Query gi|254780784|ref|YP_003065197.1| polynucleotide phosphorylase/polyadenylase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 699
No_of_seqs 217 out of 1865
Neff 5.6
Searched_HMMs 39220
Date Sun May 29 19:16:19 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780784.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11824 polynucleotide phosph 100.0 0 0 2257.2 74.2 691 2-692 1-694 (694)
2 TIGR03591 polynuc_phos polyrib 100.0 0 0 2222.8 70.5 676 10-685 1-684 (684)
3 COG1185 Pnp Polyribonucleotide 100.0 0 0 1959.6 59.7 690 1-692 1-692 (692)
4 KOG1067 consensus 100.0 0 0 1691.2 46.8 684 3-697 45-746 (760)
5 TIGR02696 pppGpp_PNP guanosine 100.0 0 0 1360.8 31.7 676 9-686 12-724 (725)
6 PRK00173 rph ribonuclease PH; 100.0 0 0 403.7 21.6 221 312-540 1-237 (237)
7 TIGR02065 ECX1 exosome complex 100.0 5.6E-45 0 384.5 16.5 225 306-541 2-229 (231)
8 PRK03983 exosome complex exonu 100.0 1.6E-41 0 356.4 16.1 236 302-548 3-240 (243)
9 PRK04282 exosome complex RNA-b 100.0 8.6E-34 2.2E-38 293.5 25.0 239 291-540 4-270 (271)
10 COG0689 Rph RNase PH [Translat 100.0 3.9E-31 1E-35 271.9 19.5 221 307-539 3-229 (230)
11 TIGR01966 RNasePH ribonuclease 100.0 4.5E-30 1.1E-34 263.3 18.6 220 313-540 1-237 (237)
12 PRK00173 rph ribonuclease PH; 100.0 4.9E-30 1.2E-34 263.0 16.3 203 13-222 11-236 (237)
13 PRK03983 exosome complex exonu 99.9 1.4E-26 3.7E-31 234.8 14.6 202 14-225 24-234 (243)
14 KOG1068 consensus 99.9 5.4E-24 1.4E-28 213.8 13.9 226 306-541 7-234 (245)
15 PRK11824 polynucleotide phosph 99.9 1.6E-20 4E-25 185.7 16.3 301 14-337 325-647 (694)
16 TIGR03591 polynuc_phos polyrib 99.9 2E-20 5.2E-25 184.7 15.7 300 14-337 321-644 (684)
17 pfam01138 RNase_PH 3' exoribon 99.8 5.3E-19 1.3E-23 173.3 13.8 128 321-454 1-128 (128)
18 PRK08582 hypothetical protein; 99.8 5.4E-19 1.4E-23 173.1 9.1 82 616-697 2-83 (139)
19 TIGR02065 ECX1 exosome complex 99.8 7.3E-18 1.9E-22 164.0 14.2 200 14-223 19-228 (231)
20 PRK05807 hypothetical protein; 99.8 8.9E-19 2.3E-23 171.4 9.1 80 616-696 2-81 (136)
21 cd05686 S1_pNO40 S1_pNO40: pNO 99.8 1.8E-18 4.6E-23 168.9 9.8 71 617-687 1-72 (73)
22 PRK07899 rpsA 30S ribosomal pr 99.7 1.7E-17 4.3E-22 161.0 11.5 85 611-695 285-370 (484)
23 PRK07899 rpsA 30S ribosomal pr 99.7 5.9E-18 1.5E-22 164.8 8.2 108 585-695 174-284 (484)
24 TIGR01966 RNasePH ribonuclease 99.7 1.2E-16 3.1E-21 154.1 14.4 193 14-222 11-236 (237)
25 PRK07252 hypothetical protein; 99.7 2E-17 5E-22 160.5 8.1 80 617-696 1-81 (120)
26 PRK07400 30S ribosomal protein 99.7 4E-17 1E-21 158.0 8.8 84 613-697 190-274 (314)
27 PRK00087 4-hydroxy-3-methylbut 99.7 1.9E-16 4.8E-21 152.5 12.2 85 613-697 559-644 (670)
28 PRK00087 4-hydroxy-3-methylbut 99.7 5E-17 1.3E-21 157.1 7.7 88 608-696 469-557 (670)
29 COG1098 VacB Predicted RNA bin 99.7 3.5E-17 9E-22 158.4 6.8 82 616-697 2-83 (129)
30 cd05684 S1_DHX8_helicase S1_DH 99.7 9.4E-17 2.4E-21 154.9 8.8 75 620-695 1-79 (79)
31 PRK13806 rpsA 30S ribosomal pr 99.7 2.1E-16 5.4E-21 152.1 10.5 81 614-694 286-368 (489)
32 cd04452 S1_IF2_alpha S1_IF2_al 99.7 9.5E-17 2.4E-21 154.9 8.1 73 617-689 1-76 (76)
33 cd05692 S1_RPS1_repeat_hs4 S1_ 99.7 9.5E-17 2.4E-21 154.9 8.1 69 620-688 1-69 (69)
34 PRK04282 exosome complex RNA-b 99.7 1.2E-14 3.1E-19 137.8 18.2 198 13-221 34-268 (271)
35 PRK08059 general stress protei 99.7 1.8E-16 4.7E-21 152.6 8.8 83 615-697 2-85 (119)
36 cd04472 S1_PNPase S1_PNPase: P 99.7 1.1E-16 2.8E-21 154.4 7.5 68 620-687 1-68 (68)
37 COG0689 Rph RNase PH [Translat 99.7 8.1E-15 2.1E-19 139.2 15.9 200 13-222 18-229 (230)
38 COG0539 RpsA Ribosomal protein 99.7 1.2E-15 3.1E-20 145.9 11.6 84 613-696 271-355 (541)
39 PRK06676 rpsA 30S ribosomal pr 99.7 6.1E-16 1.5E-20 148.4 10.0 108 585-697 247-356 (390)
40 PRK06299 rpsA 30S ribosomal pr 99.7 1.9E-15 4.9E-20 144.3 11.9 79 616-694 273-353 (556)
41 PRK12269 bifunctional cytidyla 99.7 4.2E-16 1.1E-20 149.6 8.3 247 422-695 363-656 (863)
42 PRK06299 rpsA 30S ribosomal pr 99.6 6.5E-16 1.7E-20 148.1 8.6 77 617-693 448-525 (556)
43 COG1185 Pnp Polyribonucleotide 99.6 3E-15 7.6E-20 142.7 11.5 310 14-347 323-655 (692)
44 KOG1067 consensus 99.6 5E-15 1.3E-19 140.9 12.5 194 14-223 369-585 (760)
45 PRK13806 rpsA 30S ribosomal pr 99.6 1.1E-15 2.7E-20 146.4 8.2 87 609-695 191-282 (489)
46 pfam01138 RNase_PH 3' exoribon 99.6 6.5E-15 1.7E-19 140.0 12.2 123 13-144 2-128 (128)
47 TIGR00717 rpsA ribosomal prote 99.6 2.2E-15 5.7E-20 143.7 9.4 250 422-694 68-364 (534)
48 COG0539 RpsA Ribosomal protein 99.6 1.5E-15 3.9E-20 145.1 8.1 109 585-696 158-269 (541)
49 PRK12269 bifunctional cytidyla 99.6 5.8E-15 1.5E-19 140.4 9.9 190 492-694 496-742 (863)
50 cd05708 S1_Rrp5_repeat_sc12 S1 99.6 3.7E-15 9.3E-20 142.0 8.5 73 618-690 1-75 (77)
51 PRK03987 translation initiatio 99.6 2E-15 5.1E-20 144.1 7.1 79 615-693 4-85 (262)
52 COG2123 RNase PH-related exori 99.6 4.1E-12 1.1E-16 117.2 23.6 225 299-540 11-271 (272)
53 PRK06676 rpsA 30S ribosomal pr 99.6 3.2E-14 8.1E-19 134.4 12.3 109 585-696 158-269 (390)
54 cd04473 S1_RecJ_like S1_RecJ_l 99.6 1.2E-14 3.1E-19 137.8 8.9 64 615-686 12-75 (77)
55 KOG1069 consensus 99.5 2.2E-13 5.5E-18 127.6 13.1 204 321-541 4-210 (217)
56 cd02393 PNPase_KH Polynucleoti 99.5 1.6E-14 4.1E-19 136.8 6.9 61 551-611 1-61 (61)
57 TIGR00717 rpsA ribosomal prote 99.5 1.2E-13 3E-18 129.8 9.1 89 607-696 188-279 (534)
58 cd05689 S1_RPS1_repeat_ec4 S1_ 99.5 5.9E-14 1.5E-18 132.2 7.5 68 618-685 2-71 (72)
59 cd05691 S1_RPS1_repeat_ec6 S1_ 99.5 1E-13 2.6E-18 130.2 8.1 72 620-691 1-73 (73)
60 cd05685 S1_Tex S1_Tex: The C-t 99.5 8.4E-14 2.1E-18 130.9 7.5 67 620-686 1-68 (68)
61 cd05690 S1_RPS1_repeat_ec5 S1_ 99.5 1.1E-13 2.7E-18 130.1 7.2 66 620-685 1-68 (69)
62 COG2123 RNase PH-related exori 99.5 1.8E-11 4.5E-16 112.0 17.3 198 14-223 34-271 (272)
63 cd05688 S1_RPS1_repeat_ec3 S1_ 99.4 2.6E-13 6.5E-18 127.0 7.5 66 619-685 1-67 (68)
64 cd05698 S1_Rrp5_repeat_hs6_sc5 99.4 3.6E-13 9.3E-18 125.8 8.0 69 620-688 1-70 (70)
65 cd04461 S1_Rrp5_repeat_hs8_sc7 99.4 8.1E-13 2.1E-17 123.0 7.6 73 615-687 10-83 (83)
66 pfam00575 S1 S1 RNA binding do 99.4 1.6E-12 4.1E-17 120.5 8.8 73 616-688 1-74 (74)
67 COG1093 SUI2 Translation initi 99.4 4.6E-13 1.2E-17 124.9 5.3 80 614-693 6-88 (269)
68 cd05706 S1_Rrp5_repeat_sc10 S1 99.4 1.5E-12 3.8E-17 120.8 7.6 72 617-688 1-73 (73)
69 cd05707 S1_Rrp5_repeat_sc11 S1 99.4 1.4E-12 3.6E-17 121.0 6.8 67 620-686 1-68 (68)
70 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.3 3.1E-12 8E-17 118.2 7.4 68 620-687 1-69 (69)
71 pfam03726 PNPase Polyribonucle 99.3 4E-11 1E-15 109.2 9.0 80 239-318 1-80 (80)
72 COG2183 Tex Transcriptional ac 99.2 6.8E-11 1.7E-15 107.3 8.4 79 616-694 655-734 (780)
73 cd05687 S1_RPS1_repeat_ec1_hs1 99.1 2E-10 5E-15 103.5 7.6 69 620-688 1-70 (70)
74 PRK07400 30S ribosomal protein 99.0 2.3E-09 5.9E-14 94.8 9.3 95 589-692 92-187 (314)
75 PTZ00248 eukaryotic translatio 99.0 5.2E-10 1.3E-14 100.1 5.7 79 615-693 13-94 (324)
76 cd04460 S1_RpoE S1_RpoE: RpoE, 99.0 9E-10 2.3E-14 98.1 6.8 68 621-689 1-85 (99)
77 cd00164 S1_like S1_like: Ribos 99.0 1E-09 2.7E-14 97.6 5.9 64 623-686 1-65 (65)
78 TIGR02063 RNase_R ribonuclease 98.9 3.3E-09 8.5E-14 93.5 7.3 197 479-687 518-753 (755)
79 KOG1068 consensus 98.9 4E-08 1E-12 84.7 12.4 200 14-225 24-235 (245)
80 KOG1069 consensus 98.9 6.1E-08 1.6E-12 83.3 13.1 193 14-224 6-210 (217)
81 pfam03725 RNase_PH_C 3' exorib 98.9 1.5E-09 3.8E-14 96.4 4.5 64 147-210 1-67 (67)
82 smart00316 S1 Ribosomal protei 98.8 2.3E-08 5.8E-13 86.8 8.5 71 618-688 1-72 (72)
83 cd05702 S1_Rrp5_repeat_hs11_sc 98.8 1.6E-08 4E-13 88.1 7.6 60 620-679 1-62 (70)
84 cd04471 S1_RNase_R S1_RNase_R: 98.8 2.3E-08 5.9E-13 86.7 8.1 69 619-687 1-82 (83)
85 KOG1614 consensus 98.7 1.4E-05 3.7E-10 64.0 19.6 221 305-541 15-271 (291)
86 TIGR02696 pppGpp_PNP guanosine 98.7 1.3E-08 3.3E-13 88.8 3.9 203 14-224 352-574 (725)
87 PRK11642 exoribonuclease R; Pr 98.7 1.4E-07 3.5E-12 80.4 8.9 73 615-687 639-724 (813)
88 KOG1612 consensus 98.7 9.7E-06 2.5E-10 65.4 18.1 222 308-539 17-274 (288)
89 KOG1614 consensus 98.6 1.4E-05 3.6E-10 64.1 16.8 200 14-228 33-275 (291)
90 cd05704 S1_Rrp5_repeat_hs13 S1 98.5 1.4E-06 3.6E-11 72.2 9.0 71 617-688 1-72 (72)
91 cd05705 S1_Rrp5_repeat_hs14 S1 98.4 2.3E-06 5.9E-11 70.4 8.0 70 617-686 1-74 (74)
92 KOG1613 consensus 98.3 1.5E-06 3.9E-11 71.9 6.7 224 293-530 17-291 (298)
93 TIGR03665 arCOG04150 arCOG0415 98.3 1.4E-06 3.5E-11 72.3 6.4 80 556-635 2-91 (172)
94 cd04453 S1_RNase_E S1_RNase_E: 98.3 2.6E-06 6.6E-11 70.0 7.4 74 615-688 3-82 (88)
95 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.3 5.7E-06 1.5E-10 67.2 8.9 74 616-689 3-80 (86)
96 KOG1676 consensus 98.2 3E-05 7.6E-10 61.4 10.6 102 519-621 195-305 (600)
97 cd04465 S1_RPS1_repeat_ec2_hs2 98.2 1E-05 2.6E-10 65.2 8.1 66 620-688 1-67 (67)
98 pfam00013 KH_1 KH domain. KH m 98.1 8.7E-06 2.2E-10 65.7 6.7 56 554-610 2-57 (57)
99 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.1 1E-05 2.6E-10 65.2 6.6 68 620-687 1-71 (71)
100 PRK05054 exoribonuclease II; P 98.1 2.9E-05 7.4E-10 61.5 8.6 70 616-685 556-641 (644)
101 smart00322 KH K homology RNA-b 98.0 3.2E-05 8.2E-10 61.1 8.3 63 551-614 2-68 (69)
102 KOG0119 consensus 98.0 5.1E-05 1.3E-09 59.5 9.2 153 464-616 45-230 (554)
103 cd00105 KH-I K homology RNA-bi 98.0 2.6E-05 6.7E-10 61.9 7.2 57 554-611 2-64 (64)
104 COG0557 VacB Exoribonuclease R 98.0 3.5E-05 8.9E-10 60.9 7.8 196 478-687 479-703 (706)
105 KOG1070 consensus 98.0 1E-05 2.6E-10 65.1 5.1 107 581-689 1214-1324(1710)
106 COG1095 RPB7 DNA-directed RNA 98.0 2.6E-05 6.6E-10 61.9 6.6 78 611-689 73-167 (183)
107 cd02394 vigilin_like_KH K homo 98.0 2.8E-05 7.2E-10 61.6 6.5 57 554-611 2-62 (62)
108 KOG2916 consensus 97.9 6.9E-06 1.8E-10 66.6 3.4 80 615-694 12-94 (304)
109 cd05703 S1_Rrp5_repeat_hs12_sc 97.9 5.2E-05 1.3E-09 59.5 7.8 69 620-688 1-72 (73)
110 PRK08563 DNA-directed RNA poly 97.9 2.8E-05 7.2E-10 61.6 6.1 78 611-689 73-167 (182)
111 TIGR00448 rpoE DNA-directed RN 97.9 1.5E-05 3.7E-10 63.9 4.4 117 554-677 9-153 (184)
112 cd02396 PCBP_like_KH K homolog 97.8 9.7E-05 2.5E-09 57.2 7.8 56 554-610 2-64 (65)
113 PRK13763 putative RNA-processi 97.8 0.00014 3.6E-09 55.9 8.1 84 551-634 3-96 (185)
114 PTZ00162 RNA polymerase II sub 97.7 9.3E-05 2.4E-09 57.4 5.6 68 611-679 73-150 (170)
115 PRK04163 exosome complex RNA-b 97.7 0.00023 6E-09 54.1 7.5 64 553-616 145-208 (232)
116 PRK11712 ribonuclease G; Provi 97.7 0.00027 7E-09 53.6 7.8 40 552-591 438-477 (489)
117 KOG1676 consensus 97.6 0.00033 8.3E-09 52.9 7.9 95 521-618 287-391 (600)
118 cd02395 SF1_like-KH Splicing f 97.5 0.00064 1.6E-08 50.6 8.3 58 560-617 14-96 (120)
119 COG1107 Archaea-specific RecJ- 97.5 6.7E-05 1.7E-09 58.5 3.2 50 525-574 579-628 (715)
120 PRK12704 phosphodiesterase; Pr 97.4 0.0018 4.7E-08 46.8 9.2 86 526-616 124-211 (455)
121 PRK10811 rne ribonuclease E; R 97.4 0.00023 5.8E-09 54.2 4.5 22 329-350 401-422 (1063)
122 COG1094 Predicted RNA-binding 97.4 0.00082 2.1E-08 49.7 7.3 85 549-633 5-101 (194)
123 cd04454 S1_Rrp4_like S1_Rrp4_l 97.4 0.0015 3.8E-08 47.6 8.6 74 616-689 3-76 (82)
124 KOG1070 consensus 97.4 0.00019 4.9E-09 54.8 4.0 77 614-690 1157-1234(1710)
125 PRK04163 exosome complex RNA-b 97.4 0.0014 3.5E-08 47.8 8.3 75 616-690 59-137 (232)
126 KOG2191 consensus 97.4 0.006 1.5E-07 42.7 11.4 115 494-622 82-211 (402)
127 TIGR03319 YmdA_YtgF conserved 97.3 0.0028 7E-08 45.4 9.1 54 394-454 254-307 (514)
128 KOG2190 consensus 97.2 0.0034 8.8E-08 44.6 8.9 40 549-588 335-374 (485)
129 PRK09521 exosome complex RNA-b 97.2 0.002 5.1E-08 46.6 7.4 73 615-689 60-143 (187)
130 TIGR03665 arCOG04150 arCOG0415 97.2 0.00076 1.9E-08 50.0 5.0 61 562-624 99-159 (172)
131 COG1097 RRP4 RNA-binding prote 97.1 0.0036 9.1E-08 44.5 7.8 74 616-689 61-138 (239)
132 pfam03725 RNase_PH_C 3' exorib 97.1 0.00094 2.4E-08 49.2 4.8 65 457-527 1-67 (67)
133 PRK13764 ATPase; Provisional 97.1 0.00073 1.9E-08 50.1 4.0 148 523-674 456-604 (605)
134 PRK12705 hypothetical protein; 96.9 0.0053 1.4E-07 43.1 7.2 56 394-456 224-279 (485)
135 PRK00106 hypothetical protein; 96.8 0.014 3.5E-07 39.7 9.0 55 394-455 275-329 (535)
136 COG1094 Predicted RNA-binding 96.8 0.0033 8.3E-08 44.8 5.6 60 562-623 112-171 (194)
137 KOG1613 consensus 96.8 0.0055 1.4E-07 43.0 6.7 118 14-144 47-180 (298)
138 KOG1588 consensus 96.8 0.046 1.2E-06 35.5 11.4 73 550-622 90-197 (259)
139 PRK12327 nusA transcription el 96.8 0.026 6.6E-07 37.5 10.1 229 290-589 109-340 (353)
140 COG1096 Predicted RNA-binding 96.7 0.009 2.3E-07 41.2 7.5 74 613-688 58-141 (188)
141 PRK13763 putative RNA-processi 96.7 0.0032 8.3E-08 44.8 4.9 61 562-624 105-165 (185)
142 cd05791 S1_CSL4 S1_CSL4: CSL4, 96.6 0.011 2.9E-07 40.4 7.2 73 616-688 3-85 (92)
143 cd05693 S1_Rrp5_repeat_hs1_sc1 96.6 0.0064 1.6E-07 42.4 5.9 71 618-688 2-95 (100)
144 KOG2193 consensus 96.6 0.0038 9.6E-08 44.3 4.6 59 553-612 412-477 (584)
145 COG5176 MSL5 Splicing factor ( 96.5 0.016 4.1E-07 39.2 7.4 92 527-619 121-225 (269)
146 PRK09202 nusA transcription el 96.4 0.035 9E-07 36.4 8.6 229 290-590 110-341 (428)
147 COG1530 CafA Ribonucleases G a 96.3 0.011 2.9E-07 40.4 5.9 22 98-119 83-104 (487)
148 KOG0336 consensus 96.3 0.0027 6.9E-08 45.5 2.5 31 472-511 369-399 (629)
149 COG2996 Predicted RNA-bindinin 95.9 0.038 9.6E-07 36.2 6.8 65 619-691 155-219 (287)
150 COG1097 RRP4 RNA-binding prote 95.8 0.03 7.7E-07 37.0 6.1 63 554-616 148-210 (239)
151 PRK12328 nusA transcription el 95.7 0.073 1.9E-06 33.9 7.7 230 290-593 113-349 (375)
152 cd05694 S1_Rrp5_repeat_hs2_sc2 95.6 0.1 2.6E-06 32.7 7.9 67 616-688 1-69 (74)
153 KOG2193 consensus 95.6 0.013 3.4E-07 39.8 3.4 85 529-618 473-566 (584)
154 COG1855 ATPase (PilT family) [ 95.5 0.029 7.4E-07 37.1 5.1 140 525-673 460-602 (604)
155 TIGR00757 RNaseEG ribonuclease 95.4 0.0064 1.6E-07 42.4 1.4 64 617-681 25-139 (464)
156 cd04455 S1_NusA S1_NusA: N-uti 95.4 0.055 1.4E-06 34.8 6.0 63 618-687 2-67 (67)
157 KOG2191 consensus 95.3 0.17 4.3E-06 30.9 8.4 49 158-215 57-109 (402)
158 KOG2190 consensus 95.3 0.064 1.6E-06 34.3 6.1 115 488-616 87-208 (485)
159 TIGR01953 NusA transcription t 95.2 0.15 3.8E-06 31.3 7.8 91 592-688 107-219 (366)
160 KOG1612 consensus 95.2 0.31 7.9E-06 28.7 16.7 119 14-144 32-166 (288)
161 cd05695 S1_Rrp5_repeat_hs3 S1_ 95.1 0.092 2.3E-06 33.0 6.6 65 620-686 1-66 (66)
162 PRK12329 nusA transcription el 94.9 0.23 6E-06 29.7 8.1 179 357-591 187-375 (457)
163 KOG1856 consensus 94.8 0.092 2.4E-06 33.0 5.9 71 619-689 985-1059(1299)
164 KOG2814 consensus 94.5 0.054 1.4E-06 34.9 4.1 64 553-616 58-125 (345)
165 KOG2192 consensus 94.4 0.16 4E-06 31.1 6.2 62 553-615 316-383 (390)
166 PRK08406 transcription elongat 93.7 0.18 4.5E-06 30.7 5.4 95 538-647 20-115 (142)
167 KOG2192 consensus 93.5 0.13 3.3E-06 31.8 4.4 107 530-640 101-221 (390)
168 PRK12442 translation initiatio 93.0 0.64 1.6E-05 26.2 7.3 64 622-690 8-74 (87)
169 COG2996 Predicted RNA-bindinin 92.4 0.46 1.2E-05 27.3 5.9 88 584-683 43-133 (287)
170 cd02134 NusA_KH NusA_K homolog 92.1 0.14 3.7E-06 31.4 3.1 42 547-588 20-61 (61)
171 cd05699 S1_Rrp5_repeat_hs7 S1_ 92.1 0.49 1.3E-05 27.1 5.8 67 620-688 1-72 (72)
172 TIGR00358 3_prime_RNase VacB a 91.0 0.19 4.9E-06 30.5 2.7 65 617-681 596-676 (684)
173 pfam10447 EXOSC1 Exosome compo 90.7 0.76 1.9E-05 25.6 5.6 61 616-676 1-71 (72)
174 cd04451 S1_IF1 S1_IF1: Transla 90.4 0.8 2E-05 25.4 5.4 58 622-684 2-62 (64)
175 CHL00010 infA translation init 90.3 1.3 3.2E-05 23.7 6.4 62 622-688 8-72 (78)
176 COG1847 Jag Predicted RNA-bind 90.2 1.1 2.8E-05 24.2 6.0 104 507-614 49-153 (208)
177 PRK00276 infA translation init 90.1 1 2.7E-05 24.4 5.9 59 622-685 8-69 (72)
178 cd04462 S1_RNAPII_Rpb7 S1_RNAP 90.0 1.3 3.4E-05 23.5 6.3 59 619-678 1-70 (88)
179 cd02409 KH-II KH-II (K homolo 89.9 0.74 1.9E-05 25.7 4.9 38 550-588 24-68 (68)
180 PRK02821 hypothetical protein; 88.9 0.4 1E-05 27.8 3.0 29 552-580 31-59 (77)
181 COG0195 NusA Transcription elo 88.7 0.5 1.3E-05 27.0 3.3 55 552-618 76-130 (190)
182 PRK01064 hypothetical protein; 88.2 0.48 1.2E-05 27.2 3.0 29 551-579 29-57 (78)
183 KOG3298 consensus 88.1 1.8 4.7E-05 22.5 5.9 68 611-678 73-150 (170)
184 KOG2208 consensus 88.0 0.56 1.4E-05 26.7 3.3 59 529-589 687-746 (753)
185 COG1837 Predicted RNA-binding 87.4 0.6 1.5E-05 26.4 3.1 50 531-580 5-58 (76)
186 PRK00468 hypothetical protein; 87.2 0.52 1.3E-05 26.9 2.7 30 551-580 29-58 (75)
187 COG0195 NusA Transcription elo 87.1 0.8 2E-05 25.4 3.6 39 553-591 143-181 (190)
188 TIGR00008 infA translation ini 83.5 3.2 8.1E-05 20.5 5.6 58 622-684 6-66 (69)
189 pfam07650 KH_2 KH domain. 83.2 0.98 2.5E-05 24.6 2.6 30 555-584 3-32 (55)
190 cd02411 archeal_30S_S3_KH K ho 82.0 2.7 6.8E-05 21.1 4.4 46 543-589 30-82 (85)
191 pfam00313 CSD 'Cold-shock' DNA 81.5 3.7 9.4E-05 20.0 7.1 55 624-683 2-59 (66)
192 TIGR01859 fruc_bis_ald_ fructo 80.7 3.9 1E-04 19.8 6.2 103 159-261 204-338 (339)
193 COG0514 RecQ Superfamily II DN 80.6 1.8 4.7E-05 22.5 3.2 47 340-395 275-328 (590)
194 KOG2279 consensus 79.2 1.3 3.3E-05 23.7 2.0 89 547-635 291-388 (608)
195 TIGR00202 csrA carbon storage 79.2 1.9 4.7E-05 22.4 2.8 31 658-689 6-36 (69)
196 pfam00918 Gastrin Gastrin/chol 78.1 0.74 1.9E-05 25.6 0.5 19 396-414 47-65 (111)
197 cd02414 jag_KH jag_K homology 77.5 2 5.1E-05 22.1 2.6 57 530-590 6-62 (77)
198 pfam01176 eIF-1a Translation i 77.5 4.8 0.00012 19.0 4.8 59 619-683 2-62 (65)
199 COG0361 InfA Translation initi 76.9 5 0.00013 18.9 5.7 63 617-685 4-69 (75)
200 smart00357 CSP Cold shock prot 75.7 5.3 0.00014 18.7 6.1 54 625-683 2-56 (64)
201 cd02410 archeal_CPSF_KH The ar 75.1 4.8 0.00012 19.1 4.0 42 548-589 72-113 (145)
202 LOAD_cold consensus 74.0 5.8 0.00015 18.4 5.0 56 623-683 2-60 (67)
203 PRK11057 ATP-dependent DNA hel 73.1 2.9 7.5E-05 20.8 2.5 50 339-397 280-336 (607)
204 KOG3409 consensus 72.3 6.3 0.00016 18.1 6.8 72 616-687 65-146 (193)
205 KOG3273 consensus 72.1 1.8 4.5E-05 22.6 1.2 61 562-624 179-239 (252)
206 PRK09937 stationary phase/star 71.9 6.4 0.00016 18.0 6.8 67 624-695 3-72 (74)
207 cd04458 CSP_CDS Cold-Shock Pro 70.7 6.8 0.00017 17.8 6.5 56 623-683 1-59 (65)
208 TIGR03305 alt_F1F0_F1_bet alte 70.5 6.8 0.00017 17.8 6.8 29 380-408 328-357 (449)
209 PRK10354 major cold shock prot 68.8 7.4 0.00019 17.5 7.0 57 622-683 4-63 (70)
210 PRK11776 ATP-dependent RNA hel 68.7 7.4 0.00019 17.5 4.1 72 339-418 286-370 (459)
211 KOG3548 consensus 67.6 7 0.00018 17.7 3.5 94 319-433 684-784 (1176)
212 TIGR01008 rpsC_E_A ribosomal p 67.6 4.5 0.00012 19.3 2.5 45 543-588 30-76 (204)
213 KOG2874 consensus 67.1 7.9 0.0002 17.3 5.3 21 565-585 162-182 (356)
214 PRK10943 cold shock-like prote 66.9 8 0.0002 17.2 7.1 57 622-683 3-62 (69)
215 KOG3013 consensus 66.6 8.1 0.00021 17.2 4.5 10 72-81 119-128 (301)
216 COG1782 Predicted metal-depend 66.0 4.7 0.00012 19.2 2.3 35 324-358 178-216 (637)
217 PRK10590 ATP-dependent RNA hel 65.9 8.3 0.00021 17.1 4.5 71 339-417 289-372 (457)
218 TIGR01648 hnRNP-R-Q hnRNP-R, Q 63.6 8.7 0.00022 17.0 3.3 47 591-640 236-282 (611)
219 KOG0351 consensus 63.4 8.9 0.00023 16.9 3.3 47 341-396 531-584 (941)
220 KOG3392 consensus 62.5 9.1 0.00023 16.8 3.2 27 343-369 94-120 (147)
221 cd02413 40S_S3_KH K homology R 61.9 6 0.00015 18.3 2.2 48 550-598 28-75 (81)
222 PHA02358 hypothetical protein 61.7 1.8 4.5E-05 22.6 -0.5 25 130-154 147-171 (194)
223 pfam09176 Mpt_N Methylene-tetr 61.4 1.8 4.6E-05 22.5 -0.5 50 331-386 26-75 (81)
224 COG1545 Predicted nucleic-acid 60.5 10 0.00026 16.4 6.9 64 612-682 56-128 (140)
225 PRK09507 cspE cold shock prote 59.7 10 0.00027 16.3 7.5 58 622-684 3-63 (69)
226 COG1702 PhoH Phosphate starvat 59.4 11 0.00027 16.3 5.5 20 192-211 84-103 (348)
227 PRK04537 ATP-dependent RNA hel 59.4 11 0.00027 16.3 3.9 71 338-416 300-383 (574)
228 PRK09890 cold shock protein Cs 59.1 11 0.00027 16.2 6.4 57 622-683 4-63 (70)
229 TIGR01389 recQ ATP-dependent D 58.6 8 0.0002 17.3 2.4 48 339-395 270-324 (607)
230 TIGR03675 arCOG00543 arCOG0178 57.7 11 0.00029 16.0 4.1 32 326-357 174-209 (630)
231 KOG2113 consensus 57.7 7.2 0.00018 17.6 2.0 20 322-341 279-299 (394)
232 PRK11192 ATP-dependent RNA hel 57.4 5 0.00013 18.9 1.2 70 339-416 291-373 (417)
233 COG0092 RpsC Ribosomal protein 57.3 11 0.00029 16.0 6.3 46 543-589 43-95 (233)
234 pfam05900 consensus 55.7 7.7 0.0002 17.4 1.9 22 335-356 31-52 (221)
235 TIGR00549 mevalon_kin mevalona 54.9 12 0.00032 15.7 3.2 15 129-143 144-158 (345)
236 PTZ00084 40S ribosomal protein 54.4 13 0.00032 15.6 3.3 64 515-581 10-73 (220)
237 PRK04837 ATP-dependent RNA hel 54.4 7.1 0.00018 17.7 1.6 72 339-418 300-384 (423)
238 pfam12414 Fox-1_C Calcitonin g 54.3 10 0.00027 16.3 2.4 47 29-78 19-67 (96)
239 PRK00568 carbon storage regula 54.0 13 0.00032 15.6 3.0 31 658-689 6-36 (76)
240 TIGR03562 osmo_induc_OsmC pero 54.0 12 0.00031 15.8 2.7 30 500-529 91-122 (135)
241 KOG4369 consensus 53.9 5 0.00013 18.9 0.7 30 104-134 122-151 (2131)
242 PRK09824 beta-glucoside-specif 53.6 13 0.00032 15.6 2.7 80 590-672 484-572 (625)
243 COG1551 CsrA RNA-binding globa 52.8 13 0.00033 15.6 2.7 31 658-689 6-36 (73)
244 TIGR02705 nudix_YtkD nucleosid 51.5 3.9 9.9E-05 19.8 -0.2 66 560-640 42-118 (158)
245 COG5166 Uncharacterized conser 50.7 12 0.0003 15.9 2.2 51 550-600 447-506 (657)
246 PRK01297 ATP-dependent RNA hel 50.5 8.7 0.00022 17.0 1.5 49 339-395 376-430 (472)
247 TIGR01455 glmM phosphoglucosam 50.2 5.3 0.00013 18.7 0.3 29 176-204 241-269 (450)
248 TIGR01237 D1pyr5carbox2 delta- 50.1 14 0.00037 15.2 2.9 127 289-433 129-290 (518)
249 cd07209 Pat_hypo_Ecoli_Z1214_l 49.2 10 0.00027 16.3 1.7 34 433-467 5-38 (215)
250 TIGR00959 ffh signal recogniti 49.1 6.4 0.00016 18.0 0.6 112 492-617 152-276 (439)
251 COG4044 Uncharacterized protei 48.1 15 0.00039 14.9 6.6 108 572-679 21-147 (247)
252 cd07207 Pat_ExoU_VipD_like Exo 48.1 11 0.00029 16.0 1.8 33 432-465 5-37 (194)
253 PHA00019 phage assembly protei 47.4 14 0.00035 15.3 2.1 13 193-205 66-78 (428)
254 PRK07318 dipeptidase PepV; Rev 47.2 16 0.0004 14.8 3.2 73 574-649 366-443 (469)
255 PRK04011 peptide chain release 47.1 16 0.00041 14.8 8.0 24 243-266 42-65 (409)
256 cd07198 Patatin Patatin-like p 46.8 14 0.00036 15.2 2.1 35 432-467 4-38 (172)
257 KOG1857 consensus 46.8 4.4 0.00011 19.4 -0.5 38 616-653 572-609 (623)
258 COG1665 Predicted nucleotidylt 46.6 15 0.00039 15.0 2.3 74 428-518 96-175 (315)
259 KOG4068 consensus 45.8 7.1 0.00018 17.7 0.5 15 173-187 32-46 (174)
260 TIGR02618 tyr_phenol_ly tyrosi 45.2 8.1 0.00021 17.2 0.7 32 436-467 313-344 (450)
261 TIGR01020 rpsE_arch ribosomal 45.0 11 0.00028 16.1 1.3 41 559-601 13-54 (220)
262 PRK01712 carbon storage regula 44.6 17 0.00044 14.5 2.7 31 658-689 6-36 (64)
263 cd07227 Pat_Fungal_NTE1 Fungal 44.3 14 0.00035 15.4 1.7 10 472-481 182-191 (269)
264 PRK09027 cytidine deaminase; P 44.1 18 0.00045 14.5 3.3 106 97-206 155-282 (295)
265 cd06818 PLPDE_III_cryptic_DSD 44.1 16 0.00042 14.7 2.1 55 417-472 268-323 (382)
266 COG4604 CeuD ABC-type enteroch 44.0 15 0.00038 15.1 1.8 41 555-599 21-64 (252)
267 pfam02599 CsrA Global regulato 43.7 18 0.00045 14.4 2.7 31 658-689 6-36 (53)
268 TIGR01935 NOT-MenG RraA family 43.3 10 0.00026 16.4 0.9 15 667-683 35-49 (155)
269 PRK10546 pyrimidine (deoxy)nuc 43.0 18 0.00045 14.4 2.1 14 574-587 50-63 (135)
270 KOG1423 consensus 42.9 18 0.00046 14.3 2.8 49 297-356 82-130 (379)
271 COG5009 MrcA Membrane carboxyp 42.7 18 0.00047 14.3 5.4 43 420-464 428-470 (797)
272 TIGR03676 aRF1/eRF1 peptide ch 42.3 19 0.00047 14.3 9.2 17 206-222 185-201 (403)
273 KOG0074 consensus 41.5 12 0.00031 15.7 1.1 70 36-127 29-102 (185)
274 cd03138 GATase1_AraC_2 AraC tr 41.4 9.4 0.00024 16.7 0.5 21 434-454 103-123 (195)
275 PRK12597 F0F1 ATP synthase sub 41.1 19 0.00049 14.1 6.4 31 73-103 62-95 (459)
276 pfam09364 XFP_N XFP N-terminal 40.5 20 0.0005 14.1 2.3 107 103-217 150-261 (379)
277 cd02011 TPP_PK Thiamine pyroph 40.2 20 0.00051 14.0 3.1 105 105-217 74-183 (227)
278 pfam04697 Pinin_SDK_N pinin/SD 39.9 20 0.00051 14.0 2.0 33 313-345 28-65 (134)
279 CHL00060 atpB ATP synthase CF1 39.7 20 0.00051 14.0 7.9 13 90-102 96-108 (480)
280 cd07225 Pat_PNPLA6_PNPLA7 Pata 39.7 15 0.00038 15.0 1.3 87 92-180 100-194 (306)
281 cd07210 Pat_hypo_W_succinogene 39.4 18 0.00047 14.3 1.7 35 432-467 6-40 (221)
282 CHL00192 syfB phenylalanyl-tRN 39.3 20 0.00052 13.9 6.0 48 552-609 549-596 (702)
283 PRK11750 gltB glutamate syntha 39.2 20 0.00052 13.9 4.5 80 92-189 297-384 (1483)
284 TIGR02062 RNase_B exoribonucle 39.1 21 0.00052 13.9 3.0 66 616-682 579-658 (664)
285 PTZ00110 helicase; Provisional 38.6 21 0.00053 13.9 2.1 22 56-77 49-70 (602)
286 TIGR00224 pckA phosphoenolpyru 38.6 9.6 0.00025 16.6 0.2 12 313-324 153-165 (549)
287 pfam09883 DUF2110 Uncharacteri 38.6 21 0.00053 13.9 5.5 118 571-689 20-149 (226)
288 PRK11634 ATP-dependent RNA hel 38.4 16 0.00041 14.8 1.3 71 339-417 289-372 (629)
289 PRK11162 mltA murein transglyc 38.3 8.4 0.00021 17.1 -0.1 35 378-413 133-167 (362)
290 TIGR02383 Hfq RNA chaperone Hf 37.9 21 0.00054 13.8 2.1 23 452-482 25-47 (61)
291 KOG2635 consensus 37.2 22 0.00056 13.7 4.6 41 473-517 301-341 (512)
292 pfam00358 PTS_EIIA_1 phosphoen 37.2 22 0.00056 13.7 4.5 59 611-672 32-99 (133)
293 PRK01123 shikimate kinase; Pro 37.0 22 0.00056 13.7 13.5 56 400-455 54-112 (283)
294 cd04322 LysRS_N LysRS_N: N-ter 36.9 22 0.00056 13.7 4.5 62 623-685 4-72 (108)
295 TIGR01436 glu_cys_lig_pln glut 36.9 13 0.00033 15.5 0.7 25 114-138 167-192 (446)
296 PRK13926 junction RNase; Provi 36.9 18 0.00046 14.4 1.4 128 144-281 34-171 (212)
297 TIGR02533 type_II_gspE general 36.5 21 0.00054 13.8 1.7 53 305-357 173-230 (495)
298 PRK09281 F0F1 ATP synthase sub 36.4 12 0.00031 15.8 0.4 32 74-105 84-118 (502)
299 PRK03932 asnC asparaginyl-tRNA 36.2 23 0.00058 13.6 4.4 20 444-466 415-434 (462)
300 KOG1337 consensus 36.2 20 0.00051 14.0 1.5 91 287-381 198-291 (472)
301 cd00210 PTS_IIA_glc PTS_IIA, P 36.1 23 0.00058 13.6 4.7 59 611-672 27-94 (124)
302 cd01383 MYSc_type_VIII Myosin 35.5 23 0.00059 13.5 3.8 17 128-146 258-274 (677)
303 pfam03310 Cauli_DNA-bind Cauli 35.4 16 0.00041 14.8 0.9 15 375-389 88-102 (121)
304 cd07749 NT_Pol-beta-like_1 Nuc 35.3 23 0.00059 13.5 1.9 15 132-146 22-36 (156)
305 TIGR03069 PS_II_S4 photosystem 35.3 23 0.00059 13.5 2.6 22 652-673 212-233 (257)
306 cd03135 GATase1_DJ-1 Type 1 gl 35.2 13 0.00033 15.5 0.4 18 437-454 95-112 (163)
307 TIGR02945 SUF_assoc FeS assemb 35.0 24 0.0006 13.4 2.0 31 584-614 27-68 (96)
308 pfam05314 Baculo_ODV-E27 Bacul 35.0 11 0.00028 16.1 0.1 21 121-141 72-92 (280)
309 COG1159 Era GTPase [General fu 34.9 23 0.00058 13.5 1.6 15 563-577 241-255 (298)
310 COG4130 Predicted sugar epimer 34.7 24 0.0006 13.4 1.8 10 376-385 239-248 (272)
311 TIGR01028 S7_S5_E_A ribosomal 34.7 17 0.00044 14.6 1.0 45 72-116 70-115 (206)
312 KOG0246 consensus 34.1 18 0.00046 14.4 1.0 26 339-364 294-319 (676)
313 PRK13237 tyrosine phenol-lyase 34.1 22 0.00057 13.6 1.5 73 367-466 278-350 (459)
314 COG2893 ManX Phosphotransferas 34.1 24 0.00062 13.3 3.9 94 399-523 7-104 (143)
315 pfam07867 DUF1654 Protein of u 33.7 25 0.00063 13.3 2.7 56 535-597 12-67 (73)
316 pfam01965 DJ-1_PfpI DJ-1/PfpI 33.5 13 0.00033 15.5 0.2 15 438-452 70-84 (141)
317 cd00617 Tnase_like Tryptophana 33.5 23 0.00059 13.5 1.5 74 366-466 252-325 (431)
318 cd03427 MTH1 MutT homolog-1 (M 33.2 25 0.00064 13.2 1.9 26 563-588 25-60 (137)
319 PRK08559 nusG transcription an 33.1 25 0.00064 13.2 3.7 70 591-686 47-128 (153)
320 cd03139 GATase1_PfpI_2 Type 1 32.6 14 0.00037 15.2 0.3 20 435-454 94-113 (183)
321 pfam07126 DUF1379 Protein of u 32.5 19 0.00049 14.2 0.9 72 33-113 2-82 (154)
322 PRK00089 era GTP-binding prote 32.4 26 0.00065 13.1 5.3 44 266-309 159-203 (296)
323 PRK04151 IMP cyclohydrolase; P 32.4 26 0.00065 13.1 1.7 94 59-163 98-194 (199)
324 cd03316 MR_like Mandelate race 32.4 21 0.00055 13.8 1.2 93 432-530 196-290 (357)
325 cd03140 GATase1_PfpI_3 Type 1 31.9 13 0.00033 15.6 -0.0 20 435-454 91-110 (170)
326 pfam12098 DUF3574 Protein of u 31.8 26 0.00067 13.1 2.1 24 82-107 15-38 (104)
327 TIGR02406 ectoine_EctA L-2,4-d 31.6 26 0.00067 13.0 1.7 47 395-451 75-124 (162)
328 PRK12450 foldase protein PrsA; 31.6 26 0.00067 13.0 7.1 80 176-259 20-103 (309)
329 PRK04191 rps3p 30S ribosomal p 31.5 26 0.00068 13.0 6.7 91 515-613 6-103 (225)
330 cd04690 Nudix_Hydrolase_31 Mem 31.4 26 0.00068 13.0 3.4 16 574-589 43-58 (118)
331 pfam00245 Alk_phosphatase Alka 31.4 26 0.00068 13.0 2.0 10 113-122 45-54 (421)
332 TIGR02393 RpoD_Cterm RNA polym 31.4 27 0.00068 13.0 4.4 110 191-306 100-226 (240)
333 PRK04405 prsA peptidylprolyl i 31.4 27 0.00068 13.0 9.9 66 189-258 33-101 (298)
334 COG0411 LivG ABC-type branched 31.4 27 0.00068 13.0 1.9 17 36-52 42-58 (250)
335 PRK09280 F0F1 ATP synthase sub 31.1 27 0.00068 13.0 7.3 33 71-103 64-99 (466)
336 cd03137 GATase1_AraC_1 AraC tr 31.1 12 0.00032 15.7 -0.2 20 435-454 96-115 (187)
337 cd00496 PheRS_alpha_core Pheny 30.6 20 0.00052 13.9 0.8 39 416-468 142-196 (218)
338 PRK13238 tnaA tryptophanase; P 30.6 26 0.00065 13.1 1.3 74 366-466 278-351 (461)
339 KOG3141 consensus 30.4 27 0.00068 13.0 1.4 13 134-146 40-52 (310)
340 KOG2968 consensus 30.3 28 0.0007 12.9 1.7 204 393-641 821-1105(1158)
341 pfam05382 Amidase_5 Bacterioph 30.2 28 0.00071 12.9 1.6 74 431-506 22-102 (145)
342 PRK12366 replication factor A; 30.1 28 0.00071 12.9 5.8 17 663-679 459-475 (649)
343 CHL00059 atpA ATP synthase CF1 30.0 28 0.00071 12.8 8.4 32 74-105 85-119 (501)
344 pfam08211 dCMP_cyt_deam_2 Cyti 29.7 28 0.00072 12.8 2.5 74 130-203 36-123 (124)
345 cd04092 mtEFG2_II_like mtEFG2_ 29.2 29 0.00073 12.7 2.9 44 144-187 12-60 (83)
346 COG4706 Predicted 3-hydroxylac 29.2 17 0.00042 14.7 0.2 78 32-125 28-108 (161)
347 cd03136 GATase1_AraC_ArgR_like 29.2 18 0.00046 14.4 0.3 24 435-458 95-118 (185)
348 TIGR02071 PBP_1b penicillin-bi 28.6 29 0.00075 12.7 2.4 36 641-686 639-677 (742)
349 cd07228 Pat_NTE_like_bacteria 28.4 29 0.00075 12.6 1.8 32 433-465 7-38 (175)
350 COG1685 Archaeal shikimate kin 28.3 30 0.00075 12.6 3.5 134 399-539 48-211 (278)
351 TIGR00174 miaA tRNA delta(2)-i 28.1 18 0.00047 14.3 0.2 10 173-182 89-98 (307)
352 cd04691 Nudix_Hydrolase_32 Mem 27.9 30 0.00077 12.6 1.5 24 564-587 27-60 (117)
353 cd00713 GltS Glutamine amidotr 27.8 30 0.00077 12.6 3.8 86 350-439 175-275 (413)
354 COG0056 AtpA F0F1-type ATP syn 27.7 30 0.00077 12.5 3.8 37 61-101 268-304 (504)
355 PRK11597 heat shock chaperone 27.7 30 0.00077 12.5 2.5 64 521-598 9-73 (142)
356 smart00815 AMA-1 Apical membra 27.7 21 0.00055 13.8 0.5 13 88-100 79-91 (240)
357 COG0693 ThiJ Putative intracel 27.6 18 0.00046 14.4 0.1 19 66-84 65-84 (188)
358 TIGR02730 carot_isom carotene 27.1 25 0.00064 13.2 0.8 10 418-427 245-254 (506)
359 cd03325 D-galactonate_dehydrat 26.8 27 0.00068 13.0 0.9 77 432-514 183-266 (352)
360 TIGR01009 rpsC_bact ribosomal 26.6 31 0.0008 12.4 4.5 46 543-588 57-108 (217)
361 cd03134 GATase1_PfpI_like A ty 26.2 18 0.00046 14.4 -0.1 15 438-452 97-111 (165)
362 KOG3843 consensus 26.2 19 0.00049 14.2 0.0 43 335-383 331-373 (432)
363 pfam02430 AMA-1 Apical membran 25.7 25 0.00064 13.2 0.5 14 347-360 315-328 (462)
364 COG5011 Uncharacterized protei 25.6 19 0.00049 14.2 -0.1 18 91-108 21-43 (228)
365 COG1785 PhoA Alkaline phosphat 25.6 18 0.00047 14.3 -0.2 11 63-73 76-86 (482)
366 cd04091 mtEFG1_II_like mtEFG1_ 25.5 33 0.00084 12.3 3.1 44 143-187 11-59 (81)
367 COG5159 RPN6 26S proteasome re 25.3 14 0.00035 15.3 -0.8 88 433-536 180-283 (421)
368 COG2055 Malate/L-lactate dehyd 25.2 33 0.00085 12.2 2.2 50 53-107 168-231 (349)
369 PRK00421 murC UDP-N-acetylmura 25.2 33 0.00085 12.2 3.1 14 660-673 429-442 (459)
370 PRK13366 protocatechuate 4,5-d 25.1 31 0.00078 12.5 0.9 30 382-411 147-176 (284)
371 pfam09866 DUF2093 Uncharacteri 25.0 33 0.00085 12.2 1.5 32 37-70 5-36 (42)
372 PRK00175 metX homoserine O-ace 25.0 22 0.00057 13.6 0.2 13 13-25 18-30 (379)
373 PRK11607 potG putrescine trans 25.0 34 0.00085 12.2 4.3 17 461-477 360-376 (377)
374 KOG3981 consensus 24.9 22 0.00057 13.6 0.2 73 88-169 73-150 (326)
375 PRK00629 pheT phenylalanyl-tRN 24.8 34 0.00086 12.2 5.1 47 552-608 637-683 (786)
376 PRK11067 outer membrane protei 24.8 14 0.00035 15.3 -0.9 25 89-113 53-77 (801)
377 COG0490 Putative regulatory, l 24.7 34 0.00086 12.1 2.9 47 138-184 101-149 (162)
378 PRK01326 prsA foldase protein 24.7 34 0.00086 12.1 8.4 80 176-259 18-101 (310)
379 COG0223 Fmt Methionyl-tRNA for 24.6 34 0.00086 12.2 1.1 61 494-554 127-206 (307)
380 PRK05568 flavodoxin; Provision 24.4 34 0.00087 12.1 5.8 54 561-614 82-140 (142)
381 COG2056 Predicted permease [Ge 24.4 34 0.00087 12.1 2.0 43 430-472 371-415 (444)
382 COG1278 CspC Cold shock protei 24.4 34 0.00087 12.1 6.6 57 625-687 4-64 (67)
383 TIGR01774 PFL2-3 pyruvate form 24.4 34 0.00087 12.1 3.0 59 169-227 174-233 (812)
384 cd00669 Asp_Lys_Asn_RS_core As 24.4 34 0.00087 12.1 1.2 51 393-466 195-245 (269)
385 KOG2853 consensus 24.1 35 0.00088 12.1 2.9 13 132-144 97-109 (509)
386 TIGR00770 Dcu transporter, ana 24.1 35 0.00089 12.1 2.0 12 130-141 52-63 (447)
387 cd04491 SoSSB_OBF SoSSB_OBF: A 24.0 35 0.00089 12.1 7.1 62 624-687 3-73 (82)
388 PRK10776 nucleoside triphospha 24.0 35 0.00089 12.1 3.2 16 574-589 51-66 (129)
389 pfam04348 LppC LppC putative l 24.0 19 0.00048 14.2 -0.4 21 592-613 401-421 (535)
390 COG1956 GAF domain-containing 23.9 35 0.00089 12.0 1.1 56 144-199 68-145 (163)
391 PRK00377 cbiT cobalt-precorrin 23.9 35 0.00089 12.0 5.2 90 547-642 98-187 (198)
392 pfam08292 RNA_pol_Rbc25 RNA po 23.9 35 0.00089 12.0 4.5 62 617-678 1-75 (120)
393 TIGR01800 cit_synth_II 2-methy 23.8 28 0.00073 12.8 0.5 21 433-453 193-213 (386)
394 cd01703 Pol_iota Pol iota is m 23.7 30 0.00078 12.5 0.7 23 402-426 366-388 (394)
395 pfam07286 DUF1445 Protein of u 23.5 35 0.0009 12.0 1.4 101 446-598 13-114 (143)
396 TIGR01371 met_syn_B12ind 5-met 23.4 36 0.00091 12.0 3.1 15 215-229 323-337 (778)
397 cd03169 GATase1_PfpI_1 Type 1 23.4 25 0.00065 13.2 0.2 15 438-452 111-125 (180)
398 PTZ00027 60S ribosomal protein 23.3 36 0.00091 12.0 1.8 66 563-629 24-95 (190)
399 cd02784 MopB_CT_PHLH The MopB_ 23.3 36 0.00091 12.0 3.9 52 6-60 57-108 (137)
400 pfam05783 DLIC Dynein light in 23.2 13 0.00033 15.6 -1.3 108 157-276 196-319 (490)
401 TIGR00761 argB acetylglutamate 23.1 36 0.00092 11.9 2.9 25 469-493 188-212 (254)
402 cd07367 CarBb CarBb is the B s 23.1 34 0.00087 12.1 0.8 33 382-414 136-168 (268)
403 COG4977 Transcriptional regula 23.1 27 0.00068 13.0 0.3 41 120-160 86-130 (328)
404 PRK13364 protocatechuate 4,5-d 23.1 36 0.00092 11.9 1.1 41 373-414 62-110 (279)
405 COG2428 Uncharacterized conser 22.9 36 0.00093 11.9 2.7 32 116-148 32-64 (196)
406 PRK13108 prolipoprotein diacyl 22.9 26 0.00065 13.1 0.2 72 68-145 140-218 (460)
407 pfam10646 Germane Sporulation 22.6 37 0.00094 11.8 4.9 60 99-162 46-112 (116)
408 pfam09869 DUF2096 Uncharacteri 22.6 37 0.00094 11.8 5.7 79 529-613 77-166 (169)
409 PRK07165 F0F1 ATP synthase sub 22.4 29 0.00074 12.7 0.4 20 89-108 78-97 (507)
410 pfam00347 Ribosomal_L6 Ribosom 22.3 37 0.00095 11.8 3.1 63 551-615 2-64 (76)
411 COG4717 Uncharacterized conser 22.2 37 0.00096 11.8 4.0 10 557-566 606-615 (984)
412 TIGR03303 OM_YaeT outer membra 22.2 19 0.00047 14.3 -0.7 23 91-113 32-54 (741)
413 TIGR01448 recD_rel helicase, R 22.0 29 0.00075 12.7 0.3 33 158-190 57-95 (769)
414 pfam03610 EIIA-man PTS system 22.0 38 0.00096 11.8 3.6 47 469-525 57-105 (117)
415 TIGR00614 recQ_fam ATP-depende 21.9 38 0.00097 11.7 2.8 47 340-395 286-340 (497)
416 PTZ00179 60S ribosomal protein 21.9 38 0.00097 11.7 2.2 66 562-628 22-93 (189)
417 pfam00152 tRNA-synt_2 tRNA syn 21.9 38 0.00097 11.7 1.2 67 369-466 251-317 (341)
418 pfam06951 PLA2G12 Group XII se 21.8 11 0.00028 16.2 -1.9 23 200-222 31-53 (186)
419 TIGR02941 Sigma_B RNA polymera 21.7 38 0.00097 11.7 1.2 35 189-224 4-38 (256)
420 cd08041 OBF_kDNA_ligase_like T 21.7 38 0.00098 11.7 4.8 50 633-687 21-72 (77)
421 TIGR03561 organ_hyd_perox pero 21.5 39 0.00098 11.7 2.8 27 503-529 93-119 (134)
422 cd07950 Gallate_Doxase_N The N 21.4 36 0.00092 11.9 0.7 112 382-546 147-258 (277)
423 COG1866 PckA Phosphoenolpyruva 21.2 30 0.00076 12.6 0.2 164 319-502 211-385 (529)
424 cd03319 L-Ala-DL-Glu_epimerase 21.1 36 0.00091 12.0 0.6 109 407-534 169-282 (316)
425 pfam11336 DUF3138 Protein of u 21.0 39 0.001 11.6 4.2 33 326-358 170-211 (514)
426 COG4775 Outer membrane protein 21.0 20 0.00051 14.0 -0.7 15 324-338 407-421 (766)
427 pfam11725 AvrE Pathogenicity f 20.8 40 0.001 11.6 1.5 288 376-695 1128-1497(1771)
428 KOG2473 consensus 20.8 25 0.00063 13.3 -0.3 22 322-343 280-302 (484)
429 pfam07405 DUF1506 Protein of u 20.8 40 0.001 11.6 6.8 93 596-689 8-128 (133)
430 PRK10279 hypothetical protein; 20.8 40 0.001 11.6 1.4 86 90-180 84-178 (300)
431 TIGR01051 topA_bact DNA topois 20.7 40 0.001 11.6 0.9 13 294-306 129-141 (688)
432 pfam00357 Integrin_alpha Integ 20.6 40 0.001 11.5 1.0 17 75-91 2-18 (26)
433 pfam03492 Methyltransf_7 SAM d 20.3 39 0.00098 11.7 0.6 15 65-80 84-98 (331)
434 PRK10070 glycine betaine trans 20.3 41 0.001 11.5 5.9 10 92-101 71-80 (400)
435 cd07949 PCA_45_Doxase_B_like_1 20.3 41 0.001 11.5 0.9 30 382-411 146-175 (276)
436 pfam02335 Cytochrom_C552 Cytoc 20.1 41 0.001 11.5 3.5 42 489-537 340-381 (383)
437 PRK09439 glucose-specific PTS 20.0 41 0.001 11.5 2.8 60 609-671 47-115 (169)
No 1
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=100.00 E-value=0 Score=2257.18 Aligned_cols=691 Identities=55% Similarity=0.904 Sum_probs=678.2
Q ss_pred CCEEEEEEEECCEEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCC
Q ss_conf 72089999989989999914004546728999978948999997278888777735406866523201336788873578
Q gi|254780784|r 2 FDVHTVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLTVNYQERTYAVGKIPGGYLRRE 81 (699)
Q Consensus 2 ~~~~~~~~~~ggr~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~~~~~~dFfPLtVdY~Ek~yAaGkIPGgF~kRE 81 (699)
++.++++++||||+++||||+|||||||||+++||||+||||||++++++++.|||||||||+||+||||||||||||||
T Consensus 1 ~~~~~~~~~~~g~~l~~etGklAkqA~Gsv~v~~GdT~VL~Tv~~~~~~~~~~dFfPLtVdY~Ek~yAaGkIPGgF~KRE 80 (694)
T PRK11824 1 FNPIVKSIEFGGRTLTLETGKIARQADGAVLVRYGDTVVLVTVVASKEPKEGQDFFPLTVDYQEKTYAAGKIPGGFFKRE 80 (694)
T ss_pred CCCEEEEEEECCEEEEEECCHHHHHCCCEEEEEECCEEEEEEEEECCCCCCCCCCCCCEEEEEEHHHCCCCCCCCCCCCC
T ss_conf 98479999989999999844335416842999989969999998248888999967714757882101776777562678
Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCE
Q ss_conf 98871453111123212677674688688378999982188887789999999999873268823541123552047732
Q gi|254780784|r 82 SRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQY 161 (699)
Q Consensus 82 grpsd~EiL~sRlIDR~lRPLFPkgf~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~idge~ 161 (699)
|||||+|||+|||||||||||||+||+|||||+|||||+|++|+||++|+|||||||++|||||+|||||||||++||+|
T Consensus 81 grpse~eiL~sRlIDRpiRPLFP~gf~~evQIi~tVLS~D~~~~pdvlAi~gASaAL~iSdIPF~GPVaaVRVG~idGe~ 160 (694)
T PRK11824 81 GRPSEKETLTSRLIDRPIRPLFPKGFRNEVQVVATVLSVDPENDPDILAMIGASAALSISGIPFNGPIAAVRVGYIDGEF 160 (694)
T ss_pred CCCCHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCEE
T ss_conf 89971777878863676556777788866189999997688889068899999999985089978874899999889989
Q ss_pred EECCCCCCC-CCCCEEEEEECCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC-HHH
Q ss_conf 436850002-221013553054432333124443248999988753168899999999999998388986447431-257
Q gi|254780784|r 162 VLNPRLDED-QGSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKD-FSK 239 (699)
Q Consensus 162 ViNPt~ee~-esdLDLvVAGT~d~IlMIE~~A~EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~~~~Gk~K~~~~~~~-~~~ 239 (699)
|+|||++|+ +|+|||+||||+++|+|||++|+|+||++|++||+|||++||++|++|++|++++||+|++++.+. +++
T Consensus 161 ViNPT~eqle~SdLDLvVAGT~daI~MVE~~A~EvsEe~mleAI~fahe~iq~ii~~q~el~~~~Gk~K~e~~~~~~~~e 240 (694)
T PRK11824 161 VLNPTVEELEESDLDLVVAGTKDAVLMVESEANELSEEVMLEAIEFGHEAIQELIDAQEELAAEAGKPKWEFEPPEVDEE 240 (694)
T ss_pred EECCCHHHHHHCCEEEEEECCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHH
T ss_conf 98998567742837899982478189997247767889999999999999999999999999997899764778789989
Q ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCH-HCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 999999998988888741000122489999999999730223100-0002678899999999999999872886658867
Q gi|254780784|r 240 LEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHS-SWNEGEIVSVFEDIQAKVVRTVMLDKKVRMDGRD 318 (699)
Q Consensus 240 ~~~~v~~~~~~~l~~a~~i~~K~eR~~ai~~l~~ei~e~l~ee~~-~~~~~~i~~af~~l~k~ivR~~ILeeg~R~DGR~ 318 (699)
+.+.+++.+.+++.+|+++++|++|+++++++++++.+.+.++++ +.+..+++.+|++++|++||++||++++|+|||+
T Consensus 241 l~~~v~~~~~~~i~~a~~~~~K~eR~~al~~lk~ei~e~l~ee~~~~~~~~~i~~~f~~l~K~ivR~~IL~~~~RiDGR~ 320 (694)
T PRK11824 241 LKAAVKELAEAELKEAYQITDKQERYAALDAIKEEVLEALAEEEEEEEKEKEIKEALKDLEKKIVRRRILEEGIRIDGRD 320 (694)
T ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 99999999999999998344678899999999999999754226664579999999999999999999965896668888
Q ss_pred CCCEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCHH
Q ss_conf 75337879984475466700899987976899998168652122334454420358774058875445334556765024
Q gi|254780784|r 319 SETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRRE 398 (699)
Q Consensus 319 ~dEIRpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfsvGE~~~~~~~~RRE 398 (699)
+||||||+||+|+|||+||||||||||||||||+|||++.|+|++|++.++.+||||||||||||||||+||+|+|+|||
T Consensus 321 ~dEIRPI~~EvgvLPr~HGSaLFTRGETQaL~~~TLG~~~d~Q~iD~l~~~~~krFmlHYNFPPfSvGE~g~~~~p~RRE 400 (694)
T PRK11824 321 LDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTLRDAQIIDGLEGEYKKRFMLHYNFPPYSVGETGRVGSPGRRE 400 (694)
T ss_pred CCCCCCCEEECCCCCCCCCCEEEECCCCEEEEEEEECCCCHHHHHCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCC
T ss_conf 66414525783887888743458715606999997258301010015676511047997478997678766778976310
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEECCEEEEEEE
Q ss_conf 67999999987410786446873899985311027852235667777987625950225412133200440882899863
Q gi|254780784|r 399 IGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSD 478 (699)
Q Consensus 399 iGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp~~~~VaGiamGLi~~~~~~~iLtD 478 (699)
||||+||||||.||||++++||||||||||||||||||||||||||||||||||||||+||||||||||+|+|+|+||||
T Consensus 401 IGHG~LAeRAL~~vlP~~e~FPYtIRvvSEileSNGSSSMAsVCg~sLALmdAGVPik~~VAGIAmGLi~e~~~~~iLtD 480 (694)
T PRK11824 401 IGHGALAERALEPVLPSEEEFPYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVLSD 480 (694)
T ss_pred CCCHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEECCCEEEEEEE
T ss_conf 03369999988711898566983489998800448853448898787998857996466400477777870873799974
Q ss_pred CCCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEE
Q ss_conf 14422013655100100556512443245365568899999999999999999999984356674332244875799997
Q gi|254780784|r 479 ISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAI 558 (699)
Q Consensus 479 I~G~ED~~GdMDFKvaGT~~GiTa~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i 558 (699)
|+|+||||||||||||||++||||||||||+.|||++||++||+|||+||+|||++|+++|++||.++|+||||+++++|
T Consensus 481 I~G~EDh~GDMDFKvAGT~~GITA~QmDiKi~Gi~~~il~~Al~qA~~gR~~IL~~M~~~i~~pr~~~s~~aP~i~~~~i 560 (694)
T PRK11824 481 ILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGITREIMEEALEQAKEGRLHILGKMNEAISEPRTELSPYAPRIETIKI 560 (694)
T ss_pred CCCCCCCCCCCCEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEE
T ss_conf 04441024775315623666448887403447969899999999999999999999987366654333568987999997
Q ss_pred CCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEECCEEEE
Q ss_conf 71150000378607799899986888998088089999689899999999999852475468678999999941536998
Q gi|254780784|r 559 PPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVH 638 (699)
Q Consensus 559 ~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~~~e~g~~y~~~v~~i~~fGafve 638 (699)
||+|||+||||||||||+|+++|||+|||+|||.|+||++|++++++|+++|++++++||+|++|+|+|++|++||||||
T Consensus 561 ~~~ki~~vIG~gGk~Ik~i~e~tg~~Idi~ddG~v~i~~~~~~~~~~A~~~I~~i~~~~evG~iy~g~V~~i~~fGafve 640 (694)
T PRK11824 561 DPDKIRDVIGPGGKTIREITEETGAKIDIEDDGTVKIAASDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVE 640 (694)
T ss_pred CHHHHHHEECCCHHHHHHHHHHHCCEEEEECCCEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEECEEEEE
T ss_conf 87986650686338899999988988999689179999899999999999999845768589779999999984418999
Q ss_pred CCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEECCC
Q ss_conf 287971048866314445478556032598899999978689986668730477
Q gi|254780784|r 639 FCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQ 692 (699)
Q Consensus 639 ~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk~~~~ 692 (699)
|+||++||||||||+++||++++|++++||+|+|||+++|++||++||||++++
T Consensus 641 ~~pg~~GLlHiSel~~~rv~~v~d~~~~Gd~i~Vk~~~id~~Gri~Lsrk~~l~ 694 (694)
T PRK11824 641 ILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRKAVLE 694 (694)
T ss_pred ECCCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEHHHHHC
T ss_conf 679980688800246523468645116898899999989899986666477519
No 2
>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=0 Score=2222.76 Aligned_cols=676 Identities=58% Similarity=0.933 Sum_probs=661.2
Q ss_pred EECCEEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf 98998999991400454672899997894899999727888877773540686652320133678887357898871453
Q gi|254780784|r 10 EWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLTVNYQERTYAVGKIPGGYLRRESRPTENEI 89 (699)
Q Consensus 10 ~~ggr~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~~~~~~dFfPLtVdY~Ek~yAaGkIPGgF~kREgrpsd~Ei 89 (699)
+||||+|+||||+|||||||||+++||||+||||||++++++++.|||||||||+||+||+||||||||||||||||+||
T Consensus 1 e~gg~~l~~etGklAkqA~GsV~v~~GdT~VL~T~~~~~~~~~~~DFfPLtVdY~Ek~yAaGkIPGgF~KREgrPse~Ei 80 (684)
T TIGR03591 1 EYGGRTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKEAKEGQDFFPLTVNYQEKFYAAGKIPGGFFKREGRPSEKET 80 (684)
T ss_pred CCCCCEEEEECCHHHHHCCCEEEEEECCEEEEEEEEECCCCCCCCCCCCCEEEEEEHHHHCCCCCCCCCCCCCCCCHHHH
T ss_conf 95880699974533541684299998996999999814888899997775460476633177777766477889971888
Q ss_pred HHHHHHHCCCCCCCCCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCEEECCCCCC
Q ss_conf 11112321267767468868837899998218888778999999999987326882354112355204773243685000
Q gi|254780784|r 90 LISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDE 169 (699)
Q Consensus 90 L~sRlIDR~lRPLFPkgf~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~idge~ViNPt~ee 169 (699)
|+|||||||||||||+||+|||||+|||||+|++|+||+||+|||||||++|||||+|||||||||++||+||+|||++|
T Consensus 81 L~sRlIDRpiRPLFP~gf~~evQIi~tVLS~D~~~~pDvlAi~gASaAL~iSdIPf~GPVaaVRVG~idGe~ViNPT~~q 160 (684)
T TIGR03591 81 LTSRLIDRPIRPLFPKGFRNEVQVVATVLSYDPENDPDILAIIGASAALAISGIPFNGPIAAVRVGYIDGQYVLNPTVDE 160 (684)
T ss_pred HHHHHHCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCEEEECCCHHH
T ss_conf 88887367654677667887728999999768888906889999999998608986787389999998998998998667
Q ss_pred C-CCCCEEEEEECCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC-HHHHHHHHHHH
Q ss_conf 2-221013553054432333124443248999988753168899999999999998388986447431-25799999999
Q gi|254780784|r 170 D-QGSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKD-FSKLEEEMSQM 247 (699)
Q Consensus 170 ~-esdLDLvVAGT~d~IlMIE~~A~EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~~~~Gk~K~~~~~~~-~~~~~~~v~~~ 247 (699)
+ +|+|||+||||+++|+|||++|+|+||++|++||+|||++||++|++|++|++++||+|++++... ++++.+++.+.
T Consensus 161 le~SdLDLvVAGT~daIvMVE~~A~EvsEe~mleAI~~ahe~iq~ii~~q~el~~~~Gk~K~e~~~~~~~~el~~~v~~~ 240 (684)
T TIGR03591 161 LEKSDLDLVVAGTKDAVLMVESEAKELSEEVMLGAIEFGHEEIQPVIEAIEELAEEAGKEKWEFVAPEVDEELKAKVKEL 240 (684)
T ss_pred HHHCCEEEEEECCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf 85474339998148818999756776788999999999999999999999999999789986367878998999999998
Q ss_pred HHH-HHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCH----HCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCE
Q ss_conf 898-8888741000122489999999999730223100----00026788999999999999998728866588677533
Q gi|254780784|r 248 IKE-DLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHS----SWNEGEIVSVFEDIQAKVVRTVMLDKKVRMDGRDSETV 322 (699)
Q Consensus 248 ~~~-~l~~a~~i~~K~eR~~ai~~l~~ei~e~l~ee~~----~~~~~~i~~af~~l~k~ivR~~ILeeg~R~DGR~~dEI 322 (699)
+.+ .+++++++.+|++|+++++++++++.+.+.++++ .++..+++.+|++++|++||++||++++|+|||++|||
T Consensus 241 ~~~~~i~~a~~~~~K~eR~~al~~lk~ei~e~~~~~~~~e~~~~~~~~i~~a~~~l~K~~vR~~IL~~~~R~DGR~~dEI 320 (684)
T TIGR03591 241 AYEAGLKEAYQITEKQERYAALDAIKEEVLEALAEEEEEEEEADREKEIKEAFKDLEKKIVRERILKEGKRIDGRDLDTI 320 (684)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf 62779999865666699999999999999998542144554422599999999999999999999658977889982301
Q ss_pred EEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf 78799844754667008999879768999981686521223344544203587740588754453345567650246799
Q gi|254780784|r 323 RDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHG 402 (699)
Q Consensus 323 RpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfsvGE~~~~~~~~RREiGHg 402 (699)
|||+||+|+|||+||||||||||||||||+|||++.|+|++|++.++.+||||||||||||||||+||+|+|+|||||||
T Consensus 321 RpIs~EvgvLPr~HGSaLFtRGETQaL~v~TLG~~~d~Q~iD~l~~~~~krFmlHYNFPPfSvGE~g~~~~p~RREIGHG 400 (684)
T TIGR03591 321 RPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDEQIIDDLEGEYRKRFMLHYNFPPYSVGEVGRVGGPGRREIGHG 400 (684)
T ss_pred CCHHCCCCCCCCCCCCEEEEECCCEEEEEEEECCCHHHHHHCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCHHHCCH
T ss_conf 24020338757777435788526507999950682221101145765110489974799976787677889985012267
Q ss_pred HHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEECC-EEEEEEECCC
Q ss_conf 999998741078644687389998531102785223566777798762595022541213320044088-2899863144
Q gi|254780784|r 403 RLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGD-DFIILSDISG 481 (699)
Q Consensus 403 ~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp~~~~VaGiamGLi~~~~-~~~iLtDI~G 481 (699)
+||||||.||||++++||||||||||||||||||||||||||||||||||||||+||||||||||+|+| +|+|||||+|
T Consensus 401 ~LAeRAL~~vlP~~e~FPYtIRvvSeileSNGSSSMAsVCg~sLALmdAGVPik~~VAGIAmGLi~e~d~~y~iLtDI~G 480 (684)
T TIGR03591 401 ALAERALKAVLPSEEEFPYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDERFAVLSDILG 480 (684)
T ss_pred HHHHHHHHHCCCCCCCCCCEEEEEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEECCCCCEEEEEECCC
T ss_conf 99999998518982338814899988004688434289999999998679963665025777768737874799973133
Q ss_pred CCCCCCCCCEEEEECCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCC
Q ss_conf 22013655100100556512443245365568899999999999999999999984356674332244875799997711
Q gi|254780784|r 482 DEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPD 561 (699)
Q Consensus 482 ~ED~~GdMDFKvaGT~~GiTa~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i~~~ 561 (699)
+||||||||||||||++||||||||||+.|||++||++||+|||+||+|||++|+++|++||.++|+||||+++++|||+
T Consensus 481 ~EDh~GDMDFKvaGT~~GITa~QmDiKi~Gi~~~il~~Al~qA~~~R~~IL~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ 560 (684)
T TIGR03591 481 DEDHLGDMDFKVAGTRDGITALQMDIKIDGITREIMEQALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPD 560 (684)
T ss_pred CCCCCCCCCEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECHH
T ss_conf 41014775305633666448887403558978999999999999999999999997352543344578875799997878
Q ss_pred CEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEECCEEEECCC
Q ss_conf 50000378607799899986888998088089999689899999999999852475468678999999941536998287
Q gi|254780784|r 562 QIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCG 641 (699)
Q Consensus 562 ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~~~e~g~~y~~~v~~i~~fGafve~~~ 641 (699)
|||+||||||||||+|+++|||+|||+|||.|+|+++|++++++|+++|++++++||+|++|+|||++|++|||||||+|
T Consensus 561 ki~~vIG~gGk~Ik~i~~~tg~~I~i~ddG~v~i~~~~~~~~~~A~~~I~~~~~~~evG~~y~g~V~~i~~fGafve~~p 640 (684)
T TIGR03591 561 KIRDVIGPGGKVIREITEETGAKIDIEDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILP 640 (684)
T ss_pred HHHHEECCCCHHHHHHHHHHCCEEEEECCCEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEECEEEEEECC
T ss_conf 86650787528898999988988998589089999899999999999999851668589779999999984408999679
Q ss_pred CCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEE
Q ss_conf 97104886631444547855603259889999997868998666
Q gi|254780784|r 642 ARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKL 685 (699)
Q Consensus 642 g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~l 685 (699)
|++||||||||+++||++++|++++||+|+|||+++|++||++|
T Consensus 641 g~~GLlHiSel~~~rv~~v~dv~~~Gd~i~Vk~~~id~~Gri~L 684 (684)
T TIGR03591 641 GKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDKQGRIKL 684 (684)
T ss_pred CCCEEEEEECCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCCCC
T ss_conf 98147870013653446864521689889999997889998285
No 3
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=1959.61 Aligned_cols=690 Identities=55% Similarity=0.893 Sum_probs=677.7
Q ss_pred CCCEEEEEEEECCEEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCC
Q ss_conf 97208999998998999991400454672899997894899999727888877773540686652320133678887357
Q gi|254780784|r 1 MFDVHTVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLTVNYQERTYAVGKIPGGYLRR 80 (699)
Q Consensus 1 m~~~~~~~~~~ggr~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~~~~~~dFfPLtVdY~Ek~yAaGkIPGgF~kR 80 (699)
||+++.++++||||+++||||++||||+|||+++||||+||+|||+++ +++++|||||||||+||+|||||||||||||
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
T ss_conf 976268988888846999824335525750899978979999975147-8889884431673545012067677742036
Q ss_pred CCCCCHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCC
Q ss_conf 89887145311112321267767468868837899998218888778999999999987326882354112355204773
Q gi|254780784|r 81 ESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQ 160 (699)
Q Consensus 81 Egrpsd~EiL~sRlIDR~lRPLFPkgf~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~idge 160 (699)
||||||+|||+|||||||||||||+||+||+||+++|||+|++++||++|++|||+||++|+|||+||||+||||++||+
T Consensus 80 EGrpse~e~L~sRLIDRpiRPlFp~g~~~evqIv~tvls~D~~~~pdi~a~~gaSaAl~ls~iPf~gpi~~vrvg~idg~ 159 (692)
T COG1185 80 EGRPSEKEILTSRLIDRPIRPLFPKGFRNEVQIVNTVLSVDPENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYIDGI 159 (692)
T ss_pred CCCCCCCHHHHHHHCCCCCCCCCCHHHCCCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCE
T ss_conf 77887520267764066553355212065408999998667877868899878889875137986676014899998898
Q ss_pred EEECCCCCC-CCCCCEEEEEECCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC-CHH
Q ss_conf 243685000-222101355305443233312444324899998875316889999999999999838898644743-125
Q gi|254780784|r 161 YVLNPRLDE-DQGSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSK-DFS 238 (699)
Q Consensus 161 ~ViNPt~ee-~esdLDLvVAGT~d~IlMIE~~A~EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~~~~Gk~K~~~~~~-~~~ 238 (699)
||+|||.++ .+|+|||+||||+++|+|||++|++++|+.|++|+.|||+++|.+|++|++|+..+|++++++.++ .++
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
T ss_conf 99778766654163125760786664104346666888999999998889899999999999997376553233568648
Q ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 79999999989888887410001224899999999997302231000002678899999999999999872886658867
Q gi|254780784|r 239 KLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDIQAKVVRTVMLDKKVRMDGRD 318 (699)
Q Consensus 239 ~~~~~v~~~~~~~l~~a~~i~~K~eR~~ai~~l~~ei~e~l~ee~~~~~~~~i~~af~~l~k~ivR~~ILeeg~R~DGR~ 318 (699)
++..++.+.+.+++.+++.+.+|++|+.+++++++++.+.+..++.. ...++..+|+.++++.||.+|+++++|+|||.
T Consensus 240 ~l~~~i~~~~~~~l~~a~~i~~K~eR~~~~~~~~~~i~~~~~~~e~~-~~~~~~~~~~~l~~~~vR~~Il~~~vR~DGR~ 318 (692)
T COG1185 240 ELEAKVRDLAEDELKEAVGIREKQERSAALDAIKEKIEEELSGEEES-SLKEIKAILEKLEKKPVRRLILEGKVRIDGRF 318 (692)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 99999999867889998644513334667888999999997542134-27889999998767999999863884357887
Q ss_pred CCCEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCHH
Q ss_conf 75337879984475466700899987976899998168652122334454420358774058875445334556765024
Q gi|254780784|r 319 SETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRRE 398 (699)
Q Consensus 319 ~dEIRpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfsvGE~~~~~~~~RRE 398 (699)
+++||||+||+++|||+||||||||||||+|++||||++.|+|.+|.+.+++++|||||||||||||||++|+|+|+|||
T Consensus 319 ~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~v~TLG~~~d~Qiid~l~~e~~krfm~hYNFPp~SvGE~g~~g~p~RRE 398 (692)
T COG1185 319 GDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPRDAQVIDILEGEYKKRFLLHYNFPPFSVGETGRMGSPGRRE 398 (692)
T ss_pred CCEEEEEEEEECCCCCCCCHHHCCCCCCCCEEEEECCCCCHHHHHHHCCCHHHHHEEEECCCCCCCCCCCCCCCCCCCCC
T ss_conf 65265403775478875302210068875146897577413666552053233325421267998745567788987533
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEECCEEEEEEE
Q ss_conf 67999999987410786446873899985311027852235667777987625950225412133200440882899863
Q gi|254780784|r 399 IGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSD 478 (699)
Q Consensus 399 iGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp~~~~VaGiamGLi~~~~~~~iLtD 478 (699)
||||+||+|||.|++|+.++||||||++|||||||||||||||||+||||||||||||+||||||||||+|+++|++|||
T Consensus 399 iGHG~LA~Ral~~vlp~~e~fpytiRvVsEi~eSNGSsSmaSVCg~sLaLmdAGVPIk~pVAGIAMGLI~eg~~~~vLsD 478 (692)
T COG1185 399 IGHGALAERALAPVLPSEEEFPYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVLSD 478 (692)
T ss_pred CCCCHHHHHHHHHHCCCHHCCCCEEEEEEHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCEECCCCEEEECC
T ss_conf 46736468888650995100780455220111046741222345517988757896355554300152324874476400
Q ss_pred CCCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEE
Q ss_conf 14422013655100100556512443245365568899999999999999999999984356674332244875799997
Q gi|254780784|r 479 ISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAI 558 (699)
Q Consensus 479 I~G~ED~~GdMDFKvaGT~~GiTa~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i 558 (699)
|+|+|||+||||||||||++||||||||+|+.|||.+||.+||.|||.||+|||+.|+++|+.||.++|+||||+++++|
T Consensus 479 I~G~EDhlGDMDFKVAGT~~GiTAlQMDiKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i 558 (692)
T COG1185 479 ILGDEDHLGDMDFKVAGTDDGITALQMDIKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKI 558 (692)
T ss_pred CCCCCCCCCCCEEEEECCCCCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECC
T ss_conf 26653345773268725767750104556645888999999998799999999999999875114344245872499613
Q ss_pred CCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEECCEEEE
Q ss_conf 71150000378607799899986888998088089999689899999999999852475468678999999941536998
Q gi|254780784|r 559 PPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVH 638 (699)
Q Consensus 559 ~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~~~e~g~~y~~~v~~i~~fGafve 638 (699)
+|+||+++||||||+||+|+++||++|||+|||+|+|++.|++++++|+++|++++.++|+|++|.|+|++|.+|||||+
T Consensus 559 ~~dKI~dvIG~gGk~I~~I~eetg~~IdieddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~ 638 (692)
T COG1185 559 DPDKIRDVIGPGGKTIKAITEETGVKIDIEDDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVE 638 (692)
T ss_pred CHHHHHHCCCCCCCCHHHHHHHHCCEEEECCCCCEEEEECCHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECCEEEE
T ss_conf 88887632188632034655734767984589858999565688899999999987431015289988999864125898
Q ss_pred CCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEECCC
Q ss_conf 287971048866314445478556032598899999978689986668730477
Q gi|254780784|r 639 FCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQ 692 (699)
Q Consensus 639 ~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk~~~~ 692 (699)
++||++||||||+++++||++|+|++++||+|.||++++|++||++||+|++++
T Consensus 639 l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~Gri~ls~~~~~~ 692 (692)
T COG1185 639 LLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQGRIRLSIKAVLE 692 (692)
T ss_pred ECCCCCEEEEEHHHHHHHHHCCCCEEECCCEEEEEEEEECCCCCCCCEEHHCCC
T ss_conf 338962068743533455532045354486599999633666770321121049
No 4
>KOG1067 consensus
Probab=100.00 E-value=0 Score=1691.16 Aligned_cols=684 Identities=40% Similarity=0.650 Sum_probs=663.6
Q ss_pred CEEEEEEEECCEEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCC
Q ss_conf 20899999899899999140045467289999789489999972788887777354068665232013367888735789
Q gi|254780784|r 3 DVHTVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLTVNYQERTYAVGKIPGGYLRRES 82 (699)
Q Consensus 3 ~~~~~~~~~ggr~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~~~~~~dFfPLtVdY~Ek~yAaGkIPGgF~kREg 82 (699)
|..++++.+|+|+|.||||+|||||||||++++|+|.|++|||+.+.|.|.+ |+||+||||||+||+|+||||||||||
T Consensus 45 ~~vsVeipfGnR~i~~eTG~maRfAngsvvv~~GeT~V~ttv~~a~~PSp~~-FlPL~VdYqek~aA~GRip~~f~rREg 123 (760)
T KOG1067 45 NAVSVEIPFGNREILFETGKLARFANGSVVVQMGETAVMTTVVLADKPSPPQ-FLPLVVDYQEKFAAVGRIPGNFMRREG 123 (760)
T ss_pred CCEEEEECCCCEEEEEECCHHHHHCCCCEEECCCCEEEEEEEEECCCCCCCC-CCEEEEEHHHHHHHHCCCCCCHHHCCC
T ss_conf 6504650569747999614334212785797048758999988517899644-403798756544441567763100147
Q ss_pred CCCHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCEE
Q ss_conf 88714531111232126776746886883789999821888877899999999998732688235411235520477324
Q gi|254780784|r 83 RPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYV 162 (699)
Q Consensus 83 rpsd~EiL~sRlIDR~lRPLFPkgf~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~idge~V 162 (699)
||+|+|||++||||||||||||+||+||+||+|++||+|+.++||+||+|+||+||++|||||+||+++||||++|||||
T Consensus 124 ~tkd~Eil~~rLidrsirplfp~g~~~etqi~~n~Ls~dG~~~pdvlainaas~Al~lsdvpw~gpig~vRigLi~Ge~v 203 (760)
T KOG1067 124 RTKDKEILTGRLIDRPIRPLFPKGFYHETQILCNVLSSDGVHDPDVLAINAASAALSLSDVPWNGPIGAVRIGLIDGEFV 203 (760)
T ss_pred CCCCCEEEEEECCCCCCCCCCCCCCHHHHHHHHHHEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCEEE
T ss_conf 88550146642137655667755205378887665111465580288776777776431487778421168623343388
Q ss_pred ECCCCCCC-CCCCEEEEEECCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC--CHHH
Q ss_conf 36850002-22101355305443233312444324899998875316889999999999999838898644743--1257
Q gi|254780784|r 163 LNPRLDED-QGSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSK--DFSK 239 (699)
Q Consensus 163 iNPt~ee~-esdLDLvVAGT~d~IlMIE~~A~EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~~~~Gk~K~~~~~~--~~~~ 239 (699)
+|||..|+ .|+|||+||||++.++|+|+.+++++|++++.||+.||.+.|.+|..|+.|+++.||+|+++... .+++
T Consensus 204 VNPT~kEmssS~Lnlvvagt~~~~vmle~~s~~i~qqdl~~Aikvg~~~~q~~i~~i~~L~k~~Gk~Kr~~~~~~~p~pe 283 (760)
T KOG1067 204 VNPTRKEMSSSQLNLVVAGTKSQTVMLEGSSNNILQQDLLHAIKVGVKEAQQIIQGIERLAKKYGKQKREPQKLFLPDPE 283 (760)
T ss_pred ECCCHHHHHHCCCEEEEEECCCEEEEEECCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCHH
T ss_conf 67516654015300588714652899970024220899999997430889999999999999858662432444289878
Q ss_pred HHHHHHHHHHHHHHHHHHCC--HHHHHHHHHHHHHHHHHHCCCCCCHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 99999999898888874100--0122489999999999730223100000267889999999999999987288665886
Q gi|254780784|r 240 LEEEMSQMIKEDLRVSCFIP--EKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDIQAKVVRTVMLDKKVRMDGR 317 (699)
Q Consensus 240 ~~~~v~~~~~~~l~~a~~i~--~K~eR~~ai~~l~~ei~e~l~ee~~~~~~~~i~~af~~l~k~ivR~~ILeeg~R~DGR 317 (699)
+.+.+.+.+..+|.++++.. +|.+|.+|++.++.+..+++.+.+++.+..++...|+.+-|+++|++|+++|+|||||
T Consensus 284 l~K~v~~la~erl~~vftd~shdK~sR~eAvn~i~~~~e~k~~e~~pe~e~~~i~~~fn~vskkv~Rs~i~~~gkR~DGR 363 (760)
T KOG1067 284 LVKHVHKLAMERLYAVFTDYSHDKISRDEAVNKIRLDDEDKVKEEFPEQEPSEIIESFNTVSKKVFRSRILEEGKRCDGR 363 (760)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 99999999999999985253445101566775532004777776468866789999999999999999997136556783
Q ss_pred CCCCEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCE-EEEEEEECCCCCCCCCCCCCCCCCC
Q ss_conf 775337879984475466700899987976899998168652122334454420-3587740588754453345567650
Q gi|254780784|r 318 DSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQR-NDFMMHYNFLPCATGEVSRMGAPSR 396 (699)
Q Consensus 318 ~~dEIRpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~-k~fmlHYNFPpfsvGE~~~~~~~~R 396 (699)
.+||+|||+||+++||+.||||||||||||+|||||||++..+|++|++.+..+ +||||||.||||||||+|++|+++|
T Consensus 364 ~ldelR~I~ce~~m~~~lHGSaLFqRGqTQvlctVtl~s~e~a~klD~l~~~~~~~~FmLhY~FPPyat~Evgkig~~nR 443 (760)
T KOG1067 364 DLDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGPDNGINFMLHYEFPPYATNEVGKIGGLNR 443 (760)
T ss_pred CHHHHCCCCEECCCCCCCCCHHHHHCCCEEEEEEEECCCHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCCCCCCCCCC
T ss_conf 33341354100173222441145526760599999838978843455302576675389996159754564301468760
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEECC-----
Q ss_conf 246799999998741078644687389998531102785223566777798762595022541213320044088-----
Q gi|254780784|r 397 REIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGD----- 471 (699)
Q Consensus 397 REiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp~~~~VaGiamGLi~~~~----- 471 (699)
||+|||+||||||.|++| ++|||||||.||||||||||||||||||||||||||||+++|||||||||+++.|
T Consensus 444 RE~GhgaLAEkaL~~vlP--~dfPftIRv~SeVleSnGSsSMASvCGGslALmDaGvPv~a~vAGVaiGlvt~td~e~g~ 521 (760)
T KOG1067 444 RELGHGALAEKALLPVLP--EDFPFTIRVTSEVLESNGSSSMASVCGGSLALMDAGVPVSAHVAGVAIGLVTKTDPEKGE 521 (760)
T ss_pred CCCCCHHHHHHHHHCCCC--CCCCEEEEEEEEEEECCCCCHHHHHHCCHHHHHHCCCCCCCCCCEEEEEEEECCCCCCCC
T ss_conf 004751676644302385--458637997536640589516776635216554169842132130578767614755477
Q ss_pred --EEEEEEECCCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf --289986314422013655100100556512443245365568899999999999999999999984356674332244
Q gi|254780784|r 472 --DFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEF 549 (699)
Q Consensus 472 --~~~iLtDI~G~ED~~GdMDFKvaGT~~GiTa~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m~~~~~~~~~~~~~~ 549 (699)
+|.|||||+|+|||.||||||||||++||||| ||+++|+.|||+||+++|+|||++|+++|++||...++|
T Consensus 522 i~dyriltDIlGiEd~~GDMDFKiAGt~dGvTA~-------gi~l~Iv~eal~~a~~ar~~Il~~m~k~i~~Pr~s~~~y 594 (760)
T KOG1067 522 IEDYRILTDILGIEDYNGDMDFKIAGTNDGVTAL-------GIPLKIVMEALQKAREARLQILDIMEKNINSPRGSDKEY 594 (760)
T ss_pred CCCCEEEHHHCCHHHHCCCCCEEECCCCCCCEEC-------CCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 6661431033044541687420320456761132-------774899999987616889999999985268866675345
Q ss_pred CCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHCCC-----CCCCCEEE
Q ss_conf 8757999977115000037860779989998688899808808999968989999999999985247-----54686789
Q gi|254780784|r 550 TPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDV-----PEVNKIYK 624 (699)
Q Consensus 550 ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~~-----~e~g~~y~ 624 (699)
+|++++++++|+|...+|||||++.|.|++||| .|+..|+|+++|||+++.++++|+++|..|+.+ +++|.+|+
T Consensus 595 ~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtG-ai~~vDe~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~~l~~g~vyt 673 (760)
T KOG1067 595 SPVLETLKVSPSKRATLIGPGGVLKKKIEVETG-AISQVDEGTFSIFAPTQAAMEEAKEFIDGIIKDDQVQDLEFGGVYT 673 (760)
T ss_pred CCEEEEEEECCHHHHEEECCCCCEEEEEEEECC-CEEEECCCEEEEEECCHHHHHHHHHHHHHHHCCCCCCCEEEEEEEE
T ss_conf 750357862603421021676512346764035-2244427557997068889999999988773476535258601777
Q ss_pred EEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEECCCCCCCC
Q ss_conf 9999994153699828797104886631444547855603259889999997868998666873047787899
Q gi|254780784|r 625 GQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQNTGKP 697 (699)
Q Consensus 625 ~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk~~~~~~~~~ 697 (699)
++|+++.|+|+||+|+||++||||+|||+++++.+++|+|++||+|.|||+++|++|.++||+|+|+|+|.-.
T Consensus 674 ~tIte~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~~g~~~ls~ralLp~p~~~ 746 (760)
T KOG1067 674 ATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPRGGIMLSSRALLPDPATK 746 (760)
T ss_pred EEEEEECCCCEEEEECCCCHHHCCCHHCCCCCCCCHHHHHHHCCEEEEEEEEECCCCCEEEHHHHHCCCCCCC
T ss_conf 8886641563599956874100000011512005857887520406889986657666210126526895447
No 5
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polyribonucleotide nucleotidyltransferase; InterPro: IPR014069 The of the characterization of two proteins from Streptomyces coelicolor ahs been presented . The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. It has also been shown 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=0 Score=1360.78 Aligned_cols=676 Identities=42% Similarity=0.691 Sum_probs=648.9
Q ss_pred EEECCEEEEEEECEECCCCCCEEEEEE-CCCEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf 998998999991400454672899997-8948999997278888777735406866523201336788873578988714
Q gi|254780784|r 9 IEWAGRPLKLETGRIARQSDGAVLATY-GETVVLATVVYDRSLKDGQDFFPLTVNYQERTYAVGKIPGGYLRRESRPTEN 87 (699)
Q Consensus 9 ~~~ggr~i~~ETGklArqA~GsV~v~~-G~T~VLaTv~~~~~~~~~~dFfPLtVdY~Ek~yAaGkIPGgF~kREgrpsd~ 87 (699)
..+|.|++.||||+||+||+||+++-. ++|++|++.+.++.|++..||||||||.+||+||+|||||+|||||||||+.
T Consensus 12 G~~G~~~~rfe~G~la~qa~G~~~~yld~~tm~l~~t~~~~~P~~~~dffPltvdveer~yaaG~iPGsffrreGrPs~~ 91 (725)
T TIGR02696 12 GRFGTRTIRFETGRLARQAQGSVVAYLDDETMLLSATTASKQPKDQLDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTE 91 (725)
T ss_pred CCCCCEEEEEECCHHHHHCCCCEEEEECCCEEEEEECHHCCCCHHHCCCCCEEEEHHHHHHHCCCCCCCCCCCCCCCCHH
T ss_conf 44465166640011323227737888727614664200013740224512205531000010267875110147897412
Q ss_pred HHHHHHHHHCCCCCCCCCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECC-CCEEECCC
Q ss_conf 53111123212677674688688378999982188887789999999999873268823541123552047-73243685
Q gi|254780784|r 88 EILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYIN-GQYVLNPR 166 (699)
Q Consensus 88 EiL~sRlIDR~lRPLFPkgf~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~id-ge~ViNPt 166 (699)
+||+||||||||||-|.+|.|||+||++||||.++..-+|++|+|+||++..+|++||.|||++||+++++ ++||.+|+
T Consensus 92 ail~CrlidrPlrP~f~~Glrne~q~v~tvl~~~P~~~y~~~ainaas~~t~~~GlP~sGP~~Gvr~ali~~~qWvafP~ 171 (725)
T TIGR02696 92 AILACRLIDRPLRPSFVKGLRNEVQVVVTVLSLNPDELYDVVAINAASASTQLAGLPFSGPIGGVRLALIEDGQWVAFPT 171 (725)
T ss_pred HEEEEEECCCCCCHHHHHHHHHHEEEEEEEEECCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEECCCEEECCC
T ss_conf 31231000467871255200120000123120172567666665434344331267544664424888971782586376
Q ss_pred CCCC-CCCCEEEEEEC----------CCCHHHHHCC------------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 0002-22101355305----------4432333124------------44324899998875316889999999999999
Q gi|254780784|r 167 LDED-QGSLDLFVSGT----------QDAVLMVELE------------ANQLSEDVVLDAIIFGHNECKPVIEAISKLAK 223 (699)
Q Consensus 167 ~ee~-esdLDLvVAGT----------~d~IlMIE~~------------A~EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~~ 223 (699)
.++. ++-+||+|+|. +-+|+|||++ +..-.|+.+.+.|+.|+..|+.+|.+|..|++
T Consensus 172 ~~~~~~a~f~~~v~Grv~~~~~~~~~dvaimmvea~~t~~~~~~~~~G~~~P~e~~v~~Gl~aak~fi~~l~~~q~~la~ 251 (725)
T TIGR02696 172 VEQLEEAVFDLVVAGRVLENEDGTEGDVAIMMVEAEATEKTLELVEGGAKAPTEEVVAEGLEAAKPFIKVLCRAQADLAE 251 (725)
T ss_pred HHHHHCCEEEEEEEEEEEECCCCCCCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 23220130333565112312456656458999623341789999861103732789987677678999999999999998
Q ss_pred HHCCCCCCCCC--CCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCHHCCHHHHHHHHHHHHHH
Q ss_conf 83889864474--3125799999999898888874100012248999999999973022310000026788999999999
Q gi|254780784|r 224 MCAKEPIVIDS--KDFSKLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDIQAK 301 (699)
Q Consensus 224 ~~Gk~K~~~~~--~~~~~~~~~v~~~~~~~l~~a~~i~~K~eR~~ai~~l~~ei~e~l~ee~~~~~~~~i~~af~~l~k~ 301 (699)
+..++..+++. ...+..++.+...+..++..++.+..|.+|..+.+.++..+.+.+.++... ...++..+|+.+.|+
T Consensus 252 ~~~~~~~~~~~f~~y~~~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~a~~~~~~~ 330 (725)
T TIGR02696 252 KAAKETEEFPLFLDYSDDVYEAVEEAVKDELEKVLTIADKQEREEAEDELKEKVKEKLAEELEE-REKELSAAYKAVTKK 330 (725)
T ss_pred HHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
T ss_conf 6300102564433134789999999999999999987654456789999999999999999988-899999999999999
Q ss_pred HHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCC
Q ss_conf 99999872886658867753378799844754667008999879768999981686521223344544203587740588
Q gi|254780784|r 302 VVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFL 381 (699)
Q Consensus 302 ivR~~ILeeg~R~DGR~~dEIRpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFP 381 (699)
++|..||++..|+|||++.+||++++|+.++||+||||||+|||||+|.++||.+...+|.+|++.+...||||||||||
T Consensus 331 ~~r~~~~~~~~r~dGrG~~dir~l~~ev~~~Pr~hGsa~f~rGetq~lGv~tl~ml~m~q~~d~l~P~~~~ry~h~yn~P 410 (725)
T TIGR02696 331 LVRERVLKEGVRIDGRGLTDIRSLSAEVEVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPVTSKRYLHHYNFP 410 (725)
T ss_pred HHHHHHHHCCCEECCCCHHHHHHHHCCEEEECCCCCHHHHHCCCEEEEHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCC
T ss_conf 99988862362013676445552100002413310102320576035403477888887655311620230011003788
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCE
Q ss_conf 75445334556765024679999999874107864468738999853110278522356677779876259502254121
Q gi|254780784|r 382 PCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAG 461 (699)
Q Consensus 382 pfsvGE~~~~~~~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp~~~~VaG 461 (699)
|||+||+||.|.|.|||||||.||||||.||+|+.++|||.||-+||.|.||||+||.|||+++|+|+.||||+|++|||
T Consensus 411 Pys~Ge~GrvG~PkrreiGhG~laeral~PvlP~~e~fPyair~vseal~snGstsmGsvCastl~l~~aGvPl~~~vaG 490 (725)
T TIGR02696 411 PYSTGETGRVGSPKRREIGHGALAERALVPVLPSREEFPYAIRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPVAG 490 (725)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCHHH
T ss_conf 75667645668875320256502211000344676656368999988741577630357899999998648862000201
Q ss_pred EEEEEEEEC----CEEEEEEECCCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 332004408----8289986314422013655100100556512443245365568899999999999999999999984
Q gi|254780784|r 462 IAMGLVKDG----DDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSK 537 (699)
Q Consensus 462 iamGLi~~~----~~~~iLtDI~G~ED~~GdMDFKvaGT~~GiTa~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m~~ 537 (699)
||||||.+. -+|+-||||+|.||.+||||||||||++=|||+|||.|+.|||.++|.+||.||+.+|.+||+.|.+
T Consensus 491 iamGl~~~~~~~~~~y~~ltdi~Gaeda~GdmdfkvaGt~~~~talqldtkldGiP~~vla~al~~a~~ar~~il~~~~~ 570 (725)
T TIGR02696 491 IAMGLISDEVDGETRYVALTDILGAEDALGDMDFKVAGTREFVTALQLDTKLDGIPAEVLAEALKQAKDARLAILDVLAE 570 (725)
T ss_pred HHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCEEECCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 22222222003542567642011320102553212214478777775310025764789999999889889999999999
Q ss_pred CCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHCC--
Q ss_conf 356674332244875799997711500003786077998999868889980880899996898999999999998524--
Q gi|254780784|r 538 VLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITD-- 615 (699)
Q Consensus 538 ~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~-- 615 (699)
+|..| .+++++|||+..++||.+|||++|||.||+|+.|+++||++|.|+|||+|+|.+.+..+.+.|...|+.+..
T Consensus 571 ~i~~P-~~~~~~aPr~~~~~~Pv~kiGe~iGPkGk~in~i~~~tGa~i~i~~dGt~y~~a~~~~~a~~a~~~~n~i~nP~ 649 (725)
T TIGR02696 571 AIDTP-DEMSPTAPRVITVKIPVDKIGEVIGPKGKVINSIQDETGAEISIEDDGTVYIGAADGDSAEAARAAINAIANPT 649 (725)
T ss_pred HHHCH-HHHHHCCCEEEEEEECHHHHCCCCCCCCCEEHHHHHCCCCEEEEECCCEEEEECCCCHHHHHHHHHHHHHHCCC
T ss_conf 85071-44331088279998144440411078751001010033864577068538985066224899999987650788
Q ss_pred CCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCC----CCCCCHHHHCCCCCEEEEEEEEECCCCCEEEE
Q ss_conf 754686789999999415369982879710488663144----45478556032598899999978689986668
Q gi|254780784|r 616 VPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLST----ERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLS 686 (699)
Q Consensus 616 ~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~----~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~lS 686 (699)
.|++|+-|-|+|++...||+||.|+||++||+|||++.. +|+++++|++++|+++.|.+.++|++||+.|-
T Consensus 650 ~P~vG~~~lGtvvk~~~fGafvsllPG~dGl~his~~r~l~~G~~~~~v~~v~~~G~k~~ve~~~~d~rGkl~l~ 724 (725)
T TIGR02696 650 LPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISEIRKLAGGKRVEKVEDVLSVGQKIQVEIADIDDRGKLSLV 724 (725)
T ss_pred CCCCHHHHHHHHHHCCCCCCEEEECCCCCCEEEHHHHHHHHCCCCHHHHHHHHHCCCCEEEEEEECCCCCCEEEC
T ss_conf 874001342033100233414674068875031655676315720355788872243013311111257745621
No 6
>PRK00173 rph ribonuclease PH; Reviewed
Probab=100.00 E-value=0 Score=403.72 Aligned_cols=221 Identities=24% Similarity=0.316 Sum_probs=202.2
Q ss_pred CCCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCC-
Q ss_conf 6658867753378799844754667008999879768999981686521223344544203587740588754453345-
Q gi|254780784|r 312 VRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCATGEVSR- 390 (699)
Q Consensus 312 ~R~DGR~~dEIRpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfsvGE~~~- 390 (699)
.|+|||+++|+|||++++|++|++||||||++|+|||||+||+....+.+.. +..+-.+..+|+|+|||+++..+
T Consensus 1 lR~DGR~~~E~R~i~i~~g~~~~A~GSa~v~~G~T~Vl~~v~~~~~~p~~~~----~~~~g~l~~ey~mlP~st~~R~~R 76 (237)
T PRK00173 1 MRPDGRAADQLRPVTITRNYTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLK----GQGQGWVTAEYGMLPRATHTRNDR 76 (237)
T ss_pred CCCCCCCCCCCCCEEEEECCCCCCCEEEEEEECCCEEEEEEECCCCCCCCCC----CCCCCEEEEEEECCCCCCCCCCCC
T ss_conf 9898989777446599948779987369999689299999972666753003----776533677752167677886757
Q ss_pred ---CCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHC-----------CCCCC
Q ss_conf ---5676502467999999987410786446873899985311027852235667777987625-----------95022
Q gi|254780784|r 391 ---MGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDA-----------GVPIS 456 (699)
Q Consensus 391 ---~~~~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~da-----------gvp~~ 456 (699)
.|.+++|++++++|+.|||++++|.+.+++|+|+|+|+||++|||++||||||+||||+|| |+||+
T Consensus 77 ~~~~g~~~~r~~Eisrli~ralr~~i~l~~~~~~~I~i~~~VL~aDGg~~~Asi~aa~lAL~dA~~~~~~~~~~~~~P~~ 156 (237)
T PRK00173 77 EAAKGKQGGRTQEIQRLIGRSLRAVVDLKALGERTITLDCDVLQADGGTRTASITGAYVALADALNKLVARGKLKKNPLK 156 (237)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHCCHHHCCCEEEEEEEEEEECCCCCCCEECCHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 65568876006899999999987761185549859999999861589821201235789999999999864866678854
Q ss_pred CCCCEEEEEEEEECCEEEEEEECCCCCCCCCCCCEEEEECCCC-CEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5412133200440882899863144220136551001005565-124432453655688999999999999999999999
Q gi|254780784|r 457 KPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSG-ITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEM 535 (699)
Q Consensus 457 ~~VaGiamGLi~~~~~~~iLtDI~G~ED~~GdMDFKvaGT~~G-iTa~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m 535 (699)
.+||+|+||+| +++ ++.|..+.||+.|||||+|++|.+| |+++|++-+-..+|.+.+.++|++|+.|+.+|++.|
T Consensus 157 ~~v~avs~G~i---~~~-~v~D~~~~Ed~~~d~d~~v~~~~~g~iv~iQ~~ge~~~fs~ee~~~~l~~A~~gi~~I~~~q 232 (237)
T PRK00173 157 DHVAAVSVGIV---DGE-PVLDLDYVEDSAAETDMNVVMTGDGGFVEVQGTAEGAPFSREELNALLDLAEGGIAELVALQ 232 (237)
T ss_pred CCCCEEEEEEE---CCE-EEECCCHHHHHCCCCCEEEEECCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 64111689998---786-87788846762687636999869998999971467798599999999999999999999999
Q ss_pred HHCCC
Q ss_conf 84356
Q gi|254780784|r 536 SKVLS 540 (699)
Q Consensus 536 ~~~~~ 540 (699)
+++++
T Consensus 233 ~~aLs 237 (237)
T PRK00173 233 KAALA 237 (237)
T ss_pred HHHHC
T ss_conf 99749
No 7
>TIGR02065 ECX1 exosome complex exonuclease 1; InterPro: IPR011807 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 a family of archaeal proteins that are 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 .; GO: 0016896 exoribonuclease activity producing 5'-phosphomonoesters, 0000178 exosome (RNase complex).
Probab=100.00 E-value=5.6e-45 Score=384.55 Aligned_cols=225 Identities=29% Similarity=0.465 Sum_probs=202.2
Q ss_pred HHHCCCCCCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCC
Q ss_conf 98728866588677533787998447546670089998797689999816865212233445442035877405887544
Q gi|254780784|r 306 VMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCAT 385 (699)
Q Consensus 306 ~ILeeg~R~DGR~~dEIRpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfsv 385 (699)
.|+++|+|.|||.+||+|||.+|+|||.|+.|||+|..|.|.+++.|+ |+....++.-.+-..---| .-|||.||||
T Consensus 2 l~~~dg~R~DGR~pdeLRp~KI~~GvL~rADGSA~~E~G~tki~aAVY-GPrE~hpRh~~~PDRAV~R--~RY~MAPFSv 78 (231)
T TIGR02065 2 LILEDGLRLDGRKPDELRPVKIEAGVLKRADGSAYLEFGATKIVAAVY-GPREAHPRHLQLPDRAVLR--VRYNMAPFSV 78 (231)
T ss_pred CCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHCCCCCEEEEEEE-CCCCCCCCCCCCCCCEEEE--EEECCCCCCC
T ss_conf 567888545877842012010013111127600101137979999863-7766777545788835776--0013898874
Q ss_pred -CCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEE
Q ss_conf -5334556765024679999999874107864468738999853110278522356677779876259502254121332
Q gi|254780784|r 386 -GEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAM 464 (699)
Q Consensus 386 -GE~~~~~~~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp~~~~VaGiam 464 (699)
-|.| +++|+||||+.+++...||+|+|-.|.+|...|+|+.||||+||||++|+++|+||||+||||||++.|+|+|.
T Consensus 79 kDERK-~PgPdRR~iEiSKv~~EALepai~~E~fPRt~IDVF~EvLQADaGTR~AgltAASlALADAGIpMRDLV~gvav 157 (231)
T TIGR02065 79 KDERK-RPGPDRREIEISKVIREALEPAILLEQFPRTAIDVFVEVLQADAGTRCAGLTAASLALADAGIPMRDLVVGVAV 157 (231)
T ss_pred CCCCC-CCCCCCCEEHHHHHHHHHCCCEEEEECCCCCCCEEEEEEEECCCCHHHHHHHHHHHHHHHCCCHHHHHHHEEEE
T ss_conf 34678-72229441215668888513101322388950105789985276504788999999998479402422000034
Q ss_pred EEEEECCEEEEEEECCCCCCCCCCCCEEEEEC--CCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 00440882899863144220136551001005--565124432453655688999999999999999999999843566
Q gi|254780784|r 465 GLVKDGDDFIILSDISGDEDHLGHMDFKVAGT--DSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSE 541 (699)
Q Consensus 465 GLi~~~~~~~iLtDI~G~ED~~GdMDFKvaGT--~~GiTa~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m~~~~~~ 541 (699)
|+| |..+|| |....||.||.-|..||-- -+-||-|||| +-+|.+-+++||..|.+|+..|-++-.+++.+
T Consensus 158 GKv---~G~vVL-Dl~~~ED~yGEAD~P~A~mP~~~~iTLLQld---G~~T~dEF~~A~~lA~~g~~~v~~~~r~ALk~ 229 (231)
T TIGR02065 158 GKV---DGVVVL-DLSELEDMYGEADVPLAIMPKLGEITLLQLD---GDLTPDEFRQALDLAVKGIKRVYEIQREALKK 229 (231)
T ss_pred EEE---CCEEEE-CCCCCCCCCCCCCCHHHHCCCCCCEEEEEEC---CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 556---788898-3661246757656566515899826899747---98686789999999999988999999998640
No 8
>PRK03983 exosome complex exonuclease Rrp41; Provisional
Probab=100.00 E-value=1.6e-41 Score=356.37 Aligned_cols=236 Identities=30% Similarity=0.483 Sum_probs=208.8
Q ss_pred HHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCC
Q ss_conf 99999872886658867753378799844754667008999879768999981686521223344544203587740588
Q gi|254780784|r 302 VVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFL 381 (699)
Q Consensus 302 ivR~~ILeeg~R~DGR~~dEIRpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFP 381 (699)
.+|+.++++|.|+|||+++|+|||+|++|++|++||||+|+.|+|++||+|+ |+...... ......+..+..+|+|+
T Consensus 3 ~~~~~l~~eg~R~DGR~~~elR~i~~~~g~~~~adGSa~~~~G~T~Vl~~V~-gp~e~~~~--~~~~~~~~~l~v~~~~~ 79 (243)
T PRK03983 3 EPPKLILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYVEWGNNKIIAAVY-GPREMHPR--HLQLPDRAVLRVRYNMA 79 (243)
T ss_pred CCCEEECCCCCCCCCCCCCCCCCEEEEECCCCCCCEEEEEEECCCEEEEEEC-CCCCCCCC--CCCCCCCEEEEEEEECC
T ss_conf 7744566989659995988843869996979999889999978949999975-78445732--00378748999999658
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCE
Q ss_conf 75445334556765024679999999874107864468738999853110278522356677779876259502254121
Q gi|254780784|r 382 PCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAG 461 (699)
Q Consensus 382 pfsvGE~~~~~~~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp~~~~VaG 461 (699)
|||+.+.+ .++++||+++++++.+|+|++++..+.++..+|+|+++||++|||..+|++||+||||+||||||+.+|++
T Consensus 80 pfa~~~r~-~~~~~~~~~els~~i~~~l~~~i~~~~~p~s~I~V~v~Vl~~DG~~~~aainaa~lAL~dAgIpm~d~v~a 158 (243)
T PRK03983 80 PFSVDERK-RPGPDRREIEISKVIREALEPAIMLEQFPRSVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAG 158 (243)
T ss_pred CCCCCCCC-CCCCCHHHHHHHHHHHHHHHHHCCHHHCCCEEEEEEEEEECCCCCCCEECCCCCEEEHHHCCCCCCCCEEE
T ss_conf 87667665-78998318999999999987542898879709999999991799810001035367654569872463517
Q ss_pred EEEEEEEECCEEEEEEECCCCCCCCCCCCEEEE--ECCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 332004408828998631442201365510010--055651244324536556889999999999999999999998435
Q gi|254780784|r 462 IAMGLVKDGDDFIILSDISGDEDHLGHMDFKVA--GTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVL 539 (699)
Q Consensus 462 iamGLi~~~~~~~iLtDI~G~ED~~GdMDFKva--GT~~GiTa~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m~~~~ 539 (699)
+++|++. -.++.|....|+..+++|+.|| ++.+.|+++|++ +.++.+.+.++|+.|++|+.+|++.|.+++
T Consensus 159 ~svg~~~----~~~ilDp~~~Ee~~~~~~l~va~~~~~~~i~~~q~~---G~~s~~~l~~~l~~a~~~~~~i~~~~~~~l 231 (243)
T PRK03983 159 CAVGKVD----GVIVLDLNKEEDNYGEADMPVAIMPKLGEITLLQLD---GNLTRDEFLEALELAKKGAKRIYQIQREAL 231 (243)
T ss_pred EEEEEEC----CEEEECCCHHHHCCCCCEEEEEEECCCCCEEEEEEE---CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999989----999988983774057740699996699989999998---858899999999999999999999999999
Q ss_pred CCCCCCCCC
Q ss_conf 667433224
Q gi|254780784|r 540 SESRLQLGE 548 (699)
Q Consensus 540 ~~~~~~~~~ 548 (699)
.++..++++
T Consensus 232 ~~~~~~~~~ 240 (243)
T PRK03983 232 KNKYLEIAE 240 (243)
T ss_pred HHHHHHHHH
T ss_conf 878876555
No 9
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional
Probab=100.00 E-value=8.6e-34 Score=293.52 Aligned_cols=239 Identities=19% Similarity=0.333 Sum_probs=207.4
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCC
Q ss_conf 88999999999999998728866588677533787998447546670089998797689999816865212233445442
Q gi|254780784|r 291 IVSVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQ 370 (699)
Q Consensus 291 i~~af~~l~k~ivR~~ILeeg~R~DGR~~dEIRpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~ 370 (699)
-+..+.+.+|+.+|+ .|++|+|+|||+++|.|||++++|++|++||||+|++|+|||||++|..-.... . ....
T Consensus 4 ~~~~is~~ek~~i~~-~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vla~V~~ei~~p~--~---~~p~ 77 (271)
T PRK04282 4 MEEIIPEIKRDYILN-LLKKGKRIDGRGLDEYRPIEIETGVIKKAEGSALVKLGNTQVIAGVKLELGEPF--P---DTPD 77 (271)
T ss_pred HHHHHHHHHHHHHHH-HHHHCCCCCCCCCCCCCCEEEEECCCCCCCEEEEEEECCEEEEEEEEECCCCCC--C---CCCC
T ss_conf 677888999999999-998497899989888667599979858888059999689489999872356765--6---6898
Q ss_pred EEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH--CCCC------CCCCCEEEEEEEEECCCCCCCHHHHHH
Q ss_conf 03587740588754453345567650246799999998741--0786------446873899985311027852235667
Q gi|254780784|r 371 RNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHP--VLPQ------TAQFPYTLRIVSEITESDGSSSMATVC 442 (699)
Q Consensus 371 ~k~fmlHYNFPpfsvGE~~~~~~~~RREiGHg~la~ral~~--~~P~------~~~~p~tirv~~evl~sngsssma~vc 442 (699)
+-.|..||+|+|||.-. -..|.+++|.+..+++.+|+|+. ++.. ...+.++|++.+.||++||+..+|+++
T Consensus 78 eG~~~~~v~~~~~a~~~-~~~g~~~~~~~e~~~~l~r~l~~s~~idle~LcI~~g~~~W~i~idv~VL~~dGn~~dA~~~ 156 (271)
T PRK04282 78 EGVLIVNAELLPLASPT-FEPGPPDENAIELARVVDRGIRESGAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASML 156 (271)
T ss_pred CCCEEEEEEECCCCCCC-CCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHCCCCCCCCEEEEEEEEEEECCCCHHHHHHH
T ss_conf 54379999657867776-65799763028899999988764252324763657777517999999999159968888999
Q ss_pred HHHHHHHHCCCC--------------------CCCCCCEEEEEEEEECCEEEEEEECCCCCCCCCCCCEEEEECCCCCEE
Q ss_conf 777987625950--------------------225412133200440882899863144220136551001005565124
Q gi|254780784|r 443 GSSLALMDAGVP--------------------ISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITA 502 (699)
Q Consensus 443 ~~slal~dagvp--------------------~~~~VaGiamGLi~~~~~~~iLtDI~G~ED~~GdMDFKvaGT~~GiTa 502 (699)
|+..||+|+++| |+..+..+++|++ +++ +|.|.++.||+++||||+|+.|++|.+.
T Consensus 157 A~~aAL~~~~~P~v~~~~~~~~~~~~~~~~l~i~~~Pi~vT~~~i---~~~-~l~Dpt~~EE~~~~~~~~V~~n~~g~i~ 232 (271)
T PRK04282 157 AAVAALLNTKLPAVVKEDGGVVLDLGEKVPLPINNKPVSVTFAKI---GNY-LVVDPTLEEELVMDARITITTDEDGIIC 232 (271)
T ss_pred HHHHHHHHCCCCEEEECCCCEEECCCCCCCCCCCCCCEEEEEEEE---CCE-EEECCCHHHHHCCCCEEEEEEECCCCEE
T ss_conf 999999866897168516631211366667763566137899999---999-9977998898456876999990899799
Q ss_pred EECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 43245365568899999999999999999999984356
Q gi|254780784|r 503 MQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLS 540 (699)
Q Consensus 503 ~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m~~~~~ 540 (699)
.+++.+-.+|+.+.|.+++++|+.++.+|++.|++++.
T Consensus 233 ~l~k~g~~~i~~~~l~~~~~~A~~~~~~l~~~i~~aL~ 270 (271)
T PRK04282 233 AMQKSGLGSFTEEEVEEAIDLALKKAKELREKLKEALG 270 (271)
T ss_pred EEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 99778999959999999999999999999999998629
No 10
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.9e-31 Score=271.89 Aligned_cols=221 Identities=29% Similarity=0.417 Sum_probs=194.8
Q ss_pred HHCCCCCCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCCEEEEEEE-ECCCCCCCCCCCCCCCCEEEEEEEECCCCCCC
Q ss_conf 87288665886775337879984475466700899987976899998-16865212233445442035877405887544
Q gi|254780784|r 307 MLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVT-LGTREDEQYVDSLSGTQRNDFMMHYNFLPCAT 385 (699)
Q Consensus 307 ILeeg~R~DGR~~dEIRpIs~EvgvLPrvHGSALFtRGETQaL~tvT-LG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfsv 385 (699)
..+++.|.|||.+||.|||.++.++++++.||++|.-|+|+++|+|+ .-.+...+..+.-.++.+. -|||-||||
T Consensus 3 ~~~~~~R~dgR~~~elR~i~~~~~~~~~a~GS~~~~~G~tkVic~vsGp~e~~p~~l~~~~~g~~t~----ey~m~p~sT 78 (230)
T COG0689 3 ESEDGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTA----EYGMLPRST 78 (230)
T ss_pred CCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCEEEEECCEEEEEEEECCCCCCCHHHCCCCCEEEEE----EECCCCCCC
T ss_conf 7666737788884524646887155467885379996780899997067778885443777217999----970201234
Q ss_pred CCCCCCCCCCC-HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEE
Q ss_conf 53345567650-24679999999874107864468738999853110278522356677779876259502254121332
Q gi|254780784|r 386 GEVSRMGAPSR-REIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAM 464 (699)
Q Consensus 386 GE~~~~~~~~R-REiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp~~~~VaGiam 464 (699)
.| +..+.++| |++..++|.+|||++++..+.++..+|.|+|+|+|++|+|+.|+|+|++|||+|||+||+..||+||+
T Consensus 79 ~~-R~~~~~~~gR~~eisrli~~al~~~i~L~~~p~~~I~i~~dVlqaDggTrta~It~A~lAL~DAgipl~~~vaaiSv 157 (230)
T COG0689 79 DE-RKKREADRGRTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISV 157 (230)
T ss_pred CC-CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEECCCCEEEEHHHHHHHHHHHCCCCHHHHEEEEEE
T ss_conf 33-32344334303279999999998876565447638999999998789754202667999998739945653027678
Q ss_pred EEEEECCEEEEEEECCCCCCCCCCCCEEEEECCCC----CEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 00440882899863144220136551001005565----1244324536556889999999999999999999998435
Q gi|254780784|r 465 GLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSG----ITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVL 539 (699)
Q Consensus 465 GLi~~~~~~~iLtDI~G~ED~~GdMDFKvaGT~~G----iTa~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m~~~~ 539 (699)
|++.+. ++-|....||..+.-|..|+.+.+| |+.+|+| ...+.+-|.++|..|+.|+..+.+.|..++
T Consensus 158 gi~~~~----~~lDl~~~Eds~~~~d~~v~~~~~~~~~ei~~~~~~---~~~~~del~~lL~la~~g~~~~~~~~~~al 229 (230)
T COG0689 158 GIVDGV----IVLDLDYEEDSAAEADMNVVMTGNGGLVEIQGLAED---GPFTEDELLELLDLAIKGCNELRELQREAL 229 (230)
T ss_pred EEECCC----EEECCCCHHHCCCCCCCEEEEEECCCEEEEEEEECC---CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 887793----576374321112244714999706973789986306---997999999999999999999999999975
No 11
>TIGR01966 RNasePH ribonuclease PH; InterPro: IPR002381 Prokaryotic ribonuclease PH (2.7.7.56 from EC) (RNase PH) is a phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates . There is a similar protein in Caenorhabditis elegans that belongs to this group. More information about these proteins can be found at Protein of the Month: RNA Exosomes .; GO: 0000049 tRNA binding, 0004549 tRNA-specific ribonuclease activity, 0008033 tRNA processing.
Probab=99.97 E-value=4.5e-30 Score=263.32 Aligned_cols=220 Identities=28% Similarity=0.373 Sum_probs=205.7
Q ss_pred CCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCC-
Q ss_conf 6588677533787998447546670089998797689999816865212233445442035877405887544533455-
Q gi|254780784|r 313 RMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRM- 391 (699)
Q Consensus 313 R~DGR~~dEIRpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfsvGE~~~~- 391 (699)
|+|||+.|++|||+++.++++.+-||+|-.-|+|+||||++.-..-+.++-++-.||-+.. |+|-|=||++..++
T Consensus 1 R~dGR~~dqLRpv~i~r~f~~haEGSvLi~~G~TkVlCTASv~e~VP~flrG~G~GWiTAE----Y~MLPraT~~R~~RE 76 (237)
T TIGR01966 1 RPDGRKPDQLRPVKITRDFLKHAEGSVLIEFGDTKVLCTASVEEKVPPFLRGSGEGWITAE----YGMLPRATQTRNRRE 76 (237)
T ss_pred CCCCCCCCCCCCEEECCCCCCCCCCEEEEEECCEEEEEEEEECCCCCCCCCCCCCEEEEHH----HHHHHHHHCCCCHHH
T ss_conf 9898855345362554688788887268978792466678755872852358894255041----100033030312466
Q ss_pred ---CCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHC-----------C-CCCC
Q ss_conf ---676502467999999987410786446873899985311027852235667777987625-----------9-5022
Q gi|254780784|r 392 ---GAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDA-----------G-VPIS 456 (699)
Q Consensus 392 ---~~~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~da-----------g-vp~~ 456 (699)
|.++.|..+.++|+.|||++|+..+.....||-|+|||||+||+|++|||+||..||.|| . -||+
T Consensus 77 a~~GK~~GRTqEIQRLIGRaLRavvDl~aLGErTI~iDCDVlQADGGTRTAsITGAfVAL~dAi~~L~~~~~~~~~~P~~ 156 (237)
T TIGR01966 77 AAKGKQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVLQADGGTRTASITGAFVALADAIKKLQKRGILKESEPIR 156 (237)
T ss_pred HHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 86178787505677788889887734623485027985334338876124678889999999999998578623468711
Q ss_pred CCCCEEEEEEEEECCEEEEEEECCCCCCCCCCCCEEEEECCCC-CEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5412133200440882899863144220136551001005565-124432453655688999999999999999999999
Q gi|254780784|r 457 KPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSG-ITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEM 535 (699)
Q Consensus 457 ~~VaGiamGLi~~~~~~~iLtDI~G~ED~~GdMDFKvaGT~~G-iTa~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m 535 (699)
.+||+||+|++ +.-.+| |.-..||+--|-|+.|-+|.+| +-=+|===-=..-|.+-|.+=|..|+.|....+...
T Consensus 157 ~~VAAVSVGiv---~g~~~L-DL~Y~EDs~A~vD~NvVmT~~G~fvEvQGTaE~~pFsr~EL~~LL~LA~~Gi~eL~~~Q 232 (237)
T TIGR01966 157 DFVAAVSVGIV---DGEPVL-DLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEEPFSRDELNELLDLAEKGIRELIELQ 232 (237)
T ss_pred CCCCEEEEEEE---CCEEEE-CCCCCCCCCCCCCCEEEECCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 05243898876---680676-35885556463352058857876588870578897018999999999888899999999
Q ss_pred HHCCC
Q ss_conf 84356
Q gi|254780784|r 536 SKVLS 540 (699)
Q Consensus 536 ~~~~~ 540 (699)
++++.
T Consensus 233 k~aL~ 237 (237)
T TIGR01966 233 KQALG 237 (237)
T ss_pred HHHCC
T ss_conf 99719
No 12
>PRK00173 rph ribonuclease PH; Reviewed
Probab=99.97 E-value=4.9e-30 Score=263.00 Aligned_cols=203 Identities=23% Similarity=0.260 Sum_probs=171.6
Q ss_pred CEEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCC-C--CCCCCCCCCEEEEECCCCCCCCCCCCCCCCC---CCCCH
Q ss_conf 9899999140045467289999789489999972788-8--8777735406866523201336788873578---98871
Q gi|254780784|r 13 GRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRS-L--KDGQDFFPLTVNYQERTYAVGKIPGGYLRRE---SRPTE 86 (699)
Q Consensus 13 gr~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~-~--~~~~dFfPLtVdY~Ek~yAaGkIPGgF~kRE---grpsd 86 (699)
=|+|++++| +.++|+||+++++|+|.|||||+.... | ..+.+...||++|.--.+|.+. +.+|| |+|++
T Consensus 11 ~R~i~i~~g-~~~~A~GSa~v~~G~T~Vl~~v~~~~~~p~~~~~~~~g~l~~ey~mlP~st~~----R~~R~~~~g~~~~ 85 (237)
T PRK00173 11 LRPVTITRN-YTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTAEYGMLPRATHT----RNDREAAKGKQGG 85 (237)
T ss_pred CCCEEEEEC-CCCCCCEEEEEEECCCEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCC----CCCCCCCCCCCCC
T ss_conf 446599948-77998736999968929999997266675300377653367775216767788----6757655688760
Q ss_pred HHHHHHHHHHCCCCCCCCCCCCCCEEE--EEEEEECCCCCCHHHHHHHHHHHHHHHC-----------CCCCCCCEEEEE
Q ss_conf 453111123212677674688688378--9999821888877899999999998732-----------688235411235
Q gi|254780784|r 87 NEILISRMIDRSIRPLFSKCYKNETQV--IINVMQHDLESSPHVVSMVAASAALMLS-----------GLPFEGPVVGAQ 153 (699)
Q Consensus 87 ~EiL~sRlIDR~lRPLFPkgf~~evQI--v~~VLS~D~~~dpdvlAi~aASaAL~IS-----------dIPf~GPVaaVR 153 (699)
+++.++|||||+|||.++-....+.|| .|.||++|+... ..++||||+||+-+ ++||++||+||+
T Consensus 86 r~~Eisrli~ralr~~i~l~~~~~~~I~i~~~VL~aDGg~~--~Asi~aa~lAL~dA~~~~~~~~~~~~~P~~~~v~avs 163 (237)
T PRK00173 86 RTQEIQRLIGRSLRAVVDLKALGERTITLDCDVLQADGGTR--TASITGAYVALADALNKLVARGKLKKNPLKDHVAAVS 163 (237)
T ss_pred CHHHHHHHHHHHHHHHCCHHHCCCEEEEEEEEEEECCCCCC--CEECCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEE
T ss_conf 06899999999987761185549859999999861589821--2012357899999999998648666788546411168
Q ss_pred EEECCCCEEECCCCCCC-CCCCEEEEEECCCC-HHHHHCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 52047732436850002-22101355305443-233312444--32489999887531688999999999999
Q gi|254780784|r 154 VDYINGQYVLNPRLDED-QGSLDLFVSGTQDA-VLMVELEAN--QLSEDVVLDAIIFGHNECKPVIEAISKLA 222 (699)
Q Consensus 154 VG~idge~ViNPt~ee~-esdLDLvVAGT~d~-IlMIE~~A~--EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~ 222 (699)
||++|++++++|+++|+ .++.|+-|++|+++ |+.+++.+. .+|++++.++|++||+.+++|++.|++..
T Consensus 164 ~G~i~~~~v~D~~~~Ed~~~d~d~~v~~~~~g~iv~iQ~~ge~~~fs~ee~~~~l~~A~~gi~~I~~~q~~aL 236 (237)
T PRK00173 164 VGIVDGEPVLDLDYVEDSAAETDMNVVMTGDGGFVEVQGTAEGAPFSREELNALLDLAEGGIAELVALQKAAL 236 (237)
T ss_pred EEEECCEEEECCCHHHHHCCCCCEEEEECCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9998786877888467626876369998699989999714677985999999999999999999999999974
No 13
>PRK03983 exosome complex exonuclease Rrp41; Provisional
Probab=99.95 E-value=1.4e-26 Score=234.78 Aligned_cols=202 Identities=27% Similarity=0.476 Sum_probs=172.9
Q ss_pred EEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCC----CEEEEECCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf 899999140045467289999789489999972788887777354----0686652320133678887357898871453
Q gi|254780784|r 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFP----LTVNYQERTYAVGKIPGGYLRRESRPTENEI 89 (699)
Q Consensus 14 r~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~~~~~~dFfP----LtVdY~Ek~yAaGkIPGgF~kREgrpsd~Ei 89 (699)
|++.++||.+. ||+||+++++|+|.|||+|...+++++....+| |+|+|+-..+|..+ |+.+.|+++++
T Consensus 24 R~i~~~~g~~~-~adGSa~~~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~pfa~~~------r~~~~~~~~~~ 96 (243)
T PRK03983 24 RPIKIEVGVLK-NADGSAYVEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSVDE------RKRPGPDRREI 96 (243)
T ss_pred CCEEEEECCCC-CCCEEEEEEECCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCCC------CCCCCCCHHHH
T ss_conf 38699969799-998899999789499999757844573200378748999999658876676------65789983189
Q ss_pred HHHHHHHCCCCCCCC-CCC-CCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCEEECCCC
Q ss_conf 111123212677674-688-688378999982188887789999999999873268823541123552047732436850
Q gi|254780784|r 90 LISRMIDRSIRPLFS-KCY-KNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRL 167 (699)
Q Consensus 90 L~sRlIDR~lRPLFP-kgf-~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~idge~ViNPt~ 167 (699)
..+|+|+|+|||.+. +-| +..++|.++||+.|+... ..|+||||+||..++||++++|+||.||++||+++++|++
T Consensus 97 els~~i~~~l~~~i~~~~~p~s~I~V~v~Vl~~DG~~~--~aainaa~lAL~dAgIpm~d~v~a~svg~~~~~~ilDp~~ 174 (243)
T PRK03983 97 EISKVIREALEPAIMLEQFPRSVIDVFIEVLQADAGTR--VAGITAASLALADAGIPMRDLVAGCAVGKVDGVIVLDLNK 174 (243)
T ss_pred HHHHHHHHHHHHHCCHHHCCCEEEEEEEEEECCCCCCC--EECCCCCEEEHHHCCCCCCCCEEEEEEEEECCEEEECCCH
T ss_conf 99999999987542898879709999999991799810--0010353676545698724635179999989999988983
Q ss_pred CCC-CCCCEEEEE--ECCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 002-221013553--0544323331244432489999887531688999999999999983
Q gi|254780784|r 168 DED-QGSLDLFVS--GTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMC 225 (699)
Q Consensus 168 ee~-esdLDLvVA--GT~d~IlMIE~~A~EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~~~~ 225 (699)
+|+ .++.+|.|| ++.+.|++++..+ +++++.+.+|+++|++.++++.++|++..++-
T Consensus 175 ~Ee~~~~~~l~va~~~~~~~i~~~q~~G-~~s~~~l~~~l~~a~~~~~~i~~~~~~~l~~~ 234 (243)
T PRK03983 175 EEDNYGEADMPVAIMPKLGEITLLQLDG-NLTRDEFLEALELAKKGAKRIYQIQREALKNK 234 (243)
T ss_pred HHHCCCCCEEEEEEECCCCCEEEEEEEC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 7740577406999966999899999988-58899999999999999999999999999878
No 14
>KOG1068 consensus
Probab=99.92 E-value=5.4e-24 Score=213.84 Aligned_cols=226 Identities=23% Similarity=0.340 Sum_probs=193.2
Q ss_pred HHHCCCCCCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCC
Q ss_conf 98728866588677533787998447546670089998797689999816865212233445442035877405887544
Q gi|254780784|r 306 VMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCAT 385 (699)
Q Consensus 306 ~ILeeg~R~DGR~~dEIRpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfsv 385 (699)
..-++|.|.|||.++|+|+|.+.+|+++.+.|||+|.-|+|++||+|. |+..-. .-..- ...+.-.-..||+.+||+
T Consensus 7 ~~seeg~r~dgRr~~elR~i~~~~g~~~~a~GSay~E~GnTKVl~aV~-GPre~~-~~~~~-~~~~a~lnc~~~~a~Fst 83 (245)
T KOG1068 7 TLSEEGLRTDGRRPNELRRIYARIGVLTQADGSAYMEQGNTKVLCAVY-GPREIR-GKSAR-RPDKAVLNCEVSSAQFST 83 (245)
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCHHHCCCEEEEEEEE-CCCCCC-CCCCC-CCCCCEEEEEEEEECCCC
T ss_conf 347644445778856741012111742368850100248807999984-884422-31002-666524777775420111
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEE
Q ss_conf 53345567650246799999998741078644687389998531102785223566777798762595022541213320
Q gi|254780784|r 386 GEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMG 465 (699)
Q Consensus 386 GE~~~~~~~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp~~~~VaGiamG 465 (699)
|+.+++....||+..-+-+.+++++|+|-++.++..+|+|...|||++||...|++++++|||.|||+||++.|.|++.|
T Consensus 84 ~~r~~~~~~~rr~~e~s~~L~~afe~~I~~~lyPrsqIDI~v~VleddG~~laa~inaatlAL~daGI~m~D~i~~~t~~ 163 (245)
T KOG1068 84 GDRKKRPKGDRREKELSLMLQQAFEPVILLELYPRSQIDIYVQVLEDDGSNLAAAINAATLALADAGIPMYDLITACTAG 163 (245)
T ss_pred CHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHCCCCHHHHHHHCEEE
T ss_conf 21015787627889999999999888887523765561399999977995299888788999998199744355511013
Q ss_pred EEEECCEEEEEEECCCCCCCCCCCCEEE--EECCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 0440882899863144220136551001--005565124432453655688999999999999999999999843566
Q gi|254780784|r 466 LVKDGDDFIILSDISGDEDHLGHMDFKV--AGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSE 541 (699)
Q Consensus 466 Li~~~~~~~iLtDI~G~ED~~GdMDFKv--aGT~~GiTa~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m~~~~~~ 541 (699)
+... .-|.|..-.|+.-+--..-| -++.+-|-.+||| .+++.+-++..|+-|.+|+.+|-+.|..++.+
T Consensus 164 l~~~----~~l~Dl~~~eesa~~~~ltVa~l~~~~~i~~l~~~---~~~~~d~l~~vl~~a~~~c~~v~~~l~~~l~~ 234 (245)
T KOG1068 164 LADG----TPLLDLTSLEESARAPGLTVAALPNREEIALLQLD---ERLHCDHLETVLELAIAGCKRVYERLRLVLRE 234 (245)
T ss_pred ECCC----CCCCCCCCCHHHCCCCCEEEEEECCCCEEEEEEEC---CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 2078----64336541054524786289982276527889851---88777889999999999999999999999999
No 15
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.87 E-value=1.6e-20 Score=185.70 Aligned_cols=301 Identities=19% Similarity=0.311 Sum_probs=220.8
Q ss_pred EEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCCCCC-------CCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCH
Q ss_conf 899999140045467289999789489999972788887-------7773540686652320133678887357898871
Q gi|254780784|r 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKD-------GQDFFPLTVNYQERTYAVGKIPGGYLRRESRPTE 86 (699)
Q Consensus 14 r~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~~~~-------~~dFfPLtVdY~Ek~yAaGkIPGgF~kREgrpsd 86 (699)
|+|..|+|-|.| +|||.+.+.|+|++|+|++.+..... +...-....+|+...|++|.. +|=|.|+.
T Consensus 325 RPI~~EvgvLPr-~HGSaLFTRGETQaL~~~TLG~~~d~Q~iD~l~~~~~krFmlHYNFPPfSvGE~-----g~~~~p~R 398 (694)
T PRK11824 325 RPISIEVGVLPR-THGSALFTRGETQALVVATLGTLRDAQIIDGLEGEYKKRFMLHYNFPPYSVGET-----GRVGSPGR 398 (694)
T ss_pred CCCEEECCCCCC-CCCCEEEECCCCEEEEEEEECCCCHHHHHCCCCCCCCEEEEEECCCCCCCCCCC-----CCCCCCCC
T ss_conf 452578388788-874345871560699999725830101001567651104799747899767876-----67789763
Q ss_pred HHHHHHHHHHCCCCCCCC--CCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEC--CCCEE
Q ss_conf 453111123212677674--68868837899998218888778999999999987326882354112355204--77324
Q gi|254780784|r 87 NEILISRMIDRSIRPLFS--KCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYI--NGQYV 162 (699)
Q Consensus 87 ~EiL~sRlIDR~lRPLFP--kgf~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~i--dge~V 162 (699)
|||-...|--|+|.|..| +.|.|-+.|++.+|++++... +.+++|+|+||+-+++|...|||++-+|++ +++|.
T Consensus 399 REIGHG~LAeRAL~~vlP~~e~FPYtIRvvSEileSNGSSS--MAsVCg~sLALmdAGVPik~~VAGIAmGLi~e~~~~~ 476 (694)
T PRK11824 399 REIGHGALAERALEPVLPSEEEFPYTIRVVSEILESNGSSS--MASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDKYA 476 (694)
T ss_pred CCCCCHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCCCHH--HHHHHHHHHHHHHCCCCCCCCEEEEEEEEEECCCEEE
T ss_conf 10033699999887118985669834899988004488534--4889878799885799646640047777787087379
Q ss_pred ECCCC---CCCCCCCEEEEEECCCCHHHHHCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCH
Q ss_conf 36850---00222101355305443233312444--32489999887531688999999999999983889864474312
Q gi|254780784|r 163 LNPRL---DEDQGSLDLFVSGTQDAVLMVELEAN--QLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKDF 237 (699)
Q Consensus 163 iNPt~---ee~esdLDLvVAGT~d~IlMIE~~A~--EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~~~~Gk~K~~~~~~~~ 237 (699)
+-... |+--.|||.-||||+++|.-+.+.-+ .+|.+.|.+||+.|++.-..|.+.+++...+-..+..++.+.-.
T Consensus 477 iLtDI~G~EDh~GDMDFKvAGT~~GITA~QmDiKi~Gi~~~il~~Al~qA~~gR~~IL~~M~~~i~~pr~~~s~~aP~i~ 556 (694)
T PRK11824 477 VLSDILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGITREIMEEALEQAKEGRLHILGKMNEAISEPRTELSPYAPRIE 556 (694)
T ss_pred EEEECCCCCCCCCCCCEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEE
T ss_conf 99740444102477531562366644888740344796989999999999999999999998736665433356898799
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCH------HCCHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 57999999998988888741000122489999999999730223100------000267889999999999999987288
Q gi|254780784|r 238 SKLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHS------SWNEGEIVSVFEDIQAKVVRTVMLDKK 311 (699)
Q Consensus 238 ~~~~~~v~~~~~~~l~~a~~i~~K~eR~~ai~~l~~ei~e~l~ee~~------~~~~~~i~~af~~l~k~ivR~~ILeeg 311 (699)
.- ..-.+++.+.+.... .-++.+.++.-....-+.+ ..+...+..+.+ ..+.++++ .+-|
T Consensus 557 ~~------~i~~~ki~~vIG~gG-----k~Ik~i~e~tg~~Idi~ddG~v~i~~~~~~~~~~A~~-~I~~i~~~--~evG 622 (694)
T PRK11824 557 TI------KIDPDKIRDVIGPGG-----KTIREITEETGAKIDIEDDGTVKIAASDGEAAEAAKE-RIEGITAE--PEVG 622 (694)
T ss_pred EE------EECHHHHHHEECCCH-----HHHHHHHHHHCCEEEEECCCEEEEEECCHHHHHHHHH-HHHHHCCC--CCCC
T ss_conf 99------978798665068633-----8899999988988999689179999899999999999-99984576--8589
Q ss_pred CCCCCCCCCCEEEEEEEECCCCCCCC
Q ss_conf 66588677533787998447546670
Q gi|254780784|r 312 VRMDGRDSETVRDISAQVGLLQRTHG 337 (699)
Q Consensus 312 ~R~DGR~~dEIRpIs~EvgvLPrvHG 337 (699)
.--+|+ ...|++.-+=+.++|...|
T Consensus 623 ~iy~g~-V~~i~~fGafve~~pg~~G 647 (694)
T PRK11824 623 EIYEGK-VVRIVDFGAFVEILPGKDG 647 (694)
T ss_pred CEEEEE-EEEEEECEEEEEECCCCEE
T ss_conf 779999-9999844189996799806
No 16
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=99.86 E-value=2e-20 Score=184.75 Aligned_cols=300 Identities=19% Similarity=0.321 Sum_probs=219.7
Q ss_pred EEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCCCCCCC--------CCCCCEEEEECCCCCCCCCCCCCCCCCCCCC
Q ss_conf 89999914004546728999978948999997278888777--------7354068665232013367888735789887
Q gi|254780784|r 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQ--------DFFPLTVNYQERTYAVGKIPGGYLRRESRPT 85 (699)
Q Consensus 14 r~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~~~~~~--------dFfPLtVdY~Ek~yAaGkIPGgF~kREgrps 85 (699)
|+|+.|+|-|.| +|||.+.+.|+|++|+|++.+.. .+.+ ..--...+|+...|++|.. +|=|.|+
T Consensus 321 RpIs~EvgvLPr-~HGSaLFtRGETQaL~v~TLG~~-~d~Q~iD~l~~~~~krFmlHYNFPPfSvGE~-----g~~~~p~ 393 (684)
T TIGR03591 321 RPISIEVGVLPR-THGSALFTRGETQALVVTTLGTE-RDEQIIDDLEGEYRKRFMLHYNFPPYSVGEV-----GRVGGPG 393 (684)
T ss_pred CCHHCCCCCCCC-CCCCEEEEECCCEEEEEEEECCC-HHHHHHCCCCCCCCEEEEEECCCCCCCCCCC-----CCCCCCC
T ss_conf 240203387577-77435788526507999950682-2211011457651104899747999767876-----7788998
Q ss_pred HHHHHHHHHHHCCCCCCCC--CCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEC-C--CC
Q ss_conf 1453111123212677674--68868837899998218888778999999999987326882354112355204-7--73
Q gi|254780784|r 86 ENEILISRMIDRSIRPLFS--KCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYI-N--GQ 160 (699)
Q Consensus 86 d~EiL~sRlIDR~lRPLFP--kgf~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~i-d--ge 160 (699)
.|||-...|--|+|.|+.| +.|.|.+.|++.||++++... +.+++|+|+||+-+++|...|||++-+|++ + +.
T Consensus 394 RREIGHG~LAeRAL~~vlP~~e~FPYtIRvvSeileSNGSSS--MAsVCg~sLALmdAGVPik~~VAGIAmGLi~e~d~~ 471 (684)
T TIGR03591 394 RREIGHGALAERALKAVLPSEEEFPYTIRVVSEILESNGSSS--MASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDER 471 (684)
T ss_pred CHHHCCHHHHHHHHHHCCCCCCCCCCEEEEEEEEEECCCCHH--HHHHHHHHHHHHHCCCCCCCCCCEEEEEEEECCCCC
T ss_conf 501226799999998518982338814899988004688434--289999999998679963665025777768737874
Q ss_pred EEECCCC---CCCCCCCEEEEEECCCCHHHHHCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 2436850---00222101355305443233312444--324899998875316889999999999999838898644743
Q gi|254780784|r 161 YVLNPRL---DEDQGSLDLFVSGTQDAVLMVELEAN--QLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSK 235 (699)
Q Consensus 161 ~ViNPt~---ee~esdLDLvVAGT~d~IlMIE~~A~--EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~~~~Gk~K~~~~~~ 235 (699)
|++-.-. |+--.|||.-||||+++|.-+.+.-+ .+|.+.|.+||+.|++.-..|.+.+++...+-..+...+.+.
T Consensus 472 y~iLtDI~G~EDh~GDMDFKvaGT~~GITa~QmDiKi~Gi~~~il~~Al~qA~~~R~~IL~~M~~~i~~pr~~~s~~aP~ 551 (684)
T TIGR03591 472 FAVLSDILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGITREIMEQALEQAKEGRLHILGEMNKVISEPRAELSPYAPR 551 (684)
T ss_pred EEEEEECCCCCCCCCCCCEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCE
T ss_conf 79997313341014775305633666448887403558978999999999999999999999997352543344578875
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCH------HCCHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 1257999999998988888741000122489999999999730223100------0002678899999999999999872
Q gi|254780784|r 236 DFSKLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHS------SWNEGEIVSVFEDIQAKVVRTVMLD 309 (699)
Q Consensus 236 ~~~~~~~~v~~~~~~~l~~a~~i~~K~eR~~ai~~l~~ei~e~l~ee~~------~~~~~~i~~af~~l~k~ivR~~ILe 309 (699)
-..- ..-.+++.+.+....| -++.+.++.-....-+.+ ..+...+..+.+ ..+.+++ -.+
T Consensus 552 i~~~------~i~~~ki~~vIG~gGk-----~Ik~i~~~tg~~I~i~ddG~v~i~~~~~~~~~~A~~-~I~~~~~--~~e 617 (684)
T TIGR03591 552 IETI------KINPDKIRDVIGPGGK-----VIREITEETGAKIDIEDDGTVKIAASDGEAAEAAIK-MIEGITA--EPE 617 (684)
T ss_pred EEEE------EECHHHHHHEECCCCH-----HHHHHHHHHCCEEEEECCCEEEEEECCHHHHHHHHH-HHHHHCC--CCC
T ss_conf 7999------9787886650787528-----898999988988998589089999899999999999-9998516--685
Q ss_pred CCCCCCCCCCCCEEEEEEEECCCCCCCC
Q ss_conf 8866588677533787998447546670
Q gi|254780784|r 310 KKVRMDGRDSETVRDISAQVGLLQRTHG 337 (699)
Q Consensus 310 eg~R~DGR~~dEIRpIs~EvgvLPrvHG 337 (699)
-|.--+|+ ...|.+.-+=+.++|...|
T Consensus 618 vG~~y~g~-V~~i~~fGafve~~pg~~G 644 (684)
T TIGR03591 618 VGKIYEGK-VVRIMDFGAFVEILPGKDG 644 (684)
T ss_pred CCCEEEEE-EEEEEECEEEEEECCCCCE
T ss_conf 89779999-9999844089996799814
No 17
>pfam01138 RNase_PH 3' exoribonuclease family, domain 1. This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.
Probab=99.82 E-value=5.3e-19 Score=173.26 Aligned_cols=128 Identities=34% Similarity=0.491 Sum_probs=114.6
Q ss_pred CEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCHHHH
Q ss_conf 33787998447546670089998797689999816865212233445442035877405887544533455676502467
Q gi|254780784|r 321 TVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIG 400 (699)
Q Consensus 321 EIRpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfsvGE~~~~~~~~RREiG 400 (699)
|+|||++++|++|++||||.|+-|+|+++|+++.......+. ....-.+.++|+|+||++++.. .+.+++|+..
T Consensus 1 e~R~i~~~~gv~~~a~GSa~v~~G~T~Via~V~~p~~~~~~~-----~~~~~~l~v~v~~~p~a~~~~~-~~~~~~~~~~ 74 (128)
T pfam01138 1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPPNER-----DFFPGELTVEYEEKPFASGERP-EGRPSEREIE 74 (128)
T ss_pred CCCCEEEEECCCCCCCEEEEEEECCEEEEEEEECCCCCCCCC-----CCCCCEEEEEEEECCCCCCCCC-CCCCCHHHHH
T ss_conf 973189996977998878999989979999997054355556-----7888569999867574355334-6863166899
Q ss_pred HHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf 999999987410786446873899985311027852235667777987625950
Q gi|254780784|r 401 HGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVP 454 (699)
Q Consensus 401 Hg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp 454 (699)
++.+.+|+|+++++...++.++|+|...||+.||+...|+++++++||+|||+|
T Consensus 75 l~~~l~~~l~~~~~~~~~~~~~I~i~v~vl~~dG~~~~a~~~A~~~AL~dagiP 128 (128)
T pfam01138 75 LSRLIDRALRPSFPLEGYPRWEIRIDITVLSDDGSLLDAAINAASLALADAGIP 128 (128)
T ss_pred HHHHHHHHHHHHCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHCCCC
T ss_conf 999999998864560447856999999999579998999999999999865999
No 18
>PRK08582 hypothetical protein; Provisional
Probab=99.79 E-value=5.4e-19 Score=173.14 Aligned_cols=82 Identities=37% Similarity=0.575 Sum_probs=78.1
Q ss_pred CCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEECCCCCC
Q ss_conf 75468678999999941536998287971048866314445478556032598899999978689986668730477878
Q gi|254780784|r 616 VPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQNTG 695 (699)
Q Consensus 616 ~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk~~~~~~~ 695 (699)
-+|+|++|+|+|++|.+|||||+|.+|.+|||||||+++.+|++++|+|++||+|+|||++||+.|||.||.|++.++|.
T Consensus 2 sievG~iv~G~V~~I~~fGaFV~l~~g~~GLvHISeis~~~V~~i~d~lkvGd~V~vKVi~id~~gKI~LSiK~~~~~p~ 81 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLSVGDEVEVKVLNVEDDGKIGLSIKKAKDRPR 81 (139)
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEHHHCCCCCC
T ss_conf 74478799999989964178999569966788736625665689999578999999999988899970516555454876
Q ss_pred CC
Q ss_conf 99
Q gi|254780784|r 696 KP 697 (699)
Q Consensus 696 ~~ 697 (699)
.+
T Consensus 82 ~~ 83 (139)
T PRK08582 82 RQ 83 (139)
T ss_pred CC
T ss_conf 55
No 19
>TIGR02065 ECX1 exosome complex exonuclease 1; InterPro: IPR011807 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 a family of archaeal proteins that are 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 .; GO: 0016896 exoribonuclease activity producing 5'-phosphomonoesters, 0000178 exosome (RNase complex).
Probab=99.78 E-value=7.3e-18 Score=163.98 Aligned_cols=200 Identities=27% Similarity=0.429 Sum_probs=176.1
Q ss_pred EEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCC----CEEEEECCCCCC-CCCCCCCCCCCCCCCHHH
Q ss_conf 899999140045467289999789489999972788887777354----068665232013-367888735789887145
Q gi|254780784|r 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFP----LTVNYQERTYAV-GKIPGGYLRRESRPTENE 88 (699)
Q Consensus 14 r~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~~~~~~dFfP----LtVdY~Ek~yAa-GkIPGgF~kREgrpsd~E 88 (699)
|+|++|.|.|-+ ||||.++.||.|.++|+|...+|.++-.--.| |-|-|.--.+++ =. .||-| ||.+|
T Consensus 19 Rp~KI~~GvL~r-ADGSA~~E~G~tki~aAVYGPrE~hpRh~~~PDRAV~R~RY~MAPFSvkDE-----RK~Pg-PdRR~ 91 (231)
T TIGR02065 19 RPVKIEAGVLKR-ADGSAYLEFGATKIVAAVYGPREAHPRHLQLPDRAVLRVRYNMAPFSVKDE-----RKRPG-PDRRE 91 (231)
T ss_pred CCEEEEEECCCC-CCCHHHHCCCCCEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCCCC-----CCCCC-CCCCE
T ss_conf 201001311112-760010113797999986377667775457888357760013898874346-----78722-29441
Q ss_pred HHHHHHHHCCCCC-CCCCCCC-CCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCEEECCC
Q ss_conf 3111123212677-6746886-8837899998218888778999999999987326882354112355204773243685
Q gi|254780784|r 89 ILISRMIDRSIRP-LFSKCYK-NETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPR 166 (699)
Q Consensus 89 iL~sRlIDR~lRP-LFPkgf~-~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~idge~ViNPt 166 (699)
|-+|.++--+|+| +|-+.|. ..+-|.+.||.+|+... +.++.|||.||+-++||-.--|+||-||++||..|+.++
T Consensus 92 iEiSKv~~EALepai~~E~fPRt~IDVF~EvLQADaGTR--~AgltAASlALADAGIpMRDLV~gvavGKv~G~vVLDl~ 169 (231)
T TIGR02065 92 IEISKVIREALEPAILLEQFPRTAIDVFVEVLQADAGTR--CAGLTAASLALADAGIPMRDLVVGVAVGKVDGVVVLDLS 169 (231)
T ss_pred EHHHHHHHHHCCCEEEEECCCCCCCEEEEEEEECCCCHH--HHHHHHHHHHHHHCCCHHHHHHHEEEEEEECCEEEECCC
T ss_conf 215668888513101322388950105789985276504--788999999998479402422000034556788898366
Q ss_pred CCC-CC--CCCEEEEEECCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 000-22--2101355305443233312444324899998875316889999999999999
Q gi|254780784|r 167 LDE-DQ--GSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAK 223 (699)
Q Consensus 167 ~ee-~e--sdLDLvVAGT~d~IlMIE~~A~EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~~ 223 (699)
..| +. .|+=|-+.=.-..|+.+...++ ++++++.+|+.+|-+.++.+.+.|++=.+
T Consensus 170 ~~ED~yGEAD~P~A~mP~~~~iTLLQldG~-~T~dEF~~A~~lA~~g~~~v~~~~r~ALk 228 (231)
T TIGR02065 170 ELEDMYGEADVPLAIMPKLGEITLLQLDGD-LTPDEFRQALDLAVKGIKRVYEIQREALK 228 (231)
T ss_pred CCCCCCCCCCCHHHHCCCCCCEEEEEECCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 124675765656651589982689974798-68678999999999998899999999864
No 20
>PRK05807 hypothetical protein; Provisional
Probab=99.78 E-value=8.9e-19 Score=171.39 Aligned_cols=80 Identities=39% Similarity=0.598 Sum_probs=75.8
Q ss_pred CCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEECCCCCC
Q ss_conf 75468678999999941536998287971048866314445478556032598899999978689986668730477878
Q gi|254780784|r 616 VPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQNTG 695 (699)
Q Consensus 616 ~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk~~~~~~~ 695 (699)
.+|+|++|+|+|++|++|||||+| +|++|||||||+++.+|.+++|+|++||+|.|||+++|++|||.||+|+++|++.
T Consensus 2 slevG~iv~G~V~~I~~fGaFV~l-~g~~GLvHISEis~~~Vk~i~d~lk~Gd~V~vkVl~iD~~gkI~LSiK~~~~~~~ 80 (136)
T PRK05807 2 TLEAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQAMPQKK 80 (136)
T ss_pred CCCCCCEEEEEEEEEECCEEEEEE-CCEEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCCCCEEEHHHCCCCCC
T ss_conf 745788999999999724479997-8927689856707764369999678999999999998999981433222388766
Q ss_pred C
Q ss_conf 9
Q gi|254780784|r 696 K 696 (699)
Q Consensus 696 ~ 696 (699)
.
T Consensus 81 ~ 81 (136)
T PRK05807 81 S 81 (136)
T ss_pred C
T ss_conf 6
No 21
>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=99.77 E-value=1.8e-18 Score=168.95 Aligned_cols=71 Identities=44% Similarity=0.802 Sum_probs=67.9
Q ss_pred CCCCCEEEEEEEEEEECCEEEECCC-CCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 5468678999999941536998287-9710488663144454785560325988999999786899866687
Q gi|254780784|r 617 PEVNKIYKGQVVKVMDFGAFVHFCG-ARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSM 687 (699)
Q Consensus 617 ~e~g~~y~~~v~~i~~fGafve~~~-g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSr 687 (699)
||+|++|+|+|++|++|||||+|.. +++||||||||+++|+++++|++++||+|+||++++|++||++||+
T Consensus 1 Pevg~i~~G~V~~i~~fGAFV~i~g~~~~GLvHiSeis~~rv~~~~dvv~vGd~V~Vkvi~id~~~ki~LSl 72 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSL 72 (73)
T ss_pred CCCCCEEEEEEEEEEECCEEEEECCCCCCEEEEEECCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEC
T ss_conf 978869999998997532399908988435599560541202899995579999999999886899889841
No 22
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.75 E-value=1.7e-17 Score=160.99 Aligned_cols=85 Identities=36% Similarity=0.581 Sum_probs=77.1
Q ss_pred HHHCCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEE
Q ss_conf 985247546867899999994153699828797104886631444547855603259889999997868-9986668730
Q gi|254780784|r 611 RSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKV 689 (699)
Q Consensus 611 ~~~~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~ 689 (699)
+.+.....+|.+++|+|+++.+|||||+|.||-|||+|||||+++|+++++|+|++||+|.||+++||. +-||.||.|.
T Consensus 285 ~~~~~k~~vG~vv~GkV~~l~~fGAFVel~~GIEGLVHISElS~~~v~~P~dvv~~GdeV~vkIl~ID~e~rRISLSiKQ 364 (484)
T PRK07899 285 QVFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVSVGDEVMVKVIDIDLERRRISLSLKQ 364 (484)
T ss_pred HHHHHHCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEECCEEC
T ss_conf 98986489989899999987266059993699676678776456444798884779988999999875776785423001
Q ss_pred CCCCCC
Q ss_conf 477878
Q gi|254780784|r 690 VDQNTG 695 (699)
Q Consensus 690 ~~~~~~ 695 (699)
..+.+.
T Consensus 365 a~e~~~ 370 (484)
T PRK07899 365 ANEDYD 370 (484)
T ss_pred CCCCCC
T ss_conf 678988
No 23
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.74 E-value=5.9e-18 Score=164.75 Aligned_cols=108 Identities=32% Similarity=0.549 Sum_probs=89.8
Q ss_pred EEEECC-EEEEEEECCHHHHHHHHH-HHHHHCCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHH
Q ss_conf 998088-089999689899999999-999852475468678999999941536998287971048866314445478556
Q gi|254780784|r 585 VNIDDD-GTVKIASSSLAEIEAARE-MIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSD 662 (699)
Q Consensus 585 i~i~d~-g~v~i~~~~~~~~~~a~~-~i~~~~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d 662 (699)
|.++.+ +.+-++ -+.-++...+ .-+.+...+++|++++|+|++|++|||||.| .|-+||||||+|||.|+.++++
T Consensus 174 ieid~~r~nIVlS--RRa~LEee~~~~r~e~l~~L~~G~vveG~Vk~It~fGAFVDL-GGVDGLvHiSEiSW~Rv~~Pse 250 (484)
T PRK07899 174 IELDKNRNNVVLS--RRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDL-GGVDGLVHVSELSWKHIDHPSE 250 (484)
T ss_pred EEECCCCCCEEEE--HHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCEEEEEE-CCEEEEEEHHHCCCCCCCCHHH
T ss_conf 9975766806501--999999999889999997477898799999982164689995-5723789813403567799899
Q ss_pred HCCCCCEEEEEEEEECC-CCCEEEEEEECCCCCC
Q ss_conf 03259889999997868-9986668730477878
Q gi|254780784|r 663 VVKEGDTVWVKLLDFDD-RGKIKLSMKVVDQNTG 695 (699)
Q Consensus 663 ~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~~~~~ 695 (699)
++++||+|+||++++|+ ++||.||.|++.++|=
T Consensus 251 v~~vGd~V~VkVl~iD~Ek~RISLslKql~~dPW 284 (484)
T PRK07899 251 VVEVGDEVTVEVLDVDLDRERVSLSLKATQEDPW 284 (484)
T ss_pred HCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCH
T ss_conf 5779987999998774767889886254778838
No 24
>TIGR01966 RNasePH ribonuclease PH; InterPro: IPR002381 Prokaryotic ribonuclease PH (2.7.7.56 from EC) (RNase PH) is a phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates . There is a similar protein in Caenorhabditis elegans that belongs to this group. More information about these proteins can be found at Protein of the Month: RNA Exosomes .; GO: 0000049 tRNA binding, 0004549 tRNA-specific ribonuclease activity, 0008033 tRNA processing.
Probab=99.74 E-value=1.2e-16 Score=154.09 Aligned_cols=193 Identities=26% Similarity=0.388 Sum_probs=156.6
Q ss_pred EEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCCCCC-----CCCCCCCEEEE----------ECCCCCCCCCCCCCC
Q ss_conf 899999140045467289999789489999972788887-----77735406866----------523201336788873
Q gi|254780784|r 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKD-----GQDFFPLTVNY----------QERTYAVGKIPGGYL 78 (699)
Q Consensus 14 r~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~~~~-----~~dFfPLtVdY----------~Ek~yAaGkIPGgF~ 78 (699)
|+++|+.+.+-- |.|||++.+|||.|||||....+..+ |..| +|-+| ..|=++.|||-|
T Consensus 11 Rpv~i~r~f~~h-aEGSvLi~~G~TkVlCTASv~e~VP~flrG~G~GW--iTAEY~MLPraT~~R~~REa~~GK~~G--- 84 (237)
T TIGR01966 11 RPVKITRDFLKH-AEGSVLIEFGDTKVLCTASVEEKVPPFLRGSGEGW--ITAEYGMLPRATQTRNRREAAKGKQSG--- 84 (237)
T ss_pred CCEEECCCCCCC-CCCEEEEEECCEEEEEEEEECCCCCCCCCCCCCEE--EEHHHHHHHHHHCCCCHHHHHHCCCCC---
T ss_conf 362554688788-88726897879246667875587285235889425--504110003303031246686178787---
Q ss_pred CCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCC--EEEEEEEEECCCCCCHHHHHHHHHHHHHH-----------HCC-CC
Q ss_conf 57898871453111123212677674688688--37899998218888778999999999987-----------326-88
Q gi|254780784|r 79 RRESRPTENEILISRMIDRSIRPLFSKCYKNE--TQVIINVMQHDLESSPHVVSMVAASAALM-----------LSG-LP 144 (699)
Q Consensus 79 kREgrpsd~EiL~sRlIDR~lRPLFPkgf~~e--vQIv~~VLS~D~~~dpdvlAi~aASaAL~-----------ISd-IP 144 (699)
.++|| +|||-|+||--+.=.=--| +-|-|-||.+|+... ..||+||=-||+ +.. =|
T Consensus 85 ------RTqEI--QRLIGRaLRavvDl~aLGErTI~iDCDVlQADGGTR--TAsITGAfVAL~dAi~~L~~~~~~~~~~P 154 (237)
T TIGR01966 85 ------RTQEI--QRLIGRALRAVVDLEALGERTIWIDCDVLQADGGTR--TASITGAFVALADAIKKLQKRGILKESEP 154 (237)
T ss_pred ------CHHHH--HHHHHHHHHHHHHHHHCCCEEEEEECCEEECCCCCH--HHHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf ------50567--778888988773462348502798533433887612--46788899999999999985786234687
Q ss_pred CCCCEEEEEEEECCCCEEECCCCCC-CCCCCEEEEEECCCC-HHHHHC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 2354112355204773243685000-222101355305443-233312--444324899998875316889999999999
Q gi|254780784|r 145 FEGPVVGAQVDYINGQYVLNPRLDE-DQGSLDLFVSGTQDA-VLMVEL--EANQLSEDVVLDAIIFGHNECKPVIEAISK 220 (699)
Q Consensus 145 f~GPVaaVRVG~idge~ViNPt~ee-~esdLDLvVAGT~d~-IlMIE~--~A~EVsEe~mleAI~~Ahe~Ik~iI~~Q~e 220 (699)
..++||||-||.+||+-++.-.|.| ..++-|+=|-.|.++ ++=|.| |..--|+++|.+=|.+|++-|++++++|++
T Consensus 155 ~~~~VAAVSVGiv~g~~~LDL~Y~EDs~A~vD~NvVmT~~G~fvEvQGTaE~~pFsr~EL~~LL~LA~~Gi~eL~~~Qk~ 234 (237)
T TIGR01966 155 IRDFVAAVSVGIVDGEPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEEPFSRDELNELLDLAEKGIRELIELQKQ 234 (237)
T ss_pred CCCCCCEEEEEEECCEEEECCCCCCCCCCCCCCEEEECCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 11052438988766806763588555646335205885787658887057889701899999999988889999999999
Q ss_pred HH
Q ss_conf 99
Q gi|254780784|r 221 LA 222 (699)
Q Consensus 221 L~ 222 (699)
..
T Consensus 235 aL 236 (237)
T TIGR01966 235 AL 236 (237)
T ss_pred HC
T ss_conf 71
No 25
>PRK07252 hypothetical protein; Provisional
Probab=99.72 E-value=2e-17 Score=160.46 Aligned_cols=80 Identities=28% Similarity=0.541 Sum_probs=76.2
Q ss_pred CCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEECCCCCC
Q ss_conf 546867899999994153699828797104886631444547855603259889999997868-9986668730477878
Q gi|254780784|r 617 PEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVVDQNTG 695 (699)
Q Consensus 617 ~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~~~~~ 695 (699)
+++|++|+|+|++|.+|||||+|.+|.+|||||||+++.++.++.|++++||+|.|+++++|+ ++||.||+|+|.+++.
T Consensus 1 lkvGdiv~G~V~~I~~fGaFV~l~~gv~GLiHISEis~~~v~~~~~~~kvGd~V~vkVi~ID~e~~rIsLSiK~l~e~~~ 80 (120)
T PRK07252 1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGNEVLVQVIDIDEYTKKASLSMRTLEEEKQ 80 (120)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEEECCHHHHCCCCC
T ss_conf 98888999999999754579995799578888666010200499994789999999999986899988613633224534
Q ss_pred C
Q ss_conf 9
Q gi|254780784|r 696 K 696 (699)
Q Consensus 696 ~ 696 (699)
.
T Consensus 81 ~ 81 (120)
T PRK07252 81 H 81 (120)
T ss_pred C
T ss_conf 5
No 26
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.71 E-value=4e-17 Score=158.00 Aligned_cols=84 Identities=32% Similarity=0.563 Sum_probs=78.1
Q ss_pred HCCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEECC
Q ss_conf 5247546867899999994153699828797104886631444547855603259889999997868-998666873047
Q gi|254780784|r 613 ITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVVD 691 (699)
Q Consensus 613 ~~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~ 691 (699)
.....++|.+++|+|++|++|||||+| .|-+||||||+|||.|+.+++|++++||+|+||++++|. ++||.||.|+|.
T Consensus 190 ~~~~l~vG~vv~G~V~~I~~fGaFVdi-gGvdGLlHiSeiSw~rv~~p~dv~kvGd~V~vkVi~iD~e~~rIsLSiK~l~ 268 (314)
T PRK07400 190 KMNRLEVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDQMKVMIIDLDAERGRISLSTKQLE 268 (314)
T ss_pred HHHCCCCCCEEEEEEEEEECEEEEEEE-CCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEHHHCC
T ss_conf 675088998899999999640889997-8918999814616544489878267999999999997388988997766655
Q ss_pred CCCCCC
Q ss_conf 787899
Q gi|254780784|r 692 QNTGKP 697 (699)
Q Consensus 692 ~~~~~~ 697 (699)
++|-.-
T Consensus 269 ~dPwd~ 274 (314)
T PRK07400 269 PEPGDM 274 (314)
T ss_pred CCCHHH
T ss_conf 584777
No 27
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.71 E-value=1.9e-16 Score=152.49 Aligned_cols=85 Identities=40% Similarity=0.637 Sum_probs=78.7
Q ss_pred HCCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEECC
Q ss_conf 5247546867899999994153699828797104886631444547855603259889999997868-998666873047
Q gi|254780784|r 613 ITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVVD 691 (699)
Q Consensus 613 ~~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~ 691 (699)
+.....+|++++|+|+++.+|||||+|.||-+||+|+|||+|+|+.+++|++++||+|+||++++|+ +-||.||.|++.
T Consensus 559 ~~~~~~~G~~v~g~V~~i~~fGaFVel~~gveGlih~sels~~~~~~~~~~~~~Gd~v~~kIl~id~~~krisLSiK~~~ 638 (670)
T PRK00087 559 VEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISEISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVE 638 (670)
T ss_pred HHHHCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCHHHCCCCCCEEEEEEEEECCCCCEEEEEHHHCC
T ss_conf 88648996999999999967707999579978998989948432489777489999899999998377788997846531
Q ss_pred CCCCCC
Q ss_conf 787899
Q gi|254780784|r 692 QNTGKP 697 (699)
Q Consensus 692 ~~~~~~ 697 (699)
++|+++
T Consensus 639 ~~peke 644 (670)
T PRK00087 639 EEPEKE 644 (670)
T ss_pred CCCCHH
T ss_conf 180046
No 28
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.70 E-value=5e-17 Score=157.15 Aligned_cols=88 Identities=36% Similarity=0.558 Sum_probs=81.7
Q ss_pred HHHHHHCCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEE
Q ss_conf 999985247546867899999994153699828797104886631444547855603259889999997868-9986668
Q gi|254780784|r 608 EMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLS 686 (699)
Q Consensus 608 ~~i~~~~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lS 686 (699)
+.-+.+...+++|++++|+|++|.+|||||+| .|-+||||+|+|||.|+++++|++++||+|+||++++|+ ++||.||
T Consensus 469 ~~k~~~~~~l~~G~~v~G~V~~i~~~GaFvdl-gGvdGLvHiSelSw~rv~~p~~~~~~G~~v~vkIl~iD~e~~rIsLs 547 (670)
T PRK00087 469 KQKEETWNSLEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILEIDKENKKLSLS 547 (670)
T ss_pred HHHHHHHHHCCCCCEEEEEEEEEECCCEEEEE-CCEEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEE
T ss_conf 99999997488998899999999734079997-79899998434476777898996278977999999983887889876
Q ss_pred EEECCCCCCC
Q ss_conf 7304778789
Q gi|254780784|r 687 MKVVDQNTGK 696 (699)
Q Consensus 687 rk~~~~~~~~ 696 (699)
.|+|.++|-.
T Consensus 548 ~K~l~~dPw~ 557 (670)
T PRK00087 548 LKKLLPDPWE 557 (670)
T ss_pred ECCCCCCCHH
T ss_conf 3437789478
No 29
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.70 E-value=3.5e-17 Score=158.39 Aligned_cols=82 Identities=37% Similarity=0.613 Sum_probs=77.8
Q ss_pred CCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEECCCCCC
Q ss_conf 75468678999999941536998287971048866314445478556032598899999978689986668730477878
Q gi|254780784|r 616 VPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQNTG 695 (699)
Q Consensus 616 ~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk~~~~~~~ 695 (699)
.+++|.+++|+|+.|.+|||||+|..|..||+||||+++..|.+++|+|++||+|.|||+++|++|+|.||.|++.+.|.
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKisLSIr~~~e~pe 81 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKISLSIRKLEEEPE 81 (129)
T ss_pred CCCCCCEEEEEEEEEEECCEEEEECCCCCCEEEEHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCCCCCEEHHHHHHCCC
T ss_conf 75346467888975674334898239973148835754436773998842788799999721468970335687664744
Q ss_pred CC
Q ss_conf 99
Q gi|254780784|r 696 KP 697 (699)
Q Consensus 696 ~~ 697 (699)
.+
T Consensus 82 ~~ 83 (129)
T COG1098 82 KQ 83 (129)
T ss_pred CC
T ss_conf 33
No 30
>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=99.69 E-value=9.4e-17 Score=154.94 Aligned_cols=75 Identities=63% Similarity=0.941 Sum_probs=70.5
Q ss_pred CCEEEEEEEEEEECCEEEECC---CCCCEEEEEEECCCC-CCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEECCCCCC
Q ss_conf 867899999994153699828---797104886631444-5478556032598899999978689986668730477878
Q gi|254780784|r 620 NKIYKGQVVKVMDFGAFVHFC---GARDGLVHISQLSTE-RVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQNTG 695 (699)
Q Consensus 620 g~~y~~~v~~i~~fGafve~~---~g~~gl~HiS~l~~~-~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk~~~~~~~ 695 (699)
|++|+|+|++|.+|||||+|. +|.+|||||||++|. |+.+++|++++||+|+||++++| ++||+||+|++.|++|
T Consensus 1 G~i~~G~V~~i~~fGaFV~l~~~~~~~~GLvHiSeis~~~~~~~~~~~~~~G~~V~vkVi~id-~~ki~LS~K~~~~~~G 79 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ-NGKISLSMKDVDQDTG 79 (79)
T ss_pred CCEEEEEEEEEEEEEEEEEEECCCCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEEE-CCEEEEEEEECCCCCC
T ss_conf 999999998997533999996788980678995681575555898893679999999999986-9988872261346799
No 31
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=99.69 E-value=2.1e-16 Score=152.10 Aligned_cols=81 Identities=40% Similarity=0.634 Sum_probs=73.5
Q ss_pred CCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCC-CCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEECC
Q ss_conf 24754686789999999415369982879710488663144-4547855603259889999997868-998666873047
Q gi|254780784|r 614 TDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLST-ERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVVD 691 (699)
Q Consensus 614 ~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~-~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~ 691 (699)
....++|.+|+|+|+++.+|||||||-||-+||+|+||||| +|+.++++++++||+|+||++++|. +-||.||.|++.
T Consensus 286 ~~k~~vG~~v~g~V~~i~~fGaFVel~~gieGlvHiSelSw~~~~~~p~~~~~~Gd~v~vkIl~iD~e~rrisLs~Kq~~ 365 (489)
T PRK13806 286 GDRLEADQVVEGKVVRLAPFGAFVEVLPGVEGLVHISEMSWTRRVNKPEEVVAPGDTVSVKIKELDPAKRRISLSLRDAE 365 (489)
T ss_pred HHHCCCCCEEEEEEEECCCCCEEEEECCCEEEEEEEHHCCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEHHHCC
T ss_conf 86367998379999972454069996388079998044255345789899606687299999997143378996567534
Q ss_pred CCC
Q ss_conf 787
Q gi|254780784|r 692 QNT 694 (699)
Q Consensus 692 ~~~ 694 (699)
++|
T Consensus 366 ~nP 368 (489)
T PRK13806 366 GDP 368 (489)
T ss_pred CCC
T ss_conf 695
No 32
>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=99.69 E-value=9.5e-17 Score=154.92 Aligned_cols=73 Identities=33% Similarity=0.528 Sum_probs=70.8
Q ss_pred CCCCCEEEEEEEEEEECCEEEECC--CCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEE
Q ss_conf 546867899999994153699828--797104886631444547855603259889999997868-9986668730
Q gi|254780784|r 617 PEVNKIYKGQVVKVMDFGAFVHFC--GARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKV 689 (699)
Q Consensus 617 ~e~g~~y~~~v~~i~~fGafve~~--~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~ 689 (699)
||+|++|.|+|++|.+|||||+|. +|.+||+||||++|+|+++++|++++||+|.||++++|+ +|||.||+|.
T Consensus 1 Pe~G~iv~G~V~~i~~~GafV~l~e~~g~eGlihiSEis~~~v~~~~d~~~~G~~v~~kVi~vD~~k~~i~LS~K~ 76 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEEEEEECC
T ss_conf 9889999999999973469999733699199999799684511599995589999999999997899999822369
No 33
>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=99.69 E-value=9.5e-17 Score=154.90 Aligned_cols=69 Identities=49% Similarity=0.804 Sum_probs=67.9
Q ss_pred CCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 867899999994153699828797104886631444547855603259889999997868998666873
Q gi|254780784|r 620 NKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMK 688 (699)
Q Consensus 620 g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk 688 (699)
|++|+|+|++|.||||||+|.+|.+|||||||++|.|+++++|++++||+|+||++++|++||+.||+|
T Consensus 1 G~vv~G~V~~I~~fGaFV~l~~g~~GL~HiSeis~~~v~~~~~~~~~Gd~v~vkVi~id~~~ri~LS~K 69 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEECCC
T ss_conf 999999999998538999968998899996983456557988917899999999999999996680159
No 34
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional
Probab=99.68 E-value=1.2e-14 Score=137.77 Aligned_cols=198 Identities=26% Similarity=0.356 Sum_probs=156.1
Q ss_pred CEEEEEEECEECCCCCCEEEEEECCCEEEEEEEECC-CC---CCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf 989999914004546728999978948999997278-88---87777354068665232013367888735789887145
Q gi|254780784|r 13 GRPLKLETGRIARQSDGAVLATYGETVVLATVVYDR-SL---KDGQDFFPLTVNYQERTYAVGKIPGGYLRRESRPTENE 88 (699)
Q Consensus 13 gr~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~-~~---~~~~dFfPLtVdY~Ek~yAaGkIPGgF~kREgrpsd~E 88 (699)
-|++.+++|-+.+ |+||+.+++|+|.|+|+|.+.- +| +++.++| .++|.--.+| .|. | +-|+|++++
T Consensus 34 ~R~i~i~~g~l~~-a~GSa~v~~G~T~Vla~V~~ei~~p~~~~p~eG~~--~~~v~~~~~a---~~~-~--~~g~~~~~~ 104 (271)
T PRK04282 34 YRPIEIETGVIKK-AEGSALVKLGNTQVIAGVKLELGEPFPDTPDEGVL--IVNAELLPLA---SPT-F--EPGPPDENA 104 (271)
T ss_pred CCCEEEEECCCCC-CCEEEEEEECCEEEEEEEEECCCCCCCCCCCCCCE--EEEEEECCCC---CCC-C--CCCCCCCCH
T ss_conf 6675999798588-88059999689489999872356765668985437--9999657867---776-6--579976302
Q ss_pred HHHHHHHHCCCCCC----------CCCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC--------------
Q ss_conf 31111232126776----------746886883789999821888877899999999998732688--------------
Q gi|254780784|r 89 ILISRMIDRSIRPL----------FSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLP-------------- 144 (699)
Q Consensus 89 iL~sRlIDR~lRPL----------FPkgf~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIP-------------- 144 (699)
+..+|+++|.+|-. .|.-+..-+.|-+.||++|++.- -.+.+|+.+||.-..+|
T Consensus 105 ~e~~~~l~r~l~~s~~idle~LcI~~g~~~W~i~idv~VL~~dGn~~--dA~~~A~~aAL~~~~~P~v~~~~~~~~~~~~ 182 (271)
T PRK04282 105 IELARVVDRGIRESGAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLL--DASMLAAVAALLNTKLPAVVKEDGGVVLDLG 182 (271)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHCCCCCCCCEEEEEEEEEEECCCCHH--HHHHHHHHHHHHHCCCCEEEECCCCEEECCC
T ss_conf 88999999887642523247636577775179999999991599688--8899999999986689716851663121136
Q ss_pred ------CCCCEEEEEEEECCCCEEECCCCCCC-CCCCEEEEEECCCC-HHHHHC-CCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf ------23541123552047732436850002-22101355305443-233312-4443248999988753168899999
Q gi|254780784|r 145 ------FEGPVVGAQVDYINGQYVLNPRLDED-QGSLDLFVSGTQDA-VLMVEL-EANQLSEDVVLDAIIFGHNECKPVI 215 (699)
Q Consensus 145 ------f~GPVaaVRVG~idge~ViNPt~ee~-esdLDLvVAGT~d~-IlMIE~-~A~EVsEe~mleAI~~Ahe~Ik~iI 215 (699)
++....+|-+|++++.+++.||.+|+ -++.++.|+.++++ +.-+.. +...++-+.|.++++.|.+..++++
T Consensus 183 ~~~~l~i~~~Pi~vT~~~i~~~~l~Dpt~~EE~~~~~~~~V~~n~~g~i~~l~k~g~~~i~~~~l~~~~~~A~~~~~~l~ 262 (271)
T PRK04282 183 EKVPLPINNKPVSVTFAKIGNYLVVDPTLEEELVMDARITITTDEDGIICAMQKSGLGSFTEEEVEEAIDLALKKAKELR 262 (271)
T ss_pred CCCCCCCCCCCEEEEEEEECCEEEECCCHHHHHCCCCEEEEEEECCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 66677635661378999999999977998898456876999990899799997789999599999999999999999999
Q ss_pred HHHHHH
Q ss_conf 999999
Q gi|254780784|r 216 EAISKL 221 (699)
Q Consensus 216 ~~Q~eL 221 (699)
+.|++-
T Consensus 263 ~~i~~a 268 (271)
T PRK04282 263 EKLKEA 268 (271)
T ss_pred HHHHHH
T ss_conf 999986
No 35
>PRK08059 general stress protein 13; Validated
Probab=99.68 E-value=1.8e-16 Score=152.57 Aligned_cols=83 Identities=36% Similarity=0.591 Sum_probs=78.7
Q ss_pred CCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEECCCC
Q ss_conf 47546867899999994153699828797104886631444547855603259889999997868-99866687304778
Q gi|254780784|r 615 DVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVVDQN 693 (699)
Q Consensus 615 ~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~~~ 693 (699)
...++|++|+|+|++|.+|||||++.+|.+||||||||++.+++++.+++++||+|.||++++|+ ++||.||+|++.++
T Consensus 2 ~k~kvGdiv~G~V~~I~~fG~FV~l~~gv~GLihiSEls~~~v~~~~~~~~vGd~V~vkVi~iD~e~~ri~LSlK~l~~~ 81 (119)
T PRK08059 2 EQYEVGVVVTGKVTGIQDYGAFVALDEETQGLVHISEITHGFVKDIHDFLKVGDEVKVKVLSVDEEHGKISLSIRATEEA 81 (119)
T ss_pred CCCCCCCEEEEEEEEEECEEEEEEEECCCEEEEEHHHHCCCCCCCHHHHHCCCCEEEEEEEEEECCCCEEEEECCCCCCC
T ss_conf 87899999999999997404899994395378887882456667999970589989999999989999998750357648
Q ss_pred CCCC
Q ss_conf 7899
Q gi|254780784|r 694 TGKP 697 (699)
Q Consensus 694 ~~~~ 697 (699)
|.+.
T Consensus 82 P~~~ 85 (119)
T PRK08059 82 PERK 85 (119)
T ss_pred CCCC
T ss_conf 3422
No 36
>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=99.68 E-value=1.1e-16 Score=154.42 Aligned_cols=68 Identities=60% Similarity=0.937 Sum_probs=67.0
Q ss_pred CCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 86789999999415369982879710488663144454785560325988999999786899866687
Q gi|254780784|r 620 NKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSM 687 (699)
Q Consensus 620 g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSr 687 (699)
|++|+|+|++|.+|||||+|.||.+|||||||++|.|+++++|++++||+|+||++++|+++||+|||
T Consensus 1 G~iv~G~V~~i~~fG~FV~l~~g~~GLiHiSeis~~~v~~~~~~~~~Gd~v~vkVi~iD~~~ri~LSr 68 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCCCCCCCC
T ss_conf 99999999999732999995799624888689345654698890789999999999999999720529
No 37
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]
Probab=99.67 E-value=8.1e-15 Score=139.21 Aligned_cols=200 Identities=24% Similarity=0.360 Sum_probs=155.8
Q ss_pred CEEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCCCCC----CCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCH-H
Q ss_conf 9899999140045467289999789489999972788887----7773540686652320133678887357898871-4
Q gi|254780784|r 13 GRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKD----GQDFFPLTVNYQERTYAVGKIPGGYLRRESRPTE-N 87 (699)
Q Consensus 13 gr~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~~~~----~~dFfPLtVdY~Ek~yAaGkIPGgF~kREgrpsd-~ 87 (699)
=|+++++.|.+-. |+||+++.+|+|.|+|||...+++.+ +.+.=++|++|.-...|... =.||| ++. +
T Consensus 18 lR~i~~~~~~~~~-a~GS~~~~~G~tkVic~vsGp~e~~p~~l~~~~~g~~t~ey~m~p~sT~~----R~~~~--~~~gR 90 (230)
T COG0689 18 LRPIKITRGVLKH-AEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEYGMLPRSTDE----RKKRE--ADRGR 90 (230)
T ss_pred CCCEEEEECCCCC-CCCCEEEEECCEEEEEEEECCCCCCCHHHCCCCCEEEEEEECCCCCCCCC----CCCCC--CCCCH
T ss_conf 4646887155467-88537999678089999706777888544377721799997020123433----32344--33430
Q ss_pred HHHHHHHHHCCCCCCCCCCCC--CCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCEEECC
Q ss_conf 531111232126776746886--883789999821888877899999999998732688235411235520477324368
Q gi|254780784|r 88 EILISRMIDRSIRPLFSKCYK--NETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNP 165 (699)
Q Consensus 88 EiL~sRlIDR~lRPLFPkgf~--~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~idge~ViNP 165 (699)
+..+||+|-|+|||-+.-..+ .-++|-|.|+.+|+... ..+||||+.||+-+.||...-|+|+-||.++|..++.+
T Consensus 91 ~~eisrli~~al~~~i~L~~~p~~~I~i~~dVlqaDggTr--ta~It~A~lAL~DAgipl~~~vaaiSvgi~~~~~~lDl 168 (230)
T COG0689 91 TKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADGGTR--TASITGASLALADAGIPLRDLVAAISVGIVDGVIVLDL 168 (230)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEECCCCEE--EEHHHHHHHHHHHCCCCHHHHEEEEEEEEECCCEEECC
T ss_conf 3279999999998876565447638999999998789754--20266799999873994565302767888779357637
Q ss_pred CCCCC-C--CCCEEEEEECCCCHHHHHC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 50002-2--2101355305443233312--44432489999887531688999999999999
Q gi|254780784|r 166 RLDED-Q--GSLDLFVSGTQDAVLMVEL--EANQLSEDVVLDAIIFGHNECKPVIEAISKLA 222 (699)
Q Consensus 166 t~ee~-e--sdLDLvVAGT~d~IlMIE~--~A~EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~ 222 (699)
.+.|. . +++.+++.++.. +.=|.+ +..-.+++.+..+|+.|.+.++.+.+.|++..
T Consensus 169 ~~~Eds~~~~d~~v~~~~~~~-~~ei~~~~~~~~~~~del~~lL~la~~g~~~~~~~~~~al 229 (230)
T COG0689 169 DYEEDSAAEADMNVVMTGNGG-LVEIQGLAEDGPFTEDELLELLDLAIKGCNELRELQREAL 229 (230)
T ss_pred CCHHHCCCCCCCEEEEEECCC-EEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 432111224471499970697-3789986306997999999999999999999999999975
No 38
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.67 E-value=1.2e-15 Score=145.86 Aligned_cols=84 Identities=37% Similarity=0.542 Sum_probs=66.5
Q ss_pred HCCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEECC
Q ss_conf 5247546867899999994153699828797104886631444547855603259889999997868-998666873047
Q gi|254780784|r 613 ITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVVD 691 (699)
Q Consensus 613 ~~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~ 691 (699)
+.....+|+.+.|+|+++.+||||||+.||-+||+||||+||.+.+.+++++++||+|.|+++++|+ +.||+||.|++.
T Consensus 271 i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~ 350 (541)
T COG0539 271 IEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLK 350 (541)
T ss_pred HHHHCCCCCEEEEEEEEEECCCEEEEECCCCCCEEECHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEHHCC
T ss_conf 76414788778899998614747999518843101030413133699789535687899999950720166776600000
Q ss_pred CCCCC
Q ss_conf 78789
Q gi|254780784|r 692 QNTGK 696 (699)
Q Consensus 692 ~~~~~ 696 (699)
++|-+
T Consensus 351 ~~pw~ 355 (541)
T COG0539 351 ENPWE 355 (541)
T ss_pred CCHHH
T ss_conf 39446
No 39
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.66 E-value=6.1e-16 Score=148.36 Aligned_cols=108 Identities=30% Similarity=0.528 Sum_probs=89.2
Q ss_pred EEEE-CCEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHH
Q ss_conf 9980-880899996898999999999998524754686789999999415369982879710488663144454785560
Q gi|254780784|r 585 VNID-DDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDV 663 (699)
Q Consensus 585 i~i~-d~g~v~i~~~~~~~~~~a~~~i~~~~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~ 663 (699)
++++ +++++.+.-.... . .--+.+....++|.+|+|+|++|.+||+||++.+|-+||||+||++|.++.+++++
T Consensus 247 l~id~~~~ri~LslK~l~--~---dP~~~~~~~~~vG~~v~G~V~~i~~fG~fV~l~~g~~Glih~sels~~~~~~p~~~ 321 (390)
T PRK06676 247 LSIDEETERISLSLKDTL--P---GPWEGVEEKLKEGDVIEGTVKRLTNFGAFVEVLPGVEGLVHISQISHKHIAKPSEV 321 (390)
T ss_pred EEEECCCCEEEEEEEECC--C---CCHHHHHHHCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCHHHC
T ss_conf 999467889999983267--8---95677665336998999999999473799997799689999899475333685552
Q ss_pred CCCCCEEEEEEEEECC-CCCEEEEEEECCCCCCCC
Q ss_conf 3259889999997868-998666873047787899
Q gi|254780784|r 664 VKEGDTVWVKLLDFDD-RGKIKLSMKVVDQNTGKP 697 (699)
Q Consensus 664 ~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~~~~~~~ 697 (699)
+++||+|+|++++||+ +.||.||.|++.++|.++
T Consensus 322 ~~~Gd~V~~~Vl~id~e~~ri~LS~K~l~~~p~~e 356 (390)
T PRK06676 322 LEEGQEVKVKVLEVDEEEKRISLSIKALEEAPAEE 356 (390)
T ss_pred CCCCCEEEEEEEEECCCCCEEEEEEHHCCCCHHHH
T ss_conf 78999999999998177898998814134481566
No 40
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.66 E-value=1.9e-15 Score=144.32 Aligned_cols=79 Identities=34% Similarity=0.545 Sum_probs=51.6
Q ss_pred CCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCC-CCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEECCCC
Q ss_conf 754686789999999415369982879710488663144-4547855603259889999997868-99866687304778
Q gi|254780784|r 616 VPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLST-ERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVVDQN 693 (699)
Q Consensus 616 ~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~-~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~~~ 693 (699)
..++|.+|+|+|+++.+|||||+|.||-+||+|+|||+| +|+.++.+++++||+|+||++++|+ +.||.||.|.+.++
T Consensus 273 ~~~~G~~v~g~V~~i~~fGafVel~~gveGlvhiSelsw~~~~~~p~~~~~~G~~V~~kIl~id~~~~risLS~K~~~~n 352 (556)
T PRK06299 273 KYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKEN 352 (556)
T ss_pred HCCCCCEEEEEEEEECCCEEEEEECCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEECCCCCC
T ss_conf 47899989999999827607999549958998878716754447978954479779999999724436888863236679
Q ss_pred C
Q ss_conf 7
Q gi|254780784|r 694 T 694 (699)
Q Consensus 694 ~ 694 (699)
|
T Consensus 353 P 353 (556)
T PRK06299 353 P 353 (556)
T ss_pred H
T ss_conf 7
No 41
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=99.66 E-value=4.2e-16 Score=149.64 Aligned_cols=247 Identities=25% Similarity=0.351 Sum_probs=142.3
Q ss_pred EEEEEEEECCCCCCC---HHHHHHHHHHHHHHC---CCCCCCCCC---EEEEEEEEECC--EEEE----EEEC---CCCC
Q ss_conf 899985311027852---235667777987625---950225412---13320044088--2899----8631---4422
Q gi|254780784|r 422 TLRIVSEITESDGSS---SMATVCGSSLALMDA---GVPISKPVA---GIAMGLVKDGD--DFII----LSDI---SGDE 483 (699)
Q Consensus 422 tirv~~evl~sngss---sma~vc~~slal~da---gvp~~~~Va---GiamGLi~~~~--~~~i----LtDI---~G~E 483 (699)
.+.|..|-++.-|+. --|---.++..|..| |-++..-|. .+-=|+..|-+ --+- +.|+ -..+
T Consensus 363 ~v~V~ie~~e~~~~~LSr~kA~r~~~w~~le~a~~~~~~v~G~i~~~~~vkgG~~Vdl~~gv~AFLPgSqvd~rpv~d~~ 442 (863)
T PRK12269 363 GVRVYVERVTPYGPELSKTKADRLGLKVKLRDAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPE 442 (863)
T ss_pred EEEEEEEEECCCCCEECHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCCCEEEECCCCCEEECCHHHCCCEECCCCH
T ss_conf 99999999708897561899987899999999975699079999744610453799858896786766564711368863
Q ss_pred CCCC-CCCEEEEECCCCCEEEECCCCC-----CC---CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEE
Q ss_conf 0136-5510010055651244324536-----55---6889999999999999999999998435667433224487579
Q gi|254780784|r 484 DHLG-HMDFKVAGTDSGITAMQMDMKI-----GG---ISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVE 554 (699)
Q Consensus 484 D~~G-dMDFKvaGT~~GiTa~QmDiK~-----~g---i~~~il~~al~~A~~gr~~il~~m~~~~~~~~~~~~~~ap~~~ 554 (699)
.+.| .+.||| +.||.+- +. --..+|++.....|+..+.-|.+=+-+-. --+.+.
T Consensus 443 ~~~g~~~~f~i---------ik~~~~~~~r~~~NiVvSRravlEe~~~~~r~~~l~~l~eG~vv~G-~VKnit------- 505 (863)
T PRK12269 443 SLIGLTSKFYI---------ERISQSKQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSG-VVKSFT------- 505 (863)
T ss_pred HHCCCCCCEEE---------EEEEHHHHCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCCCEEEE-EEEECC-------
T ss_conf 21588741599---------9953133126778889976798888889999999864436877889-998315-------
Q ss_pred EEEECCCCEEEEECCCCHHHHHHHHHHCC----------EEEEECCEEEEEEECCHHHHHHHHHHHHHHCCCC-------
Q ss_conf 99977115000037860779989998688----------8998088089999689899999999999852475-------
Q gi|254780784|r 555 IMAIPPDQIRNVIGMGGKVIRGIVEQTGA----------KVNIDDDGTVKIASSSLAEIEAAREMIRSITDVP------- 617 (699)
Q Consensus 555 ~~~i~~~ki~~~iG~gG~~ik~i~~~~~~----------~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~~~------- 617 (699)
--|..|--|| |-++.--|.. -+++.|+=.|+|...|.+.- +--.-++.+..+|
T Consensus 506 -------dyGaFvDLGG--vDGLLHitDiSW~Rv~hPse~~~vG~~i~vkVlk~D~e~~-riSLglKQl~~dPW~~i~~k 575 (863)
T PRK12269 506 -------SFGAFIDLGG--FDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEK-RINLSLKHFQPDPWLEFENK 575 (863)
T ss_pred -------CCEEEEECCC--CCEEEEEECCCCCCCCCHHHHHCCCCEEEEEEEEECCCCC-EEEECCCCCCCCCHHHHHHH
T ss_conf -------6405896177--1014662111357889989971279779999985256545-14311321778976788863
Q ss_pred -CCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCC-CCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEECCCCC
Q ss_conf -4686789999999415369982879710488663144-4547855603259889999997868-998666873047787
Q gi|254780784|r 618 -EVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLST-ERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVVDQNT 694 (699)
Q Consensus 618 -e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~-~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~~~~ 694 (699)
.+|..|+|+|++|+||||||||-||-|||+|+||++| ++..++.+++++||+|+|++++||. +-||.||.|.+.++|
T Consensus 576 y~vg~~v~gkVtnitdyGaFVEle~GiEGLvHvSEmsWtkk~~~P~k~v~~GdeVev~VLeID~ekrRISLg~Kq~~~NP 655 (863)
T PRK12269 576 FGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANP 655 (863)
T ss_pred CCCCCEEEEEEEEEECCCEEEEECCCCEEEEEEHHHCCCCCCCCHHHCCCCCCEEEEEEEEEECCCCEEEEEECCCCCCC
T ss_conf 88999899999997446569996389257887025020236799798076897799999988032267854410166884
Q ss_pred C
Q ss_conf 8
Q gi|254780784|r 695 G 695 (699)
Q Consensus 695 ~ 695 (699)
=
T Consensus 656 W 656 (863)
T PRK12269 656 W 656 (863)
T ss_pred H
T ss_conf 9
No 42
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.65 E-value=6.5e-16 Score=148.12 Aligned_cols=77 Identities=35% Similarity=0.589 Sum_probs=45.4
Q ss_pred CCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEECCCC
Q ss_conf 546867899999994153699828797104886631444547855603259889999997868-99866687304778
Q gi|254780784|r 617 PEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVVDQN 693 (699)
Q Consensus 617 ~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~~~ 693 (699)
..+|.+++|+|+++.+||+||++.+|-+||+|+|+|+.+|+....+.+++||+|.++++++|. +.||.||.|++.+.
T Consensus 448 ~k~G~iv~g~V~~i~~~G~fV~l~~gieglI~~sels~~~~~~~~~~~~~Gd~v~~~Ii~id~e~rkI~LSiK~le~~ 525 (556)
T PRK06299 448 HKKGSIVTGTVTEVKDKGAFVELADGVEGFIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEA 525 (556)
T ss_pred CCCCCEEEEEEEEEECCCEEEEECCCEEEEEEHHHCCCHHHHCCCCCCCCCCEEEEEEEEECCCCCEEEEEHHHHHHH
T ss_conf 899899999999997895699938990999997996800233621116899989999999827779999871595555
No 43
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.64 E-value=3e-15 Score=142.71 Aligned_cols=310 Identities=20% Similarity=0.312 Sum_probs=204.0
Q ss_pred EEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCE--------EEEECCCCCCCCCCCCCCCCCCCCC
Q ss_conf 89999914004546728999978948999997278888777735406--------8665232013367888735789887
Q gi|254780784|r 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLT--------VNYQERTYAVGKIPGGYLRRESRPT 85 (699)
Q Consensus 14 r~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~~~~~~dFfPLt--------VdY~Ek~yAaGkIPGgF~kREgrps 85 (699)
|+|.+|+|-|.| +|||.+.+.|.|..|+.++.+.. .+.+-.--|+ .+|+-..|++|.+ +|-|.|+
T Consensus 323 Rpi~~ev~~lpr-~HGS~LFtRGeTQal~v~TLG~~-~d~Qiid~l~~e~~krfm~hYNFPp~SvGE~-----g~~g~p~ 395 (692)
T COG1185 323 RPIGIEVGVLPR-THGSALFTRGETQALVVVTLGTP-RDAQVIDILEGEYKKRFLLHYNFPPFSVGET-----GRMGSPG 395 (692)
T ss_pred EEEEEEECCCCC-CCCHHHCCCCCCCCEEEEECCCC-CHHHHHHHCCCHHHHHEEEECCCCCCCCCCC-----CCCCCCC
T ss_conf 540377547887-53022100688751468975774-1366655205323332542126799874556-----7788987
Q ss_pred HHHHHHHHHHHCCCCCCCC--CCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEC-CCC-E
Q ss_conf 1453111123212677674--68868837899998218888778999999999987326882354112355204-773-2
Q gi|254780784|r 86 ENEILISRMIDRSIRPLFS--KCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYI-NGQ-Y 161 (699)
Q Consensus 86 d~EiL~sRlIDR~lRPLFP--kgf~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~i-dge-~ 161 (699)
.+||-.++|--|+|.|..| +.|.|-+.++..++.+++... +..++|+|+||+-+++|.+.|||++-.|++ +|+ |
T Consensus 396 RREiGHG~LA~Ral~~vlp~~e~fpytiRvVsEi~eSNGSsS--maSVCg~sLaLmdAGVPIk~pVAGIAMGLI~eg~~~ 473 (692)
T COG1185 396 RREIGHGALAERALAPVLPSEEEFPYTIRVVSEILESNGSSS--MASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDKY 473 (692)
T ss_pred CCCCCCCHHHHHHHHHHCCCHHCCCCEEEEEEHHHCCCCCCC--CHHHHHHHHHHHHCCCCCCCCCCCCCCCCEECCCCE
T ss_conf 533467364688886509951007804552201110467412--223455179887578963555543001523248744
Q ss_pred EECCCCC--C-CCCCCEEEEEECCCCHHHHHCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 4368500--0-222101355305443233312444--3248999988753168899999999999998388986447431
Q gi|254780784|r 162 VLNPRLD--E-DQGSLDLFVSGTQDAVLMVELEAN--QLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKD 236 (699)
Q Consensus 162 ViNPt~e--e-~esdLDLvVAGT~d~IlMIE~~A~--EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~~~~Gk~K~~~~~~~ 236 (699)
++---.. | ...|+|.-||||+++|.-..+.-+ .++.+.|-.||..|+++-..+....++-....-++...+.+..
T Consensus 474 ~vLsDI~G~EDhlGDMDFKVAGT~~GiTAlQMDiKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri 553 (692)
T COG1185 474 AVLSDILGDEDHLGDMDFKVAGTDDGITALQMDIKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYAPRI 553 (692)
T ss_pred EEECCCCCCCCCCCCCEEEEECCCCCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCE
T ss_conf 76400266533457732687257677501045566458889999999987999999999999998751143442458724
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCC-HH-----CCHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 25799999999898888874100012248999999999973022310-00-----0026788999999999999998728
Q gi|254780784|r 237 FSKLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEH-SS-----WNEGEIVSVFEDIQAKVVRTVMLDK 310 (699)
Q Consensus 237 ~~~~~~~v~~~~~~~l~~a~~i~~K~eR~~ai~~l~~ei~e~l~ee~-~~-----~~~~~i~~af~~l~k~ivR~~ILee 310 (699)
..- ..-.+++.+.+....|. ++++.++.-....-+. .. .+...++.+ .+....++|+ .+-
T Consensus 554 ~t~------~i~~dKI~dvIG~gGk~-----I~~I~eetg~~IdieddGtv~i~~s~~~~~~~a-k~~I~~i~~e--~ev 619 (692)
T COG1185 554 ETI------KIDPDKIRDVIGPGGKT-----IKAITEETGVKIDIEDDGTVKIAASDGESAKKA-KERIEAITRE--VEV 619 (692)
T ss_pred EEE------CCCHHHHHHCCCCCCCC-----HHHHHHHHCCEEEECCCCCEEEEECCHHHHHHH-HHHHHHHHHH--HCC
T ss_conf 996------13888876321886320-----346557347679845898589995656888999-9999998743--101
Q ss_pred CCCCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCCE
Q ss_conf 8665886775337879984475466700899987976
Q gi|254780784|r 311 KVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQ 347 (699)
Q Consensus 311 g~R~DGR~~dEIRpIs~EvgvLPrvHGSALFtRGETQ 347 (699)
|..-.|+... |-+.-+.++++|--.|..=-.+.-+|
T Consensus 620 g~iy~G~V~r-i~~fGaFv~l~~gkdgl~hiS~~~~~ 655 (692)
T COG1185 620 GEVYEGTVVR-IVDFGAFVELLPGKDGLVHISQLAKE 655 (692)
T ss_pred CCEEEEEEEE-EEECCEEEEECCCCCEEEEEHHHHHH
T ss_conf 5289988999-86412589833896206874353345
No 44
>KOG1067 consensus
Probab=99.64 E-value=5e-15 Score=140.89 Aligned_cols=194 Identities=21% Similarity=0.385 Sum_probs=160.2
Q ss_pred EEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCC-----------CCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCC
Q ss_conf 899999140045467289999789489999972788-----------887777354068665232013367888735789
Q gi|254780784|r 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRS-----------LKDGQDFFPLTVNYQERTYAVGKIPGGYLRRES 82 (699)
Q Consensus 14 r~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~-----------~~~~~dFfPLtVdY~Ek~yAaGkIPGgF~kREg 82 (699)
|+|.-|.+-+-+ +|||.+.+.|+|.|||||+.+.. +.++..| ..+|....||.|.+- |-|
T Consensus 369 R~I~ce~~m~~~-lHGSaLFqRGqTQvlctVtl~s~e~a~klD~l~~~~~~~~F---mLhY~FPPyat~Evg-----kig 439 (760)
T KOG1067 369 RNISCEVDMLKT-LHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGPDNGINF---MLHYEFPPYATNEVG-----KIG 439 (760)
T ss_pred CCCCEECCCCCC-CCCHHHHHCCCEEEEEEEECCCHHHHHHHHHHCCCCCCCEE---EEEECCCCCCCCCCC-----CCC
T ss_conf 354100173222-44114552676059999983897884345530257667538---999615975456430-----146
Q ss_pred CCCHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEC---CC
Q ss_conf 887145311112321267767468868837899998218888778999999999987326882354112355204---77
Q gi|254780784|r 83 RPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYI---NG 159 (699)
Q Consensus 83 rpsd~EiL~sRlIDR~lRPLFPkgf~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~i---dg 159 (699)
.++.+|+-..-|-.|+|-|..|++|.+.+.|..+||++|+... +.+++|-|+||+-+++|...|||+|-+|++ |.
T Consensus 440 ~~nRRE~GhgaLAEkaL~~vlP~dfPftIRv~SeVleSnGSsS--MASvCGGslALmDaGvPv~a~vAGVaiGlvt~td~ 517 (760)
T KOG1067 440 GLNRRELGHGALAEKALLPVLPEDFPFTIRVTSEVLESNGSSS--MASVCGGSLALMDAGVPVSAHVAGVAIGLVTKTDP 517 (760)
T ss_pred CCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEEEEEEECCCCCH--HHHHHCCHHHHHHCCCCCCCCCCEEEEEEEECCCC
T ss_conf 8760004751676644302385458637997536640589516--77663521655416984213213057876761475
Q ss_pred C------EEECCC---CCCCCCCCEEEEEECCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 3------243685---000222101355305443233312444324899998875316889999999999999
Q gi|254780784|r 160 Q------YVLNPR---LDEDQGSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAK 223 (699)
Q Consensus 160 e------~ViNPt---~ee~esdLDLvVAGT~d~IlMIE~~A~EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~~ 223 (699)
+ |-+-.. .|.-..|||.-+|||+++|.-+ .++-+.|.+||..|.++-.+|.+..++-..
T Consensus 518 e~g~i~dyriltDIlGiEd~~GDMDFKiAGt~dGvTA~-----gi~l~Iv~eal~~a~~ar~~Il~~m~k~i~ 585 (760)
T KOG1067 518 EKGEIEDYRILTDILGIEDYNGDMDFKIAGTNDGVTAL-----GIPLKIVMEALQKAREARLQILDIMEKNIN 585 (760)
T ss_pred CCCCCCCCEEEHHHCCHHHHCCCCCEEECCCCCCCEEC-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 54776661431033044541687420320456761132-----774899999987616889999999985268
No 45
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=99.63 E-value=1.1e-15 Score=146.39 Aligned_cols=87 Identities=31% Similarity=0.493 Sum_probs=54.0
Q ss_pred HHHHHCCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CC----CE
Q ss_conf 99985247546867899999994153699828797104886631444547855603259889999997868-99----86
Q gi|254780784|r 609 MIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RG----KI 683 (699)
Q Consensus 609 ~i~~~~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g----~i 683 (699)
..+.+...+++|++++|+|++|.+|||||+|-+|-+||||||||||.|++++++++++||+|+||++++|+ +. ||
T Consensus 191 ~~~~~~~~l~~G~vv~G~V~~i~~~GaFVdl~~GvdGllHiSeiSw~rv~~p~~~~~vGd~v~vkVl~id~e~~~~~~ri 270 (489)
T PRK13806 191 SLATFLEGVKEGDVLEGTVTRLAPFGAFVEIAPGVEGMVHISELSWSRVQQADEAVSVGDRVRVKVLGIGEAPKGKGLRI 270 (489)
T ss_pred HHHHHHHHHCCCCEECEEEEEECCCEEEEEECCCCEEEEEHHHCCCCCCCCHHHEECCCCEEEEEEEEEECCCCCCCEEE
T ss_conf 89999986114880042999975753899937980799983555865668888945169889999999864456665069
Q ss_pred EEEEEECCCCCC
Q ss_conf 668730477878
Q gi|254780784|r 684 KLSMKVVDQNTG 695 (699)
Q Consensus 684 ~lSrk~~~~~~~ 695 (699)
.||.|++.++|-
T Consensus 271 sLs~Kql~~dPW 282 (489)
T PRK13806 271 SLSAKQAGGDPW 282 (489)
T ss_pred EEECCCCCCCHH
T ss_conf 860166788957
No 46
>pfam01138 RNase_PH 3' exoribonuclease family, domain 1. This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.
Probab=99.63 E-value=6.5e-15 Score=139.97 Aligned_cols=123 Identities=42% Similarity=0.632 Sum_probs=104.2
Q ss_pred CEEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCC--CCEEEEECCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf 989999914004546728999978948999997278888777735--406866523201336788873578988714531
Q gi|254780784|r 13 GRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFF--PLTVNYQERTYAVGKIPGGYLRRESRPTENEIL 90 (699)
Q Consensus 13 gr~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~~~~~~dFf--PLtVdY~Ek~yAaGkIPGgF~kREgrpsd~EiL 90 (699)
-|++.+++| +..|||||+.+++|+|.|+|+|....+++...++. .|+|+|+.+.+|.++++ +|+|++++.+
T Consensus 2 ~R~i~~~~g-v~~~a~GSa~v~~G~T~Via~V~~p~~~~~~~~~~~~~l~v~v~~~p~a~~~~~------~~~~~~~~~~ 74 (128)
T pfam01138 2 LRPIEIETG-VLSQADGSALVELGDTKVLATVTGPIEPPNERDFFPGELTVEYEEKPFASGERP------EGRPSEREIE 74 (128)
T ss_pred CCCEEEEEC-CCCCCCEEEEEEECCEEEEEEEECCCCCCCCCCCCCCEEEEEEEECCCCCCCCC------CCCCCHHHHH
T ss_conf 731899969-779988789999899799999970543555567888569999867574355334------6863166899
Q ss_pred HHHHHHCCCCCCCCCC--CCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 1112321267767468--86883789999821888877899999999998732688
Q gi|254780784|r 91 ISRMIDRSIRPLFSKC--YKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLP 144 (699)
Q Consensus 91 ~sRlIDR~lRPLFPkg--f~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIP 144 (699)
.+|+++|.|||+++.. .+..++|.++||+.|+. +-..++||+++||.-++||
T Consensus 75 l~~~l~~~l~~~~~~~~~~~~~I~i~v~vl~~dG~--~~~a~~~A~~~AL~dagiP 128 (128)
T pfam01138 75 LSRLIDRALRPSFPLEGYPRWEIRIDITVLSDDGS--LLDAAINAASLALADAGIP 128 (128)
T ss_pred HHHHHHHHHHHHCCCCCCCCEEEEEEEEEECCCCC--HHHHHHHHHHHHHHHCCCC
T ss_conf 99999999886456044785699999999957999--8999999999999865999
No 47
>TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110 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 of 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 S1 contains the S1 domain that has been found in a large number of RNA-associated proteins. S1 is a prominent component of the Escherichia coli ribosome and is most probably required for translation of most, if not all, natural mRNAs in E. coli in vivo . It has been suggested that S1 is a RNA-binding protein helping polynucleotide phosphorylase (PNPase, known to be phylogenetically related to S1) to degrade mRNA, or helper molecule involved in other RNase activities . Unique among ribosomal proteins, the primary structure of S1 contains four repeating homologous stretches in the central and terminal region of the molecule. S1 is organised into at least two distinct domains; a ribosome-binding domain at the N-terminal region and a nucleic acid-binding domain at the C-terminal region . There may be a flexible region between the two domains permitting free movement of the domains relative to each other. ; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome.
Probab=99.63 E-value=2.2e-15 Score=143.73 Aligned_cols=250 Identities=26% Similarity=0.346 Sum_probs=142.3
Q ss_pred EEEEEEEECCCCCCCHH-----HHHHHHHHHHHHCCCCCCCCCCEEEEEEEEECCEEEEEEECC-CCCCCCC--CCCEEE
Q ss_conf 89998531102785223-----566777798762595022541213320044088289986314-4220136--551001
Q gi|254780784|r 422 TLRIVSEITESDGSSSM-----ATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDIS-GDEDHLG--HMDFKV 493 (699)
Q Consensus 422 tirv~~evl~sngsssm-----a~vc~~slal~dagvp~~~~VaGiamGLi~~~~~~~iLtDI~-G~ED~~G--dMDFKv 493 (699)
.|+|.-+-.+-.-|.+. |.=-.....|-+|-- =++.|-|-=.|++....-|.+ |+. |.+=+|- -.|.|=
T Consensus 68 ~v~V~l~~~~~~~g~~~LS~~ka~r~~~~~~l~~~~~-~~~~V~G~I~~kvekKGGf~V--dl~aGv~AFLP~Sq~d~k~ 144 (534)
T TIGR00717 68 EVEVYLDRVEDRIGETVLSREKAQRKEAWIKLEKAYE-EGSIVEGKIVGKVEKKGGFIV--DLEAGVEAFLPGSQVDVKK 144 (534)
T ss_pred EEEEEEEEECCCCCCCEEECCHHHHHHHHHHHHHHHH-CCCEEEEEEEEEEECCCCEEE--ECCCCEEEECCCCCCCCCC
T ss_conf 7999998442899970230452578889999999861-698456798776605657799--9236817861646046626
Q ss_pred -------EECCCCCEEEECCCCC-----CCC--CH-HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEE
Q ss_conf -------0055651244324536-----556--88-99999999999999999999984356674332244875799997
Q gi|254780784|r 494 -------AGTDSGITAMQMDMKI-----GGI--SE-NIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAI 558 (699)
Q Consensus 494 -------aGT~~GiTa~QmDiK~-----~gi--~~-~il~~al~~A~~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i 558 (699)
.|-+--+.=+.||-|- ..| |. .+|++ +++..|...|+......+- ..-++. |
T Consensus 145 ~~~~~~~~g~~~~f~i~k~d~~rqhrGn~nivvSRr~~lE~---~~~~~r~e~le~l~~g~~v-~GvVk~---------i 211 (534)
T TIGR00717 145 IKDLDSLIGKTLKFKIIKLDKKRQHRGNNNIVVSRRAYLEE---ERSQAREELLEKLKEGEVV-KGVVKN---------I 211 (534)
T ss_pred CCCCCCCCCCEEEEEEEEECCHHCCCCCCCEEEEEEEEECH---HHHHHHHHHHHHCCCCCEE-EEEEEE---------E
T ss_conf 66403034307789999863100125799769941001042---5688898887615558576-108888---------8
Q ss_pred CCCCEEEEECCCCHHHHHHHHHHCC----------EEEEECCEEEEEEECCHHHHHHHHHHH------------HHHCCC
Q ss_conf 7115000037860779989998688----------899808808999968989999999999------------985247
Q gi|254780784|r 559 PPDQIRNVIGMGGKVIRGIVEQTGA----------KVNIDDDGTVKIASSSLAEIEAAREMI------------RSITDV 616 (699)
Q Consensus 559 ~~~ki~~~iG~gG~~ik~i~~~~~~----------~i~i~d~g~v~i~~~~~~~~~~a~~~i------------~~~~~~ 616 (699)
.+-.=-.+|=-|| |.++---|.- -++..|+=.|.|...|++. .+| +.+-..
T Consensus 212 T~fGGv~Fvdlgg--~dGLLH~~d~sWkr~~~P~e~~~~G~~~~Vkv~~~D~~~-----~Ri~LsLK~~~~dPW~~i~~~ 284 (534)
T TIGR00717 212 TDFGGVAFVDLGG--VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEK-----KRISLSLKQLKEDPWEEIEKK 284 (534)
T ss_pred CCCCCEEEEECCC--EEECCCHHHCCCCCCCCCHHHCCCCCEEEEEEEEECCCC-----CEEEEEEECCCCCCCHHHHHH
T ss_conf 8987499998164--332035012147887883464007988999999652657-----607787120588830899983
Q ss_pred CCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCC-CCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEECCCCC
Q ss_conf 54686789999999415369982879710488663144-4547855603259889999997868-998666873047787
Q gi|254780784|r 617 PEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLST-ERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVVDQNT 694 (699)
Q Consensus 617 ~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~-~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~~~~ 694 (699)
..+|+..+|+|+++.||||||||..|-|||+|+||||| +...+|+++|++||+|+|++++||+ ++|++||.|.+.++|
T Consensus 285 ~~~G~~~~G~Vt~~~dyGvFvEi~eGiEGlvH~SE~sW~kk~~~P~~~v~~Gd~Ve~~vl~iD~~~rR~sLsLKQ~~~nP 364 (534)
T TIGR00717 285 FPVGDKIKGRVTNLTDYGVFVEIEEGIEGLVHVSEISWVKKNSHPSKVVKIGDEVEVMVLDIDPERRRISLSLKQCKANP 364 (534)
T ss_pred CCCCCEEEEEEEEECCCEEEEEECCCCEEEECCEEEECCCCCCCHHHCEECCCEEEEEEEEEECCCCEEEEEEECCCCCC
T ss_conf 88997889999988377079992389423423144405788558158054387999999855456784989751067781
No 48
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.62 E-value=1.5e-15 Score=145.08 Aligned_cols=109 Identities=36% Similarity=0.611 Sum_probs=90.9
Q ss_pred EEEEC-CEEEEEEECCHHHHH-HHHHHHHHHCCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHH
Q ss_conf 99808-808999968989999-9999999852475468678999999941536998287971048866314445478556
Q gi|254780784|r 585 VNIDD-DGTVKIASSSLAEIE-AAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSD 662 (699)
Q Consensus 585 i~i~d-~g~v~i~~~~~~~~~-~a~~~i~~~~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d 662 (699)
+.++. +..+-++ -...++ ...+.-..+...+++|++++|+|++|.+|||||.| .|-+||||||+|||.|+.++++
T Consensus 158 ie~d~~~n~vv~S--rR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdi-gGvdGLlHiseiS~~rv~~P~~ 234 (541)
T COG0539 158 LELDKKRNNVVLS--RRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDI-GGVDGLLHISEISWKRVDHPSE 234 (541)
T ss_pred EEECCCCCCEEEE--HHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEECCCEEEEE-CCEEEEEEHHHCCCCCCCCHHH
T ss_conf 9985334847877--177766778887999972478876699999986157479992-5716688647606555589899
Q ss_pred HCCCCCEEEEEEEEECC-CCCEEEEEEECCCCCCC
Q ss_conf 03259889999997868-99866687304778789
Q gi|254780784|r 663 VVKEGDTVWVKLLDFDD-RGKIKLSMKVVDQNTGK 696 (699)
Q Consensus 663 ~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~~~~~~ 696 (699)
++++||+|+||++.+|. +||+.||.|++.+.|-.
T Consensus 235 vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~ 269 (541)
T COG0539 235 VVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWE 269 (541)
T ss_pred HCCCCCEEEEEEEEECCCCCEEEEEEHHCCCCCHH
T ss_conf 53569889999999726788699994650469477
No 49
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=99.61 E-value=5.8e-15 Score=140.36 Aligned_cols=190 Identities=20% Similarity=0.357 Sum_probs=105.1
Q ss_pred EEEECCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC-CEEEEEEECCCCEEEEECC-
Q ss_conf 01005565124432453655688999999999999999999999843566743322448-7579999771150000378-
Q gi|254780784|r 492 KVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFT-PRVEIMAIPPDQIRNVIGM- 569 (699)
Q Consensus 492 KvaGT~~GiTa~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m~~~~~~~~~~~~~~a-p~~~~~~i~~~ki~~~iG~- 569 (699)
-|-|+-+-||-+-.=+-++|+ +|-+||-+.--.-+..|.+-++.-- =....+++++++-+--.|-
T Consensus 496 vv~G~VKnitdyGaFvDLGGv-------------DGLLHitDiSW~Rv~hPse~~~vG~~i~vkVlk~D~e~~riSLglK 562 (863)
T PRK12269 496 SVSGVVKSFTSFGAFIDLGGF-------------DGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLK 562 (863)
T ss_pred EEEEEEEECCCCEEEEECCCC-------------CEEEEEECCCCCCCCCHHHHHCCCCEEEEEEEEECCCCCEEEECCC
T ss_conf 788999831564058961771-------------0146621113578899899712797799999852565451431132
Q ss_pred ---------------CCHHHHHH---HHHHCCEEEEEC--CEEEEEEECCHHHHHH-HHHHH------------------
Q ss_conf ---------------60779989---998688899808--8089999689899999-99999------------------
Q gi|254780784|r 570 ---------------GGKVIRGI---VEQTGAKVNIDD--DGTVKIASSSLAEIEA-AREMI------------------ 610 (699)
Q Consensus 570 ---------------gG~~ik~i---~~~~~~~i~i~d--~g~v~i~~~~~~~~~~-a~~~i------------------ 610 (699)
-|..+++- ..+||+=+++++ +|.|+|+-.+-.+-.. ...++
T Consensus 563 Ql~~dPW~~i~~ky~vg~~v~gkVtnitdyGaFVEle~GiEGLvHvSEmsWtkk~~~P~k~v~~GdeVev~VLeID~ekr 642 (863)
T PRK12269 563 HFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAG 642 (863)
T ss_pred CCCCCCHHHHHHHCCCCCEEEEEEEEEECCCEEEEECCCCEEEEEEHHHCCCCCCCCHHHCCCCCCEEEEEEEEEECCCC
T ss_conf 17789767888638899989999999744656999638925788702502023679979807689779999998803226
Q ss_pred --------------HHHCCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCC-CCCCCHHHHCCCCCEEEEEEE
Q ss_conf --------------98524754686789999999415369982879710488663144-454785560325988999999
Q gi|254780784|r 611 --------------RSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLST-ERVAKTSDVVKEGDTVWVKLL 675 (699)
Q Consensus 611 --------------~~~~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~-~~v~~~~d~~~~Gd~i~vk~~ 675 (699)
+.+...-.+|.+++|+|++|.+||+||+|-+|-|||+|+|.||| ++.++....+|.||+|++|++
T Consensus 643 RISLg~Kq~~~NPW~~~~~ky~vG~~v~g~I~nitdFGiFv~le~gIDGlvH~sDlSW~~~~~~~~~~~kkGd~ve~kVL 722 (863)
T PRK12269 643 RVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVI 722 (863)
T ss_pred EEEEEECCCCCCCHHHHHHHCCCCCEEEEEEEEEECEEEEEECCCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEE
T ss_conf 78544101668849999976899898999999853308999747993678982106767877265662578987999999
Q ss_pred EECC-CCCEEEEEEECCCCC
Q ss_conf 7868-998666873047787
Q gi|254780784|r 676 DFDD-RGKIKLSMKVVDQNT 694 (699)
Q Consensus 676 ~~d~-~g~i~lSrk~~~~~~ 694 (699)
+||. +-||+|+.|+|.++|
T Consensus 723 ~Id~ekeRIsLGiKQL~~DP 742 (863)
T PRK12269 723 ECDPQARRIRLGVKQLSDNP 742 (863)
T ss_pred EECCCCCEEEEECCCCCCCC
T ss_conf 97476577774010065787
No 50
>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=99.60 E-value=3.7e-15 Score=142.02 Aligned_cols=73 Identities=34% Similarity=0.574 Sum_probs=69.9
Q ss_pred CCCCEEEEEEEEEEECCEEEECC-CCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEEC
Q ss_conf 46867899999994153699828-797104886631444547855603259889999997868-99866687304
Q gi|254780784|r 618 EVNKIYKGQVVKVMDFGAFVHFC-GARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVV 690 (699)
Q Consensus 618 e~g~~y~~~v~~i~~fGafve~~-~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~ 690 (699)
++|++|+|+|++|.+||+||++. ++.+||||+|||+|.|++++++++++||+|+||++++|+ ++||.||.|+.
T Consensus 1 kVG~~v~G~V~~i~~fG~FV~l~g~~i~GLvHiSels~~~~~~~~~~~~~Gd~V~vkVl~iD~e~~rI~LSiKa~ 75 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred CCCCEEEEEEEEEECEEEEEEECCCCEEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEEEEEEECC
T ss_conf 998999999999964178999678980799887881756568988916899999999999989999999898415
No 51
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.60 E-value=2e-15 Score=144.12 Aligned_cols=79 Identities=38% Similarity=0.650 Sum_probs=75.0
Q ss_pred CCCCCCCEEEEEEEEEEECCEEEECC--CCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEECC
Q ss_conf 47546867899999994153699828--797104886631444547855603259889999997868-998666873047
Q gi|254780784|r 615 DVPEVNKIYKGQVVKVMDFGAFVHFC--GARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVVD 691 (699)
Q Consensus 615 ~~~e~g~~y~~~v~~i~~fGafve~~--~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~ 691 (699)
.-||+|+++.|+|++|.+|||||+|+ +|.+||+|+||+++.||.++.|++++||++.|||+.+|+ +|+|.||.|.+.
T Consensus 4 ~~Pe~g~~v~~~V~~i~~~Ga~v~l~ey~~~eG~i~isEis~~~v~~i~d~~k~G~~v~~kVi~vd~~kg~IdLS~k~Vs 83 (262)
T PRK03987 4 EWPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVCKVIRVDPKKGHIDLSLKRVN 83 (262)
T ss_pred CCCCCCCEEEEEEEEEECCEEEEEECCCCCCCEEEEHHHCCHHHHHCHHHHCCCCCEEEEEEEEECCCCCEEEEECCCCC
T ss_conf 89999988999999995667999935659931678879834677519998515898899999988387887871104499
Q ss_pred CC
Q ss_conf 78
Q gi|254780784|r 692 QN 693 (699)
Q Consensus 692 ~~ 693 (699)
+.
T Consensus 84 ~~ 85 (262)
T PRK03987 84 EH 85 (262)
T ss_pred HH
T ss_conf 89
No 52
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]
Probab=99.60 E-value=4.1e-12 Score=117.19 Aligned_cols=225 Identities=20% Similarity=0.328 Sum_probs=168.9
Q ss_pred HHHHHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEE
Q ss_conf 99999999872886658867753378799844754667008999879768999981686521223344544203587740
Q gi|254780784|r 299 QAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHY 378 (699)
Q Consensus 299 ~k~ivR~~ILeeg~R~DGR~~dEIRpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHY 378 (699)
.++.+. ..++.|.|+|||+++|.|||++++|++|++.|||+.+-|.||++|-+..+.... ..|+... --|..+-
T Consensus 11 ~~~~i~-~ll~~g~R~DGR~~~efR~leI~~~vi~ka~GSa~VklG~Tqvv~gvK~eig~P--f~DtP~e---G~~~~n~ 84 (272)
T COG2123 11 KREYIL-NLLKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEIGEP--FPDTPNE---GVLVVNV 84 (272)
T ss_pred HHHHHH-HHHCCCCCCCCCCCCCCCCEEEEECCEECCCCCEEEEECCEEEEEEEECCCCCC--CCCCCCC---CEEEEEE
T ss_conf 789999-874037256898821231338895714247885799826808999997245788--8899877---5577554
Q ss_pred C-----CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC--------CCCCCCCEEEEEEEEECCCCCCCHHHHHHHHH
Q ss_conf 5-----8875445334556765024679999999874107--------86446873899985311027852235667777
Q gi|254780784|r 379 N-----FLPCATGEVSRMGAPSRREIGHGRLARRAIHPVL--------PQTAQFPYTLRIVSEITESDGSSSMATVCGSS 445 (699)
Q Consensus 379 N-----FPpfsvGE~~~~~~~~RREiGHg~la~ral~~~~--------P~~~~~p~tirv~~evl~sngsssma~vc~~s 445 (699)
. .|.|.. |.|+-++|.-.+++.|.|+..- ..+..--+.|++..-||.++|+--=|+.-|+-
T Consensus 85 El~Plas~~fE~------Gppde~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~Daa~lA~~ 158 (272)
T COG2123 85 ELSPLASPSFEP------GPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLIDAASLAAV 158 (272)
T ss_pred EEECCCCCCCCC------CCCCHHHHHHHHHHHHHHHHCCCCCHHHEEEECCCEEEEEEEEEEEECCCCCHHHHHHHHHH
T ss_conf 660232455468------99960178999999998876167565451575398899999989998689978989999999
Q ss_pred HHHHHCCCC----------------------CCCCCCEEEEEEEEECCEEEEEEECCCCCCCCCCCCEEEEECCCC-CEE
Q ss_conf 987625950----------------------225412133200440882899863144220136551001005565-124
Q gi|254780784|r 446 LALMDAGVP----------------------ISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSG-ITA 502 (699)
Q Consensus 446 lal~dagvp----------------------~~~~VaGiamGLi~~~~~~~iLtDI~G~ED~~GdMDFKvaGT~~G-iTa 502 (699)
.|||.+.+| +..++-.+.+..| ++ .++.|=.=.|...+|--.-|.-+.+| |.+
T Consensus 159 AAL~~t~vP~~~~~~~~~~v~~~~~~~~pl~~~~~pi~vt~a~i---g~-~lvvDPtleEe~v~d~~ltit~~~~~~Iv~ 234 (272)
T COG2123 159 AALLNTRVPKAVEVGDGEIVIEVEEEPVPLPVSNPPISVTFAKI---GN-VLVVDPSLEEELVADGRLTITVNEDGEIVA 234 (272)
T ss_pred HHHHHCCCCCEEECCCCCEEECCCCCCCCCCCCCCCEEEEEEEE---CC-EEEECCCCCHHHHCCCEEEEEECCCCCEEE
T ss_conf 99974679704532785056315677744556787569999998---88-898589803565237139999979985999
Q ss_pred EECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 43245365568899999999999999999999984356
Q gi|254780784|r 503 MQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLS 540 (699)
Q Consensus 503 ~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m~~~~~ 540 (699)
+|-=- ..-++.+.+.+++++|....-++++...+.+.
T Consensus 235 iqK~g-~~~~~~~~~~~~~~~A~~~~~kl~~~~~~~L~ 271 (272)
T COG2123 235 IQKVG-GGSITESDLEKALKTALSKAEKLREALKEALK 271 (272)
T ss_pred EEECC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 99718-87678999999999999999999999998633
No 53
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.59 E-value=3.2e-14 Score=134.40 Aligned_cols=109 Identities=37% Similarity=0.552 Sum_probs=87.9
Q ss_pred EEEECC-EEEEEEECCHHHHHH-HHHHHHHHCCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHH
Q ss_conf 998088-089999689899999-999999852475468678999999941536998287971048866314445478556
Q gi|254780784|r 585 VNIDDD-GTVKIASSSLAEIEA-AREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSD 662 (699)
Q Consensus 585 i~i~d~-g~v~i~~~~~~~~~~-a~~~i~~~~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d 662 (699)
++++.+ ..+.++- +..++. ....-..+....++|++++|+|++|.+|||||+| .|-+||+|+|+|+|.|+.++.+
T Consensus 158 i~vd~~~~~ivlS~--K~~l~~~~~~~~~~~~~~l~~Gdvv~G~V~~i~~~G~FV~l-ggv~glvh~sels~~~~~~~~~ 234 (390)
T PRK06676 158 IELDPEKNRVILSR--RAVVEEERAEKKKELLSSLKEGDVVEGKVARLTDFGAFVDI-GGVDGLVHISELSHERVNKPSE 234 (390)
T ss_pred EEEECCCCCEEECC--HHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCEEEEC-CCEEEEEEECCCCHHHHCCHHH
T ss_conf 99853788289703--24546667665766776346898478999999456369980-7767999961057333359888
Q ss_pred HCCCCCEEEEEEEEECC-CCCEEEEEEECCCCCCC
Q ss_conf 03259889999997868-99866687304778789
Q gi|254780784|r 663 VVKEGDTVWVKLLDFDD-RGKIKLSMKVVDQNTGK 696 (699)
Q Consensus 663 ~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~~~~~~ 696 (699)
++++||+|+|+++++|. ++||.||.|+++++|-.
T Consensus 235 ~~k~G~~v~~~Vl~id~~~~ri~LslK~l~~dP~~ 269 (390)
T PRK06676 235 VVSVGQEVEVKVLSIDEETERISLSLKDTLPGPWE 269 (390)
T ss_pred HHCCCCEEEEEEEEEECCCCEEEEEEEECCCCCHH
T ss_conf 30479757999999946788999998326789567
No 54
>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=99.57 E-value=1.2e-14 Score=137.82 Aligned_cols=64 Identities=38% Similarity=0.606 Sum_probs=60.9
Q ss_pred CCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEE
Q ss_conf 475468678999999941536998287971048866314445478556032598899999978689986668
Q gi|254780784|r 615 DVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLS 686 (699)
Q Consensus 615 ~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~lS 686 (699)
.++|+|++|+|+|++|++|||||+|.|+++||+|+|+++++ +++||+|.||+++||++|||+|+
T Consensus 12 ~dlevG~~y~G~V~~v~~fGaFV~l~~~~~GLiHiS~l~~~--------~~vGD~V~VkV~~I~~~Gki~L~ 75 (77)
T cd04473 12 EDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRD--------YEVGDEVIVQVTDIPENGNIDLI 75 (77)
T ss_pred CCCCCCCEEEEEEEEEEECCEEEECCCCCEEEEEEHHCCCC--------CCCCCEEEEEEEEECCCCCEEEE
T ss_conf 03523999999998896628899926998796893166687--------89999999999999999979318
No 55
>KOG1069 consensus
Probab=99.54 E-value=2.2e-13 Score=127.61 Aligned_cols=204 Identities=22% Similarity=0.346 Sum_probs=148.4
Q ss_pred CEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCHHHH
Q ss_conf 33787998447546670089998797689999816865212233445442035877405887544533455676502467
Q gi|254780784|r 321 TVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIG 400 (699)
Q Consensus 321 EIRpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfsvGE~~~~~~~~RREiG 400 (699)
.+|++-||.++|.|+||||-|..|.|.++|.|+ |+..---+-+..+ +.-|. |-=....|-.+++|--
T Consensus 4 ~lr~~~cei~iLsr~dGSs~fsqgdT~V~c~V~-GP~dvk~r~E~~~-----katle-------Vi~rp~~G~~~~~eK~ 70 (217)
T KOG1069 4 RLRGIACEISILSRPDGSSEFSQGDTKVICSVY-GPIDVKARQEDPE-----KATLE-------VIWRPKSGVNGTVEKV 70 (217)
T ss_pred HHHHHHHHHCEECCCCCCCCEECCCCEEEEEEE-CCCCHHHCCCCCH-----HCEEE-------EEEECCCCCCHHHHHH
T ss_conf 444355663332379986201159817999910-7863331214710-----03589-------9971256762279999
Q ss_pred HHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEECCEEEEEEECC
Q ss_conf 99999998741078644687389998531102785223566777798762595022541213320044088289986314
Q gi|254780784|r 401 HGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDIS 480 (699)
Q Consensus 401 Hg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp~~~~VaGiamGLi~~~~~~~iLtDI~ 480 (699)
..++.++.|.+++-.+-++..+|.|++.|++++||+...+|+|++|||.|||+||+..-+||++-+..|+ +.++ |=.
T Consensus 71 ~e~iI~~tl~~~I~l~l~Prt~iqVsiqvv~ddgs~LacaINaAclALvDaGIpl~~mfcai~~~~~~d~--~lv~-Dpt 147 (217)
T KOG1069 71 LERIIRKTLSKAIILELYPRTTIQVSIQVVEDDGSTLACAINAACLALVDAGIPLRSMFCAISCALHEDG--VLVL-DPT 147 (217)
T ss_pred HHHHHHHHHHHHHEEEECCCCEEEEEEEEEECCCCCHHHHHHHHHHHHHHCCCCHHHHHHHCEEEEECCC--CEEE-CCC
T ss_conf 9999999987755132157746999999993588405789988999998569856774542047884376--2897-871
Q ss_pred CCCCC--CCCCCEEEEECCCCCEE-EECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 42201--36551001005565124-432453655688999999999999999999999843566
Q gi|254780784|r 481 GDEDH--LGHMDFKVAGTDSGITA-MQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSE 541 (699)
Q Consensus 481 G~ED~--~GdMDFKvaGT~~GiTa-~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m~~~~~~ 541 (699)
-.+-- .+---|-+.++..|--- +-||.+ +-.+.+-|...|+.|.....++-..|.+.+..
T Consensus 148 ~~qek~~~~~~~lsf~~~~~~~~~vi~s~t~-G~~~~d~lf~~le~a~~~~~~~f~f~r~~~q~ 210 (217)
T KOG1069 148 AKQEKISTARATLSFEGGSLGEPKVIISETN-GEKSEDQLFYVLELAQAAAQSLFPFYREVLQR 210 (217)
T ss_pred HHHHHHHHCEEEEEEECCCCCCCCEEEEECC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 7765442224899983477887625887246-88888999999985378899999999999986
No 56
>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=99.54 E-value=1.6e-14 Score=136.80 Aligned_cols=61 Identities=57% Similarity=0.952 Sum_probs=59.9
Q ss_pred CEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHHH
Q ss_conf 7579999771150000378607799899986888998088089999689899999999999
Q gi|254780784|r 551 PRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIR 611 (699)
Q Consensus 551 p~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~ 611 (699)
||+++++||++|||+||||||||||.|+++|||+|||+|+|.|+|||+|++++++|+++|+
T Consensus 1 P~i~~~~I~~dkIg~vIGpGGk~Ik~I~e~tg~~I~I~d~G~V~I~~~~~~~~~~A~~~Ie 61 (61)
T cd02393 1 PRIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDDGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred CEEEEEEECHHHHHHHCCCCCHHHHHHHHHHCCEEEECCCCEEEEEECCHHHHHHHHHHHC
T ss_conf 9489999698998764488608999999988988998389589999899999999999749
No 57
>TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110 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 of 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 S1 contains the S1 domain that has been found in a large number of RNA-associated proteins. S1 is a prominent component of the Escherichia coli ribosome and is most probably required for translation of most, if not all, natural mRNAs in E. coli in vivo . It has been suggested that S1 is a RNA-binding protein helping polynucleotide phosphorylase (PNPase, known to be phylogenetically related to S1) to degrade mRNA, or helper molecule involved in other RNase activities . Unique among ribosomal proteins, the primary structure of S1 contains four repeating homologous stretches in the central and terminal region of the molecule. S1 is organised into at least two distinct domains; a ribosome-binding domain at the N-terminal region and a nucleic acid-binding domain at the C-terminal region . There may be a flexible region between the two domains permitting free movement of the domains relative to each other. ; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome.
Probab=99.50 E-value=1.2e-13 Score=129.75 Aligned_cols=89 Identities=35% Similarity=0.588 Sum_probs=76.8
Q ss_pred HHHHHHHCCCCCCCCEEEEEEEEEEECC--EEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCE
Q ss_conf 9999985247546867899999994153--699828797104886631444547855603259889999997868-9986
Q gi|254780784|r 607 REMIRSITDVPEVNKIYKGQVVKVMDFG--AFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKI 683 (699)
Q Consensus 607 ~~~i~~~~~~~e~g~~y~~~v~~i~~fG--afve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i 683 (699)
.+.=+.+...++.|....|.|++|.||| |||++ .|-|||||+++|||.|++||+.++++||+|+||++..|. ++||
T Consensus 188 ~~~r~e~le~l~~g~~v~GvVk~iT~fGGv~Fvdl-gg~dGLLH~~d~sWkr~~~P~e~~~~G~~~~Vkv~~~D~~~~Ri 266 (534)
T TIGR00717 188 SQAREELLEKLKEGEVVKGVVKNITDFGGVAFVDL-GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKKRI 266 (534)
T ss_pred HHHHHHHHHHCCCCCEEEEEEEEECCCCCEEEEEC-CCEEECCCHHHCCCCCCCCCHHHCCCCCEEEEEEEEECCCCCEE
T ss_conf 88898887615558576108888889874999981-64332035012147887883464007988999999652657607
Q ss_pred EEEEEECCCCCCC
Q ss_conf 6687304778789
Q gi|254780784|r 684 KLSMKVVDQNTGK 696 (699)
Q Consensus 684 ~lSrk~~~~~~~~ 696 (699)
.||.|++.++|=.
T Consensus 267 ~LsLK~~~~dPW~ 279 (534)
T TIGR00717 267 SLSLKQLKEDPWE 279 (534)
T ss_pred EEEEECCCCCCCH
T ss_conf 7871205888308
No 58
>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=99.50 E-value=5.9e-14 Score=132.21 Aligned_cols=68 Identities=35% Similarity=0.553 Sum_probs=62.7
Q ss_pred CCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCC-CCCCHHHHCCCCCEEEEEEEEECC-CCCEEE
Q ss_conf 46867899999994153699828797104886631444-547855603259889999997868-998666
Q gi|254780784|r 618 EVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTE-RVAKTSDVVKEGDTVWVKLLDFDD-RGKIKL 685 (699)
Q Consensus 618 e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~-~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~l 685 (699)
.+|++|+|+|++|.+|||||+|.||.+||||||||+|. +..++.+++++||+++||++++|+ +.||+|
T Consensus 2 ~~G~~v~G~V~~It~fG~FV~i~~g~eGLvHiSelsw~~~~~~p~~~~~~Gd~v~vkIl~iD~e~~rIsL 71 (72)
T cd05689 2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISL 71 (72)
T ss_pred CCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEECC
T ss_conf 8899999999899476239996699389999766316546679636038999999999999599799538
No 59
>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=99.49 E-value=1e-13 Score=130.24 Aligned_cols=72 Identities=32% Similarity=0.469 Sum_probs=69.3
Q ss_pred CCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEECC
Q ss_conf 867899999994153699828797104886631444547855603259889999997868-998666873047
Q gi|254780784|r 620 NKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVVD 691 (699)
Q Consensus 620 g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~ 691 (699)
|++++|+|++|.+||+||++-+|.+||+|+|||+|.|+.++.+.+++||+|++|++++|+ ++|+.||.|+|.
T Consensus 1 G~iV~G~V~~i~~~G~fV~l~~~v~G~ih~sels~~~~~~~~~~~~vGd~v~akIi~iD~~~~ri~LSiKalE 73 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAKE 73 (73)
T ss_pred CCEEEEEEEEEECCCEEEEECCCCEEEEEHHHCCCCHHHCHHHCCCCCCEEEEEEEEEECCCCEEEEEEEECC
T ss_conf 9999999999977868999289969999989978211329254389999999999999788999986742459
No 60
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=99.49 E-value=8.4e-14 Score=130.95 Aligned_cols=67 Identities=46% Similarity=0.737 Sum_probs=65.4
Q ss_pred CCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEE
Q ss_conf 867899999994153699828797104886631444547855603259889999997868-9986668
Q gi|254780784|r 620 NKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLS 686 (699)
Q Consensus 620 g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lS 686 (699)
|++|+|+|++|.+|||||+|-+|.+||||+|||++.++.++++++++||+|+||++++|+ ++||.||
T Consensus 1 G~iv~G~V~~i~~fG~FV~l~~~~~GLvhisels~~~~~~~~~~~~vGd~v~~kVi~id~e~~ri~LS 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEECEEEEEEECCCCEEEEECHHHCCCCCCCHHHCCCCCCEEEEEEEEEECCCCEEECC
T ss_conf 99999999999652899991499789998189767876798685799999999999998999988779
No 61
>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=99.48 E-value=1.1e-13 Score=130.14 Aligned_cols=66 Identities=39% Similarity=0.655 Sum_probs=62.5
Q ss_pred CCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCC-CCCCCHHHHCCCCCEEEEEEEEECC-CCCEEE
Q ss_conf 86789999999415369982879710488663144-4547855603259889999997868-998666
Q gi|254780784|r 620 NKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLST-ERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKL 685 (699)
Q Consensus 620 g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~-~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~l 685 (699)
|++|+|+|++|.+|||||++.+|.+||+|+|||+| ++++++++++++||+|+||++++|. +.||+|
T Consensus 1 G~~v~G~V~~i~~fG~FV~l~~gieGLvHiselsw~~~~~~~~~~~~~Gd~V~vkVl~iD~e~~risL 68 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68 (69)
T ss_pred CCEEEEEEEEECCCEEEEEECCCCEEEEEHHHHCCCCCCCCHHHCCCCCCEEEEEEEEEECCCCEECC
T ss_conf 99999999999131899997699659999488245666679768258999999999999798688638
No 62
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]
Probab=99.46 E-value=1.8e-11 Score=112.04 Aligned_cols=198 Identities=24% Similarity=0.317 Sum_probs=150.3
Q ss_pred EEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCC----CCCCCCCCCCEEEEECCCCCCCCCCCCCCCCC-CCCCHHH
Q ss_conf 899999140045467289999789489999972788----88777735406866523201336788873578-9887145
Q gi|254780784|r 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRS----LKDGQDFFPLTVNYQERTYAVGKIPGGYLRRE-SRPTENE 88 (699)
Q Consensus 14 r~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~----~~~~~dFfPLtVdY~Ek~yAaGkIPGgF~kRE-grpsd~E 88 (699)
|++.+++|.+-+ |+||+.+++|+|.|+|-+-+.-. -++..+.| +++-+= -|--+..+| |.|+|.+
T Consensus 34 R~leI~~~vi~k-a~GSa~VklG~Tqvv~gvK~eig~Pf~DtP~eG~~--~~n~El-------~Plas~~fE~Gppde~a 103 (272)
T COG2123 34 RPLEIETGVIPK-ANGSALVKLGNTQVVVGVKAEIGEPFPDTPNEGVL--VVNVEL-------SPLASPSFEPGPPDELA 103 (272)
T ss_pred CCEEEEECCEEC-CCCCEEEEECCEEEEEEEECCCCCCCCCCCCCCEE--EEEEEE-------ECCCCCCCCCCCCCHHH
T ss_conf 133889571424-78857998268089999972457888899877557--755466-------02324554689996017
Q ss_pred HHHHHHHHCCCCC----------CCCCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC--------------
Q ss_conf 3111123212677----------6746886883789999821888877899999999998732688--------------
Q gi|254780784|r 89 ILISRMIDRSIRP----------LFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLP-------------- 144 (699)
Q Consensus 89 iL~sRlIDR~lRP----------LFPkgf~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIP-------------- 144 (699)
|..+|++||.||- .++.....=+.+-+.||++|++ +--+|.+|+=|||.--.+|
T Consensus 104 ielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGn--l~Daa~lA~~AAL~~t~vP~~~~~~~~~~v~~~ 181 (272)
T COG2123 104 IELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGN--LIDAASLAAVAALLNTRVPKAVEVGDGEIVIEV 181 (272)
T ss_pred HHHHHHHHHHHHHCCCCCHHHEEEECCCEEEEEEEEEEEECCCCC--HHHHHHHHHHHHHHHCCCCCEEECCCCCEEECC
T ss_conf 899999999887616756545157539889999998999868997--898999999999974679704532785056315
Q ss_pred --------CCCCEEEEEEEECCCCEEECCCCCCC-CCCCEEEEEECCCC--HHHHHCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf --------23541123552047732436850002-22101355305443--23331244432489999887531688999
Q gi|254780784|r 145 --------FEGPVVGAQVDYINGQYVLNPRLDED-QGSLDLFVSGTQDA--VLMVELEANQLSEDVVLDAIIFGHNECKP 213 (699)
Q Consensus 145 --------f~GPVaaVRVG~idge~ViNPt~ee~-esdLDLvVAGT~d~--IlMIE~~A~EVsEe~mleAI~~Ahe~Ik~ 213 (699)
.+.+.=+|-++.+++.+++.||.+|+ -++--|.+.-++++ +-|--+|..-+.++++.+|++.|.+...+
T Consensus 182 ~~~~~pl~~~~~pi~vt~a~ig~~lvvDPtleEe~v~d~~ltit~~~~~~Iv~iqK~g~~~~~~~~~~~~~~~A~~~~~k 261 (272)
T COG2123 182 EEEPVPLPVSNPPISVTFAKIGNVLVVDPSLEEELVADGRLTITVNEDGEIVAIQKVGGGSITESDLEKALKTALSKAEK 261 (272)
T ss_pred CCCCCCCCCCCCCEEEEEEEECCEEEECCCCCHHHHCCCEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 67774455678756999999888898589803565237139999979985999997188767899999999999999999
Q ss_pred HHHHHHHHHH
Q ss_conf 9999999999
Q gi|254780784|r 214 VIEAISKLAK 223 (699)
Q Consensus 214 iI~~Q~eL~~ 223 (699)
+++...+..+
T Consensus 262 l~~~~~~~L~ 271 (272)
T COG2123 262 LREALKEALK 271 (272)
T ss_pred HHHHHHHHHC
T ss_conf 9999998633
No 63
>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=99.45 E-value=2.6e-13 Score=127.00 Aligned_cols=66 Identities=47% Similarity=0.734 Sum_probs=63.1
Q ss_pred CCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEE
Q ss_conf 6867899999994153699828797104886631444547855603259889999997868-998666
Q gi|254780784|r 619 VNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKL 685 (699)
Q Consensus 619 ~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~l 685 (699)
.|++|+|+|++|.+|||||++ .|.+||||+|||+|.|++++.+++++||+|++|++++|+ ++||+|
T Consensus 1 eG~iv~g~V~~i~~fG~FV~l-~gi~Glihisels~~~~~~~~~~~k~Gd~v~~kVi~iD~~k~rIsL 67 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISL 67 (68)
T ss_pred CCCEEEEEEEEEECCEEEEEE-CCEEEEEECHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEECC
T ss_conf 999999999999563889997-9989999843646666689889147999999999999999798649
No 64
>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=99.44 E-value=3.6e-13 Score=125.76 Aligned_cols=69 Identities=29% Similarity=0.392 Sum_probs=67.2
Q ss_pred CCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEE
Q ss_conf 867899999994153699828797104886631444547855603259889999997868-998666873
Q gi|254780784|r 620 NKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMK 688 (699)
Q Consensus 620 g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk 688 (699)
|.++.|+|++|.+|||||++.+|.+||+|+||+++.+++++++++++||+|+|+++++|+ ++|+.||.|
T Consensus 1 G~vv~G~V~~i~~~G~fV~~~~~i~Glvp~seis~~~v~~p~~~f~~Gq~V~v~Vl~vd~~~~ri~LS~K 70 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEECCCEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEEEEECC
T ss_conf 9999999999981718999489969998989928320289899377999999999998089999999719
No 65
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.41 E-value=8.1e-13 Score=122.95 Aligned_cols=73 Identities=29% Similarity=0.403 Sum_probs=70.1
Q ss_pred CCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEE
Q ss_conf 47546867899999994153699828797104886631444547855603259889999997868-99866687
Q gi|254780784|r 615 DVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSM 687 (699)
Q Consensus 615 ~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSr 687 (699)
.++++|.++.|+|++|.+||+||++.+|.+||+|+|++++.++.++++.+++||.|+|+++.+|+ ++||.||.
T Consensus 10 ~~lk~G~iv~G~V~~i~~~G~FV~l~~~v~Glv~~s~ls~~~~~~~~~~~~vGq~V~~~V~~iD~e~~ri~LSl 83 (83)
T cd04461 10 SDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred HHCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEEEEEC
T ss_conf 78799999999999992781999956994899899996864226989945599999999999958988788759
No 66
>pfam00575 S1 S1 RNA binding domain. The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.
Probab=99.40 E-value=1.6e-12 Score=120.53 Aligned_cols=73 Identities=41% Similarity=0.668 Sum_probs=70.8
Q ss_pred CCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEE
Q ss_conf 7546867899999994153699828797104886631444547855603259889999997868-998666873
Q gi|254780784|r 616 VPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMK 688 (699)
Q Consensus 616 ~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk 688 (699)
.|++|++++|+|++|.+||+||+|.+|.+||+|+|++++.++.++++.+++||+++++++++|+ ++|+.||+|
T Consensus 1 ~~~~G~iv~G~V~~i~~~G~fV~l~~~~~g~v~~s~ls~~~~~~~~~~~~~G~~v~~~V~~vd~~~~~i~lS~k 74 (74)
T pfam00575 1 KPEEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVLKVDKERGRIILSIR 74 (74)
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCHHHHHCCCCEEEEEEEEEECCCCEEEEEEC
T ss_conf 98899999999999987759999789979999844613655567768305999999999999999999999839
No 67
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.39 E-value=4.6e-13 Score=124.91 Aligned_cols=80 Identities=39% Similarity=0.659 Sum_probs=75.3
Q ss_pred CCCCCCCCEEEEEEEEEEECCEEEEC--CCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEEC
Q ss_conf 24754686789999999415369982--8797104886631444547855603259889999997868-99866687304
Q gi|254780784|r 614 TDVPEVNKIYKGQVVKVMDFGAFVHF--CGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVV 690 (699)
Q Consensus 614 ~~~~e~g~~y~~~v~~i~~fGafve~--~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~ 690 (699)
-.-|++|++.-|+|++|.+|||||+| +||++|++||||++..||.++.|++++||++-+||+.+|+ +|.|.||.|.+
T Consensus 6 ~~~PeeGEiVv~tV~~V~~~GA~v~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV 85 (269)
T COG1093 6 REYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRV 85 (269)
T ss_pred CCCCCCCCEEEEEEEEEECCCCEEEEECCCCEEEEEEHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCEEEEEHHHC
T ss_conf 68998886899999986046427984205996226778998778998899986169869999988868777476254338
Q ss_pred CCC
Q ss_conf 778
Q gi|254780784|r 691 DQN 693 (699)
Q Consensus 691 ~~~ 693 (699)
.+.
T Consensus 86 ~~~ 88 (269)
T COG1093 86 TEH 88 (269)
T ss_pred CHH
T ss_conf 787
No 68
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.38 E-value=1.5e-12 Score=120.77 Aligned_cols=72 Identities=26% Similarity=0.275 Sum_probs=69.5
Q ss_pred CCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEE
Q ss_conf 546867899999994153699828797104886631444547855603259889999997868-998666873
Q gi|254780784|r 617 PEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMK 688 (699)
Q Consensus 617 ~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk 688 (699)
+++|.++.|+|+++.+||+||+|-++.+||+||||+++..++++++++++||.++|+++++|. +.||+||.|
T Consensus 1 lkvG~~l~G~Vt~V~~~g~fV~L~~~~~Glvhisel~dd~~~~~~~~~~~g~~V~v~Vl~VD~~~krI~LSlr 73 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCCEEEEEEEEECCCEEEEEECCCCEEEEEHHHHCCCCCCCCHHHCCCCCEEEEEEEEEECCCCEEEEECC
T ss_conf 9889899999999888879999089947999989930460138175168999999999999888998988619
No 69
>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=99.37 E-value=1.4e-12 Score=120.96 Aligned_cols=67 Identities=25% Similarity=0.400 Sum_probs=65.4
Q ss_pred CCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEE
Q ss_conf 867899999994153699828797104886631444547855603259889999997868-9986668
Q gi|254780784|r 620 NKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLS 686 (699)
Q Consensus 620 g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lS 686 (699)
|.+.+|+|++|.+|||||+|-++.+||+|||||++.+|.++.+++++||.|++|++++|+ +|||.||
T Consensus 1 G~~v~G~V~~i~~~G~FV~l~~~~~glVhiselsd~fVkd~~~~f~vGq~V~~kV~~iD~~~~ri~LS 68 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEECCCCEEEEECCCCEEEEEHHHHCHHHHCCHHHHCCCCCEEEEEEEEEECCCCEEECC
T ss_conf 99989999980364079991799679999599172356499891799999999999982875867359
No 70
>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=99.34 E-value=3.1e-12 Score=118.16 Aligned_cols=68 Identities=25% Similarity=0.404 Sum_probs=65.8
Q ss_pred CCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEE
Q ss_conf 867899999994153699828797104886631444547855603259889999997868-99866687
Q gi|254780784|r 620 NKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSM 687 (699)
Q Consensus 620 g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSr 687 (699)
|.+.+|+|+++.+||+||+|.+|-+||+|+|+|++.++.++++.+++||+|++|++++|+ +.||.||+
T Consensus 1 G~iv~G~V~~i~~fG~fV~l~~~i~Glv~~s~lsd~~v~~p~~~fk~G~~Vk~rVl~vD~~~~ri~LSl 69 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEECCCEEEEEECCCEEEEEEHHHHCCCCCCCHHHCCCCCCEEEEEEEEEECCCCEEEEEC
T ss_conf 999999999973842799957990699878990865206988908999999999999948879988659
No 71
>pfam03726 PNPase Polyribonucleotide nucleotidyltransferase, RNA binding domain. This family contains the RNA binding domain of Polyribonucleotide nucleotidyltransferase (PNPase) PNPase is involved in mRNA degradation in a 3'-5' direction.
Probab=99.26 E-value=4e-11 Score=109.16 Aligned_cols=80 Identities=35% Similarity=0.558 Sum_probs=76.0
Q ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 79999999989888887410001224899999999997302231000002678899999999999999872886658867
Q gi|254780784|r 239 KLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDIQAKVVRTVMLDKKVRMDGRD 318 (699)
Q Consensus 239 ~~~~~v~~~~~~~l~~a~~i~~K~eR~~ai~~l~~ei~e~l~ee~~~~~~~~i~~af~~l~k~ivR~~ILeeg~R~DGR~ 318 (699)
++.++|.+.+.++|.+|+.+++|++|+++++++++++.+.|.+++++.++.+++.+|++++|++||++||++|+|+|||+
T Consensus 1 EL~~~V~~~~~~~l~~A~~i~dK~eR~~a~~~ik~~~~e~l~~e~~~~~~~~i~~~~~~lek~~vR~~Il~~~~RiDGRd 80 (80)
T pfam03726 1 ELEEKVAALAEERLSEAYTITGKQERYAALDEIKADVVAAFAEEEDEEDEKEIKDIFKALEKKVVRSRILDGGPRIDGRD 80 (80)
T ss_pred CHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 98999999999999999730135999999999999999885011541139999999999999999999985899999988
No 72
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=99.21 E-value=6.8e-11 Score=107.30 Aligned_cols=79 Identities=44% Similarity=0.628 Sum_probs=73.2
Q ss_pred CCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEECCCCC
Q ss_conf 7546867899999994153699828797104886631444547855603259889999997868-998666873047787
Q gi|254780784|r 616 VPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVVDQNT 694 (699)
Q Consensus 616 ~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~~~~ 694 (699)
+++.|.+..|+|.++.+|||||.|=-.++||+|||+++.+.|.++.+++++||.|+|+++++|- ++||.||++.-.++.
T Consensus 655 dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~~~~ 734 (780)
T COG2183 655 DLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDEEEG 734 (780)
T ss_pred HCCCCCEEEEEEEEEEECCCEEEECCCCCEEEEHHHHHHHHCCCHHHHCCCCCEEEEEEEEEECCCCEEEEEEECCCCCC
T ss_conf 50678888899887543164689456666066689854333079588401587799999998514572324763467766
No 73
>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=99.13 E-value=2e-10 Score=103.53 Aligned_cols=69 Identities=35% Similarity=0.486 Sum_probs=66.9
Q ss_pred CCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEE
Q ss_conf 867899999994153699828797104886631444547855603259889999997868-998666873
Q gi|254780784|r 620 NKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMK 688 (699)
Q Consensus 620 g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk 688 (699)
|++.+|+|++|.++||||.|-.+.+|++|+||+++.++.++++.+++||+++++++.+|+ .|++.||||
T Consensus 1 G~iV~G~V~~i~~~gv~Vdig~k~eG~ip~~E~s~~~~~~~~~~~~vGd~i~~~V~~~d~~~g~i~LS~k 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEHHHHCCCCCCCHHHCCCCCCEEEEEEEEEECCCCEEEEECC
T ss_conf 9989999999978869999689850268999945332389747126999999999999999997998509
No 74
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.02 E-value=2.3e-09 Score=94.84 Aligned_cols=95 Identities=22% Similarity=0.339 Sum_probs=73.6
Q ss_pred CCEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCC
Q ss_conf 88089999689899999999999852475468678999999941536998287971048866314445478556032598
Q gi|254780784|r 589 DDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGD 668 (699)
Q Consensus 589 d~g~v~i~~~~~~~~~~a~~~i~~~~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd 668 (699)
++|.+.++-. +....++-+.++.. .+.|++.+|+|+++.++|++|++ .|.+|+||.|+|++.+.. +.+ +|+
T Consensus 92 ~~g~i~LS~k-~~~~~~~w~~l~~~---~~~~~~V~gkV~~~~kgG~~V~i-~gl~gFiP~Sqls~~~~~---~~~-vG~ 162 (314)
T PRK07400 92 EDGQLTLSIR-RIEYMRAWERVRQL---QKEDATVRSEVFATNRGGALVRI-EGLRGFIPGSHISTRKPK---EEL-VGE 162 (314)
T ss_pred CCCCEEEEEC-HHHHHHHHHHHHHH---HHCCCEEEEEEEEEECCCEEEEE-CCEEEEEEHHHCCCCCCC---HHH-CCC
T ss_conf 8896899860-43212069999977---32598799999999638489997-686568552451635563---210-697
Q ss_pred EEEEEEEEECC-CCCEEEEEEECCC
Q ss_conf 89999997868-9986668730477
Q gi|254780784|r 669 TVWVKLLDFDD-RGKIKLSMKVVDQ 692 (699)
Q Consensus 669 ~i~vk~~~~d~-~g~i~lSrk~~~~ 692 (699)
++.||++++|+ ++|+-||||.++.
T Consensus 163 ~~~~kIieid~~~~rivlS~r~~l~ 187 (314)
T PRK07400 163 ELPLKFLEVDEERNRLVLSHRRALV 187 (314)
T ss_pred EEEEEEEEEECCCCCEEEEEEHHHH
T ss_conf 6889999971566824899833320
No 75
>PTZ00248 eukaryotic translation initiation factor 2 alpha subunit; Provisional
Probab=99.02 E-value=5.2e-10 Score=100.12 Aligned_cols=79 Identities=28% Similarity=0.465 Sum_probs=74.8
Q ss_pred CCCCCCCEEEEEEEEEEECCEEEECC--CCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEECC
Q ss_conf 47546867899999994153699828--797104886631444547855603259889999997868-998666873047
Q gi|254780784|r 615 DVPEVNKIYKGQVVKVMDFGAFVHFC--GARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVVD 691 (699)
Q Consensus 615 ~~~e~g~~y~~~v~~i~~fGafve~~--~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~ 691 (699)
.-|++|++.-++|++|.++||||.|+ ++.+|++|+|||+.+|+.++.+++++|..+.|+|+-+|+ +|.|.||.|.+.
T Consensus 13 ~~Pe~~e~V~~~V~~i~~~gayV~LlEY~~~egmI~~sEls~rrir~I~k~ikvG~~~v~~VlRVD~~KGyIDLS~rrVs 92 (324)
T PTZ00248 13 KYPEENDLVMVKVNRIEEMGVYVSLLEYDDIEGMILLSELSKRRIRSINKLVKVGRHEVVLVLRVDKDKGYIDLSKRRVT 92 (324)
T ss_pred CCCCCCCEEEEEEEEEECCEEEEEEEEECCCCCEEEHHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCCCCEECHHHCCC
T ss_conf 69998888999999980256899984008822214688863788863788710687789999998587782444150299
Q ss_pred CC
Q ss_conf 78
Q gi|254780784|r 692 QN 693 (699)
Q Consensus 692 ~~ 693 (699)
++
T Consensus 93 ~e 94 (324)
T PTZ00248 93 PE 94 (324)
T ss_pred HH
T ss_conf 88
No 76
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=99.01 E-value=9e-10 Score=98.15 Aligned_cols=68 Identities=40% Similarity=0.671 Sum_probs=60.3
Q ss_pred CEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCC-----------CCHHHHCCCCCEEEEEEEEECC------CCCE
Q ss_conf 6789999999415369982879710488663144454-----------7855603259889999997868------9986
Q gi|254780784|r 621 KIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERV-----------AKTSDVVKEGDTVWVKLLDFDD------RGKI 683 (699)
Q Consensus 621 ~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v-----------~~~~d~~~~Gd~i~vk~~~~d~------~g~i 683 (699)
++|+|.|+.+.+||+||+|- ..|||+|||+|.+.++ ++...++++||.|.||+..+|- .++|
T Consensus 1 Ev~eG~Vs~Vt~fG~FV~L~-~ieGLvHiS~l~dD~~~fd~~~~~liG~r~~~~~~~GD~V~vrV~~V~~~~r~i~~~~I 79 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI 79 (99)
T ss_pred CEEEEEEEEEEECCEEEEEC-CCEEEEEHHHCCCCEEEECHHHCEEEECCCCCEECCCCEEEEEEEEEECCCCCCCCCEE
T ss_conf 97999999588256699932-81068993675784399812446898512786984799999999998062067676466
Q ss_pred EEEEEE
Q ss_conf 668730
Q gi|254780784|r 684 KLSMKV 689 (699)
Q Consensus 684 ~lSrk~ 689 (699)
.||+|.
T Consensus 80 gLtmrq 85 (99)
T cd04460 80 GLTMRQ 85 (99)
T ss_pred EECCCC
T ss_conf 502247
No 77
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=98.97 E-value=1e-09 Score=97.62 Aligned_cols=64 Identities=47% Similarity=0.724 Sum_probs=61.1
Q ss_pred EEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEE
Q ss_conf 899999994153699828797104886631444547855603259889999997868-9986668
Q gi|254780784|r 623 YKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLS 686 (699)
Q Consensus 623 y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lS 686 (699)
++|+|+++.+||+||++.+|.+||+|+|++++.+..++.+.+++||+|.++++++|+ ++++.||
T Consensus 1 v~G~V~~i~~~G~fV~~~~~~~gli~~s~~s~~~~~~~~~~~~~G~~V~~~Vi~vd~~~~~i~LS 65 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCHHHEECCCCEEEEEEEEEECCCCEEECC
T ss_conf 98999999784599998987178898889167653595109859999999999998999989769
No 78
>TIGR02063 RNase_R ribonuclease R; InterPro: IPR011805 This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in Escherichia coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Not included in this entry are shorter, divergent forms from the Chlamydiae and the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans , .; GO: 0003723 RNA binding, 0004518 nuclease activity.
Probab=98.93 E-value=3.3e-09 Score=93.52 Aligned_cols=197 Identities=21% Similarity=0.323 Sum_probs=108.8
Q ss_pred CCCCCCCCCCCCEEEEE--CCCCCEEEECC--C-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCCCC
Q ss_conf 14422013655100100--55651244324--5-365568899999999999999999999984356674--33224487
Q gi|254780784|r 479 ISGDEDHLGHMDFKVAG--TDSGITAMQMD--M-KIGGISENIMVMALQQAKRGRLHILNEMSKVLSESR--LQLGEFTP 551 (699)
Q Consensus 479 I~G~ED~~GdMDFKvaG--T~~GiTa~QmD--i-K~~gi~~~il~~al~~A~~gr~~il~~m~~~~~~~~--~~~~~~ap 551 (699)
++-+.+++.-+.|++.| |.+.++--++- + |+.|=|-+-|-+.+ .|.-|.+|.=.|. ..+.=.+-
T Consensus 518 l~~l~~fl~~lG~~~~~~G~~~~~~P~~~~~~le~~~~~P~~~l~~~~---------lLRsM~qA~Ys~~N~GHFGLa~~ 588 (755)
T TIGR02063 518 LQNLREFLKELGLTLKGGGTSDKIQPKDLQKLLEKVKGRPEEELINTV---------LLRSMQQAKYSPENIGHFGLALE 588 (755)
T ss_pred HHHHHHHHHHCCCEECCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHH---------HHHHHHCCCCCCCCCCCHHHHHC
T ss_conf 999999998718154488888875869999999984088438999999---------99874113117678862104552
Q ss_pred EEEEEEECCCC---------EEEEECCCCHHHHHHH-------HHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHC-
Q ss_conf 57999977115---------0000378607799899-------986888998088089999689899999999999852-
Q gi|254780784|r 552 RVEIMAIPPDQ---------IRNVIGMGGKVIRGIV-------EQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSIT- 614 (699)
Q Consensus 552 ~~~~~~i~~~k---------i~~~iG~gG~~ik~i~-------~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~- 614 (699)
....|.=|-=+ |...+..+....+.-+ +.+..++ ++=| ..++..-.-+.++-.+.++-+.
T Consensus 589 ~YtHFTSPIRRYPDL~VHRlik~~L~~~~~~~~~~~~l~~~~~~~~~~~l--~~~~-~h~S~~ERrA~~AERd~~d~kka 665 (755)
T TIGR02063 589 YYTHFTSPIRRYPDLIVHRLIKKALFKGENTTKEKETLTEYAKEYLEAKL--EEIA-EHSSKTERRADEAERDVNDWKKA 665 (755)
T ss_pred CCCCCCCCHHCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH--HHHH-HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 75445884210156899999999850788875034222245456427889--9999-86112112155312779999999
Q ss_pred --CCCCCCCEEEEEEEEEEECCEEEECCC-CCCEEEEEEECCCCC-----------CCCHHHHCCCCCEEEEEEEEECC-
Q ss_conf --475468678999999941536998287-971048866314445-----------47855603259889999997868-
Q gi|254780784|r 615 --DVPEVNKIYKGQVVKVMDFGAFVHFCG-ARDGLVHISQLSTER-----------VAKTSDVVKEGDTVWVKLLDFDD- 679 (699)
Q Consensus 615 --~~~e~g~~y~~~v~~i~~fGafve~~~-g~~gl~HiS~l~~~~-----------v~~~~d~~~~Gd~i~vk~~~~d~- 679 (699)
+.-.+|++|.|.|+.|..||.||||.. .-|||+|||.|.+.- =++-.-++++||+|+|||+.+|.
T Consensus 666 eyM~~~iG~~f~G~Is~VT~FG~FVeL~~~~ieGLVhI~~L~dDYY~Fd~~~~~L~G~R~gk~frLGD~v~V~V~~ad~~ 745 (755)
T TIGR02063 666 EYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLD 745 (755)
T ss_pred HHHHHCCCCEEEEEEEEEEEEEEEEEECCCEEEEEEECCCCCCCCCEECCCCCEEEEECCCCEEECCCEEEEEEEEECCC
T ss_conf 99985079688779975662013897367411102632789885630752207886432687372487489999996103
Q ss_pred CCCEEEEE
Q ss_conf 99866687
Q gi|254780784|r 680 RGKIKLSM 687 (699)
Q Consensus 680 ~g~i~lSr 687 (699)
.|+|.|+.
T Consensus 746 ~~~idF~L 753 (755)
T TIGR02063 746 TGKIDFEL 753 (755)
T ss_pred CCEEEEEE
T ss_conf 36698997
No 79
>KOG1068 consensus
Probab=98.92 E-value=4e-08 Score=84.73 Aligned_cols=200 Identities=19% Similarity=0.330 Sum_probs=147.8
Q ss_pred EEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCCCCCCC----CCCCCEEEEECCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf 89999914004546728999978948999997278888777----73540686652320133678887357898871453
Q gi|254780784|r 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQ----DFFPLTVNYQERTYAVGKIPGGYLRRESRPTENEI 89 (699)
Q Consensus 14 r~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~~~~~~----dFfPLtVdY~Ek~yAaGkIPGgF~kREgrpsd~Ei 89 (699)
|+|...+| +..||+||++..+|+|.|||+|...++++-.. |--=|.|.|.-..++.| -+|+.-+-..++.
T Consensus 24 R~i~~~~g-~~~~a~GSay~E~GnTKVl~aV~GPre~~~~~~~~~~~a~lnc~~~~a~Fst~-----~r~~~~~~~rr~~ 97 (245)
T KOG1068 24 RRIYARIG-VLTQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLNCEVSSAQFSTG-----DRKKRPKGDRREK 97 (245)
T ss_pred HHHHHHCC-CCCCCCCCCHHHCCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEEECCCCC-----HHCCCCCCCHHHH
T ss_conf 10121117-42368850100248807999984884422310026665247777754201112-----1015787627889
Q ss_pred HHHHHHHCCCCC-----CCCCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCEEEC
Q ss_conf 111123212677-----674688688378999982188887789999999999873268823541123552047732436
Q gi|254780784|r 90 LISRMIDRSIRP-----LFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLN 164 (699)
Q Consensus 90 L~sRlIDR~lRP-----LFPkgf~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~idge~ViN 164 (699)
..|.++-..+-| |||+ .-+.|-+.||--|+.+. ..++|+|+.||+-.+||...-|.++-+|..++.+.+.
T Consensus 98 e~s~~L~~afe~~I~~~lyPr---sqIDI~v~VleddG~~l--aa~inaatlAL~daGI~m~D~i~~~t~~l~~~~~l~D 172 (245)
T KOG1068 98 ELSLMLQQAFEPVILLELYPR---SQIDIYVQVLEDDGSNL--AAAINAATLALADAGIPMYDLITACTAGLADGTPLLD 172 (245)
T ss_pred HHHHHHHHHHHHHHHHHHCCC---CCCEEEEEEEECCCCCH--HHHHHHHHHHHHHCCCCHHHHHHHCEEEECCCCCCCC
T ss_conf 999999999888887523765---56139999997799529--9888788999998199744355511013207864336
Q ss_pred CCCCCCC--C-CCEEEEEECCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8500022--2-10135530544323331244432489999887531688999999999999983
Q gi|254780784|r 165 PRLDEDQ--G-SLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMC 225 (699)
Q Consensus 165 Pt~ee~e--s-dLDLvVAGT~d~IlMIE~~A~EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~~~~ 225 (699)
|++-++. + .+-+.+-++.+.|.-.+.+.. ++++.+-..+++|-+..+.+-+.......++
T Consensus 173 l~~~eesa~~~~ltVa~l~~~~~i~~l~~~~~-~~~d~l~~vl~~a~~~c~~v~~~l~~~l~~~ 235 (245)
T KOG1068 173 LTSLEESARAPGLTVAALPNREEIALLQLDER-LHCDHLETVLELAIAGCKRVYERLRLVLREH 235 (245)
T ss_pred CCCCHHHCCCCCEEEEEECCCCEEEEEEECCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 54105452478628998227652788985188-7778899999999999999999999999999
No 80
>KOG1069 consensus
Probab=98.91 E-value=6.1e-08 Score=83.27 Aligned_cols=193 Identities=20% Similarity=0.306 Sum_probs=143.3
Q ss_pred EEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCCCCC---CCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf 899999140045467289999789489999972788887---77735406866523201336788873578988714531
Q gi|254780784|r 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKD---GQDFFPLTVNYQERTYAVGKIPGGYLRRESRPTENEIL 90 (699)
Q Consensus 14 r~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~~~~---~~dFfPLtVdY~Ek~yAaGkIPGgF~kREgrpsd~EiL 90 (699)
|++.-|-|-|-| +|||.-..+|+|.|+|.|....+++- ..+-.-|-|-||-+. |-+...|=-
T Consensus 6 r~~~cei~iLsr-~dGSs~fsqgdT~V~c~V~GP~dvk~r~E~~~katleVi~rp~~--------------G~~~~~eK~ 70 (217)
T KOG1069 6 RGIACEISILSR-PDGSSEFSQGDTKVICSVYGPIDVKARQEDPEKATLEVIWRPKS--------------GVNGTVEKV 70 (217)
T ss_pred HHHHHHHCEECC-CCCCCCEECCCCEEEEEEECCCCHHHCCCCCHHCEEEEEEECCC--------------CCCHHHHHH
T ss_conf 435566333237-99862011598179999107863331214710035899971256--------------762279999
Q ss_pred HHHHHHCCCCCCC-CCCCCC-CEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEC-CCCEEECCCC
Q ss_conf 1112321267767-468868-837899998218888778999999999987326882354112355204-7732436850
Q gi|254780784|r 91 ISRMIDRSIRPLF-SKCYKN-ETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYI-NGQYVLNPRL 167 (699)
Q Consensus 91 ~sRlIDR~lRPLF-Pkgf~~-evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~i-dge~ViNPt~ 167 (699)
.+|+|-+.|-+.. -+-|.+ -+||++.|+.-|+..- ..|||||-+||.-.+||++---.|+-..++ ||.+|+.||.
T Consensus 71 ~e~iI~~tl~~~I~l~l~Prt~iqVsiqvv~ddgs~L--acaINaAclALvDaGIpl~~mfcai~~~~~~d~~lv~Dpt~ 148 (217)
T KOG1069 71 LERIIRKTLSKAIILELYPRTTIQVSIQVVEDDGSTL--ACAINAACLALVDAGIPLRSMFCAISCALHEDGVLVLDPTA 148 (217)
T ss_pred HHHHHHHHHHHHHEEEECCCCEEEEEEEEEECCCCCH--HHHHHHHHHHHHHCCCCHHHHHHHCEEEEECCCCEEECCCH
T ss_conf 9999999987755132157746999999993588405--78998899999856985677454204788437628978717
Q ss_pred CCCC-C--CCEEEEEE---CCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 0022-2--10135530---54432333124443248999988753168899999999999998
Q gi|254780784|r 168 DEDQ-G--SLDLFVSG---TQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKM 224 (699)
Q Consensus 168 ee~e-s--dLDLvVAG---T~d~IlMIE~~A~EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~~~ 224 (699)
.|++ | ---|.+.+ .+..++|.|.-+ +.+|+++..+++.|+.+.+.+..+..++.+.
T Consensus 149 ~qek~~~~~~~lsf~~~~~~~~~vi~s~t~G-~~~~d~lf~~le~a~~~~~~~f~f~r~~~q~ 210 (217)
T KOG1069 149 KQEKISTARATLSFEGGSLGEPKVIISETNG-EKSEDQLFYVLELAQAAAQSLFPFYREVLQR 210 (217)
T ss_pred HHHHHHHCEEEEEEECCCCCCCCEEEEECCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 7654422248999834778876258872468-8888999999985378899999999999986
No 81
>pfam03725 RNase_PH_C 3' exoribonuclease family, domain 2. This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.
Probab=98.90 E-value=1.5e-09 Score=96.42 Aligned_cols=64 Identities=34% Similarity=0.625 Sum_probs=60.0
Q ss_pred CCEEEEEEEECCCCEEECCCCCC---CCCCCEEEEEECCCCHHHHHCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 54112355204773243685000---22210135530544323331244432489999887531688
Q gi|254780784|r 147 GPVVGAQVDYINGQYVLNPRLDE---DQGSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNE 210 (699)
Q Consensus 147 GPVaaVRVG~idge~ViNPt~ee---~esdLDLvVAGT~d~IlMIE~~A~EVsEe~mleAI~~Ahe~ 210 (699)
+|++|||||++||+||+|||++| .+++|+++++|+++.+.|+++++..++|+.|.+||++||+.
T Consensus 1 ~~v~avtvg~i~~~~i~dpt~~Ee~~~~~~l~v~~~~~~~~v~~~~~g~~~l~~~~l~~~l~~a~~~ 67 (67)
T pfam03725 1 GPVAAVTVGKIDGELVLDPTLEEESLADSDLTIVVAGTGDIVALMKEGGGGLTEEELLEALELAHKG 67 (67)
T ss_pred CCEEEEEEEEECCEEEECCCHHHHHHHCCEEEEEEECCCCEEEEECCCCCCCCHHHHHHHHHHHCCC
T ss_conf 9889999999999999998967863314736899968999999991899785999999999987079
No 82
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.83 E-value=2.3e-08 Score=86.77 Aligned_cols=71 Identities=44% Similarity=0.720 Sum_probs=67.8
Q ss_pred CCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCC-CCEEEEEE
Q ss_conf 468678999999941536998287971048866314445478556032598899999978689-98666873
Q gi|254780784|r 618 EVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDR-GKIKLSMK 688 (699)
Q Consensus 618 e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~-g~i~lSrk 688 (699)
+.|++++|+|+++.++|+||++.+|.+|++|+|++++.+..+..+.+++||++.+++++++.. +++.||+|
T Consensus 1 ~~G~iv~g~V~~v~~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~k 72 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCHHHEECCCCEEEEEEEEEECCCCEEEEEEC
T ss_conf 999899999999978739999769989999807505555478468363898999999999999999999859
No 83
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.83 E-value=1.6e-08 Score=88.08 Aligned_cols=60 Identities=17% Similarity=0.202 Sum_probs=55.9
Q ss_pred CCEEEEEEEEEEECCEEEECCCCCCEEEEEEEC--CCCCCCCHHHHCCCCCEEEEEEEEECC
Q ss_conf 867899999994153699828797104886631--444547855603259889999997868
Q gi|254780784|r 620 NKIYKGQVVKVMDFGAFVHFCGARDGLVHISQL--STERVAKTSDVVKEGDTVWVKLLDFDD 679 (699)
Q Consensus 620 g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l--~~~~v~~~~d~~~~Gd~i~vk~~~~d~ 679 (699)
|++.+|+|++|++||+||+|..|..|++||||+ +|.+..++.+.|++||+|+||++++-+
T Consensus 1 G~vv~g~V~sik~~~l~V~L~d~~~GrVhiSei~D~~~~~k~P~~~~k~Gq~V~~rViG~~d 62 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHD 62 (70)
T ss_pred CCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCCCHHHHCCCCCEEEEEEEEEEC
T ss_conf 97799999999467089996899577898455213555556946856899999999997654
No 84
>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=98.81 E-value=2.3e-08 Score=86.67 Aligned_cols=69 Identities=33% Similarity=0.570 Sum_probs=59.8
Q ss_pred CCCEEEEEEEEEEECCEEEECCC-CCCEEEEEEECCCCCC-----------CCHHHHCCCCCEEEEEEEEECC-CCCEEE
Q ss_conf 68678999999941536998287-9710488663144454-----------7855603259889999997868-998666
Q gi|254780784|r 619 VNKIYKGQVVKVMDFGAFVHFCG-ARDGLVHISQLSTERV-----------AKTSDVVKEGDTVWVKLLDFDD-RGKIKL 685 (699)
Q Consensus 619 ~g~~y~~~v~~i~~fGafve~~~-g~~gl~HiS~l~~~~v-----------~~~~d~~~~Gd~i~vk~~~~d~-~g~i~l 685 (699)
+|++|+|.|+.+.+||+||+|.+ +-|||+|+|+|.+.+. ++-...+++||.|+|++..+|. +++|.|
T Consensus 1 IG~~f~g~I~~v~~~GiFV~l~~~~ieGli~~~~l~~d~y~~d~~~~~l~g~~~~~~~~lGd~v~V~i~~vd~~~~~I~f 80 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80 (83)
T ss_pred CCCEEEEEEEEEEEEEEEEEEECCCEEEEEECCCCCCCCEEECCCCEEEECCCCCCEEECCCEEEEEEEEEECCCCEEEE
T ss_conf 99999999998983069999828873999982214567224474021898134775997899999999999430398989
Q ss_pred EE
Q ss_conf 87
Q gi|254780784|r 686 SM 687 (699)
Q Consensus 686 Sr 687 (699)
+.
T Consensus 81 ~l 82 (83)
T cd04471 81 EL 82 (83)
T ss_pred EE
T ss_conf 97
No 85
>KOG1614 consensus
Probab=98.71 E-value=1.4e-05 Score=63.99 Aligned_cols=221 Identities=23% Similarity=0.307 Sum_probs=144.2
Q ss_pred HHHHCCCCCCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCE-EEEEEEECCCC-
Q ss_conf 9987288665886775337879984475466700899987976899998168652122334454420-35877405887-
Q gi|254780784|r 305 TVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQR-NDFMMHYNFLP- 382 (699)
Q Consensus 305 ~~ILeeg~R~DGR~~dEIRpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~-k~fmlHYNFPp- 382 (699)
...|+.|.|.|||+++|.|.+.++.| .--||++.|-|+||+++.+|--..+ -...... -.|-..-.|.|
T Consensus 15 l~alk~g~R~DgR~l~efR~lei~fG---ke~gs~~vt~G~Tkvma~vt~~ia~------Py~dRP~eG~f~I~telsPm 85 (291)
T KOG1614 15 LNALKAGLRFDGRSLEEFRDLEIEFG---KEYGSVLVTMGNTKVMARVTAQIAQ------PYIDRPHEGSFSIFTELSPM 85 (291)
T ss_pred HHHHHHCCCCCCCCHHHHHCEEEEEC---CCCCCEEEEECCEEEEEEEEEHHCC------CCCCCCCCCEEEEEECCCCC
T ss_conf 99987253557644545331389960---1116289985670688886302167------65578877704544102424
Q ss_pred --CCCCCCCCCCCCCCHHHHHHHHHHHHHHHC--CCCC------CCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf --544533455676502467999999987410--7864------468738999853110278522356677779876259
Q gi|254780784|r 383 --CATGEVSRMGAPSRREIGHGRLARRAIHPV--LPQT------AQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAG 452 (699)
Q Consensus 383 --fsvGE~~~~~~~~RREiGHg~la~ral~~~--~P~~------~~~p~tirv~~evl~sngsssma~vc~~slal~dag 452 (699)
||. |.|+.+ --++.-++|.||+++.. |.++ ..-=+.||+.--+|.-|||---|+.-|.--|||.-+
T Consensus 86 A~~sf-E~G~~~---~~~v~l~Rliek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnlvDaA~iAviaaL~hFr 161 (291)
T KOG1614 86 ASPSF-EPGRKG---ESEVELSRLIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNLVDAACIAVIAALMHFR 161 (291)
T ss_pred CCCCC-CCCCCC---CHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCEEEEEEEEEEEECCCCCEEHHHHHHHHHHHHHCC
T ss_conf 34355-799856---21899999999998741654267777530877999998899975999840268999999999617
Q ss_pred ---------------------CC--CCCCCCEEEEEEEEECCEEEEEEECCCCCCCCCCCCEEEEECCCC-CEEEECCCC
Q ss_conf ---------------------50--225412133200440882899863144220136551001005565-124432453
Q gi|254780784|r 453 ---------------------VP--ISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSG-ITAMQMDMK 508 (699)
Q Consensus 453 ---------------------vp--~~~~VaGiamGLi~~~~~~~iLtDI~G~ED~~GdMDFKvaGT~~G-iTa~QmDiK 508 (699)
|| |...=-++..|++-.+ -.+++|=+-.|...+|=-.-|+-++++ |.++|----
T Consensus 162 rPdvTv~g~~v~ihp~eEr~PvPL~I~HmPIC~tf~ffnkG--~i~viDpt~~Ee~~~dGs~vVt~Nk~rEVc~i~k~G~ 239 (291)
T KOG1614 162 RPDVTVGGEEVIIHPVEEREPVPLSIHHMPICFTFGFFNKG--EIVVIDPTEKEEAVMDGSMVVTMNKNREVCAIQKSGG 239 (291)
T ss_pred CCCCCCCCEEEEECCHHCCCCCCEEEEECCCEEEEEEECCC--EEEEECCCHHHHHCCCCEEEEEECCCCCEEEEECCCC
T ss_conf 99720056056761610068851245421305899983476--0899687577772568519999748861899961777
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 655688999999999999999999999843566
Q gi|254780784|r 509 IGGISENIMVMALQQAKRGRLHILNEMSKVLSE 541 (699)
Q Consensus 509 ~~gi~~~il~~al~~A~~gr~~il~~m~~~~~~ 541 (699)
-.+....+..-...|+.---.+-++..+++.+
T Consensus 240 -~~~~~~~i~~C~k~A~~~a~~vt~ii~~~l~~ 271 (291)
T KOG1614 240 -EILDESVIERCYKLAKDRAVEVTGIILEALEE 271 (291)
T ss_pred -CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf -33469999999998888999888999999987
No 86
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polyribonucleotide nucleotidyltransferase; InterPro: IPR014069 The of the characterization of two proteins from Streptomyces coelicolor ahs been presented . The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. It has also been shown that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase ..
Probab=98.70 E-value=1.3e-08 Score=88.78 Aligned_cols=203 Identities=21% Similarity=0.399 Sum_probs=166.0
Q ss_pred EEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCCCC-CCCCCC-C-----CEEEEECCCCCCCCCCCCCCCCCCCCCH
Q ss_conf 89999914004546728999978948999997278888-777735-4-----0686652320133678887357898871
Q gi|254780784|r 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLK-DGQDFF-P-----LTVNYQERTYAVGKIPGGYLRRESRPTE 86 (699)
Q Consensus 14 r~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~~~-~~~dFf-P-----LtVdY~Ek~yAaGkIPGgF~kREgrpsd 86 (699)
|.+..|...+.| +|||.+.+.|+|.+|--.+.+--.. ...|-+ | ..-+|.-..|+.|.. -|=|.|..
T Consensus 352 r~l~~ev~~~Pr-~hGsa~f~rGetq~lGv~tl~ml~m~q~~d~l~P~~~~ry~h~yn~PPys~Ge~-----GrvG~Pkr 425 (725)
T TIGR02696 352 RSLSAEVEVIPR-VHGSALFERGETQILGVTTLNMLKMEQQIDSLSPVTSKRYLHHYNFPPYSTGET-----GRVGSPKR 425 (725)
T ss_pred HHHHCCEEEECC-CCCHHHHHCCCEEEEHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCCCCCCCC-----CCCCCCCC
T ss_conf 521000024133-101023205760354034778888876553116202300110037887566764-----56688753
Q ss_pred HHHHHHHHHHCCCCCCCC--CCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCC----
Q ss_conf 453111123212677674--68868837899998218888778999999999987326882354112355204773----
Q gi|254780784|r 87 NEILISRMIDRSIRPLFS--KCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQ---- 160 (699)
Q Consensus 87 ~EiL~sRlIDR~lRPLFP--kgf~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~idge---- 160 (699)
+||-...|-.|.|=|.+| +.|.|-+.-+..-|++++... +=+++|+.++|.-+++|+..||+++-+|++.++
T Consensus 426 reiGhG~laeral~PvlP~~e~fPyair~vseal~snGsts--mGsvCastl~l~~aGvPl~~~vaGiamGl~~~~~~~~ 503 (725)
T TIGR02696 426 REIGHGALAERALVPVLPSREEFPYAIRQVSEALGSNGSTS--MGSVCASTLSLLNAGVPLKAPVAGIAMGLISDEVDGE 503 (725)
T ss_pred CCCCCCCHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCCCC--HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCC
T ss_conf 20256502211000344676656368999988741577630--3578999999986488620002012222222200354
Q ss_pred --EEECCCC---CCCCCCCEEEEEECCCCHHHHHCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf --2436850---0022210135530544323331244--43248999988753168899999999999998
Q gi|254780784|r 161 --YVLNPRL---DEDQGSLDLFVSGTQDAVLMVELEA--NQLSEDVVLDAIIFGHNECKPVIEAISKLAKM 224 (699)
Q Consensus 161 --~ViNPt~---ee~esdLDLvVAGT~d~IlMIE~~A--~EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~~~ 224 (699)
|+.-... ++.-.|+|.-||||.+-|.-+.-+. +.+|-+.+..||..|+++-..+.+...+....
T Consensus 504 ~~y~~ltdi~Gaeda~GdmdfkvaGt~~~~talqldtkldGiP~~vla~al~~a~~ar~~il~~~~~~i~~ 574 (725)
T TIGR02696 504 TRYVALTDILGAEDALGDMDFKVAGTREFVTALQLDTKLDGIPAEVLAEALKQAKDARLAILDVLAEAIDT 574 (725)
T ss_pred EEEEEEEECCCCCCCCCCCCEEECCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 25676420113201025532122144787777753100257647899999998898899999999998507
No 87
>PRK11642 exoribonuclease R; Provisional
Probab=98.69 E-value=1.4e-07 Score=80.43 Aligned_cols=73 Identities=30% Similarity=0.494 Sum_probs=62.2
Q ss_pred CCCCCCCEEEEEEEEEEECCEEEECCC-CCCEEEEEEECCCCCCC-----------CHHHHCCCCCEEEEEEEEECC-CC
Q ss_conf 475468678999999941536998287-97104886631444547-----------855603259889999997868-99
Q gi|254780784|r 615 DVPEVNKIYKGQVVKVMDFGAFVHFCG-ARDGLVHISQLSTERVA-----------KTSDVVKEGDTVWVKLLDFDD-RG 681 (699)
Q Consensus 615 ~~~e~g~~y~~~v~~i~~fGafve~~~-g~~gl~HiS~l~~~~v~-----------~~~d~~~~Gd~i~vk~~~~d~-~g 681 (699)
+...+|++|.|.|+.+..||.||||.+ +-|||+|||.|.+.+-. +-.-.+++||.|.|+|..+|. ++
T Consensus 639 m~~~iGe~f~G~IsgVt~fG~FVeL~~~~vEGLVhvs~L~dD~Y~yd~~~~~LvG~rtg~~y~lGD~V~V~v~~Vd~~~~ 718 (813)
T PRK11642 639 MLDQVGNVFKGVIASVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDER 718 (813)
T ss_pred HHHHCCCEEEEEEEEEEEEEEEEEECCCCEEEEEECCCCCCCEEEECCCCCEEEEEECCCEEECCCEEEEEEEEECHHHC
T ss_conf 99744997889996076100899954886378888012888318983357889865079788269979999999742137
Q ss_pred CEEEEE
Q ss_conf 866687
Q gi|254780784|r 682 KIKLSM 687 (699)
Q Consensus 682 ~i~lSr 687 (699)
+|.|..
T Consensus 719 qIDfeL 724 (813)
T PRK11642 719 KIDFSL 724 (813)
T ss_pred EEEEEE
T ss_conf 355898
No 88
>KOG1612 consensus
Probab=98.68 E-value=9.7e-06 Score=65.36 Aligned_cols=222 Identities=21% Similarity=0.303 Sum_probs=140.5
Q ss_pred HCCCCCCCCCCCCCEEEEEEEECCCCCCCCEEEEEECC-CEEEEEEE--ECCCCCCCCCCCCCCCCEEEEEEEECCCCCC
Q ss_conf 72886658867753378799844754667008999879-76899998--1686521223344544203587740588754
Q gi|254780784|r 308 LDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGD-TQAIVVVT--LGTREDEQYVDSLSGTQRNDFMMHYNFLPCA 384 (699)
Q Consensus 308 Leeg~R~DGR~~dEIRpIs~EvgvLPrvHGSALFtRGE-TQaL~tvT--LG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfs 384 (699)
.+..+|.|||+.++.|||..|+|+||.+.|||=..-|. |-+++-+- +|++.+++..++ | +.+.-.|-|-.
T Consensus 17 ~e~~iR~DGR~~~~~Rpi~vetdVlp~tNGSaRVk~g~~tdiivgVKaEvg~~~~~~p~eg------k-~~~~VD~S~sa 89 (288)
T KOG1612 17 SEPDIRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVKAEVGSPDDETPVEG------K-YLFFVDCSPSA 89 (288)
T ss_pred CCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEEEECCCCCCCCCCCC------E-EEEEEEECCCC
T ss_conf 5701146786701001078881301489985789936873599997632057633587777------3-89999846876
Q ss_pred CCCCCCCCCCCCHHHH--HHHHHHHHHHH----C----CCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf 4533455676502467--99999998741----0----786446873899985311027852235667777987625950
Q gi|254780784|r 385 TGEVSRMGAPSRREIG--HGRLARRAIHP----V----LPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVP 454 (699)
Q Consensus 385 vGE~~~~~~~~RREiG--Hg~la~ral~~----~----~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp 454 (699)
.-+...+++ -|++ ..++-+|.|.. + +....-.-+.|-|..-|++|+|+-+-|-=-|...||.+.-.|
T Consensus 90 sp~f~gRgg---de~~~eltsaLq~~l~~~~sgv~ls~L~lt~~~~W~i~VDvlVi~s~gn~~dAiS~Ai~~AL~~T~lP 166 (288)
T KOG1612 90 SPQFQGRGG---DELVEELTSALQRVLNSLGSGVDLSKLQLTPGYCWKIYVDVLVISSDGNLLDAISIAIYAALNNTRLP 166 (288)
T ss_pred CCCCCCCCH---HHHHHHHHHHHHHHHHCCCCCCCHHHEECCCCEEEEEEEEEEEEECCCCHHHHHHHHHHHHHHCCCCC
T ss_conf 832467770---06899999999999847686545122352587069999769999549978889999999987425677
Q ss_pred C--CCCCCEEEEEEEEECCE---------------------EEEEEECCCCCCCCCCCCEEEEECCCCCEEEECCCCCCC
Q ss_conf 2--25412133200440882---------------------899863144220136551001005565124432453655
Q gi|254780784|r 455 I--SKPVAGIAMGLVKDGDD---------------------FIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGG 511 (699)
Q Consensus 455 ~--~~~VaGiamGLi~~~~~---------------------~~iLtDI~G~ED~~GdMDFKvaGT~~GiTa~QmDiK~~g 511 (699)
= .++.-+...-...-.++ +..|-|=+-.|..-----.-|-=++.||+.+---+-.++
T Consensus 167 kv~v~~dd~~~~~i~~s~~~Yd~~~~~~~~~P~ivtlskIG~~~lVD~T~eEe~~a~s~l~Isv~a~givs~~r~VG~G~ 246 (288)
T KOG1612 167 KVIVAFDDDGEVEILLSDEEYDLMVKLVENVPLIVTLSKIGTNMLVDPTAEEESVANSGLLISVSAGGIVSCTRSVGLGD 246 (288)
T ss_pred CCCCCCCCCCCEEECCCCCCCHHHHHHCCCCCEEEEEEEECCEEECCCCCCHHHHHHCCEEEEEECCCCEEEEEEECCCC
T ss_conf 43356566886146047543003454034687799998605237705782177764310699985276057888854888
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 6889999999999999999999998435
Q gi|254780784|r 512 ISENIMVMALQQAKRGRLHILNEMSKVL 539 (699)
Q Consensus 512 i~~~il~~al~~A~~gr~~il~~m~~~~ 539 (699)
+-.+-..+-|+|+++---..-....+.+
T Consensus 247 l~~s~i~~mle~~~~~~e~l~~~l~k~L 274 (288)
T KOG1612 247 LDPSSIPEMLEQGKAVVETLAPDLVKSL 274 (288)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 7704689999999999876658899875
No 89
>KOG1614 consensus
Probab=98.59 E-value=1.4e-05 Score=64.07 Aligned_cols=200 Identities=22% Similarity=0.283 Sum_probs=137.5
Q ss_pred EEEEEEECEECCCCCCEEEEEECCCEEEEEEEECC----CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf 89999914004546728999978948999997278----88877773540686652320133678887357898871453
Q gi|254780784|r 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDR----SLKDGQDFFPLTVNYQERTYAVGKIPGGYLRRESRPTENEI 89 (699)
Q Consensus 14 r~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~----~~~~~~dFfPLtVdY~Ek~yAaGkIPGgF~kREgrpsd~Ei 89 (699)
|.+.++.||. -|||.+++|+|.||+.+.+.- .-+|-.+-|-.++++-.-++.+= --||++|.++
T Consensus 33 R~lei~fGke----~gs~~vt~G~Tkvma~vt~~ia~Py~dRP~eG~f~I~telsPmA~~sf--------E~G~~~~~~v 100 (291)
T KOG1614 33 RDLEIEFGKE----YGSVLVTMGNTKVMARVTAQIAQPYIDRPHEGSFSIFTELSPMASPSF--------EPGRKGESEV 100 (291)
T ss_pred HCEEEEECCC----CCCEEEEECCEEEEEEEEEHHCCCCCCCCCCCEEEEEECCCCCCCCCC--------CCCCCCCHHH
T ss_conf 3138996011----162899856706888863021676557887770454410242434355--------7998562189
Q ss_pred HHHHHHHCCCCCCCC---CCCC-------CCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC----------------
Q ss_conf 111123212677674---6886-------88378999982188887789999999999873268----------------
Q gi|254780784|r 90 LISRMIDRSIRPLFS---KCYK-------NETQVIINVMQHDLESSPHVVSMVAASAALMLSGL---------------- 143 (699)
Q Consensus 90 L~sRlIDR~lRPLFP---kgf~-------~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdI---------------- 143 (699)
..+|+|+|.+|--=- +..+ --+.|-..+|+.|++-- -+|.+||-+||+--.=
T Consensus 101 ~l~Rliek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnlv--DaA~iAviaaL~hFrrPdvTv~g~~v~ihp~e 178 (291)
T KOG1614 101 ELSRLIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNLV--DAACIAVIAALMHFRRPDVTVGGEEVIIHPVE 178 (291)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCEEEEEEEEEEEECCCCCEE--HHHHHHHHHHHHHCCCCCCCCCCEEEEECCHH
T ss_conf 9999999998741654267777530877999998899975999840--26899999999961799720056056761610
Q ss_pred -----CC---CCCEEEEEEEECC-CC-EEECCCCCCC-CCCCEEEEEECCCC-HHHHHCCCCC-CCHHHHHHHHHHHHHH
Q ss_conf -----82---3541123552047-73-2436850002-22101355305443-2333124443-2489999887531688
Q gi|254780784|r 144 -----PF---EGPVVGAQVDYIN-GQ-YVLNPRLDED-QGSLDLFVSGTQDA-VLMVELEANQ-LSEDVVLDAIIFGHNE 210 (699)
Q Consensus 144 -----Pf---~GPVaaVRVG~id-ge-~ViNPt~ee~-esdLDLvVAGT~d~-IlMIE~~A~E-VsEe~mleAI~~Ahe~ 210 (699)
|. +=|+ |+-.|..| |+ .|+.||.+|+ --|--++|+-+++. |+-|+-.+.+ +++..++...+.|..-
T Consensus 179 Er~PvPL~I~HmPI-C~tf~ffnkG~i~viDpt~~Ee~~~dGs~vVt~Nk~rEVc~i~k~G~~~~~~~~i~~C~k~A~~~ 257 (291)
T KOG1614 179 EREPVPLSIHHMPI-CFTFGFFNKGEIVVIDPTEKEEAVMDGSMVVTMNKNREVCAIQKSGGEILDESVIERCYKLAKDR 257 (291)
T ss_pred CCCCCCEEEEECCC-EEEEEEECCCEEEEECCCHHHHHCCCCEEEEEECCCCCEEEEECCCCCCCCHHHHHHHHHHHHHH
T ss_conf 06885124542130-58999834760899687577772568519999748861899961777334699999999988889
Q ss_pred HHHHHHHHHHHHHHHCCC
Q ss_conf 999999999999983889
Q gi|254780784|r 211 CKPVIEAISKLAKMCAKE 228 (699)
Q Consensus 211 Ik~iI~~Q~eL~~~~Gk~ 228 (699)
+..+...+.+..++--++
T Consensus 258 a~~vt~ii~~~l~~d~~~ 275 (291)
T KOG1614 258 AVEVTGIILEALEEDQRE 275 (291)
T ss_pred HHHHHHHHHHHHHHHHHH
T ss_conf 998889999999878888
No 90
>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=98.47 E-value=1.4e-06 Score=72.18 Aligned_cols=71 Identities=30% Similarity=0.338 Sum_probs=66.0
Q ss_pred CCCCCEEEEEEEEEEE-CCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 5468678999999941-53699828797104886631444547855603259889999997868998666873
Q gi|254780784|r 617 PEVNKIYKGQVVKVMD-FGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMK 688 (699)
Q Consensus 617 ~e~g~~y~~~v~~i~~-fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk 688 (699)
+|.|.+-.|+|+++.+ .|+||.|++|+.|++|+++|++.+.+++-+.+++||.|.++++.. ..|++.||.|
T Consensus 1 L~~G~i~~G~V~kV~p~~Gl~Vqlp~g~~G~V~itdl~D~y~~~Pl~~f~~~qiVrc~VLs~-~~g~~~LSlR 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSK-KDGKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEECCCCCEEEECCCCCEEEEEEEEECCCCCCCCHHHCCCCCEEEEEEEEC-CCCEEEEEEC
T ss_conf 98874740399997289856998489966689999714745449677657897899999953-6998998749
No 91
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.36 E-value=2.3e-06 Score=70.41 Aligned_cols=70 Identities=21% Similarity=0.333 Sum_probs=66.4
Q ss_pred CCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHH---HHCCCCCEEEEEEEEECC-CCCEEEE
Q ss_conf 546867899999994153699828797104886631444547855---603259889999997868-9986668
Q gi|254780784|r 617 PEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTS---DVVKEGDTVWVKLLDFDD-RGKIKLS 686 (699)
Q Consensus 617 ~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~---d~~~~Gd~i~vk~~~~d~-~g~i~lS 686 (699)
++.|++..|-|+.+.+.|+||.|-+.-+|++++|++++..+.++. +.+.+|..++.|++.+|+ +|++.||
T Consensus 1 ikeGq~vRGyVk~v~~~GvFv~Ls~~v~grv~~~nls~~~v~dp~~~~~~fp~GkLv~~kVlsvd~~~~~VELS 74 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEECCCCCEEEEECCCEEEEEEEECCCHHHHCCHHHHHCCCCCCCEEEEEEEEECCCCCEEECC
T ss_conf 99887989999982687399995687489999700362120682688614899989999999986776848609
No 92
>KOG1613 consensus
Probab=98.34 E-value=1.5e-06 Score=71.90 Aligned_cols=224 Identities=23% Similarity=0.296 Sum_probs=142.2
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEE
Q ss_conf 99999999999999872886658867753378799844754667008999879768999981686521223344544203
Q gi|254780784|r 293 SVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRN 372 (699)
Q Consensus 293 ~af~~l~k~ivR~~ILeeg~R~DGR~~dEIRpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k 372 (699)
.+|+.+.-...-++-|+++.|+|||.+.|.|.+.++.|....+.||||..-|+|-++|..+-+-... --|+.. +.
T Consensus 17 ~~fkrI~Pe~~l~rhLse~~RpdgR~lgefRdt~in~g~IsTangSal~K~G~ttvi~~Ik~ei~ep--stdapd---eg 91 (298)
T KOG1613 17 EVFKRISPELYLQRHLSEGIRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICGIKAEIAEP--STDAPD---EG 91 (298)
T ss_pred HHHHHCCHHHHHHHHHHCCCCCCHHHHHHHHHHHEECCCEECCCCHHHHHCCCCEEEEEEEEEECCC--CCCCCC---CC
T ss_conf 8986539999999986435684135565776652003754036747777348808999764321166--657998---76
Q ss_pred EEEEEECCCCCCCCCCCCCCCCCCHHH----------HHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHH
Q ss_conf 587740588754453345567650246----------7999999987410786446873899985311027852235667
Q gi|254780784|r 373 DFMMHYNFLPCATGEVSRMGAPSRREI----------GHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVC 442 (699)
Q Consensus 373 ~fmlHYNFPpfsvGE~~~~~~~~RREi----------GHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc 442 (699)
-..-.|.+||-|. +..|.|.|+--+. -|+++..+-=.-+.+- ..-|..-...=+|..+|+ ---
T Consensus 92 ~Iv~n~~lpplcs-~r~RpG~p~dea~viSq~LhdtIl~S~ii~~k~Lci~~g--KaawvlYadIicLd~dG~----~fD 164 (298)
T KOG1613 92 DIVPNYALPPLCS-SRFRPGPPTDEAQVISQKLHDTILHSRIIPKKALCIKAG--KAAWVLYADIICLDYDGP----VFD 164 (298)
T ss_pred CEEECCCCCCCCC-CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHEEECC--CEEEEEEEEEEEECCCCC----HHH
T ss_conf 4541356786324-677788972377889999999998627744255311036--246577777999848884----899
Q ss_pred HHHHHHHHCCCCCCCCCCEEEEEE---------------EE-----E------------------CCEEEEEEECCCCCC
Q ss_conf 777987625950225412133200---------------44-----0------------------882899863144220
Q gi|254780784|r 443 GSSLALMDAGVPISKPVAGIAMGL---------------VK-----D------------------GDDFIILSDISGDED 484 (699)
Q Consensus 443 ~~slal~dagvp~~~~VaGiamGL---------------i~-----~------------------~~~~~iLtDI~G~ED 484 (699)
++++|||.|=-.+|-|-|-|-=-+ ++ + -++..|+-|=++.|.
T Consensus 165 a~w~al~aAlknvklP~a~ide~~~~~~~t~e~~ic~~tlt~p~~ln~e~r~~~~~n~~fS~~~vl~~~li~adpT~eEE 244 (298)
T KOG1613 165 ACWNALMAALKNVKLPRAFIDERASDLRMTIEEIICDQTLTVPLMLNAENRAFASQNSDFSEEEVLDDVLIAADPTEEEE 244 (298)
T ss_pred HHHHHHHHHHHCCCCCEEEECCCCHHHHHHHHHHHHHHHHCCHHHHCCCCCCCCCCCCCCCHHHHHCCEEEECCCCCHHH
T ss_conf 99999999984277865663564204320278887765514144414000211014788517775144368418983034
Q ss_pred CCCCCCEEEEECCCCCEEEECCCCCCC---CCHHHHHHHHHHHHHHHHH
Q ss_conf 136551001005565124432453655---6889999999999999999
Q gi|254780784|r 485 HLGHMDFKVAGTDSGITAMQMDMKIGG---ISENIMVMALQQAKRGRLH 530 (699)
Q Consensus 485 ~~GdMDFKvaGT~~GiTa~QmDiK~~g---i~~~il~~al~~A~~gr~~ 530 (699)
++-+--.-|.-...|= ..|+ .|++| ++.+.+...++.|+.--..
T Consensus 245 ~l~~~~lTIvldss~n-~v~l-~k~GG~al~~~~~iK~c~elar~Rake 291 (298)
T KOG1613 245 TLITSTLTIVLDSSGN-YVQL-TKVGGGALITPEMIKRCLELARVRAKE 291 (298)
T ss_pred HHHHCEEEEEECCCCC-EEEE-EECCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 4111158999868888-8999-944864446799999999999987999
No 93
>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=98.34 E-value=1.4e-06 Score=72.27 Aligned_cols=80 Identities=35% Similarity=0.637 Sum_probs=68.4
Q ss_pred EEECCCCEEEEECCCCHHHHHHHHHHCCEEEEE-CCEEEEEE--ECCHHHHHHHHHHHHHHCC--CCC-----CCCEEEE
Q ss_conf 997711500003786077998999868889980-88089999--6898999999999998524--754-----6867899
Q gi|254780784|r 556 MAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNID-DDGTVKIA--SSSLAEIEAAREMIRSITD--VPE-----VNKIYKG 625 (699)
Q Consensus 556 ~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~-d~g~v~i~--~~~~~~~~~a~~~i~~~~~--~~e-----~g~~y~~ 625 (699)
++||+++||.|||++|+++|.|++.+|++|+|+ ++|.|.|. ..|..++.+|.++|+.+.. .|| ..+-|.-
T Consensus 2 v~IP~~Rig~lIGk~G~~~k~Iee~~~~~i~ids~tg~V~i~~~~~Dp~~~~KA~d~I~Ai~rGf~pe~A~~Ll~dd~~l 81 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALKLLDDDYML 81 (172)
T ss_pred CCCCHHHEEEEECCCCCHHHHHHHHHCCEEEEECCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCEE
T ss_conf 66873563555568701399999997987998468634883578899899999999999987699989999873657069
Q ss_pred EEEEEEECCE
Q ss_conf 9999941536
Q gi|254780784|r 626 QVVKVMDFGA 635 (699)
Q Consensus 626 ~v~~i~~fGa 635 (699)
.|.++.+||-
T Consensus 82 evidi~~~~~ 91 (172)
T TIGR03665 82 EVIDLKEYGK 91 (172)
T ss_pred EEEEHHHHCC
T ss_conf 9998898447
No 94
>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=98.32 E-value=2.6e-06 Score=70.03 Aligned_cols=74 Identities=27% Similarity=0.447 Sum_probs=59.3
Q ss_pred CCCCCCCEEEEEEEEEEEC--CEEEECCCCCCEEEEEEECCC---CCCCCHHHHCCCCCEEEEEEEEECCCCC-EEEEEE
Q ss_conf 4754686789999999415--369982879710488663144---4547855603259889999997868998-666873
Q gi|254780784|r 615 DVPEVNKIYKGQVVKVMDF--GAFVHFCGARDGLVHISQLST---ERVAKTSDVVKEGDTVWVKLLDFDDRGK-IKLSMK 688 (699)
Q Consensus 615 ~~~e~g~~y~~~v~~i~~f--Gafve~~~g~~gl~HiS~l~~---~~v~~~~d~~~~Gd~i~vk~~~~d~~g~-i~lSrk 688 (699)
....+|.||.|+|.++.+. +|||+|-.++.|+||+|++.+ .+..+.++.+++||+|.|.|..=.-.+| -+||..
T Consensus 3 ~~~~vGnIY~GkV~~v~p~i~AAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~l~~G~~ilVQV~Ke~~~~Kgp~lT~~ 82 (88)
T cd04453 3 REPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTTN 82 (88)
T ss_pred CCCCCCCEEEEEEEEECCCCCEEEEECCCCCCEEEECHHCCHHHHCCCCCHHHHCCCCCEEEEEEEECCCCCCCCEEEEE
T ss_conf 75611248999998866687489996589868999903457235135788778377999999999766879978608845
No 95
>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=98.31 E-value=5.7e-06 Score=67.24 Aligned_cols=74 Identities=22% Similarity=0.337 Sum_probs=67.7
Q ss_pred CCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCC----CHHHHCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf 7546867899999994153699828797104886631444547----8556032598899999978689986668730
Q gi|254780784|r 616 VPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVA----KTSDVVKEGDTVWVKLLDFDDRGKIKLSMKV 689 (699)
Q Consensus 616 ~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~----~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk~ 689 (699)
.|++|++.-|+|+.+...+++|++-...+|+||+|++...|.. +...++++||-|..|+..+|+.|.+.|+.|.
T Consensus 3 ~P~~GD~ViG~V~~i~~~~w~vdi~s~~~a~L~ls~v~~~~~~~d~~~mr~~l~iGDli~a~V~~v~~~~~v~L~~r~ 80 (86)
T cd05789 3 IPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRS 80 (86)
T ss_pred CCCCCCEEEEEEEEEECCCEEEECCCCEEEEEEHHHCCCCCCCHHHHHHHHHCCCCCEEEEEEEEECCCCCEEEEECC
T ss_conf 798899999999998088189974996077987454467776314677886566898999999998899979999656
No 96
>KOG1676 consensus
Probab=98.19 E-value=3e-05 Score=61.39 Aligned_cols=102 Identities=26% Similarity=0.375 Sum_probs=75.5
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCC--CCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEE-CCE----
Q ss_conf 99999999999999999843566743--32244875799997711500003786077998999868889980-880----
Q gi|254780784|r 519 MALQQAKRGRLHILNEMSKVLSESRL--QLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNID-DDG---- 591 (699)
Q Consensus 519 ~al~~A~~gr~~il~~m~~~~~~~~~--~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~-d~g---- 591 (699)
...++|+.=-..||+.=+...+-... .....+---..++||..|.|.|||.||.+||.|+.+||++|-+- ||+
T Consensus 195 ~~ve~a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~sp 274 (600)
T KOG1676 195 DKVEQAKQLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSP 274 (600)
T ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEECCCCCEEEEEECCCHHHHHHHHCCCCEEEEECCCCCCCC
T ss_conf 89998889999998730368774445457676654136885456523468704716788876335742686238888875
Q ss_pred --EEEEEECCHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf --899996898999999999998524754686
Q gi|254780784|r 592 --TVKIASSSLAEIEAAREMIRSITDVPEVNK 621 (699)
Q Consensus 592 --~v~i~~~~~~~~~~a~~~i~~~~~~~e~g~ 621 (699)
.+.|.+ +.+.++.|.+.|++|+...+.|.
T Consensus 275 eR~~~IiG-~~d~ie~Aa~lI~eii~~~~~~~ 305 (600)
T KOG1676 275 ERPAQIIG-TVDQIEHAAELINEIIAEAEAGA 305 (600)
T ss_pred CCEEEEEC-CHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 44256526-79999999999999999986047
No 97
>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=98.19 E-value=1e-05 Score=65.16 Aligned_cols=66 Identities=23% Similarity=0.357 Sum_probs=61.8
Q ss_pred CCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEE
Q ss_conf 867899999994153699828797104886631444547855603259889999997868-998666873
Q gi|254780784|r 620 NKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMK 688 (699)
Q Consensus 620 g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk 688 (699)
|++.+|+|++..+.|.+|++ .|.+|+|+.||++..++.+.+++ +|++++|+++++|+ ++++=+|||
T Consensus 1 g~~v~g~I~~~~kGG~~v~~-~gv~~FiP~Sq~~~~~~~~~~~~--vG~~i~~~Ii~~d~~~~~ivvSrk 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCCEEEEE-CCEEEEEECHHCCCCCCCCHHHH--CCCEEEEEEEEEECCCCEEEEECC
T ss_conf 99999999999857199999-99999988025255456896897--899899999999278899999879
No 98
>pfam00013 KH_1 KH domain. KH motifs can bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Q4R966.1/333-392;
Probab=98.13 E-value=8.7e-06 Score=65.73 Aligned_cols=56 Identities=41% Similarity=0.658 Sum_probs=51.0
Q ss_pred EEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHH
Q ss_conf 999977115000037860779989998688899808808999968989999999999
Q gi|254780784|r 554 EIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMI 610 (699)
Q Consensus 554 ~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i 610 (699)
..+.||+++++.+||++|++|+.|+++|||+|.+++...|.|+| +.+.+++|++++
T Consensus 2 ~~v~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~i~i~G-~~~~v~~A~~~i 57 (57)
T pfam00013 2 EEILIPSSLVGRIIGKGGSNIKEIREETGAKIRIPDRDTVTISG-TPEAVEKAKELI 57 (57)
T ss_pred EEEEECHHHCCEEECCCCCHHHHHHHHCCCEEEECCCCEEEEEC-CHHHHHHHHHHC
T ss_conf 89998755420689989647699999739999968999799994-999999999869
No 99
>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=98.10 E-value=1e-05 Score=65.19 Aligned_cols=68 Identities=28% Similarity=0.443 Sum_probs=60.9
Q ss_pred CCEEE-EEEEEEEE-CCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCC-CCEEEEE
Q ss_conf 86789-99999941-536998287971048866314445478556032598899999978689-9866687
Q gi|254780784|r 620 NKIYK-GQVVKVMD-FGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDR-GKIKLSM 687 (699)
Q Consensus 620 g~~y~-~~v~~i~~-fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~-g~i~lSr 687 (699)
|+|++ ++|+++-+ +|+|+++.+|..|++|||+|++++++..+.-+|+|...++++++.... |...||.
T Consensus 1 G~i~~~~~V~~v~~~~G~~~~l~~g~~gfvhiS~lsD~kv~~~~~~fk~Gs~H~~RVig~s~~D~l~~lSL 71 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CCCCCEEEEEEECCCCCEEEEECCCCEEEEEEHHCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCEEEECC
T ss_conf 96233405999858853799969996899996012666423665786479988899983474341488419
No 100
>PRK05054 exoribonuclease II; Provisional
Probab=98.08 E-value=2.9e-05 Score=61.49 Aligned_cols=70 Identities=17% Similarity=0.190 Sum_probs=54.9
Q ss_pred CCCCCC--EEEEEEEEEEECCEEEECCC-CCCEEEEEEECCCCC--CC----------CHHHHCCCCCEEEEEEEEECC-
Q ss_conf 754686--78999999941536998287-971048866314445--47----------855603259889999997868-
Q gi|254780784|r 616 VPEVNK--IYKGQVVKVMDFGAFVHFCG-ARDGLVHISQLSTER--VA----------KTSDVVKEGDTVWVKLLDFDD- 679 (699)
Q Consensus 616 ~~e~g~--~y~~~v~~i~~fGafve~~~-g~~gl~HiS~l~~~~--v~----------~~~d~~~~Gd~i~vk~~~~d~- 679 (699)
.-.+|+ +|.|.|+.+.+||.||+|.. |-|||+|+|-|...+ .. +-+-.+++||.|+|++..+|.
T Consensus 556 ~~~iG~~~~f~g~Is~vt~fG~fV~L~~~~~eG~V~~~~l~~~~~~~~~~~~~~~~~~~~~~~yrlGd~v~V~v~~vd~~ 635 (644)
T PRK05054 556 KDKAGTDTRFAAEIIDISRGGMRVRLLENGAIAFIPAPFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRME 635 (644)
T ss_pred HHHCCCCCEEEEEEEEEEECCEEEEEECCCEEEEEEEEECCCCCCEEEECCHHHHEECCCCEEEECCCEEEEEEEEEECH
T ss_conf 87448987278999759817789998668508999811325677338982022103405868997899999999998000
Q ss_pred CCCEEE
Q ss_conf 998666
Q gi|254780784|r 680 RGKIKL 685 (699)
Q Consensus 680 ~g~i~l 685 (699)
+++|-+
T Consensus 636 ~r~I~~ 641 (644)
T PRK05054 636 TRSIIA 641 (644)
T ss_pred HCEEEE
T ss_conf 184876
No 101
>smart00322 KH K homology RNA-binding domain.
Probab=98.05 E-value=3.2e-05 Score=61.14 Aligned_cols=63 Identities=37% Similarity=0.591 Sum_probs=57.1
Q ss_pred CEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECC----EEEEEEECCHHHHHHHHHHHHHHC
Q ss_conf 7579999771150000378607799899986888998088----089999689899999999999852
Q gi|254780784|r 551 PRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDD----GTVKIASSSLAEIEAAREMIRSIT 614 (699)
Q Consensus 551 p~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~----g~v~i~~~~~~~~~~a~~~i~~~~ 614 (699)
|....+.||.+.+|.+||++|++||.|++.||++|++.+. ..|.|.+. .+.++.|..+|..+.
T Consensus 2 ~~~~~i~vp~~~~g~iIG~~G~~i~~i~~~~~~~I~i~~~~~~~~~v~I~g~-~~~v~~a~~~i~~~i 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGP-PENVEKAAELILEIL 68 (69)
T ss_pred CEEEEEEECHHHCCEEECCCCCCHHHHHHHHCCEEEECCCCCCCCEEEEEEC-HHHHHHHHHHHHHHH
T ss_conf 8799999897876854999984579999972888997799998878999909-999999999999983
No 102
>KOG0119 consensus
Probab=98.04 E-value=5.1e-05 Score=59.53 Aligned_cols=153 Identities=18% Similarity=0.184 Sum_probs=100.1
Q ss_pred EEEEEEC-CEEEEEEECCCCCCCCCCCCEEEEECCC-CCEEEECCCCCCCCCHHHHHH-HHHHHHHHHHHHHHHHHHCCC
Q ss_conf 2004408-8289986314422013655100100556-512443245365568899999-999999999999999984356
Q gi|254780784|r 464 MGLVKDG-DDFIILSDISGDEDHLGHMDFKVAGTDS-GITAMQMDMKIGGISENIMVM-ALQQAKRGRLHILNEMSKVLS 540 (699)
Q Consensus 464 mGLi~~~-~~~~iLtDI~G~ED~~GdMDFKvaGT~~-GiTa~QmDiK~~gi~~~il~~-al~~A~~gr~~il~~m~~~~~ 540 (699)
-||+.+. +-|.+-.-|+-.--.++--||-|.=.++ -=-..-.+.-..|.-+-.-+. +-+.-..-|..++.++.+.++
T Consensus 45 ~~lt~eq~~~y~l~~~iee~t~kLrt~d~~~p~~~e~rSPsp~p~yda~g~R~ntRe~R~r~~Le~er~e~I~~~lk~nP 124 (554)
T KOG0119 45 GGLTEEQKESYSLNLRIEEITRKLRTGDVGVPPPRELRSPSPEPVYDAKGKRLNTREQRARKKLEDERHEIIEEILKLNP 124 (554)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 65560002334578999875333045657789872235898541023220203368999998888999999999998486
Q ss_pred C--CCCCCCCCCCEEEEEEECC------CCEEEEECCCCHHHHHHHHHHCCEEEEECC----------------------
Q ss_conf 6--7433224487579999771------150000378607799899986888998088----------------------
Q gi|254780784|r 541 E--SRLQLGEFTPRVEIMAIPP------DQIRNVIGMGGKVIRGIVEQTGAKVNIDDD---------------------- 590 (699)
Q Consensus 541 ~--~~~~~~~~ap~~~~~~i~~------~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~---------------------- 590 (699)
. |-.+.+.-+-.-..+.||. .++|-||||-|.|.|.|+++||+||-|--.
T Consensus 125 ~fkpP~DYk~p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~ep 204 (554)
T KOG0119 125 GFKPPADYKPPAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEP 204 (554)
T ss_pred CCCCCCCCCCCCCCCCCEECCHHHCCCCCEEEEEECCCCCHHHHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 87787555864213441313365467762257875478528888888748758996156534465677665656666666
Q ss_pred EEEEEEECCHHHHHHHHHHHHHHCCC
Q ss_conf 08999968989999999999985247
Q gi|254780784|r 591 GTVKIASSSLAEIEAAREMIRSITDV 616 (699)
Q Consensus 591 g~v~i~~~~~~~~~~a~~~i~~~~~~ 616 (699)
=++.|.|.+++++++|+++|++|..+
T Consensus 205 LH~~Isadt~eki~~Ai~vienli~~ 230 (554)
T KOG0119 205 LHCLISADTQEKIKKAIAVIENLIQS 230 (554)
T ss_pred EEEEEECCHHHHHHHHHHHHHHHHHH
T ss_conf 16898435599999999999999985
No 103
>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=98.01 E-value=2.6e-05 Score=61.87 Aligned_cols=57 Identities=37% Similarity=0.618 Sum_probs=51.2
Q ss_pred EEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECC------EEEEEEECCHHHHHHHHHHHH
Q ss_conf 9999771150000378607799899986888998088------089999689899999999999
Q gi|254780784|r 554 EIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDD------GTVKIASSSLAEIEAAREMIR 611 (699)
Q Consensus 554 ~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~------g~v~i~~~~~~~~~~a~~~i~ 611 (699)
..+.||.+.+|.|||++|++|+.|+++||+.|.+... ..|.|.|. .+.++.|+.+|.
T Consensus 2 ~~i~ip~~~~g~vIG~~G~~I~~I~~~~~~~I~i~~~~~~~~~~~v~i~G~-~~~v~~A~~~i~ 64 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT-PEAVEKAKELIL 64 (64)
T ss_pred EEEEECHHHCCEEECCCCCHHHHHHHHCCCEEEECCCCCCCCCEEEEEEEC-HHHHHHHHHHHC
T ss_conf 899973665426799898134799997598999888899998338999969-999999999629
No 104
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=98.01 E-value=3.5e-05 Score=60.86 Aligned_cols=196 Identities=21% Similarity=0.266 Sum_probs=108.4
Q ss_pred ECCCCCCCCCCCCEEEEECCCCCEEEECCCCC---CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCC--CCCCCCCCCCE
Q ss_conf 31442201365510010055651244324536---55688999999999999999999999843566--74332244875
Q gi|254780784|r 478 DISGDEDHLGHMDFKVAGTDSGITAMQMDMKI---GGISENIMVMALQQAKRGRLHILNEMSKVLSE--SRLQLGEFTPR 552 (699)
Q Consensus 478 DI~G~ED~~GdMDFKvaGT~~GiTa~QmDiK~---~gi~~~il~~al~~A~~gr~~il~~m~~~~~~--~~~~~~~~ap~ 552 (699)
.+.-..+.+++|.|.+..+...++.-|+...+ .|-+.+.+.+ .-.|.-|.++.=. +.....-..+.
T Consensus 479 k~~~l~~~l~~lg~~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~---------~~~lRsm~~a~Ys~~~~~HfgL~~~~ 549 (706)
T COG0557 479 KLQSLREFLQNLGLVLPLGGSKPQPQDYQILLETVKGRPLEAVLQ---------TLLLRSMKQAEYSPDNVGHFGLALDY 549 (706)
T ss_pred HHHHHHHHHHHCCEEECCCCCCCCHHHHHHHHHHCCCCHHHHHHH---------HHHHHHHCCCCCCCCCCCCEECCCCC
T ss_conf 899999999966811047877568799999976303762799999---------99986430063688887760114342
Q ss_pred EEEEEECCCCEEEEECCCCHHHHHHHHHHC-CEEEEEC--CEE----E-EEEECCHHHHHHHHHHHHHHC---CCCCCCC
Q ss_conf 799997711500003786077998999868-8899808--808----9-999689899999999999852---4754686
Q gi|254780784|r 553 VEIMAIPPDQIRNVIGMGGKVIRGIVEQTG-AKVNIDD--DGT----V-KIASSSLAEIEAAREMIRSIT---DVPEVNK 621 (699)
Q Consensus 553 ~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~-~~i~i~d--~g~----v-~i~~~~~~~~~~a~~~i~~~~---~~~e~g~ 621 (699)
...|.=|--+..++| +-|.|..--. -...... ... . .+......+.+...+.+.-.. ..-.+|+
T Consensus 550 YtHFTSPIRRY~DLi-----vHR~L~~~l~~~~~~~~~~~~~~l~~i~~~~s~~er~a~~aer~~~~~~~~~~m~~~vg~ 624 (706)
T COG0557 550 YTHFTSPIRRYPDLI-----VHRQLKALLSGEPIPEKKTSEEELDELAAHISSAERRAQEAERDVIDLLKAEYMKKRVGE 624 (706)
T ss_pred HHHCCCHHHHHHHHH-----HHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 221077465243799-----999999984468887453258899999885188999999988889999999999861587
Q ss_pred EEEEEEEEEEECCEEEECCC-CCCEEEEEEECCCC-----------CCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEE
Q ss_conf 78999999941536998287-97104886631444-----------547855603259889999997868-99866687
Q gi|254780784|r 622 IYKGQVVKVMDFGAFVHFCG-ARDGLVHISQLSTE-----------RVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSM 687 (699)
Q Consensus 622 ~y~~~v~~i~~fGafve~~~-g~~gl~HiS~l~~~-----------~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSr 687 (699)
.|+|.|+.+..||.||++.. |-|||+|+|.|... .-++..-.+.+||.|+|++.++|. .+++.++.
T Consensus 625 ~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~i~~~~ 703 (706)
T COG0557 625 EFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDERKIDFEL 703 (706)
T ss_pred EEEEEEEEEECCCEEEEECCCCEEEEEECCCCCCCEEECCHHHHHHHCCCCCCCCCCCCEEEEEEEEECCCCCCEEEEE
T ss_conf 6889999873275799962754033476355886103023011232035566542338869999998705656135885
No 105
>KOG1070 consensus
Probab=98.01 E-value=1e-05 Score=65.13 Aligned_cols=107 Identities=21% Similarity=0.283 Sum_probs=75.2
Q ss_pred HCCEEEEEC-CEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEECCEEEECCCCC--CEEEEEEECCCCCC
Q ss_conf 688899808-808999968989999999999985247546867899999994153699828797--10488663144454
Q gi|254780784|r 581 TGAKVNIDD-DGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGAR--DGLVHISQLSTERV 657 (699)
Q Consensus 581 ~~~~i~i~d-~g~v~i~~~~~~~~~~a~~~i~~~~~~~e~g~~y~~~v~~i~~fGafve~~~g~--~gl~HiS~l~~~~v 657 (699)
++.-..++. .+.+.+.-.+.+. ..+.. +-....+...|+.|+|.|.+.-+||.|+++-++- -||+|+||+++.|.
T Consensus 1214 ~~rv~~ve~~s~riel~Lk~s~~-~d~~~-~~~~~~~l~~gd~~~g~v~~~~~~G~fi~l~~tv~~~g~~~~~e~~d~~~ 1291 (1710)
T KOG1070 1214 TGRVLSVEEDSKRIELSLKNSDI-KDTVK-LLKDSKDLKKGDREDGTVEVVDPFGLFIKLDVTVNMVGLCHISEEADDRG 1291 (1710)
T ss_pred EEEEEEEECCCCEEEEEEECCCC-CCCHH-HHHHHHHHHCCCCCCCEEEEECCCCEEEEECCCCEECCCCCCEEECCHHH
T ss_conf 15899852368628999852666-88444-43455664226300434999368753898337503414443101232144
Q ss_pred CCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEE
Q ss_conf 7855603259889999997868-9986668730
Q gi|254780784|r 658 AKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKV 689 (699)
Q Consensus 658 ~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~ 689 (699)
.+....+..|+.+.+.|.+.|. +.||-|+.|.
T Consensus 1292 e~it~~~~~~~~V~a~~lk~~~ek~rIsl~~k~ 1324 (1710)
T KOG1070 1292 ENITALYYAGDRVKACVLKEDSEKKRISLGLKS 1324 (1710)
T ss_pred HHCCCCEECCCEEEEEEEECCCHHHHHHHHHHH
T ss_conf 421012112440026763125113121011455
No 106
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=97.96 E-value=2.6e-05 Score=61.93 Aligned_cols=78 Identities=35% Similarity=0.601 Sum_probs=62.1
Q ss_pred HHHCCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCC----------CCCCHHH-HCCCCCEEEEEEEEECC
Q ss_conf 985247546867899999994153699828797104886631444----------5478556-03259889999997868
Q gi|254780784|r 611 RSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTE----------RVAKTSD-VVKEGDTVWVKLLDFDD 679 (699)
Q Consensus 611 ~~~~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~----------~v~~~~d-~~~~Gd~i~vk~~~~d~ 679 (699)
+.+++.|+.|++.+|+|++..+||+||.+-| .+||+|+||+-+. .+.+-+. ++++||.|.+++++..-
T Consensus 73 ~al~fkP~~gEVV~GeVv~~~~~G~fV~igp-~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~ 151 (183)
T COG1095 73 RALVFKPFRGEVVEGEVVEVVEFGAFVRIGP-LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSL 151 (183)
T ss_pred EEEEEEECCCCEEEEEEEEEEECCEEEEECC-CCCCCCHHHCCCCCCCCCCCCCEEEECCCCEEEECCCEEEEEEEEEEC
T ss_conf 9999970356389999999961446999636-222113866657532527555412403651588419889999999614
Q ss_pred CC------CEEEEEEE
Q ss_conf 99------86668730
Q gi|254780784|r 680 RG------KIKLSMKV 689 (699)
Q Consensus 680 ~g------~i~lSrk~ 689 (699)
.. +|-|++|.
T Consensus 152 ~~~~~~~~~I~lTmrq 167 (183)
T COG1095 152 KSRRPRESKIGLTMRQ 167 (183)
T ss_pred CCCCCCCCEEEEEECC
T ss_conf 6776542169999536
No 107
>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=97.95 E-value=2.8e-05 Score=61.60 Aligned_cols=57 Identities=37% Similarity=0.539 Sum_probs=51.3
Q ss_pred EEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEEC----CEEEEEEECCHHHHHHHHHHHH
Q ss_conf 999977115000037860779989998688899808----8089999689899999999999
Q gi|254780784|r 554 EIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDD----DGTVKIASSSLAEIEAAREMIR 611 (699)
Q Consensus 554 ~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d----~g~v~i~~~~~~~~~~a~~~i~ 611 (699)
+.+.||+...+.|||+||.+||.|+++|||.|++-. +..|+|.|+ .+.+++|+++|.
T Consensus 2 ~~i~vp~~~h~~iIG~~G~~i~~i~~~~~~~I~~P~~~~~~~~V~I~G~-~~~V~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGP-KENVEKAKEEIL 62 (62)
T ss_pred CEEEECHHHCCCEECCCCCCHHHHHHHHCCEEEECCCCCCCCEEEEECC-HHHHHHHHHHHC
T ss_conf 4899897881975889997399999985979995899999983999839-999999999749
No 108
>KOG2916 consensus
Probab=97.95 E-value=6.9e-06 Score=66.56 Aligned_cols=80 Identities=28% Similarity=0.473 Sum_probs=74.3
Q ss_pred CCCCCCCEEEEEEEEEEECCEEEECC--CCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEECC
Q ss_conf 47546867899999994153699828--797104886631444547855603259889999997868-998666873047
Q gi|254780784|r 615 DVPEVNKIYKGQVVKVMDFGAFVHFC--GARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVVD 691 (699)
Q Consensus 615 ~~~e~g~~y~~~v~~i~~fGafve~~--~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~~ 691 (699)
.-|+++++.-+.|+.|.+-||+|.|+ .+.||++-.||||.+|+.++.-+.++|-.=.|-|+-+|. +|.|.||.+.+.
T Consensus 12 kyPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrVs 91 (304)
T KOG2916 12 KYPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVS 91 (304)
T ss_pred CCCCCCCEEEEEEEEEHHCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCEECHHCCCC
T ss_conf 59975327998753702062167621027811110035777888898999984077534899997177870662131388
Q ss_pred CCC
Q ss_conf 787
Q gi|254780784|r 692 QNT 694 (699)
Q Consensus 692 ~~~ 694 (699)
++.
T Consensus 92 ~ed 94 (304)
T KOG2916 92 PED 94 (304)
T ss_pred HHH
T ss_conf 778
No 109
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.95 E-value=5.2e-05 Score=59.47 Aligned_cols=69 Identities=16% Similarity=0.212 Sum_probs=65.1
Q ss_pred CCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCC--CCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEE
Q ss_conf 867899999994153699828797104886631444--547855603259889999997868-998666873
Q gi|254780784|r 620 NKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTE--RVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMK 688 (699)
Q Consensus 620 g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~--~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk 688 (699)
|+.+.|-|.++.+-+++|++.|+-.|-+++.+++++ ..++++..+++|+.++++|+++|. ++++.||.+
T Consensus 1 G~~v~gfV~n~~~~~~wv~iSp~V~gri~~l~lSdd~s~l~~~e~~FpvG~avk~~V~~vD~e~~~l~LS~r 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEECCCCEEEEEECCCEEEEEEHHHHCCCHHHHCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEC
T ss_conf 987999999725984999988881899970542688568538887299984599999998287788999803
No 110
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=97.92 E-value=2.8e-05 Score=61.60 Aligned_cols=78 Identities=35% Similarity=0.634 Sum_probs=62.8
Q ss_pred HHHCCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCC-----------CHHHHCCCCCEEEEEEEEEC-
Q ss_conf 985247546867899999994153699828797104886631444547-----------85560325988999999786-
Q gi|254780784|r 611 RSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVA-----------KTSDVVKEGDTVWVKLLDFD- 678 (699)
Q Consensus 611 ~~~~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~-----------~~~d~~~~Gd~i~vk~~~~d- 678 (699)
+.+++.|..|++++|+|+++.+||+||.+-| .++++|+|++.++.+. +-.-.++.||.|.+|++++.
T Consensus 73 ~~ivfrPf~~EVv~g~V~~~~~~G~fv~~Gp-~d~~vh~sqi~dd~~~fD~~~~~~ig~~s~~~i~~Gd~VR~RIv~vs~ 151 (182)
T PRK08563 73 DALVFKPELQEVVEGEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYISYDEKNGALIGKESKRTLKVGDVVRARIVAVSL 151 (182)
T ss_pred EEEEEECCCCCEEEEEEEEEECCEEEEEEEC-CCEEEEHHHCCCCCCEECCCCCEEEEECCCEEECCCCEEEEEEEEEEC
T ss_conf 8999941368489999999966769999846-611760999477762383656519990686498289989999999771
Q ss_pred ----CC-CCEEEEEEE
Q ss_conf ----89-986668730
Q gi|254780784|r 679 ----DR-GKIKLSMKV 689 (699)
Q Consensus 679 ----~~-g~i~lSrk~ 689 (699)
++ .||.|++|.
T Consensus 152 ~~~~~~~~kIglTmrq 167 (182)
T PRK08563 152 NEREPRDSKIGLTMRQ 167 (182)
T ss_pred CCCCCCCCEEEEEECC
T ss_conf 8888776626689538
No 111
>TIGR00448 rpoE DNA-directed RNA polymerase; InterPro: IPR004519 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to Escherichia coli RpoE.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription, 0005634 nucleus.
Probab=97.90 E-value=1.5e-05 Score=63.90 Aligned_cols=117 Identities=29% Similarity=0.568 Sum_probs=78.7
Q ss_pred EEEEECCCCEEEEECCCCHHHHHH---------HHHHCCEEEEEC-----CEEEEEEECCHHHHHHHHHHHHHHCCCCCC
Q ss_conf 999977115000037860779989---------998688899808-----808999968989999999999985247546
Q gi|254780784|r 554 EIMAIPPDQIRNVIGMGGKVIRGI---------VEQTGAKVNIDD-----DGTVKIASSSLAEIEAAREMIRSITDVPEV 619 (699)
Q Consensus 554 ~~~~i~~~ki~~~iG~gG~~ik~i---------~~~~~~~i~i~d-----~g~v~i~~~~~~~~~~a~~~i~~~~~~~e~ 619 (699)
-+++|||++-+.=+ -++|+.+ ..+.|--|.|.| +|+ |-.-|+.+.-... -+.+++.|+.
T Consensus 9 D~VriPPd~f~~D~---~~~i~~~L~e~f~grld~~~G~~iti~d~~~igeG~--~~~GDGs~Y~~V~--F~A~~FkP~l 81 (184)
T TIGR00448 9 DTVRIPPDKFGEDL---EEVITKLLNEKFEGRLDKNVGLVITIKDIEDIGEGK--VIEGDGSAYHNVV--FRALVFKPEL 81 (184)
T ss_pred EEEECCCCCCCCCH---HHHHHHHHHHHCCCCCCCCCCEEEEEEEEEECCCCE--EECCCCCCCCCEE--EEEEEECCCC
T ss_conf 06665832016668---999999865420464134564489888742315435--8707984310103--4688960352
Q ss_pred CCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCC--------------HHHHCCCCCEEEEEEEEE
Q ss_conf 8678999999941536998287971048866314445478--------------556032598899999978
Q gi|254780784|r 620 NKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAK--------------TSDVVKEGDTVWVKLLDF 677 (699)
Q Consensus 620 g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~--------------~~d~~~~Gd~i~vk~~~~ 677 (699)
+++.+|.|++|.+|||||.|+.=-|||+|+||+-.+-+.= ..-+|.+||.|..++..+
T Consensus 82 ~EiVeGev~~~~efG~fV~LlGp~D~l~h~sq~~ddy~~YdPk~~~liGPmD~Etk~~ld~gd~vRaRIv~~ 153 (184)
T TIGR00448 82 GEIVEGEVIEIVEFGAFVSLLGPFDGLLHVSQVLDDYVVYDPKESALIGPMDKETKKVLDVGDKVRARIVAL 153 (184)
T ss_pred EEEEEEEEEEEEECCCEEEEECCCCCEEEEEEEEECCEEECCCCCCEECCCCHHCCCEEECCCEEEEEEEEE
T ss_conf 167865899898527426752231323441001135636626566045674012173510167566788887
No 112
>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=97.84 E-value=9.7e-05 Score=57.24 Aligned_cols=56 Identities=30% Similarity=0.531 Sum_probs=49.0
Q ss_pred EEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEEC-------CEEEEEEECCHHHHHHHHHHH
Q ss_conf 999977115000037860779989998688899808-------808999968989999999999
Q gi|254780784|r 554 EIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDD-------DGTVKIASSSLAEIEAAREMI 610 (699)
Q Consensus 554 ~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d-------~g~v~i~~~~~~~~~~a~~~i 610 (699)
..|-||.+.+|.+||.||++||.|+++||++|.+.+ |-.|.|.|. .+++++|..+|
T Consensus 2 ~rilvP~~~vG~vIGk~G~~I~~i~~~sga~I~i~~~~~~~~~eR~v~I~G~-~~~v~~A~~~I 64 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGK-PSAVQKALLLI 64 (65)
T ss_pred EEEEEEHHHEEEEECCCCHHHHHHHHHHCCEEEECCCCCCCCCCEEEEEEEC-HHHHHHHHHHH
T ss_conf 8999874672289979987899999984988999988999999469999978-99999999853
No 113
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.81 E-value=0.00014 Score=55.88 Aligned_cols=84 Identities=31% Similarity=0.547 Sum_probs=66.9
Q ss_pred CEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEE-CCEEEEEEEC--CHHHHHHHHHHHHHHCCC--CC-----CC
Q ss_conf 75799997711500003786077998999868889980-8808999968--989999999999985247--54-----68
Q gi|254780784|r 551 PRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNID-DDGTVKIASS--SLAEIEAAREMIRSITDV--PE-----VN 620 (699)
Q Consensus 551 p~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~-d~g~v~i~~~--~~~~~~~a~~~i~~~~~~--~e-----~g 620 (699)
.-...++||+++|+.|||++|++.+.|++.++++|+++ ++|.|.|... |...+.+|.++|+.+..- || .-
T Consensus 3 ~~~~~v~IP~~Ri~~Lig~~g~~~~~Iee~~~~~i~idsk~g~V~i~~~~~dp~~~~Ka~d~i~Ai~rGF~~e~A~~Ll~ 82 (185)
T PRK13763 3 RMTEYVKIPKDRIGVLIGKKGETKKEIEEKTGVKLEIDSETGEVIIEPTEEDPLAVMKARDIVKAIGRGFSPEKALKLLD 82 (185)
T ss_pred CCEEEEECCCHHEEEEECCCCCCHHHHHHHHCCEEEEECCCCEEEEEECCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHC
T ss_conf 61256417805456455788563789999979779995899759998289998999989999999984899999999846
Q ss_pred CEEEEEEEEEEECC
Q ss_conf 67899999994153
Q gi|254780784|r 621 KIYKGQVVKVMDFG 634 (699)
Q Consensus 621 ~~y~~~v~~i~~fG 634 (699)
+-|.-.|..|.+|+
T Consensus 83 dd~~leiidi~~~~ 96 (185)
T PRK13763 83 DDYVLEVIDLSEYG 96 (185)
T ss_pred CCCEEEEEEHHHHC
T ss_conf 68369999988823
No 114
>PTZ00162 RNA polymerase II subunit 7; Provisional
Probab=97.68 E-value=9.3e-05 Score=57.37 Aligned_cols=68 Identities=16% Similarity=0.172 Sum_probs=55.9
Q ss_pred HHHCCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCC----------CCHHHHCCCCCEEEEEEEEECC
Q ss_conf 98524754686789999999415369982879710488663144454----------7855603259889999997868
Q gi|254780784|r 611 RSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERV----------AKTSDVVKEGDTVWVKLLDFDD 679 (699)
Q Consensus 611 ~~~~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v----------~~~~d~~~~Gd~i~vk~~~~d~ 679 (699)
+.+++.|..|++.+|+|+++.+||+|+++=|- ++|+|.|++....+ ++-+..++.||.|.+|++++.-
T Consensus 73 ~aivfkP~~~EVvdg~V~~v~~~G~fv~~GPl-~~fv~~s~i~~d~~yd~~~~~~~~~~~~~~i~kgd~VR~rIvg~~~ 150 (170)
T PTZ00162 73 QAIVFKPFKDEVLDAIVTDVNKLGFFAQAGPL-KIFVSRTAIPPNFVYDSDSAYPCFSDGTISIKPQSEVRLRLQGIRY 150 (170)
T ss_pred EEEEEECCCCCEEEEEEEEEECCEEEEEECCE-EEEEEHHHCCCCCEECCCCCCCEECCCCCEECCCCEEEEEEEEEEE
T ss_conf 99999336798999999999640799991280-8998989999864897899860482788388889999999999873
No 115
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.67 E-value=0.00023 Score=54.13 Aligned_cols=64 Identities=28% Similarity=0.436 Sum_probs=55.3
Q ss_pred EEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHCCC
Q ss_conf 7999977115000037860779989998688899808808999968989999999999985247
Q gi|254780784|r 553 VEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDV 616 (699)
Q Consensus 553 ~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~~ 616 (699)
=..++|+|.|+..|||++|+.|+.|.++|+++|-+.++|.|-|-+.+.+....|.+.|+.+-.+
T Consensus 145 G~li~V~p~~VpRvIGk~gsmi~~ik~~t~~~I~VG~NG~IWI~g~~~~~~~~a~~aI~~Ie~e 208 (232)
T PRK04163 145 GTIVEIKPSKVPRVIGKKGSMINMLKEETGCDIIVGQNGRIWIKGKNEEDEELAIEAIKKIERE 208 (232)
T ss_pred CEEEEECHHHCCEEECCCCHHHHHHHHHHCCEEEECCCCEEEEECCCHHHHHHHHHHHHHHHHH
T ss_conf 8899973121871455883599997652195899917978999769888999999999999986
No 116
>PRK11712 ribonuclease G; Provisional
Probab=97.66 E-value=0.00027 Score=53.56 Aligned_cols=40 Identities=10% Similarity=0.133 Sum_probs=35.0
Q ss_pred EEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCE
Q ss_conf 5799997711500003786077998999868889980880
Q gi|254780784|r 552 RVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDG 591 (699)
Q Consensus 552 ~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g 591 (699)
+-.++..+|+-+.-+.+.....+..|++.+|.+|.+.-|-
T Consensus 438 ~~i~v~~~~~v~~~l~~~~~~~l~~lE~~~~~~i~i~~d~ 477 (489)
T PRK11712 438 DRFLVYASPAVAEALKGEESHALAELEVFIGKQVKVQIEP 477 (489)
T ss_pred CEEEEEECHHHHHHHHCCCHHHHHHHHHHHCCCEEEEECC
T ss_conf 7399998899999987157899999999859938999589
No 117
>KOG1676 consensus
Probab=97.64 E-value=0.00033 Score=52.94 Aligned_cols=95 Identities=23% Similarity=0.337 Sum_probs=66.2
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCE---EEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECC-------
Q ss_conf 99999999999999984356674332244875---79999771150000378607799899986888998088-------
Q gi|254780784|r 521 LQQAKRGRLHILNEMSKVLSESRLQLGEFTPR---VEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDD------- 590 (699)
Q Consensus 521 l~~A~~gr~~il~~m~~~~~~~~~~~~~~ap~---~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~------- 590 (699)
++.|.+=...|+..-++--..+ ..-.+|. ...|.||.+|-|.+||+||-|||.|..++|+.+.+.-+
T Consensus 287 ie~Aa~lI~eii~~~~~~~~~~---~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ 363 (600)
T KOG1676 287 IEHAAELINEIIAEAEAGAGGG---MGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPK 363 (600)
T ss_pred HHHHHHHHHHHHHHHHCCCCCC---CCCCCCCCEEEEEEECCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCC
T ss_conf 9999999999999986047777---6778754101588964510004454788630011103677513656789999865
Q ss_pred EEEEEEECCHHHHHHHHHHHHHHCCCCC
Q ss_conf 0899996898999999999998524754
Q gi|254780784|r 591 GTVKIASSSLAEIEAAREMIRSITDVPE 618 (699)
Q Consensus 591 g~v~i~~~~~~~~~~a~~~i~~~~~~~e 618 (699)
-++.+.--++..++-|+.+|+.-+-++-
T Consensus 364 ektf~IrG~~~QIdhAk~LIr~kvg~~~ 391 (600)
T KOG1676 364 EKTFVIRGDKRQIDHAKQLIRDKVGDIA 391 (600)
T ss_pred CEEEEEECCCCCCHHHHHHHHHHHCCCC
T ss_conf 3379883672215489999998855657
No 118
>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=97.54 E-value=0.00064 Score=50.58 Aligned_cols=58 Identities=21% Similarity=0.313 Sum_probs=50.0
Q ss_pred CCCEEEEECCCCHHHHHHHHHHCCEEEEEC-----------------------CEEEEEEECC--HHHHHHHHHHHHHHC
Q ss_conf 115000037860779989998688899808-----------------------8089999689--899999999999852
Q gi|254780784|r 560 PDQIRNVIGMGGKVIRGIVEQTGAKVNIDD-----------------------DGTVKIASSS--LAEIEAAREMIRSIT 614 (699)
Q Consensus 560 ~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d-----------------------~g~v~i~~~~--~~~~~~a~~~i~~~~ 614 (699)
-+.+|.+|||+|.+.|.|+++|||+|.|-- +=+|.|.+.+ .+++++|...|+.+.
T Consensus 14 ~Nfvg~ilGprG~t~k~l~~~t~~~i~irG~GS~Kd~~~e~~~~~~~~~hl~epLHVlI~a~~~~~e~~~~a~~~i~~ll 93 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CCEEEEEECCCCCHHHHHHHHHCCEEEEEECCCCCCCCCHHHCCCCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHH
T ss_conf 88567887798506999999879879997178766765354436899855689977999953988999999999999981
Q ss_pred CCC
Q ss_conf 475
Q gi|254780784|r 615 DVP 617 (699)
Q Consensus 615 ~~~ 617 (699)
..+
T Consensus 94 ~p~ 96 (120)
T cd02395 94 KPA 96 (120)
T ss_pred CCC
T ss_conf 789
No 119
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=97.54 E-value=6.7e-05 Score=58.54 Aligned_cols=50 Identities=6% Similarity=0.025 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHH
Q ss_conf 99999999999843566743322448757999977115000037860779
Q gi|254780784|r 525 KRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVI 574 (699)
Q Consensus 525 ~~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~i 574 (699)
+.++..+-.+|..+++.-..+.-++--.+.++.+...--.=-.-|-||+.
T Consensus 579 ~q~~~~ve~qL~aa~~~vk~~~l~nGi~~~tlDVE~yahkFtfP~pGk~~ 628 (715)
T COG1107 579 EQAKEAVEEQLRAALPHVKSERLPNGIAFNTLDVENYAHKFTFPPPGKLS 628 (715)
T ss_pred HHHHHHHHHHHHHHHHCCCEEECCCCEEEEEEEHHHCCCCCCCCCCCCCC
T ss_conf 99999999999976413432662586378986253413456579986442
No 120
>PRK12704 phosphodiesterase; Provisional
Probab=97.41 E-value=0.0018 Score=46.82 Aligned_cols=86 Identities=21% Similarity=0.348 Sum_probs=51.4
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECC-CCEEEEECCCCHHHHHHHHHHCCEEEEECC-EEEEEEECCHHHH
Q ss_conf 99999999998435667433224487579999771-150000378607799899986888998088-0899996898999
Q gi|254780784|r 526 RGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPP-DQIRNVIGMGGKVIRGIVEQTGAKVNIDDD-GTVKIASSSLAEI 603 (699)
Q Consensus 526 ~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i~~-~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~-g~v~i~~~~~~~~ 603 (699)
.+|.-|+..|+..-+..- ++ .-+.++.+|- +..|.+||.-|.|||.++.-|||.|-|+|. +.|.|++.|.---
T Consensus 124 ~Ar~Ii~~AIQR~A~e~~---~E--~tvsvV~LPsdemKGRIIGREGRNIRa~E~~TGVDlIIDDtPe~V~lS~FDpvRR 198 (455)
T PRK12704 124 KAKEILAQAIQRCAAEHA---AE--NTVSVVNLPNDEMKGRIIGREGRNIRTLETLTGVDIIIDDTPEAVILSGFDPIRR 198 (455)
T ss_pred HHHHHHHHHHHHHCCCCC---CH--HEEEEEECCCHHHHCCCCCCCCCHHHHHHHHHCCEEEECCCCCEEEEECCCHHHH
T ss_conf 999999999986364300---13--1046685485676464007775239999998696489759998378856877889
Q ss_pred HHHHHHHHHHCCC
Q ss_conf 9999999985247
Q gi|254780784|r 604 EAAREMIRSITDV 616 (699)
Q Consensus 604 ~~a~~~i~~~~~~ 616 (699)
+-|+.-++.|+.+
T Consensus 199 EiAr~aLe~Li~D 211 (455)
T PRK12704 199 EIARLALEKLVED 211 (455)
T ss_pred HHHHHHHHHHHHC
T ss_conf 9999999999884
No 121
>PRK10811 rne ribonuclease E; Reviewed
Probab=97.41 E-value=0.00023 Score=54.25 Aligned_cols=22 Identities=9% Similarity=0.172 Sum_probs=12.8
Q ss_pred ECCCCCCCCEEEEEECCCEEEE
Q ss_conf 4475466700899987976899
Q gi|254780784|r 329 VGLLQRTHGSSLFIRGDTQAIV 350 (699)
Q Consensus 329 vgvLPrvHGSALFtRGETQaL~ 350 (699)
..+-|++||++..---|+.+|.
T Consensus 401 ~~~CP~C~G~G~ir~~es~al~ 422 (1063)
T PRK10811 401 HHVCPRCSGTGTVRDNESLSLS 422 (1063)
T ss_pred CCCCCCCCCCCEECCHHHHHHH
T ss_conf 7748888770022572888999
No 122
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.40 E-value=0.00082 Score=49.71 Aligned_cols=85 Identities=32% Similarity=0.501 Sum_probs=66.3
Q ss_pred CCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEE-CCEEEEEEEC----CHHHHHHHHHHHHHHCC--CCC---
Q ss_conf 4875799997711500003786077998999868889980-8808999968----98999999999998524--754---
Q gi|254780784|r 549 FTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNID-DDGTVKIASS----SLAEIEAAREMIRSITD--VPE--- 618 (699)
Q Consensus 549 ~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~-d~g~v~i~~~----~~~~~~~a~~~i~~~~~--~~e--- 618 (699)
..+..+.+.||+++++-+||+.|++-|.|++.+++++.++ ++|.|.|... |.-++.+|.++|+.+.. .|+
T Consensus 5 ~~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~A~ 84 (194)
T COG1094 5 AEKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEKAL 84 (194)
T ss_pred CCCCEEEEECCCHHHEEEECCCCCCHHHHHHHCCEEEEEECCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCHHHHH
T ss_conf 20010455457045101225663105898861575899977877699983687788588998999999986689989999
Q ss_pred --CCCEEEEEEEEEEEC
Q ss_conf --686789999999415
Q gi|254780784|r 619 --VNKIYKGQVVKVMDF 633 (699)
Q Consensus 619 --~g~~y~~~v~~i~~f 633 (699)
.-+-|.-.|.+|.+|
T Consensus 85 ~LL~d~~~levIdi~~~ 101 (194)
T COG1094 85 KLLEDDYYLEVIDLKDV 101 (194)
T ss_pred HHHCCCCEEEEEEHHHH
T ss_conf 98627857999997884
No 123
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=97.40 E-value=0.0015 Score=47.60 Aligned_cols=74 Identities=18% Similarity=0.196 Sum_probs=67.0
Q ss_pred CCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf 75468678999999941536998287971048866314445478556032598899999978689986668730
Q gi|254780784|r 616 VPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKV 689 (699)
Q Consensus 616 ~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk~ 689 (699)
.|++|++..|+|+++..-.|.|+|..-.++.||.|.....---++...|++||.|..++..+++.|.+-|+-+.
T Consensus 3 ~P~vGDvVigrV~~v~~~~w~vdI~~~~~a~l~~~~~~~~D~~~m~~~f~~GDlI~A~V~~~~~~~~~~L~T~~ 76 (82)
T cd04454 3 LPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDDMNVLLTTAD 76 (82)
T ss_pred CCCCCCEEEEEEEEECCCEEEEEECCCEEEEEEEHHCCCCCHHHHHHHCCCCCEEEEEEEEECCCCCEEEEECC
T ss_conf 79899999999999707818999686328897302167730667987458776899999997699978999566
No 124
>KOG1070 consensus
Probab=97.39 E-value=0.00019 Score=54.85 Aligned_cols=77 Identities=23% Similarity=0.294 Sum_probs=71.9
Q ss_pred CCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEEC
Q ss_conf 247546867899999994153699828797104886631444547855603259889999997868-99866687304
Q gi|254780784|r 614 TDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVV 690 (699)
Q Consensus 614 ~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~ 690 (699)
+.+.+.|++.+|-|+.+.+-|.|+.+.++.++++-||+++.......+-.|.+|+.+..+|..+|+ .+|+-||.|.-
T Consensus 1157 ~eDlk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~s 1234 (1710)
T KOG1070 1157 IEDLKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKNS 1234 (1710)
T ss_pred HHHCCCCCEEEEEEEEECCCCEEEEECCCEEEEEECCCCCCCHHHHHHCCCCCCCEEEEEEEEEECCCCEEEEEEECC
T ss_conf 432255764688999703774899971562899983456640232221138854443158998523686289998526
No 125
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.38 E-value=0.0014 Score=47.83 Aligned_cols=75 Identities=20% Similarity=0.271 Sum_probs=66.6
Q ss_pred CCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCC----CCHHHHCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf 754686789999999415369982879710488663144454----785560325988999999786899866687304
Q gi|254780784|r 616 VPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERV----AKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVV 690 (699)
Q Consensus 616 ~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v----~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk~~ 690 (699)
.|++|++.-|+|+.+...+|+|++-.-.+++||+|+.-.++. .+...+|++||-|..++..+|+.+.+.|+.|..
T Consensus 59 ~P~~GD~VIG~V~~v~~~~W~VDI~s~~~a~L~~s~~~~r~~~~~~~~mr~~l~~GDlI~ArV~~v~~~~~~~Lt~k~~ 137 (232)
T PRK04163 59 IPKKGDLVIGKVTDVGFSGWEVDINSPYKAILPVSEVLGRPVDVESTDLRKYLDIGDYIIAKVKDVDETKDVVLTLKGR 137 (232)
T ss_pred CCCCCCEEEEEEEEECCCEEEEECCCCCEEEECHHHCCCCCCCCCHHHHHHHCCCCCEEEEEEEEECCCCCEEEEECCC
T ss_conf 5876998999999831871799869960558524445665555643567751788988999999966899789995489
No 126
>KOG2191 consensus
Probab=97.36 E-value=0.006 Score=42.68 Aligned_cols=115 Identities=24% Similarity=0.339 Sum_probs=71.8
Q ss_pred EECCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHH---HHHCCCCCCCCCCCCCC-EE--EEEEECCCCEEEEE
Q ss_conf 00556512443245365568899999999999999999999---98435667433224487-57--99997711500003
Q gi|254780784|r 494 AGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNE---MSKVLSESRLQLGEFTP-RV--EIMAIPPDQIRNVI 567 (699)
Q Consensus 494 aGT~~GiTa~QmDiK~~gi~~~il~~al~~A~~gr~~il~~---m~~~~~~~~~~~~~~ap-~~--~~~~i~~~ki~~~i 567 (699)
-||.+-|.-+|=-++ ||.. ..-.|+|+ |-....+|.+-+.+-.| |+ ..+-+|..--|-+|
T Consensus 82 PGTTeRvcli~Gt~e-----------ai~a---v~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~ii 147 (402)
T KOG2191 82 PGTTERVCLIQGTVE-----------ALNA---VHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMII 147 (402)
T ss_pred CCCCCEEEEEECCHH-----------HHHH---HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCCCCCCCEE
T ss_conf 996325899725299-----------9999---99999999987677515863234777755333047851477656233
Q ss_pred CCCCHHHHHHHHHHCCEEEEE-CC-------EEEEEEECCHHHHHHHHHHH-HHHCCCCCCCCE
Q ss_conf 786077998999868889980-88-------08999968989999999999-985247546867
Q gi|254780784|r 568 GMGGKVIRGIVEQTGAKVNID-DD-------GTVKIASSSLAEIEAAREMI-RSITDVPEVNKI 622 (699)
Q Consensus 568 G~gG~~ik~i~~~~~~~i~i~-d~-------g~v~i~~~~~~~~~~a~~~i-~~~~~~~e~g~~ 622 (699)
|+||-+||.|+|++++-|.|. .+ -+|.....+.+...+|..+| +.++.+|.-+..
T Consensus 148 gkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~sc 211 (402)
T KOG2191 148 GKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSC 211 (402)
T ss_pred CCCCCCHHHHHHHHCCEEEEECCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCCE
T ss_conf 3775208999985086389613687776500589983089899999999999986438765542
No 127
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=97.31 E-value=0.0028 Score=45.42 Aligned_cols=54 Identities=28% Similarity=0.337 Sum_probs=24.8
Q ss_pred CCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf 6502467999999987410786446873899985311027852235667777987625950
Q gi|254780784|r 394 PSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVP 454 (699)
Q Consensus 394 ~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp 454 (699)
|=|||| |.+||+..+-+.---|..|.=+-+ .+.---..-..-.|-=|+++.||+
T Consensus 254 pvRREi-----Ar~aLe~Li~DGRIhP~rIEe~v~--k~~~e~~~~i~~~Ge~a~~elgi~ 307 (514)
T TIGR03319 254 PVRREI-----ARMALEKLIQDGRIHPARIEEMVE--KATKEVDNAIREEGEQAAFDLGVH 307 (514)
T ss_pred HHHHHH-----HHHHHHHHHHCCCCCHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 688999-----999999998749948899999999--999999999999999999981999
No 128
>KOG2190 consensus
Probab=97.23 E-value=0.0034 Score=44.63 Aligned_cols=40 Identities=33% Similarity=0.496 Sum_probs=28.7
Q ss_pred CCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEE
Q ss_conf 4875799997711500003786077998999868889980
Q gi|254780784|r 549 FTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNID 588 (699)
Q Consensus 549 ~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~ 588 (699)
+.-.-..+-||.++|+-+||++|.+|-.|...||+.|.|-
T Consensus 335 ~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~ 374 (485)
T KOG2190 335 TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISIL 374 (485)
T ss_pred CCEEEEEECCCCCCCCEEECCCCCCHHHHHHHCCCCEEEC
T ss_conf 5222123215700000132566530578987328836972
No 129
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=97.19 E-value=0.002 Score=46.55 Aligned_cols=73 Identities=34% Similarity=0.417 Sum_probs=64.1
Q ss_pred CCCCCCCEEEEEEEEEEECCEEEECCC-----------CCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCE
Q ss_conf 475468678999999941536998287-----------971048866314445478556032598899999978689986
Q gi|254780784|r 615 DVPEVNKIYKGQVVKVMDFGAFVHFCG-----------ARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKI 683 (699)
Q Consensus 615 ~~~e~g~~y~~~v~~i~~fGafve~~~-----------g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i 683 (699)
..|++|++..|+|+++.+--|+|+|+- ...|.+|+|++....+.++.|.++.||.|..|++...+ .+
T Consensus 60 ~~p~vGdiVig~V~~v~~~~a~v~I~~v~g~~~~~l~~~~~g~i~i~~v~~~~~~~~~d~fr~gDIVrAkVis~~~--~~ 137 (187)
T PRK09521 60 PLLKKGDIVYGRVVDVKEQRALVRIVSIEGRGNRELATSKLGGIHISQVSDGYVEDLTDAFKIGDIVRAKVISTTD--PI 137 (187)
T ss_pred CCCCCCCEEEEEEEEECCCEEEEEEEEECCCCCCCCCCCEEEEEEECCCCHHHHHHHHHHCCCCCEEEEEEEECCC--CE
T ss_conf 7889899999999995476799999998686886256544888885437866745267524878689999973598--46
Q ss_pred EEEEEE
Q ss_conf 668730
Q gi|254780784|r 684 KLSMKV 689 (699)
Q Consensus 684 ~lSrk~ 689 (699)
.||-+.
T Consensus 138 ~Lst~~ 143 (187)
T PRK09521 138 QLSTKG 143 (187)
T ss_pred EEEECC
T ss_conf 999538
No 130
>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=97.16 E-value=0.00076 Score=49.97 Aligned_cols=61 Identities=31% Similarity=0.423 Sum_probs=54.5
Q ss_pred CEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEE
Q ss_conf 500003786077998999868889980880899996898999999999998524754686789
Q gi|254780784|r 562 QIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYK 624 (699)
Q Consensus 562 ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~~~e~g~~y~ 624 (699)
.+|.+||++|++.+.|++-||+.|.+-+ -+|.|.| +.+.++.|++.|+.|..--+-|.+|.
T Consensus 99 ~~GRIIGk~Gktr~~IE~~T~~~I~v~g-~tV~IiG-~~~~i~~Ar~aI~~Li~G~~h~~Vy~ 159 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYG-KTVGIIG-DPEQVQIAREAIEMLIEGAPHGTVYK 159 (172)
T ss_pred HHHHHCCCCCHHHHHHHHHHCCEEEECC-CEEEEEC-CHHHHHHHHHHHHHHHCCCCCHHHHH
T ss_conf 8773158996199999997687499719-8899977-98998999999999986999378999
No 131
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.08 E-value=0.0036 Score=44.50 Aligned_cols=74 Identities=24% Similarity=0.447 Sum_probs=50.4
Q ss_pred CCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCC----CHHHHCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf 7546867899999994153699828797104886631444547----8556032598899999978689986668730
Q gi|254780784|r 616 VPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVA----KTSDVVKEGDTVWVKLLDFDDRGKIKLSMKV 689 (699)
Q Consensus 616 ~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~----~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk~ 689 (699)
-|++|++.-|+|..+...++.|.|-.-...+||+|++-++.++ +...+|++||-|-.|+..+|+.+...|+-|.
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
T ss_conf 488899999999997156338972895323742666200225542234522267687899999972677753799606
No 132
>pfam03725 RNase_PH_C 3' exoribonuclease family, domain 2. This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.
Probab=97.08 E-value=0.00094 Score=49.22 Aligned_cols=65 Identities=29% Similarity=0.468 Sum_probs=55.6
Q ss_pred CCCCEEEEEEEEECCEEEEEEECCCCCCCCC--CCCEEEEECCCCCEEEECCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 5412133200440882899863144220136--5510010055651244324536556889999999999999
Q gi|254780784|r 457 KPVAGIAMGLVKDGDDFIILSDISGDEDHLG--HMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRG 527 (699)
Q Consensus 457 ~~VaGiamGLi~~~~~~~iLtDI~G~ED~~G--dMDFKvaGT~~GiTa~QmDiK~~gi~~~il~~al~~A~~g 527 (699)
.||+++++|+| +.+ ++.|-...||..+ ||+|.++||++.++-+|.+.+ +++.+.|.++|+.|+++
T Consensus 1 ~~v~avtvg~i---~~~-~i~dpt~~Ee~~~~~~l~v~~~~~~~~v~~~~~g~~--~l~~~~l~~~l~~a~~~ 67 (67)
T pfam03725 1 GPVAAVTVGKI---DGE-LVLDPTLEEESLADSDLTIVVAGTGDIVALMKEGGG--GLTEEELLEALELAHKG 67 (67)
T ss_pred CCEEEEEEEEE---CCE-EEECCCHHHHHHHCCEEEEEEECCCCEEEEECCCCC--CCCHHHHHHHHHHHCCC
T ss_conf 98899999999---999-999989678633147368999689999999918997--85999999999987079
No 133
>PRK13764 ATPase; Provisional
Probab=97.05 E-value=0.00073 Score=50.08 Aligned_cols=148 Identities=18% Similarity=0.278 Sum_probs=94.0
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHH
Q ss_conf 99999999999998435667433224487579999771150000378607799899986888998088089999689899
Q gi|254780784|r 523 QAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAE 602 (699)
Q Consensus 523 ~A~~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~ 602 (699)
..+-+...|.+.+.+.+ .++.+++--.+.-..++|+.+.|..+||.||++|..|+...|..||+...+.-..-..+...
T Consensus 456 ~~~~a~~~i~~~i~r~~-~~~~eV~~~~d~~avv~v~~~~i~~~igK~g~~i~~ie~~lgi~IdV~~~~e~~~~~~~~~~ 534 (605)
T PRK13764 456 VWKLAEEEIEREIKRYL-KGPVEVEVISDNKAVVYVPEKDIPAVIGKGGKNISKIEKKLGIDIDVRPLSEEEYEEPNSGE 534 (605)
T ss_pred HHHHHHHHHHHHHHHHC-CCCCEEEEECCCEEEEEECCCCCHHHHCCCCCCHHHHHHHHCCCEEEEECCCCCCCCCCCCC
T ss_conf 88999999999998746-89834999649868999764531366555974799999864883576576656644555456
Q ss_pred HHHHHHHHHHHCCCCCCCCEEEEEEEEEEECCEEEECC-CCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEE
Q ss_conf 99999999985247546867899999994153699828-7971048866314445478556032598899999
Q gi|254780784|r 603 IEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFC-GARDGLVHISQLSTERVAKTSDVVKEGDTVWVKL 674 (699)
Q Consensus 603 ~~~a~~~i~~~~~~~e~g~~y~~~v~~i~~fGafve~~-~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~ 674 (699)
...-....-.....+|.-|.|+.+++--=|-++--. .|+.|-+|+++=+.- -..+...++.|..|.+..
T Consensus 535 --~~~~~~t~k~~i~~v~~~~~g~~v~i~~~~eylftAtV~~~G~Ikl~k~S~i-~~~l~~a~~~g~~I~~~~ 604 (605)
T PRK13764 535 --PVKVEETKKHVILIVGPDYAGKIVDIYAGGEYLFTATVSRKGEIKLAKNSDI-AKELLRAIDKGEDIRVRP 604 (605)
T ss_pred --CCCEEEECCEEEEEECHHHCCCEEEEEECCEEEEEEEECCCCEEEECCCCHH-HHHHHHHHHCCCCEEEEE
T ss_conf --6324884347999948677898789998999999999069814996579868-999999986799669986
No 134
>PRK12705 hypothetical protein; Provisional
Probab=96.88 E-value=0.0053 Score=43.08 Aligned_cols=56 Identities=23% Similarity=0.192 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCC
Q ss_conf 650246799999998741078644687389998531102785223566777798762595022
Q gi|254780784|r 394 PSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPIS 456 (699)
Q Consensus 394 ~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp~~ 456 (699)
|=|||| |.+||+..+-+..--|. |+..-|-.+..--..-.--.|-=|+++.||+--
T Consensus 224 PiRREi-----Ar~aLe~Li~DGRIhPa--RIEe~v~ka~~e~~~~i~e~Ge~a~~elgi~~l 279 (485)
T PRK12705 224 PIRREI-----ARITLEKLLLDGRIDPA--RIEEYVQKANEEFEQKCYEIGKEVLEELGIFDL 279 (485)
T ss_pred HHHHHH-----HHHHHHHHHHCCCCCHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 789999-----99999999984891889--999999999999999999999999998099999
No 135
>PRK00106 hypothetical protein; Provisional
Probab=96.83 E-value=0.014 Score=39.70 Aligned_cols=55 Identities=20% Similarity=0.233 Sum_probs=28.4
Q ss_pred CCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf 65024679999999874107864468738999853110278522356677779876259502
Q gi|254780784|r 394 PSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPI 455 (699)
Q Consensus 394 ~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp~ 455 (699)
|=|||| |.+||+..+-+.---|.-| .--|-.+----..--.-.|-=|+++.|++-
T Consensus 275 pvRREi-----Ar~aLe~Li~DGRIhPaRI--Ee~v~k~~~e~~~~i~e~Ge~a~~elgi~~ 329 (535)
T PRK00106 275 PIRREI-----ARMTLESLIKDGRIHPARI--EELVEKNRLEMDNRIREYGEAAAYEIGAPN 329 (535)
T ss_pred HHHHHH-----HHHHHHHHHHCCCCCHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 789999-----9999999998189288889--999999999999999999999999809999
No 136
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=96.80 E-value=0.0033 Score=44.81 Aligned_cols=60 Identities=28% Similarity=0.424 Sum_probs=54.6
Q ss_pred CEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEE
Q ss_conf 50000378607799899986888998088089999689899999999999852475468678
Q gi|254780784|r 562 QIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIY 623 (699)
Q Consensus 562 ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~~~e~g~~y 623 (699)
.+|.+||++|++-+.|++-|++.|++-++- |.|.|. -+.++.|++.|+.+..--.-|++|
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~t-VaiiG~-~~~v~iAr~AVemli~G~~h~~Vy 171 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGKT-VAIIGG-FEQVEIAREAVEMLINGAPHGKVY 171 (194)
T ss_pred HHCEEECCCCHHHHHHHHHHCCEEEEECCE-EEEECC-HHHHHHHHHHHHHHHCCCCCHHHH
T ss_conf 651024888508999999868809982768-999468-266699999999997699952599
No 137
>KOG1613 consensus
Probab=96.79 E-value=0.0055 Score=42.97 Aligned_cols=118 Identities=24% Similarity=0.239 Sum_probs=74.9
Q ss_pred EEEEEEECEECCCCCCEEEEEECCCEEEEEEEEC------CCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf 8999991400454672899997894899999727------8888777735406866523201336788873578988714
Q gi|254780784|r 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYD------RSLKDGQDFFPLTVNYQERTYAVGKIPGGYLRRESRPTEN 87 (699)
Q Consensus 14 r~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~------~~~~~~~dFfPLtVdY~Ek~yAaGkIPGgF~kREgrpsd~ 87 (699)
|+..++-|-+.. ||||.+++.|+|+|+|.+.+. ..|++| +-. -+|.-..--.- .=|-|+|+|.
T Consensus 47 Rdt~in~g~IsT-angSal~K~G~ttvi~~Ik~ei~epstdapdeg-~Iv---~n~~lpplcs~------r~RpG~p~de 115 (298)
T KOG1613 47 RDTAINAGNIST-ANGSALLKSGKTTVICGIKAEIAEPSTDAPDEG-DIV---PNYALPPLCSS------RFRPGPPTDE 115 (298)
T ss_pred HHHHEECCCEEC-CCCHHHHHCCCCEEEEEEEEEECCCCCCCCCCC-CEE---ECCCCCCCCCC------CCCCCCCCHH
T ss_conf 665200375403-674777734880899976432116665799876-454---13567863246------7778897237
Q ss_pred H----------HHHHHHHHCCCCCCCCCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 5----------31111232126776746886883789999821888877899999999998732688
Q gi|254780784|r 88 E----------ILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLP 144 (699)
Q Consensus 88 E----------iL~sRlIDR~lRPLFPkgf~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIP 144 (699)
+ ||.||+|+--===+|+.-+..=.---+.+|+||+..- -++.+|+=|||.-=.+|
T Consensus 116 a~viSq~LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG~~f--Da~w~al~aAlknvklP 180 (298)
T KOG1613 116 AQVISQKLHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDGPVF--DACWNALMAALKNVKLP 180 (298)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHEEECCCEEEEEEEEEEEECCCCCHH--HHHHHHHHHHHHCCCCC
T ss_conf 788999999999862774425531103624657777799984888489--99999999998427786
No 138
>KOG1588 consensus
Probab=96.79 E-value=0.046 Score=35.50 Aligned_cols=73 Identities=21% Similarity=0.309 Sum_probs=51.3
Q ss_pred CCEEEEEEECCC------CEEEEECCCCHHHHHHHHHHCCEEEEECCE------------------------EEEEE--E
Q ss_conf 875799997711------500003786077998999868889980880------------------------89999--6
Q gi|254780784|r 550 TPRVEIMAIPPD------QIRNVIGMGGKVIRGIVEQTGAKVNIDDDG------------------------TVKIA--S 597 (699)
Q Consensus 550 ap~~~~~~i~~~------ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g------------------------~v~i~--~ 597 (699)
.-..+.+.||.+ .+|.|+||-|-++|.++++|+|+|-|--.| +|.|. +
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~ 169 (259)
T KOG1588 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEA 169 (259)
T ss_pred EEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCEEEEECCCCCCCHHHHHHHHCCCCHHHHCCCCEEEEEEEC
T ss_conf 16778888315778887611311068753199999987976999668766665779985148466774887279999738
Q ss_pred CCHHH---HHHHHHHHHHHCCCCCCCCE
Q ss_conf 89899---99999999985247546867
Q gi|254780784|r 598 SSLAE---IEAAREMIRSITDVPEVNKI 622 (699)
Q Consensus 598 ~~~~~---~~~a~~~i~~~~~~~e~g~~ 622 (699)
+-.++ +..|.+.|+.+......+.+
T Consensus 170 p~~ea~~rl~~AleeI~klL~P~~e~~d 197 (259)
T KOG1588 170 PPAEAYARLAYALEEIKKLLVPDHEDED 197 (259)
T ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCH
T ss_conf 8899999999999999986378877735
No 139
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.78 E-value=0.026 Score=37.52 Aligned_cols=229 Identities=19% Similarity=0.236 Sum_probs=108.3
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCCC-CCEEEEEECCCEEEEEEEECCCCCCCCCC-CCC
Q ss_conf 7889999999999999987288665886775337879984475466-70089998797689999816865212233-445
Q gi|254780784|r 290 EIVSVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRT-HGSSLFIRGDTQAIVVVTLGTREDEQYVD-SLS 367 (699)
Q Consensus 290 ~i~~af~~l~k~ivR~~ILeeg~R~DGR~~dEIRpIs~EvgvLPrv-HGSALFtRGETQaL~tvTLG~~~d~Q~iD-~l~ 367 (699)
..+..+.+-.+++-|+.++++-.--=| +| ++ |..-|. .|.-++.=|.|.++ .|.++|... .+.
T Consensus 109 ~AKQvi~QkireaEr~~i~~ey~~r~G----ei--V~---G~V~r~~~~~~~Vdlg~~ea~------LP~~eqip~E~~~ 173 (353)
T PRK12327 109 TAKQVIMQRLREAEREVIYNEFKEREG----DI--VT---GTVQRDDNRFVYVNLGKIEAV------LPPAEQIPGETYK 173 (353)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCC----CE--EE---EEEEEECCCCEEEEECCEEEE------CCHHHCCCCCCCC
T ss_conf 999999999999999999999987439----66--99---999997588589997882464------6879869987779
Q ss_pred CCCEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHH
Q ss_conf 44203587740588754453345567650246799999998741078644687389998531102785223566777798
Q gi|254780784|r 368 GTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLA 447 (699)
Q Consensus 368 ~~~~k~fmlHYNFPpfsvGE~~~~~~~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~sla 447 (699)
.-.+-++++. .|.. ..+|.+=-=.--|..|.++=|+.=+|.-.+. +|-+.+=.=+. |+-+=-+|-+.
T Consensus 174 ~Gdrika~i~------~V~~-~~kgp~I~lSRt~p~~v~~Lfe~EVPEI~dG--~VeIk~iaRep-G~RtKvAV~s~--- 240 (353)
T PRK12327 174 HGDRIKVYVV------KVEK-TTKGPQIFVSRTHPGLVKRLFELEVPEIYDG--TVEIVSIAREA-GDRTKIAVRSN--- 240 (353)
T ss_pred CCCEEEEEEE------EEEE-CCCCCEEEEECCCHHHHHHHHHHHCHHHHCC--EEEEEEEECCC-CCCEEEEEEEC---
T ss_conf 9997999999------9997-5997479996498899999998636686388--29999960167-87148999925---
Q ss_pred HHHCCCCCCCCCCEEEEEEEEECCEEEEEEECCCCCCCCCCCCEEEEECCCCCEEEECCC-CCCCCCHHHHHHHHHHHHH
Q ss_conf 762595022541213320044088289986314422013655100100556512443245-3655688999999999999
Q gi|254780784|r 448 LMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDM-KIGGISENIMVMALQQAKR 526 (699)
Q Consensus 448 l~dagvp~~~~VaGiamGLi~~~~~~~iLtDI~G~ED~~GdMDFKvaGT~~GiTa~QmDi-K~~gi~~~il~~al~~A~~ 526 (699)
|.+ -+|| |..+|.= +.+..-.+.-|+-| ..|| .-.-=+...+..||.-|+.
T Consensus 241 --d~~---iDpv-GAcVG~~--G~RI~~I~~EL~gE--------------------kIDii~~s~d~~~fi~nALsPA~v 292 (353)
T PRK12327 241 --NPN---VDAI-GACVGPK--GQRVQNIVNELKGE--------------------KIDIIDWSEDPAEFIANALSPAKV 292 (353)
T ss_pred --CCC---CCCC-EEEECCC--CCHHHHHHHHHCCC--------------------EEEEEECCCCHHHHHHHHCCCCCE
T ss_conf --999---8840-5888799--72599999874777--------------------788996789889999973797610
Q ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEEC
Q ss_conf 999999999843566743322448757999977115000037860779989998688899808
Q gi|254780784|r 527 GRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDD 589 (699)
Q Consensus 527 gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d 589 (699)
-+..| .+-.-+...+-+|.+.....||.+|.|+|.-..=||-+|||-.
T Consensus 293 ~~V~i---------------~de~~k~~~ViV~~~qlslAIGk~GqNvrLAs~Ltgw~IdI~s 340 (353)
T PRK12327 293 VSVEV---------------DDEEEKAARVVVPDYQLSLAIGKEGQNARLAAKLTGWKIDIKS 340 (353)
T ss_pred EEEEE---------------ECCCCCEEEEEECCHHHHHHHCCCCCHHHHHHHHHCCEEEEEE
T ss_conf 38999---------------7587866999988104157627997749999997799799856
No 140
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=96.74 E-value=0.009 Score=41.21 Aligned_cols=74 Identities=30% Similarity=0.420 Sum_probs=63.7
Q ss_pred HCCCCCCCCEEEEEEEEEEECCEEEECCC--C--------CCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCC
Q ss_conf 52475468678999999941536998287--9--------7104886631444547855603259889999997868998
Q gi|254780784|r 613 ITDVPEVNKIYKGQVVKVMDFGAFVHFCG--A--------RDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGK 682 (699)
Q Consensus 613 ~~~~~e~g~~y~~~v~~i~~fGafve~~~--g--------~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~ 682 (699)
...-|+.|++.-|.|+++..-.|.|++.. + ..|-+|||+.+...+++..|.++.||.|.-+++..- -.
T Consensus 58 ~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~--~~ 135 (188)
T COG1096 58 TPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG--DP 135 (188)
T ss_pred CCCCCCCCCEEEEEEEECCCCEEEEEEEEEECCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCEEEEEEEECC--CC
T ss_conf 7776898879999995326608999999994333367887402589782023111020134464617999998617--87
Q ss_pred EEEEEE
Q ss_conf 666873
Q gi|254780784|r 683 IKLSMK 688 (699)
Q Consensus 683 i~lSrk 688 (699)
+.||-+
T Consensus 136 ~~Lst~ 141 (188)
T COG1096 136 IQLSTK 141 (188)
T ss_pred EEEEEC
T ss_conf 189852
No 141
>PRK13763 putative RNA-processing protein; Provisional
Probab=96.69 E-value=0.0032 Score=44.84 Aligned_cols=61 Identities=33% Similarity=0.443 Sum_probs=54.3
Q ss_pred CEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEE
Q ss_conf 500003786077998999868889980880899996898999999999998524754686789
Q gi|254780784|r 562 QIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYK 624 (699)
Q Consensus 562 ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~~~e~g~~y~ 624 (699)
.+|.+||++||+-+.|++-|++.|.|-+.- |.|.| +.+.++.|++-|+.|..--+-|.+|.
T Consensus 105 ~~gRIIG~~Gktr~~IE~lT~t~I~V~g~t-V~IiG-~~~~i~~Ar~AI~~Li~Gs~h~~Vy~ 165 (185)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVKISVYGKT-VAIIG-DPEQVEIAREAIEMLIEGAPHGTVYK 165 (185)
T ss_pred HHHHHCCCCCHHHHHHHHHHCCEEEEECCE-EEEEC-CHHHHHHHHHHHHHHHCCCCCHHHHH
T ss_conf 987870899539999999878779982889-99976-88888999999999976998177999
No 142
>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=96.60 E-value=0.011 Score=40.38 Aligned_cols=73 Identities=21% Similarity=0.275 Sum_probs=62.6
Q ss_pred CCCCCCEEEEEEEEEEECCEEEECCC--------CCCEEEEEEECCCCCCCCH--HHHCCCCCEEEEEEEEECCCCCEEE
Q ss_conf 75468678999999941536998287--------9710488663144454785--5603259889999997868998666
Q gi|254780784|r 616 VPEVNKIYKGQVVKVMDFGAFVHFCG--------ARDGLVHISQLSTERVAKT--SDVVKEGDTVWVKLLDFDDRGKIKL 685 (699)
Q Consensus 616 ~~e~g~~y~~~v~~i~~fGafve~~~--------g~~gl~HiS~l~~~~v~~~--~d~~~~Gd~i~vk~~~~d~~g~i~l 685 (699)
.|++|++..++|+++.+--|+++|+- .-.|++|.+.+......++ .+-++.||.|..+++...+...+.|
T Consensus 3 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~l~~~f~g~Ir~~dVr~te~d~v~m~~~FrpGDIVrA~Vislgd~~~y~L 82 (92)
T cd05791 3 LPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSYYL 82 (92)
T ss_pred CCCCCCEEEEEEEEECCCEEEEEEEEECCEECCCEEEEEEEHHHCCCCCCCCEEHHHCCCCCCEEEEEEEECCCCCEEEE
T ss_conf 68899999999999711378999999999983762578879244343555304341354999899999997478724999
Q ss_pred EEE
Q ss_conf 873
Q gi|254780784|r 686 SMK 688 (699)
Q Consensus 686 Srk 688 (699)
|-.
T Consensus 83 STa 85 (92)
T cd05791 83 STA 85 (92)
T ss_pred EEC
T ss_conf 853
No 143
>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=96.59 E-value=0.0064 Score=42.42 Aligned_cols=71 Identities=23% Similarity=0.393 Sum_probs=59.1
Q ss_pred CCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCC-------------------CCHHHHCCCCCEEEEEEEEEC
Q ss_conf 4686789999999415369982879710488663144454-------------------785560325988999999786
Q gi|254780784|r 618 EVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERV-------------------AKTSDVVKEGDTVWVKLLDFD 678 (699)
Q Consensus 618 e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v-------------------~~~~d~~~~Gd~i~vk~~~~d 678 (699)
..|...-|.|++|.+++..|.|+.|.-|.+.|.+++..-. ...++++++||.+.++|+..|
T Consensus 2 ~~G~lvLG~V~~I~~~~l~isLP~~L~G~V~it~ISd~~t~~le~~~~~~~~~~~~~e~~~L~~lF~vGq~vr~~V~s~~ 81 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLD 81 (100)
T ss_pred CCCCEEEEEEEEECCCCEEEECCCCCEEEEEHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHCCCCCEEEEEEEECC
T ss_conf 88989999998984663899858985899887885299999999987300236763234587884768989999999845
Q ss_pred CC--C--CEEEEEE
Q ss_conf 89--9--8666873
Q gi|254780784|r 679 DR--G--KIKLSMK 688 (699)
Q Consensus 679 ~~--g--~i~lSrk 688 (699)
.. | ||.||.+
T Consensus 82 ~~~~~~krI~LSl~ 95 (100)
T cd05693 82 KSKSGKKRIELSLE 95 (100)
T ss_pred CCCCCCEEEEEECC
T ss_conf 88778548999828
No 144
>KOG2193 consensus
Probab=96.57 E-value=0.0038 Score=44.30 Aligned_cols=59 Identities=24% Similarity=0.294 Sum_probs=38.0
Q ss_pred EEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEEC-------CEEEEEEECCHHHHHHHHHHHHH
Q ss_conf 7999977115000037860779989998688899808-------80899996898999999999998
Q gi|254780784|r 553 VEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDD-------DGTVKIASSSLAEIEAAREMIRS 612 (699)
Q Consensus 553 ~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d-------~g~v~i~~~~~~~~~~a~~~i~~ 612 (699)
+..+-||...+|++||..|++||.|...+|++|.|.- +-.|.|.|+ .++.-+|..+|-+
T Consensus 412 ~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGp-peaqfKAQgrifg 477 (584)
T KOG2193 412 QVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGP-PEAQFKAQGRIFG 477 (584)
T ss_pred HEEEECCHHHHHHHHCCCCHHHHHHHHHCCCEEEECCCCCCCCCEEEEEECCC-HHHHHHHHHHHHH
T ss_conf 20144408888888712422189998742760343588887620279984498-6998765403543
No 145
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.50 E-value=0.016 Score=39.19 Aligned_cols=92 Identities=21% Similarity=0.330 Sum_probs=65.2
Q ss_pred HHHHHHHHHHHCCCC---CCCCCCCCCCEEEEEEECC------CCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEE---
Q ss_conf 999999999843566---7433224487579999771------1500003786077998999868889980880899---
Q gi|254780784|r 527 GRLHILNEMSKVLSE---SRLQLGEFTPRVEIMAIPP------DQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVK--- 594 (699)
Q Consensus 527 gr~~il~~m~~~~~~---~~~~~~~~ap~~~~~~i~~------~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~--- 594 (699)
-|+.+.+.-.+.++. |....++ +---..+.||. ..+|-+|||-|.+.|++++.++++|-|--.|.|+
T Consensus 121 er~~l~era~k~lp~fv~p~dy~rp-sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk 199 (269)
T COG5176 121 ERLWLKERAQKILPRFVLPNDYIRP-SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGK 199 (269)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCCCC-CCCCCEEEEEHHHCCCCCEEEEEECCCCCHHHHHHHHHCCEEEEECCCCCCCCC
T ss_conf 7889999998753763487433575-312322786631076654347876587426999988757748996366534575
Q ss_pred EEECCHHHHHHHHHHHHHHCC-CCCC
Q ss_conf 996898999999999998524-7546
Q gi|254780784|r 595 IASSSLAEIEAAREMIRSITD-VPEV 619 (699)
Q Consensus 595 i~~~~~~~~~~a~~~i~~~~~-~~e~ 619 (699)
+.+..++++..|-+-++.++. +.|.
T Consensus 200 ~ssd~p~~~~N~e~~lhcLI~adsed 225 (269)
T COG5176 200 ISSDTPESLKNAEAVLHCLIEADSED 225 (269)
T ss_pred CCCCCCHHHHHHHHHHHHHHHCCHHH
T ss_conf 45668433310477677775230145
No 146
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.38 E-value=0.035 Score=36.42 Aligned_cols=229 Identities=19% Similarity=0.252 Sum_probs=109.9
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCCC-CCEEEEEECCCEEEEEEEECCCCCCCCCC-CCC
Q ss_conf 7889999999999999987288665886775337879984475466-70089998797689999816865212233-445
Q gi|254780784|r 290 EIVSVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRT-HGSSLFIRGDTQAIVVVTLGTREDEQYVD-SLS 367 (699)
Q Consensus 290 ~i~~af~~l~k~ivR~~ILeeg~R~DGR~~dEIRpIs~EvgvLPrv-HGSALFtRGETQaL~tvTLG~~~d~Q~iD-~l~ 367 (699)
..+..+.+-.+++-|+.+.++-.--=| + +-.|..-|+ +|.-+..=|.|.++ .|..+|... .+.
T Consensus 110 ~AkQvi~QkireaEr~~i~~ef~~r~G----e-----iv~G~V~r~~~~~i~Vdlg~~ea~------Lp~~e~ip~E~~~ 174 (428)
T PRK09202 110 AAKQVIVQKIREAERERVYEEYKDRVG----E-----IITGTVKRVERGNIIVDLGRAEAI------LPRDEQIPRENFR 174 (428)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCC----C-----EEEEEEEEECCCCEEEEECCEEEE------CCHHHCCCCCCCC
T ss_conf 999999999999999999999987329----8-----899999997278389997882575------6478769986679
Q ss_pred CCCEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHH
Q ss_conf 44203587740588754453345567650246799999998741078644687389998531102785223566777798
Q gi|254780784|r 368 GTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLA 447 (699)
Q Consensus 368 ~~~~k~fmlHYNFPpfsvGE~~~~~~~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~sla 447 (699)
.-.+-++++. .|.. ..+|.+=-=.--|..|.+|=|+.=+|.-.+. +|.+.+=.=+. |+-+=-+|-..
T Consensus 175 ~Gdrik~~i~------~V~~-~~kg~qi~lSRt~p~~v~~Lfe~EVPEI~dG--~IeIk~iaRep-G~RtKiAV~s~--- 241 (428)
T PRK09202 175 PGDRVRAYVY------EVRK-EARGPQIILSRTHPEFLKKLFEQEVPEIAEG--LIEIKAIARDP-GSRAKIAVKSN--- 241 (428)
T ss_pred CCCEEEEEEE------EHHC-CCCCCEEEEECCCHHHHHHHHHHHHHHHHCC--EEEEEEEECCC-CCCEEEEEECC---
T ss_conf 9987999872------0212-5898579995487899999998645685388--29999861367-87237999725---
Q ss_pred HHHCCCCCCCCCCEEEEEEEEECCEEEEEEECCCCCCCCCCCCEEEEECCCCCEEEECCC-CCCCCCHHHHHHHHHHHHH
Q ss_conf 762595022541213320044088289986314422013655100100556512443245-3655688999999999999
Q gi|254780784|r 448 LMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDM-KIGGISENIMVMALQQAKR 526 (699)
Q Consensus 448 l~dagvp~~~~VaGiamGLi~~~~~~~iLtDI~G~ED~~GdMDFKvaGT~~GiTa~QmDi-K~~gi~~~il~~al~~A~~ 526 (699)
| |=-+||.. -+|.= +.+..-.+.-|+-| ..|| .-.-=+...+..||.-|+.
T Consensus 242 --d---~~iDpVGA-cVG~r--GsRI~~I~~EL~gE--------------------kIDIi~~s~d~~~fi~nAlsPA~v 293 (428)
T PRK09202 242 --D---KRIDPVGA-CVGMR--GSRIQAISNELNGE--------------------KIDIILWSDDPAQFIINALSPAEV 293 (428)
T ss_pred --C---CCCCCCEE-EECCC--CCCHHHHHHHHCCC--------------------EEEEEECCCCHHHHHHHHCCCCCC
T ss_conf --9---99785137-77788--64299999874677--------------------689996788889999981794212
Q ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECC
Q ss_conf 9999999998435667433224487579999771150000378607799899986888998088
Q gi|254780784|r 527 GRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDD 590 (699)
Q Consensus 527 gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~ 590 (699)
-+. +++ +- -+...+-+|.+.....||.+|.|+|.-..=||-+|||-.+
T Consensus 294 ~~V-~id--------------e~-~~~~~VvV~d~qlSlAIGk~GqNvrLAs~Ltgw~IdI~s~ 341 (428)
T PRK09202 294 SSI-VVD--------------ED-KHSMDVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 341 (428)
T ss_pred EEE-EEC--------------CC-CCEEEEEECCCCHHHHHCCCCEEHHHHHHHHCCEEEEEEH
T ss_conf 189-972--------------77-8889999886522477577868599999977986999558
No 147
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=96.34 E-value=0.011 Score=40.41 Aligned_cols=22 Identities=14% Similarity=0.012 Sum_probs=9.7
Q ss_pred CCCCCCCCCCCCCEEEEEEEEE
Q ss_conf 2677674688688378999982
Q gi|254780784|r 98 SIRPLFSKCYKNETQVIINVMQ 119 (699)
Q Consensus 98 ~lRPLFPkgf~~evQIv~~VLS 119 (699)
+|+.++-.++.-=|||+..-..
T Consensus 83 ~i~~~lr~~~~~~Vqv~ke~~G 104 (487)
T COG1530 83 KIKVRLRGGQATLVQVVKEPRG 104 (487)
T ss_pred CCEEEECCCCEEEEEEEEECCC
T ss_conf 5005541786289999862576
No 148
>KOG0336 consensus
Probab=96.30 E-value=0.0027 Score=45.49 Aligned_cols=31 Identities=19% Similarity=0.500 Sum_probs=19.2
Q ss_pred EEEEEEECCCCCCCCCCCCEEEEECCCCCEEEECCCCCCC
Q ss_conf 2899863144220136551001005565124432453655
Q gi|254780784|r 472 DFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGG 511 (699)
Q Consensus 472 ~~~iLtDI~G~ED~~GdMDFKvaGT~~GiTa~QmDiK~~g 511 (699)
.|.+|. .-|-.=||-|-++ |--+-+||...-
T Consensus 369 TYlVlD----EADrMLDMgFEpq-----IrkilldiRPDR 399 (629)
T KOG0336 369 TYLVLD----EADRMLDMGFEPQ-----IRKILLDIRPDR 399 (629)
T ss_pred EEEEEC----CHHHHHCCCCCHH-----HHHHHHHCCCCC
T ss_conf 889861----2666644566288-----898865227762
No 149
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=95.89 E-value=0.038 Score=36.19 Aligned_cols=65 Identities=20% Similarity=0.330 Sum_probs=57.0
Q ss_pred CCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf 6867899999994153699828797104886631444547855603259889999997868998666873047
Q gi|254780784|r 619 VNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVD 691 (699)
Q Consensus 619 ~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk~~~ 691 (699)
.++...|+|-++.+.|.||-.-.+--|++|=||-- ....+|+.+++.++++.+.|+++||-+.+.
T Consensus 155 ~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~--------~~prlG~~l~~rVi~~reDg~lnLSl~p~~ 219 (287)
T COG2996 155 KNQEVDATVYRLLESGTFVITENGYLGFIHKSERF--------AEPRLGERLTARVIGVREDGKLNLSLRPRA 219 (287)
T ss_pred HCCEEEEEEEEEECCCEEEEECCCEEEEECCHHHC--------CCCCCCCEEEEEEEEECCCCEEECCCCCCC
T ss_conf 43761059999821423999718768998606600--------666677557889999824874502215631
No 150
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=95.84 E-value=0.03 Score=36.97 Aligned_cols=63 Identities=29% Similarity=0.490 Sum_probs=52.8
Q ss_pred EEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHCCC
Q ss_conf 999977115000037860779989998688899808808999968989999999999985247
Q gi|254780784|r 554 EIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDV 616 (699)
Q Consensus 554 ~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~~ 616 (699)
..+.|+|.|...+||++|..++-+.++|+++|-+..+|.|-|-+.+...-..|...|..+-.+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG~IWV~~~~~~~e~~~~~aI~~ie~e 210 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNGRIWVDGENESLEELAIEAIRKIERE 210 (239)
T ss_pred EEEEECHHHCCEEECCCCCHHHHHHHCCCEEEEEECCCEEEECCCCCCHHHHHHHHHHHHHHH
T ss_conf 899976022524766886478876540576899966988996278863279999999987554
No 151
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.74 E-value=0.073 Score=33.85 Aligned_cols=230 Identities=18% Similarity=0.234 Sum_probs=108.7
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCCCC--CEEEEEECCCEEEEEEEECCCCCCCCCCC-C
Q ss_conf 78899999999999999872886658867753378799844754667--00899987976899998168652122334-4
Q gi|254780784|r 290 EIVSVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTH--GSSLFIRGDTQAIVVVTLGTREDEQYVDS-L 366 (699)
Q Consensus 290 ~i~~af~~l~k~ivR~~ILeeg~R~DGR~~dEIRpIs~EvgvLPrvH--GSALFtRGETQaL~tvTLG~~~d~Q~iD~-l 366 (699)
..+..+.+-.+++-|+.+.++-+--=| .+-+|..-|++ |..+..-|.|.++- |..+|.... +
T Consensus 113 ~AKQvi~QkireaEr~~i~~efk~r~G---------eiV~G~V~r~~~~~~~~vdlg~~ea~L------p~~eqip~E~y 177 (375)
T PRK12328 113 TLFKELEYHIQRLLEDSIFEKYKEKVG---------SVVFGTVVRVDNEENTFIEIDEIRAIL------PMKNRIKGEKF 177 (375)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCC---------CEEEEEEEEEECCCCEEEECCCCEEEE------CHHHCCCCCCC
T ss_conf 999999999999999999999986429---------489999999965884899739817980------27763886558
Q ss_pred CCCCEEEEEEEECCCCCCCCCCCCCCC---CCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHH
Q ss_conf 544203587740588754453345567---65024679999999874107864468738999853110278522356677
Q gi|254780784|r 367 SGTQRNDFMMHYNFLPCATGEVSRMGA---PSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCG 443 (699)
Q Consensus 367 ~~~~~k~fmlHYNFPpfsvGE~~~~~~---~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~ 443 (699)
..-.+=++++- .|....+.|. .|| -|-.|..|=|+.=+|.-.+. +|.|.+=.=+.---|-.| |-+
T Consensus 178 ~~Gdrik~~i~------~V~~~~~~gpqI~lSR---t~p~fv~~LFe~EVPEI~dG--~VeIk~IaRepG~RtKIA-V~S 245 (375)
T PRK12328 178 KVGDVVKAVLR------RVKIDKKNGIKLELSR---TSPKFLEALLELEVPEIKDG--EVIIIHCARIPGERAKVA-LFS 245 (375)
T ss_pred CCCCEEEEEEE------EEECCCCCCCEEEEEC---CCHHHHHHHHHHHHHHHHCC--CEEEEEEECCCCCCEEEE-EEE
T ss_conf 99986999999------9872789995899967---98899999999888998489--689999853788740699-992
Q ss_pred HHHHHHHCCCCCCCCCCEEEEEEEEECCEEEEEEECCCCCCCCCCCCEEEEECCCCCEEEECCCC-CCCCCHHHHHHHHH
Q ss_conf 77987625950225412133200440882899863144220136551001005565124432453-65568899999999
Q gi|254780784|r 444 SSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMK-IGGISENIMVMALQ 522 (699)
Q Consensus 444 ~slal~dagvp~~~~VaGiamGLi~~~~~~~iLtDI~G~ED~~GdMDFKvaGT~~GiTa~QmDiK-~~gi~~~il~~al~ 522 (699)
. |.+ -+||.. -+|.= +.+..-.+.-|+-| ..|+= -.-=+...+..||.
T Consensus 246 ~-----d~~---iDpVGA-cVG~k--G~RI~~I~~EL~gE--------------------kIDii~~s~d~~~fi~nALs 294 (375)
T PRK12328 246 N-----SAN---IDPVGA-TVGVK--GVRINAVSKELNGE--------------------NIDCIEYSNIPEIFIARALA 294 (375)
T ss_pred C-----CCC---CCCEEE-EECCC--CCCHHHHHHHHCCC--------------------EEEEEECCCCHHHHHHHCCC
T ss_conf 5-----998---674047-88888--63099999985796--------------------27899778888999986378
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEE
Q ss_conf 99999999999998435667433224487579999771150000378607799899986888998088089
Q gi|254780784|r 523 QAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTV 593 (699)
Q Consensus 523 ~A~~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v 593 (699)
-|+.-+..| .+ ..+-..+-+|.+.....||.+|.|+|.-..-||-+|||-.+...
T Consensus 295 PA~V~~V~i---------------~e-~~~~a~viV~~~qlSlAIGk~GqNvrLAskLtgw~IDI~s~~~~ 349 (375)
T PRK12328 295 PAIILSVKI---------------EK-IPKKAIVTLPSEQKSKAIGKNGINIRLASMLTGYEIELNEIGSV 349 (375)
T ss_pred CCCCEEEEE---------------EC-CCCEEEEEECCHHHHHHHCCCCCHHHHHHHHHCCEEEEEEHHHH
T ss_conf 553018999---------------56-88879999880143376269987199999977987998677887
No 152
>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=95.56 E-value=0.1 Score=32.72 Aligned_cols=67 Identities=18% Similarity=0.234 Sum_probs=55.2
Q ss_pred CCCCCCEEEEEEEEEEECCEEEEC-CCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCE-EEEEE
Q ss_conf 754686789999999415369982-87971048866314445478556032598899999978689986-66873
Q gi|254780784|r 616 VPEVNKIYKGQVVKVMDFGAFVHF-CGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKI-KLSMK 688 (699)
Q Consensus 616 ~~e~g~~y~~~v~~i~~fGafve~-~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i-~lSrk 688 (699)
++..|.+..|.|+++.|.|..+++ .+|..|+|--.++... .-+++|+-+.+.+.+++..|++ +||-.
T Consensus 1 dl~~g~~l~a~V~SvEDHGyild~Gi~~~~gFl~~k~~~~~------~~l~~G~v~~c~V~~v~~~g~vv~ls~~ 69 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSAD 69 (74)
T ss_pred CCCCCCEEEEEEEEEECCEEEEECCCCCCEEEEEHHHCCCC------CCCCCCCEEEEEEEEEECCCEEEEEECC
T ss_conf 96678299999856714418998477772667301334755------6334887899999999289609999668
No 153
>KOG2193 consensus
Probab=95.55 E-value=0.013 Score=39.83 Aligned_cols=85 Identities=19% Similarity=0.252 Sum_probs=58.8
Q ss_pred HHHHHHHHHCC-CCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEEC--------CEEEEEEECC
Q ss_conf 99999998435-66743322448757999977115000037860779989998688899808--------8089999689
Q gi|254780784|r 529 LHILNEMSKVL-SESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDD--------DGTVKIASSS 599 (699)
Q Consensus 529 ~~il~~m~~~~-~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d--------~g~v~i~~~~ 599 (699)
-.|..+..+.- ..|.++++- -.-+++|..-+|.+||.||||+++++--|++.+-+-. .-.|.|.|.
T Consensus 473 grifgKikEenf~~Pkeevkl----ethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGh- 547 (584)
T KOG2193 473 GRIFGKIKEENFFLPKEEVKL----ETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGH- 547 (584)
T ss_pred HHHHHHHHHHCCCCCHHHHEE----EEEEECCCHHHHHHHCCCCCCHHHHHCCCCCEEECCCCCCCCCCCEEEEEEHHH-
T ss_conf 035433312215684666233----355313405654231457743898850456458755557998664355131125-
Q ss_pred HHHHHHHHHHHHHHCCCCC
Q ss_conf 8999999999998524754
Q gi|254780784|r 600 LAEIEAAREMIRSITDVPE 618 (699)
Q Consensus 600 ~~~~~~a~~~i~~~~~~~e 618 (699)
--+-..|...|..|+..+.
T Consensus 548 fyatq~aQrki~~iv~qvk 566 (584)
T KOG2193 548 FYATQNAQRKIAHIVNQVK 566 (584)
T ss_pred HHHHHHHHHHHHHHHHHHH
T ss_conf 7778789999999999999
No 154
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=95.54 E-value=0.029 Score=37.10 Aligned_cols=140 Identities=20% Similarity=0.265 Sum_probs=78.4
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHH
Q ss_conf 99999999999843566743322448757999977115000037860779989998688899808808999968989999
Q gi|254780784|r 525 KRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIE 604 (699)
Q Consensus 525 ~~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~ 604 (699)
+.+-..|.+...+.++. +.++.-..+.-..+++|++.|+.+||.||++|+.|+.+.|.+|++..-+.=.. -+
T Consensus 460 ~~a~~~i~~~i~r~~p~-~~eVe~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~~~~-------~e 531 (604)
T COG1855 460 KLAEEEIEREIKRYLPG-DVEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEEEEE-------GE 531 (604)
T ss_pred HHHHHHHHHHHHHHCCC-CCEEEEECCCEEEEEECHHHHHHHHHCCCCHHHHHHHHHCCEEEEEECCCCCC-------CC
T ss_conf 77999999999974799-82599961871799948788567761055318999987498068888665666-------77
Q ss_pred HHHHHHHHH--CCCCCCCCEEEEEEEEEEECCEEEE-CCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEE
Q ss_conf 999999985--2475468678999999941536998-28797104886631444547855603259889999
Q gi|254780784|r 605 AAREMIRSI--TDVPEVNKIYKGQVVKVMDFGAFVH-FCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVK 673 (699)
Q Consensus 605 ~a~~~i~~~--~~~~e~g~~y~~~v~~i~~fGafve-~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk 673 (699)
++--.|.+- --.+-+|.-+.|+-++|--=+-++- -..++.|-+.|+.-+. --+.....++.|-.|.+.
T Consensus 532 ~~~~~i~~~~k~iv~~~~~~~~g~~v~i~~~~eylftatv~~~G~vri~~~~~-~g~~i~~ai~~g~~i~~~ 602 (604)
T COG1855 532 KVPVEIEEKGKHIVLYVGPDFAGKPVRIYAGDEYLFTATVSRKGVVKIRKDSE-VGKEIEEAIDNGRDIRAS 602 (604)
T ss_pred CCCEEEEECCCEEEEECCCCCCCCEEEEEECCEEEEEEECCCCCEEEEECCCH-HHHHHHHHHHCCCCEEEE
T ss_conf 47807860583799973788789816999788899999816783499851876-899999998648867996
No 155
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family; InterPro: IPR004659 The eubacterial degradosome is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria . The components of the RNA degradosome in E. coli (EBI-1169250 from INTACT) are: Ribonuclease E (Rne), P21513 from SWISSPROT, IPR004659 from INTERPRO ATP-dependent RNA helicase (RhlB), P0A8J8 from SWISSPROT, IPR000629 from INTERPRO Polynucleotide phosphorylase (Pnp), , IPR012162 from INTERPRO Enolase (Eno), P0A6P9 from SWISSPROT, IPR000941 from INTERPRO Associated components: The chaperone protein DnaK (,IPR012725 from INTERPRO) associates to abnormal complexes in which the canonical components RhlB and PNPase are not present or present in limiting amount and could be involved in repairing such incorrectly assembled degradosomes. Polyphosphate kinase (Ppk), P0A7B1 from SWISSPROT, IPR003414 from INTERPRO appears to maintain an appropriate microenvironment, removing inhibitory polyphosphate and NDPs and regenerating ATP. Subunit composition of the E. coli degradosome(see: http://biocyc.org/ECOLI/NEW-IMAGE?type=POLYPEPTIDE&object=CPLX0-2381): [(Ppk)4][(Rne)4][(RhlB)2][(Pnp)3][(Eno)2] In vitro a "minimal" degradosome composed of only RNase E, PNPase and RhlB degrades malEF REP RNA in an ATP-dependent manner in vitro, with activity equivalent to purified whole degradosomes. RNase E enzymatic function is dispensible, whereas PNPase must be catalytically active and incorporated into the degradosome for degradation to occur . RNase E provides the organizational structure for the degradosome . It is tethered to the cytoplasmic membrane via its amino-terminus and its carboxy-terminal half, which is largly unstructured and poorly conserved, cooridnates the binding of PNPase, RhlB and enolase. The loss of this portion of the protein prevents degradation of a number of degradosome substrates, including the ptsG and mukB mRNAs and RNA I , , . Ribonuclease E 3.1.4 from EC is responsible for maturing 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of ColE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in Escherichia coli, and initiates decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly A tails by an endonucleolytic process. Ribonuclease G is smaller than RNase E lacking the C-terminal region. It is involved in processing of the 5' end of 16S rRNA, and may be involved in chromosome segregation and cell division too. RNase E is a major subunit the eubacterial degradosome. It is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria . It consists of the RNA degradation enzymes RNase E (Rne) and PNPase (Pnp), as well as the ATP-dependent RNA helicase (RhlB) and the metabolic enzyme enolase (Eno) , , .; GO: 0004540 ribonuclease activity, 0006396 RNA processing, 0005737 cytoplasm.
Probab=95.43 E-value=0.0064 Score=42.44 Aligned_cols=64 Identities=31% Similarity=0.586 Sum_probs=53.0
Q ss_pred CCCCCEEEEEEEEEEE--CCEEEECCCCCCEEEEEEECCCC---------------------------CC----------
Q ss_conf 5468678999999941--53699828797104886631444---------------------------54----------
Q gi|254780784|r 617 PEVNKIYKGQVVKVMD--FGAFVHFCGARDGLVHISQLSTE---------------------------RV---------- 657 (699)
Q Consensus 617 ~e~g~~y~~~v~~i~~--fGafve~~~g~~gl~HiS~l~~~---------------------------~v---------- 657 (699)
-.+|.||.|+|++|.+ =+|||++=-.+.|+||+|++.++ .+
T Consensus 25 ~~~GnIY~G~V~~vlPsl~AAFvdiG~~~~GFLh~sdi~~~~~~~~~~~~~d~~NA~~~a~~~~~~~~~~~~kp~~~~QS 104 (464)
T TIGR00757 25 QLVGNIYKGRVTRVLPSLQAAFVDIGLEKNGFLHASDIGENSEKLEQLVDTDDDNAEAEAAPAEAKREAGQEKPEEIIQS 104 (464)
T ss_pred CCHHHHHHCEEEEECCCCCEEEEECCCCCCCCCCHHHCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCHHHHCC
T ss_conf 11002320202022037644774206883556303320332456888862021257677882332201001362132025
Q ss_pred ------------CCHHHHCCCCCEEEEEEEEECCCC
Q ss_conf ------------785560325988999999786899
Q gi|254780784|r 658 ------------AKTSDVVKEGDTVWVKLLDFDDRG 681 (699)
Q Consensus 658 ------------~~~~d~~~~Gd~i~vk~~~~d~~g 681 (699)
.+++++|+.||.|-|.|.. +|.|
T Consensus 105 ~~~~~~~~~~~~~~I~e~L~~gq~vlVQV~K-ep~G 139 (464)
T TIGR00757 105 SGDELERRQSKTASISELLRPGQSVLVQVVK-EPRG 139 (464)
T ss_pred CHHHHHHHHCCCCCHHHHHCCCCEEEEEEEE-CCCC
T ss_conf 3024554313543526661288858999885-2678
No 156
>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=95.35 E-value=0.055 Score=34.85 Aligned_cols=63 Identities=21% Similarity=0.317 Sum_probs=52.6
Q ss_pred CCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC--CC-CEEEEE
Q ss_conf 46867899999994153699828797104886631444547855603259889999997868--99-866687
Q gi|254780784|r 618 EVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD--RG-KIKLSM 687 (699)
Q Consensus 618 e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~--~g-~i~lSr 687 (699)
.+|++..|+|.++..-.++|+| .+.|++|.-+|.- +.+.++.||.|+|-+.+++. +| ++-|||
T Consensus 2 k~geiv~G~V~r~~~~~v~vdl-g~~eailp~~eqi------p~E~~~~Gdrik~~i~~V~~~~kgp~i~lSR 67 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDL-GKVEAILPKKEQI------PGESYRPGDRIKAYVLEVRKTSKGPQIILSR 67 (67)
T ss_pred CCCCEEEEEEEEEECCCEEEEE-CCCEEECCHHHCC------CCCCCCCCCEEEEEEEEEEECCCCCEEEEEC
T ss_conf 8788899999998089799998-9948973789957------8866399998999999987469988899839
No 157
>KOG2191 consensus
Probab=95.32 E-value=0.17 Score=30.90 Aligned_cols=49 Identities=18% Similarity=0.220 Sum_probs=30.0
Q ss_pred CCCEEECCCCCC----CCCCCEEEEEECCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 773243685000----2221013553054432333124443248999988753168899999
Q gi|254780784|r 158 NGQYVLNPRLDE----DQGSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVI 215 (699)
Q Consensus 158 dge~ViNPt~ee----~esdLDLvVAGT~d~IlMIE~~A~EVsEe~mleAI~~Ahe~Ik~iI 215 (699)
.|+-|++-..+- .-|.---+|-||-++|+||.+.. +||...|+.|.+-|
T Consensus 57 GG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~---------eai~av~efI~dKi 109 (402)
T KOG2191 57 GGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTV---------EALNAVHEFIADKI 109 (402)
T ss_pred CHHHHHHHHHCCCCEEEECCCCCCCCCCCCEEEEEECCH---------HHHHHHHHHHHHHH
T ss_conf 538899987504967884356666899632589972529---------99999999999999
No 158
>KOG2190 consensus
Probab=95.26 E-value=0.064 Score=34.28 Aligned_cols=115 Identities=22% Similarity=0.239 Sum_probs=78.3
Q ss_pred CCCEEEEECCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCEEEEE
Q ss_conf 55100100556512443245365568899999999999999999999984356674332244875799997711500003
Q gi|254780784|r 488 HMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVI 567 (699)
Q Consensus 488 dMDFKvaGT~~GiTa~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i~~~ki~~~i 567 (699)
+=.|.++|+ +.+. .+.=-.+||.+|.+.-...++.-...... ..+..+.-|+..-+-||-+.+|.||
T Consensus 87 eRIiti~g~---------~~~~---~~~~~~~al~ka~~~iv~~~~~d~~~~~d-~~~~~~~~~v~~RLlVp~sq~GslI 153 (485)
T KOG2190 87 ERIITITGN---------RVEL---NLSPATDALFKAFDMIVFKLEEDDEAAED-NGEDASGPEVTCRLLVPSSQVGSLI 153 (485)
T ss_pred CCEEEEECC---------CCCC---CCCCHHHHHHHHHHHHHHCCCCCCCCCCC-CCCCCCCCCEEEEEEECHHHEEEEE
T ss_conf 404897146---------5555---67823788988888875202345322446-7765647845899995125534543
Q ss_pred CCCCHHHHHHHHHHCCEEEEECC-------EEEEEEECCHHHHHHHHHHHHHHCCC
Q ss_conf 78607799899986888998088-------08999968989999999999985247
Q gi|254780784|r 568 GMGGKVIRGIVEQTGAKVNIDDD-------GTVKIASSSLAEIEAAREMIRSITDV 616 (699)
Q Consensus 568 G~gG~~ik~i~~~~~~~i~i~d~-------g~v~i~~~~~~~~~~a~~~i~~~~~~ 616 (699)
|.||++||.|.++||++|-+-.+ -.|.|.+ ..+++.+|...|..+..+
T Consensus 154 GK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG-~~~av~~al~~Is~~L~~ 208 (485)
T KOG2190 154 GKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISG-EPDAVKKALVQISSRLLE 208 (485)
T ss_pred CCCCHHHHHHHHHCCCEEEECCCCCCCCCCEEEEECC-CHHHHHHHHHHHHHHHHH
T ss_conf 0674788999985383699657889865310378738-627999999999999986
No 159
>TIGR01953 NusA transcription termination factor NusA; InterPro: IPR010213 This entry describes NusA, or N utilisation 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 Escherichia coli of phage lambda antitermination protein N with the N-utilisation substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and NusG . This entry represents a region of NusA shared by all bacterial forms, and includes the S1 (IPR003029 from INTERPRO) and KH RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this entry, with two repeats of 50-residue domain rich in acidic amino acids.; GO: 0003723 RNA binding, 0030528 transcription regulator activity.
Probab=95.20 E-value=0.15 Score=31.27 Aligned_cols=91 Identities=19% Similarity=0.287 Sum_probs=71.3
Q ss_pred EEEEEECCHHHHHHHHHHHHHHCCC-----------CCCCCEEEEEEEE--EEECC----EEEECCCCCCEEEEEEECCC
Q ss_conf 8999968989999999999985247-----------5468678999999--94153----69982879710488663144
Q gi|254780784|r 592 TVKIASSSLAEIEAAREMIRSITDV-----------PEVNKIYKGQVVK--VMDFG----AFVHFCGARDGLVHISQLST 654 (699)
Q Consensus 592 ~v~i~~~~~~~~~~a~~~i~~~~~~-----------~e~g~~y~~~v~~--i~~fG----afve~~~g~~gl~HiS~l~~ 654 (699)
.+..-.....+++.|++.+.+-..+ ..+|++-.|+|.+ ...-+ .||+|....+|+|-=+
T Consensus 107 ~~~~~~FgR~a~~~a~Q~~~Qk~re~e~~~~~~ef~~~~g~~i~g~V~r~d~~~~~~~~g~~v~l~g~~e~~lp~~---- 182 (366)
T TIGR01953 107 EINPENFGRIAAQAAKQVITQKIREAERERVYDEFKSKVGEIISGTVKRVDVNKEGNETGLIVELAGKTEAILPKK---- 182 (366)
T ss_pred ECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEEEEEECCCCCCCEEEEEECCCEEEECCHH----
T ss_conf 4276664478999999999888899998767766433318089999999752578752107999857502521353----
Q ss_pred CCCCCHHHHCCCCCEEEEEEEEECC--CC---CEEEEEE
Q ss_conf 4547855603259889999997868--99---8666873
Q gi|254780784|r 655 ERVAKTSDVVKEGDTVWVKLLDFDD--RG---KIKLSMK 688 (699)
Q Consensus 655 ~~v~~~~d~~~~Gd~i~vk~~~~d~--~g---~i~lSrk 688 (699)
---+.+.++.||.|.+-+.++-+ +| +|=|||-
T Consensus 183 --e~iP~E~~~~Gd~i~~~~~eV~~~~~g~~~~i~lSRt 219 (366)
T TIGR01953 183 --EQIPGEKFRIGDRIKAYVYEVRKTAKGGLPQIILSRT 219 (366)
T ss_pred --HCCCCCCCCCCCEEEEEEEEEEECCCCCEEEEEEECC
T ss_conf --3788875235888999999999868896689999708
No 160
>KOG1612 consensus
Probab=95.17 E-value=0.31 Score=28.72 Aligned_cols=119 Identities=21% Similarity=0.228 Sum_probs=73.9
Q ss_pred EEEEEEECEECCCCCCEEEEEECC-CEEEEEEEEC------CCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCH
Q ss_conf 899999140045467289999789-4899999727------888877773540686652320133678887357898871
Q gi|254780784|r 14 RPLKLETGRIARQSDGAVLATYGE-TVVLATVVYD------RSLKDGQDFFPLTVNYQERTYAVGKIPGGYLRRESRPTE 86 (699)
Q Consensus 14 r~i~~ETGklArqA~GsV~v~~G~-T~VLaTv~~~------~~~~~~~dFfPLtVdY~Ek~yAaGkIPGgF~kREgrpsd 86 (699)
|+|.+|||.|.. +|||+-+++|+ |-+++.+-+. ..|.++ ..-+.||.--... - -|--|+|-- =
T Consensus 32 Rpi~vetdVlp~-tNGSaRVk~g~~tdiivgVKaEvg~~~~~~p~eg--k~~~~VD~S~sas--p----~f~gRggde-~ 101 (288)
T KOG1612 32 RPIEVETDVLPG-TNGSARVKLGDGTDIIVGVKAEVGSPDDETPVEG--KYLFFVDCSPSAS--P----QFQGRGGDE-L 101 (288)
T ss_pred CEEEEEECCCCC-CCCCEEEEECCCCEEEEEEEEECCCCCCCCCCCC--EEEEEEEECCCCC--C----CCCCCCHHH-H
T ss_conf 107888130148-9985789936873599997632057633587777--3899998468768--3----246777006-8
Q ss_pred HHHHHHHHHHCCCC---------CCCCCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 45311112321267---------76746886883789999821888877899999999998732688
Q gi|254780784|r 87 NEILISRMIDRSIR---------PLFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLP 144 (699)
Q Consensus 87 ~EiL~sRlIDR~lR---------PLFPkgf~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIP 144 (699)
-|.|++-|=+=-.- -.|-++|+....|-+.|+|.|+ |..|.+++ |+=+||.---+|
T Consensus 102 ~~eltsaLq~~l~~~~sgv~ls~L~lt~~~~W~i~VDvlVi~s~g-n~~dAiS~-Ai~~AL~~T~lP 166 (288)
T KOG1612 102 VEELTSALQRVLNSLGSGVDLSKLQLTPGYCWKIYVDVLVISSDG-NLLDAISI-AIYAALNNTRLP 166 (288)
T ss_pred HHHHHHHHHHHHHCCCCCCCHHHEECCCCEEEEEEEEEEEEECCC-CHHHHHHH-HHHHHHHCCCCC
T ss_conf 999999999998476865451223525870699997699995499-78889999-999987425677
No 161
>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=95.13 E-value=0.092 Score=33.03 Aligned_cols=65 Identities=26% Similarity=0.401 Sum_probs=55.0
Q ss_pred CCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCC-CCEEEE
Q ss_conf 8678999999941536998287971048866314445478556032598899999978689-986668
Q gi|254780784|r 620 NKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDR-GKIKLS 686 (699)
Q Consensus 620 g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~-g~i~lS 686 (699)
|-+..++|.++.+.|.++.++..-.|.+..=.|+..+ ..++.+++|+++.-.++-+|+. -+|.||
T Consensus 1 GmlV~a~V~kV~~~Gl~~~fl~~F~G~Vd~~HL~~~~--~~~~~Y~~~~~v~ArIL~Vdp~tK~V~Ls 66 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEK--SSKSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEECCCCEEEEEECCEEEEEEHHHCCCCC--CCCCCCCCCCEEEEEEEEECCCCCEEECC
T ss_conf 9559999999817948999651289998876768776--87000467988999999998874788539
No 162
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.89 E-value=0.23 Score=29.72 Aligned_cols=179 Identities=22% Similarity=0.288 Sum_probs=95.2
Q ss_pred CCCCCCCCC-CCCCCEEEEEEEECCCCCCCCCCCCCC---CCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCC
Q ss_conf 652122334-454420358774058875445334556---7650246799999998741078644687389998531102
Q gi|254780784|r 357 REDEQYVDS-LSGTQRNDFMMHYNFLPCATGEVSRMG---APSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITES 432 (699)
Q Consensus 357 ~~d~Q~iD~-l~~~~~k~fmlHYNFPpfsvGE~~~~~---~~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~s 432 (699)
+.++|+... ...-.+-|+++. .|-+...+| -.|| -|-.|..|=|+.=+|.-.+. +|.|.+=.=+.
T Consensus 187 P~~EqIP~E~yr~Gdrira~i~------~V~~~~~kGpqIiLSR---t~p~fv~kLFe~EVPEI~dG--~VeIk~iARep 255 (457)
T PRK12329 187 PKREQLPNDNYRANATFKVFLK------EVSEGPRRGPQLFVSR---ANAGLVVYLFENEVPEIEEG--VVRIVAVAREA 255 (457)
T ss_pred CHHHCCCCCCCCCCCEEEEEEE------EEECCCCCCCEEEEEC---CCHHHHHHHHHHHCHHHHCC--CEEEEEEEECC
T ss_conf 7888699987899998999999------9764678885699954---87799999998645586389--48999998448
Q ss_pred C------CCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEECCEEEEEEECCCCCCCCCCCCEEEEECCCCCEEEECC
Q ss_conf 7------8522356677779876259502254121332004408828998631442201365510010055651244324
Q gi|254780784|r 433 D------GSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMD 506 (699)
Q Consensus 433 n------gsssma~vc~~slal~dagvp~~~~VaGiamGLi~~~~~~~iLtDI~G~ED~~GdMDFKvaGT~~GiTa~QmD 506 (699)
| |+-+--+|- +--|=-+||+. .+|.= +.+ |+..-.-|+ |- -|--+.-
T Consensus 256 ~~~~r~~G~RtKIAV~--------S~d~~iDPVGa-CVG~r--G~R------Iq~I~~EL~-------gE--kIDii~w- 308 (457)
T PRK12329 256 NPPSRAVGPRTKIAVD--------TLERDVDPVGA-CIGAR--GSR------IQQVVNELR-------GE--KIDVIRW- 308 (457)
T ss_pred CCCCCCCCCCEEEEEE--------ECCCCCCCEEE-EECCC--CCC------HHHHHHHHC-------CC--EEEEEEC-
T ss_conf 8777788650389998--------06999773147-88899--742------999998857-------96--3899975-
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEE
Q ss_conf 53655688999999999999999999999843566743322448757999977115000037860779989998688899
Q gi|254780784|r 507 MKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVN 586 (699)
Q Consensus 507 iK~~gi~~~il~~al~~A~~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~ 586 (699)
.-=+...+..||.-|+.-+.. +-+..-+...+-+|.+.....||.+|.|+|.-..-||-+||
T Consensus 309 ---s~d~~~~i~nALsPA~v~~v~---------------~~d~~~~~~~V~V~~dqLslAIGk~GqNvrLAa~Ltgw~Id 370 (457)
T PRK12329 309 ---SPDPATYIANSLSPARVDEVR---------------LVDPEGQHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKID 370 (457)
T ss_pred ---CCCHHHHHHHHCCCCCCCEEE---------------EECCCCCEEEEEECCCCCHHHHCCCCCHHHHHHHHHCCEEE
T ss_conf ---787899999843965351799---------------98588887999988541037627987579999997798788
Q ss_pred EECCE
Q ss_conf 80880
Q gi|254780784|r 587 IDDDG 591 (699)
Q Consensus 587 i~d~g 591 (699)
|-.+.
T Consensus 371 Iks~~ 375 (457)
T PRK12329 371 IKDSA 375 (457)
T ss_pred ECCHH
T ss_conf 56689
No 163
>KOG1856 consensus
Probab=94.81 E-value=0.092 Score=33.01 Aligned_cols=71 Identities=27% Similarity=0.328 Sum_probs=60.6
Q ss_pred CCCEEEEEEEEEEECC---EEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEE
Q ss_conf 6867899999994153---699828797104886631444547855603259889999997868-9986668730
Q gi|254780784|r 619 VNKIYKGQVVKVMDFG---AFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKV 689 (699)
Q Consensus 619 ~g~~y~~~v~~i~~fG---afve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~ 689 (699)
+|++..++|+++..-- +=|.+-.|-+|.||.+.++...|.+++.-+++|+.|.+|++.+|. +--..||-|.
T Consensus 985 ~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~ 1059 (1299)
T KOG1856 985 EGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRT 1059 (1299)
T ss_pred CCCEEEEEEEEEEECCCCEEEEEECCCCCEEEECCCCCHHHCCCHHHHHCCCCEEEEEEEEEEHHHHHHHHHHHH
T ss_conf 675677755678715653157874278731544333673421587775114762799965332854553110014
No 164
>KOG2814 consensus
Probab=94.53 E-value=0.054 Score=34.88 Aligned_cols=64 Identities=22% Similarity=0.251 Sum_probs=56.3
Q ss_pred EEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEE----ECCEEEEEEECCHHHHHHHHHHHHHHCCC
Q ss_conf 79999771150000378607799899986888998----08808999968989999999999985247
Q gi|254780784|r 553 VEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNI----DDDGTVKIASSSLAEIEAAREMIRSITDV 616 (699)
Q Consensus 553 ~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i----~d~g~v~i~~~~~~~~~~a~~~i~~~~~~ 616 (699)
..++.+++..|+-|||..|++-|.|+++|+++|.+ +.++.+.|.+.....+.+|.++|.-+...
T Consensus 58 ~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids 125 (345)
T KOG2814 58 SSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDS 125 (345)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCEECCCCCCCCCEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_conf 45530018776232146515788887863664671588888650777520199999999999999986
No 165
>KOG2192 consensus
Probab=94.35 E-value=0.16 Score=31.10 Aligned_cols=62 Identities=27% Similarity=0.519 Sum_probs=50.4
Q ss_pred EEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEEC------CEEEEEEECCHHHHHHHHHHHHHHCC
Q ss_conf 7999977115000037860779989998688899808------80899996898999999999998524
Q gi|254780784|r 553 VEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDD------DGTVKIASSSLAEIEAAREMIRSITD 615 (699)
Q Consensus 553 ~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d------~g~v~i~~~~~~~~~~a~~~i~~~~~ 615 (699)
...+.||.|.-|.+||.||..|+.|-.+.|+.|.|++ |-.+.|.+ +++.++.|.-..++-++
T Consensus 316 TaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItG-TqdQIqnAQYLlQn~Vk 383 (390)
T KOG2192 316 TAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITG-TQDQIQNAQYLLQNSVK 383 (390)
T ss_pred EEEEECCCCCCCCEECCCCHHHHHHHHCCCCEEEECCCCCCCCCEEEEEEC-CHHHHHHHHHHHHHHHH
T ss_conf 556740444676343355245665532047457845767898742799736-38887667888998898
No 166
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=93.70 E-value=0.18 Score=30.72 Aligned_cols=95 Identities=16% Similarity=0.239 Sum_probs=61.4
Q ss_pred CCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHCCCC
Q ss_conf 35667433224487579999771150000378607799899986888998088089999689899999999999852475
Q gi|254780784|r 538 VLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVP 617 (699)
Q Consensus 538 ~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~~~ 617 (699)
+-..+++.+-+.---...|-|++...|..||+||.+||.+++..|-+|+|-+ |+.| ..++|.++....
T Consensus 20 T~~~~~DCi~d~~~~riiFvV~~g~mG~AIGk~G~~Ik~l~~~lgkkIdiVe------~seD------p~~FI~N~l~Pa 87 (142)
T PRK08406 20 TGATVRDCIIDEEYDRIIFVVKEGDMGLAIGKGGENVKRLKEKLGKDIELVE------YSED------PEEFIKNLLAPA 87 (142)
T ss_pred HCCCEEEEEECCCCCEEEEEECCCHHHHHHCCCCCHHHHHHHHHCCCEEEEE------CCCC------HHHHHHHCCCCC
T ss_conf 7997235687089988999987676889758796079999998589458996------4789------999998706932
Q ss_pred CCCCEEEEEEEEEE-ECCEEEECCCCCCEEE
Q ss_conf 46867899999994-1536998287971048
Q gi|254780784|r 618 EVNKIYKGQVVKVM-DFGAFVHFCGARDGLV 647 (699)
Q Consensus 618 e~g~~y~~~v~~i~-~fGafve~~~g~~gl~ 647 (699)
++-.++ |.+-. .-=|+|...|.+-||.
T Consensus 88 ~V~~V~---i~~~~~~~~a~V~V~~~~~~lA 115 (142)
T PRK08406 88 KVKSVK---ISEKNGKKVAYVTVAPEDKGIA 115 (142)
T ss_pred EEEEEE---EECCCCCEEEEEEECHHHHHHH
T ss_conf 567999---9827996899999685652043
No 167
>KOG2192 consensus
Probab=93.50 E-value=0.13 Score=31.78 Aligned_cols=107 Identities=17% Similarity=0.262 Sum_probs=73.6
Q ss_pred HHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECC------EEEEEEECCHHHH
Q ss_conf 9999998435667433224487579999771150000378607799899986888998088------0899996898999
Q gi|254780784|r 530 HILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDD------GTVKIASSSLAEI 603 (699)
Q Consensus 530 ~il~~m~~~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~------g~v~i~~~~~~~~ 603 (699)
.|+++..++|+.--+.++.-.|.-..+-|....-|.+||-.|+.||++-|+..+.+.|-.+ .+|.+.+-.+..+
T Consensus 101 ti~~ilk~iip~lee~f~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v 180 (390)
T KOG2192 101 TIGEILKKIIPTLEEGFQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRV 180 (390)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCEECCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCCHH
T ss_conf 99999999765664088899852222133244135334367405788887642555431144899765289936885208
Q ss_pred HHHHHHHHHHCCC-CCCC-------CEEEEEEEEEEECCEEEECC
Q ss_conf 9999999985247-5468-------67899999994153699828
Q gi|254780784|r 604 EAAREMIRSITDV-PEVN-------KIYKGQVVKVMDFGAFVHFC 640 (699)
Q Consensus 604 ~~a~~~i~~~~~~-~e~g-------~~y~~~v~~i~~fGafve~~ 640 (699)
-..++.|.++..+ |-.| ..|+-. -|||-|--.+
T Consensus 181 ~~~i~~il~~i~e~pikgsa~py~p~fyd~t----~dyggf~M~f 221 (390)
T KOG2192 181 VECIKIILDLISESPIKGSAQPYDPNFYDET----YDYGGFTMMF 221 (390)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC----CCCCCCEEEC
T ss_conf 9999999998652876776876786545765----5568831105
No 168
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=92.97 E-value=0.64 Score=26.18 Aligned_cols=64 Identities=22% Similarity=0.275 Sum_probs=49.9
Q ss_pred EEEEEEEEEEECCEE-EECCCCCCEEEEEEE-CCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEEEC
Q ss_conf 789999999415369-982879710488663-1444547855603259889999997868-99866687304
Q gi|254780784|r 622 IYKGQVVKVMDFGAF-VHFCGARDGLVHISQ-LSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMKVV 690 (699)
Q Consensus 622 ~y~~~v~~i~~fGaf-ve~~~g~~gl~HiS~-l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk~~ 690 (699)
.++|+|++..+-+-| |+|-.|.+-|+|+|- +-..++. +-.||.|+|.+---|- +|||-+--|.-
T Consensus 8 e~eG~V~e~lpn~~FrV~LeNg~~Vla~~sGKmR~~~Ir-----Il~GD~V~VElSpYDltkGRIvyR~k~~ 74 (87)
T PRK12442 8 ELDGIVDEVLPDSRYRVTLENGVEVGAYASGRMRKHRIR-----ILAGDRVTLELSPYDLTKGRINFRHKDE 74 (87)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEEECCEEEEEEE-----ECCCCEEEEEECCCCCCCEEEEEEECCC
T ss_conf 987899998799879999779989999985501330277-----7689989999887778874899884788
No 169
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=92.37 E-value=0.46 Score=27.34 Aligned_cols=88 Identities=30% Similarity=0.394 Sum_probs=39.7
Q ss_pred EEEEECCEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEE-ECCEEEEC-CCCCCEEEEEEECCCCCCCCHH
Q ss_conf 899808808999968989999999999985247546867899999994-15369982-8797104886631444547855
Q gi|254780784|r 584 KVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQVVKVM-DFGAFVHF-CGARDGLVHISQLSTERVAKTS 661 (699)
Q Consensus 584 ~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~~~e~g~~y~~~v~~i~-~fGafve~-~~g~~gl~HiS~l~~~~v~~~~ 661 (699)
.+.+.|+=.|.||-...+.+...-. .-...+|+.=-++|+.+. +-||||.. +| ||-|+-+|++.. ..
T Consensus 43 e~evGdev~vFiY~D~~~rl~aTt~-----~p~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~-KDl~vp~~elp~-----~~ 111 (287)
T COG2996 43 ELEVGDEVTVFIYVDSEDRLIATTR-----EPKATVGEYGWLKVVEVNKDLGAFLDWGLP-KDLLVPLDELPT-----LK 111 (287)
T ss_pred CCCCCCEEEEEEEECCCCCEEHEEE-----CCEEEECCEEEEEEEEECCCCCEEEECCCC-CCEEEEHHHCCC-----CC
T ss_conf 5113768999999888776301010-----413740532379999873775158965987-003616253644-----31
Q ss_pred HH-CCCCCEEEEEEEEECCCCCE
Q ss_conf 60-32598899999978689986
Q gi|254780784|r 662 DV-VKEGDTVWVKLLDFDDRGKI 683 (699)
Q Consensus 662 d~-~~~Gd~i~vk~~~~d~~g~i 683 (699)
++ .+.||.+-|.+ -+|.+|||
T Consensus 112 ~~wpq~Gd~l~v~l-~~Dkk~Ri 133 (287)
T COG2996 112 SLWPQKGDKLLVYL-YVDKKGRI 133 (287)
T ss_pred CCCCCCCCEEEEEE-EECCCCCE
T ss_conf 23778798999999-98567847
No 170
>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=92.14 E-value=0.14 Score=31.45 Aligned_cols=42 Identities=26% Similarity=0.377 Sum_probs=36.2
Q ss_pred CCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEE
Q ss_conf 244875799997711500003786077998999868889980
Q gi|254780784|r 547 GEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNID 588 (699)
Q Consensus 547 ~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~ 588 (699)
.+...+...+.++++-.+..||.+|+|+|...+-||-+|||.
T Consensus 20 ~~~~~~~~~V~V~~~~~~~AIGk~G~Nvrla~~l~g~~IdI~ 61 (61)
T cd02134 20 LDDEEKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDIV 61 (61)
T ss_pred CCCCCCEEEEEECHHHHHHHHCCCCEEHHHHHHHHCCEEEEC
T ss_conf 478773799998857843876678670999999779877649
No 171
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=92.13 E-value=0.49 Score=27.09 Aligned_cols=67 Identities=25% Similarity=0.277 Sum_probs=55.5
Q ss_pred CCEEEEEEEEEEECCEEEECCC-CCCEEEEEEECCCCCCCCHHH---HCCCCCEE-EEEEEEECCCCCEEEEEE
Q ss_conf 8678999999941536998287-971048866314445478556---03259889-999997868998666873
Q gi|254780784|r 620 NKIYKGQVVKVMDFGAFVHFCG-ARDGLVHISQLSTERVAKTSD---VVKEGDTV-WVKLLDFDDRGKIKLSMK 688 (699)
Q Consensus 620 g~~y~~~v~~i~~fGafve~~~-g~~gl~HiS~l~~~~v~~~~d---~~~~Gd~i-~vk~~~~d~~g~i~lSrk 688 (699)
|+..+.+|.+-.+-|.-|.++| ...+++--..||+ ++.+..- -+++||.+ .|.|+.. .+|++-|+||
T Consensus 1 Gq~VdvkVlkkt~~GLeV~ilp~~~~afLPt~HLSD-hv~N~~LL~~~lq~GD~i~~vmCls~-~~~~iil~rK 72 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSD-HVSNCPLLWHCLQEGDTIPNLMCLSN-YKGRIILTKK 72 (72)
T ss_pred CCEEEEEEEEECCCCCEEEECCCCCCCCCCCCCCCC-CCCCCHHHHHHHHCCCCHHCEEEEEC-CCCCEEEECC
T ss_conf 960688999862887278976888542144532233-32245899998844786102578862-7882888459
No 172
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases; InterPro: IPR004476 This family is defined to identify a pair of paralogous 3'->5' exoribonucleases in Escherichia coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterised originally as required for the expression of virulence genes, but is now recognised as the exoribonuclease RNase R (Rnr). Its paralog in Escherichia coli and Haemophilus 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 cut-off to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3' exoribonucleases.; GO: 0003723 RNA binding, 0004540 ribonuclease activity, 0016070 RNA metabolic process.
Probab=91.01 E-value=0.19 Score=30.45 Aligned_cols=65 Identities=31% Similarity=0.456 Sum_probs=54.2
Q ss_pred CCCC--CEEEEEEEEEEECCEEEECC-CCCCEEEEEEECCC--C-----------CCCCHHHHCCCCCEEEEEEEEECCC
Q ss_conf 5468--67899999994153699828-79710488663144--4-----------5478556032598899999978689
Q gi|254780784|r 617 PEVN--KIYKGQVVKVMDFGAFVHFC-GARDGLVHISQLST--E-----------RVAKTSDVVKEGDTVWVKLLDFDDR 680 (699)
Q Consensus 617 ~e~g--~~y~~~v~~i~~fGafve~~-~g~~gl~HiS~l~~--~-----------~v~~~~d~~~~Gd~i~vk~~~~d~~ 680 (699)
-++| ..|.|.+..+..||.|+.+. .+-+||+|++-+.. . ..++...++++||.+.+++.+++..
T Consensus 596 ~~~g~~~~f~g~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gd~~~~~~~~~~~~ 675 (684)
T TIGR00358 596 DKVGTDEEFSGEISSVTGFGLFVRLDDNGIDGLVPVSTLPNNKDYYRFDKEKLALIGKGTGKVYRLGDRLEVKLTEVNLD 675 (684)
T ss_pred HHCCCCCCHHHHHHHHHCCCEEEEEECCCCCEEEEECCCCCCCHHEEECCCCCEEEECCCCCEEEECCEEEEEEEHHHHH
T ss_conf 54167530012221220264068750356310354122224311203421322687615673575154147752012122
Q ss_pred C
Q ss_conf 9
Q gi|254780784|r 681 G 681 (699)
Q Consensus 681 g 681 (699)
.
T Consensus 676 ~ 676 (684)
T TIGR00358 676 E 676 (684)
T ss_pred H
T ss_conf 3
No 173
>pfam10447 EXOSC1 Exosome component EXOSC1/CSL4. This family of proteins are components of the exosome 3'-5' exoribonuclease complex. The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions.
Probab=90.71 E-value=0.76 Score=25.58 Aligned_cols=61 Identities=18% Similarity=0.363 Sum_probs=47.4
Q ss_pred CCCCCCEEEEEEEEEEECCEEEECCC--------CCCEEEEEEECCCCCCCC--HHHHCCCCCEEEEEEEE
Q ss_conf 75468678999999941536998287--------971048866314445478--55603259889999997
Q gi|254780784|r 616 VPEVNKIYKGQVVKVMDFGAFVHFCG--------ARDGLVHISQLSTERVAK--TSDVVKEGDTVWVKLLD 676 (699)
Q Consensus 616 ~~e~g~~y~~~v~~i~~fGafve~~~--------g~~gl~HiS~l~~~~v~~--~~d~~~~Gd~i~vk~~~ 676 (699)
.|++|.+..++|+++..-=|+++|+- .-.|+++...+-..-..+ +.+-++.||.|..+++.
T Consensus 1 lP~vGdiV~arVtrv~~~~a~~~Il~v~~~~l~~~f~G~IR~~DVRate~Dkv~~~~~FrPGDiVrA~ViS 71 (72)
T pfam10447 1 LPKVGDIVLARVTRVTPRQAYCEILAVGGTALKETFKGIIRKQDVRATEKDRVKIYECFRPGDIVRAKVIS 71 (72)
T ss_pred CCCCCCEEEEEEEEECHHEEEEEEEEECCEECCCCEEEEEEHHHCCCCCCCEEEHHHCCCCCCEEEEEEEE
T ss_conf 99899999999999750157999999999987885558989476665641018384683999899999962
No 174
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=90.39 E-value=0.8 Score=25.40 Aligned_cols=58 Identities=28% Similarity=0.426 Sum_probs=45.4
Q ss_pred EEEEEEEEEEECCEE-EECCCCCCEEEEEEE-CCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEE
Q ss_conf 789999999415369-982879710488663-1444547855603259889999997868-99866
Q gi|254780784|r 622 IYKGQVVKVMDFGAF-VHFCGARDGLVHISQ-LSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIK 684 (699)
Q Consensus 622 ~y~~~v~~i~~fGaf-ve~~~g~~gl~HiS~-l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~ 684 (699)
..+|+|++..+-+-| |+|-.|.+-++|+|- +-..++. +-.||.|+|.+---|. +|||-
T Consensus 2 e~~G~V~e~lpn~~F~V~Leng~~v~a~~sGKmr~~~Ir-----il~GD~V~VE~SpYDltkGRI~ 62 (64)
T cd04451 2 EMEGVVTEALPNAMFRVELENGHEVLAHISGKMRMNYIR-----ILPGDRVKVELSPYDLTKGRIV 62 (64)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEECCHHEEEEEE-----ECCCCEEEEEECCCCCCCEEEE
T ss_conf 788999998799889999789989999972330412698-----4589989999886678857898
No 175
>CHL00010 infA translation initiation factor 1
Probab=90.32 E-value=1.3 Score=23.74 Aligned_cols=62 Identities=27% Similarity=0.387 Sum_probs=48.6
Q ss_pred EEEEEEEEEEECCEE-EECCCCCCEEEEEEE-CCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEEE
Q ss_conf 789999999415369-982879710488663-1444547855603259889999997868-998666873
Q gi|254780784|r 622 IYKGQVVKVMDFGAF-VHFCGARDGLVHISQ-LSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSMK 688 (699)
Q Consensus 622 ~y~~~v~~i~~fGaf-ve~~~g~~gl~HiS~-l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSrk 688 (699)
.++|+|++..+-+-| |+|-.|.+-|+|+|- +-..++ -+-.||.|.|.+---|- +|||-.-.|
T Consensus 8 e~eG~V~e~Lpn~~F~V~Leng~~Vla~~sGKmR~~~I-----ril~GD~V~VE~SpYDltkGRI~~R~k 72 (78)
T CHL00010 8 IMEGLVTESLPNGMFRVRLDNGDLVLGYISGKIRRNSI-----RILPGDRVKVELSPYDLTKGRIIYRLR 72 (78)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEECCHHEECEE-----EECCCCEEEEEECCCCCCCEEEEEEEC
T ss_conf 99899999869988999978999999999805200318-----974899899998756788578999904
No 176
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=90.18 E-value=1.1 Score=24.24 Aligned_cols=104 Identities=15% Similarity=0.154 Sum_probs=71.8
Q ss_pred CCCCCCCHH-HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEE
Q ss_conf 536556889-9999999999999999999984356674332244875799997711500003786077998999868889
Q gi|254780784|r 507 MKIGGISEN-IMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKV 585 (699)
Q Consensus 507 iK~~gi~~~-il~~al~~A~~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i 585 (699)
+++..++-+ ++++.-+++++=-.+||..|.-.+.- +++. -.+...++|.-+.++.|||..||+..+||-=+++-+
T Consensus 49 v~v~~~~~~~~~~~~~~~~~~~L~ell~~m~~~~~i---~v~~-~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l 124 (208)
T COG1847 49 VKVEPKADETVIEKIAQEAKDYLEELLELMDFEVTI---TVSE-EGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYL 124 (208)
T ss_pred CEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCEEE---EEEE-CCCEEEEEECCCCHHHHHCCCCCCHHHHHHHHHHHH
T ss_conf 035531465303579999999999999983986599---9962-475799994488610230367740179999999985
Q ss_pred EEECCEEEEEEECCHHHHHHHHHHHHHHC
Q ss_conf 98088089999689899999999999852
Q gi|254780784|r 586 NIDDDGTVKIASSSLAEIEAAREMIRSIT 614 (699)
Q Consensus 586 ~i~d~g~v~i~~~~~~~~~~a~~~i~~~~ 614 (699)
+........|.-.-..--++-++.+..|.
T Consensus 125 ~~~~g~~~~v~ldv~~yRerR~e~L~~LA 153 (208)
T COG1847 125 NKIGGKFKRVTLDVGDYRERRKETLIKLA 153 (208)
T ss_pred HHHCCCCEEEEEEHHHHHHHHHHHHHHHH
T ss_conf 35059615899982068999999999999
No 177
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=90.14 E-value=1 Score=24.43 Aligned_cols=59 Identities=27% Similarity=0.445 Sum_probs=46.9
Q ss_pred EEEEEEEEEEECCEE-EECCCCCCEEEEEEE-CCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEE
Q ss_conf 789999999415369-982879710488663-1444547855603259889999997868-998666
Q gi|254780784|r 622 IYKGQVVKVMDFGAF-VHFCGARDGLVHISQ-LSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKL 685 (699)
Q Consensus 622 ~y~~~v~~i~~fGaf-ve~~~g~~gl~HiS~-l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~l 685 (699)
.++|+|++..+-+-| |+|-.|.+-++|+|- +-..++ -+-.||.|+|.+---|. +|||-.
T Consensus 8 ~~~G~V~e~lpn~~F~V~Leng~~v~a~~sGKmR~~~I-----ril~GD~V~vE~spYDltkGRIv~ 69 (72)
T PRK00276 8 EMEGTVLETLPNAMFRVELENGHEVLAHISGKMRKNYI-----RILPGDKVTVELSPYDLTKGRITY 69 (72)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEECHHEEEEEE-----EECCCCEEEEEECCCCCCCEEEEE
T ss_conf 99999999859988999978999999997413110169-----975899899998866799578999
No 178
>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=90.00 E-value=1.3 Score=23.55 Aligned_cols=59 Identities=14% Similarity=0.179 Sum_probs=44.3
Q ss_pred CCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCC-----------CCCCHHHHCCCCCEEEEEEEEEC
Q ss_conf 6867899999994153699828797104886631444-----------54785560325988999999786
Q gi|254780784|r 619 VNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTE-----------RVAKTSDVVKEGDTVWVKLLDFD 678 (699)
Q Consensus 619 ~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~-----------~v~~~~d~~~~Gd~i~vk~~~~d 678 (699)
.|++.+|.|+++..+|.|.+.=|- ..+++-+.+... ..++-+.+++.|++|.+|+++.-
T Consensus 1 KGEVvDavVt~Vnk~G~Fa~~GPl-~~fvS~~~ip~d~~f~~~~~~p~~~~~~~~~I~k~~~VR~kIiG~r 70 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPL-SIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTR 70 (88)
T ss_pred CCCEEEEEEEEECCEEEEEEECCE-EEEEECCCCCCCEEECCCCCCCCEECCCCEEECCCCEEEEEEEEEE
T ss_conf 995799999998347899980475-8999911189970998999986282688469868999999999887
No 179
>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=89.86 E-value=0.74 Score=25.68 Aligned_cols=38 Identities=24% Similarity=0.318 Sum_probs=28.7
Q ss_pred CCEEEEEEECCCCEEEEECCCCHHHHHHHHHHC-------CEEEEE
Q ss_conf 875799997711500003786077998999868-------889980
Q gi|254780784|r 550 TPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTG-------AKVNID 588 (699)
Q Consensus 550 ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~-------~~i~i~ 588 (699)
...+....... ..|.+||.+|+||+.++..++ ..||+.
T Consensus 24 ~~~~~i~~~~~-~~g~~IGk~G~~l~~l~~ll~~~~~~~~~~i~v~ 68 (68)
T cd02409 24 RIEIIIVVARG-QPGLVIGKKGQNIRALQKLLQKLLRKKRVKIDVE 68 (68)
T ss_pred CEEEEEEECCC-CCCEEECCCCHHHHHHHHHHHHHHCCCCCEEEEC
T ss_conf 67999998777-9964898883639999999999828998438539
No 180
>PRK02821 hypothetical protein; Provisional
Probab=88.94 E-value=0.4 Score=27.79 Aligned_cols=29 Identities=28% Similarity=0.516 Sum_probs=25.9
Q ss_pred EEEEEEECCCCEEEEECCCCHHHHHHHHH
Q ss_conf 57999977115000037860779989998
Q gi|254780784|r 552 RVEIMAIPPDQIRNVIGMGGKVIRGIVEQ 580 (699)
Q Consensus 552 ~~~~~~i~~~ki~~~iG~gG~~ik~i~~~ 580 (699)
.++.+++.|+-+|.+||.+|+++|+|-.-
T Consensus 31 ~~~el~V~~eD~GkVIGk~Grta~AiRTl 59 (77)
T PRK02821 31 RTLEVRVHPDDLGKVIGRGGRTATALRTL 59 (77)
T ss_pred EEEEEEECHHHCCCEECCCCHHHHHHHHH
T ss_conf 79999999344744547786779999999
No 181
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=88.67 E-value=0.5 Score=27.05 Aligned_cols=55 Identities=22% Similarity=0.328 Sum_probs=40.9
Q ss_pred EEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHCCCCC
Q ss_conf 5799997711500003786077998999868889980880899996898999999999998524754
Q gi|254780784|r 552 RVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPE 618 (699)
Q Consensus 552 ~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~~~e 618 (699)
-..++....+.+|..||++|++||.|.++.|=+||+-+- ++|. .++|.++....+
T Consensus 76 av~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~------s~d~------~~fI~nal~Pa~ 130 (190)
T COG0195 76 AVVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW------SEDP------AEFIKNALAPAE 130 (190)
T ss_pred CEEEEECCCCCHHHHCCCCCHHHHHHHHHHCCCEEEEEE------CCCH------HHHHHHHCCCCE
T ss_conf 039961576844542177762899999986895489990------6999------999998608354
No 182
>PRK01064 hypothetical protein; Provisional
Probab=88.18 E-value=0.48 Score=27.17 Aligned_cols=29 Identities=21% Similarity=0.409 Sum_probs=26.2
Q ss_pred CEEEEEEECCCCEEEEECCCCHHHHHHHH
Q ss_conf 75799997711500003786077998999
Q gi|254780784|r 551 PRVEIMAIPPDQIRNVIGMGGKVIRGIVE 579 (699)
Q Consensus 551 p~~~~~~i~~~ki~~~iG~gG~~ik~i~~ 579 (699)
-.++.+++.|+-+|.+||..|+++|+|-.
T Consensus 29 ~~~~~l~V~~~D~GkVIGk~GrtakAIRt 57 (78)
T PRK01064 29 TIIYELTVAKPDIGKIIGKEGRTIKAIRT 57 (78)
T ss_pred EEEEEEEECCCCCCCEECCCCHHHHHHHH
T ss_conf 79999999900185587888746999999
No 183
>KOG3298 consensus
Probab=88.11 E-value=1.8 Score=22.47 Aligned_cols=68 Identities=18% Similarity=0.213 Sum_probs=45.7
Q ss_pred HHHCCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCC---CC-------CCCHHHHCCCCCEEEEEEEEEC
Q ss_conf 98524754686789999999415369982879710488663144---45-------4785560325988999999786
Q gi|254780784|r 611 RSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLST---ER-------VAKTSDVVKEGDTVWVKLLDFD 678 (699)
Q Consensus 611 ~~~~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~---~~-------v~~~~d~~~~Gd~i~vk~~~~d 678 (699)
+.+++.|=-|++.+|.|+++..-|+|++.=|-.--.+.-....+ .. -..-+++.++|++|.+|+++.-
T Consensus 73 ~av~FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr 150 (170)
T KOG3298 73 KAVTFKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTR 150 (170)
T ss_pred EEEEEEECCCCEEEEEEEEEEEEEEEEECCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEEEEEEEEE
T ss_conf 899974047768889999984244899605667532325279874217899998522664324550768999999999
No 184
>KOG2208 consensus
Probab=88.05 E-value=0.56 Score=26.67 Aligned_cols=59 Identities=17% Similarity=0.320 Sum_probs=44.6
Q ss_pred HHHHH-HHHHCCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEEC
Q ss_conf 99999-99843566743322448757999977115000037860779989998688899808
Q gi|254780784|r 529 LHILN-EMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDD 589 (699)
Q Consensus 529 ~~il~-~m~~~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d 589 (699)
.++.. .|..-+.+++.+.+ .|.-....||-+.-+.+|||+|.+.|.+..++++.+.+-.
T Consensus 687 ~~~~~~~~~~e~~~~~~~~~--~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208 687 IHVSGEKMQSEIAKIALEAK--NLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred CHHHHHHHHHHHCCCCCCCC--CCEEEEEECCHHHHHHCCCCCCCCHHHHHHHHCCCEECCC
T ss_conf 20100344544034211234--5302588566787642147887559999998565432278
No 185
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=87.35 E-value=0.6 Score=26.40 Aligned_cols=50 Identities=16% Similarity=0.261 Sum_probs=33.7
Q ss_pred HHHHHHHCCCCCCC-CCC--C-CCCEEEEEEECCCCEEEEECCCCHHHHHHHHH
Q ss_conf 99999843566743-322--4-48757999977115000037860779989998
Q gi|254780784|r 531 ILNEMSKVLSESRL-QLG--E-FTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQ 580 (699)
Q Consensus 531 il~~m~~~~~~~~~-~~~--~-~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~ 580 (699)
+.-++......|-. .++ . ..-....+.+.++-+|.+||.+|++|+.|-.-
T Consensus 5 v~~ivk~lVd~Pd~v~V~~~~~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 5 VEFIVKPLVDNPDDVRVDEEEGEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred HHHHHHHHCCCCCCEEEEEEECCCEEEEEEEECCCCCCCEECCCCHHHHHHHHH
T ss_conf 999999866896506899981697499999987200463566787059999999
No 186
>PRK00468 hypothetical protein; Provisional
Probab=87.23 E-value=0.52 Score=26.87 Aligned_cols=30 Identities=20% Similarity=0.464 Sum_probs=26.3
Q ss_pred CEEEEEEECCCCEEEEECCCCHHHHHHHHH
Q ss_conf 757999977115000037860779989998
Q gi|254780784|r 551 PRVEIMAIPPDQIRNVIGMGGKVIRGIVEQ 580 (699)
Q Consensus 551 p~~~~~~i~~~ki~~~iG~gG~~ik~i~~~ 580 (699)
-.+..+++.|+-.|.+||.+|+++|+|-.-
T Consensus 29 ~~~~~l~V~~~D~GkVIGk~GrtakAIRtl 58 (75)
T PRK00468 29 SIILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred EEEEEEEECHHHCCCEECCCCHHHHHHHHH
T ss_conf 799999999355864667787149999999
No 187
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=87.07 E-value=0.8 Score=25.38 Aligned_cols=39 Identities=36% Similarity=0.626 Sum_probs=35.9
Q ss_pred EEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCE
Q ss_conf 799997711500003786077998999868889980880
Q gi|254780784|r 553 VEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDG 591 (699)
Q Consensus 553 ~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g 591 (699)
...+.+|++-.+.+||.+|.|+|....=||-.+||++.-
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~~ 181 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETIS 181 (190)
T ss_pred EEEEEECHHHHHHCCCCCCHHHHHHHHHHCCEEEEEEHH
T ss_conf 899998989974446866588999999868877777621
No 188
>TIGR00008 infA translation initiation factor IF-1; InterPro: IPR004368 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 (IPR003029 from INTERPRO).; GO: 0003743 translation initiation factor activity, 0006413 translational initiation.
Probab=83.48 E-value=3.2 Score=20.52 Aligned_cols=58 Identities=31% Similarity=0.480 Sum_probs=45.2
Q ss_pred EEEEEEEEEEECCEE-EECCCCCCEEEEEE-ECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEE
Q ss_conf 789999999415369-98287971048866-31444547855603259889999997868-99866
Q gi|254780784|r 622 IYKGQVVKVMDFGAF-VHFCGARDGLVHIS-QLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIK 684 (699)
Q Consensus 622 ~y~~~v~~i~~fGaf-ve~~~g~~gl~HiS-~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~ 684 (699)
..+|+|++..+-+.| |+|-++..-+-||| ++..+.+. +=.||.|+|.+---|- +|||=
T Consensus 6 ~~~G~v~e~l~n~~f~V~LeN~~~v~a~iSGk~r~~~ir-----iLpGD~V~ve~SpYdl~~GRI~ 66 (69)
T TIGR00008 6 EVEGKVVESLPNAMFRVELENGHEVLAHISGKIRKNYIR-----ILPGDKVKVELSPYDLTRGRII 66 (69)
T ss_pred EECCEEEECCCCCEEEEEECCCCEEEEEECCEEECCEEE-----ECCCCEEEEEECCCCCCCCCEE
T ss_conf 742389854369826999479978989971034135175-----5479878998713648775087
No 189
>pfam07650 KH_2 KH domain.
Probab=83.16 E-value=0.98 Score=24.65 Aligned_cols=30 Identities=30% Similarity=0.417 Sum_probs=25.8
Q ss_pred EEEECCCCEEEEECCCCHHHHHHHHHHCCE
Q ss_conf 999771150000378607799899986888
Q gi|254780784|r 555 IMAIPPDQIRNVIGMGGKVIRGIVEQTGAK 584 (699)
Q Consensus 555 ~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~ 584 (699)
.+.|...+.|-+||.+|++|+.|.++..-.
T Consensus 3 ~v~i~~srpGiiIGk~G~~I~~l~~~l~k~ 32 (55)
T pfam07650 3 IVVIRTSQPGIVIGKGGSNIKKLGKELRKR 32 (55)
T ss_pred EEEEEECCCCEEECCCCCCHHHHHHHHHHH
T ss_conf 999991899679998960399999999998
No 190
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. 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=81.98 E-value=2.7 Score=21.13 Aligned_cols=46 Identities=28% Similarity=0.468 Sum_probs=34.4
Q ss_pred CCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHH----HHC---CEEEEEC
Q ss_conf 4332244875799997711500003786077998999----868---8899808
Q gi|254780784|r 543 RLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVE----QTG---AKVNIDD 589 (699)
Q Consensus 543 ~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~----~~~---~~i~i~d 589 (699)
+-++. -+|.-..+.|-..+=|-+||.+|..|+.|.+ .|| +.|+|.+
T Consensus 30 ~ieIe-Rtp~~~~I~I~t~rPG~VIGr~G~~I~~L~~~L~~~~g~~~~~I~V~E 82 (85)
T cd02411 30 GMEIL-RTPLGTQITIYAERPGMVIGRGGKNIRELTEILETKFGLENPQIDVQE 82 (85)
T ss_pred EEEEE-ECCCCEEEEEEECCCCEEECCCCHHHHHHHHHHHHHHCCCCCEEEEEE
T ss_conf 59999-889966999997899847778866599999999999689986599996
No 191
>pfam00313 CSD 'Cold-shock' DNA-binding domain.
Probab=81.54 E-value=3.7 Score=19.98 Aligned_cols=55 Identities=24% Similarity=0.359 Sum_probs=40.1
Q ss_pred EEEEEEEEE---CCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCE
Q ss_conf 999999941---536998287971048866314445478556032598899999978689986
Q gi|254780784|r 624 KGQVVKVMD---FGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKI 683 (699)
Q Consensus 624 ~~~v~~i~~---fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i 683 (699)
+|+|+.--+ ||....--.+.|-++|+|.|.... -..|++||.|+..+.. +++|..
T Consensus 2 tG~VK~f~~~kGfGFI~~~~~~~DiFvH~s~l~~~~----~~~L~~G~~V~f~v~~-~~kG~~ 59 (66)
T pfam00313 2 TGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQRVEFDIVE-GTKGPQ 59 (66)
T ss_pred CEEEEEEECCCCEEEEEECCCCCEEEEEHHHHCCCC----CCCCCCCCEEEEEEEE-CCCCCE
T ss_conf 489999959999699997899846999926812147----8617999999999997-999866
No 192
>TIGR01859 fruc_bis_ald_ fructose-1,6-bisphosphate aldolase, class II; InterPro: IPR011289 Fructose-1,6-bisphosphate (FBP) aldolases reversibly cleave FBP to two triose phosphates, glycerone phophate and D-glyceraldehyde 3-phosphate. They play a key role in both glycolysis (FBP cleavage) and gluconeogenesis (FBP synthesis). These enzymes can be divide into two classes based on their mode of catalysis. Class I FBP aldolases form a Schiff-base intermediate between glycerone phophate and an active site lysine residue, while the class II enzymes use a divalent cation such as Zn(2+) for catalysis . This entry represents class II FBP aldolases found in Gram-positive bacteria, a variety of Gram-negative baceria, and amitochondriate protists. These enzymes are homotetramers where each momomer forms a TIM barrel fold .; GO: 0004332 fructose-bisphosphate aldolase activity, 0008270 zinc ion binding, 0006096 glycolysis, 0030388 fructose 16-bisphosphate metabolic process.
Probab=80.71 E-value=3.9 Score=19.78 Aligned_cols=103 Identities=19% Similarity=0.229 Sum_probs=67.8
Q ss_pred CCEEECCCCCC--CC----C-C-CEEEEEECC----CCHHHHH------CCCCCCCHHHHHHHHHHHHHHH----HHHHH
Q ss_conf 73243685000--22----2-1-013553054----4323331------2444324899998875316889----99999
Q gi|254780784|r 159 GQYVLNPRLDE--DQ----G-S-LDLFVSGTQ----DAVLMVE------LEANQLSEDVVLDAIIFGHNEC----KPVIE 216 (699)
Q Consensus 159 ge~ViNPt~ee--~e----s-d-LDLvVAGT~----d~IlMIE------~~A~EVsEe~mleAI~~Ahe~I----k~iI~ 216 (699)
+...+-|..+. ++ . . +=||.=|-. |-+--++ .+|..|||+.+.+||.+|+--| .-.|.
T Consensus 204 DGvLiWp~LdF~~l~~I~~~~~G~PLVLHGaS~VP~e~v~~~~~~GG~L~ds~GIP~e~ikkAi~lGiaKiNidTe~riA 283 (339)
T TIGR01859 204 DGVLIWPGLDFERLKEIKELTNGIPLVLHGASSVPAEIVKEVEEYGGELKDSKGIPEEQIKKAIKLGIAKINIDTECRIA 283 (339)
T ss_pred CCEECCCCCCHHHHHHHHHHHCCCCEEECCCCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCEEEECCHHHHH
T ss_conf 72354888897899999875089766735765685889999998187677777686789999997291417658167899
Q ss_pred HHHHHHHHHC---------CCCCCCCCC-CHHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf 9999999838---------898644743-12579999999989888887410001
Q gi|254780784|r 217 AISKLAKMCA---------KEPIVIDSK-DFSKLEEEMSQMIKEDLRVSCFIPEK 261 (699)
Q Consensus 217 ~Q~eL~~~~G---------k~K~~~~~~-~~~~~~~~v~~~~~~~l~~a~~i~~K 261 (699)
+-.++++-.- -.|.+|+|. .+.+-.+++++.+.+++++.+-+..|
T Consensus 284 f~~~~R~~l~dy~a~dl~l~k~~~yDPRK~L~p~~~a~k~~v~~K~~e~fGS~gK 338 (339)
T TIGR01859 284 FTAAIRKVLEDYEAKDLELEKKDEYDPRKILGPAREAIKETVKEKMREVFGSAGK 338 (339)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 9999999984114355402588744663335316899999999862454055778
No 193
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=80.65 E-value=1.8 Score=22.45 Aligned_cols=47 Identities=26% Similarity=0.545 Sum_probs=32.1
Q ss_pred EEEECCCEEEEEEE-ECCCCCCCCCCCCCCCCEEEEEEEECCCCCC------CCCCCCCCCCC
Q ss_conf 99987976899998-1686521223344544203587740588754------45334556765
Q gi|254780784|r 340 LFIRGDTQAIVVVT-LGTREDEQYVDSLSGTQRNDFMMHYNFLPCA------TGEVSRMGAPS 395 (699)
Q Consensus 340 LFtRGETQaL~tvT-LG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfs------vGE~~~~~~~~ 395 (699)
-|.+++.+++|.+. +|+.-|- ..-||-.||+.|+-. +|.+||-|.|+
T Consensus 275 ~f~~~~~~iiVAT~AFGMGIdK---------pdVRfViH~~lP~s~EsYyQE~GRAGRDG~~a 328 (590)
T COG0514 275 AFLNDEIKVMVATNAFGMGIDK---------PDVRFVIHYDLPGSIESYYQETGRAGRDGLPA 328 (590)
T ss_pred HHHCCCCCEEEEECCCCCCCCC---------CCCEEEEEECCCCCHHHHHHHHHHCCCCCCCC
T ss_conf 9716998689996462477678---------88407998069989899999971356787702
No 194
>KOG2279 consensus
Probab=79.18 E-value=1.3 Score=23.67 Aligned_cols=89 Identities=15% Similarity=0.102 Sum_probs=58.2
Q ss_pred CCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEEC---CEEE---EEEE--CCHHHHHHHHHHHHHHCCCCC
Q ss_conf 2448757999977115000037860779989998688899808---8089---9996--898999999999998524754
Q gi|254780784|r 547 GEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDD---DGTV---KIAS--SSLAEIEAAREMIRSITDVPE 618 (699)
Q Consensus 547 ~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d---~g~v---~i~~--~~~~~~~~a~~~i~~~~~~~e 618 (699)
+.-+|-|.-|.+|....|++||-.|+.++-+...+|+.+-|-. -+.| .|+- ..+.-.+.+.+|+...+-+..
T Consensus 291 k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~egkqh~~n~vl~ml~~~~p~~~ 370 (608)
T KOG2279 291 KSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEGKQHYENSVLEMLTVHVPDIV 370 (608)
T ss_pred CCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHEECCHHHHHHHHHHHHHCCCCCCC
T ss_conf 00133330244476654102210134444656415754247752433113123230114216777777765431287320
Q ss_pred CCCEEE-EEEEEEEECCE
Q ss_conf 686789-99999941536
Q gi|254780784|r 619 VNKIYK-GQVVKVMDFGA 635 (699)
Q Consensus 619 ~g~~y~-~~v~~i~~fGa 635 (699)
+-+.|. +-+-...+.||
T Consensus 371 f~eLnl~~~~~p~lps~a 388 (608)
T KOG2279 371 FAELNLNGSWYPALPSGA 388 (608)
T ss_pred CCCCCCCCCCCCCCCCCC
T ss_conf 123345676674567653
No 195
>TIGR00202 csrA carbon storage regulator; 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, 0016071 mRNA metabolic process.
Probab=79.16 E-value=1.9 Score=22.41 Aligned_cols=31 Identities=26% Similarity=0.459 Sum_probs=26.7
Q ss_pred CCHHHHCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf 78556032598899999978689986668730
Q gi|254780784|r 658 AKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKV 689 (699)
Q Consensus 658 ~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk~ 689 (699)
+++..-+.+||.|.|+++++ +++.+||.-+|
T Consensus 6 RKvnE~i~I~ddI~v~Vl~v-~~~~VklG~~A 36 (69)
T TIGR00202 6 RKVNESIVIGDDIEVKVLSV-KGDQVKLGIEA 36 (69)
T ss_pred EECCCEEEECCCEEEEEEEE-ECCCEEEEEEC
T ss_conf 22074546589406999986-27917864338
No 196
>pfam00918 Gastrin Gastrin/cholecystokinin family.
Probab=78.05 E-value=0.74 Score=25.63 Aligned_cols=19 Identities=11% Similarity=0.174 Sum_probs=13.6
Q ss_pred CHHHHHHHHHHHHHHHCCC
Q ss_conf 0246799999998741078
Q gi|254780784|r 396 RREIGHGRLARRAIHPVLP 414 (699)
Q Consensus 396 RREiGHg~la~ral~~~~P 414 (699)
+-+.+-++|-.|-|.+.-+
T Consensus 47 ~~~~~~~~ll~r~L~~~~~ 65 (111)
T pfam00918 47 LDRLGLASLLQKYLQQKRK 65 (111)
T ss_pred CCCCCHHHHHHHHHHHHCC
T ss_conf 1335708999999987025
No 197
>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=77.48 E-value=2 Score=22.15 Aligned_cols=57 Identities=19% Similarity=0.241 Sum_probs=38.4
Q ss_pred HHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECC
Q ss_conf 9999998435667433224487579999771150000378607799899986888998088
Q gi|254780784|r 530 HILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDD 590 (699)
Q Consensus 530 ~il~~m~~~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~ 590 (699)
.+|+.|.-. ..-+.+. -.....+.|..+..+.+||+.|+++.+||.=++.-++-..+
T Consensus 6 ~ll~~mg~~---~~v~~~~-~~~~~~~~i~g~~~~~LIGk~G~tL~AlQ~L~~~~~~~~~~ 62 (77)
T cd02414 6 EVLELMGIE---ADVDVEE-EGDTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNRNTG 62 (77)
T ss_pred HHHHHCCCC---EEEEEEE-ECCEEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf 999985994---7999999-79989999944987741668986479999999999975279
No 198
>pfam01176 eIF-1a Translation initiation factor 1A / IF-1. This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1.
Probab=77.46 E-value=4.8 Score=19.05 Aligned_cols=59 Identities=29% Similarity=0.477 Sum_probs=43.0
Q ss_pred CCCEEEEEEEEEEECCEEE-ECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCE
Q ss_conf 6867899999994153699-828797104886631444547855603259889999997868-9986
Q gi|254780784|r 619 VNKIYKGQVVKVMDFGAFV-HFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKI 683 (699)
Q Consensus 619 ~g~~y~~~v~~i~~fGafv-e~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i 683 (699)
.|++ .|+|++...-|-|- .+..|.+-|+||+- +..+ .=-+..||.|.|..-+.|+ +|+|
T Consensus 2 e~e~-~g~V~~~lg~~~~~V~~~dg~~~l~~i~G----K~rk-riwi~~GD~VlV~~~~~~~~kg~I 62 (65)
T pfam01176 2 EGEM-IGQVTEMLGNGRFEVELEDGHERLAHIPG----KRRK-RIWILRGDFVLVELSPYDKVKGRI 62 (65)
T ss_pred CCEE-EEEEEEECCCCEEEEEECCCCEEEEEECC----CEEE-EEEECCCCEEEEEECCCCCCEEEE
T ss_conf 9869-99999982998899997999999999822----0545-799749999999967877863999
No 199
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=76.87 E-value=5 Score=18.93 Aligned_cols=63 Identities=30% Similarity=0.566 Sum_probs=47.6
Q ss_pred CCCCCEEEEEEEEEEECCEE-EECCCCCCEEEEEEE-CCCCCCCCHHHHCCCCCEEEEEEEEECC-CCCEEE
Q ss_conf 54686789999999415369-982879710488663-1444547855603259889999997868-998666
Q gi|254780784|r 617 PEVNKIYKGQVVKVMDFGAF-VHFCGARDGLVHISQ-LSTERVAKTSDVVKEGDTVWVKLLDFDD-RGKIKL 685 (699)
Q Consensus 617 ~e~g~~y~~~v~~i~~fGaf-ve~~~g~~gl~HiS~-l~~~~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~l 685 (699)
++.++ ..|+|.+...-+-| |++..|.+-+-|||- +-..++ -+..||.|.|..-..|. +|+|-.
T Consensus 4 ~d~~e-~~g~V~e~L~~~~f~v~~eng~~~~ahI~GKmr~~~i-----~I~~GD~V~Ve~~~~d~~kg~I~~ 69 (75)
T COG0361 4 PDEIE-MEGTVIEMLPNGRFRVELENGHERLAHISGKMRKNRI-----RILPGDVVLVELSPYDLTKGRIVY 69 (75)
T ss_pred CCCCE-EEEEEEEECCCCEEEEEECCCCEEEEECCCCCCEEEE-----EECCCCEEEEEECCCCCCCCCEEE
T ss_conf 64428-9999999738978999946996999882587440048-----857999999974566533355899
No 200
>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=75.66 E-value=5.3 Score=18.69 Aligned_cols=54 Identities=31% Similarity=0.364 Sum_probs=35.0
Q ss_pred EEEEEE-EECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCE
Q ss_conf 999999-41536998287971048866314445478556032598899999978689986
Q gi|254780784|r 625 GQVVKV-MDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKI 683 (699)
Q Consensus 625 ~~v~~i-~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i 683 (699)
|+|+-- +-||-.----.++|-++|+|++.. .. ..++.||.|+..+..-+..++.
T Consensus 2 G~Vk~f~kGfGFI~~~~g~~DvFvH~s~i~~-~~----~~l~~Gd~V~f~v~~~~~~~~~ 56 (64)
T smart00357 2 GVVKWFNKGFGFIRPDDGGKDVFVHPSQIQG-GL----KSLREGDEVEFKVVSPRGGGKP 56 (64)
T ss_pred CEEEEEECCEEEEEECCCCCCEEEEHHHHCC-CC----CCCCCCCEEEEEEEECCCCCCC
T ss_conf 4796982844888618999409998699546-77----7447587899999988999984
No 201
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. 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 domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=75.15 E-value=4.8 Score=19.05 Aligned_cols=42 Identities=26% Similarity=0.356 Sum_probs=35.8
Q ss_pred CCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEEC
Q ss_conf 448757999977115000037860779989998688899808
Q gi|254780784|r 548 EFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDD 589 (699)
Q Consensus 548 ~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d 589 (699)
-+-|..--+.|..+|=|.+||.+|.+++.|..+||=...+.-
T Consensus 72 ~FD~~~gEV~Iea~kPg~viGk~g~~l~eI~~~tGW~p~v~R 113 (145)
T cd02410 72 YFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred EECCCCCEEEEEECCCEEEECCCCHHHHHHHHHHCCEEEEEE
T ss_conf 974888579999779777972761679999997398157886
No 202
>LOAD_cold consensus
Probab=74.03 E-value=5.8 Score=18.39 Aligned_cols=56 Identities=25% Similarity=0.297 Sum_probs=39.0
Q ss_pred EEEEEEEEE---ECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCE
Q ss_conf 899999994---1536998287971048866314445478556032598899999978689986
Q gi|254780784|r 623 YKGQVVKVM---DFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKI 683 (699)
Q Consensus 623 y~~~v~~i~---~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i 683 (699)
++|+|+.-- -||...---.++|-++|+|.|... -...|++||.|+..+..- ++|..
T Consensus 2 ~~G~VK~f~~~kGfGFI~~~~g~~DvFvH~s~l~~~----~~~~l~~G~~V~f~~~~~-~kG~~ 60 (67)
T LOAD_cold 2 VKGTVKWFNVKKGFGFITPEDGGEDVFVHQSAIQGD----GFRSLTEGQEVEFDIVEG-PKGPQ 60 (67)
T ss_pred CCEEEEEEECCCCCEEEEECCCCCEEEEEHHHHCCC----CCCCCCCCCEEEEEEEEC-CCCCE
T ss_conf 986999998999947887579982189994781404----786479999999999989-99967
No 203
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=73.14 E-value=2.9 Score=20.78 Aligned_cols=50 Identities=26% Similarity=0.474 Sum_probs=36.6
Q ss_pred EEEEECCCEEEEEE-EECCCCCCCCCCCCCCCCEEEEEEEECCCCCC------CCCCCCCCCCCCH
Q ss_conf 89998797689999-81686521223344544203587740588754------4533455676502
Q gi|254780784|r 339 SLFIRGDTQAIVVV-TLGTREDEQYVDSLSGTQRNDFMMHYNFLPCA------TGEVSRMGAPSRR 397 (699)
Q Consensus 339 ALFtRGETQaL~tv-TLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfs------vGE~~~~~~~~RR 397 (699)
--|.+|+.|++|.+ .+|+.-|- ..-||..||++|.-- +|.+||-|.|++=
T Consensus 280 ~~f~~~~~~vivAT~AFGMGIdk---------~dVR~ViH~~~P~s~e~yyQE~GRAGRDG~~a~c 336 (607)
T PRK11057 280 EAFQRDDLQIVVATVAFGMGINK---------PNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEA 336 (607)
T ss_pred HHHHCCCCCEEEEEHHHHCCCCC---------CCCCEEEECCCCCCHHHHHHHHHHCCCCCCCCEE
T ss_conf 98756887589975011057677---------7766799778999999999988635258985418
No 204
>KOG3409 consensus
Probab=72.26 E-value=6.3 Score=18.08 Aligned_cols=72 Identities=19% Similarity=0.251 Sum_probs=53.1
Q ss_pred CCCCCCEEEEEEEEEEECCEEEECCC--------CCCEEEEEEECCCCCCCCHHH--HCCCCCEEEEEEEEECCCCCEEE
Q ss_conf 75468678999999941536998287--------971048866314445478556--03259889999997868998666
Q gi|254780784|r 616 VPEVNKIYKGQVVKVMDFGAFVHFCG--------ARDGLVHISQLSTERVAKTSD--VVKEGDTVWVKLLDFDDRGKIKL 685 (699)
Q Consensus 616 ~~e~g~~y~~~v~~i~~fGafve~~~--------g~~gl~HiS~l~~~~v~~~~d--~~~~Gd~i~vk~~~~d~~g~i~l 685 (699)
-|.+|.|..++|.+|-.-=|=|+|+- --.||+|--.+-..--++++- -++-||.|..|+++.+.+-+.=|
T Consensus 65 LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~L 144 (193)
T KOG3409 65 LPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLL 144 (193)
T ss_pred CCCCCCEEEEEEEEECCCEEEEEEEEECCEEHHHHHCCEEEHHHCCCCCCCHHHHHHCCCCCCEEEEEEEECCCCCCEEE
T ss_conf 77657679999876244135678999867970011211433543564440112163436988688888851477872799
Q ss_pred EE
Q ss_conf 87
Q gi|254780784|r 686 SM 687 (699)
Q Consensus 686 Sr 687 (699)
+-
T Consensus 145 Tt 146 (193)
T KOG3409 145 TT 146 (193)
T ss_pred EE
T ss_conf 87
No 205
>KOG3273 consensus
Probab=72.13 E-value=1.8 Score=22.57 Aligned_cols=61 Identities=25% Similarity=0.384 Sum_probs=49.9
Q ss_pred CEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEE
Q ss_conf 500003786077998999868889980880899996898999999999998524754686789
Q gi|254780784|r 562 QIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYK 624 (699)
Q Consensus 562 ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~~~e~g~~y~ 624 (699)
-||.++|.|||+=-.|+.-|-..|-+-| -.++|.|. -+...-|..-|-++..---.|++|-
T Consensus 179 AIGRiaGk~GkTkfaIEn~trtrIVlad-~kIHiLG~-~~niriAR~avcsLIlGsppgkVy~ 239 (252)
T KOG3273 179 AIGRIAGKGGKTKFAIENVTRTRIVLAD-SKIHILGA-FQNIRIARDAVCSLILGSPPGKVYG 239 (252)
T ss_pred HHHHHHCCCCCCEEEEECCCEEEEEECC-CEEEEEEC-CHHHHHHHHHHHHHHCCCCCHHHHH
T ss_conf 8877626788512222014304799607-66899613-1145788876676441699236788
No 206
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=71.92 E-value=6.4 Score=18.03 Aligned_cols=67 Identities=21% Similarity=0.258 Sum_probs=45.6
Q ss_pred EEEEEEEE---ECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEEECCCCCC
Q ss_conf 99999994---1536998287971048866314445478556032598899999978689986668730477878
Q gi|254780784|r 624 KGQVVKVM---DFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQNTG 695 (699)
Q Consensus 624 ~~~v~~i~---~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk~~~~~~~ 695 (699)
+|+|+-.- -||.+..--.|.|-++|+|.|...-. --|+.||.|...+..- ++|+--...+.+..++.
T Consensus 3 ~G~VKwFn~~KGyGFI~~d~gg~DvFvH~s~i~~~G~----~~L~~G~~V~f~v~~g-~kG~~A~~V~~ve~~~a 72 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGY----RTLKAGQSVQFDVHQG-PKGNHASVIVPVEVEAA 72 (74)
T ss_pred CCEEEEEECCCCEEEEEECCCCCCEEEEHHHHCCCCC----CCCCCCCEEEEEEEEC-CCCCEEEEEEECCCCCC
T ss_conf 8379788389971886207999559998588231588----4249999999999989-99851567588576667
No 207
>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=70.71 E-value=6.8 Score=17.83 Aligned_cols=56 Identities=34% Similarity=0.385 Sum_probs=39.7
Q ss_pred EEEEEEEEEE---CCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCE
Q ss_conf 8999999941---536998287971048866314445478556032598899999978689986
Q gi|254780784|r 623 YKGQVVKVMD---FGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKI 683 (699)
Q Consensus 623 y~~~v~~i~~---fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i 683 (699)
++|+|+..-+ ||-+..--.|.+-++|+|.|.... ..-+++||.|...+..- ++|..
T Consensus 1 ~~G~Vk~f~~~kGfGFI~~~~~~~diF~H~s~~~~~~----~~~l~~G~~V~f~~~~~-~~g~~ 59 (65)
T cd04458 1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEG-DKGPQ 59 (65)
T ss_pred CEEEEEEEECCCCEEEEEECCCCCCEEEEHHHHCCCC----CCCCCCCCEEEEEEEEC-CCCCE
T ss_conf 9389999979999699995799822999958924346----97479898999999989-89976
No 208
>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta. A small number of taxonomically diverse prokaryotic species 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 beta subunit of this apparent second ATP synthase.
Probab=70.50 E-value=6.8 Score=17.80 Aligned_cols=29 Identities=24% Similarity=0.241 Sum_probs=11.1
Q ss_pred CCCCCCCCC-CCCCCCCCHHHHHHHHHHHH
Q ss_conf 887544533-45567650246799999998
Q gi|254780784|r 380 FLPCATGEV-SRMGAPSRREIGHGRLARRA 408 (699)
Q Consensus 380 FPpfsvGE~-~~~~~~~RREiGHg~la~ra 408 (699)
||+.-++.- +|...+.==.-.|-.+|.+.
T Consensus 328 yPAId~l~S~SRv~~~~iv~~~H~~va~~~ 357 (449)
T TIGR03305 328 YPAIDPLQSTSKMATPGIVGERHYDLAREV 357 (449)
T ss_pred CCCCCCCCCHHHCCCCCCCCHHHHHHHHHH
T ss_conf 997177633553488100679999999999
No 209
>PRK10354 major cold shock protein; Provisional
Probab=68.82 E-value=7.4 Score=17.54 Aligned_cols=57 Identities=23% Similarity=0.286 Sum_probs=38.7
Q ss_pred EEEEEEEEEE---ECCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCE
Q ss_conf 7899999994---1536998287971048866314445478556032598899999978689986
Q gi|254780784|r 622 IYKGQVVKVM---DFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKI 683 (699)
Q Consensus 622 ~y~~~v~~i~---~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i 683 (699)
-.+|+|+--- -||...---.++|-++|+|.|..... ..|++||.|+..+..- ++|.-
T Consensus 4 ~~tG~VKwFn~~KGyGFI~~d~g~~DvFvH~s~l~~~g~----~~L~~Gq~V~f~~~~g-~kG~~ 63 (70)
T PRK10354 4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGY----KSLDEGQKVSFTIESG-AKGPA 63 (70)
T ss_pred CEEEEEEEEECCCCEEEEECCCCCCEEEEEHHHHCCCCC----CCCCCCCEEEEEEEEC-CCCCE
T ss_conf 507999987099985998427998429998589170489----7259999999999979-99862
No 210
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=68.75 E-value=7.4 Score=17.53 Aligned_cols=72 Identities=14% Similarity=0.226 Sum_probs=50.9
Q ss_pred EEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCC------CCCCCCCCCCC-------CHHHHHHHHH
Q ss_conf 8999879768999981686521223344544203587740588754------45334556765-------0246799999
Q gi|254780784|r 339 SLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCA------TGEVSRMGAPS-------RREIGHGRLA 405 (699)
Q Consensus 339 ALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfs------vGE~~~~~~~~-------RREiGHg~la 405 (699)
.-|..|.+++|+++-+.+.+ +| -..-++-.||++|.-. +|.+||.|..+ .||...=+-.
T Consensus 286 ~~F~~g~~~iLVaTDvaaRG----ID----i~~V~~VInyDlP~~~e~YvHRiGRTGRaG~~G~ait~vt~~e~~~l~~i 357 (459)
T PRK11776 286 VRFANRSCSVLVATDVAARG----LD----IKSLEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRAAAI 357 (459)
T ss_pred HHHHCCCCCEEEEHHHHHCC----CC----CCCCCEEEEECCCCCHHHHHHCCCHHHCCCCCEEEEEEECHHHHHHHHHH
T ss_conf 99977999799881043476----77----13598899978989745520205251378996579999868999999999
Q ss_pred HHHHHHCCCCCCC
Q ss_conf 9987410786446
Q gi|254780784|r 406 RRAIHPVLPQTAQ 418 (699)
Q Consensus 406 ~ral~~~~P~~~~ 418 (699)
||.+..-+|..+.
T Consensus 358 e~~~~~~i~~~~~ 370 (459)
T PRK11776 358 EDYLGRKLNWEPL 370 (459)
T ss_pred HHHHCCCCCCCCC
T ss_conf 9997899864169
No 211
>KOG3548 consensus
Probab=67.62 E-value=7 Score=17.72 Aligned_cols=94 Identities=15% Similarity=0.121 Sum_probs=56.9
Q ss_pred CCCEEEE----EEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCC-CCCCCEEEEEEEECCCCCCCCCCCCCCC
Q ss_conf 7533787----9984475466700899987976899998168652122334-4544203587740588754453345567
Q gi|254780784|r 319 SETVRDI----SAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDS-LSGTQRNDFMMHYNFLPCATGEVSRMGA 393 (699)
Q Consensus 319 ~dEIRpI----s~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~-l~~~~~k~fmlHYNFPpfsvGE~~~~~~ 393 (699)
..+.+.| .|-..|.|+.-+|. +-|+++ +-.++ |-.|+ ...--+-++-..|+|+|+|+.+++- +
T Consensus 684 ~s~a~dik~~P~~si~V~p~l~~S~-----kDQ~~v--rsDsp---qs~d~P~i~gl~v~a~w~~~fyp~s~ls~rd--~ 751 (1176)
T KOG3548 684 KSEASDIKTPPAKSIPVIPLLNLSD-----KDQLLV--RSDSP---QSDDEPHIPGLRVYAVWQKMFYPASVLSERD--G 751 (1176)
T ss_pred CCCCCCCCCCCCCCEECCCCCCCCC-----CCCEEE--ECCCC---CCCCCCCCCCEEEEEEECCCCCCCCCCEEEC--C
T ss_conf 7762101368755311255678775-----653133--05783---2246787776379998502577765320243--7
Q ss_pred CCCHHHHHHHHHHHHHHHCCCCCCCCCEE--EEEEEEECCCC
Q ss_conf 65024679999999874107864468738--99985311027
Q gi|254780784|r 394 PSRREIGHGRLARRAIHPVLPQTAQFPYT--LRIVSEITESD 433 (699)
Q Consensus 394 ~~RREiGHg~la~ral~~~~P~~~~~p~t--irv~~evl~sn 433 (699)
-+| .+++.-+.+...+.||+ |-+.+.|..++
T Consensus 752 ~gr---------~~~fft~~~~~kdi~~~diiplda~vt~~~ 784 (1176)
T KOG3548 752 LGR---------YKVFFTVDNVIKDIPNSDIIPLDALVTGKT 784 (1176)
T ss_pred CCC---------EEEEEECCCCCCCCCCCCCEECCCCCCCCC
T ss_conf 873---------799973144434542356423112123650
No 212
>TIGR01008 rpsC_E_A ribosomal protein S3; InterPro: IPR005703 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 of 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 S3 is one of the proteins from the small ribosomal subunit. This family describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=67.61 E-value=4.5 Score=19.27 Aligned_cols=45 Identities=27% Similarity=0.403 Sum_probs=33.0
Q ss_pred CCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCC--EEEEE
Q ss_conf 43322448757999977115000037860779989998688--89980
Q gi|254780784|r 543 RLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGA--KVNID 588 (699)
Q Consensus 543 ~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~--~i~i~ 588 (699)
+-++.. .|-=..+-|=.++=+.|||-||++||.|++...- +-+++
T Consensus 30 gvdv~~-TPlGT~vii~AerPg~VIGr~G~rIr~LT~~l~~Rf~Fg~e 76 (204)
T TIGR01008 30 GVDVRK-TPLGTKVIIYAERPGLVIGRGGRRIRELTEKLQKRFKFGLE 76 (204)
T ss_pred CCEEEE-CCCCCEEEEEEECCCCEECCCCCHHHHHHHHHHHHHCCCCC
T ss_conf 551687-77896799998368637727972188999999875205899
No 213
>KOG2874 consensus
Probab=67.13 E-value=7.9 Score=17.29 Aligned_cols=21 Identities=19% Similarity=0.387 Sum_probs=8.1
Q ss_pred EEECCCCHHHHHHHHHHCCEE
Q ss_conf 003786077998999868889
Q gi|254780784|r 565 NVIGMGGKVIRGIVEQTGAKV 585 (699)
Q Consensus 565 ~~iG~gG~~ik~i~~~~~~~i 585 (699)
.||||.|.++|+|+--|.|-|
T Consensus 162 RLiGpng~TLKAlelLT~CYi 182 (356)
T KOG2874 162 RLIGPNGSTLKALELLTNCYI 182 (356)
T ss_pred HHCCCCCHHHHHHHHHHHCEE
T ss_conf 731888205799999752179
No 214
>PRK10943 cold shock-like protein CspC; Provisional
Probab=66.85 E-value=8 Score=17.25 Aligned_cols=57 Identities=28% Similarity=0.386 Sum_probs=39.6
Q ss_pred EEEEEEEEEEE---CCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCE
Q ss_conf 78999999941---536998287971048866314445478556032598899999978689986
Q gi|254780784|r 622 IYKGQVVKVMD---FGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKI 683 (699)
Q Consensus 622 ~y~~~v~~i~~---fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i 683 (699)
-.+|+|+---+ ||-...--.++|-++|+|.|..... .-|.+||.|+..+..- ++|.-
T Consensus 3 ~~~G~VKwFn~~kGfGFI~~~dg~~DvFvH~s~i~~~g~----~~L~eGq~V~f~~~~g-~kG~~ 62 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGF----KTLAEGQNVEFEIQDG-QKGPA 62 (69)
T ss_pred CEEEEEEEEECCCCEEEEEECCCCCCEEEEHHHHCCCCC----CCCCCCCEEEEEEEEC-CCCCC
T ss_conf 378899998399986998617998309999388271688----3239999999999979-99863
No 215
>KOG3013 consensus
Probab=66.58 E-value=8.1 Score=17.21 Aligned_cols=10 Identities=50% Similarity=1.089 Sum_probs=5.8
Q ss_pred CCCCCCCCCC
Q ss_conf 6788873578
Q gi|254780784|r 72 KIPGGYLRRE 81 (699)
Q Consensus 72 kIPGgF~kRE 81 (699)
-.|||-+||-
T Consensus 119 NLPGg~~RRk 128 (301)
T KOG3013 119 NLPGGIQRRK 128 (301)
T ss_pred CCCCHHHHCC
T ss_conf 4886143302
No 216
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=65.96 E-value=4.7 Score=19.16 Aligned_cols=35 Identities=14% Similarity=0.156 Sum_probs=22.4
Q ss_pred EEEEEECCC---CCCCCEEE-EEECCCEEEEEEEECCCC
Q ss_conf 879984475---46670089-998797689999816865
Q gi|254780784|r 324 DISAQVGLL---QRTHGSSL-FIRGDTQAIVVVTLGTRE 358 (699)
Q Consensus 324 pIs~EvgvL---PrvHGSAL-FtRGETQaL~tvTLG~~~ 358 (699)
.=|+.+-.| --|--||+ .+-.|+.+|.-|-+-...
T Consensus 178 ~~wvRvt~LGg~~EVGRSa~lv~T~eSrVLlDcG~n~a~ 216 (637)
T COG1782 178 DRWVRVTALGGFREVGRSALLVSTPESRVLLDCGVNVAG 216 (637)
T ss_pred CCEEEEEEECCCHHCCCEEEEEECCCCEEEEECCCCCCC
T ss_conf 745999961241120625699736883389963656778
No 217
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=65.85 E-value=8.3 Score=17.11 Aligned_cols=71 Identities=20% Similarity=0.316 Sum_probs=51.1
Q ss_pred EEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCC------CCCCCCCCCCC-------CHHHHHHHHH
Q ss_conf 8999879768999981686521223344544203587740588754------45334556765-------0246799999
Q gi|254780784|r 339 SLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCA------TGEVSRMGAPS-------RREIGHGRLA 405 (699)
Q Consensus 339 ALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfs------vGE~~~~~~~~-------RREiGHg~la 405 (699)
.-|..|+.++|+++-+.+.+ +| -..-.+-.||+||... +|.++|.|..+ -.|..+=.-.
T Consensus 289 ~~F~~g~~~vLVaTDvaaRG----iD----i~~V~~VInyD~P~~~e~YvHRiGRTGRaG~~G~ait~v~~~e~~~~~~i 360 (457)
T PRK10590 289 ADFKSGDIRVLVATDIAARG----LD----IEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDI 360 (457)
T ss_pred HHHHCCCCCEEEECCCCCCC----CC----CCCCCEEEEECCCCCHHHEECCCCCCCCCCCCEEEEEEECHHHHHHHHHH
T ss_conf 99986998299957701155----66----35688799938999744500226706058995369998668999999999
Q ss_pred HHHHHHCCCCCC
Q ss_conf 998741078644
Q gi|254780784|r 406 RRAIHPVLPQTA 417 (699)
Q Consensus 406 ~ral~~~~P~~~ 417 (699)
||-+..-||...
T Consensus 361 e~~~~~~~~~~~ 372 (457)
T PRK10590 361 EKLLKKEIPRIA 372 (457)
T ss_pred HHHHCCCCCCCC
T ss_conf 999779887403
No 218
>TIGR01648 hnRNP-R-Q hnRNP-R, Q splicing factor family; InterPro: IPR006535 Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein) . These proteins contain three RNA recognition domains and a somewhat variable C-terminal domain. .
Probab=63.63 E-value=8.7 Score=16.96 Aligned_cols=47 Identities=30% Similarity=0.371 Sum_probs=25.4
Q ss_pred EEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEECCEEEECC
Q ss_conf 08999968989999999999985247546867899999994153699828
Q gi|254780784|r 591 GTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFC 640 (699)
Q Consensus 591 g~v~i~~~~~~~~~~a~~~i~~~~~~~e~g~~y~~~v~~i~~fGafve~~ 640 (699)
-.|+|.=.=--.++-.-++|+.-..+.+.|++ =+|+||.|| |||.+-
T Consensus 236 ~~VKiLyVRNL~~~ttEE~ieKsF~~f~PG~v--ERVKKirDY-AFVHF~ 282 (611)
T TIGR01648 236 AKVKILYVRNLMLETTEEIIEKSFSEFKPGAV--ERVKKIRDY-AFVHFE 282 (611)
T ss_pred CCCEEEEEECCHHHHHHHHHHHHCCCCCCCCE--EEEEEECCE-EEEEEC
T ss_conf 61027888332134214333201256799724--543110121-364016
No 219
>KOG0351 consensus
Probab=63.35 E-value=8.9 Score=16.88 Aligned_cols=47 Identities=28% Similarity=0.539 Sum_probs=29.9
Q ss_pred EEECCCEEEE-EEEECCCCCCCCCCCCCCCCEEEEEEEECCCCC------CCCCCCCCCCCCC
Q ss_conf 9987976899-998168652122334454420358774058875------4453345567650
Q gi|254780784|r 341 FIRGDTQAIV-VVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPC------ATGEVSRMGAPSR 396 (699)
Q Consensus 341 FtRGETQaL~-tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpf------svGE~~~~~~~~R 396 (699)
|.+|+-|+.| |+.+|+.-|- ..=||-+||++|.- .+|.+||-|-++.
T Consensus 531 w~~~~~~VivATVAFGMGIdK---------~DVR~ViH~~lPks~E~YYQE~GRAGRDG~~s~ 584 (941)
T KOG0351 531 WMSDKIRVIVATVAFGMGIDK---------PDVRFVIHYSLPKSFEGYYQEAGRAGRDGLPSS 584 (941)
T ss_pred HHCCCCEEEEEEEECCCCCCC---------CCEEEEEECCCCHHHHHHHHHCCCCCCCCCCCE
T ss_conf 856887089998522478777---------863599977786147888874033676788002
No 220
>KOG3392 consensus
Probab=62.47 E-value=9.1 Score=16.81 Aligned_cols=27 Identities=11% Similarity=0.185 Sum_probs=17.1
Q ss_pred ECCCEEEEEEEECCCCCCCCCCCCCCC
Q ss_conf 879768999981686521223344544
Q gi|254780784|r 343 RGDTQAIVVVTLGTREDEQYVDSLSGT 369 (699)
Q Consensus 343 RGETQaL~tvTLG~~~d~Q~iD~l~~~ 369 (699)
-+|.-.+.|+.+|+..|.|.-++.+|-
T Consensus 94 ~~ehisf~t~kigsladv~ns~dpegl 120 (147)
T KOG3392 94 GDEHISFTTSKIGSLADVNNSKDPEGL 120 (147)
T ss_pred CCEEEEEEECCCCCCHHCCCCCCCCHH
T ss_conf 882789983132110021568892430
No 221
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. 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=61.93 E-value=6 Score=18.25 Aligned_cols=48 Identities=25% Similarity=0.456 Sum_probs=33.3
Q ss_pred CCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEEC
Q ss_conf 8757999977115000037860779989998688899808808999968
Q gi|254780784|r 550 TPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASS 598 (699)
Q Consensus 550 ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~ 598 (699)
.|.-.-+-|-..+-+.|||.+|+.||+|++...-.-... ++.|.||+.
T Consensus 28 Tp~~teIiI~atrp~~ViG~kg~rIreLt~~lqkRF~~~-~~~iel~~e 75 (81)
T cd02413 28 TPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP-EGSVELYAE 75 (81)
T ss_pred CCCCEEEEEEECCCCEEECCCCEEHHHHHHHHHHHCCCC-CCCEEEEEE
T ss_conf 588619999953651556358804999999999982999-995899988
No 222
>PHA02358 hypothetical protein
Probab=61.70 E-value=1.8 Score=22.58 Aligned_cols=25 Identities=40% Similarity=0.472 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHCCCCCCCCEEEEEE
Q ss_conf 9999999987326882354112355
Q gi|254780784|r 130 SMVAASAALMLSGLPFEGPVVGAQV 154 (699)
Q Consensus 130 Ai~aASaAL~ISdIPf~GPVaaVRV 154 (699)
+-+||++|-++|.|||-|+++|=-+
T Consensus 147 ~Svga~aaPa~s~IP~VGWvaaGw~ 171 (194)
T PHA02358 147 SSIGAAAAPALSSIPFVGWVAAGWA 171 (194)
T ss_pred HHHHHHHCCHHHCCCHHHHHHHHHH
T ss_conf 2121101203207970788998999
No 223
>pfam09176 Mpt_N Methylene-tetrahydromethanopterin dehydrogenase, N-terminal. Members of this family adopt a alpha-beta structure, with a core comprising three alpha/beta/alpha layers, in which each sheet contains four strands. They are predominantly found in prokaryotic methylene-tetrahydromethanopterin dehydrogenase, which catalyses the dehydrogenation of methylene-tetrahydromethanopterin and the reversible dehydrogenation of methylene-H(4)F.
Probab=61.43 E-value=1.8 Score=22.52 Aligned_cols=50 Identities=12% Similarity=0.206 Sum_probs=34.3
Q ss_pred CCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCCC
Q ss_conf 75466700899987976899998168652122334454420358774058875445
Q gi|254780784|r 331 LLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCATG 386 (699)
Q Consensus 331 vLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfsvG 386 (699)
+-+-+|| |+||||---.-.|.-+=..+|...-..+....+|+| ||||.|.
T Consensus 26 V~~LVqd-aIFsR~p~~~~~TaIFiGG~d~~~a~~ml~~~kk~~-----~~Pf~vS 75 (81)
T pfam09176 26 VTGLVQD-AIFSRGPKDLKRTAIFIGGRDMALAEDMLEAAKKAF-----VPPFEVS 75 (81)
T ss_pred HHHHHCC-EEECCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHC-----CCCEEEE
T ss_conf 4422146-367148767720689988865999999999999835-----7983889
No 224
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=60.45 E-value=10 Score=16.39 Aligned_cols=64 Identities=20% Similarity=0.135 Sum_probs=46.0
Q ss_pred HHCCCCCCCCEEEEEEEEEEECC---------EEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCC
Q ss_conf 85247546867899999994153---------699828797104886631444547855603259889999997868998
Q gi|254780784|r 612 SITDVPEVNKIYKGQVVKVMDFG---------AFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGK 682 (699)
Q Consensus 612 ~~~~~~e~g~~y~~~v~~i~~fG---------afve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~ 682 (699)
..+..+..|.+++-+|+.+.+.| |+|+|-.+...|.|+.- .-.+-+++|.+|+.++..+.+.|.
T Consensus 56 E~vels~~G~V~t~Tv~~~~~~~~~~~~P~viaiV~l~~~~~i~~~i~~-------~dp~~v~iGm~V~~v~~~~~~~~~ 128 (140)
T COG1545 56 EWVELSGEGKVETYTVVYVKPPGFSLEEPYVIAIVELEEGGRILGQLVD-------VDPDDVEIGMKVEAVFRKREEDGG 128 (140)
T ss_pred EEEEECCCEEEEEEEEEEECCCCCCCCCCEEEEEEEECCCCEEEEEEEC-------CCCCCCCCCCEEEEEEEECCCCCC
T ss_conf 7999399769999999951788866689989999992788706999980-------685645079999999986133788
No 225
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=59.73 E-value=10 Score=16.30 Aligned_cols=58 Identities=26% Similarity=0.347 Sum_probs=40.5
Q ss_pred EEEEEEEEEEE---CCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEE
Q ss_conf 78999999941---5369982879710488663144454785560325988999999786899866
Q gi|254780784|r 622 IYKGQVVKVMD---FGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIK 684 (699)
Q Consensus 622 ~y~~~v~~i~~---fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~ 684 (699)
-.+|+|+---+ ||...---.++|-++|+|.|..... ..|.+||.|+..+..- ++|..-
T Consensus 3 ~i~G~VKwF~~~kGyGFI~~~dG~~DvFvH~s~i~~~g~----~~L~~Gq~V~f~v~~~-~kG~~A 63 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGF----KTLAEGQRVEFEITNG-AKGPSA 63 (69)
T ss_pred CEEEEEEEEECCCCEEEEECCCCCCCEEEEHHHCCCCCC----CCCCCCCEEEEEEEEC-CCCCEE
T ss_conf 478899998399987999707998329999077052578----6169999999999969-999851
No 226
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=59.44 E-value=11 Score=16.26 Aligned_cols=20 Identities=15% Similarity=-0.042 Sum_probs=11.1
Q ss_pred CCCCCHHHHHHHHHHHHHHH
Q ss_conf 44324899998875316889
Q gi|254780784|r 192 ANQLSEDVVLDAIIFGHNEC 211 (699)
Q Consensus 192 A~EVsEe~mleAI~~Ahe~I 211 (699)
...++.++++.|+.-+...-
T Consensus 84 ~~~~~~~dv~~~~~~~~~~~ 103 (348)
T COG1702 84 IASIYLEDVLSAFRGAESLQ 103 (348)
T ss_pred CCCCCHHHHHHHHHHHHHHH
T ss_conf 66678999999985324432
No 227
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=59.43 E-value=11 Score=16.26 Aligned_cols=71 Identities=15% Similarity=0.242 Sum_probs=52.4
Q ss_pred EEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCC------CCCCCCCCCCCC-------CHHHHHHHH
Q ss_conf 0899987976899998168652122334454420358774058875------445334556765-------024679999
Q gi|254780784|r 338 SSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPC------ATGEVSRMGAPS-------RREIGHGRL 404 (699)
Q Consensus 338 SALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpf------svGE~~~~~~~~-------RREiGHg~l 404 (699)
=.-|..|++++|+++-+.+.+ +|- ..-.+..||+||.. .+|.++|.|..+ -+|.++=.-
T Consensus 300 L~~Fk~G~~~VLVaTDVAARG----IDI----p~V~~VINYDlP~~~e~YVHRIGRTGRaGr~G~AITfv~~~e~~~l~~ 371 (574)
T PRK04537 300 LNRFQKGQLEILVATDVAARG----LHI----DGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYAMSLPD 371 (574)
T ss_pred HHHHHCCCCCEEEECCCCCCC----CCC----CCCCEEEEECCCCCHHHHHCCCCHHHCCCCCEEEEEEECHHHHHHHHH
T ss_conf 999976999799773500233----571----469979995796982141124535037899335999877799899999
Q ss_pred HHHHHHHCCCCC
Q ss_conf 999874107864
Q gi|254780784|r 405 ARRAIHPVLPQT 416 (699)
Q Consensus 405 a~ral~~~~P~~ 416 (699)
+|+-+..-||.+
T Consensus 372 IE~~i~~~ip~~ 383 (574)
T PRK04537 372 IEAYIEQKIPVE 383 (574)
T ss_pred HHHHHCCCCCCC
T ss_conf 999867878886
No 228
>PRK09890 cold shock protein CspG; Provisional
Probab=59.14 E-value=11 Score=16.22 Aligned_cols=57 Identities=21% Similarity=0.274 Sum_probs=39.4
Q ss_pred EEEEEEEEEEE---CCEEEECCCCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCE
Q ss_conf 78999999941---536998287971048866314445478556032598899999978689986
Q gi|254780784|r 622 IYKGQVVKVMD---FGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKI 683 (699)
Q Consensus 622 ~y~~~v~~i~~---fGafve~~~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i 683 (699)
..+|+|+-.-+ ||.+.---.++|-++|+|.|..... ..|.+||.|+..+..- ++|.-
T Consensus 4 ~~tG~VKwFn~~KGyGFI~~ddg~~DvFvH~s~i~~~~~----~~L~~Gq~V~f~v~~g-~kG~~ 63 (70)
T PRK09890 4 KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEF----RTLNENQKVEFSIEQG-QRGPA 63 (70)
T ss_pred CEEEEEEEECCCCCEEEECCCCCCCCEEEEHHHHCCCCC----CCCCCCCEEEEEEEEC-CCCCC
T ss_conf 506999988399986997038999429998689272688----3329999999999979-99861
No 229
>TIGR01389 recQ ATP-dependent DNA helicase RecQ; InterPro: IPR006293 The ATP-dependent DNA helicase RecQ (3.6.1 from EC) is involved in genome maintenance . All homologues tested to date unwind paired DNA, translocating in a 3' to 5' direction and several have a preference for forked or 4-way DNA structures (e.g. Holliday junctions) or for G-quartet DNA. The yeast protein, Sgs1, is present in numerous foci that coincide with sites of de novo synthesis DNA, such as the replication fork, and protein levels peak during S-phase. A model has been proposed for Sgs1p action in the S-phase checkpoint response, both as a 'sensor' for damage during replication and a 'resolvase' for structures that arise at paused forks, such as the four-way 'chickenfoot' structure. The action of Sgs1p may serve to maintain the proper amount and integrity of ss DNA that is necessary for the binding of RPA (replication protein A, the eukaryotic ss DNA-binding protein)DNA pol complexes. Sgs1p would thus function by detecting (or resolving) aberrant DNA structures, and would thus contribute to the full activation of the DNA-dependent protein kinase, Mec1p and the effector kinase, Rad53p. Its ability to bind both the large subunit of RPA and the RecA-like protein Rad51p, place it in a unique position to resolve inappropriate fork structures that can occur when either the leading or lagging strand synthesis is stalled. Thus, RecQ helicases integrate checkpoint activation and checkpoint response. ; GO: 0004003 ATP-dependent DNA helicase activity, 0006310 DNA recombination, 0009432 SOS response.
Probab=58.61 E-value=8 Score=17.26 Aligned_cols=48 Identities=23% Similarity=0.422 Sum_probs=34.3
Q ss_pred EEEEECCCEEEE-EEEECCCCCCCCCCCCCCCCEEEEEEEECCCCC------CCCCCCCCCCCC
Q ss_conf 899987976899-998168652122334454420358774058875------445334556765
Q gi|254780784|r 339 SLFIRGDTQAIV-VVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPC------ATGEVSRMGAPS 395 (699)
Q Consensus 339 ALFtRGETQaL~-tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpf------svGE~~~~~~~~ 395 (699)
-.|+|-++|++| |+-+|+.=|- ..=||--|||+|-- =+|.+||=|-|+
T Consensus 270 ~~Fl~d~~~vmVAT~AFGMGIdK---------pnVRFViH~d~P~~~EsYYQE~GRAGRDGlpa 324 (607)
T TIGR01389 270 EDFLYDDVKVMVATNAFGMGIDK---------PNVRFVIHADMPKNIESYYQEAGRAGRDGLPA 324 (607)
T ss_pred HHHHHHCCEEEEEEECCCCCCCC---------CCCCEEEEECCCCCHHHHHCCCCCCCCCCCHH
T ss_conf 54446255488887123587478---------76548886368742111310355468875267
No 230
>TIGR03675 arCOG00543 arCOG01782 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=57.72 E-value=11 Score=16.05 Aligned_cols=32 Identities=13% Similarity=0.135 Sum_probs=19.3
Q ss_pred EEEECCCC---CCCCEE-EEEECCCEEEEEEEECCC
Q ss_conf 99844754---667008-999879768999981686
Q gi|254780784|r 326 SAQVGLLQ---RTHGSS-LFIRGDTQAIVVVTLGTR 357 (699)
Q Consensus 326 s~EvgvLP---rvHGSA-LFtRGETQaL~tvTLG~~ 357 (699)
|+.+-.|= -|-.|| |.+-.++.+|.=|-+-..
T Consensus 174 ~vrit~LG~~~eVGRSc~l~~~~~~~illDcG~~~~ 209 (630)
T TIGR03675 174 WVRVTALGGFREVGRSALLLSTPESRILLDCGVNVG 209 (630)
T ss_pred EEEEEECCCCCCCCCEEEEEECCCEEEEEECCCCCC
T ss_conf 499983467670264589996398179998888877
No 231
>KOG2113 consensus
Probab=57.72 E-value=7.2 Score=17.63 Aligned_cols=20 Identities=10% Similarity=-0.075 Sum_probs=11.7
Q ss_pred EEEEEEE-ECCCCCCCCEEEE
Q ss_conf 3787998-4475466700899
Q gi|254780784|r 322 VRDISAQ-VGLLQRTHGSSLF 341 (699)
Q Consensus 322 IRpIs~E-vgvLPrvHGSALF 341 (699)
-||+|-. .+..|.+|-|-..
T Consensus 279 s~~~~~~~~~~~~~~~~~~~~ 299 (394)
T KOG2113 279 SRPSLGGGQSAKQDLPTYDYW 299 (394)
T ss_pred CCCCCCCCCCCCCCCCCCCCC
T ss_conf 842358863346677767710
No 232
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=57.43 E-value=5 Score=18.92 Aligned_cols=70 Identities=14% Similarity=0.228 Sum_probs=46.7
Q ss_pred EEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCC------CCCCCCCCCCCC-------CHHHHHHHHH
Q ss_conf 899987976899998168652122334454420358774058875------445334556765-------0246799999
Q gi|254780784|r 339 SLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPC------ATGEVSRMGAPS-------RREIGHGRLA 405 (699)
Q Consensus 339 ALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpf------svGE~~~~~~~~-------RREiGHg~la 405 (699)
.-|..|++++|+++-+.+.+ +| -..-++..||++|.- .+|.+||.|..| ..|..+=+-.
T Consensus 291 ~~F~~g~~~vLVaTDvaaRG----iD----i~~V~~VInyd~P~~~~~YvHRiGRTGR~G~~G~ait~v~~~d~~~~~~i 362 (417)
T PRK11192 291 KRLTDGRVNVLVATDVAARG----ID----IDDISHVINFDMPRSADTYLHRIGRTGRAGKKGTAISLVEAHDHLLLGKI 362 (417)
T ss_pred HHHHCCCCCEEEECCHHHCC----CC----CCCCCEEEEECCCCCHHHHHHHCCHHHCCCCCEEEEEEECHHHHHHHHHH
T ss_conf 99976999899981243467----77----04698899979999888923306772348995489998748999999999
Q ss_pred HHHHHHCCCCC
Q ss_conf 99874107864
Q gi|254780784|r 406 RRAIHPVLPQT 416 (699)
Q Consensus 406 ~ral~~~~P~~ 416 (699)
||-+..-+|..
T Consensus 363 e~~~~~~~~~~ 373 (417)
T PRK11192 363 ERYIEEPLKRR 373 (417)
T ss_pred HHHHCCCCCCC
T ss_conf 99977988731
No 233
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=57.35 E-value=11 Score=16.00 Aligned_cols=46 Identities=22% Similarity=0.378 Sum_probs=35.1
Q ss_pred CCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHH----HCC---EEEEEC
Q ss_conf 43322448757999977115000037860779989998----688---899808
Q gi|254780784|r 543 RLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQ----TGA---KVNIDD 589 (699)
Q Consensus 543 ~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~----~~~---~i~i~d 589 (699)
+-++.-. |.-..+.|...+=|.+||.+|++|+.|.+. ||. .|+|.+
T Consensus 43 ~veIeR~-~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I~i~E 95 (233)
T COG0092 43 GVEIERT-PKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQINIEE 95 (233)
T ss_pred EEEEEEC-CCCEEEEEEECCCCCEECCCCCCHHHHHHHHHHHHCCCCCEEEEEE
T ss_conf 4899966-9843999995798315757971099999999998499974499997
No 234
>pfam05900 consensus
Probab=55.68 E-value=7.7 Score=17.39 Aligned_cols=22 Identities=36% Similarity=0.616 Sum_probs=18.6
Q ss_pred CCCEEEEEECCCEEEEEEEECC
Q ss_conf 6700899987976899998168
Q gi|254780784|r 335 THGSSLFIRGDTQAIVVVTLGT 356 (699)
Q Consensus 335 vHGSALFtRGETQaL~tvTLG~ 356 (699)
..|--.|.||-||++|||-|--
T Consensus 31 ~~G~hvfskG~t~piCtVkL~H 52 (221)
T pfam05900 31 ADGAHVFSKGGTQPICTVKLQH 52 (221)
T ss_pred CCCCEEECCCCCCCEEEEEECC
T ss_conf 7897166268875307999516
No 235
>TIGR00549 mevalon_kin mevalonate kinase; InterPro: IPR006205 Mevalonate kinase (2.7.1.36 from EC) is well-characterised among the Eukaryotes, where it plays a role in the synthesis of isopentanyl pyrophosphate, a common intermediate for a number of pathways including cholesterol biosynthesis. It is also involved in mevalonate catabolism. Close homologs are found in the Archaea. A bacterial example is found in the Lyme disease spirochete Borrelia burgdorferi, but is not necessarily the same biosynthetic enzyme.; GO: 0004496 mevalonate kinase activity, 0005524 ATP binding, 0008299 isoprenoid biosynthetic process, 0005737 cytoplasm.
Probab=54.90 E-value=12 Score=15.71 Aligned_cols=15 Identities=20% Similarity=0.131 Sum_probs=6.9
Q ss_pred HHHHHHHHHHHHCCC
Q ss_conf 999999999873268
Q gi|254780784|r 129 VSMVAASAALMLSGL 143 (699)
Q Consensus 129 lAi~aASaAL~ISdI 143 (699)
=+..|+|||++++-|
T Consensus 144 g~GLGSSAAv~vA~~ 158 (345)
T TIGR00549 144 GRGLGSSAAVAVALI 158 (345)
T ss_pred CCCCCHHHHHHHHHH
T ss_conf 555634799999999
No 236
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=54.40 E-value=13 Score=15.65 Aligned_cols=64 Identities=19% Similarity=0.247 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHH
Q ss_conf 9999999999999999999998435667433224487579999771150000378607799899986
Q gi|254780784|r 515 NIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQT 581 (699)
Q Consensus 515 ~il~~al~~A~~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~ 581 (699)
..+.+.+.+|+- |.++-.....+ .-.+-++. ..|.-..+.|...+=|-+||.+|.+|+.|.+.-
T Consensus 10 kFv~~g~~~~~i-re~l~k~L~~A-G~s~ieIe-rt~~~~~I~I~tarPG~VIGrkG~~I~~L~~~l 73 (220)
T PTZ00084 10 KFINDGVFYAEL-NEFLSRELADD-GYAGVELR-VTPVRTEIIIRATKTREVLGEKGRRIRELTSLI 73 (220)
T ss_pred HHHHHHHHHHHH-HHHHHHHHHHC-CCCEEEEE-ECCCCEEEEEEECCCCEEECCCCHHHHHHHHHH
T ss_conf 799855699999-99999888867-87759999-889847999996898558868854699999999
No 237
>PRK04837 ATP-dependent RNA helicase RhlB; Provisional
Probab=54.40 E-value=7.1 Score=17.67 Aligned_cols=72 Identities=18% Similarity=0.264 Sum_probs=48.8
Q ss_pred EEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCC------CCCCCCCCCCC-------CHHHHHHHHH
Q ss_conf 8999879768999981686521223344544203587740588754------45334556765-------0246799999
Q gi|254780784|r 339 SLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCA------TGEVSRMGAPS-------RREIGHGRLA 405 (699)
Q Consensus 339 ALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfs------vGE~~~~~~~~-------RREiGHg~la 405 (699)
.-|..|+.++|+++-+.+.+ +| -..-.+..||+||.-+ +|.+||.|..+ ..|.-+=.-.
T Consensus 300 ~~F~~g~~~vLVaTDvaaRG----LD----i~~V~~VInyD~P~~~~~YiHRiGRTgRaG~~G~aitf~~~~~~~~l~~i 371 (423)
T PRK04837 300 EQFTRGDLDILVATDVAARG----LH----IPDVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISFACEEYALNLPAI 371 (423)
T ss_pred HHHHCCCCCEEEEHHHHHCC----CC----CCCCCEEEEECCCCCHHHEECCCCHHHCCCCCEEEEEEECHHHHHHHHHH
T ss_conf 99976999899870043277----77----26798899969989745510046541278994689998739999999999
Q ss_pred HHHHHHCCCCCCC
Q ss_conf 9987410786446
Q gi|254780784|r 406 RRAIHPVLPQTAQ 418 (699)
Q Consensus 406 ~ral~~~~P~~~~ 418 (699)
|+-+..-||..+.
T Consensus 372 e~~~~~~i~~~~~ 384 (423)
T PRK04837 372 ETYIGHSIPVSKY 384 (423)
T ss_pred HHHHCCCCCEECC
T ss_conf 9996896750136
No 238
>pfam12414 Fox-1_C Calcitonin gene-related peptide regulator C terminal. This domain family is found in eukaryotes, and is typically between 69 and 99 amino acids in length. The family is found in association with pfam00076. This family is the C terminal of Fox-1, a protein involved in the regulation of calcitonin gene-related peptide to mediate the neuron-specific splicing pattern. Fox-1, with Fox-2, functions to repress exon 4 inclusion.
Probab=54.30 E-value=10 Score=16.30 Aligned_cols=47 Identities=28% Similarity=0.306 Sum_probs=32.0
Q ss_pred CEEEEEECCC--EEEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCC
Q ss_conf 2899997894--8999997278888777735406866523201336788873
Q gi|254780784|r 29 GAVLATYGET--VVLATVVYDRSLKDGQDFFPLTVNYQERTYAVGKIPGGYL 78 (699)
Q Consensus 29 GsV~v~~G~T--~VLaTv~~~~~~~~~~dFfPLtVdY~Ek~yAaGkIPGgF~ 78 (699)
|+-+-..|.+ .|.-|..+.. |....-..|+.| |++.+|.+ +|+|||-
T Consensus 19 GahLrgrgr~~v~vynt~raA~-pp~~iPay~gvv-yqdg~yga-~~ygGya 67 (96)
T pfam12414 19 GAHLRRRRRGRVAVYNTPRAAA-PPGRIPAYPGVV-YQDGFYGA-EWYGGYA 67 (96)
T ss_pred CCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCEE-EECCCCCC-EECCCEE
T ss_conf 4411146766630001100358-999878887437-64452143-1026524
No 239
>PRK00568 carbon storage regulator; Provisional
Probab=53.99 E-value=13 Score=15.60 Aligned_cols=31 Identities=23% Similarity=0.547 Sum_probs=24.3
Q ss_pred CCHHHHCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf 78556032598899999978689986668730
Q gi|254780784|r 658 AKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKV 689 (699)
Q Consensus 658 ~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk~ 689 (699)
+++..-+.+||.|.+++++++ .|++||...|
T Consensus 6 RK~gEsI~IgddI~i~Vv~i~-g~~VrlGI~A 36 (76)
T PRK00568 6 RKVNEGIVIDDNIHIKVISID-RGSVRLGFEA 36 (76)
T ss_pred CCCCCEEEECCCEEEEEEEEC-CCEEEEEEEC
T ss_conf 338985895798699999973-9979998987
No 240
>TIGR03562 osmo_induc_OsmC peroxiredoxin, OsmC subfamily. pfam02566, OsmC-like protein, contains several deeply split clades of homologous proteins. The clade modeled here includes the protein OsmC, or osmotically induced protein C. The member from Thermus thermophilus was shown to have hydroperoxide peroxidase activity. In many species, this protein is induced by stress and helps resist oxidative stress.
Probab=53.98 E-value=12 Score=15.80 Aligned_cols=30 Identities=30% Similarity=0.440 Sum_probs=23.2
Q ss_pred CEEEECCC--CCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 12443245--3655688999999999999999
Q gi|254780784|r 500 ITAMQMDM--KIGGISENIMVMALQQAKRGRL 529 (699)
Q Consensus 500 iTa~QmDi--K~~gi~~~il~~al~~A~~gr~ 529 (699)
||++++++ +++|++.+..++.+++|++.|.
T Consensus 91 it~i~l~v~~~vpg~d~e~a~~l~~~Ah~~CP 122 (135)
T TIGR03562 91 ITGIHLTVRAKVPGIDEAKFQEIAEKAKEGCP 122 (135)
T ss_pred EEEEEEEEEEECCCCCHHHHHHHHHHHHHHCC
T ss_conf 88899999997489899999999999975496
No 241
>KOG4369 consensus
Probab=53.89 E-value=5 Score=18.92 Aligned_cols=30 Identities=17% Similarity=0.150 Sum_probs=14.9
Q ss_pred CCCCCCCEEEEEEEEECCCCCCHHHHHHHHH
Q ss_conf 4688688378999982188887789999999
Q gi|254780784|r 104 SKCYKNETQVIINVMQHDLESSPHVVSMVAA 134 (699)
Q Consensus 104 Pkgf~~evQIv~~VLS~D~~~dpdvlAi~aA 134 (699)
|-+.+.|+-|-..|.++.+. -|+|...+-|
T Consensus 122 ~a~lct~~~~~~si~a~~~~-~~ev~~~l~a 151 (2131)
T KOG4369 122 PADLCTEVTIEPSIVASAGG-YPEVVEVLLA 151 (2131)
T ss_pred HHHHHHHHHHHHHHHHHCCC-CHHHHHHHHH
T ss_conf 89888886630346654289-7058999986
No 242
>PRK09824 beta-glucoside-specific PTS system components IIABC; Provisional
Probab=53.57 E-value=13 Score=15.62 Aligned_cols=80 Identities=18% Similarity=0.186 Sum_probs=51.5
Q ss_pred CEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEE---EEEEEEEEECCEEEEC--CCCCCEEEEEE----ECCCCCCCCH
Q ss_conf 8089999689899999999999852475468678---9999999415369982--87971048866----3144454785
Q gi|254780784|r 590 DGTVKIASSSLAEIEAAREMIRSITDVPEVNKIY---KGQVVKVMDFGAFVHF--CGARDGLVHIS----QLSTERVAKT 660 (699)
Q Consensus 590 ~g~v~i~~~~~~~~~~a~~~i~~~~~~~e~g~~y---~~~v~~i~~fGafve~--~~g~~gl~HiS----~l~~~~v~~~ 660 (699)
+|.|.=...-.+.+-....+=+.+.-+|+.|++| +|+|..+.+-+-=+-+ -.|.|-|+||- +|.-+. -
T Consensus 484 ~G~~~~l~~v~D~~Fa~~~~G~g~ai~p~~g~v~aP~~g~v~~~~~t~HAig~~~~~G~e~liHiGidTV~l~G~~---F 560 (625)
T PRK09824 484 TGEIVPLIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATLHAIGIESDDGVEILIHVGIDTVKLDGKF---F 560 (625)
T ss_pred CCEEEECCCCCCHHHCCCCCCCCEEEECCCCEEECCCCCEEEEECCCCCEEEEECCCCCEEEEEECCCCCCCCCCC---C
T ss_conf 7158771318665540367779669956999698079808989747896789972898189999661650108915---4
Q ss_pred HHHCCCCCEEEE
Q ss_conf 560325988999
Q gi|254780784|r 661 SDVVKEGDTVWV 672 (699)
Q Consensus 661 ~d~~~~Gd~i~v 672 (699)
+-.+++||+|+.
T Consensus 561 ~~~v~~g~~V~~ 572 (625)
T PRK09824 561 SAHVNVGDKVNT 572 (625)
T ss_pred EEEECCCCEECC
T ss_conf 167467899679
No 243
>COG1551 CsrA RNA-binding global regulator CsrA [Signal transduction mechanisms]
Probab=52.79 E-value=13 Score=15.58 Aligned_cols=31 Identities=16% Similarity=0.416 Sum_probs=23.8
Q ss_pred CCHHHHCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf 78556032598899999978689986668730
Q gi|254780784|r 658 AKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKV 689 (699)
Q Consensus 658 ~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk~ 689 (699)
+++..-+.+||.|.|++++++ .+.+|+-..|
T Consensus 6 Rk~~Esi~IgddI~itVl~i~-gnqVkiGi~A 36 (73)
T COG1551 6 RKVGESIMIGDDIEITVLSIK-GNQVKIGINA 36 (73)
T ss_pred EECCCEEEECCCEEEEEEEEC-CCEEEEEECC
T ss_conf 133962894697399999975-9759996048
No 244
>TIGR02705 nudix_YtkD nucleoside triphosphatase YtkD; InterPro: IPR014078 The proteins in this entry belong to the nudix family and share some sequence identity with Escherichia coli MutT but appear not to be functionally interchangeable with it. The functional assignment of the proteins in this family is contentious. Reference challenges the findings of reference , both in interpretation and in enzyme assay results..
Probab=51.55 E-value=3.9 Score=19.79 Aligned_cols=66 Identities=23% Similarity=0.324 Sum_probs=44.9
Q ss_pred CCCEEEEECCCCHH----------HHHHHHHHCCEEE-EECCEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEEEE
Q ss_conf 11500003786077----------9989998688899-808808999968989999999999985247546867899999
Q gi|254780784|r 560 PDQIRNVIGMGGKV----------IRGIVEQTGAKVN-IDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQVV 628 (699)
Q Consensus 560 ~~ki~~~iG~gG~~----------ik~i~~~~~~~i~-i~d~g~v~i~~~~~~~~~~a~~~i~~~~~~~e~g~~y~~~v~ 628 (699)
.+++|=+==||||+ ||++-||||+.+. |.==|.-.|-..+++. +++ .||=+.|.
T Consensus 42 ~H~~RGlEFPGGKvE~GEt~~eAA~REv~EETGA~v~~l~Y~gQY~Ve~~~~~~----------f~K-----~vYfa~V~ 106 (158)
T TIGR02705 42 EHKRRGLEFPGGKVEEGETSKEAAIREVYEETGAIVKELHYIGQYEVEGEDDTD----------FVK-----DVYFAEVS 106 (158)
T ss_pred CCCCCCCCCCCCEECCCCCHHHHHHEECCCCCCEEEEEEEEEEEEEEECCCCCE----------EEE-----EEEEEEEE
T ss_conf 358787047888007998846765100100358075468888767875899966----------577-----76688998
Q ss_pred EEEECCEEEECC
Q ss_conf 994153699828
Q gi|254780784|r 629 KVMDFGAFVHFC 640 (699)
Q Consensus 629 ~i~~fGafve~~ 640 (699)
.+..-+.+.|-.
T Consensus 107 ~le~~~~Y~ET~ 118 (158)
T TIGR02705 107 ALESKDDYLETK 118 (158)
T ss_pred EEEECCCCCEEC
T ss_conf 732458741014
No 245
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=50.71 E-value=12 Score=15.94 Aligned_cols=51 Identities=18% Similarity=0.199 Sum_probs=37.8
Q ss_pred CCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECC---------EEEEEEECCH
Q ss_conf 87579999771150000378607799899986888998088---------0899996898
Q gi|254780784|r 550 TPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDD---------GTVKIASSSL 600 (699)
Q Consensus 550 ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~---------g~v~i~~~~~ 600 (699)
-|-=++|-|+..--..+||.||++|+++...-+|.|--... -.|-|-+|.+
T Consensus 447 Fpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrK 506 (657)
T COG5166 447 FPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRK 506 (657)
T ss_pred CCHHEEEEEECCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHCCEEEECCCC
T ss_conf 752227885123531343358541677665432445443444233233331558988866
No 246
>PRK01297 ATP-dependent RNA helicase RhlB; Provisional
Probab=50.51 E-value=8.7 Score=16.96 Aligned_cols=49 Identities=16% Similarity=0.331 Sum_probs=31.7
Q ss_pred EEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCC------CCCCCCCCCCC
Q ss_conf 8999879768999981686521223344544203587740588754------45334556765
Q gi|254780784|r 339 SLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCA------TGEVSRMGAPS 395 (699)
Q Consensus 339 ALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfs------vGE~~~~~~~~ 395 (699)
.-|..|++++|+++-+.+.+ +| -..-.+-.||+||... +|.+||.|..|
T Consensus 376 ~~F~~g~~~iLVaTDvaaRG----LD----i~~V~~VInyD~P~~~~~YIHRiGRTGRaG~~G 430 (472)
T PRK01297 376 EGFREGKIRVLVATDVAGRG----IH----IDGISHVINFTLPEDPDDYVHRIGRTGRAGASG 430 (472)
T ss_pred HHHHCCCCCEEEECCHHHCC----CC----CCCCCEEEEECCCCCHHHHHHCCCHHHCCCCCE
T ss_conf 99976999699886613366----77----578888999689897676010265312689963
No 247
>TIGR01455 glmM phosphoglucosamine mutase; InterPro: IPR006352 This family describes GlmM, phosphoglucosamine mutase, also designated MrsA and YhbF in Escherichia coli , UreC in Helicobacter pylori , and femR315 or FemD in Staphlococcus aureus . It converts glucosamine-6-phosphate to glucosamine-1-phosphate as part of the pathway toward UDP-N-acetylglucosamine for peptidoglycan and lipopolysaccharides..
Probab=50.19 E-value=5.3 Score=18.72 Aligned_cols=29 Identities=28% Similarity=0.409 Sum_probs=12.8
Q ss_pred EEEEECCCCHHHHHCCCCCCCHHHHHHHH
Q ss_conf 35530544323331244432489999887
Q gi|254780784|r 176 LFVSGTQDAVLMVELEANQLSEDVVLDAI 204 (699)
Q Consensus 176 LvVAGT~d~IlMIE~~A~EVsEe~mleAI 204 (699)
|-.=|=.|.|+||..-++-|.=+.++-=+
T Consensus 241 iAfDGDaDR~~~VD~~G~~VDGD~Il~~~ 269 (450)
T TIGR01455 241 IAFDGDADRVLAVDENGDIVDGDQILYII 269 (450)
T ss_pred EEECCCCCEEEEECCCCCCCCHHHHHHHH
T ss_conf 00128845289880665954756899999
No 248
>TIGR01237 D1pyr5carbox2 delta-1-pyrroline-5-carboxylate dehydrogenase, putative; InterPro: IPR005932 The delta(1)-pyrroline-5-carboxylate synthetase (1.5.1.12 from EC) a mitochondrial inner membrane, ATP- and NADPH-dependent, bifunctional enzyme, catalyzes the reduction of glutamate to delta1-pyrroline-5-carboxylate, a critical step in the de novo biosynthesis of proline and ornithine. It is the rate-limiting enzyme in proline biosynthesis and is subject to feedback inhibition by proline. 1-pyrroline-5-carboxylate + NAD+ + H2O = L-glutamate + NADH This model represents one of several related branches of delta-1-pyrroline-5-carboxylate dehydrogenase.; GO: 0003842 1-pyrroline-5-carboxylate dehydrogenase activity, 0006561 proline biosynthetic process.
Probab=50.12 E-value=14 Score=15.16 Aligned_cols=127 Identities=17% Similarity=0.249 Sum_probs=60.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEECCCC-CCCCEEEEE-------------------ECCCEE
Q ss_conf 678899999999999999872886658867753378799844754-667008999-------------------879768
Q gi|254780784|r 289 GEIVSVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQ-RTHGSSLFI-------------------RGDTQA 348 (699)
Q Consensus 289 ~~i~~af~~l~k~ivR~~ILeeg~R~DGR~~dEIRpIs~EvgvLP-rvHGSALFt-------------------RGETQa 348 (699)
.++..+++-+++-+ |++ .|.||=+-.+.-.+.-|.|-|= ...|=+|-- -|+|-+
T Consensus 129 aevaEAIDF~eYYA-r~m-----~~laGf~~~~~~~~eGE~N~y~y~P~Gv~vvIsPWNFp~AI~vG~tvApiVtGNcvv 202 (518)
T TIGR01237 129 AEVAEAIDFLEYYA-REM-----IKLAGFKSKEVLDIEGEKNRYVYIPLGVAVVISPWNFPMAIAVGMTVAPIVTGNCVV 202 (518)
T ss_pred HHHHHHHHHHHHHH-HHH-----HHHHCCCCCCCCCCCCCCCCEEECCCCCEEEECCCHHHHHHHHHHHHHHHHHCCEEE
T ss_conf 44888888999999-999-----986047886344478862441542541278738712589999865786776188058
Q ss_pred EEEEEECCCCCCCCCCCCCC----C-----------CEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf 99998168652122334454----4-----------20358774058875445334556765024679999999874107
Q gi|254780784|r 349 IVVVTLGTREDEQYVDSLSG----T-----------QRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVL 413 (699)
Q Consensus 349 L~tvTLG~~~d~Q~iD~l~~----~-----------~~k~fmlHYNFPpfsvGE~~~~~~~~RREiGHg~la~ral~~~~ 413 (699)
|==+-=-+.--+.+.|-|.. . .-=.||.. -| .++.+-.++=||+|--=-+.=|+. =
T Consensus 203 lKPAe~~~vIAak~veiL~eaGlP~GV~qfvPG~Gs~VG~ylv~--Hp-----kt~lItFTGSReVG~rI~e~AAkV--Q 273 (518)
T TIGR01237 203 LKPAEAATVIAAKIVEILEEAGLPKGVLQFVPGKGSEVGEYLVD--HP-----KTRLITFTGSREVGLRIYEDAAKV--Q 273 (518)
T ss_pred ECCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCCC--CC-----CEEEEEEECCHHHHHHHHHHHHCC--C
T ss_conf 71677621589999999996478976305017986120330367--88-----611787417514411357666326--9
Q ss_pred CCCCCCCEEEEEEEEECCCC
Q ss_conf 86446873899985311027
Q gi|254780784|r 414 PQTAQFPYTLRIVSEITESD 433 (699)
Q Consensus 414 P~~~~~p~tirv~~evl~sn 433 (699)
|-. .+-=||..|.=--|
T Consensus 274 PGQ---khlKRVIaEmGGKd 290 (518)
T TIGR01237 274 PGQ---KHLKRVIAEMGGKD 290 (518)
T ss_pred CCC---CEEEEEEEEECCCC
T ss_conf 885---02411333207885
No 249
>cd07209 Pat_hypo_Ecoli_Z1214_like Hypothetical patatin similar to Z1214 protein of Escherichia coli. Patatin-like phospholipase similar to Z1214 protein of Escherichia coli. This family predominantly consists of bacterial patatin glycoproteins and some representatives from eukaryotes and archaea. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates.
Probab=49.22 E-value=10 Score=16.31 Aligned_cols=34 Identities=26% Similarity=0.404 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEE
Q ss_conf 78522356677779876259502254121332004
Q gi|254780784|r 433 DGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLV 467 (699)
Q Consensus 433 ngsssma~vc~~slal~dagvp~~~~VaGiamGLi 467 (699)
-|+.+-|.-.|.--||.++|+++. .|+|+|+|=+
T Consensus 5 GGG~rGa~~~Gvl~aL~e~gi~~d-~i~GtS~GAi 38 (215)
T cd07209 5 GGGALGAYQAGVLKALAEAGIEPD-IISGTSIGAI 38 (215)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCC-EEEEECHHHH
T ss_conf 447999999999999997699988-8999889999
No 250
>TIGR00959 ffh signal recognition particle protein; InterPro: IPR004780 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes , . SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor . In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. This entry represents various SRP subunits.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle.
Probab=49.07 E-value=6.4 Score=18.02 Aligned_cols=112 Identities=26% Similarity=0.311 Sum_probs=63.1
Q ss_pred EEEECCCCCEEEE-CCCCCCC-CCHHHHHHHHHHHH-----------HHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEE
Q ss_conf 0100556512443-2453655-68899999999999-----------999999999984356674332244875799997
Q gi|254780784|r 492 KVAGTDSGITAMQ-MDMKIGG-ISENIMVMALQQAK-----------RGRLHILNEMSKVLSESRLQLGEFTPRVEIMAI 558 (699)
Q Consensus 492 KvaGT~~GiTa~Q-mDiK~~g-i~~~il~~al~~A~-----------~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i 558 (699)
++-|.+-||--|+ ..-.-+. -|.+|-++||++|+ +||+||=+.|-+.+.+=+..+.|+ |++-|
T Consensus 152 ~~Lg~Q~gVpvf~h~~~~~~p~~Pv~ia~~Al~~Ak~~~~D~vI~DTAGRL~ID~~LM~EL~~iK~~~nP~----EiLlV 227 (439)
T TIGR00959 152 KVLGEQVGVPVFAHLGKGQSPDDPVEIARQALEEAKENGFDVVIVDTAGRLQIDEELMEELAEIKEILNPD----EILLV 227 (439)
T ss_pred HHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHCCC----EEEEC
T ss_conf 99767528871100478889887789999999999974897899726751255599999999998886887----05412
Q ss_pred CCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHCCCC
Q ss_conf 71150000378607799899986888998088089999689899999999999852475
Q gi|254780784|r 559 PPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVP 617 (699)
Q Consensus 559 ~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~~~ 617 (699)
+=+--|-.+=.+-.+|+..+.+. | |-++=-|.++=--|.--|.++|..|
T Consensus 228 -------vDaM~GQdAvn~A~~F~e~lglt--G-~vltK~DGDaRGGAALS~~~~tg~P 276 (439)
T TIGR00959 228 -------VDAMTGQDAVNTAKTFNERLGLT--G-VVLTKLDGDARGGAALSVRSVTGKP 276 (439)
T ss_pred -------CHHCCHHHHHHHHHHHCCCCCCC--E-EEEECCCCCCHHHHHHHHHHHHCCC
T ss_conf -------20102169999998636600135--4-7885475660578999999996896
No 251
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=48.14 E-value=15 Score=14.93 Aligned_cols=108 Identities=17% Similarity=0.261 Sum_probs=64.9
Q ss_pred HHHHHHHHHHCCEEEEE----CCEEEEEEECCHHHHHHHHH-HHHHHC--CCCCCCCEEEEEEEEEEE--CCEEEECC--
Q ss_conf 77998999868889980----88089999689899999999-999852--475468678999999941--53699828--
Q gi|254780784|r 572 KVIRGIVEQTGAKVNID----DDGTVKIASSSLAEIEAARE-MIRSIT--DVPEVNKIYKGQVVKVMD--FGAFVHFC-- 640 (699)
Q Consensus 572 ~~ik~i~~~~~~~i~i~----d~g~v~i~~~~~~~~~~a~~-~i~~~~--~~~e~g~~y~~~v~~i~~--fGafve~~-- 640 (699)
+..++...++.|+.+|. +=-.+++-++|.+...+++. .-..+. .+++.|++|-|+....-+ ||+.|.+.
T Consensus 21 s~v~~~lgdl~vk~eisvt~~~w~~itleGed~e~sanli~eefgei~sl~~~~~Gdv~vGrl~~l~~vgyg~yvdigV~ 100 (247)
T COG4044 21 SLVKNLLGDLDVKVEISVTKKQWAKITLEGEDEEVSANLIVEEFGEIPSLSKVEEGDVYVGRLIDLGKVGYGAYVDIGVL 100 (247)
T ss_pred HHHHHHHHCEEEEEEEEEECCCCEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEECCCEEEEECCCCCC
T ss_conf 99987631115899998610234489987760788899999974777764557878679999765022115787156645
Q ss_pred -C-CCCEEEEEEECCCCCCCCH-HHH---CCCCCE--EEEEEEEECC
Q ss_conf -7-9710488663144454785-560---325988--9999997868
Q gi|254780784|r 641 -G-ARDGLVHISQLSTERVAKT-SDV---VKEGDT--VWVKLLDFDD 679 (699)
Q Consensus 641 -~-g~~gl~HiS~l~~~~v~~~-~d~---~~~Gd~--i~vk~~~~d~ 679 (699)
| -++.|+-.-+|...-=+++ .+. +--=|. +.|-+.+.|.
T Consensus 101 ~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~evnk 147 (247)
T COG4044 101 GPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEVNK 147 (247)
T ss_pred CCCCCCCCCCHHHHHHCCCCCCHHHHHHHCCCCCCCCEEEEEEECCC
T ss_conf 77742233628998731288828999987087456725899971421
No 252
>cd07207 Pat_ExoU_VipD_like ExoU and VipD-like proteins; homologus to patatin, cPLA2, and iPLA2. ExoU, a 74-kDa enzyme, is a potent virulence factor of Pseudomonas aeruginosa. One of the pathogenic mechanisms of P. aeruginosa is to induce cytotoxicity by the injection of effector proteins (e.g. ExoU) using the type III secretion (T3S) system. ExoU is homologus to patatin and also has the conserved catalytic residues of mammalian calcium-independent (iPLA2) and cytosolic (cPLA2) PLA2. In vitro, ExoU cytotoxity is blocked by the inhibitor of cytosolic and Ca2-independent phospholipase A2 (cPLA2 and iPLA2) enzymes, suggesting that phospholipase A2 inhibitors may represent a novel mode of treatment for acute P. aeruginosa infections. ExoU requires eukaryotic superoxide dismutase as a cofactor and cleaves phosphatidylcholine and phosphatidylethanolamine in vitro. VipD, a 69-kDa cytosolic protein, belongs to the members of Legionella pneumophila family and is homologus to ExoU from Pseudomona
Probab=48.08 E-value=11 Score=15.99 Aligned_cols=33 Identities=30% Similarity=0.394 Sum_probs=21.2
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEE
Q ss_conf 2785223566777798762595022541213320
Q gi|254780784|r 432 SDGSSSMATVCGSSLALMDAGVPISKPVAGIAMG 465 (699)
Q Consensus 432 sngsssma~vc~~slal~dagvp~~~~VaGiamG 465 (699)
|-|+.+.|.-.|.--||.++|++.+ .|+|+|+|
T Consensus 5 sGGG~rG~~~~Gvl~aL~e~g~~~~-~i~GtSaG 37 (194)
T cd07207 5 EGGGAKGIAYIGALKALEEAGILKK-RVAGTSAG 37 (194)
T ss_pred CCCHHHHHHHHHHHHHHHHCCCCCC-EEEEECHH
T ss_conf 6767999999999999997799966-79887799
No 253
>PHA00019 phage assembly protein
Probab=47.44 E-value=14 Score=15.34 Aligned_cols=13 Identities=15% Similarity=0.312 Sum_probs=5.8
Q ss_pred CCCCHHHHHHHHH
Q ss_conf 4324899998875
Q gi|254780784|r 193 NQLSEDVVLDAII 205 (699)
Q Consensus 193 ~EVsEe~mleAI~ 205 (699)
+.+|.+..+++|.
T Consensus 66 ~~vpw~qald~IL 78 (428)
T PHA00019 66 NPANLPQFFDSVL 78 (428)
T ss_pred CCCCHHHHHHHHH
T ss_conf 5788999999999
No 254
>PRK07318 dipeptidase PepV; Reviewed
Probab=47.23 E-value=16 Score=14.83 Aligned_cols=73 Identities=12% Similarity=0.150 Sum_probs=46.0
Q ss_pred HHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHCC-CCC----CCCEEEEEEEEEEECCEEEECCCCCCEEEE
Q ss_conf 998999868889980880899996898999999999998524-754----686789999999415369982879710488
Q gi|254780784|r 574 IRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITD-VPE----VNKIYKGQVVKVMDFGAFVHFCGARDGLVH 648 (699)
Q Consensus 574 ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~-~~e----~g~~y~~~v~~i~~fGafve~~~g~~gl~H 648 (699)
++.+.+.+++++...+...-....+|..-++...+..+..+- +++ -|.+|-....+.+.||.. +||.+.+.|
T Consensus 366 l~~~~~~~~~~~~~~~~~~p~~~~~dsplV~~l~~~~~~~tG~~~~~~~~gGgT~ar~~~~~V~fG~~---~PG~~~~aH 442 (469)
T PRK07318 366 LEKLIGVTGFELSEGHHQKPHYVPKDDPLVKTLLKVYEKQTGLKGEEQVIGGGTYARLLKRGVAFGAM---FPGEPDTMH 442 (469)
T ss_pred HHHHHHHCCEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEECCHHHHHHHHCCEEECCC---CCCCCCCCC
T ss_conf 99877654769997326887344999899999999999986999837964585266660166886775---799988653
Q ss_pred E
Q ss_conf 6
Q gi|254780784|r 649 I 649 (699)
Q Consensus 649 i 649 (699)
-
T Consensus 443 ~ 443 (469)
T PRK07318 443 Q 443 (469)
T ss_pred C
T ss_conf 7
No 255
>PRK04011 peptide chain release factor 1; Provisional
Probab=47.13 E-value=16 Score=14.82 Aligned_cols=24 Identities=13% Similarity=0.237 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf 999998988888741000122489
Q gi|254780784|r 243 EMSQMIKEDLRVSCFIPEKYVRCK 266 (699)
Q Consensus 243 ~v~~~~~~~l~~a~~i~~K~eR~~ 266 (699)
.+.....+....|-.|++|..|..
T Consensus 42 ~v~~~L~~E~~~AsNIKsk~tR~~ 65 (409)
T PRK04011 42 DVVNQLRQEYSQASNIKSKTTRKN 65 (409)
T ss_pred HHHHHHHHHHHHHCCCCCCHHHHH
T ss_conf 999999988755403202112788
No 256
>cd07198 Patatin Patatin-like phospholipase. Patatin is a storage protein of the potato tuber that shows Phospholipase A2 activity (PLA2; EC 3.1.1.4). Patatin catalyzes the nonspecific hydrolysis of phospholipids, glycolipids, sulfolipids, and mono- and diacylglycerols, thereby showing lipid acyl hydrolase activity. The active site includes an oxyanion hole with a conserved GGxR motif; it is found in almost all the members of this family. The catalytic dyad is formed by a serine and an aspartate. Patatin belongs to the alpha-beta hydrolase family which is identified by a characteristic nucleophile elbow with a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu = nucleophile). Members of this family have been found also in vertebrates. This family includes PNPLA (1-9), TGL (3-5), ExoU-like, and SDP1-like subfamilies. There are some additional hypothetical proteins included in this family.
Probab=46.79 E-value=14 Score=15.22 Aligned_cols=35 Identities=29% Similarity=0.347 Sum_probs=22.8
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEE
Q ss_conf 278522356677779876259502254121332004
Q gi|254780784|r 432 SDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLV 467 (699)
Q Consensus 432 sngsssma~vc~~slal~dagvp~~~~VaGiamGLi 467 (699)
|-|+.+-+.-+|.--+|+++|+++ +.|+|+|.|=+
T Consensus 4 sGGG~rG~~~~Gvl~~L~e~gi~~-d~i~GtSaGAi 38 (172)
T cd07198 4 SGGGALGIYHVGVAKALRERGPLI-DIIAGTSAGAI 38 (172)
T ss_pred CCCHHHHHHHHHHHHHHHHCCCCC-CEEEEECHHHH
T ss_conf 756799999999999999769998-78987450288
No 257
>KOG1857 consensus
Probab=46.78 E-value=4.4 Score=19.39 Aligned_cols=38 Identities=5% Similarity=-0.164 Sum_probs=34.9
Q ss_pred CCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECC
Q ss_conf 75468678999999941536998287971048866314
Q gi|254780784|r 616 VPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLS 653 (699)
Q Consensus 616 ~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~ 653 (699)
.+-.++-|++++-+-.|||.|..+-+|.+++-|||.+.
T Consensus 572 ~l~~~~~~Te~~~sKtD~~r~~~~g~ger~eA~I~H~~ 609 (623)
T KOG1857 572 GLIPIRNVTEAKLSKTDKRRSLGLGPGERVEAQILHID 609 (623)
T ss_pred CCCHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHCC
T ss_conf 55134320022234445561157664503231011101
No 258
>COG1665 Predicted nucleotidyltransferase [General function prediction only]
Probab=46.58 E-value=15 Score=14.95 Aligned_cols=74 Identities=31% Similarity=0.371 Sum_probs=45.1
Q ss_pred EECCCCCCCHHHHHHHHH-HHHHHCCCCCCCCCCEEEEEEEEECCEEEEEEECCCCCCCCCCCCEEEEE-----CCCCCE
Q ss_conf 311027852235667777-98762595022541213320044088289986314422013655100100-----556512
Q gi|254780784|r 428 EITESDGSSSMATVCGSS-LALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAG-----TDSGIT 501 (699)
Q Consensus 428 evl~sngsssma~vc~~s-lal~dagvp~~~~VaGiamGLi~~~~~~~iLtDI~G~ED~~GdMDFKvaG-----T~~GiT 501 (699)
|+|+|.-| -+.|-+- .-|-|||||.++ ||.- =|=.+|+.|.-.|.||=|-| -++-++
T Consensus 96 eil~s~~~---~~~~rai~~~led~gVp~~~------mGVT--------GSiL~gl~~~nSDIDfVVYG~~~~~aRea~~ 158 (315)
T COG1665 96 EILESPSS---ESKARAIVEFLEDAGVPVNS------MGVT--------GSILLGLYDENSDIDFVVYGQMWFRAREAIL 158 (315)
T ss_pred HHHHCCCC---HHHHHHHHHHHHHCCCCHHH------CCCC--------CCCCCCCCCCCCCCEEEEECHHHHHHHHHHH
T ss_conf 99838530---78999999999870984144------4432--------2111244688877309997588899999998
Q ss_pred EEECCCCCCCCCHHHHH
Q ss_conf 44324536556889999
Q gi|254780784|r 502 AMQMDMKIGGISENIMV 518 (699)
Q Consensus 502 a~QmDiK~~gi~~~il~ 518 (699)
-+|-|-++.++..+..+
T Consensus 159 ~~~e~~~l~~ldd~~W~ 175 (315)
T COG1665 159 DAIEDFPLGELDDAEWE 175 (315)
T ss_pred HHHHCCCCCCCCHHHHH
T ss_conf 66551676675889999
No 259
>KOG4068 consensus
Probab=45.84 E-value=7.1 Score=17.66 Aligned_cols=15 Identities=20% Similarity=-0.002 Sum_probs=5.3
Q ss_pred CCEEEEEECCCCHHH
Q ss_conf 101355305443233
Q gi|254780784|r 173 SLDLFVSGTQDAVLM 187 (699)
Q Consensus 173 dLDLvVAGT~d~IlM 187 (699)
++-|-+|-+..-.-|
T Consensus 32 ~lil~ycr~~k~~sm 46 (174)
T KOG4068 32 DLILQYCRHNKIWSM 46 (174)
T ss_pred HHHHHHHHHCCEEEE
T ss_conf 999999976675788
No 260
>TIGR02618 tyr_phenol_ly tyrosine phenol-lyase; InterPro: IPR013441 Tyrosine phenol-lyases (4.1.99.2 from EC) (beta-tyrosinase), are pyridoxal-phosphate enzymes which are closely related to tryptophanase (4.1.99.1 from EC) (see IPR013441 from INTERPRO). Both belong to the beta-eliminating lyase family.; GO: 0050371 tyrosine phenol-lyase activity.
Probab=45.21 E-value=8.1 Score=17.21 Aligned_cols=32 Identities=41% Similarity=0.378 Sum_probs=24.2
Q ss_pred CHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEE
Q ss_conf 22356677779876259502254121332004
Q gi|254780784|r 436 SSMATVCGSSLALMDAGVPISKPVAGIAMGLV 467 (699)
Q Consensus 436 ssma~vc~~slal~dagvp~~~~VaGiamGLi 467 (699)
.+..-+.--.=-|..|||||..||.|-|+=|=
T Consensus 313 hr~~q~~yl~~~l~~aG~Piv~P~GGhavfld 344 (450)
T TIGR02618 313 HRVKQVRYLGDKLKAAGVPIVKPVGGHAVFLD 344 (450)
T ss_pred HHHHHHHHHHHHHHHCCCCEEECCCCCHHHHH
T ss_conf 99999999999998559824404774002444
No 261
>TIGR01020 rpsE_arch ribosomal protein S5; InterPro: IPR005711 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 of 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 model finds eukaryotic ribosomal protein S2 as well as archaeal ribosomal protein S5.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=44.96 E-value=11 Score=16.11 Aligned_cols=41 Identities=20% Similarity=0.281 Sum_probs=25.4
Q ss_pred CCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEE-CCHH
Q ss_conf 711500003786077998999868889980880899996-8989
Q gi|254780784|r 559 PPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIAS-SSLA 601 (699)
Q Consensus 559 ~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~-~~~~ 601 (699)
|.-|+|.|.=-| .||+|.|=|.-+.-|-|-..|-++= |+..
T Consensus 13 P~TklGRLVKeG--kIksidEI~~~~lPIkE~EIvD~LLGP~L~ 54 (220)
T TIGR01020 13 PRTKLGRLVKEG--KIKSIDEIFRRNLPIKEPEIVDALLGPDLN 54 (220)
T ss_pred CCCCCEEEEECC--CCCCHHHHHHCCCCCCCHHHHHEECCCCCC
T ss_conf 845210065066--245679998458982123341101088878
No 262
>PRK01712 carbon storage regulator; Provisional
Probab=44.59 E-value=17 Score=14.53 Aligned_cols=31 Identities=13% Similarity=0.381 Sum_probs=24.1
Q ss_pred CCHHHHCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf 78556032598899999978689986668730
Q gi|254780784|r 658 AKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKV 689 (699)
Q Consensus 658 ~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk~ 689 (699)
.++..-+.+||.|.+++++++ .|++||-..|
T Consensus 6 Rk~gEsI~Ig~~I~i~Vl~i~-g~~VrlGI~A 36 (64)
T PRK01712 6 RRVGESLMIGDDIEVTVLGVK-GNQVRIGINA 36 (64)
T ss_pred EECCCEEEECCCEEEEEEEEC-CCEEEEEEEC
T ss_conf 208997996999799999982-9989998988
No 263
>cd07227 Pat_Fungal_NTE1 Fungal patatin-like phospholipase domain containing protein 6. These are fungal Neuropathy Target Esterase (NTE), commonly referred to as NTE1. Patatin-like phospholipase. NTE has at least two functional domains: the N-terminal domain putatively regulatory domain and the C-terminal catalytic domain which shows esterase activity. NTE shows phospholipase activity for lysophosphatidylcholine (LPC) and phosphatidylcholine (PC). Exposure of NTE to organophosphates leads to organophosphate-induced delayed neurotoxicity (OPIDN). OPIDN is a progressive neurological condition that is characterized by weakness, paralysis, pain, and paresthesia. This family includes NTE1 from fungi.
Probab=44.27 E-value=14 Score=15.38 Aligned_cols=10 Identities=20% Similarity=0.222 Sum_probs=4.6
Q ss_pred EEEEEEECCC
Q ss_conf 2899863144
Q gi|254780784|r 472 DFIILSDISG 481 (699)
Q Consensus 472 ~~~iLtDI~G 481 (699)
+.+|--|+..
T Consensus 182 d~vIaVDV~~ 191 (269)
T cd07227 182 RDIFAVDVGS 191 (269)
T ss_pred CEEEEEECCC
T ss_conf 9899998998
No 264
>PRK09027 cytidine deaminase; Provisional
Probab=44.09 E-value=18 Score=14.48 Aligned_cols=106 Identities=21% Similarity=0.334 Sum_probs=64.4
Q ss_pred CCCCCCCCCCCC-CCEEEEEEEEE-------CCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCEE------
Q ss_conf 126776746886-88378999982-------1888877899999999998732688235411235520477324------
Q gi|254780784|r 97 RSIRPLFSKCYK-NETQVIINVMQ-------HDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYV------ 162 (699)
Q Consensus 97 R~lRPLFPkgf~-~evQIv~~VLS-------~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~idge~V------ 162 (699)
.+|+-+.|..|- .+..+-.-+|. .|.. | -+ +.+|-.|..-|--|+..--++|-+-..||+..
T Consensus 155 ~~L~~~LP~aFGP~dL~~~~~Ll~~~~~~l~~~~~-d--~l-~~~Al~AAn~SyAPYS~~~SGvAL~~~~G~vy~G~YaE 230 (295)
T PRK09027 155 HTLRDYLPDAFGPKDLNITTLLMDEQDHGFALDSG-D--PL-IQAALDAANRSHAPYSQSYSGVALETKDGRIFCGRYAE 230 (295)
T ss_pred CCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-C--HH-HHHHHHHHHHCCCCCCCCCCCEEEEECCCCEEEEEEHH
T ss_conf 73788587465975558776456744445757898-9--99-99999998723388668974159995799989620033
Q ss_pred ---ECCCCCCCCCCCEEE-EEECC----CCHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf ---368500022210135-53054----432333124443248999988753
Q gi|254780784|r 163 ---LNPRLDEDQGSLDLF-VSGTQ----DAVLMVELEANQLSEDVVLDAIIF 206 (699)
Q Consensus 163 ---iNPt~ee~esdLDLv-VAGT~----d~IlMIE~~A~EVsEe~mleAI~~ 206 (699)
.|||..-+.+.|..+ .+|.. ...+|||....-+|...+..++.-
T Consensus 231 nAAfNPSl~PlQaAL~~~~~~G~~~~~I~~aVLvE~~~a~vsq~~~t~~~L~ 282 (295)
T PRK09027 231 NAAFNPSLPPLQGALNLLNLNGEDFSDIQRAVLAEKADGKLSQWDATQATLK 282 (295)
T ss_pred HHCCCCCCCHHHHHHHHHHHCCCCHHHHHHHEEEECCCCCCCHHHHHHHHHH
T ss_conf 3203899558999999998469877764552267423675436999999999
No 265
>cd06818 PLPDE_III_cryptic_DSD Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bacterial Cryptic D-Serine Dehydratase. This subfamily is composed of Burkholderia cepacia cryptic D-serine dehydratase (cryptic DSD), which is also called D-serine deaminase, and similar bacterial proteins. Members of this subfamily are fold type III PLP-dependent enzymes with similarity to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as dimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on similarity, it is possible cryptic DSDs may also form dimers. Cryptic DSDs are distinct from the ubiquitous bacterial DSDs coded by the dsdA gene, mammalian L-serine dehydratases (LSD) and mammalian serine racemase (SerRac), which are fold type II PLP-dependent enzymes. At present, the enzymatic and biochemical properties
Probab=44.08 E-value=16 Score=14.73 Aligned_cols=55 Identities=20% Similarity=0.228 Sum_probs=37.9
Q ss_pred CCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCCCCCCCEEEEEEEEECCE
Q ss_conf 468738999853110278522356677779876-25950225412133200440882
Q gi|254780784|r 417 AQFPYTLRIVSEITESDGSSSMATVCGSSLALM-DAGVPISKPVAGIAMGLVKDGDD 472 (699)
Q Consensus 417 ~~~p~tirv~~evl~sngsssma~vc~~slal~-dagvp~~~~VaGiamGLi~~~~~ 472 (699)
..|.-.++|.++|..-+. ..-|.+-+|+.+|- |+|.|.-..+.+--.|++.+.+.
T Consensus 268 ~~f~~Al~VlttViS~p~-~~~ailDaG~K~ls~D~g~P~~~~~~~~g~~~~~~~~~ 323 (382)
T cd06818 268 GALRPALEIWAYVQSRPE-PGLAILGMGKRDVAFDAGLPVPLRVFRPGGGVVRLPDG 323 (382)
T ss_pred CCCCEEEEEEEEEECCCC-CCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 222121599999964246-99699888651200246998653201588532358997
No 266
>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=44.03 E-value=15 Score=15.09 Aligned_cols=41 Identities=22% Similarity=0.412 Sum_probs=18.5
Q ss_pred EEEECCCCEEEEECCCC---HHHHHHHHHHCCEEEEECCEEEEEEECC
Q ss_conf 99977115000037860---7799899986888998088089999689
Q gi|254780784|r 555 IMAIPPDQIRNVIGMGG---KVIRGIVEQTGAKVNIDDDGTVKIASSS 599 (699)
Q Consensus 555 ~~~i~~~ki~~~iG~gG---~~ik~i~~~~~~~i~i~d~g~v~i~~~~ 599 (699)
++.||+.+|-.+|||.| ++.=++..+.= --|.|.|.|-+.+
T Consensus 21 sl~i~~g~iTs~IGPNGAGKSTLLS~~sRL~----~~d~G~i~i~g~~ 64 (252)
T COG4604 21 SLDIPKGGITSIIGPNGAGKSTLLSMMSRLL----KKDSGEITIDGLE 64 (252)
T ss_pred EEEECCCCEEEEECCCCCCHHHHHHHHHHHC----CCCCCEEEEEEEE
T ss_conf 4541588636888899864888999999852----6678638981166
No 267
>pfam02599 CsrA Global regulator protein family. This is a family of global regulator proteins. This protein is a RNA-binding protein and a global regulator of carbohydrate metabolism genes facilitating mRNA decay. In E. coli CsrA binds 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. In other bacteria such as Erwinia caratovara RmsA has been shown to regulate the production of virulence determinants, such extracellular enzymes. RmsA binds to RmsB regulatory RNA.
Probab=43.69 E-value=18 Score=14.43 Aligned_cols=31 Identities=16% Similarity=0.492 Sum_probs=24.1
Q ss_pred CCHHHHCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf 78556032598899999978689986668730
Q gi|254780784|r 658 AKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKV 689 (699)
Q Consensus 658 ~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSrk~ 689 (699)
.++..-+.+||.|.|++++++ .|++||...|
T Consensus 6 Rk~gE~I~Igd~I~i~Vl~i~-~~~VrlGi~A 36 (53)
T pfam02599 6 RKVGESIVIGDDIEITVLEVK-GGQVRIGIEA 36 (53)
T ss_pred EECCCEEEECCCEEEEEEEEE-CCEEEEEEEC
T ss_conf 138998996999899999970-9989999988
No 268
>TIGR01935 NOT-MenG RraA family; InterPro: IPR010203 This entry includes a number of closely related sequences bacteria and plants. The Escherichia coli member of this family has been characterised as a regulator of RNase E (see IPR004659 from INTERPRO), and its crystal structure has been analysed . E. coli RraA acts as a trans-acting modulator of RNA turnover, binding essential endonuclease RNase E and inhibiting RNA processing . RNase E forms the core of a large RNA-catalysis machine termed the degradosomes. RraA (and RraB) causes remodelling of degradosome composition, which is associated with alterations in RNA decay and global transcript abundance and as such is a bacterial mechanism for the regulation of RNA cleavage .; GO: 0008428 ribonuclease inhibitor activity, 0051252 regulation of RNA metabolic process.
Probab=43.26 E-value=10 Score=16.36 Aligned_cols=15 Identities=33% Similarity=0.477 Sum_probs=6.9
Q ss_pred CCEEEEEEEEECCCCCE
Q ss_conf 98899999978689986
Q gi|254780784|r 667 GDTVWVKLLDFDDRGKI 683 (699)
Q Consensus 667 Gd~i~vk~~~~d~~g~i 683 (699)
|+.++|||++ +++++
T Consensus 35 G~ivTvkcFE--DNslv 49 (155)
T TIGR01935 35 GPIVTVKCFE--DNSLV 49 (155)
T ss_pred CCCEEEEEEE--CCHHH
T ss_conf 8403899970--47368
No 269
>PRK10546 pyrimidine (deoxy)nucleoside triphosphate pyrophosphohydrolase; Provisional
Probab=43.04 E-value=18 Score=14.42 Aligned_cols=14 Identities=29% Similarity=0.558 Sum_probs=7.2
Q ss_pred HHHHHHHHCCEEEE
Q ss_conf 99899986888998
Q gi|254780784|r 574 IRGIVEQTGAKVNI 587 (699)
Q Consensus 574 ik~i~~~~~~~i~i 587 (699)
+|++.||+|.++.+
T Consensus 50 ~REl~EElgi~v~~ 63 (135)
T PRK10546 50 IRELREELGIEATV 63 (135)
T ss_pred HHHHHHHHCCEEEE
T ss_conf 88878750958984
No 270
>KOG1423 consensus
Probab=42.89 E-value=18 Score=14.34 Aligned_cols=49 Identities=22% Similarity=0.302 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECC
Q ss_conf 999999999987288665886775337879984475466700899987976899998168
Q gi|254780784|r 297 DIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGT 356 (699)
Q Consensus 297 ~l~k~ivR~~ILeeg~R~DGR~~dEIRpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~ 356 (699)
++-|..+-+..+..++-+=-|+.++-|- -=+|..|-||||..-.=|=|-
T Consensus 82 NvGKStLtN~mig~kv~~vS~K~~TTr~-----------~ilgi~ts~eTQlvf~DTPGl 130 (379)
T KOG1423 82 NVGKSTLTNQMIGQKVSAVSRKVHTTRH-----------RILGIITSGETQLVFYDTPGL 130 (379)
T ss_pred CCCHHHHHHHHHCCCCCCCCCCCCCEEE-----------EEEEEEECCCEEEEEECCCCC
T ss_conf 7654554457648721201156653020-----------135787159658999648764
No 271
>COG5009 MrcA Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]
Probab=42.66 E-value=18 Score=14.31 Aligned_cols=43 Identities=21% Similarity=0.136 Sum_probs=23.6
Q ss_pred CEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEE
Q ss_conf 738999853110278522356677779876259502254121332
Q gi|254780784|r 420 PYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAM 464 (699)
Q Consensus 420 p~tirv~~evl~sngsssma~vc~~slal~dagvp~~~~VaGiam 464 (699)
|.|=+|.+-|=-.+=+.| -.+-++=||-.-|--+|--|=..|+
T Consensus 428 p~tG~I~AlVGGfsf~~S--kFNRATQA~rQPGSsfKPfvYsAAL 470 (797)
T COG5009 428 PKTGAILALVGGFSFAQS--KFNRATQALRQPGSSFKPFVYSAAL 470 (797)
T ss_pred CCCCEEEEEECCCCCCHH--HHHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf 798708998636343222--4447777641798521278999998
No 272
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=42.34 E-value=19 Score=14.28 Aligned_cols=17 Identities=29% Similarity=0.114 Sum_probs=8.3
Q ss_pred HHHHHHHHHHHHHHHHH
Q ss_conf 31688999999999999
Q gi|254780784|r 206 FGHNECKPVIEAISKLA 222 (699)
Q Consensus 206 ~Ahe~Ik~iI~~Q~eL~ 222 (699)
..|+..+++.+.-.++.
T Consensus 185 ~~h~~~kkvae~a~~~F 201 (403)
T TIGR03676 185 AAHEFYKRVGEAANEAF 201 (403)
T ss_pred HHHHHHHHHHHHHHHHH
T ss_conf 99999999999999873
No 273
>KOG0074 consensus
Probab=41.47 E-value=12 Score=15.75 Aligned_cols=70 Identities=24% Similarity=0.343 Sum_probs=41.1
Q ss_pred CCCEEEEEEEECCCCC---CCCCCCCCEEEEECCCCCC-CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCE
Q ss_conf 8948999997278888---7777354068665232013-36788873578988714531111232126776746886883
Q gi|254780784|r 36 GETVVLATVVYDRSLK---DGQDFFPLTVNYQERTYAV-GKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNET 111 (699)
Q Consensus 36 G~T~VLaTv~~~~~~~---~~~dFfPLtVdY~Ek~yAa-GkIPGgF~kREgrpsd~EiL~sRlIDR~lRPLFPkgf~~ev 111 (699)
|.|..|--. .+.+++ +...|---+|+|.+-++-. =-| || ||.|||.+ ++|+.+|
T Consensus 29 GKTT~LKqL-~sED~~hltpT~GFn~k~v~~~g~f~LnvwDi-GG-------------------qr~IRpyW-sNYyenv 86 (185)
T KOG0074 29 GKTTFLKQL-KSEDPRHLTPTNGFNTKKVEYDGTFHLNVWDI-GG-------------------QRGIRPYW-SNYYENV 86 (185)
T ss_pred CCHHHHHHH-CCCCHHHCCCCCCCCEEEEEECCCEEEEEEEC-CC-------------------CCCCCHHH-HHHHHCC
T ss_conf 613088887-13783331566885247876247078888852-78-------------------66554456-6555305
Q ss_pred EEEEEEEECCCCCCHH
Q ss_conf 7899998218888778
Q gi|254780784|r 112 QVIINVMQHDLESSPH 127 (699)
Q Consensus 112 QIv~~VLS~D~~~dpd 127 (699)
..++.|.-+..+-..+
T Consensus 87 d~lIyVIDS~D~krfe 102 (185)
T KOG0074 87 DGLIYVIDSTDEKRFE 102 (185)
T ss_pred CEEEEEEECCCHHHHH
T ss_conf 5489998477367689
No 274
>cd03138 GATase1_AraC_2 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain. A subgroup of AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain. AraC regulators are defined by a AraC-type helix-turn-helix DNA binding domain at their C-terminal. AraC family transcriptional regulators are widespread among bacteria and are involved in regulating diverse and important biological functions, including carbon metabolism, stress responses and virulence in different microorganisms. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, in common with typical GATase1domains a reactive cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.
Probab=41.45 E-value=9.4 Score=16.69 Aligned_cols=21 Identities=24% Similarity=0.528 Sum_probs=15.3
Q ss_pred CCCHHHHHHHHHHHHHHCCCC
Q ss_conf 852235667777987625950
Q gi|254780784|r 434 GSSSMATVCGSSLALMDAGVP 454 (699)
Q Consensus 434 gsssma~vc~~slal~dagvp 454 (699)
-+...++||.|++.|..||.-
T Consensus 103 ~g~~i~sictGa~~LA~aGLL 123 (195)
T cd03138 103 NGATVAAACTGVFLLAEAGLL 123 (195)
T ss_pred HCCEEECCCHHHHHHHHCCCC
T ss_conf 271784165899999973663
No 275
>PRK12597 F0F1 ATP synthase subunit beta; Provisional
Probab=41.06 E-value=19 Score=14.13 Aligned_cols=31 Identities=26% Similarity=0.388 Sum_probs=15.8
Q ss_pred CCCCCCCCCCCCC---HHHHHHHHHHHCCCCCCC
Q ss_conf 7888735789887---145311112321267767
Q gi|254780784|r 73 IPGGYLRRESRPT---ENEILISRMIDRSIRPLF 103 (699)
Q Consensus 73 IPGgF~kREgrps---d~EiL~sRlIDR~lRPLF 103 (699)
=+|.-.++-|+|- =-+=|..|++|=.=|||=
T Consensus 62 ~~G~~V~~tg~~l~VpVG~~lLGRV~d~lG~PiD 95 (459)
T PRK12597 62 ARGDEVRNTGAPIEVPVGEAVLGRLLDVLGEPLD 95 (459)
T ss_pred CCCCEEEECCCCEEEEECHHHCCCEECCCCCCCC
T ss_conf 8999999689945987086333687678886268
No 276
>pfam09364 XFP_N XFP N-terminal domain. Bacterial enzyme splits fructose-6-P and/or xylulose-5-P with the aid of inorganic phosphate into either acetyl-P and erythrose-4-P and/or acetyl-P and glyeraldehyde-3-P EC:4.1.2.9, EC:4.1.2.22. This family is distantly related to transketolases e.g. pfam02779.
Probab=40.55 E-value=20 Score=14.08 Aligned_cols=107 Identities=16% Similarity=0.168 Sum_probs=69.8
Q ss_pred CCCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCE--EEEE-EEECCCCEEECCCCCC-C-CCCCEEE
Q ss_conf 74688688378999982188887789999999999873268823541--1235-5204773243685000-2-2210135
Q gi|254780784|r 103 FSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPV--VGAQ-VDYINGQYVLNPRLDE-D-QGSLDLF 177 (699)
Q Consensus 103 FPkgf~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPV--aaVR-VG~idge~ViNPt~ee-~-esdLDLv 177 (699)
|---|-|.-.|++.| -=|++...-- +|.+=-..-|-.|+ |||- |-..||-=|.|||.-- + +.+|.-.
T Consensus 150 ~GAv~DnPdLiva~V-vGDGEaETGP-------lAtsWhsnkFlnP~~dGaVLPILhLNGyKI~npTilar~~~~EL~~l 221 (379)
T pfam09364 150 YGAVFDNPDLIVACV-VGDGEAETGP-------LATSWHSNKFLNPATDGAVLPILHLNGYKISNPTILARISDEELRKL 221 (379)
T ss_pred CCCCCCCCCEEEEEE-ECCCCCCCCC-------CHHHHCCCCCCCCCCCCCCCEEEECCCCCCCCCEEECCCCHHHHHHH
T ss_conf 056458988689997-4686323574-------10111444335813366403024205631268745322898999999
Q ss_pred EEECCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5305443233312444324899998875316889999999
Q gi|254780784|r 178 VSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEA 217 (699)
Q Consensus 178 VAGT~d~IlMIE~~A~EVsEe~mleAI~~Ahe~Ik~iI~~ 217 (699)
..|--=...-||+.-.+.-...|..+++.+.++|+.|.+.
T Consensus 222 f~G~Gy~p~~Veg~d~~~~h~~mA~~ld~~~~~I~~iq~~ 261 (379)
T pfam09364 222 FEGYGYEPYFVEGHDPESMHRLMAETLDWAVEEIHDIQHA 261 (379)
T ss_pred HHHCCCCCEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 8427984179707985889999999999999999999999
No 277
>cd02011 TPP_PK Thiamine pyrophosphate (TPP) family, Phosphoketolase (PK) subfamily, TPP-binding module; PK catalyzes the conversion of D-xylulose 5-phosphate and phosphate to acetyl phosphate, D-glyceraldehyde-3-phosphate and H2O. This enzyme requires divalent magnesium ions and TPP for activity.
Probab=40.17 E-value=20 Score=14.03 Aligned_cols=105 Identities=16% Similarity=0.194 Sum_probs=69.5
Q ss_pred CCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCE--EEEE-EEECCCCEEECCCCCC-C-CCCCEEEEE
Q ss_conf 688688378999982188887789999999999873268823541--1235-5204773243685000-2-221013553
Q gi|254780784|r 105 KCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPV--VGAQ-VDYINGQYVLNPRLDE-D-QGSLDLFVS 179 (699)
Q Consensus 105 kgf~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPV--aaVR-VG~idge~ViNPt~ee-~-esdLDLvVA 179 (699)
--|-|.-.|++.|+ =|++...--| |+ +--..-|-.|. ++|- |-..||-=|-|||.-- + +.+|.....
T Consensus 74 A~~DnPdliva~Vv-GDGEaETGPl---At----sW~s~kflnP~~dGaVLPIlhLNGyKIsnpTilar~~~~eL~~lf~ 145 (227)
T cd02011 74 AVFDNPDLIVACVV-GDGEAETGPL---AT----SWHSNKFLNPATDGAVLPILHLNGYKISNPTILARISHEELEALFR 145 (227)
T ss_pred CCCCCCCEEEEEEE-CCCCCCCCCC---HH----HHCCCCCCCCCCCCCEEEEEECCCCCCCCCEEECCCCHHHHHHHHH
T ss_conf 53489986999985-6863235841---22----2222001583347724457741674026885431279899999984
Q ss_pred ECCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 05443233312444324899998875316889999999
Q gi|254780784|r 180 GTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEA 217 (699)
Q Consensus 180 GT~d~IlMIE~~A~EVsEe~mleAI~~Ahe~Ik~iI~~ 217 (699)
|---...-||+...+.-...|..|++.+.+.|+.|.+.
T Consensus 146 G~Gy~p~~Veg~dp~~~h~~mA~~ld~a~~~I~~iq~~ 183 (227)
T cd02011 146 GYGYEPYFVEGDDPETMHQAMAATLDWAIEEIKAIQKR 183 (227)
T ss_pred HCCCCCEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 18982179778980689999999999999999999999
No 278
>pfam04697 Pinin_SDK_N pinin/SDK conserved region. SDK2/3 is localized in nuclear speckles where as pinin is known to localize at the desmosomes where it is thought to be involved in anchoring intermediate filaments to the desmosomal plaque. The role of SDK2/3 in the nucleus is thought to be concerned with modulation of alternative pre-mRNA splicing. pinin has also been implicated as a tumour suppressor. The conserved region is found at the N-terminus of the member proteins.
Probab=39.94 E-value=20 Score=14.04 Aligned_cols=33 Identities=27% Similarity=0.386 Sum_probs=25.9
Q ss_pred CCCCCCCCCEEEEEEEECCCCCC-----CCEEEEEECC
Q ss_conf 65886775337879984475466-----7008999879
Q gi|254780784|r 313 RMDGRDSETVRDISAQVGLLQRT-----HGSSLFIRGD 345 (699)
Q Consensus 313 R~DGR~~dEIRpIs~EvgvLPrv-----HGSALFtRGE 345 (699)
++-||+++|.||..++--.|++. ||.-+.-||-
T Consensus 28 kl~GRDP~e~rp~~~rr~~~~~~~G~r~~g~~~~RR~~ 65 (134)
T pfam04697 28 KLTGRDPGDLRPGQARLLAIPGPGGGRGRGILLLRRGF 65 (134)
T ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEC
T ss_conf 87078921258863311345589888777754343211
No 279
>CHL00060 atpB ATP synthase CF1 beta subunit
Probab=39.70 E-value=20 Score=13.98 Aligned_cols=13 Identities=15% Similarity=0.347 Sum_probs=5.4
Q ss_pred HHHHHHHCCCCCC
Q ss_conf 1111232126776
Q gi|254780784|r 90 LISRMIDRSIRPL 102 (699)
Q Consensus 90 L~sRlIDR~lRPL 102 (699)
|..|++|=-=||+
T Consensus 96 lLGRV~d~lG~Pi 108 (480)
T CHL00060 96 TLGRIFNVLGEPV 108 (480)
T ss_pred HCCCEECCCCCCC
T ss_conf 3168788888835
No 280
>cd07225 Pat_PNPLA6_PNPLA7 Patatin-like phospholipase domain containing protein 6 and protein 7. Patatin-like phospholipase domain containing protein 6 (PNPLA6) and protein 7 (PNPLA7) are 60% identical to each other. PNPLA6 is commonly known as Neuropathy Target Esterase (NTE). NTE has at least two functional domains: the N-terminal domain putatively regulatory domain and the C-terminal catalytic domain which shows esterase activity. NTE shows phospholipase activity for lysophosphatidylcholine (LPC) and phosphatidylcholine (PC). Exposure of NTE to organophosphates leads to organophosphate-induced delayed neurotoxicity (OPIDN). OPIDN is a progressive neurological condition that is characterized by weakness, paralysis, pain, and paresthesia. PNPLA7 is an insulin-regulated phospholipase that is homologous to Neuropathy Target Esterase (NTE or PNPLA6) and is also known as NTE-related esterase (NRE). Human NRE is predominantly expressed in prostate, white adipose, and pancreatic tissue. NRE
Probab=39.66 E-value=15 Score=15.02 Aligned_cols=87 Identities=18% Similarity=0.195 Sum_probs=37.3
Q ss_pred HHHHHCCCCCCCCCCCCCCEEEEEEEEECCCC-----C--CHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCEEEC
Q ss_conf 11232126776746886883789999821888-----8--7789999999999873268823541123552047732436
Q gi|254780784|r 92 SRMIDRSIRPLFSKCYKNETQVIINVMQHDLE-----S--SPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLN 164 (699)
Q Consensus 92 sRlIDR~lRPLFPkgf~~evQIv~~VLS~D~~-----~--dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~idge~ViN 164 (699)
.+-..+.|+-+|+..-..|..|--.+.+.|-. . +-+....+-||+|+--.=-|+-.|+.+ | -++||..+.|
T Consensus 100 g~~~~~~l~~~~~~~~iedL~ip~~~vatDl~tg~~vv~~~G~l~~AvrAS~aiPg~f~Pv~~~~dG-~-~LVDGGv~nn 177 (306)
T cd07225 100 GAAFNRSIHSIFGDKQIEDLWLPYFTITTDITASAMRVHTDGSLWRYVRASMSLSGYLPPLCDPKDG-H-LLMDGGYINN 177 (306)
T ss_pred HHHHHHHHHHHHCCCCHHHCCCCEEEEEEECCCCCEEEEECCCHHHHHHHHHHCCCCCCCEEECCCC-E-EEEECCCCCC
T ss_conf 7999999999848898888698659998655769889980752999999997267667854746599-4-9973782766
Q ss_pred CCCCCCCC-CCEEEEEE
Q ss_conf 85000222-10135530
Q gi|254780784|r 165 PRLDEDQG-SLDLFVSG 180 (699)
Q Consensus 165 Pt~ee~es-dLDLvVAG 180 (699)
-..+...+ .-|.++|-
T Consensus 178 lPv~~~~~~gad~vIaV 194 (306)
T cd07225 178 LPADVARSMGAKTVIAI 194 (306)
T ss_pred HHHHHHHHCCCCEEEEE
T ss_conf 03999998596969999
No 281
>cd07210 Pat_hypo_W_succinogenes_WS1459_like Hypothetical patatin similar to WS1459 of Wolinella succinogenes. Patatin-like phospholipase. This family predominantly consists of bacterial patatin glycoproteins. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates.
Probab=39.42 E-value=18 Score=14.31 Aligned_cols=35 Identities=23% Similarity=0.342 Sum_probs=24.9
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEE
Q ss_conf 278522356677779876259502254121332004
Q gi|254780784|r 432 SDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLV 467 (699)
Q Consensus 432 sngsssma~vc~~slal~dagvp~~~~VaGiamGLi 467 (699)
|-|+.+=++-.|--=||.++|+++ +.|+|+|+|=+
T Consensus 6 sGGg~rG~ahiGvlkaL~e~gi~~-d~i~GtSaGAi 40 (221)
T cd07210 6 SSGFFGFYAHLGFLAALLEMGLEP-SAISGTSAGAL 40 (221)
T ss_pred CCCHHHHHHHHHHHHHHHHCCCCC-CEEEEECHHHH
T ss_conf 770899999999999999779998-88999889999
No 282
>CHL00192 syfB phenylalanyl-tRNA synthetase beta chain; Provisional
Probab=39.28 E-value=20 Score=13.93 Aligned_cols=48 Identities=17% Similarity=0.218 Sum_probs=29.8
Q ss_pred EEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHH
Q ss_conf 5799997711500003786077998999868889980880899996898999999999
Q gi|254780784|r 552 RVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREM 609 (699)
Q Consensus 552 ~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~ 609 (699)
+.-.+.++.. .||-=|..=..+.++++. +..|.+|--|-+.+......
T Consensus 549 ~sA~I~~~~~----~iG~iG~lhP~v~~~~~l------~~~v~~~Eidl~~l~~~~~~ 596 (702)
T CHL00192 549 RSAEIIYNNE----NIGIFGQLHPLLASNLGL------NTSTYLFEFDLEKLQASIEQ 596 (702)
T ss_pred CEEEEEECCE----EEEEEEEECHHHHHHCCC------CCCEEEEEEEHHHHHHHHHH
T ss_conf 5489999997----999999987999987399------99779999997994323443
No 283
>PRK11750 gltB glutamate synthase subunit alpha; Provisional
Probab=39.20 E-value=20 Score=13.92 Aligned_cols=80 Identities=16% Similarity=0.291 Sum_probs=47.9
Q ss_pred HHHHHCCCCCCCCCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCEEE--------
Q ss_conf 112321267767468868837899998218888778999999999987326882354112355204773243--------
Q gi|254780784|r 92 SRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVL-------- 163 (699)
Q Consensus 92 sRlIDR~lRPLFPkgf~~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~idge~Vi-------- 163 (699)
.|=+-++++=|+|+-|.| +...+|+.-|.--=.+.++= ||+||-+ |...||.+|.
T Consensus 297 Grsl~~A~~mliPeAw~~-----------~~~m~~~~rafYeY~s~~mE---PWDGPAa---I~ftDG~~iga~LDRNGL 359 (1483)
T PRK11750 297 GMDLFRAMRLLVPPAWQN-----------NPDMDPDLRAFYEFNSMHME---PWDGPAG---IVMTDGRYAACNLDRNGL 359 (1483)
T ss_pred CCCHHHHHHHHCCCHHCC-----------CCCCCHHHHHHHHHHHHCCC---CCCCCEE---EEEECCCEEEEECCCCCC
T ss_conf 998899998618702118-----------87789899999999872168---7778547---886069889996036788
Q ss_pred CCCCCCCCCCCEEEEEECCCCHHHHH
Q ss_conf 68500022210135530544323331
Q gi|254780784|r 164 NPRLDEDQGSLDLFVSGTQDAVLMVE 189 (699)
Q Consensus 164 NPt~ee~esdLDLvVAGT~d~IlMIE 189 (699)
-|..-....| ++++.+++-+|+=+.
T Consensus 360 RP~Ry~iT~D-~~vi~aSE~Gvv~~~ 384 (1483)
T PRK11750 360 RPARYVITKD-RLITLASEVGIWDYQ 384 (1483)
T ss_pred CCEEEEEECC-CEEEEEECCCCCCCC
T ss_conf 8515788469-889998337876798
No 284
>TIGR02062 RNase_B exoribonuclease II; InterPro: IPR011804 This family consists of exoribonuclease II (RNase 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.; GO: 0003723 RNA binding, 0008859 exoribonuclease II activity, 0006401 RNA catabolic process.
Probab=39.09 E-value=21 Score=13.91 Aligned_cols=66 Identities=23% Similarity=0.268 Sum_probs=37.6
Q ss_pred CCCCCCEEEEEEEEEEECCEEEECC--------------CCCCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCC
Q ss_conf 7546867899999994153699828--------------79710488663144454785560325988999999786899
Q gi|254780784|r 616 VPEVNKIYKGQVVKVMDFGAFVHFC--------------GARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRG 681 (699)
Q Consensus 616 ~~e~g~~y~~~v~~i~~fGafve~~--------------~g~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g 681 (699)
++--.+-|.++|..|.=-|-=|.|+ +.||=|.-..|=-.=-+ +-+-++|+||-|+|++.||....
T Consensus 579 k~~~~~~F~AEi~Dv~R~G~Rv~LleNGA~~FIPA~~Lh~~keel~~n~e~G~v~I-kge~~YKi~D~~~v~LtEv~~~t 657 (664)
T TIGR02062 579 KEAKNTRFEAEIVDVSRAGMRVRLLENGASAFIPAAFLHDNKEELVCNQEEGTVYI-KGEVVYKIGDVIEVVLTEVREET 657 (664)
T ss_pred CCCCCCCEEEEEEEECCCCCEEEEECCCCCHHCCHHHHCCCCCEEEEECCCCEEEE-EEEEEEEEEEEEEEEEEEEECCC
T ss_conf 33368612446887247874343120563111143443033213665068763887-10789866106999984540134
Q ss_pred C
Q ss_conf 8
Q gi|254780784|r 682 K 682 (699)
Q Consensus 682 ~ 682 (699)
|
T Consensus 658 R 658 (664)
T TIGR02062 658 R 658 (664)
T ss_pred C
T ss_conf 5
No 285
>PTZ00110 helicase; Provisional
Probab=38.62 E-value=21 Score=13.86 Aligned_cols=22 Identities=23% Similarity=0.147 Sum_probs=12.1
Q ss_pred CCCCEEEEECCCCCCCCCCCCC
Q ss_conf 3540686652320133678887
Q gi|254780784|r 56 FFPLTVNYQERTYAVGKIPGGY 77 (699)
Q Consensus 56 FfPLtVdY~Ek~yAaGkIPGgF 77 (699)
|---.|+|+.-.|+.+.--.||
T Consensus 49 ~~~~~~~~~~~~~~~~~~~~~~ 70 (602)
T PTZ00110 49 YDKPYVNQQAAAYSQFSNGYGF 70 (602)
T ss_pred CCCCCCCCCCCCCCCCCCCCCC
T ss_conf 4776556776433677899885
No 286
>TIGR00224 pckA phosphoenolpyruvate carboxykinase (ATP); InterPro: IPR001272 Phosphoenolpyruvate carboxykinase (PEPCK) catalyses the first committed (rate-limiting) step in hepatic gluconeogenesis, namely the reversible decarboxylation of oxaloacetate to phosphoenolpyruvate (PEP) and carbon dioxide, using either ATP or GTP as a source of phosphate. The ATP-utilising (4.1.1.49 from EC) and GTP-utilising (4.1.1.32 from EC) enzymes form two divergent subfamilies, which have little sequence similarity but which retain conserved active site residues. ATP-utilising PEPCKs are monomers or oligomers of identical subunits found in certain bacteria, yeast, trypanosomatids, and plants, while GTP-utilising PEPCKs are mainly monomers found in animals and some bacteria . Both require divalent cations for activity, such as magnesium or manganese. One cation interacts with the enzyme at metal binding site 1 to elicit activation, while the second cation interacts at metal binding site 2 to serve as a metal-nucleotide substrate. In bacteria, fungi and plants, PEPCK is involved in the glyoxylate bypass, an alternative to the tricarboxylic acid cycle. PEPCK helps to regulate blood glucose levels. The rate of gluconeogenesis can be controlled through transcriptional regulation of the PEPCK gene by cAMP (the mediator of glucagon and catecholamines), glucocorticoids and insulin. In general, PEPCK expression is induced by glucagon, catecholamines and glucocorticoids during periods of fasting and in response to stress, but is inhibited by (glucose-induced) insulin upon feeding . With type II diabetes, this regulation system can fail, resulting in increased gluconeogenesis that in turn raises glucose levels . PEPCK consists of an N-terminal and a catalytic C-terminal domain, with the active site and metal ions located in a cleft between them. Both domains have an alpha/beta topology that is partly similar to one another , . Substrate binding causes PEPCK to undergo a conformational change, which accelerates catalysis by forcing bulk solvent molecules out of the active site . PCK uses an alpha/beta/alpha motif for nucleotide binding, this motif differing from other kinase domains. GTP-utilising PEPCK has a PEP-binding domain and two kinase motifs to bind GTP and magnesium. This entry represents ATP-utilising phosphoenolpyruvate carboxykinase enzymes.; GO: 0004612 phosphoenolpyruvate carboxykinase (ATP) activity, 0005524 ATP binding, 0006094 gluconeogenesis.
Probab=38.60 E-value=9.6 Score=16.59 Aligned_cols=12 Identities=17% Similarity=0.169 Sum_probs=5.3
Q ss_pred CCCCCCCCCE-EE
Q ss_conf 6588677533-78
Q gi|254780784|r 313 RMDGRDSETV-RD 324 (699)
Q Consensus 313 R~DGR~~dEI-Rp 324 (699)
|+.+-.+..+ .|
T Consensus 153 RP~~e~l~~f~~P 165 (549)
T TIGR00224 153 RPTEEELKTFEEP 165 (549)
T ss_pred CCCHHHHCCCCCC
T ss_conf 8871323037998
No 287
>pfam09883 DUF2110 Uncharacterized protein conserved in archaea (DUF2110). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=38.57 E-value=21 Score=13.85 Aligned_cols=118 Identities=14% Similarity=0.128 Sum_probs=57.4
Q ss_pred CHHHHHHHHHHCCE--EEEECC--EEEEEEECCHHHHHHHHH-HHHHHCCCCC--CCCEEEEEEEEEEECCEEEECCCCC
Q ss_conf 07799899986888--998088--089999689899999999-9998524754--6867899999994153699828797
Q gi|254780784|r 571 GKVIRGIVEQTGAK--VNIDDD--GTVKIASSSLAEIEAARE-MIRSITDVPE--VNKIYKGQVVKVMDFGAFVHFCGAR 643 (699)
Q Consensus 571 G~~ik~i~~~~~~~--i~i~d~--g~v~i~~~~~~~~~~a~~-~i~~~~~~~e--~g~~y~~~v~~i~~fGafve~~~g~ 643 (699)
.+.++....+..|+ |.+.++ -.|++.+.|.+...+.+. .--.++...+ .|++|.|+....-+-|.-+.+- |.
T Consensus 20 ~s~v~n~lgdLdV~~~i~i~~~~w~~vtl~GeD~eva~Nll~eefGei~~~le~v~Ge~y~G~l~~~~e~G~~~~v~-G~ 98 (226)
T pfam09883 20 NSLVENELGDLDVKWEISIRDDDWVKVTLTGEDEEVAANLLREEFGEIVRSLEDVEGEVYVGTLISWDEDGYGLDVD-GV 98 (226)
T ss_pred HHHHHHHHCCEEEEEEECCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCCEEEEEC-CE
T ss_conf 99998660452689996324578339998658488999999998588760003678877899987606641699865-73
Q ss_pred CEEEEEEEC---CCCCCCCHHHHCCCCCE--EEEEEEEECCCCCEEEEEEE
Q ss_conf 104886631---44454785560325988--99999978689986668730
Q gi|254780784|r 644 DGLVHISQL---STERVAKTSDVVKEGDT--VWVKLLDFDDRGKIKLSMKV 689 (699)
Q Consensus 644 ~gl~HiS~l---~~~~v~~~~d~~~~Gd~--i~vk~~~~d~~g~i~lSrk~ 689 (699)
.+-.--++| -+..+..+..-+-.=|. +.|.++..++.-..+||-+.
T Consensus 99 ~~~ip~deL~~Lg~gs~~Qi~~rFG~V~hlPvev~v~~~e~~i~arltd~q 149 (226)
T pfam09883 99 TVPIPADELLPLGQGSPRQIRRRFGLVQHLPVEVRFVEVEDGIEARLTDKQ 149 (226)
T ss_pred ECCCCHHHHCCCCCCCHHHHHHHHCCCCCCCEEEEEEECCCCCCCCCCHHH
T ss_conf 646717885345689989999880874578538999972677643369999
No 288
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=38.38 E-value=16 Score=14.81 Aligned_cols=71 Identities=18% Similarity=0.342 Sum_probs=48.4
Q ss_pred EEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCC------CCCCCCCCCCC-------CHHHHHHHHH
Q ss_conf 8999879768999981686521223344544203587740588754------45334556765-------0246799999
Q gi|254780784|r 339 SLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCA------TGEVSRMGAPS-------RREIGHGRLA 405 (699)
Q Consensus 339 ALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfs------vGE~~~~~~~~-------RREiGHg~la 405 (699)
.-|..|.+++|+++-+.+.+ +| -..-.+-.||++|.-. +|.|||.|..+ -||...=.-+
T Consensus 289 ~~Fr~g~~~ILVaTDvaARG----LD----i~~V~~VINyDlP~d~e~YVHRiGRTGRaGr~G~Aitfv~~~e~~~l~~i 360 (629)
T PRK11634 289 ERLKDGRLDILIATDVAARG----LD----VERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNI 360 (629)
T ss_pred HHHHCCCCCEEEECCCCCCC----CC----CCCCCEEEEECCCCCHHHCCCCCCCCCCCCCCEEEEEEECHHHHHHHHHH
T ss_conf 99975999889878621055----77----25688899968989743401025833168996469998888999999999
Q ss_pred HHHHHHCCCCCC
Q ss_conf 998741078644
Q gi|254780784|r 406 RRAIHPVLPQTA 417 (699)
Q Consensus 406 ~ral~~~~P~~~ 417 (699)
||....-++..+
T Consensus 361 er~~~~~~~~~~ 372 (629)
T PRK11634 361 ERTMKLTIPEVE 372 (629)
T ss_pred HHHHCCCCEECC
T ss_conf 999779860148
No 289
>PRK11162 mltA murein transglycosylase A; Provisional
Probab=38.28 E-value=8.4 Score=17.07 Aligned_cols=35 Identities=20% Similarity=0.269 Sum_probs=24.9
Q ss_pred ECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf 058875445334556765024679999999874107
Q gi|254780784|r 378 YNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVL 413 (699)
Q Consensus 378 YNFPpfsvGE~~~~~~~~RREiGHg~la~ral~~~~ 413 (699)
|.+|=|+.-.... .-|+|+||.-|+|+.|+|+-+-
T Consensus 133 y~yPlY~~P~~~~-~~ptRaeI~~GaL~grglELaW 167 (362)
T PRK11162 133 FQYPIYRMPPKRG-RLPSRAEIYAGALSGKGLELAY 167 (362)
T ss_pred CCCCCCCCCCCCC-CCCCHHHHHCCHHCCCCCEEEE
T ss_conf 5776335897678-8989999864611288746998
No 290
>TIGR02383 Hfq RNA chaperone Hfq; InterPro: IPR005001 This entry represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory non-coding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam:RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see ). The name Hfq reflects phenomenology as a host factor for phage Q-beta RNA replication. The Hfq protein is conserved in a wide range of bacteria and varies in length from 70 to 100 amino acids. In all cases, a conserved Sm motif is located in the N-terminal halves of the molecules. The Hfq protein of E. coli is an 11 kDa polypeptide that forms a hexameric ring-shaped structure. Structural studies have suggested that the beta-4 strand in one molecule dimerises with the beta-5 strand of a neighbouring subunit to form the hexamer. These two strands move with a concerted mobility which may explain the stability of the entire structure . The architecture of the Hfq-RNA complex suggests two, not mutually exclusive, mechanisms by which Hfq might exert its function as modulator of RNA-RNA interactions. First, when Hfq binds single-stranded RNA, the target site is unwound in a circular manner. This would greatly destabilise surrounding RNA structures that are located several nucleotides on either side of the binding site, thereby permitting new RNA-RNA interactions. Secondly, the repetition of identical BPs on the Hfq hexamer implies that the binding surface can accommodate more than just a single RNA target. This would allow simultaneous binding of two RNA strands and could greatly enhance interaction between the strands .; GO: 0003723 RNA binding, 0006355 regulation of transcription DNA-dependent.
Probab=37.90 E-value=21 Score=13.78 Aligned_cols=23 Identities=35% Similarity=0.713 Sum_probs=18.8
Q ss_pred CCCCCCCCCEEEEEEEEECCEEEEEEECCCC
Q ss_conf 9502254121332004408828998631442
Q gi|254780784|r 452 GVPISKPVAGIAMGLVKDGDDFIILSDISGD 482 (699)
Q Consensus 452 gvp~~~~VaGiamGLi~~~~~~~iLtDI~G~ 482 (699)
||+++ |.|..-|+|.||-+..|.
T Consensus 25 Gv~l~--------G~i~sFD~FtVlL~~~g~ 47 (61)
T TIGR02383 25 GVQLK--------GVIKSFDNFTVLLESQGK 47 (61)
T ss_pred CEECC--------CEEEEECCEEEEECCCCE
T ss_conf 82405--------189972217998720992
No 291
>KOG2635 consensus
Probab=37.18 E-value=22 Score=13.69 Aligned_cols=41 Identities=15% Similarity=0.224 Sum_probs=24.3
Q ss_pred EEEEEECCCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCCHHHH
Q ss_conf 899863144220136551001005565124432453655688999
Q gi|254780784|r 473 FIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIM 517 (699)
Q Consensus 473 ~~iLtDI~G~ED~~GdMDFKvaGT~~GiTa~QmDiK~~gi~~~il 517 (699)
.-.|+-=. .++.||+.-.|++-.++-=|-||-- +.|..+..
T Consensus 301 qG~lsLrI-~d~e~~~i~lkl~n~~~~g~q~ktH---PNlDK~~f 341 (512)
T KOG2635 301 QGTLSLRI-KDEEYGDIELKLANGRDKGTQLKTH---PNLDKKVF 341 (512)
T ss_pred EEEEEEEE-CCCCCCCEEEEECCCCCCCEEEEEC---CCCCHHHH
T ss_conf 12699998-5602460689974788764266537---88456663
No 292
>pfam00358 PTS_EIIA_1 phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1.
Probab=37.16 E-value=22 Score=13.69 Aligned_cols=59 Identities=24% Similarity=0.317 Sum_probs=37.8
Q ss_pred HHHCCCCCCCCEE---EEEEEEEEECCE--EEECCCCCCEEEEEE----ECCCCCCCCHHHHCCCCCEEEE
Q ss_conf 9852475468678---999999941536--998287971048866----3144454785560325988999
Q gi|254780784|r 611 RSITDVPEVNKIY---KGQVVKVMDFGA--FVHFCGARDGLVHIS----QLSTERVAKTSDVVKEGDTVWV 672 (699)
Q Consensus 611 ~~~~~~~e~g~~y---~~~v~~i~~fGa--fve~~~g~~gl~HiS----~l~~~~v~~~~d~~~~Gd~i~v 672 (699)
+.+.-.|+.|++| .|+|+.+.+-+- -++--.|.|-|+||- +|.-+ .-+-.++.||+|+.
T Consensus 32 ~G~AI~P~~~~v~AP~~G~V~~v~~T~HAigi~~~~G~eiLiHiGiDTV~L~G~---gF~~~v~~Gd~V~~ 99 (133)
T pfam00358 32 DGFAIKPSDGKVVAPVDGTIVQIFPTKHAIGIESDGGVEILIHVGIDTVKLNGE---GFESHVEEGDRVKQ 99 (133)
T ss_pred CEEEEECCCCEEEECCCEEEEEECCCCCEEEEEECCCCEEEEEECCCCEECCCC---CEEEEECCCCEECC
T ss_conf 769998479979907897999986899799999689989999986452233896---31899758999989
No 293
>PRK01123 shikimate kinase; Provisional
Probab=36.99 E-value=22 Score=13.67 Aligned_cols=56 Identities=34% Similarity=0.404 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHCCCCC-CCCCEEEEEEEEECCCCC-CCHHHHHHHHHHHHHHC-CCCC
Q ss_conf 79999999874107864-468738999853110278-52235667777987625-9502
Q gi|254780784|r 400 GHGRLARRAIHPVLPQT-AQFPYTLRIVSEITESDG-SSSMATVCGSSLALMDA-GVPI 455 (699)
Q Consensus 400 GHg~la~ral~~~~P~~-~~~p~tirv~~evl~sng-sssma~vc~~slal~da-gvp~ 455 (699)
+-.+|++|+.+.+.... ...+..|++.|+|.-+-| +||-|..+++.+||.++ |.++
T Consensus 54 ~~~~l~~~~~~~~~~~~~i~~g~~i~i~s~IP~~~GL~SSSA~a~A~i~a~~~~~~~~L 112 (283)
T PRK01123 54 ADTRLVERCVELVLERFGIDYGGTVRTESEIPVASGLKSSSAAANALVLATLDALGEKL 112 (283)
T ss_pred CCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHCCCC
T ss_conf 56389999999999862998775999955898667853789999999999999858998
No 294
>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=36.90 E-value=22 Score=13.66 Aligned_cols=62 Identities=18% Similarity=0.376 Sum_probs=32.6
Q ss_pred EEEEEEEEEECC--EEEECCCCCCEEEEE----EECCCCCCCCHHHHCCCCCEEEEEEEEE-CCCCCEEE
Q ss_conf 899999994153--699828797104886----6314445478556032598899999978-68998666
Q gi|254780784|r 623 YKGQVVKVMDFG--AFVHFCGARDGLVHI----SQLSTERVAKTSDVVKEGDTVWVKLLDF-DDRGKIKL 685 (699)
Q Consensus 623 y~~~v~~i~~fG--afve~~~g~~gl~Hi----S~l~~~~v~~~~d~~~~Gd~i~vk~~~~-d~~g~i~l 685 (699)
..|.|.++.+.| +|+.|-.+. |.+-+ .++.....+.....++.||.|.|+=.-. -++|-+.+
T Consensus 4 v~GrV~~~R~~G~l~FidLrD~~-g~iQv~~~~~~~~~~~~~~~~~~~~~gDvv~v~G~v~~t~tGel~v 72 (108)
T cd04322 4 VAGRIMSKRGSGKLSFADLQDES-GKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKTGELSI 72 (108)
T ss_pred EEEEEEEEECCCCCEEEEEEECC-CCEEEEEECCCCCHHHHHHHHHCCCCCEEEEEEEEEECCCCCEEEE
T ss_conf 99999847067982999999699-6189999756477567777763444344999997875179934999
No 295
>TIGR01436 glu_cys_lig_pln glutamate--cysteine ligase; InterPro: IPR011556 These sequences represent one of two highly dissimilar forms of glutamate--cysteine ligase (gamma-glutamylcysteine synthetase), an enzyme of glutathione biosynthesis. The other group is represented by IPR006335 from INTERPRO. This form is found in plants (with a probable transit peptide), root nodule and other bacteria, but not Escherichia coli and closely related species. ; GO: 0004357 glutamate-cysteine ligase activity, 0006750 glutathione biosynthetic process, 0009507 chloroplast.
Probab=36.89 E-value=13 Score=15.52 Aligned_cols=25 Identities=28% Similarity=0.307 Sum_probs=11.4
Q ss_pred EEEEEEC-CCCCCHHHHHHHHHHHHH
Q ss_conf 9999821-888877899999999998
Q gi|254780784|r 114 IINVMQH-DLESSPHVVSMVAASAAL 138 (699)
Q Consensus 114 v~~VLS~-D~~~dpdvlAi~aASaAL 138 (699)
+|||+|. |=....|+.-=-=+|+||
T Consensus 167 TCTvQ~N~DfsSEADMv~KFR~slAL 192 (446)
T TIGR01436 167 TCTVQANLDFSSEADMVKKFRVSLAL 192 (446)
T ss_pred HHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf 52443056634057788998776555
No 296
>PRK13926 junction RNase; Provisional
Probab=36.88 E-value=18 Score=14.35 Aligned_cols=128 Identities=15% Similarity=0.088 Sum_probs=53.3
Q ss_pred CCCCCEEEEEEEEC--CCCEEECCCCCCCC---CCC-EEEEEECCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 82354112355204--77324368500022---210-1355305443233312444324899998875316889999999
Q gi|254780784|r 144 PFEGPVVGAQVDYI--NGQYVLNPRLDEDQ---GSL-DLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEA 217 (699)
Q Consensus 144 Pf~GPVaaVRVG~i--dge~ViNPt~ee~e---sdL-DLvVAGT~d~IlMIE~~A~EVsEe~mleAI~~Ahe~Ik~iI~~ 217 (699)
||.|||-+.-|..- ..++-++-|....+ ..| +.+ --..-.+.-.+..++|+.+-.+++|...|-.. +
T Consensus 34 ~laGPvvvaaVil~~~~~~~~~~DSKkLs~kkRe~l~~~I-~~~~~~~~i~~~s~~eID~~nI~~At~~am~r------a 106 (212)
T PRK13926 34 AWAGPITVAAVILPGTPGEYPFRDSKQLSPAARERLAAKV-REVAVAWAVEHAWPEEIDRLNVLGATHAAAER------A 106 (212)
T ss_pred CCHHHHEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHH-HHHHHHHEEEEECHHHHHHHCHHHHHHHHHHH------H
T ss_conf 5534334799997886663578703539999999999999-86412331366589998750709999999999------9
Q ss_pred HHHHHHHHCCCCCCC-CC---CCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 999999838898644-74---31257999999998988888741000122489999999999730223
Q gi|254780784|r 218 ISKLAKMCAKEPIVI-DS---KDFSKLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSS 281 (699)
Q Consensus 218 Q~eL~~~~Gk~K~~~-~~---~~~~~~~~~v~~~~~~~l~~a~~i~~K~eR~~ai~~l~~ei~e~l~e 281 (699)
+..|. -++...+ .. +..-.....++.-.....-.|-.+--|..|++-+.++.++.-.+--+
T Consensus 107 i~~l~---~~~~~v~~D~~~~~~~~~~~~~~KGD~~~~~IAAASIiAKV~RD~~M~~l~~~yP~Ygf~ 171 (212)
T PRK13926 107 LARLP---PPPQALVTDYLRLRTPLPLLAPPKADALSYSVAAASLLAKTERDRLMAELDALYPGYGFA 171 (212)
T ss_pred HHHCC---CCCCEEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 98658---887679856874799988050278634433127889999999899999999878799820
No 297
>TIGR02533 type_II_gspE general secretory pathway protein E; InterPro: IPR013369 GspE, the E protein of the type II secretion system, is also referred to as the main terminal branch of the general secretion pathway. ; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex.
Probab=36.46 E-value=21 Score=13.80 Aligned_cols=53 Identities=28% Similarity=0.435 Sum_probs=32.4
Q ss_pred HHHHCCCCCCCCCCCCCE--EEEEEEECCCCCCCCEEEEEE---CCCEEEEEEEECCC
Q ss_conf 998728866588677533--787998447546670089998---79768999981686
Q gi|254780784|r 305 TVMLDKKVRMDGRDSETV--RDISAQVGLLQRTHGSSLFIR---GDTQAIVVVTLGTR 357 (699)
Q Consensus 305 ~~ILeeg~R~DGR~~dEI--RpIs~EvgvLPrvHGSALFtR---GETQaL~tvTLG~~ 357 (699)
=.|=|+..=-|||=.=-| |+|++.|..+|.-||=-+-=| =++|.|.-.+||..
T Consensus 173 LnIAEKRLPQDGRI~Lrv~Gr~~DiRVSt~Pt~fGERvVMRLLDK~~~~l~L~~LGm~ 230 (495)
T TIGR02533 173 LNIAEKRLPQDGRISLRVAGRDIDIRVSTVPTSFGERVVMRLLDKDAVRLDLEALGMS 230 (495)
T ss_pred CCHHHCCCCCCCCEEEEECCEEEEEEEEECCCCCCCEEEHHHHCHHHHHHHHHHCCCC
T ss_conf 7723217899872666673744667885305899710000011204777758864888
No 298
>PRK09281 F0F1 ATP synthase subunit alpha; Validated
Probab=36.38 E-value=12 Score=15.80 Aligned_cols=32 Identities=28% Similarity=0.456 Sum_probs=19.1
Q ss_pred CCCCCCCCCCCCH---HHHHHHHHHHCCCCCCCCC
Q ss_conf 8887357898871---4531111232126776746
Q gi|254780784|r 74 PGGYLRRESRPTE---NEILISRMIDRSIRPLFSK 105 (699)
Q Consensus 74 PGgF~kREgrpsd---~EiL~sRlIDR~lRPLFPk 105 (699)
+|.-.||-|++-+ -+=|..|++|=-=||+=-+
T Consensus 84 ~G~~V~~TG~~~~VPVG~~lLGRVvd~lG~PiDGk 118 (502)
T PRK09281 84 EGDTVKRTGRILEVPVGEALLGRVVNPLGQPIDGK 118 (502)
T ss_pred CCCEEEECCCCEEEECCHHHHCCEECCCCCCCCCC
T ss_conf 99989857982577567523033206774526899
No 299
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=36.23 E-value=23 Score=13.58 Aligned_cols=20 Identities=30% Similarity=0.472 Sum_probs=16.3
Q ss_pred HHHHHHHCCCCCCCCCCEEEEEE
Q ss_conf 77987625950225412133200
Q gi|254780784|r 444 SSLALMDAGVPISKPVAGIAMGL 466 (699)
Q Consensus 444 ~slal~dagvp~~~~VaGiamGL 466 (699)
-.|.++.-|.| |-||+++|+
T Consensus 415 ~yl~~~~yG~P---P~gG~GiGi 434 (462)
T PRK03932 415 WYLDLRRYGSV---PHSGFGLGF 434 (462)
T ss_pred HHHHHHHCCCC---CCCEEEEHH
T ss_conf 99999767999---877376779
No 300
>KOG1337 consensus
Probab=36.21 E-value=20 Score=14.03 Aligned_cols=91 Identities=8% Similarity=0.159 Sum_probs=56.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC---CEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCC
Q ss_conf 0267889999999999999987288665886775---3378799844754667008999879768999981686521223
Q gi|254780784|r 287 NEGEIVSVFEDIQAKVVRTVMLDKKVRMDGRDSE---TVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYV 363 (699)
Q Consensus 287 ~~~~i~~af~~l~k~ivR~~ILeeg~R~DGR~~d---EIRpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~i 363 (699)
+.....+++-.+....++..++.. .-.+..+ ..=|+.-..+--|.+-+..++++.+ +..++++---..-+|..
T Consensus 198 ~~~~~~w~~~~~~sr~~~~~~~~~---~~~~~~~~~~~L~P~~D~~NH~~~~~~~~~~~~d~-~~~l~~~~~v~~geevf 273 (472)
T KOG1337 198 TFSAFKWAYSIVNSRAFYLPSLQR---LTAGDPDDNEALAPLIDLLNHSPEVIKAGYNQEDE-AVELVAERDVSAGEEVF 273 (472)
T ss_pred CHHHHHHHHHHHCCHHHCCCCCCC---CCCCCCCCCHHHHHHHHHCCCCCHHHHCCCCCCCC-CEEEEEECCCCCCCEEE
T ss_conf 033333355301222102465432---46789854244414577517981432044336786-38999802467897489
Q ss_pred CCCCCCCEEEEEEEECCC
Q ss_conf 344544203587740588
Q gi|254780784|r 364 DSLSGTQRNDFMMHYNFL 381 (699)
Q Consensus 364 D~l~~~~~k~fmlHYNFP 381 (699)
-........++++||.|-
T Consensus 274 i~YG~~~N~eLL~~YGFv 291 (472)
T KOG1337 274 INYGPKSNAELLLHYGFV 291 (472)
T ss_pred EEECCCCHHHHHHHCCCC
T ss_conf 950887779999748964
No 301
>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=36.13 E-value=23 Score=13.57 Aligned_cols=59 Identities=22% Similarity=0.273 Sum_probs=37.7
Q ss_pred HHHCCCCCCCCEE---EEEEEEEEECC--EEEECCCCCCEEEEEE----ECCCCCCCCHHHHCCCCCEEEE
Q ss_conf 9852475468678---99999994153--6998287971048866----3144454785560325988999
Q gi|254780784|r 611 RSITDVPEVNKIY---KGQVVKVMDFG--AFVHFCGARDGLVHIS----QLSTERVAKTSDVVKEGDTVWV 672 (699)
Q Consensus 611 ~~~~~~~e~g~~y---~~~v~~i~~fG--afve~~~g~~gl~HiS----~l~~~~v~~~~d~~~~Gd~i~v 672 (699)
+.+.-.|+.|++| .|+|+.+.+-+ .-++-..|.|-|+||. +|.-+ .-+-.++.||+|+.
T Consensus 27 ~G~AI~P~~~~v~AP~~G~V~~v~~T~HAigi~t~~G~evLiHiGiDTV~L~G~---gF~~~v~~Gd~V~~ 94 (124)
T cd00210 27 DGFAIKPSDGKVVAPVDGTIVQIFPTKHAIGIESDSGVEILIHIGIDTVKLNGE---GFTSHVEEGQRVKQ 94 (124)
T ss_pred CEEEEECCCCEEECCCCEEEEEECCCCCEEEEEECCCCEEEEEEEECCCCCCCC---CEEEEECCCCEECC
T ss_conf 769998479989907897999986789699999689989999973042014895---31899748899989
No 302
>cd01383 MYSc_type_VIII Myosin motor domain, plant-specific type VIII myosins, a subgroup which has been associated with endocytosis, cytokinesis, cell-to-cell coupling and gating at plasmodesmata. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates f
Probab=35.46 E-value=23 Score=13.49 Aligned_cols=17 Identities=41% Similarity=0.638 Sum_probs=8.3
Q ss_pred HHHHHHHHHHHHHCCCCCC
Q ss_conf 9999999999873268823
Q gi|254780784|r 128 VVSMVAASAALMLSGLPFE 146 (699)
Q Consensus 128 vlAi~aASaAL~ISdIPf~ 146 (699)
+..++|| -|++.+|=|.
T Consensus 258 I~~ilaa--ILhLGni~F~ 274 (677)
T cd01383 258 VFAMLAA--VLWLGNVSFT 274 (677)
T ss_pred HHHHHHH--HHHHCCCCEE
T ss_conf 9999999--9831575135
No 303
>pfam03310 Cauli_DNA-bind Caulimovirus DNA-binding protein.
Probab=35.40 E-value=16 Score=14.81 Aligned_cols=15 Identities=13% Similarity=0.448 Sum_probs=11.4
Q ss_pred EEEECCCCCCCCCCC
Q ss_conf 774058875445334
Q gi|254780784|r 375 MMHYNFLPCATGEVS 389 (699)
Q Consensus 375 mlHYNFPpfsvGE~~ 389 (699)
+-.|.||.|-||-..
T Consensus 88 l~Kysypn~~vgn~~ 102 (121)
T pfam03310 88 LVKYSYPNWNVGNEE 102 (121)
T ss_pred CCCCCCCCCCCCCHH
T ss_conf 640257887878631
No 304
>cd07749 NT_Pol-beta-like_1 Nucleotidyltransferase (NT) domain of an uncharacterized subgroup of the Pol beta-like NT superfamily. The Pol beta-like NT superfamily includes DNA polymerase beta and other family X DNA Polymerases, as well as Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly(A) polymerases, terminal uridylyl transferases, Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. Proteins belonging to this subgroup are uncharacterized. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations essential for catalysis. These divalent metal ions are involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are conserved in this subgroup.
Probab=35.31 E-value=23 Score=13.48 Aligned_cols=15 Identities=33% Similarity=0.671 Sum_probs=6.8
Q ss_pred HHHHHHHHHCCCCCC
Q ss_conf 999999873268823
Q gi|254780784|r 132 VAASAALMLSGLPFE 146 (699)
Q Consensus 132 ~aASaAL~ISdIPf~ 146 (699)
.++|++|++-++|.+
T Consensus 22 v~gS~~l~~~Gl~~~ 36 (156)
T cd07749 22 LTGSLSFALQGVPVE 36 (156)
T ss_pred EHHHHHHHHCCCCCC
T ss_conf 313588997599999
No 305
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=35.29 E-value=23 Score=13.47 Aligned_cols=22 Identities=27% Similarity=0.392 Sum_probs=9.7
Q ss_pred CCCCCCCCHHHHCCCCCEEEEE
Q ss_conf 1444547855603259889999
Q gi|254780784|r 652 LSTERVAKTSDVVKEGDTVWVK 673 (699)
Q Consensus 652 l~~~~v~~~~d~~~~Gd~i~vk 673 (699)
+.|..++++.-.+++||.|+|+
T Consensus 212 vN~~~v~~~s~~v~~gDiiSvR 233 (257)
T TIGR03069 212 LNWKTVTQPSRELKVGDRLQLR 233 (257)
T ss_pred ECCEEECCCCCCCCCCCEEEEE
T ss_conf 8999905787566899999990
No 306
>cd03135 GATase1_DJ-1 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1. Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1. DJ-1 is involved in multiple physiological processes including cancer, Parkinson's disease and male fertility. It is unclear how DJ-1 functions in these. DJ-1 has been shown to possess chaperone activity. DJ-1 is preferentially expressed in the testis and moderately in other tissues; it is induced together with genes involved in oxidative stress response. The Drosophila homologue (DJ-1A) plays an essential role in oxidative stress response and neuronal maintenance. Inhibition of DJ-1A function through RNAi, results in the cellular accumulation of reactive oxygen species, organismal hypersensitivity to oxidative stress, and dysfunction and degeneration of dopaminergic and photoreceptor neurons. DJ-1 has lacks enzymatic activity and the catalytic triad of typical GATase1 domains, however it does contain the highly
Probab=35.15 E-value=13 Score=15.52 Aligned_cols=18 Identities=28% Similarity=0.578 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHHCCCC
Q ss_conf 235667777987625950
Q gi|254780784|r 437 SMATVCGSSLALMDAGVP 454 (699)
Q Consensus 437 sma~vc~~slal~dagvp 454 (699)
..++||.|+..|..||+=
T Consensus 95 ~i~aiC~G~~~La~agll 112 (163)
T cd03135 95 LIAAICAAPAVLAKAGLL 112 (163)
T ss_pred EEEEECHHHHHHHHCCCC
T ss_conf 479864548999986998
No 307
>TIGR02945 SUF_assoc FeS assembly SUF system protein; InterPro: IPR014291 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry is a subset of the larger DUF59 family. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here are all found as part of the FeS assembly SUF system locus, in a subset of SUF-positive proteobacteria. .
Probab=34.98 E-value=24 Score=13.44 Aligned_cols=31 Identities=29% Similarity=0.383 Sum_probs=19.6
Q ss_pred EEEEECCEEEEE-----------EECCHHHHHHHHHHHHHHC
Q ss_conf 899808808999-----------9689899999999999852
Q gi|254780784|r 584 KVNIDDDGTVKI-----------ASSSLAEIEAAREMIRSIT 614 (699)
Q Consensus 584 ~i~i~d~g~v~i-----------~~~~~~~~~~a~~~i~~~~ 614 (699)
+|+|+||++|.| .+.=...++.|+..|.++.
T Consensus 27 ~i~i~Dd~~V~I~MTLTaPgCPvAgemP~~V~~aV~~v~GV~ 68 (96)
T TIGR02945 27 KIEISDDRHVHIDMTLTAPGCPVAGEMPGWVEDAVGQVPGVS 68 (96)
T ss_pred EEEECCCCEEEEEEEECCCCCCCCCCCHHHHHHHHCCCCCCC
T ss_conf 887658986788775178568422452268899733388985
No 308
>pfam05314 Baculo_ODV-E27 Baculovirus occlusion-derived virus envelope protein EC27. This family consists of several baculovirus occlusion-derived virus envelope proteins (EC27 or E27). The ODV-E27 protein has distinct functional characteristics compared to cellular and viral cyclins. Depending on the cdk protein, and perhaps other viral or cellular proteins yet to be described, the kinase-EC27 complex may have either cyclin B- or D-like activity.
Probab=34.95 E-value=11 Score=16.07 Aligned_cols=21 Identities=29% Similarity=0.389 Sum_probs=14.8
Q ss_pred CCCCCHHHHHHHHHHHHHHHC
Q ss_conf 888877899999999998732
Q gi|254780784|r 121 DLESSPHVVSMVAASAALMLS 141 (699)
Q Consensus 121 D~~~dpdvlAi~aASaAL~IS 141 (699)
|....-++.++.=||+|.-=.
T Consensus 72 ~rn~~~~I~siV~~SLgFVhN 92 (280)
T pfam05314 72 DRNATREIVSIVYASLGFVHN 92 (280)
T ss_pred CCCCHHHHHHHHHHHHHHHHC
T ss_conf 885178889999887676751
No 309
>COG1159 Era GTPase [General function prediction only]
Probab=34.88 E-value=23 Score=13.53 Aligned_cols=15 Identities=33% Similarity=0.538 Sum_probs=8.2
Q ss_pred EEEEECCCCHHHHHH
Q ss_conf 000037860779989
Q gi|254780784|r 563 IRNVIGMGGKVIRGI 577 (699)
Q Consensus 563 i~~~iG~gG~~ik~i 577 (699)
.+-+||.+|..||.|
T Consensus 241 K~IiIGk~G~~iK~I 255 (298)
T COG1159 241 KGIIIGKNGAMIKKI 255 (298)
T ss_pred CCEEECCCCHHHHHH
T ss_conf 435987881999999
No 310
>COG4130 Predicted sugar epimerase [Carbohydrate transport and metabolism]
Probab=34.71 E-value=24 Score=13.41 Aligned_cols=10 Identities=40% Similarity=0.634 Sum_probs=6.0
Q ss_pred EEECCCCCCC
Q ss_conf 7405887544
Q gi|254780784|r 376 MHYNFLPCAT 385 (699)
Q Consensus 376 lHYNFPpfsv 385 (699)
=-|.|-||+.
T Consensus 239 Gp~sFePFa~ 248 (272)
T COG4130 239 GPYSFEPFAS 248 (272)
T ss_pred CCCCCCCCHH
T ss_conf 8624574166
No 311
>TIGR01028 S7_S5_E_A ribosomal protein S7; InterPro: IPR005716 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 of 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 family describes the members from the eukaryotic cytosol and the Archaea of the family that includes ribosomal protein S7 of bacteria and S5 of eukaryotes.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=34.70 E-value=17 Score=14.57 Aligned_cols=45 Identities=20% Similarity=0.434 Sum_probs=20.9
Q ss_pred CCCCCCCCCCCC-CCHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEE
Q ss_conf 678887357898-871453111123212677674688688378999
Q gi|254780784|r 72 KIPGGYLRRESR-PTENEILISRMIDRSIRPLFSKCYKNETQVIIN 116 (699)
Q Consensus 72 kIPGgF~kREgr-psd~EiL~sRlIDR~lRPLFPkgf~~evQIv~~ 116 (699)
|+.|.|+|||-. .+-+=+.+-|+|--++-=.=-..=.|++||+++
T Consensus 70 kvaghf~Rre~n~l~GKK~~A~~IVk~AFeII~~~T~~NPiQVLV~ 115 (206)
T TIGR01028 70 KVAGHFMRRERNSLNGKKLKAYKIVKEAFEIIEKRTKKNPIQVLVD 115 (206)
T ss_pred EEHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEE
T ss_conf 0011212023324540268899999999999875508996489845
No 312
>KOG0246 consensus
Probab=34.11 E-value=18 Score=14.38 Aligned_cols=26 Identities=23% Similarity=0.207 Sum_probs=18.5
Q ss_pred EEEEECCCEEEEEEEECCCCCCCCCC
Q ss_conf 89998797689999816865212233
Q gi|254780784|r 339 SLFIRGDTQAIVVVTLGTREDEQYVD 364 (699)
Q Consensus 339 ALFtRGETQaL~tvTLG~~~d~Q~iD 364 (699)
-.|.-|||-+=-|-|.|..-....-|
T Consensus 294 TCFAYGQTGSGKT~TMggdfsgk~q~ 319 (676)
T KOG0246 294 TCFAYGQTGSGKTYTMGGDFSGKAQD 319 (676)
T ss_pred EEEEECCCCCCCEEECCCCCCCCCCC
T ss_conf 45651257887415514666764433
No 313
>PRK13237 tyrosine phenol-lyase; Provisional
Probab=34.10 E-value=22 Score=13.64 Aligned_cols=73 Identities=23% Similarity=0.278 Sum_probs=44.1
Q ss_pred CCCCEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHH
Q ss_conf 54420358774058875445334556765024679999999874107864468738999853110278522356677779
Q gi|254780784|r 367 SGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSL 446 (699)
Q Consensus 367 ~~~~~k~fmlHYNFPpfsvGE~~~~~~~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~sl 446 (699)
...-+....+.+-||.| ||.+.|++. +|| ..|.-++ .+++- +.+...|--=-=
T Consensus 278 ~~~~~~~~i~~EGf~TY--------GGlagRDme--AlA-~GL~E~~-de~yl---------------~~Ri~qv~yl~~ 330 (459)
T PRK13237 278 FQEAKELVVVYEGMPSY--------GGMAGRDME--AMA-IGIEESV-QDDYI---------------RHRIGQVRYLGE 330 (459)
T ss_pred HHHHHHHEEECCCCCCC--------CCCCHHHHH--HHH-CCHHHHC-CHHHH---------------HHHHHHHHHHHH
T ss_conf 99998551120587554--------562264699--996-3437543-67999---------------988999999999
Q ss_pred HHHHCCCCCCCCCCEEEEEE
Q ss_conf 87625950225412133200
Q gi|254780784|r 447 ALMDAGVPISKPVAGIAMGL 466 (699)
Q Consensus 447 al~dagvp~~~~VaGiamGL 466 (699)
.|.+||||+..|+.|-|+=+
T Consensus 331 ~L~~~GVPvv~P~GGHav~i 350 (459)
T PRK13237 331 KLLAAGVPIVEPVGGHAVFL 350 (459)
T ss_pred HHHHCCCCEECCCCCEEEEE
T ss_conf 99987997036898528997
No 314
>COG2893 ManX Phosphotransferase system, mannose/fructose-specific component IIA [Carbohydrate transport and metabolism]
Probab=34.06 E-value=24 Score=13.33 Aligned_cols=94 Identities=21% Similarity=0.320 Sum_probs=53.0
Q ss_pred HHHHHHHHHHH---HHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEECCEEEE
Q ss_conf 67999999987---410786446873899985311027852235667777987625950225412133200440882899
Q gi|254780784|r 399 IGHGRLARRAI---HPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFII 475 (699)
Q Consensus 399 iGHg~la~ral---~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp~~~~VaGiamGLi~~~~~~~i 475 (699)
.+||.+|+--+ +-++. .+-.++.++=..+.|++......-..-++..|. ++...+
T Consensus 7 ~tHG~~A~~l~~s~emi~G----~q~nv~~v~~~~~~~~~~~l~~~~~~~~~~~d~------------------~eevl~ 64 (143)
T COG2893 7 ATHGRFAEGLLNSLEMILG----EQENVEAVDFVPGEDSEDLLTKQIAAAIAALDS------------------GEGVLF 64 (143)
T ss_pred EECHHHHHHHHHHHHHHHC----CHHCEEEEEEECCCCHHHHHHHHHHHHHHHCCC------------------CCCEEE
T ss_conf 8277899999999998858----673238998535887277999999998720689------------------885799
Q ss_pred EEECCCCCCCCCCCCEEEEECCCCCEEEECC-CCCCCCCHHHHHHHHHH
Q ss_conf 8631442201365510010055651244324-53655688999999999
Q gi|254780784|r 476 LSDISGDEDHLGHMDFKVAGTDSGITAMQMD-MKIGGISENIMVMALQQ 523 (699)
Q Consensus 476 LtDI~G~ED~~GdMDFKvaGT~~GiTa~QmD-iK~~gi~~~il~~al~~ 523 (699)
||||.| ---|.+|-+- -.--=. -=+.|+++.+|-+++.-
T Consensus 65 ltDl~G------GSP~N~A~~l---~~~~~~~~viaGvNLPmLle~~~~ 104 (143)
T COG2893 65 LTDLFG------GSPFNVASRL---AMEGPRVEVIAGVNLPMLLEALLA 104 (143)
T ss_pred EEECCC------CCHHHHHHHH---HHHCCCCEEEECCCHHHHHHHHHC
T ss_conf 985688------9876999999---851998269864889999999846
No 315
>pfam07867 DUF1654 Protein of unknown function (DUF1654). This family consists of proteins from the Pseudomonadaceae.
Probab=33.70 E-value=25 Score=13.29 Aligned_cols=56 Identities=23% Similarity=0.305 Sum_probs=31.8
Q ss_pred HHHCCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEE
Q ss_conf 984356674332244875799997711500003786077998999868889980880899996
Q gi|254780784|r 535 MSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIAS 597 (699)
Q Consensus 535 m~~~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~ 597 (699)
.++.|..|+.+-. -....++-|-+--. -=...+..|.|.-|+.++.+|||.|.|+=
T Consensus 12 vq~~InsP~AQ~~---r~v~I~Rl~~e~~~----~We~vle~i~etdgi~l~~~dDGsV~i~W 67 (73)
T pfam07867 12 VQKMINSPTAQKQ---RWVTIHRLDDEGDD----EWEEVLEEIAETDGIDLAFNDDGSVTIRW 67 (73)
T ss_pred HHHHHCCHHHHHE---EEEEEEECCCCCHH----HHHHHHHHHHCCCCCEEEECCCCEEEEEE
T ss_conf 9999769576450---28999977999888----99999999835678057755898499988
No 316
>pfam01965 DJ-1_PfpI DJ-1/PfpI family. The family includes the protease PfpI. This domain is also found in transcriptional regulators.
Probab=33.51 E-value=13 Score=15.53 Aligned_cols=15 Identities=33% Similarity=0.713 Sum_probs=6.4
Q ss_pred HHHHHHHHHHHHHCC
Q ss_conf 356677779876259
Q gi|254780784|r 438 MATVCGSSLALMDAG 452 (699)
Q Consensus 438 ma~vc~~slal~dag 452 (699)
+|+||.|++.|..+|
T Consensus 70 i~aiC~g~~~La~~g 84 (141)
T pfam01965 70 IAAICHGPVLLAAAG 84 (141)
T ss_pred EEEECHHHHHHHHCC
T ss_conf 999876689999869
No 317
>cd00617 Tnase_like Tryptophanase family (Tnase). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to tryptophanase (Tnase) and tyrosine phenol-lyase (TPL). Tnase and TPL are active as tetramers and catalyze beta-elimination reactions. Tnase catalyzes degradation of L-tryptophan to yield indole, pyruvate and ammonia and TPL catalyzes degradation of L-tyrosine to yield phenol, pyruvate and ammonia.
Probab=33.47 E-value=23 Score=13.50 Aligned_cols=74 Identities=24% Similarity=0.332 Sum_probs=43.9
Q ss_pred CCCCCEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHH
Q ss_conf 45442035877405887544533455676502467999999987410786446873899985311027852235667777
Q gi|254780784|r 366 LSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSS 445 (699)
Q Consensus 366 l~~~~~k~fmlHYNFPpfsvGE~~~~~~~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~s 445 (699)
+..+.+.+..+..-||.| ||.+.|++ -+||. .|.-++. +.| =+.+...|-==-
T Consensus 252 l~~~~~~~~i~~EGf~TY--------GGlaGRD~--eAlA~-GL~E~~d----~~y------------l~~Ri~qv~yL~ 304 (431)
T cd00617 252 LYEEARQRVVLYEGFVTY--------GGMAGRDM--EALAQ-GLREAVE----EDY------------LRHRVEQVRYLG 304 (431)
T ss_pred HHHHHHHHCCCCCCCCCC--------CCCCHHHH--HHHHC-CHHHHCC----HHH------------HHHHHHHHHHHH
T ss_conf 999997543200587443--------56325349--99865-4075436----799------------997799999999
Q ss_pred HHHHHCCCCCCCCCCEEEEEE
Q ss_conf 987625950225412133200
Q gi|254780784|r 446 LALMDAGVPISKPVAGIAMGL 466 (699)
Q Consensus 446 lal~dagvp~~~~VaGiamGL 466 (699)
=.|.+||||+..|+.|-|+=+
T Consensus 305 ~~L~~~GvPvv~P~GGHav~i 325 (431)
T cd00617 305 DRLDEAGVPIVEPAGGHAVFI 325 (431)
T ss_pred HHHHHCCCCEECCCCCEEEEE
T ss_conf 999988996666897438997
No 318
>cd03427 MTH1 MutT homolog-1 (MTH1) is a member of the Nudix hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the incorporation of such oxygen radicals during replication. This is an important step in the repair mechanism in genomic and mitochondrial DNA. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for activity, and contain the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. MTH1 is predominantly localized in the cytoplasm and mitochondria. Structurally, this enzyme adopts a similar fold to MutT despite low sequence similarity outside the conserved nudix motif. The most distinctive structural difference between MutT and MTH1 is the presence of a beta-hairpin, which is absent in MutT. This results in a m
Probab=33.17 E-value=25 Score=13.22 Aligned_cols=26 Identities=38% Similarity=0.475 Sum_probs=20.5
Q ss_pred EEEEECCCCHH----------HHHHHHHHCCEEEEE
Q ss_conf 00003786077----------998999868889980
Q gi|254780784|r 563 IRNVIGMGGKV----------IRGIVEQTGAKVNID 588 (699)
Q Consensus 563 i~~~iG~gG~~----------ik~i~~~~~~~i~i~ 588 (699)
.|.--.||||+ +|++.||||..++..
T Consensus 25 ~G~W~~PGGkvE~gEt~~~a~~REl~EEtGl~v~~~ 60 (137)
T cd03427 25 WGGWNGPGGKVEPGETPEECAIRELKEETGLTIDNL 60 (137)
T ss_pred CCEEECCEEECCCCCCHHHHHHHHHHHHHCEEEEEE
T ss_conf 995979556567997999999999989869288713
No 319
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=33.14 E-value=25 Score=13.22 Aligned_cols=70 Identities=23% Similarity=0.336 Sum_probs=41.5
Q ss_pred EEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCCCCHHHH-CCCCCE
Q ss_conf 0899996898999999999998524754686789999999415369982879710488663144454785560-325988
Q gi|254780784|r 591 GTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDV-VKEGDT 669 (699)
Q Consensus 591 g~v~i~~~~~~~~~~a~~~i~~~~~~~e~g~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v~~~~d~-~~~Gd~ 669 (699)
|.|.|=|.....+..|+.-+..+. | . ..|++.++|+.+---.+.... +++||+
T Consensus 47 GYV~VEa~~~~~v~~~i~gi~~v~----------g----~------------~p~~v~~~Ei~~~L~~~~~~~~i~~G~~ 100 (153)
T PRK08559 47 GYVFVEAESKGAVEEAIRGIPHVR----------G----V------------VPGEISFEEVEHFLKPKPIVEGIKEGDI 100 (153)
T ss_pred CEEEEEECCHHHHHHHHHCCCCEE----------E----E------------CCCCCCHHHHHHHCCCCCCCCCCCCCCE
T ss_conf 179999567889999984776468----------5----6------------4776798999876375765234689999
Q ss_pred EEE----------EEEEECC-CCCEEEE
Q ss_conf 999----------9997868-9986668
Q gi|254780784|r 670 VWV----------KLLDFDD-RGKIKLS 686 (699)
Q Consensus 670 i~v----------k~~~~d~-~g~i~lS 686 (699)
|.| ++..+|+ ++++.++
T Consensus 101 V~v~~Gpfkg~~a~V~~Vd~~k~~vtV~ 128 (153)
T PRK08559 101 VELIAGPFKGEKARVVRVDESKEEVTVE 128 (153)
T ss_pred EEEECCCCCCCCEEEEEECCCCCEEEEE
T ss_conf 9991357699617999981668899999
No 320
>cd03139 GATase1_PfpI_2 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. PfpI is an ATP-independent intracellular proteases which may hydrolyze small peptides to provide a nutritional source. Only Cys of the catalytic triad typical of GATase1 domains is conserved in this group. This Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.
Probab=32.63 E-value=14 Score=15.15 Aligned_cols=20 Identities=30% Similarity=0.544 Sum_probs=15.1
Q ss_pred CCHHHHHHHHHHHHHHCCCC
Q ss_conf 52235667777987625950
Q gi|254780784|r 435 SSSMATVCGSSLALMDAGVP 454 (699)
Q Consensus 435 sssma~vc~~slal~dagvp 454 (699)
+...+++|+|++-|..||+=
T Consensus 94 g~~i~siCtGa~~LA~aGlL 113 (183)
T cd03139 94 AKYVTSVCTGALLLAAAGLL 113 (183)
T ss_pred CCEEEEECHHHHHHHHCCCC
T ss_conf 98389873767999974776
No 321
>pfam07126 DUF1379 Protein of unknown function (DUF1379). This family consists of several hypothetical bacterial proteins of around 180 residues in length. The function of this family is unknown.
Probab=32.54 E-value=19 Score=14.16 Aligned_cols=72 Identities=17% Similarity=0.220 Sum_probs=44.1
Q ss_pred EEECCCEEEEEEEECCCCCCCCCCC--CCEE-------EEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCC
Q ss_conf 9978948999997278888777735--4068-------665232013367888735789887145311112321267767
Q gi|254780784|r 33 ATYGETVVLATVVYDRSLKDGQDFF--PLTV-------NYQERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLF 103 (699)
Q Consensus 33 v~~G~T~VLaTv~~~~~~~~~~dFf--PLtV-------dY~Ek~yAaGkIPGgF~kREgrpsd~EiL~sRlIDR~lRPLF 103 (699)
+..||.++..|-...|--.+.. |- +.+| .|.|+... ..+.. --.-.-+|.+=..-|=++|+.
T Consensus 2 LdLgd~M~F~t~~~~k~L~~~a-~~~~~FsvdDAa~Y~~~~E~~~~-l~ls~-------~~~~el~LNA~aA~rF~KP~m 72 (154)
T pfam07126 2 LDLGDGMVFRTPYKAKMLVPDA-FKEQEFSVEDAALYQQFKEQLAS-LDLSD-------AQRVQLALNATAAKRFLKPQM 72 (154)
T ss_pred CCCCCCCEEECCCCHHHCCHHH-CCCCCCCHHHHHHHHHHHHHHHC-CCCCH-------HHHHHHHHHHHHHHHHCCCCC
T ss_conf 6467998897678613288524-04788678899999999999843-89988-------999999999999998669988
Q ss_pred CCCCCCCEEE
Q ss_conf 4688688378
Q gi|254780784|r 104 SKCYKNETQV 113 (699)
Q Consensus 104 Pkgf~~evQI 113 (699)
||.|++++|-
T Consensus 73 PKSW~F~~~~ 82 (154)
T pfam07126 73 PKSWFFDTSD 82 (154)
T ss_pred CCCCCEECCC
T ss_conf 9746453268
No 322
>PRK00089 era GTP-binding protein Era; Reviewed
Probab=32.42 E-value=26 Score=13.13 Aligned_cols=44 Identities=18% Similarity=0.347 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHCCCCCCHHCCHHHHH-HHHHHHHHHHHHHHHHC
Q ss_conf 999999999973022310000026788-99999999999999872
Q gi|254780784|r 266 KQIDDLKKKMVSYFSSEHSSWNEGEIV-SVFEDIQAKVVRTVMLD 309 (699)
Q Consensus 266 ~ai~~l~~ei~e~l~ee~~~~~~~~i~-~af~~l~k~ivR~~ILe 309 (699)
..++.+.+.+.+.+.+....+....+. .-...+..+++|+.+++
T Consensus 159 ~gi~~L~~~l~~~lp~~~~~y~~d~~Td~~~~~~v~EiIREki~~ 203 (296)
T PRK00089 159 DNVDELLDLIAKYLPEGPPLYPEDQITDRPERFLAAEIIREKILR 203 (296)
T ss_pred CCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 898999999998679886568730145784889999999999999
No 323
>PRK04151 IMP cyclohydrolase; Provisional
Probab=32.38 E-value=26 Score=13.13 Aligned_cols=94 Identities=17% Similarity=0.224 Sum_probs=56.2
Q ss_pred CEEEEECCCCCCCCCCCCCCCCC---CCCCHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEEEECCCCCCHHHHHHHHHH
Q ss_conf 06866523201336788873578---988714531111232126776746886883789999821888877899999999
Q gi|254780784|r 59 LTVNYQERTYAVGKIPGGYLRRE---SRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSMVAAS 135 (699)
Q Consensus 59 LtVdY~Ek~yAaGkIPGgF~kRE---grpsd~EiL~sRlIDR~lRPLFPkgf~~evQIv~~VLS~D~~~dpdvlAi~aAS 135 (699)
|.-||+---|-.-||-|=.-+.+ |..++.+++..++-=..=-| ..++| --.|.-.+-+.-+-.+..
T Consensus 98 lamDYEkDdy~TPRIA~vv~~~~aylG~V~~d~l~V~~v~l~~ge~----------~~vat-Ye~~~~~~~~~~~~~aee 166 (199)
T PRK04151 98 LAMDYEKDDYNTPRIAGVVTGDGAYLGIVTDDDLRVRKVELEDGEA----------YLVST-YEKTEPEAISLDAETAEE 166 (199)
T ss_pred HHCCCCCCCCCCCCEEEEECCCCEEEEEEECCCEEEEEEECCCCCE----------EEEEE-ECCCCCCCEEECCCCHHH
T ss_conf 5300455679998589998699479999851618999960579937----------99999-437898404662799999
Q ss_pred HHHHHCCCCCCCCEEEEEEEECCCCEEE
Q ss_conf 9987326882354112355204773243
Q gi|254780784|r 136 AALMLSGLPFEGPVVGAQVDYINGQYVL 163 (699)
Q Consensus 136 aAL~ISdIPf~GPVaaVRVG~idge~Vi 163 (699)
+|-.+=+.+|.-||.|+-+-..+|.|-+
T Consensus 167 ~a~~i~~~~fEhpV~aa~a~~~~~~~~l 194 (199)
T PRK04151 167 AAKFVYDLEFEHPVCAAGAVHDGDGFEL 194 (199)
T ss_pred HHHHHHCCCCCCCEEEEEEEECCCCEEE
T ss_conf 9998755546673679999981893788
No 324
>cd03316 MR_like Mandelate racemase (MR)-like subfamily of the enolase superfamily. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues, a Lys-X-Lys motif and a conserved histidine-aspartate dyad. Members of the MR subgroup are mandelate racemase, D-glucarate/L-idarate dehydratase (GlucD), D-altronate/D-mannonate dehydratase , D-galactonate dehydratase (GalD) , D-gluconate dehydratase (GlcD), and L-rhamnonate dehydratase (RhamD).
Probab=32.37 E-value=21 Score=13.77 Aligned_cols=93 Identities=19% Similarity=0.204 Sum_probs=47.7
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCC-CCCCCCEEEEEEEEECCEEEEEEECCCCCCCCCCCCEEEEECCCCCEEEECCC-CC
Q ss_conf 27852235667777987625950-22541213320044088289986314422013655100100556512443245-36
Q gi|254780784|r 432 SDGSSSMATVCGSSLALMDAGVP-ISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDM-KI 509 (699)
Q Consensus 432 sngsssma~vc~~slal~dagvp-~~~~VaGiamGLi~~~~~~~iLtDI~G~ED~~GdMDFKvaGT~~GiTa~QmDi-K~ 509 (699)
+|++=+....-.-.=+|-+.++- +-.|+..=..--...- .-..-+-|...|..++-.||+=+=..+.+..+|.|+ |+
T Consensus 196 aN~~~~~~~A~~~~~~l~~~~l~~iEqP~~~~d~~~~~~l-~~~~~~pI~~~Es~~~~~~~~~~i~~~a~di~~~d~~~~ 274 (357)
T cd03316 196 ANGRWDLAEAIRLARALEEYDLFWFEEPVPPDDLEGLARL-RQATSVPIAAGENLYTRWEFRDLLEAGAVDIIQPDVTKV 274 (357)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH-HHCCCCCEEECCCCCCHHHHHHHHHCCCCCEEEECCCCC
T ss_conf 7655579999999998865446650589895579999999-862899688178878878888888707776376267446
Q ss_pred CCCCHHHHHHHHHHHHHHHHH
Q ss_conf 556889999999999999999
Q gi|254780784|r 510 GGISENIMVMALQQAKRGRLH 530 (699)
Q Consensus 510 ~gi~~~il~~al~~A~~gr~~ 530 (699)
+||+ ++++.|.-++.+
T Consensus 275 GGit-----~~~~i~~~A~~~ 290 (357)
T cd03316 275 GGIT-----EAKKIAALAEAH 290 (357)
T ss_pred CCHH-----HHHHHHHHHHHC
T ss_conf 9879-----999999999986
No 325
>cd03140 GATase1_PfpI_3 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. PfpI is an ATP-independent intracellular proteases which may hydrolyze small peptides to provide a nutritional source. Only Cys of the catalytic triad typical of GATase1 domains is conserved in this group. This Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.
Probab=31.89 E-value=13 Score=15.56 Aligned_cols=20 Identities=40% Similarity=0.787 Sum_probs=11.4
Q ss_pred CCHHHHHHHHHHHHHHCCCC
Q ss_conf 52235667777987625950
Q gi|254780784|r 435 SSSMATVCGSSLALMDAGVP 454 (699)
Q Consensus 435 sssma~vc~~slal~dagvp 454 (699)
+...|+||+|.+.|..||+=
T Consensus 91 gk~iaaIC~g~~vLa~aGlL 110 (170)
T cd03140 91 GKPVAAICGATLALARAGLL 110 (170)
T ss_pred CCCEEEECHHHHHHHHCCCC
T ss_conf 99099986558999985986
No 326
>pfam12098 DUF3574 Protein of unknown function (DUF3574). This family of proteins is functionally uncharacterized. This protein is found in bacteria and viruses. Proteins in this family are typically between 144 to 163 amino acids in length. This protein has a conserved TPRF sequence motif.
Probab=31.76 E-value=26 Score=13.06 Aligned_cols=24 Identities=25% Similarity=0.459 Sum_probs=19.9
Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 98871453111123212677674688
Q gi|254780784|r 82 SRPTENEILISRMIDRSIRPLFSKCY 107 (699)
Q Consensus 82 grpsd~EiL~sRlIDR~lRPLFPkgf 107 (699)
|.-||.|- .+-+|+-+-|-||+||
T Consensus 15 g~Vs~~~w--~~F~~~~VtPrFpdGl 38 (104)
T pfam12098 15 PGVSEAEW--QRFLDEEVTPRFPDGL 38 (104)
T ss_pred CCCCHHHH--HHHHHHCCCCCCCCCE
T ss_conf 95399999--9999840566789970
No 327
>TIGR02406 ectoine_EctA L-2,4-diaminobutyric acid acetyltransferase; InterPro: IPR012772 This enzyme family is the EctA of ectoine biosynthesis. Ectoine is a compatible solute, analogous to trehalose, betaines, etc., found often in halotolerant organisms. EctA is L-2,4-diaminobutyric acid acetyltransferase, also called DABA acetyltransferase.; GO: 0008415 acyltransferase activity, 0019491 ectoine biosynthetic process.
Probab=31.64 E-value=26 Score=13.04 Aligned_cols=47 Identities=23% Similarity=0.387 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHHHHHHHCCCC--CCCCCEEEE-EEEEECCCCCCCHHHHHHHHHHHHHHC
Q ss_conf 502467999999987410786--446873899-985311027852235667777987625
Q gi|254780784|r 395 SRREIGHGRLARRAIHPVLPQ--TAQFPYTLR-IVSEITESDGSSSMATVCGSSLALMDA 451 (699)
Q Consensus 395 ~RREiGHg~la~ral~~~~P~--~~~~p~tir-v~~evl~sngsssma~vc~~slal~da 451 (699)
+-|..||| ||.|.|..++-- -+.-.|.|. |...|+.+|- +|=||+.+
T Consensus 75 ~~~~RG~G-LA~rll~all~R~~~~~v~~~I~~~EtTiTPdN~---------AS~aLF~~ 124 (162)
T TIGR02406 75 DPKARGKG-LASRLLEALLERVALERVRHCIQAVETTITPDNE---------ASRALFKK 124 (162)
T ss_pred CCCCCCCH-HHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCHH---------HHHHHHHH
T ss_conf 71314316-8999999976103331379821046621076666---------89999998
No 328
>PRK12450 foldase protein PrsA; Reviewed
Probab=31.61 E-value=26 Score=13.04 Aligned_cols=80 Identities=6% Similarity=0.113 Sum_probs=50.3
Q ss_pred EEEEECC-CCHHHHHCCCCCCCHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 3553054-432333124443248999988753---168899999999999998388986447431257999999998988
Q gi|254780784|r 176 LFVSGTQ-DAVLMVELEANQLSEDVVLDAIIF---GHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIKED 251 (699)
Q Consensus 176 LvVAGT~-d~IlMIE~~A~EVsEe~mleAI~~---Ahe~Ik~iI~~Q~eL~~~~Gk~K~~~~~~~~~~~~~~v~~~~~~~ 251 (699)
|--||+. +.-.-+..-+..|+++++.+.+.- |+..++.++ .++-|.++.|.. +.....+..++...+-|++.
T Consensus 20 LaAC~s~~~~~~v~t~kgg~IT~~efy~~~K~t~~gq~~L~~mi-~~KvLe~kYg~k---VsdkeVd~~~~~~k~qyG~~ 95 (309)
T PRK12450 20 LSACQSSHNNTKLVSMKGDTITVSDFYNETKNTELAQKAMLSLV-ISRVFETQYANK---VSDKEVEKAYKQTADQYGTS 95 (309)
T ss_pred HHHHCCCCCCCEEEEECCCCCCHHHHHHHHHCCCHHHHHHHHHH-HHHHHHHHHCCC---CCHHHHHHHHHHHHHHHHHH
T ss_conf 98605899983689835992409999999853415899999999-999999985351---78899999999999998689
Q ss_pred HHHHHHCC
Q ss_conf 88874100
Q gi|254780784|r 252 LRVSCFIP 259 (699)
Q Consensus 252 l~~a~~i~ 259 (699)
+..++...
T Consensus 96 F~~~L~q~ 103 (309)
T PRK12450 96 FKTVLAQS 103 (309)
T ss_pred HHHHHHHC
T ss_conf 99999987
No 329
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=31.46 E-value=26 Score=13.02 Aligned_cols=91 Identities=18% Similarity=0.299 Sum_probs=50.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHH----HC---CEEEE
Q ss_conf 999999999999999999999843566743322448757999977115000037860779989998----68---88998
Q gi|254780784|r 515 NIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQ----TG---AKVNI 587 (699)
Q Consensus 515 ~il~~al~~A~~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~----~~---~~i~i 587 (699)
..+...+..+.- |.++-....++- -.+-++.. .|.-..+.|...+=|.+||.+|.+|+.|.+. |+ +.|+|
T Consensus 6 ~fi~~~~~~~~I-reyl~k~l~~Ag-is~IeIeR-t~~~~~I~I~tarPG~vIGr~G~~i~~L~~~L~k~~~~~~~~I~V 82 (225)
T PRK04191 6 KFVQEGVKKTLI-DEYLAKELERAG-YGGMEIKK-TPLGTRITIYAERPGMVIGRGGKTIRELTETLEKKFGLENPQIDV 82 (225)
T ss_pred HHHHHHHHHHHH-HHHHHHHHHHCC-CCEEEEEE-CCCCEEEEEEECCCCEEECCCHHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf 999830289999-999998777678-54599998-689469999948985155578377999999999983999744999
Q ss_pred ECCEEEEEEECCHHHHHHHHHHHHHH
Q ss_conf 08808999968989999999999985
Q gi|254780784|r 588 DDDGTVKIASSSLAEIEAAREMIRSI 613 (699)
Q Consensus 588 ~d~g~v~i~~~~~~~~~~a~~~i~~~ 613 (699)
. .|--|+.++.--|...-..|
T Consensus 83 ~-----EV~~P~l~A~lvAe~IA~qL 103 (225)
T PRK04191 83 K-----EVENPELNARVVAFRIANAL 103 (225)
T ss_pred E-----EEECCCCCHHHHHHHHHHHH
T ss_conf 9-----95187748899999999998
No 330
>cd04690 Nudix_Hydrolase_31 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=31.45 E-value=26 Score=13.02 Aligned_cols=16 Identities=31% Similarity=0.547 Sum_probs=9.2
Q ss_pred HHHHHHHHCCEEEEEC
Q ss_conf 9989998688899808
Q gi|254780784|r 574 IRGIVEQTGAKVNIDD 589 (699)
Q Consensus 574 ik~i~~~~~~~i~i~d 589 (699)
+|++.||||+.++...
T Consensus 43 ~REl~EE~Gl~v~~~~ 58 (118)
T cd04690 43 IRELSEELGLDLDPDS 58 (118)
T ss_pred HHHHHHHHCCEEECCE
T ss_conf 9999897594986020
No 331
>pfam00245 Alk_phosphatase Alkaline phosphatase.
Probab=31.44 E-value=26 Score=13.02 Aligned_cols=10 Identities=10% Similarity=-0.011 Sum_probs=4.0
Q ss_pred EEEEEEECCC
Q ss_conf 8999982188
Q gi|254780784|r 113 VIINVMQHDL 122 (699)
Q Consensus 113 Iv~~VLS~D~ 122 (699)
=.++.-|.|.
T Consensus 45 Gl~~T~s~d~ 54 (421)
T pfam00245 45 GLSKTYNVDK 54 (421)
T ss_pred EEEECCCCCC
T ss_conf 5773155889
No 332
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD; InterPro: IPR012760 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the C-terminal region of sigma 70 (RpoD) which contains the well-conserved regions 2, 3 and 4. Region 2 of sigma-70 is the most conserved region of the entire protein. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime , . The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation , . Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme .Region 4 is involved in binding to the -35 promoter element via a helix-turn-helix motif .; GO: 0003677 DNA binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=31.43 E-value=27 Score=13.01 Aligned_cols=110 Identities=10% Similarity=0.103 Sum_probs=52.7
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHCCCCCC----CC--CCCHHHHHHHHHHHHHHHHHHHHH-CCH
Q ss_conf 444324899998875316889999999999---99983889864----47--431257999999998988888741-000
Q gi|254780784|r 191 EANQLSEDVVLDAIIFGHNECKPVIEAISK---LAKMCAKEPIV----ID--SKDFSKLEEEMSQMIKEDLRVSCF-IPE 260 (699)
Q Consensus 191 ~A~EVsEe~mleAI~~Ahe~Ik~iI~~Q~e---L~~~~Gk~K~~----~~--~~~~~~~~~~v~~~~~~~l~~a~~-i~~ 260 (699)
-+.|-+.+.+.+.+.+.-+-++.|.+.-.+ |-+.+|.+.-. |- .....+....-.....+.|.+++. .-
T Consensus 100 ~Gr~Pt~EelAe~~g~~~~Kv~~i~~~~~~PiSLe~piG~e~dS~l~DFi~D~~~~~P~~~~~~~~l~~~l~~vL~~~L- 178 (240)
T TIGR02393 100 LGREPTDEELAERMGLPVEKVREIKKIAQEPISLETPIGEEEDSSLGDFIEDESIESPEDAAAKELLREQLEEVLENTL- 178 (240)
T ss_pred HCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCC-
T ss_conf 2889987789987089989999999862488656667788777744265257444685899999999999999986017-
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHCCHHHHHHHH-------HHHHHHHHHHH
Q ss_conf 12248999999999973022310000026788999-------99999999999
Q gi|254780784|r 261 KYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVF-------EDIQAKVVRTV 306 (699)
Q Consensus 261 K~eR~~ai~~l~~ei~e~l~ee~~~~~~~~i~~af-------~~l~k~ivR~~ 306 (699)
.+|.+.+=..+--+ .+........+|...| .+++.+++|++
T Consensus 179 -~~rE~~Vl~~RyGL----~d~~~~~TLEEVG~~f~VTRERIRQIE~KALRKL 226 (240)
T TIGR02393 179 -TERERKVLRMRYGL----LDGEKPKTLEEVGKEFNVTRERIRQIESKALRKL 226 (240)
T ss_pred -CHHHHHHHHHHCCC----CCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHC
T ss_conf -88899999874389----9887653378887651787114568889998850
No 333
>PRK04405 prsA peptidylprolyl isomerase; Provisional
Probab=31.41 E-value=27 Score=13.01 Aligned_cols=66 Identities=12% Similarity=0.150 Sum_probs=36.8
Q ss_pred HCCCCCCCHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 124443248999988753---1688999999999999983889864474312579999999989888887410
Q gi|254780784|r 189 ELEANQLSEDVVLDAIIF---GHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIKEDLRVSCFI 258 (699)
Q Consensus 189 E~~A~EVsEe~mleAI~~---Ahe~Ik~iI~~Q~eL~~~~Gk~K~~~~~~~~~~~~~~v~~~~~~~l~~a~~i 258 (699)
...+..|+++++.+.+.- |+...+.++ .++-|..+.|+. +.....+..++...+-+.+.+..++..
T Consensus 33 t~kg~~IT~~e~y~~~k~~~~g~~~l~~mi-~~kvl~~~yg~k---VsdkeV~~~~~~~k~qyg~~f~~~L~q 101 (298)
T PRK04405 33 TYKGGKITESQYYKEMKQSSAGKQTLANMI-IYRALEKQYGKK---VSTKKVNKQYNSYKKQYGSSFDSVLSQ 101 (298)
T ss_pred EECCCCCCHHHHHHHHHCCHHHHHHHHHHH-HHHHHHHHHCCC---CCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 863987259999999864423679999999-999999987460---679999999999999971889999998
No 334
>COG0411 LivG ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]
Probab=31.38 E-value=27 Score=13.01 Aligned_cols=17 Identities=12% Similarity=0.075 Sum_probs=6.7
Q ss_pred CCCEEEEEEEECCCCCC
Q ss_conf 89489999972788887
Q gi|254780784|r 36 GETVVLATVVYDRSLKD 52 (699)
Q Consensus 36 G~T~VLaTv~~~~~~~~ 52 (699)
|.|+++-..+..-+|..
T Consensus 42 GKTTlfNlitG~~~P~~ 58 (250)
T COG0411 42 GKTTLFNLITGFYKPSS 58 (250)
T ss_pred CCEEEEEEECCCCCCCC
T ss_conf 82456653236405887
No 335
>PRK09280 F0F1 ATP synthase subunit beta; Validated
Probab=31.14 E-value=27 Score=12.98 Aligned_cols=33 Identities=15% Similarity=0.294 Sum_probs=17.8
Q ss_pred CCCCCCCCCCCCCCCH---HHHHHHHHHHCCCCCCC
Q ss_conf 3678887357898871---45311112321267767
Q gi|254780784|r 71 GKIPGGYLRRESRPTE---NEILISRMIDRSIRPLF 103 (699)
Q Consensus 71 GkIPGgF~kREgrpsd---~EiL~sRlIDR~lRPLF 103 (699)
|--+|.-.++-|+|-. -+-|..|++|=.=||+=
T Consensus 64 Gl~~G~~V~~tg~~l~VpVG~~lLGRV~d~lG~PiD 99 (466)
T PRK09280 64 GLVRGMEVKDTGAPISVPVGKATLGRIFNVLGEPID 99 (466)
T ss_pred CCCCCCEEEECCCCEEEEECHHHCCCEECCCCCCCC
T ss_conf 878999999589954987086442788687775267
No 336
>cd03137 GATase1_AraC_1 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain. A subgroup of AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain. AraC regulators are defined by a AraC-type helix-turn-helix DNA binding domain at their C-terminal. AraC family transcriptional regulators are widespread among bacteria and are involved in regulating diverse and important biological functions, including carbon metabolism, stress responses and virulence in different microorganisms. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, in common with typical GATase1domains a reactive cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.
Probab=31.10 E-value=12 Score=15.68 Aligned_cols=20 Identities=30% Similarity=0.645 Sum_probs=14.2
Q ss_pred CCHHHHHHHHHHHHHHCCCC
Q ss_conf 52235667777987625950
Q gi|254780784|r 435 SSSMATVCGSSLALMDAGVP 454 (699)
Q Consensus 435 sssma~vc~~slal~dagvp 454 (699)
+...++||.|+..|..||+-
T Consensus 96 ~~~l~~ictG~~~LA~aGLL 115 (187)
T cd03137 96 GARVASVCTGAFVLAEAGLL 115 (187)
T ss_pred CCEEEEECCCCHHHHHCCCC
T ss_conf 86688753140988745665
No 337
>cd00496 PheRS_alpha_core Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer.
Probab=30.57 E-value=20 Score=13.95 Aligned_cols=39 Identities=26% Similarity=0.548 Sum_probs=23.0
Q ss_pred CCCCCEE-----EEEEEEECCCCCCCHHHHHHHHHHHHH-----------HCCCCCCCCCCEEEEEEEE
Q ss_conf 4468738-----999853110278522356677779876-----------2595022541213320044
Q gi|254780784|r 416 TAQFPYT-----LRIVSEITESDGSSSMATVCGSSLALM-----------DAGVPISKPVAGIAMGLVK 468 (699)
Q Consensus 416 ~~~~p~t-----irv~~evl~sngsssma~vc~~slal~-----------dagvp~~~~VaGiamGLi~ 468 (699)
..+|||| +.+.|.. |+++|-++ .+|++ ....|.|.|+=.
T Consensus 142 p~yFPFTePS~Evdv~~~~------------~~~WlEv~G~G~v~p~vL~~~G~d--~~~~g~AfG~Gl 196 (218)
T cd00496 142 PSYFPFTEPSFEVDVYCPG------------CLGWLEILGCGMVRPEVLENAGID--EEYSGFAFGIGL 196 (218)
T ss_pred CCCCCCCCCCEEEEEEECC------------CCCCEEEECCCCCCHHHHHHCCCC--CCCEEEEEEECH
T ss_conf 7889999982699999658------------787148850465488999866979--998899985258
No 338
>PRK13238 tnaA tryptophanase; Provisional
Probab=30.55 E-value=26 Score=13.14 Aligned_cols=74 Identities=23% Similarity=0.269 Sum_probs=45.7
Q ss_pred CCCCCEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHH
Q ss_conf 45442035877405887544533455676502467999999987410786446873899985311027852235667777
Q gi|254780784|r 366 LSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSS 445 (699)
Q Consensus 366 l~~~~~k~fmlHYNFPpfsvGE~~~~~~~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~s 445 (699)
+...-+.+..+.+-||.| ||.+.|++ -+||. .|.-++ .+++- +.+...|-==-
T Consensus 278 l~~~~~~~~i~~EGf~TY--------GGlaGRDm--eAlAv-GL~E~~-d~dyl---------------~~Ri~qv~yLg 330 (461)
T PRK13238 278 LYTKCRTLCILYEGFPTY--------GGLAGRDM--EALAV-GLYEGM-DEDYL---------------AYRIAQVEYLG 330 (461)
T ss_pred HHHHHHHHEEECCCCCCC--------CCCCHHHH--HHHHC-CHHHHC-CHHHH---------------HHHHHHHHHHH
T ss_conf 999987442420587566--------88338779--99973-578760-77999---------------97799999999
Q ss_pred HHHHHCCCCCCCCCCEEEEEE
Q ss_conf 987625950225412133200
Q gi|254780784|r 446 LALMDAGVPISKPVAGIAMGL 466 (699)
Q Consensus 446 lal~dagvp~~~~VaGiamGL 466 (699)
=-|.++|||+..|+.|-|+=+
T Consensus 331 ~~L~~~GVPvv~P~GGHAv~i 351 (461)
T PRK13238 331 EGLEEAGVPVVTPAGGHAVFV 351 (461)
T ss_pred HHHHHCCCCEECCCCCEEEEE
T ss_conf 999977997056798518997
No 339
>KOG3141 consensus
Probab=30.41 E-value=27 Score=12.99 Aligned_cols=13 Identities=31% Similarity=0.299 Sum_probs=5.3
Q ss_pred HHHHHHHCCCCCC
Q ss_conf 9999873268823
Q gi|254780784|r 134 ASAALMLSGLPFE 146 (699)
Q Consensus 134 ASaAL~ISdIPf~ 146 (699)
+|+++.+++.|+.
T Consensus 40 ~~~l~~~~~~~~~ 52 (310)
T KOG3141 40 KSILLLLKEEPNA 52 (310)
T ss_pred HHHHCCCCCCCCC
T ss_conf 1121027676565
No 340
>KOG2968 consensus
Probab=30.34 E-value=28 Score=12.88 Aligned_cols=204 Identities=23% Similarity=0.348 Sum_probs=103.6
Q ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEE----
Q ss_conf 7650246799999998741078644687389998531102785223566777798762595022541213320044----
Q gi|254780784|r 393 APSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVK---- 468 (699)
Q Consensus 393 ~~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp~~~~VaGiamGLi~---- 468 (699)
.++|+ =-.++||..-.-. +|-+|- .-|+.+=|+--|---||-.||||+ +.|.|.+||-..
T Consensus 821 ~~~r~-sDFsRLAR~LtGn----------aIgLVL----GGGGARG~ahiGvl~ALeE~GIPv-D~VGGTSIGafiGaLY 884 (1158)
T KOG2968 821 EPDRH-SDFSRLARILTGN----------AIGLVL----GGGGARGAAHIGVLQALEEAGIPV-DMVGGTSIGAFIGALY 884 (1158)
T ss_pred CCCCC-CHHHHHHHHHHCC----------EEEEEE----CCCCHHHHHHHHHHHHHHHCCCCE-EEECCCCHHHHHHHHH
T ss_conf 75410-0499999987177----------479995----176400156888999999739974-5456625777521242
Q ss_pred --ECCEE-----------------EEEEEC--------CC------CCCCCCCC---CEEE---EECCCCCEEEECCCCC
Q ss_conf --08828-----------------998631--------44------22013655---1001---0055651244324536
Q gi|254780784|r 469 --DGDDF-----------------IILSDI--------SG------DEDHLGHM---DFKV---AGTDSGITAMQMDMKI 509 (699)
Q Consensus 469 --~~~~~-----------------~iLtDI--------~G------~ED~~GdM---DFKv---aGT~~GiTa~QmDiK~ 509 (699)
|-|.+ ..|.|. .| +-+-+||- ||=+ |=| .-||+--|+|--
T Consensus 885 A~e~d~~~v~~rak~f~~~mssiw~~llDLTyP~tsmftGh~FNrsI~~~Fgd~~IEDlWi~yfciT-TdIt~S~mriH~ 963 (1158)
T KOG2968 885 AEERDLVPVFGRAKKFAGKMSSIWRLLLDLTYPITSMFTGHEFNRSIHSTFGDVLIEDLWIPYFCIT-TDITSSEMRVHR 963 (1158)
T ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHCCCHHHHHHHHHHHHCCCCHHHHHHEEEECC-CCCCHHHHHHHC
T ss_conf 0667612799999999877889999998556520200033345268998845542255311000100-344245653441
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHH-------HHHHHHHHC
Q ss_conf 5568899999999999999999999984356674332244875799997711500003786077-------998999868
Q gi|254780784|r 510 GGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKV-------IRGIVEQTG 582 (699)
Q Consensus 510 ~gi~~~il~~al~~A~~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~-------ik~i~~~~~ 582 (699)
.|.--.-++. .-.++-|.|-+. -.|=|.+.=-||++ .+++..++=
T Consensus 964 ~G~~WrYvRA-----------------------SMsLaGylPPlc-----dp~dGhlLlDGGYvnNlPadvmrslGa~~i 1015 (1158)
T KOG2968 964 NGSLWRYVRA-----------------------SMSLAGYLPPLC-----DPKDGHLLLDGGYVNNLPADVMRSLGAKVI 1015 (1158)
T ss_pred CCCHHHHHHH-----------------------HCCCCCCCCCCC-----CCCCCCEEECCCCCCCCCHHHHHHCCCCEE
T ss_conf 7831788876-----------------------420214689777-----888887874364405675899974688679
Q ss_pred CEEEEE--CC-----------EEEEEEE-----------CCHHHHHHHHHHHHHHCC--CC--CCCCEEEE---EEEEEE
Q ss_conf 889980--88-----------0899996-----------898999999999998524--75--46867899---999994
Q gi|254780784|r 583 AKVNID--DD-----------GTVKIAS-----------SSLAEIEAAREMIRSITD--VP--EVNKIYKG---QVVKVM 631 (699)
Q Consensus 583 ~~i~i~--d~-----------g~v~i~~-----------~~~~~~~~a~~~i~~~~~--~~--e~g~~y~~---~v~~i~ 631 (699)
-.||+. |+ |.--+|- +|.+.++.-..+|...-. ++ --+..|-- .--+++
T Consensus 1016 iAiDVGS~detdl~~YGDslSG~W~L~krwnPf~~~~kv~nm~EIQsRLaYVscVrqlE~vK~~~yc~YlRPPI~~f~Tl 1095 (1158)
T KOG2968 1016 IAIDVGSQDETDLMNYGDSLSGFWILFKRWNPFGTKVKVPNMAEIQSRLAYVSCVRQLEVVKNSPYCEYLRPPIEKFKTL 1095 (1158)
T ss_pred EEEECCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCHHCCCC
T ss_conf 99942674567700026654532333421365678778888899987778887898899873489738978873011535
Q ss_pred ECCEEEECCC
Q ss_conf 1536998287
Q gi|254780784|r 632 DFGAFVHFCG 641 (699)
Q Consensus 632 ~fGafve~~~ 641 (699)
|||-|=||..
T Consensus 1096 dF~kFdeI~~ 1105 (1158)
T KOG2968 1096 DFGKFDEIYE 1105 (1158)
T ss_pred CCCCHHHHHH
T ss_conf 6200899999
No 341
>pfam05382 Amidase_5 Bacteriophage peptidoglycan hydrolase. At least one of the members of this family, the Pal protein from the pneumococcal bacteriophage Dp-1 has been shown to be a N-acetylmuramoyl-L-alanine amidase. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside at the N-terminal domain whereas the C-terminal domain binds to the choline residues of the cell wall teichoic acids. This family appears to be related to pfam00877.
Probab=30.18 E-value=28 Score=12.86 Aligned_cols=74 Identities=18% Similarity=0.188 Sum_probs=46.3
Q ss_pred CCCCCCHHHHHHHHHHHHHHCCCCCCC-CCCEEEEEEEEECCEEEEEEECCCCCCCCCCCCEEEEEC------CCCCEEE
Q ss_conf 027852235667777987625950225-412133200440882899863144220136551001005------5651244
Q gi|254780784|r 431 ESDGSSSMATVCGSSLALMDAGVPISK-PVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGT------DSGITAM 503 (699)
Q Consensus 431 ~sngsssma~vc~~slal~dagvp~~~-~VaGiamGLi~~~~~~~iLtDI~G~ED~~GdMDFKvaGT------~~GiTa~ 503 (699)
.-||+.++-|=-+-+-||.+||..... ...-..++-......|.+.++...-+=..||.=+ .|+ ..|-|.+
T Consensus 22 ~RnG~d~~DCSssvy~AL~~aG~~~~g~~~nTetL~~~L~~nG~~~i~~~~~~~~q~GDI~I--wG~~g~S~Ga~GHvgi 99 (145)
T pfam05382 22 SRNGPDSYDCSSSVYFALRSAGASSAGWAVNTETLHDWLIKNGFKLIAENEDWNAKRGDIFI--WGKRGASAGAGGHVGM 99 (145)
T ss_pred CCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHCCCEEEECCCCCCCCCCCEEE--EECCCCCCCCCCEEEE
T ss_conf 16799877643899999997578888753641678899863773996027766777688999--9268997777754899
Q ss_pred ECC
Q ss_conf 324
Q gi|254780784|r 504 QMD 506 (699)
Q Consensus 504 QmD 506 (699)
=+|
T Consensus 100 ~~d 102 (145)
T pfam05382 100 FID 102 (145)
T ss_pred EEC
T ss_conf 947
No 342
>PRK12366 replication factor A; Reviewed
Probab=30.15 E-value=28 Score=12.86 Aligned_cols=17 Identities=24% Similarity=0.231 Sum_probs=7.8
Q ss_pred HCCCCCEEEEEEEEECC
Q ss_conf 03259889999997868
Q gi|254780784|r 663 VVKEGDTVWVKLLDFDD 679 (699)
Q Consensus 663 ~~~~Gd~i~vk~~~~d~ 679 (699)
-+++||.|+|.---+..
T Consensus 459 ~i~eGDviki~~a~vke 475 (649)
T PRK12366 459 EIKEGDVIKIIHGYAKE 475 (649)
T ss_pred CCCCCCEEEEECCEEEC
T ss_conf 44689789995256700
No 343
>CHL00059 atpA ATP synthase CF1 alpha subunit
Probab=29.95 E-value=28 Score=12.83 Aligned_cols=32 Identities=16% Similarity=0.401 Sum_probs=18.0
Q ss_pred CCCCCCCCCCCCH---HHHHHHHHHHCCCCCCCCC
Q ss_conf 8887357898871---4531111232126776746
Q gi|254780784|r 74 PGGYLRRESRPTE---NEILISRMIDRSIRPLFSK 105 (699)
Q Consensus 74 PGgF~kREgrpsd---~EiL~sRlIDR~lRPLFPk 105 (699)
.|.-.||-|++-+ -+=|..|+||=-=|||=-+
T Consensus 85 eG~~V~~TG~~l~VPVG~~lLGRVvd~LG~PiDgk 119 (501)
T CHL00059 85 EGSSVKATGKIAQIPVSEAYLGRVVNALAKPIDGK 119 (501)
T ss_pred CCCEEEECCCEEEEECCHHHCCCEECCCEEECCCC
T ss_conf 99988857972477457523147406877544799
No 344
>pfam08211 dCMP_cyt_deam_2 Cytidine and deoxycytidylate deaminase zinc-binding region.
Probab=29.66 E-value=28 Score=12.80 Aligned_cols=74 Identities=26% Similarity=0.308 Sum_probs=48.9
Q ss_pred HHHHHHHHHHHCCCCCCCCEEEEEEEECCCCEE---------ECCCCCCCCCCCEEEE-EECC----CCHHHHHCCCCCC
Q ss_conf 999999998732688235411235520477324---------3685000222101355-3054----4323331244432
Q gi|254780784|r 130 SMVAASAALMLSGLPFEGPVVGAQVDYINGQYV---------LNPRLDEDQGSLDLFV-SGTQ----DAVLMVELEANQL 195 (699)
Q Consensus 130 Ai~aASaAL~ISdIPf~GPVaaVRVG~idge~V---------iNPt~ee~esdLDLvV-AGT~----d~IlMIE~~A~EV 195 (699)
-+.+|-.|..-|-.|+..--.+|-+-..||++. .|||..-+++.|..++ +|-. ...++||.....|
T Consensus 36 L~~~Al~Aa~~syaPYS~~~~G~Al~~~~G~i~~G~~~EnAAfnPSl~PlQaAL~~~~~~G~~~~~I~~avLvE~~~a~v 115 (124)
T pfam08211 36 LVQRALAAANRSHAPYSKSPSGVALEDKDGKVYAGRYAENAAFNPSLPPLQAALVDFVAAGKDFNDIVRAVLVEKADAKL 115 (124)
T ss_pred HHHHHHHHHHHCCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCCCCCHHHHHHHHHHHCCCCHHHHHEEEEEECCCCCC
T ss_conf 99999999982558856796017999379999985652302268983589999999997499876501136885378802
Q ss_pred CHHHHHHH
Q ss_conf 48999988
Q gi|254780784|r 196 SEDVVLDA 203 (699)
Q Consensus 196 sEe~mleA 203 (699)
|...+..+
T Consensus 116 sq~~~a~~ 123 (124)
T pfam08211 116 SQEATARI 123 (124)
T ss_pred CHHHHHHC
T ss_conf 23987533
No 345
>cd04092 mtEFG2_II_like mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG1s are n
Probab=29.24 E-value=29 Score=12.74 Aligned_cols=44 Identities=16% Similarity=0.229 Sum_probs=25.0
Q ss_pred CCCCCEEEEEE--EEC-CCCEEECCCCCCCC--CCCEEEEEECCCCHHH
Q ss_conf 82354112355--204-77324368500022--2101355305443233
Q gi|254780784|r 144 PFEGPVVGAQV--DYI-NGQYVLNPRLDEDQ--GSLDLFVSGTQDAVLM 187 (699)
Q Consensus 144 Pf~GPVaaVRV--G~i-dge~ViNPt~ee~e--sdLDLvVAGT~d~IlM 187 (699)
||.|.++=+|| |.+ .|.-+.|++....+ +.+-.+.+.....+--
T Consensus 12 ~~~G~ls~vRVysG~l~~g~~v~n~~~~~~ekv~~l~~~~g~~~~~v~~ 60 (83)
T cd04092 12 PQRGPLTFVRVYSGTLKRGSALYNTNTGKKERISRLLQPFADQYQEIPS 60 (83)
T ss_pred CCCCCEEEEEEEECEECCCCEEEECCCCCEEEEEEEEEEECCCCEECCE
T ss_conf 9844099999970789789999968899629730888975799329978
No 346
>COG4706 Predicted 3-hydroxylacyl-(acyl carrier protein) dehydratase [Lipid metabolism]
Probab=29.23 E-value=17 Score=14.66 Aligned_cols=78 Identities=15% Similarity=0.111 Sum_probs=41.8
Q ss_pred EEEECCCEEEEEEEECCCCCC---CCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 999789489999972788887---77735406866523201336788873578988714531111232126776746886
Q gi|254780784|r 32 LATYGETVVLATVVYDRSLKD---GQDFFPLTVNYQERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYK 108 (699)
Q Consensus 32 ~v~~G~T~VLaTv~~~~~~~~---~~dFfPLtVdY~Ek~yAaGkIPGgF~kREgrpsd~EiL~sRlIDR~lRPLFPkgf~ 108 (699)
+++|+|+.+-|+++.++.+-. .-+-+|-+.-.+--.-|+|--.|=-.-|+|+|| +|+=|=-|-|
T Consensus 28 VvtwdDd~~rc~atvsp~~a~~l~~dg~Lpa~~gIElmAQAv~vh~g~l~~rq~~ps-------------~r~GfLlg~R 94 (161)
T COG4706 28 VVTWDDDSARCRATVSPSGAPFLDPDGNLPAWFGIELMAQAVGVHSGWLRHRQGKPS-------------IRLGFLLGAR 94 (161)
T ss_pred EEEECCCEEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCC-------------CCCEEEEEEE
T ss_conf 423348837887676788887637677754555699999999998988875027976-------------5412463000
Q ss_pred CCEEEEEEEEECCCCCC
Q ss_conf 88378999982188887
Q gi|254780784|r 109 NETQVIINVMQHDLESS 125 (699)
Q Consensus 109 ~evQIv~~VLS~D~~~d 125 (699)
.+-|.+-+.+....
T Consensus 95 ---kleaha~~l~~~q~ 108 (161)
T COG4706 95 ---KLEAHAGILPAGQT 108 (161)
T ss_pred ---EEEEECCCCCCCCC
T ss_conf ---11221354577653
No 347
>cd03136 GATase1_AraC_ArgR_like AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain. A subgroup of AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to the Pseudomonas aeruginosa ArgR regulator. ArgR functions in the control of expression of certain genes of arginine biosynthesis and catabolism. AraC regulators are defined by a AraC-type helix-turn-helix DNA binding domain at their C-terminal. AraC family transcriptional regulators are widespread among bacteria and are involved in regulating diverse and important biological functions, including carbon metabolism, stress responses and virulence in different microorganisms. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, in common with typical GATase1domains a reactive cys residue is found in some sequences in the sharp turn betwee
Probab=29.17 E-value=18 Score=14.38 Aligned_cols=24 Identities=13% Similarity=0.192 Sum_probs=17.9
Q ss_pred CCHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 522356677779876259502254
Q gi|254780784|r 435 SSSMATVCGSSLALMDAGVPISKP 458 (699)
Q Consensus 435 sssma~vc~~slal~dagvp~~~~ 458 (699)
++..+++|.|+..|..||+-=...
T Consensus 95 g~~v~svctGa~~LA~aGlL~g~~ 118 (185)
T cd03136 95 GVALGGIDTGAFLLARAGLLDGRR 118 (185)
T ss_pred CCEEEEECHHHHHHHHCCCCCCCE
T ss_conf 998998647999999818879990
No 348
>TIGR02071 PBP_1b penicillin-binding protein 1B; InterPro: IPR011813 Bacterial that synthesize a cell wall of peptidoglycan (murein) generally have several transglycosylases and transpeptidases for the task. This family consists of a particular bifunctional transglycosylase/transpeptidase in Escherichia coli and other Proteobacteria, designated penicillin-binding protein 1B.; GO: 0008233 peptidase activity, 0008955 peptidoglycan glycosyltransferase activity, 0009252 peptidoglycan biosynthetic process, 0046677 response to antibiotic, 0009274 peptidoglycan-based cell wall.
Probab=28.64 E-value=29 Score=12.67 Aligned_cols=36 Identities=31% Similarity=0.469 Sum_probs=25.9
Q ss_pred CCCCEEEEEEECCCCCCCCHHHH--C-CCCCEEEEEEEEECCCCCEEEE
Q ss_conf 79710488663144454785560--3-2598899999978689986668
Q gi|254780784|r 641 GARDGLVHISQLSTERVAKTSDV--V-KEGDTVWVKLLDFDDRGKIKLS 686 (699)
Q Consensus 641 ~g~~gl~HiS~l~~~~v~~~~d~--~-~~Gd~i~vk~~~~d~~g~i~lS 686 (699)
=||.|= .|+-.|= . =-|++|.|-|+|+|++|.-+|.
T Consensus 639 AGKTGT----------tNd~RDsWF~G~dG~~~~~~W~GRD~N~~TkLt 677 (742)
T TIGR02071 639 AGKTGT----------TNDSRDSWFVGIDGKEVTIVWLGRDDNGPTKLT 677 (742)
T ss_pred CCCCCC----------CCCCCCEEEEEECCCEEEEEEEECCCCCCCCCC
T ss_conf 456365----------688851047764387899999852789884764
No 349
>cd07228 Pat_NTE_like_bacteria Bacterial patatin-like phospholipase domain containing protein 6. Bacterial patatin-like phospholipase domain containing protein 6. PNPLA6 is commonly known as Neuropathy Target Esterase (NTE). NTE has at least two functional domains: the N-terminal domain putatively regulatory domain and the C-terminal catalytic domain which shows esterase activity. NTE shows phospholipase activity for lysophosphatidylcholine (LPC) and phosphatidylcholine (PC). Exposure of NTE to organophosphates leads to organophosphate-induced delayed neurotoxicity (OPIDN). OPIDN is a progressive neurological condition that is characterized by weakness, paralysis, pain, and paresthesia. This group includes YCHK and rssA from Escherichia coli as well as Ylbk from Bacillus amyloliquefaciens.
Probab=28.42 E-value=29 Score=12.64 Aligned_cols=32 Identities=28% Similarity=0.405 Sum_probs=15.5
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEE
Q ss_conf 785223566777798762595022541213320
Q gi|254780784|r 433 DGSSSMATVCGSSLALMDAGVPISKPVAGIAMG 465 (699)
Q Consensus 433 ngsssma~vc~~slal~dagvp~~~~VaGiamG 465 (699)
-|+.+-+.-.|.--+|.+.|+++ +.++|+|+|
T Consensus 7 GGG~rG~~~~Gvl~~L~e~gi~~-d~i~GtSaG 38 (175)
T cd07228 7 SGGARGWAHIGVLRALEEEGIEI-DIIAGSSIG 38 (175)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCC-CEEEEECHH
T ss_conf 76899999999999999869986-789864489
No 350
>COG1685 Archaeal shikimate kinase [Amino acid transport and metabolism / Coenzyme metabolism]
Probab=28.35 E-value=30 Score=12.63 Aligned_cols=134 Identities=21% Similarity=0.297 Sum_probs=81.1
Q ss_pred HHHHHHHHHHHHHCCCCC-CCCCEEEEEEEEECCCCC-CCHHHHHHHHHHHHHHC-CCCCCC-----------CCCEEEE
Q ss_conf 679999999874107864-468738999853110278-52235667777987625-950225-----------4121332
Q gi|254780784|r 399 IGHGRLARRAIHPVLPQT-AQFPYTLRIVSEITESDG-SSSMATVCGSSLALMDA-GVPISK-----------PVAGIAM 464 (699)
Q Consensus 399 iGHg~la~ral~~~~P~~-~~~p~tirv~~evl~sng-sssma~vc~~slal~da-gvp~~~-----------~VaGiam 464 (699)
-+-.+|.+|.++.+.-.. ..++..+++.||+...-| +||-|.+++-.+|+.++ |+++.. -=||+++
T Consensus 48 ~~d~~li~~~~~~v~e~~g~~~~~~v~v~SeiP~~~GLkSSSA~~nAlv~A~~~~~g~~~~~~~i~~l~a~~S~~aGvSv 127 (278)
T COG1685 48 EGDTRLIERCVERVREKYGIPLGVEVEVESEIPVGSGLKSSSAASNALVKAVLKALGEEIDDFEILRLGARASKEAGVSV 127 (278)
T ss_pred CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCEE
T ss_conf 78747999999999987298865599982578766674245899999999999971898881488887779887459447
Q ss_pred E-------------E-EEECCEEEEEEECCCCCCCCCCCCEEEEECCCCCEEEECCCCCCC--CCHHHHHHHHHHHHHHH
Q ss_conf 0-------------0-440882899863144220136551001005565124432453655--68899999999999999
Q gi|254780784|r 465 G-------------L-VKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGG--ISENIMVMALQQAKRGR 528 (699)
Q Consensus 465 G-------------L-i~~~~~~~iLtDI~G~ED~~GdMDFKvaGT~~GiTa~QmDiK~~g--i~~~il~~al~~A~~gr 528 (699)
- + |+|+.+..||--- .++ +.+|.=--.|-+.++-++.+.+ .-....+.|...|-.|+
T Consensus 128 TGA~DDa~AS~~GG~~iTDN~~m~Ilrr~--~~~-----~~~vlI~~p~~k~~~~~vdv~~~r~~a~~~e~A~~lA~~G~ 200 (278)
T COG1685 128 TGAFDDACASYLGGIVITDNRKMRILRRL--DLP-----ELTVLILAPGEKRLSANVDVNRLRLIAPVVEEAFRLALKGE 200 (278)
T ss_pred ECCCHHHHHHHHCCEEEECCHHHEEHHCC--CCC-----CCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 41406889997588688616111000003--467-----74089981687652554787898774389999999985352
Q ss_pred HHHHHHHHHCC
Q ss_conf 99999998435
Q gi|254780784|r 529 LHILNEMSKVL 539 (699)
Q Consensus 529 ~~il~~m~~~~ 539 (699)
.+=--.+|-.+
T Consensus 201 ~~~Am~lNG~~ 211 (278)
T COG1685 201 YFKAMVLNGIL 211 (278)
T ss_pred HHHHHHHHHHH
T ss_conf 88888876799
No 351
>TIGR00174 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; InterPro: IPR002627 tRNA isopentenyltransferases 2.5.1.8 from EC also known as tRNA delta(2)-isopentenylpyrophosphate transferases or IPP transferases. These enzymes modify both cytoplasmic and mitochondrial tRNAs at A(37) to give isopentenyl A(37) .; GO: 0004811 tRNA isopentenyltransferase activity, 0005524 ATP binding, 0008033 tRNA processing.
Probab=28.08 E-value=18 Score=14.33 Aligned_cols=10 Identities=40% Similarity=0.670 Sum_probs=6.0
Q ss_pred CCEEEEEECC
Q ss_conf 1013553054
Q gi|254780784|r 173 SLDLFVSGTQ 182 (699)
Q Consensus 173 dLDLvVAGT~ 182 (699)
.+=|+|+||.
T Consensus 89 kipl~VGGT~ 98 (307)
T TIGR00174 89 KIPLLVGGTG 98 (307)
T ss_pred CCEEEECCHH
T ss_conf 8348868578
No 352
>cd04691 Nudix_Hydrolase_32 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=27.90 E-value=30 Score=12.57 Aligned_cols=24 Identities=21% Similarity=0.303 Sum_probs=18.1
Q ss_pred EEEECCCCHH----------HHHHHHHHCCEEEE
Q ss_conf 0003786077----------99899986888998
Q gi|254780784|r 564 RNVIGMGGKV----------IRGIVEQTGAKVNI 587 (699)
Q Consensus 564 ~~~iG~gG~~----------ik~i~~~~~~~i~i 587 (699)
|.--.||||. +|++.||+|+++..
T Consensus 27 G~WefPGGkvE~gEt~~~Al~REl~EElgI~v~~ 60 (117)
T cd04691 27 GKLNIPGGHIEAGESQEEALLREVQEELGVDPLS 60 (117)
T ss_pred CEEECCEECCCCCCCHHHHHHHHHHHHHCEEEEC
T ss_conf 9698974517798899999999988981915622
No 353
>cd00713 GltS Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The N-terminal glutaminase domain catalyzes the hydrolysis of glutamine to glutamic acid and ammonia, and has a fold similar to that of other glutamine amidotransferases such as glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), and beta lactam synthetase (beta-LS), as well as the Ntn hydrolase folds of the proteasomal alpha and beta subunits.
Probab=27.82 E-value=30 Score=12.56 Aligned_cols=86 Identities=23% Similarity=0.229 Sum_probs=42.6
Q ss_pred EEEEECCCCCCCCCC---CCCCCCEE--EEEEEECCCCCCCCCCCCCC-CCCCHHHHH--------HHHH-HHHHHHCCC
Q ss_conf 999816865212233---44544203--58774058875445334556-765024679--------9999-998741078
Q gi|254780784|r 350 VVVTLGTREDEQYVD---SLSGTQRN--DFMMHYNFLPCATGEVSRMG-APSRREIGH--------GRLA-RRAIHPVLP 414 (699)
Q Consensus 350 ~tvTLG~~~d~Q~iD---~l~~~~~k--~fmlHYNFPpfsvGE~~~~~-~~~RREiGH--------g~la-~ral~~~~P 414 (699)
++|.=|....+|..+ +|.....+ -.+.|= =||||.-.... ++-=|-++| ||.- -||-++.+-
T Consensus 175 tIVYKGml~~~ql~~fY~DL~d~~~~s~~al~H~---RFSTNTfPsW~lAqPfR~laHNGEINTi~GN~nwm~aRe~~~~ 251 (413)
T cd00713 175 TIVYKGMLLPEQLGQFYPDLQDPRFESAFALVHS---RFSTNTFPSWPLAQPFRYLAHNGEINTIRGNRNWMRAREGLLK 251 (413)
T ss_pred EEEEECCCCHHHHHHHHHHHCCCCEEEEEEEEEE---ECCCCCCCCCCCCCCCHHHHCCCCCHHHHHHHHHHHHHHHHHC
T ss_conf 1786412578999886166369765899987883---0568999987302755000027630015657999998777641
Q ss_pred CCCCCCEEEEEEEEECCCCCCCHHH
Q ss_conf 6446873899985311027852235
Q gi|254780784|r 415 QTAQFPYTLRIVSEITESDGSSSMA 439 (699)
Q Consensus 415 ~~~~~p~tirv~~evl~sngsssma 439 (699)
++ .|..-+.-.--|+..+||-|..
T Consensus 252 s~-~~~~~~~~l~Pi~~~~~SDSa~ 275 (413)
T cd00713 252 SP-LFGEDLKKLKPIINPGGSDSAS 275 (413)
T ss_pred CC-CCHHHHHHCCCCCCCCCCHHHH
T ss_conf 87-5302188647876999844668
No 354
>COG0056 AtpA F0F1-type ATP synthase, alpha subunit [Energy production and conversion]
Probab=27.71 E-value=30 Score=12.55 Aligned_cols=37 Identities=32% Similarity=0.554 Sum_probs=29.5
Q ss_pred EEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCC
Q ss_conf 86652320133678887357898871453111123212677
Q gi|254780784|r 61 VNYQERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRP 101 (699)
Q Consensus 61 VdY~Ek~yAaGkIPGgF~kREgrpsd~EiL~sRlIDR~lRP 101 (699)
|-|||-+-=.+|=|| ||.=|.|-=-|.|||-.|+-|=
T Consensus 268 ~AYReiSLLlrRPPG----REAyPGDVFYlHSrLLERAakl 304 (504)
T COG0056 268 VAYREISLLLRRPPG----REAYPGDVFYLHSRLLERAAKL 304 (504)
T ss_pred HHHHHHHHHHCCCCC----CCCCCCCEEEHHHHHHHHHHHH
T ss_conf 999999998369998----6578886400117999998862
No 355
>PRK11597 heat shock chaperone IbpB; Provisional
Probab=27.68 E-value=30 Score=12.54 Aligned_cols=64 Identities=13% Similarity=0.175 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEE-CCEEEEEEEC
Q ss_conf 99999999999999984356674332244875799997711500003786077998999868889980-8808999968
Q gi|254780784|r 521 LQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNID-DDGTVKIASS 598 (699)
Q Consensus 521 l~~A~~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~-d~g~v~i~~~ 598 (699)
|...-.|=.++.+.++..-. +.+-|-.-..+.+-+.-.--+--.|-.-. .|+|+ +++..+|.|.
T Consensus 9 ~~~~~vGFD~lf~~l~~~~~------~~~yPpYNI~k~~e~~y~IeiAvaGf~k~--------di~I~~~~~~LtI~g~ 73 (142)
T PRK11597 9 LLRQWIGFDKLANALQNAGE------SQSFPPYNIEKSDDNHYRITLALAGFRQE--------DLDIQLEGTRLTVKGT 73 (142)
T ss_pred HHHCCCCHHHHHHHHHHCCC------CCCCCCCEEEEECCCEEEEEEEECCCCHH--------HEEEEEECCEEEEECC
T ss_conf 67454387799999864266------78999966999179729999996887757--------7899997899999715
No 356
>smart00815 AMA-1 Apical membrane antigen 1. Apical membrane antigen 1 (AMA-1) is a Plasmodium asexual blood-stage antigen. It has been suggested that positive selection operates on the AMA-1 gene in regions coding for antigenic sites.
Probab=27.66 E-value=21 Score=13.77 Aligned_cols=13 Identities=15% Similarity=0.460 Sum_probs=6.7
Q ss_pred HHHHHHHHHCCCC
Q ss_conf 5311112321267
Q gi|254780784|r 88 EILISRMIDRSIR 100 (699)
Q Consensus 88 EiL~sRlIDR~lR 100 (699)
.++.|++..-.||
T Consensus 79 ~~~iSPis~~~Lk 91 (240)
T smart00815 79 NVLLSPISADELK 91 (240)
T ss_pred CCCCCCCCHHHHH
T ss_conf 7753747789999
No 357
>COG0693 ThiJ Putative intracellular protease/amidase [General function prediction only]
Probab=27.57 E-value=18 Score=14.37 Aligned_cols=19 Identities=37% Similarity=0.459 Sum_probs=8.5
Q ss_pred CCCCCCCCCCC-CCCCCCCC
Q ss_conf 32013367888-73578988
Q gi|254780784|r 66 RTYAVGKIPGG-YLRRESRP 84 (699)
Q Consensus 66 k~yAaGkIPGg-F~kREgrp 84 (699)
.-|.+=-|||| +-.+--++
T Consensus 65 ~~ydal~ipGG~~~~~~~~~ 84 (188)
T COG0693 65 ADYDALVIPGGDHGPEYLRP 84 (188)
T ss_pred CCCCEEEECCCCCCHHHCCC
T ss_conf 35989998899752322135
No 358
>TIGR02730 carot_isom carotene isomerase; InterPro: IPR014101 Members of this family, including sll0033 (crtH) of Synechocystis sp. (strain PCC 6803), catalyse a cis-trans isomerization of carotenes to the all-trans lycopene, a reaction that can also occur non-enzymatically in light through photoisomerization..
Probab=27.14 E-value=25 Score=13.23 Aligned_cols=10 Identities=20% Similarity=0.541 Sum_probs=3.4
Q ss_pred CCCEEEEEEE
Q ss_conf 6873899985
Q gi|254780784|r 418 QFPYTLRIVS 427 (699)
Q Consensus 418 ~~p~tirv~~ 427 (699)
.-.|.-||.+
T Consensus 245 ~I~Y~A~Vt~ 254 (506)
T TIGR02730 245 KIRYKARVTK 254 (506)
T ss_pred CEEEEEEEEE
T ss_conf 0563002455
No 359
>cd03325 D-galactonate_dehydratase D-galactonate dehydratase catalyses the dehydration of galactonate to 2-keto-3-deoxygalactnate (KDGal), as part of the D-galactonate nonphosphorolytic catabolic Entner-Doudoroff pathway. D-galactonate dehydratase belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion.
Probab=26.85 E-value=27 Score=12.97 Aligned_cols=77 Identities=23% Similarity=0.233 Sum_probs=46.9
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCC-CCCCCCEEEEEEEEECCE-----EEEEEECCCCCCCCCCCCEEEEECCCCCEEEEC
Q ss_conf 27852235667777987625950-225412133200440882-----899863144220136551001005565124432
Q gi|254780784|r 432 SDGSSSMATVCGSSLALMDAGVP-ISKPVAGIAMGLVKDGDD-----FIILSDISGDEDHLGHMDFKVAGTDSGITAMQM 505 (699)
Q Consensus 432 sngsssma~vc~~slal~dagvp-~~~~VaGiamGLi~~~~~-----~~iLtDI~G~ED~~GdMDFKvaGT~~GiTa~Qm 505 (699)
+|++-+....---.=+|-+.++- +-.|+..- +-+. -..-+.|.+.|..++--||+=.=..+.+..+|.
T Consensus 183 an~~~~~~~A~~~~~~l~~~~l~w~EeP~~~~------d~~~~~~l~~~~~~PIa~gE~~~~~~~~~~~i~~~a~di~~~ 256 (352)
T cd03325 183 FHGRVSKPMAKDLAKELEPYRLLFIEEPVLPE------NVEALAEIAARTTIPIATGERLFSRWDFKELLEDGAVDIIQP 256 (352)
T ss_pred CCCCCCHHHHHHHHHHHHHCCCHHEECCCCCC------CHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHCCCCCEEEC
T ss_conf 89998999999999986104623112788988------999999999876999971783787677899997687766821
Q ss_pred CC-CCCCCCH
Q ss_conf 45-3655688
Q gi|254780784|r 506 DM-KIGGISE 514 (699)
Q Consensus 506 Di-K~~gi~~ 514 (699)
|+ |++||+.
T Consensus 257 d~~~~GGit~ 266 (352)
T cd03325 257 DISHAGGITE 266 (352)
T ss_pred CCCCCCCHHH
T ss_conf 7773598999
No 360
>TIGR01009 rpsC_bact ribosomal protein S3; InterPro: IPR005704 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 of 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 S3 is one of the proteins from the small ribosomal subunit. This family describes the bacterial type of ribosomal protein S3 and also and many chloroplast forms. Chloroplast and mitochondrial forms have large, variable inserts between conserved N-terminal and C-terminal domains. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=26.61 E-value=31 Score=12.41 Aligned_cols=46 Identities=22% Similarity=0.295 Sum_probs=35.4
Q ss_pred CCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHH----HHC--CEEEEE
Q ss_conf 4332244875799997711500003786077998999----868--889980
Q gi|254780784|r 543 RLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVE----QTG--AKVNID 588 (699)
Q Consensus 543 ~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~----~~~--~~i~i~ 588 (699)
+-++.-.+++-..+.|..-+=|-|||.+|++|-.|.+ .++ -+|+|+
T Consensus 57 ~veIeR~~~~~v~V~IhtArPg~vIGkkG~~iE~l~~~l~k~~~~~k~v~i~ 108 (217)
T TIGR01009 57 DVEIERTADKKVRVTIHTARPGIVIGKKGSEIEKLKKALQKLTGSVKEVQIN 108 (217)
T ss_pred EEEEEECCCCEEEEEEEECCCCEEECCCCCHHHHHHHHHHHHHCCEEEEEEE
T ss_conf 2799816997889999827886588578845899999999884783589998
No 361
>cd03134 GATase1_PfpI_like A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus. A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus. This group includes proteins similar to PfpI from P. furiosus. and PH1704 from Pyrococcus horikoshii. These enzymes are ATP-independent intracellular proteases and may hydrolyze small peptides to provide a nutritional source. Only Cys of the catalytic triad typical of GATase1 domains is conserved in this group. This Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. For PH1704, it is believed that this Cys together with a different His in one monomer and Glu (from an adjacent monomer) forms a different catalytic triad from the typical GATase1domain. PfpI is homooligomeric. Protease activity is only found for oligomeric forms of PH1704.
Probab=26.19 E-value=18 Score=14.40 Aligned_cols=15 Identities=33% Similarity=0.756 Sum_probs=9.0
Q ss_pred HHHHHHHHHHHHHCC
Q ss_conf 356677779876259
Q gi|254780784|r 438 MATVCGSSLALMDAG 452 (699)
Q Consensus 438 ma~vc~~slal~dag 452 (699)
.|+||+|.+.|..||
T Consensus 97 iaaIC~gp~~L~~~g 111 (165)
T cd03134 97 VAAICHGPWVLISAG 111 (165)
T ss_pred EEEECCHHHHHHHCC
T ss_conf 999987578774578
No 362
>KOG3843 consensus
Probab=26.16 E-value=19 Score=14.18 Aligned_cols=43 Identities=37% Similarity=0.477 Sum_probs=33.3
Q ss_pred CCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCC
Q ss_conf 6700899987976899998168652122334454420358774058875
Q gi|254780784|r 335 THGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPC 383 (699)
Q Consensus 335 vHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpf 383 (699)
.-||-||+.|-|-+-++ ||| |+.-+++|.+.-.||-|-|=-|-
T Consensus 331 ~~gsilfak~isgarvv-~~~-----q~kttieg~ef~~f~sht~e~~~ 373 (432)
T KOG3843 331 LFGSILFAKGISGARVV-PLG-----QMKTTIEGCEFIGFGSHTNEQHC 373 (432)
T ss_pred HHHHHHHHCCCCCCEEE-ECC-----CCCEEEECEEEECCCCCCCCCCH
T ss_conf 98878875156674586-535-----44002403277612335675752
No 363
>pfam02430 AMA-1 Apical membrane antigen 1. Apical membrane antigen 1 (AMA-1) is a Plasmodium asexual blood-stage antigen. It has been suggested that positive selection operates on the AMA-1 gene in regions coding for antigenic sites.
Probab=25.69 E-value=25 Score=13.23 Aligned_cols=14 Identities=21% Similarity=0.238 Sum_probs=10.1
Q ss_pred EEEEEEEECCCCCC
Q ss_conf 68999981686521
Q gi|254780784|r 347 QAIVVVTLGTREDE 360 (699)
Q Consensus 347 QaL~tvTLG~~~d~ 360 (699)
-.++++.||++..+
T Consensus 315 ~~iA~TAlssp~E~ 328 (462)
T pfam02430 315 GFIATTALSSPLEE 328 (462)
T ss_pred CCEEEECCCCCCHH
T ss_conf 61454002781032
No 364
>COG5011 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.57 E-value=19 Score=14.18 Aligned_cols=18 Identities=33% Similarity=0.733 Sum_probs=13.8
Q ss_pred HHHHHHCCCCC-----CCCCCCC
Q ss_conf 11123212677-----6746886
Q gi|254780784|r 91 ISRMIDRSIRP-----LFSKCYK 108 (699)
Q Consensus 91 ~sRlIDR~lRP-----LFPkgf~ 108 (699)
..||+||++|- -|-+||+
T Consensus 21 lmRlidR~iRRAglpiayT~GFh 43 (228)
T COG5011 21 LMRLIDRTIRRAGLPIAYTGGFH 43 (228)
T ss_pred HHHHHHHHHHHCCCCEEECCCCC
T ss_conf 99999999886498535437889
No 365
>COG1785 PhoA Alkaline phosphatase [Inorganic ion transport and metabolism]
Probab=25.55 E-value=18 Score=14.32 Aligned_cols=11 Identities=27% Similarity=0.347 Sum_probs=6.0
Q ss_pred EECCCCCCCCC
Q ss_conf 65232013367
Q gi|254780784|r 63 YQERTYAVGKI 73 (699)
Q Consensus 63 Y~Ek~yAaGkI 73 (699)
.--|+|+.|.-
T Consensus 76 taaR~~~~~~~ 86 (482)
T COG1785 76 TAARSYKGGPN 86 (482)
T ss_pred HHHHHHCCCCC
T ss_conf 89887514777
No 366
>cd04091 mtEFG1_II_like mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals
Probab=25.50 E-value=33 Score=12.26 Aligned_cols=44 Identities=18% Similarity=0.194 Sum_probs=28.2
Q ss_pred CCCCCCEEEEEE--EEC-CCCEEECCCCCCCC--CCCEEEEEECCCCHHH
Q ss_conf 882354112355--204-77324368500022--2101355305443233
Q gi|254780784|r 143 LPFEGPVVGAQV--DYI-NGQYVLNPRLDEDQ--GSLDLFVSGTQDAVLM 187 (699)
Q Consensus 143 IPf~GPVaaVRV--G~i-dge~ViNPt~ee~e--sdLDLvVAGT~d~IlM 187 (699)
=|| |.++=+|| |.+ .|+.+.|++....+ +.|-.+.+-....|--
T Consensus 11 d~~-G~lsf~RVysG~l~~g~~v~n~~~~~~eri~~l~~~~~~~~~~v~~ 59 (81)
T cd04091 11 GRF-GQLTYMRIYQGKLKKGDTIYNVRTGKKVRVPRLVRMHSNEMEEVEE 59 (81)
T ss_pred CCC-CCEEEEEEEEEEECCCCEEEECCCCCEEEEEEEEEEECCCCEECCE
T ss_conf 899-8899999967288799999978689168720228997898507656
No 367
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=25.26 E-value=14 Score=15.34 Aligned_cols=88 Identities=25% Similarity=0.262 Sum_probs=47.2
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEECCEEEEEEECCCCCCCCCCCCEEEEEC-----CCCCEEEECCC
Q ss_conf 7852235667777987625950225412133200440882899863144220136551001005-----56512443245
Q gi|254780784|r 433 DGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGT-----DSGITAMQMDM 507 (699)
Q Consensus 433 ngsssma~vc~~slal~dagvp~~~~VaGiamGLi~~~~~~~iLtDI~G~ED~~GdMDFKvaGT-----~~GiTa~QmDi 507 (699)
|=|-|-||.+++--+--.|=-|-. |. .+..+++-|+ |.-|||||+|-. -+|.|.+.||.
T Consensus 180 nv~KskaSLTaArt~Ans~YCPpq---------lq---a~lDL~sGIl----hcdd~dyktA~SYF~Ea~Egft~l~~d~ 243 (421)
T COG5159 180 NVSKSKASLTAARTLANSAYCPPQ---------LQ---AQLDLLSGIL----HCDDRDYKTASSYFIEALEGFTLLKMDV 243 (421)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCHH---------HH---HHHHHHCCCE----EECCCCCHHHHHHHHHHHHCCCCCCCHH
T ss_conf 102435577899988511478888---------88---7888863621----2045551058999999982402342429
Q ss_pred CC-CCCCHHHHH----------HHHHHHHHHHHHHHHHHH
Q ss_conf 36-556889999----------999999999999999998
Q gi|254780784|r 508 KI-GGISENIMV----------MALQQAKRGRLHILNEMS 536 (699)
Q Consensus 508 K~-~gi~~~il~----------~al~~A~~gr~~il~~m~ 536 (699)
|- .-+-+-+|. .|+-.+|....|--+.|-
T Consensus 244 kAc~sLkYmlLSkIMlN~~~evk~vl~~K~t~~~y~~r~I 283 (421)
T COG5159 244 KACVSLKYMLLSKIMLNRREEVKAVLRNKNTLKHYDDRMI 283 (421)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 9999999999999998549999999816026766314568
No 368
>COG2055 Malate/L-lactate dehydrogenases [Energy production and conversion]
Probab=25.23 E-value=33 Score=12.22 Aligned_cols=50 Identities=30% Similarity=0.459 Sum_probs=33.7
Q ss_pred CCCCCCCEEEEECCCCCCCC----------CCCC-CCCCCCCCCHH--HHHHHHHHHCCCCCC-CCCCC
Q ss_conf 77735406866523201336----------7888-73578988714--531111232126776-74688
Q gi|254780784|r 53 GQDFFPLTVNYQERTYAVGK----------IPGG-YLRRESRPTEN--EILISRMIDRSIRPL-FSKCY 107 (699)
Q Consensus 53 ~~dFfPLtVdY~Ek~yAaGk----------IPGg-F~kREgrpsd~--EiL~sRlIDR~lRPL-FPkgf 107 (699)
..|-.|+.+|+=--.+|-|| ||-| -+-+||+|++. +.|-+ .++|+ .+|||
T Consensus 168 ~~~~~P~vlDmATS~va~Gki~~ar~~g~~iP~gwavD~~G~pTtDP~~a~~g-----~llp~Gg~KG~ 231 (349)
T COG2055 168 RKDGAPFVLDMATSAVARGKILVARRAGKPIPEGWAVDAEGNPTTDPEAALEG-----ALLPFGGHKGY 231 (349)
T ss_pred CCCCCCEEEECHHHHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCHHHHHHC-----CCCCCCCCCHH
T ss_conf 79999459974111877779999998299689870478999847998999613-----75356673158
No 369
>PRK00421 murC UDP-N-acetylmuramate--L-alanine ligase; Provisional
Probab=25.22 E-value=33 Score=12.22 Aligned_cols=14 Identities=36% Similarity=0.525 Sum_probs=6.3
Q ss_pred HHHHCCCCCEEEEE
Q ss_conf 55603259889999
Q gi|254780784|r 660 TSDVVKEGDTVWVK 673 (699)
Q Consensus 660 ~~d~~~~Gd~i~vk 673 (699)
..+..+.||.|-++
T Consensus 429 ~~~~a~~gDvVL~~ 442 (459)
T PRK00421 429 LADVLQPGDLVLTM 442 (459)
T ss_pred HHHHCCCCCEEEEE
T ss_conf 99858998999997
No 370
>PRK13366 protocatechuate 4,5-dioxygenase subunit beta; Provisional
Probab=25.08 E-value=31 Score=12.49 Aligned_cols=30 Identities=30% Similarity=0.365 Sum_probs=14.3
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 754453345567650246799999998741
Q gi|254780784|r 382 PCATGEVSRMGAPSRREIGHGRLARRAIHP 411 (699)
Q Consensus 382 pfsvGE~~~~~~~~RREiGHg~la~ral~~ 411 (699)
|.+||-.-..-.+.||-.--|....||+++
T Consensus 147 Pv~vN~~~~P~Ps~~Rc~~LG~Air~AIes 176 (284)
T PRK13366 147 PFAVNVVQYPVPSGRRCFALGQAIRRAVES 176 (284)
T ss_pred EEEECCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 888715679999989999999999999985
No 371
>pfam09866 DUF2093 Uncharacterized protein conserved in bacteria (DUF2093). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=25.05 E-value=33 Score=12.20 Aligned_cols=32 Identities=22% Similarity=0.229 Sum_probs=21.5
Q ss_pred CCEEEEEEEECCCCCCCCCCCCCEEEEECCCCCC
Q ss_conf 9489999972788887777354068665232013
Q gi|254780784|r 37 ETVVLATVVYDRSLKDGQDFFPLTVNYQERTYAV 70 (699)
Q Consensus 37 ~T~VLaTv~~~~~~~~~~dFfPLtVdY~Ek~yAa 70 (699)
++-|+|+|+..+=|-+...+. +||.||-|+++
T Consensus 5 G~~V~CAVsgk~IpL~~L~YW--sV~~QEaY~s~ 36 (42)
T pfam09866 5 GSFVLCAVTGEPIPLDELRYW--SVERQEAYASA 36 (42)
T ss_pred CCEEEEEEECCEECHHHCCCC--CHHHCCCCCCH
T ss_conf 999899740980026454746--61022034799
No 372
>PRK00175 metX homoserine O-acetyltransferase; Provisional
Probab=25.01 E-value=22 Score=13.63 Aligned_cols=13 Identities=38% Similarity=0.708 Sum_probs=6.9
Q ss_pred CEEEEEEECEECC
Q ss_conf 9899999140045
Q gi|254780784|r 13 GRPLKLETGRIAR 25 (699)
Q Consensus 13 gr~i~~ETGklAr 25 (699)
..++.||.|..=+
T Consensus 18 ~~~f~le~G~~L~ 30 (379)
T PRK00175 18 DEPLPLESGAVLP 30 (379)
T ss_pred CCCCCCCCCCCCC
T ss_conf 9980168988769
No 373
>PRK11607 potG putrescine transporter ATP-binding subunit; Provisional
Probab=24.96 E-value=34 Score=12.18 Aligned_cols=17 Identities=24% Similarity=0.456 Sum_probs=9.5
Q ss_pred EEEEEEEEECCEEEEEE
Q ss_conf 13320044088289986
Q gi|254780784|r 461 GIAMGLVKDGDDFIILS 477 (699)
Q Consensus 461 GiamGLi~~~~~~~iLt 477 (699)
|=.+.|-.+.|+-.+||
T Consensus 360 G~~V~l~w~~~~~~vl~ 376 (377)
T PRK11607 360 GDEVRLCWEADSCVVLT 376 (377)
T ss_pred CCEEEEEEECCCEEEEE
T ss_conf 99899998257389992
No 374
>KOG3981 consensus
Probab=24.87 E-value=22 Score=13.61 Aligned_cols=73 Identities=25% Similarity=0.369 Sum_probs=44.9
Q ss_pred HHHHHHHHHCCCCC----CCCCCCCCCEEEEEE-EEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCEE
Q ss_conf 53111123212677----674688688378999-9821888877899999999998732688235411235520477324
Q gi|254780784|r 88 EILISRMIDRSIRP----LFSKCYKNETQVIIN-VMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYV 162 (699)
Q Consensus 88 EiL~sRlIDR~lRP----LFPkgf~~evQIv~~-VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~idge~V 162 (699)
.--+-||.-|.+-| +|.+-|..+-.|-+- |--|- .-+.-|-.||.-|+ .|-||++|--|.--|||-
T Consensus 73 asnv~rLc~rA~yP~~p~~~~~~~~~dp~ihtaaVCVYP-------aRv~Da~kal~~~~--~n~~iasVA~GFPsGQyh 143 (326)
T KOG3981 73 ASNVVRLCKRAIYPVEPQFFDKFFATDPSIHTAAVCVYP-------ARVADAKKALASSK--LNSNIASVAGGFPSGQYH 143 (326)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCEEEEEEEH-------HHHHHHHHHHHHCC--CCCCHHHHHCCCCCCCHH
T ss_conf 889999999732888877888874138764223478504-------88888999998656--886237775388775057
Q ss_pred ECCCCCC
Q ss_conf 3685000
Q gi|254780784|r 163 LNPRLDE 169 (699)
Q Consensus 163 iNPt~ee 169 (699)
+....+|
T Consensus 144 Lktrl~E 150 (326)
T KOG3981 144 LKTRLLE 150 (326)
T ss_pred HHHHHHH
T ss_conf 7889999
No 375
>PRK00629 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=24.79 E-value=34 Score=12.16 Aligned_cols=47 Identities=15% Similarity=0.251 Sum_probs=31.0
Q ss_pred EEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHH
Q ss_conf 579999771150000378607799899986888998088089999689899999999
Q gi|254780784|r 552 RVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAARE 608 (699)
Q Consensus 552 ~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~ 608 (699)
|...+.++.. .||-=|+.-..+.++++.+ ..|.+|--|-+.+.....
T Consensus 637 rsA~I~~~~~----~IG~iG~lhP~i~~~~~i~------~~v~~~Ei~l~~l~~~~~ 683 (786)
T PRK00629 637 RSAAIYLGGK----VIGFIGQLHPEVLKKYDLP------GRTYVFELDLDALLERKK 683 (786)
T ss_pred CEEEEEECCE----EEEEEEEECHHHHHHCCCC------CCEEEEEEEHHHHHHHHH
T ss_conf 5799999998----9999999989999973979------988999999899443130
No 376
>PRK11067 outer membrane protein assembly factor YaeT; Provisional
Probab=24.78 E-value=14 Score=15.32 Aligned_cols=25 Identities=24% Similarity=0.343 Sum_probs=19.1
Q ss_pred HHHHHHHHCCCCCCCCCCCCCCEEE
Q ss_conf 3111123212677674688688378
Q gi|254780784|r 89 ILISRMIDRSIRPLFSKCYKNETQV 113 (699)
Q Consensus 89 iL~sRlIDR~lRPLFPkgf~~evQI 113 (699)
.+....+++.||-||-.||+.+|+|
T Consensus 53 ~~~~~~i~~~ik~L~~tg~F~dV~v 77 (801)
T PRK11067 53 TVNDEDISNTIRALFATGNFEDVRV 77 (801)
T ss_pred CCCHHHHHHHHHHHHHCCCCCEEEE
T ss_conf 2798999999999985899524899
No 377
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=24.71 E-value=34 Score=12.15 Aligned_cols=47 Identities=15% Similarity=0.184 Sum_probs=24.5
Q ss_pred HHHCCCCCCCCEEEEEEEEC-CCCEEECCCCCC-CCCCCEEEEEECCCC
Q ss_conf 87326882354112355204-773243685000-222101355305443
Q gi|254780784|r 138 LMLSGLPFEGPVVGAQVDYI-NGQYVLNPRLDE-DQGSLDLFVSGTQDA 184 (699)
Q Consensus 138 L~ISdIPf~GPVaaVRVG~i-dge~ViNPt~ee-~esdLDLvVAGT~d~ 184 (699)
.+|++.-+.---||--|+-+ |++++++|.+.. .+.-=-|+|.|+++.
T Consensus 101 ksiGdl~irq~TGaTIIAI~r~~e~I~SPgPy~vle~gDtlvviG~~~~ 149 (162)
T COG0490 101 KTIGDLNIRQNTGATVIAIVRNEEKILSPGPYTVLEAGDTLVVIGEETG 149 (162)
T ss_pred CCHHHCCCCCCCCCEEEEEEECCCEECCCCCHHHHCCCCEEEEEECCHH
T ss_conf 6144342200169689999866867128993133238999999935417
No 378
>PRK01326 prsA foldase protein PrsA; Reviewed
Probab=24.67 E-value=34 Score=12.14 Aligned_cols=80 Identities=5% Similarity=0.129 Sum_probs=51.9
Q ss_pred EEEEECCC-CHHHHHCCCCCCCHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 35530544-3233312444324899998875---3168899999999999998388986447431257999999998988
Q gi|254780784|r 176 LFVSGTQD-AVLMVELEANQLSEDVVLDAII---FGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIKED 251 (699)
Q Consensus 176 LvVAGT~d-~IlMIE~~A~EVsEe~mleAI~---~Ahe~Ik~iI~~Q~eL~~~~Gk~K~~~~~~~~~~~~~~v~~~~~~~ 251 (699)
|--||+.+ .-.-+...+..|.++++.+.++ .|+..++.++ .++=|-++.|.. +...+.+..++...+.|.+.
T Consensus 18 LaaCs~~~~~~~vat~kgg~IT~~e~Y~~~K~~~~g~q~l~~mi-~~kvLe~~Yg~k---VsdkeV~~~~~~~k~qyG~~ 93 (310)
T PRK01326 18 LAACSKTNDNTKVISMKGDTITVSDFYNEVKNNEVAQQAMLNLV-ISRVFEKQYGDK---VSDKEVEKAYHKTAKQYGAS 93 (310)
T ss_pred HHHHCCCCCCCEEEEECCCCEEHHHHHHHHHCCCHHHHHHHHHH-HHHHHHHHHCCC---CCHHHHHHHHHHHHHHHHHH
T ss_conf 98716999880689824993429999999846642899999999-999999986261---78999999999999998689
Q ss_pred HHHHHHCC
Q ss_conf 88874100
Q gi|254780784|r 252 LRVSCFIP 259 (699)
Q Consensus 252 l~~a~~i~ 259 (699)
+..++...
T Consensus 94 F~~~L~q~ 101 (310)
T PRK01326 94 FSAALAQA 101 (310)
T ss_pred HHHHHHHC
T ss_conf 99999986
No 379
>COG0223 Fmt Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]
Probab=24.64 E-value=34 Score=12.17 Aligned_cols=61 Identities=21% Similarity=0.330 Sum_probs=30.8
Q ss_pred EE-CCCCCEEEECCCCCC-C-------------CCHHHHHHHH-HHHHHHHHHHHHHHHHC--CCCCC-CCCCCCCCEEE
Q ss_conf 00-556512443245365-5-------------6889999999-99999999999999843--56674-33224487579
Q gi|254780784|r 494 AG-TDSGITAMQMDMKIG-G-------------ISENIMVMAL-QQAKRGRLHILNEMSKV--LSESR-LQLGEFTPRVE 554 (699)
Q Consensus 494 aG-T~~GiTa~QmDiK~~-g-------------i~~~il~~al-~~A~~gr~~il~~m~~~--~~~~~-~~~~~~ap~~~ 554 (699)
+| |+.|+|-+|||-++. | -|...|...| +.+.+.-.+.|..+.+- .+.|- ++-..|||++.
T Consensus 127 ~Gd~~TGvTim~M~~~lDaG~Il~q~~~~I~~~dta~~L~~kLa~~ga~lL~~~L~~i~~g~~~~~~Q~e~~~tya~ki~ 206 (307)
T COG0223 127 NGDTETGVTIMQMDEGLDAGDILAQREVPIEPDDTAGSLHDKLAELGAELLLETLPQLEAGTLTPIPQDEEEATYAPKIT 206 (307)
T ss_pred CCCCCCCEEEEECCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
T ss_conf 59860124988822457876640267704577425889999999999999999999996599877788755474034778
No 380
>PRK05568 flavodoxin; Provisional
Probab=24.45 E-value=34 Score=12.11 Aligned_cols=54 Identities=17% Similarity=0.266 Sum_probs=41.2
Q ss_pred CCEEEEECC----CCHHHHHHHHHH-CCEEEEECCEEEEEEECCHHHHHHHHHHHHHHC
Q ss_conf 150000378----607799899986-888998088089999689899999999999852
Q gi|254780784|r 561 DQIRNVIGM----GGKVIRGIVEQT-GAKVNIDDDGTVKIASSSLAEIEAAREMIRSIT 614 (699)
Q Consensus 561 ~ki~~~iG~----gG~~ik~i~~~~-~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~ 614 (699)
.|+..+.|+ +|.-++.++++. +...++-+++...-+.|+.+.+++++++=+.+.
T Consensus 82 gK~~a~FGSyGWg~Ge~v~~~~e~l~~~g~~~v~~~l~v~~~P~~e~l~~c~e~G~~~A 140 (142)
T PRK05568 82 GKKTLLFGSYGWGTGEWMEDWKERMEGYGANLVNDGLIVNNTPEGEGIEKCKALGKALA 140 (142)
T ss_pred CCEEEEEEECCCCCCHHHHHHHHHHHHCCCEEECCCEEEEECCCHHHHHHHHHHHHHHH
T ss_conf 99899999434898739999999999769978178679960799899999999999995
No 381
>COG2056 Predicted permease [General function prediction only]
Probab=24.41 E-value=34 Score=12.11 Aligned_cols=43 Identities=40% Similarity=0.517 Sum_probs=35.5
Q ss_pred CCCCCCCHHHHHH--HHHHHHHHCCCCCCCCCCEEEEEEEEECCE
Q ss_conf 1027852235667--777987625950225412133200440882
Q gi|254780784|r 430 TESDGSSSMATVC--GSSLALMDAGVPISKPVAGIAMGLVKDGDD 472 (699)
Q Consensus 430 l~sngsssma~vc--~~slal~dagvp~~~~VaGiamGLi~~~~~ 472 (699)
--+=|=|-||+|. |..-||=|||-|-++.--|=.+||=.|+..
T Consensus 371 c~~lGFSp~ati~liG~AaALGDAGSPASDSTLGPTsGLNaDGQH 415 (444)
T COG2056 371 CLKLGFSPLATIALIGTAAALGDAGSPASDSTLGPTSGLNADGQH 415 (444)
T ss_pred HHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 887188798999999999884478998644777876677887775
No 382
>COG1278 CspC Cold shock proteins [Transcription]
Probab=24.41 E-value=34 Score=12.11 Aligned_cols=57 Identities=23% Similarity=0.333 Sum_probs=33.8
Q ss_pred EEEEEEEE---CCEEEECCCC-CCEEEEEEECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 99999941---5369982879-710488663144454785560325988999999786899866687
Q gi|254780784|r 625 GQVVKVMD---FGAFVHFCGA-RDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSM 687 (699)
Q Consensus 625 ~~v~~i~~---fGafve~~~g-~~gl~HiS~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSr 687 (699)
|+|+---+ ||- +.=-.| +|-++|+|.+...... -|.+||+|..-+.. +++|..-...
T Consensus 4 GtVKwfn~~KGfGF-I~p~~G~~DvFVH~Sai~~~g~~----~L~eGQ~V~f~~~~-g~kgp~A~nv 64 (67)
T COG1278 4 GTVKWFNATKGFGF-ITPEDGGKDVFVHISAIQRAGFR----TLREGQKVEFEVEQ-GRKGPSAANV 64 (67)
T ss_pred CEEEEEECCCCCEE-ECCCCCCCCEEEEEEEECCCCCC----CCCCCCEEEEEEEC-CCCCCCEEEE
T ss_conf 16888508986337-07899985779980125127886----55799889999952-8999722678
No 383
>TIGR01774 PFL2-3 pyruvate formate-lyase; InterPro: IPR010098 This entry represents isoforms of the pyruvate-formate lyases found in a limited number of species including Escherichia coli. This enzyme converts pyruvate + CoA to acetyl-CoA + formate, which is a step in the fermentation of glucose..
Probab=24.40 E-value=34 Score=12.11 Aligned_cols=59 Identities=20% Similarity=0.162 Sum_probs=41.8
Q ss_pred CCCCCCEEEEEECCCCHHHHHC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 0222101355305443233312-4443248999988753168899999999999998388
Q gi|254780784|r 169 EDQGSLDLFVSGTQDAVLMVEL-EANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAK 227 (699)
Q Consensus 169 e~esdLDLvVAGT~d~IlMIE~-~A~EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~~~~Gk 227 (699)
..+.-|+-+++-.+..+--||- +-.+.+++.+++|++.=.++.++-|.=.-+|+++...
T Consensus 174 LL~~Gl~~l~ee~~~r~~~~~~~~~~~~~~~~FyqAa~ivleAv~~hilRya~LAeemAa 233 (812)
T TIGR01774 174 LLEKGLDELLEEVERRIRALELSVLEELEEESFYQAAKIVLEAVSEHILRYAKLAEEMAA 233 (812)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 888878999999999999876431014642028999999999999888899999999973
No 384
>cd00669 Asp_Lys_Asn_RS_core Asp_Lys_Asn_tRNA synthetase class II core domain. This domain is the core catalytic domain of class II aminoacyl-tRNA synthetases of the subgroup containing aspartyl, lysyl, and asparaginyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. Nearly all class II tRNA synthetases are dimers and enzymes in this subgroup are homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.
Probab=24.37 E-value=34 Score=12.10 Aligned_cols=51 Identities=20% Similarity=0.211 Sum_probs=30.8
Q ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEE
Q ss_conf 76502467999999987410786446873899985311027852235667777987625950225412133200
Q gi|254780784|r 393 APSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGL 466 (699)
Q Consensus 393 ~~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp~~~~VaGiamGL 466 (699)
+.+-|+.-.-.|.+|--+..+..++ ....-.-.|+++..|.| |.||+|+|+
T Consensus 195 nG~~r~~d~~~~~~r~~~~~~~~~~--------------------~~~~~~~yl~a~~~G~p---p~~G~glG~ 245 (269)
T cd00669 195 NGSSRLHDPDIQAEVFQEQGINKEA--------------------GMEYFEFYLKALEYGLP---PHGGLGIGI 245 (269)
T ss_pred CCCCCCCCHHHHHHHHHHHCCCHHH--------------------HHHHHHHHHHHHHCCCC---CCEEEEEHH
T ss_conf 3252048889999999985607445--------------------56658999999877999---971663479
No 385
>KOG2853 consensus
Probab=24.14 E-value=35 Score=12.07 Aligned_cols=13 Identities=23% Similarity=0.212 Sum_probs=7.1
Q ss_pred HHHHHHHHHCCCC
Q ss_conf 9999998732688
Q gi|254780784|r 132 VAASAALMLSGLP 144 (699)
Q Consensus 132 ~aASaAL~ISdIP 144 (699)
.|+|.|.-+-.--
T Consensus 97 ~GsS~AfWLKer~ 109 (509)
T KOG2853 97 SGSSTAFWLKERA 109 (509)
T ss_pred CCHHHHHHHHHHH
T ss_conf 5226589998876
No 386
>TIGR00770 Dcu transporter, anaerobic C4-dicarboxylate uptake (Dcu) family; InterPro: IPR004668 These proteins are members of the C4-Dicarboxylate Uptake (Dcu) family. Most proteins in this family are predicted to have 12 GES predicted transmembrane regions; however the one member whose membrane topology has been experimentally determined has 10 transmembrane regions, with both the N- and C-termini localized to the periplasm . The DcuA and DcuB proteins are involved in the transport of aspartate, malate, fumarate and succinate in many species , , , and are thought to function as antiporters with any two of these substrates. Since DcuA is encoded in an operon with the gene for aspartase, and DcuB is encoded in an operon with the gene for fumarase, their physiological functions may be to catalyze aspartate:fumarate and fumarate:malate exchange during the anaerobic utilization of aspartate and fumarate, respectively . The Escherichia coli DcuA and DcuB proteins have very different expression patterns . DcuA is constitutively expressed; DcuB is strongly induced anaerobically by FNR and C4-dicarboxylates, while it is repressed by nitrate and subject to CRP-mediated catabolite repression.; GO: 0015556 C4-dicarboxylate transmembrane transporter activity, 0015740 C4-dicarboxylate transport, 0016021 integral to membrane.
Probab=24.06 E-value=35 Score=12.06 Aligned_cols=12 Identities=33% Similarity=0.426 Sum_probs=4.3
Q ss_pred HHHHHHHHHHHC
Q ss_conf 999999998732
Q gi|254780784|r 130 SMVAASAALMLS 141 (699)
Q Consensus 130 Ai~aASaAL~IS 141 (699)
|++||++|++.|
T Consensus 52 AViAAiaAmQ~A 63 (447)
T TIGR00770 52 AVIAAIAAMQAA 63 (447)
T ss_pred HHHHHHHHHHHH
T ss_conf 999999998751
No 387
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=24.04 E-value=35 Score=12.06 Aligned_cols=62 Identities=23% Similarity=0.394 Sum_probs=35.3
Q ss_pred EEEEEEEEECCEEEECCCCCCEEEEEEECCCC--------CCCCHHHHCCCCCEEEEEEEEECC-CCCEEEEE
Q ss_conf 99999994153699828797104886631444--------547855603259889999997868-99866687
Q gi|254780784|r 624 KGQVVKVMDFGAFVHFCGARDGLVHISQLSTE--------RVAKTSDVVKEGDTVWVKLLDFDD-RGKIKLSM 687 (699)
Q Consensus 624 ~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~--------~v~~~~d~~~~Gd~i~vk~~~~d~-~g~i~lSr 687 (699)
.|+|+.+-+-=-|- -.|.+|.+..=.+.++ +-++..+-+++||.|+++-.-+.. +|+++|+.
T Consensus 3 ~~~V~~~~~~r~f~--~dg~~~~v~~~~i~D~TG~ir~t~W~~~~~~~l~~Gd~v~i~~~~v~~~~g~~el~~ 73 (82)
T cd04491 3 EGKVLSISEPREFT--RDGSEGKVQSGLVGDETGTIRFTLWDEKAADDLEPGDVVRIENAYVREFNGRLELSV 73 (82)
T ss_pred EEEEEECCCCEEEE--ECCCEEEEEEEEEECCCCEEEEEEECCCCCCCCCCCCEEEEEEEEEEEECCEEEEEE
T ss_conf 99999877887997--399768999999998998799999687444555899999996899988899799998
No 388
>PRK10776 nucleoside triphosphate pyrophosphohydrolase; Provisional
Probab=24.02 E-value=35 Score=12.05 Aligned_cols=16 Identities=25% Similarity=0.358 Sum_probs=9.1
Q ss_pred HHHHHHHHCCEEEEEC
Q ss_conf 9989998688899808
Q gi|254780784|r 574 IRGIVEQTGAKVNIDD 589 (699)
Q Consensus 574 ik~i~~~~~~~i~i~d 589 (699)
+|+|.||+|++|++.+
T Consensus 51 ~REl~EElgi~v~~~~ 66 (129)
T PRK10776 51 IRELQEEVGITPQQAT 66 (129)
T ss_pred HHHHHHHHCEEEEECC
T ss_conf 9998775171676052
No 389
>pfam04348 LppC LppC putative lipoprotein. This family includes several bacterial outer membrane antigens, whose molecular function is unknown.
Probab=24.01 E-value=19 Score=14.25 Aligned_cols=21 Identities=10% Similarity=0.278 Sum_probs=10.9
Q ss_pred EEEEEECCHHHHHHHHHHHHHH
Q ss_conf 8999968989999999999985
Q gi|254780784|r 592 TVKIASSSLAEIEAAREMIRSI 613 (699)
Q Consensus 592 ~v~i~~~~~~~~~~a~~~i~~~ 613 (699)
-|++.| +.+.+..-|-+|+..
T Consensus 401 aIfl~a-~~~~ar~ikP~l~~~ 421 (535)
T pfam04348 401 AVYIVA-NSPQLAEIKPTLANL 421 (535)
T ss_pred EEEEEC-CHHHHHHHHHHHHCC
T ss_conf 799966-889998875546403
No 390
>COG1956 GAF domain-containing protein [Signal transduction mechanisms]
Probab=23.93 E-value=35 Score=12.04 Aligned_cols=56 Identities=20% Similarity=0.348 Sum_probs=27.5
Q ss_pred CCCCCEEEEEEEEC---------CCC-EEE-----CCCCCC--CCCC----CEEEEEECCCCHHHHHCCCCC-CCHHH
Q ss_conf 82354112355204---------773-243-----685000--2221----013553054432333124443-24899
Q gi|254780784|r 144 PFEGPVVGAQVDYI---------NGQ-YVL-----NPRLDE--DQGS----LDLFVSGTQDAVLMVELEANQ-LSEDV 199 (699)
Q Consensus 144 Pf~GPVaaVRVG~i---------dge-~Vi-----NPt~ee--~esd----LDLvVAGT~d~IlMIE~~A~E-VsEe~ 199 (699)
||+|.+++||+..= .++ .++ +|.+-. ..|. .-+++-|.-=+++=|++...+ -+|++
T Consensus 68 PFqG~~acv~I~~GkGVCg~A~~~~~t~~V~DV~~~~ghiaCD~as~SEIVvPi~~~g~~iGvlDiDS~~~~~Fd~~D 145 (163)
T COG1956 68 PFQGKVACVRIPFGKGVCGTAAATGETVRVDDVHAFPGHIACDAASNSEIVVPIFKDGKLIGVLDIDSPTPGRFDEED 145 (163)
T ss_pred CCCCCCCEEEECCCCCHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCCEEEEEEEECCEEEEEEECCCCCCCCCCHHH
T ss_conf 466875448843675215778733976995112547996314644577289999889989999956899735689899
No 391
>PRK00377 cbiT cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
Probab=23.87 E-value=35 Score=12.03 Aligned_cols=90 Identities=19% Similarity=0.219 Sum_probs=58.5
Q ss_pred CCCCCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEE
Q ss_conf 24487579999771150000378607799899986888998088089999689899999999999852475468678999
Q gi|254780784|r 547 GEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQ 626 (699)
Q Consensus 547 ~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~~~e~g~~y~~~ 626 (699)
.-.||.... ..+|+-=.-+||=||.+++.|.+.....+ ...|++-+.+..-+++..|.+..+..-..+| +-+-.
T Consensus 98 ~G~ap~~l~-~l~p~pD~vFIGG~~g~l~~il~~~~~~L--~~gGriVinaVtlet~~~~~~~l~~~~~~~e---v~qv~ 171 (198)
T PRK00377 98 EGEAPEVLP-KLNPKSDRYFIGGGGEELPEIIQAALEKI--GKGGRIVADAILLESLNKALSALEELGYKYE---VTEVI 171 (198)
T ss_pred ECCHHHHHH-CCCCCCCEEEEECCCCCHHHHHHHHHHHC--CCCCEEEEEEECHHHHHHHHHHHHHCCCCCE---EEEEE
T ss_conf 525488772-08998898999788777899999999857--9998999983629889999999997699814---99999
Q ss_pred EEEEEECCEEEECCCC
Q ss_conf 9999415369982879
Q gi|254780784|r 627 VVKVMDFGAFVHFCGA 642 (699)
Q Consensus 627 v~~i~~fGafve~~~g 642 (699)
|.+-.+-|-+.-+.|.
T Consensus 172 vsr~~~lg~~~~~~~~ 187 (198)
T PRK00377 172 IAKGMKTGKGTAMIAR 187 (198)
T ss_pred EEECCCCCCCCEEECC
T ss_conf 4647325787666068
No 392
>pfam08292 RNA_pol_Rbc25 RNA polymerase III subunit Rpc25. 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.
Probab=23.85 E-value=35 Score=12.03 Aligned_cols=62 Identities=21% Similarity=0.177 Sum_probs=41.6
Q ss_pred CCCCCEEEEEEEEEEECCEEEEC------CCCCCEEEEEEECCCC---CC----CCHHHHCCCCCEEEEEEEEEC
Q ss_conf 54686789999999415369982------8797104886631444---54----785560325988999999786
Q gi|254780784|r 617 PEVNKIYKGQVVKVMDFGAFVHF------CGARDGLVHISQLSTE---RV----AKTSDVVKEGDTVWVKLLDFD 678 (699)
Q Consensus 617 ~e~g~~y~~~v~~i~~fGafve~------~~g~~gl~HiS~l~~~---~v----~~~~d~~~~Gd~i~vk~~~~d 678 (699)
|=+|+|..|+|++-..-|..|.| +=-..-|-+-|..+.. ++ +..+-++..|++|..+|.+.-
T Consensus 1 PF~gEIl~G~I~s~~~eGi~vslgFFdDI~IP~~~L~~ps~fd~~eq~WvW~~d~~~~l~~d~~e~IRFRV~~~~ 75 (120)
T pfam08292 1 PFVGEIITGKIKSSTAEGIKVSLGFFDDIFIPPDLLPEPSEFDEEEQAWVWEYDEETELYFDVGEEIRFRVESEI 75 (120)
T ss_pred CCCCCEEEEEEEECCCCCEEEEEECCCEEEECHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCCCEEEEEEEEEE
T ss_conf 987658999994058784799710242068998997886630733467992489864010368996999998879
No 393
>TIGR01800 cit_synth_II 2-methylcitrate synthase/citrate synthase II; InterPro: IPR011278 Citrate synthase 2.3.3.1 from EC is a member of a small family of enzymes that can directly form a carbon-carbon bond without the presence of metal ion cofactors. It catalyses the first reaction in the Krebs' cycle, namely the conversion of oxaloacetate and acetyl-coenzyme A into citrate and coenzyme A. This reaction is important for energy generation and for carbon assimilation. The reaction proceeds via a non-covalently bound citryl-coenzyme A intermediate in a 2-step process (aldol-Claisen condensation followed by the hydrolysis of citryl-CoA). Citrate synthase enzymes are found in two distinct structural types: type I enzymes (found in eukaryotes, Gram-positive bacteria and archaea) form homodimers and have shorter sequences than type II enzymes, which are found in Gram-negative bacteria and are hexameric in structure. In both types, the monomer is composed of two domains: a large alpha-helical domain consisting of two structural repeats, where the second repeat is interrupted by a small alpha-helical domain. The cleft between these domains forms the active site, where both citrate and acetyl-coenzyme A bind. The enzyme undergoes a conformational change upon binding of the oxaloacetate ligand, whereby the active site cleft closes over in order to form the acetyl-CoA binding site . The energy required for domain closure comes from the interaction of the enzyme with the substrate. Type II enzymes possess an extra N-terminal beta-sheet domain, and some type II enzymes are allosterically inhibited by NADH . This entry represents type I homodimeric citrate synthase enzymes (predominantly from Gram-positive bacteria and archaea), as well as 2-methylcitrate synthase; some enzyme in this entry may be bifunctional citrate synthase/2-methylcitrate synthase enzymes. Members of this family appear as a second citrate synthase isozyme but typically are associated with propionate metabolism and synthesise 2-methylcitrate from propionyl-CoA; citrate synthase activity may be incidental. A number of species, including Thermoplasma acidophilum, Pyrococcus furiosus, and the Antarctic bacterium DS2-3R have a bifunctional member of this family as the only citrate synthase isozyme . 2-methylcitrate (2.3.3.5 from EC) synthase catalyses the conversion of oxaloacetate and propanoyl-CoA into (2R,3S)-2-hydroxybutane-1,2,3-tricarboxylate and coenzyme A. This enzyme is induced during bacterial growth on propionate, while type II hexameric citrate synthase is constitutive . ; GO: 0046912 transferase activity transferring acyl groups acyl groups converted into alkyl on transfer, 0044262 cellular carbohydrate metabolic process, 0005737 cytoplasm.
Probab=23.75 E-value=28 Score=12.76 Aligned_cols=21 Identities=24% Similarity=0.273 Sum_probs=13.1
Q ss_pred CCCCHHHHHHHHHHHHHHCCC
Q ss_conf 785223566777798762595
Q gi|254780784|r 433 DGSSSMATVCGSSLALMDAGV 453 (699)
Q Consensus 433 ngsssma~vc~~slal~dagv 453 (699)
|.||-.|=||+||||=|=++|
T Consensus 193 NASTFaarv~aSTLSD~YSai 213 (386)
T TIGR01800 193 NASTFAARVIASTLSDIYSAI 213 (386)
T ss_pred CHHHHHHHHHHHHHHHHHHHH
T ss_conf 566799999998888899999
No 394
>cd01703 Pol_iota Pol iota is member of the DNA polymerase Y-family, and has also been called Rad30 homolog B. Unlike classic DNA polymerases,Y-family polymerases are induced by DNA damage. They can transverse normal replication-blocking DNA lesions. Unlike Pol eta, Pol iota is unable to replicate through a cis-syn T-T dimer. In human Pol iota, the base-pairing mode in the active site at the replicative end mat bee Hoogsteen instead of Watson-Click. Human Pol iota can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine. Pol iota prefers to insert Guanosine instead of Adenosine opposite Thymidine.
Probab=23.72 E-value=30 Score=12.52 Aligned_cols=23 Identities=13% Similarity=0.278 Sum_probs=13.4
Q ss_pred HHHHHHHHHHCCCCCCCCCEEEEEE
Q ss_conf 9999998741078644687389998
Q gi|254780784|r 402 GRLARRAIHPVLPQTAQFPYTLRIV 426 (699)
Q Consensus 402 g~la~ral~~~~P~~~~~p~tirv~ 426 (699)
=.||.+=|..++|.. -||-||+-
T Consensus 366 ~~~~~~Lf~~~~~~~--~~~~i~ll 388 (394)
T cd01703 366 LELLMKLFRRLVDVK--KPFNLTLL 388 (394)
T ss_pred HHHHHHHHHHHCCCC--CCCEEEEE
T ss_conf 999999999713468--98257798
No 395
>pfam07286 DUF1445 Protein of unknown function (DUF1445). This family represents a conserved region approximately 150 residues long within a number of hypothetical bacterial and eukaryotic proteins of unknown function.
Probab=23.54 E-value=35 Score=11.99 Aligned_cols=101 Identities=21% Similarity=0.270 Sum_probs=50.0
Q ss_pred HHHHHCCCCCCCCCCEEEEEEEEECCEEEEEEECCCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCCHHHHHHHHHHHH
Q ss_conf 98762595022541213320044088289986314422013655100100556512443245365568899999999999
Q gi|254780784|r 446 LALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAK 525 (699)
Q Consensus 446 lal~dagvp~~~~VaGiamGLi~~~~~~~iLtDI~G~ED~~GdMDFKvaGT~~GiTa~QmDiK~~gi~~~il~~al~~A~ 525 (699)
-||+.||+|++....|.-+.+..-. | .-. .-|.=...|=+-...++.+-+.+|.+-..
T Consensus 13 ~aL~~aGip~rhi~~~~nV~MY~Tn--------i----------~~~----~aG~F~g~mVVSMRp~~~~~~~~a~~iT~ 70 (143)
T pfam07286 13 EALLAAGIPVRHIEEGRNVPMYRTN--------I----------PCR----PAGPFSGPMVVSMRPIPADDVIRAVQITS 70 (143)
T ss_pred HHHHHCCCCCCCCCCCCCCCEEECC--------C----------CCC----CCCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf 9999879985332358666838658--------6----------553----56775675478740389899889996762
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCHHHHHHHH-HHCCEEEEECCEEEEEEEC
Q ss_conf 999999999984356674332244875799997711500003786077998999-8688899808808999968
Q gi|254780784|r 526 RGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVE-QTGAKVNIDDDGTVKIASS 598 (699)
Q Consensus 526 ~gr~~il~~m~~~~~~~~~~~~~~ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~-~~~~~i~i~d~g~v~i~~~ 598 (699)
.+ | ..--||.-.- +|+.|| |+.|.. ++|-.+.+. +|.|-+|=.
T Consensus 71 --------~f------p---~~HGaPihiG---dP~~iG---------I~Dl~~PD~Gd~~~~~-~gevPVFWa 114 (143)
T pfam07286 71 --------RF------P---AVHGAPVHIG---DPALIG---------IKDLSKPDFGDAVEIK-PGEVPVFWA 114 (143)
T ss_pred --------CC------C---CCCCCCEEEC---CHHHCC---------CCCCCCCCCCCCCCCC-CCCEEEEEE
T ss_conf --------38------5---5478732408---976728---------4446899899875458-997547887
No 396
>TIGR01371 met_syn_B12ind 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; InterPro: IPR006276 This group represents cobalamin-independent methionine synthase. A family of uncharacterised archaeal proteins having substantial homology to the C-terminal region of this family, are not included in this group, though they are contained in a larger family of vitamin-B12 independent methionine synthase.; GO: 0003871 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity, 0009086 methionine biosynthetic process.
Probab=23.38 E-value=36 Score=11.96 Aligned_cols=15 Identities=20% Similarity=0.286 Sum_probs=6.1
Q ss_pred HHHHHHHHHHHCCCC
Q ss_conf 999999999838898
Q gi|254780784|r 215 IEAISKLAKMCAKEP 229 (699)
Q Consensus 215 I~~Q~eL~~~~Gk~K 229 (699)
....++|.+..|+++
T Consensus 323 l~~~~~l~~~~~~~~ 337 (778)
T TIGR01371 323 LALLKKLLAHLGKDR 337 (778)
T ss_pred HHHHHHHHHHHCCCE
T ss_conf 999999998640886
No 397
>cd03169 GATase1_PfpI_1 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. PfpI is an ATP-independent intracellular proteases which may hydrolyze small peptides to provide a nutritional source. Only Cys of the catalytic triad typical of GATase1 domains is conserved in this group. This Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow.
Probab=23.37 E-value=25 Score=13.18 Aligned_cols=15 Identities=33% Similarity=0.627 Sum_probs=7.2
Q ss_pred HHHHHHHHHHHHHCC
Q ss_conf 356677779876259
Q gi|254780784|r 438 MATVCGSSLALMDAG 452 (699)
Q Consensus 438 ma~vc~~slal~dag 452 (699)
.|+||.|..+|..||
T Consensus 111 iaaIChgp~~L~~ag 125 (180)
T cd03169 111 VAAICHGPQILAAAG 125 (180)
T ss_pred EEEECCHHHHHHHCC
T ss_conf 997781689998769
No 398
>PTZ00027 60S ribosomal protein L6; Provisional
Probab=23.34 E-value=36 Score=11.96 Aligned_cols=66 Identities=18% Similarity=0.208 Sum_probs=37.2
Q ss_pred EEEEECCCCHHHHHHHHHHCCEEEEECCE-EEEEEE--CCHHH---HHHHHHHHHHHCCCCCCCCEEEEEEEE
Q ss_conf 00003786077998999868889980880-899996--89899---999999999852475468678999999
Q gi|254780784|r 563 IRNVIGMGGKVIRGIVEQTGAKVNIDDDG-TVKIAS--SSLAE---IEAAREMIRSITDVPEVNKIYKGQVVK 629 (699)
Q Consensus 563 i~~~iG~gG~~ik~i~~~~~~~i~i~d~g-~v~i~~--~~~~~---~~~a~~~i~~~~~~~e~g~~y~~~v~~ 629 (699)
.-.+=||.|..-|...- ..++|.+++++ .+.+-. .+... +--....|++|..-+..|=.|+-+++-
T Consensus 24 ~VtVkGp~G~l~r~f~h-~~v~i~~~~~~~~i~v~~~~~~rk~~A~v~T~~shI~NMikGVt~Gf~Ykmk~vy 95 (190)
T PTZ00027 24 KVTVKGKYGTLTRSFRH-LPIDLRLSKDKKYVKVVMWFGTPSKIAAIRTVCSHIKNMMTGVTKKFQYKMRLVH 95 (190)
T ss_pred EEEEECCCCEEEEEEEC-CCEEEEEECCCCEEEEEEECCCCHHEEEHHHHHHHHHHHHHHCCCCCEEEEEEEE
T ss_conf 99999189479999405-8479999479989999995697002244252999998788532378099999999
No 399
>cd02784 MopB_CT_PHLH The MopB_CT_PHLH CD includes a group of related uncharacterized putative hydrogenase-like homologs (PHLH) of molybdopterin binding proteins. This CD is of the PHLH region homologous to the conserved molybdopterin-binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=23.33 E-value=36 Score=11.96 Aligned_cols=52 Identities=25% Similarity=0.313 Sum_probs=32.0
Q ss_pred EEEEEECCEEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCE
Q ss_conf 9999989989999914004546728999978948999997278888777735406
Q gi|254780784|r 6 TVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLT 60 (699)
Q Consensus 6 ~~~~~~ggr~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~~~~~~dFfPLt 60 (699)
.+++..+++.|++-.=...-||+++|.+..|==.--+--+. ..-|.+++||.
T Consensus 57 ~v~l~~~~~si~~Pv~i~PG~~~~tv~l~lGyGr~~~g~v~---~g~G~Naypl~ 108 (137)
T cd02784 57 VVRIRRGGRTIELPVWIQPGHAEGVVLLALGYGRTHAGKVG---NGVGHNAYPFR 108 (137)
T ss_pred EEEEEECCCEEEEEEEECCCCCCCCEEECCCCCCCCCCCCC---CCCCCCCHHCC
T ss_conf 89999689279975898678689938977578855476342---55646020020
No 400
>pfam05783 DLIC Dynein light intermediate chain (DLIC). This family consists of several eukaryotic dynein light intermediate chain proteins. The light intermediate chains (LICs) of cytoplasmic dynein consist of multiple isoforms, which undergo post-translational modification to produce a large number of species. DLIC1 is known to be involved in assembly, organisation, and function of centrosomes and mitotic spindles when bound to pericentrin. DLIC2 is a subunit of cytoplasmic dynein 2 that may play a role in maintaining Golgi organisation by binding cytoplasmic dynein 2 to its Golgi-associated cargo.
Probab=23.18 E-value=13 Score=15.59 Aligned_cols=108 Identities=17% Similarity=0.171 Sum_probs=45.5
Q ss_pred CCCCEEECCCCCC-CC--CCCEEEE-EECCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 4773243685000-22--2101355-305443233312444324899998875316889999999999999838898644
Q gi|254780784|r 157 INGQYVLNPRLDE-DQ--GSLDLFV-SGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVI 232 (699)
Q Consensus 157 idge~ViNPt~ee-~e--sdLDLvV-AGT~d~IlMIE~~A~EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~~~~Gk~K~~~ 232 (699)
.+++.++.|-.+- .. -.++++| +-..|.+-++|-+-. -.||. ++|=+.+++.+| =.+|---+--
T Consensus 196 ~~d~~v~LPLgeg~Lt~NLGiPIvVV~tKsD~me~LEKe~d-y~dEh----FDfIqq~LR~fC-------LqyGAALiYT 263 (490)
T pfam05783 196 SDDDSVLLPLGENVLTHNLGIPVVVVCTKCDAMSVLEKEHD-YRDEH----FDFIQSHIRRFC-------LQYGAALIYT 263 (490)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHCC-CCHHH----HHHHHHHHHHHH-------HHCCCEEEEE
T ss_conf 66664214689871000479877999946418888765126-20677----899999999999-------8619657885
Q ss_pred C---CCCHHHHHHHHHHH-HHHHH--------HHHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf 7---43125799999999-89888--------887410001224899999999997
Q gi|254780784|r 233 D---SKDFSKLEEEMSQM-IKEDL--------RVSCFIPEKYVRCKQIDDLKKKMV 276 (699)
Q Consensus 233 ~---~~~~~~~~~~v~~~-~~~~l--------~~a~~i~~K~eR~~ai~~l~~ei~ 276 (699)
. ....+-+++++.-. |.-.+ +++++++.--+-.++|..+.+...
T Consensus 264 SvKe~kN~dlLykYl~HRiYgfpF~~pa~vvekDaVFIPaGWD~~kKI~il~EN~~ 319 (490)
T pfam05783 264 SVKEEKNLDLLYKYLVHKIYGFPFNTPALVVEKDAVFIPAGWDNEKKIGILHENFQ 319 (490)
T ss_pred ECCCCCCHHHHHHHHHHHHCCCCCCCCCEEEECCCEEECCCCCCHHHHHHHHHHCC
T ss_conf 23545018999999998861887798644640353573278772766556676432
No 401
>TIGR00761 argB acetylglutamate kinase; InterPro: IPR004662 N -Acetylglutamate (NAG) fulfils distinct biological roles in lower and higher organisms. In prokaryotes, lower eukaryotes and plants it is the first intermediate in the biosynthesis of arginine, whereas in ureotelic (excreting nitrogen mostly in the form of urea) vertebrates, it is an essential allosteric cofactor for carbamyl phosphate synthetase I (CPSI), the first enzyme of the urea cycle. The pathway that leads from glutamate to arginine in lower organisms employs eight steps, starting with the acetylation of glutamate to form NAG. In these species, NAG can be produced by two enzymatic reactions: one catalysed by NAG synthase (NAGS) and the other by ornithine acetyltransferase (OAT). In ureotelic species, NAG is produced exclusively by NAGS. In lower organisms, NAGS is feedback-inhibited by L-arginine, whereas mammalian NAGS activity is significantly enhanced by this amino acid. The NAGS genes of bacteria, fungi and mammals are more diverse than other arginine-biosynthesis and urea-cycle genes. The evolutionary relationship between the distinctly different roles of NAG and its metabolism in lower and higher organisms remains to be determined . The pathway from glutamate to arginine is: NAGS; N-acetylglutamate synthase (2.3.1.1 from EC) (glutamate to N-acetylglutamate) NAGK; N-acetylglutamate kinase (2.7.2.8 from EC) (N-acetylglutamate to N-acetylglutamate-5P) NAGSA; N-acetyl-gamma-glutamyl-phosphate reductase (1.2.1.38 from EC) (N-acetylglutamate-5P to N-acetylglumate semialdehyde) Acetylornithine aminotransferase (2.6.1.11 from EC) (N-acetylglumate semialdehyde to N-acetylornithine) Acetylornithine deacetylase (3.5.1.16 from EC) (N-acetylornithine to ornithine) Arginase (3.5.3.1 from EC) (ornithine to arginine) This entry describes N-acetylglutamate kinases (ArgB) of many prokaryotes and the N-acetylglutamate kinase domains of multifunctional proteins from yeasts as well as some, as yet, uncharacterised proteins.; GO: 0003991 acetylglutamate kinase activity, 0006526 arginine biosynthetic process, 0005737 cytoplasm.
Probab=23.12 E-value=36 Score=11.93 Aligned_cols=25 Identities=12% Similarity=0.304 Sum_probs=18.2
Q ss_pred ECCEEEEEEECCCCCCCCCCCCEEE
Q ss_conf 0882899863144220136551001
Q gi|254780784|r 469 DGDDFIILSDISGDEDHLGHMDFKV 493 (699)
Q Consensus 469 ~~~~~~iLtDI~G~ED~~GdMDFKv 493 (699)
+-++-..|||+-|.=.+|-|-+-.|
T Consensus 188 ~A~kL~~LtDv~Gi~~~y~d~~~~i 212 (254)
T TIGR00761 188 GAEKLVLLTDVPGILNGYPDKQSLI 212 (254)
T ss_pred CCCEEEEECCCHHHHCCCCCCCCEE
T ss_conf 9953888417403225888746140
No 402
>cd07367 CarBb CarBb is the B subunit of the Class III Extradiol ring-cleavage dioxygenase, 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBb is the B subunit of 2-aminophenol 1,6-dioxygenase (CarB), which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. It is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, it has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=23.10 E-value=34 Score=12.13 Aligned_cols=33 Identities=15% Similarity=0.197 Sum_probs=18.4
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 754453345567650246799999998741078
Q gi|254780784|r 382 PCATGEVSRMGAPSRREIGHGRLARRAIHPVLP 414 (699)
Q Consensus 382 pfsvGE~~~~~~~~RREiGHg~la~ral~~~~P 414 (699)
|-.+|-.-..-.+.||-.--|+...||++...|
T Consensus 136 Pv~vN~~~~P~p~~~R~~~lG~air~ai~~~~~ 168 (268)
T cd07367 136 PLIVNINTDPAPSPRRCWALGKVLAQYVEKRRP 168 (268)
T ss_pred EEEECCCCCCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf 986212058999989999999999999997187
No 403
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=23.09 E-value=27 Score=13.00 Aligned_cols=41 Identities=17% Similarity=0.232 Sum_probs=17.5
Q ss_pred CCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEE----EEEECCCC
Q ss_conf 188887789999999999873268823541123----55204773
Q gi|254780784|r 120 HDLESSPHVVSMVAASAALMLSGLPFEGPVVGA----QVDYINGQ 160 (699)
Q Consensus 120 ~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaV----RVG~idge 160 (699)
.+....+..-+.+++=-..+=.+++.-|.-.++ +-|+.||.
T Consensus 86 ~~~~~~~~~~~l~~~Lr~~~~~G~~l~gictGaf~LA~aGLLdGr 130 (328)
T COG4977 86 LGPERPVNAPALLAWLRRAARRGARLGGLCTGAFVLAEAGLLDGR 130 (328)
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCCEEEEEHHHHHHHHHHCCCCCC
T ss_conf 775444564999999999984699588860869999971153799
No 404
>PRK13364 protocatechuate 4,5-dioxygenase subunit beta; Provisional
Probab=23.05 E-value=36 Score=11.92 Aligned_cols=41 Identities=20% Similarity=0.374 Sum_probs=18.2
Q ss_pred EEEEEECCCCCCCCCCCC-------CCCCCCH-HHHHHHHHHHHHHHCCC
Q ss_conf 587740588754453345-------5676502-46799999998741078
Q gi|254780784|r 373 DFMMHYNFLPCATGEVSR-------MGAPSRR-EIGHGRLARRAIHPVLP 414 (699)
Q Consensus 373 ~fmlHYNFPpfsvGE~~~-------~~~~~RR-EiGHg~la~ral~~~~P 414 (699)
+|++. |+|+|++|-.-. .|.+..+ =-||..||+.-+..++.
T Consensus 62 nFf~d-~~P~FaIG~a~~y~~~deg~g~~~~~~v~G~~~lA~hi~~~l~~ 110 (279)
T PRK13364 62 NFFLD-KMPTFAVGAAPEYSNADEGWGIPTLAPFKGDTELSWHIIESLVE 110 (279)
T ss_pred HCCCC-CCCCEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 42645-78976997530107777667888788788989999999999987
No 405
>COG2428 Uncharacterized conserved protein [Function unknown]
Probab=22.93 E-value=36 Score=11.90 Aligned_cols=32 Identities=19% Similarity=0.358 Sum_probs=16.4
Q ss_pred EEEECCCCCCHHHHHHHH-HHHHHHHCCCCCCCC
Q ss_conf 998218888778999999-999987326882354
Q gi|254780784|r 116 NVMQHDLESSPHVVSMVA-ASAALMLSGLPFEGP 148 (699)
Q Consensus 116 ~VLS~D~~~dpdvlAi~a-ASaAL~ISdIPf~GP 148 (699)
.|.+++++ .|.++|-++ +...-++++.|++++
T Consensus 32 ~vtna~pe-~p~vlak~g~~~i~e~~~~~~l~r~ 64 (196)
T COG2428 32 IVTNAKPE-EPEVLAKIGLSGIPESITRLPLDRS 64 (196)
T ss_pred EEECCCCC-HHHHHHHHCCCCCCHHHHHCCCCCC
T ss_conf 66057862-1579998265668636762636789
No 406
>PRK13108 prolipoprotein diacylglyceryl transferase; Reviewed
Probab=22.90 E-value=26 Score=13.14 Aligned_cols=72 Identities=19% Similarity=0.165 Sum_probs=33.5
Q ss_pred CCCCCCCCCCCCCC--CCCCHHHHHHHHHHHCCCCCCCCCCCCCCEEEEE----EEE-ECCCCCCHHHHHHHHHHHHHHH
Q ss_conf 01336788873578--9887145311112321267767468868837899----998-2188887789999999999873
Q gi|254780784|r 68 YAVGKIPGGYLRRE--SRPTENEILISRMIDRSIRPLFSKCYKNETQVII----NVM-QHDLESSPHVVSMVAASAALML 140 (699)
Q Consensus 68 yAaGkIPGgF~kRE--grpsd~EiL~sRlIDR~lRPLFPkgf~~evQIv~----~VL-S~D~~~dpdvlAi~aASaAL~I 140 (699)
-|.||+ |+||-.| |||++--= .=-|+---|| .+|.+.-.+.. .+. -+-+..-++.|=-.+.-+.|..
T Consensus 140 QAIGRw-GNFFNQELyGrPTdLPW--GLeI~~~~~p---~g~~~~~~~~G~~~g~v~~~fHPTFLYEsLWNl~va~lLl~ 213 (460)
T PRK13108 140 QAIGRL-GNYFNQELYGRETTMPW--GLEIFYRRDP---SGFDVPNSLDGVSTGQVAFVVQPTFLYELIWNVLVFVALIY 213 (460)
T ss_pred HHHCHH-HHHHCHHHCCCCCCCCC--CEECCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHE
T ss_conf 984404-64305122389888864--0135501386---54567533466556655665173389999999999999730
Q ss_pred CCCCC
Q ss_conf 26882
Q gi|254780784|r 141 SGLPF 145 (699)
Q Consensus 141 SdIPf 145 (699)
-+--|
T Consensus 214 ldRr~ 218 (460)
T PRK13108 214 IDRRF 218 (460)
T ss_pred ECCCC
T ss_conf 22130
No 407
>pfam10646 Germane Sporulation and spore germination. The GerMN domain is a region of approximately 100 residues that is found, duplicated, in the Bacillus GerM protein and is implicated in both sporulation and spore germination. The domain is found in a number of different bacterial species both alone and in association with other domains such as Amidase_3 pfam01520, Gmad1 and Gmad2. It is predicted to have a novel alpha-beta fold.
Probab=22.58 E-value=37 Score=11.85 Aligned_cols=60 Identities=18% Similarity=0.206 Sum_probs=37.7
Q ss_pred CCCCCCCCCCCCEEEEEE-EEECCC------CCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCEE
Q ss_conf 677674688688378999-982188------8877899999999998732688235411235520477324
Q gi|254780784|r 99 IRPLFSKCYKNETQVIIN-VMQHDL------ESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYV 162 (699)
Q Consensus 99 lRPLFPkgf~~evQIv~~-VLS~D~------~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~idge~V 162 (699)
+++.||++....+.+.-. ++-.|= ..+++......+|...++...|- |..|++ +++|+-+
T Consensus 46 ~~~~iP~~~~l~~~~~~~~~~~Vdfs~~~~~~~~~~~e~~~~~qiv~TL~~~~~---v~~V~i-~v~G~~~ 112 (116)
T pfam10646 46 LVSALPPGTKLSVSLKDGGVATVDLSSEFLDGGGSAAEELLLAQLVLTLTQFPG---VDKVQI-LVDGKPL 112 (116)
T ss_pred CCCCCCCCCEEEEEECCCCEEEEECCHHHHHCCCHHHHHHHHHHHHHHHHCCCC---CCEEEE-EECCEEC
T ss_conf 001388872887898349879997577776337828999999999999974899---536999-9999983
No 408
>pfam09869 DUF2096 Uncharacterized protein conserved in archaea (DUF2096). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=22.56 E-value=37 Score=11.85 Aligned_cols=79 Identities=18% Similarity=0.222 Sum_probs=46.6
Q ss_pred HHHHHHHHHCCCC-----CCCCCCCC------CCEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEE
Q ss_conf 9999999843566-----74332244------875799997711500003786077998999868889980880899996
Q gi|254780784|r 529 LHILNEMSKVLSE-----SRLQLGEF------TPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIAS 597 (699)
Q Consensus 529 ~~il~~m~~~~~~-----~~~~~~~~------ap~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~ 597 (699)
..-|+.|.++..- ....-|.| -|..++++|.-.+=- .=-....|.|-.|+-++-+|+..|.|+|
T Consensus 77 ~~~l~km~kA~rge~~~efp~~kS~Fn~~vk~~~g~e~iRv~l~~~l-----~~Erl~el~E~~GvIfE~ee~dkV~i~G 151 (169)
T pfam09869 77 KEYLDKMGKALRGEEVFEFPLKKSKFNVEVKRPKGFETIRVNLPEPL-----HEERLGELSEYHGVIFEFEENDKVIIEG 151 (169)
T ss_pred HHHHHHHHHHHCCCHHHCCCCCHHHCCHHCCCCCCCEEEEEECCCCC-----HHHHHHHHHHHHCEEEEECCCCEEEEEC
T ss_conf 99999999986065100275201002220389998606898578511-----2999988888745478834786799966
Q ss_pred CCHHHHHHHHHHHHHH
Q ss_conf 8989999999999985
Q gi|254780784|r 598 SSLAEIEAAREMIRSI 613 (699)
Q Consensus 598 ~~~~~~~~a~~~i~~~ 613 (699)
+++.+.+|..-...+
T Consensus 152 -~kd~i~~ALKe~~~~ 166 (169)
T pfam09869 152 -DKDRIKKALKEFSSF 166 (169)
T ss_pred -CHHHHHHHHHHHHHH
T ss_conf -689999999999988
No 409
>PRK07165 F0F1 ATP synthase subunit alpha; Validated
Probab=22.42 E-value=29 Score=12.70 Aligned_cols=20 Identities=15% Similarity=0.243 Sum_probs=10.2
Q ss_pred HHHHHHHHCCCCCCCCCCCC
Q ss_conf 31111232126776746886
Q gi|254780784|r 89 ILISRMIDRSIRPLFSKCYK 108 (699)
Q Consensus 89 iL~sRlIDR~lRPLFPkgf~ 108 (699)
=|..|+||=-=+|+-|++..
T Consensus 78 ~lLGRVVD~LG~pidp~~~~ 97 (507)
T PRK07165 78 EYFGKIIDIDGNIIYPKAAN 97 (507)
T ss_pred CCCCCEECCCCCCCCCCCCC
T ss_conf 64463688999867898988
No 410
>pfam00347 Ribosomal_L6 Ribosomal protein L6.
Probab=22.34 E-value=37 Score=11.81 Aligned_cols=63 Identities=16% Similarity=0.229 Sum_probs=47.8
Q ss_pred CEEEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHCC
Q ss_conf 75799997711500003786077998999868889980880899996898999999999998524
Q gi|254780784|r 551 PRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITD 615 (699)
Q Consensus 551 p~~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~~ 615 (699)
|.=.++.++-..+-.+.||-|..-+.+-+ +++|.+++.-.+.+++.|++.+.+..++|..+..
T Consensus 2 p~Gv~v~i~g~~l~~v~G~kg~l~~~i~~--~v~i~~~~~~~~~~~~~dk~~v~~~aa~i~~~r~ 64 (76)
T pfam00347 2 PVGVRVSIDGVNLVLVLGPKGELTREIPP--GVTVKVEKITVIIVSGIDKEKVGQFAALIGTYRA 64 (76)
T ss_pred CCCEEEEEECCEEEEEECCCCCEEEECCC--CEEEEECCCCEEEEECCCHHHHHHHHHHHHHHCC
T ss_conf 97689999699899938688368887899--8899978997899836988998999999876179
No 411
>COG4717 Uncharacterized conserved protein [Function unknown]
Probab=22.18 E-value=37 Score=11.79 Aligned_cols=10 Identities=20% Similarity=0.581 Sum_probs=4.7
Q ss_pred EECCCCEEEE
Q ss_conf 9771150000
Q gi|254780784|r 557 AIPPDQIRNV 566 (699)
Q Consensus 557 ~i~~~ki~~~ 566 (699)
.++|+.+-++
T Consensus 606 el~~~~~~d~ 615 (984)
T COG4717 606 ELSPEQQLDI 615 (984)
T ss_pred CCCCHHHHHH
T ss_conf 5891889999
No 412
>TIGR03303 OM_YaeT outer membrane protein assembly complex, YaeT protein. Members of this protein family are the YaeT protein of the YaeT/YfiO complex for assembling proteins into the outer membrane of Gram-negative bacteria. This protein is similar in sequence and function to a non-essential paralog, YtfM, that is also in the Omp85 family. Members of this family typically have five tandem copies of the surface antigen variable number repeat (pfam07244), followed by an outer membrane beta-barrel domain (pfam01103), while the YtfM family typically has a single pfam07244 repeat.
Probab=22.16 E-value=19 Score=14.28 Aligned_cols=23 Identities=22% Similarity=0.521 Sum_probs=11.2
Q ss_pred HHHHHHCCCCCCCCCCCCCCEEE
Q ss_conf 11123212677674688688378
Q gi|254780784|r 91 ISRMIDRSIRPLFSKCYKNETQV 113 (699)
Q Consensus 91 ~sRlIDR~lRPLFPkgf~~evQI 113 (699)
....+++.||-|+-.||..+++|
T Consensus 32 ~~~~i~~~ik~L~~tg~F~dv~v 54 (741)
T TIGR03303 32 SDEKIDEAIKALYATGYFEDVKI 54 (741)
T ss_pred CHHHHHHHHHHHHHCCCCEEEEE
T ss_conf 99999999999996799005899
No 413
>TIGR01448 recD_rel helicase, RecD/TraA family; InterPro: IPR006345 These sequences represent a family similar to RecD, the exodeoxyribonuclease V alpha chain of IPR006344 from INTERPRO. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. .
Probab=21.98 E-value=29 Score=12.65 Aligned_cols=33 Identities=9% Similarity=0.190 Sum_probs=17.7
Q ss_pred CCCEEECCCCC-CCC-CCCEEE---EEECCCC-HHHHHC
Q ss_conf 77324368500-022-210135---5305443-233312
Q gi|254780784|r 158 NGQYVLNPRLD-EDQ-GSLDLF---VSGTQDA-VLMVEL 190 (699)
Q Consensus 158 dge~ViNPt~e-e~e-sdLDLv---VAGT~d~-IlMIE~ 190 (699)
.|+|+-|+.|- |.+ +.++.. ---++++ |.-.++
T Consensus 57 ~Gq~~~h~~yG~q~~~~~~~~~amP~~~~~~gi~~Yl~S 95 (769)
T TIGR01448 57 EGQWEEHAKYGKQFKAERMEKEAMPAPTSKEGIVAYLSS 95 (769)
T ss_pred EEEEEECCCCCEEEEEEEEHHHHCCCCCHHHHHHHHHHC
T ss_conf 898888754451523352014307886506787655522
No 414
>pfam03610 EIIA-man PTS system fructose IIA component.
Probab=21.96 E-value=38 Score=11.76 Aligned_cols=47 Identities=23% Similarity=0.455 Sum_probs=27.3
Q ss_pred ECCEEEEEEECCCCCCCCCCCCEEEEECCCCCEEE-ECCCC-CCCCCHHHHHHHHHHHH
Q ss_conf 08828998631442201365510010055651244-32453-65568899999999999
Q gi|254780784|r 469 DGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAM-QMDMK-IGGISENIMVMALQQAK 525 (699)
Q Consensus 469 ~~~~~~iLtDI~G~ED~~GdMDFKvaGT~~GiTa~-QmDiK-~~gi~~~il~~al~~A~ 525 (699)
+++...||||+.|-- -|..|-. -.+ .-+++ +.|+++.++.+|+...-
T Consensus 57 ~~~~vliltDl~GGt------p~n~a~~----~~~~~~~v~visG~NLPmllea~~~r~ 105 (117)
T pfam03610 57 SGDGVLVLVDLGGGT------PFNEAAL----ELLEKPDIEVITGVNLPMVEEAVAARA 105 (117)
T ss_pred CCCEEEEEEECCCCC------HHHHHHH----HHCCCCCEEEEEECCHHHHHHHHHHHH
T ss_conf 998099998679997------8999999----970479879999624999999999756
No 415
>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family; InterPro: IPR004589 The ATP-dependent DNA helicase RecQ (3.6.1 from EC) is involved in genome maintenance . All homologues tested to date unwind paired DNA, translocating in a 3' to 5' direction and several have a preference for forked or 4-way DNA structures (e.g. Holliday junctions) or for G-quartet DNA. The yeast protein, Sgs1, is present in numerous foci that coincide with sites of de novo synthesis DNA, such as the replication fork, and protein levels peak during S-phase. A model has been proposed for Sgs1p action in the S-phase checkpoint response, both as a 'sensor' for damage during replication and a 'resolvase' for structures that arise at paused forks, such as the four-way 'chickenfoot' structure. The action of Sgs1p may serve to maintain the proper amount and integrity of ss DNA that is necessary for the binding of RPA (replication protein A, the eukaryotic ss DNA-binding protein)DNA pol complexes. Sgs1p would thus function by detecting (or resolving) aberrant DNA structures, and would thus contribute to the full activation of the DNA-dependent protein kinase, Mec1p and the effector kinase, Rad53p. Its ability to bind both the large subunit of RPA and the RecA-like protein Rad51p, place it in a unique position to resolve inappropriate fork structures that can occur when either the leading or lagging strand synthesis is stalled. Thus, RecQ helicases integrate checkpoint activation and checkpoint response. ; GO: 0008026 ATP-dependent helicase activity, 0006310 DNA recombination.
Probab=21.87 E-value=38 Score=11.75 Aligned_cols=47 Identities=28% Similarity=0.536 Sum_probs=30.5
Q ss_pred EEE-ECCCEEE-EEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCC------CCCCCCCCCCCC
Q ss_conf 999-8797689-9998168652122334454420358774058875------445334556765
Q gi|254780784|r 340 LFI-RGDTQAI-VVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPC------ATGEVSRMGAPS 395 (699)
Q Consensus 340 LFt-RGETQaL-~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpf------svGE~~~~~~~~ 395 (699)
=|. |-|-|+. +|+.+|+.=|- ..=||-.||..|=- =+|.+||-|-++
T Consensus 286 ~f~nrD~~QvVvATvAFGMGInK---------pdvRfViH~~~Pk~~EsYYQE~GRAGRDgl~s 340 (497)
T TIGR00614 286 KFQNRDEIQVVVATVAFGMGINK---------PDVRFVIHYSLPKSMESYYQESGRAGRDGLPS 340 (497)
T ss_pred HHHCCCCCEEEEEEEECCCCCCC---------CCCCEEEEECCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 87503885799987212688876---------35367885078856211013555567897320
No 416
>PTZ00179 60S ribosomal protein L9; Provisional
Probab=21.87 E-value=38 Score=11.74 Aligned_cols=66 Identities=15% Similarity=0.178 Sum_probs=25.5
Q ss_pred CEEEEECCCCHHHHHHHHHHCCEEEEECC-EEEEEEE--CCHHH---HHHHHHHHHHHCCCCCCCCEEEEEEE
Q ss_conf 50000378607799899986888998088-0899996--89899---99999999985247546867899999
Q gi|254780784|r 562 QIRNVIGMGGKVIRGIVEQTGAKVNIDDD-GTVKIAS--SSLAE---IEAAREMIRSITDVPEVNKIYKGQVV 628 (699)
Q Consensus 562 ki~~~iG~gG~~ik~i~~~~~~~i~i~d~-g~v~i~~--~~~~~---~~~a~~~i~~~~~~~e~g~~y~~~v~ 628 (699)
+.-.+=||.|..-|...- ..++|.++++ ..+.+.. .++.. +--...+|++|..-+..|=.|+-+++
T Consensus 22 ~~VtVkGp~G~L~r~f~h-~~v~i~i~~~~~~i~v~~~~~~rk~~A~igT~~shI~NMikGVT~Gf~Ykmk~v 93 (189)
T PTZ00179 22 RIVTVKGKRGTLTKDLRH-LQLDFRVNKKNRTFTAVRWFGSKIPNSTINTALSHVRNMITGVTKGFRFKVRFA 93 (189)
T ss_pred CEEEEECCCCEEEEEEEC-CCEEEEEECCCCEEEEEECCCCHHHEEEHHHHHHHHHHHHHHCCCCEEEEEEEE
T ss_conf 999999899589989556-957999957974899987378741400046199999987753018749999999
No 417
>pfam00152 tRNA-synt_2 tRNA synthetases class II (D, K and N).
Probab=21.86 E-value=38 Score=11.74 Aligned_cols=67 Identities=25% Similarity=0.313 Sum_probs=39.5
Q ss_pred CCEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf 42035877405887544533455676502467999999987410786446873899985311027852235667777987
Q gi|254780784|r 369 TQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLAL 448 (699)
Q Consensus 369 ~~~k~fmlHYNFPpfsvGE~~~~~~~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal 448 (699)
...+||-|-++ -+|.. +.+-|+.---.+.+|--..-+.. .+ .-..-.-.|..
T Consensus 251 ~~a~rFel~~~-----G~Ei~---nG~~el~d~~~~~~rf~~~~~~~-------------------~~-~~~~d~~yl~a 302 (341)
T pfam00152 251 GLAERFDLVLN-----GGEIG---GGSIRIHDPEEQRKRFEELGLDP-------------------EE-AEEKFGFYLDA 302 (341)
T ss_pred CCHHEEEECCC-----CEEEE---CCCCCCCCHHHHHHHHHHHCCCH-------------------HH-HHHHHHHHHHH
T ss_conf 50121575269-----74982---57534599999999999819890-------------------23-35658999999
Q ss_pred HHCCCCCCCCCCEEEEEE
Q ss_conf 625950225412133200
Q gi|254780784|r 449 MDAGVPISKPVAGIAMGL 466 (699)
Q Consensus 449 ~dagvp~~~~VaGiamGL 466 (699)
+..|.| |.||++||+
T Consensus 303 ~~~G~P---P~~G~glGi 317 (341)
T pfam00152 303 LKYGMP---PHGGIGLGL 317 (341)
T ss_pred HHCCCC---CCEEEEEHH
T ss_conf 866979---970565789
No 418
>pfam06951 PLA2G12 Group XII secretory phospholipase A2 precursor (PLA2G12). This family consists of several group XII secretory phospholipase A2 precursor (PLA2G12) (EC:3.1.1.4) proteins. Group XII and group V PLA(2)s are thought to participate in helper T cell immune response through release of immediate second signals and generation of downstream eicosanoids.
Probab=21.79 E-value=11 Score=16.16 Aligned_cols=23 Identities=22% Similarity=0.255 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99887531688999999999999
Q gi|254780784|r 200 VLDAIIFGHNECKPVIEAISKLA 222 (699)
Q Consensus 200 mleAI~~Ahe~Ik~iI~~Q~eL~ 222 (699)
-+..|.-+.+.|-...++--||.
T Consensus 31 ~l~tir~~f~~v~~yfdaalel~ 53 (186)
T pfam06951 31 TLKTIRNGFHKVDGYFDAALELL 53 (186)
T ss_pred HHHHHHHHCCHHHHHHHHHHHHH
T ss_conf 89999862034989999999984
No 419
>TIGR02941 Sigma_B RNA polymerase sigma-B factor; InterPro: IPR014288 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the sigma factor, sigmaB. It is restricted to certain species within the order Bacillales including Staphylococcus aureus , Listeria monocytogenes and Bacillus cereus (strain ATCC 14579 / DSM 31) ..
Probab=21.75 E-value=38 Score=11.73 Aligned_cols=35 Identities=26% Similarity=0.161 Sum_probs=18.6
Q ss_pred HCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 124443248999988753168899999999999998
Q gi|254780784|r 189 ELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKM 224 (699)
Q Consensus 189 E~~A~EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~~~ 224 (699)
...+++++.+++..=|+.=|+.-+ --++|++|+.+
T Consensus 4 ~sqp~n~~~e~v~~wI~e~Q~nP~-n~eaQeklV~h 38 (256)
T TIGR02941 4 KSQPTNLTKEDVIQWIKEFQKNPK-NEEAQEKLVKH 38 (256)
T ss_pred CCCCCCCCHHHHHHHHHHHCCCCC-CHHHHHHHHHH
T ss_conf 657655788789999999636998-32578999999
No 420
>cd08041 OBF_kDNA_ligase_like The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. The mitochondrial DNA of parasitic protozoan is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-de
Probab=21.66 E-value=38 Score=11.71 Aligned_cols=50 Identities=20% Similarity=0.222 Sum_probs=31.1
Q ss_pred CCEEEECCC-CCCEEEEE-EECCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 536998287-97104886-63144454785560325988999999786899866687
Q gi|254780784|r 633 FGAFVHFCG-ARDGLVHI-SQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSM 687 (699)
Q Consensus 633 fGafve~~~-g~~gl~Hi-S~l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~g~i~lSr 687 (699)
.|+|+--.+ |++ ..| |.++++.- ++..++|..|+||+.+..+.|..|+-+
T Consensus 21 lG~~~~~~~~G~~--F~vgsG~td~~R---~~~~~iG~~it~ky~~~t~~g~PRFP~ 72 (77)
T cd08041 21 LGALVVETKDGIR--FKIGSGFSDEQR---RNPPPIGSIITYKYQGLTKNGLPRFPV 72 (77)
T ss_pred EEEEEEEECCCCE--EECCCCCCHHHH---HCCCCCCCEEEEEEECCCCCCCCCCCE
T ss_conf 3799999899988--972787699998---366458979999996407899854757
No 421
>TIGR03561 organ_hyd_perox peroxiredoxin, Ohr subfamily. pfam02566, OsmC-like protein, contains several deeply split clades of homologous proteins. The clade modeled here includes the protein Ohr, or organic hydroperoxide resistance protein.
Probab=21.47 E-value=39 Score=11.69 Aligned_cols=27 Identities=7% Similarity=0.170 Sum_probs=21.1
Q ss_pred EECCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 432453655688999999999999999
Q gi|254780784|r 503 MQMDMKIGGISENIMVMALQQAKRGRL 529 (699)
Q Consensus 503 ~QmDiK~~gi~~~il~~al~~A~~gr~ 529 (699)
..++++++|+..+-.++.+++|++.|.
T Consensus 93 v~l~v~vpg~d~~~a~~lv~~A~~~CP 119 (134)
T TIGR03561 93 VELKVTLPGLDQAEAEALVEAAHQVCP 119 (134)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHCC
T ss_conf 999996799899999999999986494
No 422
>cd07950 Gallate_Doxase_N The N-terminal domain of the Class III extradiol dioxygenase, Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. In this subfamily, the subunits A and B are fused to make a single polypeptide chain. The dimer interface for this subfamily may resemble the tetramer interface of classical LigAB en
Probab=21.36 E-value=36 Score=11.92 Aligned_cols=112 Identities=22% Similarity=0.286 Sum_probs=52.4
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCE
Q ss_conf 75445334556765024679999999874107864468738999853110278522356677779876259502254121
Q gi|254780784|r 382 PCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAG 461 (699)
Q Consensus 382 pfsvGE~~~~~~~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp~~~~VaG 461 (699)
|-.+|-.-..-.+.||-.--|....||+++ .| --.||. |+-|-|=|-. |.|
T Consensus 147 Pv~vN~~~~P~p~~~Rc~~LG~Air~aies-~p------~D~RVa--vigTGGLSH~--------------------v~g 197 (277)
T cd07950 147 PLQVGVLQFPLPTARRCYKLGQALRRAIES-YP------EDLKVA--VVGTGGLSHQ--------------------VHG 197 (277)
T ss_pred EEEECCCCCCCCCHHHHHHHHHHHHHHHHH-CC------CCCEEE--EEECCCCCCC--------------------CCC
T ss_conf 898647679998989999999999999985-78------885299--9946865465--------------------687
Q ss_pred EEEEEEEECCEEEEEEECCCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 33200440882899863144220136551001005565124432453655688999999999999999999999843566
Q gi|254780784|r 462 IAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSE 541 (699)
Q Consensus 462 iamGLi~~~~~~~iLtDI~G~ED~~GdMDFKvaGT~~GiTa~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m~~~~~~ 541 (699)
=-+|+|-+.=+...| | ++.+..+.++++. ..+++++|=.+.-+=|+-+ .|..+++.
T Consensus 198 ~raG~iN~efD~~fL-------------d-~l~~d~~~l~~~~--------~~e~~~~aG~~g~Ei~~Wl--~m~gAl~~ 253 (277)
T cd07950 198 ERAGFNNTEWDMEFL-------------D-LIENDPESLAAMT--------HADYATLGGAEGAEVIMWL--IMRGALSD 253 (277)
T ss_pred CCCCCCCHHHHHHHH-------------H-HHHCCHHHHHCCC--------HHHHHHHCCCCCHHHHHHH--HHHHHCCC
T ss_conf 644457999999999-------------9-9850999997389--------9999987287619999999--99844578
Q ss_pred CCCCC
Q ss_conf 74332
Q gi|254780784|r 542 SRLQL 546 (699)
Q Consensus 542 ~~~~~ 546 (699)
...++
T Consensus 254 ~~~~~ 258 (277)
T cd07950 254 RVREL 258 (277)
T ss_pred CCCEE
T ss_conf 66666
No 423
>COG1866 PckA Phosphoenolpyruvate carboxykinase (ATP) [Energy production and conversion]
Probab=21.21 E-value=30 Score=12.58 Aligned_cols=164 Identities=17% Similarity=0.178 Sum_probs=68.7
Q ss_pred CCCEEEEEEEECCCCCCCCEEEEEE-CCCEEEEEEEECCCCCCCCC-CCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCC
Q ss_conf 7533787998447546670089998-79768999981686521223-344544203587740588754453345567650
Q gi|254780784|r 319 SETVRDISAQVGLLQRTHGSSLFIR-GDTQAIVVVTLGTREDEQYV-DSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSR 396 (699)
Q Consensus 319 ~dEIRpIs~EvgvLPrvHGSALFtR-GETQaL~tvTLG~~~d~Q~i-D~l~~~~~k~fmlHYNFPpfsvGE~~~~~~~~R 396 (699)
...|=|+.|-.++=|. +-.|||-- -.| .-+||-.......| |+..+|...-. +||-.=|---+=....-+-
T Consensus 211 ~~~i~~MHcsANvG~~-gdvalFFGLSGT---GKTTLSaDp~R~LIGDDEHgW~d~GV---FN~EGGCYAK~I~Ls~e~E 283 (529)
T COG1866 211 LKGILSMHCSANVGEK-GDVALFFGLSGT---GKTTLSADPHRRLIGDDEHGWDDRGV---FNFEGGCYAKTINLSEEKE 283 (529)
T ss_pred CCCCCCCEECCCCCCC-CCEEEEEECCCC---CCCEECCCCCCCCCCCCCCCCCCCCE---EEECCCCCCCCCCCCHHHC
T ss_conf 0455440000343767-876999952678---85213348764201676336677765---8612752311046761105
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCC--CEEEEEEEEEC-C--
Q ss_conf 246799999998741078644687389998531102785223566777798762595022541--21332004408-8--
Q gi|254780784|r 397 REIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPV--AGIAMGLVKDG-D-- 471 (699)
Q Consensus 397 REiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp~~~~V--aGiamGLi~~~-~-- 471 (699)
-||-.--.-.--|+.|+-.++ -.+==.|||----+-|+-.+--.+ ...|+ +|..--+|.=. |
T Consensus 284 P~I~~Ai~~~avLENVVvded---------g~~Df~D~SlTeNTR~aYpi~~Ip----n~~~~~~~ghp~~iIfLTaDaf 350 (529)
T COG1866 284 PEIYAAIKRGAVLENVVVDED---------GTPDFDDGSLTENTRAAYPIEHIP----NVSPSVKAGHPKNVIFLTADAF 350 (529)
T ss_pred HHHHHHHHCCCEEEEEEECCC---------CCCCCCCCCCCCCCCCCCHHHHCC----CCCCCCCCCCCCEEEEEECCCC
T ss_conf 468877613621234787578---------886776665464431106176655----5586544689855999965324
Q ss_pred ----EEEEEEECCCCCCCCCCCCEEEEECCCCCEE
Q ss_conf ----2899863144220136551001005565124
Q gi|254780784|r 472 ----DFIILSDISGDEDHLGHMDFKVAGTDSGITA 502 (699)
Q Consensus 472 ----~~~iLtDI~G~ED~~GdMDFKvaGT~~GiTa 502 (699)
...-||--|-.=-++.--.+|+|||..|+|-
T Consensus 351 GVlPPvsrLTpeQamYhFlsG~TaK~agTE~Gvte 385 (529)
T COG1866 351 GVLPPVSRLTPEQAMYHFLSGYTAKLAGTERGVTE 385 (529)
T ss_pred CCCCCCHHCCHHHHHHHHHCCHHHHCCCCCCCCCC
T ss_conf 78896111599999999871202201343468899
No 424
>cd03319 L-Ala-DL-Glu_epimerase L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism of the murein peptide of peptidoglycan, of which L-Ala-D-Glu is a component. L-Ala-D/L-Glu epimerase is a member of the enolase-superfamily, which is characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion.
Probab=21.09 E-value=36 Score=11.95 Aligned_cols=109 Identities=23% Similarity=0.290 Sum_probs=60.3
Q ss_pred HHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCC-CCCCCCE---EEEEEEEECCEEEEEEECCCC
Q ss_conf 987410786446873899985311027852235667777987625950-2254121---332004408828998631442
Q gi|254780784|r 407 RAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVP-ISKPVAG---IAMGLVKDGDDFIILSDISGD 482 (699)
Q Consensus 407 ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~dagvp-~~~~VaG---iamGLi~~~~~~~iLtDI~G~ 482 (699)
++++..+|. ..+|+. +|++=+....-.-.-.|-+.++- +-.|+.- -.|..+.+ ..-+-|...
T Consensus 169 ~~vr~~~~~-----~~l~vD-----aN~~~~~~~A~~~~~~l~~~~i~~iEqP~~~~d~~~~~~l~~----~~~~pIa~d 234 (316)
T cd03319 169 RAIREAAPD-----ARLRVD-----ANQGWTPEEAVELLRELAELGVELIEQPVPAGDDDGLAYLRD----KSPLPIMAD 234 (316)
T ss_pred HHHHHHCCC-----CEEEEE-----CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH----HCCCCEEEC
T ss_conf 999966899-----629984-----688889999999999752443444308989999999999999----689999935
Q ss_pred CCCCCCCCEEEEECCCCCEEEECCC-CCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 2013655100100556512443245-365568899999999999999999999
Q gi|254780784|r 483 EDHLGHMDFKVAGTDSGITAMQMDM-KIGGISENIMVMALQQAKRGRLHILNE 534 (699)
Q Consensus 483 ED~~GdMDFKvaGT~~GiTa~QmDi-K~~gi~~~il~~al~~A~~gr~~il~~ 534 (699)
|..++--||+=+=..+.+..+|.|+ |++||+ ++++.|..++.+=+..
T Consensus 235 Es~~~~~d~~~~~~~~a~d~v~~k~~~~GGit-----~~~~ia~~A~~~gi~~ 282 (316)
T cd03319 235 ESCFSAADAARLAGGGAYDGINIKLMKTGGLT-----EALRIADLARAAGLKV 282 (316)
T ss_pred CCCCCHHHHHHHHHCCCCCEEEECCHHHCCHH-----HHHHHHHHHHHCCCEE
T ss_conf 88799999999997699886984514408989-----9999999999869949
No 425
>pfam11336 DUF3138 Protein of unknown function (DUF3138). This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=21.04 E-value=39 Score=11.62 Aligned_cols=33 Identities=33% Similarity=0.578 Sum_probs=22.4
Q ss_pred EEEECCCC-CCCCEEEEE--ECC------CEEEEEEEECCCC
Q ss_conf 99844754-667008999--879------7689999816865
Q gi|254780784|r 326 SAQVGLLQ-RTHGSSLFI--RGD------TQAIVVVTLGTRE 358 (699)
Q Consensus 326 s~EvgvLP-rvHGSALFt--RGE------TQaL~tvTLG~~~ 358 (699)
+.|+-+.| |-.|-.||+ ||. +++.++|-|....
T Consensus 170 saeiTl~PNRG~G~~l~~ns~g~~G~nIvntAvV~VPLs~tt 211 (514)
T pfam11336 170 SAEITIMPNRGFGNTLLSNSHGGSGNNIINTAVVTVPLSTTT 211 (514)
T ss_pred CCEEEECCCCCCCCEEECCCCCCCCCCEEEEEEEEEECCCCE
T ss_conf 612897567776723310356774312200268987427861
No 426
>COG4775 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]
Probab=21.04 E-value=20 Score=14.03 Aligned_cols=15 Identities=27% Similarity=0.505 Sum_probs=8.8
Q ss_pred EEEEEECCCCCCCCE
Q ss_conf 879984475466700
Q gi|254780784|r 324 DISAQVGLLQRTHGS 338 (699)
Q Consensus 324 pIs~EvgvLPrvHGS 338 (699)
.++.-++|-.+.-||
T Consensus 407 ~vdvvv~VkE~~Tgs 421 (766)
T COG4775 407 QVDVVVDVKERSTGS 421 (766)
T ss_pred EEEEEEEEEECCCEE
T ss_conf 079999987567205
No 427
>pfam11725 AvrE Pathogenicity factor. This family is secreted by gram-negative Gammaproteobacteria such as Pseudomonas syringae of tomato and the fire blight plant pathogen Erwinia amylovora, amongst others. It is an essential pathogenicity factor of approximately 198 kDa. Its injection into the host-plant is dependent upon the bacterial type III or Hrp secretion system. The family is long and carries a number of predicted functional regions, including an ERMS or endoplasmic reticulum membrane retention signal at both the C- and the N-termini, a leucine-zipper motif from residues 539-560, and a nuclear localisation signal at 1358-1361. this conserved AvrE-family of effectors is among the few that are required for full virulence of many phytopathogenic pseudomonads, erwinias and pantoeas.
Probab=20.83 E-value=40 Score=11.59 Aligned_cols=288 Identities=18% Similarity=0.200 Sum_probs=148.3
Q ss_pred EEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEE-EECCCCCCCHHHHHHHHHHHHHHCC--
Q ss_conf 7405887544533455676502467999999987410786446873899985-3110278522356677779876259--
Q gi|254780784|r 376 MHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVS-EITESDGSSSMATVCGSSLALMDAG-- 452 (699)
Q Consensus 376 lHYNFPpfsvGE~~~~~~~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~-evl~sngsssma~vc~~slal~dag-- 452 (699)
.||.=-|-- -+--||...---++-+.=|=+|+....-.+ ...+-|.+ .+|+|-+.+.+|.---.+|-=.|.|
T Consensus 1128 ~~YG~NPVK--~vTDMGFT~n~aLEa~YDaVKaFlnaFkK~---~haVsvnmRta~gs~dqaeLa~K~K~~LksLe~gdd 1202 (1771)
T pfam11725 1128 KTYGDNPVK--VVTDMGFTHNKALEANYDAVKAFLNAFKKE---DHAVSVNMRTATGSQGQAELADKLKSTLKSLEHGDD 1202 (1771)
T ss_pred CCCCCCCCE--EEECCCCCCCHHHHCCHHHHHHHHHHHCCC---CCCEEEEEHHHHCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf 545778732--551366655254441508999999863685---541114413233367509999999999873127875
Q ss_pred ----------------CCCCCCCC-----------------------EEEEEEEEECC---------EEEEE--------
Q ss_conf ----------------50225412-----------------------13320044088---------28998--------
Q gi|254780784|r 453 ----------------VPISKPVA-----------------------GIAMGLVKDGD---------DFIIL-------- 476 (699)
Q Consensus 453 ----------------vp~~~~Va-----------------------GiamGLi~~~~---------~~~iL-------- 476 (699)
||++..+. ||.+.++.|+. -+.++
T Consensus 1203 eis~sRsYG~~lsTpFv~l~~~~~gp~P~ag~T~~RnY~l~aeR~egGv~vy~~regg~~~s~gvg~G~D~~P~~t~~~~ 1282 (1771)
T pfam11725 1203 EISFSRSYGGGLSTPFVPLAKLPTGPWPGAGITGDRNYNLSAERTDGGVTVYFIREGGVTGSGGVGGGKDVWPYFTGKNT 1282 (1771)
T ss_pred EEEEEECCCCCCCCCEEECCCCCCCCCCCCCCCCCCCEEEEEECCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCCCCC
T ss_conf 04665013886454405625677798887862453202540001579879998713673023331378444776456887
Q ss_pred ---EECCCCCCCCCCCCEEEEECCC-CCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCE
Q ss_conf ---6314422013655100100556-512443245365568899999999999999999999984356674332244875
Q gi|254780784|r 477 ---SDISGDEDHLGHMDFKVAGTDS-GITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPR 552 (699)
Q Consensus 477 ---tDI~G~ED~~GdMDFKvaGT~~-GiTa~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m~~~~~~~~~~~~~~ap~ 552 (699)
||-+| -+|-+-+||.+-|+-. +.++-|---=+=.++-|-|-.=+.---.|.+.=|+.|.+.+..--.+ -+
T Consensus 1283 ~a~s~dl~-nk~~~~pdfR~G~~vta~~~~tqr~gl~F~v~deei~~Fvd~Lf~Gklnpl~llkKg~dH~~~q-----~~ 1356 (1771)
T pfam11725 1283 PARSDDLG-NKHKISPDFRLGADVTATLQGTQRNGLNFTVPDEEIDGFVDGLFEGKLNPLDLLKKGIEHEMKQ-----GK 1356 (1771)
T ss_pred CCCCCCCC-CCCCCCCCEEECCEEEHHHHHHHHCCEEEECCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH-----HC
T ss_conf 13332246-6630375456622455022244224514634667756787654037657999987655655543-----12
Q ss_pred EEEEEECCCCEEEEECCCCHHHHHHHHHHCCEEEEECCEEEEEEECCH------HHHHHHHHHHHHHCCCCCCCCEEEEE
Q ss_conf 799997711500003786077998999868889980880899996898------99999999999852475468678999
Q gi|254780784|r 553 VEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSL------AEIEAAREMIRSITDVPEVNKIYKGQ 626 (699)
Q Consensus 553 ~~~~~i~~~ki~~~iG~gG~~ik~i~~~~~~~i~i~d~g~v~i~~~~~------~~~~~a~~~i~~~~~~~e~g~~y~~~ 626 (699)
-..|.|+.. ...+.-+-|+|.|+|.....+.-. .++.-+--.=..++..=+.++.+++-
T Consensus 1357 r~~fdvt~~---------------~~~dlRaginltd~~s~p~sA~aR~gvg~~a~~NL~s~t~~~~tq~nd~t~~~~~s 1421 (1771)
T pfam11725 1357 RFNFDLTAG---------------AALDLRAGINLTEPGSKPLTATARAGVGLNASANLASYTDYSSTQKNDKSSTREAS 1421 (1771)
T ss_pred EEEEEECCC---------------CCHHHEECCCCCCCCCCCCEEEEEEEEEEEEEEEEEECCHHHHHHCCCCCCCCCCC
T ss_conf 688884366---------------33100002466679988751367764102015442002311332047532001145
Q ss_pred -----EEEEEECCEEEECCCCCCEEEEEEE------CCCCCCCCHHHHCCCCCEEEEEEEEECCC--CCEEEEEEECCCC
Q ss_conf -----9999415369982879710488663------14445478556032598899999978689--9866687304778
Q gi|254780784|r 627 -----VVKVMDFGAFVHFCGARDGLVHISQ------LSTERVAKTSDVVKEGDTVWVKLLDFDDR--GKIKLSMKVVDQN 693 (699)
Q Consensus 627 -----v~~i~~fGafve~~~g~~gl~HiS~------l~~~~v~~~~d~~~~Gd~i~vk~~~~d~~--g~i~lSrk~~~~~ 693 (699)
--.-..+||+....- |.-|--- -....+.........|-.+.+ .+|.+ -+|++-.|...|=
T Consensus 1422 ~NRprF~N~~~~Ga~ar~q~---g~~ht~pt~~ptsap~~~pgtq~a~~s~~v~~~~---siD~rT~krIkf~~k~A~P~ 1495 (1771)
T pfam11725 1422 DNRPRFLNSAAAGANARAQA---GGAHTNPTAAPTSAPGKTPGTQPAFNSPNVTVTV---AIDNRTTKRIKFEMKVAEPM 1495 (1771)
T ss_pred CCCHHHHHHCCCCCEEEEEE---CCCCCCCCCCCCCCCCCCCCCEECCCCCCCEEEE---EECCCCCEEEEEEECCCCCC
T ss_conf 67324654203230123210---3445787777767888997640011478715899---86265410588873266765
Q ss_pred CC
Q ss_conf 78
Q gi|254780784|r 694 TG 695 (699)
Q Consensus 694 ~~ 695 (699)
..
T Consensus 1496 t~ 1497 (1771)
T pfam11725 1496 TT 1497 (1771)
T ss_pred CC
T ss_conf 31
No 428
>KOG2473 consensus
Probab=20.81 E-value=25 Score=13.26 Aligned_cols=22 Identities=18% Similarity=0.235 Sum_probs=12.7
Q ss_pred EEEEEEEECCCCCC-CCEEEEEE
Q ss_conf 37879984475466-70089998
Q gi|254780784|r 322 VRDISAQVGLLQRT-HGSSLFIR 343 (699)
Q Consensus 322 IRpIs~EvgvLPrv-HGSALFtR 343 (699)
-|.+||.-|+=||- -+|+++|+
T Consensus 280 wr~~wirFGyDPRkD~~~~~YQt 302 (484)
T KOG2473 280 WRRLWIRFGYDPRKDPNSRVYQT 302 (484)
T ss_pred HHCEEEEECCCCCCCCCCCEEEE
T ss_conf 10121331678777867530578
No 429
>pfam07405 DUF1506 Protein of unknown function (DUF1506). This family consists of several bacterial proteins of around 130 residues in length. Members of this family seem to be specific to Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown.
Probab=20.78 E-value=40 Score=11.58 Aligned_cols=93 Identities=20% Similarity=0.287 Sum_probs=67.3
Q ss_pred EECCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEE----------------CCEEEECCCCCCEEEEEEECCCCC---
Q ss_conf 9689899999999999852475468678999999941----------------536998287971048866314445---
Q gi|254780784|r 596 ASSSLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMD----------------FGAFVHFCGARDGLVHISQLSTER--- 656 (699)
Q Consensus 596 ~~~~~~~~~~a~~~i~~~~~~~e~g~~y~~~v~~i~~----------------fGafve~~~g~~gl~HiS~l~~~~--- 656 (699)
.+.-+.-.+.+..||+ ...+|+.=..|+|.|++..+ -|+...+-|---..++-|.+++-.
T Consensus 8 ~gvRkrladMs~rmIn-~Fkdp~pLrfYK~n~~kle~d~SyqrIfdKn~ytEF~GviidIkPqel~~lydSn~~Diqgys 86 (133)
T pfam07405 8 NGVRKRLSDMSFRMIN-VFKDPKPLKFYKGTVVKLENDSSYQRVFDKNKYTEFAGVIIDIKPQELAILYDSDMSDIQGYS 86 (133)
T ss_pred CHHHHHHHHHHHHHHH-HHCCCCCEEEECCCEEECCCCHHHHHHHCCCCCEEEEEEEEECCHHHEEEECCCCCHHHHHHH
T ss_conf 1088899887799998-617975516330518982585489988454542077789997271653421127805541023
Q ss_pred --------CCCHHHHCCCCCEEEEEEEEECCC-CCEEEEEEE
Q ss_conf --------478556032598899999978689-986668730
Q gi|254780784|r 657 --------VAKTSDVVKEGDTVWVKLLDFDDR-GKIKLSMKV 689 (699)
Q Consensus 657 --------v~~~~d~~~~Gd~i~vk~~~~d~~-g~i~lSrk~ 689 (699)
--...|-.+++|-+-..++.||.. |..-|..|.
T Consensus 87 kLYTy~~LnyElkDRISi~d~~yfEIfSIdsSigYfTLvLKe 128 (133)
T pfam07405 87 KLYTYQDLNYELKDRISIADLIYFEIFSIDSSIGYFTLVLKE 128 (133)
T ss_pred HEEEHHCCCCHHHCCCCCCCEEEEEEEEEECCCEEEEEEHHH
T ss_conf 100122057023302313323899999970642054402123
No 430
>PRK10279 hypothetical protein; Provisional
Probab=20.78 E-value=40 Score=11.58 Aligned_cols=86 Identities=13% Similarity=0.161 Sum_probs=40.2
Q ss_pred HHHHHHHCCCCCCCCCC----CCCCEEEEEEEEECCCC---CCHHHHHHHHHHHHHHHCCCC-CCCCEEEEEEEECCCCE
Q ss_conf 11112321267767468----86883789999821888---877899999999998732688-23541123552047732
Q gi|254780784|r 90 LISRMIDRSIRPLFSKC----YKNETQVIINVMQHDLE---SSPHVVSMVAASAALMLSGLP-FEGPVVGAQVDYINGQY 161 (699)
Q Consensus 90 L~sRlIDR~lRPLFPkg----f~~evQIv~~VLS~D~~---~dpdvlAi~aASaAL~ISdIP-f~GPVaaVRVG~idge~ 161 (699)
+..+-+.+-++.+|+.. ..-...+++|=|..-.. ...++.-.+.||+| || +--||--=---++||.+
T Consensus 84 ~~g~~~~~~l~~~~~~~~~edl~ip~~~vatdl~~g~~v~~~~G~l~~AvrAS~a-----iPgif~Pv~~~g~~lvDGGv 158 (300)
T PRK10279 84 LRGERVFNQYREIMPETEIENCSRRFGAVATNLSTGRELWFTEGDLHLAIRASCS-----MPGLMAPVAHNGYWLVDGAV 158 (300)
T ss_pred CCHHHHHHHHHHHCCCCCHHHCCCCEEEEEEECCCCCEEEECCCCHHHHHHHHCC-----CCCCCCCEEECCEEEEECCC
T ss_conf 4528999999997599997987987599978768898899579889999998656-----66675887989999973773
Q ss_pred EECCCCCCC-CCCCEEEEEE
Q ss_conf 436850002-2210135530
Q gi|254780784|r 162 VLNPRLDED-QGSLDLFVSG 180 (699)
Q Consensus 162 ViNPt~ee~-esdLDLvVAG 180 (699)
+.|-..+.. +-.-|.++|-
T Consensus 159 ~nn~Pv~~~~~~gad~vIaV 178 (300)
T PRK10279 159 VNPVPISLTRALGADIVIAV 178 (300)
T ss_pred CCCHHHHHHHHCCCCEEEEE
T ss_conf 76321999998499989999
No 431
>TIGR01051 topA_bact DNA topoisomerase I; InterPro: IPR005733 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry describes topoisomerase I from bacteria, which is more closely related to archaeal than to eukaryotic topoisomerase I . Topoisomerase I is the major enzyme for relaxing negatively supercoiled DNA, and its presence is balanced by reverse gyrase, which can introduce negative supercoils. Prokaryotic topoisomerase I folds in an unusual way to give 4 distinct domains, enclosing a hole large enough to accommodate a double-stranded DNA segment. A tyrosine at the active site, which lies at the interface of 2 domains, is involved in transient breakage of a DNA strand, and the formation of a covalent protein-DNA intermediate through a 5-phosphotyrosine linkage. The structure reveals a plausible mechanism by which this and related enzymes could catalyse the passage of one DNA strand through a transient break in another strand . Topoisomerase I require Mg2+ as a cofactor for catalysis to take place. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003917 DNA topoisomerase type I activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=20.70 E-value=40 Score=11.57 Aligned_cols=13 Identities=38% Similarity=0.754 Sum_probs=6.2
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 9999999999999
Q gi|254780784|r 294 VFEDIQAKVVRTV 306 (699)
Q Consensus 294 af~~l~k~ivR~~ 306 (699)
.|++++++++|+.
T Consensus 129 VFnEIT~~AI~~A 141 (688)
T TIGR01051 129 VFNEITKKAIRAA 141 (688)
T ss_pred ECCCCCHHHHHHH
T ss_conf 0247677899999
No 432
>pfam00357 Integrin_alpha Integrin alpha cytoplasmic region. This family contains the short intracellular region of integrin alpha chains.
Probab=20.57 E-value=40 Score=11.55 Aligned_cols=17 Identities=29% Similarity=0.651 Sum_probs=10.8
Q ss_pred CCCCCCCCCCCHHHHHH
Q ss_conf 88735789887145311
Q gi|254780784|r 75 GGYLRRESRPTENEILI 91 (699)
Q Consensus 75 GgF~kREgrpsd~EiL~ 91 (699)
-|||||--.|-+.+...
T Consensus 2 ~GFFKR~~p~~~e~~~~ 18 (26)
T pfam00357 2 CGFFKRKYPPQEEEXXX 18 (26)
T ss_pred CCCCCCCCCCCHHHHCC
T ss_conf 77445559870655022
No 433
>pfam03492 Methyltransf_7 SAM dependent carboxyl methyltransferase. This family of plant methyltransferases contains enzymes that act on a variety of substrates including salicylic acid, jasmonic acid and 7-Methylxanthine. Caffeine is synthesized through sequential three-step methylation of xanthine derivatives at positions 7-N, 3-N, and 1-N. The protein 7-methylxanthine methyltransferase (designated as CaMXMT) catalyses the second step to produce theobromine.
Probab=20.32 E-value=39 Score=11.69 Aligned_cols=15 Identities=27% Similarity=0.791 Sum_probs=11.7
Q ss_pred CCCCCCCCCCCCCCCC
Q ss_conf 2320133678887357
Q gi|254780784|r 65 ERTYAVGKIPGGYLRR 80 (699)
Q Consensus 65 Ek~yAaGkIPGgF~kR 80 (699)
..+|++| +||+|..|
T Consensus 84 ~~~f~~g-vpGSFy~R 98 (331)
T pfam03492 84 RSYFVSG-VPGSFYGR 98 (331)
T ss_pred CCEEEEE-CCCCCCCC
T ss_conf 8769996-58643255
No 434
>PRK10070 glycine betaine transporter ATP-binding subunit; Provisional
Probab=20.30 E-value=41 Score=11.51 Aligned_cols=10 Identities=40% Similarity=0.870 Sum_probs=6.3
Q ss_pred HHHHHCCCCC
Q ss_conf 1123212677
Q gi|254780784|r 92 SRMIDRSIRP 101 (699)
Q Consensus 92 sRlIDR~lRP 101 (699)
.|+|-|-++|
T Consensus 71 lr~i~gL~~P 80 (400)
T PRK10070 71 VRLLNRLIEP 80 (400)
T ss_pred HHHHHCCCCC
T ss_conf 9999759998
No 435
>cd07949 PCA_45_Doxase_B_like_1 The B subunit of unknown Class III extradiol dioxygenases with similarity to Protocatechuate 4,5-dioxygenase. This subfamily is composed of proteins of unknown function with similarity to the B subunit of Protocatechuate 4,5-dioxygenase (LigAB). LigAB belongs to the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Dioxygenases play key roles in the degradation of aromatic compounds. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B.
Probab=20.25 E-value=41 Score=11.50 Aligned_cols=30 Identities=23% Similarity=0.294 Sum_probs=16.2
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 754453345567650246799999998741
Q gi|254780784|r 382 PCATGEVSRMGAPSRREIGHGRLARRAIHP 411 (699)
Q Consensus 382 pfsvGE~~~~~~~~RREiGHg~la~ral~~ 411 (699)
|-.||-....-.+.||-.--|....||++.
T Consensus 146 Pv~vN~~~~P~p~~~Rc~~lG~air~ai~~ 175 (276)
T cd07949 146 PVSINTVQHPLPSPKRCFKLGQAIGRAIES 175 (276)
T ss_pred EEEECCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 898726679999989999999999999985
No 436
>pfam02335 Cytochrom_C552 Cytochrome c552. Cytochrome c552 (cytochrome c nitrite reductase) is a crucial enzyme in the nitrogen cycle catalysing the reduction of nitrite to ammonia. The crystal structure of cytochrome c552 reveals it to be a dimer, with with 10 close-packed type c haem groups.
Probab=20.12 E-value=41 Score=11.48 Aligned_cols=42 Identities=26% Similarity=0.392 Sum_probs=31.1
Q ss_pred CCEEEEECCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5100100556512443245365568899999999999999999999984
Q gi|254780784|r 489 MDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSK 537 (699)
Q Consensus 489 MDFKvaGT~~GiTa~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m~~ 537 (699)
-||=.|-+..|.-+=| -.+.+|.+|+..|+.||..+...+.+
T Consensus 340 WDf~~AeNs~GFHnP~-------ea~r~L~~s~~~a~~A~~~l~~~lak 381 (383)
T pfam02335 340 WDFAIAENSVGFHAPE-------EALRILGTALDKAAKARTKLRQALAK 381 (383)
T ss_pred EEEEEECCCCCCCCHH-------HHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 2654302566457819-------99999999999999999999999744
No 437
>PRK09439 glucose-specific PTS system component; Provisional
Probab=20.00 E-value=41 Score=11.46 Aligned_cols=60 Identities=23% Similarity=0.280 Sum_probs=38.0
Q ss_pred HHHHHCCCCCCCCEE---EEEEEEEEECCE--EEECCCCCCEEEEEE----ECCCCCCCCHHHHCCCCCEEE
Q ss_conf 999852475468678---999999941536--998287971048866----314445478556032598899
Q gi|254780784|r 609 MIRSITDVPEVNKIY---KGQVVKVMDFGA--FVHFCGARDGLVHIS----QLSTERVAKTSDVVKEGDTVW 671 (699)
Q Consensus 609 ~i~~~~~~~e~g~~y---~~~v~~i~~fGa--fve~~~g~~gl~HiS----~l~~~~v~~~~d~~~~Gd~i~ 671 (699)
+=+.+.-.|+-|.+| .|+|+.+.+-+- -++-..|.|-|+||- +|.-+- -+-.++.||+|+
T Consensus 47 mGdG~AI~P~~~~v~AP~~G~V~~vf~T~HAigi~~~~G~eiLIHiGiDTV~L~G~g---F~~~v~~Gd~Vk 115 (169)
T PRK09439 47 VGDGIAIKPTGNKIVAPVDGTIGKIFETNHAFSIESDSGVELFVHFGIDTVELKGEG---FKRIAEEGQRVK 115 (169)
T ss_pred CCCEEEEECCCCEEECCCCEEEEEECCCCCEEEEECCCCCEEEEEECCCCEECCCCC---EEEEEECCCEEC
T ss_conf 247489986799899188959999778893899992899899999762402338967---269992769988
Done!