Query 026737
Match_columns 234
No_of_seqs 246 out of 2184
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 11:59:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026737.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026737hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0539 RpsA Ribosomal protein 100.0 1.5E-42 3.2E-47 324.4 17.1 195 16-234 143-365 (541)
2 COG0539 RpsA Ribosomal protein 100.0 4.6E-41 1E-45 314.4 15.7 203 1-233 224-450 (541)
3 PRK12269 bifunctional cytidyla 100.0 2.5E-36 5.4E-41 298.1 18.3 205 1-234 525-754 (863)
4 PRK13806 rpsA 30S ribosomal pr 100.0 1.5E-33 3.2E-38 265.8 17.6 193 20-234 157-381 (491)
5 PRK13806 rpsA 30S ribosomal pr 100.0 6.4E-33 1.4E-37 261.5 17.9 197 2-228 236-466 (491)
6 PRK12269 bifunctional cytidyla 100.0 6E-33 1.3E-37 274.1 18.3 195 17-234 440-667 (863)
7 PRK07899 rpsA 30S ribosomal pr 100.0 5.1E-32 1.1E-36 253.8 18.5 181 18-222 161-369 (486)
8 PRK06299 rpsA 30S ribosomal pr 100.0 3E-31 6.5E-36 254.1 18.4 192 20-234 156-375 (565)
9 PRK06676 rpsA 30S ribosomal pr 100.0 1.6E-30 3.5E-35 238.8 18.7 186 20-229 147-360 (390)
10 TIGR00717 rpsA ribosomal prote 100.0 1.3E-30 2.9E-35 247.1 17.8 204 2-234 220-448 (516)
11 PRK06299 rpsA 30S ribosomal pr 100.0 2.9E-30 6.2E-35 247.4 17.4 204 2-234 234-462 (565)
12 TIGR00717 rpsA ribosomal prote 100.0 1.9E-29 4.2E-34 239.2 17.6 193 19-234 141-361 (516)
13 PRK07899 rpsA 30S ribosomal pr 100.0 5.4E-29 1.2E-33 233.5 16.1 184 22-233 82-294 (486)
14 PRK07400 30S ribosomal protein 100.0 8.2E-29 1.8E-33 221.9 15.8 178 22-231 78-280 (318)
15 PRK00087 4-hydroxy-3-methylbut 99.9 5.7E-27 1.2E-31 227.7 17.5 181 18-222 429-638 (647)
16 PRK06676 rpsA 30S ribosomal pr 99.9 8.5E-27 1.9E-31 214.2 16.3 185 22-233 65-278 (390)
17 PRK00087 4-hydroxy-3-methylbut 99.9 5.1E-25 1.1E-29 214.0 16.2 185 22-233 349-563 (647)
18 PRK07400 30S ribosomal protein 99.8 1.5E-20 3.2E-25 168.7 13.8 112 20-137 158-274 (318)
19 PTZ00248 eukaryotic translatio 99.7 1.4E-17 3.1E-22 148.1 8.1 105 54-162 12-140 (319)
20 COG1098 VacB Predicted RNA bin 99.7 2E-17 4.4E-22 126.8 5.5 75 55-135 2-81 (129)
21 cd05705 S1_Rrp5_repeat_hs14 S1 99.6 8.5E-15 1.8E-19 104.5 7.1 66 56-126 1-74 (74)
22 PRK08582 hypothetical protein; 99.6 1.7E-14 3.8E-19 114.9 9.1 77 55-137 2-83 (139)
23 PLN00207 polyribonucleotide nu 99.5 7.3E-14 1.6E-18 138.2 10.2 87 49-141 744-836 (891)
24 cd05703 S1_Rrp5_repeat_hs12_sc 99.5 1.1E-13 2.3E-18 98.5 8.1 65 59-128 1-72 (73)
25 cd05704 S1_Rrp5_repeat_hs13 S1 99.5 1.2E-13 2.6E-18 97.9 7.8 66 56-128 1-72 (72)
26 KOG1070 rRNA processing protei 99.5 4.1E-13 8.8E-18 135.1 14.2 175 22-218 1115-1325(1710)
27 cd04461 S1_Rrp5_repeat_hs8_sc7 99.5 1.3E-13 2.9E-18 100.0 8.1 72 51-127 7-83 (83)
28 PF00575 S1: S1 RNA binding do 99.5 1.5E-13 3.3E-18 97.2 7.5 69 55-128 1-74 (74)
29 PHA02945 interferon resistance 99.4 4.7E-13 1E-17 97.0 8.4 75 54-133 7-87 (88)
30 cd04452 S1_IF2_alpha S1_IF2_al 99.4 7E-13 1.5E-17 94.2 9.3 71 56-129 1-76 (76)
31 cd05698 S1_Rrp5_repeat_hs6_sc5 99.4 3.6E-13 7.7E-18 94.4 7.7 65 59-128 1-70 (70)
32 cd05686 S1_pNO40 S1_pNO40: pNO 99.4 5.3E-13 1.2E-17 94.7 8.6 67 56-127 1-72 (73)
33 cd05706 S1_Rrp5_repeat_sc10 S1 99.4 5.5E-13 1.2E-17 94.2 8.4 68 56-128 1-73 (73)
34 KOG1070 rRNA processing protei 99.4 8.3E-13 1.8E-17 132.9 11.5 210 1-226 538-780 (1710)
35 PRK07252 hypothetical protein; 99.4 8.5E-13 1.8E-17 102.7 9.1 75 57-136 2-82 (120)
36 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.4 8.9E-13 1.9E-17 92.3 7.9 64 59-127 1-69 (69)
37 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.4 7E-13 1.5E-17 93.7 7.1 57 66-127 15-71 (71)
38 PTZ00248 eukaryotic translatio 99.4 4.9E-13 1.1E-17 119.3 7.3 86 103-234 14-107 (319)
39 PRK08059 general stress protei 99.4 2E-12 4.4E-17 101.0 9.4 76 54-134 3-83 (123)
40 cd05691 S1_RPS1_repeat_ec6 S1_ 99.4 2.3E-12 4.9E-17 90.6 8.6 68 59-131 1-73 (73)
41 cd05694 S1_Rrp5_repeat_hs2_sc2 99.4 2.5E-12 5.4E-17 91.8 8.8 68 55-132 1-73 (74)
42 cd05707 S1_Rrp5_repeat_sc11 S1 99.4 1.8E-12 3.9E-17 90.5 6.8 63 59-126 1-68 (68)
43 PRK05807 hypothetical protein; 99.4 2.9E-12 6.4E-17 101.8 8.8 70 55-131 2-76 (136)
44 COG1093 SUI2 Translation initi 99.4 1E-12 2.2E-17 112.8 6.4 76 56-134 9-89 (269)
45 cd05708 S1_Rrp5_repeat_sc12 S1 99.4 5.2E-12 1.1E-16 89.6 9.0 70 57-130 1-75 (77)
46 cd05690 S1_RPS1_repeat_ec5 S1_ 99.3 2.9E-12 6.3E-17 89.3 7.1 63 59-126 1-69 (69)
47 cd05684 S1_DHX8_helicase S1_DH 99.3 6.9E-12 1.5E-16 90.1 9.0 71 59-133 1-77 (79)
48 cd05687 S1_RPS1_repeat_ec1_hs1 99.3 8.6E-12 1.9E-16 87.4 7.9 65 59-128 1-70 (70)
49 COG1098 VacB Predicted RNA bin 99.3 1.7E-12 3.7E-17 99.8 4.6 77 103-225 3-83 (129)
50 cd05692 S1_RPS1_repeat_hs4 S1_ 99.3 1.3E-11 2.9E-16 85.2 8.3 64 59-128 1-69 (69)
51 cd05689 S1_RPS1_repeat_ec4 S1_ 99.3 1.2E-11 2.6E-16 87.1 7.6 66 56-126 1-72 (72)
52 cd05693 S1_Rrp5_repeat_hs1_sc1 99.2 2E-11 4.4E-16 92.0 6.9 71 56-131 1-98 (100)
53 cd05685 S1_Tex S1_Tex: The C-t 99.2 4.3E-11 9.4E-16 82.4 7.1 63 59-126 1-68 (68)
54 cd04465 S1_RPS1_repeat_ec2_hs2 99.2 7.8E-11 1.7E-15 81.9 8.0 62 59-128 1-67 (67)
55 PRK03987 translation initiatio 99.2 6.9E-11 1.5E-15 103.5 9.3 76 56-134 6-86 (262)
56 cd05688 S1_RPS1_repeat_ec3 S1_ 99.2 7.8E-11 1.7E-15 81.3 7.7 63 58-126 1-68 (68)
57 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.2 8.6E-11 1.9E-15 85.6 7.8 70 55-130 3-81 (86)
58 cd04472 S1_PNPase S1_PNPase: P 99.2 1.1E-10 2.4E-15 80.6 7.8 63 59-127 1-68 (68)
59 TIGR02696 pppGpp_PNP guanosine 99.2 1.1E-10 2.5E-15 113.6 10.5 89 31-126 611-718 (719)
60 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.2 7.3E-11 1.6E-15 82.2 6.5 61 59-126 1-66 (66)
61 PRK11824 polynucleotide phosph 99.2 1.5E-10 3.3E-15 113.7 10.2 93 31-130 587-692 (693)
62 smart00316 S1 Ribosomal protei 99.1 4.1E-10 8.9E-15 77.6 8.4 67 57-128 1-72 (72)
63 cd04453 S1_RNase_E S1_RNase_E: 99.1 3.6E-10 7.7E-15 83.3 8.1 69 55-128 4-82 (88)
64 PRK08582 hypothetical protein; 99.1 3.4E-10 7.3E-15 90.3 7.7 77 103-225 3-83 (139)
65 COG2183 Tex Transcriptional ac 99.1 2.5E-10 5.5E-15 110.9 7.4 75 53-132 653-732 (780)
66 cd04471 S1_RNase_R S1_RNase_R: 99.1 9.6E-10 2.1E-14 79.1 8.4 66 58-127 1-82 (83)
67 PLN00207 polyribonucleotide nu 99.0 7E-11 1.5E-15 117.3 2.5 110 66-228 713-835 (891)
68 COG1185 Pnp Polyribonucleotide 99.0 5.8E-10 1.3E-14 107.0 8.2 94 31-131 585-691 (692)
69 PRK09521 exosome complex RNA-b 99.0 2.1E-09 4.5E-14 89.9 9.5 100 23-129 30-142 (189)
70 cd04454 S1_Rrp4_like S1_Rrp4_l 99.0 2.3E-09 4.9E-14 77.5 8.0 68 56-129 4-76 (82)
71 TIGR03591 polynuc_phos polyrib 98.9 2.6E-09 5.6E-14 104.9 9.0 88 31-125 584-684 (684)
72 cd05702 S1_Rrp5_repeat_hs11_sc 98.9 5.1E-09 1.1E-13 73.4 6.6 57 59-120 1-64 (70)
73 cd00164 S1_like S1_like: Ribos 98.9 4.9E-09 1.1E-13 70.8 6.0 56 66-126 10-65 (65)
74 cd04473 S1_RecJ_like S1_RecJ_l 98.9 1.4E-08 3.1E-13 72.6 8.5 61 53-127 11-76 (77)
75 cd04460 S1_RpoE S1_RpoE: RpoE, 98.9 1.3E-08 2.8E-13 76.3 8.0 65 66-136 12-92 (99)
76 cd05703 S1_Rrp5_repeat_hs12_sc 98.8 5.9E-09 1.3E-13 74.0 5.6 67 106-216 1-72 (73)
77 cd05705 S1_Rrp5_repeat_hs14 S1 98.8 8.6E-09 1.9E-13 73.4 6.4 69 103-214 1-74 (74)
78 cd05704 S1_Rrp5_repeat_hs13 S1 98.7 1.9E-08 4.2E-13 71.1 5.7 69 103-216 1-72 (72)
79 PF00575 S1: S1 RNA binding do 98.7 6.1E-08 1.3E-12 68.2 6.9 68 103-216 2-74 (74)
80 COG2996 Predicted RNA-bindinin 98.7 4.2E-07 9E-12 79.0 13.3 158 22-219 46-219 (287)
81 KOG1067 Predicted RNA-binding 98.7 2.1E-08 4.5E-13 94.2 5.7 77 54-136 664-745 (760)
82 PRK09202 nusA transcription el 98.7 2.2E-08 4.7E-13 94.3 5.7 96 20-129 87-200 (470)
83 TIGR02696 pppGpp_PNP guanosine 98.7 1.5E-08 3.2E-13 99.1 3.6 100 66-214 606-718 (719)
84 TIGR00448 rpoE DNA-directed RN 98.6 7.1E-08 1.5E-12 80.0 7.0 79 51-135 74-173 (179)
85 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.6 7.7E-08 1.7E-12 67.8 6.0 50 149-215 17-71 (71)
86 PRK05807 hypothetical protein; 98.6 9.4E-08 2E-12 76.0 7.0 70 103-219 3-76 (136)
87 cd05706 S1_Rrp5_repeat_sc10 S1 98.6 1.3E-07 2.9E-12 66.5 6.8 68 103-216 1-73 (73)
88 PRK07252 hypothetical protein; 98.6 1E-07 2.2E-12 74.2 6.7 75 104-224 2-82 (120)
89 PRK04163 exosome complex RNA-b 98.6 1.2E-07 2.7E-12 81.9 7.8 71 54-130 59-138 (235)
90 cd05698 S1_Rrp5_repeat_hs6_sc5 98.6 1.2E-07 2.5E-12 66.1 5.7 65 106-216 1-70 (70)
91 cd05689 S1_RPS1_repeat_ec4 S1_ 98.6 3.3E-07 7.1E-12 64.2 7.8 63 103-210 1-64 (72)
92 cd05684 S1_DHX8_helicase S1_DH 98.6 2E-07 4.4E-12 66.7 6.6 57 149-221 15-77 (79)
93 cd05690 S1_RPS1_repeat_ec5 S1_ 98.6 2.2E-07 4.7E-12 64.5 6.5 50 149-214 15-69 (69)
94 cd05694 S1_Rrp5_repeat_hs2_sc2 98.6 2E-07 4.3E-12 66.4 6.4 66 103-220 2-73 (74)
95 PRK08059 general stress protei 98.6 1.6E-07 3.4E-12 73.4 6.2 74 103-222 5-83 (123)
96 cd05686 S1_pNO40 S1_pNO40: pNO 98.5 3E-07 6.4E-12 65.0 6.9 66 104-215 2-72 (73)
97 cd04452 S1_IF2_alpha S1_IF2_al 98.5 2.4E-07 5.3E-12 65.4 6.4 68 104-217 2-76 (76)
98 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.5 2E-07 4.4E-12 64.9 5.7 63 106-214 1-68 (69)
99 cd04455 S1_NusA S1_NusA: N-uti 98.5 3.3E-07 7.2E-12 63.8 6.8 59 57-127 2-67 (67)
100 cd04461 S1_Rrp5_repeat_hs8_sc7 98.5 2.4E-07 5.2E-12 67.0 5.9 67 103-215 12-83 (83)
101 cd05691 S1_RPS1_repeat_ec6 S1_ 98.5 3.3E-07 7.2E-12 64.1 5.9 54 149-219 15-73 (73)
102 PRK08563 DNA-directed RNA poly 98.5 3.1E-07 6.8E-12 76.5 6.6 79 49-133 72-171 (187)
103 TIGR02063 RNase_R ribonuclease 98.4 6.8E-07 1.5E-11 88.5 8.9 69 55-127 624-708 (709)
104 cd05708 S1_Rrp5_repeat_sc12 S1 98.4 7E-07 1.5E-11 63.0 6.3 69 104-218 1-75 (77)
105 cd05707 S1_Rrp5_repeat_sc11 S1 98.4 8.1E-07 1.8E-11 61.7 6.1 45 149-210 15-60 (68)
106 COG1185 Pnp Polyribonucleotide 98.4 3.7E-07 8E-12 88.0 5.5 110 57-219 569-691 (692)
107 PHA02858 EIF2a-like PKR inhibi 98.4 1.2E-06 2.6E-11 63.2 6.7 69 54-127 12-85 (86)
108 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.3 8.9E-07 1.9E-11 64.3 5.4 74 103-218 4-81 (86)
109 PRK11824 polynucleotide phosph 98.3 2.6E-07 5.7E-12 91.1 3.1 101 66-219 582-693 (693)
110 cd05693 S1_Rrp5_repeat_hs1_sc1 98.3 6.7E-07 1.4E-11 67.4 4.6 80 103-218 1-97 (100)
111 COG1095 RPB7 DNA-directed RNA 98.3 1.9E-06 4.2E-11 71.0 7.4 82 49-136 72-176 (183)
112 PRK03987 translation initiatio 98.3 1.1E-06 2.4E-11 77.1 6.3 75 101-221 4-85 (262)
113 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.3 2.7E-06 5.9E-11 59.0 6.6 61 106-214 1-66 (66)
114 cd05687 S1_RPS1_repeat_ec1_hs1 98.3 2.3E-06 5E-11 59.5 5.8 65 106-216 1-70 (70)
115 PRK11642 exoribonuclease R; Pr 98.3 3.3E-06 7.1E-11 84.6 8.7 70 57-130 642-727 (813)
116 COG1093 SUI2 Translation initi 98.2 7.8E-07 1.7E-11 76.9 3.6 74 102-221 8-88 (269)
117 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.2 4.9E-06 1.1E-10 61.7 7.0 73 56-129 4-86 (92)
118 TIGR00358 3_prime_RNase VacB a 98.2 4.4E-06 9.5E-11 82.1 8.8 68 56-127 570-653 (654)
119 cd05692 S1_RPS1_repeat_hs4 S1_ 98.2 3.6E-06 7.8E-11 57.6 5.9 51 149-216 15-69 (69)
120 TIGR01953 NusA transcription t 98.2 2.2E-06 4.8E-11 77.8 6.1 97 19-129 83-198 (341)
121 PHA02945 interferon resistance 98.2 5E-06 1.1E-10 60.5 6.7 54 149-221 25-87 (88)
122 TIGR03591 polynuc_phos polyrib 98.1 1.9E-06 4E-11 85.0 3.8 92 66-210 579-678 (684)
123 cd04453 S1_RNase_E S1_RNase_E: 98.1 8.1E-06 1.8E-10 60.0 6.1 67 102-209 4-71 (88)
124 cd05702 S1_Rrp5_repeat_hs11_sc 98.1 1.2E-05 2.6E-10 56.2 6.5 61 106-210 1-62 (70)
125 cd05685 S1_Tex S1_Tex: The C-t 98.1 1E-05 2.2E-10 55.3 5.8 45 149-210 15-60 (68)
126 PRK12327 nusA transcription el 98.1 9.5E-06 2E-10 74.2 7.1 97 19-128 86-199 (362)
127 COG2996 Predicted RNA-bindinin 98.1 4.4E-05 9.5E-10 66.6 10.6 96 22-133 117-221 (287)
128 cd04465 S1_RPS1_repeat_ec2_hs2 98.0 1.3E-05 2.8E-10 55.4 5.7 62 106-216 1-67 (67)
129 cd04471 S1_RNase_R S1_RNase_R: 98.0 3E-05 6.6E-10 55.4 7.3 56 149-210 16-73 (83)
130 cd04472 S1_PNPase S1_PNPase: P 98.0 2.6E-05 5.7E-10 53.4 6.2 45 149-210 15-60 (68)
131 KOG2916 Translation initiation 98.0 7.1E-06 1.5E-10 71.0 3.9 79 56-137 14-97 (304)
132 smart00316 S1 Ribosomal protei 97.9 3.5E-05 7.6E-10 52.5 6.2 66 104-215 1-71 (72)
133 cd05688 S1_RPS1_repeat_ec3 S1_ 97.9 5.2E-05 1.1E-09 51.8 6.5 59 105-210 1-60 (68)
134 cd04460 S1_RpoE S1_RpoE: RpoE, 97.8 0.0001 2.3E-09 55.0 7.9 74 149-229 14-97 (99)
135 cd04454 S1_Rrp4_like S1_Rrp4_l 97.7 9.9E-05 2.1E-09 53.0 6.0 68 104-217 5-76 (82)
136 cd04473 S1_RecJ_like S1_RecJ_l 97.6 0.00024 5.2E-09 50.6 6.6 52 103-208 14-66 (77)
137 PRK09521 exosome complex RNA-b 97.6 0.0002 4.3E-09 59.9 6.6 52 149-217 79-142 (189)
138 COG1097 RRP4 RNA-binding prote 97.5 0.00046 9.9E-09 59.3 7.9 71 54-130 60-139 (239)
139 TIGR00757 RNaseEG ribonuclease 97.4 0.0006 1.3E-08 63.6 8.2 58 54-116 21-97 (414)
140 cd05699 S1_Rrp5_repeat_hs7 S1_ 97.4 0.00075 1.6E-08 47.7 6.6 64 59-128 1-72 (72)
141 PRK05054 exoribonuclease II; P 97.4 0.0006 1.3E-08 67.0 7.9 65 59-127 562-643 (644)
142 PRK04163 exosome complex RNA-b 97.3 0.0011 2.5E-08 57.2 8.3 74 103-218 61-138 (235)
143 KOG1067 Predicted RNA-binding 97.2 0.00031 6.6E-09 66.8 4.1 61 149-226 683-747 (760)
144 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.2 0.0017 3.7E-08 47.7 7.2 59 58-122 1-75 (88)
145 COG1096 Predicted RNA-binding 97.2 0.0028 6.1E-08 52.5 9.2 74 53-129 59-142 (188)
146 cd00164 S1_like S1_like: Ribos 97.2 0.00052 1.1E-08 45.7 4.0 45 149-210 12-57 (65)
147 cd04455 S1_NusA S1_NusA: N-uti 97.1 0.0017 3.6E-08 44.9 5.8 54 104-210 2-56 (67)
148 TIGR00448 rpoE DNA-directed RN 96.9 0.0028 6.1E-08 52.5 6.9 84 105-224 81-174 (179)
149 PTZ00162 DNA-directed RNA poly 96.8 0.0043 9.3E-08 51.4 7.2 74 50-129 73-165 (176)
150 COG0557 VacB Exoribonuclease R 96.8 0.003 6.5E-08 62.8 7.1 71 54-128 618-704 (706)
151 TIGR02063 RNase_R ribonuclease 96.8 0.0036 7.9E-08 62.3 7.4 71 104-210 626-699 (709)
152 cd05790 S1_Rrp40 S1_Rrp40: Rrp 96.8 0.0058 1.3E-07 44.7 6.6 68 55-129 3-75 (86)
153 COG2183 Tex Transcriptional ac 96.8 0.0018 3.9E-08 63.9 5.0 54 149-219 673-731 (780)
154 TIGR02062 RNase_B exoribonucle 96.7 0.0048 1E-07 60.7 7.4 64 59-126 558-638 (639)
155 PRK11642 exoribonuclease R; Pr 96.5 0.0082 1.8E-07 60.6 7.6 77 104-215 642-724 (813)
156 PF13509 S1_2: S1 domain; PDB: 96.5 0.011 2.3E-07 40.3 5.9 48 66-128 14-61 (61)
157 TIGR00358 3_prime_RNase VacB a 96.4 0.0096 2.1E-07 58.8 7.4 72 104-210 571-644 (654)
158 PRK08563 DNA-directed RNA poly 96.4 0.014 3.1E-07 48.4 7.3 79 104-218 80-168 (187)
159 PRK12328 nusA transcription el 96.2 0.012 2.7E-07 54.0 6.5 61 56-128 136-205 (374)
160 PF10447 EXOSC1: Exosome compo 96.2 0.033 7.2E-07 40.4 7.3 79 104-208 3-82 (82)
161 KOG1856 Transcription elongati 96.1 0.0051 1.1E-07 62.7 3.8 72 54-130 981-1060(1299)
162 PRK09202 nusA transcription el 96.0 0.0017 3.7E-08 61.5 0.1 87 103-216 87-199 (470)
163 COG1095 RPB7 DNA-directed RNA 96.0 0.057 1.2E-06 44.8 8.9 84 105-224 81-176 (183)
164 COG1107 Archaea-specific RecJ- 95.7 0.0089 1.9E-07 57.4 3.3 68 53-131 117-189 (715)
165 PF10447 EXOSC1: Exosome compo 95.4 0.045 9.7E-07 39.7 5.4 36 81-116 45-82 (82)
166 KOG2916 Translation initiation 95.3 0.012 2.6E-07 51.3 2.4 66 149-231 31-103 (304)
167 PHA02858 EIF2a-like PKR inhibi 94.7 0.047 1E-06 39.6 3.8 44 149-210 30-76 (86)
168 PRK11712 ribonuclease G; Provi 94.7 0.23 5.1E-06 47.4 9.7 59 54-117 34-111 (489)
169 PRK10811 rne ribonuclease E; R 94.7 0.096 2.1E-06 53.4 7.3 61 56-121 36-112 (1068)
170 cd05791 S1_CSL4 S1_CSL4: CSL4, 94.7 0.077 1.7E-06 39.1 5.1 79 103-217 4-86 (92)
171 PRK12329 nusA transcription el 94.1 0.15 3.3E-06 47.9 6.7 67 56-128 150-224 (449)
172 PRK12327 nusA transcription el 93.7 0.17 3.7E-06 46.5 6.3 57 101-210 128-187 (362)
173 TIGR00757 RNaseEG ribonuclease 93.5 0.22 4.8E-06 46.6 6.8 79 98-208 18-97 (414)
174 TIGR01953 NusA transcription t 93.0 0.25 5.4E-06 45.1 6.2 64 101-217 125-198 (341)
175 PRK05054 exoribonuclease II; P 91.1 0.87 1.9E-05 45.1 7.9 55 149-210 576-634 (644)
176 COG1096 Predicted RNA-binding 89.0 1.9 4.1E-05 36.0 7.0 81 100-216 59-141 (188)
177 COG1097 RRP4 RNA-binding prote 87.9 3.3 7.1E-05 35.9 8.1 73 103-217 62-138 (239)
178 cd05699 S1_Rrp5_repeat_hs7 S1_ 87.1 1.7 3.6E-05 30.7 4.8 53 149-216 15-72 (72)
179 COG0557 VacB Exoribonuclease R 86.0 2 4.4E-05 43.0 6.6 56 149-210 637-694 (706)
180 cd04462 S1_RNAPII_Rpb7 S1_RNAP 85.8 7.6 0.00017 28.2 8.0 68 105-209 1-70 (88)
181 KOG3298 DNA-directed RNA polym 84.4 3.9 8.5E-05 33.4 6.3 60 54-119 77-152 (170)
182 TIGR02062 RNase_B exoribonucle 82.8 4.8 0.0001 39.9 7.6 55 149-210 572-630 (639)
183 COG4044 Uncharacterized protei 80.8 2.5 5.4E-05 36.0 4.1 74 53-127 70-156 (247)
184 COG1530 CafA Ribonucleases G a 79.5 2.5 5.3E-05 40.5 4.2 72 50-127 29-112 (487)
185 PRK10811 rne ribonuclease E; R 77.9 6.2 0.00013 40.8 6.5 70 104-208 37-107 (1068)
186 PF08292 RNA_pol_Rbc25: RNA po 77.4 7.7 0.00017 30.1 5.7 56 58-118 3-76 (122)
187 PTZ00162 DNA-directed RNA poly 72.1 21 0.00046 29.4 7.4 69 105-209 81-151 (176)
188 PRK11712 ribonuclease G; Provi 71.2 12 0.00026 35.9 6.5 81 96-208 29-110 (489)
189 KOG3409 Exosomal 3'-5' exoribo 71.2 12 0.00026 31.0 5.5 72 103-209 66-137 (193)
190 KOG3409 Exosomal 3'-5' exoribo 70.3 44 0.00095 27.7 8.6 70 56-127 66-146 (193)
191 KOG1856 Transcription elongati 66.5 5.2 0.00011 41.8 3.1 50 152-218 1006-1060(1299)
192 PRK15464 cold shock-like prote 60.5 19 0.00041 25.1 4.2 42 66-115 15-57 (70)
193 PRK12442 translation initiatio 60.1 30 0.00065 25.3 5.2 54 66-129 18-73 (87)
194 PRK12328 nusA transcription el 58.7 14 0.0003 34.3 4.1 27 22-48 179-208 (374)
195 COG1551 CsrA RNA-binding globa 57.5 7.8 0.00017 27.2 1.8 29 189-217 6-36 (73)
196 COG1530 CafA Ribonucleases G a 57.3 26 0.00057 33.6 5.9 75 95-209 27-102 (487)
197 cd05700 S1_Rrp5_repeat_hs9 S1_ 55.2 16 0.00034 24.9 2.9 27 101-127 39-65 (65)
198 PF10246 MRP-S35: Mitochondria 54.7 51 0.0011 24.9 5.8 49 57-117 22-75 (104)
199 PRK09507 cspE cold shock prote 54.0 35 0.00076 23.5 4.7 39 70-116 19-57 (69)
200 KOG1999 RNA polymerase II tran 52.0 1.3E+02 0.0027 31.5 9.8 40 195-234 408-464 (1024)
201 PF02599 CsrA: Global regulato 50.5 8 0.00017 25.7 0.9 30 190-219 7-38 (54)
202 PF13509 S1_2: S1 domain; PDB: 50.4 27 0.00058 23.4 3.5 21 22-44 40-60 (61)
203 PRK01712 carbon storage regula 49.4 12 0.00026 25.8 1.7 30 189-218 6-37 (64)
204 PRK00568 carbon storage regula 48.6 12 0.00026 26.7 1.6 29 189-217 6-36 (76)
205 PRK09937 stationary phase/star 47.9 89 0.0019 21.9 6.0 54 67-130 13-67 (74)
206 TIGR00008 infA translation ini 46.0 69 0.0015 22.3 5.1 50 66-125 16-67 (68)
207 PF00313 CSD: 'Cold-shock' DNA 46.0 87 0.0019 20.8 6.8 31 81-115 23-53 (66)
208 PRK15463 cold shock-like prote 44.8 39 0.00084 23.4 3.7 42 66-115 15-57 (70)
209 TIGR00202 csrA carbon storage 43.3 17 0.00038 25.4 1.7 29 189-217 6-36 (69)
210 PRK09890 cold shock protein Cs 40.7 72 0.0016 22.0 4.6 38 70-115 20-57 (70)
211 PRK14998 cold shock-like prote 39.7 1.3E+02 0.0028 21.0 5.8 48 70-127 17-64 (73)
212 KOG3754 Gamma-glutamylcysteine 38.4 34 0.00074 32.6 3.3 27 22-48 47-73 (640)
213 COG1278 CspC Cold shock protei 37.8 54 0.0012 22.8 3.5 31 81-115 24-54 (67)
214 TIGR02381 cspD cold shock doma 35.8 68 0.0015 21.9 3.8 38 70-115 17-54 (68)
215 PRK10354 RNA chaperone/anti-te 35.0 93 0.002 21.4 4.4 38 70-115 20-57 (70)
216 PRK10943 cold shock-like prote 33.4 93 0.002 21.4 4.2 38 70-115 19-56 (69)
217 PF11813 DUF3334: Protein of u 31.3 34 0.00074 29.1 2.0 21 149-169 51-71 (229)
218 COG2100 Predicted Fe-S oxidore 31.2 1.1E+02 0.0024 28.2 5.2 71 1-73 335-412 (414)
219 PRK12329 nusA transcription el 30.7 84 0.0018 29.9 4.6 27 22-48 198-227 (449)
220 cd04480 RPA1_DBD_A_like RPA1_D 28.7 1.6E+02 0.0035 20.6 5.0 44 22-67 17-60 (86)
221 cd04474 RPA1_DBD_A RPA1_DBD_A: 28.4 2.1E+02 0.0045 21.0 5.7 41 23-65 34-74 (104)
222 PF01835 A2M_N: MG2 domain; I 27.6 71 0.0015 22.9 3.0 31 100-130 8-45 (99)
223 KOG3013 Exosomal 3'-5' exoribo 26.9 1.1E+02 0.0025 27.0 4.5 71 54-130 81-166 (301)
224 PF03152 UFD1: Ubiquitin fusio 26.3 90 0.002 25.8 3.6 95 22-132 56-158 (176)
225 COG0361 InfA Translation initi 24.2 2.7E+02 0.0058 19.8 5.8 50 69-128 22-72 (75)
226 PF09876 DUF2103: Predicted me 22.6 2E+02 0.0043 21.8 4.5 54 156-210 33-86 (103)
227 PF07405 DUF1506: Protein of u 22.5 73 0.0016 24.6 2.2 57 68-129 55-122 (127)
228 KOG1004 Exosomal 3'-5' exoribo 21.6 3.1E+02 0.0067 23.6 5.9 58 55-118 62-124 (230)
229 PF02721 DUF223: Domain of unk 20.4 3.3E+02 0.0072 19.5 5.7 39 31-69 3-41 (95)
No 1
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.5e-42 Score=324.43 Aligned_cols=195 Identities=26% Similarity=0.488 Sum_probs=176.5
Q ss_pred hhcccCCCCEEEEEEEEEeCCCCEEEEEechhh-------HhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeE
Q 026737 16 EIAKGLTGSIISVKVIQANEEMKKLVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLT 83 (234)
Q Consensus 16 ~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~~-------~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~ 83 (234)
+++.+++|+++.|+|+++|.+++++++|+|... .+.+++++++|+++.|+ +|||||+|+ |++
T Consensus 143 ~d~~~~~Gk~~~~kiie~d~~~n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdig------Gvd 216 (541)
T COG0539 143 RDLDPLIGKELEFKILELDKKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIG------GVD 216 (541)
T ss_pred ccccccCCceEEEEEEEEccccCcEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEec------Cee
Confidence 345678999999999999999999999999752 45678999999999999 999999997 699
Q ss_pred EEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc-----------ceee
Q 026737 84 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE-----------PYLK 152 (234)
Q Consensus 84 glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~-----------G~fV 152 (234)
||+|++++||.++.+|.++|++||+|+|+|+++|++++|++||+|++.++||.....+ ++.|.. ||||
T Consensus 217 GLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~-~~~g~~v~G~Vt~i~~~GafV 295 (541)
T COG0539 217 GLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKK-YPVGDKVEGKVTNLTDYGAFV 295 (541)
T ss_pred eEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhh-cCCCCEEEEEEEEeecCcEEE
Confidence 9999999999999999999999999999999999999999999999999999866555 777631 9999
Q ss_pred eecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHH
Q 026737 153 SFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFH 227 (234)
Q Consensus 153 ~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~ 227 (234)
++.+|++||+ +|++ +|.... .++.++++||.|+|+||++|+ ||||+||+.+|||+.|+
T Consensus 296 ei~~GvEGlvhvSEi------------sw~~~~-----~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~ 358 (541)
T COG0539 296 EIEEGVEGLVHVSEI------------SWTKKN-----VPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFA 358 (541)
T ss_pred EecCCccceeechhh------------cccccC-----CHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhh
Confidence 9999999999 8999 555433 266799999999999999996 99999999999999999
Q ss_pred hhcccCC
Q 026737 228 ETAIVNN 234 (234)
Q Consensus 228 ~~~~~~~ 234 (234)
++|++|.
T Consensus 359 ~~~~~g~ 365 (541)
T COG0539 359 DKHPVGD 365 (541)
T ss_pred hhcCCCC
Confidence 9999874
No 2
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.6e-41 Score=314.38 Aligned_cols=203 Identities=30% Similarity=0.452 Sum_probs=185.7
Q ss_pred CCCCCCCCCCcchhhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhhcCCCCCcEEEEE-----EeeEEEE
Q 026737 1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIH 72 (234)
Q Consensus 1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~iv~g~-----~~G~fV~ 72 (234)
|||.| ..||+..+. +||+|+|+|+++|.+++|++||+|+. +|+.+..++++|+.+.|+ +|||||+
T Consensus 224 iS~~r-v~~P~~vvk------vGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVe 296 (541)
T COG0539 224 ISWKR-VDHPSEVVK------VGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVE 296 (541)
T ss_pred ccccc-cCCHHHhcc------cCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEEeecCcEEEE
Confidence 68888 899999987 99999999999999999999999986 699999999999999999 9999999
Q ss_pred EecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc----
Q 026737 73 LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE---- 148 (234)
Q Consensus 73 l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~---- 148 (234)
+. +|++||+|+||+||.+...|.+++++||+|.|+|+++|++++||+||+|++..|||..+.+. ++.|..
T Consensus 297 i~-----~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~-~~~g~~v~g~ 370 (541)
T COG0539 297 IE-----EGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADK-HPVGDVVEGK 370 (541)
T ss_pred ec-----CCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhh-cCCCCeEEEE
Confidence 98 58999999999999998889999999999999999999999999999999999999987776 788742
Q ss_pred -------ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737 149 -------PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK 216 (234)
Q Consensus 149 -------G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K 216 (234)
|+||++++|++||+ .|.+ +|.... +....++.|++++++||.+|. |+||+|
T Consensus 371 v~~~t~~g~fv~le~gidG~vh~~d~------------sw~~~~-----~~~~~~k~Gd~v~~~vl~vd~~~~~isLgiK 433 (541)
T COG0539 371 VKSITDFGAFVELEGGIDGLVHLSDL------------SWDRPG-----EEAEKYKKGDEVEAKVLAVDKEKERISLGIK 433 (541)
T ss_pred EeeecccceEEccCCCccceEEHHhc------------CccccC-----cHHHhhccCcEEEEEEEEEecccceeeeehh
Confidence 99999999999999 6766 554332 223378999999999999997 999999
Q ss_pred ccccchhHHHHhhcccC
Q 026737 217 RHCNEYWNVFHETAIVN 233 (234)
Q Consensus 217 ~~~~~p~~~~~~~~~~~ 233 (234)
|+.++||+.+.+.|++|
T Consensus 434 ql~~~p~~~~~~~~~~~ 450 (541)
T COG0539 434 QLEESPWEEFSEKYKKG 450 (541)
T ss_pred hhccCchhhhHhhccCC
Confidence 99999999999999987
No 3
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=2.5e-36 Score=298.09 Aligned_cols=205 Identities=26% Similarity=0.489 Sum_probs=178.7
Q ss_pred CCCCCCCCCCcchhhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhhcCCCCCcEEEEE-----EeeEEEE
Q 026737 1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIH 72 (234)
Q Consensus 1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~iv~g~-----~~G~fV~ 72 (234)
|||++ ..+|...+. +||+++|+|+++|++++++.||+|+. +|+.+.+.+++|++++|+ +||+||+
T Consensus 525 iS~~~-v~~~~~~~k------vGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVe 597 (863)
T PRK12269 525 MSWGH-VARPREFVK------KGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIE 597 (863)
T ss_pred ccccc-cCCHHHhcc------CCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEEEEEEEEeCCeEEEE
Confidence 34555 456655443 99999999999999999999999975 588888999999999999 9999999
Q ss_pred EecCCCcceeEEEEEceeccc-ccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc---
Q 026737 73 LRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE--- 148 (234)
Q Consensus 73 l~~~~g~~g~~glv~isels~-~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~--- 148 (234)
|+ +|++||+|+|+++| .++.+|.+.|++||+|+|+|+++|++++|++||+|++.+|||..+.++ +++|.+
T Consensus 598 L~-----~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~-~~vG~~v~G 671 (863)
T PRK12269 598 LA-----EGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEAR-YPVGARFTR 671 (863)
T ss_pred ec-----CCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHh-CCCCCEEEE
Confidence 97 47999999999999 578999999999999999999999999999999999999999877665 677732
Q ss_pred --------ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhh
Q 026737 149 --------PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKAS 215 (234)
Q Consensus 149 --------G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~ 215 (234)
|+||+|.+|++||+ +|++ +|.... .+++..+++||.|+|+|+++|. |+||+
T Consensus 672 ~V~~i~~~G~fV~l~~gV~GlIh~sel------------s~~~~~----~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~ 735 (863)
T PRK12269 672 RIVKVTNAGAFIEMEEGIDGFLHVDDL------------SWVKRT----RPADHELEVGKEIECMVIECDPQARRIRLGV 735 (863)
T ss_pred EEEEEecceEEEEeCCCcEEEEEhHHh------------hccccc----cchhhccCCCCEEEEEEEEEeccCCEEEEEe
Confidence 99999999999999 6776 454432 2344579999999999999986 99999
Q ss_pred cccccchhHHHHhhcccCC
Q 026737 216 KRHCNEYWNVFHETAIVNN 234 (234)
Q Consensus 216 K~~~~~p~~~~~~~~~~~~ 234 (234)
|++.++||+.|.++|++|.
T Consensus 736 K~l~~dpw~~~~~~~~vG~ 754 (863)
T PRK12269 736 KQLSDNPWQVFANAYGVGS 754 (863)
T ss_pred cccccChHHHHHhhCCCCC
Confidence 9999999999999999874
No 4
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=1.5e-33 Score=265.85 Aligned_cols=193 Identities=24% Similarity=0.388 Sum_probs=170.0
Q ss_pred cCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEE
Q 026737 20 GLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVH 87 (234)
Q Consensus 20 ~~vG~~v~~~Vi~id~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~ 87 (234)
.++|++++|+|+++|++++++.||+++. .|+.+..++++|++++|+ ++|+||+|+ ++++||||
T Consensus 157 ~~vG~~i~~~V~~id~~~~~v~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~-----~gv~g~v~ 231 (491)
T PRK13806 157 SYVGQTFQFLITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELA-----PGVEGMVH 231 (491)
T ss_pred HcCCCeEEEEEEEEECCCCeEEEEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcC-----CCcEEEEE
Confidence 4699999999999999999999999865 366777889999999998 999999996 37999999
Q ss_pred ceecccccccchhhhhCCCCEEEEEEEEEeCCC----CeEEEEEeecccCcchhhhhcccccccc-----------ceee
Q 026737 88 VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK----SRITLSIKQLEEDPLLETLEKVIPQGLE-----------PYLK 152 (234)
Q Consensus 88 isels~~~~~~~~~~~~vGd~v~vkVl~id~~~----~ri~LS~K~~~~~p~~~~~~~~~~~G~~-----------G~fV 152 (234)
+++++|.++.++.+.|++||.++|+|+++|.++ .|+.||+|++.++||..+.++ ++.|.+ |+||
T Consensus 232 ~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~-~~~G~~v~G~V~~v~~~G~fV 310 (491)
T PRK13806 232 ISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDR-LKAGDKVTGKVVRLAPFGAFV 310 (491)
T ss_pred HHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhcc-CCCCCEEEEEEEEEeCceEEE
Confidence 999999999999999999999999999999876 479999999999999876665 566632 9999
Q ss_pred eecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHH
Q 026737 153 SFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFH 227 (234)
Q Consensus 153 ~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~ 227 (234)
++.+|++||+ +|+++ |.... .++...+++||.|+|+|+++|. |+||+|++.++||+.+.
T Consensus 311 ~l~~gv~Glvh~sels------------~~~~~----~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~ 374 (491)
T PRK13806 311 EILPGIEGLVHVSEMS------------WTRRV----NKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVA 374 (491)
T ss_pred EeCCCcEEEEEHHHcC------------ccccc----CCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhh
Confidence 9999999999 78884 42221 3456689999999999999985 99999999999999999
Q ss_pred hhcccCC
Q 026737 228 ETAIVNN 234 (234)
Q Consensus 228 ~~~~~~~ 234 (234)
+.|++|.
T Consensus 375 ~~~~vG~ 381 (491)
T PRK13806 375 ERFAPGT 381 (491)
T ss_pred hhCCCCC
Confidence 9999884
No 5
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=6.4e-33 Score=261.55 Aligned_cols=197 Identities=25% Similarity=0.409 Sum_probs=167.6
Q ss_pred CCCCCCCCCcchhhhhcccCCCCEEEEEEEEEeCCC----CEEEEEechh---hHhhhhcCCCCCcEEEEE-----EeeE
Q 026737 2 SPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM----KKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGA 69 (234)
Q Consensus 2 ~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~----~~i~lS~k~~---~~~~~~~~~~~G~iv~g~-----~~G~ 69 (234)
+|++ ..+|...+. +||.+.|+|+++|.++ +++.||+|++ +|+.+..++++|+++.|+ +||+
T Consensus 236 s~~~-~~~~~~~~~------vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~G~ 308 (491)
T PRK13806 236 SWSR-VQKADEAVS------VGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGA 308 (491)
T ss_pred CCcc-ccChhHhcC------CCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEEEEEeCceE
Confidence 4444 445554443 9999999999999876 4799999986 698999999999999999 9999
Q ss_pred EEEEecCCCcceeEEEEEceeccc-ccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc
Q 026737 70 FIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE 148 (234)
Q Consensus 70 fV~l~~~~g~~g~~glv~isels~-~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~ 148 (234)
||+++ +|++||||+|+++| .++.++.+.|++||.|+|+|+++|+++++|.||+|++..+||..+.++ +++|.+
T Consensus 309 fV~l~-----~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~-~~vG~~ 382 (491)
T PRK13806 309 FVEIL-----PGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAER-FAPGTT 382 (491)
T ss_pred EEEeC-----CCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhh-CCCCCE
Confidence 99997 47999999999999 478899999999999999999999999999999999999999987766 666632
Q ss_pred -----------ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----ch
Q 026737 149 -----------PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IR 212 (234)
Q Consensus 149 -----------G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ 212 (234)
|+||++++|++||| +|++++++ . .++...+++||+|+|+|+++|. |+
T Consensus 383 v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~~~------------~-----~~~~~~~~~Gd~v~~~V~~id~e~~ri~ 445 (491)
T PRK13806 383 VTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAG------------K-----PATYEKLKPGDSVTLVVEEIDTAKRKIS 445 (491)
T ss_pred EEEEEEEEecCceEEEcCCCcEEEEEHHHcCccc------------c-----cchhhcCCCCCEEEEEEEEEeCCCCEEE
Confidence 99999999999999 78884322 1 2344578999999999999985 99
Q ss_pred hhhccc-----ccchhHHHHh
Q 026737 213 KASKRH-----CNEYWNVFHE 228 (234)
Q Consensus 213 ls~K~~-----~~~p~~~~~~ 228 (234)
||+|++ ..+||+.+..
T Consensus 446 Ls~~~~~~~~~~~~~~~~~~~ 466 (491)
T PRK13806 446 LAPAGAAGSGADDDDWKQFAP 466 (491)
T ss_pred EEeehhhhhhhhhhHHHhhcc
Confidence 999987 3589999853
No 6
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=6e-33 Score=274.14 Aligned_cols=195 Identities=22% Similarity=0.426 Sum_probs=169.9
Q ss_pred hcccCCCCEEEEEEEEEeC-----CCCEEEEEechhh-------HhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCc
Q 026737 17 IAKGLTGSIISVKVIQANE-----EMKKLVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGL 79 (234)
Q Consensus 17 ~~~~~vG~~v~~~Vi~id~-----~~~~i~lS~k~~~-------~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~ 79 (234)
+++.++|++++|+|+++|+ +++++++|+|... .+++++++++|++++|+ +||+||+++
T Consensus 440 ~~~~~vG~~ie~~V~~~~~~~~~~~~~~iVlSrr~~l~e~~~~~~ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl~----- 514 (863)
T PRK12269 440 APESLIGLTSKFYIERISQSKQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLG----- 514 (863)
T ss_pred chHHhCCCeEEEEEEEEecccccCCCCeEEEEHHHHHHHHHHHHHHHHHhcCCCCCEEEEEEEEEeCCcEEEEEC-----
Confidence 3456799999999999975 3468999998742 34567889999999998 899999996
Q ss_pred ceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc-----------
Q 026737 80 YHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE----------- 148 (234)
Q Consensus 80 ~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~----------- 148 (234)
|++||||+|+++|.++.+|.+.|++||+++|+|+++|++++++.||+|++.++||..+.++ +++|.+
T Consensus 515 -Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~-~~vG~iV~G~V~~I~~f 592 (863)
T PRK12269 515 -GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENK-FGVNDVVKGRVTKIADF 592 (863)
T ss_pred -CEEEEEEchhccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhcc-CCCCCEEEEEEEEEeCC
Confidence 6999999999999999999999999999999999999999999999999999999876665 666632
Q ss_pred ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchh
Q 026737 149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYW 223 (234)
Q Consensus 149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~ 223 (234)
|+||+|.+|++||+ +|+++ |.... .++...+++||+|+|+|+++|. |+||+|++.+|||
T Consensus 593 G~fVeL~~gveGLvhiSEls------------~~~~~----~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw 656 (863)
T PRK12269 593 GAFIELAEGIEGLAHISEFS------------WVKKT----SKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPW 656 (863)
T ss_pred eEEEEecCCceeeeEHHHhc------------Ccccc----CCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCch
Confidence 99999999999999 78884 43221 3456689999999999999995 9999999999999
Q ss_pred HHHHhhcccCC
Q 026737 224 NVFHETAIVNN 234 (234)
Q Consensus 224 ~~~~~~~~~~~ 234 (234)
+.|.++|++|.
T Consensus 657 ~~~~~~~~vG~ 667 (863)
T PRK12269 657 EEIEARYPVGA 667 (863)
T ss_pred HHHHHhCCCCC
Confidence 99999999874
No 7
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=5.1e-32 Score=253.82 Aligned_cols=181 Identities=23% Similarity=0.379 Sum_probs=158.5
Q ss_pred cccCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEE
Q 026737 18 AKGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL 85 (234)
Q Consensus 18 ~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~gl 85 (234)
++.++|++|+|+|+++|.++++++||+|.. .|+.+..++++|++++|+ +||+||+|+ +++||
T Consensus 161 ~~~~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlg------gv~Gl 234 (486)
T PRK07899 161 LQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLG------GVDGL 234 (486)
T ss_pred hhhcCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEEE
Confidence 345799999999999999999999999852 477788899999999999 999999996 69999
Q ss_pred EEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc-----------ceeeee
Q 026737 86 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE-----------PYLKSF 154 (234)
Q Consensus 86 v~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~-----------G~fV~l 154 (234)
||+|+++|.++.+|.+.|++||.|+|+|+++|++++||.||+|++.++||..+.+. +..|.+ |+||+|
T Consensus 235 v~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~-~~vG~vv~G~V~~I~~fGvFVeL 313 (486)
T PRK07899 235 VHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFART-HAIGQIVPGKVTKLVPFGAFVRV 313 (486)
T ss_pred EEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHh-cCCCCEEEEEEEEEeccEEEEEe
Confidence 99999999999999999999999999999999999999999999999999877665 555521 999999
Q ss_pred cCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccch
Q 026737 155 YKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEY 222 (234)
Q Consensus 155 ~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p 222 (234)
.+|++||| +|+++++.. ..+...+++||+|+|+|+++|. |+||+|++.++-
T Consensus 314 ~~gieGLvh~SeLs~~~v-----------------~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~~~~~~ 369 (486)
T PRK07899 314 EEGIEGLVHISELAERHV-----------------EVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQANEGV 369 (486)
T ss_pred CCCcEEEEEHHHcCcccc-----------------cCccceeCCCCEEEEEEEEEECCCCEEEEEEEEcccCC
Confidence 99999999 788853221 1234589999999999999985 999999997654
No 8
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.97 E-value=3e-31 Score=254.13 Aligned_cols=192 Identities=28% Similarity=0.497 Sum_probs=169.7
Q ss_pred cCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEE
Q 026737 20 GLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVH 87 (234)
Q Consensus 20 ~~vG~~v~~~Vi~id~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~ 87 (234)
.++|++++|+|+++|++++++.+|+|++ .|+.++.++++|++++|+ ++|+||+++ |++||+|
T Consensus 156 ~~vG~~i~~~V~~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~------g~~glv~ 229 (565)
T PRK06299 156 PLEGKELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLG------GVDGLLH 229 (565)
T ss_pred HhCCCEEEEEEEEEECCCCEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEEC------CEEEEEE
Confidence 4699999999999999999999999975 366778899999999999 999999996 6999999
Q ss_pred ceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc-----------ceeeeecC
Q 026737 88 VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE-----------PYLKSFYK 156 (234)
Q Consensus 88 isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~-----------G~fV~l~~ 156 (234)
+++++|.++.++.+.|++||.|+|+|+++|++++++.||+|++.++||....+. ++.|.+ |+||++.+
T Consensus 230 ~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~-~~~G~~v~g~V~~i~~~G~fV~l~~ 308 (565)
T PRK06299 230 ITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKK-YPVGSKVKGKVTNITDYGAFVELEE 308 (565)
T ss_pred HHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHhh-CCCCCEEEEEEEEEeCCeEEEEeCC
Confidence 999999999999999999999999999999999999999999999999876555 666632 99999999
Q ss_pred CceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhcc
Q 026737 157 KMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETAI 231 (234)
Q Consensus 157 gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~~ 231 (234)
|++||+ +|+++|+.+ . .++...+++||.|+|+|+++|. |+||+|++..+||+.+.+.|+
T Consensus 309 ~v~Glv~~sel~~~~~------------~----~~~~~~~~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~~~ 372 (565)
T PRK06299 309 GIEGLVHVSEMSWTKK------------N----KHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYP 372 (565)
T ss_pred CCEEEEEHHHcCcccc------------c----cCHHHhcCCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHhCC
Confidence 999999 788854322 1 2344578999999999999985 999999999999999999998
Q ss_pred cCC
Q 026737 232 VNN 234 (234)
Q Consensus 232 ~~~ 234 (234)
+|.
T Consensus 373 ~G~ 375 (565)
T PRK06299 373 VGD 375 (565)
T ss_pred CCC
Confidence 873
No 9
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.97 E-value=1.6e-30 Score=238.85 Aligned_cols=186 Identities=24% Similarity=0.364 Sum_probs=163.2
Q ss_pred cCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEE
Q 026737 20 GLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVH 87 (234)
Q Consensus 20 ~~vG~~v~~~Vi~id~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~ 87 (234)
.++|+++.|+|+++|++++++.||+|.. .|..++.++++|++++|+ ++|+||+++ +++||||
T Consensus 147 ~~vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~------~v~g~v~ 220 (390)
T PRK06676 147 DFKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIG------GVDGLVH 220 (390)
T ss_pred HcCCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeC------CeEEEEE
Confidence 4599999999999999999999999874 356677889999999998 999999996 6999999
Q ss_pred ceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc-----------ceeeeecC
Q 026737 88 VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE-----------PYLKSFYK 156 (234)
Q Consensus 88 isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~-----------G~fV~l~~ 156 (234)
+++++|.++.++.+.|++||.|+|+|+++|+++++|.||+|++.++||..+.++ +..|.+ |+||++.+
T Consensus 221 ~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~-~~~G~~v~g~V~~i~~~G~fV~l~~ 299 (390)
T PRK06676 221 ISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEK-LPEGDVIEGTVKRLTDFGAFVEVLP 299 (390)
T ss_pred HHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhh-hcCCcEEEEEEEEEeCceEEEEECC
Confidence 999999999999999999999999999999999999999999999999876655 555521 99999999
Q ss_pred CceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhh
Q 026737 157 KMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHET 229 (234)
Q Consensus 157 gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~ 229 (234)
|++||+ +|++++.. . .++...+++||.|+|+|+++|. |+||+|++.++||+.+.++
T Consensus 300 gi~Glv~~se~~~~~------------~-----~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~~~~~~~~~~~~ 360 (390)
T PRK06676 300 GVEGLVHISQISHKH------------I-----ATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAPAEEEDRR 360 (390)
T ss_pred CCeEEEEhHHcCccc------------c-----CChhhccCCCCEEEEEEEEEECCCCEEEEEEEecccChhhhhhhh
Confidence 999999 78774221 1 2345578999999999999985 9999999999999999776
No 10
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=99.97 E-value=1.3e-30 Score=247.10 Aligned_cols=204 Identities=27% Similarity=0.472 Sum_probs=173.2
Q ss_pred CCCCCCCCCcchhhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhhcCCCCCcEEEEE-----EeeEEEEE
Q 026737 2 SPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHL 73 (234)
Q Consensus 2 ~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~iv~g~-----~~G~fV~l 73 (234)
++++ ..+|...+. +|+++.|+|+++|++++++.+|++.. +|+.+...+++|+++.|+ ++|+||++
T Consensus 220 s~~~-~~~~~~~~~------vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l 292 (516)
T TIGR00717 220 SWKR-VKHPSEYVK------VGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEI 292 (516)
T ss_pred CCCC-CCCHHHhcc------CCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHHhhccCCCEEEEEEEEeeCCcEEEEe
Confidence 4444 445554443 99999999999999999999999965 688888889999999998 99999999
Q ss_pred ecCCCcceeEEEEEceecccc-cccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc----
Q 026737 74 RFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE---- 148 (234)
Q Consensus 74 ~~~~g~~g~~glv~isels~~-~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~---- 148 (234)
+ ++++||+|+++++|. ...++.+.|++||.++|+|+++|++++++.||+|++..+||..+.+. +..|.+
T Consensus 293 ~-----~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~-~~~G~~v~g~ 366 (516)
T TIGR00717 293 E-----EGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEK-HPVGDRVTGK 366 (516)
T ss_pred C-----CCCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHh-CCCCCEEEEE
Confidence 7 479999999999987 46778888999999999999999999999999999999999877665 555532
Q ss_pred -------ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737 149 -------PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK 216 (234)
Q Consensus 149 -------G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K 216 (234)
|+||++.+|++||+ +|+++|... . .++...+++||.|.|+|+++|. |.||+|
T Consensus 367 V~~v~~~G~fV~l~~~v~glv~~s~ls~~~~------------~----~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K 430 (516)
T TIGR00717 367 IKKITDFGAFVELEGGIDGLIHLSDISWDKD------------G----READHLYKKGDEIEAVVLAVDKEKKRISLGVK 430 (516)
T ss_pred EEEEecceEEEECCCCCEEEEEHHHCcCccc------------C----CCHhHccCCCCEEEEEEEEEeCcCCEEEEeec
Confidence 99999999999999 788754321 1 1234578999999999999985 999999
Q ss_pred ccccchhHHHHhhcccCC
Q 026737 217 RHCNEYWNVFHETAIVNN 234 (234)
Q Consensus 217 ~~~~~p~~~~~~~~~~~~ 234 (234)
++.++||+.+.+.|++|.
T Consensus 431 ~~~~~p~~~~~~~~~~G~ 448 (516)
T TIGR00717 431 QLTENPWEKFAAKYKVGS 448 (516)
T ss_pred cccCCchhhhhhccCcce
Confidence 999999999999888773
No 11
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.97 E-value=2.9e-30 Score=247.39 Aligned_cols=204 Identities=28% Similarity=0.453 Sum_probs=174.3
Q ss_pred CCCCCCCCCcchhhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhhcCCCCCcEEEEE-----EeeEEEEE
Q 026737 2 SPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHL 73 (234)
Q Consensus 2 ~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~iv~g~-----~~G~fV~l 73 (234)
+|++ ..+|...+. +||++.|+|+++|.+++++.||++.. +|+.+...+++|+++.|+ ++|+||++
T Consensus 234 s~~~-~~~~~~~~k------vG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l 306 (565)
T PRK06299 234 SWKR-VNHPSEVVN------VGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKYPVGSKVKGKVTNITDYGAFVEL 306 (565)
T ss_pred cccc-cCCHhhcCC------CCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEe
Confidence 4444 445655544 99999999999999999999999965 698888899999999999 99999999
Q ss_pred ecCCCcceeEEEEEceecccc-cccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc----
Q 026737 74 RFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE---- 148 (234)
Q Consensus 74 ~~~~g~~g~~glv~isels~~-~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~---- 148 (234)
+ ++++||+|+++++|. +..+|.+.|++||.|+|+|+++|++++++.||+|++..+||..+... +..|.+
T Consensus 307 ~-----~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~-~~~G~~v~g~ 380 (565)
T PRK06299 307 E-----EGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEK-YPVGDVVEGK 380 (565)
T ss_pred C-----CCCEEEEEHHHcCccccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHh-CCCCCEEEEE
Confidence 7 479999999999987 46788899999999999999999999999999999999999877665 566621
Q ss_pred -------ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737 149 -------PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK 216 (234)
Q Consensus 149 -------G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K 216 (234)
|+||+|.+|++|++ +|+++++. .. .++...+++||.|+|+|+++|. |.||+|
T Consensus 381 V~~v~~~G~fV~l~~~v~g~i~~s~l~~~~------------~~----~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k 444 (565)
T PRK06299 381 VKNITDFGAFVGLEGGIDGLVHLSDISWDK------------KG----EEAVELYKKGDEVEAVVLKVDVEKERISLGIK 444 (565)
T ss_pred EEEEecceEEEECCCCCEEEEEHHHcCccc------------cc----cChHhhCCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence 99999988999999 78874321 10 2345688999999999999984 999999
Q ss_pred ccccchhHHHHhhcccCC
Q 026737 217 RHCNEYWNVFHETAIVNN 234 (234)
Q Consensus 217 ~~~~~p~~~~~~~~~~~~ 234 (234)
++..+||..+.+.+++|.
T Consensus 445 ~~~~~p~~~~~~~~~~G~ 462 (565)
T PRK06299 445 QLEEDPFEEFAKKHKKGS 462 (565)
T ss_pred hhhcCchhHHHhhcCCCC
Confidence 999999999999888873
No 12
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=99.97 E-value=1.9e-29 Score=239.16 Aligned_cols=193 Identities=26% Similarity=0.485 Sum_probs=168.1
Q ss_pred ccCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEE
Q 026737 19 KGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLV 86 (234)
Q Consensus 19 ~~~vG~~v~~~Vi~id~~~~~i~lS~k~~-------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv 86 (234)
..++|++++|+|+++|++++++++|+|.. .++.++..+++|++++|+ ++|+||+++ +++||+
T Consensus 141 ~~~vG~~i~~~v~~~~~~~~~iv~Srk~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l~------g~~g~l 214 (516)
T TIGR00717 141 DSLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKGVVKNITDFGAFVDLG------GVDGLL 214 (516)
T ss_pred hhhCCCEEEEEEEEEECCCCcEEEEHHHHHHHHHHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEEEE
Confidence 45699999999999999999999999865 255667889999999999 899999996 699999
Q ss_pred EceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc-----------ceeeeec
Q 026737 87 HVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE-----------PYLKSFY 155 (234)
Q Consensus 87 ~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~-----------G~fV~l~ 155 (234)
|.++++|.++.++.+.|++||.+.|+|+++|++++++.||+|++.++||....+. +..|.+ |+||++.
T Consensus 215 p~~e~s~~~~~~~~~~~~vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~-~~~G~i~~g~V~~v~~~G~fV~l~ 293 (516)
T TIGR00717 215 HITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKK-FPVGDKITGRVTNLTDYGVFVEIE 293 (516)
T ss_pred EHHHcCCCCCCCHHHhccCCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHHhh-ccCCCEEEEEEEEeeCCcEEEEeC
Confidence 9999999999999999999999999999999999999999999999999876654 555521 9999999
Q ss_pred CCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhc
Q 026737 156 KKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETA 230 (234)
Q Consensus 156 ~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~ 230 (234)
+|++||+ +|+++++.. . .++...+++||.|+|+|+++|. |.||+|++.++||+.+.+.+
T Consensus 294 ~~v~g~v~~sels~~~~------------~----~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~ 357 (516)
T TIGR00717 294 EGIEGLVHVSEMSWVKK------------N----SHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKH 357 (516)
T ss_pred CCCEEEEEHHHcCCccc------------c----CCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhC
Confidence 9999999 688743321 1 2344578999999999999985 99999999999999999988
Q ss_pred ccCC
Q 026737 231 IVNN 234 (234)
Q Consensus 231 ~~~~ 234 (234)
.+|.
T Consensus 358 ~~G~ 361 (516)
T TIGR00717 358 PVGD 361 (516)
T ss_pred CCCC
Confidence 8874
No 13
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.96 E-value=5.4e-29 Score=233.48 Aligned_cols=184 Identities=19% Similarity=0.368 Sum_probs=158.6
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecc
Q 026737 22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS 92 (234)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~----~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels 92 (234)
+|++|+|+|+++|.++++++||+|++ .|+.+...++.|++++|+ ++|+||+++ ++||||.|+++
T Consensus 82 vGd~Ie~~V~~~~~~~g~liLS~k~~~~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~VdlG-------i~gflP~Sel~ 154 (486)
T PRK07899 82 VGDEVEALVLQKEDKEGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDIG-------LRGFLPASLVE 154 (486)
T ss_pred CCCEEEEEEEEEECCCCeEEEEehhhcccchHHHHHHHhcCCCEEEEEEEEEECCeEEEEEC-------CEEEEEhhHhc
Confidence 99999999999999999999999975 477777777899999998 889999994 89999999999
Q ss_pred cccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeeccc----Ccchhhhhcccccccc-----------ceeeeecCC
Q 026737 93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE----DPLLETLEKVIPQGLE-----------PYLKSFYKK 157 (234)
Q Consensus 93 ~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~----~p~~~~~~~~~~~G~~-----------G~fV~l~~g 157 (234)
+.++.++..+ +||.|+|+|+++|++++++.||+|.+.. ++|..++.. +..|.+ |+||+| +|
T Consensus 155 ~~~~~~~~~~--vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~-lk~G~iv~G~V~~i~~~G~FVdl-gg 230 (486)
T PRK07899 155 MRRVRDLQPY--IGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQ-LQKGQVRKGVVSSIVNFGAFVDL-GG 230 (486)
T ss_pred ccccCChhhc--CCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHh-ccCCCEEEEEEEEEECCeEEEEE-CC
Confidence 9988888763 8999999999999999999999996543 678777665 566521 999999 58
Q ss_pred ceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhccc
Q 026737 158 MDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETAIV 232 (234)
Q Consensus 158 i~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~~~ 232 (234)
++||+ +|+++ |-.. .++...+++||.|+++|+++|+ |+||+|++.++||+.+.++|++
T Consensus 231 v~Glv~~Sels------------~~~v-----~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~v 293 (486)
T PRK07899 231 VDGLVHVSELS------------WKHI-----DHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAI 293 (486)
T ss_pred EEEEEEHHHCC------------Cccc-----CCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCC
Confidence 99999 78884 4221 2455689999999999999985 9999999999999999999987
Q ss_pred C
Q 026737 233 N 233 (234)
Q Consensus 233 ~ 233 (234)
|
T Consensus 294 G 294 (486)
T PRK07899 294 G 294 (486)
T ss_pred C
Confidence 6
No 14
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.96 E-value=8.2e-29 Score=221.94 Aligned_cols=178 Identities=14% Similarity=0.221 Sum_probs=148.4
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecc
Q 026737 22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS 92 (234)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~----~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels 92 (234)
+|++++|+|+++|.+++++.||+|+. .|+.+...+..|++++|+ ++|+||+++ |++||||+|+++
T Consensus 78 ~G~~v~~~Vi~~~~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l~------Gv~gfip~s~ls 151 (318)
T PRK07400 78 PNETREFFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIE------GLRGFIPGSHIS 151 (318)
T ss_pred CCCEEEEEEEEEeCCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHcC
Confidence 89999999999999999999999874 488888888899999998 899999996 699999999999
Q ss_pred cccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccc-----c------ceeeeecCCceEE
Q 026737 93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGL-----E------PYLKSFYKKMDDV 161 (234)
Q Consensus 93 ~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~-----~------G~fV~l~~gi~Gl 161 (234)
|.+.. +.+ +|+.+.++|+++|+++++|.||+|++..++ ...+ +..|. + |+||++ .|++||
T Consensus 152 ~~~~~---~~~-vG~~i~~kVl~id~~~~~i~lS~K~~~~~~---~~~~-~k~G~vv~G~V~~I~~~G~fV~i-~gv~Gl 222 (318)
T PRK07400 152 TRKPK---EEL-VGEELPLKFLEVDEERNRLVLSHRRALVER---KMNR-LEVGEVVVGTVRGIKPYGAFIDI-GGVSGL 222 (318)
T ss_pred ccCCc---ccc-CCCEEEEEEEEEEcccCEEEEEhhHhhhhh---hhcc-CCCCCEEEEEEEEEECCeEEEEE-CCEEEE
Confidence 96533 333 999999999999999999999999765543 2222 45552 1 999999 599999
Q ss_pred E-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhcc
Q 026737 162 R-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETAI 231 (234)
Q Consensus 162 ~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~~ 231 (234)
+ +|+++++. . .++...+++||.|+|+|+++|. |+||+|++.++||+.+....+
T Consensus 223 lhisels~~~------------~-----~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~~P~~~~~~~~~ 280 (318)
T PRK07400 223 LHISEISHEH------------I-----ETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEPGDMLKDPQK 280 (318)
T ss_pred EEHHHccccc------------c-----cChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccccChhhhhhhHHH
Confidence 9 78885432 1 2355689999999999999984 999999999999998876543
No 15
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.95 E-value=5.7e-27 Score=227.69 Aligned_cols=181 Identities=29% Similarity=0.458 Sum_probs=158.1
Q ss_pred cccCCCCEEEEEEEEEeCCCCE-EEEEechhh-------HhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEE
Q 026737 18 AKGLTGSIISVKVIQANEEMKK-LVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTG 84 (234)
Q Consensus 18 ~~~~vG~~v~~~Vi~id~~~~~-i~lS~k~~~-------~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~g 84 (234)
++.++|+++.|+|+++|+++++ +.+|+|... ++..+.++++|+++.|+ ++|+||+++ +++|
T Consensus 429 ~~~~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l~------gv~G 502 (647)
T PRK00087 429 LSEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIG------GVDG 502 (647)
T ss_pred HHHhCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEEC------CEEE
Confidence 3446999999999999999998 999998752 45677889999999998 899999995 6999
Q ss_pred EEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhcccccccc-----------ceeee
Q 026737 85 LVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE-----------PYLKS 153 (234)
Q Consensus 85 lv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~-----------G~fV~ 153 (234)
|+|+++++|.++.++.+.|++||.++++|+++|++++++.||+|++.++||....++ +..|.+ |+||+
T Consensus 503 ll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~-~~~G~~v~g~V~~i~~~G~fV~ 581 (647)
T PRK00087 503 LLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEK-YPVGSIVLGKVVRIAPFGAFVE 581 (647)
T ss_pred EEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhh-ccCCeEEEEEEEEEECCeEEEE
Confidence 999999999999999999999999999999999999999999999999999876665 555621 99999
Q ss_pred ecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccch
Q 026737 154 FYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEY 222 (234)
Q Consensus 154 l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p 222 (234)
+.+|++||+ +|+++++.. .++...+++||+|+|+|+++|. |+||+|++.++|
T Consensus 582 l~~~i~Gli~~sel~~~~~-----------------~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~~~~ 638 (647)
T PRK00087 582 LEPGVDGLVHISQISWKRI-----------------DKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEP 638 (647)
T ss_pred ECCCCEEEEEhhhcCcccc-----------------CCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence 999999999 788743221 2345578999999999999985 999999999999
No 16
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.95 E-value=8.5e-27 Score=214.20 Aligned_cols=185 Identities=21% Similarity=0.332 Sum_probs=158.4
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecc
Q 026737 22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS 92 (234)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~----~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels 92 (234)
+|++++|+|+++|.+++++.||++.. .|+.+...++.|+++.|+ ++|+||+++ |++||||+++++
T Consensus 65 vGd~v~~~V~~v~~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~------G~~gflp~~el~ 138 (390)
T PRK06676 65 VGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVE------GVRGFIPASLIS 138 (390)
T ss_pred CCCEEEEEEEEEECCCCCEEEEHHHhhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHcC
Confidence 99999999999999999999999974 488887888999999999 889999996 589999999999
Q ss_pred cccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeeccc----Ccchhhhhcccccccc-----------ceeeeecCC
Q 026737 93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE----DPLLETLEKVIPQGLE-----------PYLKSFYKK 157 (234)
Q Consensus 93 ~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~----~p~~~~~~~~~~~G~~-----------G~fV~l~~g 157 (234)
+.+..++..+ +||.+.|+|+++|.+++++.||+|++.. ++|...... +..|.+ |+||++ +|
T Consensus 139 ~~~~~~~~~~--vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~-~~~G~~v~g~V~~v~~~G~fV~l-~~ 214 (390)
T PRK06676 139 TRFVEDFSDF--KGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSS-LKEGDVVEGTVARLTDFGAFVDI-GG 214 (390)
T ss_pred CccCCChHHc--CCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhh-CCCCCEEEEEEEEEecceEEEEe-CC
Confidence 9988888764 8999999999999999999999998765 466655554 455521 999999 58
Q ss_pred ceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhccc
Q 026737 158 MDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETAIV 232 (234)
Q Consensus 158 i~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~~~ 232 (234)
++|++ +|++++. .. .++...+++||.|+++|+++|. |.||+|++.++||+.+.+.+.+
T Consensus 215 v~g~v~~sels~~------------~~-----~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~ 277 (390)
T PRK06676 215 VDGLVHISELSHE------------RV-----EKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPE 277 (390)
T ss_pred eEEEEEHHHcCcc------------cc-----CCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhhhcC
Confidence 99999 7887432 11 2355678999999999999985 9999999999999999888887
Q ss_pred C
Q 026737 233 N 233 (234)
Q Consensus 233 ~ 233 (234)
|
T Consensus 278 G 278 (390)
T PRK06676 278 G 278 (390)
T ss_pred C
Confidence 7
No 17
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.93 E-value=5.1e-25 Score=214.05 Aligned_cols=185 Identities=20% Similarity=0.342 Sum_probs=158.3
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecc
Q 026737 22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS 92 (234)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~----~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels 92 (234)
+|++++|+|+++|.+.+++.||++.. .|+.+...+++|+++.|+ ++|+||+++ +++||||.++++
T Consensus 349 vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lg------gi~gfiP~sel~ 422 (647)
T PRK00087 349 VGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYG------GVRAFLPASHVE 422 (647)
T ss_pred CCCEEEEEEEEEECCCCcEEEEeehhcchhHHHHHHHHhhCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHhC
Confidence 99999999999999999999999865 477887888999999998 889999997 599999999999
Q ss_pred cccccchhhhhCCCCEEEEEEEEEeCCCCe-EEEEEeeccc----Ccchhhhhccccccc-----c------ceeeeecC
Q 026737 93 WDLIQDIRDILNEGDEVRVKVIKIDREKSR-ITLSIKQLEE----DPLLETLEKVIPQGL-----E------PYLKSFYK 156 (234)
Q Consensus 93 ~~~~~~~~~~~~vGd~v~vkVl~id~~~~r-i~LS~K~~~~----~p~~~~~~~~~~~G~-----~------G~fV~l~~ 156 (234)
+.+..++..+ +|+.++++|+++|+++++ +.+|+|.+.. ++|....++ +..|. + |+||++ +
T Consensus 423 ~~~~~d~~~~--vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~-l~~G~iV~g~V~~v~~~G~fV~l-~ 498 (647)
T PRK00087 423 LGYVEDLSEY--KGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNS-LEEGDVVEGEVKRLTDFGAFVDI-G 498 (647)
T ss_pred ccccCCHHHh--CCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHh-CCCCCEEEEEEEEEeCCcEEEEE-C
Confidence 9998888764 899999999999998888 9999998753 566555554 44542 1 999999 8
Q ss_pred CceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhcc
Q 026737 157 KMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETAI 231 (234)
Q Consensus 157 gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~~ 231 (234)
|++||+ +|++++. .. .++...+++||.|+++|+++|+ |.||+|++.++||+.+.++|+
T Consensus 499 gv~Gll~~sels~~------------~~-----~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~ 561 (647)
T PRK00087 499 GVDGLLHVSEISWG------------RV-----EKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYP 561 (647)
T ss_pred CEEEEEEHHHcCcc------------cc-----CCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhhcc
Confidence 999999 7887432 11 2355679999999999999985 999999999999999999888
Q ss_pred cC
Q 026737 232 VN 233 (234)
Q Consensus 232 ~~ 233 (234)
+|
T Consensus 562 ~G 563 (647)
T PRK00087 562 VG 563 (647)
T ss_pred CC
Confidence 86
No 18
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.85 E-value=1.5e-20 Score=168.68 Aligned_cols=112 Identities=37% Similarity=0.637 Sum_probs=106.6
Q ss_pred cCCCCEEEEEEEEEeCCCCEEEEEechhhHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccc
Q 026737 20 GLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD 94 (234)
Q Consensus 20 ~~vG~~v~~~Vi~id~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~ 94 (234)
.++|+++.|+|+++|+++++++||+|.+.++....++++|+++.|+ +||+||+++ |++||+|+++++|.
T Consensus 158 ~~vG~~i~~kVl~id~~~~~i~lS~K~~~~~~~~~~~k~G~vv~G~V~~I~~~G~fV~i~------gv~Gllhisels~~ 231 (318)
T PRK07400 158 ELVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDIG------GVSGLLHISEISHE 231 (318)
T ss_pred ccCCCEEEEEEEEEEcccCEEEEEhhHhhhhhhhccCCCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHcccc
Confidence 3599999999999999999999999988888888899999999999 999999996 69999999999999
Q ss_pred cccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchh
Q 026737 95 LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLE 137 (234)
Q Consensus 95 ~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~ 137 (234)
++.++.+.|++||.|+|+|+++|.++++|.||+|++.+|||+.
T Consensus 232 ~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~~P~~~ 274 (318)
T PRK07400 232 HIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEPGDM 274 (318)
T ss_pred cccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccccChhhh
Confidence 9999999999999999999999999999999999999999964
No 19
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.71 E-value=1.4e-17 Score=148.13 Aligned_cols=105 Identities=22% Similarity=0.356 Sum_probs=90.2
Q ss_pred cCCC-CCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737 54 SRVN-VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (234)
Q Consensus 54 ~~~~-~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~ 127 (234)
++++ +|++|.|+ +||+||+|.+++ |++||||+|++||.++.++++.+++||.+.|+|+++|+++++|.||+
T Consensus 12 ~~~P~~GdvV~g~V~~I~d~GafV~L~EY~---gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~ 88 (319)
T PTZ00248 12 QKFPEEDDLVMVKVVRITEMGAYVSLLEYD---DIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSK 88 (319)
T ss_pred hhCCCCCCEEEEEEEEEeCCeEEEEecCCC---CcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEe
Confidence 3455 89999998 999999996322 69999999999999999999999999999999999999999999999
Q ss_pred eecccCcchhhhhcccccccc------------ceeee------ecCCceEEE
Q 026737 128 KQLEEDPLLETLEKVIPQGLE------------PYLKS------FYKKMDDVR 162 (234)
Q Consensus 128 K~~~~~p~~~~~~~~~~~G~~------------G~fV~------l~~gi~Gl~ 162 (234)
|++.++||...... ++.|.+ |+|++ ..++++++.
T Consensus 89 K~v~~~pw~~~~e~-~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~g 140 (319)
T PTZ00248 89 KRVSPEDIEACEEK-FSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYG 140 (319)
T ss_pred eecccchHHHHHHh-CcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcC
Confidence 99999999987776 666521 77776 456777776
No 20
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.70 E-value=2e-17 Score=126.75 Aligned_cols=75 Identities=45% Similarity=0.756 Sum_probs=70.5
Q ss_pred CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (234)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~ 129 (234)
.+++|++++|+ +|||||+|+ .|-.|||||||+++.|++++.+++++||+|+|+|+++|. +++|+||+|.
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~-----~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~ 75 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELE-----GGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRK 75 (129)
T ss_pred CccccceEEEEEEeeEecceEEEec-----CCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcceehHH
Confidence 47899999998 999999998 268999999999999999999999999999999999997 9999999999
Q ss_pred cccCcc
Q 026737 130 LEEDPL 135 (234)
Q Consensus 130 ~~~~p~ 135 (234)
+...|-
T Consensus 76 ~~e~pe 81 (129)
T COG1098 76 LEEEPE 81 (129)
T ss_pred hhhCcc
Confidence 998874
No 21
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.56 E-value=8.5e-15 Score=104.51 Aligned_cols=66 Identities=26% Similarity=0.423 Sum_probs=60.5
Q ss_pred CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccch---hhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI---RDILNEGDEVRVKVIKIDREKSRITLS 126 (234)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~---~~~~~vGd~v~vkVl~id~~~~ri~LS 126 (234)
+++|+++.|+ +||+||+|+ ++++|+||++++||.++.++ .+.|++||.++|+|+++|+++++|.||
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~-----~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS 74 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLS-----SSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeC-----CCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 5789999999 999999997 47999999999999997765 588999999999999999999999886
No 22
>PRK08582 hypothetical protein; Provisional
Probab=99.56 E-value=1.7e-14 Score=114.92 Aligned_cols=77 Identities=40% Similarity=0.679 Sum_probs=71.6
Q ss_pred CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (234)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~ 129 (234)
.+++|++|.|+ +||+||+|+ ++++||||+++++|.++.++.+.|++||.|+|+|+++|. .++|.||+|+
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~fV~L~-----~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~ 75 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELP-----EGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKK 75 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEEEEEC-----CCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEe
Confidence 37899999998 999999997 379999999999999999999999999999999999997 5999999999
Q ss_pred cccCcchh
Q 026737 130 LEEDPLLE 137 (234)
Q Consensus 130 ~~~~p~~~ 137 (234)
+.++||.+
T Consensus 76 ~~~~~~~~ 83 (139)
T PRK08582 76 AKDRPKRQ 83 (139)
T ss_pred cccCchhh
Confidence 99999964
No 23
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.50 E-value=7.3e-14 Score=138.18 Aligned_cols=87 Identities=28% Similarity=0.435 Sum_probs=78.3
Q ss_pred HhhhhcCCCCCcEEE-EE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCe
Q 026737 49 WNKYSSRVNVEDIFV-GR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSR 122 (234)
Q Consensus 49 ~~~~~~~~~~G~iv~-g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~r 122 (234)
++.+....++|++|+ |+ +||+||+|. ++.+||||+|+++|.++.++.+.|++||.|+|+|+++|. ++|
T Consensus 744 I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~-----~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~gr 817 (891)
T PLN00207 744 ISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIA-----PGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQ 817 (891)
T ss_pred HHHHhcCcCCCcEEECcEEEEEeccEEEEEeC-----CCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC-CCc
Confidence 445556789999995 45 999999997 479999999999999999999999999999999999997 899
Q ss_pred EEEEEeecccCcchhhhhc
Q 026737 123 ITLSIKQLEEDPLLETLEK 141 (234)
Q Consensus 123 i~LS~K~~~~~p~~~~~~~ 141 (234)
|.||+|++.++||.++.+.
T Consensus 818 I~LSlK~l~~~Pw~~~~~~ 836 (891)
T PLN00207 818 LRLSRRALLPEANSEKSSQ 836 (891)
T ss_pred EEEEEeccccCchhhhhhh
Confidence 9999999999999987664
No 24
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.50 E-value=1.1e-13 Score=98.51 Aligned_cols=65 Identities=17% Similarity=0.305 Sum_probs=60.4
Q ss_pred CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccc--ccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (234)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~--~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K 128 (234)
|++++|+ ++|+||+|+ ++++|+||+++++|.. ..++.+.|++||.++|+|+++|+++++|.||+|
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~-----~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTIS-----PDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeC-----CCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 7888888 999999997 4799999999999874 889999999999999999999999999999986
No 25
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.49 E-value=1.2e-13 Score=97.89 Aligned_cols=66 Identities=20% Similarity=0.305 Sum_probs=60.8
Q ss_pred CCCCcEEEEE-----E-eeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737 56 VNVEDIFVGR-----D-YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (234)
Q Consensus 56 ~~~G~iv~g~-----~-~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K 128 (234)
+++|+++.|+ + +|+|++++ ++.+|++|+|+++|++..++.+.|++||.++|+|+++|. +++.||+|
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~-----~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~--~~i~LSl~ 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLP-----FGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECC-----CCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEEEEeC
Confidence 4689999998 4 89999997 479999999999999999999999999999999999984 99999986
No 26
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.48 E-value=4.1e-13 Score=135.08 Aligned_cols=175 Identities=22% Similarity=0.247 Sum_probs=141.6
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh-----------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEE
Q 026737 22 TGSIISVKVIQANEEMKKLVFSEKDA-----------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL 85 (234)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~-----------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~gl 85 (234)
.++.+.+.++.++..++.+.||.+.. .-.+..++++.|+++.|. +.|+|+.+. ++++|+
T Consensus 1115 ~~~~v~~~~L~vs~~n~~leLslr~sr~~~t~~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glfi~ls-----~~v~a~ 1189 (1710)
T KOG1070|consen 1115 KIQIVYVCVLSVSALNKGLELSLRESRTKITPVDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLFIALS-----RKVEAF 1189 (1710)
T ss_pred cccEEEEEEEEEecccccceeecccccccCccccccCCcccchhhcccCceeEEEEEEecCCcEEEEEc-----cceEEE
Confidence 67999999999999988899998832 123457889999999999 889999998 589999
Q ss_pred EEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhh--ccccc-----ccc------ceee
Q 026737 86 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLE--KVIPQ-----GLE------PYLK 152 (234)
Q Consensus 86 v~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~--~~~~~-----G~~------G~fV 152 (234)
+++++++..+.+.++..|++|+.+.++|++++...+|+.||+|.....--..... ..+.. |++ |.||
T Consensus 1190 v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~v~~~~~~G~fi 1269 (1710)
T KOG1070|consen 1190 VPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKNSDIKDTVKLLKDSKDLKKGDREDGTVEVVDPFGLFI 1269 (1710)
T ss_pred EEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEeccccCCchhhhhhhhhhhccccccceEEEecCCceEE
Confidence 9999999999999999999999999999999999999999999865422111111 11222 332 9999
Q ss_pred eecCCc--eEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhccc
Q 026737 153 SFYKKM--DDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRH 218 (234)
Q Consensus 153 ~l~~gi--~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~ 218 (234)
++++++ .|+| +++++.++. .+++..+..|++|+|.+++.+. |+|++|.+
T Consensus 1270 ~l~~tv~~~g~~~~~e~~d~~~-----------------e~it~~~~~~~~V~a~~lk~~~ek~rIsl~~k~s 1325 (1710)
T KOG1070|consen 1270 KLDVTVNMVGLCHISEEADDRG-----------------ENITALYYAGDRVKACVLKEDSEKKRISLGLKSS 1325 (1710)
T ss_pred EecCcceecccccceeecchhh-----------------hhcccceeccceeeeEeeeccchhhhhhhhhhhh
Confidence 999855 9999 888753321 3456688999999999999985 99999987
No 27
>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=99.48 E-value=1.3e-13 Score=100.04 Aligned_cols=72 Identities=31% Similarity=0.390 Sum_probs=66.4
Q ss_pred hhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEE
Q 026737 51 KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125 (234)
Q Consensus 51 ~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~L 125 (234)
..+.++++|+++.|+ ++|+||+++ ++++||+|+++++++++.++.+.|++||.++|+|+++|.+++++.|
T Consensus 7 ~~~~~~~~G~i~~g~V~~v~~~G~fv~l~-----~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~l 81 (83)
T cd04461 7 TNFSDLKPGMVVHGYVRNITPYGVFVEFL-----GGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLL 81 (83)
T ss_pred hhHHhCCCCCEEEEEEEEEeeceEEEEcC-----CCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEE
Confidence 345668999999999 999999997 3699999999999999999999999999999999999999999999
Q ss_pred EE
Q 026737 126 SI 127 (234)
Q Consensus 126 S~ 127 (234)
|+
T Consensus 82 sl 83 (83)
T cd04461 82 SL 83 (83)
T ss_pred eC
Confidence 85
No 28
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=99.47 E-value=1.5e-13 Score=97.19 Aligned_cols=69 Identities=43% Similarity=0.731 Sum_probs=64.6
Q ss_pred CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (234)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K 128 (234)
++++|+++.|+ ++|+||+++ .+++||||++++++.+..++...|++||.++|+|+++|.+++++.||+|
T Consensus 1 k~~~G~iv~g~V~~v~~~g~~V~l~-----~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k 74 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDFGVFVDLG-----NGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEES-----TSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCCEEEEEEEEEECCEEEEEEC-----CcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 47899999999 899999997 3799999999999999999999999999999999999999999999986
No 29
>PHA02945 interferon resistance protein; Provisional
Probab=99.45 E-value=4.7e-13 Score=97.03 Aligned_cols=75 Identities=31% Similarity=0.396 Sum_probs=67.5
Q ss_pred cCCCCCcEEEEE----EeeEEEEEecCCCcceeEEEEEceec--ccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737 54 SRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVSEV--SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (234)
Q Consensus 54 ~~~~~G~iv~g~----~~G~fV~l~~~~g~~g~~glv~isel--s~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~ 127 (234)
.-+++|+++.|+ +||+||.|.+++ |.+||+|+|+. +..++++ ++++ .||++.|||+++|+.++.|.||+
T Consensus 7 ~~P~~GelvigtV~~~d~ga~v~L~EY~---g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSl 81 (88)
T PHA02945 7 SLPNVGDVLKGKVYENGYALYIDLFDYP---HSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNY 81 (88)
T ss_pred cCCCCCcEEEEEEEecCceEEEEecccC---CcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEe
Confidence 346899999999 999999998643 69999999955 9999999 9999 99999999999999999999999
Q ss_pred eecccC
Q 026737 128 KQLEED 133 (234)
Q Consensus 128 K~~~~~ 133 (234)
|++.++
T Consensus 82 K~V~~~ 87 (88)
T PHA02945 82 KRMCRH 87 (88)
T ss_pred eEcccC
Confidence 998654
No 30
>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=99.45 E-value=7e-13 Score=94.18 Aligned_cols=71 Identities=34% Similarity=0.489 Sum_probs=64.1
Q ss_pred CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (234)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~ 129 (234)
++.|+++.|+ ++|+||++.+. ++.+||+|+++++++++.++.+.|++||.++|+|+++|.+++++.||+|+
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~---~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~ 76 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEY---GNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCC---CCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 3679999998 99999999621 14899999999999999999999999999999999999989999999975
No 31
>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=99.45 E-value=3.6e-13 Score=94.36 Aligned_cols=65 Identities=29% Similarity=0.396 Sum_probs=60.5
Q ss_pred CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (234)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K 128 (234)
|+++.|+ ++|+||++. ++++||+|+++++++++.++.+.|++||.++++|+++|++++++.||+|
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~-----~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k 70 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFY-----NNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEEC-----CCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 6788888 999999997 3699999999999999999999999999999999999999999999986
No 32
>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=99.44 E-value=5.3e-13 Score=94.72 Aligned_cols=67 Identities=33% Similarity=0.541 Sum_probs=60.0
Q ss_pred CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (234)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~ 127 (234)
++.|++++|+ +||+||++.+ .+.+||+|+++++|.++.++.+.|++||+++|+|+++|.++ ++.||+
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~~----~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~ 72 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPG----CRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL 72 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEECC----CCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence 3579999998 9999999962 23699999999999999999999999999999999999865 999986
No 33
>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=99.44 E-value=5.5e-13 Score=94.22 Aligned_cols=68 Identities=26% Similarity=0.418 Sum_probs=63.0
Q ss_pred CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (234)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K 128 (234)
+++|+++.|+ ++|+||+|+ ++++|++|++++++++..++.+.|++||.++++|+++|.+++++.||+|
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~-----~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~ 73 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLG-----NKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeC-----CCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 4689999998 999999997 4799999999999998888889999999999999999999999999985
No 34
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.42 E-value=8.3e-13 Score=132.89 Aligned_cols=210 Identities=20% Similarity=0.249 Sum_probs=151.5
Q ss_pred CCCCCCCCCCcchhhhhcccCCCCEEEEEEEEEeCCCCEEEEEechhhHh------hhhcCCCCCcEEEEE-----EeeE
Q 026737 1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWN------KYSSRVNVEDIFVGR-----DYGA 69 (234)
Q Consensus 1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~~~~------~~~~~~~~G~iv~g~-----~~G~ 69 (234)
+++.|+..||........ .+|..+.++|+.++.+.+++.|+++.+..+ .-.++..+|+++.|+ ++||
T Consensus 538 lp~~hlsd~~~~~p~~~f--~v~~~~k~RVl~~~~~~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~~G~l~~~~~~g~ 615 (1710)
T KOG1070|consen 538 LPKEHLSDHPLQPPLRDF--KVGSGVKLRVLSVNRDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLCAIKENGA 615 (1710)
T ss_pred cChHhhhhccccccccee--eeccccEEEEEEEEccCCeeEEEechhhhcccCCCccchhhcCCCceEEEEEeeeccCCe
Confidence 467788888877664332 388888889999999999999999987532 234567899999999 9999
Q ss_pred EEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchh----hhhccccc
Q 026737 70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLE----TLEKVIPQ 145 (234)
Q Consensus 70 fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~----~~~~~~~~ 145 (234)
||.+.+ |++||.|.++++++++.++++.|.+||++.++|+++|++++||.||+|+... |.. ..+. +..
T Consensus 616 ~V~F~g-----~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~~--~~a~~~~~~e~-~~~ 687 (1710)
T KOG1070|consen 616 FVTFTG-----GLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASSC--ARACVKRSVEN-FVK 687 (1710)
T ss_pred EEEecC-----ccccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhhhhhh--HHHHHHHHHHH-hhc
Confidence 999983 7999999999999999999999999999999999999999999999997653 321 1222 222
Q ss_pred c-cc----------ceeeeecC-CceEEE-EccccccccccccccccccccCCCCCccee-eeeeCCCEEEEEEeeecc-
Q 026737 146 G-LE----------PYLKSFYK-KMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFT-LLARAGRQVQEIQLSHSL- 210 (234)
Q Consensus 146 G-~~----------G~fV~l~~-gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~G~~v~~~vl~~d~- 210 (234)
| +. -+.|++.+ |+.|++ +.++....-+.+....-.+. .+.+ ..+-+|+.+.++|++++.
T Consensus 688 g~v~s~~~~~~tkd~viVei~~~~~~~v~~~~~L~dg~v~~~~~~~~kl~------~~t~~~~lv~gq~~~~~i~~isl~ 761 (1710)
T KOG1070|consen 688 GGVKSLKSIDKTKDSVIVEIVDQGITGVGVFGELVDGSVVVNKVLENKLR------KNTSLLHLVVGQVTVGVILSISLK 761 (1710)
T ss_pred cccccceeehhccccEEEEccCcceEEEEEEEEEccCceEEccchhhhhh------hcchhheeeecceeEEEEEEeehh
Confidence 3 21 45777765 588877 66654333333322211111 1111 135899999999999996
Q ss_pred ---chhhhcccccchhHHH
Q 026737 211 ---IRKASKRHCNEYWNVF 226 (234)
Q Consensus 211 ---i~ls~K~~~~~p~~~~ 226 (234)
+.+++++-+++-...+
T Consensus 762 k~lv~~s~~~~L~~~~~~l 780 (1710)
T KOG1070|consen 762 KSLVLISLCTDLPNNATKL 780 (1710)
T ss_pred hhhhhccccccccchHHHH
Confidence 6666666665443333
No 35
>PRK07252 hypothetical protein; Provisional
Probab=99.42 E-value=8.5e-13 Score=102.68 Aligned_cols=75 Identities=36% Similarity=0.657 Sum_probs=68.8
Q ss_pred CCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 026737 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131 (234)
Q Consensus 57 ~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~ 131 (234)
++|+++.|+ ++|+||+|+ ++++||+|++++++.++.++.+.|++||.|+|+|+++|.+++++.||+|++.
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~-----~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~ 76 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALE-----NGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLE 76 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEEC-----CCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence 579999998 999999997 3699999999999999999999999999999999999999999999999998
Q ss_pred cCc-ch
Q 026737 132 EDP-LL 136 (234)
Q Consensus 132 ~~p-~~ 136 (234)
+++ |.
T Consensus 77 ~~~~~~ 82 (120)
T PRK07252 77 EEKQHF 82 (120)
T ss_pred cCcccc
Confidence 754 53
No 36
>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=99.41 E-value=8.9e-13 Score=92.29 Aligned_cols=64 Identities=22% Similarity=0.437 Sum_probs=59.5
Q ss_pred CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (234)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~ 127 (234)
|++++|+ ++|+||+++ ++++||+|++++++.+..++.+.|++||.++++|+++|++++++.||+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~-----~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls~ 69 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLS-----DHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEec-----CCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 6788888 999999997 379999999999999999999999999999999999999999999985
No 37
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.41 E-value=7e-13 Score=93.73 Aligned_cols=57 Identities=26% Similarity=0.402 Sum_probs=53.7
Q ss_pred EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (234)
Q Consensus 66 ~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~ 127 (234)
+||+||++. ++++||+|+|++++.+..++.+.|++||.++++|+++|+.++++.||+
T Consensus 15 ~~G~~V~l~-----~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 15 DLGAVFELK-----DGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CceEEEEeC-----CCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 799999997 379999999999999999999999999999999999999999999985
No 38
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.40 E-value=4.9e-13 Score=119.29 Aligned_cols=86 Identities=21% Similarity=0.227 Sum_probs=74.7
Q ss_pred hC-CCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeec--CCceEEE-Eccccccccccccccc
Q 026737 103 LN-EGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY--KKMDDVR-ITRQGFEKRVVSQDLQ 178 (234)
Q Consensus 103 ~~-vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~--~gi~Gl~-~s~~~~~~~~~~~~~~ 178 (234)
|. +|+.|.++|.++.. + |+||+|. +|++||+ +|+++|.
T Consensus 14 ~P~~GdvV~g~V~~I~d-----------------------~------GafV~L~EY~gvEGlIhiSElS~~--------- 55 (319)
T PTZ00248 14 FPEEDDLVMVKVVRITE-----------------------M------GAYVSLLEYDDIEGMILMSELSKR--------- 55 (319)
T ss_pred CCCCCCEEEEEEEEEeC-----------------------C------eEEEEecCCCCcEEEEEHHHhccc---------
Confidence 44 89999999999864 5 9999996 6999999 8998542
Q ss_pred cccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccchhHHHHhhcccCC
Q 026737 179 LWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEYWNVFHETAIVNN 234 (234)
Q Consensus 179 ~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p~~~~~~~~~~~~ 234 (234)
.. .+++.++++||+|.|+||++|+ |+||+|++.++||+.+.++|+.|+
T Consensus 56 ---ri-----~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~~pw~~~~e~~~~g~ 107 (319)
T PTZ00248 56 ---RI-----RSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVSPEDIEACEEKFSKSK 107 (319)
T ss_pred ---cc-----CCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeecccchHHHHHHhCcCCC
Confidence 21 4577799999999999999986 999999999999999999999874
No 39
>PRK08059 general stress protein 13; Validated
Probab=99.39 E-value=2e-12 Score=100.97 Aligned_cols=76 Identities=46% Similarity=0.813 Sum_probs=71.4
Q ss_pred cCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737 54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (234)
Q Consensus 54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K 128 (234)
+++++|+++.|+ ++|+||++. ++++|++|+++++++++.++.+.|++||.|+|+|+++|.+++++.||+|
T Consensus 3 ~~~k~G~iv~G~V~~i~~~G~fV~i~-----~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk 77 (123)
T PRK08059 3 SQYEVGSVVTGKVTGIQPYGAFVALD-----EETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77 (123)
T ss_pred ccCCCCCEEEEEEEEEecceEEEEEC-----CCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEE
Confidence 468999999999 999999997 3699999999999999999999999999999999999999999999999
Q ss_pred ecccCc
Q 026737 129 QLEEDP 134 (234)
Q Consensus 129 ~~~~~p 134 (234)
++..+|
T Consensus 78 ~~~~~~ 83 (123)
T PRK08059 78 ATEEAP 83 (123)
T ss_pred EcccCc
Confidence 998888
No 40
>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=99.39 E-value=2.3e-12 Score=90.64 Aligned_cols=68 Identities=34% Similarity=0.562 Sum_probs=62.5
Q ss_pred CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 026737 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131 (234)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~ 131 (234)
|+++.|+ ++|+||++. ++++|++|+++++++++.++.+.|++||.++|+|+++|++++++.||+|+++
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~-----~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~~ 73 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLG-----DGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAKE 73 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeC-----CCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEcC
Confidence 6778887 999999997 3699999999999999999999999999999999999998899999999763
No 41
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.39 E-value=2.5e-12 Score=91.78 Aligned_cols=68 Identities=16% Similarity=0.149 Sum_probs=60.7
Q ss_pred CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (234)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~ 129 (234)
++++|+++.|+ ++|+||+++ . .+++||+|.++++|. +.+++||.+.|+|+++|++++++.||+|+
T Consensus 1 dl~~G~~v~g~V~si~d~G~~v~~g-~---~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~ 70 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHGYILDIG-I---PGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADP 70 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeC-C---CCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEee
Confidence 37899999999 999999995 1 169999999999986 66899999999999999999999999998
Q ss_pred ccc
Q 026737 130 LEE 132 (234)
Q Consensus 130 ~~~ 132 (234)
+.+
T Consensus 71 ~~~ 73 (74)
T cd05694 71 SKV 73 (74)
T ss_pred ccc
Confidence 764
No 42
>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=99.36 E-value=1.8e-12 Score=90.46 Aligned_cols=63 Identities=29% Similarity=0.470 Sum_probs=58.4
Q ss_pred CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (234)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS 126 (234)
|+++.|+ ++|+||++. ++++||+|++++++++..++.+.|++||.++|+|+++|++++++.||
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~-----~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls 68 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLG-----RGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeC-----CCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 6778887 999999997 36999999999999999999999999999999999999999999886
No 43
>PRK05807 hypothetical protein; Provisional
Probab=99.36 E-value=2.9e-12 Score=101.77 Aligned_cols=70 Identities=46% Similarity=0.722 Sum_probs=65.6
Q ss_pred CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (234)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~ 129 (234)
.+++|++++|+ ++|+||+|+ +..||||++++++.++.++.+.|++||.|+|+|+++|. +++|.||+|+
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L~------~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~ 74 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEVE------GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQ 74 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEEC------CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEe
Confidence 36889999999 999999995 58999999999999999999999999999999999998 7999999999
Q ss_pred cc
Q 026737 130 LE 131 (234)
Q Consensus 130 ~~ 131 (234)
+.
T Consensus 75 ~~ 76 (136)
T PRK05807 75 AM 76 (136)
T ss_pred cc
Confidence 86
No 44
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.36 E-value=1e-12 Score=112.80 Aligned_cols=76 Identities=36% Similarity=0.639 Sum_probs=71.7
Q ss_pred CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeec
Q 026737 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (234)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~ 130 (234)
+.+|++|-|+ +||+||.|..++ |++||+|+||++..+++++++++++||.+-|+|+++|+.++.|.||+|.+
T Consensus 9 PeeGEiVv~tV~~V~~~GAyv~L~EY~---g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV 85 (269)
T COG1093 9 PEEGEIVVGTVKQVADYGAYVELDEYP---GKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRV 85 (269)
T ss_pred CCCCcEEEEEEEEeeccccEEEeeccC---CeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhC
Confidence 6899999999 999999998654 69999999999999999999999999999999999999999999999999
Q ss_pred ccCc
Q 026737 131 EEDP 134 (234)
Q Consensus 131 ~~~p 134 (234)
.++.
T Consensus 86 ~~~q 89 (269)
T COG1093 86 TEHQ 89 (269)
T ss_pred CHHH
Confidence 8765
No 45
>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=99.36 E-value=5.2e-12 Score=89.60 Aligned_cols=70 Identities=41% Similarity=0.643 Sum_probs=63.8
Q ss_pred CCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeec
Q 026737 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (234)
Q Consensus 57 ~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~ 130 (234)
++|+++.|+ ++|+||++.+ .+.+|++|++++++.+..++.+.|++||.++|+|+++|.+++++.||+|+.
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~~----~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~ 75 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDG----TNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECC----CCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence 368999998 9999999972 258999999999999988999999999999999999999999999999975
No 46
>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=99.35 E-value=2.9e-12 Score=89.29 Aligned_cols=63 Identities=37% Similarity=0.748 Sum_probs=56.7
Q ss_pred CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccc-ccccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (234)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~-~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS 126 (234)
|+++.|+ +||+||+++ ++++||+|+++++| .+..++.+.|++||.|+|+|+++|.+++++.||
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~-----~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLD-----GGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeC-----CCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence 6777887 999999997 37999999999997 467889999999999999999999999999875
No 47
>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=99.34 E-value=6.9e-12 Score=90.09 Aligned_cols=71 Identities=35% Similarity=0.663 Sum_probs=61.8
Q ss_pred CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc-cchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeeccc
Q 026737 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE 132 (234)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~-~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~ 132 (234)
|+++.|+ +||+||+|++. .++.+||+|+++++|.++ .++.+.|++||.|+|+|+++| ++++.||+|++.+
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~--~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~~~ 76 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGL--KGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDVDQ 76 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCC--CCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEeccc
Confidence 5677777 99999999721 014899999999999986 899999999999999999999 8999999999876
Q ss_pred C
Q 026737 133 D 133 (234)
Q Consensus 133 ~ 133 (234)
+
T Consensus 77 ~ 77 (79)
T cd05684 77 D 77 (79)
T ss_pred C
Confidence 5
No 48
>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=99.31 E-value=8.6e-12 Score=87.37 Aligned_cols=65 Identities=32% Similarity=0.532 Sum_probs=60.2
Q ss_pred CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (234)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K 128 (234)
|+++.|+ ++|+||+++ .+.+|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||+|
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~-----~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIG-----YKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeC-----CCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 6788888 889999997 3699999999999999999999999999999999999988899999986
No 49
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.31 E-value=1.7e-12 Score=99.75 Aligned_cols=77 Identities=13% Similarity=0.082 Sum_probs=66.3
Q ss_pred hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
+++|+.++++|..+-+ + ||||+|++|-.||+ |||.+. .++
T Consensus 3 ~kvG~~l~GkItgI~~-----------------------y------GAFV~l~~g~tGLVHISEIa~----------~fV 43 (129)
T COG1098 3 MKVGSKLKGKITGITP-----------------------Y------GAFVELEGGKTGLVHISEIAD----------GFV 43 (129)
T ss_pred ccccceEEEEEEeeEe-----------------------c------ceEEEecCCCcceEEehHhhh----------hhH
Confidence 6789999999998864 6 99999999999999 999852 233
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcccccchhHH
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRHCNEYWNV 225 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~~~~p~~~ 225 (234)
.++.+.+++||+|+|+||.+|. |+||||.+.+.|-..
T Consensus 44 -------kdI~d~L~vG~eV~vKVl~ide~GKisLSIr~~~e~pe~~ 83 (129)
T COG1098 44 -------KDIHDHLKVGQEVKVKVLDIDENGKISLSIRKLEEEPEKQ 83 (129)
T ss_pred -------HhHHHHhcCCCEEEEEEEeeccCCCcceehHHhhhCcccc
Confidence 3567799999999999999997 999999999888644
No 50
>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=99.30 E-value=1.3e-11 Score=85.17 Aligned_cols=64 Identities=44% Similarity=0.830 Sum_probs=58.9
Q ss_pred CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (234)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K 128 (234)
|+++.|+ ++|+||+++ ++.+||+|.++++++++.++.+.|++||.++++|+++|. ++++.||+|
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~-----~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~-~~~i~ls~k 69 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELG-----GGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEEC-----CCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence 6777777 999999997 369999999999999999999999999999999999998 899999986
No 51
>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=99.29 E-value=1.2e-11 Score=87.06 Aligned_cols=66 Identities=39% Similarity=0.674 Sum_probs=58.4
Q ss_pred CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccc-cccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (234)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~-~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS 126 (234)
+++|+++.|+ +||+||++. ++.+||+|+++++|. +..++.+.|++||.++|+|+++|.+++++.|+
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~-----~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELE-----EGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcC-----CCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence 5789999998 999999997 369999999999976 45577788999999999999999999998874
No 52
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.24 E-value=2e-11 Score=92.00 Aligned_cols=71 Identities=30% Similarity=0.466 Sum_probs=62.5
Q ss_pred CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc-------------------cchhhhhCCCCEEEE
Q 026737 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------------------QDIRDILNEGDEVRV 111 (234)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~-------------------~~~~~~~~vGd~v~v 111 (234)
+++|+++.|+ ++|+||.|+ .+++|++|+++++|.+. .++.+.|++||.|+|
T Consensus 1 L~~G~vV~G~V~~v~~~gl~v~L~-----~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~ 75 (100)
T cd05693 1 LSEGMLVLGQVKEITKLDLVISLP-----NGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRC 75 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEECC-----CCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEE
Confidence 5789999998 999999997 37999999999999763 347788999999999
Q ss_pred EEEEEeCC---CCeEEEEEeecc
Q 026737 112 KVIKIDRE---KSRITLSIKQLE 131 (234)
Q Consensus 112 kVl~id~~---~~ri~LS~K~~~ 131 (234)
+|+++|++ +++|.||+|...
T Consensus 76 kVi~~d~~~~~~~~i~LSlr~~~ 98 (100)
T cd05693 76 KVVSLDKSKSGKKRIELSLEPEL 98 (100)
T ss_pred EEEEccCCcCCCcEEEEEecHHH
Confidence 99999987 799999998643
No 53
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=99.22 E-value=4.3e-11 Score=82.42 Aligned_cols=63 Identities=38% Similarity=0.670 Sum_probs=57.3
Q ss_pred CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (234)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS 126 (234)
|+++.|+ ++|+||+++ ++.+||+|.+++++.++.++.+.|++||.++|+|+++|.+++++.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~-----~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIG-----VKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcC-----CCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 5677777 999999997 36999999999999998899999999999999999999989999876
No 54
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.21 E-value=7.8e-11 Score=81.94 Aligned_cols=62 Identities=27% Similarity=0.545 Sum_probs=55.9
Q ss_pred CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (234)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K 128 (234)
|++++|+ ++|+||+++ +++||+|.+++++.+..++... +||.++|+|+++|.+++++.||+|
T Consensus 1 G~iv~g~V~~v~~~G~~v~l~------g~~gfip~s~~~~~~~~~~~~~--vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDIE------GVRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHCCCcccCChHHh--CCCEEEEEEEEEeCCCCEEEEEcC
Confidence 6788887 999999995 6999999999999888877763 899999999999999999999985
No 55
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.20 E-value=6.9e-11 Score=103.47 Aligned_cols=76 Identities=37% Similarity=0.629 Sum_probs=69.4
Q ss_pred CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeec
Q 026737 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (234)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~ 130 (234)
+++|+++.|+ ++|+||+|...+ +++||+|+|+++++++.++.+.|++||.+.|+|+++|.++++|.||+|++
T Consensus 6 P~~GdiV~G~V~~I~~~G~fV~L~e~~---gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v 82 (262)
T PRK03987 6 PEEGELVVGTVKEVKDFGAFVTLDEYP---GKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRV 82 (262)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCC---CcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEec
Confidence 6899999998 999999997321 59999999999999999999999999999999999999999999999988
Q ss_pred ccCc
Q 026737 131 EEDP 134 (234)
Q Consensus 131 ~~~p 134 (234)
.++.
T Consensus 83 ~~~e 86 (262)
T PRK03987 83 NEHQ 86 (262)
T ss_pred ccch
Confidence 7654
No 56
>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=99.20 E-value=7.8e-11 Score=81.34 Aligned_cols=63 Identities=44% Similarity=0.865 Sum_probs=58.1
Q ss_pred CCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737 58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (234)
Q Consensus 58 ~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS 126 (234)
+|+++.|+ ++|+||+++ +.+|++|.+++++.++.++.+.|++||.++|+|+++|.+++++.||
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~------~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLG------GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC------CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence 48888888 999999996 5999999999999889899999999999999999999999999876
No 57
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.19 E-value=8.6e-11 Score=85.65 Aligned_cols=70 Identities=23% Similarity=0.363 Sum_probs=62.0
Q ss_pred CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccc----ccccchhhhhCCCCEEEEEEEEEeCCCCeEEE
Q 026737 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW----DLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125 (234)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~----~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~L 125 (234)
.+++|++|.|+ ++|++|+++ ++.+|++|++++++ .+..++.+.+++||.++|+|++++++ +++.|
T Consensus 3 ~p~~GdiV~g~V~~i~~~g~~v~i~-----~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~L 76 (86)
T cd05789 3 IPEVGDVVIGRVTEVGFKRWKVDIN-----SPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSL 76 (86)
T ss_pred cCCCCCEEEEEEEEECCCEEEEECC-----CCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEE
Confidence 36899999999 999999997 37999999999996 45577888899999999999999875 99999
Q ss_pred EEeec
Q 026737 126 SIKQL 130 (234)
Q Consensus 126 S~K~~ 130 (234)
|+|+.
T Consensus 77 S~~~~ 81 (86)
T cd05789 77 HTRSL 81 (86)
T ss_pred EeCcc
Confidence 99874
No 58
>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=99.18 E-value=1.1e-10 Score=80.63 Aligned_cols=63 Identities=44% Similarity=0.783 Sum_probs=57.3
Q ss_pred CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (234)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~ 127 (234)
|+++.|+ ++|+||+++ .+.+||+|+++++++++.++.+.|++||.++|+|+++|+ ++++.||+
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~-----~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~-~~~i~ls~ 68 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEIL-----PGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeC-----CCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence 5677777 999999997 369999999999999998999999999999999999998 99999985
No 59
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=99.18 E-value=1.1e-10 Score=113.60 Aligned_cols=89 Identities=24% Similarity=0.506 Sum_probs=73.0
Q ss_pred EEEeCCCCEEEEEechh--------hHhhhhc--CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecc---
Q 026737 31 IQANEEMKKLVFSEKDA--------VWNKYSS--RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS--- 92 (234)
Q Consensus 31 i~id~~~~~i~lS~k~~--------~~~~~~~--~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels--- 92 (234)
|++++ .+.+.++.... ..+.+.. .+++|++|+|+ +||+||+|. +|.+||||+|+++
T Consensus 611 Idi~d-~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~dfGaFVel~-----~G~eGLvHISeisdls 684 (719)
T TIGR02696 611 ISIED-DGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFVSLL-----PGKDGLLHISQIRKLA 684 (719)
T ss_pred EEEec-CcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECceEEEEec-----CCceEEEEhhhccccc
Confidence 67775 57777765432 1333444 58999999999 999999997 4799999999996
Q ss_pred -cccccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737 93 -WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (234)
Q Consensus 93 -~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS 126 (234)
|.++.++.+.|++||.|+|||+++|. ++||+|+
T Consensus 685 ~~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~ 718 (719)
T TIGR02696 685 GGKRVENVEDVLSVGQKIQVEIADIDD-RGKLSLV 718 (719)
T ss_pred cccCcCCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence 46899999999999999999999995 8899986
No 60
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.17 E-value=7.3e-11 Score=82.22 Aligned_cols=61 Identities=20% Similarity=0.333 Sum_probs=53.4
Q ss_pred CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (234)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS 126 (234)
|++++|+ ++|+||+|. .+++||+|.++++..+.. .+.|++||.++|+|+++|+++++|.||
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~-----~~v~g~v~~~~l~~~~~~--~~~~~~G~~i~~kVi~id~~~~~i~LS 66 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFL-----SSFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEc-----CCceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 6788888 999999996 269999999999865544 677999999999999999999999886
No 61
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.15 E-value=1.5e-10 Score=113.71 Aligned_cols=93 Identities=34% Similarity=0.615 Sum_probs=77.4
Q ss_pred EEEeCCCCEEEEEechh--------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc
Q 026737 31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ 97 (234)
Q Consensus 31 i~id~~~~~i~lS~k~~--------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~ 97 (234)
+++++ .+.+.++.... ..+.+...+++|+++.|+ +||+||+|. ++.+||+|+|+++|.++.
T Consensus 587 idi~d-~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafVei~-----~~~~GllhiSels~~~v~ 660 (693)
T PRK11824 587 IDIED-DGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEIL-----PGKDGLVHISEIADERVE 660 (693)
T ss_pred cccCC-CceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEECCeEEEEEC-----CCCEEEEEeeeccCcccc
Confidence 44443 46666665321 234455678999999999 999999997 479999999999999999
Q ss_pred chhhhhCCCCEEEEEEEEEeCCCCeEEEEEeec
Q 026737 98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (234)
Q Consensus 98 ~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~ 130 (234)
++.+.|++||.|+|+|+++|.+ +++.||+|.+
T Consensus 661 ~~~~v~kvGD~V~VkV~~iD~~-grI~LS~k~~ 692 (693)
T PRK11824 661 KVEDVLKEGDEVKVKVLEIDKR-GRIRLSRKAV 692 (693)
T ss_pred CccceeCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence 9999999999999999999986 9999999976
No 62
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=99.12 E-value=4.1e-10 Score=77.60 Aligned_cols=67 Identities=43% Similarity=0.725 Sum_probs=61.1
Q ss_pred CCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (234)
Q Consensus 57 ~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K 128 (234)
++|+++.|+ ++|+||+++ +++.|++|.+++++.+..++...|++||.++++|++++.+++++.||++
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~-----~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLG-----NGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeC-----CCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 368999998 889999997 3699999999999998888888999999999999999998899999975
No 63
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=99.11 E-value=3.6e-10 Score=83.27 Aligned_cols=69 Identities=26% Similarity=0.411 Sum_probs=59.1
Q ss_pred CCCCCcEEEEE-----Ee--eEEEEEecCCCcceeEEEEEceeccc---ccccchhhhhCCCCEEEEEEEEEeCCCCeEE
Q 026737 55 RVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSW---DLIQDIRDILNEGDEVRVKVIKIDREKSRIT 124 (234)
Q Consensus 55 ~~~~G~iv~g~-----~~--G~fV~l~~~~g~~g~~glv~isels~---~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~ 124 (234)
.+++|++|.|+ ++ ||||+|+ ++.+||||+|+++| .++.++.+.+++||.|.|+|++.....+...
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~-----~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~ 78 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIG-----LGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPR 78 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeC-----CCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCce
Confidence 57899999999 65 9999997 37999999999999 6788899999999999999999876665555
Q ss_pred EEEe
Q 026737 125 LSIK 128 (234)
Q Consensus 125 LS~K 128 (234)
||.+
T Consensus 79 lt~~ 82 (88)
T cd04453 79 LTTN 82 (88)
T ss_pred EEEE
Confidence 5554
No 64
>PRK08582 hypothetical protein; Provisional
Probab=99.09 E-value=3.4e-10 Score=90.27 Aligned_cols=77 Identities=14% Similarity=0.087 Sum_probs=64.8
Q ss_pred hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
+++|+.+.++|..+.. + |+||+|.++++||+ +|+++++. +
T Consensus 3 ~kvG~iv~G~V~~I~~-----------------------f------G~fV~L~~~~~GlVhiSels~~~----------v 43 (139)
T PRK08582 3 IEVGSKLQGKVTGITN-----------------------F------GAFVELPEGKTGLVHISEVADNY----------V 43 (139)
T ss_pred CcCCCEEEEEEEEEEC-----------------------C------eEEEEECCCCEEEEEeeccCccc----------c
Confidence 6789999999999864 4 99999999999999 88885321 1
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcccccchhHH
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRHCNEYWNV 225 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~~~~p~~~ 225 (234)
.++...+++||.|+|+|+++|. |.||+|++.++||..
T Consensus 44 -------~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk~~~~~~~~~ 83 (139)
T PRK08582 44 -------KDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRPKRQ 83 (139)
T ss_pred -------cccccccCCCCEEEEEEEEECCCCcEEEEEEecccCchhh
Confidence 1234589999999999999984 999999999999964
No 65
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=99.07 E-value=2.5e-10 Score=110.90 Aligned_cols=75 Identities=37% Similarity=0.648 Sum_probs=70.1
Q ss_pred hcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737 53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (234)
Q Consensus 53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~ 127 (234)
+.++++|++++|+ +||+||+|+ .+.+|+||+|+++..++.+|.+++++||.|+|+|+++|..+++|.|||
T Consensus 653 i~dLk~Gm~leg~Vrnv~~fgafVdIg-----v~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsm 727 (780)
T COG2183 653 ITDLKPGMILEGTVRNVVDFGAFVDIG-----VHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSM 727 (780)
T ss_pred HhhccCCCEEEEEEEEeeeccceEEec-----cccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEe
Confidence 3579999999999 999999997 478999999999999999999999999999999999999999999999
Q ss_pred eeccc
Q 026737 128 KQLEE 132 (234)
Q Consensus 128 K~~~~ 132 (234)
+....
T Consensus 728 r~~~~ 732 (780)
T COG2183 728 RLDEE 732 (780)
T ss_pred eccCC
Confidence 97654
No 66
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=99.06 E-value=9.6e-10 Score=79.05 Aligned_cols=66 Identities=30% Similarity=0.610 Sum_probs=55.7
Q ss_pred CCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc-----------chhhhhCCCCEEEEEEEEEeCCCC
Q 026737 58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREKS 121 (234)
Q Consensus 58 ~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~-----------~~~~~~~vGd~v~vkVl~id~~~~ 121 (234)
+|++++|+ ++|+||+++. ++.+|++|++++++.++. +....|++||.|+|+|.++|.+++
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~----~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~ 76 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDN----LTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRR 76 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecC----CCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccC
Confidence 37888888 9999999972 269999999999876432 345779999999999999999899
Q ss_pred eEEEEE
Q 026737 122 RITLSI 127 (234)
Q Consensus 122 ri~LS~ 127 (234)
++.|++
T Consensus 77 ~i~~~l 82 (83)
T cd04471 77 KIDFEL 82 (83)
T ss_pred EEEEEE
Confidence 999986
No 67
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.04 E-value=7e-11 Score=117.28 Aligned_cols=110 Identities=12% Similarity=0.056 Sum_probs=81.3
Q ss_pred EeeEE-EEEecCCCcceeEEEEEceecccccccch-------hhhhCCCCEEE-EEEEEEeCCCCeEEEEEeecccCcch
Q 026737 66 DYGAF-IHLRFPDGLYHLTGLVHVSEVSWDLIQDI-------RDILNEGDEVR-VKVIKIDREKSRITLSIKQLEEDPLL 136 (234)
Q Consensus 66 ~~G~f-V~l~~~~g~~g~~glv~isels~~~~~~~-------~~~~~vGd~v~-vkVl~id~~~~ri~LS~K~~~~~p~~ 136 (234)
++|+- +++. -+|-+++.--+...+... -...++|+.+. ++|.++-.
T Consensus 713 etg~~~Idi~-------ddg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy~~g~V~~I~~------------------ 767 (891)
T PLN00207 713 ETGVEAIDTQ-------DDGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIYRNCEIKSIAP------------------ 767 (891)
T ss_pred HHCCCccCcC-------CCeeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcEEECcEEEEEec------------------
Confidence 67775 7775 357776664443333222 22356888885 57877743
Q ss_pred hhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc---ch
Q 026737 137 ETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL---IR 212 (234)
Q Consensus 137 ~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ 212 (234)
+ |+||+|.+|++||+ +|+++++.. .++..++++||.|+|+|+++|. |+
T Consensus 768 -----F------GaFVeL~~g~EGLVHISeLs~~rv-----------------~~~~dv~kvGD~V~VkVi~ID~~grI~ 819 (891)
T PLN00207 768 -----Y------GAFVEIAPGREGLCHISELSSNWL-----------------AKPEDAFKVGDRIDVKLIEVNDKGQLR 819 (891)
T ss_pred -----c------EEEEEeCCCCEEEEEhhhcCCccc-----------------cCHHHhcCCCCEEEEEEEEECCCCcEE
Confidence 4 99999999999999 899854321 2344589999999999999995 99
Q ss_pred hhhcccccchhHHHHh
Q 026737 213 KASKRHCNEYWNVFHE 228 (234)
Q Consensus 213 ls~K~~~~~p~~~~~~ 228 (234)
||+|++.++||+.+.+
T Consensus 820 LSlK~l~~~Pw~~~~~ 835 (891)
T PLN00207 820 LSRRALLPEANSEKSS 835 (891)
T ss_pred EEEeccccCchhhhhh
Confidence 9999999999998866
No 68
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.03 E-value=5.8e-10 Score=106.96 Aligned_cols=94 Identities=36% Similarity=0.631 Sum_probs=80.8
Q ss_pred EEEeCCCCEEEEEechh--------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc
Q 026737 31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ 97 (234)
Q Consensus 31 i~id~~~~~i~lS~k~~--------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~ 97 (234)
++++ +.+.+.++.... ..+.....+++|++|.|+ +||+||++. +|-+|+||+|++++.++.
T Consensus 585 Idie-ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~-----~gkdgl~hiS~~~~~rv~ 658 (692)
T COG1185 585 IDIE-DDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELL-----PGKDGLVHISQLAKERVE 658 (692)
T ss_pred EEec-CCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEEEec-----CCcceeEEehhhhhhhhh
Confidence 6676 566666665432 245667889999999999 999999998 479999999999999999
Q ss_pred chhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecc
Q 026737 98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131 (234)
Q Consensus 98 ~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~ 131 (234)
...+.+++||.+.||++.+|. .+|+.||+|...
T Consensus 659 kv~dvlk~Gd~v~Vkv~~iD~-~Gri~ls~~~~~ 691 (692)
T COG1185 659 KVEDVLKEGDEVKVKVIEIDK-QGRIRLSIKAVL 691 (692)
T ss_pred cccceeecCceEEEEEeeecc-cCCccceehhcc
Confidence 999999999999999999996 899999998754
No 69
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=99.00 E-value=2.1e-09 Score=89.88 Aligned_cols=100 Identities=23% Similarity=0.318 Sum_probs=79.9
Q ss_pred CCEEEEEE---EEEeCCCCEEEEEechhhHhhhhcCCCCCcEEEEE-----EeeEEEEEecCC--C---cceeEEEEEce
Q 026737 23 GSIISVKV---IQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPD--G---LYHLTGLVHVS 89 (234)
Q Consensus 23 G~~v~~~V---i~id~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~--g---~~g~~glv~is 89 (234)
+..+.+.+ +++|.+++++.+. +|..+...+++|++|.|+ ++|+||+|...+ + .++.+|++|.+
T Consensus 30 ~~~i~as~~G~~~id~~~~~Isv~----P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s 105 (189)
T PRK09521 30 NGEVYASVVGKVFIDDINRKISVI----PFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHIS 105 (189)
T ss_pred CCEEEEEeeEEEEEcCCCCEEEEe----cCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhh
Confidence 45555544 5668888888775 355555678999999999 999999996221 0 02578999999
Q ss_pred ecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737 90 EVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (234)
Q Consensus 90 els~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~ 129 (234)
++++.+..++.+.|++||.|.|+|++++ +++.||+|+
T Consensus 106 ~i~~~~~~~~~~~~~~GD~V~akV~~i~---~~i~LS~k~ 142 (189)
T PRK09521 106 QVSDGYVESLTDAFKIGDIVRAKVISYT---DPLQLSTKG 142 (189)
T ss_pred HcChhhhhhHHhccCCCCEEEEEEEecC---CcEEEEEec
Confidence 9999988899999999999999999998 789999985
No 70
>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=98.99 E-value=2.3e-09 Score=77.51 Aligned_cols=68 Identities=22% Similarity=0.226 Sum_probs=62.6
Q ss_pred CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (234)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~ 129 (234)
+++|+++.|+ +.|++|+++ .+.+|++|.++++..+..++.+.|++||.+.|+|++++.+ +++.||++.
T Consensus 4 p~~GdiV~G~V~~v~~~~~~V~i~-----~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~ 76 (82)
T cd04454 4 PDVGDIVIGIVTEVNSRFWKVDIL-----SRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTAD 76 (82)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEeC-----CCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECC
Confidence 5899999999 889999997 3699999999999888888999999999999999999986 899999986
No 71
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=98.94 E-value=2.6e-09 Score=104.94 Aligned_cols=88 Identities=34% Similarity=0.647 Sum_probs=72.2
Q ss_pred EEEeCCCCEEEEEech-h-------hHhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc
Q 026737 31 IQANEEMKKLVFSEKD-A-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ 97 (234)
Q Consensus 31 i~id~~~~~i~lS~k~-~-------~~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~ 97 (234)
+++++ .|.+.++... . ..+.+...+++|++|.|+ +||+||++. ++.+||+|+|+++|.++.
T Consensus 584 I~i~d-dG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~-----~g~~GllHiSei~~~~v~ 657 (684)
T TIGR03591 584 IDIED-DGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEIL-----PGKDGLVHISEIANERVE 657 (684)
T ss_pred EEEec-CeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEEC-----CCcEEEEEHHHcCCCccc
Confidence 56665 4666666432 1 233455678999999999 999999997 479999999999999999
Q ss_pred chhhhhCCCCEEEEEEEEEeCCCCeEEE
Q 026737 98 DIRDILNEGDEVRVKVIKIDREKSRITL 125 (234)
Q Consensus 98 ~~~~~~~vGd~v~vkVl~id~~~~ri~L 125 (234)
++.+.|++||.|+|+|+++|. +++++|
T Consensus 658 ~~~~~~kvGD~V~VkVi~id~-~gki~L 684 (684)
T TIGR03591 658 KVEDVLKEGDEVKVKVLEIDK-QGRIKL 684 (684)
T ss_pred ChhhccCCCCEEEEEEEEECC-CCCccC
Confidence 999999999999999999997 787764
No 72
>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=98.89 E-value=5.1e-09 Score=73.44 Aligned_cols=57 Identities=21% Similarity=0.256 Sum_probs=50.9
Q ss_pred CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccc--ccchhhhhCCCCEEEEEEEEEeCCC
Q 026737 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREK 120 (234)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~--~~~~~~~~~vGd~v~vkVl~id~~~ 120 (234)
|+++.|+ ++|+||+++ ++++|++|++++++++ ..++.+.|++||.++|+|+++|.++
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~-----~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~ 64 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLA-----DNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK 64 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeC-----CCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcc
Confidence 6788887 889999997 4799999999999885 7889999999999999999999754
No 73
>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=98.88 E-value=4.9e-09 Score=70.77 Aligned_cols=56 Identities=45% Similarity=0.781 Sum_probs=51.7
Q ss_pred EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEE
Q 026737 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (234)
Q Consensus 66 ~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS 126 (234)
++|+||+++ ++.+|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||
T Consensus 10 ~~g~~v~l~-----~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 10 KFGVFVELE-----DGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred eeeEEEEec-----CCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 899999997 36999999999999988888999999999999999999988888875
No 74
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=98.87 E-value=1.4e-08 Score=72.65 Aligned_cols=61 Identities=34% Similarity=0.578 Sum_probs=53.7
Q ss_pred hcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737 53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (234)
Q Consensus 53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~ 127 (234)
..+++.|+++.|+ ++|+||++. ++.+||+|.+++. +.|++||.++++|.++ .+++++.+|+
T Consensus 11 ~~~~~~G~~~~g~V~~i~~~G~fV~l~-----~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i-~e~~~i~l~~ 76 (77)
T cd04473 11 MEDLEVGKLYKGKVNGVAKYGVFVDLN-----DHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI-PENGNIDLIP 76 (77)
T ss_pred hhhCCCCCEEEEEEEeEecceEEEEEC-----CCcEEEEEchhcc--------CcCCCCCEEEEEEEEE-CCCCcEEEEE
Confidence 3458999999999 999999997 3699999999864 4489999999999999 7899999986
No 75
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=98.85 E-value=1.3e-08 Score=76.31 Aligned_cols=65 Identities=31% Similarity=0.567 Sum_probs=56.4
Q ss_pred EeeEEEEEecCCCcceeEEEEEceecccccccch-----------hhhhCCCCEEEEEEEEEeCCC-----CeEEEEEee
Q 026737 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-----------RDILNEGDEVRVKVIKIDREK-----SRITLSIKQ 129 (234)
Q Consensus 66 ~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~-----------~~~~~vGd~v~vkVl~id~~~-----~ri~LS~K~ 129 (234)
++|+||++. +++|++|+++++++++... ...|++||.++++|.++|.+. .++.||+|+
T Consensus 12 ~~GifV~l~------~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i~ls~k~ 85 (99)
T cd04460 12 DFGAFVRIG------PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIGLTMRQ 85 (99)
T ss_pred eccEEEEEc------CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceEEEEEec
Confidence 999999996 4999999999998876533 477999999999999999764 589999999
Q ss_pred cccCcch
Q 026737 130 LEEDPLL 136 (234)
Q Consensus 130 ~~~~p~~ 136 (234)
....||+
T Consensus 86 ~~~g~~~ 92 (99)
T cd04460 86 PGLGKLE 92 (99)
T ss_pred CCCCcHH
Confidence 9888875
No 76
>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=98.84 E-value=5.9e-09 Score=73.99 Aligned_cols=67 Identities=9% Similarity=0.018 Sum_probs=53.0
Q ss_pred CCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccC
Q 026737 106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNA 184 (234)
Q Consensus 106 Gd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~ 184 (234)
|+.|.++|.++.. + |+||+|.++++|++ .|+++++.. ..
T Consensus 1 G~~V~g~V~~i~~-----------------------~------g~~V~l~~~i~G~i~~~~ls~~~~-----------~~ 40 (73)
T cd05703 1 GQEVTGFVNNVSK-----------------------E------FVWLTISPDVKGRIPLLDLSDDVS-----------VL 40 (73)
T ss_pred CCEEEEEEEEEeC-----------------------C------EEEEEeCCCcEEEEEHHHcCCccc-----------cc
Confidence 7888888888763 4 99999999999999 788753310 00
Q ss_pred CCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737 185 PPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK 216 (234)
Q Consensus 185 ~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K 216 (234)
.++...+++||.|+++|+++|+ |.||+|
T Consensus 41 ----~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 41 ----EHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred ----cCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 2355689999999999999996 999886
No 77
>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=98.84 E-value=8.6e-09 Score=73.40 Aligned_cols=69 Identities=12% Similarity=0.064 Sum_probs=54.0
Q ss_pred hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
+++||.|.++|.++.. + |+||+|.+|++|++ ++++++.. .
T Consensus 1 ~k~G~~V~g~V~~i~~-----------------------~------G~fV~l~~~v~G~v~~~~ls~~~----------~ 41 (74)
T cd05705 1 IKEGQLLRGYVSSVTK-----------------------Q------GVFFRLSSSIVGRVLFQNVTKYF----------V 41 (74)
T ss_pred CCCCCEEEEEEEEEeC-----------------------C------cEEEEeCCCCEEEEEHHHccCcc----------c
Confidence 4789999999998853 4 99999999999999 78885432 1
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeeecc----chhh
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKA 214 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls 214 (234)
. + ..++...+++||.|+++|+++|. |.||
T Consensus 42 ~--~--~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS 74 (74)
T cd05705 42 S--D--PSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred c--C--hhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 1 1 12355689999999999999985 6664
No 78
>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=98.75 E-value=1.9e-08 Score=71.09 Aligned_cols=69 Identities=14% Similarity=-0.006 Sum_probs=54.8
Q ss_pred hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
+++|+.+.++|.++.+ .+ |+|++|.+|.+|++ +|+++++ |.
T Consensus 1 l~~G~iv~G~V~~i~~----------------------~~------g~~v~l~~~~~Glvhis~~s~~----------~~ 42 (72)
T cd05704 1 LEEGAVTLGMVTKVIP----------------------HS------GLTVQLPFGKTGLVSIFHLSDS----------YT 42 (72)
T ss_pred CCCCCEEEEEEEEeeC----------------------Cc------EEEEECCCCCEEEEEHHHhcCc----------cc
Confidence 3689999999998742 03 89999999999999 8888532 21
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeeecc--chhhhc
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL--IRKASK 216 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~--i~ls~K 216 (234)
.++.+.+++||.|+|+|+++|. |+||+|
T Consensus 43 -------~~~~~~~~~Gd~v~~kV~~~~~~~i~LSl~ 72 (72)
T cd05704 43 -------ENPLEGFKPGKIVRCCILSKKDGKYQLSLR 72 (72)
T ss_pred -------CCHHHhCCCCCEEEEEEEEecCCEEEEEeC
Confidence 2345688999999999999984 888875
No 79
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=98.70 E-value=6.1e-08 Score=68.25 Aligned_cols=68 Identities=19% Similarity=0.218 Sum_probs=55.7
Q ss_pred hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
+++|+.+.++|.++++ + |+||+|..|++|++ .++++++..
T Consensus 2 ~~~G~iv~g~V~~v~~-----------------------~------g~~V~l~~~~~g~ip~~~l~~~~~---------- 42 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVED-----------------------F------GVFVDLGNGIEGFIPISELSDDRI---------- 42 (74)
T ss_dssp SSTTSEEEEEEEEEET-----------------------T------EEEEEESTSSEEEEEGGGSSSSEE----------
T ss_pred CCCCCEEEEEEEEEEC-----------------------C------EEEEEECCcEEEEEEeehhcCccc----------
Confidence 5789999999999974 3 99999999999999 788743311
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK 216 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K 216 (234)
..+...+++||.++|+|+++|. +.||+|
T Consensus 43 -------~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k 74 (74)
T PF00575_consen 43 -------DDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp -------SSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred -------cccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 1234588999999999999996 888876
No 80
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=98.69 E-value=4.2e-07 Score=78.96 Aligned_cols=158 Identities=14% Similarity=0.092 Sum_probs=105.8
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechhhHhhhhcCCCCCcEEEEE-EeeEEEEEecCCCcceeEEEEEceecccccccchh
Q 026737 22 TGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIR 100 (234)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~-~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~ 100 (234)
+|++|++. +..|. .+++.++.+.... ....+--++++.-. +-|+|++.+ ..-+-+||++++...+ .
T Consensus 46 vGdev~vF-iY~D~-~~rl~aTt~~p~~--tvg~~g~~~Vv~v~~~lGaFlD~G-----l~KDl~vp~~elp~~~----~ 112 (287)
T COG2996 46 VGDEVTVF-IYVDS-EDRLIATTREPKA--TVGEYGWLKVVEVNKDLGAFLDWG-----LPKDLLVPLDELPTLK----S 112 (287)
T ss_pred cCcEEEEE-EEECC-CCceeheeecceE--eecceeEEEEEEEcCCcceEEecC-----CCcceeeehhhccccc----c
Confidence 99999998 45565 5667777765420 11122333444444 889999996 3479999999987531 0
Q ss_pred hhhCCCCEEEEEEEEEeCCCCeEEEEEeec-----ccCcchhhhhcccccccc------ceeeeecCCceEEE-Eccccc
Q 026737 101 DILNEGDEVRVKVIKIDREKSRITLSIKQL-----EEDPLLETLEKVIPQGLE------PYLKSFYKKMDDVR-ITRQGF 168 (234)
Q Consensus 101 ~~~~vGd~v~vkVl~id~~~~ri~LS~K~~-----~~~p~~~~~~~~~~~G~~------G~fV~l~~gi~Gl~-~s~~~~ 168 (234)
--+++||.+-|.+ .+|. ++||.-+++.- .+.|....+.+....|++ |.||-++++.-|++ .||..
T Consensus 113 ~wpq~Gd~l~v~l-~~Dk-k~Ri~g~~a~~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~- 189 (287)
T COG2996 113 LWPQKGDKLLVYL-YVDK-KGRIWGTLAIEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFIHKSERF- 189 (287)
T ss_pred cCCCCCCEEEEEE-EEcc-CCcEEEEecchhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhc-
Confidence 1167999999988 8887 66998877631 223322222221222433 99999999999999 45531
Q ss_pred cccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcccc
Q 026737 169 EKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRHC 219 (234)
Q Consensus 169 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~~ 219 (234)
...+.|+++++.|+.+.. |.||++...
T Consensus 190 ------------------------~~prlG~~l~~rVi~~reDg~lnLSl~p~~ 219 (287)
T COG2996 190 ------------------------AEPRLGERLTARVIGVREDGKLNLSLRPRA 219 (287)
T ss_pred ------------------------ccccCCceEEEEEEEEccCCeeeccccccc
Confidence 134899999999999965 999888654
No 81
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=98.69 E-value=2.1e-08 Score=94.24 Aligned_cols=77 Identities=29% Similarity=0.453 Sum_probs=70.1
Q ss_pred cCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737 54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (234)
Q Consensus 54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K 128 (234)
.++..|-+|+|+ ++|+||++. ++..||+|+|+|+..++.+|.+.+.+||.|.+|.++.|+ .+.+.+|.|
T Consensus 664 ~~l~~g~vy~~tIt~~rd~G~~V~l~-----p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~-~g~~~ls~r 737 (760)
T KOG1067|consen 664 QDLEFGGVYTATITEIRDTGVMVELY-----PMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDP-RGGIMLSSR 737 (760)
T ss_pred cceEeeeEEEEEEeeecccceEEEec-----CCchhhccchhcccccccChHHHHhhcceeEEEEEeecC-ccceeehhh
Confidence 356777888888 999999998 578999999999999999999999999999999999997 888999999
Q ss_pred ecccCcch
Q 026737 129 QLEEDPLL 136 (234)
Q Consensus 129 ~~~~~p~~ 136 (234)
.+.++|-.
T Consensus 738 alLp~p~~ 745 (760)
T KOG1067|consen 738 ALLPDPAT 745 (760)
T ss_pred hhcCCccc
Confidence 99999853
No 82
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.69 E-value=2.2e-08 Score=94.28 Aligned_cols=96 Identities=19% Similarity=0.277 Sum_probs=78.0
Q ss_pred cCCCCEEEEEEEEEeCCCCEEEEEe-chh--------hHhhhhcCCC--CCcEEEEE-----EeeEEEEEecCCCcceeE
Q 026737 20 GLTGSIISVKVIQANEEMKKLVFSE-KDA--------VWNKYSSRVN--VEDIFVGR-----DYGAFIHLRFPDGLYHLT 83 (234)
Q Consensus 20 ~~vG~~v~~~Vi~id~~~~~i~lS~-k~~--------~~~~~~~~~~--~G~iv~g~-----~~G~fV~l~~~~g~~g~~ 83 (234)
..+|+.+.+.|...+ .+++.++. |+. .++.++..|+ .|+++.|+ ++|+||+++ +++
T Consensus 87 ~~vGD~ie~~I~~~~--fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~~giiVDLg------gve 158 (470)
T PRK09202 87 AEVGDYIEEEIESVD--FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLG------RAE 158 (470)
T ss_pred ccCCCeEEEEEcccc--CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCEEEEEC------CeE
Confidence 459999999988766 44444443 332 2446777787 99999999 889999996 699
Q ss_pred EEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCC--eEEEEEee
Q 026737 84 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIKQ 129 (234)
Q Consensus 84 glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~--ri~LS~K~ 129 (234)
||+|.++++ |.+.|++||.++|+|++++++++ +|.||++.
T Consensus 159 a~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~ 200 (470)
T PRK09202 159 AILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTH 200 (470)
T ss_pred EEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCc
Confidence 999999986 67889999999999999999877 99999864
No 83
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.65 E-value=1.5e-08 Score=99.06 Aligned_cols=100 Identities=15% Similarity=0.113 Sum_probs=74.3
Q ss_pred EeeEEEEEecCCCcceeEEEEEceecccccc-------cchhh--hhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcch
Q 026737 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------QDIRD--ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLL 136 (234)
Q Consensus 66 ~~G~fV~l~~~~g~~g~~glv~isels~~~~-------~~~~~--~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~ 136 (234)
.+|+-++|. -+|.|.++..+.... ..... .+++|+.++++|.++..
T Consensus 606 ~tg~~Idi~-------d~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~d------------------ 660 (719)
T TIGR02696 606 ETGAEISIE-------DDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTA------------------ 660 (719)
T ss_pred HHCCEEEEe-------cCcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEEC------------------
Confidence 889999997 468888875443322 23333 36799999999999864
Q ss_pred hhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc---ch
Q 026737 137 ETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL---IR 212 (234)
Q Consensus 137 ~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ 212 (234)
+ |+||+|.+|++||+ +|+++ ++ +|-..+ .++.+++++||+|+|+|+++|. |+
T Consensus 661 -----f------GaFVel~~G~eGLvHISeis--------dl-s~~~rv----~~~~dv~kvGd~V~VKVl~ID~~gKI~ 716 (719)
T TIGR02696 661 -----F------GAFVSLLPGKDGLLHISQIR--------KL-AGGKRV----ENVEDVLSVGQKIQVEIADIDDRGKLS 716 (719)
T ss_pred -----c------eEEEEecCCceEEEEhhhcc--------cc-ccccCc----CCHHHcCCCCCEEEEEEEEECCCCCee
Confidence 5 99999999999999 78874 11 232222 3567799999999999999995 66
Q ss_pred hh
Q 026737 213 KA 214 (234)
Q Consensus 213 ls 214 (234)
|+
T Consensus 717 L~ 718 (719)
T TIGR02696 717 LV 718 (719)
T ss_pred ec
Confidence 64
No 84
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=98.65 E-value=7.1e-08 Score=79.99 Aligned_cols=79 Identities=32% Similarity=0.574 Sum_probs=64.3
Q ss_pred hhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc-----------chhhhhCCCCEEEEEEE
Q 026737 51 KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVI 114 (234)
Q Consensus 51 ~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~-----------~~~~~~~vGd~v~vkVl 114 (234)
.+.-+...|+++.|+ ++|+||+++ ..+|++|.+++.+++.. +....++.||.|+++|+
T Consensus 74 ~i~f~p~~gEvv~G~V~~v~~~GifV~lg------~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~ 147 (179)
T TIGR00448 74 ALVFKPELGEIVEGEVIEIVEFGAFVSLG------PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIV 147 (179)
T ss_pred EEEEeccCCCEEEEEEEEEEeeEEEEEeC------CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEE
Confidence 334467789999999 999999996 49999999998866542 23467999999999999
Q ss_pred EEe-----CCCCeEEEEEeecccCcc
Q 026737 115 KID-----REKSRITLSIKQLEEDPL 135 (234)
Q Consensus 115 ~id-----~~~~ri~LS~K~~~~~p~ 135 (234)
+++ ++..+|.+|+|+..-.|+
T Consensus 148 ~v~~~~~~~~~~~I~lt~k~~~LG~~ 173 (179)
T TIGR00448 148 ALSLKDRRPEGSKIGLTMRQPLLGKL 173 (179)
T ss_pred EEEccCCCCCcceEEEEeccCcCCcc
Confidence 998 567899999998665553
No 85
>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=98.64 E-value=7.7e-08 Score=67.81 Aligned_cols=50 Identities=12% Similarity=-0.045 Sum_probs=39.5
Q ss_pred ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhh
Q 026737 149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKAS 215 (234)
Q Consensus 149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~ 215 (234)
|+||+|.+|++||+ +|+++++.. .++...+++||.++++|+++|+ |+||+
T Consensus 17 G~~V~l~~gv~G~i~~s~l~~~~~-----------------~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 17 GAVFELKDGLLGFVHISHLSDDKV-----------------PSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred eEEEEeCCCCEEEEEHHHCCcchh-----------------cCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 99999999999999 788743211 1234579999999999999996 77764
No 86
>PRK05807 hypothetical protein; Provisional
Probab=98.63 E-value=9.4e-08 Score=75.95 Aligned_cols=70 Identities=14% Similarity=0.124 Sum_probs=57.8
Q ss_pred hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
+++|+.+.++|..+.+ + |+||+| ++..||+ +|+++.+ |+
T Consensus 3 ~~vG~vv~G~Vt~i~~-----------------------~------GafV~L-~~~~Glvhiseis~~----------~v 42 (136)
T PRK05807 3 LKAGSILEGTVVNITN-----------------------F------GAFVEV-EGKTGLVHISEVADT----------YV 42 (136)
T ss_pred ccCCCEEEEEEEEEEC-----------------------C------eEEEEE-CCEEEEEEhhhcccc----------cc
Confidence 6789999999999864 4 999999 7899999 8887532 22
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcccc
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRHC 219 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~~ 219 (234)
.++...+++||.|+|+|+++|. |+||+|++.
T Consensus 43 -------~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk~~~ 76 (136)
T PRK05807 43 -------KDIREHLKEQDKVKVKVISIDDNGKISLSIKQAM 76 (136)
T ss_pred -------cCccccCCCCCEEEEEEEEECCCCcEEEEEEecc
Confidence 2344578999999999999984 999999987
No 87
>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=98.62 E-value=1.3e-07 Score=66.45 Aligned_cols=68 Identities=19% Similarity=0.135 Sum_probs=53.1
Q ss_pred hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
+++|+.+.++|.++.. + |+||+|+++++|++ +|+++++. .
T Consensus 1 ~~~G~iv~g~V~~v~~-----------------------~------gi~v~l~~~~~g~v~~s~l~~~~----------~ 41 (73)
T cd05706 1 LKVGDILPGRVTKVND-----------------------R------YVLVQLGNKVTGPSFITDALDDY----------S 41 (73)
T ss_pred CCCCCEEEEEEEEEeC-----------------------C------eEEEEeCCCcEEEEEhhhccCcc----------c
Confidence 3689999999998853 3 99999999999999 77774321 0
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK 216 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K 216 (234)
.++...+++||.++++|+++|. |.||+|
T Consensus 42 -------~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~ 73 (73)
T cd05706 42 -------EALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred -------cccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 1234578999999999999984 777754
No 88
>PRK07252 hypothetical protein; Provisional
Probab=98.62 E-value=1e-07 Score=74.21 Aligned_cols=75 Identities=9% Similarity=0.055 Sum_probs=60.1
Q ss_pred CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccccc
Q 026737 104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLS 182 (234)
Q Consensus 104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~ 182 (234)
++|+.+.++|.++.. + |+||++.++++||+ +|+++++. .
T Consensus 2 kvG~iv~G~V~~V~~-----------------------~------G~fVei~~~~~GllhiseLs~~~----------~- 41 (120)
T PRK07252 2 KIGDKLKGTITGIKP-----------------------Y------GAFVALENGTTGLIHISEIKTGF----------I- 41 (120)
T ss_pred CCCCEEEEEEEEEeC-----------------------c------EEEEEECCCCEEEEEHHHcCCcc----------c-
Confidence 479999999998864 4 99999999999999 78875321 1
Q ss_pred cCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhccccc-chhH
Q 026737 183 NAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCN-EYWN 224 (234)
Q Consensus 183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~-~p~~ 224 (234)
.++...+++||.|+|+|+++|. |.||+|++++ .+|.
T Consensus 42 ------~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~~~~~ 82 (120)
T PRK07252 42 ------DNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEEEKQHF 82 (120)
T ss_pred ------cChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecccCcccc
Confidence 1234578999999999999986 9999999977 4453
No 89
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.61 E-value=1.2e-07 Score=81.85 Aligned_cols=71 Identities=27% Similarity=0.355 Sum_probs=62.9
Q ss_pred cCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc----cchhhhhCCCCEEEEEEEEEeCCCCeEE
Q 026737 54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----QDIRDILNEGDEVRVKVIKIDREKSRIT 124 (234)
Q Consensus 54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~----~~~~~~~~vGd~v~vkVl~id~~~~ri~ 124 (234)
..+++|++|.|+ ++|+||+|+ .+.+|++|++++++.++ .++.+.|++||.|.|+|+++++ .+++.
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~-----~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~-~~~~~ 132 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDIN-----SPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDR-TRDVV 132 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeC-----CCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECC-CCcEE
Confidence 346999999999 889999997 36899999999999987 7899999999999999999996 45699
Q ss_pred EEEeec
Q 026737 125 LSIKQL 130 (234)
Q Consensus 125 LS~K~~ 130 (234)
||+|+.
T Consensus 133 LS~k~~ 138 (235)
T PRK04163 133 LTLKGK 138 (235)
T ss_pred EEEcCC
Confidence 999753
No 90
>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=98.59 E-value=1.2e-07 Score=66.14 Aligned_cols=65 Identities=18% Similarity=0.171 Sum_probs=50.4
Q ss_pred CCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccC
Q 026737 106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNA 184 (234)
Q Consensus 106 Gd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~ 184 (234)
|+.+.++|.++.+ + |+||+|.++++||+ +|+++.+. .
T Consensus 1 g~~~~g~V~~v~~-----------------------~------G~~V~l~~~~~gli~~s~l~~~~-~------------ 38 (70)
T cd05698 1 GLKTHGTIVKVKP-----------------------N------GCIVSFYNNVKGFLPKSELSEAF-I------------ 38 (70)
T ss_pred CCEEEEEEEEEec-----------------------C------cEEEEECCCCEEEEEHHHcChhh-c------------
Confidence 6778888887753 4 99999999999999 78774321 1
Q ss_pred CCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737 185 PPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK 216 (234)
Q Consensus 185 ~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K 216 (234)
.++...+++||.++++|+++|+ +.||+|
T Consensus 39 ----~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k 70 (70)
T cd05698 39 ----KDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred ----CCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 2244579999999999999986 777765
No 91
>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=98.58 E-value=3.3e-07 Score=64.25 Aligned_cols=63 Identities=13% Similarity=0.197 Sum_probs=49.4
Q ss_pred hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
|++|+.+.++|.++.+ + |+||+|.+|++||+ ++++.++..
T Consensus 1 ~~~g~~~~g~V~~i~~-----------------------~------G~fv~l~~~~~Gl~~~~~l~~~~~---------- 41 (72)
T cd05689 1 YPEGTRLFGKVTNLTD-----------------------Y------GCFVELEEGVEGLVHVSEMDWTNK---------- 41 (72)
T ss_pred CcCCCEEEEEEEEEEe-----------------------e------EEEEEcCCCCEEEEEEEeccCccc----------
Confidence 4689999999988864 4 99999999999999 787743211
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL 210 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~ 210 (234)
. .+....++.||+|+|+++++|.
T Consensus 42 -~-----~~~~~~~~~Gd~v~v~v~~id~ 64 (72)
T cd05689 42 -N-----IHPSKVVSLGDEVEVMVLDIDE 64 (72)
T ss_pred -c-----cCcccEeCCCCEEEEEEEEeeC
Confidence 0 1234579999999999999985
No 92
>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=98.56 E-value=2e-07 Score=66.70 Aligned_cols=57 Identities=16% Similarity=0.179 Sum_probs=45.4
Q ss_pred ceeeeec---CCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc--chhhhcccccc
Q 026737 149 PYLKSFY---KKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL--IRKASKRHCNE 221 (234)
Q Consensus 149 G~fV~l~---~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~--i~ls~K~~~~~ 221 (234)
|+||+|+ ++++||+ +|+++++.. . .++...++.||.|+|+++++|. +.||+|++.++
T Consensus 15 G~fv~l~~~~~~~~gll~~s~l~~~~~------------~----~~~~~~~~~Gd~v~v~v~~vd~~~i~~s~k~~~~~ 77 (79)
T cd05684 15 GCFVQLEGLKGRKEGLVHISQLSFEGR------------V----ANPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQD 77 (79)
T ss_pred eEEEEEeCCCCCcEEEEEhHhccCCCC------------c----CChhheeCCCCEEEEEEEEEeCCEEEEEEEecccC
Confidence 9999998 4799999 788754321 0 1234589999999999999986 99999998865
No 93
>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=98.56 E-value=2.2e-07 Score=64.45 Aligned_cols=50 Identities=14% Similarity=0.274 Sum_probs=38.2
Q ss_pred ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhh
Q 026737 149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKA 214 (234)
Q Consensus 149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls 214 (234)
|+||+|+++++||+ +|+++|..+ . .++...+++||+|+|+|+++|. |+||
T Consensus 15 G~fv~l~~~~~Glv~~~~l~~~~~------------~----~~~~~~~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 15 GIFVGLDGGIDGLVHISDISWTQR------------V----RHPSEIYKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred eEEEEeCCCCEEEEEHHHCCCccc------------c----CChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence 99999999999999 777742211 1 2345589999999999999985 5554
No 94
>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=98.56 E-value=2e-07 Score=66.38 Aligned_cols=66 Identities=11% Similarity=0.012 Sum_probs=54.6
Q ss_pred hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeec-CCceEEE-Eccccccccccccccccc
Q 026737 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY-KKMDDVR-ITRQGFEKRVVSQDLQLW 180 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~-~gi~Gl~-~s~~~~~~~~~~~~~~~~ 180 (234)
++.|+.+.+.|.++.. + |+||++. +|++||+ .++++ |
T Consensus 2 l~~G~~v~g~V~si~d-----------------------~------G~~v~~g~~gv~Gfl~~~~~~------------~ 40 (74)
T cd05694 2 LVEGMVLSGCVSSVED-----------------------H------GYILDIGIPGTTGFLPKKDAG------------N 40 (74)
T ss_pred CCCCCEEEEEEEEEeC-----------------------C------EEEEEeCCCCcEEEEEHHHCC------------c
Confidence 5689999999988864 4 9999996 6999999 56652 2
Q ss_pred cccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhccccc
Q 026737 181 LSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCN 220 (234)
Q Consensus 181 ~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~ 220 (234)
. ..+++||.+.|+|+++|+ +.||+|++.+
T Consensus 41 ~-----------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~~ 73 (74)
T cd05694 41 F-----------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73 (74)
T ss_pred c-----------cccCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence 1 368999999999999986 9999998864
No 95
>PRK08059 general stress protein 13; Validated
Probab=98.55 E-value=1.6e-07 Score=73.35 Aligned_cols=74 Identities=16% Similarity=0.091 Sum_probs=61.3
Q ss_pred hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
+++|+.+.++|.++.+ + |+||++.++++|++ +|+++.+. .
T Consensus 5 ~k~G~iv~G~V~~i~~-----------------------~------G~fV~i~~~~~Gli~~sel~~~~----------~ 45 (123)
T PRK08059 5 YEVGSVVTGKVTGIQP-----------------------Y------GAFVALDEETQGLVHISEITHGF----------V 45 (123)
T ss_pred CCCCCEEEEEEEEEec-----------------------c------eEEEEECCCCEEEEEHHHCCccc----------c
Confidence 6789999999999864 4 99999999999999 77774321 1
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccch
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNEY 222 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~p 222 (234)
.++...+++||.|+|+|+++|. +.||+|++..+|
T Consensus 46 -------~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~~~ 83 (123)
T PRK08059 46 -------KDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEAP 83 (123)
T ss_pred -------cCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEcccCc
Confidence 2234578999999999999975 999999999888
No 96
>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=98.54 E-value=3e-07 Score=65.03 Aligned_cols=66 Identities=8% Similarity=0.024 Sum_probs=50.5
Q ss_pred CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC-CceEEE-Ecccccccccccccccccc
Q 026737 104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK-KMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~-gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
..|+.++++|.++.+ + |+||++.+ +.+||+ +|+++++ +.
T Consensus 2 ~~g~~~~g~V~~i~~-----------------------f------G~fv~l~~~~~eGlvh~sel~~~-~~--------- 42 (73)
T cd05686 2 ALYQIFKGEVASVTE-----------------------Y------GAFVKIPGCRKQGLVHKSHMSSC-RV--------- 42 (73)
T ss_pred cCCCEEEEEEEEEEe-----------------------e------eEEEEECCCCeEEEEEchhhCCC-cc---------
Confidence 468999999988864 5 99999943 369999 8888543 11
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhh
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKAS 215 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~ 215 (234)
.++...+++||+|+|+|+++|. |+||+
T Consensus 43 -------~~~~~~~~~Gd~v~vkv~~vd~~~ki~ls~ 72 (73)
T cd05686 43 -------DDPSEVVDVGEKVWVKVIGREMKDKMKLSL 72 (73)
T ss_pred -------cCHhhEECCCCEEEEEEEEECCCCcEEEEe
Confidence 2445689999999999999986 56654
No 97
>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=98.54 E-value=2.4e-07 Score=65.42 Aligned_cols=68 Identities=19% Similarity=0.249 Sum_probs=53.6
Q ss_pred CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC--CceEEE-Eccccccccccccccccc
Q 026737 104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK--KMDDVR-ITRQGFEKRVVSQDLQLW 180 (234)
Q Consensus 104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~--gi~Gl~-~s~~~~~~~~~~~~~~~~ 180 (234)
+.|+.+.++|.++.. + |+||++.+ |++||+ +|+++++..
T Consensus 2 ~~G~~~~g~V~~v~~-----------------------~------g~~v~l~~~~~~~gll~~s~l~~~~~--------- 43 (76)
T cd04452 2 EEGELVVVTVKSIAD-----------------------M------GAYVSLLEYGNIEGMILLSELSRRRI--------- 43 (76)
T ss_pred CCCCEEEEEEEEEEc-----------------------c------EEEEEEcCCCCeEEEEEhHHcCCccc---------
Confidence 478999999988853 3 99999974 699999 788753221
Q ss_pred cccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcc
Q 026737 181 LSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKR 217 (234)
Q Consensus 181 ~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~ 217 (234)
.++...++.||.|+|+|+++|. +.||+|+
T Consensus 44 --------~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~ 76 (76)
T cd04452 44 --------RSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred --------CCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 2345689999999999999985 8888875
No 98
>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=98.53 E-value=2e-07 Score=64.92 Aligned_cols=63 Identities=13% Similarity=0.041 Sum_probs=48.7
Q ss_pred CCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccC
Q 026737 106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNA 184 (234)
Q Consensus 106 Gd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~ 184 (234)
|+.+.++|.++.. + |+||+|.+|++|++ .++++++..
T Consensus 1 G~~v~g~V~~v~~-----------------------~------Gv~V~l~~~v~g~i~~~~l~~~~~------------- 38 (69)
T cd05697 1 GQVVKGTIRKLRP-----------------------S------GIFVKLSDHIKGLVPPMHLADVRL------------- 38 (69)
T ss_pred CCEEEEEEEEEec-----------------------c------EEEEEecCCcEEEEEHHHCCCccc-------------
Confidence 6888888888753 3 99999999999999 677743311
Q ss_pred CCCCcceeeeeeCCCEEEEEEeeecc----chhh
Q 026737 185 PPSGKKFTLLARAGRQVQEIQLSHSL----IRKA 214 (234)
Q Consensus 185 ~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls 214 (234)
.++...++.||.++++|+++|+ |.||
T Consensus 39 ----~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls 68 (69)
T cd05697 39 ----KHPEKKFKPGLKVKCRVLSVEPERKRLVLT 68 (69)
T ss_pred ----cCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence 1234579999999999999985 5555
No 99
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=98.53 E-value=3.3e-07 Score=63.77 Aligned_cols=59 Identities=17% Similarity=0.281 Sum_probs=49.1
Q ss_pred CCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCC--CeEEEEE
Q 026737 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRITLSI 127 (234)
Q Consensus 57 ~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~--~ri~LS~ 127 (234)
..|++++|+ ++|+||+++ +.+|++|.++++. .+.|++||.+++.|++++.++ .+|.||.
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig------~~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lSr 67 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLG------KVEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILSR 67 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcC------CeEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence 468999998 889999996 4899999999873 356899999999999999643 4677773
No 100
>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=98.52 E-value=2.4e-07 Score=66.99 Aligned_cols=67 Identities=15% Similarity=0.009 Sum_probs=53.9
Q ss_pred hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
+++|+.+.++|.++.. + |+||+|.+|++|++ +++++++..
T Consensus 12 ~~~G~i~~g~V~~v~~-----------------------~------G~fv~l~~~~~g~v~~~el~~~~~---------- 52 (83)
T cd04461 12 LKPGMVVHGYVRNITP-----------------------Y------GVFVEFLGGLTGLAPKSYISDEFV---------- 52 (83)
T ss_pred CCCCCEEEEEEEEEee-----------------------c------eEEEEcCCCCEEEEEHHHCCcccc----------
Confidence 7899999999998864 4 99999999999999 677743211
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhh
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKAS 215 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~ 215 (234)
.++...+++||.++|+|+++|. |.||+
T Consensus 53 -------~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl 83 (83)
T cd04461 53 -------TDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred -------cCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence 2345689999999999999985 66664
No 101
>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=98.49 E-value=3.3e-07 Score=64.08 Aligned_cols=54 Identities=9% Similarity=0.000 Sum_probs=42.9
Q ss_pred ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccc
Q 026737 149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHC 219 (234)
Q Consensus 149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~ 219 (234)
|+||++.++++|++ +|+++.+. . .++...+++||.++++|+++|. +.||+|+++
T Consensus 15 g~~v~l~~~~~g~i~~~~~~~~~----------~-------~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~~ 73 (73)
T cd05691 15 GATVKLGDGVEGFLRAAELSRDR----------V-------EDATERFKVGDEVEAKITNVDRKNRKISLSIKAKE 73 (73)
T ss_pred eEEEEeCCCCEEEEEHHHCCCcc----------c-------cCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEcC
Confidence 99999999999999 67764221 1 2345678999999999999985 899988753
No 102
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.48 E-value=3.1e-07 Score=76.51 Aligned_cols=79 Identities=24% Similarity=0.563 Sum_probs=63.1
Q ss_pred HhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc-----------chhhhhCCCCEEEEE
Q 026737 49 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVK 112 (234)
Q Consensus 49 ~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~-----------~~~~~~~vGd~v~vk 112 (234)
+..+...+..|+++.|+ ++|+||+++ .++|++|.+++.+++.. +....+++||.|+++
T Consensus 72 f~~lvf~P~~GEVv~g~V~~v~~~Gi~V~lg------~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~Vrvr 145 (187)
T PRK08563 72 FDALVFKPELQEVVEGEVVEVVEFGAFVRIG------PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRAR 145 (187)
T ss_pred EEEEEEeccCCCEEEEEEEEEEccEEEEEEe------CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEE
Confidence 33445568899999999 999999997 49999999999876532 345678999999999
Q ss_pred EEEEeCCC-----CeEEEEEeecccC
Q 026737 113 VIKIDREK-----SRITLSIKQLEED 133 (234)
Q Consensus 113 Vl~id~~~-----~ri~LS~K~~~~~ 133 (234)
|++++.+. .+|.+|+|+..--
T Consensus 146 V~~v~~~~~~~~~~~I~ls~~~~~LG 171 (187)
T PRK08563 146 IVAVSLKERRPRGSKIGLTMRQPGLG 171 (187)
T ss_pred EEEEEcccCCCCCCEEEEEecCCCCC
Confidence 99999754 3899999975443
No 103
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=98.44 E-value=6.8e-07 Score=88.50 Aligned_cols=69 Identities=28% Similarity=0.549 Sum_probs=58.7
Q ss_pred CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc-----------cchhhhhCCCCEEEEEEEEEeC
Q 026737 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDR 118 (234)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~-----------~~~~~~~~vGd~v~vkVl~id~ 118 (234)
..++|++++|+ +||+||+|.+ ++++|+||+++++++++ .+....|++||.|+|+|.++|.
T Consensus 624 ~~~iG~~~~g~V~~v~~fGifV~L~~----~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~ 699 (709)
T TIGR02063 624 SEKIGEEFEGVISGVTSFGLFVELEN----NTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADL 699 (709)
T ss_pred hccCCcEEEEEEEEEEeCCEEEEecC----CceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEec
Confidence 45789999998 9999999972 26999999999987653 2334679999999999999999
Q ss_pred CCCeEEEEE
Q 026737 119 EKSRITLSI 127 (234)
Q Consensus 119 ~~~ri~LS~ 127 (234)
.+++|.|++
T Consensus 700 ~~~~I~~~l 708 (709)
T TIGR02063 700 DTGKIDFEL 708 (709)
T ss_pred ccCeEEEEE
Confidence 999999986
No 104
>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=98.43 E-value=7e-07 Score=62.99 Aligned_cols=69 Identities=13% Similarity=0.121 Sum_probs=54.3
Q ss_pred CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC-CceEEE-Ecccccccccccccccccc
Q 026737 104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK-KMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~-gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
++|+.+.++|.++.+ . |+||++.+ +++|++ +++++++..
T Consensus 1 ~~g~~v~g~V~~i~~-----------------------~------g~~v~l~~~~~~g~i~~~~l~~~~~---------- 41 (77)
T cd05708 1 KVGQKIDGTVRRVED-----------------------Y------GVFIDIDGTNVSGLCHKSEISDNRV---------- 41 (77)
T ss_pred CCCCEEEEEEEEEEc-----------------------c------eEEEEECCCCeEEEEEHHHCCCCcc----------
Confidence 368899999988864 3 99999985 899999 677743211
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhccc
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRH 218 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~ 218 (234)
.++...+++||.|+|+|+++|. +.|++|+.
T Consensus 42 -------~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~ 75 (77)
T cd05708 42 -------ADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred -------CCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence 2245689999999999999985 88998875
No 105
>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=98.40 E-value=8.1e-07 Score=61.65 Aligned_cols=45 Identities=13% Similarity=0.139 Sum_probs=36.3
Q ss_pred ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737 149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 210 (234)
Q Consensus 149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~ 210 (234)
|+||+|.++++||+ +|+++++ |. .++...+++||.++|+|+++|+
T Consensus 15 Gv~V~l~~~~~G~v~~s~l~~~----------~~-------~~~~~~~~~Gd~v~~~v~~~d~ 60 (68)
T cd05707 15 GVFVTLGRGVDARVRVSELSDS----------YL-------KDWKKRFKVGQLVKGKIVSIDP 60 (68)
T ss_pred cEEEEeCCCCEEEEEHHHCCch----------hh-------cCHhhccCCCCEEEEEEEEEeC
Confidence 99999999999999 7777422 11 2345688999999999999996
No 106
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.40 E-value=3.7e-07 Score=88.00 Aligned_cols=110 Identities=18% Similarity=0.184 Sum_probs=84.8
Q ss_pred CCCcEEEEE--EeeEEEEEecCCCcceeEEEEEceeccc-------ccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737 57 NVEDIFVGR--DYGAFIHLRFPDGLYHLTGLVHVSEVSW-------DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (234)
Q Consensus 57 ~~G~iv~g~--~~G~fV~l~~~~g~~g~~glv~isels~-------~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~ 127 (234)
+-|+++.+. .+|+-++|+ -+|.|.++--+. .++......+.+|+.+.++|.++..
T Consensus 569 ~gGk~I~~I~eetg~~Idie-------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~--------- 632 (692)
T COG1185 569 PGGKTIKAITEETGVKIDIE-------DDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVD--------- 632 (692)
T ss_pred CcccchhhhhhhhCcEEEec-------CCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEee---------
Confidence 445666666 999999997 456666653332 2345556668999999999988753
Q ss_pred eecccCcchhhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEe
Q 026737 128 KQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQL 206 (234)
Q Consensus 128 K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl 206 (234)
+ |+||+|.+|-+||| +|++++. |+ .+.+++++.||.+.|+++
T Consensus 633 --------------f------GaFv~l~~gkdgl~hiS~~~~~-rv----------------~kv~dvlk~Gd~v~Vkv~ 675 (692)
T COG1185 633 --------------F------GAFVELLPGKDGLVHISQLAKE-RV----------------EKVEDVLKEGDEVKVKVI 675 (692)
T ss_pred --------------c------ceEEEecCCcceeEEehhhhhh-hh----------------hcccceeecCceEEEEEe
Confidence 5 99999999999999 8998533 21 345569999999999999
Q ss_pred eecc---chhhhcccc
Q 026737 207 SHSL---IRKASKRHC 219 (234)
Q Consensus 207 ~~d~---i~ls~K~~~ 219 (234)
++|+ ++|++|...
T Consensus 676 ~iD~~Gri~ls~~~~~ 691 (692)
T COG1185 676 EIDKQGRIRLSIKAVL 691 (692)
T ss_pred eecccCCccceehhcc
Confidence 9998 999999764
No 107
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=98.39 E-value=1.2e-06 Score=63.18 Aligned_cols=69 Identities=25% Similarity=0.340 Sum_probs=62.7
Q ss_pred cCCCCCcEEEEE----EeeEEEEEecCCCcceeEEEEE-ceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737 54 SRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVH-VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (234)
Q Consensus 54 ~~~~~G~iv~g~----~~G~fV~l~~~~g~~g~~glv~-isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~ 127 (234)
.-+++|+++.|. +.|+||.|-+ ++.+|++. .+|++.+++....+.+ +|....|+|+.+|+++|.|.||.
T Consensus 12 ~~P~v~dvv~~Vv~i~d~~~YV~Lle----Y~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 12 VFPNINEVTKGIVFVKDNIFYVKLID----YGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred ecCCCCeEEEEEEEEeccEEEEEEec----CccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence 447899999987 9999999984 56899988 9999999999999999 99999999999999999999984
No 108
>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=98.35 E-value=8.9e-07 Score=64.31 Aligned_cols=74 Identities=11% Similarity=0.033 Sum_probs=56.5
Q ss_pred hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
+++||.|.++|+++.. . |+||++.++++|++ +|++++++.. .+
T Consensus 4 p~~GdiV~g~V~~i~~-----------------------~------g~~v~i~~~~~G~l~~se~~~~~~~------~~- 47 (86)
T cd05789 4 PEVGDVVIGRVTEVGF-----------------------K------RWKVDINSPYDAVLPLSEVNLPRTD------ED- 47 (86)
T ss_pred CCCCCEEEEEEEEECC-----------------------C------EEEEECCCCeEEEEEHHHccCCCCc------cc-
Confidence 4689999999999864 3 88999999999999 7777432100 01
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhccc
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRH 218 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~ 218 (234)
..++...+++||.++++|++++. +.||+|+.
T Consensus 48 ------~~~~~~~l~vGd~i~~~V~~~~~~~~i~LS~~~~ 81 (86)
T cd05789 48 ------ELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRSL 81 (86)
T ss_pred ------hHHHHhhCCCCCEEEEEEEEECCCCCEEEEeCcc
Confidence 12345578999999999999984 89998874
No 109
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.34 E-value=2.6e-07 Score=91.08 Aligned_cols=101 Identities=20% Similarity=0.204 Sum_probs=75.7
Q ss_pred EeeEEEEEecCCCcceeEEEEEceecccccc-------cchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhh
Q 026737 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLET 138 (234)
Q Consensus 66 ~~G~fV~l~~~~g~~g~~glv~isels~~~~-------~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~ 138 (234)
.+|+-+++. -+|.+++.-.....+ ......+++|+.+.++|.++..
T Consensus 582 ~~~~~idi~-------d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~-------------------- 634 (693)
T PRK11824 582 ETGAKIDIE-------DDGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVD-------------------- 634 (693)
T ss_pred HHCCccccC-------CCceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEEC--------------------
Confidence 778877765 467777764443322 2223347899999999998864
Q ss_pred hhccccccccceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc---chhh
Q 026737 139 LEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKA 214 (234)
Q Consensus 139 ~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls 214 (234)
+ |+||+|.+|++||+ +|+++++. + .++...+++||.|+|+|+++|. |+||
T Consensus 635 ---f------GafVei~~~~~GllhiSels~~~----------v-------~~~~~v~kvGD~V~VkV~~iD~~grI~LS 688 (693)
T PRK11824 635 ---F------GAFVEILPGKDGLVHISEIADER----------V-------EKVEDVLKEGDEVKVKVLEIDKRGRIRLS 688 (693)
T ss_pred ---C------eEEEEECCCCEEEEEeeeccCcc----------c-------cCccceeCCCCEEEEEEEEECCCCcEEEE
Confidence 4 99999999999999 89885332 1 2345689999999999999984 9999
Q ss_pred hcccc
Q 026737 215 SKRHC 219 (234)
Q Consensus 215 ~K~~~ 219 (234)
+|++.
T Consensus 689 ~k~~~ 693 (693)
T PRK11824 689 RKAVL 693 (693)
T ss_pred EEecC
Confidence 99763
No 110
>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=98.33 E-value=6.7e-07 Score=67.37 Aligned_cols=80 Identities=19% Similarity=0.084 Sum_probs=58.8
Q ss_pred hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
+++|+.|.++|.++.. . |+||+|.+|++|++ +++++++.. .|.
T Consensus 1 L~~G~vV~G~V~~v~~-----------------------~------gl~v~L~~g~~G~v~~seis~~~~-------~~~ 44 (100)
T cd05693 1 LSEGMLVLGQVKEITK-----------------------L------DLVISLPNGLTGYVPITNISDAYT-------ERL 44 (100)
T ss_pred CCCCCEEEEEEEEEcC-----------------------C------CEEEECCCCcEEEEEHHHhhHHHH-------HHH
Confidence 4689999999998853 3 89999999999999 888864321 121
Q ss_pred cc---------CCCCCcceeeeeeCCCEEEEEEeeecc-------chhhhccc
Q 026737 182 SN---------APPSGKKFTLLARAGRQVQEIQLSHSL-------IRKASKRH 218 (234)
Q Consensus 182 ~~---------~~~~~~~~~~~~~~G~~v~~~vl~~d~-------i~ls~K~~ 218 (234)
.. .+....++...+++||.|+|+|+++|. |.||+|..
T Consensus 45 ~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~d~~~~~~~~i~LSlr~~ 97 (100)
T cd05693 45 EELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLDKSKSGKKRIELSLEPE 97 (100)
T ss_pred HHhhhhccccccccccCCHHHhccCCCEEEEEEEEccCCcCCCcEEEEEecHH
Confidence 11 111123467789999999999999983 78888753
No 111
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.32 E-value=1.9e-06 Score=71.03 Aligned_cols=82 Identities=27% Similarity=0.513 Sum_probs=65.0
Q ss_pred HhhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc----------c-hhhhhCCCCEEEEE
Q 026737 49 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ----------D-IRDILNEGDEVRVK 112 (234)
Q Consensus 49 ~~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~----------~-~~~~~~vGd~v~vk 112 (234)
+..+...+..|++|.|. +||+||.++ ..+||+|.+++.++++. . ....+++|+.|+++
T Consensus 72 f~al~fkP~~gEVV~GeVv~~~~~G~fV~ig------p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~R 145 (183)
T COG1095 72 FRALVFKPFRGEVVEGEVVEVVEFGAFVRIG------PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRAR 145 (183)
T ss_pred EEEEEEEeccccEEEEEEEEEeecceEEEec------cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEE
Confidence 44455678889999998 999999997 59999999999988431 1 23468999999999
Q ss_pred EEEEeCCC-----CeEEEEEeeccc--Ccch
Q 026737 113 VIKIDREK-----SRITLSIKQLEE--DPLL 136 (234)
Q Consensus 113 Vl~id~~~-----~ri~LS~K~~~~--~p~~ 136 (234)
|+.+.... .+|.+|||+.-. -+|.
T Consensus 146 Iv~~s~~~~~~~~~~I~lTmrq~~LGklew~ 176 (183)
T COG1095 146 IVGVSLKSRRPRESKIGLTMRQPGLGKLEWI 176 (183)
T ss_pred EEEEecccCccccceEEEEeccccCCcchhh
Confidence 99998755 578999998644 3464
No 112
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.32 E-value=1.1e-06 Score=77.08 Aligned_cols=75 Identities=16% Similarity=0.174 Sum_probs=60.3
Q ss_pred hhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC--CceEEE-Ecccccccccccccc
Q 026737 101 DILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK--KMDDVR-ITRQGFEKRVVSQDL 177 (234)
Q Consensus 101 ~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~--gi~Gl~-~s~~~~~~~~~~~~~ 177 (234)
.+.++|+.+.++|.++.. + |+||+|.+ |++||+ +|+++++
T Consensus 4 ~~P~~GdiV~G~V~~I~~-----------------------~------G~fV~L~e~~gieGlI~iSEls~~-------- 46 (262)
T PRK03987 4 EWPEEGELVVGTVKEVKD-----------------------F------GAFVTLDEYPGKEGFIHISEVASG-------- 46 (262)
T ss_pred CCCCCCCEEEEEEEEEEC-----------------------C------EEEEEECCCCCcEEEEEHHHcCcc--------
Confidence 345789999999998864 4 99999975 899999 7887532
Q ss_pred ccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccc
Q 026737 178 QLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNE 221 (234)
Q Consensus 178 ~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~ 221 (234)
|. .++...+++||.|.|+|+++|. |.||+|++.++
T Consensus 47 --~i-------~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v~~~ 85 (262)
T PRK03987 47 --WV-------KNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVNEH 85 (262)
T ss_pred --cc-------cCHHHhCCCCCEEEEEEEEEecccCeEEEEEEecccc
Confidence 22 2345589999999999999995 99999988764
No 113
>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=98.29 E-value=2.7e-06 Score=59.03 Aligned_cols=61 Identities=15% Similarity=0.096 Sum_probs=46.2
Q ss_pred CCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccC
Q 026737 106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNA 184 (234)
Q Consensus 106 Gd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~ 184 (234)
|+.|.++|.++.. + |+||+|.++++|++ .|+++.+ +
T Consensus 1 G~~V~g~V~~i~~-----------------------~------G~~v~l~~~v~g~v~~~~l~~~----------~---- 37 (66)
T cd05695 1 GMLVNARVKKVLS-----------------------N------GLILDFLSSFTGTVDFLHLDPE----------K---- 37 (66)
T ss_pred CCEEEEEEEEEeC-----------------------C------cEEEEEcCCceEEEEHHHcCCc----------c----
Confidence 6788888888753 3 99999988999999 6765211 0
Q ss_pred CCCCcceeeeeeCCCEEEEEEeeecc----chhh
Q 026737 185 PPSGKKFTLLARAGRQVQEIQLSHSL----IRKA 214 (234)
Q Consensus 185 ~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls 214 (234)
.. ...+++||+++|+|+.+|+ |.||
T Consensus 38 ----~~-~~~~~~G~~i~~kVi~id~~~~~i~LS 66 (66)
T cd05695 38 ----SS-KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred ----Cc-ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 01 3368999999999999995 6554
No 114
>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=98.26 E-value=2.3e-06 Score=59.54 Aligned_cols=65 Identities=17% Similarity=0.132 Sum_probs=50.1
Q ss_pred CCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccC
Q 026737 106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNA 184 (234)
Q Consensus 106 Gd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~ 184 (234)
|+.|.++|.++.. . |+||+|..+.+|++ ++++++.. .
T Consensus 1 G~iv~g~V~~i~~-----------------------~------~~~v~l~~~~~g~l~~~e~~~~~------------~- 38 (70)
T cd05687 1 GDIVKGTVVSVDD-----------------------D------EVLVDIGYKSEGIIPISEFSDDP------------I- 38 (70)
T ss_pred CCEEEEEEEEEeC-----------------------C------EEEEEeCCCceEEEEHHHhCccc------------c-
Confidence 6788888888763 3 89999988999999 67764221 1
Q ss_pred CCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737 185 PPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK 216 (234)
Q Consensus 185 ~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K 216 (234)
.++...+++||.++++|+++|+ |.||+|
T Consensus 39 ----~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 39 ----ENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred ----CCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 2355689999999999999984 777765
No 115
>PRK11642 exoribonuclease R; Provisional
Probab=98.25 E-value=3.3e-06 Score=84.65 Aligned_cols=70 Identities=30% Similarity=0.544 Sum_probs=59.5
Q ss_pred CCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc-----------chhhhhCCCCEEEEEEEEEeCCC
Q 026737 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREK 120 (234)
Q Consensus 57 ~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~-----------~~~~~~~vGd~v~vkVl~id~~~ 120 (234)
++|+++.|+ +||+||+|+ + .+++||||++++.++++. +....|++||.|+|+|.++|.++
T Consensus 642 ~iGe~f~G~Is~V~~fGifVeL~--~--~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~ 717 (813)
T PRK11642 642 QVGNVFKGVISSVTGFGFFVRLD--D--LFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDE 717 (813)
T ss_pred cCCcEEEEEEEEeecCceEEEEC--C--CCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCC
Confidence 789999998 999999997 2 259999999999987432 22467999999999999999999
Q ss_pred CeEEEEEeec
Q 026737 121 SRITLSIKQL 130 (234)
Q Consensus 121 ~ri~LS~K~~ 130 (234)
++|.|++-..
T Consensus 718 rkI~f~l~~~ 727 (813)
T PRK11642 718 RKIDFSLISS 727 (813)
T ss_pred CeEEEEEecc
Confidence 9999998543
No 116
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.25 E-value=7.8e-07 Score=76.88 Aligned_cols=74 Identities=16% Similarity=0.151 Sum_probs=60.5
Q ss_pred hhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC--CceEEE-Eccccccccccccccc
Q 026737 102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK--KMDDVR-ITRQGFEKRVVSQDLQ 178 (234)
Q Consensus 102 ~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~--gi~Gl~-~s~~~~~~~~~~~~~~ 178 (234)
+...|+.|-++|.++-. + |+||.|++ |++||+ +||++.
T Consensus 8 ~PeeGEiVv~tV~~V~~-----------------------~------GAyv~L~EY~g~Eg~ihiSEvas---------- 48 (269)
T COG1093 8 YPEEGEIVVGTVKQVAD-----------------------Y------GAYVELDEYPGKEGFIHISEVAS---------- 48 (269)
T ss_pred CCCCCcEEEEEEEEeec-----------------------c------ccEEEeeccCCeeeeEEHHHHHH----------
Confidence 34578888888877642 4 99999975 999999 899852
Q ss_pred cccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccc
Q 026737 179 LWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNE 221 (234)
Q Consensus 179 ~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~ 221 (234)
.|++ ++.+++|+||+|-|+||.+|+ |-||||++.++
T Consensus 49 ~wVk-------nIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~~ 88 (269)
T COG1093 49 GWVK-------NIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTEH 88 (269)
T ss_pred HHHH-------HHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCCHH
Confidence 6875 456699999999999999998 99999999654
No 117
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.22 E-value=4.9e-06 Score=61.73 Aligned_cols=73 Identities=22% Similarity=0.276 Sum_probs=56.5
Q ss_pred CCCCcEEEEE-----EeeEEEEEecCCC---cceeEEEEEceeccccccc--chhhhhCCCCEEEEEEEEEeCCCCeEEE
Q 026737 56 VNVEDIFVGR-----DYGAFIHLRFPDG---LYHLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKIDREKSRITL 125 (234)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g---~~g~~glv~isels~~~~~--~~~~~~~vGd~v~vkVl~id~~~~ri~L 125 (234)
+++|++|.|+ ...++|+|...++ .....|++|++++...+.. ++.+.|++||.|+|||++++. ...+.|
T Consensus 4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~-~~~~~L 82 (92)
T cd05791 4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD-ASSYYL 82 (92)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCC-CCCcEE
Confidence 5789998888 5568888821100 0257899999999877665 788999999999999999975 567889
Q ss_pred EEee
Q 026737 126 SIKQ 129 (234)
Q Consensus 126 S~K~ 129 (234)
|++.
T Consensus 83 st~~ 86 (92)
T cd05791 83 STAE 86 (92)
T ss_pred EecC
Confidence 8875
No 118
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=98.22 E-value=4.4e-06 Score=82.06 Aligned_cols=68 Identities=26% Similarity=0.485 Sum_probs=58.0
Q ss_pred CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc-----------cchhhhhCCCCEEEEEEEEEeCC
Q 026737 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDRE 119 (234)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~-----------~~~~~~~~vGd~v~vkVl~id~~ 119 (234)
-++|+++.|+ +||+||+|++ ++++||||++++.+++. .+....|++||.|+|+|.++|.+
T Consensus 570 ~~iG~~~~g~I~~v~~~GifV~L~~----~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~ 645 (654)
T TIGR00358 570 DKVGTEFSGEISSVTRFGMFVRLDD----NGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNME 645 (654)
T ss_pred hCCCcEEEEEEEeEEcCcEEEEecC----CceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecc
Confidence 3679999998 9999999972 47999999999998752 22346799999999999999999
Q ss_pred CCeEEEEE
Q 026737 120 KSRITLSI 127 (234)
Q Consensus 120 ~~ri~LS~ 127 (234)
+++|.+++
T Consensus 646 ~~~I~f~l 653 (654)
T TIGR00358 646 TRSIIFEL 653 (654)
T ss_pred cCeEEEEE
Confidence 99999985
No 119
>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=98.22 E-value=3.6e-06 Score=57.60 Aligned_cols=51 Identities=16% Similarity=0.137 Sum_probs=39.2
Q ss_pred ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhc
Q 026737 149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASK 216 (234)
Q Consensus 149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K 216 (234)
|+||++.++++||+ +++++++.. .++...++.||.++++|+++|. +.||+|
T Consensus 15 g~~v~i~~~~~g~l~~~~l~~~~~-----------------~~~~~~~~~Gd~v~v~v~~~~~~~~i~ls~k 69 (69)
T cd05692 15 GAFVELGGGISGLVHISQIAHKRV-----------------KDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69 (69)
T ss_pred eEEEEECCCCEEEEEhHHcCCccc-----------------CCHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence 99999999999999 777743211 2234578999999999999984 666654
No 120
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=98.22 E-value=2.2e-06 Score=77.81 Aligned_cols=97 Identities=15% Similarity=0.265 Sum_probs=72.1
Q ss_pred ccCCCCEEEEEEEEEeCCCCEEEEEe-ch--------hhHhhhhcCC--CCCcEEEEE-----Eee-EEEEEecCCCcce
Q 026737 19 KGLTGSIISVKVIQANEEMKKLVFSE-KD--------AVWNKYSSRV--NVEDIFVGR-----DYG-AFIHLRFPDGLYH 81 (234)
Q Consensus 19 ~~~vG~~v~~~Vi~id~~~~~i~lS~-k~--------~~~~~~~~~~--~~G~iv~g~-----~~G-~fV~l~~~~g~~g 81 (234)
+..+|+.+.+.+..- +-++..++. ++ +.++.++..| +.|++++|+ +.| +||+++ +
T Consensus 83 ~~~vGD~I~~~I~~~--~fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG------~ 154 (341)
T TIGR01953 83 DVQIGDEVKKEIPPE--NFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELG------K 154 (341)
T ss_pred ccccCCEEEEEeccc--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEEC------C
Confidence 345999999887542 234444443 33 1255666677 599999999 546 699996 6
Q ss_pred eEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCC--CCeEEEEEee
Q 026737 82 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDRE--KSRITLSIKQ 129 (234)
Q Consensus 82 ~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~--~~ri~LS~K~ 129 (234)
.+|++|.+++. |.+.|++||.+++.|++++.. ..+|.||++.
T Consensus 155 ~ea~LP~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~ 198 (341)
T TIGR01953 155 TEGILPKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTH 198 (341)
T ss_pred eEEEecHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCc
Confidence 99999999887 345599999999999999954 3689999975
No 121
>PHA02945 interferon resistance protein; Provisional
Probab=98.21 E-value=5e-06 Score=60.54 Aligned_cols=54 Identities=13% Similarity=0.181 Sum_probs=44.5
Q ss_pred ceeeeecC--CceEEE-Eccc--cccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccc
Q 026737 149 PYLKSFYK--KMDDVR-ITRQ--GFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHC 219 (234)
Q Consensus 149 G~fV~l~~--gi~Gl~-~s~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~ 219 (234)
|+||.|++ |.+||+ +|+. + ..|++. .+.+ +||++-|+||.+|+ |-||+|+..
T Consensus 25 ga~v~L~EY~g~eg~i~~seveva----------~~wvK~--------rd~l-~GqkvV~KVirVd~~kg~IDlSlK~V~ 85 (88)
T PHA02945 25 ALYIDLFDYPHSEAILAESVQMHM----------NRYFKY--------RDKL-VGKTVKVKVIRVDYTKGYIDVNYKRMC 85 (88)
T ss_pred eEEEEecccCCcEEEEEeehhhhc----------cceEee--------eeEe-cCCEEEEEEEEECCCCCEEEeEeeEcc
Confidence 99999975 999999 8854 3 257753 3477 99999999999997 999999986
Q ss_pred cc
Q 026737 220 NE 221 (234)
Q Consensus 220 ~~ 221 (234)
++
T Consensus 86 ~~ 87 (88)
T PHA02945 86 RH 87 (88)
T ss_pred cC
Confidence 53
No 122
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=98.12 E-value=1.9e-06 Score=84.99 Aligned_cols=92 Identities=21% Similarity=0.233 Sum_probs=69.7
Q ss_pred EeeEEEEEecCCCcceeEEEEEceecccc-------cccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhh
Q 026737 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-------LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLET 138 (234)
Q Consensus 66 ~~G~fV~l~~~~g~~g~~glv~isels~~-------~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~ 138 (234)
.+|+-+++. .+|.|.+.-.... .+......+++|+.+.++|.++..
T Consensus 579 ~tg~~I~i~-------ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~-------------------- 631 (684)
T TIGR03591 579 ETGAKIDIE-------DDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMD-------------------- 631 (684)
T ss_pred HHCCEEEEe-------cCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeC--------------------
Confidence 889999997 4677777643322 233334447889999999998853
Q ss_pred hhccccccccceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737 139 LEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 210 (234)
Q Consensus 139 ~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~ 210 (234)
+ |+||++.+|++||+ +|+++++ + + .++...+++||.|+|+|+++|.
T Consensus 632 ---~------GafVei~~g~~GllHiSei~~~-~---------v-------~~~~~~~kvGD~V~VkVi~id~ 678 (684)
T TIGR03591 632 ---F------GAFVEILPGKDGLVHISEIANE-R---------V-------EKVEDVLKEGDEVKVKVLEIDK 678 (684)
T ss_pred ---C------EEEEEECCCcEEEEEHHHcCCC-c---------c-------cChhhccCCCCEEEEEEEEECC
Confidence 4 99999999999999 8988432 1 1 2455689999999999999985
No 123
>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=98.11 E-value=8.1e-06 Score=60.02 Aligned_cols=67 Identities=13% Similarity=-0.014 Sum_probs=50.8
Q ss_pred hhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccc
Q 026737 102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLW 180 (234)
Q Consensus 102 ~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~ 180 (234)
.+++|+.+.++|.++.+ ++ . ||||+|.+|.+||+ +|+++|..+
T Consensus 4 ~~~~G~iy~g~V~~i~~-------------------~~--~------GaFV~l~~g~~Gllh~seis~~~~--------- 47 (88)
T cd04453 4 EPIVGNIYLGRVKKIVP-------------------GL--Q------AAFVDIGLGKNGFLHLSDILPAYF--------- 47 (88)
T ss_pred cCCCCCEEEEEEEEecc-------------------CC--c------EEEEEeCCCCEEEEEhHHcCchhc---------
Confidence 36789999999999864 11 2 99999999999999 788854221
Q ss_pred cccCCCCCcceeeeeeCCCEEEEEEeeec
Q 026737 181 LSNAPPSGKKFTLLARAGRQVQEIQLSHS 209 (234)
Q Consensus 181 ~~~~~~~~~~~~~~~~~G~~v~~~vl~~d 209 (234)
. .. .++...+++||.|.|+|++..
T Consensus 48 ~-~v----~~~~~~~~~Gd~v~VqV~~~~ 71 (88)
T cd04453 48 K-KH----KKIAKLLKEGQEILVQVVKEP 71 (88)
T ss_pred c-cc----CCHHHcCCCCCEEEEEEEEec
Confidence 0 01 344568999999999999975
No 124
>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=98.09 E-value=1.2e-05 Score=56.15 Aligned_cols=61 Identities=15% Similarity=0.158 Sum_probs=46.6
Q ss_pred CCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccC
Q 026737 106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNA 184 (234)
Q Consensus 106 Gd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~ 184 (234)
|+.|.++|++++. . |+||++.+|++|++ +++++++ |...
T Consensus 1 G~iV~g~V~~i~~-----------------------~------gi~v~l~~~i~g~i~~~~i~~~----------~~~~- 40 (70)
T cd05702 1 GDLVKAKVKSVKP-----------------------T------QLNVQLADNVHGRIHVSEVFDE----------WPDG- 40 (70)
T ss_pred CCEEEEEEEEEEC-----------------------C------cEEEEeCCCcEEEEEHHHhccc----------cccc-
Confidence 7888889988864 3 88999999999999 7777422 1011
Q ss_pred CCCCcceeeeeeCCCEEEEEEeeecc
Q 026737 185 PPSGKKFTLLARAGRQVQEIQLSHSL 210 (234)
Q Consensus 185 ~~~~~~~~~~~~~G~~v~~~vl~~d~ 210 (234)
.++...+++||.|+|+|+++|.
T Consensus 41 ----~~~~~~~~~Gd~i~~kVl~~d~ 62 (70)
T cd05702 41 ----KNPLSKFKIGQKIKARVIGGHD 62 (70)
T ss_pred ----cChhHhCCCCCEEEEEEEEEeC
Confidence 2345578999999999999985
No 125
>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=98.08 E-value=1e-05 Score=55.26 Aligned_cols=45 Identities=13% Similarity=0.014 Sum_probs=35.1
Q ss_pred ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737 149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 210 (234)
Q Consensus 149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~ 210 (234)
|+||++.++.+|++ .++++.+. . .++...+++||.++|+|+++|.
T Consensus 15 G~fv~l~~~~~g~~~~~~l~~~~----------~-------~~~~~~~~~Gd~v~v~i~~vd~ 60 (68)
T cd05685 15 GAFVDIGVKQDGLIHISKMADRF----------V-------SHPSDVVSVGDIVEVKVISIDE 60 (68)
T ss_pred cEEEEcCCCCEEEEEHHHCCCcc----------c-------cCHHHhcCCCCEEEEEEEEEEC
Confidence 99999999999999 67664221 1 1234578999999999999985
No 126
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.07 E-value=9.5e-06 Score=74.24 Aligned_cols=97 Identities=16% Similarity=0.243 Sum_probs=69.9
Q ss_pred ccCCCCEEEEEEEEEeCCCCEEEEEechh--------hHhhhhcCC--CCCcEEEEE-----EeeEEEEEecCCCcceeE
Q 026737 19 KGLTGSIISVKVIQANEEMKKLVFSEKDA--------VWNKYSSRV--NVEDIFVGR-----DYGAFIHLRFPDGLYHLT 83 (234)
Q Consensus 19 ~~~vG~~v~~~Vi~id~~~~~i~lS~k~~--------~~~~~~~~~--~~G~iv~g~-----~~G~fV~l~~~~g~~g~~ 83 (234)
+..+|+.+.+.+...+- ++....+.++. ..+..+..| +.|++++|+ ++|+||+++ +++
T Consensus 86 ~~~vGD~i~~~I~~~~f-gR~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg------~vE 158 (362)
T PRK12327 86 AYELGDVIEIEVTPKDF-GRIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLG------KIE 158 (362)
T ss_pred cccCCCEEEEecCcCCC-ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeC------CeE
Confidence 34589999988655332 12222222221 244566677 999999999 889999997 699
Q ss_pred EEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCC--eEEEEEe
Q 026737 84 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIK 128 (234)
Q Consensus 84 glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~--ri~LS~K 128 (234)
|++|.+++. |.+.|++||.++|.|++++.+++ +|.||+.
T Consensus 159 a~LP~~E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt 199 (362)
T PRK12327 159 AVLPPAEQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRT 199 (362)
T ss_pred EEecHHHcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence 999988775 35679999999999999996554 5777764
No 127
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=98.06 E-value=4.4e-05 Score=66.56 Aligned_cols=96 Identities=14% Similarity=0.211 Sum_probs=74.4
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh-hHhhhhcCCCC---CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecc
Q 026737 22 TGSIISVKVIQANEEMKKLVFSEKDA-VWNKYSSRVNV---EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS 92 (234)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~-~~~~~~~~~~~---G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels 92 (234)
+|+++-|. +.+|+++ |+....+.. ..+........ ++.+.|+ ..|.||-++ .++-||||-||..
T Consensus 117 ~Gd~l~v~-l~~Dkk~-Ri~g~~a~~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e-----~~~~GfIh~sEr~ 189 (287)
T COG2996 117 KGDKLLVY-LYVDKKG-RIWGTLAIEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITE-----NGYLGFIHKSERF 189 (287)
T ss_pred CCCEEEEE-EEEccCC-cEEEEecchhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEc-----CCeEEEEcchhhc
Confidence 89999999 6778755 777776654 34444444444 8888888 889999997 3799999988754
Q ss_pred cccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccC
Q 026737 93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEED 133 (234)
Q Consensus 93 ~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~ 133 (234)
- .++.|+.+.++|+.+.+ .++|.||++....+
T Consensus 190 ~--------~prlG~~l~~rVi~~re-Dg~lnLSl~p~~~E 221 (287)
T COG2996 190 A--------EPRLGERLTARVIGVRE-DGKLNLSLRPRAHE 221 (287)
T ss_pred c--------cccCCceEEEEEEEEcc-CCeeecccccccHH
Confidence 2 26789999999999986 99999999876443
No 128
>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=98.04 E-value=1.3e-05 Score=55.44 Aligned_cols=62 Identities=10% Similarity=0.089 Sum_probs=45.4
Q ss_pred CCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-EccccccccccccccccccccC
Q 026737 106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNA 184 (234)
Q Consensus 106 Gd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~ 184 (234)
|+.+.++|.++.. . |+||++ +|++||+ .|++++.. ..
T Consensus 1 G~iv~g~V~~v~~-----------------------~------G~~v~l-~g~~gfip~s~~~~~~------------~~ 38 (67)
T cd04465 1 GEIVEGKVTEKVK-----------------------G------GLIVDI-EGVRAFLPASQVDLRP------------VE 38 (67)
T ss_pred CCEEEEEEEEEEC-----------------------C------eEEEEE-CCEEEEEEHHHCCCcc------------cC
Confidence 6778888887753 3 999999 8999999 67773211 11
Q ss_pred CCCCcceeeeeeCCCEEEEEEeeecc----chhhhc
Q 026737 185 PPSGKKFTLLARAGRQVQEIQLSHSL----IRKASK 216 (234)
Q Consensus 185 ~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K 216 (234)
++.. .+||.++++|+++|+ |.||+|
T Consensus 39 -----~~~~--~vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 39 -----DLDE--YVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred -----ChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 1111 489999999999995 777765
No 129
>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=98.00 E-value=3e-05 Score=55.35 Aligned_cols=56 Identities=9% Similarity=0.042 Sum_probs=37.5
Q ss_pred ceeeeecC-CceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737 149 PYLKSFYK-KMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 210 (234)
Q Consensus 149 G~fV~l~~-gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~ 210 (234)
|+||++.+ |++|++ .|++.++... -++- .|.... .+....+++||.|+|+|+++|.
T Consensus 16 G~fv~l~~~~~~G~v~~~~l~~~~~~-~d~~-~~~~~~----~~~~~~~~~gd~v~v~v~~vd~ 73 (83)
T cd04471 16 GLFVELDNLTVEGLVHVSTLGDDYYE-FDEE-NHALVG----ERTGKVFRLGDKVKVRVVRVDL 73 (83)
T ss_pred eEEEEecCCCEEEEEEEEecCCCcEE-Eccc-ceEEEe----ccCCCEEcCCCEEEEEEEEecc
Confidence 99999998 999999 7877543321 1111 111111 1234589999999999999985
No 130
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=97.96 E-value=2.6e-05 Score=53.38 Aligned_cols=45 Identities=13% Similarity=0.122 Sum_probs=35.4
Q ss_pred ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737 149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 210 (234)
Q Consensus 149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~ 210 (234)
|+||++.++++|++ +++++++. . .++...++.||.++|+|+++|.
T Consensus 15 G~~v~l~~~~~g~l~~~~l~~~~----------~-------~~~~~~~~~Gd~v~v~v~~~d~ 60 (68)
T cd04472 15 GAFVEILPGKDGLVHISELSDER----------V-------EKVEDVLKVGDEVKVKVIEVDD 60 (68)
T ss_pred EEEEEeCCCCEEEEEhHHcCCcc----------c-------cCHHHccCCCCEEEEEEEEECC
Confidence 99999998999999 77774321 1 1234578999999999999985
No 131
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=97.96 E-value=7.1e-06 Score=70.96 Aligned_cols=79 Identities=27% Similarity=0.464 Sum_probs=71.0
Q ss_pred CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeec
Q 026737 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (234)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~ 130 (234)
+.++++|-+. +-|+||.|-.++ +++|+|-+||||.+++....+..++|..=-|.|+.+|+++|.|.||.+.+
T Consensus 14 Pev~e~VmvnV~sIaemGayv~LlEYn---niEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrV 90 (304)
T KOG2916|consen 14 PEVEEIVMVNVRSIAEMGAYVKLLEYN---NIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRV 90 (304)
T ss_pred CCcccEEEEEeeEehhccceEeeeecC---CcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccC
Confidence 5788888877 889999998655 59999999999999999999999999999999999999999999999999
Q ss_pred ccCcchh
Q 026737 131 EEDPLLE 137 (234)
Q Consensus 131 ~~~p~~~ 137 (234)
.++....
T Consensus 91 s~ed~~k 97 (304)
T KOG2916|consen 91 SPEDKEK 97 (304)
T ss_pred CHHHHHH
Confidence 8766433
No 132
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=97.92 E-value=3.5e-05 Score=52.54 Aligned_cols=66 Identities=18% Similarity=0.122 Sum_probs=50.2
Q ss_pred CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccccc
Q 026737 104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLS 182 (234)
Q Consensus 104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~ 182 (234)
++|+.+.++|.++.. . |+|+++.+++.|++ .+++....
T Consensus 1 ~~G~~v~g~V~~v~~-----------------------~------g~~v~i~~~~~g~l~~~~~~~~~------------ 39 (72)
T smart00316 1 EVGDVVEGTVTEITP-----------------------F------GAFVDLGNGVEGLIPISELSDKR------------ 39 (72)
T ss_pred CCCCEEEEEEEEEEc-----------------------c------EEEEEeCCCCEEEEEHHHCCccc------------
Confidence 369999999998864 3 89999998999999 67663211
Q ss_pred cCCCCCcceeeeeeCCCEEEEEEeeecc----chhhh
Q 026737 183 NAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKAS 215 (234)
Q Consensus 183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~ 215 (234)
..++...++.||.++++|++++. +.|++
T Consensus 40 -----~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~ 71 (72)
T smart00316 40 -----VKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71 (72)
T ss_pred -----cCCHHHeecCCCEEEEEEEEEeCCCCEEEEEe
Confidence 02344578999999999999985 55554
No 133
>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=97.88 E-value=5.2e-05 Score=51.79 Aligned_cols=59 Identities=20% Similarity=0.186 Sum_probs=44.8
Q ss_pred CCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccccc
Q 026737 105 EGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSN 183 (234)
Q Consensus 105 vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~ 183 (234)
+|+.+.++|.++.. . |+||++. +++|++ .+++++. ..
T Consensus 1 ~g~~~~g~V~~v~~-----------------------~------g~~v~l~-~~~g~l~~~e~~~~------------~~ 38 (68)
T cd05688 1 EGDVVEGTVKSITD-----------------------F------GAFVDLG-GVDGLLHISDMSWG------------RV 38 (68)
T ss_pred CCCEEEEEEEEEEe-----------------------e------eEEEEEC-CeEEEEEhHHCCCc------------cc
Confidence 47888888888863 3 8999996 799999 6766321 11
Q ss_pred CCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737 184 APPSGKKFTLLARAGRQVQEIQLSHSL 210 (234)
Q Consensus 184 ~~~~~~~~~~~~~~G~~v~~~vl~~d~ 210 (234)
.++...++.||.|+|+|+++|.
T Consensus 39 -----~~~~~~~~~Gd~v~v~i~~vd~ 60 (68)
T cd05688 39 -----KHPSEVVNVGDEVEVKVLKIDK 60 (68)
T ss_pred -----cCHhHEECCCCEEEEEEEEEEC
Confidence 2345579999999999999985
No 134
>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=97.83 E-value=0.0001 Score=54.97 Aligned_cols=74 Identities=9% Similarity=-0.010 Sum_probs=51.4
Q ss_pred ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeec---------cchhhhccc
Q 026737 149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHS---------LIRKASKRH 218 (234)
Q Consensus 149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d---------~i~ls~K~~ 218 (234)
|+||++. +++|++ +++++.+.....+.-..|.. .+....++.||.|+++|+++| .+.||+|+-
T Consensus 14 GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~------~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i~ls~k~~ 86 (99)
T cd04460 14 GAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIG------EETKRVLKVGDVVRARIVAVSLKERRPRESKIGLTMRQP 86 (99)
T ss_pred cEEEEEc-CeEEEEEEEEccCCceEechhheeecc------cCcCCEECCCCEEEEEEEEEeHHHCcCCCceEEEEEecC
Confidence 9999997 599999 77775433210000001111 123457899999999999997 399999999
Q ss_pred ccchhHHHHhh
Q 026737 219 CNEYWNVFHET 229 (234)
Q Consensus 219 ~~~p~~~~~~~ 229 (234)
..-||+-+.+.
T Consensus 87 ~~g~~~~~~~~ 97 (99)
T cd04460 87 GLGKLEWIEEE 97 (99)
T ss_pred CCCcHHHhhhh
Confidence 99999776653
No 135
>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=97.72 E-value=9.9e-05 Score=53.04 Aligned_cols=68 Identities=10% Similarity=0.008 Sum_probs=53.9
Q ss_pred CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccccc
Q 026737 104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLS 182 (234)
Q Consensus 104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~ 182 (234)
++||.|.++|++++. . +++|++..+.+|++ .|+++.+.
T Consensus 5 ~~GdiV~G~V~~v~~-----------------------~------~~~V~i~~~~~g~l~~~~~~~~~------------ 43 (82)
T cd04454 5 DVGDIVIGIVTEVNS-----------------------R------FWKVDILSRGTARLEDSSATEKD------------ 43 (82)
T ss_pred CCCCEEEEEEEEEcC-----------------------C------EEEEEeCCCceEEeechhccCcc------------
Confidence 689999999999864 2 78999988999999 77763221
Q ss_pred cCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcc
Q 026737 183 NAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKR 217 (234)
Q Consensus 183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~ 217 (234)
..++...+++||.+.|+|+++|. +.||++.
T Consensus 44 -----~~~~~~~~~~GD~i~~~V~~~~~~~~i~LS~~~ 76 (82)
T cd04454 44 -----KKEIRKSLQPGDLILAKVISLGDDMNVLLTTAD 76 (82)
T ss_pred -----hHHHHhcCCCCCEEEEEEEEeCCCCCEEEEECC
Confidence 12345578999999999999985 8888775
No 136
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=97.61 E-value=0.00024 Score=50.60 Aligned_cols=52 Identities=12% Similarity=0.022 Sum_probs=43.9
Q ss_pred hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
+++|+.+.++|.++.. + |+||+++++++||+ .|++
T Consensus 14 ~~~G~~~~g~V~~i~~-----------------------~------G~fV~l~~~~~Glv~~se~--------------- 49 (77)
T cd04473 14 LEVGKLYKGKVNGVAK-----------------------Y------GVFVDLNDHVRGLIHRSNL--------------- 49 (77)
T ss_pred CCCCCEEEEEEEeEec-----------------------c------eEEEEECCCcEEEEEchhc---------------
Confidence 6789999999988753 4 99999999999999 5553
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeee
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSH 208 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~ 208 (234)
...++.||.++++|.++
T Consensus 50 ----------~~~~~iGd~v~v~I~~i 66 (77)
T cd04473 50 ----------LRDYEVGDEVIVQVTDI 66 (77)
T ss_pred ----------cCcCCCCCEEEEEEEEE
Confidence 12579999999999998
No 137
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=97.57 E-value=0.0002 Score=59.85 Aligned_cols=52 Identities=13% Similarity=-0.001 Sum_probs=37.8
Q ss_pred ceeeeec----------CCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc-chhhhc
Q 026737 149 PYLKSFY----------KKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL-IRKASK 216 (234)
Q Consensus 149 G~fV~l~----------~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~-i~ls~K 216 (234)
|+||+|. ++++|++ .|++++.. . .++...+++||.|+|+|++++. +.||+|
T Consensus 79 g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~------------~-----~~~~~~~~~GD~V~akV~~i~~~i~LS~k 141 (189)
T PRK09521 79 RALVRIVSIEGSERELATSKLAYIHISQVSDGY------------V-----ESLTDAFKIGDIVRAKVISYTDPLQLSTK 141 (189)
T ss_pred eEEEEEEEecccccccCCCceeeEEhhHcChhh------------h-----hhHHhccCCCCEEEEEEEecCCcEEEEEe
Confidence 6667663 4789999 67663211 0 2345578999999999999976 888888
Q ss_pred c
Q 026737 217 R 217 (234)
Q Consensus 217 ~ 217 (234)
+
T Consensus 142 ~ 142 (189)
T PRK09521 142 G 142 (189)
T ss_pred c
Confidence 6
No 138
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.50 E-value=0.00046 Score=59.35 Aligned_cols=71 Identities=27% Similarity=0.432 Sum_probs=61.2
Q ss_pred cCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc----cchhhhhCCCCEEEEEEEEEeCCCCeEE
Q 026737 54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----QDIRDILNEGDEVRVKVIKIDREKSRIT 124 (234)
Q Consensus 54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~----~~~~~~~~vGd~v~vkVl~id~~~~ri~ 124 (234)
..++.||+|-|. ..+..|+|+ ..+.|++|+|++.++.+ .+++.+|++||-|.|+|..+|+ .+...
T Consensus 60 YiP~~gD~VIG~I~~v~~~~W~VDI~-----sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~ 133 (239)
T COG1097 60 YIPEVGDVVIGKIIEVGPSGWKVDIG-----SPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVE 133 (239)
T ss_pred ccCCCCCEEEEEEEEEcccceEEEcC-----CccceEeehhhhhcccccccccccccccccCCEEEEEEEEccC-CCceE
Confidence 357899999999 788999997 36999999999976653 4778899999999999999997 88999
Q ss_pred EEEeec
Q 026737 125 LSIKQL 130 (234)
Q Consensus 125 LS~K~~ 130 (234)
|++|..
T Consensus 134 L~~k~~ 139 (239)
T COG1097 134 LTLKDE 139 (239)
T ss_pred EEeecC
Confidence 999654
No 139
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=97.41 E-value=0.0006 Score=63.63 Aligned_cols=58 Identities=29% Similarity=0.477 Sum_probs=47.7
Q ss_pred cCCCCCcEEEEE-----Ee--eEEEEEecCCCcceeEEEEEceecccc------------cccchhhhhCCCCEEEEEEE
Q 026737 54 SRVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKVI 114 (234)
Q Consensus 54 ~~~~~G~iv~g~-----~~--G~fV~l~~~~g~~g~~glv~isels~~------------~~~~~~~~~~vGd~v~vkVl 114 (234)
....+|.+|.|+ ++ ||||+|+ .+..||+|++++.+. +..++.+.+++||.|.|+|.
T Consensus 21 ~~~~vGnIY~GrV~~i~p~l~aAFVdiG-----~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~ 95 (414)
T TIGR00757 21 SRQLKGNIYKGRVTRILPSLQAAFVDIG-----LEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVV 95 (414)
T ss_pred CcCCCCCEEEEEEeeecCCCceEEEEcC-----CCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEe
Confidence 346789999999 66 8999997 368999999998763 23456778999999999998
Q ss_pred EE
Q 026737 115 KI 116 (234)
Q Consensus 115 ~i 116 (234)
+-
T Consensus 96 Ke 97 (414)
T TIGR00757 96 KE 97 (414)
T ss_pred eC
Confidence 83
No 140
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.39 E-value=0.00075 Score=47.69 Aligned_cols=64 Identities=19% Similarity=0.222 Sum_probs=50.1
Q ss_pred CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccc--hhhhhCCCCEE-EEEEEEEeCCCCeEEEEEe
Q 026737 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD--IRDILNEGDEV-RVKVIKIDREKSRITLSIK 128 (234)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~--~~~~~~vGd~v-~vkVl~id~~~~ri~LS~K 128 (234)
|+++.|+ +-+++|++.+ .++.|++|..++|+..-++ .-..+++||++ ++.|+ +...+.|.||.|
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~----~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL--~~~~r~i~lt~K 72 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILP----EEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecC----CCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence 6777787 6679999983 3799999999999943332 34558999999 99999 777888888865
No 141
>PRK05054 exoribonuclease II; Provisional
Probab=97.36 E-value=0.0006 Score=67.03 Aligned_cols=65 Identities=15% Similarity=0.148 Sum_probs=51.8
Q ss_pred CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccc---ccc--c-------hhhhhCCCCEEEEEEEEEeCCCC
Q 026737 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD---LIQ--D-------IRDILNEGDEVRVKVIKIDREKS 121 (234)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~---~~~--~-------~~~~~~vGd~v~vkVl~id~~~~ 121 (234)
|+.+.|. +||+||+|.. .+++||||++.+... +.- + -...|++||.|+|+|.++|..++
T Consensus 562 ~~~f~g~I~~v~~~G~fV~l~~----~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~ 637 (644)
T PRK05054 562 DTRFAAEIIDISRGGMRVRLLE----NGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETR 637 (644)
T ss_pred CeEEEEEEEeeecCcEEEEEeC----CceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccC
Confidence 4488887 9999999973 479999999998653 110 1 12469999999999999999999
Q ss_pred eEEEEE
Q 026737 122 RITLSI 127 (234)
Q Consensus 122 ri~LS~ 127 (234)
+|.+++
T Consensus 638 ~i~~~~ 643 (644)
T PRK05054 638 SIIARP 643 (644)
T ss_pred eEEEEE
Confidence 998865
No 142
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.31 E-value=0.0011 Score=57.24 Aligned_cols=74 Identities=11% Similarity=-0.002 Sum_probs=55.5
Q ss_pred hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
.++||.|.++|.++.. . |+||++..+++|++ +|++++.. .
T Consensus 61 P~vGDiViG~V~~i~~-----------------------~------~~~vdI~~~~~g~L~~s~i~~~~----------~ 101 (235)
T PRK04163 61 PKVGDLVIGKVTDVTF-----------------------S------GWEVDINSPYKAYLPVSEVLGRP----------V 101 (235)
T ss_pred CCCCCEEEEEEEEEeC-----------------------c------eEEEEeCCCceeEEEHHHcCCCc----------c
Confidence 4789999999998864 2 67999988999999 77764221 1
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhccc
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRH 218 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~ 218 (234)
. ....++...+++||.|.|+|+++++ +.||+|+-
T Consensus 102 ~---~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~~ 138 (235)
T PRK04163 102 N---VEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGK 138 (235)
T ss_pred c---cchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcCC
Confidence 0 0113456689999999999999976 77888753
No 143
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=97.24 E-value=0.00031 Score=66.80 Aligned_cols=61 Identities=11% Similarity=0.015 Sum_probs=52.0
Q ss_pred ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcccccchhH
Q 026737 149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKRHCNEYWN 224 (234)
Q Consensus 149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~~~~~p~~ 224 (234)
|+||+|.++..||| .|++.. -|+ .++++++.+||+++++-++.|. +.|+.|.++++|..
T Consensus 683 G~~V~l~p~~~~Llh~sqL~~----------e~i-------akpsd~levGq~I~vk~ie~d~~g~~~ls~ralLp~p~~ 745 (760)
T KOG1067|consen 683 GVMVELYPMQQGLLHNSQLDQ----------EKI-------AKPSDLLEVGQEIQVKYIERDPRGGIMLSSRALLPDPAT 745 (760)
T ss_pred ceEEEecCCchhhccchhccc----------ccc-------cChHHHHhhcceeEEEEEeecCccceeehhhhhcCCccc
Confidence 99999999999999 898842 243 4567789999999999999997 99999999999975
Q ss_pred HH
Q 026737 225 VF 226 (234)
Q Consensus 225 ~~ 226 (234)
..
T Consensus 746 ~~ 747 (760)
T KOG1067|consen 746 KE 747 (760)
T ss_pred CC
Confidence 43
No 144
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=97.22 E-value=0.0017 Score=47.68 Aligned_cols=59 Identities=17% Similarity=0.230 Sum_probs=45.5
Q ss_pred CCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccch-----------hhhhCCCCEEEEEEEEEeCCCC
Q 026737 58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-----------RDILNEGDEVRVKVIKIDREKS 121 (234)
Q Consensus 58 ~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~-----------~~~~~vGd~v~vkVl~id~~~~ 121 (234)
.|+++.|+ ++|+||.++ ++++|+|.+.+......++ ...++.|+.|++||+.+..+.+
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G------pl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~ 74 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG------PLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDAT 74 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc------CceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccC
Confidence 47889998 999999997 5999999987765533222 3447899999999999876544
Q ss_pred e
Q 026737 122 R 122 (234)
Q Consensus 122 r 122 (234)
.
T Consensus 75 ~ 75 (88)
T cd04462 75 D 75 (88)
T ss_pred c
Confidence 3
No 145
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=97.22 E-value=0.0028 Score=52.54 Aligned_cols=74 Identities=28% Similarity=0.344 Sum_probs=57.2
Q ss_pred hcCCCCCcEEEEE-----EeeEEEEEecCCCc-----ceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCe
Q 026737 53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGL-----YHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSR 122 (234)
Q Consensus 53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~-----~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~r 122 (234)
...++.|++|-|. ...+.|++-+.++. +...|-+|+|+....++++..+.|++||.|+|+|++.- ..
T Consensus 59 ~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~---~~ 135 (188)
T COG1096 59 PPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG---DP 135 (188)
T ss_pred CCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC---CC
Confidence 3457899999998 55677777543320 12467899999999999999999999999999999974 45
Q ss_pred EEEEEee
Q 026737 123 ITLSIKQ 129 (234)
Q Consensus 123 i~LS~K~ 129 (234)
+.||++.
T Consensus 136 ~~Lst~~ 142 (188)
T COG1096 136 IQLSTKG 142 (188)
T ss_pred eEEEecC
Confidence 6676653
No 146
>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=97.20 E-value=0.00052 Score=45.67 Aligned_cols=45 Identities=11% Similarity=0.040 Sum_probs=34.7
Q ss_pred ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737 149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 210 (234)
Q Consensus 149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~ 210 (234)
|+||++.++++|++ .++++... + .++...+++||.|+++|+++|.
T Consensus 12 g~~v~l~~~~~g~~~~~~~~~~~---------~--------~~~~~~~~~G~~v~~~v~~~d~ 57 (65)
T cd00164 12 GVFVELEDGVEGLVHISELSDKF---------V--------KDPSEVFKVGDEVEVKVLEVDP 57 (65)
T ss_pred eEEEEecCCCEEEEEHHHCCCcc---------c--------cCHhhEeCCCCEEEEEEEEEcC
Confidence 89999999999999 67663211 0 1234578999999999999984
No 147
>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=97.09 E-value=0.0017 Score=44.93 Aligned_cols=54 Identities=20% Similarity=0.168 Sum_probs=42.0
Q ss_pred CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccccc
Q 026737 104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLS 182 (234)
Q Consensus 104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~ 182 (234)
+.|+.|+++|++++. . |+||++. +++|++ .+++.
T Consensus 2 ~~g~iV~G~V~~~~~-----------------------~------~~~vdig-~~eg~lp~~e~~--------------- 36 (67)
T cd04455 2 REGEIVTGIVKRVDR-----------------------G------NVIVDLG-KVEAILPKKEQI--------------- 36 (67)
T ss_pred CCCCEEEEEEEEEcC-----------------------C------CEEEEcC-CeEEEeeHHHCC---------------
Confidence 369999999998874 2 7899995 599999 55541
Q ss_pred cCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737 183 NAPPSGKKFTLLARAGRQVQEIQLSHSL 210 (234)
Q Consensus 183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d~ 210 (234)
+.+.+++||++++.|.+++.
T Consensus 37 --------~~~~~~~Gd~v~v~v~~v~~ 56 (67)
T cd04455 37 --------PGESYRPGDRIKAYVLEVRK 56 (67)
T ss_pred --------CCCcCCCCCEEEEEEEEEec
Confidence 11256999999999999973
No 148
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=96.95 E-value=0.0028 Score=52.45 Aligned_cols=84 Identities=13% Similarity=0.062 Sum_probs=57.2
Q ss_pred CCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccccc
Q 026737 105 EGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSN 183 (234)
Q Consensus 105 vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~ 183 (234)
+|+.+.++|.+++. . |+||++. .++|++ ++++..+...-..+-..|.-.
T Consensus 81 ~gEvv~G~V~~v~~-----------------------~------GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~ 130 (179)
T TIGR00448 81 LGEIVEGEVIEIVE-----------------------F------GAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGK 130 (179)
T ss_pred CCCEEEEEEEEEEe-----------------------e------EEEEEeC-CceEEEEcHHhCCCceEEccccceEEEc
Confidence 68888888888864 3 9999995 599999 666643321111111133321
Q ss_pred CCCCCcceeeeeeCCCEEEEEEeeec---------cchhhhcccccchhH
Q 026737 184 APPSGKKFTLLARAGRQVQEIQLSHS---------LIRKASKRHCNEYWN 224 (234)
Q Consensus 184 ~~~~~~~~~~~~~~G~~v~~~vl~~d---------~i~ls~K~~~~~p~~ 224 (234)
+....++.||.|+++|+++| +|.|+||+-.--|++
T Consensus 131 ------~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~~I~lt~k~~~LG~~~ 174 (179)
T TIGR00448 131 ------ETKKVLDEGDKVRARIVALSLKDRRPEGSKIGLTMRQPLLGKLE 174 (179)
T ss_pred ------cCCeEEcCCCEEEEEEEEEEccCCCCCcceEEEEeccCcCCccc
Confidence 12358999999999999997 299999986555554
No 149
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=96.85 E-value=0.0043 Score=51.39 Aligned_cols=74 Identities=16% Similarity=0.208 Sum_probs=54.7
Q ss_pred hhhhcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccc------------cchhhhhCCCCEEEEE
Q 026737 50 NKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI------------QDIRDILNEGDEVRVK 112 (234)
Q Consensus 50 ~~~~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~------------~~~~~~~~vGd~v~vk 112 (234)
....-++-.|+++.|. ++|+||.++ ..++|||.+++..... .+-+..++.|+.|++|
T Consensus 73 raivFrPf~gEVv~g~V~~v~~~G~~v~~G------p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~r 146 (176)
T PTZ00162 73 QAIVFKPFKDEVLDAIVTDVNKLGFFAQAG------PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLR 146 (176)
T ss_pred EEEEEecCCCCEEEEEEEEEecceEEEEee------CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEE
Confidence 3445678899999999 999999997 4789999998864321 1224568999999999
Q ss_pred EEEEeCCCC--eEEEEEee
Q 026737 113 VIKIDREKS--RITLSIKQ 129 (234)
Q Consensus 113 Vl~id~~~~--ri~LS~K~ 129 (234)
|+.+..+.+ ++..|+|+
T Consensus 147 V~~v~~~~~~~~~i~T~~~ 165 (176)
T PTZ00162 147 LQGVRYDASNLFAIATINS 165 (176)
T ss_pred EEEEEecCCCcEEEEEecC
Confidence 988875433 34556654
No 150
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=96.82 E-value=0.003 Score=62.83 Aligned_cols=71 Identities=31% Similarity=0.515 Sum_probs=57.5
Q ss_pred cCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccccccc-----------chhhhhCCCCEEEEEEEEEe
Q 026737 54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKID 117 (234)
Q Consensus 54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~-----------~~~~~~~vGd~v~vkVl~id 117 (234)
-+-.+|+++.|+ .||+||.|.+ .+++|+||++.+..+++. .....++.||.|++++.+++
T Consensus 618 m~~~vg~~f~g~V~~v~~~g~~V~l~~----~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~ 693 (706)
T COG0557 618 MKKRVGEEFDGVVTGVTSFGFFVELPE----LGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVD 693 (706)
T ss_pred HHHhcCCEEEEEEEEEEeccEEEEecc----cccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEc
Confidence 345788998888 8999999973 468999999999965432 22335899999999999999
Q ss_pred CCCCeEEEEEe
Q 026737 118 REKSRITLSIK 128 (234)
Q Consensus 118 ~~~~ri~LS~K 128 (234)
...+++.+++-
T Consensus 694 ~~~~~i~~~~v 704 (706)
T COG0557 694 LDERKIDFELV 704 (706)
T ss_pred ccccceEEEec
Confidence 99999988763
No 151
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=96.78 E-value=0.0036 Score=62.25 Aligned_cols=71 Identities=11% Similarity=0.149 Sum_probs=48.6
Q ss_pred CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC-CceEEE-Ecccccccccccccccccc
Q 026737 104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK-KMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~-gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
++|+.+.++|.++.. + |+||+|.+ |++||+ +|++..+.. .|.
T Consensus 626 ~iG~~~~g~V~~v~~-----------------------f------GifV~L~~~~~eGlvhis~l~~d~~-------~~d 669 (709)
T TIGR02063 626 KIGEEFEGVISGVTS-----------------------F------GLFVELENNTIEGLVHISTLKDDYY-------VFD 669 (709)
T ss_pred cCCcEEEEEEEEEEe-----------------------C------CEEEEecCCceEEEEEeeecCCCcE-------EEc
Confidence 578888888888753 4 99999988 899999 888853321 111
Q ss_pred ccCCC-CCcceeeeeeCCCEEEEEEeeecc
Q 026737 182 SNAPP-SGKKFTLLARAGRQVQEIQLSHSL 210 (234)
Q Consensus 182 ~~~~~-~~~~~~~~~~~G~~v~~~vl~~d~ 210 (234)
..... ...+....++.||+|+|+|.++|.
T Consensus 670 ~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~ 699 (709)
T TIGR02063 670 EKGLALVGERTGKVFRLGDRVKVRVVKADL 699 (709)
T ss_pred ccceEEEeccCCcEECCCCEEEEEEEEEec
Confidence 00000 001123478999999999999985
No 152
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=96.78 E-value=0.0058 Score=44.75 Aligned_cols=68 Identities=19% Similarity=0.079 Sum_probs=53.9
Q ss_pred CCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (234)
Q Consensus 55 ~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~ 129 (234)
.+++|+.|-|+ ....+|+|+ ....|++|.+++... .+..+..+++||-|.|+|.++++ .....||...
T Consensus 3 ~P~~gD~VIG~V~~~~~~~~~VdI~-----s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~-~~~~eLtc~~ 75 (86)
T cd05790 3 VPAKGDHVIGIVVAKAGDFFKVDIG-----GSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANR-DMEPELSCVD 75 (86)
T ss_pred cCCCCCEEEEEEEEEcCCeEEEEcC-----CCcceEechHHcccc-cccccccCCCCCEEEEEEEecCC-CCCeEEEEeC
Confidence 36889999998 456899997 357899999876543 34456779999999999999997 4567888765
No 153
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=96.77 E-value=0.0018 Score=63.94 Aligned_cols=54 Identities=11% Similarity=0.019 Sum_probs=44.3
Q ss_pred ceeeeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccc
Q 026737 149 PYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHC 219 (234)
Q Consensus 149 G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~ 219 (234)
|+||.+.=..+||+ +|+++... + .++..++++||.|+|+|+++|- |+|||+.-.
T Consensus 673 gafVdIgv~qDglvHis~ls~~f----------v-------~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~ 731 (780)
T COG2183 673 GAFVDIGVHQDGLVHISQLSDKF----------V-------KDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDE 731 (780)
T ss_pred cceEEeccccceeeeHHHhhhhh----------c-------CChHHhcccCCEEEEEEEEEecccCeeeeEeeccC
Confidence 99999988999999 89885221 1 3356799999999999999995 999998654
No 154
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=96.69 E-value=0.0048 Score=60.73 Aligned_cols=64 Identities=16% Similarity=0.200 Sum_probs=49.8
Q ss_pred CcEEEEE-----EeeEEEEEecCCCcceeEEEEEceeccc--ccc---cc-----h--hhhhCCCCEEEEEEEEEeCCCC
Q 026737 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW--DLI---QD-----I--RDILNEGDEVRVKVIKIDREKS 121 (234)
Q Consensus 59 G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~--~~~---~~-----~--~~~~~vGd~v~vkVl~id~~~~ 121 (234)
|+.+.|. .+|+||+|.. .+++||||++.+.. ++. .+ . ...|+.||.|+|+|.++|.+++
T Consensus 558 ~~~f~g~I~~v~~~g~~v~l~~----~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~ 633 (639)
T TIGR02062 558 NTRFAAEIVDISRGGMRVRLLE----NGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETR 633 (639)
T ss_pred CcEEEEEEEeeeCCcEEEEEec----CceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccC
Confidence 4478887 8999999972 47999999999865 221 10 1 1259999999999999999999
Q ss_pred eEEEE
Q 026737 122 RITLS 126 (234)
Q Consensus 122 ri~LS 126 (234)
+|.+.
T Consensus 634 ~i~~~ 638 (639)
T TIGR02062 634 SIIAR 638 (639)
T ss_pred cEeee
Confidence 98764
No 155
>PRK11642 exoribonuclease R; Provisional
Probab=96.48 E-value=0.0082 Score=60.61 Aligned_cols=77 Identities=10% Similarity=0.054 Sum_probs=51.6
Q ss_pred CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecC-CceEEE-Ecccccccccccccccccc
Q 026737 104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYK-KMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~-gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
++|+.+.++|.++.. + |+||+|++ +++||+ +|++.++-...... ...+
T Consensus 642 ~iGe~f~G~Is~V~~-----------------------f------GifVeL~~~~vEGlV~vs~L~~d~y~~d~~-~~~L 691 (813)
T PRK11642 642 QVGNVFKGVISSVTG-----------------------F------GFFVRLDDLFIDGLVHVSSLDNDYYRFDQV-GQRL 691 (813)
T ss_pred cCCcEEEEEEEEeec-----------------------C------ceEEEECCCCeeeeEEEeecCCcceEecch-heEE
Confidence 589999999988753 4 99999987 599999 88875432110000 0001
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhh
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKAS 215 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~ 215 (234)
. . .+....++.||.|+|+|+++|. |.|++
T Consensus 692 ~-g----~~~~~~~~lGD~V~VkV~~vD~~~rkI~f~l 724 (813)
T PRK11642 692 I-G----ESSGQTYRLGDRVEVRVEAVNMDERKIDFSL 724 (813)
T ss_pred e-c----ccCCcEECCCCEEEEEEEEeecCCCeEEEEE
Confidence 1 0 1223478999999999999985 66655
No 156
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=96.47 E-value=0.011 Score=40.31 Aligned_cols=48 Identities=33% Similarity=0.422 Sum_probs=31.4
Q ss_pred EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (234)
Q Consensus 66 ~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K 128 (234)
++|+|++-+ .+-+-++|.++.... +++||+|.|-| ..|. .+|+..|+|
T Consensus 14 ~~g~fL~~~-----~~~~vlLp~~e~~~~--------~~~Gd~v~VFv-Y~D~-~~rl~AT~k 61 (61)
T PF13509_consen 14 EFGYFLDDG-----EGKEVLLPKSEVPEP--------LKVGDEVEVFV-YLDK-EGRLVATTK 61 (61)
T ss_dssp SSEEEEEET-----T-EEEEEEGGG--------------TTSEEEEEE-EE-T-TS-EEEE--
T ss_pred CCEEEEECC-----CCCEEEechHHcCCC--------CCCCCEEEEEE-EECC-CCCEEEecC
Confidence 899999975 258999999987633 78999999877 6776 678888775
No 157
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=96.39 E-value=0.0096 Score=58.77 Aligned_cols=72 Identities=15% Similarity=0.141 Sum_probs=48.8
Q ss_pred CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeec-CCceEEE-Ecccccccccccccccccc
Q 026737 104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY-KKMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~-~gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
++|+++.++|.++.. + |+||+|+ .|++||+ +|++.++..... +-...+
T Consensus 571 ~iG~~~~g~I~~v~~-----------------------~------GifV~L~~~~veGlV~~s~l~~d~y~~d-~~~~~l 620 (654)
T TIGR00358 571 KVGTEFSGEISSVTR-----------------------F------GMFVRLDDNGIDGLIHISTLHNDYYVFD-QEKMAL 620 (654)
T ss_pred CCCcEEEEEEEeEEc-----------------------C------cEEEEecCCceEEEEEeEeCCCcceEEe-ccccEE
Confidence 578888888888753 3 9999997 6999999 888865432100 000001
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL 210 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~ 210 (234)
. . .+....++.||+|+|+|+++|.
T Consensus 621 ~-g----~~~~~~~~lGD~V~Vki~~vd~ 644 (654)
T TIGR00358 621 I-G----KGTGKVYRIGDRVTVKLTEVNM 644 (654)
T ss_pred E-e----ccCCcEECCCCEEEEEEEEEec
Confidence 0 0 1123478999999999999985
No 158
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=96.38 E-value=0.014 Score=48.43 Aligned_cols=79 Identities=11% Similarity=0.058 Sum_probs=52.6
Q ss_pred CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccccc
Q 026737 104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLS 182 (234)
Q Consensus 104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~ 182 (234)
.+|+.+.++|.+++. . |+||++. .++|++ .+++..+...-..+=..|..
T Consensus 80 ~~GEVv~g~V~~v~~-----------------------~------Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~ 129 (187)
T PRK08563 80 ELQEVVEGEVVEVVE-----------------------F------GAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIG 129 (187)
T ss_pred cCCCEEEEEEEEEEc-----------------------c------EEEEEEe-CceEEEEcHHcCCCceEEccccceEEE
Confidence 468888888888864 3 9999996 499999 66664332110011113432
Q ss_pred cCCCCCcceeeeeeCCCEEEEEEeeecc---------chhhhccc
Q 026737 183 NAPPSGKKFTLLARAGRQVQEIQLSHSL---------IRKASKRH 218 (234)
Q Consensus 183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d~---------i~ls~K~~ 218 (234)
. +....++.||.|+++|++++. |.||+|+-
T Consensus 130 ~------~~~~~i~~Gd~VrvrV~~v~~~~~~~~~~~I~ls~~~~ 168 (187)
T PRK08563 130 K------ESKRVLKVGDVVRARIVAVSLKERRPRGSKIGLTMRQP 168 (187)
T ss_pred c------cCCeEEcCCCEEEEEEEEEEcccCCCCCCEEEEEecCC
Confidence 1 124578999999999999972 77788774
No 159
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.20 E-value=0.012 Score=53.99 Aligned_cols=61 Identities=21% Similarity=0.345 Sum_probs=50.7
Q ss_pred CCCCcEEEEE----E--eeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCC---eEEEE
Q 026737 56 VNVEDIFVGR----D--YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS---RITLS 126 (234)
Q Consensus 56 ~~~G~iv~g~----~--~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~---ri~LS 126 (234)
-+.|+++.|+ + .++||+|+ +.+|++|.++.. |.+.|++||.++|.|.+++...+ +|.||
T Consensus 136 ~~~Geiv~g~V~r~~~~~~i~vdlg------~~ea~LP~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~IilS 203 (374)
T PRK12328 136 KKVGKIVFGTVVRVDNEENTFIEID------EIRAVLPMKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIELS 203 (374)
T ss_pred HhcCcEEEEEEEEEecCCCEEEEcC------CeEEEeCHHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEEE
Confidence 4799999999 3 34999996 699999988755 55779999999999999998655 78888
Q ss_pred Ee
Q 026737 127 IK 128 (234)
Q Consensus 127 ~K 128 (234)
+.
T Consensus 204 Rt 205 (374)
T PRK12328 204 RT 205 (374)
T ss_pred cC
Confidence 74
No 160
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=96.16 E-value=0.033 Score=40.37 Aligned_cols=79 Identities=14% Similarity=0.064 Sum_probs=39.4
Q ss_pred CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccccc
Q 026737 104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLS 182 (234)
Q Consensus 104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~ 182 (234)
++|+.|.++|.++. ..+..+.+-.++..++...- +--..+.....|++ .+..+...
T Consensus 3 ~vGdiV~~rVtrv~--~~~a~v~Il~v~~~~~~~~~---------~~~~~l~~~f~GiIR~~DVR~te------------ 59 (82)
T PF10447_consen 3 KVGDIVIARVTRVN--PRQAKVEILCVEGKGNDSIN---------AGDRPLKEPFQGIIRKQDVRATE------------ 59 (82)
T ss_dssp -TT-EEEEEEEEE---SSEEEEEEEES-------------------SSS----SS-S-EEEEGGGT-S------------
T ss_pred CCCCEEEEEEEEEe--ccEEEEEEEEEEeccccccc---------cCCcccccccEEEEEeeeecccc------------
Confidence 68999999999997 57777777766555542111 11235566888888 44443211
Q ss_pred cCCCCCcceeeeeeCCCEEEEEEeee
Q 026737 183 NAPPSGKKFTLLARAGRQVQEIQLSH 208 (234)
Q Consensus 183 ~~~~~~~~~~~~~~~G~~v~~~vl~~ 208 (234)
.| .-++.+.|++||-|+|+|+++
T Consensus 60 -~D--kv~~~~~FrpGDIVrA~ViSl 82 (82)
T PF10447_consen 60 -KD--KVKMYDCFRPGDIVRARVISL 82 (82)
T ss_dssp -S------GGGT--SSSEEEEEEEEE
T ss_pred -cc--hhhHHhccCCCCEEEEEEeeC
Confidence 11 123566899999999999974
No 161
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=96.11 E-value=0.0051 Score=62.73 Aligned_cols=72 Identities=24% Similarity=0.275 Sum_probs=59.2
Q ss_pred cCCCCCcEEEEE------EeeE--EEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEE
Q 026737 54 SRVNVEDIFVGR------DYGA--FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125 (234)
Q Consensus 54 ~~~~~G~iv~g~------~~G~--fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~L 125 (234)
+.+..|.+|.++ ..|. -|.+. +|+.|+|+.+++|.+.+.+|...+++||.|.+||+++|.++=-+.|
T Consensus 981 et~~~g~iV~~~V~~vt~rr~~Cv~v~ld-----~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~L 1055 (1299)
T KOG1856|consen 981 ETFYEGAIVPVTVTKVTHRRGICVRVRLD-----CGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVEL 1055 (1299)
T ss_pred hHhccCceEEEeeeEEEecccceeEEEec-----CCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhh
Confidence 357788888866 3333 34554 5799999999999999999999999999999999999988877888
Q ss_pred EEeec
Q 026737 126 SIKQL 130 (234)
Q Consensus 126 S~K~~ 130 (234)
|.|..
T Consensus 1056 s~r~s 1060 (1299)
T KOG1856|consen 1056 SCRTS 1060 (1299)
T ss_pred hhhhH
Confidence 88743
No 162
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.04 E-value=0.0017 Score=61.53 Aligned_cols=87 Identities=16% Similarity=0.149 Sum_probs=58.0
Q ss_pred hCCCCEEEEEEEEEeCCCCeEE-EEEeecccCcch-----hhhhcccc--cc-----cc------ceeeeecCCceEEE-
Q 026737 103 LNEGDEVRVKVIKIDREKSRIT-LSIKQLEEDPLL-----ETLEKVIP--QG-----LE------PYLKSFYKKMDDVR- 162 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~-LS~K~~~~~p~~-----~~~~~~~~--~G-----~~------G~fV~l~~gi~Gl~- 162 (234)
+++||.+++.|...+. +|+. .+.|+....-|. ..++. |. .| ++ |+||+| +|++|++
T Consensus 87 ~~vGD~ie~~I~~~~f--gRia~q~aKq~i~Qkire~ere~i~~e-yk~~~GeIV~G~V~ri~~~giiVDL-ggvea~LP 162 (470)
T PRK09202 87 AEVGDYIEEEIESVDF--GRIAAQTAKQVIVQKIREAERERVYEE-YKDRVGEIITGVVKRVERGNIIVDL-GRAEAILP 162 (470)
T ss_pred ccCCCeEEEEEccccC--ChHHHHHHHHHHHHHHHHHHHHHHHHH-HHhhcCCEEEEEEEEEecCCEEEEE-CCeEEEec
Confidence 7899999999988773 4443 333444333343 22333 32 33 32 899999 6999999
Q ss_pred EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc------chhhhc
Q 026737 163 ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL------IRKASK 216 (234)
Q Consensus 163 ~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~------i~ls~K 216 (234)
.|++. +.+.+++||+++|+|+++++ |-||++
T Consensus 163 ~sE~i-----------------------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt 199 (470)
T PRK09202 163 RKEQI-----------------------PRENFRPGDRVRAYVYEVRKEARGPQIILSRT 199 (470)
T ss_pred HHHcC-----------------------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence 45541 23478999999999999986 556654
No 163
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=96.02 E-value=0.057 Score=44.83 Aligned_cols=84 Identities=12% Similarity=0.147 Sum_probs=56.8
Q ss_pred CCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccccc
Q 026737 105 EGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSN 183 (234)
Q Consensus 105 vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~ 183 (234)
.|+.|.+.|++++. + |+||.+. -++||+ .|++-.+.-.-.+.-..|.-.
T Consensus 81 ~gEVV~GeVv~~~~-----------------------~------G~fV~ig-p~dglvh~sqi~dd~~~~d~~~~~~~g~ 130 (183)
T COG1095 81 RGEVVEGEVVEVVE-----------------------F------GAFVRIG-PLDGLVHVSQIMDDYIDYDEKNKVLIGE 130 (183)
T ss_pred cccEEEEEEEEEee-----------------------c------ceEEEec-cccccccHhhccCcccccCcccceeeec
Confidence 48888888888874 4 9999996 789999 777755521111222223322
Q ss_pred CCCCCcceeeeeeCCCEEEEEEeeecc---------chhhhcccc--cchhH
Q 026737 184 APPSGKKFTLLARAGRQVQEIQLSHSL---------IRKASKRHC--NEYWN 224 (234)
Q Consensus 184 ~~~~~~~~~~~~~~G~~v~~~vl~~d~---------i~ls~K~~~--~~p~~ 224 (234)
. =...+++||.|+++|+..+. |-|+|||-- .-+|-
T Consensus 131 ~------tk~~i~~gd~VR~RIv~~s~~~~~~~~~~I~lTmrq~~LGklew~ 176 (183)
T COG1095 131 E------TKRVLKVGDKVRARIVGVSLKSRRPRESKIGLTMRQPGLGKLEWI 176 (183)
T ss_pred c------cceEEecCCEEEEEEEEEecccCccccceEEEEeccccCCcchhh
Confidence 1 13389999999999999863 777888863 35663
No 164
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=95.70 E-value=0.0089 Score=57.37 Aligned_cols=68 Identities=29% Similarity=0.496 Sum_probs=57.8
Q ss_pred hcCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737 53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (234)
Q Consensus 53 ~~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~ 127 (234)
..+++.|..+.|+ +||+||+++ ..+.|++|-++++.. ..|.+|+++-+++..+-+.++.|.|..
T Consensus 117 ~~Dve~g~~Y~g~v~~v~~~GvFv~Ln-----~~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~ 185 (715)
T COG1107 117 MEDVEAGKYYKGIVSRVEKYGVFVELN-----SHVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEP 185 (715)
T ss_pred hhhcccceeeeccccchhhhcceeecC-----hhhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceee
Confidence 4578999999999 999999997 479999999998863 227899999999999998889888877
Q ss_pred eecc
Q 026737 128 KQLE 131 (234)
Q Consensus 128 K~~~ 131 (234)
..+.
T Consensus 186 ~~~~ 189 (715)
T COG1107 186 VGLD 189 (715)
T ss_pred cCCc
Confidence 6554
No 165
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=95.39 E-value=0.045 Score=39.70 Aligned_cols=36 Identities=25% Similarity=0.438 Sum_probs=23.9
Q ss_pred eeEEEEEceeccccccc--chhhhhCCCCEEEEEEEEE
Q 026737 81 HLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKI 116 (234)
Q Consensus 81 g~~glv~isels~~~~~--~~~~~~~vGd~v~vkVl~i 116 (234)
...|++|.+++-..... .+.+.|++||.|+|+|++.
T Consensus 45 ~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViSl 82 (82)
T PF10447_consen 45 PFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVISL 82 (82)
T ss_dssp SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEEE
T ss_pred ccEEEEEeeeecccccchhhHHhccCCCCEEEEEEeeC
Confidence 47899999987665443 4678899999999999974
No 166
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=95.29 E-value=0.012 Score=51.33 Aligned_cols=66 Identities=15% Similarity=0.186 Sum_probs=52.2
Q ss_pred ceeeeec--CCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhcccccc
Q 026737 149 PYLKSFY--KKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRHCNE 221 (234)
Q Consensus 149 G~fV~l~--~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~~~~ 221 (234)
|++|.|- ++++|++ +||++. +| + +.++.+.|+|..=-|.||.+|+ |-||.+++.++
T Consensus 31 Gayv~LlEYnniEGmiLlsELSr-RR---------I-------RSI~klirVGr~E~vvVlrVDkekGYIDLSkrrVs~e 93 (304)
T KOG2916|consen 31 GAYVKLLEYNNIEGMILLSELSR-RR---------I-------RSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVSPE 93 (304)
T ss_pred cceEeeeecCCcccchhhhHHHH-HH---------H-------HHHHHHHhcCCcceEEEEEEcCCCCceechhccCCHH
Confidence 9999985 4999999 899841 11 1 4466689999999999999998 99999999877
Q ss_pred hhHHHHhhcc
Q 026737 222 YWNVFHETAI 231 (234)
Q Consensus 222 p~~~~~~~~~ 231 (234)
--..-.++|.
T Consensus 94 d~~kC~Er~~ 103 (304)
T KOG2916|consen 94 DKEKCEERFA 103 (304)
T ss_pred HHHHHHHHHH
Confidence 6666666553
No 167
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=94.74 E-value=0.047 Score=39.59 Aligned_cols=44 Identities=5% Similarity=0.130 Sum_probs=33.7
Q ss_pred ceeeeecC-CceEEE--EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737 149 PYLKSFYK-KMDDVR--ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 210 (234)
Q Consensus 149 G~fV~l~~-gi~Gl~--~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~ 210 (234)
|++|.|-+ |++|++ .|+++.++. ++++..+ +|....|.|+.+|+
T Consensus 30 ~~YV~LleY~iegmIl~~selsr~ri-----------------rsi~kll-VGk~e~v~ViRVDk 76 (86)
T PHA02858 30 IFYVKLIDYGLEALIVNYVNVNADRA-----------------EKLKKKL-VGKTINVQVIRTDK 76 (86)
T ss_pred EEEEEEecCccceEEecHHHHhHHHH-----------------Hhhhhhh-cCCeeEEEEEEECC
Confidence 88999865 899998 477743221 3455577 99999999999997
No 168
>PRK11712 ribonuclease G; Provisional
Probab=94.74 E-value=0.23 Score=47.43 Aligned_cols=59 Identities=25% Similarity=0.511 Sum_probs=44.6
Q ss_pred cCCCCCcEEEEE-------EeeEEEEEecCCCcceeEEEEEceecccc------------cccchhhhhCCCCEEEEEEE
Q 026737 54 SRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKVI 114 (234)
Q Consensus 54 ~~~~~G~iv~g~-------~~G~fV~l~~~~g~~g~~glv~isels~~------------~~~~~~~~~~vGd~v~vkVl 114 (234)
....+|.+|.|+ =.+|||+|+ .+-.||+|++++... ......+.+++||.+-|.|.
T Consensus 34 ~~~~vGnIY~G~V~~v~pg~~AAFVdIG-----~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~ 108 (489)
T PRK11712 34 KRGIVGNIYKGRVSRVLPGMQAAFVDIG-----LDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVV 108 (489)
T ss_pred cccccccEEEEEEeecCCCCceeEEeeC-----CCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEE
Confidence 445789999999 336999998 478999999987321 11234566999999999998
Q ss_pred EEe
Q 026737 115 KID 117 (234)
Q Consensus 115 ~id 117 (234)
+--
T Consensus 109 Ke~ 111 (489)
T PRK11712 109 KDP 111 (489)
T ss_pred eCC
Confidence 754
No 169
>PRK10811 rne ribonuclease E; Reviewed
Probab=94.72 E-value=0.096 Score=53.36 Aligned_cols=61 Identities=26% Similarity=0.480 Sum_probs=46.1
Q ss_pred CCCCcEEEEE-------EeeEEEEEecCCCcceeEEEEEceeccccccc---------chhhhhCCCCEEEEEEEEEeCC
Q 026737 56 VNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ---------DIRDILNEGDEVRVKVIKIDRE 119 (234)
Q Consensus 56 ~~~G~iv~g~-------~~G~fV~l~~~~g~~g~~glv~isels~~~~~---------~~~~~~~vGd~v~vkVl~id~~ 119 (234)
..+|.||.|+ =.++||+|+ .+..||+|+++....++. .....+++||.|-|.|.+--..
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDIG-----~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~g 110 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDYG-----AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERG 110 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEec-----CCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccC
Confidence 3589999999 447999998 368999999998654322 2245688999999999885543
Q ss_pred CC
Q 026737 120 KS 121 (234)
Q Consensus 120 ~~ 121 (234)
++
T Consensus 111 tK 112 (1068)
T PRK10811 111 NK 112 (1068)
T ss_pred CC
Confidence 33
No 170
>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=94.69 E-value=0.077 Score=39.13 Aligned_cols=79 Identities=13% Similarity=0.058 Sum_probs=48.9
Q ss_pred hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
.++||.|-++|.++.. .+..+.+-.+.. ..+.....|++ +|+.+.. .
T Consensus 4 P~~GDiVig~V~~v~~--~~~~v~I~~v~~-------------------~~l~~~~~g~l~~~dv~~~-~---------- 51 (92)
T cd05791 4 PKVGSIVIARVTRINP--RFAKVDILCVGG-------------------RPLKESFRGVIRKEDIRAT-E---------- 51 (92)
T ss_pred CCCCCEEEEEEEEEcC--CEEEEEEEEecC-------------------eecCCCcccEEEHHHcccc-c----------
Confidence 3789999999999863 344443322210 12234567888 5654311 0
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcc
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKR 217 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~ 217 (234)
....++.+.+++||-|+|+|++++. +.||++.
T Consensus 52 ----~d~~~~~~~f~~GDiV~AkVis~~~~~~~~Lst~~ 86 (92)
T cd05791 52 ----KDKVEMYKCFRPGDIVRAKVISLGDASSYYLSTAE 86 (92)
T ss_pred ----cchHHHHhhcCCCCEEEEEEEEcCCCCCcEEEecC
Confidence 0112356689999999999999963 6666653
No 171
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.09 E-value=0.15 Score=47.89 Aligned_cols=67 Identities=9% Similarity=0.050 Sum_probs=49.9
Q ss_pred CCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCC---CeEEEEE
Q 026737 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK---SRITLSI 127 (234)
Q Consensus 56 ~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~---~ri~LS~ 127 (234)
-++|+++.|+ ..+++|+++..-|..+++|++|.++.. |.+.|++||.++|.|.++.... -+|.||+
T Consensus 150 ~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~y~~Gdrika~i~~V~~~~~kGpqIilSR 223 (449)
T PRK12329 150 DLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDNYRANATFKVFLKEVSEGPRRGPQLFVSR 223 (449)
T ss_pred HhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCcCCCCCEEEEEEEEeecCCCCCCEEEEEc
Confidence 4789999999 557999983100101389999988754 5577999999999999998652 4688887
Q ss_pred e
Q 026737 128 K 128 (234)
Q Consensus 128 K 128 (234)
.
T Consensus 224 t 224 (449)
T PRK12329 224 A 224 (449)
T ss_pred C
Confidence 3
No 172
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=93.72 E-value=0.17 Score=46.54 Aligned_cols=57 Identities=18% Similarity=0.091 Sum_probs=44.6
Q ss_pred hhh--CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEEE-cccccccccccccc
Q 026737 101 DIL--NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVRI-TRQGFEKRVVSQDL 177 (234)
Q Consensus 101 ~~~--~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~~-s~~~~~~~~~~~~~ 177 (234)
+.| +.|+.|.++|.+++. . |+||++ +|++|+++ +++.
T Consensus 128 ~ef~~k~GeiV~G~V~~~~~-----------------------~------~~~Vdl-g~vEa~LP~~E~i---------- 167 (362)
T PRK12327 128 NEFSEREGDIVTGVVQRRDN-----------------------R------FVYVNL-GKIEAVLPPAEQI---------- 167 (362)
T ss_pred HHHHHhcCCEEEEEEEEEeC-----------------------C------cEEEEe-CCeEEEecHHHcC----------
Confidence 336 899999999998763 2 789999 57999995 4431
Q ss_pred ccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737 178 QLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 210 (234)
Q Consensus 178 ~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~ 210 (234)
+.+.+++||++++.|++++.
T Consensus 168 -------------p~e~~~~Gd~Ika~V~~V~~ 187 (362)
T PRK12327 168 -------------PGETYKHGDRIKVYVVKVEK 187 (362)
T ss_pred -------------CCCCCCCCCEEEEEEEEEec
Confidence 13468999999999999984
No 173
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=93.51 E-value=0.22 Score=46.63 Aligned_cols=79 Identities=13% Similarity=0.096 Sum_probs=50.1
Q ss_pred chhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccc
Q 026737 98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQD 176 (234)
Q Consensus 98 ~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~ 176 (234)
.+.....+|+.+.++|.++.+ .+. ||||++..|-.||+ +++.......
T Consensus 18 ~~~~~~~vGnIY~GrV~~i~p-----------------------~l~----aAFVdiG~~k~gfL~~~d~~~~~~~---- 66 (414)
T TIGR00757 18 RPKSRQLKGNIYKGRVTRILP-----------------------SLQ----AAFVDIGLEKNGFLHASDIGPNYEC---- 66 (414)
T ss_pred cCcCcCCCCCEEEEEEeeecC-----------------------CCc----eEEEEcCCCceEEEEHHHcCchhhc----
Confidence 344445789999999998875 111 89999999999999 7776321000
Q ss_pred cccccccCCCCCcceeeeeeCCCEEEEEEeee
Q 026737 177 LQLWLSNAPPSGKKFTLLARAGRQVQEIQLSH 208 (234)
Q Consensus 177 ~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~ 208 (234)
... .........++...+++||.|-|.|.+-
T Consensus 67 ~~~-~~~~~~~~~~i~~~l~~G~~IlVQV~Ke 97 (414)
T TIGR00757 67 LAP-AEAKREAGPSISELLRPGQSVLVQVVKE 97 (414)
T ss_pred ccc-ccccccccCCHHHhCcCCCEEEEEEeeC
Confidence 000 0000000124566899999999998873
No 174
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=93.04 E-value=0.25 Score=45.11 Aligned_cols=64 Identities=16% Similarity=0.140 Sum_probs=48.0
Q ss_pred hhh--CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccc-eeeeecCCceEEE-Eccccccccccccc
Q 026737 101 DIL--NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEP-YLKSFYKKMDDVR-ITRQGFEKRVVSQD 176 (234)
Q Consensus 101 ~~~--~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G-~fV~l~~gi~Gl~-~s~~~~~~~~~~~~ 176 (234)
+.| +.|+.|.++|.+++. . | +||++ +|++|++ .+++.
T Consensus 125 ~ey~~k~GeiV~G~V~~v~~-----------------------~------g~v~Vdi-G~~ea~LP~~E~i--------- 165 (341)
T TIGR01953 125 DEFSSKEGEIISGTVKRVNR-----------------------R------GNLYVEL-GKTEGILPKKEQI--------- 165 (341)
T ss_pred HHHHhhcCCEEEEEEEEEec-----------------------C------CcEEEEE-CCeEEEecHHHcC---------
Confidence 345 499999999999864 1 4 58999 5999999 45431
Q ss_pred cccccccCCCCCcceeeeeeCCCEEEEEEeeecc------chhhhcc
Q 026737 177 LQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL------IRKASKR 217 (234)
Q Consensus 177 ~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~------i~ls~K~ 217 (234)
+.+.+++||++++.|++++. |-||.+.
T Consensus 166 --------------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~ 198 (341)
T TIGR01953 166 --------------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTH 198 (341)
T ss_pred --------------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCc
Confidence 12358999999999999984 6666653
No 175
>PRK05054 exoribonuclease II; Provisional
Probab=91.09 E-value=0.87 Score=45.06 Aligned_cols=55 Identities=5% Similarity=-0.110 Sum_probs=34.1
Q ss_pred ceeeeecC-CceEEE-Eccccccc--cccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737 149 PYLKSFYK-KMDDVR-ITRQGFEK--RVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 210 (234)
Q Consensus 149 G~fV~l~~-gi~Gl~-~s~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~ 210 (234)
|+||+|++ |++||+ +|.+..+. ..-.++- ..+... + ...++.||+|+|+|.++|.
T Consensus 576 G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~-~~~~~~----~--~~~~~lGd~V~V~v~~vd~ 634 (644)
T PRK05054 576 GMRVRLLENGAVAFIPASFLHAVRDELVCNQEN-GTVQIK----G--ETVYKLGDVIDVTLAEVRM 634 (644)
T ss_pred cEEEEEeCCceEEEEEccccCCCccceEEcccc-ceEEEe----C--CEEEcCCCEEEEEEEEEcc
Confidence 99999976 899999 77663221 1000000 000000 1 1378999999999999985
No 176
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=88.98 E-value=1.9 Score=35.98 Aligned_cols=81 Identities=19% Similarity=0.250 Sum_probs=48.9
Q ss_pred hhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeec-CCceEEEEccccccccccccccc
Q 026737 100 RDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY-KKMDDVRITRQGFEKRVVSQDLQ 178 (234)
Q Consensus 100 ~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~-~gi~Gl~~s~~~~~~~~~~~~~~ 178 (234)
....+.|+.|-++|+++.. .+..+.+-.++..+ -++. .+.-++.+|+.+..
T Consensus 59 ~~~~K~GdiV~grV~~v~~--~~a~V~i~~ve~~~-----------------r~~~~~~~~~ihvs~~~~~--------- 110 (188)
T COG1096 59 PPLPKGGDIVYGRVTDVRE--QRALVRIVGVEGKE-----------------RELATSGAADIHVSQVRDG--------- 110 (188)
T ss_pred CCCCCCCCEEEEEEeeccc--eEEEEEEEEEeccc-----------------ccCCCCceeeEEEEecccc---------
Confidence 3457889999999999863 34443332222111 0111 13333446665321
Q ss_pred cccccCCCCCcceeeeeeCCCEEEEEEeee-ccchhhhc
Q 026737 179 LWLSNAPPSGKKFTLLARAGRQVQEIQLSH-SLIRKASK 216 (234)
Q Consensus 179 ~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~-d~i~ls~K 216 (234)
+. .++++.+++||-|+|+|++. +++.||.+
T Consensus 111 -~~-------~~~~d~f~~GDivrA~Vis~~~~~~Lst~ 141 (188)
T COG1096 111 -YV-------EKLSDAFRIGDIVRARVISTGDPIQLSTK 141 (188)
T ss_pred -cc-------cccccccccccEEEEEEEecCCCeEEEec
Confidence 11 34667999999999999998 66666654
No 177
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=87.92 E-value=3.3 Score=35.90 Aligned_cols=73 Identities=12% Similarity=0.046 Sum_probs=49.0
Q ss_pred hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccccccccccc
Q 026737 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWL 181 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~ 181 (234)
.++||.|-.+|+++-+. +-.|++..-..+++ +|++- |-
T Consensus 62 P~~gD~VIG~I~~v~~~-----------------------------~W~VDI~sp~~A~L~ls~~~------------~r 100 (239)
T COG1097 62 PEVGDVVIGKIIEVGPS-----------------------------GWKVDIGSPYPALLSLSDFL------------RR 100 (239)
T ss_pred CCCCCEEEEEEEEEccc-----------------------------ceEEEcCCccceEeehhhhh------------cc
Confidence 46799999999988541 33577766677777 66651 11
Q ss_pred ccCCCCCcceeeeeeCCCEEEEEEeeecc---chhhhcc
Q 026737 182 SNAPPSGKKFTLLARAGRQVQEIQLSHSL---IRKASKR 217 (234)
Q Consensus 182 ~~~~~~~~~~~~~~~~G~~v~~~vl~~d~---i~ls~K~ 217 (234)
.. +....++...+++||-|-|+|..+|. ..|.+|.
T Consensus 101 ~~-~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~ 138 (239)
T COG1097 101 KF-ENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKD 138 (239)
T ss_pred cc-cccccccccccccCCEEEEEEEEccCCCceEEEeec
Confidence 10 11124566799999999999999997 5555543
No 178
>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=87.07 E-value=1.7 Score=30.73 Aligned_cols=53 Identities=13% Similarity=0.070 Sum_probs=32.1
Q ss_pred ceeeeecC-CceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEE-EEEEeeecc--chhhhc
Q 026737 149 PYLKSFYK-KMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV-QEIQLSHSL--IRKASK 216 (234)
Q Consensus 149 G~fV~l~~-gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v-~~~vl~~d~--i~ls~K 216 (234)
+++|++.+ |+.|++ ...++. ..-.++. .| .-+++||++ ++.+|.... |.++.|
T Consensus 15 ~l~v~l~~~~l~a~l~~~HLsD-~~~k~~~--~~------------~klrvG~~L~~~lvL~~~~r~i~lt~K 72 (72)
T cd05699 15 GLEVAILPEEIRAFLPTMHLSD-HVSNCPL--LW------------HCLQEGDTIPNLMCLSNYKGRIILTKK 72 (72)
T ss_pred cEEEEecCCCcEEEEEccccCC-chhhCHH--HH------------hhhhcCCCccceEEEeccccEEEEecC
Confidence 77899988 999999 444432 1111111 12 146999999 888882221 555543
No 179
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=86.03 E-value=2 Score=42.95 Aligned_cols=56 Identities=14% Similarity=0.074 Sum_probs=36.8
Q ss_pred ceeeeecC-CceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737 149 PYLKSFYK-KMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 210 (234)
Q Consensus 149 G~fV~l~~-gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~ 210 (234)
|+||+|.+ |++|++ +|.+..+-....+.- .. ....+....++.||.|++++.+++.
T Consensus 637 g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~--~~----l~~~~~~~~~~lgd~v~v~v~~v~~ 694 (706)
T COG0557 637 GFFVELPELGLEGLVHISSLPDDYYHFDERG--QA----LVGEKSGKVYRLGDEVKVKVTSVDL 694 (706)
T ss_pred cEEEEecccccccceEcccCCCceeeecccc--ce----eeccccccccccCCEEEEEEEEEcc
Confidence 99999977 799999 888743222111000 00 0113445578999999999999985
No 180
>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=85.85 E-value=7.6 Score=28.20 Aligned_cols=68 Identities=6% Similarity=0.066 Sum_probs=41.3
Q ss_pred CCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccc-cccccccc
Q 026737 105 EGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVS-QDLQLWLS 182 (234)
Q Consensus 105 vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~-~~~~~~~~ 182 (234)
.|+.+.++|.++++ . |+|+.+ +.+++|+ .+.+-.+--... +..-.|.
T Consensus 1 kgEVi~g~V~~v~~-----------------------~------G~~v~~-Gpl~~f~~~~~ip~~~~~~~~~~~~~~~- 49 (88)
T cd04462 1 KGEVVDAIVTSVNK-----------------------T------GFFAEV-GPLSIFISRHLIPSDMEFDPNASPPCFT- 49 (88)
T ss_pred CCcEEEEEEEEEec-----------------------c------EEEEEE-cCceEEEEeeecCccceECCcCCCCeEe-
Confidence 47888888888875 3 889998 4567776 333211100001 1111342
Q ss_pred cCCCCCcceeeeeeCCCEEEEEEeeec
Q 026737 183 NAPPSGKKFTLLARAGRQVQEIQLSHS 209 (234)
Q Consensus 183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d 209 (234)
.+ -...++.|+.|+++|+.+.
T Consensus 50 -~~-----~~~~i~~g~~VR~rV~~v~ 70 (88)
T cd04462 50 -SN-----EDIVIKKDTEVRLKIIGTR 70 (88)
T ss_pred -CC-----CcEEECCCCEEEEEEEEEE
Confidence 11 1458999999999998885
No 181
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=84.40 E-value=3.9 Score=33.36 Aligned_cols=60 Identities=18% Similarity=0.236 Sum_probs=41.1
Q ss_pred cCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecc----cccccc-------hhhhhCCCCEEEEEEEEEe
Q 026737 54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS----WDLIQD-------IRDILNEGDEVRVKVIKID 117 (234)
Q Consensus 54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels----~~~~~~-------~~~~~~vGd~v~vkVl~id 117 (234)
-++-.|+++.|+ +.|+|++++ .++.++.---.. ...-.+ -.+..++|.+|++||+...
T Consensus 77 FkpfKGEVvdgvV~~Vnk~G~F~~~G------Pl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr 150 (170)
T KOG3298|consen 77 FKPFKGEVVDGVVTKVNKMGVFARSG------PLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTR 150 (170)
T ss_pred EeecCCcEEEEEEEEEeeeeEEEecc------ceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEE
Confidence 356789999998 899999997 477776433222 111112 1235789999999999886
Q ss_pred CC
Q 026737 118 RE 119 (234)
Q Consensus 118 ~~ 119 (234)
.+
T Consensus 151 ~~ 152 (170)
T KOG3298|consen 151 VD 152 (170)
T ss_pred Ee
Confidence 53
No 182
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=82.76 E-value=4.8 Score=39.86 Aligned_cols=55 Identities=4% Similarity=-0.028 Sum_probs=32.9
Q ss_pred ceeeeec-CCceEEE-EccccccccccccccccccccCCCCCcce--eeeeeCCCEEEEEEeeecc
Q 026737 149 PYLKSFY-KKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKF--TLLARAGRQVQEIQLSHSL 210 (234)
Q Consensus 149 G~fV~l~-~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~G~~v~~~vl~~d~ 210 (234)
|+||+|. .|++||+ ++.+.... + .|.-..+.....+ ...++.||+|+|+|.++|.
T Consensus 572 g~~v~l~~~~~~g~v~~~~l~~~~-----~--~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~ 630 (639)
T TIGR02062 572 GMRVRLLENGAIAFIPAAFLHANR-----E--ELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRM 630 (639)
T ss_pred cEEEEEecCceEEEEEhhhcCCCC-----c--ceEEcccccEEEEeccEEEecCCEEEEEEEEecc
Confidence 9999995 4899999 66653210 0 0100000000001 1269999999999999985
No 183
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=80.77 E-value=2.5 Score=35.97 Aligned_cols=74 Identities=24% Similarity=0.367 Sum_probs=52.3
Q ss_pred hcCCCCCcEEEEE-------EeeEEEEEecCCCcceeEEEEEceecccccccch-hh---hh--CCCCEEEEEEEEEeCC
Q 026737 53 SSRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-RD---IL--NEGDEVRVKVIKIDRE 119 (234)
Q Consensus 53 ~~~~~~G~iv~g~-------~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~-~~---~~--~vGd~v~vkVl~id~~ 119 (234)
+.++++|+++-|+ -||+||+++ +.|....++++|..+|....-..| ++ .| -.-..++|-|.++|..
T Consensus 70 l~~~~~Gdv~vGrl~~l~~vgyg~yvdig-V~~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~evnk~ 148 (247)
T COG4044 70 LSKVEEGDVYVGRLIDLGKVGYGAYVDIG-VLGPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEVNKL 148 (247)
T ss_pred cccCCCCcEEEEEEeeeccceeEEEcccc-ccCCCcccccccHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEeccch
Confidence 3788999999999 889999996 344235689999998876554444 22 22 2346788889888876
Q ss_pred CCeEEEEE
Q 026737 120 KSRITLSI 127 (234)
Q Consensus 120 ~~ri~LS~ 127 (234)
.+.|...+
T Consensus 149 ~~EIea~l 156 (247)
T COG4044 149 AQEIEARL 156 (247)
T ss_pred hhhhhhhh
Confidence 66665443
No 184
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=79.50 E-value=2.5 Score=40.53 Aligned_cols=72 Identities=24% Similarity=0.379 Sum_probs=51.2
Q ss_pred hhhhcCCCCCcEEEEE-----E--eeEEEEEecCCCcceeEEEEEceecccccccch-----hhhhCCCCEEEEEEEEEe
Q 026737 50 NKYSSRVNVEDIFVGR-----D--YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-----RDILNEGDEVRVKVIKID 117 (234)
Q Consensus 50 ~~~~~~~~~G~iv~g~-----~--~G~fV~l~~~~g~~g~~glv~isels~~~~~~~-----~~~~~vGd~v~vkVl~id 117 (234)
+.-.....+|.+|.|+ + -.+||+++ ..-.||+|++++.+ +...+ ...++.||.+-+.|+.-.
T Consensus 29 e~~~~~~~~gniy~grv~~i~p~~~aafvdig-----~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~ 102 (487)
T COG1530 29 ERGAKEQIVGNIYKGRVTRVLPSLEAAFVDIG-----LERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEP 102 (487)
T ss_pred ecCCcEeeecCceEEEecccCccchhheeecc-----CCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeec
Confidence 3334456789999999 2 25899997 25789999999998 54433 347899999999998765
Q ss_pred CCCCeEEEEE
Q 026737 118 REKSRITLSI 127 (234)
Q Consensus 118 ~~~~ri~LS~ 127 (234)
..++--.||.
T Consensus 103 ~G~Kga~lT~ 112 (487)
T COG1530 103 RGTKGARLTT 112 (487)
T ss_pred Ccccccccee
Confidence 4333333333
No 185
>PRK10811 rne ribonuclease E; Reviewed
Probab=77.94 E-value=6.2 Score=40.80 Aligned_cols=70 Identities=11% Similarity=0.090 Sum_probs=45.2
Q ss_pred CCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccccccccccc
Q 026737 104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLS 182 (234)
Q Consensus 104 ~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~ 182 (234)
.+|+.+.++|.++.+ |+-++||+|..|..|++ +++........ .+..
T Consensus 37 ~vGnIYkGkVenIvP---------------------------GInAAFVDIG~gknGFL~L~Di~~~~f~~-----~~~~ 84 (1068)
T PRK10811 37 KKANIYKGKITRIEP---------------------------SLEAAFVDYGAERHGFLPLKEIAREYFPA-----NYSA 84 (1068)
T ss_pred CccceEEEEEecccC---------------------------CcceeEEEecCCcceEEEhhhcccccccc-----cccc
Confidence 579999999977754 22289999999999999 66652111000 0000
Q ss_pred cCCCCCcceeeeeeCCCEEEEEEeee
Q 026737 183 NAPPSGKKFTLLARAGRQVQEIQLSH 208 (234)
Q Consensus 183 ~~~~~~~~~~~~~~~G~~v~~~vl~~ 208 (234)
....+++..++.||.|-|-|.+-
T Consensus 85 ---~~~~~i~~~Lk~GqeILVQV~KE 107 (1068)
T PRK10811 85 ---HGRPNIKDVLREGQEVIVQIDKE 107 (1068)
T ss_pred ---ccccccccccCCCCEEEEEEeec
Confidence 00123456789999998888774
No 186
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=77.40 E-value=7.7 Score=30.14 Aligned_cols=56 Identities=16% Similarity=0.197 Sum_probs=34.3
Q ss_pred CCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccc-------------cccchhhhhCCCCEEEEEEEEEeC
Q 026737 58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-------------LIQDIRDILNEGDEVRVKVIKIDR 118 (234)
Q Consensus 58 ~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~-------------~~~~~~~~~~vGd~v~vkVl~id~ 118 (234)
+|+++.|+ ..|+.|.|+ .--+-+||-+.|... +-..-.-++..|+.|+.||.++..
T Consensus 3 ~gEvl~g~I~~~~~~Gi~vslg-----FFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f 76 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAEGIRVSLG-----FFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF 76 (122)
T ss_dssp TT-EEEEEEEEEETTEEEEEEC-----CEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred CCCEEEEEEEecCCCcEEEEec-----ccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence 57777777 667888875 234677777655421 112333447899999999998875
No 187
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=72.13 E-value=21 Score=29.39 Aligned_cols=69 Identities=4% Similarity=0.016 Sum_probs=44.0
Q ss_pred CCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccc-ccccccccc
Q 026737 105 EGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVV-SQDLQLWLS 182 (234)
Q Consensus 105 vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~-~~~~~~~~~ 182 (234)
.|+.+.++|.++++ . |+||++. -+++++ .+.+..+-.-. .+....|..
T Consensus 81 ~gEVv~g~V~~v~~-----------------------~------G~~v~~G-p~~ifI~~~~l~~~~~fd~~~~~~~~~~ 130 (176)
T PTZ00162 81 KDEVLDAIVTDVNK-----------------------L------GFFAQAG-PLKAFVSRSAIPPDFVYDSDSAYPCYIS 130 (176)
T ss_pred CCCEEEEEEEEEec-----------------------c------eEEEEee-CeEEEEcHHHCCCccEECCCCCcceEec
Confidence 58888888888874 3 9999995 455888 56663221110 111113431
Q ss_pred cCCCCCcceeeeeeCCCEEEEEEeeec
Q 026737 183 NAPPSGKKFTLLARAGRQVQEIQLSHS 209 (234)
Q Consensus 183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d 209 (234)
. + -...++.|+.|+++|+.+.
T Consensus 131 ~---~---~~~~i~~g~~VR~rV~~v~ 151 (176)
T PTZ00162 131 S---D---GQIQIKPNTEVRLRLQGVR 151 (176)
T ss_pred C---C---CcEEECCCCEEEEEEEEEE
Confidence 1 1 1458999999999998885
No 188
>PRK11712 ribonuclease G; Provisional
Probab=71.20 E-value=12 Score=35.90 Aligned_cols=81 Identities=9% Similarity=-0.003 Sum_probs=48.3
Q ss_pred ccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Eccccccccccc
Q 026737 96 IQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVVS 174 (234)
Q Consensus 96 ~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~~ 174 (234)
+........+|+.+.++|.++.+ |+-+|||++..+-.|++ +++.....
T Consensus 29 iE~~~~~~~vGnIY~G~V~~v~p---------------------------g~~AAFVdIG~~k~gFL~~~d~~~~~---- 77 (489)
T PRK11712 29 IEREAKRGIVGNIYKGRVSRVLP---------------------------GMQAAFVDIGLDKAAFLHASDIVPHT---- 77 (489)
T ss_pred EecCCcccccccEEEEEEeecCC---------------------------CCceeEEeeCCCccEEEEhhhccchh----
Confidence 33333445589999999988764 12289999999999999 66542100
Q ss_pred cccccccccCCCCCcceeeeeeCCCEEEEEEeee
Q 026737 175 QDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSH 208 (234)
Q Consensus 175 ~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~ 208 (234)
+.++. .........+++..+++||.|-|.|.+-
T Consensus 78 ~~~~~-~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke 110 (489)
T PRK11712 78 ECVAG-EEQKQFVVRDISELVRQGQDIMVQVVKD 110 (489)
T ss_pred hhccc-ccccccccccHHHhccCCCEEEEEEEeC
Confidence 00000 0000000123566799999998887765
No 189
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=71.19 E-value=12 Score=31.01 Aligned_cols=72 Identities=17% Similarity=0.127 Sum_probs=44.0
Q ss_pred hCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEEEccccccccccccccccccc
Q 026737 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVRITRQGFEKRVVSQDLQLWLS 182 (234)
Q Consensus 103 ~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~~s~~~~~~~~~~~~~~~~~~ 182 (234)
...|+.|.++|..++...-++.+.- +|. +-+.+-..|++.++. + +
T Consensus 66 P~~G~IVtarV~~i~~rfAkv~I~~-----------------V~d----~~lk~~Frglirkqd----------v----R 110 (193)
T KOG3409|consen 66 PFVGAIVTARVSRINLRFAKVDILS-----------------VGD----KPLKKSFRGLIRKQD----------V----R 110 (193)
T ss_pred CccCcEEEEEEEeeccceeeEEEEE-----------------EcC----EEhhhhhcceeehhh----------c----c
Confidence 4689999999999875222222111 111 125567888886543 1 1
Q ss_pred cCCCCCcceeeeeeCCCEEEEEEeeec
Q 026737 183 NAPPSGKKFTLLARAGRQVQEIQLSHS 209 (234)
Q Consensus 183 ~~~~~~~~~~~~~~~G~~v~~~vl~~d 209 (234)
..+++.-++-..|++||-|.|+|++.+
T Consensus 111 ~tEkdrv~v~ksFrPgDiVlAkVis~~ 137 (193)
T KOG3409|consen 111 ATEKDRVKVYKSFRPGDIVLAKVISLG 137 (193)
T ss_pred ccccchhhhhhccCCCcEEEEEEeecC
Confidence 111222345568999999999999954
No 190
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=70.33 E-value=44 Score=27.74 Aligned_cols=70 Identities=21% Similarity=0.220 Sum_probs=43.0
Q ss_pred CCCCcEEEEE------EeeEEEEEecCCC---cceeEEEEEceeccccc--ccchhhhhCCCCEEEEEEEEEeCCCCeEE
Q 026737 56 VNVEDIFVGR------DYGAFIHLRFPDG---LYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREKSRIT 124 (234)
Q Consensus 56 ~~~G~iv~g~------~~G~fV~l~~~~g---~~g~~glv~isels~~~--~~~~~~~~~vGd~v~vkVl~id~~~~ri~ 124 (234)
+..|++|.++ .| +-|+|--++. .....|+||..++--.. --++-+.|++||.|.++|++... .....
T Consensus 66 P~~G~IVtarV~~i~~rf-Akv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~-~~~y~ 143 (193)
T KOG3409|consen 66 PFVGAIVTARVSRINLRF-AKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGD-GSNYL 143 (193)
T ss_pred CccCcEEEEEEEeeccce-eeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCC-CCcEE
Confidence 6789999998 22 3333321000 01468999987653221 12455668999999999999654 45555
Q ss_pred EEE
Q 026737 125 LSI 127 (234)
Q Consensus 125 LS~ 127 (234)
||.
T Consensus 144 LTt 146 (193)
T KOG3409|consen 144 LTT 146 (193)
T ss_pred EEE
Confidence 554
No 191
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=66.47 E-value=5.2 Score=41.81 Aligned_cols=50 Identities=6% Similarity=0.043 Sum_probs=35.6
Q ss_pred eeecCCceEEE-EccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc----chhhhccc
Q 026737 152 KSFYKKMDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKRH 218 (234)
Q Consensus 152 V~l~~gi~Gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~----i~ls~K~~ 218 (234)
|.++.|++|+| .++.+ ++.+ .++..-+++||.|.++|+++|. +-||.+..
T Consensus 1006 v~ld~G~~g~i~~~~~S-d~~v----------------~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~s 1060 (1299)
T KOG1856|consen 1006 VRLDCGVTGFILAKNLS-DRDV----------------RRPENRVKVGQTVYCKVIKIDKERFSVELSCRTS 1060 (1299)
T ss_pred EEecCCCceeeeccccC-hhhc----------------cCHHHhhccCceEEEEeeeeeHhhhhhhhhhhhH
Confidence 57788999999 44442 2111 3455678999999999999997 55565544
No 192
>PRK15464 cold shock-like protein CspH; Provisional
Probab=60.50 E-value=19 Score=25.08 Aligned_cols=42 Identities=26% Similarity=0.276 Sum_probs=29.5
Q ss_pred EeeE-EEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEE
Q 026737 66 DYGA-FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (234)
Q Consensus 66 ~~G~-fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~ 115 (234)
+.|. |+.-+ +| +-+.|+|++.+...-. ..+.+||.|+..+..
T Consensus 15 ~KGfGFI~~~--~g--~~DvFvH~s~l~~~g~----~~l~~G~~V~f~v~~ 57 (70)
T PRK15464 15 KSGKGFIIPS--DG--RKEVQVHISAFTPRDA----EVLIPGLRVEFCRVN 57 (70)
T ss_pred CCCeEEEccC--CC--CccEEEEehhehhcCC----CCCCCCCEEEEEEEE
Confidence 4454 77665 22 5799999999864422 237899999988855
No 193
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=60.13 E-value=30 Score=25.33 Aligned_cols=54 Identities=22% Similarity=0.207 Sum_probs=37.6
Q ss_pred EeeEE-EEEecCCCcceeEEEEEceecc-cccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737 66 DYGAF-IHLRFPDGLYHLTGLVHVSEVS-WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (234)
Q Consensus 66 ~~G~f-V~l~~~~g~~g~~glv~isels-~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~ 129 (234)
..+.| |.|+ +|..-+.|+|--- ..++. +-+||.|.+.+-..|..+++|..-.|.
T Consensus 18 p~~~frV~Le-----nG~~vla~isGKmR~~rIr-----Il~GD~V~VE~spYDltkGRIiyR~~~ 73 (87)
T PRK12442 18 PDSRFRVTLE-----NGVEVGAYASGRMRKHRIR-----ILAGDRVTLELSPYDLTKGRINFRHKD 73 (87)
T ss_pred CCCEEEEEeC-----CCCEEEEEeccceeeeeEE-----ecCCCEEEEEECcccCCceeEEEEecC
Confidence 44444 4665 2577777776221 11222 568999999999999999999998874
No 194
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=58.72 E-value=14 Score=34.28 Aligned_cols=27 Identities=7% Similarity=0.198 Sum_probs=24.0
Q ss_pred CCCEEEEEEEEEeCCCC---EEEEEechhh
Q 026737 22 TGSIISVKVIQANEEMK---KLVFSEKDAV 48 (234)
Q Consensus 22 vG~~v~~~Vi~id~~~~---~i~lS~k~~~ 48 (234)
+|+.+.|+|.+++...+ .+.||+....
T Consensus 179 ~Gdrik~~i~~V~~~~k~gp~IilSRt~p~ 208 (374)
T PRK12328 179 VGDVVKAVLKRVKIDKNNGILIELSRTSPK 208 (374)
T ss_pred CCCEEEEEEEEEecCCCCCCEEEEEcCCHH
Confidence 99999999999998765 8999998764
No 195
>COG1551 CsrA RNA-binding global regulator CsrA [Signal transduction mechanisms]
Probab=57.46 E-value=7.8 Score=27.25 Aligned_cols=29 Identities=14% Similarity=0.074 Sum_probs=23.7
Q ss_pred cceeeeeeCCCEEEEEEeeecc--chhhhcc
Q 026737 189 KKFTLLARAGRQVQEIQLSHSL--IRKASKR 217 (234)
Q Consensus 189 ~~~~~~~~~G~~v~~~vl~~d~--i~ls~K~ 217 (234)
++.++.+..||.+.+.|++++. +++|+.+
T Consensus 6 Rk~~Esi~IgddI~itVl~i~gnqVkiGi~A 36 (73)
T COG1551 6 RKVGESIMIGDDIEITVLSIKGNQVKIGINA 36 (73)
T ss_pred eecCceEEecCCeEEEEEEEcCCeEEEeecC
Confidence 3456688999999999999987 7777764
No 196
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=57.31 E-value=26 Score=33.60 Aligned_cols=75 Identities=8% Similarity=0.029 Sum_probs=51.0
Q ss_pred cccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeecccCcchhhhhccccccccceeeeecCCceEEE-Ecccccccccc
Q 026737 95 LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMDDVR-ITRQGFEKRVV 173 (234)
Q Consensus 95 ~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~~p~~~~~~~~~~~G~~G~fV~l~~gi~Gl~-~s~~~~~~~~~ 173 (234)
.+....+...+|+.++++|.++.+. +. .|||++..+-.||+ .++...
T Consensus 27 ~ie~~~~~~~~gniy~grv~~i~p~-----------------------~~----aafvdig~~r~gfl~~~~~~~----- 74 (487)
T COG1530 27 DIERGAKEQIVGNIYKGRVTRVLPS-----------------------LE----AAFVDIGLERNGFLHLSEIVP----- 74 (487)
T ss_pred EEecCCcEeeecCceEEEecccCcc-----------------------ch----hheeeccCCccceEEecccch-----
Confidence 3444445566788888888877751 11 78999999999999 677632
Q ss_pred ccccccccccCCCCCcceeeeeeCCCEEEEEEeeec
Q 026737 174 SQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHS 209 (234)
Q Consensus 174 ~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d 209 (234)
+.... ...+++..++.||.+-+.+++-.
T Consensus 75 ------~~~~~--~~~~i~~~lr~~~~~~Vqv~ke~ 102 (487)
T COG1530 75 ------YFRAV--LEEKIKVRLRGGQATLVQVVKEP 102 (487)
T ss_pred ------hhhhc--ccccceeeecCCceEEEEEEeec
Confidence 11111 11357789999999888777764
No 197
>cd05700 S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=55.25 E-value=16 Score=24.94 Aligned_cols=27 Identities=19% Similarity=0.363 Sum_probs=21.4
Q ss_pred hhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737 101 DILNEGDEVRVKVIKIDREKSRITLSI 127 (234)
Q Consensus 101 ~~~~vGd~v~vkVl~id~~~~ri~LS~ 127 (234)
..+.+||++++.|+.+|.-+.++.+|+
T Consensus 39 ~nl~pGqK~kaviLhvD~l~~~VhVSl 65 (65)
T cd05700 39 VNVTPGCKLKAVILHVDFVKSQVHVSL 65 (65)
T ss_pred eecCCCceeEEEEEEEeeEEeEEEEeC
Confidence 347799999999999998666666653
No 198
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=54.70 E-value=51 Score=24.90 Aligned_cols=49 Identities=16% Similarity=0.311 Sum_probs=36.5
Q ss_pred CCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEe
Q 026737 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKID 117 (234)
Q Consensus 57 ~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id 117 (234)
..|.+|.|+ +--+||++++ ...+.|+...... +.|..|..|.+++.+.+
T Consensus 22 ~~gk~V~G~I~hvv~ddLYIDfG~-----KFhcVc~rp~~~~-------~~y~~G~rV~lrLkdlE 75 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDDDLYIDFGG-----KFHCVCKRPAVNG-------EKYVRGSRVRLRLKDLE 75 (104)
T ss_pred ccCCEEEEEEEEEecCceEEEeCC-----ceeEEEecccccc-------cccccCCEEEEEECCHh
Confidence 578888888 5579999973 6789998665433 23788999998886543
No 199
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=53.98 E-value=35 Score=23.52 Aligned_cols=39 Identities=28% Similarity=0.393 Sum_probs=27.2
Q ss_pred EEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEE
Q 026737 70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 116 (234)
Q Consensus 70 fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~i 116 (234)
||.-. +| +-+-|+|+|.+...-. ..+.+||.|...+..-
T Consensus 19 FI~~~--~g--~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~~ 57 (69)
T PRK09507 19 FITPE--DG--SKDVFVHFSAIQTNGF----KTLAEGQRVEFEITNG 57 (69)
T ss_pred EEecC--CC--CeeEEEEeecccccCC----CCCCCCCEEEEEEEEC
Confidence 66654 22 5799999999875422 3367899999877553
No 200
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=52.00 E-value=1.3e+02 Score=31.48 Aligned_cols=40 Identities=15% Similarity=-0.067 Sum_probs=27.1
Q ss_pred eeCCCEEEEE----------Eeeecc----chhh---hcccccchhHHHHhhcccCC
Q 026737 195 ARAGRQVQEI----------QLSHSL----IRKA---SKRHCNEYWNVFHETAIVNN 234 (234)
Q Consensus 195 ~~~G~~v~~~----------vl~~d~----i~ls---~K~~~~~p~~~~~~~~~~~~ 234 (234)
|.+||.|+|. |..||. |... ++.-..-|...+.+-|.+|+
T Consensus 408 F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~~e~l~~pl~~~~~eLrKyF~~GD 464 (1024)
T KOG1999|consen 408 FSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSKHEDLKGPLEVPASELRKYFEPGD 464 (1024)
T ss_pred cCCCCeEEEeeeeeccceeEEEeccCceEEEeeccccCCCccccchHhhhhhccCCC
Confidence 8999998654 666665 3333 34445567778888888875
No 201
>PF02599 CsrA: Global regulator protein family; InterPro: IPR003751 The RNA-binding protein CsrA (carbon storage regulator) is a new kind of global regulator, which facilitates specific mRNA decay []. CsrA is entirely contained within a globular complex of approximately 18 CsrA-H6 subunits and a single RNA, CsrB. CsrA binds to the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis [].; GO: 0003723 RNA binding, 0006109 regulation of carbohydrate metabolic process, 0006402 mRNA catabolic process; PDB: 1Y00_B 2JPP_A 1T3O_A 1VPZ_A.
Probab=50.52 E-value=8 Score=25.69 Aligned_cols=30 Identities=13% Similarity=-0.007 Sum_probs=23.5
Q ss_pred ceeeeeeCCCEEEEEEeeecc--chhhhcccc
Q 026737 190 KFTLLARAGRQVQEIQLSHSL--IRKASKRHC 219 (234)
Q Consensus 190 ~~~~~~~~G~~v~~~vl~~d~--i~ls~K~~~ 219 (234)
+..+.+..|+.+++.|++++. ++||+.+=.
T Consensus 7 k~gE~I~Ig~~I~I~Vl~i~~~~VklgI~AP~ 38 (54)
T PF02599_consen 7 KVGESIVIGDDIEITVLEISGGQVKLGIDAPK 38 (54)
T ss_dssp ETT-EEEETTTEEEEEEEEETTEEEEEEEECT
T ss_pred cCCCEEEECCCEEEEEEEEcCCEEEEEEECCC
Confidence 445578889999999999976 999887643
No 202
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=50.43 E-value=27 Score=23.38 Aligned_cols=21 Identities=24% Similarity=0.300 Sum_probs=11.6
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEe
Q 026737 22 TGSIISVKVIQANEEMKKLVFSE 44 (234)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~ 44 (234)
+|+++.+.|. .|. .+++++|.
T Consensus 40 ~Gd~v~VFvY-~D~-~~rl~AT~ 60 (61)
T PF13509_consen 40 VGDEVEVFVY-LDK-EGRLVATT 60 (61)
T ss_dssp TTSEEEEEEE-E-T-TS-EEEE-
T ss_pred CCCEEEEEEE-ECC-CCCEEEec
Confidence 7888888744 343 44666664
No 203
>PRK01712 carbon storage regulator; Provisional
Probab=49.44 E-value=12 Score=25.77 Aligned_cols=30 Identities=13% Similarity=0.068 Sum_probs=24.1
Q ss_pred cceeeeeeCCCEEEEEEeeecc--chhhhccc
Q 026737 189 KKFTLLARAGRQVQEIQLSHSL--IRKASKRH 218 (234)
Q Consensus 189 ~~~~~~~~~G~~v~~~vl~~d~--i~ls~K~~ 218 (234)
++..+.+..|+.++++|++++. ++||+.+=
T Consensus 6 Rk~gE~I~Igd~I~I~V~~i~~~~VrlGI~AP 37 (64)
T PRK01712 6 RKVGESLMIGDDIEVTVLGVKGNQVRIGINAP 37 (64)
T ss_pred ccCCCEEEeCCCEEEEEEEEeCCEEEEEEECC
Confidence 3455688899999999999976 88888753
No 204
>PRK00568 carbon storage regulator; Provisional
Probab=48.63 E-value=12 Score=26.69 Aligned_cols=29 Identities=10% Similarity=-0.005 Sum_probs=23.1
Q ss_pred cceeeeeeCCCEEEEEEeeecc--chhhhcc
Q 026737 189 KKFTLLARAGRQVQEIQLSHSL--IRKASKR 217 (234)
Q Consensus 189 ~~~~~~~~~G~~v~~~vl~~d~--i~ls~K~ 217 (234)
++..+.+..||.+++.|++++. ++||+.+
T Consensus 6 RK~gEsI~Igd~I~I~Vl~i~g~~VrlGI~A 36 (76)
T PRK00568 6 RKVNEGIVIDDNIHIKVISIDRGSVRLGFEA 36 (76)
T ss_pred eeCCCeEEeCCCeEEEEEEEcCCEEEEEEEC
Confidence 3455688999999999999976 8877754
No 205
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=47.91 E-value=89 Score=21.91 Aligned_cols=54 Identities=24% Similarity=0.228 Sum_probs=34.7
Q ss_pred eeE-EEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEeec
Q 026737 67 YGA-FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (234)
Q Consensus 67 ~G~-fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~~ 130 (234)
.|. ||.-. +| +-+.|+|+|.+...-. ..+..||.|+..+..-. +++-...+..+
T Consensus 13 KGfGFI~~~--~g--g~dVFvH~s~i~~~g~----~~l~~G~~V~f~~~~~~--~G~~A~~V~~~ 67 (74)
T PRK09937 13 KGFGFICPE--GG--GEDIFAHYSTIQMDGY----RTLKAGQSVQFDVHQGP--KGNHASVIVPV 67 (74)
T ss_pred CCeEEEeeC--CC--CccEEEEEeeccccCC----CCCCCCCEEEEEEEECC--CCceeeEEEEC
Confidence 344 66654 22 6899999999874421 33789999999886543 45544444433
No 206
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=46.04 E-value=69 Score=22.30 Aligned_cols=50 Identities=28% Similarity=0.361 Sum_probs=32.7
Q ss_pred EeeEE-EEEecCCCcceeEEEEEceeccc-ccccchhhhhCCCCEEEEEEEEEeCCCCeEEE
Q 026737 66 DYGAF-IHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125 (234)
Q Consensus 66 ~~G~f-V~l~~~~g~~g~~glv~isels~-~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~L 125 (234)
+.+.| |.+. .|..-+.|++---. .++ .+.+||.|.+.+-..|.++++|..
T Consensus 16 ~~~~f~V~l~-----ng~~vla~i~GKmr~~rI-----~I~~GD~V~Ve~spyd~tkgrIi~ 67 (68)
T TIGR00008 16 PNAMFRVELE-----NGHEVLAHISGKIRMHYI-----RILPGDKVKVELSPYDLTRGRITY 67 (68)
T ss_pred CCCEEEEEEC-----CCCEEEEEecCcchhccE-----EECCCCEEEEEECcccCCcEeEEe
Confidence 44444 4665 25777777763221 122 267899999999999988888753
No 207
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=45.96 E-value=87 Score=20.78 Aligned_cols=31 Identities=29% Similarity=0.292 Sum_probs=23.2
Q ss_pred eeEEEEEceecccccccchhhhhCCCCEEEEEEEE
Q 026737 81 HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (234)
Q Consensus 81 g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~ 115 (234)
+-+-|+|++++.... -..++.|+.|+..+..
T Consensus 23 ~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 23 GEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE 53 (66)
T ss_dssp SSEEEEEGGGBCSSS----STS--TTSEEEEEEEE
T ss_pred ceeEEeccccccccc----cccCCCCCEEEEEEEE
Confidence 459999999988664 2347789999999977
No 208
>PRK15463 cold shock-like protein CspF; Provisional
Probab=44.78 E-value=39 Score=23.45 Aligned_cols=42 Identities=26% Similarity=0.286 Sum_probs=29.2
Q ss_pred EeeE-EEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEE
Q 026737 66 DYGA-FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (234)
Q Consensus 66 ~~G~-fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~ 115 (234)
+.|. |+.-. +| +-+.|+|++.+...-. ..+++||.|...+..
T Consensus 15 ~kGfGFI~~~--~g--~~DvFvH~sal~~~g~----~~l~~G~~V~f~v~~ 57 (70)
T PRK15463 15 KSGKGLITPS--DG--RKDVQVHISALNLRDA----EELTTGLRVEFCRIN 57 (70)
T ss_pred CCceEEEecC--CC--CccEEEEehhhhhcCC----CCCCCCCEEEEEEEE
Confidence 3454 77665 22 5799999999875422 237799999997754
No 209
>TIGR00202 csrA carbon storage regulator (csrA). Modulates the expression of genes in the glycogen biosynthesis and gluconeogenesis pathways by accelerating the 5'-to-3' degradation of these transcripts through selective RNA binding. The N-terminal end of the sequence (AA 11-45) contains the KH motif which is characteristic of a set of RNA-binding proteins.
Probab=43.25 E-value=17 Score=25.38 Aligned_cols=29 Identities=14% Similarity=0.127 Sum_probs=23.4
Q ss_pred cceeeeeeCCCEEEEEEeeecc--chhhhcc
Q 026737 189 KKFTLLARAGRQVQEIQLSHSL--IRKASKR 217 (234)
Q Consensus 189 ~~~~~~~~~G~~v~~~vl~~d~--i~ls~K~ 217 (234)
++..+.+..|+.++++|+++.. ++||+.+
T Consensus 6 Rk~gE~I~Igd~I~I~Vl~i~g~~VrlGI~A 36 (69)
T TIGR00202 6 RKVNESIQIGDDIEVKVLSVKGDQVKLGIEA 36 (69)
T ss_pred ccCCCEEEeCCCEEEEEEEEcCCeEEEEEEC
Confidence 3455688999999999999976 8888765
No 210
>PRK09890 cold shock protein CspG; Provisional
Probab=40.67 E-value=72 Score=21.99 Aligned_cols=38 Identities=26% Similarity=0.405 Sum_probs=27.0
Q ss_pred EEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEE
Q 026737 70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (234)
Q Consensus 70 fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~ 115 (234)
|+.-+ +| +-+-|+|+|.+...-. ..+.+||.|+..+..
T Consensus 20 FI~~~--~g--~~dvFvH~s~l~~~~~----~~l~~G~~V~f~~~~ 57 (70)
T PRK09890 20 FITPD--DG--SKDVFVHFTAIQSNEF----RTLNENQKVEFSIEQ 57 (70)
T ss_pred EEecC--CC--CceEEEEEeeeccCCC----CCCCCCCEEEEEEEE
Confidence 66654 22 5799999999875532 236789999997644
No 211
>PRK14998 cold shock-like protein CspD; Provisional
Probab=39.69 E-value=1.3e+02 Score=21.00 Aligned_cols=48 Identities=27% Similarity=0.264 Sum_probs=31.7
Q ss_pred EEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeCCCCeEEEEE
Q 026737 70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (234)
Q Consensus 70 fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~ 127 (234)
||.-. +| +-+.|+|+|.+...-. ..+..||.|...+..-+ +++-...+
T Consensus 17 FI~~~--~g--~~dVFvH~s~l~~~g~----~~l~~G~~V~f~~~~~~--~G~~A~~V 64 (73)
T PRK14998 17 FICPE--GG--GEDIFAHYSTIQMDGY----RTLKAGQSVRFDVHQGP--KGNHASVI 64 (73)
T ss_pred EEecC--CC--CccEEEEeeeecccCC----CCCCCCCEEEEEEEECC--CCceeEEE
Confidence 66654 22 5799999999864421 34789999999886643 44433333
No 212
>KOG3754 consensus Gamma-glutamylcysteine synthetase [Coenzyme transport and metabolism]
Probab=38.44 E-value=34 Score=32.61 Aligned_cols=27 Identities=22% Similarity=0.195 Sum_probs=24.8
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechhh
Q 026737 22 TGSIISVKVIQANEEMKKLVFSEKDAV 48 (234)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~~ 48 (234)
=|++|++.|++.|.+++++.+|.++..
T Consensus 47 WGDEiEy~vV~fDd~~kk~rv~l~~e~ 73 (640)
T KOG3754|consen 47 WGDEIEYMVVKFDDKNKKARVSLRAEK 73 (640)
T ss_pred ccceeEEEEEecccccceeeeeeeHHH
Confidence 699999999999999999999998763
No 213
>COG1278 CspC Cold shock proteins [Transcription]
Probab=37.78 E-value=54 Score=22.78 Aligned_cols=31 Identities=26% Similarity=0.353 Sum_probs=23.2
Q ss_pred eeEEEEEceecccccccchhhhhCCCCEEEEEEEE
Q 026737 81 HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (234)
Q Consensus 81 g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~ 115 (234)
+-+.|||+|.+...-.. .+..||.|..-+..
T Consensus 24 ~~DvFVH~Sai~~~g~~----~L~eGQ~V~f~~~~ 54 (67)
T COG1278 24 GKDVFVHISAIQRAGFR----TLREGQKVEFEVEQ 54 (67)
T ss_pred CcCEEEEeeeeccCCCc----ccCCCCEEEEEEec
Confidence 47999999998655332 36789999987743
No 214
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=35.79 E-value=68 Score=21.93 Aligned_cols=38 Identities=24% Similarity=0.318 Sum_probs=26.7
Q ss_pred EEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEE
Q 026737 70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (234)
Q Consensus 70 fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~ 115 (234)
|+.-. + .+-+.|+|+|.+...-. ..+..||.|+..+..
T Consensus 17 FI~~~--~--g~~dvfvH~s~~~~~g~----~~l~~G~~V~f~~~~ 54 (68)
T TIGR02381 17 FICPE--G--VDGDIFAHYSTIQMDGY----RTLKAGQKVQFEVVQ 54 (68)
T ss_pred EEecC--C--CCccEEEEHHHhhhcCC----CCCCCCCEEEEEEEE
Confidence 66654 2 25899999999864421 337899999987754
No 215
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=34.99 E-value=93 Score=21.37 Aligned_cols=38 Identities=32% Similarity=0.421 Sum_probs=27.0
Q ss_pred EEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEE
Q 026737 70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (234)
Q Consensus 70 fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~ 115 (234)
|+.-. +| +-+-|+|+|.+...-. ..+.+||.|+..+..
T Consensus 20 FI~~~--~g--~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~ 57 (70)
T PRK10354 20 FITPD--DG--SKDVFVHFSAIQNDGY----KSLDEGQKVSFTIES 57 (70)
T ss_pred EEecC--CC--CccEEEEEeeccccCC----CCCCCCCEEEEEEEE
Confidence 66654 22 5799999999875421 337899999987754
No 216
>PRK10943 cold shock-like protein CspC; Provisional
Probab=33.40 E-value=93 Score=21.36 Aligned_cols=38 Identities=29% Similarity=0.420 Sum_probs=27.0
Q ss_pred EEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEE
Q 026737 70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (234)
Q Consensus 70 fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~ 115 (234)
|+.-. +| +-+-|+|+|.+..... ..+..||.|...+..
T Consensus 19 FI~~~--~g--~~dvFvH~s~l~~~g~----~~l~~G~~V~f~~~~ 56 (69)
T PRK10943 19 FITPA--DG--SKDVFVHFSAIQGNGF----KTLAEGQNVEFEIQD 56 (69)
T ss_pred EEecC--CC--CeeEEEEhhHccccCC----CCCCCCCEEEEEEEE
Confidence 66654 22 5799999999875422 336789999998754
No 217
>PF11813 DUF3334: Protein of unknown function (DUF3334); InterPro: IPR024513 This family of proteins are functionally uncharacterised. This family is only found in bacteria. Proteins in this family are typically between 227 to 238 amino acids in length.
Probab=31.32 E-value=34 Score=29.13 Aligned_cols=21 Identities=5% Similarity=0.004 Sum_probs=17.7
Q ss_pred ceeeeecCCceEEEEcccccc
Q 026737 149 PYLKSFYKKMDDVRITRQGFE 169 (234)
Q Consensus 149 G~fV~l~~gi~Gl~~s~~~~~ 169 (234)
|+||-+++|..||++-+++..
T Consensus 51 GCFvlFDGGFsGLVviNFsa~ 71 (229)
T PF11813_consen 51 GCFVLFDGGFSGLVVINFSAQ 71 (229)
T ss_pred ceEEEecCCcceEEEEecChH
Confidence 999999999999996666544
No 218
>COG2100 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=31.15 E-value=1.1e+02 Score=28.23 Aligned_cols=71 Identities=15% Similarity=0.244 Sum_probs=44.1
Q ss_pred CCCCCCCCCCcchhhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh--h-HhhhhcCCCCCcEEEEE----EeeEEEEE
Q 026737 1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA--V-WNKYSSRVNVEDIFVGR----DYGAFIHL 73 (234)
Q Consensus 1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~--~-~~~~~~~~~~G~iv~g~----~~G~fV~l 73 (234)
++|.|.-.||.+.+..-.+ .|+.+.+.|+-=-.-+|....-.+.- + .........+|+.++.. +.|+||..
T Consensus 335 lkP~~fG~~pRp~lp~PF~--rGevv~aevV~~Gr~kGEmlavArdRvIav~~~~~~~~~vG~~vkvrIvr~khnI~Ia~ 412 (414)
T COG2100 335 LKPGEFGMHPRPRLPKPFK--RGEVVKAEVVLPGRLKGEMLAVARDRVIAVINSNEGALLVGDRVKVRIVRTKHNIYIAV 412 (414)
T ss_pred cChhhcCCCcCCCCCCccc--cCcEEEEEEEecceecceEEEEecccEEEEecCchhhhccCceEEEEEEEccCceEEee
Confidence 4688888888888764444 89999999875333233332222211 0 11111257899999988 77888865
No 219
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=30.68 E-value=84 Score=29.90 Aligned_cols=27 Identities=19% Similarity=0.176 Sum_probs=22.7
Q ss_pred CCCEEEEEEEEEeCCC---CEEEEEechhh
Q 026737 22 TGSIISVKVIQANEEM---KKLVFSEKDAV 48 (234)
Q Consensus 22 vG~~v~~~Vi~id~~~---~~i~lS~k~~~ 48 (234)
.|+.+.|+|.++.... -.+.||+....
T Consensus 198 ~Gdrika~i~~V~~~~~kGpqIilSRt~p~ 227 (449)
T PRK12329 198 ANATFKVFLKEVSEGPRRGPQLFVSRANAG 227 (449)
T ss_pred CCCEEEEEEEEeecCCCCCCEEEEEcCCHH
Confidence 9999999999998753 37999998763
No 220
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=28.65 E-value=1.6e+02 Score=20.57 Aligned_cols=44 Identities=7% Similarity=0.169 Sum_probs=32.6
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechhhHhhhhcCCCCCcEEEEEEe
Q 026737 22 TGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDY 67 (234)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~~~ 67 (234)
.|..+++. =+|+++.++.++......+.+...+++|.++.=.+|
T Consensus 17 ~~~~~~mi--L~De~G~~I~a~i~~~~~~~f~~~L~eg~vy~is~f 60 (86)
T cd04480 17 SGESLEMV--LVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNF 60 (86)
T ss_pred CCcEEEEE--EEcCCCCEEEEEECHHHHHhhhhhceeCCEEEEeeE
Confidence 34555554 456778899999998888888889999988764433
No 221
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=28.40 E-value=2.1e+02 Score=20.99 Aligned_cols=41 Identities=12% Similarity=0.216 Sum_probs=30.6
Q ss_pred CCEEEEEEEEEeCCCCEEEEEechhhHhhhhcCCCCCcEEEEE
Q 026737 23 GSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR 65 (234)
Q Consensus 23 G~~v~~~Vi~id~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~ 65 (234)
|..+.+.+ .|++++.+.++.-....+.+...+++|+++.=.
T Consensus 34 g~~~~~~l--~De~~~~I~~t~~~~~~~~f~~~l~eG~vy~i~ 74 (104)
T cd04474 34 GKLFSFDL--LDEDGGEIRATFFNDAVDKFYDLLEVGKVYYIS 74 (104)
T ss_pred cEEEEEEE--EECCCCEEEEEEehHHHHHhhcccccccEEEEe
Confidence 44444443 567788999998877778888899999987644
No 222
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=27.62 E-value=71 Score=22.89 Aligned_cols=31 Identities=32% Similarity=0.493 Sum_probs=20.1
Q ss_pred hhhhCCCCEEEEEEEEEeCC-------CCeEEEEEeec
Q 026737 100 RDILNEGDEVRVKVIKIDRE-------KSRITLSIKQL 130 (234)
Q Consensus 100 ~~~~~vGd~v~vkVl~id~~-------~~ri~LS~K~~ 130 (234)
+..|++||+|.++++-.+.+ ...+.+.++..
T Consensus 8 r~iYrPGetV~~~~~~~~~~~~~~~~~~~~~~v~i~dp 45 (99)
T PF01835_consen 8 RPIYRPGETVHFRAIVRDLDNDFKPPANSPVTVTIKDP 45 (99)
T ss_dssp SSEE-TTSEEEEEEEEEEECTTCSCESSEEEEEEEEET
T ss_pred ccCcCCCCEEEEEEEEeccccccccccCCceEEEEECC
Confidence 45689999999999955443 23556666544
No 223
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=26.86 E-value=1.1e+02 Score=26.97 Aligned_cols=71 Identities=23% Similarity=0.318 Sum_probs=51.4
Q ss_pred cCCCCCcEEEEE-----EeeEEEEEecCCCcceeEEEEEceecccc------cc----cchhhhhCCCCEEEEEEEEEeC
Q 026737 54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD------LI----QDIRDILNEGDEVRVKVIKIDR 118 (234)
Q Consensus 54 ~~~~~G~iv~g~-----~~G~fV~l~~~~g~~g~~glv~isels~~------~~----~~~~~~~~vGd~v~vkVl~id~ 118 (234)
...++|++|-|. ..-.-|+++ ...++.+.+|.+.-. +. ...+.+|+.||-+-+-|-.+-.
T Consensus 81 Y~pEvGDvVVgRV~eVq~KRWkvd~n-----sk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~ 155 (301)
T KOG3013|consen 81 YAPEVGDVVVGRVIEVQQKRWKVDLN-----SKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFH 155 (301)
T ss_pred cCCccCCEEEEEeeeeecceeEEecc-----cccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhcc
Confidence 357899999998 556778886 357888888754321 11 2467889999999999988754
Q ss_pred CCCeEEEEEeec
Q 026737 119 EKSRITLSIKQL 130 (234)
Q Consensus 119 ~~~ri~LS~K~~ 130 (234)
+|-++|-.|.+
T Consensus 156 -dGs~sLhTRS~ 166 (301)
T KOG3013|consen 156 -DGSLSLHTRSL 166 (301)
T ss_pred -CCeEEEEecch
Confidence 78888766644
No 224
>PF03152 UFD1: Ubiquitin fusion degradation protein UFD1; InterPro: IPR004854 Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified []. This family includes UFD1, a 40kDa protein that is essential for vegetative cell viability []. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterised by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1ZC1_A 2YUJ_A.
Probab=26.32 E-value=90 Score=25.81 Aligned_cols=95 Identities=15% Similarity=0.276 Sum_probs=49.0
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechhhHhhhhcCCCCCcEEEEE----EeeEEEEEecCCCcceeEEEEEceecccccc-
Q 026737 22 TGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI- 96 (234)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~----~~G~fV~l~~~~g~~g~~glv~isels~~~~- 96 (234)
.+..+.|-|++...+.|.+.+..-- ++.+ .+++|+.+.-. +.|-||.|. |.-.+|..+++ |+.+
T Consensus 56 ~~~~th~GVlEFsA~eG~i~lP~wm--m~~L--~l~~g~~V~v~~~~LPkgt~vkLq-----P~~~~F~~i~n--~KavL 124 (176)
T PF03152_consen 56 NGKRTHCGVLEFSAEEGTIYLPPWM--MQNL--GLQEGDIVRVEYVSLPKGTFVKLQ-----PQSSDFLDISN--PKAVL 124 (176)
T ss_dssp TTEEEEEEEEEE--CTTEEEE-CHH--HHHH--T--TTEEEEEEEEE----SEEEEE-----ESCHHHHCSS---HHHHH
T ss_pred CCcEEEEEEEEeEcCCCeEEeCccH--Hhhc--CCCCCCEEEEEEeECCCCCEEEEe-----ECCCccccccc--hHHHH
Confidence 5677788888888788888777532 2222 57899998765 889999997 22234444332 1111
Q ss_pred -cchh--hhhCCCCEEEEEEEEEeCCCCeEEEEEeeccc
Q 026737 97 -QDIR--DILNEGDEVRVKVIKIDREKSRITLSIKQLEE 132 (234)
Q Consensus 97 -~~~~--~~~~vGd~v~vkVl~id~~~~ri~LS~K~~~~ 132 (234)
..++ ..+..||.+.+. ..+....|.+-++.+
T Consensus 125 E~~Lr~ystLT~Gd~I~i~-----~~~~~y~l~V~e~kP 158 (176)
T PF03152_consen 125 ERALRNYSTLTKGDTISIE-----YNNKTYELDVVEVKP 158 (176)
T ss_dssp HHHHCC-SEEETTSEEEEE-----CTTEEEEEEEEEECS
T ss_pred HhhcccCceeecCCEEEEE-----eCCEEEEEEEEEEcC
Confidence 0111 126789887753 234455555555544
No 225
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=24.17 E-value=2.7e+02 Score=19.77 Aligned_cols=50 Identities=28% Similarity=0.246 Sum_probs=32.8
Q ss_pred EEEEEecCCCcceeEEEEEceecccc-cccchhhhhCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026737 69 AFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (234)
Q Consensus 69 ~fV~l~~~~g~~g~~glv~isels~~-~~~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K 128 (234)
+.|.+. .|..-+-|++---.. ++ -+.+||.|.+..-..|.++++|..-.+
T Consensus 22 f~v~~e-----dg~~~~ahI~GKmr~~~i-----~I~~GD~V~Ve~~~~d~~kg~I~~Ry~ 72 (75)
T COG0361 22 FRVELE-----NGHERLAHISGKMRKNRI-----RILPGDVVLVELSPYDLTKGRIVYRYK 72 (75)
T ss_pred EEEEec-----CCcEEEEEccCcchheeE-----EeCCCCEEEEEecccccccccEEEEec
Confidence 455665 256666666532222 22 167899999999999988888876544
No 226
>PF09876 DUF2103: Predicted metal-binding protein (DUF2103); InterPro: IPR018664 This family of various putative metal binding prokaryotic proteins has no known function.
Probab=22.57 E-value=2e+02 Score=21.75 Aligned_cols=54 Identities=26% Similarity=0.305 Sum_probs=31.8
Q ss_pred CCceEEEEccccccccccccccccccccCCCCCcceeeeeeCCCEEEEEEeeecc
Q 026737 156 KKMDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 210 (234)
Q Consensus 156 ~gi~Gl~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~vl~~d~ 210 (234)
++|..+++..+...+......+..|+...+. .+++.++++.|..||+.-+-.+.
T Consensus 33 ~~Vk~IiPG~I~~~~~~~~~gl~lkvt~~~~-~Gn~Kllar~G~SvQEvfVVT~~ 86 (103)
T PF09876_consen 33 PGVKKIIPGVISRSGGRSSGGLRLKVTRPTR-GGNFKLLARSGSSVQEVFVVTTL 86 (103)
T ss_pred CCCCEEecccEEcCCCCCCCCeEEEEEEecC-CCcEEEEEecCCeeEEEEEEeeC
Confidence 4555555433332222212334455554433 36799999999999988776653
No 227
>PF07405 DUF1506: Protein of unknown function (DUF1506); InterPro: IPR010875 This entry represents proteins found primarily in Borrelia species. Their function is unknown.
Probab=22.55 E-value=73 Score=24.62 Aligned_cols=57 Identities=19% Similarity=0.207 Sum_probs=38.8
Q ss_pred eEEEEEecCCCcceeEEEEEceecccccc-----------cchhhhhCCCCEEEEEEEEEeCCCCeEEEEEee
Q 026737 68 GAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (234)
Q Consensus 68 G~fV~l~~~~g~~g~~glv~isels~~~~-----------~~~~~~~~vGd~v~vkVl~id~~~~ri~LS~K~ 129 (234)
|+|+.|. |.--..++-+++++... -...+.++++|.+-.-|+++|..=+..+|.+|+
T Consensus 55 Gv~i~I~-----P~E~v~i~~sNi~D~~~y~klYT~~~l~fE~~DrIsi~D~~yfeI~sid~si~Y~TLvLk~ 122 (127)
T PF07405_consen 55 GVIIDIK-----PQELVEIYDSNIFDIQGYSKLYTYQNLNFELKDRISISDDVYFEIFSIDSSIGYFTLVLKE 122 (127)
T ss_pred EEEEEeC-----hHHeeeeccCCchhhhhhhheeehhhccchhhceeehhheeeeEEEeeeccccchhhhHhh
Confidence 7888886 33344555566654211 234666888999999999999766777777765
No 228
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=21.62 E-value=3.1e+02 Score=23.58 Aligned_cols=58 Identities=16% Similarity=0.094 Sum_probs=37.0
Q ss_pred CCCCCcEEEEE---Eee--EEEEEecCCCcceeEEEEEceecccccccchhhhhCCCCEEEEEEEEEeC
Q 026737 55 RVNVEDIFVGR---DYG--AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDR 118 (234)
Q Consensus 55 ~~~~G~iv~g~---~~G--~fV~l~~~~g~~g~~glv~isels~~~~~~~~~~~~vGd~v~vkVl~id~ 118 (234)
-+.+|+.|-|. .+| .-|+|++ ...+.++.-.....- +.-+-.+++||-|.++|...++
T Consensus 62 iP~~~D~VIGiV~~~~gd~ykVDigg-----~~~a~L~~laFe~At-krNrPnl~vGdliyakv~~a~~ 124 (230)
T KOG1004|consen 62 IPVKGDHVIGIVTSKSGDIYKVDIGG-----SEPASLSYLAFEGAT-KRNRPNLQVGDLIYAKVVDANK 124 (230)
T ss_pred cCCCCCEEEEEEEeccCceEEEecCC-----CCeeeeeeccccCcc-ccCCCccccccEEEEEEEecCC
Confidence 36789999998 444 5677762 245555544333221 1122338999999999998875
No 229
>PF02721 DUF223: Domain of unknown function DUF223; InterPro: IPR003871 The function of this domain has not been characterised, but may be involved in nucleic acid or nucleotide binding.
Probab=20.44 E-value=3.3e+02 Score=19.45 Aligned_cols=39 Identities=8% Similarity=0.189 Sum_probs=31.7
Q ss_pred EEEeCCCCEEEEEechhhHhhhhcCCCCCcEEEEEEeeE
Q 026737 31 IQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGA 69 (234)
Q Consensus 31 i~id~~~~~i~lS~k~~~~~~~~~~~~~G~iv~g~~~G~ 69 (234)
+=+|+++.++.++.+......+...+++|..+.=.+|.+
T Consensus 3 vL~De~G~~I~A~I~~~~~~~f~~~l~Eg~~y~i~~F~V 41 (95)
T PF02721_consen 3 VLVDEKGDKIQATIPKELVDKFKDSLKEGSWYTISNFTV 41 (95)
T ss_pred EEEecCCCEEEEEECHHHHHHHHhhcccCCEEEeEeEEE
Confidence 346888999999999888888888999999887656543
Done!