Query 026794
Match_columns 233
No_of_seqs 275 out of 1656
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 12:48:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026794.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026794hhsearch_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 3E-38 6.6E-43 296.4 16.5 188 16-224 143-350 (541)
2 COG0539 RpsA Ribosomal protein 100.0 1.7E-37 3.6E-42 291.4 16.1 198 1-225 224-437 (541)
3 PRK13806 rpsA 30S ribosomal pr 100.0 2.9E-32 6.3E-37 257.7 19.4 197 1-224 235-452 (491)
4 PRK12269 bifunctional cytidyla 100.0 4.5E-32 9.7E-37 268.7 18.8 196 1-223 525-738 (863)
5 PRK07899 rpsA 30S ribosomal pr 100.0 1.2E-31 2.6E-36 252.0 19.3 188 17-225 160-367 (486)
6 PRK12269 bifunctional cytidyla 100.0 2.2E-30 4.7E-35 256.7 18.0 200 2-227 612-831 (863)
7 PRK13806 rpsA 30S ribosomal pr 100.0 1.1E-29 2.4E-34 240.2 17.2 187 18-224 155-366 (491)
8 PRK06299 rpsA 30S ribosomal pr 100.0 3.6E-28 7.8E-33 233.3 18.3 183 20-223 156-359 (565)
9 PRK06676 rpsA 30S ribosomal pr 100.0 7.9E-28 1.7E-32 221.4 19.0 186 19-225 146-351 (390)
10 TIGR00717 rpsA ribosomal prote 100.0 3.4E-27 7.4E-32 224.1 18.9 180 22-221 320-516 (516)
11 PRK06299 rpsA 30S ribosomal pr 99.9 5E-27 1.1E-31 225.4 18.3 184 22-225 334-534 (565)
12 TIGR00717 rpsA ribosomal prote 99.9 8.3E-27 1.8E-31 221.5 19.3 196 1-223 219-432 (516)
13 PRK00087 4-hydroxy-3-methylbut 99.9 3.6E-26 7.9E-31 222.5 18.6 187 17-224 428-635 (647)
14 PRK07400 30S ribosomal protein 99.9 5.3E-25 1.1E-29 197.9 17.4 174 22-224 78-268 (318)
15 PRK07899 rpsA 30S ribosomal pr 99.9 4.1E-25 8.9E-30 207.9 17.4 178 22-224 82-280 (486)
16 PRK06676 rpsA 30S ribosomal pr 99.9 1.7E-23 3.6E-28 192.7 18.1 180 21-224 64-264 (390)
17 PRK07400 30S ribosomal protein 99.9 3.2E-22 7E-27 179.9 13.3 111 20-136 158-273 (318)
18 PRK00087 4-hydroxy-3-methylbut 99.9 2.1E-21 4.5E-26 189.3 17.3 178 22-223 349-548 (647)
19 PTZ00248 eukaryotic translatio 99.8 3.4E-19 7.4E-24 159.0 10.3 101 54-166 12-118 (319)
20 COG1098 VacB Predicted RNA bin 99.8 5.6E-19 1.2E-23 135.9 4.8 75 55-135 2-81 (129)
21 PRK08582 hypothetical protein; 99.6 3E-15 6.5E-20 119.7 9.6 77 55-137 2-83 (139)
22 cd05705 S1_Rrp5_repeat_hs14 S1 99.6 2.2E-15 4.7E-20 107.9 7.6 66 56-126 1-74 (74)
23 PLN00207 polyribonucleotide nu 99.6 1.4E-14 3.1E-19 143.6 10.4 88 49-142 744-837 (891)
24 PF00575 S1: S1 RNA binding do 99.5 2.5E-14 5.3E-19 101.5 8.1 69 55-128 1-74 (74)
25 cd04461 S1_Rrp5_repeat_hs8_sc7 99.5 2.2E-14 4.9E-19 104.4 7.8 71 52-127 8-83 (83)
26 cd05686 S1_pNO40 S1_pNO40: pNO 99.5 4.2E-14 9.1E-19 100.7 9.0 67 56-127 1-72 (73)
27 cd05704 S1_Rrp5_repeat_hs13 S1 99.5 2.5E-14 5.5E-19 101.7 7.7 66 56-128 1-72 (72)
28 cd05703 S1_Rrp5_repeat_hs12_sc 99.5 3.2E-14 6.9E-19 101.6 8.1 65 59-128 1-72 (73)
29 cd04452 S1_IF2_alpha S1_IF2_al 99.5 9.6E-14 2.1E-18 98.9 9.5 71 56-129 1-76 (76)
30 cd05698 S1_Rrp5_repeat_hs6_sc5 99.5 6E-14 1.3E-18 98.5 7.7 65 59-128 1-70 (70)
31 PHA02945 interferon resistance 99.5 1E-13 2.2E-18 101.0 8.9 75 54-133 7-87 (88)
32 cd05706 S1_Rrp5_repeat_sc10 S1 99.5 1.3E-13 2.8E-18 97.7 9.0 68 56-128 1-73 (73)
33 PRK07252 hypothetical protein; 99.5 1.6E-13 3.6E-18 107.0 9.4 75 57-136 2-82 (120)
34 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.5 1.8E-13 3.9E-18 96.1 8.0 64 59-127 1-69 (69)
35 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.5 1.6E-13 3.5E-18 97.3 7.7 57 66-127 15-71 (71)
36 cd05694 S1_Rrp5_repeat_hs2_sc2 99.5 3.5E-13 7.7E-18 96.5 9.4 68 55-132 1-73 (74)
37 cd05691 S1_RPS1_repeat_ec6 S1_ 99.5 4.2E-13 9.2E-18 94.6 8.6 68 59-131 1-73 (73)
38 PRK08059 general stress protei 99.4 5.1E-13 1.1E-17 104.6 9.5 77 53-134 2-83 (123)
39 cd05708 S1_Rrp5_repeat_sc12 S1 99.4 7.4E-13 1.6E-17 94.2 9.3 70 57-130 1-75 (77)
40 cd05684 S1_DHX8_helicase S1_DH 99.4 7.2E-13 1.6E-17 95.5 9.3 72 59-134 1-78 (79)
41 PRK05807 hypothetical protein; 99.4 5.4E-13 1.2E-17 106.3 9.4 70 55-131 2-76 (136)
42 COG1093 SUI2 Translation initi 99.4 1.3E-13 2.9E-18 118.7 6.2 77 55-134 8-89 (269)
43 cd05707 S1_Rrp5_repeat_sc11 S1 99.4 3.6E-13 7.9E-18 94.2 7.0 63 59-126 1-68 (68)
44 cd05690 S1_RPS1_repeat_ec5 S1_ 99.4 5.1E-13 1.1E-17 93.4 7.5 63 59-126 1-69 (69)
45 cd05687 S1_RPS1_repeat_ec1_hs1 99.4 2.2E-12 4.7E-17 90.6 8.1 65 59-128 1-70 (70)
46 cd05692 S1_RPS1_repeat_hs4 S1_ 99.4 2.9E-12 6.3E-17 88.7 8.3 64 59-128 1-69 (69)
47 cd05689 S1_RPS1_repeat_ec4 S1_ 99.4 2.7E-12 5.9E-17 90.6 8.0 66 56-126 1-72 (72)
48 KOG1070 rRNA processing protei 99.4 1.2E-12 2.7E-17 132.1 8.5 124 1-131 538-672 (1710)
49 PRK03987 translation initiatio 99.3 8.4E-12 1.8E-16 109.5 9.9 77 55-134 5-86 (262)
50 TIGR02696 pppGpp_PNP guanosine 99.3 6.3E-12 1.4E-16 122.7 9.5 111 8-126 575-718 (719)
51 KOG1070 rRNA processing protei 99.3 2.3E-11 5E-16 123.1 13.4 185 22-225 1115-1327(1710)
52 cd05693 S1_Rrp5_repeat_hs1_sc1 99.3 5.6E-12 1.2E-16 95.4 6.5 70 56-130 1-97 (100)
53 cd04465 S1_RPS1_repeat_ec2_hs2 99.3 1.5E-11 3.3E-16 85.8 8.0 62 59-128 1-67 (67)
54 cd05688 S1_RPS1_repeat_ec3 S1_ 99.3 1.6E-11 3.5E-16 85.0 8.0 63 58-126 1-68 (68)
55 cd05685 S1_Tex S1_Tex: The C-t 99.3 1E-11 2.3E-16 85.7 7.0 63 59-126 1-68 (68)
56 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.3 1.5E-11 3.2E-16 86.0 7.1 61 59-126 1-66 (66)
57 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.3 2.2E-11 4.8E-16 89.0 7.7 70 55-130 3-81 (86)
58 cd04472 S1_PNPase S1_PNPase: P 99.3 3E-11 6.5E-16 83.7 7.9 63 59-127 1-68 (68)
59 PRK11824 polynucleotide phosph 99.2 4.5E-11 9.9E-16 117.7 10.6 93 31-130 587-692 (693)
60 smart00316 S1 Ribosomal protei 99.2 1.2E-10 2.7E-15 80.4 8.5 67 57-128 1-72 (72)
61 cd04453 S1_RNase_E S1_RNase_E: 99.2 9.8E-11 2.1E-15 86.6 8.2 70 54-128 3-82 (88)
62 cd04471 S1_RNase_R S1_RNase_R: 99.2 2.4E-10 5.2E-15 82.4 9.0 66 58-127 1-82 (83)
63 COG1185 Pnp Polyribonucleotide 99.1 1.4E-10 3E-15 111.6 8.5 94 31-131 585-691 (692)
64 PRK09521 exosome complex RNA-b 99.1 4.3E-10 9.3E-15 94.3 9.7 101 22-129 29-142 (189)
65 cd04454 S1_Rrp4_like S1_Rrp4_l 99.1 5.7E-10 1.2E-14 80.9 8.0 69 56-130 4-77 (82)
66 COG2183 Tex Transcriptional ac 99.1 2.2E-10 4.8E-15 111.7 7.0 75 53-132 653-732 (780)
67 TIGR03591 polynuc_phos polyrib 99.0 7.3E-10 1.6E-14 109.1 9.2 88 31-125 584-684 (684)
68 cd05702 S1_Rrp5_repeat_hs11_sc 99.0 1.1E-09 2.4E-14 77.0 6.7 58 59-121 1-65 (70)
69 cd00164 S1_like S1_like: Ribos 99.0 1.1E-09 2.4E-14 74.1 6.4 56 66-126 10-65 (65)
70 cd04473 S1_RecJ_like S1_RecJ_l 99.0 3.7E-09 8E-14 76.0 8.8 61 53-127 11-76 (77)
71 cd04460 S1_RpoE S1_RpoE: RpoE, 99.0 3E-09 6.6E-14 79.9 8.3 65 66-136 12-92 (99)
72 TIGR00448 rpoE DNA-directed RN 98.9 7.6E-09 1.6E-13 86.0 8.6 129 1-135 13-173 (179)
73 PRK09202 nusA transcription el 98.8 6.1E-09 1.3E-13 98.3 6.0 98 18-129 85-200 (470)
74 PRK08563 DNA-directed RNA poly 98.8 3.7E-08 8E-13 82.3 9.3 128 1-134 13-172 (187)
75 KOG1067 Predicted RNA-binding 98.7 7.8E-09 1.7E-13 97.4 4.1 76 55-136 665-745 (760)
76 PRK04163 exosome complex RNA-b 98.7 3.8E-08 8.2E-13 85.3 8.1 70 54-129 59-137 (235)
77 PTZ00248 eukaryotic translatio 98.7 9.4E-10 2E-14 98.6 -2.5 100 1-112 52-169 (319)
78 cd04455 S1_NusA S1_NusA: N-uti 98.7 1.1E-07 2.3E-12 66.5 7.6 59 57-127 2-67 (67)
79 PHA02858 EIF2a-like PKR inhibi 98.6 1.1E-07 2.3E-12 68.8 6.2 70 53-127 11-85 (86)
80 TIGR02063 RNase_R ribonuclease 98.6 1.8E-07 3.8E-12 92.8 9.5 70 54-127 623-708 (709)
81 COG1098 VacB Predicted RNA bin 98.6 2.5E-08 5.4E-13 77.3 2.1 65 154-225 6-78 (129)
82 COG1095 RPB7 DNA-directed RNA 98.5 3.2E-07 6.9E-12 75.9 7.8 82 49-136 72-176 (183)
83 TIGR01953 NusA transcription t 98.5 2.7E-07 5.9E-12 84.0 8.1 98 18-129 82-198 (341)
84 COG2996 Predicted RNA-bindinin 98.5 1.4E-06 3.1E-11 76.0 11.0 100 22-137 117-225 (287)
85 PRK12327 nusA transcription el 98.5 2.3E-07 4.9E-12 85.0 6.0 98 18-128 85-199 (362)
86 cd05703 S1_Rrp5_repeat_hs12_sc 98.4 2.6E-07 5.5E-12 65.8 4.4 61 155-221 2-72 (73)
87 PRK11642 exoribonuclease R; Pr 98.4 7E-07 1.5E-11 89.6 9.1 71 57-131 642-728 (813)
88 cd05705 S1_Rrp5_repeat_hs14 S1 98.4 2.7E-07 6E-12 65.8 4.2 60 154-219 4-74 (74)
89 TIGR00358 3_prime_RNase VacB a 98.4 9.7E-07 2.1E-11 86.8 9.1 68 56-127 570-653 (654)
90 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.4 1E-06 2.3E-11 65.5 6.9 74 56-130 4-87 (92)
91 COG2996 Predicted RNA-bindinin 98.4 5.5E-06 1.2E-10 72.4 11.9 172 21-224 45-219 (287)
92 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.2 1.6E-06 3.5E-11 61.2 4.4 59 157-220 4-71 (71)
93 KOG2916 Translation initiation 98.2 1.4E-06 3E-11 75.6 3.8 85 55-142 13-102 (304)
94 cd05694 S1_Rrp5_repeat_hs2_sc2 98.1 4.3E-06 9.3E-11 59.7 5.0 64 154-225 5-73 (74)
95 cd05698 S1_Rrp5_repeat_hs6_sc5 98.1 4.7E-06 1E-10 58.1 4.6 60 156-221 3-70 (70)
96 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.1 4.8E-06 1E-10 58.0 4.1 58 156-219 3-68 (69)
97 cd05704 S1_Rrp5_repeat_hs13 S1 98.0 1E-05 2.3E-10 57.2 4.5 61 154-221 4-72 (72)
98 cd05706 S1_Rrp5_repeat_sc10 S1 98.0 1.5E-05 3.2E-10 56.0 5.3 62 154-221 4-73 (73)
99 PF00575 S1: S1 RNA binding do 98.0 1.3E-05 2.8E-10 56.4 4.7 59 157-221 8-74 (74)
100 cd05707 S1_Rrp5_repeat_sc11 S1 97.9 8.4E-06 1.8E-10 56.6 3.4 58 156-219 3-68 (68)
101 cd04461 S1_Rrp5_repeat_hs8_sc7 97.9 1.6E-05 3.5E-10 57.5 4.7 64 143-220 12-83 (83)
102 cd05690 S1_RPS1_repeat_ec5 S1_ 97.9 1.3E-05 2.9E-10 55.4 3.3 57 157-219 4-69 (69)
103 cd04465 S1_RPS1_repeat_ec2_hs2 97.8 2.4E-05 5.2E-10 54.2 4.3 59 156-221 3-67 (67)
104 PRK08582 hypothetical protein; 97.8 3.1E-05 6.7E-10 61.9 5.4 63 156-225 8-78 (139)
105 cd05695 S1_Rrp5_repeat_hs3 S1_ 97.8 2E-05 4.4E-10 54.8 3.6 58 156-219 3-66 (66)
106 PTZ00162 DNA-directed RNA poly 97.7 0.0001 2.2E-09 61.2 7.3 123 1-129 13-165 (176)
107 PRK07252 hypothetical protein; 97.7 4.3E-05 9.4E-10 59.6 4.7 66 154-225 4-77 (120)
108 cd04452 S1_IF2_alpha S1_IF2_al 97.7 7.2E-05 1.6E-09 52.7 4.7 62 155-222 5-76 (76)
109 PRK05054 exoribonuclease II; P 97.7 0.00015 3.2E-09 71.4 8.5 65 59-127 562-643 (644)
110 cd05691 S1_RPS1_repeat_ec6 S1_ 97.7 7E-05 1.5E-09 52.2 4.6 62 156-223 3-72 (73)
111 cd05689 S1_RPS1_repeat_ec4 S1_ 97.7 5.9E-05 1.3E-09 52.8 4.1 57 157-219 7-72 (72)
112 COG1096 Predicted RNA-binding 97.7 0.00041 9E-09 57.7 9.6 75 52-129 58-142 (188)
113 cd05686 S1_pNO40 S1_pNO40: pNO 97.6 8.1E-05 1.8E-09 52.6 4.2 59 154-220 4-72 (73)
114 cd05708 S1_Rrp5_repeat_sc12 S1 97.6 0.00011 2.4E-09 51.7 4.7 64 154-223 3-75 (77)
115 TIGR02696 pppGpp_PNP guanosine 97.6 9.6E-05 2.1E-09 73.0 5.6 59 154-219 648-718 (719)
116 PRK05807 hypothetical protein; 97.6 0.00013 2.7E-09 58.2 5.3 60 157-224 9-76 (136)
117 cd05699 S1_Rrp5_repeat_hs7 S1_ 97.5 0.00029 6.3E-09 50.0 6.1 64 59-128 1-72 (72)
118 cd05692 S1_RPS1_repeat_hs4 S1_ 97.5 0.00018 3.9E-09 49.1 4.3 58 157-221 4-69 (69)
119 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.4 0.00075 1.6E-08 49.7 7.6 58 58-121 1-74 (88)
120 cd05687 S1_RPS1_repeat_ec1_hs1 97.4 0.0002 4.2E-09 49.8 4.2 60 156-221 3-70 (70)
121 PRK08059 general stress protei 97.4 0.00024 5.1E-09 55.5 5.1 68 143-224 5-80 (123)
122 TIGR00757 RNaseEG ribonuclease 97.4 0.00036 7.8E-09 65.3 7.0 59 53-116 20-97 (414)
123 cd05685 S1_Tex S1_Tex: The C-t 97.4 0.00016 3.4E-09 49.3 3.5 57 157-219 4-68 (68)
124 PLN00207 polyribonucleotide nu 97.4 0.00018 3.9E-09 72.5 4.9 60 157-223 757-825 (891)
125 COG1097 RRP4 RNA-binding prote 97.3 0.00079 1.7E-08 58.1 7.5 98 22-130 32-139 (239)
126 cd05693 S1_Rrp5_repeat_hs1_sc1 97.3 0.00026 5.7E-09 53.4 3.8 63 154-222 4-96 (100)
127 cd05684 S1_DHX8_helicase S1_DH 97.2 0.00049 1.1E-08 49.1 4.4 61 156-224 3-75 (79)
128 cd04473 S1_RecJ_like S1_RecJ_l 97.2 0.00083 1.8E-08 47.9 5.2 63 143-220 14-76 (77)
129 TIGR02062 RNase_B exoribonucle 97.2 0.0011 2.4E-08 65.3 7.6 64 59-126 558-638 (639)
130 COG0557 VacB Exoribonuclease R 97.1 0.0011 2.4E-08 66.1 7.3 72 53-128 617-704 (706)
131 PRK09521 exosome complex RNA-b 97.1 0.0022 4.8E-08 53.7 7.3 95 103-222 27-142 (189)
132 PRK03987 translation initiatio 97.0 0.00086 1.9E-08 59.1 4.8 63 157-225 12-84 (262)
133 PRK11824 polynucleotide phosph 97.0 0.00068 1.5E-08 67.4 4.5 63 154-223 622-692 (693)
134 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 97.0 0.0013 2.9E-08 47.5 4.8 62 155-223 8-81 (86)
135 COG2183 Tex Transcriptional ac 97.0 0.00062 1.3E-08 67.3 3.6 67 153-225 658-732 (780)
136 cd04472 S1_PNPase S1_PNPase: P 96.9 0.0012 2.5E-08 45.1 3.8 57 157-220 4-68 (68)
137 cd05790 S1_Rrp40 S1_Rrp40: Rrp 96.9 0.0057 1.2E-07 45.0 7.5 68 55-129 3-75 (86)
138 PF10447 EXOSC1: Exosome compo 96.9 0.0026 5.6E-08 46.4 5.4 36 81-116 45-82 (82)
139 cd04471 S1_RNase_R S1_RNase_R: 96.9 0.0021 4.7E-08 45.7 4.9 60 155-220 3-82 (83)
140 COG1185 Pnp Polyribonucleotide 96.8 0.0017 3.8E-08 63.4 5.1 94 114-223 585-690 (692)
141 COG1107 Archaea-specific RecJ- 96.7 0.0021 4.5E-08 61.8 4.8 68 53-131 117-189 (715)
142 cd04453 S1_RNase_E S1_RNase_E: 96.7 0.0033 7.1E-08 46.2 4.6 59 157-219 11-80 (88)
143 cd05688 S1_RPS1_repeat_ec3 S1_ 96.6 0.002 4.4E-08 43.8 3.3 58 155-219 3-68 (68)
144 smart00316 S1 Ribosomal protei 96.6 0.0039 8.4E-08 42.2 4.6 62 154-221 3-72 (72)
145 cd00164 S1_like S1_like: Ribos 96.6 0.0027 5.9E-08 42.2 3.4 56 158-219 2-65 (65)
146 PRK12328 nusA transcription el 96.5 0.0086 1.9E-07 55.2 7.3 61 56-128 136-205 (374)
147 KOG1856 Transcription elongati 96.3 0.0033 7.1E-08 64.3 3.7 72 54-130 981-1060(1299)
148 PRK09202 nusA transcription el 96.3 0.00086 1.9E-08 63.7 -0.5 122 84-227 73-205 (470)
149 cd05702 S1_Rrp5_repeat_hs11_sc 95.9 0.0081 1.8E-07 41.8 3.2 53 156-214 3-65 (70)
150 cd04454 S1_Rrp4_like S1_Rrp4_l 95.5 0.02 4.3E-07 41.0 3.9 63 154-223 7-77 (82)
151 TIGR03591 polynuc_phos polyrib 95.4 0.01 2.2E-07 59.1 2.7 58 154-218 619-684 (684)
152 PF09876 DUF2103: Predicted me 95.3 0.069 1.5E-06 40.5 6.4 59 173-232 25-83 (103)
153 PF13509 S1_2: S1 domain; PDB: 95.2 0.087 1.9E-06 35.9 6.0 48 66-128 14-61 (61)
154 PRK12329 nusA transcription el 95.1 0.09 2E-06 49.5 7.7 67 56-128 150-224 (449)
155 PRK11712 ribonuclease G; Provi 95.0 0.12 2.5E-06 49.6 8.3 62 51-117 31-111 (489)
156 PRK10811 rne ribonuclease E; R 94.8 0.078 1.7E-06 54.1 7.0 57 56-117 36-108 (1068)
157 TIGR01953 NusA transcription t 94.8 0.0056 1.2E-07 55.9 -0.9 115 98-227 79-203 (341)
158 PHA02945 interferon resistance 94.7 0.048 1E-06 40.1 3.9 62 157-225 15-86 (88)
159 cd04460 S1_RpoE S1_RpoE: RpoE, 94.4 0.043 9.3E-07 40.8 3.2 60 157-223 3-86 (99)
160 KOG1067 Predicted RNA-binding 93.8 0.046 9.9E-07 52.7 2.9 66 153-225 668-741 (760)
161 cd04455 S1_NusA S1_NusA: N-uti 93.7 0.11 2.5E-06 35.7 4.1 59 154-219 4-66 (67)
162 TIGR02063 RNase_R ribonuclease 93.6 0.083 1.8E-06 52.8 4.4 61 154-220 628-708 (709)
163 COG1093 SUI2 Translation initi 92.9 0.076 1.7E-06 46.5 2.5 63 157-225 15-87 (269)
164 PRK11642 exoribonuclease R; Pr 92.5 0.16 3.6E-06 51.5 4.7 61 154-220 644-724 (813)
165 PRK12327 nusA transcription el 89.8 0.15 3.2E-06 47.1 1.2 106 100-221 84-199 (362)
166 TIGR00358 3_prime_RNase VacB a 88.7 0.67 1.5E-05 46.0 5.0 61 154-220 573-653 (654)
167 TIGR00448 rpoE DNA-directed RN 88.6 0.7 1.5E-05 38.2 4.3 59 157-222 85-167 (179)
168 KOG3298 DNA-directed RNA polym 86.9 3.3 7.2E-05 33.9 7.1 63 51-119 74-152 (170)
169 KOG3409 Exosomal 3'-5' exoribo 85.1 4.5 9.8E-05 33.6 7.1 72 55-127 65-146 (193)
170 PRK04163 exosome complex RNA-b 84.8 6.3 0.00014 34.1 8.4 59 157-222 67-137 (235)
171 COG1530 CafA Ribonucleases G a 83.2 1.9 4.1E-05 41.4 4.8 73 50-128 29-113 (487)
172 cd05699 S1_Rrp5_repeat_hs7 S1_ 81.9 1.4 3.1E-05 31.2 2.6 42 2-45 30-72 (72)
173 PRK08563 DNA-directed RNA poly 80.6 2.8 6.2E-05 34.7 4.5 59 157-222 85-167 (187)
174 PF08292 RNA_pol_Rbc25: RNA po 79.8 9.3 0.0002 29.8 6.8 56 58-118 3-76 (122)
175 COG4044 Uncharacterized protei 79.2 1.6 3.4E-05 37.3 2.4 73 54-127 71-156 (247)
176 PF13509 S1_2: S1 domain; PDB: 70.5 11 0.00023 25.5 4.4 55 157-219 5-59 (61)
177 PRK05054 exoribonuclease II; P 68.0 6.7 0.00015 39.0 4.2 58 157-219 565-642 (644)
178 PRK12442 translation initiatio 64.3 39 0.00085 24.8 6.5 55 66-129 18-73 (87)
179 PF02599 CsrA: Global regulato 64.2 16 0.00035 24.3 4.2 39 186-226 2-40 (54)
180 TIGR00008 infA translation ini 60.7 31 0.00067 24.1 5.3 51 66-125 16-67 (68)
181 PF00313 CSD: 'Cold-shock' DNA 60.4 49 0.0011 22.1 7.7 31 81-115 23-53 (66)
182 PF10246 MRP-S35: Mitochondria 58.6 37 0.00081 25.7 5.7 49 57-117 22-75 (104)
183 COG1107 Archaea-specific RecJ- 57.1 7.5 0.00016 38.2 2.2 59 157-221 126-186 (715)
184 cd05700 S1_Rrp5_repeat_hs9 S1_ 54.3 17 0.00037 24.9 2.9 28 100-127 38-65 (65)
185 KOG1856 Transcription elongati 53.2 6.4 0.00014 41.3 1.1 66 154-222 986-1059(1299)
186 PRK01712 carbon storage regula 52.6 27 0.00058 24.2 3.8 39 186-226 2-40 (64)
187 PHA02858 EIF2a-like PKR inhibi 52.5 27 0.00058 25.6 3.9 26 19-44 60-85 (86)
188 KOG2916 Translation initiation 50.8 7.8 0.00017 34.3 1.1 62 157-222 20-89 (304)
189 PRK09937 stationary phase/star 49.2 82 0.0018 22.2 6.0 54 66-130 14-67 (74)
190 COG1097 RRP4 RNA-binding prote 47.4 52 0.0011 28.7 5.6 37 22-63 115-151 (239)
191 PRK09507 cspE cold shock prote 46.8 59 0.0013 22.4 4.9 43 66-117 16-58 (69)
192 PRK12328 nusA transcription el 45.8 28 0.00061 32.3 4.0 45 21-65 178-225 (374)
193 PRK00568 carbon storage regula 45.7 34 0.00074 24.5 3.5 38 186-225 2-39 (76)
194 PRK15464 cold shock-like prote 44.7 57 0.0012 22.8 4.6 39 70-116 20-58 (70)
195 PRK15463 cold shock-like prote 43.4 49 0.0011 23.0 4.1 39 70-116 20-58 (70)
196 PRK10943 cold shock-like prote 42.5 73 0.0016 22.0 4.8 42 66-116 16-57 (69)
197 TIGR02062 RNase_B exoribonucle 41.8 33 0.00071 34.2 4.0 57 157-218 561-637 (639)
198 COG1551 CsrA RNA-binding globa 41.4 41 0.00088 23.8 3.3 37 186-224 2-38 (73)
199 COG0250 NusG Transcription ant 40.9 80 0.0017 26.2 5.7 29 101-129 122-160 (178)
200 COG1278 CspC Cold shock protei 40.8 44 0.00094 23.4 3.4 32 81-116 24-55 (67)
201 PF03152 UFD1: Ubiquitin fusio 39.8 33 0.00071 28.5 3.2 99 20-133 54-159 (176)
202 PRK01712 carbon storage regula 39.4 51 0.0011 22.8 3.5 34 99-134 8-41 (64)
203 PRK14998 cold shock-like prote 39.3 1.3E+02 0.0028 21.1 5.7 43 66-117 14-56 (73)
204 COG1545 Predicted nucleic-acid 38.9 85 0.0019 24.9 5.3 43 69-123 88-130 (140)
205 PF01835 A2M_N: MG2 domain; I 38.9 41 0.00088 24.3 3.3 21 99-119 7-27 (99)
206 TIGR00202 csrA carbon storage 38.8 56 0.0012 22.9 3.7 38 186-225 2-39 (69)
207 COG0361 InfA Translation initi 38.4 1.5E+02 0.0032 21.2 6.0 52 68-128 21-72 (75)
208 PRK12442 translation initiatio 37.4 50 0.0011 24.3 3.4 60 157-221 9-72 (87)
209 PRK09890 cold shock protein Cs 36.1 1.1E+02 0.0024 21.1 5.0 42 66-116 17-58 (70)
210 KOG3297 DNA-directed RNA polym 35.3 1.1E+02 0.0024 25.7 5.6 63 51-118 74-158 (202)
211 TIGR00757 RNaseEG ribonuclease 34.9 72 0.0016 30.0 5.0 50 157-210 29-98 (414)
212 KOG3754 Gamma-glutamylcysteine 33.5 44 0.00096 32.0 3.2 27 22-48 47-73 (640)
213 TIGR02381 cspD cold shock doma 32.4 87 0.0019 21.5 3.9 43 66-117 14-56 (68)
214 PRK00568 carbon storage regula 32.1 69 0.0015 22.9 3.3 34 99-134 8-41 (76)
215 PRK10354 RNA chaperone/anti-te 31.0 1.1E+02 0.0024 21.0 4.3 42 66-116 17-58 (70)
216 PF06347 SH3_4: Bacterial SH3 29.3 1.3E+02 0.0027 19.3 4.2 38 51-92 16-54 (55)
217 cd04458 CSP_CDS Cold-Shock Pro 29.1 1.7E+02 0.0038 19.3 5.4 32 81-116 23-54 (65)
218 cd04474 RPA1_DBD_A RPA1_DBD_A: 26.3 2.4E+02 0.0052 20.7 5.7 34 32-65 41-74 (104)
219 COG4031 Predicted metal-bindin 25.7 2.3E+02 0.005 24.0 5.8 54 178-232 150-203 (227)
220 cd05701 S1_Rrp5_repeat_hs10 S1 25.1 2E+02 0.0043 20.1 4.5 45 69-118 16-61 (69)
221 cd04480 RPA1_DBD_A_like RPA1_D 24.9 2E+02 0.0043 20.2 4.8 37 31-67 24-60 (86)
222 cd05793 S1_IF1A S1_IF1A: Trans 24.6 1.9E+02 0.0041 20.5 4.6 42 81-127 22-63 (77)
223 PF07405 DUF1506: Protein of u 23.4 77 0.0017 24.6 2.5 59 67-130 54-123 (127)
224 PF02721 DUF223: Domain of unk 23.3 2.8E+02 0.0062 19.9 5.5 39 31-69 3-41 (95)
225 COG0557 VacB Exoribonuclease R 23.2 93 0.002 31.3 3.7 60 156-221 625-704 (706)
226 PF11604 CusF_Ec: Copper bindi 22.3 1.9E+02 0.0041 19.9 4.2 38 28-65 1-52 (70)
227 PRK12329 nusA transcription el 21.3 1.4E+02 0.003 28.6 4.2 28 21-48 197-227 (449)
228 COG0195 NusA Transcription elo 21.1 1.7E+02 0.0038 24.5 4.4 41 82-128 2-43 (190)
No 1
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3e-38 Score=296.40 Aligned_cols=188 Identities=26% Similarity=0.488 Sum_probs=171.6
Q ss_pred hhcccCCCCEEEEEEEEEeCCCCEEEEEechhh-------HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEE
Q 026794 16 EIAKGLTGSIISVKVIQANEEMKKLVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLT 83 (233)
Q Consensus 16 ~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~~-------~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~ 83 (233)
++...++|+++.|+|+++|.+++++++|+|... .+.+++.+++|+++.|+ +|||||+|+ |++
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 556678999999999999999999999999763 45678999999999999 999999997 799
Q ss_pred EEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeee
Q 026794 84 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNT 163 (233)
Q Consensus 84 Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~ 163 (233)
||+|+|+|||.++.+|+++|++||.|+|+|+++|.+++|++||+|++.+|||+ ..++.+++|+. +.|+|++
T Consensus 217 GLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~-~i~~~~~~g~~--------v~G~Vt~ 287 (541)
T COG0539 217 GLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWE-GIEKKYPVGDK--------VEGKVTN 287 (541)
T ss_pred eEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHH-HHhhhcCCCCE--------EEEEEEE
Confidence 99999999999999999999999999999999999999999999999999996 45566898988 6799999
Q ss_pred eccCCChhhhhhhhcccCCeeEE----Eeeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794 164 IEPLPGLGAIFEELLQEDGIDDV----RITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR 224 (233)
Q Consensus 164 v~~~~g~~~~~~~l~~~~gv~gl----~~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~ 224 (233)
++| ||+|+++.+||+|| +++|.+...| .+||+++|+|.++|++++||+|++|+..
T Consensus 288 i~~------~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~ 350 (541)
T COG0539 288 LTD------YGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLK 350 (541)
T ss_pred eec------CcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhh
Confidence 885 58999999999999 3899887766 6899999999999999999999999754
No 2
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-37 Score=291.42 Aligned_cols=198 Identities=28% Similarity=0.424 Sum_probs=182.4
Q ss_pred CCCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEE
Q 026794 1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIH 72 (233)
Q Consensus 1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~vv~g~-----~~G~fV~ 72 (233)
|||.|+ .||+..+. +||+|+++|+++|++++|++||+|++ +|+.+..++++|+.+.|+ +|||||+
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 789996 79999987 99999999999999999999999987 699999999999999999 9999999
Q ss_pred EccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeec
Q 026794 73 LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISD 152 (233)
Q Consensus 73 l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~ 152 (233)
+. +|++||+|+||+||.+...|++++++||.|.|+|+++|++++||+||+|++..|||..+.+. ++.|++
T Consensus 297 i~-----~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~-~~~g~~---- 366 (541)
T COG0539 297 IE-----EGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADK-HPVGDV---- 366 (541)
T ss_pred ec-----CCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhh-cCCCCe----
Confidence 98 59999999999999999889999999999999999999999999999999999999876665 898888
Q ss_pred CCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR 224 (233)
Q Consensus 153 ~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~ 224 (233)
++|.+.+++ ++++|+++++|++|+. ++|.....+ ..|+++++++..+|.++.||+|++|+..
T Consensus 367 ----v~g~v~~~t------~~g~fv~le~gidG~vh~~d~sw~~~~~~~~~~k~Gd~v~~~vl~vd~~~~~isLgiKql~ 436 (541)
T COG0539 367 ----VEGKVKSIT------DFGAFVELEGGIDGLVHLSDLSWDRPGEEAEKYKKGDEVEAKVLAVDKEKERISLGIKQLE 436 (541)
T ss_pred ----EEEEEeeec------ccceEEccCCCccceEEHHhcCccccCcHHHhhccCcEEEEEEEEEecccceeeeehhhhc
Confidence 789999888 5588899999999995 888765545 4699999999999999999999999876
Q ss_pred e
Q 026794 225 C 225 (233)
Q Consensus 225 ~ 225 (233)
.
T Consensus 437 ~ 437 (541)
T COG0539 437 E 437 (541)
T ss_pred c
Confidence 3
No 3
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=2.9e-32 Score=257.68 Aligned_cols=197 Identities=25% Similarity=0.417 Sum_probs=170.5
Q ss_pred CCCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCC----CEEEEEechh---hHhhhccCCCCCCEEEEE-----eee
Q 026794 1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM----KKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYG 68 (233)
Q Consensus 1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~----~~i~lS~k~~---~~~~~~~~~~~G~vv~g~-----~~G 68 (233)
|||+|. .+|...+. +||.|.|+|+++|.++ +++.||+|++ +|+.+...+++|+++.|+ +||
T Consensus 235 ls~~~~-~~~~~~~~------vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~G 307 (491)
T PRK13806 235 LSWSRV-QKADEAVS------VGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFG 307 (491)
T ss_pred CCCccc-cChhHhcC------CCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEEEEEeCce
Confidence 355554 35555444 9999999999999876 4799999987 598999999999999999 999
Q ss_pred EEEEEccCCCCccEEEEEEccccCc-ccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCC
Q 026794 69 AFIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDG 147 (233)
Q Consensus 69 ~fV~l~~~~~~~gv~Glv~~sels~-~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~ 147 (233)
+||++. +|++||+|+|+++| .++.++.+.|++||.|+|+|+++|+++++|.||+|++.++||....+ .+++|+
T Consensus 308 ~fV~l~-----~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~-~~~vG~ 381 (491)
T PRK13806 308 AFVEIL-----PGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAE-RFAPGT 381 (491)
T ss_pred EEEEeC-----CCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhh-hCCCCC
Confidence 999997 48999999999999 57889999999999999999999999999999999999999976655 467788
Q ss_pred eeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794 148 SVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLL 219 (233)
Q Consensus 148 ~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls 219 (233)
+ ++|+|+++++ +|+|+++++|++||+ +++.+.+++ .+||+++++|.++|++++|++||
T Consensus 382 ~--------v~G~V~~i~~------~G~FV~l~~gv~Gli~~se~s~~~~~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls 447 (491)
T PRK13806 382 T--------VTGTVEKRAQ------FGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLA 447 (491)
T ss_pred E--------EEEEEEEEec------CceEEEcCCCcEEEEEHHHcCcccccchhhcCCCCCEEEEEEEEEeCCCCEEEEE
Confidence 7 6799999985 478888899999995 666655433 68999999999999999999999
Q ss_pred Ecccc
Q 026794 220 ARAGR 224 (233)
Q Consensus 220 ~r~~~ 224 (233)
.|+..
T Consensus 448 ~~~~~ 452 (491)
T PRK13806 448 PAGAA 452 (491)
T ss_pred eehhh
Confidence 99653
No 4
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=4.5e-32 Score=268.68 Aligned_cols=196 Identities=26% Similarity=0.437 Sum_probs=170.4
Q ss_pred CCCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEE
Q 026794 1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIH 72 (233)
Q Consensus 1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~vv~g~-----~~G~fV~ 72 (233)
|||+|. .+|...+. +||++.|+|+++|++++++.||+|+. +|+.+.+.+++|++++|+ +||+||+
T Consensus 525 iS~~~v-~~~~~~~k------vGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVe 597 (863)
T PRK12269 525 MSWGHV-ARPREFVK------KGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIE 597 (863)
T ss_pred cccccc-CCHHHhcc------CCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEEEEEEEEeCCeEEEE
Confidence 456664 45655443 89999999999999999999999976 588888999999999999 9999999
Q ss_pred EccCCCCccEEEEEEccccCc-ccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeee
Q 026794 73 LRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVIS 151 (233)
Q Consensus 73 l~~~~~~~gv~Glv~~sels~-~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~ 151 (233)
|. +|++||+|+||++| .++.+|.+.|++||+|+|+|+++|.+++|++||+|++.+|||....+ .++.|++
T Consensus 598 L~-----~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~-~~~vG~~--- 668 (863)
T PRK12269 598 LA-----EGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEA-RYPVGAR--- 668 (863)
T ss_pred ec-----CCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHH-hCCCCCE---
Confidence 97 48999999999999 57899999999999999999999999999999999999999976544 5788888
Q ss_pred cCCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc-----cccCceEEEEeecCCCCCEEEEEEcc
Q 026794 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR-----VVSQDLQLWLSNAPPSGKKFTLLARA 222 (233)
Q Consensus 152 ~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~-----~vg~~~~v~i~~~d~~~~ki~Ls~r~ 222 (233)
++|+|++++++ |+|+++++||+|+. ++|.+...+ .+||.++++|.++|++++|++||.|+
T Consensus 669 -----v~G~V~~i~~~------G~fV~l~~gV~GlIh~sels~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~ 737 (863)
T PRK12269 669 -----FTRRIVKVTNA------GAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVKQ 737 (863)
T ss_pred -----EEEEEEEEecc------eEEEEeCCCcEEEEEhHHhhccccccchhhccCCCCEEEEEEEEEeccCCEEEEEecc
Confidence 67999999854 78888899999995 566443222 58999999999999999999999986
Q ss_pred c
Q 026794 223 G 223 (233)
Q Consensus 223 ~ 223 (233)
.
T Consensus 738 l 738 (863)
T PRK12269 738 L 738 (863)
T ss_pred c
Confidence 5
No 5
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.98 E-value=1.2e-31 Score=252.05 Aligned_cols=188 Identities=22% Similarity=0.396 Sum_probs=165.8
Q ss_pred hcccCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEE
Q 026794 17 IAKGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTG 84 (233)
Q Consensus 17 ~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~-------~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~G 84 (233)
+++.++|++|.|+|+++|++++++.||+|.. .|+.+...+++|++++|+ +||+||+|+ |++|
T Consensus 160 ~~~~~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlg------gv~G 233 (486)
T PRK07899 160 DLQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLG------GVDG 233 (486)
T ss_pred ChhhcCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEE
Confidence 3445799999999999999999999999853 377788899999999999 999999996 7999
Q ss_pred EEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeeee
Q 026794 85 LVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTI 164 (233)
Q Consensus 85 lv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v 164 (233)
|||+|+++|.++.++.+.|++||.|+|+|+++|++++||.||+|++.++||..+.++ ++.|++ ++|+|+++
T Consensus 234 lv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~-~~vG~v--------v~G~V~~I 304 (486)
T PRK07899 234 LVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFART-HAIGQI--------VPGKVTKL 304 (486)
T ss_pred EEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHh-cCCCCE--------EEEEEEEE
Confidence 999999999999999999999999999999999999999999999999999766554 567777 67999998
Q ss_pred ccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794 165 EPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC 225 (233)
Q Consensus 165 ~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~ 225 (233)
.+ +|+|+++.+|++||. ++++++..+ .+||.++|+|.++|.+++|++||.|+...
T Consensus 305 ~~------fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~~~~ 367 (486)
T PRK07899 305 VP------FGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQANE 367 (486)
T ss_pred ec------cEEEEEeCCCcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCCEEEEEEEEccc
Confidence 85 477888899999995 666665444 58999999999999999999999986543
No 6
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=99.97 E-value=2.2e-30 Score=256.74 Aligned_cols=200 Identities=18% Similarity=0.296 Sum_probs=170.5
Q ss_pred CCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEEE
Q 026794 2 SPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHL 73 (233)
Q Consensus 2 ~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~vv~g~-----~~G~fV~l 73 (233)
||.+-..+|...+. +||+|+|+|+++|.+++++.||+|++ +|+.+.+++++|++++|+ +||+||++
T Consensus 612 s~~~~~~~p~~~~k------vGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l 685 (863)
T PRK12269 612 SWVKKTSKPSDMVK------IGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEM 685 (863)
T ss_pred cCccccCCHHHcCC------CCCEEEEEEEEEecccCceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEecceEEEEe
Confidence 45322356666655 99999999999999999999999976 599999999999999999 99999999
Q ss_pred ccCCCCccEEEEEEccccCcccc-cCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeec
Q 026794 74 RFPDGLYHLTGLVHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISD 152 (233)
Q Consensus 74 ~~~~~~~gv~Glv~~sels~~~~-~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~ 152 (233)
. +|++||||+|+++|.+. .++.+.|++||.|+|+|+++|++++||.||+|++..|||..+. +.++.|+.
T Consensus 686 ~-----~gV~GlIh~sels~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~l~~dpw~~~~-~~~~vG~i---- 755 (863)
T PRK12269 686 E-----EGIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVFA-NAYGVGST---- 755 (863)
T ss_pred C-----CCcEEEEEhHHhhccccccchhhccCCCCEEEEEEEEEeccCCEEEEEecccccChHHHHH-hhCCCCCE----
Confidence 8 48999999999999765 4556689999999999999999999999999999999997654 44778888
Q ss_pred CCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc-------cccCceEEEEeecCCCCCEEEEEEc
Q 026794 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR-------VVSQDLQLWLSNAPPSGKKFTLLAR 221 (233)
Q Consensus 153 ~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~-------~vg~~~~v~i~~~d~~~~ki~Ls~r 221 (233)
++|+|+++++ +|+|+++++||+|+. +++++...+ .+||.++++|.++|++++||+||.|
T Consensus 756 ----V~GkV~~v~~------~GvFVeL~~gVeGlI~~s~lsdd~~~~~~~~~~~f~vGD~V~v~Vl~iD~~~rkI~LSlk 825 (863)
T PRK12269 756 ----VEGEVSSVTD------FGIFVRVPGGVEGLVRKQHLVENRDGDPGEALRKYAVGDRVKAVIVDMNVKDRKVAFSVR 825 (863)
T ss_pred ----EEEEEEEEec------CeEEEEcCCCeEEEEEHHHcCCcccccchhhccccCCCCEEEEEEEEEEcCCCEEEEEEe
Confidence 6799999885 477888899999995 666654322 5899999999999999999999999
Q ss_pred ccceee
Q 026794 222 AGRCKR 227 (233)
Q Consensus 222 ~~~~vq 227 (233)
+.++.+
T Consensus 826 ~~~~~~ 831 (863)
T PRK12269 826 DYQRKV 831 (863)
T ss_pred chhhHH
Confidence 776543
No 7
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=99.97 E-value=1.1e-29 Score=240.18 Aligned_cols=187 Identities=24% Similarity=0.415 Sum_probs=162.6
Q ss_pred cccCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEE
Q 026794 18 AKGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL 85 (233)
Q Consensus 18 ~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~-------~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Gl 85 (233)
++.++|+++.|+|+++|++++++.+|+++. .|+.+...+++|++++|+ +||+||+|+ .|++||
T Consensus 155 ~~~~vG~~i~~~V~~id~~~~~v~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~-----~gv~g~ 229 (491)
T PRK13806 155 PESYVGQTFQFLITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELA-----PGVEGM 229 (491)
T ss_pred hHHcCCCeEEEEEEEEECCCCeEEEEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcC-----CCcEEE
Confidence 345699999999999999999999999975 366777889999999998 999999997 389999
Q ss_pred EEccccCcccccCcccccCCCCEEEEEEEEEeCCC----CeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCe
Q 026794 86 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK----SRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNS 161 (233)
Q Consensus 86 v~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~----~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v 161 (233)
||+|+++|.++.++.+.|++||.|+|+|+++|.++ +|++||+|++.++||....+ .++.|++ +.|+|
T Consensus 230 v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~-~~~~G~~--------v~G~V 300 (491)
T PRK13806 230 VHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGD-RLKAGDK--------VTGKV 300 (491)
T ss_pred EEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhc-cCCCCCE--------EEEEE
Confidence 99999999999999999999999999999999876 48999999999999975544 4677887 67999
Q ss_pred eeeccCCChhhhhhhhcccCCeeEEE----eec-cccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794 162 NTIEPLPGLGAIFEELLQEDGIDDVR----ITR-QGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR 224 (233)
Q Consensus 162 ~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~-~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~ 224 (233)
+.+.+ +|+|+++.+|++|+. ++| .++.++ .+||.++++|.++|++++|+.||.|+..
T Consensus 301 ~~v~~------~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~ 366 (491)
T PRK13806 301 VRLAP------FGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAE 366 (491)
T ss_pred EEEeC------ceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecc
Confidence 99885 478888899999995 566 334333 6899999999999999999999998653
No 8
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.96 E-value=3.6e-28 Score=233.31 Aligned_cols=183 Identities=26% Similarity=0.454 Sum_probs=161.3
Q ss_pred cCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEE
Q 026794 20 GLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVH 87 (233)
Q Consensus 20 ~~vG~~v~~~Vi~id~~~~~i~lS~k~~-------~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~ 87 (233)
.++|+++.|+|+++|++++++.+|+|++ .|+.++..+++|++++|+ +||+||+++ |++||+|
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 5699999999999999999999999975 266778899999999999 999999996 7999999
Q ss_pred ccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeeeeccC
Q 026794 88 VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPL 167 (233)
Q Consensus 88 ~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~ 167 (233)
+++++|.++.++.+.|++||.|+|+|+++|.+++++.||+|++.++||....+ .++.|++ ++|+|+++.+
T Consensus 230 ~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~-~~~~G~~--------v~g~V~~i~~- 299 (565)
T PRK06299 230 ITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEK-KYPVGSK--------VKGKVTNITD- 299 (565)
T ss_pred HHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHh-hCCCCCE--------EEEEEEEEeC-
Confidence 99999999999999999999999999999999999999999999999976544 4777887 6799999875
Q ss_pred CChhhhhhhhcccCCeeEEE----eeccc-cccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794 168 PGLGAIFEELLQEDGIDDVR----ITRQG-FEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG 223 (233)
Q Consensus 168 ~g~~~~~~~l~~~~gv~gl~----~~~~~-~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~ 223 (233)
+|+|+++.+|+.|+. ++|.. ..+| .+||+++|+|.++|++++++.||.|+.
T Consensus 300 -----~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V~~id~~~~~i~ls~k~~ 359 (565)
T PRK06299 300 -----YGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQC 359 (565)
T ss_pred -----CeEEEEeCCCCEEEEEHHHcCccccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEehHHh
Confidence 477888899999995 45432 3333 589999999999999999999999865
No 9
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.96 E-value=7.9e-28 Score=221.44 Aligned_cols=186 Identities=23% Similarity=0.385 Sum_probs=162.0
Q ss_pred ccCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEE
Q 026794 19 KGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLV 86 (233)
Q Consensus 19 ~~~vG~~v~~~Vi~id~~~~~i~lS~k~~-------~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv 86 (233)
+.++|+.+.|+|+++|++++++.+|+|.. .|..++..+++|++++|+ ++|+||+++ +++|||
T Consensus 146 ~~~vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~------~v~g~v 219 (390)
T PRK06676 146 SDFKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIG------GVDGLV 219 (390)
T ss_pred HHcCCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeC------CeEEEE
Confidence 34699999999999999999999999974 356677889999999998 999999996 799999
Q ss_pred EccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeeeecc
Q 026794 87 HVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEP 166 (233)
Q Consensus 87 ~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~ 166 (233)
|+|+++|.++.++.+.|++||.|+|+|+++|+++++|.||+|++.++||....+ .++.|++ +.|.|+.+.+
T Consensus 220 ~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~-~~~~G~~--------v~g~V~~i~~ 290 (390)
T PRK06676 220 HISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEE-KLPEGDV--------IEGTVKRLTD 290 (390)
T ss_pred EHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchh-hhcCCcE--------EEEEEEEEeC
Confidence 999999999999999999999999999999999999999999999999976555 4667777 6799998875
Q ss_pred CCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794 167 LPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC 225 (233)
Q Consensus 167 ~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~ 225 (233)
+|+|+++.+|++|+. +++.+..++ .+||.++++|.++|+++++++||+|+...
T Consensus 291 ------~G~fV~l~~gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~~~ 351 (390)
T PRK06676 291 ------FGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEE 351 (390)
T ss_pred ------ceEEEEECCCCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEECCCCEEEEEEEeccc
Confidence 477788899999994 555554433 58999999999999999999999986543
No 10
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=99.95 E-value=3.4e-27 Score=224.15 Aligned_cols=180 Identities=23% Similarity=0.465 Sum_probs=158.2
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCc
Q 026794 22 TGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW 93 (233)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~ 93 (233)
+||.+.|+|+++|++++++.||++++ +|+.+.+.+++|+++.|+ ++|+||+++ .+++||+|+++++|
T Consensus 320 vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~-----~~v~glv~~s~ls~ 394 (516)
T TIGR00717 320 KGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELE-----GGIDGLIHLSDISW 394 (516)
T ss_pred CCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEecceEEEECC-----CCCEEEEEHHHCcC
Confidence 99999999999999999999999875 588888889999999999 999999997 48999999999999
Q ss_pred ccc-cCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeeeeccCCChhh
Q 026794 94 DLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGA 172 (233)
Q Consensus 94 ~~~-~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~ 172 (233)
.+. .++...|++||.|.|+|+++|.++++|.||+|++.+|||....+ .++.|++ ++|.|..+++
T Consensus 395 ~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p~~~~~~-~~~~G~~--------v~g~V~~v~~------ 459 (516)
T TIGR00717 395 DKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAA-KYKVGSV--------VKGKVTEIKD------ 459 (516)
T ss_pred cccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCCchhhhhh-ccCcceE--------EEEEEEEEec------
Confidence 764 56778899999999999999999999999999999999975544 3567777 6799999885
Q ss_pred hhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEc
Q 026794 173 IFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLAR 221 (233)
Q Consensus 173 ~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r 221 (233)
+|+|+++.+|++|+. +++++.+++ .+||.++++|.++|.+++|++||.|
T Consensus 460 ~G~fV~l~~~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~id~~~~~i~ls~k 516 (516)
T TIGR00717 460 FGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516 (516)
T ss_pred ceEEEEcCCCeEEEEEHHHcCccccccccccCCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 477888899999995 566554333 6899999999999999999999986
No 11
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.95 E-value=5e-27 Score=225.42 Aligned_cols=184 Identities=29% Similarity=0.517 Sum_probs=161.6
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCc
Q 026794 22 TGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW 93 (233)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~ 93 (233)
+|+.|.|+|+++|++++++.||+|+. +|..+...+++|+++.|+ ++|+||+|+ .+++||+|+++++|
T Consensus 334 ~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~-----~~v~g~i~~s~l~~ 408 (565)
T PRK06299 334 VGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGAFVGLE-----GGIDGLVHLSDISW 408 (565)
T ss_pred CCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHhCCCCCEEEEEEEEEecceEEEECC-----CCCEEEEEHHHcCc
Confidence 89999999999999999999999976 588888889999999999 999999997 38999999999999
Q ss_pred ccc-cCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeeeeccCCChhh
Q 026794 94 DLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGA 172 (233)
Q Consensus 94 ~~~-~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~ 172 (233)
.+. .++.+.|++||.|+|+|+++|.++++|.||+|++..+||....+. ++.|++ +.|+|.++.+
T Consensus 409 ~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~~-~~~G~v--------V~G~V~~v~~------ 473 (565)
T PRK06299 409 DKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKK-HKKGSI--------VTGTVTEVKD------ 473 (565)
T ss_pred cccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehhhcCchhHHHhh-cCCCCE--------EEEEEEEEec------
Confidence 887 889999999999999999999999999999999999999766554 577887 6799999885
Q ss_pred hhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794 173 IFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC 225 (233)
Q Consensus 173 ~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~ 225 (233)
+|+|+.+.+|+.|++ ++..++.++ .+||.+++++.++|.+++|++||.+....
T Consensus 474 ~G~fV~l~~gi~g~i~~se~s~~~~~~~~~~~~~Gd~v~~~V~~vd~~~~~i~LS~k~~~~ 534 (565)
T PRK06299 474 KGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDE 534 (565)
T ss_pred CceEEecCCCcEEEEEHHHhcchhccCccccCCCCCEEEEEEEEEccccCEEEEEeeehhh
Confidence 477788889999995 444444332 68999999999999999999999986544
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=99.95 E-value=8.3e-27 Score=221.53 Aligned_cols=196 Identities=28% Similarity=0.425 Sum_probs=166.2
Q ss_pred CCCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEE
Q 026794 1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIH 72 (233)
Q Consensus 1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~vv~g~-----~~G~fV~ 72 (233)
|+|++. .+|+..+. +|+.+.|+|+.+|++++++.+|+|.. +|+.+...+++|+++.|+ ++|+||+
T Consensus 219 ~s~~~~-~~~~~~~~------vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~ 291 (516)
T TIGR00717 219 MSWKRV-KHPSEYVK------VGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVE 291 (516)
T ss_pred cCCCCC-CCHHHhcc------CCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHHhhccCCCEEEEEEEEeeCCcEEEE
Confidence 355553 45554444 89999999999999999999999975 588888889999999998 9999999
Q ss_pred EccCCCCccEEEEEEccccCcc-cccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeee
Q 026794 73 LRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVIS 151 (233)
Q Consensus 73 l~~~~~~~gv~Glv~~sels~~-~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~ 151 (233)
++ ++++||+|+|+++|. ...++.+.|++||.|+|+|+++|++++++.||+|++..+||....+. ++.|+.
T Consensus 292 l~-----~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~-~~~G~~--- 362 (516)
T TIGR00717 292 IE-----EGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEK-HPVGDR--- 362 (516)
T ss_pred eC-----CCCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHh-CCCCCE---
Confidence 97 489999999999986 46778888999999999999999999999999999999999766554 677777
Q ss_pred cCCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccc-cc----cccCceEEEEeecCCCCCEEEEEEcc
Q 026794 152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFE-KR----VVSQDLQLWLSNAPPSGKKFTLLARA 222 (233)
Q Consensus 152 ~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~-~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~ 222 (233)
+.|+|.++.+ +|+|+++.+|++|+. ++|.... ++ .+||.+.++|.++|.+++|+.||+|.
T Consensus 363 -----v~g~V~~v~~------~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~ 431 (516)
T TIGR00717 363 -----VTGKIKKITD------FGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQ 431 (516)
T ss_pred -----EEEEEEEEec------ceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeecc
Confidence 6799998874 578888899999995 5554321 11 58999999999999999999999997
Q ss_pred c
Q 026794 223 G 223 (233)
Q Consensus 223 ~ 223 (233)
.
T Consensus 432 ~ 432 (516)
T TIGR00717 432 L 432 (516)
T ss_pred c
Confidence 4
No 13
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.94 E-value=3.6e-26 Score=222.55 Aligned_cols=187 Identities=27% Similarity=0.462 Sum_probs=163.2
Q ss_pred hcccCCCCEEEEEEEEEeCCCCE-EEEEechhh-------HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEE
Q 026794 17 IAKGLTGSIISVKVIQANEEMKK-LVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLT 83 (233)
Q Consensus 17 ~~~~~vG~~v~~~Vi~id~~~~~-i~lS~k~~~-------~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~ 83 (233)
+++.++|+.+.|+|+++|+++++ +.+|+|... ++..++.+++|+++.|+ ++|+||+++ +++
T Consensus 428 d~~~~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l~------gv~ 501 (647)
T PRK00087 428 DLSEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIG------GVD 501 (647)
T ss_pred CHHHhCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEEC------CEE
Confidence 34456999999999999999988 999998762 45677789999999999 999999995 799
Q ss_pred EEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeee
Q 026794 84 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNT 163 (233)
Q Consensus 84 Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~ 163 (233)
||+|+|+++|.++.++.+.|++||.|+|+|+++|++++++.||+|++.++||....++ ++.|+. +.|.|..
T Consensus 502 Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~-~~~G~~--------v~g~V~~ 572 (647)
T PRK00087 502 GLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEK-YPVGSI--------VLGKVVR 572 (647)
T ss_pred EEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhh-ccCCeE--------EEEEEEE
Confidence 9999999999999999999999999999999999999999999999999999765544 566776 6799999
Q ss_pred eccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794 164 IEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR 224 (233)
Q Consensus 164 v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~ 224 (233)
+.++ |+|+++.+|+.|+. +++.+++.+ .+||.+++++.++|.+++|+.||.|+..
T Consensus 573 i~~~------G~fV~l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~ 635 (647)
T PRK00087 573 IAPF------GAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVE 635 (647)
T ss_pred EECC------eEEEEECCCCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence 8854 77788899999994 566555444 6899999999999999999999998754
No 14
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.93 E-value=5.3e-25 Score=197.87 Aligned_cols=174 Identities=15% Similarity=0.260 Sum_probs=147.7
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccC
Q 026794 22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS 92 (233)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~----~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels 92 (233)
+|+++.|+|+++|.+++++.||+|+. .|+.+.+.++.|++++|+ ++|+||+++ |++||||+|++|
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 89999999999999999999999975 488888888899999998 899999996 899999999999
Q ss_pred cccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeeeeccCCChhh
Q 026794 93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGA 172 (233)
Q Consensus 93 ~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~ 172 (233)
|.+.. +.+ +|+.+.++|+++|+++++|.||+|.+..++ ... .++.|++ +.|+|+++.++
T Consensus 152 ~~~~~---~~~-vG~~i~~kVl~id~~~~~i~lS~K~~~~~~---~~~-~~k~G~v--------v~G~V~~I~~~----- 210 (318)
T PRK07400 152 TRKPK---EEL-VGEELPLKFLEVDEERNRLVLSHRRALVER---KMN-RLEVGEV--------VVGTVRGIKPY----- 210 (318)
T ss_pred ccCCc---ccc-CCCEEEEEEEEEEcccCEEEEEhhHhhhhh---hhc-cCCCCCE--------EEEEEEEEECC-----
Confidence 96533 334 899999999999999999999999765543 222 3667777 67999998854
Q ss_pred hhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794 173 IFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR 224 (233)
Q Consensus 173 ~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~ 224 (233)
|+|+++ .|++|+. ++++++.++ .+||.+++++.++|.++++++||.|+..
T Consensus 211 -G~fV~i-~gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~ 268 (318)
T PRK07400 211 -GAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLE 268 (318)
T ss_pred -eEEEEE-CCEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccc
Confidence 777777 4899994 777776555 6899999999999999999999999765
No 15
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.93 E-value=4.1e-25 Score=207.89 Aligned_cols=178 Identities=17% Similarity=0.316 Sum_probs=154.1
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccC
Q 026794 22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS 92 (233)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~----~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels 92 (233)
+|+.|+|+|+++|.+++++.||+|++ .|+.+.+.++.|++++|+ ++|+||++ |++||||.|+++
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 99999999999999999999999976 477777777899999998 89999999 489999999999
Q ss_pred cccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccc----cChhhHHhhhhcCCCCeeeecCCccccCCeeeeccCC
Q 026794 93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE----EDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLP 168 (233)
Q Consensus 93 ~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~----~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~~ 168 (233)
+.++.++.++ +||.|+|+|+++|.+++++.||+|.+. .++|....+. ++.|++ ++|+|.+++++
T Consensus 155 ~~~~~~~~~~--vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~-lk~G~i--------v~G~V~~i~~~- 222 (486)
T PRK07899 155 MRRVRDLQPY--IGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQ-LQKGQV--------RKGVVSSIVNF- 222 (486)
T ss_pred ccccCChhhc--CCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHh-ccCCCE--------EEEEEEEEECC-
Confidence 9988888774 799999999999999999999999643 3678666554 677887 77999998854
Q ss_pred ChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794 169 GLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR 224 (233)
Q Consensus 169 g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~ 224 (233)
|+|+++. |++|+. ++|.++.++ .+||.++++|.++|++++||+||.|+..
T Consensus 223 -----G~FVdlg-gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~ 280 (486)
T PRK07899 223 -----GAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQ 280 (486)
T ss_pred -----eEEEEEC-CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeecc
Confidence 7778774 899994 788777666 4899999999999999999999999653
No 16
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.91 E-value=1.7e-23 Score=192.74 Aligned_cols=180 Identities=18% Similarity=0.325 Sum_probs=152.9
Q ss_pred CCCCEEEEEEEEEeCCCCEEEEEechh----hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEcccc
Q 026794 21 LTGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEV 91 (233)
Q Consensus 21 ~vG~~v~~~Vi~id~~~~~i~lS~k~~----~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sel 91 (233)
.+|+.|.|+|+.+|.+++++.||++.. .|+.+...++.|++++|+ ++|+||+++ |++||||++++
T Consensus 64 ~vGd~v~~~V~~v~~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~------G~~gflp~~el 137 (390)
T PRK06676 64 KVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVE------GVRGFIPASLI 137 (390)
T ss_pred CCCCEEEEEEEEEECCCCCEEEEHHHhhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHc
Confidence 399999999999999999999999974 488888888999999999 899999996 68999999999
Q ss_pred CcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecccc----ChhhHHhhhhcCCCCeeeecCCccccCCeeeeccC
Q 026794 92 SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE----DPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPL 167 (233)
Q Consensus 92 s~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~----dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~ 167 (233)
+|.+..++.++ +||.++|+|+++|.+++++.||+|.+.. ++|...... ++.|++ ++|+|..+.++
T Consensus 138 ~~~~~~~~~~~--vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~-~~~G~~--------v~g~V~~v~~~ 206 (390)
T PRK06676 138 STRFVEDFSDF--KGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSS-LKEGDV--------VEGTVARLTDF 206 (390)
T ss_pred CCccCCChHHc--CCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhh-CCCCCE--------EEEEEEEEecc
Confidence 99998888774 8999999999999999999999998765 466554443 567777 67999988754
Q ss_pred CChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794 168 PGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR 224 (233)
Q Consensus 168 ~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~ 224 (233)
|+|+++ .|++|+. +++.++.++ .+||.++++|.++|.+++++.||.|+..
T Consensus 207 ------G~fV~l-~~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~ 264 (390)
T PRK06676 207 ------GAFVDI-GGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTL 264 (390)
T ss_pred ------eEEEEe-CCeEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence 667777 4899994 666555544 5799999999999999999999998543
No 17
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.88 E-value=3.2e-22 Score=179.87 Aligned_cols=111 Identities=37% Similarity=0.649 Sum_probs=106.5
Q ss_pred cCCCCEEEEEEEEEeCCCCEEEEEechhhHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcc
Q 026794 20 GLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD 94 (233)
Q Consensus 20 ~~vG~~v~~~Vi~id~~~~~i~lS~k~~~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~ 94 (233)
.++|+.+.|+|+++|++++++.||+|.+.++.....+++|+++.|+ +||+||++. |++||+|+|+++|+
T Consensus 158 ~~vG~~i~~kVl~id~~~~~i~lS~K~~~~~~~~~~~k~G~vv~G~V~~I~~~G~fV~i~------gv~Gllhisels~~ 231 (318)
T PRK07400 158 ELVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDIG------GVSGLLHISEISHE 231 (318)
T ss_pred ccCCCEEEEEEEEEEcccCEEEEEhhHhhhhhhhccCCCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHcccc
Confidence 4699999999999999999999999998888888999999999999 999999996 79999999999999
Q ss_pred cccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhh
Q 026794 95 LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLL 136 (233)
Q Consensus 95 ~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~ 136 (233)
++.++.+.|++||.|+|+|+++|.++++|.||+|++++|||+
T Consensus 232 ~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~~P~~ 273 (318)
T PRK07400 232 HIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEPGD 273 (318)
T ss_pred cccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccccChhh
Confidence 999999999999999999999999999999999999999995
No 18
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.87 E-value=2.1e-21 Score=189.27 Aligned_cols=178 Identities=21% Similarity=0.362 Sum_probs=152.4
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccC
Q 026794 22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS 92 (233)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~----~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels 92 (233)
+|++++|+|+++|.+++++.||++.. .|+.+.+.++.|+++.|+ ++|+||+++ +++||+|.++++
T Consensus 349 vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lg------gi~gfiP~sel~ 422 (647)
T PRK00087 349 VGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYG------GVRAFLPASHVE 422 (647)
T ss_pred CCCEEEEEEEEEECCCCcEEEEeehhcchhHHHHHHHHhhCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHhC
Confidence 99999999999999999999999865 477888888999999998 889999997 699999999999
Q ss_pred cccccCcccccCCCCEEEEEEEEEeCCCCe-EEEEEecccc----ChhhHHhhhhcCCCCeeeecCCccccCCeeeeccC
Q 026794 93 WDLIQDIRDILNEGDEVRVKVIKIDREKSR-ITLSIKQLEE----DPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPL 167 (233)
Q Consensus 93 ~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~r-i~LS~k~~~~----dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~ 167 (233)
+.+..++..+ +||.++|+|+++|.++++ +.+|+|.+.. ++|....+. ++.|+. +.|+|..+.+
T Consensus 423 ~~~~~d~~~~--vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~-l~~G~i--------V~g~V~~v~~- 490 (647)
T PRK00087 423 LGYVEDLSEY--KGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNS-LEEGDV--------VEGEVKRLTD- 490 (647)
T ss_pred ccccCCHHHh--CCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHh-CCCCCE--------EEEEEEEEeC-
Confidence 9998888764 899999999999999998 9999999753 566555554 566777 6799998875
Q ss_pred CChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794 168 PGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG 223 (233)
Q Consensus 168 ~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~ 223 (233)
+|+|+++ +|++|+. ++|.++.++ .+||.++++|.++|++++++.||.|..
T Consensus 491 -----~G~fV~l-~gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~ 548 (647)
T PRK00087 491 -----FGAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKL 548 (647)
T ss_pred -----CcEEEEE-CCEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeecc
Confidence 4778888 7999995 566555444 589999999999999999999999853
No 19
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.79 E-value=3.4e-19 Score=159.02 Aligned_cols=101 Identities=25% Similarity=0.386 Sum_probs=89.0
Q ss_pred cCCC-CCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794 54 SRVN-VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (233)
Q Consensus 54 ~~~~-~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~ 127 (233)
++++ +|+++.|+ +||+||+|.+++ |++||||+||+||+++.++++++++||.|.|+|+++|+++++|.||+
T Consensus 12 ~~~P~~GdvV~g~V~~I~d~GafV~L~EY~---gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~ 88 (319)
T PTZ00248 12 QKFPEEDDLVMVKVVRITEMGAYVSLLEYD---DIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSK 88 (319)
T ss_pred hhCCCCCCEEEEEEEEEeCCeEEEEecCCC---CcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEe
Confidence 4555 89999998 999999996433 79999999999999999999999999999999999999999999999
Q ss_pred eccccChhhHHhhhhcCCCCeeeecCCccccCCeeeecc
Q 026794 128 KQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEP 166 (233)
Q Consensus 128 k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~ 166 (233)
|++.++||..+.++ ++.|+. +.|.|..+..
T Consensus 89 K~v~~~pw~~~~e~-~~~g~~--------v~~~V~~ia~ 118 (319)
T PTZ00248 89 KRVSPEDIEACEEK-FSKSKK--------VHSIMRHIAQ 118 (319)
T ss_pred eecccchHHHHHHh-CcCCCE--------EEEEEEEchh
Confidence 99999999766655 777887 5678877753
No 20
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.76 E-value=5.6e-19 Score=135.91 Aligned_cols=75 Identities=45% Similarity=0.751 Sum_probs=71.2
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (233)
Q Consensus 55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~ 129 (233)
.+++|++++|+ +|||||+|++ |-.|||||||++++|++|+.+++++||.|+|+|+++|. +++|+||+|+
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 47899999998 9999999984 78999999999999999999999999999999999997 9999999999
Q ss_pred cccChh
Q 026794 130 LEEDPL 135 (233)
Q Consensus 130 ~~~dp~ 135 (233)
++..|-
T Consensus 76 ~~e~pe 81 (129)
T COG1098 76 LEEEPE 81 (129)
T ss_pred hhhCcc
Confidence 999885
No 21
>PRK08582 hypothetical protein; Provisional
Probab=99.61 E-value=3e-15 Score=119.69 Aligned_cols=77 Identities=40% Similarity=0.679 Sum_probs=71.9
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (233)
Q Consensus 55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~ 129 (233)
.+++|++|.|+ +||+||+|. ++++||||+|+++|+++.++.+.|++||.|+|+|+++|. +++|.||+|+
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 36899999998 999999998 489999999999999999999999999999999999997 5999999999
Q ss_pred cccChhhH
Q 026794 130 LEEDPLLE 137 (233)
Q Consensus 130 ~~~dp~~~ 137 (233)
+.++||.+
T Consensus 76 ~~~~~~~~ 83 (139)
T PRK08582 76 AKDRPKRQ 83 (139)
T ss_pred cccCchhh
Confidence 99999964
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=99.61 E-value=2.2e-15 Score=107.91 Aligned_cols=66 Identities=26% Similarity=0.423 Sum_probs=60.9
Q ss_pred CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCc---ccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI---RDILNEGDEVRVKVIKIDREKSRITLS 126 (233)
Q Consensus 56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~---~~~~~~Gd~V~vkVi~vd~e~~ri~LS 126 (233)
+++|+++.|+ +||+||+|. ++++|++|++++||+++.++ .+.|++||.++|+|+++|+++++|.||
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~-----~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS 74 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLS-----SSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeC-----CCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 5789999999 999999997 48999999999999997775 588999999999999999999999986
No 23
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.56 E-value=1.4e-14 Score=143.59 Aligned_cols=88 Identities=27% Similarity=0.423 Sum_probs=78.5
Q ss_pred HhhhccCCCCCCEEE-EE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCe
Q 026794 49 WNKYSSRVNVEDIFV-GR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSR 122 (233)
Q Consensus 49 ~~~~~~~~~~G~vv~-g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~r 122 (233)
.+.+....++|++|. |+ +||+||+|. +|++||||+|+++|+++.++.+.|++||.|+|+|+++|. ++|
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 345556789999995 45 999999998 489999999999999999999999999999999999997 899
Q ss_pred EEEEEeccccChhhHHhhhh
Q 026794 123 ITLSIKQLEEDPLLETLEKV 142 (233)
Q Consensus 123 i~LS~k~~~~dp~~~~~~~~ 142 (233)
|.||+|++.++||++..++.
T Consensus 818 I~LSlK~l~~~Pw~~~~~~~ 837 (891)
T PLN00207 818 LRLSRRALLPEANSEKSSQK 837 (891)
T ss_pred EEEEEeccccCchhhhhhhh
Confidence 99999999999998766543
No 24
>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=99.54 E-value=2.5e-14 Score=101.53 Aligned_cols=69 Identities=43% Similarity=0.731 Sum_probs=65.0
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (233)
Q Consensus 55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k 128 (233)
++++|+++.|+ ++|+||+|+ .+++||||++++++.+..++.+.|++||+++|+|+++|.+++++.||+|
T Consensus 1 k~~~G~iv~g~V~~v~~~g~~V~l~-----~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k 74 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDFGVFVDLG-----NGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEES-----TSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCCEEEEEEEEEECCEEEEEEC-----CcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 47899999999 899999998 3899999999999999999999999999999999999999999999986
No 25
>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=99.54 E-value=2.2e-14 Score=104.42 Aligned_cols=71 Identities=31% Similarity=0.389 Sum_probs=66.4
Q ss_pred hccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794 52 YSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (233)
Q Consensus 52 ~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS 126 (233)
.+.++++|+++.|+ +||+||++.+ +++||+|+++++++++.++.+.|++||.|+|+|+++|.+++++.||
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 NFSDLKPGMVVHGYVRNITPYGVFVEFLG-----GLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLS 82 (83)
T ss_pred hHHhCCCCCEEEEEEEEEeeceEEEEcCC-----CCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEe
Confidence 35668999999999 9999999973 8999999999999999999999999999999999999999999998
Q ss_pred E
Q 026794 127 I 127 (233)
Q Consensus 127 ~ 127 (233)
+
T Consensus 83 l 83 (83)
T cd04461 83 L 83 (83)
T ss_pred C
Confidence 5
No 26
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=99.54 E-value=4.2e-14 Score=100.71 Aligned_cols=67 Identities=33% Similarity=0.541 Sum_probs=60.4
Q ss_pred CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (233)
Q Consensus 56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~ 127 (233)
++.|++++|+ +||+||++.+ .+.+||+|+|+++|.++.++.+.|++||+|+|+|+++|.++ ++.||+
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~~----~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~ 72 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPG----CRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL 72 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEECC----CCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence 3589999998 9999999962 23799999999999999999999999999999999999865 999986
No 27
>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=99.54 E-value=2.5e-14 Score=101.72 Aligned_cols=66 Identities=20% Similarity=0.305 Sum_probs=61.1
Q ss_pred CCCCCEEEEE-----e-eeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794 56 VNVEDIFVGR-----D-YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (233)
Q Consensus 56 ~~~G~vv~g~-----~-~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k 128 (233)
+++|+++.|+ + ||+|++|. ++.+|++|+|+++|++..++.+.|++||.|+|+|+++|. +++.||+|
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 4789999998 4 89999998 489999999999999999999999999999999999984 89999986
No 28
>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=99.54 E-value=3.2e-14 Score=101.56 Aligned_cols=65 Identities=17% Similarity=0.305 Sum_probs=60.7
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccc--ccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (233)
Q Consensus 59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~--~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k 128 (233)
|++++|+ ++|+||+|. ++++|+||+++++|.+ ..++.+.|++||.|+|+|+++|+++++|.||+|
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~-----~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTIS-----PDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeC-----CCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 7888888 999999997 4899999999999874 889999999999999999999999999999987
No 29
>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=99.52 E-value=9.6e-14 Score=98.86 Aligned_cols=71 Identities=34% Similarity=0.489 Sum_probs=64.4
Q ss_pred CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (233)
Q Consensus 56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~ 129 (233)
++.|+++.|+ ++|+||++.+. .+++||+|+|+++++++.++.+.|++||.|+|+|+++|.+++++.||+|+
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~---~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~ 76 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEY---GNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCC---CCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 3679999998 99999999631 15999999999999999999999999999999999999999999999985
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=99.51 E-value=6e-14 Score=98.55 Aligned_cols=65 Identities=29% Similarity=0.387 Sum_probs=60.9
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (233)
Q Consensus 59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k 128 (233)
|+++.|+ ++|+||++.+ +++||+|+|++++++..++.+.|++||.++|+|+++|.+++++.||+|
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 GLKTHGTIVKVKPNGCIVSFYN-----NVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECC-----CCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 6788888 9999999983 799999999999999999999999999999999999999999999986
No 31
>PHA02945 interferon resistance protein; Provisional
Probab=99.51 E-value=1e-13 Score=100.96 Aligned_cols=75 Identities=31% Similarity=0.396 Sum_probs=68.1
Q ss_pred cCCCCCCEEEEE----eeeEEEEEccCCCCccEEEEEEcccc--CcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794 54 SRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVSEV--SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (233)
Q Consensus 54 ~~~~~G~vv~g~----~~G~fV~l~~~~~~~gv~Glv~~sel--s~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~ 127 (233)
.-+.+|+++.|+ +||+||.|.+++ |.+||||+|++ +..++++ ++++ .||++.|||+++|+.++.|.||+
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 446899999999 999999999754 79999999955 9999999 9999 99999999999999999999999
Q ss_pred eccccC
Q 026794 128 KQLEED 133 (233)
Q Consensus 128 k~~~~d 133 (233)
|+..++
T Consensus 82 K~V~~~ 87 (88)
T PHA02945 82 KRMCRH 87 (88)
T ss_pred eEcccC
Confidence 997653
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=99.50 E-value=1.3e-13 Score=97.68 Aligned_cols=68 Identities=26% Similarity=0.418 Sum_probs=63.4
Q ss_pred CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (233)
Q Consensus 56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k 128 (233)
+++|+++.|+ ++|+||+|+ .+++|++|++++++++..++.+.|++||.++|+|+++|.+++++.||+|
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 4789999998 999999998 4899999999999999888899999999999999999999999999985
No 33
>PRK07252 hypothetical protein; Provisional
Probab=99.49 E-value=1.6e-13 Score=107.03 Aligned_cols=75 Identities=36% Similarity=0.657 Sum_probs=69.4
Q ss_pred CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccc
Q 026794 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131 (233)
Q Consensus 57 ~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~ 131 (233)
++|+++.|+ ++|+||+|. .+++||+|+++++++++.++.+.|++||.|+|+|+++|.+++++.||+|+++
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~-----~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~ 76 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALE-----NGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLE 76 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEEC-----CCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence 579999998 999999997 3799999999999999999999999999999999999999999999999998
Q ss_pred cCh-hh
Q 026794 132 EDP-LL 136 (233)
Q Consensus 132 ~dp-~~ 136 (233)
+++ |.
T Consensus 77 ~~~~~~ 82 (120)
T PRK07252 77 EEKQHF 82 (120)
T ss_pred cCcccc
Confidence 865 64
No 34
>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=99.48 E-value=1.8e-13 Score=96.07 Aligned_cols=64 Identities=22% Similarity=0.437 Sum_probs=59.9
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (233)
Q Consensus 59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~ 127 (233)
|++++|+ ++|+||++. .+++||+|+++++|.+..++.+.|++||.++|+|+++|.+++++.||+
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 389999999999999999999999999999999999999999999985
No 35
>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=99.48 E-value=1.6e-13 Score=97.34 Aligned_cols=57 Identities=26% Similarity=0.402 Sum_probs=54.1
Q ss_pred eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (233)
Q Consensus 66 ~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~ 127 (233)
+||+||+|. +|++||+|+|++++.+..++.+.|++||.++|+|+++|+.++++.||+
T Consensus 15 ~~G~~V~l~-----~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 15 DLGAVFELK-----DGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CceEEEEeC-----CCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 799999997 389999999999999999999999999999999999999999999985
No 36
>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=99.47 E-value=3.5e-13 Score=96.47 Aligned_cols=68 Identities=16% Similarity=0.166 Sum_probs=61.3
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (233)
Q Consensus 55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~ 129 (233)
.+++|+++.|+ ++|+||+++- .|++||+|.++++|. +.+++||.+.|+|+++|.+++++.||+|+
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 36899999999 9999999951 279999999999986 77999999999999999999999999998
Q ss_pred ccc
Q 026794 130 LEE 132 (233)
Q Consensus 130 ~~~ 132 (233)
+.+
T Consensus 71 ~~~ 73 (74)
T cd05694 71 SKV 73 (74)
T ss_pred ccc
Confidence 765
No 37
>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=99.45 E-value=4.2e-13 Score=94.61 Aligned_cols=68 Identities=34% Similarity=0.562 Sum_probs=62.9
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccc
Q 026794 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131 (233)
Q Consensus 59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~ 131 (233)
|+++.|+ ++|+||++. .+++|++|+++++++++.++.+.|++||.++|+|+++|.+++++.||+|+++
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~-----~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~~ 73 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLG-----DGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAKE 73 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeC-----CCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEcC
Confidence 6788887 999999998 3799999999999999999999999999999999999999999999999763
No 38
>PRK08059 general stress protein 13; Validated
Probab=99.45 E-value=5.1e-13 Score=104.65 Aligned_cols=77 Identities=45% Similarity=0.796 Sum_probs=72.2
Q ss_pred ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794 53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (233)
Q Consensus 53 ~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~ 127 (233)
.+.+++|+++.|+ ++|+||++. .+++||+|+++++++++.++.+.|++||.|+|+|+++|.+++++.||+
T Consensus 2 ~~~~k~G~iv~G~V~~i~~~G~fV~i~-----~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lsl 76 (123)
T PRK08059 2 MSQYEVGSVVTGKVTGIQPYGAFVALD-----EETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSI 76 (123)
T ss_pred cccCCCCCEEEEEEEEEecceEEEEEC-----CCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEE
Confidence 3568899999999 999999998 479999999999999999999999999999999999999999999999
Q ss_pred eccccCh
Q 026794 128 KQLEEDP 134 (233)
Q Consensus 128 k~~~~dp 134 (233)
|++..+|
T Consensus 77 k~~~~~~ 83 (123)
T PRK08059 77 RATEEAP 83 (123)
T ss_pred EEcccCc
Confidence 9999888
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=99.44 E-value=7.4e-13 Score=94.19 Aligned_cols=70 Identities=41% Similarity=0.643 Sum_probs=64.1
Q ss_pred CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecc
Q 026794 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (233)
Q Consensus 57 ~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~ 130 (233)
++|+++.|+ ++|+||++.+ .+.+|++|++++++++..++.+.|++||.|+|+|+++|.+++++.||+|+.
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~~----~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~ 75 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDG----TNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECC----CCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence 368999998 9999999973 269999999999999999999999999999999999999999999999975
No 40
>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=99.44 E-value=7.2e-13 Score=95.50 Aligned_cols=72 Identities=35% Similarity=0.666 Sum_probs=62.6
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccc-cCcccccCCCCEEEEEEEEEeCCCCeEEEEEecccc
Q 026794 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE 132 (233)
Q Consensus 59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~-~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~ 132 (233)
|+++.|+ +||+||+|.+.- .+.+||+|+++++|++. .++.+.|++||.|+|+|+++| ++++.||+|++++
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 15899999999999986 899999999999999999999 8999999999877
Q ss_pred Ch
Q 026794 133 DP 134 (233)
Q Consensus 133 dp 134 (233)
+.
T Consensus 77 ~~ 78 (79)
T cd05684 77 DT 78 (79)
T ss_pred CC
Confidence 53
No 41
>PRK05807 hypothetical protein; Provisional
Probab=99.44 E-value=5.4e-13 Score=106.29 Aligned_cols=70 Identities=46% Similarity=0.722 Sum_probs=65.8
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (233)
Q Consensus 55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~ 129 (233)
.+++|++++|+ +||+||+|. +..||||+|++++.++.++.++|++||.|+|+|+++|. +++|.||+|+
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 36789999999 999999995 68999999999999999999999999999999999997 7999999999
Q ss_pred cc
Q 026794 130 LE 131 (233)
Q Consensus 130 ~~ 131 (233)
+.
T Consensus 75 ~~ 76 (136)
T PRK05807 75 AM 76 (136)
T ss_pred cc
Confidence 86
No 42
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.44 E-value=1.3e-13 Score=118.73 Aligned_cols=77 Identities=35% Similarity=0.623 Sum_probs=72.3
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (233)
Q Consensus 55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~ 129 (233)
-+.+|++|-|+ +||+||.|.+++ |++||+|+||++.+++.+++++++.||.+-|+||++|+.++.|.||+|.
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 999999999876 6999999999999999999999999999999999999999999999999
Q ss_pred cccCh
Q 026794 130 LEEDP 134 (233)
Q Consensus 130 ~~~dp 134 (233)
..++.
T Consensus 85 V~~~q 89 (269)
T COG1093 85 VTEHQ 89 (269)
T ss_pred CCHHH
Confidence 87664
No 43
>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=99.43 E-value=3.6e-13 Score=94.24 Aligned_cols=63 Identities=29% Similarity=0.470 Sum_probs=58.8
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (233)
Q Consensus 59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS 126 (233)
|+++.|+ ++|+||+|. .+++||+|++++++++..++.+.|++||.++|+|+++|++++++.||
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 37999999999999999999999999999999999999999999886
No 44
>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=99.43 E-value=5.1e-13 Score=93.35 Aligned_cols=63 Identities=37% Similarity=0.748 Sum_probs=57.2
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCc-ccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (233)
Q Consensus 59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~-~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS 126 (233)
|+++.|+ +||+||+|. ++++||+|+++++| .+..++.+.|++||.|+|+|+++|.+++++.||
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 6778887 999999998 38999999999997 577889999999999999999999999999875
No 45
>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=99.38 E-value=2.2e-12 Score=90.65 Aligned_cols=65 Identities=32% Similarity=0.532 Sum_probs=60.6
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (233)
Q Consensus 59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k 128 (233)
|+++.|+ ++|+||++. .+.+|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||+|
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 899999997 3799999999999999999999999999999999999988899999986
No 46
>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=99.37 E-value=2.9e-12 Score=88.66 Aligned_cols=64 Identities=44% Similarity=0.830 Sum_probs=59.3
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (233)
Q Consensus 59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k 128 (233)
|+++.|+ ++|+||++. .+.+||+|.++++++++.++.+.|++||.++|+|+++|. ++++.||+|
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 6778887 999999998 379999999999999999999999999999999999998 899999986
No 47
>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=99.37 E-value=2.7e-12 Score=90.61 Aligned_cols=66 Identities=39% Similarity=0.674 Sum_probs=58.9
Q ss_pred CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcc-cccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (233)
Q Consensus 56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~-~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS 126 (233)
+++|+++.|+ +||+||+|. ++++||+|+++++|. +..++.+.|++||.|+|+|+++|.+++++.||
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~-----~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELE-----EGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcC-----CCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence 5789999998 999999998 379999999999985 55577788999999999999999999999874
No 48
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.37 E-value=1.2e-12 Score=132.09 Aligned_cols=124 Identities=23% Similarity=0.355 Sum_probs=106.1
Q ss_pred CCCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCCCEEEEEechhhHh------hhccCCCCCCEEEEE-----eeeE
Q 026794 1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWN------KYSSRVNVEDIFVGR-----DYGA 69 (233)
Q Consensus 1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~~~~------~~~~~~~~G~vv~g~-----~~G~ 69 (233)
+++.|++.||...+... ..+|..+..+|+.++.+.+++.+++|.+..+ .-.....+|.++.|+ ++||
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 LPKEHLSDHPLQPPLRD--FKVGSGVKLRVLSVNRDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLCAIKENGA 615 (1710)
T ss_pred cChHhhhhcccccccce--eeeccccEEEEEEEEccCCeeEEEechhhhcccCCCccchhhcCCCceEEEEEeeeccCCe
Confidence 46778877777655432 2478888889999999999999999987532 234456789999999 9999
Q ss_pred EEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccc
Q 026794 70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131 (233)
Q Consensus 70 fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~ 131 (233)
||.+.+ |++||.|.|+++++++.++++.|.+||++.|+|.++|.+++||.||+|+..
T Consensus 616 ~V~F~g-----~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~ 672 (1710)
T KOG1070|consen 616 FVTFTG-----GLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASS 672 (1710)
T ss_pred EEEecC-----ccccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhhhhh
Confidence 999985 899999999999999999999999999999999999999999999999864
No 49
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.32 E-value=8.4e-12 Score=109.53 Aligned_cols=77 Identities=36% Similarity=0.614 Sum_probs=70.4
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (233)
Q Consensus 55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~ 129 (233)
.+++|+++.|+ ++|+||+|.+++ |++||+|+|+++++++.++.+.|++||.|.|+|+++|.+++++.||+|+
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 46889999998 999999997422 6999999999999999999999999999999999999999999999998
Q ss_pred cccCh
Q 026794 130 LEEDP 134 (233)
Q Consensus 130 ~~~dp 134 (233)
+.++.
T Consensus 82 v~~~e 86 (262)
T PRK03987 82 VNEHQ 86 (262)
T ss_pred cccch
Confidence 87765
No 50
>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=99.31 E-value=6.3e-12 Score=122.65 Aligned_cols=111 Identities=23% Similarity=0.448 Sum_probs=85.6
Q ss_pred CCCchhHhhhcccCCCCEEE--------------EEEEEEeCCCCEEEEEechhh--------Hhhhcc--CCCCCCEEE
Q 026794 8 KEPQKSIHEIAKGLTGSIIS--------------VKVIQANEEMKKLVFSEKDAV--------WNKYSS--RVNVEDIFV 63 (233)
Q Consensus 8 ~~p~~~~~~~~~~~vG~~v~--------------~~Vi~id~~~~~i~lS~k~~~--------~~~~~~--~~~~G~vv~ 63 (233)
..|+....+...+.+|+.|- ++ |+++. .+.+.++-.... .+.+.. .+++|++|+
T Consensus 575 ~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~-Idi~d-~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~ 652 (719)
T TIGR02696 575 YAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAE-ISIED-DGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFL 652 (719)
T ss_pred CCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCE-EEEec-CcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEE
Confidence 45665555555555665553 23 77775 677777765431 233444 489999999
Q ss_pred EE-----eeeEEEEEccCCCCccEEEEEEccccC----cccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794 64 GR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS----WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (233)
Q Consensus 64 g~-----~~G~fV~l~~~~~~~gv~Glv~~sels----~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS 126 (233)
|+ +||+||+|. +|.+||+|+|+++ |.++.++.++|++||.|+|||+++|. ++||+|+
T Consensus 653 GkV~~I~dfGaFVel~-----~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~ 718 (719)
T TIGR02696 653 GTVVKTTAFGAFVSLL-----PGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDD-RGKLSLV 718 (719)
T ss_pred EEEEEEECceEEEEec-----CCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence 99 999999997 4899999999996 46899999999999999999999995 8899986
No 51
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.31 E-value=2.3e-11 Score=123.13 Aligned_cols=185 Identities=17% Similarity=0.183 Sum_probs=147.5
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechhh-----------HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEE
Q 026794 22 TGSIISVKVIQANEEMKKLVFSEKDAV-----------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL 85 (233)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~~-----------~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Gl 85 (233)
.++.+.+++|.++..++.+.+|.+... --+..++++.|+++.|. +.|+|+.+. ++++++
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 579999999999998888999988321 12356789999999999 899999998 699999
Q ss_pred EEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHH--hhhhcCCCCeeeecCCccccCCeee
Q 026794 86 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLET--LEKVIPQDGSVISDSSSMSSSNSNT 163 (233)
Q Consensus 86 v~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~--~~~~~~~g~~~~~~~~~~~~g~v~~ 163 (233)
+|+|+++..+...++..|++||.|.++|++++...+|+.|++|.....--... ....+..|+. ..|.+..
T Consensus 1190 v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~~~~~~~~~~l~~gd~--------~~g~v~~ 1261 (1710)
T KOG1070|consen 1190 VPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKNSDIKDTVKLLKDSKDLKKGDR--------EDGTVEV 1261 (1710)
T ss_pred EEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEeccccCCchhhhhhhhhhhcccc--------ccceEEE
Confidence 99999999999999999999999999999999999999999998544322111 1223566777 6799998
Q ss_pred eccCCChhhhhhhhcccCCe--eEE----Eeeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794 164 IEPLPGLGAIFEELLQEDGI--DDV----RITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC 225 (233)
Q Consensus 164 v~~~~g~~~~~~~l~~~~gv--~gl----~~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~ 225 (233)
+.|+ |.|+++..++ .|+ +++.++.+.. ..|+.+...+.+.+.++++|+|.+++...
T Consensus 1262 ~~~~------G~fi~l~~tv~~~g~~~~~e~~d~~~e~it~~~~~~~~V~a~~lk~~~ek~rIsl~~k~s~~ 1327 (1710)
T KOG1070|consen 1262 VDPF------GLFIKLDVTVNMVGLCHISEEADDRGENITALYYAGDRVKACVLKEDSEKKRISLGLKSSYL 1327 (1710)
T ss_pred ecCC------ceEEEecCcceecccccceeecchhhhhcccceeccceeeeEeeeccchhhhhhhhhhhhcc
Confidence 8865 5566666665 676 3444443322 56899999999999999999999776543
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=99.30 E-value=5.6e-12 Score=95.39 Aligned_cols=70 Identities=30% Similarity=0.478 Sum_probs=62.4
Q ss_pred CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccc-------------------cCcccccCCCCEEEE
Q 026794 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------------------QDIRDILNEGDEVRV 111 (233)
Q Consensus 56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~-------------------~~~~~~~~~Gd~V~v 111 (233)
+++|+++.|+ ++|+||.|.+ +++|++|+++++|++. .++.+.|++||.|+|
T Consensus 1 L~~G~vV~G~V~~v~~~gl~v~L~~-----g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~ 75 (100)
T cd05693 1 LSEGMLVLGQVKEITKLDLVISLPN-----GLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRC 75 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEECCC-----CcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEE
Confidence 5789999999 9999999983 8999999999999763 347889999999999
Q ss_pred EEEEEeCC---CCeEEEEEecc
Q 026794 112 KVIKIDRE---KSRITLSIKQL 130 (233)
Q Consensus 112 kVi~vd~e---~~ri~LS~k~~ 130 (233)
+|+++|.+ +++|.||+|..
T Consensus 76 kVi~~d~~~~~~~~i~LSlr~~ 97 (100)
T cd05693 76 KVVSLDKSKSGKKRIELSLEPE 97 (100)
T ss_pred EEEEccCCcCCCcEEEEEecHH
Confidence 99999987 79999999864
No 53
>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=99.29 E-value=1.5e-11 Score=85.76 Aligned_cols=62 Identities=27% Similarity=0.545 Sum_probs=56.2
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (233)
Q Consensus 59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k 128 (233)
|++++|+ ++|+||+++ |++||+|.|++++.+..++.+. +||.++|+|+++|.+++++.||+|
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 999999994 7999999999999988877774 799999999999999999999985
No 54
>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=99.29 E-value=1.6e-11 Score=84.97 Aligned_cols=63 Identities=44% Similarity=0.865 Sum_probs=58.4
Q ss_pred CCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794 58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (233)
Q Consensus 58 ~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS 126 (233)
+|+++.|+ ++|+||++. +.+|++|.+++++.+..++.+.|++||.|+|+|+++|.+++++.||
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 999999996 6999999999999999999999999999999999999999999886
No 55
>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=99.29 E-value=1e-11 Score=85.73 Aligned_cols=63 Identities=38% Similarity=0.670 Sum_probs=57.7
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (233)
Q Consensus 59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS 126 (233)
|+++.|+ ++|+||++. ++.+||+|.+++++.++.++.+.|++||.++|+|+++|.+++++.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~-----~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIG-----VKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcC-----CCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 5677777 999999997 47999999999999999999999999999999999999999999886
No 56
>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=99.27 E-value=1.5e-11 Score=86.01 Aligned_cols=61 Identities=20% Similarity=0.328 Sum_probs=54.2
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (233)
Q Consensus 59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS 126 (233)
|++++|+ ++|+||+|.+ +++||+|.++++..+.. .+.|++||.++|+|+++|+++++|.||
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 GMLVNARVKKVLSNGLILDFLS-----SFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcC-----CceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 6788888 9999999973 79999999999866544 778999999999999999999999886
No 57
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.26 E-value=2.2e-11 Score=89.00 Aligned_cols=70 Identities=23% Similarity=0.363 Sum_probs=62.3
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCc----ccccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 026794 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW----DLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125 (233)
Q Consensus 55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~----~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~L 125 (233)
.+++|+++.|+ ++|+||++. ++.+|++|++++++ .+..++.+.+++||.++|+|+++|++ +++.|
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 35899999999 999999998 48999999999997 45577888899999999999999975 99999
Q ss_pred EEecc
Q 026794 126 SIKQL 130 (233)
Q Consensus 126 S~k~~ 130 (233)
|+|+.
T Consensus 77 S~~~~ 81 (86)
T cd05789 77 HTRSL 81 (86)
T ss_pred EeCcc
Confidence 99875
No 58
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=99.25 E-value=3e-11 Score=83.73 Aligned_cols=63 Identities=44% Similarity=0.783 Sum_probs=57.5
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (233)
Q Consensus 59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~ 127 (233)
|+++.|+ ++|+||++. .+.+||+|.++++++++.++.+.|++||.++|+|+++|. ++++.||+
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~-----~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~-~~~i~ls~ 68 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEIL-----PGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeC-----CCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence 5677777 999999997 379999999999999998999999999999999999998 99999985
No 59
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.23 E-value=4.5e-11 Score=117.67 Aligned_cols=93 Identities=34% Similarity=0.615 Sum_probs=78.0
Q ss_pred EEEeCCCCEEEEEechh--------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc
Q 026794 31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ 97 (233)
Q Consensus 31 i~id~~~~~i~lS~k~~--------~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~ 97 (233)
++++ +++.+.++.... ..+.+...+++|+++.|+ +||+||+|. ++.+||+|+|+++|.++.
T Consensus 587 idi~-d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafVei~-----~~~~GllhiSels~~~v~ 660 (693)
T PRK11824 587 IDIE-DDGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEIL-----PGKDGLVHISEIADERVE 660 (693)
T ss_pred cccC-CCceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEECCeEEEEEC-----CCCEEEEEeeeccCcccc
Confidence 4444 356666665432 134455678999999999 999999998 489999999999999999
Q ss_pred CcccccCCCCEEEEEEEEEeCCCCeEEEEEecc
Q 026794 98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (233)
Q Consensus 98 ~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~ 130 (233)
++.+.|++||.|+|+|+++|.+ +++.||+|.+
T Consensus 661 ~~~~v~kvGD~V~VkV~~iD~~-grI~LS~k~~ 692 (693)
T PRK11824 661 KVEDVLKEGDEVKVKVLEIDKR-GRIRLSRKAV 692 (693)
T ss_pred CccceeCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence 9999999999999999999986 9999999976
No 60
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=99.19 E-value=1.2e-10 Score=80.37 Aligned_cols=67 Identities=43% Similarity=0.725 Sum_probs=61.5
Q ss_pred CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (233)
Q Consensus 57 ~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k 128 (233)
++|+++.|+ ++|+||+++ +++.|++|.+++++.+..++.+.|++||.++|+|+++|.+++++.||++
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 468999998 899999998 3799999999999998888889999999999999999998899999975
No 61
>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=99.19 E-value=9.8e-11 Score=86.55 Aligned_cols=70 Identities=26% Similarity=0.404 Sum_probs=59.8
Q ss_pred cCCCCCCEEEEE-----ee--eEEEEEccCCCCccEEEEEEccccCc---ccccCcccccCCCCEEEEEEEEEeCCCCeE
Q 026794 54 SRVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSW---DLIQDIRDILNEGDEVRVKVIKIDREKSRI 123 (233)
Q Consensus 54 ~~~~~G~vv~g~-----~~--G~fV~l~~~~~~~gv~Glv~~sels~---~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri 123 (233)
.+++.|++|.|+ +| ||||+|. .|.+||||+||+|| .++.++.+.+++||.|.|+|++......-.
T Consensus 3 ~~~~~G~iy~g~V~~i~~~~~GaFV~l~-----~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~ 77 (88)
T cd04453 3 REPIVGNIYLGRVKKIVPGLQAAFVDIG-----LGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGP 77 (88)
T ss_pred CcCCCCCEEEEEEEEeccCCcEEEEEeC-----CCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCc
Confidence 357899999999 65 9999998 37999999999999 678889999999999999999987766555
Q ss_pred EEEEe
Q 026794 124 TLSIK 128 (233)
Q Consensus 124 ~LS~k 128 (233)
.|+.+
T Consensus 78 ~lt~~ 82 (88)
T cd04453 78 RLTTN 82 (88)
T ss_pred eEEEE
Confidence 55544
No 62
>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=99.16 E-value=2.4e-10 Score=82.39 Aligned_cols=66 Identities=30% Similarity=0.610 Sum_probs=56.2
Q ss_pred CCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc-----------CcccccCCCCEEEEEEEEEeCCCC
Q 026794 58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREKS 121 (233)
Q Consensus 58 ~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~-----------~~~~~~~~Gd~V~vkVi~vd~e~~ 121 (233)
+|++++|+ ++|+||++.. ++++|++|.++++++++. +....|++||.|+|+|+++|.+++
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 9999999972 379999999999976532 345789999999999999999999
Q ss_pred eEEEEE
Q 026794 122 RITLSI 127 (233)
Q Consensus 122 ri~LS~ 127 (233)
++.|++
T Consensus 77 ~i~~~l 82 (83)
T cd04471 77 KIDFEL 82 (83)
T ss_pred EEEEEE
Confidence 999986
No 63
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.13 E-value=1.4e-10 Score=111.59 Aligned_cols=94 Identities=36% Similarity=0.631 Sum_probs=81.8
Q ss_pred EEEeCCCCEEEEEechh--------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc
Q 026794 31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ 97 (233)
Q Consensus 31 i~id~~~~~i~lS~k~~--------~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~ 97 (233)
++++ +.+.+.++-... ..+.+...+++|++|.|+ +||+||+|. +|-+||||+|++++.++.
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 667777665542 245677889999999999 999999998 589999999999999999
Q ss_pred CcccccCCCCEEEEEEEEEeCCCCeEEEEEeccc
Q 026794 98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131 (233)
Q Consensus 98 ~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~ 131 (233)
...+.+++||.+.||++++|. ++|+.||+|...
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 999999999999999999995 899999999764
No 64
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=99.11 E-value=4.3e-10 Score=94.26 Aligned_cols=101 Identities=23% Similarity=0.315 Sum_probs=82.8
Q ss_pred CCCEEEEEE---EEEeCCCCEEEEEechhhHhhhccCCCCCCEEEEE-----eeeEEEEEccCC--C---CccEEEEEEc
Q 026794 22 TGSIISVKV---IQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPD--G---LYHLTGLVHV 88 (233)
Q Consensus 22 vG~~v~~~V---i~id~~~~~i~lS~k~~~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~--~---~~gv~Glv~~ 88 (233)
.+..+.+.+ +++|.+++++.+. +|..+...+++|++|.|+ ++|+||+|...+ + ..+++|++|+
T Consensus 29 ~~~~i~as~~G~~~id~~~~~Isv~----P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~ 104 (189)
T PRK09521 29 DNGEVYASVVGKVFIDDINRKISVI----PFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHI 104 (189)
T ss_pred eCCEEEEEeeEEEEEcCCCCEEEEe----cCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEh
Confidence 456666554 5668888888885 466666788999999999 999999996321 0 1268999999
Q ss_pred cccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794 89 SEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (233)
Q Consensus 89 sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~ 129 (233)
+++++.+..++.+.|++||.|+|+|++++ +++.||+|+
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 99999999999999999999999999998 789999985
No 65
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.08 E-value=5.7e-10 Score=80.88 Aligned_cols=69 Identities=22% Similarity=0.208 Sum_probs=63.5
Q ss_pred CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecc
Q 026794 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (233)
Q Consensus 56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~ 130 (233)
+++|+++.|+ +.+++|++. .+.+|++|.++++..+..++.+.|++||.+.|+|+++|.+ +++.||++..
T Consensus 4 p~~GdiV~G~V~~v~~~~~~V~i~-----~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~~ 77 (82)
T cd04454 4 PDVGDIVIGIVTEVNSRFWKVDIL-----SRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTADN 77 (82)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEeC-----CCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECCC
Confidence 5899999999 899999997 3799999999999988889999999999999999999986 8999999873
No 66
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=99.07 E-value=2.2e-10 Score=111.66 Aligned_cols=75 Identities=37% Similarity=0.648 Sum_probs=70.0
Q ss_pred ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794 53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (233)
Q Consensus 53 ~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~ 127 (233)
+..+++|++++|+ +||+||+|+ -+.+|+||+|++|..++.+|.+++++||.|+|+|+++|..++||.|||
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 999999997 478999999999999999999999999999999999999999999999
Q ss_pred ecccc
Q 026794 128 KQLEE 132 (233)
Q Consensus 128 k~~~~ 132 (233)
+.-..
T Consensus 728 r~~~~ 732 (780)
T COG2183 728 RLDEE 732 (780)
T ss_pred eccCC
Confidence 97544
No 67
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=99.04 E-value=7.3e-10 Score=109.05 Aligned_cols=88 Identities=34% Similarity=0.649 Sum_probs=73.2
Q ss_pred EEEeCCCCEEEEEechh--------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc
Q 026794 31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ 97 (233)
Q Consensus 31 i~id~~~~~i~lS~k~~--------~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~ 97 (233)
|+++. ++.+.++.... ..+.+...+++|++|.|+ +||+||++. ++.+||+|+|+++|.++.
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 66764 56776665432 133455678999999999 999999998 489999999999999999
Q ss_pred CcccccCCCCEEEEEEEEEeCCCCeEEE
Q 026794 98 DIRDILNEGDEVRVKVIKIDREKSRITL 125 (233)
Q Consensus 98 ~~~~~~~~Gd~V~vkVi~vd~e~~ri~L 125 (233)
++.+.|++||.|+|+|+++|. +++++|
T Consensus 658 ~~~~~~kvGD~V~VkVi~id~-~gki~L 684 (684)
T TIGR03591 658 KVEDVLKEGDEVKVKVLEIDK-QGRIKL 684 (684)
T ss_pred ChhhccCCCCEEEEEEEEECC-CCCccC
Confidence 999999999999999999997 787764
No 68
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.00 E-value=1.1e-09 Score=77.04 Aligned_cols=58 Identities=21% Similarity=0.260 Sum_probs=51.8
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccc--ccCcccccCCCCEEEEEEEEEeCCCC
Q 026794 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREKS 121 (233)
Q Consensus 59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~--~~~~~~~~~~Gd~V~vkVi~vd~e~~ 121 (233)
|+++.|+ ++|+||+++ .+++|++|++++++++ ..++.+.|++||.|+|+|+++|.++.
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~-----~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~ 65 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLA-----DNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT 65 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeC-----CCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence 6788887 899999998 4899999999999985 78899999999999999999997543
No 69
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=99.00 E-value=1.1e-09 Score=74.10 Aligned_cols=56 Identities=45% Similarity=0.781 Sum_probs=52.2
Q ss_pred eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126 (233)
Q Consensus 66 ~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS 126 (233)
++|+||++. .+.+|++|.+++++.+..++.+.|++||.|+|+|+++|.+++++.||
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 47999999999999988888999999999999999999999998875
No 70
>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=98.98 E-value=3.7e-09 Score=75.95 Aligned_cols=61 Identities=34% Similarity=0.578 Sum_probs=54.3
Q ss_pred ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794 53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (233)
Q Consensus 53 ~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~ 127 (233)
...++.|+.++|+ +||+||++. .+.+||+|.|++. +.|++||+++++|.++ .+++++.||+
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 4568999999999 999999998 3799999999973 5599999999999999 7899999986
No 71
>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=98.97 E-value=3e-09 Score=79.93 Aligned_cols=65 Identities=31% Similarity=0.584 Sum_probs=56.9
Q ss_pred eeeEEEEEccCCCCccEEEEEEccccCcccccC-----------cccccCCCCEEEEEEEEEeCCC-----CeEEEEEec
Q 026794 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD-----------IRDILNEGDEVRVKVIKIDREK-----SRITLSIKQ 129 (233)
Q Consensus 66 ~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~-----------~~~~~~~Gd~V~vkVi~vd~e~-----~ri~LS~k~ 129 (233)
++|+||++. +++||+|++++++++... ....|++||.|+|+|.++|.+. .++.||+|+
T Consensus 12 ~~GifV~l~------~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i~ls~k~ 85 (99)
T cd04460 12 DFGAFVRIG------PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIGLTMRQ 85 (99)
T ss_pred eccEEEEEc------CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceEEEEEec
Confidence 999999996 599999999999887653 3477999999999999999764 589999999
Q ss_pred cccChhh
Q 026794 130 LEEDPLL 136 (233)
Q Consensus 130 ~~~dp~~ 136 (233)
....||.
T Consensus 86 ~~~g~~~ 92 (99)
T cd04460 86 PGLGKLE 92 (99)
T ss_pred CCCCcHH
Confidence 9999974
No 72
>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=98.89 E-value=7.6e-09 Score=86.00 Aligned_cols=129 Identities=22% Similarity=0.452 Sum_probs=87.2
Q ss_pred CCCCCCCCCCchhHhhhcc-cCCCCEEE-----EEEEEEeC-CCCEEEEEe----chhhHhhhccCCCCCCEEEEE----
Q 026794 1 MSPSHSCKEPQKSIHEIAK-GLTGSIIS-----VKVIQANE-EMKKLVFSE----KDAVWNKYSSRVNVEDIFVGR---- 65 (233)
Q Consensus 1 ~~~~~~~~~p~~~~~~~~~-~~vG~~v~-----~~Vi~id~-~~~~i~lS~----k~~~~~~~~~~~~~G~vv~g~---- 65 (233)
++|+++.+++.....+.++ .+.|+.+. +.|.++.. +.+++.-.- -......+.-+...|++++|+
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 4577776666655544433 34444332 34444433 344443111 011233344567789999999
Q ss_pred -eeeEEEEEccCCCCccEEEEEEccccCccccc-----------CcccccCCCCEEEEEEEEEe-----CCCCeEEEEEe
Q 026794 66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKID-----REKSRITLSIK 128 (233)
Q Consensus 66 -~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~-----------~~~~~~~~Gd~V~vkVi~vd-----~e~~ri~LS~k 128 (233)
++|+||+++ .++|++|.+++.+++.. +....|+.||.|+++|+++| ++..+|.+|+|
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 59999999999876542 23467999999999999998 56789999999
Q ss_pred ccccChh
Q 026794 129 QLEEDPL 135 (233)
Q Consensus 129 ~~~~dp~ 135 (233)
+...-|+
T Consensus 167 ~~~LG~~ 173 (179)
T TIGR00448 167 QPLLGKL 173 (179)
T ss_pred cCcCCcc
Confidence 9766664
No 73
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.80 E-value=6.1e-09 Score=98.26 Aligned_cols=98 Identities=18% Similarity=0.275 Sum_probs=79.8
Q ss_pred cccCCCCEEEEEEEEEeCCCCEEEEE-echh--------hHhhhccCCC--CCCEEEEE-----eeeEEEEEccCCCCcc
Q 026794 18 AKGLTGSIISVKVIQANEEMKKLVFS-EKDA--------VWNKYSSRVN--VEDIFVGR-----DYGAFIHLRFPDGLYH 81 (233)
Q Consensus 18 ~~~~vG~~v~~~Vi~id~~~~~i~lS-~k~~--------~~~~~~~~~~--~G~vv~g~-----~~G~fV~l~~~~~~~g 81 (233)
++..+|+.+.+.|...+ .+++.++ .|+. .++.++..|+ .|++++|+ ++|+||+++ +
T Consensus 85 ~~~~vGD~ie~~I~~~~--fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~~giiVDLg------g 156 (470)
T PRK09202 85 PDAEVGDYIEEEIESVD--FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLG------R 156 (470)
T ss_pred ccccCCCeEEEEEcccc--CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCEEEEEC------C
Confidence 44579999999998877 3444333 2332 2446777887 99999999 899999996 7
Q ss_pred EEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCC--eEEEEEec
Q 026794 82 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIKQ 129 (233)
Q Consensus 82 v~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~--ri~LS~k~ 129 (233)
++||+|.++++ |.+.|++||.|+|.|++++.+++ +|.||.+.
T Consensus 157 vea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~ 200 (470)
T PRK09202 157 AEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTH 200 (470)
T ss_pred eEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCc
Confidence 99999999985 78889999999999999999877 89999875
No 74
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.78 E-value=3.7e-08 Score=82.30 Aligned_cols=128 Identities=21% Similarity=0.433 Sum_probs=86.1
Q ss_pred CCCCCCCCCCchhHhhhccc-CCCCEE-----EEEEEEEeC-CCCEEEEEec----hhhHhhhccCCCCCCEEEEE----
Q 026794 1 MSPSHSCKEPQKSIHEIAKG-LTGSII-----SVKVIQANE-EMKKLVFSEK----DAVWNKYSSRVNVEDIFVGR---- 65 (233)
Q Consensus 1 ~~~~~~~~~p~~~~~~~~~~-~vG~~v-----~~~Vi~id~-~~~~i~lS~k----~~~~~~~~~~~~~G~vv~g~---- 65 (233)
++|+++.+++.....+.++. +.|+.+ -+.|++++. +.+++.-.-- .+....+..+...|+++.|+
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 35777766666555444433 334433 245555554 3444431111 11234445568899999999
Q ss_pred -eeeEEEEEccCCCCccEEEEEEccccCccccc-----------CcccccCCCCEEEEEEEEEeCCC-----CeEEEEEe
Q 026794 66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREK-----SRITLSIK 128 (233)
Q Consensus 66 -~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~-----------~~~~~~~~Gd~V~vkVi~vd~e~-----~ri~LS~k 128 (233)
++|+||+++ .++|++|.+++.+++.. +....+++||.|+++|.+++.+. .+|.+|++
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 999999996 59999999999876532 34567999999999999999754 38999999
Q ss_pred ccccCh
Q 026794 129 QLEEDP 134 (233)
Q Consensus 129 ~~~~dp 134 (233)
+.-.-+
T Consensus 167 ~~~LG~ 172 (187)
T PRK08563 167 QPGLGK 172 (187)
T ss_pred CCCCCc
Confidence 854444
No 75
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=98.73 E-value=7.8e-09 Score=97.41 Aligned_cols=76 Identities=29% Similarity=0.458 Sum_probs=69.4
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (233)
Q Consensus 55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~ 129 (233)
.+..|.+|+|+ +||+||+|. ++..||+|+|+|+..++.+|++.+++||.|.+|.++.|+ ++.+.+|.|.
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 56777888888 999999998 588999999999999999999999999999999999997 7788889999
Q ss_pred cccChhh
Q 026794 130 LEEDPLL 136 (233)
Q Consensus 130 ~~~dp~~ 136 (233)
+.++|-.
T Consensus 739 lLp~p~~ 745 (760)
T KOG1067|consen 739 LLPDPAT 745 (760)
T ss_pred hcCCccc
Confidence 9999954
No 76
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.73 E-value=3.8e-08 Score=85.26 Aligned_cols=70 Identities=27% Similarity=0.370 Sum_probs=62.6
Q ss_pred cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccc----cCcccccCCCCEEEEEEEEEeCCCCeEE
Q 026794 54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----QDIRDILNEGDEVRVKVIKIDREKSRIT 124 (233)
Q Consensus 54 ~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~----~~~~~~~~~Gd~V~vkVi~vd~e~~ri~ 124 (233)
..+++||+|.|+ ++|+||+|. .+..|++|+++++|.++ .++++.|++||.|+|+|++++. .+++.
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 456999999999 999999997 37899999999999987 7899999999999999999996 44699
Q ss_pred EEEec
Q 026794 125 LSIKQ 129 (233)
Q Consensus 125 LS~k~ 129 (233)
||+|+
T Consensus 133 LS~k~ 137 (235)
T PRK04163 133 LTLKG 137 (235)
T ss_pred EEEcC
Confidence 99975
No 77
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=98.71 E-value=9.4e-10 Score=98.65 Aligned_cols=100 Identities=13% Similarity=0.132 Sum_probs=84.0
Q ss_pred CCCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE------eeeEEE
Q 026794 1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR------DYGAFI 71 (233)
Q Consensus 1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~vv~g~------~~G~fV 71 (233)
|||.|. ++|+..+. +||++.|+|+.+|+++++|.||.|+. +|+.+...++.|++++|+ +||+|+
T Consensus 52 lS~~ri-~~i~d~vk------vGd~v~vkVl~VD~ekg~IdLS~K~v~~~pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~ 124 (319)
T PTZ00248 52 LSKRRI-RSINKLIR------VGRHEVVVVLRVDKEKGYIDLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSV 124 (319)
T ss_pred hccccc-CCHHHhcC------CCCEEEEEEEEEeCCCCEEEEEeeecccchHHHHHHhCcCCCEEEEEEEEchhhcCCCH
Confidence 578775 78887776 99999999999999999999999986 599999999999999999 699999
Q ss_pred E------EccCCCCccEEEEEEccccCcccccCcccccC---CCCEEEEE
Q 026794 72 H------LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILN---EGDEVRVK 112 (233)
Q Consensus 72 ~------l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~---~Gd~V~vk 112 (233)
+ .. +..++|.|+.++....+.++.+.|+ +++.+..+
T Consensus 125 eely~~i~~-----pl~~~~gh~y~af~~~v~~~~evl~~l~i~~ev~~~ 169 (319)
T PTZ00248 125 EELYTKIIW-----PLYKKYGHALDALKEALTNPDNVFEGLDIPEEVKES 169 (319)
T ss_pred HHHHHHHHH-----HHHHhcCCHHHHHHHHhcCchhhhccCCCCHHHHHH
Confidence 8 33 4789999999998888888877765 55544433
No 78
>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=98.68 E-value=1.1e-07 Score=66.48 Aligned_cols=59 Identities=17% Similarity=0.281 Sum_probs=49.7
Q ss_pred CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCC--CeEEEEE
Q 026794 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRITLSI 127 (233)
Q Consensus 57 ~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~--~ri~LS~ 127 (233)
+.|++++|+ ++|+||+++ +.+|++|.+|++. .+.|++||.++|.|++++.++ .+|.||.
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig------~~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lSr 67 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLG------KVEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILSR 67 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcC------CeEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence 468999998 889999996 5999999999973 456899999999999999654 4677773
No 79
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=98.61 E-value=1.1e-07 Score=68.84 Aligned_cols=70 Identities=24% Similarity=0.327 Sum_probs=64.2
Q ss_pred ccCCCCCCEEEEE----eeeEEEEEccCCCCccEEEEEE-ccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794 53 SSRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVH-VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (233)
Q Consensus 53 ~~~~~~G~vv~g~----~~G~fV~l~~~~~~~gv~Glv~-~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~ 127 (233)
..-+++|+++.|. +.|+||.|.+ ++++|+|. .+|++.+++.++.+.+ +|..+.|+|+.+|.++|.|.||.
T Consensus 11 y~~P~v~dvv~~Vv~i~d~~~YV~Lle----Y~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 11 YVFPNINEVTKGIVFVKDNIFYVKLID----YGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred EecCCCCeEEEEEEEEeccEEEEEEec----CccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence 4457899999987 9999999986 67999998 9999999999999999 99999999999999999999985
No 80
>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=98.60 E-value=1.8e-07 Score=92.80 Aligned_cols=70 Identities=27% Similarity=0.535 Sum_probs=59.6
Q ss_pred cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccc-----------cCcccccCCCCEEEEEEEEEe
Q 026794 54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKID 117 (233)
Q Consensus 54 ~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~-----------~~~~~~~~~Gd~V~vkVi~vd 117 (233)
-..++|++++|+ +||+||+|.+ ++++||+|+|+++++++ .+....|++||.|+|+|.++|
T Consensus 623 l~~~iG~~~~g~V~~v~~fGifV~L~~----~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd 698 (709)
T TIGR02063 623 MSEKIGEEFEGVISGVTSFGLFVELEN----NTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKAD 698 (709)
T ss_pred hhccCCcEEEEEEEEEEeCCEEEEecC----CceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEe
Confidence 345789999998 9999999973 36999999999997653 234567999999999999999
Q ss_pred CCCCeEEEEE
Q 026794 118 REKSRITLSI 127 (233)
Q Consensus 118 ~e~~ri~LS~ 127 (233)
.++++|.|++
T Consensus 699 ~~~~~I~~~l 708 (709)
T TIGR02063 699 LDTGKIDFEL 708 (709)
T ss_pred cccCeEEEEE
Confidence 9999999986
No 81
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=98.57 E-value=2.5e-08 Score=77.26 Aligned_cols=65 Identities=17% Similarity=0.080 Sum_probs=52.5
Q ss_pred CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC 225 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~ 225 (233)
|+.++|+++.+++ ||||++++.|=+||. ++...++.- .+||+|+|+|.++|. ++|++||+|+...
T Consensus 6 G~~l~GkItgI~~------yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~~~e 78 (129)
T COG1098 6 GSKLKGKITGITP------YGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRKLEE 78 (129)
T ss_pred cceEEEEEEeeEe------cceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcceehHHhhh
Confidence 3338899998885 589999999999993 455445433 689999999999997 9999999998765
No 82
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.53 E-value=3.2e-07 Score=75.93 Aligned_cols=82 Identities=27% Similarity=0.529 Sum_probs=65.4
Q ss_pred HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc----------C-cccccCCCCEEEEE
Q 026794 49 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ----------D-IRDILNEGDEVRVK 112 (233)
Q Consensus 49 ~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~----------~-~~~~~~~Gd~V~vk 112 (233)
...+.-++..|+++.|. +||+||.++ ..+||+|.|++.++++. . ...++++||.|++|
T Consensus 72 f~al~fkP~~gEVV~GeVv~~~~~G~fV~ig------p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~R 145 (183)
T COG1095 72 FRALVFKPFRGEVVEGEVVEVVEFGAFVRIG------PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRAR 145 (183)
T ss_pred EEEEEEEeccccEEEEEEEEEeecceEEEec------cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEE
Confidence 44556678889999998 999999997 69999999999988542 1 23369999999999
Q ss_pred EEEEeCCC-----CeEEEEEeccccC--hhh
Q 026794 113 VIKIDREK-----SRITLSIKQLEED--PLL 136 (233)
Q Consensus 113 Vi~vd~e~-----~ri~LS~k~~~~d--p~~ 136 (233)
|+..+... .+|.+++|+.-.. +|.
T Consensus 146 Iv~~s~~~~~~~~~~I~lTmrq~~LGklew~ 176 (183)
T COG1095 146 IVGVSLKSRRPRESKIGLTMRQPGLGKLEWI 176 (183)
T ss_pred EEEEecccCccccceEEEEeccccCCcchhh
Confidence 99998654 6899999985443 464
No 83
>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=98.53 E-value=2.7e-07 Score=83.96 Aligned_cols=98 Identities=16% Similarity=0.273 Sum_probs=73.4
Q ss_pred cccCCCCEEEEEEEEEeCCCCEEEEE-ech--------hhHhhhccCC--CCCCEEEEE-----eee-EEEEEccCCCCc
Q 026794 18 AKGLTGSIISVKVIQANEEMKKLVFS-EKD--------AVWNKYSSRV--NVEDIFVGR-----DYG-AFIHLRFPDGLY 80 (233)
Q Consensus 18 ~~~~vG~~v~~~Vi~id~~~~~i~lS-~k~--------~~~~~~~~~~--~~G~vv~g~-----~~G-~fV~l~~~~~~~ 80 (233)
++..+|+.+.+.+..-+ -+++.++ .|+ +.++.++..| +.|++++|+ +.| +||+++
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 55679999998875433 2333333 233 1255666677 599999999 546 699996
Q ss_pred cEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCC--CCeEEEEEec
Q 026794 81 HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDRE--KSRITLSIKQ 129 (233)
Q Consensus 81 gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e--~~ri~LS~k~ 129 (233)
+++|++|.+|.. +.+.|++||.++|.|++++.+ ..+|.||.+.
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 456699999999999999954 3579999875
No 84
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=98.49 E-value=1.4e-06 Score=76.01 Aligned_cols=100 Identities=15% Similarity=0.196 Sum_probs=78.4
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechhh-HhhhccCCCC---CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccC
Q 026794 22 TGSIISVKVIQANEEMKKLVFSEKDAV-WNKYSSRVNV---EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS 92 (233)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~~-~~~~~~~~~~---G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels 92 (233)
+|+.+-+. +.+|+.+ |+....+... .+......-. ++.++|+ ..|.||-+++ ++-||||-||.-
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-RIWGTLAIEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITEN-----GYLGFIHKSERF 189 (287)
T ss_pred CCCEEEEE-EEEccCC-cEEEEecchhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcC-----CeEEEEcchhhc
Confidence 89999999 8888765 7776665443 4445555444 8888888 8899999973 899999999963
Q ss_pred cccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhH
Q 026794 93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLE 137 (233)
Q Consensus 93 ~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~ 137 (233)
...+.||.++++|+.+.+ .++|.||++....+-.++
T Consensus 190 --------~~prlG~~l~~rVi~~re-Dg~lnLSl~p~~~E~l~~ 225 (287)
T COG2996 190 --------AEPRLGERLTARVIGVRE-DGKLNLSLRPRAHEMLDE 225 (287)
T ss_pred --------ccccCCceEEEEEEEEcc-CCeeecccccccHHhhhh
Confidence 336789999999999996 999999999876555443
No 85
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.47 E-value=2.3e-07 Score=85.02 Aligned_cols=98 Identities=16% Similarity=0.236 Sum_probs=71.6
Q ss_pred cccCCCCEEEEEEEEEeCCCCEEEEEechh--------hHhhhccCC--CCCCEEEEE-----eeeEEEEEccCCCCccE
Q 026794 18 AKGLTGSIISVKVIQANEEMKKLVFSEKDA--------VWNKYSSRV--NVEDIFVGR-----DYGAFIHLRFPDGLYHL 82 (233)
Q Consensus 18 ~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~--------~~~~~~~~~--~~G~vv~g~-----~~G~fV~l~~~~~~~gv 82 (233)
++..+|+.+.+.+...+..+ +...+.|+. ..+..+..| +.|++++|+ ++|+||+++ ++
T Consensus 85 ~~~~vGD~i~~~I~~~~fgR-~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg------~v 157 (362)
T PRK12327 85 PAYELGDVIEIEVTPKDFGR-IAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLG------KI 157 (362)
T ss_pred ccccCCCEEEEecCcCCCCh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeC------Ce
Confidence 45578999998876544322 111112221 245566777 999999999 889999996 79
Q ss_pred EEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCC--eEEEEEe
Q 026794 83 TGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIK 128 (233)
Q Consensus 83 ~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~--ri~LS~k 128 (233)
+|++|.+++. +.+.|++||.++|.|++++.+++ +|.||.-
T Consensus 158 Ea~LP~~E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt 199 (362)
T PRK12327 158 EAVLPPAEQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRT 199 (362)
T ss_pred EEEecHHHcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence 9999998874 36779999999999999996554 4666653
No 86
>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=98.44 E-value=2.6e-07 Score=65.75 Aligned_cols=61 Identities=16% Similarity=0.125 Sum_probs=49.7
Q ss_pred ccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccc--cccc----cccCceEEEEeecCCCCCEEEEEEc
Q 026794 155 SMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQG--FEKR----VVSQDLQLWLSNAPPSGKKFTLLAR 221 (233)
Q Consensus 155 ~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~--~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r 221 (233)
..++|+|.++. ++|+++++++||+|+. +++.. .+++ .+||.++++|.++|++++|++||.|
T Consensus 2 ~~V~g~V~~i~------~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 2 QEVTGFVNNVS------KEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CEEEEEEEEEe------CCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 34779999887 4578888899999995 56542 3333 6899999999999999999999986
No 87
>PRK11642 exoribonuclease R; Provisional
Probab=98.44 E-value=7e-07 Score=89.58 Aligned_cols=71 Identities=30% Similarity=0.511 Sum_probs=60.4
Q ss_pred CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc-----------CcccccCCCCEEEEEEEEEeCCC
Q 026794 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREK 120 (233)
Q Consensus 57 ~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~-----------~~~~~~~~Gd~V~vkVi~vd~e~ 120 (233)
++|++++|+ +||+||+|.+ .+++||||+++++++++. +....|++||.|+|+|.++|.++
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 689999998 9999999973 359999999999987432 23467999999999999999999
Q ss_pred CeEEEEEeccc
Q 026794 121 SRITLSIKQLE 131 (233)
Q Consensus 121 ~ri~LS~k~~~ 131 (233)
++|.|++-...
T Consensus 718 rkI~f~l~~~~ 728 (813)
T PRK11642 718 RKIDFSLISSE 728 (813)
T ss_pred CeEEEEEeccc
Confidence 99999996443
No 88
>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=98.43 E-value=2.7e-07 Score=65.83 Aligned_cols=60 Identities=7% Similarity=-0.096 Sum_probs=50.2
Q ss_pred CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc-------cccCceEEEEeecCCCCCEEEEE
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR-------VVSQDLQLWLSNAPPSGKKFTLL 219 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~-------~vg~~~~v~i~~~d~~~~ki~Ls 219 (233)
|..+.|+|.++.+ +|+|+.+.+|++|+. +++..+.++ .+||.++++|.++|.+++++.||
T Consensus 4 G~~V~g~V~~i~~------~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS 74 (74)
T cd05705 4 GQLLRGYVSSVTK------QGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCEEEEEEEEEeC------CcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 3347899999884 578888899999995 788775553 68999999999999999999986
No 89
>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=98.41 E-value=9.7e-07 Score=86.83 Aligned_cols=68 Identities=26% Similarity=0.485 Sum_probs=58.5
Q ss_pred CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccc-----------cCcccccCCCCEEEEEEEEEeCC
Q 026794 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDRE 119 (233)
Q Consensus 56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~-----------~~~~~~~~~Gd~V~vkVi~vd~e 119 (233)
-+.|++++|+ +||+||+|.+ ++++||||++++.|++. .+....|++||.|+|+|.++|.+
T Consensus 570 ~~iG~~~~g~I~~v~~~GifV~L~~----~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~ 645 (654)
T TIGR00358 570 DKVGTEFSGEISSVTRFGMFVRLDD----NGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNME 645 (654)
T ss_pred hCCCcEEEEEEEeEEcCcEEEEecC----CceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecc
Confidence 3679999998 9999999974 47999999999998752 22346799999999999999999
Q ss_pred CCeEEEEE
Q 026794 120 KSRITLSI 127 (233)
Q Consensus 120 ~~ri~LS~ 127 (233)
+++|.+++
T Consensus 646 ~~~I~f~l 653 (654)
T TIGR00358 646 TRSIIFEL 653 (654)
T ss_pred cCeEEEEE
Confidence 99999985
No 90
>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=98.40 E-value=1e-06 Score=65.54 Aligned_cols=74 Identities=22% Similarity=0.259 Sum_probs=58.0
Q ss_pred CCCCCEEEEE-----eeeEEEEEccCCC---CccEEEEEEccccCccccc--CcccccCCCCEEEEEEEEEeCCCCeEEE
Q 026794 56 VNVEDIFVGR-----DYGAFIHLRFPDG---LYHLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKIDREKSRITL 125 (233)
Q Consensus 56 ~~~G~vv~g~-----~~G~fV~l~~~~~---~~gv~Glv~~sels~~~~~--~~~~~~~~Gd~V~vkVi~vd~e~~ri~L 125 (233)
+++|++|.|+ ...+++++...++ .....|++|+|++...+.. ++.+.|++||.|+|||++++. .+.+.|
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 5788998888 5568888821111 0367899999999887776 789999999999999999984 566889
Q ss_pred EEecc
Q 026794 126 SIKQL 130 (233)
Q Consensus 126 S~k~~ 130 (233)
|+++-
T Consensus 83 st~~~ 87 (92)
T cd05791 83 STAEN 87 (92)
T ss_pred EecCC
Confidence 98763
No 91
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=98.38 E-value=5.5e-06 Score=72.36 Aligned_cols=172 Identities=16% Similarity=0.145 Sum_probs=112.6
Q ss_pred CCCCEEEEEEEEEeCCCCEEEEEechhhHhhhccCCCCCCEEEEE-eeeEEEEEccCCCCccEEEEEEccccCcccccCc
Q 026794 21 LTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI 99 (233)
Q Consensus 21 ~vG~~v~~~Vi~id~~~~~i~lS~k~~~~~~~~~~~~~G~vv~g~-~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~ 99 (233)
-+|++|++- +..|.+ +++.++.+.... ....+--+.++.-. +-|+|++.+ -.-+-++|.++++..+
T Consensus 45 evGdev~vF-iY~D~~-~rl~aTt~~p~~--tvg~~g~~~Vv~v~~~lGaFlD~G-----l~KDl~vp~~elp~~~---- 111 (287)
T COG2996 45 EVGDEVTVF-IYVDSE-DRLIATTREPKA--TVGEYGWLKVVEVNKDLGAFLDWG-----LPKDLLVPLDELPTLK---- 111 (287)
T ss_pred ccCcEEEEE-EEECCC-CceeheeecceE--eecceeEEEEEEEcCCcceEEecC-----CCcceeeehhhccccc----
Confidence 489999988 777854 456555543210 01122223344444 789999996 3478999999986531
Q ss_pred ccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcC--CCCeeeecCCccccCCeeeeccCCChhhhhhhh
Q 026794 100 RDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIP--QDGSVISDSSSMSSSNSNTIEPLPGLGAIFEEL 177 (233)
Q Consensus 100 ~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~--~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l 177 (233)
+-..++||.+-|.+ .+|. ++||.-.++. +.+.+..+...+. .+.. +.|+|-+.. ..|.|+
T Consensus 112 ~~wpq~Gd~l~v~l-~~Dk-k~Ri~g~~a~--~~~l~~l~~~~~~~l~nq~--------v~~tVYr~~------~~G~fv 173 (287)
T COG2996 112 SLWPQKGDKLLVYL-YVDK-KGRIWGTLAI--EKILENLATPAYNNLKNQE--------VDATVYRLL------ESGTFV 173 (287)
T ss_pred ccCCCCCCEEEEEE-EEcc-CCcEEEEecc--hhHHHhcCCccchhhhcCe--------eeeEEEEEe------ccceEE
Confidence 23478999998775 5675 5577765542 2222222222111 1222 556766654 345555
Q ss_pred cccCCeeEEEeeccccccccccCceEEEEeecCCCCCEEEEEEcccc
Q 026794 178 LQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGR 224 (233)
Q Consensus 178 ~~~~gv~gl~~~~~~~~~~~vg~~~~v~i~~~d~~~~ki~Ls~r~~~ 224 (233)
-.++|.-|++....+..+|.+|+.++.+|..+.. |++++||.|...
T Consensus 174 ~~e~~~~GfIh~sEr~~~prlG~~l~~rVi~~re-Dg~lnLSl~p~~ 219 (287)
T COG2996 174 ITENGYLGFIHKSERFAEPRLGERLTARVIGVRE-DGKLNLSLRPRA 219 (287)
T ss_pred EEcCCeEEEEcchhhcccccCCceEEEEEEEEcc-CCeeeccccccc
Confidence 5599999998888888889999999999999775 999999997543
No 92
>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=98.23 E-value=1.6e-06 Score=61.18 Aligned_cols=59 Identities=8% Similarity=0.063 Sum_probs=47.0
Q ss_pred cc-CCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEE
Q 026794 157 SS-SNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLA 220 (233)
Q Consensus 157 ~~-g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~ 220 (233)
++ |+|+++. .++|+++++.+|++|+. +++.+.+.+ .+||+++++|.++|+++++|+||.
T Consensus 4 ~~~g~V~~v~-----~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 4 VDSVKVTKVE-----PDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred eeeeEEEEEc-----cCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 44 7887762 15688899999999995 556555544 689999999999999999999984
No 93
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.18 E-value=1.4e-06 Score=75.62 Aligned_cols=85 Identities=26% Similarity=0.437 Sum_probs=76.1
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (233)
Q Consensus 55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~ 129 (233)
.+.++++|-+. +.|+||.|-+++ .++|+|-.||||.+|+.++....++|..=.|.|+.+|.++|.|.||.+.
T Consensus 13 yPev~e~VmvnV~sIaemGayv~LlEYn---niEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrr 89 (304)
T KOG2916|consen 13 YPEVEEIVMVNVRSIAEMGAYVKLLEYN---NIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRR 89 (304)
T ss_pred CCCcccEEEEEeeEehhccceEeeeecC---CcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhcc
Confidence 35778888776 899999998876 6999999999999999999999999999999999999999999999999
Q ss_pred cccChhhHHhhhh
Q 026794 130 LEEDPLLETLEKV 142 (233)
Q Consensus 130 ~~~dp~~~~~~~~ 142 (233)
+.++.-.++.+++
T Consensus 90 Vs~ed~~kC~Er~ 102 (304)
T KOG2916|consen 90 VSPEDKEKCEERF 102 (304)
T ss_pred CCHHHHHHHHHHH
Confidence 9887766666665
No 94
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.14 E-value=4.3e-06 Score=59.69 Aligned_cols=64 Identities=17% Similarity=0.051 Sum_probs=49.9
Q ss_pred CccccCCeeeeccCCChhhhhhhhccc-CCeeEEE----eeccccccccccCceEEEEeecCCCCCEEEEEEcccce
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQE-DGIDDVR----ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRC 225 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~-~gv~gl~----~~~~~~~~~~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~ 225 (233)
|..+.|.|.++++ +|+++++. +|++|+. +++. +.=.+||.+.++|.++|.+++++.||.|+.+.
T Consensus 5 G~~v~g~V~si~d------~G~~v~~g~~gv~Gfl~~~~~~~~--~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~~ 73 (74)
T cd05694 5 GMVLSGCVSSVED------HGYILDIGIPGTTGFLPKKDAGNF--SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73 (74)
T ss_pred CCEEEEEEEEEeC------CEEEEEeCCCCcEEEEEHHHCCcc--cccCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence 3347899998884 57778776 6899995 4442 11267999999999999999999999997654
No 95
>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=98.10 E-value=4.7e-06 Score=58.09 Aligned_cols=60 Identities=8% Similarity=0.087 Sum_probs=48.4
Q ss_pred cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEc
Q 026794 156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLAR 221 (233)
Q Consensus 156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r 221 (233)
.+.|+|..+.+ +|+++++.++++|+. +++++..++ .+||.+++++.++|++.+++.||.|
T Consensus 3 ~~~g~V~~v~~------~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k 70 (70)
T cd05698 3 KTHGTIVKVKP------NGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred EEEEEEEEEec------CcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 36788888874 578888899999995 555444433 6799999999999999999999975
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=98.07 E-value=4.8e-06 Score=58.03 Aligned_cols=58 Identities=9% Similarity=0.078 Sum_probs=47.9
Q ss_pred cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794 156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLL 219 (233)
Q Consensus 156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls 219 (233)
.++|+|..+. ++|+++++++|++|+. ++++...++ .+||.+++++.++|.+++++.||
T Consensus 3 ~v~g~V~~v~------~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls 68 (69)
T cd05697 3 VVKGTIRKLR------PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLT 68 (69)
T ss_pred EEEEEEEEEe------ccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence 3678998887 4588888899999995 666655443 67999999999999999999987
No 97
>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=97.98 E-value=1e-05 Score=57.17 Aligned_cols=61 Identities=10% Similarity=0.030 Sum_probs=48.7
Q ss_pred CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEc
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLAR 221 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r 221 (233)
|..+.|+|.++.+ .+++|+++.+|.+|+. +++++++++ .+||.+++++.+++. +|+.||.|
T Consensus 4 G~iv~G~V~~i~~-----~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~--~~i~LSl~ 72 (72)
T cd05704 4 GAVTLGMVTKVIP-----HSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLSLR 72 (72)
T ss_pred CCEEEEEEEEeeC-----CcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEEEEeC
Confidence 3447899999874 3577888899999994 777777665 579999999988874 89999986
No 98
>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=97.98 E-value=1.5e-05 Score=56.03 Aligned_cols=62 Identities=8% Similarity=0.025 Sum_probs=49.1
Q ss_pred CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEc
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLAR 221 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r 221 (233)
|..+.|.|..+.+ +++++++++|++|+. ++++..+++ .+||.+++++.++|.+++++.||.|
T Consensus 4 G~iv~g~V~~v~~------~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~ 73 (73)
T cd05706 4 GDILPGRVTKVND------RYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCEEEEEEEEEeC------CeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 3347799988874 577888899999994 555544332 6899999999999999999999975
No 99
>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=97.96 E-value=1.3e-05 Score=56.36 Aligned_cols=59 Identities=8% Similarity=0.143 Sum_probs=47.3
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEc
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLAR 221 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r 221 (233)
++|+|..+.++ +.++++..|++|+. +++.....+ .+||.+++++.++|.+++++.||.|
T Consensus 8 v~g~V~~v~~~------g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k 74 (74)
T PF00575_consen 8 VEGKVTSVEDF------GVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp EEEEEEEEETT------EEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred EEEEEEEEECC------EEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 77999998854 67788889999995 443322223 6899999999999999999999986
No 100
>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=97.94 E-value=8.4e-06 Score=56.62 Aligned_cols=58 Identities=10% Similarity=0.045 Sum_probs=47.0
Q ss_pred cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794 156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLL 219 (233)
Q Consensus 156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls 219 (233)
.+.|.|.++.+ +++++++.++++|+. ++++..+++ .+||.+++++.++|++.+++.||
T Consensus 3 ~v~g~V~~v~~------~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls 68 (68)
T cd05707 3 VVRGFVKNIAN------NGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred EEEEEEEEEEC------ccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 36788888874 578888899999995 555555544 68999999999999999999876
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=97.92 E-value=1.6e-05 Score=57.49 Aligned_cols=64 Identities=11% Similarity=0.059 Sum_probs=51.8
Q ss_pred cCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCC
Q 026794 143 IPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGK 214 (233)
Q Consensus 143 ~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ 214 (233)
++.|++ +.|+|..+.+ +++|+++.+|++|+. +++++..++ .+||+++|+|.++|.+++
T Consensus 12 ~~~G~i--------~~g~V~~v~~------~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~ 77 (83)
T cd04461 12 LKPGMV--------VHGYVRNITP------YGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQ 77 (83)
T ss_pred CCCCCE--------EEEEEEEEee------ceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCC
Confidence 566777 6799998885 577888899999994 666655444 579999999999999999
Q ss_pred EEEEEE
Q 026794 215 KFTLLA 220 (233)
Q Consensus 215 ki~Ls~ 220 (233)
++.||+
T Consensus 78 ~i~lsl 83 (83)
T cd04461 78 RFLLSL 83 (83)
T ss_pred EEEEeC
Confidence 999984
No 102
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.86 E-value=1.3e-05 Score=55.43 Aligned_cols=57 Identities=18% Similarity=0.139 Sum_probs=44.8
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eec-cccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITR-QGFEKR----VVSQDLQLWLSNAPPSGKKFTLL 219 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~-~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls 219 (233)
+.|.|..+.++ |.|+++++|++|+. ++| .+..++ .+||.+++++.++|.+++|++|+
T Consensus 4 ~~g~V~~i~~~------G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 4 VSGKIKSITDF------GIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred EEEEEEEEEee------eEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence 66888888754 77888899999995 443 233333 68999999999999999999875
No 103
>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=97.85 E-value=2.4e-05 Score=54.19 Aligned_cols=59 Identities=10% Similarity=0.054 Sum_probs=45.8
Q ss_pred cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc--cccCceEEEEeecCCCCCEEEEEEc
Q 026794 156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR--VVSQDLQLWLSNAPPSGKKFTLLAR 221 (233)
Q Consensus 156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~--~vg~~~~v~i~~~d~~~~ki~Ls~r 221 (233)
.++|+|.++.+ .|.++++ +|++|+. +++...+.+ .+||.++++|.++|.+++++.||.|
T Consensus 3 iv~g~V~~v~~------~G~~v~l-~g~~gfip~s~~~~~~~~~~~~~vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 3 IVEGKVTEKVK------GGLIVDI-EGVRAFLPASQVDLRPVEDLDEYVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred EEEEEEEEEEC------CeEEEEE-CCEEEEEEHHHCCCcccCChHHhCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 36788888874 4677777 7999995 444443322 5899999999999999999999975
No 104
>PRK08582 hypothetical protein; Provisional
Probab=97.84 E-value=3.1e-05 Score=61.93 Aligned_cols=63 Identities=10% Similarity=0.056 Sum_probs=49.9
Q ss_pred cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794 156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC 225 (233)
Q Consensus 156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~ 225 (233)
.+.|.|+.+++ +++|+++.+|++|+. +++..+... .+||.++|+|.+++. +++|.||.++...
T Consensus 8 iv~G~V~~I~~------fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~~~~ 78 (139)
T PRK08582 8 KLQGKVTGITN------FGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKKAKD 78 (139)
T ss_pred EEEEEEEEEEC------CeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEeccc
Confidence 37799999885 478888899999994 555555433 579999999999997 4899999987543
No 105
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.82 E-value=2e-05 Score=54.77 Aligned_cols=58 Identities=12% Similarity=-0.003 Sum_probs=44.6
Q ss_pred cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc--cccCceEEEEeecCCCCCEEEEE
Q 026794 156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR--VVSQDLQLWLSNAPPSGKKFTLL 219 (233)
Q Consensus 156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~--~vg~~~~v~i~~~d~~~~ki~Ls 219 (233)
.++|+|.++.+ +|+++++.+|++|+. ++..+.... .+||+++++|..+|++++++.||
T Consensus 3 ~V~g~V~~i~~------~G~~v~l~~~v~g~v~~~~l~~~~~~~~~~~~G~~i~~kVi~id~~~~~i~LS 66 (66)
T cd05695 3 LVNARVKKVLS------NGLILDFLSSFTGTVDFLHLDPEKSSKSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred EEEEEEEEEeC------CcEEEEEcCCceEEEEHHHcCCccCcccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 36789988874 578888888999995 333222211 68999999999999999999886
No 106
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.75 E-value=0.0001 Score=61.20 Aligned_cols=123 Identities=16% Similarity=0.202 Sum_probs=75.0
Q ss_pred CCCCCCCCCCchhHhhhcc-cCCCCEE-----EEEEEEEeC-CCCEEEEEech----hhHhhhccCCCCCCEEEEE----
Q 026794 1 MSPSHSCKEPQKSIHEIAK-GLTGSII-----SVKVIQANE-EMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR---- 65 (233)
Q Consensus 1 ~~~~~~~~~p~~~~~~~~~-~~vG~~v-----~~~Vi~id~-~~~~i~lS~k~----~~~~~~~~~~~~G~vv~g~---- 65 (233)
|.|+++..+......+.++ .+.|+.+ -+.|++++. +.+++.-.--. .....+.-++..|++++|+
T Consensus 13 i~P~~f~~~~~~~i~~~L~~~~egkv~~~~GliV~v~di~~i~~G~I~~gdG~~~~~V~FraivFrPf~gEVv~g~V~~v 92 (176)
T PTZ00162 13 LKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDV 92 (176)
T ss_pred ECHHHcCccHHHHHHHHHHHHHCCCCcCcccEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEEecCCCCEEEEEEEEE
Confidence 3566666555555544443 2334322 234444433 33444321111 1234556678999999999
Q ss_pred -eeeEEEEEccCCCCccEEEEEEccccCcccc------------cCcccccCCCCEEEEEEEEEeCCCC--eEEEEEec
Q 026794 66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI------------QDIRDILNEGDEVRVKVIKIDREKS--RITLSIKQ 129 (233)
Q Consensus 66 -~~G~fV~l~~~~~~~gv~Glv~~sels~~~~------------~~~~~~~~~Gd~V~vkVi~vd~e~~--ri~LS~k~ 129 (233)
++|+||.++ ..++|+|.+.+..+.. .+-...++.|+.|++||..+..+.+ ++..++|+
T Consensus 93 ~~~G~~v~~G------p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~~i~T~~~ 165 (176)
T PTZ00162 93 NKLGFFAQAG------PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLFAIATINS 165 (176)
T ss_pred ecceEEEEee------CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcEEEEEecC
Confidence 999999997 6889999999974321 1123468999999999988865433 34445544
No 107
>PRK07252 hypothetical protein; Provisional
Probab=97.74 E-value=4.3e-05 Score=59.62 Aligned_cols=66 Identities=14% Similarity=0.061 Sum_probs=52.3
Q ss_pred CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC 225 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~ 225 (233)
|..+.|.|+.+.+ +|+|+++.++++|+. +++.++..+ .+||.++|+|.++|.+.+++.||.+....
T Consensus 4 G~iv~G~V~~V~~------~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~ 77 (120)
T PRK07252 4 GDKLKGTITGIKP------YGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEE 77 (120)
T ss_pred CCEEEEEEEEEeC------cEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeeccc
Confidence 3347799998875 477888899999994 565555444 68999999999999999999999986543
No 108
>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=97.68 E-value=7.2e-05 Score=52.73 Aligned_cols=62 Identities=8% Similarity=0.044 Sum_probs=47.7
Q ss_pred ccccCCeeeeccCCChhhhhhhhccc--CCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcc
Q 026794 155 SMSSSNSNTIEPLPGLGAIFEELLQE--DGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARA 222 (233)
Q Consensus 155 ~~~~g~v~~v~~~~g~~~~~~~l~~~--~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~ 222 (233)
..+.|+|..+.+ +++++++. +|++|+. +++++...+ .+||.+++++.++|.+++++.||.|+
T Consensus 5 ~~~~g~V~~v~~------~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~ 76 (76)
T cd04452 5 ELVVVTVKSIAD------MGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CEEEEEEEEEEc------cEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 336799988874 46777776 3699994 555554433 58999999999999999999999874
No 109
>PRK05054 exoribonuclease II; Provisional
Probab=97.68 E-value=0.00015 Score=71.45 Aligned_cols=65 Identities=14% Similarity=0.111 Sum_probs=52.5
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcc--cc-c--C-------cccccCCCCEEEEEEEEEeCCCC
Q 026794 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD--LI-Q--D-------IRDILNEGDEVRVKVIKIDREKS 121 (233)
Q Consensus 59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~--~~-~--~-------~~~~~~~Gd~V~vkVi~vd~e~~ 121 (233)
|+.+.|. +||+||+|.. .+++||||++.+..+ +. - + -...|+.||.|+|+|.++|.+++
T Consensus 562 ~~~f~g~I~~v~~~G~fV~l~~----~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~ 637 (644)
T PRK05054 562 DTRFAAEIIDISRGGMRVRLLE----NGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETR 637 (644)
T ss_pred CeEEEEEEEeeecCcEEEEEeC----CceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccC
Confidence 4488887 9999999974 589999999999653 11 1 1 12469999999999999999999
Q ss_pred eEEEEE
Q 026794 122 RITLSI 127 (233)
Q Consensus 122 ri~LS~ 127 (233)
+|.+.+
T Consensus 638 ~i~~~~ 643 (644)
T PRK05054 638 SIIARP 643 (644)
T ss_pred eEEEEE
Confidence 999865
No 110
>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=97.68 E-value=7e-05 Score=52.24 Aligned_cols=62 Identities=15% Similarity=0.283 Sum_probs=48.8
Q ss_pred cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794 156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG 223 (233)
Q Consensus 156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~ 223 (233)
.+.|+|..+.+ .+.++++.++++|+. ++.+...++ .+||.+++++.++|.+++++.||.|..
T Consensus 3 ~v~g~V~~v~~------~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~ 72 (73)
T cd05691 3 IVTGKVTEVDA------KGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK 72 (73)
T ss_pred EEEEEEEEEEC------CeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence 36788888874 477788889999995 444444333 589999999999999999999998764
No 111
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.67 E-value=5.9e-05 Score=52.80 Aligned_cols=57 Identities=5% Similarity=0.070 Sum_probs=43.7
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecc-ccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQ-GFEKR----VVSQDLQLWLSNAPPSGKKFTLL 219 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~-~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls 219 (233)
..|.|..+.++ |.|+++.+|++|+. ++|. ...++ .+||.++|++.++|.+++++.|+
T Consensus 7 ~~g~V~~i~~~------G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 7 LFGKVTNLTDY------GCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred EEEEEEEEEee------EEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence 67999988854 77788899999994 4432 11111 67999999999999999999764
No 112
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=97.67 E-value=0.00041 Score=57.66 Aligned_cols=75 Identities=28% Similarity=0.331 Sum_probs=59.3
Q ss_pred hccCCCCCCEEEEE-----eeeEEEEEccCCCC-----ccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCC
Q 026794 52 YSSRVNVEDIFVGR-----DYGAFIHLRFPDGL-----YHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS 121 (233)
Q Consensus 52 ~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~-----~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ 121 (233)
....++.|++|-|. .-.+.|++.+.++- ....|-+|+|+++..++++.++.|++||.|+|+|++.- .
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 45678999999998 55677777654331 12578899999999999999999999999999999973 4
Q ss_pred eEEEEEec
Q 026794 122 RITLSIKQ 129 (233)
Q Consensus 122 ri~LS~k~ 129 (233)
.+.||.+.
T Consensus 135 ~~~Lst~~ 142 (188)
T COG1096 135 PIQLSTKG 142 (188)
T ss_pred CeEEEecC
Confidence 46777654
No 113
>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=97.62 E-value=8.1e-05 Score=52.58 Aligned_cols=59 Identities=7% Similarity=0.007 Sum_probs=45.9
Q ss_pred CccccCCeeeeccCCChhhhhhhhcccCC--eeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEE
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDG--IDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLA 220 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~g--v~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~ 220 (233)
|...+|+|+++.+ +|+|+++ +| ++|+. ++++++.++ .+||++.|++.++|.++ |++||.
T Consensus 4 g~~~~g~V~~i~~------fG~fv~l-~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~ 72 (73)
T cd05686 4 YQIFKGEVASVTE------YGAFVKI-PGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL 72 (73)
T ss_pred CCEEEEEEEEEEe------eeEEEEE-CCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence 3447799998885 4778887 45 68883 777766554 57999999999999976 899885
No 114
>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=97.60 E-value=0.00011 Score=51.66 Aligned_cols=64 Identities=9% Similarity=0.074 Sum_probs=48.6
Q ss_pred CccccCCeeeeccCCChhhhhhhhcccC-CeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG 223 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~-gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~ 223 (233)
|..+.|.|..+.++ ++|+++.+ +++|+. +++++...+ .+||.+++++.++|.+++++.|+.|+.
T Consensus 3 g~~v~g~V~~i~~~------g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~ 75 (77)
T cd05708 3 GQKIDGTVRRVEDY------GVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred CCEEEEEEEEEEcc------eEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence 33477999888754 67777774 799995 444443322 689999999999999999999998863
No 115
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.58 E-value=9.6e-05 Score=72.96 Aligned_cols=59 Identities=17% Similarity=0.111 Sum_probs=47.1
Q ss_pred CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----ee----ccccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----IT----RQGFEKR----VVSQDLQLWLSNAPPSGKKFTLL 219 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~----~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls 219 (233)
|..++|+|+++. +||+|+++.+|++||. ++ +.++.++ .+||+++|+|.++| +++|++|+
T Consensus 648 G~i~~GkV~~I~------dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID-~~gKI~L~ 718 (719)
T TIGR02696 648 GERFLGTVVKTT------AFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADID-DRGKLSLV 718 (719)
T ss_pred CCEEEEEEEEEE------CceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEEC-CCCCeeec
Confidence 444789999998 4588899999999994 43 3456555 57999999999999 47899986
No 116
>PRK05807 hypothetical protein; Provisional
Probab=97.58 E-value=0.00013 Score=58.19 Aligned_cols=60 Identities=7% Similarity=0.010 Sum_probs=47.5
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR 224 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~ 224 (233)
++|+|..+.++ |+|+++ +|.+|+. +++..+... .+||.++|+|.+++. +++|.||.|+..
T Consensus 9 v~G~Vt~i~~~------GafV~L-~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~~~ 76 (136)
T PRK05807 9 LEGTVVNITNF------GAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQAM 76 (136)
T ss_pred EEEEEEEEECC------eEEEEE-CCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEecc
Confidence 77999988754 777888 6889994 555444333 689999999999998 799999998754
No 117
>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=97.54 E-value=0.00029 Score=49.98 Aligned_cols=64 Identities=19% Similarity=0.222 Sum_probs=50.6
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccC--cccccCCCCEE-EEEEEEEeCCCCeEEEEEe
Q 026794 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD--IRDILNEGDEV-RVKVIKIDREKSRITLSIK 128 (233)
Q Consensus 59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~--~~~~~~~Gd~V-~vkVi~vd~e~~ri~LS~k 128 (233)
|++++|+ +-+++|++.+ .++.|++|...+|++.-++ .-..+++||++ .+.|+ +...+.|.||.|
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 6778887 6679999984 4899999999999933333 23348899999 99999 777888888865
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=97.47 E-value=0.00018 Score=49.09 Aligned_cols=58 Identities=9% Similarity=0.130 Sum_probs=45.3
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEc
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLAR 221 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r 221 (233)
+.|+|..+.+ +++|+++.++++|+. ++++.+.++ .+||.+++++.+++. ++++.||.|
T Consensus 4 ~~g~V~~i~~------~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~-~~~i~ls~k 69 (69)
T cd05692 4 VEGTVTRLKP------FGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK 69 (69)
T ss_pred EEEEEEEEEe------eeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence 5688888774 477888899999994 444443332 579999999999998 889999875
No 119
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=97.45 E-value=0.00075 Score=49.73 Aligned_cols=58 Identities=17% Similarity=0.236 Sum_probs=46.0
Q ss_pred CCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCc-----------ccccCCCCEEEEEEEEEeCCCC
Q 026794 58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-----------RDILNEGDEVRVKVIKIDREKS 121 (233)
Q Consensus 58 ~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~-----------~~~~~~Gd~V~vkVi~vd~e~~ 121 (233)
.|++++|+ ++|+||.++ ++++|+|.+.+..+...++ ...++.|+.|++||+.+..+.+
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G------pl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~ 74 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG------PLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDAT 74 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc------CceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccC
Confidence 47889998 999999997 7999999998876544332 3448899999999999876543
No 120
>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=97.44 E-value=0.0002 Score=49.82 Aligned_cols=60 Identities=7% Similarity=0.067 Sum_probs=46.5
Q ss_pred cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEc
Q 026794 156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLAR 221 (233)
Q Consensus 156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r 221 (233)
.++|+|.++.+ .++++++..+++|+. +++...+.+ .+||.++++|.+++.+++++.||.+
T Consensus 3 iv~g~V~~i~~------~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 3 IVKGTVVSVDD------DEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred EEEEEEEEEeC------CEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 36789888874 477888888899994 444433323 6799999999999988999999875
No 121
>PRK08059 general stress protein 13; Validated
Probab=97.44 E-value=0.00024 Score=55.55 Aligned_cols=68 Identities=13% Similarity=0.116 Sum_probs=53.2
Q ss_pred cCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCC
Q 026794 143 IPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGK 214 (233)
Q Consensus 143 ~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ 214 (233)
++.|++ +.|.|..+.+ +|+++++.++++|+. ++++.+.++ .+||.++|+|.++|.+++
T Consensus 5 ~k~G~i--------v~G~V~~i~~------~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~ 70 (123)
T PRK08059 5 YEVGSV--------VTGKVTGIQP------YGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKG 70 (123)
T ss_pred CCCCCE--------EEEEEEEEec------ceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCC
Confidence 455666 6799988875 477888899999995 444444333 579999999999999999
Q ss_pred EEEEEEcccc
Q 026794 215 KFTLLARAGR 224 (233)
Q Consensus 215 ki~Ls~r~~~ 224 (233)
++.||.|...
T Consensus 71 ~i~lslk~~~ 80 (123)
T PRK08059 71 KISLSIRATE 80 (123)
T ss_pred eEEEEEEEcc
Confidence 9999998653
No 122
>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=97.43 E-value=0.00036 Score=65.28 Aligned_cols=59 Identities=29% Similarity=0.469 Sum_probs=48.9
Q ss_pred ccCCCCCCEEEEE-----ee--eEEEEEccCCCCccEEEEEEccccCcc------------cccCcccccCCCCEEEEEE
Q 026794 53 SSRVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKV 113 (233)
Q Consensus 53 ~~~~~~G~vv~g~-----~~--G~fV~l~~~~~~~gv~Glv~~sels~~------------~~~~~~~~~~~Gd~V~vkV 113 (233)
.....+|++|.|+ ++ ||||+++ .+-.||+|++++.+. +..++.+.+++||.|.|+|
T Consensus 20 ~~~~~vGnIY~GrV~~i~p~l~aAFVdiG-----~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV 94 (414)
T TIGR00757 20 KSRQLKGNIYKGRVTRILPSLQAAFVDIG-----LEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQV 94 (414)
T ss_pred cCcCCCCCEEEEEEeeecCCCceEEEEcC-----CCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEE
Confidence 4456799999999 66 8999998 478999999999763 2345677899999999999
Q ss_pred EEE
Q 026794 114 IKI 116 (233)
Q Consensus 114 i~v 116 (233)
..-
T Consensus 95 ~Ke 97 (414)
T TIGR00757 95 VKE 97 (414)
T ss_pred eeC
Confidence 983
No 123
>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=97.42 E-value=0.00016 Score=49.31 Aligned_cols=57 Identities=5% Similarity=-0.063 Sum_probs=44.1
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLL 219 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls 219 (233)
..|+|+.+.+ +|.|+++.++++|+. +++....++ .+||.++|++.++|.+++++.||
T Consensus 4 ~~g~V~~i~~------~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 4 LEGVVTNVTD------FGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred EEEEEEEEec------ccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 5688888875 477788899999995 443333222 67999999999999999999875
No 124
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.40 E-value=0.00018 Score=72.53 Aligned_cols=60 Identities=13% Similarity=0.083 Sum_probs=50.5
Q ss_pred c-cCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794 157 S-SSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG 223 (233)
Q Consensus 157 ~-~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~ 223 (233)
+ .|+|+++. +||+|+++.+|++||. ++|+++..+ .+||.++|++.++|. ++||+||.|+.
T Consensus 757 y~~g~V~~I~------~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~grI~LSlK~l 825 (891)
T PLN00207 757 YRNCEIKSIA------PYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQLRLSRRAL 825 (891)
T ss_pred EECcEEEEEe------ccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC-CCcEEEEEecc
Confidence 5 36888887 5588899999999994 888877666 579999999999997 78999999874
No 125
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.33 E-value=0.00079 Score=58.11 Aligned_cols=98 Identities=23% Similarity=0.330 Sum_probs=72.3
Q ss_pred CCCEEEEEEEEE-eCCCCEEEEEechhhHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccc
Q 026794 22 TGSIISVKVIQA-NEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL 95 (233)
Q Consensus 22 vG~~v~~~Vi~i-d~~~~~i~lS~k~~~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~ 95 (233)
-|+++...+... +..++.+.+=. .+. ...++.||+|-|+ ..+..|+|.. ...+++|.|++-++.
T Consensus 32 ~~~~iyssv~G~~~~~~~~v~VIp----l~g-~YiP~~gD~VIG~I~~v~~~~W~VDI~s-----p~~A~L~ls~~~~r~ 101 (239)
T COG1097 32 EGGKIYSSVVGLLDVKGKLVRVIP----LEG-RYIPEVGDVVIGKIIEVGPSGWKVDIGS-----PYPALLSLSDFLRRK 101 (239)
T ss_pred cCCEEEEEEEeEEEEeCCEEEEEe----CCC-cccCCCCCEEEEEEEEEcccceEEEcCC-----ccceEeehhhhhccc
Confidence 566666666542 32233332221 222 3457899999998 8899999983 689999999997766
Q ss_pred c----cCcccccCCCCEEEEEEEEEeCCCCeEEEEEecc
Q 026794 96 I----QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (233)
Q Consensus 96 ~----~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~ 130 (233)
+ .+++.+|++||-|.|+|.++|. .+...|++|..
T Consensus 102 ~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~L~~k~~ 139 (239)
T COG1097 102 FENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVELTLKDE 139 (239)
T ss_pred ccccccccccccccCCEEEEEEEEccC-CCceEEEeecC
Confidence 4 4688899999999999999996 78889988543
No 126
>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=97.31 E-value=0.00026 Score=53.39 Aligned_cols=63 Identities=16% Similarity=0.075 Sum_probs=48.9
Q ss_pred CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecccc----------------------ccc-cccCceEEEE
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGF----------------------EKR-VVSQDLQLWL 206 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~----------------------~~~-~vg~~~~v~i 206 (233)
|..+.|+|..+.++ +.++.+..|++|+. +++.+. .+. .+||.+.++|
T Consensus 4 G~vV~G~V~~v~~~------gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kV 77 (100)
T cd05693 4 GMLVLGQVKEITKL------DLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKV 77 (100)
T ss_pred CCEEEEEEEEEcCC------CEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEE
Confidence 44478999998754 67778899999994 665331 111 6899999999
Q ss_pred eecCCC---CCEEEEEEcc
Q 026794 207 SNAPPS---GKKFTLLARA 222 (233)
Q Consensus 207 ~~~d~~---~~ki~Ls~r~ 222 (233)
.++|.+ +++|.||.|.
T Consensus 78 i~~d~~~~~~~~i~LSlr~ 96 (100)
T cd05693 78 VSLDKSKSGKKRIELSLEP 96 (100)
T ss_pred EEccCCcCCCcEEEEEecH
Confidence 999997 7899999985
No 127
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=97.24 E-value=0.00049 Score=49.12 Aligned_cols=61 Identities=10% Similarity=0.048 Sum_probs=46.4
Q ss_pred cccCCeeeeccCCChhhhhhhhccc---CCeeEEE----eecccc-ccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794 156 MSSSNSNTIEPLPGLGAIFEELLQE---DGIDDVR----ITRQGF-EKR----VVSQDLQLWLSNAPPSGKKFTLLARAG 223 (233)
Q Consensus 156 ~~~g~v~~v~~~~g~~~~~~~l~~~---~gv~gl~----~~~~~~-~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~ 223 (233)
.+.|.|+.+.++ ++|+++. .|++|+. +++++. .++ .+||+++|++.++| .+++.+|.|+.
T Consensus 3 ~~~g~V~~v~~~------G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~ 74 (79)
T cd05684 3 IYKGKVTSIMDF------GCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDV 74 (79)
T ss_pred EEEEEEEEEEee------eEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEec
Confidence 366888888854 7777777 5799994 555543 434 58999999999999 78999999864
Q ss_pred c
Q 026794 224 R 224 (233)
Q Consensus 224 ~ 224 (233)
.
T Consensus 75 ~ 75 (79)
T cd05684 75 D 75 (79)
T ss_pred c
Confidence 3
No 128
>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=97.20 E-value=0.00083 Score=47.94 Aligned_cols=63 Identities=8% Similarity=0.067 Sum_probs=48.0
Q ss_pred cCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEEEeeccccccccccCceEEEEeecCCCCCEEEEEE
Q 026794 143 IPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLA 220 (233)
Q Consensus 143 ~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~~~~~~~~~~~vg~~~~v~i~~~d~~~~ki~Ls~ 220 (233)
++.|+. .+|++..+.+ +|.|++++++++|+....+-.+.-.+||.+++++.++ .+++|+.++.
T Consensus 14 ~~~G~~--------~~g~V~~i~~------~G~fV~l~~~~~Glv~~se~~~~~~iGd~v~v~I~~i-~e~~~i~l~~ 76 (77)
T cd04473 14 LEVGKL--------YKGKVNGVAK------YGVFVDLNDHVRGLIHRSNLLRDYEVGDEVIVQVTDI-PENGNIDLIP 76 (77)
T ss_pred CCCCCE--------EEEEEEeEec------ceEEEEECCCcEEEEEchhccCcCCCCCEEEEEEEEE-CCCCcEEEEE
Confidence 566777 6689988875 4777888999999953332222237899999999999 8999999875
No 129
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=97.18 E-value=0.0011 Score=65.27 Aligned_cols=64 Identities=14% Similarity=0.165 Sum_probs=50.4
Q ss_pred CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCc--ccc---cCc-------ccccCCCCEEEEEEEEEeCCCC
Q 026794 59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW--DLI---QDI-------RDILNEGDEVRVKVIKIDREKS 121 (233)
Q Consensus 59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~--~~~---~~~-------~~~~~~Gd~V~vkVi~vd~e~~ 121 (233)
|+.+.|. ++|+||+|.. .|++||||++.+.. ++. .+. ...|+.||.|+|+|.++|.+++
T Consensus 558 ~~~f~g~I~~v~~~g~~v~l~~----~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~ 633 (639)
T TIGR02062 558 NTRFAAEIVDISRGGMRVRLLE----NGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETR 633 (639)
T ss_pred CcEEEEEEEeeeCCcEEEEEec----CceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccC
Confidence 4478887 8999999974 58999999999965 221 111 1259999999999999999999
Q ss_pred eEEEE
Q 026794 122 RITLS 126 (233)
Q Consensus 122 ri~LS 126 (233)
+|.+.
T Consensus 634 ~i~~~ 638 (639)
T TIGR02062 634 SIIAR 638 (639)
T ss_pred cEeee
Confidence 98863
No 130
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=97.14 E-value=0.0011 Score=66.06 Aligned_cols=72 Identities=31% Similarity=0.499 Sum_probs=58.6
Q ss_pred ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc-----------CcccccCCCCEEEEEEEEE
Q 026794 53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKI 116 (233)
Q Consensus 53 ~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~-----------~~~~~~~~Gd~V~vkVi~v 116 (233)
+-.-.+|+.++|+ .||+||.|.+ .+++|++|++.+..++.. .....|+.||.|+|++.++
T Consensus 617 ~m~~~vg~~f~g~V~~v~~~g~~V~l~~----~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v 692 (706)
T COG0557 617 YMKKRVGEEFDGVVTGVTSFGFFVELPE----LGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSV 692 (706)
T ss_pred HHHHhcCCEEEEEEEEEEeccEEEEecc----cccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEE
Confidence 3345788888888 8999999985 579999999999965432 2233589999999999999
Q ss_pred eCCCCeEEEEEe
Q 026794 117 DREKSRITLSIK 128 (233)
Q Consensus 117 d~e~~ri~LS~k 128 (233)
+...+++.+++-
T Consensus 693 ~~~~~~i~~~~v 704 (706)
T COG0557 693 DLDERKIDFELV 704 (706)
T ss_pred cccccceEEEec
Confidence 999999998764
No 131
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=97.06 E-value=0.0022 Score=53.68 Aligned_cols=95 Identities=11% Similarity=0.084 Sum_probs=63.2
Q ss_pred cCCCCEEEEEEEE---EeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcc
Q 026794 103 LNEGDEVRVKVIK---IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179 (233)
Q Consensus 103 ~~~Gd~V~vkVi~---vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~ 179 (233)
|..++.+.+.+.. +|.++++|+| +||.... ...+.|++ +.|+|+++.+. ++++++
T Consensus 27 y~~~~~i~as~~G~~~id~~~~~Isv-------~P~~~~~-~~~~~Gdi--------V~GkV~~i~~~------g~~V~I 84 (189)
T PRK09521 27 YEDNGEVYASVVGKVFIDDINRKISV-------IPFKKTP-PLLKKGDI--------VYGRVVDVKEQ------RALVRI 84 (189)
T ss_pred EeeCCEEEEEeeEEEEEcCCCCEEEE-------ecCcCCC-CCCCCCCE--------EEEEEEEEcCC------eEEEEE
Confidence 4446667665544 4767777877 5885432 23567777 67999998754 444443
Q ss_pred ----------cCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcc
Q 026794 180 ----------EDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARA 222 (233)
Q Consensus 180 ----------~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~ 222 (233)
.++++|+. +++...++. .+||.+.++|.+++ +++.||.|.
T Consensus 85 ~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~---~~i~LS~k~ 142 (189)
T PRK09521 85 VSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT---DPLQLSTKG 142 (189)
T ss_pred EEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC---CcEEEEEec
Confidence 45788884 333222211 57999999998888 689999985
No 132
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=97.03 E-value=0.00086 Score=59.10 Aligned_cols=63 Identities=6% Similarity=0.004 Sum_probs=49.9
Q ss_pred ccCCeeeeccCCChhhhhhhhcccC--CeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQED--GIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC 225 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~--gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~ 225 (233)
+.|+|..+.+ +|+|+++.+ |++|+. ++++++... .+||.+.+++.++|.+++++.||.|....
T Consensus 12 V~G~V~~I~~------~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v~~ 84 (262)
T PRK03987 12 VVGTVKEVKD------FGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVNE 84 (262)
T ss_pred EEEEEEEEEC------CEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEeccc
Confidence 6799998875 477777775 899995 555555433 58999999999999999999999986553
No 133
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.03 E-value=0.00068 Score=67.37 Aligned_cols=63 Identities=13% Similarity=0.060 Sum_probs=51.8
Q ss_pred CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG 223 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~ 223 (233)
|..+.|+|+.+.+ +|+|+++.+|++|+. +++.+++++ .+||.++|++.++|.+ +|+.||.|+.
T Consensus 622 G~v~~G~V~~I~~------fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~-grI~LS~k~~ 692 (693)
T PRK11824 622 GEIYEGKVVRIVD------FGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLSRKAV 692 (693)
T ss_pred CeEEEEEEEEEEC------CeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence 4447899999884 588888899999993 677766655 6899999999999987 9999999864
No 134
>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=97.00 E-value=0.0013 Score=47.52 Aligned_cols=62 Identities=6% Similarity=-0.107 Sum_probs=46.2
Q ss_pred ccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecc----cccc----ccccCceEEEEeecCCCCCEEEEEEcc
Q 026794 155 SMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQ----GFEK----RVVSQDLQLWLSNAPPSGKKFTLLARA 222 (233)
Q Consensus 155 ~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~----~~~~----~~vg~~~~v~i~~~d~~~~ki~Ls~r~ 222 (233)
..+.|+|..+.+ .++++++.++++|+. ++++ ..++ -.+||.+.++|.+++.+ +++.||.|.
T Consensus 8 diV~g~V~~i~~------~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~LS~~~ 80 (86)
T cd05789 8 DVVIGRVTEVGF------KRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLHTRS 80 (86)
T ss_pred CEEEEEEEEECC------CEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEEeCc
Confidence 337899998874 467788899999995 3321 1111 15899999999999876 889999986
Q ss_pred c
Q 026794 223 G 223 (233)
Q Consensus 223 ~ 223 (233)
.
T Consensus 81 ~ 81 (86)
T cd05789 81 L 81 (86)
T ss_pred c
Confidence 4
No 135
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=96.97 E-value=0.00062 Score=67.32 Aligned_cols=67 Identities=7% Similarity=-0.001 Sum_probs=55.7
Q ss_pred CCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR 224 (233)
Q Consensus 153 ~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~ 224 (233)
+|+.++|.|.+++ +||+|+++.-..+|+. ++...+..| .+||.++||+.++|..++||+||+|.-.
T Consensus 658 ~Gm~leg~Vrnv~------~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~ 731 (780)
T COG2183 658 PGMILEGTVRNVV------DFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDE 731 (780)
T ss_pred CCCEEEEEEEEee------eccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccC
Confidence 4555899999998 5588887777778884 778778777 5899999999999999999999998654
Q ss_pred e
Q 026794 225 C 225 (233)
Q Consensus 225 ~ 225 (233)
.
T Consensus 732 ~ 732 (780)
T COG2183 732 E 732 (780)
T ss_pred C
Confidence 3
No 136
>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=96.93 E-value=0.0012 Score=45.13 Aligned_cols=57 Identities=12% Similarity=0.098 Sum_probs=43.8
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEE
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLA 220 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~ 220 (233)
..|.|..+.+ +++++++.++++|+. ++++....+ .+||.+.|++.++|+ .+++.||.
T Consensus 4 ~~g~V~~v~~------~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~-~~~i~ls~ 68 (68)
T cd04472 4 YEGKVVKIKD------FGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR 68 (68)
T ss_pred EEEEEEEEEE------eEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence 5688888875 477888888999994 444443322 579999999999999 88898873
No 137
>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=96.91 E-value=0.0057 Score=44.98 Aligned_cols=68 Identities=19% Similarity=0.073 Sum_probs=54.0
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794 55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (233)
Q Consensus 55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~ 129 (233)
.+++||.|-|+ ....+|+|.. ...|++|.+++... .+..+..|++||-|.|+|.++|+ .....||+..
T Consensus 3 ~P~~gD~VIG~V~~~~~~~~~VdI~s-----~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~-~~~~eLtc~~ 75 (86)
T cd05790 3 VPAKGDHVIGIVVAKAGDFFKVDIGG-----SEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANR-DMEPELSCVD 75 (86)
T ss_pred cCCCCCEEEEEEEEEcCCeEEEEcCC-----CcceEechHHcccc-cccccccCCCCCEEEEEEEecCC-CCCeEEEEeC
Confidence 35789999998 5678999973 57899999887543 34456779999999999999997 4567888765
No 138
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=96.88 E-value=0.0026 Score=46.36 Aligned_cols=36 Identities=25% Similarity=0.438 Sum_probs=25.0
Q ss_pred cEEEEEEccccCccccc--CcccccCCCCEEEEEEEEE
Q 026794 81 HLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKI 116 (233)
Q Consensus 81 gv~Glv~~sels~~~~~--~~~~~~~~Gd~V~vkVi~v 116 (233)
...|+||.+++.....+ ++.+.|++||.|+|+|+++
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 57899999999766554 4688899999999999974
No 139
>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=96.87 E-value=0.0021 Score=45.72 Aligned_cols=60 Identities=3% Similarity=0.067 Sum_probs=44.4
Q ss_pred ccccCCeeeeccCCChhhhhhhhcccC-CeeEEE----eeccccc-----------c--c--cccCceEEEEeecCCCCC
Q 026794 155 SMSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR----ITRQGFE-----------K--R--VVSQDLQLWLSNAPPSGK 214 (233)
Q Consensus 155 ~~~~g~v~~v~~~~g~~~~~~~l~~~~-gv~gl~----~~~~~~~-----------~--~--~vg~~~~v~i~~~d~~~~ 214 (233)
...+|.|+++.+ +|+|+++++ |++|+. ++++.+. . . .+||.++|++.++|.+++
T Consensus 3 ~~~~g~V~~v~~------~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~ 76 (83)
T cd04471 3 EEFDGVISGVTS------FGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRR 76 (83)
T ss_pred CEEEEEEEeEEe------eeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccC
Confidence 346788888875 477787788 899994 3332110 1 1 579999999999999999
Q ss_pred EEEEEE
Q 026794 215 KFTLLA 220 (233)
Q Consensus 215 ki~Ls~ 220 (233)
++.++.
T Consensus 77 ~i~~~l 82 (83)
T cd04471 77 KIDFEL 82 (83)
T ss_pred EEEEEE
Confidence 998874
No 140
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.80 E-value=0.0017 Score=63.35 Aligned_cols=94 Identities=12% Similarity=0.134 Sum_probs=67.2
Q ss_pred EEEeCCCCeEEEEEeccccC----hhhHHhhhhcCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEEE--
Q 026794 114 IKIDREKSRITLSIKQLEED----PLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-- 187 (233)
Q Consensus 114 i~vd~e~~ri~LS~k~~~~d----p~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~-- 187 (233)
++++ +++.+..+-...... .|-+...+..++|.+ ..|+|+++.+ ||+|+++-+|=+|++
T Consensus 585 Idie-ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~i--------y~G~V~ri~~------fGaFv~l~~gkdgl~hi 649 (692)
T COG1185 585 IDIE-DDGTVKIAASDGESAKKAKERIEAITREVEVGEV--------YEGTVVRIVD------FGAFVELLPGKDGLVHI 649 (692)
T ss_pred EEec-CCCcEEEEecchHHHHHHHHHHHHHHhhcccccE--------EEEEEEEEee------cceEEEecCCcceeEEe
Confidence 4555 678888777553221 132333344667776 6799999984 688999999988883
Q ss_pred --eeccccccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794 188 --ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG 223 (233)
Q Consensus 188 --~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~ 223 (233)
++++++++. .+||.+.||+.++|. ++|+.||+++.
T Consensus 650 S~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~-~Gri~ls~~~~ 690 (692)
T COG1185 650 SQLAKERVEKVEDVLKEGDEVKVKVIEIDK-QGRIRLSIKAV 690 (692)
T ss_pred hhhhhhhhhcccceeecCceEEEEEeeecc-cCCccceehhc
Confidence 777776655 579999999988884 47799998864
No 141
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=96.71 E-value=0.0021 Score=61.78 Aligned_cols=68 Identities=29% Similarity=0.496 Sum_probs=58.1
Q ss_pred ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794 53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (233)
Q Consensus 53 ~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~ 127 (233)
.+.++.|..+.|+ .||+||+|+ ..+.||+|.++++.. .-|.+|+.+-|++..+-++++.|.|..
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 489999999999862 237899999999999999889888876
Q ss_pred eccc
Q 026794 128 KQLE 131 (233)
Q Consensus 128 k~~~ 131 (233)
..+.
T Consensus 186 ~~~~ 189 (715)
T COG1107 186 VGLD 189 (715)
T ss_pred cCCc
Confidence 6554
No 142
>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=96.66 E-value=0.0033 Score=46.24 Aligned_cols=59 Identities=15% Similarity=0.012 Sum_probs=43.2
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eec---cccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITR---QGFEKR----VVSQDLQLWLSNAPPSGKKFTLL 219 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~---~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls 219 (233)
..|+|+++.++ -+++|+++.+|.+|+. ++| .++.++ .+||++.|++...+...+--.|+
T Consensus 11 y~g~V~~i~~~----~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt 80 (88)
T cd04453 11 YLGRVKKIVPG----LQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLT 80 (88)
T ss_pred EEEEEEEeccC----CcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEE
Confidence 67999999864 3489999999999994 555 233222 57999999999977665544444
No 143
>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=96.65 E-value=0.002 Score=43.83 Aligned_cols=58 Identities=10% Similarity=0.135 Sum_probs=43.1
Q ss_pred ccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794 155 SMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLL 219 (233)
Q Consensus 155 ~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls 219 (233)
..+.|+|..+.++ +.++++. +++|+. +++.+...+ .+||.+++++.++|.+++++.||
T Consensus 3 ~~~~g~V~~v~~~------g~~v~l~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05688 3 DVVEGTVKSITDF------GAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CEEEEEEEEEEee------eEEEEEC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence 3467888888754 5666665 688985 344344333 68999999999999999999876
No 144
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=96.62 E-value=0.0039 Score=42.21 Aligned_cols=62 Identities=8% Similarity=0.136 Sum_probs=45.6
Q ss_pred CccccCCeeeeccCCChhhhhhhhcccCCeeEEEe----ecccccc----ccccCceEEEEeecCCCCCEEEEEEc
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRI----TRQGFEK----RVVSQDLQLWLSNAPPSGKKFTLLAR 221 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~~----~~~~~~~----~~vg~~~~v~i~~~d~~~~ki~Ls~r 221 (233)
|..+.|.|..+.+ .+.++++.+++.|+.. ++....+ -.+||.+.+++.+++.+++++.|+.|
T Consensus 3 G~~v~g~V~~v~~------~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 3 GDVVEGTVTEITP------FGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCEEEEEEEEEEc------cEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 3447789988875 3667777889999952 2221111 15799999999999999999999875
No 145
>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=96.56 E-value=0.0027 Score=42.16 Aligned_cols=56 Identities=13% Similarity=0.203 Sum_probs=40.4
Q ss_pred cCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794 158 SSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLL 219 (233)
Q Consensus 158 ~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls 219 (233)
.|.|..+.+ .+.++++.+|++|+. +++....++ .+||.+++++.++|.+++++.||
T Consensus 2 ~g~V~~v~~------~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 2 TGKVVSITK------FGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred EEEEEEEEe------eeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 366666653 466777788999995 333222112 57999999999999999998875
No 146
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.52 E-value=0.0086 Score=55.17 Aligned_cols=61 Identities=21% Similarity=0.345 Sum_probs=51.3
Q ss_pred CCCCCEEEEE----e-e-eEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCC---eEEEE
Q 026794 56 VNVEDIFVGR----D-Y-GAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS---RITLS 126 (233)
Q Consensus 56 ~~~G~vv~g~----~-~-G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~---ri~LS 126 (233)
-++|++++|+ + . ++||+|+ +.+|++|.++.. |.+.|++||.++|-|.+++...+ +|.||
T Consensus 136 ~~~Geiv~g~V~r~~~~~~i~vdlg------~~ea~LP~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~IilS 203 (374)
T PRK12328 136 KKVGKIVFGTVVRVDNEENTFIEID------EIRAVLPMKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIELS 203 (374)
T ss_pred HhcCcEEEEEEEEEecCCCEEEEcC------CeEEEeCHHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEEE
Confidence 4789999999 3 2 4899996 799999999864 57789999999999999998665 77888
Q ss_pred Ee
Q 026794 127 IK 128 (233)
Q Consensus 127 ~k 128 (233)
+.
T Consensus 204 Rt 205 (374)
T PRK12328 204 RT 205 (374)
T ss_pred cC
Confidence 74
No 147
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=96.32 E-value=0.0033 Score=64.30 Aligned_cols=72 Identities=24% Similarity=0.275 Sum_probs=60.0
Q ss_pred cCCCCCCEEEEE------eeeE--EEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 026794 54 SRVNVEDIFVGR------DYGA--FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125 (233)
Q Consensus 54 ~~~~~G~vv~g~------~~G~--fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~L 125 (233)
+.+.+|.+|.++ .+|. =|.++ .|++|+||.+++|...+.+|...+++||+|.+||+++|.++=-+.|
T Consensus 981 et~~~g~iV~~~V~~vt~rr~~Cv~v~ld-----~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~L 1055 (1299)
T KOG1856|consen 981 ETFYEGAIVPVTVTKVTHRRGICVRVRLD-----CGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVEL 1055 (1299)
T ss_pred hHhccCceEEEeeeEEEecccceeEEEec-----CCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhh
Confidence 357788888866 3332 35565 5999999999999999999999999999999999999998888888
Q ss_pred EEecc
Q 026794 126 SIKQL 130 (233)
Q Consensus 126 S~k~~ 130 (233)
|+|..
T Consensus 1056 s~r~s 1060 (1299)
T KOG1856|consen 1056 SCRTS 1060 (1299)
T ss_pred hhhhH
Confidence 88753
No 148
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.30 E-value=0.00086 Score=63.70 Aligned_cols=122 Identities=8% Similarity=0.034 Sum_probs=79.7
Q ss_pred EEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhh-----HHhhhhcC--CCCeeeecCCcc
Q 026794 84 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLL-----ETLEKVIP--QDGSVISDSSSM 156 (233)
Q Consensus 84 Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~-----~~~~~~~~--~g~~~~~~~~~~ 156 (233)
+.++.++.. .....+++||.+.+.|...+. .+....+.|+....-|. ...+. |+ .|.+
T Consensus 73 ~eI~L~eAk-----~~~~~~~vGD~ie~~I~~~~f-gRia~q~aKq~i~Qkire~ere~i~~e-yk~~~GeI-------- 137 (470)
T PRK09202 73 KEISLEEAR-----KIDPDAEVGDYIEEEIESVDF-GRIAAQTAKQVIVQKIREAERERVYEE-YKDRVGEI-------- 137 (470)
T ss_pred ceeeHHHHh-----hhCccccCCCeEEEEEccccC-ChHHHHHHHHHHHHHHHHHHHHHHHHH-HHhhcCCE--------
Confidence 555555542 122337899999999998873 22333334455444454 33333 43 6776
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEEeeccccc--cccccCceEEEEeecCCCCC--EEEEEEcccceee
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFE--KRVVSQDLQLWLSNAPPSGK--KFTLLARAGRCKR 227 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~~~~~~~~--~~~vg~~~~v~i~~~d~~~~--ki~Ls~r~~~~vq 227 (233)
++|+|.++... +.++++ .|++|+.+..+... .-.+||.++++|.+++.+.+ +|.||-+.-.-+.
T Consensus 138 V~G~V~ri~~~------giiVDL-ggvea~LP~sE~ip~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~p~~l~ 205 (470)
T PRK09202 138 ITGVVKRVERG------NIIVDL-GRAEAILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLK 205 (470)
T ss_pred EEEEEEEEecC------CEEEEE-CCeEEEecHHHcCCCccCCCCCEEEEEEEEEecCCCCCeEEEEeCcHHHHH
Confidence 77999988743 566766 58999965444331 11689999999999999877 8999987665544
No 149
>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=95.93 E-value=0.0081 Score=41.77 Aligned_cols=53 Identities=6% Similarity=0.121 Sum_probs=39.6
Q ss_pred cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecc--ccccc----cccCceEEEEeecCCCCC
Q 026794 156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQ--GFEKR----VVSQDLQLWLSNAPPSGK 214 (233)
Q Consensus 156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~--~~~~~----~vg~~~~v~i~~~d~~~~ 214 (233)
.+.|+|+++.+ .++++++.+|++|+. ++++ ..+.+ .+||.++++|.+++.++.
T Consensus 3 iV~g~V~~i~~------~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~ 65 (70)
T cd05702 3 LVKAKVKSVKP------TQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT 65 (70)
T ss_pred EEEEEEEEEEC------CcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence 46789988874 467788899999995 4443 23333 679999999999887765
No 150
>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=95.52 E-value=0.02 Score=41.03 Aligned_cols=63 Identities=5% Similarity=-0.118 Sum_probs=45.1
Q ss_pred CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG 223 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~ 223 (233)
|..+.|+|+.+.+. ++++++..+.+|+. ++....++. .+||.+.++|.+++.+ +++.||.+..
T Consensus 7 GdiV~G~V~~v~~~------~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~~ 77 (82)
T cd04454 7 GDIVIGIVTEVNSR------FWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTADN 77 (82)
T ss_pred CCEEEEEEEEEcCC------EEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECCC
Confidence 33477999988743 56677777888884 332222211 6899999999999987 8899999863
No 151
>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=95.40 E-value=0.01 Score=59.07 Aligned_cols=58 Identities=12% Similarity=0.072 Sum_probs=46.0
Q ss_pred CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEE
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTL 218 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~L 218 (233)
|..+.|+|+++. ++|+|+++.+|++|+. +++.++.++ .+||.+.|++.++|. ++|++|
T Consensus 619 G~i~~G~V~~I~------~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~-~gki~L 684 (684)
T TIGR03591 619 GKIYEGKVVRIM------DFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK-QGRIKL 684 (684)
T ss_pred CcEEEEEEEEEe------CCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECC-CCCccC
Confidence 334779999987 4588898899999994 677666544 579999999999997 677765
No 152
>PF09876 DUF2103: Predicted metal-binding protein (DUF2103); InterPro: IPR018664 This family of various putative metal binding prokaryotic proteins has no known function.
Probab=95.35 E-value=0.069 Score=40.50 Aligned_cols=59 Identities=24% Similarity=0.314 Sum_probs=43.4
Q ss_pred hhhhhcccCCeeEEEeeccccccccccCceEEEEeecCCCCCEEEEEEcccceeeeeEec
Q 026794 173 IFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRCKRYNFHI 232 (233)
Q Consensus 173 ~~~~l~~~~gv~gl~~~~~~~~~~~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~vq~~~~~ 232 (233)
+...|...++|..+++++-..........+.+|++.-+ ..+-+.|.+|.|..+||+|=|
T Consensus 25 ~L~~la~~~~Vk~IiPG~I~~~~~~~~~gl~lkvt~~~-~~Gn~Kllar~G~SvQEvfVV 83 (103)
T PF09876_consen 25 WLEKLAKHPGVKKIIPGVISRSGGRSSGGLRLKVTRPT-RGGNFKLLARSGSSVQEVFVV 83 (103)
T ss_pred HHHHHhcCCCCCEEecccEEcCCCCCCCCeEEEEEEec-CCCcEEEEEecCCeeEEEEEE
Confidence 45666777899988877765443343456999998644 444499999999999999954
No 153
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=95.17 E-value=0.087 Score=35.93 Aligned_cols=48 Identities=33% Similarity=0.385 Sum_probs=30.3
Q ss_pred eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (233)
Q Consensus 66 ~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k 128 (233)
++|+|++-+ .+-+-|+|.+++.. .+++||.|.|-|-. |. .+|+..++|
T Consensus 14 ~~g~fL~~~-----~~~~vlLp~~e~~~--------~~~~Gd~v~VFvY~-D~-~~rl~AT~k 61 (61)
T PF13509_consen 14 EFGYFLDDG-----EGKEVLLPKSEVPE--------PLKVGDEVEVFVYL-DK-EGRLVATTK 61 (61)
T ss_dssp SSEEEEEET-----T-EEEEEEGGG--------------TTSEEEEEEEE--T-TS-EEEE--
T ss_pred CCEEEEECC-----CCCEEEechHHcCC--------CCCCCCEEEEEEEE-CC-CCCEEEecC
Confidence 899999976 26899999999852 37899999987654 53 567777764
No 154
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.05 E-value=0.09 Score=49.50 Aligned_cols=67 Identities=9% Similarity=0.041 Sum_probs=50.7
Q ss_pred CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCC---CeEEEEE
Q 026794 56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK---SRITLSI 127 (233)
Q Consensus 56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~---~ri~LS~ 127 (233)
-++|++++|+ +.+++|++...-|..+++|++|.++. -|.+.|++||.++|-|.++.... -+|.||.
T Consensus 150 ~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eq------ip~E~y~~Gdrika~i~~V~~~~~kGpqIilSR 223 (449)
T PRK12329 150 DLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQ------LPNDNYRANATFKVFLKEVSEGPRRGPQLFVSR 223 (449)
T ss_pred HhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHc------CCCCcCCCCCEEEEEEEEeecCCCCCCEEEEEc
Confidence 4789999999 55799998410010148999999886 45678999999999999998752 3678876
Q ss_pred e
Q 026794 128 K 128 (233)
Q Consensus 128 k 128 (233)
-
T Consensus 224 t 224 (449)
T PRK12329 224 A 224 (449)
T ss_pred C
Confidence 4
No 155
>PRK11712 ribonuclease G; Provisional
Probab=94.96 E-value=0.12 Score=49.61 Aligned_cols=62 Identities=24% Similarity=0.492 Sum_probs=46.5
Q ss_pred hhccCCCCCCEEEEE-------eeeEEEEEccCCCCccEEEEEEccccCcc------------cccCcccccCCCCEEEE
Q 026794 51 KYSSRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRV 111 (233)
Q Consensus 51 ~~~~~~~~G~vv~g~-------~~G~fV~l~~~~~~~gv~Glv~~sels~~------------~~~~~~~~~~~Gd~V~v 111 (233)
.......+|.+|.|+ =.+|||+|+ .+-.||+|++++... ...++.+.+++||.|-|
T Consensus 31 ~~~~~~~vGnIY~G~V~~v~pg~~AAFVdIG-----~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLV 105 (489)
T PRK11712 31 REAKRGIVGNIYKGRVSRVLPGMQAAFVDIG-----LDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMV 105 (489)
T ss_pred cCCcccccccEEEEEEeecCCCCceeEEeeC-----CCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEE
Confidence 334455799999999 346999998 488999999998321 11234566999999999
Q ss_pred EEEEEe
Q 026794 112 KVIKID 117 (233)
Q Consensus 112 kVi~vd 117 (233)
+|..--
T Consensus 106 QV~Ke~ 111 (489)
T PRK11712 106 QVVKDP 111 (489)
T ss_pred EEEeCC
Confidence 998853
No 156
>PRK10811 rne ribonuclease E; Reviewed
Probab=94.81 E-value=0.078 Score=54.15 Aligned_cols=57 Identities=26% Similarity=0.486 Sum_probs=45.3
Q ss_pred CCCCCEEEEE-------eeeEEEEEccCCCCccEEEEEEccccCccccc---------CcccccCCCCEEEEEEEEEe
Q 026794 56 VNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ---------DIRDILNEGDEVRVKVIKID 117 (233)
Q Consensus 56 ~~~G~vv~g~-------~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~---------~~~~~~~~Gd~V~vkVi~vd 117 (233)
..+|+||.|+ =.++||+|+ .|..||+|++++...++. +..+.++.||.|-|.|..-.
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDIG-----~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa 108 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDYG-----AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEE 108 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEec-----CCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecc
Confidence 4589999999 457999998 388999999999654332 23456899999999999854
No 157
>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=94.81 E-value=0.0056 Score=55.93 Aligned_cols=115 Identities=10% Similarity=0.097 Sum_probs=72.7
Q ss_pred CcccccCCCCEEEEEEEEEeCCCCeEEEEEecc-----ccChhhHHhhhhc-CCCCeeeecCCccccCCeeeeccCCChh
Q 026794 98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQL-----EEDPLLETLEKVI-PQDGSVISDSSSMSSSNSNTIEPLPGLG 171 (233)
Q Consensus 98 ~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~-----~~dp~~~~~~~~~-~~g~~~~~~~~~~~~g~v~~v~~~~g~~ 171 (233)
.....+++||.+.+.+...+. .+....+.|+. ....++...+.+. ..|.+ ++|+|.++.+.
T Consensus 79 ~~d~~~~vGD~I~~~I~~~~f-gR~aaq~aKqvi~Qkire~ere~i~~ey~~k~Gei--------V~G~V~~v~~~---- 145 (341)
T TIGR01953 79 EIDPDVQIGDEVKKEIPPENF-GRIAAQTAKQVILQKIREAERERVYDEFSSKEGEI--------ISGTVKRVNRR---- 145 (341)
T ss_pred hhccccccCCEEEEEecccCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCE--------EEEEEEEEecC----
Confidence 344558899999998865543 22333334442 2333444444432 35666 78999988753
Q ss_pred hhhhhhcccCCeeEEEeeccccc--cccccCceEEEEeecCCC--CCEEEEEEcccceee
Q 026794 172 AIFEELLQEDGIDDVRITRQGFE--KRVVSQDLQLWLSNAPPS--GKKFTLLARAGRCKR 227 (233)
Q Consensus 172 ~~~~~l~~~~gv~gl~~~~~~~~--~~~vg~~~~v~i~~~d~~--~~ki~Ls~r~~~~vq 227 (233)
+ +.++++ .|++|+.+.+.... .-.+||.+++++.+++.. ...+.||.+..+-+.
T Consensus 146 g-~v~Vdi-G~~ea~LP~~E~ip~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~~~v~ 203 (341)
T TIGR01953 146 G-NLYVEL-GKTEGILPKKEQIPGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHPEFVK 203 (341)
T ss_pred C-cEEEEE-CCeEEEecHHHcCCCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcHHHHH
Confidence 2 135666 48999965554432 226899999999999854 457999988766554
No 158
>PHA02945 interferon resistance protein; Provisional
Probab=94.72 E-value=0.048 Score=40.08 Aligned_cols=62 Identities=5% Similarity=-0.083 Sum_probs=42.4
Q ss_pred ccCCeeeeccCCChhhhhhhhccc--CCeeEEE-ee-----ccccccc--cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQE--DGIDDVR-IT-----RQGFEKR--VVSQDLQLWLSNAPPSGKKFTLLARAGRC 225 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~--~gv~gl~-~~-----~~~~~~~--~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~ 225 (233)
+-|+|.. . ++++++.+. +|.+|+. +| ...++.+ .+||.+.+++..+|+.++.|-||.|+-.+
T Consensus 15 vigtV~~-~------d~ga~v~L~EY~g~eg~i~~seveva~~wvK~rd~l~GqkvV~KVirVd~~kg~IDlSlK~V~~ 86 (88)
T PHA02945 15 LKGKVYE-N------GYALYIDLFDYPHSEAILAESVQMHMNRYFKYRDKLVGKTVKVKVIRVDYTKGYIDVNYKRMCR 86 (88)
T ss_pred EEEEEEe-c------CceEEEEecccCCcEEEEEeehhhhccceEeeeeEecCCEEEEEEEEECCCCCEEEeEeeEccc
Confidence 4577665 5 445555444 3788873 23 1122222 57999999999999999999999986543
No 159
>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=94.41 E-value=0.043 Score=40.84 Aligned_cols=60 Identities=12% Similarity=0.030 Sum_probs=41.9
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecccccc-------------c--cccCceEEEEeecCCCC----
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEK-------------R--VVSQDLQLWLSNAPPSG---- 213 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~-------------~--~vg~~~~v~i~~~d~~~---- 213 (233)
+.|.|..+.++ +.|+++. +++|+. ++++.... . .+||.++|++.++|.+.
T Consensus 3 v~g~V~~i~~~------GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~ 75 (99)
T cd04460 3 VEGEVVEVVDF------GAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPR 75 (99)
T ss_pred EEEEEEEEEec------cEEEEEc-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCC
Confidence 45777777744 6666666 588884 33333321 1 67999999999999874
Q ss_pred -CEEEEEEccc
Q 026794 214 -KKFTLLARAG 223 (233)
Q Consensus 214 -~ki~Ls~r~~ 223 (233)
.++.||++..
T Consensus 76 ~~~i~ls~k~~ 86 (99)
T cd04460 76 ESKIGLTMRQP 86 (99)
T ss_pred CceEEEEEecC
Confidence 5899999754
No 160
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=93.85 E-value=0.046 Score=52.66 Aligned_cols=66 Identities=15% Similarity=0.091 Sum_probs=53.9
Q ss_pred CCccccCCeeeeccCCChhhhhhhhcccCCeeEE----Eeeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794 153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDV----RITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR 224 (233)
Q Consensus 153 ~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl----~~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~ 224 (233)
.|++.+++++.+. ++|+++++.+|..|| +++...+.+| .|||+++||..+.|+..+ +.||.|+.-
T Consensus 668 ~g~vy~~tIt~~r------d~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~~g~-~~ls~ralL 740 (760)
T KOG1067|consen 668 FGGVYTATITEIR------DTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPRGG-IMLSSRALL 740 (760)
T ss_pred eeeEEEEEEeeec------ccceEEEecCCchhhccchhcccccccChHHHHhhcceeEEEEEeecCccc-eeehhhhhc
Confidence 5666777777766 568889999999998 4788778888 589999999999999888 888888754
Q ss_pred e
Q 026794 225 C 225 (233)
Q Consensus 225 ~ 225 (233)
+
T Consensus 741 p 741 (760)
T KOG1067|consen 741 P 741 (760)
T ss_pred C
Confidence 3
No 161
>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=93.72 E-value=0.11 Score=35.70 Aligned_cols=59 Identities=3% Similarity=0.041 Sum_probs=39.8
Q ss_pred CccccCCeeeeccCCChhhhhhhhcccCCeeEEEeecccc--ccccccCceEEEEeecCCCC--CEEEEE
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGF--EKRVVSQDLQLWLSNAPPSG--KKFTLL 219 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~~~~~~~--~~~~vg~~~~v~i~~~d~~~--~ki~Ls 219 (233)
|..++|+|..+.+. ++++++. +++|+.+..... +.-.+||.+++++.+++.++ .+|.||
T Consensus 4 g~iV~G~V~~~~~~------~~~vdig-~~eg~lp~~e~~~~~~~~~Gd~v~v~v~~v~~~~~~~~i~lS 66 (67)
T cd04455 4 GEIVTGIVKRVDRG------NVIVDLG-KVEAILPKKEQIPGESYRPGDRIKAYVLEVRKTSKGPQIILS 66 (67)
T ss_pred CCEEEEEEEEEcCC------CEEEEcC-CeEEEeeHHHCCCCCcCCCCCEEEEEEEEEecCCCCCEEEEe
Confidence 34478999888753 5667775 488985433322 11268999999999998654 456665
No 162
>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=93.62 E-value=0.083 Score=52.78 Aligned_cols=61 Identities=10% Similarity=0.048 Sum_probs=45.4
Q ss_pred CccccCCeeeeccCCChhhhhhhhcccC-CeeEEE----eecccc-----------c---c-ccccCceEEEEeecCCCC
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR----ITRQGF-----------E---K-RVVSQDLQLWLSNAPPSG 213 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~-gv~gl~----~~~~~~-----------~---~-~~vg~~~~v~i~~~d~~~ 213 (233)
|...+|.|+.++++ |.|+++++ |++|+. ++.+.. + . -.+||.++|++.++|.++
T Consensus 628 G~~~~g~V~~v~~f------GifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~ 701 (709)
T TIGR02063 628 GEEFEGVISGVTSF------GLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDT 701 (709)
T ss_pred CcEEEEEEEEEEeC------CEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEeccc
Confidence 44578999988855 66777788 899994 332211 1 1 157999999999999999
Q ss_pred CEEEEEE
Q 026794 214 KKFTLLA 220 (233)
Q Consensus 214 ~ki~Ls~ 220 (233)
++|.++.
T Consensus 702 ~~I~~~l 708 (709)
T TIGR02063 702 GKIDFEL 708 (709)
T ss_pred CeEEEEE
Confidence 9999874
No 163
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=92.90 E-value=0.076 Score=46.52 Aligned_cols=63 Identities=6% Similarity=-0.056 Sum_probs=46.9
Q ss_pred ccCCeeeeccCCChhhhhhhhcc--cCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQ--EDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC 225 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~--~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~ 225 (233)
+-|+|..+.++ |+++.| =+|++|+. +++..+.+- .+||.+-+++..+|++++.|-||+|.-++
T Consensus 15 Vv~tV~~V~~~------GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~ 87 (269)
T COG1093 15 VVGTVKQVADY------GAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTE 87 (269)
T ss_pred EEEEEEEeecc------ccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCCH
Confidence 55888888754 666644 46899994 444334332 47999999999999999999999987554
No 164
>PRK11642 exoribonuclease R; Provisional
Probab=92.52 E-value=0.16 Score=51.51 Aligned_cols=61 Identities=8% Similarity=0.110 Sum_probs=45.2
Q ss_pred CccccCCeeeeccCCChhhhhhhhcccCC-eeEEE----eecc--ccc------------c-ccccCceEEEEeecCCCC
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDG-IDDVR----ITRQ--GFE------------K-RVVSQDLQLWLSNAPPSG 213 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~g-v~gl~----~~~~--~~~------------~-~~vg~~~~v~i~~~d~~~ 213 (233)
|...+|.|+.++++ |.|++++++ |+|+. ++++ ... . -.+||.|+|+|.++|+++
T Consensus 644 Ge~f~G~Is~V~~f------GifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~ 717 (813)
T PRK11642 644 GNVFKGVISSVTGF------GFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDE 717 (813)
T ss_pred CcEEEEEEEEeecC------ceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCC
Confidence 44478999888755 666777875 99994 3332 111 1 157999999999999999
Q ss_pred CEEEEEE
Q 026794 214 KKFTLLA 220 (233)
Q Consensus 214 ~ki~Ls~ 220 (233)
++|.++.
T Consensus 718 rkI~f~l 724 (813)
T PRK11642 718 RKIDFSL 724 (813)
T ss_pred CeEEEEE
Confidence 9999987
No 165
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=89.77 E-value=0.15 Score=47.11 Aligned_cols=106 Identities=9% Similarity=0.057 Sum_probs=62.0
Q ss_pred ccccCCCCEEEEEEEEEeCCCCeEEEEEeccccCh-----hhHHhhhh-cCCCCeeeecCCccccCCeeeeccCCChhhh
Q 026794 100 RDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP-----LLETLEKV-IPQDGSVISDSSSMSSSNSNTIEPLPGLGAI 173 (233)
Q Consensus 100 ~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp-----~~~~~~~~-~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~ 173 (233)
....++||.+...+...+..+.. ..+.|+....- .+...+.+ -+.|++ ++|+|.+..+.
T Consensus 84 ~~~~~vGD~i~~~I~~~~fgR~a-aq~akqvI~Qkire~ere~v~~ef~~k~Gei--------V~G~V~~~~~~------ 148 (362)
T PRK12327 84 NPAYELGDVIEIEVTPKDFGRIA-AQTAKQVIMQRLREAEREIIYNEFSEREGDI--------VTGVVQRRDNR------ 148 (362)
T ss_pred CccccCCCEEEEecCcCCCChHH-HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCE--------EEEEEEEEeCC------
Confidence 34478899999988776643322 22222221111 11122222 145666 78999987753
Q ss_pred hhhhcccCCeeEEEeeccccccc--cccCceEEEEeecCCCCC--EEEEEEc
Q 026794 174 FEELLQEDGIDDVRITRQGFEKR--VVSQDLQLWLSNAPPSGK--KFTLLAR 221 (233)
Q Consensus 174 ~~~l~~~~gv~gl~~~~~~~~~~--~vg~~~~v~i~~~d~~~~--ki~Ls~r 221 (233)
+.++++. |++|+.+.+...... .+||.+++++.+++.+.+ .+.||--
T Consensus 149 ~~~Vdlg-~vEa~LP~~E~ip~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt 199 (362)
T PRK12327 149 FVYVNLG-KIEAVLPPAEQIPGETYKHGDRIKVYVVKVEKTTKGPQIFVSRT 199 (362)
T ss_pred cEEEEeC-CeEEEecHHHcCCCCCCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence 4456664 699996533332211 579999999999986543 4766654
No 166
>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=88.67 E-value=0.67 Score=46.01 Aligned_cols=61 Identities=10% Similarity=0.122 Sum_probs=44.4
Q ss_pred CccccCCeeeeccCCChhhhhhhhccc-CCeeEEE----eeccc---------c--c---c-ccccCceEEEEeecCCCC
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQE-DGIDDVR----ITRQG---------F--E---K-RVVSQDLQLWLSNAPPSG 213 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~-~gv~gl~----~~~~~---------~--~---~-~~vg~~~~v~i~~~d~~~ 213 (233)
|...+|.|+.+.++ |.|++++ .|++|+. ++++. + + . -.+||.++|++.++|+++
T Consensus 573 G~~~~g~I~~v~~~------GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~ 646 (654)
T TIGR00358 573 GTEFSGEISSVTRF------GMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMET 646 (654)
T ss_pred CcEEEEEEEeEEcC------cEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEeccc
Confidence 34477999888855 6667777 7899984 43331 0 1 1 158999999999999999
Q ss_pred CEEEEEE
Q 026794 214 KKFTLLA 220 (233)
Q Consensus 214 ~ki~Ls~ 220 (233)
++|.++.
T Consensus 647 ~~I~f~l 653 (654)
T TIGR00358 647 RSIIFEL 653 (654)
T ss_pred CeEEEEE
Confidence 9998874
No 167
>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=88.63 E-value=0.7 Score=38.22 Aligned_cols=59 Identities=15% Similarity=0.070 Sum_probs=40.3
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEEe----ecccc--------------ccc-cccCceEEEEeecC-----CC
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVRI----TRQGF--------------EKR-VVSQDLQLWLSNAP-----PS 212 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~~----~~~~~--------------~~~-~vg~~~~v~i~~~d-----~~ 212 (233)
++|.|+++.++ |.|+++. .++|+.. ..+.. +.. .+||.+.++|.+++ ++
T Consensus 85 v~G~V~~v~~~------GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~ 157 (179)
T TIGR00448 85 VEGEVIEIVEF------GAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPE 157 (179)
T ss_pred EEEEEEEEEee------EEEEEeC-CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCC
Confidence 66888888855 5556554 4777742 11111 011 57999999999998 67
Q ss_pred CCEEEEEEcc
Q 026794 213 GKKFTLLARA 222 (233)
Q Consensus 213 ~~ki~Ls~r~ 222 (233)
..++.|++|+
T Consensus 158 ~~~I~lt~k~ 167 (179)
T TIGR00448 158 GSKIGLTMRQ 167 (179)
T ss_pred cceEEEEecc
Confidence 7899999986
No 168
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=86.94 E-value=3.3 Score=33.91 Aligned_cols=63 Identities=17% Similarity=0.180 Sum_probs=43.2
Q ss_pred hhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcc----cccC-------cccccCCCCEEEEEEE
Q 026794 51 KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LIQD-------IRDILNEGDEVRVKVI 114 (233)
Q Consensus 51 ~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~----~~~~-------~~~~~~~Gd~V~vkVi 114 (233)
...-+.-.|++++|+ ..|+|++.+ .++.++..-....+ .-+| -.+..++|..|+++|+
T Consensus 74 av~FkpfKGEVvdgvV~~Vnk~G~F~~~G------Pl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kii 147 (170)
T KOG3298|consen 74 AVTFKPFKGEVVDGVVTKVNKMGVFARSG------PLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKII 147 (170)
T ss_pred EEEEeecCCcEEEEEEEEEeeeeEEEecc------ceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEE
Confidence 334467789999999 889999997 57777654333322 2222 1225788999999999
Q ss_pred EEeCC
Q 026794 115 KIDRE 119 (233)
Q Consensus 115 ~vd~e 119 (233)
....+
T Consensus 148 gtr~~ 152 (170)
T KOG3298|consen 148 GTRVD 152 (170)
T ss_pred EEEEe
Confidence 87643
No 169
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=85.09 E-value=4.5 Score=33.57 Aligned_cols=72 Identities=21% Similarity=0.126 Sum_probs=46.1
Q ss_pred CCCCCCEEEEE-----eeeEEEEEccCCC---CccEEEEEEccccCcc--cccCcccccCCCCEEEEEEEEEeCCCCeEE
Q 026794 55 RVNVEDIFVGR-----DYGAFIHLRFPDG---LYHLTGLVHVSEVSWD--LIQDIRDILNEGDEVRVKVIKIDREKSRIT 124 (233)
Q Consensus 55 ~~~~G~vv~g~-----~~G~fV~l~~~~~---~~gv~Glv~~sels~~--~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~ 124 (233)
....|++|.++ ..-+=|+|--.++ -...+|+||..++... ---++...|++||.|.|+|++.+. .....
T Consensus 65 LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~-~~~y~ 143 (193)
T KOG3409|consen 65 LPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGD-GSNYL 143 (193)
T ss_pred CCccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCC-CCcEE
Confidence 46799999998 1113333321111 0257899999888542 123466679999999999999764 45555
Q ss_pred EEE
Q 026794 125 LSI 127 (233)
Q Consensus 125 LS~ 127 (233)
|+.
T Consensus 144 LTt 146 (193)
T KOG3409|consen 144 LTT 146 (193)
T ss_pred EEE
Confidence 554
No 170
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=84.84 E-value=6.3 Score=34.09 Aligned_cols=59 Identities=3% Similarity=-0.091 Sum_probs=41.7
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecccc----ccc----cccCceEEEEeecCCCCCEEEEEEcc
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGF----EKR----VVSQDLQLWLSNAPPSGKKFTLLARA 222 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~----~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~ 222 (233)
+-|+|+.+.+. +.++++.++.+|+. +++.++ .+. .+||.+.++|.+++.++. +.||.|.
T Consensus 67 ViG~V~~i~~~------~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~-~~LS~k~ 137 (235)
T PRK04163 67 VIGKVTDVTFS------GWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRD-VVLTLKG 137 (235)
T ss_pred EEEEEEEEeCc------eEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCc-EEEEEcC
Confidence 56888887743 56677787788773 444432 111 569999999999986654 9999875
No 171
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=83.22 E-value=1.9 Score=41.41 Aligned_cols=73 Identities=23% Similarity=0.371 Sum_probs=53.5
Q ss_pred hhhccCCCCCCEEEEE-------eeeEEEEEccCCCCccEEEEEEccccCcccccCc-----ccccCCCCEEEEEEEEEe
Q 026794 50 NKYSSRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-----RDILNEGDEVRVKVIKID 117 (233)
Q Consensus 50 ~~~~~~~~~G~vv~g~-------~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~-----~~~~~~Gd~V~vkVi~vd 117 (233)
+.-.....+|.+|.|+ =-.+||+++. .-.||+|.+++.+ +...+ ...++.||.+-|.|+.-.
T Consensus 29 e~~~~~~~~gniy~grv~~i~p~~~aafvdig~-----~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~ 102 (487)
T COG1530 29 ERGAKEQIVGNIYKGRVTRVLPSLEAAFVDIGL-----ERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEP 102 (487)
T ss_pred ecCCcEeeecCceEEEecccCccchhheeeccC-----CccceEEecccch-hhhhcccccceeeecCCceEEEEEEeec
Confidence 3445566789999999 2358999983 6789999999998 54433 457999999999999876
Q ss_pred CCCCeEEEEEe
Q 026794 118 REKSRITLSIK 128 (233)
Q Consensus 118 ~e~~ri~LS~k 128 (233)
..+.--.||..
T Consensus 103 ~G~Kga~lT~~ 113 (487)
T COG1530 103 RGTKGARLTTD 113 (487)
T ss_pred CccccccceeE
Confidence 54443344443
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=81.94 E-value=1.4 Score=31.23 Aligned_cols=42 Identities=10% Similarity=0.099 Sum_probs=30.4
Q ss_pred CCCCCCCCCchhHhhhcccCCCCEE-EEEEEEEeCCCCEEEEEec
Q 026794 2 SPSHSCKEPQKSIHEIAKGLTGSII-SVKVIQANEEMKKLVFSEK 45 (233)
Q Consensus 2 ~~~~~~~~p~~~~~~~~~~~vG~~v-~~~Vi~id~~~~~i~lS~k 45 (233)
+.+||+.++++.......-.+||++ ++.|+ |...+.+.+|.|
T Consensus 30 ~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL--~~~~r~i~lt~K 72 (72)
T cd05699 30 PTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK 72 (72)
T ss_pred EccccCCchhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence 4578877666555433444599999 88888 888888888865
No 173
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=80.57 E-value=2.8 Score=34.66 Aligned_cols=59 Identities=14% Similarity=0.085 Sum_probs=39.0
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccc-------------cc--cccCceEEEEeecCCCCC---
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFE-------------KR--VVSQDLQLWLSNAPPSGK--- 214 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~-------------~~--~vg~~~~v~i~~~d~~~~--- 214 (233)
+.|.|+.+.+. |.++++. .++|+. +..++.. .. .+||.+.++|.+++.++.
T Consensus 85 v~g~V~~v~~~------Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~ 157 (187)
T PRK08563 85 VEGEVVEVVEF------GAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPR 157 (187)
T ss_pred EEEEEEEEEcc------EEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCC
Confidence 56888888754 5555555 377773 2222111 01 569999999999987653
Q ss_pred --EEEEEEcc
Q 026794 215 --KFTLLARA 222 (233)
Q Consensus 215 --ki~Ls~r~ 222 (233)
++.|+++.
T Consensus 158 ~~~I~ls~~~ 167 (187)
T PRK08563 158 GSKIGLTMRQ 167 (187)
T ss_pred CCEEEEEecC
Confidence 89999884
No 174
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=79.75 E-value=9.3 Score=29.77 Aligned_cols=56 Identities=16% Similarity=0.197 Sum_probs=31.2
Q ss_pred CCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcc-------------cccCcccccCCCCEEEEEEEEEeC
Q 026794 58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-------------LIQDIRDILNEGDEVRVKVIKIDR 118 (233)
Q Consensus 58 ~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~-------------~~~~~~~~~~~Gd~V~vkVi~vd~ 118 (233)
+|+++.|+ ..|+.|.|+ .=-+-+||.+.|... +-.+-.-++..|+.|+.||.++..
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 45666665 456666664 223455666655421 113334457899999999999875
No 175
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=79.20 E-value=1.6 Score=37.31 Aligned_cols=73 Identities=26% Similarity=0.411 Sum_probs=51.9
Q ss_pred cCCCCCCEEEEE-------eeeEEEEEccCCCCccEEEEEEccccCcccccCc-ccc---c--CCCCEEEEEEEEEeCCC
Q 026794 54 SRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-RDI---L--NEGDEVRVKVIKIDREK 120 (233)
Q Consensus 54 ~~~~~G~vv~g~-------~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~-~~~---~--~~Gd~V~vkVi~vd~e~ 120 (233)
.+++.|+++-|+ .||+||+++ ..+-...++|+|.-+|....-..| ++. | =.-..++|-|.++|...
T Consensus 71 ~~~~~Gdv~vGrl~~l~~vgyg~yvdig-V~~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~evnk~~ 149 (247)
T COG4044 71 SKVEEGDVYVGRLIDLGKVGYGAYVDIG-VLGPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEVNKLA 149 (247)
T ss_pred ccCCCCcEEEEEEeeeccceeEEEcccc-ccCCCcccccccHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEeccchh
Confidence 788999999999 899999986 222124689999999877665454 222 2 23457888899998766
Q ss_pred CeEEEEE
Q 026794 121 SRITLSI 127 (233)
Q Consensus 121 ~ri~LS~ 127 (233)
+.|...+
T Consensus 150 ~EIea~l 156 (247)
T COG4044 150 QEIEARL 156 (247)
T ss_pred hhhhhhh
Confidence 6665443
No 176
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=70.55 E-value=11 Score=25.48 Aligned_cols=55 Identities=9% Similarity=0.030 Sum_probs=26.9
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEEeeccccccccccCceEEEEeecCCCCCEEEEE
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLL 219 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~~~~~~~~~~~vg~~~~v~i~~~d~~~~ki~Ls 219 (233)
.+.+|.... ++++||....+-+-+.+.+.-.++..+||+++|.+=. |.++ |+...
T Consensus 5 ~~L~V~~~~------~~g~fL~~~~~~~vlLp~~e~~~~~~~Gd~v~VFvY~-D~~~-rl~AT 59 (61)
T PF13509_consen 5 NTLKVVDKN------EFGYFLDDGEGKEVLLPKSEVPEPLKVGDEVEVFVYL-DKEG-RLVAT 59 (61)
T ss_dssp ----EEEE-------SSEEEEEETT-EEEEEEGGG------TTSEEEEEEEE--TTS--EEEE
T ss_pred cceEEEEEe------CCEEEEECCCCCEEEechHHcCCCCCCCCEEEEEEEE-CCCC-CEEEe
Confidence 456777666 4577786555555554444333344899999999965 6554 45443
No 177
>PRK05054 exoribonuclease II; Provisional
Probab=68.03 E-value=6.7 Score=38.97 Aligned_cols=58 Identities=10% Similarity=0.035 Sum_probs=40.1
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecc--c--c---------c---cccccCceEEEEeecCCCCCEE
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQ--G--F---------E---KRVVSQDLQLWLSNAPPSGKKF 216 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~--~--~---------~---~~~vg~~~~v~i~~~d~~~~ki 216 (233)
.+|.|+.+.++ ++++.|+ +.|++|+. +..+ . . . .-.+||.++|++.++|+++++|
T Consensus 565 f~g~I~~v~~~----G~fV~l~-~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~~i 639 (644)
T PRK05054 565 FAAEIIDISRG----GMRVRLL-ENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETRSI 639 (644)
T ss_pred EEEEEEeeecC----cEEEEEe-CCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccCeE
Confidence 66888888866 5655553 45788883 2221 0 0 0 1157999999999999999998
Q ss_pred EEE
Q 026794 217 TLL 219 (233)
Q Consensus 217 ~Ls 219 (233)
.+.
T Consensus 640 ~~~ 642 (644)
T PRK05054 640 IAR 642 (644)
T ss_pred EEE
Confidence 765
No 178
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=64.27 E-value=39 Score=24.83 Aligned_cols=55 Identities=22% Similarity=0.163 Sum_probs=38.6
Q ss_pred eeeEE-EEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794 66 DYGAF-IHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129 (233)
Q Consensus 66 ~~G~f-V~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~ 129 (233)
+.+.| |.|++ |..-+.|+|-=-.. -.-.+-+||.|.|.+-..|.++++|..-.|.
T Consensus 18 p~~~frV~Len-----G~~vla~isGKmR~----~rIrIl~GD~V~VE~spYDltkGRIiyR~~~ 73 (87)
T PRK12442 18 PDSRFRVTLEN-----GVEVGAYASGRMRK----HRIRILAGDRVTLELSPYDLTKGRINFRHKD 73 (87)
T ss_pred CCCEEEEEeCC-----CCEEEEEeccceee----eeEEecCCCEEEEEECcccCCceeEEEEecC
Confidence 44444 57763 67777777642211 1122678999999999999999999998873
No 179
>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=64.20 E-value=16 Score=24.34 Aligned_cols=39 Identities=18% Similarity=0.208 Sum_probs=27.9
Q ss_pred EEeeccccccccccCceEEEEeecCCCCCEEEEEEccccee
Q 026794 186 VRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRCK 226 (233)
Q Consensus 186 l~~~~~~~~~~~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~v 226 (233)
|.++|..-+.-.+|+++++.+.+++ ++++.|...|-+.+
T Consensus 2 LvLsRk~gE~I~Ig~~I~I~Vl~i~--~~~VklgI~AP~~v 40 (54)
T PF02599_consen 2 LVLSRKVGESIVIGDDIEITVLEIS--GGQVKLGIDAPKEV 40 (54)
T ss_dssp EEEEEETT-EEEETTTEEEEEEEEE--TTEEEEEEEECTTS
T ss_pred eEEEccCCCEEEECCCEEEEEEEEc--CCEEEEEEECCCCC
Confidence 4577866555588999999998877 66677776665544
No 180
>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=60.68 E-value=31 Score=24.13 Aligned_cols=51 Identities=25% Similarity=0.244 Sum_probs=35.0
Q ss_pred eeeEE-EEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 026794 66 DYGAF-IHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125 (233)
Q Consensus 66 ~~G~f-V~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~L 125 (233)
+.+.| |.|.+ |.+-++|+|-=-. .-+-.+.+||.|.|.+-..|.++++|..
T Consensus 16 ~~~~f~V~l~n-----g~~vla~i~GKmr----~~rI~I~~GD~V~Ve~spyd~tkgrIi~ 67 (68)
T TIGR00008 16 PNAMFRVELEN-----GHEVLAHISGKIR----MHYIRILPGDKVKVELSPYDLTRGRITY 67 (68)
T ss_pred CCCEEEEEECC-----CCEEEEEecCcch----hccEEECCCCEEEEEECcccCCcEeEEe
Confidence 44444 47763 7778888765222 1123377899999999999998888864
No 181
>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=60.38 E-value=49 Score=22.15 Aligned_cols=31 Identities=29% Similarity=0.292 Sum_probs=23.6
Q ss_pred cEEEEEEccccCcccccCcccccCCCCEEEEEEEE
Q 026794 81 HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115 (233)
Q Consensus 81 gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~ 115 (233)
+-+-|+|+|++.... -..++.|+.|...+..
T Consensus 23 ~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 23 GEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE 53 (66)
T ss_dssp SSEEEEEGGGBCSSS----STS--TTSEEEEEEEE
T ss_pred ceeEEeccccccccc----cccCCCCCEEEEEEEE
Confidence 458999999998654 2457889999999988
No 182
>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=58.55 E-value=37 Score=25.74 Aligned_cols=49 Identities=16% Similarity=0.311 Sum_probs=36.7
Q ss_pred CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEe
Q 026794 57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKID 117 (233)
Q Consensus 57 ~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd 117 (233)
..|.++.|+ +.-+|+++++ ...+.|+..+... +.|..|..|.+++.+..
T Consensus 22 ~~gk~V~G~I~hvv~ddLYIDfG~-----KFhcVc~rp~~~~-------~~y~~G~rV~lrLkdlE 75 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDDDLYIDFGG-----KFHCVCKRPAVNG-------EKYVRGSRVRLRLKDLE 75 (104)
T ss_pred ccCCEEEEEEEEEecCceEEEeCC-----ceeEEEecccccc-------cccccCCEEEEEECCHh
Confidence 467788887 5579999984 6899999776533 34788999988876643
No 183
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=57.10 E-value=7.5 Score=38.16 Aligned_cols=59 Identities=8% Similarity=0.001 Sum_probs=44.9
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEEeecccc--ccccccCceEEEEeecCCCCCEEEEEEc
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGF--EKRVVSQDLQLWLSNAPPSGKKFTLLAR 221 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~~~~~~~--~~~~vg~~~~v~i~~~d~~~~ki~Ls~r 221 (233)
..|+|.+++ .|++|+++.+.+.||.-.++-. .+..+|+++-|.++.+-++++.+++--.
T Consensus 126 Y~g~v~~v~------~~GvFv~Ln~~v~GL~~~~d~~~~~~~~vgdeiiV~v~~vr~~~geidf~~~ 186 (715)
T COG1107 126 YKGIVSRVE------KYGVFVELNSHVRGLIHRRDLGGDPDYAVGDEIIVQVSDVRPEKGEIDFEPV 186 (715)
T ss_pred eeccccchh------hhcceeecChhhhccccccccCCCCCCCCCCeEEEEeeccCCCCCccceeec
Confidence 458877766 7799999999999995333221 2337899999999999999888887654
No 184
>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=54.26 E-value=17 Score=24.93 Aligned_cols=28 Identities=18% Similarity=0.338 Sum_probs=22.2
Q ss_pred ccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794 100 RDILNEGDEVRVKVIKIDREKSRITLSI 127 (233)
Q Consensus 100 ~~~~~~Gd~V~vkVi~vd~e~~ri~LS~ 127 (233)
...+-+||++++.|+.+|.-+.++.+|+
T Consensus 38 g~nl~pGqK~kaviLhvD~l~~~VhVSl 65 (65)
T cd05700 38 GVNVTPGCKLKAVILHVDFVKSQVHVSL 65 (65)
T ss_pred ceecCCCceeEEEEEEEeeEEeEEEEeC
Confidence 3447789999999999998776666653
No 185
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=53.16 E-value=6.4 Score=41.29 Aligned_cols=66 Identities=9% Similarity=0.096 Sum_probs=46.4
Q ss_pred CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcc
Q 026794 154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARA 222 (233)
Q Consensus 154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~ 222 (233)
|..+.+.|.+++.. .+.|+.+.+..|++|++ +|...+..| .|||.+.++|..+|.++=..-||.|.
T Consensus 986 g~iV~~~V~~vt~r---r~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~ 1059 (1299)
T KOG1856|consen 986 GAIVPVTVTKVTHR---RGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRT 1059 (1299)
T ss_pred CceEEEeeeEEEec---ccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhh
Confidence 44466777777643 26788889999999996 444333333 58999999999999876555555553
No 186
>PRK01712 carbon storage regulator; Provisional
Probab=52.62 E-value=27 Score=24.20 Aligned_cols=39 Identities=15% Similarity=0.194 Sum_probs=27.8
Q ss_pred EEeeccccccccccCceEEEEeecCCCCCEEEEEEccccee
Q 026794 186 VRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRCK 226 (233)
Q Consensus 186 l~~~~~~~~~~~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~v 226 (233)
|.++|..-+.-.+|+++++++.++. ++++.|...|=+.+
T Consensus 2 LvLtRk~gE~I~Igd~I~I~V~~i~--~~~VrlGI~AP~~v 40 (64)
T PRK01712 2 LILTRKVGESLMIGDDIEVTVLGVK--GNQVRIGINAPKEV 40 (64)
T ss_pred eeEEccCCCEEEeCCCEEEEEEEEe--CCEEEEEEECCCCc
Confidence 4577866565588999999996655 66777777665543
No 187
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=52.45 E-value=27 Score=25.56 Aligned_cols=26 Identities=27% Similarity=0.356 Sum_probs=22.8
Q ss_pred ccCCCCEEEEEEEEEeCCCCEEEEEe
Q 026794 19 KGLTGSIISVKVIQANEEMKKLVFSE 44 (233)
Q Consensus 19 ~~~vG~~v~~~Vi~id~~~~~i~lS~ 44 (233)
+.++|..+.+.|+.+|.++|=|-||.
T Consensus 60 kllVGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 60 KKLVGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred hhhcCCeeEEEEEEECCCCCEEEeEc
Confidence 34599999999999999999988874
No 188
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=50.79 E-value=7.8 Score=34.31 Aligned_cols=62 Identities=15% Similarity=0.226 Sum_probs=44.4
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEE----Eeeccccccc----cccCceEEEEeecCCCCCEEEEEEcc
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDV----RITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARA 222 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl----~~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~ 222 (233)
+.+.|..+..+ |.-+.|.-=+.|+|+ ++||+|+..- .||-.=.|.+..+|.++|-|-||.|.
T Consensus 20 VmvnV~sIaem----Gayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrr 89 (304)
T KOG2916|consen 20 VMVNVRSIAEM----GAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRR 89 (304)
T ss_pred EEEEeeEehhc----cceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhcc
Confidence 45677766643 222233333468888 4899887544 58988889999999999999999875
No 189
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=49.20 E-value=82 Score=22.18 Aligned_cols=54 Identities=22% Similarity=0.183 Sum_probs=34.7
Q ss_pred eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecc
Q 026794 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (233)
Q Consensus 66 ~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~ 130 (233)
-|| |+.-++ .+-+-|+|+|.+...- ...+..||.|...+..-. +++-...+..+
T Consensus 14 GfG-FI~~~~----gg~dVFvH~s~i~~~g----~~~l~~G~~V~f~~~~~~--~G~~A~~V~~~ 67 (74)
T PRK09937 14 GFG-FICPEG----GGEDIFAHYSTIQMDG----YRTLKAGQSVQFDVHQGP--KGNHASVIVPV 67 (74)
T ss_pred CeE-EEeeCC----CCccEEEEEeeccccC----CCCCCCCCEEEEEEEECC--CCceeeEEEEC
Confidence 344 565542 2689999999996432 234778999999887754 45444444433
No 190
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=47.42 E-value=52 Score=28.73 Aligned_cols=37 Identities=16% Similarity=0.278 Sum_probs=25.4
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechhhHhhhccCCCCCCEEE
Q 026794 22 TGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFV 63 (233)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~~~~~~~~~~~~G~vv~ 63 (233)
+|+.|.++|..+|+ .+.+.|+.|... .-+++.|.++.
T Consensus 115 vGD~v~AkV~~vd~-~~~~~L~~k~~~----~GkL~~G~iv~ 151 (239)
T COG1097 115 VGDLVYAKVVDVDR-DGEVELTLKDEG----LGKLKNGQIVK 151 (239)
T ss_pred cCCEEEEEEEEccC-CCceEEEeecCC----CccccCCEEEE
Confidence 89999999999996 466777775443 33444444433
No 191
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=46.76 E-value=59 Score=22.45 Aligned_cols=43 Identities=23% Similarity=0.292 Sum_probs=29.1
Q ss_pred eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEe
Q 026794 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKID 117 (233)
Q Consensus 66 ~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd 117 (233)
.|| |+.-.+ .+-+-|+|+|.+..... ..+..||.|...+..-+
T Consensus 16 GyG-FI~~~~----g~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~~~ 58 (69)
T PRK09507 16 GFG-FITPED----GSKDVFVHFSAIQTNGF----KTLAEGQRVEFEITNGA 58 (69)
T ss_pred CcE-EEecCC----CCeeEEEEeecccccCC----CCCCCCCEEEEEEEECC
Confidence 455 565542 25799999999964321 34678999998776643
No 192
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=45.84 E-value=28 Score=32.35 Aligned_cols=45 Identities=11% Similarity=0.170 Sum_probs=30.3
Q ss_pred CCCCEEEEEEEEEeCCCC---EEEEEechhhHhhhccCCCCCCEEEEE
Q 026794 21 LTGSIISVKVIQANEEMK---KLVFSEKDAVWNKYSSRVNVEDIFVGR 65 (233)
Q Consensus 21 ~vG~~v~~~Vi~id~~~~---~i~lS~k~~~~~~~~~~~~~G~vv~g~ 65 (233)
.+|+.++|.|.+++...+ .+.||+....+-.-+-..++=++.+|+
T Consensus 178 ~~Gdrik~~i~~V~~~~k~gp~IilSRt~p~~v~~Lfe~EVPEI~dG~ 225 (374)
T PRK12328 178 KVGDVVKAVLKRVKIDKNNGILIELSRTSPKFLEALLELEVPEIKDGE 225 (374)
T ss_pred CCCCEEEEEEEEEecCCCCCCEEEEEcCCHHHHHHHHHHhCccccCCe
Confidence 389999999999998765 899999876432222223444444444
No 193
>PRK00568 carbon storage regulator; Provisional
Probab=45.67 E-value=34 Score=24.50 Aligned_cols=38 Identities=13% Similarity=0.119 Sum_probs=26.0
Q ss_pred EEeeccccccccccCceEEEEeecCCCCCEEEEEEcccce
Q 026794 186 VRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRC 225 (233)
Q Consensus 186 l~~~~~~~~~~~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~ 225 (233)
|.++|..-+.-.+|+++++++.++. ++++.|-.-|=+.
T Consensus 2 LVLtRK~gEsI~Igd~I~I~Vl~i~--g~~VrlGI~AP~~ 39 (76)
T PRK00568 2 LILSRKVNEGIVIDDNIHIKVISID--RGSVRLGFEAPES 39 (76)
T ss_pred ceEEeeCCCeEEeCCCeEEEEEEEc--CCEEEEEEECCCC
Confidence 3577766565588999999996555 5666666655443
No 194
>PRK15464 cold shock-like protein CspH; Provisional
Probab=44.70 E-value=57 Score=22.76 Aligned_cols=39 Identities=21% Similarity=0.051 Sum_probs=28.0
Q ss_pred EEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEE
Q 026794 70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 116 (233)
Q Consensus 70 fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~v 116 (233)
|+.-++ .+-+-|+|+|.+...- ...+..||.|...+..-
T Consensus 20 FI~~~~----g~~DvFvH~s~l~~~g----~~~l~~G~~V~f~v~~~ 58 (70)
T PRK15464 20 FIIPSD----GRKEVQVHISAFTPRD----AEVLIPGLRVEFCRVNG 58 (70)
T ss_pred EEccCC----CCccEEEEehhehhcC----CCCCCCCCEEEEEEEEC
Confidence 666652 2579999999996432 23477899999888774
No 195
>PRK15463 cold shock-like protein CspF; Provisional
Probab=43.35 E-value=49 Score=23.01 Aligned_cols=39 Identities=21% Similarity=0.060 Sum_probs=27.9
Q ss_pred EEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEE
Q 026794 70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 116 (233)
Q Consensus 70 fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~v 116 (233)
|++-++ .+-+-|+|+|.+...-. ..++.||.|...+..-
T Consensus 20 FI~~~~----g~~DvFvH~sal~~~g~----~~l~~G~~V~f~v~~~ 58 (70)
T PRK15463 20 LITPSD----GRKDVQVHISALNLRDA----EELTTGLRVEFCRING 58 (70)
T ss_pred EEecCC----CCccEEEEehhhhhcCC----CCCCCCCEEEEEEEEC
Confidence 666652 25799999999975422 3477899999977663
No 196
>PRK10943 cold shock-like protein CspC; Provisional
Probab=42.51 E-value=73 Score=21.98 Aligned_cols=42 Identities=24% Similarity=0.248 Sum_probs=28.9
Q ss_pred eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEE
Q 026794 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 116 (233)
Q Consensus 66 ~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~v 116 (233)
.|| |+.-.+ .+-+-|+|+|.+.... ...+..||.|...+..-
T Consensus 16 GfG-FI~~~~----g~~dvFvH~s~l~~~g----~~~l~~G~~V~f~~~~~ 57 (69)
T PRK10943 16 GFG-FITPAD----GSKDVFVHFSAIQGNG----FKTLAEGQNVEFEIQDG 57 (69)
T ss_pred CcE-EEecCC----CCeeEEEEhhHccccC----CCCCCCCCEEEEEEEEC
Confidence 344 565542 2579999999997542 23467899999887664
No 197
>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=41.82 E-value=33 Score=34.17 Aligned_cols=57 Identities=11% Similarity=0.112 Sum_probs=37.3
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eec--ccc-----c-------c--ccccCceEEEEeecCCCCCEE
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITR--QGF-----E-------K--RVVSQDLQLWLSNAPPSGKKF 216 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~--~~~-----~-------~--~~vg~~~~v~i~~~d~~~~ki 216 (233)
..|.|+.+.++ ++++.|+ +.|++|+. +.. +.. + . -.+||.|+|++.++|.++++|
T Consensus 561 f~g~I~~v~~~----g~~v~l~-~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i 635 (639)
T TIGR02062 561 FAAEIVDISRG----GMRVRLL-ENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSI 635 (639)
T ss_pred EEEEEEeeeCC----cEEEEEe-cCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccCcE
Confidence 55777777755 4444442 56788883 221 100 0 1 147999999999999999988
Q ss_pred EE
Q 026794 217 TL 218 (233)
Q Consensus 217 ~L 218 (233)
.+
T Consensus 636 ~~ 637 (639)
T TIGR02062 636 IA 637 (639)
T ss_pred ee
Confidence 65
No 198
>COG1551 CsrA RNA-binding global regulator CsrA [Signal transduction mechanisms]
Probab=41.38 E-value=41 Score=23.81 Aligned_cols=37 Identities=14% Similarity=0.244 Sum_probs=25.2
Q ss_pred EEeeccccccccccCceEEEEeecCCCCCEEEEEEcccc
Q 026794 186 VRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGR 224 (233)
Q Consensus 186 l~~~~~~~~~~~vg~~~~v~i~~~d~~~~ki~Ls~r~~~ 224 (233)
|.++|..-+.-.+||++++.+.+++ .+.+.+-..|-+
T Consensus 2 LILsRk~~Esi~IgddI~itVl~i~--gnqVkiGi~APk 38 (73)
T COG1551 2 LILSRKVGESIMIGDDIEITVLSIK--GNQVKIGINAPK 38 (73)
T ss_pred eeEEeecCceEEecCCeEEEEEEEc--CCeEEEeecCCh
Confidence 4577866665689999999996665 555555554433
No 199
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=40.89 E-value=80 Score=26.17 Aligned_cols=29 Identities=31% Similarity=0.526 Sum_probs=23.8
Q ss_pred cccCCCCEEEE----------EEEEEeCCCCeEEEEEec
Q 026794 101 DILNEGDEVRV----------KVIKIDREKSRITLSIKQ 129 (233)
Q Consensus 101 ~~~~~Gd~V~v----------kVi~vd~e~~ri~LS~k~ 129 (233)
..|.+||.|++ +|.++|.+++++.+.+-.
T Consensus 122 ~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~i 160 (178)
T COG0250 122 VDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSI 160 (178)
T ss_pred ccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEEEEE
Confidence 45889999987 699999998888887643
No 200
>COG1278 CspC Cold shock proteins [Transcription]
Probab=40.83 E-value=44 Score=23.35 Aligned_cols=32 Identities=25% Similarity=0.295 Sum_probs=23.7
Q ss_pred cEEEEEEccccCcccccCcccccCCCCEEEEEEEEE
Q 026794 81 HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 116 (233)
Q Consensus 81 gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~v 116 (233)
+-+.|+|+|.+...-.. .+..||+|...+..=
T Consensus 24 ~~DvFVH~Sai~~~g~~----~L~eGQ~V~f~~~~g 55 (67)
T COG1278 24 GKDVFVHISAIQRAGFR----TLREGQKVEFEVEQG 55 (67)
T ss_pred CcCEEEEeeeeccCCCc----ccCCCCEEEEEEecC
Confidence 47999999999654332 366799999877653
No 201
>PF03152 UFD1: Ubiquitin fusion degradation protein UFD1; InterPro: IPR004854 Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified []. This family includes UFD1, a 40kDa protein that is essential for vegetative cell viability []. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterised by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1ZC1_A 2YUJ_A.
Probab=39.82 E-value=33 Score=28.50 Aligned_cols=99 Identities=14% Similarity=0.273 Sum_probs=55.3
Q ss_pred cCCCCEEEEEEEEEeCCCCEEEEEechhhHhhhccCCCCCCEEEEE----eeeEEEEEccCCCCccEEEEEEccccCc--
Q 026794 20 GLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVSEVSW-- 93 (233)
Q Consensus 20 ~~vG~~v~~~Vi~id~~~~~i~lS~k~~~~~~~~~~~~~G~vv~g~----~~G~fV~l~~~~~~~gv~Glv~~sels~-- 93 (233)
...++.+.|-|+++.-+.|.+.+.. |.--.-.++.|+.+.-+ +.|-||.|. +--.+|..+++...
T Consensus 54 ~~~~~~th~GVlEFsA~eG~i~lP~----wmm~~L~l~~g~~V~v~~~~LPkgt~vkLq-----P~~~~F~~i~n~KavL 124 (176)
T PF03152_consen 54 PDNGKRTHCGVLEFSAEEGTIYLPP----WMMQNLGLQEGDIVRVEYVSLPKGTFVKLQ-----PQSSDFLDISNPKAVL 124 (176)
T ss_dssp TTTTEEEEEEEEEE--CTTEEEE-C----HHHHHHT--TTEEEEEEEEE----SEEEEE-----ESCHHHHCSS-HHHHH
T ss_pred CCCCcEEEEEEEEeEcCCCeEEeCc----cHHhhcCCCCCCEEEEEEeECCCCCEEEEe-----ECCCccccccchHHHH
Confidence 3468889999999998889988876 43333467899998765 889999997 22234444333211
Q ss_pred -ccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccC
Q 026794 94 -DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEED 133 (233)
Q Consensus 94 -~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~d 133 (233)
....+ ...+..||.+.+. ..+....|.+-+++++
T Consensus 125 E~~Lr~-ystLT~Gd~I~i~-----~~~~~y~l~V~e~kP~ 159 (176)
T PF03152_consen 125 ERALRN-YSTLTKGDTISIE-----YNNKTYELDVVEVKPE 159 (176)
T ss_dssp HHHHCC--SEEETTSEEEEE-----CTTEEEEEEEEEECSS
T ss_pred Hhhccc-CceeecCCEEEEE-----eCCEEEEEEEEEEcCC
Confidence 01111 2337789988753 3455666666666443
No 202
>PRK01712 carbon storage regulator; Provisional
Probab=39.41 E-value=51 Score=22.80 Aligned_cols=34 Identities=21% Similarity=0.431 Sum_probs=26.8
Q ss_pred cccccCCCCEEEEEEEEEeCCCCeEEEEEeccccCh
Q 026794 99 IRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134 (233)
Q Consensus 99 ~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp 134 (233)
+.+.+.+|+.+.++|+++. .+++.|++.+-..-|
T Consensus 8 ~gE~I~Igd~I~I~V~~i~--~~~VrlGI~AP~~v~ 41 (64)
T PRK01712 8 VGESLMIGDDIEVTVLGVK--GNQVRIGINAPKEVS 41 (64)
T ss_pred CCCEEEeCCCEEEEEEEEe--CCEEEEEEECCCCce
Confidence 4566778999999999997 778999987654444
No 203
>PRK14998 cold shock-like protein CspD; Provisional
Probab=39.30 E-value=1.3e+02 Score=21.10 Aligned_cols=43 Identities=26% Similarity=0.230 Sum_probs=30.0
Q ss_pred eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEe
Q 026794 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKID 117 (233)
Q Consensus 66 ~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd 117 (233)
-|| |+.-.+ .+-+-|+|+|.+...- ...+..||.|...+..-+
T Consensus 14 GfG-FI~~~~----g~~dVFvH~s~l~~~g----~~~l~~G~~V~f~~~~~~ 56 (73)
T PRK14998 14 GFG-FICPEG----GGEDIFAHYSTIQMDG----YRTLKAGQSVRFDVHQGP 56 (73)
T ss_pred ceE-EEecCC----CCccEEEEeeeecccC----CCCCCCCCEEEEEEEECC
Confidence 344 565542 2679999999996432 244778999999887754
No 204
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=38.93 E-value=85 Score=24.85 Aligned_cols=43 Identities=19% Similarity=0.077 Sum_probs=27.2
Q ss_pred EEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeE
Q 026794 69 AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRI 123 (233)
Q Consensus 69 ~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri 123 (233)
+.|+|++ +-..+.|+.. .++. .+++|+.|++++.....+...+
T Consensus 88 aiV~l~~-----~~~i~~~i~~------~~p~-~v~iGm~V~~v~~~~~~~~~~~ 130 (140)
T COG1545 88 AIVELEE-----GGRILGQLVD------VDPD-DVEIGMKVEAVFRKREEDGGRG 130 (140)
T ss_pred EEEEeCC-----CCceEEEEEe------cCcc-cccCCCEEEEEEEEccccCCce
Confidence 4667753 2355555554 1233 4789999999999877554433
No 205
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=38.88 E-value=41 Score=24.25 Aligned_cols=21 Identities=29% Similarity=0.401 Sum_probs=15.6
Q ss_pred cccccCCCCEEEEEEEEEeCC
Q 026794 99 IRDILNEGDEVRVKVIKIDRE 119 (233)
Q Consensus 99 ~~~~~~~Gd~V~vkVi~vd~e 119 (233)
.+..|++||+|.++++-.+.+
T Consensus 7 Dr~iYrPGetV~~~~~~~~~~ 27 (99)
T PF01835_consen 7 DRPIYRPGETVHFRAIVRDLD 27 (99)
T ss_dssp SSSEE-TTSEEEEEEEEEEEC
T ss_pred CccCcCCCCEEEEEEEEeccc
Confidence 356799999999999955543
No 206
>TIGR00202 csrA carbon storage regulator (csrA). Modulates the expression of genes in the glycogen biosynthesis and gluconeogenesis pathways by accelerating the 5'-to-3' degradation of these transcripts through selective RNA binding. The N-terminal end of the sequence (AA 11-45) contains the KH motif which is characteristic of a set of RNA-binding proteins.
Probab=38.77 E-value=56 Score=22.95 Aligned_cols=38 Identities=16% Similarity=0.211 Sum_probs=26.6
Q ss_pred EEeeccccccccccCceEEEEeecCCCCCEEEEEEcccce
Q 026794 186 VRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRC 225 (233)
Q Consensus 186 l~~~~~~~~~~~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~ 225 (233)
|.++|..-+.-.+|+++++++.++. ++++.|-..|=+.
T Consensus 2 LiLtRk~gE~I~Igd~I~I~Vl~i~--g~~VrlGI~AP~~ 39 (69)
T TIGR00202 2 LILSRKVNESIQIGDDIEVKVLSVK--GDQVKLGIEAPKE 39 (69)
T ss_pred eeEEccCCCEEEeCCCEEEEEEEEc--CCeEEEEEECCCC
Confidence 4577766555588999999996655 6667776655444
No 207
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=38.39 E-value=1.5e+02 Score=21.20 Aligned_cols=52 Identities=27% Similarity=0.196 Sum_probs=36.0
Q ss_pred eEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794 68 GAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128 (233)
Q Consensus 68 G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k 128 (233)
-+.|.+.+ |..-+.|+|-=-.. -.-.+.+||.|.|..-..|.++++|..-.+
T Consensus 21 ~f~v~~ed-----g~~~~ahI~GKmr~----~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~ 72 (75)
T COG0361 21 RFRVELEN-----GHERLAHISGKMRK----NRIRILPGDVVLVELSPYDLTKGRIVYRYK 72 (75)
T ss_pred EEEEEecC-----CcEEEEEccCcchh----eeEEeCCCCEEEEEecccccccccEEEEec
Confidence 35567763 67777776643222 122377899999999999988888887554
No 208
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=37.36 E-value=50 Score=24.30 Aligned_cols=60 Identities=12% Similarity=0.119 Sum_probs=38.8
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEE-eecccccc---ccccCceEEEEeecCCCCCEEEEEEc
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEK---RVVSQDLQLWLSNAPPSGKKFTLLAR 221 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~-~~~~~~~~---~~vg~~~~v~i~~~d~~~~ki~Ls~r 221 (233)
++|+|+..-|- +.| .+++++|..-+. ++-.--.+ -..||.|.|-++.-|..+++|.--.+
T Consensus 9 ~~G~V~e~Lp~----~~f-rV~LenG~~vla~isGKmR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~ 72 (87)
T PRK12442 9 LDGIVDEVLPD----SRF-RVTLENGVEVGAYASGRMRKHRIRILAGDRVTLELSPYDLTKGRINFRHK 72 (87)
T ss_pred EEEEEEEECCC----CEE-EEEeCCCCEEEEEeccceeeeeEEecCCCEEEEEECcccCCceeEEEEec
Confidence 56777765432 222 346688877663 33211111 16799999999999999999987655
No 209
>PRK09890 cold shock protein CspG; Provisional
Probab=36.10 E-value=1.1e+02 Score=21.11 Aligned_cols=42 Identities=21% Similarity=0.268 Sum_probs=28.6
Q ss_pred eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEE
Q 026794 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 116 (233)
Q Consensus 66 ~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~v 116 (233)
.|| |+.-++ .+-+-|+|+|.+...-. ..++.||.|...+..-
T Consensus 17 GfG-FI~~~~----g~~dvFvH~s~l~~~~~----~~l~~G~~V~f~~~~~ 58 (70)
T PRK09890 17 GFG-FITPDD----GSKDVFVHFTAIQSNEF----RTLNENQKVEFSIEQG 58 (70)
T ss_pred CcE-EEecCC----CCceEEEEEeeeccCCC----CCCCCCCEEEEEEEEC
Confidence 344 566552 25799999999975422 3467899999876553
No 210
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=35.32 E-value=1.1e+02 Score=25.70 Aligned_cols=63 Identities=16% Similarity=0.182 Sum_probs=40.5
Q ss_pred hhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc-----------------CcccccCCCCE
Q 026794 51 KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------------DIRDILNEGDE 108 (233)
Q Consensus 51 ~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~-----------------~~~~~~~~Gd~ 108 (233)
-..-++-+|+++.|+ ..|+-|.|.- =-+-|||.+-|...... ...=++.+|..
T Consensus 74 ~vVFrPF~gEVi~gki~~cs~eG~rvtl~F-----FdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~ 148 (202)
T KOG3297|consen 74 VVVFRPFVGEVITGKIKECSEEGLRVTLGF-----FDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEE 148 (202)
T ss_pred EEEEecccceEEEEEeecCCccceEEEEEe-----eeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCe
Confidence 345577899999999 6777777741 12456666555432111 12234778999
Q ss_pred EEEEEEEEeC
Q 026794 109 VRVKVIKIDR 118 (233)
Q Consensus 109 V~vkVi~vd~ 118 (233)
|+.+|.+...
T Consensus 149 IRFRV~~e~f 158 (202)
T KOG3297|consen 149 IRFRVEDESF 158 (202)
T ss_pred EEEEEeeecc
Confidence 9999988754
No 211
>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=34.89 E-value=72 Score=30.05 Aligned_cols=50 Identities=12% Similarity=0.003 Sum_probs=33.0
Q ss_pred ccCCeeeeccCCChhhhhhhhcccCCeeEEE-eeccc---------------c---cc-ccccCceEEEEeecC
Q 026794 157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQG---------------F---EK-RVVSQDLQLWLSNAP 210 (233)
Q Consensus 157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~-~~~~~---------------~---~~-~~vg~~~~v~i~~~d 210 (233)
..|+|.++.| |++ ++|+++..|-.|+. ++.-. . .+ -..||++-|.|+.-.
T Consensus 29 Y~GrV~~i~p--~l~--aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~ 98 (414)
T TIGR00757 29 YKGRVTRILP--SLQ--AAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEP 98 (414)
T ss_pred EEEEEeeecC--CCc--eEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCC
Confidence 5699999875 444 56777799988984 22210 0 00 145999999998843
No 212
>KOG3754 consensus Gamma-glutamylcysteine synthetase [Coenzyme transport and metabolism]
Probab=33.46 E-value=44 Score=32.02 Aligned_cols=27 Identities=22% Similarity=0.195 Sum_probs=24.8
Q ss_pred CCCEEEEEEEEEeCCCCEEEEEechhh
Q 026794 22 TGSIISVKVIQANEEMKKLVFSEKDAV 48 (233)
Q Consensus 22 vG~~v~~~Vi~id~~~~~i~lS~k~~~ 48 (233)
=|++|+..|+++|.+++++.+|.++..
T Consensus 47 WGDEiEy~vV~fDd~~kk~rv~l~~e~ 73 (640)
T KOG3754|consen 47 WGDEIEYMVVKFDDKNKKARVSLRAEK 73 (640)
T ss_pred ccceeEEEEEecccccceeeeeeeHHH
Confidence 599999999999999999999998764
No 213
>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=32.44 E-value=87 Score=21.46 Aligned_cols=43 Identities=23% Similarity=0.283 Sum_probs=29.0
Q ss_pred eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEe
Q 026794 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKID 117 (233)
Q Consensus 66 ~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd 117 (233)
.|| |+.-++ .+-+-|+|+|.+...- ...++.||.|...+..=+
T Consensus 14 GfG-FI~~~~----g~~dvfvH~s~~~~~g----~~~l~~G~~V~f~~~~~~ 56 (68)
T TIGR02381 14 GFG-FICPEG----VDGDIFAHYSTIQMDG----YRTLKAGQKVQFEVVQGP 56 (68)
T ss_pred CeE-EEecCC----CCccEEEEHHHhhhcC----CCCCCCCCEEEEEEEECC
Confidence 355 555542 2679999999996432 234778999998766543
No 214
>PRK00568 carbon storage regulator; Provisional
Probab=32.11 E-value=69 Score=22.95 Aligned_cols=34 Identities=24% Similarity=0.421 Sum_probs=26.5
Q ss_pred cccccCCCCEEEEEEEEEeCCCCeEEEEEeccccCh
Q 026794 99 IRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134 (233)
Q Consensus 99 ~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp 134 (233)
..+.+.+||.++++|+++. .+++.|.+.+-..-+
T Consensus 8 ~gEsI~Igd~I~I~Vl~i~--g~~VrlGI~AP~~v~ 41 (76)
T PRK00568 8 VNEGIVIDDNIHIKVISID--RGSVRLGFEAPESTL 41 (76)
T ss_pred CCCeEEeCCCeEEEEEEEc--CCEEEEEEECCCCCe
Confidence 3456778999999999997 778999887654444
No 215
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=31.01 E-value=1.1e+02 Score=21.01 Aligned_cols=42 Identities=26% Similarity=0.274 Sum_probs=28.9
Q ss_pred eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEE
Q 026794 66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 116 (233)
Q Consensus 66 ~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~v 116 (233)
.|| |+.-++ .+-+-|+|+|.+...- ...++.||.|...+..-
T Consensus 17 GfG-FI~~~~----g~~dvfvH~s~l~~~g----~~~l~~G~~V~f~~~~~ 58 (70)
T PRK10354 17 GFG-FITPDD----GSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESG 58 (70)
T ss_pred CcE-EEecCC----CCccEEEEEeeccccC----CCCCCCCCEEEEEEEEC
Confidence 455 565542 2578999999996532 23478899999877663
No 216
>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=29.26 E-value=1.3e+02 Score=19.28 Aligned_cols=38 Identities=24% Similarity=0.153 Sum_probs=26.4
Q ss_pred hhccCCCCCCEEEEE-eeeEEEEEccCCCCccEEEEEEccccC
Q 026794 51 KYSSRVNVEDIFVGR-DYGAFIHLRFPDGLYHLTGLVHVSEVS 92 (233)
Q Consensus 51 ~~~~~~~~G~vv~g~-~~G~fV~l~~~~~~~gv~Glv~~sels 92 (233)
.....++.|..++-. ..|-|..+. .+ |..|.|+.+.|+
T Consensus 16 ~vv~~l~~g~~v~v~~~~~~W~~V~-~~---g~~GWv~~~~lw 54 (55)
T PF06347_consen 16 PVVARLEPGVPVRVIECRGGWCKVR-AD---GRTGWVHKSLLW 54 (55)
T ss_pred CEEEEECCCCEEEEEEccCCeEEEE-EC---CeEEeEEeeecc
Confidence 345667888888877 455445554 23 789999998875
No 217
>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=29.14 E-value=1.7e+02 Score=19.26 Aligned_cols=32 Identities=28% Similarity=0.244 Sum_probs=25.0
Q ss_pred cEEEEEEccccCcccccCcccccCCCCEEEEEEEEE
Q 026794 81 HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 116 (233)
Q Consensus 81 gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~v 116 (233)
+-+-|+|.+++...- ...+++||.|...+..-
T Consensus 23 g~diffh~~~~~~~~----~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 23 GEDVFVHISALEGDG----FRSLEEGDRVEFELEEG 54 (65)
T ss_pred CcCEEEEhhHhhccC----CCcCCCCCEEEEEEEEC
Confidence 678999999997542 24578899999887765
No 218
>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=26.32 E-value=2.4e+02 Score=20.74 Aligned_cols=34 Identities=9% Similarity=0.096 Sum_probs=27.3
Q ss_pred EEeCCCCEEEEEechhhHhhhccCCCCCCEEEEE
Q 026794 32 QANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR 65 (233)
Q Consensus 32 ~id~~~~~i~lS~k~~~~~~~~~~~~~G~vv~g~ 65 (233)
=.|.+++.+.++.-....+.+...+++|+++.=.
T Consensus 41 l~De~~~~I~~t~~~~~~~~f~~~l~eG~vy~i~ 74 (104)
T cd04474 41 LLDEDGGEIRATFFNDAVDKFYDLLEVGKVYYIS 74 (104)
T ss_pred EEECCCCEEEEEEehHHHHHhhcccccccEEEEe
Confidence 3566688999988877777888899999988754
No 219
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=25.65 E-value=2.3e+02 Score=24.04 Aligned_cols=54 Identities=15% Similarity=0.081 Sum_probs=35.7
Q ss_pred cccCCeeEEEeeccccccccccCceEEEEeecCCCCCEEEEEEcccceeeeeEec
Q 026794 178 LQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRCKRYNFHI 232 (233)
Q Consensus 178 ~~~~gv~gl~~~~~~~~~~~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~vq~~~~~ 232 (233)
...|.|--++++.-......-|--+..|++..|...| +.|..+.|.-+||++-|
T Consensus 150 a~~P~VKkVIPg~I~~~gs~~g~Gvr~KvtRaD~~GN-lrlLl~eGss~Qei~vV 203 (227)
T COG4031 150 AQHPYVKKVIPGVISAKGSAGGGGVRLKVTRADARGN-LRLLLSEGSSVQEIRVV 203 (227)
T ss_pred hcCCceeecccceeecCcccCCCceEEEEEeecCCCC-EEEEeecCCceeEEEEE
Confidence 3344444443333222222345569999999996666 99999999999999854
No 220
>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=25.11 E-value=2e+02 Score=20.07 Aligned_cols=45 Identities=11% Similarity=-0.000 Sum_probs=26.9
Q ss_pred EEEEEccCCCCccEEEEEEcc-ccCcccccCcccccCCCCEEEEEEEEEeC
Q 026794 69 AFIHLRFPDGLYHLTGLVHVS-EVSWDLIQDIRDILNEGDEVRVKVIKIDR 118 (233)
Q Consensus 69 ~fV~l~~~~~~~gv~Glv~~s-els~~~~~~~~~~~~~Gd~V~vkVi~vd~ 118 (233)
+.|.|.+ .+--..+|.+ .+.+- +..-++.+++||.+.|.+...+.
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 5566653 3444444443 34332 33335669999999999887654
No 221
>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=24.88 E-value=2e+02 Score=20.21 Aligned_cols=37 Identities=5% Similarity=0.143 Sum_probs=29.4
Q ss_pred EEEeCCCCEEEEEechhhHhhhccCCCCCCEEEEEee
Q 026794 31 IQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDY 67 (233)
Q Consensus 31 i~id~~~~~i~lS~k~~~~~~~~~~~~~G~vv~g~~~ 67 (233)
+=+|+++.+|.++......+.+...+++|.++.=.+|
T Consensus 24 iL~De~G~~I~a~i~~~~~~~f~~~L~eg~vy~is~f 60 (86)
T cd04480 24 VLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNF 60 (86)
T ss_pred EEEcCCCCEEEEEECHHHHHhhhhhceeCCEEEEeeE
Confidence 4456777799999998888889999999988764433
No 222
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=24.61 E-value=1.9e+02 Score=20.50 Aligned_cols=42 Identities=24% Similarity=0.288 Sum_probs=29.2
Q ss_pred cEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794 81 HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127 (233)
Q Consensus 81 gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~ 127 (233)
|..-++|++-= +.. .-.+++||.|.|.....|..+++|..-.
T Consensus 22 g~~~la~i~gK----~rk-~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~ 63 (77)
T cd05793 22 GKKRLCRIRGK----MRK-RVWINEGDIVLVAPWDFQDDKADIIYKY 63 (77)
T ss_pred CCEEEEEEchh----hcc-cEEEcCCCEEEEEeccccCCEEEEEEEc
Confidence 56666665542 222 3458899999999988887777776544
No 223
>PF07405 DUF1506: Protein of unknown function (DUF1506); InterPro: IPR010875 This entry represents proteins found primarily in Borrelia species. Their function is unknown.
Probab=23.35 E-value=77 Score=24.60 Aligned_cols=59 Identities=19% Similarity=0.214 Sum_probs=40.7
Q ss_pred eeEEEEEccCCCCccEEEEEEccccCccc--c---------cCcccccCCCCEEEEEEEEEeCCCCeEEEEEecc
Q 026794 67 YGAFIHLRFPDGLYHLTGLVHVSEVSWDL--I---------QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 130 (233)
Q Consensus 67 ~G~fV~l~~~~~~~gv~Glv~~sels~~~--~---------~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~ 130 (233)
.|+|+.+. |.--..++-+++++-. . -...|.++++|.+-..|+++|..-+...|-+|+.
T Consensus 54 ~Gv~i~I~-----P~E~v~i~~sNi~D~~~y~klYT~~~l~fE~~DrIsi~D~~yfeI~sid~si~Y~TLvLk~~ 123 (127)
T PF07405_consen 54 KGVIIDIK-----PQELVEIYDSNIFDIQGYSKLYTYQNLNFELKDRISISDDVYFEIFSIDSSIGYFTLVLKEF 123 (127)
T ss_pred EEEEEEeC-----hHHeeeeccCCchhhhhhhheeehhhccchhhceeehhheeeeEEEeeeccccchhhhHhhH
Confidence 38888886 3344556666666421 1 1356778899999999999998777777776653
No 224
>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=23.29 E-value=2.8e+02 Score=19.88 Aligned_cols=39 Identities=8% Similarity=0.189 Sum_probs=32.3
Q ss_pred EEEeCCCCEEEEEechhhHhhhccCCCCCCEEEEEeeeE
Q 026794 31 IQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGA 69 (233)
Q Consensus 31 i~id~~~~~i~lS~k~~~~~~~~~~~~~G~vv~g~~~G~ 69 (233)
+=+|+++.+|.++.+......+...+++|.++.=.+|.+
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 457888999999999888888899999999887666653
No 225
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=23.22 E-value=93 Score=31.32 Aligned_cols=60 Identities=3% Similarity=0.020 Sum_probs=39.1
Q ss_pred cccCCeeeeccCCChhhhhhhhcccCC-eeEEE----eeccc--ccc-------------ccccCceEEEEeecCCCCCE
Q 026794 156 MSSSNSNTIEPLPGLGAIFEELLQEDG-IDDVR----ITRQG--FEK-------------RVVSQDLQLWLSNAPPSGKK 215 (233)
Q Consensus 156 ~~~g~v~~v~~~~g~~~~~~~l~~~~g-v~gl~----~~~~~--~~~-------------~~vg~~~~v~i~~~d~~~~k 215 (233)
..+|.|..++.+ |.|+.+++- ++|+. +..+. .++ -.+||.++|++.+++...++
T Consensus 625 ~f~g~V~~v~~~------g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~ 698 (706)
T COG0557 625 EFDGVVTGVTSF------GFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDERK 698 (706)
T ss_pred EEEEEEEEEEec------cEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccccc
Confidence 367888888755 444544543 77773 33111 111 15799999999999999888
Q ss_pred EEEEEc
Q 026794 216 FTLLAR 221 (233)
Q Consensus 216 i~Ls~r 221 (233)
+.+..-
T Consensus 699 i~~~~v 704 (706)
T COG0557 699 IDFELV 704 (706)
T ss_pred eEEEec
Confidence 877653
No 226
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=22.30 E-value=1.9e+02 Score=19.90 Aligned_cols=38 Identities=13% Similarity=0.060 Sum_probs=25.7
Q ss_pred EEEEEEeCCCCEEEEEechhh---H-----------hhhccCCCCCCEEEEE
Q 026794 28 VKVIQANEEMKKLVFSEKDAV---W-----------NKYSSRVNVEDIFVGR 65 (233)
Q Consensus 28 ~~Vi~id~~~~~i~lS~k~~~---~-----------~~~~~~~~~G~vv~g~ 65 (233)
+.|.++|.+.+.+.++....+ | ......+++|+.+.-.
T Consensus 1 G~V~~vd~~~~~iti~H~pIp~l~wpaMTM~F~v~~~~~l~~l~~Gd~V~F~ 52 (70)
T PF11604_consen 1 GVVKSVDPEAGTITISHEPIPELGWPAMTMDFPVADPVDLAGLKPGDKVRFT 52 (70)
T ss_dssp EEEEEEETTTTEEEEEE--BCCCTB-SEEEEEE--TTSEESS-STT-EEEEE
T ss_pred CEEEEEecCCCEEEEecCccccCCCCCeEEEEEcCChhhhhcCCCCCEEEEE
Confidence 368899999999999987642 2 2345788999988755
No 227
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=21.30 E-value=1.4e+02 Score=28.56 Aligned_cols=28 Identities=18% Similarity=0.144 Sum_probs=22.9
Q ss_pred CCCCEEEEEEEEEeCCC---CEEEEEechhh
Q 026794 21 LTGSIISVKVIQANEEM---KKLVFSEKDAV 48 (233)
Q Consensus 21 ~vG~~v~~~Vi~id~~~---~~i~lS~k~~~ 48 (233)
..|+.++|.|.+++... -.+.||+....
T Consensus 197 ~~Gdrika~i~~V~~~~~kGpqIilSRt~p~ 227 (449)
T PRK12329 197 RANATFKVFLKEVSEGPRRGPQLFVSRANAG 227 (449)
T ss_pred CCCCEEEEEEEEeecCCCCCCEEEEEcCCHH
Confidence 38999999999998753 37999998653
No 228
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=21.11 E-value=1.7e+02 Score=24.51 Aligned_cols=41 Identities=20% Similarity=0.332 Sum_probs=31.0
Q ss_pred EEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCC-CeEEEEEe
Q 026794 82 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK-SRITLSIK 128 (233)
Q Consensus 82 v~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~-~ri~LS~k 128 (233)
++|++|..+.. +.+.|++|+++++.+.++.... +.+.+|+-
T Consensus 2 ~~~~l~~~~~~------~~e~~~~g~ri~~~~~~v~~~~~g~~~~srt 43 (190)
T COG0195 2 VEAILPKREQI------PGENFKVGDRIRALLYEVQKEAKGQIELSRT 43 (190)
T ss_pred ceeEcchhhcC------CCcccccCcEEEEEEeeeeecCcccEEEEec
Confidence 46888877764 4677999999999999998533 45677653
Done!