Query 020356
Match_columns 327
No_of_seqs 246 out of 961
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 09:05:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020356.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020356hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3013 Exosomal 3'-5' exoribo 100.0 1.2E-80 2.7E-85 572.7 20.1 300 4-324 1-300 (301)
2 COG1097 RRP4 RNA-binding prote 100.0 1.6E-48 3.6E-53 359.1 21.6 225 31-279 6-235 (239)
3 PRK04163 exosome complex RNA-b 100.0 3.3E-42 7.1E-47 320.0 23.1 183 31-221 6-193 (235)
4 KOG1004 Exosomal 3'-5' exoribo 100.0 1.3E-33 2.7E-38 254.9 16.7 177 34-221 2-195 (230)
5 PRK09521 exosome complex RNA-b 99.9 3.7E-26 8E-31 205.8 16.4 134 31-177 3-149 (189)
6 COG1096 Predicted RNA-binding 99.9 3.1E-24 6.8E-29 191.6 12.5 134 31-177 3-149 (188)
7 KOG3409 Exosomal 3'-5' exoribo 99.9 5.6E-21 1.2E-25 168.5 12.9 159 33-194 5-178 (193)
8 cd05790 S1_Rrp40 S1_Rrp40: Rrp 99.8 4.4E-21 9.5E-26 153.2 9.8 75 85-170 1-75 (86)
9 cd05791 S1_CSL4 S1_CSL4: CSL4, 99.8 1.1E-19 2.4E-24 146.5 9.9 83 86-176 2-92 (92)
10 cd04454 S1_Rrp4_like S1_Rrp4_l 99.7 1.3E-16 2.8E-21 124.7 10.4 82 85-176 1-82 (82)
11 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.6 9.2E-15 2E-19 114.9 10.1 86 85-176 1-86 (86)
12 PF10447 EXOSC1: Exosome compo 99.4 9.1E-13 2E-17 104.5 7.1 69 87-158 1-82 (82)
13 PF14382 ECR1_N: Exosome compl 99.2 1.4E-11 2.9E-16 84.8 3.2 39 35-74 1-39 (39)
14 COG1098 VacB Predicted RNA bin 98.9 2.3E-09 5.1E-14 90.7 6.5 77 87-173 2-78 (129)
15 cd05704 S1_Rrp5_repeat_hs13 S1 98.9 1.2E-08 2.6E-13 78.2 8.2 70 89-169 2-72 (72)
16 cd05687 S1_RPS1_repeat_ec1_hs1 98.8 3.9E-08 8.5E-13 74.0 8.4 69 91-169 1-70 (70)
17 cd04452 S1_IF2_alpha S1_IF2_al 98.7 1.3E-07 2.8E-12 71.9 9.0 72 88-169 1-75 (76)
18 cd05692 S1_RPS1_repeat_hs4 S1_ 98.7 2E-07 4.4E-12 68.6 9.0 69 91-169 1-69 (69)
19 cd05691 S1_RPS1_repeat_ec6 S1_ 98.6 2E-07 4.3E-12 70.2 8.7 71 91-171 1-72 (73)
20 PF00575 S1: S1 RNA binding do 98.6 3E-07 6.5E-12 69.7 9.0 72 88-169 2-74 (74)
21 cd05705 S1_Rrp5_repeat_hs14 S1 98.6 1.8E-07 3.9E-12 72.3 7.6 72 89-167 2-74 (74)
22 smart00316 S1 Ribosomal protei 98.6 4.3E-07 9.4E-12 66.5 8.7 71 89-169 1-72 (72)
23 cd05706 S1_Rrp5_repeat_sc10 S1 98.6 5.6E-07 1.2E-11 68.2 9.1 71 89-169 2-73 (73)
24 cd05708 S1_Rrp5_repeat_sc12 S1 98.5 6.1E-07 1.3E-11 68.0 8.8 74 89-172 1-76 (77)
25 PRK08582 hypothetical protein; 98.5 6.2E-07 1.3E-11 77.7 9.9 76 88-173 3-78 (139)
26 cd05686 S1_pNO40 S1_pNO40: pNO 98.5 9.3E-07 2E-11 67.7 9.3 71 88-168 1-72 (73)
27 PTZ00248 eukaryotic translatio 98.5 4.3E-07 9.3E-12 88.5 8.9 74 87-170 14-90 (319)
28 cd05693 S1_Rrp5_repeat_hs1_sc1 98.5 4.3E-07 9.4E-12 74.3 7.3 81 89-170 2-96 (100)
29 TIGR00448 rpoE DNA-directed RN 98.4 9.6E-07 2.1E-11 79.1 9.0 89 86-177 77-174 (179)
30 PRK08563 DNA-directed RNA poly 98.4 9.5E-07 2.1E-11 79.4 8.5 90 85-177 76-174 (187)
31 PRK03987 translation initiatio 98.4 1.1E-06 2.4E-11 83.6 9.2 76 86-171 4-82 (262)
32 PRK07252 hypothetical protein; 98.4 2E-06 4.3E-11 72.8 9.3 73 89-171 2-75 (120)
33 PRK08059 general stress protei 98.4 2E-06 4.4E-11 72.7 9.2 76 88-173 5-81 (123)
34 cd05707 S1_Rrp5_repeat_sc11 S1 98.4 1.6E-06 3.5E-11 65.0 7.3 67 91-167 1-68 (68)
35 PRK05807 hypothetical protein; 98.4 2.5E-06 5.5E-11 73.6 9.4 72 89-171 4-75 (136)
36 cd05698 S1_Rrp5_repeat_hs6_sc5 98.3 3.1E-06 6.8E-11 63.5 8.4 69 91-169 1-70 (70)
37 COG1093 SUI2 Translation initi 98.3 9.7E-07 2.1E-11 83.3 6.8 79 82-170 3-84 (269)
38 cd05702 S1_Rrp5_repeat_hs11_sc 98.3 2.7E-06 5.9E-11 64.4 7.6 64 91-162 1-64 (70)
39 cd05703 S1_Rrp5_repeat_hs12_sc 98.3 4.5E-06 9.7E-11 64.2 8.7 71 91-169 1-72 (73)
40 cd04461 S1_Rrp5_repeat_hs8_sc7 98.3 5.5E-06 1.2E-10 64.7 8.3 73 86-168 10-83 (83)
41 COG1095 RPB7 DNA-directed RNA 98.2 3.8E-06 8.3E-11 75.8 7.8 90 85-177 76-174 (183)
42 cd04453 S1_RNase_E S1_RNase_E: 98.2 8.4E-06 1.8E-10 65.2 8.9 74 88-168 5-81 (88)
43 cd04472 S1_PNPase S1_PNPase: P 98.2 9.4E-06 2E-10 59.9 8.4 67 91-167 1-67 (68)
44 PHA02945 interferon resistance 98.2 8.8E-06 1.9E-10 65.3 8.4 73 85-170 5-83 (88)
45 COG0539 RpsA Ribosomal protein 98.2 4.7E-06 1E-10 86.2 8.4 76 87-173 189-265 (541)
46 cd05688 S1_RPS1_repeat_ec3 S1_ 98.2 7.3E-06 1.6E-10 60.4 7.2 66 90-166 1-67 (68)
47 cd05694 S1_Rrp5_repeat_hs2_sc2 98.2 1.4E-05 3E-10 61.9 8.8 67 89-171 3-71 (74)
48 cd05685 S1_Tex S1_Tex: The C-t 98.2 8.5E-06 1.8E-10 59.8 7.0 67 91-167 1-68 (68)
49 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.1 1.5E-05 3.2E-10 59.9 8.1 67 91-167 1-68 (69)
50 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.0 3.4E-05 7.4E-10 58.9 7.7 68 91-168 1-71 (71)
51 cd00164 S1_like S1_like: Ribos 97.9 3.3E-05 7.2E-10 55.4 6.4 63 94-166 1-64 (65)
52 cd04460 S1_RpoE S1_RpoE: RpoE, 97.9 4.9E-05 1.1E-09 61.4 8.0 83 92-177 1-92 (99)
53 cd05684 S1_DHX8_helicase S1_DH 97.9 7.5E-05 1.6E-09 57.6 8.5 70 91-170 1-73 (79)
54 cd05695 S1_Rrp5_repeat_hs3 S1_ 97.9 6.1E-05 1.3E-09 56.7 7.2 65 91-167 1-66 (66)
55 TIGR02696 pppGpp_PNP guanosine 97.9 5.1E-05 1.1E-09 81.0 8.9 75 86-167 643-718 (719)
56 PRK11824 polynucleotide phosph 97.8 6.6E-05 1.4E-09 80.3 9.5 99 58-170 591-691 (693)
57 cd04473 S1_RecJ_like S1_RecJ_l 97.8 0.00026 5.7E-09 54.7 10.1 64 87-168 13-76 (77)
58 cd04455 S1_NusA S1_NusA: N-uti 97.8 0.00011 2.4E-09 55.3 7.7 56 89-161 2-57 (67)
59 PRK07400 30S ribosomal protein 97.8 9.3E-05 2E-09 72.2 9.2 74 87-171 193-267 (318)
60 PRK07400 30S ribosomal protein 97.8 8.1E-05 1.8E-09 72.6 8.5 76 86-171 27-103 (318)
61 PTZ00162 DNA-directed RNA poly 97.8 0.00062 1.3E-08 61.3 13.5 90 85-177 76-172 (176)
62 cd05690 S1_RPS1_repeat_ec5 S1_ 97.7 0.00016 3.5E-09 53.7 7.2 67 91-166 1-68 (69)
63 cd04465 S1_RPS1_repeat_ec2_hs2 97.7 0.00032 7E-09 52.4 8.1 66 91-169 1-67 (67)
64 TIGR03591 polynuc_phos polyrib 97.6 0.00014 3E-09 77.7 7.8 94 58-165 588-683 (684)
65 PRK07899 rpsA 30S ribosomal pr 97.6 0.00027 5.9E-09 72.7 9.2 71 89-170 207-278 (486)
66 PRK13806 rpsA 30S ribosomal pr 97.6 0.00027 5.8E-09 72.7 8.8 75 87-171 199-278 (491)
67 cd05689 S1_RPS1_repeat_ec4 S1_ 97.6 0.00041 8.9E-09 52.3 7.6 64 89-161 2-65 (72)
68 PLN00207 polyribonucleotide nu 97.5 0.00029 6.2E-09 76.9 8.8 75 87-171 750-825 (891)
69 PRK06676 rpsA 30S ribosomal pr 97.5 0.00059 1.3E-08 67.7 9.4 74 87-171 189-263 (390)
70 PRK07899 rpsA 30S ribosomal pr 97.5 0.00045 9.8E-09 71.2 8.8 74 88-171 33-107 (486)
71 PRK06299 rpsA 30S ribosomal pr 97.4 0.00057 1.2E-08 71.1 9.4 73 87-170 198-271 (565)
72 PRK06299 rpsA 30S ribosomal pr 97.4 0.0016 3.4E-08 67.8 11.8 73 89-171 459-532 (565)
73 PRK06676 rpsA 30S ribosomal pr 97.4 0.00066 1.4E-08 67.3 8.4 74 87-170 14-89 (390)
74 cd04471 S1_RNase_R S1_RNase_R: 97.3 0.0017 3.6E-08 49.8 8.6 72 90-167 1-81 (83)
75 COG2183 Tex Transcriptional ac 97.3 0.00054 1.2E-08 73.4 7.3 73 89-171 657-730 (780)
76 TIGR00717 rpsA ribosomal prote 97.3 0.0011 2.4E-08 68.0 9.2 73 87-170 184-257 (516)
77 PRK00087 4-hydroxy-3-methylbut 97.2 0.001 2.2E-08 70.6 8.8 72 88-170 475-547 (647)
78 COG0539 RpsA Ribosomal protein 97.2 0.00092 2E-08 69.5 7.9 73 89-171 276-349 (541)
79 PRK13806 rpsA 30S ribosomal pr 97.2 0.0012 2.7E-08 67.8 8.4 73 89-171 378-451 (491)
80 PRK12269 bifunctional cytidyla 97.2 0.0039 8.4E-08 68.4 12.4 105 57-171 625-738 (863)
81 TIGR00717 rpsA ribosomal prote 97.2 0.0016 3.6E-08 66.7 9.1 73 89-170 271-344 (516)
82 PRK12269 bifunctional cytidyla 97.1 0.0013 2.9E-08 71.9 8.5 74 88-170 576-650 (863)
83 PRK00087 4-hydroxy-3-methylbut 97.1 0.0022 4.8E-08 68.1 9.0 77 86-172 298-375 (647)
84 TIGR01953 NusA transcription t 97.0 0.0022 4.8E-08 63.4 8.1 113 85-214 126-255 (341)
85 PRK12327 nusA transcription el 97.0 0.0022 4.8E-08 63.9 7.6 112 86-214 130-257 (362)
86 cd04462 S1_RNAPII_Rpb7 S1_RNAP 96.8 0.01 2.2E-07 47.6 8.8 81 90-174 1-88 (88)
87 PRK09202 nusA transcription el 96.5 0.0054 1.2E-07 63.1 6.6 72 85-173 129-203 (470)
88 TIGR00757 RNaseEG ribonuclease 96.1 0.042 9.1E-07 55.8 10.7 81 86-169 21-109 (414)
89 COG1185 Pnp Polyribonucleotide 96.0 0.015 3.3E-07 61.7 6.9 75 86-170 615-689 (692)
90 TIGR02063 RNase_R ribonuclease 94.1 0.18 4E-06 54.2 8.5 81 87-168 624-708 (709)
91 PRK12328 nusA transcription el 93.8 0.14 3E-06 51.4 6.3 69 85-170 133-206 (374)
92 PRK12329 nusA transcription el 93.7 0.14 3.1E-06 52.3 6.3 84 85-184 147-248 (449)
93 PHA02858 EIF2a-like PKR inhibi 93.3 0.41 8.9E-06 38.4 7.0 71 85-167 10-84 (86)
94 PF13509 S1_2: S1 domain; PDB: 93.2 0.55 1.2E-05 34.9 7.3 61 90-169 1-61 (61)
95 PRK10811 rne ribonuclease E; R 93.2 0.56 1.2E-05 52.2 10.2 78 88-169 36-119 (1068)
96 PRK11642 exoribonuclease R; Pr 92.7 0.47 1E-05 52.1 8.8 76 87-168 640-724 (813)
97 TIGR00358 3_prime_RNase VacB a 91.7 0.72 1.6E-05 49.4 8.7 75 87-167 569-652 (654)
98 KOG1070 rRNA processing protei 91.7 0.66 1.4E-05 53.2 8.5 73 89-171 1161-1234(1710)
99 KOG2916 Translation initiation 91.7 0.22 4.8E-06 47.8 4.2 74 86-169 12-88 (304)
100 PRK11712 ribonuclease G; Provi 91.7 1.4 3.1E-05 45.7 10.5 95 74-169 22-122 (489)
101 KOG1856 Transcription elongati 90.0 0.41 8.9E-06 53.7 4.9 76 89-174 984-1063(1299)
102 COG2996 Predicted RNA-bindinin 84.9 3 6.6E-05 40.3 6.9 64 91-172 156-219 (287)
103 cd05699 S1_Rrp5_repeat_hs7 S1_ 84.6 5 0.00011 31.3 6.8 69 91-168 1-71 (72)
104 KOG1070 rRNA processing protei 84.2 1.6 3.5E-05 50.2 5.5 77 82-168 877-955 (1710)
105 KOG3298 DNA-directed RNA polym 82.6 7.1 0.00015 35.1 7.8 88 85-176 76-170 (170)
106 PF08292 RNA_pol_Rbc25: RNA po 81.8 6.6 0.00014 33.5 7.1 67 88-159 1-75 (122)
107 PF10246 MRP-S35: Mitochondria 79.3 6.2 0.00013 32.9 5.9 53 89-158 22-74 (104)
108 KOG1067 Predicted RNA-binding 78.4 4.7 0.0001 42.8 6.0 89 72-170 632-738 (760)
109 CHL00121 rpl27 ribosomal prote 76.8 5.1 0.00011 32.3 4.6 53 30-82 25-84 (86)
110 COG1530 CafA Ribonucleases G a 73.5 6 0.00013 41.1 5.4 74 89-168 36-112 (487)
111 KOG3297 DNA-directed RNA polym 72.2 16 0.00035 33.6 7.1 71 86-158 77-156 (202)
112 cd02393 PNPase_KH Polynucleoti 68.7 2.6 5.6E-05 31.2 1.1 39 181-219 5-48 (61)
113 PRK05435 rpmA 50S ribosomal pr 67.1 12 0.00026 29.9 4.6 45 29-73 24-70 (82)
114 PF01016 Ribosomal_L27: Riboso 64.4 9.8 0.00021 30.4 3.7 46 28-73 22-69 (81)
115 PF03961 DUF342: Protein of un 63.0 16 0.00035 37.3 6.0 35 48-82 144-181 (451)
116 COG1315 Uncharacterized conser 62.8 12 0.00027 39.1 5.0 52 48-99 220-276 (543)
117 PRK05054 exoribonuclease II; P 62.2 37 0.0008 36.5 8.7 73 86-160 554-634 (644)
118 TIGR00008 infA translation ini 57.4 57 0.0012 25.2 6.7 54 93-160 6-60 (68)
119 PLN00208 translation initiatio 54.3 57 0.0012 28.8 7.0 56 87-158 28-84 (145)
120 PRK12442 translation initiatio 52.5 66 0.0014 26.1 6.6 54 93-160 8-62 (87)
121 cd04456 S1_IF1A_like S1_IF1A_l 51.6 1.1E+02 0.0024 23.9 7.7 50 94-158 2-52 (78)
122 PRK04012 translation initiatio 51.6 81 0.0018 26.0 7.2 58 86-159 16-74 (100)
123 PF01176 eIF-1a: Translation i 50.5 39 0.00084 25.3 4.8 52 92-158 3-55 (65)
124 TIGR00062 L27 ribosomal protei 49.5 20 0.00044 28.7 3.2 45 29-73 24-70 (83)
125 PF08970 Sda: Sporulation inhi 49.3 31 0.00066 24.7 3.7 36 281-323 4-39 (46)
126 COG2932 Predicted transcriptio 48.1 1E+02 0.0022 27.9 8.1 67 34-102 135-210 (214)
127 cd05791 S1_CSL4 S1_CSL4: CSL4, 47.8 24 0.00053 28.2 3.5 28 89-116 62-90 (92)
128 COG0361 InfA Translation initi 45.7 99 0.0022 24.3 6.5 56 91-160 6-62 (75)
129 cd05793 S1_IF1A S1_IF1A: Trans 42.9 1.1E+02 0.0024 23.9 6.4 50 94-158 2-52 (77)
130 KOG4134 DNA-dependent RNA poly 42.0 30 0.00065 32.8 3.6 70 76-160 93-162 (253)
131 PTZ00329 eukaryotic translatio 36.3 1.5E+02 0.0033 26.4 7.0 76 87-193 28-104 (155)
132 PF14398 ATPgrasp_YheCD: YheC/ 36.2 19 0.00042 34.0 1.4 22 199-220 209-230 (262)
133 COG0557 VacB Exoribonuclease R 36.0 1.5E+02 0.0033 32.2 8.4 78 88-167 620-702 (706)
134 PF07494 Reg_prop: Two compone 33.4 31 0.00066 20.8 1.5 15 204-218 8-22 (24)
135 PTZ00329 eukaryotic translatio 33.3 58 0.0013 29.1 3.8 51 34-98 25-81 (155)
136 PF15057 DUF4537: Domain of un 32.9 3E+02 0.0065 23.2 8.8 49 96-155 17-66 (124)
137 COG1096 Predicted RNA-binding 32.3 95 0.0021 28.6 5.1 38 78-118 111-148 (188)
138 PLN00208 translation initiatio 31.6 89 0.0019 27.6 4.7 54 34-101 25-84 (145)
139 cd04454 S1_Rrp4_like S1_Rrp4_l 29.2 94 0.002 23.5 4.0 30 87-116 50-80 (82)
140 smart00652 eIF1a eukaryotic tr 28.7 2.9E+02 0.0064 21.8 7.0 54 88-157 2-56 (83)
141 cd05839 BR140_related The PWWP 28.1 52 0.0011 27.7 2.5 68 145-219 1-73 (111)
142 PRK04012 translation initiatio 27.8 58 0.0013 26.9 2.7 54 34-101 14-73 (100)
143 PF12508 DUF3714: Protein of u 27.6 3.3E+02 0.0072 25.2 7.9 56 57-114 50-111 (200)
144 PF11848 DUF3368: Domain of un 26.2 1.1E+02 0.0024 21.4 3.7 29 264-292 18-46 (48)
145 COG2996 Predicted RNA-bindinin 25.9 1.7E+02 0.0037 28.6 5.9 58 86-157 69-127 (287)
146 PF10844 DUF2577: Protein of u 25.4 1.4E+02 0.0031 24.2 4.6 23 88-112 14-36 (100)
147 PF01336 tRNA_anti-codon: OB-f 25.4 2.1E+02 0.0044 20.5 5.2 62 94-168 3-69 (75)
148 KOG4078 Putative mitochondrial 24.8 2E+02 0.0043 25.6 5.6 54 87-157 79-132 (173)
149 cd02394 vigilin_like_KH K homo 24.6 46 0.00099 23.9 1.4 38 182-219 4-50 (62)
150 KOG4600 Mitochondrial ribosoma 24.3 1.6E+02 0.0035 25.9 4.9 55 31-85 53-116 (144)
151 PF01959 DHQS: 3-dehydroquinat 24.3 7.5E+02 0.016 25.0 10.4 91 36-159 247-340 (354)
152 COG1792 MreC Cell shape-determ 24.2 1.5E+02 0.0032 28.7 5.2 22 94-115 156-177 (284)
153 smart00293 PWWP domain with co 24.1 49 0.0011 24.4 1.5 14 145-158 1-14 (63)
154 PRK00276 infA translation init 23.9 3.3E+02 0.0071 20.6 6.3 34 59-103 28-62 (72)
155 TIGR02062 RNase_B exoribonucle 23.6 2.3E+02 0.0049 30.6 7.0 72 86-160 550-630 (639)
156 COG3822 ABC-type sugar transpo 23.3 2.3E+02 0.0049 26.5 5.9 70 35-104 92-191 (225)
157 PF14444 S1-like: S1-like 22.3 2.7E+02 0.0059 20.9 5.1 16 85-100 31-46 (58)
158 PF14698 ASL_C2: Argininosucci 22.2 1.8E+02 0.0038 22.1 4.3 51 260-310 18-68 (70)
159 PF05257 CHAP: CHAP domain; I 21.1 1E+02 0.0022 25.2 3.1 27 85-111 60-98 (124)
160 PRK02290 3-dehydroquinate synt 21.1 8.6E+02 0.019 24.5 10.3 92 35-159 236-330 (344)
161 cd05834 HDGF_related The PWWP 20.9 61 0.0013 25.5 1.6 15 145-159 3-17 (83)
162 TIGR00523 eIF-1A eukaryotic/ar 20.9 4.7E+02 0.01 21.4 8.6 57 86-157 12-70 (99)
163 PRK06763 F0F1 ATP synthase sub 20.7 1.6E+02 0.0034 27.6 4.4 61 92-158 118-178 (213)
164 COG1107 Archaea-specific RecJ- 20.7 1.4E+02 0.0029 32.4 4.4 80 75-170 106-187 (715)
165 PRK00215 LexA repressor; Valid 20.7 3.3E+02 0.0071 24.3 6.5 35 69-103 165-203 (205)
166 PRK09521 exosome complex RNA-b 20.4 1.6E+02 0.0034 26.5 4.3 29 89-118 120-148 (189)
167 COG0211 RpmA Ribosomal protein 20.2 2E+02 0.0044 23.2 4.3 54 30-83 25-85 (87)
168 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 20.1 1.7E+02 0.0036 22.3 3.9 24 88-111 55-79 (86)
No 1
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=100.00 E-value=1.2e-80 Score=572.74 Aligned_cols=300 Identities=46% Similarity=0.757 Sum_probs=270.7
Q ss_pred ccccchhhHHHHHHHHHHHHhhccCCCCCCceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEECcEEEEEecC
Q 020356 4 LQLSFNQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALR 83 (327)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~nk~v~V~pl~ 83 (327)
++++++|.++++.+++.+.. +++.+....++|+||+.++. +++||+|||||+.||.|+||++|.++++||+++|+|++
T Consensus 1 ~~~~~s~~~~v~~~~~~e~~-~a~~~~~~~~ivtPG~~V~~-d~~fmRGHGTy~~d~~i~ssvaG~v~rvNkLi~V~plk 78 (301)
T KOG3013|consen 1 LQFPLSQALKVNFERMSERE-SASDTSDHSTIVTPGELVTD-DPGFMRGHGTYVRDGEIYSSVAGVVQRVNKLISVKPLK 78 (301)
T ss_pred CCccccCCccccchhcchhh-hhcccccCceeecCCccccC-chhhhhcccceecCCeEEEeecchhhhhcceEEEeehh
Confidence 47899999999999999987 33344556789999999975 44699999999999999999999999999999999999
Q ss_pred CccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCc
Q 020356 84 ARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGS 163 (327)
Q Consensus 84 ~rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~ 163 (327)
.||.|++||+|+|||++|++++|+||+|+.++|+|+||++|+|||++|||...||++||+||++||+|+||||+++.||+
T Consensus 79 ~rY~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~dGs 158 (301)
T KOG3013|consen 79 SRYAPEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFHDGS 158 (301)
T ss_pred hhcCCccCCEEEEEeeeeecceeEEecccccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhccCCe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEccCCCccCCCCeEEEeChhhhhhccccccccCccceEEEEeecceeeeccccccccccccccCCCchhhhhhccC
Q 020356 164 LQLQARNQKYGKLERGQLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIAKCDK 243 (327)
Q Consensus 164 i~Lstr~~~lGkL~~G~lv~V~~~li~r~~~h~~~L~~~~~eiivG~NG~IWI~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (327)
+.||||+.+||||.+|++++|||.|++|.|.|||.|+ +|+++|+||||||||.+..... .++ +...+++..
T Consensus 159 ~sLhTRS~KYGKL~~G~lvkVpp~Lvkr~K~hfh~lp-~g~~vIlG~NGyIWv~~s~~~~-------~ee-~~~~~~~~~ 229 (301)
T KOG3013|consen 159 LSLHTRSLKYGKLGQGILVKVPPALVKRSKTHFHNLP-GGVDVILGCNGYIWVGPSIKDQ-------EEE-ESIGSYSSE 229 (301)
T ss_pred EEEEecchhcccccCceEEEeCHHHhhhhhhhhccCC-CCeEEEEecCceEEecCCCCcc-------hhh-hcccccccC
Confidence 9999999999999999999999999999999999998 9999999999999999854311 111 111122211
Q ss_pred CCCccccCCCCCCCHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHhhhhCCCCchhcccchHHHHHHHHHHHHhhhh
Q 020356 244 NSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLDIHDMLGSEFYVLVAESEAERRSLS 323 (327)
Q Consensus 244 ~~~~~~~~~~~~~~~~~r~~i~r~~n~i~~l~~~~~~i~~~~i~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 323 (327)
.++.||.++|++|||++|||++|+.++++||+++|+++||+| +-++++|||.+++|..+|+.+++|+..+
T Consensus 230 --------~~~~v~~~~R~~i~Rl~n~i~~La~~~~~i~~~sI~~~ye~S--~~~~i~ell~~~~~~~ia~~~~~rl~~~ 299 (301)
T KOG3013|consen 230 --------NDEHVSLNTRVNICRLANCIRALANCSIMITLTSITYCYEAS--LPYEIHELLEQEFMEVIAMEIAARLRTK 299 (301)
T ss_pred --------cccCCCHHHHHHHHHHHHHHHHHHhcCeeeeHHHHHHHHHhc--CcchHHHHhhhhHHHHHHHHHHHHHHhh
Confidence 124599999999999999999999999999999999999999 5569999999999999999999998765
Q ss_pred h
Q 020356 324 K 324 (327)
Q Consensus 324 ~ 324 (327)
.
T Consensus 300 ~ 300 (301)
T KOG3013|consen 300 R 300 (301)
T ss_pred c
Confidence 3
No 2
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-48 Score=359.07 Aligned_cols=225 Identities=29% Similarity=0.462 Sum_probs=189.6
Q ss_pred CCCceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEECcEEEEEecCCccCCCCCCEEEEEEEEEecceEEEEE
Q 020356 31 NPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEI 110 (327)
Q Consensus 31 ~~~~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~nk~v~V~pl~~rY~P~vGDiVIGrV~~V~~~~w~VDI 110 (327)
+..++|+|||.|.. ++.+++|||||..++++||+++|.+..+++.+.|+|++++|.|++||+|||+|+++.+++|+|||
T Consensus 6 ~~~~iV~PGd~vl~-~~~~~~G~Gty~~~~~iyssv~G~~~~~~~~v~VIpl~g~YiP~~gD~VIG~I~~v~~~~W~VDI 84 (239)
T COG1097 6 SMRKIVLPGDLVLA-EGSYKLGHGTYFEGGKIYSSVVGLLDVKGKLVRVIPLEGRYIPEVGDVVIGKIIEVGPSGWKVDI 84 (239)
T ss_pred cccceecCCCccCC-CCCEecCCCcEecCCEEEEEEEeEEEEeCCEEEEEeCCCcccCCCCCEEEEEEEEEcccceEEEc
Confidence 44689999997754 44699999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEccCCCccCCCCeEEEeChhhhh
Q 020356 111 NFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVK 190 (327)
Q Consensus 111 ~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~~~lGkL~~G~lv~V~~~li~ 190 (327)
++++.|.||+|++ ++|+.+.++.+|+.+|++||+|+|||+++++++++.||||+.+||+|++|++++|+|++++
T Consensus 85 ~sp~~A~L~ls~~------~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p~kVp 158 (239)
T COG1097 85 GSPYPALLSLSDF------LRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPPSKVP 158 (239)
T ss_pred CCccceEeehhhh------hcccccccccccccccccCCEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEchhhcc
Confidence 9999999999976 3677777788999999999999999999999999999999999999999999999999999
Q ss_pred hcccc----ccccC-ccceEEEEeecceeeeccccccccccccccCCCchhhhhhccCCCCccccCCCCCCCHHHHHHHH
Q 020356 191 RRKQH----FHHLE-EYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIAKCDKNSMDLDEQDGTCTPREARQNIC 265 (327)
Q Consensus 191 r~~~h----~~~L~-~~~~eiivG~NG~IWI~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~i~ 265 (327)
|...| +.+|+ +++|+|+||+||||||++..+...... ....+..+... -++--|++.++
T Consensus 159 Rvig~~~sm~~~l~~~~~~~I~VG~NG~IWV~~~~~~~e~~~--------~~aI~~ie~ea--------~~~gltdr~~~ 222 (239)
T COG1097 159 RVIGKKGSMLNMLKEKTGCEIIVGQNGRIWVDGENESLEELA--------IEAIRKIEREA--------HTSGLTDRIKE 222 (239)
T ss_pred eEecCCCcHHHHhhhhcCeEEEEecCCEEEecCCCcchHHHH--------HHHHHHHhhhh--------hhhhHHHHHHH
Confidence 98644 55563 789999999999999999765321110 01111111101 16778899999
Q ss_pred HHHHHHHHHHhCCC
Q 020356 266 RIANAIRVLSRLGF 279 (327)
Q Consensus 266 r~~n~i~~l~~~~~ 279 (327)
++.+++ .|++.+.
T Consensus 223 ~i~~~~-~~~~~~~ 235 (239)
T COG1097 223 FLKKLL-RLKESKD 235 (239)
T ss_pred HHHHHH-hcccccc
Confidence 999988 5554443
No 3
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=100.00 E-value=3.3e-42 Score=319.98 Aligned_cols=183 Identities=31% Similarity=0.521 Sum_probs=165.7
Q ss_pred CCCceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEECcEEEEEecCCccCCCCCCEEEEEEEEEecceEEEEE
Q 020356 31 NPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEI 110 (327)
Q Consensus 31 ~~~~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~nk~v~V~pl~~rY~P~vGDiVIGrV~~V~~~~w~VDI 110 (327)
....+|+|||.|+ +++|++|+|||..+|+++||++|.+..+++.++|+|++++|.|++||+|+|+|+++++++|+|||
T Consensus 6 ~~~~~V~PGd~l~--~~~~~~G~Gty~~~g~i~As~~G~~~~~~~~i~V~p~~~~y~P~vGDiViG~V~~i~~~~~~vdI 83 (235)
T PRK04163 6 EDRKIVVPGDLLA--EGEFKAGRGTYKENGKIYSTVVGLVDIKDDKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGWEVDI 83 (235)
T ss_pred eCCcEECCCCCcC--cCCeecCCceEEeCCEEEEEEeEEEEEECCEEEEEECCCcccCCCCCEEEEEEEEEeCceEEEEe
Confidence 3468999999996 34599999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEccCCCccCCCCeEEEeChhhhh
Q 020356 111 NFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVK 190 (327)
Q Consensus 111 ~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~~~lGkL~~G~lv~V~~~li~ 190 (327)
++++.|+||++++. +++.+.|+.+|+++|++||+|+|+|+++++++.+.|||++.+||+|.+|++++|+|.+++
T Consensus 84 ~~~~~g~L~~s~i~------~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~~~lG~L~~G~~~~V~~~~i~ 157 (235)
T PRK04163 84 NSPYKAYLPVSEVL------GRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGKGLGKIEGGTIVEIKPVKVP 157 (235)
T ss_pred CCCceeEEEHHHcC------CCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcCCCCCccCCCEEEEECHHHHH
Confidence 99999999999874 344456778999999999999999999998888999999999999999999999999999
Q ss_pred hcc----cccccc-CccceEEEEeecceeeeccccc
Q 020356 191 RRK----QHFHHL-EEYGIDLIIGCNGYIWIGEHVE 221 (327)
Q Consensus 191 r~~----~h~~~L-~~~~~eiivG~NG~IWI~~~~~ 221 (327)
++. .++..| +.++|+|++|.||+|||.+++.
T Consensus 158 ~lig~~g~~i~~l~~~~~~~I~ig~NG~VwI~~~~~ 193 (235)
T PRK04163 158 RVIGKKGSMINMLKEETGCDIIVGQNGRIWIKGPDE 193 (235)
T ss_pred hhcCCCChhHhhhhhhhCcEEEEcCCcEEEEeeCCH
Confidence 983 345555 3689999999999999988654
No 4
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-33 Score=254.94 Aligned_cols=177 Identities=26% Similarity=0.412 Sum_probs=157.4
Q ss_pred ceEecCCccCCCC-CceeecCCEEeeCCeEEEEEeeEEEEE--Cc----EEEEEecCCccCCCCCCEEEEEEEEEecceE
Q 020356 34 SCVTVGDTIPVYE-DGILKGHGTSDQKGELAATVCGVVERI--NK----LIYVRALRARYKPETGDIVIGRVIEVVPKRW 106 (327)
Q Consensus 34 ~iV~PGD~I~~~e-e~~~~G~Gty~~~g~i~Ssv~G~v~~~--nk----~v~V~pl~~rY~P~vGDiVIGrV~~V~~~~w 106 (327)
.+.+|||.++... ....+|+|.+..++.+..+.+|.+... ++ ..||...++||+|.+||.|||+|+...++.|
T Consensus 2 ~~~~pg~~~~~~~~~sv~~G~g~~~~g~~~~~~~~G~~~~~~~gk~~~~v~~vds~~kRYiP~~~D~VIGiV~~~~gd~y 81 (230)
T KOG1004|consen 2 TFYFPGDSIPRPRLCSVVLGPGLRRRGQERLVTKCGRLRHKEPGKGGGGVYWVDSQQKRYIPVKGDHVIGIVTSKSGDIY 81 (230)
T ss_pred ceecCCcccccCccCceeecCCccccCceEEeccccceeeccCCcccceeEEEecccceecCCCCCEEEEEEEeccCceE
Confidence 5789999997542 248899999999999999999977663 33 6799999999999999999999999999999
Q ss_pred EEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEccC-----CCccCCCCeE
Q 020356 107 KLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQ-----KYGKLERGQL 181 (327)
Q Consensus 107 ~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~~-----~lGkL~~G~l 181 (327)
+|||+.++.|. |+.++|+|+++|+||+ |+.||+|||+|...+++.+++|+|-+. +||+|++|++
T Consensus 82 kVDigg~~~a~--L~~laFe~AtkrNrPn---------l~vGdliyakv~~a~~~~Epel~Cids~graaGfG~LkdG~i 150 (230)
T KOG1004|consen 82 KVDIGGSEPAS--LSYLAFEGATKRNRPN---------LQVGDLIYAKVVDANKDMEPELTCIDSTGRAAGFGVLKDGMI 150 (230)
T ss_pred EEecCCCCeee--eeeccccCccccCCCc---------cccccEEEEEEEecCCCcCcceEEEcccCcccCcccccCceE
Confidence 99999999988 6889999999999998 899999999999999999999999555 9999999999
Q ss_pred EEeChhhhhhccc-ccccc----CccceEEEEeecceeeeccccc
Q 020356 182 LTVDPYLVKRRKQ-HFHHL----EEYGIDLIIGCNGYIWIGEHVE 221 (327)
Q Consensus 182 v~V~~~li~r~~~-h~~~L----~~~~~eiivG~NG~IWI~~~~~ 221 (327)
++++++++|++.. -+..| +.++|||++|+||+|||++.+.
T Consensus 151 f~vs~~~~R~Ll~p~~~iLq~vGk~~~FEia~GlNGriWV~ae~~ 195 (230)
T KOG1004|consen 151 FKVSLGLCRKLLLPDCPILQTVGKKYPFEIAFGLNGRIWVKAETL 195 (230)
T ss_pred EEecHHHHHHHHcCCCcHHHHhhcccceEEEEecCceEEEeccCc
Confidence 9999999999864 35555 4789999999999999988654
No 5
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=99.94 E-value=3.7e-26 Score=205.78 Aligned_cols=134 Identities=31% Similarity=0.401 Sum_probs=117.7
Q ss_pred CCCceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEE--CcEEEEEecCC-ccCCCCCCEEEEEEEEEecceEE
Q 020356 31 NPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERI--NKLIYVRALRA-RYKPETGDIVIGRVIEVVPKRWK 107 (327)
Q Consensus 31 ~~~~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~--nk~v~V~pl~~-rY~P~vGDiVIGrV~~V~~~~w~ 107 (327)
+..++|+|||.|+..++ |++|+|||+++|.|+||++|.++.+ ++.++|.|++. .|.|++||+|+|+|+++.+++|+
T Consensus 3 ~~~~~V~PGe~l~~~~e-~~~G~Gty~~~~~i~as~~G~~~id~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~i~~~g~~ 81 (189)
T PRK09521 3 KQGDLVLPGDYLAVIEE-YLPGEGTYEDNGEVYASVVGKVFIDDINRKISVIPFKKTPPLLKKGDIVYGRVVDVKEQRAL 81 (189)
T ss_pred ccCCEECCCCccccccc-eEcCCCEEeeCCEEEEEeeEEEEEcCCCCEEEEecCcCCCCCCCCCCEEEEEEEEEcCCeEE
Confidence 35689999999987666 9999999999999999999999874 56899999987 89999999999999999999999
Q ss_pred EEEcC----------ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEccCCCccCC
Q 020356 108 LEINF----------TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLE 177 (327)
Q Consensus 108 VDI~s----------~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~~~lGkL~ 177 (327)
|||.+ ...|++|.++++ ....+ +|+++|++||+|.|+|++++ +.+.||+++.+||+|.
T Consensus 82 V~I~~~~~~~~~l~~~~~G~l~~s~i~--------~~~~~--~~~~~~~~GD~V~akV~~i~--~~i~LS~k~~~lGvv~ 149 (189)
T PRK09521 82 VRIVSIEGSERELATSKLAYIHISQVS--------DGYVE--SLTDAFKIGDIVRAKVISYT--DPLQLSTKGKDLGVIY 149 (189)
T ss_pred EEEEEecccccccCCCceeeEEhhHcC--------hhhhh--hHHhccCCCCEEEEEEEecC--CcEEEEEecCCceEEE
Confidence 99964 467888887664 12222 78999999999999999998 7899999999999996
No 6
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=3.1e-24 Score=191.59 Aligned_cols=134 Identities=31% Similarity=0.452 Sum_probs=117.7
Q ss_pred CCCceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEE--ECcEEEEEecCC-ccCCCCCCEEEEEEEEEecceEE
Q 020356 31 NPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVER--INKLIYVRALRA-RYKPETGDIVIGRVIEVVPKRWK 107 (327)
Q Consensus 31 ~~~~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~--~nk~v~V~pl~~-rY~P~vGDiVIGrV~~V~~~~w~ 107 (327)
....+|+|||.|+..|| |++|.|||+++|.|+|+..|.+.+ .|..++|+|.++ ..+|+.||+|+|+|+++..+++.
T Consensus 3 ~~g~~v~PGd~~a~~EE-~~~G~gt~~~~g~i~Aa~~G~~~~d~~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~~~~a~ 81 (188)
T COG1096 3 KDGTFVLPGDVLAVIEE-FLPGEGTYEEGGEIRAAATGVVRRDDKNRVISVKPGKKTPPLPKGGDIVYGRVTDVREQRAL 81 (188)
T ss_pred ccCcEEcCcceeeeeee-eecCCCeEeECCEEEEeecccEEEcccceEEEeccCCCCCCCCCCCCEEEEEEeeccceEEE
Confidence 35789999999998888 999999999999999999999998 578999999998 78999999999999999999999
Q ss_pred EEEcC----------ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEccCCCccCC
Q 020356 108 LEINF----------TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLE 177 (327)
Q Consensus 108 VDI~s----------~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~~~lGkL~ 177 (327)
|.|-+ +..|.+|+|++. ..+.. +++++|++||+|+|+|.+.. ..+.|||+++.||++.
T Consensus 82 V~i~~ve~~~r~~~~~~~~~ihvs~~~--------~~~~~--~~~d~f~~GDivrA~Vis~~--~~~~Lst~~~dlGVI~ 149 (188)
T COG1096 82 VRIVGVEGKERELATSGAADIHVSQVR--------DGYVE--KLSDAFRIGDIVRARVISTG--DPIQLSTKGNDLGVIY 149 (188)
T ss_pred EEEEEEecccccCCCCceeeEEEEecc--------ccccc--ccccccccccEEEEEEEecC--CCeEEEecCCcceEEE
Confidence 99854 356778888763 12222 56789999999999999987 5799999999999986
No 7
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=99.85 E-value=5.6e-21 Score=168.46 Aligned_cols=159 Identities=25% Similarity=0.252 Sum_probs=129.7
Q ss_pred CceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEE--CcEEEEEecC----CccCCCCCCEEEEEEEEEecceE
Q 020356 33 NSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERI--NKLIYVRALR----ARYKPETGDIVIGRVIEVVPKRW 106 (327)
Q Consensus 33 ~~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~--nk~v~V~pl~----~rY~P~vGDiVIGrV~~V~~~~w 106 (327)
..+|+|||++|..++.+..|.|||+.+++|+||++|...+. ++.+.|.... ..-+|.+||||..+|..++.+++
T Consensus 5 ~~~~lpG~~~c~~e~~~~~g~Gtye~~~yI~aS~ag~~~~~~~~~~~~v~~~~~~~~~~~LP~~G~IVtarV~~i~~rfA 84 (193)
T KOG3409|consen 5 ETLVLPGEVVCRAEGEYRMGEGTYERNGYIFASVAGVNFRDNLVQKIEVVSVEKQLFNELLPFVGAIVTARVSRINLRFA 84 (193)
T ss_pred eEEEcccceeeecccccccccceeecCCeEEeccccceeecCCccceeeeeecccchhhcCCccCcEEEEEEEeecccee
Confidence 57899999999887779999999999999999999955443 3455554433 35799999999999999999999
Q ss_pred EEEEcCccceeeecccccCCCccc---ccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEccCCCccC------C
Q 020356 107 KLEINFTQDAILMLSSMNLPDGIQ---RRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKL------E 177 (327)
Q Consensus 107 ~VDI~s~~~a~L~ls~v~fpg~i~---rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~~~lGkL------~ 177 (327)
+|+|-+..+-.|.- .|.|.++ .|.++.|.+++.+.|+|||+|.|+|.+.+...++.|||.++.||++ .
T Consensus 85 kv~I~~V~d~~lk~---~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LTtAeneLGVV~a~as~~ 161 (193)
T KOG3409|consen 85 KVDILSVGDKPLKK---SFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLTTAENELGVVFARASET 161 (193)
T ss_pred eEEEEEEcCEEhhh---hhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcEEEEEecccceEEEEecccc
Confidence 99999876655321 3666555 4567788899999999999999999997766689999999999998 3
Q ss_pred CCeEEEeChhhhhhccc
Q 020356 178 RGQLLTVDPYLVKRRKQ 194 (327)
Q Consensus 178 ~G~lv~V~~~li~r~~~ 194 (327)
++.|++|+...+.--+.
T Consensus 162 g~~M~pvdw~~mqsp~T 178 (193)
T KOG3409|consen 162 GEPMVPVDWQEMQSPKT 178 (193)
T ss_pred CCceeeccceeEEcCcc
Confidence 78899988776554333
No 8
>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=99.85 E-value=4.4e-21 Score=153.19 Aligned_cols=75 Identities=29% Similarity=0.421 Sum_probs=68.5
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCce
Q 020356 85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSL 164 (327)
Q Consensus 85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i 164 (327)
||+|++||+|||+|+++..++|+|||++++.|.||+ .+|+|+++|+|+. |++||+|+|||++++++.++
T Consensus 1 rY~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~--~~f~gatk~~rp~---------L~~GDlV~ArV~~~~~~~~~ 69 (86)
T cd05790 1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSY--LAFEGATKRNRPN---------LNVGDLVYARVVKANRDMEP 69 (86)
T ss_pred CCcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEech--HHccccccccccc---------CCCCCEEEEEEEecCCCCCe
Confidence 699999999999999999999999999999999877 4699997776544 89999999999999999999
Q ss_pred EEEEcc
Q 020356 165 QLQARN 170 (327)
Q Consensus 165 ~Lstr~ 170 (327)
+|+|.+
T Consensus 70 eLtc~~ 75 (86)
T cd05790 70 ELSCVD 75 (86)
T ss_pred EEEEeC
Confidence 999965
No 9
>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=99.81 E-value=1.1e-19 Score=146.54 Aligned_cols=83 Identities=28% Similarity=0.396 Sum_probs=75.3
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEE--------cCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEe
Q 020356 86 YKPETGDIVIGRVIEVVPKRWKLEI--------NFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRS 157 (327)
Q Consensus 86 Y~P~vGDiVIGrV~~V~~~~w~VDI--------~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~s 157 (327)
|.|++||+|+|+|++++.++|.||| ++++.|.||.+++ +..+.|+++|+++|++||+|+|||++
T Consensus 2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv--------~~~~~d~~~~~~~f~~GDiV~AkVis 73 (92)
T cd05791 2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDI--------RATEKDKVEMYKCFRPGDIVRAKVIS 73 (92)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHc--------cccccchHHHHhhcCCCCEEEEEEEE
Confidence 8999999999999999999999999 7788888888765 34667888999999999999999999
Q ss_pred cCCCCceEEEEccCCCccC
Q 020356 158 SQGDGSLQLQARNQKYGKL 176 (327)
Q Consensus 158 v~~~g~i~Lstr~~~lGkL 176 (327)
+++..++.|||++++||++
T Consensus 74 ~~~~~~~~Lst~~~~lGVv 92 (92)
T cd05791 74 LGDASSYYLSTAENELGVV 92 (92)
T ss_pred cCCCCCcEEEecCCCCccC
Confidence 9877789999999999985
No 10
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.70 E-value=1.3e-16 Score=124.73 Aligned_cols=82 Identities=35% Similarity=0.477 Sum_probs=73.9
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCce
Q 020356 85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSL 164 (327)
Q Consensus 85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i 164 (327)
+|+|++||+|+|+|+++..+.|.|||++..+|++|+++++-+ ...+|++.|++||+|.|+|++++.++.+
T Consensus 1 ~y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~----------~~~~~~~~~~~GD~i~~~V~~~~~~~~i 70 (82)
T cd04454 1 RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEK----------DKKEIRKSLQPGDLILAKVISLGDDMNV 70 (82)
T ss_pred CCCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCc----------chHHHHhcCCCCCEEEEEEEEeCCCCCE
Confidence 699999999999999999999999999999999999987521 1237888999999999999999877889
Q ss_pred EEEEccCCCccC
Q 020356 165 QLQARNQKYGKL 176 (327)
Q Consensus 165 ~Lstr~~~lGkL 176 (327)
.||+++.+||+|
T Consensus 71 ~LS~~~~~~Gvi 82 (82)
T cd04454 71 LLTTADNELGVI 82 (82)
T ss_pred EEEECCCCCccC
Confidence 999999999986
No 11
>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=99.59 E-value=9.2e-15 Score=114.90 Aligned_cols=86 Identities=62% Similarity=0.925 Sum_probs=74.7
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCce
Q 020356 85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSL 164 (327)
Q Consensus 85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i 164 (327)
+|.|++||+|.|+|+++.+++|+|+|+....|+||++++.-+ +......++.+.|++||.|.|+|+++++++.+
T Consensus 1 ~y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~------~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~~i 74 (86)
T cd05789 1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLP------RTDEDELNMRSYLDEGDLIVAEVQSVDSDGSV 74 (86)
T ss_pred CCcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCC------CCccchHHHHhhCCCCCEEEEEEEEECCCCCE
Confidence 699999999999999999999999999999999999987521 11112237788899999999999999888899
Q ss_pred EEEEccCCCccC
Q 020356 165 QLQARNQKYGKL 176 (327)
Q Consensus 165 ~Lstr~~~lGkL 176 (327)
.||++..+||+|
T Consensus 75 ~LS~~~~~~g~~ 86 (86)
T cd05789 75 SLHTRSLKYGKL 86 (86)
T ss_pred EEEeCcccccCC
Confidence 999999999986
No 12
>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=99.38 E-value=9.1e-13 Score=104.50 Aligned_cols=69 Identities=38% Similarity=0.484 Sum_probs=44.0
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEcCc----------cceeeecccccCCCcccc---cccccchhhhhcccCCCCEEEE
Q 020356 87 KPETGDIVIGRVIEVVPKRWKLEINFT----------QDAILMLSSMNLPDGIQR---RRTAVDELNMRSIFTENDLVCA 153 (327)
Q Consensus 87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~----------~~a~L~ls~v~fpg~i~r---rr~~~de~~mr~~~~~GDlV~A 153 (327)
+|++||+|+|+|++++++++.|+|.+. .... +.+ .|.|.+++ |.++.|+++|.++|+|||+|+|
T Consensus 1 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~--l~~-~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA 77 (82)
T PF10447_consen 1 LPKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRP--LKE-PFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRA 77 (82)
T ss_dssp ---TT-EEEEEEEEE-SSEEEEEEEES----------SSS-------SS-S-EEEEGGGT-SS----GGGT--SSSEEEE
T ss_pred CCCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcc--ccc-ccEEEEEeeeecccccchhhHHhccCCCCEEEE
Confidence 599999999999999999999999876 2222 222 47777764 5678899999999999999999
Q ss_pred EEEec
Q 020356 154 EVRSS 158 (327)
Q Consensus 154 eV~sv 158 (327)
+|.|+
T Consensus 78 ~ViSl 82 (82)
T PF10447_consen 78 RVISL 82 (82)
T ss_dssp EEEEE
T ss_pred EEeeC
Confidence 99984
No 13
>PF14382 ECR1_N: Exosome complex exonuclease RRP4 N-terminal region; PDB: 2NN6_I 3M7N_C 2BA1_A 3M85_C.
Probab=99.19 E-value=1.4e-11 Score=84.79 Aligned_cols=39 Identities=36% Similarity=0.525 Sum_probs=33.9
Q ss_pred eEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEEC
Q 020356 35 CVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERIN 74 (327)
Q Consensus 35 iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~n 74 (327)
+|+|||.|+..++ |++|+|||+.+|+|+||++|.++++|
T Consensus 1 iV~PG~~l~~~~e-~~~G~GTY~~~g~I~asv~G~v~~~n 39 (39)
T PF14382_consen 1 IVVPGDRLGSSEE-YMPGHGTYVRDGNIYASVAGTVKIDN 39 (39)
T ss_dssp EE-TT-EEEETTT-SEESTTEEEETTEEEESSSEEEEEET
T ss_pred CCCCCCEeecCCC-EecCCCEEEeCCEEEEEeeEEEEEcC
Confidence 6999999998665 99999999999999999999998865
No 14
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=98.92 E-value=2.3e-09 Score=90.68 Aligned_cols=77 Identities=14% Similarity=0.231 Sum_probs=69.1
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEE
Q 020356 87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQL 166 (327)
Q Consensus 87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~L 166 (327)
.+++||+|-|+||++++.++||++.....+++|||+++ ..++. ++.+++.+||-|.++|++++++|.+.|
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa--------~~fVk--dI~d~L~vG~eV~vKVl~ide~GKisL 71 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIA--------DGFVK--DIHDHLKVGQEVKVKVLDIDENGKISL 71 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecCCCcceEEehHhh--------hhhHH--hHHHHhcCCCEEEEEEEeeccCCCcce
Confidence 46899999999999999999999999999999999985 23444 789999999999999999999999999
Q ss_pred EEccCCC
Q 020356 167 QARNQKY 173 (327)
Q Consensus 167 str~~~l 173 (327)
|+|....
T Consensus 72 SIr~~~e 78 (129)
T COG1098 72 SIRKLEE 78 (129)
T ss_pred ehHHhhh
Confidence 9997544
No 15
>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=98.86 E-value=1.2e-08 Score=78.24 Aligned_cols=70 Identities=21% Similarity=0.398 Sum_probs=59.1
Q ss_pred CCCCEEEEEEEEEec-ceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEE
Q 020356 89 ETGDIVIGRVIEVVP-KRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQ 167 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~-~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Ls 167 (327)
++||+|.|+|+++.+ .+++|++....+|.+|+|+++ ..+ .. ++.+.|++||.|.|+|.+++. +.+.||
T Consensus 2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s------~~~--~~--~~~~~~~~Gd~v~~kV~~~~~-~~i~LS 70 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLS------DSY--TE--NPLEGFKPGKIVRCCILSKKD-GKYQLS 70 (72)
T ss_pred CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhc------Ccc--cC--CHHHhCCCCCEEEEEEEEecC-CEEEEE
Confidence 589999999999986 799999999999999999875 111 11 446789999999999999975 789998
Q ss_pred Ec
Q 020356 168 AR 169 (327)
Q Consensus 168 tr 169 (327)
+|
T Consensus 71 l~ 72 (72)
T cd05704 71 LR 72 (72)
T ss_pred eC
Confidence 75
No 16
>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=98.77 E-value=3.9e-08 Score=74.03 Aligned_cols=69 Identities=25% Similarity=0.355 Sum_probs=57.5
Q ss_pred CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEEEc
Q 020356 91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQAR 169 (327)
Q Consensus 91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Lstr 169 (327)
||+|.|+|+++.+++|+|+++....|+||.+++.-+ + .+ ++.++|++||.|.|+|.++++ .+.+.||.+
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~------~--~~--~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDD------P--IE--NGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCcc------c--cC--CHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 899999999999999999999899999999987521 1 11 567889999999999999984 456877753
No 17
>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=98.69 E-value=1.3e-07 Score=71.92 Aligned_cols=72 Identities=17% Similarity=0.290 Sum_probs=59.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEEcC--ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCce
Q 020356 88 PETGDIVIGRVIEVVPKRWKLEINF--TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSL 164 (327)
Q Consensus 88 P~vGDiVIGrV~~V~~~~w~VDI~s--~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i 164 (327)
|+.|++|.|+|+++...+|+|++.. ...|++|++++... + . . ++.+.|+.||.|.|+|.+++. .+.+
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~------~-~-~--~~~~~~~~Gd~v~vkv~~~d~~~~~i 70 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRR------R-I-R--SIRKLVKVGRKEVVKVIRVDKEKGYI 70 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCc------c-c-C--CHHHeeCCCCEEEEEEEEEECCCCEE
Confidence 7899999999999999999999974 37999999987511 1 1 1 457889999999999999986 4678
Q ss_pred EEEEc
Q 020356 165 QLQAR 169 (327)
Q Consensus 165 ~Lstr 169 (327)
.|+++
T Consensus 71 ~ls~k 75 (76)
T cd04452 71 DLSKK 75 (76)
T ss_pred EEEEc
Confidence 99886
No 18
>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=98.66 E-value=2e-07 Score=68.59 Aligned_cols=69 Identities=23% Similarity=0.386 Sum_probs=58.1
Q ss_pred CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEc
Q 020356 91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQAR 169 (327)
Q Consensus 91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr 169 (327)
||+|.|+|+++.+.+|+|+|.....|++|.+++. + .+ .. ++.+.|++||.|.++|.+++..+.+.||++
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 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIA--H----KR--VK--DVKDVLKEGDKVKVKVLSIDARGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcC--C----cc--cC--CHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence 8999999999999999999999999999998764 1 11 11 445779999999999999987778999875
No 19
>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=98.64 E-value=2e-07 Score=70.17 Aligned_cols=71 Identities=23% Similarity=0.328 Sum_probs=59.7
Q ss_pred CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEEEEc
Q 020356 91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQLQAR 169 (327)
Q Consensus 91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~Lstr 169 (327)
||+|.|+|+++.+++|+|+|.....|++|.+++.-+ . .+ ++.+.|++||.|.|+|.+++.. +.+.|+++
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~------~--~~--~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k 70 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRD------R--VE--DATERFKVGDEVEAKITNVDRKNRKISLSIK 70 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCc------c--cc--CHHHccCCCCEEEEEEEEEeCCCCEEEEEEE
Confidence 899999999999999999999889999999987511 1 11 4567799999999999999875 67999987
Q ss_pred cC
Q 020356 170 NQ 171 (327)
Q Consensus 170 ~~ 171 (327)
..
T Consensus 71 ~~ 72 (73)
T cd05691 71 AK 72 (73)
T ss_pred Ec
Confidence 54
No 20
>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=98.61 E-value=3e-07 Score=69.69 Aligned_cols=72 Identities=19% Similarity=0.314 Sum_probs=60.9
Q ss_pred CCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEE
Q 020356 88 PETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQL 166 (327)
Q Consensus 88 P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~L 166 (327)
|++||+|-|+|+++..++++|+++....|++|+++++.. . .+ +....|++||.|.|+|.+++.+ +.+.|
T Consensus 2 ~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~------~--~~--~~~~~~~~G~~v~v~v~~vd~~~~~i~l 71 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDD------R--ID--DPSEVYKIGQTVRVKVIKVDKEKGRIRL 71 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSS------E--ES--SSHGTCETTCEEEEEEEEEETTTTEEEE
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCc------c--cc--ccccccCCCCEEEEEEEEEECCCCeEEE
Confidence 689999999999999999999999999999999988621 1 11 4456799999999999999875 45888
Q ss_pred EEc
Q 020356 167 QAR 169 (327)
Q Consensus 167 str 169 (327)
|+|
T Consensus 72 S~k 74 (74)
T PF00575_consen 72 SLK 74 (74)
T ss_dssp EST
T ss_pred EEC
Confidence 875
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=98.60 E-value=1.8e-07 Score=72.33 Aligned_cols=72 Identities=14% Similarity=0.153 Sum_probs=57.6
Q ss_pred CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEEE
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQLQ 167 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~Ls 167 (327)
++||+|.|+|+++++.+++|+++....|.+|+++++... ...+ -++.+.|++||.|.|+|.+++++ +.+.||
T Consensus 2 k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~---~~~~----~~~~~~~~~G~~v~~kVl~id~~~~~i~LS 74 (74)
T cd05705 2 KEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYF---VSDP----SLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCcc---ccCh----hhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 589999999999999999999998899999999886221 0111 13568899999999999999864 456553
No 22
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.57 E-value=4.3e-07 Score=66.49 Aligned_cols=71 Identities=23% Similarity=0.332 Sum_probs=58.8
Q ss_pred CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEEE
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQLQ 167 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~Ls 167 (327)
++||+|.|+|+++...+|+|+++....|++|.+++.-+ . ..++.+.|++||.|.|+|.+++.+ +.+.|+
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~------~----~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls 70 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDK------R----VKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCcc------c----cCCHHHeecCCCEEEEEEEEEeCCCCEEEEE
Confidence 47999999999999999999999889999999877511 1 114456799999999999999875 778887
Q ss_pred Ec
Q 020356 168 AR 169 (327)
Q Consensus 168 tr 169 (327)
++
T Consensus 71 ~~ 72 (72)
T smart00316 71 LK 72 (72)
T ss_pred eC
Confidence 64
No 23
>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=98.55 E-value=5.6e-07 Score=68.22 Aligned_cols=71 Identities=23% Similarity=0.226 Sum_probs=59.1
Q ss_pred CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ 167 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls 167 (327)
++|++|.|+|+++.+++++|++.....|++|+++++- .. . .+..+.|++||.|.|+|.+++. .+.+.||
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~------~~--~--~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls 71 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALD------DY--S--EALPYKFKKNDIVRACVLSVDVPNKKIALS 71 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccC------cc--c--cccccccCCCCEEEEEEEEEeCCCCEEEEE
Confidence 5899999999999999999999999999999998741 11 1 1346779999999999999986 4688888
Q ss_pred Ec
Q 020356 168 AR 169 (327)
Q Consensus 168 tr 169 (327)
+|
T Consensus 72 ~~ 73 (73)
T cd05706 72 LR 73 (73)
T ss_pred EC
Confidence 74
No 24
>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=98.53 E-value=6.1e-07 Score=68.03 Aligned_cols=74 Identities=18% Similarity=0.196 Sum_probs=60.8
Q ss_pred CCCCEEEEEEEEEecceEEEEEcC-ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEE
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEINF-TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQL 166 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~s-~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~L 166 (327)
++|++|.|+|+++...+|+|++.. ...|++|++++. +. + . .++.+.|++||.|.|+|.+++. .+.+.|
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~-~~-----~-~---~~~~~~~~~Gd~v~v~i~~vd~~~~~i~l 70 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEIS-DN-----R-V---ADASKLFRVGDKVRAKVLKIDAEKKRISL 70 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCC-CC-----c-c---CCHhHeecCCCEEEEEEEEEeCCCCEEEE
Confidence 469999999999999999999984 789999999874 11 1 1 1356789999999999999987 578999
Q ss_pred EEccCC
Q 020356 167 QARNQK 172 (327)
Q Consensus 167 str~~~ 172 (327)
+++...
T Consensus 71 s~k~~~ 76 (77)
T cd05708 71 GLKASY 76 (77)
T ss_pred EEEeec
Confidence 987653
No 25
>PRK08582 hypothetical protein; Provisional
Probab=98.53 E-value=6.2e-07 Score=77.68 Aligned_cols=76 Identities=18% Similarity=0.211 Sum_probs=64.2
Q ss_pred CCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEE
Q 020356 88 PETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQ 167 (327)
Q Consensus 88 P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Ls 167 (327)
.++|++|.|+|+++++.+++|+|.....|++|++++.-. . . .++.+.|++||.|.|+|.+++.++.+.|+
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~------~--v--~~~~~~l~vGD~VkvkV~~id~~gkI~LS 72 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADN------Y--V--KDINDHLKVGDEVEVKVLNVEDDGKIGLS 72 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcc------c--c--cccccccCCCCEEEEEEEEECCCCcEEEE
Confidence 468999999999999999999999989999999987511 1 1 14567899999999999999877899999
Q ss_pred EccCCC
Q 020356 168 ARNQKY 173 (327)
Q Consensus 168 tr~~~l 173 (327)
++....
T Consensus 73 lk~~~~ 78 (139)
T PRK08582 73 IKKAKD 78 (139)
T ss_pred EEeccc
Confidence 976533
No 26
>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=98.51 E-value=9.3e-07 Score=67.67 Aligned_cols=71 Identities=20% Similarity=0.197 Sum_probs=58.8
Q ss_pred CCCCCEEEEEEEEEecceEEEEEcC-ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEE
Q 020356 88 PETGDIVIGRVIEVVPKRWKLEINF-TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQL 166 (327)
Q Consensus 88 P~vGDiVIGrV~~V~~~~w~VDI~s-~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~L 166 (327)
|+.|+++-|+|+++.+.+++|++.. ...|++|++++.- .+ .+ +..++|++||.|.++|.+++..+.+.|
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~------~~--~~--~~~~~~~~Gd~v~vkv~~vd~~~ki~l 70 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSS------CR--VD--DPSEVVDVGEKVWVKVIGREMKDKMKL 70 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCC------Cc--cc--CHhhEECCCCEEEEEEEEECCCCcEEE
Confidence 6899999999999999999999954 2689999998751 11 22 567789999999999999987667777
Q ss_pred EE
Q 020356 167 QA 168 (327)
Q Consensus 167 st 168 (327)
|+
T Consensus 71 s~ 72 (73)
T cd05686 71 SL 72 (73)
T ss_pred Ee
Confidence 75
No 27
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=98.49 E-value=4.3e-07 Score=88.48 Aligned_cols=74 Identities=15% Similarity=0.290 Sum_probs=64.6
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEc--CccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCc
Q 020356 87 KPETGDIVIGRVIEVVPKRWKLEIN--FTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGS 163 (327)
Q Consensus 87 ~P~vGDiVIGrV~~V~~~~w~VDI~--s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~ 163 (327)
.|++||+|.|+|+.+...+++|+|. ....|++|+|.++ +++.. ++++++++||.|.++|++++. .+.
T Consensus 14 ~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS------~~ri~----~i~d~vkvGd~v~vkVl~VD~ekg~ 83 (319)
T PTZ00248 14 FPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELS------KRRIR----SINKLIRVGRHEVVVVLRVDKEKGY 83 (319)
T ss_pred CCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhc------ccccC----CHHHhcCCCCEEEEEEEEEeCCCCE
Confidence 7999999999999999999999996 3589999999987 33332 788999999999999999975 578
Q ss_pred eEEEEcc
Q 020356 164 LQLQARN 170 (327)
Q Consensus 164 i~Lstr~ 170 (327)
+.||.|.
T Consensus 84 IdLS~K~ 90 (319)
T PTZ00248 84 IDLSKKR 90 (319)
T ss_pred EEEEeee
Confidence 9999875
No 28
>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=98.48 E-value=4.3e-07 Score=74.34 Aligned_cols=81 Identities=15% Similarity=0.226 Sum_probs=63.1
Q ss_pred CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccc----------cccccchhhhhcccCCCCEEEEEEEec
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQR----------RRTAVDELNMRSIFTENDLVCAEVRSS 158 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~r----------rr~~~de~~mr~~~~~GDlV~AeV~sv 158 (327)
++||+|.|+|+++.+.+.+|++.....|++|+++++- ..+++ ...+.+..++.+.|++||+|.|+|.++
T Consensus 2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~ 80 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISD-AYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL 80 (100)
T ss_pred CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhH-HHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence 5899999999999999999999988999999998751 10011 011222346789999999999999999
Q ss_pred CCC----CceEEEEcc
Q 020356 159 QGD----GSLQLQARN 170 (327)
Q Consensus 159 ~~~----g~i~Lstr~ 170 (327)
+.. ..+.||.|.
T Consensus 81 d~~~~~~~~i~LSlr~ 96 (100)
T cd05693 81 DKSKSGKKRIELSLEP 96 (100)
T ss_pred cCCcCCCcEEEEEecH
Confidence 874 578888874
No 29
>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=98.44 E-value=9.6e-07 Score=79.10 Aligned_cols=89 Identities=27% Similarity=0.388 Sum_probs=68.1
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccc---cccccchhhhhcccCCCCEEEEEEEecC---
Q 020356 86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQR---RRTAVDELNMRSIFTENDLVCAEVRSSQ--- 159 (327)
Q Consensus 86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~r---rr~~~de~~mr~~~~~GDlV~AeV~sv~--- 159 (327)
|.|.+|+++.|+|++++..+++|+++ +.++++|.+++. |....- +..-.. -+....|+.||.|+++|.+++
T Consensus 77 f~p~~gEvv~G~V~~v~~~GifV~lg-~~~gi~~~~~l~-~~~~~~d~~~~~~~~-~~~~~~~~~Gd~VrvrV~~v~~~~ 153 (179)
T TIGR00448 77 FKPELGEIVEGEVIEIVEFGAFVSLG-PFDGLFHVSQVT-DDYCYYDPKESALIG-KETKKVLDEGDKVRARIVALSLKD 153 (179)
T ss_pred EeccCCCEEEEEEEEEEeeEEEEEeC-CceEEEEcHHhC-CCceEEccccceEEE-ccCCeEEcCCCEEEEEEEEEEccC
Confidence 67899999999999999999999995 689999888764 321110 000000 023567999999999999986
Q ss_pred ---CCCceEEEEccCCCccCC
Q 020356 160 ---GDGSLQLQARNQKYGKLE 177 (327)
Q Consensus 160 ---~~g~i~Lstr~~~lGkL~ 177 (327)
+...+.||+|+++||+++
T Consensus 154 ~~~~~~~I~lt~k~~~LG~~~ 174 (179)
T TIGR00448 154 RRPEGSKIGLTMRQPLLGKLE 174 (179)
T ss_pred CCCCcceEEEEeccCcCCccc
Confidence 235799999999999986
No 30
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.42 E-value=9.5e-07 Score=79.39 Aligned_cols=90 Identities=27% Similarity=0.362 Sum_probs=67.8
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccc---cccccchhhhhcccCCCCEEEEEEEecCCC
Q 020356 85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQR---RRTAVDELNMRSIFTENDLVCAEVRSSQGD 161 (327)
Q Consensus 85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~r---rr~~~de~~mr~~~~~GDlV~AeV~sv~~~ 161 (327)
-|.|.+|++|.|+|+++...+|+|+++ +.+++++.+++. +....- +..-.. .+...+++.||.|+++|.+++.+
T Consensus 76 vf~P~~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~~l~-~~~~~~d~~~~~~~~-~~~~~~i~~Gd~VrvrV~~v~~~ 152 (187)
T PRK08563 76 VFKPELQEVVEGEVVEVVEFGAFVRIG-PVDGLLHISQIM-DDYISYDPKNGRLIG-KESKRVLKVGDVVRARIVAVSLK 152 (187)
T ss_pred EEeccCCCEEEEEEEEEEccEEEEEEe-CceEEEEcHHcC-CCceEEccccceEEE-ccCCeEEcCCCEEEEEEEEEEcc
Confidence 356999999999999999999999998 688998887663 211110 000000 13467799999999999999753
Q ss_pred ------CceEEEEccCCCccCC
Q 020356 162 ------GSLQLQARNQKYGKLE 177 (327)
Q Consensus 162 ------g~i~Lstr~~~lGkL~ 177 (327)
..+.||+++++||+++
T Consensus 153 ~~~~~~~~I~ls~~~~~LG~~~ 174 (187)
T PRK08563 153 ERRPRGSKIGLTMRQPGLGKLE 174 (187)
T ss_pred cCCCCCCEEEEEecCCCCCcHH
Confidence 3689999999999985
No 31
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.41 E-value=1.1e-06 Score=83.61 Aligned_cols=76 Identities=21% Similarity=0.298 Sum_probs=63.6
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEEcC--ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-C
Q 020356 86 YKPETGDIVIGRVIEVVPKRWKLEINF--TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-G 162 (327)
Q Consensus 86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s--~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g 162 (327)
-.|++||+|.|+|+++.+.+|+|++.. ...|++|+|+++ .++.. ++++.|++||.|.|+|.+++.. +
T Consensus 4 ~~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls------~~~i~----~i~~~~kvGd~V~vkVi~VD~~k~ 73 (262)
T PRK03987 4 EWPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVA------SGWVK----NIRDHVKEGQKVVCKVIRVDPRKG 73 (262)
T ss_pred CCCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcC------ccccc----CHHHhCCCCCEEEEEEEEEecccC
Confidence 479999999999999999999999975 479999999875 11111 5678899999999999999864 6
Q ss_pred ceEEEEccC
Q 020356 163 SLQLQARNQ 171 (327)
Q Consensus 163 ~i~Lstr~~ 171 (327)
.+.||++..
T Consensus 74 ~I~LSlK~v 82 (262)
T PRK03987 74 HIDLSLKRV 82 (262)
T ss_pred eEEEEEEec
Confidence 799999753
No 32
>PRK07252 hypothetical protein; Provisional
Probab=98.39 E-value=2e-06 Score=72.83 Aligned_cols=73 Identities=16% Similarity=0.269 Sum_probs=60.9
Q ss_pred CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ 167 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls 167 (327)
++||+|.|+|+++...+|+|+|.....|++|++++.-. + .+ +..+.|++||.|.|+|.+++. .+.+.|+
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~------~--~~--~~~~~~~vGD~V~VkI~~iD~~~~ri~lS 71 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTG------F--ID--NIHQLLKVGEEVLVQVVDFDEYTGKASLS 71 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCc------c--cc--ChhhccCCCCEEEEEEEEEeCCCCEEEEE
Confidence 47999999999999999999999889999999987411 1 11 345779999999999999987 5788898
Q ss_pred EccC
Q 020356 168 ARNQ 171 (327)
Q Consensus 168 tr~~ 171 (327)
++..
T Consensus 72 lk~~ 75 (120)
T PRK07252 72 LRTL 75 (120)
T ss_pred Eeec
Confidence 8764
No 33
>PRK08059 general stress protein 13; Validated
Probab=98.38 E-value=2e-06 Score=72.69 Aligned_cols=76 Identities=20% Similarity=0.291 Sum_probs=63.3
Q ss_pred CCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEE
Q 020356 88 PETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQL 166 (327)
Q Consensus 88 P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~L 166 (327)
.++|++|.|+|+++...+|+|+|.....|++|++++.-+ + . -++.+.|++||.|.|+|.+++. .+.+.|
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~------~--~--~~~~~~~~vGD~I~vkI~~id~~~~~i~l 74 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHG------F--V--KDIHDFLSVGDEVKVKVLSVDEEKGKISL 74 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcc------c--c--cCHHHcCCCCCEEEEEEEEEECCCCeEEE
Confidence 468999999999999999999999999999999987411 1 1 1456789999999999999965 678999
Q ss_pred EEccCCC
Q 020356 167 QARNQKY 173 (327)
Q Consensus 167 str~~~l 173 (327)
+++....
T Consensus 75 slk~~~~ 81 (123)
T PRK08059 75 SIRATEE 81 (123)
T ss_pred EEEEccc
Confidence 9987644
No 34
>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=98.36 E-value=1.6e-06 Score=64.99 Aligned_cols=67 Identities=19% Similarity=0.282 Sum_probs=54.6
Q ss_pred CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356 91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ 167 (327)
Q Consensus 91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls 167 (327)
|++|.|+|+++.+.+++|++.....|++|+++++- .. .. +..+.|++||.|.|+|.++++ .+.+.||
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 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSD------SY--LK--DWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCc------hh--hc--CHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 89999999999999999999988999999998741 11 11 456779999999999999987 4455553
No 35
>PRK05807 hypothetical protein; Provisional
Probab=98.36 E-value=2.5e-06 Score=73.59 Aligned_cols=72 Identities=21% Similarity=0.358 Sum_probs=60.7
Q ss_pred CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEE
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQA 168 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lst 168 (327)
++|++|.|+|+++++.+++|+|. ...|++|++.+. ++ ... +..++|++||.|.++|.+++.++.+.||+
T Consensus 4 ~vG~vv~G~Vt~i~~~GafV~L~-~~~Glvhiseis-~~-------~v~--~~~~~~kvGd~V~VkV~~id~~gkI~LSl 72 (136)
T PRK05807 4 KAGSILEGTVVNITNFGAFVEVE-GKTGLVHISEVA-DT-------YVK--DIREHLKEQDKVKVKVISIDDNGKISLSI 72 (136)
T ss_pred cCCCEEEEEEEEEECCeEEEEEC-CEEEEEEhhhcc-cc-------ccc--CccccCCCCCEEEEEEEEECCCCcEEEEE
Confidence 58999999999999999999995 568999999875 11 111 44677999999999999998888999999
Q ss_pred ccC
Q 020356 169 RNQ 171 (327)
Q Consensus 169 r~~ 171 (327)
+..
T Consensus 73 k~~ 75 (136)
T PRK05807 73 KQA 75 (136)
T ss_pred Eec
Confidence 864
No 36
>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=98.34 E-value=3.1e-06 Score=63.50 Aligned_cols=69 Identities=17% Similarity=0.202 Sum_probs=57.4
Q ss_pred CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEEEc
Q 020356 91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQAR 169 (327)
Q Consensus 91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Lstr 169 (327)
||+|.|+|+++.+.+++|++.....|++|++++.-+ + .. +..+.|++||.|.++|.+++. .+.+.||++
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 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEA------F--IK--DPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChh------h--cC--CHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 899999999999999999998779999999987511 1 11 345679999999999999987 567888874
No 37
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.34 E-value=9.7e-07 Score=83.34 Aligned_cols=79 Identities=24% Similarity=0.383 Sum_probs=66.3
Q ss_pred cCCccCCCCCCEEEEEEEEEecceEEEEEcC--ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecC
Q 020356 82 LRARYKPETGDIVIGRVIEVVPKRWKLEINF--TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQ 159 (327)
Q Consensus 82 l~~rY~P~vGDiVIGrV~~V~~~~w~VDI~s--~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~ 159 (327)
+..+-.|++||+|||+|.+|.+.+++|.+.- ...|++|+|+++ ..|-| ++|+++++|..+.|+|++++
T Consensus 3 ~~~~~~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEva----s~wVk------nIrd~vkegqkvV~kVlrVd 72 (269)
T COG1093 3 MKRREYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVA----SGWVK------NIRDYVKEGQKVVAKVLRVD 72 (269)
T ss_pred ccccCCCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHH----HHHHH------HHHHHhhcCCeEEEEEEEEc
Confidence 3445689999999999999999999999974 467999999996 12222 88999999999999999999
Q ss_pred C-CCceEEEEcc
Q 020356 160 G-DGSLQLQARN 170 (327)
Q Consensus 160 ~-~g~i~Lstr~ 170 (327)
+ -|.+.||.|.
T Consensus 73 ~~rg~IDLSlkr 84 (269)
T COG1093 73 PKRGHIDLSLKR 84 (269)
T ss_pred CCCCeEeeehhh
Confidence 7 4678998863
No 38
>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=98.31 E-value=2.7e-06 Score=64.37 Aligned_cols=64 Identities=20% Similarity=0.194 Sum_probs=52.8
Q ss_pred CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCC
Q 020356 91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDG 162 (327)
Q Consensus 91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g 162 (327)
||+|.|+|+++..++++|++....+|.+|++++.- +. .+..++.+.|++||.|.|+|.+++...
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~------~~--~~~~~~~~~~~~Gd~i~~kVl~~d~~~ 64 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFD------EW--PDGKNPLSKFKIGQKIKARVIGGHDAK 64 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhcc------cc--ccccChhHhCCCCCEEEEEEEEEeCcc
Confidence 89999999999999999999999999999998741 10 011256788999999999999997653
No 39
>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=98.30 E-value=4.5e-06 Score=64.24 Aligned_cols=71 Identities=21% Similarity=0.138 Sum_probs=58.1
Q ss_pred CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEEEEc
Q 020356 91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQLQAR 169 (327)
Q Consensus 91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~Lstr 169 (327)
||+|-|.|+++.+++++|.+...-.|.+|+++++-+. ... .+..+.|++||.|.|+|.+++.. ..+.||.+
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 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDV------SVL--EHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCcc------ccc--cCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 8999999999999999999988899999999885220 001 14567799999999999999864 57888875
No 40
>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=98.25 E-value=5.5e-06 Score=64.67 Aligned_cols=73 Identities=19% Similarity=0.087 Sum_probs=60.7
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCce
Q 020356 86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSL 164 (327)
Q Consensus 86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i 164 (327)
..+++|+++.|+|+++...+.+|++.....|++|++++.-. + . .++.+.|++||.|.++|.+++. .+.+
T Consensus 10 ~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~------~--~--~~~~~~~~~Gd~v~vkV~~id~~~~~i 79 (83)
T cd04461 10 SDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDE------F--V--TDPSFGFKKGQSVTAKVTSVDEEKQRF 79 (83)
T ss_pred HhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcc------c--c--cCHHHhcCCCCEEEEEEEEEcCCCCEE
Confidence 35789999999999999999999998889999999987521 1 1 1467889999999999999986 4677
Q ss_pred EEEE
Q 020356 165 QLQA 168 (327)
Q Consensus 165 ~Lst 168 (327)
.||+
T Consensus 80 ~lsl 83 (83)
T cd04461 80 LLSL 83 (83)
T ss_pred EEeC
Confidence 7764
No 41
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.23 E-value=3.8e-06 Score=75.77 Aligned_cols=90 Identities=27% Similarity=0.398 Sum_probs=69.5
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcc---cccccccchhhhhcccCCCCEEEEEEEecCCC
Q 020356 85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGI---QRRRTAVDELNMRSIFTENDLVCAEVRSSQGD 161 (327)
Q Consensus 85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i---~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~ 161 (327)
.|.|..|.+|-|.|+++...+++|.|+ |.++++|.|++. ++-. .++.....+ .-...|+.||.|+|||.++..+
T Consensus 76 ~fkP~~gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~-dd~~~~d~~~~~~~g~-~tk~~i~~gd~VR~RIv~~s~~ 152 (183)
T COG1095 76 VFKPFRGEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIM-DDYIDYDEKNKVLIGE-ETKRVLKVGDKVRARIVGVSLK 152 (183)
T ss_pred EEEeccccEEEEEEEEEeecceEEEec-cccccccHhhcc-CcccccCcccceeeec-ccceEEecCCEEEEEEEEEecc
Confidence 478999999999999999999999999 999999999873 2211 111111111 2234699999999999987642
Q ss_pred ------CceEEEEccCCCccCC
Q 020356 162 ------GSLQLQARNQKYGKLE 177 (327)
Q Consensus 162 ------g~i~Lstr~~~lGkL~ 177 (327)
..+.||+|++++|+++
T Consensus 153 ~~~~~~~~I~lTmrq~~LGkle 174 (183)
T COG1095 153 SRRPRESKIGLTMRQPGLGKLE 174 (183)
T ss_pred cCccccceEEEEeccccCCcch
Confidence 4589999999999996
No 42
>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=98.22 E-value=8.4e-06 Score=65.20 Aligned_cols=74 Identities=20% Similarity=0.321 Sum_probs=57.2
Q ss_pred CCCCCEEEEEEEEEecc--eEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCC-ce
Q 020356 88 PETGDIVIGRVIEVVPK--RWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDG-SL 164 (327)
Q Consensus 88 P~vGDiVIGrV~~V~~~--~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g-~i 164 (327)
|++|+++.|+|+.+.+. +++|||+....|+||+|+++... .++. .+..+.|++||.|.++|.....++ .+
T Consensus 5 ~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~---~~~v----~~~~~~~~~Gd~v~VqV~~~~~~~K~~ 77 (88)
T cd04453 5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAY---FKKH----KKIAKLLKEGQEILVQVVKEPIGTKGP 77 (88)
T ss_pred CCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchh---cccc----CCHHHcCCCCCEEEEEEEEecCCCCCc
Confidence 57999999999999996 99999998889999999885310 0111 144567999999999999976543 45
Q ss_pred EEEE
Q 020356 165 QLQA 168 (327)
Q Consensus 165 ~Lst 168 (327)
.||+
T Consensus 78 ~lt~ 81 (88)
T cd04453 78 RLTT 81 (88)
T ss_pred eEEE
Confidence 5555
No 43
>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=98.21 E-value=9.4e-06 Score=59.90 Aligned_cols=67 Identities=24% Similarity=0.376 Sum_probs=54.7
Q ss_pred CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEE
Q 020356 91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQ 167 (327)
Q Consensus 91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Ls 167 (327)
|+++.|+|+++...+|+|+|.....|++|++++. . .+ .. ...+.|++||.|.++|.+++..+.+.||
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~--~----~~--~~--~~~~~~~~Gd~v~v~v~~~d~~~~i~ls 67 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELS--D----ER--VE--KVEDVLKVGDEVKVKVIEVDDRGRISLS 67 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcC--C----cc--cc--CHHHccCCCCEEEEEEEEECCCCcEEee
Confidence 7899999999999999999998899999998764 1 11 11 3346799999999999999876677776
No 44
>PHA02945 interferon resistance protein; Provisional
Probab=98.20 E-value=8.8e-06 Score=65.28 Aligned_cols=73 Identities=21% Similarity=0.225 Sum_probs=59.1
Q ss_pred cc-CCCCCCEEEEEEEEEecceEEEEEcC--ccceeeecccc--cCCCcccccccccchhhhhcccCCCCEEEEEEEecC
Q 020356 85 RY-KPETGDIVIGRVIEVVPKRWKLEINF--TQDAILMLSSM--NLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQ 159 (327)
Q Consensus 85 rY-~P~vGDiVIGrV~~V~~~~w~VDI~s--~~~a~L~ls~v--~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~ 159 (327)
.| .|++||+|+|+|.. .+.+++|++.- ...|++|+|.+ + +| +-| + |+++ +|..|.|+|+.++
T Consensus 5 cy~~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva-~~---wvK------~-rd~l-~GqkvV~KVirVd 71 (88)
T PHA02945 5 CYSLPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHM-NR---YFK------Y-RDKL-VGKTVKVKVIRVD 71 (88)
T ss_pred eecCCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhc-cc---eEe------e-eeEe-cCCEEEEEEEEEC
Confidence 35 89999999999999 99999999974 57899999954 4 22 222 4 6788 9999999999999
Q ss_pred CC-CceEEEEcc
Q 020356 160 GD-GSLQLQARN 170 (327)
Q Consensus 160 ~~-g~i~Lstr~ 170 (327)
+. |.+-||.+.
T Consensus 72 ~~kg~IDlSlK~ 83 (88)
T PHA02945 72 YTKGYIDVNYKR 83 (88)
T ss_pred CCCCEEEeEeeE
Confidence 74 678888763
No 45
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=98.18 E-value=4.7e-06 Score=86.17 Aligned_cols=76 Identities=22% Similarity=0.272 Sum_probs=65.9
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceE
Q 020356 87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQ 165 (327)
Q Consensus 87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~ 165 (327)
.-++||+|-|+|+++++.+++|||+. -+|.||+++++. .+.. ...++|++||-|.++|++++. .+.++
T Consensus 189 ~l~~G~vV~G~V~~It~~GafVdigG-vdGLlHiseiS~------~rv~----~P~~vvkvGd~VkvkVi~~D~e~~RVs 257 (541)
T COG0539 189 KLEVGEVVEGVVKNITDYGAFVDIGG-VDGLLHISEISW------KRVD----HPSEVVKVGDEVKVKVISLDEERGRVS 257 (541)
T ss_pred cCCCCceEEEEEEEeecCcEEEEecC-eeeEEehhhccc------cccC----CHHHhcccCCEEEEEEEEEccCCCeEE
Confidence 45899999999999999999999998 999999999973 3322 667889999999999999995 56899
Q ss_pred EEEccCCC
Q 020356 166 LQARNQKY 173 (327)
Q Consensus 166 Lstr~~~l 173 (327)
||++...-
T Consensus 258 LSlK~l~~ 265 (541)
T COG0539 258 LSLKQLEE 265 (541)
T ss_pred EEehhccc
Confidence 99987544
No 46
>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=98.18 E-value=7.3e-06 Score=60.37 Aligned_cols=66 Identities=21% Similarity=0.270 Sum_probs=52.6
Q ss_pred CCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEE
Q 020356 90 TGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQL 166 (327)
Q Consensus 90 vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~L 166 (327)
+|++|.|+|+++...+|+|+++ ...|++|.+++... +. ..+.+.|++||.|.|+|.+++.. +.+.|
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~-~~~g~l~~~e~~~~------~~----~~~~~~~~~Gd~v~v~i~~vd~~~~~i~l 67 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWG------RV----KHPSEVVNVGDEVEVKVLKIDKERKRISL 67 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCCc------cc----cCHhHEECCCCEEEEEEEEEECCCCEEec
Confidence 5999999999999999999998 58899999887521 11 13457799999999999999763 44544
No 47
>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=98.17 E-value=1.4e-05 Score=61.94 Aligned_cols=67 Identities=19% Similarity=0.187 Sum_probs=56.6
Q ss_pred CCCCEEEEEEEEEecceEEEEEc-CccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEE
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEIN-FTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQL 166 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~-s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~L 166 (327)
+.|++|.|.|.++.+.+++||++ ....|++|.++++ +. +.|++||.+.|+|.++++. ..+.|
T Consensus 3 ~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~------~~----------~~~~~Gq~v~~~V~~vd~~~~~v~l 66 (74)
T cd05694 3 VEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAG------NF----------SKLKVGQLLLCVVEKVKDDGRVVSL 66 (74)
T ss_pred CCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCC------cc----------cccCCCCEEEEEEEEEECCCCEEEE
Confidence 57999999999999999999997 4578999988775 11 4589999999999999864 57899
Q ss_pred EEccC
Q 020356 167 QARNQ 171 (327)
Q Consensus 167 str~~ 171 (327)
|++..
T Consensus 67 s~k~~ 71 (74)
T cd05694 67 SADPS 71 (74)
T ss_pred EEeec
Confidence 98764
No 48
>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=98.15 E-value=8.5e-06 Score=59.78 Aligned_cols=67 Identities=24% Similarity=0.310 Sum_probs=53.8
Q ss_pred CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356 91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ 167 (327)
Q Consensus 91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls 167 (327)
|+++.|+|+++.+.+|+|+++....|++|.+++. ++ + .. ++.+.|++||.|.|+|.+++. .+.+.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~-~~---~----~~--~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMA-DR---F----VS--HPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCC-Cc---c----cc--CHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 7899999999999999999998889999998764 11 1 11 446779999999999999986 4555553
No 49
>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=98.13 E-value=1.5e-05 Score=59.91 Aligned_cols=67 Identities=15% Similarity=0.107 Sum_probs=54.7
Q ss_pred CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356 91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ 167 (327)
Q Consensus 91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls 167 (327)
|++|.|+|+++...+++|++.....|++|.++++-. .. .+..+.|++||.|.++|.+++. .+.+.|+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~-------~~---~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls 68 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADV-------RL---KHPEKKFKPGLKVKCRVLSVEPERKRLVLT 68 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCc-------cc---cCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence 799999999999999999998779999999877411 11 1345679999999999999986 4567776
No 50
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.99 E-value=3.4e-05 Score=58.87 Aligned_cols=68 Identities=21% Similarity=0.152 Sum_probs=55.0
Q ss_pred CCEEE-EEEEEE-ecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356 91 GDIVI-GRVIEV-VPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ 167 (327)
Q Consensus 91 GDiVI-GrV~~V-~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls 167 (327)
|+++- |+|+++ .+.+++|++....+|++|.|+++-+ + .+ +..+.|++||.+.|+|.++++ ++.+.||
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~------~--~~--~~~~~~~vG~~v~~kV~~id~~~~~i~lS 70 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDD------K--VP--SDTGPFKAGTTHKARIIGYSPMDGLLQLS 70 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcc------h--hc--CcccccCCCCEEEEEEEEEeCCCCEEEEe
Confidence 78888 999999 7999999998778999999987511 1 11 345679999999999999986 5578887
Q ss_pred E
Q 020356 168 A 168 (327)
Q Consensus 168 t 168 (327)
+
T Consensus 71 ~ 71 (71)
T cd05696 71 L 71 (71)
T ss_pred C
Confidence 4
No 51
>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=97.93 E-value=3.3e-05 Score=55.35 Aligned_cols=63 Identities=17% Similarity=0.237 Sum_probs=49.8
Q ss_pred EEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEE
Q 020356 94 VIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQL 166 (327)
Q Consensus 94 VIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~L 166 (327)
|.|+|+++.+.+|+|++.....|++|.+++.-. . . .++.+.|++||.|.|+|.+++. ++.+.|
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~------~-~---~~~~~~~~~G~~v~~~v~~~d~~~~~i~l 64 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDK------F-V---KDPSEVFKVGDEVEVKVLEVDPEKGRISL 64 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCc------c-c---cCHhhEeCCCCEEEEEEEEEcCCcCEEec
Confidence 479999999999999999889999999876411 1 1 1456779999999999999975 344544
No 52
>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=97.92 E-value=4.9e-05 Score=61.45 Aligned_cols=83 Identities=25% Similarity=0.334 Sum_probs=60.8
Q ss_pred CEEEEEEEEEecceEEEEEcCccceeeecccccCCCccccc--c-cccchhhhhcccCCCCEEEEEEEecCCC------C
Q 020356 92 DIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRR--R-TAVDELNMRSIFTENDLVCAEVRSSQGD------G 162 (327)
Q Consensus 92 DiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rr--r-~~~de~~mr~~~~~GDlV~AeV~sv~~~------g 162 (327)
++|.|+|+++...+++|++. +..|++|++++. ++..... . ...+ -.-.+.|++||.|.++|.+++.. .
T Consensus 1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~~~l~-~~~~~~~~~~~~~~~-~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~ 77 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIM-DDYISYDPKNKRLIG-EETKRVLKVGDVVRARIVAVSLKERRPRES 77 (99)
T ss_pred CEEEEEEEEEEeccEEEEEc-CeEEEEEEEEcc-CCceEechhheeecc-cCcCCEECCCCEEEEEEEEEeHHHCcCCCc
Confidence 47899999999999999998 488999988764 1100000 0 0000 01235689999999999999853 5
Q ss_pred ceEEEEccCCCccCC
Q 020356 163 SLQLQARNQKYGKLE 177 (327)
Q Consensus 163 ~i~Lstr~~~lGkL~ 177 (327)
.+.||+++..+|++.
T Consensus 78 ~i~ls~k~~~~g~~~ 92 (99)
T cd04460 78 KIGLTMRQPGLGKLE 92 (99)
T ss_pred eEEEEEecCCCCcHH
Confidence 799999999999874
No 53
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=97.91 E-value=7.5e-05 Score=57.59 Aligned_cols=70 Identities=19% Similarity=0.316 Sum_probs=57.5
Q ss_pred CCEEEEEEEEEecceEEEEEc---CccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEE
Q 020356 91 GDIVIGRVIEVVPKRWKLEIN---FTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQ 167 (327)
Q Consensus 91 GDiVIGrV~~V~~~~w~VDI~---s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Ls 167 (327)
|+++-|+|+++.+.+++|+|. ....|++|++++. ++ + . .+ ++.+.|+.||.|.++|.+++ .+.+.|+
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~-~~---~--~-~~--~~~~~~~~Gd~v~v~v~~vd-~~~i~~s 70 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLS-FE---G--R-VA--NPSDVVKRGQKVKVKVISIQ-NGKISLS 70 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhcc-CC---C--C-cC--ChhheeCCCCEEEEEEEEEe-CCEEEEE
Confidence 789999999999999999998 3578999999875 11 1 1 12 45678999999999999998 7889998
Q ss_pred Ecc
Q 020356 168 ARN 170 (327)
Q Consensus 168 tr~ 170 (327)
++.
T Consensus 71 ~k~ 73 (79)
T cd05684 71 MKD 73 (79)
T ss_pred EEe
Confidence 875
No 54
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.87 E-value=6.1e-05 Score=56.74 Aligned_cols=65 Identities=17% Similarity=0.202 Sum_probs=52.1
Q ss_pred CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEEE
Q 020356 91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQLQ 167 (327)
Q Consensus 91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~Ls 167 (327)
||+|-|+|+++.+++.+|++....+|++|.++++-+ +. . .+.|++||.|.|+|.++++. +.+.||
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 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPE----KS-------S-KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCc----cC-------c-ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 899999999999999999997678999999877411 10 1 45699999999999999864 455553
No 55
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.85 E-value=5.1e-05 Score=80.98 Aligned_cols=75 Identities=20% Similarity=0.351 Sum_probs=61.5
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEEcCccceeeeccccc-CCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCce
Q 020356 86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMN-LPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSL 164 (327)
Q Consensus 86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~-fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i 164 (327)
+.|++|++|.|+|+++.+.+++|+|....+|++|+|++. +.. .++.. ++.+.|++||.|.++|.+++..+.+
T Consensus 643 ~~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~---~~rv~----~~~dv~kvGd~V~VKVl~ID~~gKI 715 (719)
T TIGR02696 643 TMPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAG---GKRVE----NVEDVLSVGQKIQVEIADIDDRGKL 715 (719)
T ss_pred CcCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhcccccc---ccCcC----CHHHcCCCCCEEEEEEEEECCCCCe
Confidence 358999999999999999999999987789999999873 100 11111 6688899999999999999977778
Q ss_pred EEE
Q 020356 165 QLQ 167 (327)
Q Consensus 165 ~Ls 167 (327)
.|+
T Consensus 716 ~L~ 718 (719)
T TIGR02696 716 SLV 718 (719)
T ss_pred eec
Confidence 774
No 56
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.84 E-value=6.6e-05 Score=80.26 Aligned_cols=99 Identities=20% Similarity=0.289 Sum_probs=76.9
Q ss_pred eCCeEEEEEeeEEEEE--CcEEEEEecCCccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccc
Q 020356 58 QKGELAATVCGVVERI--NKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTA 135 (327)
Q Consensus 58 ~~g~i~Ssv~G~v~~~--nk~v~V~pl~~rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~ 135 (327)
++|.++++..|..... ...+...+ ..|++|+++.|+|+++.+.+++|+|....+|++|+|++. ..+.
T Consensus 591 d~G~v~i~~~~~~~~~~a~~~I~~~~----~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels------~~~v- 659 (693)
T PRK11824 591 DDGTVKIAATDGEAAEAAKERIEGIT----AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIA------DERV- 659 (693)
T ss_pred CCceEEEEcccHHHHHHHHHHHHHhc----ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeecc------Cccc-
Confidence 4778888777766542 22222222 247899999999999999999999998899999999875 1111
Q ss_pred cchhhhhcccCCCCEEEEEEEecCCCCceEEEEcc
Q 020356 136 VDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARN 170 (327)
Q Consensus 136 ~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~ 170 (327)
. +..+.|++||.|.++|.+++..+.+.||++.
T Consensus 660 -~--~~~~v~kvGD~V~VkV~~iD~~grI~LS~k~ 691 (693)
T PRK11824 660 -E--KVEDVLKEGDEVKVKVLEIDKRGRIRLSRKA 691 (693)
T ss_pred -c--CccceeCCCCEEEEEEEEECCCCcEEEEEEe
Confidence 1 4567899999999999999877899999875
No 57
>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=97.81 E-value=0.00026 Score=54.72 Aligned_cols=64 Identities=19% Similarity=0.229 Sum_probs=55.1
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEE
Q 020356 87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQL 166 (327)
Q Consensus 87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~L 166 (327)
-.++|+.+.|+|+++++.+++|++.....|.+|.+++. +.++.||.+.++|.++.+++.+.|
T Consensus 13 ~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~------------------~~~~iGd~v~v~I~~i~e~~~i~l 74 (77)
T cd04473 13 DLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL------------------RDYEVGDEVIVQVTDIPENGNIDL 74 (77)
T ss_pred hCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc------------------CcCCCCCEEEEEEEEECCCCcEEE
Confidence 46799999999999999999999998899999887642 338999999999999966777877
Q ss_pred EE
Q 020356 167 QA 168 (327)
Q Consensus 167 st 168 (327)
+.
T Consensus 75 ~~ 76 (77)
T cd04473 75 IP 76 (77)
T ss_pred EE
Confidence 64
No 58
>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=97.81 E-value=0.00011 Score=55.32 Aligned_cols=56 Identities=23% Similarity=0.225 Sum_probs=47.9
Q ss_pred CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD 161 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~ 161 (327)
..|++|-|+|..+..++++|||+. .+|+||.++.. | .+.|++||-|.+.|.+++.+
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~-~eg~lp~~e~~-~---------------~~~~~~Gd~v~v~v~~v~~~ 57 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGK-VEAILPKKEQI-P---------------GESYRPGDRIKAYVLEVRKT 57 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCC-eEEEeeHHHCC-C---------------CCcCCCCCEEEEEEEEEecC
Confidence 579999999999999999999986 89999888764 1 23489999999999998753
No 59
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=97.80 E-value=9.3e-05 Score=72.22 Aligned_cols=74 Identities=20% Similarity=0.339 Sum_probs=61.7
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceE
Q 020356 87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQ 165 (327)
Q Consensus 87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~ 165 (327)
..++||+|.|+|+.+.+.+++|+++ ...|++|++.++- .+. .+..+.|++||.|.|+|.+++. .+.+.
T Consensus 193 ~~k~G~vv~G~V~~I~~~G~fV~i~-gv~Gllhisels~------~~~----~~~~~~~~vGd~VkvkVl~iD~e~~rI~ 261 (318)
T PRK07400 193 RLEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISH------EHI----ETPHSVFNVNDEMKVMIIDLDAERGRIS 261 (318)
T ss_pred cCCCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHccc------ccc----cChhhccCCCCEEEEEEEEEeCCCCEEE
Confidence 4678999999999999999999997 4679999998862 111 1456889999999999999975 57899
Q ss_pred EEEccC
Q 020356 166 LQARNQ 171 (327)
Q Consensus 166 Lstr~~ 171 (327)
|+++..
T Consensus 262 LS~K~l 267 (318)
T PRK07400 262 LSTKQL 267 (318)
T ss_pred EEEecc
Confidence 999864
No 60
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=97.79 E-value=8.1e-05 Score=72.64 Aligned_cols=76 Identities=25% Similarity=0.396 Sum_probs=63.5
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCce
Q 020356 86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSL 164 (327)
Q Consensus 86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i 164 (327)
|..++||+|-|+|+.+..++.+|||+....|+||++++... +. . +..+.|++||.|.+.|.+++. ++.+
T Consensus 27 ~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~------~~--~--~~~~~~~~G~~v~~~Vi~~~~~~~~i 96 (318)
T PRK07400 27 YHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSIN------RV--E--GPEEVLQPNETREFFILSDENEDGQL 96 (318)
T ss_pred hhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccc------cc--c--CHHHccCCCCEEEEEEEEEeCCCCeE
Confidence 45689999999999999999999999888999999988622 11 1 445779999999999999875 5689
Q ss_pred EEEEccC
Q 020356 165 QLQARNQ 171 (327)
Q Consensus 165 ~Lstr~~ 171 (327)
.||+|..
T Consensus 97 ~lS~k~~ 103 (318)
T PRK07400 97 TLSIRRI 103 (318)
T ss_pred EEehhhh
Confidence 9999864
No 61
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.79 E-value=0.00062 Score=61.28 Aligned_cols=90 Identities=11% Similarity=0.070 Sum_probs=65.8
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeeccccc----CCCcccccccccchhhhhcccCCCCEEEEEEEecCC
Q 020356 85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMN----LPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG 160 (327)
Q Consensus 85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~----fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~ 160 (327)
-|.|..|.+|.|+|+++...+++|+++ +.+..+|.+++. |....+.. ...++ +-...++.||.|++||.++.-
T Consensus 76 vFrPf~gEVv~g~V~~v~~~G~~v~~G-p~~ifI~~~~l~~~~~fd~~~~~~-~~~~~-~~~~~i~~g~~VR~rV~~v~~ 152 (176)
T PTZ00162 76 VFKPFKDEVLDAIVTDVNKLGFFAQAG-PLKAFVSRSAIPPDFVYDSDSAYP-CYISS-DGQIQIKPNTEVRLRLQGVRY 152 (176)
T ss_pred EEecCCCCEEEEEEEEEecceEEEEee-CeEEEEcHHHCCCccEECCCCCcc-eEecC-CCcEEECCCCEEEEEEEEEEe
Confidence 478999999999999999999999997 666888777662 21111100 00111 225679999999999988753
Q ss_pred ---CCceEEEEccCCCccCC
Q 020356 161 ---DGSLQLQARNQKYGKLE 177 (327)
Q Consensus 161 ---~g~i~Lstr~~~lGkL~ 177 (327)
+.....|+|++.||+++
T Consensus 153 ~~~~~~~i~T~~~~~LG~~~ 172 (176)
T PTZ00162 153 DASNLFAIATINSDYLGPIE 172 (176)
T ss_pred cCCCcEEEEEecCCCcCccc
Confidence 23577799999999995
No 62
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.70 E-value=0.00016 Score=53.74 Aligned_cols=67 Identities=16% Similarity=0.241 Sum_probs=52.9
Q ss_pred CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEE
Q 020356 91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQL 166 (327)
Q Consensus 91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~L 166 (327)
|+++-|+|+++.+.+++|++.....|++|.+++..+. + . .+..+.|++||.|.|+|.+++.. +.+.|
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~---~--~----~~~~~~~~~G~~v~v~v~~id~~~~~i~l 68 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQ---R--V----RHPSEIYKKGQEVEAVVLNIDVERERISL 68 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCcc---c--c----CChhhEECCCCEEEEEEEEEECCcCEEeC
Confidence 7899999999999999999998899999999875211 1 0 13356799999999999999754 34444
No 63
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.65 E-value=0.00032 Score=52.35 Aligned_cols=66 Identities=21% Similarity=0.237 Sum_probs=51.8
Q ss_pred CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEEEc
Q 020356 91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQAR 169 (327)
Q Consensus 91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Lstr 169 (327)
|++|.|+|+++...+++|++ ....|++|.+++..+ +.. +..+ .+||.+.|+|.+++. .+.+.||.|
T Consensus 1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~~~~------~~~----~~~~--~vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLR------PVE----DLDE--YVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCc------ccC----ChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 79999999999999999999 468999999987521 110 1111 389999999999986 567888764
No 64
>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=97.62 E-value=0.00014 Score=77.72 Aligned_cols=94 Identities=20% Similarity=0.289 Sum_probs=69.0
Q ss_pred eCCeEEEEEeeEEEEE--CcEEEEEecCCccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccc
Q 020356 58 QKGELAATVCGVVERI--NKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTA 135 (327)
Q Consensus 58 ~~g~i~Ssv~G~v~~~--nk~v~V~pl~~rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~ 135 (327)
++|.++....+..... ...+.... ..|++|+++.|+|+++.+.+++|+|....+|+||+|++. ..+.
T Consensus 588 ddG~V~i~~~~~~~~~~a~~~I~~~~----~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~------~~~v- 656 (684)
T TIGR03591 588 DDGTVKIAASDGEAAEAAIKMIEGIT----AEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIA------NERV- 656 (684)
T ss_pred cCeEEEEEECcHHHHHHHHHHHHhhh----cccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcC------CCcc-
Confidence 4666666665554332 22333322 258999999999999999999999998899999999885 1111
Q ss_pred cchhhhhcccCCCCEEEEEEEecCCCCceE
Q 020356 136 VDELNMRSIFTENDLVCAEVRSSQGDGSLQ 165 (327)
Q Consensus 136 ~de~~mr~~~~~GDlV~AeV~sv~~~g~i~ 165 (327)
+ +..+.|++||.|.++|.+++..+.+.
T Consensus 657 -~--~~~~~~kvGD~V~VkVi~id~~gki~ 683 (684)
T TIGR03591 657 -E--KVEDVLKEGDEVKVKVLEIDKQGRIK 683 (684)
T ss_pred -c--ChhhccCCCCEEEEEEEEECCCCCcc
Confidence 1 56788999999999999998655443
No 65
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.58 E-value=0.00027 Score=72.73 Aligned_cols=71 Identities=15% Similarity=0.201 Sum_probs=60.0
Q ss_pred CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ 167 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls 167 (327)
++||+|-|+|+++.+.+++|||+. ..|++|+|+++. .+. + +..+.|++||.|.++|.+++. .+.+.||
T Consensus 207 k~G~iv~G~V~~i~~~G~FVdlgg-v~Glv~~Sels~------~~v--~--~~~~~~kvGd~V~vkVl~iD~e~~rI~LS 275 (486)
T PRK07899 207 QKGQVRKGVVSSIVNFGAFVDLGG-VDGLVHVSELSW------KHI--D--HPSEVVEVGQEVTVEVLDVDMDRERVSLS 275 (486)
T ss_pred cCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHCCC------ccc--C--CHHHhcCCCCEEEEEEEEEECCCCEEEEE
Confidence 589999999999999999999974 889999998862 221 1 456789999999999999986 4789999
Q ss_pred Ecc
Q 020356 168 ARN 170 (327)
Q Consensus 168 tr~ 170 (327)
+|.
T Consensus 276 lK~ 278 (486)
T PRK07899 276 LKA 278 (486)
T ss_pred Eee
Confidence 875
No 66
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=97.56 E-value=0.00027 Score=72.71 Aligned_cols=75 Identities=19% Similarity=0.272 Sum_probs=61.9
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCC----
Q 020356 87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDG---- 162 (327)
Q Consensus 87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g---- 162 (327)
..++||+|-|+|+++...+++|+|+....|++|+++++. .+ .+ ++.++|++||.|.|+|.+++.+.
T Consensus 199 ~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~------~~--~~--~~~~~~~vGd~i~vkVl~id~~~~~~~ 268 (491)
T PRK13806 199 TVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSW------SR--VQ--KADEAVSVGDTVRVKVLGIERAKKGKG 268 (491)
T ss_pred hCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCC------cc--cc--ChhHhcCCCCEEEEEEEEEecccCCcc
Confidence 468999999999999999999999877899999998862 11 11 45677999999999999998653
Q ss_pred -ceEEEEccC
Q 020356 163 -SLQLQARNQ 171 (327)
Q Consensus 163 -~i~Lstr~~ 171 (327)
.+.||+|..
T Consensus 269 ~ri~lS~K~~ 278 (491)
T PRK13806 269 LRISLSIKQA 278 (491)
T ss_pred eEEEEEehhh
Confidence 588998653
No 67
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.55 E-value=0.00041 Score=52.26 Aligned_cols=64 Identities=14% Similarity=0.236 Sum_probs=51.9
Q ss_pred CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD 161 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~ 161 (327)
.+|+++.|+|+++...+++|++.....|++|++++.-++ + ..+..+.|+.||.|.++|.+++..
T Consensus 2 ~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~-----~----~~~~~~~~~~Gd~v~v~v~~id~~ 65 (72)
T cd05689 2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTN-----K----NIHPSKVVSLGDEVEVMVLDIDEE 65 (72)
T ss_pred cCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcc-----c----ccCcccEeCCCCEEEEEEEEeeCC
Confidence 379999999999999999999987789999998774110 1 113457799999999999999764
No 68
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.53 E-value=0.00029 Score=76.90 Aligned_cols=75 Identities=20% Similarity=0.276 Sum_probs=63.4
Q ss_pred CCCCCCEEE-EEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceE
Q 020356 87 KPETGDIVI-GRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQ 165 (327)
Q Consensus 87 ~P~vGDiVI-GrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~ 165 (327)
.|++|+++. |+|++|.+.+++|+|....+|++|+|++. .++.. +..+.|++||.|.++|.+++..+.+.
T Consensus 750 ~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs------~~rv~----~~~dv~kvGD~V~VkVi~ID~~grI~ 819 (891)
T PLN00207 750 VPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELS------SNWLA----KPEDAFKVGDRIDVKLIEVNDKGQLR 819 (891)
T ss_pred CcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcC------Ccccc----CHHHhcCCCCEEEEEEEEECCCCcEE
Confidence 589999995 69999999999999987789999999885 22221 44578999999999999999878899
Q ss_pred EEEccC
Q 020356 166 LQARNQ 171 (327)
Q Consensus 166 Lstr~~ 171 (327)
|+++..
T Consensus 820 LSlK~l 825 (891)
T PLN00207 820 LSRRAL 825 (891)
T ss_pred EEEecc
Confidence 998753
No 69
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.46 E-value=0.00059 Score=67.67 Aligned_cols=74 Identities=19% Similarity=0.232 Sum_probs=61.1
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceE
Q 020356 87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQ 165 (327)
Q Consensus 87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~ 165 (327)
..++||+|-|+|+++.+.+++|+++. ..|++|+++++.. + .+ ++.+.|++||.|.|+|.+++. ++.+.
T Consensus 189 ~~~~G~~v~g~V~~v~~~G~fV~l~~-v~g~v~~sels~~------~--~~--~~~~~~~vGd~i~~~Vl~vd~~~~~i~ 257 (390)
T PRK06676 189 SLKEGDVVEGTVARLTDFGAFVDIGG-VDGLVHISELSHE------R--VE--KPSEVVSVGQEVEVKVLSIDWETERIS 257 (390)
T ss_pred hCCCCCEEEEEEEEEecceEEEEeCC-eEEEEEHHHcCcc------c--cC--CHHHhcCCCCEEEEEEEEEeCCCCEEE
Confidence 35799999999999999999999975 8899999987621 1 11 456779999999999999976 57899
Q ss_pred EEEccC
Q 020356 166 LQARNQ 171 (327)
Q Consensus 166 Lstr~~ 171 (327)
||+|..
T Consensus 258 lS~k~~ 263 (390)
T PRK06676 258 LSLKDT 263 (390)
T ss_pred EEEeec
Confidence 998753
No 70
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.46 E-value=0.00045 Score=71.16 Aligned_cols=74 Identities=22% Similarity=0.349 Sum_probs=61.2
Q ss_pred CCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEE
Q 020356 88 PETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQL 166 (327)
Q Consensus 88 P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~L 166 (327)
.+.||+|.|+|+.+..+.++|||+....|+||.++++.. +. .+..+.|++||.|.|.|.++++ .+.+.|
T Consensus 33 ~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~------~~----~~~~~~~~vGd~Ie~~V~~~~~~~g~liL 102 (486)
T PRK07899 33 FNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIK------HD----VDPNEVVEVGDEVEALVLQKEDKEGRLIL 102 (486)
T ss_pred CCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhccc------cc----CChhhcCCCCCEEEEEEEEEECCCCeEEE
Confidence 579999999999999999999999888999999887621 11 1345669999999999999865 568999
Q ss_pred EEccC
Q 020356 167 QARNQ 171 (327)
Q Consensus 167 str~~ 171 (327)
|.+..
T Consensus 103 S~k~~ 107 (486)
T PRK07899 103 SKKRA 107 (486)
T ss_pred Eehhh
Confidence 99864
No 71
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.44 E-value=0.00057 Score=71.05 Aligned_cols=73 Identities=16% Similarity=0.214 Sum_probs=61.5
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceE
Q 020356 87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQ 165 (327)
Q Consensus 87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~ 165 (327)
..++|++|-|+|+.+...+++||++ ...|.+|+++++.. +. .++.+.|++||-|.|+|.+++. ++.+.
T Consensus 198 ~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~------~~----~~~~~~~kvG~~v~v~V~~~d~~~~~i~ 266 (565)
T PRK06299 198 NLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWK------RV----NHPSEVVNVGDEVKVKVLKFDKEKKRVS 266 (565)
T ss_pred cCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhccc------cc----CCHhhcCCCCCEEEEEEEEEeCCCCeEE
Confidence 3579999999999999999999998 78999999988632 11 1556779999999999999986 57899
Q ss_pred EEEcc
Q 020356 166 LQARN 170 (327)
Q Consensus 166 Lstr~ 170 (327)
||++.
T Consensus 267 lS~k~ 271 (565)
T PRK06299 267 LGLKQ 271 (565)
T ss_pred EEEEe
Confidence 99874
No 72
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.38 E-value=0.0016 Score=67.80 Aligned_cols=73 Identities=23% Similarity=0.302 Sum_probs=61.0
Q ss_pred CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ 167 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls 167 (327)
++||+|.|+|+.+.+.+.+|.+.....|++|.|+++- .+ .. +..+.|++||.|.|+|.+++. .+.+.||
T Consensus 459 ~~G~vV~G~V~~v~~~G~fV~l~~gi~g~i~~se~s~------~~--~~--~~~~~~~~Gd~v~~~V~~vd~~~~~i~LS 528 (565)
T PRK06299 459 KKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSR------DR--VE--DATEVLKVGDEVEAKVINIDRKNRRISLS 528 (565)
T ss_pred CCCCEEEEEEEEEecCceEEecCCCcEEEEEHHHhcc------hh--cc--CccccCCCCCEEEEEEEEEccccCEEEEE
Confidence 6899999999999999999999877899999998751 11 11 456779999999999999986 5789999
Q ss_pred EccC
Q 020356 168 ARNQ 171 (327)
Q Consensus 168 tr~~ 171 (327)
++..
T Consensus 529 ~k~~ 532 (565)
T PRK06299 529 IKAL 532 (565)
T ss_pred eeeh
Confidence 9753
No 73
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.36 E-value=0.00066 Score=67.33 Aligned_cols=74 Identities=22% Similarity=0.376 Sum_probs=59.7
Q ss_pred CCCCCCEEEEEEEEEecceEEEEE-cCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-Cce
Q 020356 87 KPETGDIVIGRVIEVVPKRWKLEI-NFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSL 164 (327)
Q Consensus 87 ~P~vGDiVIGrV~~V~~~~w~VDI-~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i 164 (327)
..++||+|.|+|+.+..+++.||| +....|+||.+++... +.. +....|++||.|.|.|.+++.+ +.+
T Consensus 14 ~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~------~~~----~~~~~~~vGd~v~~~V~~v~~~~~~i 83 (390)
T PRK06676 14 EVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSND------HIE----DINDVVKVGDELEVYVLKVEDGEGNL 83 (390)
T ss_pred cccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhccc------ccc----CcccccCCCCEEEEEEEEEECCCCCE
Confidence 457999999999999999999999 7788999999887521 000 2345589999999999999864 469
Q ss_pred EEEEcc
Q 020356 165 QLQARN 170 (327)
Q Consensus 165 ~Lstr~ 170 (327)
.||.+.
T Consensus 84 ~lS~k~ 89 (390)
T PRK06676 84 LLSKRR 89 (390)
T ss_pred EEEHHH
Confidence 999875
No 74
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=97.33 E-value=0.0017 Score=49.81 Aligned_cols=72 Identities=18% Similarity=0.218 Sum_probs=53.4
Q ss_pred CCCEEEEEEEEEecceEEEEEcC-ccceeeecccccCCCcccccccccchh-------hhhcccCCCCEEEEEEEecCC-
Q 020356 90 TGDIVIGRVIEVVPKRWKLEINF-TQDAILMLSSMNLPDGIQRRRTAVDEL-------NMRSIFTENDLVCAEVRSSQG- 160 (327)
Q Consensus 90 vGDiVIGrV~~V~~~~w~VDI~s-~~~a~L~ls~v~fpg~i~rrr~~~de~-------~mr~~~~~GDlV~AeV~sv~~- 160 (327)
+|+++-|.|+.+.+.+++|++.. ...|.+|++++. +. + -..|+. .....|++||.|.++|.+++.
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~--~~--~--~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~ 74 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLG--DD--Y--YEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLD 74 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecC--CC--c--EEEcccceEEEeccCCCEEcCCCEEEEEEEEeccc
Confidence 48999999999999999999986 578899998764 11 0 001111 234679999999999999986
Q ss_pred CCceEEE
Q 020356 161 DGSLQLQ 167 (327)
Q Consensus 161 ~g~i~Ls 167 (327)
.+.+.|+
T Consensus 75 ~~~i~~~ 81 (83)
T cd04471 75 RRKIDFE 81 (83)
T ss_pred cCEEEEE
Confidence 3556654
No 75
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=97.29 E-value=0.00054 Score=73.38 Aligned_cols=73 Identities=22% Similarity=0.287 Sum_probs=62.1
Q ss_pred CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEEE
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQLQ 167 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~Ls 167 (327)
++|.++.|+|+.|...+++|||+..++|.+|+|.++ .+ .+. +..+.++.||+|.++|..++.. ..+.||
T Consensus 657 k~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls------~~--fv~--~P~~vv~vGdiV~v~V~~vD~~r~rI~Ls 726 (780)
T COG2183 657 KPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLS------DK--FVK--DPNEVVKVGDIVKVKVIEVDTARKRIALS 726 (780)
T ss_pred cCCCEEEEEEEEeeeccceEEeccccceeeeHHHhh------hh--hcC--ChHHhcccCCEEEEEEEEEecccCeeeeE
Confidence 789999999999999999999999999999999886 11 111 3367799999999999999864 579999
Q ss_pred EccC
Q 020356 168 ARNQ 171 (327)
Q Consensus 168 tr~~ 171 (327)
+|..
T Consensus 727 mr~~ 730 (780)
T COG2183 727 MRLD 730 (780)
T ss_pred eecc
Confidence 9864
No 76
>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=97.27 E-value=0.0011 Score=67.96 Aligned_cols=73 Identities=18% Similarity=0.226 Sum_probs=60.4
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceE
Q 020356 87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQ 165 (327)
Q Consensus 87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~ 165 (327)
..++||+|-|.|+.+.+.+++||++. ..|++|.++++.. +.. +..+.|++||.|.|+|.+++. .+.+.
T Consensus 184 ~l~~G~~v~g~V~~i~~~G~~V~l~g-~~g~lp~~e~s~~------~~~----~~~~~~~vG~~v~v~Vl~~d~~~~~i~ 252 (516)
T TIGR00717 184 NLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWK------RVK----HPSEYVKVGQEVKVKVIKFDKEKGRIS 252 (516)
T ss_pred hccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHcCCC------CCC----CHHHhccCCCEEEEEEEEEECCCCcEE
Confidence 56899999999999999999999975 7899999988631 111 455679999999999999986 46799
Q ss_pred EEEcc
Q 020356 166 LQARN 170 (327)
Q Consensus 166 Lstr~ 170 (327)
||.+.
T Consensus 253 lS~k~ 257 (516)
T TIGR00717 253 LSLKQ 257 (516)
T ss_pred EEEEe
Confidence 99874
No 77
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.24 E-value=0.001 Score=70.63 Aligned_cols=72 Identities=19% Similarity=0.244 Sum_probs=60.1
Q ss_pred CCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEE
Q 020356 88 PETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQL 166 (327)
Q Consensus 88 P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~L 166 (327)
.++||+|.|+|+++.+.+++|++ ....|++|+++++.. +. . ++.+.|++||.|.|+|.+++. ++.+.|
T Consensus 475 l~~G~iV~g~V~~v~~~G~fV~l-~gv~Gll~~sels~~------~~--~--~~~~~~~vGd~V~vkV~~id~~~~~I~l 543 (647)
T PRK00087 475 LEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWG------RV--E--KPSDVLKVGDEIKVYILDIDKENKKLSL 543 (647)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEHHHcCcc------cc--C--CHHHhcCCCCEEEEEEEEEECCCCEEEE
Confidence 46899999999999999999999 568899999987521 11 1 456779999999999999975 578999
Q ss_pred EEcc
Q 020356 167 QARN 170 (327)
Q Consensus 167 str~ 170 (327)
|+|.
T Consensus 544 S~K~ 547 (647)
T PRK00087 544 SLKK 547 (647)
T ss_pred Eeec
Confidence 9975
No 78
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=97.23 E-value=0.00092 Score=69.50 Aligned_cols=73 Identities=15% Similarity=0.172 Sum_probs=62.8
Q ss_pred CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEEE
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQLQ 167 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~Ls 167 (327)
.+||.+.|+|+.+++++++|+|.....|++|+|+++- .+.. ...+.+++||.|.++|++++++ ..+.|+
T Consensus 276 ~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw------~~~~----~P~evv~~Gq~V~V~Vl~id~e~rRIsL~ 345 (541)
T COG0539 276 PVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISW------TKKN----VPSEVVKVGQEVEVKVLDIDPERRRISLG 345 (541)
T ss_pred CCCCEEEEEEEEeecCcEEEEecCCccceeechhhcc------cccC----CHHHhcccCCEEEEEEEeeCchhceEEee
Confidence 4899999999999999999999999999999999872 2211 2467899999999999999974 689999
Q ss_pred EccC
Q 020356 168 ARNQ 171 (327)
Q Consensus 168 tr~~ 171 (327)
||..
T Consensus 346 iKq~ 349 (541)
T COG0539 346 LKQL 349 (541)
T ss_pred ehhh
Confidence 9864
No 79
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=97.18 E-value=0.0012 Score=67.84 Aligned_cols=73 Identities=14% Similarity=0.076 Sum_probs=60.3
Q ss_pred CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEEE
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQLQ 167 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~Ls 167 (327)
.+|++|-|+|+++.+.+++|++....+|++|.|+++-. + . -+..+.|++||.|.|+|.+++.+ ..+.|+
T Consensus 378 ~vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~~----~--~----~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls 447 (491)
T PRK13806 378 APGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRA----G--K----PATYEKLKPGDSVTLVVEEIDTAKRKISLA 447 (491)
T ss_pred CCCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCcc----c--c----cchhhcCCCCCEEEEEEEEEeCCCCEEEEE
Confidence 47999999999999999999998789999999988621 1 1 13456689999999999999864 579999
Q ss_pred EccC
Q 020356 168 ARNQ 171 (327)
Q Consensus 168 tr~~ 171 (327)
++..
T Consensus 448 ~~~~ 451 (491)
T PRK13806 448 PAGA 451 (491)
T ss_pred eehh
Confidence 8843
No 80
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=97.17 E-value=0.0039 Score=68.40 Aligned_cols=105 Identities=11% Similarity=0.132 Sum_probs=73.2
Q ss_pred eeCCeEEEEEeeEEEEECcEE--EEEecC-Cc---c--CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCc
Q 020356 57 DQKGELAATVCGVVERINKLI--YVRALR-AR---Y--KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDG 128 (327)
Q Consensus 57 ~~~g~i~Ssv~G~v~~~nk~v--~V~pl~-~r---Y--~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~ 128 (327)
..++++.+.+.+. ...++.+ +++-+. .+ + .-.+|++|-|.|+.+++.+++|++...-.|++|.|+++..
T Consensus 625 kvGd~V~vkVl~i-D~e~~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~sels~~-- 701 (863)
T PRK12269 625 KIGDEVECMILGY-DIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWV-- 701 (863)
T ss_pred CCCCEEEEEEEEE-ecccCceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEecceEEEEeCCCcEEEEEhHHhhcc--
Confidence 3456677777665 3223333 333221 11 1 1147999999999999999999998888999999988621
Q ss_pred ccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEEEccC
Q 020356 129 IQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQARNQ 171 (327)
Q Consensus 129 i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Lstr~~ 171 (327)
++ .. ...+.|++||.|.|+|.+++. ...+.||+|..
T Consensus 702 --~~-~~----~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~l 738 (863)
T PRK12269 702 --KR-TR----PADHELEVGKEIECMVIECDPQARRIRLGVKQL 738 (863)
T ss_pred --cc-cc----chhhccCCCCEEEEEEEEEeccCCEEEEEeccc
Confidence 11 11 233569999999999999986 46899999853
No 81
>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=97.17 E-value=0.0016 Score=66.71 Aligned_cols=73 Identities=18% Similarity=0.219 Sum_probs=60.0
Q ss_pred CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ 167 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls 167 (327)
++||++-|+|+++...+++|+++....|++|++++.... .. .+..+.|++||.|.|+|.+++. .+.+.||
T Consensus 271 ~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~-----~~----~~~~~~~~vG~~v~v~V~~id~~~~~i~lS 341 (516)
T TIGR00717 271 PVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVK-----KN----SHPSKVVKKGDEVEVMILDIDPERRRLSLG 341 (516)
T ss_pred cCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCcc-----cc----CCHHHhccCCCEEEEEEEEEcCCCCEEEEE
Confidence 589999999999999999999988889999999875321 00 1234569999999999999986 4689999
Q ss_pred Ecc
Q 020356 168 ARN 170 (327)
Q Consensus 168 tr~ 170 (327)
++.
T Consensus 342 ~k~ 344 (516)
T TIGR00717 342 LKQ 344 (516)
T ss_pred ehh
Confidence 875
No 82
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=97.14 E-value=0.0013 Score=71.92 Aligned_cols=74 Identities=16% Similarity=0.169 Sum_probs=61.7
Q ss_pred CCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEE
Q 020356 88 PETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQL 166 (327)
Q Consensus 88 P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~L 166 (327)
..+||+|-|+|+++.+.+++|++.....|++|+|+++.. ++. .+..+.|++||.|.|+|.+++. .+.+.|
T Consensus 576 ~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~-----~~~----~~p~~~~kvGd~V~vkVl~iD~e~~rIsL 646 (863)
T PRK12269 576 FGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWV-----KKT----SKPSDMVKIGDEVECMILGYDIQAGRVSL 646 (863)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCc-----ccc----CCHHHcCCCCCEEEEEEEEEecccCceEE
Confidence 468999999999999999999998888999999998631 111 1456779999999999999985 568999
Q ss_pred EEcc
Q 020356 167 QARN 170 (327)
Q Consensus 167 str~ 170 (327)
|++.
T Consensus 647 S~K~ 650 (863)
T PRK12269 647 GLKQ 650 (863)
T ss_pred Eehh
Confidence 9875
No 83
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.05 E-value=0.0022 Score=68.12 Aligned_cols=77 Identities=18% Similarity=0.329 Sum_probs=63.4
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecC-CCCce
Q 020356 86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQ-GDGSL 164 (327)
Q Consensus 86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~-~~g~i 164 (327)
+..++|++|.|+|+++..++++||++....|+||.+++.... ..+..+.|++||.|.++|.+++ .++.+
T Consensus 298 ~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~----------~~~~~~~~~vGd~V~v~V~~vd~~~g~i 367 (647)
T PRK00087 298 KQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDE----------ISSLKESVKVGDEIEVKVLKLEDEDGYV 367 (647)
T ss_pred hhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccc----------cCChhhccCCCCEEEEEEEEEECCCCcE
Confidence 467899999999999999999999998889999998875221 1134566999999999999986 46789
Q ss_pred EEEEccCC
Q 020356 165 QLQARNQK 172 (327)
Q Consensus 165 ~Lstr~~~ 172 (327)
.||.+...
T Consensus 368 ~LS~k~~~ 375 (647)
T PRK00087 368 VLSKKEAD 375 (647)
T ss_pred EEEeehhc
Confidence 99998653
No 84
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=97.02 E-value=0.0022 Score=63.35 Aligned_cols=113 Identities=16% Similarity=0.186 Sum_probs=76.8
Q ss_pred ccCCCCCCEEEEEEEEEecce-EEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC--
Q 020356 85 RYKPETGDIVIGRVIEVVPKR-WKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-- 161 (327)
Q Consensus 85 rY~P~vGDiVIGrV~~V~~~~-w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-- 161 (327)
.|..+.|++|.|+|.++..++ |.|||+ ...|+||.++.. | .+.|++||-|.|.|.++..+
T Consensus 126 ey~~k~GeiV~G~V~~v~~~g~v~VdiG-~~ea~LP~~E~i-p---------------~E~~~~Gd~ik~~V~~V~~~~k 188 (341)
T TIGR01953 126 EFSSKEGEIISGTVKRVNRRGNLYVELG-KTEGILPKKEQI-P---------------GEKFRIGDRIKAYVYEVRKTAK 188 (341)
T ss_pred HHHhhcCCEEEEEEEEEecCCcEEEEEC-CeEEEecHHHcC-C---------------CcCCCCCCEEEEEEEEEEcCCC
Confidence 488899999999999999866 799997 578898877653 2 22389999999999999743
Q ss_pred -CceEEEEccCCC---------ccCCCCeEEEeChhhhhhcccccccc---C-ccceEEEEeeccee
Q 020356 162 -GSLQLQARNQKY---------GKLERGQLLTVDPYLVKRRKQHFHHL---E-EYGIDLIIGCNGYI 214 (327)
Q Consensus 162 -g~i~Lstr~~~l---------GkL~~G~lv~V~~~li~r~~~h~~~L---~-~~~~eiivG~NG~I 214 (327)
+.+.||.+.++| -.+.+|.+-=...+-..=.++.+... + --++-.|||.+|-=
T Consensus 189 g~qIivSRt~~~~v~~Lfe~EVPEI~dG~VeI~~iaR~pG~RtKvAV~s~~~~iDpvga~vG~~G~r 255 (341)
T TIGR01953 189 GPQIILSRTHPEFVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVESNDENIDPVGACVGPKGSR 255 (341)
T ss_pred CCeEEEEeCcHHHHHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCcceeeECCCCch
Confidence 368888877554 45567766543332222112211111 1 12667788988853
No 85
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.97 E-value=0.0022 Score=63.87 Aligned_cols=112 Identities=13% Similarity=0.103 Sum_probs=74.9
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCC---
Q 020356 86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDG--- 162 (327)
Q Consensus 86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g--- 162 (327)
|.+++|++|.|+|..+....|+|||+. ..|+||.++.. | ++.|++||-|.|.|.++..+.
T Consensus 130 f~~k~GeiV~G~V~~~~~~~~~Vdlg~-vEa~LP~~E~i-p---------------~e~~~~Gd~Ika~V~~V~~~~kgp 192 (362)
T PRK12327 130 FSEREGDIVTGVVQRRDNRFVYVNLGK-IEAVLPPAEQI-P---------------GETYKHGDRIKVYVVKVEKTTKGP 192 (362)
T ss_pred HHHhcCCEEEEEEEEEeCCcEEEEeCC-eEEEecHHHcC-C---------------CCCCCCCCEEEEEEEEEecCCCCC
Confidence 899999999999999999999999986 78898866542 2 244899999999999998432
Q ss_pred ceEEEEccCCC---------ccCCCCeEEEeChhhhhhcccccccc---Cc-cceEEEEeeccee
Q 020356 163 SLQLQARNQKY---------GKLERGQLLTVDPYLVKRRKQHFHHL---EE-YGIDLIIGCNGYI 214 (327)
Q Consensus 163 ~i~Lstr~~~l---------GkL~~G~lv~V~~~li~r~~~h~~~L---~~-~~~eiivG~NG~I 214 (327)
.+.||-..++| -.+.+|.+-=...+-.+=.++.+... +. -++-.|||.+|-=
T Consensus 193 ~IivSRt~p~~v~~Lfe~EVPEI~~G~VeIk~iaR~pG~RtKVAV~s~~~~iDpvGa~iG~~G~r 257 (362)
T PRK12327 193 QIFVSRTHPGLVKRLFELEVPEIYDGTVEIKSIAREAGDRTKIAVRSNNPNVDAKGACVGPKGQR 257 (362)
T ss_pred eEEEEeCCHHHHHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCchheeECCCChh
Confidence 57777655443 34556765533322211111111111 11 2566688888853
No 86
>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=96.81 E-value=0.01 Score=47.56 Aligned_cols=81 Identities=11% Similarity=0.115 Sum_probs=51.7
Q ss_pred CCCEEEEEEEEEecceEEEEEcCccceeeecccc----cCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-Cc-
Q 020356 90 TGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSM----NLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GS- 163 (327)
Q Consensus 90 vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v----~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~- 163 (327)
+|.+|.|+|+++...+++|+++ |.+++++-+.+ -|.+..+ .-...+ +-..+++.||.|++||.++.-+ ..
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G-pl~~f~~~~~ip~~~~~~~~~~-~~~~~~--~~~~~i~~g~~VR~rV~~v~~~~~~~ 76 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG-PLSIFISRHLIPSDMEFDPNAS-PPCFTS--NEDIVIKKDTEVRLKIIGTRVDATDI 76 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc-CceEEEEeeecCccceECCcCC-CCeEeC--CCcEEECCCCEEEEEEEEEEEccCce
Confidence 5899999999999999999998 45555544433 1211000 001111 1256799999999999887532 11
Q ss_pred -eEEEEccCCCc
Q 020356 164 -LQLQARNQKYG 174 (327)
Q Consensus 164 -i~Lstr~~~lG 174 (327)
..-|++++.||
T Consensus 77 ~~igt~~~~~LG 88 (88)
T cd04462 77 FAIGTIKDDYLG 88 (88)
T ss_pred EEEEEccCCCCC
Confidence 22266777776
No 87
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.51 E-value=0.0054 Score=63.08 Aligned_cols=72 Identities=25% Similarity=0.350 Sum_probs=59.4
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC---
Q 020356 85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD--- 161 (327)
Q Consensus 85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~--- 161 (327)
.|..++|++|.|+|.++...+++||++ ...|+||.+++. | ++.|++||-|.|.|..++..
T Consensus 129 eyk~~~GeIV~G~V~ri~~~giiVDLg-gvea~LP~sE~i-p---------------~E~~~~GdrIka~I~~Vd~~~kg 191 (470)
T PRK09202 129 EYKDRVGEIITGVVKRVERGNIIVDLG-RAEAILPRKEQI-P---------------RENFRPGDRVRAYVYEVRKEARG 191 (470)
T ss_pred HHHhhcCCEEEEEEEEEecCCEEEEEC-CeEEEecHHHcC-C---------------CccCCCCCEEEEEEEEEecCCCC
Confidence 388899999999999999999999997 468898887763 2 34589999999999999763
Q ss_pred CceEEEEccCCC
Q 020356 162 GSLQLQARNQKY 173 (327)
Q Consensus 162 g~i~Lstr~~~l 173 (327)
..+.||-+.+.|
T Consensus 192 ~qIilSRt~p~~ 203 (470)
T PRK09202 192 PQIILSRTHPEF 203 (470)
T ss_pred CeEEEEeCcHHH
Confidence 268888777554
No 88
>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=96.15 E-value=0.042 Score=55.75 Aligned_cols=81 Identities=19% Similarity=0.295 Sum_probs=57.7
Q ss_pred cCCCCCCEEEEEEEEEecc--eEEEEEcCccceeeecccccCCCccc-----ccccccchhhhhcccCCCCEEEEEEEec
Q 020356 86 YKPETGDIVIGRVIEVVPK--RWKLEINFTQDAILMLSSMNLPDGIQ-----RRRTAVDELNMRSIFTENDLVCAEVRSS 158 (327)
Q Consensus 86 Y~P~vGDiVIGrV~~V~~~--~w~VDI~s~~~a~L~ls~v~fpg~i~-----rrr~~~de~~mr~~~~~GDlV~AeV~sv 158 (327)
..+.+|||..|+|..+.+. .+||||+...+|+||++++. |+.-. .++... -++.+.+++||.|.+.|..-
T Consensus 21 ~~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~-~~~~~~~~~~~~~~~~--~~i~~~l~~G~~IlVQV~Ke 97 (414)
T TIGR00757 21 SRQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIG-PNYECLAPAEAKREAG--PSISELLRPGQSVLVQVVKE 97 (414)
T ss_pred CcCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcC-chhhcccccccccccc--CCHHHhCcCCCEEEEEEeeC
Confidence 3445899999999999998 99999999999999999874 21000 000011 14566799999999999883
Q ss_pred CC-CCceEEEEc
Q 020356 159 QG-DGSLQLQAR 169 (327)
Q Consensus 159 ~~-~g~i~Lstr 169 (327)
.. +..+.||+.
T Consensus 98 ~~~~Kgp~lT~~ 109 (414)
T TIGR00757 98 PRGNKGARLTTD 109 (414)
T ss_pred CcCCCCCeEEEE
Confidence 22 234666663
No 89
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.01 E-value=0.015 Score=61.74 Aligned_cols=75 Identities=20% Similarity=0.328 Sum_probs=64.8
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceE
Q 020356 86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQ 165 (327)
Q Consensus 86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~ 165 (327)
--|++|.+-.|+|+.+.+.+++|.+....++.+|+|.+.-. |. + +..+.+++||.|+.+|..+++-|.+.
T Consensus 615 ~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~------rv--~--kv~dvlk~Gd~v~Vkv~~iD~~Gri~ 684 (692)
T COG1185 615 REVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKE------RV--E--KVEDVLKEGDEVKVKVIEIDKQGRIR 684 (692)
T ss_pred hhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhh------hh--h--cccceeecCceEEEEEeeecccCCcc
Confidence 36799999999999999999999999999999999988611 11 1 45588999999999999999989999
Q ss_pred EEEcc
Q 020356 166 LQARN 170 (327)
Q Consensus 166 Lstr~ 170 (327)
|+++.
T Consensus 685 ls~~~ 689 (692)
T COG1185 685 LSIKA 689 (692)
T ss_pred ceehh
Confidence 98864
No 90
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=94.12 E-value=0.18 Score=54.22 Aligned_cols=81 Identities=16% Similarity=0.165 Sum_probs=57.1
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEcC-ccceeeecccccCCCccccc--ccccchhhhhcccCCCCEEEEEEEecCC-CC
Q 020356 87 KPETGDIVIGRVIEVVPKRWKLEINF-TQDAILMLSSMNLPDGIQRR--RTAVDELNMRSIFTENDLVCAEVRSSQG-DG 162 (327)
Q Consensus 87 ~P~vGDiVIGrV~~V~~~~w~VDI~s-~~~a~L~ls~v~fpg~i~rr--r~~~de~~mr~~~~~GDlV~AeV~sv~~-~g 162 (327)
.+++|.++-|+|++++..+++|.+.. ...|.+|++++. .+..... .....-......|++||.|.++|.+++. .+
T Consensus 624 ~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~-~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~ 702 (709)
T TIGR02063 624 SEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLK-DDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTG 702 (709)
T ss_pred hccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecC-CCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccC
Confidence 56889999999999999999999986 589999999874 1100000 0000000223569999999999999986 46
Q ss_pred ceEEEE
Q 020356 163 SLQLQA 168 (327)
Q Consensus 163 ~i~Lst 168 (327)
.+.++.
T Consensus 703 ~I~~~l 708 (709)
T TIGR02063 703 KIDFEL 708 (709)
T ss_pred eEEEEE
Confidence 666653
No 91
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=93.77 E-value=0.14 Score=51.35 Aligned_cols=69 Identities=26% Similarity=0.388 Sum_probs=51.7
Q ss_pred ccCCCCCCEEEEEEEEEec-ceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCC-
Q 020356 85 RYKPETGDIVIGRVIEVVP-KRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDG- 162 (327)
Q Consensus 85 rY~P~vGDiVIGrV~~V~~-~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g- 162 (327)
.|.+++|++|-|+|..+.. ..+.||++ ...|+||-++. .| ++.|++||-|.|-|..+..+.
T Consensus 133 ey~~~~Geiv~g~V~r~~~~~~i~vdlg-~~ea~LP~~eq-ip---------------~E~~~~Gdrik~~i~~V~~~~k 195 (374)
T PRK12328 133 KYKKKVGKIVFGTVVRVDNEENTFIEID-EIRAVLPMKNR-IK---------------GEKFKVGDVVKAVLKRVKIDKN 195 (374)
T ss_pred HHHHhcCcEEEEEEEEEecCCCEEEEcC-CeEEEeCHHHc-CC---------------CCcCCCCCEEEEEEEEEecCCC
Confidence 4999999999999999986 46889998 46788765443 12 345999999999999997532
Q ss_pred ---ceEEEEcc
Q 020356 163 ---SLQLQARN 170 (327)
Q Consensus 163 ---~i~Lstr~ 170 (327)
.+.||...
T Consensus 196 ~gp~IilSRt~ 206 (374)
T PRK12328 196 NGILIELSRTS 206 (374)
T ss_pred CCCEEEEEcCC
Confidence 34455443
No 92
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=93.73 E-value=0.14 Score=52.32 Aligned_cols=84 Identities=15% Similarity=0.222 Sum_probs=61.3
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEEcC-----ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecC
Q 020356 85 RYKPETGDIVIGRVIEVVPKRWKLEINF-----TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQ 159 (327)
Q Consensus 85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s-----~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~ 159 (327)
.|.+++|++|.|+|..+....+.||+++ ...|+||-++. .| ++.|++||.|+|-|..+.
T Consensus 147 ef~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eq-ip---------------~E~y~~Gdrika~i~~V~ 210 (449)
T PRK12329 147 EFQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQ-LP---------------NDNYRANATFKVFLKEVS 210 (449)
T ss_pred HHHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHc-CC---------------CCcCCCCCEEEEEEEEee
Confidence 3899999999999999999999999953 25677665443 22 345999999999999996
Q ss_pred CC---C-ceEEEEccCCC---------ccCCCCeEEEe
Q 020356 160 GD---G-SLQLQARNQKY---------GKLERGQLLTV 184 (327)
Q Consensus 160 ~~---g-~i~Lstr~~~l---------GkL~~G~lv~V 184 (327)
.+ | .+.||-..++| -.+.+|.+--.
T Consensus 211 ~~~~kGpqIilSRt~p~lv~~Lfe~EVPEI~dG~VeIk 248 (449)
T PRK12329 211 EGPRRGPQLFVSRANAGLVVYLFENEVPEIEEGVVRIV 248 (449)
T ss_pred cCCCCCCEEEEEcCCHHHHHHHHHhhCcccccCeEEEE
Confidence 53 2 46777655443 45567766544
No 93
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=93.29 E-value=0.41 Score=38.44 Aligned_cols=71 Identities=11% Similarity=0.242 Sum_probs=52.1
Q ss_pred cc-CCCCCCEEEEEEEEEecceEEEEEcC-ccceeee-cccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC
Q 020356 85 RY-KPETGDIVIGRVIEVVPKRWKLEINF-TQDAILM-LSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD 161 (327)
Q Consensus 85 rY-~P~vGDiVIGrV~~V~~~~w~VDI~s-~~~a~L~-ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~ 161 (327)
.| .|++||+|. .|+.++...+.|.+-. ...|.+. .++++ |+|.. .+++.+ +|-.+.+.|..++..
T Consensus 10 cy~~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~sels------r~rir----si~kll-VGk~e~v~ViRVDk~ 77 (86)
T PHA02858 10 CYVFPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVN------ADRAE----KLKKKL-VGKTINVQVIRTDKL 77 (86)
T ss_pred EEecCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHh------HHHHH----hhhhhh-cCCeeEEEEEEECCC
Confidence 45 899999999 7888999999998753 2455554 66664 44333 667778 999999999999865
Q ss_pred -CceEEE
Q 020356 162 -GSLQLQ 167 (327)
Q Consensus 162 -g~i~Ls 167 (327)
|=+-|+
T Consensus 78 KGYIDLs 84 (86)
T PHA02858 78 KGYIDVR 84 (86)
T ss_pred CCEEEeE
Confidence 334443
No 94
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=93.22 E-value=0.55 Score=34.89 Aligned_cols=61 Identities=18% Similarity=0.141 Sum_probs=33.4
Q ss_pred CCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEc
Q 020356 90 TGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQAR 169 (327)
Q Consensus 90 vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr 169 (327)
+|+++-.+|++++..+|++|.+...+-.||.+++. .-+++||-|.+-|-. +.++.+..||+
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~------------------~~~~~Gd~v~VFvY~-D~~~rl~AT~k 61 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVP------------------EPLKVGDEVEVFVYL-DKEGRLVATTK 61 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG------------------------TTSEEEEEEEE--TTS-EEEE--
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcC------------------CCCCCCCEEEEEEEE-CCCCCEEEecC
Confidence 58999999999999999999887777776665442 227899999998866 34456766663
No 95
>PRK10811 rne ribonuclease E; Reviewed
Probab=93.22 E-value=0.56 Score=52.19 Aligned_cols=78 Identities=12% Similarity=0.232 Sum_probs=54.5
Q ss_pred CCCCCEEEEEEEEE--ecceEEEEEcCccceeeeccccc---CCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-
Q 020356 88 PETGDIVIGRVIEV--VPKRWKLEINFTQDAILMLSSMN---LPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD- 161 (327)
Q Consensus 88 P~vGDiVIGrV~~V--~~~~w~VDI~s~~~a~L~ls~v~---fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~- 161 (327)
+.+|+|-+|+|..| +-+.+||||+....|+|+|+++. |+.... .. ..-++...+++||.|...|..-...
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~--~~--~~~~i~~~Lk~GqeILVQV~KEa~gt 111 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYS--AH--GRPNIKDVLREGQEVIVQIDKEERGN 111 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccc--cc--cccccccccCCCCEEEEEEeecccCC
Confidence 35899999999999 46789999999999999998874 221110 00 0013455689999999999874432
Q ss_pred CceEEEEc
Q 020356 162 GSLQLQAR 169 (327)
Q Consensus 162 g~i~Lstr 169 (327)
.-+.||++
T Consensus 112 KGp~LTt~ 119 (1068)
T PRK10811 112 KGAALTTF 119 (1068)
T ss_pred CCCceeee
Confidence 23555554
No 96
>PRK11642 exoribonuclease R; Provisional
Probab=92.67 E-value=0.47 Score=52.11 Aligned_cols=76 Identities=13% Similarity=0.200 Sum_probs=56.7
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEcCc-cceeeecccccCCCcccccccccch-------hhhhcccCCCCEEEEEEEec
Q 020356 87 KPETGDIVIGRVIEVVPKRWKLEINFT-QDAILMLSSMNLPDGIQRRRTAVDE-------LNMRSIFTENDLVCAEVRSS 158 (327)
Q Consensus 87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~-~~a~L~ls~v~fpg~i~rrr~~~de-------~~mr~~~~~GDlV~AeV~sv 158 (327)
...+|+++-|+|++|+..+++|.|... -.|++|++++. +. ....|+ ......|+.||.|.++|.++
T Consensus 640 ~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~--~d----~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~v 713 (813)
T PRK11642 640 LDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLD--ND----YYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAV 713 (813)
T ss_pred hccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecC--Cc----ceEecchheEEecccCCcEECCCCEEEEEEEEe
Confidence 447999999999999999999999754 89999998764 10 000111 12346699999999999999
Q ss_pred CC-CCceEEEE
Q 020356 159 QG-DGSLQLQA 168 (327)
Q Consensus 159 ~~-~g~i~Lst 168 (327)
+. .+.+.|+.
T Consensus 714 D~~~rkI~f~l 724 (813)
T PRK11642 714 NMDERKIDFSL 724 (813)
T ss_pred ecCCCeEEEEE
Confidence 75 45677765
No 97
>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=91.74 E-value=0.72 Score=49.40 Aligned_cols=75 Identities=12% Similarity=0.190 Sum_probs=55.7
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEc-CccceeeecccccCCCcccccccccch-------hhhhcccCCCCEEEEEEEec
Q 020356 87 KPETGDIVIGRVIEVVPKRWKLEIN-FTQDAILMLSSMNLPDGIQRRRTAVDE-------LNMRSIFTENDLVCAEVRSS 158 (327)
Q Consensus 87 ~P~vGDiVIGrV~~V~~~~w~VDI~-s~~~a~L~ls~v~fpg~i~rrr~~~de-------~~mr~~~~~GDlV~AeV~sv 158 (327)
..++|+.+-|+|++++..+++|.|. ....|.+|++++. +. ....|+ ......|+.||.|..+|.++
T Consensus 569 ~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~--~d----~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~v 642 (654)
T TIGR00358 569 LDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLH--ND----YYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEV 642 (654)
T ss_pred hhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCC--Cc----ceEEeccccEEEeccCCcEECCCCEEEEEEEEE
Confidence 4578999999999999999999997 5689999998764 21 011111 12236799999999999999
Q ss_pred CC-CCceEEE
Q 020356 159 QG-DGSLQLQ 167 (327)
Q Consensus 159 ~~-~g~i~Ls 167 (327)
+. .+.+.++
T Consensus 643 d~~~~~I~f~ 652 (654)
T TIGR00358 643 NMETRSIIFE 652 (654)
T ss_pred ecccCeEEEE
Confidence 75 4455554
No 98
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=91.70 E-value=0.66 Score=53.23 Aligned_cols=73 Identities=25% Similarity=0.296 Sum_probs=60.6
Q ss_pred CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCC-ceEEE
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDG-SLQLQ 167 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g-~i~Ls 167 (327)
++||+|-|.|..+..++.++-+.....|.+++|... +-. +..-+..|.+|++|.++|.+++++. .++|+
T Consensus 1161 k~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~-ds~---------~k~w~k~~~~gklv~~rv~~ve~~s~riel~ 1230 (1710)
T KOG1070|consen 1161 KIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLS-DSF---------EKEWEKHLPVGKLVTGRVLSVEEDSKRIELS 1230 (1710)
T ss_pred ccCceeEEEEEEecCCcEEEEEccceEEEEEccccc-cch---------hhhhhccCCccceeeeEEEEeeccCceEEEE
Confidence 689999999999999999999999999999988763 211 1234567999999999999998764 78998
Q ss_pred EccC
Q 020356 168 ARNQ 171 (327)
Q Consensus 168 tr~~ 171 (327)
.+..
T Consensus 1231 Lk~s 1234 (1710)
T KOG1070|consen 1231 LKNS 1234 (1710)
T ss_pred Eecc
Confidence 7653
No 99
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=91.68 E-value=0.22 Score=47.78 Aligned_cols=74 Identities=19% Similarity=0.271 Sum_probs=60.1
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEEcC--ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-C
Q 020356 86 YKPETGDIVIGRVIEVVPKRWKLEINF--TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-G 162 (327)
Q Consensus 86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s--~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g 162 (327)
-.|+++|+|++.|..++.-++.|.+-- ...|.+.||.++ |||.. .+....++|-.=.+-|+.++.. |
T Consensus 12 kyPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELS------rRRIR----SI~klirVGr~E~vvVlrVDkekG 81 (304)
T KOG2916|consen 12 KYPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELS------RRRIR----SIQKLIRVGRNEPVVVLRVDKEKG 81 (304)
T ss_pred cCCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHH------HHHHH----HHHHHHhcCCcceEEEEEEcCCCC
Confidence 379999999999999999999999853 446677788876 55544 6677899999999999999864 5
Q ss_pred ceEEEEc
Q 020356 163 SLQLQAR 169 (327)
Q Consensus 163 ~i~Lstr 169 (327)
=+.||.|
T Consensus 82 YIDLSkr 88 (304)
T KOG2916|consen 82 YIDLSKR 88 (304)
T ss_pred ceechhc
Confidence 6888875
No 100
>PRK11712 ribonuclease G; Provisional
Probab=91.66 E-value=1.4 Score=45.73 Aligned_cols=95 Identities=16% Similarity=0.171 Sum_probs=60.6
Q ss_pred CcEEEEEecCCccCCCCCCEEEEEEEEEe--cceEEEEEcCccceeeecccccCCCccc-cc--ccccchhhhhcccCCC
Q 020356 74 NKLIYVRALRARYKPETGDIVIGRVIEVV--PKRWKLEINFTQDAILMLSSMNLPDGIQ-RR--RTAVDELNMRSIFTEN 148 (327)
Q Consensus 74 nk~v~V~pl~~rY~P~vGDiVIGrV~~V~--~~~w~VDI~s~~~a~L~ls~v~fpg~i~-rr--r~~~de~~mr~~~~~G 148 (327)
++++.+.--+......+|+|-.|+|..|- -+.+||||+...+|+||++++ +|..-. .. +.......+.+.+++|
T Consensus 22 g~l~e~~iE~~~~~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~-~~~~~~~~~~~~~~~~~~~i~~~l~~G 100 (489)
T PRK11712 22 GILQEIHIEREAKRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDI-VPHTECVAGEEQKQFVVRDISELVRQG 100 (489)
T ss_pred CEEEEEEEecCCcccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhc-cchhhhcccccccccccccHHHhccCC
Confidence 34443333333345568999999999995 467999999999999999987 231000 00 0000011356679999
Q ss_pred CEEEEEEEecCC-CCceEEEEc
Q 020356 149 DLVCAEVRSSQG-DGSLQLQAR 169 (327)
Q Consensus 149 DlV~AeV~sv~~-~g~i~Lstr 169 (327)
|.|...|..-.- ..-+.||+.
T Consensus 101 q~iLVQV~Ke~~~~KG~~lT~~ 122 (489)
T PRK11712 101 QDIMVQVVKDPLGTKGARLTTD 122 (489)
T ss_pred CEEEEEEEeCCcCCCCCeEEEE
Confidence 999999987432 234666663
No 101
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=89.95 E-value=0.41 Score=53.75 Aligned_cols=76 Identities=17% Similarity=0.223 Sum_probs=58.8
Q ss_pred CCCCEEEEEEEEEecce---EEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-Cce
Q 020356 89 ETGDIVIGRVIEVVPKR---WKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSL 164 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~---w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i 164 (327)
.+|-+|.++|++|+..+ .+|-+.+..+++++..+++ + -..+ +..+-+++|+.|+|+|.+++.. -++
T Consensus 984 ~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~S--d-~~v~-------~p~~~v~vgq~v~~kvi~id~e~f~v 1053 (1299)
T KOG1856|consen 984 YEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLS--D-RDVR-------RPENRVKVGQTVYCKVIKIDKERFSV 1053 (1299)
T ss_pred ccCceEEEeeeEEEecccceeEEEecCCCceeeeccccC--h-hhcc-------CHHHhhccCceEEEEeeeeeHhhhhh
Confidence 47999999999999998 6668888889998877654 1 1112 3445588999999999999864 478
Q ss_pred EEEEccCCCc
Q 020356 165 QLQARNQKYG 174 (327)
Q Consensus 165 ~Lstr~~~lG 174 (327)
.||||...|-
T Consensus 1054 ~Ls~r~sdlk 1063 (1299)
T KOG1856|consen 1054 ELSCRTSDLK 1063 (1299)
T ss_pred hhhhhhHHhh
Confidence 9999876554
No 102
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=84.86 E-value=3 Score=40.32 Aligned_cols=64 Identities=16% Similarity=0.037 Sum_probs=47.7
Q ss_pred CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEcc
Q 020356 91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARN 170 (327)
Q Consensus 91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~ 170 (327)
++.|-|.|.+....+.+|=+...+-+++|-|++ ....+.|+.+.|+|..+.+||++.||++-
T Consensus 156 nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr------------------~~~prlG~~l~~rVi~~reDg~lnLSl~p 217 (287)
T COG2996 156 NQEVDATVYRLLESGTFVITENGYLGFIHKSER------------------FAEPRLGERLTARVIGVREDGKLNLSLRP 217 (287)
T ss_pred cCeeeeEEEEEeccceEEEEcCCeEEEEcchhh------------------cccccCCceEEEEEEEEccCCeeeccccc
Confidence 566666777776667776666666777665543 23368999999999999999999999975
Q ss_pred CC
Q 020356 171 QK 172 (327)
Q Consensus 171 ~~ 172 (327)
..
T Consensus 218 ~~ 219 (287)
T COG2996 218 RA 219 (287)
T ss_pred cc
Confidence 43
No 103
>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=84.57 E-value=5 Score=31.30 Aligned_cols=69 Identities=19% Similarity=0.183 Sum_probs=46.2
Q ss_pred CCEEEEEEEEEecceEEEEEcC-ccceeeecccccCCCcccccccccchhhhhcccCCCCEE-EEEEEecCCCCceEEEE
Q 020356 91 GDIVIGRVIEVVPKRWKLEINF-TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLV-CAEVRSSQGDGSLQLQA 168 (327)
Q Consensus 91 GDiVIGrV~~V~~~~w~VDI~s-~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV-~AeV~sv~~~g~i~Lst 168 (327)
|++|-|+|.+++.+...|++.. ...|+|+...++ .....++ .+-..+++||-+ .+-|.+. ....+.||.
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLs--D~~~k~~------~~~~klrvG~~L~~~lvL~~-~~r~i~lt~ 71 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLS--DHVSNCP------LLWHCLQEGDTIPNLMCLSN-YKGRIILTK 71 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccC--CchhhCH------HHHhhhhcCCCccceEEEec-cccEEEEec
Confidence 7999999999999999999975 677887655443 1111222 345568999988 6666621 223455553
No 104
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=84.21 E-value=1.6 Score=50.22 Aligned_cols=77 Identities=16% Similarity=0.180 Sum_probs=59.9
Q ss_pred cCCccCCCCCCEEEEEEEEEecceEEEEEcCccceeeeccccc--CCCcccccccccchhhhhcccCCCCEEEEEEEecC
Q 020356 82 LRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMN--LPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQ 159 (327)
Q Consensus 82 l~~rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~--fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~ 159 (327)
++..|.-.+|+||-|.|+++.++...|++.+...+-+|+|++- ++.. . +.-+-|+.||-|.|+|..-+
T Consensus 877 ~k~~~~~~igsiv~a~v~svKp~~L~v~l~~~~~gri~isev~d~~~ei-------t---Dp~~k~~vG~~I~vrviG~~ 946 (1710)
T KOG1070|consen 877 IKSTEDLSIGSIVRAYVKSVKPDQLNVLLAANHHGRIHISEVLDNLHEI-------T---DPLDKFKVGDGIFVRVIGGH 946 (1710)
T ss_pred cccccceeeeeEEEEEEeeecccceEEeccccccCceehHHhhcccccc-------C---ChhhhcccCCeEEEEEEcCC
Confidence 3456778899999999999999999999999999999999873 3321 1 24456999999999999875
Q ss_pred CCCceEEEE
Q 020356 160 GDGSLQLQA 168 (327)
Q Consensus 160 ~~g~i~Lst 168 (327)
+-.++-.|+
T Consensus 947 D~k~lpith 955 (1710)
T KOG1070|consen 947 DVKDLPITH 955 (1710)
T ss_pred ccccCcccc
Confidence 433444443
No 105
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=82.61 E-value=7.1 Score=35.10 Aligned_cols=88 Identities=14% Similarity=0.138 Sum_probs=53.6
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEEcCccceee---ecccccC-CCcccccccccchhhhhcccCCCCEEEEEEEecCC
Q 020356 85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAIL---MLSSMNL-PDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG 160 (327)
Q Consensus 85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L---~ls~v~f-pg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~ 160 (327)
.+.|-.|++|=|.|+.|...+++++++.-.-.++ .-+.+.| || -+.+.....++. .++.|+.|+-+|..+--
T Consensus 76 ~FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~p~---~n~P~f~~~d~s-~I~~~~~VR~kiigtr~ 151 (170)
T KOG3298|consen 76 TFKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPG---ENPPNFQTEDES-VIQKGVEVRLKIIGTRV 151 (170)
T ss_pred EEeecCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccCCC---CCCCcccccccc-eeeeCcEEEEEEEEEEE
Confidence 4788999999999999999999999985333331 1122222 22 111211111222 57899999999987643
Q ss_pred CC--ceEE-EEccCCCccC
Q 020356 161 DG--SLQL-QARNQKYGKL 176 (327)
Q Consensus 161 ~g--~i~L-str~~~lGkL 176 (327)
+- -+.| |+.++.||.+
T Consensus 152 ~~~~i~algtl~~D~LG~i 170 (170)
T KOG3298|consen 152 DETEIFALGTLKGDYLGPI 170 (170)
T ss_pred eeeeEEEEEEecCcccccC
Confidence 22 1223 5567777753
No 106
>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=81.76 E-value=6.6 Score=33.45 Aligned_cols=67 Identities=15% Similarity=0.267 Sum_probs=42.4
Q ss_pred CCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccc--------cccccchhhhhcccCCCCEEEEEEEecC
Q 020356 88 PETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQR--------RRTAVDELNMRSIFTENDLVCAEVRSSQ 159 (327)
Q Consensus 88 P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~r--------rr~~~de~~mr~~~~~GDlV~AeV~sv~ 159 (327)
|-+|.++.|+|.+...++.+|.++--.+-. ++.-.||....- -... -+-.-+|..|+.|+=||.++.
T Consensus 1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~--IP~~~L~~ps~fd~~~~~W~W~~~---~~~~l~~d~ge~IRFRV~~~~ 75 (122)
T PF08292_consen 1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIF--IPPSLLPEPSRFDEEEQAWVWEYD---EEQELFFDIGEEIRFRVESEI 75 (122)
T ss_dssp --TT-EEEEEEEEEETTEEEEEECCEEEEE--EECCCC-TTEEEECCCTEEEEEES---SSEEEEE-TT-EEEEEEEEEE
T ss_pred CCCCCEEEEEEEecCCCcEEEEecccccEE--ECHHHCCCCCccCccCCEEEEECC---CCceeEccCCCEEEEEEeEEE
Confidence 789999999999999999999998766644 344444432210 0010 133456899999999998864
No 107
>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=79.31 E-value=6.2 Score=32.89 Aligned_cols=53 Identities=17% Similarity=0.283 Sum_probs=41.8
Q ss_pred CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEec
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSS 158 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv 158 (327)
..|-+|+|+|..+-.+-..+|.+...+++..-+..+ .+.+..|+-|.-++...
T Consensus 22 ~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~-----------------~~~y~~G~rV~lrLkdl 74 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVN-----------------GEKYVRGSRVRLRLKDL 74 (104)
T ss_pred ccCCEEEEEEEEEecCceEEEeCCceeEEEeccccc-----------------ccccccCCEEEEEECCH
Confidence 468899999999999999999999888886543322 13378899999888553
No 108
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=78.35 E-value=4.7 Score=42.80 Aligned_cols=89 Identities=12% Similarity=0.132 Sum_probs=67.4
Q ss_pred EECcEEEEEecCC-------------ccCCCCCCEEE-----EEEEEEecceEEEEEcCccceeeecccccCCCcccccc
Q 020356 72 RINKLIYVRALRA-------------RYKPETGDIVI-----GRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRR 133 (327)
Q Consensus 72 ~~nk~v~V~pl~~-------------rY~P~vGDiVI-----GrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr 133 (327)
.++.+++|..... .-.|+++|++. +.|+++.+.+.+|.+..-..+.||.|++. .++
T Consensus 632 vDe~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~------~e~ 705 (760)
T KOG1067|consen 632 VDEGTFSIFAPTQAAMEEAKEFIDGIIKDDQVQDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLD------QEK 705 (760)
T ss_pred ecCceEEEEecCHHHHHHHHHHHHHHhcCccccceEeeeEEEEEEeeecccceEEEecCCchhhccchhcc------ccc
Confidence 3566777765431 13688999987 68899999999999999899999999886 122
Q ss_pred cccchhhhhcccCCCCEEEEEEEecCCCCceEEEEcc
Q 020356 134 TAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARN 170 (327)
Q Consensus 134 ~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~ 170 (327)
.. ...+.+++||-|-.+-...++.+.+.|+-|.
T Consensus 706 ia----kpsd~levGq~I~vk~ie~d~~g~~~ls~ra 738 (760)
T KOG1067|consen 706 IA----KPSDLLEVGQEIQVKYIERDPRGGIMLSSRA 738 (760)
T ss_pred cc----ChHHHHhhcceeEEEEEeecCccceeehhhh
Confidence 22 3345699999999998888877777777664
No 109
>CHL00121 rpl27 ribosomal protein L27; Reviewed
Probab=76.80 E-value=5.1 Score=32.29 Aligned_cols=53 Identities=19% Similarity=0.095 Sum_probs=39.0
Q ss_pred CCCCceEecCCccCCC-CCceeecCCEEe-eCCeEEEEEeeEEEEE-----CcEEEEEec
Q 020356 30 SNPNSCVTVGDTIPVY-EDGILKGHGTSD-QKGELAATVCGVVERI-----NKLIYVRAL 82 (327)
Q Consensus 30 ~~~~~iV~PGD~I~~~-ee~~~~G~Gty~-~~g~i~Ssv~G~v~~~-----nk~v~V~pl 82 (327)
.....+|.||+.|.-- ...|.+|.++-. .|..|+|.+.|.|... .+.|+|.|.
T Consensus 25 ~~~gq~V~~G~IivRQRGtk~hPG~NVg~GrD~TlfAl~~G~V~f~~~~~~~~~vsv~~~ 84 (86)
T CHL00121 25 RFGGEKVSAGNILIRQRGTKFKPGLNVGCGKDFTLYALIDGFVKFKKKNKKQKSINVINI 84 (86)
T ss_pred EcCCEEEcCCcEEEEcCCCeECCCCcccccCCceEEEccceEEEEEEeCCCCEEEEEeec
Confidence 4456789999988532 235888888755 5889999999999873 346677664
No 110
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=73.49 E-value=6 Score=41.14 Aligned_cols=74 Identities=19% Similarity=0.266 Sum_probs=54.2
Q ss_pred CCCCEEEEEEEEEe--cceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceE
Q 020356 89 ETGDIVIGRVIEVV--PKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQ 165 (327)
Q Consensus 89 ~vGDiVIGrV~~V~--~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~ 165 (327)
.+|+|-.|+|+.|- -+.+||||+...+|+||++.+. | ..+....+ ++...++.|+.+...|..-... .-..
T Consensus 36 ~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~-~---~~~~~~~~--~i~~~lr~~~~~~Vqv~ke~~G~Kga~ 109 (487)
T COG1530 36 IVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIV-P---YFRAVLEE--KIKVRLRGGQATLVQVVKEPRGTKGAR 109 (487)
T ss_pred eecCceEEEecccCccchhheeeccCCccceEEecccc-h---hhhhcccc--cceeeecCCceEEEEEEeecCcccccc
Confidence 48999999999985 5679999999999999999875 2 11222222 5677899999999988775432 2244
Q ss_pred EEE
Q 020356 166 LQA 168 (327)
Q Consensus 166 Lst 168 (327)
||+
T Consensus 110 lT~ 112 (487)
T COG1530 110 LTT 112 (487)
T ss_pred cee
Confidence 544
No 111
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=72.16 E-value=16 Score=33.55 Aligned_cols=71 Identities=15% Similarity=0.311 Sum_probs=46.7
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccc-------cc--cchhhhhcccCCCCEEEEEEE
Q 020356 86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRR-------TA--VDELNMRSIFTENDLVCAEVR 156 (327)
Q Consensus 86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr-------~~--~de~~mr~~~~~GDlV~AeV~ 156 (327)
+.|-+|.+|.|+|.+-...+.+|.|+--.+-.+|-+. +|.+..-.. .+ .|--.-.-+|++|..|+=||.
T Consensus 77 FrPF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~--L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~ 154 (202)
T KOG3297|consen 77 FRPFVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEM--LPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVE 154 (202)
T ss_pred EecccceEEEEEeecCCccceEEEEEeeeceeechhh--CCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEe
Confidence 6788999999999999999999999865554433332 332221100 00 010123456999999999998
Q ss_pred ec
Q 020356 157 SS 158 (327)
Q Consensus 157 sv 158 (327)
+.
T Consensus 155 ~e 156 (202)
T KOG3297|consen 155 DE 156 (202)
T ss_pred ee
Confidence 86
No 112
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=68.65 E-value=2.6 Score=31.20 Aligned_cols=39 Identities=15% Similarity=0.359 Sum_probs=31.4
Q ss_pred EEEeChhhhhhc----cccccccC-ccceEEEEeecceeeeccc
Q 020356 181 LLTVDPYLVKRR----KQHFHHLE-EYGIDLIIGCNGYIWIGEH 219 (327)
Q Consensus 181 lv~V~~~li~r~----~~h~~~L~-~~~~eiivG~NG~IWI~~~ 219 (327)
.+.|++.++.++ ++++..|. .+++.|-+..||.|||.+.
T Consensus 5 ~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~g~v~I~G~ 48 (61)
T cd02393 5 TMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDDGTVYIAAS 48 (61)
T ss_pred EEEeChhheeeeECCCchHHHHHHHHHCCEEEeCCCCEEEEEeC
Confidence 467888877765 46677774 6899999999999999885
No 113
>PRK05435 rpmA 50S ribosomal protein L27; Validated
Probab=67.06 E-value=12 Score=29.94 Aligned_cols=45 Identities=24% Similarity=0.167 Sum_probs=35.2
Q ss_pred CCCCCceEecCCccCCC-CCceeecCCEEe-eCCeEEEEEeeEEEEE
Q 020356 29 KSNPNSCVTVGDTIPVY-EDGILKGHGTSD-QKGELAATVCGVVERI 73 (327)
Q Consensus 29 ~~~~~~iV~PGD~I~~~-ee~~~~G~Gty~-~~g~i~Ssv~G~v~~~ 73 (327)
.......|.||..|.-- ...|.+|.++-. .|..|+|.+.|.|...
T Consensus 24 K~~~g~~V~~G~IivRQRGtk~~PG~nVg~GrD~TlfA~~~G~V~f~ 70 (82)
T PRK05435 24 KRFGGQFVKAGNIIVRQRGTKFHPGVNVGRGKDHTLFALVDGVVKFE 70 (82)
T ss_pred EecCCEEEcCCcEEEEeCCCeECCCCCEeecCCceEEEecceEEEEE
Confidence 34567899999988532 236889999876 4789999999999874
No 114
>PF01016 Ribosomal_L27: Ribosomal L27 protein; InterPro: IPR001684 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 [, ]. L27 is a protein from the large (50S) subunit; it is essential for ribosome function, but its exact role is unclear. It belongs to a family of ribosomal proteins, examples of which are found in bacteria, chloroplasts of plants and red algae and the mitochondria of fungi (e.g. MRP7 from yeast mitochondria). The schematic relationship between these groups of proteins is shown below. Bacterial L27 Nxxxxxxxxx Algal L27 Nxxxxxxxxx Plant L27 tttttNxxxxxxxxxxxxx Yeast MRP7 tttNxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 't': transit peptide. 'N': N-terminal of mature protein. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZJQ_T 2ZJP_T 3PIP_T 3DLL_T 3PIO_T 1Y69_U 3CF5_T 2ZJR_T 1VSA_U 3PYT_W ....
Probab=64.43 E-value=9.8 Score=30.39 Aligned_cols=46 Identities=22% Similarity=0.114 Sum_probs=36.2
Q ss_pred CCCCCCceEecCCccCCC-CCceeecCCEEee-CCeEEEEEeeEEEEE
Q 020356 28 SKSNPNSCVTVGDTIPVY-EDGILKGHGTSDQ-KGELAATVCGVVERI 73 (327)
Q Consensus 28 ~~~~~~~iV~PGD~I~~~-ee~~~~G~Gty~~-~g~i~Ssv~G~v~~~ 73 (327)
.......+|.||+.|.-- ...|.||.++... |..|+|.+.|.|...
T Consensus 22 vK~~~G~~V~~G~IivRQRgtk~hPG~NVg~GrD~TLfAl~~G~V~f~ 69 (81)
T PF01016_consen 22 VKKFGGQFVKAGNIIVRQRGTKFHPGENVGMGRDHTLFALVDGRVKFT 69 (81)
T ss_dssp ESSSTTCEESSTSEEEEBSSSSSEEBTTEEEETTSEEEESSSCEEEEE
T ss_pred EEEeCCEEEcCCCEEEEeCCCcCcCCCCEEECCCCcEEEecCEEEEEE
Confidence 345667899999988532 2369999999874 789999999999874
No 115
>PF03961 DUF342: Protein of unknown function (DUF342); InterPro: IPR005646 This family of bacterial proteins has no known function. The proteins are in the region of 500-600 amino acid residues in length.
Probab=63.04 E-value=16 Score=37.25 Aligned_cols=35 Identities=23% Similarity=0.139 Sum_probs=30.4
Q ss_pred ceeecCCEEee---CCeEEEEEeeEEEEECcEEEEEec
Q 020356 48 GILKGHGTSDQ---KGELAATVCGVVERINKLIYVRAL 82 (327)
Q Consensus 48 ~~~~G~Gty~~---~g~i~Ssv~G~v~~~nk~v~V~pl 82 (327)
.+..|.||... +..++|++.|.+...++.++|.|.
T Consensus 144 ~~~~g~~~~~~~~d~~~~~A~~~G~~~~~~~~i~V~~~ 181 (451)
T PF03961_consen 144 PLKAGKNTEVSEEDGNKLYAAIDGRPVFENGKISVDPV 181 (451)
T ss_pred ceeCCCCEEEEcCCCCEEEEecCCEEEEECCEEEEEEe
Confidence 57789999875 358999999999999999999985
No 116
>COG1315 Uncharacterized conserved protein [Function unknown]
Probab=62.77 E-value=12 Score=39.11 Aligned_cols=52 Identities=23% Similarity=0.252 Sum_probs=40.4
Q ss_pred ceeecCCE-EeeCCeEEEEEeeEEEEECcEEEEEecC---CccCCCCCCEE-EEEEE
Q 020356 48 GILKGHGT-SDQKGELAATVCGVVERINKLIYVRALR---ARYKPETGDIV-IGRVI 99 (327)
Q Consensus 48 ~~~~G~Gt-y~~~g~i~Ssv~G~v~~~nk~v~V~pl~---~rY~P~vGDiV-IGrV~ 99 (327)
.+.+|.|| +.+++.+.|+..|.+-..+++|+|.|.- +--.++.|+|. +|.|.
T Consensus 220 ~l~lG~nt~~kd~~tlvA~~~G~~~~s~~tI~V~~iyeV~gdV~~kTGnI~F~G~Vv 276 (543)
T COG1315 220 KLNLGKNTAFKDNNTLVAKRDGQPIVSKNTISVYPIYEVNGDVDVKTGNIKFVGNVV 276 (543)
T ss_pred eeecCCCCccCCCCEEEEeeCCeEEecCCeeEEEEEEEecCCccccccceeecceEE
Confidence 47789999 6778899999999999999999999963 34566677765 34443
No 117
>PRK05054 exoribonuclease II; Provisional
Probab=62.19 E-value=37 Score=36.54 Aligned_cols=73 Identities=10% Similarity=0.144 Sum_probs=48.8
Q ss_pred c-CCCCCC--EEEEEEEEEecceEEEEEcC-ccceeeecccccCCCcccccccccch--h--hhhcccCCCCEEEEEEEe
Q 020356 86 Y-KPETGD--IVIGRVIEVVPKRWKLEINF-TQDAILMLSSMNLPDGIQRRRTAVDE--L--NMRSIFTENDLVCAEVRS 157 (327)
Q Consensus 86 Y-~P~vGD--iVIGrV~~V~~~~w~VDI~s-~~~a~L~ls~v~fpg~i~rrr~~~de--~--~mr~~~~~GDlV~AeV~s 157 (327)
| ...+|+ ..-|.|++|+..+++|.|.. .-.+++|++++. +.--.-+...++ + .=+..|+.||-|..+|.+
T Consensus 554 y~~~~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~--~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~ 631 (644)
T PRK05054 554 YLKDKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLH--AVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAE 631 (644)
T ss_pred HHhhccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccC--CCccceEEccccceEEEeCCEEEcCCCEEEEEEEE
Confidence 5 456765 99999999999999999964 467888888763 100000000010 0 112469999999999999
Q ss_pred cCC
Q 020356 158 SQG 160 (327)
Q Consensus 158 v~~ 160 (327)
++.
T Consensus 632 vd~ 634 (644)
T PRK05054 632 VRM 634 (644)
T ss_pred Ecc
Confidence 975
No 118
>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=57.42 E-value=57 Score=25.17 Aligned_cols=54 Identities=15% Similarity=0.199 Sum_probs=35.7
Q ss_pred EEEEEEEEEe-cceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC
Q 020356 93 IVIGRVIEVV-PKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG 160 (327)
Q Consensus 93 iVIGrV~~V~-~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~ 160 (327)
.+.|.|++.- +..|.|.+.....-.-| ++|-.++++.. +.+||.|..+....+.
T Consensus 6 e~~G~V~e~L~~~~f~V~l~ng~~vla~-----i~GKmr~~rI~---------I~~GD~V~Ve~spyd~ 60 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELENGHEVLAH-----ISGKIRMHYIR---------ILPGDKVKVELSPYDL 60 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEE-----ecCcchhccEE---------ECCCCEEEEEECcccC
Confidence 3679999984 56778888754443333 34644444433 7899999999876543
No 119
>PLN00208 translation initiation factor (eIF); Provisional
Probab=54.30 E-value=57 Score=28.80 Aligned_cols=56 Identities=11% Similarity=0.144 Sum_probs=36.9
Q ss_pred CCCCCCEEEEEEEEE-ecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEec
Q 020356 87 KPETGDIVIGRVIEV-VPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSS 158 (327)
Q Consensus 87 ~P~vGDiVIGrV~~V-~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv 158 (327)
.|..|+ ++|+|++. .+..+.|.+.....-+.+ +||-.++ + =.+++||+|.+++-..
T Consensus 28 ~p~egq-~~g~V~~~lGn~~~~V~c~dG~~rLa~-----IpGKmRK-r---------IWI~~GD~VlVel~~~ 84 (145)
T PLN00208 28 FKEDGQ-EYAQVLRMLGNGRCEALCIDGTKRLCH-----IRGKMRK-K---------VWIAAGDIILVGLRDY 84 (145)
T ss_pred cCCCCc-EEEEEEEEcCCCEEEEEECCCCEEEEE-----Eecccee-e---------EEecCCCEEEEEccCC
Confidence 577666 88999987 567788887754443333 4553333 2 2389999999986544
No 120
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=52.48 E-value=66 Score=26.07 Aligned_cols=54 Identities=17% Similarity=0.178 Sum_probs=36.4
Q ss_pred EEEEEEEEEe-cceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC
Q 020356 93 IVIGRVIEVV-PKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG 160 (327)
Q Consensus 93 iVIGrV~~V~-~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~ 160 (327)
.+.|.|++.- +..|+|.+.....-.-| ++|-.++++.. +.+||.|..++...+.
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG~~vla~-----isGKmR~~rIr---------Il~GD~V~VE~spYDl 62 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENGVEVGAY-----ASGRMRKHRIR---------ILAGDRVTLELSPYDL 62 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEE-----eccceeeeeEE---------ecCCCEEEEEECcccC
Confidence 3679999984 66788888754443333 34544444433 7899999999987664
No 121
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=51.63 E-value=1.1e+02 Score=23.91 Aligned_cols=50 Identities=16% Similarity=0.259 Sum_probs=33.4
Q ss_pred EEEEEEEE-ecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEec
Q 020356 94 VIGRVIEV-VPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSS 158 (327)
Q Consensus 94 VIGrV~~V-~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv 158 (327)
++|+|++. .+..+.|.+.....-..+ +||-.+++ =.+++||.|.++....
T Consensus 2 ~i~~V~~~lG~~~~~V~~~dg~~~l~~-----i~gK~Rk~----------iwI~~GD~VlV~~~~~ 52 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECADGQRRLVS-----IPGKLRKN----------IWIKRGDFLIVDPIEE 52 (78)
T ss_pred eEEEEEEECCCCEEEEEECCCCEEEEE-----EchhhccC----------EEEcCCCEEEEEeccc
Confidence 68999997 467788888754443333 45533321 2389999999987665
No 122
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=51.61 E-value=81 Score=26.01 Aligned_cols=58 Identities=21% Similarity=0.217 Sum_probs=37.7
Q ss_pred cCCCCCCEEEEEEEEE-ecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecC
Q 020356 86 YKPETGDIVIGRVIEV-VPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQ 159 (327)
Q Consensus 86 Y~P~vGDiVIGrV~~V-~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~ 159 (327)
..|. .+-++|+|++. .+..+.|.+.....-..+ +||-.++ + =.+++||.|.++....+
T Consensus 16 ~~p~-e~e~~g~V~~~lG~~~~~V~~~dG~~~la~-----i~GK~Rk-~---------IwI~~GD~VlVe~~~~~ 74 (100)
T PRK04012 16 PMPE-EGEVFGVVEQMLGANRVRVRCMDGVERMGR-----IPGKMKK-R---------MWIREGDVVIVAPWDFQ 74 (100)
T ss_pred cCCC-CCEEEEEEEEEcCCCEEEEEeCCCCEEEEE-----Echhhcc-c---------EEecCCCEEEEEecccC
Confidence 3555 44589999997 466788887654443322 4553332 2 23899999999987665
No 123
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=50.47 E-value=39 Score=25.28 Aligned_cols=52 Identities=25% Similarity=0.351 Sum_probs=31.6
Q ss_pred CEEEEEEEEE-ecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEec
Q 020356 92 DIVIGRVIEV-VPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSS 158 (327)
Q Consensus 92 DiVIGrV~~V-~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv 158 (327)
+-++|+|++. .++.+.|.+.....-.. .+||- .+++ =.+++||.|.+++...
T Consensus 3 ~e~~~~V~~~lG~~~~~V~~~dg~~~l~-----~i~gK-~r~~---------iwI~~GD~V~V~~~~~ 55 (65)
T PF01176_consen 3 GEVIGRVTEMLGNNLFEVECEDGEERLA-----RIPGK-FRKR---------IWIKRGDFVLVEPSPY 55 (65)
T ss_dssp TEEEEEEEEEESSSEEEEEETTSEEEEE-----EE-HH-HHTC---------C---TTEEEEEEESTT
T ss_pred cEEEEEEEEECCCCEEEEEeCCCCEEEE-----Eeccc-eeee---------EecCCCCEEEEEeccc
Confidence 4688999997 46778888875444332 34553 2322 2389999999888443
No 124
>TIGR00062 L27 ribosomal protein L27. Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.
Probab=49.54 E-value=20 Score=28.75 Aligned_cols=45 Identities=22% Similarity=0.144 Sum_probs=34.8
Q ss_pred CCCCCceEecCCccCCC-CCceeecCCEEe-eCCeEEEEEeeEEEEE
Q 020356 29 KSNPNSCVTVGDTIPVY-EDGILKGHGTSD-QKGELAATVCGVVERI 73 (327)
Q Consensus 29 ~~~~~~iV~PGD~I~~~-ee~~~~G~Gty~-~~g~i~Ssv~G~v~~~ 73 (327)
.......|.||..|.-- ...|.+|.++-. .|..|+|.+.|.|...
T Consensus 24 K~~~gq~V~~G~IivRQRGtk~hPG~nVg~GrD~TlfAl~~G~V~f~ 70 (83)
T TIGR00062 24 KRAGGQFVRAGSIIVRQRGTKFHPGNNVGMGKDHTLFALSDGVVKFE 70 (83)
T ss_pred EecCCEEEcCCcEEEEcCCceECCCCcccccCCCeEEEecceEEEEE
Confidence 34567889999988532 236889998876 5889999999999874
No 125
>PF08970 Sda: Sporulation inhibitor A; InterPro: IPR015064 Members of this protein group contain two antiparallel alpha helices that are linked by a highly structured inter-helix loop to form a helical hairpin; the structure is stabilised by numerous hydrophobic and electrostatic interactions. These sporulation inhibitors are antikinases that bind to the histidine kinase KinA phosphotransfer domain and act as a molecular barricade that inhibit productive interaction between the ATP binding site and the phosphorylatable KinA His residue. This results in the inhibition of sporulation (by preventing phosphorylation of spo0A) []. ; PDB: 3FYR_B 1PV0_A.
Probab=49.33 E-value=31 Score=24.75 Aligned_cols=36 Identities=36% Similarity=0.583 Sum_probs=24.5
Q ss_pred ccHHHHHHHHHhhhhCCCCchhcccchHHHHHHHHHHHHhhhh
Q 020356 281 ITVEVILETVNLSNSLNLDIHDMLGSEFYVLVAESEAERRSLS 323 (327)
Q Consensus 281 i~~~~i~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 323 (327)
++++.++++|..|+++++ ++||+..+.+ +-.||+-.
T Consensus 4 LSDe~LiesY~~A~el~L------~~dFI~Ll~~-Ei~rR~L~ 39 (46)
T PF08970_consen 4 LSDELLIESYHKAIELNL------DPDFIRLLEE-EIQRRSLK 39 (46)
T ss_dssp S-HHHHHHHHHHHHHTT--------HHHHHHHHH-HHHHCT-T
T ss_pred ccHHHHHHHHHHHHHhCC------CHHHHHHHHH-HHHHcCCc
Confidence 789999999999988875 5788776654 44566543
No 126
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=48.09 E-value=1e+02 Score=27.94 Aligned_cols=67 Identities=25% Similarity=0.265 Sum_probs=38.4
Q ss_pred ceEecCCccCCC-CCceeecCCEEee--CCeEEEEEeeEEEEECcEEEEEecCCcc----CCCCCC-E-EEEEEEEEe
Q 020356 34 SCVTVGDTIPVY-EDGILKGHGTSDQ--KGELAATVCGVVERINKLIYVRALRARY----KPETGD-I-VIGRVIEVV 102 (327)
Q Consensus 34 ~iV~PGD~I~~~-ee~~~~G~Gty~~--~g~i~Ssv~G~v~~~nk~v~V~pl~~rY----~P~vGD-i-VIGrV~~V~ 102 (327)
....|||.|... ......|.+.|+. +|..+....... .++.+.+.++...| .+...| + +||+|+.+.
T Consensus 135 P~~~~Gd~ilVd~~~~~~~gd~v~v~~~g~~~~VK~l~~~--~~~~~~l~S~N~~~~~~~~~~~~~~v~iIgrVv~~~ 210 (214)
T COG2932 135 PTYEDGDTLLVDPGVNTRRGDRVYVETDGGELYVKKLQRE--PGGLLRLVSLNPDYYPDEIFSEDDDVEIIGRVVWVS 210 (214)
T ss_pred ccccCCCEEEECCCCceeeCCEEEEEEeCCeEEEEEEEEe--cCCeEEEEeCCCCCCcccccCccceEEEEEEEEEEe
Confidence 356788866432 2234455555542 334444443222 25566688876655 556666 6 899999764
No 127
>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=47.79 E-value=24 Score=28.18 Aligned_cols=28 Identities=25% Similarity=0.304 Sum_probs=21.9
Q ss_pred CCCCEEEEEEEEEec-ceEEEEEcCccce
Q 020356 89 ETGDIVIGRVIEVVP-KRWKLEINFTQDA 116 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~-~~w~VDI~s~~~a 116 (327)
.+||+|.++|.+... ..+.+.+.....|
T Consensus 62 ~~GDiV~AkVis~~~~~~~~Lst~~~~lG 90 (92)
T cd05791 62 RPGDIVRAKVISLGDASSYYLSTAENELG 90 (92)
T ss_pred CCCCEEEEEEEEcCCCCCcEEEecCCCCc
Confidence 799999999999875 6677777655444
No 128
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=45.73 E-value=99 Score=24.35 Aligned_cols=56 Identities=18% Similarity=0.265 Sum_probs=37.9
Q ss_pred CCEEEEEEEEE-ecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC
Q 020356 91 GDIVIGRVIEV-VPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG 160 (327)
Q Consensus 91 GDiVIGrV~~V-~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~ 160 (327)
..-+.|.|++. .+..++|.+.....-.-|| ||-.++++ =.+.+||+|..+....+.
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~edg~~~~ahI-----~GKmr~~~---------i~I~~GD~V~Ve~~~~d~ 62 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELENGHERLAHI-----SGKMRKNR---------IRILPGDVVLVELSPYDL 62 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEecCCcEEEEEc-----cCcchhee---------EEeCCCCEEEEEeccccc
Confidence 44678999996 5778889887665544444 34222222 238899999999877663
No 129
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=42.92 E-value=1.1e+02 Score=23.90 Aligned_cols=50 Identities=14% Similarity=0.190 Sum_probs=33.2
Q ss_pred EEEEEEEEe-cceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEec
Q 020356 94 VIGRVIEVV-PKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSS 158 (327)
Q Consensus 94 VIGrV~~V~-~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv 158 (327)
++|+|++.. +..+.|.+.....-.. .+||-.++ + =.+++||.|.++....
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g~~~la-----~i~gK~rk-~---------iwI~~GD~V~Ve~~~~ 52 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDGKKRLC-----RIRGKMRK-R---------VWINEGDIVLVAPWDF 52 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEE-----EEchhhcc-c---------EEEcCCCEEEEEeccc
Confidence 689999974 6778888875444332 24563332 2 2389999999987654
No 130
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=41.99 E-value=30 Score=32.79 Aligned_cols=70 Identities=19% Similarity=0.209 Sum_probs=49.9
Q ss_pred EEEEEecCCccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEE
Q 020356 76 LIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEV 155 (327)
Q Consensus 76 ~v~V~pl~~rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV 155 (327)
.+||..---.|.|++||+.-|.|--+.....-+=|-...+|.++-.++. .| +.++..++-..++|
T Consensus 93 hlwi~adfyVf~Pk~Gd~LeG~Vn~vS~sHIglLIhg~FNASIpk~nip-----------~d----w~fI~md~eee~~v 157 (253)
T KOG4134|consen 93 HLWINADFYVFRPKAGDILEGVVNHVSRSHIGLLIHGVFNASIPKTNIP-----------AD----WEFIAMDQEEEIRV 157 (253)
T ss_pred EEEEeeeEEEECCCCCCeeeeeeeecchhhhceeehhhhhccCCCCCCc-----------cc----eeeecCCchhhhce
Confidence 4455555456899999999999999988877776766666664433321 12 34678888888999
Q ss_pred EecCC
Q 020356 156 RSSQG 160 (327)
Q Consensus 156 ~sv~~ 160 (327)
..++.
T Consensus 158 ~ntD~ 162 (253)
T KOG4134|consen 158 KNTDI 162 (253)
T ss_pred eeccc
Confidence 88864
No 131
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=36.33 E-value=1.5e+02 Score=26.44 Aligned_cols=76 Identities=14% Similarity=0.145 Sum_probs=45.7
Q ss_pred CCCCCCEEEEEEEEE-ecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceE
Q 020356 87 KPETGDIVIGRVIEV-VPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQ 165 (327)
Q Consensus 87 ~P~vGDiVIGrV~~V-~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~ 165 (327)
.|+.|. ++|+|++. .+..+.|.+.....-+.| +||-.++ + =.+.+||+|.++....+.
T Consensus 28 ~~eegq-~~g~V~~~LGn~~f~V~c~dG~~rLa~-----I~GKmRK-~---------IWI~~GD~VlVel~~yd~----- 86 (155)
T PTZ00329 28 FKEEGQ-EYAQVLRMLGNGRLEAYCFDGVKRLCH-----IRGKMRK-R---------VWINIGDIILVSLRDFQD----- 86 (155)
T ss_pred cCCCCc-EEEEEEEEcCCCEEEEEECCCCEEEEE-----eecccee-e---------EEecCCCEEEEeccCCCC-----
Confidence 466666 78999987 466777777654443333 4553333 2 238999999997643321
Q ss_pred EEEccCCCccCCCCeEEEeChhhhhhcc
Q 020356 166 LQARNQKYGKLERGQLLTVDPYLVKRRK 193 (327)
Q Consensus 166 Lstr~~~lGkL~~G~lv~V~~~li~r~~ 193 (327)
-.+=+++.-.+.-++.++
T Consensus 87 ----------~KgdIi~Ry~~devr~Lk 104 (155)
T PTZ00329 87 ----------SKADVILKYTPDEARALK 104 (155)
T ss_pred ----------CEEEEEEEcCHHHHHHHH
Confidence 122344555666677765
No 132
>PF14398 ATPgrasp_YheCD: YheC/D like ATP-grasp
Probab=36.18 E-value=19 Score=34.03 Aligned_cols=22 Identities=55% Similarity=0.714 Sum_probs=18.2
Q ss_pred cCccceEEEEeecceeeecccc
Q 020356 199 LEEYGIDLIIGCNGYIWIGEHV 220 (327)
Q Consensus 199 L~~~~~eiivG~NG~IWI~~~~ 220 (327)
+-++|+|++|..||.|||=+.+
T Consensus 209 ~gElGiDl~iD~~g~iWliEvN 230 (262)
T PF14398_consen 209 LGELGIDLGIDKNGKIWLIEVN 230 (262)
T ss_pred eeEEEEEEEEcCCCCEEEEEEe
Confidence 4468999999999999995543
No 133
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=35.98 E-value=1.5e+02 Score=32.17 Aligned_cols=78 Identities=19% Similarity=0.213 Sum_probs=52.8
Q ss_pred CCCCCEEEEEEEEEecceEEEEEcCc-cceeeecccccCCCccc---ccccccchhhhhcccCCCCEEEEEEEecCCC-C
Q 020356 88 PETGDIVIGRVIEVVPKRWKLEINFT-QDAILMLSSMNLPDGIQ---RRRTAVDELNMRSIFTENDLVCAEVRSSQGD-G 162 (327)
Q Consensus 88 P~vGDiVIGrV~~V~~~~w~VDI~s~-~~a~L~ls~v~fpg~i~---rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g 162 (327)
=.+|+.--|.|++|...+.+|.+... .++..|++.+. +--- .......-......|+.||-|..+|.+++.+ +
T Consensus 620 ~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~--~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~ 697 (706)
T COG0557 620 KRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLP--DDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDER 697 (706)
T ss_pred HhcCCEEEEEEEEEEeccEEEEecccccccceEcccCC--CceeeeccccceeeccccccccccCCEEEEEEEEEccccc
Confidence 37899999999999999999999875 78888888654 1000 0000001113344599999999999998753 3
Q ss_pred ceEEE
Q 020356 163 SLQLQ 167 (327)
Q Consensus 163 ~i~Ls 167 (327)
.+.++
T Consensus 698 ~i~~~ 702 (706)
T COG0557 698 KIDFE 702 (706)
T ss_pred ceEEE
Confidence 44443
No 134
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=33.41 E-value=31 Score=20.77 Aligned_cols=15 Identities=27% Similarity=0.762 Sum_probs=11.3
Q ss_pred eEEEEeecceeeecc
Q 020356 204 IDLIIGCNGYIWIGE 218 (327)
Q Consensus 204 ~eiivG~NG~IWI~~ 218 (327)
..|+.-.+|++||..
T Consensus 8 ~~i~~D~~G~lWigT 22 (24)
T PF07494_consen 8 YSIYEDSDGNLWIGT 22 (24)
T ss_dssp EEEEE-TTSCEEEEE
T ss_pred EEEEEcCCcCEEEEe
Confidence 356788999999975
No 135
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=33.33 E-value=58 Score=29.08 Aligned_cols=51 Identities=16% Similarity=0.296 Sum_probs=34.1
Q ss_pred ceEec--CCccCCCCCceeecCCEEe----eCCeEEEEEeeEEEEECcEEEEEecCCccCCCCCCEEEEEE
Q 020356 34 SCVTV--GDTIPVYEDGILKGHGTSD----QKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRV 98 (327)
Q Consensus 34 ~iV~P--GD~I~~~ee~~~~G~Gty~----~~g~i~Ssv~G~v~~~nk~v~V~pl~~rY~P~vGDiVIGrV 98 (327)
.+++| ||.++... -+.|.|.|. .+..+.|.+.|.+++ .|||.+ ||+|+-..
T Consensus 25 el~~~eegq~~g~V~--~~LGn~~f~V~c~dG~~rLa~I~GKmRK---~IWI~~---------GD~VlVel 81 (155)
T PTZ00329 25 ELVFKEEGQEYAQVL--RMLGNGRLEAYCFDGVKRLCHIRGKMRK---RVWINI---------GDIILVSL 81 (155)
T ss_pred eeccCCCCcEEEEEE--EEcCCCEEEEEECCCCEEEEEeecccee---eEEecC---------CCEEEEec
Confidence 45556 66666444 378888875 245789999999976 377654 67666543
No 136
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=32.91 E-value=3e+02 Score=23.21 Aligned_cols=49 Identities=18% Similarity=0.135 Sum_probs=27.0
Q ss_pred EEEEEE-ecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEE
Q 020356 96 GRVIEV-VPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEV 155 (327)
Q Consensus 96 GrV~~V-~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV 155 (327)
|+|... ....+.|+-.+...-..+.+.+-+- .-.|+..+++||-|.|..
T Consensus 17 GtV~~~~~~~~~lV~f~~~~~~~v~~~~iI~~-----------~~~~~~~L~~GD~VLA~~ 66 (124)
T PF15057_consen 17 GTVKKCVSSGQFLVEFDDGDTQEVPISDIIAL-----------SDAMRHSLQVGDKVLAPW 66 (124)
T ss_pred EEEEEccCCCEEEEEECCCCEEEeChHHeEEc-----------cCcccCcCCCCCEEEEec
Confidence 455543 5666666664433333333333110 113466699999999983
No 137
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=32.34 E-value=95 Score=28.60 Aligned_cols=38 Identities=29% Similarity=0.414 Sum_probs=30.4
Q ss_pred EEEecCCccCCCCCCEEEEEEEEEecceEEEEEcCccceee
Q 020356 78 YVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAIL 118 (327)
Q Consensus 78 ~V~pl~~rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L 118 (327)
++++++..| ++||+|-++|++.. +.+.+.+..+..+++
T Consensus 111 ~~~~~~d~f--~~GDivrA~Vis~~-~~~~Lst~~~dlGVI 148 (188)
T COG1096 111 YVEKLSDAF--RIGDIVRARVISTG-DPIQLSTKGNDLGVI 148 (188)
T ss_pred ccccccccc--ccccEEEEEEEecC-CCeEEEecCCcceEE
Confidence 344444444 58999999999999 999999999988885
No 138
>PLN00208 translation initiation factor (eIF); Provisional
Probab=31.57 E-value=89 Score=27.62 Aligned_cols=54 Identities=13% Similarity=0.298 Sum_probs=35.2
Q ss_pred ceEec--CCccCCCCCceeecCCEEe----eCCeEEEEEeeEEEEECcEEEEEecCCccCCCCCCEEEEEEEEE
Q 020356 34 SCVTV--GDTIPVYEDGILKGHGTSD----QKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEV 101 (327)
Q Consensus 34 ~iV~P--GD~I~~~ee~~~~G~Gty~----~~g~i~Ssv~G~v~~~nk~v~V~pl~~rY~P~vGDiVIGrV~~V 101 (327)
.+++| ||.++... -+.|.|.|. .+....+.+.|.+.+ .+||. .||+|+-.+..-
T Consensus 25 el~~p~egq~~g~V~--~~lGn~~~~V~c~dG~~rLa~IpGKmRK---rIWI~---------~GD~VlVel~~~ 84 (145)
T PLN00208 25 ELIFKEDGQEYAQVL--RMLGNGRCEALCIDGTKRLCHIRGKMRK---KVWIA---------AGDIILVGLRDY 84 (145)
T ss_pred ecccCCCCcEEEEEE--EEcCCCEEEEEECCCCEEEEEEecccee---eEEec---------CCCEEEEEccCC
Confidence 34555 55555433 378888875 245789999999975 47775 477777664443
No 139
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=29.22 E-value=94 Score=23.55 Aligned_cols=30 Identities=17% Similarity=0.220 Sum_probs=21.6
Q ss_pred CCCCCCEEEEEEEEEec-ceEEEEEcCccce
Q 020356 87 KPETGDIVIGRVIEVVP-KRWKLEINFTQDA 116 (327)
Q Consensus 87 ~P~vGDiVIGrV~~V~~-~~w~VDI~s~~~a 116 (327)
.-++||++.++|+++.. ....+.+.++..+
T Consensus 50 ~~~~GD~i~~~V~~~~~~~~i~LS~~~~~~G 80 (82)
T cd04454 50 SLQPGDLILAKVISLGDDMNVLLTTADNELG 80 (82)
T ss_pred cCCCCCEEEEEEEEeCCCCCEEEEECCCCCc
Confidence 35899999999999876 4556666554433
No 140
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=28.69 E-value=2.9e+02 Score=21.78 Aligned_cols=54 Identities=13% Similarity=0.235 Sum_probs=34.9
Q ss_pred CCCCCEEEEEEEEE-ecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEe
Q 020356 88 PETGDIVIGRVIEV-VPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRS 157 (327)
Q Consensus 88 P~vGDiVIGrV~~V-~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~s 157 (327)
|+. +-++|+|++. .+..+.|.+.....-..+ +||-.++ + =.++.||.|.++...
T Consensus 2 p~e-~q~~g~V~~~lG~~~~~V~~~dG~~~la~-----ipgK~Rk-~---------iwI~~GD~VlVe~~~ 56 (83)
T smart00652 2 KED-GQEIAQVVKMLGNGRLEVMCADGKERLAR-----IPGKMRK-K---------VWIRRGDIVLVDPWD 56 (83)
T ss_pred CCC-CcEEEEEEEEcCCCEEEEEECCCCEEEEE-----Echhhcc-c---------EEEcCCCEEEEEecC
Confidence 554 4488999987 467788888754443332 4553332 2 238999999998754
No 141
>cd05839 BR140_related The PWWP domain is found in the BR140 family, which includes peregrin and BR140-like proteins 1 and 2. BR140 is the only family to contain the PWWP domain at the C terminus, with PHD and bromo domains in the N-terminal region. In myeloid leukemias, BR140 is disrupted by chromosomal translocations, similar to translocations of WHSC1 in lymphoid multiple myeloma. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding proteins, that function as transcription factors regulating a variety of developmental processes.
Probab=28.14 E-value=52 Score=27.72 Aligned_cols=68 Identities=15% Similarity=0.193 Sum_probs=34.3
Q ss_pred cCCCCEEEEEEEecCCCCceEEEEccCCCccCCCCeEEEeChhhhhhc---c-ccccccCccceEEEEee-cceeeeccc
Q 020356 145 FTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRR---K-QHFHHLEEYGIDLIIGC-NGYIWIGEH 219 (327)
Q Consensus 145 ~~~GDlV~AeV~sv~~~g~i~Lstr~~~lGkL~~G~lv~V~~~li~r~---~-~h~~~L~~~~~eiivG~-NG~IWI~~~ 219 (327)
+.+||+|-|++...---..+.+.-.....|.+.+|+-.+|.-.--.+. . +++. +. .++. +.++||...
T Consensus 1 ~~pg~lVwaK~~g~P~wPa~iidp~~~~~~~~~~~~p~~~l~~~~~~~~~~~~~~~l------V~-FFd~~~s~~Wv~~~ 73 (111)
T cd05839 1 LEPLTLVWAKCRGYPSYPALIIDPKMPRDGVFHNGVPPDVLTLGEARAQNADERLYL------VL-FFDNKRTWQWLPGD 73 (111)
T ss_pred CCCcCEeeeeecCCCCCCeEeeCCCCCCcccccCCCCchhhhHHHHHhccCCCcEEE------EE-EecCCCcceecCHH
Confidence 468999999996543222233322233446666665322211111111 1 1221 12 3665 899999775
No 142
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=27.76 E-value=58 Score=26.85 Aligned_cols=54 Identities=20% Similarity=0.306 Sum_probs=34.8
Q ss_pred ceEec--CCccCCCCCceeecCCEEe----eCCeEEEEEeeEEEEECcEEEEEecCCccCCCCCCEEEEEEEEE
Q 020356 34 SCVTV--GDTIPVYEDGILKGHGTSD----QKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEV 101 (327)
Q Consensus 34 ~iV~P--GD~I~~~ee~~~~G~Gty~----~~g~i~Ssv~G~v~~~nk~v~V~pl~~rY~P~vGDiVIGrV~~V 101 (327)
.++.| |+.++... -+.|.|.|. .+..+.|.+.|.+.+ .+||. .||+|+-....-
T Consensus 14 ~~~~p~e~e~~g~V~--~~lG~~~~~V~~~dG~~~la~i~GK~Rk---~IwI~---------~GD~VlVe~~~~ 73 (100)
T PRK04012 14 RLPMPEEGEVFGVVE--QMLGANRVRVRCMDGVERMGRIPGKMKK---RMWIR---------EGDVVIVAPWDF 73 (100)
T ss_pred EccCCCCCEEEEEEE--EEcCCCEEEEEeCCCCEEEEEEchhhcc---cEEec---------CCCEEEEEeccc
Confidence 34555 44554333 367888885 245689999999974 47765 577777665443
No 143
>PF12508 DUF3714: Protein of unknown function (DUF3714) ; InterPro: IPR022187 Proteins in this entry are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage.
Probab=27.58 E-value=3.3e+02 Score=25.18 Aligned_cols=56 Identities=21% Similarity=0.316 Sum_probs=43.6
Q ss_pred eeCCeEEEEEeeEEEEEC-cEEEEEec-----CCccCCCCCCEEEEEEEEEecceEEEEEcCcc
Q 020356 57 DQKGELAATVCGVVERIN-KLIYVRAL-----RARYKPETGDIVIGRVIEVVPKRWKLEINFTQ 114 (327)
Q Consensus 57 ~~~g~i~Ssv~G~v~~~n-k~v~V~pl-----~~rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~ 114 (327)
...+.|.|.+-|.....+ ..+.++=+ .+..+|+ |-++.| +..+.+.+..+.|.+..
T Consensus 50 ~~~n~I~A~V~~~qtv~~Gs~vrlRLle~i~i~g~~IPk-gt~l~G-~~~~~~~Rl~i~I~SI~ 111 (200)
T PF12508_consen 50 TEKNTIRAVVDGTQTVVDGSRVRLRLLEDIQIGGILIPK-GTYLYG-VASFQGQRLLITITSIE 111 (200)
T ss_pred CCCCeEEEEEecceEEeCCCEEEEEEcCceEECCEEeCC-CCEEEE-EEeeeccEEEEEEEEEE
Confidence 356789999999987754 35555533 4567876 999999 99999999999998743
No 144
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=26.23 E-value=1.1e+02 Score=21.43 Aligned_cols=29 Identities=24% Similarity=0.401 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHhCCCcccHHHHHHHHHh
Q 020356 264 ICRIANAIRVLSRLGFNITVEVILETVNL 292 (327)
Q Consensus 264 i~r~~n~i~~l~~~~~~i~~~~i~~~~~~ 292 (327)
|..++-++..|...|+.|+++.+..+.+.
T Consensus 18 I~~~~~~l~~l~~~g~~is~~l~~~~L~~ 46 (48)
T PF11848_consen 18 ISEVKPLLDRLQQAGFRISPKLIEEILRR 46 (48)
T ss_pred hhhHHHHHHHHHHcCcccCHHHHHHHHHH
Confidence 45678889999999999999999888765
No 145
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=25.88 E-value=1.7e+02 Score=28.61 Aligned_cols=58 Identities=16% Similarity=0.101 Sum_probs=45.9
Q ss_pred cCCCCCCEEEEEEEEEe-cceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEe
Q 020356 86 YKPETGDIVIGRVIEVV-PKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRS 157 (327)
Q Consensus 86 Y~P~vGDiVIGrV~~V~-~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~s 157 (327)
..-.+|+.=-++|+++. .-+++||.+-+.+.+++++... .-+ +-++++||-+++.+.-
T Consensus 69 p~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp------~~~--------~~wpq~Gd~l~v~l~~ 127 (287)
T COG2996 69 PKATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELP------TLK--------SLWPQKGDKLLVYLYV 127 (287)
T ss_pred ceEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhcc------ccc--------ccCCCCCCEEEEEEEE
Confidence 34478999999999999 8999999999999998887653 100 2347999999988754
No 146
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=25.44 E-value=1.4e+02 Score=24.17 Aligned_cols=23 Identities=43% Similarity=0.676 Sum_probs=18.0
Q ss_pred CCCCCEEEEEEEEEecceEEEEEcC
Q 020356 88 PETGDIVIGRVIEVVPKRWKLEINF 112 (327)
Q Consensus 88 P~vGDiVIGrV~~V~~~~w~VDI~s 112 (327)
.++=++++|+|+++.+ .+|.++.
T Consensus 14 ~~p~~i~~G~V~s~~P--L~I~i~~ 36 (100)
T PF10844_consen 14 SNPVDIVIGTVVSVPP--LKIKIDQ 36 (100)
T ss_pred CCCceeEEEEEEeccc--EEEEECC
Confidence 3455779999999999 7777775
No 147
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=25.35 E-value=2.1e+02 Score=20.50 Aligned_cols=62 Identities=21% Similarity=0.232 Sum_probs=35.2
Q ss_pred EEEEEEEE---ecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEE--EEecCCCCceEEEE
Q 020356 94 VIGRVIEV---VPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAE--VRSSQGDGSLQLQA 168 (327)
Q Consensus 94 VIGrV~~V---~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~Ae--V~sv~~~g~i~Lst 168 (327)
|.|+|+.+ ..+..+++|.... +.+ ..+.|+ .+-....+.+++||.|.++ |... .+++++|+.
T Consensus 3 v~G~V~~~~~~~~~~~~~~l~D~t-g~i--~~~~~~---------~~~~~~~~~l~~g~~v~v~G~v~~~-~~~~~~l~~ 69 (75)
T PF01336_consen 3 VEGRVTSIRRSGGKIVFFTLEDGT-GSI--QVVFFN---------EEYERFREKLKEGDIVRVRGKVKRY-NGGELELIV 69 (75)
T ss_dssp EEEEEEEEEEEETTEEEEEEEETT-EEE--EEEEET---------HHHHHHHHTS-TTSEEEEEEEEEEE-TTSSEEEEE
T ss_pred EEEEEEEEEcCCCCEEEEEEEECC-ccE--EEEEcc---------HHhhHHhhcCCCCeEEEEEEEEEEE-CCccEEEEE
Confidence 67888887 5667777776544 442 222232 1112556779999998754 4443 222366654
No 148
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=24.76 E-value=2e+02 Score=25.58 Aligned_cols=54 Identities=13% Similarity=0.265 Sum_probs=40.5
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEe
Q 020356 87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRS 157 (327)
Q Consensus 87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~s 157 (327)
-|..|-+|+|+|-.+-.+-..+|.+...+++..-+.++ .+.++-|--|+-++..
T Consensus 79 g~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n-----------------~e~Y~~GaRVrlRl~D 132 (173)
T KOG4078|consen 79 GDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALN-----------------GEAYQKGARVRLRLID 132 (173)
T ss_pred cCcCCcEEEeeeeeeeccceEEecCCeEEEEEcCcCcC-----------------HHHhhcCceEEEEEcC
Confidence 46789999999999999999999998888775444332 1236778777777654
No 149
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=24.55 E-value=46 Score=23.89 Aligned_cols=38 Identities=13% Similarity=0.115 Sum_probs=27.8
Q ss_pred EEeChhhhhhc----cccccccC-ccceEEEEee----cceeeeccc
Q 020356 182 LTVDPYLVKRR----KQHFHHLE-EYGIDLIIGC----NGYIWIGEH 219 (327)
Q Consensus 182 v~V~~~li~r~----~~h~~~L~-~~~~eiivG~----NG~IWI~~~ 219 (327)
+.||+.+++.+ +.++..|. .+++.|.+.. ++.|||.+.
T Consensus 4 i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~ 50 (62)
T cd02394 4 VEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGP 50 (62)
T ss_pred EEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcC
Confidence 56677766554 46676663 6899999988 788888775
No 150
>KOG4600 consensus Mitochondrial ribosomal protein MRP7 (L2) [Translation, ribosomal structure and biogenesis]
Probab=24.33 E-value=1.6e+02 Score=25.87 Aligned_cols=55 Identities=18% Similarity=0.059 Sum_probs=36.1
Q ss_pred CCCceEecCCccCCCC-CceeecCCEEe-eCCeEEEEEeeEEEEE-------CcEEEEEecCCc
Q 020356 31 NPNSCVTVGDTIPVYE-DGILKGHGTSD-QKGELAATVCGVVERI-------NKLIYVRALRAR 85 (327)
Q Consensus 31 ~~~~iV~PGD~I~~~e-e~~~~G~Gty~-~~g~i~Ssv~G~v~~~-------nk~v~V~pl~~r 85 (327)
.....|.||+.|..-- ..|-+|..+=. .|..|||-.-|.|+.. .+.+.|.|....
T Consensus 53 ~egq~V~~G~IIvrQRgtkfHPG~nVGiGKDhtifaL~eG~Vrf~k~~~~~~Rk~i~V~~~~~~ 116 (144)
T KOG4600|consen 53 YEGQSVIPGNIIVRQRGTKFHPGDNVGIGKDHTIFALEEGRVRFEKSKITPPRKWIGVDPRGGL 116 (144)
T ss_pred cCCeeeecccEEEEecccccCCCcccccCCcceEEEeeccEEEEEEccCCCCcceEEEeecCCc
Confidence 3456899999885321 24666654433 4678999999999873 256677665543
No 151
>PF01959 DHQS: 3-dehydroquinate synthase (EC 4.6.1.3); InterPro: IPR002812 3-Dehydroquinate synthase (4.2.3.4 from EC) is an enzyme in the common pathway of aromatic amino acid biosynthesis that catalyses the conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) into 3-dehydroquinic acid []. This synthesis of aromatic amino acids is an essential metabolic function for most prokaryotic as well as lower eukaryotic cells, including plants. The pathway is absent in humans; therefore, DHQS represents a potential target for the development of novel and selective antimicrobial agents. Owing to the threat posed by the spread of pathogenic bacteria resistant to many currently used antimicrobial drugs, there is clearly a need to develop new anti-infective drugs acting at novel targets. A further potential use for DHQS inhibitors is as herbicides [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process
Probab=24.31 E-value=7.5e+02 Score=25.01 Aligned_cols=91 Identities=11% Similarity=0.158 Sum_probs=55.2
Q ss_pred EecCCccCCCCCceeecCCEEe--eCCeEEEEEeeEEEEEC-cEEEEEecCCccCCCCCCEEEEEEEEEecceEEEEEcC
Q 020356 36 VTVGDTIPVYEDGILKGHGTSD--QKGELAATVCGVVERIN-KLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINF 112 (327)
Q Consensus 36 V~PGD~I~~~ee~~~~G~Gty~--~~g~i~Ssv~G~v~~~n-k~v~V~pl~~rY~P~vGDiVIGrV~~V~~~~w~VDI~s 112 (327)
..||+.=...+| ...|.-+.. .+|+-+....|.+++.. .++.|+.- + ++ .++.=+-++-|.|-+-.
T Consensus 247 ~~pg~kT~YLSE-L~sG~~VlvVd~~G~tR~~~VGRvKIE~RPLllIeA~---~----~g---~~~svilQnaetIRlv~ 315 (354)
T PF01959_consen 247 LMPGGKTRYLSE-LRSGDEVLVVDADGRTRTAIVGRVKIERRPLLLIEAE---A----DG---KRISVILQNAETIRLVG 315 (354)
T ss_pred EcCCCceeehhh-hcCCCEEEEEeCCCCEEEEEeeEEEEeecceEEEEEE---e----CC---eEEEEEEecCcEEEEEC
Confidence 445554332233 334444332 47889999999998753 35565553 2 22 23344567889998887
Q ss_pred ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecC
Q 020356 113 TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQ 159 (327)
Q Consensus 113 ~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~ 159 (327)
+....+++. + +++||-|.+.+..-.
T Consensus 316 p~G~~vsVt---------------~-------Lk~GD~vL~~~~~~~ 340 (354)
T PF01959_consen 316 PDGEPVSVT---------------E-------LKPGDEVLVYLEEAG 340 (354)
T ss_pred CCCCEeeee---------------e-------cCCCCEEEEEecCCC
Confidence 765543221 1 799999999987644
No 152
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=24.17 E-value=1.5e+02 Score=28.75 Aligned_cols=22 Identities=18% Similarity=0.356 Sum_probs=17.5
Q ss_pred EEEEEEEEecceEEEEEcCccc
Q 020356 94 VIGRVIEVVPKRWKLEINFTQD 115 (327)
Q Consensus 94 VIGrV~~V~~~~w~VDI~s~~~ 115 (327)
++|+|+.|.....+|.+-+..+
T Consensus 156 LVG~V~~V~~~tS~V~Lltd~~ 177 (284)
T COG1792 156 LVGKVVEVSKNTSRVLLLTDVN 177 (284)
T ss_pred eEEEEEEEcCceeEEEEeeccc
Confidence 8999999999999887655433
No 153
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=24.09 E-value=49 Score=24.39 Aligned_cols=14 Identities=36% Similarity=0.562 Sum_probs=12.2
Q ss_pred cCCCCEEEEEEEec
Q 020356 145 FTENDLVCAEVRSS 158 (327)
Q Consensus 145 ~~~GDlV~AeV~sv 158 (327)
|++||+|-||+...
T Consensus 1 f~~GdlVwaK~~G~ 14 (63)
T smart00293 1 FKPGDLVWAKMKGF 14 (63)
T ss_pred CCCCCEEEEECCCC
Confidence 68999999999774
No 154
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=23.87 E-value=3.3e+02 Score=20.65 Aligned_cols=34 Identities=21% Similarity=0.207 Sum_probs=20.3
Q ss_pred CC-eEEEEEeeEEEEECcEEEEEecCCccCCCCCCEEEEEEEEEec
Q 020356 59 KG-ELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVP 103 (327)
Q Consensus 59 ~g-~i~Ssv~G~v~~~nk~v~V~pl~~rY~P~vGDiVIGrV~~V~~ 103 (327)
+| .+.+...|.+... .-.|.+||.|.-.+.....
T Consensus 28 ~g~~~~c~~~Gklr~~-----------~i~i~vGD~V~ve~~~~~~ 62 (72)
T PRK00276 28 NGHEVLAHISGKMRKN-----------YIRILPGDKVTVELSPYDL 62 (72)
T ss_pred CCCEEEEEEccceeeC-----------CcccCCCCEEEEEEcccCC
Confidence 44 4556666666532 1127899999766554443
No 155
>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=23.57 E-value=2.3e+02 Score=30.64 Aligned_cols=72 Identities=3% Similarity=0.141 Sum_probs=47.8
Q ss_pred c-CCCCCC--EEEEEEEEEecceEEEEEc-Cccceeeeccccc-CCCcccccccccch--hhh--hcccCCCCEEEEEEE
Q 020356 86 Y-KPETGD--IVIGRVIEVVPKRWKLEIN-FTQDAILMLSSMN-LPDGIQRRRTAVDE--LNM--RSIFTENDLVCAEVR 156 (327)
Q Consensus 86 Y-~P~vGD--iVIGrV~~V~~~~w~VDI~-s~~~a~L~ls~v~-fpg~i~rrr~~~de--~~m--r~~~~~GDlV~AeV~ 156 (327)
| ..++|+ .--|.|+++...+++|.+. ....+++|++++. +++... -..++ +.+ +..|+.||-|..+|.
T Consensus 550 yl~~~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~---~~~~~~~~~l~g~~~~~lgd~v~V~v~ 626 (639)
T TIGR02062 550 FLADKAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELV---CNQENGTVQIKGETVYKIGDVIDVVLT 626 (639)
T ss_pred HHhhccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceE---EcccccEEEEeccEEEecCCEEEEEEE
Confidence 5 345654 7899999999999999994 4578888887652 111000 00111 011 126999999999999
Q ss_pred ecCC
Q 020356 157 SSQG 160 (327)
Q Consensus 157 sv~~ 160 (327)
+++.
T Consensus 627 ~vd~ 630 (639)
T TIGR02062 627 EVRM 630 (639)
T ss_pred Eecc
Confidence 9874
No 156
>COG3822 ABC-type sugar transport system, auxiliary component [General function prediction only]
Probab=23.26 E-value=2.3e+02 Score=26.49 Aligned_cols=70 Identities=24% Similarity=0.303 Sum_probs=42.6
Q ss_pred eEecCCccCCC------CCceeecCCEEee--------C-----CeEEEEEeeEE---------EEE-CcEEEEEecC-C
Q 020356 35 CVTVGDTIPVY------EDGILKGHGTSDQ--------K-----GELAATVCGVV---------ERI-NKLIYVRALR-A 84 (327)
Q Consensus 35 iV~PGD~I~~~------ee~~~~G~Gty~~--------~-----g~i~Ssv~G~v---------~~~-nk~v~V~pl~-~ 84 (327)
+|.||++-+.- |+..-+|.||.+. + ..+..++-|.. +.. ...|.+-|-. .
T Consensus 92 ~vr~gQvtPmHrH~~k~eDiinrgggtlv~el~~~d~~~~~~~ks~vtv~~dg~r~~~~ag~~lkL~PGesitL~Pg~~H 171 (225)
T COG3822 92 HVRPGQVTPMHRHWRKPEDIINRGGGTLVVELWNVDLVEGQDEKSDVTVPVDGCRQTHTAGSQLKLSPGESITLPPGLYH 171 (225)
T ss_pred EeccCCcCcccccccchhhhhhcCCceEEEEEeccccccCcCCCCCeEecCCCcEEEeccceeEEECCCCcEecCCCcee
Confidence 68899876532 3456678888531 1 11333333333 322 2355555543 3
Q ss_pred ccCCCCCCEEEEEEEEEecc
Q 020356 85 RYKPETGDIVIGRVIEVVPK 104 (327)
Q Consensus 85 rY~P~vGDiVIGrV~~V~~~ 104 (327)
.|-.+.|++++|.|..++.+
T Consensus 172 sFwae~g~vlvgEvSsvndD 191 (225)
T COG3822 172 SFWAEEGGVLVGEVSSVNDD 191 (225)
T ss_pred eeeecCCcEEEEEEeeccCc
Confidence 57889999999999998765
No 157
>PF14444 S1-like: S1-like
Probab=22.34 E-value=2.7e+02 Score=20.92 Aligned_cols=16 Identities=31% Similarity=0.383 Sum_probs=13.2
Q ss_pred ccCCCCCCEEEEEEEE
Q 020356 85 RYKPETGDIVIGRVIE 100 (327)
Q Consensus 85 rY~P~vGDiVIGrV~~ 100 (327)
-++|++||-|+..-+.
T Consensus 31 G~~P~vGdrV~v~A~~ 46 (58)
T PF14444_consen 31 GNVPKVGDRVLVEAIY 46 (58)
T ss_pred cCCCccCCEEEEEEEe
Confidence 4799999999987664
No 158
>PF14698 ASL_C2: Argininosuccinate lyase C-terminal; PDB: 1XWO_A 2E9F_A 1TJW_C 1TJU_A 1DCN_B 1K7W_B 1HY1_C 1TJV_B 1AUW_A 1U15_B ....
Probab=22.21 E-value=1.8e+02 Score=22.15 Aligned_cols=51 Identities=18% Similarity=0.215 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHhhhhCCCCchhcccchHHH
Q 020356 260 ARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLDIHDMLGSEFYV 310 (327)
Q Consensus 260 ~r~~i~r~~n~i~~l~~~~~~i~~~~i~~~~~~s~~~~~~~~~~l~~~~~~ 310 (327)
=|++=..|+.+++...+.|.++.+-+....=+.+...+-++.+.|+|+..+
T Consensus 18 FR~AH~iVg~~V~~a~~~~~~l~~l~~~~~~~~~~~~~~~~~~~l~~~~~V 68 (70)
T PF14698_consen 18 FREAHHIVGRLVRLAEEEGKPLSELTLEELQEISPEFEEDVREALDPEASV 68 (70)
T ss_dssp HHHHHHHHHHHHHHHHHTTS-GGGS-HHHHHHH-TT--GGGGGGSSHHHHH
T ss_pred HHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHhHHhHHHHHHHCCHHHHh
Confidence 366667788999999999999888777666666666777799999998765
No 159
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=21.13 E-value=1e+02 Score=25.23 Aligned_cols=27 Identities=30% Similarity=0.272 Sum_probs=16.3
Q ss_pred ccCCCCCCEE------------EEEEEEEecceEEEEEc
Q 020356 85 RYKPETGDIV------------IGRVIEVVPKRWKLEIN 111 (327)
Q Consensus 85 rY~P~vGDiV------------IGrV~~V~~~~w~VDI~ 111 (327)
...|++||+| +|+|+++..+....-+.
T Consensus 60 ~~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~~~~i~v~e 98 (124)
T PF05257_consen 60 GSTPQPGDIVVWDSGSGGGYGHVAIVESVNDGGTITVIE 98 (124)
T ss_dssp CS---TTEEEEEEECTTTTT-EEEEEEEE-TTSEEEEEE
T ss_pred CcccccceEEEeccCCCCCCCeEEEEEEECCCCEEEEEE
Confidence 5689999999 48999985555554444
No 160
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=21.06 E-value=8.6e+02 Score=24.50 Aligned_cols=92 Identities=17% Similarity=0.279 Sum_probs=55.4
Q ss_pred eEecCCccCCCCCceeecCCEE--eeCCeEEEEEeeEEEEEC-cEEEEEecCCccCCCCCCEEEEEEEEEecceEEEEEc
Q 020356 35 CVTVGDTIPVYEDGILKGHGTS--DQKGELAATVCGVVERIN-KLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEIN 111 (327)
Q Consensus 35 iV~PGD~I~~~ee~~~~G~Gty--~~~g~i~Ssv~G~v~~~n-k~v~V~pl~~rY~P~vGDiVIGrV~~V~~~~w~VDI~ 111 (327)
+..||+.-...++ ...|.-+. ..+|+-+..+.|.+++.. .++-|+.- | +. -++.-+-++-|.|-+-
T Consensus 236 v~~pgg~T~YLsE-L~sG~eVlvVd~~G~tR~~~VGRvKIE~RPL~lIeAe---~----~g---~~~~viLQnaetIrlv 304 (344)
T PRK02290 236 VRVPGDKTRYLSE-LRSGDEVLVVDADGNTREAIVGRVKIEKRPLLLIEAE---Y----GG---KRIRTILQNAETIRLV 304 (344)
T ss_pred EEcCCCcchhhHh-hcCCCEEEEEeCCCCEEEEEeeEEEEeeccEEEEEEE---e----CC---eEEEEEEecCcEEEEE
Confidence 3556665433333 34444432 347889999999998753 35555543 2 22 2233345788888887
Q ss_pred CccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecC
Q 020356 112 FTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQ 159 (327)
Q Consensus 112 s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~ 159 (327)
.+.... +|-. + +++||-|.+.+....
T Consensus 305 ~~dG~~--vsVt-------------~-------Lk~GD~VL~~~~~~~ 330 (344)
T PRK02290 305 TPDGKP--VSVV-------------D-------LKPGDEVLGYLEEAA 330 (344)
T ss_pred CCCCCE--eeee-------------e-------cCCCCEEEEEecCCc
Confidence 765443 2211 1 799999999987644
No 161
>cd05834 HDGF_related The PWWP domain is an essential part of the Hepatoma Derived Growth Factor (HDGF) family of proteins, and is necessary for DNA binding by HDGF. This family of endogenous nuclear-targeted mitogens includes HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, HPR2, HPR3, HPR4, respectively) and lens epithelium-derived growth factor, LEDGF. Members of the HDGF family have been linked to human diseases, and HDGF is a prognostic factor in several types of cancer. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=20.93 E-value=61 Score=25.54 Aligned_cols=15 Identities=40% Similarity=0.596 Sum_probs=12.8
Q ss_pred cCCCCEEEEEEEecC
Q 020356 145 FTENDLVCAEVRSSQ 159 (327)
Q Consensus 145 ~~~GDlV~AeV~sv~ 159 (327)
|++||+|.|++...-
T Consensus 3 f~~GdlVwaK~kGyp 17 (83)
T cd05834 3 FKAGDLVFAKVKGYP 17 (83)
T ss_pred CCCCCEEEEecCCCC
Confidence 899999999997653
No 162
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=20.92 E-value=4.7e+02 Score=21.42 Aligned_cols=57 Identities=16% Similarity=0.220 Sum_probs=35.2
Q ss_pred cCCC-CCCEEEEEEEEE-ecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEe
Q 020356 86 YKPE-TGDIVIGRVIEV-VPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRS 157 (327)
Q Consensus 86 Y~P~-vGDiVIGrV~~V-~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~s 157 (327)
-+|. .-+-++|+|++. .+..+.|.+.....-.. .+||-.++ + =.+++||.|.+..-.
T Consensus 12 ~~p~~~e~e~~g~V~~~lG~~~~~V~~~dG~~~la-----~i~GK~Rk-~---------iwI~~GD~VlVsp~d 70 (99)
T TIGR00523 12 RLPRKEEGEILGVIEQMLGAGRVKVRCLDGKTRLG-----RIPGKLKK-R---------IWIREGDVVIVKPWE 70 (99)
T ss_pred eCCCCCCCEEEEEEEEEcCCCEEEEEeCCCCEEEE-----EEchhhcc-c---------EEecCCCEEEEEEcc
Confidence 3554 356799999998 46677888764333222 24553332 2 238999999984433
No 163
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=20.75 E-value=1.6e+02 Score=27.56 Aligned_cols=61 Identities=18% Similarity=0.160 Sum_probs=30.2
Q ss_pred CEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEec
Q 020356 92 DIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSS 158 (327)
Q Consensus 92 DiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv 158 (327)
|.|||.|+++....+ |.+.+.+-++ +.+|+---....-.=.+.-.+-|+.||.|+..-..+
T Consensus 118 dYvIG~Iskv~k~~~--~~~~~~dyVv----V~YP~~~G~~~~V~V~LT~GQkFnVGDkVKV~~~~~ 178 (213)
T PRK06763 118 DYVIGEVSKVYTMED--DGDGATKYVV----VEYPSLNGKKLIIDVFLTKGQVFHVGDKVKVDMKYV 178 (213)
T ss_pred ceEEEEEEEeccccc--CCCCcccEEE----EEcCCCCCCeeEEEEEeccCCEEecCCEEEEEeeec
Confidence 899999999976543 1112222111 112221000000000123345699999999886554
No 164
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=20.73 E-value=1.4e+02 Score=32.41 Aligned_cols=80 Identities=16% Similarity=0.216 Sum_probs=59.2
Q ss_pred cEEEEEecCC-ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEE
Q 020356 75 KLIYVRALRA-RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCA 153 (327)
Q Consensus 75 k~v~V~pl~~-rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~A 153 (327)
+.+++-..+. -+-=+.|-+=-|.|.++...+.+|++|+...+.+|-+++. +. .-|.+||-|..
T Consensus 106 ~~vy~l~~~c~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~-------~~---------~~~~vgdeiiV 169 (715)
T COG1107 106 KIVYVLDNSCTMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLG-------GD---------PDYAVGDEIIV 169 (715)
T ss_pred ceeEEeccccchhhcccceeeeccccchhhhcceeecChhhhccccccccC-------CC---------CCCCCCCeEEE
Confidence 4455554443 3345889999999999999999999999888887655543 11 22899999999
Q ss_pred EEEecCCC-CceEEEEcc
Q 020356 154 EVRSSQGD-GSLQLQARN 170 (327)
Q Consensus 154 eV~sv~~~-g~i~Lstr~ 170 (327)
.|..+.+. +.+.+.-..
T Consensus 170 ~v~~vr~~~geidf~~~~ 187 (715)
T COG1107 170 QVSDVRPEKGEIDFEPVG 187 (715)
T ss_pred EeeccCCCCCccceeecC
Confidence 99999875 666665433
No 165
>PRK00215 LexA repressor; Validated
Probab=20.65 E-value=3.3e+02 Score=24.26 Aligned_cols=35 Identities=17% Similarity=0.268 Sum_probs=23.9
Q ss_pred EEEEECcEEEEEecCCccCCCC----CCEEEEEEEEEec
Q 020356 69 VVERINKLIYVRALRARYKPET----GDIVIGRVIEVVP 103 (327)
Q Consensus 69 ~v~~~nk~v~V~pl~~rY~P~v----GDiVIGrV~~V~~ 103 (327)
.+...++.+.+.|....|-|.. .-.|+|+|+.+-.
T Consensus 165 rl~~~~~~~~L~s~Np~y~~~~~~~~~~~IiG~Vv~~~r 203 (205)
T PRK00215 165 RFRREGGHIRLEPENPAYEPIIVDPDRVTIEGKVVGLIR 203 (205)
T ss_pred EEEEeCCEEEEEcCCCCCCCEEeCCCcEEEEEEEEEEEE
Confidence 3334567888999877775522 4588999988653
No 166
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=20.41 E-value=1.6e+02 Score=26.47 Aligned_cols=29 Identities=24% Similarity=0.342 Sum_probs=24.3
Q ss_pred CCCCEEEEEEEEEecceEEEEEcCccceee
Q 020356 89 ETGDIVIGRVIEVVPKRWKLEINFTQDAIL 118 (327)
Q Consensus 89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L 118 (327)
++||+|.++|..+. ..+.+.+-....+.|
T Consensus 120 ~~GD~V~akV~~i~-~~i~LS~k~~~lGvv 148 (189)
T PRK09521 120 KIGDIVRAKVISYT-DPLQLSTKGKDLGVI 148 (189)
T ss_pred CCCCEEEEEEEecC-CcEEEEEecCCceEE
Confidence 78999999999999 778888776666665
No 167
>COG0211 RpmA Ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=20.17 E-value=2e+02 Score=23.23 Aligned_cols=54 Identities=22% Similarity=0.130 Sum_probs=36.8
Q ss_pred CCCCceEecCCccCCC-CCceeecCCEEe-eCCeEEEEEeeEEEEE-----CcEEEEEecC
Q 020356 30 SNPNSCVTVGDTIPVY-EDGILKGHGTSD-QKGELAATVCGVVERI-----NKLIYVRALR 83 (327)
Q Consensus 30 ~~~~~iV~PGD~I~~~-ee~~~~G~Gty~-~~g~i~Ssv~G~v~~~-----nk~v~V~pl~ 83 (327)
.....+|.+|+.|--- -..|-+|.++=. .|..|+|.+.|.|+.. .+.++|.|..
T Consensus 25 ~~~Gq~v~aG~IivRQRGTk~hpG~NVG~GkDhTlFAl~dG~Vkf~~k~~~rk~vsV~~~~ 85 (87)
T COG0211 25 KFGGQFVKAGSIIVRQRGTKFHPGVNVGRGKDHTLFALVDGVVKFETKGKNRKYVSVVPEA 85 (87)
T ss_pred eeCCeEEecccEEEEeccccccCCcccccCCCceEEEeeccEEEEEEccCCccEEEEEeec
Confidence 3456788899887421 124666666533 4778999999999763 2488888764
No 168
>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=20.13 E-value=1.7e+02 Score=22.26 Aligned_cols=24 Identities=21% Similarity=0.363 Sum_probs=17.3
Q ss_pred CCCCCEEEEEEEEEecc-eEEEEEc
Q 020356 88 PETGDIVIGRVIEVVPK-RWKLEIN 111 (327)
Q Consensus 88 P~vGDiVIGrV~~V~~~-~w~VDI~ 111 (327)
-++||.|.++|+++..+ ...+.+.
T Consensus 55 l~vGd~i~~~V~~~~~~~~i~LS~~ 79 (86)
T cd05789 55 LDEGDLIVAEVQSVDSDGSVSLHTR 79 (86)
T ss_pred CCCCCEEEEEEEEECCCCCEEEEeC
Confidence 38999999999998653 3444443
Done!