Query 028346
Match_columns 210
No_of_seqs 168 out of 903
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 10:05:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028346.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028346hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1096 Predicted RNA-binding 100.0 1.1E-44 2.4E-49 296.7 18.6 169 6-188 3-174 (188)
2 PRK09521 exosome complex RNA-b 100.0 2.3E-43 5.1E-48 293.2 20.6 170 7-189 4-176 (189)
3 KOG3409 Exosomal 3'-5' exoribo 100.0 1.4E-43 3.1E-48 285.9 16.4 176 7-188 4-181 (193)
4 PRK04163 exosome complex RNA-b 100.0 9E-32 1.9E-36 230.8 15.7 176 7-208 7-190 (235)
5 COG1097 RRP4 RNA-binding prote 100.0 2.6E-29 5.6E-34 213.5 15.8 138 6-163 6-145 (239)
6 KOG3013 Exosomal 3'-5' exoribo 100.0 1.6E-29 3.5E-34 215.5 3.2 184 5-208 26-212 (301)
7 cd05791 S1_CSL4 S1_CSL4: CSL4, 99.9 1.4E-27 3E-32 177.6 9.2 91 72-162 2-92 (92)
8 PF10447 EXOSC1: Exosome compo 99.9 3.4E-22 7.4E-27 145.5 7.5 72 73-144 1-82 (82)
9 cd04454 S1_Rrp4_like S1_Rrp4_l 99.8 2.6E-18 5.7E-23 124.1 9.7 82 71-162 1-82 (82)
10 KOG1004 Exosomal 3'-5' exoribo 99.7 5.2E-16 1.1E-20 129.6 14.3 172 9-208 2-183 (230)
11 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.6 7.4E-16 1.6E-20 112.0 8.9 84 71-162 1-86 (86)
12 cd05790 S1_Rrp40 S1_Rrp40: Rrp 99.6 1.1E-14 2.3E-19 107.1 9.6 75 71-156 1-75 (86)
13 PF14382 ECR1_N: Exosome compl 99.4 4.9E-13 1.1E-17 84.3 3.7 37 10-48 1-37 (39)
14 COG1098 VacB Predicted RNA bin 99.4 9.6E-13 2.1E-17 101.9 5.2 76 74-159 3-78 (129)
15 cd05704 S1_Rrp5_repeat_hs13 S1 99.3 6.3E-12 1.4E-16 88.9 7.9 70 75-155 2-72 (72)
16 cd05687 S1_RPS1_repeat_ec1_hs1 99.2 7.4E-11 1.6E-15 82.2 8.5 69 77-155 1-70 (70)
17 cd05706 S1_Rrp5_repeat_sc10 S1 99.2 4.1E-10 9E-15 79.0 9.8 71 75-155 2-73 (73)
18 cd05691 S1_RPS1_repeat_ec6 S1_ 99.1 4.1E-10 8.8E-15 78.5 8.9 72 77-158 1-73 (73)
19 cd05705 S1_Rrp5_repeat_hs14 S1 99.1 2.8E-10 6E-15 81.1 7.9 71 75-153 2-74 (74)
20 cd04452 S1_IF2_alpha S1_IF2_al 99.1 6E-10 1.3E-14 78.5 8.7 74 74-155 1-75 (76)
21 PRK08582 hypothetical protein; 99.1 1.2E-09 2.5E-14 87.1 10.6 76 74-159 3-78 (139)
22 cd05702 S1_Rrp5_repeat_hs11_sc 99.1 8.2E-10 1.8E-14 77.3 7.7 66 77-150 1-66 (70)
23 cd05693 S1_Rrp5_repeat_hs1_sc1 99.0 5.7E-10 1.2E-14 84.1 7.1 76 74-157 1-97 (100)
24 cd05703 S1_Rrp5_repeat_hs12_sc 99.0 1.4E-09 3.1E-14 77.1 8.5 71 77-155 1-72 (73)
25 cd05692 S1_RPS1_repeat_hs4 S1_ 99.0 1.8E-09 3.9E-14 73.8 8.6 69 77-155 1-69 (69)
26 cd05686 S1_pNO40 S1_pNO40: pNO 99.0 2.5E-09 5.3E-14 75.6 9.2 72 74-154 1-72 (73)
27 PF00575 S1: S1 RNA binding do 99.0 2.5E-09 5.5E-14 75.0 9.0 72 74-155 2-74 (74)
28 cd05707 S1_Rrp5_repeat_sc11 S1 99.0 1.6E-09 3.4E-14 75.2 7.7 67 77-153 1-68 (68)
29 cd05708 S1_Rrp5_repeat_sc12 S1 99.0 2.9E-09 6.3E-14 74.8 8.8 74 75-157 1-75 (77)
30 PRK07252 hypothetical protein; 99.0 5.4E-09 1.2E-13 81.3 9.8 73 75-157 2-75 (120)
31 PRK05807 hypothetical protein; 99.0 7.1E-09 1.5E-13 82.3 10.5 74 74-158 3-76 (136)
32 cd05698 S1_Rrp5_repeat_hs6_sc5 99.0 4.6E-09 1E-13 73.0 8.4 69 77-155 1-70 (70)
33 PTZ00248 eukaryotic translatio 98.9 4E-09 8.7E-14 94.3 8.6 77 72-157 13-91 (319)
34 smart00316 S1 Ribosomal protei 98.9 7.9E-09 1.7E-13 70.3 8.1 71 75-155 1-72 (72)
35 PRK08059 general stress protei 98.9 1E-08 2.2E-13 79.9 9.6 76 74-159 5-81 (123)
36 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.9 1.8E-08 3.8E-13 71.0 8.4 68 77-154 1-71 (71)
37 cd04461 S1_Rrp5_repeat_hs8_sc7 98.9 1.6E-08 3.6E-13 72.9 8.3 72 73-154 11-83 (83)
38 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.9 1.6E-08 3.6E-13 70.2 8.0 68 77-154 1-69 (69)
39 PRK03987 translation initiatio 98.8 1.8E-08 3.9E-13 88.1 9.7 79 72-158 4-83 (262)
40 COG0539 RpsA Ribosomal protein 98.8 1.1E-08 2.3E-13 97.0 8.1 75 73-158 189-264 (541)
41 cd05694 S1_Rrp5_repeat_hs2_sc2 98.8 7.3E-08 1.6E-12 68.7 9.5 69 74-158 2-72 (74)
42 cd05688 S1_RPS1_repeat_ec3 S1_ 98.8 3.9E-08 8.5E-13 67.2 7.3 67 76-153 1-68 (68)
43 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.8 5.6E-08 1.2E-12 67.5 8.1 65 77-153 1-66 (66)
44 cd04472 S1_PNPase S1_PNPase: P 98.8 6.8E-08 1.5E-12 66.1 8.4 68 77-154 1-68 (68)
45 cd05685 S1_Tex S1_Tex: The C-t 98.7 4E-08 8.6E-13 66.9 6.9 67 77-153 1-68 (68)
46 cd04453 S1_RNase_E S1_RNase_E: 98.7 1.2E-07 2.7E-12 69.7 8.7 74 74-155 5-82 (88)
47 PRK11824 polynucleotide phosph 98.7 2.2E-08 4.8E-13 98.0 5.9 101 32-156 591-691 (693)
48 PHA02945 interferon resistance 98.7 2.2E-07 4.9E-12 68.1 8.9 73 72-156 7-83 (88)
49 COG1093 SUI2 Translation initi 98.6 5.9E-08 1.3E-12 84.0 6.1 77 71-156 6-84 (269)
50 PRK08563 DNA-directed RNA poly 98.6 1.8E-07 3.9E-12 77.5 8.6 83 72-163 77-174 (187)
51 PRK07400 30S ribosomal protein 98.6 2.2E-07 4.7E-12 83.3 9.7 76 72-158 192-268 (318)
52 cd05684 S1_DHX8_helicase S1_DH 98.6 4E-07 8.6E-12 64.9 9.0 72 77-156 1-73 (79)
53 cd05690 S1_RPS1_repeat_ec5 S1_ 98.6 2.4E-07 5.3E-12 63.9 7.1 66 77-152 1-68 (69)
54 TIGR00448 rpoE DNA-directed RN 98.6 3.1E-07 6.8E-12 75.8 8.8 83 72-163 77-174 (179)
55 cd04460 S1_RpoE S1_RpoE: RpoE, 98.5 4E-07 8.7E-12 67.9 8.0 77 78-163 1-92 (99)
56 TIGR02696 pppGpp_PNP guanosine 98.5 3.3E-07 7.2E-12 89.5 8.7 71 73-153 644-718 (719)
57 TIGR03591 polynuc_phos polyrib 98.5 1.1E-07 2.3E-12 93.1 4.1 94 33-150 589-682 (684)
58 cd00164 S1_like S1_like: Ribos 98.5 5.8E-07 1.3E-11 59.9 6.5 64 80-153 1-65 (65)
59 PRK07400 30S ribosomal protein 98.4 8.9E-07 1.9E-11 79.4 8.5 76 72-157 27-103 (318)
60 cd05689 S1_RPS1_repeat_ec4 S1_ 98.4 1.9E-06 4E-11 60.1 8.4 64 75-147 2-65 (72)
61 cd04455 S1_NusA S1_NusA: N-uti 98.4 2E-06 4.4E-11 59.7 8.4 62 75-153 2-66 (67)
62 PRK13806 rpsA 30S ribosomal pr 98.4 1.1E-06 2.3E-11 83.1 8.9 75 74-158 377-452 (491)
63 COG1095 RPB7 DNA-directed RNA 98.4 8.8E-07 1.9E-11 73.3 7.0 83 72-163 77-174 (183)
64 cd04473 S1_RecJ_like S1_RecJ_l 98.4 7.7E-06 1.7E-10 58.3 10.7 64 73-154 13-76 (77)
65 cd04465 S1_RPS1_repeat_ec2_hs2 98.4 3.3E-06 7.1E-11 58.3 8.1 66 77-155 1-67 (67)
66 COG0539 RpsA Ribosomal protein 98.3 1.2E-06 2.7E-11 83.1 7.6 74 74-157 275-349 (541)
67 PRK13806 rpsA 30S ribosomal pr 98.3 2.1E-06 4.5E-11 81.1 8.5 75 73-157 199-278 (491)
68 PRK07899 rpsA 30S ribosomal pr 98.3 2.7E-06 5.8E-11 80.4 9.0 74 74-157 33-107 (486)
69 PLN00207 polyribonucleotide nu 98.3 2.5E-06 5.4E-11 85.2 8.6 74 73-156 750-824 (891)
70 PRK07899 rpsA 30S ribosomal pr 98.3 3E-06 6.4E-11 80.1 8.7 73 74-157 206-279 (486)
71 PRK06299 rpsA 30S ribosomal pr 98.3 3.8E-06 8.3E-11 80.3 8.9 75 74-158 458-533 (565)
72 PRK12269 bifunctional cytidyla 98.2 2.9E-06 6.3E-11 84.9 8.2 74 74-156 576-650 (863)
73 PRK06676 rpsA 30S ribosomal pr 98.2 6.9E-06 1.5E-10 75.0 9.5 75 74-158 275-350 (390)
74 PRK06676 rpsA 30S ribosomal pr 98.2 6.4E-06 1.4E-10 75.2 8.9 73 74-157 190-263 (390)
75 PRK06299 rpsA 30S ribosomal pr 98.2 9.3E-06 2E-10 77.6 9.6 73 73-156 198-271 (565)
76 cd04471 S1_RNase_R S1_RNase_R: 98.2 2.2E-05 4.8E-10 55.7 9.1 71 76-154 1-82 (83)
77 PRK00087 4-hydroxy-3-methylbut 98.1 1.5E-05 3.3E-10 77.7 9.5 75 74-158 560-635 (647)
78 TIGR00717 rpsA ribosomal prote 98.1 1.4E-05 3E-10 75.5 8.9 72 74-155 444-516 (516)
79 PTZ00162 DNA-directed RNA poly 98.0 2.4E-05 5.3E-10 64.6 8.4 85 72-165 77-174 (176)
80 PRK12269 bifunctional cytidyla 98.0 2.1E-05 4.6E-10 78.8 9.1 74 74-156 663-737 (863)
81 TIGR00717 rpsA ribosomal prote 98.0 3.4E-05 7.4E-10 72.8 8.8 73 73-156 184-257 (516)
82 PRK00087 4-hydroxy-3-methylbut 97.9 4.1E-05 8.9E-10 74.6 9.4 77 72-158 298-375 (647)
83 COG2183 Tex Transcriptional ac 97.9 2.2E-05 4.7E-10 77.0 7.1 77 73-159 655-732 (780)
84 COG1185 Pnp Polyribonucleotide 97.7 0.00011 2.3E-09 71.4 7.2 75 73-157 616-690 (692)
85 PRK09202 nusA transcription el 97.6 0.00014 3.1E-09 68.5 7.3 71 72-159 130-203 (470)
86 PRK12327 nusA transcription el 97.5 0.00028 6.1E-09 64.5 7.2 72 71-159 129-203 (362)
87 TIGR01953 NusA transcription t 97.5 0.00031 6.7E-09 63.8 7.2 72 71-159 126-201 (341)
88 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.4 0.0018 4E-08 47.5 8.7 74 76-160 1-88 (88)
89 PHA02858 EIF2a-like PKR inhibi 97.2 0.0017 3.7E-08 47.4 7.1 72 72-154 12-85 (86)
90 TIGR00757 RNaseEG ribonuclease 97.0 0.0042 9.2E-08 57.8 9.0 82 62-154 14-108 (414)
91 TIGR02063 RNase_R ribonuclease 96.8 0.0061 1.3E-07 60.2 9.3 74 73-154 624-708 (709)
92 PRK12328 nusA transcription el 96.6 0.0052 1.1E-07 56.4 6.7 72 71-159 133-209 (374)
93 KOG1070 rRNA processing protei 96.6 0.0096 2.1E-07 62.0 9.1 76 74-159 1160-1236(1710)
94 PRK12329 nusA transcription el 96.5 0.0072 1.6E-07 56.5 7.1 77 71-159 147-228 (449)
95 PRK11642 exoribonuclease R; Pr 96.5 0.015 3.2E-07 58.5 9.5 73 75-155 642-725 (813)
96 KOG1070 rRNA processing protei 96.5 0.0039 8.4E-08 64.8 5.1 74 70-151 879-952 (1710)
97 TIGR00358 3_prime_RNase VacB a 96.1 0.03 6.5E-07 54.9 9.2 73 74-154 570-653 (654)
98 cd05699 S1_Rrp5_repeat_hs7 S1_ 95.9 0.039 8.5E-07 39.2 6.4 70 77-154 1-71 (72)
99 KOG1067 Predicted RNA-binding 95.6 0.021 4.5E-07 54.9 5.3 83 73-165 660-751 (760)
100 KOG1856 Transcription elongati 95.5 0.018 3.9E-07 59.0 4.9 78 73-160 982-1063(1299)
101 COG2996 Predicted RNA-bindinin 95.5 0.064 1.4E-06 47.3 7.5 63 77-157 156-218 (287)
102 KOG2916 Translation initiation 95.2 0.015 3.2E-07 51.0 2.9 76 73-156 13-89 (304)
103 PRK11712 ribonuclease G; Provi 94.8 0.15 3.3E-06 48.6 8.6 82 62-154 27-121 (489)
104 PRK10811 rne ribonuclease E; R 94.6 0.14 3E-06 52.2 8.0 83 62-155 27-119 (1068)
105 COG1571 Predicted DNA-binding 92.7 0.19 4.1E-06 46.9 5.0 62 127-189 312-377 (421)
106 PF13509 S1_2: S1 domain; PDB: 91.9 1.6 3.5E-05 29.5 7.6 60 76-154 1-60 (61)
107 KOG3298 DNA-directed RNA polym 91.7 0.97 2.1E-05 37.0 7.4 85 72-162 77-170 (170)
108 PF09297 zf-NADH-PPase: NADH p 90.5 0.2 4.4E-06 29.6 1.8 25 165-189 5-31 (32)
109 PF01016 Ribosomal_L27: Riboso 89.4 0.5 1.1E-05 34.4 3.5 44 4-49 23-69 (81)
110 smart00659 RPOLCX RNA polymera 89.2 0.2 4.3E-06 32.2 1.1 28 164-191 3-31 (44)
111 CHL00121 rpl27 ribosomal prote 89.1 0.79 1.7E-05 33.6 4.3 58 4-67 24-84 (86)
112 PRK05054 exoribonuclease II; P 88.3 2.9 6.4E-05 41.1 9.1 71 75-152 558-641 (644)
113 PRK05435 rpmA 50S ribosomal pr 88.2 1.3 2.7E-05 32.3 4.8 44 4-49 24-70 (82)
114 PF07754 DUF1610: Domain of un 86.6 0.4 8.7E-06 27.0 1.2 20 167-186 3-23 (24)
115 COG1530 CafA Ribonucleases G a 85.1 1.9 4.1E-05 41.1 5.7 64 74-145 35-102 (487)
116 PF07497 Rho_RNA_bind: Rho ter 83.8 1.8 4E-05 31.2 3.9 61 33-103 12-75 (78)
117 TIGR00062 L27 ribosomal protei 83.2 2.3 4.9E-05 31.1 4.1 44 4-49 24-70 (83)
118 COG0557 VacB Exoribonuclease R 82.8 6.6 0.00014 39.1 8.6 74 75-155 621-704 (706)
119 PF03604 DNA_RNApol_7kD: DNA d 82.5 0.22 4.7E-06 29.9 -1.2 26 165-190 2-28 (32)
120 PF01959 DHQS: 3-dehydroquinat 80.6 19 0.00041 33.1 10.0 96 10-146 246-341 (354)
121 PF08292 RNA_pol_Rbc25: RNA po 79.2 9.6 0.00021 29.6 6.7 69 74-144 1-74 (122)
122 PTZ00248 eukaryotic translatio 78.7 2.9 6.4E-05 37.8 4.2 58 71-146 61-118 (319)
123 PRK02290 3-dehydroquinate synt 78.3 22 0.00048 32.5 9.7 93 10-145 236-330 (344)
124 smart00661 RPOL9 RNA polymeras 78.3 1.3 2.7E-05 28.6 1.3 25 165-189 2-30 (52)
125 PRK00398 rpoP DNA-directed RNA 78.3 1.5 3.4E-05 27.9 1.7 28 164-191 4-33 (46)
126 COG1645 Uncharacterized Zn-fin 78.3 1.3 2.9E-05 35.0 1.6 23 165-188 30-53 (131)
127 KOG3507 DNA-directed RNA polym 77.9 2.1 4.7E-05 29.2 2.3 30 162-191 19-49 (62)
128 PF14446 Prok-RING_1: Prokaryo 77.0 1.2 2.6E-05 30.0 0.9 27 164-191 6-33 (54)
129 TIGR02062 RNase_B exoribonucle 76.3 10 0.00023 37.3 7.6 65 75-146 554-630 (639)
130 PRK00420 hypothetical protein; 74.8 1.8 3.8E-05 33.4 1.5 27 164-190 24-51 (112)
131 KOG4134 DNA-dependent RNA poly 74.3 2.7 5.9E-05 36.2 2.6 61 72-147 103-163 (253)
132 COG2816 NPY1 NTP pyrophosphohy 74.2 1.4 3.1E-05 39.1 0.9 27 165-191 113-141 (279)
133 PF10080 DUF2318: Predicted me 72.9 5.5 0.00012 30.1 3.7 36 157-192 29-65 (102)
134 COG1107 Archaea-specific RecJ- 71.4 10 0.00022 37.2 5.9 67 71-153 117-184 (715)
135 PF10246 MRP-S35: Mitochondria 71.2 27 0.00058 26.6 7.0 53 75-144 22-74 (104)
136 TIGR01384 TFS_arch transcripti 70.7 2.2 4.9E-05 31.6 1.2 25 165-190 2-27 (104)
137 KOG4600 Mitochondrial ribosoma 69.7 13 0.00029 29.6 5.3 61 4-68 51-114 (144)
138 PF08274 PhnA_Zn_Ribbon: PhnA 69.5 2.6 5.7E-05 24.9 1.0 25 165-189 4-29 (30)
139 COG3364 Zn-ribbon containing p 68.8 0.88 1.9E-05 34.5 -1.4 29 165-193 4-34 (112)
140 COG1996 RPC10 DNA-directed RNA 68.3 2.1 4.6E-05 28.2 0.5 28 164-191 7-36 (49)
141 COG1656 Uncharacterized conser 67.2 1.7 3.8E-05 35.6 -0.1 31 161-191 95-142 (165)
142 TIGR00767 rho transcription te 66.7 4.8 0.0001 37.7 2.7 129 23-171 48-182 (415)
143 PF04085 MreC: rod shape-deter 66.3 23 0.0005 28.2 6.3 60 80-139 36-102 (152)
144 PF09538 FYDLN_acid: Protein o 66.1 2.3 5E-05 32.5 0.4 36 155-191 2-38 (108)
145 COG1158 Rho Transcription term 64.9 8.6 0.00019 35.5 3.9 72 22-103 50-126 (422)
146 PTZ00329 eukaryotic translatio 64.3 11 0.00024 30.6 4.1 40 7-48 23-67 (155)
147 cd04454 S1_Rrp4_like S1_Rrp4_l 64.2 17 0.00037 25.3 4.7 33 132-165 5-37 (82)
148 PRK12380 hydrogenase nickel in 63.6 4.5 9.7E-05 30.9 1.6 27 162-189 69-96 (113)
149 COG1594 RPB9 DNA-directed RNA 63.5 5.5 0.00012 30.6 2.1 25 165-189 4-32 (113)
150 PRK03681 hypA hydrogenase nick 63.4 4.5 9.7E-05 31.0 1.6 28 162-189 69-97 (114)
151 PF01927 Mut7-C: Mut7-C RNAse 63.2 3 6.5E-05 33.1 0.6 34 158-191 86-136 (147)
152 TIGR00100 hypA hydrogenase nic 63.2 4.7 0.0001 30.9 1.7 27 162-189 69-96 (115)
153 PRK00564 hypA hydrogenase nick 62.4 3.2 6.9E-05 32.0 0.6 29 162-190 70-99 (117)
154 TIGR00686 phnA alkylphosphonat 60.9 5.8 0.00012 30.4 1.7 26 165-191 4-31 (109)
155 cd05790 S1_Rrp40 S1_Rrp40: Rrp 60.5 10 0.00022 27.7 2.9 29 71-100 47-75 (86)
156 PF09953 DUF2187: Uncharacteri 60.1 24 0.00051 24.0 4.4 21 80-100 16-36 (57)
157 TIGR02300 FYDLN_acid conserved 60.0 3.6 7.8E-05 32.4 0.5 36 155-191 2-38 (129)
158 PF06677 Auto_anti-p27: Sjogre 59.9 6.9 0.00015 24.7 1.7 23 164-186 18-41 (41)
159 PF08792 A2L_zn_ribbon: A2L zi 58.5 11 0.00023 22.6 2.3 24 165-188 5-30 (33)
160 KOG3297 DNA-directed RNA polym 58.2 70 0.0015 26.9 7.8 69 74-144 79-156 (202)
161 PRK13922 rod shape-determining 57.5 47 0.001 28.8 7.2 91 38-138 120-222 (276)
162 COG3357 Predicted transcriptio 57.4 3.6 7.8E-05 30.6 0.1 34 156-190 51-87 (97)
163 COG0211 RpmA Ribosomal protein 55.7 26 0.00056 25.7 4.3 59 4-68 24-85 (87)
164 PRK14890 putative Zn-ribbon RN 54.4 7.5 0.00016 26.6 1.2 27 165-191 9-37 (59)
165 PRK10220 hypothetical protein; 53.7 9.6 0.00021 29.3 1.9 27 165-191 5-32 (111)
166 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 53.1 31 0.00068 24.1 4.5 32 131-163 4-35 (86)
167 COG0375 HybF Zn finger protein 52.7 9.2 0.0002 29.6 1.7 28 162-190 69-97 (115)
168 PF10844 DUF2577: Protein of u 52.0 95 0.0021 23.0 7.7 71 76-150 16-94 (100)
169 PF07282 OrfB_Zn_ribbon: Putat 51.9 7.4 0.00016 26.5 0.9 24 165-188 30-55 (69)
170 cd05791 S1_CSL4 S1_CSL4: CSL4, 51.7 20 0.00044 26.1 3.3 23 74-96 61-84 (92)
171 PF01155 HypA: Hydrogenase exp 51.2 4.7 0.0001 30.7 -0.2 28 162-190 69-97 (113)
172 PF10447 EXOSC1: Exosome compo 51.1 14 0.00031 26.7 2.4 16 132-147 3-18 (82)
173 cd05704 S1_Rrp5_repeat_hs13 S1 50.9 39 0.00085 23.1 4.6 32 131-162 1-32 (72)
174 PLN00208 translation initiatio 50.5 25 0.00055 28.3 3.9 39 8-48 24-67 (145)
175 TIGR00219 mreC rod shape-deter 50.2 67 0.0014 28.4 7.0 61 78-138 155-223 (283)
176 PF09862 DUF2089: Protein of u 50.0 12 0.00025 28.9 1.8 19 166-187 1-20 (113)
177 PRK09521 exosome complex RNA-b 49.9 24 0.00053 29.0 3.9 24 72-96 117-140 (189)
178 cd05705 S1_Rrp5_repeat_hs14 S1 49.8 44 0.00096 23.1 4.7 32 131-163 1-32 (74)
179 COG1545 Predicted nucleic-acid 49.6 11 0.00024 29.9 1.7 27 160-189 25-53 (140)
180 PRK00432 30S ribosomal protein 49.2 8 0.00017 25.4 0.7 26 164-190 21-48 (50)
181 PF08810 KapB: Kinase associat 48.6 29 0.00063 26.7 3.8 21 80-100 6-26 (112)
182 smart00293 PWWP domain with co 48.3 12 0.00026 25.2 1.6 14 131-144 1-14 (63)
183 PRK03824 hypA hydrogenase nick 48.3 12 0.00026 29.4 1.8 28 162-189 69-117 (135)
184 TIGR00739 yajC preprotein tran 47.9 41 0.00088 24.3 4.4 23 74-96 38-66 (84)
185 smart00652 eIF1a eukaryotic tr 47.8 1E+02 0.0022 22.2 7.0 56 74-145 2-58 (83)
186 PF03961 DUF342: Protein of un 46.4 42 0.00091 31.4 5.4 36 22-66 144-180 (451)
187 smart00834 CxxC_CXXC_SSSS Puta 46.2 13 0.00028 22.4 1.3 24 164-187 6-34 (41)
188 PLN00208 translation initiatio 45.9 1.1E+02 0.0025 24.6 7.0 57 73-145 28-85 (145)
189 cd05706 S1_Rrp5_repeat_sc10 S1 45.4 57 0.0012 21.9 4.7 33 131-164 1-33 (73)
190 PF02150 RNA_POL_M_15KD: RNA p 45.1 21 0.00046 21.5 2.1 24 165-188 3-29 (35)
191 PRK08402 replication factor A; 44.5 83 0.0018 28.9 6.8 27 160-186 209-237 (355)
192 PRK00276 infA translation init 44.2 1.1E+02 0.0023 21.2 7.1 53 80-146 9-62 (72)
193 PF09723 Zn-ribbon_8: Zinc rib 42.3 17 0.00037 22.7 1.5 23 165-187 7-34 (42)
194 cd05836 N_Pac_NP60 The PWWP do 42.2 16 0.00035 26.4 1.5 14 131-144 1-14 (86)
195 COG4416 Com Mu-like prophage p 42.1 2.9 6.2E-05 28.2 -2.2 29 165-193 6-38 (60)
196 cd04459 Rho_CSD Rho_CSD: Rho p 41.9 15 0.00032 25.7 1.2 27 61-87 28-54 (68)
197 cd05834 HDGF_related The PWWP 41.6 17 0.00038 26.1 1.6 15 130-144 2-16 (83)
198 PRK06763 F0F1 ATP synthase sub 41.5 1E+02 0.0022 26.3 6.3 21 76-96 38-58 (213)
199 TIGR00008 infA translation ini 41.4 85 0.0018 22.0 5.0 52 80-145 7-59 (68)
200 cd05840 SPBC215_ISWI_like The 41.2 17 0.00037 26.8 1.5 14 131-144 1-14 (93)
201 cd05693 S1_Rrp5_repeat_hs1_sc1 40.9 63 0.0014 23.8 4.6 31 131-162 1-31 (100)
202 TIGR01206 lysW lysine biosynth 40.6 15 0.00033 24.6 1.1 26 164-189 3-32 (54)
203 PF10571 UPF0547: Uncharacteri 40.2 9.8 0.00021 21.6 0.1 21 166-189 3-24 (26)
204 PRK07252 hypothetical protein; 39.9 80 0.0017 24.2 5.2 27 73-99 47-75 (120)
205 PRK09376 rho transcription ter 39.9 31 0.00067 32.4 3.3 71 23-103 48-123 (416)
206 cd06850 biotinyl_domain The bi 39.1 1E+02 0.0022 19.7 5.9 63 38-137 2-64 (67)
207 PRK04012 translation initiatio 39.0 1.7E+02 0.0036 22.0 7.2 58 73-146 17-75 (100)
208 COG0361 InfA Translation initi 39.0 1.4E+02 0.0031 21.3 6.3 56 77-146 6-62 (75)
209 PF14803 Nudix_N_2: Nudix N-te 38.6 21 0.00045 21.6 1.3 23 165-187 2-30 (34)
210 PF01176 eIF-1a: Translation i 38.6 1.2E+02 0.0027 20.4 5.9 52 78-144 3-55 (65)
211 PF10122 Mu-like_Com: Mu-like 38.1 8.2 0.00018 25.6 -0.5 27 165-191 6-36 (51)
212 PHA02325 hypothetical protein 37.8 9.6 0.00021 26.6 -0.3 13 179-191 3-15 (72)
213 PF09567 RE_MamI: MamI restric 37.8 23 0.00051 31.2 2.0 57 150-209 61-141 (314)
214 PF13375 RnfC_N: RnfC Barrel s 37.7 29 0.00063 26.0 2.3 11 38-48 69-79 (101)
215 PRK05585 yajC preprotein trans 37.6 68 0.0015 24.3 4.3 23 74-96 53-81 (106)
216 PF03966 Trm112p: Trm112p-like 37.6 28 0.00061 23.8 2.1 16 174-189 48-63 (68)
217 TIGR02605 CxxC_CxxC_SSSS putat 37.5 20 0.00043 23.0 1.2 24 165-188 7-35 (52)
218 PRK11032 hypothetical protein; 37.1 17 0.00037 29.7 1.1 26 165-190 126-153 (160)
219 PF01938 TRAM: TRAM domain; I 36.9 66 0.0014 21.1 3.8 24 73-96 37-60 (61)
220 PRK05886 yajC preprotein trans 36.7 71 0.0015 24.4 4.3 23 74-96 39-67 (109)
221 PRK12442 translation initiatio 36.1 1.2E+02 0.0026 22.3 5.3 53 80-146 9-62 (87)
222 KOG1999 RNA polymerase II tran 36.0 3.2E+02 0.007 28.6 9.9 113 70-192 404-547 (1024)
223 PF03558 TBSV_P22: TBSV core p 35.3 2E+02 0.0044 23.7 6.9 79 106-188 73-158 (189)
224 PRK00241 nudC NADH pyrophospha 35.2 18 0.00039 31.4 1.0 27 165-191 101-129 (256)
225 COG1792 MreC Cell shape-determ 35.2 1.7E+02 0.0037 25.8 7.2 22 80-101 156-177 (284)
226 PF13717 zinc_ribbon_4: zinc-r 35.0 16 0.00034 22.2 0.4 19 172-190 18-36 (36)
227 TIGR01053 LSD1 zinc finger dom 34.8 29 0.00063 20.5 1.5 23 166-188 4-28 (31)
228 COG2996 Predicted RNA-bindinin 34.8 1.2E+02 0.0026 27.0 6.0 39 72-118 69-108 (287)
229 PRK12678 transcription termina 34.7 49 0.0011 32.9 3.9 69 23-103 293-371 (672)
230 PF12172 DUF35_N: Rubredoxin-l 34.5 27 0.0006 20.9 1.5 26 161-189 9-35 (37)
231 PF13453 zf-TFIIB: Transcripti 34.3 24 0.00052 21.7 1.2 26 166-191 2-31 (41)
232 cd05835 Dnmt3b_related The PWW 33.9 27 0.00058 25.2 1.5 14 131-144 1-14 (87)
233 COG1315 Uncharacterized conser 33.8 49 0.0011 31.9 3.6 48 22-80 220-270 (543)
234 COG2824 PhnA Uncharacterized Z 33.6 29 0.00064 26.6 1.8 26 165-190 5-31 (112)
235 COG4873 Uncharacterized protei 33.2 56 0.0012 23.1 3.0 26 74-99 24-55 (81)
236 PHA02942 putative transposase; 33.2 23 0.0005 32.6 1.4 24 165-188 327-351 (383)
237 PF13240 zinc_ribbon_2: zinc-r 32.8 12 0.00026 20.5 -0.3 20 166-188 2-22 (23)
238 cd05841 BS69_related The PWWP 32.4 33 0.00071 25.0 1.8 18 128-145 4-21 (83)
239 PF01336 tRNA_anti-codon: OB-f 31.7 1E+02 0.0023 20.2 4.2 49 80-140 3-54 (75)
240 PF13719 zinc_ribbon_5: zinc-r 31.6 23 0.00049 21.5 0.7 26 165-190 4-36 (37)
241 PF15616 TerY-C: TerY-C metal 31.5 46 0.001 26.3 2.6 30 159-188 83-114 (131)
242 cd04322 LysRS_N LysRS_N: N-ter 30.7 1.8E+02 0.0038 21.3 5.7 55 79-140 3-59 (108)
243 cd05793 S1_IF1A S1_IF1A: Trans 30.4 2E+02 0.0043 20.4 6.3 51 80-145 2-53 (77)
244 TIGR00638 Mop molybdenum-pteri 30.3 1.6E+02 0.0035 19.2 6.1 55 77-143 6-61 (69)
245 COG1096 Predicted RNA-binding 30.3 93 0.002 26.1 4.3 23 73-96 118-140 (188)
246 PRK05889 putative acetyl-CoA c 29.7 1.8E+02 0.0039 19.6 5.9 50 38-116 5-54 (71)
247 cd05162 PWWP The PWWP domain, 29.5 35 0.00076 24.2 1.6 14 131-144 1-14 (87)
248 CHL00010 infA translation init 29.3 2.1E+02 0.0045 20.2 6.7 52 80-145 9-61 (78)
249 COG4393 Predicted membrane pro 29.3 73 0.0016 29.3 3.8 36 156-191 327-363 (405)
250 PRK12495 hypothetical protein; 29.2 27 0.00058 30.1 1.0 25 164-189 43-68 (226)
251 COG1862 YajC Preprotein transl 28.8 1.1E+02 0.0023 23.0 4.1 23 74-96 44-72 (97)
252 PF07295 DUF1451: Protein of u 28.5 25 0.00053 28.3 0.6 26 165-190 114-141 (146)
253 PF06943 zf-LSD1: LSD1 zinc fi 28.4 39 0.00085 19.1 1.3 21 167-187 3-24 (25)
254 PF13597 NRDD: Anaerobic ribon 28.0 16 0.00035 35.3 -0.5 35 163-205 491-526 (546)
255 PF08271 TF_Zn_Ribbon: TFIIB z 27.8 55 0.0012 20.2 2.1 22 166-187 3-27 (43)
256 PRK06386 replication factor A; 27.5 4.9E+02 0.011 24.0 9.0 21 162-187 235-256 (358)
257 PRK07218 replication factor A; 27.2 2.1E+02 0.0046 26.9 6.7 36 136-188 282-318 (423)
258 PTZ00329 eukaryotic translatio 27.1 1.6E+02 0.0035 23.9 5.1 55 73-143 28-83 (155)
259 PF12508 DUF3714: Protein of u 27.0 3.9E+02 0.0084 22.6 8.1 55 36-100 53-111 (200)
260 PRK08579 anaerobic ribonucleos 26.7 24 0.00051 34.9 0.3 35 164-205 569-604 (625)
261 PF00855 PWWP: PWWP domain; I 26.7 40 0.00086 23.5 1.4 13 131-143 1-13 (86)
262 PRK00004 rplX 50S ribosomal pr 26.5 2.7E+02 0.0059 20.8 6.1 19 81-99 22-40 (105)
263 PRK14351 ligA NAD-dependent DN 26.3 1.1E+02 0.0025 30.5 5.0 52 129-184 388-444 (689)
264 PF09845 DUF2072: Zn-ribbon co 26.1 13 0.00027 29.5 -1.4 29 165-193 3-33 (131)
265 COG3877 Uncharacterized protei 25.9 40 0.00088 25.9 1.3 22 163-187 6-28 (122)
266 PF04319 NifZ: NifZ domain; I 25.6 2.5E+02 0.0055 20.0 5.6 21 127-147 1-21 (75)
267 PF04351 PilP: Pilus assembly 25.4 81 0.0018 25.0 3.1 28 68-95 99-129 (149)
268 PRK04163 exosome complex RNA-b 25.2 2.4E+02 0.0052 24.1 6.2 30 132-162 62-91 (235)
269 cd03478 Rieske_AIFL_N AIFL (ap 25.0 1.9E+02 0.004 20.5 4.8 53 130-189 8-66 (95)
270 COG0675 Transposase and inacti 24.8 36 0.00078 29.3 1.1 19 166-188 312-331 (364)
271 PRK08059 general stress protei 24.8 1.9E+02 0.0041 21.9 5.0 27 129-156 3-29 (123)
272 cd04476 RPA1_DBD_C RPA1_DBD_C: 24.7 1.3E+02 0.0027 23.9 4.2 41 136-188 19-60 (166)
273 COG3269 Predicted RNA-binding 24.6 1.3E+02 0.0029 21.4 3.7 23 75-97 47-69 (73)
274 cd06080 MUM1_like Mutated mela 24.5 49 0.0011 23.8 1.6 15 131-145 1-15 (80)
275 PF00394 Cu-oxidase: Multicopp 24.5 2.3E+02 0.0051 22.1 5.7 35 130-164 63-97 (159)
276 PF08646 Rep_fac-A_C: Replicat 24.4 1.7E+02 0.0038 22.6 4.9 40 137-188 4-46 (146)
277 PF01835 A2M_N: MG2 domain; I 23.9 2.6E+02 0.0057 19.7 5.4 34 129-162 9-50 (99)
278 cd00350 rubredoxin_like Rubred 23.8 36 0.00078 20.0 0.6 24 165-189 3-27 (33)
279 PF00467 KOW: KOW motif; Inte 23.7 1.2E+02 0.0026 17.5 2.9 16 80-95 15-30 (32)
280 COG1592 Rubrerythrin [Energy p 23.6 34 0.00074 28.1 0.6 25 163-189 134-159 (166)
281 COG0777 AccD Acetyl-CoA carbox 23.2 36 0.00078 30.4 0.7 46 162-207 27-78 (294)
282 PRK14350 ligA NAD-dependent DN 22.6 1.5E+02 0.0031 29.7 4.9 52 129-184 363-419 (669)
283 TIGR02098 MJ0042_CXXC MJ0042 f 22.6 40 0.00086 20.1 0.6 11 179-189 2-12 (38)
284 COG1465 Predicted alternative 22.5 1.7E+02 0.0036 26.7 4.7 48 10-65 268-315 (376)
285 PF13248 zf-ribbon_3: zinc-rib 22.2 32 0.00069 19.1 0.2 21 165-188 4-25 (26)
286 PHA00626 hypothetical protein 21.9 71 0.0015 21.7 1.8 25 166-190 3-34 (59)
287 TIGR01385 TFSII transcription 21.8 36 0.00077 30.5 0.4 13 180-192 287-299 (299)
288 COG4956 Integral membrane prot 21.7 1.3E+02 0.0029 27.4 4.0 28 8-35 288-319 (356)
289 PF09889 DUF2116: Uncharacteri 21.5 16 0.00034 25.0 -1.5 19 166-187 6-26 (59)
290 cd03528 Rieske_RO_ferredoxin R 21.3 1.7E+02 0.0037 20.6 4.0 57 131-191 10-69 (98)
291 TIGR00074 hypC_hupF hydrogenas 21.3 2E+02 0.0043 20.5 4.1 16 81-96 6-21 (76)
292 PF02699 YajC: Preprotein tran 21.2 32 0.00069 24.7 0.0 24 74-97 37-66 (82)
293 PF07191 zinc-ribbons_6: zinc- 20.9 76 0.0016 22.4 1.9 27 164-191 2-29 (70)
294 PRK00762 hypA hydrogenase nick 20.8 53 0.0011 25.4 1.2 27 163-189 70-102 (124)
295 smart00532 LIGANc Ligase N fam 20.6 1.5E+02 0.0034 27.9 4.4 68 129-203 361-436 (441)
296 PRK14873 primosome assembly pr 20.4 73 0.0016 31.7 2.3 26 164-189 393-420 (665)
297 PF09926 DUF2158: Uncharacteri 20.2 71 0.0015 21.2 1.5 24 131-158 1-24 (53)
298 KOG1004 Exosomal 3'-5' exoribo 20.1 2.7E+02 0.006 24.0 5.4 35 131-166 63-97 (230)
No 1
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-44 Score=296.69 Aligned_cols=169 Identities=31% Similarity=0.394 Sum_probs=158.7
Q ss_pred CCceEEecCCccCCCCCeeeCCcEEEeCCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 028346 6 EEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT 85 (210)
Q Consensus 6 ~~~~iV~PGd~l~~~ee~~~G~GtY~~~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V~ 85 (210)
.++.+|+|||.|+..|||+||.|||+++|+ |+|+.+|.+.+ |++++.++|.|.+..+.+|+.||+|+|+|+
T Consensus 3 ~~g~~v~PGd~~a~~EE~~~G~gt~~~~g~--i~Aa~~G~~~~-------d~~n~~~~V~p~~~~~~~~K~GdiV~grV~ 73 (188)
T COG1096 3 KDGTFVLPGDVLAVIEEFLPGEGTYEEGGE--IRAAATGVVRR-------DDKNRVISVKPGKKTPPLPKGGDIVYGRVT 73 (188)
T ss_pred ccCcEEcCcceeeeeeeeecCCCeEeECCE--EEEeecccEEE-------cccceEEEeccCCCCCCCCCCCCEEEEEEe
Confidence 367789999999999999999999999999 99999999999 667889999999876889999999999999
Q ss_pred EEecCeEEEEEeeecccc--ccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEEEeecCCceeeE
Q 028346 86 KVMTRMASADIMCVGAKS--VREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVS 163 (210)
Q Consensus 86 ~v~~~~a~V~I~~v~~~~--l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv~ 163 (210)
+++.+.|.|+|.++++.. +..++.|.||+||++..+.. +++++|++||+|+|+|+|.+ .++.|||++++||||+
T Consensus 74 ~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~--~~~d~f~~GDivrA~Vis~~--~~~~Lst~~~dlGVI~ 149 (188)
T COG1096 74 DVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVE--KLSDAFRIGDIVRARVISTG--DPIQLSTKGNDLGVIY 149 (188)
T ss_pred eccceEEEEEEEEEecccccCCCCceeeEEEEeccccccc--ccccccccccEEEEEEEecC--CCeEEEecCCcceEEE
Confidence 999999999999999954 88899999999999998887 89999999999999999987 4799999999999999
Q ss_pred EEc-CCCCeeEEcccceEEecccchh
Q 028346 164 AES-TAGKLVYCISKYDLNIILFYSF 188 (210)
Q Consensus 164 a~~-~~G~~m~~~~~~~l~C~~~~~~ 188 (210)
|+| +||++|.+ .|++|.||+|+..
T Consensus 150 A~CsrC~~~L~~-~~~~l~Cp~Cg~t 174 (188)
T COG1096 150 ARCSRCRAPLVK-KGNMLKCPNCGNT 174 (188)
T ss_pred EEccCCCcceEE-cCcEEECCCCCCE
Confidence 999 99999999 8899999999864
No 2
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=100.00 E-value=2.3e-43 Score=293.23 Aligned_cols=170 Identities=26% Similarity=0.329 Sum_probs=157.1
Q ss_pred CceEEecCCccCCCCCeeeCCcEEEeCCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEE
Q 028346 7 EMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTK 86 (210)
Q Consensus 7 ~~~iV~PGd~l~~~ee~~~G~GtY~~~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V~~ 86 (210)
++++|+|||+|+..+||++|+|||+++|+ ||||++|.+++ |..++.|+|.|.+...+.|++||+|+|+|++
T Consensus 4 ~~~~V~PGe~l~~~~e~~~G~Gty~~~~~--i~as~~G~~~i-------d~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~ 74 (189)
T PRK09521 4 QGDLVLPGDYLAVIEEYLPGEGTYEDNGE--VYASVVGKVFI-------DDINRKISVIPFKKTPPLLKKGDIVYGRVVD 74 (189)
T ss_pred cCCEECCCCccccccceEcCCCEEeeCCE--EEEEeeEEEEE-------cCCCCEEEEecCcCCCCCCCCCCEEEEEEEE
Confidence 56789999999998999999999999999 99999999998 3456789999988668999999999999999
Q ss_pred EecCeEEEEEeeec--cccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEEEeecCCceeeEE
Q 028346 87 VMTRMASADIMCVG--AKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSA 164 (210)
Q Consensus 87 v~~~~a~V~I~~v~--~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv~a 164 (210)
+.+++|+|+|.+++ +++++.++.|+||.+|++..+.+ ++.+.|++||+|+|+|++++ +.+.||+++++||||+|
T Consensus 75 i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~--~~~~~~~~GD~V~akV~~i~--~~i~LS~k~~~lGvv~a 150 (189)
T PRK09521 75 VKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVE--SLTDAFKIGDIVRAKVISYT--DPLQLSTKGKDLGVIYA 150 (189)
T ss_pred EcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhh--hHHhccCCCCEEEEEEEecC--CcEEEEEecCCceEEEE
Confidence 99999999999887 67788889999999999877665 79999999999999999998 57999999999999999
Q ss_pred Ec-CCCCeeEEcccceEEecccchhh
Q 028346 165 ES-TAGKLVYCISKYDLNIILFYSFW 189 (210)
Q Consensus 165 ~~-~~G~~m~~~~~~~l~C~~~~~~~ 189 (210)
+| +||.+|+|.+|++|.||+|+++.
T Consensus 151 ~~~~~g~~~~~~~~~~~~c~~~~~~e 176 (189)
T PRK09521 151 MCSRCRTPLVKKGENELKCPNCGNIE 176 (189)
T ss_pred EccccCCceEECCCCEEECCCCCCEE
Confidence 99 89999999999999999999764
No 3
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-43 Score=285.86 Aligned_cols=176 Identities=38% Similarity=0.554 Sum_probs=157.6
Q ss_pred CceEEecCCccCCCCC-eeeCCcEEEeCCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 028346 7 EMVLVTPGEVLGKATE-VKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT 85 (210)
Q Consensus 7 ~~~iV~PGd~l~~~ee-~~~G~GtY~~~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V~ 85 (210)
...+|+|||+++..++ +..|.|||+.++. |+||.+|...+. +..+++.+.+++.......+|.+||||++||.
T Consensus 4 a~~~~lpG~~~c~~e~~~~~g~Gtye~~~y--I~aS~ag~~~~~----~~~~~~~v~~~~~~~~~~~LP~~G~IVtarV~ 77 (193)
T KOG3409|consen 4 AETLVLPGEVVCRAEGEYRMGEGTYERNGY--IFASVAGVNFRD----NLVQKIEVVSVEKQLFNELLPFVGAIVTARVS 77 (193)
T ss_pred ceEEEcccceeeecccccccccceeecCCe--EEeccccceeec----CCccceeeeeecccchhhcCCccCcEEEEEEE
Confidence 4578999999998765 9999999999999 999999955442 11223444555544445789999999999999
Q ss_pred EEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEEEeecCCceeeEEE
Q 028346 86 KVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAE 165 (210)
Q Consensus 86 ~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv~a~ 165 (210)
+++.++|.|+|+++++.+|...|+|+||.+|+|++++|++++.++|+|||+|+|+|+|.+++.+|.|||+++|||||+|+
T Consensus 78 ~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LTtAeneLGVV~a~ 157 (193)
T KOG3409|consen 78 RINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLTTAENELGVVFAR 157 (193)
T ss_pred eeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcEEEEEecccceEEEEe
Confidence 99999999999999999999999999999999999999999999999999999999999988999999999999999999
Q ss_pred c-CCCCeeEEcccceEEecccchh
Q 028346 166 S-TAGKLVYCISKYDLNIILFYSF 188 (210)
Q Consensus 166 ~-~~G~~m~~~~~~~l~C~~~~~~ 188 (210)
+ +.|.+|+|++|++|+||.+++-
T Consensus 158 as~~g~~M~pvdw~~mqsp~Tg~t 181 (193)
T KOG3409|consen 158 ASETGEPMVPVDWQEMQSPKTGKT 181 (193)
T ss_pred ccccCCceeeccceeEEcCccCcc
Confidence 9 9999999999999999998864
No 4
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=99.98 E-value=9e-32 Score=230.79 Aligned_cols=176 Identities=22% Similarity=0.293 Sum_probs=140.7
Q ss_pred CceEEecCCccCCCCCeeeCCcEEEeCCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEE
Q 028346 7 EMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTK 86 (210)
Q Consensus 7 ~~~iV~PGd~l~~~ee~~~G~GtY~~~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V~~ 86 (210)
+..+|+|||.|+ .++|.+|+|||+++|+ |+||++|.+... ++.++|.|.+. +|.|++||+|+|+|++
T Consensus 7 ~~~~V~PGd~l~-~~~~~~G~Gty~~~g~--i~As~~G~~~~~---------~~~i~V~p~~~-~y~P~vGDiViG~V~~ 73 (235)
T PRK04163 7 DRKIVVPGDLLA-EGEFKAGRGTYKENGK--IYSTVVGLVDIK---------DDKVRVIPLEG-KYIPKVGDLVIGKVTD 73 (235)
T ss_pred CCcEECCCCCcC-cCCeecCCceEEeCCE--EEEEEeEEEEEE---------CCEEEEEECCC-cccCCCCCEEEEEEEE
Confidence 347899999997 5789999999999999 999999999982 25899999986 4999999999999999
Q ss_pred EecCeEEEEEeeeccccccCceeEEEeccccccccc--cccccCCCCCCCCEEEEEEEEeCCCcceEEEeecCCceeeEE
Q 028346 87 VMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI--DKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSA 164 (210)
Q Consensus 87 v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~--d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv~a 164 (210)
+++++|+|+| ..++.|+||.++++..+. |..+++++|++||+|+|||+++++.+.+.||+++++||++.
T Consensus 74 i~~~~~~vdI--------~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~~~lG~L~- 144 (235)
T PRK04163 74 VTFSGWEVDI--------NSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGKGLGKIE- 144 (235)
T ss_pred EeCceEEEEe--------CCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcCCCCCccC-
Confidence 9999999999 778999999999986643 55689999999999999999998766799999999999993
Q ss_pred EcCCCCeeEEcccc---eEEecccchhhhH---HHHHHhhcccceEEEee
Q 028346 165 ESTAGKLVYCISKY---DLNIILFYSFWIF---CILQIASNIISFITLFK 208 (210)
Q Consensus 165 ~~~~G~~m~~~~~~---~l~C~~~~~~~~~---~~~~~~~~~~~~~~~~~ 208 (210)
++.+..++-. .+.=|.|.....+ +..+|+-+.+++|..+.
T Consensus 145 ----~G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~NG~VwI~~ 190 (235)
T PRK04163 145 ----GGTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQNGRIWIKG 190 (235)
T ss_pred ----CCEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCCcEEEEee
Confidence 2332222211 1222233322222 46677777777777664
No 5
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=2.6e-29 Score=213.51 Aligned_cols=138 Identities=25% Similarity=0.360 Sum_probs=125.3
Q ss_pred CCceEEecCCccCCCCCeeeCCcEEEeCCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 028346 6 EEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT 85 (210)
Q Consensus 6 ~~~~iV~PGd~l~~~ee~~~G~GtY~~~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V~ 85 (210)
.++++|+|||.|...+.+..|+|||..+++ |||+++|.+..+ ++.+.|.|+++ +|+|++||+|+|+|+
T Consensus 6 ~~~~iV~PGd~vl~~~~~~~G~Gty~~~~~--iyssv~G~~~~~---------~~~v~VIpl~g-~YiP~~gD~VIG~I~ 73 (239)
T COG1097 6 SMRKIVLPGDLVLAEGSYKLGHGTYFEGGK--IYSSVVGLLDVK---------GKLVRVIPLEG-RYIPEVGDVVIGKII 73 (239)
T ss_pred cccceecCCCccCCCCCEecCCCcEecCCE--EEEEEEeEEEEe---------CCEEEEEeCCC-cccCCCCCEEEEEEE
Confidence 467899999987777889999999999999 999999999983 46799999997 899999999999999
Q ss_pred EEecCeEEEEEeeeccccccCceeEEEeccccc--cccccccccCCCCCCCCEEEEEEEEeCCCcceEEEeecCCceeeE
Q 028346 86 KVMTRMASADIMCVGAKSVREKFSGIIRQQDVR--ATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVS 163 (210)
Q Consensus 86 ~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~--~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv~ 163 (210)
++.+++|.||| ++++.+.||.|++. ..+.++.+|+++|++||+|+|||.+++....+.|++++..||.+.
T Consensus 74 ~v~~~~W~VDI--------~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~~GkL~ 145 (239)
T COG1097 74 EVGPSGWKVDI--------GSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLGKLK 145 (239)
T ss_pred EEcccceEEEc--------CCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCceEEEeecCCCcccc
Confidence 99999999999 89999999999983 223346689999999999999999999888899999999999984
No 6
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=99.95 E-value=1.6e-29 Score=215.49 Aligned_cols=184 Identities=20% Similarity=0.261 Sum_probs=153.6
Q ss_pred cCCceEEecCCccCCCCCeeeCCcEEEeCCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEE
Q 028346 5 EEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARV 84 (210)
Q Consensus 5 ~~~~~iV~PGd~l~~~ee~~~G~GtY~~~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V 84 (210)
+...++|+||+.+.....|+.|+|||..+|. |+||++|.+++ .|+.++|+|++ .+|.|++||+|+|||
T Consensus 26 ~~~~~ivtPG~~V~~d~~fmRGHGTy~~d~~--i~ssvaG~v~r---------vNkLi~V~plk-~rY~pEvGDvVVgRV 93 (301)
T KOG3013|consen 26 SDHSTIVTPGELVTDDPGFMRGHGTYVRDGE--IYSSVAGVVQR---------VNKLISVKPLK-SRYAPEVGDVVVGRV 93 (301)
T ss_pred ccCceeecCCccccCchhhhhcccceecCCe--EEEeecchhhh---------hcceEEEeehh-hhcCCccCCEEEEEe
Confidence 4456899999999998889999999999999 99999999988 57899999998 589999999999999
Q ss_pred EEEecCeEEEEEeeeccccccC---ceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEEEeecCCcee
Q 028346 85 TKVMTRMASADIMCVGAKSVRE---KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGV 161 (210)
Q Consensus 85 ~~v~~~~a~V~I~~v~~~~l~~---~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LSt~~~~LGV 161 (210)
..|.+++|+||+++-.+..|.. ...|- .+.|....|+..|+++|+.||+|.|+|+++...++..|+||+..||+
T Consensus 94 ~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg---~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~dGs~sLhTRS~KYGK 170 (301)
T KOG3013|consen 94 IEVQQKRWKVDLNSKQDAVLMLSSVNLPGG---IQRRKSEEDELQMRSFLKEGDLIVAEVQNVFHDGSLSLHTRSLKYGK 170 (301)
T ss_pred eeeecceeEEecccccceEEEeecccCCch---hhhccchhhHHHHHHHhhccCeehHHHHHhccCCeEEEEecchhccc
Confidence 9999999999997766655432 22222 13455677888999999999999999999976678999999999999
Q ss_pred eEEEcCCCCeeEEcccceEEecccchhhhHHHHHHhhcccceEEEee
Q 028346 162 VSAESTAGKLVYCISKYDLNIILFYSFWIFCILQIASNIISFITLFK 208 (210)
Q Consensus 162 v~a~~~~G~~m~~~~~~~l~C~~~~~~~~~~~~~~~~~~~~~~~~~~ 208 (210)
+ ..| .++++.-..++=...+.++++|.+.++.+-++||-.-+
T Consensus 171 L----~~G-~lvkVpp~Lvkr~K~hfh~lp~g~~vIlG~NGyIWv~~ 212 (301)
T KOG3013|consen 171 L----GQG-ILVKVPPALVKRSKTHFHNLPGGVDVILGCNGYIWVGP 212 (301)
T ss_pred c----cCc-eEEEeCHHHhhhhhhhhccCCCCeEEEEecCceEEecC
Confidence 8 333 34555555666667777888899999999999997643
No 7
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.95 E-value=1.4e-27 Score=177.59 Aligned_cols=91 Identities=60% Similarity=1.022 Sum_probs=88.3
Q ss_pred CCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceE
Q 028346 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYF 151 (210)
Q Consensus 72 y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~ 151 (210)
|+|++||+|+|+|++++.++|.|+|.++++++++.+|.|+||+||+++++.++.+|+++|++||+|+|||+|+++.++|+
T Consensus 2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~~~ 81 (92)
T cd05791 2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSYY 81 (92)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCCcE
Confidence 78999999999999999999999999999999999999999999999999998899999999999999999999878899
Q ss_pred EEeecCCceee
Q 028346 152 LSTAKNDLGVV 162 (210)
Q Consensus 152 LSt~~~~LGVv 162 (210)
|||++++||||
T Consensus 82 Lst~~~~lGVv 92 (92)
T cd05791 82 LSTAENELGVV 92 (92)
T ss_pred EEecCCCCccC
Confidence 99999999996
No 8
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=99.87 E-value=3.4e-22 Score=145.51 Aligned_cols=72 Identities=61% Similarity=0.963 Sum_probs=52.3
Q ss_pred CCCCCCEEEEEEEEEecCeEEEEEeee----------ccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEE
Q 028346 73 VPEPGSVVIARVTKVMTRMASADIMCV----------GAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVL 142 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~a~V~I~~v----------~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~ 142 (210)
+|++||+|+|+|+++++++|.|+|+++ ++.++..+|+|+||++|+|++++|+++|.++|+|||+|+|+|+
T Consensus 1 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~Vi 80 (82)
T PF10447_consen 1 LPKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVI 80 (82)
T ss_dssp ---TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEE
T ss_pred CCCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEe
Confidence 589999999999999999999999999 6778889999999999999999999999999999999999999
Q ss_pred Ee
Q 028346 143 SL 144 (210)
Q Consensus 143 s~ 144 (210)
|+
T Consensus 81 Sl 82 (82)
T PF10447_consen 81 SL 82 (82)
T ss_dssp EE
T ss_pred eC
Confidence 85
No 9
>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=99.77 E-value=2.6e-18 Score=124.14 Aligned_cols=82 Identities=33% Similarity=0.552 Sum_probs=74.7
Q ss_pred CCCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcce
Q 028346 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAY 150 (210)
Q Consensus 71 ~y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~ 150 (210)
+|.|++||+|+|+|+++.++.|.|+| ...++|+||.+++...+.. ++.+.|++||+|+|+|+++++.+.+
T Consensus 1 ~y~p~~GdiV~G~V~~v~~~~~~V~i--------~~~~~g~l~~~~~~~~~~~--~~~~~~~~GD~i~~~V~~~~~~~~i 70 (82)
T cd04454 1 RYLPDVGDIVIGIVTEVNSRFWKVDI--------LSRGTARLEDSSATEKDKK--EIRKSLQPGDLILAKVISLGDDMNV 70 (82)
T ss_pred CCCCCCCCEEEEEEEEEcCCEEEEEe--------CCCceEEeechhccCcchH--HHHhcCCCCCEEEEEEEEeCCCCCE
Confidence 48999999999999999999999999 6779999999999755443 7899999999999999999866789
Q ss_pred EEEeecCCceee
Q 028346 151 FLSTAKNDLGVV 162 (210)
Q Consensus 151 ~LSt~~~~LGVv 162 (210)
.||+++++||||
T Consensus 71 ~LS~~~~~~Gvi 82 (82)
T cd04454 71 LLTTADNELGVI 82 (82)
T ss_pred EEEECCCCCccC
Confidence 999999999986
No 10
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=99.69 E-value=5.2e-16 Score=129.58 Aligned_cols=172 Identities=22% Similarity=0.263 Sum_probs=129.4
Q ss_pred eEEecCCccCCC--CCeeeCCcEEEeCCeeEEEEeEeeeEEEcCCCCCCCCC--CCeEEEecCCCCCCCCCCCCEEEEEE
Q 028346 9 VLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQ--RPTVEVTGHKAHGPVPEPGSVVIARV 84 (210)
Q Consensus 9 ~iV~PGd~l~~~--ee~~~G~GtY~~~g~~~I~Asv~G~v~~~~~~~~~d~~--~~~i~V~p~~~~~y~p~vGDiViG~V 84 (210)
...+|||.+... .+..+|+|.+..++. +.++..|.+...+ +.+ -...+|... .++|+|.+||.|+|.|
T Consensus 2 ~~~~pg~~~~~~~~~sv~~G~g~~~~g~~--~~~~~~G~~~~~~-----~gk~~~~v~~vds~-~kRYiP~~~D~VIGiV 73 (230)
T KOG1004|consen 2 TFYFPGDSIPRPRLCSVVLGPGLRRRGQE--RLVTKCGRLRHKE-----PGKGGGGVYWVDSQ-QKRYIPVKGDHVIGIV 73 (230)
T ss_pred ceecCCcccccCccCceeecCCccccCce--EEeccccceeecc-----CCcccceeEEEecc-cceecCCCCCEEEEEE
Confidence 457899987642 347899999998877 9999999887743 111 125577765 4799999999999999
Q ss_pred EEEecCeEEEEEeeecccccc-CceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEEEeecCCceeeE
Q 028346 85 TKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVS 163 (210)
Q Consensus 85 ~~v~~~~a~V~I~~v~~~~l~-~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv~ 163 (210)
++-..+.++|||...+-+.|+ .+|+|. +++ -++.|+.||+|+|||...+.. . |+||-|+.
T Consensus 74 ~~~~gd~ykVDigg~~~a~L~~laFe~A--------tkr----NrPnl~vGdliyakv~~a~~~--~-----Epel~Cid 134 (230)
T KOG1004|consen 74 TSKSGDIYKVDIGGSEPASLSYLAFEGA--------TKR----NRPNLQVGDLIYAKVVDANKD--M-----EPELTCID 134 (230)
T ss_pred EeccCceEEEecCCCCeeeeeeccccCc--------ccc----CCCccccccEEEEEEEecCCC--c-----CcceEEEc
Confidence 999999999999664444555 356663 443 458899999999999988643 2 78888888
Q ss_pred EEc-CCCCeeEEcccceEEecccchhhhH---H-HHHHhhcccceEEEee
Q 028346 164 AES-TAGKLVYCISKYDLNIILFYSFWIF---C-ILQIASNIISFITLFK 208 (210)
Q Consensus 164 a~~-~~G~~m~~~~~~~l~C~~~~~~~~~---~-~~~~~~~~~~~~~~~~ 208 (210)
+.. ..|-.-++ +...+.-+..+.|.|+ | +||++++..+|=..|-
T Consensus 135 s~graaGfG~Lk-dG~if~vs~~~~R~Ll~p~~~iLq~vGk~~~FEia~G 183 (230)
T KOG1004|consen 135 STGRAAGFGVLK-DGMIFKVSLGLCRKLLLPDCPILQTVGKKYPFEIAFG 183 (230)
T ss_pred ccCcccCccccc-CceEEEecHHHHHHHHcCCCcHHHHhhcccceEEEEe
Confidence 855 44543333 5567777777888887 6 9999999999876653
No 11
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.65 E-value=7.4e-16 Score=112.03 Aligned_cols=84 Identities=27% Similarity=0.396 Sum_probs=73.0
Q ss_pred CCCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccc--cccccccCCCCCCCCEEEEEEEEeCCCc
Q 028346 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT--EIDKVDMHLSFRPGDIVRASVLSLGDAR 148 (210)
Q Consensus 71 ~y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~--~~d~~~~~~~~~~GDiV~AkV~s~~d~~ 148 (210)
+|.|++||+|.|+|+++.++.|+|+| ...++|+||.+|++.. .....++.+.|++||.|.|+|+++++.+
T Consensus 1 ~y~p~~GdiV~g~V~~i~~~g~~v~i--------~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~ 72 (86)
T cd05789 1 RYIPEVGDVVIGRVTEVGFKRWKVDI--------NSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDG 72 (86)
T ss_pred CCcCCCCCEEEEEEEEECCCEEEEEC--------CCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCCC
Confidence 48899999999999999999999999 6789999999999731 1112367889999999999999997657
Q ss_pred ceEEEeecCCceee
Q 028346 149 AYFLSTAKNDLGVV 162 (210)
Q Consensus 149 ~~~LSt~~~~LGVv 162 (210)
.+.||++.++||++
T Consensus 73 ~i~LS~~~~~~g~~ 86 (86)
T cd05789 73 SVSLHTRSLKYGKL 86 (86)
T ss_pred CEEEEeCcccccCC
Confidence 89999999999985
No 12
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.59 E-value=1.1e-14 Score=107.09 Aligned_cols=75 Identities=20% Similarity=0.157 Sum_probs=63.8
Q ss_pred CCCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcce
Q 028346 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAY 150 (210)
Q Consensus 71 ~y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~ 150 (210)
+|+|++||+|+|+|+++..+.|+|+| ++++.|+||.+++... .. ++++.|++||+|+|||.+++.....
T Consensus 1 rY~P~~gD~VIG~V~~~~~~~~~VdI--------~s~~~a~L~~~~f~ga-tk--~~rp~L~~GDlV~ArV~~~~~~~~~ 69 (86)
T cd05790 1 RYVPAKGDHVIGIVVAKAGDFFKVDI--------GGSEPASLSYLAFEGA-TK--RNRPNLNVGDLVYARVVKANRDMEP 69 (86)
T ss_pred CCcCCCCCEEEEEEEEEcCCeEEEEc--------CCCcceEechHHcccc-cc--cccccCCCCCEEEEEEEecCCCCCe
Confidence 59999999999999999999999999 6778899998876422 12 5789999999999999999866667
Q ss_pred EEEeec
Q 028346 151 FLSTAK 156 (210)
Q Consensus 151 ~LSt~~ 156 (210)
.||..+
T Consensus 70 eLtc~~ 75 (86)
T cd05790 70 ELSCVD 75 (86)
T ss_pred EEEEeC
Confidence 777755
No 13
>PF14382 ECR1_N: Exosome complex exonuclease RRP4 N-terminal region; PDB: 2NN6_I 3M7N_C 2BA1_A 3M85_C.
Probab=99.37 E-value=4.9e-13 Score=84.28 Aligned_cols=37 Identities=41% Similarity=0.803 Sum_probs=33.7
Q ss_pred EEecCCccCCCCCeeeCCcEEEeCCeeEEEEeEeeeEEE
Q 028346 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRT 48 (210)
Q Consensus 10 iV~PGd~l~~~ee~~~G~GtY~~~g~~~I~Asv~G~v~~ 48 (210)
+|+|||+|+..++|++|+|||+++|+ ||||++|.+++
T Consensus 1 iV~PG~~l~~~~e~~~G~GTY~~~g~--I~asv~G~v~~ 37 (39)
T PF14382_consen 1 IVVPGDRLGSSEEYMPGHGTYVRDGN--IYASVAGTVKI 37 (39)
T ss_dssp EE-TT-EEEETTTSEESTTEEEETTE--EEESSSEEEEE
T ss_pred CCCCCCEeecCCCEecCCCEEEeCCE--EEEEeeEEEEE
Confidence 69999999999999999999999999 99999999987
No 14
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.35 E-value=9.6e-13 Score=101.91 Aligned_cols=76 Identities=18% Similarity=0.274 Sum_probs=71.0
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLS 153 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LS 153 (210)
+++|+++.|+|+.|++..|+|++ ...-+|++|+|++...+++ ++.|.+++||.|.|+|+++++.+.+.||
T Consensus 3 ~kvG~~l~GkItgI~~yGAFV~l--------~~g~tGLVHISEIa~~fVk--dI~d~L~vG~eV~vKVl~ide~GKisLS 72 (129)
T COG1098 3 MKVGSKLKGKITGITPYGAFVEL--------EGGKTGLVHISEIADGFVK--DIHDHLKVGQEVKVKVLDIDENGKISLS 72 (129)
T ss_pred ccccceEEEEEEeeEecceEEEe--------cCCCcceEEehHhhhhhHH--hHHHHhcCCCEEEEEEEeeccCCCccee
Confidence 68999999999999999999999 6778899999999999988 8999999999999999999988889999
Q ss_pred eecCCc
Q 028346 154 TAKNDL 159 (210)
Q Consensus 154 t~~~~L 159 (210)
+|..+-
T Consensus 73 Ir~~~e 78 (129)
T COG1098 73 IRKLEE 78 (129)
T ss_pred hHHhhh
Confidence 987654
No 15
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.33 E-value=6.3e-12 Score=88.95 Aligned_cols=70 Identities=29% Similarity=0.408 Sum_probs=62.0
Q ss_pred CCCCEEEEEEEEEec-CeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEEE
Q 028346 75 EPGSVVIARVTKVMT-RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLS 153 (210)
Q Consensus 75 ~vGDiViG~V~~v~~-~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LS 153 (210)
++||+|.|+|+++.+ ..+++++ ....+|++|++|++..+.. ++.+.|++||.|+|+|+++++ +.+.||
T Consensus 2 ~~G~iv~G~V~~i~~~~g~~v~l--------~~~~~Glvhis~~s~~~~~--~~~~~~~~Gd~v~~kV~~~~~-~~i~LS 70 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQL--------PFGKTGLVSIFHLSDSYTE--NPLEGFKPGKIVRCCILSKKD-GKYQLS 70 (72)
T ss_pred CCCCEEEEEEEEeeCCcEEEEEC--------CCCCEEEEEHHHhcCcccC--CHHHhCCCCCEEEEEEEEecC-CEEEEE
Confidence 689999999999987 6899998 7789999999999877655 677899999999999999975 679999
Q ss_pred ee
Q 028346 154 TA 155 (210)
Q Consensus 154 t~ 155 (210)
++
T Consensus 71 l~ 72 (72)
T cd05704 71 LR 72 (72)
T ss_pred eC
Confidence 85
No 16
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.22 E-value=7.4e-11 Score=82.20 Aligned_cols=69 Identities=28% Similarity=0.295 Sum_probs=60.3
Q ss_pred CCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEEEee
Q 028346 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLSTA 155 (210)
Q Consensus 77 GDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~LSt~ 155 (210)
||+|.|+|+++.++.|+|++ ...++|+||.++++..+.+ ++.+.|++||.++|+|+++++ .+.+.||.+
T Consensus 1 G~iv~g~V~~i~~~~~~v~l--------~~~~~g~l~~~e~~~~~~~--~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDI--------GYKSEGIIPISEFSDDPIE--NGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEe--------CCCceEEEEHHHhCccccC--CHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 89999999999999999999 5568999999999876655 788999999999999999973 456888863
No 17
>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=99.15 E-value=4.1e-10 Score=79.01 Aligned_cols=71 Identities=30% Similarity=0.354 Sum_probs=61.7
Q ss_pred CCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEEE
Q 028346 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS 153 (210)
Q Consensus 75 ~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~LS 153 (210)
++|++|.|+|+++.+++++|++ ....+|.+|.++++..+.. +..+.|++||.|+|+|++++. .+.+.||
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l--------~~~~~g~v~~s~l~~~~~~--~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls 71 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQL--------GNKVTGPSFITDALDDYSE--ALPYKFKKNDIVRACVLSVDVPNKKIALS 71 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEe--------CCCcEEEEEhhhccCcccc--ccccccCCCCEEEEEEEEEeCCCCEEEEE
Confidence 6899999999999999999999 6679999999999865433 567889999999999999975 4678888
Q ss_pred ee
Q 028346 154 TA 155 (210)
Q Consensus 154 t~ 155 (210)
++
T Consensus 72 ~~ 73 (73)
T cd05706 72 LR 73 (73)
T ss_pred EC
Confidence 74
No 18
>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=99.13 E-value=4.1e-10 Score=78.55 Aligned_cols=72 Identities=25% Similarity=0.439 Sum_probs=63.1
Q ss_pred CCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCC-cceEEEee
Q 028346 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RAYFLSTA 155 (210)
Q Consensus 77 GDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~-~~~~LSt~ 155 (210)
|++|.|+|+++.++.|+|+| ....+|.+|.++++..+.+ ++.+.|++||.|+|+|++++.. +.+.||++
T Consensus 1 G~~v~g~V~~v~~~g~~v~l--------~~~~~g~i~~~~~~~~~~~--~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k 70 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKL--------GDGVEGFLRAAELSRDRVE--DATERFKVGDEVEAKITNVDRKNRKISLSIK 70 (73)
T ss_pred CCEEEEEEEEEECCeEEEEe--------CCCCEEEEEHHHCCCcccc--CHHHccCCCCEEEEEEEEEeCCCCEEEEEEE
Confidence 79999999999999999999 5679999999999866554 6788999999999999999754 56899998
Q ss_pred cCC
Q 028346 156 KND 158 (210)
Q Consensus 156 ~~~ 158 (210)
..+
T Consensus 71 ~~~ 73 (73)
T cd05691 71 AKE 73 (73)
T ss_pred EcC
Confidence 754
No 19
>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=99.13 E-value=2.8e-10 Score=81.11 Aligned_cols=71 Identities=18% Similarity=0.178 Sum_probs=59.4
Q ss_pred CCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEecccccccccc-ccccCCCCCCCCEEEEEEEEeCCC-cceEE
Q 028346 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID-KVDMHLSFRPGDIVRASVLSLGDA-RAYFL 152 (210)
Q Consensus 75 ~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d-~~~~~~~~~~GDiV~AkV~s~~d~-~~~~L 152 (210)
++||+|.|+|+++++..++|++ ....+|.+|+++++..... ..++.+.|++||.|.|+|+++++. +.+.|
T Consensus 2 k~G~~V~g~V~~i~~~G~fV~l--------~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~L 73 (74)
T cd05705 2 KEGQLLRGYVSSVTKQGVFFRL--------SSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVEL 73 (74)
T ss_pred CCCCEEEEEEEEEeCCcEEEEe--------CCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEec
Confidence 6899999999999999999999 6789999999999866533 113668999999999999999753 45666
Q ss_pred E
Q 028346 153 S 153 (210)
Q Consensus 153 S 153 (210)
|
T Consensus 74 S 74 (74)
T cd05705 74 S 74 (74)
T ss_pred C
Confidence 4
No 20
>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=99.10 E-value=6e-10 Score=78.51 Aligned_cols=74 Identities=18% Similarity=0.244 Sum_probs=62.2
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~L 152 (210)
|++|++|.|+|+++.+..++|++... ...+|++|+++++..+.. ++.+.|++||.|+|+|++++. .+.+.|
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~------~~~~gll~~s~l~~~~~~--~~~~~~~~Gd~v~vkv~~~d~~~~~i~l 72 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEY------GNIEGMILLSELSRRRIR--SIRKLVKVGRKEVVKVIRVDKEKGYIDL 72 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCC------CCeEEEEEhHHcCCcccC--CHHHeeCCCCEEEEEEEEEECCCCEEEE
Confidence 67899999999999999999999311 248999999999865544 678899999999999999975 356888
Q ss_pred Eee
Q 028346 153 STA 155 (210)
Q Consensus 153 St~ 155 (210)
|++
T Consensus 73 s~k 75 (76)
T cd04452 73 SKK 75 (76)
T ss_pred EEc
Confidence 875
No 21
>PRK08582 hypothetical protein; Provisional
Probab=99.09 E-value=1.2e-09 Score=87.10 Aligned_cols=76 Identities=25% Similarity=0.283 Sum_probs=66.8
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLS 153 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LS 153 (210)
+++|++|.|+|+.|++..++|+| .....|++|+++++..+.. ++.+.|++||.|.|+|++++..+.+.||
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L--------~~~~~GlVhiSels~~~v~--~~~~~l~vGD~VkvkV~~id~~gkI~LS 72 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVEL--------PEGKTGLVHISEVADNYVK--DINDHLKVGDEVEVKVLNVEDDGKIGLS 72 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEE--------CCCCEEEEEeeccCccccc--ccccccCCCCEEEEEEEEECCCCcEEEE
Confidence 57899999999999999999999 6679999999999866654 6779999999999999999865789999
Q ss_pred eecCCc
Q 028346 154 TAKNDL 159 (210)
Q Consensus 154 t~~~~L 159 (210)
++...-
T Consensus 73 lk~~~~ 78 (139)
T PRK08582 73 IKKAKD 78 (139)
T ss_pred EEeccc
Confidence 987543
No 22
>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=99.06 E-value=8.2e-10 Score=77.31 Aligned_cols=66 Identities=23% Similarity=0.287 Sum_probs=56.3
Q ss_pred CCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcce
Q 028346 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAY 150 (210)
Q Consensus 77 GDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~ 150 (210)
|++|.|+|+++.+++++|++ ...++|.+|.++++..+.+..++.+.|++||.|.|+|+++++.+.+
T Consensus 1 G~iV~g~V~~i~~~gi~v~l--------~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~~ 66 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQL--------ADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTH 66 (70)
T ss_pred CCEEEEEEEEEECCcEEEEe--------CCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcccc
Confidence 89999999999999999999 6789999999999865312237789999999999999999865443
No 23
>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=99.05 E-value=5.7e-10 Score=84.07 Aligned_cols=76 Identities=18% Similarity=0.291 Sum_probs=63.7
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccc-----------------cccccCCCCCCCCE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI-----------------DKVDMHLSFRPGDI 136 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~-----------------d~~~~~~~~~~GDi 136 (210)
+++|++|.|+|+++.+..++|++ ....+|++|++|++..+. +..++.+.|++||+
T Consensus 1 L~~G~vV~G~V~~v~~~gl~v~L--------~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~ 72 (100)
T cd05693 1 LSEGMLVLGQVKEITKLDLVISL--------PNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQL 72 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEEC--------CCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCE
Confidence 36899999999999999999998 677999999999975331 12257899999999
Q ss_pred EEEEEEEeCCC----cceEEEeecC
Q 028346 137 VRASVLSLGDA----RAYFLSTAKN 157 (210)
Q Consensus 137 V~AkV~s~~d~----~~~~LSt~~~ 157 (210)
|+|+|+++++. +.+.||++..
T Consensus 73 V~~kVi~~d~~~~~~~~i~LSlr~~ 97 (100)
T cd05693 73 VRCKVVSLDKSKSGKKRIELSLEPE 97 (100)
T ss_pred EEEEEEEccCCcCCCcEEEEEecHH
Confidence 99999999863 5789998754
No 24
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.04 E-value=1.4e-09 Score=77.11 Aligned_cols=71 Identities=20% Similarity=0.181 Sum_probs=60.7
Q ss_pred CCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEEEee
Q 028346 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLSTA 155 (210)
Q Consensus 77 GDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~LSt~ 155 (210)
||+|.|+|+++.++.++|++ ....+|.+|.++++.......+..+.|++||.|.|+|++++. .+.+.||.+
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 GQEVTGFVNNVSKEFVWLTI--------SPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEe--------CCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 89999999999999999999 677999999999975431222678999999999999999985 467899875
No 25
>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=99.04 E-value=1.8e-09 Score=73.79 Aligned_cols=69 Identities=26% Similarity=0.352 Sum_probs=59.3
Q ss_pred CCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEEEee
Q 028346 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTA 155 (210)
Q Consensus 77 GDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LSt~ 155 (210)
||++.|+|+++.+..|+|+| ....+|+||.++++..+.. ++.+.|++||.|.++|.+++..+.+.||++
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 GSVVEGTVTRLKPFGAFVEL--------GGGISGLVHISQIAHKRVK--DVKDVLKEGDKVKVKVLSIDARGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEE--------CCCCEEEEEhHHcCCcccC--CHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence 79999999999999999999 5679999999999755443 566889999999999999976556888864
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=99.02 E-value=2.5e-09 Score=75.61 Aligned_cols=72 Identities=18% Similarity=0.160 Sum_probs=61.5
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLS 153 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LS 153 (210)
|+.|+++.|+|+++.+.+++|++. ....+|++|+++++..+.+ +..+.|++||.|+++|++++..+.+.||
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~-------~~~~eGlvh~sel~~~~~~--~~~~~~~~Gd~v~vkv~~vd~~~ki~ls 71 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIP-------GCRKQGLVHKSHMSSCRVD--DPSEVVDVGEKVWVKVIGREMKDKMKLS 71 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEEC-------CCCeEEEEEchhhCCCccc--CHhhEECCCCEEEEEEEEECCCCcEEEE
Confidence 578999999999999999999992 1236999999999876665 7888999999999999999865567777
Q ss_pred e
Q 028346 154 T 154 (210)
Q Consensus 154 t 154 (210)
+
T Consensus 72 ~ 72 (73)
T cd05686 72 L 72 (73)
T ss_pred e
Confidence 5
No 27
>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=99.02 E-value=2.5e-09 Score=74.99 Aligned_cols=72 Identities=24% Similarity=0.310 Sum_probs=63.6
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCC-cceEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RAYFL 152 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~-~~~~L 152 (210)
+++||++.|+|+++.++.++|++ ....+|++|.+++.....+ +..+.|++||.|.|+|++++.. +.+.|
T Consensus 2 ~~~G~iv~g~V~~v~~~g~~V~l--------~~~~~g~ip~~~l~~~~~~--~~~~~~~~G~~v~v~v~~vd~~~~~i~l 71 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDFGVFVDL--------GNGIEGFIPISELSDDRID--DPSEVYKIGQTVRVKVIKVDKEKGRIRL 71 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEE--------STSSEEEEEGGGSSSSEES--SSHGTCETTCEEEEEEEEEETTTTEEEE
T ss_pred CCCCCEEEEEEEEEECCEEEEEE--------CCcEEEEEEeehhcCcccc--ccccccCCCCEEEEEEEEEECCCCeEEE
Confidence 68999999999999999999999 6789999999999876544 6789999999999999999754 55888
Q ss_pred Eee
Q 028346 153 STA 155 (210)
Q Consensus 153 St~ 155 (210)
|++
T Consensus 72 S~k 74 (74)
T PF00575_consen 72 SLK 74 (74)
T ss_dssp EST
T ss_pred EEC
Confidence 864
No 28
>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=99.01 E-value=1.6e-09 Score=75.22 Aligned_cols=67 Identities=15% Similarity=0.283 Sum_probs=57.6
Q ss_pred CCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEEE
Q 028346 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS 153 (210)
Q Consensus 77 GDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~LS 153 (210)
|++|.|+|+++.++.++|++ .....|++|.++++..... +..+.|++||.|.|+|++++. .+.+.||
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 GDVVRGFVKNIANNGVFVTL--------GRGVDARVRVSELSDSYLK--DWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEe--------CCCCEEEEEHHHCCchhhc--CHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 79999999999999999999 5569999999999865544 678999999999999999985 3456554
No 29
>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=99.00 E-value=2.9e-09 Score=74.83 Aligned_cols=74 Identities=24% Similarity=0.320 Sum_probs=62.4
Q ss_pred CCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEEE
Q 028346 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS 153 (210)
Q Consensus 75 ~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~LS 153 (210)
++|++|.|+|+++++..++|++. ....+|++|.++++..+.. ++.+.|++||.|+|+|.+++. .+.+.||
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~-------~~~~~g~i~~~~l~~~~~~--~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 71 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDID-------GTNVSGLCHKSEISDNRVA--DASKLFRVGDKVRAKVLKIDAEKKRISLG 71 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEEC-------CCCeEEEEEHHHCCCCccC--CHhHeecCCCEEEEEEEEEeCCCCEEEEE
Confidence 46999999999999999999992 1368999999999865533 577899999999999999975 4678888
Q ss_pred eecC
Q 028346 154 TAKN 157 (210)
Q Consensus 154 t~~~ 157 (210)
++..
T Consensus 72 ~k~~ 75 (77)
T cd05708 72 LKAS 75 (77)
T ss_pred EEee
Confidence 8764
No 30
>PRK07252 hypothetical protein; Provisional
Probab=98.96 E-value=5.4e-09 Score=81.31 Aligned_cols=73 Identities=18% Similarity=0.257 Sum_probs=63.3
Q ss_pred CCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEEE
Q 028346 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS 153 (210)
Q Consensus 75 ~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~LS 153 (210)
++|++|.|+|+++.+.+++|+| .....|++|+++++..+.+ +..+.|++||.|.|+|++++. .+.+.||
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei--------~~~~~GllhiseLs~~~~~--~~~~~~~vGD~V~VkI~~iD~~~~ri~lS 71 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVAL--------ENGTTGLIHISEIKTGFID--NIHQLLKVGEEVLVQVVDFDEYTGKASLS 71 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEE--------CCCCEEEEEHHHcCCcccc--ChhhccCCCCEEEEEEEEEeCCCCEEEEE
Confidence 5799999999999999999999 5668999999999865554 567889999999999999975 4678888
Q ss_pred eecC
Q 028346 154 TAKN 157 (210)
Q Consensus 154 t~~~ 157 (210)
++..
T Consensus 72 lk~~ 75 (120)
T PRK07252 72 LRTL 75 (120)
T ss_pred Eeec
Confidence 8765
No 31
>PRK05807 hypothetical protein; Provisional
Probab=98.96 E-value=7.1e-09 Score=82.25 Aligned_cols=74 Identities=20% Similarity=0.295 Sum_probs=64.7
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLS 153 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LS 153 (210)
.++|++|.|+|+.+++..|+|+| . ..+|++|+++++..+.. ++.+.|++||.|.++|++++..+.+.||
T Consensus 3 ~~vG~vv~G~Vt~i~~~GafV~L--------~-~~~Glvhiseis~~~v~--~~~~~~kvGd~V~VkV~~id~~gkI~LS 71 (136)
T PRK05807 3 LKAGSILEGTVVNITNFGAFVEV--------E-GKTGLVHISEVADTYVK--DIREHLKEQDKVKVKVISIDDNGKISLS 71 (136)
T ss_pred ccCCCEEEEEEEEEECCeEEEEE--------C-CEEEEEEhhhccccccc--CccccCCCCCEEEEEEEEECCCCcEEEE
Confidence 46899999999999999999999 2 35899999999877665 6789999999999999999866679999
Q ss_pred eecCC
Q 028346 154 TAKND 158 (210)
Q Consensus 154 t~~~~ 158 (210)
++...
T Consensus 72 lk~~~ 76 (136)
T PRK05807 72 IKQAM 76 (136)
T ss_pred EEecc
Confidence 98743
No 32
>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=98.96 E-value=4.6e-09 Score=72.98 Aligned_cols=69 Identities=22% Similarity=0.316 Sum_probs=59.7
Q ss_pred CCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEEEee
Q 028346 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLSTA 155 (210)
Q Consensus 77 GDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~LSt~ 155 (210)
|+++.|+|+++.+..++|++ ....+|++|.++++..+.. +..+.|++||.|.++|++++. .+.+.||.+
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 GLKTHGTIVKVKPNGCIVSF--------YNNVKGFLPKSELSEAFIK--DPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEE--------CCCCEEEEEHHHcChhhcC--CHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 89999999999999999999 5568999999999865544 677889999999999999975 456888864
No 33
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=98.92 E-value=4e-09 Score=94.27 Aligned_cols=77 Identities=18% Similarity=0.280 Sum_probs=67.2
Q ss_pred CCCCCCCEEEEEEEEEecCeEEEEEeeecccccc-CceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-Ccc
Q 028346 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARA 149 (210)
Q Consensus 72 y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~-~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~ 149 (210)
..|++||+|.|+|++|.+.+++|+|. . ...+|+||+|+++..+.. ++++.+++||.|.++|++++. .+.
T Consensus 13 ~~P~~GdvV~g~V~~I~d~GafV~L~-------EY~gvEGlIhiSElS~~ri~--~i~d~vkvGd~v~vkVl~VD~ekg~ 83 (319)
T PTZ00248 13 KFPEEDDLVMVKVVRITEMGAYVSLL-------EYDDIEGMILMSELSKRRIR--SINKLIRVGRHEVVVVLRVDKEKGY 83 (319)
T ss_pred hCCCCCCEEEEEEEEEeCCeEEEEec-------CCCCcEEEEEHHHhcccccC--CHHHhcCCCCEEEEEEEEEeCCCCE
Confidence 35899999999999999999999993 1 268999999999877665 899999999999999999974 456
Q ss_pred eEEEeecC
Q 028346 150 YFLSTAKN 157 (210)
Q Consensus 150 ~~LSt~~~ 157 (210)
+.||++..
T Consensus 84 IdLS~K~v 91 (319)
T PTZ00248 84 IDLSKKRV 91 (319)
T ss_pred EEEEeeec
Confidence 89999874
No 34
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.92 E-value=7.9e-09 Score=70.34 Aligned_cols=71 Identities=27% Similarity=0.356 Sum_probs=59.8
Q ss_pred CCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCC-cceEEE
Q 028346 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RAYFLS 153 (210)
Q Consensus 75 ~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~-~~~~LS 153 (210)
++|++|.|+|+++.+..++|++ ...+.|.+|.+++...... ++.+.|++||.|+|+|.+++.. +.+.||
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i--------~~~~~g~l~~~~~~~~~~~--~~~~~~~~G~~v~~~V~~~~~~~~~i~ls 70 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDL--------GNGVEGLIPISELSDKRVK--DPEEVLKVGDEVKVKVLSVDEEKGRIILS 70 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEe--------CCCCEEEEEHHHCCccccC--CHHHeecCCCEEEEEEEEEeCCCCEEEEE
Confidence 4699999999999999999999 5579999999998865433 5667899999999999999754 667777
Q ss_pred ee
Q 028346 154 TA 155 (210)
Q Consensus 154 t~ 155 (210)
++
T Consensus 71 ~~ 72 (72)
T smart00316 71 LK 72 (72)
T ss_pred eC
Confidence 64
No 35
>PRK08059 general stress protein 13; Validated
Probab=98.91 E-value=1e-08 Score=79.86 Aligned_cols=76 Identities=26% Similarity=0.323 Sum_probs=65.6
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~L 152 (210)
+++|++|.|+|+++.+..|+|+| .....|++|.++++..+.. ++.+.|++||.|.|+|++++. .+.+.|
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i--------~~~~~Gli~~sel~~~~~~--~~~~~~~vGD~I~vkI~~id~~~~~i~l 74 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVAL--------DEETQGLVHISEITHGFVK--DIHDFLSVGDEVKVKVLSVDEEKGKISL 74 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEE--------CCCCEEEEEHHHCCccccc--CHHHcCCCCCEEEEEEEEEECCCCeEEE
Confidence 57899999999999999999999 6679999999999765543 667889999999999999964 467999
Q ss_pred EeecCCc
Q 028346 153 STAKNDL 159 (210)
Q Consensus 153 St~~~~L 159 (210)
|++..+.
T Consensus 75 slk~~~~ 81 (123)
T PRK08059 75 SIRATEE 81 (123)
T ss_pred EEEEccc
Confidence 9987644
No 36
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.86 E-value=1.8e-08 Score=71.02 Aligned_cols=68 Identities=21% Similarity=0.293 Sum_probs=58.2
Q ss_pred CCEEE-EEEEEE-ecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEEE
Q 028346 77 GSVVI-ARVTKV-MTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS 153 (210)
Q Consensus 77 GDiVi-G~V~~v-~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~LS 153 (210)
|+++- |+|+++ .+.+++|++ ....+|.+|+++++..+.+ +..+.|++||.+.|+|++++. .+.+.||
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l--------~~gv~G~i~~s~l~~~~~~--~~~~~~~vG~~v~~kV~~id~~~~~i~lS 70 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFEL--------KDGLLGFVHISHLSDDKVP--SDTGPFKAGTTHKARIIGYSPMDGLLQLS 70 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEe--------CCCCEEEEEHHHCCcchhc--CcccccCCCCEEEEEEEEEeCCCCEEEEe
Confidence 78888 999999 689999999 5679999999999866555 577899999999999999985 3568887
Q ss_pred e
Q 028346 154 T 154 (210)
Q Consensus 154 t 154 (210)
+
T Consensus 71 ~ 71 (71)
T cd05696 71 L 71 (71)
T ss_pred C
Confidence 4
No 37
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.85 E-value=1.6e-08 Score=72.87 Aligned_cols=72 Identities=21% Similarity=0.319 Sum_probs=62.3
Q ss_pred CCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceE
Q 028346 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF 151 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~ 151 (210)
-+++|+++.|+|+++.+..++|++ ....+|++|.++++..+.. ++.+.|++||.|+++|++++. .+.+.
T Consensus 11 ~~~~G~i~~g~V~~v~~~G~fv~l--------~~~~~g~v~~~el~~~~~~--~~~~~~~~Gd~v~vkV~~id~~~~~i~ 80 (83)
T cd04461 11 DLKPGMVVHGYVRNITPYGVFVEF--------LGGLTGLAPKSYISDEFVT--DPSFGFKKGQSVTAKVTSVDEEKQRFL 80 (83)
T ss_pred hCCCCCEEEEEEEEEeeceEEEEc--------CCCCEEEEEHHHCCccccc--CHHHhcCCCCEEEEEEEEEcCCCCEEE
Confidence 378999999999999999999999 5568999999999865544 678999999999999999975 36678
Q ss_pred EEe
Q 028346 152 LST 154 (210)
Q Consensus 152 LSt 154 (210)
||+
T Consensus 81 lsl 83 (83)
T cd04461 81 LSL 83 (83)
T ss_pred EeC
Confidence 774
No 38
>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=98.85 E-value=1.6e-08 Score=70.23 Aligned_cols=68 Identities=19% Similarity=0.345 Sum_probs=58.3
Q ss_pred CCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEEEe
Q 028346 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLST 154 (210)
Q Consensus 77 GDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~LSt 154 (210)
|+++.|+|+++.+..++|++ ....+|++|.++++..... +..+.|++||.+.++|++++. .+.+.||+
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 GQVVKGTIRKLRPSGIFVKL--------SDHIKGLVPPMHLADVRLK--HPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEe--------cCCcEEEEEHHHCCCcccc--CHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 79999999999999999999 6679999999999765443 567889999999999999975 46677773
No 39
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.84 E-value=1.8e-08 Score=88.06 Aligned_cols=79 Identities=19% Similarity=0.198 Sum_probs=66.5
Q ss_pred CCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCC-cce
Q 028346 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RAY 150 (210)
Q Consensus 72 y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~-~~~ 150 (210)
-.|++||+|.|+|+++.+.+|+|++... ...+|+||.++++..... ++++.|++||.|.|+|++++.. +.+
T Consensus 4 ~~P~~GdiV~G~V~~I~~~G~fV~L~e~------~gieGlI~iSEls~~~i~--~i~~~~kvGd~V~vkVi~VD~~k~~I 75 (262)
T PRK03987 4 EWPEEGELVVGTVKEVKDFGAFVTLDEY------PGKEGFIHISEVASGWVK--NIRDHVKEGQKVVCKVIRVDPRKGHI 75 (262)
T ss_pred CCCCCCCEEEEEEEEEECCEEEEEECCC------CCcEEEEEHHHcCccccc--CHHHhCCCCCEEEEEEEEEecccCeE
Confidence 4689999999999999999999999311 157999999999866554 7889999999999999999853 568
Q ss_pred EEEeecCC
Q 028346 151 FLSTAKND 158 (210)
Q Consensus 151 ~LSt~~~~ 158 (210)
.||++.-+
T Consensus 76 ~LSlK~v~ 83 (262)
T PRK03987 76 DLSLKRVN 83 (262)
T ss_pred EEEEEecc
Confidence 99998543
No 40
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=98.82 E-value=1.1e-08 Score=97.02 Aligned_cols=75 Identities=24% Similarity=0.277 Sum_probs=68.3
Q ss_pred CCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeC-CCcceE
Q 028346 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG-DARAYF 151 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~-d~~~~~ 151 (210)
..++||+|.|+|+++++..|+|+| ..++|++|++|++..+.+ .+++.|++||.|+++|++++ +.+.+.
T Consensus 189 ~l~~G~vV~G~V~~It~~GafVdi---------gGvdGLlHiseiS~~rv~--~P~~vvkvGd~VkvkVi~~D~e~~RVs 257 (541)
T COG0539 189 KLEVGEVVEGVVKNITDYGAFVDI---------GGVDGLLHISEISWKRVD--HPSEVVKVGDEVKVKVISLDEERGRVS 257 (541)
T ss_pred cCCCCceEEEEEEEeecCcEEEEe---------cCeeeEEehhhccccccC--CHHHhcccCCEEEEEEEEEccCCCeEE
Confidence 478999999999999999999999 449999999999988887 89999999999999999998 456799
Q ss_pred EEeecCC
Q 028346 152 LSTAKND 158 (210)
Q Consensus 152 LSt~~~~ 158 (210)
||++...
T Consensus 258 LSlK~l~ 264 (541)
T COG0539 258 LSLKQLE 264 (541)
T ss_pred EEehhcc
Confidence 9998754
No 41
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.78 E-value=7.3e-08 Score=68.66 Aligned_cols=69 Identities=20% Similarity=0.214 Sum_probs=58.8
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeecccccc-CceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCC-cceE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RAYF 151 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~-~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~-~~~~ 151 (210)
.++|++|.|.|.++.+..+++++ . ..+.|++|.++++.. +.|++||.+.|+|++++.+ +.+.
T Consensus 2 l~~G~~v~g~V~si~d~G~~v~~--------g~~gv~Gfl~~~~~~~~--------~~~~~Gq~v~~~V~~vd~~~~~v~ 65 (74)
T cd05694 2 LVEGMVLSGCVSSVEDHGYILDI--------GIPGTTGFLPKKDAGNF--------SKLKVGQLLLCVVEKVKDDGRVVS 65 (74)
T ss_pred CCCCCEEEEEEEEEeCCEEEEEe--------CCCCcEEEEEHHHCCcc--------cccCCCCEEEEEEEEEECCCCEEE
Confidence 46899999999999999999999 4 468999999987632 7799999999999999754 5689
Q ss_pred EEeecCC
Q 028346 152 LSTAKND 158 (210)
Q Consensus 152 LSt~~~~ 158 (210)
||++...
T Consensus 66 ls~k~~~ 72 (74)
T cd05694 66 LSADPSK 72 (74)
T ss_pred EEEeecc
Confidence 9987643
No 42
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.76 E-value=3.9e-08 Score=67.19 Aligned_cols=67 Identities=21% Similarity=0.259 Sum_probs=55.1
Q ss_pred CCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCC-cceEEE
Q 028346 76 PGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RAYFLS 153 (210)
Q Consensus 76 vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~-~~~~LS 153 (210)
+|+++.|+|+++.+..++|++ . ..+|++|.++++..+.. ++.+.|++||.|+|+|.+++.. +.+.||
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 EGDVVEGTVKSITDFGAFVDL--------G-GVDGLLHISDMSWGRVK--HPSEVVNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEE--------C-CeEEEEEhHHCCCcccc--CHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence 499999999999999999999 3 47899999998754443 5678899999999999999743 445553
No 43
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.76 E-value=5.6e-08 Score=67.54 Aligned_cols=65 Identities=26% Similarity=0.377 Sum_probs=54.6
Q ss_pred CCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEEE
Q 028346 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS 153 (210)
Q Consensus 77 GDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~LS 153 (210)
||+|.|+|+++.+++++|++ ...++|.+|.+++..... . .+.|++||.|.|||++++. .+.+.||
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 GMLVNARVKKVLSNGLILDF--------LSSFTGTVDFLHLDPEKS---S-KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEE--------cCCceEEEEHHHcCCccC---c-ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 89999999999999999999 556999999999864332 2 6889999999999999985 3456665
No 44
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=98.75 E-value=6.8e-08 Score=66.08 Aligned_cols=68 Identities=19% Similarity=0.299 Sum_probs=56.9
Q ss_pred CCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEEEe
Q 028346 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLST 154 (210)
Q Consensus 77 GDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LSt 154 (210)
|+++.|+|+++.+..++|+| .....|++|.++++..... +..+.|++||.|.++|.+++..+.+.||+
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 GKIYEGKVVKIKDFGAFVEI--------LPGKDGLVHISELSDERVE--KVEDVLKVGDEVKVKVIEVDDRGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEe--------CCCCEEEEEhHHcCCcccc--CHHHccCCCCEEEEEEEEECCCCcEEeeC
Confidence 78999999999999999999 5568999999999755433 45678999999999999997645567763
No 45
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=98.74 E-value=4e-08 Score=66.93 Aligned_cols=67 Identities=28% Similarity=0.267 Sum_probs=56.0
Q ss_pred CCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEEE
Q 028346 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLS 153 (210)
Q Consensus 77 GDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~LS 153 (210)
|+++.|+|+++.+..++|++ .....|++|.++++..... ++.+.|++||.|.|+|.+++. .+.+.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l--------~~~~~g~~~~~~l~~~~~~--~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDI--------GVKQDGLIHISKMADRFVS--HPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEc--------CCCCEEEEEHHHCCCcccc--CHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 78999999999999999999 5568999999999765444 567789999999999999975 3455554
No 46
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=98.69 E-value=1.2e-07 Score=69.70 Aligned_cols=74 Identities=19% Similarity=0.239 Sum_probs=57.7
Q ss_pred CCCCCEEEEEEEEEecC--eEEEEEeeeccccccCceeEEEecccccccc-ccccccCCCCCCCCEEEEEEEEeCC-Ccc
Q 028346 74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATE-IDKVDMHLSFRPGDIVRASVLSLGD-ARA 149 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~--~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~-~d~~~~~~~~~~GDiV~AkV~s~~d-~~~ 149 (210)
+++|+++.|+|+++.+. .|+|+| ....+|+||.++++... ....+..+.|++||.|.++|+.... +..
T Consensus 5 ~~~G~iy~g~V~~i~~~~~GaFV~l--------~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~ 76 (88)
T cd04453 5 PIVGNIYLGRVKKIVPGLQAAFVDI--------GLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKG 76 (88)
T ss_pred CCCCCEEEEEEEEeccCCcEEEEEe--------CCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCC
Confidence 57999999999999996 999999 55689999999986411 1112567899999999999999753 344
Q ss_pred eEEEee
Q 028346 150 YFLSTA 155 (210)
Q Consensus 150 ~~LSt~ 155 (210)
..||+.
T Consensus 77 ~~lt~~ 82 (88)
T cd04453 77 PRLTTN 82 (88)
T ss_pred ceEEEE
Confidence 556553
No 47
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.69 E-value=2.2e-08 Score=98.01 Aligned_cols=101 Identities=17% Similarity=0.215 Sum_probs=80.0
Q ss_pred eCCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEE
Q 028346 32 AKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGI 111 (210)
Q Consensus 32 ~~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gi 111 (210)
++|. ++++..+..... ..+..|+..+. .+++|+++.|+|+++.+.+++|+| ....+|+
T Consensus 591 d~G~--v~i~~~~~~~~~-------~a~~~I~~~~~-----~~~vG~v~~G~V~~I~~fGafVei--------~~~~~Gl 648 (693)
T PRK11824 591 DDGT--VKIAATDGEAAE-------AAKERIEGITA-----EPEVGEIYEGKVVRIVDFGAFVEI--------LPGKDGL 648 (693)
T ss_pred CCce--EEEEcccHHHHH-------HHHHHHHHhcc-----cCcCCeEEEEEEEEEECCeEEEEE--------CCCCEEE
Confidence 3566 888777776652 22233443332 378999999999999999999999 4568999
Q ss_pred EeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEEEeec
Q 028346 112 IRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAK 156 (210)
Q Consensus 112 i~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LSt~~ 156 (210)
+|+++++..+.+ +..+.|++||.|+++|++++..+.+.||++.
T Consensus 649 lhiSels~~~v~--~~~~v~kvGD~V~VkV~~iD~~grI~LS~k~ 691 (693)
T PRK11824 649 VHISEIADERVE--KVEDVLKEGDEVKVKVLEIDKRGRIRLSRKA 691 (693)
T ss_pred EEeeeccCcccc--CccceeCCCCEEEEEEEEECCCCcEEEEEEe
Confidence 999999876665 6789999999999999999765789999875
No 48
>PHA02945 interferon resistance protein; Provisional
Probab=98.65 E-value=2.2e-07 Score=68.10 Aligned_cols=73 Identities=12% Similarity=0.128 Sum_probs=61.1
Q ss_pred CCCCCCCEEEEEEEEEecCeEEEEEeeeccccccC-ceeEEEecccc--ccccccccccCCCCCCCCEEEEEEEEeCCC-
Q 028346 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDV--RATEIDKVDMHLSFRPGDIVRASVLSLGDA- 147 (210)
Q Consensus 72 y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~-~~~Gii~~s~v--~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~- 147 (210)
-.|.+||+|+|+|.. .+..++|.+. .. ..+|+||+|++ ...-.+ + ++.+ .|..|.|||+.++..
T Consensus 7 ~~P~~GelvigtV~~-~d~ga~v~L~-------EY~g~eg~i~~seveva~~wvK--~-rd~l-~GqkvV~KVirVd~~k 74 (88)
T PHA02945 7 SLPNVGDVLKGKVYE-NGYALYIDLF-------DYPHSEAILAESVQMHMNRYFK--Y-RDKL-VGKTVKVKVIRVDYTK 74 (88)
T ss_pred cCCCCCcEEEEEEEe-cCceEEEEec-------ccCCcEEEEEeehhhhccceEe--e-eeEe-cCCEEEEEEEEECCCC
Confidence 369999999999999 9999999993 23 67999999955 665554 5 8999 999999999999865
Q ss_pred cceEEEeec
Q 028346 148 RAYFLSTAK 156 (210)
Q Consensus 148 ~~~~LSt~~ 156 (210)
+.+.||++.
T Consensus 75 g~IDlSlK~ 83 (88)
T PHA02945 75 GYIDVNYKR 83 (88)
T ss_pred CEEEeEeeE
Confidence 457898864
No 49
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.63 E-value=5.9e-08 Score=84.03 Aligned_cols=77 Identities=22% Similarity=0.254 Sum_probs=67.7
Q ss_pred CCCCCCCCEEEEEEEEEecCeEEEEEeeeccccccC-ceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCC-c
Q 028346 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-R 148 (210)
Q Consensus 71 ~y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~-~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~-~ 148 (210)
+-.|.+||+|+|+|.+|.+.+|+|.+. .+ +.+|.+|+|+++..-+. ++++.+++|.-|.|+|++++.. +
T Consensus 6 ~~~PeeGEiVv~tV~~V~~~GAyv~L~-------EY~g~Eg~ihiSEvas~wVk--nIrd~vkegqkvV~kVlrVd~~rg 76 (269)
T COG1093 6 REYPEEGEIVVGTVKQVADYGAYVELD-------EYPGKEGFIHISEVASGWVK--NIRDYVKEGQKVVAKVLRVDPKRG 76 (269)
T ss_pred cCCCCCCcEEEEEEEEeeccccEEEee-------ccCCeeeeEEHHHHHHHHHH--HHHHHhhcCCeEEEEEEEEcCCCC
Confidence 356999999999999999999999994 23 47899999999988777 8999999999999999999875 4
Q ss_pred ceEEEeec
Q 028346 149 AYFLSTAK 156 (210)
Q Consensus 149 ~~~LSt~~ 156 (210)
.+.||++.
T Consensus 77 ~IDLSlkr 84 (269)
T COG1093 77 HIDLSLKR 84 (269)
T ss_pred eEeeehhh
Confidence 46899865
No 50
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.62 E-value=1.8e-07 Score=77.46 Aligned_cols=83 Identities=22% Similarity=0.262 Sum_probs=66.9
Q ss_pred CCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEecccccccccc--c-------cccCCCCCCCCEEEEEEE
Q 028346 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID--K-------VDMHLSFRPGDIVRASVL 142 (210)
Q Consensus 72 y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d--~-------~~~~~~~~~GDiV~AkV~ 142 (210)
+.|.+|++|.|+|++++..++++++ . +++|++|.+++...+.. . .+....++.||.|++||.
T Consensus 77 f~P~~GEVv~g~V~~v~~~Gi~V~l--------g-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~ 147 (187)
T PRK08563 77 FKPELQEVVEGEVVEVVEFGAFVRI--------G-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIV 147 (187)
T ss_pred EeccCCCEEEEEEEEEEccEEEEEE--------e-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEE
Confidence 4588999999999999999999999 3 58999999988643211 0 124567899999999999
Q ss_pred EeCCC------cceEEEeecCCceeeE
Q 028346 143 SLGDA------RAYFLSTAKNDLGVVS 163 (210)
Q Consensus 143 s~~d~------~~~~LSt~~~~LGVv~ 163 (210)
+++-. ..+.||++++.||++.
T Consensus 148 ~v~~~~~~~~~~~I~ls~~~~~LG~~~ 174 (187)
T PRK08563 148 AVSLKERRPRGSKIGLTMRQPGLGKLE 174 (187)
T ss_pred EEEcccCCCCCCEEEEEecCCCCCcHH
Confidence 98621 2589999999999874
No 51
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.61 E-value=2.2e-07 Score=83.32 Aligned_cols=76 Identities=24% Similarity=0.290 Sum_probs=65.6
Q ss_pred CCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-Ccce
Q 028346 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAY 150 (210)
Q Consensus 72 y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~ 150 (210)
.-+++|++|.|+|+++++.+++|++. ...|++|+++++..+.. ++.+.|++||.|+|+|++++. .+.+
T Consensus 192 ~~~k~G~vv~G~V~~I~~~G~fV~i~---------gv~Gllhisels~~~~~--~~~~~~~vGd~VkvkVl~iD~e~~rI 260 (318)
T PRK07400 192 NRLEVGEVVVGTVRGIKPYGAFIDIG---------GVSGLLHISEISHEHIE--TPHSVFNVNDEMKVMIIDLDAERGRI 260 (318)
T ss_pred ccCCCCCEEEEEEEEEECCeEEEEEC---------CEEEEEEHHHccccccc--ChhhccCCCCEEEEEEEEEeCCCCEE
Confidence 34789999999999999999999982 46899999999876654 688999999999999999974 4679
Q ss_pred EEEeecCC
Q 028346 151 FLSTAKND 158 (210)
Q Consensus 151 ~LSt~~~~ 158 (210)
.||++..+
T Consensus 261 ~LS~K~l~ 268 (318)
T PRK07400 261 SLSTKQLE 268 (318)
T ss_pred EEEEeccc
Confidence 99998754
No 52
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=98.60 E-value=4e-07 Score=64.91 Aligned_cols=72 Identities=15% Similarity=0.206 Sum_probs=59.3
Q ss_pred CCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccc-cccccCCCCCCCCEEEEEEEEeCCCcceEEEee
Q 028346 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI-DKVDMHLSFRPGDIVRASVLSLGDARAYFLSTA 155 (210)
Q Consensus 77 GDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~-d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LSt~ 155 (210)
|+++.|+|+++.+..++|+|... ..+.+|++|.++++.... + +..+.|++||.|+++|.+++ .+.+.||++
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~-----~~~~~gll~~s~l~~~~~~~--~~~~~~~~Gd~v~v~v~~vd-~~~i~~s~k 72 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGL-----KGRKEGLVHISQLSFEGRVA--NPSDVVKRGQKVKVKVISIQ-NGKISLSMK 72 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCC-----CCCcEEEEEhHhccCCCCcC--ChhheeCCCCEEEEEEEEEe-CCEEEEEEE
Confidence 78999999999999999999310 035799999999975543 3 67788999999999999998 667888886
Q ss_pred c
Q 028346 156 K 156 (210)
Q Consensus 156 ~ 156 (210)
.
T Consensus 73 ~ 73 (79)
T cd05684 73 D 73 (79)
T ss_pred e
Confidence 5
No 53
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.58 E-value=2.4e-07 Score=63.86 Aligned_cols=66 Identities=17% Similarity=0.263 Sum_probs=54.1
Q ss_pred CCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEecccccc-ccccccccCCCCCCCCEEEEEEEEeCCC-cceEE
Q 028346 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRA-TEIDKVDMHLSFRPGDIVRASVLSLGDA-RAYFL 152 (210)
Q Consensus 77 GDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~-~~~d~~~~~~~~~~GDiV~AkV~s~~d~-~~~~L 152 (210)
|+++.|+|+++++..++|++ ....+|++|.++++. .... +..+.|++||.|+|+|++++.. +.+.|
T Consensus 1 G~~~~g~V~~i~~~G~fv~l--------~~~~~Glv~~~~l~~~~~~~--~~~~~~~~G~~v~v~v~~id~~~~~i~l 68 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGL--------DGGIDGLVHISDISWTQRVR--HPSEIYKKGQEVEAVVLNIDVERERISL 68 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEe--------CCCCEEEEEHHHCCCccccC--ChhhEECCCCEEEEEEEEEECCcCEEeC
Confidence 78999999999999999999 556899999999973 2222 5668899999999999999743 44544
No 54
>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=98.57 E-value=3.1e-07 Score=75.77 Aligned_cols=83 Identities=23% Similarity=0.312 Sum_probs=67.0
Q ss_pred CCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccc--ccc-------ccCCCCCCCCEEEEEEE
Q 028346 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI--DKV-------DMHLSFRPGDIVRASVL 142 (210)
Q Consensus 72 y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~--d~~-------~~~~~~~~GDiV~AkV~ 142 (210)
+.|.+|+++.|+|+++++.++++++ .+++|++|++++...+. |.. +....++.||.|++||.
T Consensus 77 f~p~~gEvv~G~V~~v~~~GifV~l---------g~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~ 147 (179)
T TIGR00448 77 FKPELGEIVEGEVIEIVEFGAFVSL---------GPFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIV 147 (179)
T ss_pred EeccCCCEEEEEEEEEEeeEEEEEe---------CCceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEE
Confidence 4578999999999999999999999 35899999998863321 111 23467999999999999
Q ss_pred EeC------CCcceEEEeecCCceeeE
Q 028346 143 SLG------DARAYFLSTAKNDLGVVS 163 (210)
Q Consensus 143 s~~------d~~~~~LSt~~~~LGVv~ 163 (210)
+++ +...+.||++++.||.+.
T Consensus 148 ~v~~~~~~~~~~~I~lt~k~~~LG~~~ 174 (179)
T TIGR00448 148 ALSLKDRRPEGSKIGLTMRQPLLGKLE 174 (179)
T ss_pred EEEccCCCCCcceEEEEeccCcCCccc
Confidence 985 234699999999999875
No 55
>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=98.55 E-value=4e-07 Score=67.89 Aligned_cols=77 Identities=21% Similarity=0.264 Sum_probs=61.6
Q ss_pred CEEEEEEEEEecCeEEEEEeeeccccccCceeEEEecccccccccccc---------ccCCCCCCCCEEEEEEEEeCCC-
Q 028346 78 SVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKV---------DMHLSFRPGDIVRASVLSLGDA- 147 (210)
Q Consensus 78 DiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~---------~~~~~~~~GDiV~AkV~s~~d~- 147 (210)
+++.|+|+++.+.+++|++ . +..|++|.++++..+.... .....|++||.|.++|.+++..
T Consensus 1 ~vv~g~V~~i~~~GifV~l--------~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~ 71 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRI--------G-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKE 71 (99)
T ss_pred CEEEEEEEEEEeccEEEEE--------c-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHH
Confidence 4789999999999999999 3 3789999999875433210 1246789999999999999732
Q ss_pred -----cceEEEeecCCceeeE
Q 028346 148 -----RAYFLSTAKNDLGVVS 163 (210)
Q Consensus 148 -----~~~~LSt~~~~LGVv~ 163 (210)
..+.||++++.||.+.
T Consensus 72 ~~~~~~~i~ls~k~~~~g~~~ 92 (99)
T cd04460 72 RRPRESKIGLTMRQPGLGKLE 92 (99)
T ss_pred CcCCCceEEEEEecCCCCcHH
Confidence 4699999999999864
No 56
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.52 E-value=3.3e-07 Score=89.53 Aligned_cols=71 Identities=15% Similarity=0.281 Sum_probs=61.1
Q ss_pred CCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccc---c-ccccccccCCCCCCCCEEEEEEEEeCCCc
Q 028346 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVR---A-TEIDKVDMHLSFRPGDIVRASVLSLGDAR 148 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~---~-~~~d~~~~~~~~~~GDiV~AkV~s~~d~~ 148 (210)
.|++|+++.|+|+++.+.+++|+| ....+|++|+|+++ . .+.. ++++.|++||.|.++|+++++.+
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel--------~~G~eGLvHISeisdls~~~rv~--~~~dv~kvGd~V~VKVl~ID~~g 713 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSL--------LPGKDGLLHISQIRKLAGGKRVE--NVEDVLSVGQKIQVEIADIDDRG 713 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEe--------cCCceEEEEhhhccccccccCcC--CHHHcCCCCCEEEEEEEEECCCC
Confidence 489999999999999999999999 56789999999985 2 2333 78999999999999999998656
Q ss_pred ceEEE
Q 028346 149 AYFLS 153 (210)
Q Consensus 149 ~~~LS 153 (210)
.+.|+
T Consensus 714 KI~L~ 718 (719)
T TIGR02696 714 KLSLV 718 (719)
T ss_pred Ceeec
Confidence 67765
No 57
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=98.47 E-value=1.1e-07 Score=93.11 Aligned_cols=94 Identities=16% Similarity=0.216 Sum_probs=72.0
Q ss_pred CCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEE
Q 028346 33 KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGII 112 (210)
Q Consensus 33 ~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii 112 (210)
+|. ++++..+..... ..+..|.... ..|++|+++.|+|+++.+.+++|+| ....+|++
T Consensus 589 dG~--V~i~~~~~~~~~-------~a~~~I~~~~-----~~~~~G~i~~G~V~~I~~~GafVei--------~~g~~Gll 646 (684)
T TIGR03591 589 DGT--VKIAASDGEAAE-------AAIKMIEGIT-----AEPEVGKIYEGKVVRIMDFGAFVEI--------LPGKDGLV 646 (684)
T ss_pred CeE--EEEEECcHHHHH-------HHHHHHHhhh-----cccccCcEEEEEEEEEeCCEEEEEE--------CCCcEEEE
Confidence 555 777777665542 1222343332 2478999999999999999999999 45689999
Q ss_pred eccccccccccccccCCCCCCCCEEEEEEEEeCCCcce
Q 028346 113 RQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAY 150 (210)
Q Consensus 113 ~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~ 150 (210)
|+|+++..+.+ ++.+.|++||.|+++|++++..+.+
T Consensus 647 HiSei~~~~v~--~~~~~~kvGD~V~VkVi~id~~gki 682 (684)
T TIGR03591 647 HISEIANERVE--KVEDVLKEGDEVKVKVLEIDKQGRI 682 (684)
T ss_pred EHHHcCCCccc--ChhhccCCCCEEEEEEEEECCCCCc
Confidence 99999876665 7889999999999999999753333
No 58
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=98.47 E-value=5.8e-07 Score=59.87 Aligned_cols=64 Identities=19% Similarity=0.285 Sum_probs=51.7
Q ss_pred EEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCC-cceEEE
Q 028346 80 VIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RAYFLS 153 (210)
Q Consensus 80 ViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~-~~~~LS 153 (210)
|.|+|+++.+..++|++ ....+|++|.++++..... ++.+.|++||.|+|+|++++.. +.+.||
T Consensus 1 v~g~V~~v~~~g~~v~l--------~~~~~g~~~~~~~~~~~~~--~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 1 VTGKVVSITKFGVFVEL--------EDGVEGLVHISELSDKFVK--DPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEEEEEEEEeeeEEEEe--------cCCCEEEEEHHHCCCcccc--CHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 47999999999999999 5678999999998755432 5678899999999999999743 344443
No 59
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.43 E-value=8.9e-07 Score=79.41 Aligned_cols=76 Identities=20% Similarity=0.202 Sum_probs=66.0
Q ss_pred CCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-Ccce
Q 028346 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAY 150 (210)
Q Consensus 72 y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~ 150 (210)
+..++||+|.|+|+++.+++++|+| ....+|.||.+|++..+.. ++.+.|++||.|.++|++.++ .+.+
T Consensus 27 ~~~~~G~iv~G~V~~i~~~g~~Vdi--------g~k~~g~lp~sEis~~~~~--~~~~~~~~G~~v~~~Vi~~~~~~~~i 96 (318)
T PRK07400 27 YHFKPGDIVNGTVFSLEPRGALIDI--------GAKTAAFMPIQEMSINRVE--GPEEVLQPNETREFFILSDENEDGQL 96 (318)
T ss_pred hhcCCCCEEEEEEEEEECCEEEEEE--------CCCeEEEEEHHHhcccccc--CHHHccCCCCEEEEEEEEEeCCCCeE
Confidence 3479999999999999999999999 6678999999999876654 678899999999999999864 4678
Q ss_pred EEEeecC
Q 028346 151 FLSTAKN 157 (210)
Q Consensus 151 ~LSt~~~ 157 (210)
.||.+..
T Consensus 97 ~lS~k~~ 103 (318)
T PRK07400 97 TLSIRRI 103 (318)
T ss_pred EEehhhh
Confidence 9998864
No 60
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.43 E-value=1.9e-06 Score=60.11 Aligned_cols=64 Identities=17% Similarity=0.285 Sum_probs=53.3
Q ss_pred CCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCC
Q 028346 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA 147 (210)
Q Consensus 75 ~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~ 147 (210)
.+|+++.|+|+.+++..++|++ ....+|++|.++++..+. ..+..+.|++||.|+++|++++..
T Consensus 2 ~~g~~~~g~V~~i~~~G~fv~l--------~~~~~Gl~~~~~l~~~~~-~~~~~~~~~~Gd~v~v~v~~id~~ 65 (72)
T cd05689 2 PEGTRLFGKVTNLTDYGCFVEL--------EEGVEGLVHVSEMDWTNK-NIHPSKVVSLGDEVEVMVLDIDEE 65 (72)
T ss_pred cCCCEEEEEEEEEEeeEEEEEc--------CCCCEEEEEEEeccCccc-ccCcccEeCCCCEEEEEEEEeeCC
Confidence 4799999999999999999999 556899999999963211 225668899999999999999743
No 61
>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=98.42 E-value=2e-06 Score=59.71 Aligned_cols=62 Identities=26% Similarity=0.401 Sum_probs=51.1
Q ss_pred CCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCC---cceE
Q 028346 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA---RAYF 151 (210)
Q Consensus 75 ~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~---~~~~ 151 (210)
+.|++|.|+|.++.++.++|+| .. .+|+||.+++.. .+.|++||.|.+.|.++++. .++.
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdi--------g~-~eg~lp~~e~~~--------~~~~~~Gd~v~v~v~~v~~~~~~~~i~ 64 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDL--------GK-VEAILPKKEQIP--------GESYRPGDRIKAYVLEVRKTSKGPQII 64 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEc--------CC-eEEEeeHHHCCC--------CCcCCCCCEEEEEEEEEecCCCCCEEE
Confidence 5799999999999999999999 44 899999988752 25689999999999999643 2355
Q ss_pred EE
Q 028346 152 LS 153 (210)
Q Consensus 152 LS 153 (210)
||
T Consensus 65 lS 66 (67)
T cd04455 65 LS 66 (67)
T ss_pred Ee
Confidence 55
No 62
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.41 E-value=1.1e-06 Score=83.08 Aligned_cols=75 Identities=19% Similarity=0.212 Sum_probs=65.1
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~L 152 (210)
.++|++|.|+|+++++.+++|++ .....|++|.++++..+.. +..+.|++||.|.|+|++++. .+.+.|
T Consensus 377 ~~vG~~v~G~V~~i~~~G~FV~l--------~~gv~Gli~~se~s~~~~~--~~~~~~~~Gd~v~~~V~~id~e~~ri~L 446 (491)
T PRK13806 377 FAPGTTVTGTVEKRAQFGLFVNL--------APGVTGLLPASVISRAGKP--ATYEKLKPGDSVTLVVEEIDTAKRKISL 446 (491)
T ss_pred CCCCCEEEEEEEEEecCceEEEc--------CCCcEEEEEHHHcCccccc--chhhcCCCCCEEEEEEEEEeCCCCEEEE
Confidence 46899999999999999999999 5679999999999865553 678899999999999999974 467999
Q ss_pred EeecCC
Q 028346 153 STAKND 158 (210)
Q Consensus 153 St~~~~ 158 (210)
|++..+
T Consensus 447 s~~~~~ 452 (491)
T PRK13806 447 APAGAA 452 (491)
T ss_pred Eeehhh
Confidence 998543
No 63
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.40 E-value=8.8e-07 Score=73.30 Aligned_cols=83 Identities=25% Similarity=0.302 Sum_probs=67.0
Q ss_pred CCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEecccccccccc-----ccc----cCCCCCCCCEEEEEEE
Q 028346 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID-----KVD----MHLSFRPGDIVRASVL 142 (210)
Q Consensus 72 y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d-----~~~----~~~~~~~GDiV~AkV~ 142 (210)
+.|..|++|-|.|+++....++|.| .+++|++|++|+...+.+ ... -...|+.||.|+|||.
T Consensus 77 fkP~~gEVV~GeVv~~~~~G~fV~i---------gp~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv 147 (183)
T COG1095 77 FKPFRGEVVEGEVVEVVEFGAFVRI---------GPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIV 147 (183)
T ss_pred EEeccccEEEEEEEEEeecceEEEe---------ccccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEE
Confidence 4588899999999999999999999 489999999998755322 111 2238999999999999
Q ss_pred EeC--CC----cceEEEeecCCceeeE
Q 028346 143 SLG--DA----RAYFLSTAKNDLGVVS 163 (210)
Q Consensus 143 s~~--d~----~~~~LSt~~~~LGVv~ 163 (210)
+.. .. ..+.||++++-||++.
T Consensus 148 ~~s~~~~~~~~~~I~lTmrq~~LGkle 174 (183)
T COG1095 148 GVSLKSRRPRESKIGLTMRQPGLGKLE 174 (183)
T ss_pred EEecccCccccceEEEEeccccCCcch
Confidence 974 21 3479999999999875
No 64
>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=98.38 E-value=7.7e-06 Score=58.28 Aligned_cols=64 Identities=19% Similarity=0.239 Sum_probs=54.5
Q ss_pred CCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEE
Q 028346 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFL 152 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~L 152 (210)
-+++|+.+.|+|+++++.++++++ .....|++|.+++ .+.++.||.+.++|.++.+.+.+.|
T Consensus 13 ~~~~G~~~~g~V~~i~~~G~fV~l--------~~~~~Glv~~se~----------~~~~~iGd~v~v~I~~i~e~~~i~l 74 (77)
T cd04473 13 DLEVGKLYKGKVNGVAKYGVFVDL--------NDHVRGLIHRSNL----------LRDYEVGDEVIVQVTDIPENGNIDL 74 (77)
T ss_pred hCCCCCEEEEEEEeEecceEEEEE--------CCCcEEEEEchhc----------cCcCCCCCEEEEEEEEECCCCcEEE
Confidence 368999999999999999999999 5569999999874 2569999999999999954566777
Q ss_pred Ee
Q 028346 153 ST 154 (210)
Q Consensus 153 St 154 (210)
|.
T Consensus 75 ~~ 76 (77)
T cd04473 75 IP 76 (77)
T ss_pred EE
Confidence 64
No 65
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.35 E-value=3.3e-06 Score=58.26 Aligned_cols=66 Identities=18% Similarity=0.289 Sum_probs=53.4
Q ss_pred CCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEEEee
Q 028346 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFLSTA 155 (210)
Q Consensus 77 GDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~LSt~ 155 (210)
|++|.|+|+++.+..++|++ ...+|.+|.+++...+.+ +..+ .+||.+.|+|++++. .+.+.||.+
T Consensus 1 G~iv~g~V~~v~~~G~~v~l---------~g~~gfip~s~~~~~~~~--~~~~--~vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI---------EGVRAFLPASQVDLRPVE--DLDE--YVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE---------CCEEEEEEHHHCCCcccC--ChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 78999999999999999999 358999999998755433 2333 389999999999985 466788753
No 66
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=98.34 E-value=1.2e-06 Score=83.13 Aligned_cols=74 Identities=20% Similarity=0.207 Sum_probs=67.2
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~L 152 (210)
..+|+.+.|+|+.+++++|+|+| ..+.+|++|+|+++.+++. .+++.+++||.|.++|++++. .+.+.|
T Consensus 275 ~~~g~~v~G~Vt~i~~~GafVei--------~~GvEGlvhvSEisw~~~~--~P~evv~~Gq~V~V~Vl~id~e~rRIsL 344 (541)
T COG0539 275 YPVGDKVEGKVTNLTDYGAFVEI--------EEGVEGLVHVSEISWTKKN--VPSEVVKVGQEVEVKVLDIDPERRRISL 344 (541)
T ss_pred cCCCCEEEEEEEEeecCcEEEEe--------cCCccceeechhhcccccC--CHHHhcccCCEEEEEEEeeCchhceEEe
Confidence 46899999999999999999999 7899999999999988776 499999999999999999984 477999
Q ss_pred EeecC
Q 028346 153 STAKN 157 (210)
Q Consensus 153 St~~~ 157 (210)
|++..
T Consensus 345 ~iKq~ 349 (541)
T COG0539 345 GLKQL 349 (541)
T ss_pred eehhh
Confidence 99873
No 67
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.31 E-value=2.1e-06 Score=81.11 Aligned_cols=75 Identities=21% Similarity=0.278 Sum_probs=64.5
Q ss_pred CCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCC-----
Q 028346 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA----- 147 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~----- 147 (210)
.+++|++|.|+|+++.+..++|+| .....|++|.++++..+.+ ++.+.|++||.|+|+|++++..
T Consensus 199 ~l~~G~iv~G~V~~v~~~G~fV~l--------~~gv~g~v~~sels~~~~~--~~~~~~~vGd~i~vkVl~id~~~~~~~ 268 (491)
T PRK13806 199 TVKEGDVVEGTVTRLAPFGAFVEL--------APGVEGMVHISELSWSRVQ--KADEAVSVGDTVRVKVLGIERAKKGKG 268 (491)
T ss_pred hCCCCCEEEEEEEEEeCCeEEEEc--------CCCcEEEEEHHHCCCcccc--ChhHhcCCCCEEEEEEEEEecccCCcc
Confidence 368999999999999999999999 5568999999999876655 7889999999999999999753
Q ss_pred cceEEEeecC
Q 028346 148 RAYFLSTAKN 157 (210)
Q Consensus 148 ~~~~LSt~~~ 157 (210)
..+.||++..
T Consensus 269 ~ri~lS~K~~ 278 (491)
T PRK13806 269 LRISLSIKQA 278 (491)
T ss_pred eEEEEEehhh
Confidence 2488998654
No 68
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.30 E-value=2.7e-06 Score=80.36 Aligned_cols=74 Identities=27% Similarity=0.250 Sum_probs=64.1
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~L 152 (210)
.+.||+|.|+|+++.++.++|+| ....+|+||.++++..... ++.+.|++||.|.|+|+++++ .+.+.|
T Consensus 33 ~~~GdiV~G~V~~v~~~gv~VdI--------g~k~eG~Ip~~Els~~~~~--~~~~~~~vGd~Ie~~V~~~~~~~g~liL 102 (486)
T PRK07899 33 FNDGDIVEGTVVKVDRDEVLLDI--------GYKTEGVIPSRELSIKHDV--DPNEVVEVGDEVEALVLQKEDKEGRLIL 102 (486)
T ss_pred CCCCCEEEEEEEEEECCcEEEEE--------CCCcEEEEEHHHhcccccC--ChhhcCCCCCEEEEEEEEEECCCCeEEE
Confidence 68999999999999999999999 6678999999999864432 677889999999999999975 457899
Q ss_pred EeecC
Q 028346 153 STAKN 157 (210)
Q Consensus 153 St~~~ 157 (210)
|.+..
T Consensus 103 S~k~~ 107 (486)
T PRK07899 103 SKKRA 107 (486)
T ss_pred Eehhh
Confidence 99864
No 69
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.28 E-value=2.5e-06 Score=85.17 Aligned_cols=74 Identities=16% Similarity=0.258 Sum_probs=64.9
Q ss_pred CCCCCCEEE-EEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceE
Q 028346 73 VPEPGSVVI-ARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYF 151 (210)
Q Consensus 73 ~p~vGDiVi-G~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~ 151 (210)
.|++|+++. |+|++|.+.+++|+| ....+|++|+|+++..+.. +..+.|++||.|.++|++++..+.+.
T Consensus 750 ~~~vG~iy~~g~V~~I~~FGaFVeL--------~~g~EGLVHISeLs~~rv~--~~~dv~kvGD~V~VkVi~ID~~grI~ 819 (891)
T PLN00207 750 VPTVGDIYRNCEIKSIAPYGAFVEI--------APGREGLCHISELSSNWLA--KPEDAFKVGDRIDVKLIEVNDKGQLR 819 (891)
T ss_pred CcCCCcEEECcEEEEEeccEEEEEe--------CCCCEEEEEhhhcCCcccc--CHHHhcCCCCEEEEEEEEECCCCcEE
Confidence 378999995 699999999999999 5568999999999876655 67799999999999999998766799
Q ss_pred EEeec
Q 028346 152 LSTAK 156 (210)
Q Consensus 152 LSt~~ 156 (210)
||++.
T Consensus 820 LSlK~ 824 (891)
T PLN00207 820 LSRRA 824 (891)
T ss_pred EEEec
Confidence 99875
No 70
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.28 E-value=3e-06 Score=80.05 Aligned_cols=73 Identities=19% Similarity=0.194 Sum_probs=63.6
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~L 152 (210)
.++|++|.|+|+++.+..++|+| . ...|+||+++++..+.+ ++.+.|++||.|.++|++++. .+.+.|
T Consensus 206 lk~G~iv~G~V~~i~~~G~FVdl--------g-gv~Glv~~Sels~~~v~--~~~~~~kvGd~V~vkVl~iD~e~~rI~L 274 (486)
T PRK07899 206 LQKGQVRKGVVSSIVNFGAFVDL--------G-GVDGLVHVSELSWKHID--HPSEVVEVGQEVTVEVLDVDMDRERVSL 274 (486)
T ss_pred ccCCCEEEEEEEEEECCeEEEEE--------C-CEEEEEEHHHCCCcccC--CHHHhcCCCCEEEEEEEEEECCCCEEEE
Confidence 57999999999999999999999 3 48999999999876655 677899999999999999974 467899
Q ss_pred EeecC
Q 028346 153 STAKN 157 (210)
Q Consensus 153 St~~~ 157 (210)
|++..
T Consensus 275 SlK~~ 279 (486)
T PRK07899 275 SLKAT 279 (486)
T ss_pred EEeec
Confidence 98754
No 71
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.25 E-value=3.8e-06 Score=80.25 Aligned_cols=75 Identities=27% Similarity=0.412 Sum_probs=65.8
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~L 152 (210)
.++||+|.|+|+++.+.+++|.+ .....|++|.++++..+.+ ++.+.|++||.|+|+|++++. .+.+.|
T Consensus 458 ~~~G~vV~G~V~~v~~~G~fV~l--------~~gi~g~i~~se~s~~~~~--~~~~~~~~Gd~v~~~V~~vd~~~~~i~L 527 (565)
T PRK06299 458 HKKGSIVTGTVTEVKDKGAFVEL--------EDGVEGLIRASELSRDRVE--DATEVLKVGDEVEAKVINIDRKNRRISL 527 (565)
T ss_pred cCCCCEEEEEEEEEecCceEEec--------CCCcEEEEEHHHhcchhcc--CccccCCCCCEEEEEEEEEccccCEEEE
Confidence 47899999999999999999999 4578999999999876665 788999999999999999974 467999
Q ss_pred EeecCC
Q 028346 153 STAKND 158 (210)
Q Consensus 153 St~~~~ 158 (210)
|++...
T Consensus 528 S~k~~~ 533 (565)
T PRK06299 528 SIKALD 533 (565)
T ss_pred Eeeehh
Confidence 998643
No 72
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=98.25 E-value=2.9e-06 Score=84.89 Aligned_cols=74 Identities=20% Similarity=0.151 Sum_probs=63.1
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~L 152 (210)
+++||+|.|+|+++.+.+++|++ ....+|++|++|++... +..++.+.|++||.|.|+|++++. .+.+.|
T Consensus 576 ~~vG~iV~G~V~~I~~fG~fVeL--------~~gveGLvhiSEls~~~-~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsL 646 (863)
T PRK12269 576 FGVNDVVKGRVTKIADFGAFIEL--------AEGIEGLAHISEFSWVK-KTSKPSDMVKIGDEVECMILGYDIQAGRVSL 646 (863)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEe--------cCCceeeeEHHHhcCcc-ccCCHHHcCCCCCEEEEEEEEEecccCceEE
Confidence 57999999999999999999999 56789999999997522 122677899999999999999974 467899
Q ss_pred Eeec
Q 028346 153 STAK 156 (210)
Q Consensus 153 St~~ 156 (210)
|++.
T Consensus 647 S~K~ 650 (863)
T PRK12269 647 GLKQ 650 (863)
T ss_pred Eehh
Confidence 9975
No 73
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.22 E-value=6.9e-06 Score=75.01 Aligned_cols=75 Identities=16% Similarity=0.230 Sum_probs=64.3
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~L 152 (210)
.++|+++.|+|+++.+..++|++ .....|++|.++++..+.. +..+.|++||.|.|+|++++. .+.+.|
T Consensus 275 ~~~G~~v~g~V~~i~~~G~fV~l--------~~gi~Glv~~se~~~~~~~--~~~~~~~~Gd~v~v~V~~id~e~~~i~l 344 (390)
T PRK06676 275 LPEGDVIEGTVKRLTDFGAFVEV--------LPGVEGLVHISQISHKHIA--TPSEVLEEGQEVKVKVLEVNEEEKRISL 344 (390)
T ss_pred hcCCcEEEEEEEEEeCceEEEEE--------CCCCeEEEEhHHcCccccC--ChhhccCCCCEEEEEEEEEECCCCEEEE
Confidence 57899999999999999999999 5568999999999765544 667889999999999999974 467899
Q ss_pred EeecCC
Q 028346 153 STAKND 158 (210)
Q Consensus 153 St~~~~ 158 (210)
|++..+
T Consensus 345 s~k~~~ 350 (390)
T PRK06676 345 SIKALE 350 (390)
T ss_pred EEEecc
Confidence 988654
No 74
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.20 E-value=6.4e-06 Score=75.22 Aligned_cols=73 Identities=21% Similarity=0.229 Sum_probs=62.6
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~L 152 (210)
+++|++|.|+|+++.+.+++|++ . ...|++|.++++....+ ++.+.|++||.|.|+|++++. .+.+.|
T Consensus 190 ~~~G~~v~g~V~~v~~~G~fV~l--------~-~v~g~v~~sels~~~~~--~~~~~~~vGd~i~~~Vl~vd~~~~~i~l 258 (390)
T PRK06676 190 LKEGDVVEGTVARLTDFGAFVDI--------G-GVDGLVHISELSHERVE--KPSEVVSVGQEVEVKVLSIDWETERISL 258 (390)
T ss_pred CCCCCEEEEEEEEEecceEEEEe--------C-CeEEEEEHHHcCccccC--CHHHhcCCCCEEEEEEEEEeCCCCEEEE
Confidence 58999999999999999999999 2 47899999999865544 677889999999999999974 467899
Q ss_pred EeecC
Q 028346 153 STAKN 157 (210)
Q Consensus 153 St~~~ 157 (210)
|++..
T Consensus 259 S~k~~ 263 (390)
T PRK06676 259 SLKDT 263 (390)
T ss_pred EEeec
Confidence 98753
No 75
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.17 E-value=9.3e-06 Score=77.60 Aligned_cols=73 Identities=21% Similarity=0.255 Sum_probs=64.1
Q ss_pred CCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceE
Q 028346 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF 151 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~ 151 (210)
-+++|++|.|+|+++.+..++|++ . ...|++|.++++..+.. ++.+.|++||.|.|+|++++. .+.+.
T Consensus 198 ~l~~G~iv~g~V~~v~~~G~~V~i--------~-g~~glv~~se~s~~~~~--~~~~~~kvG~~v~v~V~~~d~~~~~i~ 266 (565)
T PRK06299 198 NLEEGQVVEGVVKNITDYGAFVDL--------G-GVDGLLHITDISWKRVN--HPSEVVNVGDEVKVKVLKFDKEKKRVS 266 (565)
T ss_pred cCCCCCEEEEEEEEEeCCeEEEEE--------C-CEEEEEEHHHhcccccC--CHhhcCCCCCEEEEEEEEEeCCCCeEE
Confidence 368999999999999999999999 5 78999999999866554 788899999999999999974 46789
Q ss_pred EEeec
Q 028346 152 LSTAK 156 (210)
Q Consensus 152 LSt~~ 156 (210)
||++.
T Consensus 267 lS~k~ 271 (565)
T PRK06299 267 LGLKQ 271 (565)
T ss_pred EEEEe
Confidence 99874
No 76
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=98.16 E-value=2.2e-05 Score=55.73 Aligned_cols=71 Identities=15% Similarity=0.171 Sum_probs=54.8
Q ss_pred CCCEEEEEEEEEecCeEEEEEeeeccccccC-ceeEEEeccccccccc--cc-------cccCCCCCCCCEEEEEEEEeC
Q 028346 76 PGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEI--DK-------VDMHLSFRPGDIVRASVLSLG 145 (210)
Q Consensus 76 vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~-~~~Gii~~s~v~~~~~--d~-------~~~~~~~~~GDiV~AkV~s~~ 145 (210)
+|+++.|+|+++++..++|++ .. ..+|++|.++++.... |. ....+.|++||.|+++|.+++
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l--------~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd 72 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVEL--------DNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVD 72 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEe--------cCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEec
Confidence 489999999999999999999 43 6899999999864321 00 034578999999999999997
Q ss_pred C-CcceEEEe
Q 028346 146 D-ARAYFLST 154 (210)
Q Consensus 146 d-~~~~~LSt 154 (210)
. .+.+.|++
T Consensus 73 ~~~~~i~~~l 82 (83)
T cd04471 73 LDRRKIDFEL 82 (83)
T ss_pred cccCEEEEEE
Confidence 4 34566653
No 77
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=98.10 E-value=1.5e-05 Score=77.67 Aligned_cols=75 Identities=19% Similarity=0.298 Sum_probs=64.9
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~L 152 (210)
.++|++|.|+|+++++..++|++ .....|++|.++++..+.. ++.+.|++||.|+|+|++++. .+.+.|
T Consensus 560 ~~~G~~v~g~V~~i~~~G~fV~l--------~~~i~Gli~~sel~~~~~~--~~~~~~kvGd~V~vkV~~id~e~~rI~l 629 (647)
T PRK00087 560 YPVGSIVLGKVVRIAPFGAFVEL--------EPGVDGLVHISQISWKRID--KPEDVLSEGEEVKAKILEVDPEEKRIRL 629 (647)
T ss_pred ccCCeEEEEEEEEEECCeEEEEE--------CCCCEEEEEhhhcCccccC--CHhhcCCCCCEEEEEEEEEeCCCCEEEE
Confidence 46899999999999999999999 5679999999999865544 677889999999999999974 577899
Q ss_pred EeecCC
Q 028346 153 STAKND 158 (210)
Q Consensus 153 St~~~~ 158 (210)
|++...
T Consensus 630 slk~~~ 635 (647)
T PRK00087 630 SIKEVE 635 (647)
T ss_pred EEeecc
Confidence 987653
No 78
>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=98.09 E-value=1.4e-05 Score=75.48 Aligned_cols=72 Identities=26% Similarity=0.334 Sum_probs=62.9
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~L 152 (210)
.++|++|.|+|+++++.+++|.+ .....|++|.++++..+.+ ++.+.|++||.|.|+|++++. .+.+.|
T Consensus 444 ~~~G~~v~g~V~~v~~~G~fV~l--------~~~~~Glv~~s~l~~~~~~--~~~~~~~~Gd~v~~~V~~id~~~~~i~l 513 (516)
T TIGR00717 444 YKVGSVVKGKVTEIKDFGAFVEL--------PGGVEGLIRNSELSENRDE--DKTDEIKVGDEVEAKVVDIDKKNRKVSL 513 (516)
T ss_pred cCcceEEEEEEEEEecceEEEEc--------CCCeEEEEEHHHcCccccc--cccccCCCCCEEEEEEEEEeCCCCEEEE
Confidence 46899999999999999999999 5679999999999876654 788999999999999999964 467888
Q ss_pred Eee
Q 028346 153 STA 155 (210)
Q Consensus 153 St~ 155 (210)
|++
T Consensus 514 s~k 516 (516)
T TIGR00717 514 SVK 516 (516)
T ss_pred EEC
Confidence 864
No 79
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=98.04 E-value=2.4e-05 Score=64.64 Aligned_cols=85 Identities=19% Similarity=0.177 Sum_probs=64.6
Q ss_pred CCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccc-ccc---c------cccCCCCCCCCEEEEEE
Q 028346 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT-EID---K------VDMHLSFRPGDIVRASV 141 (210)
Q Consensus 72 y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~-~~d---~------~~~~~~~~~GDiV~AkV 141 (210)
+.|.+|++|.|+|++++..++++.+ .++++.+|.+++.+. .-| + .+-...++.||.|++||
T Consensus 77 FrPf~gEVv~g~V~~v~~~G~~v~~---------Gp~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV 147 (176)
T PTZ00162 77 FKPFKDEVLDAIVTDVNKLGFFAQA---------GPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRL 147 (176)
T ss_pred EecCCCCEEEEEEEEEecceEEEEe---------eCeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEE
Confidence 4588999999999999999999999 467788888877521 111 0 01235689999999999
Q ss_pred EEeC-CC--cceEEEeecCCceeeEEE
Q 028346 142 LSLG-DA--RAYFLSTAKNDLGVVSAE 165 (210)
Q Consensus 142 ~s~~-d~--~~~~LSt~~~~LGVv~a~ 165 (210)
.++. +. .....|++++-||.+.|+
T Consensus 148 ~~v~~~~~~~~~i~T~~~~~LG~~~~~ 174 (176)
T PTZ00162 148 QGVRYDASNLFAIATINSDYLGPIESS 174 (176)
T ss_pred EEEEecCCCcEEEEEecCCCcCccccc
Confidence 8873 22 235789999999999663
No 80
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=98.02 E-value=2.1e-05 Score=78.85 Aligned_cols=74 Identities=18% Similarity=0.205 Sum_probs=62.2
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~L 152 (210)
.++|++|.|+|+.+++..++|++ ....+|+||.+|++..... ....+.|++||.|.|+|++++. .+.+.|
T Consensus 663 ~~vG~~v~G~V~~i~~~G~fV~l--------~~gV~GlIh~sels~~~~~-~~~~~~~kvGq~VkvkVl~ID~e~rrI~L 733 (863)
T PRK12269 663 YPVGARFTRRIVKVTNAGAFIEM--------EEGIDGFLHVDDLSWVKRT-RPADHELEVGKEIECMVIECDPQARRIRL 733 (863)
T ss_pred CCCCCEEEEEEEEEecceEEEEe--------CCCcEEEEEhHHhhccccc-cchhhccCCCCEEEEEEEEEeccCCEEEE
Confidence 46899999999999999999999 6789999999999753321 2455689999999999999974 467999
Q ss_pred Eeec
Q 028346 153 STAK 156 (210)
Q Consensus 153 St~~ 156 (210)
|++.
T Consensus 734 S~K~ 737 (863)
T PRK12269 734 GVKQ 737 (863)
T ss_pred Eecc
Confidence 9874
No 81
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=97.95 E-value=3.4e-05 Score=72.80 Aligned_cols=73 Identities=18% Similarity=0.205 Sum_probs=62.6
Q ss_pred CCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceE
Q 028346 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF 151 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~ 151 (210)
-+++|++|.|+|+++.+..++|++ . ..+|.+|.++++..... ++.+.|++||.|.|+|++++. .+.+.
T Consensus 184 ~l~~G~~v~g~V~~i~~~G~~V~l--------~-g~~g~lp~~e~s~~~~~--~~~~~~~vG~~v~v~Vl~~d~~~~~i~ 252 (516)
T TIGR00717 184 NLKEGDVVKGVVKNITDFGAFVDL--------G-GVDGLLHITDMSWKRVK--HPSEYVKVGQEVKVKVIKFDKEKGRIS 252 (516)
T ss_pred hccCCCEEEEEEEEEECCeEEEEE--------C-CEEEEEEHHHcCCCCCC--CHHHhccCCCEEEEEEEEEECCCCcEE
Confidence 468999999999999999999998 3 47999999999865544 677889999999999999975 45689
Q ss_pred EEeec
Q 028346 152 LSTAK 156 (210)
Q Consensus 152 LSt~~ 156 (210)
||++.
T Consensus 253 lS~k~ 257 (516)
T TIGR00717 253 LSLKQ 257 (516)
T ss_pred EEEEe
Confidence 99885
No 82
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.94 E-value=4.1e-05 Score=74.64 Aligned_cols=77 Identities=26% Similarity=0.324 Sum_probs=65.5
Q ss_pred CCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-Ccce
Q 028346 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAY 150 (210)
Q Consensus 72 y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~ 150 (210)
..+++|++|.|+|.++.++.++|++ .....|.|+.++++..... +..+.|++||.|+|+|+++++ .+.+
T Consensus 298 ~~l~~G~iV~G~V~~v~~~gv~Vdi--------g~~~~G~lp~~els~~~~~--~~~~~~~vGd~V~v~V~~vd~~~g~i 367 (647)
T PRK00087 298 KQIRRGDIVKGTVVSVNENEVFVDV--------GYKSEGVIPLRELTLDEIS--SLKESVKVGDEIEVKVLKLEDEDGYV 367 (647)
T ss_pred hhccCCCEEEEEEEEEECCEEEEEE--------CCCeEEEEEHHHhcccccC--ChhhccCCCCEEEEEEEEEECCCCcE
Confidence 3478999999999999999999999 6678999999998754333 677889999999999999964 4678
Q ss_pred EEEeecCC
Q 028346 151 FLSTAKND 158 (210)
Q Consensus 151 ~LSt~~~~ 158 (210)
.||.+..+
T Consensus 368 ~LS~k~~~ 375 (647)
T PRK00087 368 VLSKKEAD 375 (647)
T ss_pred EEEeehhc
Confidence 99998775
No 83
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=97.93 E-value=2.2e-05 Score=77.04 Aligned_cols=77 Identities=21% Similarity=0.283 Sum_probs=68.7
Q ss_pred CCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceE
Q 028346 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYF 151 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~ 151 (210)
-+++|-++.|.|+.+.+.+++|+| .-.-.|++|+|+.+...++ +..+.+++||+|.++|++++- ...+.
T Consensus 655 dLk~Gm~leg~Vrnv~~fgafVdI--------gv~qDglvHis~ls~~fv~--~P~~vv~vGdiV~v~V~~vD~~r~rI~ 724 (780)
T COG2183 655 DLKPGMILEGTVRNVVDFGAFVDI--------GVHQDGLVHISQLSDKFVK--DPNEVVKVGDIVKVKVIEVDTARKRIA 724 (780)
T ss_pred hccCCCEEEEEEEEeeeccceEEe--------ccccceeeeHHHhhhhhcC--ChHHhcccCCEEEEEEEEEecccCeee
Confidence 368999999999999999999999 7778999999999877766 678999999999999999974 46799
Q ss_pred EEeecCCc
Q 028346 152 LSTAKNDL 159 (210)
Q Consensus 152 LSt~~~~L 159 (210)
||++.++.
T Consensus 725 Lsmr~~~~ 732 (780)
T COG2183 725 LSMRLDEE 732 (780)
T ss_pred eEeeccCC
Confidence 99998765
No 84
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.67 E-value=0.00011 Score=71.36 Aligned_cols=75 Identities=16% Similarity=0.224 Sum_probs=67.7
Q ss_pred CCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEE
Q 028346 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFL 152 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~L 152 (210)
-+++|.+-.|+|+++.+..|+|.+ ...-.|++|+|++...+++ +..+.++.||.|+.||+++++.+.+.|
T Consensus 616 e~evg~iy~G~V~ri~~fGaFv~l--------~~gkdgl~hiS~~~~~rv~--kv~dvlk~Gd~v~Vkv~~iD~~Gri~l 685 (692)
T COG1185 616 EVEVGEVYEGTVVRIVDFGAFVEL--------LPGKDGLVHISQLAKERVE--KVEDVLKEGDEVKVKVIEIDKQGRIRL 685 (692)
T ss_pred hcccccEEEEEEEEEeecceEEEe--------cCCcceeEEehhhhhhhhh--cccceeecCceEEEEEeeecccCCccc
Confidence 479999999999999999999999 6778999999999887777 677999999999999999998778888
Q ss_pred EeecC
Q 028346 153 STAKN 157 (210)
Q Consensus 153 St~~~ 157 (210)
|+...
T Consensus 686 s~~~~ 690 (692)
T COG1185 686 SIKAV 690 (692)
T ss_pred eehhc
Confidence 88653
No 85
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=97.64 E-value=0.00014 Score=68.53 Aligned_cols=71 Identities=23% Similarity=0.330 Sum_probs=59.8
Q ss_pred CCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC---Cc
Q 028346 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD---AR 148 (210)
Q Consensus 72 y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d---~~ 148 (210)
|..++|++|.|+|.++....++|++ ....|+||.++.. .++.|++||.|+|.|++++. +.
T Consensus 130 yk~~~GeIV~G~V~ri~~~giiVDL---------ggvea~LP~sE~i--------p~E~~~~GdrIka~I~~Vd~~~kg~ 192 (470)
T PRK09202 130 YKDRVGEIITGVVKRVERGNIIVDL---------GRAEAILPRKEQI--------PRENFRPGDRVRAYVYEVRKEARGP 192 (470)
T ss_pred HHhhcCCEEEEEEEEEecCCEEEEE---------CCeEEEecHHHcC--------CCccCCCCCEEEEEEEEEecCCCCC
Confidence 5567999999999999999999999 3589999998864 33779999999999999964 34
Q ss_pred ceEEEeecCCc
Q 028346 149 AYFLSTAKNDL 159 (210)
Q Consensus 149 ~~~LSt~~~~L 159 (210)
++.||-+.++|
T Consensus 193 qIilSRt~p~~ 203 (470)
T PRK09202 193 QIILSRTHPEF 203 (470)
T ss_pred eEEEEeCcHHH
Confidence 68999888754
No 86
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.51 E-value=0.00028 Score=64.50 Aligned_cols=72 Identities=15% Similarity=0.287 Sum_probs=58.6
Q ss_pred CCCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC---C
Q 028346 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD---A 147 (210)
Q Consensus 71 ~y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d---~ 147 (210)
.|..+.|++|.|+|.++..+.++|+| . ..+|+||.++... ++.|++||.|+|.|.+++. +
T Consensus 129 ef~~k~GeiV~G~V~~~~~~~~~Vdl--------g-~vEa~LP~~E~ip--------~e~~~~Gd~Ika~V~~V~~~~kg 191 (362)
T PRK12327 129 EFSEREGDIVTGVVQRRDNRFVYVNL--------G-KIEAVLPPAEQIP--------GETYKHGDRIKVYVVKVEKTTKG 191 (362)
T ss_pred HHHHhcCCEEEEEEEEEeCCcEEEEe--------C-CeEEEecHHHcCC--------CCCCCCCCEEEEEEEEEecCCCC
Confidence 36679999999999999999999999 3 3799999766432 3779999999999999973 3
Q ss_pred cceEEEeecCCc
Q 028346 148 RAYFLSTAKNDL 159 (210)
Q Consensus 148 ~~~~LSt~~~~L 159 (210)
..+.||-..++|
T Consensus 192 p~IivSRt~p~~ 203 (362)
T PRK12327 192 PQIFVSRTHPGL 203 (362)
T ss_pred CeEEEEeCCHHH
Confidence 458888887653
No 87
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=97.49 E-value=0.00031 Score=63.75 Aligned_cols=72 Identities=21% Similarity=0.319 Sum_probs=58.4
Q ss_pred CCCCCCCCEEEEEEEEEecCe-EEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCC--
Q 028346 71 GPVPEPGSVVIARVTKVMTRM-ASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-- 147 (210)
Q Consensus 71 ~y~p~vGDiViG~V~~v~~~~-a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~-- 147 (210)
.|..++|++|.|+|.++..+. ++|+| . ..+|+||.++... .+.|++||.|+|.|.++++.
T Consensus 126 ey~~k~GeiV~G~V~~v~~~g~v~Vdi--------G-~~ea~LP~~E~ip--------~E~~~~Gd~ik~~V~~V~~~~k 188 (341)
T TIGR01953 126 EFSSKEGEIISGTVKRVNRRGNLYVEL--------G-KTEGILPKKEQIP--------GEKFRIGDRIKAYVYEVRKTAK 188 (341)
T ss_pred HHHhhcCCEEEEEEEEEecCCcEEEEE--------C-CeEEEecHHHcCC--------CcCCCCCCEEEEEEEEEEcCCC
Confidence 355689999999999999865 79999 3 5799999887653 24599999999999999743
Q ss_pred -cceEEEeecCCc
Q 028346 148 -RAYFLSTAKNDL 159 (210)
Q Consensus 148 -~~~~LSt~~~~L 159 (210)
..+.||.+.++|
T Consensus 189 g~qIivSRt~~~~ 201 (341)
T TIGR01953 189 GPQIILSRTHPEF 201 (341)
T ss_pred CCeEEEEeCcHHH
Confidence 458999988764
No 88
>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=97.36 E-value=0.0018 Score=47.54 Aligned_cols=74 Identities=22% Similarity=0.183 Sum_probs=47.3
Q ss_pred CCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccc-----------cccccccCCCCCCCCEEEEEEEEe
Q 028346 76 PGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT-----------EIDKVDMHLSFRPGDIVRASVLSL 144 (210)
Q Consensus 76 vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~-----------~~d~~~~~~~~~~GDiV~AkV~s~ 144 (210)
+|+++.|+|+++....+++.+. |.++.++.+++.+. ..+ +-...+++||.|++||.++
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G---------pl~~f~~~~~ip~~~~~~~~~~~~~~~~--~~~~~i~~g~~VR~rV~~v 69 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG---------PLSIFISRHLIPSDMEFDPNASPPCFTS--NEDIVIKKDTEVRLKIIGT 69 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc---------CceEEEEeeecCccceECCcCCCCeEeC--CCcEEECCCCEEEEEEEEE
Confidence 5899999999999999999995 23333333333211 011 1245689999999999987
Q ss_pred C-CCcc--eEEEeecCCce
Q 028346 145 G-DARA--YFLSTAKNDLG 160 (210)
Q Consensus 145 ~-d~~~--~~LSt~~~~LG 160 (210)
. +.+. ..-|++++-||
T Consensus 70 ~~~~~~~~~igt~~~~~LG 88 (88)
T cd04462 70 RVDATDIFAIGTIKDDYLG 88 (88)
T ss_pred EEccCceEEEEEccCCCCC
Confidence 4 2222 13355666665
No 89
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=97.23 E-value=0.0017 Score=47.42 Aligned_cols=72 Identities=11% Similarity=0.177 Sum_probs=59.5
Q ss_pred CCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEe-ccccccccccccccCCCCCCCCEEEEEEEEeCCCcc-
Q 028346 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR-QQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARA- 149 (210)
Q Consensus 72 y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~-~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~- 149 (210)
-.|++||+|. .|+.+++..+.|.++ ....+|.|. -++++..+.+ ++++.+ +|-.+.++|+.++..+.
T Consensus 12 ~~P~v~dvv~-~Vv~i~d~~~YV~Ll-------eY~iegmIl~~selsr~rir--si~kll-VGk~e~v~ViRVDk~KGY 80 (86)
T PHA02858 12 VFPNINEVTK-GIVFVKDNIFYVKLI-------DYGLEALIVNYVNVNADRAE--KLKKKL-VGKTINVQVIRTDKLKGY 80 (86)
T ss_pred ecCCCCeEEE-EEEEEeccEEEEEEe-------cCccceEEecHHHHhHHHHH--hhhhhh-cCCeeEEEEEEECCCCCE
Confidence 3589999999 899999999999995 455888887 8888876666 788888 99999999999985433
Q ss_pred eEEEe
Q 028346 150 YFLST 154 (210)
Q Consensus 150 ~~LSt 154 (210)
+.||.
T Consensus 81 IDLs~ 85 (86)
T PHA02858 81 IDVRH 85 (86)
T ss_pred EEeEc
Confidence 46663
No 90
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=96.97 E-value=0.0042 Score=57.79 Aligned_cols=82 Identities=21% Similarity=0.263 Sum_probs=58.9
Q ss_pred EEEecCCCCCCCCCCCCEEEEEEEEEecC--eEEEEEeeeccccccCceeEEEecccccccc----------ccccccCC
Q 028346 62 VEVTGHKAHGPVPEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATE----------IDKVDMHL 129 (210)
Q Consensus 62 i~V~p~~~~~y~p~vGDiViG~V~~v~~~--~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~----------~d~~~~~~ 129 (210)
+.+.+... ...+|++..|+|+++.+. .|+|+| ...-.|.||.+|+.... ....++.+
T Consensus 14 ~~ie~~~~---~~~vGnIY~GrV~~i~p~l~aAFVdi--------G~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~ 82 (414)
T TIGR00757 14 LIIERPKS---RQLKGNIYKGRVTRILPSLQAAFVDI--------GLEKNGFLHASDIGPNYECLAPAEAKREAGPSISE 82 (414)
T ss_pred EEEecCcC---cCCCCCEEEEEEeeecCCCceEEEEc--------CCCceEEEEHHHcCchhhccccccccccccCCHHH
Confidence 45565432 246899999999999998 899999 66778999999985321 01114567
Q ss_pred CCCCCCEEEEEEEEeC-CCcceEEEe
Q 028346 130 SFRPGDIVRASVLSLG-DARAYFLST 154 (210)
Q Consensus 130 ~~~~GDiV~AkV~s~~-d~~~~~LSt 154 (210)
.+++||.|.++|..-. ..+...||+
T Consensus 83 ~l~~G~~IlVQV~Ke~~~~Kgp~lT~ 108 (414)
T TIGR00757 83 LLRPGQSVLVQVVKEPRGNKGARLTT 108 (414)
T ss_pred hCcCCCEEEEEEeeCCcCCCCCeEEE
Confidence 8999999999999842 123345555
No 91
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=96.83 E-value=0.0061 Score=60.18 Aligned_cols=74 Identities=14% Similarity=0.152 Sum_probs=57.5
Q ss_pred CCCCCCEEEEEEEEEecCeEEEEEeeeccccccC-ceeEEEeccccccccc--cc-------cccCCCCCCCCEEEEEEE
Q 028346 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEI--DK-------VDMHLSFRPGDIVRASVL 142 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~-~~~Gii~~s~v~~~~~--d~-------~~~~~~~~~GDiV~AkV~ 142 (210)
..++|+++.|+|++|++.+++|++ .. ..+|++|++++..... ++ ......|++||.|.++|.
T Consensus 624 ~~~iG~~~~g~V~~v~~fGifV~L--------~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~ 695 (709)
T TIGR02063 624 SEKIGEEFEGVISGVTSFGLFVEL--------ENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVV 695 (709)
T ss_pred hccCCcEEEEEEEEEEeCCEEEEe--------cCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEE
Confidence 357899999999999999999999 43 5899999999874321 10 123467999999999999
Q ss_pred EeCC-CcceEEEe
Q 028346 143 SLGD-ARAYFLST 154 (210)
Q Consensus 143 s~~d-~~~~~LSt 154 (210)
+++. .+.+.+++
T Consensus 696 ~vd~~~~~I~~~l 708 (709)
T TIGR02063 696 KADLDTGKIDFEL 708 (709)
T ss_pred EEecccCeEEEEE
Confidence 9974 45676664
No 92
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.64 E-value=0.0052 Score=56.40 Aligned_cols=72 Identities=17% Similarity=0.201 Sum_probs=56.8
Q ss_pred CCCCCCCCEEEEEEEEEec-CeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC---
Q 028346 71 GPVPEPGSVVIARVTKVMT-RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD--- 146 (210)
Q Consensus 71 ~y~p~vGDiViG~V~~v~~-~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d--- 146 (210)
.|..++|++|.|+|.++.. ..++|++ . ..+|+||.++.- ..+.|++||-|+|.|.++..
T Consensus 133 ey~~~~Geiv~g~V~r~~~~~~i~vdl--------g-~~ea~LP~~eqi--------p~E~~~~Gdrik~~i~~V~~~~k 195 (374)
T PRK12328 133 KYKKKVGKIVFGTVVRVDNEENTFIEI--------D-EIRAVLPMKNRI--------KGEKFKVGDVVKAVLKRVKIDKN 195 (374)
T ss_pred HHHHhcCcEEEEEEEEEecCCCEEEEc--------C-CeEEEeCHHHcC--------CCCcCCCCCEEEEEEEEEecCCC
Confidence 4778999999999999986 4588888 3 578999877643 33779999999999999953
Q ss_pred -CcceEEEeecCCc
Q 028346 147 -ARAYFLSTAKNDL 159 (210)
Q Consensus 147 -~~~~~LSt~~~~L 159 (210)
+..+.||-..++|
T Consensus 196 ~gp~IilSRt~p~~ 209 (374)
T PRK12328 196 NGILIELSRTSPKF 209 (374)
T ss_pred CCCEEEEEcCCHHH
Confidence 2357888877654
No 93
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=96.62 E-value=0.0096 Score=62.00 Aligned_cols=76 Identities=18% Similarity=0.223 Sum_probs=67.4
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC-CcceEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD-ARAYFL 152 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d-~~~~~L 152 (210)
.+.||+|.|.|..+.++..++.+ ...+++..++++...+... .-+..|.+|++|.+||.+++. .+.+.|
T Consensus 1160 lk~g~iv~G~V~nv~~~glfi~l--------s~~v~a~v~is~~~ds~~k--~w~k~~~~gklv~~rv~~ve~~s~riel 1229 (1710)
T KOG1070|consen 1160 LKIGDIVRGFVKNVETKGLFIAL--------SRKVEAFVPISGLSDSFEK--EWEKHLPVGKLVTGRVLSVEEDSKRIEL 1229 (1710)
T ss_pred cccCceeEEEEEEecCCcEEEEE--------ccceEEEEEccccccchhh--hhhccCCccceeeeEEEEeeccCceEEE
Confidence 58999999999999999999999 7889999999999887755 678899999999999999974 567999
Q ss_pred EeecCCc
Q 028346 153 STAKNDL 159 (210)
Q Consensus 153 St~~~~L 159 (210)
|++..+-
T Consensus 1230 ~Lk~s~~ 1236 (1710)
T KOG1070|consen 1230 SLKNSDI 1236 (1710)
T ss_pred EEecccc
Confidence 9987654
No 94
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.54 E-value=0.0072 Score=56.52 Aligned_cols=77 Identities=12% Similarity=0.162 Sum_probs=58.4
Q ss_pred CCCCCCCCEEEEEEEEEecCeEEEEEeeeccccccC-ceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCC--
Q 028346 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-- 147 (210)
Q Consensus 71 ~y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~-~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~-- 147 (210)
.|..++|++|.|+|.++..+.+.|++.+ .+.. ..+|+|+.++.- ..+.|++||.|+|.|.++..+
T Consensus 147 ef~~~~GeIV~G~V~r~e~~~viv~l~~----~~g~~~~EaiLP~~Eqi--------p~E~y~~Gdrika~i~~V~~~~~ 214 (449)
T PRK12329 147 EFQDLEDTVLTARVLRFERQSVIMAVSS----GFGQPEVEAELPKREQL--------PNDNYRANATFKVFLKEVSEGPR 214 (449)
T ss_pred HHHHhcCcEEEEEEEEEcCCCEEEEecc----cCCCcceEEEecHHHcC--------CCCcCCCCCEEEEEEEEeecCCC
Confidence 4678999999999999999989998831 0111 378999877643 337799999999999999532
Q ss_pred --cceEEEeecCCc
Q 028346 148 --RAYFLSTAKNDL 159 (210)
Q Consensus 148 --~~~~LSt~~~~L 159 (210)
..+.||-..++|
T Consensus 215 kGpqIilSRt~p~l 228 (449)
T PRK12329 215 RGPQLFVSRANAGL 228 (449)
T ss_pred CCCEEEEEcCCHHH
Confidence 347888877654
No 95
>PRK11642 exoribonuclease R; Provisional
Probab=96.52 E-value=0.015 Score=58.52 Aligned_cols=73 Identities=16% Similarity=0.203 Sum_probs=57.2
Q ss_pred CCCCEEEEEEEEEecCeEEEEEeeeccccccC-ceeEEEeccccccc--cccc-------cccCCCCCCCCEEEEEEEEe
Q 028346 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRAT--EIDK-------VDMHLSFRPGDIVRASVLSL 144 (210)
Q Consensus 75 ~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~-~~~Gii~~s~v~~~--~~d~-------~~~~~~~~~GDiV~AkV~s~ 144 (210)
++|+++.|+|++|++.+++|+| .. ..+|++|++++... ..++ ......|++||.|.++|.++
T Consensus 642 ~iGe~f~G~Is~V~~fGifVeL--------~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~v 713 (813)
T PRK11642 642 QVGNVFKGVISSVTGFGFFVRL--------DDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAV 713 (813)
T ss_pred cCCcEEEEEEEEeecCceEEEE--------CCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEe
Confidence 6899999999999999999999 43 48999999988632 1111 02346799999999999998
Q ss_pred CC-CcceEEEee
Q 028346 145 GD-ARAYFLSTA 155 (210)
Q Consensus 145 ~d-~~~~~LSt~ 155 (210)
+. .+.+.|++.
T Consensus 714 D~~~rkI~f~l~ 725 (813)
T PRK11642 714 NMDERKIDFSLI 725 (813)
T ss_pred ecCCCeEEEEEe
Confidence 73 466888774
No 96
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=96.46 E-value=0.0039 Score=64.77 Aligned_cols=74 Identities=20% Similarity=0.133 Sum_probs=63.8
Q ss_pred CCCCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcc
Q 028346 70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARA 149 (210)
Q Consensus 70 ~~y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~ 149 (210)
..+-.++|++|.|.|+++++++..|.+ ...+.|-||++++-.+...-.++.+-|++||-|.|||+.-.|.++
T Consensus 879 ~~~~~~igsiv~a~v~svKp~~L~v~l--------~~~~~gri~isev~d~~~eitDp~~k~~vG~~I~vrviG~~D~k~ 950 (1710)
T KOG1070|consen 879 STEDLSIGSIVRAYVKSVKPDQLNVLL--------AANHHGRIHISEVLDNLHEITDPLDKFKVGDGIFVRVIGGHDVKD 950 (1710)
T ss_pred cccceeeeeEEEEEEeeecccceEEec--------cccccCceehHHhhccccccCChhhhcccCCeEEEEEEcCCcccc
Confidence 356789999999999999999999999 778999999999987666666788999999999999998766554
Q ss_pred eE
Q 028346 150 YF 151 (210)
Q Consensus 150 ~~ 151 (210)
+-
T Consensus 951 lp 952 (1710)
T KOG1070|consen 951 LP 952 (1710)
T ss_pred Cc
Confidence 43
No 97
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=96.13 E-value=0.03 Score=54.93 Aligned_cols=73 Identities=14% Similarity=0.203 Sum_probs=56.2
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeecccccc-CceeEEEecccccccc--ccc-------cccCCCCCCCCEEEEEEEE
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATE--IDK-------VDMHLSFRPGDIVRASVLS 143 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~-~~~~Gii~~s~v~~~~--~d~-------~~~~~~~~~GDiV~AkV~s 143 (210)
-++|+.+-|+|+++++.+++|+| . ...+|++|++++.... .|+ ......|++||.|+++|.+
T Consensus 570 ~~iG~~~~g~I~~v~~~GifV~L--------~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~ 641 (654)
T TIGR00358 570 DKVGTEFSGEISSVTRFGMFVRL--------DDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTE 641 (654)
T ss_pred hCCCcEEEEEEEeEEcCcEEEEe--------cCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEE
Confidence 36799999999999999999999 5 5689999999986432 111 1223679999999999999
Q ss_pred eCC-CcceEEEe
Q 028346 144 LGD-ARAYFLST 154 (210)
Q Consensus 144 ~~d-~~~~~LSt 154 (210)
++. .+.+.+++
T Consensus 642 vd~~~~~I~f~l 653 (654)
T TIGR00358 642 VNMETRSIIFEL 653 (654)
T ss_pred EecccCeEEEEE
Confidence 974 34566553
No 98
>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=95.87 E-value=0.039 Score=39.24 Aligned_cols=70 Identities=19% Similarity=0.177 Sum_probs=52.9
Q ss_pred CCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEE-EEEEEEeCCCcceEEEe
Q 028346 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIV-RASVLSLGDARAYFLST 154 (210)
Q Consensus 77 GDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV-~AkV~s~~d~~~~~LSt 154 (210)
|++|.|+|.+-+.+...|++. .....|.|+..+++........+...+++||-+ .+-|++. ..+.+.||.
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~-------~~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL~~-~~r~i~lt~ 71 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAIL-------PEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLSN-YKGRIILTK 71 (72)
T ss_pred CceEEEEEEEEcCCcEEEEec-------CCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEEec-cccEEEEec
Confidence 789999999999999999994 357889988877765333333577889999999 8888832 234456653
No 99
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=95.59 E-value=0.021 Score=54.89 Aligned_cols=83 Identities=10% Similarity=0.090 Sum_probs=65.8
Q ss_pred CCCCCCEE-----EEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCC
Q 028346 73 VPEPGSVV-----IARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA 147 (210)
Q Consensus 73 ~p~vGDiV-----iG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~ 147 (210)
.++++|+. .|+|+++++..++|++ ....+|++|.+|+.+.... +.++.+.+||.|..+-+..+..
T Consensus 660 ~~~~~~l~~g~vy~~tIt~~rd~G~~V~l--------~p~~~~Llh~sqL~~e~ia--kpsd~levGq~I~vk~ie~d~~ 729 (760)
T KOG1067|consen 660 DDQVQDLEFGGVYTATITEIRDTGVMVEL--------YPMQQGLLHNSQLDQEKIA--KPSDLLEVGQEIQVKYIERDPR 729 (760)
T ss_pred CccccceEeeeEEEEEEeeecccceEEEe--------cCCchhhccchhccccccc--ChHHHHhhcceeEEEEEeecCc
Confidence 35566655 5899999999999999 4467899999999887766 7889999999999999998877
Q ss_pred cceEEEeec----CCceeeEEE
Q 028346 148 RAYFLSTAK----NDLGVVSAE 165 (210)
Q Consensus 148 ~~~~LSt~~----~~LGVv~a~ 165 (210)
+.+.||-|. +..++....
T Consensus 730 g~~~ls~ralLp~p~~~~~st~ 751 (760)
T KOG1067|consen 730 GGIMLSSRALLPDPATKESSTL 751 (760)
T ss_pred cceeehhhhhcCCcccCCcccc
Confidence 778877654 445544443
No 100
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=95.52 E-value=0.018 Score=58.96 Aligned_cols=78 Identities=21% Similarity=0.251 Sum_probs=63.6
Q ss_pred CCCCCCEEEEEEEEEecCeEEE---EEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCC-c
Q 028346 73 VPEPGSVVIARVTKVMTRMASA---DIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-R 148 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~a~V---~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~-~ 148 (210)
...+|.+|.+.|++++.....| .. ..+..|.|+.++++...+. ++.+-+++|+.|.+||++++.. -
T Consensus 982 t~~~g~iV~~~V~~vt~rr~~Cv~v~l--------d~G~~g~i~~~~~Sd~~v~--~p~~~v~vgq~v~~kvi~id~e~f 1051 (1299)
T KOG1856|consen 982 TFYEGAIVPVTVTKVTHRRGICVRVRL--------DCGVTGFILAKNLSDRDVR--RPENRVKVGQTVYCKVIKIDKERF 1051 (1299)
T ss_pred HhccCceEEEeeeEEEecccceeEEEe--------cCCCceeeeccccChhhcc--CHHHhhccCceEEEEeeeeeHhhh
Confidence 3568999999999999998554 44 7889999999999875554 7888899999999999999743 3
Q ss_pred ceEEEeecCCce
Q 028346 149 AYFLSTAKNDLG 160 (210)
Q Consensus 149 ~~~LSt~~~~LG 160 (210)
...||++..+|-
T Consensus 1052 ~v~Ls~r~sdlk 1063 (1299)
T KOG1856|consen 1052 SVELSCRTSDLK 1063 (1299)
T ss_pred hhhhhhhhHHhh
Confidence 468888887763
No 101
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=95.46 E-value=0.064 Score=47.25 Aligned_cols=63 Identities=17% Similarity=0.167 Sum_probs=47.7
Q ss_pred CCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEEEeec
Q 028346 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAK 156 (210)
Q Consensus 77 GDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LSt~~ 156 (210)
++.|-|.|-+......++-+ ...+.|.||.|++. ...+.|+.+.|||+.+.+.+++.||++.
T Consensus 156 nq~v~~tVYr~~~~G~fv~~--------e~~~~GfIh~sEr~----------~~prlG~~l~~rVi~~reDg~lnLSl~p 217 (287)
T COG2996 156 NQEVDATVYRLLESGTFVIT--------ENGYLGFIHKSERF----------AEPRLGERLTARVIGVREDGKLNLSLRP 217 (287)
T ss_pred cCeeeeEEEEEeccceEEEE--------cCCeEEEEcchhhc----------ccccCCceEEEEEEEEccCCeeeccccc
Confidence 55566666666666655555 56789999998754 3357999999999999877789999975
Q ss_pred C
Q 028346 157 N 157 (210)
Q Consensus 157 ~ 157 (210)
-
T Consensus 218 ~ 218 (287)
T COG2996 218 R 218 (287)
T ss_pred c
Confidence 3
No 102
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=95.25 E-value=0.015 Score=50.99 Aligned_cols=76 Identities=18% Similarity=0.264 Sum_probs=64.6
Q ss_pred CCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcc-eE
Q 028346 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARA-YF 151 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~-~~ 151 (210)
.|.++|+|++.|.+|..-+|.|.++-. ...+|.|-.|+++..++. +++...++|-.=.+-|+.++..+. +.
T Consensus 13 yPev~e~VmvnV~sIaemGayv~LlEY------nniEGmiLlsELSrRRIR--SI~klirVGr~E~vvVlrVDkekGYID 84 (304)
T KOG2916|consen 13 YPEVEEIVMVNVRSIAEMGAYVKLLEY------NNIEGMILLSELSRRRIR--SIQKLIRVGRNEPVVVLRVDKEKGYID 84 (304)
T ss_pred CCCcccEEEEEeeEehhccceEeeeec------CCcccchhhhHHHHHHHH--HHHHHHhcCCcceEEEEEEcCCCCcee
Confidence 499999999999999999999999632 357899999999877766 788999999999999999986544 58
Q ss_pred EEeec
Q 028346 152 LSTAK 156 (210)
Q Consensus 152 LSt~~ 156 (210)
||.+.
T Consensus 85 LSkrr 89 (304)
T KOG2916|consen 85 LSKRR 89 (304)
T ss_pred chhcc
Confidence 88875
No 103
>PRK11712 ribonuclease G; Provisional
Probab=94.81 E-value=0.15 Score=48.56 Aligned_cols=82 Identities=18% Similarity=0.188 Sum_probs=57.0
Q ss_pred EEEecCCCCCCCCCCCCEEEEEEEEEecCe--EEEEEeeeccccccCceeEEEecccccccc--------c--cccccCC
Q 028346 62 VEVTGHKAHGPVPEPGSVVIARVTKVMTRM--ASADIMCVGAKSVREKFSGIIRQQDVRATE--------I--DKVDMHL 129 (210)
Q Consensus 62 i~V~p~~~~~y~p~vGDiViG~V~~v~~~~--a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~--------~--d~~~~~~ 129 (210)
+.+++... ...+|+|-.|+|.+|-+.. |+||| ...-.|.||.+|+.... . ....+.+
T Consensus 27 ~~iE~~~~---~~~vGnIY~G~V~~v~pg~~AAFVdI--------G~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~ 95 (489)
T PRK11712 27 IHIEREAK---RGIVGNIYKGRVSRVLPGMQAAFVDI--------GLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISE 95 (489)
T ss_pred EEEecCCc---ccccccEEEEEEeecCCCCceeEEee--------CCCccEEEEhhhccchhhhcccccccccccccHHH
Confidence 45555442 2458999999999998865 99999 67788999999874210 0 0113456
Q ss_pred CCCCCCEEEEEEEEeCC-CcceEEEe
Q 028346 130 SFRPGDIVRASVLSLGD-ARAYFLST 154 (210)
Q Consensus 130 ~~~~GDiV~AkV~s~~d-~~~~~LSt 154 (210)
.+++||.|.++|..-.- .+...||+
T Consensus 96 ~l~~Gq~iLVQV~Ke~~~~KG~~lT~ 121 (489)
T PRK11712 96 LVRQGQDIMVQVVKDPLGTKGARLTT 121 (489)
T ss_pred hccCCCEEEEEEEeCCcCCCCCeEEE
Confidence 79999999999998431 23345555
No 104
>PRK10811 rne ribonuclease E; Reviewed
Probab=94.57 E-value=0.14 Score=52.24 Aligned_cols=83 Identities=11% Similarity=0.171 Sum_probs=57.4
Q ss_pred EEEecCCCCCCCCCCCCEEEEEEEEEecCe--EEEEEeeeccccccCceeEEEecccccccc-cc------ccccCCCCC
Q 028346 62 VEVTGHKAHGPVPEPGSVVIARVTKVMTRM--ASADIMCVGAKSVREKFSGIIRQQDVRATE-ID------KVDMHLSFR 132 (210)
Q Consensus 62 i~V~p~~~~~y~p~vGDiViG~V~~v~~~~--a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~-~d------~~~~~~~~~ 132 (210)
+.+.+... -+.+|+|-.|+|.+|-+.. |||+| ...-.|.||.+|+.... .+ ..++.+.++
T Consensus 27 L~IEr~~~---e~~vGnIYkGkVenIvPGInAAFVDI--------G~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk 95 (1068)
T PRK10811 27 LDIESPGH---EQKKANIYKGKITRIEPSLEAAFVDY--------GAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLR 95 (1068)
T ss_pred EEeccCcc---ccCccceEEEEEecccCCcceeEEEe--------cCCcceEEEhhhccccccccccccccccccccccC
Confidence 45555332 2368999999999998754 99999 66788999999984221 11 113456799
Q ss_pred CCCEEEEEEEEeC-CCcceEEEee
Q 028346 133 PGDIVRASVLSLG-DARAYFLSTA 155 (210)
Q Consensus 133 ~GDiV~AkV~s~~-d~~~~~LSt~ 155 (210)
+||.|...|..-. .++...||++
T Consensus 96 ~GqeILVQV~KEa~gtKGp~LTt~ 119 (1068)
T PRK10811 96 EGQEVIVQIDKEERGNKGAALTTF 119 (1068)
T ss_pred CCCEEEEEEeecccCCCCCceeee
Confidence 9999999999853 2233445443
No 105
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=92.73 E-value=0.19 Score=46.91 Aligned_cols=62 Identities=8% Similarity=-0.000 Sum_probs=38.4
Q ss_pred cCCCCCCCCEEEEEEEEeCCC---cceEEEeecCCceeeEEEc-CCCCeeEEcccceEEecccchhh
Q 028346 127 MHLSFRPGDIVRASVLSLGDA---RAYFLSTAKNDLGVVSAES-TAGKLVYCISKYDLNIILFYSFW 189 (210)
Q Consensus 127 ~~~~~~~GDiV~AkV~s~~d~---~~~~LSt~~~~LGVv~a~~-~~G~~m~~~~~~~l~C~~~~~~~ 189 (210)
+-..+.+||.|.+-=.--... ..+++..-.. +-...-+| .||+.|.-.+.+-++|+.|+++.
T Consensus 312 ~a~~L~pGD~i~~~G~~~~~~~n~ek~~v~~l~~-~~~~~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~ 377 (421)
T COG1571 312 LARKLIPGDEITVYGSVKPGTLNLEKFQVLKLAR-YERVNPVCPRCGGRMKSAGRNGFRCKKCGTRA 377 (421)
T ss_pred HHHhcCCCCEEEEecCccccceeEEEEEEEEeee-eEEcCCCCCccCCchhhcCCCCcccccccccC
Confidence 335678999986421100000 1122222222 55555689 99999988887799999999874
No 106
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=91.86 E-value=1.6 Score=29.54 Aligned_cols=60 Identities=17% Similarity=0.080 Sum_probs=31.1
Q ss_pred CCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEEEe
Q 028346 76 PGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLST 154 (210)
Q Consensus 76 vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LSt 154 (210)
+|+++..+|++.++..|+++- ...-+-.||.++.. .-+++||.|.+-|=- +..+.+..||
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~--------~~~~~vlLp~~e~~----------~~~~~Gd~v~VFvY~-D~~~rl~AT~ 60 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDD--------GEGKEVLLPKSEVP----------EPLKVGDEVEVFVYL-DKEGRLVATT 60 (61)
T ss_dssp --------EEEE-SSEEEEEE--------TT-EEEEEEGGG----------------TTSEEEEEEEE--TTS-EEEE-
T ss_pred CCCCcceEEEEEeCCEEEEEC--------CCCCEEEechHHcC----------CCCCCCCEEEEEEEE-CCCCCEEEec
Confidence 589999999999999999987 55567777766543 347899999988764 2223444444
No 107
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=91.68 E-value=0.97 Score=37.02 Aligned_cols=85 Identities=20% Similarity=0.071 Sum_probs=51.6
Q ss_pred CCCCCCCEEEEEEEEEecCeEEEEEeeecccccc------CceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeC
Q 028346 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR------EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG 145 (210)
Q Consensus 72 y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~------~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~ 145 (210)
..|-.|++|-|.|+++....+++++...+--.++ ..|. +-++-. .... .+.+ ..+.|+.|+.+|+...
T Consensus 77 FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~---p~~n~P-~f~~-~d~s-~I~~~~~VR~kiigtr 150 (170)
T KOG3298|consen 77 FKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFD---PGENPP-NFQT-EDES-VIQKGVEVRLKIIGTR 150 (170)
T ss_pred EeecCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccC---CCCCCC-cccc-cccc-eeeeCcEEEEEEEEEE
Confidence 4577899999999999999999999644332111 1122 222211 1111 1233 6899999999999873
Q ss_pred -CCcce-E-EEeecCCceee
Q 028346 146 -DARAY-F-LSTAKNDLGVV 162 (210)
Q Consensus 146 -d~~~~-~-LSt~~~~LGVv 162 (210)
+...+ . =|+.++-||.+
T Consensus 151 ~~~~~i~algtl~~D~LG~i 170 (170)
T KOG3298|consen 151 VDETEIFALGTLKGDYLGPI 170 (170)
T ss_pred EeeeeEEEEEEecCcccccC
Confidence 33333 3 35556666753
No 108
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=90.50 E-value=0.2 Score=29.65 Aligned_cols=25 Identities=4% Similarity=-0.262 Sum_probs=14.9
Q ss_pred Ec-CCCCeeEEccc-ceEEecccchhh
Q 028346 165 ES-TAGKLVYCISK-YDLNIILFYSFW 189 (210)
Q Consensus 165 ~~-~~G~~m~~~~~-~~l~C~~~~~~~ 189 (210)
.| +||++|.+..+ ..++||.|+...
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-EE
T ss_pred ccCcCCccccCCCCcCEeECCCCcCEe
Confidence 47 89999987743 499999998764
No 109
>PF01016 Ribosomal_L27: Ribosomal L27 protein; InterPro: IPR001684 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. L27 is a protein from the large (50S) subunit; it is essential for ribosome function, but its exact role is unclear. It belongs to a family of ribosomal proteins, examples of which are found in bacteria, chloroplasts of plants and red algae and the mitochondria of fungi (e.g. MRP7 from yeast mitochondria). The schematic relationship between these groups of proteins is shown below. Bacterial L27 Nxxxxxxxxx Algal L27 Nxxxxxxxxx Plant L27 tttttNxxxxxxxxxxxxx Yeast MRP7 tttNxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 't': transit peptide. 'N': N-terminal of mature protein. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZJQ_T 2ZJP_T 3PIP_T 3DLL_T 3PIO_T 1Y69_U 3CF5_T 2ZJR_T 1VSA_U 3PYT_W ....
Probab=89.42 E-value=0.5 Score=34.37 Aligned_cols=44 Identities=18% Similarity=0.352 Sum_probs=35.8
Q ss_pred ccCCceEEecCCccCC--CCCeeeCCcEEEe-CCeeEEEEeEeeeEEEc
Q 028346 4 KEEEMVLVTPGEVLGK--ATEVKAGKGAYVA-KHNGLVYASLTGLLRTL 49 (210)
Q Consensus 4 ~~~~~~iV~PGd~l~~--~ee~~~G~GtY~~-~g~~~I~Asv~G~v~~~ 49 (210)
|.-+.+.|.||+.|.. -..|.||.++... |.. |+|..-|.|..+
T Consensus 23 K~~~G~~V~~G~IivRQRgtk~hPG~NVg~GrD~T--LfAl~~G~V~f~ 69 (81)
T PF01016_consen 23 KKFGGQFVKAGNIIVRQRGTKFHPGENVGMGRDHT--LFALVDGRVKFT 69 (81)
T ss_dssp SSSTTCEESSTSEEEEBSSSSSEEBTTEEEETTSE--EEESSSCEEEEE
T ss_pred EEeCCEEEcCCCEEEEeCCCcCcCCCCEEECCCCc--EEEecCEEEEEE
Confidence 4456788999999864 2459999999886 666 999999999885
No 110
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=89.15 E-value=0.2 Score=32.20 Aligned_cols=28 Identities=11% Similarity=-0.167 Sum_probs=22.1
Q ss_pred EEc-CCCCeeEEcccceEEecccchhhhH
Q 028346 164 AES-TAGKLVYCISKYDLNIILFYSFWIF 191 (210)
Q Consensus 164 a~~-~~G~~m~~~~~~~l~C~~~~~~~~~ 191 (210)
-+| .||........+.+.||.|++|-|+
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~rIly 31 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGYRILY 31 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCceEEE
Confidence 368 8999865555679999999998764
No 111
>CHL00121 rpl27 ribosomal protein L27; Reviewed
Probab=89.10 E-value=0.79 Score=33.63 Aligned_cols=58 Identities=19% Similarity=0.280 Sum_probs=40.8
Q ss_pred ccCCceEEecCCccCCC--CCeeeCCcEEEe-CCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecC
Q 028346 4 KEEEMVLVTPGEVLGKA--TEVKAGKGAYVA-KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH 67 (210)
Q Consensus 4 ~~~~~~iV~PGd~l~~~--ee~~~G~GtY~~-~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~ 67 (210)
|.-+.+.|.||+.|..- ..|.||.++-.- |.. |+|...|.|+.... ...++.|+|.|.
T Consensus 24 K~~~gq~V~~G~IivRQRGtk~hPG~NVg~GrD~T--lfAl~~G~V~f~~~----~~~~~~vsv~~~ 84 (86)
T CHL00121 24 KRFGGEKVSAGNILIRQRGTKFKPGLNVGCGKDFT--LYALIDGFVKFKKK----NKKQKSINVINI 84 (86)
T ss_pred EEcCCEEEcCCcEEEEcCCCeECCCCcccccCCce--EEEccceEEEEEEe----CCCCEEEEEeec
Confidence 34466889999988642 358999988654 656 99999999998521 123446777764
No 112
>PRK05054 exoribonuclease II; Provisional
Probab=88.28 E-value=2.9 Score=41.14 Aligned_cols=71 Identities=11% Similarity=0.228 Sum_probs=51.0
Q ss_pred CCCC--EEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccc---c-c--c--cccc--CCCCCCCCEEEEEEE
Q 028346 75 EPGS--VVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT---E-I--D--KVDM--HLSFRPGDIVRASVL 142 (210)
Q Consensus 75 ~vGD--iViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~---~-~--d--~~~~--~~~~~~GDiV~AkV~ 142 (210)
++|+ ...|.|+.++..+.+|+|. ....+|++|.+.+... + - + ...+ ...|+.||-|+.+|.
T Consensus 558 ~~G~~~~f~g~I~~v~~~G~fV~l~-------~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~ 630 (644)
T PRK05054 558 KAGTDTRFAAEIIDISRGGMRVRLL-------ENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLA 630 (644)
T ss_pred ccCCCeEEEEEEEeeecCcEEEEEe-------CCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEE
Confidence 4554 9999999999999999993 3568899999887531 1 0 1 0111 247999999999999
Q ss_pred EeCC-CcceEE
Q 028346 143 SLGD-ARAYFL 152 (210)
Q Consensus 143 s~~d-~~~~~L 152 (210)
+++. .+.+..
T Consensus 631 ~vd~~~~~i~~ 641 (644)
T PRK05054 631 EVRMETRSIIA 641 (644)
T ss_pred EEccccCeEEE
Confidence 9974 344443
No 113
>PRK05435 rpmA 50S ribosomal protein L27; Validated
Probab=88.18 E-value=1.3 Score=32.30 Aligned_cols=44 Identities=18% Similarity=0.311 Sum_probs=34.9
Q ss_pred ccCCceEEecCCccCCC--CCeeeCCcEEEe-CCeeEEEEeEeeeEEEc
Q 028346 4 KEEEMVLVTPGEVLGKA--TEVKAGKGAYVA-KHNGLVYASLTGLLRTL 49 (210)
Q Consensus 4 ~~~~~~iV~PGd~l~~~--ee~~~G~GtY~~-~g~~~I~Asv~G~v~~~ 49 (210)
|.-+.+.|.||..|..- ..|.||.++-.- |.. |+|.+.|.|+..
T Consensus 24 K~~~g~~V~~G~IivRQRGtk~~PG~nVg~GrD~T--lfA~~~G~V~f~ 70 (82)
T PRK05435 24 KRFGGQFVKAGNIIVRQRGTKFHPGVNVGRGKDHT--LFALVDGVVKFE 70 (82)
T ss_pred EecCCEEEcCCcEEEEeCCCeECCCCCEeecCCce--EEEecceEEEEE
Confidence 34456889999988642 359999999875 666 999999999985
No 114
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=86.64 E-value=0.4 Score=26.96 Aligned_cols=20 Identities=5% Similarity=-0.130 Sum_probs=17.3
Q ss_pred CCCCeeEEcc-cceEEecccc
Q 028346 167 TAGKLVYCIS-KYDLNIILFY 186 (210)
Q Consensus 167 ~~G~~m~~~~-~~~l~C~~~~ 186 (210)
.||..|.|.. ...+.||.|+
T Consensus 3 sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 3 SCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred cCCCcccCcccCceEeCCCCC
Confidence 7899998876 6799999997
No 115
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=85.05 E-value=1.9 Score=41.10 Aligned_cols=64 Identities=19% Similarity=0.259 Sum_probs=50.5
Q ss_pred CCCCCEEEEEEEEEecCe--EEEEEeeeccccccCceeEEEecccccccccc--ccccCCCCCCCCEEEEEEEEeC
Q 028346 74 PEPGSVVIARVTKVMTRM--ASADIMCVGAKSVREKFSGIIRQQDVRATEID--KVDMHLSFRPGDIVRASVLSLG 145 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~--a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d--~~~~~~~~~~GDiV~AkV~s~~ 145 (210)
-.+|++-.|+|++|-+.+ |+||| ...-.|+||.+++.+.... ...++..++.|+.+...|..-.
T Consensus 35 ~~~gniy~grv~~i~p~~~aafvdi--------g~~r~gfl~~~~~~~~~~~~~~~~i~~~lr~~~~~~Vqv~ke~ 102 (487)
T COG1530 35 QIVGNIYKGRVTRVLPSLEAAFVDI--------GLERNGFLHLSEIVPYFRAVLEEKIKVRLRGGQATLVQVVKEP 102 (487)
T ss_pred eeecCceEEEecccCccchhheeec--------cCCccceEEecccchhhhhcccccceeeecCCceEEEEEEeec
Confidence 468999999999998876 99999 5677899999998752111 1135678999999999999864
No 116
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=83.85 E-value=1.8 Score=31.17 Aligned_cols=61 Identities=15% Similarity=0.120 Sum_probs=36.2
Q ss_pred CCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecC---eEEEEEeeecccc
Q 028346 33 KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTR---MASADIMCVGAKS 103 (210)
Q Consensus 33 ~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V~~v~~~---~a~V~I~~v~~~~ 103 (210)
+|.|.++++..|.... ..-|+|-|..-+++-++.||.|.|.|..-++. .+.+.|.+|++.+
T Consensus 12 dGyGFLR~~~~~y~~~----------~~DvYVs~~qIrrf~LR~GD~V~G~vr~p~~~ek~~aL~~V~~VNg~~ 75 (78)
T PF07497_consen 12 DGYGFLRSPDNNYLPS----------PDDVYVSPSQIRRFGLRTGDLVEGQVRPPREGEKYFALLRVESVNGRP 75 (78)
T ss_dssp TS-EEEE-GGGTTS-S----------TTSEEE-CCCCCCTT--TTEEEEEEEE--STTSSSEEECEECEETTEC
T ss_pred CCcEEeECCCcCCCCC----------CCCEEECHHHHHHcCCCCCCEEEEEEeCCCCCCcceeeEEEEeECCcC
Confidence 4455566655454432 12488888766788899999999999987643 3777777776643
No 117
>TIGR00062 L27 ribosomal protein L27. Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.
Probab=83.25 E-value=2.3 Score=31.09 Aligned_cols=44 Identities=18% Similarity=0.349 Sum_probs=34.7
Q ss_pred ccCCceEEecCCccCCC--CCeeeCCcEEEe-CCeeEEEEeEeeeEEEc
Q 028346 4 KEEEMVLVTPGEVLGKA--TEVKAGKGAYVA-KHNGLVYASLTGLLRTL 49 (210)
Q Consensus 4 ~~~~~~iV~PGd~l~~~--ee~~~G~GtY~~-~g~~~I~Asv~G~v~~~ 49 (210)
|.-+.+.|.||+.|..- ..|.||.++-.- |.. |+|.+.|.|...
T Consensus 24 K~~~gq~V~~G~IivRQRGtk~hPG~nVg~GrD~T--lfAl~~G~V~f~ 70 (83)
T TIGR00062 24 KRAGGQFVRAGSIIVRQRGTKFHPGNNVGMGKDHT--LFALSDGVVKFE 70 (83)
T ss_pred EecCCEEEcCCcEEEEcCCceECCCCcccccCCCe--EEEecceEEEEE
Confidence 34456889999988642 359999998764 666 999999999884
No 118
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=82.82 E-value=6.6 Score=39.06 Aligned_cols=74 Identities=16% Similarity=0.092 Sum_probs=53.9
Q ss_pred CCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccc---------cccccCCCCCCCCEEEEEEEEeC
Q 028346 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI---------DKVDMHLSFRPGDIVRASVLSLG 145 (210)
Q Consensus 75 ~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~---------d~~~~~~~~~~GDiV~AkV~s~~ 145 (210)
++|+.-.|.|+++...+++|.+. ....+|.+|++.+...+- ........++.||.|+++|.+++
T Consensus 621 ~vg~~f~g~V~~v~~~g~~V~l~-------~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~ 693 (706)
T COG0557 621 RVGEEFDGVVTGVTSFGFFVELP-------ELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVD 693 (706)
T ss_pred hcCCEEEEEEEEEEeccEEEEec-------ccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEc
Confidence 67899999999999999999993 234788888887762110 11134457999999999999986
Q ss_pred C-CcceEEEee
Q 028346 146 D-ARAYFLSTA 155 (210)
Q Consensus 146 d-~~~~~LSt~ 155 (210)
. .+.+.++..
T Consensus 694 ~~~~~i~~~~v 704 (706)
T COG0557 694 LDERKIDFELV 704 (706)
T ss_pred ccccceEEEec
Confidence 3 345555543
No 119
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=82.50 E-value=0.22 Score=29.91 Aligned_cols=26 Identities=8% Similarity=-0.208 Sum_probs=18.5
Q ss_pred Ec-CCCCeeEEcccceEEecccchhhh
Q 028346 165 ES-TAGKLVYCISKYDLNIILFYSFWI 190 (210)
Q Consensus 165 ~~-~~G~~m~~~~~~~l~C~~~~~~~~ 190 (210)
.| +||....-...+.++|+.|+.|-|
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~RIl 28 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGHRIL 28 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-SEE
T ss_pred CCCcCCCeeEcCCCCcEECCcCCCeEE
Confidence 36 899886544557899999999865
No 120
>PF01959 DHQS: 3-dehydroquinate synthase (EC 4.6.1.3); InterPro: IPR002812 3-Dehydroquinate synthase (4.2.3.4 from EC) is an enzyme in the common pathway of aromatic amino acid biosynthesis that catalyses the conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) into 3-dehydroquinic acid []. This synthesis of aromatic amino acids is an essential metabolic function for most prokaryotic as well as lower eukaryotic cells, including plants. The pathway is absent in humans; therefore, DHQS represents a potential target for the development of novel and selective antimicrobial agents. Owing to the threat posed by the spread of pathogenic bacteria resistant to many currently used antimicrobial drugs, there is clearly a need to develop new anti-infective drugs acting at novel targets. A further potential use for DHQS inhibitors is as herbicides [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process
Probab=80.57 E-value=19 Score=33.12 Aligned_cols=96 Identities=18% Similarity=0.386 Sum_probs=64.3
Q ss_pred EEecCCccCCCCCeeeCCcEEEeCCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEec
Q 028346 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMT 89 (210)
Q Consensus 10 iV~PGd~l~~~ee~~~G~GtY~~~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V~~v~~ 89 (210)
+..||+.=...+|..+|.-+..-+..|.-+..++|++++. +++.+.|+-.. -| -++.-+-.
T Consensus 246 v~~pg~kT~YLSEL~sG~~VlvVd~~G~tR~~~VGRvKIE--------~RPLllIeA~~-------~g----~~~svilQ 306 (354)
T PF01959_consen 246 VLMPGGKTRYLSELRSGDEVLVVDADGRTRTAIVGRVKIE--------RRPLLLIEAEA-------DG----KRISVILQ 306 (354)
T ss_pred EEcCCCceeehhhhcCCCEEEEEeCCCCEEEEEeeEEEEe--------ecceEEEEEEe-------CC----eEEEEEEe
Confidence 4678888777788888888765533333999999999984 56677776321 12 23334567
Q ss_pred CeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC
Q 028346 90 RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD 146 (210)
Q Consensus 90 ~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d 146 (210)
+-|.|.+...++.+++ + -.++|||.|.+++..-+.
T Consensus 307 naetIRlv~p~G~~vs----------------V------t~Lk~GD~vL~~~~~~~R 341 (354)
T PF01959_consen 307 NAETIRLVGPDGEPVS----------------V------TELKPGDEVLVYLEEAGR 341 (354)
T ss_pred cCcEEEEECCCCCEee----------------e------eecCCCCEEEEEecCCCc
Confidence 7899999654433222 1 237899999999987543
No 121
>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=79.16 E-value=9.6 Score=29.64 Aligned_cols=69 Identities=19% Similarity=0.175 Sum_probs=38.1
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeecccc-----ccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEe
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKS-----VREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSL 144 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~-----l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~ 144 (210)
|-+|+++.|+|.+.+.++..|.+...++-- |..+ ...=+.+++=-...+ .+-.-++..|+.|+=||.+.
T Consensus 1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~p-s~fd~~~~~W~W~~~-~~~~l~~d~ge~IRFRV~~~ 74 (122)
T PF08292_consen 1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEP-SRFDEEEQAWVWEYD-EEQELFFDIGEEIRFRVESE 74 (122)
T ss_dssp --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TT-EEEECCCTEEEEEES-SSEEEEE-TT-EEEEEEEEE
T ss_pred CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCC-CccCccCCEEEEECC-CCceeEccCCCEEEEEEeEE
Confidence 568999999999999999999996555521 1110 011011111000010 13335679999999999986
No 122
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=78.67 E-value=2.9 Score=37.78 Aligned_cols=58 Identities=14% Similarity=0.200 Sum_probs=40.6
Q ss_pred CCCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC
Q 028346 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD 146 (210)
Q Consensus 71 ~y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d 146 (210)
.-..++||.|..+|.++....-.+++ + ..++...... .....|+.|+.|.++|..+-+
T Consensus 61 ~d~vkvGd~v~vkVl~VD~ekg~IdL--------S--------~K~v~~~pw~--~~~e~~~~g~~v~~~V~~ia~ 118 (319)
T PTZ00248 61 NKLIRVGRHEVVVVLRVDKEKGYIDL--------S--------KKRVSPEDIE--ACEEKFSKSKKVHSIMRHIAQ 118 (319)
T ss_pred HHhcCCCCEEEEEEEEEeCCCCEEEE--------E--------eeecccchHH--HHHHhCcCCCEEEEEEEEchh
Confidence 34579999999999999776655665 1 1122222212 456789999999999999843
No 123
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=78.34 E-value=22 Score=32.52 Aligned_cols=93 Identities=18% Similarity=0.378 Sum_probs=62.8
Q ss_pred EEecCCccCCCCCeeeCCcEEEe--CCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEE
Q 028346 10 LVTPGEVLGKATEVKAGKGAYVA--KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKV 87 (210)
Q Consensus 10 iV~PGd~l~~~ee~~~G~GtY~~--~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V~~v 87 (210)
+..||+.=...+|...|.-+-.- +|+ -+..++|++++. +++.+-|+-. + -| -++.-+
T Consensus 236 v~~pgg~T~YLsEL~sG~eVlvVd~~G~--tR~~~VGRvKIE--------~RPL~lIeAe----~---~g----~~~~vi 294 (344)
T PRK02290 236 VRVPGDKTRYLSELRSGDEVLVVDADGN--TREAIVGRVKIE--------KRPLLLIEAE----Y---GG----KRIRTI 294 (344)
T ss_pred EEcCCCcchhhHhhcCCCEEEEEeCCCC--EEEEEeeEEEEe--------eccEEEEEEE----e---CC----eEEEEE
Confidence 46789987777888888887654 566 999999999984 4566666632 1 12 233344
Q ss_pred ecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeC
Q 028346 88 MTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG 145 (210)
Q Consensus 88 ~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~ 145 (210)
-.+-+.+.+...++++++ + -.++|||.|.+++...+
T Consensus 295 LQnaetIrlv~~dG~~vs----------------V------t~Lk~GD~VL~~~~~~~ 330 (344)
T PRK02290 295 LQNAETIRLVTPDGKPVS----------------V------VDLKPGDEVLGYLEEAA 330 (344)
T ss_pred EecCcEEEEECCCCCEee----------------e------eecCCCCEEEEEecCCc
Confidence 577788888543332221 1 23789999999998644
No 124
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=78.28 E-value=1.3 Score=28.60 Aligned_cols=25 Identities=4% Similarity=-0.274 Sum_probs=19.3
Q ss_pred Ec-CCCCeeEEccc---ceEEecccchhh
Q 028346 165 ES-TAGKLVYCISK---YDLNIILFYSFW 189 (210)
Q Consensus 165 ~~-~~G~~m~~~~~---~~l~C~~~~~~~ 189 (210)
.| .||..|.+..+ +.+.||.|+..+
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 37 89998877654 379999999654
No 125
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=78.27 E-value=1.5 Score=27.87 Aligned_cols=28 Identities=11% Similarity=-0.092 Sum_probs=20.5
Q ss_pred EEc-CCCCeeEEcccc-eEEecccchhhhH
Q 028346 164 AES-TAGKLVYCISKY-DLNIILFYSFWIF 191 (210)
Q Consensus 164 a~~-~~G~~m~~~~~~-~l~C~~~~~~~~~ 191 (210)
-+| .||..+...... .+.||.|+++.++
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 468 899987444333 7999999987664
No 126
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=78.25 E-value=1.3 Score=34.99 Aligned_cols=23 Identities=4% Similarity=-0.081 Sum_probs=19.1
Q ss_pred Ec-CCCCeeEEcccceEEecccchh
Q 028346 165 ES-TAGKLVYCISKYDLNIILFYSF 188 (210)
Q Consensus 165 ~~-~~G~~m~~~~~~~l~C~~~~~~ 188 (210)
.| +||.|+.... .++.||+|.++
T Consensus 30 hCp~Cg~PLF~Kd-G~v~CPvC~~~ 53 (131)
T COG1645 30 HCPKCGTPLFRKD-GEVFCPVCGYR 53 (131)
T ss_pred hCcccCCcceeeC-CeEECCCCCce
Confidence 36 9999998855 59999999964
No 127
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=77.94 E-value=2.1 Score=29.23 Aligned_cols=30 Identities=3% Similarity=-0.229 Sum_probs=24.6
Q ss_pred eEEEc-CCCCeeEEcccceEEecccchhhhH
Q 028346 162 VSAES-TAGKLVYCISKYDLNIILFYSFWIF 191 (210)
Q Consensus 162 v~a~~-~~G~~m~~~~~~~l~C~~~~~~~~~ 191 (210)
+.-.| .||......+.+.++|.+|+.|-|+
T Consensus 19 miYiCgdC~~en~lk~~D~irCReCG~RIly 49 (62)
T KOG3507|consen 19 MIYICGDCGQENTLKRGDVIRCRECGYRILY 49 (62)
T ss_pred EEEEeccccccccccCCCcEehhhcchHHHH
Confidence 44468 8998876667789999999999876
No 128
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=77.00 E-value=1.2 Score=29.95 Aligned_cols=27 Identities=7% Similarity=-0.262 Sum_probs=21.8
Q ss_pred EEc-CCCCeeEEcccceEEecccchhhhH
Q 028346 164 AES-TAGKLVYCISKYDLNIILFYSFWIF 191 (210)
Q Consensus 164 a~~-~~G~~m~~~~~~~l~C~~~~~~~~~ 191 (210)
.+| .||.++.+.+ +.+.||.|++.|--
T Consensus 6 ~~C~~Cg~~~~~~d-DiVvCp~CgapyHR 33 (54)
T PF14446_consen 6 CKCPVCGKKFKDGD-DIVVCPECGAPYHR 33 (54)
T ss_pred ccChhhCCcccCCC-CEEECCCCCCcccH
Confidence 467 8999987655 79999999998754
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=76.33 E-value=10 Score=37.30 Aligned_cols=65 Identities=9% Similarity=0.176 Sum_probs=48.2
Q ss_pred CCC--CEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccc---c-cc--c--cccC--CCCCCCCEEEEEEE
Q 028346 75 EPG--SVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT---E-ID--K--VDMH--LSFRPGDIVRASVL 142 (210)
Q Consensus 75 ~vG--DiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~---~-~d--~--~~~~--~~~~~GDiV~AkV~ 142 (210)
++| ..--|.|++++..+.+|++. .....|++|.+.+... + -+ . ..+. ..|+.||-|+.+|.
T Consensus 554 ~~g~~~~f~g~I~~v~~~g~~v~l~-------~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~ 626 (639)
T TIGR02062 554 KAAKNTRFAAEIVDISRGGMRVRLL-------ENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLT 626 (639)
T ss_pred ccCCCcEEEEEEEeeeCCcEEEEEe-------cCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEE
Confidence 454 48999999999999999994 4568999998887541 1 01 1 1221 25999999999999
Q ss_pred EeCC
Q 028346 143 SLGD 146 (210)
Q Consensus 143 s~~d 146 (210)
+++.
T Consensus 627 ~vd~ 630 (639)
T TIGR02062 627 EVRM 630 (639)
T ss_pred Eecc
Confidence 9973
No 130
>PRK00420 hypothetical protein; Validated
Probab=74.83 E-value=1.8 Score=33.38 Aligned_cols=27 Identities=7% Similarity=0.134 Sum_probs=21.5
Q ss_pred EEc-CCCCeeEEcccceEEecccchhhh
Q 028346 164 AES-TAGKLVYCISKYDLNIILFYSFWI 190 (210)
Q Consensus 164 a~~-~~G~~m~~~~~~~l~C~~~~~~~~ 190 (210)
..| .||.++.........||.|+....
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCeee
Confidence 467 899999874556999999998554
No 131
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=74.29 E-value=2.7 Score=36.23 Aligned_cols=61 Identities=15% Similarity=0.068 Sum_probs=49.1
Q ss_pred CCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCC
Q 028346 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA 147 (210)
Q Consensus 72 y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~ 147 (210)
..|++||+..|.|-.++++..-+-| ..-|.+.|+..++.+.- .++..+|...++|..++++
T Consensus 103 f~Pk~Gd~LeG~Vn~vS~sHIglLI--------hg~FNASIpk~nip~dw-------~fI~md~eee~~v~ntD~g 163 (253)
T KOG4134|consen 103 FRPKAGDILEGVVNHVSRSHIGLLI--------HGVFNASIPKTNIPADW-------EFIAMDQEEEIRVKNTDIG 163 (253)
T ss_pred ECCCCCCeeeeeeeecchhhhceee--------hhhhhccCCCCCCccce-------eeecCCchhhhceeecccc
Confidence 4599999999999999999888888 45677878777654322 4678999999999999754
No 132
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=74.21 E-value=1.4 Score=39.06 Aligned_cols=27 Identities=7% Similarity=-0.199 Sum_probs=22.6
Q ss_pred Ec-CCCCeeEEcc-cceEEecccchhhhH
Q 028346 165 ES-TAGKLVYCIS-KYDLNIILFYSFWIF 191 (210)
Q Consensus 165 ~~-~~G~~m~~~~-~~~l~C~~~~~~~~~ 191 (210)
.| +||++|.+.. ...++||.|++..++
T Consensus 113 FCg~CG~~~~~~~~g~~~~C~~cg~~~fP 141 (279)
T COG2816 113 FCGRCGTKTYPREGGWARVCPKCGHEHFP 141 (279)
T ss_pred CCCCCCCcCccccCceeeeCCCCCCccCC
Confidence 37 8999998773 349999999999987
No 133
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=72.93 E-value=5.5 Score=30.14 Aligned_cols=36 Identities=11% Similarity=-0.092 Sum_probs=29.4
Q ss_pred CCceeeEEEc-CCCCeeEEcccceEEecccchhhhHH
Q 028346 157 NDLGVVSAES-TAGKLVYCISKYDLNIILFYSFWIFC 192 (210)
Q Consensus 157 ~~LGVv~a~~-~~G~~m~~~~~~~l~C~~~~~~~~~~ 192 (210)
..+++.+.-| -||..-+-...+.|.|..|..+|.+=
T Consensus 29 g~~~va~daCeiC~~~GY~q~g~~lvC~~C~~~~~~~ 65 (102)
T PF10080_consen 29 GSYRVAFDACEICGPKGYYQEGDQLVCKNCGVRFNLP 65 (102)
T ss_pred CCEEEEEEeccccCCCceEEECCEEEEecCCCEEehh
Confidence 4567888889 89876666777899999999999874
No 134
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=71.35 E-value=10 Score=37.20 Aligned_cols=67 Identities=16% Similarity=0.198 Sum_probs=54.8
Q ss_pred CCCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCC-cc
Q 028346 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA-RA 149 (210)
Q Consensus 71 ~y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~-~~ 149 (210)
..-.+.|.+=.|.|+++....+++++ ++...|++|.++... + .-|.+||.+..+|.++.+. +.
T Consensus 117 ~~Dve~g~~Y~g~v~~v~~~GvFv~L--------n~~v~GL~~~~d~~~---~-----~~~~vgdeiiV~v~~vr~~~ge 180 (715)
T COG1107 117 MEDVEAGKYYKGIVSRVEKYGVFVEL--------NSHVRGLIHRRDLGG---D-----PDYAVGDEIIVQVSDVRPEKGE 180 (715)
T ss_pred hhhcccceeeeccccchhhhcceeec--------ChhhhccccccccCC---C-----CCCCCCCeEEEEeeccCCCCCc
Confidence 45568899999999999999999999 888999999988764 1 5588999999999998654 44
Q ss_pred eEEE
Q 028346 150 YFLS 153 (210)
Q Consensus 150 ~~LS 153 (210)
+.+.
T Consensus 181 idf~ 184 (715)
T COG1107 181 IDFE 184 (715)
T ss_pred ccee
Confidence 4333
No 135
>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=71.18 E-value=27 Score=26.59 Aligned_cols=53 Identities=23% Similarity=0.339 Sum_probs=42.6
Q ss_pred CCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEe
Q 028346 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSL 144 (210)
Q Consensus 75 ~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~ 144 (210)
..|-+|+|+|..+-++-..+|. ...|.++.+..... .+.+..|+-|+.++.+.
T Consensus 22 ~~gk~V~G~I~hvv~ddLYIDf--------G~KFhcVc~rp~~~---------~~~y~~G~rV~lrLkdl 74 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDDDLYIDF--------GGKFHCVCKRPAVN---------GEKYVRGSRVRLRLKDL 74 (104)
T ss_pred ccCCEEEEEEEEEecCceEEEe--------CCceeEEEeccccc---------ccccccCCEEEEEECCH
Confidence 3688999999999999999999 67888887654321 14578899999999875
No 136
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=70.69 E-value=2.2 Score=31.64 Aligned_cols=25 Identities=8% Similarity=-0.380 Sum_probs=20.6
Q ss_pred Ec-CCCCeeEEcccceEEecccchhhh
Q 028346 165 ES-TAGKLVYCISKYDLNIILFYSFWI 190 (210)
Q Consensus 165 ~~-~~G~~m~~~~~~~l~C~~~~~~~~ 190 (210)
.| .||..|.|.+ +.+.|+.|+..+-
T Consensus 2 fC~~Cg~~l~~~~-~~~~C~~C~~~~~ 27 (104)
T TIGR01384 2 FCPKCGSLMTPKN-GVYVCPSCGYEKE 27 (104)
T ss_pred CCcccCcccccCC-CeEECcCCCCccc
Confidence 47 8999999876 6899999997643
No 137
>KOG4600 consensus Mitochondrial ribosomal protein MRP7 (L2) [Translation, ribosomal structure and biogenesis]
Probab=69.72 E-value=13 Score=29.61 Aligned_cols=61 Identities=20% Similarity=0.268 Sum_probs=41.2
Q ss_pred ccCCceEEecCCccCCCC--CeeeCCcEEEe-CCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCC
Q 028346 4 KEEEMVLVTPGEVLGKAT--EVKAGKGAYVA-KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHK 68 (210)
Q Consensus 4 ~~~~~~iV~PGd~l~~~e--e~~~G~GtY~~-~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~ 68 (210)
|+.+.+.|.||+.|..-- .|-||.++=.- |. .|||-.-|.|+......+- .++.|.|.|..
T Consensus 51 Kk~egq~V~~G~IIvrQRgtkfHPG~nVGiGKDh--tifaL~eG~Vrf~k~~~~~--~Rk~i~V~~~~ 114 (144)
T KOG4600|consen 51 KKYEGQSVIPGNIIVRQRGTKFHPGDNVGIGKDH--TIFALEEGRVRFEKSKITP--PRKWIGVDPRG 114 (144)
T ss_pred eecCCeeeecccEEEEecccccCCCcccccCCcc--eEEEeeccEEEEEEccCCC--CcceEEEeecC
Confidence 455668899999987533 36777666443 44 4999999999986432221 35678888754
No 138
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=69.52 E-value=2.6 Score=24.87 Aligned_cols=25 Identities=12% Similarity=-0.110 Sum_probs=14.0
Q ss_pred Ec-CCCCeeEEcccceEEecccchhh
Q 028346 165 ES-TAGKLVYCISKYDLNIILFYSFW 189 (210)
Q Consensus 165 ~~-~~G~~m~~~~~~~l~C~~~~~~~ 189 (210)
.| .|+..-.-.+...|.||.|++-|
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCPECGHEW 29 (30)
T ss_dssp --TTT-----EE-SSSEEETTTTEEE
T ss_pred CCCCCCCcceeccCCEEeCCcccccC
Confidence 56 78876544566899999999866
No 139
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=68.76 E-value=0.88 Score=34.54 Aligned_cols=29 Identities=7% Similarity=-0.172 Sum_probs=20.2
Q ss_pred Ec-CCCCeeEEcccc-eEEecccchhhhHHH
Q 028346 165 ES-TAGKLVYCISKY-DLNIILFYSFWIFCI 193 (210)
Q Consensus 165 ~~-~~G~~m~~~~~~-~l~C~~~~~~~~~~~ 193 (210)
+| +||..--..+.. .=-||.|+.++|+|.
T Consensus 4 ~CtrCG~vf~~g~~~il~GCp~CG~nkF~yv 34 (112)
T COG3364 4 QCTRCGEVFDDGSEEILSGCPKCGCNKFLYV 34 (112)
T ss_pred eecccccccccccHHHHccCccccchheEec
Confidence 57 899875443322 224999999999874
No 140
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=68.31 E-value=2.1 Score=28.19 Aligned_cols=28 Identities=11% Similarity=-0.059 Sum_probs=21.2
Q ss_pred EEc-CCCCeeE-EcccceEEecccchhhhH
Q 028346 164 AES-TAGKLVY-CISKYDLNIILFYSFWIF 191 (210)
Q Consensus 164 a~~-~~G~~m~-~~~~~~l~C~~~~~~~~~ 191 (210)
-+| +||.... ........||.|+++-|+
T Consensus 7 Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~ 36 (49)
T COG1996 7 YKCARCGREVELDQETRGIRCPYCGSRILV 36 (49)
T ss_pred EEhhhcCCeeehhhccCceeCCCCCcEEEE
Confidence 468 8998864 334568999999998764
No 141
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=67.16 E-value=1.7 Score=35.62 Aligned_cols=31 Identities=3% Similarity=-0.122 Sum_probs=25.2
Q ss_pred eeEEEc-CCCCeeEEcccceEE----------------ecccchhhhH
Q 028346 161 VVSAES-TAGKLVYCISKYDLN----------------IILFYSFWIF 191 (210)
Q Consensus 161 Vv~a~~-~~G~~m~~~~~~~l~----------------C~~~~~~~~~ 191 (210)
--+++| .|++++.+++..+.. ||.|+.-|..
T Consensus 95 ~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~ 142 (165)
T COG1656 95 PEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWK 142 (165)
T ss_pred cccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccC
Confidence 347899 999999999877744 9999987765
No 142
>TIGR00767 rho transcription termination factor Rho. Members of this family differ in the specificity of RNA binding.
Probab=66.75 E-value=4.8 Score=37.71 Aligned_cols=129 Identities=16% Similarity=0.192 Sum_probs=73.9
Q ss_pred eeeCCcEEEe--CCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecC---eEEEEEe
Q 028346 23 VKAGKGAYVA--KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTR---MASADIM 97 (210)
Q Consensus 23 ~~~G~GtY~~--~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V~~v~~~---~a~V~I~ 97 (210)
...+.|+-+- +|.|.+++.-.+.+.. ..-|+|.|..-+++-++.||.|.|.|..-... ...+++-
T Consensus 48 ~~~~~g~le~~~~g~gflr~~~~~~~~~----------~~d~yvs~~~i~~~~lr~gd~v~g~~R~~~~~ER~~~Ll~v~ 117 (415)
T TIGR00767 48 LIFGEGVLEILPDGFGFLRSPDSSYLPG----------PDDIYVSPSQIRRFNLRTGDTIEGQIRSPKEGERYFALLKVE 117 (415)
T ss_pred ceEEEEEEEEcCCCCeEEeCCCcCCCCC----------CCCeeeCHHHHHhcCCCCCCEEEEEEeccccHhHHHHHhCCC
Confidence 4567777653 5666677765555432 12488988765678899999999999876432 2445555
Q ss_pred eeccccccCceeEEEeccccccccccccccCCCCC-CCCEEEEEEEEeCCCcceEEEeecCCceeeEEEcCCCCe
Q 028346 98 CVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFR-PGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGKL 171 (210)
Q Consensus 98 ~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~-~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv~a~~~~G~~ 171 (210)
.+++.+. ....+-++.+++...+.++ . ..+. -.+-+-.|+++ +.+.+..-+-+.|.+...||..
T Consensus 118 ~vn~~~~-e~~~~ri~Fe~LTf~YP~e-r--~~Le~~~~~~~~R~id------~~~pig~Gq~~~IvG~~g~GKT 182 (415)
T TIGR00767 118 SVNGDDP-EKAKNRVLFENLTPLYPNE-R--LRLETSTEDLSTRVLD------LFAPIGKGQRGLIVAPPKAGKT 182 (415)
T ss_pred ccCCCCc-cccCCCeEEEEeeecCCCc-c--ceeecCccccceeeee------eEEEeCCCCEEEEECCCCCChh
Confidence 5544332 2344556666665544331 0 1111 12444455553 3455555556666666666654
No 143
>PF04085 MreC: rod shape-determining protein MreC; InterPro: IPR007221 MreC (murein formation C) is involved in the rod shape determination in Escherichia coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped.; GO: 0008360 regulation of cell shape; PDB: 2J5U_B 2QF4_B 2QF5_A.
Probab=66.29 E-value=23 Score=28.17 Aligned_cols=60 Identities=20% Similarity=0.298 Sum_probs=34.1
Q ss_pred EEEEEEEEecCeEEEEEeeecccc-----ccCceeEEEecccccc--ccccccccCCCCCCCCEEEE
Q 028346 80 VIARVTKVMTRMASADIMCVGAKS-----VREKFSGIIRQQDVRA--TEIDKVDMHLSFRPGDIVRA 139 (210)
Q Consensus 80 ViG~V~~v~~~~a~V~I~~v~~~~-----l~~~~~Gii~~s~v~~--~~~d~~~~~~~~~~GDiV~A 139 (210)
++|+|+++.++.+.|..+.-.+.. ......|+++-..-.. -..........+++||.|.-
T Consensus 36 lVG~V~~V~~~~S~V~li~d~~~~v~v~i~~~~~~Gi~~G~~~~~~~~~l~~i~~~~~i~~GD~V~T 102 (152)
T PF04085_consen 36 LVGRVTEVGPNTSRVLLITDPNSRVSVKIERSGDRGILRGDGSNTGLLKLEYIPKDADIKKGDIVVT 102 (152)
T ss_dssp EEEEEEEE-SS-EEEEETTSSBCEEEEEEECTTEEEEEEEEETTTTEEEEEEECTTS---TT-EEEE
T ss_pred cEEEEEEECCCEEEEEEEeCCCceEEEEEecCCeeEEEEeCCCCCceEEEEECCCCCCCCCCCEEEE
Confidence 589999999999999986544321 2345568876655432 22233345677889998763
No 144
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=66.10 E-value=2.3 Score=32.48 Aligned_cols=36 Identities=19% Similarity=0.138 Sum_probs=28.3
Q ss_pred ecCCceeeEEEc-CCCCeeEEcccceEEecccchhhhH
Q 028346 155 AKNDLGVVSAES-TAGKLVYCISKYDLNIILFYSFWIF 191 (210)
Q Consensus 155 ~~~~LGVv~a~~-~~G~~m~~~~~~~l~C~~~~~~~~~ 191 (210)
+.++||.= -.| .||..-|=+...-+.||.|++-|=+
T Consensus 2 akpelGtK-R~Cp~CG~kFYDLnk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 2 AKPELGTK-RTCPSCGAKFYDLNKDPIVCPKCGTEFPP 38 (108)
T ss_pred CccccCCc-ccCCCCcchhccCCCCCccCCCCCCccCc
Confidence 45677753 358 9999988888889999999987743
No 145
>COG1158 Rho Transcription termination factor [Transcription]
Probab=64.88 E-value=8.6 Score=35.47 Aligned_cols=72 Identities=15% Similarity=0.123 Sum_probs=49.5
Q ss_pred CeeeCCcEEEe--CCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEec---CeEEEEE
Q 028346 22 EVKAGKGAYVA--KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMT---RMASADI 96 (210)
Q Consensus 22 e~~~G~GtY~~--~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V~~v~~---~~a~V~I 96 (210)
++..+.|+.+. +|.|.++++-.-.+.- ..-|+|.|..-+++-++.||.|.|+|..=++ +++.+.+
T Consensus 50 ~~~~~~GvLeil~dGfGFLR~~~~~yl~~----------~~DiYvSpSQIRrf~LrtGD~v~G~vR~Pke~Ery~aLl~v 119 (422)
T COG1158 50 EEIFGDGVLEILPDGFGFLRSADSSYLPG----------PDDIYVSPSQIRRFNLRTGDTVEGKVRPPKEGERYFALLKV 119 (422)
T ss_pred ceEeeeeEEEeccCCcceeecCccccCCC----------CCceEECHHHHhhccCccCCEEeeeecCCCcccceeeeEEE
Confidence 46677777653 5665566543322211 1348999987678889999999999987654 5688888
Q ss_pred eeecccc
Q 028346 97 MCVGAKS 103 (210)
Q Consensus 97 ~~v~~~~ 103 (210)
-++++.+
T Consensus 120 e~vN~~~ 126 (422)
T COG1158 120 EAVNGDD 126 (422)
T ss_pred eecCCCC
Confidence 8887754
No 146
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=64.32 E-value=11 Score=30.63 Aligned_cols=40 Identities=18% Similarity=0.184 Sum_probs=26.1
Q ss_pred CceEEec--CCccCCCCCeeeCCcEEE---eCCeeEEEEeEeeeEEE
Q 028346 7 EMVLVTP--GEVLGKATEVKAGKGAYV---AKHNGLVYASLTGLLRT 48 (210)
Q Consensus 7 ~~~iV~P--Gd~l~~~ee~~~G~GtY~---~~g~~~I~Asv~G~v~~ 48 (210)
.+.+++| ||.++... -..|.|.|. .+|. .+.|.+.|+++.
T Consensus 23 ~rel~~~eegq~~g~V~-~~LGn~~f~V~c~dG~-~rLa~I~GKmRK 67 (155)
T PTZ00329 23 KRELVFKEEGQEYAQVL-RMLGNGRLEAYCFDGV-KRLCHIRGKMRK 67 (155)
T ss_pred eeeeccCCCCcEEEEEE-EEcCCCEEEEEECCCC-EEEEEeecccee
Confidence 3567777 66666544 356777775 2443 378888888864
No 147
>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=64.15 E-value=17 Score=25.33 Aligned_cols=33 Identities=15% Similarity=0.163 Sum_probs=25.3
Q ss_pred CCCCEEEEEEEEeCCCcceEEEeecCCceeeEEE
Q 028346 132 RPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAE 165 (210)
Q Consensus 132 ~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv~a~ 165 (210)
++||+|.++|+++.+. .+.+.+.+.-.|.+...
T Consensus 5 ~~GdiV~G~V~~v~~~-~~~V~i~~~~~g~l~~~ 37 (82)
T cd04454 5 DVGDIVIGIVTEVNSR-FWKVDILSRGTARLEDS 37 (82)
T ss_pred CCCCEEEEEEEEEcCC-EEEEEeCCCceEEeech
Confidence 6999999999999754 57777766666666553
No 148
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=63.63 E-value=4.5 Score=30.92 Aligned_cols=27 Identities=15% Similarity=-0.038 Sum_probs=19.5
Q ss_pred eEEEc-CCCCeeEEcccceEEecccchhh
Q 028346 162 VSAES-TAGKLVYCISKYDLNIILFYSFW 189 (210)
Q Consensus 162 v~a~~-~~G~~m~~~~~~~l~C~~~~~~~ 189 (210)
..++| .||..- +.....+.||.|+.+-
T Consensus 69 ~~~~C~~Cg~~~-~~~~~~~~CP~Cgs~~ 96 (113)
T PRK12380 69 AQAWCWDCSQVV-EIHQHDAQCPHCHGER 96 (113)
T ss_pred cEEEcccCCCEE-ecCCcCccCcCCCCCC
Confidence 45689 899774 4444567899999764
No 149
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=63.52 E-value=5.5 Score=30.58 Aligned_cols=25 Identities=16% Similarity=-0.146 Sum_probs=20.0
Q ss_pred Ec-CCCCeeEEc---ccceEEecccchhh
Q 028346 165 ES-TAGKLVYCI---SKYDLNIILFYSFW 189 (210)
Q Consensus 165 ~~-~~G~~m~~~---~~~~l~C~~~~~~~ 189 (210)
.| +||+.|+|. ....|.|+.|+.-.
T Consensus 4 FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 4 FCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred ccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 47 899999994 23599999998754
No 150
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=63.41 E-value=4.5 Score=30.98 Aligned_cols=28 Identities=7% Similarity=-0.165 Sum_probs=19.5
Q ss_pred eEEEc-CCCCeeEEcccceEEecccchhh
Q 028346 162 VSAES-TAGKLVYCISKYDLNIILFYSFW 189 (210)
Q Consensus 162 v~a~~-~~G~~m~~~~~~~l~C~~~~~~~ 189 (210)
..++| .||..--...+..+.||.|+.+-
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 69 AECWCETCQQYVTLLTQRVRRCPQCHGDM 97 (114)
T ss_pred cEEEcccCCCeeecCCccCCcCcCcCCCC
Confidence 45789 89976433244448899999764
No 151
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=63.25 E-value=3 Score=33.13 Aligned_cols=34 Identities=9% Similarity=-0.065 Sum_probs=25.9
Q ss_pred CceeeEEEc-CCCCeeEEcccce----------------EEecccchhhhH
Q 028346 158 DLGVVSAES-TAGKLVYCISKYD----------------LNIILFYSFWIF 191 (210)
Q Consensus 158 ~LGVv~a~~-~~G~~m~~~~~~~----------------l~C~~~~~~~~~ 191 (210)
++.-++++| .|++++.+++..+ ..||.|+..|.-
T Consensus 86 ~~~~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 86 RLDPIFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWE 136 (147)
T ss_pred ccCCCCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecc
Confidence 345567899 9999998887663 489999987653
No 152
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=63.24 E-value=4.7 Score=30.87 Aligned_cols=27 Identities=11% Similarity=-0.106 Sum_probs=19.9
Q ss_pred eEEEc-CCCCeeEEcccceEEecccchhh
Q 028346 162 VSAES-TAGKLVYCISKYDLNIILFYSFW 189 (210)
Q Consensus 162 v~a~~-~~G~~m~~~~~~~l~C~~~~~~~ 189 (210)
+.++| .||..- +.....+.||.|+.+-
T Consensus 69 ~~~~C~~Cg~~~-~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 69 VECECEDCSEEV-SPEIDLYRCPKCHGIM 96 (115)
T ss_pred cEEEcccCCCEE-ecCCcCccCcCCcCCC
Confidence 45789 899764 4444578899999864
No 153
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=62.38 E-value=3.2 Score=31.96 Aligned_cols=29 Identities=10% Similarity=-0.252 Sum_probs=19.9
Q ss_pred eEEEc-CCCCeeEEcccceEEecccchhhh
Q 028346 162 VSAES-TAGKLVYCISKYDLNIILFYSFWI 190 (210)
Q Consensus 162 v~a~~-~~G~~m~~~~~~~l~C~~~~~~~~ 190 (210)
..++| .||...-+..+..+.||.|+.+.+
T Consensus 70 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~ 99 (117)
T PRK00564 70 VELECKDCSHVFKPNALDYGVCEKCHSKNV 99 (117)
T ss_pred CEEEhhhCCCccccCCccCCcCcCCCCCce
Confidence 46789 899775433344556999998753
No 154
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=60.91 E-value=5.8 Score=30.39 Aligned_cols=26 Identities=12% Similarity=-0.023 Sum_probs=20.1
Q ss_pred Ec-CCCCee-EEcccceEEecccchhhhH
Q 028346 165 ES-TAGKLV-YCISKYDLNIILFYSFWIF 191 (210)
Q Consensus 165 ~~-~~G~~m-~~~~~~~l~C~~~~~~~~~ 191 (210)
.| +|+..- ++ ....+.||+|.+-|-.
T Consensus 4 ~CP~C~seytY~-dg~~~iCpeC~~EW~~ 31 (109)
T TIGR00686 4 PCPKCNSEYTYH-DGTQLICPSCLYEWNE 31 (109)
T ss_pred cCCcCCCcceEe-cCCeeECccccccccc
Confidence 47 888764 55 4479999999999954
No 155
>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=60.47 E-value=10 Score=27.75 Aligned_cols=29 Identities=34% Similarity=0.550 Sum_probs=20.9
Q ss_pred CCCCCCCCEEEEEEEEEecCeEEEEEeeec
Q 028346 71 GPVPEPGSVVIARVTKVMTRMASADIMCVG 100 (210)
Q Consensus 71 ~y~p~vGDiViG~V~~v~~~~a~V~I~~v~ 100 (210)
+...++||+|++||.++...+ ..++.+++
T Consensus 47 rp~L~~GDlV~ArV~~~~~~~-~~eLtc~~ 75 (86)
T cd05790 47 RPNLNVGDLVYARVVKANRDM-EPELSCVD 75 (86)
T ss_pred cccCCCCCEEEEEEEecCCCC-CeEEEEeC
Confidence 455799999999999998763 34544443
No 156
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=60.09 E-value=24 Score=24.00 Aligned_cols=21 Identities=24% Similarity=0.197 Sum_probs=18.0
Q ss_pred EEEEEEEEecCeEEEEEeeec
Q 028346 80 VIARVTKVMTRMASADIMCVG 100 (210)
Q Consensus 80 ViG~V~~v~~~~a~V~I~~v~ 100 (210)
..|+|..+..+.+.|+|...+
T Consensus 16 ~~G~V~kv~eNSVIVdIT~m~ 36 (57)
T PF09953_consen 16 FTGIVEKVYENSVIVDITIME 36 (57)
T ss_pred cEEEEEEEecCcEEEEEEecC
Confidence 589999999999999995433
No 157
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=59.96 E-value=3.6 Score=32.42 Aligned_cols=36 Identities=19% Similarity=0.097 Sum_probs=28.6
Q ss_pred ecCCceeeEEEc-CCCCeeEEcccceEEecccchhhhH
Q 028346 155 AKNDLGVVSAES-TAGKLVYCISKYDLNIILFYSFWIF 191 (210)
Q Consensus 155 ~~~~LGVv~a~~-~~G~~m~~~~~~~l~C~~~~~~~~~ 191 (210)
..++||.= -.| .||...|-....-..||.|++-|-+
T Consensus 2 ~k~elGtK-r~Cp~cg~kFYDLnk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 2 AKPDLGTK-RICPNTGSKFYDLNRRPAVSPYTGEQFPP 38 (129)
T ss_pred CchhhCcc-ccCCCcCccccccCCCCccCCCcCCccCc
Confidence 34667753 358 9999999888899999999998754
No 158
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=59.86 E-value=6.9 Score=24.70 Aligned_cols=23 Identities=4% Similarity=-0.075 Sum_probs=17.9
Q ss_pred EEc-CCCCeeEEcccceEEecccc
Q 028346 164 AES-TAGKLVYCISKYDLNIILFY 186 (210)
Q Consensus 164 a~~-~~G~~m~~~~~~~l~C~~~~ 186 (210)
..| .||.||.........|+.|.
T Consensus 18 ~~Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEEecCCCEECCCCC
Confidence 467 89999877445689999984
No 159
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=58.47 E-value=11 Score=22.64 Aligned_cols=24 Identities=13% Similarity=-0.165 Sum_probs=18.9
Q ss_pred Ec-CCCCeeEE-cccceEEecccchh
Q 028346 165 ES-TAGKLVYC-ISKYDLNIILFYSF 188 (210)
Q Consensus 165 ~~-~~G~~m~~-~~~~~l~C~~~~~~ 188 (210)
.| .||+.++- .....+.|+.|++.
T Consensus 5 ~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 5 KCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred EcCCCCCCeEEEecCCeEEcccCCcE
Confidence 57 69998865 55679999999864
No 160
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=58.24 E-value=70 Score=26.93 Aligned_cols=69 Identities=16% Similarity=0.179 Sum_probs=42.5
Q ss_pred CCCCCEEEEEEEEEecCeEEEEEeeecccc-----ccCc--e--eEEEeccccccccccccccCCCCCCCCEEEEEEEEe
Q 028346 74 PEPGSVVIARVTKVMTRMASADIMCVGAKS-----VREK--F--SGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSL 144 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~~a~V~I~~v~~~~-----l~~~--~--~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~ 144 (210)
|-+|+++.|+|..-+..+..|.|...++-- |..+ | ....=+=+.... |.-.-.-+|++|..|+=||.+.
T Consensus 79 PF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~E--dg~~~~Ly~D~~e~IRFRV~~e 156 (202)
T KOG3297|consen 79 PFVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQE--DGPGTKLYFDVGEEIRFRVEDE 156 (202)
T ss_pred cccceEEEEEeecCCccceEEEEEeeeceeechhhCCCCcccccccEEEEEEeccc--CCCCceeEecCCCeEEEEEeee
Confidence 678999999999999999999997666532 1111 1 111000011100 0001224689999999999986
No 161
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=57.53 E-value=47 Score=28.76 Aligned_cols=91 Identities=14% Similarity=0.183 Sum_probs=52.6
Q ss_pred EEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCE------EEEEEEEEecCeEEEEEeeecccc----c-cC
Q 028346 38 VYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSV------VIARVTKVMTRMASADIMCVGAKS----V-RE 106 (210)
Q Consensus 38 I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDi------ViG~V~~v~~~~a~V~I~~v~~~~----l-~~ 106 (210)
+.|.+.+.-. +...+.+.+... ...=.++|+. ++|+|+++.++.+.|..+.-.+.. + ..
T Consensus 120 i~A~Vi~~~~--------~~~~~~i~Id~G--~~~Gv~~g~~Vv~~~GlVG~V~~v~~~~s~V~li~d~~~~v~v~i~~~ 189 (276)
T PRK13922 120 ITARVISRSP--------DPWSQQVTIDKG--SNDGVKKGMPVIDPGGLVGRVIEVSPNTSRVLLLTDPNSRVPVQVGRN 189 (276)
T ss_pred EEEEEEEeCC--------CCceeEEEEccC--cccCCCCCCceEcCCCCeEEEEEECCCeeEEEEEEcCCCceEEEEEcC
Confidence 6676666442 112345555422 2223456666 599999999999999887644321 1 23
Q ss_pred ceeEEEecccccc-ccccccccCCCCCCCCEEE
Q 028346 107 KFSGIIRQQDVRA-TEIDKVDMHLSFRPGDIVR 138 (210)
Q Consensus 107 ~~~Gii~~s~v~~-~~~d~~~~~~~~~~GDiV~ 138 (210)
...|+++-+.-.. -..+-..-...+++||.|.
T Consensus 190 ~~~gi~~G~g~~~~l~l~~i~~~~~i~~GD~Vv 222 (276)
T PRK13922 190 GIRGILSGNGSGDNLKLEFIPRSADIKVGDLVV 222 (276)
T ss_pred CceEEEEecCCCCceEEEecCCCCCCCCCCEEE
Confidence 4567777663211 1222223446689999863
No 162
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=57.35 E-value=3.6 Score=30.61 Aligned_cols=34 Identities=24% Similarity=0.073 Sum_probs=25.2
Q ss_pred cCCceeeEEEc-CCCCeeEE--cccceEEecccchhhh
Q 028346 156 KNDLGVVSAES-TAGKLVYC--ISKYDLNIILFYSFWI 190 (210)
Q Consensus 156 ~~~LGVv~a~~-~~G~~m~~--~~~~~l~C~~~~~~~~ 190 (210)
+..|=+.-|+| +||..--+ +. .-=.||.|.+-||
T Consensus 51 g~~Llv~Pa~CkkCGfef~~~~ik-~pSRCP~CKSE~I 87 (97)
T COG3357 51 GKRLLVRPARCKKCGFEFRDDKIK-KPSRCPKCKSEWI 87 (97)
T ss_pred CceEEecChhhcccCccccccccC-CcccCCcchhhcc
Confidence 44566778999 99987544 22 2567999999997
No 163
>COG0211 RpmA Ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=55.68 E-value=26 Score=25.66 Aligned_cols=59 Identities=19% Similarity=0.278 Sum_probs=40.0
Q ss_pred ccCCceEEecCCccCCC--CCeeeCCcEEEe-CCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCC
Q 028346 4 KEEEMVLVTPGEVLGKA--TEVKAGKGAYVA-KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHK 68 (210)
Q Consensus 4 ~~~~~~iV~PGd~l~~~--ee~~~G~GtY~~-~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~ 68 (210)
|..+.+.|.+|+.|--- ..|-||.++=.- |.. ++|.+-|.|+.... ...++.++|.|..
T Consensus 24 K~~~Gq~v~aG~IivRQRGTk~hpG~NVG~GkDhT--lFAl~dG~Vkf~~k----~~~rk~vsV~~~~ 85 (87)
T COG0211 24 KKFGGQFVKAGSIIVRQRGTKFHPGVNVGRGKDHT--LFALVDGVVKFETK----GKNRKYVSVVPEA 85 (87)
T ss_pred eeeCCeEEecccEEEEeccccccCCcccccCCCce--EEEeeccEEEEEEc----cCCccEEEEEeec
Confidence 44567889999987532 347788777443 444 99999999977421 1345678888753
No 164
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=54.41 E-value=7.5 Score=26.59 Aligned_cols=27 Identities=7% Similarity=-0.063 Sum_probs=19.4
Q ss_pred Ec-CCCCeeEEcc-cceEEecccchhhhH
Q 028346 165 ES-TAGKLVYCIS-KYDLNIILFYSFWIF 191 (210)
Q Consensus 165 ~~-~~G~~m~~~~-~~~l~C~~~~~~~~~ 191 (210)
.| .||..|.|.+ .-.+.||.|+.-.|+
T Consensus 9 ~CtSCg~~i~~~~~~~~F~CPnCG~~~I~ 37 (59)
T PRK14890 9 KCTSCGIEIAPREKAVKFLCPNCGEVIIY 37 (59)
T ss_pred cccCCCCcccCCCccCEeeCCCCCCeeEe
Confidence 35 7888887776 568888888875444
No 165
>PRK10220 hypothetical protein; Provisional
Probab=53.65 E-value=9.6 Score=29.26 Aligned_cols=27 Identities=4% Similarity=-0.276 Sum_probs=20.2
Q ss_pred Ec-CCCCeeEEcccceEEecccchhhhH
Q 028346 165 ES-TAGKLVYCISKYDLNIILFYSFWIF 191 (210)
Q Consensus 165 ~~-~~G~~m~~~~~~~l~C~~~~~~~~~ 191 (210)
.| +|.....=.....+.||+|.+-|-.
T Consensus 5 ~CP~C~seytY~d~~~~vCpeC~hEW~~ 32 (111)
T PRK10220 5 HCPKCNSEYTYEDNGMYICPECAHEWND 32 (111)
T ss_pred cCCCCCCcceEcCCCeEECCcccCcCCc
Confidence 47 7887653334479999999999964
No 166
>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=53.14 E-value=31 Score=24.10 Aligned_cols=32 Identities=19% Similarity=0.173 Sum_probs=22.3
Q ss_pred CCCCCEEEEEEEEeCCCcceEEEeecCCceeeE
Q 028346 131 FRPGDIVRASVLSLGDARAYFLSTAKNDLGVVS 163 (210)
Q Consensus 131 ~~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv~ 163 (210)
.++||+|.|+|.++.+. .+.+.+...--|.+.
T Consensus 4 p~~GdiV~g~V~~i~~~-g~~v~i~~~~~G~l~ 35 (86)
T cd05789 4 PEVGDVVIGRVTEVGFK-RWKVDINSPYDAVLP 35 (86)
T ss_pred CCCCCEEEEEEEEECCC-EEEEECCCCeEEEEE
Confidence 47999999999999753 456655544445544
No 167
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=52.70 E-value=9.2 Score=29.61 Aligned_cols=28 Identities=14% Similarity=-0.071 Sum_probs=21.4
Q ss_pred eEEEc-CCCCeeEEcccceEEecccchhhh
Q 028346 162 VSAES-TAGKLVYCISKYDLNIILFYSFWI 190 (210)
Q Consensus 162 v~a~~-~~G~~m~~~~~~~l~C~~~~~~~~ 190 (210)
..+.| .|+.+..+..| .+.||.|++..+
T Consensus 69 ~~~~C~~C~~~~~~e~~-~~~CP~C~s~~~ 97 (115)
T COG0375 69 AECWCLDCGQEVELEEL-DYRCPKCGSINL 97 (115)
T ss_pred cEEEeccCCCeecchhh-eeECCCCCCCce
Confidence 45678 89999888777 556999997643
No 168
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=52.01 E-value=95 Score=22.95 Aligned_cols=71 Identities=20% Similarity=0.252 Sum_probs=35.2
Q ss_pred CCCEEEEEEEEEecCeEEEEEee-e--cc--ccccC---ceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCC
Q 028346 76 PGSVVIARVTKVMTRMASADIMC-V--GA--KSVRE---KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDA 147 (210)
Q Consensus 76 vGDiViG~V~~v~~~~a~V~I~~-v--~~--~~l~~---~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~ 147 (210)
+=++++|+|+++.| ..+.+.. . .. -.+.. .+.--+..+....+........+.|++||.|. ++...++
T Consensus 16 p~~i~~G~V~s~~P--L~I~i~~~liL~~~~L~i~~~l~~~~~~~~~~~~~~~~~~~i~~~~~Lk~GD~V~--ll~~~~g 91 (100)
T PF10844_consen 16 PVDIVIGTVVSVPP--LKIKIDQKLILDKDFLIIPELLKDYTRDITIEHNSETDNITITFTDGLKVGDKVL--LLRVQGG 91 (100)
T ss_pred CceeEEEEEEeccc--EEEEECCeEEEchHHEEeehhccceEEEEEEeccccccceeEEEecCCcCCCEEE--EEEecCC
Confidence 44668999999998 5565532 0 00 00111 11111111111111111135678999999987 5555444
Q ss_pred cce
Q 028346 148 RAY 150 (210)
Q Consensus 148 ~~~ 150 (210)
..|
T Consensus 92 Q~y 94 (100)
T PF10844_consen 92 QKY 94 (100)
T ss_pred CEE
Confidence 455
No 169
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=51.91 E-value=7.4 Score=26.50 Aligned_cols=24 Identities=8% Similarity=-0.323 Sum_probs=19.4
Q ss_pred Ec-CCCCeeEE-cccceEEecccchh
Q 028346 165 ES-TAGKLVYC-ISKYDLNIILFYSF 188 (210)
Q Consensus 165 ~~-~~G~~m~~-~~~~~l~C~~~~~~ 188 (210)
.| .||..+.. .++..+.||.|+..
T Consensus 30 ~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCcccccccccccceEEcCCCCCE
Confidence 46 79998865 56789999999875
No 170
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=51.68 E-value=20 Score=26.14 Aligned_cols=23 Identities=22% Similarity=0.215 Sum_probs=18.6
Q ss_pred CCCCCEEEEEEEEEec-CeEEEEE
Q 028346 74 PEPGSVVIARVTKVMT-RMASADI 96 (210)
Q Consensus 74 p~vGDiViG~V~~v~~-~~a~V~I 96 (210)
.++||+|.|+|.+..+ ....+.+
T Consensus 61 f~~GDiV~AkVis~~~~~~~~Lst 84 (92)
T cd05791 61 FRPGDIVRAKVISLGDASSYYLST 84 (92)
T ss_pred cCCCCEEEEEEEEcCCCCCcEEEe
Confidence 5899999999999976 4566555
No 171
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=51.21 E-value=4.7 Score=30.72 Aligned_cols=28 Identities=14% Similarity=-0.037 Sum_probs=18.4
Q ss_pred eEEEc-CCCCeeEEcccceEEecccchhhh
Q 028346 162 VSAES-TAGKLVYCISKYDLNIILFYSFWI 190 (210)
Q Consensus 162 v~a~~-~~G~~m~~~~~~~l~C~~~~~~~~ 190 (210)
..++| .||...-+.. ..+.||.|+++.+
T Consensus 69 ~~~~C~~Cg~~~~~~~-~~~~CP~Cgs~~~ 97 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDE-FDFSCPRCGSPDV 97 (113)
T ss_dssp -EEEETTTS-EEECHH-CCHH-SSSSSS-E
T ss_pred CcEECCCCCCEEecCC-CCCCCcCCcCCCc
Confidence 46789 8999965544 4588999998753
No 172
>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=51.10 E-value=14 Score=26.71 Aligned_cols=16 Identities=38% Similarity=0.463 Sum_probs=11.7
Q ss_pred CCCCEEEEEEEEeCCC
Q 028346 132 RPGDIVRASVLSLGDA 147 (210)
Q Consensus 132 ~~GDiV~AkV~s~~d~ 147 (210)
++||+|.|||+++...
T Consensus 3 ~vGdiV~~rVtrv~~~ 18 (82)
T PF10447_consen 3 KVGDIVIARVTRVNPR 18 (82)
T ss_dssp -TT-EEEEEEEEE-SS
T ss_pred CCCCEEEEEEEEEecc
Confidence 5899999999999754
No 173
>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=50.88 E-value=39 Score=23.09 Aligned_cols=32 Identities=13% Similarity=0.142 Sum_probs=20.3
Q ss_pred CCCCCEEEEEEEEeCCCcceEEEeecCCceee
Q 028346 131 FRPGDIVRASVLSLGDARAYFLSTAKNDLGVV 162 (210)
Q Consensus 131 ~~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv 162 (210)
+++||++.|+|.++.+.....+++...--|-+
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glv 32 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLV 32 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEE
Confidence 46999999999998542234555443333444
No 174
>PLN00208 translation initiation factor (eIF); Provisional
Probab=50.47 E-value=25 Score=28.27 Aligned_cols=39 Identities=18% Similarity=0.234 Sum_probs=23.8
Q ss_pred ceEEec--CCccCCCCCeeeCCcEEEe---CCeeEEEEeEeeeEEE
Q 028346 8 MVLVTP--GEVLGKATEVKAGKGAYVA---KHNGLVYASLTGLLRT 48 (210)
Q Consensus 8 ~~iV~P--Gd~l~~~ee~~~G~GtY~~---~g~~~I~Asv~G~v~~ 48 (210)
+.+++| ||.++... -..|.|.|.- +|. ...|.+.|+.+.
T Consensus 24 ~el~~p~egq~~g~V~-~~lGn~~~~V~c~dG~-~rLa~IpGKmRK 67 (145)
T PLN00208 24 RELIFKEDGQEYAQVL-RMLGNGRCEALCIDGT-KRLCHIRGKMRK 67 (145)
T ss_pred eecccCCCCcEEEEEE-EEcCCCEEEEEECCCC-EEEEEEecccee
Confidence 466776 45555433 3567777652 433 377888888764
No 175
>TIGR00219 mreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.
Probab=50.24 E-value=67 Score=28.38 Aligned_cols=61 Identities=13% Similarity=0.237 Sum_probs=38.0
Q ss_pred CEEEEEEEEEecCeEEEEEeeecccc-----ccCceeEEEecccccc---ccccccccCCCCCCCCEEE
Q 028346 78 SVVIARVTKVMTRMASADIMCVGAKS-----VREKFSGIIRQQDVRA---TEIDKVDMHLSFRPGDIVR 138 (210)
Q Consensus 78 DiViG~V~~v~~~~a~V~I~~v~~~~-----l~~~~~Gii~~s~v~~---~~~d~~~~~~~~~~GDiV~ 138 (210)
+=++|+|+++.+..+.|.++.-.+.. ......|+++-.+-.. -..........+++||.|.
T Consensus 155 ~GLVG~V~~V~~~~S~V~litd~~~~v~v~v~~t~~~gi~~G~~~g~~~~l~l~~~~~~~~v~~GD~Vv 223 (283)
T TIGR00219 155 KGLVGKVVSVGSNTSRVLLLTDYTNFVPAQILRSDFRGLIEGNGYGKTLEMNLVNRPAEKDIKKGDLIV 223 (283)
T ss_pred CceEEEEEEECCCeEEEEEEEcCCCceEEEEecCCceEEEEecCCCCCcEEEEEECCCCCCCCCCCEEE
Confidence 34789999999999999997654322 2345678887664111 0111112346789999863
No 176
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=49.97 E-value=12 Score=28.94 Aligned_cols=19 Identities=11% Similarity=-0.041 Sum_probs=15.7
Q ss_pred c-CCCCeeEEcccceEEecccch
Q 028346 166 S-TAGKLVYCISKYDLNIILFYS 187 (210)
Q Consensus 166 ~-~~G~~m~~~~~~~l~C~~~~~ 187 (210)
| .||+.|.- ..|.|+.|.+
T Consensus 1 CPvCg~~l~v---t~l~C~~C~t 20 (113)
T PF09862_consen 1 CPVCGGELVV---TRLKCPSCGT 20 (113)
T ss_pred CCCCCCceEE---EEEEcCCCCC
Confidence 6 79999874 4699999986
No 177
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=49.85 E-value=24 Score=29.02 Aligned_cols=24 Identities=17% Similarity=0.095 Sum_probs=19.5
Q ss_pred CCCCCCCEEEEEEEEEecCeEEEEE
Q 028346 72 PVPEPGSVVIARVTKVMTRMASADI 96 (210)
Q Consensus 72 y~p~vGDiViG~V~~v~~~~a~V~I 96 (210)
...++||+|.++|.++. +.+.+.+
T Consensus 117 ~~~~~GD~V~akV~~i~-~~i~LS~ 140 (189)
T PRK09521 117 DAFKIGDIVRAKVISYT-DPLQLST 140 (189)
T ss_pred hccCCCCEEEEEEEecC-CcEEEEE
Confidence 34689999999999998 6666666
No 178
>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=49.78 E-value=44 Score=23.10 Aligned_cols=32 Identities=22% Similarity=0.376 Sum_probs=21.6
Q ss_pred CCCCCEEEEEEEEeCCCcceEEEeecCCceeeE
Q 028346 131 FRPGDIVRASVLSLGDARAYFLSTAKNDLGVVS 163 (210)
Q Consensus 131 ~~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv~ 163 (210)
+++||+|.++|.++.+. ...+++...=-|-|.
T Consensus 1 ~k~G~~V~g~V~~i~~~-G~fV~l~~~v~G~v~ 32 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQ-GVFFRLSSSIVGRVL 32 (74)
T ss_pred CCCCCEEEEEEEEEeCC-cEEEEeCCCCEEEEE
Confidence 57999999999999754 355666432224443
No 179
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=49.61 E-value=11 Score=29.89 Aligned_cols=27 Identities=11% Similarity=0.006 Sum_probs=21.6
Q ss_pred eee-EEEc-CCCCeeEEcccceEEecccchhh
Q 028346 160 GVV-SAES-TAGKLVYCISKYDLNIILFYSFW 189 (210)
Q Consensus 160 GVv-~a~~-~~G~~m~~~~~~~l~C~~~~~~~ 189 (210)
|.+ -++| +||....|- ...||.|+++-
T Consensus 25 ~kl~g~kC~~CG~v~~PP---r~~Cp~C~~~~ 53 (140)
T COG1545 25 GKLLGTKCKKCGRVYFPP---RAYCPKCGSET 53 (140)
T ss_pred CcEEEEEcCCCCeEEcCC---cccCCCCCCCC
Confidence 554 4689 999999884 47899999983
No 180
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=49.21 E-value=8 Score=25.37 Aligned_cols=26 Identities=4% Similarity=-0.325 Sum_probs=20.1
Q ss_pred EEc-CCCC-eeEEcccceEEecccchhhh
Q 028346 164 AES-TAGK-LVYCISKYDLNIILFYSFWI 190 (210)
Q Consensus 164 a~~-~~G~-~m~~~~~~~l~C~~~~~~~~ 190 (210)
..| +||. .|.+-. +.+.|..|+..++
T Consensus 21 ~fCP~Cg~~~m~~~~-~r~~C~~Cgyt~~ 48 (50)
T PRK00432 21 KFCPRCGSGFMAEHL-DRWHCGKCGYTEF 48 (50)
T ss_pred CcCcCCCcchheccC-CcEECCCcCCEEe
Confidence 357 8998 777655 7999999987654
No 181
>PF08810 KapB: Kinase associated protein B; InterPro: IPR014916 This bacterial protein forms an anti-parallel beta sheet with an extending alpha helical region. ; PDB: 1Y71_B.
Probab=48.60 E-value=29 Score=26.71 Aligned_cols=21 Identities=14% Similarity=0.145 Sum_probs=18.9
Q ss_pred EEEEEEEEecCeEEEEEeeec
Q 028346 80 VIARVTKVMTRMASADIMCVG 100 (210)
Q Consensus 80 ViG~V~~v~~~~a~V~I~~v~ 100 (210)
=+|.|++++++.+.|.|++|-
T Consensus 6 Yigei~e~~~~~~lVkVlaVl 26 (112)
T PF08810_consen 6 YIGEITEERPQHYLVKVLAVL 26 (112)
T ss_dssp EEEEEEEEETTEEEEEEEEEE
T ss_pred eEEEEEeecCCeEEEEEEEEe
Confidence 479999999999999998874
No 182
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=48.34 E-value=12 Score=25.24 Aligned_cols=14 Identities=43% Similarity=0.895 Sum_probs=12.4
Q ss_pred CCCCCEEEEEEEEe
Q 028346 131 FRPGDIVRASVLSL 144 (210)
Q Consensus 131 ~~~GDiV~AkV~s~ 144 (210)
|++||+|-||+.+.
T Consensus 1 f~~GdlVwaK~~G~ 14 (63)
T smart00293 1 FKPGDLVWAKMKGF 14 (63)
T ss_pred CCCCCEEEEECCCC
Confidence 68999999999874
No 183
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=48.25 E-value=12 Score=29.43 Aligned_cols=28 Identities=11% Similarity=-0.249 Sum_probs=19.4
Q ss_pred eEEEc-CCCCeeEEcc--------------------cceEEecccchhh
Q 028346 162 VSAES-TAGKLVYCIS--------------------KYDLNIILFYSFW 189 (210)
Q Consensus 162 v~a~~-~~G~~m~~~~--------------------~~~l~C~~~~~~~ 189 (210)
..++| .||..--... ...+.||.|+++-
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRD 117 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCC
Confidence 56789 8997643221 3567899999874
No 184
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=47.86 E-value=41 Score=24.34 Aligned_cols=23 Identities=26% Similarity=0.369 Sum_probs=20.5
Q ss_pred CCCCCEE------EEEEEEEecCeEEEEE
Q 028346 74 PEPGSVV------IARVTKVMTRMASADI 96 (210)
Q Consensus 74 p~vGDiV------iG~V~~v~~~~a~V~I 96 (210)
.++||.| +|+|+++.++.+.+++
T Consensus 38 L~~Gd~VvT~gGi~G~V~~i~d~~v~vei 66 (84)
T TIGR00739 38 LKKGDKVLTIGGIIGTVTKIAENTIVIEL 66 (84)
T ss_pred CCCCCEEEECCCeEEEEEEEeCCEEEEEE
Confidence 6789987 8999999999888888
No 185
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=47.75 E-value=1e+02 Score=22.16 Aligned_cols=56 Identities=21% Similarity=0.217 Sum_probs=31.2
Q ss_pred CCCCCEEEEEEEEEecC-eEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeC
Q 028346 74 PEPGSVVIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG 145 (210)
Q Consensus 74 p~vGDiViG~V~~v~~~-~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~ 145 (210)
|..| -++|+|++..++ .+.|... ++ ....+.|+- +.. -+=.++.||.|.+.....+
T Consensus 2 p~e~-q~~g~V~~~lG~~~~~V~~~--dG----~~~la~ipg------K~R---k~iwI~~GD~VlVe~~~~~ 58 (83)
T smart00652 2 KEDG-QEIAQVVKMLGNGRLEVMCA--DG----KERLARIPG------KMR---KKVWIRRGDIVLVDPWDFQ 58 (83)
T ss_pred CCCC-cEEEEEEEEcCCCEEEEEEC--CC----CEEEEEEch------hhc---ccEEEcCCCEEEEEecCCC
Confidence 4434 489999999754 4666661 11 122232221 111 1244689999998876544
No 186
>PF03961 DUF342: Protein of unknown function (DUF342); InterPro: IPR005646 This family of bacterial proteins has no known function. The proteins are in the region of 500-600 amino acid residues in length.
Probab=46.41 E-value=42 Score=31.41 Aligned_cols=36 Identities=25% Similarity=0.323 Sum_probs=26.1
Q ss_pred CeeeCCcEEEe-CCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEec
Q 028346 22 EVKAGKGAYVA-KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTG 66 (210)
Q Consensus 22 e~~~G~GtY~~-~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p 66 (210)
.+.+|+|+..+ ++...++|++-|.+... +..++|.|
T Consensus 144 ~~~~g~~~~~~~~d~~~~~A~~~G~~~~~---------~~~i~V~~ 180 (451)
T PF03961_consen 144 PLKAGKNTEVSEEDGNKLYAAIDGRPVFE---------NGKISVDP 180 (451)
T ss_pred ceeCCCCEEEEcCCCCEEEEecCCEEEEE---------CCEEEEEE
Confidence 47889999986 32223899999999984 24566665
No 187
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=46.17 E-value=13 Score=22.40 Aligned_cols=24 Identities=13% Similarity=-0.136 Sum_probs=16.3
Q ss_pred EEc-CCCCe---eEEcc-cceEEecccch
Q 028346 164 AES-TAGKL---VYCIS-KYDLNIILFYS 187 (210)
Q Consensus 164 a~~-~~G~~---m~~~~-~~~l~C~~~~~ 187 (210)
-+| .||.. +.+.+ .....||.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 367 88884 34333 45788999987
No 188
>PLN00208 translation initiation factor (eIF); Provisional
Probab=45.87 E-value=1.1e+02 Score=24.57 Aligned_cols=57 Identities=14% Similarity=0.183 Sum_probs=31.9
Q ss_pred CCCCCCEEEEEEEEEecC-eEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeC
Q 028346 73 VPEPGSVVIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG 145 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~-~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~ 145 (210)
.|..|+ ++|+|++..++ .+.|.. .....-+.|++- +. .-+-.+++||+|.+..-..+
T Consensus 28 ~p~egq-~~g~V~~~lGn~~~~V~c--------~dG~~rLa~IpG----Km---RKrIWI~~GD~VlVel~~~d 85 (145)
T PLN00208 28 FKEDGQ-EYAQVLRMLGNGRCEALC--------IDGTKRLCHIRG----KM---RKKVWIAAGDIILVGLRDYQ 85 (145)
T ss_pred cCCCCc-EEEEEEEEcCCCEEEEEE--------CCCCEEEEEEec----cc---eeeEEecCCCEEEEEccCCC
Confidence 456565 89999999765 455555 222222222221 11 11245679999998855543
No 189
>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=45.45 E-value=57 Score=21.85 Aligned_cols=33 Identities=18% Similarity=0.258 Sum_probs=22.9
Q ss_pred CCCCCEEEEEEEEeCCCcceEEEeecCCceeeEE
Q 028346 131 FRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSA 164 (210)
Q Consensus 131 ~~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv~a 164 (210)
+++||++.|+|..+.+. .+.+.+...--|.+..
T Consensus 1 ~~~G~iv~g~V~~v~~~-gi~v~l~~~~~g~v~~ 33 (73)
T cd05706 1 LKVGDILPGRVTKVNDR-YVLVQLGNKVTGPSFI 33 (73)
T ss_pred CCCCCEEEEEEEEEeCC-eEEEEeCCCcEEEEEh
Confidence 46899999999999753 4677765543344443
No 190
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=45.07 E-value=21 Score=21.51 Aligned_cols=24 Identities=13% Similarity=-0.032 Sum_probs=16.4
Q ss_pred Ec-CCCCeeEEcc--cceEEecccchh
Q 028346 165 ES-TAGKLVYCIS--KYDLNIILFYSF 188 (210)
Q Consensus 165 ~~-~~G~~m~~~~--~~~l~C~~~~~~ 188 (210)
.| +||..|+|.. +....|+.|.+-
T Consensus 3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~ 29 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRVACRTCGYE 29 (35)
T ss_dssp BETTTTSBEEEEEETTTTEEESSSS-E
T ss_pred eCCCCCccceEcCCCccCcCCCCCCCc
Confidence 47 8999998875 223369988753
No 191
>PRK08402 replication factor A; Reviewed
Probab=44.54 E-value=83 Score=28.87 Aligned_cols=27 Identities=7% Similarity=-0.257 Sum_probs=19.0
Q ss_pred eeeEEEc-CCCCeeE-EcccceEEecccc
Q 028346 160 GVVSAES-TAGKLVY-CISKYDLNIILFY 186 (210)
Q Consensus 160 GVv~a~~-~~G~~m~-~~~~~~l~C~~~~ 186 (210)
+-++..| .|...|. ..+...-.|+.|.
T Consensus 209 ~~~y~aCp~CnKkv~~~~~~~~~~Ce~~~ 237 (355)
T PRK08402 209 VLVYDACPECRRKVDYDPATDTWICPEHG 237 (355)
T ss_pred CeeEecCCCCCeEEEEecCCCCEeCCCCC
Confidence 3467788 8999886 3333467899887
No 192
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=44.16 E-value=1.1e+02 Score=21.24 Aligned_cols=53 Identities=19% Similarity=0.305 Sum_probs=30.7
Q ss_pred EEEEEEEEecC-eEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC
Q 028346 80 VIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD 146 (210)
Q Consensus 80 ViG~V~~v~~~-~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d 146 (210)
..|+|++..++ .+.|.. .++........|-++.+. ....+||.|..++...++
T Consensus 9 ~~G~Vi~~~~~~~y~V~~--~~g~~~~c~~~Gklr~~~------------i~i~vGD~V~ve~~~~~~ 62 (72)
T PRK00276 9 MEGTVVEALPNAMFRVEL--ENGHEVLAHISGKMRKNY------------IRILPGDKVTVELSPYDL 62 (72)
T ss_pred EEEEEEEEcCCCEEEEEe--CCCCEEEEEEccceeeCC------------cccCCCCEEEEEEcccCC
Confidence 46899998866 666643 233233333445443221 225799999988765543
No 193
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=42.28 E-value=17 Score=22.66 Aligned_cols=23 Identities=17% Similarity=0.086 Sum_probs=17.1
Q ss_pred Ec-CCCC---eeEEccc-ceEEecccch
Q 028346 165 ES-TAGK---LVYCISK-YDLNIILFYS 187 (210)
Q Consensus 165 ~~-~~G~---~m~~~~~-~~l~C~~~~~ 187 (210)
+| +||+ .+.+++. ....||.|+.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 57 7885 3566654 5899999987
No 194
>cd05836 N_Pac_NP60 The PWWP domain is an essential part of the cytokine-like nuclear factor n-pac protein, or NP60, which enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In a variety of cell lines, NP60 has been shown to localize to the nucleus. In addition to the PWWP domain, NP60 also contains an AT-hook and a C-terminal NAD-binding domain. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding proteins, that function as transcription factors regulating a variety of developmental processes.
Probab=42.20 E-value=16 Score=26.42 Aligned_cols=14 Identities=29% Similarity=0.541 Sum_probs=12.0
Q ss_pred CCCCCEEEEEEEEe
Q 028346 131 FRPGDIVRASVLSL 144 (210)
Q Consensus 131 ~~~GDiV~AkV~s~ 144 (210)
|++||+|-||+-..
T Consensus 1 f~~GDlVwaK~~g~ 14 (86)
T cd05836 1 LKLGDLVWAKMKGF 14 (86)
T ss_pred CCCCCEEEEeCCCC
Confidence 68999999998754
No 195
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=42.08 E-value=2.9 Score=28.19 Aligned_cols=29 Identities=14% Similarity=0.011 Sum_probs=21.0
Q ss_pred Ec-CCCCeeEEccc---ceEEecccchhhhHHH
Q 028346 165 ES-TAGKLVYCISK---YDLNIILFYSFWIFCI 193 (210)
Q Consensus 165 ~~-~~G~~m~~~~~---~~l~C~~~~~~~~~~~ 193 (210)
+| .|+..+...+. -+.+||.|..-..+|+
T Consensus 6 RC~~CnKlLa~a~~~~yle~KCPrCK~vN~~~~ 38 (60)
T COG4416 6 RCAKCNKLLAEAEGQAYLEKKCPRCKEVNEFYI 38 (60)
T ss_pred ehHHHhHHHHhcccceeeeecCCccceeeeeec
Confidence 57 78887755543 3789999998777754
No 196
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=41.89 E-value=15 Score=25.74 Aligned_cols=27 Identities=11% Similarity=0.151 Sum_probs=21.2
Q ss_pred eEEEecCCCCCCCCCCCCEEEEEEEEE
Q 028346 61 TVEVTGHKAHGPVPEPGSVVIARVTKV 87 (210)
Q Consensus 61 ~i~V~p~~~~~y~p~vGDiViG~V~~v 87 (210)
-++|-+.--+++-++.||.|.|.|..-
T Consensus 28 DvyVs~~~Irr~~LR~GD~V~G~vr~p 54 (68)
T cd04459 28 DIYVSPSQIRRFNLRTGDTVVGQIRPP 54 (68)
T ss_pred CEEECHHHHHHhCCCCCCEEEEEEeCC
Confidence 378877654578899999999998753
No 197
>cd05834 HDGF_related The PWWP domain is an essential part of the Hepatoma Derived Growth Factor (HDGF) family of proteins, and is necessary for DNA binding by HDGF. This family of endogenous nuclear-targeted mitogens includes HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, HPR2, HPR3, HPR4, respectively) and lens epithelium-derived growth factor, LEDGF. Members of the HDGF family have been linked to human diseases, and HDGF is a prognostic factor in several types of cancer. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=41.62 E-value=17 Score=26.10 Aligned_cols=15 Identities=40% Similarity=0.638 Sum_probs=12.7
Q ss_pred CCCCCCEEEEEEEEe
Q 028346 130 SFRPGDIVRASVLSL 144 (210)
Q Consensus 130 ~~~~GDiV~AkV~s~ 144 (210)
.|++||+|-||+...
T Consensus 2 ~f~~GdlVwaK~kGy 16 (83)
T cd05834 2 QFKAGDLVFAKVKGY 16 (83)
T ss_pred CCCCCCEEEEecCCC
Confidence 489999999998654
No 198
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=41.54 E-value=1e+02 Score=26.28 Aligned_cols=21 Identities=19% Similarity=0.064 Sum_probs=16.5
Q ss_pred CCCEEEEEEEEEecCeEEEEE
Q 028346 76 PGSVVIARVTKVMTRMASADI 96 (210)
Q Consensus 76 vGDiViG~V~~v~~~~a~V~I 96 (210)
--+.+-|||+.+......++.
T Consensus 38 n~~tiEGrVvEV~~~~i~ies 58 (213)
T PRK06763 38 NFSTIEGRVVEVDNGVIVIKS 58 (213)
T ss_pred ccceeeeEEEEEeCCEEEEEe
Confidence 356788999999888877776
No 199
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=41.35 E-value=85 Score=21.98 Aligned_cols=52 Identities=15% Similarity=0.258 Sum_probs=29.1
Q ss_pred EEEEEEEEecC-eEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeC
Q 028346 80 VIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG 145 (210)
Q Consensus 80 ViG~V~~v~~~-~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~ 145 (210)
+.|.|++..++ .+.|.+ ....+-+-|++- +.. .-+-...+||.|..+....+
T Consensus 7 ~~G~V~e~L~~~~f~V~l--------~ng~~vla~i~G----Kmr--~~rI~I~~GD~V~Ve~spyd 59 (68)
T TIGR00008 7 MEGKVTESLPNAMFRVEL--------ENGHEVLAHISG----KIR--MHYIRILPGDKVKVELSPYD 59 (68)
T ss_pred EEEEEEEECCCCEEEEEE--------CCCCEEEEEecC----cch--hccEEECCCCEEEEEECccc
Confidence 68999998654 466666 222222222221 100 01233679999999877654
No 200
>cd05840 SPBC215_ISWI_like The PWWP domain is a component of the S. pombe hypothetical protein SPBC215, as well as ISWI complex protein 4. The ISWI (imitation switch) proteins are ATPases responsible for chromatin remodeling in eukaryotes, and SPBC215 is proposed to also bind chromatin. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=41.22 E-value=17 Score=26.77 Aligned_cols=14 Identities=50% Similarity=0.771 Sum_probs=12.3
Q ss_pred CCCCCEEEEEEEEe
Q 028346 131 FRPGDIVRASVLSL 144 (210)
Q Consensus 131 ~~~GDiV~AkV~s~ 144 (210)
|++||+|-||+-+.
T Consensus 1 f~~GDlVwaK~~Gy 14 (93)
T cd05840 1 FQPGDRVLAKVKGF 14 (93)
T ss_pred CCCCCEEEEeCCCC
Confidence 68999999999864
No 201
>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=40.91 E-value=63 Score=23.84 Aligned_cols=31 Identities=19% Similarity=0.224 Sum_probs=21.7
Q ss_pred CCCCCEEEEEEEEeCCCcceEEEeecCCceee
Q 028346 131 FRPGDIVRASVLSLGDARAYFLSTAKNDLGVV 162 (210)
Q Consensus 131 ~~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv 162 (210)
+++||+|.|+|.++.+. .+.+++...--|-+
T Consensus 1 L~~G~vV~G~V~~v~~~-gl~v~L~~g~~G~v 31 (100)
T cd05693 1 LSEGMLVLGQVKEITKL-DLVISLPNGLTGYV 31 (100)
T ss_pred CCCCCEEEEEEEEEcCC-CEEEECCCCcEEEE
Confidence 57999999999999753 56676654333333
No 202
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=40.61 E-value=15 Score=24.56 Aligned_cols=26 Identities=8% Similarity=-0.308 Sum_probs=17.2
Q ss_pred EEc-CCCCee-EEc--ccceEEecccchhh
Q 028346 164 AES-TAGKLV-YCI--SKYDLNIILFYSFW 189 (210)
Q Consensus 164 a~~-~~G~~m-~~~--~~~~l~C~~~~~~~ 189 (210)
+.| .||..+ +|- ....+.||.|++..
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCEE
Confidence 567 788765 221 24688899998764
No 203
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=40.16 E-value=9.8 Score=21.60 Aligned_cols=21 Identities=10% Similarity=-0.306 Sum_probs=14.6
Q ss_pred c-CCCCeeEEcccceEEecccchhh
Q 028346 166 S-TAGKLVYCISKYDLNIILFYSFW 189 (210)
Q Consensus 166 ~-~~G~~m~~~~~~~l~C~~~~~~~ 189 (210)
| .|+.. +|.+ ...||.|++.+
T Consensus 3 CP~C~~~-V~~~--~~~Cp~CG~~F 24 (26)
T PF10571_consen 3 CPECGAE-VPES--AKFCPHCGYDF 24 (26)
T ss_pred CCCCcCC-chhh--cCcCCCCCCCC
Confidence 5 67766 4544 68899998754
No 204
>PRK07252 hypothetical protein; Provisional
Probab=39.89 E-value=80 Score=24.23 Aligned_cols=27 Identities=19% Similarity=0.194 Sum_probs=20.0
Q ss_pred CCCCCCEEEEEEEEEecC--eEEEEEeee
Q 028346 73 VPEPGSVVIARVTKVMTR--MASADIMCV 99 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~--~a~V~I~~v 99 (210)
..++||.|.++|.++... .+.+.+-.+
T Consensus 47 ~~~vGD~V~VkI~~iD~~~~ri~lSlk~~ 75 (120)
T PRK07252 47 LLKVGEEVLVQVVDFDEYTGKASLSLRTL 75 (120)
T ss_pred ccCCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence 468999999999999863 455555333
No 205
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=39.86 E-value=31 Score=32.40 Aligned_cols=71 Identities=13% Similarity=0.096 Sum_probs=48.9
Q ss_pred eeeCCcEEEe--CCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEe---cCeEEEEEe
Q 028346 23 VKAGKGAYVA--KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVM---TRMASADIM 97 (210)
Q Consensus 23 ~~~G~GtY~~--~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V~~v~---~~~a~V~I~ 97 (210)
...+.|+-+- +|.|.+++.-.+.... ..-|+|.|..-+++-++.||.|.|.|..-+ ...+.+.+.
T Consensus 48 ~~~~~g~le~~~~g~gflr~~~~~y~~~----------~~d~yvs~~~ir~~~lr~gd~v~g~~r~~~~~e~~~~l~~v~ 117 (416)
T PRK09376 48 DIFGEGVLEILPDGFGFLRSPDANYLPG----------PDDIYVSPSQIRRFNLRTGDTVEGKIRPPKEGERYFALLKVE 117 (416)
T ss_pred ceEEEEEEEEcCCCCeEEeCCCcCCCCC----------CCCeeeCHHHHHhcCCCCCCEEEEEeeCCCCCCCccceEEEe
Confidence 4566676653 4666677655554432 123888887656788999999999998643 345888888
Q ss_pred eecccc
Q 028346 98 CVGAKS 103 (210)
Q Consensus 98 ~v~~~~ 103 (210)
.|++.+
T Consensus 118 ~vng~~ 123 (416)
T PRK09376 118 TVNGED 123 (416)
T ss_pred eeCCCC
Confidence 888854
No 206
>cd06850 biotinyl_domain The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase, oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, transcarboxylase and urea amidolyase. This domain functions in transferring CO2 from one subsite to another, allowing carboxylation, decarboxylation, or transcarboxylation. During this process, biotin is covalently attached to a specific lysine.
Probab=39.08 E-value=1e+02 Score=19.67 Aligned_cols=63 Identities=16% Similarity=0.260 Sum_probs=34.6
Q ss_pred EEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEecccc
Q 028346 38 VYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDV 117 (210)
Q Consensus 38 I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v 117 (210)
++|+..|++.. ..+.+.. ..+.||.+. .+. ......+| .+++.|.+....+
T Consensus 2 v~a~~~G~v~~-------------~~v~~G~----~v~~g~~l~-~i~---~~~~~~~i--------~ap~~G~v~~~~~ 52 (67)
T cd06850 2 VTAPMPGTVVK-------------VLVKEGD----KVEAGQPLA-VLE---AMKMENEV--------TAPVAGVVKEILV 52 (67)
T ss_pred ccCCccEEEEE-------------EEeCCCC----EECCCCEEE-EEE---cccEEEEE--------eCCCCEEEEEEEE
Confidence 67788887753 2233221 246677554 443 23345556 7788898764433
Q ss_pred ccccccccccCCCCCCCCEE
Q 028346 118 RATEIDKVDMHLSFRPGDIV 137 (210)
Q Consensus 118 ~~~~~d~~~~~~~~~~GDiV 137 (210)
.. .+.+.+||.+
T Consensus 53 ~~--------G~~V~~G~~l 64 (67)
T cd06850 53 KE--------GDQVEAGQLL 64 (67)
T ss_pred CC--------CCEECCCCEE
Confidence 21 2456677754
No 207
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=39.01 E-value=1.7e+02 Score=21.99 Aligned_cols=58 Identities=17% Similarity=0.267 Sum_probs=33.7
Q ss_pred CCCCCCEEEEEEEEEecC-eEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC
Q 028346 73 VPEPGSVVIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD 146 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~-~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d 146 (210)
.|. .+-++|+|++..++ .+.|.. .....-+-|++- +.. .+=.+++||.|.+.....++
T Consensus 17 ~p~-e~e~~g~V~~~lG~~~~~V~~--------~dG~~~la~i~G----K~R---k~IwI~~GD~VlVe~~~~~~ 75 (100)
T PRK04012 17 MPE-EGEVFGVVEQMLGANRVRVRC--------MDGVERMGRIPG----KMK---KRMWIREGDVVIVAPWDFQD 75 (100)
T ss_pred CCC-CCEEEEEEEEEcCCCEEEEEe--------CCCCEEEEEEch----hhc---ccEEecCCCEEEEEecccCC
Confidence 354 44599999999754 466666 222222222221 111 13457899999999876653
No 208
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=38.95 E-value=1.4e+02 Score=21.28 Aligned_cols=56 Identities=9% Similarity=0.165 Sum_probs=33.9
Q ss_pred CCEEEEEEEEEec-CeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC
Q 028346 77 GSVVIARVTKVMT-RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD 146 (210)
Q Consensus 77 GDiViG~V~~v~~-~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d 146 (210)
..-+.|+|++.-+ ..+.|.+ .....-.-|++. +.. ..+-.+.|||+|.++....++
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~--------edg~~~~ahI~G----Kmr--~~~i~I~~GD~V~Ve~~~~d~ 62 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVEL--------ENGHERLAHISG----KMR--KNRIRILPGDVVLVELSPYDL 62 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEe--------cCCcEEEEEccC----cch--heeEEeCCCCEEEEEeccccc
Confidence 4458899999865 4567766 333333333332 111 113457899999999877653
No 209
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=38.64 E-value=21 Score=21.59 Aligned_cols=23 Identities=9% Similarity=-0.234 Sum_probs=11.1
Q ss_pred Ec-CCCCee---EE--cccceEEecccch
Q 028346 165 ES-TAGKLV---YC--ISKYDLNIILFYS 187 (210)
Q Consensus 165 ~~-~~G~~m---~~--~~~~~l~C~~~~~ 187 (210)
.| .||++| +| -+..-+.|+.|+.
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCC
Confidence 36 789876 45 2345788999874
No 210
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=38.60 E-value=1.2e+02 Score=20.44 Aligned_cols=52 Identities=19% Similarity=0.203 Sum_probs=28.2
Q ss_pred CEEEEEEEEEecC-eEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEe
Q 028346 78 SVVIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSL 144 (210)
Q Consensus 78 DiViG~V~~v~~~-~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~ 144 (210)
+-++|+|++..++ .+.|... ++ ....+.|+-. ... +=.+++||.|.+.+-..
T Consensus 3 ~e~~~~V~~~lG~~~~~V~~~--dg----~~~l~~i~gK-----~r~----~iwI~~GD~V~V~~~~~ 55 (65)
T PF01176_consen 3 GEVIGRVTEMLGNNLFEVECE--DG----EERLARIPGK-----FRK----RIWIKRGDFVLVEPSPY 55 (65)
T ss_dssp TEEEEEEEEEESSSEEEEEET--TS----EEEEEEE-HH-----HHT----CC---TTEEEEEEESTT
T ss_pred cEEEEEEEEECCCCEEEEEeC--CC----CEEEEEeccc-----eee----eEecCCCCEEEEEeccc
Confidence 4589999998754 5777661 11 1233443322 111 13578999999887443
No 211
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=38.14 E-value=8.2 Score=25.63 Aligned_cols=27 Identities=7% Similarity=-0.022 Sum_probs=17.9
Q ss_pred Ec-CCCCeeEEc---ccceEEecccchhhhH
Q 028346 165 ES-TAGKLVYCI---SKYDLNIILFYSFWIF 191 (210)
Q Consensus 165 ~~-~~G~~m~~~---~~~~l~C~~~~~~~~~ 191 (210)
+| .|+..+-.. ..-+++||.|++.+.+
T Consensus 6 RC~~CnklLa~~g~~~~leIKCpRC~tiN~~ 36 (51)
T PF10122_consen 6 RCGHCNKLLAKAGEVIELEIKCPRCKTINHV 36 (51)
T ss_pred eccchhHHHhhhcCccEEEEECCCCCccceE
Confidence 56 677766442 2348999999987643
No 212
>PHA02325 hypothetical protein
Probab=37.80 E-value=9.6 Score=26.59 Aligned_cols=13 Identities=8% Similarity=-0.128 Sum_probs=10.5
Q ss_pred eEEecccchhhhH
Q 028346 179 DLNIILFYSFWIF 191 (210)
Q Consensus 179 ~l~C~~~~~~~~~ 191 (210)
.-.||.|.++||=
T Consensus 3 ~k~CPkC~A~Wld 15 (72)
T PHA02325 3 TKICPKCGARWLD 15 (72)
T ss_pred ccccCccCCEeEc
Confidence 3479999999973
No 213
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=37.78 E-value=23 Score=31.22 Aligned_cols=57 Identities=18% Similarity=0.221 Sum_probs=34.7
Q ss_pred eEEEeecCCceeeEE--------Ec-CCCCeeEEcccceEEecccch---------hhhH------HHHHHhhcccceEE
Q 028346 150 YFLSTAKNDLGVVSA--------ES-TAGKLVYCISKYDLNIILFYS---------FWIF------CILQIASNIISFIT 205 (210)
Q Consensus 150 ~~LSt~~~~LGVv~a--------~~-~~G~~m~~~~~~~l~C~~~~~---------~~~~------~~~~~~~~~~~~~~ 205 (210)
..|++...+++-|.+ .| .||.... .| +..||.|.+ +|++ =.-|.|.-..=|+-
T Consensus 61 ~DL~~~n~d~sEiKsC~rvDQl~~C~~CGa~V~--~~-e~~Cp~C~StnI~r~DdSkWl~~ir~d~E~~e~L~P~~~ylv 137 (314)
T PF09567_consen 61 DDLVMNNDDGSEIKSCYRVDQLGKCNNCGANVS--RL-EESCPNCGSTNIKRKDDSKWLFGIRSDDEFEEYLNPRMIYLV 137 (314)
T ss_pred ccccccCCCcchhhhhhhhhhhhhhccccceee--eh-hhcCCCCCcccccccCCcceecccccHHHHHHhcCccEEEEE
Confidence 455555555555543 47 7998753 35 889999986 5655 13455554444555
Q ss_pred Eeee
Q 028346 206 LFKF 209 (210)
Q Consensus 206 ~~~~ 209 (210)
||.|
T Consensus 138 lfd~ 141 (314)
T PF09567_consen 138 LFDF 141 (314)
T ss_pred Eecc
Confidence 5765
No 214
>PF13375 RnfC_N: RnfC Barrel sandwich hybrid domain
Probab=37.70 E-value=29 Score=25.96 Aligned_cols=11 Identities=27% Similarity=0.495 Sum_probs=9.6
Q ss_pred EEEeEeeeEEE
Q 028346 38 VYASLTGLLRT 48 (210)
Q Consensus 38 I~Asv~G~v~~ 48 (210)
|.||+.|+|.-
T Consensus 69 iHAsvSG~V~~ 79 (101)
T PF13375_consen 69 IHASVSGTVTA 79 (101)
T ss_pred EEcCCCeEEEE
Confidence 99999999875
No 215
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=37.63 E-value=68 Score=24.27 Aligned_cols=23 Identities=30% Similarity=0.410 Sum_probs=21.0
Q ss_pred CCCCCEE------EEEEEEEecCeEEEEE
Q 028346 74 PEPGSVV------IARVTKVMTRMASADI 96 (210)
Q Consensus 74 p~vGDiV------iG~V~~v~~~~a~V~I 96 (210)
.++||.| +|+|+++.++.+.++|
T Consensus 53 Lk~Gd~VvT~gGi~G~Vv~i~~~~v~lei 81 (106)
T PRK05585 53 LAKGDEVVTNGGIIGKVTKVSEDFVIIEL 81 (106)
T ss_pred cCCCCEEEECCCeEEEEEEEeCCEEEEEE
Confidence 6889998 8999999999899888
No 216
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=37.56 E-value=28 Score=23.81 Aligned_cols=16 Identities=13% Similarity=-0.209 Sum_probs=11.9
Q ss_pred EcccceEEecccchhh
Q 028346 174 CISKYDLNIILFYSFW 189 (210)
Q Consensus 174 ~~~~~~l~C~~~~~~~ 189 (210)
-+-...|.||.|+..|
T Consensus 48 ~i~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 48 EIVEGELICPECGREY 63 (68)
T ss_dssp ETTTTEEEETTTTEEE
T ss_pred cccCCEEEcCCCCCEE
Confidence 4555799999998654
No 217
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=37.54 E-value=20 Score=22.98 Aligned_cols=24 Identities=8% Similarity=-0.129 Sum_probs=15.8
Q ss_pred Ec-CCCC---eeEEccc-ceEEecccchh
Q 028346 165 ES-TAGK---LVYCISK-YDLNIILFYSF 188 (210)
Q Consensus 165 ~~-~~G~---~m~~~~~-~~l~C~~~~~~ 188 (210)
+| +||. .+.+.+. ....||.|++.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGGE 35 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCCC
Confidence 57 7887 3444442 35679999974
No 218
>PRK11032 hypothetical protein; Provisional
Probab=37.08 E-value=17 Score=29.67 Aligned_cols=26 Identities=0% Similarity=-0.400 Sum_probs=19.3
Q ss_pred Ec-CCCCeeEE-cccceEEecccchhhh
Q 028346 165 ES-TAGKLVYC-ISKYDLNIILFYSFWI 190 (210)
Q Consensus 165 ~~-~~G~~m~~-~~~~~l~C~~~~~~~~ 190 (210)
.| +||..|.- -....--||.|+..+|
T Consensus 126 vC~~Cg~~~~~~~p~~i~pCp~C~~~~F 153 (160)
T PRK11032 126 VCEKCHHHLAFYTPEVLPLCPKCGHDQF 153 (160)
T ss_pred EecCCCCEEEecCCCcCCCCCCCCCCee
Confidence 68 99998832 2345778999998765
No 219
>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain. The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets []. Secondary structure prediction indicates that the TRAM domain adopts a simple beta-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five beta-strands in the predicted secondary structure [].; PDB: 1YEZ_A 2BH2_A 1UWV_A 1YVC_A.
Probab=36.93 E-value=66 Score=21.09 Aligned_cols=24 Identities=25% Similarity=0.372 Sum_probs=17.7
Q ss_pred CCCCCCEEEEEEEEEecCeEEEEE
Q 028346 73 VPEPGSVVIARVTKVMTRMASADI 96 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~a~V~I 96 (210)
.|.+||.|..+|++.+...++-++
T Consensus 37 ~~~iG~~v~v~I~~~~~~~l~G~~ 60 (61)
T PF01938_consen 37 LPLIGEFVKVRITKAKKNYLFGEL 60 (61)
T ss_dssp -T--TEEEEEEEEEE-SSEEEEEE
T ss_pred CCCCCCEEEEEEEEeeCCcEEEEE
Confidence 355899999999999999887665
No 220
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=36.69 E-value=71 Score=24.42 Aligned_cols=23 Identities=22% Similarity=0.371 Sum_probs=20.8
Q ss_pred CCCCCEE------EEEEEEEecCeEEEEE
Q 028346 74 PEPGSVV------IARVTKVMTRMASADI 96 (210)
Q Consensus 74 p~vGDiV------iG~V~~v~~~~a~V~I 96 (210)
.++||-| +|+|+++.++.+.+++
T Consensus 39 Lk~GD~VvT~gGi~G~V~~I~d~~v~lei 67 (109)
T PRK05886 39 LQPGDRVHTTSGLQATIVGITDDTVDLEI 67 (109)
T ss_pred cCCCCEEEECCCeEEEEEEEeCCEEEEEE
Confidence 6889988 7999999999899888
No 221
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=36.12 E-value=1.2e+02 Score=22.31 Aligned_cols=53 Identities=17% Similarity=0.165 Sum_probs=30.5
Q ss_pred EEEEEEEEec-CeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCC
Q 028346 80 VIARVTKVMT-RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGD 146 (210)
Q Consensus 80 ViG~V~~v~~-~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d 146 (210)
+.|.|+++.+ ..+.|.+. ++........|=++... -.+.+||.|..++...+.
T Consensus 9 ~~G~V~e~Lp~~~frV~Le--nG~~vla~isGKmR~~r------------IrIl~GD~V~VE~spYDl 62 (87)
T PRK12442 9 LDGIVDEVLPDSRFRVTLE--NGVEVGAYASGRMRKHR------------IRILAGDRVTLELSPYDL 62 (87)
T ss_pred EEEEEEEECCCCEEEEEeC--CCCEEEEEeccceeeee------------EEecCCCEEEEEECcccC
Confidence 6899999865 45777771 22222222333222211 235699999998876543
No 222
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=35.96 E-value=3.2e+02 Score=28.63 Aligned_cols=113 Identities=19% Similarity=0.230 Sum_probs=63.3
Q ss_pred CCCCCCCCCEEEEEEEEEecCeEEEEEeeecccc--cc---CceeEEEeccccccccccccccCCCCCCCCEEEE-----
Q 028346 70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKS--VR---EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRA----- 139 (210)
Q Consensus 70 ~~y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~--l~---~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~A----- 139 (210)
+....++||.|.-.+-+..+-+..| ..|.+.. .. ..+.+-| ......|+..|++||.|+.
T Consensus 404 ~~~~F~~GD~VeV~~Gel~glkG~v--e~vdg~~vti~~~~e~l~~pl--------~~~~~eLrKyF~~GDhVKVi~G~~ 473 (1024)
T KOG1999|consen 404 KKHLFSPGDAVEVIVGELKGLKGKV--ESVDGTIVTIMSKHEDLKGPL--------EVPASELRKYFEPGDHVKVIAGRY 473 (1024)
T ss_pred cccccCCCCeEEEeeeeeccceeEE--EeccCceEEEeeccccCCCcc--------ccchHhhhhhccCCCeEEEEeccc
Confidence 3445789999976666655533222 2222210 00 1112211 1112267899999999874
Q ss_pred -----EEEEeCCCcceEEEeecCCceeeEEEc--C---------C-C----CeeEEcccceEEecccchhhhHH
Q 028346 140 -----SVLSLGDARAYFLSTAKNDLGVVSAES--T---------A-G----KLVYCISKYDLNIILFYSFWIFC 192 (210)
Q Consensus 140 -----kV~s~~d~~~~~LSt~~~~LGVv~a~~--~---------~-G----~~m~~~~~~~l~C~~~~~~~~~~ 192 (210)
-|+.+.++.-+.||.-..+-..|+|.. . | | +.|+..+.+.+-|-.++-+..|=
T Consensus 474 eG~tGlVvrVe~~~vi~~Sd~t~eel~Vf~~dlq~c~ev~~gv~~~ge~e~hdlVqLd~~~vgvI~rle~e~~~ 547 (1024)
T KOG1999|consen 474 EGDTGLVVRVEQGDVILLSDLTMEELKVFARDLQLCSEVTLGVEKSGEYELHDLVQLDNQNVGVIVRLERETFQ 547 (1024)
T ss_pred cCCcceEEEEeCCeEEEEecCccceeeEEehhcccchheeecccccccccccceeecCCCcEEEEEEecchhee
Confidence 244454444467777776667777742 1 1 1 24666666677888888777663
No 223
>PF03558 TBSV_P22: TBSV core protein P21/P22; InterPro: IPR005332 Two small nested genes (p19 and p22) are located near the 3' end of the genome of tomato bushy stunt virus (TBSV) - the p19 gene encodes a soluble protein, whereas the p22 gene specifies a membrane-associated protein. p22 is required for cell-to-cell movement in all plants tested [].; GO: 0019028 viral capsid
Probab=35.26 E-value=2e+02 Score=23.70 Aligned_cols=79 Identities=19% Similarity=0.200 Sum_probs=52.0
Q ss_pred CceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEEEeecC---CceeeEEEc--CCCCeeEEc--ccc
Q 028346 106 EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKN---DLGVVSAES--TAGKLVYCI--SKY 178 (210)
Q Consensus 106 ~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LSt~~~---~LGVv~a~~--~~G~~m~~~--~~~ 178 (210)
....|.+..-|++++.-.+.--.+.|..|--|+-.-.- -++.|+++++ .+|+=..++ ..|..|.-. .|.
T Consensus 73 AgV~g~l~L~D~sD~ssr~L~~Tk~fnLG~~i~le~~q----L~F~l~~~gd~PI~F~~t~l~S~F~e~r~LfStSleWq 148 (189)
T PF03558_consen 73 AGVSGVLKLRDISDTSSRKLHCTKEFNLGHGIRLEGSQ----LPFCLPTRGDYPIVFEVTVLVSQFREGRELFSTSLEWQ 148 (189)
T ss_pred cCceEEEEEEEccccccceeeeehhccCCcceEEeecc----CceeeecCCCcceEEEEEEeechhhccceeEEeEeEEE
Confidence 34566666666655443333445778888877655433 3478888775 457766677 788888655 597
Q ss_pred eEEecccchh
Q 028346 179 DLNIILFYSF 188 (210)
Q Consensus 179 ~l~C~~~~~~ 188 (210)
.|..+.|+.+
T Consensus 149 ~~~S~t~~S~ 158 (189)
T PF03558_consen 149 MMLSPTPYSR 158 (189)
T ss_pred eeccCCcccc
Confidence 7777888765
No 224
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=35.21 E-value=18 Score=31.45 Aligned_cols=27 Identities=4% Similarity=-0.134 Sum_probs=21.7
Q ss_pred Ec-CCCCeeEEc-ccceEEecccchhhhH
Q 028346 165 ES-TAGKLVYCI-SKYDLNIILFYSFWIF 191 (210)
Q Consensus 165 ~~-~~G~~m~~~-~~~~l~C~~~~~~~~~ 191 (210)
.| .||.+|... +...+.|+.|+..+++
T Consensus 101 fC~~CG~~~~~~~~~~~~~C~~c~~~~yp 129 (256)
T PRK00241 101 FCGYCGHPMHPSKTEWAMLCPHCRERYYP 129 (256)
T ss_pred cccccCCCCeecCCceeEECCCCCCEECC
Confidence 68 899998654 4458999999988876
No 225
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=35.20 E-value=1.7e+02 Score=25.82 Aligned_cols=22 Identities=9% Similarity=0.155 Sum_probs=19.2
Q ss_pred EEEEEEEEecCeEEEEEeeecc
Q 028346 80 VIARVTKVMTRMASADIMCVGA 101 (210)
Q Consensus 80 ViG~V~~v~~~~a~V~I~~v~~ 101 (210)
++|+|+.|......|.++.-.+
T Consensus 156 LVG~V~~V~~~tS~V~Lltd~~ 177 (284)
T COG1792 156 LVGKVVEVSKNTSRVLLLTDVN 177 (284)
T ss_pred eEEEEEEEcCceeEEEEeeccc
Confidence 7999999999999999987443
No 226
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=35.01 E-value=16 Score=22.21 Aligned_cols=19 Identities=0% Similarity=-0.235 Sum_probs=14.4
Q ss_pred eEEcccceEEecccchhhh
Q 028346 172 VYCISKYDLNIILFYSFWI 190 (210)
Q Consensus 172 m~~~~~~~l~C~~~~~~~~ 190 (210)
.+|.....++|+.|++.|.
T Consensus 18 ~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 18 KIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred HCCCCCcEEECCCCCCEeC
Confidence 3555667899999998773
No 227
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=34.81 E-value=29 Score=20.51 Aligned_cols=23 Identities=13% Similarity=0.124 Sum_probs=18.9
Q ss_pred c-CCCCe-eEEcccceEEecccchh
Q 028346 166 S-TAGKL-VYCISKYDLNIILFYSF 188 (210)
Q Consensus 166 ~-~~G~~-m~~~~~~~l~C~~~~~~ 188 (210)
| .|+.. |+|.+-..++|+.|.+-
T Consensus 4 C~~C~t~L~yP~gA~~vrCs~C~~v 28 (31)
T TIGR01053 4 CGGCRTLLMYPRGASSVRCALCQTV 28 (31)
T ss_pred cCCCCcEeecCCCCCeEECCCCCeE
Confidence 5 68876 59998889999999764
No 228
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=34.81 E-value=1.2e+02 Score=27.04 Aligned_cols=39 Identities=15% Similarity=0.038 Sum_probs=28.6
Q ss_pred CCCCCCCEEEEEEEEEe-cCeEEEEEeeeccccccCceeEEEeccccc
Q 028346 72 PVPEPGSVVIARVTKVM-TRMASADIMCVGAKSVREKFSGIIRQQDVR 118 (210)
Q Consensus 72 y~p~vGDiViG~V~~v~-~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~ 118 (210)
...++|+.-.++|++++ .-.|++|. ..+-+-+++.++.+
T Consensus 69 p~~tvg~~g~~~Vv~v~~~lGaFlD~--------Gl~KDl~vp~~elp 108 (287)
T COG2996 69 PKATVGEYGWLKVVEVNKDLGAFLDW--------GLPKDLLVPLDELP 108 (287)
T ss_pred ceEeecceeEEEEEEEcCCcceEEec--------CCCcceeeehhhcc
Confidence 34689999999999999 77899999 33344555555443
No 229
>PRK12678 transcription termination factor Rho; Provisional
Probab=34.70 E-value=49 Score=32.87 Aligned_cols=69 Identities=17% Similarity=0.100 Sum_probs=44.8
Q ss_pred eeeCCcEEEe-CCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecC---------eE
Q 028346 23 VKAGKGAYVA-KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTR---------MA 92 (210)
Q Consensus 23 ~~~G~GtY~~-~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V~~v~~~---------~a 92 (210)
+.+..|+... +|.+.++.+ |.+.- ..-|+|.+..-+++-++.||.|.|.|..-+.. .+
T Consensus 293 ~~~~~GiLdi~dg~gFlR~~--~y~~~----------~~Dvyvs~~qirr~~Lr~Gd~v~G~vr~p~~~e~~~~r~k~~~ 360 (672)
T PRK12678 293 LVPVAGILDVLDNYAFVRTS--GYLPG----------PNDVYVSMNQVRKNGLRKGDAVTGAVRAPREGEQGNQRQKFNP 360 (672)
T ss_pred eeEeeEEEEecCCeeEeeCC--CCCCC----------CCCeeeCHHHHHHcCCCCCCEEEEeecCCCCCccccccceeee
Confidence 5566665432 455555553 33321 12478887654577889999999999876533 37
Q ss_pred EEEEeeecccc
Q 028346 93 SADIMCVGAKS 103 (210)
Q Consensus 93 ~V~I~~v~~~~ 103 (210)
.+.|..|++.+
T Consensus 361 l~~v~~vNg~~ 371 (672)
T PRK12678 361 LVRLDSVNGMS 371 (672)
T ss_pred eeeEeeeCCCC
Confidence 88888888754
No 230
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=34.52 E-value=27 Score=20.86 Aligned_cols=26 Identities=8% Similarity=-0.098 Sum_probs=14.4
Q ss_pred eeEEEc-CCCCeeEEcccceEEecccchhh
Q 028346 161 VVSAES-TAGKLVYCISKYDLNIILFYSFW 189 (210)
Q Consensus 161 Vv~a~~-~~G~~m~~~~~~~l~C~~~~~~~ 189 (210)
.+..+| .||....|-. ..||.|+...
T Consensus 9 l~~~rC~~Cg~~~~pPr---~~Cp~C~s~~ 35 (37)
T PF12172_consen 9 LLGQRCRDCGRVQFPPR---PVCPHCGSDE 35 (37)
T ss_dssp EEEEE-TTT--EEES-----SEETTTT---
T ss_pred EEEEEcCCCCCEecCCC---cCCCCcCccc
Confidence 455788 8999977633 7899998753
No 231
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=34.30 E-value=24 Score=21.70 Aligned_cols=26 Identities=8% Similarity=-0.143 Sum_probs=18.1
Q ss_pred c-CCCCeeEEcccc---eEEecccchhhhH
Q 028346 166 S-TAGKLVYCISKY---DLNIILFYSFWIF 191 (210)
Q Consensus 166 ~-~~G~~m~~~~~~---~l~C~~~~~~~~~ 191 (210)
| +|+..|.+.... .-.|+.|+-.||-
T Consensus 2 CP~C~~~l~~~~~~~~~id~C~~C~G~W~d 31 (41)
T PF13453_consen 2 CPRCGTELEPVRLGDVEIDVCPSCGGIWFD 31 (41)
T ss_pred cCCCCcccceEEECCEEEEECCCCCeEEcc
Confidence 5 777777555432 4569999888885
No 232
>cd05835 Dnmt3b_related The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of Dnmt3b has been identified in patients with ICF syndrome (immunodeficiency, centromeric instability, and facial anomalies), a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=33.91 E-value=27 Score=25.25 Aligned_cols=14 Identities=29% Similarity=0.605 Sum_probs=12.0
Q ss_pred CCCCCEEEEEEEEe
Q 028346 131 FRPGDIVRASVLSL 144 (210)
Q Consensus 131 ~~~GDiV~AkV~s~ 144 (210)
|.+||+|-||+-..
T Consensus 1 f~vGDlVWaK~kg~ 14 (87)
T cd05835 1 FNVGDLVWGKIKGF 14 (87)
T ss_pred CCCCCEEEEecCCC
Confidence 68999999998764
No 233
>COG1315 Uncharacterized conserved protein [Function unknown]
Probab=33.82 E-value=49 Score=31.95 Aligned_cols=48 Identities=15% Similarity=0.181 Sum_probs=33.4
Q ss_pred CeeeCCcE-EEeCCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCC--CCCCCCCCCCEE
Q 028346 22 EVKAGKGA-YVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHK--AHGPVPEPGSVV 80 (210)
Q Consensus 22 e~~~G~Gt-Y~~~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~--~~~y~p~vGDiV 80 (210)
.+.+|.|| ..+++. +.|+..|..-+ .+++|+|.|.- ....-++.|+|.
T Consensus 220 ~l~lG~nt~~kd~~t--lvA~~~G~~~~---------s~~tI~V~~iyeV~gdV~~kTGnI~ 270 (543)
T COG1315 220 KLNLGKNTAFKDNNT--LVAKRDGQPIV---------SKNTISVYPIYEVNGDVDVKTGNIK 270 (543)
T ss_pred eeecCCCCccCCCCE--EEEeeCCeEEe---------cCCeeEEEEEEEecCCcccccccee
Confidence 38889999 666777 99999999988 34688988731 112334555554
No 234
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=33.63 E-value=29 Score=26.56 Aligned_cols=26 Identities=8% Similarity=-0.164 Sum_probs=18.7
Q ss_pred Ec-CCCCeeEEcccceEEecccchhhh
Q 028346 165 ES-TAGKLVYCISKYDLNIILFYSFWI 190 (210)
Q Consensus 165 ~~-~~G~~m~~~~~~~l~C~~~~~~~~ 190 (210)
.| .|...-.--....|.||.|.+.|-
T Consensus 5 ~cp~c~sEytYed~~~~~cpec~~ew~ 31 (112)
T COG2824 5 PCPKCNSEYTYEDGGQLICPECAHEWN 31 (112)
T ss_pred CCCccCCceEEecCceEeCchhccccc
Confidence 46 676654334445999999999985
No 235
>COG4873 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.24 E-value=56 Score=23.05 Aligned_cols=26 Identities=19% Similarity=0.304 Sum_probs=21.3
Q ss_pred CCCCCEE------EEEEEEEecCeEEEEEeee
Q 028346 74 PEPGSVV------IARVTKVMTRMASADIMCV 99 (210)
Q Consensus 74 p~vGDiV------iG~V~~v~~~~a~V~I~~v 99 (210)
.++|+++ .|+|.++.++.+.||+.--
T Consensus 24 a~vgniief~dgl~g~vek~nensvivdlt~m 55 (81)
T COG4873 24 AKVGNIIEFKDGLTGVVEKVNENSVIVDLTIM 55 (81)
T ss_pred eeccceEEEcccceeeeeeecCCcEEEEEEee
Confidence 4567776 8999999999999999543
No 236
>PHA02942 putative transposase; Provisional
Probab=33.22 E-value=23 Score=32.65 Aligned_cols=24 Identities=8% Similarity=-0.117 Sum_probs=18.8
Q ss_pred Ec-CCCCeeEEcccceEEecccchh
Q 028346 165 ES-TAGKLVYCISKYDLNIILFYSF 188 (210)
Q Consensus 165 ~~-~~G~~m~~~~~~~l~C~~~~~~ 188 (210)
.| .||..+.+.+...+.|+.|+..
T Consensus 327 ~Cs~CG~~~~~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 327 SCPKCGHKMVEIAHRYFHCPSCGYE 351 (383)
T ss_pred cCCCCCCccCcCCCCEEECCCCCCE
Confidence 47 7999876556568999999973
No 237
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=32.78 E-value=12 Score=20.49 Aligned_cols=20 Identities=5% Similarity=-0.336 Sum_probs=14.4
Q ss_pred c-CCCCeeEEcccceEEecccchh
Q 028346 166 S-TAGKLVYCISKYDLNIILFYSF 188 (210)
Q Consensus 166 ~-~~G~~m~~~~~~~l~C~~~~~~ 188 (210)
| .||..+-+ +...||.|++.
T Consensus 2 Cp~CG~~~~~---~~~fC~~CG~~ 22 (23)
T PF13240_consen 2 CPNCGAEIED---DAKFCPNCGTP 22 (23)
T ss_pred CcccCCCCCC---cCcchhhhCCc
Confidence 6 78888643 45679999874
No 238
>cd05841 BS69_related The PWWP domain is part of BS69 protein, a nuclear protein that specifically binds adenoviral E1A and Epstein-Barr viral EBNA2 proteins, suppressing their transactivation functions. BS69 is a multi-domain protein, containing bromo, PHD, PWWP, and MYND domains. The specific role of the PWWP domain within BS69 is not clearly identified, but BS69 functions in chromatin remodeling, consistent with other PWWP-containing proteins. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=32.43 E-value=33 Score=24.97 Aligned_cols=18 Identities=17% Similarity=0.198 Sum_probs=15.0
Q ss_pred CCCCCCCCEEEEEEEEeC
Q 028346 128 HLSFRPGDIVRASVLSLG 145 (210)
Q Consensus 128 ~~~~~~GDiV~AkV~s~~ 145 (210)
..|..+||+|-||+...-
T Consensus 4 ~pc~~p~dLVwAK~kGyp 21 (83)
T cd05841 4 EPCRPPHELVWAKLKGFP 21 (83)
T ss_pred cccCCCCCEEEEeCCCCC
Confidence 478999999999987653
No 239
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=31.66 E-value=1e+02 Score=20.16 Aligned_cols=49 Identities=22% Similarity=0.246 Sum_probs=25.5
Q ss_pred EEEEEEEEe---cCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEE
Q 028346 80 VIARVTKVM---TRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRAS 140 (210)
Q Consensus 80 ViG~V~~v~---~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~Ak 140 (210)
|.|+|+++. ...+++.|- ...|.+..-=.. .+.....+.+++||.|.++
T Consensus 3 v~G~V~~~~~~~~~~~~~~l~---------D~tg~i~~~~~~---~~~~~~~~~l~~g~~v~v~ 54 (75)
T PF01336_consen 3 VEGRVTSIRRSGGKIVFFTLE---------DGTGSIQVVFFN---EEYERFREKLKEGDIVRVR 54 (75)
T ss_dssp EEEEEEEEEEEETTEEEEEEE---------ETTEEEEEEEET---HHHHHHHHTS-TTSEEEEE
T ss_pred EEEEEEEEEcCCCCEEEEEEE---------ECCccEEEEEcc---HHhhHHhhcCCCCeEEEEE
Confidence 678888883 344566652 111332222111 0111456789999998765
No 240
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=31.61 E-value=23 Score=21.53 Aligned_cols=26 Identities=0% Similarity=-0.193 Sum_probs=17.7
Q ss_pred Ec-CCCCee------EEcccceEEecccchhhh
Q 028346 165 ES-TAGKLV------YCISKYDLNIILFYSFWI 190 (210)
Q Consensus 165 ~~-~~G~~m------~~~~~~~l~C~~~~~~~~ 190 (210)
.| .|+... ++.....++||.|++.|.
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 46 666532 344456899999998874
No 241
>PF15616 TerY-C: TerY-C metal binding domain
Probab=31.45 E-value=46 Score=26.31 Aligned_cols=30 Identities=17% Similarity=-0.025 Sum_probs=21.7
Q ss_pred ceee--EEEcCCCCeeEEcccceEEecccchh
Q 028346 159 LGVV--SAESTAGKLVYCISKYDLNIILFYSF 188 (210)
Q Consensus 159 LGVv--~a~~~~G~~m~~~~~~~l~C~~~~~~ 188 (210)
.|-- +|.|.||+.|=--+..+..||-|++.
T Consensus 83 CGn~~~fa~C~CGkl~Ci~g~~~~~CPwCg~~ 114 (131)
T PF15616_consen 83 CGNQYAFAVCGCGKLFCIDGEGEVTCPWCGNE 114 (131)
T ss_pred CcChhcEEEecCCCEEEeCCCCCEECCCCCCe
Confidence 3544 45679999984344569999999864
No 242
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=30.73 E-value=1.8e+02 Score=21.31 Aligned_cols=55 Identities=20% Similarity=0.325 Sum_probs=31.4
Q ss_pred EEEEEEEEEec--CeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEE
Q 028346 79 VVIARVTKVMT--RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRAS 140 (210)
Q Consensus 79 iViG~V~~v~~--~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~Ak 140 (210)
.|.|+|.+++. +.++++|.. + ....+.++..++....... +....++.||.|.++
T Consensus 3 ~v~GwV~~~R~~g~~~Fi~lrd--~---~~~lQ~v~~~~~~~~~~~~--~~~~~l~~g~~V~v~ 59 (108)
T cd04322 3 SVAGRIMSKRGSGKLSFADLQD--E---SGKIQVYVNKDDLGEEEFE--DFKKLLDLGDIIGVT 59 (108)
T ss_pred EEEEEEEEEecCCCeEEEEEEE--C---CeEEEEEEECCCCCHHHHH--HHHhcCCCCCEEEEE
Confidence 47899999985 457788732 1 1345566544432111111 223348999998764
No 243
>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=30.40 E-value=2e+02 Score=20.35 Aligned_cols=51 Identities=18% Similarity=0.189 Sum_probs=28.8
Q ss_pred EEEEEEEEecC-eEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeC
Q 028346 80 VIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG 145 (210)
Q Consensus 80 ViG~V~~v~~~-~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~ 145 (210)
++|+|++..++ .+.|... ++ ....+.|+- +. .-+=.+++||.|.+.....+
T Consensus 2 ~~g~V~~~~g~~~~~V~~~--~g----~~~la~i~g------K~---rk~iwI~~GD~V~Ve~~~~d 53 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCF--DG----KKRLCRIRG------KM---RKRVWINEGDIVLVAPWDFQ 53 (77)
T ss_pred EEEEEEEEcCCCEEEEEEC--CC----CEEEEEEch------hh---cccEEEcCCCEEEEEecccc
Confidence 68999998754 4666661 11 112232221 11 11345689999999866553
No 244
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=30.30 E-value=1.6e+02 Score=19.25 Aligned_cols=55 Identities=20% Similarity=0.353 Sum_probs=32.8
Q ss_pred CCEEEEEEEEEecCeEEEEEee-eccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEE
Q 028346 77 GSVVIARVTKVMTRMASADIMC-VGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLS 143 (210)
Q Consensus 77 GDiViG~V~~v~~~~a~V~I~~-v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s 143 (210)
...+-|+|.++......+++.. .++ ...+.+.++.+.+. +-.+++||-|.|.+.+
T Consensus 6 ~N~l~g~I~~i~~~g~~~~v~l~~~~---~~~l~a~i~~~~~~---------~l~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 6 RNQLKGKVVAIEDGDVNAEVDLLLGG---GTKLTAVITLESVA---------ELGLKPGKEVYAVIKA 61 (69)
T ss_pred ccEEEEEEEEEEECCCeEEEEEEECC---CCEEEEEecHHHHh---------hCCCCCCCEEEEEEEC
Confidence 3568899999966554444421 111 11455555543322 1347899999999875
No 245
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=30.29 E-value=93 Score=26.14 Aligned_cols=23 Identities=22% Similarity=0.106 Sum_probs=19.6
Q ss_pred CCCCCCEEEEEEEEEecCeEEEEE
Q 028346 73 VPEPGSVVIARVTKVMTRMASADI 96 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~a~V~I 96 (210)
-.++||+|.|+|++.. +...+.+
T Consensus 118 ~f~~GDivrA~Vis~~-~~~~Lst 140 (188)
T COG1096 118 AFRIGDIVRARVISTG-DPIQLST 140 (188)
T ss_pred ccccccEEEEEEEecC-CCeEEEe
Confidence 3589999999999998 6677777
No 246
>PRK05889 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Provisional
Probab=29.72 E-value=1.8e+02 Score=19.62 Aligned_cols=50 Identities=12% Similarity=0.147 Sum_probs=29.9
Q ss_pred EEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccc
Q 028346 38 VYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQD 116 (210)
Q Consensus 38 I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~ 116 (210)
|+|...|.+.. +.|..-. ..+.||.+. .| ........| .++..|.+....
T Consensus 5 v~a~~~G~i~~-------------~~v~~Gd----~V~~g~~l~-~v---e~~K~~~~I--------~a~~~G~V~~i~ 54 (71)
T PRK05889 5 VRAEIVASVLE-------------VVVNEGD----QIGKGDTLV-LL---ESMKMEIPV--------LAEVAGTVSKVS 54 (71)
T ss_pred EeCCCCEEEEE-------------EEeCCCC----EECCCCEEE-EE---EeccceeEE--------eCCCCEEEEEEE
Confidence 88888898754 3444321 246777665 33 333355556 677888776544
No 247
>cd05162 PWWP The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.
Probab=29.54 E-value=35 Score=24.18 Aligned_cols=14 Identities=50% Similarity=0.895 Sum_probs=12.2
Q ss_pred CCCCCEEEEEEEEe
Q 028346 131 FRPGDIVRASVLSL 144 (210)
Q Consensus 131 ~~~GDiV~AkV~s~ 144 (210)
|++||+|-||+.+.
T Consensus 1 f~~GdlVwaK~~g~ 14 (87)
T cd05162 1 FRPGDLVWAKMKGY 14 (87)
T ss_pred CCCCCEEEEeCCCC
Confidence 68999999999864
No 248
>CHL00010 infA translation initiation factor 1
Probab=29.35 E-value=2.1e+02 Score=20.21 Aligned_cols=52 Identities=23% Similarity=0.300 Sum_probs=30.4
Q ss_pred EEEEEEEEe-cCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeC
Q 028346 80 VIARVTKVM-TRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLG 145 (210)
Q Consensus 80 ViG~V~~v~-~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~ 145 (210)
+.|+|+++. ...+.|.. -++........|-++.+ .-...+||.|..++...+
T Consensus 9 ~~G~Vik~lg~~~y~V~~--~~g~~~~c~~rGklr~~------------~i~~~vGD~V~ve~~~~~ 61 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRL--DNGCQVLGYISGKIRRN------------SIRILPGDRVKVELSPYD 61 (78)
T ss_pred EEEEEEEEcCCCEEEEEe--CCCCEEEEEeccceecC------------CcccCCCCEEEEEEcccC
Confidence 579999998 46677753 23322233344544311 122468999998875544
No 249
>COG4393 Predicted membrane protein [Function unknown]
Probab=29.31 E-value=73 Score=29.34 Aligned_cols=36 Identities=14% Similarity=0.122 Sum_probs=27.2
Q ss_pred cCCceeeEEEc-CCCCeeEEcccceEEecccchhhhH
Q 028346 156 KNDLGVVSAES-TAGKLVYCISKYDLNIILFYSFWIF 191 (210)
Q Consensus 156 ~~~LGVv~a~~-~~G~~m~~~~~~~l~C~~~~~~~~~ 191 (210)
+..+|.++--| -||..-+-+..+++.|.-|.-|-+.
T Consensus 327 r~s~~avfDAC~iCGd~GYv~e~dqvICv~C~Vrmfi 363 (405)
T COG4393 327 RLSLGAVFDACDICGDQGYVMEGDQVICVRCDVRMFI 363 (405)
T ss_pred CCCceeeehHHHhccccceEeECCEEEEEEccEEEEc
Confidence 34568888778 8988766666789999999876543
No 250
>PRK12495 hypothetical protein; Provisional
Probab=29.21 E-value=27 Score=30.11 Aligned_cols=25 Identities=8% Similarity=-0.134 Sum_probs=19.4
Q ss_pred EEc-CCCCeeEEcccceEEecccchhh
Q 028346 164 AES-TAGKLVYCISKYDLNIILFYSFW 189 (210)
Q Consensus 164 a~~-~~G~~m~~~~~~~l~C~~~~~~~ 189 (210)
..| .||.++-.+. ....||.|...+
T Consensus 43 ~hC~~CG~PIpa~p-G~~~Cp~CQ~~~ 68 (226)
T PRK12495 43 AHCDECGDPIFRHD-GQEFCPTCQQPV 68 (226)
T ss_pred hhcccccCcccCCC-CeeECCCCCCcc
Confidence 357 8999986665 489999998653
No 251
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=28.77 E-value=1.1e+02 Score=22.98 Aligned_cols=23 Identities=26% Similarity=0.341 Sum_probs=19.6
Q ss_pred CCCCCEE------EEEEEEEecCeEEEEE
Q 028346 74 PEPGSVV------IARVTKVMTRMASADI 96 (210)
Q Consensus 74 p~vGDiV------iG~V~~v~~~~a~V~I 96 (210)
.++||.| .|+|+++.++...+++
T Consensus 44 L~kGD~VvT~gGi~G~V~~v~d~~v~I~l 72 (97)
T COG1862 44 LKKGDEVVTIGGIVGTVTKVGDDTVEIEL 72 (97)
T ss_pred ccCCCEEEEcCCeEEEEEEEecCcEEEEE
Confidence 5789988 7999999998877777
No 252
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=28.54 E-value=25 Score=28.27 Aligned_cols=26 Identities=8% Similarity=-0.293 Sum_probs=18.7
Q ss_pred Ec-CCCCeeEE-cccceEEecccchhhh
Q 028346 165 ES-TAGKLVYC-ISKYDLNIILFYSFWI 190 (210)
Q Consensus 165 ~~-~~G~~m~~-~~~~~l~C~~~~~~~~ 190 (210)
.| +||..|.- -....-.||.|+...|
T Consensus 114 ~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F 141 (146)
T PF07295_consen 114 VCENCGHEVELTHPERLPPCPKCGHTEF 141 (146)
T ss_pred ecccCCCEEEecCCCcCCCCCCCCCCee
Confidence 68 89998732 2345788999987654
No 253
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=28.38 E-value=39 Score=19.09 Aligned_cols=21 Identities=10% Similarity=0.018 Sum_probs=16.8
Q ss_pred CCCCe-eEEcccceEEecccch
Q 028346 167 TAGKL-VYCISKYDLNIILFYS 187 (210)
Q Consensus 167 ~~G~~-m~~~~~~~l~C~~~~~ 187 (210)
.|+.. |+|.+-...+|+.|.+
T Consensus 3 ~Cr~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 3 GCRTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CCCceEEcCCCCCCeECCccCc
Confidence 56654 7999888999999975
No 254
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=27.99 E-value=16 Score=35.27 Aligned_cols=35 Identities=9% Similarity=-0.031 Sum_probs=16.0
Q ss_pred EEEc-CCCCeeEEcccceEEecccchhhhHHHHHHhhcccceEE
Q 028346 163 SAES-TAGKLVYCISKYDLNIILFYSFWIFCILQIASNIISFIT 205 (210)
Q Consensus 163 ~a~~-~~G~~m~~~~~~~l~C~~~~~~~~~~~~~~~~~~~~~~~ 205 (210)
..+| .||.... . ...||.|+... ++++.-+.+|+.
T Consensus 491 ~~~C~~CG~~~~---~-~~~CP~CGs~~----~~~~~Rv~GYl~ 526 (546)
T PF13597_consen 491 IDICPDCGYIGG---E-GDKCPKCGSEN----IEVYSRVTGYLR 526 (546)
T ss_dssp EEEETTT---S------EEE-CCC--------EEEEB-SSSS-B
T ss_pred cccccCCCcCCC---C-CCCCCCCCCcc----cceEEEeecccc
Confidence 3578 8998643 2 68899999987 555666666653
No 255
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=27.82 E-value=55 Score=20.25 Aligned_cols=22 Identities=9% Similarity=-0.192 Sum_probs=13.4
Q ss_pred c-CCCCeeE--EcccceEEecccch
Q 028346 166 S-TAGKLVY--CISKYDLNIILFYS 187 (210)
Q Consensus 166 ~-~~G~~m~--~~~~~~l~C~~~~~ 187 (210)
| .||...+ .-...++.|+.|+.
T Consensus 3 Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 3 CPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp BTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CcCCcCCceEEcCCCCeEECCCCCC
Confidence 5 6777542 22345888888874
No 256
>PRK06386 replication factor A; Reviewed
Probab=27.50 E-value=4.9e+02 Score=23.98 Aligned_cols=21 Identities=5% Similarity=-0.107 Sum_probs=15.9
Q ss_pred eEEEc-CCCCeeEEcccceEEecccch
Q 028346 162 VSAES-TAGKLVYCISKYDLNIILFYS 187 (210)
Q Consensus 162 v~a~~-~~G~~m~~~~~~~l~C~~~~~ 187 (210)
+..+| .|+..+.. | +||.|+.
T Consensus 235 li~rCP~C~R~l~~--g---~C~~HG~ 256 (358)
T PRK06386 235 IFTKCSVCNKIIED--G---VCKDHPD 256 (358)
T ss_pred eEecCcCCCeEccC--C---cCCCCCC
Confidence 56678 89988873 3 8988875
No 257
>PRK07218 replication factor A; Provisional
Probab=27.21 E-value=2.1e+02 Score=26.92 Aligned_cols=36 Identities=8% Similarity=0.072 Sum_probs=24.0
Q ss_pred EEEEEEEEeCCCcceEEEeecCCceeeEEEc-CCCCeeEEcccceEEecccchh
Q 028346 136 IVRASVLSLGDARAYFLSTAKNDLGVVSAES-TAGKLVYCISKYDLNIILFYSF 188 (210)
Q Consensus 136 iV~AkV~s~~d~~~~~LSt~~~~LGVv~a~~-~~G~~m~~~~~~~l~C~~~~~~ 188 (210)
.|...|+++.++. -+..+| .|+..|.. -+||.|+.-
T Consensus 282 ev~G~Iv~i~~gs------------gli~rCP~C~r~v~~-----~~C~~hG~v 318 (423)
T PRK07218 282 ELVGNIISVRDGS------------GLIERCPECGRVIQK-----GQCRSHGAV 318 (423)
T ss_pred EEEEEEEEeccCC------------cceecCcCccccccC-----CcCCCCCCc
Confidence 4777788775431 244578 88888743 378888754
No 258
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=27.10 E-value=1.6e+02 Score=23.95 Aligned_cols=55 Identities=16% Similarity=0.204 Sum_probs=29.7
Q ss_pred CCCCCCEEEEEEEEEecCe-EEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEE
Q 028346 73 VPEPGSVVIARVTKVMTRM-ASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLS 143 (210)
Q Consensus 73 ~p~vGDiViG~V~~v~~~~-a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s 143 (210)
.|..|+ ++|+|++..++. +.|.. -++ ..-+-|++- +.. .+-.+++||+|.+..-.
T Consensus 28 ~~eegq-~~g~V~~~LGn~~f~V~c--~dG------~~rLa~I~G----KmR---K~IWI~~GD~VlVel~~ 83 (155)
T PTZ00329 28 FKEEGQ-EYAQVLRMLGNGRLEAYC--FDG------VKRLCHIRG----KMR---KRVWINIGDIILVSLRD 83 (155)
T ss_pred cCCCCc-EEEEEEEEcCCCEEEEEE--CCC------CEEEEEeec----cce---eeEEecCCCEEEEeccC
Confidence 355565 799999997653 55555 222 222222221 111 12446789999886543
No 259
>PF12508 DUF3714: Protein of unknown function (DUF3714) ; InterPro: IPR022187 Proteins in this entry are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage.
Probab=26.98 E-value=3.9e+02 Score=22.56 Aligned_cols=55 Identities=13% Similarity=0.162 Sum_probs=38.8
Q ss_pred eEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCC----CCCCCCCCCCEEEEEEEEEecCeEEEEEeeec
Q 028346 36 GLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHK----AHGPVPEPGSVVIARVTKVMTRMASADIMCVG 100 (210)
Q Consensus 36 ~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~----~~~y~p~vGDiViG~V~~v~~~~a~V~I~~v~ 100 (210)
..|+|.+-|..+... . ..+..+=+. +...+|+ |..++| +.++.+.+..+.|.++.
T Consensus 53 n~I~A~V~~~qtv~~------G--s~vrlRLle~i~i~g~~IPk-gt~l~G-~~~~~~~Rl~i~I~SI~ 111 (200)
T PF12508_consen 53 NTIRAVVDGTQTVVD------G--SRVRLRLLEDIQIGGILIPK-GTYLYG-VASFQGQRLLITITSIE 111 (200)
T ss_pred CeEEEEEecceEEeC------C--CEEEEEEcCceEECCEEeCC-CCEEEE-EEeeeccEEEEEEEEEE
Confidence 459999999887742 1 234433111 2345565 999999 99999999999997654
No 260
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=26.71 E-value=24 Score=34.89 Aligned_cols=35 Identities=14% Similarity=0.038 Sum_probs=25.3
Q ss_pred EEc-CCCCeeEEcccceEEecccchhhhHHHHHHhhcccceEE
Q 028346 164 AES-TAGKLVYCISKYDLNIILFYSFWIFCILQIASNIISFIT 205 (210)
Q Consensus 164 a~~-~~G~~m~~~~~~~l~C~~~~~~~~~~~~~~~~~~~~~~~ 205 (210)
++| .||..+ ....-.||.|+... ++++.-+.+|+.
T Consensus 569 ~~C~~CG~~~---~g~~~~CP~CGs~~----~~v~~Rv~GYl~ 604 (625)
T PRK08579 569 TVCNKCGRST---TGLYTRCPRCGSED----VEVWSRIIGYYR 604 (625)
T ss_pred ccCCCCCCcc---CCCCCcCcCCCCch----hHHHHHHHhhhc
Confidence 478 899854 23467999999863 677777777764
No 261
>PF00855 PWWP: PWWP domain; InterPro: IPR000313 Upon characterisation of WHSC1, a gene mapping to the Wolf-Hirschhornsyndrome critical region and at its C terminus similar to the Drosophila melanogaster ASH1/trithorax group proteins, a novel protein domain designated PWWP domain was identified []. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. It is present in proteins of nuclear origin and plays a role in cell growth and differentiation. Due to its position, the composition of amino acids close to the PWWP motif and the pattern of other domains present it has been suggested that the domain is involved in protein-protein interactions [].; PDB: 3LYI_B 2L89_A 2NLU_A 1RI0_A 1KHC_A 3QKJ_C 2DAQ_A 1N27_A 3PFS_B 3QJ6_A ....
Probab=26.71 E-value=40 Score=23.46 Aligned_cols=13 Identities=54% Similarity=0.969 Sum_probs=10.3
Q ss_pred CCCCCEEEEEEEE
Q 028346 131 FRPGDIVRASVLS 143 (210)
Q Consensus 131 ~~~GDiV~AkV~s 143 (210)
|++||+|-||+-.
T Consensus 1 f~~GdlVWaK~~g 13 (86)
T PF00855_consen 1 FRPGDLVWAKLKG 13 (86)
T ss_dssp -STTEEEEEEETT
T ss_pred CCCCCEEEEEeCC
Confidence 6899999999843
No 262
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=26.50 E-value=2.7e+02 Score=20.83 Aligned_cols=19 Identities=21% Similarity=0.218 Sum_probs=14.1
Q ss_pred EEEEEEEecCeEEEEEeee
Q 028346 81 IARVTKVMTRMASADIMCV 99 (210)
Q Consensus 81 iG~V~~v~~~~a~V~I~~v 99 (210)
+|+|.+|..+...|-+-.+
T Consensus 22 ~G~V~~V~~~~~~V~Vegv 40 (105)
T PRK00004 22 RGKVLKVLPKKNKVIVEGV 40 (105)
T ss_pred EEEEEEEEcCCCEEEEcCc
Confidence 5999999877777666433
No 263
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=26.29 E-value=1.1e+02 Score=30.53 Aligned_cols=52 Identities=19% Similarity=0.114 Sum_probs=32.2
Q ss_pred CCCCCCCEEEEEEEEeCCCcceEEEe----ecCCceeeEEEc-CCCCeeEEcccceEEecc
Q 028346 129 LSFRPGDIVRASVLSLGDARAYFLST----AKNDLGVVSAES-TAGKLVYCISKYDLNIIL 184 (210)
Q Consensus 129 ~~~~~GDiV~AkV~s~~d~~~~~LSt----~~~~LGVv~a~~-~~G~~m~~~~~~~l~C~~ 184 (210)
.-+++||.|. |...|+--+..... +..++ .+-..| .||++++. ....+.|+.
T Consensus 388 ~di~iGD~V~--V~raGdVIPkI~~vv~~~~~~~~-~~P~~CP~C~~~l~~-~~~~~~C~n 444 (689)
T PRK14351 388 LGVNVGDRVR--VKRAGDVIPYVEEVVEKDSEGTF-EFPDTCPVCDSAVER-DGPLAFCTG 444 (689)
T ss_pred cCCCCCCEEE--EEecCCccceeeeeecccCCCCC-cCCCCCCCCCCEeee-CCceEEcCC
Confidence 4468999998 66666653333332 11222 334578 99999876 345777874
No 264
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=26.10 E-value=13 Score=29.52 Aligned_cols=29 Identities=7% Similarity=-0.184 Sum_probs=20.3
Q ss_pred Ec-CCCCeeEEcc-cceEEecccchhhhHHH
Q 028346 165 ES-TAGKLVYCIS-KYDLNIILFYSFWIFCI 193 (210)
Q Consensus 165 ~~-~~G~~m~~~~-~~~l~C~~~~~~~~~~~ 193 (210)
+| +||...--.+ ...--||.|+-..|.|+
T Consensus 3 ~Ct~Cg~~f~dgs~eil~GCP~CGg~kF~yv 33 (131)
T PF09845_consen 3 QCTKCGRVFEDGSKEILSGCPECGGNKFQYV 33 (131)
T ss_pred ccCcCCCCcCCCcHHHHccCcccCCcceEEc
Confidence 57 8998754444 22345999999998874
No 265
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.86 E-value=40 Score=25.89 Aligned_cols=22 Identities=9% Similarity=0.077 Sum_probs=17.3
Q ss_pred EEEc-CCCCeeEEcccceEEecccch
Q 028346 163 SAES-TAGKLVYCISKYDLNIILFYS 187 (210)
Q Consensus 163 ~a~~-~~G~~m~~~~~~~l~C~~~~~ 187 (210)
.-+| .||..|+- .+|+|+.|.+
T Consensus 6 ~~~cPvcg~~~iV---TeL~c~~~et 28 (122)
T COG3877 6 INRCPVCGRKLIV---TELKCSNCET 28 (122)
T ss_pred CCCCCccccccee---EEEecCCCCc
Confidence 3468 89999873 5799999976
No 266
>PF04319 NifZ: NifZ domain; InterPro: IPR007415 NifZ is a short protein is found in the nif (nitrogen fixation) operon. It is required for the maturation of the nitrogenase MoFe protein. In the absence of NifZ, only one of the two P-clusters of the MoFe protein is matured to the ultimate [8Fe-7S] structure. The other P-cluster site in the protein contains a [4Fe-4S] cluster pair, suggesting that NifZ is specifically required for the formation of the second P-cluster [, , ].; GO: 0009399 nitrogen fixation
Probab=25.59 E-value=2.5e+02 Score=20.00 Aligned_cols=21 Identities=38% Similarity=0.295 Sum_probs=17.5
Q ss_pred cCCCCCCCCEEEEEEEEeCCC
Q 028346 127 MHLSFRPGDIVRASVLSLGDA 147 (210)
Q Consensus 127 ~~~~~~~GDiV~AkV~s~~d~ 147 (210)
|.+.|++||.|+|...-.+|+
T Consensus 1 ~~p~f~~G~~V~a~~~irNDG 21 (75)
T PF04319_consen 1 MPPRFEWGDKVRARKDIRNDG 21 (75)
T ss_pred CCCccCCCCEEEEEEEeEcCC
Confidence 347799999999998887775
No 267
>PF04351 PilP: Pilus assembly protein, PilP; InterPro: IPR007446 The PilP family are periplasmic proteins involved in the biogenesis of type IV pili [].; PDB: 2Y4Y_B 2Y4X_A 2IVW_A 2LC4_A.
Probab=25.41 E-value=81 Score=25.00 Aligned_cols=28 Identities=11% Similarity=0.065 Sum_probs=20.7
Q ss_pred CCCCCCCCCCCEE---EEEEEEEecCeEEEE
Q 028346 68 KAHGPVPEPGSVV---IARVTKVMTRMASAD 95 (210)
Q Consensus 68 ~~~~y~p~vGDiV---iG~V~~v~~~~a~V~ 95 (210)
.+..|..++||.+ .|+|++|+++.+.+.
T Consensus 99 dg~v~~V~~G~yiG~n~G~I~~Is~~~I~l~ 129 (149)
T PF04351_consen 99 DGKVYRVKVGDYIGQNYGRITSISEDSIELV 129 (149)
T ss_dssp TTEEEEEETTEEETTTTEEEEEEETTEEEEE
T ss_pred CCCEEEecCCCEeccCCCEEEEEeCCeEEEE
Confidence 3455666777777 799999999886654
No 268
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=25.19 E-value=2.4e+02 Score=24.05 Aligned_cols=30 Identities=13% Similarity=0.159 Sum_probs=20.7
Q ss_pred CCCCEEEEEEEEeCCCcceEEEeecCCceee
Q 028346 132 RPGDIVRASVLSLGDARAYFLSTAKNDLGVV 162 (210)
Q Consensus 132 ~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv 162 (210)
++||+|.++|.++.+. .+.+.+.+.-.|.+
T Consensus 62 ~vGDiViG~V~~i~~~-~~~vdI~~~~~g~L 91 (235)
T PRK04163 62 KVGDLVIGKVTDVTFS-GWEVDINSPYKAYL 91 (235)
T ss_pred CCCCEEEEEEEEEeCc-eEEEEeCCCceeEE
Confidence 7999999999998643 35666554433433
No 269
>cd03478 Rieske_AIFL_N AIFL (apoptosis-inducing factor like) family, N-terminal Rieske domain; members of this family show similarity to human AIFL, containing an N-terminal Rieske domain and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain (Pyr_redox). The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. AIFL shares 35% homology with human AIF (apoptosis-inducing factor), mainly in the Pyr_redox domain. AIFL is predominantly localized to the mitochondria. AIFL induces apoptosis in a caspase-dependent manner.
Probab=25.02 E-value=1.9e+02 Score=20.49 Aligned_cols=53 Identities=15% Similarity=0.196 Sum_probs=29.1
Q ss_pred CCCCCCEEEEEEEEeCCCcceEEEeecCCceeeEEEc-CC---CCeeEE--cccceEEecccchhh
Q 028346 130 SFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAES-TA---GKLVYC--ISKYDLNIILFYSFW 189 (210)
Q Consensus 130 ~~~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv~a~~-~~---G~~m~~--~~~~~l~C~~~~~~~ 189 (210)
.+.+|+....++ + +..+.|.-.+ |.++|.. .| |.+|.. ...+.+.||--+.+|
T Consensus 8 ~l~~g~~~~~~~---~-~~~v~v~r~~---g~~~A~~~~CpH~g~~L~~g~~~~~~i~CP~Hg~~F 66 (95)
T cd03478 8 DLGDGEMKEVDV---G-DGKVLLVRQG---GEVHAIGAKCPHYGAPLAKGVLTDGRIRCPWHGACF 66 (95)
T ss_pred hCCCCCEEEEEe---C-CcEEEEEEEC---CEEEEEcCcCcCCCCccCCCeEeCCEEEcCCCCCEE
Confidence 356777766555 2 3456554333 5666654 43 444421 124689999765554
No 270
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.85 E-value=36 Score=29.28 Aligned_cols=19 Identities=11% Similarity=-0.088 Sum_probs=15.2
Q ss_pred c-CCCCeeEEcccceEEecccchh
Q 028346 166 S-TAGKLVYCISKYDLNIILFYSF 188 (210)
Q Consensus 166 ~-~~G~~m~~~~~~~l~C~~~~~~ 188 (210)
| .||. .+...+.||.|+..
T Consensus 312 C~~cg~----~~~r~~~C~~cg~~ 331 (364)
T COG0675 312 CPCCGH----LSGRLFKCPRCGFV 331 (364)
T ss_pred ccccCC----ccceeEECCCCCCe
Confidence 5 6999 44578999999974
No 271
>PRK08059 general stress protein 13; Validated
Probab=24.80 E-value=1.9e+02 Score=21.94 Aligned_cols=27 Identities=15% Similarity=0.310 Sum_probs=19.6
Q ss_pred CCCCCCCEEEEEEEEeCCCcceEEEeec
Q 028346 129 LSFRPGDIVRASVLSLGDARAYFLSTAK 156 (210)
Q Consensus 129 ~~~~~GDiV~AkV~s~~d~~~~~LSt~~ 156 (210)
..+++||++.|+|.++.+. .+.+.+..
T Consensus 3 ~~~k~G~iv~G~V~~i~~~-G~fV~i~~ 29 (123)
T PRK08059 3 SQYEVGSVVTGKVTGIQPY-GAFVALDE 29 (123)
T ss_pred ccCCCCCEEEEEEEEEecc-eEEEEECC
Confidence 3478999999999999753 35555543
No 272
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, 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-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=24.72 E-value=1.3e+02 Score=23.92 Aligned_cols=41 Identities=12% Similarity=-0.037 Sum_probs=29.4
Q ss_pred EEEEEEEEeCCCcceEEEeecCCceeeEEEc-CCCCeeEEcccceEEecccchh
Q 028346 136 IVRASVLSLGDARAYFLSTAKNDLGVVSAES-TAGKLVYCISKYDLNIILFYSF 188 (210)
Q Consensus 136 iV~AkV~s~~d~~~~~LSt~~~~LGVv~a~~-~~G~~m~~~~~~~l~C~~~~~~ 188 (210)
.|+|.|..+.. + +-.+.-| .|+..|.+.......|+.|...
T Consensus 19 ~v~a~I~~I~~-----------~-~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~ 60 (166)
T cd04476 19 TVKATIVFIKP-----------D-NWWYPACPGCNKKVVEEGNGTYRCEKCNKS 60 (166)
T ss_pred EEEEEEEEEcC-----------C-CeEEccccccCcccEeCCCCcEECCCCCCc
Confidence 46677776642 2 4556778 8999988765458999999875
No 273
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=24.56 E-value=1.3e+02 Score=21.39 Aligned_cols=23 Identities=35% Similarity=0.483 Sum_probs=21.2
Q ss_pred CCCCEEEEEEEEEecCeEEEEEe
Q 028346 75 EPGSVVIARVTKVMTRMASADIM 97 (210)
Q Consensus 75 ~vGDiViG~V~~v~~~~a~V~I~ 97 (210)
++||.|.=+|+++.++.|+-++.
T Consensus 47 ~~Gd~V~vkI~~v~~~~afaevv 69 (73)
T COG3269 47 EVGDEVKVKITKVKPNFAFAEVV 69 (73)
T ss_pred CCCCeeeEEEEEeeccceeeEEe
Confidence 68999999999999999998884
No 274
>cd06080 MUM1_like Mutated melanoma-associated antigen 1 (MUM-1) is a melanoma-associated antigen (MAA). MUM-1 belongs to the mutated or aberrantly expressed type of MAAs, along with antigens such as CDK4, beta-catenin, gp100-in4, p15, and N-acetylglucosaminyltransferase V. It is highly expressed in several types of human cancers. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=24.51 E-value=49 Score=23.82 Aligned_cols=15 Identities=27% Similarity=0.430 Sum_probs=12.5
Q ss_pred CCCCCEEEEEEEEeC
Q 028346 131 FRPGDIVRASVLSLG 145 (210)
Q Consensus 131 ~~~GDiV~AkV~s~~ 145 (210)
|++||+|-||+.+.-
T Consensus 1 f~~gdlVWaK~~g~P 15 (80)
T cd06080 1 FEKNDLVWAKIQGYP 15 (80)
T ss_pred CCCCCEEEEeCCCCC
Confidence 689999999987653
No 275
>PF00394 Cu-oxidase: Multicopper oxidase; InterPro: IPR001117 Copper is one of the most prevalent transition metals in living organisms and its biological function is intimately related to its redox properties. Since free copper is toxic, even at very low concentrations, its homeostasis in living organisms is tightly controlled by subtle molecular mechanisms. In eukaryotes, before being transported inside the cell via the high-affinity copper transporters of the CTR family, the copper (II) ion is reduced to copper (I). In blue copper proteins such as cupredoxin, the copper (I) ion form is stabilised by a constrained His2Cys coordination environment. Multicopper oxidases oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre; dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water []. There are three spectroscopically different copper centres found in multicopper oxidases: type 1 (or blue), type 2 (or normal) and type 3 (or coupled binuclear) [, ]. Multicopper oxidases consist of 2, 3 or 6 of these homologous domains, which also share homology to the cupredoxins azurin and plastocyanin. Structurally, these domains consist of a cupredoxin-like fold, a beta-sandwich consisting of 7 strands in 2 beta-sheets, arranged in a Greek-key beta-barrel []. Multicopper oxidases include: Ceruloplasmin (1.16.3.1 from EC) (ferroxidase), a 6-domain enzyme found in the serum of mammals and birds that oxidizes different inorganic and organic substances; exhibits internal sequence homology that appears to have evolved from the triplication of a Cu-binding domain similar to that of laccase and ascorbate oxidase. Laccase (1.10.3.2 from EC) (urishiol oxidase), a 3-domain enzyme found in fungi and plants, which oxidizes different phenols and diamines. CueO is a laccase found in Escherichia coli that is involved in copper-resistance []. Ascorbate oxidase (1.10.3.3 from EC), a 3-domain enzyme found in higher plants. Nitrite reductase (1.7.2.1 from EC), a 2-domain enzyme containing type-1 and type-2 copper centres [, ]. In addition to the above enzymes there are a number of other proteins that are similar to the multi-copper oxidases in terms of structure and sequence, some of which have lost the ability to bind copper. These include: copper resistance protein A (copA) from a plasmid in Pseudomonas syringae; domain A of (non-copper binding) blood coagulation factors V (Fa V) and VIII (Fa VIII) []; yeast FET3 required for ferrous iron uptake []; yeast hypothetical protein YFL041w; and the fission yeast homologue SpAC1F7.08. This entry represents multicopper oxidase type 1 (blue) domains. These domains are also present in proteins that have lost the ability to bind copper.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1RZP_A 2AVF_D 1NIA_A 1KCB_A 2NRD_A 1NIB_A 2BW4_A 1RZQ_C 2BWD_A 2BWI_A ....
Probab=24.50 E-value=2.3e+02 Score=22.14 Aligned_cols=35 Identities=20% Similarity=0.464 Sum_probs=29.2
Q ss_pred CCCCCCEEEEEEEEeCCCcceEEEeecCCceeeEE
Q 028346 130 SFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSA 164 (210)
Q Consensus 130 ~~~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv~a 164 (210)
.+++|+-++-|+++.+....+.|++.+..+-||.+
T Consensus 63 ~v~~g~~~rlRliNa~~~~~~~~~i~gh~~~Via~ 97 (159)
T PF00394_consen 63 KVKPGERYRLRLINAGASTSFNFSIDGHPMTVIAA 97 (159)
T ss_dssp EEETTTEEEEEEEEESSS-BEEEEETTBCEEEEEE
T ss_pred EEcCCcEEEEEEEeccCCeeEEEEeeccceeEeee
Confidence 47899999999999986667899999988877766
No 276
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=24.35 E-value=1.7e+02 Score=22.58 Aligned_cols=40 Identities=13% Similarity=-0.002 Sum_probs=25.1
Q ss_pred EEEEEEEeCCCcceEEEeecCCceeeEEEcC---CCCeeEEcccceEEecccchh
Q 028346 137 VRASVLSLGDARAYFLSTAKNDLGVVSAEST---AGKLVYCISKYDLNIILFYSF 188 (210)
Q Consensus 137 V~AkV~s~~d~~~~~LSt~~~~LGVv~a~~~---~G~~m~~~~~~~l~C~~~~~~ 188 (210)
|+|.|..+... +-.+.-|. |+..+.+.+.+...|+.|...
T Consensus 4 v~a~I~~I~~~------------~~~Y~aC~~~~C~kKv~~~~~~~y~C~~C~~~ 46 (146)
T PF08646_consen 4 VRATIVEIKSD------------NWYYPACPNEKCNKKVTENGDGSYRCEKCNKT 46 (146)
T ss_dssp EEEEEEEEETT------------TTEEEE-TSTTTS-B-EEETTTEEEETTTTEE
T ss_pred EEEEEEEEECC------------CcEECCCCCccCCCEeecCCCcEEECCCCCCc
Confidence 67777776432 23555564 888887775568999998865
No 277
>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=23.91 E-value=2.6e+02 Score=19.71 Aligned_cols=34 Identities=18% Similarity=0.292 Sum_probs=22.0
Q ss_pred CCCCCCCEEEEEEE--EeCC------CcceEEEeecCCceee
Q 028346 129 LSFRPGDIVRASVL--SLGD------ARAYFLSTAKNDLGVV 162 (210)
Q Consensus 129 ~~~~~GDiV~AkV~--s~~d------~~~~~LSt~~~~LGVv 162 (210)
..++|||.|..+++ ..+. ...+.|++..++--.|
T Consensus 9 ~iYrPGetV~~~~~~~~~~~~~~~~~~~~~~v~i~dp~g~~v 50 (99)
T PF01835_consen 9 PIYRPGETVHFRAIVRDLDNDFKPPANSPVTVTIKDPSGNEV 50 (99)
T ss_dssp SEE-TTSEEEEEEEEEEECTTCSCESSEEEEEEEEETTSEEE
T ss_pred cCcCCCCEEEEEEEEeccccccccccCCceEEEEECCCCCEE
Confidence 78899999999998 4431 1346777777743333
No 278
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=23.82 E-value=36 Score=20.01 Aligned_cols=24 Identities=4% Similarity=-0.289 Sum_probs=16.4
Q ss_pred Ec-CCCCeeEEcccceEEecccchhh
Q 028346 165 ES-TAGKLVYCISKYDLNIILFYSFW 189 (210)
Q Consensus 165 ~~-~~G~~m~~~~~~~l~C~~~~~~~ 189 (210)
+| .||....+.. ..-.||+|++..
T Consensus 3 ~C~~CGy~y~~~~-~~~~CP~Cg~~~ 27 (33)
T cd00350 3 VCPVCGYIYDGEE-APWVCPVCGAPK 27 (33)
T ss_pred ECCCCCCEECCCc-CCCcCcCCCCcH
Confidence 46 7888765432 456999998753
No 279
>PF00467 KOW: KOW motif; InterPro: IPR005824 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 KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=23.72 E-value=1.2e+02 Score=17.48 Aligned_cols=16 Identities=6% Similarity=0.171 Sum_probs=11.5
Q ss_pred EEEEEEEEecCeEEEE
Q 028346 80 VIARVTKVMTRMASAD 95 (210)
Q Consensus 80 ViG~V~~v~~~~a~V~ 95 (210)
-.|+|.++..+...+.
T Consensus 15 ~~G~I~~i~~~~~~V~ 30 (32)
T PF00467_consen 15 KIGKIVEIDRSKVRVT 30 (32)
T ss_dssp EEEEEEEEETTTTEEE
T ss_pred ceEEEEEEECCCCEEE
Confidence 4788888887765544
No 280
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=23.56 E-value=34 Score=28.12 Aligned_cols=25 Identities=4% Similarity=-0.369 Sum_probs=18.6
Q ss_pred EEEc-CCCCeeEEcccceEEecccchhh
Q 028346 163 SAES-TAGKLVYCISKYDLNIILFYSFW 189 (210)
Q Consensus 163 ~a~~-~~G~~m~~~~~~~l~C~~~~~~~ 189 (210)
.=+| .||....- ..-=.||+|+++.
T Consensus 134 ~~vC~vCGy~~~g--e~P~~CPiCga~k 159 (166)
T COG1592 134 VWVCPVCGYTHEG--EAPEVCPICGAPK 159 (166)
T ss_pred EEEcCCCCCcccC--CCCCcCCCCCChH
Confidence 4579 89988643 4567899999764
No 281
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=23.24 E-value=36 Score=30.39 Aligned_cols=46 Identities=13% Similarity=-0.028 Sum_probs=31.1
Q ss_pred eEEEc-CCCCeeEEcc--cceEEecccchhhhHH---HHHHhhcccceEEEe
Q 028346 162 VSAES-TAGKLVYCIS--KYDLNIILFYSFWIFC---ILQIASNIISFITLF 207 (210)
Q Consensus 162 v~a~~-~~G~~m~~~~--~~~l~C~~~~~~~~~~---~~~~~~~~~~~~~~~ 207 (210)
+...| .||..|+... .|...||.|.++.=.= -+..+.---+|..|+
T Consensus 27 lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri~A~~Ri~~llD~gsf~el~ 78 (294)
T COG0777 27 LWTKCPSCGEMLYRKELESNLKVCPKCGHHMRISARERLEALLDEGSFEELD 78 (294)
T ss_pred ceeECCCccceeeHHHHHhhhhcccccCcccccCHHHHHHHhhCCCcceecc
Confidence 56789 9999997653 5688999999876541 444444444555443
No 282
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=22.61 E-value=1.5e+02 Score=29.72 Aligned_cols=52 Identities=12% Similarity=0.105 Sum_probs=32.3
Q ss_pred CCCCCCCEEEEEEEEeCCCcceEEE----eecCCceeeEEEc-CCCCeeEEcccceEEecc
Q 028346 129 LSFRPGDIVRASVLSLGDARAYFLS----TAKNDLGVVSAES-TAGKLVYCISKYDLNIIL 184 (210)
Q Consensus 129 ~~~~~GDiV~AkV~s~~d~~~~~LS----t~~~~LGVv~a~~-~~G~~m~~~~~~~l~C~~ 184 (210)
.-+++||.|. |...||--+..+. .+..++ ++-..| .||.+++.. ...+.|+.
T Consensus 363 ~di~iGD~V~--V~raGdVIP~I~~v~~~~r~~~~-~~P~~CP~C~s~l~~~-~~~~~C~n 419 (669)
T PRK14350 363 IGLNVGDVVK--ISRRGDVIPAVELVIEKLSVGFF-KIPDNCPSCKTALIKE-GAHLFCVN 419 (669)
T ss_pred cCCCCCCEEE--EEecCCCCCceeeecccccCCCC-CCCCCCCCCCCEeeeC-CEEEEECC
Confidence 4468999996 7777765333222 222222 233578 899998763 36788874
No 283
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=22.56 E-value=40 Score=20.10 Aligned_cols=11 Identities=0% Similarity=-0.121 Sum_probs=6.5
Q ss_pred eEEecccchhh
Q 028346 179 DLNIILFYSFW 189 (210)
Q Consensus 179 ~l~C~~~~~~~ 189 (210)
.+.||.|++.|
T Consensus 2 ~~~CP~C~~~~ 12 (38)
T TIGR02098 2 RIQCPNCKTSF 12 (38)
T ss_pred EEECCCCCCEE
Confidence 35666666654
No 284
>COG1465 Predicted alternative 3-dehydroquinate synthase [Amino acid transport and metabolism]
Probab=22.47 E-value=1.7e+02 Score=26.69 Aligned_cols=48 Identities=21% Similarity=0.404 Sum_probs=32.3
Q ss_pred EEecCCccCCCCCeeeCCcEEEeCCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEe
Q 028346 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVT 65 (210)
Q Consensus 10 iV~PGd~l~~~ee~~~G~GtY~~~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~ 65 (210)
+-.||..=-...|..+|.-+-.-+..|.-+++++|++++. +++.+-|+
T Consensus 268 i~vPg~kTkYLaEL~aGDeV~iVD~dGr~R~aiVGRvKIE--------rRPl~lIe 315 (376)
T COG1465 268 IRVPGGKTKYLAELKAGDEVLIVDFDGRTRSAIVGRVKIE--------RRPLMLIE 315 (376)
T ss_pred EEcCCCceEEhhhhcCCCeEEEEecCCceeEEEEEEEEee--------cCceEEEE
Confidence 4567776555556777777654433333999999999984 45666666
No 285
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=22.22 E-value=32 Score=19.14 Aligned_cols=21 Identities=5% Similarity=-0.347 Sum_probs=13.9
Q ss_pred Ec-CCCCeeEEcccceEEecccchh
Q 028346 165 ES-TAGKLVYCISKYDLNIILFYSF 188 (210)
Q Consensus 165 ~~-~~G~~m~~~~~~~l~C~~~~~~ 188 (210)
.| .||... + .+.-.||.|+++
T Consensus 4 ~Cp~Cg~~~-~--~~~~fC~~CG~~ 25 (26)
T PF13248_consen 4 FCPNCGAEI-D--PDAKFCPNCGAK 25 (26)
T ss_pred CCcccCCcC-C--cccccChhhCCC
Confidence 46 788853 3 245788888864
No 286
>PHA00626 hypothetical protein
Probab=21.88 E-value=71 Score=21.74 Aligned_cols=25 Identities=8% Similarity=-0.395 Sum_probs=15.9
Q ss_pred c-CCCCe-eEE-----cccceEEecccchhhh
Q 028346 166 S-TAGKL-VYC-----ISKYDLNIILFYSFWI 190 (210)
Q Consensus 166 ~-~~G~~-m~~-----~~~~~l~C~~~~~~~~ 190 (210)
| +||.. .++ ..-+...|+.|+.++-
T Consensus 3 CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 3 CPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCceeeeeceecccCcceEcCCCCCeec
Confidence 5 67763 333 2126899999987653
No 287
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=21.75 E-value=36 Score=30.54 Aligned_cols=13 Identities=23% Similarity=0.493 Sum_probs=10.8
Q ss_pred EEecccchhhhHH
Q 028346 180 LNIILFYSFWIFC 192 (210)
Q Consensus 180 l~C~~~~~~~~~~ 192 (210)
..|..|+++|-||
T Consensus 287 ~~C~~Cg~~w~fc 299 (299)
T TIGR01385 287 VTCEECGNRWKFC 299 (299)
T ss_pred EEcCCCCCeeeeC
Confidence 4799999999776
No 288
>COG4956 Integral membrane protein (PIN domain superfamily) [General function prediction only]
Probab=21.70 E-value=1.3e+02 Score=27.39 Aligned_cols=28 Identities=29% Similarity=0.478 Sum_probs=20.6
Q ss_pred ceEEecCCccCC---CCCeeeCCcE-EEeCCe
Q 028346 8 MVLVTPGEVLGK---ATEVKAGKGA-YVAKHN 35 (210)
Q Consensus 8 ~~iV~PGd~l~~---~ee~~~G~Gt-Y~~~g~ 35 (210)
+-.|+|||.+.. .+...+|+|+ |.+||.
T Consensus 288 kP~vlpGe~l~v~iiK~GkE~~QGVgYLdDGT 319 (356)
T COG4956 288 KPVVLPGEELTVQIIKDGKEPGQGVGYLDDGT 319 (356)
T ss_pred CCcccCCCeeEEEEeecCcccCCceEEecCCe
Confidence 346899998753 2446789996 888887
No 289
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=21.48 E-value=16 Score=24.98 Aligned_cols=19 Identities=11% Similarity=-0.146 Sum_probs=13.1
Q ss_pred c-CCCCeeEEcccceEEe-cccch
Q 028346 166 S-TAGKLVYCISKYDLNI-ILFYS 187 (210)
Q Consensus 166 ~-~~G~~m~~~~~~~l~C-~~~~~ 187 (210)
| .||.++-| ++--| +.|..
T Consensus 6 C~~CG~~Ip~---~~~fCS~~C~~ 26 (59)
T PF09889_consen 6 CPVCGKPIPP---DESFCSPKCRE 26 (59)
T ss_pred CCcCCCcCCc---chhhhCHHHHH
Confidence 6 79988543 47888 47764
No 290
>cd03528 Rieske_RO_ferredoxin Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The ferredoxin component contains either a plant-type or Rieske-type [2Fe-2S] cluster. The Rieske ferredoxin component in this family carries an electron from the RO reductase component to the terminal RO oxygenase component. BPDO degrades biphenyls and polychlorinated biphenyls. BPDO ferredoxin (BphF) has structural features consistent with a minimal and perhaps archetypical Rieske protein in that the in
Probab=21.34 E-value=1.7e+02 Score=20.60 Aligned_cols=57 Identities=9% Similarity=0.004 Sum_probs=31.6
Q ss_pred CCCCCEEEEEEEEeCCCcceEEEeecCCceeeEEEc-CCCCeeEE--cccceEEecccchhhhH
Q 028346 131 FRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAES-TAGKLVYC--ISKYDLNIILFYSFWIF 191 (210)
Q Consensus 131 ~~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv~a~~-~~G~~m~~--~~~~~l~C~~~~~~~~~ 191 (210)
+.+|+.+..++. +.++.|.-.+.++-.+.++| -.|.+|.. ...+.+.||--+.+|=+
T Consensus 10 l~~g~~~~~~~~----g~~~~v~r~~~~~~a~~~~CpH~g~~L~~g~~~~~~i~Cp~Hg~~fd~ 69 (98)
T cd03528 10 LPEGEPKRVDVG----GRPIAVYRVDGEFYATDDLCTHGDASLSEGYVEGGVIECPLHGGRFDL 69 (98)
T ss_pred cCCCCEEEEEEC----CeEEEEEEECCEEEEECCcCCCCCCCCCCCeEeCCEEEeCCcCCEEEC
Confidence 467887766653 23555543333333344455 34555532 23468999987766543
No 291
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=21.25 E-value=2e+02 Score=20.45 Aligned_cols=16 Identities=13% Similarity=0.229 Sum_probs=13.4
Q ss_pred EEEEEEEecCeEEEEE
Q 028346 81 IARVTKVMTRMASADI 96 (210)
Q Consensus 81 iG~V~~v~~~~a~V~I 96 (210)
=|+|.++.++.+.|+.
T Consensus 6 P~~V~~i~~~~A~v~~ 21 (76)
T TIGR00074 6 PGQVVEIDENIALVEF 21 (76)
T ss_pred ceEEEEEcCCEEEEEc
Confidence 3788999888888887
No 292
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=21.25 E-value=32 Score=24.68 Aligned_cols=24 Identities=21% Similarity=0.313 Sum_probs=0.0
Q ss_pred CCCCCEE------EEEEEEEecCeEEEEEe
Q 028346 74 PEPGSVV------IARVTKVMTRMASADIM 97 (210)
Q Consensus 74 p~vGDiV------iG~V~~v~~~~a~V~I~ 97 (210)
.++||-| +|+|+++.++.+.+++.
T Consensus 37 Lk~Gd~VvT~gGi~G~V~~i~~~~v~lei~ 66 (82)
T PF02699_consen 37 LKPGDEVVTIGGIYGTVVEIDDDTVVLEIA 66 (82)
T ss_dssp ------------------------------
T ss_pred CCCCCEEEECCcEEEEEEEEeCCEEEEEEC
Confidence 5778877 89999999999999993
No 293
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=20.92 E-value=76 Score=22.43 Aligned_cols=27 Identities=0% Similarity=-0.256 Sum_probs=16.1
Q ss_pred EEc-CCCCeeEEcccceEEecccchhhhH
Q 028346 164 AES-TAGKLVYCISKYDLNIILFYSFWIF 191 (210)
Q Consensus 164 a~~-~~G~~m~~~~~~~l~C~~~~~~~~~ 191 (210)
+.| .|..+|.+.+ ....|+.|...+..
T Consensus 2 ~~CP~C~~~L~~~~-~~~~C~~C~~~~~~ 29 (70)
T PF07191_consen 2 NTCPKCQQELEWQG-GHYHCEACQKDYKK 29 (70)
T ss_dssp -B-SSS-SBEEEET-TEEEETTT--EEEE
T ss_pred CcCCCCCCccEEeC-CEEECcccccccee
Confidence 457 7888888776 57888888776543
No 294
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.82 E-value=53 Score=25.41 Aligned_cols=27 Identities=15% Similarity=0.012 Sum_probs=14.7
Q ss_pred EEEcCCCCeeE----Ecccc--eEEecccchhh
Q 028346 163 SAESTAGKLVY----CISKY--DLNIILFYSFW 189 (210)
Q Consensus 163 ~a~~~~G~~m~----~~~~~--~l~C~~~~~~~ 189 (210)
.++|.||..-- +.... .+.||.|+.+-
T Consensus 70 ~~~C~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~ 102 (124)
T PRK00762 70 EIECECGYEGVVDEDEIDHYAAVIECPVCGNKR 102 (124)
T ss_pred eEEeeCcCcccccccchhccccCCcCcCCCCCC
Confidence 45667875521 11111 26799998654
No 295
>smart00532 LIGANc Ligase N family.
Probab=20.62 E-value=1.5e+02 Score=27.93 Aligned_cols=68 Identities=24% Similarity=0.303 Sum_probs=40.3
Q ss_pred CCCCCCCEEEEEEEEeCCCcceEEEeecC-Cce-----eeEEEc-CCCCeeEEcc-cceEEecccchhhhHHHHHHhhcc
Q 028346 129 LSFRPGDIVRASVLSLGDARAYFLSTAKN-DLG-----VVSAES-TAGKLVYCIS-KYDLNIILFYSFWIFCILQIASNI 200 (210)
Q Consensus 129 ~~~~~GDiV~AkV~s~~d~~~~~LSt~~~-~LG-----Vv~a~~-~~G~~m~~~~-~~~l~C~~~~~~~~~~~~~~~~~~ 200 (210)
.-+++||.|. |...|+--+..+....+ .-+ .+-..| .||+.+.... .-.+.|+.. .|-.|++..+
T Consensus 361 ~~i~iGd~V~--V~raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~C~s~l~~~~~~~~~~C~n~-----~C~aq~~~~l 433 (441)
T smart00532 361 KDIRIGDTVV--VRKAGDVIPKVVGVVKEKRPGDEREIEMPTHCPSCGSELVREEGEVDIRCPNP-----LCPAQLIERI 433 (441)
T ss_pred cCCCCCCEEE--EEECCCcCcceeecccccCCCCCccCcCCCCCCCCCCEeEecCCceEEEeCCC-----CCHHHHHHHH
Confidence 4578999998 66767654433333221 111 234578 8999987543 236789842 2666666665
Q ss_pred cce
Q 028346 201 ISF 203 (210)
Q Consensus 201 ~~~ 203 (210)
.-|
T Consensus 434 ~hf 436 (441)
T smart00532 434 IHF 436 (441)
T ss_pred Hhh
Confidence 544
No 296
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.43 E-value=73 Score=31.72 Aligned_cols=26 Identities=4% Similarity=-0.376 Sum_probs=16.8
Q ss_pred EEc-CCCCeeE-EcccceEEecccchhh
Q 028346 164 AES-TAGKLVY-CISKYDLNIILFYSFW 189 (210)
Q Consensus 164 a~~-~~G~~m~-~~~~~~l~C~~~~~~~ 189 (210)
++| .|+.+|. ..+.+.|.|.-|+...
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~~~ 420 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGRAA 420 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcCCC
Confidence 357 6888874 3344578777777654
No 297
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=20.16 E-value=71 Score=21.18 Aligned_cols=24 Identities=21% Similarity=0.386 Sum_probs=13.9
Q ss_pred CCCCCEEEEEEEEeCCCcceEEEeecCC
Q 028346 131 FRPGDIVRASVLSLGDARAYFLSTAKND 158 (210)
Q Consensus 131 ~~~GDiV~AkV~s~~d~~~~~LSt~~~~ 158 (210)
|++||+|+-| | .++...++..++.
T Consensus 1 f~~GDvV~LK--S--GGp~MTV~~v~~~ 24 (53)
T PF09926_consen 1 FKIGDVVQLK--S--GGPRMTVTEVGPN 24 (53)
T ss_pred CCCCCEEEEc--c--CCCCeEEEEcccc
Confidence 6899998744 2 2344555544443
No 298
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=20.13 E-value=2.7e+02 Score=23.98 Aligned_cols=35 Identities=20% Similarity=0.106 Sum_probs=28.2
Q ss_pred CCCCCEEEEEEEEeCCCcceEEEeecCCceeeEEEc
Q 028346 131 FRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAES 166 (210)
Q Consensus 131 ~~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv~a~~ 166 (210)
=.+||.|.+.|++.. +..|.+.+.+++++-+.+..
T Consensus 63 P~~~D~VIGiV~~~~-gd~ykVDigg~~~a~L~~la 97 (230)
T KOG1004|consen 63 PVKGDHVIGIVTSKS-GDIYKVDIGGSEPASLSYLA 97 (230)
T ss_pred CCCCCEEEEEEEecc-CceEEEecCCCCeeeeeecc
Confidence 369999999999974 24688999888888877765
Done!