Query 024995
Match_columns 259
No_of_seqs 225 out of 1749
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 09:07:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024995.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024995hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0539 RpsA Ribosomal protein 100.0 3.3E-43 7.2E-48 335.0 16.7 206 16-259 143-365 (541)
2 COG0539 RpsA Ribosomal protein 100.0 4.8E-41 1E-45 320.3 15.6 214 1-258 224-450 (541)
3 PRK12269 bifunctional cytidyla 100.0 3.3E-36 7.2E-41 303.1 18.6 202 22-259 539-754 (863)
4 PRK13806 rpsA 30S ribosomal pr 100.0 5.9E-34 1.3E-38 274.0 17.3 204 20-259 157-381 (491)
5 PRK13806 rpsA 30S ribosomal pr 100.0 2.2E-33 4.7E-38 270.1 18.5 195 22-253 249-466 (491)
6 PRK12269 bifunctional cytidyla 100.0 2.7E-33 5.9E-38 282.0 18.2 206 17-259 440-667 (863)
7 PRK07899 rpsA 30S ribosomal pr 100.0 6.6E-32 1.4E-36 258.0 18.0 192 18-247 161-369 (486)
8 PRK06299 rpsA 30S ribosomal pr 100.0 2.3E-31 5E-36 260.2 18.3 203 20-259 156-375 (565)
9 TIGR00717 rpsA ribosomal prote 100.0 9.9E-31 2.1E-35 253.1 17.7 202 22-259 233-448 (516)
10 PRK06676 rpsA 30S ribosomal pr 100.0 1.3E-30 2.8E-35 244.4 17.7 197 20-254 147-360 (390)
11 PRK06299 rpsA 30S ribosomal pr 100.0 5.1E-30 1.1E-34 250.7 17.5 202 22-259 247-462 (565)
12 TIGR00717 rpsA ribosomal prote 100.0 1.6E-29 3.4E-34 244.7 17.3 205 18-259 140-361 (516)
13 PRK07899 rpsA 30S ribosomal pr 100.0 5.1E-29 1.1E-33 238.2 16.0 196 22-259 82-295 (486)
14 PRK07400 30S ribosomal protein 100.0 1.1E-28 2.4E-33 225.4 15.0 189 22-256 78-280 (318)
15 PRK00087 4-hydroxy-3-methylbut 99.9 5.6E-27 1.2E-31 232.4 17.1 191 19-247 430-638 (647)
16 PRK06676 rpsA 30S ribosomal pr 99.9 3.8E-27 8.3E-32 220.9 14.6 197 22-259 65-279 (390)
17 PRK00087 4-hydroxy-3-methylbut 99.9 3.4E-25 7.3E-30 219.7 15.2 197 22-259 349-564 (647)
18 PRK07400 30S ribosomal protein 99.8 1.3E-20 2.8E-25 172.4 13.8 165 49-258 22-197 (318)
19 PTZ00248 eukaryotic translatio 99.7 4.2E-18 9.2E-23 154.4 9.9 116 55-187 13-140 (319)
20 COG1098 VacB Predicted RNA bin 99.7 4.6E-17 9.9E-22 127.0 5.2 76 55-136 2-82 (129)
21 KOG1070 rRNA processing protei 99.6 2.6E-14 5.6E-19 146.1 15.1 190 22-243 1115-1325(1710)
22 cd05705 S1_Rrp5_repeat_hs14 S1 99.5 1.6E-14 3.4E-19 105.0 7.3 66 56-126 1-74 (74)
23 PRK08582 hypothetical protein; 99.5 4.8E-14 1E-18 114.5 9.3 77 55-137 2-83 (139)
24 cd05704 S1_Rrp5_repeat_hs13 S1 99.5 1.5E-13 3.2E-18 99.2 7.6 66 56-128 1-72 (72)
25 PF00575 S1: S1 RNA binding do 99.5 1.8E-13 3.9E-18 98.6 7.7 69 55-128 1-74 (74)
26 cd04461 S1_Rrp5_repeat_hs8_sc7 99.5 1.8E-13 3.8E-18 101.3 7.7 71 52-127 8-83 (83)
27 cd05703 S1_Rrp5_repeat_hs12_sc 99.5 2.2E-13 4.7E-18 98.7 8.0 65 59-128 1-72 (73)
28 cd05686 S1_pNO40 S1_pNO40: pNO 99.5 3.9E-13 8.5E-18 97.2 8.9 66 57-127 2-72 (73)
29 PLN00207 polyribonucleotide nu 99.5 1.4E-13 3.1E-18 138.8 8.4 87 49-141 744-836 (891)
30 cd05698 S1_Rrp5_repeat_hs6_sc5 99.4 4.6E-13 9.9E-18 95.5 7.5 65 59-128 1-70 (70)
31 cd04452 S1_IF2_alpha S1_IF2_al 99.4 1.1E-12 2.3E-17 95.0 9.3 71 56-129 1-76 (76)
32 cd05706 S1_Rrp5_repeat_sc10 S1 99.4 8.7E-13 1.9E-17 94.9 8.6 68 56-128 1-73 (73)
33 PHA02945 interferon resistance 99.4 9.4E-13 2E-17 97.1 8.5 75 54-133 7-87 (88)
34 PRK07252 hypothetical protein; 99.4 1.2E-12 2.7E-17 103.6 9.1 73 57-134 2-79 (120)
35 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.4 1.1E-12 2.3E-17 93.6 7.8 64 59-127 1-69 (69)
36 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.4 9.2E-13 2E-17 94.8 7.2 57 66-127 15-71 (71)
37 cd05694 S1_Rrp5_repeat_hs2_sc2 99.4 2.3E-12 5E-17 93.6 8.9 68 55-132 1-73 (74)
38 KOG1070 rRNA processing protei 99.4 3.3E-12 7.1E-17 131.1 11.1 221 1-245 538-774 (1710)
39 cd05708 S1_Rrp5_repeat_sc12 S1 99.4 4.8E-12 1E-16 91.5 9.0 70 57-130 1-75 (77)
40 PRK08059 general stress protei 99.4 3.9E-12 8.5E-17 101.2 9.3 76 54-134 3-83 (123)
41 cd05707 S1_Rrp5_repeat_sc11 S1 99.4 2E-12 4.4E-17 91.9 6.8 63 59-126 1-68 (68)
42 cd05691 S1_RPS1_repeat_ec6 S1_ 99.4 4.2E-12 9.2E-17 90.9 8.4 67 59-130 1-72 (73)
43 cd05690 S1_RPS1_repeat_ec5 S1_ 99.3 3.5E-12 7.7E-17 90.5 7.4 63 59-126 1-69 (69)
44 PTZ00248 eukaryotic translatio 99.3 7E-13 1.5E-17 120.5 4.4 85 154-259 18-107 (319)
45 cd05684 S1_DHX8_helicase S1_DH 99.3 7.5E-12 1.6E-16 91.6 9.0 71 59-133 1-77 (79)
46 COG1093 SUI2 Translation initi 99.3 1.5E-12 3.2E-17 113.8 6.1 77 55-134 8-89 (269)
47 PRK05807 hypothetical protein; 99.3 5.5E-12 1.2E-16 102.1 9.0 70 55-131 2-76 (136)
48 COG2996 Predicted RNA-bindinin 99.3 1.2E-11 2.6E-16 108.7 11.8 167 21-222 45-217 (287)
49 cd05687 S1_RPS1_repeat_ec1_hs1 99.3 1.1E-11 2.4E-16 88.4 7.9 65 59-128 1-70 (70)
50 cd05692 S1_RPS1_repeat_hs4 S1_ 99.3 1.5E-11 3.3E-16 86.5 8.2 64 59-128 1-69 (69)
51 cd05689 S1_RPS1_repeat_ec4 S1_ 99.3 1.7E-11 3.7E-16 87.9 8.1 66 56-126 1-72 (72)
52 cd05693 S1_Rrp5_repeat_hs1_sc1 99.2 1.7E-11 3.8E-16 94.1 6.6 71 56-131 1-98 (100)
53 cd05685 S1_Tex S1_Tex: The C-t 99.2 4.2E-11 9.2E-16 84.0 7.1 63 59-126 1-68 (68)
54 cd04465 S1_RPS1_repeat_ec2_hs2 99.2 7.1E-11 1.5E-15 83.7 7.9 62 59-128 1-67 (67)
55 PRK03987 translation initiatio 99.2 8E-11 1.7E-15 105.1 9.5 77 55-134 5-86 (262)
56 cd05688 S1_RPS1_repeat_ec3 S1_ 99.2 9.3E-11 2E-15 82.5 7.9 63 58-126 1-68 (68)
57 cd04472 S1_PNPase S1_PNPase: P 99.2 1.1E-10 2.4E-15 82.2 7.8 63 59-127 1-68 (68)
58 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.2 9.1E-11 2E-15 83.2 6.8 61 59-126 1-66 (66)
59 TIGR02696 pppGpp_PNP guanosine 99.2 1.6E-10 3.6E-15 114.7 10.7 89 31-126 611-718 (719)
60 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.2 1.4E-10 3.1E-15 86.1 7.7 70 55-130 3-81 (86)
61 COG1098 VacB Predicted RNA bin 99.1 2.2E-11 4.7E-16 95.3 2.7 76 152-251 4-84 (129)
62 smart00316 S1 Ribosomal protei 99.1 3.8E-10 8.2E-15 79.2 8.3 67 57-128 1-72 (72)
63 PRK11824 polynucleotide phosph 99.1 3.2E-10 6.9E-15 113.7 10.9 93 31-130 587-692 (693)
64 cd04453 S1_RNase_E S1_RNase_E: 99.1 4.4E-10 9.6E-15 84.3 8.2 69 55-128 4-82 (88)
65 cd04471 S1_RNase_R S1_RNase_R: 99.1 1.1E-09 2.3E-14 80.3 9.0 66 58-127 1-82 (83)
66 COG1185 Pnp Polyribonucleotide 99.0 5.9E-10 1.3E-14 108.9 8.4 94 31-131 585-691 (692)
67 COG2183 Tex Transcriptional ac 99.0 4.4E-10 9.5E-15 111.3 7.0 75 53-132 653-732 (780)
68 cd04454 S1_Rrp4_like S1_Rrp4_l 99.0 2.6E-09 5.7E-14 78.6 7.9 69 55-129 3-76 (82)
69 PRK09521 exosome complex RNA-b 99.0 3.5E-09 7.5E-14 90.3 9.1 101 22-129 29-142 (189)
70 TIGR03591 polynuc_phos polyrib 98.9 4.4E-09 9.4E-14 105.4 9.5 88 31-125 584-684 (684)
71 cd00164 S1_like S1_like: Ribos 98.9 4.5E-09 9.7E-14 72.3 6.2 56 66-126 10-65 (65)
72 cd05702 S1_Rrp5_repeat_hs11_sc 98.9 6.3E-09 1.4E-13 74.3 6.6 57 59-120 1-64 (70)
73 cd04473 S1_RecJ_like S1_RecJ_l 98.9 1.4E-08 3.1E-13 74.0 8.4 61 53-127 11-76 (77)
74 cd05705 S1_Rrp5_repeat_hs14 S1 98.9 2.7E-09 5.8E-14 77.4 4.2 68 152-239 2-74 (74)
75 cd04460 S1_RpoE S1_RpoE: RpoE, 98.8 1.8E-08 4E-13 76.9 8.4 65 66-136 12-92 (99)
76 cd05703 S1_Rrp5_repeat_hs12_sc 98.8 3.1E-09 6.7E-14 76.9 2.8 67 154-241 1-72 (73)
77 PRK08582 hypothetical protein; 98.8 8.4E-09 1.8E-13 83.8 4.8 75 152-250 4-83 (139)
78 cd05694 S1_Rrp5_repeat_hs2_sc2 98.7 9.2E-09 2E-13 74.6 3.8 65 152-245 3-73 (74)
79 PRK09202 nusA transcription el 98.7 1.5E-08 3.3E-13 97.2 6.3 97 19-129 86-200 (470)
80 TIGR00448 rpoE DNA-directed RN 98.7 4.5E-08 9.8E-13 82.7 8.0 128 1-134 13-172 (179)
81 PLN00207 polyribonucleotide nu 98.7 7.5E-09 1.6E-13 105.0 3.7 78 152-253 752-835 (891)
82 COG1093 SUI2 Translation initi 98.7 1.1E-08 2.4E-13 89.7 2.6 77 153-250 11-92 (269)
83 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.6 3E-08 6.4E-13 71.2 4.0 64 154-240 1-71 (71)
84 cd05690 S1_RPS1_repeat_ec5 S1_ 98.6 3.7E-08 8E-13 69.7 3.9 64 154-239 1-69 (69)
85 KOG1067 Predicted RNA-binding 98.6 4E-08 8.7E-13 94.0 4.4 77 55-137 665-746 (760)
86 PRK04163 exosome complex RNA-b 98.6 1.5E-07 3.3E-12 82.9 7.8 70 54-129 59-137 (235)
87 PRK08563 DNA-directed RNA poly 98.6 1.9E-07 4E-12 79.4 7.4 126 1-132 13-170 (187)
88 COG1095 RPB7 DNA-directed RNA 98.6 1.9E-07 4.2E-12 78.3 7.2 129 2-136 14-176 (183)
89 cd04455 S1_NusA S1_NusA: N-uti 98.6 3E-07 6.5E-12 65.2 7.1 58 57-126 2-66 (67)
90 cd05698 S1_Rrp5_repeat_hs6_sc5 98.5 5.6E-08 1.2E-12 69.0 3.2 65 154-241 1-70 (70)
91 PRK07252 hypothetical protein; 98.5 8.2E-08 1.8E-12 76.1 3.7 81 152-255 2-88 (120)
92 PF00575 S1: S1 RNA binding do 98.5 1.1E-07 2.4E-12 68.2 3.8 67 152-241 3-74 (74)
93 TIGR02063 RNase_R ribonuclease 98.5 6.7E-07 1.4E-11 90.4 9.4 69 55-127 624-708 (709)
94 cd04452 S1_IF2_alpha S1_IF2_al 98.4 2.1E-07 4.6E-12 66.9 3.9 70 152-242 2-76 (76)
95 cd05689 S1_RPS1_repeat_ec4 S1_ 98.4 3.8E-07 8.3E-12 65.1 5.1 65 153-239 3-72 (72)
96 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.4 1.8E-07 3.8E-12 66.4 3.1 64 154-240 1-69 (69)
97 cd05706 S1_Rrp5_repeat_sc10 S1 98.4 3.6E-07 7.9E-12 65.4 4.6 67 152-241 2-73 (73)
98 cd05704 S1_Rrp5_repeat_hs13 S1 98.4 2E-07 4.3E-12 67.1 3.0 67 152-241 2-72 (72)
99 PHA02945 interferon resistance 98.4 3E-07 6.4E-12 68.1 3.9 70 153-246 11-87 (88)
100 PHA02858 EIF2a-like PKR inhibi 98.4 9.6E-07 2.1E-11 64.7 6.1 69 54-127 12-85 (86)
101 cd04461 S1_Rrp5_repeat_hs8_sc7 98.4 3.2E-07 6.9E-12 67.6 3.4 66 152-240 13-83 (83)
102 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.4 5.6E-07 1.2E-11 63.7 4.5 61 154-239 1-66 (66)
103 cd05707 S1_Rrp5_repeat_sc11 S1 98.3 4.9E-07 1.1E-11 63.9 3.7 63 154-239 1-68 (68)
104 cd05691 S1_RPS1_repeat_ec6 S1_ 98.3 4.2E-07 9.2E-12 64.7 3.3 67 154-243 1-72 (73)
105 cd05686 S1_pNO40 S1_pNO40: pNO 98.3 6.6E-07 1.4E-11 64.4 4.1 64 153-240 3-72 (73)
106 PRK11642 exoribonuclease R; Pr 98.3 2.1E-06 4.6E-11 87.7 9.1 69 57-129 642-726 (813)
107 cd05684 S1_DHX8_helicase S1_DH 98.3 5.8E-07 1.2E-11 65.5 3.6 71 154-246 1-77 (79)
108 cd05693 S1_Rrp5_repeat_hs1_sc1 98.3 5E-07 1.1E-11 69.3 3.0 79 152-243 2-97 (100)
109 TIGR00358 3_prime_RNase VacB a 98.3 2.7E-06 5.9E-11 85.2 9.0 68 56-127 570-653 (654)
110 PRK05807 hypothetical protein; 98.3 8.8E-07 1.9E-11 71.7 4.3 68 152-244 4-76 (136)
111 cd05708 S1_Rrp5_repeat_sc12 S1 98.2 1.1E-06 2.4E-11 63.2 3.8 68 153-243 2-75 (77)
112 PRK08059 general stress protei 98.2 9.3E-07 2E-11 70.3 3.6 73 152-247 6-83 (123)
113 TIGR01953 NusA transcription t 98.2 1.9E-06 4.1E-11 79.8 6.0 98 18-129 82-198 (341)
114 COG2996 Predicted RNA-bindinin 98.2 1.1E-05 2.4E-10 71.5 10.4 96 22-133 117-221 (287)
115 PRK12327 nusA transcription el 98.2 1.6E-06 3.4E-11 80.8 5.2 98 18-128 85-199 (362)
116 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.2 5.7E-06 1.2E-10 62.5 7.0 73 56-129 4-86 (92)
117 PRK03987 translation initiatio 98.2 1.5E-06 3.3E-11 77.7 4.0 74 153-247 8-86 (262)
118 cd05692 S1_RPS1_repeat_hs4 S1_ 98.1 3.3E-06 7.1E-11 58.9 3.1 64 154-241 1-69 (69)
119 cd05687 S1_RPS1_repeat_ec1_hs1 98.0 5.1E-06 1.1E-10 58.9 3.6 65 154-241 1-70 (70)
120 TIGR02696 pppGpp_PNP guanosine 98.0 4.7E-06 1E-10 83.4 4.1 68 152-239 646-718 (719)
121 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.0 4.5E-06 9.9E-11 61.7 3.1 72 152-243 5-81 (86)
122 cd05685 S1_Tex S1_Tex: The C-t 98.0 7.2E-06 1.6E-10 57.1 3.5 63 154-239 1-68 (68)
123 cd04471 S1_RNase_R S1_RNase_R: 97.9 1.5E-05 3.3E-10 58.0 4.5 75 154-240 2-82 (83)
124 cd04465 S1_RPS1_repeat_ec2_hs2 97.9 1E-05 2.3E-10 56.9 3.5 62 154-241 1-67 (67)
125 PRK11824 polynucleotide phosph 97.9 1.3E-05 2.8E-10 80.9 4.8 69 152-244 620-693 (693)
126 KOG2916 Translation initiation 97.9 1.2E-05 2.7E-10 70.7 3.8 80 56-138 14-98 (304)
127 cd04472 S1_PNPase S1_PNPase: P 97.8 2.4E-05 5.2E-10 54.6 3.5 63 154-240 1-68 (68)
128 cd05688 S1_RPS1_repeat_ec3 S1_ 97.7 4.5E-05 9.8E-10 53.1 4.2 62 154-239 2-68 (68)
129 smart00316 S1 Ribosomal protei 97.7 3.4E-05 7.5E-10 53.6 3.6 66 153-241 2-72 (72)
130 cd04453 S1_RNase_E S1_RNase_E: 97.7 3.4E-05 7.4E-10 57.7 3.4 54 153-226 7-63 (88)
131 cd04473 S1_RecJ_like S1_RecJ_l 97.6 7.5E-05 1.6E-09 54.2 4.2 56 153-240 16-76 (77)
132 COG2183 Tex Transcriptional ac 97.6 3E-05 6.5E-10 77.6 2.7 72 150-244 655-731 (780)
133 PRK09521 exosome complex RNA-b 97.5 0.00013 2.8E-09 62.1 5.3 100 103-242 27-142 (189)
134 PRK05054 exoribonuclease II; P 97.5 0.00027 5.8E-09 70.9 8.0 65 59-127 562-643 (644)
135 PTZ00162 DNA-directed RNA poly 97.5 0.0003 6.5E-09 59.4 7.2 122 2-129 14-165 (176)
136 cd05702 S1_Rrp5_repeat_hs11_sc 97.5 0.00019 4.2E-09 50.9 4.5 60 154-234 1-65 (70)
137 cd05699 S1_Rrp5_repeat_hs7 S1_ 97.4 0.00052 1.1E-08 49.3 6.4 64 59-128 1-72 (72)
138 cd04460 S1_RpoE S1_RpoE: RpoE, 97.4 0.00024 5.1E-09 54.1 4.6 86 156-254 2-97 (99)
139 COG1097 RRP4 RNA-binding prote 97.4 0.0018 4E-08 56.7 10.5 71 54-130 60-139 (239)
140 COG1096 Predicted RNA-binding 97.3 0.0019 4.1E-08 54.6 9.5 74 52-128 58-141 (188)
141 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.3 0.0014 3E-08 49.1 7.8 59 58-122 1-75 (88)
142 PRK09202 nusA transcription el 97.3 8.7E-05 1.9E-09 71.5 1.5 115 84-242 73-200 (470)
143 COG1185 Pnp Polyribonucleotide 97.3 0.00026 5.7E-09 70.0 4.1 70 152-244 618-691 (692)
144 TIGR00757 RNaseEG ribonuclease 97.2 0.00076 1.6E-08 64.2 7.0 57 55-116 22-97 (414)
145 cd04454 S1_Rrp4_like S1_Rrp4_l 97.2 0.00033 7.1E-09 51.3 3.5 67 152-242 5-76 (82)
146 TIGR03591 polynuc_phos polyrib 97.2 0.00039 8.5E-09 70.1 4.3 63 152-238 617-684 (684)
147 cd00164 S1_like S1_like: Ribos 97.0 0.00081 1.8E-08 45.6 3.6 60 157-239 1-65 (65)
148 TIGR02062 RNase_B exoribonucle 97.0 0.002 4.3E-08 64.6 7.4 64 59-126 558-638 (639)
149 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.0 0.0036 7.9E-08 46.7 7.0 68 55-129 3-75 (86)
150 COG0557 VacB Exoribonuclease R 96.9 0.0021 4.6E-08 65.2 7.3 70 55-128 619-704 (706)
151 PF13509 S1_2: S1 domain; PDB: 96.8 0.0048 1E-07 42.9 5.9 48 66-128 14-61 (61)
152 KOG1067 Predicted RNA-binding 96.7 0.00093 2E-08 64.7 2.3 76 152-251 667-747 (760)
153 TIGR00448 rpoE DNA-directed RN 96.7 0.0021 4.4E-08 54.3 4.2 83 154-249 82-174 (179)
154 TIGR02063 RNase_R ribonuclease 96.7 0.0024 5.2E-08 64.8 5.2 71 153-240 627-708 (709)
155 PRK11642 exoribonuclease R; Pr 96.6 0.003 6.4E-08 65.0 5.1 77 153-245 643-729 (813)
156 cd04455 S1_NusA S1_NusA: N-uti 96.5 0.0041 9E-08 43.7 4.3 32 153-191 3-35 (67)
157 COG1107 Archaea-specific RecJ- 96.4 0.014 3E-07 57.1 8.5 68 53-131 117-189 (715)
158 PRK12328 nusA transcription el 96.2 0.013 2.9E-07 54.8 6.8 62 55-128 135-205 (374)
159 COG1095 RPB7 DNA-directed RNA 96.2 0.0033 7.2E-08 53.0 2.4 87 154-253 82-180 (183)
160 PRK04163 exosome complex RNA-b 96.1 0.0051 1.1E-07 54.2 3.5 70 153-242 63-137 (235)
161 KOG2916 Translation initiation 96.1 0.0024 5.2E-08 56.5 1.1 83 153-256 16-103 (304)
162 KOG1856 Transcription elongati 96.0 0.0062 1.3E-07 63.3 4.1 71 55-130 982-1060(1299)
163 TIGR00358 3_prime_RNase VacB a 96.0 0.0088 1.9E-07 60.2 5.1 76 153-240 572-653 (654)
164 TIGR01953 NusA transcription t 95.9 0.0028 6.1E-08 58.9 0.9 106 100-242 81-198 (341)
165 PF10447 EXOSC1: Exosome compo 95.7 0.031 6.8E-07 41.3 5.4 36 81-116 45-82 (82)
166 PRK08563 DNA-directed RNA poly 95.2 0.022 4.8E-07 48.2 4.0 76 154-242 82-167 (187)
167 PRK12327 nusA transcription el 94.9 0.0088 1.9E-07 56.0 0.5 100 102-239 86-197 (362)
168 PRK10811 rne ribonuclease E; R 94.8 0.07 1.5E-06 55.3 6.7 61 56-121 36-112 (1068)
169 PRK11712 ribonuclease G; Provi 94.6 0.14 3.1E-06 49.8 8.0 59 54-117 34-111 (489)
170 PRK12329 nusA transcription el 93.9 0.19 4E-06 48.2 7.0 68 55-128 149-224 (449)
171 PRK05054 exoribonuclease II; P 90.9 0.26 5.6E-06 49.7 4.1 72 155-239 563-642 (644)
172 cd05699 S1_Rrp5_repeat_hs7 S1_ 89.8 0.54 1.2E-05 33.8 3.9 68 154-241 1-72 (72)
173 PRK12328 nusA transcription el 87.5 0.2 4.3E-06 47.1 0.4 97 101-234 89-195 (374)
174 KOG3298 DNA-directed RNA polym 87.4 3.2 6.9E-05 34.5 7.3 62 54-121 77-154 (170)
175 COG0557 VacB Exoribonuclease R 85.7 0.86 1.9E-05 46.5 3.9 73 153-240 622-703 (706)
176 COG4044 Uncharacterized protei 82.3 1.1 2.3E-05 38.8 2.5 74 53-127 70-156 (247)
177 PF09876 DUF2103: Predicted me 82.1 1.4 2.9E-05 34.0 2.7 54 180-234 32-85 (103)
178 TIGR02062 RNase_B exoribonucle 81.5 2 4.4E-05 43.3 4.6 70 155-238 559-637 (639)
179 cd05791 S1_CSL4 S1_CSL4: CSL4, 81.4 2.1 4.6E-05 32.0 3.6 72 152-242 5-86 (92)
180 PTZ00162 DNA-directed RNA poly 81.2 2.3 5.1E-05 35.8 4.2 59 154-226 82-143 (176)
181 COG1530 CafA Ribonucleases G a 80.4 2.3 4.9E-05 41.6 4.4 71 53-129 32-114 (487)
182 PRK10811 rne ribonuclease E; R 78.6 3.3 7.1E-05 43.5 5.0 35 153-191 38-73 (1068)
183 cd04462 S1_RNAPII_Rpb7 S1_RNAP 77.0 2.7 5.9E-05 31.2 2.9 58 154-226 2-62 (88)
184 PF08292 RNA_pol_Rbc25: RNA po 76.8 8.7 0.00019 30.4 6.0 56 58-118 3-76 (122)
185 PHA02858 EIF2a-like PKR inhibi 72.8 1.9 4.2E-05 31.9 1.2 62 154-239 17-84 (86)
186 KOG3409 Exosomal 3'-5' exoribo 72.8 26 0.00056 29.6 7.9 71 55-127 65-146 (193)
187 PF00313 CSD: 'Cold-shock' DNA 71.7 29 0.00063 23.7 7.2 41 66-115 13-53 (66)
188 PF10447 EXOSC1: Exosome compo 71.5 4.4 9.5E-05 29.9 2.8 25 152-180 3-27 (82)
189 COG1107 Archaea-specific RecJ- 70.7 2.9 6.3E-05 41.5 2.2 31 153-189 122-152 (715)
190 TIGR00757 RNaseEG ribonuclease 67.0 5.1 0.00011 38.4 3.0 36 153-192 25-61 (414)
191 PF13509 S1_2: S1 domain; PDB: 66.7 6 0.00013 27.1 2.6 30 154-189 2-31 (61)
192 PRK09937 stationary phase/star 64.3 32 0.00069 24.7 6.1 54 66-130 14-67 (74)
193 KOG1856 Transcription elongati 61.4 7.8 0.00017 41.3 3.3 69 153-242 985-1059(1299)
194 COG1530 CafA Ribonucleases G a 61.3 9.9 0.00022 37.2 3.9 57 153-226 37-94 (487)
195 PRK15464 cold shock-like prote 57.7 24 0.00052 25.0 4.4 41 66-115 17-57 (70)
196 PF10246 MRP-S35: Mitochondria 57.2 37 0.0008 26.1 5.5 48 57-116 22-74 (104)
197 PRK09507 cspE cold shock prote 55.2 35 0.00076 24.0 4.9 41 66-115 16-56 (69)
198 PRK15463 cold shock-like prote 55.1 22 0.00048 25.2 3.9 41 66-115 17-57 (70)
199 PRK14998 cold shock-like prote 55.0 50 0.0011 23.5 5.7 51 66-127 14-64 (73)
200 TIGR00830 PTBA PTS system, glu 54.1 30 0.00066 27.3 4.9 51 157-226 42-92 (121)
201 PRK09439 PTS system glucose-sp 53.5 31 0.00067 28.9 5.1 57 157-232 64-126 (169)
202 PRK10943 cold shock-like prote 52.2 36 0.00078 23.9 4.6 41 66-115 16-56 (69)
203 cd00210 PTS_IIA_glc PTS_IIA, P 51.7 32 0.00069 27.3 4.7 30 157-190 42-71 (124)
204 PF00358 PTS_EIIA_1: phosphoen 51.6 32 0.0007 27.6 4.7 28 157-188 46-73 (132)
205 COG2190 NagE Phosphotransferas 50.4 27 0.00059 28.9 4.2 29 157-189 49-77 (156)
206 PRK12442 translation initiatio 50.2 72 0.0016 23.8 6.0 54 66-129 18-73 (87)
207 cd05700 S1_Rrp5_repeat_hs9 S1_ 48.7 22 0.00048 24.7 2.8 27 101-127 39-65 (65)
208 PRK12329 nusA transcription el 48.1 31 0.00067 33.4 4.7 56 152-233 151-213 (449)
209 PRK11712 ribonuclease G; Provi 48.0 16 0.00034 35.8 2.8 35 153-191 38-73 (489)
210 PRK10354 RNA chaperone/anti-te 47.9 44 0.00095 23.5 4.5 41 66-115 17-57 (70)
211 PRK09890 cold shock protein Cs 47.6 48 0.001 23.3 4.7 41 66-115 17-57 (70)
212 TIGR02381 cspD cold shock doma 47.6 31 0.00068 24.1 3.6 41 66-115 14-54 (68)
213 cd04458 CSP_CDS Cold-Shock Pro 45.5 68 0.0015 21.7 5.1 32 81-116 23-54 (65)
214 TIGR00008 infA translation ini 41.9 74 0.0016 22.6 4.8 51 66-125 16-67 (68)
215 COG1278 CspC Cold shock protei 41.7 40 0.00087 23.9 3.4 30 81-114 24-53 (67)
216 COG1097 RRP4 RNA-binding prote 40.9 99 0.0022 27.4 6.4 55 153-226 64-119 (239)
217 KOG3754 Gamma-glutamylcysteine 39.0 32 0.0007 33.4 3.3 26 22-47 47-72 (640)
218 PF02599 CsrA: Global regulato 36.8 59 0.0013 21.9 3.5 33 98-132 7-39 (54)
219 PRK01712 carbon storage regula 29.9 1E+02 0.0022 21.6 3.8 34 98-133 7-40 (64)
220 COG2100 Predicted Fe-S oxidore 29.5 1.1E+02 0.0023 28.7 5.0 71 1-73 335-412 (414)
221 PF08206 OB_RNB: Ribonuclease 28.8 1.8E+02 0.0039 19.4 5.4 26 81-115 19-44 (58)
222 cd04474 RPA1_DBD_A RPA1_DBD_A: 28.5 2E+02 0.0043 21.5 5.7 41 23-65 34-74 (104)
223 cd04480 RPA1_DBD_A_like RPA1_D 26.9 1.5E+02 0.0033 21.2 4.6 43 23-67 18-60 (86)
224 COG0250 NusG Transcription ant 25.5 95 0.0021 26.1 3.7 70 173-242 75-160 (178)
225 PF02721 DUF223: Domain of unk 24.7 2.6E+02 0.0055 20.5 5.6 39 31-69 3-41 (95)
226 KOG1004 Exosomal 3'-5' exoribo 24.5 2.6E+02 0.0055 24.5 6.1 57 55-118 62-124 (230)
227 cd05701 S1_Rrp5_repeat_hs10 S1 24.1 1.8E+02 0.004 20.5 4.2 45 69-118 16-61 (69)
228 PRK00568 carbon storage regula 23.7 1.3E+02 0.0029 21.8 3.7 32 99-132 8-39 (76)
229 COG1545 Predicted nucleic-acid 23.0 2.5E+02 0.0055 22.5 5.6 42 69-122 88-129 (140)
230 COG1551 CsrA RNA-binding globa 22.6 1.1E+02 0.0024 22.0 2.9 28 100-129 9-36 (73)
231 TIGR01995 PTS-II-ABC-beta PTS 22.5 1.5E+02 0.0032 30.0 5.0 57 157-232 506-568 (610)
232 COG1096 Predicted RNA-binding 22.1 1.4E+02 0.0031 25.5 4.0 54 152-226 63-125 (188)
233 PF08845 SymE_toxin: Toxin Sym 20.7 1.3E+02 0.0028 20.5 2.9 19 103-126 38-56 (57)
234 PF06347 SH3_4: Bacterial SH3 20.6 2.3E+02 0.005 18.3 4.2 36 53-92 18-54 (55)
235 PRK09824 PTS system beta-gluco 20.1 1.6E+02 0.0034 29.9 4.6 57 157-232 522-584 (627)
No 1
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.3e-43 Score=335.03 Aligned_cols=206 Identities=26% Similarity=0.524 Sum_probs=187.1
Q ss_pred hhcccCCCCEEEEEEEEEeCCCCEEEEEechhh-------HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEE
Q 024995 16 EIAKGLTGSIISVKVIQANEEMKKLVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLT 83 (259)
Q Consensus 16 ~~~~~~vG~~v~~~Vl~id~~~~~v~lS~k~~~-------~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~ 83 (259)
+++..++|+++.++|+++|.+++++++|+|... ++.+++.+++|+++.|+ +|||||+|+ |++
T Consensus 143 ~d~~~~~Gk~~~~kiie~d~~~n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdig------Gvd 216 (541)
T COG0539 143 RDLDPLIGKELEFKILELDKKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIG------GVD 216 (541)
T ss_pred ccccccCCceEEEEEEEEccccCcEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEec------Cee
Confidence 445678999999999999999999999999753 45678999999999999 999999998 899
Q ss_pred EEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceee
Q 024995 84 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNT 163 (259)
Q Consensus 84 glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~ 163 (259)
||||++||||.++.+|++.|++||+|+|+|+++|.+++||+||+|++.++||.... +.++. |+.+.|+|++
T Consensus 217 GLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~-~~~~~--------g~~v~G~Vt~ 287 (541)
T COG0539 217 GLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIE-KKYPV--------GDKVEGKVTN 287 (541)
T ss_pred eEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHh-hhcCC--------CCEEEEEEEE
Confidence 99999999999999999999999999999999999999999999999999997654 44675 4559999999
Q ss_pred eccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhh
Q 024995 164 IEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRK 238 (259)
Q Consensus 164 i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~l 238 (259)
++||| +|+++ .+||+||+ +|+++ |..... |.. +++.||.| ++||++++||||
T Consensus 288 i~~~G----afVei--~~GvEGlvhvSEis------------w~~~~~-P~e----vv~~Gq~V~V~Vl~id~e~rRIsL 344 (541)
T COG0539 288 LTDYG----AFVEI--EEGVEGLVHVSEIS------------WTKKNV-PSE----VVKVGQEVEVKVLDIDPERRRISL 344 (541)
T ss_pred eecCc----EEEEe--cCCccceeechhhc------------ccccCC-HHH----hcccCCEEEEEEEeeCchhceEEe
Confidence 99999 99999 99999999 89998 665554 554 77999999 899999999999
Q ss_pred hhchhhhhhhHHhhhhcccCC
Q 024995 239 ASKRHCNEYWNVFHETAIVNN 259 (259)
Q Consensus 239 s~k~~~~~p~~~~~~~~~~~~ 259 (259)
||||+.++||+.++++|++|.
T Consensus 345 ~iKq~~~~pw~~~~~~~~~g~ 365 (541)
T COG0539 345 GLKQLKENPWEEFADKHPVGD 365 (541)
T ss_pred eehhhhcChhhhhhhhcCCCC
Confidence 999999999999999999984
No 2
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.8e-41 Score=320.25 Aligned_cols=214 Identities=31% Similarity=0.505 Sum_probs=194.5
Q ss_pred CCCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEE
Q 024995 1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIH 72 (259)
Q Consensus 1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vl~id~~~~~v~lS~k~~---~~~~~~~~l~~G~iv~G~-----~~G~fV~ 72 (259)
|||.|+ .||+..+. +||+|.|+|+++|.+++|++||+|+. +|+.+...+.+|+.+.|+ +|||||+
T Consensus 224 iS~~rv-~~P~~vvk------vGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVe 296 (541)
T COG0539 224 ISWKRV-DHPSEVVK------VGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVE 296 (541)
T ss_pred cccccc-CCHHHhcc------cCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEEeecCcEEEE
Confidence 688886 89998877 99999999999999999999999986 699999999999999999 9999999
Q ss_pred EccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccC
Q 024995 73 LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISD 152 (259)
Q Consensus 73 l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~ 152 (259)
+. +|++||+|+|||||.+...|++++++||+|.|+|+++|++++||+||+|++..|||..+.+. ++.|
T Consensus 297 i~-----~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~-~~~g------ 364 (541)
T COG0539 297 IE-----EGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADK-HPVG------ 364 (541)
T ss_pred ec-----CCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhh-cCCC------
Confidence 99 69999999999999998889999999999999999999999999999999999999877665 6765
Q ss_pred CCCccccceeeeccCCCccceeeeecccCCeeEEEE-ccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q 227 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~ 227 (259)
..++|.|.++++|| +|++| ++|++||+| |.++ |.....+.+ +| +.|+++ +
T Consensus 365 --~~v~g~v~~~t~~g----~fv~l--e~gidG~vh~~d~s------------w~~~~~~~~-~~----k~Gd~v~~~vl 419 (541)
T COG0539 365 --DVVEGKVKSITDFG----AFVEL--EGGIDGLVHLSDLS------------WDRPGEEAE-KY----KKGDEVEAKVL 419 (541)
T ss_pred --CeEEEEEeeecccc----eEEcc--CCCccceEEHHhcC------------ccccCcHHH-hh----ccCcEEEEEEE
Confidence 44999999999999 99888 889999995 5555 665555444 45 999999 8
Q ss_pred EEecccchhhhhhchhhhhhhHHhhhhcccC
Q 024995 228 EIQLSHSLIRKASKRHCNEYWNVFHETAIVN 258 (259)
Q Consensus 228 ~v~~~~~~i~ls~k~~~~~p~~~~~~~~~~~ 258 (259)
.||.++++|||++|||.++||+.+.+.|+.|
T Consensus 420 ~vd~~~~~isLgiKql~~~p~~~~~~~~~~~ 450 (541)
T COG0539 420 AVDKEKERISLGIKQLEESPWEEFSEKYKKG 450 (541)
T ss_pred EEecccceeeeehhhhccCchhhhHhhccCC
Confidence 9999999999999999999999999999987
No 3
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=3.3e-36 Score=303.07 Aligned_cols=202 Identities=28% Similarity=0.500 Sum_probs=180.9
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCc
Q 024995 22 TGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW 93 (259)
Q Consensus 22 vG~~v~~~Vl~id~~~~~v~lS~k~~---~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~ 93 (259)
+||+++|+|+.+|++++++.||+|+. +|+.+.+.+++|+++.|+ +||+||+++ .|++||+|+||++|
T Consensus 539 vGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~-----~gveGLvhiSEls~ 613 (863)
T PRK12269 539 KGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIELA-----EGIEGLAHISEFSW 613 (863)
T ss_pred CCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEEEEEEEEeCCeEEEEec-----CCceeeeEHHHhcC
Confidence 89999999999999999999999975 588888899999999999 999999997 48999999999999
Q ss_pred -ccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCccc
Q 024995 94 -DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGA 172 (259)
Q Consensus 94 -~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~ 172 (259)
.++.+|.+.|++||+|+|+|+++|++++|++||+|++.+|||....++ +++ |++++|+|+++++||
T Consensus 614 ~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~-~~v--------G~~v~G~V~~i~~~G---- 680 (863)
T PRK12269 614 VKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEAR-YPV--------GARFTRRIVKVTNAG---- 680 (863)
T ss_pred ccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHh-CCC--------CCEEEEEEEEEecce----
Confidence 578899999999999999999999999999999999999999876554 554 566999999999999
Q ss_pred eeeeecccCCeeEEEE-ccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchhhhhh
Q 024995 173 IFEELLQEDGIDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRHCNEY 247 (259)
Q Consensus 173 ~fv~l~~~~gv~gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~~~~p 247 (259)
+||+| .+||+||+| |+++ |.....+++. .+++||.| ++||+++++|+||+|++.++|
T Consensus 681 ~fV~l--~~gV~GlIh~sels------------~~~~~~~~~~----~~kvGq~VkvkVl~ID~e~rrI~LS~K~l~~dp 742 (863)
T PRK12269 681 AFIEM--EEGIDGFLHVDDLS------------WVKRTRPADH----ELEVGKEIECMVIECDPQARRIRLGVKQLSDNP 742 (863)
T ss_pred EEEEe--CCCcEEEEEhHHhh------------ccccccchhh----ccCCCCEEEEEEEEEeccCCEEEEEecccccCh
Confidence 99999 899999994 5555 6554444444 45999999 799999999999999999999
Q ss_pred hHHhhhhcccCC
Q 024995 248 WNVFHETAIVNN 259 (259)
Q Consensus 248 ~~~~~~~~~~~~ 259 (259)
|+.+.++|++|.
T Consensus 743 w~~~~~~~~vG~ 754 (863)
T PRK12269 743 WQVFANAYGVGS 754 (863)
T ss_pred HHHHHhhCCCCC
Confidence 999999999884
No 4
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=5.9e-34 Score=273.96 Aligned_cols=204 Identities=25% Similarity=0.439 Sum_probs=178.2
Q ss_pred cCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEE
Q 024995 20 GLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVH 87 (259)
Q Consensus 20 ~~vG~~v~~~Vl~id~~~~~v~lS~k~~-------~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~ 87 (259)
.++|++++|+|+.+|++++++.+|+|.. .|+.++..+++|+++.|+ +||+||+++ .|++||||
T Consensus 157 ~~vG~~i~~~V~~id~~~~~v~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~-----~gv~g~v~ 231 (491)
T PRK13806 157 SYVGQTFQFLITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELA-----PGVEGMVH 231 (491)
T ss_pred HcCCCeEEEEEEEEECCCCeEEEEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcC-----CCcEEEEE
Confidence 4699999999999999999999999875 356667789999999999 899999997 38999999
Q ss_pred ceecCcccccChhhhcCCCCeEEEEEEEEeCCC----CeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceee
Q 024995 88 VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK----SRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNT 163 (259)
Q Consensus 88 isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~----~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~ 163 (259)
+++++|.++.++.+.|++||.|+|+|+++|.++ +||.||+|++.++||....++ ++. |+++.|+|++
T Consensus 232 ~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~-~~~--------G~~v~G~V~~ 302 (491)
T PRK13806 232 ISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDR-LKA--------GDKVTGKVVR 302 (491)
T ss_pred HHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhcc-CCC--------CCEEEEEEEE
Confidence 999999999999999999999999999999866 479999999999999765544 444 6669999999
Q ss_pred eccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhh
Q 024995 164 IEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRK 238 (259)
Q Consensus 164 i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~l 238 (259)
+++|| +|++| .+|++||+ .|+++ |..+...+.. .+++||.| +++|.++++|+|
T Consensus 303 v~~~G----~fV~l--~~gv~Glvh~sels------------~~~~~~~~~~----~~~~Gd~v~vkVl~iD~e~~ri~L 360 (491)
T PRK13806 303 LAPFG----AFVEI--LPGIEGLVHVSEMS------------WTRRVNKPED----VVAPGDAVAVKIKDIDPAKRRISL 360 (491)
T ss_pred EeCce----EEEEe--CCCcEEEEEHHHcC------------cccccCCHHH----cCCCCCEEEEEEEEEEccCCEEEE
Confidence 99999 99988 78999999 57766 4333333333 56999999 789999999999
Q ss_pred hhchhhhhhhHHhhhhcccCC
Q 024995 239 ASKRHCNEYWNVFHETAIVNN 259 (259)
Q Consensus 239 s~k~~~~~p~~~~~~~~~~~~ 259 (259)
|+|++..+||+.+.++|++|.
T Consensus 361 s~K~~~~~p~~~~~~~~~vG~ 381 (491)
T PRK13806 361 SLRDAEGDPWADVAERFAPGT 381 (491)
T ss_pred EEeecccChhHHhhhhCCCCC
Confidence 999999999999999999984
No 5
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=2.2e-33 Score=270.06 Aligned_cols=195 Identities=27% Similarity=0.479 Sum_probs=169.9
Q ss_pred CCCEEEEEEEEEeCCC----CEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEce
Q 024995 22 TGSIISVKVIQANEEM----KKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVS 89 (259)
Q Consensus 22 vG~~v~~~Vl~id~~~----~~v~lS~k~~---~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~is 89 (259)
+||.|+|+|+.+|.++ +++.||+|++ +|+.+...+++|+++.|+ +||+||+++ .|++||+|+|
T Consensus 249 vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~-----~gv~Glvh~s 323 (491)
T PRK13806 249 VGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEIL-----PGIEGLVHVS 323 (491)
T ss_pred CCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEEEEEeCceEEEEeC-----CCcEEEEEHH
Confidence 9999999999999876 4799999986 588888899999999999 999999997 4899999999
Q ss_pred ecCc-ccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccCC
Q 024995 90 EVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLP 168 (259)
Q Consensus 90 els~-~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G 168 (259)
+|+| .++.++.+.|++||.|+|+|+++|+++++|.||+|++.++||....++ +++ |++++|+|+++++||
T Consensus 324 els~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~-~~v--------G~~v~G~V~~i~~~G 394 (491)
T PRK13806 324 EMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAER-FAP--------GTTVTGTVEKRAQFG 394 (491)
T ss_pred HcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhh-CCC--------CCEEEEEEEEEecCc
Confidence 9999 477899999999999999999999999999999999999999876554 454 666999999999999
Q ss_pred CccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchh
Q 024995 169 GLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRH 243 (259)
Q Consensus 169 ~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~ 243 (259)
+|+++ ++|++||| +|++++++ . ..+.. .+++||.| +++|.+++||+||+|++
T Consensus 395 ----~FV~l--~~gv~Gli~~se~s~~~------------~-~~~~~----~~~~Gd~v~~~V~~id~e~~ri~Ls~~~~ 451 (491)
T PRK13806 395 ----LFVNL--APGVTGLLPASVISRAG------------K-PATYE----KLKPGDSVTLVVEEIDTAKRKISLAPAGA 451 (491)
T ss_pred ----eEEEc--CCCcEEEEEHHHcCccc------------c-cchhh----cCCCCCEEEEEEEEEeCCCCEEEEEeehh
Confidence 99988 78999999 67777332 1 22223 45999999 79999999999999987
Q ss_pred -----hhhhhHHhhh
Q 024995 244 -----CNEYWNVFHE 253 (259)
Q Consensus 244 -----~~~p~~~~~~ 253 (259)
..+||+.+..
T Consensus 452 ~~~~~~~~~~~~~~~ 466 (491)
T PRK13806 452 AGSGADDDDWKQFAP 466 (491)
T ss_pred hhhhhhhhHHHhhcc
Confidence 4589999854
No 6
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=2.7e-33 Score=282.04 Aligned_cols=206 Identities=23% Similarity=0.460 Sum_probs=179.1
Q ss_pred hcccCCCCEEEEEEEEEeC-----CCCEEEEEechhh-------HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCC
Q 024995 17 IAKGLTGSIISVKVIQANE-----EMKKLVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGL 79 (259)
Q Consensus 17 ~~~~~vG~~v~~~Vl~id~-----~~~~v~lS~k~~~-------~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~ 79 (259)
+++.++|++++|+|+.+|. +++++++|+|... .+++++.+++|+++.|+ +||+||+++
T Consensus 440 ~~~~~vG~~ie~~V~~~~~~~~~~~~~~iVlSrr~~l~e~~~~~~ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl~----- 514 (863)
T PRK12269 440 APESLIGLTSKFYIERISQSKQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLG----- 514 (863)
T ss_pred chHHhCCCeEEEEEEEEecccccCCCCeEEEEHHHHHHHHHHHHHHHHHhcCCCCCEEEEEEEEEeCCcEEEEEC-----
Confidence 3456799999999999975 3469999998742 34567889999999998 899999996
Q ss_pred ccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCcccc
Q 024995 80 YHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSS 159 (259)
Q Consensus 80 ~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G 159 (259)
|++||||+|+++|.++.+|.+.|++||+++|+|+++|++++++.||+|++.++||....++ +++ |++++|
T Consensus 515 -Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~-~~v--------G~iV~G 584 (863)
T PRK12269 515 -GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENK-FGV--------NDVVKG 584 (863)
T ss_pred -CEEEEEEchhccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhcc-CCC--------CCEEEE
Confidence 8999999999999999999999999999999999999999999999999999999765544 454 666999
Q ss_pred ceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccc
Q 024995 160 NSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHS 234 (259)
Q Consensus 160 ~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~ 234 (259)
+|+++++|| +|++| .+|++||+ +|+++ |.....++.. .+++||.| +.+|.+++
T Consensus 585 ~V~~I~~fG----~fVeL--~~gveGLvhiSEls------------~~~~~~~p~~----~~kvGd~V~vkVl~iD~e~~ 642 (863)
T PRK12269 585 RVTKIADFG----AFIEL--AEGIEGLAHISEFS------------WVKKTSKPSD----MVKIGDEVECMILGYDIQAG 642 (863)
T ss_pred EEEEEeCCe----EEEEe--cCCceeeeEHHHhc------------CccccCCHHH----cCCCCCEEEEEEEEEecccC
Confidence 999999999 99988 78999999 57776 5433443443 56999999 79999999
Q ss_pred hhhhhhchhhhhhhHHhhhhcccCC
Q 024995 235 LIRKASKRHCNEYWNVFHETAIVNN 259 (259)
Q Consensus 235 ~i~ls~k~~~~~p~~~~~~~~~~~~ 259 (259)
+|+||+|++.++||+.+.++|++|.
T Consensus 643 rIsLS~K~l~~~Pw~~~~~~~~vG~ 667 (863)
T PRK12269 643 RVSLGLKQVTANPWEEIEARYPVGA 667 (863)
T ss_pred ceEEEehhcccCchHHHHHhCCCCC
Confidence 9999999999999999999999984
No 7
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.98 E-value=6.6e-32 Score=258.04 Aligned_cols=192 Identities=24% Similarity=0.452 Sum_probs=166.5
Q ss_pred cccCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEE
Q 024995 18 AKGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL 85 (259)
Q Consensus 18 ~~~~vG~~v~~~Vl~id~~~~~v~lS~k~~-------~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~gl 85 (259)
++.++|++|+|+|+++|.+++++.+|+|.. .|+.++..+++|+++.|+ +||+||+|+ |++||
T Consensus 161 ~~~~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlg------gv~Gl 234 (486)
T PRK07899 161 LQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLG------GVDGL 234 (486)
T ss_pred hhhcCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEEE
Confidence 345799999999999999999999999852 366778899999999999 999999996 79999
Q ss_pred EEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeec
Q 024995 86 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIE 165 (259)
Q Consensus 86 v~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~ 165 (259)
||+|+++|.++.+|.+.|++||.|+|+|+++|++++||.||+|++.++||..+... ++. |+++.|+|+++.
T Consensus 235 v~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~-~~v--------G~vv~G~V~~I~ 305 (486)
T PRK07899 235 VHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFART-HAI--------GQIVPGKVTKLV 305 (486)
T ss_pred EEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHh-cCC--------CCEEEEEEEEEe
Confidence 99999999999999999999999999999999999999999999999999766554 343 566999999999
Q ss_pred cCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhh
Q 024995 166 PLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKAS 240 (259)
Q Consensus 166 ~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~ 240 (259)
+|| +|++| .+|++||+ +|+++.+. ...+.. .+++||.| ++||.++++|+||+
T Consensus 306 ~fG----vFVeL--~~gieGLvh~SeLs~~~-------------v~~~~~----~~kvGd~V~VkIi~ID~e~rrI~LSl 362 (486)
T PRK07899 306 PFG----AFVRV--EEGIEGLVHISELAERH-------------VEVPEQ----VVQVGDEVFVKVIDIDLERRRISLSL 362 (486)
T ss_pred ccE----EEEEe--CCCcEEEEEHHHcCccc-------------ccCccc----eeCCCCEEEEEEEEEECCCCEEEEEE
Confidence 999 99998 78999999 67776331 111222 56999999 68999999999999
Q ss_pred chhhhhh
Q 024995 241 KRHCNEY 247 (259)
Q Consensus 241 k~~~~~p 247 (259)
|++.++.
T Consensus 363 K~~~~~~ 369 (486)
T PRK07899 363 KQANEGV 369 (486)
T ss_pred EEcccCC
Confidence 9987654
No 8
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.97 E-value=2.3e-31 Score=260.19 Aligned_cols=203 Identities=30% Similarity=0.536 Sum_probs=178.1
Q ss_pred cCCCCEEEEEEEEEeCCCCEEEEEechhh-------HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEE
Q 024995 20 GLTGSIISVKVIQANEEMKKLVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVH 87 (259)
Q Consensus 20 ~~vG~~v~~~Vl~id~~~~~v~lS~k~~~-------~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~ 87 (259)
.++|++++|+|+.+|.+++++.+|+|.+. |+.++..+++|+++.|+ +||+||+++ |++||+|
T Consensus 156 ~~vG~~i~~~V~~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~------g~~glv~ 229 (565)
T PRK06299 156 PLEGKELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLG------GVDGLLH 229 (565)
T ss_pred HhCCCEEEEEEEEEECCCCEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEEC------CEEEEEE
Confidence 56999999999999999999999999753 55677899999999999 999999997 7999999
Q ss_pred ceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccC
Q 024995 88 VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPL 167 (259)
Q Consensus 88 isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~ 167 (259)
+++++|.++.++.+.|++||.|+|+|+++|++++++.||+|++.++||....+. ++. |+++.|+|+++++|
T Consensus 230 ~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~-~~~--------G~~v~g~V~~i~~~ 300 (565)
T PRK06299 230 ITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKK-YPV--------GSKVKGKVTNITDY 300 (565)
T ss_pred HHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHhh-CCC--------CCEEEEEEEEEeCC
Confidence 999999999999999999999999999999999999999999999999865444 454 66699999999999
Q ss_pred CCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhch
Q 024995 168 PGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKR 242 (259)
Q Consensus 168 G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~ 242 (259)
| +|++| .+|+.||+ .|+++ |.....++.. .+++||.| +++|.++++|+||+|+
T Consensus 301 G----~fV~l--~~~v~Glv~~sel~------------~~~~~~~~~~----~~~~G~~v~v~V~~id~~~~~i~ls~k~ 358 (565)
T PRK06299 301 G----AFVEL--EEGIEGLVHVSEMS------------WTKKNKHPSK----VVSVGQEVEVMVLEIDEEKRRISLGLKQ 358 (565)
T ss_pred e----EEEEe--CCCCEEEEEHHHcC------------ccccccCHHH----hcCCCCEEEEEEEEEcCCCCEEEEehHH
Confidence 9 99988 78999999 57765 3332333332 45899998 7999999999999999
Q ss_pred hhhhhhHHhhhhcccCC
Q 024995 243 HCNEYWNVFHETAIVNN 259 (259)
Q Consensus 243 ~~~~p~~~~~~~~~~~~ 259 (259)
+..+||..+.++|++|.
T Consensus 359 ~~~~p~~~~~~~~~~G~ 375 (565)
T PRK06299 359 CKENPWEEFAEKYPVGD 375 (565)
T ss_pred hccchhhhHHHhCCCCC
Confidence 99999999999999874
No 9
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=99.97 E-value=9.9e-31 Score=253.08 Aligned_cols=202 Identities=29% Similarity=0.504 Sum_probs=175.6
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCc
Q 024995 22 TGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW 93 (259)
Q Consensus 22 vG~~v~~~Vl~id~~~~~v~lS~k~~---~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~ 93 (259)
+|+++.|+|+.+|++++++.+|+|.. +|+.+...+++|+++.|+ ++|+||+++ .+++||+|+++++|
T Consensus 233 vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~-----~~v~g~v~~sels~ 307 (516)
T TIGR00717 233 VGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIE-----EGIEGLVHVSEMSW 307 (516)
T ss_pred CCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHHhhccCCCEEEEEEEEeeCCcEEEEeC-----CCCEEEEEHHHcCC
Confidence 89999999999999999999999965 588888889999999999 999999997 48999999999998
Q ss_pred c-cccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCccc
Q 024995 94 D-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGA 172 (259)
Q Consensus 94 ~-~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~ 172 (259)
. ...++.+.|++||.|+|+|+++|++++++.||+|++..+||....+. +.. |+.+.|+|+++.+||
T Consensus 308 ~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~-~~~--------G~~v~g~V~~v~~~G---- 374 (516)
T TIGR00717 308 VKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEK-HPV--------GDRVTGKIKKITDFG---- 374 (516)
T ss_pred ccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHh-CCC--------CCEEEEEEEEEecce----
Confidence 6 46678888999999999999999999999999999999999866554 343 667999999999999
Q ss_pred eeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchhhhhh
Q 024995 173 IFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRHCNEY 247 (259)
Q Consensus 173 ~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~~~~p 247 (259)
+|++| .+|++||+ .++++ |.....++.. .+++||.| +++|.++++|.||+|++..+|
T Consensus 375 ~fV~l--~~~v~glv~~s~ls------------~~~~~~~~~~----~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p 436 (516)
T TIGR00717 375 AFVEL--EGGIDGLIHLSDIS------------WDKDGREADH----LYKKGDEIEAVVLAVDKEKKRISLGVKQLTENP 436 (516)
T ss_pred EEEEC--CCCCEEEEEHHHCc------------CcccCCCHhH----ccCCCCEEEEEEEEEeCcCCEEEEeeccccCCc
Confidence 99888 78999999 67766 3322222223 45999997 899999999999999999999
Q ss_pred hHHhhhhcccCC
Q 024995 248 WNVFHETAIVNN 259 (259)
Q Consensus 248 ~~~~~~~~~~~~ 259 (259)
|..+.+.|++|.
T Consensus 437 ~~~~~~~~~~G~ 448 (516)
T TIGR00717 437 WEKFAAKYKVGS 448 (516)
T ss_pred hhhhhhccCcce
Confidence 999999898874
No 10
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.97 E-value=1.3e-30 Score=244.41 Aligned_cols=197 Identities=24% Similarity=0.404 Sum_probs=170.8
Q ss_pred cCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEE
Q 024995 20 GLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVH 87 (259)
Q Consensus 20 ~~vG~~v~~~Vl~id~~~~~v~lS~k~~-------~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~ 87 (259)
.++|+++.|+|+++|++++++.+|+|.. .|..++..+++|+++.|+ ++|+||+++ +++||||
T Consensus 147 ~~vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~------~v~g~v~ 220 (390)
T PRK06676 147 DFKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIG------GVDGLVH 220 (390)
T ss_pred HcCCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeC------CeEEEEE
Confidence 4599999999999999999999999874 245567789999999999 899999996 7999999
Q ss_pred ceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccC
Q 024995 88 VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPL 167 (259)
Q Consensus 88 isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~ 167 (259)
+++++|.++.++.+.|++||.|+|+|+++|+++++|.||+|++.++||....+. +. +|+.+.|+|+++.+|
T Consensus 221 ~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~-~~--------~G~~v~g~V~~i~~~ 291 (390)
T PRK06676 221 ISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEK-LP--------EGDVIEGTVKRLTDF 291 (390)
T ss_pred HHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhh-hc--------CCcEEEEEEEEEeCc
Confidence 999999999999999999999999999999999999999999999999765443 33 366699999999999
Q ss_pred CCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhch
Q 024995 168 PGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKR 242 (259)
Q Consensus 168 G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~ 242 (259)
| +|+++ .+|+.||+ +|+++... ...++. .+++||.| +++|.++++|+||+|+
T Consensus 292 G----~fV~l--~~gi~Glv~~se~~~~~-------------~~~~~~----~~~~Gd~v~v~V~~id~e~~~i~ls~k~ 348 (390)
T PRK06676 292 G----AFVEV--LPGVEGLVHISQISHKH-------------IATPSE----VLEEGQEVKVKVLEVNEEEKRISLSIKA 348 (390)
T ss_pred e----EEEEE--CCCCeEEEEhHHcCccc-------------cCChhh----ccCCCCEEEEEEEEEECCCCEEEEEEEe
Confidence 9 99988 78999999 67765221 122222 56999999 7999999999999999
Q ss_pred hhhhhhHHhhhh
Q 024995 243 HCNEYWNVFHET 254 (259)
Q Consensus 243 ~~~~p~~~~~~~ 254 (259)
+..+||+.+.++
T Consensus 349 ~~~~~~~~~~~~ 360 (390)
T PRK06676 349 LEEAPAEEEDRR 360 (390)
T ss_pred cccChhhhhhhh
Confidence 999999998765
No 11
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.97 E-value=5.1e-30 Score=250.70 Aligned_cols=202 Identities=29% Similarity=0.481 Sum_probs=175.4
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCc
Q 024995 22 TGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW 93 (259)
Q Consensus 22 vG~~v~~~Vl~id~~~~~v~lS~k~~---~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~ 93 (259)
+||+|.|+|+.+|++++++.||++.. +|+.+...+++|+++.|+ ++|+||+++ .|++||+|+++++|
T Consensus 247 vG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~-----~~v~Glv~~sel~~ 321 (565)
T PRK06299 247 VGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKYPVGSKVKGKVTNITDYGAFVELE-----EGIEGLVHVSEMSW 321 (565)
T ss_pred CCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeC-----CCCEEEEEHHHcCc
Confidence 89999999999999999999999964 588888889999999999 999999998 58999999999998
Q ss_pred c-cccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCccc
Q 024995 94 D-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGA 172 (259)
Q Consensus 94 ~-~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~ 172 (259)
. +..+|.+.|++||.|+|+|+++|++++++.||+|++..+||....+. ++. |+++.|+|.++.++|
T Consensus 322 ~~~~~~~~~~~~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~-~~~--------G~~v~g~V~~v~~~G---- 388 (565)
T PRK06299 322 TKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEK-YPV--------GDVVEGKVKNITDFG---- 388 (565)
T ss_pred cccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHh-CCC--------CCEEEEEEEEEecce----
Confidence 6 46788888999999999999999999999999999999999866554 443 666999999999999
Q ss_pred eeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchhhhhh
Q 024995 173 IFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRHCNEY 247 (259)
Q Consensus 173 ~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~~~~p 247 (259)
+|++| .+|++|++ .|++++. .....+.. .+++||.| +++|.++++|.||+|++..+|
T Consensus 389 ~fV~l--~~~v~g~i~~s~l~~~------------~~~~~~~~----~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p 450 (565)
T PRK06299 389 AFVGL--EGGIDGLVHLSDISWD------------KKGEEAVE----LYKKGDEVEAVVLKVDVEKERISLGIKQLEEDP 450 (565)
T ss_pred EEEEC--CCCCEEEEEHHHcCcc------------ccccChHh----hCCCCCEEEEEEEEEeCCCCEEEEEEehhhcCc
Confidence 99988 77999999 6776622 11122222 55999999 789999999999999999999
Q ss_pred hHHhhhhcccCC
Q 024995 248 WNVFHETAIVNN 259 (259)
Q Consensus 248 ~~~~~~~~~~~~ 259 (259)
|..+.+.+++|.
T Consensus 451 ~~~~~~~~~~G~ 462 (565)
T PRK06299 451 FEEFAKKHKKGS 462 (565)
T ss_pred hhHHHhhcCCCC
Confidence 999999888874
No 12
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=99.97 E-value=1.6e-29 Score=244.72 Aligned_cols=205 Identities=27% Similarity=0.525 Sum_probs=176.4
Q ss_pred cccCCCCEEEEEEEEEeCCCCEEEEEechhh-------HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEE
Q 024995 18 AKGLTGSIISVKVIQANEEMKKLVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL 85 (259)
Q Consensus 18 ~~~~vG~~v~~~Vl~id~~~~~v~lS~k~~~-------~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~gl 85 (259)
...++|++++|+|+.+|..++++.+|+|... ++..+..+++|++++|+ ++|+||+++ |++||
T Consensus 140 ~~~~vG~~i~~~v~~~~~~~~~iv~Srk~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l~------g~~g~ 213 (516)
T TIGR00717 140 LDSLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKGVVKNITDFGAFVDLG------GVDGL 213 (516)
T ss_pred hhhhCCCEEEEEEEEEECCCCcEEEEHHHHHHHHHHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEEE
Confidence 3457999999999999999999999998752 44567789999999999 899999996 79999
Q ss_pred EEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeec
Q 024995 86 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIE 165 (259)
Q Consensus 86 v~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~ 165 (259)
+|.++++|.+..++.+.|++||.+.|+|+++|++++++.||+|.+.++||....+. +. +|++++|+|+++.
T Consensus 214 lp~~e~s~~~~~~~~~~~~vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~-~~--------~G~i~~g~V~~v~ 284 (516)
T TIGR00717 214 LHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKK-FP--------VGDKITGRVTNLT 284 (516)
T ss_pred EEHHHcCCCCCCCHHHhccCCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHHhh-cc--------CCCEEEEEEEEee
Confidence 99999999999999999999999999999999999999999999999999865443 34 3677999999999
Q ss_pred cCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhh
Q 024995 166 PLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKAS 240 (259)
Q Consensus 166 ~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~ 240 (259)
++| +|++| .+|+.||+ .|+++ |.....++. ..+++||.| +++|.++++|.||+
T Consensus 285 ~~G----~fV~l--~~~v~g~v~~sels------------~~~~~~~~~----~~~~vG~~v~v~V~~id~~~~~i~lS~ 342 (516)
T TIGR00717 285 DYG----VFVEI--EEGIEGLVHVSEMS------------WVKKNSHPS----KVVKKGDEVEVMILDIDPERRRLSLGL 342 (516)
T ss_pred CCc----EEEEe--CCCCEEEEEHHHcC------------CccccCCHH----HhccCCCEEEEEEEEEcCCCCEEEEEe
Confidence 999 99988 78999999 57765 322122222 246899999 68899999999999
Q ss_pred chhhhhhhHHhhhhcccCC
Q 024995 241 KRHCNEYWNVFHETAIVNN 259 (259)
Q Consensus 241 k~~~~~p~~~~~~~~~~~~ 259 (259)
|++.++||..+.+.+++|.
T Consensus 343 k~~~~~p~~~~~~~~~~G~ 361 (516)
T TIGR00717 343 KQCKANPWEQFEEKHPVGD 361 (516)
T ss_pred hhcccCcHHHHHHhCCCCC
Confidence 9999999999999998874
No 13
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.96 E-value=5.1e-29 Score=238.20 Aligned_cols=196 Identities=19% Similarity=0.405 Sum_probs=165.8
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecC
Q 024995 22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS 92 (259)
Q Consensus 22 vG~~v~~~Vl~id~~~~~v~lS~k~~----~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels 92 (259)
+|++|+|+|+.+|.+++++.||+|.+ .|+.+...++.|+++.|+ ++|+||++ |++||||.|+++
T Consensus 82 vGd~Ie~~V~~~~~~~g~liLS~k~~~~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~Vdl-------Gi~gflP~Sel~ 154 (486)
T PRK07899 82 VGDEVEALVLQKEDKEGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDI-------GLRGFLPASLVE 154 (486)
T ss_pred CCCEEEEEEEEEECCCCeEEEEehhhcccchHHHHHHHhcCCCEEEEEEEEEECCeEEEEE-------CCEEEEEhhHhc
Confidence 99999999999999999999999975 366666667899999999 88999999 489999999999
Q ss_pred cccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEecccc----CcchHhhhhhcCCCCccccCCCCccccceeeeccCC
Q 024995 93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE----DPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLP 168 (259)
Q Consensus 93 ~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~----~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G 168 (259)
+.++.++..+ +||.|+|+|+++|++++++.||+|.... .+|..+... ++ +|+++.|+|+++++||
T Consensus 155 ~~~~~~~~~~--vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~-lk--------~G~iv~G~V~~i~~~G 223 (486)
T PRK07899 155 MRRVRDLQPY--IGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQ-LQ--------KGQVRKGVVSSIVNFG 223 (486)
T ss_pred ccccCChhhc--CCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHh-cc--------CCCEEEEEEEEEECCe
Confidence 9888887763 8999999999999999999999996443 567655443 33 4777999999999999
Q ss_pred CccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchh
Q 024995 169 GLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRH 243 (259)
Q Consensus 169 ~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~ 243 (259)
+|++| +|++||+ .|+++ |-. +.+++. .+++||.| +++|.++++|+||+|++
T Consensus 224 ----~FVdl---ggv~Glv~~Sels------------~~~-v~~~~~----~~kvGd~V~vkVl~iD~e~~rI~LSlK~~ 279 (486)
T PRK07899 224 ----AFVDL---GGVDGLVHVSELS------------WKH-IDHPSE----VVEVGQEVTVEVLDVDMDRERVSLSLKAT 279 (486)
T ss_pred ----EEEEE---CCEEEEEEHHHCC------------Ccc-cCCHHH----hcCCCCEEEEEEEEEECCCCEEEEEEeec
Confidence 99998 5899999 67777 322 232333 56999999 78999999999999999
Q ss_pred hhhhhHHhhhhcccCC
Q 024995 244 CNEYWNVFHETAIVNN 259 (259)
Q Consensus 244 ~~~p~~~~~~~~~~~~ 259 (259)
.++||+.+.++|++|.
T Consensus 280 ~~dPw~~~~~~~~vG~ 295 (486)
T PRK07899 280 QEDPWQQFARTHAIGQ 295 (486)
T ss_pred cccchhhhHHhcCCCC
Confidence 9999999999998873
No 14
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.96 E-value=1.1e-28 Score=225.40 Aligned_cols=189 Identities=15% Similarity=0.266 Sum_probs=156.7
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecC
Q 024995 22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS 92 (259)
Q Consensus 22 vG~~v~~~Vl~id~~~~~v~lS~k~~----~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels 92 (259)
+|++++|+|+++|.+++++.||+|.. .|+.+....+.|+++.|+ ++|+||+++ |++||||+|+++
T Consensus 78 ~G~~v~~~Vi~~~~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l~------Gv~gfip~s~ls 151 (318)
T PRK07400 78 PNETREFFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIE------GLRGFIPGSHIS 151 (318)
T ss_pred CCCEEEEEEEEEeCCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHcC
Confidence 89999999999999999999999875 477777778889999998 899999996 899999999999
Q ss_pred cccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCccc
Q 024995 93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGA 172 (259)
Q Consensus 93 ~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~ 172 (259)
|.+.. +.+ +|+.+.++|+++|+++++|.||+|.+...+ .... ++ +|+++.|+|+++++||
T Consensus 152 ~~~~~---~~~-vG~~i~~kVl~id~~~~~i~lS~K~~~~~~---~~~~-~k--------~G~vv~G~V~~I~~~G---- 211 (318)
T PRK07400 152 TRKPK---EEL-VGEELPLKFLEVDEERNRLVLSHRRALVER---KMNR-LE--------VGEVVVGTVRGIKPYG---- 211 (318)
T ss_pred ccCCc---ccc-CCCEEEEEEEEEEcccCEEEEEhhHhhhhh---hhcc-CC--------CCCEEEEEEEEEECCe----
Confidence 96433 334 899999999999999999999999765432 1222 33 4777999999999999
Q ss_pred eeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchhhhhh
Q 024995 173 IFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRHCNEY 247 (259)
Q Consensus 173 ~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~~~~p 247 (259)
+|+++ +|+.||+ +|++++.+ ... ....+++||.| +++|.++++|+||+|++.++|
T Consensus 212 ~fV~i---~gv~Gllhisels~~~-------------~~~----~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~~P 271 (318)
T PRK07400 212 AFIDI---GGVSGLLHISEISHEH-------------IET----PHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEP 271 (318)
T ss_pred EEEEE---CCEEEEEEHHHccccc-------------ccC----hhhccCCCCEEEEEEEEEeCCCCEEEEEEeccccCh
Confidence 99988 5899999 67776331 111 22356999999 688999999999999999999
Q ss_pred hHHhhhhcc
Q 024995 248 WNVFHETAI 256 (259)
Q Consensus 248 ~~~~~~~~~ 256 (259)
|+.+.....
T Consensus 272 ~~~~~~~~~ 280 (318)
T PRK07400 272 GDMLKDPQK 280 (318)
T ss_pred hhhhhhHHH
Confidence 988876644
No 15
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.95 E-value=5.6e-27 Score=232.37 Aligned_cols=191 Identities=30% Similarity=0.519 Sum_probs=165.5
Q ss_pred ccCCCCEEEEEEEEEeCCCCE-EEEEechhh-------HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEE
Q 024995 19 KGLTGSIISVKVIQANEEMKK-LVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL 85 (259)
Q Consensus 19 ~~~vG~~v~~~Vl~id~~~~~-v~lS~k~~~-------~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~gl 85 (259)
+.++|+++.|+|+++|+++++ +.+|+|... ++..+..+++|+++.|+ ++|+||+++ +++||
T Consensus 430 ~~~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l~------gv~Gl 503 (647)
T PRK00087 430 SEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIG------GVDGL 503 (647)
T ss_pred HHhCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEEC------CEEEE
Confidence 346999999999999999888 999998763 44567789999999999 899999995 89999
Q ss_pred EEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeec
Q 024995 86 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIE 165 (259)
Q Consensus 86 v~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~ 165 (259)
+|+++++|.++.++.+.|++||.|+|+|+++|++++++.||+|++.++||.....+ +.. |+.+.|+|+++.
T Consensus 504 l~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~-~~~--------G~~v~g~V~~i~ 574 (647)
T PRK00087 504 LHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEK-YPV--------GSIVLGKVVRIA 574 (647)
T ss_pred EEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhh-ccC--------CeEEEEEEEEEE
Confidence 99999999999999999999999999999999999999999999999999765444 343 666999999999
Q ss_pred cCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhh
Q 024995 166 PLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKAS 240 (259)
Q Consensus 166 ~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~ 240 (259)
+|| +|++| .+|+.||+ .++++++. ...+.. .+++||.| +++|.++++|+||+
T Consensus 575 ~~G----~fV~l--~~~i~Gli~~sel~~~~-------------~~~~~~----~~kvGd~V~vkV~~id~e~~rI~lsl 631 (647)
T PRK00087 575 PFG----AFVEL--EPGVDGLVHISQISWKR-------------IDKPED----VLSEGEEVKAKILEVDPEEKRIRLSI 631 (647)
T ss_pred CCe----EEEEE--CCCCEEEEEhhhcCccc-------------cCCHhh----cCCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 999 99988 78999999 67766331 122222 56999999 79999999999999
Q ss_pred chhhhhh
Q 024995 241 KRHCNEY 247 (259)
Q Consensus 241 k~~~~~p 247 (259)
|++.++|
T Consensus 632 k~~~~~~ 638 (647)
T PRK00087 632 KEVEEEP 638 (647)
T ss_pred eecccCc
Confidence 9999998
No 16
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.95 E-value=3.8e-27 Score=220.91 Aligned_cols=197 Identities=20% Similarity=0.360 Sum_probs=166.3
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecC
Q 024995 22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS 92 (259)
Q Consensus 22 vG~~v~~~Vl~id~~~~~v~lS~k~~----~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels 92 (259)
+|++|+|+|+.+|.+++++.||++.. .|+.+...++.|+++.|+ ++|+||+++ |++||||+++++
T Consensus 65 vGd~v~~~V~~v~~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~------G~~gflp~~el~ 138 (390)
T PRK06676 65 VGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVE------GVRGFIPASLIS 138 (390)
T ss_pred CCCEEEEEEEEEECCCCCEEEEHHHhhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHcC
Confidence 99999999999999999999999974 477777788999999999 899999996 789999999999
Q ss_pred cccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccC----cchHhhhhhcCCCCccccCCCCccccceeeeccCC
Q 024995 93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEED----PLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLP 168 (259)
Q Consensus 93 ~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~----p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G 168 (259)
+.+..++.++ +||.+.|+|+++|.+++++.||+|.+... +|...... +. +|++++|+|.++.++|
T Consensus 139 ~~~~~~~~~~--vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~-~~--------~G~~v~g~V~~v~~~G 207 (390)
T PRK06676 139 TRFVEDFSDF--KGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSS-LK--------EGDVVEGTVARLTDFG 207 (390)
T ss_pred CccCCChHHc--CCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhh-CC--------CCCEEEEEEEEEecce
Confidence 9988888764 89999999999999999999999987653 55443333 23 4777999999999999
Q ss_pred CccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchh
Q 024995 169 GLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRH 243 (259)
Q Consensus 169 ~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~ 243 (259)
+|+.+ +|++||+ .|++++. + .. ++...+++||.| +++|.++++|.||+|++
T Consensus 208 ----~fV~l---~~v~g~v~~sels~~----------~---~~----~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~ 263 (390)
T PRK06676 208 ----AFVDI---GGVDGLVHISELSHE----------R---VE----KPSEVVSVGQEVEVKVLSIDWETERISLSLKDT 263 (390)
T ss_pred ----EEEEe---CCeEEEEEHHHcCcc----------c---cC----CHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence 99988 5899999 5776632 1 12 133356999999 68899999999999999
Q ss_pred hhhhhHHhhhhcccCC
Q 024995 244 CNEYWNVFHETAIVNN 259 (259)
Q Consensus 244 ~~~p~~~~~~~~~~~~ 259 (259)
..+||+.+.+.|.+|.
T Consensus 264 ~~~~~~~~~~~~~~G~ 279 (390)
T PRK06676 264 LPGPWEGVEEKLPEGD 279 (390)
T ss_pred ccCccccchhhhcCCc
Confidence 9999999998888873
No 17
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.93 E-value=3.4e-25 Score=219.72 Aligned_cols=197 Identities=19% Similarity=0.369 Sum_probs=166.2
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecC
Q 024995 22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS 92 (259)
Q Consensus 22 vG~~v~~~Vl~id~~~~~v~lS~k~~----~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels 92 (259)
+|++++|+|+.+|.+++++.||++.. .|+.+...+++|+++.|+ ++|+||+++ |++||||.++++
T Consensus 349 vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lg------gi~gfiP~sel~ 422 (647)
T PRK00087 349 VGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYG------GVRAFLPASHVE 422 (647)
T ss_pred CCCEEEEEEEEEECCCCcEEEEeehhcchhHHHHHHHHhhCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHhC
Confidence 99999999999999999999999875 377777788999999999 889999997 799999999999
Q ss_pred cccccChhhhcCCCCeEEEEEEEEeCCCCe-eEEEEecccc----CcchHhhhhhcCCCCccccCCCCccccceeeeccC
Q 024995 93 WDLIQDIRDILNEGDEVRVKVIKIDREKSR-ITLSIKQLEE----DPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPL 167 (259)
Q Consensus 93 ~~~~~~~~~~~~~Gd~V~vkVl~id~~~~r-i~lS~K~~~~----~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~ 167 (259)
+.+..++.++ +|+.++|+|+++|.++++ +.+|+|.... .+|....++ +. +|+.+.|+|.++.++
T Consensus 423 ~~~~~d~~~~--vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~-l~--------~G~iV~g~V~~v~~~ 491 (647)
T PRK00087 423 LGYVEDLSEY--KGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNS-LE--------EGDVVEGEVKRLTDF 491 (647)
T ss_pred ccccCCHHHh--CCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHh-CC--------CCCEEEEEEEEEeCC
Confidence 9988888764 899999999999998888 9999998753 455444333 23 477799999999999
Q ss_pred CCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhch
Q 024995 168 PGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKR 242 (259)
Q Consensus 168 G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~ 242 (259)
| +|+++ +|++||+ +|++++. . ... .+..+++||.| +++|.++++|.||+|+
T Consensus 492 G----~fV~l---~gv~Gll~~sels~~------------~-~~~----~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~ 547 (647)
T PRK00087 492 G----AFVDI---GGVDGLLHVSEISWG------------R-VEK----PSDVLKVGDEIKVYILDIDKENKKLSLSLKK 547 (647)
T ss_pred c----EEEEE---CCEEEEEEHHHcCcc------------c-cCC----HHHhcCCCCEEEEEEEEEECCCCEEEEEeec
Confidence 9 99888 7999999 5776632 1 121 23356999999 6889999999999999
Q ss_pred hhhhhhHHhhhhcccCC
Q 024995 243 HCNEYWNVFHETAIVNN 259 (259)
Q Consensus 243 ~~~~p~~~~~~~~~~~~ 259 (259)
+.++||..+.++|++|.
T Consensus 548 ~~~~p~~~~~~~~~~G~ 564 (647)
T PRK00087 548 LLPDPWENVEEKYPVGS 564 (647)
T ss_pred cccChhhhhhhhccCCe
Confidence 99999999999998873
No 18
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.85 E-value=1.3e-20 Score=172.41 Aligned_cols=165 Identities=15% Similarity=0.199 Sum_probs=134.0
Q ss_pred HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCee
Q 024995 49 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRI 123 (259)
Q Consensus 49 ~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri 123 (259)
++++...++.|+++.|+ ++|+||+|+ .+.+||||.+|++|.++.++.+.|++||.++|+|+++|.+++++
T Consensus 22 le~~~~~~~~G~iv~G~V~~i~~~g~~Vdig-----~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i 96 (318)
T PRK07400 22 LDKYDYHFKPGDIVNGTVFSLEPRGALIDIG-----AKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQL 96 (318)
T ss_pred HHhhHhhcCCCCEEEEEEEEEECCEEEEEEC-----CCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeE
Confidence 44444568999999999 799999997 47899999999999999999999999999999999999999999
Q ss_pred EEEEecccc-CcchHhhhhhcCCCCccccCCCCccccceeeeccCCCccceeeeecccCCeeEEE-Eccccccccccchh
Q 024995 124 TLSIKQLEE-DPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQD 201 (259)
Q Consensus 124 ~lS~K~~~~-~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~ 201 (259)
.||+|++.. ++|.... ..+.. |+.++|+|.++.++| +|+.| +|++||+ .|++++.
T Consensus 97 ~lS~k~~~~~~~w~~l~-~~~~~--------~~~V~g~V~~~~~~G----~~V~l---~Gv~gfip~s~ls~~------- 153 (318)
T PRK07400 97 TLSIRRIEYMRAWERVR-QLQKE--------DATVRSEVFATNRGG----ALVRI---EGLRGFIPGSHISTR------- 153 (318)
T ss_pred EEehhhhhhhhHHHHHH-HhccC--------CCEEEEEEEEEECCe----EEEEE---CCEEEEEEHHHcCcc-------
Confidence 999998764 8897543 33443 556999999999999 99988 5999999 6776521
Q ss_pred hhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchhhhhhhHHhhhhcccC
Q 024995 202 LQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRHCNEYWNVFHETAIVN 258 (259)
Q Consensus 202 ~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~~~~p~~~~~~~~~~~ 258 (259)
. .. . . .+|+.+ +++|+++++|.||+|++..+ ....+|++|
T Consensus 154 -----~-~~---~-~----~vG~~i~~kVl~id~~~~~i~lS~K~~~~~---~~~~~~k~G 197 (318)
T PRK07400 154 -----K-PK---E-E----LVGEELPLKFLEVDEERNRLVLSHRRALVE---RKMNRLEVG 197 (318)
T ss_pred -----C-Cc---c-c----cCCCEEEEEEEEEEcccCEEEEEhhHhhhh---hhhccCCCC
Confidence 0 00 1 1 388887 89999999999999986643 345566766
No 19
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.75 E-value=4.2e-18 Score=154.38 Aligned_cols=116 Identities=23% Similarity=0.304 Sum_probs=99.6
Q ss_pred CCC-CCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995 55 RVN-VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (259)
Q Consensus 55 ~l~-~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K 128 (259)
.+. +|+++.|+ +||+||+|.+|+ |++||||+|||||.++.++++.+++||.+.|+|+++|+++++|.||+|
T Consensus 13 ~~P~~GdvV~g~V~~I~d~GafV~L~EY~---gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K 89 (319)
T PTZ00248 13 KFPEEDDLVMVKVVRITEMGAYVSLLEYD---DIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKK 89 (319)
T ss_pred hCCCCCCEEEEEEEEEeCCeEEEEecCCC---CcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEee
Confidence 455 89999998 999999996432 799999999999999999999999999999999999999999999999
Q ss_pred ccccCcchHhhhhhcCCCCccccCCCCccccceeeecc-CCCccceeee-----ecccCCeeEEE
Q 024995 129 QLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEP-LPGLGAIFEE-----LLQEDGIDDVR 187 (259)
Q Consensus 129 ~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~-~G~~~~~fv~-----l~~~~gv~gl~ 187 (259)
++.++||.....+ ++. |..++|+|.++.+ || +|++ + ..|++.++-
T Consensus 90 ~v~~~pw~~~~e~-~~~--------g~~v~~~V~~ia~~~g----~~~eely~~i-~~pl~~~~g 140 (319)
T PTZ00248 90 RVSPEDIEACEEK-FSK--------SKKVHSIMRHIAQKHG----MSVEELYTKI-IWPLYKKYG 140 (319)
T ss_pred ecccchHHHHHHh-CcC--------CCEEEEEEEEchhhcC----CCHHHHHHHH-HHHHHHhcC
Confidence 9999999876665 555 5559999999954 99 6654 1 247778876
No 20
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.67 E-value=4.6e-17 Score=126.96 Aligned_cols=76 Identities=45% Similarity=0.732 Sum_probs=71.3
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (259)
Q Consensus 55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~ 129 (259)
.+++|++++|+ +|||||+|++ |-.|||||||+++.|+.++.+++++||+|.|+|+++|. +++|+||+|.
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~-----g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~ 75 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEG-----GKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRK 75 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecC-----CCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcceehHH
Confidence 57899999999 9999999983 89999999999999999999999999999999999997 9999999999
Q ss_pred cccCcch
Q 024995 130 LEEDPLL 136 (259)
Q Consensus 130 ~~~~p~~ 136 (259)
+...|-.
T Consensus 76 ~~e~pe~ 82 (129)
T COG1098 76 LEEEPEK 82 (129)
T ss_pred hhhCccc
Confidence 9888753
No 21
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.58 E-value=2.6e-14 Score=146.11 Aligned_cols=190 Identities=20% Similarity=0.229 Sum_probs=151.2
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechhh-----------HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEE
Q 024995 22 TGSIISVKVIQANEEMKKLVFSEKDAV-----------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL 85 (259)
Q Consensus 22 vG~~v~~~Vl~id~~~~~v~lS~k~~~-----------~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~gl 85 (259)
.++.+.++++.++..++.+.+|.|... -....++++.|+++.|+ +.|+|+.+. +++++|
T Consensus 1115 ~~~~v~~~~L~vs~~n~~leLslr~sr~~~t~~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glfi~ls-----~~v~a~ 1189 (1710)
T KOG1070|consen 1115 KIQIVYVCVLSVSALNKGLELSLRESRTKITPVDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLFIALS-----RKVEAF 1189 (1710)
T ss_pred cccEEEEEEEEEecccccceeecccccccCccccccCCcccchhhcccCceeEEEEEEecCCcEEEEEc-----cceEEE
Confidence 679999999999999888999998421 12346789999999999 889999998 699999
Q ss_pred EEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeec
Q 024995 86 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIE 165 (259)
Q Consensus 86 v~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~ 165 (259)
+|+|++++.+...|+..|++||.+.++|++++...+|+.|++|.....--...+.. + .....|+...|+|.++.
T Consensus 1190 v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~~~~~~~-~-----~~l~~gd~~~g~v~~~~ 1263 (1710)
T KOG1070|consen 1190 VPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKNSDIKDTVKLLKD-S-----KDLKKGDREDGTVEVVD 1263 (1710)
T ss_pred EEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEeccccCCchhhhhh-h-----hhhhccccccceEEEec
Confidence 99999999999999999999999999999999999999999998654322221111 1 11245777999999999
Q ss_pred cCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhh
Q 024995 166 PLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKAS 240 (259)
Q Consensus 166 ~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~ 240 (259)
||| .|+.+.....+.|+| +++++..+. . .++.....|+.| ++++.+.++|++++
T Consensus 1264 ~~G----~fi~l~~tv~~~g~~~~~e~~d~~~----------e-------~it~~~~~~~~V~a~~lk~~~ek~rIsl~~ 1322 (1710)
T KOG1070|consen 1264 PFG----LFIKLDVTVNMVGLCHISEEADDRG----------E-------NITALYYAGDRVKACVLKEDSEKKRISLGL 1322 (1710)
T ss_pred CCc----eEEEecCcceecccccceeecchhh----------h-------hcccceeccceeeeEeeeccchhhhhhhhh
Confidence 999 999995545569999 777774431 1 122233677777 89999999999999
Q ss_pred chh
Q 024995 241 KRH 243 (259)
Q Consensus 241 k~~ 243 (259)
|..
T Consensus 1323 k~s 1325 (1710)
T KOG1070|consen 1323 KSS 1325 (1710)
T ss_pred hhh
Confidence 973
No 22
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.55 E-value=1.6e-14 Score=105.01 Aligned_cols=66 Identities=26% Similarity=0.423 Sum_probs=60.6
Q ss_pred CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccCh---hhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI---RDILNEGDEVRVKVIKIDREKSRITLS 126 (259)
Q Consensus 56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~---~~~~~~Gd~V~vkVl~id~~~~ri~lS 126 (259)
+++|+++.|+ +||+||+++ ++++||+|++++||.++.++ .+.|++||.++|+|+++|+++++|.||
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~-----~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS 74 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLS-----SSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeC-----CCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 5789999999 999999998 58999999999999987765 588999999999999999999999886
No 23
>PRK08582 hypothetical protein; Provisional
Probab=99.52 E-value=4.8e-14 Score=114.50 Aligned_cols=77 Identities=40% Similarity=0.679 Sum_probs=71.7
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (259)
Q Consensus 55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~ 129 (259)
.+++|++|.|+ +||+||+|+ .+++||||++++++.++.++.+.|++||.|+|+|+++|. .++|.||+|+
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~fV~L~-----~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~ 75 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELP-----EGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKK 75 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEEEEEC-----CCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEe
Confidence 47899999999 999999998 489999999999999999999999999999999999997 5999999999
Q ss_pred cccCcchH
Q 024995 130 LEEDPLLE 137 (259)
Q Consensus 130 ~~~~p~~~ 137 (259)
+.++||.+
T Consensus 76 ~~~~~~~~ 83 (139)
T PRK08582 76 AKDRPKRQ 83 (139)
T ss_pred cccCchhh
Confidence 99999964
No 24
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.47 E-value=1.5e-13 Score=99.22 Aligned_cols=66 Identities=20% Similarity=0.305 Sum_probs=61.1
Q ss_pred CCCCCEEEEE-----e-eeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995 56 VNVEDIFVGR-----D-YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (259)
Q Consensus 56 l~~G~iv~G~-----~-~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K 128 (259)
+++|+++.|+ + ||+||+++ .+.+|++|+|++++++..++.+.|++||.|+|+|+++|. +|+.||+|
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~-----~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~--~~i~LSl~ 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLP-----FGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECC-----CCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEEEEeC
Confidence 4789999999 4 89999998 589999999999999999999999999999999999984 99999986
No 25
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=99.47 E-value=1.8e-13 Score=98.63 Aligned_cols=69 Identities=43% Similarity=0.731 Sum_probs=64.7
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (259)
Q Consensus 55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K 128 (259)
++++|+++.|+ ++|+||+++ .+++||||++++++.+..++.+.|++||.++|+|+++|.+++++.||+|
T Consensus 1 k~~~G~iv~g~V~~v~~~g~~V~l~-----~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k 74 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDFGVFVDLG-----NGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEES-----TSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCCEEEEEEEEEECCEEEEEEC-----CcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 36899999999 899999998 4899999999999999999999999999999999999999999999986
No 26
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.47 E-value=1.8e-13 Score=101.28 Aligned_cols=71 Identities=31% Similarity=0.395 Sum_probs=66.1
Q ss_pred hccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995 52 YSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (259)
Q Consensus 52 ~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS 126 (259)
.+.++++|+++.|+ +||+||+++ .+++||+|+++++++++.++.+.|++||.|+|+|+++|.+++++.||
T Consensus 8 ~~~~~~~G~i~~g~V~~v~~~G~fv~l~-----~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~ls 82 (83)
T cd04461 8 NFSDLKPGMVVHGYVRNITPYGVFVEFL-----GGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLS 82 (83)
T ss_pred hHHhCCCCCEEEEEEEEEeeceEEEEcC-----CCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEe
Confidence 35578999999999 999999998 38999999999999999999999999999999999999999999998
Q ss_pred E
Q 024995 127 I 127 (259)
Q Consensus 127 ~ 127 (259)
+
T Consensus 83 l 83 (83)
T cd04461 83 L 83 (83)
T ss_pred C
Confidence 5
No 27
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.47 E-value=2.2e-13 Score=98.68 Aligned_cols=65 Identities=17% Similarity=0.305 Sum_probs=60.4
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccc--ccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (259)
Q Consensus 59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~--~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K 128 (259)
|+++.|+ ++|+||++. .+++|+||+++++|.. ..++.+.|++||.|+|+|+++|++++||.||+|
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~-----~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTIS-----PDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeC-----CCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 7788888 899999998 4899999999999864 789999999999999999999999999999986
No 28
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=99.46 E-value=3.9e-13 Score=97.15 Aligned_cols=66 Identities=33% Similarity=0.559 Sum_probs=59.7
Q ss_pred CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (259)
Q Consensus 57 ~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~ 127 (259)
+.|+++.|+ +||+||++.+ .+.+||+|+|+++|.++.++.+.|++||.|+|+|+++|.++ |+.||+
T Consensus 2 ~~g~~~~g~V~~i~~fG~fv~l~~----~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~ 72 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIPG----CRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL 72 (73)
T ss_pred cCCCEEEEEEEEEEeeeEEEEECC----CCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence 579999999 9999999962 24799999999999999999999999999999999999865 999986
No 29
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.45 E-value=1.4e-13 Score=138.80 Aligned_cols=87 Identities=28% Similarity=0.435 Sum_probs=77.7
Q ss_pred HhhhccCCCCCCEEE-EE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCe
Q 024995 49 WNKYSSRVNVEDIFV-GR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSR 122 (259)
Q Consensus 49 ~~~~~~~l~~G~iv~-G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~r 122 (259)
++.+....++|++|. |+ +||+||+|. .|++||||+|+|+|.++.++.+.|++||.|+|+|+++|. ++|
T Consensus 744 I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~-----~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~gr 817 (891)
T PLN00207 744 ISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIA-----PGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQ 817 (891)
T ss_pred HHHHhcCcCCCcEEECcEEEEEeccEEEEEeC-----CCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC-CCc
Confidence 445556789999995 45 999999998 489999999999999999999999999999999999997 899
Q ss_pred eEEEEeccccCcchHhhhh
Q 024995 123 ITLSIKQLEEDPLLETLEK 141 (259)
Q Consensus 123 i~lS~K~~~~~p~~~~~~~ 141 (259)
|.||+|++.++||.++...
T Consensus 818 I~LSlK~l~~~Pw~~~~~~ 836 (891)
T PLN00207 818 LRLSRRALLPEANSEKSSQ 836 (891)
T ss_pred EEEEEeccccCchhhhhhh
Confidence 9999999999999876543
No 30
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.43 E-value=4.6e-13 Score=95.55 Aligned_cols=65 Identities=29% Similarity=0.396 Sum_probs=60.6
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (259)
Q Consensus 59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K 128 (259)
|+++.|+ ++|+||++. .+++||+|++++++.+..++.+.|++||.++|+|+++|++++++.||+|
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~-----~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k 70 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFY-----NNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEEC-----CCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 6788888 999999998 3799999999999998889999999999999999999999999999986
No 31
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=99.43 E-value=1.1e-12 Score=94.96 Aligned_cols=71 Identities=34% Similarity=0.489 Sum_probs=64.1
Q ss_pred CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (259)
Q Consensus 56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~ 129 (259)
++.|+++.|+ ++|+||++.+. .+++||+|+++++++++.++.+.|++||.|+|+|+++|.+++++.||+|+
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~---~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~ 76 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEY---GNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCC---CCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 3689999999 99999999631 15999999999999999999999999999999999999989999999874
No 32
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.42 E-value=8.7e-13 Score=94.92 Aligned_cols=68 Identities=26% Similarity=0.418 Sum_probs=63.1
Q ss_pred CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (259)
Q Consensus 56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K 128 (259)
+++|+++.|+ ++|+||+++ .+++|++|++++++++..++.+.|++||.++++|+++|.+++++.||+|
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~-----~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~ 73 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLG-----NKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeC-----CCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 4789999999 899999998 5899999999999998888889999999999999999999999999975
No 33
>PHA02945 interferon resistance protein; Provisional
Probab=99.42 E-value=9.4e-13 Score=97.09 Aligned_cols=75 Identities=31% Similarity=0.396 Sum_probs=67.6
Q ss_pred cCCCCCCEEEEE----eeeEEEEEccCCCCccEEEEEEceec--CcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995 54 SRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVSEV--SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (259)
Q Consensus 54 ~~l~~G~iv~G~----~~G~fV~l~~~~g~~gi~glv~isel--s~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~ 127 (259)
.-.++|+++.|+ +||+||.|..|+ |.+||+|+|+. +..++++ ++++ +||++.|||+++|+.++.|.||+
T Consensus 7 ~~P~~GelvigtV~~~d~ga~v~L~EY~---g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSl 81 (88)
T PHA02945 7 SLPNVGDVLKGKVYENGYALYIDLFDYP---HSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNY 81 (88)
T ss_pred cCCCCCcEEEEEEEecCceEEEEecccC---CcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEe
Confidence 345899999999 999999999754 79999999955 9999999 9999 99999999999999999999999
Q ss_pred eccccC
Q 024995 128 KQLEED 133 (259)
Q Consensus 128 K~~~~~ 133 (259)
|+..++
T Consensus 82 K~V~~~ 87 (88)
T PHA02945 82 KRMCRH 87 (88)
T ss_pred eEcccC
Confidence 987643
No 34
>PRK07252 hypothetical protein; Provisional
Probab=99.41 E-value=1.2e-12 Score=103.65 Aligned_cols=73 Identities=37% Similarity=0.674 Sum_probs=67.8
Q ss_pred CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccc
Q 024995 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131 (259)
Q Consensus 57 ~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~ 131 (259)
++|+++.|+ ++|+||++. .+++||+|++++++.++.++.+.|++||.|+|+|+++|.+++++.||+|.+.
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~-----~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~ 76 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALE-----NGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLE 76 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEEC-----CCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence 579999999 999999997 4799999999999999999999999999999999999999999999999988
Q ss_pred cCc
Q 024995 132 EDP 134 (259)
Q Consensus 132 ~~p 134 (259)
+++
T Consensus 77 ~~~ 79 (120)
T PRK07252 77 EEK 79 (120)
T ss_pred cCc
Confidence 744
No 35
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.40 E-value=1.1e-12 Score=93.56 Aligned_cols=64 Identities=22% Similarity=0.437 Sum_probs=59.6
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (259)
Q Consensus 59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~ 127 (259)
|+++.|+ ++|+||+++ .+++||+|++++++.+..++.+.|++||.++|+|+++|++++++.||+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~-----~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls~ 69 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLS-----DHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEec-----CCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 6788888 999999997 489999999999999888999999999999999999999999999985
No 36
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.40 E-value=9.2e-13 Score=94.81 Aligned_cols=57 Identities=26% Similarity=0.402 Sum_probs=53.8
Q ss_pred eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (259)
Q Consensus 66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~ 127 (259)
+||+||++. .|++||+|+|++++.+..++.+.|++||.++|+|+++|+.++++.||+
T Consensus 15 ~~G~~V~l~-----~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 15 DLGAVFELK-----DGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CceEEEEeC-----CCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 799999998 489999999999999988899999999999999999999999999985
No 37
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.39 E-value=2.3e-12 Score=93.62 Aligned_cols=68 Identities=16% Similarity=0.166 Sum_probs=60.9
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (259)
Q Consensus 55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~ 129 (259)
++++|+++.|+ ++|+||+++- .|++||+|.++++|. +.+++||.+.|+|+++|++++++.||+|+
T Consensus 1 dl~~G~~v~g~V~si~d~G~~v~~g~----~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~ 70 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHGYILDIGI----PGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADP 70 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeCC----CCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEee
Confidence 47899999999 9999999961 279999999999986 67899999999999999999999999998
Q ss_pred ccc
Q 024995 130 LEE 132 (259)
Q Consensus 130 ~~~ 132 (259)
..+
T Consensus 71 ~~~ 73 (74)
T cd05694 71 SKV 73 (74)
T ss_pred ccc
Confidence 754
No 38
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.36 E-value=3.3e-12 Score=131.06 Aligned_cols=221 Identities=21% Similarity=0.250 Sum_probs=152.6
Q ss_pred CCCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCCCEEEEEechhhHh------hhccCCCCCCEEEEE-----eeeE
Q 024995 1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWN------KYSSRVNVEDIFVGR-----DYGA 69 (259)
Q Consensus 1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vl~id~~~~~v~lS~k~~~~~------~~~~~l~~G~iv~G~-----~~G~ 69 (259)
+.++|++.+|-..+...+. +|..+.++|+.++.+.+++.++++.+... .-.....+|.++.|+ ++||
T Consensus 538 lp~~hlsd~~~~~p~~~f~--v~~~~k~RVl~~~~~~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~~G~l~~~~~~g~ 615 (1710)
T KOG1070|consen 538 LPKEHLSDHPLQPPLRDFK--VGSGVKLRVLSVNRDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLCAIKENGA 615 (1710)
T ss_pred cChHhhhhcccccccceee--eccccEEEEEEEEccCCeeEEEechhhhcccCCCccchhhcCCCceEEEEEeeeccCCe
Confidence 4678888888877765444 88888889999999999999999976432 223456799999999 8999
Q ss_pred EEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCcc
Q 024995 70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSV 149 (259)
Q Consensus 70 fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~ 149 (259)
||.+.+ |++||.|.+++++.++.++++.|.+||++.++|.++|.+++||.+++|+..- |......... .
T Consensus 616 ~V~F~g-----~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~~--~~a~~~~~~e--~-- 684 (1710)
T KOG1070|consen 616 FVTFTG-----GLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASSC--ARACVKRSVE--N-- 684 (1710)
T ss_pred EEEecC-----ccccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhhhhhh--HHHHHHHHHH--H--
Confidence 999984 8999999999999999999999999999999999999999999999997642 4321111100 0
Q ss_pred ccCCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee--
Q 024995 150 ISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV-- 226 (259)
Q Consensus 150 ~~~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V-- 226 (259)
..+|.+..+.+...+. + .+.|++ .+.|+.|+. ..++.+....++....-.+.. ..+. + .+-+|+.+
T Consensus 685 -~~~g~v~s~~~~~~tk-d---~viVei-~~~~~~~v~~~~~L~dg~v~~~~~~~~kl~~-~t~~--~--~lv~gq~~~~ 753 (1710)
T KOG1070|consen 685 -FVKGGVKSLKSIDKTK-D---SVIVEI-VDQGITGVGVFGELVDGSVVVNKVLENKLRK-NTSL--L--HLVVGQVTVG 753 (1710)
T ss_pred -hhccccccceeehhcc-c---cEEEEc-cCcceEEEEEEEEEccCceEEccchhhhhhh-cchh--h--eeeecceeEE
Confidence 0123334555555544 2 466666 133588886 666665544333332111111 1011 1 23566665
Q ss_pred --EEEecccchhhhhhchhhh
Q 024995 227 --QEIQLSHSLIRKASKRHCN 245 (259)
Q Consensus 227 --~~v~~~~~~i~ls~k~~~~ 245 (259)
+.|+..++.+.+|.++=++
T Consensus 754 ~i~~isl~k~lv~~s~~~~L~ 774 (1710)
T KOG1070|consen 754 VILSISLKKSLVLISLCTDLP 774 (1710)
T ss_pred EEEEeehhhhhhhcccccccc
Confidence 6777777777777766443
No 39
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.36 E-value=4.8e-12 Score=91.46 Aligned_cols=70 Identities=41% Similarity=0.643 Sum_probs=63.8
Q ss_pred CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEecc
Q 024995 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (259)
Q Consensus 57 ~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~ 130 (259)
++|+++.|+ ++|+||++.+ .+.+|++|++++++.+..++.+.|++||.|+|+|+++|.+++++.||+|+.
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~~----~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~ 75 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDG----TNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECC----CCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence 468899998 9999999972 269999999999999988899999999999999999999999999999874
No 40
>PRK08059 general stress protein 13; Validated
Probab=99.36 E-value=3.9e-12 Score=101.21 Aligned_cols=76 Identities=46% Similarity=0.813 Sum_probs=71.2
Q ss_pred cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995 54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (259)
Q Consensus 54 ~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K 128 (259)
..+++|+++.|+ ++|+||++. .+++||+|++++++.++.++.+.|++||.|+|+|+++|.+++++.||+|
T Consensus 3 ~~~k~G~iv~G~V~~i~~~G~fV~i~-----~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk 77 (123)
T PRK08059 3 SQYEVGSVVTGKVTGIQPYGAFVALD-----EETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77 (123)
T ss_pred ccCCCCCEEEEEEEEEecceEEEEEC-----CCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEE
Confidence 468999999999 999999998 4899999999999999989999999999999999999999999999999
Q ss_pred ccccCc
Q 024995 129 QLEEDP 134 (259)
Q Consensus 129 ~~~~~p 134 (259)
.+..+|
T Consensus 78 ~~~~~~ 83 (123)
T PRK08059 78 ATEEAP 83 (123)
T ss_pred EcccCc
Confidence 998877
No 41
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.36 E-value=2e-12 Score=91.86 Aligned_cols=63 Identities=29% Similarity=0.470 Sum_probs=58.5
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (259)
Q Consensus 59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS 126 (259)
|+++.|+ ++|+||++. .+++||+|++++++.+..++.+.|++||.++|+|+++|++++++.||
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~-----~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls 68 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLG-----RGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeC-----CCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 6778887 999999998 48999999999999999999999999999999999999999999876
No 42
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.35 E-value=4.2e-12 Score=90.92 Aligned_cols=67 Identities=33% Similarity=0.553 Sum_probs=62.0
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEecc
Q 024995 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (259)
Q Consensus 59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~ 130 (259)
|+++.|+ ++|+||++. .+++|++|+++++++++.++.+.|++||.++|+|+++|.+++++.||+|.+
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~-----~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~ 72 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLG-----DGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK 72 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeC-----CCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence 6777777 899999998 489999999999999999999999999999999999999889999999875
No 43
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.34 E-value=3.5e-12 Score=90.51 Aligned_cols=63 Identities=37% Similarity=0.748 Sum_probs=56.8
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCc-ccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (259)
Q Consensus 59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~-~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS 126 (259)
|+++.|+ +||+||++. .+++||+|+++++| .+..++.+.|++||.|+|+|+++|.+++++.||
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~-----~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLD-----GGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeC-----CCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence 6777887 999999998 48999999999997 567888899999999999999999999999875
No 44
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.34 E-value=7e-13 Score=120.50 Aligned_cols=85 Identities=16% Similarity=0.200 Sum_probs=73.1
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE 228 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~ 228 (259)
|+++.|+|++|.+|| +||.|.-.+|++||+ +|++++. |+ . +++.++++||.| ++
T Consensus 18 GdvV~g~V~~I~d~G----afV~L~EY~gvEGlIhiSElS~~----------ri---~----~i~d~vkvGd~v~vkVl~ 76 (319)
T PTZ00248 18 DDLVMVKVVRITEMG----AYVSLLEYDDIEGMILMSELSKR----------RI---R----SINKLIRVGRHEVVVVLR 76 (319)
T ss_pred CCEEEEEEEEEeCCe----EEEEecCCCCcEEEEEHHHhccc----------cc---C----CHHHhcCCCCEEEEEEEE
Confidence 667999999999999 999995457999999 7888742 23 3 244478999999 79
Q ss_pred EecccchhhhhhchhhhhhhHHhhhhcccCC
Q 024995 229 IQLSHSLIRKASKRHCNEYWNVFHETAIVNN 259 (259)
Q Consensus 229 v~~~~~~i~ls~k~~~~~p~~~~~~~~~~~~ 259 (259)
||.++++|+||+|++.++||..+.++|+.|+
T Consensus 77 VD~ekg~IdLS~K~v~~~pw~~~~e~~~~g~ 107 (319)
T PTZ00248 77 VDKEKGYIDLSKKRVSPEDIEACEEKFSKSK 107 (319)
T ss_pred EeCCCCEEEEEeeecccchHHHHHHhCcCCC
Confidence 9999999999999999999999999999874
No 45
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=99.34 E-value=7.5e-12 Score=91.58 Aligned_cols=71 Identities=35% Similarity=0.675 Sum_probs=61.7
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccc-cChhhhcCCCCeEEEEEEEEeCCCCeeEEEEecccc
Q 024995 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE 132 (259)
Q Consensus 59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~-~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~ 132 (259)
|+++.|+ +||+||++.+.- .+.+||+|+++++|.+. .++.+.|++||.|+|+|+++| ++++.+|+|++.+
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~--~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~~~ 76 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLK--GRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDVDQ 76 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCC--CCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEeccc
Confidence 5677777 999999997310 05899999999999986 899999999999999999999 7999999999876
Q ss_pred C
Q 024995 133 D 133 (259)
Q Consensus 133 ~ 133 (259)
+
T Consensus 77 ~ 77 (79)
T cd05684 77 D 77 (79)
T ss_pred C
Confidence 5
No 46
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.34 E-value=1.5e-12 Score=113.84 Aligned_cols=77 Identities=35% Similarity=0.623 Sum_probs=72.3
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (259)
Q Consensus 55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~ 129 (259)
-..+|+++-|+ +||+||.|..|+ |++||+|+||++..|+.+..+++++||.+-|+|+++|+.++.|.||+|.
T Consensus 8 ~PeeGEiVv~tV~~V~~~GAyv~L~EY~---g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkr 84 (269)
T COG1093 8 YPEEGEIVVGTVKQVADYGAYVELDEYP---GKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKR 84 (269)
T ss_pred CCCCCcEEEEEEEEeeccccEEEeeccC---CeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhh
Confidence 46899999999 999999999776 6999999999999999999999999999999999999999999999999
Q ss_pred cccCc
Q 024995 130 LEEDP 134 (259)
Q Consensus 130 ~~~~p 134 (259)
..++.
T Consensus 85 V~~~q 89 (269)
T COG1093 85 VTEHQ 89 (269)
T ss_pred CCHHH
Confidence 88765
No 47
>PRK05807 hypothetical protein; Provisional
Probab=99.33 E-value=5.5e-12 Score=102.07 Aligned_cols=70 Identities=46% Similarity=0.722 Sum_probs=65.5
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (259)
Q Consensus 55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~ 129 (259)
.+++|+++.|+ +||+||+|. +..||||++++++.++.++.+.|++||.|+|+|+++|. +++|.||+|+
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L~------~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~ 74 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEVE------GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQ 74 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEEC------CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEe
Confidence 46789999999 999999995 68999999999999999999999999999999999997 7999999999
Q ss_pred cc
Q 024995 130 LE 131 (259)
Q Consensus 130 ~~ 131 (259)
+.
T Consensus 75 ~~ 76 (136)
T PRK05807 75 AM 76 (136)
T ss_pred cc
Confidence 76
No 48
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.33 E-value=1.2e-11 Score=108.73 Aligned_cols=167 Identities=19% Similarity=0.188 Sum_probs=120.6
Q ss_pred CCCCEEEEEEEEEeCCCCEEEEEechhhHhhhccCCCCCCEEEEE------eeeEEEEEccCCCCccEEEEEEceecCcc
Q 024995 21 LTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR------DYGAFIHLRFPDGLYHLTGLVHVSEVSWD 94 (259)
Q Consensus 21 ~vG~~v~~~Vl~id~~~~~v~lS~k~~~~~~~~~~l~~G~iv~G~------~~G~fV~l~~~~g~~gi~glv~isels~~ 94 (259)
.+||+|++. ++.|.+ +++.++.+.. ...+|+.-.++ +-|+|++.+ ...+-+||.++++..
T Consensus 45 evGdev~vF-iY~D~~-~rl~aTt~~p-------~~tvg~~g~~~Vv~v~~~lGaFlD~G-----l~KDl~vp~~elp~~ 110 (287)
T COG2996 45 EVGDEVTVF-IYVDSE-DRLIATTREP-------KATVGEYGWLKVVEVNKDLGAFLDWG-----LPKDLLVPLDELPTL 110 (287)
T ss_pred ccCcEEEEE-EEECCC-Cceeheeecc-------eEeecceeEEEEEEEcCCcceEEecC-----CCcceeeehhhcccc
Confidence 399999999 889965 7788888776 34556554444 789999997 568999999999764
Q ss_pred cccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCcccee
Q 024995 95 LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIF 174 (259)
Q Consensus 95 ~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~~f 174 (259)
+ +-++++||++.|.+ .+|. ++||.-.++.- .|.+.++...-.+. -++.+.|+|++...-| .|
T Consensus 111 ~----~~wpq~Gd~l~v~l-~~Dk-k~Ri~g~~a~~---~~l~~l~~~~~~~l-----~nq~v~~tVYr~~~~G----~f 172 (287)
T COG2996 111 K----SLWPQKGDKLLVYL-YVDK-KGRIWGTLAIE---KILENLATPAYNNL-----KNQEVDATVYRLLESG----TF 172 (287)
T ss_pred c----ccCCCCCCEEEEEE-EEcc-CCcEEEEecch---hHHHhcCCccchhh-----hcCeeeeEEEEEeccc----eE
Confidence 2 23588999999998 8997 66998877532 12222221111111 1566999999999999 99
Q ss_pred eeecccCCeeEEEEccccccccccchhhhhhcccCCCCCcceeeeccC
Q 024995 175 EELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARA 222 (259)
Q Consensus 175 v~l~~~~gv~gl~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~ 222 (259)
+.+ ++|.-||+|+..+...+.+|+.++.++...+. |+++++++++
T Consensus 173 v~~--e~~~~GfIh~sEr~~~prlG~~l~~rVi~~re-Dg~lnLSl~p 217 (287)
T COG2996 173 VIT--ENGYLGFIHKSERFAEPRLGERLTARVIGVRE-DGKLNLSLRP 217 (287)
T ss_pred EEE--cCCeEEEEcchhhcccccCCceEEEEEEEEcc-CCeeeccccc
Confidence 877 89999999655555667777777777766663 6666666665
No 49
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.30 E-value=1.1e-11 Score=88.41 Aligned_cols=65 Identities=32% Similarity=0.532 Sum_probs=60.3
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (259)
Q Consensus 59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K 128 (259)
|+++.|+ ++|+||+++ .+.+|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||+|
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~-----~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIG-----YKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeC-----CCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 6788888 889999997 4799999999999999999999999999999999999988899999985
No 50
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.29 E-value=1.5e-11 Score=86.48 Aligned_cols=64 Identities=44% Similarity=0.830 Sum_probs=59.0
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (259)
Q Consensus 59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K 128 (259)
|+++.|+ ++|+||+++ .+.+||+|+++++++++.++.+.|++||.++|+|+++|. ++++.||+|
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~-----~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~-~~~i~ls~k 69 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELG-----GGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEEC-----CCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence 6777777 999999998 489999999999999999999999999999999999998 899999986
No 51
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.28 E-value=1.7e-11 Score=87.94 Aligned_cols=66 Identities=39% Similarity=0.674 Sum_probs=58.4
Q ss_pred CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcc-cccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (259)
Q Consensus 56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~-~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS 126 (259)
+++|+++.|+ +||+||++. .+++||+|+++++|. +..++.+.|++||.|+|+|+++|.+++++.++
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~-----~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELE-----EGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcC-----CCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence 4689999999 999999998 479999999999975 45577788999999999999999999998864
No 52
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.24 E-value=1.7e-11 Score=94.07 Aligned_cols=71 Identities=30% Similarity=0.466 Sum_probs=62.8
Q ss_pred CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccc-------------------cChhhhcCCCCeEEE
Q 024995 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------------------QDIRDILNEGDEVRV 111 (259)
Q Consensus 56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~-------------------~~~~~~~~~Gd~V~v 111 (259)
+++|+++.|+ ++|+||.++ .|++|++|+++++|.+. .++.+.|++||.|+|
T Consensus 1 L~~G~vV~G~V~~v~~~gl~v~L~-----~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~ 75 (100)
T cd05693 1 LSEGMLVLGQVKEITKLDLVISLP-----NGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRC 75 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEECC-----CCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEE
Confidence 5789999999 899999998 48999999999998753 347789999999999
Q ss_pred EEEEEeCC---CCeeEEEEeccc
Q 024995 112 KVIKIDRE---KSRITLSIKQLE 131 (259)
Q Consensus 112 kVl~id~~---~~ri~lS~K~~~ 131 (259)
+|+++|++ +++|.||+|...
T Consensus 76 kVi~~d~~~~~~~~i~LSlr~~~ 98 (100)
T cd05693 76 KVVSLDKSKSGKKRIELSLEPEL 98 (100)
T ss_pred EEEEccCCcCCCcEEEEEecHHH
Confidence 99999987 789999998654
No 53
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=99.21 E-value=4.2e-11 Score=84.04 Aligned_cols=63 Identities=38% Similarity=0.670 Sum_probs=57.4
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (259)
Q Consensus 59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS 126 (259)
|+++.|+ ++|+||++. .+.+||+|.+++++.++.++.+.|++||.++|+|+++|.+++++.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~-----~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIG-----VKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcC-----CCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 5677777 999999998 47999999999999988899999999999999999999988999876
No 54
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.21 E-value=7.1e-11 Score=83.67 Aligned_cols=62 Identities=27% Similarity=0.545 Sum_probs=55.7
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (259)
Q Consensus 59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K 128 (259)
|+++.|+ ++|+||+++ |++||+|.+++++.+..++.+. +||.++|+|+++|.+++++.||+|
T Consensus 1 G~iv~g~V~~v~~~G~~v~l~------g~~gfip~s~~~~~~~~~~~~~--vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDIE------GVRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHCCCcccCChHHh--CCCEEEEEEEEEeCCCCEEEEEcC
Confidence 6788887 999999995 8999999999999887777763 899999999999999999999975
No 55
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.19 E-value=8e-11 Score=105.06 Aligned_cols=77 Identities=36% Similarity=0.614 Sum_probs=69.7
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (259)
Q Consensus 55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~ 129 (259)
-+++|+++.|+ ++|+||+|..++ |++||+|+|+++++++.++.+.|++||.|.|+|+++|.++++|.||+|+
T Consensus 5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~---gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~ 81 (262)
T PRK03987 5 WPEEGELVVGTVKEVKDFGAFVTLDEYP---GKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKR 81 (262)
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCC---CcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEe
Confidence 45899999999 999999997422 7999999999999999999999999999999999999999999999998
Q ss_pred cccCc
Q 024995 130 LEEDP 134 (259)
Q Consensus 130 ~~~~p 134 (259)
+.++.
T Consensus 82 v~~~e 86 (262)
T PRK03987 82 VNEHQ 86 (262)
T ss_pred cccch
Confidence 77654
No 56
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.19 E-value=9.3e-11 Score=82.45 Aligned_cols=63 Identities=44% Similarity=0.865 Sum_probs=58.0
Q ss_pred CCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995 58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (259)
Q Consensus 58 ~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS 126 (259)
+|+++.|+ ++|+||+++ +.+|++|.+++++.+..++.+.|++||.|+|+|+++|.+++++.||
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~------~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLG------GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC------CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence 47888888 899999996 6999999999999888889999999999999999999989999876
No 57
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=99.18 E-value=1.1e-10 Score=82.21 Aligned_cols=63 Identities=44% Similarity=0.783 Sum_probs=57.3
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (259)
Q Consensus 59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~ 127 (259)
|+++.|+ ++|+||+++ .+.+||+|++++++.++.++.+.|++||.++|+|+++|. ++++.||+
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~-----~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~-~~~i~ls~ 68 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEIL-----PGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeC-----CCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence 5677777 999999998 479999999999999988889999999999999999998 89999884
No 58
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.16 E-value=9.1e-11 Score=83.21 Aligned_cols=61 Identities=20% Similarity=0.333 Sum_probs=53.4
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (259)
Q Consensus 59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS 126 (259)
|+++.|+ ++|+||++. .+++||+|.++++..+.. .+.|++||+++|+|+++|+++++|.||
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~-----~~v~g~v~~~~l~~~~~~--~~~~~~G~~i~~kVi~id~~~~~i~LS 66 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFL-----SSFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEc-----CCceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 6788888 999999997 279999999999765544 677999999999999999999999886
No 59
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=99.16 E-value=1.6e-10 Score=114.66 Aligned_cols=89 Identities=24% Similarity=0.493 Sum_probs=73.9
Q ss_pred EEEeCCCCEEEEEechhh--------Hhhhcc--CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecC---
Q 024995 31 IQANEEMKKLVFSEKDAV--------WNKYSS--RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS--- 92 (259)
Q Consensus 31 l~id~~~~~v~lS~k~~~--------~~~~~~--~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels--- 92 (259)
|+++. .+.+.++..... .+.+.. .+++|++|.|+ +||+||+|. .|++||||+||++
T Consensus 611 Idi~d-~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~dfGaFVel~-----~G~eGLvHISeisdls 684 (719)
T TIGR02696 611 ISIED-DGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFVSLL-----PGKDGLLHISQIRKLA 684 (719)
T ss_pred EEEec-CcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECceEEEEec-----CCceEEEEhhhccccc
Confidence 77775 588887765421 233444 58999999999 999999997 4899999999996
Q ss_pred -cccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995 93 -WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (259)
Q Consensus 93 -~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS 126 (259)
|.++.++.+.|++||.|+|+|+++|. ++||.|+
T Consensus 685 ~~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~ 718 (719)
T TIGR02696 685 GGKRVENVEDVLSVGQKIQVEIADIDD-RGKLSLV 718 (719)
T ss_pred cccCcCCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence 46899999999999999999999995 8999986
No 60
>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=99.15 E-value=1.4e-10 Score=86.07 Aligned_cols=70 Identities=23% Similarity=0.363 Sum_probs=62.0
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCc----ccccChhhhcCCCCeEEEEEEEEeCCCCeeEE
Q 024995 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW----DLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125 (259)
Q Consensus 55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~----~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~l 125 (259)
.+++|+++.|+ ++|+||+++ .+.+|++|++++++ .+..++.+.+++||.+.|+|+++|++ +++.|
T Consensus 3 ~p~~GdiV~g~V~~i~~~g~~v~i~-----~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~L 76 (86)
T cd05789 3 IPEVGDVVIGRVTEVGFKRWKVDIN-----SPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSL 76 (86)
T ss_pred cCCCCCEEEEEEEEECCCEEEEECC-----CCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEE
Confidence 45899999999 899999998 48999999999996 45567788899999999999999975 99999
Q ss_pred EEecc
Q 024995 126 SIKQL 130 (259)
Q Consensus 126 S~K~~ 130 (259)
|+|+.
T Consensus 77 S~~~~ 81 (86)
T cd05789 77 HTRSL 81 (86)
T ss_pred EeCcc
Confidence 99874
No 61
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.14 E-value=2.2e-11 Score=95.28 Aligned_cols=76 Identities=18% Similarity=0.189 Sum_probs=63.1
Q ss_pred CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
+.|+.++|+|+.|++|| +||+| ++|=+||+ +|+++.. |++ +++..+++||+|
T Consensus 4 kvG~~l~GkItgI~~yG----AFV~l--~~g~tGLVHISEIa~~----------fVk-------dI~d~L~vG~eV~vKV 60 (129)
T COG1098 4 KVGSKLKGKITGITPYG----AFVEL--EGGKTGLVHISEIADG----------FVK-------DIHDHLKVGQEVKVKV 60 (129)
T ss_pred cccceEEEEEEeeEecc----eEEEe--cCCCcceEEehHhhhh----------hHH-------hHHHHhcCCCEEEEEE
Confidence 45788999999999999 99999 88999998 8998733 443 355688999999
Q ss_pred EEEecccchhhhhhchhhhhhhHHh
Q 024995 227 QEIQLSHSLIRKASKRHCNEYWNVF 251 (259)
Q Consensus 227 ~~v~~~~~~i~ls~k~~~~~p~~~~ 251 (259)
+.||. +.+|+||||.+.++|-...
T Consensus 61 l~ide-~GKisLSIr~~~e~pe~~~ 84 (129)
T COG1098 61 LDIDE-NGKISLSIRKLEEEPEKQH 84 (129)
T ss_pred Eeecc-CCCcceehHHhhhCccccc
Confidence 56666 7799999999999887654
No 62
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=99.12 E-value=3.8e-10 Score=79.25 Aligned_cols=67 Identities=43% Similarity=0.725 Sum_probs=61.2
Q ss_pred CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (259)
Q Consensus 57 ~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K 128 (259)
++|+++.|+ ++|+||+++ .++.|++|.+++++.+..++.+.|++||.++|+|+++|.+++++.+|++
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~-----~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLG-----NGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeC-----CCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 368899988 899999998 4899999999999988888888999999999999999998899999975
No 63
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.12 E-value=3.2e-10 Score=113.70 Aligned_cols=93 Identities=34% Similarity=0.615 Sum_probs=78.1
Q ss_pred EEEeCCCCEEEEEechh--------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccccc
Q 024995 31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ 97 (259)
Q Consensus 31 l~id~~~~~v~lS~k~~--------~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~ 97 (259)
++++. ++.+.++.... ..+.+...+++|++|.|+ +||+||++. .+.+||+|+|++++.++.
T Consensus 587 idi~d-~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafVei~-----~~~~GllhiSels~~~v~ 660 (693)
T PRK11824 587 IDIED-DGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEIL-----PGKDGLVHISEIADERVE 660 (693)
T ss_pred cccCC-CceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEECCeEEEEEC-----CCCEEEEEeeeccCcccc
Confidence 44443 47777765432 134455678999999999 999999998 489999999999999999
Q ss_pred ChhhhcCCCCeEEEEEEEEeCCCCeeEEEEecc
Q 024995 98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (259)
Q Consensus 98 ~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~ 130 (259)
++.+.|++||.|+|+|+++|.+ +++.||+|.+
T Consensus 661 ~~~~v~kvGD~V~VkV~~iD~~-grI~LS~k~~ 692 (693)
T PRK11824 661 KVEDVLKEGDEVKVKVLEIDKR-GRIRLSRKAV 692 (693)
T ss_pred CccceeCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence 9999999999999999999986 9999999975
No 64
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=99.10 E-value=4.4e-10 Score=84.30 Aligned_cols=69 Identities=26% Similarity=0.411 Sum_probs=59.2
Q ss_pred CCCCCCEEEEE-----ee--eEEEEEccCCCCccEEEEEEceecCc---ccccChhhhcCCCCeEEEEEEEEeCCCCeeE
Q 024995 55 RVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSW---DLIQDIRDILNEGDEVRVKVIKIDREKSRIT 124 (259)
Q Consensus 55 ~l~~G~iv~G~-----~~--G~fV~l~~~~g~~gi~glv~isels~---~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~ 124 (259)
.++.|++|.|+ +| ||||+++ .|.+||||+||++| .++.++.+.+++||.|.|+|++.....+-..
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~-----~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~ 78 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIG-----LGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPR 78 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeC-----CCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCce
Confidence 57899999999 65 9999998 48999999999999 6688889999999999999999877666555
Q ss_pred EEEe
Q 024995 125 LSIK 128 (259)
Q Consensus 125 lS~K 128 (259)
||.+
T Consensus 79 lt~~ 82 (88)
T cd04453 79 LTTN 82 (88)
T ss_pred EEEE
Confidence 5543
No 65
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=99.06 E-value=1.1e-09 Score=80.33 Aligned_cols=66 Identities=30% Similarity=0.610 Sum_probs=55.8
Q ss_pred CCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccccc-----------ChhhhcCCCCeEEEEEEEEeCCCC
Q 024995 58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREKS 121 (259)
Q Consensus 58 ~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~-----------~~~~~~~~Gd~V~vkVl~id~~~~ 121 (259)
+|+++.|+ ++|+||+++. ++++|++|.+++++.++. ++.+.|++||.|+|+|.++|.+++
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~----~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~ 76 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDN----LTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRR 76 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecC----CCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccC
Confidence 37788888 9999999982 379999999999876422 345789999999999999999899
Q ss_pred eeEEEE
Q 024995 122 RITLSI 127 (259)
Q Consensus 122 ri~lS~ 127 (259)
++.+++
T Consensus 77 ~i~~~l 82 (83)
T cd04471 77 KIDFEL 82 (83)
T ss_pred EEEEEE
Confidence 999986
No 66
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.03 E-value=5.9e-10 Score=108.91 Aligned_cols=94 Identities=36% Similarity=0.631 Sum_probs=82.1
Q ss_pred EEEeCCCCEEEEEechh--------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccccc
Q 024995 31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ 97 (259)
Q Consensus 31 l~id~~~~~v~lS~k~~--------~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~ 97 (259)
++++ +.+.+..+.... .++.+...+++|++|.|+ +||+||++. +|.+||||+|++++.++.
T Consensus 585 Idie-ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~-----~gkdgl~hiS~~~~~rv~ 658 (692)
T COG1185 585 IDIE-DDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELL-----PGKDGLVHISQLAKERVE 658 (692)
T ss_pred EEec-CCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEEEec-----CCcceeEEehhhhhhhhh
Confidence 6777 667777776542 245567889999999999 999999998 589999999999999999
Q ss_pred ChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccc
Q 024995 98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131 (259)
Q Consensus 98 ~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~ 131 (259)
+.++.+++||.+.||++.+|. .+|+.||+|...
T Consensus 659 kv~dvlk~Gd~v~Vkv~~iD~-~Gri~ls~~~~~ 691 (692)
T COG1185 659 KVEDVLKEGDEVKVKVIEIDK-QGRIRLSIKAVL 691 (692)
T ss_pred cccceeecCceEEEEEeeecc-cCCccceehhcc
Confidence 999999999999999999996 899999998753
No 67
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=99.02 E-value=4.4e-10 Score=111.31 Aligned_cols=75 Identities=37% Similarity=0.648 Sum_probs=70.2
Q ss_pred ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995 53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (259)
Q Consensus 53 ~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~ 127 (259)
+.+|++|+++.|+ +||+||+|+ .+.+|+||+|+++..++.+|.+.+++||.|+|+|+++|..++||.|||
T Consensus 653 i~dLk~Gm~leg~Vrnv~~fgafVdIg-----v~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsm 727 (780)
T COG2183 653 ITDLKPGMILEGTVRNVVDFGAFVDIG-----VHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSM 727 (780)
T ss_pred HhhccCCCEEEEEEEEeeeccceEEec-----cccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEe
Confidence 3489999999999 999999998 689999999999999999999999999999999999999999999999
Q ss_pred ecccc
Q 024995 128 KQLEE 132 (259)
Q Consensus 128 K~~~~ 132 (259)
+....
T Consensus 728 r~~~~ 732 (780)
T COG2183 728 RLDEE 732 (780)
T ss_pred eccCC
Confidence 87543
No 68
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.97 E-value=2.6e-09 Score=78.64 Aligned_cols=69 Identities=22% Similarity=0.212 Sum_probs=63.0
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (259)
Q Consensus 55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~ 129 (259)
.+++|+++.|+ +.|++|+++ .+.+|++|+++++..+..++.+.|++||.+.|+|+++|.+ +++.||++.
T Consensus 3 ~p~~GdiV~G~V~~v~~~~~~V~i~-----~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~ 76 (82)
T cd04454 3 LPDVGDIVIGIVTEVNSRFWKVDIL-----SRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTAD 76 (82)
T ss_pred CCCCCCEEEEEEEEEcCCEEEEEeC-----CCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECC
Confidence 35899999999 889999998 4899999999999888888899999999999999999985 999999986
No 69
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.95 E-value=3.5e-09 Score=90.27 Aligned_cols=101 Identities=23% Similarity=0.319 Sum_probs=80.2
Q ss_pred CCCEEEEEE---EEEeCCCCEEEEEechhhHhhhccCCCCCCEEEEE-----eeeEEEEEccCC--C---CccEEEEEEc
Q 024995 22 TGSIISVKV---IQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPD--G---LYHLTGLVHV 88 (259)
Q Consensus 22 vG~~v~~~V---l~id~~~~~v~lS~k~~~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~--g---~~gi~glv~i 88 (259)
.+..+.+.+ +++|.+++++.+.. |......+++|+++.|+ ++|+||+|..++ + ..+.+|++|+
T Consensus 29 ~~~~i~as~~G~~~id~~~~~Isv~P----~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~ 104 (189)
T PRK09521 29 DNGEVYASVVGKVFIDDINRKISVIP----FKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHI 104 (189)
T ss_pred eCCEEEEEeeEEEEEcCCCCEEEEec----CcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEh
Confidence 455666555 45577777887753 44445678999999999 899999996321 0 0268999999
Q ss_pred eecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995 89 SEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (259)
Q Consensus 89 sels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~ 129 (259)
+++++.+..++.+.|++||.|.|+|++++ +++.||+|+
T Consensus 105 s~i~~~~~~~~~~~~~~GD~V~akV~~i~---~~i~LS~k~ 142 (189)
T PRK09521 105 SQVSDGYVESLTDAFKIGDIVRAKVISYT---DPLQLSTKG 142 (189)
T ss_pred hHcChhhhhhHHhccCCCCEEEEEEEecC---CcEEEEEec
Confidence 99999888889999999999999999997 789999985
No 70
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=98.91 E-value=4.4e-09 Score=105.42 Aligned_cols=88 Identities=34% Similarity=0.649 Sum_probs=73.2
Q ss_pred EEEeCCCCEEEEEechh--------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccccc
Q 024995 31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ 97 (259)
Q Consensus 31 l~id~~~~~v~lS~k~~--------~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~ 97 (259)
++++. ++.+.++.... .++.+...+++|++|.|+ +||+||++. .+.+||||+|+++|.++.
T Consensus 584 I~i~d-dG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~-----~g~~GllHiSei~~~~v~ 657 (684)
T TIGR03591 584 IDIED-DGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEIL-----PGKDGLVHISEIANERVE 657 (684)
T ss_pred EEEec-CeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEEC-----CCcEEEEEHHHcCCCccc
Confidence 56664 47777775432 133455678999999999 999999998 489999999999999999
Q ss_pred ChhhhcCCCCeEEEEEEEEeCCCCeeEE
Q 024995 98 DIRDILNEGDEVRVKVIKIDREKSRITL 125 (259)
Q Consensus 98 ~~~~~~~~Gd~V~vkVl~id~~~~ri~l 125 (259)
++.+.|++||.|+|+|+++|. ++|+.|
T Consensus 658 ~~~~~~kvGD~V~VkVi~id~-~gki~L 684 (684)
T TIGR03591 658 KVEDVLKEGDEVKVKVLEIDK-QGRIKL 684 (684)
T ss_pred ChhhccCCCCEEEEEEEEECC-CCCccC
Confidence 999999999999999999997 788764
No 71
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=98.89 E-value=4.5e-09 Score=72.32 Aligned_cols=56 Identities=45% Similarity=0.781 Sum_probs=51.8
Q ss_pred eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (259)
Q Consensus 66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS 126 (259)
++|+||+++ .+.+|++|.+++++.+..++.+.|++||.|+|+|+++|.+++++.||
T Consensus 10 ~~g~~v~l~-----~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 10 KFGVFVELE-----DGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred eeeEEEEec-----CCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 899999998 48999999999999888888899999999999999999988888875
No 72
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.87 E-value=6.3e-09 Score=74.32 Aligned_cols=57 Identities=21% Similarity=0.256 Sum_probs=50.8
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccc--ccChhhhcCCCCeEEEEEEEEeCCC
Q 024995 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREK 120 (259)
Q Consensus 59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~--~~~~~~~~~~Gd~V~vkVl~id~~~ 120 (259)
|+++.|+ ++|+||+++ .+++|++|++++++++ ..++.+.|++||.|+|+|+++|.++
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~-----~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~ 64 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLA-----DNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK 64 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeC-----CCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcc
Confidence 6777887 889999998 5899999999999885 7888899999999999999999743
No 73
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=98.86 E-value=1.4e-08 Score=73.99 Aligned_cols=61 Identities=34% Similarity=0.578 Sum_probs=54.1
Q ss_pred ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995 53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (259)
Q Consensus 53 ~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~ 127 (259)
..+++.|+.+.|+ +||+||++. .+.+||+|.+++. +.|++||.++++|.++ .+++++.+|+
T Consensus 11 ~~~~~~G~~~~g~V~~i~~~G~fV~l~-----~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i-~e~~~i~l~~ 76 (77)
T cd04473 11 MEDLEVGKLYKGKVNGVAKYGVFVDLN-----DHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI-PENGNIDLIP 76 (77)
T ss_pred hhhCCCCCEEEEEEEeEecceEEEEEC-----CCcEEEEEchhcc--------CcCCCCCEEEEEEEEE-CCCCcEEEEE
Confidence 3468999999999 999999998 4799999999973 4589999999999999 7899999986
No 74
>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=98.85 E-value=2.7e-09 Score=77.42 Aligned_cols=68 Identities=9% Similarity=0.154 Sum_probs=53.7
Q ss_pred CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
++|+++.|+|.++++|| +|+.| .+|++|++ .+++++. |... +. ++...+++||.|
T Consensus 2 k~G~~V~g~V~~i~~~G----~fV~l--~~~v~G~v~~~~ls~~----------~~~~---~~-~~~~~~~~G~~v~~kV 61 (74)
T cd05705 2 KEGQLLRGYVSSVTKQG----VFFRL--SSSIVGRVLFQNVTKY----------FVSD---PS-LYNKYLPEGKLLTAKV 61 (74)
T ss_pred CCCCEEEEEEEEEeCCc----EEEEe--CCCCEEEEEHHHccCc----------cccC---hh-hHhcccCCCCEEEEEE
Confidence 46888999999999999 99988 89999999 6887743 2211 11 133466999999
Q ss_pred EEEecccchhhhh
Q 024995 227 QEIQLSHSLIRKA 239 (259)
Q Consensus 227 ~~v~~~~~~i~ls 239 (259)
+++|.++++|.||
T Consensus 62 l~id~~~~~i~LS 74 (74)
T cd05705 62 LSVNSEKNLVELS 74 (74)
T ss_pred EEEECCCCEEecC
Confidence 7999999999886
No 75
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=98.83 E-value=1.8e-08 Score=76.88 Aligned_cols=65 Identities=31% Similarity=0.584 Sum_probs=55.9
Q ss_pred eeeEEEEEccCCCCccEEEEEEceecCcccccC-----------hhhhcCCCCeEEEEEEEEeCCC-----CeeEEEEec
Q 024995 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD-----------IRDILNEGDEVRVKVIKIDREK-----SRITLSIKQ 129 (259)
Q Consensus 66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~-----------~~~~~~~Gd~V~vkVl~id~~~-----~ri~lS~K~ 129 (259)
++|+||++. +++||+|+++++++++.. +.+.|++||.|+|+|.++|.+. .++.||+|+
T Consensus 12 ~~GifV~l~------~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i~ls~k~ 85 (99)
T cd04460 12 DFGAFVRIG------PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIGLTMRQ 85 (99)
T ss_pred eccEEEEEc------CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceEEEEEec
Confidence 999999997 599999999999876543 3477999999999999999764 589999999
Q ss_pred cccCcch
Q 024995 130 LEEDPLL 136 (259)
Q Consensus 130 ~~~~p~~ 136 (259)
....||.
T Consensus 86 ~~~g~~~ 92 (99)
T cd04460 86 PGLGKLE 92 (99)
T ss_pred CCCCcHH
Confidence 8888874
No 76
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.80 E-value=3.1e-09 Score=76.86 Aligned_cols=67 Identities=10% Similarity=0.110 Sum_probs=52.6
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE 228 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~ 228 (259)
|++++|+|.++.++| +|++| .+||+|++ .++++++. .....+.. .+++||.| ++
T Consensus 1 G~~V~g~V~~i~~~g----~~V~l--~~~i~G~i~~~~ls~~~-----------~~~~~~~~----~~~vG~~v~~kV~~ 59 (73)
T cd05703 1 GQEVTGFVNNVSKEF----VWLTI--SPDVKGRIPLLDLSDDV-----------SVLEHPEK----KFPIGQALKAKVVG 59 (73)
T ss_pred CCEEEEEEEEEeCCE----EEEEe--CCCcEEEEEHHHcCCcc-----------ccccCHHH----hCCCCCEEEEEEEE
Confidence 567999999999999 99988 88999999 67776321 11122223 45999999 79
Q ss_pred Eecccchhhhhhc
Q 024995 229 IQLSHSLIRKASK 241 (259)
Q Consensus 229 v~~~~~~i~ls~k 241 (259)
+|+++++|.||+|
T Consensus 60 id~~~~~i~Ls~k 72 (73)
T cd05703 60 VDKEHKLLRLSAR 72 (73)
T ss_pred EeCCCCEEEEEec
Confidence 9999999999986
No 77
>PRK08582 hypothetical protein; Provisional
Probab=98.77 E-value=8.4e-09 Score=83.79 Aligned_cols=75 Identities=15% Similarity=0.152 Sum_probs=60.1
Q ss_pred CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
++|+++.|+|++|++|| +||+| .++++||+ +|+++++ |+. . ....+++||.|
T Consensus 4 kvG~iv~G~V~~I~~fG----~fV~L--~~~~~GlVhiSels~~----------~v~---~----~~~~l~vGD~VkvkV 60 (139)
T PRK08582 4 EVGSKLQGKVTGITNFG----AFVEL--PEGKTGLVHISEVADN----------YVK---D----INDHLKVGDEVEVKV 60 (139)
T ss_pred cCCCEEEEEEEEEECCe----EEEEE--CCCCEEEEEeeccCcc----------ccc---c----cccccCCCCEEEEEE
Confidence 45888999999999999 99988 78999999 7777633 221 1 22356999999
Q ss_pred EEEecccchhhhhhchhhhhhhHH
Q 024995 227 QEIQLSHSLIRKASKRHCNEYWNV 250 (259)
Q Consensus 227 ~~v~~~~~~i~ls~k~~~~~p~~~ 250 (259)
+.|+. ..+|.||+|++.++||..
T Consensus 61 ~~id~-~gkI~LSlk~~~~~~~~~ 83 (139)
T PRK08582 61 LNVED-DGKIGLSIKKAKDRPKRQ 83 (139)
T ss_pred EEECC-CCcEEEEEEecccCchhh
Confidence 57776 489999999999999975
No 78
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.74 E-value=9.2e-09 Score=74.65 Aligned_cols=65 Identities=8% Similarity=0.081 Sum_probs=53.4
Q ss_pred CCCCccccceeeeccCCCccceeeeeccc-CCeeEEEE-ccccccccccchhhhhhcccCCCCCcceeeeccCCCee---
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQE-DGIDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV--- 226 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~-~gv~gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V--- 226 (259)
+.|+++.|+|.+|++|| +|+++ . +|++||++ ++++ |. ..+++||.+
T Consensus 3 ~~G~~v~g~V~si~d~G----~~v~~--g~~gv~Gfl~~~~~~------------~~-----------~~~~~Gq~v~~~ 53 (74)
T cd05694 3 VEGMVLSGCVSSVEDHG----YILDI--GIPGTTGFLPKKDAG------------NF-----------SKLKVGQLLLCV 53 (74)
T ss_pred CCCCEEEEEEEEEeCCE----EEEEe--CCCCcEEEEEHHHCC------------cc-----------cccCCCCEEEEE
Confidence 56888999999999999 99888 4 69999994 5544 11 145899998
Q ss_pred -EEEecccchhhhhhchhhh
Q 024995 227 -QEIQLSHSLIRKASKRHCN 245 (259)
Q Consensus 227 -~~v~~~~~~i~ls~k~~~~ 245 (259)
+.||.+++++.||+|++.+
T Consensus 54 V~~vd~~~~~v~ls~k~~~~ 73 (74)
T cd05694 54 VEKVKDDGRVVSLSADPSKV 73 (74)
T ss_pred EEEEECCCCEEEEEEeeccc
Confidence 6889999999999998764
No 79
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.73 E-value=1.5e-08 Score=97.18 Aligned_cols=97 Identities=19% Similarity=0.276 Sum_probs=78.5
Q ss_pred ccCCCCEEEEEEEEEeCCCCEEEEEe-chh--------hHhhhccCCC--CCCEEEEE-----eeeEEEEEccCCCCccE
Q 024995 19 KGLTGSIISVKVIQANEEMKKLVFSE-KDA--------VWNKYSSRVN--VEDIFVGR-----DYGAFIHLRFPDGLYHL 82 (259)
Q Consensus 19 ~~~vG~~v~~~Vl~id~~~~~v~lS~-k~~--------~~~~~~~~l~--~G~iv~G~-----~~G~fV~l~~~~g~~gi 82 (259)
+..+|+.+.+.|...+ .+|+.++. |+. .++.++..++ .|+++.|+ ++|+||+++ |+
T Consensus 86 ~~~vGD~ie~~I~~~~--fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~~giiVDLg------gv 157 (470)
T PRK09202 86 DAEVGDYIEEEIESVD--FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLG------RA 157 (470)
T ss_pred cccCCCeEEEEEcccc--CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCEEEEEC------Ce
Confidence 4569999999988776 34444443 332 2345677787 99999999 899999997 79
Q ss_pred EEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCC--eeEEEEec
Q 024995 83 TGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIKQ 129 (259)
Q Consensus 83 ~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~--ri~lS~K~ 129 (259)
+||||.++++ |.+.|++||.|+|+|++++++++ +|.||++.
T Consensus 158 ea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~ 200 (470)
T PRK09202 158 EAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTH 200 (470)
T ss_pred EEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCc
Confidence 9999999985 67789999999999999999777 89999864
No 80
>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=98.72 E-value=4.5e-08 Score=82.70 Aligned_cols=128 Identities=22% Similarity=0.436 Sum_probs=85.7
Q ss_pred CCCCCCCCCCchhHhhhcc-cCCCCEEE-----EEEEEEeC-CCCEEEEEech----hhHhhhccCCCCCCEEEEE----
Q 024995 1 MSPSHSCKEPQKSIHEIAK-GLTGSIIS-----VKVIQANE-EMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR---- 65 (259)
Q Consensus 1 ~~~~~~~~~p~~~~~~~~~-~~vG~~v~-----~~Vl~id~-~~~~v~lS~k~----~~~~~~~~~l~~G~iv~G~---- 65 (259)
+.|++|.+++...+.+.++ .+.|+.+. +.|.++.. ..+++.-.--. ..+..+.-+...|+++.|+
T Consensus 13 i~P~~~~~~~~~~i~~~l~~~~~gk~~~~~G~~i~v~di~~i~~g~i~~gdG~~~~~V~f~~i~f~p~~gEvv~G~V~~v 92 (179)
T TIGR00448 13 IPPDQFGEDLEEVITHQLNEKFEGRLDKNVGLCITIYDIEDIGEGKVIPGDGSAYHNVTFRALVFKPELGEIVEGEVIEI 92 (179)
T ss_pred ECHHHhCccHHHHHHHHHHHHhcCcCcCCcCEEEEEEEeEEecCCEEECCCCCEEEEEEEEEEEEeccCCCEEEEEEEEE
Confidence 3577777666655554443 35555433 33444433 33444311111 1123334467789999999
Q ss_pred -eeeEEEEEccCCCCccEEEEEEceecCccccc-----------ChhhhcCCCCeEEEEEEEEe-----CCCCeeEEEEe
Q 024995 66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKID-----REKSRITLSIK 128 (259)
Q Consensus 66 -~~G~fV~l~~~~g~~gi~glv~isels~~~~~-----------~~~~~~~~Gd~V~vkVl~id-----~~~~ri~lS~K 128 (259)
++|+||+++ .++|++|.+++.+.+.. +....|+.||.|+++|.++| ++..+|.+|+|
T Consensus 93 ~~~GifV~lg------~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~~I~lt~k 166 (179)
T TIGR00448 93 VEFGAFVSLG------PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPEGSKIGLTMR 166 (179)
T ss_pred EeeEEEEEeC------CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCCcceEEEEec
Confidence 999999996 59999999999866432 23467999999999999998 56789999999
Q ss_pred ccccCc
Q 024995 129 QLEEDP 134 (259)
Q Consensus 129 ~~~~~p 134 (259)
+.-..|
T Consensus 167 ~~~LG~ 172 (179)
T TIGR00448 167 QPLLGK 172 (179)
T ss_pred cCcCCc
Confidence 865444
No 81
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.71 E-value=7.5e-09 Score=105.01 Aligned_cols=78 Identities=15% Similarity=0.249 Sum_probs=63.6
Q ss_pred CCCCccc-cceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee---
Q 024995 152 DSSSMSS-SNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV--- 226 (259)
Q Consensus 152 ~~g~~v~-G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V--- 226 (259)
+.|+++. |+|++|++|| +||+| .+|++||+ +|++++. |+ ..+.. ++++||.|
T Consensus 752 ~vG~iy~~g~V~~I~~FG----aFVeL--~~g~EGLVHISeLs~~----------rv---~~~~d----v~kvGD~V~Vk 808 (891)
T PLN00207 752 TVGDIYRNCEIKSIAPYG----AFVEI--APGREGLCHISELSSN----------WL---AKPED----AFKVGDRIDVK 808 (891)
T ss_pred CCCcEEECcEEEEEeccE----EEEEe--CCCCEEEEEhhhcCCc----------cc---cCHHH----hcCCCCEEEEE
Confidence 3588894 6999999999 99999 78999999 7888743 22 22223 56999999
Q ss_pred -EEEecccchhhhhhchhhhhhhHHhhh
Q 024995 227 -QEIQLSHSLIRKASKRHCNEYWNVFHE 253 (259)
Q Consensus 227 -~~v~~~~~~i~ls~k~~~~~p~~~~~~ 253 (259)
++||. +++|+||+|++.++||+.+.+
T Consensus 809 Vi~ID~-~grI~LSlK~l~~~Pw~~~~~ 835 (891)
T PLN00207 809 LIEVND-KGQLRLSRRALLPEANSEKSS 835 (891)
T ss_pred EEEECC-CCcEEEEEeccccCchhhhhh
Confidence 68886 689999999999999998876
No 82
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.66 E-value=1.1e-08 Score=89.75 Aligned_cols=77 Identities=14% Similarity=0.197 Sum_probs=66.4
Q ss_pred CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q 227 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~ 227 (259)
.|+.+-|+|.+|.+|| +|+.|+-.+|++||+ +||++ +.|+++++ ..+|.||.| +
T Consensus 11 eGEiVv~tV~~V~~~G----Ayv~L~EY~g~Eg~ihiSEva----------s~wVknIr-------d~vkegqkvV~kVl 69 (269)
T COG1093 11 EGEIVVGTVKQVADYG----AYVELDEYPGKEGFIHISEVA----------SGWVKNIR-------DYVKEGQKVVAKVL 69 (269)
T ss_pred CCcEEEEEEEEeeccc----cEEEeeccCCeeeeEEHHHHH----------HHHHHHHH-------HHhhcCCeEEEEEE
Confidence 3777999999999999 999999889999998 79987 24998765 267999998 8
Q ss_pred EEecccchhhhhhchhhhhhhHH
Q 024995 228 EIQLSHSLIRKASKRHCNEYWNV 250 (259)
Q Consensus 228 ~v~~~~~~i~ls~k~~~~~p~~~ 250 (259)
.||++++.|.||||++.++--..
T Consensus 70 rVd~~rg~IDLSlkrV~~~q~~~ 92 (269)
T COG1093 70 RVDPKRGHIDLSLKRVTEHQRRK 92 (269)
T ss_pred EEcCCCCeEeeehhhCCHHHHHH
Confidence 99999999999999988765443
No 83
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.64 E-value=3e-08 Score=71.22 Aligned_cols=64 Identities=17% Similarity=0.187 Sum_probs=49.6
Q ss_pred CCccc-cceeee-ccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 154 SSMSS-SNSNTI-EPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 154 g~~v~-G~V~~i-~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
|++++ |+|+++ .+|| +|++| .+|++||+ .|+++.++ ...+.. .+++||.+
T Consensus 1 G~v~~~g~V~~v~~~~G----~~V~l--~~gv~G~i~~s~l~~~~-------------~~~~~~----~~~vG~~v~~kV 57 (71)
T cd05696 1 GAVVDSVKVTKVEPDLG----AVFEL--KDGLLGFVHISHLSDDK-------------VPSDTG----PFKAGTTHKARI 57 (71)
T ss_pred CcEeeeeEEEEEccCce----EEEEe--CCCCEEEEEHHHCCcch-------------hcCccc----ccCCCCEEEEEE
Confidence 45678 899998 6999 99988 78999999 57766321 121223 45999999
Q ss_pred EEEecccchhhhhh
Q 024995 227 QEIQLSHSLIRKAS 240 (259)
Q Consensus 227 ~~v~~~~~~i~ls~ 240 (259)
+++|+.+++|+||+
T Consensus 58 ~~id~~~~~i~lS~ 71 (71)
T cd05696 58 IGYSPMDGLLQLSL 71 (71)
T ss_pred EEEeCCCCEEEEeC
Confidence 79999999999985
No 84
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.62 E-value=3.7e-08 Score=69.66 Aligned_cols=64 Identities=22% Similarity=0.421 Sum_probs=49.2
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE 228 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~ 228 (259)
|+.+.|+|.++++|| +|++| ++|++||+ .++++ |......+.. .+++||.| ++
T Consensus 1 G~~~~g~V~~i~~~G----~fv~l--~~~~~Glv~~~~l~------------~~~~~~~~~~----~~~~G~~v~v~v~~ 58 (69)
T cd05690 1 GTVVSGKIKSITDFG----IFVGL--DGGIDGLVHISDIS------------WTQRVRHPSE----IYKKGQEVEAVVLN 58 (69)
T ss_pred CCEEEEEEEEEEeee----EEEEe--CCCCEEEEEHHHCC------------CccccCChhh----EECCCCEEEEEEEE
Confidence 456999999999999 99999 78999999 55554 3222222333 55999999 69
Q ss_pred Eecccchhhhh
Q 024995 229 IQLSHSLIRKA 239 (259)
Q Consensus 229 v~~~~~~i~ls 239 (259)
+|.++++|+||
T Consensus 59 id~~~~~i~l~ 69 (69)
T cd05690 59 IDVERERISLG 69 (69)
T ss_pred EECCcCEEeCC
Confidence 99999999875
No 85
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=98.59 E-value=4e-08 Score=94.00 Aligned_cols=77 Identities=29% Similarity=0.457 Sum_probs=70.0
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (259)
Q Consensus 55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~ 129 (259)
++..|.+|+|+ ++|+||++. ++..||+|+|+|+..++.+|++.+.+||.|.+|.++.|+ .+.+.+|.|.
T Consensus 665 ~l~~g~vy~~tIt~~rd~G~~V~l~-----p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~-~g~~~ls~ra 738 (760)
T KOG1067|consen 665 DLEFGGVYTATITEIRDTGVMVELY-----PMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDP-RGGIMLSSRA 738 (760)
T ss_pred ceEeeeEEEEEEeeecccceEEEec-----CCchhhccchhcccccccChHHHHhhcceeEEEEEeecC-ccceeehhhh
Confidence 57778888888 999999998 589999999999999999999999999999999999997 7888888899
Q ss_pred cccCcchH
Q 024995 130 LEEDPLLE 137 (259)
Q Consensus 130 ~~~~p~~~ 137 (259)
++++|-..
T Consensus 739 lLp~p~~~ 746 (760)
T KOG1067|consen 739 LLPDPATK 746 (760)
T ss_pred hcCCcccC
Confidence 99988643
No 86
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.59 E-value=1.5e-07 Score=82.91 Aligned_cols=70 Identities=27% Similarity=0.370 Sum_probs=62.9
Q ss_pred cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccc----cChhhhcCCCCeEEEEEEEEeCCCCeeE
Q 024995 54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----QDIRDILNEGDEVRVKVIKIDREKSRIT 124 (259)
Q Consensus 54 ~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~----~~~~~~~~~Gd~V~vkVl~id~~~~ri~ 124 (259)
..+++|++|.|+ ++|+||+|+ .+.+|+||++++++.++ .++.+.|++||.|.|+|+++++ .+++.
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~-----~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~-~~~~~ 132 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDIN-----SPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDR-TRDVV 132 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeC-----CCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECC-CCcEE
Confidence 466999999999 899999998 47999999999999887 7889999999999999999996 56699
Q ss_pred EEEec
Q 024995 125 LSIKQ 129 (259)
Q Consensus 125 lS~K~ 129 (259)
||+|+
T Consensus 133 LS~k~ 137 (235)
T PRK04163 133 LTLKG 137 (235)
T ss_pred EEEcC
Confidence 99975
No 87
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.56 E-value=1.9e-07 Score=79.40 Aligned_cols=126 Identities=21% Similarity=0.432 Sum_probs=84.6
Q ss_pred CCCCCCCCCCchhHhhhccc-CCCCEEE-----EEEEEEeC-CCCEEEEEech----hhHhhhccCCCCCCEEEEE----
Q 024995 1 MSPSHSCKEPQKSIHEIAKG-LTGSIIS-----VKVIQANE-EMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR---- 65 (259)
Q Consensus 1 ~~~~~~~~~p~~~~~~~~~~-~vG~~v~-----~~Vl~id~-~~~~v~lS~k~----~~~~~~~~~l~~G~iv~G~---- 65 (259)
+.|++|.++....+.+.++. +.|+.+. +.|++++. ..+++.-.-.. ..+..+.-....|+++.|+
T Consensus 13 i~P~~~~~~~~~~i~~~l~~~~~~k~~~~~G~~v~v~di~~i~~g~i~~gdg~~~~~v~f~~lvf~P~~GEVv~g~V~~v 92 (187)
T PRK08563 13 IPPEMFGEDLEEAALEVLREKYEGRIDKELGIIVAVLDVKVIGEGKIVPGDGATYHEVEFDALVFKPELQEVVEGEVVEV 92 (187)
T ss_pred ECHHHcCccHHHHHHHHHHHHhhCcCcCCcCEEEEEEEeEEecccEEecCCCCcEEEEEEEEEEEeccCCCEEEEEEEEE
Confidence 35777776666655554443 3454432 44455544 33444311111 1133344567899999999
Q ss_pred -eeeEEEEEccCCCCccEEEEEEceecCccccc-----------ChhhhcCCCCeEEEEEEEEeCCCC-----eeEEEEe
Q 024995 66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREKS-----RITLSIK 128 (259)
Q Consensus 66 -~~G~fV~l~~~~g~~gi~glv~isels~~~~~-----------~~~~~~~~Gd~V~vkVl~id~~~~-----ri~lS~K 128 (259)
++|+||+++ .++|++|.+++.+.+.. +....+++||.|+++|.+++.+.+ +|.+|+|
T Consensus 93 ~~~Gi~V~lg------~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~~~~I~ls~~ 166 (187)
T PRK08563 93 VEFGAFVRIG------PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPRGSKIGLTMR 166 (187)
T ss_pred EccEEEEEEe------CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCCCCEEEEEec
Confidence 899999997 59999999999876432 345678999999999999997543 8999998
Q ss_pred cccc
Q 024995 129 QLEE 132 (259)
Q Consensus 129 ~~~~ 132 (259)
+.-.
T Consensus 167 ~~~L 170 (187)
T PRK08563 167 QPGL 170 (187)
T ss_pred CCCC
Confidence 7443
No 88
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.56 E-value=1.9e-07 Score=78.29 Aligned_cols=129 Identities=24% Similarity=0.402 Sum_probs=86.0
Q ss_pred CCCCCCCCCchhHhhhcc-cCCCCEEE-----EEEEEEeC-CCCEEEEEechh----hHhhhccCCCCCCEEEEE-----
Q 024995 2 SPSHSCKEPQKSIHEIAK-GLTGSIIS-----VKVIQANE-EMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR----- 65 (259)
Q Consensus 2 ~~~~~~~~p~~~~~~~~~-~~vG~~v~-----~~Vl~id~-~~~~v~lS~k~~----~~~~~~~~l~~G~iv~G~----- 65 (259)
.|+.|-.+.+....+.+. .+.|+... +.|.++.. ..+++...--.. .+..+.-....|+++.|.
T Consensus 14 pP~~fg~~~~~~v~~~L~~k~eG~~~~~~G~~v~V~~v~~igeG~I~~GDG~~y~~V~f~al~fkP~~gEVV~GeVv~~~ 93 (183)
T COG1095 14 PPSYFGEDLEEAVKEELKEKYEGKLDGDVGLVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALVFKPFRGEVVEGEVVEVV 93 (183)
T ss_pred CHHHcCccHHHHHHHHHHHHhcceEccccCEEEEEEEeeEeeccEEecCCCcEEEEEEEEEEEEEeccccEEEEEEEEEe
Confidence 566665555555544443 45565543 33344432 345555332211 234445577889999998
Q ss_pred eeeEEEEEccCCCCccEEEEEEceecCcccc----------cC-hhhhcCCCCeEEEEEEEEeCCC-----CeeEEEEec
Q 024995 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----------QD-IRDILNEGDEVRVKVIKIDREK-----SRITLSIKQ 129 (259)
Q Consensus 66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~----------~~-~~~~~~~Gd~V~vkVl~id~~~-----~ri~lS~K~ 129 (259)
+||+||.++ .++||+|++++.++++ .+ ....+++||.|+++|+.+.... .+|.+++|+
T Consensus 94 ~~G~fV~ig------p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~~~I~lTmrq 167 (183)
T COG1095 94 EFGAFVRIG------PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRESKIGLTMRQ 167 (183)
T ss_pred ecceEEEec------cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCccccceEEEEecc
Confidence 999999998 6999999999998743 12 2336999999999999998755 578999998
Q ss_pred ccc--Ccch
Q 024995 130 LEE--DPLL 136 (259)
Q Consensus 130 ~~~--~p~~ 136 (259)
.-. -+|.
T Consensus 168 ~~LGklew~ 176 (183)
T COG1095 168 PGLGKLEWI 176 (183)
T ss_pred ccCCcchhh
Confidence 543 4564
No 89
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=98.55 E-value=3e-07 Score=65.19 Aligned_cols=58 Identities=17% Similarity=0.300 Sum_probs=48.8
Q ss_pred CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCC--CeeEEE
Q 024995 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRITLS 126 (259)
Q Consensus 57 ~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~--~ri~lS 126 (259)
+.|++++|+ ++|+||+++ +.+|+||.+|++. .+.|++||.+++.|++++.++ .+|.||
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig------~~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lS 66 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLG------KVEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILS 66 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcC------CeEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEe
Confidence 468999998 789999997 5999999999873 346899999999999999643 467777
No 90
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.54 E-value=5.6e-08 Score=69.02 Aligned_cols=65 Identities=8% Similarity=0.055 Sum_probs=51.0
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE 228 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~ 228 (259)
|+++.|+|.+++++| +|++| .++++||+ .|+++.+ + ...+.. .+++||.+ ++
T Consensus 1 g~~~~g~V~~v~~~G----~~V~l--~~~~~gli~~s~l~~~----------~---~~~~~~----~~~~G~~i~v~v~~ 57 (70)
T cd05698 1 GLKTHGTIVKVKPNG----CIVSF--YNNVKGFLPKSELSEA----------F---IKDPEE----HFRVGQVVKVKVLS 57 (70)
T ss_pred CCEEEEEEEEEecCc----EEEEE--CCCCEEEEEHHHcChh----------h---cCCHHH----cccCCCEEEEEEEE
Confidence 566999999999999 99999 78899999 5666522 1 122222 56999999 68
Q ss_pred Eecccchhhhhhc
Q 024995 229 IQLSHSLIRKASK 241 (259)
Q Consensus 229 v~~~~~~i~ls~k 241 (259)
+|.+++++.||+|
T Consensus 58 ~d~~~~~i~ls~k 70 (70)
T cd05698 58 CDPEQQRLLLSCK 70 (70)
T ss_pred EcCCCCEEEEEeC
Confidence 9999999999986
No 91
>PRK07252 hypothetical protein; Provisional
Probab=98.51 E-value=8.2e-08 Score=76.09 Aligned_cols=81 Identities=12% Similarity=0.110 Sum_probs=62.1
Q ss_pred CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
++|+++.|+|++|+++| +|++| .++++||+ .|+++.+ ++ ..+. ..+++||.|
T Consensus 2 kvG~iv~G~V~~V~~~G----~fVei--~~~~~GllhiseLs~~----------~~---~~~~----~~~~vGD~V~VkI 58 (120)
T PRK07252 2 KIGDKLKGTITGIKPYG----AFVAL--ENGTTGLIHISEIKTG----------FI---DNIH----QLLKVGEEVLVQV 58 (120)
T ss_pred CCCCEEEEEEEEEeCcE----EEEEE--CCCCEEEEEHHHcCCc----------cc---cChh----hccCCCCEEEEEE
Confidence 35888999999999999 99998 78899999 6776632 12 1122 256999999
Q ss_pred EEEecccchhhhhhchhhh-hhhHHhhhhc
Q 024995 227 QEIQLSHSLIRKASKRHCN-EYWNVFHETA 255 (259)
Q Consensus 227 ~~v~~~~~~i~ls~k~~~~-~p~~~~~~~~ 255 (259)
+++|.++++|.+|+|.+.+ .+|......|
T Consensus 59 ~~iD~~~~ri~lSlk~~~~~~~~~~~~~~~ 88 (120)
T PRK07252 59 VDFDEYTGKASLSLRTLEEEKQHFPHRHRF 88 (120)
T ss_pred EEEeCCCCEEEEEEeecccCccccCccccc
Confidence 6899999999999999887 5565444433
No 92
>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=98.50 E-value=1.1e-07 Score=68.18 Aligned_cols=67 Identities=16% Similarity=0.333 Sum_probs=53.4
Q ss_pred CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
..|++++|+|.++.++| +|+.| ..|++|++ .++++... .+.+.. .+++||.|
T Consensus 3 ~~G~iv~g~V~~v~~~g----~~V~l--~~~~~g~ip~~~l~~~~-------------~~~~~~----~~~~G~~v~v~v 59 (74)
T PF00575_consen 3 KEGDIVEGKVTSVEDFG----VFVDL--GNGIEGFIPISELSDDR-------------IDDPSE----VYKIGQTVRVKV 59 (74)
T ss_dssp STTSEEEEEEEEEETTE----EEEEE--STSSEEEEEGGGSSSSE-------------ESSSHG----TCETTCEEEEEE
T ss_pred CCCCEEEEEEEEEECCE----EEEEE--CCcEEEEEEeehhcCcc-------------cccccc----ccCCCCEEEEEE
Confidence 35888999999999999 99999 58999999 56666321 122333 45999999
Q ss_pred EEEecccchhhhhhc
Q 024995 227 QEIQLSHSLIRKASK 241 (259)
Q Consensus 227 ~~v~~~~~~i~ls~k 241 (259)
+++|.+++++.+|+|
T Consensus 60 ~~vd~~~~~i~lS~k 74 (74)
T PF00575_consen 60 IKVDKEKGRIRLSLK 74 (74)
T ss_dssp EEEETTTTEEEEEST
T ss_pred EEEECCCCeEEEEEC
Confidence 799999999999987
No 93
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=98.45 E-value=6.7e-07 Score=90.35 Aligned_cols=69 Identities=28% Similarity=0.549 Sum_probs=59.0
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccc-----------cChhhhcCCCCeEEEEEEEEeC
Q 024995 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDR 118 (259)
Q Consensus 55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~-----------~~~~~~~~~Gd~V~vkVl~id~ 118 (259)
.-+.|+++.|+ +||+||++.+ ++++||+|+++++++++ .+..+.|++||.|+|+|.++|.
T Consensus 624 ~~~iG~~~~g~V~~v~~fGifV~L~~----~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~ 699 (709)
T TIGR02063 624 SEKIGEEFEGVISGVTSFGLFVELEN----NTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADL 699 (709)
T ss_pred hccCCcEEEEEEEEEEeCCEEEEecC----CceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEec
Confidence 45789999999 9999999973 37999999999987643 2345679999999999999999
Q ss_pred CCCeeEEEE
Q 024995 119 EKSRITLSI 127 (259)
Q Consensus 119 ~~~ri~lS~ 127 (259)
.+++|.+++
T Consensus 700 ~~~~I~~~l 708 (709)
T TIGR02063 700 DTGKIDFEL 708 (709)
T ss_pred ccCeEEEEE
Confidence 999999986
No 94
>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=98.43 E-value=2.1e-07 Score=66.95 Aligned_cols=70 Identities=14% Similarity=0.287 Sum_probs=53.4
Q ss_pred CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
+.|+.+.|+|.++.+|| +|+++...+|++||+ .|+++... + . +....+++||.|
T Consensus 2 ~~G~~~~g~V~~v~~~g----~~v~l~~~~~~~gll~~s~l~~~~----------~---~----~~~~~~~~Gd~v~vkv 60 (76)
T cd04452 2 EEGELVVVTVKSIADMG----AYVSLLEYGNIEGMILLSELSRRR----------I---R----SIRKLVKVGRKEVVKV 60 (76)
T ss_pred CCCCEEEEEEEEEEccE----EEEEEcCCCCeEEEEEhHHcCCcc----------c---C----CHHHeeCCCCEEEEEE
Confidence 35788999999999999 999994335799999 67766321 1 1 123356999999
Q ss_pred EEEecccchhhhhhch
Q 024995 227 QEIQLSHSLIRKASKR 242 (259)
Q Consensus 227 ~~v~~~~~~i~ls~k~ 242 (259)
.++|.+++++.||+|+
T Consensus 61 ~~~d~~~~~i~ls~k~ 76 (76)
T cd04452 61 IRVDKEKGYIDLSKKR 76 (76)
T ss_pred EEEECCCCEEEEEEcC
Confidence 5888888899999885
No 95
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.43 E-value=3.8e-07 Score=65.10 Aligned_cols=65 Identities=17% Similarity=0.318 Sum_probs=49.0
Q ss_pred CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q 227 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~ 227 (259)
+|+.+.|+|.++++|| +|++| .+|++||+ .+++. |......+.. .++.||.| +
T Consensus 3 ~g~~~~g~V~~i~~~G----~fv~l--~~~~~Gl~~~~~l~------------~~~~~~~~~~----~~~~Gd~v~v~v~ 60 (72)
T cd05689 3 EGTRLFGKVTNLTDYG----CFVEL--EEGVEGLVHVSEMD------------WTNKNIHPSK----VVSLGDEVEVMVL 60 (72)
T ss_pred CCCEEEEEEEEEEeeE----EEEEc--CCCCEEEEEEEecc------------CcccccCccc----EeCCCCEEEEEEE
Confidence 4677999999999999 99999 78999999 56654 2111111222 56999999 6
Q ss_pred EEecccchhhhh
Q 024995 228 EIQLSHSLIRKA 239 (259)
Q Consensus 228 ~v~~~~~~i~ls 239 (259)
++|.++++|.+|
T Consensus 61 ~id~~~~~i~~~ 72 (72)
T cd05689 61 DIDEERRRISLG 72 (72)
T ss_pred EeeCCcCEEeCC
Confidence 889998888775
No 96
>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=98.42 E-value=1.8e-07 Score=66.43 Aligned_cols=64 Identities=14% Similarity=0.148 Sum_probs=49.1
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE 228 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~ 228 (259)
|++++|+|.++.++| +|++| .+|++||+ .+++++.. . ..+ ...+++||.+ ++
T Consensus 1 G~~v~g~V~~v~~~G----v~V~l--~~~v~g~i~~~~l~~~~----------~---~~~----~~~~~~Gd~i~~~V~~ 57 (69)
T cd05697 1 GQVVKGTIRKLRPSG----IFVKL--SDHIKGLVPPMHLADVR----------L---KHP----EKKFKPGLKVKCRVLS 57 (69)
T ss_pred CCEEEEEEEEEeccE----EEEEe--cCCcEEEEEHHHCCCcc----------c---cCH----HHcCCCCCEEEEEEEE
Confidence 567999999999999 99988 78999999 45655221 1 111 2245999999 79
Q ss_pred Eecccchhhhhh
Q 024995 229 IQLSHSLIRKAS 240 (259)
Q Consensus 229 v~~~~~~i~ls~ 240 (259)
+|.++++|.||+
T Consensus 58 id~~~~~i~ls~ 69 (69)
T cd05697 58 VEPERKRLVLTL 69 (69)
T ss_pred EECCCCEEEEEC
Confidence 999999988874
No 97
>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=98.41 E-value=3.6e-07 Score=65.41 Aligned_cols=67 Identities=7% Similarity=0.106 Sum_probs=51.7
Q ss_pred CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
++|+++.|+|.++.++| +|++| ++|++|++ .++++++ |.. . ....+++||.|
T Consensus 2 ~~G~iv~g~V~~v~~~g----i~v~l--~~~~~g~v~~s~l~~~----------~~~---~----~~~~~~~Gd~v~~~V 58 (73)
T cd05706 2 KVGDILPGRVTKVNDRY----VLVQL--GNKVTGPSFITDALDD----------YSE---A----LPYKFKKNDIVRACV 58 (73)
T ss_pred CCCCEEEEEEEEEeCCe----EEEEe--CCCcEEEEEhhhccCc----------ccc---c----cccccCCCCEEEEEE
Confidence 45888999999999999 99988 88999999 5665522 111 1 12256999999
Q ss_pred EEEecccchhhhhhc
Q 024995 227 QEIQLSHSLIRKASK 241 (259)
Q Consensus 227 ~~v~~~~~~i~ls~k 241 (259)
+++|.+++++.||++
T Consensus 59 ~~~d~~~~~i~ls~~ 73 (73)
T cd05706 59 LSVDVPNKKIALSLR 73 (73)
T ss_pred EEEeCCCCEEEEEEC
Confidence 688888889998875
No 98
>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=98.40 E-value=2e-07 Score=67.06 Aligned_cols=67 Identities=9% Similarity=0.046 Sum_probs=49.2
Q ss_pred CCCCccccceeeecc-CCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee--E
Q 024995 152 DSSSMSSSNSNTIEP-LPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV--Q 227 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~-~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V--~ 227 (259)
++|+++.|+|.++.+ || +|++| .+|.+|++ +|+++++ |.. .+ ...+++||.| .
T Consensus 2 ~~G~iv~G~V~~i~~~~g----~~v~l--~~~~~Glvhis~~s~~----------~~~---~~----~~~~~~Gd~v~~k 58 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSG----LTVQL--PFGKTGLVSIFHLSDS----------YTE---NP----LEGFKPGKIVRCC 58 (72)
T ss_pred CCCCEEEEEEEEeeCCcE----EEEEC--CCCCEEEEEHHHhcCc----------ccC---CH----HHhCCCCCEEEEE
Confidence 468889999999986 89 99888 89999999 6777633 222 12 2256999999 2
Q ss_pred EEecccchhhhhhc
Q 024995 228 EIQLSHSLIRKASK 241 (259)
Q Consensus 228 ~v~~~~~~i~ls~k 241 (259)
-++.++++++||+|
T Consensus 59 V~~~~~~~i~LSl~ 72 (72)
T cd05704 59 ILSKKDGKYQLSLR 72 (72)
T ss_pred EEEecCCEEEEEeC
Confidence 23333488999875
No 99
>PHA02945 interferon resistance protein; Provisional
Probab=98.40 E-value=3e-07 Score=68.08 Aligned_cols=70 Identities=11% Similarity=0.199 Sum_probs=58.1
Q ss_pred CCCccccceeeeccCCCccceeeeecccCCeeEEE-Eccc--cccccccchhhhhhcccCCCCCcceeeeccCCCee---
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQ--GFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV--- 226 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V--- 226 (259)
+|+.+.|+|.. .+|| +|+.|+-.+|.+||+ +|+. + +.|+++ + + .+ .|+.|
T Consensus 11 ~GelvigtV~~-~d~g----a~v~L~EY~g~eg~i~~seveva----------~~wvK~-r---d----~l-~GqkvV~K 66 (88)
T PHA02945 11 VGDVLKGKVYE-NGYA----LYIDLFDYPHSEAILAESVQMHM----------NRYFKY-R---D----KL-VGKTVKVK 66 (88)
T ss_pred CCcEEEEEEEe-cCce----EEEEecccCCcEEEEEeehhhhc----------cceEee-e---e----Ee-cCCEEEEE
Confidence 58889999999 9999 999998889999999 7854 5 238876 3 1 45 99988
Q ss_pred -EEEecccchhhhhhchhhhh
Q 024995 227 -QEIQLSHSLIRKASKRHCNE 246 (259)
Q Consensus 227 -~~v~~~~~~i~ls~k~~~~~ 246 (259)
+.||+.++.|-||+|+..++
T Consensus 67 VirVd~~kg~IDlSlK~V~~~ 87 (88)
T PHA02945 67 VIRVDYTKGYIDVNYKRMCRH 87 (88)
T ss_pred EEEECCCCCEEEeEeeEcccC
Confidence 78899999999999997653
No 100
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=98.38 E-value=9.6e-07 Score=64.74 Aligned_cols=69 Identities=25% Similarity=0.340 Sum_probs=63.1
Q ss_pred cCCCCCCEEEEE----eeeEEEEEccCCCCccEEEEEE-ceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995 54 SRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVH-VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (259)
Q Consensus 54 ~~l~~G~iv~G~----~~G~fV~l~~~~g~~gi~glv~-isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~ 127 (259)
.-.++|+++.|. +.|+||.|.. ++++|++. .+|++.+++....+.+ +|..+.|+|+++|+++|.|.||.
T Consensus 12 ~~P~v~dvv~~Vv~i~d~~~YV~Lle----Y~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 12 VFPNINEVTKGIVFVKDNIFYVKLID----YGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred ecCCCCeEEEEEEEEeccEEEEEEec----CccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence 456899999877 8999999986 67999998 9999999999999999 99999999999999999999985
No 101
>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=98.36 E-value=3.2e-07 Score=67.60 Aligned_cols=66 Identities=12% Similarity=0.188 Sum_probs=51.1
Q ss_pred CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
++|+.+.|+|.++.+|| +|++| .+|++||+ .++++.+ +. .++. ..+++||.|
T Consensus 13 ~~G~i~~g~V~~v~~~G----~fv~l--~~~~~g~v~~~el~~~----------~~---~~~~----~~~~~Gd~v~vkV 69 (83)
T cd04461 13 KPGMVVHGYVRNITPYG----VFVEF--LGGLTGLAPKSYISDE----------FV---TDPS----FGFKKGQSVTAKV 69 (83)
T ss_pred CCCCEEEEEEEEEeece----EEEEc--CCCCEEEEEHHHCCcc----------cc---cCHH----HhcCCCCEEEEEE
Confidence 35788999999999999 99888 78999999 5666532 11 1222 356999999
Q ss_pred EEEecccchhhhhh
Q 024995 227 QEIQLSHSLIRKAS 240 (259)
Q Consensus 227 ~~v~~~~~~i~ls~ 240 (259)
.++|.++++|.|||
T Consensus 70 ~~id~~~~~i~lsl 83 (83)
T cd04461 70 TSVDEEKQRFLLSL 83 (83)
T ss_pred EEEcCCCCEEEEeC
Confidence 58888899999886
No 102
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.36 E-value=5.6e-07 Score=63.67 Aligned_cols=61 Identities=8% Similarity=0.069 Sum_probs=47.2
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE 228 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~ 228 (259)
|++++|+|.++.++| +|++| .+|++|++ .++++.. +. ...+ +++|+.+ +.
T Consensus 1 G~~V~g~V~~i~~~G----~~v~l--~~~v~g~v~~~~l~~~----------~~-----~~~~----~~~G~~i~~kVi~ 55 (66)
T cd05695 1 GMLVNARVKKVLSNG----LILDF--LSSFTGTVDFLHLDPE----------KS-----SKST----YKEGQKVRARILY 55 (66)
T ss_pred CCEEEEEEEEEeCCc----EEEEE--cCCceEEEEHHHcCCc----------cC-----cccC----cCCCCEEEEEEEE
Confidence 566999999999999 99988 67999999 4555411 11 1233 4999999 79
Q ss_pred Eecccchhhhh
Q 024995 229 IQLSHSLIRKA 239 (259)
Q Consensus 229 v~~~~~~i~ls 239 (259)
+|+++++|.||
T Consensus 56 id~~~~~i~LS 66 (66)
T cd05695 56 VDPSTKVVGLS 66 (66)
T ss_pred EeCCCCEEecC
Confidence 99999998886
No 103
>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=98.34 E-value=4.9e-07 Score=63.93 Aligned_cols=63 Identities=17% Similarity=0.199 Sum_probs=48.4
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE 228 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~ 228 (259)
|+++.|+|+++.++| +|++| .++++||+ .++++.+ |.. .+.. .+++||.| ++
T Consensus 1 G~~v~g~V~~v~~~G----v~V~l--~~~~~G~v~~s~l~~~----------~~~---~~~~----~~~~Gd~v~~~v~~ 57 (68)
T cd05707 1 GDVVRGFVKNIANNG----VFVTL--GRGVDARVRVSELSDS----------YLK---DWKK----RFKVGQLVKGKIVS 57 (68)
T ss_pred CCEEEEEEEEEECcc----EEEEe--CCCCEEEEEHHHCCch----------hhc---CHhh----ccCCCCEEEEEEEE
Confidence 566999999999999 99988 78999999 5666522 222 1222 45999999 68
Q ss_pred Eecccchhhhh
Q 024995 229 IQLSHSLIRKA 239 (259)
Q Consensus 229 v~~~~~~i~ls 239 (259)
+|.++++|.||
T Consensus 58 ~d~~~~~i~ls 68 (68)
T cd05707 58 IDPDNGRIEMT 68 (68)
T ss_pred EeCCCCEEecC
Confidence 89988888775
No 104
>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=98.33 E-value=4.2e-07 Score=64.72 Aligned_cols=67 Identities=13% Similarity=0.170 Sum_probs=52.1
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE 228 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~ 228 (259)
|+++.|+|+++.++| +|++| .++++|++ .++++.. +. .. ....+++||.+ ++
T Consensus 1 G~~v~g~V~~v~~~g----~~v~l--~~~~~g~i~~~~~~~~----------~~---~~----~~~~~~~Gd~v~~~v~~ 57 (73)
T cd05691 1 GSIVTGKVTEVDAKG----ATVKL--GDGVEGFLRAAELSRD----------RV---ED----ATERFKVGDEVEAKITN 57 (73)
T ss_pred CCEEEEEEEEEECCe----EEEEe--CCCCEEEEEHHHCCCc----------cc---cC----HHHccCCCCEEEEEEEE
Confidence 566999999999999 99988 78999999 5665522 11 11 22245999999 68
Q ss_pred Eecccchhhhhhchh
Q 024995 229 IQLSHSLIRKASKRH 243 (259)
Q Consensus 229 v~~~~~~i~ls~k~~ 243 (259)
+|.+++++.||+|++
T Consensus 58 ~d~~~~~i~ls~k~~ 72 (73)
T cd05691 58 VDRKNRKISLSIKAK 72 (73)
T ss_pred EeCCCCEEEEEEEEc
Confidence 899899999999875
No 105
>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=98.32 E-value=6.6e-07 Score=64.42 Aligned_cols=64 Identities=5% Similarity=0.063 Sum_probs=47.6
Q ss_pred CCCccccceeeeccCCCccceeeeecccC-CeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~-gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
.|+.+.|+|+++++|| +|++| .+ +++||+ +|++++.. ...+ ...+++||.|
T Consensus 3 ~g~~~~g~V~~i~~fG----~fv~l--~~~~~eGlvh~sel~~~~-------------~~~~----~~~~~~Gd~v~vkv 59 (73)
T cd05686 3 LYQIFKGEVASVTEYG----AFVKI--PGCRKQGLVHKSHMSSCR-------------VDDP----SEVVDVGEKVWVKV 59 (73)
T ss_pred CCCEEEEEEEEEEeee----EEEEE--CCCCeEEEEEchhhCCCc-------------ccCH----hhEECCCCEEEEEE
Confidence 4788999999999999 99998 22 379999 67776321 1222 2356999999
Q ss_pred EEEecccchhhhhh
Q 024995 227 QEIQLSHSLIRKAS 240 (259)
Q Consensus 227 ~~v~~~~~~i~ls~ 240 (259)
+++|.++ +|+||+
T Consensus 60 ~~vd~~~-ki~ls~ 72 (73)
T cd05686 60 IGREMKD-KMKLSL 72 (73)
T ss_pred EEECCCC-cEEEEe
Confidence 5778876 888876
No 106
>PRK11642 exoribonuclease R; Provisional
Probab=98.31 E-value=2.1e-06 Score=87.70 Aligned_cols=69 Identities=29% Similarity=0.518 Sum_probs=59.4
Q ss_pred CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccccc-----------ChhhhcCCCCeEEEEEEEEeCCC
Q 024995 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREK 120 (259)
Q Consensus 57 ~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~-----------~~~~~~~~Gd~V~vkVl~id~~~ 120 (259)
++|+++.|+ +||+||+|.. .+++||||+++|+++++. +....|++||.|+|+|.++|.++
T Consensus 642 ~iGe~f~G~Is~V~~fGifVeL~~----~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~ 717 (813)
T PRK11642 642 QVGNVFKGVISSVTGFGFFVRLDD----LFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDE 717 (813)
T ss_pred cCCcEEEEEEEEeecCceEEEECC----CCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCC
Confidence 789999999 9999999973 369999999999876432 23467999999999999999999
Q ss_pred CeeEEEEec
Q 024995 121 SRITLSIKQ 129 (259)
Q Consensus 121 ~ri~lS~K~ 129 (259)
++|.|++..
T Consensus 718 rkI~f~l~~ 726 (813)
T PRK11642 718 RKIDFSLIS 726 (813)
T ss_pred CeEEEEEec
Confidence 999999854
No 107
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=98.31 E-value=5.8e-07 Score=65.53 Aligned_cols=71 Identities=17% Similarity=0.182 Sum_probs=52.4
Q ss_pred CCccccceeeeccCCCccceeeeeccc-CCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQE-DGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q 227 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~-~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~ 227 (259)
|+++.|+|+++++|| +|++|... +|++||+ .++++++ |. ...+. ..+++||.| .
T Consensus 1 G~~~~g~V~~v~~~G----~fv~l~~~~~~~~gll~~s~l~~~----------~~--~~~~~----~~~~~Gd~v~v~v~ 60 (79)
T cd05684 1 GKIYKGKVTSIMDFG----CFVQLEGLKGRKEGLVHISQLSFE----------GR--VANPS----DVVKRGQKVKVKVI 60 (79)
T ss_pred CCEEEEEEEEEEeee----EEEEEeCCCCCcEEEEEhHhccCC----------CC--cCChh----heeCCCCEEEEEEE
Confidence 456899999999999 99999322 4799999 6776633 21 12222 256999999 5
Q ss_pred EEecccchhhhhhchhhhh
Q 024995 228 EIQLSHSLIRKASKRHCNE 246 (259)
Q Consensus 228 ~v~~~~~~i~ls~k~~~~~ 246 (259)
++| ++++.+|+|++.++
T Consensus 61 ~vd--~~~i~~s~k~~~~~ 77 (79)
T cd05684 61 SIQ--NGKISLSMKDVDQD 77 (79)
T ss_pred EEe--CCEEEEEEEecccC
Confidence 777 78999999998764
No 108
>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=98.29 E-value=5e-07 Score=69.34 Aligned_cols=79 Identities=15% Similarity=0.119 Sum_probs=56.6
Q ss_pred CCCCccccceeeeccCCCccceeeeecccCCeeEEE-Eccccccccccchhhhhhccc---------CCCCCcceeeecc
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSN---------APPSGKKFTLLAR 221 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~r 221 (259)
++|+++.|+|.++.++| +|+.| ++|++|++ .++++++ +..|+.. ...........++
T Consensus 2 ~~G~vV~G~V~~v~~~g----l~v~L--~~g~~G~v~~seis~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~f~ 68 (100)
T cd05693 2 SEGMLVLGQVKEITKLD----LVISL--PNGLTGYVPITNISDA-------YTERLEELDEESEEEDDEEELPDLEDLFS 68 (100)
T ss_pred CCCCEEEEEEEEEcCCC----EEEEC--CCCcEEEEEHHHhhHH-------HHHHHHHhhhhccccccccccCCHHHhcc
Confidence 46888999999999999 99888 88999999 6777632 2223221 0011112334669
Q ss_pred CCCee----EEEecc---cchhhhhhchh
Q 024995 222 AGRQV----QEIQLS---HSLIRKASKRH 243 (259)
Q Consensus 222 ~G~~V----~~v~~~---~~~i~ls~k~~ 243 (259)
+||.| +.++.+ +++|.||+|.-
T Consensus 69 vGd~V~~kVi~~d~~~~~~~~i~LSlr~~ 97 (100)
T cd05693 69 VGQLVRCKVVSLDKSKSGKKRIELSLEPE 97 (100)
T ss_pred CCCEEEEEEEEccCCcCCCcEEEEEecHH
Confidence 99999 688887 67899999964
No 109
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=98.28 E-value=2.7e-06 Score=85.22 Aligned_cols=68 Identities=26% Similarity=0.485 Sum_probs=58.3
Q ss_pred CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccc-----------cChhhhcCCCCeEEEEEEEEeCC
Q 024995 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDRE 119 (259)
Q Consensus 56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~-----------~~~~~~~~~Gd~V~vkVl~id~~ 119 (259)
-+.|++++|+ +||+||+|.. .+++||||++++.++++ .+....|++||.|+|+|.++|.+
T Consensus 570 ~~iG~~~~g~I~~v~~~GifV~L~~----~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~ 645 (654)
T TIGR00358 570 DKVGTEFSGEISSVTRFGMFVRLDD----NGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNME 645 (654)
T ss_pred hCCCcEEEEEEEeEEcCcEEEEecC----CceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecc
Confidence 3679999999 9999999973 58999999999998742 22346799999999999999999
Q ss_pred CCeeEEEE
Q 024995 120 KSRITLSI 127 (259)
Q Consensus 120 ~~ri~lS~ 127 (259)
+++|.+++
T Consensus 646 ~~~I~f~l 653 (654)
T TIGR00358 646 TRSIIFEL 653 (654)
T ss_pred cCeEEEEE
Confidence 99999985
No 110
>PRK05807 hypothetical protein; Provisional
Probab=98.27 E-value=8.8e-07 Score=71.69 Aligned_cols=68 Identities=15% Similarity=0.176 Sum_probs=53.5
Q ss_pred CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
.+|++++|+|+.+++|| +||+| +|..||+ +|+++.. |+.. +...+++||.|
T Consensus 4 ~vG~vv~G~Vt~i~~~G----afV~L---~~~~Glvhiseis~~----------~v~~-------~~~~~kvGd~V~VkV 59 (136)
T PRK05807 4 KAGSILEGTVVNITNFG----AFVEV---EGKTGLVHISEVADT----------YVKD-------IREHLKEQDKVKVKV 59 (136)
T ss_pred cCCCEEEEEEEEEECCe----EEEEE---CCEEEEEEhhhcccc----------cccC-------ccccCCCCCEEEEEE
Confidence 35788999999999999 99988 5789999 7777632 3322 22356999999
Q ss_pred EEEecccchhhhhhchhh
Q 024995 227 QEIQLSHSLIRKASKRHC 244 (259)
Q Consensus 227 ~~v~~~~~~i~ls~k~~~ 244 (259)
++++. .++|+||+|++.
T Consensus 60 ~~id~-~gkI~LSlk~~~ 76 (136)
T PRK05807 60 ISIDD-NGKISLSIKQAM 76 (136)
T ss_pred EEECC-CCcEEEEEEecc
Confidence 56776 689999999986
No 111
>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=98.24 E-value=1.1e-06 Score=63.16 Aligned_cols=68 Identities=13% Similarity=0.192 Sum_probs=52.7
Q ss_pred CCCccccceeeeccCCCccceeeeeccc-CCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQE-DGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~-~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
+|+.+.|+|.+++++| +|++| . .+++|++ .++++.+. . .. ....+++||.|
T Consensus 2 ~g~~v~g~V~~i~~~g----~~v~l--~~~~~~g~i~~~~l~~~~----------~---~~----~~~~~~~Gd~v~v~i 58 (77)
T cd05708 2 VGQKIDGTVRRVEDYG----VFIDI--DGTNVSGLCHKSEISDNR----------V---AD----ASKLFRVGDKVRAKV 58 (77)
T ss_pred CCCEEEEEEEEEEcce----EEEEE--CCCCeEEEEEHHHCCCCc----------c---CC----HhHeecCCCEEEEEE
Confidence 4788999999999999 99998 4 3799999 56665321 1 11 22356999999
Q ss_pred EEEecccchhhhhhchh
Q 024995 227 QEIQLSHSLIRKASKRH 243 (259)
Q Consensus 227 ~~v~~~~~~i~ls~k~~ 243 (259)
.+++.+++++.+++|+.
T Consensus 59 ~~vd~~~~~i~ls~k~~ 75 (77)
T cd05708 59 LKIDAEKKRISLGLKAS 75 (77)
T ss_pred EEEeCCCCEEEEEEEee
Confidence 68899999999999874
No 112
>PRK08059 general stress protein 13; Validated
Probab=98.23 E-value=9.3e-07 Score=70.27 Aligned_cols=73 Identities=12% Similarity=0.195 Sum_probs=57.8
Q ss_pred CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
++|+++.|+|.++.++| +|++| .++++|++ .++++.+ |. .. ....+++||.|
T Consensus 6 k~G~iv~G~V~~i~~~G----~fV~i--~~~~~Gli~~sel~~~----------~~---~~----~~~~~~vGD~I~vkI 62 (123)
T PRK08059 6 EVGSVVTGKVTGIQPYG----AFVAL--DEETQGLVHISEITHG----------FV---KD----IHDFLSVGDEVKVKV 62 (123)
T ss_pred CCCCEEEEEEEEEecce----EEEEE--CCCCEEEEEHHHCCcc----------cc---cC----HHHcCCCCCEEEEEE
Confidence 35778999999999999 99988 78999999 5666522 11 11 12256999999
Q ss_pred EEEecccchhhhhhchhhhhh
Q 024995 227 QEIQLSHSLIRKASKRHCNEY 247 (259)
Q Consensus 227 ~~v~~~~~~i~ls~k~~~~~p 247 (259)
.++|.+++++.+|+|++..+|
T Consensus 63 ~~id~~~~~i~lslk~~~~~~ 83 (123)
T PRK08059 63 LSVDEEKGKISLSIRATEEAP 83 (123)
T ss_pred EEEECCCCeEEEEEEEcccCc
Confidence 588888999999999998888
No 113
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=98.23 E-value=1.9e-06 Score=79.80 Aligned_cols=98 Identities=16% Similarity=0.273 Sum_probs=72.5
Q ss_pred cccCCCCEEEEEEEEEeCCCCEEEEEe-ch--------hhHhhhccCC--CCCCEEEEE-----eee-EEEEEccCCCCc
Q 024995 18 AKGLTGSIISVKVIQANEEMKKLVFSE-KD--------AVWNKYSSRV--NVEDIFVGR-----DYG-AFIHLRFPDGLY 80 (259)
Q Consensus 18 ~~~~vG~~v~~~Vl~id~~~~~v~lS~-k~--------~~~~~~~~~l--~~G~iv~G~-----~~G-~fV~l~~~~g~~ 80 (259)
.+..+|+++++.|...+ -++..++. |+ ..++.++..+ +.|++++|+ +.| +||+++
T Consensus 82 ~~~~vGD~I~~~I~~~~--fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG------ 153 (341)
T TIGR01953 82 PDVQIGDEVKKEIPPEN--FGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELG------ 153 (341)
T ss_pred cccccCCEEEEEecccC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEEC------
Confidence 44569999999874333 24444443 32 1244566666 599999999 556 699997
Q ss_pred cEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCC--CCeeEEEEec
Q 024995 81 HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDRE--KSRITLSIKQ 129 (259)
Q Consensus 81 gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~--~~ri~lS~K~ 129 (259)
+++|++|.+|.. |.+.|++||.++|.|++++.. ..+|.||++.
T Consensus 154 ~~ea~LP~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~ 198 (341)
T TIGR01953 154 KTEGILPKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTH 198 (341)
T ss_pred CeEEEecHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCc
Confidence 799999999987 345699999999999999954 3579999865
No 114
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=98.23 E-value=1.1e-05 Score=71.53 Aligned_cols=96 Identities=14% Similarity=0.206 Sum_probs=76.4
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechhh-HhhhccCCCC---CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecC
Q 024995 22 TGSIISVKVIQANEEMKKLVFSEKDAV-WNKYSSRVNV---EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS 92 (259)
Q Consensus 22 vG~~v~~~Vl~id~~~~~v~lS~k~~~-~~~~~~~l~~---G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels 92 (259)
+||.+-|. +.+|+++ |+...++... .+........ ++.+.|+ ..|.||-+. .+.-||||-||..
T Consensus 117 ~Gd~l~v~-l~~Dkk~-Ri~g~~a~~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e-----~~~~GfIh~sEr~ 189 (287)
T COG2996 117 KGDKLLVY-LYVDKKG-RIWGTLAIEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITE-----NGYLGFIHKSERF 189 (287)
T ss_pred CCCEEEEE-EEEccCC-cEEEEecchhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEc-----CCeEEEEcchhhc
Confidence 89999999 8999764 8888877643 4444444444 8888888 789999997 3899999999863
Q ss_pred cccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccC
Q 024995 93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEED 133 (259)
Q Consensus 93 ~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~ 133 (259)
..++.|+.+.++|+.+.. .++|.||++....+
T Consensus 190 --------~~prlG~~l~~rVi~~re-Dg~lnLSl~p~~~E 221 (287)
T COG2996 190 --------AEPRLGERLTARVIGVRE-DGKLNLSLRPRAHE 221 (287)
T ss_pred --------ccccCCceEEEEEEEEcc-CCeeecccccccHH
Confidence 236789999999999996 89999999876443
No 115
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.22 E-value=1.6e-06 Score=80.85 Aligned_cols=98 Identities=16% Similarity=0.243 Sum_probs=71.1
Q ss_pred cccCCCCEEEEEEEEEeCCCCEEEEEechh--------hHhhhccCC--CCCCEEEEE-----eeeEEEEEccCCCCccE
Q 024995 18 AKGLTGSIISVKVIQANEEMKKLVFSEKDA--------VWNKYSSRV--NVEDIFVGR-----DYGAFIHLRFPDGLYHL 82 (259)
Q Consensus 18 ~~~~vG~~v~~~Vl~id~~~~~v~lS~k~~--------~~~~~~~~l--~~G~iv~G~-----~~G~fV~l~~~~g~~gi 82 (259)
.+..+|+.+.+.+...+-. +....+.|+. .++..+..+ +.|+++.|+ ++|+||+++ ++
T Consensus 85 ~~~~vGD~i~~~I~~~~fg-R~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg------~v 157 (362)
T PRK12327 85 PAYELGDVIEIEVTPKDFG-RIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLG------KI 157 (362)
T ss_pred ccccCCCEEEEecCcCCCC-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeC------Ce
Confidence 3456899999886544322 2222222221 244566777 999999999 789999997 79
Q ss_pred EEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCC--eeEEEEe
Q 024995 83 TGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIK 128 (259)
Q Consensus 83 ~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~--ri~lS~K 128 (259)
+||||.+++.. .+.|++||.++|.|++++.+++ +|.||+.
T Consensus 158 Ea~LP~~E~ip------~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt 199 (362)
T PRK12327 158 EAVLPPAEQIP------GETYKHGDRIKVYVVKVEKTTKGPQIFVSRT 199 (362)
T ss_pred EEEecHHHcCC------CCCCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence 99999888743 5679999999999999996544 5777763
No 116
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.19 E-value=5.7e-06 Score=62.50 Aligned_cols=73 Identities=22% Similarity=0.276 Sum_probs=56.8
Q ss_pred CCCCCEEEEE-----eeeEEEEEccCCC---CccEEEEEEceecCccccc--ChhhhcCCCCeEEEEEEEEeCCCCeeEE
Q 024995 56 VNVEDIFVGR-----DYGAFIHLRFPDG---LYHLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKIDREKSRITL 125 (259)
Q Consensus 56 l~~G~iv~G~-----~~G~fV~l~~~~g---~~gi~glv~isels~~~~~--~~~~~~~~Gd~V~vkVl~id~~~~ri~l 125 (259)
+++|+++.|+ ...++|++...++ .....|++|++++...+.. ++.+.|++||.|+|+|++++. .+.+.|
T Consensus 4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~-~~~~~L 82 (92)
T cd05791 4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD-ASSYYL 82 (92)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCC-CCCcEE
Confidence 5788888888 5568888821111 0367999999999877665 788999999999999999985 577889
Q ss_pred EEec
Q 024995 126 SIKQ 129 (259)
Q Consensus 126 S~K~ 129 (259)
|+++
T Consensus 83 st~~ 86 (92)
T cd05791 83 STAE 86 (92)
T ss_pred EecC
Confidence 9875
No 117
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.17 E-value=1.5e-06 Score=77.67 Aligned_cols=74 Identities=15% Similarity=0.223 Sum_probs=58.5
Q ss_pred CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q 227 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~ 227 (259)
+|+.+.|+|.++.+|| +|++|...+|++||+ .|+++.. |+.. ....+++||.| +
T Consensus 8 ~GdiV~G~V~~I~~~G----~fV~L~e~~gieGlI~iSEls~~----------~i~~-------i~~~~kvGd~V~vkVi 66 (262)
T PRK03987 8 EGELVVGTVKEVKDFG----AFVTLDEYPGKEGFIHISEVASG----------WVKN-------IRDHVKEGQKVVCKVI 66 (262)
T ss_pred CCCEEEEEEEEEECCE----EEEEECCCCCcEEEEEHHHcCcc----------cccC-------HHHhCCCCCEEEEEEE
Confidence 5788999999999999 999995435999999 6777632 3322 12256999999 6
Q ss_pred EEecccchhhhhhchhhhhh
Q 024995 228 EIQLSHSLIRKASKRHCNEY 247 (259)
Q Consensus 228 ~v~~~~~~i~ls~k~~~~~p 247 (259)
++|.++++|.||+|++.++-
T Consensus 67 ~VD~~k~~I~LSlK~v~~~e 86 (262)
T PRK03987 67 RVDPRKGHIDLSLKRVNEHQ 86 (262)
T ss_pred EEecccCeEEEEEEecccch
Confidence 89999999999999887654
No 118
>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=98.06 E-value=3.3e-06 Score=58.93 Aligned_cols=64 Identities=20% Similarity=0.321 Sum_probs=47.4
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE 228 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~ 228 (259)
|+++.|+|.+++++| +|+.+ .++++||+ .++++.+. . ..+. ..+++||.+ .+
T Consensus 1 G~~~~g~V~~i~~~g----~~v~i--~~~~~g~l~~~~l~~~~----------~---~~~~----~~~~~Gd~v~v~v~~ 57 (69)
T cd05692 1 GSVVEGTVTRLKPFG----AFVEL--GGGISGLVHISQIAHKR----------V---KDVK----DVLKEGDKVKVKVLS 57 (69)
T ss_pred CCEEEEEEEEEEeee----EEEEE--CCCCEEEEEhHHcCCcc----------c---CCHH----HccCCCCEEEEEEEE
Confidence 566999999999999 99988 78999999 56665321 1 1122 245999999 46
Q ss_pred Eecccchhhhhhc
Q 024995 229 IQLSHSLIRKASK 241 (259)
Q Consensus 229 v~~~~~~i~ls~k 241 (259)
++. .+++.||+|
T Consensus 58 ~~~-~~~i~ls~k 69 (69)
T cd05692 58 IDA-RGRISLSIK 69 (69)
T ss_pred ECC-CCcEEEEEC
Confidence 776 678888875
No 119
>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=98.02 E-value=5.1e-06 Score=58.88 Aligned_cols=65 Identities=5% Similarity=0.053 Sum_probs=49.2
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE 228 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~ 228 (259)
|+++.|+|.++.++| +|++| ..+++|++ .++++... ... +...+++||.+ ++
T Consensus 1 G~iv~g~V~~i~~~~----~~v~l--~~~~~g~l~~~e~~~~~-------------~~~----~~~~~~~Gd~i~~~i~~ 57 (70)
T cd05687 1 GDIVKGTVVSVDDDE----VLVDI--GYKSEGIIPISEFSDDP-------------IEN----GEDEVKVGDEVEVYVLR 57 (70)
T ss_pred CCEEEEEEEEEeCCE----EEEEe--CCCceEEEEHHHhCccc-------------cCC----HhHcCCCCCEEEEEEEE
Confidence 567999999999999 99888 77899999 56655221 111 22356999999 68
Q ss_pred Eecccchhhhhhc
Q 024995 229 IQLSHSLIRKASK 241 (259)
Q Consensus 229 v~~~~~~i~ls~k 241 (259)
++.+..+|.||+|
T Consensus 58 ~~~~~~~i~lS~~ 70 (70)
T cd05687 58 VEDEEGNVVLSKR 70 (70)
T ss_pred EECCCCeEEEEeC
Confidence 8877788988875
No 120
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.01 E-value=4.7e-06 Score=83.37 Aligned_cols=68 Identities=12% Similarity=0.065 Sum_probs=51.2
Q ss_pred CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
..|+++.|+|++|++|| +|++| .+|++||+ +|+++. + .|..++.++ ..++++||.|
T Consensus 646 ~vG~i~~GkV~~I~dfG----aFVel--~~G~eGLvHISeisd--------l-s~~~rv~~~----~dv~kvGd~V~VKV 706 (719)
T TIGR02696 646 EVGERFLGTVVKTTAFG----AFVSL--LPGKDGLLHISQIRK--------L-AGGKRVENV----EDVLSVGQKIQVEI 706 (719)
T ss_pred CCCCEEEEEEEEEECce----EEEEe--cCCceEEEEhhhccc--------c-ccccCcCCH----HHcCCCCCEEEEEE
Confidence 46888999999999999 99998 79999999 677751 1 133333433 3367999999
Q ss_pred EEEecccchhhhh
Q 024995 227 QEIQLSHSLIRKA 239 (259)
Q Consensus 227 ~~v~~~~~~i~ls 239 (259)
++||. ++||+|+
T Consensus 707 l~ID~-~gKI~L~ 718 (719)
T TIGR02696 707 ADIDD-RGKLSLV 718 (719)
T ss_pred EEECC-CCCeeec
Confidence 67773 6788875
No 121
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.00 E-value=4.5e-06 Score=61.69 Aligned_cols=72 Identities=6% Similarity=0.034 Sum_probs=51.6
Q ss_pred CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
++|+++.|+|.++.++| +++++ .++++|++ .|+++..+ .+.+. ......+++||.+
T Consensus 5 ~~GdiV~g~V~~i~~~g----~~v~i--~~~~~G~l~~se~~~~~------~~~~~-------~~~~~~l~vGd~i~~~V 65 (86)
T cd05789 5 EVGDVVIGRVTEVGFKR----WKVDI--NSPYDAVLPLSEVNLPR------TDEDE-------LNMRSYLDEGDLIVAEV 65 (86)
T ss_pred CCCCEEEEEEEEECCCE----EEEEC--CCCeEEEEEHHHccCCC------Cccch-------HHHHhhCCCCCEEEEEE
Confidence 46888999999999999 99888 78999999 56655210 00011 1122356999999
Q ss_pred EEEecccchhhhhhchh
Q 024995 227 QEIQLSHSLIRKASKRH 243 (259)
Q Consensus 227 ~~v~~~~~~i~ls~k~~ 243 (259)
++++.+ +++.||+|+.
T Consensus 66 ~~~~~~-~~i~LS~~~~ 81 (86)
T cd05789 66 QSVDSD-GSVSLHTRSL 81 (86)
T ss_pred EEECCC-CCEEEEeCcc
Confidence 577665 7899999874
No 122
>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=97.97 E-value=7.2e-06 Score=57.05 Aligned_cols=63 Identities=13% Similarity=0.143 Sum_probs=46.9
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE 228 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~ 228 (259)
|+.+.|+|++++++| +|+++ .+++.|++ .++++.+ |.. .+ ...+++||.+ ++
T Consensus 1 g~~~~g~V~~i~~~G----~fv~l--~~~~~g~~~~~~l~~~----------~~~---~~----~~~~~~Gd~v~v~i~~ 57 (68)
T cd05685 1 GMVLEGVVTNVTDFG----AFVDI--GVKQDGLIHISKMADR----------FVS---HP----SDVVSVGDIVEVKVIS 57 (68)
T ss_pred CCEEEEEEEEEeccc----EEEEc--CCCCEEEEEHHHCCCc----------ccc---CH----HHhcCCCCEEEEEEEE
Confidence 456899999999999 99888 78899999 5555422 221 11 2245999999 68
Q ss_pred Eecccchhhhh
Q 024995 229 IQLSHSLIRKA 239 (259)
Q Consensus 229 v~~~~~~i~ls 239 (259)
+|.+++++.||
T Consensus 58 vd~~~~~i~ls 68 (68)
T cd05685 58 IDEERGRISLS 68 (68)
T ss_pred EECCCCEEecC
Confidence 88888888765
No 123
>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=97.92 E-value=1.5e-05 Score=58.04 Aligned_cols=75 Identities=13% Similarity=0.130 Sum_probs=49.3
Q ss_pred CCccccceeeeccCCCccceeeeecccC-CeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q 227 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~-gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~ 227 (259)
|+.++|+|++++++| +|++| .+ |++|++ .+++..+.- ..+-..|...... ....+++||.| .
T Consensus 2 g~~~~g~V~~v~~~G----~fv~l--~~~~~~G~v~~~~l~~~~~--~~d~~~~~~~~~~----~~~~~~~gd~v~v~v~ 69 (83)
T cd04471 2 GEEFDGVISGVTSFG----LFVEL--DNLTVEGLVHVSTLGDDYY--EFDEENHALVGER----TGKVFRLGDKVKVRVV 69 (83)
T ss_pred CCEEEEEEEeEEeee----EEEEe--cCCCEEEEEEEEecCCCcE--EEcccceEEEecc----CCCEEcCCCEEEEEEE
Confidence 667999999999999 99999 66 899999 666552210 0000000001111 12356999999 6
Q ss_pred EEecccchhhhhh
Q 024995 228 EIQLSHSLIRKAS 240 (259)
Q Consensus 228 ~v~~~~~~i~ls~ 240 (259)
++|.++++|.+++
T Consensus 70 ~vd~~~~~i~~~l 82 (83)
T cd04471 70 RVDLDRRKIDFEL 82 (83)
T ss_pred EeccccCEEEEEE
Confidence 8888888888775
No 124
>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=97.91 E-value=1e-05 Score=56.93 Aligned_cols=62 Identities=8% Similarity=0.161 Sum_probs=46.4
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE 228 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~ 228 (259)
|++++|+|.++.++| +|+++ +|++||+ .|+++... . ..+.. .+||.+ ++
T Consensus 1 G~iv~g~V~~v~~~G----~~v~l---~g~~gfip~s~~~~~~----------~---~~~~~------~vG~~i~~~i~~ 54 (67)
T cd04465 1 GEIVEGKVTEKVKGG----LIVDI---EGVRAFLPASQVDLRP----------V---EDLDE------YVGKELKFKIIE 54 (67)
T ss_pred CCEEEEEEEEEECCe----EEEEE---CCEEEEEEHHHCCCcc----------c---CChHH------hCCCEEEEEEEE
Confidence 566999999999999 99888 6899999 56665221 1 11111 478888 79
Q ss_pred Eecccchhhhhhc
Q 024995 229 IQLSHSLIRKASK 241 (259)
Q Consensus 229 v~~~~~~i~ls~k 241 (259)
+|.++++|.||.|
T Consensus 55 vd~~~~~i~lS~k 67 (67)
T cd04465 55 IDRERNNIVLSRR 67 (67)
T ss_pred EeCCCCEEEEEcC
Confidence 9998899999875
No 125
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.88 E-value=1.3e-05 Score=80.87 Aligned_cols=69 Identities=20% Similarity=0.216 Sum_probs=55.3
Q ss_pred CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
++|+++.|+|+++.+|| +|++| .+|++||+ +|+++++. + ..+. ..+++||.|
T Consensus 620 ~vG~v~~G~V~~I~~fG----afVei--~~~~~GllhiSels~~~----------v---~~~~----~v~kvGD~V~VkV 676 (693)
T PRK11824 620 EVGEIYEGKVVRIVDFG----AFVEI--LPGKDGLVHISEIADER----------V---EKVE----DVLKEGDEVKVKV 676 (693)
T ss_pred cCCeEEEEEEEEEECCe----EEEEE--CCCCEEEEEeeeccCcc----------c---cCcc----ceeCCCCEEEEEE
Confidence 56889999999999999 99999 78999999 78877331 2 2222 366999999
Q ss_pred EEEecccchhhhhhchhh
Q 024995 227 QEIQLSHSLIRKASKRHC 244 (259)
Q Consensus 227 ~~v~~~~~~i~ls~k~~~ 244 (259)
+++|.+ ++|+||+|.+.
T Consensus 677 ~~iD~~-grI~LS~k~~~ 693 (693)
T PRK11824 677 LEIDKR-GRIRLSRKAVL 693 (693)
T ss_pred EEECCC-CcEEEEEEecC
Confidence 678877 89999999763
No 126
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=97.87 E-value=1.2e-05 Score=70.68 Aligned_cols=80 Identities=26% Similarity=0.456 Sum_probs=71.5
Q ss_pred CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEecc
Q 024995 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (259)
Q Consensus 56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~ 130 (259)
..++++|-+. +.|+||.|-.|+ .++|++-.||||..++....+..++|..=.|.|+++|+++|.|.||.+.+
T Consensus 14 Pev~e~VmvnV~sIaemGayv~LlEYn---niEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrV 90 (304)
T KOG2916|consen 14 PEVEEIVMVNVRSIAEMGAYVKLLEYN---NIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRV 90 (304)
T ss_pred CCcccEEEEEeeEehhccceEeeeecC---CcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccC
Confidence 5778888777 899999998766 69999999999999999999999999999999999999999999999998
Q ss_pred ccCcchHh
Q 024995 131 EEDPLLET 138 (259)
Q Consensus 131 ~~~p~~~~ 138 (259)
.++.-.+.
T Consensus 91 s~ed~~kC 98 (304)
T KOG2916|consen 91 SPEDKEKC 98 (304)
T ss_pred CHHHHHHH
Confidence 87655443
No 127
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=97.78 E-value=2.4e-05 Score=54.59 Aligned_cols=63 Identities=17% Similarity=0.194 Sum_probs=46.3
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE 228 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~ 228 (259)
|+.+.|+|.++.+|| +|+++ .+++.||+ .++++.. |+. .+. ..+++||.| .+
T Consensus 1 g~~~~g~V~~v~~~G----~~v~l--~~~~~g~l~~~~l~~~----------~~~---~~~----~~~~~Gd~v~v~v~~ 57 (68)
T cd04472 1 GKIYEGKVVKIKDFG----AFVEI--LPGKDGLVHISELSDE----------RVE---KVE----DVLKVGDEVKVKVIE 57 (68)
T ss_pred CCEEEEEEEEEEEeE----EEEEe--CCCCEEEEEhHHcCCc----------ccc---CHH----HccCCCCEEEEEEEE
Confidence 456899999999999 99988 67899999 5665522 121 111 256999999 57
Q ss_pred Eecccchhhhhh
Q 024995 229 IQLSHSLIRKAS 240 (259)
Q Consensus 229 v~~~~~~i~ls~ 240 (259)
+|. ++++.+|+
T Consensus 58 ~d~-~~~i~ls~ 68 (68)
T cd04472 58 VDD-RGRISLSR 68 (68)
T ss_pred ECC-CCcEEeeC
Confidence 787 77887774
No 128
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.73 E-value=4.5e-05 Score=53.11 Aligned_cols=62 Identities=16% Similarity=0.283 Sum_probs=46.3
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE 228 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~ 228 (259)
|+.+.|+|.++.++| +|+++ . +++|++ .++++.. . ...+. ..+++||.| .+
T Consensus 2 g~~~~g~V~~v~~~g----~~v~l--~-~~~g~l~~~e~~~~------------~-~~~~~----~~~~~Gd~v~v~i~~ 57 (68)
T cd05688 2 GDVVEGTVKSITDFG----AFVDL--G-GVDGLLHISDMSWG------------R-VKHPS----EVVNVGDEVEVKVLK 57 (68)
T ss_pred CCEEEEEEEEEEeee----EEEEE--C-CeEEEEEhHHCCCc------------c-ccCHh----HEECCCCEEEEEEEE
Confidence 677999999999999 99988 3 799999 5554411 1 11122 256999999 68
Q ss_pred Eecccchhhhh
Q 024995 229 IQLSHSLIRKA 239 (259)
Q Consensus 229 v~~~~~~i~ls 239 (259)
+|.+++++.||
T Consensus 58 vd~~~~~i~ls 68 (68)
T cd05688 58 IDKERKRISLG 68 (68)
T ss_pred EECCCCEEecC
Confidence 88888888775
No 129
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=97.72 E-value=3.4e-05 Score=53.58 Aligned_cols=66 Identities=15% Similarity=0.232 Sum_probs=49.7
Q ss_pred CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q 227 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~ 227 (259)
+|+.+.|+|.++.++| +|+++ .+++.|++ .+++... + .. +....+++||.+ .
T Consensus 2 ~G~~v~g~V~~v~~~g----~~v~i--~~~~~g~l~~~~~~~~----------~---~~----~~~~~~~~G~~v~~~V~ 58 (72)
T smart00316 2 VGDVVEGTVTEITPFG----AFVDL--GNGVEGLIPISELSDK----------R---VK----DPEEVLKVGDEVKVKVL 58 (72)
T ss_pred CCCEEEEEEEEEEccE----EEEEe--CCCCEEEEEHHHCCcc----------c---cC----CHHHeecCCCEEEEEEE
Confidence 4788999999999999 99888 77999999 5555522 1 11 122256999999 6
Q ss_pred EEecccchhhhhhc
Q 024995 228 EIQLSHSLIRKASK 241 (259)
Q Consensus 228 ~v~~~~~~i~ls~k 241 (259)
.++.+++++.+|++
T Consensus 59 ~~~~~~~~i~ls~~ 72 (72)
T smart00316 59 SVDEEKGRIILSLK 72 (72)
T ss_pred EEeCCCCEEEEEeC
Confidence 88888888888764
No 130
>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=97.70 E-value=3.4e-05 Score=57.74 Aligned_cols=54 Identities=11% Similarity=0.158 Sum_probs=39.6
Q ss_pred CCCccccceeeeccC--CCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee
Q 024995 153 SSSMSSSNSNTIEPL--PGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV 226 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~--G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V 226 (259)
.|+++.|+|+++.+| | +|++| .+|.+||+ .|++++.. ..++.+ ....+++||.|
T Consensus 7 ~G~iy~g~V~~i~~~~~G----aFV~l--~~g~~Gllh~seis~~~----------~~~v~~----~~~~~~~Gd~v 63 (88)
T cd04453 7 VGNIYLGRVKKIVPGLQA----AFVDI--GLGKNGFLHLSDILPAY----------FKKHKK----IAKLLKEGQEI 63 (88)
T ss_pred CCCEEEEEEEEeccCCcE----EEEEe--CCCCEEEEEhHHcCchh----------ccccCC----HHHcCCCCCEE
Confidence 578899999999997 8 99988 78999999 67776210 011222 22367999999
No 131
>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=97.62 E-value=7.5e-05 Score=54.25 Aligned_cols=56 Identities=14% Similarity=0.193 Sum_probs=43.0
Q ss_pred CCCccccceeeeccCCCccceeeeecccCCeeEEEE-ccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q 227 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~ 227 (259)
.|+.+.|+|+++++|| +|+++ .++++||++ |++. . .++.||.+ +
T Consensus 16 ~G~~~~g~V~~i~~~G----~fV~l--~~~~~Glv~~se~~---------------------~----~~~iGd~v~v~I~ 64 (77)
T cd04473 16 VGKLYKGKVNGVAKYG----VFVDL--NDHVRGLIHRSNLL---------------------R----DYEVGDEVIVQVT 64 (77)
T ss_pred CCCEEEEEEEeEecce----EEEEE--CCCcEEEEEchhcc---------------------C----cCCCCCEEEEEEE
Confidence 4677999999999999 99998 788999995 4421 1 24888888 5
Q ss_pred EEecccchhhhhh
Q 024995 228 EIQLSHSLIRKAS 240 (259)
Q Consensus 228 ~v~~~~~~i~ls~ 240 (259)
++ .++++|.+++
T Consensus 65 ~i-~e~~~i~l~~ 76 (77)
T cd04473 65 DI-PENGNIDLIP 76 (77)
T ss_pred EE-CCCCcEEEEE
Confidence 66 6777777764
No 132
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=97.62 E-value=3e-05 Score=77.57 Aligned_cols=72 Identities=10% Similarity=0.115 Sum_probs=59.2
Q ss_pred ccCCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee--
Q 024995 150 ISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV-- 226 (259)
Q Consensus 150 ~~~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V-- 226 (259)
+.++|+.+.|+|+++++|| +||.| .-..+||+ +|+++.. | ++.|.. ++++||.|
T Consensus 655 dLk~Gm~leg~Vrnv~~fg----afVdI--gv~qDglvHis~ls~~-------f------v~~P~~----vv~vGdiV~v 711 (780)
T COG2183 655 DLKPGMILEGTVRNVVDFG----AFVDI--GVHQDGLVHISQLSDK-------F------VKDPNE----VVKVGDIVKV 711 (780)
T ss_pred hccCCCEEEEEEEEeeecc----ceEEe--ccccceeeeHHHhhhh-------h------cCChHH----hcccCCEEEE
Confidence 3678999999999999999 99988 67889998 7887733 1 343444 77999999
Q ss_pred --EEEecccchhhhhhchhh
Q 024995 227 --QEIQLSHSLIRKASKRHC 244 (259)
Q Consensus 227 --~~v~~~~~~i~ls~k~~~ 244 (259)
++||..+++|+|||+.-.
T Consensus 712 ~V~~vD~~r~rI~Lsmr~~~ 731 (780)
T COG2183 712 KVIEVDTARKRIALSMRLDE 731 (780)
T ss_pred EEEEEecccCeeeeEeeccC
Confidence 799999999999999643
No 133
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=97.55 E-value=0.00013 Score=62.13 Aligned_cols=100 Identities=13% Similarity=0.140 Sum_probs=65.3
Q ss_pred cCCCCeEEEEEE---EEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCccceeeeecc
Q 024995 103 LNEGDEVRVKVI---KIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (259)
Q Consensus 103 ~~~Gd~V~vkVl---~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~~fv~l~~ 179 (259)
|..++.+.+.+. ++|.++++|.+ +||..... .+. +|+++.|+|+++.++| +|++|..
T Consensus 27 y~~~~~i~as~~G~~~id~~~~~Isv-------~P~~~~~~-~~~--------~GdiV~GkV~~i~~~g----~~V~I~~ 86 (189)
T PRK09521 27 YEDNGEVYASVVGKVFIDDINRKISV-------IPFKKTPP-LLK--------KGDIVYGRVVDVKEQR----ALVRIVS 86 (189)
T ss_pred EeeCCEEEEEeeEEEEEcCCCCEEEE-------ecCcCCCC-CCC--------CCCEEEEEEEEEcCCe----EEEEEEE
Confidence 445666776554 44766777776 47753221 122 4777999999999999 9998832
Q ss_pred --------cCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhch
Q 024995 180 --------EDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKR 242 (259)
Q Consensus 180 --------~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~ 242 (259)
.+++.|++ .++++... . . +....+++||.| +.++ +++.||+|.
T Consensus 87 ~~~~~~~l~~~~~G~l~~s~i~~~~----------~---~----~~~~~~~~GD~V~akV~~i~---~~i~LS~k~ 142 (189)
T PRK09521 87 IEGSERELATSKLAYIHISQVSDGY----------V---E----SLTDAFKIGDIVRAKVISYT---DPLQLSTKG 142 (189)
T ss_pred ecccccccCCCceeeEEhhHcChhh----------h---h----hHHhccCCCCEEEEEEEecC---CcEEEEEec
Confidence 35799999 55554211 1 1 122356999999 3444 789999886
No 134
>PRK05054 exoribonuclease II; Provisional
Probab=97.53 E-value=0.00027 Score=70.88 Aligned_cols=65 Identities=14% Similarity=0.114 Sum_probs=52.7
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccc--c-c--C-------hhhhcCCCCeEEEEEEEEeCCCC
Q 024995 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--I-Q--D-------IRDILNEGDEVRVKVIKIDREKS 121 (259)
Q Consensus 59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~--~-~--~-------~~~~~~~Gd~V~vkVl~id~~~~ 121 (259)
|+.+.|. +||+||+|.. .+++||||++.|...+ . - + -...|++||.|+|+|.++|.+++
T Consensus 562 ~~~f~g~I~~v~~~G~fV~l~~----~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~ 637 (644)
T PRK05054 562 DTRFAAEIIDISRGGMRVRLLE----NGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETR 637 (644)
T ss_pred CeEEEEEEEeeecCcEEEEEeC----CceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccC
Confidence 4588888 9999999974 5899999999996531 1 1 1 12469999999999999999999
Q ss_pred eeEEEE
Q 024995 122 RITLSI 127 (259)
Q Consensus 122 ri~lS~ 127 (259)
+|.+++
T Consensus 638 ~i~~~~ 643 (644)
T PRK05054 638 SIIARP 643 (644)
T ss_pred eEEEEE
Confidence 998875
No 135
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.53 E-value=0.0003 Score=59.36 Aligned_cols=122 Identities=16% Similarity=0.205 Sum_probs=74.4
Q ss_pred CCCCCCCCCchhHhhhcc-cCCCCEEE-----EEEEEEeC-CCCEEEEEechh----hHhhhccCCCCCCEEEEE-----
Q 024995 2 SPSHSCKEPQKSIHEIAK-GLTGSIIS-----VKVIQANE-EMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR----- 65 (259)
Q Consensus 2 ~~~~~~~~p~~~~~~~~~-~~vG~~v~-----~~Vl~id~-~~~~v~lS~k~~----~~~~~~~~l~~G~iv~G~----- 65 (259)
.|++|..+....+.+.++ .+.|+.+. +.|.+++. ..+++.=.--.+ .+..+.-+...|++++|.
T Consensus 14 ~P~~f~~~~~~~i~~~L~~~~egkv~~~~GliV~v~di~~i~~G~I~~gdG~~~~~V~FraivFrPf~gEVv~g~V~~v~ 93 (176)
T PTZ00162 14 KPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDVN 93 (176)
T ss_pred CHHHcCccHHHHHHHHHHHHHCCCCcCcccEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEEecCCCCEEEEEEEEEe
Confidence 467776655555544443 34454332 33344433 234443221111 133345578999999999
Q ss_pred eeeEEEEEccCCCCccEEEEEEceecCcccc------------cChhhhcCCCCeEEEEEEEEeCCCCe--eEEEEec
Q 024995 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI------------QDIRDILNEGDEVRVKVIKIDREKSR--ITLSIKQ 129 (259)
Q Consensus 66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~------------~~~~~~~~~Gd~V~vkVl~id~~~~r--i~lS~K~ 129 (259)
++|+||.++ .+++|+|.++|..... .+-...++.|+.|++||..+..+.+. ...|+|+
T Consensus 94 ~~G~~v~~G------p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~~i~T~~~ 165 (176)
T PTZ00162 94 KLGFFAQAG------PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLFAIATINS 165 (176)
T ss_pred cceEEEEee------CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcEEEEEecC
Confidence 899999998 5889999999974321 11234589999999999888654433 3445543
No 136
>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=97.46 E-value=0.00019 Score=50.90 Aligned_cols=60 Identities=10% Similarity=0.183 Sum_probs=42.6
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE 228 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~ 228 (259)
|+++.|+|+++.++| +|++| .+|++|++ .++++.+ |.. ...+.. .+++||.| ++
T Consensus 1 G~iV~g~V~~i~~~g----i~v~l--~~~i~g~i~~~~i~~~----------~~~-~~~~~~----~~~~Gd~i~~kVl~ 59 (70)
T cd05702 1 GDLVKAKVKSVKPTQ----LNVQL--ADNVHGRIHVSEVFDE----------WPD-GKNPLS----KFKIGQKIKARVIG 59 (70)
T ss_pred CCEEEEEEEEEECCc----EEEEe--CCCcEEEEEHHHhccc----------ccc-ccChhH----hCCCCCEEEEEEEE
Confidence 567999999999999 99888 78999999 5666532 211 111222 45999999 56
Q ss_pred Eecccc
Q 024995 229 IQLSHS 234 (259)
Q Consensus 229 v~~~~~ 234 (259)
++.+++
T Consensus 60 ~d~~~~ 65 (70)
T cd05702 60 GHDAKT 65 (70)
T ss_pred EeCccc
Confidence 666554
No 137
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.44 E-value=0.00052 Score=49.33 Aligned_cols=64 Identities=19% Similarity=0.222 Sum_probs=50.3
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccC--hhhhcCCCCeE-EEEEEEEeCCCCeeEEEEe
Q 024995 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD--IRDILNEGDEV-RVKVIKIDREKSRITLSIK 128 (259)
Q Consensus 59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~--~~~~~~~Gd~V-~vkVl~id~~~~ri~lS~K 128 (259)
|++++|+ +-+++|++.+ .|+.|++|..++|++.-+. .-..+++||++ .+.|+ |...+.|.+|.|
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~----~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL--~~~~r~i~lt~K 72 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILP----EEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecC----CCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence 5677777 5679999985 5899999999999943222 34558999999 99998 777888888865
No 138
>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=97.41 E-value=0.00024 Score=54.05 Aligned_cols=86 Identities=10% Similarity=0.075 Sum_probs=57.3
Q ss_pred ccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEe
Q 024995 156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQ 230 (259)
Q Consensus 156 ~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~ 230 (259)
++.|+|..+.++| +|++| . +++|++ .++++.+.-..-+.-..|... +....+++||.| .++|
T Consensus 2 vv~g~V~~i~~~G----ifV~l--~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~------~~~~~~~~Gd~v~vkI~~vd 68 (99)
T cd04460 2 VVEGEVVEVVDFG----AFVRI--G-PVDGLLHISQIMDDYISYDPKNKRLIGE------ETKRVLKVGDVVRARIVAVS 68 (99)
T ss_pred EEEEEEEEEEecc----EEEEE--c-CeEEEEEEEEccCCceEechhheeeccc------CcCCEECCCCEEEEEEEEEe
Confidence 4789999999999 99999 4 599999 566653321000000011110 112356999999 5777
Q ss_pred ccc-----chhhhhhchhhhhhhHHhhhh
Q 024995 231 LSH-----SLIRKASKRHCNEYWNVFHET 254 (259)
Q Consensus 231 ~~~-----~~i~ls~k~~~~~p~~~~~~~ 254 (259)
.+. .++.||+|+----||+-+.+.
T Consensus 69 ~~~~~~~~~~i~ls~k~~~~g~~~~~~~~ 97 (99)
T cd04460 69 LKERRPRESKIGLTMRQPGLGKLEWIEEE 97 (99)
T ss_pred HHHCcCCCceEEEEEecCCCCcHHHhhhh
Confidence 764 479999999888888877664
No 139
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.40 E-value=0.0018 Score=56.71 Aligned_cols=71 Identities=27% Similarity=0.414 Sum_probs=61.1
Q ss_pred cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccc----ccChhhhcCCCCeEEEEEEEEeCCCCeeE
Q 024995 54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL----IQDIRDILNEGDEVRVKVIKIDREKSRIT 124 (259)
Q Consensus 54 ~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~----~~~~~~~~~~Gd~V~vkVl~id~~~~ri~ 124 (259)
...+.||.|.|. ..+..|+|+ ....+++|+|++.+.. ..+++.+|++||.|.|+|..+|+ .+...
T Consensus 60 YiP~~gD~VIG~I~~v~~~~W~VDI~-----sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~ 133 (239)
T COG1097 60 YIPEVGDVVIGKIIEVGPSGWKVDIG-----SPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVE 133 (239)
T ss_pred ccCCCCCEEEEEEEEEcccceEEEcC-----CccceEeehhhhhcccccccccccccccccCCEEEEEEEEccC-CCceE
Confidence 467899999999 789999998 3699999999996654 35778899999999999999997 79999
Q ss_pred EEEecc
Q 024995 125 LSIKQL 130 (259)
Q Consensus 125 lS~K~~ 130 (259)
|++|..
T Consensus 134 L~~k~~ 139 (239)
T COG1097 134 LTLKDE 139 (239)
T ss_pred EEeecC
Confidence 998643
No 140
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=97.33 E-value=0.0019 Score=54.56 Aligned_cols=74 Identities=28% Similarity=0.344 Sum_probs=58.1
Q ss_pred hccCCCCCCEEEEE-----eeeEEEEEccCCC-----CccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCC
Q 024995 52 YSSRVNVEDIFVGR-----DYGAFIHLRFPDG-----LYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS 121 (259)
Q Consensus 52 ~~~~l~~G~iv~G~-----~~G~fV~l~~~~g-----~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ 121 (259)
....++.|++|.|. ...+.|++-+.++ .....|-+|+|+.+..++.+.++.|++||.|+++|++.- -
T Consensus 58 ~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~---~ 134 (188)
T COG1096 58 TPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG---D 134 (188)
T ss_pred CCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC---C
Confidence 34578999999999 5567777765433 012568899999999999999999999999999999973 4
Q ss_pred eeEEEEe
Q 024995 122 RITLSIK 128 (259)
Q Consensus 122 ri~lS~K 128 (259)
.+.||.+
T Consensus 135 ~~~Lst~ 141 (188)
T COG1096 135 PIQLSTK 141 (188)
T ss_pred CeEEEec
Confidence 5666654
No 141
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=97.32 E-value=0.0014 Score=49.06 Aligned_cols=59 Identities=17% Similarity=0.230 Sum_probs=46.1
Q ss_pred CCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccCh-----------hhhcCCCCeEEEEEEEEeCCCC
Q 024995 58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-----------RDILNEGDEVRVKVIKIDREKS 121 (259)
Q Consensus 58 ~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~-----------~~~~~~Gd~V~vkVl~id~~~~ 121 (259)
.|++++|+ ++|+||.++ ++++|+|.+.+......++ ...++.|+.|++||+.+..+.+
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G------pl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~ 74 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG------PLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDAT 74 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc------CceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccC
Confidence 47888888 899999998 7999999999976543332 3348899999999998876544
Q ss_pred e
Q 024995 122 R 122 (259)
Q Consensus 122 r 122 (259)
.
T Consensus 75 ~ 75 (88)
T cd04462 75 D 75 (88)
T ss_pred c
Confidence 3
No 142
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=97.31 E-value=8.7e-05 Score=71.54 Aligned_cols=115 Identities=17% Similarity=0.182 Sum_probs=75.5
Q ss_pred EEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEE-EEeccccCcch-----HhhhhhcCCCCccccCCCCcc
Q 024995 84 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL-SIKQLEEDPLL-----ETLEKVIPQDGSVISDSSSMS 157 (259)
Q Consensus 84 glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~l-S~K~~~~~p~~-----~~~~~~~~~g~~~~~~~g~~v 157 (259)
+.+++++.... +| .+++||.+.+.|...+. +|+.+ +.|+....-|. ...+.+ . .+.|+++
T Consensus 73 ~eI~L~eAk~~---~~--~~~vGD~ie~~I~~~~f--gRia~q~aKq~i~Qkire~ere~i~~ey-k------~~~GeIV 138 (470)
T PRK09202 73 KEISLEEARKI---DP--DAEVGDYIEEEIESVDF--GRIAAQTAKQVIVQKIREAERERVYEEY-K------DRVGEII 138 (470)
T ss_pred ceeeHHHHhhh---Cc--cccCCCeEEEEEccccC--ChHHHHHHHHHHHHHHHHHHHHHHHHHH-H------hhcCCEE
Confidence 55555554321 22 37899999999988874 44443 33444333343 233332 2 1247789
Q ss_pred ccceeeeccCCCccceeeeecccCCeeEEEE-ccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecc
Q 024995 158 SSNSNTIEPLPGLGAIFEELLQEDGIDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLS 232 (259)
Q Consensus 158 ~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~ 232 (259)
+|+|.++..+| +|+.| +|++||++ +++. +...| ++||.| ++|+.+
T Consensus 139 ~G~V~ri~~~g----iiVDL---ggvea~LP~sE~i-------------------p~E~~----~~GdrIka~I~~Vd~~ 188 (470)
T PRK09202 139 TGVVKRVERGN----IIVDL---GRAEAILPRKEQI-------------------PRENF----RPGDRVRAYVYEVRKE 188 (470)
T ss_pred EEEEEEEecCC----EEEEE---CCeEEEecHHHcC-------------------CCccC----CCCCEEEEEEEEEecC
Confidence 99999999999 99888 79999995 4432 22334 899998 788888
Q ss_pred cc--hhhhhhch
Q 024995 233 HS--LIRKASKR 242 (259)
Q Consensus 233 ~~--~i~ls~k~ 242 (259)
++ .|-||.+.
T Consensus 189 ~kg~qIilSRt~ 200 (470)
T PRK09202 189 ARGPQIILSRTH 200 (470)
T ss_pred CCCCeEEEEeCc
Confidence 77 67777653
No 143
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.25 E-value=0.00026 Score=69.98 Aligned_cols=70 Identities=21% Similarity=0.258 Sum_probs=54.3
Q ss_pred CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee--EE
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV--QE 228 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V--~~ 228 (259)
.+|+++.|+|+++.+|| +|++| .||-+||| +|+++.++ +. +...+++.||.| ..
T Consensus 618 evg~iy~G~V~ri~~fG----aFv~l--~~gkdgl~hiS~~~~~r-------------v~----kv~dvlk~Gd~v~Vkv 674 (692)
T COG1185 618 EVGEVYEGTVVRIVDFG----AFVEL--LPGKDGLVHISQLAKER-------------VE----KVEDVLKEGDEVKVKV 674 (692)
T ss_pred ccccEEEEEEEEEeecc----eEEEe--cCCcceeEEehhhhhhh-------------hh----cccceeecCceEEEEE
Confidence 35888999999999999 99999 89999999 78887442 12 233477999999 45
Q ss_pred Eeccc-chhhhhhchhh
Q 024995 229 IQLSH-SLIRKASKRHC 244 (259)
Q Consensus 229 v~~~~-~~i~ls~k~~~ 244 (259)
++.++ .|++|++|...
T Consensus 675 ~~iD~~Gri~ls~~~~~ 691 (692)
T COG1185 675 IEIDKQGRIRLSIKAVL 691 (692)
T ss_pred eeecccCCccceehhcc
Confidence 55555 58999998654
No 144
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=97.24 E-value=0.00076 Score=64.18 Aligned_cols=57 Identities=28% Similarity=0.472 Sum_probs=47.6
Q ss_pred CCCCCCEEEEE-----ee--eEEEEEccCCCCccEEEEEEceecCcc------------cccChhhhcCCCCeEEEEEEE
Q 024995 55 RVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKVIK 115 (259)
Q Consensus 55 ~l~~G~iv~G~-----~~--G~fV~l~~~~g~~gi~glv~isels~~------------~~~~~~~~~~~Gd~V~vkVl~ 115 (259)
...+|++|.|+ ++ ||||+++ .+..||+|++++.+. +..++.+.+++||.|.|.|.+
T Consensus 22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG-----~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~K 96 (414)
T TIGR00757 22 RQLKGNIYKGRVTRILPSLQAAFVDIG-----LEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVK 96 (414)
T ss_pred cCCCCCEEEEEEeeecCCCceEEEEcC-----CCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEee
Confidence 56799999999 66 8999998 489999999999753 234566789999999999988
Q ss_pred E
Q 024995 116 I 116 (259)
Q Consensus 116 i 116 (259)
-
T Consensus 97 e 97 (414)
T TIGR00757 97 E 97 (414)
T ss_pred C
Confidence 3
No 145
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=97.23 E-value=0.00033 Score=51.26 Aligned_cols=67 Identities=4% Similarity=-0.099 Sum_probs=50.0
Q ss_pred CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
.+|+++.|+|.++.+.+ +++.+ ..+.+|++ .++++... . .+....+++||.+
T Consensus 5 ~~GdiV~G~V~~v~~~~----~~V~i--~~~~~g~l~~~~~~~~~----------~-------~~~~~~~~~GD~i~~~V 61 (82)
T cd04454 5 DVGDIVIGIVTEVNSRF----WKVDI--LSRGTARLEDSSATEKD----------K-------KEIRKSLQPGDLILAKV 61 (82)
T ss_pred CCCCEEEEEEEEEcCCE----EEEEe--CCCceEEeechhccCcc----------h-------HHHHhcCCCCCEEEEEE
Confidence 46888999999999999 99888 77899999 66665220 1 1122256999999
Q ss_pred EEEecccchhhhhhch
Q 024995 227 QEIQLSHSLIRKASKR 242 (259)
Q Consensus 227 ~~v~~~~~~i~ls~k~ 242 (259)
++++.+ +++.||++.
T Consensus 62 ~~~~~~-~~i~LS~~~ 76 (82)
T cd04454 62 ISLGDD-MNVLLTTAD 76 (82)
T ss_pred EEeCCC-CCEEEEECC
Confidence 566765 789999875
No 146
>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=97.16 E-value=0.00039 Score=70.14 Aligned_cols=63 Identities=19% Similarity=0.226 Sum_probs=47.6
Q ss_pred CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
++|+++.|+|+++.+|| +|++| .+|++||+ +|+++++ |+ .. +...+++||.|
T Consensus 617 ~~G~i~~G~V~~I~~~G----afVei--~~g~~GllHiSei~~~----------~v---~~----~~~~~kvGD~V~VkV 673 (684)
T TIGR03591 617 EVGKIYEGKVVRIMDFG----AFVEI--LPGKDGLVHISEIANE----------RV---EK----VEDVLKEGDEVKVKV 673 (684)
T ss_pred ccCcEEEEEEEEEeCCE----EEEEE--CCCcEEEEEHHHcCCC----------cc---cC----hhhccCCCCEEEEEE
Confidence 46888999999999999 99999 78999999 6887633 22 21 23356999999
Q ss_pred EEEecccchhhh
Q 024995 227 QEIQLSHSLIRK 238 (259)
Q Consensus 227 ~~v~~~~~~i~l 238 (259)
+++|. +++|+|
T Consensus 674 i~id~-~gki~L 684 (684)
T TIGR03591 674 LEIDK-QGRIKL 684 (684)
T ss_pred EEECC-CCCccC
Confidence 56665 566654
No 147
>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=97.01 E-value=0.00081 Score=45.59 Aligned_cols=60 Identities=20% Similarity=0.340 Sum_probs=42.5
Q ss_pred cccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEec
Q 024995 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQL 231 (259)
Q Consensus 157 v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~ 231 (259)
+.|+|.++.++| +|+++ .+|++|++ .++++.. +. . +....+++||.| .++|.
T Consensus 1 v~g~V~~v~~~g----~~v~l--~~~~~g~~~~~~~~~~----------~~---~----~~~~~~~~G~~v~~~v~~~d~ 57 (65)
T cd00164 1 VTGKVVSITKFG----VFVEL--EDGVEGLVHISELSDK----------FV---K----DPSEVFKVGDEVEVKVLEVDP 57 (65)
T ss_pred CEEEEEEEEeee----EEEEe--cCCCEEEEEHHHCCCc----------cc---c----CHhhEeCCCCEEEEEEEEEcC
Confidence 368999999999 99888 68999999 5555422 11 1 112256999999 57777
Q ss_pred ccchhhhh
Q 024995 232 SHSLIRKA 239 (259)
Q Consensus 232 ~~~~i~ls 239 (259)
+++++.||
T Consensus 58 ~~~~i~ls 65 (65)
T cd00164 58 EKGRISLS 65 (65)
T ss_pred CcCEEecC
Confidence 77777664
No 148
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=96.98 E-value=0.002 Score=64.64 Aligned_cols=64 Identities=13% Similarity=0.136 Sum_probs=50.6
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCc--ccc-cC--h-------hhhcCCCCeEEEEEEEEeCCCC
Q 024995 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW--DLI-QD--I-------RDILNEGDEVRVKVIKIDREKS 121 (259)
Q Consensus 59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~--~~~-~~--~-------~~~~~~Gd~V~vkVl~id~~~~ 121 (259)
|+.+.|. +||+||+|.. .|++||||++.|.. ++. -+ . ...|+.||.|+|+|.++|.+++
T Consensus 558 ~~~f~g~I~~v~~~g~~v~l~~----~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~ 633 (639)
T TIGR02062 558 NTRFAAEIVDISRGGMRVRLLE----NGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETR 633 (639)
T ss_pred CcEEEEEEEeeeCCcEEEEEec----CceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccC
Confidence 4478888 8999999973 58999999999965 221 11 1 1259999999999999999999
Q ss_pred eeEEE
Q 024995 122 RITLS 126 (259)
Q Consensus 122 ri~lS 126 (259)
+|.+.
T Consensus 634 ~i~~~ 638 (639)
T TIGR02062 634 SIIAR 638 (639)
T ss_pred cEeee
Confidence 98864
No 149
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=96.97 E-value=0.0036 Score=46.65 Aligned_cols=68 Identities=19% Similarity=0.079 Sum_probs=54.3
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (259)
Q Consensus 55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~ 129 (259)
..++||.|.|+ ....+|+|+ ....|++|.+++... .++.+..|++||.|.|+|..+|+ .....||+..
T Consensus 3 ~P~~gD~VIG~V~~~~~~~~~VdI~-----s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~-~~~~eLtc~~ 75 (86)
T cd05790 3 VPAKGDHVIGIVVAKAGDFFKVDIG-----GSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANR-DMEPELSCVD 75 (86)
T ss_pred cCCCCCEEEEEEEEEcCCeEEEEcC-----CCcceEechHHcccc-cccccccCCCCCEEEEEEEecCC-CCCeEEEEeC
Confidence 35789999999 457899998 367899999887543 34456679999999999999997 4678888765
No 150
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=96.94 E-value=0.0021 Score=65.18 Aligned_cols=70 Identities=31% Similarity=0.529 Sum_probs=57.8
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccccc-----------ChhhhcCCCCeEEEEEEEEeC
Q 024995 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDR 118 (259)
Q Consensus 55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~-----------~~~~~~~~Gd~V~vkVl~id~ 118 (259)
.-.+|+.+.|+ .||+||.+.+ .+++|++|++.+...++. .....|+.||.|++++.++|.
T Consensus 619 ~~~vg~~f~g~V~~v~~~g~~V~l~~----~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~ 694 (706)
T COG0557 619 KKRVGEEFDGVVTGVTSFGFFVELPE----LGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDL 694 (706)
T ss_pred HHhcCCEEEEEEEEEEeccEEEEecc----cccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcc
Confidence 45788888888 8999999984 579999999999965321 223458999999999999999
Q ss_pred CCCeeEEEEe
Q 024995 119 EKSRITLSIK 128 (259)
Q Consensus 119 ~~~ri~lS~K 128 (259)
..+++.+++-
T Consensus 695 ~~~~i~~~~v 704 (706)
T COG0557 695 DERKIDFELV 704 (706)
T ss_pred cccceEEEec
Confidence 9999998763
No 151
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=96.78 E-value=0.0048 Score=42.86 Aligned_cols=48 Identities=33% Similarity=0.409 Sum_probs=32.5
Q ss_pred eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (259)
Q Consensus 66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K 128 (259)
++|+|++.+ .+-+-|+|.++++. .+++||.|.|-| ..|. .+|+..|+|
T Consensus 14 ~~g~fL~~~-----~~~~vlLp~~e~~~--------~~~~Gd~v~VFv-Y~D~-~~rl~AT~k 61 (61)
T PF13509_consen 14 EFGYFLDDG-----EGKEVLLPKSEVPE--------PLKVGDEVEVFV-YLDK-EGRLVATTK 61 (61)
T ss_dssp SSEEEEEET-----T-EEEEEEGGG--------------TTSEEEEEE-EE-T-TS-EEEE--
T ss_pred CCEEEEECC-----CCCEEEechHHcCC--------CCCCCCEEEEEE-EECC-CCCEEEecC
Confidence 899999987 36899999998753 378999999887 7886 678888875
No 152
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=96.69 E-value=0.00093 Score=64.75 Aligned_cols=76 Identities=13% Similarity=0.056 Sum_probs=57.4
Q ss_pred CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCeeE---
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQ--- 227 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V~--- 227 (259)
-.|.+++++|+.+.||| +||+| .||..||+ .|+++.+ |+.. +.. ++.+||+++
T Consensus 667 ~~g~vy~~tIt~~rd~G----~~V~l--~p~~~~Llh~sqL~~e----------~iak---psd----~levGq~I~vk~ 723 (760)
T KOG1067|consen 667 EFGGVYTATITEIRDTG----VMVEL--YPMQQGLLHNSQLDQE----------KIAK---PSD----LLEVGQEIQVKY 723 (760)
T ss_pred EeeeEEEEEEeeecccc----eEEEe--cCCchhhccchhcccc----------cccC---hHH----HHhhcceeEEEE
Confidence 45888999999999999 99999 99999999 7887744 5532 333 679999993
Q ss_pred -EEecccchhhhhhchhhhhhhHHh
Q 024995 228 -EIQLSHSLIRKASKRHCNEYWNVF 251 (259)
Q Consensus 228 -~v~~~~~~i~ls~k~~~~~p~~~~ 251 (259)
+.|+.. .+.++.|.++++|....
T Consensus 724 ie~d~~g-~~~ls~ralLp~p~~~~ 747 (760)
T KOG1067|consen 724 IERDPRG-GIMLSSRALLPDPATKE 747 (760)
T ss_pred EeecCcc-ceeehhhhhcCCcccCC
Confidence 444433 46677777888887544
No 153
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=96.68 E-value=0.0021 Score=54.30 Aligned_cols=83 Identities=10% Similarity=0.052 Sum_probs=53.5
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE 228 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~ 228 (259)
|++++|+|++++++| +|+++ . .++|++ .+++..+.-..-++-..|... .. ...++.||.| .+
T Consensus 82 gEvv~G~V~~v~~~G----ifV~l--g-~~~gi~~~~~l~~~~~~~d~~~~~~~~~--~~----~~~~~~Gd~VrvrV~~ 148 (179)
T TIGR00448 82 GEIVEGEVIEIVEFG----AFVSL--G-PFDGLFHVSQVTDDYCYYDPKESALIGK--ET----KKVLDEGDKVRARIVA 148 (179)
T ss_pred CCEEEEEEEEEEeeE----EEEEe--C-CceEEEEcHHhCCCceEEccccceEEEc--cC----CeEEcCCCEEEEEEEE
Confidence 667999999999999 99998 3 499998 555543321111111223321 11 2356999999 56
Q ss_pred Ee-----cccchhhhhhchhhhhhhH
Q 024995 229 IQ-----LSHSLIRKASKRHCNEYWN 249 (259)
Q Consensus 229 v~-----~~~~~i~ls~k~~~~~p~~ 249 (259)
++ ++.++|.++||+----|++
T Consensus 149 v~~~~~~~~~~~I~lt~k~~~LG~~~ 174 (179)
T TIGR00448 149 LSLKDRRPEGSKIGLTMRQPLLGKLE 174 (179)
T ss_pred EEccCCCCCcceEEEEeccCcCCccc
Confidence 66 5667899999984333433
No 154
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=96.66 E-value=0.0024 Score=64.78 Aligned_cols=71 Identities=18% Similarity=0.216 Sum_probs=50.9
Q ss_pred CCCccccceeeeccCCCccceeeeecccC-CeeEEE-Eccccccccccchhhhhhccc-----CCCCCcceeeeccCCCe
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR-ITRQGFEKRVVSQDLQLWLSN-----APPSGKKFTLLARAGRQ 225 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~-gv~gl~-~s~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~r~G~~ 225 (259)
.|+.++|+|++|++|| +||+| .+ |++||+ +|++..+. -.|... ...... .++.||.
T Consensus 627 iG~~~~g~V~~v~~fG----ifV~L--~~~~~eGlvhis~l~~d~-------~~~d~~~~~l~g~~~~~----~~~lGd~ 689 (709)
T TIGR02063 627 IGEEFEGVISGVTSFG----LFVEL--ENNTIEGLVHISTLKDDY-------YVFDEKGLALVGERTGK----VFRLGDR 689 (709)
T ss_pred CCcEEEEEEEEEEeCC----EEEEe--cCCceEEEEEeeecCCCc-------EEEcccceEEEeccCCc----EECCCCE
Confidence 4888999999999999 99999 56 899999 67765221 011110 011112 4599999
Q ss_pred e----EEEecccchhhhhh
Q 024995 226 V----QEIQLSHSLIRKAS 240 (259)
Q Consensus 226 V----~~v~~~~~~i~ls~ 240 (259)
| .+||.++++|.+++
T Consensus 690 V~Vkv~~vd~~~~~I~~~l 708 (709)
T TIGR02063 690 VKVRVVKADLDTGKIDFEL 708 (709)
T ss_pred EEEEEEEEecccCeEEEEE
Confidence 9 68899999998875
No 155
>PRK11642 exoribonuclease R; Provisional
Probab=96.56 E-value=0.003 Score=64.97 Aligned_cols=77 Identities=13% Similarity=0.154 Sum_probs=52.9
Q ss_pred CCCccccceeeeccCCCccceeeeecccC-CeeEEE-EccccccccccchhhhhhcccCCC----CCcceeeeccCCCee
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR-ITRQGFEKRVVSQDLQLWLSNAPP----SGKKFTLLARAGRQV 226 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~-gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~r~G~~V 226 (259)
.|+.++|+|++|++|| +||+| ++ +|+||+ .+.+..+ |+..... ...+-...++.||.|
T Consensus 643 iGe~f~G~Is~V~~fG----ifVeL--~~~~vEGlV~vs~L~~d----------~y~~d~~~~~L~g~~~~~~~~lGD~V 706 (813)
T PRK11642 643 VGNVFKGVISSVTGFG----FFVRL--DDLFIDGLVHVSSLDND----------YYRFDQVGQRLIGESSGQTYRLGDRV 706 (813)
T ss_pred CCcEEEEEEEEeecCc----eEEEE--CCCCeeeeEEEeecCCc----------ceEecchheEEecccCCcEECCCCEE
Confidence 4888999999999999 99999 55 599999 6666522 2221100 000111245999999
Q ss_pred ----EEEecccchhhhhhchhhh
Q 024995 227 ----QEIQLSHSLIRKASKRHCN 245 (259)
Q Consensus 227 ----~~v~~~~~~i~ls~k~~~~ 245 (259)
.++|.++++|.+++-....
T Consensus 707 ~VkV~~vD~~~rkI~f~l~~~~~ 729 (813)
T PRK11642 707 EVRVEAVNMDERKIDFSLISSER 729 (813)
T ss_pred EEEEEEeecCCCeEEEEEecccc
Confidence 5789999999888754333
No 156
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=96.53 E-value=0.0041 Score=43.74 Aligned_cols=32 Identities=6% Similarity=0.164 Sum_probs=26.6
Q ss_pred CCCccccceeeeccCCCccceeeeecccCCeeEEEE-ccc
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRI-TRQ 191 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~-s~~ 191 (259)
.|++++|+|.++.++| +|+.+ ++++|+++ +++
T Consensus 3 ~g~iV~G~V~~~~~~~----~~vdi---g~~eg~lp~~e~ 35 (67)
T cd04455 3 EGEIVTGIVKRVDRGN----VIVDL---GKVEAILPKKEQ 35 (67)
T ss_pred CCCEEEEEEEEEcCCC----EEEEc---CCeEEEeeHHHC
Confidence 5888999999999999 99888 45999994 443
No 157
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=96.45 E-value=0.014 Score=57.13 Aligned_cols=68 Identities=29% Similarity=0.496 Sum_probs=58.2
Q ss_pred ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995 53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (259)
Q Consensus 53 ~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~ 127 (259)
+.+++.|..|.|+ .||+||+++ ..+.||+|-++++.. .-|.+|+.+-|.+..+-++++.|.+..
T Consensus 117 ~~Dve~g~~Y~g~v~~v~~~GvFv~Ln-----~~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~ 185 (715)
T COG1107 117 MEDVEAGKYYKGIVSRVEKYGVFVELN-----SHVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEP 185 (715)
T ss_pred hhhcccceeeeccccchhhhcceeecC-----hhhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceee
Confidence 4678999999999 999999998 589999999999862 237899999999999998889888877
Q ss_pred eccc
Q 024995 128 KQLE 131 (259)
Q Consensus 128 K~~~ 131 (259)
..+.
T Consensus 186 ~~~~ 189 (715)
T COG1107 186 VGLD 189 (715)
T ss_pred cCCc
Confidence 6554
No 158
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.19 E-value=0.013 Score=54.78 Aligned_cols=62 Identities=21% Similarity=0.353 Sum_probs=51.4
Q ss_pred CCCCCCEEEEE----e--eeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCC---eeEE
Q 024995 55 RVNVEDIFVGR----D--YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS---RITL 125 (259)
Q Consensus 55 ~l~~G~iv~G~----~--~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~---ri~l 125 (259)
.-+.|+++.|+ + .++||+++ +.+|++|.++.. |.+.|++||.++|.|.+++...+ +|.|
T Consensus 135 ~~~~Geiv~g~V~r~~~~~~i~vdlg------~~ea~LP~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~Iil 202 (374)
T PRK12328 135 KKKVGKIVFGTVVRVDNEENTFIEID------EIRAVLPMKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIEL 202 (374)
T ss_pred HHhcCcEEEEEEEEEecCCCEEEEcC------CeEEEeCHHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEE
Confidence 35799999999 3 34899997 799999988864 46779999999999999998655 7888
Q ss_pred EEe
Q 024995 126 SIK 128 (259)
Q Consensus 126 S~K 128 (259)
|+.
T Consensus 203 SRt 205 (374)
T PRK12328 203 SRT 205 (374)
T ss_pred EcC
Confidence 863
No 159
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=96.17 E-value=0.0033 Score=53.02 Aligned_cols=87 Identities=10% Similarity=0.108 Sum_probs=57.8
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE 228 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~ 228 (259)
|+++.|.|+++..|| +|+.| .-.+||+ .|++.++ .+..|-..|.-... +. +..+++||.| ..
T Consensus 82 gEVV~GeVv~~~~~G----~fV~i---gp~dglvh~sqi~dd--~~~~d~~~~~~~g~-~t---k~~i~~gd~VR~RIv~ 148 (183)
T COG1095 82 GEVVEGEVVEVVEFG----AFVRI---GPLDGLVHVSQIMDD--YIDYDEKNKVLIGE-ET---KRVLKVGDKVRARIVG 148 (183)
T ss_pred ccEEEEEEEEEeecc----eEEEe---ccccccccHhhccCc--ccccCcccceeeec-cc---ceEEecCCEEEEEEEE
Confidence 677999999999999 99999 5789998 6777655 23333333332222 22 2267999999 22
Q ss_pred Eecc-----cchhhhhhch--hhhhhhHHhhh
Q 024995 229 IQLS-----HSLIRKASKR--HCNEYWNVFHE 253 (259)
Q Consensus 229 v~~~-----~~~i~ls~k~--~~~~p~~~~~~ 253 (259)
+... ..+|-++||| |-.-+|-..+.
T Consensus 149 ~s~~~~~~~~~~I~lTmrq~~LGklew~~~~~ 180 (183)
T COG1095 149 VSLKSRRPRESKIGLTMRQPGLGKLEWIEEEK 180 (183)
T ss_pred EecccCccccceEEEEeccccCCcchhhhhhh
Confidence 2222 3568899998 55566765543
No 160
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.11 E-value=0.0051 Score=54.22 Aligned_cols=70 Identities=4% Similarity=-0.023 Sum_probs=48.1
Q ss_pred CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q 227 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~ 227 (259)
+|++|.|+|+++.+++ +|++| ..+..|++ .++++.. |. ..+..+....+++||.| +
T Consensus 63 vGDiViG~V~~i~~~~----~~vdI--~~~~~g~L~~s~i~~~----------~~---~~d~~~~~~~~~~GDlV~akV~ 123 (235)
T PRK04163 63 VGDLVIGKVTDVTFSG----WEVDI--NSPYKAYLPVSEVLGR----------PV---NVEGTDLRKYLDIGDYIIAKVK 123 (235)
T ss_pred CCCEEEEEEEEEeCce----EEEEe--CCCceeEEEHHHcCCC----------cc---ccchhhhHhhCCCCCEEEEEEE
Confidence 4788999999999999 99888 77899999 5665522 11 00112233467999999 4
Q ss_pred EEecccchhhhhhch
Q 024995 228 EIQLSHSLIRKASKR 242 (259)
Q Consensus 228 ~v~~~~~~i~ls~k~ 242 (259)
.++.+. .+.||+|+
T Consensus 124 ~i~~~~-~~~LS~k~ 137 (235)
T PRK04163 124 DVDRTR-DVVLTLKG 137 (235)
T ss_pred EECCCC-cEEEEEcC
Confidence 555443 37777765
No 161
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=96.05 E-value=0.0024 Score=56.52 Aligned_cols=83 Identities=17% Similarity=0.233 Sum_probs=67.0
Q ss_pred CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCe----eE
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQ----VQ 227 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~----V~ 227 (259)
.+++|-+.|..|.+.| +++.|.-.++++|++ .|++|-. +++. ++-+.|+|.. |+
T Consensus 16 v~e~VmvnV~sIaemG----ayv~LlEYnniEGmiLlsELSrR----------RIRS-------I~klirVGr~E~vvVl 74 (304)
T KOG2916|consen 16 VEEIVMVNVRSIAEMG----AYVKLLEYNNIEGMILLSELSRR----------RIRS-------IQKLIRVGRNEPVVVL 74 (304)
T ss_pred cccEEEEEeeEehhcc----ceEeeeecCCcccchhhhHHHHH----------HHHH-------HHHHHhcCCcceEEEE
Confidence 3677999999999999 999998889999998 8998822 2322 3336688863 38
Q ss_pred EEecccchhhhhhchhhhhhhHHhhhhcc
Q 024995 228 EIQLSHSLIRKASKRHCNEYWNVFHETAI 256 (259)
Q Consensus 228 ~v~~~~~~i~ls~k~~~~~p~~~~~~~~~ 256 (259)
.||.++.-|.||.+++.++-...-.|+|+
T Consensus 75 rVDkekGYIDLSkrrVs~ed~~kC~Er~~ 103 (304)
T KOG2916|consen 75 RVDKEKGYIDLSKRRVSPEDKEKCEERFA 103 (304)
T ss_pred EEcCCCCceechhccCCHHHHHHHHHHHH
Confidence 99999999999999999887777777664
No 162
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=96.04 E-value=0.0062 Score=63.29 Aligned_cols=71 Identities=24% Similarity=0.278 Sum_probs=59.5
Q ss_pred CCCCCCEEEEE------eeeE--EEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995 55 RVNVEDIFVGR------DYGA--FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (259)
Q Consensus 55 ~l~~G~iv~G~------~~G~--fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS 126 (259)
.+.+|.++.++ .+|. =|.+. +|++|+||.+++|...+.+|...+++||.|.++|+++|.++=-+.||
T Consensus 982 t~~~g~iV~~~V~~vt~rr~~Cv~v~ld-----~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls 1056 (1299)
T KOG1856|consen 982 TFYEGAIVPVTVTKVTHRRGICVRVRLD-----CGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELS 1056 (1299)
T ss_pred HhccCceEEEeeeEEEecccceeEEEec-----CCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhh
Confidence 47788888866 3443 34555 59999999999999999999999999999999999999988888888
Q ss_pred Eecc
Q 024995 127 IKQL 130 (259)
Q Consensus 127 ~K~~ 130 (259)
.|..
T Consensus 1057 ~r~s 1060 (1299)
T KOG1856|consen 1057 CRTS 1060 (1299)
T ss_pred hhhH
Confidence 8753
No 163
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=96.02 E-value=0.0088 Score=60.24 Aligned_cols=76 Identities=21% Similarity=0.287 Sum_probs=50.3
Q ss_pred CCCccccceeeeccCCCccceeeeeccc-CCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQE-DGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~-~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
.|+.++|+|+++++|| +|++| + .|++||+ .+++..+.-.. ++-+.-+ ....... .++.||.|
T Consensus 572 iG~~~~g~I~~v~~~G----ifV~L--~~~~veGlV~~s~l~~d~y~~-d~~~~~l-~g~~~~~----~~~lGD~V~Vki 639 (654)
T TIGR00358 572 VGTEFSGEISSVTRFG----MFVRL--DDNGIDGLIHISTLHNDYYVF-DQEKMAL-IGKGTGK----VYRIGDRVTVKL 639 (654)
T ss_pred CCcEEEEEEEeEEcCc----EEEEe--cCCceEEEEEeEeCCCcceEE-eccccEE-EeccCCc----EECCCCEEEEEE
Confidence 4888999999999999 99999 5 7899999 66665321000 0000000 0011112 46999999
Q ss_pred EEEecccchhhhhh
Q 024995 227 QEIQLSHSLIRKAS 240 (259)
Q Consensus 227 ~~v~~~~~~i~ls~ 240 (259)
.+||.++++|.+++
T Consensus 640 ~~vd~~~~~I~f~l 653 (654)
T TIGR00358 640 TEVNMETRSIIFEL 653 (654)
T ss_pred EEEecccCeEEEEE
Confidence 68899999988764
No 164
>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=95.91 E-value=0.0028 Score=58.86 Aligned_cols=106 Identities=18% Similarity=0.215 Sum_probs=65.0
Q ss_pred hhhcCCCCeEEEEEEEEeCCCCeeEEEEeccc-----cCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCcccee
Q 024995 100 RDILNEGDEVRVKVIKIDREKSRITLSIKQLE-----EDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIF 174 (259)
Q Consensus 100 ~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~-----~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~~f 174 (259)
...+++||.+.+.+..-+. .+....+.|+.. ...+....+.+. ...|++++|+|.++.+.| .+|
T Consensus 81 d~~~~vGD~I~~~I~~~~f-gR~aaq~aKqvi~Qkire~ere~i~~ey~-------~k~GeiV~G~V~~v~~~g---~v~ 149 (341)
T TIGR01953 81 DPDVQIGDEVKKEIPPENF-GRIAAQTAKQVILQKIREAERERVYDEFS-------SKEGEIISGTVKRVNRRG---NLY 149 (341)
T ss_pred ccccccCCEEEEEecccCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------hhcCCEEEEEEEEEecCC---cEE
Confidence 3458899999998855543 233333344422 222333333332 134888999999999877 258
Q ss_pred eeecccCCeeEEEE-ccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccc--hhhhhhch
Q 024995 175 EELLQEDGIDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHS--LIRKASKR 242 (259)
Q Consensus 175 v~l~~~~gv~gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~--~i~ls~k~ 242 (259)
+.| +|++|+++ +++. +..+| ++||.+ ++|+.+.+ .|-+|.+.
T Consensus 150 Vdi---G~~ea~LP~~E~i-------------------p~E~~----~~Gd~ik~~V~~V~~~~kg~qIivSRt~ 198 (341)
T TIGR01953 150 VEL---GKTEGILPKKEQI-------------------PGEKF----RIGDRIKAYVYEVRKTAKGPQIILSRTH 198 (341)
T ss_pred EEE---CCeEEEecHHHcC-------------------CCcCC----CCCCEEEEEEEEEEcCCCCCeEEEEeCc
Confidence 777 69999995 4433 11224 899987 67776554 46666553
No 165
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=95.65 E-value=0.031 Score=41.25 Aligned_cols=36 Identities=25% Similarity=0.438 Sum_probs=24.2
Q ss_pred cEEEEEEceecCccccc--ChhhhcCCCCeEEEEEEEE
Q 024995 81 HLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKI 116 (259)
Q Consensus 81 gi~glv~isels~~~~~--~~~~~~~~Gd~V~vkVl~i 116 (259)
...|.++.+++...... ++.+-|++||.|+|+|+++
T Consensus 45 ~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViSl 82 (82)
T PF10447_consen 45 PFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVISL 82 (82)
T ss_dssp SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEEE
T ss_pred ccEEEEEeeeecccccchhhHHhccCCCCEEEEEEeeC
Confidence 57899999998765443 4688899999999999874
No 166
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=95.25 E-value=0.022 Score=48.23 Aligned_cols=76 Identities=11% Similarity=0.105 Sum_probs=49.7
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE 228 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~ 228 (259)
|+++.|+|+++.++| +|+++ . .++|++ .+++..+.-...++=+.|+.. .. ...++.||.| ..
T Consensus 82 GEVv~g~V~~v~~~G----i~V~l--g-~~~g~v~~~~l~~~~~~~d~~~~~~~~~--~~----~~~i~~Gd~VrvrV~~ 148 (187)
T PRK08563 82 QEVVEGEVVEVVEFG----AFVRI--G-PVDGLLHISQIMDDYISYDPKNGRLIGK--ES----KRVLKVGDVVRARIVA 148 (187)
T ss_pred CCEEEEEEEEEEccE----EEEEE--e-CceEEEEcHHcCCCceEEccccceEEEc--cC----CeEEcCCCEEEEEEEE
Confidence 677999999999999 99998 3 499998 555543211111112234432 11 2356999999 56
Q ss_pred Eecccc-----hhhhhhch
Q 024995 229 IQLSHS-----LIRKASKR 242 (259)
Q Consensus 229 v~~~~~-----~i~ls~k~ 242 (259)
++.+.+ +|.+|||+
T Consensus 149 v~~~~~~~~~~~I~ls~~~ 167 (187)
T PRK08563 149 VSLKERRPRGSKIGLTMRQ 167 (187)
T ss_pred EEcccCCCCCCEEEEEecC
Confidence 665543 78889987
No 167
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=94.86 E-value=0.0088 Score=55.96 Aligned_cols=100 Identities=13% Similarity=0.113 Sum_probs=61.5
Q ss_pred hcCCCCeEEEEEEEEeCCCCeeEEEEeccccCc-----chHhhhhhcCCCCccccCCCCccccceeeeccCCCccceeee
Q 024995 102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP-----LLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEE 176 (259)
Q Consensus 102 ~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p-----~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~~fv~ 176 (259)
..++||.+...+...+.. +.-..+.|+....- .....+.+. .+.|++++|+|.++.+.| +|+.
T Consensus 86 ~~~vGD~i~~~I~~~~fg-R~aaq~akqvI~Qkire~ere~v~~ef~-------~k~GeiV~G~V~~~~~~~----~~Vd 153 (362)
T PRK12327 86 AYELGDVIEIEVTPKDFG-RIAAQTAKQVIMQRLREAEREIIYNEFS-------EREGDIVTGVVQRRDNRF----VYVN 153 (362)
T ss_pred cccCCCEEEEecCcCCCC-hHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HhcCCEEEEEEEEEeCCc----EEEE
Confidence 478999999988666542 22222233322111 111222221 235888999999999988 9988
Q ss_pred ecccCCeeEEEE-ccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccch--hhhh
Q 024995 177 LLQEDGIDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSL--IRKA 239 (259)
Q Consensus 177 l~~~~gv~gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~--i~ls 239 (259)
| +|++|+++ +++. +.. .+++||.+ ++|+.+++. |.+|
T Consensus 154 l---g~vEa~LP~~E~i-------------------p~e----~~~~Gd~Ika~V~~V~~~~kgp~IivS 197 (362)
T PRK12327 154 L---GKIEAVLPPAEQI-------------------PGE----TYKHGDRIKVYVVKVEKTTKGPQIFVS 197 (362)
T ss_pred e---CCeEEEecHHHcC-------------------CCC----CCCCCCEEEEEEEEEecCCCCCeEEEE
Confidence 8 67999996 4432 122 33899998 678776664 4444
No 168
>PRK10811 rne ribonuclease E; Reviewed
Probab=94.78 E-value=0.07 Score=55.27 Aligned_cols=61 Identities=26% Similarity=0.480 Sum_probs=46.4
Q ss_pred CCCCCEEEEE-------eeeEEEEEccCCCCccEEEEEEceecCccccc---------ChhhhcCCCCeEEEEEEEEeCC
Q 024995 56 VNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ---------DIRDILNEGDEVRVKVIKIDRE 119 (259)
Q Consensus 56 l~~G~iv~G~-------~~G~fV~l~~~~g~~gi~glv~isels~~~~~---------~~~~~~~~Gd~V~vkVl~id~~ 119 (259)
..+|.||.|+ =.++||+|+ .|..||+|+++.....+. .....+++||.|.|.|.+-...
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDIG-----~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~g 110 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDYG-----AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERG 110 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEec-----CCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccC
Confidence 4689999999 357999999 489999999999644322 2245688999999999875443
Q ss_pred CC
Q 024995 120 KS 121 (259)
Q Consensus 120 ~~ 121 (259)
++
T Consensus 111 tK 112 (1068)
T PRK10811 111 NK 112 (1068)
T ss_pred CC
Confidence 33
No 169
>PRK11712 ribonuclease G; Provisional
Probab=94.56 E-value=0.14 Score=49.77 Aligned_cols=59 Identities=25% Similarity=0.511 Sum_probs=45.1
Q ss_pred cCCCCCCEEEEE-------eeeEEEEEccCCCCccEEEEEEceecCcc------------cccChhhhcCCCCeEEEEEE
Q 024995 54 SRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKVI 114 (259)
Q Consensus 54 ~~l~~G~iv~G~-------~~G~fV~l~~~~g~~gi~glv~isels~~------------~~~~~~~~~~~Gd~V~vkVl 114 (259)
....+|.+|.|+ =.+|||+|+ .+..||+|++++... ......+.+++||.|-|.|.
T Consensus 34 ~~~~vGnIY~G~V~~v~pg~~AAFVdIG-----~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~ 108 (489)
T PRK11712 34 KRGIVGNIYKGRVSRVLPGMQAAFVDIG-----LDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVV 108 (489)
T ss_pred cccccccEEEEEEeecCCCCceeEEeeC-----CCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEE
Confidence 355799999999 346999998 589999999997321 01234566999999999997
Q ss_pred EEe
Q 024995 115 KID 117 (259)
Q Consensus 115 ~id 117 (259)
+--
T Consensus 109 Ke~ 111 (489)
T PRK11712 109 KDP 111 (489)
T ss_pred eCC
Confidence 753
No 170
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=93.87 E-value=0.19 Score=48.16 Aligned_cols=68 Identities=9% Similarity=0.057 Sum_probs=50.4
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCC---CeeEEE
Q 024995 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK---SRITLS 126 (259)
Q Consensus 55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~---~ri~lS 126 (259)
.-+.|+++.|+ +.+++|+++..-|-.+++|++|.++.. |.+.|++||.++|.|.++.... -+|.||
T Consensus 149 ~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~y~~Gdrika~i~~V~~~~~kGpqIilS 222 (449)
T PRK12329 149 QDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDNYRANATFKVFLKEVSEGPRRGPQLFVS 222 (449)
T ss_pred HHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCcCCCCCEEEEEEEEeecCCCCCCEEEEE
Confidence 34799999999 557999983100001389999988863 4677999999999999998642 368888
Q ss_pred Ee
Q 024995 127 IK 128 (259)
Q Consensus 127 ~K 128 (259)
+.
T Consensus 223 Rt 224 (449)
T PRK12329 223 RA 224 (449)
T ss_pred cC
Confidence 63
No 171
>PRK05054 exoribonuclease II; Provisional
Probab=90.89 E-value=0.26 Score=49.68 Aligned_cols=72 Identities=13% Similarity=0.076 Sum_probs=46.5
Q ss_pred CccccceeeeccCCCccceeeeecccCCeeEEE-Eccccccccc--cch-hhhhhcccCCCCCcceeeeccCCCee----
Q 024995 155 SMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRV--VSQ-DLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 155 ~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~--~~~-~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
+.+.|.|+.+++|| +||+|. +.|++||+ .+.+...... ..+ +..... . -.. .++.||.|
T Consensus 563 ~~f~g~I~~v~~~G----~fV~l~-~~~veglV~~~~l~~~~~~y~~~~~~~~~~~---~-~~~----~~~lGd~V~V~v 629 (644)
T PRK05054 563 TRFAAEIIDISRGG----MRVRLL-ENGAVAFIPASFLHAVRDELVCNQENGTVQI---K-GET----VYKLGDVIDVTL 629 (644)
T ss_pred eEEEEEEEeeecCc----EEEEEe-CCceEEEEEccccCCCccceEEccccceEEE---e-CCE----EEcCCCEEEEEE
Confidence 37999999999999 999995 57999998 5655421000 000 000000 0 011 45999998
Q ss_pred EEEecccchhhhh
Q 024995 227 QEIQLSHSLIRKA 239 (259)
Q Consensus 227 ~~v~~~~~~i~ls 239 (259)
.+||.++++|.+.
T Consensus 630 ~~vd~~~~~i~~~ 642 (644)
T PRK05054 630 AEVRMETRSIIAR 642 (644)
T ss_pred EEEccccCeEEEE
Confidence 5888888887654
No 172
>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=89.80 E-value=0.54 Score=33.81 Aligned_cols=68 Identities=13% Similarity=0.070 Sum_probs=44.7
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee---EEE
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---QEI 229 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---~~v 229 (259)
|+.++|+|..-++-+ ++++|. +.|+.|++ ...+++ . .++.-..|- ++ |+||.+ +-+
T Consensus 1 G~lV~~~V~EKt~D~----l~v~l~-~~~l~a~l~~~HLsD-~--~~k~~~~~~--------kl----rvG~~L~~~lvL 60 (72)
T cd05699 1 GKLVDARVLKKTLNG----LEVAIL-PEEIRAFLPTMHLSD-H--VSNCPLLWH--------CL----QEGDTIPNLMCL 60 (72)
T ss_pred CceEEEEEEEEcCCc----EEEEec-CCCcEEEEEccccCC-c--hhhCHHHHh--------hh----hcCCCccceEEE
Confidence 456899999988877 888883 34999998 445553 1 233322233 23 889887 445
Q ss_pred ecccchhhhhhc
Q 024995 230 QLSHSLIRKASK 241 (259)
Q Consensus 230 ~~~~~~i~ls~k 241 (259)
+..++.|.++.|
T Consensus 61 ~~~~r~i~lt~K 72 (72)
T cd05699 61 SNYKGRIILTKK 72 (72)
T ss_pred eccccEEEEecC
Confidence 777777777654
No 173
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=87.46 E-value=0.2 Score=47.05 Aligned_cols=97 Identities=18% Similarity=0.213 Sum_probs=57.9
Q ss_pred hhcCCCCeEEEEEEEEeCCCCeeE-EEEeccccCc-----chHhhhhhcCCCCccccCCCCccccceeeeccCCCcccee
Q 024995 101 DILNEGDEVRVKVIKIDREKSRIT-LSIKQLEEDP-----LLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIF 174 (259)
Q Consensus 101 ~~~~~Gd~V~vkVl~id~~~~ri~-lS~K~~~~~p-----~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~~f 174 (259)
..+++||.+...+---+. +|+. -+.|+....- .....+.+. .+.|++++|+|.++...| .+|
T Consensus 89 ~~~~vGd~i~~~i~~~~f--gRiaaq~akq~i~Qkir~~er~~i~~ey~-------~~~Geiv~g~V~r~~~~~---~i~ 156 (374)
T PRK12328 89 PSVEIGDELTYELSLENM--GRTAANTLFKELEYHIQRLLEESIFEKYK-------KKVGKIVFGTVVRVDNEE---NTF 156 (374)
T ss_pred CCCCCCCEEEEecChhhC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HhcCcEEEEEEEEEecCC---CEE
Confidence 348899999987744433 3332 2233322100 011122221 235888999999998755 378
Q ss_pred eeecccCCeeEEEEccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccc
Q 024995 175 EELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHS 234 (259)
Q Consensus 175 v~l~~~~gv~gl~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~ 234 (259)
+.| ++++|+++.+.- .+..+| ++||.+ .+|..+++
T Consensus 157 vdl---g~~ea~LP~~eq------------------ip~E~~----~~Gdrik~~i~~V~~~~k 195 (374)
T PRK12328 157 IEI---DEIRAVLPMKNR------------------IKGEKF----KVGDVVKAVLKRVKIDKN 195 (374)
T ss_pred EEc---CCeEEEeCHHHc------------------CCCCcC----CCCCEEEEEEEEEecCCC
Confidence 777 589999954321 133345 899998 67877766
No 174
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=87.37 E-value=3.2 Score=34.48 Aligned_cols=62 Identities=18% Similarity=0.197 Sum_probs=42.1
Q ss_pred cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcc----cccC-------hhhhcCCCCeEEEEEEEEe
Q 024995 54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LIQD-------IRDILNEGDEVRVKVIKID 117 (259)
Q Consensus 54 ~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~----~~~~-------~~~~~~~Gd~V~vkVl~id 117 (259)
-+.-.|++++|+ ..|+|++++ .++.|+.---+..+ ...+ -.+.+++|..|+++|+..-
T Consensus 77 FkpfKGEVvdgvV~~Vnk~G~F~~~G------Pl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr 150 (170)
T KOG3298|consen 77 FKPFKGEVVDGVVTKVNKMGVFARSG------PLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTR 150 (170)
T ss_pred EeecCCcEEEEEEEEEeeeeEEEecc------ceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEE
Confidence 367789999999 889999998 57777643222211 1111 1225889999999998876
Q ss_pred CCCC
Q 024995 118 REKS 121 (259)
Q Consensus 118 ~~~~ 121 (259)
.+..
T Consensus 151 ~~~~ 154 (170)
T KOG3298|consen 151 VDET 154 (170)
T ss_pred Eeee
Confidence 5333
No 175
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=85.70 E-value=0.86 Score=46.46 Aligned_cols=73 Identities=18% Similarity=0.186 Sum_probs=48.9
Q ss_pred CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCC----CCCcceeeeccCCCee-
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAP----PSGKKFTLLARAGRQV- 226 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~r~G~~V- 226 (259)
+|....|.|.+++.|| +|++|. ..|++|++ ++.+..+ |+.... ....+-...++.||.|
T Consensus 622 vg~~f~g~V~~v~~~g----~~V~l~-~~~ieglV~~s~L~~d----------~y~~~~~~~~l~~~~~~~~~~lgd~v~ 686 (706)
T COG0557 622 VGEEFDGVVTGVTSFG----FFVELP-ELGLEGLVHISSLPDD----------YYHFDERGQALVGEKSGKVYRLGDEVK 686 (706)
T ss_pred cCCEEEEEEEEEEecc----EEEEec-ccccccceEcccCCCc----------eeeeccccceeeccccccccccCCEEE
Confidence 4778999999999999 999993 34699998 6666521 121111 0112233356999999
Q ss_pred ---EEEecccchhhhhh
Q 024995 227 ---QEIQLSHSLIRKAS 240 (259)
Q Consensus 227 ---~~v~~~~~~i~ls~ 240 (259)
.+++...++|.+++
T Consensus 687 v~v~~v~~~~~~i~~~~ 703 (706)
T COG0557 687 VKVTSVDLDERKIDFEL 703 (706)
T ss_pred EEEEEEcccccceEEEe
Confidence 47777777776654
No 176
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=82.33 E-value=1.1 Score=38.79 Aligned_cols=74 Identities=24% Similarity=0.376 Sum_probs=52.6
Q ss_pred ccCCCCCCEEEEE-------eeeEEEEEccCCCCccEEEEEEceecCcccccCh-hh---hc--CCCCeEEEEEEEEeCC
Q 024995 53 SSRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-RD---IL--NEGDEVRVKVIKIDRE 119 (259)
Q Consensus 53 ~~~l~~G~iv~G~-------~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~-~~---~~--~~Gd~V~vkVl~id~~ 119 (259)
+.++++|+++-|+ .||++|+++- .|....++|+|.-+|....-..| ++ .| -.--.++|-|.++|..
T Consensus 70 l~~~~~Gdv~vGrl~~l~~vgyg~yvdigV-~~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~evnk~ 148 (247)
T COG4044 70 LSKVEEGDVYVGRLIDLGKVGYGAYVDIGV-LGPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEVNKL 148 (247)
T ss_pred cccCCCCcEEEEEEeeeccceeEEEccccc-cCCCcccccccHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEeccch
Confidence 4788999999999 7999999973 33235789999999876655444 22 22 2345677888888876
Q ss_pred CCeeEEEE
Q 024995 120 KSRITLSI 127 (259)
Q Consensus 120 ~~ri~lS~ 127 (259)
.+.|...+
T Consensus 149 ~~EIea~l 156 (247)
T COG4044 149 AQEIEARL 156 (247)
T ss_pred hhhhhhhh
Confidence 66665544
No 177
>PF09876 DUF2103: Predicted metal-binding protein (DUF2103); InterPro: IPR018664 This family of various putative metal binding prokaryotic proteins has no known function.
Probab=82.06 E-value=1.4 Score=33.99 Aligned_cols=54 Identities=26% Similarity=0.343 Sum_probs=32.9
Q ss_pred cCCeeEEEEccccccccccchhhhhhcccCCCCCcceeeeccCCCeeEEEecccc
Q 024995 180 EDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHS 234 (259)
Q Consensus 180 ~~gv~gl~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V~~v~~~~~ 234 (259)
.++|..++++.+...+...++.+..|+.+. ...++|++++|.|-.||||-.-+.
T Consensus 32 ~~~Vk~IiPG~I~~~~~~~~~gl~lkvt~~-~~~Gn~Kllar~G~SvQEvfVVT~ 85 (103)
T PF09876_consen 32 HPGVKKIIPGVISRSGGRSSGGLRLKVTRP-TRGGNFKLLARSGSSVQEVFVVTT 85 (103)
T ss_pred CCCCCEEecccEEcCCCCCCCCeEEEEEEe-cCCCcEEEEEecCCeeEEEEEEee
Confidence 355555554444433322233455566543 356679999999999999866544
No 178
>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=81.48 E-value=2 Score=43.29 Aligned_cols=70 Identities=11% Similarity=0.077 Sum_probs=44.6
Q ss_pred CccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCccee----eeccCCCee---
Q 024995 155 SMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFT----LLARAGRQV--- 226 (259)
Q Consensus 155 ~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~r~G~~V--- 226 (259)
....|.|..++++| +||+|. ..|++||+ .+.+.... +. |. ... ....+. -.++.||.|
T Consensus 559 ~~f~g~I~~v~~~g----~~v~l~-~~~~~g~v~~~~l~~~~-----~~--~~-~~~-~~~~~~l~g~~~~~lgd~v~V~ 624 (639)
T TIGR02062 559 TRFAAEIVDISRGG----MRVRLL-ENGAIAFIPAAFLHANR-----EE--LV-CNQ-ENGTVQIKGETVYKIGDVIDVV 624 (639)
T ss_pred cEEEEEEEeeeCCc----EEEEEe-cCceEEEEEhhhcCCCC-----cc--eE-Ecc-cccEEEEeccEEEecCCEEEEE
Confidence 36899999999999 999995 57999998 44443210 10 10 000 000000 046899999
Q ss_pred -EEEecccchhhh
Q 024995 227 -QEIQLSHSLIRK 238 (259)
Q Consensus 227 -~~v~~~~~~i~l 238 (259)
.+||.++++|.+
T Consensus 625 v~~vd~~~~~i~~ 637 (639)
T TIGR02062 625 LTEVRMETRSIIA 637 (639)
T ss_pred EEEeccccCcEee
Confidence 588888887754
No 179
>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=81.42 E-value=2.1 Score=31.97 Aligned_cols=72 Identities=15% Similarity=0.107 Sum_probs=41.8
Q ss_pred CCCCccccceeeeccCCCccceeeeecc------cCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCC
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQ------EDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGR 224 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~------~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~ 224 (259)
++|+++.|+|+++..-. +++++.. .....|++ +|+.+.. .....+....+++||
T Consensus 5 ~~GDiVig~V~~v~~~~----~~v~I~~v~~~~l~~~~~g~l~~~dv~~~---------------~~d~~~~~~~f~~GD 65 (92)
T cd05791 5 KVGSIVIARVTRINPRF----AKVDILCVGGRPLKESFRGVIRKEDIRAT---------------EKDKVEMYKCFRPGD 65 (92)
T ss_pred CCCCEEEEEEEEEcCCE----EEEEEEEecCeecCCCcccEEEHHHcccc---------------ccchHHHHhhcCCCC
Confidence 56888999999998776 6666621 33456777 3443311 001012333679999
Q ss_pred eeE-E-Eeccc-chhhhhhch
Q 024995 225 QVQ-E-IQLSH-SLIRKASKR 242 (259)
Q Consensus 225 ~V~-~-v~~~~-~~i~ls~k~ 242 (259)
.|. + +.... +.+.||++.
T Consensus 66 iV~AkVis~~~~~~~~Lst~~ 86 (92)
T cd05791 66 IVRAKVISLGDASSYYLSTAE 86 (92)
T ss_pred EEEEEEEEcCCCCCcEEEecC
Confidence 993 2 33332 456666653
No 180
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=81.20 E-value=2.3 Score=35.78 Aligned_cols=59 Identities=8% Similarity=0.131 Sum_probs=37.9
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-Eccccccccccch--hhhhhcccCCCCCcceeeeccCCCee
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQ--DLQLWLSNAPPSGKKFTLLARAGRQV 226 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~r~G~~V 226 (259)
|++++|.|+++.++| +|+.+ +=+++++ .+.+. +.-..-. ....|... +. +..++.|+.|
T Consensus 82 gEVv~g~V~~v~~~G----~~v~~---Gp~~ifI~~~~l~-~~~~fd~~~~~~~~~~~----~~--~~~i~~g~~V 143 (176)
T PTZ00162 82 DEVLDAIVTDVNKLG----FFAQA---GPLKAFVSRSAIP-PDFVYDSDSAYPCYISS----DG--QIQIKPNTEV 143 (176)
T ss_pred CCEEEEEEEEEecce----EEEEe---eCeEEEEcHHHCC-CccEECCCCCcceEecC----CC--cEEECCCCEE
Confidence 677999999999999 99888 4567888 45553 2222111 22244421 12 2367999999
No 181
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=80.38 E-value=2.3 Score=41.55 Aligned_cols=71 Identities=24% Similarity=0.365 Sum_probs=52.0
Q ss_pred ccCCCCCCEEEEE-------eeeEEEEEccCCCCccEEEEEEceecCcccccCh-----hhhcCCCCeEEEEEEEEeCCC
Q 024995 53 SSRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-----RDILNEGDEVRVKVIKIDREK 120 (259)
Q Consensus 53 ~~~l~~G~iv~G~-------~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~-----~~~~~~Gd~V~vkVl~id~~~ 120 (259)
.....+|.+|.|+ =-.+||+++ ..-.||+|.+++.+ +...+ ...++.||.+-|.+..-...+
T Consensus 32 ~~~~~~gniy~grv~~i~p~~~aafvdig-----~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~ 105 (487)
T COG1530 32 AKEQIVGNIYKGRVTRVLPSLEAAFVDIG-----LERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEPRGT 105 (487)
T ss_pred CcEeeecCceEEEecccCccchhheeecc-----CCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeecCcc
Confidence 4466789999999 235899998 47899999999998 43333 357999999999998776544
Q ss_pred CeeEEEEec
Q 024995 121 SRITLSIKQ 129 (259)
Q Consensus 121 ~ri~lS~K~ 129 (259)
+=-.||-.-
T Consensus 106 Kga~lT~~I 114 (487)
T COG1530 106 KGARLTTDI 114 (487)
T ss_pred ccccceeEE
Confidence 433444433
No 182
>PRK10811 rne ribonuclease E; Reviewed
Probab=78.56 E-value=3.3 Score=43.47 Aligned_cols=35 Identities=17% Similarity=0.251 Sum_probs=29.1
Q ss_pred CCCccccceeeeccCCCccceeeeecccCCeeEEE-Eccc
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQ 191 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~ 191 (259)
+|.++.|+|.+|.+ |+.++||+| ..|-.||+ .++.
T Consensus 38 vGnIYkGkVenIvP--GInAAFVDI--G~gknGFL~L~Di 73 (1068)
T PRK10811 38 KANIYKGKITRIEP--SLEAAFVDY--GAERHGFLPLKEI 73 (1068)
T ss_pred ccceEEEEEecccC--CcceeEEEe--cCCcceEEEhhhc
Confidence 47889999999975 677899999 78999998 5554
No 183
>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=76.98 E-value=2.7 Score=31.19 Aligned_cols=58 Identities=7% Similarity=0.080 Sum_probs=37.4
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE-Ecccccccccc--chhhhhhcccCCCCCcceeeeccCCCee
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVV--SQDLQLWLSNAPPSGKKFTLLARAGRQV 226 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~r~G~~V 226 (259)
|+++.|+|+++.++| +|+.+ ..+++|+ .+.+..+ -.. .+...+|.. . . ...++.|+.|
T Consensus 2 gEVi~g~V~~v~~~G----~~v~~---Gpl~~f~~~~~ip~~-~~~~~~~~~~~~~~----~-~--~~~i~~g~~V 62 (88)
T cd04462 2 GEVVDAIVTSVNKTG----FFAEV---GPLSIFISRHLIPSD-MEFDPNASPPCFTS----N-E--DIVIKKDTEV 62 (88)
T ss_pred CcEEEEEEEEEeccE----EEEEE---cCceEEEEeeecCcc-ceECCcCCCCeEeC----C-C--cEEECCCCEE
Confidence 788999999999999 99888 6688887 3333211 111 122224531 1 1 2367999999
No 184
>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=76.83 E-value=8.7 Score=30.41 Aligned_cols=56 Identities=16% Similarity=0.213 Sum_probs=35.6
Q ss_pred CCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccc-c------------cChhhhcCCCCeEEEEEEEEeC
Q 024995 58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-I------------QDIRDILNEGDEVRVKVIKIDR 118 (259)
Q Consensus 58 ~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~-~------------~~~~~~~~~Gd~V~vkVl~id~ 118 (259)
+|+++.|+ .-|+.|.|+ .--+-+||.+.|.... + .+-.-++..|+.|++||.++..
T Consensus 3 ~gEvl~g~I~~~~~~Gi~vslg-----FFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f 76 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAEGIRVSLG-----FFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF 76 (122)
T ss_dssp TT-EEEEEEEEEETTEEEEEEC-----CEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred CCCEEEEEEEecCCCcEEEEec-----ccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence 57777777 568888886 4557788888876321 1 2223347889999999988865
No 185
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=72.81 E-value=1.9 Score=31.87 Aligned_cols=62 Identities=8% Similarity=0.153 Sum_probs=41.7
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEE--EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR--ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q 227 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~--~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~ 227 (259)
|+.+. .|+.+.+.| +++.|.-. |++|++ .|+++..+ +. +++-++ +|... +
T Consensus 17 ~dvv~-~Vv~i~d~~----~YV~LleY-~iegmIl~~selsr~r----------ir-------si~kll-VGk~e~v~Vi 72 (86)
T PHA02858 17 NEVTK-GIVFVKDNI----FYVKLIDY-GLEALIVNYVNVNADR----------AE-------KLKKKL-VGKTINVQVI 72 (86)
T ss_pred CeEEE-EEEEEeccE----EEEEEecC-ccceEEecHHHHhHHH----------HH-------hhhhhh-cCCeeEEEEE
Confidence 55577 788999999 99999644 599997 46766221 21 123344 66654 6
Q ss_pred EEecccchhhhh
Q 024995 228 EIQLSHSLIRKA 239 (259)
Q Consensus 228 ~v~~~~~~i~ls 239 (259)
.+|.++.=|.||
T Consensus 73 RVDk~KGYIDLs 84 (86)
T PHA02858 73 RTDKLKGYIDVR 84 (86)
T ss_pred EECCCCCEEEeE
Confidence 788877766665
No 186
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=72.79 E-value=26 Score=29.59 Aligned_cols=71 Identities=21% Similarity=0.201 Sum_probs=45.9
Q ss_pred CCCCCCEEEEE------eeeEEEEEccCCC---CccEEEEEEceecCcc--cccChhhhcCCCCeEEEEEEEEeCCCCee
Q 024995 55 RVNVEDIFVGR------DYGAFIHLRFPDG---LYHLTGLVHVSEVSWD--LIQDIRDILNEGDEVRVKVIKIDREKSRI 123 (259)
Q Consensus 55 ~l~~G~iv~G~------~~G~fV~l~~~~g---~~gi~glv~isels~~--~~~~~~~~~~~Gd~V~vkVl~id~~~~ri 123 (259)
....|+++.++ .| +=|+|-.++. -....|+||..++... .--++.+-|++||.|.++|++.+. ....
T Consensus 65 LP~~G~IVtarV~~i~~rf-Akv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~-~~~y 142 (193)
T KOG3409|consen 65 LPFVGAIVTARVSRINLRF-AKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGD-GSNY 142 (193)
T ss_pred CCccCcEEEEEEEeeccce-eeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCC-CCcE
Confidence 46789999888 22 3333321110 0246899998887542 223556679999999999999764 5556
Q ss_pred EEEE
Q 024995 124 TLSI 127 (259)
Q Consensus 124 ~lS~ 127 (259)
.|+.
T Consensus 143 ~LTt 146 (193)
T KOG3409|consen 143 LLTT 146 (193)
T ss_pred EEEE
Confidence 6654
No 187
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=71.72 E-value=29 Score=23.67 Aligned_cols=41 Identities=27% Similarity=0.254 Sum_probs=28.0
Q ss_pred eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEE
Q 024995 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (259)
Q Consensus 66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~ 115 (259)
.||....-+ .+-+-|+|++++.... ...++.|+.|...+..
T Consensus 13 gyGFI~~~~-----~~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 13 GYGFITSDD-----GGEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE 53 (66)
T ss_dssp TEEEEEETT-----SSSEEEEEGGGBCSSS----STS--TTSEEEEEEEE
T ss_pred CceEEEEcc-----cceeEEeccccccccc----cccCCCCCEEEEEEEE
Confidence 465544433 2559999999998754 2357899999999976
No 188
>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=71.51 E-value=4.4 Score=29.85 Aligned_cols=25 Identities=12% Similarity=0.137 Sum_probs=17.0
Q ss_pred CCCCccccceeeeccCCCccceeeeeccc
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQE 180 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~ 180 (259)
++|++|.|+|+++.+-- +.++|..-
T Consensus 3 ~vGdiV~~rVtrv~~~~----a~v~Il~v 27 (82)
T PF10447_consen 3 KVGDIVIARVTRVNPRQ----AKVEILCV 27 (82)
T ss_dssp -TT-EEEEEEEEE-SSE----EEEEEEES
T ss_pred CCCCEEEEEEEEEeccE----EEEEEEEE
Confidence 35888999999998866 66666444
No 189
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=70.70 E-value=2.9 Score=41.45 Aligned_cols=31 Identities=13% Similarity=0.186 Sum_probs=27.6
Q ss_pred CCCccccceeeeccCCCccceeeeecccCCeeEEEEc
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRIT 189 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~s 189 (259)
.|..+.|+|.+++.|| +|++| .+.+.||+++
T Consensus 122 ~g~~Y~g~v~~v~~~G----vFv~L--n~~v~GL~~~ 152 (715)
T COG1107 122 AGKYYKGIVSRVEKYG----VFVEL--NSHVRGLIHR 152 (715)
T ss_pred cceeeeccccchhhhc----ceeec--Chhhhccccc
Confidence 4777999999999999 99888 8999999953
No 190
>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=66.99 E-value=5.1 Score=38.35 Aligned_cols=36 Identities=17% Similarity=0.202 Sum_probs=28.7
Q ss_pred CCCccccceeeeccCCCccceeeeecccCCeeEEE-Ecccc
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQG 192 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~ 192 (259)
+|.++.|+|.++.|. +.++||+| ..|-.||+ .+++.
T Consensus 25 vGnIY~GrV~~i~p~--l~aAFVdi--G~~k~gfL~~~d~~ 61 (414)
T TIGR00757 25 KGNIYKGRVTRILPS--LQAAFVDI--GLEKNGFLHASDIG 61 (414)
T ss_pred CCCEEEEEEeeecCC--CceEEEEc--CCCceEEEEHHHcC
Confidence 477799999999986 33499999 78899999 56543
No 191
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=66.66 E-value=6 Score=27.11 Aligned_cols=30 Identities=7% Similarity=0.060 Sum_probs=15.4
Q ss_pred CCccccceeeeccCCCccceeeeecccCCeeEEEEc
Q 024995 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRIT 189 (259)
Q Consensus 154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~s 189 (259)
|++.+.+|.++.++| +|... ..+-+-|++.
T Consensus 2 G~~~~L~V~~~~~~g----~fL~~--~~~~~vlLp~ 31 (61)
T PF13509_consen 2 GQINTLKVVDKNEFG----YFLDD--GEGKEVLLPK 31 (61)
T ss_dssp -------EEEE-SSE----EEEEE--TT-EEEEEEG
T ss_pred CCCcceEEEEEeCCE----EEEEC--CCCCEEEech
Confidence 667889999999999 88543 5556667753
No 192
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=64.28 E-value=32 Score=24.67 Aligned_cols=54 Identities=22% Similarity=0.191 Sum_probs=35.2
Q ss_pred eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEecc
Q 024995 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (259)
Q Consensus 66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~ 130 (259)
-|| ||.-.+ .+-+.|+|+|.+...-. ..++.||.|...+..- .+++-...+..+
T Consensus 14 GfG-FI~~~~----gg~dVFvH~s~i~~~g~----~~l~~G~~V~f~~~~~--~~G~~A~~V~~~ 67 (74)
T PRK09937 14 GFG-FICPEG----GGEDIFAHYSTIQMDGY----RTLKAGQSVQFDVHQG--PKGNHASVIVPV 67 (74)
T ss_pred CeE-EEeeCC----CCccEEEEEeeccccCC----CCCCCCCEEEEEEEEC--CCCceeeEEEEC
Confidence 345 555542 26899999999975432 3478899999998553 256555554433
No 193
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=61.36 E-value=7.8 Score=41.30 Aligned_cols=69 Identities=9% Similarity=0.101 Sum_probs=47.4
Q ss_pred CCCccccceeeecc-CCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995 153 SSSMSSSNSNTIEP-LPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---- 226 (259)
Q Consensus 153 ~g~~v~G~V~~i~~-~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---- 226 (259)
.|..+.++|++++. .| +||.+.+..|++|+| ....+.. + +..|.. .+++|+.|
T Consensus 985 ~g~iV~~~V~~vt~rr~----~Cv~v~ld~G~~g~i~~~~~Sd~------~-------v~~p~~----~v~vgq~v~~kv 1043 (1299)
T KOG1856|consen 985 EGAIVPVTVTKVTHRRG----ICVRVRLDCGVTGFILAKNLSDR------D-------VRRPEN----RVKVGQTVYCKV 1043 (1299)
T ss_pred cCceEEEeeeEEEeccc----ceeEEEecCCCceeeeccccChh------h-------ccCHHH----hhccCceEEEEe
Confidence 37778899999873 45 777787899999999 4555521 1 344555 44899998
Q ss_pred EEEecccchhhhhhch
Q 024995 227 QEIQLSHSLIRKASKR 242 (259)
Q Consensus 227 ~~v~~~~~~i~ls~k~ 242 (259)
+.+|.+.=.+-||++.
T Consensus 1044 i~id~e~f~v~Ls~r~ 1059 (1299)
T KOG1856|consen 1044 IKIDKERFSVELSCRT 1059 (1299)
T ss_pred eeeeHhhhhhhhhhhh
Confidence 5677666556666554
No 194
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=61.32 E-value=9.9 Score=37.16 Aligned_cols=57 Identities=12% Similarity=0.180 Sum_probs=40.9
Q ss_pred CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV 226 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V 226 (259)
+|.++.|+|++|.| +.+++||++ ..+=.||+ .++... +... ..+.+++..+|.||.+
T Consensus 37 ~gniy~grv~~i~p--~~~aafvdi--g~~r~gfl~~~~~~~-----------~~~~--~~~~~i~~~lr~~~~~ 94 (487)
T COG1530 37 VGNIYKGRVTRVLP--SLEAAFVDI--GLERNGFLHLSEIVP-----------YFRA--VLEEKIKVRLRGGQAT 94 (487)
T ss_pred ecCceEEEecccCc--cchhheeec--cCCccceEEecccch-----------hhhh--cccccceeeecCCceE
Confidence 37779999999986 678899999 77889998 555442 1111 1222566788999998
No 195
>PRK15464 cold shock-like protein CspH; Provisional
Probab=57.67 E-value=24 Score=25.04 Aligned_cols=41 Identities=22% Similarity=0.121 Sum_probs=28.9
Q ss_pred eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEE
Q 024995 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (259)
Q Consensus 66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~ 115 (259)
-|| |+.-++ .+-+.|+|++.+..... +.+++||.|...+..
T Consensus 17 GfG-FI~~~~----g~~DvFvH~s~l~~~g~----~~l~~G~~V~f~v~~ 57 (70)
T PRK15464 17 GKG-FIIPSD----GRKEVQVHISAFTPRDA----EVLIPGLRVEFCRVN 57 (70)
T ss_pred CeE-EEccCC----CCccEEEEehhehhcCC----CCCCCCCEEEEEEEE
Confidence 344 566552 26799999999965432 347889999998854
No 196
>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=57.19 E-value=37 Score=26.13 Aligned_cols=48 Identities=17% Similarity=0.299 Sum_probs=35.8
Q ss_pred CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEE
Q 024995 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 116 (259)
Q Consensus 57 ~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~i 116 (259)
..|.++.|+ +--+||++++ ...+.|+..+... +.|+.|..|.+++.+.
T Consensus 22 ~~gk~V~G~I~hvv~ddLYIDfG~-----KFhcVc~rp~~~~-------~~y~~G~rV~lrLkdl 74 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDDDLYIDFGG-----KFHCVCKRPAVNG-------EKYVRGSRVRLRLKDL 74 (104)
T ss_pred ccCCEEEEEEEEEecCceEEEeCC-----ceeEEEecccccc-------cccccCCEEEEEECCH
Confidence 477788888 5579999983 7899998766532 3478899998888544
No 197
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=55.20 E-value=35 Score=23.96 Aligned_cols=41 Identities=24% Similarity=0.345 Sum_probs=28.4
Q ss_pred eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEE
Q 024995 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (259)
Q Consensus 66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~ 115 (259)
-|| |+.-.+ .+-+.|+|+|.+..... ..+++||.|...+..
T Consensus 16 GyG-FI~~~~----g~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~ 56 (69)
T PRK09507 16 GFG-FITPED----GSKDVFVHFSAIQTNGF----KTLAEGQRVEFEITN 56 (69)
T ss_pred CcE-EEecCC----CCeeEEEEeecccccCC----CCCCCCCEEEEEEEE
Confidence 455 455542 26799999999975422 347789999997744
No 198
>PRK15463 cold shock-like protein CspF; Provisional
Probab=55.09 E-value=22 Score=25.17 Aligned_cols=41 Identities=22% Similarity=0.131 Sum_probs=28.8
Q ss_pred eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEE
Q 024995 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (259)
Q Consensus 66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~ 115 (259)
-|| |+.-.+ .+-+.|+|++.+..... ..+++||.|...+..
T Consensus 17 GfG-FI~~~~----g~~DvFvH~sal~~~g~----~~l~~G~~V~f~v~~ 57 (70)
T PRK15463 17 GKG-LITPSD----GRKDVQVHISALNLRDA----EELTTGLRVEFCRIN 57 (70)
T ss_pred ceE-EEecCC----CCccEEEEehhhhhcCC----CCCCCCCEEEEEEEE
Confidence 344 566542 26799999999975422 247899999998744
No 199
>PRK14998 cold shock-like protein CspD; Provisional
Probab=54.98 E-value=50 Score=23.54 Aligned_cols=51 Identities=25% Similarity=0.222 Sum_probs=33.5
Q ss_pred eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (259)
Q Consensus 66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~ 127 (259)
-|| |+.-.+ .+-+.|+|+|.+..... ..+..||.|...+..-+ +++....+
T Consensus 14 GfG-FI~~~~----g~~dVFvH~s~l~~~g~----~~l~~G~~V~f~~~~~~--~G~~A~~V 64 (73)
T PRK14998 14 GFG-FICPEG----GGEDIFAHYSTIQMDGY----RTLKAGQSVRFDVHQGP--KGNHASVI 64 (73)
T ss_pred ceE-EEecCC----CCccEEEEeeeecccCC----CCCCCCCEEEEEEEECC--CCceeEEE
Confidence 344 555542 26899999999975432 35788999999985543 45544443
No 200
>TIGR00830 PTBA PTS system, glucose subfamily, IIA component. These are part of the The PTS Glucose-Glucoside (Glc) SuperFamily. The Glc family includes permeases specific for glucose, N-acetylglucosamine and a large variety of a- and b-glucosides. However, not all b-glucoside PTS permeases are in this class, as the cellobiose (Cel) b-glucoside PTS permease is in the Lac family (TC #4.A.3). The IIA, IIB and IIC domains of all of the permeases listed below are demonstrably homologous. These permeases show limited sequence similarity with members of the Fru family (TC #4.A.2). Several of the PTS permeases in the Glc family lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). Most of these permeases have the B and C domains linked together in a single polypeptide chain, and a cysteyl residue in the IIB domain is phosphorylated by direct phosphoryl transfer from IIAglc(his~P). Those permeases which lack a IIA domain include the maltose (Mal), arbutin-salicin-c
Probab=54.10 E-value=30 Score=27.30 Aligned_cols=51 Identities=18% Similarity=0.232 Sum_probs=32.4
Q ss_pred cccceeeeccCCCccceeeeecccCCeeEEEEccccccccccchhhhhhcccCCCCCcceeeeccCCCee
Q 024995 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV 226 (259)
Q Consensus 157 v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V 226 (259)
+.|+|..+.+-+ ++|. |..++|++-|+|--+-.- .-....|+..++.||.|
T Consensus 42 ~~G~v~~v~~T~---HA~g-i~~~~G~evLiHiGidTV---------------~L~G~gF~~~v~~Gd~V 92 (121)
T TIGR00830 42 VDGKIGKIFPTK---HAFG-IESDSGVEILIHIGIDTV---------------KLNGEGFTSHVEEGQRV 92 (121)
T ss_pred CCeEEEEEccCC---CEEE-EEeCCCcEEEEEeeecee---------------ecCCCceEEEecCCCEE
Confidence 578899998866 5554 556789999986433211 11222366677777776
No 201
>PRK09439 PTS system glucose-specific transporter subunit; Provisional
Probab=53.54 E-value=31 Score=28.92 Aligned_cols=57 Identities=18% Similarity=0.248 Sum_probs=36.7
Q ss_pred cccceeeeccCCCccceeeeecccCCeeEEEEccccccccccchhhhhhcccCCCCCcceeeeccCCCee------EEEe
Q 024995 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV------QEIQ 230 (259)
Q Consensus 157 v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V------~~v~ 230 (259)
+.|+|..+.+-+ ++|. |..++|++-|+|--+. ++ .-...-|+..++.||.| .++|
T Consensus 64 ~dG~V~~vf~T~---HAig-i~t~~G~eiLIHiGiD--------TV-------~L~G~gF~~~Vk~Gd~Vk~G~~L~~~D 124 (169)
T PRK09439 64 VDGTIGKIFETN---HAFS-IESDSGVELFVHFGID--------TV-------ELKGEGFKRIAEEGQRVKVGDPIIEFD 124 (169)
T ss_pred CCeEEEEEcCCC---CEEE-EEeCCCcEEEEEEeec--------cc-------ccCCCceEEEecCCCEEeCCCEEEEEc
Confidence 578899998866 5664 5567899999864332 11 11222377777777777 5666
Q ss_pred cc
Q 024995 231 LS 232 (259)
Q Consensus 231 ~~ 232 (259)
.+
T Consensus 125 ~~ 126 (169)
T PRK09439 125 LP 126 (169)
T ss_pred HH
Confidence 54
No 202
>PRK10943 cold shock-like protein CspC; Provisional
Probab=52.25 E-value=36 Score=23.92 Aligned_cols=41 Identities=24% Similarity=0.324 Sum_probs=28.6
Q ss_pred eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEE
Q 024995 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (259)
Q Consensus 66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~ 115 (259)
.|| |+.-.+ .+-+-|+|+|.+..... ..+.+||.|...+..
T Consensus 16 GfG-FI~~~~----g~~dvFvH~s~l~~~g~----~~l~~G~~V~f~~~~ 56 (69)
T PRK10943 16 GFG-FITPAD----GSKDVFVHFSAIQGNGF----KTLAEGQNVEFEIQD 56 (69)
T ss_pred CcE-EEecCC----CCeeEEEEhhHccccCC----CCCCCCCEEEEEEEE
Confidence 344 555542 26899999999975432 347789999998744
No 203
>cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=51.65 E-value=32 Score=27.28 Aligned_cols=30 Identities=10% Similarity=0.096 Sum_probs=22.2
Q ss_pred cccceeeeccCCCccceeeeecccCCeeEEEEcc
Q 024995 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITR 190 (259)
Q Consensus 157 v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~s~ 190 (259)
+.|+|..+.+-+ ++|. |..++|++-|+|-.
T Consensus 42 ~~G~v~~i~~T~---HA~~-i~~~~G~eiLiHiG 71 (124)
T cd00210 42 VDGTIVQIFPTK---HAIG-IESDSGVEILIHIG 71 (124)
T ss_pred CCeEEEEEccCC---CEEE-EEeCCCcEEEEEee
Confidence 578999998866 5553 55578999998643
No 204
>PF00358 PTS_EIIA_1: phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1; InterPro: IPR001127 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. ; GO: 0005351 sugar:hydrogen symporter activity, 0006810 transport, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016020 membrane; PDB: 3OUR_D 1GPR_A 1F3G_A 2F3G_B 1F3Z_A 1O2F_A 1GLB_F 1GGR_A 1GLA_F 1GLE_F ....
Probab=51.63 E-value=32 Score=27.56 Aligned_cols=28 Identities=11% Similarity=0.183 Sum_probs=20.7
Q ss_pred cccceeeeccCCCccceeeeecccCCeeEEEE
Q 024995 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVRI 188 (259)
Q Consensus 157 v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~ 188 (259)
+.|+|..+.+-+ ++|. |...+|++-|+|
T Consensus 46 ~~G~v~~i~~T~---HAi~-i~s~~G~eiLiH 73 (132)
T PF00358_consen 46 VDGTVTMIFPTK---HAIG-IRSDNGVEILIH 73 (132)
T ss_dssp SSEEEEEE-TTS---SEEE-EEETTSEEEEEE
T ss_pred eeEEEEEEcCCC---CEEE-EEeCCCCEEEEE
Confidence 579999998866 4554 666899999985
No 205
>COG2190 NagE Phosphotransferase system IIA components [Carbohydrate transport and metabolism]
Probab=50.38 E-value=27 Score=28.91 Aligned_cols=29 Identities=10% Similarity=0.127 Sum_probs=22.4
Q ss_pred cccceeeeccCCCccceeeeecccCCeeEEEEc
Q 024995 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVRIT 189 (259)
Q Consensus 157 v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~s 189 (259)
+.|+|..+.|-+ ++|. |..++|++=|+|=
T Consensus 49 vdG~v~~iFpTk---HAig-i~t~~GvEiLiHi 77 (156)
T COG2190 49 VDGTVVLIFPTK---HAIG-IETDEGVEILIHI 77 (156)
T ss_pred cCcEEEEEeeCC---cEEE-EEcCCCcEEEEEe
Confidence 568899998876 5665 6668899999863
No 206
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=50.19 E-value=72 Score=23.78 Aligned_cols=54 Identities=22% Similarity=0.183 Sum_probs=37.8
Q ss_pred eeeEE-EEEccCCCCccEEEEEEceecC-cccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995 66 DYGAF-IHLRFPDGLYHLTGLVHVSEVS-WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (259)
Q Consensus 66 ~~G~f-V~l~~~~g~~gi~glv~isels-~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~ 129 (259)
+.+.| |.|. .|..-+.|+|-=- ..++ .+-+||.|.|.+-.+|..+++|..-.|.
T Consensus 18 p~~~frV~Le-----nG~~vla~isGKmR~~rI-----rIl~GD~V~VE~spYDltkGRIiyR~~~ 73 (87)
T PRK12442 18 PDSRFRVTLE-----NGVEVGAYASGRMRKHRI-----RILAGDRVTLELSPYDLTKGRINFRHKD 73 (87)
T ss_pred CCCEEEEEeC-----CCCEEEEEeccceeeeeE-----EecCCCEEEEEECcccCCceeEEEEecC
Confidence 34443 4776 2677777766421 1122 3668999999999999999999998874
No 207
>cd05700 S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=48.68 E-value=22 Score=24.68 Aligned_cols=27 Identities=19% Similarity=0.363 Sum_probs=21.4
Q ss_pred hhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995 101 DILNEGDEVRVKVIKIDREKSRITLSI 127 (259)
Q Consensus 101 ~~~~~Gd~V~vkVl~id~~~~ri~lS~ 127 (259)
..+.+||++++.|+.+|.-+.++-+|+
T Consensus 39 ~nl~pGqK~kaviLhvD~l~~~VhVSl 65 (65)
T cd05700 39 VNVTPGCKLKAVILHVDFVKSQVHVSL 65 (65)
T ss_pred eecCCCceeEEEEEEEeeEEeEEEEeC
Confidence 346789999999999998766666653
No 208
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=48.09 E-value=31 Score=33.36 Aligned_cols=56 Identities=9% Similarity=0.127 Sum_probs=37.4
Q ss_pred CCCCccccceeeeccCCCccceeeeec---ccCCeeEEEEccccccccccchhhhhhcccCCCCCcceeeeccCCCee--
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELL---QEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV-- 226 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~---~~~gv~gl~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V-- 226 (259)
+.|++++|+|.++..-+ +++.|. ..++++|+++.+.. .+..+| ++||.+
T Consensus 151 ~~GeIV~G~V~r~e~~~----viv~l~~~~g~~~~EaiLP~~Eq------------------ip~E~y----~~Gdrika 204 (449)
T PRK12329 151 LEDTVLTARVLRFERQS----VIMAVSSGFGQPEVEAELPKREQ------------------LPNDNY----RANATFKV 204 (449)
T ss_pred hcCcEEEEEEEEEcCCC----EEEEecccCCCcceEEEecHHHc------------------CCCCcC----CCCCEEEE
Confidence 35888999999998776 887772 11248999853311 133345 899998
Q ss_pred --EEEeccc
Q 024995 227 --QEIQLSH 233 (259)
Q Consensus 227 --~~v~~~~ 233 (259)
++|....
T Consensus 205 ~i~~V~~~~ 213 (449)
T PRK12329 205 FLKEVSEGP 213 (449)
T ss_pred EEEEeecCC
Confidence 5776663
No 209
>PRK11712 ribonuclease G; Provisional
Probab=47.99 E-value=16 Score=35.85 Aligned_cols=35 Identities=11% Similarity=0.182 Sum_probs=29.4
Q ss_pred CCCccccceeeeccCCCccceeeeecccCCeeEEE-Eccc
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQ 191 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~ 191 (259)
+|.++.|+|.+|.| ++.++||++ ..+-.||+ .++.
T Consensus 38 vGnIY~G~V~~v~p--g~~AAFVdI--G~~k~gFL~~~d~ 73 (489)
T PRK11712 38 VGNIYKGRVSRVLP--GMQAAFVDI--GLDKAAFLHASDI 73 (489)
T ss_pred cccEEEEEEeecCC--CCceeEEee--CCCccEEEEhhhc
Confidence 47789999999986 778899999 88999998 4543
No 210
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=47.94 E-value=44 Score=23.49 Aligned_cols=41 Identities=27% Similarity=0.326 Sum_probs=28.7
Q ss_pred eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEE
Q 024995 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (259)
Q Consensus 66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~ 115 (259)
.|| |+.-.+ .+-+.|+|+|.+..... ..+++||.|...+..
T Consensus 17 GfG-FI~~~~----g~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~ 57 (70)
T PRK10354 17 GFG-FITPDD----GSKDVFVHFSAIQNDGY----KSLDEGQKVSFTIES 57 (70)
T ss_pred CcE-EEecCC----CCccEEEEEeeccccCC----CCCCCCCEEEEEEEE
Confidence 455 455542 25899999999975421 347889999998754
No 211
>PRK09890 cold shock protein CspG; Provisional
Probab=47.59 E-value=48 Score=23.32 Aligned_cols=41 Identities=22% Similarity=0.311 Sum_probs=28.5
Q ss_pred eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEE
Q 024995 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (259)
Q Consensus 66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~ 115 (259)
.|| |+.-.+ .+-+.|+|+|.+..... ..+++||.|...+..
T Consensus 17 GfG-FI~~~~----g~~dvFvH~s~l~~~~~----~~l~~G~~V~f~~~~ 57 (70)
T PRK09890 17 GFG-FITPDD----GSKDVFVHFTAIQSNEF----RTLNENQKVEFSIEQ 57 (70)
T ss_pred CcE-EEecCC----CCceEEEEEeeeccCCC----CCCCCCCEEEEEEEE
Confidence 345 555542 25899999999976532 347789999997743
No 212
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=47.58 E-value=31 Score=24.11 Aligned_cols=41 Identities=24% Similarity=0.348 Sum_probs=28.4
Q ss_pred eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEE
Q 024995 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (259)
Q Consensus 66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~ 115 (259)
.|| |+.-.+ .+-+.|+|+|.+..... ..+++||.|...+..
T Consensus 14 GfG-FI~~~~----g~~dvfvH~s~~~~~g~----~~l~~G~~V~f~~~~ 54 (68)
T TIGR02381 14 GFG-FICPEG----VDGDIFAHYSTIQMDGY----RTLKAGQKVQFEVVQ 54 (68)
T ss_pred CeE-EEecCC----CCccEEEEHHHhhhcCC----CCCCCCCEEEEEEEE
Confidence 455 555542 26899999999975431 347889999998744
No 213
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=45.47 E-value=68 Score=21.69 Aligned_cols=32 Identities=28% Similarity=0.244 Sum_probs=25.1
Q ss_pred cEEEEEEceecCcccccChhhhcCCCCeEEEEEEEE
Q 024995 81 HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 116 (259)
Q Consensus 81 gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~i 116 (259)
+-+-|+|.+++...- ...+++||.|...+..-
T Consensus 23 g~diffh~~~~~~~~----~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 23 GEDVFVHISALEGDG----FRSLEEGDRVEFELEEG 54 (65)
T ss_pred CcCEEEEhhHhhccC----CCcCCCCCEEEEEEEEC
Confidence 789999999997642 24578999999988554
No 214
>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=41.89 E-value=74 Score=22.56 Aligned_cols=51 Identities=25% Similarity=0.255 Sum_probs=33.5
Q ss_pred eeeEE-EEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEE
Q 024995 66 DYGAF-IHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125 (259)
Q Consensus 66 ~~G~f-V~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~l 125 (259)
+.+.| |.+. .|..-+.|++-=-. .-.-.+.+||.|.|.+-..|..+++|..
T Consensus 16 ~~~~f~V~l~-----ng~~vla~i~GKmr----~~rI~I~~GD~V~Ve~spyd~tkgrIi~ 67 (68)
T TIGR00008 16 PNAMFRVELE-----NGHEVLAHISGKIR----MHYIRILPGDKVKVELSPYDLTRGRITY 67 (68)
T ss_pred CCCEEEEEEC-----CCCEEEEEecCcch----hccEEECCCCEEEEEECcccCCcEeEEe
Confidence 34443 4666 26777777664211 1122477899999999999988888763
No 215
>COG1278 CspC Cold shock proteins [Transcription]
Probab=41.66 E-value=40 Score=23.87 Aligned_cols=30 Identities=27% Similarity=0.328 Sum_probs=23.3
Q ss_pred cEEEEEEceecCcccccChhhhcCCCCeEEEEEE
Q 024995 81 HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVI 114 (259)
Q Consensus 81 gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl 114 (259)
+-+.|+|+|.+..... ..+..||+|...+.
T Consensus 24 ~~DvFVH~Sai~~~g~----~~L~eGQ~V~f~~~ 53 (67)
T COG1278 24 GKDVFVHISAIQRAGF----RTLREGQKVEFEVE 53 (67)
T ss_pred CcCEEEEeeeeccCCC----cccCCCCEEEEEEe
Confidence 5799999999965543 24778999998873
No 216
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=40.87 E-value=99 Score=27.40 Aligned_cols=55 Identities=9% Similarity=0.017 Sum_probs=35.2
Q ss_pred CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee
Q 024995 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV 226 (259)
Q Consensus 153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V 226 (259)
.|+.|-|.|..+.+.+ -.++| ..-..+++ .|++-..+ .++...+..-.+++||.|
T Consensus 64 ~gD~VIG~I~~v~~~~----W~VDI--~sp~~A~L~ls~~~~r~-------------~~~~~~~~r~~l~vGD~v 119 (239)
T COG1097 64 VGDVVIGKIIEVGPSG----WKVDI--GSPYPALLSLSDFLRRK-------------FENAEKDLRPFLNVGDLV 119 (239)
T ss_pred CCCEEEEEEEEEcccc----eEEEc--CCccceEeehhhhhccc-------------ccccccccccccccCCEE
Confidence 5777999999999888 77777 44467776 55542110 011222344478999998
No 217
>KOG3754 consensus Gamma-glutamylcysteine synthetase [Coenzyme transport and metabolism]
Probab=38.97 E-value=32 Score=33.37 Aligned_cols=26 Identities=23% Similarity=0.224 Sum_probs=24.2
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh
Q 024995 22 TGSIISVKVIQANEEMKKLVFSEKDA 47 (259)
Q Consensus 22 vG~~v~~~Vl~id~~~~~v~lS~k~~ 47 (259)
=|++|+..|++.|.+++++.+|.+..
T Consensus 47 WGDEiEy~vV~fDd~~kk~rv~l~~e 72 (640)
T KOG3754|consen 47 WGDEIEYMVVKFDDKNKKARVSLRAE 72 (640)
T ss_pred ccceeEEEEEecccccceeeeeeeHH
Confidence 59999999999999999999999875
No 218
>PF02599 CsrA: Global regulator protein family; InterPro: IPR003751 The RNA-binding protein CsrA (carbon storage regulator) is a new kind of global regulator, which facilitates specific mRNA decay []. CsrA is entirely contained within a globular complex of approximately 18 CsrA-H6 subunits and a single RNA, CsrB. CsrA binds to the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis [].; GO: 0003723 RNA binding, 0006109 regulation of carbohydrate metabolic process, 0006402 mRNA catabolic process; PDB: 1Y00_B 2JPP_A 1T3O_A 1VPZ_A.
Probab=36.78 E-value=59 Score=21.94 Aligned_cols=33 Identities=21% Similarity=0.498 Sum_probs=25.8
Q ss_pred ChhhhcCCCCeEEEEEEEEeCCCCeeEEEEecccc
Q 024995 98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE 132 (259)
Q Consensus 98 ~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~ 132 (259)
.+.+.+.+|+.+.++|++++ .+++.|.+.+...
T Consensus 7 k~gE~I~Ig~~I~I~Vl~i~--~~~VklgI~AP~~ 39 (54)
T PF02599_consen 7 KVGESIVIGDDIEITVLEIS--GGQVKLGIDAPKE 39 (54)
T ss_dssp ETT-EEEETTTEEEEEEEEE--TTEEEEEEEECTT
T ss_pred cCCCEEEECCCEEEEEEEEc--CCEEEEEEECCCC
Confidence 34566778999999999998 6889998876544
No 219
>PRK01712 carbon storage regulator; Provisional
Probab=29.90 E-value=1e+02 Score=21.63 Aligned_cols=34 Identities=21% Similarity=0.432 Sum_probs=26.4
Q ss_pred ChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccC
Q 024995 98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEED 133 (259)
Q Consensus 98 ~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~ 133 (259)
.+.+.+.+|+.+.++|+++. .+++.|.+.+...-
T Consensus 7 k~gE~I~Igd~I~I~V~~i~--~~~VrlGI~AP~~v 40 (64)
T PRK01712 7 KVGESLMIGDDIEVTVLGVK--GNQVRIGINAPKEV 40 (64)
T ss_pred cCCCEEEeCCCEEEEEEEEe--CCEEEEEEECCCCc
Confidence 34566788999999999997 68899988765443
No 220
>COG2100 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=29.48 E-value=1.1e+02 Score=28.75 Aligned_cols=71 Identities=17% Similarity=0.259 Sum_probs=45.6
Q ss_pred CCCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCCCEEEEEechhh---HhhhccCCCCCCEEEEE----eeeEEEEE
Q 024995 1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR----DYGAFIHL 73 (259)
Q Consensus 1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vl~id~~~~~v~lS~k~~~---~~~~~~~l~~G~iv~G~----~~G~fV~l 73 (259)
++|.|+--||...++.-+. .|+.+.+.|+---.-+|....-.+.-. .......+.+|+.++.+ .-|+||..
T Consensus 335 lkP~~fG~~pRp~lp~PF~--rGevv~aevV~~Gr~kGEmlavArdRvIav~~~~~~~~~vG~~vkvrIvr~khnI~Ia~ 412 (414)
T COG2100 335 LKPGEFGMHPRPRLPKPFK--RGEVVKAEVVLPGRLKGEMLAVARDRVIAVINSNEGALLVGDRVKVRIVRTKHNIYIAV 412 (414)
T ss_pred cChhhcCCCcCCCCCCccc--cCcEEEEEEEecceecceEEEEecccEEEEecCchhhhccCceEEEEEEEccCceEEee
Confidence 4788887788877765444 999999998765444444444433211 11111257899998887 66788764
No 221
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=28.78 E-value=1.8e+02 Score=19.37 Aligned_cols=26 Identities=15% Similarity=0.192 Sum_probs=18.1
Q ss_pred cEEEEEEceecCcccccChhhhcCCCCeEEEEEEE
Q 024995 81 HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (259)
Q Consensus 81 gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~ 115 (259)
+-+-|||..+|... --||+|.|+++.
T Consensus 19 ~~DifIp~~~l~~A---------~~gD~V~v~i~~ 44 (58)
T PF08206_consen 19 GEDIFIPPRNLNGA---------MDGDKVLVRITP 44 (58)
T ss_dssp TEEEEE-HHHHTTS----------TT-EEEEEEEE
T ss_pred CCCEEECHHHHCCC---------CCCCEEEEEEec
Confidence 67888887777543 259999999988
No 222
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=28.50 E-value=2e+02 Score=21.53 Aligned_cols=41 Identities=12% Similarity=0.188 Sum_probs=30.6
Q ss_pred CCEEEEEEEEEeCCCCEEEEEechhhHhhhccCCCCCCEEEEE
Q 024995 23 GSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR 65 (259)
Q Consensus 23 G~~v~~~Vl~id~~~~~v~lS~k~~~~~~~~~~l~~G~iv~G~ 65 (259)
|....+. -.|.+++.+.++.-....+.+...+++|+++.=.
T Consensus 34 g~~~~~~--l~De~~~~I~~t~~~~~~~~f~~~l~eG~vy~i~ 74 (104)
T cd04474 34 GKLFSFD--LLDEDGGEIRATFFNDAVDKFYDLLEVGKVYYIS 74 (104)
T ss_pred cEEEEEE--EEECCCCEEEEEEehHHHHHhhcccccccEEEEe
Confidence 4444443 4677788999998887778888899999998644
No 223
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=26.90 E-value=1.5e+02 Score=21.17 Aligned_cols=43 Identities=7% Similarity=0.161 Sum_probs=32.4
Q ss_pred CCEEEEEEEEEeCCCCEEEEEechhhHhhhccCCCCCCEEEEEee
Q 024995 23 GSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDY 67 (259)
Q Consensus 23 G~~v~~~Vl~id~~~~~v~lS~k~~~~~~~~~~l~~G~iv~G~~~ 67 (259)
|..+++. -+|.++.++.++......+.+...+++|+++.=.+|
T Consensus 18 ~~~~~mi--L~De~G~~I~a~i~~~~~~~f~~~L~eg~vy~is~f 60 (86)
T cd04480 18 GESLEMV--LVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNF 60 (86)
T ss_pred CcEEEEE--EEcCCCCEEEEEECHHHHHhhhhhceeCCEEEEeeE
Confidence 4555444 467777799999998888888899999998864443
No 224
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=25.46 E-value=95 Score=26.13 Aligned_cols=70 Identities=10% Similarity=0.073 Sum_probs=36.1
Q ss_pred eeeeecccCCeeEEEEccccccccccchhhhhhcccCCC--CCcceeeeccCCCee--------------EEEecccchh
Q 024995 173 IFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPP--SGKKFTLLARAGRQV--------------QEIQLSHSLI 236 (259)
Q Consensus 173 ~fv~l~~~~gv~gl~~s~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~r~G~~V--------------~~v~~~~~~i 236 (259)
++--+...|||.||+-+.-+.-.+....++.--+..... ...+....+++||.| ++||.+++++
T Consensus 75 ~w~~Vr~tpgV~GfVg~~~~~P~pi~~~ei~~~l~~~~~~~~~~~~~~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~ 154 (178)
T COG0250 75 AWHLVRNTPGVTGFVGSGGAKPVPLSEEEIEHILGFLEEEVAPKKPKVDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKL 154 (178)
T ss_pred eEEEEecCCCcEEEeccCCCCCcccCHHHHHHHHhhccccccCCcccccCCCCCEEEEeccCCCCccEEEEEEcCcCcEE
Confidence 444466679999998432011111111122111111110 012334467999999 6999998887
Q ss_pred hhhhch
Q 024995 237 RKASKR 242 (259)
Q Consensus 237 ~ls~k~ 242 (259)
++.+-.
T Consensus 155 ~v~v~i 160 (178)
T COG0250 155 KVEVSI 160 (178)
T ss_pred EEEEEE
Confidence 666543
No 225
>PF02721 DUF223: Domain of unknown function DUF223; InterPro: IPR003871 The function of this domain has not been characterised, but may be involved in nucleic acid or nucleotide binding.
Probab=24.65 E-value=2.6e+02 Score=20.47 Aligned_cols=39 Identities=8% Similarity=0.189 Sum_probs=32.2
Q ss_pred EEEeCCCCEEEEEechhhHhhhccCCCCCCEEEEEeeeE
Q 024995 31 IQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGA 69 (259)
Q Consensus 31 l~id~~~~~v~lS~k~~~~~~~~~~l~~G~iv~G~~~G~ 69 (259)
+-+|.++.++.++.+......+...+++|.++.=.+|.+
T Consensus 3 vL~De~G~~I~A~I~~~~~~~f~~~l~Eg~~y~i~~F~V 41 (95)
T PF02721_consen 3 VLVDEKGDKIQATIPKELVDKFKDSLKEGSWYTISNFTV 41 (95)
T ss_pred EEEecCCCEEEEEECHHHHHHHHhhcccCCEEEeEeEEE
Confidence 557888999999999888888888999999986556653
No 226
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=24.53 E-value=2.6e+02 Score=24.52 Aligned_cols=57 Identities=14% Similarity=0.050 Sum_probs=37.5
Q ss_pred CCCCCCEEEEE---eee--EEEEEccCCCCccEEEEEEceecCcc-cccChhhhcCCCCeEEEEEEEEeC
Q 024995 55 RVNVEDIFVGR---DYG--AFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDR 118 (259)
Q Consensus 55 ~l~~G~iv~G~---~~G--~fV~l~~~~g~~gi~glv~isels~~-~~~~~~~~~~~Gd~V~vkVl~id~ 118 (259)
-..+||.|.|. .+| .-|+|++ .-.+.++.-.+... +-..| .+++||.|.++|...++
T Consensus 62 iP~~~D~VIGiV~~~~gd~ykVDigg-----~~~a~L~~laFe~AtkrNrP--nl~vGdliyakv~~a~~ 124 (230)
T KOG1004|consen 62 IPVKGDHVIGIVTSKSGDIYKVDIGG-----SEPASLSYLAFEGATKRNRP--NLQVGDLIYAKVVDANK 124 (230)
T ss_pred cCCCCCEEEEEEEeccCceEEEecCC-----CCeeeeeeccccCccccCCC--ccccccEEEEEEEecCC
Confidence 46789999998 343 5677762 34566665444332 22223 38999999999988764
No 227
>cd05701 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: 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 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=24.13 E-value=1.8e+02 Score=20.48 Aligned_cols=45 Identities=11% Similarity=-0.000 Sum_probs=25.9
Q ss_pred EEEEEccCCCCccEEEEEEce-ecCcccccChhhhcCCCCeEEEEEEEEeC
Q 024995 69 AFIHLRFPDGLYHLTGLVHVS-EVSWDLIQDIRDILNEGDEVRVKVIKIDR 118 (259)
Q Consensus 69 ~fV~l~~~~g~~gi~glv~is-els~~~~~~~~~~~~~Gd~V~vkVl~id~ 118 (259)
+.|.+.. ++--..+|.+ .+-+- ...-++.+++||.+.+++...+.
T Consensus 16 AvvSL~~----t~~L~a~p~~sHLNdt-frf~seklkvG~~l~v~lk~~~~ 61 (69)
T cd05701 16 AIVSLAT----TGDLAAFPTRSHLNDT-FRFDSEKLSVGQCLDVTLKDPNC 61 (69)
T ss_pred EEEEeec----cccEEEEEchhhcccc-ccccceeeeccceEEEEEecCcc
Confidence 4555542 3444444443 33222 23335679999999999876543
No 228
>PRK00568 carbon storage regulator; Provisional
Probab=23.73 E-value=1.3e+02 Score=21.76 Aligned_cols=32 Identities=25% Similarity=0.471 Sum_probs=25.4
Q ss_pred hhhhcCCCCeEEEEEEEEeCCCCeeEEEEecccc
Q 024995 99 IRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE 132 (259)
Q Consensus 99 ~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~ 132 (259)
..+.+.+||.|.++|+++. .+++.+.+.+...
T Consensus 8 ~gEsI~Igd~I~I~Vl~i~--g~~VrlGI~AP~~ 39 (76)
T PRK00568 8 VNEGIVIDDNIHIKVISID--RGSVRLGFEAPES 39 (76)
T ss_pred CCCeEEeCCCeEEEEEEEc--CCEEEEEEECCCC
Confidence 4556788999999999996 6889988866443
No 229
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=22.99 E-value=2.5e+02 Score=22.48 Aligned_cols=42 Identities=19% Similarity=0.114 Sum_probs=26.1
Q ss_pred EEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCe
Q 024995 69 AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSR 122 (259)
Q Consensus 69 ~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~r 122 (259)
+.|+|++ +-..+.|+.. .+++ .+++|++|++++.........
T Consensus 88 aiV~l~~-----~~~i~~~i~~------~~p~-~v~iGm~V~~v~~~~~~~~~~ 129 (140)
T COG1545 88 AIVELEE-----GGRILGQLVD------VDPD-DVEIGMKVEAVFRKREEDGGR 129 (140)
T ss_pred EEEEeCC-----CCceEEEEEe------cCcc-cccCCCEEEEEEEEccccCCc
Confidence 5667752 3356666555 1233 378999999999877654333
No 230
>COG1551 CsrA RNA-binding global regulator CsrA [Signal transduction mechanisms]
Probab=22.61 E-value=1.1e+02 Score=21.95 Aligned_cols=28 Identities=18% Similarity=0.496 Sum_probs=22.5
Q ss_pred hhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995 100 RDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (259)
Q Consensus 100 ~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~ 129 (259)
.+.+.+||.|.++|++++ .+.+.+.+.+
T Consensus 9 ~Esi~IgddI~itVl~i~--gnqVkiGi~A 36 (73)
T COG1551 9 GESIMIGDDIEITVLSIK--GNQVKIGINA 36 (73)
T ss_pred CceEEecCCeEEEEEEEc--CCeEEEeecC
Confidence 456789999999999997 5777777654
No 231
>TIGR01995 PTS-II-ABC-beta PTS system, beta-glucoside-specific IIABC component. This model represents a family of PTS enzyme II proteins in which all three domains are found in the same polypeptide chain and which appear to have a broad specificity for beta-glucosides including salicin (beta-D-glucose-1-salicylate) and arbutin (Hydroquinone-O-beta-D-glucopyranoside). These are distinct from the closely related sucrose-specific and trehalose-specific PTS transporters.
Probab=22.54 E-value=1.5e+02 Score=29.96 Aligned_cols=57 Identities=16% Similarity=0.285 Sum_probs=35.7
Q ss_pred cccceeeeccCCCccceeeeecccCCeeEEEEccccccccccchhhhhhcccCCCCCcceeeeccCCCee------EEEe
Q 024995 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV------QEIQ 230 (259)
Q Consensus 157 v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V------~~v~ 230 (259)
+.|+|..+.|-+ |+|. ++.++|++-|+|--+.. +.-....|+..++.||+| .++|
T Consensus 506 ~~G~v~~~~~t~---Ha~g-i~~~~G~eiliHiGidT---------------v~l~g~gF~~~v~~g~~V~~G~~l~~~d 566 (610)
T TIGR01995 506 VDGTVTAVFPTK---HAIG-IRSDNGIEILIHVGIDT---------------VELNGEGFEILVKVGDHVKAGQLLLTFD 566 (610)
T ss_pred CCeEEEEEcCCC---CEEE-EEECCCcEEEEEeccch---------------hccCCCCeEEEecCcCEEcCCCEEEEec
Confidence 578888888866 5553 55678999998643321 111223466677777776 5666
Q ss_pred cc
Q 024995 231 LS 232 (259)
Q Consensus 231 ~~ 232 (259)
.+
T Consensus 567 ~~ 568 (610)
T TIGR01995 567 LD 568 (610)
T ss_pred HH
Confidence 54
No 232
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=22.07 E-value=1.4e+02 Score=25.46 Aligned_cols=54 Identities=11% Similarity=0.207 Sum_probs=32.0
Q ss_pred CCCCccccceeeeccCCCccceeeeeccc---------CCeeEEEEccccccccccchhhhhhcccCCCCCcceeeeccC
Q 024995 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQE---------DGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARA 222 (259)
Q Consensus 152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~---------~gv~gl~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~ 222 (259)
++|++|-|.|+++..-. +.+++-.- ++.-++++|+.+.. +.. +++..+++
T Consensus 63 K~GdiV~grV~~v~~~~----a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~----------~~~-------~~~d~f~~ 121 (188)
T COG1096 63 KGGDIVYGRVTDVREQR----ALVRIVGVEGKERELATSGAADIHVSQVRDG----------YVE-------KLSDAFRI 121 (188)
T ss_pred CCCCEEEEEEeeccceE----EEEEEEEEecccccCCCCceeeEEEEecccc----------ccc-------cccccccc
Confidence 35777999999987665 55554111 23444556665422 222 23346799
Q ss_pred CCee
Q 024995 223 GRQV 226 (259)
Q Consensus 223 G~~V 226 (259)
||-|
T Consensus 122 GDiv 125 (188)
T COG1096 122 GDIV 125 (188)
T ss_pred ccEE
Confidence 9999
No 233
>PF08845 SymE_toxin: Toxin SymE, type I toxin-antitoxin system; InterPro: IPR014944 This entry represents a SOS-induced gene whose product shows homology to the antitoxin MazE (SymE), the coding region contains a cis-encoded antisense RNA. The small antisense RNA and the gene have the all the hallmarks of a toxin-antitoxin module. The synthesis of the SymE is tightly repressed at multiple levels; at the transcriptional level by the LexA repressor, at the level of mRNA stability and translation by the SymR RNA and at the level of protein stability by the Lon protease. SymE co-purifies with ribosomes and overproduction of the protein leads to cell growth inhibition, decreased protein synthesis and increased RNA degradation. These properties are shared with several RNA endonuclease toxins of toxin-antitoxin modules. It seems probable that the SymE protein represents an evolutionary derivative of a toxin containing the AbrB fold, whose representatives are typically antitoxins. The SymE promoted cleavage of RNA cleavage may be important for the recycling of RNAs damaged under SOS-inducing conditions []. ; GO: 0003723 RNA binding, 0016788 hydrolase activity, acting on ester bonds, 0016070 RNA metabolic process, 0005737 cytoplasm
Probab=20.66 E-value=1.3e+02 Score=20.48 Aligned_cols=19 Identities=26% Similarity=0.508 Sum_probs=15.4
Q ss_pred cCCCCeEEEEEEEEeCCCCeeEEE
Q 024995 103 LNEGDEVRVKVIKIDREKSRITLS 126 (259)
Q Consensus 103 ~~~Gd~V~vkVl~id~~~~ri~lS 126 (259)
|.+|+.|+++| ..++|.++
T Consensus 38 F~~G~~v~V~v-----~~g~lvIt 56 (57)
T PF08845_consen 38 FTIGDPVKVRV-----MPGCLVIT 56 (57)
T ss_pred CCCCCEEEEEE-----ECCEEEEe
Confidence 88999999998 46777664
No 234
>PF06347 SH3_4: Bacterial SH3 domain; InterPro: IPR010466 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This family consists of several hypothetical bacterial proteins of unknown function, but that contain an SH-3 region.
Probab=20.59 E-value=2.3e+02 Score=18.31 Aligned_cols=36 Identities=25% Similarity=0.177 Sum_probs=24.1
Q ss_pred ccCCCCCCEEEEE-eeeEEEEEccCCCCccEEEEEEceecC
Q 024995 53 SSRVNVEDIFVGR-DYGAFIHLRFPDGLYHLTGLVHVSEVS 92 (259)
Q Consensus 53 ~~~l~~G~iv~G~-~~G~fV~l~~~~g~~gi~glv~isels 92 (259)
...++.|..+.-. ..|-|+.+. .+ |..|.|+.+.|+
T Consensus 18 v~~l~~g~~v~v~~~~~~W~~V~-~~---g~~GWv~~~~lw 54 (55)
T PF06347_consen 18 VARLEPGVPVRVIECRGGWCKVR-AD---GRTGWVHKSLLW 54 (55)
T ss_pred EEEECCCCEEEEEEccCCeEEEE-EC---CeEEeEEeeecc
Confidence 4567888888777 444444443 22 789999988874
No 235
>PRK09824 PTS system beta-glucoside-specific transporter subunits IIABC; Provisional
Probab=20.06 E-value=1.6e+02 Score=29.92 Aligned_cols=57 Identities=18% Similarity=0.228 Sum_probs=36.2
Q ss_pred cccceeeeccCCCccceeeeecccCCeeEEEEccccccccccchhhhhhcccCCCCCcceeeeccCCCee------EEEe
Q 024995 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV------QEIQ 230 (259)
Q Consensus 157 v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V------~~v~ 230 (259)
+.|+|..+.|-+ |+|. +..++|++-|+|--+. ++ .-....|+..++.||+| .++|
T Consensus 522 ~~G~v~~vf~T~---HAig-i~t~~G~eiLiHiGiD--------TV-------~L~G~gF~~~v~~Gd~V~~G~~l~~~D 582 (627)
T PRK09824 522 VAGRVASLFATL---HAIG-LESDDGVEVLIHVGID--------TV-------KLDGKFFTAHVNVGDKVNTGDLLIEFD 582 (627)
T ss_pred CCeEEEEEcCCC---cEEE-EEeCCCcEEEEEechh--------hh-------hcCCCCceEEecCCCEEcCCCEEEEEc
Confidence 578888888766 5664 6668899999864432 11 11222366677777777 5666
Q ss_pred cc
Q 024995 231 LS 232 (259)
Q Consensus 231 ~~ 232 (259)
.+
T Consensus 583 ~~ 584 (627)
T PRK09824 583 IP 584 (627)
T ss_pred HH
Confidence 55
Done!