Query psy3754
Match_columns 755
No_of_seqs 650 out of 4044
Neff 6.9
Searched_HMMs 46136
Date Sat Aug 17 00:42:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3754.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3754hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02696 pppGpp_PNP guanosine 100.0 3E-167 6E-172 1426.8 78.4 681 69-752 9-718 (719)
2 COG1185 Pnp Polyribonucleotide 100.0 2E-168 3E-173 1400.5 62.9 689 64-755 1-689 (692)
3 PLN00207 polyribonucleotide nu 100.0 5E-159 1E-163 1383.2 77.8 690 66-755 78-824 (891)
4 PRK11824 polynucleotide phosph 100.0 7E-153 2E-157 1340.1 80.0 691 64-755 1-691 (693)
5 TIGR03591 polynuc_phos polyrib 100.0 2E-152 4E-157 1333.0 77.6 678 74-751 2-684 (684)
6 KOG1067|consensus 100.0 6E-152 1E-156 1221.3 53.9 675 68-754 47-737 (760)
7 TIGR02065 ECX1 archaeal exosom 100.0 1.8E-39 3.8E-44 336.5 25.1 225 372-608 2-229 (230)
8 PRK03983 exosome complex exonu 100.0 1.1E-38 2.3E-43 333.5 26.0 225 372-608 8-235 (244)
9 PRK00173 rph ribonuclease PH; 100.0 2.6E-37 5.6E-42 321.7 25.7 221 378-606 1-237 (238)
10 TIGR01966 RNasePH ribonuclease 100.0 2.8E-36 6E-41 313.7 26.2 218 379-605 1-235 (236)
11 PRK04282 exosome complex RNA-b 100.0 8.7E-36 1.9E-40 316.3 28.3 235 360-606 7-270 (271)
12 PLN00207 polyribonucleotide nu 100.0 2.1E-36 4.6E-41 354.5 24.7 243 75-328 447-707 (891)
13 COG0689 Rph RNase PH [Translat 100.0 3.5E-36 7.5E-41 304.6 22.5 224 374-606 4-230 (230)
14 TIGR02065 ECX1 archaeal exosom 100.0 6E-36 1.3E-40 310.1 24.2 204 76-289 18-229 (230)
15 PRK00173 rph ribonuclease PH; 100.0 3.4E-34 7.4E-39 298.3 23.2 205 76-287 11-237 (238)
16 KOG1068|consensus 100.0 5.5E-35 1.2E-39 294.0 16.4 226 373-609 8-236 (245)
17 PRK03983 exosome complex exonu 100.0 1.1E-33 2.3E-38 295.9 22.7 206 76-291 24-237 (244)
18 COG2123 RNase PH-related exori 100.0 2.9E-32 6.4E-37 278.1 27.0 231 364-606 10-271 (272)
19 TIGR01966 RNasePH ribonuclease 100.0 1.1E-32 2.3E-37 286.9 23.3 204 76-286 10-235 (236)
20 TIGR03591 polynuc_phos polyrib 100.0 3.7E-32 8E-37 319.4 24.8 241 76-328 320-573 (684)
21 PRK11824 polynucleotide phosph 100.0 5.6E-32 1.2E-36 318.7 23.1 240 76-327 324-575 (693)
22 COG0689 Rph RNase PH [Translat 100.0 3.9E-30 8.5E-35 260.6 20.5 200 76-286 18-229 (230)
23 KOG1614|consensus 100.0 1.7E-29 3.7E-34 250.8 22.4 239 364-615 9-279 (291)
24 KOG1069|consensus 100.0 1.5E-29 3.1E-34 245.6 15.2 203 387-609 4-212 (217)
25 TIGR02696 pppGpp_PNP guanosine 100.0 3.6E-28 7.8E-33 280.3 20.4 237 77-329 346-601 (719)
26 PRK04282 exosome complex RNA-b 100.0 2.4E-27 5.2E-32 251.8 23.2 203 76-287 34-270 (271)
27 KOG1069|consensus 99.9 1.4E-26 3.1E-31 224.8 16.5 195 77-289 6-211 (217)
28 KOG1068|consensus 99.9 6.5E-26 1.4E-30 228.6 15.4 206 77-291 24-237 (245)
29 COG2123 RNase PH-related exori 99.9 1.4E-24 3.1E-29 221.9 22.1 201 76-287 33-271 (272)
30 KOG1613|consensus 99.9 2E-24 4.4E-29 214.2 17.0 239 358-602 16-297 (298)
31 KOG1612|consensus 99.9 1.2E-22 2.7E-27 203.4 24.6 234 374-617 17-288 (288)
32 PF01138 RNase_PH: 3' exoribon 99.9 4E-23 8.8E-28 195.7 15.6 131 387-520 1-132 (132)
33 PRK05626 rpsO 30S ribosomal pr 99.9 3.6E-22 7.8E-27 173.8 6.2 63 1-63 1-63 (89)
34 TIGR00952 S15_bact ribosomal p 99.8 5.7E-21 1.2E-25 165.2 5.8 60 4-63 1-60 (86)
35 KOG1614|consensus 99.8 5.5E-19 1.2E-23 176.3 19.7 204 76-293 32-276 (291)
36 COG1185 Pnp Polyribonucleotide 99.8 4.5E-20 9.7E-25 208.5 13.2 341 389-753 14-377 (692)
37 COG0184 RpsO Ribosomal protein 99.8 5.2E-20 1.1E-24 159.5 6.2 63 1-63 1-63 (89)
38 KOG1067|consensus 99.8 2.2E-18 4.7E-23 188.3 15.0 209 77-298 369-596 (760)
39 PF01138 RNase_PH: 3' exoribon 99.8 1.4E-18 3.1E-23 164.6 11.3 123 77-207 3-132 (132)
40 COG1098 VacB Predicted RNA bin 99.8 8.2E-19 1.8E-23 158.5 5.9 74 682-755 2-75 (129)
41 COG0539 RpsA Ribosomal protein 99.7 2.9E-18 6.3E-23 192.9 8.4 164 580-755 96-262 (541)
42 PTZ00119 40S ribosomal protein 99.7 3.6E-18 7.8E-23 173.0 5.0 85 2-86 104-199 (302)
43 cd00353 Ribosomal_S15p_S13e Ri 99.7 5.3E-18 1.1E-22 146.3 5.3 56 8-63 2-57 (80)
44 COG0539 RpsA Ribosomal protein 99.7 3.1E-17 6.8E-22 184.6 10.0 123 629-755 192-348 (541)
45 CHL00027 rps15 ribosomal prote 99.7 5.5E-18 1.2E-22 146.9 2.9 53 11-63 6-60 (90)
46 PF00312 Ribosomal_S15: Riboso 99.7 7.9E-17 1.7E-21 140.0 5.4 57 7-63 2-58 (83)
47 cd05704 S1_Rrp5_repeat_hs13 S1 99.6 4.7E-15 1E-19 125.9 8.3 71 683-754 1-72 (72)
48 cd05686 S1_pNO40 S1_pNO40: pNO 99.6 1.6E-14 3.5E-19 122.9 10.0 71 683-753 1-72 (73)
49 cd05705 S1_Rrp5_repeat_hs14 S1 99.6 1E-14 2.2E-19 124.4 8.0 70 683-752 1-74 (74)
50 PRK08582 hypothetical protein; 99.5 4.4E-14 9.5E-19 134.9 10.1 74 682-755 2-75 (139)
51 cd04461 S1_Rrp5_repeat_hs8_sc7 99.5 7.4E-14 1.6E-18 121.8 8.7 74 680-753 9-83 (83)
52 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.5 7E-14 1.5E-18 118.4 8.2 68 686-753 1-71 (71)
53 cd05698 S1_Rrp5_repeat_hs6_sc5 99.5 8.7E-14 1.9E-18 117.1 8.4 69 686-754 1-70 (70)
54 cd04452 S1_IF2_alpha S1_IF2_al 99.5 1.5E-13 3.2E-18 117.5 9.6 73 683-755 1-76 (76)
55 PTZ00248 eukaryotic translatio 99.5 8.5E-14 1.8E-18 148.5 8.8 73 683-755 15-90 (319)
56 PRK07899 rpsA 30S ribosomal pr 99.5 3.1E-13 6.7E-18 153.4 12.9 133 611-755 143-278 (486)
57 cd05706 S1_Rrp5_repeat_sc10 S1 99.5 2.8E-13 6.1E-18 115.0 9.6 72 683-754 1-73 (73)
58 PF00575 S1: S1 RNA binding do 99.5 2.6E-13 5.7E-18 115.4 9.0 73 682-754 1-74 (74)
59 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.5 2.3E-13 4.9E-18 114.4 8.3 68 686-753 1-69 (69)
60 cd05703 S1_Rrp5_repeat_hs12_sc 99.4 3.1E-13 6.7E-18 115.1 8.5 69 686-754 1-72 (73)
61 cd05707 S1_Rrp5_repeat_sc11 S1 99.4 2.3E-13 4.9E-18 114.0 7.5 67 686-752 1-68 (68)
62 cd05690 S1_RPS1_repeat_ec5 S1_ 99.4 2.9E-13 6.4E-18 113.4 8.2 67 686-752 1-69 (69)
63 PRK05807 hypothetical protein; 99.4 4.5E-13 9.8E-18 127.6 10.1 73 682-755 2-74 (136)
64 PRK07252 hypothetical protein; 99.4 6.4E-13 1.4E-17 123.7 9.7 72 684-755 2-74 (120)
65 PRK07400 30S ribosomal protein 99.4 8.7E-13 1.9E-17 143.0 11.9 126 610-755 139-266 (318)
66 cd05684 S1_DHX8_helicase S1_DH 99.4 9.3E-13 2E-17 113.7 9.6 69 686-755 1-73 (79)
67 cd05692 S1_RPS1_repeat_hs4 S1_ 99.4 1E-12 2.2E-17 109.3 9.5 69 686-754 1-69 (69)
68 PRK12269 bifunctional cytidyla 99.4 5.4E-13 1.2E-17 160.1 10.8 133 611-755 515-650 (863)
69 cd05689 S1_RPS1_repeat_ec4 S1_ 99.4 9.4E-13 2E-17 111.4 8.8 70 683-752 1-72 (72)
70 PHA02945 interferon resistance 99.4 9.5E-13 2.1E-17 112.8 8.6 71 682-755 8-83 (88)
71 cd05708 S1_Rrp5_repeat_sc12 S1 99.4 1.3E-12 2.7E-17 111.8 9.4 72 684-755 1-74 (77)
72 PRK07899 rpsA 30S ribosomal pr 99.4 1E-12 2.2E-17 149.1 11.4 81 675-755 283-364 (486)
73 PRK13806 rpsA 30S ribosomal pr 99.4 3.3E-13 7.2E-18 154.7 6.7 136 610-755 136-277 (491)
74 cd05691 S1_RPS1_repeat_ec6 S1_ 99.4 1.8E-12 4E-17 109.6 8.7 70 686-755 1-71 (73)
75 PRK13806 rpsA 30S ribosomal pr 99.4 1.9E-12 4.2E-17 148.5 10.7 80 675-754 369-449 (491)
76 PRK06299 rpsA 30S ribosomal pr 99.4 8E-13 1.7E-17 154.8 7.6 133 610-754 135-270 (565)
77 PF03726 PNPase: Polyribonucle 99.4 4.6E-12 9.9E-17 110.6 10.3 81 304-384 1-83 (83)
78 cd05687 S1_RPS1_repeat_ec1_hs1 99.3 3.2E-12 6.9E-17 107.6 8.6 69 686-754 1-70 (70)
79 cd04472 S1_PNPase S1_PNPase: P 99.3 4.2E-12 9.1E-17 105.7 9.1 68 686-753 1-68 (68)
80 PRK08059 general stress protei 99.3 3.5E-12 7.6E-17 119.7 9.0 76 680-755 2-78 (123)
81 COG1093 SUI2 Translation initi 99.3 1E-12 2.3E-17 133.8 5.7 74 682-755 8-84 (269)
82 KOG1612|consensus 99.3 1.9E-10 4E-15 116.5 21.3 201 77-288 32-276 (288)
83 cd05685 S1_Tex S1_Tex: The C-t 99.3 3.4E-12 7.3E-17 106.0 7.4 67 686-752 1-68 (68)
84 cd05694 S1_Rrp5_repeat_hs2_sc2 99.3 7.2E-12 1.6E-16 106.9 9.4 68 682-755 1-70 (74)
85 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.3 7.6E-12 1.7E-16 109.8 8.3 74 682-755 3-80 (86)
86 PRK12269 bifunctional cytidyla 99.3 1.4E-11 3.1E-16 148.0 12.7 136 611-755 423-563 (863)
87 cd04453 S1_RNase_E S1_RNase_E: 99.3 1.1E-11 2.4E-16 109.3 8.7 64 682-745 4-72 (88)
88 TIGR00717 rpsA ribosomal prote 99.3 7.4E-12 1.6E-16 145.1 8.5 133 610-754 121-256 (516)
89 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.2 2E-11 4.3E-16 101.8 7.8 65 686-752 1-66 (66)
90 cd04471 S1_RNase_R S1_RNase_R: 99.2 4.3E-11 9.3E-16 103.8 9.9 70 685-754 1-83 (83)
91 cd05688 S1_RPS1_repeat_ec3 S1_ 99.2 2.9E-11 6.3E-16 100.5 8.5 67 685-752 1-68 (68)
92 KOG1613|consensus 99.2 5.5E-11 1.2E-15 119.2 11.3 195 77-282 47-296 (298)
93 PRK06676 rpsA 30S ribosomal pr 99.2 6.3E-11 1.4E-15 132.7 12.0 103 651-755 158-262 (390)
94 PRK00087 4-hydroxy-3-methylbut 99.2 2.4E-11 5.2E-16 144.0 8.9 133 611-755 411-547 (647)
95 PRK06676 rpsA 30S ribosomal pr 99.2 4E-11 8.7E-16 134.3 10.2 99 651-754 247-347 (390)
96 cd04465 S1_RPS1_repeat_ec2_hs2 99.2 5.8E-11 1.3E-15 99.1 8.5 66 686-754 1-67 (67)
97 cd05693 S1_Rrp5_repeat_hs1_sc1 99.2 2.9E-11 6.2E-16 109.3 6.9 72 683-754 1-95 (100)
98 PRK03987 translation initiatio 99.2 5.6E-11 1.2E-15 125.1 9.2 73 682-754 5-80 (262)
99 smart00316 S1 Ribosomal protei 99.1 1.8E-10 3.9E-15 95.9 9.0 71 684-754 1-72 (72)
100 cd04473 S1_RecJ_like S1_RecJ_l 99.1 2.3E-10 5.1E-15 98.4 9.7 66 680-753 11-76 (77)
101 PRK00087 4-hydroxy-3-methylbut 99.1 1.8E-10 4E-15 136.6 10.5 100 651-755 532-633 (647)
102 cd04454 S1_Rrp4_like S1_Rrp4_l 99.1 3.2E-10 7E-15 98.6 8.8 73 683-755 4-76 (82)
103 TIGR00717 rpsA ribosomal prote 99.1 4.9E-10 1.1E-14 130.0 11.9 99 651-754 416-516 (516)
104 cd05702 S1_Rrp5_repeat_hs11_sc 99.1 3.1E-10 6.7E-15 95.7 7.4 64 686-749 1-66 (70)
105 PRK06299 rpsA 30S ribosomal pr 99.1 3.6E-10 7.8E-15 132.5 10.3 99 651-754 256-357 (565)
106 COG2183 Tex Transcriptional ac 99.0 3.3E-10 7.2E-15 131.3 7.5 75 681-755 654-729 (780)
107 cd00164 S1_like S1_like: Ribos 99.0 9.9E-10 2.2E-14 89.6 7.3 64 689-752 1-65 (65)
108 cd00677 S15_NS1_EPRS_RNA-bind 99.0 5E-10 1.1E-14 86.5 3.6 38 26-63 1-38 (46)
109 PRK09521 exosome complex RNA-b 98.9 1.1E-09 2.5E-14 110.4 5.2 74 680-755 59-142 (189)
110 PRK07400 30S ribosomal protein 98.9 4.2E-09 9.1E-14 114.4 9.9 75 680-754 26-101 (318)
111 PF03725 RNase_PH_C: 3' exorib 98.9 6.1E-09 1.3E-13 87.3 8.5 65 210-274 1-68 (68)
112 cd02393 PNPase_KH Polynucleoti 98.9 1.4E-09 3E-14 89.3 3.8 60 617-676 1-60 (61)
113 cd04460 S1_RpoE S1_RpoE: RpoE, 98.9 7.9E-09 1.7E-13 93.2 8.8 68 687-755 1-85 (99)
114 PRK04163 exosome complex RNA-b 98.8 7.3E-09 1.6E-13 107.9 9.0 74 682-755 60-137 (235)
115 TIGR02063 RNase_R ribonuclease 98.8 1.5E-08 3.2E-13 121.8 11.9 73 681-753 623-708 (709)
116 PRK13763 putative RNA-processi 98.8 2.1E-09 4.6E-14 107.4 3.6 83 618-700 3-96 (180)
117 TIGR03665 arCOG04150 arCOG0415 98.8 3.2E-09 6.9E-14 105.4 2.4 79 622-700 2-90 (172)
118 PRK11642 exoribonuclease R; Pr 98.7 2.2E-08 4.8E-13 120.7 9.0 91 664-754 619-725 (813)
119 TIGR00448 rpoE DNA-directed RN 98.7 8.5E-08 1.8E-12 96.0 9.1 76 679-755 75-167 (179)
120 cd04455 S1_NusA S1_NusA: N-uti 98.6 1E-07 2.2E-12 79.7 7.8 63 684-753 2-67 (67)
121 TIGR00358 3_prime_RNase VacB a 98.6 1.3E-07 2.8E-12 112.4 11.7 72 682-753 569-653 (654)
122 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.6 1E-07 2.2E-12 84.9 7.8 74 682-755 3-86 (92)
123 COG1095 RPB7 DNA-directed RNA 98.5 3.4E-07 7.4E-12 89.9 7.2 76 679-755 75-167 (183)
124 PRK08563 DNA-directed RNA poly 98.4 8.4E-07 1.8E-11 89.4 8.9 76 679-755 75-167 (187)
125 PRK09202 nusA transcription el 98.4 7.5E-07 1.6E-11 101.2 8.3 70 678-754 125-199 (470)
126 PF03725 RNase_PH_C: 3' exorib 98.3 1.5E-06 3.2E-11 72.8 7.2 67 523-593 1-68 (68)
127 KOG2815|consensus 98.3 4.5E-07 9.7E-12 93.3 2.9 50 15-64 176-225 (256)
128 PHA02858 EIF2a-like PKR inhibi 98.2 2.7E-06 5.9E-11 72.6 6.4 70 682-753 13-85 (86)
129 PRK05054 exoribonuclease II; P 98.1 5.2E-06 1.1E-10 98.6 8.9 71 683-753 557-643 (644)
130 PRK08561 rps15p 30S ribosomal 98.1 1.5E-06 3.4E-11 82.4 3.0 34 30-63 89-122 (151)
131 cd02395 SF1_like-KH Splicing f 98.0 3.9E-06 8.4E-11 78.3 4.0 61 626-686 14-99 (120)
132 KOG1070|consensus 98.0 3.9E-06 8.5E-11 101.7 5.0 132 612-754 534-669 (1710)
133 COG1097 RRP4 RNA-binding prote 97.9 2.9E-05 6.3E-10 79.5 8.4 74 682-755 61-138 (239)
134 TIGR01953 NusA transcription t 97.9 2.2E-05 4.9E-10 85.9 8.2 72 677-755 121-198 (341)
135 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.9 5.1E-05 1.1E-09 66.5 8.7 72 682-754 3-74 (86)
136 COG0557 VacB Exoribonuclease R 97.9 3.2E-05 7E-10 93.1 9.6 95 660-754 594-704 (706)
137 PRK12327 nusA transcription el 97.8 9.4E-05 2E-09 81.5 10.5 84 664-754 102-199 (362)
138 TIGR00757 RNaseEG ribonuclease 97.8 3.3E-05 7.2E-10 86.8 6.7 61 682-742 22-96 (414)
139 TIGR02062 RNase_B exoribonucle 97.8 4.2E-05 9E-10 90.8 7.9 92 661-752 528-638 (639)
140 KOG2916|consensus 97.7 1.6E-05 3.5E-10 81.4 3.0 73 682-754 13-88 (304)
141 COG1096 Predicted RNA-binding 97.7 4.2E-05 9E-10 75.4 5.7 73 680-754 59-141 (188)
142 COG2996 Predicted RNA-bindinin 97.7 0.00018 3.9E-09 74.6 10.2 91 649-754 123-216 (287)
143 cd02394 vigilin_like_KH K homo 97.7 2.9E-05 6.4E-10 63.6 3.0 56 620-676 2-61 (62)
144 PRK04163 exosome complex RNA-b 97.5 6.9E-05 1.5E-09 78.3 4.0 63 620-682 147-209 (235)
145 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.4 0.00047 1E-08 60.9 7.7 60 685-745 1-71 (88)
146 PTZ00162 DNA-directed RNA poly 97.4 0.00047 1E-08 68.8 8.3 75 679-754 75-164 (176)
147 PF10447 EXOSC1: Exosome compo 97.4 0.00042 9.1E-09 60.2 6.7 61 683-743 2-82 (82)
148 COG1107 Archaea-specific RecJ- 97.4 0.00012 2.5E-09 82.7 3.7 68 680-753 117-185 (715)
149 KOG1070|consensus 97.3 0.0006 1.3E-08 83.5 8.7 76 680-755 1157-1233(1710)
150 PF13509 S1_2: S1 domain; PDB: 97.2 0.0012 2.6E-08 54.2 7.3 61 685-754 1-61 (61)
151 PF00013 KH_1: KH domain syndr 97.1 0.00017 3.6E-09 58.7 1.2 55 621-676 3-60 (60)
152 cd00105 KH-I K homology RNA-bi 96.9 0.00088 1.9E-08 54.8 3.7 54 621-675 3-62 (64)
153 cd05699 S1_Rrp5_repeat_hs7 S1_ 96.9 0.0027 5.9E-08 53.6 6.2 66 686-754 1-72 (72)
154 smart00322 KH K homology RNA-b 96.4 0.0046 9.9E-08 50.4 4.5 60 618-678 3-66 (69)
155 PRK12328 nusA transcription el 96.4 0.018 3.9E-07 63.5 10.0 84 664-754 106-205 (374)
156 PRK10811 rne ribonuclease E; R 96.3 0.0067 1.4E-07 73.1 7.1 61 683-743 36-107 (1068)
157 PTZ00248 eukaryotic translatio 96.3 0.00018 3.9E-09 77.7 -5.5 110 629-742 17-172 (319)
158 PRK11712 ribonuclease G; Provi 96.2 0.0074 1.6E-07 69.3 6.2 61 683-743 36-110 (489)
159 cd02396 PCBP_like_KH K homolog 95.9 0.0068 1.5E-07 50.2 3.3 54 621-675 3-63 (65)
160 KOG1676|consensus 95.4 0.043 9.3E-07 62.9 7.9 99 587-686 197-304 (600)
161 PRK12329 nusA transcription el 95.3 0.09 2E-06 59.1 9.9 66 683-754 150-224 (449)
162 KOG1856|consensus 95.3 0.023 4.9E-07 69.1 5.5 72 683-754 983-1058(1299)
163 TIGR03665 arCOG04150 arCOG0415 95.2 0.017 3.6E-07 57.6 3.6 55 628-684 99-153 (172)
164 PRK13763 putative RNA-processi 95.0 0.014 3E-07 58.6 2.3 59 628-688 105-163 (180)
165 COG1098 VacB Predicted RNA bin 94.5 0.066 1.4E-06 49.7 5.3 53 640-700 13-67 (129)
166 KOG2191|consensus 94.3 0.16 3.5E-06 54.3 8.4 116 560-689 82-212 (402)
167 PRK12442 translation initiatio 94.1 0.2 4.3E-06 43.8 7.0 63 688-754 8-72 (87)
168 TIGR00008 infA translation ini 93.5 0.29 6.3E-06 41.0 6.8 60 688-751 6-67 (68)
169 PF13014 KH_3: KH domain 93.5 0.024 5.2E-07 42.9 0.3 27 629-655 2-28 (43)
170 COG1094 Predicted RNA-binding 93.0 0.13 2.9E-06 51.5 4.8 68 615-682 5-77 (194)
171 KOG3409|consensus 92.7 0.39 8.5E-06 47.0 7.3 71 682-753 65-146 (193)
172 COG1530 CafA Ribonucleases G a 92.3 0.14 3.1E-06 59.2 4.6 62 682-744 34-102 (487)
173 KOG1676|consensus 90.7 0.66 1.4E-05 53.5 7.5 95 584-682 284-389 (600)
174 KOG3298|consensus 89.8 1.5 3.3E-05 42.6 8.1 65 680-745 76-151 (170)
175 COG2183 Tex Transcriptional ac 89.5 0.46 9.9E-06 56.8 5.2 109 578-697 607-717 (780)
176 COG2996 Predicted RNA-bindinin 86.4 2.8 6.2E-05 44.2 8.2 64 683-754 3-67 (287)
177 cd05686 S1_pNO40 S1_pNO40: pNO 86.0 1.1 2.5E-05 37.7 4.2 57 640-705 11-70 (73)
178 cd05705 S1_Rrp5_repeat_hs14 S1 85.7 0.98 2.1E-05 38.4 3.7 54 640-698 11-66 (74)
179 PF00313 CSD: 'Cold-shock' DNA 85.7 7.6 0.00016 31.9 9.0 54 689-747 1-57 (66)
180 COG0361 InfA Translation initi 84.7 5 0.00011 34.3 7.4 64 686-753 6-71 (75)
181 cd05704 S1_Rrp5_repeat_hs13 S1 83.4 1.4 2.9E-05 37.2 3.6 53 639-698 10-64 (72)
182 cd02134 NusA_KH NusA_K homolog 83.1 0.44 9.5E-06 39.0 0.4 36 618-653 25-60 (61)
183 KOG0119|consensus 82.8 3.4 7.4E-05 46.9 7.3 57 626-682 152-230 (554)
184 cd05696 S1_Rrp5_repeat_hs4 S1_ 82.1 1.9 4E-05 36.3 3.9 53 639-698 8-62 (71)
185 PTZ00072 40S ribosomal protein 81.8 1.3 2.8E-05 42.4 3.0 31 31-61 87-117 (148)
186 PF08292 RNA_pol_Rbc25: RNA po 79.9 7.4 0.00016 36.6 7.4 63 683-745 1-76 (122)
187 TIGR03319 YmdA_YtgF conserved 79.5 3.7 8.1E-05 48.0 6.6 61 620-680 206-268 (514)
188 PRK15464 cold shock-like prote 79.2 5.5 0.00012 33.7 5.7 54 689-748 5-62 (70)
189 COG1097 RRP4 RNA-binding prote 77.5 3.3 7.1E-05 43.1 4.7 53 620-672 148-200 (239)
190 PRK09507 cspE cold shock prote 77.3 7.1 0.00015 32.8 5.9 50 688-742 3-56 (69)
191 PRK00106 hypothetical protein; 77.3 5.3 0.00012 46.8 6.9 61 620-680 227-289 (535)
192 PRK15463 cold shock-like prote 77.2 6.8 0.00015 33.1 5.8 54 689-747 5-61 (70)
193 PRK13764 ATPase; Provisional 77.1 0.79 1.7E-05 54.3 0.1 143 593-740 457-601 (602)
194 PRK04012 translation initiatio 76.3 10 0.00022 34.4 7.0 61 686-751 20-82 (100)
195 KOG2190|consensus 76.1 1.9 4.1E-05 49.9 2.8 63 617-680 137-206 (485)
196 KOG2193|consensus 74.5 2.7 5.9E-05 46.6 3.3 62 589-654 255-316 (584)
197 COG4044 Uncharacterized protei 74.4 11 0.00023 38.4 7.1 102 644-745 27-147 (247)
198 PRK10943 cold shock-like prote 74.3 9 0.0002 32.2 5.8 50 688-742 3-56 (69)
199 PRK09890 cold shock protein Cs 73.8 10 0.00023 31.9 6.0 54 689-748 5-62 (70)
200 KOG3013|consensus 73.6 3.3 7.2E-05 43.2 3.5 71 682-752 82-162 (301)
201 PRK12704 phosphodiesterase; Pr 73.2 8.1 0.00018 45.3 7.1 61 620-680 212-274 (520)
202 PRK09937 stationary phase/star 73.2 10 0.00022 32.5 5.8 53 690-748 3-59 (74)
203 COG1094 Predicted RNA-binding 72.7 2.1 4.5E-05 43.2 1.8 59 629-689 113-171 (194)
204 PRK08582 hypothetical protein; 72.7 5.2 0.00011 38.4 4.5 53 640-700 13-67 (139)
205 cd05793 S1_IF1A S1_IF1A: Trans 71.2 11 0.00024 32.5 5.6 58 689-751 2-61 (77)
206 cd05694 S1_Rrp5_repeat_hs2_sc2 70.5 8.1 0.00018 32.8 4.7 49 640-702 12-63 (74)
207 cd05703 S1_Rrp5_repeat_hs12_sc 70.1 6.3 0.00014 33.3 3.9 53 640-698 8-62 (73)
208 PRK10354 RNA chaperone/anti-te 69.5 15 0.00031 31.0 6.0 53 689-747 5-61 (70)
209 KOG1004|consensus 68.6 23 0.0005 36.2 8.0 63 682-746 62-125 (230)
210 TIGR02381 cspD cold shock doma 67.3 13 0.00028 31.1 5.2 48 690-742 3-54 (68)
211 PRK14998 cold shock-like prote 67.2 15 0.00033 31.2 5.7 53 690-748 3-59 (73)
212 cd05693 S1_Rrp5_repeat_hs1_sc1 65.9 16 0.00036 32.9 6.0 65 640-705 11-94 (100)
213 PF10246 MRP-S35: Mitochondria 64.3 25 0.00054 31.9 6.6 55 683-744 21-75 (104)
214 smart00652 eIF1a eukaryotic tr 63.5 27 0.00059 30.5 6.6 60 687-751 5-66 (83)
215 COG1855 ATPase (PilT family) [ 63.3 3.9 8.5E-05 46.3 1.7 60 594-654 463-522 (604)
216 KOG2192|consensus 62.9 9.3 0.0002 40.1 4.1 50 626-675 56-109 (390)
217 cd05707 S1_Rrp5_repeat_sc11 S1 61.0 14 0.00031 30.2 4.4 51 640-698 8-60 (68)
218 KOG2193|consensus 59.7 7 0.00015 43.5 2.8 33 621-653 496-528 (584)
219 TIGR03324 alt_F1F0_F1_al alter 59.0 1E+02 0.0022 36.0 12.1 164 124-337 268-438 (497)
220 TIGR03498 FliI_clade3 flagella 58.5 69 0.0015 36.6 10.6 94 124-245 244-338 (418)
221 cd05706 S1_Rrp5_repeat_sc10 S1 58.3 21 0.00046 29.6 5.0 51 640-698 11-63 (73)
222 PRK12705 hypothetical protein; 57.6 15 0.00033 42.8 5.2 61 620-680 200-262 (508)
223 PRK05807 hypothetical protein; 57.0 12 0.00025 35.9 3.5 53 640-700 13-66 (136)
224 cd04458 CSP_CDS Cold-Shock Pro 56.7 56 0.0012 26.6 7.2 57 690-751 2-61 (65)
225 cd04456 S1_IF1A_like S1_IF1A_l 56.5 42 0.00092 29.0 6.5 58 689-751 2-62 (78)
226 PRK00468 hypothetical protein; 56.0 4.4 9.6E-05 34.7 0.4 24 621-644 33-56 (75)
227 cd04452 S1_IF2_alpha S1_IF2_al 55.9 20 0.00042 29.9 4.4 47 645-698 15-65 (76)
228 PF09883 DUF2110: Uncharacteri 55.5 28 0.0006 35.8 6.0 104 646-751 28-144 (225)
229 PRK02821 hypothetical protein; 55.1 4.5 9.8E-05 34.9 0.3 25 620-644 33-57 (77)
230 cd05687 S1_RPS1_repeat_ec1_hs1 54.6 18 0.0004 29.7 4.0 53 640-700 8-62 (70)
231 cd05684 S1_DHX8_helicase S1_DH 53.9 18 0.00038 30.7 3.8 51 640-697 8-63 (79)
232 cd05692 S1_RPS1_repeat_hs4 S1_ 52.5 21 0.00045 28.7 4.0 51 640-698 8-60 (69)
233 cd05690 S1_RPS1_repeat_ec5 S1_ 52.4 14 0.0003 30.2 2.8 52 640-698 8-61 (69)
234 cd05700 S1_Rrp5_repeat_hs9 S1_ 51.1 44 0.00096 27.3 5.3 63 686-752 1-64 (65)
235 COG1278 CspC Cold shock protei 50.9 27 0.00059 29.3 4.3 48 690-742 3-54 (67)
236 PF01176 eIF-1a: Translation i 50.7 16 0.00034 30.3 2.9 59 687-750 3-63 (65)
237 cd05697 S1_Rrp5_repeat_hs5 S1_ 50.6 24 0.00051 29.0 4.0 51 640-698 8-60 (69)
238 PRK13343 F0F1 ATP synthase sub 50.5 1.8E+02 0.0039 34.1 12.4 164 126-337 270-438 (502)
239 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 50.4 18 0.0004 31.1 3.5 65 629-700 6-72 (86)
240 COG1837 Predicted RNA-binding 50.3 5.8 0.00013 34.1 0.3 24 621-644 33-56 (76)
241 KOG0336|consensus 49.9 14 0.00031 41.4 3.1 56 621-677 50-108 (629)
242 KOG2192|consensus 49.8 25 0.00053 37.0 4.7 55 621-676 318-378 (390)
243 PRK08972 fliI flagellum-specif 49.6 85 0.0019 36.1 9.4 82 126-235 268-349 (444)
244 cd04322 LysRS_N LysRS_N: N-ter 49.5 32 0.00068 31.2 5.0 52 688-739 3-59 (108)
245 cd04472 S1_PNPase S1_PNPase: P 48.5 28 0.00062 28.0 4.1 51 640-698 8-60 (68)
246 cd05685 S1_Tex S1_Tex: The C-t 48.2 29 0.00064 27.7 4.2 51 640-698 8-60 (68)
247 cd05689 S1_RPS1_repeat_ec4 S1_ 48.2 31 0.00067 28.5 4.4 51 640-697 11-63 (72)
248 cd04453 S1_RNase_E S1_RNase_E: 48.1 22 0.00048 31.3 3.6 53 640-696 15-70 (88)
249 PRK07252 hypothetical protein; 48.0 29 0.00063 32.5 4.6 51 640-698 11-63 (120)
250 cd04461 S1_Rrp5_repeat_hs8_sc7 48.0 29 0.00063 29.7 4.3 51 640-698 22-74 (83)
251 CHL00010 infA translation init 47.4 91 0.002 26.9 7.2 61 689-753 9-71 (78)
252 cd05691 S1_RPS1_repeat_ec6 S1_ 44.5 53 0.0011 26.9 5.3 51 640-698 8-60 (73)
253 cd05698 S1_Rrp5_repeat_hs6_sc5 44.1 22 0.00048 29.2 2.8 51 640-698 8-60 (70)
254 PTZ00329 eukaryotic translatio 44.0 60 0.0013 31.8 6.1 63 683-751 29-93 (155)
255 PRK08149 ATP synthase SpaL; Va 44.0 2.5E+02 0.0055 32.2 12.1 90 124-243 255-345 (428)
256 CHL00059 atpA ATP synthase CF1 43.7 2.9E+02 0.0063 32.2 12.6 86 124-235 247-332 (485)
257 KOG2814|consensus 43.7 11 0.00025 40.9 1.3 62 620-681 59-124 (345)
258 KOG2191|consensus 43.4 28 0.00061 37.9 4.1 56 621-676 42-105 (402)
259 PRK05922 type III secretion sy 43.3 2.2E+02 0.0048 32.7 11.5 88 126-244 263-350 (434)
260 COG1093 SUI2 Translation initi 43.2 37 0.0008 36.0 4.8 59 639-705 18-80 (269)
261 PRK00276 infA translation init 42.9 1.3E+02 0.0028 25.3 7.4 61 688-752 8-70 (72)
262 TIGR03497 FliI_clade2 flagella 42.4 2E+02 0.0042 32.9 10.9 91 126-246 243-334 (413)
263 cd05695 S1_Rrp5_repeat_hs3 S1_ 42.0 34 0.00073 28.2 3.6 49 640-698 8-58 (66)
264 PRK06820 type III secretion sy 42.0 1.8E+02 0.0039 33.6 10.5 90 124-243 267-357 (440)
265 cd05702 S1_Rrp5_repeat_hs11_sc 41.7 29 0.00064 28.7 3.2 49 645-698 12-62 (70)
266 TIGR00523 eIF-1A eukaryotic/ar 40.1 1.5E+02 0.0034 26.8 7.7 60 686-750 18-80 (99)
267 PRK08406 transcription elongat 39.8 11 0.00023 36.4 0.3 34 620-653 34-67 (140)
268 TIGR01952 nusA_arch NusA famil 39.5 13 0.00027 36.0 0.7 35 620-654 35-69 (141)
269 PF13184 KH_5: NusA-like KH do 39.3 5.9 0.00013 33.4 -1.3 27 627-653 17-44 (69)
270 TIGR00638 Mop molybdenum-pteri 39.3 40 0.00086 27.5 3.7 54 687-742 7-61 (69)
271 PRK01064 hypothetical protein; 38.9 13 0.00028 32.2 0.6 24 621-644 33-56 (78)
272 cd05708 S1_Rrp5_repeat_sc12 S1 38.9 42 0.00092 27.8 3.8 51 640-698 10-63 (77)
273 cd05688 S1_RPS1_repeat_ec3 S1_ 38.5 37 0.0008 27.2 3.3 47 645-698 13-60 (68)
274 COG5176 MSL5 Splicing factor ( 38.0 19 0.00041 36.6 1.7 53 626-678 162-217 (269)
275 PLN00208 translation initiatio 37.6 86 0.0019 30.4 6.0 63 683-751 29-93 (145)
276 PRK08406 transcription elongat 36.6 9.7 0.00021 36.7 -0.5 60 595-654 72-135 (140)
277 PRK07165 F0F1 ATP synthase sub 36.4 3.7E+02 0.008 31.6 12.0 83 124-235 247-329 (507)
278 KOG1588|consensus 36.4 11 0.00024 39.7 -0.1 27 628-654 108-134 (259)
279 PRK09521 exosome complex RNA-b 35.7 1.5E+02 0.0033 29.8 8.0 58 629-697 64-133 (189)
280 COG0195 NusA Transcription elo 35.6 13 0.00029 37.6 0.3 35 619-653 77-111 (190)
281 PRK07594 type III secretion sy 34.6 1.2E+02 0.0026 34.9 7.6 80 126-235 261-340 (433)
282 PRK06002 fliI flagellum-specif 34.4 1.6E+02 0.0034 34.1 8.6 93 125-245 269-362 (450)
283 cd04473 S1_RecJ_like S1_RecJ_l 34.0 50 0.0011 28.0 3.5 42 640-697 24-67 (77)
284 PRK09099 type III secretion sy 33.9 2E+02 0.0044 33.1 9.3 91 126-246 269-360 (441)
285 cd02414 jag_KH jag_K homology 33.1 32 0.0007 29.3 2.2 27 618-644 24-50 (77)
286 PRK08472 fliI flagellum-specif 32.8 2E+02 0.0044 33.0 9.1 81 126-235 262-342 (434)
287 PRK05688 fliI flagellum-specif 32.3 2E+02 0.0043 33.3 8.9 89 125-241 273-362 (451)
288 PRK08927 fliI flagellum-specif 32.2 2.1E+02 0.0045 33.1 9.0 94 125-246 263-357 (442)
289 smart00316 S1 Ribosomal protei 32.1 91 0.002 24.7 4.7 47 645-698 14-62 (72)
290 TIGR03496 FliI_clade1 flagella 31.1 2.5E+02 0.0054 32.1 9.5 93 126-246 243-336 (411)
291 PRK12597 F0F1 ATP synthase sub 30.6 1.7E+02 0.0037 33.9 8.1 91 126-246 253-344 (461)
292 smart00357 CSP Cold shock prot 29.9 1.2E+02 0.0027 23.7 5.1 47 691-743 2-50 (64)
293 TIGR02546 III_secr_ATP type II 29.8 2.3E+02 0.005 32.4 9.0 91 126-246 251-342 (422)
294 PF03459 TOBE: TOBE domain; I 29.6 1.4E+02 0.0031 23.8 5.4 48 687-741 5-58 (64)
295 PF13083 KH_4: KH domain; PDB: 29.4 9.8 0.00021 32.0 -1.6 28 617-644 28-55 (73)
296 CHL00060 atpB ATP synthase CF1 28.3 2.5E+02 0.0054 32.9 8.9 88 126-243 278-366 (494)
297 cd00164 S1_like S1_like: Ribos 27.9 88 0.0019 24.2 3.9 46 646-698 10-57 (65)
298 PRK09280 F0F1 ATP synthase sub 27.5 94 0.002 36.0 5.3 91 126-246 254-345 (463)
299 PRK01712 carbon storage regula 27.1 82 0.0018 26.3 3.4 29 725-754 7-35 (64)
300 PF01336 tRNA_anti-codon: OB-f 26.8 1.7E+02 0.0038 23.7 5.6 63 688-753 2-69 (75)
301 PHA02945 interferon resistance 26.7 76 0.0016 28.1 3.3 52 645-705 22-79 (88)
302 PRK07960 fliI flagellum-specif 26.6 3.8E+02 0.0082 31.1 9.9 92 126-245 281-373 (455)
303 PF02599 CsrA: Global regulato 26.5 59 0.0013 26.1 2.4 29 725-754 7-35 (54)
304 PRK08059 general stress protei 26.1 65 0.0014 30.1 3.1 51 640-698 15-67 (123)
305 cd00210 PTS_IIA_glc PTS_IIA, P 25.0 1.6E+02 0.0034 27.9 5.4 56 689-744 42-102 (124)
306 COG1545 Predicted nucleic-acid 24.9 2.7E+02 0.0059 26.7 7.2 55 684-745 62-125 (140)
307 PRK07196 fliI flagellum-specif 24.4 5.1E+02 0.011 29.9 10.4 83 124-235 259-341 (434)
308 cd02409 KH-II KH-II (K homolo 24.3 40 0.00088 27.0 1.2 26 623-648 30-55 (68)
309 KOG3273|consensus 24.3 81 0.0017 32.1 3.5 60 628-689 179-238 (252)
310 PRK06418 transcription elongat 24.1 28 0.00061 34.6 0.3 33 621-654 64-96 (166)
311 PF00575 S1: S1 RNA binding do 23.3 39 0.00084 27.9 1.0 51 640-698 12-64 (74)
312 KOG2190|consensus 23.3 36 0.00079 39.5 1.0 35 620-654 340-374 (485)
313 PRK00568 carbon storage regula 22.6 98 0.0021 26.7 3.2 29 725-754 7-35 (76)
314 PRK03987 translation initiatio 22.5 1.1E+02 0.0023 32.8 4.2 52 640-699 16-71 (262)
315 cd04454 S1_Rrp4_like S1_Rrp4_l 22.5 2.1E+02 0.0045 24.3 5.4 47 645-698 18-66 (82)
316 TIGR01041 ATP_syn_B_arch ATP s 22.0 1.5E+02 0.0033 34.3 5.6 90 126-243 254-344 (458)
317 COG3269 Predicted RNA-binding 21.3 2.9E+02 0.0062 23.7 5.6 51 681-745 11-61 (73)
318 PF12907 zf-met2: Zinc-binding 20.4 70 0.0015 24.1 1.7 22 28-49 9-31 (40)
No 1
>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=2.6e-167 Score=1426.80 Aligned_cols=681 Identities=42% Similarity=0.705 Sum_probs=657.0
Q ss_pred eEeeeeCCeeEEEEeCccCcCCCcEEEEEE-CCeEEEEEEEecCCCCCCCCcceeeEEeEeeccccCCCCCCcccccCCC
Q psy3754 69 IKSFKYGSYKISIEIGEIARQATSSVLVSI-EDTVILATVVSCKDPTSTYNFFPLTVDYIEKAYAAGRIPGSFFKREGKP 147 (755)
Q Consensus 69 ~~~~~~~~r~i~~e~G~la~~A~GSa~v~~-G~T~Vl~tv~~~~~~~~~~~f~pl~v~y~e~~~a~g~ip~~~~kReg~p 147 (755)
.+++++|++++.+|||++|+||||||++++ |+|+|||||+..++++++.|||||+|+|+||+||+|||||||+||||+|
T Consensus 9 ~~~~~~~~~~~~~etG~~A~qA~Gav~v~~~G~t~vl~t~~~~~~~~~~~dF~PLtV~y~Ek~yA~GkiPggf~kREgrp 88 (719)
T TIGR02696 9 IDNGRFGTRTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQPKDQFDFFPLTVDVEERMYAAGRIPGSFFRREGRP 88 (719)
T ss_pred EEEEEECCEEEEEEcchhHhhCCceEEEEecCCeEEEEEEEecCCCCCCCCCcceeEeeeehhhhcCccCCceeccCCCC
Confidence 345667666999999999999999999999 9999999999988899999999999999999999999999999999999
Q ss_pred CchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEc
Q psy3754 148 SERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILN 227 (755)
Q Consensus 148 ~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP~~~~vaav~vg~~~g~~vld 227 (755)
+++|+|+|||||||||||||++|+++|||+++|||+|++++|+++|+||||+||++|+|||+|||||||||++||+||+|
T Consensus 89 s~~eiL~sRliDR~iRPLFp~~~~~e~qi~~~vls~D~~~~pdvla~~~ASaAl~iSdiPf~gPv~~vrVg~i~g~~viN 168 (719)
T TIGR02696 89 STDAILTCRLIDRPLRPSFVKGLRNEVQVVVTVLSLNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALIDGQWVAF 168 (719)
T ss_pred ChhhhHHHHhhCCCCccCCCCCCCcceEEEEEEEEcCCCCChHHHHHHHHHHHHHhcCCCCCCceEEEEEEEECCEEEEC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCHHHHhcCcccEEEEeec----C-ceEEEEc------------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q psy3754 228 PTTEQLKKSHLDLLVAGTE----K-AIITVES------------ESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVG 290 (755)
Q Consensus 228 Pt~~E~~~s~~~l~va~~~----~-~i~mie~------------~~~~~se~~~~~al~~a~~~~~~i~~~~~~~~~~~~ 290 (755)
||.+|++.|++||+||||+ + +++|||+ +++++||++|++||++||++++++|++|+++.+++|
T Consensus 169 Pt~~~~~~s~ldLvvagt~~~~~~~~i~MiE~~a~~~~~~~~~~~a~e~~e~~~~~Ai~~a~~~i~~~~~~~~~l~~~~g 248 (719)
T TIGR02696 169 PTHEQLEGAVFDMVVAGRVLENGDVAIMMVEAEATEKTWDLVKGGAEAPTEEVVAEGLEAAKPFIKVLCRAQADLAEKAA 248 (719)
T ss_pred cCHHHHhhCeeeEEEEeeecCCCCccEEEEecCCccccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 9999999999999999998 6 8999998 899999999999999999999999999999999999
Q ss_pred CCcccCC-CCCCChhHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHhhcccCCcCChhhHHHHHHHHHHHHH
Q psy3754 291 QKKVNWD-PIVKDKTLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYDLESKII 369 (755)
Q Consensus 291 ~~k~~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 369 (755)
|+|+++. ....+++|.+.+++.+.++|++++.+.+|.+|+++++++++++.++|.+.. +....++..+|++++++.+
T Consensus 249 k~k~~~~~~~~~~~~l~~~v~~~~~~~~~~~~~~~~K~~R~~~~~~~~~~~~~~~~~~~--~~~~~~i~~~~~~~~k~~~ 326 (719)
T TIGR02696 249 KPTGEFPLFPDYQDDVYEAVEGAVKDELSAALTIAGKQEREEALDEVKALVAAKLAEQF--EGREKEISAAYRAVTKKLV 326 (719)
T ss_pred CCccccCCCCCCCHHHHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHhhccc--cccHHHHHHHHHHHHHHHH
Confidence 9999998 677889999999999999999999999999999999999999999996531 2244689999999999999
Q ss_pred HHHHHccCCcCCCCCCCCccceEEEeCCCCCCCceeEEEeCCeEEEEEEEecCCccccccccccCCcccEEEEEeecCCC
Q psy3754 370 RKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPF 449 (755)
Q Consensus 370 r~~~l~~~~R~DGR~~~e~R~i~ie~g~l~~a~GSal~~~G~T~Vl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~f~p~ 449 (755)
|++++++|+|+|||.++++|||+|++|++|++||||+|++|+|||+|++++||..+++..+.+.+++.++|+|||+||||
T Consensus 327 r~~il~~g~R~DGR~~~eiR~i~~~~g~l~~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~~~~~~~~~~YnfpPF 406 (719)
T TIGR02696 327 RERVLTEGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPETSKRYMHHYNFPPY 406 (719)
T ss_pred HHHHhcCCCCCCCCCccccccceeecCCCCCCCceEEEEecCcEEEEEEeCCCchhhhhcccccccccceEEEEEeCCCC
Confidence 99999999999999999999999999999999999999999999999999999999998888877889999999999999
Q ss_pred CcccccCCCCCChhHHHHHHHHHHhccccCCCCCCCceEEEEEEEEEccCCChhhHHHHHHHHHHHhCCCCcccceEEEE
Q psy3754 450 ATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIA 529 (755)
Q Consensus 450 s~~e~~~~g~~~~rei~~~~lieral~~vi~~~~~~p~tI~V~v~VLe~dGs~~~Aav~a~slAL~daGvPi~~~va~vs 529 (755)
|++|+++.++++||+++|++|++|+|++++|..++|||+|+++++||++|||++|||+||+|||||||||||+++|+|||
T Consensus 407 St~er~~~~~~~RReighg~La~rALe~vI~~~e~fP~TIrvvseVLeSdGSss~AsIcaasLALmDAGVPmkd~VAgis 486 (719)
T TIGR02696 407 STGETGRVGSPKRREIGHGALAERALVPVLPSREEFPYAIRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPVAGIA 486 (719)
T ss_pred cccCCCCCCCCCccHHHHHHHHHHHHHHhhCcHhhCCCEEEEEEEeeccCCcHHHHHHHHHHHHHHHcCcchhheeeEEE
Confidence 99999999999999999999999999999996689999999999999999999999999999999999999999999999
Q ss_pred EEEEec---Cc-eEEEEecCCccccccCCccEEEEeecCcEEEEEeeecccccCHHHHHHHHHHHHhhhHHHHHHHHhhc
Q psy3754 530 MGLIKD---GE-KVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEV 605 (755)
Q Consensus 530 ~gli~~---~~-~~~vL~Dp~~~Ee~~gd~~~~Va~t~~gi~alq~~~k~~~is~~~l~~al~~A~~~~~~I~~~~~~~l 605 (755)
||++.+ ++ +|.+|+||++.||+.|+|||+|+++.+|||++|||++..|++.++|.+||++|+++|.+|++.|++++
T Consensus 487 ~Gli~e~~~~~~~~~iL~Di~g~ED~~Gdmdfkvagt~~gIt~lQmd~ki~gi~~e~l~~aL~~A~~g~~~Il~~m~~al 566 (719)
T TIGR02696 487 MGLISDEVDGETRYVALTDILGAEDAFGDMDFKVAGTSEFVTALQLDTKLDGIPASVLASALKQARDARLAILDVMAEAI 566 (719)
T ss_pred EEEeccccCCCcceeEEeCCCchhhhcCCceEEEEecCCCEEEEEEEeeECCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999976 54 79999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccccCCCceeEEeeCCcccceeeccccceeeeeccccceEEeecCceeEEEEecChhhhHHHHHHHHHhhh--cc
Q psy3754 606 PKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTE--SV 683 (755)
Q Consensus 606 ~~~r~~~~~~~P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~G~v~i~~~~~~~~~~a~~~i~~~~~--~~ 683 (755)
..| .++++++|++++++|||+||+++||||||+||+|+++||++|||+++|.|.|++.+...+++|+++|+.+.. .+
T Consensus 567 ~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~ 645 (719)
T TIGR02696 567 DTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDDGTVYIGAADGPSAEAARAMINAIANPTMP 645 (719)
T ss_pred hCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecCcEEEEEeCCHHHHHHHHHHHHHhhCcCcC
Confidence 999 899999999999999999999999999999999999999999999999999999999999999999999998 69
Q ss_pred cCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccC----cccccCcccccCCCCEEEEEEEEEcCCCcEEEE
Q psy3754 684 QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS----SKRVNIITDFLKENQKVRVKVLGIDDRGRIKLS 752 (755)
Q Consensus 684 ~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~----~~~~~~~~~~~kvGd~V~VkV~~id~~gki~LS 752 (755)
++|++|+|+|++|++||+||+|.+|.+||||+|||+ |.++.++.++|++||+|+|||+++|.+|||+|+
T Consensus 646 ~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~~gKI~L~ 718 (719)
T TIGR02696 646 EVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDDRGKLSLV 718 (719)
T ss_pred CCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECCCCCeeec
Confidence 999999999999999999999999999999999996 478999999999999999999999988999986
No 2
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-168 Score=1400.47 Aligned_cols=689 Identities=56% Similarity=0.918 Sum_probs=676.0
Q ss_pred ccceeeEeeeeCCeeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecCCCCCCCCcceeeEEeEeeccccCCCCCCcccc
Q psy3754 64 LFNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYIEKAYAAGRIPGSFFKR 143 (755)
Q Consensus 64 ~~~~~~~~~~~~~r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~~~~~~~~f~pl~v~y~e~~~a~g~ip~~~~kR 143 (755)
||+.+.++++||||++.+|||++|+||+|||+++||+|.|||||++++ ++++.|||||+|+|+||+||+|||||||+||
T Consensus 1 ~~~~~~~~~~~~~~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~-~~~~~dF~PLtV~y~Ek~yaaGkiPGgf~kR 79 (692)
T COG1185 1 MFNKIVKTIEWGGRTLTLETGKIARQANGAVLVRYGDTVVLATVVASK-PKEGQDFFPLTVNYEEKTYAAGKIPGGFFKR 79 (692)
T ss_pred CCcceEEEEEECCeeEEEEcchhhhhcCccEEEEECCeEEEEEEeecC-CCCCCCccceeEeeeeehhccCcCCCccccc
Confidence 567788899999999999999999999999999999999999999998 8899999999999999999999999999999
Q ss_pred cCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCE
Q psy3754 144 EGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGK 223 (755)
Q Consensus 144 eg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP~~~~vaav~vg~~~g~ 223 (755)
||||+++|+|+|||||||||||||++|++++||+++|+|+|+.++|+++|++|||+||++|+|||.+|+|+||||++||+
T Consensus 80 EGrpse~e~L~sRLIDRpiRPlFp~g~~~evqIv~tvls~D~~~~pdi~a~~gaSaAl~is~iPf~gpi~~vrvg~idg~ 159 (692)
T COG1185 80 EGRPSEKEILTSRLIDRPIRPLFPKGFRNEVQIVNTVLSVDPENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYIDGI 159 (692)
T ss_pred CCCCCccchhhhhhcccccccccchhhccceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCccCccceEEEEEECCE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEcCCHHHHhcCcccEEEEeecCceEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCCCCCCh
Q psy3754 224 YILNPTTEQLKKSHLDLLVAGTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 303 (755)
Q Consensus 224 ~vldPt~~E~~~s~~~l~va~~~~~i~mie~~~~~~se~~~~~al~~a~~~~~~i~~~~~~~~~~~~~~k~~~~~~~~~~ 303 (755)
|++|||.+|.+.|++||+||||+++|+|+|+++++++|++|++|+.+||++++.+|++|+++....|+++++|.+...++
T Consensus 160 ~vlNPt~~e~~~s~lDlvVAGT~~aV~MVE~~a~~l~E~~ml~Av~fg~~~~~~~~~~qe~l~~~~g~~~~~~~~~~~~~ 239 (692)
T COG1185 160 FVLNPTLEELEESKLDLVVAGTKDAVNMVESEADELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKWELEPPSLDE 239 (692)
T ss_pred EEECCChHHhhhcceeeEecCChhhhheeecccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccccCccH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999888999
Q ss_pred hHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHhhcccCCcCChhhHHHHHHHHHHHHHHHHHHccCCcCCCC
Q psy3754 304 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYDLESKIIRKQILDKGLRIDNR 383 (755)
Q Consensus 304 ~l~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~l~~~~R~DGR 383 (755)
++...+++.+.+++.+++.+.+|++|..+++++++++.++|...+ .....++..+|+.++++.+|.+|++.++|+|||
T Consensus 240 ~l~~~i~~~~~~~l~~a~~i~~K~eR~~~~~~~~~~i~~~~~~~e--~~~~~~~~~~~~~l~~~~vR~~Il~~~vR~DGR 317 (692)
T COG1185 240 ELEAKVRDLAEDELKEAVGIREKQERSAALDAIKEKIEEELSGEE--ESSLKEIKAILEKLEKKPVRRLILEGKVRIDGR 317 (692)
T ss_pred HHHHHHHHHhHHHHHHHhcccchhhhhhhHHHHHHHHHHHHhhhc--cccHHHHHHHHHHHhHHHHHHHHhcCCcccCCC
Confidence 999999999999999999999999999999999999999997642 223679999999999999999999999999999
Q ss_pred CCCCccceEEEeCCCCCCCceeEEEeCCeEEEEEEEecCCccccccccccCCcccEEEEEeecCCCCcccccCCCCCChh
Q psy3754 384 GVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRR 463 (755)
Q Consensus 384 ~~~e~R~i~ie~g~l~~a~GSal~~~G~T~Vl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~f~p~s~~e~~~~g~~~~r 463 (755)
..+++||+.|++|+||++|||++|+||+||+++++|||+..+.|..|.+.++..++|++||||||||+||++|.|.|+||
T Consensus 318 ~~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~v~TLG~~~d~Qvid~l~~e~~krfm~hYNFPp~SvGE~g~~g~p~RR 397 (692)
T COG1185 318 FGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPRDAQVIDILEGEYKKRFLLHYNFPPFSVGETGRMGSPGRR 397 (692)
T ss_pred CcceeeeeeEEecCCCCccchhhhccCCCcceEEEEcCCcchhhhhhhccchhhhheeeeccCCCCCccccCCCCCCCcc
Confidence 99999999999999999999999999999999999999999999999999888999999999999999999999999999
Q ss_pred HHHHHHHHHHhccccCCCCCCCceEEEEEEEEEccCCChhhHHHHHHHHHHHhCCCCcccceEEEEEEEEecCceEEEEe
Q psy3754 464 EIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILS 543 (755)
Q Consensus 464 ei~~~~lieral~~vi~~~~~~p~tI~V~v~VLe~dGs~~~Aav~a~slAL~daGvPi~~~va~vs~gli~~~~~~~vL~ 543 (755)
|+|||+|++|++.+++|..+.|||+||++++|++||||++||++|+++|||||||||++.+|||++|||+.++|+|.+|+
T Consensus 398 EiGHG~LA~Ral~~vlp~~e~fpytiRvVsEi~eSNGSsSmaSVCg~sLaLmdAGVPIk~pVAGIAMGLI~eg~~~~vLs 477 (692)
T COG1185 398 EIGHGALAERALAPVLPSEEEFPYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVLS 477 (692)
T ss_pred cccCchhhHHHHhhhCCchhcCCceeeeeehhhcccCcccchhhhhhHHHHHhCCCcccccccchhccceecCCceEeec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCccccccCCccEEEEeecCcEEEEEeeecccccCHHHHHHHHHHHHhhhHHHHHHHHhhccccccccccCCCceeEEe
Q psy3754 544 DILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIK 623 (755)
Q Consensus 544 Dp~~~Ee~~gd~~~~Va~t~~gi~alq~~~k~~~is~~~l~~al~~A~~~~~~I~~~~~~~l~~~r~~~~~~~P~~~~~~ 623 (755)
|+.+.|||+|||||+||+|.+||||+|||.|+.|++.+++.+||.+|+.++.+|+..|.+++..+|++++.|+|++++++
T Consensus 478 DI~G~EDhlGDMDFKVAGT~~GiTAlQMDiKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~ 557 (692)
T COG1185 478 DILGDEDHLGDMDFKVAGTDDGITALQMDIKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIK 557 (692)
T ss_pred cccccccccCCceeEEecCCCcceeeeeeeeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eCCcccceeeccccceeeeeccccceEEeecCceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEeeeEEE
Q psy3754 624 IDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAII 703 (755)
Q Consensus 624 i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~fG~FV 703 (755)
|+|+||+++||||||+|++|+++||++|+|++||+|.|++.+....++|++.|+.+..++++|++|.|+|++|.+||+||
T Consensus 558 i~~dKI~dvIG~gGk~I~~I~eetg~~IdieddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv 637 (692)
T COG1185 558 IDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFV 637 (692)
T ss_pred cCHHHHhhccCCcccchhhhhhhhCcEEEecCCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcEEEEEeC
Q psy3754 704 RILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRIKLSMIY 755 (755)
Q Consensus 704 el~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki~LS~k~ 755 (755)
+|.+|.+||+|+|++++.|+.+.++++++||.|.||++++|.+||++||++.
T Consensus 638 ~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~Gri~ls~~~ 689 (692)
T COG1185 638 ELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQGRIRLSIKA 689 (692)
T ss_pred EecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeecccCCccceehh
Confidence 9999999999999999999999999999999999999999999999999973
No 3
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=100.00 E-value=4.6e-159 Score=1383.20 Aligned_cols=690 Identities=41% Similarity=0.697 Sum_probs=660.5
Q ss_pred ceeeEeeeeCCeeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecCCCCCCCCcceeeEEeEeeccccCCCCCCcccccC
Q psy3754 66 NKIIKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYIEKAYAAGRIPGSFFKREG 145 (755)
Q Consensus 66 ~~~~~~~~~~~r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~~~~~~~~f~pl~v~y~e~~~a~g~ip~~~~kReg 145 (755)
++..+.+++|+|++.+|||++|+||+|||++++|+|.|||||+..++++++.|||||+|+|+||+||+|||||||+||||
T Consensus 78 ~~~~~~~~~g~~~~~~etG~~a~qA~gav~v~~g~t~vl~t~~~~~~~~~~~dF~PLtV~y~Ek~~AaGkipggf~kREg 157 (891)
T PLN00207 78 QQFSVKIPVGDRHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPSEPSDFFPLSVHYQERFSAAGRTSGGFFKREG 157 (891)
T ss_pred cceEEEEEECCEEEEEEhhHHHHhCCCcEEEEECCeEEEEEEEeccCCCCCCCccceeEeeeeehhhcCccCCceeccCC
Confidence 34556778887899999999999999999999999999999999888999999999999999999999999999999999
Q ss_pred CCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEE
Q psy3754 146 KPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYI 225 (755)
Q Consensus 146 ~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP~~~~vaav~vg~~~g~~v 225 (755)
+|+++|+|+||+|||+|||+||++|++++||+++||++||+++|+++||||||+||++|||||++||+|||||++||++|
T Consensus 158 rp~d~eiL~sRlIdR~lRPlfp~~~~~etQI~i~VLsaDg~~~pd~~AInAASaAL~~SgIP~~gpVaAVrVG~idg~~V 237 (891)
T PLN00207 158 RTKDHEVLICRLIDRPLRPTMPKGFYHETQILSWVLSYDGLHSPDSLAVTAAGIAVALSEVPNLKAIAGVRVGLIGGKFI 237 (891)
T ss_pred CCChHHHHHHHHHCccchhhccccCCCCcEEEEEEEeeCCCCChhhHHHHHHHHHHHhhCCCccCceEEEEEEEECCEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcCCHHHHhcCcccEEEEeecCceEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCCCCCChhH
Q psy3754 226 LNPTTEQLKKSHLDLLVAGTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDKTL 305 (755)
Q Consensus 226 ldPt~~E~~~s~~~l~va~~~~~i~mie~~~~~~se~~~~~al~~a~~~~~~i~~~~~~~~~~~~~~k~~~~~~~~~~~l 305 (755)
||||++|++.|++||+|+|++++|+|+|++++++++++|.+||++||++|+.++++|+++++++|++|+++.....+++|
T Consensus 238 lnPt~~E~~~s~ldLvvagt~~~IvMIE~~a~e~see~l~~Al~~a~~aik~i~~~~~el~~~~gk~k~~~~~~~~~~~l 317 (891)
T PLN00207 238 VNPTTKEMEESELDLIMAGTDSAILMIEGYCNFLPEEKLLEAVEVGQDAVRAICKEIEVLVKKCGKPKMLDAIKLPPPEL 317 (891)
T ss_pred ECCCHHHHhcCCeeEEEEEcCCeEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCCCCCCCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999988889999
Q ss_pred HHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHhhccc--------------------CCc--------------
Q psy3754 306 ISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNE--------------------NLT-------------- 351 (755)
Q Consensus 306 ~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~--------------------~~~-------------- 351 (755)
.+.+++.+.++|++++.+.+|.+|++++++|++++.+.|.+.. ...
T Consensus 318 ~~~v~~~~~~~~~~~~~~~~K~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 397 (891)
T PLN00207 318 YKHVKEIAGDELVKALQIRGKIPRRKALSSLEEKVLSILTEEGYVSKDESFGTSETRADLLEDEDEDEEVVVDGEVDEGD 397 (891)
T ss_pred HHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHhhccccccccccccccccccccccccccchhccccccccccc
Confidence 9999999999999999999999999999999999999885430 000
Q ss_pred --------------CChhhHHHHHHHHHHHHHHHHHHccCCcCCCCCCCCccceEEEeCCCCCCCceeEEEeCCeEEEEE
Q psy3754 352 --------------IDINDINCILYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVV 417 (755)
Q Consensus 352 --------------~~~~~~~~~~~~~~~~~~r~~~l~~~~R~DGR~~~e~R~i~ie~g~l~~a~GSal~~~G~T~Vl~~ 417 (755)
....++..+|++++++++|++++++|+|+|||.++|+|||+|++|++|++||||+|++|+|||||+
T Consensus 398 ~~~~~~~~~~~~~~~~~~~i~~~~~~~~k~~~R~~i~~~g~R~DGR~~~eiRpI~~e~G~Lp~A~GSAlf~~G~TqVLat 477 (891)
T PLN00207 398 VHIKPIPRKSSPLLFSEVDVKLVFKEVTSKFLRRRIVEGGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAV 477 (891)
T ss_pred ccccccccccccccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCcCccceEEEEeCCcCCCCceEEEEECCeEEEEE
Confidence 023469999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecCCccccccccccC-CcccEEEEEeecCCCCcccccCCCCCChhHHHHHHHHHHhccccCCCCCCCceEEEEEEEEE
Q psy3754 418 ATLGTSRDEQKIDALMG-EFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEIT 496 (755)
Q Consensus 418 Vt~Gp~~~~~~~d~~~~-~~~~~~~~~~~f~p~s~~e~~~~g~~~~rei~~~~lieral~~vi~~~~~~p~tI~V~v~VL 496 (755)
|++||.+..+..|++.. +..++|++||+|||||+++.++.|++++||++|++|++|+|++++|.+++|||+|+|+++||
T Consensus 478 VtlGp~~~~q~~d~l~~~~~~~~f~~~y~fPPfs~ge~~r~g~psrREi~hg~L~eRALrpvip~~~~fP~tIrV~~~VL 557 (891)
T PLN00207 478 VTLGDKQMAQRIDNLVDADEVKRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERALEPILPSEDDFPYTIRVESTIT 557 (891)
T ss_pred EEecCccccccccccccccceeeEEEEEEcCCCCCccccCCCCCCHHHHHHHHHHHHHHHHhCCcccCCCEEEEEEEEEE
Confidence 99999988887776533 56789999999999999999999999999999999999999999998778999999999999
Q ss_pred ccCCChhhHHHHHHHHHHHhCCCCcccceEEEEEEEEec-----C-ceEEEEecCCccccccCCccEEEEeecCcEEEEE
Q psy3754 497 ESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKD-----G-EKVVILSDILGDEDRCGDMDFKVAGTVNGITALQ 570 (755)
Q Consensus 497 e~dGs~~~Aav~a~slAL~daGvPi~~~va~vs~gli~~-----~-~~~~vL~Dp~~~Ee~~gd~~~~Va~t~~gi~alq 570 (755)
++|||++||++||+|||||||||||+++|+|++||++.+ + ++|.+|+||++.|++.|+|||+|++|.+||+++|
T Consensus 558 esDGSssmAaV~aaSLALmDAGIPmk~~VAGvsvGli~d~~~~~~~g~~~IL~Dp~g~Ed~~gdmDfkVAgT~~gIt~iq 637 (891)
T PLN00207 558 ESNGSSSMASVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEEFGGDGSPLILSDITGSEDASGDMDFKVAGNEDGITAFQ 637 (891)
T ss_pred eCCCChHHHHHHHHHHHHHhcCCCccCceeEEEEEEEecccccCCCCcEEEEeCCCHHHHhcCCceEEEEecccceEEEE
Confidence 999999999999999999999999999999999999954 2 2678999999999999999999999999999999
Q ss_pred eeecccccCHHHHHHHHHHHHhhhHHHHHHHHhhccccccccccCCCceeEEeeCCcccceeeccccceeeeeccccceE
Q psy3754 571 MDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQ 650 (755)
Q Consensus 571 ~~~k~~~is~~~l~~al~~A~~~~~~I~~~~~~~l~~~r~~~~~~~P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~ 650 (755)
|++++.+++.++|.+||++|++++.+|++.|++++..||.++++++|++++++|+|+||+++||+|||+||+|+++||++
T Consensus 638 md~k~~gis~e~l~eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~ 717 (891)
T PLN00207 638 MDIKVGGITLPIMERALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVE 717 (891)
T ss_pred EecccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred -EeecCceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEE-EEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCccc
Q psy3754 651 -IDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYT-GIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITD 728 (755)
Q Consensus 651 -I~i~~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~-G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~ 728 (755)
||++++|.|.|++.+...+++++++|+.+..++++|++|+ |+|++|++||+||+|.++.+||||+|+|+|+++.++.+
T Consensus 718 ~Idi~ddg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~d 797 (891)
T PLN00207 718 AIDTQDDGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPED 797 (891)
T ss_pred ccCcCCCeeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHH
Confidence 9999999999999999999999999999999999999996 69999999999999999999999999999999999999
Q ss_pred ccCCCCEEEEEEEEEcCCCcEEEEEeC
Q psy3754 729 FLKENQKVRVKVLGIDDRGRIKLSMIY 755 (755)
Q Consensus 729 ~~kvGd~V~VkV~~id~~gki~LS~k~ 755 (755)
+|++||.|+|||+++|.+|||.||+|.
T Consensus 798 v~kvGD~V~VkVi~ID~~grI~LSlK~ 824 (891)
T PLN00207 798 AFKVGDRIDVKLIEVNDKGQLRLSRRA 824 (891)
T ss_pred hcCCCCEEEEEEEEECCCCcEEEEEec
Confidence 999999999999999988999999983
No 4
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=100.00 E-value=7.1e-153 Score=1340.11 Aligned_cols=691 Identities=57% Similarity=0.938 Sum_probs=669.4
Q ss_pred ccceeeEeeeeCCeeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecCCCCCCCCcceeeEEeEeeccccCCCCCCcccc
Q psy3754 64 LFNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYIEKAYAAGRIPGSFFKR 143 (755)
Q Consensus 64 ~~~~~~~~~~~~~r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~~~~~~~~f~pl~v~y~e~~~a~g~ip~~~~kR 143 (755)
||+.+.+++++|+|++++|||++|+||||||++++|+|+|||||+++.+|+++.+|+||+|+|+|++||+|||||||+||
T Consensus 1 ~~~~~~~~~~~~~r~i~~e~G~ia~qAdGSa~v~~G~T~VlatV~~~~~~~~~~df~pL~v~y~e~~~A~gkiP~~f~kr 80 (693)
T PRK11824 1 MFNKIVKSIEFGGRTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKEPKEGQDFFPLTVDYEEKTYAAGKIPGGFFKR 80 (693)
T ss_pred CCceEEEEEEECCccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCCCCCeeeeEEEEEehhhhccCCCcccccC
Confidence 45666778888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCE
Q psy3754 144 EGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGK 223 (755)
Q Consensus 144 eg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP~~~~vaav~vg~~~g~ 223 (755)
||+|+++|+|++|+|||+|||+||++|+|++||+++||++||+++++++|+||||+||++|+|||.+||+||++|++||+
T Consensus 81 eg~pse~eil~srlIdR~lrplfp~~~~~~i~I~~~VL~~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~i~g~ 160 (693)
T PRK11824 81 EGRPSEKETLTSRLIDRPIRPLFPKGFRNEVQVVATVLSVDPENDPDILAMIGASAALSISGIPFNGPIAAVRVGYIDGE 160 (693)
T ss_pred CCCCChHHHHHHHHHhhhHHHhCCCCCCeEEEEEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEcCCHHHHhcCcccEEEEeecCceEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCCCCCCh
Q psy3754 224 YILNPTTEQLKKSHLDLLVAGTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 303 (755)
Q Consensus 224 ~vldPt~~E~~~s~~~l~va~~~~~i~mie~~~~~~se~~~~~al~~a~~~~~~i~~~~~~~~~~~~~~k~~~~~~~~~~ 303 (755)
+|+|||.+|++.|++||+|+++.+.|+|+|++++++++++|.+||++|+++|++++++|+++++++| +|+++.....++
T Consensus 161 ~ivdPt~~E~~~s~~~l~va~t~~~i~mie~~~~~l~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~-~~~~~~~~~~~~ 239 (693)
T PRK11824 161 FVLNPTVEELEESDLDLVVAGTKDAVLMVESEAKELSEEVMLEAIEFGHEAIQELIDAQEELAAEAG-PKWEWQPPEVDE 239 (693)
T ss_pred EEEcCCHHHHhhCcceEEEEEccCceEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCcccCCCCCCH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999 999999888999
Q ss_pred hHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHhhcccCCcCChhhHHHHHHHHHHHHHHHHHHccCCcCCCC
Q psy3754 304 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYDLESKIIRKQILDKGLRIDNR 383 (755)
Q Consensus 304 ~l~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~l~~~~R~DGR 383 (755)
+|.+.+++++.++|++++.+.+|.+|+++++++++++.++|.+...++.+..++..+|++++++.+|++++++|+|+|||
T Consensus 240 ~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~g~R~DGR 319 (693)
T PRK11824 240 ELKAAVKELAEAKLKEAYQITDKQEREAALDAIKEEVLEALAAEEEEEEDEKEIKEAFKKLEKKIVRRRILEEGIRIDGR 319 (693)
T ss_pred HHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCCC
Confidence 99999999999999999999999999999999999999999753223446679999999999999999999999999999
Q ss_pred CCCCccceEEEeCCCCCCCceeEEEeCCeEEEEEEEecCCccccccccccCCcccEEEEEeecCCCCcccccCCCCCChh
Q psy3754 384 GVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRR 463 (755)
Q Consensus 384 ~~~e~R~i~ie~g~l~~a~GSal~~~G~T~Vl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~f~p~s~~e~~~~g~~~~r 463 (755)
.++|+|||+|++|++|++||||+|++|+|||+|+||+||..+.+..+.+..++.++|++||+|||||++++++.|+|++|
T Consensus 320 ~~~e~Rpi~~~~g~l~~a~GSal~~~G~T~Vl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~~~~~~~rr 399 (693)
T PRK11824 320 KLDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTLRDEQIIDGLEGEYKKRFMLHYNFPPYSVGETGRVGSPGRR 399 (693)
T ss_pred CcCcccceEEEeCCCCCCCceEEEEECCeEEEEEEecCCCcccccccccCCCCcEEEEEEEEcCCCCCCCcCCCCCCChh
Confidence 99999999999999999999999999999999999999987777777776778999999999999999999999999999
Q ss_pred HHHHHHHHHHhccccCCCCCCCceEEEEEEEEEccCCChhhHHHHHHHHHHHhCCCCcccceEEEEEEEEecCceEEEEe
Q psy3754 464 EIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILS 543 (755)
Q Consensus 464 ei~~~~lieral~~vi~~~~~~p~tI~V~v~VLe~dGs~~~Aav~a~slAL~daGvPi~~~va~vs~gli~~~~~~~vL~ 543 (755)
+++|+++++|+|++++|++++|||+|+|+++||++|||++|||+||+++|||||||||+++|+|++||+++++++|.+|+
T Consensus 400 e~~~~~li~ral~~vi~~~~~~p~~I~v~~~VLe~dGs~~~Aai~aaslAL~dAgvP~~~~Va~vs~gli~~~~~~~il~ 479 (693)
T PRK11824 400 EIGHGALAERALEPVLPSEEEFPYTIRVVSEILESNGSSSMASVCGSSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVLT 479 (693)
T ss_pred HHHHHHHHHHHHHHhcCcccCCCEEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCccCceeEEEEEEEcCCCceEEEc
Confidence 99999999999999999888999999999999999999999999999999999999999999999999998777789999
Q ss_pred cCCccccccCCccEEEEeecCcEEEEEeeecccccCHHHHHHHHHHHHhhhHHHHHHHHhhccccccccccCCCceeEEe
Q psy3754 544 DILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIK 623 (755)
Q Consensus 544 Dp~~~Ee~~gd~~~~Va~t~~gi~alq~~~k~~~is~~~l~~al~~A~~~~~~I~~~~~~~l~~~r~~~~~~~P~~~~~~ 623 (755)
||++.||+.++|+|+|++|.+|||++||++|.++++.++|.+|+++|+.++.+|++.|++++..+++++++++|++++++
T Consensus 480 D~~~~Ed~~~d~d~~va~t~~gi~~lq~d~k~~~i~~~~l~~al~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~ 559 (693)
T PRK11824 480 DILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGITREILEEALEQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIK 559 (693)
T ss_pred CCChhhHhhCCceEEEEecCCceEEEEEecccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhhhcccCchheeec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eCCcccceeeccccceeeeeccccceEEeecCceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEeeeEEE
Q psy3754 624 IDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAII 703 (755)
Q Consensus 624 i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~fG~FV 703 (755)
|||+||+++||+||++||.|+++||+.||++++|.+++++.+...+++|+++++.+..++++|++|.|+|++|.+||+||
T Consensus 560 I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafV 639 (693)
T PRK11824 560 IPPDKIRDVIGPGGKTIREITEETGAKIDIEDDGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFV 639 (693)
T ss_pred CCHHHHHHHhcCCchhHHHHHHHHCCccccCCCceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEECCeEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcEEEEEeC
Q psy3754 704 RILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRIKLSMIY 755 (755)
Q Consensus 704 el~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki~LS~k~ 755 (755)
+|.++.+||+|+|+++|+++.++.++|++||.|+|||+++|..|+|.||+|.
T Consensus 640 ei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~grI~LS~k~ 691 (693)
T PRK11824 640 EILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRKA 691 (693)
T ss_pred EECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCCCcEEEEEEe
Confidence 9999999999999999999999999999999999999999988999999984
No 5
>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=2e-152 Score=1332.98 Aligned_cols=678 Identities=56% Similarity=0.918 Sum_probs=656.2
Q ss_pred eCCeeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecCCCCCCCCcceeeEEeEeeccccCCCCCCcccccCCCCchhhH
Q psy3754 74 YGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYIEKAYAAGRIPGSFFKREGKPSERETI 153 (755)
Q Consensus 74 ~~~r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~~~~~~~~f~pl~v~y~e~~~a~g~ip~~~~kReg~p~~~e~l 153 (755)
+|+|++++|||++|+||||||++++|+|+|||||+++.+++++.+|+||+|+|+|++||+|+|||||+||||+|+++|+|
T Consensus 2 ~~~R~i~ie~G~la~~AdGSa~v~~G~T~VlatV~~~~~~~~~~df~pL~vey~e~~~A~gkipg~f~kReg~p~~~eil 81 (684)
T TIGR03591 2 YGGRTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKEAKEGQDFFPLTVNYQEKFYAAGKIPGGFFKREGRPSEKETL 81 (684)
T ss_pred CCCccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCCCCceEeEEEEEEehhhhccCCCCCcccCCCCCCHHHHH
Confidence 36789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCCHHHH
Q psy3754 154 ISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQL 233 (755)
Q Consensus 154 ~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP~~~~vaav~vg~~~g~~vldPt~~E~ 233 (755)
++|+|||+|||+||++|+|++||+++||++||+++|+++|+||||+||++|+|||++||+||+||++||++++|||.+|+
T Consensus 82 ~srlIdR~lrplfp~~~~~~i~V~~~VLs~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~idg~~ildPt~~E~ 161 (684)
T TIGR03591 82 TSRLIDRPIRPLFPKGFRNEVQVVATVLSYDPENDPDILAIIGASAALAISGIPFNGPIAAVRVGYIDGQYVLNPTVDEL 161 (684)
T ss_pred HHHHHhhHHHHhcCCCCCceEEEEEEEEecCcCCchHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCEEEEcCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCcccEEEEeecCceEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCCCCCChhHHHHHHHHH
Q psy3754 234 KKSHLDLLVAGTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDKTLISKIINIS 313 (755)
Q Consensus 234 ~~s~~~l~va~~~~~i~mie~~~~~~se~~~~~al~~a~~~~~~i~~~~~~~~~~~~~~k~~~~~~~~~~~l~~~~~~~~ 313 (755)
+.|++||+|+++.++++|+|++++++++++|.+||++|+++|++++++|+++++++|++|+++.....+++|.+.+++++
T Consensus 162 ~~s~~~l~va~t~~~i~mie~~~~~i~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~ 241 (684)
T TIGR03591 162 EKSDLDLVVAGTKDAVLMVESEAKELSEEVMLGAIEFGHEEIQPVIEAIEELAEEAGKEKWEFVAPEVDEELKAKVKELA 241 (684)
T ss_pred hhCCceEEEEccCCcEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCCCCCCCHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999998889999999999999
Q ss_pred HH-HHHHHHhccchhHHHHHHHHHHHHHHHHhhccc-CCc--CChhhHHHHHHHHHHHHHHHHHHccCCcCCCCCCCCcc
Q psy3754 314 EH-KIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNE-NLT--IDINDINCILYDLESKIIRKQILDKGLRIDNRGVNDIR 389 (755)
Q Consensus 314 ~~-~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~-~~~--~~~~~~~~~~~~~~~~~~r~~~l~~~~R~DGR~~~e~R 389 (755)
.+ +|++++.+.+|.+|+++++++++++.++|.+.. .++ ....++..+|++++++.+|++++++|+|+|||+++|+|
T Consensus 242 ~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~g~R~DGR~~~e~R 321 (684)
T TIGR03591 242 YEAGLKEAYQITEKQERYAALDAIKEEVLEALAEEEEEEEEADREKEIKEAFKDLEKKIVRERILKEGKRIDGRDLDTIR 321 (684)
T ss_pred hhHHHHHHhhccchHHHHHHHHHHHHHHHHHhhhhcccccccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCcC
Confidence 99 899999999999999999999999999996531 111 24468999999999999999999999999999999999
Q ss_pred ceEEEeCCCCCCCceeEEEeCCeEEEEEEEecCCccccccccccCCcccEEEEEeecCCCCcccccCCCCCChhHHHHHH
Q psy3754 390 PISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGR 469 (755)
Q Consensus 390 ~i~ie~g~l~~a~GSal~~~G~T~Vl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~f~p~s~~e~~~~g~~~~rei~~~~ 469 (755)
||+|++|++|++||||+|++|+|||+|+||+||.++.+..+.+.++..++|++||+|||||++++++.|+|++|+++|++
T Consensus 322 pi~~~~g~l~~a~GSa~~~~G~Tqvl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~~~g~~~rrei~~~~ 401 (684)
T TIGR03591 322 PISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDEQIIDDLEGEYRKRFMLHYNFPPYSVGEVGRVGGPGRREIGHGA 401 (684)
T ss_pred ceEEEeCCCCCCCceEEEEeCCeEEEEEEecCCcccccCCcccCCCccEEEEEEEEcCCCCCCCcCCCCCCChHHHHHHH
Confidence 99999999999999999999999999999999999888777787788999999999999999999999999999999999
Q ss_pred HHHHhccccCCCCCCCceEEEEEEEEEccCCChhhHHHHHHHHHHHhCCCCcccceEEEEEEEEecCc-eEEEEecCCcc
Q psy3754 470 LAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGE-KVVILSDILGD 548 (755)
Q Consensus 470 lieral~~vi~~~~~~p~tI~V~v~VLe~dGs~~~Aav~a~slAL~daGvPi~~~va~vs~gli~~~~-~~~vL~Dp~~~ 548 (755)
|++|+|++++|++++|||+|+|+++||++|||++|||+||+++|||||||||+++|+|+|||++.+++ +|.+|+||++.
T Consensus 402 l~~ral~~~i~~~~~~p~tI~v~~~VLesdGs~~~Aai~aaslAL~dAgvP~~~~Vagvs~gli~~~~~~~~il~D~~~~ 481 (684)
T TIGR03591 402 LAERALKAVLPSEEEFPYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDERFAVLSDILGD 481 (684)
T ss_pred HHHHHHHHhcCccccCCeEEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCCcCCEEEEEEEEEcCCCcceEEEeCCChH
Confidence 99999999999878999999999999999999999999999999999999999999999999997664 58899999999
Q ss_pred ccccCCccEEEEeecCcEEEEEeeecccccCHHHHHHHHHHHHhhhHHHHHHHHhhccccccccccCCCceeEEeeCCcc
Q psy3754 549 EDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSK 628 (755)
Q Consensus 549 Ee~~gd~~~~Va~t~~gi~alq~~~k~~~is~~~l~~al~~A~~~~~~I~~~~~~~l~~~r~~~~~~~P~~~~~~i~~~k 628 (755)
||+.+||+|+|++|.+|||++|++++..+++.++|.+|+++|++++.+|++.|++++..++.++++|+|++++++|||+|
T Consensus 482 Ed~~~d~d~~va~t~~gI~~lq~d~k~~~i~~~~l~~al~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~k 561 (684)
T TIGR03591 482 EDHLGDMDFKVAGTRDGITALQMDIKIDGITREIMEQALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDK 561 (684)
T ss_pred HHhcCCceEEEEEcCCceEEEEEEcCcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceeeccccceeeeeccccceEEeecCceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEeeeEEEEEcCC
Q psy3754 629 IRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSG 708 (755)
Q Consensus 629 i~~~IG~gGk~ik~i~~~~g~~I~i~~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~fG~FVel~~g 708 (755)
|+++||||||+||.|+++||++|+|+++|.|+|++.+...+++|+++++.+...+++|++|.|+|++|.+||+||+|.++
T Consensus 562 I~~vIG~gGk~Ik~I~~~tg~~I~i~ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g 641 (684)
T TIGR03591 562 IRDVIGPGGKVIREITEETGAKIDIEDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPG 641 (684)
T ss_pred HHhhcCCCcHHHHHHHHHHCCEEEEecCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcEEE
Q psy3754 709 KDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRIKL 751 (755)
Q Consensus 709 ~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki~L 751 (755)
.+||||+|+++|+|+.++.++|++||+|+|||+++|.+|+|+|
T Consensus 642 ~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~~gki~L 684 (684)
T TIGR03591 642 KDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDKQGRIKL 684 (684)
T ss_pred cEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECCCCCccC
Confidence 9999999999999999999999999999999999998788865
No 6
>KOG1067|consensus
Probab=100.00 E-value=6e-152 Score=1221.29 Aligned_cols=675 Identities=40% Similarity=0.672 Sum_probs=646.2
Q ss_pred eeEeeeeCCeeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecCCCCCCCCcceeeEEeEeeccccCCCCCCcccccCCC
Q psy3754 68 IIKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYIEKAYAAGRIPGSFFKREGKP 147 (755)
Q Consensus 68 ~~~~~~~~~r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~~~~~~~~f~pl~v~y~e~~~a~g~ip~~~~kReg~p 147 (755)
..+++.+|+|.+.+|||++|++|+|||++++|+|.|++||+...+|.|++ |+||.|+|+||+||.|+||+||+||||+|
T Consensus 47 vsveipfGnR~i~~etGklaRfAngsvvv~~GeT~Vm~Tv~~a~~PSp~q-FlPL~VdYqeK~aAvGRip~~fmRREg~t 125 (760)
T KOG1067|consen 47 VSVEIPFGNREILFETGKLARFANGSVVVQMGETAVMTTVVLADKPSPPQ-FLPLVVDYQEKFAAVGRIPGNFMRREGRT 125 (760)
T ss_pred eeeeeccCCeEEEEecchhhhhcCCcEEEccCCeEEEEEEEecCCCCccc-cceEEEehhhhhhhhccCCCcccccccCC
Confidence 34555569999999999999999999999999999999999999888877 99999999999999999999999999999
Q ss_pred CchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEc
Q psy3754 148 SERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILN 227 (755)
Q Consensus 148 ~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP~~~~vaav~vg~~~g~~vld 227 (755)
+++|+|++|||||+|||+||++|++++|+.|++|++||-.+||++|+|+|++||++|+|||++|+++||+|++||+||+|
T Consensus 126 kdkEiL~~rLidrsirplfp~g~~~etqi~~n~Ls~dG~~~pdvlainaas~Al~lsdvpw~gpig~vRigLi~Ge~vVN 205 (760)
T KOG1067|consen 126 KDKEILTGRLIDRPIRPLFPKGFYHETQILCNVLSSDGVHDPDVLAINAASAALSLSDVPWNGPIGAVRIGLIDGEFVVN 205 (760)
T ss_pred cchhheeeeccccccccCCcccchhHHHHHhhheecccccCchHHHHhHHHHHhhhccCCCCCceeeeEeeeecceEEeC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCHHHHhcCcccEEEEeecCceEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCC-CCCChhHH
Q psy3754 228 PTTEQLKKSHLDLLVAGTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDP-IVKDKTLI 306 (755)
Q Consensus 228 Pt~~E~~~s~~~l~va~~~~~i~mie~~~~~~se~~~~~al~~a~~~~~~i~~~~~~~~~~~~~~k~~~~~-~~~~~~l~ 306 (755)
||.+|++.|++||+|||+++.++|+|+.++++++++|++|++.++++.+.++..|+.+.+++|++|++++. ..+++||.
T Consensus 206 PT~kEmssS~Lnlvvagt~~~~vmle~~s~~i~qqdl~~Aikvg~~~~q~~i~~i~~L~k~~Gk~Kr~~~~~~~p~pel~ 285 (760)
T KOG1067|consen 206 PTRKEMSSSQLNLVVAGTKSQTVMLEGSSNNILQQDLLHAIKVGVKEAQQIIQGIERLAKKYGKQKREPQKLFLPDPELV 285 (760)
T ss_pred cchhhhhhccceeEEEeccceEEEEEcccccccHHHHHHHHHhccHHHHHHHHHHHHHHHHhCccccchhhhcCCCHHHH
Confidence 99999999999999999988999999999999999999999999999999999999999999999999875 55888999
Q ss_pred HHHHHHHHHHHHHHHh--ccchhHHHHHHHHHHHHHHHHhhcccCCcCChhhHHHHHHHHHHHHHHHHHHccCCcCCCCC
Q psy3754 307 SKIINISEHKIRKAYQ--IKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYDLESKIIRKQILDKGLRIDNRG 384 (755)
Q Consensus 307 ~~~~~~~~~~~~~~~~--~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~l~~~~R~DGR~ 384 (755)
.++++++.++|+++++ .+||.+|++|+++|+.+..++..+.+ |+....++.+.|+.+.++.+|++++++|+|+|||.
T Consensus 286 K~v~~la~erl~~vftd~shdK~sR~eAvn~i~~~~e~~~~e~~-pe~e~~~i~~~fn~vskkv~Rs~i~~~gkR~DGR~ 364 (760)
T KOG1067|consen 286 KHVHKLAMERLYAVFTDYSHDKISRDEAVNKIRLDDEDKVKEEF-PEQEPSEIIESFNTVSKKVFRSRILEEGKRCDGRD 364 (760)
T ss_pred HHHHHHHHHHHHHHhcccccccchhhhHHhhhccchHHHHHhhc-CCccHHHHHHHHHHHHHHHHHHHHHhcccccCCcc
Confidence 9999999999999998 56899999999999988888887765 45667899999999999999999999999999999
Q ss_pred CCCccceEEEeCCCCCCCceeEEEeCCeEEEEEEEecCCccccccccccCCccc-EEEEEeecCCCCcccccCCCCCChh
Q psy3754 385 VNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTD-SFMLHYNMPPFATGDIGRIGVPKRR 463 (755)
Q Consensus 385 ~~e~R~i~ie~g~l~~a~GSal~~~G~T~Vl~~Vt~Gp~~~~~~~d~~~~~~~~-~~~~~~~f~p~s~~e~~~~g~~~~r 463 (755)
++|+|||+|+++++++.|||++|+||+|||||+||+|..+..++.|.+.+++++ +||+||+|||||++|.++.|+++||
T Consensus 365 ldelR~I~ce~~m~~~lHGSaLFqRGqTQvlctVtl~s~e~a~klD~l~~~~~~~~FmLhY~FPPyat~Evgkig~~nRR 444 (760)
T KOG1067|consen 365 LDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGPDNGINFMLHYEFPPYATNEVGKIGGLNRR 444 (760)
T ss_pred hhhhcccceecCccccccchhhhhcCceeEEEEEEcCCHHHhhhhhhhccCccCceEEEEeccCCccccccccccCCccc
Confidence 999999999999999999999999999999999999999999999999877776 9999999999999999999999999
Q ss_pred HHHHHHHHHHhccccCCCCCCCceEEEEEEEEEccCCChhhHHHHHHHHHHHhCCCCcccceEEEEEEEEecC-------
Q psy3754 464 EIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDG------- 536 (755)
Q Consensus 464 ei~~~~lieral~~vi~~~~~~p~tI~V~v~VLe~dGs~~~Aav~a~slAL~daGvPi~~~va~vs~gli~~~------- 536 (755)
|++|+.|+||+|.+++| +.|||+|||.++||+||||++||++|++|+||||||||++.+||||+|||+.+-
T Consensus 445 E~GhgaLAEkaL~~vlP--~dfPftIRv~SeVleSnGSsSMASvCGGslALmDaGvPv~a~vAGvaiGlvt~td~e~g~i 522 (760)
T KOG1067|consen 445 ELGHGALAEKALLPVLP--EDFPFTIRVTSEVLESNGSSSMASVCGGSLALMDAGVPVSAHVAGVAIGLVTKTDPEKGEI 522 (760)
T ss_pred ccCchhHhhhhhhccCc--ccCceEEEEeeeeeecCCcchHHhhhcchhhhhhcCCccccccceeEEEeEeccCcccCCc
Confidence 99999999999999999 899999999999999999999999999999999999999999999999999752
Q ss_pred ceEEEEecCCccccccCCccEEEEeecCcEEEEEeeecccccCHHHHHHHHHHHHhhhHHHHHHHHhhccccccccccCC
Q psy3754 537 EKVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCKNELSKFA 616 (755)
Q Consensus 537 ~~~~vL~Dp~~~Ee~~gd~~~~Va~t~~gi~alq~~~k~~~is~~~l~~al~~A~~~~~~I~~~~~~~l~~~r~~~~~~~ 616 (755)
++|.+|+|+++.||+.|||||+||||.+|+||+ ||+.+++++++++|+.++.+|++.|.+++..||...+.|+
T Consensus 523 ~dyriltDIlGiEd~~GDMDFKiAGt~dGvTA~-------gi~l~Iv~eal~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~ 595 (760)
T KOG1067|consen 523 EDYRILTDILGIEDYNGDMDFKIAGTNDGVTAL-------GIPLKIVMEALQKAREARLQILDIMEKNINSPRGSDKEYS 595 (760)
T ss_pred ccceeehhhcchhhhcCCcceeeccccCcceec-------CCcHHHHHHHHHhhhHHHHHHHHHHHhhcCCcccCccccC
Confidence 269999999999999999999999999999998 5789999999999999999999999999999999999999
Q ss_pred CceeEEeeCCcccceeeccccceeeeeccccceEEeecCceeEEEEecChhhhHHHHHHHHHhhh-----cccCCcEEEE
Q psy3754 617 PRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTE-----SVQIGKVYTG 691 (755)
Q Consensus 617 P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~G~v~i~~~~~~~~~~a~~~i~~~~~-----~~~~G~~~~G 691 (755)
|.+++++++|+|...+|||||+..|.|+.+|| .|+..|+|.+.|++++..++++|++.|..+.. +++.|-+|++
T Consensus 596 P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtG-ai~~vDe~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~~l~~g~vy~~ 674 (760)
T KOG1067|consen 596 PVLETLKVSPSKRATLIGPGGVLKKKIEVETG-AISQVDEGTFSIFAPTQAAMEEAKEFIDGIIKDDQVQDLEFGGVYTA 674 (760)
T ss_pred ceeeEEeecchhhheeecCccceeeeEeeecc-ceeeecCceEEEEecCHHHHHHHHHHHHHHhcCccccceEeeeEEEE
Confidence 99999999999999999999999999999999 67777999999999999999999999988875 4678888999
Q ss_pred EEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcEEEEEe
Q psy3754 692 IVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRIKLSMI 754 (755)
Q Consensus 692 ~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki~LS~k 754 (755)
+|+++.++|+||+|+|+..||+|+|||+.+++.+|++.+++||+|.||.++.|+.|.+.||.+
T Consensus 675 tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~~g~~~ls~r 737 (760)
T KOG1067|consen 675 TITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPRGGIMLSSR 737 (760)
T ss_pred EEeeecccceEEEecCCchhhccchhcccccccChHHHHhhcceeEEEEEeecCccceeehhh
Confidence 999999999999999999999999999999999999999999999999999999766666543
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=1.8e-39 Score=336.50 Aligned_cols=225 Identities=30% Similarity=0.487 Sum_probs=202.7
Q ss_pred HHHccCCcCCCCCCCCccceEEEeCCCCCCCceeEEEeCCeEEEEEEEecCCccccccccccCCcccEEEEEeecCCCCc
Q psy3754 372 QILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFAT 451 (755)
Q Consensus 372 ~~l~~~~R~DGR~~~e~R~i~ie~g~l~~a~GSal~~~G~T~Vl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~f~p~s~ 451 (755)
.++++|+|+|||.++|+|++.+++|+++++||||+|++|+|+|+|+|+ ||++..+. ....++.+.+.++|+++||++
T Consensus 2 ~~~~~~~R~DGR~~~e~R~~~~~~g~~~~a~GSa~~~~G~T~Vl~~V~-gp~e~~~~--~~~~~~~~~l~v~~~~~~~a~ 78 (230)
T TIGR02065 2 LILEDGVRLDGRKPDELRPIKIEAGVLKNADGSAYVEFGGTKIIAAVY-GPREMHPR--HLQLPDRAVLRVRYHMAPFST 78 (230)
T ss_pred cccCCCcCCCCCCcccccCeEEEECCCCCCCeEEEEEECCcEEEEEEe-CCCccccc--cccCCCceEEEEEEEeCCccc
Confidence 368899999999999999999999999999999999999999999995 99765433 223356889999999999999
Q ss_pred ccccCCCCCChhHHHHHHHHHHhccccCCCCCCCceE-EEEEEEEEccCCChhhHHHHHHHHHHHhCCCCcccceEEEEE
Q psy3754 452 GDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYS-IRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAM 530 (755)
Q Consensus 452 ~e~~~~g~~~~rei~~~~lieral~~vi~~~~~~p~t-I~V~v~VLe~dGs~~~Aav~a~slAL~daGvPi~~~va~vs~ 530 (755)
.+.++. ++++++++++++++|+|+++++. +.||++ |+|.++||++||+..+|++||+++||+|+||||+++|+++++
T Consensus 79 ~~~~~~-~~~~~~~~~s~~l~~~l~~~i~~-~~~p~~~i~i~v~vl~~DG~~~~aai~aa~lAL~dagIp~~~~v~avtv 156 (230)
T TIGR02065 79 DERKRP-GPSRREIEISKVIREALEPAILL-EQFPRTAIDVFIEVLQADAGTRCAGLTAASLALADAGIPMRDLVVGVAV 156 (230)
T ss_pred CCccCC-CCCccHHHHHHHHHHHHHHHhCh-hhcCCeEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCCccccceeeEEE
Confidence 776654 48899999999999999999997 689987 999999999999999999999999999999999999999999
Q ss_pred EEEecCceEEEEecCCccccccCCccEEEEe--ecCcEEEEEeeecccccCHHHHHHHHHHHHhhhHHHHHHHHhhcccc
Q psy3754 531 GLIKDGEKVVILSDILGDEDRCGDMDFKVAG--TVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKC 608 (755)
Q Consensus 531 gli~~~~~~~vL~Dp~~~Ee~~gd~~~~Va~--t~~gi~alq~~~k~~~is~~~l~~al~~A~~~~~~I~~~~~~~l~~~ 608 (755)
|++++ .+++||+..|+..++++++|+. +.+.++++++++ .++.+++.+|++.|.+++..+.+.|+++++.+
T Consensus 157 ~~~~~----~~v~Dpt~~Ee~~~~~~l~va~~~~~~~i~~i~~~g---~~~~e~~~~~l~~a~~~~~~l~~~~~~~l~~~ 229 (230)
T TIGR02065 157 GKVDG----VVVLDLNEEEDMYGEADMPVAMMPKLGEITLLQLDG---DMTPDEFRQALDLAVKGIKIIYQIQREALKNK 229 (230)
T ss_pred EEECC----eEEECCCHHHhhcCCCceEEEEeCCCCCEEEEEEec---CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 99854 5788999999999999999986 456699999975 58999999999999999999999999998764
No 8
>PRK03983 exosome complex exonuclease Rrp41; Provisional
Probab=100.00 E-value=1.1e-38 Score=333.47 Aligned_cols=225 Identities=31% Similarity=0.488 Sum_probs=203.8
Q ss_pred HHHccCCcCCCCCCCCccceEEEeCCCCCCCceeEEEeCCeEEEEEEEecCCccccccccccCCcccEEEEEeecCCCCc
Q psy3754 372 QILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFAT 451 (755)
Q Consensus 372 ~~l~~~~R~DGR~~~e~R~i~ie~g~l~~a~GSal~~~G~T~Vl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~f~p~s~ 451 (755)
.++++|+|+|||.++|+|++++++|++++++|||+|++|+|+|+|+|+ ||.+..+. ....++++.+.++|+|+||++
T Consensus 8 ~~~~~~~R~DGR~~~~~R~i~i~~G~l~~a~GSa~v~~G~T~Vl~~V~-gp~e~~~~--~~~~~~~~~l~v~~~~~p~~~ 84 (244)
T PRK03983 8 LILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVY-GPREMHPR--HLQLPDRAVLRVRYNMAPFSV 84 (244)
T ss_pred hhccCCCCCCCCCcCcccceEEEeCCCCCCCeEEEEEECCeEEEEEEe-cCCccccc--cccCCCcEEEEEEEEcCCCcc
Confidence 478999999999999999999999999999999999999999999996 99765432 334467899999999999999
Q ss_pred ccccCCCCCChhHHHHHHHHHHhccccCCCCCCCceE-EEEEEEEEccCCChhhHHHHHHHHHHHhCCCCcccceEEEEE
Q psy3754 452 GDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYS-IRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAM 530 (755)
Q Consensus 452 ~e~~~~g~~~~rei~~~~lieral~~vi~~~~~~p~t-I~V~v~VLe~dGs~~~Aav~a~slAL~daGvPi~~~va~vs~ 530 (755)
.+.++. ++++++++++++++|+|+++++. +.||++ |+|.++||++|||..+||+||+++||+|+||||+++++++++
T Consensus 85 ~~~~~~-~~~~~~~~~s~~l~~~l~~~i~~-~~~p~~~I~I~i~VL~~DG~~~~aai~Aa~lAL~dagIp~~~~v~avtv 162 (244)
T PRK03983 85 DERKRP-GPDRRSIEISKVIREALEPAIML-ELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAV 162 (244)
T ss_pred ccccCC-CCChhHHHHHHHHHHHHHHhccH-HhCCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHhcCCccccceeEEEE
Confidence 776544 58899999999999999999997 778987 999999999999999999999999999999999999999999
Q ss_pred EEEecCceEEEEecCCccccccCCccEEEEee-cCc-EEEEEeeecccccCHHHHHHHHHHHHhhhHHHHHHHHhhcccc
Q psy3754 531 GLIKDGEKVVILSDILGDEDRCGDMDFKVAGT-VNG-ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKC 608 (755)
Q Consensus 531 gli~~~~~~~vL~Dp~~~Ee~~gd~~~~Va~t-~~g-i~alq~~~k~~~is~~~l~~al~~A~~~~~~I~~~~~~~l~~~ 608 (755)
+++++ .+++||+..|+..++++++|+.+ ..| |+++++++ .++.+++.+|++.|++++..|.+.|+++++..
T Consensus 163 ~~~~~----~~i~DPt~~Ee~~~~~~l~va~~~~~~~I~~l~~~G---~~~~~~~~~~i~~A~~~~~~i~~~i~~~l~~~ 235 (244)
T PRK03983 163 GKVDG----VIVLDLNKEEDNYGEADMPVAIMPRLGEITLLQLDG---NLTREEFLEALELAKKGIKRIYQLQREALKSK 235 (244)
T ss_pred EEECC----EEEECCCHHHhccCCceEEEEEECCCCCEEEEEEec---CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99865 58899999999999999999987 344 99999975 58999999999999999999999999998864
No 9
>PRK00173 rph ribonuclease PH; Reviewed
Probab=100.00 E-value=2.6e-37 Score=321.75 Aligned_cols=221 Identities=24% Similarity=0.325 Sum_probs=196.6
Q ss_pred CcCCCCCCCCccceEEEeCCCCCCCceeEEEeCCeEEEEEEEecCCccccccccccCCcccEEEEEeecCCCCcccccC-
Q psy3754 378 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGR- 456 (755)
Q Consensus 378 ~R~DGR~~~e~R~i~ie~g~l~~a~GSal~~~G~T~Vl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~f~p~s~~e~~~- 456 (755)
+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|+ ++... +.....++.+.++++|+++|||+.+..+
T Consensus 1 ~R~DGR~~~e~R~i~~~~g~~~~a~GSa~v~~G~T~Vla~V~-~~~~~---p~~~~~~~~g~l~v~~~~~p~a~~~~~~~ 76 (238)
T PRK00173 1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTAS-VEEGV---PRFLKGQGQGWVTAEYGMLPRATHTRNDR 76 (238)
T ss_pred CCCCCCCcccccCeEEEeCCCCCCCeeEEEEecCcEEEEEEE-cCCCC---CCccCCCCcEEEEEEEecCCCCCcccccc
Confidence 599999999999999999999999999999999999999997 55432 1122345689999999999999987632
Q ss_pred ---CCCCChhHHHHHHHHHHhccccCCCCCCCceEEEEEEEEEccCCChhhHHHHHHHHHHHhC-----------CCCcc
Q psy3754 457 ---IGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDA-----------GVPIS 522 (755)
Q Consensus 457 ---~g~~~~rei~~~~lieral~~vi~~~~~~p~tI~V~v~VLe~dGs~~~Aav~a~slAL~da-----------GvPi~ 522 (755)
.|++++++++++++++|+|+++++++.+..++|+|+++||++|||..+|+++|+++||+|| |+||+
T Consensus 77 ~~~~g~~~~~~~~~sr~i~r~lr~~i~l~~l~~~~i~v~v~VL~~DG~~~~aai~Aa~~AL~da~~~~~~~~~~~~ip~~ 156 (238)
T PRK00173 77 EAAKGKQGGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKNPLK 156 (238)
T ss_pred cccCCCCCccHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhhhhhhccCcccCCccc
Confidence 3567889999999999999999998444345699999999999999999999999999999 99999
Q ss_pred cceEEEEEEEEecCceEEEEecCCccccccCCccEEEEeecCc-EEEEEeeecccccCHHHHHHHHHHHHhhhHHHHHHH
Q psy3754 523 EHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 601 (755)
Q Consensus 523 ~~va~vs~gli~~~~~~~vL~Dp~~~Ee~~gd~~~~Va~t~~g-i~alq~~~k~~~is~~~l~~al~~A~~~~~~I~~~~ 601 (755)
++|+++++|++.+ .+|+||+..|+..++.+++|+.+.+| |+++|++++..+++.++|.+|++.|++.+.+|.+.|
T Consensus 157 ~~~~~vt~~~~~~----~~lvDpt~~Ee~~~~~~l~v~~~~~~~i~~v~~~g~g~~~~~e~l~~~i~~A~~~~~~l~~~~ 232 (238)
T PRK00173 157 DQVAAVSVGIVDG----EPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTAEGAPFSREELDALLDLAEKGIAELVALQ 232 (238)
T ss_pred CceeEEEEEEECC----EEEECCCHHHHhcCCceEEEEECCCCCEEEEEccCCCCCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999965 58899999999999999999998866 999999766668999999999999999999999999
Q ss_pred Hhhcc
Q psy3754 602 KTEVP 606 (755)
Q Consensus 602 ~~~l~ 606 (755)
++++.
T Consensus 233 ~~~l~ 237 (238)
T PRK00173 233 KAALA 237 (238)
T ss_pred HHHhc
Confidence 99875
No 10
>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=2.8e-36 Score=313.70 Aligned_cols=218 Identities=28% Similarity=0.368 Sum_probs=191.6
Q ss_pred cCCCCCCCCccceEEEeCCCCCCCceeEEEeCCeEEEEEEEecCCccccccccccCCcccEEEEEeecCCCCcccc-cC-
Q psy3754 379 RIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDI-GR- 456 (755)
Q Consensus 379 R~DGR~~~e~R~i~ie~g~l~~a~GSal~~~G~T~Vl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~f~p~s~~e~-~~- 456 (755)
|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|+ ++... + .....++++.+.++|+|+||++.+. ++
T Consensus 1 R~DGR~~~e~R~i~i~~G~~~~A~GSa~v~~G~T~Vla~V~-~~~~~-p--~~~~~~~~g~l~v~~~~~p~a~~~~~~r~ 76 (236)
T TIGR01966 1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTAS-VEEKV-P--PFLRGSGEGWITAEYGMLPRATQTRNRRE 76 (236)
T ss_pred CCCCCCCCCccCeEEEeCCcCCCCceEEEEecCCEEEEEEE-ccCcc-C--CcccCCCcEEEEEEEecCCCCCCCCcccc
Confidence 89999999999999999999999999999999999999997 44322 1 1122356899999999999999866 22
Q ss_pred --CCCCChhHHHHHHHHHHhccccCCCCCCCc-eEEEEEEEEEccCCChhhHHHHHHHHHHHhC-----------CCCcc
Q psy3754 457 --IGVPKRREIGHGRLAKRALLPVLPNNNKFN-YSIRLVSEITESNGSSSMASVCGGCLALLDA-----------GVPIS 522 (755)
Q Consensus 457 --~g~~~~rei~~~~lieral~~vi~~~~~~p-~tI~V~v~VLe~dGs~~~Aav~a~slAL~da-----------GvPi~ 522 (755)
.|.+++++.+++++++|+|++++++ +.|| ++|+|+++||++|||..+||+||+++||+|| |+||+
T Consensus 77 ~~~g~~~~~~~e~~~~i~r~lr~~i~l-~~l~~~~i~I~v~VL~~DG~~~~aai~Aa~aAL~da~~~~~~~~~~~~ip~~ 155 (236)
T TIGR01966 77 SAKGKQSGRTQEIQRLIGRALRAVVDL-EALGERTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIR 155 (236)
T ss_pred ccCCCCCccHHHHHHHHHHHHHHhcCH-hhcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHHHHhhhhcCcccCCCcc
Confidence 3567778999999999999999998 4455 5699999999999999999999999999999 99999
Q ss_pred cceEEEEEEEEecCceEEEEecCCccccccCCccEEEEeecCc-EEEEEeeecccccCHHHHHHHHHHHHhhhHHHHHHH
Q psy3754 523 EHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 601 (755)
Q Consensus 523 ~~va~vs~gli~~~~~~~vL~Dp~~~Ee~~gd~~~~Va~t~~g-i~alq~~~k~~~is~~~l~~al~~A~~~~~~I~~~~ 601 (755)
++|+++++|++++ .+++||+..|+..++..++++.+.++ |+.+|+.+..+.++.+++.+|++.|++++..|.+.|
T Consensus 156 ~~~~~vt~~~~~~----~~v~Dpt~~Ee~~~~~~l~l~~~~~~~i~~i~~~g~~~~~~~~~l~~~i~~a~~~~~~l~~~~ 231 (236)
T TIGR01966 156 DFVAAVSVGIVDG----EPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGIRELIELQ 231 (236)
T ss_pred CceeEEEEEEECC----EEEECCChhHHhccCceEEEEEcCCCCEEEEEecCCCCCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999975 58899999999999888888877666 899998765678999999999999999999999999
Q ss_pred Hhhc
Q psy3754 602 KTEV 605 (755)
Q Consensus 602 ~~~l 605 (755)
++++
T Consensus 232 ~~~l 235 (236)
T TIGR01966 232 KQAL 235 (236)
T ss_pred HHHh
Confidence 9876
No 11
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional
Probab=100.00 E-value=8.7e-36 Score=316.34 Aligned_cols=235 Identities=23% Similarity=0.333 Sum_probs=206.4
Q ss_pred HHHHHHHHHHHHHHHccCCcCCCCCCCCccceEEEeCCCCCCCceeEEEeCCeEEEEEEEecCCccccccccccCCcccE
Q psy3754 360 ILYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDS 439 (755)
Q Consensus 360 ~~~~~~~~~~r~~~l~~~~R~DGR~~~e~R~i~ie~g~l~~a~GSal~~~G~T~Vl~~Vt~Gp~~~~~~~d~~~~~~~~~ 439 (755)
+.+..+++.+++ .+++|+|+|||+++|+|++++++|++++++|||+++.|+|+|+|+|+.++.. + ....+++|.
T Consensus 7 ~~~~~e~~~i~~-~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~vl~~V~~~~~~--p---~~~~~~~g~ 80 (271)
T PRK04282 7 IIPEIKKDYILS-LLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGE--P---FPDTPNEGV 80 (271)
T ss_pred hhhHHHHHHHHH-HHhcCCCCCCCCCccccCeEEEeCCccCCCcEEEEEECCCEEEEEEEEEEec--C---CCCCCCCCE
Confidence 366778888877 6699999999999999999999999999999999999999999999864322 2 233467899
Q ss_pred EEEEeecCCCCcccccCCCCCChhHHHHHHHHHHhcccc--CCCC------CCCceEEEEEEEEEccCCChhhHHHHHHH
Q psy3754 440 FMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPV--LPNN------NKFNYSIRLVSEITESNGSSSMASVCGGC 511 (755)
Q Consensus 440 ~~~~~~f~p~s~~e~~~~g~~~~rei~~~~lieral~~v--i~~~------~~~p~tI~V~v~VLe~dGs~~~Aav~a~s 511 (755)
+.++|+|+|+|+... +.++++++++.++++++|+|++. ++++ ..++|+|+|+++||++|||..+|+++|++
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 999999999998754 55778899999999999999864 3321 34689999999999999999999999999
Q ss_pred HHHHhCCCC--------------------cccceEEEEEEEEecCceEEEEecCCccccccCCccEEEEeecCc-EEEEE
Q psy3754 512 LALLDAGVP--------------------ISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQ 570 (755)
Q Consensus 512 lAL~daGvP--------------------i~~~va~vs~gli~~~~~~~vL~Dp~~~Ee~~gd~~~~Va~t~~g-i~alq 570 (755)
+||+|+++| |+++|.++++|++.+ .+|+||+..|+..++..++|+.+.+| +++++
T Consensus 160 aAL~~~~iP~~~~~~~~~~~~~~~~~~l~~~~~p~~vt~~~~~~----~~v~Dpt~~Ee~~~~~~l~va~~~~g~i~~l~ 235 (271)
T PRK04282 160 AALLNTKVPAVEEGEDGVVDKLGEDFPLPVNDKPVTVTFAKIGN----YLIVDPTLEEESVMDARITITTDEDGNIVAIQ 235 (271)
T ss_pred HHHHhCCCCcEEEcCCceeccCCCcccCCCCCeeEEEEEEEECC----EEEECCCHHHHhhcCceEEEEECCCCcEEEEE
Confidence 999999995 999999999999965 58899999999999999999999885 88888
Q ss_pred eeecccccCHHHHHHHHHHHHhhhHHHHHHHHhhcc
Q psy3754 571 MDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVP 606 (755)
Q Consensus 571 ~~~k~~~is~~~l~~al~~A~~~~~~I~~~~~~~l~ 606 (755)
..+ .++++.+.+.+|++.|.+.+..+.+.|+++++
T Consensus 236 ~~g-~~~~~~~~l~~~i~~A~~~~~~l~~~~~~~l~ 270 (271)
T PRK04282 236 KSG-IGSFTEEEVDKAIDIALEKAKELREKLKEALG 270 (271)
T ss_pred cCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 764 46799999999999999999999999999874
No 12
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=100.00 E-value=2.1e-36 Score=354.49 Aligned_cols=243 Identities=20% Similarity=0.290 Sum_probs=210.1
Q ss_pred CCeeEEEEeCccCcCCCcEEEEEECCeEEEEEEE-ecCCCCCCCCcceeeEEeEeeccccCCCCCCcc---cccCCCCch
Q psy3754 75 GSYKISIEIGEIARQATSSVLVSIEDTVILATVV-SCKDPTSTYNFFPLTVDYIEKAYAAGRIPGSFF---KREGKPSER 150 (755)
Q Consensus 75 ~~r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~-~~~~~~~~~~f~pl~v~y~e~~~a~g~ip~~~~---kReg~p~~~ 150 (755)
.-|++.+|+|.++ .|+|||++++|+|+|||+|+ |+.+.....+++ +.++|.+++|..+++|+.+. +|+|+|+++
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 4689999999995 59999999999999999997 665444456766 68899999999999999665 889999999
Q ss_pred hhHHHHHhcCcccccccCC--CcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEE-C------
Q psy3754 151 ETIISRLIDRPIRPLFPEG--YLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYI-D------ 221 (755)
Q Consensus 151 e~l~sRlIdr~lrpl~p~~--~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP~~~~vaav~vg~~-~------ 221 (755)
|++.+|+++|+|||+||.+ |.|.++|+++||++||+.+ +||+|||||||++|||||++|||||++|++ |
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 999999999999999999999999999998 3
Q ss_pred -CEE--EEcCCHHHHhcCcccEEEEeecCceEEEEcCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccC
Q psy3754 222 -GKY--ILNPTTEQLKKSHLDLLVAGTEKAIITVESES--KQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNW 296 (755)
Q Consensus 222 -g~~--vldPt~~E~~~s~~~l~va~~~~~i~mie~~~--~~~se~~~~~al~~a~~~~~~i~~~~~~~~~~~~~~k~~~ 296 (755)
|++ ++||+..|+..+++||.||||.++|+|+|+++ ++++++.|.+||+.|+++|..|++.|++.+.+...+...+
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 46999999999999999999999999999855 5689999999999999999999999999998877666666
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHHhccchhH
Q psy3754 297 DPIVKDKTLISKIINISEHKIRKAYQIKNKQI 328 (755)
Q Consensus 297 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~k~~ 328 (755)
.|....-.+. .++|.+++....|.-
T Consensus 683 aP~i~~~~i~-------~~ki~~vIG~GGktI 707 (891)
T PLN00207 683 APLIHIMKVK-------PEKVNMIIGSGGKKV 707 (891)
T ss_pred CCeeEEEEcC-------HHHHHHHhcCCchhH
Confidence 6543222221 466777777666654
No 13
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.5e-36 Score=304.63 Aligned_cols=224 Identities=29% Similarity=0.404 Sum_probs=199.6
Q ss_pred HccCCcCCCCCCCCccceEEEeCCCCCCCceeEEEeCCeEEEEEEEecCCccccccccccCCcccEEEEEeecCCCCccc
Q psy3754 374 LDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGD 453 (755)
Q Consensus 374 l~~~~R~DGR~~~e~R~i~ie~g~l~~a~GSal~~~G~T~Vl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~f~p~s~~e 453 (755)
..+++|+|||.++|+|||.++.|++++++||++|+.|+|+|+|+|+ ||++ +.+.++.++..++++++|++.|||+.+
T Consensus 4 ~~~~~R~dgR~~delR~i~~~~~~~~~a~GS~~~~~G~tkVic~vs-Gp~e--~~p~~l~~~~~g~~t~ey~m~p~sT~~ 80 (230)
T COG0689 4 SEDGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVS-GPRE--PVPRFLRGTGKGWLTAEYGMLPRSTDE 80 (230)
T ss_pred cccCcCCCCCCcccccceEEEeccccCCCccEEEEeCCeEEEEEEe-cCCC--CCChhhcCCCceEEEEEEecccccccc
Confidence 4689999999999999999999999999999999999999999997 9975 455578888999999999999999966
Q ss_pred ccCCCCCCh-hHHHHHHHHHHhccccCCCCCCCceE-EEEEEEEEccCCChhhHHHHHHHHHHHhCCCCcccceEEEEEE
Q psy3754 454 IGRIGVPKR-REIGHGRLAKRALLPVLPNNNKFNYS-IRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMG 531 (755)
Q Consensus 454 ~~~~g~~~~-rei~~~~lieral~~vi~~~~~~p~t-I~V~v~VLe~dGs~~~Aav~a~slAL~daGvPi~~~va~vs~g 531 (755)
+.+.. +.+ |++++++++.|+|++++.+ +.||.+ |+|+++|++.||+...|+++|+++||+|||+||+++++++|+|
T Consensus 81 R~~~~-~~~gR~~eisrli~~al~~~i~L-~~~p~~~I~i~~dVlqaDggTrta~It~A~lAL~DAgipl~~~vaaiSvg 158 (230)
T COG0689 81 RKKRE-ADRGRTKEISRLIGRALRAVIDL-ELLPESTIDIDCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISVG 158 (230)
T ss_pred ccccc-ccccchhHHHHHHHHHHHHHhhh-hhcCccEEEEEEEEEECCCCeeeehhhHHHHHHHHcCCchhhheeEeEEE
Confidence 54444 445 9999999999999999998 889997 9999999999999999999999999999999999999999999
Q ss_pred EEecCceEEEEecCCccccccCCccEEEEeecCc-EEEEEeeecccccCHHHHHHHHHHHHhhhHHHHHHHHhhcc
Q psy3754 532 LIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVP 606 (755)
Q Consensus 532 li~~~~~~~vL~Dp~~~Ee~~gd~~~~Va~t~~g-i~alq~~~k~~~is~~~l~~al~~A~~~~~~I~~~~~~~l~ 606 (755)
++++ .+++|+...||..+..+..|+++.+| +.-+|.-...++++.++|.++|+.|.+++..+.+.|+++|.
T Consensus 159 i~~~----~~~lDl~~~Eds~~~~d~~v~~~~~~~~~ei~~~~~~~~~~~del~~lL~la~~g~~~~~~~~~~al~ 230 (230)
T COG0689 159 IVDG----VIVLDLDYEEDSAAEADMNVVMTGNGGLVEIQGLAEDGPFTEDELLELLDLAIKGCNELRELQREALA 230 (230)
T ss_pred EECC----ceEecCcchhhcccccCceEEEEecCCeEEEEEEeccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 9987 48899999999988888888776655 34444444456799999999999999999999999998863
No 14
>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=6e-36 Score=310.12 Aligned_cols=204 Identities=23% Similarity=0.268 Sum_probs=180.8
Q ss_pred CeeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecCCCCCC----CCcceeeEEeEeeccccCCCCCCcccccCCCCchh
Q psy3754 76 SYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTST----YNFFPLTVDYIEKAYAAGRIPGSFFKREGKPSERE 151 (755)
Q Consensus 76 ~r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~~~~~~----~~f~pl~v~y~e~~~a~g~ip~~~~kReg~p~~~e 151 (755)
=|++++++|.+ .+|||||++++|+|+|+|+|+||++.+++ .++.+|+|+|....||. +.+|+++|+++|
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 47899999999 89999999999999999999998865432 45678999998776654 345567899999
Q ss_pred hHHHHHhcCcccccccCCCcCe--EEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCC
Q psy3754 152 TIISRLIDRPIRPLFPEGYLNE--IQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPT 229 (755)
Q Consensus 152 ~l~sRlIdr~lrpl~p~~~~~~--~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP~~~~vaav~vg~~~g~~vldPt 229 (755)
++++|+|+|+|||+++.++++. ++|.++||+.||+ +.++|+|||++||.+|||||.++|+||++++++|++|+|||
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 9999999999999999887554 5555669998887 45999999999999999999999999999999999999999
Q ss_pred HHHHhcCcccEEEEe--ecCceEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy3754 230 TEQLKKSHLDLLVAG--TEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNV 289 (755)
Q Consensus 230 ~~E~~~s~~~l~va~--~~~~i~mie~~~~~~se~~~~~al~~a~~~~~~i~~~~~~~~~~~ 289 (755)
.+|+..++++++|+. +.+.|+|++..| ++++++|.+|+++|+++|++++++|++.++++
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 456699999998 69999999999999999999999999998764
No 15
>PRK00173 rph ribonuclease PH; Reviewed
Probab=100.00 E-value=3.4e-34 Score=298.31 Aligned_cols=205 Identities=22% Similarity=0.239 Sum_probs=178.6
Q ss_pred CeeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecCCCC---CCCCcceeeEEeEeeccccCCCCCCcccc---cCCCCc
Q psy3754 76 SYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPT---STYNFFPLTVDYIEKAYAAGRIPGSFFKR---EGKPSE 149 (755)
Q Consensus 76 ~r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~~~~---~~~~f~pl~v~y~e~~~a~g~ip~~~~kR---eg~p~~ 149 (755)
=|++++++|.+ ++|+|||++++|+|+|+|+|+++...+ .+.+..+|+|+|....++..+. .+| .|+|++
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-KHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTAEYGMLPRATHTR----NDREAAKGKQGG 85 (238)
T ss_pred ccCeEEEeCCC-CCCCeeEEEEecCcEEEEEEEcCCCCCCccCCCCcEEEEEEEecCCCCCccc----ccccccCCCCCc
Confidence 48999999988 899999999999999999999866432 2345678999997554443322 112 378999
Q ss_pred hhhHHHHHhcCcccccccCCCcCe--EEEEEEEEecCCCCChhhHHHHHHHHHhhcC-----------CCCCCCCeEEEE
Q psy3754 150 RETIISRLIDRPIRPLFPEGYLNE--IQIVVYVLSVNPQIDPDIASIIGVSTALSIS-----------ELPFLGPLGVAK 216 (755)
Q Consensus 150 ~e~l~sRlIdr~lrpl~p~~~~~~--~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s-----------~IP~~~~vaav~ 216 (755)
++++++|+|||+|||+|+..+++. ++|+++||++||+.. .+|+|||++||+++ ++||++++++|+
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 RTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGTR--TASITGAYVALADALNKLVARGKLKKNPLKDQVAAVS 163 (238)
T ss_pred cHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHH--HHHHHHHHHHHHHhhhhhhccCcccCCcccCceeEEE
Confidence 999999999999999999777655 999999999999875 99999999999977 999999999999
Q ss_pred EEEECCEEEEcCCHHHHhcCcccEEEEeecCc-eEEEEc--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3754 217 VGYIDGKYILNPTTEQLKKSHLDLLVAGTEKA-IITVES--ESKQLPEDIILNAIIFGHEKMKIAINAINELVQ 287 (755)
Q Consensus 217 vg~~~g~~vldPt~~E~~~s~~~l~va~~~~~-i~mie~--~~~~~se~~~~~al~~a~~~~~~i~~~~~~~~~ 287 (755)
+|+++|++|+|||.+|++.++.+|+|+.+.++ |+|++. ++.++++++|.+|+++|++++++++++|++.++
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 99999999999999999999999999998865 999997 356899999999999999999999999998764
No 16
>KOG1068|consensus
Probab=100.00 E-value=5.5e-35 Score=294.02 Aligned_cols=226 Identities=25% Similarity=0.363 Sum_probs=203.4
Q ss_pred HHccCCcCCCCCCCCccceEEEeCCCCCCCceeEEEeCCeEEEEEEEecCCccccccccccCCcccEEEEEeecCCCCcc
Q psy3754 373 ILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATG 452 (755)
Q Consensus 373 ~l~~~~R~DGR~~~e~R~i~ie~g~l~~a~GSal~~~G~T~Vl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~f~p~s~~ 452 (755)
..++|.|.|||.++|+|+|.+..|++++++||||++.|||+|+|+| +||++...... ..++...+++.|++.+|+++
T Consensus 8 ~seeg~r~dgRr~~elR~i~~~~g~~~~a~GSay~E~GnTKVl~aV-~GPre~~~~~~--~~~~~a~lnc~~~~a~Fst~ 84 (245)
T KOG1068|consen 8 LSEEGLRTDGRRPNELRRIYARIGVLTQADGSAYMEQGNTKVLCAV-YGPREIRGKSA--RRPDKAVLNCEVSSAQFSTG 84 (245)
T ss_pred cCccccccCCCChhHhhhhhhhcCccccCCccchhhcCCeEEEEEE-eCCcccccccc--cccccceEEEEEeeeccccc
Confidence 4679999999999999999999999999999999999999999999 59987655332 25678899999999999999
Q ss_pred cccCCCCCChhHHHHHHHHHHhccccCCCCCCCceE-EEEEEEEEccCCChhhHHHHHHHHHHHhCCCCcccceEEEEEE
Q psy3754 453 DIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYS-IRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMG 531 (755)
Q Consensus 453 e~~~~g~~~~rei~~~~lieral~~vi~~~~~~p~t-I~V~v~VLe~dGs~~~Aav~a~slAL~daGvPi~~~va~vs~g 531 (755)
++++....++|+.+++.+++++|+++|.+ ++||++ |+|.++||++||+.+.+++||+++||.||||||++++.|+|+|
T Consensus 85 ~r~~~~~~~rr~~e~s~~L~~afe~~I~~-~lyPrsqIDI~v~VleddG~~laa~inaatlAL~daGI~m~D~i~~~t~~ 163 (245)
T KOG1068|consen 85 DRKKRPKGDRREKELSLMLQQAFEPVILL-ELYPRSQIDIYVQVLEDDGSNLAAAINAATLALADAGIPMYDLITACTAG 163 (245)
T ss_pred hhccCCCccHHHHHHHHHHHHHHHHHHHh-hhCccccceEEEEEEECCCccHHHHHHHHHHHHHHcCCChhhhhhhceee
Confidence 99866667899999999999999999998 899998 9999999999999999999999999999999999999999999
Q ss_pred EEecCceEEEEecCCccccccCCccEEEE--eecCcEEEEEeeecccccCHHHHHHHHHHHHhhhHHHHHHHHhhccccc
Q psy3754 532 LIKDGEKVVILSDILGDEDRCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCK 609 (755)
Q Consensus 532 li~~~~~~~vL~Dp~~~Ee~~gd~~~~Va--~t~~gi~alq~~~k~~~is~~~l~~al~~A~~~~~~I~~~~~~~l~~~r 609 (755)
+.++ ..++|++..||..+...++|+ ++.+.|..+|++.+ ++.+.|...++.|..+|..+.+.++..+..+.
T Consensus 164 l~~~----~~l~Dl~~~eesa~~~~ltVa~l~~~~~i~~l~~~~~---~~~d~l~~vl~~a~~~c~~v~~~l~~~l~~~l 236 (245)
T KOG1068|consen 164 LADG----TPLLDLTSLEESARAPGLTVAALPNREEIALLQLDER---LHCDHLETVLELAIAGCKRVYERLRLVLREHL 236 (245)
T ss_pred ecCC----ccccccccchhhccCCceEEEEecCcceEEEEEecCC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9986 588999999998877666665 56666999999865 68999999999999999999999998887653
No 17
>PRK03983 exosome complex exonuclease Rrp41; Provisional
Probab=100.00 E-value=1.1e-33 Score=295.87 Aligned_cols=206 Identities=21% Similarity=0.294 Sum_probs=176.5
Q ss_pred CeeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecCCCCCCCCcce----eeEEeEeeccccCCCCCCcccccCCCCchh
Q psy3754 76 SYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFP----LTVDYIEKAYAAGRIPGSFFKREGKPSERE 151 (755)
Q Consensus 76 ~r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~~~~~~~~f~p----l~v~y~e~~~a~g~ip~~~~kReg~p~~~e 151 (755)
=|++++++|.+ ++|+|||++++|+|+|+|+|+||++..+.....| +.++|.-..++. . .+++++|++++
T Consensus 24 ~R~i~i~~G~l-~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~p~~~-----~-~~~~~~~~~~~ 96 (244)
T PRK03983 24 LRPIKIEVGVL-KNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSV-----D-ERKRPGPDRRS 96 (244)
T ss_pred ccceEEEeCCC-CCCCeEEEEEECCeEEEEEEecCCccccccccCCCcEEEEEEEEcCCCcc-----c-cccCCCCChhH
Confidence 37899999999 8999999999999999999999987654444444 455554322222 1 24456799999
Q ss_pred hHHHHHhcCcccccccCCCcCe--EEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCC
Q psy3754 152 TIISRLIDRPIRPLFPEGYLNE--IQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPT 229 (755)
Q Consensus 152 ~l~sRlIdr~lrpl~p~~~~~~--~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP~~~~vaav~vg~~~g~~vldPt 229 (755)
++++|+|+|+|||+++.++++. ++|.++||+.||+. .++|+|||++||.+|||||.++++||++++.+|++++|||
T Consensus 97 ~~~s~~l~~~l~~~i~~~~~p~~~I~I~i~VL~~DG~~--~~aai~Aa~lAL~dagIp~~~~v~avtv~~~~~~~i~DPt 174 (244)
T PRK03983 97 IEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGT--RVAGITAASLALADAGIPMRDLVAGCAVGKVDGVIVLDLN 174 (244)
T ss_pred HHHHHHHHHHHHHhccHHhCCCeEEEEEEEEEECCCCH--HHHHHHHHHHHHHhcCCccccceeEEEEEEECCEEEECCC
Confidence 9999999999999998777777 55666699999874 4899999999999999999999999999999999999999
Q ss_pred HHHHhcCcccEEEEeec--CceEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q psy3754 230 TEQLKKSHLDLLVAGTE--KAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQ 291 (755)
Q Consensus 230 ~~E~~~s~~~l~va~~~--~~i~mie~~~~~~se~~~~~al~~a~~~~~~i~~~~~~~~~~~~~ 291 (755)
.+|++.++.+|+|+++. +.|+|++..| .++++++.+|+++|+++|++++++|++.++++..
T Consensus 175 ~~Ee~~~~~~l~va~~~~~~~I~~l~~~G-~~~~~~~~~~i~~A~~~~~~i~~~i~~~l~~~~~ 237 (244)
T PRK03983 175 KEEDNYGEADMPVAIMPRLGEITLLQLDG-NLTREEFLEALELAKKGIKRIYQLQREALKSKYG 237 (244)
T ss_pred HHHhccCCceEEEEEECCCCCEEEEEEec-CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999973 4599999998 6999999999999999999999999998876654
No 18
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.9e-32 Score=278.13 Aligned_cols=231 Identities=24% Similarity=0.334 Sum_probs=202.2
Q ss_pred HHHHHHHHHHHccCCcCCCCCCCCccceEEEeCCCCCCCceeEEEeCCeEEEEEEEecCCccccccccccCCcccEEEEE
Q psy3754 364 LESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLH 443 (755)
Q Consensus 364 ~~~~~~r~~~l~~~~R~DGR~~~e~R~i~ie~g~l~~a~GSal~~~G~T~Vl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~ 443 (755)
+.++.+.. .++.|+|+|||.++|+||+.+++|+++.++|||+++.|+|||+|+|+.+. .+ |+++.+++|.+.++
T Consensus 10 ~~~~~i~~-ll~~g~R~DGR~~~efR~ieI~~~vi~ka~GSa~VklG~Tqvv~gvK~ei--g~---Pf~DtP~eG~~~~n 83 (272)
T COG2123 10 IKREYILN-LLKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEI--GE---PFPDTPNEGVLVVN 83 (272)
T ss_pred hHHHHHHH-HhccCcccCCCCcccccceEEEeCceecCCCcEEEEecCeEEEEEEEccc--CC---CCCCCCCCceEEee
Confidence 34444444 78899999999999999999999999999999999999999999999733 33 35556779999999
Q ss_pred eecCCCCcccccCCCCCChhHHHHHHHHHHhccc--cCCCC------CCCceEEEEEEEEEccCCChhhHHHHHHHHHHH
Q psy3754 444 YNMPPFATGDIGRIGVPKRREIGHGRLAKRALLP--VLPNN------NKFNYSIRLVSEITESNGSSSMASVCGGCLALL 515 (755)
Q Consensus 444 ~~f~p~s~~e~~~~g~~~~rei~~~~lieral~~--vi~~~------~~~p~tI~V~v~VLe~dGs~~~Aav~a~slAL~ 515 (755)
+++.|.++..+ -.|+|+..+++++++++|.++. .++++ ..+.|.++++++||++|||..+|++.|+.+||+
T Consensus 84 ~El~Plas~~f-E~Gppde~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~Da~~lA~~aAL~ 162 (272)
T COG2123 84 VELSPLASPSF-EPGPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLIDAASLAAVAALL 162 (272)
T ss_pred eeeeccccccc-cCCCCchhHHHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHH
Confidence 99999887644 4577889999999999999985 33322 457999999999999999999999999999999
Q ss_pred hCCCC----------------------cccceEEEEEEEEecCceEEEEecCCccccccCCccEEEEeecCc-EEEEEee
Q psy3754 516 DAGVP----------------------ISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMD 572 (755)
Q Consensus 516 daGvP----------------------i~~~va~vs~gli~~~~~~~vL~Dp~~~Ee~~gd~~~~Va~t~~g-i~alq~~ 572 (755)
++++| +.++|.+++++.+.+ .+++||+.+|+..++..+++..+.+| |+++|..
T Consensus 163 ~t~vP~~~~~~~~~~v~~~~~~~~pl~~~~~pi~vt~a~ig~----~lvvDPsleEe~v~d~~ltit~~~~~~Iv~iqK~ 238 (272)
T COG2123 163 NTRVPKAVEVGDGEIVIEVEEEPVPLPVSNPPISVTFAKIGN----VLVVDPSLEEELVADGRLTITVNEDGEIVAIQKV 238 (272)
T ss_pred hcCCCceeecCCcceeecccCCCcccccCCCceEEEEEEECC----EEEeCCCcchhhhcCceEEEEECCCCcEEEEEEc
Confidence 99888 678899999999976 78999999999999999999999998 8999985
Q ss_pred ecccccCHHHHHHHHHHHHhhhHHHHHHHHhhcc
Q psy3754 573 IKIFGITYDIIQIALYKAKKGLSYILEKMKTEVP 606 (755)
Q Consensus 573 ~k~~~is~~~l~~al~~A~~~~~~I~~~~~~~l~ 606 (755)
+ .+.++.+.+.+|++.|.....++.+.+.+.|+
T Consensus 239 g-~~~~~~~~~~~~~~~A~~~~~kl~~~~~~~L~ 271 (272)
T COG2123 239 G-GGSITESDLEKALKTALSKAEKLREALKEALK 271 (272)
T ss_pred C-CCcCCHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 5 57899999999999999999999999988875
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=1.1e-32 Score=286.88 Aligned_cols=204 Identities=24% Similarity=0.249 Sum_probs=172.4
Q ss_pred CeeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecCCCCC---CCCcceeeEEeEeeccccCCCCCCccccc---CCCCc
Q psy3754 76 SYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTS---TYNFFPLTVDYIEKAYAAGRIPGSFFKRE---GKPSE 149 (755)
Q Consensus 76 ~r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~~~~~---~~~f~pl~v~y~e~~~a~g~ip~~~~kRe---g~p~~ 149 (755)
=|++++++|.+ ++|+|||++++|+|+|+|+|+++...+. ..+..+|+|+|.-..++... +.+|+ |+|++
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-KHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQT----RNRRESAKGKQSG 84 (236)
T ss_pred ccCeEEEeCCc-CCCCceEEEEecCCEEEEEEEccCccCCcccCCCcEEEEEEEecCCCCCCC----CccccccCCCCCc
Confidence 48899999965 9999999999999999999997554222 12446788888644433321 12344 78888
Q ss_pred hhhHHHHHhcCcccccccCCCcCeE--EEEEEEEecCCCCChhhHHHHHHHHHhhcC-----------CCCCCCCeEEEE
Q psy3754 150 RETIISRLIDRPIRPLFPEGYLNEI--QIVVYVLSVNPQIDPDIASIIGVSTALSIS-----------ELPFLGPLGVAK 216 (755)
Q Consensus 150 ~e~l~sRlIdr~lrpl~p~~~~~~~--qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s-----------~IP~~~~vaav~ 216 (755)
++++++|+|||+|||+|+.++++.. +|+++||++||+.. .+|+|||++||+++ +|||++++++|+
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 RTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADGGTR--TASITGAFVALADAISKLHKRGILKESPIRDFVAAVS 162 (236)
T ss_pred cHHHHHHHHHHHHHHhcCHhhcCCeEEEEEEEEEeCCCCHH--HHHHHHHHHHHHHHHHhhhhcCcccCCCccCceeEEE
Confidence 8999999999999999998766544 88999999999874 99999999999977 999999999999
Q ss_pred EEEECCEEEEcCCHHHHhcCcccEEEEeecCc-eEEEEcC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3754 217 VGYIDGKYILNPTTEQLKKSHLDLLVAGTEKA-IITVESE--SKQLPEDIILNAIIFGHEKMKIAINAINELV 286 (755)
Q Consensus 217 vg~~~g~~vldPt~~E~~~s~~~l~va~~~~~-i~mie~~--~~~~se~~~~~al~~a~~~~~~i~~~~~~~~ 286 (755)
+|++++++|+|||.+|++.++..|+++.+.++ |+|++.+ +.+++++++.+|+++|++++++++++|++.+
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 99999999999999999999888888877664 9999973 5789999999999999999999999998864
No 20
>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=3.7e-32 Score=319.44 Aligned_cols=241 Identities=22% Similarity=0.297 Sum_probs=205.2
Q ss_pred CeeEEEEeCccCcCCCcEEEEEECCeEEEEEEE-ecCCCCCCCCcceeeEEeEeeccccCCCCC---CcccccCCCCchh
Q psy3754 76 SYKISIEIGEIARQATSSVLVSIEDTVILATVV-SCKDPTSTYNFFPLTVDYIEKAYAAGRIPG---SFFKREGKPSERE 151 (755)
Q Consensus 76 ~r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~-~~~~~~~~~~f~pl~v~y~e~~~a~g~ip~---~~~kReg~p~~~e 151 (755)
=||+.+++|.+ .+|+|||++++|+|+|||+|+ ||.+. .+.+.++..+++.+++..+++|+ |+.+|.|+|+++|
T Consensus 320 ~Rpi~~~~g~l-~~a~GSa~~~~G~Tqvl~~vt~g~~~~--~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~~~g~~~rre 396 (684)
T TIGR03591 320 IRPISIEVGVL-PRTHGSALFTRGETQALVVTTLGTERD--EQIIDDLEGEYRKRFMLHYNFPPYSVGEVGRVGGPGRRE 396 (684)
T ss_pred cCceEEEeCCC-CCCCceEEEEeCCeEEEEEEecCCccc--ccCCcccCCCccEEEEEEEEcCCCCCCCcCCCCCCChHH
Confidence 37899999999 679999999999999999995 66542 23445566666777777777776 7778889999999
Q ss_pred hHHHHHhcCccccccc--CCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEEC-C----EE
Q psy3754 152 TIISRLIDRPIRPLFP--EGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYID-G----KY 224 (755)
Q Consensus 152 ~l~sRlIdr~lrpl~p--~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP~~~~vaav~vg~~~-g----~~ 224 (755)
++.+++++|+|||++| +.|.|.++|+++||++||+.. +||+||||+||++|||||.++|+||++|+++ | .+
T Consensus 397 i~~~~l~~ral~~~i~~~~~~p~tI~v~~~VLesdGs~~--~Aai~aaslAL~dAgvP~~~~Vagvs~gli~~~~~~~~i 474 (684)
T TIGR03591 397 IGHGALAERALKAVLPSEEEFPYTIRVVSEILESNGSSS--MASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDERFAV 474 (684)
T ss_pred HHHHHHHHHHHHHhcCccccCCeEEEEEEEEEeCCCChH--HHHHHHHHHHHHhcCCCCcCCEEEEEEEEEcCCCcceEE
Confidence 9999999999999999 789999999999999999888 9999999999999999999999999999984 3 48
Q ss_pred EEcCCHHHHhcCcccEEEEeecCceEEEEcCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCCCCCC
Q psy3754 225 ILNPTTEQLKKSHLDLLVAGTEKAIITVESES--KQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKD 302 (755)
Q Consensus 225 vldPt~~E~~~s~~~l~va~~~~~i~mie~~~--~~~se~~~~~al~~a~~~~~~i~~~~~~~~~~~~~~k~~~~~~~~~ 302 (755)
++||+..|+..+++||.|++|.++|++++.++ ..++.+.|.+|++.|+++++.|++.|++.+.+++++..++.|....
T Consensus 475 l~D~~~~Ed~~~d~d~~va~t~~gI~~lq~d~k~~~i~~~~l~~al~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~ 554 (684)
T TIGR03591 475 LSDILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGITREIMEQALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIET 554 (684)
T ss_pred EeCCChHHHhcCCceEEEEEcCCceEEEEEEcCcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccccCCeEEE
Confidence 99999999999999999999999999998844 4589999999999999999999999999999999988888773211
Q ss_pred hhHHHHHHHHHHHHHHHHHhccchhH
Q psy3754 303 KTLISKIINISEHKIRKAYQIKNKQI 328 (755)
Q Consensus 303 ~~l~~~~~~~~~~~~~~~~~~~~k~~ 328 (755)
-.+- .++|.+++...+|.-
T Consensus 555 ~~I~-------~~kI~~vIG~gGk~I 573 (684)
T TIGR03591 555 IKIN-------PDKIRDVIGPGGKVI 573 (684)
T ss_pred EecC-------HHHHHhhcCCCcHHH
Confidence 1111 355666665555543
No 21
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=100.00 E-value=5.6e-32 Score=318.65 Aligned_cols=240 Identities=23% Similarity=0.309 Sum_probs=195.7
Q ss_pred CeeEEEEeCccCcCCCcEEEEEECCeEEEEEEE-ecCCCCCCCCcceeeEEeEeeccccCCCCC---CcccccCCCCchh
Q psy3754 76 SYKISIEIGEIARQATSSVLVSIEDTVILATVV-SCKDPTSTYNFFPLTVDYIEKAYAAGRIPG---SFFKREGKPSERE 151 (755)
Q Consensus 76 ~r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~-~~~~~~~~~~f~pl~v~y~e~~~a~g~ip~---~~~kReg~p~~~e 151 (755)
=||+.+++|.+ .+|+|||++++|+|+|||+|+ |+.. +.+.+.++..+++.+++..+++|+ ++.+|.|+|+++|
T Consensus 324 ~Rpi~~~~g~l-~~a~GSal~~~G~T~Vl~~vt~g~~~--~~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~~~~~~~rre 400 (693)
T PRK11824 324 IRPISIEVGVL-PRTHGSALFTRGETQALVVATLGTLR--DEQIIDGLEGEYKKRFMLHYNFPPYSVGETGRVGSPGRRE 400 (693)
T ss_pred ccceEEEeCCC-CCCCceEEEEECCeEEEEEEecCCCc--ccccccccCCCCcEEEEEEEEcCCCCCCCcCCCCCCChhH
Confidence 37899999999 679999999999999999995 5532 223334444555555555556665 6678889999999
Q ss_pred hHHHHHhcCccccccc--CCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEEC-C---EEE
Q psy3754 152 TIISRLIDRPIRPLFP--EGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYID-G---KYI 225 (755)
Q Consensus 152 ~l~sRlIdr~lrpl~p--~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP~~~~vaav~vg~~~-g---~~v 225 (755)
++++++++|+|||++| ..|.|.++|+++||++||+.. +||+||||+||++|||||.++|+||++|+++ | .++
T Consensus 401 ~~~~~li~ral~~vi~~~~~~p~~I~v~~~VLe~dGs~~--~Aai~aaslAL~dAgvP~~~~Va~vs~gli~~~~~~~il 478 (693)
T PRK11824 401 IGHGALAERALEPVLPSEEEFPYTIRVVSEILESNGSSS--MASVCGSSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVL 478 (693)
T ss_pred HHHHHHHHHHHHHhcCcccCCCEEEEEEEEEEecCCCHH--HHHHHHHHHHHHhcCCCccCceeEEEEEEEcCCCceEEE
Confidence 9999999999999999 488999999999999999888 9999999999999999999999999999984 4 278
Q ss_pred EcCCHHHHhcCcccEEEEeecCceEEEEcCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCCCCCCh
Q psy3754 226 LNPTTEQLKKSHLDLLVAGTEKAIITVESESK--QLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 303 (755)
Q Consensus 226 ldPt~~E~~~s~~~l~va~~~~~i~mie~~~~--~~se~~~~~al~~a~~~~~~i~~~~~~~~~~~~~~k~~~~~~~~~~ 303 (755)
+||+..|+..+++||.|++|.+++++++.+++ .++.+.|.+|++.|+++++.|++.|++.+.+.......+.|....-
T Consensus 479 ~D~~~~Ed~~~d~d~~va~t~~gi~~lq~d~k~~~i~~~~l~~al~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~ 558 (693)
T PRK11824 479 TDILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGITREILEEALEQAKEGRLHILGKMNEAISEPRAELSPYAPRIETI 558 (693)
T ss_pred cCCChhhHhhCCceEEEEecCCceEEEEEecccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhhhcccCchheee
Confidence 89999999999999999999999999997754 4899999999999999999999999998876655444444322111
Q ss_pred hHHHHHHHHHHHHHHHHHhccchh
Q psy3754 304 TLISKIINISEHKIRKAYQIKNKQ 327 (755)
Q Consensus 304 ~l~~~~~~~~~~~~~~~~~~~~k~ 327 (755)
.+ -.++|.+.+....|.
T Consensus 559 ~I-------~~~kI~~vIG~gg~~ 575 (693)
T PRK11824 559 KI-------PPDKIRDVIGPGGKT 575 (693)
T ss_pred cC-------CHHHHHHHhcCCchh
Confidence 11 135566665555544
No 22
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=3.9e-30 Score=260.64 Aligned_cols=200 Identities=24% Similarity=0.276 Sum_probs=170.9
Q ss_pred CeeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecCCCCC----CCCcceeeEEeEeeccccCCCCCCccccc-CCCCc-
Q psy3754 76 SYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTS----TYNFFPLTVDYIEKAYAAGRIPGSFFKRE-GKPSE- 149 (755)
Q Consensus 76 ~r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~~~~~----~~~f~pl~v~y~e~~~a~g~ip~~~~kRe-g~p~~- 149 (755)
=|++.++.|.+ ++|+||+++++|||+|+|+|+||+++.+ +.+..|++++|.-..++. ..|. ..++.
T Consensus 18 lR~i~~~~~~~-~~a~GS~~~~~G~tkVic~vsGp~e~~p~~l~~~~~g~~t~ey~m~p~sT-------~~R~~~~~~~g 89 (230)
T COG0689 18 LRPIKITRGVL-KHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEYGMLPRST-------DERKKREADRG 89 (230)
T ss_pred ccceEEEeccc-cCCCccEEEEeCCeEEEEEEecCCCCCChhhcCCCceEEEEEEecccccc-------ccccccccccc
Confidence 48999999999 8999999999999999999999988754 457789999996554433 3332 23344
Q ss_pred hhhHHHHHhcCcccccccCCC--cCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEc
Q psy3754 150 RETIISRLIDRPIRPLFPEGY--LNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILN 227 (755)
Q Consensus 150 ~e~l~sRlIdr~lrpl~p~~~--~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP~~~~vaav~vg~~~g~~vld 227 (755)
++.+++|+|.|+||+.+.... +..++|+|+|+++||++. .+|||||++||++++||+.+.|+|++||+++|.+++|
T Consensus 90 R~~eisrli~~al~~~i~L~~~p~~~I~i~~dVlqaDggTr--ta~It~A~lAL~DAgipl~~~vaaiSvgi~~~~~~lD 167 (230)
T COG0689 90 RTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADGGTR--TASITGASLALADAGIPLRDLVAAISVGIVDGVIVLD 167 (230)
T ss_pred chhHHHHHHHHHHHHHhhhhhcCccEEEEEEEEEECCCCee--eehhhHHHHHHHHcCCchhhheeEeEEEEECCceEec
Confidence 799999999999999543222 227888899999999888 9999999999999999999999999999999999999
Q ss_pred CCHHHHhcCcccEEEEeecCc----eEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3754 228 PTTEQLKKSHLDLLVAGTEKA----IITVESESKQLPEDIILNAIIFGHEKMKIAINAINELV 286 (755)
Q Consensus 228 Pt~~E~~~s~~~l~va~~~~~----i~mie~~~~~~se~~~~~al~~a~~~~~~i~~~~~~~~ 286 (755)
|++.|++.+..|++|+++.++ |...+.++ .+++++|.++|+.|.++|+++++.|++++
T Consensus 168 l~~~Eds~~~~d~~v~~~~~~~~~ei~~~~~~~-~~~~del~~lL~la~~g~~~~~~~~~~al 229 (230)
T COG0689 168 LDYEEDSAAEADMNVVMTGNGGLVEIQGLAEDG-PFTEDELLELLDLAIKGCNELRELQREAL 229 (230)
T ss_pred CcchhhcccccCceEEEEecCCeEEEEEEeccC-CcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999888775 44444555 59999999999999999999999999875
No 23
>KOG1614|consensus
Probab=99.97 E-value=1.7e-29 Score=250.80 Aligned_cols=239 Identities=22% Similarity=0.267 Sum_probs=203.7
Q ss_pred HHHHHHHHHHHccCCcCCCCCCCCccceEEEeCCCCCCCceeEEEeCCeEEEEEEEecCCccccccccccCCcccEEEEE
Q psy3754 364 LESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLH 443 (755)
Q Consensus 364 ~~~~~~r~~~l~~~~R~DGR~~~e~R~i~ie~g~l~~a~GSal~~~G~T~Vl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~ 443 (755)
-+++++.+ .|+.|.|.|||+++|+|.+.+++| .-.||+.++.|+|+|+|.||. +...|..+.|.+|.|.+.
T Consensus 9 ~e~~fvl~-alk~g~R~DgR~l~efR~lei~fG---ke~gs~~vt~G~Tkvm~~vt~-----~ia~Py~dRP~eG~~~I~ 79 (291)
T KOG1614|consen 9 NESKFVLN-ALKAGLRFDGRSLEEFRDLEIEFG---KEYGSVLVTMGNTKVMARVTA-----QIAQPYIDRPHEGSFSIF 79 (291)
T ss_pred chHHHHHH-HHHhcccccccchhhhhceEEEec---cccccEEEEecCeeEEEEeeh-----hhcCcccCCCCCCeeeee
Confidence 34555555 789999999999999999999999 578999999999999999985 333344556779999999
Q ss_pred eecCCCCcccccCCCCCChhHHHHHHHHHHhccc--cCCCCC------CCceEEEEEEEEEccCCChhhHHHHHHHHHHH
Q psy3754 444 YNMPPFATGDIGRIGVPKRREIGHGRLAKRALLP--VLPNNN------KFNYSIRLVSEITESNGSSSMASVCGGCLALL 515 (755)
Q Consensus 444 ~~f~p~s~~e~~~~g~~~~rei~~~~lieral~~--vi~~~~------~~p~tI~V~v~VLe~dGs~~~Aav~a~slAL~ 515 (755)
.+++|++.... ..|+++..+..++++++++++. .++.+. .-.|.||+++++|+.|||+.+||..|+.+|||
T Consensus 80 telsPmA~~sf-E~Gr~~~~~v~l~Rliek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnlvDaA~iAviaaL~ 158 (291)
T KOG1614|consen 80 TELSPMASPSF-EPGRKGESEVELSRLIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNLVDAACIAVIAALM 158 (291)
T ss_pred ecccccccccc-CCCCccchHHHHHHHHHHHHHhccccchHHHHhhhCCeEEEEEEEEEEEcCCCCeehhHHHHHHHHHH
Confidence 99999987644 3355778899999999999984 333322 35999999999999999999999999999999
Q ss_pred hCCCC-----------------------cccceEEEEEEEEecCceEEEEecCCccccccCCccEEEEeecCc-EEEEEe
Q psy3754 516 DAGVP-----------------------ISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQM 571 (755)
Q Consensus 516 daGvP-----------------------i~~~va~vs~gli~~~~~~~vL~Dp~~~Ee~~gd~~~~Va~t~~g-i~alq~ 571 (755)
+.+-| |+++|.++++|+++.|+ .+++|||..|+..+|..++|+.++++ +|++|.
T Consensus 159 hFrrPdvTv~g~ev~ihp~eEr~PvPL~I~HmPIC~tf~ffnkG~--ivviDpt~~Ee~~~dGs~vVt~Nk~rEVc~i~k 236 (291)
T KOG1614|consen 159 HFRRPDVTVGGEEVIIHPVEEREPVPLSIHHMPICFTFGFFNKGE--IVVIDPTEKEEAVMDGSMVVTMNKNREVCAIQK 236 (291)
T ss_pred hcCCCCcccccceeEecChhccCCcceeeeeccceEEEEEecCce--EEEeCCcHHHHhccCceEEEEEcCCccEEEEec
Confidence 99833 89999999999999876 78899999999999999999999988 899998
Q ss_pred eecccccCHHHHHHHHHHHHhhhHHHHHHHHhhccccccccccC
Q psy3754 572 DIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCKNELSKF 615 (755)
Q Consensus 572 ~~k~~~is~~~l~~al~~A~~~~~~I~~~~~~~l~~~r~~~~~~ 615 (755)
.++ -.++..++..|...|......+.+.+.+++++...+-+.+
T Consensus 237 ~G~-~~~~~~~i~~C~k~A~~~a~~vt~ii~e~l~~d~~~r~~~ 279 (291)
T KOG1614|consen 237 SGG-EILDESVIERCYKLAKDRAVEVTGIILEALEEDQRERSAQ 279 (291)
T ss_pred CCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 764 4678999999999999999999999999998765444444
No 24
>KOG1069|consensus
Probab=99.96 E-value=1.5e-29 Score=245.61 Aligned_cols=203 Identities=21% Similarity=0.307 Sum_probs=178.8
Q ss_pred CccceEEEeCCCCCCCceeEEEeCCeEEEEEEEecCCccccccccccCCcccEEEEEeecCCCCcccccCCCCCChhHHH
Q psy3754 387 DIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIG 466 (755)
Q Consensus 387 e~R~i~ie~g~l~~a~GSal~~~G~T~Vl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~f~p~s~~e~~~~g~~~~rei~ 466 (755)
.+|++.|+.|+|+++|||+.|++|+|+|+|+|+ ||.+...+. ++..+..+++...|.+ |-++..|..
T Consensus 4 ~lr~~~cei~iLsr~dGSs~fsqgdT~V~c~V~-GP~dvk~r~-----E~~~katleVi~rp~~-------G~~~~~eK~ 70 (217)
T KOG1069|consen 4 RLRGIACEISILSRPDGSSEFSQGDTKVICSVY-GPIDVKARQ-----EDPEKATLEVIWRPKS-------GVNGTVEKV 70 (217)
T ss_pred hhhhhhhhhceecCCCCccceecCCcEEEEEee-CCcchhhcc-----cCchhceEEEEEeccc-------CcchHHHHH
Confidence 789999999999999999999999999999996 999876654 4456789999999986 457899999
Q ss_pred HHHHHHHhccccCCCCCCCceE-EEEEEEEEccCCChhhHHHHHHHHHHHhCCCCcccceEEEEEEEEecCceEEEEecC
Q psy3754 467 HGRLAKRALLPVLPNNNKFNYS-IRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDI 545 (755)
Q Consensus 467 ~~~lieral~~vi~~~~~~p~t-I~V~v~VLe~dGs~~~Aav~a~slAL~daGvPi~~~va~vs~gli~~~~~~~vL~Dp 545 (755)
++++|++.|++++.+ +.||++ |+|.++|+++|||.+.+|+||+++||.||||||+.+++|+++.+.+++ .+++||
T Consensus 71 ~e~iI~~tl~~~I~l-~l~Prt~iqVsiqvv~ddgs~LacaINaAclALvDaGIpl~~mfcai~~~~~~d~---~lv~Dp 146 (217)
T KOG1069|consen 71 LERIIRKTLSKAIIL-ELYPRTTIQVSIQVVEDDGSTLACAINAACLALVDAGIPLRSMFCAISCALHEDG---VLVLDP 146 (217)
T ss_pred HHHHHHHHHHHhhee-eecCCceEEEEEEEEecCCcchHHHHHHHHHHHHhcCCchHHhhhhceEEEecCc---cEEECC
Confidence 999999999999998 899998 999999999999999999999999999999999999999999999987 578899
Q ss_pred Cccccc--cCCccEEEEeecC---cEEEEEeeecccccCHHHHHHHHHHHHhhhHHHHHHHHhhccccc
Q psy3754 546 LGDEDR--CGDMDFKVAGTVN---GITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCK 609 (755)
Q Consensus 546 ~~~Ee~--~gd~~~~Va~t~~---gi~alq~~~k~~~is~~~l~~al~~A~~~~~~I~~~~~~~l~~~r 609 (755)
+..++. .+...+++.++.. +++. ++. .|.++.++|..+++.|...+..++.++++.+++..
T Consensus 147 t~~qek~~~~~~~lsf~~~~~~~~~vi~--s~t-~G~~~~d~lf~~le~a~~~~~~~f~f~r~~~q~~~ 212 (217)
T KOG1069|consen 147 TAKQEKISTARATLSFEGGSLGEPKVII--SET-NGEKSEDQLFYVLELAQAAAQSLFPFYREVLQRKY 212 (217)
T ss_pred cHHhhhhhhceEEEEEecCCCCCcceEE--Eec-cCCCCHHHHHHHHHhhHHHHHHHHHHHHHHHHhhc
Confidence 999887 5666777765433 3443 332 46789999999999999999999999999988753
No 25
>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=3.6e-28 Score=280.29 Aligned_cols=237 Identities=19% Similarity=0.282 Sum_probs=199.7
Q ss_pred eeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecC---CCCC----CCCcceeeEEeEeeccccCCCCCCcccccCCCCc
Q psy3754 77 YKISIEIGEIARQATSSVLVSIEDTVILATVVSCK---DPTS----TYNFFPLTVDYIEKAYAAGRIPGSFFKREGKPSE 149 (755)
Q Consensus 77 r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~---~~~~----~~~f~pl~v~y~e~~~a~g~ip~~~~kReg~p~~ 149 (755)
|++.+++|.+ .+|+|||+++.|+|+|||+++... +.+. +.+.-.+.++|....|+.|.. +|.+.|+.
T Consensus 346 R~i~~~~g~l-~~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~~~~~~~~~~YnfpPFSt~er-----~~~~~~~R 419 (719)
T TIGR02696 346 RPLDAEVQVI-PRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPETSKRYMHHYNFPPYSTGET-----GRVGSPKR 419 (719)
T ss_pred ccceeecCCC-CCCCceEEEEecCcEEEEEEeCCCchhhhhcccccccccceEEEEEeCCCCcccCC-----CCCCCCCc
Confidence 7899999999 889999999999999999987521 1111 233456779998888887754 55577889
Q ss_pred hhhHHHHHhcCccccccc--CCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEEC----CE
Q psy3754 150 RETIISRLIDRPIRPLFP--EGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYID----GK 223 (755)
Q Consensus 150 ~e~l~sRlIdr~lrpl~p--~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP~~~~vaav~vg~~~----g~ 223 (755)
+|+..++++.|+|+|.+| ..|.+.+.+++.||++||+.. +|||||||+||++|||||+++||||++|+++ |+
T Consensus 420 Reighg~La~rALe~vI~~~e~fP~TIrvvseVLeSdGSss--~AsIcaasLALmDAGVPmkd~VAgis~Gli~e~~~~~ 497 (719)
T TIGR02696 420 REIGHGALAERALVPVLPSREEFPYAIRQVSEALGSNGSTS--MGSVCASTLSLLNAGVPLKAPVAGIAMGLISDEVDGE 497 (719)
T ss_pred cHHHHHHHHHHHHHHhhCcHhhCCCEEEEEEEeeccCCcHH--HHHHHHHHHHHHHcCcchhheeeEEEEEEeccccCCC
Confidence 999999999999999998 888888999999999999888 9999999999999999999999999999983 33
Q ss_pred ----EEEcCCHHHHhcCcccEEEEeecCceEEEEcCCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCC
Q psy3754 224 ----YILNPTTEQLKKSHLDLLVAGTEKAIITVESESKQ--LPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWD 297 (755)
Q Consensus 224 ----~vldPt~~E~~~s~~~l~va~~~~~i~mie~~~~~--~se~~~~~al~~a~~~~~~i~~~~~~~~~~~~~~k~~~~ 297 (755)
+++||+..|+..+++|+.|++|.++++.++.+++- ++.+.|.+||+.|.++|..|++.|++.+.+. .+..++.
T Consensus 498 ~~~~iL~Di~g~ED~~Gdmdfkvagt~~gIt~lQmd~ki~gi~~e~l~~aL~~A~~g~~~Il~~m~~al~~p-~~~s~~a 576 (719)
T TIGR02696 498 TRYVALTDILGAEDAFGDMDFKVAGTSEFVTALQLDTKLDGIPASVLASALKQARDARLAILDVMAEAIDTP-DEMSPYA 576 (719)
T ss_pred cceeEEeCCCchhhhcCCceEEEEecCCCEEEEEEEeeECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCc-cccccCC
Confidence 89999999999999999999999999999998863 6999999999999999999999999999988 5555555
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHHhccchhHH
Q psy3754 298 PIVKDKTLISKIINISEHKIRKAYQIKNKQIR 329 (755)
Q Consensus 298 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~k~~r 329 (755)
|....-.+. .++|.+++...+|.-|
T Consensus 577 P~~~~~~I~-------~~ki~~vIG~gGk~I~ 601 (719)
T TIGR02696 577 PRIITVKIP-------VDKIGEVIGPKGKMIN 601 (719)
T ss_pred CeeEEEEeC-------hHHhhheeCCCcHhHH
Confidence 543221221 4677777777777654
No 26
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional
Probab=99.95 E-value=2.4e-27 Score=251.81 Aligned_cols=203 Identities=26% Similarity=0.275 Sum_probs=171.8
Q ss_pred CeeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecC-CCCC-CCCcceeeEEeEeeccccCCCCCCcccccCCCCchhhH
Q psy3754 76 SYKISIEIGEIARQATSSVLVSIEDTVILATVVSCK-DPTS-TYNFFPLTVDYIEKAYAAGRIPGSFFKREGKPSERETI 153 (755)
Q Consensus 76 ~r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~-~~~~-~~~f~pl~v~y~e~~~a~g~ip~~~~kReg~p~~~e~l 153 (755)
-|++.+++|.+ ++|+|||++++|+|+|+|+|+++. +|.+ ..+-.-++++|.-..++. |. .|.|+|++++++
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-KKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLAS---PT---FEPGPPDENAIE 106 (271)
T ss_pred ccCeEEEeCCc-cCCCcEEEEEECCCEEEEEEEEEEecCCCCCCCCCEEEEEEEECCCcC---cc---ccCCCCCHHHHH
Confidence 48999999999 899999999999999999999643 2321 112223556655443332 21 256899999999
Q ss_pred HHHHhcCccccc----------ccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCC----------------
Q psy3754 154 ISRLIDRPIRPL----------FPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELP---------------- 207 (755)
Q Consensus 154 ~sRlIdr~lrpl----------~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP---------------- 207 (755)
++|+|+|+||+. .|+.++|.++|+++||+.||+.. .+|++||++||.+++||
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 999999999984 36677899999999999999844 69999999999999995
Q ss_pred ----CCCCeEEEEEEEECCEEEEcCCHHHHhcCcccEEEEeecC-ceEEEEc-CCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy3754 208 ----FLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEK-AIITVES-ESKQLPEDIILNAIIFGHEKMKIAINA 281 (755)
Q Consensus 208 ----~~~~vaav~vg~~~g~~vldPt~~E~~~s~~~l~va~~~~-~i~mie~-~~~~~se~~~~~al~~a~~~~~~i~~~ 281 (755)
|++++.++++|++++.+|+|||.+|++.++.+++|+.+++ .|++++. ++.++++++|.+|++.|.+.+++++++
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 9999999999999999999999999999999999999988 5777774 567799999999999999999999999
Q ss_pred HHHHHH
Q psy3754 282 INELVQ 287 (755)
Q Consensus 282 ~~~~~~ 287 (755)
+++.++
T Consensus 265 ~~~~l~ 270 (271)
T PRK04282 265 LKEALG 270 (271)
T ss_pred HHHHhc
Confidence 998763
No 27
>KOG1069|consensus
Probab=99.94 E-value=1.4e-26 Score=224.80 Aligned_cols=195 Identities=21% Similarity=0.234 Sum_probs=167.8
Q ss_pred eeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecCCCCCC---CCcceeeEEeEeeccccCCCCCCcccccCCCCchhhH
Q psy3754 77 YKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTST---YNFFPLTVDYIEKAYAAGRIPGSFFKREGKPSERETI 153 (755)
Q Consensus 77 r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~~~~~~---~~f~pl~v~y~e~~~a~g~ip~~~~kReg~p~~~e~l 153 (755)
|++..|.|.| +++|||+-+++|+|+|+|+|+||.+++.+ .+-..|.|-||++. |-+...|..
T Consensus 6 r~~~cei~iL-sr~dGSs~fsqgdT~V~c~V~GP~dvk~r~E~~~katleVi~rp~~--------------G~~~~~eK~ 70 (217)
T KOG1069|consen 6 RGIACEISIL-SRPDGSSEFSQGDTKVICSVYGPIDVKARQEDPEKATLEVIWRPKS--------------GVNGTVEKV 70 (217)
T ss_pred hhhhhhhcee-cCCCCccceecCCcEEEEEeeCCcchhhcccCchhceEEEEEeccc--------------CcchHHHHH
Confidence 5788899999 88999999999999999999999987543 34566899999887 888999999
Q ss_pred HHHHhcCcccccccCCC--cCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEE-CCEEEEcCCH
Q psy3754 154 ISRLIDRPIRPLFPEGY--LNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYI-DGKYILNPTT 230 (755)
Q Consensus 154 ~sRlIdr~lrpl~p~~~--~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP~~~~vaav~vg~~-~g~~vldPt~ 230 (755)
++|+|.+.|.+++-... +..+||+++|++.||+.. ++|||||++||.|+||||+..++|+.+.+. ||.+++|||.
T Consensus 71 ~e~iI~~tl~~~I~l~l~Prt~iqVsiqvv~ddgs~L--acaINaAclALvDaGIpl~~mfcai~~~~~~d~~lv~Dpt~ 148 (217)
T KOG1069|consen 71 LERIIRKTLSKAIILELYPRTTIQVSIQVVEDDGSTL--ACAINAACLALVDAGIPLRSMFCAISCALHEDGVLVLDPTA 148 (217)
T ss_pred HHHHHHHHHHHhheeeecCCceEEEEEEEEecCCcch--HHHHHHHHHHHHhcCCchHHhhhhceEEEecCccEEECCcH
Confidence 99999999988433222 338999999999999866 999999999999999999999999999986 4689999999
Q ss_pred HHHhcC--cccEEEEe---ecCceEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy3754 231 EQLKKS--HLDLLVAG---TEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNV 289 (755)
Q Consensus 231 ~E~~~s--~~~l~va~---~~~~i~mie~~~~~~se~~~~~al~~a~~~~~~i~~~~~~~~~~~ 289 (755)
.|++.+ ...|++.+ ...++++.++.| +++++++..+++.|..+++.++.++++.+++.
T Consensus 149 ~qek~~~~~~~lsf~~~~~~~~~vi~s~t~G-~~~~d~lf~~le~a~~~~~~~f~f~r~~~q~~ 211 (217)
T KOG1069|consen 149 KQEKISTARATLSFEGGSLGEPKVIISETNG-EKSEDQLFYVLELAQAAAQSLFPFYREVLQRK 211 (217)
T ss_pred HhhhhhhceEEEEEecCCCCCcceEEEeccC-CCCHHHHHHHHHhhHHHHHHHHHHHHHHHHhh
Confidence 999954 44555543 334699999999 59999999999999999999999999988754
No 28
>KOG1068|consensus
Probab=99.93 E-value=6.5e-26 Score=228.59 Aligned_cols=206 Identities=19% Similarity=0.230 Sum_probs=172.7
Q ss_pred eeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecCCCCC----CCCcceeeEEeEeeccccCCCCCCcccccCCCCchhh
Q psy3754 77 YKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTS----TYNFFPLTVDYIEKAYAAGRIPGSFFKREGKPSERET 152 (755)
Q Consensus 77 r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~~~~~----~~~f~pl~v~y~e~~~a~g~ip~~~~kReg~p~~~e~ 152 (755)
|++...+|.+ .+|+||||+++|||||+|+|+||++++. +.+-.-+.+.|.-..|+.|.. ++..+.+.++.
T Consensus 24 R~i~~~~g~~-~~a~GSay~E~GnTKVl~aV~GPre~~~~~~~~~~~a~lnc~~~~a~Fst~~r-----~~~~~~~rr~~ 97 (245)
T KOG1068|consen 24 RRIYARIGVL-TQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLNCEVSSAQFSTGDR-----KKRPKGDRREK 97 (245)
T ss_pred hhhhhhcCcc-ccCCccchhhcCCeEEEEEEeCCcccccccccccccceEEEEEeeeccccchh-----ccCCCccHHHH
Confidence 6799999977 8999999999999999999999998754 234456899998777666533 33456678899
Q ss_pred HHHHHhcCcccccccCCCcC--eEEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCCH
Q psy3754 153 IISRLIDRPIRPLFPEGYLN--EIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTT 230 (755)
Q Consensus 153 l~sRlIdr~lrpl~p~~~~~--~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP~~~~vaav~vg~~~g~~vldPt~ 230 (755)
+++.++.+++.|.+....++ .+.|.++||+.||++. ++|||||++||+++||||.+.|.|+++|+.+|.+++|||.
T Consensus 98 e~s~~L~~afe~~I~~~lyPrsqIDI~v~VleddG~~l--aa~inaatlAL~daGI~m~D~i~~~t~~l~~~~~l~Dl~~ 175 (245)
T KOG1068|consen 98 ELSLMLQQAFEPVILLELYPRSQIDIYVQVLEDDGSNL--AAAINAATLALADAGIPMYDLITACTAGLADGTPLLDLTS 175 (245)
T ss_pred HHHHHHHHHHHHHHHhhhCccccceEEEEEEECCCccH--HHHHHHHHHHHHHcCCChhhhhhhceeeecCCcccccccc
Confidence 99999999999955444444 5555567777777555 9999999999999999999999999999999999999999
Q ss_pred HHHhcCcccEEEEe--ecCceEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q psy3754 231 EQLKKSHLDLLVAG--TEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQ 291 (755)
Q Consensus 231 ~E~~~s~~~l~va~--~~~~i~mie~~~~~~se~~~~~al~~a~~~~~~i~~~~~~~~~~~~~ 291 (755)
-|+......++|+. +.+.+..++.++. ++.+.+...++.|.++|+++.+.++..+.++.+
T Consensus 176 ~eesa~~~~ltVa~l~~~~~i~~l~~~~~-~~~d~l~~vl~~a~~~c~~v~~~l~~~l~~~l~ 237 (245)
T KOG1068|consen 176 LEESARAPGLTVAALPNREEIALLQLDER-LHCDHLETVLELAIAGCKRVYERLRLVLREHLK 237 (245)
T ss_pred chhhccCCceEEEEecCcceEEEEEecCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99988766677664 4555999999986 999999999999999999999999998887754
No 29
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=1.4e-24 Score=221.92 Aligned_cols=201 Identities=19% Similarity=0.201 Sum_probs=175.0
Q ss_pred CeeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecCC----CCCCCCcceeeEEeEeeccccCCCCCCcccccCCCCchh
Q psy3754 76 SYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKD----PTSTYNFFPLTVDYIEKAYAAGRIPGSFFKREGKPSERE 151 (755)
Q Consensus 76 ~r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~~----~~~~~~f~pl~v~y~e~~~a~g~ip~~~~kReg~p~~~e 151 (755)
=|++++++|.+ +.|+|||+|++|+|+|+|.|..... -.|.++.+-.+++..+.+|..+.. |+|++.+
T Consensus 33 fR~ieI~~~vi-~ka~GSa~VklG~Tqvv~gvK~eig~Pf~DtP~eG~~~~n~El~Plas~~fE~--------Gppde~a 103 (272)
T COG2123 33 FRPLEIETGVI-PKANGSALVKLGNTQVVVGVKAEIGEPFPDTPNEGVLVVNVELSPLASPSFEP--------GPPDELA 103 (272)
T ss_pred ccceEEEeCce-ecCCCcEEEEecCeEEEEEEEcccCCCCCCCCCCceEEeeeeeeccccccccC--------CCCchhH
Confidence 37899999999 8899999999999999999997542 245555556677777666555444 8999999
Q ss_pred hHHHHHhcCcccc----------cccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCC--------------
Q psy3754 152 TIISRLIDRPIRP----------LFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELP-------------- 207 (755)
Q Consensus 152 ~l~sRlIdr~lrp----------l~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP-------------- 207 (755)
++++|++||.||. +.++.+.|-+.++++||++|||.- .||..|+.+||....+|
T Consensus 104 ielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~--Da~~lA~~aAL~~t~vP~~~~~~~~~~v~~~ 181 (272)
T COG2123 104 IELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLI--DAASLAAVAALLNTRVPKAVEVGDGEIVIEV 181 (272)
T ss_pred HHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHH--HHHHHHHHHHHHhcCCCceeecCCcceeecc
Confidence 9999999999998 578999999999999999999755 68888888888887666
Q ss_pred --------CCCCeEEEEEEEECCEEEEcCCHHHHhcCcccEEEEeecCc--eEEEEcCCCCCCHHHHHHHHHHHHHHHHH
Q psy3754 208 --------FLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEKA--IITVESESKQLPEDIILNAIIFGHEKMKI 277 (755)
Q Consensus 208 --------~~~~vaav~vg~~~g~~vldPt~~E~~~s~~~l~va~~~~~--i~mie~~~~~~se~~~~~al~~a~~~~~~ 277 (755)
+..++-+|+++.+|+.+++|||.+|+..++..|+++.++++ +.|.++|+..++++.+.+|++.|.+...+
T Consensus 182 ~~~~~pl~~~~~pi~vt~a~ig~~lvvDPsleEe~v~d~~ltit~~~~~~Iv~iqK~g~~~~~~~~~~~~~~~A~~~~~k 261 (272)
T COG2123 182 EEEPVPLPVSNPPISVTFAKIGNVLVVDPSLEEELVADGRLTITVNEDGEIVAIQKVGGGSITESDLEKALKTALSKAEK 261 (272)
T ss_pred cCCCcccccCCCceEEEEEEECCEEEeCCCcchhhhcCceEEEEECCCCcEEEEEEcCCCcCCHHHHHHHHHHHHHHHHH
Confidence 56788899999999999999999999999999999999997 67777888889999999999999999999
Q ss_pred HHHHHHHHHH
Q psy3754 278 AINAINELVQ 287 (755)
Q Consensus 278 i~~~~~~~~~ 287 (755)
+++.+.+.++
T Consensus 262 l~~~~~~~L~ 271 (272)
T COG2123 262 LREALKEALK 271 (272)
T ss_pred HHHHHHHhhc
Confidence 9999988764
No 30
>KOG1613|consensus
Probab=99.92 E-value=2e-24 Score=214.22 Aligned_cols=239 Identities=16% Similarity=0.200 Sum_probs=192.8
Q ss_pred HHHHHHHHHHHHHHHHHccCCcCCCCCCCCccceEEEeCCCCCCCceeEEEeCCeEEEEEEEecCCccccccccccCCcc
Q psy3754 358 NCILYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFT 437 (755)
Q Consensus 358 ~~~~~~~~~~~~r~~~l~~~~R~DGR~~~e~R~i~ie~g~l~~a~GSal~~~G~T~Vl~~Vt~Gp~~~~~~~d~~~~~~~ 437 (755)
-++|+++.|..+.++.|++++|+|||...|+|.+.++.|.++.++|||++..|+|.|+|+++.+ ...++.+.+++
T Consensus 16 p~~fkrI~Pe~~l~rhLse~~RpdgR~lgefRdt~in~g~IsTangSal~K~G~ttvi~~Ik~e-----i~epstdapde 90 (298)
T KOG1613|consen 16 PEVFKRISPELYLQRHLSEGIRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICGIKAE-----IAEPSTDAPDE 90 (298)
T ss_pred HHHHhhcCHHHHHHHHhhcccCcchhhhhHHhhhheecCceeccCcHHHHhcCCcEEEEEeeee-----ecccccCCCCC
Confidence 3789999999999999999999999999999999999999999999999999999999999852 22234445679
Q ss_pred cEEEEEeecCCCCcccccCCCCCChhHHHHHHHHHHhccc--cCCCCC------CCceEEEEEEEEEccCCChhhHHHHH
Q psy3754 438 DSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLP--VLPNNN------KFNYSIRLVSEITESNGSSSMASVCG 509 (755)
Q Consensus 438 ~~~~~~~~f~p~s~~e~~~~g~~~~rei~~~~lieral~~--vi~~~~------~~p~tI~V~v~VLe~dGs~~~Aav~a 509 (755)
|.+..+|.+||.|+. +.|.|+|...+.-+++.+...+.. +|++++ +..|.+|.++.||+.||+.++||++|
T Consensus 91 g~Iv~n~~lpplcs~-r~RpG~p~dea~viSq~LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG~~fDa~w~a 169 (298)
T KOG1613|consen 91 GDIVPNYALPPLCSS-RFRPGPPTDEAQVISQKLHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDGPVFDACWNA 169 (298)
T ss_pred cceeecccCCccccc-CCCCCCCchHHHHHHHHHHHHHHhcCCcchhhheeeccceeeEEEEEEEEEcCCCcHHHHHHHH
Confidence 999999999999975 457888999888888877777653 555443 36789999999999999999999999
Q ss_pred HHHHHHhCCCCcc---c-----------ceEE--------EE-----EEEEec----C---ceEEEEecCCccccccCCc
Q psy3754 510 GCLALLDAGVPIS---E-----------HVAG--------IA-----MGLIKD----G---EKVVILSDILGDEDRCGDM 555 (755)
Q Consensus 510 ~slAL~daGvPi~---~-----------~va~--------vs-----~gli~~----~---~~~~vL~Dp~~~Ee~~gd~ 555 (755)
.++||..-.+|.- . ..+. ++ +++-+. . ++..++.|||.+||+..+.
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 9999999988821 0 0000 00 111000 0 1235668999999999999
Q ss_pred cEEEEeecCc-EEEEEeeecccccCHHHHHHHHHHHHhhhHHHHHHHH
Q psy3754 556 DFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMK 602 (755)
Q Consensus 556 ~~~Va~t~~g-i~alq~~~k~~~is~~~l~~al~~A~~~~~~I~~~~~ 602 (755)
.++|..+..| ++.+...|+.+-++++.++.|++.|+...+.+.+.|.
T Consensus 250 ~lTIvldss~n~v~l~k~GG~al~~~~~iK~c~elar~Rakelk~~~~ 297 (298)
T KOG1613|consen 250 TLTIVLDSSGNYVQLTKVGGGALITPEMIKRCLELARVRAKELKTRFN 297 (298)
T ss_pred eEEEEEcCCCCEEEEEecCcccccCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999987777 7888877665556779999999999999988877664
No 31
>KOG1612|consensus
Probab=99.91 E-value=1.2e-22 Score=203.45 Aligned_cols=234 Identities=17% Similarity=0.194 Sum_probs=189.0
Q ss_pred HccCCcCCCCCCCCccceEEEeCCCCCCCceeEEEeCC-eEEEEEEEecCCccccccccccCCcccEEEEEeecCCCCcc
Q psy3754 374 LDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGD-TQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATG 452 (755)
Q Consensus 374 l~~~~R~DGR~~~e~R~i~ie~g~l~~a~GSal~~~G~-T~Vl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~f~p~s~~ 452 (755)
.+..+|.|||..+++|||.+++|+||+++|||++..|+ |-++++|+. +...+....++++.+.+.+++.|.+.+
T Consensus 17 ~e~~iR~DGR~~~~~Rpi~vetdVlp~tNGSaRVk~g~~tdiivgVKa-----Evg~~~~~~p~egk~~~~VD~S~sasp 91 (288)
T KOG1612|consen 17 SEPDIRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVKA-----EVGSPDDETPVEGKYLFFVDCSPSASP 91 (288)
T ss_pred cCcccccCCcCccccceEEEEeccccCCCCcEEEEecCCceEEEEEee-----eccCccccCCCCCeEEEEEEecCCcCc
Confidence 45789999999999999999999999999999999999 999999985 222233445778899999999999887
Q ss_pred cccCCCCCChhHHHHHHHHHHhccc--------cCCCCCCCceEEEEEEEEEccCCChhhHHHHHHHHHHHhCCCC----
Q psy3754 453 DIGRIGVPKRREIGHGRLAKRALLP--------VLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVP---- 520 (755)
Q Consensus 453 e~~~~g~~~~rei~~~~lieral~~--------vi~~~~~~p~tI~V~v~VLe~dGs~~~Aav~a~slAL~daGvP---- 520 (755)
++..+ ..+.--.++.+.++|+|.. -+.....|.|.|+|++.|+++|||.++|-..|+.+||.+..+|
T Consensus 92 ~f~gR-ggde~~~eltsaLq~~l~~~~sgv~ls~L~lt~~~~W~i~VDvlVi~s~gn~~dAiS~Ai~~AL~~T~lPkv~v 170 (288)
T KOG1612|consen 92 QFQGR-GGDELVEELTSALQRVLNSLGSGVDLSKLQLTPGYCWKIYVDVLVISSDGNLLDAISIAIYAALNNTRLPKVIV 170 (288)
T ss_pred cccCC-ChhhHHHHHHHHHHHHHhCcCcccchhheeccCCeeEEEEEeEEEEecCCCHHHHHHHHHHHHHhcccCCcccc
Confidence 66322 2344445677888888886 1222245999999999999999999999999999999999888
Q ss_pred -----------------------cccceEEEEEEEEecCceEEEEecCCccccccCCccEEEEeecCcEEEEEeeecccc
Q psy3754 521 -----------------------ISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFG 577 (755)
Q Consensus 521 -----------------------i~~~va~vs~gli~~~~~~~vL~Dp~~~Ee~~gd~~~~Va~t~~gi~alq~~~k~~~ 577 (755)
+..++.-++...+.. .+|+||+.+|+.+....+.|..+..|++.+....+.++
T Consensus 171 ~~dd~~~~~i~~s~~~Yd~~~~~~~~~P~ivtlskIG~----~~lVD~T~eEe~~a~s~l~Isv~a~givs~~r~VG~G~ 246 (288)
T KOG1612|consen 171 AFDDDGEVEILLSDEEYDLMVKLVENVPLIVTLSKIGT----NMLVDPTAEEESVANSGLLISVSAGGIVSCTRSVGLGD 246 (288)
T ss_pred ccccCCceeeccCcccchhhhhhcccCCEEEEEEeecc----eEEccCCccHHHhhhcceEEEEecCcceEEEEEecCCC
Confidence 233556666666643 68899999999999999999999999888777666667
Q ss_pred cCHHHHHHHHHHHHhhhHHHHHHHHhhcccc--ccccccCCC
Q psy3754 578 ITYDIIQIALYKAKKGLSYILEKMKTEVPKC--KNELSKFAP 617 (755)
Q Consensus 578 is~~~l~~al~~A~~~~~~I~~~~~~~l~~~--r~~~~~~~P 617 (755)
+.++-+.+++++++.....+...+.+.|... +...+.|+|
T Consensus 247 l~~s~i~~mle~~~~~~e~l~~~l~k~L~~~e~~~~~~~fl~ 288 (288)
T KOG1612|consen 247 LDPSSIPEMLEQGKAVVETLAPDLVKSLENEEDILSFKGFLP 288 (288)
T ss_pred CChhhHHHHHHHHHHHHHhhhHHHHHHhhhhhhccCccccCC
Confidence 9999999999999999998888888887652 233444544
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=99.90 E-value=4e-23 Score=195.73 Aligned_cols=131 Identities=29% Similarity=0.494 Sum_probs=116.1
Q ss_pred CccceEEEeCCCCCCCceeEEEeCCeEEEEEEEecCCccccccccccCCcccEEEEEeecCCCCcccccCCCCCChhHHH
Q psy3754 387 DIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIG 466 (755)
Q Consensus 387 e~R~i~ie~g~l~~a~GSal~~~G~T~Vl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~f~p~s~~e~~~~g~~~~rei~ 466 (755)
|+|++.+++|++++++|||+|++|+|+|+|+|+ ||....+..+. ...+|.+.++|+++|++.++.++.+.+++++..
T Consensus 1 e~R~i~i~~~~~~~a~GSa~v~~G~T~V~~~V~-~~~~~~~~~~~--~~~~g~~~v~v~~~~~~~~~~~~~~~~~~~~~~ 77 (132)
T PF01138_consen 1 ELRPISIETGVLPRADGSARVSLGNTKVICSVK-GPIEPPPSNER--DDAEGRLTVEVEFSPFASPSFRRGGRPDEEERE 77 (132)
T ss_dssp CBEEEEEEESSSSSSSEEEEEEETTEEEEEEEE-EEEEGCSCSTT--SSSSEEEEEEEEECCCGSTSSSSSSSTHHHHHH
T ss_pred CCccEEEEeCCCCCCCeEEEEEECCeEEEEEEE-ecccccchhcc--cCCCceEEEEEEeccccccccccccccchhHHH
Confidence 799999999999999999999999999999997 77665322221 122589999999999999888777889999999
Q ss_pred HHHHHHHhccccCCCCCCCceEEEEEEEEEccCC-ChhhHHHHHHHHHHHhCCCC
Q psy3754 467 HGRLAKRALLPVLPNNNKFNYSIRLVSEITESNG-SSSMASVCGGCLALLDAGVP 520 (755)
Q Consensus 467 ~~~lieral~~vi~~~~~~p~tI~V~v~VLe~dG-s~~~Aav~a~slAL~daGvP 520 (755)
++++++++|++++..+..+.|+|+|+++||++|| |..+|+++|+++||+|+|+|
T Consensus 78 l~~~l~~~l~~~~~~~~~~~~~i~v~v~vl~~dG~~~~~a~~~A~~~AL~~~~iP 132 (132)
T PF01138_consen 78 LSSLLERALRSSILLEGYPRWQIHVDVQVLSDDGGNLLDAAINAACLALLDAGIP 132 (132)
T ss_dssp HHHHHHHHHHHTBSTTTTSSEEEEEEEEEEECSSSSHHHHHHHHHHHHHHHHTCS
T ss_pred HHHHHhhhccccccccccCceEEEEEEEEEecCCCCHHHHHHHHHHHHHHhcCCC
Confidence 9999999999999985545689999999999999 99999999999999999998
No 33
>PRK05626 rpsO 30S ribosomal protein S15; Reviewed
Probab=99.86 E-value=3.6e-22 Score=173.78 Aligned_cols=63 Identities=59% Similarity=0.818 Sum_probs=62.6
Q ss_pred CCCChhHHHHHHHHhcCCCCCCCCchhhHHHHHHHHHHHHHHHhhccCcccchhhhhhhhhcc
Q psy3754 1 MTIKNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKGNF 63 (755)
Q Consensus 1 m~~~~~~k~~~~~~~~~~~~d~gs~evqia~lt~~I~~l~~h~~~~~kd~~~~~~l~~~v~~r 63 (755)
|+++.++|+++|++|+++++||||+|||||+||+||++|++||+.||||+||+|||++||++|
T Consensus 1 m~~~~~~k~~li~~f~~~~~DTGS~eVQiA~LT~rI~~L~~Hlk~~~KD~~srrgL~~lv~kR 63 (89)
T PRK05626 1 MSLTKEKKAEIIKEYGRHEGDTGSPEVQVALLTERINHLTEHLKEHKKDHHSRRGLLKMVGQR 63 (89)
T ss_pred CCCCHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHcccchhhHHHHHHHHHhH
Confidence 899999999999999999999999999999999999999999999999999999999999999
No 34
>TIGR00952 S15_bact ribosomal protein S15, bacterial/organelle. This model is built to recognize specifically bacterial, chloroplast, and mitochondrial ribosomal protein S15. The homologous proteins of Archaea and Eukarya are designated S13.
Probab=99.83 E-value=5.7e-21 Score=165.22 Aligned_cols=60 Identities=52% Similarity=0.722 Sum_probs=58.3
Q ss_pred ChhHHHHHHHHhcCCCCCCCCchhhHHHHHHHHHHHHHHHhhccCcccchhhhhhhhhcc
Q psy3754 4 KNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKGNF 63 (755)
Q Consensus 4 ~~~~k~~~~~~~~~~~~d~gs~evqia~lt~~I~~l~~h~~~~~kd~~~~~~l~~~v~~r 63 (755)
+.++|+++|++|+++++||||+|||||+||+||++|++||+.||||+||+|||++||++|
T Consensus 1 ~~~~k~~li~~~~~~~~DtGS~eVQiA~LT~rI~~L~~Hl~~h~KD~~srrgL~~lv~kR 60 (86)
T TIGR00952 1 TKERKQEIIKEFQLHEKDTGSPEVQIALLTERINQLTEHLKANKKDHHSRRGLLKLVGRR 60 (86)
T ss_pred CHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHH
Confidence 357899999999999999999999999999999999999999999999999999999999
No 35
>KOG1614|consensus
Probab=99.82 E-value=5.5e-19 Score=176.27 Aligned_cols=204 Identities=20% Similarity=0.246 Sum_probs=164.9
Q ss_pred CeeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecC----CCCCCCCcceeeEEeEeeccccCCCCCCcccccCCCCchh
Q psy3754 76 SYKISIEIGEIARQATSSVLVSIEDTVILATVVSCK----DPTSTYNFFPLTVDYIEKAYAAGRIPGSFFKREGKPSERE 151 (755)
Q Consensus 76 ~r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~----~~~~~~~f~pl~v~y~e~~~a~g~ip~~~~kReg~p~~~e 151 (755)
=|.+++++|+. -||+.+++|+|+|+|.++... .-+|..+.+.+.+++.++++.++.. |++++.+
T Consensus 32 fR~lei~fGke----~gs~~vt~G~Tkvm~~vt~~ia~Py~dRP~eG~~~I~telsPmA~~sfE~--------Gr~~~~~ 99 (291)
T KOG1614|consen 32 FRDLEIEFGKE----YGSVLVTMGNTKVMARVTAQIAQPYIDRPHEGSFSIFTELSPMASPSFEP--------GRKGESE 99 (291)
T ss_pred hhceEEEeccc----cccEEEEecCeeEEEEeehhhcCcccCCCCCCeeeeeeccccccccccCC--------CCccchH
Confidence 47899999965 699999999999999999754 2356667788999999999888776 8999999
Q ss_pred hHHHHHhcCcccc----------cccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCC----------------
Q psy3754 152 TIISRLIDRPIRP----------LFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISE---------------- 205 (755)
Q Consensus 152 ~l~sRlIdr~lrp----------l~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~---------------- 205 (755)
++++|+|++.+|. +......|.+.|++++|+.||+.- .||..||.+||+--.
T Consensus 100 v~l~Rliek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnlv--DaA~iAviaaL~hFrrPdvTv~g~ev~ihp~ 177 (291)
T KOG1614|consen 100 VELSRLIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNLV--DAACIAVIAALMHFRRPDVTVGGEEVIIHPV 177 (291)
T ss_pred HHHHHHHHHHHHhccccchHHHHhhhCCeEEEEEEEEEEEcCCCCee--hhHHHHHHHHHHhcCCCCcccccceeEecCh
Confidence 9999999999998 466788999999999999999944 344555555554322
Q ss_pred -----CC--CCCCeEEEEEEEEC-CE-EEEcCCHHHHhcCcccEEEEeecCc-eEEEE-cCCCCCCHHHHHHHHHHHHHH
Q psy3754 206 -----LP--FLGPLGVAKVGYID-GK-YILNPTTEQLKKSHLDLLVAGTEKA-IITVE-SESKQLPEDIILNAIIFGHEK 274 (755)
Q Consensus 206 -----IP--~~~~vaav~vg~~~-g~-~vldPt~~E~~~s~~~l~va~~~~~-i~mie-~~~~~~se~~~~~al~~a~~~ 274 (755)
+| ++....+++.+..| |+ .|+|||.+|+...+.-++|+.+++. |+.++ +++-.+++.+++.|.+.|...
T Consensus 178 eEr~PvPL~I~HmPIC~tf~ffnkG~ivviDpt~~Ee~~~dGs~vVt~Nk~rEVc~i~k~G~~~~~~~~i~~C~k~A~~~ 257 (291)
T KOG1614|consen 178 EEREPVPLSIHHMPICFTFGFFNKGEIVVIDPTEKEEAVMDGSMVVTMNKNREVCAIQKSGGEILDESVIERCYKLAKDR 257 (291)
T ss_pred hccCCcceeeeeccceEEEEEecCceEEEeCCcHHHHhccCceEEEEEcCCccEEEEecCCCccccHHHHHHHHHHHHHH
Confidence 22 23444567777665 55 6899999999999999999999997 55555 555558899999999999999
Q ss_pred HHHHHHHHHHHHHHhCCCc
Q psy3754 275 MKIAINAINELVQNVGQKK 293 (755)
Q Consensus 275 ~~~i~~~~~~~~~~~~~~k 293 (755)
+.++...+.+.+++.-+++
T Consensus 258 a~~vt~ii~e~l~~d~~~r 276 (291)
T KOG1614|consen 258 AVEVTGIILEALEEDQRER 276 (291)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 9999999999888765444
No 36
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.82 E-value=4.5e-20 Score=208.54 Aligned_cols=341 Identities=18% Similarity=0.280 Sum_probs=240.9
Q ss_pred cceEEEeCCCCC-CCceeEEEeCCeEEEEEEEecCCccccccccccCCcccEEEEEeecCCCCcc-----cccCCCCCCh
Q psy3754 389 RPISIRTGILPR-THGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATG-----DIGRIGVPKR 462 (755)
Q Consensus 389 R~i~ie~g~l~~-a~GSal~~~G~T~Vl~~Vt~Gp~~~~~~~d~~~~~~~~~~~~~~~f~p~s~~-----e~~~~g~~~~ 462 (755)
|++.+++|-+.+ ++||++++.|+|.||++|+ +.+ .....|++ .++++|.-.-|+.| ..+|.|+|+.
T Consensus 14 ~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~-~~~-~~~~~dF~------PLtV~y~Ek~yaaGkiPGgf~kREGrpse 85 (692)
T COG1185 14 RTLTLETGKIARQANGAVLVRYGDTVVLATVV-ASK-PKEGQDFF------PLTVNYEEKTYAAGKIPGGFFKREGRPSE 85 (692)
T ss_pred eeEEEEcchhhhhcCccEEEEECCeEEEEEEe-ecC-CCCCCCcc------ceeEeeeeehhccCcCCCcccccCCCCCc
Confidence 789999999985 9999999999999999997 444 33334444 58889988888885 4579999999
Q ss_pred hHHHHHHHHHHhccccCCCCCCCceEEEEEEEEEccCCCh--hhHHHHHHHHHHHhCCCCcccceEEEEEEEEecCceEE
Q psy3754 463 REIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSS--SMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVV 540 (755)
Q Consensus 463 rei~~~~lieral~~vi~~~~~~p~tI~V~v~VLe~dGs~--~~Aav~a~slAL~daGvPi~~~va~vs~gli~~~~~~~ 540 (755)
+++..++|++|.++|++| +.|-+-++|.++|++.|+.. ...+++++|+||.-+++|+.++++++.+|++++ .
T Consensus 86 ~e~L~sRLIDRpiRPlFp--~g~~~evqIv~tvls~D~~~~pdi~a~~gaSaAl~is~iPf~gpi~~vrvg~idg----~ 159 (692)
T COG1185 86 KEILTSRLIDRPIRPLFP--KGFRNEVQIVNTVLSVDPENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYIDG----I 159 (692)
T ss_pred cchhhhhhcccccccccc--hhhccceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCccCccceEEEEEECC----E
Confidence 999999999999999999 67777899999999999876 568999999999999999999999999999965 4
Q ss_pred EEecCCccccccCCccEEEEeecCcEEEEEeeecccccCHHHHHHHHHHHHhhhHHHHHHHHhhccccccccccCCCcee
Q psy3754 541 ILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLI 620 (755)
Q Consensus 541 vL~Dp~~~Ee~~gd~~~~Va~t~~gi~alq~~~k~~~is~~~l~~al~~A~~~~~~I~~~~~~~l~~~r~~~~~~~P~~~ 620 (755)
.++.|+..|-+.+++|++|+||.+.|.++..+.+ .++++++.+|+..+++..+.+.+++++......+....+.|...
T Consensus 160 ~vlNPt~~e~~~s~lDlvVAGT~~aV~MVE~~a~--~l~E~~ml~Av~fg~~~~~~~~~~qe~l~~~~g~~~~~~~~~~~ 237 (692)
T COG1185 160 FVLNPTLEELEESKLDLVVAGTKDAVNMVESEAD--ELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKWELEPPSL 237 (692)
T ss_pred EEECCChHHhhhcceeeEecCChhhhheeecccc--cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccccCc
Confidence 6689999999999999999999998888887654 58999999999999999999999998887765433333333211
Q ss_pred -------EEeeCCcccceeeccccceeeeeccccce---EEeecCceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEE
Q psy3754 621 -------TIKIDPSKIRDVIGKGGSTIRTLTEETGT---QIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYT 690 (755)
Q Consensus 621 -------~~~i~~~ki~~~IG~gGk~ik~i~~~~g~---~I~i~~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~ 690 (755)
...+-.+++.+.++..+|.-|... ..+ +|.-.-.+. .... ...-....+.+...+---.+++
T Consensus 238 ~~~l~~~i~~~~~~~l~~a~~i~~K~eR~~~--~~~~~~~i~~~~~~~---e~~~---~~~~~~~~~~l~~~~vR~~Il~ 309 (692)
T COG1185 238 DEELEAKVRDLAEDELKEAVGIREKQERSAA--LDAIKEKIEEELSGE---EESS---LKEIKAILEKLEKKPVRRLILE 309 (692)
T ss_pred cHHHHHHHHHHhHHHHHHHhcccchhhhhhh--HHHHHHHHHHHHhhh---cccc---HHHHHHHHHHHhHHHHHHHHhc
Confidence 000111123333333333222110 000 000000000 0000 1111112222223333345566
Q ss_pred EEEEEEEeeeEEEEEcC---CeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC--CCcEEEEE
Q psy3754 691 GIVLRLFDFGAIIRILS---GKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD--RGRIKLSM 753 (755)
Q Consensus 691 G~V~~I~~fG~FVel~~---g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~--~gki~LS~ 753 (755)
++|.-...++.||.... ++-...|.|.|..+.-..+-.+...|+...+++++... .++..|+.
T Consensus 310 ~~vR~DGR~~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~v~TLG~~~d~Qvid~l~~e~~krfm~h 377 (692)
T COG1185 310 GKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPRDAQVIDILEGEYKKRFLLH 377 (692)
T ss_pred CCcccCCCCcceeeeeeEEecCCCCccchhhhccCCCcceEEEEcCCcchhhhhhhccchhhhheeee
Confidence 66655555555555433 23334899999888777888899999999999988764 34555543
No 37
>COG0184 RpsO Ribosomal protein S15P/S13E [Translation, ribosomal structure and biogenesis]
Probab=99.80 E-value=5.2e-20 Score=159.51 Aligned_cols=63 Identities=48% Similarity=0.673 Sum_probs=62.5
Q ss_pred CCCChhHHHHHHHHhcCCCCCCCCchhhHHHHHHHHHHHHHHHhhccCcccchhhhhhhhhcc
Q psy3754 1 MTIKNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKGNF 63 (755)
Q Consensus 1 m~~~~~~k~~~~~~~~~~~~d~gs~evqia~lt~~I~~l~~h~~~~~kd~~~~~~l~~~v~~r 63 (755)
|+++++.|++|+++|+.++.||||+|||+|+||+||++|++||+.||||+||||||+.||+||
T Consensus 1 m~~~~~~k~~l~~eyg~~~~dtgs~evq~a~Lt~ri~~L~~Hlk~hkKD~~srRGL~~~vskr 63 (89)
T COG0184 1 MSLTSEIKQELRDEYGIPEVDTGSGEVQLALLTERINNLTEHLKEHKKDHHSRRGLLLLVSKR 63 (89)
T ss_pred CCchHHHHHHHHHHhCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHCCcchhHHHHHHHHHHHH
Confidence 899999999999999999999999999999999999999999999999999999999999999
No 38
>KOG1067|consensus
Probab=99.78 E-value=2.2e-18 Score=188.30 Aligned_cols=209 Identities=21% Similarity=0.302 Sum_probs=172.3
Q ss_pred eeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecCCCC-C------CC-CcceeeEEeEeeccccCCCCCCcccccCCCC
Q psy3754 77 YKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPT-S------TY-NFFPLTVDYIEKAYAAGRIPGSFFKREGKPS 148 (755)
Q Consensus 77 r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~~~~-~------~~-~f~pl~v~y~e~~~a~g~ip~~~~kReg~p~ 148 (755)
|+|.+|.+.+ +..+||++++.|+|+|||||+-..... . +. ..--+...|....||.+.+ -|-|.++
T Consensus 369 R~I~ce~~m~-~~lHGSaLFqRGqTQvlctVtl~s~e~a~klD~l~~~~~~~~FmLhY~FPPyat~Ev-----gkig~~n 442 (760)
T KOG1067|consen 369 RNISCEVDML-KTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGPDNGINFMLHYEFPPYATNEV-----GKIGGLN 442 (760)
T ss_pred cccceecCcc-ccccchhhhhcCceeEEEEEEcCCHHHhhhhhhhccCccCceEEEEeccCCcccccc-----ccccCCc
Confidence 7899999999 889999999999999999999644210 0 00 1113567787788888765 2236777
Q ss_pred chhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEE---C---C
Q psy3754 149 ERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYI---D---G 222 (755)
Q Consensus 149 ~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP~~~~vaav~vg~~---~---g 222 (755)
.+|+-...|-+|+|-|.+|++|.+.+.|...||+.+|..+ .|+++|.|+||++||+|...+||+|.+|++ | |
T Consensus 443 RRE~GhgaLAEkaL~~vlP~dfPftIRv~SeVleSnGSsS--MASvCGGslALmDaGvPv~a~vAGvaiGlvt~td~e~g 520 (760)
T KOG1067|consen 443 RRELGHGALAEKALLPVLPEDFPFTIRVTSEVLESNGSSS--MASVCGGSLALMDAGVPVSAHVAGVAIGLVTKTDPEKG 520 (760)
T ss_pred ccccCchhHhhhhhhccCcccCceEEEEeeeeeecCCcch--HHhhhcchhhhhhcCCccccccceeEEEeEeccCcccC
Confidence 7777778899999999999999999999999999999988 999999999999999999999999999985 1 1
Q ss_pred -----EEEEcCCHHHHhcCcccEEEEeecCceEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCC
Q psy3754 223 -----KYILNPTTEQLKKSHLDLLVAGTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWD 297 (755)
Q Consensus 223 -----~~vldPt~~E~~~s~~~l~va~~~~~i~mie~~~~~~se~~~~~al~~a~~~~~~i~~~~~~~~~~~~~~k~~~~ 297 (755)
.++-|-.--|.-..|+|+-||||.++|..+ .++.+.+.+|+..|.++-.+|.+.+.+.+.+......+|.
T Consensus 521 ~i~dyriltDIlGiEd~~GDMDFKiAGt~dGvTA~-----gi~l~Iv~eal~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~ 595 (760)
T KOG1067|consen 521 EIEDYRILTDILGIEDYNGDMDFKIAGTNDGVTAL-----GIPLKIVMEALQKAREARLQILDIMEKNINSPRGSDKEYS 595 (760)
T ss_pred CcccceeehhhcchhhhcCCcceeeccccCcceec-----CCcHHHHHHHHHhhhHHHHHHHHHHHhhcCCcccCccccC
Confidence 145565667777799999999999998888 4899999999999999999999999887766554444443
Q ss_pred C
Q psy3754 298 P 298 (755)
Q Consensus 298 ~ 298 (755)
|
T Consensus 596 P 596 (760)
T KOG1067|consen 596 P 596 (760)
T ss_pred c
Confidence 3
No 39
>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=99.77 E-value=1.4e-18 Score=164.59 Aligned_cols=123 Identities=28% Similarity=0.332 Sum_probs=105.8
Q ss_pred eeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecCCCCCCC--Ccce--eeEEeEeeccccCCCCCCcccccCCCCchhh
Q psy3754 77 YKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTY--NFFP--LTVDYIEKAYAAGRIPGSFFKREGKPSERET 152 (755)
Q Consensus 77 r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~~~~~~~--~f~p--l~v~y~e~~~a~g~ip~~~~kReg~p~~~e~ 152 (755)
|++.+++|.+ .+|+||+++++|+|+|+|+|++|..+++.. +..+ +++++.-..++.+++ +|+|++++.+.
T Consensus 3 R~i~i~~~~~-~~a~GSa~v~~G~T~V~~~V~~~~~~~~~~~~~~~~g~~~v~v~~~~~~~~~~-----~~~~~~~~~~~ 76 (132)
T PF01138_consen 3 RPISIETGVL-PRADGSARVSLGNTKVICSVKGPIEPPPSNERDDAEGRLTVEVEFSPFASPSF-----RRGGRPDEEER 76 (132)
T ss_dssp EEEEEEESSS-SSSSEEEEEEETTEEEEEEEEEEEEGCSCSTTSSSSEEEEEEEEECCCGSTSS-----SSSSSTHHHHH
T ss_pred ccEEEEeCCC-CCCCeEEEEEECCeEEEEEEEecccccchhcccCCCceEEEEEEecccccccc-----ccccccchhHH
Confidence 8999999999 899999999999999999999988763322 4444 888887777766655 66688999999
Q ss_pred HHHHHhcCccccccc--CCCcCeEEEEEEEEecCC-CCChhhHHHHHHHHHhhcCCCC
Q psy3754 153 IISRLIDRPIRPLFP--EGYLNEIQIVVYVLSVNP-QIDPDIASIIGVSTALSISELP 207 (755)
Q Consensus 153 l~sRlIdr~lrpl~p--~~~~~~~qi~~~Vls~Dg-~~~~~~~ai~aAs~AL~~s~IP 207 (755)
+++++|++.|++.+. +.++|.++|+++||+.|| +.. .+|+|||++||.+++||
T Consensus 77 ~l~~~l~~~l~~~~~~~~~~~~~i~v~v~vl~~dG~~~~--~a~~~A~~~AL~~~~iP 132 (132)
T PF01138_consen 77 ELSSLLERALRSSILLEGYPRWQIHVDVQVLSDDGGNLL--DAAINAACLALLDAGIP 132 (132)
T ss_dssp HHHHHHHHHHHHTBSTTTTSSEEEEEEEEEEECSSSSHH--HHHHHHHHHHHHHHTCS
T ss_pred HHHHHHhhhccccccccccCceEEEEEEEEEecCCCCHH--HHHHHHHHHHHHhcCCC
Confidence 999999999999544 555799999999999999 655 89999999999999998
No 40
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.75 E-value=8.2e-19 Score=158.47 Aligned_cols=74 Identities=41% Similarity=0.644 Sum_probs=71.6
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcEEEEEeC
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRIKLSMIY 755 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki~LS~k~ 755 (755)
.+++|++++|+|++|++|||||+|++|..|||||||+.+.++.++.+++++||+|+|||+++|++|+|+||+|.
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKisLSIr~ 75 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKISLSIRK 75 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCCcceehHH
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999873
No 41
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.73 E-value=2.9e-18 Score=192.85 Aligned_cols=164 Identities=26% Similarity=0.427 Sum_probs=119.6
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHhhccccccccccCCCceeEEeeCCcccceeeccccceeeeeccccceEEeec-Ccee
Q psy3754 580 YDIIQIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN-DEGI 658 (755)
Q Consensus 580 ~~~l~~al~~A~~~~~~I~~~~~~~l~~~r~~~~~~~P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~-~~G~ 658 (755)
|+.|.++++........|....+..+....+++++|+|.+++-.-+.+....++ |+.+...+ +.++ .+++
T Consensus 96 w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi~gvr~FlP~S~v~~r~v~d~~~~~---Gk~~~~ki------ie~d~~~n~ 166 (541)
T COG0539 96 WEKLEEAFENGEIVEGKITGKVKGGLTVDIEGVRAFLPGSLVDVRPVRDLDPLI---GKELEFKI------LELDKKRNN 166 (541)
T ss_pred HHHHHHHHhcCCeEEEEEEEEecCcEEEEECCEEEeccHHHhcccccccccccC---CceEEEEE------EEEccccCc
Confidence 444444444443444444445555555566689999999983333323333445 44555543 5566 4566
Q ss_pred EEEEecChhhhH-HHHHHHHHhhhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEE
Q psy3754 659 ITIASFNSVSGQ-EAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVR 737 (755)
Q Consensus 659 v~i~~~~~~~~~-~a~~~i~~~~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~ 737 (755)
+.+|.. ..++ ...+....++..+++|++++|+|++|++|||||+| +|++||||+|+|+|.|+.+|+++|++||+|+
T Consensus 167 vv~SrR--~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdi-gGvdGLlHiseiS~~rv~~P~~vvkvGd~Vk 243 (541)
T COG0539 167 VVLSRR--AVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDI-GGVDGLLHISEISWKRVDHPSEVVKVGDEVK 243 (541)
T ss_pred EEEEhH--HHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEe-cCeeeEEehhhccccccCCHHHhcccCCEEE
Confidence 766544 3333 22334556788999999999999999999999997 4599999999999999999999999999999
Q ss_pred EEEEEEcC-CCcEEEEEeC
Q psy3754 738 VKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 738 VkV~~id~-~gki~LS~k~ 755 (755)
|+|+++|. ++||+||+|.
T Consensus 244 vkVi~~D~e~~RVsLSlK~ 262 (541)
T COG0539 244 VKVISLDEERGRVSLSLKQ 262 (541)
T ss_pred EEEEEEccCCCeEEEEehh
Confidence 99999998 9999999984
No 42
>PTZ00119 40S ribosomal protein S15; Provisional
Probab=99.72 E-value=3.6e-18 Score=173.04 Aligned_cols=85 Identities=27% Similarity=0.259 Sum_probs=69.9
Q ss_pred CCChhHHHHHHHHhcCCCCCCCCchhhHHHHHHHHHHHHHHHhhccCcccchhhhhhhhhcc--ccc----e----e-eE
Q psy3754 2 TIKNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKGNF--LFN----K----I-IK 70 (755)
Q Consensus 2 ~~~~~~k~~~~~~~~~~~~d~gs~evqia~lt~~I~~l~~h~~~~~kd~~~~~~l~~~v~~r--~~~----~----~-~~ 70 (755)
.+++++|++++++|+++++||||+|||||+||+||++|++||+.|+||+||+|||++||+|| +++ . . ..
T Consensus 104 Ei~K~rK~eIIkkfqr~~~DTGS~EVQIAiLTeRI~~LTeHLk~hkKD~~SrRGLlkLV~KRRKLLkYLKrkD~erY~~l 183 (302)
T PTZ00119 104 QIHKYKKLCIRRCLQRRPFDTGSAPVQIGCLTEKILNLRAHLILRCKDHPKKRTMSILLARRQKLMKYLYKTDFELYKHT 183 (302)
T ss_pred HHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhCCCccHhHHHHHHHHHHHHHHHHHHHhcCHHHHHHH
Confidence 45678999999999999999999999999999999999999999999999999999999999 111 1 0 01
Q ss_pred eeeeCCeeEEEEeCcc
Q psy3754 71 SFKYGSYKISIEIGEI 86 (755)
Q Consensus 71 ~~~~~~r~i~~e~G~l 86 (755)
.-.+|=|.+.+.+--.
T Consensus 184 IkkLGLRkv~f~~~~~ 199 (302)
T PTZ00119 184 CNLLKIKCILFAIPDS 199 (302)
T ss_pred HHHhCCceEEeecccc
Confidence 1235667777766543
No 43
>cd00353 Ribosomal_S15p_S13e Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome. S15 also plays an important autoregulatory role by binding and preventing its own mRNA from being translated. S15 has a predominantly alpha-helical fold that is highly structured except for the N-terminal alpha helix.
Probab=99.72 E-value=5.3e-18 Score=146.27 Aligned_cols=56 Identities=45% Similarity=0.668 Sum_probs=55.2
Q ss_pred HHHHHHHhcCCCCCCCCchhhHHHHHHHHHHHHHHHhhccCcccchhhhhhhhhcc
Q psy3754 8 KASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKGNF 63 (755)
Q Consensus 8 k~~~~~~~~~~~~d~gs~evqia~lt~~I~~l~~h~~~~~kd~~~~~~l~~~v~~r 63 (755)
+++++++|+++++||||+|||||+||+||++|++||+.||||+||+|||++|+++|
T Consensus 2 ~~~i~~~~~~~~~DtGs~evQia~LT~rI~~L~~Hl~~~~KD~~~krgL~~lv~kR 57 (80)
T cd00353 2 KQEILKEFGLAEGDTGSPEVQLALLTERIVNLTEHLEKNKKDKHSKRGLLLLVSKR 57 (80)
T ss_pred HHHHHHHhCCCCCCCCChHHHHHHHHHHHHHHHHHHHHccccchHHHhHHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999
No 44
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.70 E-value=3.1e-17 Score=184.61 Aligned_cols=123 Identities=31% Similarity=0.531 Sum_probs=109.4
Q ss_pred cceeeccccceeeeeccccceEEeec-CceeEEEEecChhhhHHHHHH--------------------------------
Q psy3754 629 IRDVIGKGGSTIRTLTEETGTQIDIN-DEGIITIASFNSVSGQEAKRR-------------------------------- 675 (755)
Q Consensus 629 i~~~IG~gGk~ik~i~~~~g~~I~i~-~~G~v~i~~~~~~~~~~a~~~-------------------------------- 675 (755)
.++++ .| +++.|. .||+++|++ -||.+|++..+|...+...+.
T Consensus 192 ~G~vV--~G-~V~~It-~~GafVdigGvdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dP 267 (541)
T COG0539 192 VGEVV--EG-VVKNIT-DYGAFVDIGGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDP 267 (541)
T ss_pred CCceE--EE-EEEEee-cCcEEEEecCeeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCc
Confidence 44444 34 678886 699999997 799999999999998777664
Q ss_pred HHHhhhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 676 IEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 676 i~~~~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
|..+...+++|+.+.|+|+++++|||||++.+|++||+|+||++|.+...|.+++++||+|.|+|++||+ ++||+||+|
T Consensus 268 w~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iK 347 (541)
T COG0539 268 WEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLK 347 (541)
T ss_pred HHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeeh
Confidence 3455577899999999999999999999999999999999999999999999999999999999999999 899999998
Q ss_pred C
Q psy3754 755 Y 755 (755)
Q Consensus 755 ~ 755 (755)
+
T Consensus 348 q 348 (541)
T COG0539 348 Q 348 (541)
T ss_pred h
Confidence 5
No 45
>CHL00027 rps15 ribosomal protein S15
Probab=99.70 E-value=5.5e-18 Score=146.86 Aligned_cols=53 Identities=38% Similarity=0.471 Sum_probs=49.1
Q ss_pred HHHHhcC--CCCCCCCchhhHHHHHHHHHHHHHHHhhccCcccchhhhhhhhhcc
Q psy3754 11 IILDNSR--TKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKGNF 63 (755)
Q Consensus 11 ~~~~~~~--~~~d~gs~evqia~lt~~I~~l~~h~~~~~kd~~~~~~l~~~v~~r 63 (755)
.|..+.. +++||||+|||||+||+||++|++||+.||||+||+|||++||++|
T Consensus 6 ~i~~~~~~~~~~DTGS~evQiA~LT~rI~~Lt~Hlk~hkKD~~s~RgL~~lv~kR 60 (90)
T CHL00027 6 FISVISQEEKEENRGSVEFQVFSFTNKIRRLTSHLELHKKDYSSQRGLRKILGKR 60 (90)
T ss_pred ceeeeecccCCCCCCChHHHHHHHHHHHHHHHHHHHHCCCcchhHHHHHHHHHHH
Confidence 3455555 8999999999999999999999999999999999999999999999
No 46
>PF00312 Ribosomal_S15: Ribosomal protein S15; InterPro: IPR000589 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 [, ]. Ribosomal protein S15 is one of the proteins from the small ribosomal subunit. In Escherichia coli, this protein binds to 16S ribosomal RNA and functions at early steps in ribosome assembly. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ,], groups bacterial and plant chloroplast S15; archaeal Haloarcula marismortui HmaS15 (HS11); yeast mitochondrial S28; and mammalian, yeast, Brugia pahangi and Wuchereria bancrofti S13. S15 is a protein of 80 to 250 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YSH_E 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 1S1H_O 3MR8_O 3D5C_O 3MS0_O ....
Probab=99.66 E-value=7.9e-17 Score=140.03 Aligned_cols=57 Identities=47% Similarity=0.649 Sum_probs=55.9
Q ss_pred HHHHHHHHhcCCCCCCCCchhhHHHHHHHHHHHHHHHhhccCcccchhhhhhhhhcc
Q psy3754 7 IKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKGNF 63 (755)
Q Consensus 7 ~k~~~~~~~~~~~~d~gs~evqia~lt~~I~~l~~h~~~~~kd~~~~~~l~~~v~~r 63 (755)
.|++++.+|+++++||||+|||||+||.||++|++||+.||||++|+|+|..+|++|
T Consensus 2 ~k~~~i~~~~~~~~dtgs~evqia~LT~rI~~L~~Hl~~~kkD~~skr~L~~lv~kR 58 (83)
T PF00312_consen 2 RKQKSIKKFQRHPNDTGSPEVQIAILTERIRNLQEHLKKNKKDKHSKRGLLKLVSKR 58 (83)
T ss_dssp HHHHHHHHHSSSTTSSSSHHHHHHHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHhccccccceehhHHHHHH
Confidence 488999999999999999999999999999999999999999999999999999999
No 47
>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=99.58 E-value=4.7e-15 Score=125.88 Aligned_cols=71 Identities=27% Similarity=0.398 Sum_probs=67.4
Q ss_pred ccCCcEEEEEEEEEEe-eeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcEEEEEe
Q psy3754 683 VQIGKVYTGIVLRLFD-FGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRIKLSMI 754 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~-fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki~LS~k 754 (755)
+++|++|.|+|++|.+ ||+||+|.++.+|++|+|+++|++..++.++|++||.|+|+|+++|. +++.||++
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~-~~i~LSl~ 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD-GKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC-CEEEEEeC
Confidence 4689999999999986 99999999999999999999999999999999999999999999985 99999986
No 48
>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=99.56 E-value=1.6e-14 Score=122.93 Aligned_cols=71 Identities=32% Similarity=0.551 Sum_probs=65.7
Q ss_pred ccCCcEEEEEEEEEEeeeEEEEEcC-CeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcEEEEE
Q psy3754 683 VQIGKVYTGIVLRLFDFGAIIRILS-GKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRIKLSM 753 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~fG~FVel~~-g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki~LS~ 753 (755)
+++|++|+|+|++|.+||+||+|.+ +.+||+|+|+++|.++.++.+.|++||+|+|+|+++|..+++.||+
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~ki~ls~ 72 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSL 72 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCCcEEEEe
Confidence 4689999999999999999999944 2799999999999999999999999999999999999866999997
No 49
>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=99.55 E-value=1e-14 Score=124.43 Aligned_cols=70 Identities=21% Similarity=0.354 Sum_probs=65.5
Q ss_pred ccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCc---ccccCCCCEEEEEEEEEcC-CCcEEEE
Q psy3754 683 VQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNII---TDFLKENQKVRVKVLGIDD-RGRIKLS 752 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~---~~~~kvGd~V~VkV~~id~-~gki~LS 752 (755)
+++|+++.|+|+++++||+||+|.++++|++|+++++|.++.++ .+.|++||.|+++|+++|+ +++|.||
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 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 47899999999999999999999999999999999999997775 5899999999999999998 8899886
No 50
>PRK08582 hypothetical protein; Provisional
Probab=99.52 E-value=4.4e-14 Score=134.95 Aligned_cols=74 Identities=39% Similarity=0.662 Sum_probs=70.7
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcEEEEEeC
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRIKLSMIY 755 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki~LS~k~ 755 (755)
.+++|++|.|+|++|++||+||+|.++.+||||+|+++|+++.++.+.|++||.|+|+|+++|.+|+|.||++.
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk~ 75 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKK 75 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcEEEEEEe
Confidence 47899999999999999999999999999999999999999999999999999999999999988999999973
No 51
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.49 E-value=7.4e-14 Score=121.80 Aligned_cols=74 Identities=30% Similarity=0.380 Sum_probs=70.8
Q ss_pred hhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEE
Q psy3754 680 TESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSM 753 (755)
Q Consensus 680 ~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~ 753 (755)
+.++++|++|.|+|+++.+||+||+|.++.+||+|+++++++++.++.+.|++||.|+|+|+++|. +++|.||+
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 FSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred HHhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence 556899999999999999999999999999999999999999999999999999999999999998 89999986
No 52
>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=99.49 E-value=7e-14 Score=118.37 Aligned_cols=68 Identities=28% Similarity=0.463 Sum_probs=65.0
Q ss_pred CcEEE-EEEEEE-EeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEE
Q psy3754 686 GKVYT-GIVLRL-FDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSM 753 (755)
Q Consensus 686 G~~~~-G~V~~I-~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~ 753 (755)
|++|+ |+|+++ .+||+||+|.++++||+|+|++++++..++.+.|++||+++++|+++|+ +++|.||+
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 78999 999999 6999999999999999999999999999999999999999999999998 89999985
No 53
>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=99.49 E-value=8.7e-14 Score=117.07 Aligned_cols=69 Identities=26% Similarity=0.366 Sum_probs=66.6
Q ss_pred CcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
|++|.|+|+++.+||+||+|.++.+||+|+|++++++..++.+.|++||.++|+|+++|+ ++++.||+|
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k 70 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 789999999999999999999899999999999999999999999999999999999998 899999986
No 54
>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=99.48 E-value=1.5e-13 Score=117.46 Aligned_cols=73 Identities=29% Similarity=0.474 Sum_probs=68.5
Q ss_pred ccCCcEEEEEEEEEEeeeEEEEEc--CCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEeC
Q psy3754 683 VQIGKVYTGIVLRLFDFGAIIRIL--SGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~fG~FVel~--~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k~ 755 (755)
+++|++|.|+|+++.+||+||+|. ++.+||+|+|+++++++.++.+.|++||.|+|+|+++|. ++++.||+|.
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 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 468999999999999999999996 369999999999999999999999999999999999998 7999999974
No 55
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.47 E-value=8.5e-14 Score=148.47 Aligned_cols=73 Identities=25% Similarity=0.438 Sum_probs=69.5
Q ss_pred ccCCcEEEEEEEEEEeeeEEEEEc--CCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEeC
Q psy3754 683 VQIGKVYTGIVLRLFDFGAIIRIL--SGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~fG~FVel~--~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k~ 755 (755)
+++|+++.|+|++|.+||+||+|. +|++||||+|||+|+|+.++.+++++||+|.|+|+++|+ +|+|.||+|.
T Consensus 15 P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~ 90 (319)
T PTZ00248 15 PEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKR 90 (319)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeee
Confidence 348999999999999999999996 789999999999999999999999999999999999998 8999999984
No 56
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.46 E-value=3.1e-13 Score=153.36 Aligned_cols=133 Identities=25% Similarity=0.425 Sum_probs=100.6
Q ss_pred ccccCCCceeEEeeCCcccceeeccccceeeeeccccceEEeec-CceeEEEEecChhhhH-HHHHHHHHhhhcccCCcE
Q psy3754 611 ELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN-DEGIITIASFNSVSGQ-EAKRRIEKLTESVQIGKV 688 (755)
Q Consensus 611 ~~~~~~P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~-~~G~v~i~~~~~~~~~-~a~~~i~~~~~~~~~G~~ 688 (755)
+++.|+|.+++-.-....+.+++ |+.|+..+ ++++ +++++.+|... .++ .....+..++..+++|++
T Consensus 143 Gi~gflP~Sel~~~~~~~~~~~v---Gq~V~vkV------leid~~~~~ivLSrr~--~l~~~~~~~~~~~~~~lk~G~i 211 (486)
T PRK07899 143 GLRGFLPASLVEMRRVRDLQPYI---GQEIEAKI------IELDKNRNNVVLSRRA--WLEQTQSEVRSEFLNQLQKGQV 211 (486)
T ss_pred CCEEEEEhhHhcccccCChhhcC---CCEEEEEE------EEEECCCCEEEEEhHH--HHHhhhHHHHHHHHHhccCCCE
Confidence 57889888763221112223333 45555433 4565 45677776442 222 122345566788999999
Q ss_pred EEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEeC
Q psy3754 689 YTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 689 ~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k~ 755 (755)
+.|+|+++++||+||+| ++++||||+|+++|.++.+|.++|++||.|+|+|+++|+ +++|.||+|.
T Consensus 212 v~G~V~~i~~~G~FVdl-ggv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~ 278 (486)
T PRK07899 212 RKGVVSSIVNFGAFVDL-GGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKA 278 (486)
T ss_pred EEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEee
Confidence 99999999999999998 679999999999999999999999999999999999998 8999999984
No 57
>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=99.46 E-value=2.8e-13 Score=114.98 Aligned_cols=72 Identities=22% Similarity=0.306 Sum_probs=68.2
Q ss_pred ccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 683 VQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
+++|++|.|+|+++.+||+||+|.++.+|++|++++++++..++.+.|++||.|+++|+++|. ++++.||++
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~ 73 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 468999999999999999999999999999999999999888889999999999999999998 799999985
No 58
>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=99.45 E-value=2.6e-13 Score=115.36 Aligned_cols=73 Identities=34% Similarity=0.613 Sum_probs=69.6
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
++++|+++.|+|+++.++|+||+|.++.+|+||.+++++.+..++...|++||.|+|+|+++|. ++++.||+|
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 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 4789999999999999999999999899999999999999999999999999999999999999 889999986
No 59
>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=99.45 E-value=2.3e-13 Score=114.38 Aligned_cols=68 Identities=24% Similarity=0.418 Sum_probs=65.4
Q ss_pred CcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEE
Q psy3754 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSM 753 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~ 753 (755)
|++|+|+|++|.+||+||+|.++++||+|+++++|.++.++.+.|++||.++|+|+++|+ ++++.||+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls~ 69 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 789999999999999999999999999999999999999999999999999999999998 89999985
No 60
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.44 E-value=3.1e-13 Score=115.06 Aligned_cols=69 Identities=20% Similarity=0.245 Sum_probs=65.7
Q ss_pred CcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCccc--ccCcccccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKR--VNIITDFLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~--~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
|+++.|+|+++.++|+||+|.++++|++|+++++|.+ ..++.+.|++||.|+++|+++|+ +++|.||+|
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 7899999999999999999999999999999999874 88999999999999999999998 899999987
No 61
>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=99.44 E-value=2.3e-13 Score=114.04 Aligned_cols=67 Identities=27% Similarity=0.434 Sum_probs=64.7
Q ss_pred CcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEE
Q psy3754 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLS 752 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS 752 (755)
|++|.|+|+++.++|+||+|.++.+||+|+|++++++..++.+.|++||.|+|+|+++|+ +++|.||
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 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 789999999999999999999999999999999999999999999999999999999998 8999886
No 62
>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=99.44 E-value=2.9e-13 Score=113.38 Aligned_cols=67 Identities=42% Similarity=0.626 Sum_probs=62.9
Q ss_pred CcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCc-ccccCcccccCCCCEEEEEEEEEcC-CCcEEEE
Q psy3754 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISS-KRVNIITDFLKENQKVRVKVLGIDD-RGRIKLS 752 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~-~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS 752 (755)
|++|.|+|++|.+||+||+|.++.+||+|+++++| .+..++.+.|++||.|+|+|+++|. +++|.||
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence 78999999999999999999999999999999997 5788889999999999999999998 7999875
No 63
>PRK05807 hypothetical protein; Provisional
Probab=99.43 E-value=4.5e-13 Score=127.59 Aligned_cols=73 Identities=41% Similarity=0.752 Sum_probs=69.3
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcEEEEEeC
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRIKLSMIY 755 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki~LS~k~ 755 (755)
.+++|++|+|+|++|.+||+||+| ++.+||||+|++++.++.++.+.|++||.|+|+|+++|.+|+|.||+|.
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L-~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk~ 74 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQ 74 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEEe
Confidence 478999999999999999999999 7889999999999999999999999999999999999988999999973
No 64
>PRK07252 hypothetical protein; Provisional
Probab=99.42 E-value=6.4e-13 Score=123.72 Aligned_cols=72 Identities=31% Similarity=0.561 Sum_probs=69.0
Q ss_pred cCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEeC
Q psy3754 684 QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 684 ~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k~ 755 (755)
++|++|.|+|++|.+||+||+|.++.+||+|+|+++++++.++.+.|++||.|+|+|+++|. ++++.||++.
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~ 74 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRT 74 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEee
Confidence 57999999999999999999999999999999999999999999999999999999999998 8999999974
No 65
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.41 E-value=8.7e-13 Score=143.00 Aligned_cols=126 Identities=25% Similarity=0.439 Sum_probs=96.7
Q ss_pred cccccCCCceeEEeeCCcccceeeccccceeeeeccccceEEeecC-ceeEEEEecChhhhHHHHHHHHHhhhcccCCcE
Q psy3754 610 NELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND-EGIITIASFNSVSGQEAKRRIEKLTESVQIGKV 688 (755)
Q Consensus 610 ~~~~~~~P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~-~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~ 688 (755)
.++..|+|.++. +.....+. .-|+.++.. .++++. .+++.+|.. ... .+..+.++++|++
T Consensus 139 ~Gv~gfip~s~l---s~~~~~~~--~vG~~i~~k------Vl~id~~~~~i~lS~K--~~~------~~~~~~~~k~G~v 199 (318)
T PRK07400 139 EGLRGFIPGSHI---STRKPKEE--LVGEELPLK------FLEVDEERNRLVLSHR--RAL------VERKMNRLEVGEV 199 (318)
T ss_pred CCEEEEEEHHHc---CccCCccc--cCCCEEEEE------EEEEEcccCEEEEEhh--Hhh------hhhhhccCCCCCE
Confidence 478889998873 22112221 134455433 366774 466666543 221 1224677999999
Q ss_pred EEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEeC
Q psy3754 689 YTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 689 ~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k~ 755 (755)
|.|+|++|++||+||++ +|.+||+|+|+++|+++.++.+.|++||.|+|+|+++|. +++|.||+|.
T Consensus 200 v~G~V~~I~~~G~fV~i-~gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~ 266 (318)
T PRK07400 200 VVGTVRGIKPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQ 266 (318)
T ss_pred EEEEEEEEECCeEEEEE-CCEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEec
Confidence 99999999999999998 689999999999999999999999999999999999998 8999999984
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=99.41 E-value=9.3e-13 Score=113.70 Aligned_cols=69 Identities=43% Similarity=0.700 Sum_probs=65.0
Q ss_pred CcEEEEEEEEEEeeeEEEEEc---CCeeEEEeccccCcccc-cCcccccCCCCEEEEEEEEEcCCCcEEEEEeC
Q psy3754 686 GKVYTGIVLRLFDFGAIIRIL---SGKDGLLHISQISSKRV-NIITDFLKENQKVRVKVLGIDDRGRIKLSMIY 755 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~FVel~---~g~~Gllhisel~~~~~-~~~~~~~kvGd~V~VkV~~id~~gki~LS~k~ 755 (755)
|++|.|+|+++.+||+||+|. ++.+||+|+|+++|+++ .++.+.|++||+|+|+|+++| ++++.||+|.
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd-~~~i~~s~k~ 73 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ-NGKISLSMKD 73 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe-CCEEEEEEEe
Confidence 789999999999999999997 46999999999999986 899999999999999999999 9999999974
No 67
>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=99.41 E-value=1e-12 Score=109.34 Aligned_cols=69 Identities=55% Similarity=0.799 Sum_probs=66.2
Q ss_pred CcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcEEEEEe
Q psy3754 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRIKLSMI 754 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki~LS~k 754 (755)
|++|.|+|+++.+||+||++.++.+||+|+++++++++.++.+.|++||.|+|+|+++|.++++.||+|
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 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence 789999999999999999999899999999999999999999999999999999999998889999986
No 68
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=99.41 E-value=5.4e-13 Score=160.14 Aligned_cols=133 Identities=25% Similarity=0.331 Sum_probs=101.8
Q ss_pred ccccCCCceeEEeeCCcccceeeccccceeeeeccccceEEeec-CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEE
Q psy3754 611 ELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN-DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVY 689 (755)
Q Consensus 611 ~~~~~~P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~-~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~ 689 (755)
++..|+|.++.-.-...+..++. +-|..++..+ |+++ +++++.+|...-. .+.|..+...+++|+++
T Consensus 515 Gv~Gfvp~SeiS~~~v~~~~~~~-kvGq~v~vkV------i~iD~e~~rI~LSlK~l~-----~~p~~~~~~~~~vG~iV 582 (863)
T PRK12269 515 GFDGLLHVNDMSWGHVARPREFV-KKGQTIELKV------IRLDQAEKRINLSLKHFQ-----PDPWLEFENKFGVNDVV 582 (863)
T ss_pred CEEEEEEchhccccccCCHHHhc-cCCCEEEEEE------EEEecCCCeEEEEEeccc-----cchhhhhhccCCCCCEE
Confidence 45667776652111122233444 4455665543 6676 4788887765421 24466667789999999
Q ss_pred EEEEEEEEeeeEEEEEcCCeeEEEeccccCc-ccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEeC
Q psy3754 690 TGIVLRLFDFGAIIRILSGKDGLLHISQISS-KRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 690 ~G~V~~I~~fG~FVel~~g~~Gllhisel~~-~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k~ 755 (755)
+|+|++|.+||+||+|.+|++||+|+||++| .++.+|.+.|++||+|+|+|+++|+ +++|.||+|.
T Consensus 583 ~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~ 650 (863)
T PRK12269 583 KGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQ 650 (863)
T ss_pred EEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehh
Confidence 9999999999999999999999999999999 6789999999999999999999998 8999999984
No 69
>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=99.40 E-value=9.4e-13 Score=111.45 Aligned_cols=70 Identities=30% Similarity=0.476 Sum_probs=63.8
Q ss_pred ccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcc-cccCcccccCCCCEEEEEEEEEcC-CCcEEEE
Q psy3754 683 VQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSK-RVNIITDFLKENQKVRVKVLGIDD-RGRIKLS 752 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~-~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS 752 (755)
+.+|++|.|+|++|.+||+||+|.++.+||+|+++++|. +..++.+.|++||.|+|+|.++|. ++++.|+
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence 468999999999999999999999999999999999875 555778899999999999999998 7888874
No 70
>PHA02945 interferon resistance protein; Provisional
Probab=99.40 E-value=9.5e-13 Score=112.79 Aligned_cols=71 Identities=23% Similarity=0.329 Sum_probs=66.2
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEE--cCCeeEEEecccc--CcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEeC
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRI--LSGKDGLLHISQI--SSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel--~~g~~Gllhisel--~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k~ 755 (755)
-|++|+++.|+|+. .+||+||.| ++|.+||+|+|++ +..|+++ ++++ .||+|.+||+++|+ +|.|.||+|.
T Consensus 8 ~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSlK~ 83 (88)
T PHA02945 8 LPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNYKR 83 (88)
T ss_pred CCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEeeE
Confidence 36899999999999 999999999 4689999999955 9999999 9999 99999999999999 8999999984
No 71
>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=99.40 E-value=1.3e-12 Score=111.76 Aligned_cols=72 Identities=38% Similarity=0.553 Sum_probs=67.8
Q ss_pred cCCcEEEEEEEEEEeeeEEEEEcC-CeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEeC
Q psy3754 684 QIGKVYTGIVLRLFDFGAIIRILS-GKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 684 ~~G~~~~G~V~~I~~fG~FVel~~-g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k~ 755 (755)
++|++|.|+|+++.+||+||+|.+ +.+||+|++++++++..++.+.|++||.|+|+|+++|. ++++.||+|.
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~ 74 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKA 74 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEe
Confidence 469999999999999999999985 79999999999999998999999999999999999998 8999999984
No 72
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.40 E-value=1e-12 Score=149.14 Aligned_cols=81 Identities=33% Similarity=0.581 Sum_probs=74.9
Q ss_pred HHHHhhhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEE
Q psy3754 675 RIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSM 753 (755)
Q Consensus 675 ~i~~~~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~ 753 (755)
.|+.+...+++|++|.|+|++|.+||+||+|.+|++||+|+|+++++++.++.+.|++||+|+|+|+++|. ++||.||+
T Consensus 283 Pw~~~~~~~~vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSl 362 (486)
T PRK07899 283 PWQQFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSL 362 (486)
T ss_pred chhhhHHhcCCCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCCEEEEEE
Confidence 34555667889999999999999999999999999999999999999999999999999999999999998 89999999
Q ss_pred eC
Q psy3754 754 IY 755 (755)
Q Consensus 754 k~ 755 (755)
|.
T Consensus 363 K~ 364 (486)
T PRK07899 363 KQ 364 (486)
T ss_pred EE
Confidence 83
No 73
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=99.39 E-value=3.3e-13 Score=154.74 Aligned_cols=136 Identities=29% Similarity=0.405 Sum_probs=101.6
Q ss_pred cccccCCCceeEEeeCCcccceeeccccceeeeeccccceEEeec-CceeEEEEecChhhhHHHHHHHHHhhhcccCCcE
Q psy3754 610 NELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN-DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKV 688 (755)
Q Consensus 610 ~~~~~~~P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~-~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~ 688 (755)
.++..|+|.++.-.-+......++ |+.++..+ +.++ +++.+.+|... .......+.+..++..+++|++
T Consensus 136 ~g~~~flP~s~~~~~~~~~~~~~v---G~~i~~~V------~~id~~~~~v~lSrk~-~~~~~~~~~~~~~~~~l~~G~i 205 (491)
T PRK13806 136 LGRRAFCPVSQIDLRYVEDPESYV---GQTFQFLI------TRVEENGRNIVVSRRA-LLEREQKEALEAFMETVKEGDV 205 (491)
T ss_pred CCEEEEEEHHHhccccCCChHHcC---CCeEEEEE------EEEECCCCeEEEEeeh-hhhhhhHHHHHHHHhhCCCCCE
Confidence 468889998873221222223343 44555543 4565 45677765432 1112233455666778999999
Q ss_pred EEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-C----CcEEEEEeC
Q psy3754 689 YTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-R----GRIKLSMIY 755 (755)
Q Consensus 689 ~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~----gki~LS~k~ 755 (755)
|+|+|+++.+||+||+|.++++||||+|+++|.++.+|.+.|++||.|+|+|+++|. + ++|.||+|.
T Consensus 206 v~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~ 277 (491)
T PRK13806 206 VEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQ 277 (491)
T ss_pred EEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehh
Confidence 999999999999999998899999999999999999999999999999999999997 4 379999873
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=99.37 E-value=1.8e-12 Score=109.64 Aligned_cols=70 Identities=29% Similarity=0.442 Sum_probs=66.9
Q ss_pred CcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEeC
Q psy3754 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k~ 755 (755)
|++|.|+|+++.++|+||+|.++++|++|+++++++++.++.+.|++||.++++|+++|. ++++.||+|.
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~ 71 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKA 71 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEE
Confidence 789999999999999999999999999999999999999999999999999999999998 6899999873
No 75
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=99.36 E-value=1.9e-12 Score=148.49 Aligned_cols=80 Identities=28% Similarity=0.336 Sum_probs=74.8
Q ss_pred HHHHhhhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEE
Q psy3754 675 RIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSM 753 (755)
Q Consensus 675 ~i~~~~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~ 753 (755)
.|..+...+++|++++|+|+++++||+||++.+|++||||+|+++|.+..++.+.|++||+|+|+|+++|+ ++||+||+
T Consensus 369 p~~~~~~~~~vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~~~~~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls~ 448 (491)
T PRK13806 369 PWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLAP 448 (491)
T ss_pred hhHHhhhhCCCCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCcccccchhhcCCCCCEEEEEEEEEeCCCCEEEEEe
Confidence 35556678899999999999999999999999999999999999999999999999999999999999998 88999998
Q ss_pred e
Q psy3754 754 I 754 (755)
Q Consensus 754 k 754 (755)
|
T Consensus 449 ~ 449 (491)
T PRK13806 449 A 449 (491)
T ss_pred e
Confidence 7
No 76
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.36 E-value=8e-13 Score=154.78 Aligned_cols=133 Identities=31% Similarity=0.479 Sum_probs=101.1
Q ss_pred cccccCCCceeEEeeCCcccceeeccccceeeeeccccceEEeec-CceeEEEEecChhhhHH-HHHHHHHhhhcccCCc
Q psy3754 610 NELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN-DEGIITIASFNSVSGQE-AKRRIEKLTESVQIGK 687 (755)
Q Consensus 610 ~~~~~~~P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~-~~G~v~i~~~~~~~~~~-a~~~i~~~~~~~~~G~ 687 (755)
.++..|+|.++ ++...++++--.-|+.++..+ +.++ +.+++.+|... ..+. ..+.+..++..+++|+
T Consensus 135 ~g~~gfip~s~---~~~~~~~~~~~~vG~~i~~~V------~~~d~~~~~i~lS~k~--~~~~~~~~~~~~~~~~l~~G~ 203 (565)
T PRK06299 135 NGVEAFLPGSQ---VDVRPVRDTDPLEGKELEFKV------IKLDKKRNNIVVSRRA--VLEEERAEEREELLENLEEGQ 203 (565)
T ss_pred CCEEEEEEHHH---ccCcCCCChHHhCCCEEEEEE------EEEECCCCEEEEEhHH--hhhhhhhhHHHHHHhcCCCCC
Confidence 47888999886 333333322122455665543 5566 44566555432 2222 2234556678899999
Q ss_pred EEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 688 VYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 688 ~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
+++|+|+++.+||+||++. |.+||+|+|+++|.++.+|.+.|++||.|+|+|+++|+ ++++.||+|
T Consensus 204 iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k 270 (565)
T PRK06299 204 VVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLK 270 (565)
T ss_pred EEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEE
Confidence 9999999999999999986 99999999999999999999999999999999999998 899999997
No 77
>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=99.35 E-value=4.6e-12 Score=110.62 Aligned_cols=81 Identities=30% Similarity=0.476 Sum_probs=73.3
Q ss_pred hHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHhhccc--CCcCChhhHHHHHHHHHHHHHHHHHHccCCcCC
Q psy3754 304 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNE--NLTIDINDINCILYDLESKIIRKQILDKGLRID 381 (755)
Q Consensus 304 ~l~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~r~~~l~~~~R~D 381 (755)
+|.+.|.+++.++|.+|+.+++|++|++++++|++++.++|.+.. .++....+|..+|+.++++.+|.+||++|+|+|
T Consensus 1 el~~~v~~~~~~~l~~a~~~~~K~eR~~a~~~i~~~~~~~~~~~~~e~~~~~~~~i~~~~~~l~k~~vR~~Il~~~~R~D 80 (83)
T PF03726_consen 1 ELKEAVKELAGEKLKEALQIPDKQEREEALDAIKEEVIEELEEEYEEEDEEDEKEIKEAFEELEKKIVREMILEEGIRID 80 (83)
T ss_dssp HHHHHHHHHHHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHHHCCCHHSTTSHHHHHHHHHHHHHHHHHHHHHHCTSBTTT
T ss_pred CHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Confidence 588999999999999999999999999999999999999998542 235577899999999999999999999999999
Q ss_pred CCC
Q psy3754 382 NRG 384 (755)
Q Consensus 382 GR~ 384 (755)
||.
T Consensus 81 GR~ 83 (83)
T PF03726_consen 81 GRK 83 (83)
T ss_dssp S-B
T ss_pred CCC
Confidence 995
No 78
>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=99.35 E-value=3.2e-12 Score=107.59 Aligned_cols=69 Identities=28% Similarity=0.390 Sum_probs=66.2
Q ss_pred CcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
|++|.|+|.++.++|+||+|.++.+|++|.+++++.+..++.+.|++||.++++|+++|+ +++|.||+|
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 799999999999999999998889999999999999999999999999999999999997 789999986
No 79
>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=99.34 E-value=4.2e-12 Score=105.73 Aligned_cols=68 Identities=54% Similarity=0.937 Sum_probs=65.0
Q ss_pred CcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcEEEEE
Q psy3754 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRIKLSM 753 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki~LS~ 753 (755)
|++|.|+|+++.+||+||+|.++.+||+|+++++++++.++.+.|++||.|+|+|.++|+++++.||+
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 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECCCCcEEeeC
Confidence 78999999999999999999889999999999999999999999999999999999999888999985
No 80
>PRK08059 general stress protein 13; Validated
Probab=99.33 E-value=3.5e-12 Score=119.67 Aligned_cols=76 Identities=37% Similarity=0.597 Sum_probs=71.6
Q ss_pred hhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEeC
Q psy3754 680 TESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 680 ~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k~ 755 (755)
+.++++|++|.|+|+++.+||+||+|.++.+||+|+|+++++++.++.+.|++||.|+|+|+++|. ++++.||++.
T Consensus 2 ~~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~ 78 (123)
T PRK08059 2 MSQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRA 78 (123)
T ss_pred cccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEE
Confidence 356899999999999999999999999999999999999999999999999999999999999997 8999999873
No 81
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.33 E-value=1e-12 Score=133.79 Aligned_cols=74 Identities=41% Similarity=0.673 Sum_probs=70.7
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEE--cCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEeC
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRI--LSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel--~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k~ 755 (755)
-|++|+++-|+|++|.+||+||.| ++|.+||+|+||++..|++++.+++++||++-+||+++|+ +|.|+||+|.
T Consensus 8 ~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkr 84 (269)
T COG1093 8 YPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKR 84 (269)
T ss_pred CCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhh
Confidence 378999999999999999999999 5799999999999999999999999999999999999999 8999999973
No 82
>KOG1612|consensus
Probab=99.33 E-value=1.9e-10 Score=116.50 Aligned_cols=201 Identities=20% Similarity=0.230 Sum_probs=142.7
Q ss_pred eeEEEEeCccCcCCCcEEEEEECC-eEEEEEEEecCC----CCCCCCcceeeEEeEeeccccCCCCCCcccccCCCCchh
Q psy3754 77 YKISIEIGEIARQATSSVLVSIED-TVILATVVSCKD----PTSTYNFFPLTVDYIEKAYAAGRIPGSFFKREGKPSERE 151 (755)
Q Consensus 77 r~i~~e~G~la~~A~GSa~v~~G~-T~Vl~tv~~~~~----~~~~~~f~pl~v~y~e~~~a~g~ip~~~~kReg~p~~~e 151 (755)
|||.+|||++ .+++|||.|++|+ |-|+++|..... ..|..+..-+.||+.+.... .|.-|+| ++-.
T Consensus 32 Rpi~vetdVl-p~tNGSaRVk~g~~tdiivgVKaEvg~~~~~~p~egk~~~~VD~S~sasp------~f~gRgg--de~~ 102 (288)
T KOG1612|consen 32 RPIEVETDVL-PGTNGSARVKLGDGTDIIVGVKAEVGSPDDETPVEGKYLFFVDCSPSASP------QFQGRGG--DELV 102 (288)
T ss_pred ceEEEEeccc-cCCCCcEEEEecCCceEEEEEeeeccCccccCCCCCeEEEEEEecCCcCc------cccCCCh--hhHH
Confidence 7899999999 8999999999999 999999997443 23444555677888654321 2333432 2223
Q ss_pred hHHHHHhcCcccc----------cccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCC--------------
Q psy3754 152 TIISRLIDRPIRP----------LFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELP-------------- 207 (755)
Q Consensus 152 ~l~sRlIdr~lrp----------l~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP-------------- 207 (755)
.+++-.+.|.|.. .|.++|+|.+.|++.|++.||+.. .|--.|+.+||...-+|
T Consensus 103 ~eltsaLq~~l~~~~sgv~ls~L~lt~~~~W~i~VDvlVi~s~gn~~--dAiS~Ai~~AL~~T~lPkv~v~~dd~~~~~i 180 (288)
T KOG1612|consen 103 EELTSALQRVLNSLGSGVDLSKLQLTPGYCWKIYVDVLVISSDGNLL--DAISIAIYAALNNTRLPKVIVAFDDDGEVEI 180 (288)
T ss_pred HHHHHHHHHHHhCcCcccchhheeccCCeeEEEEEeEEEEecCCCHH--HHHHHHHHHHHhcccCCccccccccCCceee
Confidence 3344455555554 366679999999999999999733 33335666677666555
Q ss_pred ------C-------CCCeEEEEEEEECCEEEEcCCHHHHhcCcccEEEEeecCc-eEEEEc-CCCCCCHHHHHHHHHHHH
Q psy3754 208 ------F-------LGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEKA-IITVES-ESKQLPEDIILNAIIFGH 272 (755)
Q Consensus 208 ------~-------~~~vaav~vg~~~g~~vldPt~~E~~~s~~~l~va~~~~~-i~mie~-~~~~~se~~~~~al~~a~ 272 (755)
. ..+..-+++..++..+++|||.+|+..+...|.|+-+..+ +..+.. +.+.+..+-..++++.+.
T Consensus 181 ~~s~~~Yd~~~~~~~~~P~ivtlskIG~~~lVD~T~eEe~~a~s~l~Isv~a~givs~~r~VG~G~l~~s~i~~mle~~~ 260 (288)
T KOG1612|consen 181 LLSDEEYDLMVKLVENVPLIVTLSKIGTNMLVDPTAEEESVANSGLLISVSAGGIVSCTRSVGLGDLDPSSIPEMLEQGK 260 (288)
T ss_pred ccCcccchhhhhhcccCCEEEEEEeecceEEccCCccHHHhhhcceEEEEecCcceEEEEEecCCCCChhhHHHHHHHHH
Confidence 1 1122356778899999999999999999999999888777 334432 333388888899999999
Q ss_pred HHHHHHHHHHHHHHHH
Q psy3754 273 EKMKIAINAINELVQN 288 (755)
Q Consensus 273 ~~~~~i~~~~~~~~~~ 288 (755)
+-.+.+.....+.+++
T Consensus 261 ~~~e~l~~~l~k~L~~ 276 (288)
T KOG1612|consen 261 AVVETLAPDLVKSLEN 276 (288)
T ss_pred HHHHhhhHHHHHHhhh
Confidence 9888888777666543
No 83
>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=99.32 E-value=3.4e-12 Score=106.01 Aligned_cols=67 Identities=43% Similarity=0.691 Sum_probs=64.0
Q ss_pred CcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEE
Q psy3754 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLS 752 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS 752 (755)
|++|.|+|+++.+||+||++.++.+||+|.++++++++.++.+.|++||.|+|+|+++|. ++++.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 789999999999999999999899999999999999999999999999999999999998 8999886
No 84
>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=99.32 E-value=7.2e-12 Score=106.89 Aligned_cols=68 Identities=26% Similarity=0.244 Sum_probs=62.8
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEEc-CCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEeC
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRIL-SGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel~-~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k~ 755 (755)
++++|+++.|+|++|.+||+||++. ++++||+|.++++|+ +.+++||.+.++|+++|+ ++++.||+|.
T Consensus 1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~ 70 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADP 70 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEee
Confidence 4688999999999999999999995 689999999999986 679999999999999998 8899999974
No 85
>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=99.29 E-value=7.6e-12 Score=109.75 Aligned_cols=74 Identities=20% Similarity=0.223 Sum_probs=67.5
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCc----ccccCcccccCCCCEEEEEEEEEcCCCcEEEEEeC
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISS----KRVNIITDFLKENQKVRVKVLGIDDRGRIKLSMIY 755 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~----~~~~~~~~~~kvGd~V~VkV~~id~~gki~LS~k~ 755 (755)
.|++|++|.|+|+++.++|+||++.++.+|++|+|++++ .+..++.+.+++||.|+++|+++|+++++.||++.
T Consensus 3 ~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~~i~LS~~~ 80 (86)
T cd05789 3 IPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRS 80 (86)
T ss_pred cCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCCCCEEEEeCc
Confidence 368999999999999999999999989999999999996 45567788899999999999999888999999873
No 86
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=99.28 E-value=1.4e-11 Score=148.01 Aligned_cols=136 Identities=28% Similarity=0.389 Sum_probs=101.3
Q ss_pred ccccCCCceeEEeeCCcccceeeccccceeeeeccccceEEee---c-CceeEEEEecChhhhHHHHHHHHHhhhcccCC
Q psy3754 611 ELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI---N-DEGIITIASFNSVSGQEAKRRIEKLTESVQIG 686 (755)
Q Consensus 611 ~~~~~~P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i---~-~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G 686 (755)
+...|+|.++.-.-+.+....++| +.++..+. .++- + ++|++.+|...- ..+.+.+.++.++..+++|
T Consensus 423 ~~~gfiP~se~~~~~~~~~~~~vG---~~ie~~V~----~~~~~~~~~~~~~iVlSrr~~-l~e~~~~~~ee~~~~l~~G 494 (863)
T PRK12269 423 GMMAFLPISQSDCQKVDAPESLIG---LTSKFYIE----RISQSKQHRGNDNIVINRRRY-LEERARQAREEFFNSVHIE 494 (863)
T ss_pred CcEEEEEHHHhccccccchHHhCC---CeEEEEEE----EEecccccCCCCeEEEEHHHH-HHHHHHHHHHHHHhcCCCC
Confidence 467888888732111222333554 34443321 1211 1 346777764432 2244556667778889999
Q ss_pred cEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEeC
Q psy3754 687 KVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 687 ~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k~ 755 (755)
++|+|+|+++.+||+||++ +|++||||+|+++|.++.+|.+.|++||+|+|+|+++|+ ++++.||+|.
T Consensus 495 ~~V~G~Vk~i~~~G~fVdl-~Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~ 563 (863)
T PRK12269 495 DSVSGVVKSFTSFGAFIDL-GGFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKH 563 (863)
T ss_pred CEEEEEEEEEeCCcEEEEE-CCEEEEEEchhccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEEec
Confidence 9999999999999999998 789999999999999999999999999999999999998 8999999984
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=99.28 E-value=1.1e-11 Score=109.27 Aligned_cols=64 Identities=33% Similarity=0.482 Sum_probs=59.9
Q ss_pred cccCCcEEEEEEEEEEee--eEEEEEcCCeeEEEeccccCc---ccccCcccccCCCCEEEEEEEEEcC
Q psy3754 682 SVQIGKVYTGIVLRLFDF--GAIIRILSGKDGLLHISQISS---KRVNIITDFLKENQKVRVKVLGIDD 745 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~f--G~FVel~~g~~Gllhisel~~---~~~~~~~~~~kvGd~V~VkV~~id~ 745 (755)
.+++|++|.|+|++|.+| ||||+|.++.+||||+||++| .++.++.+.+++||.|.|+|++...
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~ 72 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPI 72 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecC
Confidence 578999999999999997 999999999999999999999 6788889999999999999999765
No 88
>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=99.26 E-value=7.4e-12 Score=145.13 Aligned_cols=133 Identities=34% Similarity=0.531 Sum_probs=99.2
Q ss_pred cccccCCCceeEEeeCCcccceeeccccceeeeeccccceEEeecC-ceeEEEEecChhhhHH-HHHHHHHhhhcccCCc
Q psy3754 610 NELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND-EGIITIASFNSVSGQE-AKRRIEKLTESVQIGK 687 (755)
Q Consensus 610 ~~~~~~~P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~-~G~v~i~~~~~~~~~~-a~~~i~~~~~~~~~G~ 687 (755)
.++..|+|.++. +.....+.--.-|+.++..+ +.++. .+.+.+|.. ..++. ....+...+..+++|+
T Consensus 121 ~g~~~flP~s~~---~~~~~~~~~~~vG~~i~~~v------~~~~~~~~~iv~Srk--~~l~~~~~~~~~~~~~~l~~G~ 189 (516)
T TIGR00717 121 NGVEAFLPGSQV---DVKPIKDLDSLIGKTLKFKI------IKLDQKRNNIVVSRR--AYLEEERSQAREELLENLKEGD 189 (516)
T ss_pred CCEEEEEeHHHh---cCcccCchhhhCCCEEEEEE------EEEECCCCcEEEEHH--HHHHHHHHHHHHHHHHhccCCC
Confidence 367889998873 22211111112355665543 44553 455666533 23322 2334556677899999
Q ss_pred EEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 688 VYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 688 ~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
+++|+|+++.++|+||++ ++.+||+|.++++|.++.++.+.|++||.|.|+|+++|+ ++++.||+|
T Consensus 190 ~v~g~V~~i~~~G~~V~l-~g~~g~lp~~e~s~~~~~~~~~~~~vG~~v~v~Vl~~d~~~~~i~lS~k 256 (516)
T TIGR00717 190 VVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLK 256 (516)
T ss_pred EEEEEEEEEECCeEEEEE-CCEEEEEEHHHcCCCCCCCHHHhccCCCEEEEEEEEEECCCCcEEEEEE
Confidence 999999999999999998 689999999999999999999999999999999999998 889999987
No 89
>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=99.24 E-value=2e-11 Score=101.83 Aligned_cols=65 Identities=26% Similarity=0.404 Sum_probs=59.6
Q ss_pred CcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEE
Q psy3754 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLS 752 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS 752 (755)
|++++|+|+++.++|+||+|.++++|++|.++++..+.. .+.|++||+|+++|+++|+ +++|.||
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~~~~--~~~~~~G~~i~~kVi~id~~~~~i~LS 66 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 789999999999999999998899999999999766544 7789999999999999998 7888886
No 90
>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=99.24 E-value=4.3e-11 Score=103.85 Aligned_cols=70 Identities=21% Similarity=0.517 Sum_probs=62.5
Q ss_pred CCcEEEEEEEEEEeeeEEEEEcC-CeeEEEeccccCccccc-----------CcccccCCCCEEEEEEEEEcC-CCcEEE
Q psy3754 685 IGKVYTGIVLRLFDFGAIIRILS-GKDGLLHISQISSKRVN-----------IITDFLKENQKVRVKVLGIDD-RGRIKL 751 (755)
Q Consensus 685 ~G~~~~G~V~~I~~fG~FVel~~-g~~Gllhisel~~~~~~-----------~~~~~~kvGd~V~VkV~~id~-~gki~L 751 (755)
+|++|+|+|++|++||+||+|.+ +.+|++|.++++++++. ++.+.|++||.|+|+|.++|. ++++.|
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~~ 80 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEEE
Confidence 48999999999999999999988 89999999999876532 456789999999999999998 899999
Q ss_pred EEe
Q psy3754 752 SMI 754 (755)
Q Consensus 752 S~k 754 (755)
+++
T Consensus 81 ~l~ 83 (83)
T cd04471 81 ELV 83 (83)
T ss_pred EEC
Confidence 863
No 91
>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=99.24 E-value=2.9e-11 Score=100.55 Aligned_cols=67 Identities=45% Similarity=0.643 Sum_probs=63.1
Q ss_pred CCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEE
Q psy3754 685 IGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLS 752 (755)
Q Consensus 685 ~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS 752 (755)
+|++|.|+|+++.++|+||++. +.+|++|.+++++.++.++.+.|++||.|+|+|+++|. ++++.||
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence 5899999999999999999985 79999999999999999999999999999999999998 8999886
No 92
>KOG1613|consensus
Probab=99.23 E-value=5.5e-11 Score=119.20 Aligned_cols=195 Identities=14% Similarity=0.116 Sum_probs=136.1
Q ss_pred eeEEEEeCccCcCCCcEEEEEECCeEEEEEEEecC-CC---CCCCCcceeeEEeEeeccccCCCCCCcccccCCCCchhh
Q psy3754 77 YKISIEIGEIARQATSSVLVSIEDTVILATVVSCK-DP---TSTYNFFPLTVDYIEKAYAAGRIPGSFFKREGKPSERET 152 (755)
Q Consensus 77 r~i~~e~G~la~~A~GSa~v~~G~T~Vl~tv~~~~-~~---~~~~~f~pl~v~y~e~~~a~g~ip~~~~kReg~p~~~e~ 152 (755)
|...++.|-+ ..||||++++.|+|.|+|++.+.. +| .+..+.---.++|-+--...+ |-|+|++.+.
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-STANGSALLKSGKTTVICGIKAEIAEPSTDAPDEGDIVPNYALPPLCSSRF--------RPGPPTDEAQ 117 (298)
T ss_pred hhhheecCce-eccCcHHHHhcCCcEEEEEeeeeecccccCCCCCcceeecccCCcccccCC--------CCCCCchHHH
Confidence 5677889999 899999999999999999999854 22 222222222222222211112 3499999998
Q ss_pred HHHHHhcCcccc----------cccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCCCCC---CCCe-------
Q psy3754 153 IISRLIDRPIRP----------LFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPF---LGPL------- 212 (755)
Q Consensus 153 l~sRlIdr~lrp----------l~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~IP~---~~~v------- 212 (755)
.+|.-+..+|.. ++++.+.|-...++.+|++||..- .+|.+|+.+||..-.+|- +.-.
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 888777554443 688999999999999999999865 788999999998777772 1100
Q ss_pred ----E---------------EE-------EEE-EECCEEE-EcCCHHHHhcCcccEEEEeecCc--eEEEEcCC-CCCCH
Q psy3754 213 ----G---------------VA-------KVG-YIDGKYI-LNPTTEQLKKSHLDLLVAGTEKA--IITVESES-KQLPE 261 (755)
Q Consensus 213 ----a---------------av-------~vg-~~~g~~v-ldPt~~E~~~s~~~l~va~~~~~--i~mie~~~-~~~se 261 (755)
+ ++ +-. ..|+.++ .|||.+|+..++..++|.....+ +.+...|| .-.+.
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 0 00 001 1244444 89999999999988888776665 55556555 34566
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q psy3754 262 DIILNAIIFGHEKMKIAINAI 282 (755)
Q Consensus 262 ~~~~~al~~a~~~~~~i~~~~ 282 (755)
+-+.+|+++|..-.+++-..+
T Consensus 276 ~~iK~c~elar~Rakelk~~~ 296 (298)
T KOG1613|consen 276 EMIKRCLELARVRAKELKTRF 296 (298)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 889999999998888775543
No 93
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.21 E-value=6.3e-11 Score=132.68 Aligned_cols=103 Identities=38% Similarity=0.567 Sum_probs=83.2
Q ss_pred Eeec-CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccc
Q psy3754 651 IDIN-DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDF 729 (755)
Q Consensus 651 I~i~-~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~ 729 (755)
++++ +++.+.+|...-.. +.....+..+...+++|+++.|+|+++.++|+||++ ++++||+|+|+++|.++.++.+.
T Consensus 158 l~~d~~~~~i~lS~k~~~~-~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l-~~v~g~v~~sels~~~~~~~~~~ 235 (390)
T PRK06676 158 IELDPEKNRVILSRRAVVE-EERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELSHERVEKPSEV 235 (390)
T ss_pred EEEECCCCEEEEEeHHHhh-hhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEe-CCeEEEEEHHHcCccccCCHHHh
Confidence 3555 45677776442111 111123445567789999999999999999999998 67999999999999999999999
Q ss_pred cCCCCEEEEEEEEEcC-CCcEEEEEeC
Q psy3754 730 LKENQKVRVKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 730 ~kvGd~V~VkV~~id~-~gki~LS~k~ 755 (755)
|++||.|+|+|+++|+ +++|.||+|.
T Consensus 236 ~~vGd~i~~~Vl~vd~~~~~i~lS~k~ 262 (390)
T PRK06676 236 VSVGQEVEVKVLSIDWETERISLSLKD 262 (390)
T ss_pred cCCCCEEEEEEEEEeCCCCEEEEEEee
Confidence 9999999999999998 8999999973
No 94
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.20 E-value=2.4e-11 Score=143.99 Aligned_cols=133 Identities=30% Similarity=0.458 Sum_probs=96.7
Q ss_pred ccccCCCceeEEeeCCcccceeeccccceeeeeccccceEEeecC-cee-EEEEecChhhhHHH-HHHHHHhhhcccCCc
Q psy3754 611 ELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND-EGI-ITIASFNSVSGQEA-KRRIEKLTESVQIGK 687 (755)
Q Consensus 611 ~~~~~~P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~-~G~-v~i~~~~~~~~~~a-~~~i~~~~~~~~~G~ 687 (755)
++..|+|..+. +.....++--.-|..++..+ +++++ ++. +.+|. +...+.. .+.....+..+++|+
T Consensus 411 gi~gfiP~sel---~~~~~~d~~~~vG~~v~v~V------l~vd~e~~~~l~lS~--k~~~~~~~~~~~~~~~~~l~~G~ 479 (647)
T PRK00087 411 GVRAFLPASHV---ELGYVEDLSEYKGQELEVKI------IEFNRKRRKKVVLSR--KAILEEEKEKKKEETWNSLEEGD 479 (647)
T ss_pred CEEEEEEHHHh---CccccCCHHHhCCCEEEEEE------EEEEcCCCcEEEEEe--HHHhhhhhhhHHHHHHHhCCCCC
Confidence 46777887652 21212211101344454332 46664 455 55553 3333221 234455667789999
Q ss_pred EEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEeC
Q psy3754 688 VYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 688 ~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k~ 755 (755)
+|.|+|+++.+||+||++ ++++||+|+|+++|.++.++.+.|++||.|+|+|+++|+ ++++.||+|.
T Consensus 480 iV~g~V~~v~~~G~fV~l-~gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~ 547 (647)
T PRK00087 480 VVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKK 547 (647)
T ss_pred EEEEEEEEEeCCcEEEEE-CCEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeec
Confidence 999999999999999999 899999999999999999999999999999999999998 8999999974
No 95
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.20 E-value=4e-11 Score=134.26 Aligned_cols=99 Identities=37% Similarity=0.609 Sum_probs=84.4
Q ss_pred Eeec-CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccc
Q psy3754 651 IDIN-DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDF 729 (755)
Q Consensus 651 I~i~-~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~ 729 (755)
++++ +++.+.++..... .+.+..+...+++|+++.|+|+++.+||+||++.++++||+|+|++++.++.++.+.
T Consensus 247 l~vd~~~~~i~lS~k~~~-----~~~~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~~~~~~~~~ 321 (390)
T PRK06676 247 LSIDWETERISLSLKDTL-----PGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEV 321 (390)
T ss_pred EEEeCCCCEEEEEEeecc-----cCccccchhhhcCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCccccCChhhc
Confidence 4565 4688877754322 123444566799999999999999999999999999999999999999999999999
Q ss_pred cCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 730 LKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 730 ~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
|++||.|+|+|+++|. ++++.||+|
T Consensus 322 ~~~Gd~v~v~V~~id~e~~~i~ls~k 347 (390)
T PRK06676 322 LEEGQEVKVKVLEVNEEEKRISLSIK 347 (390)
T ss_pred cCCCCEEEEEEEEEECCCCEEEEEEE
Confidence 9999999999999997 899999987
No 96
>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=99.20 E-value=5.8e-11 Score=99.14 Aligned_cols=66 Identities=27% Similarity=0.405 Sum_probs=61.3
Q ss_pred CcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
|++|+|+|+++.++|+||++ ++++||+|.|++++.+..++.+ .+||.++|+|+++|. +++|.||+|
T Consensus 1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~~~~~~~~~~~--~vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLRPVEDLDE--YVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCcccCChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 78999999999999999999 8999999999999988877766 389999999999998 899999986
No 97
>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=99.20 E-value=2.9e-11 Score=109.26 Aligned_cols=72 Identities=28% Similarity=0.426 Sum_probs=65.4
Q ss_pred ccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccc-------------------cCcccccCCCCEEEEEEEEE
Q psy3754 683 VQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRV-------------------NIITDFLKENQKVRVKVLGI 743 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~-------------------~~~~~~~kvGd~V~VkV~~i 743 (755)
+++|+++.|+|++|.++|+||+|+++.+|++|+++++|++. .++.+.|++||.|+++|+++
T Consensus 1 L~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~ 80 (100)
T cd05693 1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL 80 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence 47899999999999999999999999999999999998752 34778999999999999999
Q ss_pred cC----CCcEEEEEe
Q psy3754 744 DD----RGRIKLSMI 754 (755)
Q Consensus 744 d~----~gki~LS~k 754 (755)
|+ +++|.||+|
T Consensus 81 d~~~~~~~~i~LSlr 95 (100)
T cd05693 81 DKSKSGKKRIELSLE 95 (100)
T ss_pred cCCcCCCcEEEEEec
Confidence 97 479999987
No 98
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.18 E-value=5.6e-11 Score=125.08 Aligned_cols=73 Identities=40% Similarity=0.624 Sum_probs=69.4
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEEcC--CeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRILS--GKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel~~--g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
-|++|++|.|+|++|.+||+||+|.. +.+||+|+|+++++++.++.+.|++||.|.|+|+++|. +++|.||+|
T Consensus 5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK 80 (262)
T PRK03987 5 WPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80 (262)
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEE
Confidence 36899999999999999999999964 79999999999999999999999999999999999998 899999997
No 99
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=99.15 E-value=1.8e-10 Score=95.91 Aligned_cols=71 Identities=41% Similarity=0.681 Sum_probs=66.6
Q ss_pred cCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 684 QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 684 ~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
++|++|.|+|+++.++|+||++.++.+|++|.+++.+.+..++.+.|++||.|+|+|+++|. ++++.||++
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 46999999999999999999998899999999999998888888899999999999999998 699999975
No 100
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=99.14 E-value=2.3e-10 Score=98.38 Aligned_cols=66 Identities=27% Similarity=0.451 Sum_probs=60.1
Q ss_pred hhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcEEEEE
Q psy3754 680 TESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRIKLSM 753 (755)
Q Consensus 680 ~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki~LS~ 753 (755)
..++++|+.|.|+|+++++||+||++.++.+||+|+|++. +.+++||.++|+|.++..+|++.||+
T Consensus 11 ~~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i~e~~~i~l~~ 76 (77)
T cd04473 11 MEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDIPENGNIDLIP 76 (77)
T ss_pred hhhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEEEEECCCCcEEEEE
Confidence 4568999999999999999999999999999999999973 45999999999999994489999986
No 101
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.11 E-value=1.8e-10 Score=136.56 Aligned_cols=100 Identities=34% Similarity=0.544 Sum_probs=85.0
Q ss_pred Eeec-CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccc
Q psy3754 651 IDIN-DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDF 729 (755)
Q Consensus 651 I~i~-~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~ 729 (755)
++++ +++.+.++.... . .+.+..+...+++|++|.|+|+++.+||+||+|.++++||+|+|+++++++.++.+.
T Consensus 532 ~~id~~~~~I~lS~K~~--~---~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~~~~~~~~~ 606 (647)
T PRK00087 532 LDIDKENKKLSLSLKKL--L---PDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDV 606 (647)
T ss_pred EEEECCCCEEEEEeecc--c---cChhhhhhhhccCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCccccCCHhhc
Confidence 4555 467777765432 1 123455566789999999999999999999999999999999999999999999999
Q ss_pred cCCCCEEEEEEEEEcC-CCcEEEEEeC
Q psy3754 730 LKENQKVRVKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 730 ~kvGd~V~VkV~~id~-~gki~LS~k~ 755 (755)
|++||+|+|+|+++|. ++++.||+|.
T Consensus 607 ~kvGd~V~vkV~~id~e~~rI~lslk~ 633 (647)
T PRK00087 607 LSEGEEVKAKILEVDPEEKRIRLSIKE 633 (647)
T ss_pred CCCCCEEEEEEEEEeCCCCEEEEEEee
Confidence 9999999999999998 8999999974
No 102
>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=99.10 E-value=3.2e-10 Score=98.58 Aligned_cols=73 Identities=22% Similarity=0.204 Sum_probs=68.8
Q ss_pred ccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcEEEEEeC
Q psy3754 683 VQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRIKLSMIY 755 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki~LS~k~ 755 (755)
|++|+++.|+|+++.+.|++|++..+.+|++|+++++..+..++.+.|++||.+.++|+++|..+++.||++.
T Consensus 4 p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~~~i~LS~~~ 76 (82)
T cd04454 4 PDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDDMNVLLTTAD 76 (82)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCCCCEEEEECC
Confidence 6899999999999999999999988999999999999888888899999999999999999977899999863
No 103
>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=99.08 E-value=4.9e-10 Score=130.01 Aligned_cols=99 Identities=27% Similarity=0.448 Sum_probs=84.9
Q ss_pred Eeec-CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccc
Q psy3754 651 IDIN-DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDF 729 (755)
Q Consensus 651 I~i~-~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~ 729 (755)
+.++ +++.+.++..... .+.+..+...+++|++++|+|+++++||+||++.++++||+|.|+++++++.++.+.
T Consensus 416 l~vd~~~~~i~ls~K~~~-----~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~~~Glv~~s~l~~~~~~~~~~~ 490 (516)
T TIGR00717 416 LAVDKEKKRISLGVKQLT-----ENPWEKFAAKYKVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDE 490 (516)
T ss_pred EEEeCcCCEEEEeecccc-----CCchhhhhhccCcceEEEEEEEEEecceEEEEcCCCeEEEEEHHHcCcccccccccc
Confidence 5566 5678877765321 123444556789999999999999999999999999999999999999999999999
Q ss_pred cCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 730 LKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 730 ~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
|++||.|+++|+++|. ++++.||+|
T Consensus 491 ~~~Gd~v~~~V~~id~~~~~i~ls~k 516 (516)
T TIGR00717 491 IKVGDEVEAKVVDIDKKNRKVSLSVK 516 (516)
T ss_pred CCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 9999999999999998 899999987
No 104
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.08 E-value=3.1e-10 Score=95.67 Aligned_cols=64 Identities=17% Similarity=0.206 Sum_probs=59.0
Q ss_pred CcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCccc--ccCcccccCCCCEEEEEEEEEcCCCcE
Q psy3754 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKR--VNIITDFLKENQKVRVKVLGIDDRGRI 749 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~--~~~~~~~~kvGd~V~VkV~~id~~gki 749 (755)
|+++.|+|+++.++|+||+|.++++|++|++++++++ ..++.+.|++||.|+++|+++|..+..
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~~ 66 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTH 66 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcccc
Confidence 7899999999999999999999999999999999885 888999999999999999999974433
No 105
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.07 E-value=3.6e-10 Score=132.55 Aligned_cols=99 Identities=23% Similarity=0.416 Sum_probs=83.6
Q ss_pred Eeec-CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcc-cccCccc
Q psy3754 651 IDIN-DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSK-RVNIITD 728 (755)
Q Consensus 651 I~i~-~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~-~~~~~~~ 728 (755)
+.++ ++|++.+|..... .+.|..+...+++|+++.|+|+++.+||+||+|.++++||+|+|+++|. +..+|.+
T Consensus 256 ~~~d~~~~~i~lS~k~~~-----~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~ 330 (565)
T PRK06299 256 LKFDKEKKRVSLGLKQLG-----EDPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSK 330 (565)
T ss_pred EEEeCCCCeEEEEEEecc-----cChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHHcCccccccCHHH
Confidence 4566 4688887765322 1245556677999999999999999999999999999999999999986 4678888
Q ss_pred ccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 729 FLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 729 ~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
.|++||.|+|+|+++|+ ++++.||+|
T Consensus 331 ~~~~G~~v~v~V~~id~~~~~i~ls~k 357 (565)
T PRK06299 331 VVSVGQEVEVMVLEIDEEKRRISLGLK 357 (565)
T ss_pred hcCCCCEEEEEEEEEcCCCCEEEEehH
Confidence 99999999999999998 899999986
No 106
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=99.03 E-value=3.3e-10 Score=131.26 Aligned_cols=75 Identities=40% Similarity=0.573 Sum_probs=72.0
Q ss_pred hcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEeC
Q psy3754 681 ESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 681 ~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k~ 755 (755)
.++++|.+..|+|+++.+||+||+|.-+.+||||+|+++++++.+|.+++++||.|+|+|+++|. +++|.|||+.
T Consensus 654 ~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~ 729 (780)
T COG2183 654 TDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRL 729 (780)
T ss_pred hhccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeec
Confidence 46899999999999999999999998899999999999999999999999999999999999998 8999999974
No 107
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=99.00 E-value=9.9e-10 Score=89.60 Aligned_cols=64 Identities=41% Similarity=0.659 Sum_probs=60.1
Q ss_pred EEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEE
Q psy3754 689 YTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLS 752 (755)
Q Consensus 689 ~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS 752 (755)
|.|+|+++.++|+||++.++.+|++|.+++++.++.++.+.|++||.|+|+|+++|. ++++.||
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 579999999999999999899999999999999888888999999999999999998 8888876
No 108
>cd00677 S15_NS1_EPRS_RNA-bind S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism.
Probab=98.96 E-value=5e-10 Score=86.52 Aligned_cols=38 Identities=47% Similarity=0.672 Sum_probs=37.4
Q ss_pred hhhHHHHHHHHHHHHHHHhhccCcccchhhhhhhhhcc
Q psy3754 26 EVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKGNF 63 (755)
Q Consensus 26 evqia~lt~~I~~l~~h~~~~~kd~~~~~~l~~~v~~r 63 (755)
|||||.+|+||++|++|++.||||++++|+|..+|++|
T Consensus 1 ~vqia~lt~~i~~L~~hl~~~~kD~~~kr~L~~~v~kr 38 (46)
T cd00677 1 EVQIALLTERIRNLKEHLAKNKKDKHSKRGLDLLVSKR 38 (46)
T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCcchHHHHHHHHHHH
Confidence 69999999999999999999999999999999999998
No 109
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.91 E-value=1.1e-09 Score=110.39 Aligned_cols=74 Identities=30% Similarity=0.388 Sum_probs=68.0
Q ss_pred hhcccCCcEEEEEEEEEEeeeEEEEEc----------CCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcE
Q psy3754 680 TESVQIGKVYTGIVLRLFDFGAIIRIL----------SGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRI 749 (755)
Q Consensus 680 ~~~~~~G~~~~G~V~~I~~fG~FVel~----------~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki 749 (755)
...+++|++|.|+|++|.++|+||+|. ++.+|++|++++++.+..++.+.|++||.|+++|++++ +++
T Consensus 59 ~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~--~~i 136 (189)
T PRK09521 59 PPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT--DPL 136 (189)
T ss_pred CCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC--CcE
Confidence 456899999999999999999999984 36899999999999988889999999999999999998 899
Q ss_pred EEEEeC
Q psy3754 750 KLSMIY 755 (755)
Q Consensus 750 ~LS~k~ 755 (755)
.||+|+
T Consensus 137 ~LS~k~ 142 (189)
T PRK09521 137 QLSTKG 142 (189)
T ss_pred EEEEec
Confidence 999874
No 110
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.90 E-value=4.2e-09 Score=114.42 Aligned_cols=75 Identities=24% Similarity=0.347 Sum_probs=70.7
Q ss_pred hhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 680 TESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 680 ~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
...++.|+++.|+|+++.++|+||+|.++.+|++|.+|++|.++.++.+.|++||.|+|+|+++|. +|++.||+|
T Consensus 26 ~~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k 101 (318)
T PRK07400 26 DYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIR 101 (318)
T ss_pred HhhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehh
Confidence 345899999999999999999999997779999999999999999999999999999999999987 899999987
No 111
>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=98.90 E-value=6.1e-09 Score=87.27 Aligned_cols=65 Identities=28% Similarity=0.342 Sum_probs=52.6
Q ss_pred CCeEEEEEEEECCEEEEcCCHHHHhcCcccEEEEeecC--ceEEEEcCCCC-CCHHHHHHHHHHHHHH
Q psy3754 210 GPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEK--AIITVESESKQ-LPEDIILNAIIFGHEK 274 (755)
Q Consensus 210 ~~vaav~vg~~~g~~vldPt~~E~~~s~~~l~va~~~~--~i~mie~~~~~-~se~~~~~al~~a~~~ 274 (755)
++++||+++++||++|+|||.+|+..++.+|+++.+.. .+.|++.++.. +++++|.+|+++|+++
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 58999999999999999999999888766666665544 46777777655 9999999999999985
No 112
>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=1.4e-09 Score=89.27 Aligned_cols=60 Identities=52% Similarity=0.850 Sum_probs=57.2
Q ss_pred CceeEEeeCCcccceeeccccceeeeeccccceEEeecCceeEEEEecChhhhHHHHHHH
Q psy3754 617 PRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRI 676 (755)
Q Consensus 617 P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~G~v~i~~~~~~~~~~a~~~i 676 (755)
|+++++.||+++++.+||+||++||.|+++||++|+++++|.+.|+..+...++.|++++
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 PRIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDDGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred CeEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCCCCEEEEEeCCHHHHHHHHHHh
Confidence 889999999999999999999999999999999999999999999999899999998875
No 113
>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=98.87 E-value=7.9e-09 Score=93.23 Aligned_cols=68 Identities=37% Similarity=0.550 Sum_probs=59.6
Q ss_pred cEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccC-----------cccccCCCCEEEEEEEEEcC-C-----CcE
Q psy3754 687 KVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNI-----------ITDFLKENQKVRVKVLGIDD-R-----GRI 749 (755)
Q Consensus 687 ~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~-----------~~~~~kvGd~V~VkV~~id~-~-----gki 749 (755)
++|.|+|++|.++|+||+|. +.+||+|+++++++++.. +...|++||.|+|+|.++|. . +++
T Consensus 1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i 79 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI 79 (99)
T ss_pred CEEEEEEEEEEeccEEEEEc-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceE
Confidence 47999999999999999997 599999999999887653 35789999999999999996 2 589
Q ss_pred EEEEeC
Q psy3754 750 KLSMIY 755 (755)
Q Consensus 750 ~LS~k~ 755 (755)
.||+|.
T Consensus 80 ~ls~k~ 85 (99)
T cd04460 80 GLTMRQ 85 (99)
T ss_pred EEEEec
Confidence 999974
No 114
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.85 E-value=7.3e-09 Score=107.91 Aligned_cols=74 Identities=19% Similarity=0.217 Sum_probs=69.1
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccc----cCcccccCCCCEEEEEEEEEcCCCcEEEEEeC
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRV----NIITDFLKENQKVRVKVLGIDDRGRIKLSMIY 755 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~----~~~~~~~kvGd~V~VkV~~id~~gki~LS~k~ 755 (755)
.|++||++.|+|+++.++|+||+|.++.+|+||++++++.++ .++.+.|++||.|.+||+++++.+++.||+++
T Consensus 60 ~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~ 137 (235)
T PRK04163 60 IPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKG 137 (235)
T ss_pred cCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcC
Confidence 479999999999999999999999889999999999999987 78889999999999999999987789999874
No 115
>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=98.83 E-value=1.5e-08 Score=121.80 Aligned_cols=73 Identities=23% Similarity=0.483 Sum_probs=65.2
Q ss_pred hcccCCcEEEEEEEEEEeeeEEEEEcC-CeeEEEeccccCcccc-----------cCcccccCCCCEEEEEEEEEcC-CC
Q psy3754 681 ESVQIGKVYTGIVLRLFDFGAIIRILS-GKDGLLHISQISSKRV-----------NIITDFLKENQKVRVKVLGIDD-RG 747 (755)
Q Consensus 681 ~~~~~G~~~~G~V~~I~~fG~FVel~~-g~~Gllhisel~~~~~-----------~~~~~~~kvGd~V~VkV~~id~-~g 747 (755)
...++|++|+|+|++|++||+||+|.+ +.+||+|+|+++++++ ++..+.|++||+|+|+|.++|. ++
T Consensus 623 l~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~ 702 (709)
T TIGR02063 623 MSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTG 702 (709)
T ss_pred hhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccC
Confidence 455889999999999999999999987 7999999999987654 3456789999999999999998 89
Q ss_pred cEEEEE
Q psy3754 748 RIKLSM 753 (755)
Q Consensus 748 ki~LS~ 753 (755)
+|.|++
T Consensus 703 ~I~~~l 708 (709)
T TIGR02063 703 KIDFEL 708 (709)
T ss_pred eEEEEE
Confidence 999986
No 116
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.82 E-value=2.1e-09 Score=107.37 Aligned_cols=83 Identities=27% Similarity=0.443 Sum_probs=76.3
Q ss_pred ceeEEeeCCcccceeeccccceeeeeccccceEEeecCc-eeEEEE---ecChhhhHHHHHHHHHhhh--ccc-----CC
Q psy3754 618 RLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDE-GIITIA---SFNSVSGQEAKRRIEKLTE--SVQ-----IG 686 (755)
Q Consensus 618 ~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~-G~v~i~---~~~~~~~~~a~~~i~~~~~--~~~-----~G 686 (755)
.+.++.||+++++.+||+||++|+.|+++||++|+++++ |.|.|. ..+...+++|+++++.+.. +++ .|
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~e~A~~l~g 82 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSPEKALRLLD 82 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECCCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCHHHHHHHhC
Confidence 457889999999999999999999999999999999976 999999 8899999999999998887 566 79
Q ss_pred cEEEEEEEEEEeee
Q psy3754 687 KVYTGIVLRLFDFG 700 (755)
Q Consensus 687 ~~~~G~V~~I~~fG 700 (755)
+.|.|+|+++.+|+
T Consensus 83 d~y~~~Vi~i~~~~ 96 (180)
T PRK13763 83 DDYVLEVIDLSDYG 96 (180)
T ss_pred CCceEEEEEhhhcc
Confidence 99999999999983
No 117
>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=98.75 E-value=3.2e-09 Score=105.41 Aligned_cols=79 Identities=29% Similarity=0.519 Sum_probs=72.6
Q ss_pred EeeCCcccceeeccccceeeeeccccceEEeecCc-eeEEE--EecChhhhHHHHHHHHHhhh--ccc-----CCcEEEE
Q psy3754 622 IKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDE-GIITI--ASFNSVSGQEAKRRIEKLTE--SVQ-----IGKVYTG 691 (755)
Q Consensus 622 ~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~-G~v~i--~~~~~~~~~~a~~~i~~~~~--~~~-----~G~~~~G 691 (755)
+.||+++++.+||+||++||.|+++||+.|+++++ |.|.| ...+...+++|+++++.+.. .++ +|+.|.+
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~~ 81 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALKLLDDDYML 81 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHHHhcCCcceE
Confidence 57999999999999999999999999999999965 99999 78888999999999998887 566 7999999
Q ss_pred EEEEEEeee
Q psy3754 692 IVLRLFDFG 700 (755)
Q Consensus 692 ~V~~I~~fG 700 (755)
.|++|.+|+
T Consensus 82 ~Vi~I~~~~ 90 (172)
T TIGR03665 82 EVIDLKEYG 90 (172)
T ss_pred EEEEhhhcc
Confidence 999999983
No 118
>PRK11642 exoribonuclease R; Provisional
Probab=98.73 E-value=2.2e-08 Score=120.73 Aligned_cols=91 Identities=21% Similarity=0.369 Sum_probs=71.2
Q ss_pred cChhhhHHHHHHHHHhh---hcccCCcEEEEEEEEEEeeeEEEEEcCC-eeEEEeccccCccccc-----------Cccc
Q psy3754 664 FNSVSGQEAKRRIEKLT---ESVQIGKVYTGIVLRLFDFGAIIRILSG-KDGLLHISQISSKRVN-----------IITD 728 (755)
Q Consensus 664 ~~~~~~~~a~~~i~~~~---~~~~~G~~~~G~V~~I~~fG~FVel~~g-~~Gllhisel~~~~~~-----------~~~~ 728 (755)
..+.+.++.++....+. ..-++|++|+|+|++|++||+||+|.+. ++||||+++|.++|+. +...
T Consensus 619 ~er~A~~aeR~~~~~~~~~~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~ 698 (813)
T PRK11642 619 TERRADEATRDVADWLKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQ 698 (813)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCc
Confidence 33444444444433222 3347999999999999999999999765 9999999999987532 3457
Q ss_pred ccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 729 FLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 729 ~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
.|++||.|+|+|.++|. +++|.|++.
T Consensus 699 ~~~lGD~V~VkV~~vD~~~rkI~f~l~ 725 (813)
T PRK11642 699 TYRLGDRVEVRVEAVNMDERKIDFSLI 725 (813)
T ss_pred EECCCCEEEEEEEEeecCCCeEEEEEe
Confidence 89999999999999998 899999874
No 119
>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=98.65 E-value=8.5e-08 Score=95.98 Aligned_cols=76 Identities=28% Similarity=0.528 Sum_probs=64.9
Q ss_pred hhhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCccccc-----------CcccccCCCCEEEEEEEEEc---
Q psy3754 679 LTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVN-----------IITDFLKENQKVRVKVLGID--- 744 (755)
Q Consensus 679 ~~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~-----------~~~~~~kvGd~V~VkV~~id--- 744 (755)
+...+.+|++++|+|+++.++|+||++ +..+|++|.+++.+++.. +....+++||.|++||.++|
T Consensus 75 i~f~p~~gEvv~G~V~~v~~~GifV~l-g~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 153 (179)
T TIGR00448 75 LVFKPELGEIVEGEVIEIVEFGAFVSL-GPFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKD 153 (179)
T ss_pred EEEeccCCCEEEEEEEEEEeeEEEEEe-CCceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccC
Confidence 345688999999999999999999998 569999999999866532 34578999999999999998
Q ss_pred --C-CCcEEEEEeC
Q psy3754 745 --D-RGRIKLSMIY 755 (755)
Q Consensus 745 --~-~gki~LS~k~ 755 (755)
+ ..+|.||+|+
T Consensus 154 ~~~~~~~I~lt~k~ 167 (179)
T TIGR00448 154 RRPEGSKIGLTMRQ 167 (179)
T ss_pred CCCCcceEEEEecc
Confidence 3 5689999985
No 120
>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=98.64 E-value=1e-07 Score=79.72 Aligned_cols=63 Identities=21% Similarity=0.259 Sum_probs=55.1
Q ss_pred cCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC---CCcEEEEE
Q psy3754 684 QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD---RGRIKLSM 753 (755)
Q Consensus 684 ~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~---~gki~LS~ 753 (755)
..|++++|+|.++.++|+||++. +.+|+||.+|++ +.+.|++||.|+|.|.+++. .++|.||+
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig-~~eg~lp~~e~~------~~~~~~~Gd~v~v~v~~v~~~~~~~~i~lSr 67 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLG-KVEAILPKKEQI------PGESYRPGDRIKAYVLEVRKTSKGPQIILSR 67 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcC-CeEEEeeHHHCC------CCCcCCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence 47999999999999999999984 599999999996 34568999999999999985 35788885
No 121
>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=98.63 E-value=1.3e-07 Score=112.44 Aligned_cols=72 Identities=22% Similarity=0.412 Sum_probs=63.9
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEEc-CCeeEEEeccccCcccc-----------cCcccccCCCCEEEEEEEEEcC-CCc
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRIL-SGKDGLLHISQISSKRV-----------NIITDFLKENQKVRVKVLGIDD-RGR 748 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel~-~g~~Gllhisel~~~~~-----------~~~~~~~kvGd~V~VkV~~id~-~gk 748 (755)
.-++|++|+|+|++|++||+||+|. .+++||||++++.++++ ++....|++||+|+|+|.++|. +++
T Consensus 569 ~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~ 648 (654)
T TIGR00358 569 LDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRS 648 (654)
T ss_pred hhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCe
Confidence 3478999999999999999999997 67999999999998752 3345789999999999999998 899
Q ss_pred EEEEE
Q psy3754 749 IKLSM 753 (755)
Q Consensus 749 i~LS~ 753 (755)
|.|++
T Consensus 649 I~f~l 653 (654)
T TIGR00358 649 IIFEL 653 (654)
T ss_pred EEEEE
Confidence 99986
No 122
>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=98.62 E-value=1e-07 Score=84.87 Aligned_cols=74 Identities=19% Similarity=0.220 Sum_probs=66.0
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEE--------cCCeeEEEeccccCccccc--CcccccCCCCEEEEEEEEEcCCCcEEE
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRI--------LSGKDGLLHISQISSKRVN--IITDFLKENQKVRVKVLGIDDRGRIKL 751 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel--------~~g~~Gllhisel~~~~~~--~~~~~~kvGd~V~VkV~~id~~gki~L 751 (755)
.|++|+++.|+|+++....|+|+| .....|++|+|++...+.. ++.+.|++||.|++||++.+....+.|
T Consensus 3 ~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~~~L 82 (92)
T cd05791 3 LPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSYYL 82 (92)
T ss_pred CCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCCcEE
Confidence 368999999999999999999999 6679999999999877766 678999999999999999986677999
Q ss_pred EEeC
Q psy3754 752 SMIY 755 (755)
Q Consensus 752 S~k~ 755 (755)
|+++
T Consensus 83 st~~ 86 (92)
T cd05791 83 STAE 86 (92)
T ss_pred EecC
Confidence 9863
No 123
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.46 E-value=3.4e-07 Score=89.85 Aligned_cols=76 Identities=34% Similarity=0.524 Sum_probs=64.3
Q ss_pred hhhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccc----------cC-cccccCCCCEEEEEEEEEcC-C
Q psy3754 679 LTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRV----------NI-ITDFLKENQKVRVKVLGIDD-R 746 (755)
Q Consensus 679 ~~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~----------~~-~~~~~kvGd~V~VkV~~id~-~ 746 (755)
++..|..|++++|.|+++.+||+||.+ +..+||+|+|++.++++ .+ ...++++||.|++||++.+. .
T Consensus 75 l~fkP~~gEVV~GeVv~~~~~G~fV~i-gp~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~ 153 (183)
T COG1095 75 LVFKPFRGEVVEGEVVEVVEFGAFVRI-GPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKS 153 (183)
T ss_pred EEEEeccccEEEEEEEEEeecceEEEe-ccccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEeccc
Confidence 456789999999999999999999997 57899999999998843 22 44589999999999999875 2
Q ss_pred -----CcEEEEEeC
Q psy3754 747 -----GRIKLSMIY 755 (755)
Q Consensus 747 -----gki~LS~k~ 755 (755)
-+|.|+|++
T Consensus 154 ~~~~~~~I~lTmrq 167 (183)
T COG1095 154 RRPRESKIGLTMRQ 167 (183)
T ss_pred CccccceEEEEecc
Confidence 478888875
No 124
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.41 E-value=8.4e-07 Score=89.44 Aligned_cols=76 Identities=33% Similarity=0.478 Sum_probs=64.6
Q ss_pred hhhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCccccc-----------CcccccCCCCEEEEEEEEEcC-C
Q psy3754 679 LTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVN-----------IITDFLKENQKVRVKVLGIDD-R 746 (755)
Q Consensus 679 ~~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~-----------~~~~~~kvGd~V~VkV~~id~-~ 746 (755)
+...+.+|+++.|+|+++.++|+||++. ..+|++|.+++.+++.. +....+++||.|++||.+++. .
T Consensus 75 lvf~P~~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~ 153 (187)
T PRK08563 75 LVFKPELQEVVEGEVVEVVEFGAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKE 153 (187)
T ss_pred EEEeccCCCEEEEEEEEEEccEEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccc
Confidence 4556889999999999999999999985 59999999999877532 346789999999999999986 3
Q ss_pred -----CcEEEEEeC
Q psy3754 747 -----GRIKLSMIY 755 (755)
Q Consensus 747 -----gki~LS~k~ 755 (755)
.+|.+|+++
T Consensus 154 ~~~~~~~I~ls~~~ 167 (187)
T PRK08563 154 RRPRGSKIGLTMRQ 167 (187)
T ss_pred CCCCCCEEEEEecC
Confidence 378999874
No 125
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.37 E-value=7.5e-07 Score=101.15 Aligned_cols=70 Identities=20% Similarity=0.317 Sum_probs=62.6
Q ss_pred Hhhhccc--CCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CC--cEEEE
Q psy3754 678 KLTESVQ--IGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RG--RIKLS 752 (755)
Q Consensus 678 ~~~~~~~--~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~g--ki~LS 752 (755)
.+...|+ +|+++.|+|+++.++|+||+| ++.+||||.|+++ |.+.|++||+|+|+|++++. ++ +|.||
T Consensus 125 ~i~~eyk~~~GeIV~G~V~ri~~~giiVDL-ggvea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilS 197 (470)
T PRK09202 125 RVYEEYKDRVGEIITGVVKRVERGNIIVDL-GRAEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILS 197 (470)
T ss_pred HHHHHHHhhcCCEEEEEEEEEecCCEEEEE-CCeEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEE
Confidence 4556676 999999999999999999998 7899999999984 77889999999999999997 34 89999
Q ss_pred Ee
Q psy3754 753 MI 754 (755)
Q Consensus 753 ~k 754 (755)
++
T Consensus 198 Rt 199 (470)
T PRK09202 198 RT 199 (470)
T ss_pred eC
Confidence 86
No 126
>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=98.33 E-value=1.5e-06 Score=72.82 Aligned_cols=67 Identities=22% Similarity=0.266 Sum_probs=52.3
Q ss_pred cceEEEEEEEEecCceEEEEecCCccccccCCccEEEEeecCc-EEEEEeeecccccCHHHHHHHHHHHHhh
Q psy3754 523 EHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKG 593 (755)
Q Consensus 523 ~~va~vs~gli~~~~~~~vL~Dp~~~Ee~~gd~~~~Va~t~~g-i~alq~~~k~~~is~~~l~~al~~A~~~ 593 (755)
++|+++++|++++ .+++||+..||..++..++++.+.++ ++.++..+...+++.+++.+|++.|+++
T Consensus 1 ~~~~avt~~~i~~----~~v~Dpt~~Ee~~~~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~l~~~i~~A~~~ 68 (68)
T PF03725_consen 1 DPPVAVTVGIIDG----ELVVDPTAEEESLSDSSLTLAVDGTGNICTLQKSGGGSELSEDQLEEAIELAKKA 68 (68)
T ss_dssp SEEEEEEEEEETT----EEEES--HHHHHHSSEEEEEEEETTSSEEEEEEEEESSEEEHHHHHHHHHHHHHH
T ss_pred CCeEEEEEEEECC----EEEECCCHHHHhhcCCcEEEEEECCCCEEEEEEcCCCCCCCHHHHHHHHHHHhcC
Confidence 5899999999975 48899999999999888888877666 5555554433359999999999999864
No 127
>KOG2815|consensus
Probab=98.26 E-value=4.5e-07 Score=93.30 Aligned_cols=50 Identities=42% Similarity=0.414 Sum_probs=48.7
Q ss_pred hcCCCCCCCCchhhHHHHHHHHHHHHHHHhhccCcccchhhhhhhhhccc
Q psy3754 15 NSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKGNFL 64 (755)
Q Consensus 15 ~~~~~~d~gs~evqia~lt~~I~~l~~h~~~~~kd~~~~~~l~~~v~~r~ 64 (755)
|++.+.||||++||+|..|.+|+++..|++.|+||.+++++|+.++.+|+
T Consensus 176 ~~~~e~dtgs~~vQ~~~~t~~i~~~~r~~~~Hkkd~~~~~~l~~~~qkR~ 225 (256)
T KOG2815|consen 176 FQRFESDTGSAEVQAAFPTVEIRKLSRHEELHKKDQASVRGLRQEVQKRQ 225 (256)
T ss_pred cccccccccchhHhHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 88899999999999999999999999999999999999999999999994
No 128
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=98.23 E-value=2.7e-06 Score=72.58 Aligned_cols=70 Identities=17% Similarity=0.289 Sum_probs=64.9
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEEcC-CeeEEEe-ccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEE
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRILS-GKDGLLH-ISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSM 753 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel~~-g~~Gllh-isel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~ 753 (755)
-|++|+++. .|+.+.+.|++|.|.+ +.+|++. .||++.+|+++..+.+ +|-.+.|+|+.+|+ +|-|+||.
T Consensus 13 ~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 13 FPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred cCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence 378999999 8999999999999954 5999998 9999999999999999 99999999999999 99999985
No 129
>PRK05054 exoribonuclease II; Provisional
Probab=98.14 E-value=5.2e-06 Score=98.55 Aligned_cols=71 Identities=15% Similarity=0.185 Sum_probs=58.6
Q ss_pred ccCC--cEEEEEEEEEEeeeEEEEEcC-CeeEEEeccccCccc--c--c--------CcccccCCCCEEEEEEEEEcC-C
Q psy3754 683 VQIG--KVYTGIVLRLFDFGAIIRILS-GKDGLLHISQISSKR--V--N--------IITDFLKENQKVRVKVLGIDD-R 746 (755)
Q Consensus 683 ~~~G--~~~~G~V~~I~~fG~FVel~~-g~~Gllhisel~~~~--~--~--------~~~~~~kvGd~V~VkV~~id~-~ 746 (755)
-++| +.|.|.|++|++||+||+|.+ +++||||+|.|.+.+ + . .-...|++||.|+|+|.++|. +
T Consensus 557 ~~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~ 636 (644)
T PRK05054 557 DKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMET 636 (644)
T ss_pred hccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEcccc
Confidence 3565 499999999999999999954 699999999997642 1 0 112579999999999999998 8
Q ss_pred CcEEEEE
Q psy3754 747 GRIKLSM 753 (755)
Q Consensus 747 gki~LS~ 753 (755)
++|.+++
T Consensus 637 ~~i~~~~ 643 (644)
T PRK05054 637 RSIIARP 643 (644)
T ss_pred CeEEEEE
Confidence 9999875
No 130
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=98.11 E-value=1.5e-06 Score=82.44 Aligned_cols=34 Identities=26% Similarity=0.459 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHHhhccCcccchhhhhhhhhcc
Q psy3754 30 ALLTSRINDLNIHFKLHIKDHHSRRGLIMMKGNF 63 (755)
Q Consensus 30 a~lt~~I~~l~~h~~~~~kd~~~~~~l~~~v~~r 63 (755)
-.||+||.+|++||+.|+||+||||||+.+++||
T Consensus 89 ~~L~~ri~~L~~HL~~nkKD~~skRgL~~~~skr 122 (151)
T PRK08561 89 RNLIKKAVNLRKHLEENPKDLHNKRGLQLIESKI 122 (151)
T ss_pred HHHHHHHHHHHHHHHhCCCcchhHHHHHHHHHHH
Confidence 4599999999999999999999999999999999
No 131
>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=98.04 E-value=3.9e-06 Score=78.28 Aligned_cols=61 Identities=25% Similarity=0.320 Sum_probs=54.7
Q ss_pred CcccceeeccccceeeeeccccceEEeecCc-----------------------eeEEEEecC--hhhhHHHHHHHHHhh
Q psy3754 626 PSKIRDVIGKGGSTIRTLTEETGTQIDINDE-----------------------GIITIASFN--SVSGQEAKRRIEKLT 680 (755)
Q Consensus 626 ~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~-----------------------G~v~i~~~~--~~~~~~a~~~i~~~~ 680 (755)
-.+|+.+|||+|+++|.|+++||++|+|..+ +.|.|++.+ ...+++|.++|+.++
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll 93 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence 4589999999999999999999999999766 889999999 999999999999888
Q ss_pred hcccCC
Q psy3754 681 ESVQIG 686 (755)
Q Consensus 681 ~~~~~G 686 (755)
..+...
T Consensus 94 ~~~~~~ 99 (120)
T cd02395 94 KPAIEG 99 (120)
T ss_pred ccCCCc
Confidence 765543
No 132
>KOG1070|consensus
Probab=98.04 E-value=3.9e-06 Score=101.66 Aligned_cols=132 Identities=20% Similarity=0.270 Sum_probs=93.8
Q ss_pred cccCCCceeEEeeC--CcccceeeccccceeeeeccccceEEeec-CceeEEEEecChhhhHHHHHHHHHhhhcccCCcE
Q psy3754 612 LSKFAPRLITIKID--PSKIRDVIGKGGSTIRTLTEETGTQIDIN-DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKV 688 (755)
Q Consensus 612 ~~~~~P~~~~~~i~--~~ki~~~IG~gGk~ik~i~~~~g~~I~i~-~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~ 688 (755)
+++++|..+....+ +--+.-.+|+|-+- |- +.++ +.|++.++.... ....+..... -.....+|.+
T Consensus 534 i~g~lp~~hlsd~~~~~p~~~f~v~~~~k~-RV--------l~~~~~~~~v~l~~K~s-lv~~~~plp~-d~~~~~pg~~ 602 (1710)
T KOG1070|consen 534 IKGVLPKEHLSDHPLQPPLRDFKVGSGVKL-RV--------LSVNRDRNRVALTLKKS-LVNTQLPLPS-DFEQAIPGKI 602 (1710)
T ss_pred eeeecChHhhhhcccccccceeeeccccEE-EE--------EEEEccCCeeEEEechh-hhcccCCCcc-chhhcCCCce
Confidence 66777766533322 11233355554432 22 3344 567777765432 1111111111 1234578999
Q ss_pred EEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 689 YTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 689 ~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
+.|.|-.+.++||||++++|++||.|.|+++++++.++.+.|.+||+|.|+|.++|+ +.||.|+++
T Consensus 603 ~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r 669 (1710)
T KOG1070|consen 603 TKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLR 669 (1710)
T ss_pred EEEEEeeeccCCeEEEecCccccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhh
Confidence 999999999999999999999999999999999999999999999999999999998 889999876
No 133
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.93 E-value=2.9e-05 Score=79.53 Aligned_cols=74 Identities=23% Similarity=0.332 Sum_probs=67.0
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccc----cCcccccCCCCEEEEEEEEEcCCCcEEEEEeC
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRV----NIITDFLKENQKVRVKVLGIDDRGRIKLSMIY 755 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~----~~~~~~~kvGd~V~VkV~~id~~gki~LS~k~ 755 (755)
.|++||++.|+|..+...++.|+|...+.++||+|++.+..+ .+++.+|++||-|.+||..+|..+...|++|.
T Consensus 61 iP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~ 138 (239)
T COG1097 61 IPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKD 138 (239)
T ss_pred cCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCceEEEeec
Confidence 489999999999999999999999889999999999976653 46678899999999999999999999998863
No 134
>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=97.93 E-value=2.2e-05 Score=85.88 Aligned_cols=72 Identities=17% Similarity=0.290 Sum_probs=61.1
Q ss_pred HHhhhcc--cCCcEEEEEEEEEEeee-EEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC---CCcEE
Q psy3754 677 EKLTESV--QIGKVYTGIVLRLFDFG-AIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD---RGRIK 750 (755)
Q Consensus 677 ~~~~~~~--~~G~~~~G~V~~I~~fG-~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~---~gki~ 750 (755)
+.+..+| ++|++++|+|.++.+.| +||+| ++.+|+||.+|.. |.+.|++||.++|.|++++. .++|.
T Consensus 121 e~i~~ey~~k~GeiV~G~V~~v~~~g~v~Vdi-G~~ea~LP~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIi 193 (341)
T TIGR01953 121 ERVYDEFSSKEGEIISGTVKRVNRRGNLYVEL-GKTEGILPKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQII 193 (341)
T ss_pred HHHHHHHHhhcCCEEEEEEEEEecCCcEEEEE-CCeEEEecHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEE
Confidence 3445566 59999999999999988 69998 7899999999986 45569999999999999985 35899
Q ss_pred EEEeC
Q psy3754 751 LSMIY 755 (755)
Q Consensus 751 LS~k~ 755 (755)
||++.
T Consensus 194 vSRt~ 198 (341)
T TIGR01953 194 LSRTH 198 (341)
T ss_pred EEeCc
Confidence 99863
No 135
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=97.92 E-value=5.1e-05 Score=66.46 Aligned_cols=72 Identities=15% Similarity=0.031 Sum_probs=62.8
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcEEEEEe
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRIKLSMI 754 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki~LS~k 754 (755)
.|++||.|-|+|+++....++|+|.....|+||.+++... .++.+..|++||.|-++|.++|+.....||+.
T Consensus 3 ~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~ 74 (86)
T cd05790 3 VPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRDMEPELSCV 74 (86)
T ss_pred cCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc-cccccccCCCCCEEEEEEEecCCCCCeEEEEe
Confidence 3789999999999999999999998889999999988644 34445679999999999999998778888875
No 136
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=97.90 E-value=3.2e-05 Score=93.07 Aligned_cols=95 Identities=21% Similarity=0.382 Sum_probs=74.8
Q ss_pred EEEecChhhhHHHHHHHHHhh---hcccCCcEEEEEEEEEEeeeEEEEEcCC-eeEEEeccccCcccc-----------c
Q psy3754 660 TIASFNSVSGQEAKRRIEKLT---ESVQIGKVYTGIVLRLFDFGAIIRILSG-KDGLLHISQISSKRV-----------N 724 (755)
Q Consensus 660 ~i~~~~~~~~~~a~~~i~~~~---~~~~~G~~~~G~V~~I~~fG~FVel~~g-~~Gllhisel~~~~~-----------~ 724 (755)
+++...+.+.++.++....+. ..-.+|+.++|.|+++..||+||+|.+. ++|++|++.|..+++ .
T Consensus 594 ~~s~~er~a~~aer~~~~~~~~~~m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~ 673 (706)
T COG0557 594 HISSAERRAQEAERDVIDLLKAEYMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGE 673 (706)
T ss_pred HhCHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeecc
Confidence 455566666666666443333 3448999999999999999999999764 999999999987542 2
Q ss_pred CcccccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 725 IITDFLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 725 ~~~~~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
+....+++||.|+|++.+++. .++|.+++.
T Consensus 674 ~~~~~~~lgd~v~v~v~~v~~~~~~i~~~~v 704 (706)
T COG0557 674 KSGKVYRLGDEVKVKVTSVDLDERKIDFELV 704 (706)
T ss_pred ccccccccCCEEEEEEEEEcccccceEEEec
Confidence 344579999999999999998 899998864
No 137
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.81 E-value=9.4e-05 Score=81.54 Aligned_cols=84 Identities=20% Similarity=0.299 Sum_probs=66.9
Q ss_pred cChhhhHHHHHHH---------HHhhhcc--cCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCC
Q psy3754 664 FNSVSGQEAKRRI---------EKLTESV--QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKE 732 (755)
Q Consensus 664 ~~~~~~~~a~~~i---------~~~~~~~--~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kv 732 (755)
.++.++..+++.+ +.++.+| ++|+++.|+|.++.+.|+||+| ++.+|+||.+++. |++.|++
T Consensus 102 fgR~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdl-g~vEa~LP~~E~i------p~e~~~~ 174 (362)
T PRK12327 102 FGRIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNL-GKIEAVLPPAEQI------PGETYKH 174 (362)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEe-CCeEEEecHHHcC------CCCCCCC
Confidence 3345555555544 3444566 8999999999999999999997 6699999988873 3677999
Q ss_pred CCEEEEEEEEEcC--C-CcEEEEEe
Q psy3754 733 NQKVRVKVLGIDD--R-GRIKLSMI 754 (755)
Q Consensus 733 Gd~V~VkV~~id~--~-gki~LS~k 754 (755)
||.++|.|.+++. + .+|.||+.
T Consensus 175 Gd~Ika~V~~V~~~~kgp~IivSRt 199 (362)
T PRK12327 175 GDRIKVYVVKVEKTTKGPQIFVSRT 199 (362)
T ss_pred CCEEEEEEEEEecCCCCCeEEEEeC
Confidence 9999999999995 2 37999975
No 138
>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=97.79 E-value=3.3e-05 Score=86.82 Aligned_cols=61 Identities=31% Similarity=0.459 Sum_probs=53.6
Q ss_pred cccCCcEEEEEEEEEEee--eEEEEEcCCeeEEEeccccCcc------------cccCcccccCCCCEEEEEEEE
Q psy3754 682 SVQIGKVYTGIVLRLFDF--GAIIRILSGKDGLLHISQISSK------------RVNIITDFLKENQKVRVKVLG 742 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~f--G~FVel~~g~~Gllhisel~~~------------~~~~~~~~~kvGd~V~VkV~~ 742 (755)
...+|++|.|+|++|.++ ||||+|..+..||||++++.+. +..++.+.+++||.|.|+|.+
T Consensus 22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~K 96 (414)
T TIGR00757 22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVK 96 (414)
T ss_pred cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEee
Confidence 357899999999999999 9999999999999999999753 233556789999999999998
No 139
>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=97.79 E-value=4.2e-05 Score=90.84 Aligned_cols=92 Identities=11% Similarity=0.122 Sum_probs=65.4
Q ss_pred EEecChhhhHHHHHHHHHhh---hcccCC--cEEEEEEEEEEeeeEEEEE-cCCeeEEEeccccCc--ccc-----c---
Q psy3754 661 IASFNSVSGQEAKRRIEKLT---ESVQIG--KVYTGIVLRLFDFGAIIRI-LSGKDGLLHISQISS--KRV-----N--- 724 (755)
Q Consensus 661 i~~~~~~~~~~a~~~i~~~~---~~~~~G--~~~~G~V~~I~~fG~FVel-~~g~~Gllhisel~~--~~~-----~--- 724 (755)
++...+.+.++.++....+. ..-++| +.|.|.|+++.+||+||+| ..+++||||++.|.+ +++ .
T Consensus 528 ~s~~er~a~~aeR~~~~~~~~~yl~~~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~ 607 (639)
T TIGR02062 528 LAERRRLNRIAERDVADWLYARFLADKAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTV 607 (639)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEE
Confidence 44444445454443332222 233565 4999999999999999999 457999999999975 221 1
Q ss_pred Cc--ccccCCCCEEEEEEEEEcC-CCcEEEE
Q psy3754 725 II--TDFLKENQKVRVKVLGIDD-RGRIKLS 752 (755)
Q Consensus 725 ~~--~~~~kvGd~V~VkV~~id~-~gki~LS 752 (755)
.. ...|++||.|+|+|.++|. +++|.+.
T Consensus 608 ~l~g~~~~~lgd~v~V~v~~vd~~~~~i~~~ 638 (639)
T TIGR02062 608 QIKGETVYKIGDVIDVVLTEVRMETRSIIAR 638 (639)
T ss_pred EEeccEEEecCCEEEEEEEEeccccCcEeee
Confidence 11 1369999999999999998 8888874
No 140
>KOG2916|consensus
Probab=97.75 E-value=1.6e-05 Score=81.37 Aligned_cols=73 Identities=22% Similarity=0.426 Sum_probs=69.0
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEE--cCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRI--LSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel--~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
-|++++++-+.|..|.+.|+||.| +++++||+-.||||..|++++...+++|-.=-|.|+.+|. +|-|.||.+
T Consensus 13 yPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkr 88 (304)
T KOG2916|consen 13 YPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKR 88 (304)
T ss_pred CCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhc
Confidence 378999999999999999999999 5689999999999999999999999999999999999998 999999975
No 141
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=97.74 E-value=4.2e-05 Score=75.38 Aligned_cols=73 Identities=23% Similarity=0.325 Sum_probs=63.1
Q ss_pred hhcccCCcEEEEEEEEEEeeeEEEEEcC----------CeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcE
Q psy3754 680 TESVQIGKVYTGIVLRLFDFGAIIRILS----------GKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRI 749 (755)
Q Consensus 680 ~~~~~~G~~~~G~V~~I~~fG~FVel~~----------g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki 749 (755)
..-++.|+++.|.|+++....+.|++.. ...|-+|+|+....++++.++.|++||.|+++|++.- -.+
T Consensus 59 ~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~--~~~ 136 (188)
T COG1096 59 PPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG--DPI 136 (188)
T ss_pred CCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC--CCe
Confidence 4567999999999999999999998842 2678999999999999999999999999999999973 456
Q ss_pred EEEEe
Q psy3754 750 KLSMI 754 (755)
Q Consensus 750 ~LS~k 754 (755)
.||.+
T Consensus 137 ~Lst~ 141 (188)
T COG1096 137 QLSTK 141 (188)
T ss_pred EEEec
Confidence 67664
No 142
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=97.72 E-value=0.00018 Score=74.64 Aligned_cols=91 Identities=19% Similarity=0.322 Sum_probs=70.1
Q ss_pred eEEeecCceeEEEEecChhhhHHHHHHHHHhhhcccC---CcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccC
Q psy3754 649 TQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQI---GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNI 725 (755)
Q Consensus 649 ~~I~i~~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~---G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~ 725 (755)
+.+.+|..|++.-..... +.++.+...... ++.+.|+|.++...|.||-+.+++-||+|-||--.+
T Consensus 123 v~l~~Dkk~Ri~g~~a~~-------~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~~~---- 191 (287)
T COG2996 123 VYLYVDKKGRIWGTLAIE-------KILENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFIHKSERFAE---- 191 (287)
T ss_pred EEEEEccCCcEEEEecch-------hHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhccc----
Confidence 345667777544332221 223444444444 999999999999999999999999999999986433
Q ss_pred cccccCCCCEEEEEEEEEcCCCcEEEEEe
Q psy3754 726 ITDFLKENQKVRVKVLGIDDRGRIKLSMI 754 (755)
Q Consensus 726 ~~~~~kvGd~V~VkV~~id~~gki~LS~k 754 (755)
.++||+++++|+++.++|+++||++
T Consensus 192 ----prlG~~l~~rVi~~reDg~lnLSl~ 216 (287)
T COG2996 192 ----PRLGERLTARVIGVREDGKLNLSLR 216 (287)
T ss_pred ----ccCCceEEEEEEEEccCCeeecccc
Confidence 7899999999999999999999975
No 143
>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=97.67 E-value=2.9e-05 Score=63.62 Aligned_cols=56 Identities=38% Similarity=0.472 Sum_probs=48.2
Q ss_pred eEEeeCCcccceeeccccceeeeeccccceEEeecC----ceeEEEEecChhhhHHHHHHH
Q psy3754 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND----EGIITIASFNSVSGQEAKRRI 676 (755)
Q Consensus 620 ~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~----~G~v~i~~~~~~~~~~a~~~i 676 (755)
+.+.||+++++.+||++|++|+.|+++||++|++.+ ++.|.|+.. .+.+..|.+++
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~-~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGP-KENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcC-HHHHHHHHHHh
Confidence 467899999999999999999999999999999975 799999988 55666666553
No 144
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.53 E-value=6.9e-05 Score=78.30 Aligned_cols=63 Identities=35% Similarity=0.475 Sum_probs=57.9
Q ss_pred eEEeeCCcccceeeccccceeeeeccccceEEeecCceeEEEEecChhhhHHHHHHHHHhhhc
Q psy3754 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTES 682 (755)
Q Consensus 620 ~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~G~v~i~~~~~~~~~~a~~~i~~~~~~ 682 (755)
..++||+++++.+||++|++++.|.++||++|+++++|.|.|++.+...+++|.++|+.+-.+
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~NG~VwI~~~~~~~~~~a~~~I~~~e~~ 209 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQNGRIWIKGPDEEDEEIAIEAIKKIERE 209 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCCcEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence 468999999999999999999999999999999999999999999999999999988765543
No 145
>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=97.45 E-value=0.00047 Score=60.91 Aligned_cols=60 Identities=20% Similarity=0.197 Sum_probs=50.0
Q ss_pred CCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccC-----------cccccCCCCEEEEEEEEEcC
Q psy3754 685 IGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNI-----------ITDFLKENQKVRVKVLGIDD 745 (755)
Q Consensus 685 ~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~-----------~~~~~kvGd~V~VkV~~id~ 745 (755)
.|++++|+|+++.++|+||.+ +.+++|+|.+.++.+..-+ -...++.|+.|++||.++..
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~-Gpl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~ 71 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEV-GPLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRV 71 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEE-cCceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEE
Confidence 489999999999999999996 7789999999987553222 23469999999999999864
No 146
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.42 E-value=0.00047 Score=68.79 Aligned_cols=75 Identities=15% Similarity=0.100 Sum_probs=59.1
Q ss_pred hhhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCccc-----------c-cCcccccCCCCEEEEEEEEEcC-
Q psy3754 679 LTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKR-----------V-NIITDFLKENQKVRVKVLGIDD- 745 (755)
Q Consensus 679 ~~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~-----------~-~~~~~~~kvGd~V~VkV~~id~- 745 (755)
+...|..|++++|+|+++.++|+||.+ +..++++|.++++++. . ++-+..++.||.|++||.++..
T Consensus 75 ivFrPf~gEVv~g~V~~v~~~G~~v~~-Gp~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~ 153 (176)
T PTZ00162 75 IVFKPFKDEVLDAIVTDVNKLGFFAQA-GPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYD 153 (176)
T ss_pred EEEecCCCCEEEEEEEEEecceEEEEe-eCeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEec
Confidence 456789999999999999999999997 5677999999997431 1 1224579999999999998864
Q ss_pred --CCcEEEEEe
Q psy3754 746 --RGRIKLSMI 754 (755)
Q Consensus 746 --~gki~LS~k 754 (755)
+.+.-.|||
T Consensus 154 ~~~~~~i~T~~ 164 (176)
T PTZ00162 154 ASNLFAIATIN 164 (176)
T ss_pred CCCcEEEEEec
Confidence 234555665
No 147
>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=97.41 E-value=0.00042 Score=60.19 Aligned_cols=61 Identities=18% Similarity=0.334 Sum_probs=42.4
Q ss_pred ccCCcEEEEEEEEEEeeeEEEEEc------------------CCeeEEEeccccCccccc--CcccccCCCCEEEEEEEE
Q psy3754 683 VQIGKVYTGIVLRLFDFGAIIRIL------------------SGKDGLLHISQISSKRVN--IITDFLKENQKVRVKVLG 742 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~fG~FVel~------------------~g~~Gllhisel~~~~~~--~~~~~~kvGd~V~VkV~~ 742 (755)
|++|+++.|+|++|.+--|+++|. ..+.|++|.+++-..... .+.+.|++||.|+++|++
T Consensus 2 P~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViS 81 (82)
T PF10447_consen 2 PKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVIS 81 (82)
T ss_dssp --TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEE
T ss_pred CCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEee
Confidence 689999999999999999999883 146799999998655444 357889999999999987
Q ss_pred E
Q psy3754 743 I 743 (755)
Q Consensus 743 i 743 (755)
.
T Consensus 82 l 82 (82)
T PF10447_consen 82 L 82 (82)
T ss_dssp E
T ss_pred C
Confidence 4
No 148
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=97.38 E-value=0.00012 Score=82.66 Aligned_cols=68 Identities=26% Similarity=0.463 Sum_probs=60.6
Q ss_pred hhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEE
Q psy3754 680 TESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSM 753 (755)
Q Consensus 680 ~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~ 753 (755)
+.+++.|..|+|+|+++.+||+||+|...+.||+|-++++.. .-+.+||++-|++..+.+ +|.|+|..
T Consensus 117 ~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~ 185 (715)
T COG1107 117 MEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEP 185 (715)
T ss_pred hhhcccceeeeccccchhhhcceeecChhhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceee
Confidence 467899999999999999999999999999999999998762 228999999999999988 69888764
No 149
>KOG1070|consensus
Probab=97.31 E-value=0.0006 Score=83.48 Aligned_cols=76 Identities=24% Similarity=0.324 Sum_probs=72.2
Q ss_pred hhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEeC
Q psy3754 680 TESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMIY 755 (755)
Q Consensus 680 ~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k~ 755 (755)
..++++|+++.|.|..+.+.|+|+.|..++++++++|++++.+...++..|.+||.|.++|.++++ .++|.|++|.
T Consensus 1157 ~eDlk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~ 1233 (1710)
T KOG1070|consen 1157 IEDLKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKN 1233 (1710)
T ss_pred hhhcccCceeEEEEEEecCCcEEEEEccceEEEEEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEec
Confidence 567999999999999999999999999999999999999999999999999999999999999998 7899999873
No 150
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=97.24 E-value=0.0012 Score=54.17 Aligned_cols=61 Identities=31% Similarity=0.364 Sum_probs=37.2
Q ss_pred CCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcEEEEEe
Q psy3754 685 IGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRIKLSMI 754 (755)
Q Consensus 685 ~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki~LS~k 754 (755)
+|++...+|+++.++|+|++-..+.+-|||.+|.... +++||.|.|-|-. |.++++..|+|
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~~--------~~~Gd~v~VFvY~-D~~~rl~AT~k 61 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPEP--------LKVGDEVEVFVYL-DKEGRLVATTK 61 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG--------------TTSEEEEEEEE--TTS-EEEE--
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCCC--------CCCCCEEEEEEEE-CCCCCEEEecC
Confidence 5899999999999999999976679999999998543 8999999999876 56788888775
No 151
>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=97.13 E-value=0.00017 Score=58.71 Aligned_cols=55 Identities=38% Similarity=0.621 Sum_probs=48.1
Q ss_pred EEeeCCcccceeeccccceeeeeccccceEEeecCc---eeEEEEecChhhhHHHHHHH
Q psy3754 621 TIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDE---GIITIASFNSVSGQEAKRRI 676 (755)
Q Consensus 621 ~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~---G~v~i~~~~~~~~~~a~~~i 676 (755)
.+.||++.++.+||++|.+|+.|.++||+.|.+.++ ..+.|.+ +.+.++.|.++|
T Consensus 3 ~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G-~~~~v~~A~~~I 60 (60)
T PF00013_consen 3 RIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISG-SPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEE-SHHHHHHHHHHH
T ss_pred EEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEe-CHHHHHHHHhhC
Confidence 567899999999999999999999999999999753 6788988 788888887764
No 152
>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=96.92 E-value=0.00088 Score=54.78 Aligned_cols=54 Identities=41% Similarity=0.607 Sum_probs=43.9
Q ss_pred EEeeCCcccceeeccccceeeeeccccceEEeecC------ceeEEEEecChhhhHHHHHH
Q psy3754 621 TIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND------EGIITIASFNSVSGQEAKRR 675 (755)
Q Consensus 621 ~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~------~G~v~i~~~~~~~~~~a~~~ 675 (755)
.+.||.+.++.+||++|++|+.|.++||+.|.+.+ +..+.+... .+.+..|..+
T Consensus 3 ~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~-~~~v~~a~~~ 62 (64)
T cd00105 3 RVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT-PEAVEKAKEL 62 (64)
T ss_pred EEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcC-HHHHHHHHHH
Confidence 57899999999999999999999999999999964 466777766 4555555544
No 153
>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=96.88 E-value=0.0027 Score=53.55 Aligned_cols=66 Identities=26% Similarity=0.343 Sum_probs=55.9
Q ss_pred CcEEEEEEEEEEeeeEEEEEcC-CeeEEEeccccCcccccC---cccccCCCCEE-EEEEEEEcC-CCcEEEEEe
Q psy3754 686 GKVYTGIVLRLFDFGAIIRILS-GKDGLLHISQISSKRVNI---ITDFLKENQKV-RVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~FVel~~-g~~Gllhisel~~~~~~~---~~~~~kvGd~V-~VkV~~id~-~gki~LS~k 754 (755)
|++++|+|..-++-+++|++.+ ++.|+++...|++ .+++ .-..+++||++ .+-|+ |. .+.|.||.|
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 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSD-HVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC-chhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence 7899999999999999999977 7999999999999 4432 23459999999 99999 66 778888865
No 154
>smart00322 KH K homology RNA-binding domain.
Probab=96.39 E-value=0.0046 Score=50.38 Aligned_cols=60 Identities=37% Similarity=0.529 Sum_probs=48.7
Q ss_pred ceeEEeeCCcccceeeccccceeeeeccccceEEeecC----ceeEEEEecChhhhHHHHHHHHH
Q psy3754 618 RLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND----EGIITIASFNSVSGQEAKRRIEK 678 (755)
Q Consensus 618 ~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~----~G~v~i~~~~~~~~~~a~~~i~~ 678 (755)
....+.|+++.++.+||++|++|+.|.+.+|+.|.+.. ...+.+... ......+...+..
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~-~~~v~~a~~~i~~ 66 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGP-PENVEKAAELILE 66 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcC-HHHHHHHHHHHHH
Confidence 34567899999999999999999999999999999865 377888777 5666667666554
No 155
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.36 E-value=0.018 Score=63.50 Aligned_cols=84 Identities=18% Similarity=0.190 Sum_probs=63.6
Q ss_pred cChhhhHHHHHHHHHh---------hhc--ccCCcEEEEEEEEEEee-eEEEEEcCCeeEEEeccccCcccccCcccccC
Q psy3754 664 FNSVSGQEAKRRIEKL---------TES--VQIGKVYTGIVLRLFDF-GAIIRILSGKDGLLHISQISSKRVNIITDFLK 731 (755)
Q Consensus 664 ~~~~~~~~a~~~i~~~---------~~~--~~~G~~~~G~V~~I~~f-G~FVel~~g~~Gllhisel~~~~~~~~~~~~k 731 (755)
.++.+++.|+..+... ..+ -++|+++.|+|.++... ++||+| ++.+|+||.++.. |.+.|+
T Consensus 106 fgRiaaq~akq~i~Qkir~~er~~i~~ey~~~~Geiv~g~V~r~~~~~~i~vdl-g~~ea~LP~~eqi------p~E~~~ 178 (374)
T PRK12328 106 MGRTAANTLFKELEYHIQRLLEESIFEKYKKKVGKIVFGTVVRVDNEENTFIEI-DEIRAVLPMKNRI------KGEKFK 178 (374)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEecCCCEEEEc-CCeEEEeCHHHcC------CCCcCC
Confidence 4455666666654222 222 37999999999999875 489997 6899999988753 567799
Q ss_pred CCCEEEEEEEEEcC--C--CcEEEEEe
Q psy3754 732 ENQKVRVKVLGIDD--R--GRIKLSMI 754 (755)
Q Consensus 732 vGd~V~VkV~~id~--~--gki~LS~k 754 (755)
+||.++|-|.+++. + -+|.||+.
T Consensus 179 ~Gdrik~~i~~V~~~~k~gp~IilSRt 205 (374)
T PRK12328 179 VGDVVKAVLKRVKIDKNNGILIELSRT 205 (374)
T ss_pred CCCEEEEEEEEEecCCCCCCEEEEEcC
Confidence 99999999999986 3 27888874
No 156
>PRK10811 rne ribonuclease E; Reviewed
Probab=96.35 E-value=0.0067 Score=73.08 Aligned_cols=61 Identities=23% Similarity=0.340 Sum_probs=50.7
Q ss_pred ccCCcEEEEEEEEEEe--eeEEEEEcCCeeEEEeccccCccccc---------CcccccCCCCEEEEEEEEE
Q psy3754 683 VQIGKVYTGIVLRLFD--FGAIIRILSGKDGLLHISQISSKRVN---------IITDFLKENQKVRVKVLGI 743 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~--fG~FVel~~g~~Gllhisel~~~~~~---------~~~~~~kvGd~V~VkV~~i 743 (755)
..+|.||.|+|.+|.+ -++||+|..+..||||++++....+. +..+.+++||.|-|.|.+-
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KE 107 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE 107 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeec
Confidence 3579999999999965 67999999999999999999654322 2345799999999999984
No 157
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=96.33 E-value=0.00018 Score=77.66 Aligned_cols=110 Identities=15% Similarity=0.169 Sum_probs=84.6
Q ss_pred cceeeccccceeeeeccccceEEeec----CceeEEEEecChhhhHHHHHH-----------------------------
Q psy3754 629 IRDVIGKGGSTIRTLTEETGTQIDIN----DEGIITIASFNSVSGQEAKRR----------------------------- 675 (755)
Q Consensus 629 i~~~IG~gGk~ik~i~~~~g~~I~i~----~~G~v~i~~~~~~~~~~a~~~----------------------------- 675 (755)
+++++ .|+ |+.| .++|++++++ -+|.+|+|..+|.......+.
T Consensus 17 ~GdvV--~g~-V~~I-~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~ 92 (319)
T PTZ00248 17 EDDLV--MVK-VVRI-TEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVS 92 (319)
T ss_pred CCCEE--EEE-EEEE-eCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeecc
Confidence 34444 343 4555 5899999993 589999999988877666553
Q ss_pred ---HHHhhhcccCCcEEEEEEEEEE-eeeEEEE------EcCCeeEEEeccccCcccccCcccccC---CCCEEEEEEEE
Q psy3754 676 ---IEKLTESVQIGKVYTGIVLRLF-DFGAIIR------ILSGKDGLLHISQISSKRVNIITDFLK---ENQKVRVKVLG 742 (755)
Q Consensus 676 ---i~~~~~~~~~G~~~~G~V~~I~-~fG~FVe------l~~g~~Gllhisel~~~~~~~~~~~~k---vGd~V~VkV~~ 742 (755)
|+.+...++.|++++|+|..+. .||+|++ ..+..+++.|+++.....+.++.++|+ +++.++.+++.
T Consensus 93 ~~pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y~af~~~v~~~~evl~~l~i~~ev~~~l~~ 172 (319)
T PTZ00248 93 PEDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKEALTNPDNVFEGLDIPEEVKESLLQ 172 (319)
T ss_pred cchHHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCHHHHHHHHhcCchhhhccCCCCHHHHHHHHH
Confidence 3555677899999999999995 5999998 467899999999998888888887777 77776655543
No 158
>PRK11712 ribonuclease G; Provisional
Probab=96.19 E-value=0.0074 Score=69.35 Aligned_cols=61 Identities=28% Similarity=0.425 Sum_probs=49.7
Q ss_pred ccCCcEEEEEEEEEEe--eeEEEEEcCCeeEEEeccccCcc------------cccCcccccCCCCEEEEEEEEE
Q psy3754 683 VQIGKVYTGIVLRLFD--FGAIIRILSGKDGLLHISQISSK------------RVNIITDFLKENQKVRVKVLGI 743 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~--fG~FVel~~g~~Gllhisel~~~------------~~~~~~~~~kvGd~V~VkV~~i 743 (755)
..+|.+|.|+|.+|.+ .+|||+|..+..||||++++... ...+..+.+++||.|-|.|.+=
T Consensus 36 ~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke 110 (489)
T PRK11712 36 GIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKD 110 (489)
T ss_pred cccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeC
Confidence 4689999999999976 57999999999999999997321 0123356699999999999984
No 159
>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=95.94 E-value=0.0068 Score=50.22 Aligned_cols=54 Identities=33% Similarity=0.516 Sum_probs=41.2
Q ss_pred EEeeCCcccceeeccccceeeeeccccceEEeecCc-------eeEEEEecChhhhHHHHHH
Q psy3754 621 TIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDE-------GIITIASFNSVSGQEAKRR 675 (755)
Q Consensus 621 ~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~-------G~v~i~~~~~~~~~~a~~~ 675 (755)
.+.||.++++.+||++|.+|+.|+++||+.|.+.++ -.+.|... .+...+|..+
T Consensus 3 r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~-~~~v~~A~~~ 63 (65)
T cd02396 3 RLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGK-PSAVQKALLL 63 (65)
T ss_pred EEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeC-HHHHHHHHHh
Confidence 467899999999999999999999999999998632 24555544 4445555544
No 160
>KOG1676|consensus
Probab=95.38 E-value=0.043 Score=62.88 Aligned_cols=99 Identities=26% Similarity=0.353 Sum_probs=65.9
Q ss_pred HHHHHhhhHHHHHHHHhhccc--cccccccCCCceeEEeeCCcccceeeccccceeeeeccccceEEeec-Cce------
Q psy3754 587 LYKAKKGLSYILEKMKTEVPK--CKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN-DEG------ 657 (755)
Q Consensus 587 l~~A~~~~~~I~~~~~~~l~~--~r~~~~~~~P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~-~~G------ 657 (755)
+++|+.....|++.=.+.... ...+.+.-.-....+.||..+.+-+||++|.+||.|..+||++|-+- ||+
T Consensus 197 ve~a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR 276 (600)
T KOG1676|consen 197 VEQAKQLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPER 276 (600)
T ss_pred HHHHHHHHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccc
Confidence 456655555555531111111 11233333333445788999999999999999999999999999984 333
Q ss_pred eEEEEecChhhhHHHHHHHHHhhhcccCC
Q psy3754 658 IITIASFNSVSGQEAKRRIEKLTESVQIG 686 (755)
Q Consensus 658 ~v~i~~~~~~~~~~a~~~i~~~~~~~~~G 686 (755)
.+.|... .+.++.|.+.|.+++.....|
T Consensus 277 ~~~IiG~-~d~ie~Aa~lI~eii~~~~~~ 304 (600)
T KOG1676|consen 277 PAQIIGT-VDQIEHAAELINEIIAEAEAG 304 (600)
T ss_pred eeeeecC-HHHHHHHHHHHHHHHHHHhcc
Confidence 3455433 567888999998888776655
No 161
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.27 E-value=0.09 Score=59.10 Aligned_cols=66 Identities=17% Similarity=0.139 Sum_probs=55.1
Q ss_pred ccCCcEEEEEEEEEEeeeEEEEEc---C--CeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCC----CcEEEEE
Q psy3754 683 VQIGKVYTGIVLRLFDFGAIIRIL---S--GKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDR----GRIKLSM 753 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~fG~FVel~---~--g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~----gki~LS~ 753 (755)
-++|+++.|+|.++..-+++|+|. + +.+|+||.++. -|++.|++||.|+|-|.+++.. -+|.||+
T Consensus 150 ~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eq------ip~E~y~~Gdrika~i~~V~~~~~kGpqIilSR 223 (449)
T PRK12329 150 DLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQ------LPNDNYRANATFKVFLKEVSEGPRRGPQLFVSR 223 (449)
T ss_pred HhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHc------CCCCcCCCCCEEEEEEEEeecCCCCCCEEEEEc
Confidence 379999999999999999999983 3 38999998875 3567799999999999999752 3688987
Q ss_pred e
Q psy3754 754 I 754 (755)
Q Consensus 754 k 754 (755)
.
T Consensus 224 t 224 (449)
T PRK12329 224 A 224 (449)
T ss_pred C
Confidence 4
No 162
>KOG1856|consensus
Probab=95.25 E-value=0.023 Score=69.13 Aligned_cols=72 Identities=24% Similarity=0.265 Sum_probs=61.5
Q ss_pred ccCCcEEEEEEEEEEeee---EEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 683 VQIGKVYTGIVLRLFDFG---AIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~fG---~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
+.+|.++.++|++|+.-- +=|.+..|++|+||.+++++..+.+|...+++||.|.+||+++|. +=-+.||++
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 1058 (1299)
T KOG1856|consen 983 FYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCR 1058 (1299)
T ss_pred hccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhh
Confidence 678999999999997544 456788999999999999999999999999999999999999996 434455543
No 163
>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=95.22 E-value=0.017 Score=57.61 Aligned_cols=55 Identities=31% Similarity=0.401 Sum_probs=47.3
Q ss_pred ccceeeccccceeeeeccccceEEeecCceeEEEEecChhhhHHHHHHHHHhhhccc
Q psy3754 628 KIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQ 684 (755)
Q Consensus 628 ki~~~IG~gGk~ik~i~~~~g~~I~i~~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~ 684 (755)
.++.+||++|++++.|++.||+.|.+.+ ..|+|.. +....+.|++.+..++..-.
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~-~~v~i~G-~~~~~~~A~~~i~~li~~~~ 153 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYG-KTVGIIG-DPEQVQIAREAIEMLIEGAP 153 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcC-CEEEEEC-CHHHHHHHHHHHHHHHcCCC
Confidence 5778999999999999999999999865 6799988 78889999999988775433
No 164
>PRK13763 putative RNA-processing protein; Provisional
Probab=94.99 E-value=0.014 Score=58.59 Aligned_cols=59 Identities=31% Similarity=0.439 Sum_probs=47.7
Q ss_pred ccceeeccccceeeeeccccceEEeecCceeEEEEecChhhhHHHHHHHHHhhhcccCCcE
Q psy3754 628 KIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKV 688 (755)
Q Consensus 628 ki~~~IG~gGk~ik~i~~~~g~~I~i~~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~ 688 (755)
.++.+||+||+++|.|++.||+.|.+.++ .++|.. +....+.|++.++.+......+.+
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~-~v~i~G-~~~~~~~A~~~I~~li~g~~~~~~ 163 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGK-TVAIIG-DPEQVEIAREAIEMLIEGAPHGTV 163 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCC-EEEEEe-CHHHHHHHHHHHHHHHcCCCcHHH
Confidence 56779999999999999999999999754 488876 678889999998887765544433
No 165
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=94.53 E-value=0.066 Score=49.66 Aligned_cols=53 Identities=15% Similarity=0.364 Sum_probs=41.8
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEeee
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFG 700 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~fG 700 (755)
|..| ..||||++++ ..|.||||...... ++++-.-+++|+.|..+|.+|.+.|
T Consensus 13 ItgI-~~yGAFV~l~~g~tGLVHISEIa~~f-------VkdI~d~L~vG~eV~vKVl~ide~G 67 (129)
T COG1098 13 ITGI-TPYGAFVELEGGKTGLVHISEIADGF-------VKDIHDHLKVGQEVKVKVLDIDENG 67 (129)
T ss_pred EEee-EecceEEEecCCCcceEEehHhhhhh-------HHhHHHHhcCCCEEEEEEEeeccCC
Confidence 5556 4899999996 68999999776554 4455555899999999999987755
No 166
>KOG2191|consensus
Probab=94.33 E-value=0.16 Score=54.26 Aligned_cols=116 Identities=23% Similarity=0.372 Sum_probs=67.4
Q ss_pred EeecCcEEEEEeeecccccCHHHHHHHHHHHHhhhHHHHHHHHhhccccccccccCCCce------eEEeeCCcccceee
Q psy3754 560 AGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRL------ITIKIDPSKIRDVI 633 (755)
Q Consensus 560 a~t~~gi~alq~~~k~~~is~~~l~~al~~A~~~~~~I~~~~~~~l~~~r~~~~~~~P~~------~~~~i~~~ki~~~I 633 (755)
-+|.+.||.+|- +.+.|+..++. |.+++++-...-.+-...+-|+- ..+-+|..--+-+|
T Consensus 82 PGTTeRvcli~G-------t~eai~av~ef-------I~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~ii 147 (402)
T KOG2191|consen 82 PGTTERVCLIQG-------TVEALNAVHEF-------IADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMII 147 (402)
T ss_pred CCccceEEEEec-------cHHHHHHHHHH-------HHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCccccee
Confidence 467788888775 35556655554 33333333222111122333332 12335666677899
Q ss_pred ccccceeeeeccccceEEeec---------CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEE
Q psy3754 634 GKGGSTIRTLTEETGTQIDIN---------DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVY 689 (755)
Q Consensus 634 G~gGk~ik~i~~~~g~~I~i~---------~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~ 689 (755)
|+||.+||.|+|++|+-|.|. .+-.+.++..-...++++...++.+.++++-+..+
T Consensus 148 gkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scl 212 (402)
T KOG2191|consen 148 GKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCL 212 (402)
T ss_pred cCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCccccee
Confidence 999999999999999877764 13344554444444444444456666777666554
No 167
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=94.14 E-value=0.2 Score=43.81 Aligned_cols=63 Identities=17% Similarity=0.160 Sum_probs=50.2
Q ss_pred EEEEEEEEEEeeeEE-EEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEEe
Q psy3754 688 VYTGIVLRLFDFGAI-IRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSMI 754 (755)
Q Consensus 688 ~~~G~V~~I~~fG~F-Vel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~k 754 (755)
.++|+|+.+.+.+.| |+|.+|.+-+.|+|- +...-.-.+-+||.|+|.+-..|. +|+|..-.+
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG~~vla~isG----KmR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~ 72 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASG----RMRKHRIRILAGDRVTLELSPYDLTKGRINFRHK 72 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEecc----ceeeeeEEecCCCEEEEEECcccCCceeEEEEec
Confidence 589999999999987 588999999999883 222222238899999999999988 899876543
No 168
>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=93.51 E-value=0.29 Score=41.02 Aligned_cols=60 Identities=25% Similarity=0.323 Sum_probs=47.8
Q ss_pred EEEEEEEEEEeeeEE-EEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEE
Q psy3754 688 VYTGIVLRLFDFGAI-IRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKL 751 (755)
Q Consensus 688 ~~~G~V~~I~~fG~F-Vel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~L 751 (755)
.+.|+|++..+.|.| |.+.+|.+-+.|+|- +.....--+.+||.|.|.+-..|. +|+|..
T Consensus 6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~G----Kmr~~rI~I~~GD~V~Ve~spyd~tkgrIi~ 67 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELENGHEVLAHISG----KIRMHYIRILPGDKVKVELSPYDLTRGRITY 67 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEecC----cchhccEEECCCCEEEEEECcccCCcEeEEe
Confidence 578999999999988 688999999999874 222223348999999999998887 788753
No 169
>PF13014 KH_3: KH domain
Probab=93.48 E-value=0.024 Score=42.89 Aligned_cols=27 Identities=52% Similarity=0.882 Sum_probs=24.5
Q ss_pred cceeeccccceeeeeccccceEEeecC
Q psy3754 629 IRDVIGKGGSTIRTLTEETGTQIDIND 655 (755)
Q Consensus 629 i~~~IG~gGk~ik~i~~~~g~~I~i~~ 655 (755)
.+.+||++|.+|+.|++++|++|.+.+
T Consensus 2 vg~iIG~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 2 VGRIIGKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred cCeEECCCChHHHHHHHHhCcEEEECC
Confidence 567899999999999999999999864
No 170
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=93.02 E-value=0.13 Score=51.51 Aligned_cols=68 Identities=22% Similarity=0.368 Sum_probs=57.6
Q ss_pred CCCceeEEeeCCcccceeeccccceeeeeccccceEEeec-CceeEEEEec----ChhhhHHHHHHHHHhhhc
Q psy3754 615 FAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN-DEGIITIASF----NSVSGQEAKRRIEKLTES 682 (755)
Q Consensus 615 ~~P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~-~~G~v~i~~~----~~~~~~~a~~~i~~~~~~ 682 (755)
..+.+....||++.++-+||+.|++.+.|.+.+|+++.+| ++|.|.|... +.....+|++.++.+-..
T Consensus 5 ~~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrG 77 (194)
T COG1094 5 AEKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRG 77 (194)
T ss_pred cccceeeeecCchhheeeecccccchHHHHhhcCeEEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHhcC
Confidence 3456677899999999999999999999999999999998 6799999887 556788888888766543
No 171
>KOG3409|consensus
Probab=92.70 E-value=0.39 Score=47.01 Aligned_cols=71 Identities=23% Similarity=0.250 Sum_probs=54.5
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEEc--------CCeeEEEeccccCc---ccccCcccccCCCCEEEEEEEEEcCCCcEE
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRIL--------SGKDGLLHISQISS---KRVNIITDFLKENQKVRVKVLGIDDRGRIK 750 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel~--------~g~~Gllhisel~~---~~~~~~~~~~kvGd~V~VkV~~id~~gki~ 750 (755)
-+.+|+++.++|..|..--|=|+|. ..+.|++|..++-. +++ ++-.-|++||.|.++|++.+...+.-
T Consensus 65 LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv-~v~ksFrPgDiVlAkVis~~~~~~y~ 143 (193)
T KOG3409|consen 65 LPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRV-KVYKSFRPGDIVLAKVISLGDGSNYL 143 (193)
T ss_pred CCccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchh-hhhhccCCCcEEEEEEeecCCCCcEE
Confidence 3789999999999998877777764 25899999887732 222 34556999999999999966555666
Q ss_pred EEE
Q psy3754 751 LSM 753 (755)
Q Consensus 751 LS~ 753 (755)
||.
T Consensus 144 LTt 146 (193)
T KOG3409|consen 144 LTT 146 (193)
T ss_pred EEE
Confidence 765
No 172
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=92.32 E-value=0.14 Score=59.18 Aligned_cols=62 Identities=26% Similarity=0.396 Sum_probs=52.3
Q ss_pred cccCCcEEEEEEEEEEee--eEEEEEcCCeeEEEeccccCcccccCc-----ccccCCCCEEEEEEEEEc
Q psy3754 682 SVQIGKVYTGIVLRLFDF--GAIIRILSGKDGLLHISQISSKRVNII-----TDFLKENQKVRVKVLGID 744 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~f--G~FVel~~g~~Gllhisel~~~~~~~~-----~~~~kvGd~V~VkV~~id 744 (755)
...+|.+|.|+|++|.+. .+||++.....||+|.+++.+ +.+.+ ...++.||.+-|.|..-.
T Consensus 34 ~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~ 102 (487)
T COG1530 34 EQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEP 102 (487)
T ss_pred EeeecCceEEEecccCccchhheeeccCCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeec
Confidence 456899999999999874 489999989999999999988 54433 347999999999998854
No 173
>KOG1676|consensus
Probab=90.67 E-value=0.66 Score=53.52 Aligned_cols=95 Identities=21% Similarity=0.284 Sum_probs=65.4
Q ss_pred HHHHHHHHhhhHHHHHHHHhhccccccccccCCCce---eEEeeCCcccceeeccccceeeeeccccceEEeecC-----
Q psy3754 584 QIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRL---ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND----- 655 (755)
Q Consensus 584 ~~al~~A~~~~~~I~~~~~~~l~~~r~~~~~~~P~~---~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~----- 655 (755)
.++++.|.+....|+. ++-......+..-.|.. ..+.||.+|-+-+||+||.+||.|..++|+.+.+-.
T Consensus 284 ~d~ie~Aa~lI~eii~---~~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~ 360 (600)
T KOG1676|consen 284 VDQIEHAAELINEIIA---EAEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNG 360 (600)
T ss_pred HHHHHHHHHHHHHHHH---HHhccCCCCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCC
Confidence 3455555444444443 34333333455666755 478899999999999999999999999999987631
Q ss_pred ---ceeEEEEecChhhhHHHHHHHHHhhhc
Q psy3754 656 ---EGIITIASFNSVSGQEAKRRIEKLTES 682 (755)
Q Consensus 656 ---~G~v~i~~~~~~~~~~a~~~i~~~~~~ 682 (755)
+-++.| .-++..++.|+..|+..+..
T Consensus 361 ~~~ektf~I-rG~~~QIdhAk~LIr~kvg~ 389 (600)
T KOG1676|consen 361 NPKEKTFVI-RGDKRQIDHAKQLIRDKVGD 389 (600)
T ss_pred CccceEEEE-ecCcccchHHHHHHHHHhcc
Confidence 234444 45577889999998865544
No 174
>KOG3298|consensus
Probab=89.83 E-value=1.5 Score=42.64 Aligned_cols=65 Identities=17% Similarity=0.193 Sum_probs=44.2
Q ss_pred hhcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEec----cccCcccccC-------cccccCCCCEEEEEEEEEcC
Q psy3754 680 TESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHI----SQISSKRVNI-------ITDFLKENQKVRVKVLGIDD 745 (755)
Q Consensus 680 ~~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhi----sel~~~~~~~-------~~~~~kvGd~V~VkV~~id~ 745 (755)
...+-.|++++|+|+++...|+|++..| .+-++-- .++.....++ -.+++++|++|++||++...
T Consensus 76 ~FkpfKGEVvdgvV~~Vnk~G~F~~~GP-l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~ 151 (170)
T KOG3298|consen 76 TFKPFKGEVVDGVVTKVNKMGVFARSGP-LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRV 151 (170)
T ss_pred EEeecCCcEEEEEEEEEeeeeEEEeccc-eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEE
Confidence 4457789999999999999999999643 3333321 1221111222 12379999999999998753
No 175
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=89.53 E-value=0.46 Score=56.79 Aligned_cols=109 Identities=17% Similarity=0.217 Sum_probs=61.7
Q ss_pred cCHHHHHHHHHHHHhhhHHHHHHHHhhccccccccccCCCceeEEeeCCcccceeeccccceeeeeccccceEEeec--C
Q psy3754 578 ITYDIIQIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN--D 655 (755)
Q Consensus 578 is~~~l~~al~~A~~~~~~I~~~~~~~l~~~r~~~~~~~P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~--~ 655 (755)
+..+++.+-..........|...+.+--..+|.+...-.+...+..+..=|.+-++ .| +++.. ..||+++||+ +
T Consensus 607 L~~~~~a~~~~~gl~Tl~dIi~eL~kp~rdpR~~f~~~~~~~~v~~i~dLk~Gm~l--eg-~Vrnv-~~fgafVdIgv~q 682 (780)
T COG2183 607 LNLEEFADELDFGLPTLEDIILELEKPGRDPRDEFHTPTLDEGVESITDLKPGMIL--EG-TVRNV-VDFGAFVDIGVHQ 682 (780)
T ss_pred cCHHHHHHHHhcCCchHHHHHHHhhcCCCCCcccccccchhhhhhhHhhccCCCEE--EE-EEEEe-eeccceEEecccc
Confidence 33333333333333333444444444444455544444444444444433333222 12 34544 4899999997 8
Q ss_pred ceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEE
Q psy3754 656 EGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLF 697 (755)
Q Consensus 656 ~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~ 697 (755)
||.|||+..+...+... ..-+++|++|+++|.+|-
T Consensus 683 DglvHis~ls~~fv~~P-------~~vv~vGdiV~v~V~~vD 717 (780)
T COG2183 683 DGLVHISQLSDKFVKDP-------NEVVKVGDIVKVKVIEVD 717 (780)
T ss_pred ceeeeHHHhhhhhcCCh-------HHhcccCCEEEEEEEEEe
Confidence 99999987765554433 234789999999999983
No 176
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=86.42 E-value=2.8 Score=44.24 Aligned_cols=64 Identities=23% Similarity=0.273 Sum_probs=47.7
Q ss_pred ccCCcEEEEEEEEEEeeeEEEEEcCC-eeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcEEEEEe
Q psy3754 683 VQIGKVYTGIVLRLFDFGAIIRILSG-KDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRIKLSMI 754 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~fG~FVel~~g-~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki~LS~k 754 (755)
..+|++....|.+..+||+|+.=..+ ..=++|.++.. ++.+.+||+|+|-+-- |.++++..+++
T Consensus 3 ~~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~-------~~e~evGdev~vFiY~-D~~~rl~aTt~ 67 (287)
T COG2996 3 IKIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPE-------EDELEVGDEVTVFIYV-DSEDRLIATTR 67 (287)
T ss_pred ccccceEEEEEEEeeceeEEEecCCCceEEeccccCCc-------CCccccCcEEEEEEEE-CCCCceeheee
Confidence 57899999999999999999983222 36788888653 2347899999987653 55667666654
No 177
>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=85.99 E-value=1.1 Score=37.70 Aligned_cols=57 Identities=16% Similarity=0.225 Sum_probs=42.0
Q ss_pred eeeeccccceEEeecC---ceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEeeeEEEEE
Q psy3754 640 IRTLTEETGTQIDIND---EGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRI 705 (755)
Q Consensus 640 ik~i~~~~g~~I~i~~---~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~fG~FVel 705 (755)
|..+ .+||++++++. +|.+|++...+...+ ..-.-+++||.++.+|.++...+ .+.|
T Consensus 11 V~~i-~~fG~fv~l~~~~~eGlvh~sel~~~~~~-------~~~~~~~~Gd~v~vkv~~vd~~~-ki~l 70 (73)
T cd05686 11 VASV-TEYGAFVKIPGCRKQGLVHKSHMSSCRVD-------DPSEVVDVGEKVWVKVIGREMKD-KMKL 70 (73)
T ss_pred EEEE-EeeeEEEEECCCCeEEEEEchhhCCCccc-------CHhhEECCCCEEEEEEEEECCCC-cEEE
Confidence 4455 47999999953 799999988765322 33344799999999999997766 5543
No 178
>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=85.69 E-value=0.98 Score=38.41 Aligned_cols=54 Identities=13% Similarity=0.188 Sum_probs=40.3
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
++.+ ..+|++++++ -+|.++++..++...... ..+...+++|+.++++|.++.+
T Consensus 11 V~~i-~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~----~~~~~~~~~G~~v~~kVl~id~ 66 (74)
T cd05705 11 VSSV-TKQGVFFRLSSSIVGRVLFQNVTKYFVSDP----SLYNKYLPEGKLLTAKVLSVNS 66 (74)
T ss_pred EEEE-eCCcEEEEeCCCCEEEEEHHHccCccccCh----hhHhcccCCCCEEEEEEEEEEC
Confidence 5555 4899999996 589999888777653322 1134568999999999999864
No 179
>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=85.68 E-value=7.6 Score=31.92 Aligned_cols=54 Identities=31% Similarity=0.405 Sum_probs=39.1
Q ss_pred EEEEEEEEE---eeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCC
Q psy3754 689 YTGIVLRLF---DFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRG 747 (755)
Q Consensus 689 ~~G~V~~I~---~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~g 747 (755)
..|+|+... .||....-.++.+-++|+|++.... -+.++.||.|+..+.. +++|
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~-~~~g 57 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE-GKKG 57 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSS----STS--TTSEEEEEEEE-CTTS
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEeccccccccc----cccCCCCCEEEEEEEE-CCCC
Confidence 479999986 4776655334469999999997764 2458999999999988 4444
No 180
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=84.69 E-value=5 Score=34.34 Aligned_cols=64 Identities=23% Similarity=0.272 Sum_probs=49.8
Q ss_pred CcEEEEEEEEEEeeeEE-EEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEE
Q psy3754 686 GKVYTGIVLRLFDFGAI-IRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSM 753 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~F-Vel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~ 753 (755)
.-.+.|+|.+..+-+-| |++.+|..-+-|+|-=-.. ..--+.+||.|.|..-..|. +|+|..-.
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~GKmr~----~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry 71 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELENGHERLAHISGKMRK----NRIRILPGDVVLVELSPYDLTKGRIVYRY 71 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEecCCcEEEEEccCcchh----eeEEeCCCCEEEEEecccccccccEEEEe
Confidence 45688999999998876 8889999999998842221 12238899999999999986 78887654
No 181
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=83.38 E-value=1.4 Score=37.21 Aligned_cols=53 Identities=15% Similarity=0.304 Sum_probs=39.9
Q ss_pred eeeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 639 TIRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 639 ~ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
.|+.+.+.+|+++++. .+|.+|++..++.... .....+++||.+.++|.++.+
T Consensus 10 ~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~-------~~~~~~~~Gd~v~~kV~~~~~ 64 (72)
T cd05704 10 MVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTE-------NPLEGFKPGKIVRCCILSKKD 64 (72)
T ss_pred EEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccC-------CHHHhCCCCCEEEEEEEEecC
Confidence 3566766799999985 5899999877665432 223457999999999999864
No 182
>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=83.12 E-value=0.44 Score=39.03 Aligned_cols=36 Identities=28% Similarity=0.508 Sum_probs=31.2
Q ss_pred ceeEEeeCCcccceeeccccceeeeeccccceEEee
Q psy3754 618 RLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI 653 (755)
Q Consensus 618 ~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i 653 (755)
....+.++++.++..||++|.+|+.+.+-+|..|++
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 455678899999999999999999998888877765
No 183
>KOG0119|consensus
Probab=82.82 E-value=3.4 Score=46.85 Aligned_cols=57 Identities=32% Similarity=0.360 Sum_probs=47.0
Q ss_pred CcccceeeccccceeeeeccccceEEeec-----Ccee-----------------EEEEecChhhhHHHHHHHHHhhhc
Q psy3754 626 PSKIRDVIGKGGSTIRTLTEETGTQIDIN-----DEGI-----------------ITIASFNSVSGQEAKRRIEKLTES 682 (755)
Q Consensus 626 ~~ki~~~IG~gGk~ik~i~~~~g~~I~i~-----~~G~-----------------v~i~~~~~~~~~~a~~~i~~~~~~ 682 (755)
-..++-+||+.|.|.|.++++||++|-|- .+|. ..|++...+.+++|.++|+.++.+
T Consensus 152 ~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 152 INFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS 230 (554)
T ss_pred cceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence 34677899999999999999999999883 2332 567888889999999999888864
No 184
>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=82.08 E-value=1.9 Score=36.26 Aligned_cols=53 Identities=9% Similarity=0.213 Sum_probs=38.9
Q ss_pred eeeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 639 TIRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 639 ~ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
.|..+..++|+++++. -+|.+|++...+.. +......+++|+.++++|.++.+
T Consensus 8 ~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~-------~~~~~~~~~vG~~v~~kV~~id~ 62 (71)
T cd05696 8 KVTKVEPDLGAVFELKDGLLGFVHISHLSDDK-------VPSDTGPFKAGTTHKARIIGYSP 62 (71)
T ss_pred EEEEEccCceEEEEeCCCCEEEEEHHHCCcch-------hcCcccccCCCCEEEEEEEEEeC
Confidence 3555546899999995 47999988665433 22334568999999999998854
No 185
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=81.79 E-value=1.3 Score=42.41 Aligned_cols=31 Identities=23% Similarity=0.390 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHhhccCcccchhhhhhhhh
Q psy3754 31 LLTSRINDLNIHFKLHIKDHHSRRGLIMMKG 61 (755)
Q Consensus 31 ~lt~~I~~l~~h~~~~~kd~~~~~~l~~~v~ 61 (755)
.|-.|-.++..|++.|+||.+||++|.-.-+
T Consensus 87 ~LikKAv~iRkHLe~n~kD~~sK~~LiLiES 117 (148)
T PTZ00072 87 FLIKKAVSIRKHLEKNRKDKDSKFRLILVES 117 (148)
T ss_pred HHHHHHHHHHHHHHHcccchhhhHHHHHHHH
Confidence 3777888999999999999999999975544
No 186
>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=79.88 E-value=7.4 Score=36.62 Aligned_cols=63 Identities=17% Similarity=0.095 Sum_probs=43.6
Q ss_pred ccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcc-c-----------c-cCcccccCCCCEEEEEEEEEcC
Q psy3754 683 VQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSK-R-----------V-NIITDFLKENQKVRVKVLGIDD 745 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~-~-----------~-~~~~~~~kvGd~V~VkV~~id~ 745 (755)
+-+|++..|+|++-..-|+.|.|.---+=+||.+.|... + . ..-.-.+..|+.|+.||.++..
T Consensus 1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f 76 (122)
T PF08292_consen 1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF 76 (122)
T ss_dssp --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence 357999999999999999999984345677777777532 1 1 2334468999999999998753
No 187
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=79.52 E-value=3.7 Score=47.97 Aligned_cols=61 Identities=26% Similarity=0.455 Sum_probs=48.3
Q ss_pred eEEeeCC-cccceeeccccceeeeeccccceEEeecCc-eeEEEEecChhhhHHHHHHHHHhh
Q psy3754 620 ITIKIDP-SKIRDVIGKGGSTIRTLTEETGTQIDINDE-GIITIASFNSVSGQEAKRRIEKLT 680 (755)
Q Consensus 620 ~~~~i~~-~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~-G~v~i~~~~~~~~~~a~~~i~~~~ 680 (755)
.++.+|. +..+.+||..|.|||.+..-||+.|-|||+ +.|.+|+.+....+-|+..++.++
T Consensus 206 ~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~fdp~rreia~~~l~~li 268 (514)
T TIGR03319 206 SVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPVRREIARMALEKLI 268 (514)
T ss_pred eeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCCCeEEecCCchHHHHHHHHHHHHHH
Confidence 4566765 566779999999999999999999999875 678888888887777776554444
No 188
>PRK15464 cold shock-like protein CspH; Provisional
Probab=79.17 E-value=5.5 Score=33.68 Aligned_cols=54 Identities=26% Similarity=0.283 Sum_probs=38.7
Q ss_pred EEEEEEEEEe---eeEEEEEcC-CeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCc
Q psy3754 689 YTGIVLRLFD---FGAIIRILS-GKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGR 748 (755)
Q Consensus 689 ~~G~V~~I~~---fG~FVel~~-g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gk 748 (755)
++|+|+.-.+ || |+.-.+ +.+-|+|+|.|..... +.+.+||.|...+.. +++|.
T Consensus 5 ~~G~Vk~fn~~KGfG-FI~~~~g~~DvFvH~s~l~~~g~----~~l~~G~~V~f~v~~-~~kG~ 62 (70)
T PRK15464 5 MTGIVKTFDRKSGKG-FIIPSDGRKEVQVHISAFTPRDA----EVLIPGLRVEFCRVN-GLRGP 62 (70)
T ss_pred ceEEEEEEECCCCeE-EEccCCCCccEEEEehhehhcCC----CCCCCCCEEEEEEEE-CCCCc
Confidence 5799999843 55 565444 5899999999964422 348999999999876 33453
No 189
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=77.55 E-value=3.3 Score=43.14 Aligned_cols=53 Identities=38% Similarity=0.497 Sum_probs=46.0
Q ss_pred eEEeeCCcccceeeccccceeeeeccccceEEeecCceeEEEEecChhhhHHH
Q psy3754 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEA 672 (755)
Q Consensus 620 ~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~G~v~i~~~~~~~~~~a 672 (755)
..+.|+|.|...+||++|..++-+.+++++.|-++.+|.+.+...+......+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG~IWV~~~~~~~e~~~ 200 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNGRIWVDGENESLEELA 200 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecCCEEEecCCCcchHHHH
Confidence 35789999999999999999999999999999999999999998887433333
No 190
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=77.33 E-value=7.1 Score=32.81 Aligned_cols=50 Identities=28% Similarity=0.364 Sum_probs=36.8
Q ss_pred EEEEEEEEEE---eeeEEEEE-cCCeeEEEeccccCcccccCcccccCCCCEEEEEEEE
Q psy3754 688 VYTGIVLRLF---DFGAIIRI-LSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLG 742 (755)
Q Consensus 688 ~~~G~V~~I~---~fG~FVel-~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~ 742 (755)
.++|+|+... .|| |+.- .++.+-|+|+|.+..... +.+.+||.|...+..
T Consensus 3 ~~~G~Vk~f~~~kGyG-FI~~~~g~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~ 56 (69)
T PRK09507 3 KIKGNVKWFNESKGFG-FITPEDGSKDVFVHFSAIQTNGF----KTLAEGQRVEFEITN 56 (69)
T ss_pred ccceEEEEEeCCCCcE-EEecCCCCeeEEEEeecccccCC----CCCCCCCEEEEEEEE
Confidence 4679999874 466 4554 345899999999965422 348899999998776
No 191
>PRK00106 hypothetical protein; Provisional
Probab=77.29 E-value=5.3 Score=46.75 Aligned_cols=61 Identities=26% Similarity=0.498 Sum_probs=48.5
Q ss_pred eEEeeCC-cccceeeccccceeeeeccccceEEeecCc-eeEEEEecChhhhHHHHHHHHHhh
Q psy3754 620 ITIKIDP-SKIRDVIGKGGSTIRTLTEETGTQIDINDE-GIITIASFNSVSGQEAKRRIEKLT 680 (755)
Q Consensus 620 ~~~~i~~-~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~-G~v~i~~~~~~~~~~a~~~i~~~~ 680 (755)
.++.+|. +..+.+||..|.|||.+..-||+.+-|||+ +.|.+|+.+....+-|+..++.++
T Consensus 227 s~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp~~v~lS~fdpvRReiAr~~le~Li 289 (535)
T PRK00106 227 TTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTPEVVVLSGFDPIRREIARMTLESLI 289 (535)
T ss_pred eeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCCCeEEEeCCChHHHHHHHHHHHHHH
Confidence 4566765 566789999999999999999999999865 668888888888777776655444
No 192
>PRK15463 cold shock-like protein CspF; Provisional
Probab=77.20 E-value=6.8 Score=33.07 Aligned_cols=54 Identities=28% Similarity=0.318 Sum_probs=38.0
Q ss_pred EEEEEEEEEe-eeE-EEEEc-CCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCC
Q psy3754 689 YTGIVLRLFD-FGA-IIRIL-SGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRG 747 (755)
Q Consensus 689 ~~G~V~~I~~-fG~-FVel~-~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~g 747 (755)
+.|+|+.-.+ -|. |++-. ++.+-|+|+|.+..... ..+++||.|...+.. +.+|
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~----~~l~~G~~V~f~v~~-~~~G 61 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDA----EELTTGLRVEFCRIN-GLRG 61 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCC----CCCCCCCEEEEEEEE-CCCC
Confidence 4799999843 333 56544 45899999999975422 348899999998765 3344
No 193
>PRK13764 ATPase; Provisional
Probab=77.06 E-value=0.79 Score=54.30 Aligned_cols=143 Identities=17% Similarity=0.244 Sum_probs=86.2
Q ss_pred hhHHHHHHHHhhccccccccccCCCceeEEeeCCcccceeeccccceeeeeccccceEEeecCceeEEEEecC-hhhhHH
Q psy3754 593 GLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFN-SVSGQE 671 (755)
Q Consensus 593 ~~~~I~~~~~~~l~~~r~~~~~~~P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~G~v~i~~~~-~~~~~~ 671 (755)
+...|.+.+++.+..+ -++.---+....+.++.+.|..+||+||++|+.|.+++|..|++.....-...... .....
T Consensus 457 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~- 534 (602)
T PRK13764 457 AEKEIEREIKRYLPGP-VEVEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEPGEEAEEGEEVT- 534 (602)
T ss_pred HHHHHHHHHHHhcCCc-eEEEEecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccccccccccCccc-
Confidence 3556777777777333 23433345556788999999999999999999999999999998521111100000 00000
Q ss_pred HHHHHHHhhhcccCCcEEEEEEEEEEeeeEEEEE-cCCeeEEEeccccCcccccCcccccCCCCEEEEEE
Q psy3754 672 AKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRI-LSGKDGLLHISQISSKRVNIITDFLKENQKVRVKV 740 (755)
Q Consensus 672 a~~~i~~~~~~~~~G~~~~G~V~~I~~fG~FVel-~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV 740 (755)
-.....-.-+.+|.-|.|+.+.|.--|=|+-. .-+-.|-+|++.=+. -.....+.++-|..|.+++
T Consensus 535 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~g~i~~~~~~~-~~~~~~~~~~~~~~i~~~~ 601 (602)
T PRK13764 535 --VEETKKHVILIVGPDYAGKTVDVYAGGEYLFTATVSRKGEIKVAKNSA-IAKELLRAIDEGEDIRVRP 601 (602)
T ss_pred --eEEeccEEEEEcChhhCCCeEEEEECCEEEEEEEcCCCceEEeccCCh-HHHHHHHHHhCCCcEEEee
Confidence 00000011246677788888888666655433 346678888765321 1234456688888888764
No 194
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=76.27 E-value=10 Score=34.40 Aligned_cols=61 Identities=16% Similarity=0.294 Sum_probs=47.2
Q ss_pred CcEEEEEEEEEEeeeEE-EEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEE
Q psy3754 686 GKVYTGIVLRLFDFGAI-IRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKL 751 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~F-Vel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~L 751 (755)
...+.|+|+.....+.| |++.+|..-|+|++- ++++ .--++.||.|.|.....|. +|+|..
T Consensus 20 e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~G----K~Rk-~IwI~~GD~VlVe~~~~~~~kg~Iv~ 82 (100)
T PRK04012 20 EGEVFGVVEQMLGANRVRVRCMDGVERMGRIPG----KMKK-RMWIREGDVVIVAPWDFQDEKADIIW 82 (100)
T ss_pred CCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEch----hhcc-cEEecCCCEEEEEecccCCCEEEEEE
Confidence 34588999999999987 688899999999873 2333 3348999999999888876 676654
No 195
>KOG2190|consensus
Probab=76.11 E-value=1.9 Score=49.86 Aligned_cols=63 Identities=27% Similarity=0.408 Sum_probs=45.5
Q ss_pred CceeEEeeCCcccceeeccccceeeeeccccceEEeecCc-------eeEEEEecChhhhHHHHHHHHHhh
Q psy3754 617 PRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDE-------GIITIASFNSVSGQEAKRRIEKLT 680 (755)
Q Consensus 617 P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~-------G~v~i~~~~~~~~~~a~~~i~~~~ 680 (755)
|..--+-|+-.+++-+||+||+.||.|.++||++|-+-.+ -.|.|+.. ..++.+|...+-..+
T Consensus 137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~-~~av~~al~~Is~~L 206 (485)
T KOG2190|consen 137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGE-PDAVKKALVQISSRL 206 (485)
T ss_pred ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCc-hHHHHHHHHHHHHHH
Confidence 5666677899999999999999999999999999987432 23555443 345555555554333
No 196
>KOG2193|consensus
Probab=74.54 E-value=2.7 Score=46.56 Aligned_cols=62 Identities=29% Similarity=0.430 Sum_probs=42.5
Q ss_pred HHHhhhHHHHHHHHhhccccccccccCCCceeEEeeCCcccceeeccccceeeeeccccceEEeec
Q psy3754 589 KAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN 654 (755)
Q Consensus 589 ~A~~~~~~I~~~~~~~l~~~r~~~~~~~P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~ 654 (755)
.+.++|..|++.|.+--.... +..-.|.- +.-.....+.+||+.|.++|+|..+||++|.|.
T Consensus 255 g~s~Ac~~ILeimqkEA~~~k--~~~e~pLk--~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis 316 (584)
T KOG2193|consen 255 GTSKACKMILEIMQKEAVDDK--VAEEIPLK--ILAHNNLVGRLIGKEGRNLKKIEQDTGTKITIS 316 (584)
T ss_pred chHHHHHHHHHHHHHhhhccc--hhhhcchh--hhhhcchhhhhhhhccccHHHHHhhcCCceeee
Confidence 466778899999877544432 22222311 112344577899999999999999999999874
No 197
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=74.40 E-value=11 Score=38.36 Aligned_cols=102 Identities=19% Similarity=0.229 Sum_probs=60.4
Q ss_pred ccccceEEeec--CceeEEEEecChhhhHHHHHHHH---Hhh--hcccCCcEEEEEEEEEE--eeeEEEEEc----CCee
Q psy3754 644 TEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIE---KLT--ESVQIGKVYTGIVLRLF--DFGAIIRIL----SGKD 710 (755)
Q Consensus 644 ~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~---~~~--~~~~~G~~~~G~V~~I~--~fG~FVel~----~g~~ 710 (755)
+.++.++++|. .+--..++-...+....|+...+ .+. .+++.|++|-|+..... .||++|.+. ...+
T Consensus 27 lgdl~vk~eisvt~~~w~~itleGed~e~sanli~eefgei~sl~~~~~Gdv~vGrl~~l~~vgyg~yvdigV~~p~~~d 106 (247)
T COG4044 27 LGDLDVKVEISVTKKQWAKITLEGEDEEVSANLIVEEFGEIPSLSKVEEGDVYVGRLIDLGKVGYGAYVDIGVLGPRPKD 106 (247)
T ss_pred hhceeEEEEEEeecccceEEEEECccHHHHHHHHHHHhCCCCccccCCCCcEEEEEEeeeccceeEEEccccccCCCccc
Confidence 33455555543 33334444333333333333332 222 57789999999999984 588898873 2489
Q ss_pred EEEeccccCcccccCc----ccccCC--CCEEEEEEEEEcC
Q psy3754 711 GLLHISQISSKRVNII----TDFLKE--NQKVRVKVLGIDD 745 (755)
Q Consensus 711 Gllhisel~~~~~~~~----~~~~kv--Gd~V~VkV~~id~ 745 (755)
+|+|.-+|....-++| .+.|-- --.|+|-|.++|.
T Consensus 107 alvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~evnk 147 (247)
T COG4044 107 ALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEVNK 147 (247)
T ss_pred ccccHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEeccc
Confidence 9999988865554444 222333 3346667777765
No 198
>PRK10943 cold shock-like protein CspC; Provisional
Probab=74.30 E-value=9 Score=32.19 Aligned_cols=50 Identities=28% Similarity=0.382 Sum_probs=37.0
Q ss_pred EEEEEEEEEEe---eeEEEEEc-CCeeEEEeccccCcccccCcccccCCCCEEEEEEEE
Q psy3754 688 VYTGIVLRLFD---FGAIIRIL-SGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLG 742 (755)
Q Consensus 688 ~~~G~V~~I~~---fG~FVel~-~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~ 742 (755)
.++|+|+.-.+ || |++-. ++.+-|+|+|.+..... +.+..||.|...+..
T Consensus 3 ~~~G~Vk~f~~~kGfG-FI~~~~g~~dvFvH~s~l~~~g~----~~l~~G~~V~f~~~~ 56 (69)
T PRK10943 3 KIKGQVKWFNESKGFG-FITPADGSKDVFVHFSAIQGNGF----KTLAEGQNVEFEIQD 56 (69)
T ss_pred ccceEEEEEeCCCCcE-EEecCCCCeeEEEEhhHccccCC----CCCCCCCEEEEEEEE
Confidence 46899998743 55 55543 46899999999975432 348899999998765
No 199
>PRK09890 cold shock protein CspG; Provisional
Probab=73.80 E-value=10 Score=31.91 Aligned_cols=54 Identities=35% Similarity=0.481 Sum_probs=38.1
Q ss_pred EEEEEEEEE---eeeEEEEEcC-CeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCc
Q psy3754 689 YTGIVLRLF---DFGAIIRILS-GKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGR 748 (755)
Q Consensus 689 ~~G~V~~I~---~fG~FVel~~-g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gk 748 (755)
+.|+|+... .|| |++-.+ +.+-|+|+|.+...-. +.+++||.|...+.. +++|.
T Consensus 5 ~~G~Vk~f~~~kGfG-FI~~~~g~~dvFvH~s~l~~~~~----~~l~~G~~V~f~~~~-~~~G~ 62 (70)
T PRK09890 5 MTGLVKWFNADKGFG-FITPDDGSKDVFVHFTAIQSNEF----RTLNENQKVEFSIEQ-GQRGP 62 (70)
T ss_pred ceEEEEEEECCCCcE-EEecCCCCceEEEEEeeeccCCC----CCCCCCCEEEEEEEE-CCCCc
Confidence 579999874 466 555444 5899999999975532 348899999997755 33453
No 200
>KOG3013|consensus
Probab=73.55 E-value=3.3 Score=43.24 Aligned_cols=71 Identities=23% Similarity=0.327 Sum_probs=57.7
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCc--c--cc------cCcccccCCCCEEEEEEEEEcCCCcEEE
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISS--K--RV------NIITDFLKENQKVRVKVLGIDDRGRIKL 751 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~--~--~~------~~~~~~~kvGd~V~VkV~~id~~gki~L 751 (755)
.+++||++-|+|..|...-+=|++....++.|..|.+.- . |- ...+++|+.||-|.+.|-.+-.+|-+.|
T Consensus 82 ~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~dGs~sL 161 (301)
T KOG3013|consen 82 APEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFHDGSLSL 161 (301)
T ss_pred CCccCCEEEEEeeeeecceeEEecccccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhccCCeEEE
Confidence 478999999999999999999999889999999997642 1 11 1456789999999998887755777766
Q ss_pred E
Q psy3754 752 S 752 (755)
Q Consensus 752 S 752 (755)
-
T Consensus 162 h 162 (301)
T KOG3013|consen 162 H 162 (301)
T ss_pred E
Confidence 4
No 201
>PRK12704 phosphodiesterase; Provisional
Probab=73.23 E-value=8.1 Score=45.31 Aligned_cols=61 Identities=25% Similarity=0.454 Sum_probs=47.1
Q ss_pred eEEeeCC-cccceeeccccceeeeeccccceEEeecCc-eeEEEEecChhhhHHHHHHHHHhh
Q psy3754 620 ITIKIDP-SKIRDVIGKGGSTIRTLTEETGTQIDINDE-GIITIASFNSVSGQEAKRRIEKLT 680 (755)
Q Consensus 620 ~~~~i~~-~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~-G~v~i~~~~~~~~~~a~~~i~~~~ 680 (755)
.++.+|. +.-+.+||..|.|||.+..-||+.|-|||+ +.|.+|+.+....+-|+..++.++
T Consensus 212 ~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~~~~~rre~a~~~l~~l~ 274 (520)
T PRK12704 212 SVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPIRREIARLALEKLV 274 (520)
T ss_pred eeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCCCeEEEecCChhhHHHHHHHHHHHH
Confidence 3556765 556779999999999999999999999875 667888878777666666554444
No 202
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=73.18 E-value=10 Score=32.47 Aligned_cols=53 Identities=30% Similarity=0.319 Sum_probs=37.4
Q ss_pred EEEEEEEE---eeeEEEEE-cCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCc
Q psy3754 690 TGIVLRLF---DFGAIIRI-LSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGR 748 (755)
Q Consensus 690 ~G~V~~I~---~fG~FVel-~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gk 748 (755)
+|+|+... -|| |+.- .++.+-|+|+|.+...-. ..+..||.|...+..- ++|+
T Consensus 3 ~G~Vkwfn~~KGfG-FI~~~~gg~dVFvH~s~i~~~g~----~~l~~G~~V~f~~~~~-~~G~ 59 (74)
T PRK09937 3 KGTVKWFNNAKGFG-FICPEGGGEDIFAHYSTIQMDGY----RTLKAGQSVQFDVHQG-PKGN 59 (74)
T ss_pred CeEEEEEeCCCCeE-EEeeCCCCccEEEEEeeccccCC----CCCCCCCEEEEEEEEC-CCCc
Confidence 48888874 355 5544 446999999999964422 3489999999998763 3554
No 203
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=72.68 E-value=2.1 Score=43.19 Aligned_cols=59 Identities=29% Similarity=0.378 Sum_probs=46.5
Q ss_pred cceeeccccceeeeeccccceEEeecCceeEEEEecChhhhHHHHHHHHHhhhcccCCcEE
Q psy3754 629 IRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVY 689 (755)
Q Consensus 629 i~~~IG~gGk~ik~i~~~~g~~I~i~~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~ 689 (755)
.+.+||++|++-+.|++-||+.|.+-+ -+|+|... ...++.|++.++.++..-+.|.+|
T Consensus 113 kgRIIG~~GkTr~~IE~lt~~~I~V~g-~tVaiiG~-~~~v~iAr~AVemli~G~~h~~Vy 171 (194)
T COG1094 113 KGRIIGREGKTRRAIEELTGVYISVYG-KTVAIIGG-FEQVEIAREAVEMLINGAPHGKVY 171 (194)
T ss_pred hceeeCCCchHHHHHHHHhCCeEEEeC-cEEEEecC-hhhhHHHHHHHHHHHcCCCchhHH
Confidence 456999999999999989999998754 35666544 567788899898888777777666
No 204
>PRK08582 hypothetical protein; Provisional
Probab=72.68 E-value=5.2 Score=38.44 Aligned_cols=53 Identities=15% Similarity=0.323 Sum_probs=40.1
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEeee
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFG 700 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~fG 700 (755)
|..| ..+|++|+++ .+|.||++...+... ......+++|+.++++|.+|..-|
T Consensus 13 V~~I-~~fG~fV~L~~~~~GlVhiSels~~~v-------~~~~~~l~vGD~VkvkV~~id~~g 67 (139)
T PRK08582 13 VTGI-TNFGAFVELPEGKTGLVHISEVADNYV-------KDINDHLKVGDEVEVKVLNVEDDG 67 (139)
T ss_pred EEEE-ECCeEEEEECCCCEEEEEeeccCcccc-------cccccccCCCCEEEEEEEEECCCC
Confidence 4444 5799999997 589999998876543 223356899999999999986433
No 205
>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=71.16 E-value=11 Score=32.49 Aligned_cols=58 Identities=22% Similarity=0.352 Sum_probs=44.9
Q ss_pred EEEEEEEEEeeeEE-EEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEE
Q psy3754 689 YTGIVLRLFDFGAI-IRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKL 751 (755)
Q Consensus 689 ~~G~V~~I~~fG~F-Vel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~L 751 (755)
..|+|+.....+.| |++.+|..-|.|++- ++++ .--++.||.|.|.....|. +|+|..
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g~~~la~i~g----K~rk-~iwI~~GD~V~Ve~~~~d~~kg~Iv~ 61 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDGKKRLCRIRG----KMRK-RVWINEGDIVLVAPWDFQDDKADIIY 61 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEEch----hhcc-cEEEcCCCEEEEEeccccCCEEEEEE
Confidence 57999999999987 688889999999874 2232 3348999999999887776 677654
No 206
>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=70.46 E-value=8.1 Score=32.82 Aligned_cols=49 Identities=18% Similarity=0.422 Sum_probs=36.4
Q ss_pred eeeeccccceEEeec---CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEeeeEE
Q psy3754 640 IRTLTEETGTQIDIN---DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAI 702 (755)
Q Consensus 640 ik~i~~~~g~~I~i~---~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~fG~F 702 (755)
|+.| +++|++++++ -+|.++.+..++. ..+++|+.+.++|.++.+.+--
T Consensus 12 V~si-~d~G~~v~~g~~gv~Gfl~~~~~~~~-------------~~~~~Gq~v~~~V~~vd~~~~~ 63 (74)
T cd05694 12 VSSV-EDHGYILDIGIPGTTGFLPKKDAGNF-------------SKLKVGQLLLCVVEKVKDDGRV 63 (74)
T ss_pred EEEE-eCCEEEEEeCCCCcEEEEEHHHCCcc-------------cccCCCCEEEEEEEEEECCCCE
Confidence 6666 5899999986 2677776555433 5689999999999999755433
No 207
>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=70.06 E-value=6.3 Score=33.28 Aligned_cols=53 Identities=13% Similarity=0.202 Sum_probs=37.8
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
|+.+ .++|+++++. -+|.++++..++... ..+.....+++|+.++++|.++.+
T Consensus 8 V~~i-~~~g~~V~l~~~i~G~i~~~~ls~~~~-----~~~~~~~~~~vG~~v~~kV~~id~ 62 (73)
T cd05703 8 VNNV-SKEFVWLTISPDVKGRIPLLDLSDDVS-----VLEHPEKKFPIGQALKAKVVGVDK 62 (73)
T ss_pred EEEE-eCCEEEEEeCCCcEEEEEHHHcCCccc-----cccCHHHhCCCCCEEEEEEEEEeC
Confidence 4445 5789999995 489999887764310 122345569999999999999853
No 208
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=69.53 E-value=15 Score=31.00 Aligned_cols=53 Identities=34% Similarity=0.422 Sum_probs=37.7
Q ss_pred EEEEEEEE---EeeeEEEEEc-CCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCC
Q psy3754 689 YTGIVLRL---FDFGAIIRIL-SGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRG 747 (755)
Q Consensus 689 ~~G~V~~I---~~fG~FVel~-~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~g 747 (755)
..|+|+.. +.||. ++-. ++.+-|+|+|.+...-. +.+++||.|...+.. +++|
T Consensus 5 ~~G~Vk~f~~~kGfGF-I~~~~g~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~-~~~G 61 (70)
T PRK10354 5 MTGIVKWFNADKGFGF-ITPDDGSKDVFVHFSAIQNDGY----KSLDEGQKVSFTIES-GAKG 61 (70)
T ss_pred ceEEEEEEeCCCCcEE-EecCCCCccEEEEEeeccccCC----CCCCCCCEEEEEEEE-CCCC
Confidence 47999887 44664 5544 35899999999965422 348999999998765 3344
No 209
>KOG1004|consensus
Probab=68.62 E-value=23 Score=36.23 Aligned_cols=63 Identities=16% Similarity=0.050 Sum_probs=48.8
Q ss_pred cccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcc-cccCcccccCCCCEEEEEEEEEcCC
Q psy3754 682 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSK-RVNIITDFLKENQKVRVKVLGIDDR 746 (755)
Q Consensus 682 ~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~-~~~~~~~~~kvGd~V~VkV~~id~~ 746 (755)
.|.+||.|.|.|+.-..-+.-|+|.+...+.|+.-.+... +-..|+ +++||.|.+||...+++
T Consensus 62 iP~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~AtkrNrPn--l~vGdliyakv~~a~~~ 125 (230)
T KOG1004|consen 62 IPVKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGATKRNRPN--LQVGDLIYAKVVDANKD 125 (230)
T ss_pred cCCCCCEEEEEEEeccCceEEEecCCCCeeeeeeccccCccccCCCc--cccccEEEEEEEecCCC
Confidence 3789999999999998888889987767777776555432 223444 99999999999987653
No 210
>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=67.25 E-value=13 Score=31.14 Aligned_cols=48 Identities=33% Similarity=0.340 Sum_probs=34.7
Q ss_pred EEEEEEEE---eeeEEEEEc-CCeeEEEeccccCcccccCcccccCCCCEEEEEEEE
Q psy3754 690 TGIVLRLF---DFGAIIRIL-SGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLG 742 (755)
Q Consensus 690 ~G~V~~I~---~fG~FVel~-~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~ 742 (755)
+|+|+... .|| |+.-. ++.+-++|+|.+..... +.++.||.|...+..
T Consensus 3 ~G~Vk~f~~~kGfG-FI~~~~g~~dvfvH~s~~~~~g~----~~l~~G~~V~f~~~~ 54 (68)
T TIGR02381 3 IGIVKWFNNAKGFG-FICPEGVDGDIFAHYSTIQMDGY----RTLKAGQKVQFEVVQ 54 (68)
T ss_pred CeEEEEEeCCCCeE-EEecCCCCccEEEEHHHhhhcCC----CCCCCCCEEEEEEEE
Confidence 48888863 455 55444 46899999999965422 348999999998765
No 211
>PRK14998 cold shock-like protein CspD; Provisional
Probab=67.21 E-value=15 Score=31.23 Aligned_cols=53 Identities=34% Similarity=0.349 Sum_probs=37.3
Q ss_pred EEEEEEEE---eeeEEEEE-cCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCc
Q psy3754 690 TGIVLRLF---DFGAIIRI-LSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGR 748 (755)
Q Consensus 690 ~G~V~~I~---~fG~FVel-~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gk 748 (755)
.|+|+.-. -|| |+.- .++.+-|+|+|.|.... ...+..||.|...+..- ++|+
T Consensus 3 ~G~Vkwfn~~kGfG-FI~~~~g~~dVFvH~s~l~~~g----~~~l~~G~~V~f~~~~~-~~G~ 59 (73)
T PRK14998 3 TGTVKWFNNAKGFG-FICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVRFDVHQG-PKGN 59 (73)
T ss_pred CeEEEEEeCCCceE-EEecCCCCccEEEEeeeecccC----CCCCCCCCEEEEEEEEC-CCCc
Confidence 48888874 355 5544 44689999999996442 24589999999998763 3453
No 212
>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=65.85 E-value=16 Score=32.91 Aligned_cols=65 Identities=11% Similarity=0.210 Sum_probs=43.3
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHH------------HHHhhhcccCCcEEEEEEEEEEee-----e
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRR------------IEKLTESVQIGKVYTGIVLRLFDF-----G 700 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~------------i~~~~~~~~~G~~~~G~V~~I~~f-----G 700 (755)
|+.+ .++|++|++. -+|.++++...+......... ...+...+++|+++.++|.++.+. .
T Consensus 11 V~~v-~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~d~~~~~~~~ 89 (100)
T cd05693 11 VKEI-TKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLDKSKSGKKR 89 (100)
T ss_pred EEEE-cCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEccCCcCCCcE
Confidence 4454 5789999984 589999887766543222211 112445689999999999999764 4
Q ss_pred EEEEE
Q psy3754 701 AIIRI 705 (755)
Q Consensus 701 ~FVel 705 (755)
+-+.|
T Consensus 90 i~LSl 94 (100)
T cd05693 90 IELSL 94 (100)
T ss_pred EEEEe
Confidence 55544
No 213
>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=64.30 E-value=25 Score=31.93 Aligned_cols=55 Identities=13% Similarity=0.202 Sum_probs=45.2
Q ss_pred ccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEc
Q psy3754 683 VQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGID 744 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id 744 (755)
...|.++.|+|..|.+--.|+++.....+.+.-.+... +.|..|++|.+++.+..
T Consensus 21 ~~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~~-------~~y~~G~rV~lrLkdlE 75 (104)
T PF10246_consen 21 DPEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVNG-------EKYVRGSRVRLRLKDLE 75 (104)
T ss_pred CccCCEEEEEEEEEecCceEEEeCCceeEEEecccccc-------cccccCCEEEEEECCHh
Confidence 35899999999999999999998888999988555432 34888999999987643
No 214
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=63.47 E-value=27 Score=30.51 Aligned_cols=60 Identities=17% Similarity=0.288 Sum_probs=45.4
Q ss_pred cEEEEEEEEEEeeeEE-EEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEE
Q psy3754 687 KVYTGIVLRLFDFGAI-IRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKL 751 (755)
Q Consensus 687 ~~~~G~V~~I~~fG~F-Vel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~L 751 (755)
..+.|+|+.....+.| |.+.+|..=|+|++- ++++ .--++.||.|.|.....+. +|.|..
T Consensus 5 ~q~~g~V~~~lG~~~~~V~~~dG~~~la~ipg----K~Rk-~iwI~~GD~VlVe~~~~~~~kg~Iv~ 66 (83)
T smart00652 5 GQEIAQVVKMLGNGRLEVMCADGKERLARIPG----KMRK-KVWIRRGDIVLVDPWDFQDVKADIIY 66 (83)
T ss_pred CcEEEEEEEEcCCCEEEEEECCCCEEEEEEch----hhcc-cEEEcCCCEEEEEecCCCCCEEEEEE
Confidence 4478999999999987 677889999999874 2222 3348999999998877665 666654
No 215
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=63.29 E-value=3.9 Score=46.31 Aligned_cols=60 Identities=27% Similarity=0.431 Sum_probs=47.4
Q ss_pred hHHHHHHHHhhccccccccccCCCceeEEeeCCcccceeeccccceeeeeccccceEEeec
Q psy3754 594 LSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN 654 (755)
Q Consensus 594 ~~~I~~~~~~~l~~~r~~~~~~~P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~ 654 (755)
...|.+.+++.+.. ..+++---+....+.+|++-|..+||++|++|+.|..++|.+|++.
T Consensus 463 ~~~i~~~i~r~~p~-~~eVe~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~ 522 (604)
T COG1855 463 EEEIEREIKRYLPG-DVEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVK 522 (604)
T ss_pred HHHHHHHHHHhCCC-CceEEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEE
Confidence 45566677777775 2334444566677899999999999999999999999999999885
No 216
>KOG2192|consensus
Probab=62.86 E-value=9.3 Score=40.06 Aligned_cols=50 Identities=30% Similarity=0.473 Sum_probs=34.9
Q ss_pred CcccceeeccccceeeeeccccceEEeecC----ceeEEEEecChhhhHHHHHH
Q psy3754 626 PSKIRDVIGKGGSTIRTLTEETGTQIDIND----EGIITIASFNSVSGQEAKRR 675 (755)
Q Consensus 626 ~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~----~G~v~i~~~~~~~~~~a~~~ 675 (755)
...-+.+||+||+|||.+..+|++.|.+-| +-..+|++..+...+-.++.
T Consensus 56 sk~agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad~~ti~~ilk~i 109 (390)
T KOG2192|consen 56 SKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISADIETIGEILKKI 109 (390)
T ss_pred cccccceeccccccHHHHhhhccceeeccCCCCCceeEEEeccHHHHHHHHHHH
Confidence 334678999999999999999999998742 44566665544444433333
No 217
>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=60.99 E-value=14 Score=30.21 Aligned_cols=51 Identities=6% Similarity=0.293 Sum_probs=38.2
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
|+.+ .++|+++++. -+|.++++..++... +.....+++|+.++++|.++.+
T Consensus 8 V~~v-~~~Gv~V~l~~~~~G~v~~s~l~~~~~-------~~~~~~~~~Gd~v~~~v~~~d~ 60 (68)
T cd05707 8 VKNI-ANNGVFVTLGRGVDARVRVSELSDSYL-------KDWKKRFKVGQLVKGKIVSIDP 60 (68)
T ss_pred EEEE-ECccEEEEeCCCCEEEEEHHHCCchhh-------cCHhhccCCCCEEEEEEEEEeC
Confidence 4455 4799999985 589999887765432 2334568999999999999865
No 218
>KOG2193|consensus
Probab=59.65 E-value=7 Score=43.49 Aligned_cols=33 Identities=33% Similarity=0.564 Sum_probs=29.4
Q ss_pred EEeeCCcccceeeccccceeeeeccccceEEee
Q psy3754 621 TIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI 653 (755)
Q Consensus 621 ~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i 653 (755)
-+.+|..-++.+||+|||++++++.-|++.+-+
T Consensus 496 hirVPs~~aGRvIGKGGktVnELQnlt~AeV~v 528 (584)
T KOG2193|consen 496 HIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVV 528 (584)
T ss_pred eeeccchhhhhhhccccccHHHHhccccceEEc
Confidence 357888899999999999999999999988876
No 219
>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha. A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase.
Probab=58.99 E-value=1e+02 Score=36.01 Aligned_cols=164 Identities=20% Similarity=0.225 Sum_probs=93.8
Q ss_pred EEeEeeccccCCCCCCcccccCCCCchhhHHHHHhcCccc--ccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHh
Q psy3754 124 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIR--PLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTAL 201 (755)
Q Consensus 124 v~y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lr--pl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL 201 (755)
.-|||-.-+.|++|+ |+|=|.+-=-+.+||++|+=+ ....++ .+...-+|+--.++..
T Consensus 268 ~A~REisL~lgepPg----r~gYPg~vF~~~srLlERag~~~~~~~~G---SITal~~V~~~~dD~s------------- 327 (497)
T TIGR03324 268 RAYRELSLLLRRPPG----REAFPGDIFYVHSRLLERSTHLNEELGGG---SLTALPIIETEAQNIS------------- 327 (497)
T ss_pred HHHHHHHhhccCCCc----cCcCCccHHHHhHHHHHhhhhccCCCCCc---ceeEEEEEEcCCCCCC-------------
Confidence 446888889999998 667788777889999999865 222233 6666656665554433
Q ss_pred hcCCCCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CcccEEEEeecCceEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy3754 202 SISELPFLGPLGVAKVGYIDGKYILNPTTEQLKK-SHLDLLVAGTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAIN 280 (755)
Q Consensus 202 ~~s~IP~~~~vaav~vg~~~g~~vldPt~~E~~~-s~~~l~va~~~~~i~mie~~~~~~se~~~~~al~~a~~~~~~i~~ 280 (755)
.|++--..++.||+++++....+.-. ...|...+-++ + ++.-.+ ++........+..+.
T Consensus 328 --------~pI~d~v~sItDGqIvLsr~La~~G~~PAIDv~~SvSR---v----~~~~~~-----~~~~~~a~~lr~~la 387 (497)
T TIGR03324 328 --------AYIPTNLISITDGQIYLSPTLFELGVLPAVDVGKSVSR---V----GGKAQL-----AAYRAVAGDLKLAYA 387 (497)
T ss_pred --------CcchHhheeccceEEEEcHHHHhCCCCCcCCCcccccc---C----CccccC-----HHHHHHHHHHHHHHH
Confidence 34444445668999999987776644 33343333332 1 111111 233333344444455
Q ss_pred HHHHHH--HHhCCCcccCCCCCCChhHHHHHHHHHHHHHHHHHhcc--chhHHHHHHHHHH
Q psy3754 281 AINELV--QNVGQKKVNWDPIVKDKTLISKIINISEHKIRKAYQIK--NKQIRDLTFKNIS 337 (755)
Q Consensus 281 ~~~~~~--~~~~~~k~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~--~k~~r~~~~~~~~ 337 (755)
.++++. ...|.. .+++....++. ..+|++.+++. ....-.+.+..+.
T Consensus 388 ~y~e~e~~~~~G~~--------ld~~~~~~i~~--~~~i~~fL~Q~~~~~~~~~~~~~~l~ 438 (497)
T TIGR03324 388 QFEELETFARFGAR--------LDENTRKTIEH--GRRIRACLKQTQSSPLTVPQQIAILL 438 (497)
T ss_pred HHHHHHHHHHhhhh--------cCHHHHHHHHh--HHHHHHHhCCCCCCCCCHHHHHHHHH
Confidence 555443 223311 45566666653 67787777643 4444455555554
No 220
>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=58.46 E-value=69 Score=36.62 Aligned_cols=94 Identities=20% Similarity=0.238 Sum_probs=62.5
Q ss_pred EEeEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhc
Q psy3754 124 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSI 203 (755)
Q Consensus 124 v~y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~ 203 (755)
--|+|-.-+.|++|+ |+|=|..--.+++|+++|+=+- +. -...+...-+|+.-.++.+
T Consensus 244 ~A~REisl~~gepP~----~~gyp~~vf~~l~~L~ERag~~-~~--~~GSIT~~~tVl~~gdd~~--------------- 301 (418)
T TIGR03498 244 MAQREIGLAAGEPPV----ARGYTPSVFSELPRLLERAGPG-AE--GKGSITGIFTVLVDGDDHN--------------- 301 (418)
T ss_pred HHHHHHHHhcCCCCc----cccCCchhhhhhhHHHHHhccC-CC--CCcceeeeEEEeccCCCCC---------------
Confidence 346888888999998 5577777777899999998763 22 1237777777774433322
Q ss_pred CCCCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CcccEEEEee
Q psy3754 204 SELPFLGPLGVAKVGYIDGKYILNPTTEQLKK-SHLDLLVAGT 245 (755)
Q Consensus 204 s~IP~~~~vaav~vg~~~g~~vldPt~~E~~~-s~~~l~va~~ 245 (755)
+|++--..+..||+++++-...+... ...|...+.+
T Consensus 302 ------dpi~d~~~si~DG~ivLsr~la~~g~~PAIDv~~S~S 338 (418)
T TIGR03498 302 ------EPVADAVRGILDGHIVLDRAIAERGRYPAINVLASVS 338 (418)
T ss_pred ------CcchhhhheeeeeEEEECHHHHhCCCCCccCCccccc
Confidence 45555555678999999877766644 3344444433
No 221
>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=58.28 E-value=21 Score=29.59 Aligned_cols=51 Identities=10% Similarity=0.059 Sum_probs=37.2
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
|+.+ ..+|++++++ -+|.++++...+.... .....+++|+.++++|.++..
T Consensus 11 V~~v-~~~gi~v~l~~~~~g~v~~s~l~~~~~~-------~~~~~~~~Gd~v~~~V~~~d~ 63 (73)
T cd05706 11 VTKV-NDRYVLVQLGNKVTGPSFITDALDDYSE-------ALPYKFKKNDIVRACVLSVDV 63 (73)
T ss_pred EEEE-eCCeEEEEeCCCcEEEEEhhhccCcccc-------ccccccCCCCEEEEEEEEEeC
Confidence 4444 5689999886 5899999877654321 123458999999999999865
No 222
>PRK12705 hypothetical protein; Provisional
Probab=57.56 E-value=15 Score=42.78 Aligned_cols=61 Identities=30% Similarity=0.474 Sum_probs=45.2
Q ss_pred eEEeeCC-cccceeeccccceeeeeccccceEEeecCc-eeEEEEecChhhhHHHHHHHHHhh
Q psy3754 620 ITIKIDP-SKIRDVIGKGGSTIRTLTEETGTQIDINDE-GIITIASFNSVSGQEAKRRIEKLT 680 (755)
Q Consensus 620 ~~~~i~~-~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~-G~v~i~~~~~~~~~~a~~~i~~~~ 680 (755)
.++.+|. +.-+.+||..|.|||.+...||+.+-|+|. ..|.++..+....+.++..++.++
T Consensus 200 s~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp~~V~ls~fdp~rreia~~~l~~Li 262 (508)
T PRK12705 200 SVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTPEAVVISSFNPIRREIARLTLEKLL 262 (508)
T ss_pred eeeecCChHhhccccCccchhHHHHHHhhCCceEecCCccchhhcccCccchHHHHHHHHHHH
Confidence 3455654 556779999999999999999999989864 556777777766666666554444
No 223
>PRK05807 hypothetical protein; Provisional
Probab=56.97 E-value=12 Score=35.91 Aligned_cols=53 Identities=13% Similarity=0.271 Sum_probs=39.0
Q ss_pred eeeeccccceEEeec-CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEeee
Q psy3754 640 IRTLTEETGTQIDIN-DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFG 700 (755)
Q Consensus 640 ik~i~~~~g~~I~i~-~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~fG 700 (755)
|..| ..+|++++++ .+|.++++........ .....+++|+.++++|.++.+-|
T Consensus 13 Vt~i-~~~GafV~L~~~~Glvhiseis~~~v~-------~~~~~~kvGd~V~VkV~~id~~g 66 (136)
T PRK05807 13 VVNI-TNFGAFVEVEGKTGLVHISEVADTYVK-------DIREHLKEQDKVKVKVISIDDNG 66 (136)
T ss_pred EEEE-ECCeEEEEECCEEEEEEhhhccccccc-------CccccCCCCCEEEEEEEEECCCC
Confidence 4444 4799999996 4799999877654422 23345899999999999987544
No 224
>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=56.68 E-value=56 Score=26.58 Aligned_cols=57 Identities=30% Similarity=0.373 Sum_probs=39.6
Q ss_pred EEEEEEEEe---eeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcCCCcEEE
Q psy3754 690 TGIVLRLFD---FGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDDRGRIKL 751 (755)
Q Consensus 690 ~G~V~~I~~---fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~~gki~L 751 (755)
.|+|+...+ ||....-..+-+-++|.|++...- .+.+++||.|...+..- .+|....
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~----~~~~~~G~~V~f~~~~~-~~g~~A~ 61 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEG-DKGPQAV 61 (65)
T ss_pred cEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccC----CCcCCCCCEEEEEEEEC-CCCCeEE
Confidence 588888754 665544333799999999997542 24589999999988764 3454433
No 225
>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=56.49 E-value=42 Score=28.99 Aligned_cols=58 Identities=17% Similarity=0.232 Sum_probs=43.7
Q ss_pred EEEEEEEEEeeeEE-EEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEE-cC-CCcEEE
Q psy3754 689 YTGIVLRLFDFGAI-IRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGI-DD-RGRIKL 751 (755)
Q Consensus 689 ~~G~V~~I~~fG~F-Vel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~i-d~-~gki~L 751 (755)
.-|+|+.....+.| |++.+|..-|+|++- ++++- --++.||.|.|..... |. +|.|..
T Consensus 2 ~i~~V~~~lG~~~~~V~~~dg~~~l~~i~g----K~Rk~-iwI~~GD~VlV~~~~~~~~~kg~Iv~ 62 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECADGQRRLVSIPG----KLRKN-IWIKRGDFLIVDPIEEGEDVKADIIF 62 (78)
T ss_pred eEEEEEEECCCCEEEEEECCCCEEEEEEch----hhccC-EEEcCCCEEEEEecccCCCceEEEEE
Confidence 46899999999987 688889999999874 22221 3489999999998887 45 676654
No 226
>PRK00468 hypothetical protein; Provisional
Probab=55.96 E-value=4.4 Score=34.75 Aligned_cols=24 Identities=29% Similarity=0.641 Sum_probs=21.3
Q ss_pred EEeeCCcccceeeccccceeeeec
Q psy3754 621 TIKIDPSKIRDVIGKGGSTIRTLT 644 (755)
Q Consensus 621 ~~~i~~~ki~~~IG~gGk~ik~i~ 644 (755)
.+.++++-++.+||++|+++++|.
T Consensus 33 ~l~v~~~D~GrVIGk~Gr~i~AIR 56 (75)
T PRK00468 33 ELKVAPEDMGKVIGKQGRIAKAIR 56 (75)
T ss_pred EEEEChhhCcceecCCChhHHHHH
Confidence 467889999999999999999874
No 227
>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=55.92 E-value=20 Score=29.91 Aligned_cols=47 Identities=17% Similarity=0.301 Sum_probs=35.4
Q ss_pred cccceEEeec----CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 645 EETGTQIDIN----DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 645 ~~~g~~I~i~----~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
..+|+++++. -+|.++++..++.... .....+++|+.++.+|.++..
T Consensus 15 ~~~g~~v~l~~~~~~~gll~~s~l~~~~~~-------~~~~~~~~Gd~v~vkv~~~d~ 65 (76)
T cd04452 15 ADMGAYVSLLEYGNIEGMILLSELSRRRIR-------SIRKLVKVGRKEVVKVIRVDK 65 (76)
T ss_pred EccEEEEEEcCCCCeEEEEEhHHcCCcccC-------CHHHeeCCCCEEEEEEEEEEC
Confidence 4799999985 4799999876654322 234458999999999999865
No 228
>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=55.53 E-value=28 Score=35.83 Aligned_cols=104 Identities=14% Similarity=0.168 Sum_probs=58.4
Q ss_pred ccceEEee--cCceeEEEEecChhhhHHHHHHHHH----hhhcccC--CcEEEEEEEEEEeeeEEEEEcCCeeEEEeccc
Q psy3754 646 ETGTQIDI--NDEGIITIASFNSVSGQEAKRRIEK----LTESVQI--GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQ 717 (755)
Q Consensus 646 ~~g~~I~i--~~~G~v~i~~~~~~~~~~a~~~i~~----~~~~~~~--G~~~~G~V~~I~~fG~FVel~~g~~Gllhise 717 (755)
++.++.+| .+++.++++-...+.-- |...+.+ +...++. |++|.|++.+..+-|.-+.+. |...-+|.++
T Consensus 28 dLdV~~~i~~~~~~wv~vtl~GeD~ev-a~Nll~eefGei~~~le~v~Ge~y~G~l~s~~~~G~~~~v~-G~~~~ip~d~ 105 (225)
T PF09883_consen 28 DLDVEWDIGITKDDWVKVTLEGEDEEV-AANLLREEFGEIVYSLEPVKGETYVGTLISWDEDGYGVDVD-GIFVPIPKDE 105 (225)
T ss_pred CeeEEEEeccccCCceEEEEecCcHHH-HHHHHHHHhCCCCchhcccCCceEEEEEEeecccceEEEee-cccccCcHHH
Confidence 34455444 47788777766555433 3333322 2233455 999999999998777666665 7777777777
Q ss_pred cCc---ccccCcccccCCCCE--EEEEEEEEcCCCcEEE
Q psy3754 718 ISS---KRVNIITDFLKENQK--VRVKVLGIDDRGRIKL 751 (755)
Q Consensus 718 l~~---~~~~~~~~~~kvGd~--V~VkV~~id~~gki~L 751 (755)
|.. ...+.+.+.|-.=|- |++++...+.....+|
T Consensus 106 L~~Lg~g~~~Qi~~rFG~V~hlPvev~~v~~~~~~~~rl 144 (225)
T PF09883_consen 106 LKPLGPGSPRQIRRRFGLVQHLPVEVEFVKVEDGIEARL 144 (225)
T ss_pred hcccCCCCHHHHHHHhCcccCCceEEEEEEcccCccccc
Confidence 622 222222333433333 4477777654333333
No 229
>PRK02821 hypothetical protein; Provisional
Probab=55.08 E-value=4.5 Score=34.88 Aligned_cols=25 Identities=32% Similarity=0.780 Sum_probs=21.9
Q ss_pred eEEeeCCcccceeeccccceeeeec
Q psy3754 620 ITIKIDPSKIRDVIGKGGSTIRTLT 644 (755)
Q Consensus 620 ~~~~i~~~ki~~~IG~gGk~ik~i~ 644 (755)
..+.++++-++.+||++|+++++|.
T Consensus 33 i~l~v~~~D~GrVIGk~Gr~i~AIR 57 (77)
T PRK02821 33 LEVRVHPDDLGKVIGRGGRTATALR 57 (77)
T ss_pred EEEEEChhhCcceeCCCCchHHHHH
Confidence 4567899999999999999999874
No 230
>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=54.65 E-value=18 Score=29.67 Aligned_cols=53 Identities=30% Similarity=0.469 Sum_probs=36.2
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEeee
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFG 700 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~fG 700 (755)
|..+ .++|+++++. .+|.++++...+.. ....-..+++|+.++++|.++.+-+
T Consensus 8 V~~i-~~~~~~v~l~~~~~g~l~~~e~~~~~-------~~~~~~~~~~Gd~i~~~i~~~~~~~ 62 (70)
T cd05687 8 VVSV-DDDEVLVDIGYKSEGIIPISEFSDDP-------IENGEDEVKVGDEVEVYVLRVEDEE 62 (70)
T ss_pred EEEE-eCCEEEEEeCCCceEEEEHHHhCccc-------cCCHhHcCCCCCEEEEEEEEEECCC
Confidence 4445 4678999985 57888876554432 2223345899999999999997533
No 231
>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=53.93 E-value=18 Score=30.73 Aligned_cols=51 Identities=14% Similarity=0.326 Sum_probs=36.8
Q ss_pred eeeeccccceEEeec-----CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEE
Q psy3754 640 IRTLTEETGTQIDIN-----DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLF 697 (755)
Q Consensus 640 ik~i~~~~g~~I~i~-----~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~ 697 (755)
|..+ ..+|++++++ .+|.++++...+... +...-..+++|+.++.+|.++.
T Consensus 8 V~~v-~~~G~fv~l~~~~~~~~gll~~s~l~~~~~------~~~~~~~~~~Gd~v~v~v~~vd 63 (79)
T cd05684 8 VTSI-MDFGCFVQLEGLKGRKEGLVHISQLSFEGR------VANPSDVVKRGQKVKVKVISIQ 63 (79)
T ss_pred EEEE-EeeeEEEEEeCCCCCcEEEEEhHhccCCCC------cCChhheeCCCCEEEEEEEEEe
Confidence 3444 4789999997 479999987766532 1222345799999999998875
No 232
>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=52.53 E-value=21 Score=28.68 Aligned_cols=51 Identities=14% Similarity=0.251 Sum_probs=35.9
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
|..+ .++|++++++ .+|.++++...+... ......+++|+.+.++|.++..
T Consensus 8 V~~i-~~~g~~v~i~~~~~g~l~~~~l~~~~~-------~~~~~~~~~Gd~v~v~v~~~~~ 60 (69)
T cd05692 8 VTRL-KPFGAFVELGGGISGLVHISQIAHKRV-------KDVKDVLKEGDKVKVKVLSIDA 60 (69)
T ss_pred EEEE-EeeeEEEEECCCCEEEEEhHHcCCccc-------CCHHHccCCCCEEEEEEEEECC
Confidence 3344 4689999997 579998876654332 1222458999999999998865
No 233
>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=52.37 E-value=14 Score=30.24 Aligned_cols=52 Identities=17% Similarity=0.375 Sum_probs=36.6
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
|..+ ..+|++++++ .+|.++++...+.. .+......+++|+.++.+|.++..
T Consensus 8 V~~i-~~~G~fv~l~~~~~Glv~~~~l~~~~------~~~~~~~~~~~G~~v~v~v~~id~ 61 (69)
T cd05690 8 IKSI-TDFGIFVGLDGGIDGLVHISDISWTQ------RVRHPSEIYKKGQEVEAVVLNIDV 61 (69)
T ss_pred EEEE-EeeeEEEEeCCCCEEEEEHHHCCCcc------ccCChhhEECCCCEEEEEEEEEEC
Confidence 4454 4799999997 68999987765321 122223458999999999998853
No 234
>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=51.13 E-value=44 Score=27.35 Aligned_cols=63 Identities=16% Similarity=0.198 Sum_probs=40.0
Q ss_pred CcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEE
Q psy3754 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLS 752 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS 752 (755)
|+..+=.|-.+++-|--+--.+.+.|+. +.-.|+..-...+-+|+++++.|+.+|. +-++-.|
T Consensus 1 G~~L~LvV~~~~edgsv~fs~g~v~g~t----v~AtryH~~g~nl~pGqK~kaviLhvD~l~~~VhVS 64 (65)
T cd05700 1 GDQLKLVVQDVTEDGSVMFSGGQVSGLT----VLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVS 64 (65)
T ss_pred CceEEEEEeeeccCCcEEEecCCcCCcE----EEEEEEEecceecCCCceeEEEEEEEeeEEeEEEEe
Confidence 4556667777766664333245566662 1223333334458999999999999997 6666655
No 235
>COG1278 CspC Cold shock proteins [Transcription]
Probab=50.94 E-value=27 Score=29.32 Aligned_cols=48 Identities=40% Similarity=0.486 Sum_probs=32.9
Q ss_pred EEEEEEEE---eeeEEEEEcCC-eeEEEeccccCcccccCcccccCCCCEEEEEEEE
Q psy3754 690 TGIVLRLF---DFGAIIRILSG-KDGLLHISQISSKRVNIITDFLKENQKVRVKVLG 742 (755)
Q Consensus 690 ~G~V~~I~---~fG~FVel~~g-~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~ 742 (755)
.|+|+... -|| |+.=.+| .|-|+|+|.+...... .+..||+|...+..
T Consensus 3 ~GtVKwfn~~KGfG-FI~p~~G~~DvFVH~Sai~~~g~~----~L~eGQ~V~f~~~~ 54 (67)
T COG1278 3 TGTVKWFNATKGFG-FITPEDGGKDVFVHISAIQRAGFR----TLREGQKVEFEVEQ 54 (67)
T ss_pred cceEEEeeCCCcce-EcCCCCCCcCEEEEeeeeccCCCc----ccCCCCEEEEEEec
Confidence 46676663 344 4433344 8999999999654433 38899999998865
No 236
>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=50.72 E-value=16 Score=30.31 Aligned_cols=59 Identities=20% Similarity=0.208 Sum_probs=39.6
Q ss_pred cEEEEEEEEEEeeeEE-EEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEE
Q psy3754 687 KVYTGIVLRLFDFGAI-IRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIK 750 (755)
Q Consensus 687 ~~~~G~V~~I~~fG~F-Vel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~ 750 (755)
..+.|+|++....+.| |++.+|..=++|++-= +-.. --++.||.|.|.+-..|. +|+|.
T Consensus 3 ~e~~~~V~~~lG~~~~~V~~~dg~~~l~~i~gK---~r~~--iwI~~GD~V~V~~~~~d~~kG~Ii 63 (65)
T PF01176_consen 3 GEVIGRVTEMLGNNLFEVECEDGEERLARIPGK---FRKR--IWIKRGDFVLVEPSPYDKVKGRII 63 (65)
T ss_dssp TEEEEEEEEEESSSEEEEEETTSEEEEEEE-HH---HHTC--C---TTEEEEEEESTTCTTEEEEE
T ss_pred cEEEEEEEEECCCCEEEEEeCCCCEEEEEeccc---eeee--EecCCCCEEEEEecccCCCeEEEE
Confidence 4578999999988876 7888898888887742 2222 238999999998865554 45553
No 237
>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=50.63 E-value=24 Score=29.02 Aligned_cols=51 Identities=18% Similarity=0.223 Sum_probs=37.1
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
|..+ ..+|++++++ -+|.++++..++... ......+++|+.++.+|.++.+
T Consensus 8 V~~v-~~~Gv~V~l~~~v~g~i~~~~l~~~~~-------~~~~~~~~~Gd~i~~~V~~id~ 60 (69)
T cd05697 8 IRKL-RPSGIFVKLSDHIKGLVPPMHLADVRL-------KHPEKKFKPGLKVKCRVLSVEP 60 (69)
T ss_pred EEEE-eccEEEEEecCCcEEEEEHHHCCCccc-------cCHHHcCCCCCEEEEEEEEEEC
Confidence 4444 4789999995 489998876665432 2234569999999999999854
No 238
>PRK13343 F0F1 ATP synthase subunit alpha; Provisional
Probab=50.47 E-value=1.8e+02 Score=34.08 Aligned_cols=164 Identities=17% Similarity=0.197 Sum_probs=91.4
Q ss_pred eEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCC
Q psy3754 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISE 205 (755)
Q Consensus 126 y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~ 205 (755)
|||-.-+.|++|+ |+|=|.+---+.+||++|+=+ +-+..-...+...-+|+--.++..
T Consensus 270 ~REisL~l~epPg----r~gYP~~vf~~~srLlERAg~-~~~~~~gGSITal~~V~~~~dD~s----------------- 327 (502)
T PRK13343 270 YRELSLLLRRPPG----REAYPGDIFYLHSRLLERAAK-LSPELGGGSLTALPIIETLAGELS----------------- 327 (502)
T ss_pred HHHHHHhcCCCCC----cCCcCcchHhhhHHHHHhhcc-CCCCCCCcceEEEEEEEcCCCCCC-----------------
Confidence 7888888999998 667777777789999999865 211101236666656665444432
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CcccEEEEeecCceEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3754 206 LPFLGPLGVAKVGYIDGKYILNPTTEQLKK-SHLDLLVAGTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINE 284 (755)
Q Consensus 206 IP~~~~vaav~vg~~~g~~vldPt~~E~~~-s~~~l~va~~~~~i~mie~~~~~~se~~~~~al~~a~~~~~~i~~~~~~ 284 (755)
.||+--..++.||+++++....+.-. ...|...+-++- | +.-.+ +++......++.....+++
T Consensus 328 ----~pI~~~v~sItDGqIvLsr~La~~G~~PAIDv~~SvSRv---~----~~~~~-----~~~~~~a~~lr~~la~y~e 391 (502)
T PRK13343 328 ----AYIPTNLISITDGQIYLDSDLFAAGQRPAVDVGLSVSRV---G----GKAQH-----PAIRKESGRLRLDYAQFLE 391 (502)
T ss_pred ----CcchhhhhcccceEEEECHHHHhCCCCCccCCccchhcc---C----ccccC-----HHHHHHHHHHHHHHHHHHH
Confidence 34544455668999999988776643 233433333221 1 11122 2334444555555555555
Q ss_pred HH--HHhCCCcccCCCCCCChhHHHHHHHHHHHHHHHHHhcc--chhHHHHHHHHHH
Q psy3754 285 LV--QNVGQKKVNWDPIVKDKTLISKIINISEHKIRKAYQIK--NKQIRDLTFKNIS 337 (755)
Q Consensus 285 ~~--~~~~~~k~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~--~k~~r~~~~~~~~ 337 (755)
+. ...|.. .+++....+.. ..+|.+.+.+. +...-.+.+..+.
T Consensus 392 ~e~~~~~G~~--------ld~~~~~~i~~--~~~i~~~L~Q~~~~~~~~~~~~~~l~ 438 (502)
T PRK13343 392 LEAFTRFGGL--------LDAGTQKQITR--GRRLRELLKQPRFSPLSVEEQIALLY 438 (502)
T ss_pred HHHHHHHhhh--------cCHHHHHHHHH--HHHHHHHhcCCCCCCCCHHHHHHHHH
Confidence 42 333321 45555555553 56677766532 3444444444443
No 239
>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=50.37 E-value=18 Score=31.10 Aligned_cols=65 Identities=17% Similarity=0.217 Sum_probs=41.5
Q ss_pred cceeeccccceeeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEeee
Q psy3754 629 IRDVIGKGGSTIRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFG 700 (755)
Q Consensus 629 i~~~IG~gGk~ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~fG 700 (755)
+++++ .|++++ + ...|+.++++ -+|.++++...+...+. ..+.+...+++||.+.++|.++.+-|
T Consensus 6 ~GdiV--~g~V~~-i-~~~g~~v~i~~~~~G~l~~se~~~~~~~~---~~~~~~~~l~vGd~i~~~V~~~~~~~ 72 (86)
T cd05789 6 VGDVV--IGRVTE-V-GFKRWKVDINSPYDAVLPLSEVNLPRTDE---DELNMRSYLDEGDLIVAEVQSVDSDG 72 (86)
T ss_pred CCCEE--EEEEEE-E-CCCEEEEECCCCeEEEEEHHHccCCCCcc---chHHHHhhCCCCCEEEEEEEEECCCC
Confidence 44544 344433 3 5788899886 47999987665421111 12334456899999999999985433
No 240
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=50.29 E-value=5.8 Score=34.08 Aligned_cols=24 Identities=33% Similarity=0.727 Sum_probs=20.9
Q ss_pred EEeeCCcccceeeccccceeeeec
Q psy3754 621 TIKIDPSKIRDVIGKGGSTIRTLT 644 (755)
Q Consensus 621 ~~~i~~~ki~~~IG~gGk~ik~i~ 644 (755)
.+.+.++-++.+||++|++|++|.
T Consensus 33 ~l~v~~~D~GkvIGk~GRti~AIR 56 (76)
T COG1837 33 ELRVAPEDMGKVIGKQGRTIQAIR 56 (76)
T ss_pred EEEECcccccceecCCChhHHHHH
Confidence 456789999999999999999874
No 241
>KOG0336|consensus
Probab=49.94 E-value=14 Score=41.36 Aligned_cols=56 Identities=34% Similarity=0.519 Sum_probs=41.8
Q ss_pred EEeeCCcccceeeccccceeeeeccccceEEeec---CceeEEEEecChhhhHHHHHHHH
Q psy3754 621 TIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN---DEGIITIASFNSVSGQEAKRRIE 677 (755)
Q Consensus 621 ~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~---~~G~v~i~~~~~~~~~~a~~~i~ 677 (755)
.+.|..+..+.+||.||..|+.|+..|++.|.|. .+-.|.|++.+.-. .+|+..+.
T Consensus 50 cf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg~~~m~-~kaka~id 108 (629)
T KOG0336|consen 50 CFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFGINHMR-KKAKASID 108 (629)
T ss_pred hhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCceeEEEEechHHHH-HHHHhhHh
Confidence 4567788899999999999999999999999875 35667777665332 33444443
No 242
>KOG2192|consensus
Probab=49.84 E-value=25 Score=37.03 Aligned_cols=55 Identities=31% Similarity=0.481 Sum_probs=41.2
Q ss_pred EEeeCCcccceeeccccceeeeeccccceEEeecC------ceeEEEEecChhhhHHHHHHH
Q psy3754 621 TIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND------EGIITIASFNSVSGQEAKRRI 676 (755)
Q Consensus 621 ~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~------~G~v~i~~~~~~~~~~a~~~i 676 (755)
.+.||.|.=+.+||+||..|+.|..+.|+.|.+++ |-.+.|... ++.++.|.-..
T Consensus 318 Qvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGT-qdQIqnAQYLl 378 (390)
T KOG2192|consen 318 QVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT-QDQIQNAQYLL 378 (390)
T ss_pred eEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEecc-HHHHhhHHHHH
Confidence 46789999999999999999999999999999873 344555544 34445554433
No 243
>PRK08972 fliI flagellum-specific ATP synthase; Validated
Probab=49.61 E-value=85 Score=36.09 Aligned_cols=82 Identities=22% Similarity=0.280 Sum_probs=56.6
Q ss_pred eEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCC
Q psy3754 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISE 205 (755)
Q Consensus 126 y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~ 205 (755)
|+|-.-+.|++|+ |+|=|..--..++|+++|+=+ .... ...+...-+|+--.++..
T Consensus 268 ~REIsl~~gepP~----~~GYPpsvfs~l~~L~ERAg~-~~~~--~GSITai~tVl~~gdD~~----------------- 323 (444)
T PRK08972 268 QREIALAVGEPPA----TKGYPPSVFAKLPALVERAGN-GGPG--QGSITAFYTVLTEGDDLQ----------------- 323 (444)
T ss_pred HHHHHHhcCCCCc----cccCCchHHHHhHHHHHHhcC-CCCC--CceeeeEEEEEEeCCCCC-----------------
Confidence 5888888999998 457777777788999999864 1121 237777777766544432
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhc
Q psy3754 206 LPFLGPLGVAKVGYIDGKYILNPTTEQLKK 235 (755)
Q Consensus 206 IP~~~~vaav~vg~~~g~~vldPt~~E~~~ 235 (755)
+|++--..++.||+++||-...+...
T Consensus 324 ----dpI~d~~~silDGhIvLsr~La~~g~ 349 (444)
T PRK08972 324 ----DPIADASRAILDGHIVLSRELADSGH 349 (444)
T ss_pred ----cchHHhhhhhcceEEEEcHHHHhCCC
Confidence 45555555668999999887776644
No 244
>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=49.46 E-value=32 Score=31.22 Aligned_cols=52 Identities=8% Similarity=0.124 Sum_probs=34.3
Q ss_pred EEEEEEEEEEeee--EEEEEcCC---eeEEEeccccCcccccCcccccCCCCEEEEE
Q psy3754 688 VYTGIVLRLFDFG--AIIRILSG---KDGLLHISQISSKRVNIITDFLKENQKVRVK 739 (755)
Q Consensus 688 ~~~G~V~~I~~fG--~FVel~~g---~~Gllhisel~~~~~~~~~~~~kvGd~V~Vk 739 (755)
.+.|.|.++...| +|++|..+ +..++..++.....+.+....++.||.|.|.
T Consensus 3 ~v~GwV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~ 59 (108)
T cd04322 3 SVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVT 59 (108)
T ss_pred EEEEEEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEE
Confidence 4789999998877 89999554 5566655543222222222338899998874
No 245
>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=48.46 E-value=28 Score=27.99 Aligned_cols=51 Identities=16% Similarity=0.380 Sum_probs=36.3
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
|..+ .++|++++++ .+|.++++...+.... .....+++|+.+..+|.++.+
T Consensus 8 V~~v-~~~G~~v~l~~~~~g~l~~~~l~~~~~~-------~~~~~~~~Gd~v~v~v~~~d~ 60 (68)
T cd04472 8 VVKI-KDFGAFVEILPGKDGLVHISELSDERVE-------KVEDVLKVGDEVKVKVIEVDD 60 (68)
T ss_pred EEEE-EEeEEEEEeCCCCEEEEEhHHcCCcccc-------CHHHccCCCCEEEEEEEEECC
Confidence 3344 3689999987 6899998766544321 222458999999999999865
No 246
>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=48.24 E-value=29 Score=27.74 Aligned_cols=51 Identities=18% Similarity=0.374 Sum_probs=36.0
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
|..+ ..+|++++++ .+|.++.+........ ..-..+++|+.+..+|.++..
T Consensus 8 V~~i-~~~G~fv~l~~~~~g~~~~~~l~~~~~~-------~~~~~~~~Gd~v~v~i~~vd~ 60 (68)
T cd05685 8 VTNV-TDFGAFVDIGVKQDGLIHISKMADRFVS-------HPSDVVSVGDIVEVKVISIDE 60 (68)
T ss_pred EEEE-ecccEEEEcCCCCEEEEEHHHCCCcccc-------CHHHhcCCCCEEEEEEEEEEC
Confidence 4444 4789999987 5788887655443322 223458999999999999865
No 247
>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=48.21 E-value=31 Score=28.48 Aligned_cols=51 Identities=16% Similarity=0.316 Sum_probs=36.4
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEE
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLF 697 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~ 697 (755)
|..| .++|++++++ .+|.++++..++... .......+++|+.++.+|.++.
T Consensus 11 V~~i-~~~G~fv~l~~~~~Gl~~~~~l~~~~~------~~~~~~~~~~Gd~v~v~v~~id 63 (72)
T cd05689 11 VTNL-TDYGCFVELEEGVEGLVHVSEMDWTNK------NIHPSKVVSLGDEVEVMVLDID 63 (72)
T ss_pred EEEE-EeeEEEEEcCCCCEEEEEEEeccCccc------ccCcccEeCCCCEEEEEEEEee
Confidence 3444 5799999997 589999988865310 1112355899999999998875
No 248
>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=48.11 E-value=22 Score=31.26 Aligned_cols=53 Identities=11% Similarity=0.255 Sum_probs=36.7
Q ss_pred eeeeccc-cceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEE
Q psy3754 640 IRTLTEE-TGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRL 696 (755)
Q Consensus 640 ik~i~~~-~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I 696 (755)
|..|..- +|++++++ .+|.+|++..++... ..+......+++|+.+..+|.+.
T Consensus 15 V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~----~~v~~~~~~~~~Gd~v~VqV~~~ 70 (88)
T cd04453 15 VKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYF----KKHKKIAKLLKEGQEILVQVVKE 70 (88)
T ss_pred EEEeccCCcEEEEEeCCCCEEEEEhHHcCchhc----cccCCHHHcCCCCCEEEEEEEEe
Confidence 5566543 59999997 589999987765221 11222344589999999999884
No 249
>PRK07252 hypothetical protein; Provisional
Probab=48.04 E-value=29 Score=32.50 Aligned_cols=51 Identities=14% Similarity=0.263 Sum_probs=38.1
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
|..+ ..+|++++++ .+|.++++...+.... .....+++||.++.+|.++..
T Consensus 11 V~~V-~~~G~fVei~~~~~GllhiseLs~~~~~-------~~~~~~~vGD~V~VkI~~iD~ 63 (120)
T PRK07252 11 ITGI-KPYGAFVALENGTTGLIHISEIKTGFID-------NIHQLLKVGEEVLVQVVDFDE 63 (120)
T ss_pred EEEE-eCcEEEEEECCCCEEEEEHHHcCCcccc-------ChhhccCCCCEEEEEEEEEeC
Confidence 4445 4799999996 5899999877654332 223458999999999999975
No 250
>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=47.96 E-value=29 Score=29.73 Aligned_cols=51 Identities=12% Similarity=0.154 Sum_probs=37.9
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
|+.+ .++|++++++ -+|.++++...+.. +......+++|+.++.+|.++..
T Consensus 22 V~~v-~~~G~fv~l~~~~~g~v~~~el~~~~-------~~~~~~~~~~Gd~v~vkV~~id~ 74 (83)
T cd04461 22 VRNI-TPYGVFVEFLGGLTGLAPKSYISDEF-------VTDPSFGFKKGQSVTAKVTSVDE 74 (83)
T ss_pred EEEE-eeceEEEEcCCCCEEEEEHHHCCccc-------ccCHHHhcCCCCEEEEEEEEEcC
Confidence 5555 4799999985 47889887766543 22344568999999999999854
No 251
>CHL00010 infA translation initiation factor 1
Probab=47.41 E-value=91 Score=26.85 Aligned_cols=61 Identities=23% Similarity=0.291 Sum_probs=38.4
Q ss_pred EEEEEEEEEeeeEE-EEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEEE
Q psy3754 689 YTGIVLRLFDFGAI-IRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLSM 753 (755)
Q Consensus 689 ~~G~V~~I~~fG~F-Vel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS~ 753 (755)
++|.|+++.+.|.| |.+.+|..=++|+.- .+.+..-.+.+||.|.+.+...+. +|.|..-.
T Consensus 9 ~~G~Vik~lg~~~y~V~~~~g~~~~c~~rG----klr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~ 71 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLDNGCQVLGYISG----KIRRNSIRILPGDRVKVELSPYDLTKGRIIYRL 71 (78)
T ss_pred EEEEEEEEcCCCEEEEEeCCCCEEEEEecc----ceecCCcccCCCCEEEEEEcccCCCeEEEEEEe
Confidence 68999998865654 555566555555432 222222336889999999766665 67776543
No 252
>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=44.46 E-value=53 Score=26.88 Aligned_cols=51 Identities=16% Similarity=0.298 Sum_probs=36.8
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
|..+ ..+|++++++ -+|.++++....... ......+++|+.++++|.++..
T Consensus 8 V~~v-~~~g~~v~l~~~~~g~i~~~~~~~~~~-------~~~~~~~~~Gd~v~~~v~~~d~ 60 (73)
T cd05691 8 VTEV-DAKGATVKLGDGVEGFLRAAELSRDRV-------EDATERFKVGDEVEAKITNVDR 60 (73)
T ss_pred EEEE-ECCeEEEEeCCCCEEEEEHHHCCCccc-------cCHHHccCCCCEEEEEEEEEeC
Confidence 4444 4788899885 479998876655432 2334558999999999999865
No 253
>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=44.07 E-value=22 Score=29.15 Aligned_cols=51 Identities=16% Similarity=0.196 Sum_probs=36.7
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
|+.+ ..+|+++++. -+|.++++........ .....+++|+.++.+|.++.+
T Consensus 8 V~~v-~~~G~~V~l~~~~~gli~~s~l~~~~~~-------~~~~~~~~G~~i~v~v~~~d~ 60 (70)
T cd05698 8 IVKV-KPNGCIVSFYNNVKGFLPKSELSEAFIK-------DPEEHFRVGQVVKVKVLSCDP 60 (70)
T ss_pred EEEE-ecCcEEEEECCCCEEEEEHHHcChhhcC-------CHHHcccCCCEEEEEEEEEcC
Confidence 4455 4799999996 4788988766544322 223458999999999999865
No 254
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=44.02 E-value=60 Score=31.82 Aligned_cols=63 Identities=19% Similarity=0.285 Sum_probs=46.2
Q ss_pred ccCCcEEEEEEEEEEeeeEE-EEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEE
Q psy3754 683 VQIGKVYTGIVLRLFDFGAI-IRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKL 751 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~fG~F-Vel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~L 751 (755)
++.|+ ..|+|+.....|.| |.+.+|..-|.||+-= ++. .--++.||.|.|..-..+. +|+|..
T Consensus 29 ~eegq-~~g~V~~~LGn~~f~V~c~dG~~rLa~I~GK----mRK-~IWI~~GD~VlVel~~yd~~KgdIi~ 93 (155)
T PTZ00329 29 KEEGQ-EYAQVLRMLGNGRLEAYCFDGVKRLCHIRGK----MRK-RVWINIGDIILVSLRDFQDSKADVIL 93 (155)
T ss_pred CCCCc-EEEEEEEEcCCCEEEEEECCCCEEEEEeecc----cee-eEEecCCCEEEEeccCCCCCEEEEEE
Confidence 34566 56899999999987 6888999999998742 221 1238999999998866655 566654
No 255
>PRK08149 ATP synthase SpaL; Validated
Probab=43.99 E-value=2.5e+02 Score=32.24 Aligned_cols=90 Identities=24% Similarity=0.346 Sum_probs=63.2
Q ss_pred EEeEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhc
Q psy3754 124 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSI 203 (755)
Q Consensus 124 v~y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~ 203 (755)
--|+|-.-+.|++|+ |+|=|..--..++++++|+=+- .. ..+...-+|+--.++.+
T Consensus 255 ~A~rEi~l~~ge~P~----~~Gyp~~vfs~l~~l~ERag~~--~~---GSIT~~~tVl~~~dD~~--------------- 310 (428)
T PRK08149 255 RALRDVALAAGELPA----RRGYPASVFDSLPRLLERPGAT--LA---GSITAFYTVLLESEEEP--------------- 310 (428)
T ss_pred HHHHHhHhhcCCCCc----ccccCccHHHHHHHHHHhccCC--CC---CCceEEEEEEecCCCCC---------------
Confidence 346888888999998 4577777777889999998653 23 47777777776665533
Q ss_pred CCCCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CcccEEEE
Q psy3754 204 SELPFLGPLGVAKVGYIDGKYILNPTTEQLKK-SHLDLLVA 243 (755)
Q Consensus 204 s~IP~~~~vaav~vg~~~g~~vldPt~~E~~~-s~~~l~va 243 (755)
+|++--..+..||++++|-...+... ...|..-+
T Consensus 311 ------dpi~d~~~~ilDg~ivLsr~La~~g~yPAIDvl~S 345 (428)
T PRK08149 311 ------DPIGDEIRSILDGHIYLSRKLAAKGHYPAIDVLKS 345 (428)
T ss_pred ------CCchhhhheeccEEEEEcHHHHhCCCCCcccCccc
Confidence 56666666778999999988876643 33444433
No 256
>CHL00059 atpA ATP synthase CF1 alpha subunit
Probab=43.68 E-value=2.9e+02 Score=32.23 Aligned_cols=86 Identities=19% Similarity=0.211 Sum_probs=56.4
Q ss_pred EEeEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhc
Q psy3754 124 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSI 203 (755)
Q Consensus 124 v~y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~ 203 (755)
.-|||..-+.|+.|+ |||=|.+---+.+||++|+=+ +-...-...+...-.|+--+++.
T Consensus 247 ~A~REisl~l~epPg----r~gYP~~vF~~~srLlERag~-~~~~~~~GSITal~~V~~~~dD~---------------- 305 (485)
T CHL00059 247 QAYRQMSLLLRRPPG----REAYPGDVFYLHSRLLERAAK-LSSQLGEGSMTALPIVETQAGDV---------------- 305 (485)
T ss_pred HHHHHHHHhcCCCCC----cCCcCchHHHHhHHHHHhhhc-ccCCCCCcceEEEEEEEccCCCC----------------
Confidence 447899999999998 567777777789999999865 21100023666665565544442
Q ss_pred CCCCCCCCeEEEEEEEECCEEEEcCCHHHHhc
Q psy3754 204 SELPFLGPLGVAKVGYIDGKYILNPTTEQLKK 235 (755)
Q Consensus 204 s~IP~~~~vaav~vg~~~g~~vldPt~~E~~~ 235 (755)
..|++--..++.||+++++....+.-.
T Consensus 306 -----s~pI~~~v~sItDGqIvLsr~La~~G~ 332 (485)
T CHL00059 306 -----SAYIPTNVISITDGQIFLSADLFNAGI 332 (485)
T ss_pred -----CCcchHhhhhhcceEEEEcHHHHhCCC
Confidence 234444445567999999887766643
No 257
>KOG2814|consensus
Probab=43.67 E-value=11 Score=40.85 Aligned_cols=62 Identities=34% Similarity=0.360 Sum_probs=51.6
Q ss_pred eEEeeCCcccceeeccccceeeeeccccceEEee----cCceeEEEEecChhhhHHHHHHHHHhhh
Q psy3754 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI----NDEGIITIASFNSVSGQEAKRRIEKLTE 681 (755)
Q Consensus 620 ~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i----~~~G~v~i~~~~~~~~~~a~~~i~~~~~ 681 (755)
.++.+.+.-++-+||..|++-+.|.++|++.|-+ +.++.+.+.......+..|.+.+..++.
T Consensus 59 ~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~id 124 (345)
T KOG2814|consen 59 SSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLID 124 (345)
T ss_pred hhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHH
Confidence 3456778889999999999999999999998876 2578899999999999999888765543
No 258
>KOG2191|consensus
Probab=43.40 E-value=28 Score=37.87 Aligned_cols=56 Identities=25% Similarity=0.346 Sum_probs=39.7
Q ss_pred EEeeCCcccceeeccccceeeeeccccceEEeecC--------ceeEEEEecChhhhHHHHHHH
Q psy3754 621 TIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND--------EGIITIASFNSVSGQEAKRRI 676 (755)
Q Consensus 621 ~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~--------~G~v~i~~~~~~~~~~a~~~i 676 (755)
.+-||..-.+.+||+||.+|..++.++|+.|.+.. .-+|..-.-.-+++....+.|
T Consensus 42 kvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI 105 (402)
T KOG2191|consen 42 KVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFI 105 (402)
T ss_pred EEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHH
Confidence 45578888899999999999999999999998742 234444444444554444444
No 259
>PRK05922 type III secretion system ATPase; Validated
Probab=43.28 E-value=2.2e+02 Score=32.75 Aligned_cols=88 Identities=18% Similarity=0.209 Sum_probs=58.3
Q ss_pred eEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCC
Q psy3754 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISE 205 (755)
Q Consensus 126 y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~ 205 (755)
|||-.-+.|++|+ |+|=|..--..++|+++|+=+. .+ ..+..+-+||-..+.++
T Consensus 263 ~REisl~~ge~P~----~~gyp~svfs~l~~l~ERag~~--~~---GSIT~~~tVl~~~~~~d----------------- 316 (434)
T PRK05922 263 LQEVALARGETLS----AHHYAASVFHHVSEFTERAGNN--DK---GSITALYAILHYPNHPD----------------- 316 (434)
T ss_pred HHHHHHhcCCCCC----cCCcCchHHHHhHHHHHhhcCC--CC---cceeEEEEEEecCCCCC-----------------
Confidence 5888889999998 4576666667889999998762 23 47777777775444333
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhcCcccEEEEe
Q psy3754 206 LPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAG 244 (755)
Q Consensus 206 IP~~~~vaav~vg~~~g~~vldPt~~E~~~s~~~l~va~ 244 (755)
|++.--.++.||++|++....+.-....|+.-+.
T Consensus 317 -----pi~d~~rsilDGhIvLsr~la~~~~PAIDvl~S~ 350 (434)
T PRK05922 317 -----IFTDYLKSLLDGHFFLTPQGKALASPPIDILTSL 350 (434)
T ss_pred -----ccccchhhhcCcEEEEcHHHHhCCCCCcCCcccc
Confidence 2222234557999999987755444444544433
No 260
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=43.17 E-value=37 Score=35.96 Aligned_cols=59 Identities=22% Similarity=0.345 Sum_probs=44.5
Q ss_pred eeeeeccccceEEeec----CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEeeeEEEEE
Q psy3754 639 TIRTLTEETGTQIDIN----DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRI 705 (755)
Q Consensus 639 ~ik~i~~~~g~~I~i~----~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~fG~FVel 705 (755)
+++.| .++|++++++ .+|.+|+|......+. .+-.-+++|+.+-.+|.+|.+--=+|+|
T Consensus 18 tV~~V-~~~GAyv~L~EY~g~Eg~ihiSEvas~wVk-------nIrd~vkegqkvV~kVlrVd~~rg~IDL 80 (269)
T COG1093 18 TVKQV-ADYGAYVELDEYPGKEGFIHISEVASGWVK-------NIRDYVKEGQKVVAKVLRVDPKRGHIDL 80 (269)
T ss_pred EEEEe-eccccEEEeeccCCeeeeEEHHHHHHHHHH-------HHHHHhhcCCeEEEEEEEEcCCCCeEee
Confidence 46666 5899999986 3899999877655544 3334478999999999999776666665
No 261
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=42.89 E-value=1.3e+02 Score=25.35 Aligned_cols=61 Identities=23% Similarity=0.283 Sum_probs=37.8
Q ss_pred EEEEEEEEEEeeeEE-EEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEEE
Q psy3754 688 VYTGIVLRLFDFGAI-IRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKLS 752 (755)
Q Consensus 688 ~~~G~V~~I~~fG~F-Vel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~LS 752 (755)
.++|.|++...-+.| |.+.+|..=++|+.- .+........+||.|.+.+-..+. +|.|-.-
T Consensus 8 ~~~G~Vi~~~~~~~y~V~~~~g~~~~c~~~G----klr~~~i~i~vGD~V~ve~~~~~~~~g~Iv~r 70 (72)
T PRK00276 8 EMEGTVVEALPNAMFRVELENGHEVLAHISG----KMRKNYIRILPGDKVTVELSPYDLTKGRITYR 70 (72)
T ss_pred EEEEEEEEEcCCCEEEEEeCCCCEEEEEEcc----ceeeCCcccCCCCEEEEEEcccCCCeEEEEEE
Confidence 467999988766543 455566554555332 122222237899999999866665 6776543
No 262
>TIGR03497 FliI_clade2 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=42.44 E-value=2e+02 Score=32.93 Aligned_cols=91 Identities=20% Similarity=0.290 Sum_probs=64.1
Q ss_pred eEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCC
Q psy3754 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISE 205 (755)
Q Consensus 126 y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~ 205 (755)
|+|-.-+.|++|+ |+|=|..--..++++++|+=.. . ...+...-+|+--.++.+
T Consensus 243 ~rEisl~~ge~P~----~~gyp~~~f~~l~~l~ERag~~--~---~GSIT~~~tVl~~gdD~~----------------- 296 (413)
T TIGR03497 243 QREIGLAVGEPPT----TRGYTPSVFSLLPKLLERSGNS--Q---KGSITGFYTVLVDGDDMN----------------- 296 (413)
T ss_pred HHHHHHhcCCCCC----CCCcCchHHHHhHHHHHHhcCC--C---CcceeEEEEEEccCCCCC-----------------
Confidence 5888888999998 4576777777888999998651 2 347777777776655433
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CcccEEEEeec
Q psy3754 206 LPFLGPLGVAKVGYIDGKYILNPTTEQLKK-SHLDLLVAGTE 246 (755)
Q Consensus 206 IP~~~~vaav~vg~~~g~~vldPt~~E~~~-s~~~l~va~~~ 246 (755)
+|++--..+..||++++|-...+.-. ...|...+.++
T Consensus 297 ----dpi~~~~~si~dg~ivLsr~la~~g~~PAId~~~S~SR 334 (413)
T TIGR03497 297 ----EPIADAVRGILDGHIVLSRELAAKNHYPAIDVLASVSR 334 (413)
T ss_pred ----CcchhhccccccEEEEECHHHHhCCCCCccCCcccccc
Confidence 56666566678999999988877654 44555554444
No 263
>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=42.04 E-value=34 Score=28.16 Aligned_cols=49 Identities=10% Similarity=0.183 Sum_probs=34.5
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
|..+ .++|+++++. -+|.++.+........ ...+++|+.++++|..+.+
T Consensus 8 V~~i-~~~G~~v~l~~~v~g~v~~~~l~~~~~~---------~~~~~~G~~i~~kVi~id~ 58 (66)
T cd05695 8 VKKV-LSNGLILDFLSSFTGTVDFLHLDPEKSS---------KSTYKEGQKVRARILYVDP 58 (66)
T ss_pred EEEE-eCCcEEEEEcCCceEEEEHHHcCCccCc---------ccCcCCCCEEEEEEEEEeC
Confidence 4455 4899999985 4788887655322111 4458999999999998853
No 264
>PRK06820 type III secretion system ATPase; Validated
Probab=41.95 E-value=1.8e+02 Score=33.56 Aligned_cols=90 Identities=19% Similarity=0.249 Sum_probs=63.0
Q ss_pred EEeEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhc
Q psy3754 124 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSI 203 (755)
Q Consensus 124 v~y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~ 203 (755)
--|||-.-+.|+.|+ |+|=|..--..++|+++|+=+- .+ ..+..+-+|+--.++..
T Consensus 267 ~A~REisl~~gepP~----~~GYP~~vf~~l~~L~ERag~~--~~---GSIT~i~tVl~~gdD~~--------------- 322 (440)
T PRK06820 267 RAAREIGLAAGEPPA----AGSFPPSVFANLPRLLERTGNS--DR---GSITAFYTVLVEGDDMN--------------- 322 (440)
T ss_pred HHHHHHHHhcCCCCc----cccCCccHHHHHHHHHHhhccC--CC---cceeEEEEEEccCCCCC---------------
Confidence 346888888999987 5576777777889999998762 33 47888777776655533
Q ss_pred CCCCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CcccEEEE
Q psy3754 204 SELPFLGPLGVAKVGYIDGKYILNPTTEQLKK-SHLDLLVA 243 (755)
Q Consensus 204 s~IP~~~~vaav~vg~~~g~~vldPt~~E~~~-s~~~l~va 243 (755)
+||+--..+..||++++|-...+... ...|..-+
T Consensus 323 ------dpI~d~~~~ilDg~ivLsr~La~~g~yPAIDvl~S 357 (440)
T PRK06820 323 ------EPVADEVRSLLDGHIVLSRRLAGAGHYPAIDIAAS 357 (440)
T ss_pred ------CcchhhhccccceEEEECHHHHhCCCCCccCCccc
Confidence 46665556778999999988777644 33444333
No 265
>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=41.67 E-value=29 Score=28.66 Aligned_cols=49 Identities=14% Similarity=0.120 Sum_probs=33.9
Q ss_pred cccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 645 EETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 645 ~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
.+.|+.++++ -+|.++++...+... ........+++|+.+.++|.++.+
T Consensus 12 ~~~gi~v~l~~~i~g~i~~~~i~~~~~-----~~~~~~~~~~~Gd~i~~kVl~~d~ 62 (70)
T cd05702 12 KPTQLNVQLADNVHGRIHVSEVFDEWP-----DGKNPLSKFKIGQKIKARVIGGHD 62 (70)
T ss_pred ECCcEEEEeCCCcEEEEEHHHhccccc-----cccChhHhCCCCCEEEEEEEEEeC
Confidence 4678888885 588888876654320 022234558999999999998854
No 266
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=40.05 E-value=1.5e+02 Score=26.79 Aligned_cols=60 Identities=23% Similarity=0.369 Sum_probs=43.1
Q ss_pred CcEEEEEEEEEEeeeEE-EEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEc-C-CCcEE
Q psy3754 686 GKVYTGIVLRLFDFGAI-IRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGID-D-RGRIK 750 (755)
Q Consensus 686 G~~~~G~V~~I~~fG~F-Vel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id-~-~gki~ 750 (755)
-..+.|+|+.....+.| |.+.+|..=|+|++- ++.+ .--++.||.|.|...+.. . +|+|.
T Consensus 18 e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~G----K~Rk-~iwI~~GD~VlVsp~d~~~~~kg~Iv 80 (99)
T TIGR00523 18 EGEILGVIEQMLGAGRVKVRCLDGKTRLGRIPG----KLKK-RIWIREGDVVIVKPWEFQGDDKCDIV 80 (99)
T ss_pred CCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEch----hhcc-cEEecCCCEEEEEEccCCCCccEEEE
Confidence 45589999999999987 688889999999874 2222 334899999999654443 2 45554
No 267
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=39.81 E-value=11 Score=36.42 Aligned_cols=34 Identities=29% Similarity=0.609 Sum_probs=29.6
Q ss_pred eEEeeCCcccceeeccccceeeeeccccceEEee
Q psy3754 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI 653 (755)
Q Consensus 620 ~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i 653 (755)
..+-+++..++..||++|+.|+.+.+..|.+|++
T Consensus 34 vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdV 67 (140)
T PRK08406 34 IIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIEL 67 (140)
T ss_pred EEEEEeCCCccccCCcCchHHHHHHHHhCCceEE
Confidence 4556788899999999999999999889988886
No 268
>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=39.46 E-value=13 Score=35.98 Aligned_cols=35 Identities=26% Similarity=0.566 Sum_probs=30.4
Q ss_pred eEEeeCCcccceeeccccceeeeeccccceEEeec
Q psy3754 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN 654 (755)
Q Consensus 620 ~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~ 654 (755)
..+-+.+..++..||++|.+|+.+.+..|-+|++-
T Consensus 35 iifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV 69 (141)
T TIGR01952 35 VVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI 69 (141)
T ss_pred EEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE
Confidence 35678899999999999999999988889888863
No 269
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=39.32 E-value=5.9 Score=33.37 Aligned_cols=27 Identities=41% Similarity=0.745 Sum_probs=21.9
Q ss_pred cccceeeccccceeeeecccc-ceEEee
Q psy3754 627 SKIRDVIGKGGSTIRTLTEET-GTQIDI 653 (755)
Q Consensus 627 ~ki~~~IG~gGk~ik~i~~~~-g~~I~i 653 (755)
|.++..||++|..|+.|.+++ |.+|++
T Consensus 17 d~vG~~iG~~G~rik~i~~~L~gekIdv 44 (69)
T PF13184_consen 17 DPVGACIGKKGSRIKAISEELNGEKIDV 44 (69)
T ss_dssp -HHHHHH-CCCCCHHHHHHHTTT-EEEE
T ss_pred CcceecCccccHHHHHHHHHhCCCeEEE
Confidence 348889999999999999999 888886
No 270
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=39.30 E-value=40 Score=27.51 Aligned_cols=54 Identities=17% Similarity=-0.006 Sum_probs=31.5
Q ss_pred cEEEEEEEEEEeeeEEEEEcCCeeEE-EeccccCcccccCcccccCCCCEEEEEEEE
Q psy3754 687 KVYTGIVLRLFDFGAIIRILSGKDGL-LHISQISSKRVNIITDFLKENQKVRVKVLG 742 (755)
Q Consensus 687 ~~~~G~V~~I~~fG~FVel~~g~~Gl-lhisel~~~~~~~~~~~~kvGd~V~VkV~~ 742 (755)
-.+.|+|.+|.+.|.++++.=...|- -=.+.++.+...+ -.+++||.|.+.+..
T Consensus 7 N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~~~--l~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 7 NQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESVAE--LGLKPGKEVYAVIKA 61 (69)
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHHhh--CCCCCCCEEEEEEEC
Confidence 46899999999888776653111111 0111222222222 238999999998864
No 271
>PRK01064 hypothetical protein; Provisional
Probab=38.88 E-value=13 Score=32.18 Aligned_cols=24 Identities=29% Similarity=0.616 Sum_probs=20.8
Q ss_pred EEeeCCcccceeeccccceeeeec
Q psy3754 621 TIKIDPSKIRDVIGKGGSTIRTLT 644 (755)
Q Consensus 621 ~~~i~~~ki~~~IG~gGk~ik~i~ 644 (755)
.+.++++.++.+||++|+++++|.
T Consensus 33 ~l~v~~~D~g~vIGk~G~~i~air 56 (78)
T PRK01064 33 ELTVAKPDIGKIIGKEGRTIKAIR 56 (78)
T ss_pred EEEECcccceEEECCCCccHHHHH
Confidence 466789999999999999999774
No 272
>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=38.85 E-value=42 Score=27.77 Aligned_cols=51 Identities=20% Similarity=0.321 Sum_probs=37.4
Q ss_pred eeeeccccceEEeec---CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 640 IRTLTEETGTQIDIN---DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 640 ik~i~~~~g~~I~i~---~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
|..+ ..+|+++++. .+|.++++...+.... .....+++||.++.+|.++..
T Consensus 10 V~~i-~~~g~~v~l~~~~~~g~i~~~~l~~~~~~-------~~~~~~~~Gd~v~v~i~~vd~ 63 (77)
T cd05708 10 VRRV-EDYGVFIDIDGTNVSGLCHKSEISDNRVA-------DASKLFRVGDKVRAKVLKIDA 63 (77)
T ss_pred EEEE-EcceEEEEECCCCeEEEEEHHHCCCCccC-------CHhHeecCCCEEEEEEEEEeC
Confidence 4455 4799999986 4788998776654321 234568999999999999875
No 273
>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=38.52 E-value=37 Score=27.25 Aligned_cols=47 Identities=19% Similarity=0.359 Sum_probs=33.0
Q ss_pred cccceEEeec-CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 645 EETGTQIDIN-DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 645 ~~~g~~I~i~-~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
.++|++++++ .+|.++.+...+.. +......+++|+.++.+|.++..
T Consensus 13 ~~~g~~v~l~~~~g~l~~~e~~~~~-------~~~~~~~~~~Gd~v~v~i~~vd~ 60 (68)
T cd05688 13 TDFGAFVDLGGVDGLLHISDMSWGR-------VKHPSEVVNVGDEVEVKVLKIDK 60 (68)
T ss_pred EeeeEEEEECCeEEEEEhHHCCCcc-------ccCHhHEECCCCEEEEEEEEEEC
Confidence 4678888886 67888876554322 12223458999999999999854
No 274
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=38.01 E-value=19 Score=36.60 Aligned_cols=53 Identities=25% Similarity=0.301 Sum_probs=37.8
Q ss_pred CcccceeeccccceeeeeccccceEEeecCceeE---EEEecChhhhHHHHHHHHH
Q psy3754 626 PSKIRDVIGKGGSTIRTLTEETGTQIDINDEGII---TIASFNSVSGQEAKRRIEK 678 (755)
Q Consensus 626 ~~ki~~~IG~gGk~ik~i~~~~g~~I~i~~~G~v---~i~~~~~~~~~~a~~~i~~ 678 (755)
...++-+|||.|.+.|.+++.++++|.|--.|.+ .+++........+.+.+..
T Consensus 162 ~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhc 217 (269)
T COG5176 162 SNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHC 217 (269)
T ss_pred cceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHH
Confidence 3467889999999999999999999999654444 3444445555555555433
No 275
>PLN00208 translation initiation factor (eIF); Provisional
Probab=37.61 E-value=86 Score=30.43 Aligned_cols=63 Identities=19% Similarity=0.264 Sum_probs=46.2
Q ss_pred ccCCcEEEEEEEEEEeeeEE-EEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCcEEE
Q psy3754 683 VQIGKVYTGIVLRLFDFGAI-IRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGRIKL 751 (755)
Q Consensus 683 ~~~G~~~~G~V~~I~~fG~F-Vel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gki~L 751 (755)
+..|+ ..|+|+.....|.| |.+.+|..-|+|++-= ++. .--++.||.|.|.+-..+. ++.|..
T Consensus 29 p~egq-~~g~V~~~lGn~~~~V~c~dG~~rLa~IpGK----mRK-rIWI~~GD~VlVel~~~d~~KgdIv~ 93 (145)
T PLN00208 29 KEDGQ-EYAQVLRMLGNGRCEALCIDGTKRLCHIRGK----MRK-KVWIAAGDIILVGLRDYQDDKADVIL 93 (145)
T ss_pred CCCCc-EEEEEEEEcCCCEEEEEECCCCEEEEEEecc----cee-eEEecCCCEEEEEccCCCCCEEEEEE
Confidence 45555 66899999999987 6778899999998742 221 2238999999999777665 566654
No 276
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=36.56 E-value=9.7 Score=36.68 Aligned_cols=60 Identities=18% Similarity=0.243 Sum_probs=39.3
Q ss_pred HHHHHHHHhhcccccc---ccccC-CCceeEEeeCCcccceeeccccceeeeeccccceEEeec
Q psy3754 595 SYILEKMKTEVPKCKN---ELSKF-APRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN 654 (755)
Q Consensus 595 ~~I~~~~~~~l~~~r~---~~~~~-~P~~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~ 654 (755)
....+++++++....- .+... --+...+.++++..+.+||++|+|++.+..-+|-.++++
T Consensus 72 ~d~~~fI~n~l~Pa~V~~v~I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 72 DDPEEFIKNIFAPAAVRSVTIKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred CCHHHHHHHHcCCCEEEEEEEEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 4455666666554321 11111 113345678999999999999999999877777777764
No 277
>PRK07165 F0F1 ATP synthase subunit alpha; Validated
Probab=36.41 E-value=3.7e+02 Score=31.59 Aligned_cols=83 Identities=18% Similarity=0.193 Sum_probs=57.8
Q ss_pred EEeEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhc
Q psy3754 124 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSI 203 (755)
Q Consensus 124 v~y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~ 203 (755)
.-|||..-+.|++|| |||=|.+-=.+++||++|+=+- .. ...++-.-.|+--+++..
T Consensus 247 ~A~REisLllgepPg----regYPg~vF~~~srLlERAg~~--~g--~GSITalpiV~t~~dDis--------------- 303 (507)
T PRK07165 247 NIYREIALLTNKPVG----KEAFPGDMFFAHSKLLERAGKF--KN--RKTITALPILQTVDNDIT--------------- 303 (507)
T ss_pred HHHHHHHhhccCCCC----ccCCCchHHHHhHHHHHhccCC--CC--CCceEEEEEEECCCCCCC---------------
Confidence 347898999999997 6788888888999999998762 21 125555545554444433
Q ss_pred CCCCCCCCeEEEEEEEECCEEEEcCCHHHHhc
Q psy3754 204 SELPFLGPLGVAKVGYIDGKYILNPTTEQLKK 235 (755)
Q Consensus 204 s~IP~~~~vaav~vg~~~g~~vldPt~~E~~~ 235 (755)
.|++--...+.||+++++.+.-+.-.
T Consensus 304 ------~pIpdnv~sItDGqIvLsr~L~~~G~ 329 (507)
T PRK07165 304 ------SLISSNIISITDGQIVTSSDLFASGK 329 (507)
T ss_pred ------CcchhhhccccCeEEEEcHHHHhCCC
Confidence 35555555667999999887776644
No 278
>KOG1588|consensus
Probab=36.40 E-value=11 Score=39.71 Aligned_cols=27 Identities=33% Similarity=0.620 Sum_probs=24.7
Q ss_pred ccceeeccccceeeeeccccceEEeec
Q psy3754 628 KIRDVIGKGGSTIRTLTEETGTQIDIN 654 (755)
Q Consensus 628 ki~~~IG~gGk~ik~i~~~~g~~I~i~ 654 (755)
.++.++||.|-++|.++++||++|-|-
T Consensus 108 FVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 108 FVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred cccccccCCcchHHHHHHHHCCeEEEe
Confidence 578899999999999999999999873
No 279
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=35.72 E-value=1.5e+02 Score=29.75 Aligned_cols=58 Identities=21% Similarity=0.293 Sum_probs=38.5
Q ss_pred cceeeccccceeeeeccccceEEeec------------CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEE
Q psy3754 629 IRDVIGKGGSTIRTLTEETGTQIDIN------------DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRL 696 (755)
Q Consensus 629 i~~~IG~gGk~ik~i~~~~g~~I~i~------------~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I 696 (755)
+++++ -|+ |..+ ...|+++++. -+|.++++..++... ..+...+++||++.++|.++
T Consensus 64 ~GdiV--~Gk-V~~i-~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~-------~~~~~~~~~GD~V~akV~~i 132 (189)
T PRK09521 64 KGDIV--YGR-VVDV-KEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYV-------ESLTDAFKIGDIVRAKVISY 132 (189)
T ss_pred CCCEE--EEE-EEEE-cCCeEEEEEEEecccccccCCCceeeEEhhHcChhhh-------hhHHhccCCCCEEEEEEEec
Confidence 55544 333 4444 4678888873 258888876654322 23455689999999999998
Q ss_pred E
Q psy3754 697 F 697 (755)
Q Consensus 697 ~ 697 (755)
.
T Consensus 133 ~ 133 (189)
T PRK09521 133 T 133 (189)
T ss_pred C
Confidence 6
No 280
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=35.57 E-value=13 Score=37.62 Aligned_cols=35 Identities=29% Similarity=0.585 Sum_probs=30.4
Q ss_pred eeEEeeCCcccceeeccccceeeeeccccceEEee
Q psy3754 619 LITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI 653 (755)
Q Consensus 619 ~~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i 653 (755)
..++....+.++..||++|.+|+.+.+++|-+||+
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdV 111 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDV 111 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEE
Confidence 35566677889999999999999999999988886
No 281
>PRK07594 type III secretion system ATPase SsaN; Validated
Probab=34.64 E-value=1.2e+02 Score=34.89 Aligned_cols=80 Identities=21% Similarity=0.231 Sum_probs=55.7
Q ss_pred eEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCC
Q psy3754 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISE 205 (755)
Q Consensus 126 y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~ 205 (755)
|||-.-+.|++|+ |+|=|..--..++|+++|+=.. .+ ..+...-+|+--.++.+
T Consensus 261 ~REisl~~ge~P~----~~Gyp~svf~~l~~l~ERag~~--~~---GSIT~~~tVl~~gdD~~----------------- 314 (433)
T PRK07594 261 AREIALAAGETAV----SGEYPPGVFSALPRLLERTGMG--EK---GSITAFYTVLVEGDDMN----------------- 314 (433)
T ss_pred HHHHHHhcCCCCC----CCCcCchhHHHhHHHHHhhcCC--CC---cchheeeeeeecCCCCC-----------------
Confidence 5888888999998 4476777777889999998532 23 36666666665544432
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhc
Q psy3754 206 LPFLGPLGVAKVGYIDGKYILNPTTEQLKK 235 (755)
Q Consensus 206 IP~~~~vaav~vg~~~g~~vldPt~~E~~~ 235 (755)
+|++-...++.||+++|+-...+...
T Consensus 315 ----dpi~d~~~~ilDG~IvLsr~la~~g~ 340 (433)
T PRK07594 315 ----EPLADEVRSLLDGHIVLSRRLAERGH 340 (433)
T ss_pred ----CchHHHhhhhcceEEEEcHHHHhCCC
Confidence 45665555668999999877766644
No 282
>PRK06002 fliI flagellum-specific ATP synthase; Validated
Probab=34.43 E-value=1.6e+02 Score=34.06 Aligned_cols=93 Identities=23% Similarity=0.242 Sum_probs=61.4
Q ss_pred EeEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcC
Q psy3754 125 DYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSIS 204 (755)
Q Consensus 125 ~y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s 204 (755)
-|+|-.-+.|++|+ |+|-|..--.+++|+++|+=+- +. -...+...-+|+.-.++.+
T Consensus 269 A~rEisl~~ge~P~----~~gyp~~vf~~l~~l~ERag~~-~~--~~GSIT~~~tvl~~~dd~~---------------- 325 (450)
T PRK06002 269 AAREVALAAGEPPV----ARGYPPSVFSELPRLLERAGPG-AE--GGGSITGIFSVLVDGDDHN---------------- 325 (450)
T ss_pred HHHHHHHhcCCCCc----cccCCccHHHHhhHHHHHhccC-CC--CCeeeeEEEEEEecCCCCC----------------
Confidence 35777788899987 5577777778899999999763 22 1237777777776655533
Q ss_pred CCCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CcccEEEEee
Q psy3754 205 ELPFLGPLGVAKVGYIDGKYILNPTTEQLKK-SHLDLLVAGT 245 (755)
Q Consensus 205 ~IP~~~~vaav~vg~~~g~~vldPt~~E~~~-s~~~l~va~~ 245 (755)
+|++--..+..||+++++-...+... ...|..-+.+
T Consensus 326 -----dpI~d~~~~i~Dg~ivLsr~la~~g~~PAIDv~~S~S 362 (450)
T PRK06002 326 -----DPVADSIRGTLDGHIVLDRAIAEQGRYPAVDPLASIS 362 (450)
T ss_pred -----CccHHHHHhhcceEEEEcHHHHhCCCCCccCCccccC
Confidence 34444445567999999877766644 3345444443
No 283
>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=34.01 E-value=50 Score=27.97 Aligned_cols=42 Identities=17% Similarity=0.290 Sum_probs=32.6
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEE
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLF 697 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~ 697 (755)
|..+ .++|++++++ .+|.++.+.. ...+++|+.++.+|.++.
T Consensus 24 V~~i-~~~G~fV~l~~~~~Glv~~se~---------------~~~~~iGd~v~v~I~~i~ 67 (77)
T cd04473 24 VNGV-AKYGVFVDLNDHVRGLIHRSNL---------------LRDYEVGDEVIVQVTDIP 67 (77)
T ss_pred EEeE-ecceEEEEECCCcEEEEEchhc---------------cCcCCCCCEEEEEEEEEC
Confidence 4444 5799999997 5788888652 245899999999999984
No 284
>PRK09099 type III secretion system ATPase; Provisional
Probab=33.90 E-value=2e+02 Score=33.14 Aligned_cols=91 Identities=24% Similarity=0.312 Sum_probs=63.6
Q ss_pred eEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCC
Q psy3754 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISE 205 (755)
Q Consensus 126 y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~ 205 (755)
|+|-.-+.|++|+ |+|=|..--..++|+++|+=+. . ...+...-+|+.-+++..
T Consensus 269 ~REisl~~gepP~----~~gyP~~vf~~l~~l~ERag~~--~---~GSIT~i~tVl~~~dd~~----------------- 322 (441)
T PRK09099 269 QREIGLAAGEPPA----RRGFPPSVFAELPRLLERAGMG--E---TGSITALYTVLAEDESGS----------------- 322 (441)
T ss_pred HHHHHHhcCCCCc----cccCCccHHHHhHHHHHhhcCC--C---CcchheeEEEEecCCCcC-----------------
Confidence 6888888999998 5577888888899999998531 2 337777777776655533
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CcccEEEEeec
Q psy3754 206 LPFLGPLGVAKVGYIDGKYILNPTTEQLKK-SHLDLLVAGTE 246 (755)
Q Consensus 206 IP~~~~vaav~vg~~~g~~vldPt~~E~~~-s~~~l~va~~~ 246 (755)
+||+--..++.||+++++-...+... ...|...+.++
T Consensus 323 ----dpI~d~~~~i~DG~ivLsr~La~~g~yPAIDvl~S~SR 360 (441)
T PRK09099 323 ----DPIAEEVRGILDGHMILSREIAARNQYPAIDVLGSLSR 360 (441)
T ss_pred ----CcchhhhheecceEEEEcHHHHhCCCCCccCCccccCc
Confidence 46666566678999999987776644 33454444443
No 285
>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=33.07 E-value=32 Score=29.30 Aligned_cols=27 Identities=30% Similarity=0.484 Sum_probs=22.8
Q ss_pred ceeEEeeCCcccceeeccccceeeeec
Q psy3754 618 RLITIKIDPSKIRDVIGKGGSTIRTLT 644 (755)
Q Consensus 618 ~~~~~~i~~~ki~~~IG~gGk~ik~i~ 644 (755)
....+.++++..+-+||+.|+++.+|+
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ 50 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQ 50 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHH
Confidence 334578889999999999999999875
No 286
>PRK08472 fliI flagellum-specific ATP synthase; Validated
Probab=32.79 E-value=2e+02 Score=33.01 Aligned_cols=81 Identities=20% Similarity=0.313 Sum_probs=57.1
Q ss_pred eEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCC
Q psy3754 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISE 205 (755)
Q Consensus 126 y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~ 205 (755)
++|-.-+.|++|+ |+|=|..--..++++++|+=+ +. + ...+...-+|+--.++.+
T Consensus 262 ~REi~l~~ge~P~----~~Gyp~~vf~~l~~l~ERag~--~~-g-~GSIT~~~tVlv~gdD~~----------------- 316 (434)
T PRK08472 262 QREIGLALGEPPT----SKGYPPSVLSLLPQLMERAGK--EE-G-KGSITAFFTVLVEGDDMS----------------- 316 (434)
T ss_pred HHHHHHhcCCCCC----ccCcCchHHHHHHHHHHHhcc--CC-C-CceeeEeEEEEecCCCCC-----------------
Confidence 5888888899998 557777777788999999875 33 1 237777777774333322
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhc
Q psy3754 206 LPFLGPLGVAKVGYIDGKYILNPTTEQLKK 235 (755)
Q Consensus 206 IP~~~~vaav~vg~~~g~~vldPt~~E~~~ 235 (755)
+|++--..++.||+++++....+...
T Consensus 317 ----dpi~d~~~~i~Dg~ivLsr~la~~g~ 342 (434)
T PRK08472 317 ----DPIADQSRSILDGHIVLSRELTDFGI 342 (434)
T ss_pred ----CCchHHhhhhcceEEEEcHHHHhCCC
Confidence 45555555678999999988877644
No 287
>PRK05688 fliI flagellum-specific ATP synthase; Validated
Probab=32.30 E-value=2e+02 Score=33.31 Aligned_cols=89 Identities=21% Similarity=0.271 Sum_probs=60.1
Q ss_pred EeEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcC
Q psy3754 125 DYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSIS 204 (755)
Q Consensus 125 ~y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s 204 (755)
-|+|-.-+.|++|+ |+|=|..--..++|+++|+=+. . +-...+...-+|+--.++..
T Consensus 273 A~REisl~~gepP~----~~GYp~svfs~l~~l~ERag~~--~-~~~GSITai~tVl~~gdD~~---------------- 329 (451)
T PRK05688 273 AQREIALAIGEPPA----TKGYPPSVFAKLPKLVERAGNA--E-PGGGSITAFYTVLSEGDDQQ---------------- 329 (451)
T ss_pred HHHHHHHhcCCCCc----ccCCCchHHHHhHHHHHHhcCC--C-CCCceeeEEEEEEecCCCCC----------------
Confidence 36888889999998 5577777777889999998742 2 11347777777776655533
Q ss_pred CCCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CcccEE
Q psy3754 205 ELPFLGPLGVAKVGYIDGKYILNPTTEQLKK-SHLDLL 241 (755)
Q Consensus 205 ~IP~~~~vaav~vg~~~g~~vldPt~~E~~~-s~~~l~ 241 (755)
+||+-...++.||+++|+-...+... ...|..
T Consensus 330 -----dpI~d~~~silDGhIvLsr~La~~g~yPAIDvl 362 (451)
T PRK05688 330 -----DPIADSARGVLDGHIVLSRRLAEEGHYPAIDIE 362 (451)
T ss_pred -----CchHHHHHhhccEEEEEcHHHHhCCCCCccCCc
Confidence 34444444567999999877766644 334443
No 288
>PRK08927 fliI flagellum-specific ATP synthase; Validated
Probab=32.20 E-value=2.1e+02 Score=33.06 Aligned_cols=94 Identities=18% Similarity=0.209 Sum_probs=62.4
Q ss_pred EeEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcC
Q psy3754 125 DYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSIS 204 (755)
Q Consensus 125 ~y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s 204 (755)
-|+|-.-+.|+.|+ |+|=|..--..++|+++|+=+-.-. ...+..+-+|+--.++.
T Consensus 263 A~REisl~~ge~P~----~~Gyp~~~f~~l~~l~ERaG~~~~~---~GSIT~i~tVlv~gdD~----------------- 318 (442)
T PRK08927 263 AQREIGLSAGEPPT----TKGYTPTVFAELPRLLERAGPGPIG---EGTITGLFTVLVDGDDH----------------- 318 (442)
T ss_pred hhhHHHHhcCCCCc----ccCCCcchHHHhhHHHHHhcCCCCC---CeeeeeeeeeEccCCCC-----------------
Confidence 36888888899997 5577777778899999998751111 23677777777333332
Q ss_pred CCCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CcccEEEEeec
Q psy3754 205 ELPFLGPLGVAKVGYIDGKYILNPTTEQLKK-SHLDLLVAGTE 246 (755)
Q Consensus 205 ~IP~~~~vaav~vg~~~g~~vldPt~~E~~~-s~~~l~va~~~ 246 (755)
++|++--..+..||+++++....+... ...|..-+.++
T Consensus 319 ----~dpi~d~~~~i~Dg~ivLsr~La~~g~~PAIDvl~S~SR 357 (442)
T PRK08927 319 ----NEPVADAVRGILDGHIVMERAIAERGRYPAINVLKSVSR 357 (442)
T ss_pred ----CCchhhhhhccccEEEEEcHHHHhCCCCCccCCcccccc
Confidence 245555556678999999988777654 44455444443
No 289
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=32.08 E-value=91 Score=24.69 Aligned_cols=47 Identities=21% Similarity=0.364 Sum_probs=32.4
Q ss_pred cccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 645 EETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 645 ~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
...|++++++ .+|.++.+...... .......+++|+.+.++|.++..
T Consensus 14 ~~~g~~v~i~~~~~g~l~~~~~~~~~-------~~~~~~~~~~G~~v~~~V~~~~~ 62 (72)
T smart00316 14 TPFGAFVDLGNGVEGLIPISELSDKR-------VKDPEEVLKVGDEVKVKVLSVDE 62 (72)
T ss_pred EccEEEEEeCCCCEEEEEHHHCCccc-------cCCHHHeecCCCEEEEEEEEEeC
Confidence 3478888886 46777776555433 11123458999999999999865
No 290
>TIGR03496 FliI_clade1 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=31.10 E-value=2.5e+02 Score=32.06 Aligned_cols=93 Identities=20% Similarity=0.250 Sum_probs=62.4
Q ss_pred eEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCC
Q psy3754 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISE 205 (755)
Q Consensus 126 y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~ 205 (755)
|+|-.-+.|++|+ |+|=|..--..++|+++|+=+-. . -...+...-+|+.-.++.+
T Consensus 243 ~REisl~~ge~P~----~~gyp~~~f~~l~~l~ERag~~~-~--~~GSIT~~~tv~~~~dd~~----------------- 298 (411)
T TIGR03496 243 QREIALAIGEPPA----TKGYPPSVFAKLPQLVERAGNGE-E--GKGSITAFYTVLVEGDDQQ----------------- 298 (411)
T ss_pred HHHHHHhcCCCCC----ccCcCHHHHHHhHHHHHHhcccC-C--CCcceeEEEEEEccCCCCC-----------------
Confidence 5788888899988 55777777778899999986521 1 1237777777775554433
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CcccEEEEeec
Q psy3754 206 LPFLGPLGVAKVGYIDGKYILNPTTEQLKK-SHLDLLVAGTE 246 (755)
Q Consensus 206 IP~~~~vaav~vg~~~g~~vldPt~~E~~~-s~~~l~va~~~ 246 (755)
+|++--..+..||+++++-...+... ...|...+.++
T Consensus 299 ----dpi~~~~~~i~dg~ivLsr~la~~g~~PAId~~~S~SR 336 (411)
T TIGR03496 299 ----DPIADAARAILDGHIVLSRELAEQGHYPAIDILASISR 336 (411)
T ss_pred ----CcchhhhcccccEEEEEchhHHhCCCCCccCCCccccc
Confidence 46665556678999999987777644 33444444433
No 291
>PRK12597 F0F1 ATP synthase subunit beta; Provisional
Probab=30.56 E-value=1.7e+02 Score=33.88 Aligned_cols=91 Identities=19% Similarity=0.220 Sum_probs=58.4
Q ss_pred eEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCC
Q psy3754 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISE 205 (755)
Q Consensus 126 y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~ 205 (755)
|||-.-+.|++|+ |+|=|..--..++++.+|+-+. . ...+...-+|+--.++..
T Consensus 253 ~REisl~~gepP~----~~GYPpsvfs~l~~l~ERag~~----~-~GSIT~i~tVl~~~dD~~----------------- 306 (461)
T PRK12597 253 GSEVSGLLGRMPS----RVGYQPTLASEVAELQERIAST----K-NGSITSIQAVYVPADDLT----------------- 306 (461)
T ss_pred HHHHHHhcCCCCC----cCCcCchhHHHHHHHHHhhcCC----C-CccccEEEEEEecCCCCC-----------------
Confidence 5788888999998 4465655555678888887532 2 347777777776655522
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CcccEEEEeec
Q psy3754 206 LPFLGPLGVAKVGYIDGKYILNPTTEQLKK-SHLDLLVAGTE 246 (755)
Q Consensus 206 IP~~~~vaav~vg~~~g~~vldPt~~E~~~-s~~~l~va~~~ 246 (755)
+|++....+..||+++++-...+... ...|..-+.++
T Consensus 307 ----dPI~d~~~~ilDG~IvLsr~La~~g~yPAIDvl~S~SR 344 (461)
T PRK12597 307 ----DPAAVAIFSHLDSTVVLSRAQAAKGIYPAIDPLASSSN 344 (461)
T ss_pred ----CccHHHHHhhcceEEEEcHHHHhCCCCCccCCcccccc
Confidence 34444334567899999987777644 34455444444
No 292
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=29.87 E-value=1.2e+02 Score=23.70 Aligned_cols=47 Identities=36% Similarity=0.449 Sum_probs=29.3
Q ss_pred EEEEEEE-eeeEEEEEcCC-eeEEEeccccCcccccCcccccCCCCEEEEEEEEE
Q psy3754 691 GIVLRLF-DFGAIIRILSG-KDGLLHISQISSKRVNIITDFLKENQKVRVKVLGI 743 (755)
Q Consensus 691 G~V~~I~-~fG~FVel~~g-~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~i 743 (755)
|+|.... .||.+.. .+. .+-++|.+.+.. . ...+..||.|.+++..-
T Consensus 2 G~i~~~~~g~gfv~~-~~~~~~i~v~~~~~~~-~----~~~~~~Gd~V~~~i~~~ 50 (64)
T smart00357 2 GVVKWFNKGFGFIRP-DDGGKDVFVHPSQIQG-G----LKSLREGDEVEFKVVSP 50 (64)
T ss_pred eEEEEEcCCeeEEec-CCCCccEEEEhHHhhc-C----CCcCCCCCEEEEEEEEc
Confidence 5555443 4665443 333 578888876532 1 12377799999999864
No 293
>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase.
Probab=29.78 E-value=2.3e+02 Score=32.42 Aligned_cols=91 Identities=22% Similarity=0.334 Sum_probs=63.5
Q ss_pred eEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCC
Q psy3754 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISE 205 (755)
Q Consensus 126 y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~ 205 (755)
|+|-.-+.|++|+ |+|=|..--..++|+++|+=+. . ...+..+-+|+.-.++.+
T Consensus 251 ~rei~l~~ge~P~----~~gyp~~~f~~l~~l~ERag~~--~---~GSIT~~~tv~~~~dd~~----------------- 304 (422)
T TIGR02546 251 LREIGLAAGEPPA----RGGYPPSVFSSLPRLLERAGNG--E---KGSITALYTVLVEGDDMN----------------- 304 (422)
T ss_pred HHHHHHhcCCCCc----ccccChhHHHHhHHHHHHhcCC--C---CCceeEEEEEeccCCCCC-----------------
Confidence 4666778899987 5577877778899999998762 2 347777777776655533
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CcccEEEEeec
Q psy3754 206 LPFLGPLGVAKVGYIDGKYILNPTTEQLKK-SHLDLLVAGTE 246 (755)
Q Consensus 206 IP~~~~vaav~vg~~~g~~vldPt~~E~~~-s~~~l~va~~~ 246 (755)
+||+-...+..||++++|-...+... ...|...+.++
T Consensus 305 ----~pi~~~~~~i~dg~i~Lsr~la~~g~yPAId~~~S~SR 342 (422)
T TIGR02546 305 ----DPIADEVRSILDGHIVLSRALAERNHYPAIDVLASLSR 342 (422)
T ss_pred ----CCchhhhhccccEEEEEcHHHHhCCCCCccCCcccccc
Confidence 56666666778999999987776644 33454444443
No 294
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=29.65 E-value=1.4e+02 Score=23.85 Aligned_cols=48 Identities=15% Similarity=0.144 Sum_probs=27.5
Q ss_pred cEEEEEEEEEEeee----EEEEEcCC--eeEEEeccccCcccccCcccccCCCCEEEEEEE
Q psy3754 687 KVYTGIVLRLFDFG----AIIRILSG--KDGLLHISQISSKRVNIITDFLKENQKVRVKVL 741 (755)
Q Consensus 687 ~~~~G~V~~I~~fG----~FVel~~g--~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~ 741 (755)
-.+.|+|..|.+-| +.+++.++ +...+.... ... -.+++||+|.+.+.
T Consensus 5 N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~-----~~~--L~L~~G~~V~~~ik 58 (64)
T PF03459_consen 5 NQLPGTVESIENLGSEVEVTLDLGGGETLTARITPES-----AEE--LGLKPGDEVYASIK 58 (64)
T ss_dssp EEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHH-----HHH--CT-STT-EEEEEE-
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHH-----HHH--cCCCCCCEEEEEEe
Confidence 46899999999999 34444444 233333221 111 12889999998874
No 295
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=29.37 E-value=9.8 Score=32.05 Aligned_cols=28 Identities=32% Similarity=0.495 Sum_probs=23.9
Q ss_pred CceeEEeeCCcccceeeccccceeeeec
Q psy3754 617 PRLITIKIDPSKIRDVIGKGGSTIRTLT 644 (755)
Q Consensus 617 P~~~~~~i~~~ki~~~IG~gGk~ik~i~ 644 (755)
.....+.++++..+.+||+.|+++++|+
T Consensus 28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq 55 (73)
T PF13083_consen 28 GDTIVVNIDGEDAGRLIGKHGKTLNALQ 55 (73)
T ss_dssp TTEEEEEEESCCCHHHCTTHHHHHHHHH
T ss_pred ceEEEEEECCCccceEECCCCeeHHHHH
Confidence 4455678899999999999999999885
No 296
>CHL00060 atpB ATP synthase CF1 beta subunit
Probab=28.34 E-value=2.5e+02 Score=32.86 Aligned_cols=88 Identities=18% Similarity=0.172 Sum_probs=60.7
Q ss_pred eEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCC
Q psy3754 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISE 205 (755)
Q Consensus 126 y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~ 205 (755)
|||-.-+.|++|+ |+|=|..--..++||++|+=. +.+ ..+...=+|+--.++..
T Consensus 278 ~REIsl~~gepP~----~~GYPpsvfs~l~~LlERaG~--~~~---GSITai~tVl~~gdD~t----------------- 331 (494)
T CHL00060 278 GSEVSALLGRMPS----AVGYQPTLSTEMGSLQERITS--TKE---GSITSIQAVYVPADDLT----------------- 331 (494)
T ss_pred HHHHHHhcCCCCC----CCCcCCCHHHHhHHHHHhccC--CCC---CCeeEEEEEECCCCCCC-----------------
Confidence 5888889999998 557777777789999999764 233 37777766766655533
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CcccEEEE
Q psy3754 206 LPFLGPLGVAKVGYIDGKYILNPTTEQLKK-SHLDLLVA 243 (755)
Q Consensus 206 IP~~~~vaav~vg~~~g~~vldPt~~E~~~-s~~~l~va 243 (755)
+||+--..++.||+++++....+... ...|..-+
T Consensus 332 ----dPI~d~~~silDGhIvLsr~La~~G~yPAIDvl~S 366 (494)
T CHL00060 332 ----DPAPATTFAHLDATTVLSRGLAAKGIYPAVDPLDS 366 (494)
T ss_pred ----CcchHhhhhhcceEEEEcHHHHhCCCCCCcCCccc
Confidence 45555555568999999887776654 33444433
No 297
>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=27.92 E-value=88 Score=24.23 Aligned_cols=46 Identities=17% Similarity=0.273 Sum_probs=32.2
Q ss_pred ccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 646 ETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 646 ~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
.+|++++++ .+|.++.+...+... ......+++|+.+.++|.++.+
T Consensus 10 ~~g~~v~l~~~~~g~~~~~~~~~~~~-------~~~~~~~~~G~~v~~~v~~~d~ 57 (65)
T cd00164 10 KFGVFVELEDGVEGLVHISELSDKFV-------KDPSEVFKVGDEVEVKVLEVDP 57 (65)
T ss_pred eeeEEEEecCCCEEEEEHHHCCCccc-------cCHhhEeCCCCEEEEEEEEEcC
Confidence 577888876 578887766554332 2223458999999999999854
No 298
>PRK09280 F0F1 ATP synthase subunit beta; Validated
Probab=27.46 E-value=94 Score=35.99 Aligned_cols=91 Identities=19% Similarity=0.191 Sum_probs=64.2
Q ss_pred eEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCC
Q psy3754 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISE 205 (755)
Q Consensus 126 y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~ 205 (755)
|||-.-+.|++|+ |+|=|..---.++++++|+-. .. ...+...-+|+--.++..
T Consensus 254 ~REisl~~gepP~----~~GYPpsvfs~l~~L~ERag~--~~---~GSITai~tVl~~gdD~~----------------- 307 (463)
T PRK09280 254 GSEVSALLGRMPS----AVGYQPTLATEMGQLQERITS--TK---KGSITSVQAVYVPADDLT----------------- 307 (463)
T ss_pred HHHHHHhcCCCCc----ccCcCchHHHHHHHHHHHhcC--CC---CCceeEEEEEECcCCCCC-----------------
Confidence 5788889999998 456666666788899999853 12 448888888887776644
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CcccEEEEeec
Q psy3754 206 LPFLGPLGVAKVGYIDGKYILNPTTEQLKK-SHLDLLVAGTE 246 (755)
Q Consensus 206 IP~~~~vaav~vg~~~g~~vldPt~~E~~~-s~~~l~va~~~ 246 (755)
+||+-...+..||+++++....+... ...|...+.++
T Consensus 308 ----dPI~d~~~silDGhIvLsr~La~~g~yPAIDvl~S~SR 345 (463)
T PRK09280 308 ----DPAPATTFAHLDATTVLSRQIAELGIYPAVDPLDSTSR 345 (463)
T ss_pred ----CcchHhhhhhcceEEEEcHHHHhCCCCCccCCcccccc
Confidence 46666566678999999988877754 44555544443
No 299
>PRK01712 carbon storage regulator; Provisional
Probab=27.14 E-value=82 Score=26.27 Aligned_cols=29 Identities=17% Similarity=0.411 Sum_probs=23.7
Q ss_pred CcccccCCCCEEEEEEEEEcCCCcEEEEEe
Q psy3754 725 IITDFLKENQKVRVKVLGIDDRGRIKLSMI 754 (755)
Q Consensus 725 ~~~~~~kvGd~V~VkV~~id~~gki~LS~k 754 (755)
++.+.+.+||.++++|++++ .++++|.+.
T Consensus 7 k~gE~I~Igd~I~I~V~~i~-~~~VrlGI~ 35 (64)
T PRK01712 7 KVGESLMIGDDIEVTVLGVK-GNQVRIGIN 35 (64)
T ss_pred cCCCEEEeCCCEEEEEEEEe-CCEEEEEEE
Confidence 45677899999999999997 577888763
No 300
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=26.83 E-value=1.7e+02 Score=23.66 Aligned_cols=63 Identities=21% Similarity=0.321 Sum_probs=36.7
Q ss_pred EEEEEEEEE-Eeee--EEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC-CCc-EEEEE
Q psy3754 688 VYTGIVLRL-FDFG--AIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD-RGR-IKLSM 753 (755)
Q Consensus 688 ~~~G~V~~I-~~fG--~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~-~gk-i~LS~ 753 (755)
.+.|.|.++ ...+ +|+.|..+. |-+.+.-.. +......+.+++|+.|.|+ =.+.. +++ +.|..
T Consensus 2 ~v~G~V~~~~~~~~~~~~~~l~D~t-g~i~~~~~~-~~~~~~~~~l~~g~~v~v~-G~v~~~~~~~~~l~~ 69 (75)
T PF01336_consen 2 TVEGRVTSIRRSGGKIVFFTLEDGT-GSIQVVFFN-EEYERFREKLKEGDIVRVR-GKVKRYNGGELELIV 69 (75)
T ss_dssp EEEEEEEEEEEEETTEEEEEEEETT-EEEEEEEET-HHHHHHHHTS-TTSEEEEE-EEEEEETTSSEEEEE
T ss_pred EEEEEEEEEEcCCCCEEEEEEEECC-ccEEEEEcc-HHhhHHhhcCCCCeEEEEE-EEEEEECCccEEEEE
Confidence 468999999 4444 567765543 444433322 2233445669999999987 33443 444 77654
No 301
>PHA02945 interferon resistance protein; Provisional
Probab=26.74 E-value=76 Score=28.12 Aligned_cols=52 Identities=17% Similarity=0.165 Sum_probs=36.3
Q ss_pred cccceEEeec----CceeEEEEec--ChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEeeeEEEEE
Q psy3754 645 EETGTQIDIN----DEGIITIASF--NSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRI 705 (755)
Q Consensus 645 ~~~g~~I~i~----~~G~v~i~~~--~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~fG~FVel 705 (755)
+.+|++++++ -+|.+++|.. .... ++. -..+ +|+.+..+|.++.+---.|++
T Consensus 22 ~d~ga~v~L~EY~g~eg~i~~seveva~~w-------vK~-rd~l-~GqkvV~KVirVd~~kg~IDl 79 (88)
T PHA02945 22 NGYALYIDLFDYPHSEAILAESVQMHMNRY-------FKY-RDKL-VGKTVKVKVIRVDYTKGYIDV 79 (88)
T ss_pred cCceEEEEecccCCcEEEEEeehhhhccce-------Eee-eeEe-cCCEEEEEEEEECCCCCEEEe
Confidence 6899999886 3799999833 3332 232 2235 899999999998766555554
No 302
>PRK07960 fliI flagellum-specific ATP synthase; Validated
Probab=26.63 E-value=3.8e+02 Score=31.09 Aligned_cols=92 Identities=18% Similarity=0.250 Sum_probs=62.1
Q ss_pred eEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCC
Q psy3754 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISE 205 (755)
Q Consensus 126 y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~ 205 (755)
|+|-..+.|++|+ |+|=|..--..++++++|+=+-.-.+ ..+..+-+|+--.++.+
T Consensus 281 ~rEisl~~ge~P~----~~gypp~~f~~l~~l~ERag~~~~~~---GSIT~i~tVlv~~dD~~----------------- 336 (455)
T PRK07960 281 QREIALAIGEPPA----TKGYPPSVFAKLPALVERAGNGISGG---GSITAFYTVLTEGDDQQ----------------- 336 (455)
T ss_pred HHHHHHhcCCCCc----cccCCcchhhhhhHHHHHHhcCCCCC---eeeeeEEEEEEcCCCCC-----------------
Confidence 5788888899987 45777777778899999987621122 47777777776655433
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CcccEEEEee
Q psy3754 206 LPFLGPLGVAKVGYIDGKYILNPTTEQLKK-SHLDLLVAGT 245 (755)
Q Consensus 206 IP~~~~vaav~vg~~~g~~vldPt~~E~~~-s~~~l~va~~ 245 (755)
+|++--..+..||+++|+-...+... ...|..-+.+
T Consensus 337 ----dpi~d~~~~i~dg~ivLsr~la~~g~yPAID~l~S~S 373 (455)
T PRK07960 337 ----DPIADSARAILDGHIVLSRRLAEAGHYPAIDIEASIS 373 (455)
T ss_pred ----cchHHHhhhhcceEEEECHHHHhCCCCCccCcCcccC
Confidence 45554455567999999987777654 4455544444
No 303
>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=26.46 E-value=59 Score=26.14 Aligned_cols=29 Identities=21% Similarity=0.395 Sum_probs=22.9
Q ss_pred CcccccCCCCEEEEEEEEEcCCCcEEEEEe
Q psy3754 725 IITDFLKENQKVRVKVLGIDDRGRIKLSMI 754 (755)
Q Consensus 725 ~~~~~~kvGd~V~VkV~~id~~gki~LS~k 754 (755)
++.+.+.+||.|.++|++++ .++++|.+.
T Consensus 7 k~gE~I~Ig~~I~I~Vl~i~-~~~VklgI~ 35 (54)
T PF02599_consen 7 KVGESIVIGDDIEITVLEIS-GGQVKLGID 35 (54)
T ss_dssp ETT-EEEETTTEEEEEEEEE-TTEEEEEEE
T ss_pred cCCCEEEECCCEEEEEEEEc-CCEEEEEEE
Confidence 45667889999999999998 677887653
No 304
>PRK08059 general stress protein 13; Validated
Probab=26.14 E-value=65 Score=30.12 Aligned_cols=51 Identities=12% Similarity=0.322 Sum_probs=36.8
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
|..+ .++|++++++ .+|.++++...... +......+++|+.+.++|.++..
T Consensus 15 V~~i-~~~G~fV~i~~~~~Gli~~sel~~~~-------~~~~~~~~~vGD~I~vkI~~id~ 67 (123)
T PRK08059 15 VTGI-QPYGAFVALDEETQGLVHISEITHGF-------VKDIHDFLSVGDEVKVKVLSVDE 67 (123)
T ss_pred EEEE-ecceEEEEECCCCEEEEEHHHCCccc-------ccCHHHcCCCCCEEEEEEEEEEC
Confidence 3344 4699999997 58999987665443 22233458999999999999853
No 305
>cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=24.98 E-value=1.6e+02 Score=27.89 Aligned_cols=56 Identities=32% Similarity=0.408 Sum_probs=37.2
Q ss_pred EEEEEEEEEeee-EE-EEEcCCeeEEEeccccCccc-ccCcccccCCCCEEEE--EEEEEc
Q psy3754 689 YTGIVLRLFDFG-AI-IRILSGKDGLLHISQISSKR-VNIITDFLKENQKVRV--KVLGID 744 (755)
Q Consensus 689 ~~G~V~~I~~fG-~F-Vel~~g~~Gllhisel~~~~-~~~~~~~~kvGd~V~V--kV~~id 744 (755)
+.|+|+.+.+-| +| ++..+|.+-|+|+.-=+.+- -+-....++.||+|++ .+.++|
T Consensus 42 ~~G~v~~i~~T~HA~~i~~~~G~eiLiHiGidTv~l~g~gF~~~vk~Gd~V~~G~~l~~~D 102 (124)
T cd00210 42 VDGTIVQIFPTKHAIGIESDSGVEILIHIGIDTVKLNGEGFTSHVEEGQRVKQGDKLLEFD 102 (124)
T ss_pred CCeEEEEEccCCCEEEEEeCCCcEEEEEeeeeeeecCCCceEEEecCCCEEcCCCEEEEEc
Confidence 679999997755 23 55567999999997533221 1122344778888876 677777
No 306
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=24.92 E-value=2.7e+02 Score=26.72 Aligned_cols=55 Identities=24% Similarity=0.137 Sum_probs=35.6
Q ss_pred cCCcEEEEEEEEEEeee---------EEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC
Q psy3754 684 QIGKVYTGIVLRLFDFG---------AIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD 745 (755)
Q Consensus 684 ~~G~~~~G~V~~I~~fG---------~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~ 745 (755)
..|.++.=+|+.+.+.| +.|+|.++-..|.|+.. .+ -+.+++|++|++++.....
T Consensus 62 ~~G~V~t~Tv~~~~~~~~~~~~P~viaiV~l~~~~~i~~~i~~------~~-p~~v~iGm~V~~v~~~~~~ 125 (140)
T COG1545 62 GEGKVETYTVVYVKPPGFSLEEPYVIAIVELEEGGRILGQLVD------VD-PDDVEIGMKVEAVFRKREE 125 (140)
T ss_pred CCeEEEEEEEEeeCCCCcccCCCEEEEEEEeCCCCceEEEEEe------cC-cccccCCCEEEEEEEEccc
Confidence 44555555555555544 45666655567777665 11 1348999999999998765
No 307
>PRK07196 fliI flagellum-specific ATP synthase; Validated
Probab=24.41 E-value=5.1e+02 Score=29.86 Aligned_cols=83 Identities=20% Similarity=0.297 Sum_probs=57.4
Q ss_pred EEeEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhc
Q psy3754 124 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSI 203 (755)
Q Consensus 124 v~y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~ 203 (755)
.-|||-..+.|++|+ |+|=|..---.++|+++|+=+- . + ...+..+-+|+.-.++..
T Consensus 259 ~A~REisl~~ge~P~----~~Gyp~svf~~l~~l~ERag~~--~-~-~GSIT~~~tVl~~~dD~~--------------- 315 (434)
T PRK07196 259 MAQREIALSLGEPPA----TKGYPPSAFSIIPRLAESAGNS--S-G-NGTMTAIYTVLAEGDDQQ--------------- 315 (434)
T ss_pred hhhhHHHHhcCCCCc----ccCcCHHHHHHhHHHHHHhhcC--C-C-CEEeeeeeEEEccCCCCC---------------
Confidence 346888888999998 4577777777889999998431 2 1 247777777776655533
Q ss_pred CCCCCCCCeEEEEEEEECCEEEEcCCHHHHhc
Q psy3754 204 SELPFLGPLGVAKVGYIDGKYILNPTTEQLKK 235 (755)
Q Consensus 204 s~IP~~~~vaav~vg~~~g~~vldPt~~E~~~ 235 (755)
+|++--..++.||+++++-...+...
T Consensus 316 ------dpi~d~~~~ilDG~ivLsr~la~~g~ 341 (434)
T PRK07196 316 ------DPIVDCARAVLDGHIVLSRKLAEAGH 341 (434)
T ss_pred ------CchhHhhhhhcceEEEEcHHHHhCCC
Confidence 45555555668999999877766644
No 308
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. 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 addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=24.32 E-value=40 Score=26.96 Aligned_cols=26 Identities=31% Similarity=0.351 Sum_probs=19.9
Q ss_pred eeCCcccceeeccccceeeeeccccc
Q psy3754 623 KIDPSKIRDVIGKGGSTIRTLTEETG 648 (755)
Q Consensus 623 ~i~~~ki~~~IG~gGk~ik~i~~~~g 648 (755)
.......+.+||++|++++.++..++
T Consensus 30 ~~~~~~~g~lIGk~G~~l~~l~~l~~ 55 (68)
T cd02409 30 VVARGQPGLVIGKKGQNIRALQKLLQ 55 (68)
T ss_pred EECCCCCceEECCCCccHHHHHHHHH
Confidence 33433578899999999999876666
No 309
>KOG3273|consensus
Probab=24.29 E-value=81 Score=32.09 Aligned_cols=60 Identities=28% Similarity=0.309 Sum_probs=43.5
Q ss_pred ccceeeccccceeeeeccccceEEeecCceeEEEEecChhhhHHHHHHHHHhhhcccCCcEE
Q psy3754 628 KIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVY 689 (755)
Q Consensus 628 ki~~~IG~gGk~ik~i~~~~g~~I~i~~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~ 689 (755)
.|+.+.|+|||+--.|.+-+-..|-+ .+-.+||... ...+..|++.+-.++..-.+|++|
T Consensus 179 AIGRiaGk~GkTkfaIEn~trtrIVl-ad~kIHiLG~-~~niriAR~avcsLIlGsppgkVy 238 (252)
T KOG3273|consen 179 AIGRIAGKGGKTKFAIENVTRTRIVL-ADSKIHILGA-FQNIRIARDAVCSLILGSPPGKVY 238 (252)
T ss_pred HHHHhhcCCCcceeeeeccceeEEEe-cCceEEEeec-chhhHHHHHhhHhhhccCCchhHH
Confidence 47789999999887887666666654 5667888766 455677777776666666677665
No 310
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=24.10 E-value=28 Score=34.55 Aligned_cols=33 Identities=24% Similarity=0.498 Sum_probs=27.7
Q ss_pred EEeeCCcccceeeccccceeeeeccccceEEeec
Q psy3754 621 TIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN 654 (755)
Q Consensus 621 ~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~ 654 (755)
++-+.+.. +..||++|++++.+++.+|-.|.+-
T Consensus 64 IfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevV 96 (166)
T PRK06418 64 ILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVV 96 (166)
T ss_pred EEEEeCCC-cccccccchHHHHHHHHhCCcEEEE
Confidence 45566666 8899999999999999999888763
No 311
>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=23.34 E-value=39 Score=27.94 Aligned_cols=51 Identities=24% Similarity=0.419 Sum_probs=37.3
Q ss_pred eeeeccccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 640 IRTLTEETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 640 ik~i~~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
|..+ +++|++++++ -+|.++++...... .......+++|+.+..+|.++..
T Consensus 12 V~~v-~~~g~~V~l~~~~~g~ip~~~l~~~~-------~~~~~~~~~~G~~v~v~v~~vd~ 64 (74)
T PF00575_consen 12 VTSV-EDFGVFVDLGNGIEGFIPISELSDDR-------IDDPSEVYKIGQTVRVKVIKVDK 64 (74)
T ss_dssp EEEE-ETTEEEEEESTSSEEEEEGGGSSSSE-------ESSSHGTCETTCEEEEEEEEEET
T ss_pred EEEE-ECCEEEEEECCcEEEEEEeehhcCcc-------ccccccccCCCCEEEEEEEEEEC
Confidence 4444 4699999997 57888887776541 22234568999999999999854
No 312
>KOG2190|consensus
Probab=23.29 E-value=36 Score=39.54 Aligned_cols=35 Identities=31% Similarity=0.522 Sum_probs=31.9
Q ss_pred eEEeeCCcccceeeccccceeeeeccccceEEeec
Q psy3754 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIN 654 (755)
Q Consensus 620 ~~~~i~~~ki~~~IG~gGk~ik~i~~~~g~~I~i~ 654 (755)
+.+.++.+.|+-+||++|.+|-+|.+.||+.|.|-
T Consensus 340 ~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~ 374 (485)
T KOG2190|consen 340 QRLLVPSDLIGCIIGKGGAKISEIRQRTGASISIL 374 (485)
T ss_pred eeeccCccccceeecccccchHHHHHhcCCceEEc
Confidence 45678999999999999999999999999999984
No 313
>PRK00568 carbon storage regulator; Provisional
Probab=22.64 E-value=98 Score=26.69 Aligned_cols=29 Identities=24% Similarity=0.539 Sum_probs=23.4
Q ss_pred CcccccCCCCEEEEEEEEEcCCCcEEEEEe
Q psy3754 725 IITDFLKENQKVRVKVLGIDDRGRIKLSMI 754 (755)
Q Consensus 725 ~~~~~~kvGd~V~VkV~~id~~gki~LS~k 754 (755)
++.+.+.+||.|+++|++++ .++++|.+.
T Consensus 7 K~gEsI~Igd~I~I~Vl~i~-g~~VrlGI~ 35 (76)
T PRK00568 7 KVNEGIVIDDNIHIKVISID-RGSVRLGFE 35 (76)
T ss_pred eCCCeEEeCCCeEEEEEEEc-CCEEEEEEE
Confidence 45667899999999999997 677887653
No 314
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=22.48 E-value=1.1e+02 Score=32.83 Aligned_cols=52 Identities=19% Similarity=0.319 Sum_probs=38.0
Q ss_pred eeeeccccceEEeec----CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEee
Q psy3754 640 IRTLTEETGTQIDIN----DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDF 699 (755)
Q Consensus 640 ik~i~~~~g~~I~i~----~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~f 699 (755)
|..+ .++|++++++ -+|.++++...+... ..+-..+++|+.+..+|.++...
T Consensus 16 V~~I-~~~G~fV~L~e~~gieGlI~iSEls~~~i-------~~i~~~~kvGd~V~vkVi~VD~~ 71 (262)
T PRK03987 16 VKEV-KDFGAFVTLDEYPGKEGFIHISEVASGWV-------KNIRDHVKEGQKVVCKVIRVDPR 71 (262)
T ss_pred EEEE-ECCEEEEEECCCCCcEEEEEHHHcCcccc-------cCHHHhCCCCCEEEEEEEEEecc
Confidence 4555 5899999985 379999887655432 22334589999999999999653
No 315
>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=22.47 E-value=2.1e+02 Score=24.28 Aligned_cols=47 Identities=19% Similarity=0.165 Sum_probs=34.0
Q ss_pred cccceEEeec--CceeEEEEecChhhhHHHHHHHHHhhhcccCCcEEEEEEEEEEe
Q psy3754 645 EETGTQIDIN--DEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFD 698 (755)
Q Consensus 645 ~~~g~~I~i~--~~G~v~i~~~~~~~~~~a~~~i~~~~~~~~~G~~~~G~V~~I~~ 698 (755)
...++.+++. -+|.++++...... .+.+...+++||.+.++|.++.+
T Consensus 18 ~~~~~~V~i~~~~~g~l~~~~~~~~~-------~~~~~~~~~~GD~i~~~V~~~~~ 66 (82)
T cd04454 18 NSRFWKVDILSRGTARLEDSSATEKD-------KKEIRKSLQPGDLILAKVISLGD 66 (82)
T ss_pred cCCEEEEEeCCCceEEeechhccCcc-------hHHHHhcCCCCCEEEEEEEEeCC
Confidence 4567788885 47888887665432 22344558999999999999865
No 316
>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit. Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.
Probab=22.04 E-value=1.5e+02 Score=34.33 Aligned_cols=90 Identities=18% Similarity=0.192 Sum_probs=61.5
Q ss_pred eEeeccccCCCCCCcccccCCCCchhhHHHHHhcCcccccccCCCcCeEEEEEEEEecCCCCChhhHHHHHHHHHhhcCC
Q psy3754 126 YIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISE 205 (755)
Q Consensus 126 y~e~~~a~g~ip~~~~kReg~p~~~e~l~sRlIdr~lrpl~p~~~~~~~qi~~~Vls~Dg~~~~~~~ai~aAs~AL~~s~ 205 (755)
|||-.-+.|++|+ |+|=|..---+++||++|+=+--=.+ ..+...=+|+--.++..
T Consensus 254 ~REIsl~~gepP~----~~GYP~svfs~l~~LlERaG~~~~~~---GSITai~tV~~~gdD~~----------------- 309 (458)
T TIGR01041 254 LREISAAREEVPG----RRGYPGYMYTDLATIYERAGRVKGKK---GSITQMPILTMPGDDIT----------------- 309 (458)
T ss_pred HHHHHHhcCCCCC----CCCcCccHHHHhHHHHHhcccCCCCC---cceEEEEEEEcCCCCCC-----------------
Confidence 5888888999998 56778877888999999985411013 37777777776666533
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CcccEEEE
Q psy3754 206 LPFLGPLGVAKVGYIDGKYILNPTTEQLKK-SHLDLLVA 243 (755)
Q Consensus 206 IP~~~~vaav~vg~~~g~~vldPt~~E~~~-s~~~l~va 243 (755)
+||+--..++.||+++|+....+... ...|...+
T Consensus 310 ----dPI~d~~~sIlDGhivLsr~La~~G~yPAIDvl~S 344 (458)
T TIGR01041 310 ----HPIPDLTGYITEGQIVLSRELHRKGIYPPINVLPS 344 (458)
T ss_pred ----CchHHhhhhhcceEEEEcHHHHhCCCCCccCCccc
Confidence 35555555568999999887777644 33444433
No 317
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=21.31 E-value=2.9e+02 Score=23.73 Aligned_cols=51 Identities=20% Similarity=0.177 Sum_probs=33.0
Q ss_pred hcccCCcEEEEEEEEEEeeeEEEEEcCCeeEEEeccccCcccccCcccccCCCCEEEEEEEEEcC
Q psy3754 681 ESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGIDD 745 (755)
Q Consensus 681 ~~~~~G~~~~G~V~~I~~fG~FVel~~g~~Gllhisel~~~~~~~~~~~~kvGd~V~VkV~~id~ 745 (755)
.-+++|++|+-.|..+.+.|==+.-..|+--|+| -.+.||+|+++|..+-+
T Consensus 11 ~PVeeGe~y~V~I~d~g~~GDGiarveGfvVFVp--------------~a~~Gd~V~vkI~~v~~ 61 (73)
T COG3269 11 PPVEEGETYEVEIEDVGDQGDGIARVEGFVVFVP--------------GAEVGDEVKVKITKVKP 61 (73)
T ss_pred CCcccCCEEEEEEEEeccCCCceEEEEEEEEEeC--------------CCCCCCeeeEEEEEeec
Confidence 3468899999999988766521111112222332 16789999999998853
No 318
>PF12907 zf-met2: Zinc-binding
Probab=20.36 E-value=70 Score=24.10 Aligned_cols=22 Identities=27% Similarity=0.258 Sum_probs=18.3
Q ss_pred hHHHHHHHHHHHHHHHh-hccCc
Q psy3754 28 QVALLTSRINDLNIHFK-LHIKD 49 (755)
Q Consensus 28 qia~lt~~I~~l~~h~~-~~~kd 49 (755)
|-.+.|.+-..|.+|+. +|+|.
T Consensus 9 qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 9 QTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred HHHHhcCCHHHHHHHHHccCCCC
Confidence 55668999999999998 78885
Done!