Query 032397
Match_columns 141
No_of_seqs 106 out of 525
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 13:34:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032397.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032397hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3409 Exosomal 3'-5' exoribo 100.0 6E-33 1.3E-37 210.5 10.0 129 7-141 4-144 (193)
2 COG1096 Predicted RNA-binding 100.0 8.7E-28 1.9E-32 184.5 11.1 122 5-135 2-134 (188)
3 PRK09521 exosome complex RNA-b 99.9 7.2E-26 1.6E-30 174.9 14.4 121 5-134 2-133 (189)
4 PRK04163 exosome complex RNA-b 99.9 1.8E-23 3.9E-28 166.7 13.0 116 5-141 5-133 (235)
5 COG1097 RRP4 RNA-binding prote 99.9 1.3E-21 2.9E-26 155.5 11.5 114 3-136 3-118 (239)
6 cd05791 S1_CSL4 S1_CSL4: CSL4, 99.8 2.6E-21 5.7E-26 134.3 6.8 71 71-141 1-82 (92)
7 PF10447 EXOSC1: Exosome compo 99.8 8.5E-22 1.9E-26 134.3 4.2 61 73-133 1-82 (82)
8 KOG3013 Exosomal 3'-5' exoribo 99.8 2.3E-19 5E-24 143.9 6.4 117 6-134 27-149 (301)
9 PF14382 ECR1_N: Exosome compl 99.5 1.3E-14 2.8E-19 86.0 3.2 37 10-48 1-37 (39)
10 cd04454 S1_Rrp4_like S1_Rrp4_l 98.9 8.3E-09 1.8E-13 69.1 6.3 58 71-136 1-67 (82)
11 KOG1004 Exosomal 3'-5' exoribo 98.7 8.4E-08 1.8E-12 75.6 7.9 101 9-115 2-105 (230)
12 cd05790 S1_Rrp40 S1_Rrp40: Rrp 98.7 3.5E-08 7.7E-13 67.8 4.7 39 71-117 1-39 (86)
13 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.4 7E-07 1.5E-11 60.1 6.1 40 71-118 1-40 (86)
14 cd05702 S1_Rrp5_repeat_hs11_sc 97.6 0.00011 2.5E-09 47.5 4.8 55 77-139 1-66 (70)
15 cd05705 S1_Rrp5_repeat_hs14 S1 97.6 0.00019 4.1E-09 47.5 5.0 37 75-119 2-38 (74)
16 cd05693 S1_Rrp5_repeat_hs1_sc1 97.2 0.00077 1.7E-08 47.2 5.2 37 75-119 2-38 (100)
17 cd05687 S1_RPS1_repeat_ec1_hs1 97.2 0.00078 1.7E-08 43.2 4.6 44 77-128 1-46 (70)
18 cd04452 S1_IF2_alpha S1_IF2_al 97.1 0.0013 2.9E-08 42.6 4.8 40 74-119 1-40 (76)
19 cd05704 S1_Rrp5_repeat_hs13 S1 97.0 0.0016 3.4E-08 42.6 4.9 37 75-119 2-39 (72)
20 PF00575 S1: S1 RNA binding do 96.9 0.0033 7.2E-08 40.5 5.7 38 74-119 2-39 (74)
21 cd05706 S1_Rrp5_repeat_sc10 S1 96.8 0.0034 7.3E-08 40.5 5.2 37 75-119 2-38 (73)
22 COG1098 VacB Predicted RNA bin 96.7 0.0031 6.7E-08 46.2 4.7 55 74-136 3-66 (129)
23 cd05691 S1_RPS1_repeat_ec6 S1_ 96.7 0.0044 9.6E-08 39.6 4.9 35 77-119 1-35 (73)
24 PRK07252 hypothetical protein; 96.7 0.0043 9.4E-08 44.9 5.3 37 75-119 2-38 (120)
25 PTZ00248 eukaryotic translatio 96.6 0.0035 7.6E-08 52.5 5.2 41 71-119 12-54 (319)
26 cd05707 S1_Rrp5_repeat_sc11 S1 96.6 0.0061 1.3E-07 38.9 5.2 35 77-119 1-35 (68)
27 PRK08582 hypothetical protein; 96.6 0.0057 1.2E-07 45.3 5.5 38 74-119 3-40 (139)
28 cd05708 S1_Rrp5_repeat_sc12 S1 96.6 0.0057 1.2E-07 39.4 4.8 37 75-119 1-38 (77)
29 PRK08059 general stress protei 96.6 0.0056 1.2E-07 44.2 5.2 38 74-119 5-42 (123)
30 smart00316 S1 Ribosomal protei 96.5 0.0065 1.4E-07 37.7 4.9 37 75-119 1-37 (72)
31 cd05686 S1_pNO40 S1_pNO40: pNO 96.5 0.0086 1.9E-07 39.0 5.4 39 74-119 1-39 (73)
32 cd05703 S1_Rrp5_repeat_hs12_sc 96.5 0.0069 1.5E-07 39.7 4.7 35 77-119 1-35 (73)
33 PRK03987 translation initiatio 96.4 0.0081 1.8E-07 48.9 5.9 43 71-119 3-45 (262)
34 cd05692 S1_RPS1_repeat_hs4 S1_ 96.3 0.01 2.2E-07 37.0 4.6 35 77-119 1-35 (69)
35 cd05697 S1_Rrp5_repeat_hs5 S1_ 96.2 0.013 2.8E-07 37.4 4.8 35 77-119 1-35 (69)
36 cd05698 S1_Rrp5_repeat_hs6_sc5 96.2 0.014 3E-07 37.2 4.8 35 77-119 1-35 (70)
37 cd04453 S1_RNase_E S1_RNase_E: 96.0 0.017 3.7E-07 39.4 5.1 37 74-118 5-43 (88)
38 cd05685 S1_Tex S1_Tex: The C-t 95.7 0.025 5.5E-07 35.1 4.5 35 77-119 1-35 (68)
39 TIGR03591 polynuc_phos polyrib 95.7 0.0049 1.1E-07 56.3 1.4 64 36-119 590-653 (684)
40 cd05695 S1_Rrp5_repeat_hs3 S1_ 95.5 0.037 8E-07 35.5 4.7 35 77-119 1-35 (66)
41 cd04472 S1_PNPase S1_PNPase: P 95.5 0.041 8.9E-07 34.3 4.8 35 77-119 1-35 (68)
42 cd04461 S1_Rrp5_repeat_hs8_sc7 95.4 0.042 9E-07 36.4 5.0 38 74-119 12-49 (83)
43 cd05688 S1_RPS1_repeat_ec3 S1_ 95.4 0.043 9.4E-07 34.1 4.7 35 76-119 1-35 (68)
44 PRK05807 hypothetical protein; 95.3 0.049 1.1E-06 40.1 5.4 37 74-119 3-39 (136)
45 cd05694 S1_Rrp5_repeat_hs2_sc2 95.2 0.056 1.2E-06 35.6 4.9 37 75-119 3-40 (74)
46 PRK11824 polynucleotide phosph 95.0 0.01 2.2E-07 54.3 1.2 64 36-119 593-656 (693)
47 cd04455 S1_NusA S1_NusA: N-uti 94.9 0.066 1.4E-06 34.3 4.6 35 75-118 2-36 (67)
48 PHA02945 interferon resistance 94.8 0.087 1.9E-06 36.4 5.2 40 71-117 6-45 (88)
49 PF01016 Ribosomal_L27: Riboso 94.2 0.06 1.3E-06 36.7 3.2 47 3-50 22-70 (81)
50 cd04473 S1_RecJ_like S1_RecJ_l 94.1 0.26 5.7E-06 32.3 6.3 38 74-119 14-51 (77)
51 cd05690 S1_RPS1_repeat_ec5 S1_ 94.0 0.12 2.7E-06 32.5 4.4 34 77-118 1-34 (69)
52 cd05689 S1_RPS1_repeat_ec4 S1_ 94.0 0.17 3.6E-06 32.3 4.9 36 75-118 2-37 (72)
53 COG1093 SUI2 Translation initi 93.9 0.13 2.8E-06 42.1 5.2 43 71-119 6-48 (269)
54 PRK05435 rpmA 50S ribosomal pr 93.9 0.18 3.9E-06 34.4 5.0 46 3-49 23-70 (82)
55 PRK08563 DNA-directed RNA poly 93.6 0.15 3.3E-06 38.9 5.0 39 72-119 77-115 (187)
56 TIGR02696 pppGpp_PNP guanosine 93.4 0.12 2.7E-06 47.6 4.7 38 73-118 644-681 (719)
57 COG0539 RpsA Ribosomal protein 93.3 0.14 3.1E-06 45.7 5.0 46 73-127 189-236 (541)
58 CHL00121 rpl27 ribosomal prote 93.1 0.22 4.7E-06 34.2 4.4 60 3-67 23-84 (86)
59 PRK07400 30S ribosomal protein 92.6 0.26 5.7E-06 41.1 5.3 38 74-119 29-66 (318)
60 PRK07400 30S ribosomal protein 92.4 0.3 6.6E-06 40.7 5.4 38 73-119 193-230 (318)
61 PRK07899 rpsA 30S ribosomal pr 92.0 0.25 5.3E-06 43.7 4.6 38 74-119 33-70 (486)
62 cd05684 S1_DHX8_helicase S1_DH 91.9 0.38 8.3E-06 31.3 4.4 38 77-119 1-38 (79)
63 TIGR00062 L27 ribosomal protei 91.1 0.48 1E-05 32.4 4.3 46 3-49 23-70 (83)
64 cd05696 S1_Rrp5_repeat_hs4 S1_ 90.8 0.6 1.3E-05 30.1 4.5 35 77-119 1-37 (71)
65 TIGR00448 rpoE DNA-directed RN 90.4 0.58 1.3E-05 35.6 4.8 39 72-119 77-115 (179)
66 COG0539 RpsA Ribosomal protein 90.4 0.45 9.7E-06 42.7 4.6 41 71-119 16-56 (541)
67 PRK13806 rpsA 30S ribosomal pr 90.4 0.46 9.9E-06 41.8 4.7 37 75-119 378-414 (491)
68 cd04465 S1_RPS1_repeat_ec2_hs2 89.7 1 2.2E-05 28.3 4.8 34 77-119 1-34 (67)
69 PRK13806 rpsA 30S ribosomal pr 89.6 0.63 1.4E-05 40.9 4.9 46 74-127 200-247 (491)
70 PRK12269 bifunctional cytidyla 89.4 0.6 1.3E-05 44.0 4.9 55 74-137 750-806 (863)
71 cd04471 S1_RNase_R S1_RNase_R: 89.4 1.2 2.6E-05 28.7 5.1 36 76-119 1-37 (83)
72 TIGR00757 RNaseEG ribonuclease 88.6 0.81 1.8E-05 39.7 4.8 37 74-118 23-61 (414)
73 cd04460 S1_RpoE S1_RpoE: RpoE, 87.9 1.1 2.4E-05 30.5 4.3 33 78-119 1-33 (99)
74 cd00164 S1_like S1_like: Ribos 87.3 0.97 2.1E-05 27.0 3.4 32 80-119 1-32 (65)
75 TIGR00717 rpsA ribosomal prote 86.9 1.4 2.9E-05 38.6 5.3 38 74-119 16-53 (516)
76 PLN00207 polyribonucleotide nu 86.4 1.2 2.5E-05 42.3 4.8 39 73-119 750-789 (891)
77 PRK12269 bifunctional cytidyla 85.5 1.4 3E-05 41.7 4.8 36 74-117 319-354 (863)
78 PRK06299 rpsA 30S ribosomal pr 85.5 1.3 2.9E-05 39.2 4.6 37 75-119 372-408 (565)
79 cd05790 S1_Rrp40 S1_Rrp40: Rrp 84.0 2.2 4.8E-05 29.2 4.1 30 71-101 47-76 (86)
80 PRK07899 rpsA 30S ribosomal pr 84.0 1.9 4E-05 38.2 4.7 37 75-119 292-328 (486)
81 KOG4600 Mitochondrial ribosoma 82.4 4.1 8.8E-05 30.4 5.2 69 3-75 50-120 (144)
82 PRK00087 4-hydroxy-3-methylbut 81.0 2.8 6E-05 38.1 4.8 40 72-119 298-337 (647)
83 TIGR00717 rpsA ribosomal prote 80.7 2.9 6.3E-05 36.5 4.7 37 74-118 270-306 (516)
84 PRK00087 4-hydroxy-3-methylbut 80.2 3.3 7E-05 37.7 5.0 37 75-119 561-597 (647)
85 PRK06676 rpsA 30S ribosomal pr 80.2 4 8.7E-05 34.4 5.3 37 74-119 190-226 (390)
86 PTZ00162 DNA-directed RNA poly 80.1 3.8 8.3E-05 31.4 4.7 40 71-119 76-115 (176)
87 PF01959 DHQS: 3-dehydroquinat 80.0 9.8 0.00021 32.5 7.4 40 10-49 246-285 (354)
88 PHA02858 EIF2a-like PKR inhibi 79.2 7.6 0.00017 26.7 5.3 40 71-118 11-51 (86)
89 PRK06676 rpsA 30S ribosomal pr 78.2 4.5 9.7E-05 34.1 5.0 38 74-119 275-312 (390)
90 PRK02290 3-dehydroquinate synt 77.5 13 0.00028 31.7 7.4 41 10-50 236-276 (344)
91 PRK06299 rpsA 30S ribosomal pr 77.1 5.1 0.00011 35.5 5.2 37 74-119 199-235 (565)
92 PRK12327 nusA transcription el 76.7 3.9 8.4E-05 34.9 4.1 38 71-117 129-166 (362)
93 PRK09202 nusA transcription el 73.4 4.8 0.0001 35.5 4.0 39 71-118 129-167 (470)
94 PRK11712 ribonuclease G; Provi 72.9 5.2 0.00011 35.5 4.1 37 74-118 36-74 (489)
95 COG1465 Predicted alternative 72.6 17 0.00037 30.8 6.8 77 10-86 268-360 (376)
96 cd05791 S1_CSL4 S1_CSL4: CSL4, 72.6 5.3 0.00011 27.2 3.3 22 75-96 62-84 (92)
97 COG0211 RpmA Ribosomal protein 70.7 11 0.00024 25.8 4.4 61 3-68 23-85 (87)
98 PF07497 Rho_RNA_bind: Rho ter 70.4 12 0.00026 25.2 4.5 45 60-104 29-76 (78)
99 PF01938 TRAM: TRAM domain; I 70.3 9.3 0.0002 23.6 3.8 25 73-97 37-61 (61)
100 PRK10811 rne ribonuclease E; R 67.8 7.6 0.00017 37.4 4.2 37 74-118 36-74 (1068)
101 PRK04012 translation initiatio 67.6 16 0.00034 25.7 4.9 64 9-98 14-82 (100)
102 COG1095 RPB7 DNA-directed RNA 67.5 7.6 0.00016 30.3 3.5 40 71-119 76-115 (183)
103 cd04462 S1_RNAPII_Rpb7 S1_RNAP 66.2 19 0.00041 24.3 5.0 22 76-97 1-22 (88)
104 TIGR01953 NusA transcription t 65.8 9.2 0.0002 32.4 4.0 39 71-118 126-165 (341)
105 PF10447 EXOSC1: Exosome compo 65.5 6.3 0.00014 26.7 2.4 13 75-87 70-82 (82)
106 cd04454 S1_Rrp4_like S1_Rrp4_l 62.4 15 0.00032 23.8 3.8 25 72-96 49-74 (82)
107 cd05699 S1_Rrp5_repeat_hs7 S1_ 59.1 49 0.0011 21.9 5.7 36 77-119 1-36 (72)
108 COG1315 Uncharacterized conser 59.0 16 0.00035 32.8 4.4 48 22-80 220-270 (543)
109 COG1530 CafA Ribonucleases G a 56.8 10 0.00022 33.6 2.8 38 74-119 35-74 (487)
110 PRK09521 exosome complex RNA-b 54.3 26 0.00057 26.7 4.4 22 74-96 119-140 (189)
111 PF08810 KapB: Kinase associat 52.7 61 0.0013 23.3 5.7 40 80-119 6-66 (112)
112 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 51.0 28 0.0006 22.6 3.6 23 74-96 55-78 (86)
113 TIGR02063 RNase_R ribonuclease 50.8 32 0.00069 31.7 5.1 40 72-119 623-663 (709)
114 KOG1070 rRNA processing protei 49.1 17 0.00036 36.6 3.1 59 71-137 880-949 (1710)
115 cd05704 S1_Rrp5_repeat_hs13 S1 48.8 38 0.00083 21.5 4.0 23 74-96 49-71 (72)
116 PF03961 DUF342: Protein of un 48.6 46 0.00099 28.8 5.5 28 22-49 144-172 (451)
117 PTZ00329 eukaryotic translatio 48.6 31 0.00067 26.2 3.9 66 8-99 24-94 (155)
118 COG1096 Predicted RNA-binding 48.4 36 0.00077 26.7 4.3 22 74-96 119-140 (188)
119 PRK12696 flgH flagellar basal 47.4 1.5E+02 0.0032 23.9 8.0 12 108-119 184-195 (236)
120 KOG2916 Translation initiation 46.3 28 0.0006 29.0 3.5 30 72-101 12-41 (304)
121 COG3269 Predicted RNA-binding 45.9 44 0.00096 22.2 3.9 24 75-98 47-70 (73)
122 PF08292 RNA_pol_Rbc25: RNA po 43.9 42 0.0009 24.2 3.9 28 74-101 1-28 (122)
123 PF09953 DUF2187: Uncharacteri 43.4 64 0.0014 20.5 4.2 22 80-101 16-37 (57)
124 cd05693 S1_Rrp5_repeat_hs1_sc1 43.2 44 0.00094 23.0 3.8 23 74-96 67-94 (100)
125 PRK11642 exoribonuclease R; Pr 43.0 47 0.001 31.4 5.0 38 74-119 641-679 (813)
126 PF02107 FlgH: Flagellar L-rin 42.7 49 0.0011 25.3 4.3 41 79-119 95-139 (179)
127 PRK12328 nusA transcription el 41.3 32 0.00068 29.7 3.3 26 71-96 133-159 (374)
128 KOG4134 DNA-dependent RNA poly 41.3 19 0.00042 29.1 1.9 41 71-119 102-142 (253)
129 KOG1856 Transcription elongati 40.5 35 0.00076 33.7 3.8 41 74-119 983-1023(1299)
130 PF12508 DUF3714: Protein of u 40.0 1.8E+02 0.004 22.8 7.8 55 36-100 53-111 (200)
131 COG2183 Tex Transcriptional ac 39.2 37 0.0008 32.0 3.6 38 74-119 656-693 (780)
132 PRK04163 exosome complex RNA-b 38.3 48 0.001 26.4 3.8 23 74-96 112-135 (235)
133 PRK12329 nusA transcription el 37.6 32 0.00069 30.4 2.8 26 71-96 147-172 (449)
134 cd06541 ASCH ASC-1 homology or 36.9 1.4E+02 0.003 20.5 5.6 24 59-82 16-39 (105)
135 CHL00010 infA translation init 35.4 1.3E+02 0.0028 19.8 6.2 21 72-92 45-65 (78)
136 PLN00208 translation initiatio 34.4 90 0.0019 23.4 4.5 42 71-114 26-67 (145)
137 PF14444 S1-like: S1-like 34.2 45 0.00098 21.3 2.4 16 71-86 31-46 (58)
138 TIGR00358 3_prime_RNase VacB a 31.8 98 0.0021 28.3 5.1 38 74-119 570-608 (654)
139 smart00652 eIF1a eukaryotic tr 30.4 76 0.0016 21.3 3.2 61 13-98 4-66 (83)
140 COG2928 Uncharacterized conser 29.4 73 0.0016 25.6 3.4 60 73-136 127-198 (222)
141 PF11720 Inhibitor_I78: Peptid 28.8 97 0.0021 19.3 3.3 35 8-44 26-60 (60)
142 smart00293 PWWP domain with co 28.5 39 0.00085 21.1 1.5 12 75-86 2-13 (63)
143 PF13509 S1_2: S1 domain; PDB: 28.5 1.5E+02 0.0032 18.3 4.2 21 76-96 1-21 (61)
144 PRK12700 flgH flagellar basal 28.0 1.2E+02 0.0026 24.3 4.5 38 79-119 145-189 (230)
145 KOG3298 DNA-directed RNA polym 28.0 84 0.0018 24.2 3.4 29 71-99 76-104 (170)
146 cd05838 WHSC1_related The PWWP 27.1 43 0.00093 22.9 1.6 23 74-98 1-23 (95)
147 KOG0171 Mitochondrial inner me 26.4 53 0.0012 25.4 2.1 19 65-83 57-75 (176)
148 PRK00249 flgH flagellar basal 26.4 1.2E+02 0.0027 24.0 4.3 41 79-119 137-181 (222)
149 PRK00276 infA translation init 25.2 1.8E+02 0.0038 18.7 4.2 37 80-118 9-46 (72)
150 COG1097 RRP4 RNA-binding prote 25.0 2.4E+02 0.0053 22.9 5.7 26 71-96 110-136 (239)
151 PRK12701 flgH flagellar basal 24.4 1.5E+02 0.0033 23.7 4.5 38 79-119 144-188 (230)
152 PF13375 RnfC_N: RnfC Barrel s 24.2 89 0.0019 21.7 2.8 13 36-48 67-79 (101)
153 PRK12788 flgH flagellar basal 23.7 1.4E+02 0.0031 24.0 4.2 38 79-119 149-193 (234)
154 PF12059 DUF3540: Protein of u 23.5 3.2E+02 0.0069 21.3 6.1 35 62-98 23-59 (202)
155 TIGR00219 mreC rod shape-deter 23.4 1.8E+02 0.0039 23.8 4.8 38 79-116 156-198 (283)
156 PRK12698 flgH flagellar basal 23.3 1.7E+02 0.0036 23.4 4.5 41 79-119 138-182 (224)
157 PRK12697 flgH flagellar basal 22.9 1.6E+02 0.0034 23.7 4.3 38 79-119 141-185 (226)
158 KOG1070 rRNA processing protei 22.8 2.1E+02 0.0046 29.3 5.8 45 74-126 1160-1205(1710)
159 cd05793 S1_IF1A S1_IF1A: Trans 22.5 1.6E+02 0.0034 19.5 3.6 49 24-96 9-59 (77)
160 PF04085 MreC: rod shape-deter 22.4 1.5E+02 0.0034 21.7 3.9 39 80-118 36-79 (152)
161 PF05257 CHAP: CHAP domain; I 22.3 1.2E+02 0.0025 21.0 3.1 19 71-89 60-90 (124)
162 PRK05585 yajC preprotein trans 22.1 1.8E+02 0.0039 20.4 4.0 23 74-96 53-81 (106)
163 cd05840 SPBC215_ISWI_like The 22.0 57 0.0012 22.3 1.4 20 75-96 2-21 (93)
164 PRK12407 flgH flagellar basal 22.0 1.7E+02 0.0037 23.3 4.3 41 79-119 135-179 (221)
165 COG2932 Predicted transcriptio 21.0 3.8E+02 0.0083 20.4 8.6 69 10-89 136-211 (214)
166 COG1185 Pnp Polyribonucleotide 21.0 1.5E+02 0.0033 27.7 4.3 40 72-119 615-654 (692)
167 PRK13922 rod shape-determining 20.2 2.3E+02 0.0051 22.5 4.9 37 80-116 158-199 (276)
No 1
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6e-33 Score=210.54 Aligned_cols=129 Identities=29% Similarity=0.402 Sum_probs=113.0
Q ss_pred CCcEEecCCccCCCCC-eeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 032397 7 EMVLVTPGEVLGKATE-VKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT 85 (141)
Q Consensus 7 ~~~iVlPGd~L~~~~e-~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V~ 85 (141)
...+|+|||+++..++ |..|.|||+++ |+|+||..|...++ +.....++.+++.......+|.+||||++||+
T Consensus 4 a~~~~lpG~~~c~~e~~~~~g~Gtye~~--~yI~aS~ag~~~~~----~~~~~~~v~~~~~~~~~~~LP~~G~IVtarV~ 77 (193)
T KOG3409|consen 4 AETLVLPGEVVCRAEGEYRMGEGTYERN--GYIFASVAGVNFRD----NLVQKIEVVSVEKQLFNELLPFVGAIVTARVS 77 (193)
T ss_pred ceEEEcccceeeecccccccccceeecC--CeEEeccccceeec----CCccceeeeeecccchhhcCCccCcEEEEEEE
Confidence 4568999999987765 99999999999 99999999955441 11233456666665556899999999999999
Q ss_pred EeccceEEEEEEEecCeecccceeEEEeccccch----hhhHHHHhh-------hhccccccceeeC
Q 032397 86 KVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI----ELLMHLLYG-------YLGSCKMQLNYSL 141 (141)
Q Consensus 86 ~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~----~v~~~~~f~-------~vis~gd~~~y~l 141 (141)
+++.+||+|+|++|++++|++.|+|+||+||||+ ++++++||| +|||+||++||||
T Consensus 78 ~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~L 144 (193)
T KOG3409|consen 78 RINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLL 144 (193)
T ss_pred eeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcEEE
Confidence 9999999999999999999999999999999997 799999995 9999999999997
No 2
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=8.7e-28 Score=184.52 Aligned_cols=122 Identities=25% Similarity=0.301 Sum_probs=113.0
Q ss_pred ccCCcEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEE
Q 032397 5 EEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARV 84 (141)
Q Consensus 5 ~~~~~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V 84 (141)
..++.+|+|||.|+.+|||.+|+|||+.+ |+|+|+.+|.+.. |+++..++|.|.+..+.+|+.||+|+|+|
T Consensus 2 ~~~g~~v~PGd~~a~~EE~~~G~gt~~~~--g~i~Aa~~G~~~~-------d~~n~~~~V~p~~~~~~~~K~GdiV~grV 72 (188)
T COG1096 2 VKDGTFVLPGDVLAVIEEFLPGEGTYEEG--GEIRAAATGVVRR-------DDKNRVISVKPGKKTPPLPKGGDIVYGRV 72 (188)
T ss_pred cccCcEEcCcceeeeeeeeecCCCeEeEC--CEEEEeecccEEE-------cccceEEEeccCCCCCCCCCCCCEEEEEE
Confidence 45788999999999999999999999999 9999999999998 67889999999997799999999999999
Q ss_pred EEeccceEEEEEEEecCe--ecccceeEEEeccccch--hhhHHHHhh-------hhccccc
Q 032397 85 TKVMTRMASADIMCVGAK--SVREKFSGIIRFFIFYI--ELLMHLLYG-------YLGSCKM 135 (141)
Q Consensus 85 ~~v~~~~a~v~I~~v~~~--~l~~~~~G~Ir~~dvr~--~v~~~~~f~-------~vis~gd 135 (141)
+++..++|.|+|..|.++ .+.+++.|.||.|++++ .-++.++|+ +|||+||
T Consensus 73 ~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~~ 134 (188)
T COG1096 73 TDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTGD 134 (188)
T ss_pred eeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecCC
Confidence 999999999999999994 59999999999999998 456668885 9999994
No 3
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=99.94 E-value=7.2e-26 Score=174.87 Aligned_cols=121 Identities=23% Similarity=0.266 Sum_probs=108.6
Q ss_pred ccCCcEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEE
Q 032397 5 EEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARV 84 (141)
Q Consensus 5 ~~~~~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V 84 (141)
++++.+|+|||+|+..++|.+|+|||+++ |.||||++|.+++ |..++.|+|.|.+...+.|++||+|+|+|
T Consensus 2 ~~~~~~V~PGe~l~~~~e~~~G~Gty~~~--~~i~as~~G~~~i-------d~~~~~Isv~P~~~~~~~~~~GdiV~GkV 72 (189)
T PRK09521 2 VKQGDLVLPGDYLAVIEEYLPGEGTYEDN--GEVYASVVGKVFI-------DDINRKISVIPFKKTPPLLKKGDIVYGRV 72 (189)
T ss_pred cccCCEECCCCccccccceEcCCCEEeeC--CEEEEEeeEEEEE-------cCCCCEEEEecCcCCCCCCCCCCEEEEEE
Confidence 34778999999999989999999999999 9999999999998 44578999999886689999999999999
Q ss_pred EEeccceEEEEEEEec--CeecccceeEEEeccccch--hhhHHHHhh-------hhcccc
Q 032397 85 TKVMTRMASADIMCVG--AKSVREKFSGIIRFFIFYI--ELLMHLLYG-------YLGSCK 134 (141)
Q Consensus 85 ~~v~~~~a~v~I~~v~--~~~l~~~~~G~Ir~~dvr~--~v~~~~~f~-------~vis~g 134 (141)
+++.++.|.|+|.+++ ++++..++.|+||.++++. ..+|.++|+ ++++++
T Consensus 73 ~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~ 133 (189)
T PRK09521 73 VDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT 133 (189)
T ss_pred EEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC
Confidence 9999999999999988 7888899999999999986 356778884 777776
No 4
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=99.91 E-value=1.8e-23 Score=166.69 Aligned_cols=116 Identities=23% Similarity=0.351 Sum_probs=101.7
Q ss_pred ccCCcEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEE
Q 032397 5 EEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARV 84 (141)
Q Consensus 5 ~~~~~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V 84 (141)
..++.+|+|||.|+ +++|.+|+|||+++ |.|+||++|.+... +..++|.|.+. .|+|++||+|+|+|
T Consensus 5 ~~~~~~V~PGd~l~-~~~~~~G~Gty~~~--g~i~As~~G~~~~~---------~~~i~V~p~~~-~y~P~vGDiViG~V 71 (235)
T PRK04163 5 VEDRKIVVPGDLLA-EGEFKAGRGTYKEN--GKIYSTVVGLVDIK---------DDKVRVIPLEG-KYIPKVGDLVIGKV 71 (235)
T ss_pred eeCCcEECCCCCcC-cCCeecCCceEEeC--CEEEEEEeEEEEEE---------CCEEEEEECCC-cccCCCCCEEEEEE
Confidence 34568999999997 57899999999999 99999999999983 35999999986 59999999999999
Q ss_pred EEeccceEEEEEEEecCeecccceeEEEeccccch-h-----hhHHHHhh-------hhccccccceeeC
Q 032397 85 TKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI-E-----LLMHLLYG-------YLGSCKMQLNYSL 141 (141)
Q Consensus 85 ~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~-~-----v~~~~~f~-------~vis~gd~~~y~l 141 (141)
++++++.|.|+| .+++.|+||.++++. + .+|.++|+ +|+++++...+.|
T Consensus 72 ~~i~~~~~~vdI--------~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~L 133 (235)
T PRK04163 72 TDVTFSGWEVDI--------NSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVL 133 (235)
T ss_pred EEEeCceEEEEe--------CCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEE
Confidence 999999999999 788999999999986 3 78999994 8888877655543
No 5
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=99.87 E-value=1.3e-21 Score=155.53 Aligned_cols=114 Identities=22% Similarity=0.290 Sum_probs=100.0
Q ss_pred ccccCCcEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEE
Q 032397 3 VKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIA 82 (141)
Q Consensus 3 ~~~~~~~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig 82 (141)
......++|+|||.|.....+..|+|||..+ +.|||+++|.++++ ++.+.|+|.++ +|+|++||+|||
T Consensus 3 ~~~~~~~iV~PGd~vl~~~~~~~G~Gty~~~--~~iyssv~G~~~~~---------~~~v~VIpl~g-~YiP~~gD~VIG 70 (239)
T COG1097 3 LSVSMRKIVLPGDLVLAEGSYKLGHGTYFEG--GKIYSSVVGLLDVK---------GKLVRVIPLEG-RYIPEVGDVVIG 70 (239)
T ss_pred eeccccceecCCCccCCCCCEecCCCcEecC--CEEEEEEEeEEEEe---------CCEEEEEeCCC-cccCCCCCEEEE
Confidence 4456788999999887778899999999999 99999999999994 57899999996 999999999999
Q ss_pred EEEEeccceEEEEEEEecCeecccceeEEEeccccch-hhh-HHHHhhhhcccccc
Q 032397 83 RVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI-ELL-MHLLYGYLGSCKMQ 136 (141)
Q Consensus 83 ~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~-~v~-~~~~f~~vis~gd~ 136 (141)
+|+.+.+..|+||| .++|.++|+.+++-. +.+ .....|.+++.||.
T Consensus 71 ~I~~v~~~~W~VDI--------~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~ 118 (239)
T COG1097 71 KIIEVGPSGWKVDI--------GSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDL 118 (239)
T ss_pred EEEEEcccceEEEc--------CCccceEeehhhhhcccccccccccccccccCCE
Confidence 99999999999999 999999999999954 333 23556788888875
No 6
>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=99.84 E-value=2.6e-21 Score=134.27 Aligned_cols=71 Identities=35% Similarity=0.508 Sum_probs=67.4
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch----hhhHHHHhh-------hhcccccccee
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI----ELLMHLLYG-------YLGSCKMQLNY 139 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~----~v~~~~~f~-------~vis~gd~~~y 139 (141)
.|+|++||+|+|+|++++.++|.|+|+++++++++++|+|+||+||+|+ +++|++||+ +++|+||+.+|
T Consensus 1 ~~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~~ 80 (92)
T cd05791 1 LVLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSY 80 (92)
T ss_pred CCCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCCc
Confidence 3789999999999999999999999999999999999999999999997 678999995 99999999999
Q ss_pred eC
Q 032397 140 SL 141 (141)
Q Consensus 140 ~l 141 (141)
||
T Consensus 81 ~L 82 (92)
T cd05791 81 YL 82 (92)
T ss_pred EE
Confidence 86
No 7
>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=99.84 E-value=8.5e-22 Score=134.33 Aligned_cols=61 Identities=38% Similarity=0.564 Sum_probs=43.0
Q ss_pred CCCCCCEEEEEEEEeccceEEEEEEEe----------cCeecccceeEEEeccccch----hhhHHHHhh-------hhc
Q 032397 73 VPEPGSVVIARVTKVMTRMASADIMCV----------GAKSVREKFSGIIRFFIFYI----ELLMHLLYG-------YLG 131 (141)
Q Consensus 73 ~P~~GdiVig~V~~v~~~~a~v~I~~v----------~~~~l~~~~~G~Ir~~dvr~----~v~~~~~f~-------~vi 131 (141)
+|++||+|+|||+++++++|+|+|+|+ ++.+|.++|+|+||+||||+ +++|++||| +||
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 699999999999999999999999999 88899999999999999997 799999996 888
Q ss_pred cc
Q 032397 132 SC 133 (141)
Q Consensus 132 s~ 133 (141)
|+
T Consensus 81 Sl 82 (82)
T PF10447_consen 81 SL 82 (82)
T ss_dssp EE
T ss_pred eC
Confidence 75
No 8
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=99.78 E-value=2.3e-19 Score=143.86 Aligned_cols=117 Identities=26% Similarity=0.347 Sum_probs=100.2
Q ss_pred cCCcEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 032397 6 EEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT 85 (141)
Q Consensus 6 ~~~~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V~ 85 (141)
....+|+||+.+.....|..|+|||..+ |.|+||++|.++.. ++.|+|+|.+ .+|.|++||+|.|||+
T Consensus 27 ~~~~ivtPG~~V~~d~~fmRGHGTy~~d--~~i~ssvaG~v~rv---------NkLi~V~plk-~rY~pEvGDvVVgRV~ 94 (301)
T KOG3013|consen 27 DHSTIVTPGELVTDDPGFMRGHGTYVRD--GEIYSSVAGVVQRV---------NKLISVKPLK-SRYAPEVGDVVVGRVI 94 (301)
T ss_pred cCceeecCCccccCchhhhhcccceecC--CeEEEeecchhhhh---------cceEEEeehh-hhcCCccCCEEEEEee
Confidence 4557999999999988899999999999 99999999999874 7999999999 6999999999999999
Q ss_pred EeccceEEEEEEEecCeecc--c--ceeEEEeccccchhhhHHHHhh--hhcccc
Q 032397 86 KVMTRMASADIMCVGAKSVR--E--KFSGIIRFFIFYIELLMHLLYG--YLGSCK 134 (141)
Q Consensus 86 ~v~~~~a~v~I~~v~~~~l~--~--~~~G~Ir~~dvr~~v~~~~~f~--~vis~g 134 (141)
.|.+++|+|++.+-.+..|- + =.-|++|+.+..++..|.+-|. .+|+..
T Consensus 95 eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AE 149 (301)
T KOG3013|consen 95 EVQQKRWKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAE 149 (301)
T ss_pred eeecceeEEecccccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHH
Confidence 99999999999877766653 2 2567888888888899987774 444433
No 9
>PF14382 ECR1_N: Exosome complex exonuclease RRP4 N-terminal region; PDB: 2NN6_I 3M7N_C 2BA1_A 3M85_C.
Probab=99.50 E-value=1.3e-14 Score=86.02 Aligned_cols=37 Identities=41% Similarity=0.814 Sum_probs=33.8
Q ss_pred EEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEe
Q 032397 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRT 48 (141)
Q Consensus 10 iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~ 48 (141)
+|+|||+|+.+++|.+|+|||+++ |+||||++|.+++
T Consensus 1 iV~PG~~l~~~~e~~~G~GTY~~~--g~I~asv~G~v~~ 37 (39)
T PF14382_consen 1 IVVPGDRLGSSEEYMPGHGTYVRD--GNIYASVAGTVKI 37 (39)
T ss_dssp EE-TT-EEEETTTSEESTTEEEET--TEEEESSSEEEEE
T ss_pred CCCCCCEeecCCCEecCCCEEEeC--CEEEEEeeEEEEE
Confidence 699999999999999999999999 9999999999987
No 10
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.85 E-value=8.3e-09 Score=69.14 Aligned_cols=58 Identities=19% Similarity=0.074 Sum_probs=48.5
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch--hhhHHHHhh-------hhcccccc
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI--ELLMHLLYG-------YLGSCKMQ 136 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~--~v~~~~~f~-------~vis~gd~ 136 (141)
.|+|++||+|+|+|+++..+.|.|+| .+.+.|+|+.+++.. .-+|.+.|+ +++++.+.
T Consensus 1 ~y~p~~GdiV~G~V~~v~~~~~~V~i--------~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~ 67 (82)
T cd04454 1 RYLPDVGDIVIGIVTEVNSRFWKVDI--------LSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD 67 (82)
T ss_pred CCCCCCCCEEEEEEEEEcCCEEEEEe--------CCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC
Confidence 48999999999999999999999999 677999999999975 455666663 66666553
No 11
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=98.68 E-value=8.4e-08 Score=75.59 Aligned_cols=101 Identities=21% Similarity=0.195 Sum_probs=74.5
Q ss_pred cEEecCCccCC--CCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEE
Q 032397 9 VLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTK 86 (141)
Q Consensus 9 ~iVlPGd~L~~--~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V~~ 86 (141)
.+.+|||.+.. ..+..+|+|.+.++ +.+..+..|.+....+. .......+|.... .+|+|.+||.|||+|+.
T Consensus 2 ~~~~pg~~~~~~~~~sv~~G~g~~~~g--~~~~~~~~G~~~~~~~g---k~~~~v~~vds~~-kRYiP~~~D~VIGiV~~ 75 (230)
T KOG1004|consen 2 TFYFPGDSIPRPRLCSVVLGPGLRRRG--QERLVTKCGRLRHKEPG---KGGGGVYWVDSQQ-KRYIPVKGDHVIGIVTS 75 (230)
T ss_pred ceecCCcccccCccCceeecCCccccC--ceEEeccccceeeccCC---cccceeEEEeccc-ceecCCCCCEEEEEEEe
Confidence 46789998753 24589999999988 99999999988774200 0011356777766 69999999999999999
Q ss_pred eccceEEEEEEEecCeecc-cceeEEEecc
Q 032397 87 VMTRMASADIMCVGAKSVR-EKFSGIIRFF 115 (141)
Q Consensus 87 v~~~~a~v~I~~v~~~~l~-~~~~G~Ir~~ 115 (141)
-+++..+|||-.-.-..|+ ..|.|.-+++
T Consensus 76 ~~gd~ykVDigg~~~a~L~~laFe~AtkrN 105 (230)
T KOG1004|consen 76 KSGDIYKVDIGGSEPASLSYLAFEGATKRN 105 (230)
T ss_pred ccCceEEEecCCCCeeeeeeccccCccccC
Confidence 9999999999332222233 2688877665
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=98.66 E-value=3.5e-08 Score=67.85 Aligned_cols=39 Identities=23% Similarity=0.290 Sum_probs=34.8
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEecccc
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIF 117 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dv 117 (141)
+|+|++||+|||+|++++.+.|+|+| ++++.|+|+..+.
T Consensus 1 rY~P~~gD~VIG~V~~~~~~~~~VdI--------~s~~~a~L~~~~f 39 (86)
T cd05790 1 RYVPAKGDHVIGIVVAKAGDFFKVDI--------GGSEPASLSYLAF 39 (86)
T ss_pred CCcCCCCCEEEEEEEEEcCCeEEEEc--------CCCcceEechHHc
Confidence 48999999999999999999999999 7777777777665
No 13
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.43 E-value=7e-07 Score=60.07 Aligned_cols=40 Identities=30% Similarity=0.408 Sum_probs=37.6
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccc
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY 118 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr 118 (141)
.|.|++||+|.|+|+++.+..|.|+| ...+.|+|+.+++.
T Consensus 1 ~y~p~~GdiV~g~V~~i~~~g~~v~i--------~~~~~G~l~~se~~ 40 (86)
T cd05789 1 RYIPEVGDVVIGRVTEVGFKRWKVDI--------NSPYDAVLPLSEVN 40 (86)
T ss_pred CCcCCCCCEEEEEEEEECCCEEEEEC--------CCCeEEEEEHHHcc
Confidence 47899999999999999999999999 77899999999996
No 14
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.64 E-value=0.00011 Score=47.51 Aligned_cols=55 Identities=13% Similarity=0.051 Sum_probs=45.3
Q ss_pred CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch----hhhHHHHhh-------hhcccccccee
Q 032397 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI----ELLMHLLYG-------YLGSCKMQLNY 139 (141)
Q Consensus 77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~----~v~~~~~f~-------~vis~gd~~~y 139 (141)
|++|.|+|+++....+.|++ ...+.|.|+.++++. ...+.++|+ +++++.+...+
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 678999999999974 234567774 78888776654
No 15
>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=97.56 E-value=0.00019 Score=47.49 Aligned_cols=37 Identities=14% Similarity=0.125 Sum_probs=34.6
Q ss_pred CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
++||+|.|+|+++++..++|++ .....|.||.+|+..
T Consensus 2 k~G~~V~g~V~~i~~~G~fV~l--------~~~v~G~v~~~~ls~ 38 (74)
T cd05705 2 KEGQLLRGYVSSVTKQGVFFRL--------SSSIVGRVLFQNVTK 38 (74)
T ss_pred CCCCEEEEEEEEEeCCcEEEEe--------CCCCEEEEEHHHccC
Confidence 6899999999999999999999 778999999999986
No 16
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.23 E-value=0.00077 Score=47.19 Aligned_cols=37 Identities=11% Similarity=0.174 Sum_probs=34.2
Q ss_pred CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
++|++|.|+|+++.+..+.+++ .....|+++.+|+.+
T Consensus 2 ~~G~vV~G~V~~v~~~gl~v~L--------~~g~~G~v~~seis~ 38 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISL--------PNGLTGYVPITNISD 38 (100)
T ss_pred CCCCEEEEEEEEEcCCCEEEEC--------CCCcEEEEEHHHhhH
Confidence 6899999999999999999988 778999999999975
No 17
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.20 E-value=0.00078 Score=43.19 Aligned_cols=44 Identities=25% Similarity=0.072 Sum_probs=36.4
Q ss_pred CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch-h-hhHHHHhh
Q 032397 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI-E-LLMHLLYG 128 (141)
Q Consensus 77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~-~-v~~~~~f~ 128 (141)
||+|.|+|+++.+..|.|++ ...+.|+|+.+++.. + ..+.++|+
T Consensus 1 G~iv~g~V~~i~~~~~~v~l--------~~~~~g~l~~~e~~~~~~~~~~~~~~ 46 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDI--------GYKSEGIIPISEFSDDPIENGEDEVK 46 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEe--------CCCceEEEEHHHhCccccCCHhHcCC
Confidence 89999999999999999999 556899999999975 3 34555553
No 18
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=97.08 E-value=0.0013 Score=42.56 Aligned_cols=40 Identities=20% Similarity=0.296 Sum_probs=34.4
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
|++|++|.|+|+++....|.+++... ....|+||.++++.
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~------~~~~gll~~s~l~~ 40 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEY------GNIEGMILLSELSR 40 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCC------CCeEEEEEhHHcCC
Confidence 68999999999999999999999321 13899999999976
No 19
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.04 E-value=0.0016 Score=42.61 Aligned_cols=37 Identities=24% Similarity=0.344 Sum_probs=33.0
Q ss_pred CCCCEEEEEEEEecc-ceEEEEEEEecCeecccceeEEEeccccch
Q 032397 75 EPGSVVIARVTKVMT-RMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 75 ~~GdiVig~V~~v~~-~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
++|++|.|+|+++.+ ..+.+++ .....|++|.+++..
T Consensus 2 ~~G~iv~G~V~~i~~~~g~~v~l--------~~~~~Glvhis~~s~ 39 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQL--------PFGKTGLVSIFHLSD 39 (72)
T ss_pred CCCCEEEEEEEEeeCCcEEEEEC--------CCCCEEEEEHHHhcC
Confidence 689999999999987 4688887 888999999999976
No 20
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=96.93 E-value=0.0033 Score=40.50 Aligned_cols=38 Identities=21% Similarity=0.183 Sum_probs=35.6
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
|++|++|.|+|+++.+..+.++| .....|+|+.+++..
T Consensus 2 ~~~G~iv~g~V~~v~~~g~~V~l--------~~~~~g~ip~~~l~~ 39 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDFGVFVDL--------GNGIEGFIPISELSD 39 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEE--------STSSEEEEEGGGSSS
T ss_pred CCCCCEEEEEEEEEECCEEEEEE--------CCcEEEEEEeehhcC
Confidence 68999999999999999999999 788999999999974
No 21
>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=96.84 E-value=0.0034 Score=40.51 Aligned_cols=37 Identities=24% Similarity=0.211 Sum_probs=34.5
Q ss_pred CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
++|++|.|+|+++....+.|++ ....+|++|.+++..
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l--------~~~~~g~v~~s~l~~ 38 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQL--------GNKVTGPSFITDALD 38 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEe--------CCCcEEEEEhhhccC
Confidence 5899999999999999999998 778999999999986
No 22
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=96.71 E-value=0.0031 Score=46.20 Aligned_cols=55 Identities=9% Similarity=-0.074 Sum_probs=44.9
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch-hhhHHHHh--------hhhcccccc
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI-ELLMHLLY--------GYLGSCKMQ 136 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~-~v~~~~~f--------~~vis~gd~ 136 (141)
+++||++.|+||.|++=-|+|++ ...-+|++|++.|.. .|+-.+.+ .+||++.+.
T Consensus 3 ~kvG~~l~GkItgI~~yGAFV~l--------~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~ 66 (129)
T COG1098 3 MKVGSKLKGKITGITPYGAFVEL--------EGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDEN 66 (129)
T ss_pred ccccceEEEEEEeeEecceEEEe--------cCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccC
Confidence 68999999999999999999999 777889999999997 65544333 277777663
No 23
>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=96.68 E-value=0.0044 Score=39.58 Aligned_cols=35 Identities=26% Similarity=0.372 Sum_probs=32.4
Q ss_pred CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
|++|.|+|+++....|.|+| .....|+++.+++..
T Consensus 1 G~~v~g~V~~v~~~g~~v~l--------~~~~~g~i~~~~~~~ 35 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKL--------GDGVEGFLRAAELSR 35 (73)
T ss_pred CCEEEEEEEEEECCeEEEEe--------CCCCEEEEEHHHCCC
Confidence 89999999999999999999 567999999999876
No 24
>PRK07252 hypothetical protein; Provisional
Probab=96.68 E-value=0.0043 Score=44.87 Aligned_cols=37 Identities=14% Similarity=0.133 Sum_probs=34.0
Q ss_pred CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
++|++|.|+|++|....|.|+| .....|+|+.++++.
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei--------~~~~~GllhiseLs~ 38 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVAL--------ENGTTGLIHISEIKT 38 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEE--------CCCCEEEEEHHHcCC
Confidence 5799999999999999999999 667899999999975
No 25
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=96.65 E-value=0.0035 Score=52.51 Aligned_cols=41 Identities=17% Similarity=0.284 Sum_probs=36.6
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecc--cceeEEEeccccch
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR--EKFSGIIRFFIFYI 119 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~--~~~~G~Ir~~dvr~ 119 (141)
.-.|++||+|.|+|++|..-.|.|+| . ....|+||.+++..
T Consensus 12 ~~~P~~GdvV~g~V~~I~d~GafV~L--------~EY~gvEGlIhiSElS~ 54 (319)
T PTZ00248 12 QKFPEEDDLVMVKVVRITEMGAYVSL--------LEYDDIEGMILMSELSK 54 (319)
T ss_pred hhCCCCCCEEEEEEEEEeCCeEEEEe--------cCCCCcEEEEEHHHhcc
Confidence 45699999999999999999999999 4 35899999999965
No 26
>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=96.63 E-value=0.0061 Score=38.86 Aligned_cols=35 Identities=14% Similarity=0.085 Sum_probs=32.4
Q ss_pred CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
|++|.|+|+++.+..+.|++ ...+.|++|.+++..
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l--------~~~~~G~v~~s~l~~ 35 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTL--------GRGVDARVRVSELSD 35 (68)
T ss_pred CCEEEEEEEEEECccEEEEe--------CCCCEEEEEHHHCCc
Confidence 79999999999999999999 567999999999975
No 27
>PRK08582 hypothetical protein; Provisional
Probab=96.60 E-value=0.0057 Score=45.31 Aligned_cols=38 Identities=21% Similarity=0.162 Sum_probs=35.0
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.++|++|.|+|+.|++..|.|+| .....|+||.+++..
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L--------~~~~~GlVhiSels~ 40 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVEL--------PEGKTGLVHISEVAD 40 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEE--------CCCCEEEEEeeccCc
Confidence 57899999999999999999999 667999999999975
No 28
>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=96.57 E-value=0.0057 Score=39.38 Aligned_cols=37 Identities=19% Similarity=0.087 Sum_probs=33.1
Q ss_pred CCCCEEEEEEEEeccceEEEEEEEecCeecc-cceeEEEeccccch
Q 032397 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRFFIFYI 119 (141)
Q Consensus 75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~-~~~~G~Ir~~dvr~ 119 (141)
++|++|.|+|+++.+..|.|++ . ....|+++.+++..
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l--------~~~~~~g~i~~~~l~~ 38 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDI--------DGTNVSGLCHKSEISD 38 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEE--------CCCCeEEEEEHHHCCC
Confidence 4699999999999999999999 4 36899999999986
No 29
>PRK08059 general stress protein 13; Validated
Probab=96.56 E-value=0.0056 Score=44.15 Aligned_cols=38 Identities=26% Similarity=0.254 Sum_probs=34.9
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.++|++|.|+|+++.+..|.|+| ...+.|+|+.++++.
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i--------~~~~~Gli~~sel~~ 42 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVAL--------DEETQGLVHISEITH 42 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEE--------CCCCEEEEEHHHCCc
Confidence 57899999999999999999999 667999999999975
No 30
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=96.54 E-value=0.0065 Score=37.67 Aligned_cols=37 Identities=27% Similarity=0.244 Sum_probs=33.7
Q ss_pred CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
++|++|.|+|++++...+.|+| ...+.|+++.+++..
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i--------~~~~~g~l~~~~~~~ 37 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDL--------GNGVEGLIPISELSD 37 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEe--------CCCCEEEEEHHHCCc
Confidence 4699999999999999999999 657999999999986
No 31
>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=96.51 E-value=0.0086 Score=38.98 Aligned_cols=39 Identities=15% Similarity=0.067 Sum_probs=33.3
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
|+.|+++.|+|+++.+..+.+++ ++. ...|++|.+++..
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l---~~~----~~eGlvh~sel~~ 39 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKI---PGC----RKQGLVHKSHMSS 39 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEE---CCC----CeEEEEEchhhCC
Confidence 67999999999999999999999 111 2589999999976
No 32
>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=96.45 E-value=0.0069 Score=39.70 Aligned_cols=35 Identities=20% Similarity=0.166 Sum_probs=32.6
Q ss_pred CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
||+|.|+|+++.+..++|++ .....|.|+.+|+..
T Consensus 1 G~~V~g~V~~i~~~g~~V~l--------~~~i~G~i~~~~ls~ 35 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTI--------SPDVKGRIPLLDLSD 35 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEe--------CCCcEEEEEHHHcCC
Confidence 89999999999999999999 778999999999964
No 33
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=96.41 E-value=0.0081 Score=48.95 Aligned_cols=43 Identities=21% Similarity=0.129 Sum_probs=36.5
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.-+|++||+|.|+|+++.+..|.|++... ....|+||.+++..
T Consensus 3 ~~~P~~GdiV~G~V~~I~~~G~fV~L~e~------~gieGlI~iSEls~ 45 (262)
T PRK03987 3 KEWPEEGELVVGTVKEVKDFGAFVTLDEY------PGKEGFIHISEVAS 45 (262)
T ss_pred CCCCCCCCEEEEEEEEEECCEEEEEECCC------CCcEEEEEHHHcCc
Confidence 45799999999999999999999999321 14799999999875
No 34
>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=96.29 E-value=0.01 Score=36.98 Aligned_cols=35 Identities=26% Similarity=0.260 Sum_probs=32.4
Q ss_pred CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
|++|.|+|+++.+..|.|+| ...+.|+|+.++++.
T Consensus 1 G~~~~g~V~~i~~~g~~v~i--------~~~~~g~l~~~~l~~ 35 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVEL--------GGGISGLVHISQIAH 35 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEE--------CCCCEEEEEhHHcCC
Confidence 79999999999999999999 667999999999875
No 35
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=96.19 E-value=0.013 Score=37.45 Aligned_cols=35 Identities=14% Similarity=0.208 Sum_probs=32.4
Q ss_pred CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
|++|.|+|+++....+.|++ .....|++|.+++..
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l--------~~~v~g~i~~~~l~~ 35 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKL--------SDHIKGLVPPMHLAD 35 (69)
T ss_pred CCEEEEEEEEEeccEEEEEe--------cCCcEEEEEHHHCCC
Confidence 79999999999999999999 667999999999975
No 36
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=96.16 E-value=0.014 Score=37.19 Aligned_cols=35 Identities=11% Similarity=0.046 Sum_probs=32.1
Q ss_pred CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
|+++.|+|+++.+..+.|++ .....|+||.+++..
T Consensus 1 g~~~~g~V~~v~~~G~~V~l--------~~~~~gli~~s~l~~ 35 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSF--------YNNVKGFLPKSELSE 35 (70)
T ss_pred CCEEEEEEEEEecCcEEEEE--------CCCCEEEEEHHHcCh
Confidence 89999999999999999999 556899999999975
No 37
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=96.04 E-value=0.017 Score=39.38 Aligned_cols=37 Identities=24% Similarity=0.352 Sum_probs=33.0
Q ss_pred CCCCCEEEEEEEEeccc--eEEEEEEEecCeecccceeEEEeccccc
Q 032397 74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRFFIFY 118 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~--~a~v~I~~v~~~~l~~~~~G~Ir~~dvr 118 (141)
|++|+++.|+|+++.+. .|.|+| .....|+||.+++.
T Consensus 5 ~~~G~iy~g~V~~i~~~~~GaFV~l--------~~g~~Gllh~seis 43 (88)
T cd04453 5 PIVGNIYLGRVKKIVPGLQAAFVDI--------GLGKNGFLHLSDIL 43 (88)
T ss_pred CCCCCEEEEEEEEeccCCcEEEEEe--------CCCCEEEEEhHHcC
Confidence 68999999999999996 899999 55678999999884
No 38
>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=95.71 E-value=0.025 Score=35.08 Aligned_cols=35 Identities=31% Similarity=0.205 Sum_probs=31.9
Q ss_pred CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
|+++.|+|+++++..|.+++ .....|+++.++++.
T Consensus 1 g~~~~g~V~~i~~~G~fv~l--------~~~~~g~~~~~~l~~ 35 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDI--------GVKQDGLIHISKMAD 35 (68)
T ss_pred CCEEEEEEEEEecccEEEEc--------CCCCEEEEEHHHCCC
Confidence 78999999999999999999 556899999999976
No 39
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=95.67 E-value=0.0049 Score=56.28 Aligned_cols=64 Identities=17% Similarity=0.134 Sum_probs=48.7
Q ss_pred CeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEecc
Q 032397 36 GLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFF 115 (141)
Q Consensus 36 g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~ 115 (141)
|.++++..+.... +.....|.... ..|++|+++.|+|+++.+..+.|+| .....|+||++
T Consensus 590 G~V~i~~~~~~~~-------~~a~~~I~~~~-----~~~~~G~i~~G~V~~I~~~GafVei--------~~g~~GllHiS 649 (684)
T TIGR03591 590 GTVKIAASDGEAA-------EAAIKMIEGIT-----AEPEVGKIYEGKVVRIMDFGAFVEI--------LPGKDGLVHIS 649 (684)
T ss_pred eEEEEEECcHHHH-------HHHHHHHHhhh-----cccccCcEEEEEEEEEeCCEEEEEE--------CCCcEEEEEHH
Confidence 7888777776555 11223444432 2489999999999999999999999 44689999999
Q ss_pred ccch
Q 032397 116 IFYI 119 (141)
Q Consensus 116 dvr~ 119 (141)
++..
T Consensus 650 ei~~ 653 (684)
T TIGR03591 650 EIAN 653 (684)
T ss_pred HcCC
Confidence 9975
No 40
>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=95.50 E-value=0.037 Score=35.45 Aligned_cols=35 Identities=31% Similarity=0.441 Sum_probs=31.5
Q ss_pred CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
||+|.|+|+++.+..+.+++ ...+.|+++..++..
T Consensus 1 G~~V~g~V~~i~~~G~~v~l--------~~~v~g~v~~~~l~~ 35 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDF--------LSSFTGTVDFLHLDP 35 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEE--------cCCceEEEEHHHcCC
Confidence 89999999999999999999 566999999988864
No 41
>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=95.45 E-value=0.041 Score=34.34 Aligned_cols=35 Identities=17% Similarity=0.150 Sum_probs=31.9
Q ss_pred CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
|+++.|+|+++.+..|.++| .....|+++.++++.
T Consensus 1 g~~~~g~V~~v~~~G~~v~l--------~~~~~g~l~~~~l~~ 35 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEI--------LPGKDGLVHISELSD 35 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEe--------CCCCEEEEEhHHcCC
Confidence 78999999999999999999 556899999999976
No 42
>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=95.44 E-value=0.042 Score=36.41 Aligned_cols=38 Identities=16% Similarity=0.116 Sum_probs=34.9
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
+++|+++.|+|+++....+.|++ .....|++|.+++..
T Consensus 12 ~~~G~i~~g~V~~v~~~G~fv~l--------~~~~~g~v~~~el~~ 49 (83)
T cd04461 12 LKPGMVVHGYVRNITPYGVFVEF--------LGGLTGLAPKSYISD 49 (83)
T ss_pred CCCCCEEEEEEEEEeeceEEEEc--------CCCCEEEEEHHHCCc
Confidence 68999999999999999999999 556899999999975
No 43
>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=95.36 E-value=0.043 Score=34.15 Aligned_cols=35 Identities=20% Similarity=0.204 Sum_probs=30.9
Q ss_pred CCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 76 PGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 76 ~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
+|+++.|+|+++....|.++| . ...|+|+.+++..
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l--------~-~~~g~l~~~e~~~ 35 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDL--------G-GVDGLLHISDMSW 35 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEE--------C-CeEEEEEhHHCCC
Confidence 599999999999999999998 3 4789999999864
No 44
>PRK05807 hypothetical protein; Provisional
Probab=95.28 E-value=0.049 Score=40.12 Aligned_cols=37 Identities=14% Similarity=0.156 Sum_probs=32.4
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.++|++|.|+|+.+++..|.|++ ++ ..|+||.+++..
T Consensus 3 ~~vG~vv~G~Vt~i~~~GafV~L---~~------~~Glvhiseis~ 39 (136)
T PRK05807 3 LKAGSILEGTVVNITNFGAFVEV---EG------KTGLVHISEVAD 39 (136)
T ss_pred ccCCCEEEEEEEEEECCeEEEEE---CC------EEEEEEhhhccc
Confidence 36899999999999999999999 22 489999999975
No 45
>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=95.18 E-value=0.056 Score=35.59 Aligned_cols=37 Identities=19% Similarity=-0.014 Sum_probs=33.1
Q ss_pred CCCCEEEEEEEEeccceEEEEEEEecCeecc-cceeEEEeccccch
Q 032397 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRFFIFYI 119 (141)
Q Consensus 75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~-~~~~G~Ir~~dvr~ 119 (141)
+.|++|.|.|.++.+..+.+++ . ..+.|+|+++++..
T Consensus 3 ~~G~~v~g~V~si~d~G~~v~~--------g~~gv~Gfl~~~~~~~ 40 (74)
T cd05694 3 VEGMVLSGCVSSVEDHGYILDI--------GIPGTTGFLPKKDAGN 40 (74)
T ss_pred CCCCEEEEEEEEEeCCEEEEEe--------CCCCcEEEEEHHHCCc
Confidence 6899999999999999999998 4 46899999999864
No 46
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.00 E-value=0.01 Score=54.35 Aligned_cols=64 Identities=17% Similarity=0.144 Sum_probs=49.3
Q ss_pred CeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEecc
Q 032397 36 GLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFF 115 (141)
Q Consensus 36 g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~ 115 (141)
|.++++..+...+ +..+..|+.... .|++|+++.|+|+++.+..+.|+| .....|++|.+
T Consensus 593 G~v~i~~~~~~~~-------~~a~~~I~~~~~-----~~~vG~v~~G~V~~I~~fGafVei--------~~~~~GllhiS 652 (693)
T PRK11824 593 GTVKIAATDGEAA-------EAAKERIEGITA-----EPEVGEIYEGKVVRIVDFGAFVEI--------LPGKDGLVHIS 652 (693)
T ss_pred ceEEEEcccHHHH-------HHHHHHHHHhcc-----cCcCCeEEEEEEEEEECCeEEEEE--------CCCCEEEEEee
Confidence 8888887777665 222334444332 379999999999999999999999 45689999999
Q ss_pred ccch
Q 032397 116 IFYI 119 (141)
Q Consensus 116 dvr~ 119 (141)
++..
T Consensus 653 els~ 656 (693)
T PRK11824 653 EIAD 656 (693)
T ss_pred eccC
Confidence 9975
No 47
>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=94.92 E-value=0.066 Score=34.26 Aligned_cols=35 Identities=17% Similarity=0.136 Sum_probs=30.8
Q ss_pred CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccc
Q 032397 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY 118 (141)
Q Consensus 75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr 118 (141)
+.|++|.|+|.++....+.++| .. ..|+|+.++..
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdi--------g~-~eg~lp~~e~~ 36 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDL--------GK-VEAILPKKEQI 36 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEc--------CC-eEEEeeHHHCC
Confidence 5799999999999999999999 44 78899988875
No 48
>PHA02945 interferon resistance protein; Provisional
Probab=94.82 E-value=0.087 Score=36.39 Aligned_cols=40 Identities=15% Similarity=0.120 Sum_probs=32.0
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEecccc
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIF 117 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dv 117 (141)
--+|++|++|+|+|+. ....|.+++.-- ...+|+|+.+.+
T Consensus 6 y~~P~~GelvigtV~~-~d~ga~v~L~EY------~g~eg~i~~sev 45 (88)
T PHA02945 6 YSLPNVGDVLKGKVYE-NGYALYIDLFDY------PHSEAILAESVQ 45 (88)
T ss_pred ecCCCCCcEEEEEEEe-cCceEEEEeccc------CCcEEEEEeehh
Confidence 3579999999999999 888899999321 147888888855
No 49
>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=94.17 E-value=0.06 Score=36.66 Aligned_cols=47 Identities=17% Similarity=0.316 Sum_probs=39.4
Q ss_pred ccccCCcEEecCCccCCC--CCeeecCcEEEeCCCCeEEEEEeeEEEeeC
Q 032397 3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTLS 50 (141)
Q Consensus 3 ~~~~~~~iVlPGd~L~~~--~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~ 50 (141)
+|..+++.|.||+.|... ..|-||.++..-. |..|+|..-|.+.++.
T Consensus 22 vK~~~G~~V~~G~IivRQRgtk~hPG~NVg~Gr-D~TLfAl~~G~V~f~~ 70 (81)
T PF01016_consen 22 VKKFGGQFVKAGNIIVRQRGTKFHPGENVGMGR-DHTLFALVDGRVKFTK 70 (81)
T ss_dssp ESSSTTCEESSTSEEEEBSSSSSEEBTTEEEET-TSEEEESSSCEEEEEE
T ss_pred EEEeCCEEEcCCCEEEEeCCCcCcCCCCEEECC-CCcEEEecCEEEEEEE
Confidence 577889999999999643 4599999998773 4899999999999963
No 50
>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=94.15 E-value=0.26 Score=32.26 Aligned_cols=38 Identities=18% Similarity=0.190 Sum_probs=33.9
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.++|+++.|+|+++++..+.+++ .....|+++.+++..
T Consensus 14 ~~~G~~~~g~V~~i~~~G~fV~l--------~~~~~Glv~~se~~~ 51 (77)
T cd04473 14 LEVGKLYKGKVNGVAKYGVFVDL--------NDHVRGLIHRSNLLR 51 (77)
T ss_pred CCCCCEEEEEEEeEecceEEEEE--------CCCcEEEEEchhccC
Confidence 68999999999999999999999 557999999998653
No 51
>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=94.03 E-value=0.12 Score=32.45 Aligned_cols=34 Identities=12% Similarity=0.205 Sum_probs=31.0
Q ss_pred CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccc
Q 032397 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY 118 (141)
Q Consensus 77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr 118 (141)
|+++.|+|+++++..+.|++ .....|++|.+++.
T Consensus 1 G~~~~g~V~~i~~~G~fv~l--------~~~~~Glv~~~~l~ 34 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGL--------DGGIDGLVHISDIS 34 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEe--------CCCCEEEEEHHHCC
Confidence 78999999999999999999 45689999999986
No 52
>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=93.96 E-value=0.17 Score=32.30 Aligned_cols=36 Identities=14% Similarity=0.249 Sum_probs=32.5
Q ss_pred CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccc
Q 032397 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY 118 (141)
Q Consensus 75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr 118 (141)
.+|+++.|+|+++++..+.|++ .....|++|.+++.
T Consensus 2 ~~g~~~~g~V~~i~~~G~fv~l--------~~~~~Gl~~~~~l~ 37 (72)
T cd05689 2 PEGTRLFGKVTNLTDYGCFVEL--------EEGVEGLVHVSEMD 37 (72)
T ss_pred cCCCEEEEEEEEEEeeEEEEEc--------CCCCEEEEEEEecc
Confidence 4799999999999999999999 55689999999986
No 53
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=93.93 E-value=0.13 Score=42.13 Aligned_cols=43 Identities=21% Similarity=0.198 Sum_probs=36.5
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.-.|.+|++|+|+|.+|..-.|.+.+.-- ...+|+||.+.|..
T Consensus 6 ~~~PeeGEiVv~tV~~V~~~GAyv~L~EY------~g~Eg~ihiSEvas 48 (269)
T COG1093 6 REYPEEGEIVVGTVKQVADYGAYVELDEY------PGKEGFIHISEVAS 48 (269)
T ss_pred cCCCCCCcEEEEEEEEeeccccEEEeecc------CCeeeeEEHHHHHH
Confidence 56799999999999999999999999321 13789999999976
No 54
>PRK05435 rpmA 50S ribosomal protein L27; Validated
Probab=93.88 E-value=0.18 Score=34.37 Aligned_cols=46 Identities=20% Similarity=0.291 Sum_probs=38.1
Q ss_pred ccccCCcEEecCCccCCC--CCeeecCcEEEeCCCCeEEEEEeeEEEee
Q 032397 3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTL 49 (141)
Q Consensus 3 ~~~~~~~iVlPGd~L~~~--~e~~~G~GtY~~~~~g~I~Asv~G~~~~~ 49 (141)
+|......|.||+.|... ..|-||.++-.-. |..|+|.+.|.+++.
T Consensus 23 vK~~~g~~V~~G~IivRQRGtk~~PG~nVg~Gr-D~TlfA~~~G~V~f~ 70 (82)
T PRK05435 23 VKRFGGQFVKAGNIIVRQRGTKFHPGVNVGRGK-DHTLFALVDGVVKFE 70 (82)
T ss_pred eEecCCEEEcCCcEEEEeCCCeECCCCCEeecC-CceEEEecceEEEEE
Confidence 577788999999998644 3499999987653 489999999999995
No 55
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=93.63 E-value=0.15 Score=38.94 Aligned_cols=39 Identities=23% Similarity=0.164 Sum_probs=34.6
Q ss_pred CCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
+-|.+|++|.|+|++++...+.+++ . ++.|+++.+++..
T Consensus 77 f~P~~GEVv~g~V~~v~~~Gi~V~l--------g-~~~g~v~~~~l~~ 115 (187)
T PRK08563 77 FKPELQEVVEGEVVEVVEFGAFVRI--------G-PVDGLLHISQIMD 115 (187)
T ss_pred EeccCCCEEEEEEEEEEccEEEEEE--------e-CceEEEEcHHcCC
Confidence 4599999999999999999999999 3 5889999988865
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=93.36 E-value=0.12 Score=47.57 Aligned_cols=38 Identities=18% Similarity=0.209 Sum_probs=34.4
Q ss_pred CCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccc
Q 032397 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY 118 (141)
Q Consensus 73 ~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr 118 (141)
.|++|+++.|+|+++.+-.|.|+| .....|++|++++.
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel--------~~G~eGLvHISeis 681 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSL--------LPGKDGLLHISQIR 681 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEe--------cCCceEEEEhhhcc
Confidence 489999999999999999999999 45689999999774
No 57
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=93.34 E-value=0.14 Score=45.74 Aligned_cols=46 Identities=20% Similarity=0.084 Sum_probs=38.3
Q ss_pred CCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch-h-hhHHHHh
Q 032397 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI-E-LLMHLLY 127 (141)
Q Consensus 73 ~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~-~-v~~~~~f 127 (141)
-.++|++|.|.|+++++-.|.|+| .. +.|++|++++.- + ..+.+-|
T Consensus 189 ~l~~G~vV~G~V~~It~~GafVdi--------gG-vdGLlHiseiS~~rv~~P~~vv 236 (541)
T COG0539 189 KLEVGEVVEGVVKNITDYGAFVDI--------GG-VDGLLHISEISWKRVDHPSEVV 236 (541)
T ss_pred cCCCCceEEEEEEEeecCcEEEEe--------cC-eeeEEehhhccccccCCHHHhc
Confidence 368999999999999999999999 44 999999999985 2 4455544
No 58
>CHL00121 rpl27 ribosomal protein L27; Reviewed
Probab=93.07 E-value=0.22 Score=34.25 Aligned_cols=60 Identities=20% Similarity=0.268 Sum_probs=43.5
Q ss_pred ccccCCcEEecCCccCCC--CCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecC
Q 032397 3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH 67 (141)
Q Consensus 3 ~~~~~~~iVlPGd~L~~~--~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~ 67 (141)
+|......|.||+.|... ..|-||.++=.- +|..|+|...|.++++. ...++..|+|.|.
T Consensus 23 vK~~~gq~V~~G~IivRQRGtk~hPG~NVg~G-rD~TlfAl~~G~V~f~~----~~~~~~~vsv~~~ 84 (86)
T CHL00121 23 VKRFGGEKVSAGNILIRQRGTKFKPGLNVGCG-KDFTLYALIDGFVKFKK----KNKKQKSINVINI 84 (86)
T ss_pred eEEcCCEEEcCCcEEEEcCCCeECCCCccccc-CCceEEEccceEEEEEE----eCCCCEEEEEeec
Confidence 567788999999998654 348888887554 24899999999999952 1123457777653
No 59
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=92.60 E-value=0.26 Score=41.06 Aligned_cols=38 Identities=26% Similarity=0.267 Sum_probs=34.4
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.++|++|.|+|+++....+.|+| .....|+|+.+++..
T Consensus 29 ~~~G~iv~G~V~~i~~~g~~Vdi--------g~k~~g~lp~sEis~ 66 (318)
T PRK07400 29 FKPGDIVNGTVFSLEPRGALIDI--------GAKTAAFMPIQEMSI 66 (318)
T ss_pred cCCCCEEEEEEEEEECCEEEEEE--------CCCeEEEEEHHHhcc
Confidence 69999999999999999999999 666789999999875
No 60
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=92.39 E-value=0.3 Score=40.70 Aligned_cols=38 Identities=26% Similarity=0.208 Sum_probs=33.4
Q ss_pred CCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 73 ~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
-.++|++|.|+|+++++..+.|++. ...|++|.+++..
T Consensus 193 ~~k~G~vv~G~V~~I~~~G~fV~i~---------gv~Gllhisels~ 230 (318)
T PRK07400 193 RLEVGEVVVGTVRGIKPYGAFIDIG---------GVSGLLHISEISH 230 (318)
T ss_pred cCCCCCEEEEEEEEEECCeEEEEEC---------CEEEEEEHHHccc
Confidence 3688999999999999999999982 3579999999986
No 61
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=91.99 E-value=0.25 Score=43.68 Aligned_cols=38 Identities=29% Similarity=0.206 Sum_probs=34.6
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.++||+|.|+|+++....+.|+| .....|+|+..++..
T Consensus 33 ~~~GdiV~G~V~~v~~~gv~VdI--------g~k~eG~Ip~~Els~ 70 (486)
T PRK07899 33 FNDGDIVEGTVVKVDRDEVLLDI--------GYKTEGVIPSRELSI 70 (486)
T ss_pred CCCCCEEEEEEEEEECCcEEEEE--------CCCcEEEEEHHHhcc
Confidence 68999999999999999999999 667899999998864
No 62
>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=91.91 E-value=0.38 Score=31.33 Aligned_cols=38 Identities=13% Similarity=0.246 Sum_probs=30.9
Q ss_pred CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
|+++.|+|+++.+..+.++|.-. ..+..|+++.+++..
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~-----~~~~~gll~~s~l~~ 38 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGL-----KGRKEGLVHISQLSF 38 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCC-----CCCcEEEEEhHhccC
Confidence 78999999999999999999210 035789999999875
No 63
>TIGR00062 L27 ribosomal protein L27. Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.
Probab=91.14 E-value=0.48 Score=32.37 Aligned_cols=46 Identities=20% Similarity=0.328 Sum_probs=37.6
Q ss_pred ccccCCcEEecCCccCCC--CCeeecCcEEEeCCCCeEEEEEeeEEEee
Q 032397 3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTL 49 (141)
Q Consensus 3 ~~~~~~~iVlPGd~L~~~--~e~~~G~GtY~~~~~g~I~Asv~G~~~~~ 49 (141)
+|......|.||+.|-.. ..|-||.++-.-. |..|+|.+.|.++++
T Consensus 23 vK~~~gq~V~~G~IivRQRGtk~hPG~nVg~Gr-D~TlfAl~~G~V~f~ 70 (83)
T TIGR00062 23 VKRAGGQFVRAGSIIVRQRGTKFHPGNNVGMGK-DHTLFALSDGVVKFE 70 (83)
T ss_pred eEecCCEEEcCCcEEEEcCCceECCCCcccccC-CCeEEEecceEEEEE
Confidence 577788999999998654 3489999887652 489999999999995
No 64
>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=90.78 E-value=0.6 Score=30.08 Aligned_cols=35 Identities=26% Similarity=0.290 Sum_probs=30.4
Q ss_pred CCEEE-EEEEEe-ccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 77 GSVVI-ARVTKV-MTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 77 GdiVi-g~V~~v-~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
|+++- |+|+++ ....|.|++ .....|+||.+++..
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l--------~~gv~G~i~~s~l~~ 37 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFEL--------KDGLLGFVHISHLSD 37 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEe--------CCCCEEEEEHHHCCc
Confidence 67888 999999 578899999 667999999999964
No 65
>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=90.43 E-value=0.58 Score=35.65 Aligned_cols=39 Identities=21% Similarity=0.228 Sum_probs=34.7
Q ss_pred CCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
+-|.+|+++.|+|++++...+.+++ . ++.|+++.++...
T Consensus 77 f~p~~gEvv~G~V~~v~~~GifV~l--------g-~~~gi~~~~~l~~ 115 (179)
T TIGR00448 77 FKPELGEIVEGEVIEIVEFGAFVSL--------G-PFDGLFHVSQVTD 115 (179)
T ss_pred EeccCCCEEEEEEEEEEeeEEEEEe--------C-CceEEEEcHHhCC
Confidence 4588999999999999999999998 3 5899999998874
No 66
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=90.38 E-value=0.45 Score=42.66 Aligned_cols=41 Identities=29% Similarity=0.280 Sum_probs=33.3
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
..-+++||+|.|.|+.+..++|.|+| ..--.|+|+.+.+..
T Consensus 16 ~~~~~~G~vV~G~Vv~i~~~~v~Vdi--------g~Kseg~ip~~E~~~ 56 (541)
T COG0539 16 DEEFEPGDVVKGTVVSIEKDGVLVDI--------GGKSEGVIPISEFSN 56 (541)
T ss_pred hhccCCCCEEEEEEEEEeCCeEEEEe--------cCccccEeEHHHhcc
Confidence 45689999999999999999999999 444567777766654
No 67
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=90.36 E-value=0.46 Score=41.81 Aligned_cols=37 Identities=16% Similarity=0.204 Sum_probs=33.5
Q ss_pred CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
++|++|.|+|+++++..+.|++ .....|++|.+++..
T Consensus 378 ~vG~~v~G~V~~i~~~G~FV~l--------~~gv~Gli~~se~s~ 414 (491)
T PRK13806 378 APGTTVTGTVEKRAQFGLFVNL--------APGVTGLLPASVISR 414 (491)
T ss_pred CCCCEEEEEEEEEecCceEEEc--------CCCcEEEEEHHHcCc
Confidence 4799999999999999999999 667999999998874
No 68
>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=89.68 E-value=1 Score=28.27 Aligned_cols=34 Identities=18% Similarity=0.177 Sum_probs=29.7
Q ss_pred CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
|++|.|+|+++....+.+++ . ...|.|+.+++..
T Consensus 1 G~iv~g~V~~v~~~G~~v~l--------~-g~~gfip~s~~~~ 34 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI--------E-GVRAFLPASQVDL 34 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE--------C-CEEEEEEHHHCCC
Confidence 78999999999999999998 3 4899999988864
No 69
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=89.60 E-value=0.63 Score=40.92 Aligned_cols=46 Identities=15% Similarity=0.109 Sum_probs=37.7
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch-h-hhHHHHh
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI-E-LLMHLLY 127 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~-~-v~~~~~f 127 (141)
.++|++|.|+|+++.+..+.|+| .....|+||.+++.. + ..+.+.|
T Consensus 200 l~~G~iv~G~V~~v~~~G~fV~l--------~~gv~g~v~~sels~~~~~~~~~~~ 247 (491)
T PRK13806 200 VKEGDVVEGTVTRLAPFGAFVEL--------APGVEGMVHISELSWSRVQKADEAV 247 (491)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEc--------CCCcEEEEEHHHCCCccccChhHhc
Confidence 68999999999999999999998 556889999999975 3 3344444
No 70
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=89.45 E-value=0.6 Score=44.01 Aligned_cols=55 Identities=13% Similarity=-0.106 Sum_probs=41.3
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch-hhh-HHHHhhhhccccccc
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI-ELL-MHLLYGYLGSCKMQL 137 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~-~v~-~~~~f~~vis~gd~~ 137 (141)
.++||+|.|+|+++++..++|++ .....|+++.+++.. +.+ ..+. .+.++.||..
T Consensus 750 ~~vG~iV~GkV~~v~~~GvFVeL--------~~gVeGlI~~s~lsdd~~~~~~~~-~~~f~vGD~V 806 (863)
T PRK12269 750 YGVGSTVEGEVSSVTDFGIFVRV--------PGGVEGLVRKQHLVENRDGDPGEA-LRKYAVGDRV 806 (863)
T ss_pred CCCCCEEEEEEEEEecCeEEEEc--------CCCeEEEEEHHHcCCcccccchhh-ccccCCCCEE
Confidence 46899999999999999999999 667999999999875 322 2222 3345556543
No 71
>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=89.41 E-value=1.2 Score=28.70 Aligned_cols=36 Identities=8% Similarity=0.054 Sum_probs=31.3
Q ss_pred CCCEEEEEEEEeccceEEEEEEEecCeeccc-ceeEEEeccccch
Q 032397 76 PGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRFFIFYI 119 (141)
Q Consensus 76 ~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~-~~~G~Ir~~dvr~ 119 (141)
+|+++-|.|++++...+.+++ .. ...|+++.+++..
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l--------~~~~~~G~v~~~~l~~ 37 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVEL--------DNLTVEGLVHVSTLGD 37 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEe--------cCCCEEEEEEEEecCC
Confidence 489999999999999999999 43 5889999998864
No 72
>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=88.57 E-value=0.81 Score=39.66 Aligned_cols=37 Identities=22% Similarity=0.229 Sum_probs=33.6
Q ss_pred CCCCCEEEEEEEEeccc--eEEEEEEEecCeecccceeEEEeccccc
Q 032397 74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRFFIFY 118 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~--~a~v~I~~v~~~~l~~~~~G~Ir~~dvr 118 (141)
+.+|+|..|+|+++.+. .|+|+| ...-.|+||.+|+.
T Consensus 23 ~~vGnIY~GrV~~i~p~l~aAFVdi--------G~~k~gfL~~~d~~ 61 (414)
T TIGR00757 23 QLKGNIYKGRVTRILPSLQAAFVDI--------GLEKNGFLHASDIG 61 (414)
T ss_pred CCCCCEEEEEEeeecCCCceEEEEc--------CCCceEEEEHHHcC
Confidence 46899999999999999 799999 77788999999985
No 73
>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=87.89 E-value=1.1 Score=30.54 Aligned_cols=33 Identities=21% Similarity=0.170 Sum_probs=28.6
Q ss_pred CEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 78 SVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 78 diVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
+++.|+|+++....+.|++ . +..|++|.++++.
T Consensus 1 ~vv~g~V~~i~~~GifV~l--------~-~v~G~v~~~~l~~ 33 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRI--------G-PVDGLLHISQIMD 33 (99)
T ss_pred CEEEEEEEEEEeccEEEEE--------c-CeEEEEEEEEccC
Confidence 4789999999999999999 2 3689999999875
No 74
>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=87.30 E-value=0.97 Score=26.99 Aligned_cols=32 Identities=9% Similarity=0.163 Sum_probs=28.2
Q ss_pred EEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 80 VIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 80 Vig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
|.|+|+++....|.|++ .....|+++.+++..
T Consensus 1 v~g~V~~v~~~g~~v~l--------~~~~~g~~~~~~~~~ 32 (65)
T cd00164 1 VTGKVVSITKFGVFVEL--------EDGVEGLVHISELSD 32 (65)
T ss_pred CEEEEEEEEeeeEEEEe--------cCCCEEEEEHHHCCC
Confidence 57999999999999999 567899999999875
No 75
>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=86.86 E-value=1.4 Score=38.57 Aligned_cols=38 Identities=26% Similarity=0.241 Sum_probs=33.9
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.++|++|.|.|+++.++.+.|+| .....|+|+.+++..
T Consensus 16 ~~~G~~v~g~V~~i~~~~~~v~~--------g~k~~g~i~~~E~~~ 53 (516)
T TIGR00717 16 TRPGSIVKGTVVAINKDTVFVDV--------GLKSEGRIPKEEFLD 53 (516)
T ss_pred CCCCCEEEEEEEEEECCEEEEEc--------CCCcEEEEEHHHhcC
Confidence 58899999999999999999999 666899999888863
No 76
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=86.43 E-value=1.2 Score=42.31 Aligned_cols=39 Identities=15% Similarity=0.182 Sum_probs=34.5
Q ss_pred CCCCCCEEE-EEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 73 VPEPGSVVI-ARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 73 ~P~~GdiVi-g~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.|++|+++. |+|++|.+-.++|+| .....|++|++++..
T Consensus 750 ~~~vG~iy~~g~V~~I~~FGaFVeL--------~~g~EGLVHISeLs~ 789 (891)
T PLN00207 750 VPTVGDIYRNCEIKSIAPYGAFVEI--------APGREGLCHISELSS 789 (891)
T ss_pred CcCCCcEEECcEEEEEeccEEEEEe--------CCCCEEEEEhhhcCC
Confidence 489999995 699999999999999 555799999999975
No 77
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=85.52 E-value=1.4 Score=41.67 Aligned_cols=36 Identities=36% Similarity=0.452 Sum_probs=28.9
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEecccc
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIF 117 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dv 117 (141)
+++|++|.|+|++++.+.+.|+| ..-..|+|..+++
T Consensus 319 ~~~G~iV~G~Vv~i~~~~v~Vdi--------G~K~eGiI~~~E~ 354 (863)
T PRK12269 319 PEPGSVRMGTVVQVNAGTVFVDI--------GGKSEGRVPVEEF 354 (863)
T ss_pred CCCCCEEEEEEEEEECCEEEEEe--------CCCceEEeEHHHh
Confidence 68999999999999999999999 4444555555544
No 78
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=85.47 E-value=1.3 Score=39.17 Aligned_cols=37 Identities=16% Similarity=0.187 Sum_probs=33.6
Q ss_pred CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
++|++|.|+|++++...+.|+| .....|+||.+|+..
T Consensus 372 ~~G~~v~g~V~~v~~~G~fV~l--------~~~v~g~i~~s~l~~ 408 (565)
T PRK06299 372 PVGDVVEGKVKNITDFGAFVGL--------EGGIDGLVHLSDISW 408 (565)
T ss_pred CCCCEEEEEEEEEecceEEEEC--------CCCCEEEEEHHHcCc
Confidence 6899999999999999999999 667889999999874
No 79
>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=83.97 E-value=2.2 Score=29.16 Aligned_cols=30 Identities=33% Similarity=0.544 Sum_probs=22.8
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEecC
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGA 101 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~ 101 (141)
++..++||+|+|||..+...+ ..++-|++.
T Consensus 47 rp~L~~GDlV~ArV~~~~~~~-~~eLtc~~~ 76 (86)
T cd05790 47 RPNLNVGDLVYARVVKANRDM-EPELSCVDS 76 (86)
T ss_pred cccCCCCCEEEEEEEecCCCC-CeEEEEeCC
Confidence 455699999999999998764 456666653
No 80
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=83.97 E-value=1.9 Score=38.23 Aligned_cols=37 Identities=22% Similarity=0.267 Sum_probs=33.3
Q ss_pred CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
++|++|.|+|+++.+..+.|++ .....|++|.+++..
T Consensus 292 ~vG~vv~G~V~~I~~fGvFVeL--------~~gieGLvh~SeLs~ 328 (486)
T PRK07899 292 AIGQIVPGKVTKLVPFGAFVRV--------EEGIEGLVHISELAE 328 (486)
T ss_pred CCCCEEEEEEEEEeccEEEEEe--------CCCcEEEEEHHHcCc
Confidence 5799999999999999999999 557899999998875
No 81
>KOG4600 consensus Mitochondrial ribosomal protein MRP7 (L2) [Translation, ribosomal structure and biogenesis]
Probab=82.41 E-value=4.1 Score=30.41 Aligned_cols=69 Identities=22% Similarity=0.293 Sum_probs=47.2
Q ss_pred ccccCCcEEecCCccCCCCC--eeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCC
Q 032397 3 VKEEEMVLVTPGEVLGKATE--VKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPE 75 (141)
Q Consensus 3 ~~~~~~~iVlPGd~L~~~~e--~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~ 75 (141)
+|..++..|.||+.|...-. |-||..+=+-. |-.|||-.-|.++..+..... .++.|.|.+... ..+|.
T Consensus 50 vKk~egq~V~~G~IIvrQRgtkfHPG~nVGiGK-DhtifaL~eG~Vrf~k~~~~~--~Rk~i~V~~~~~-~~l~~ 120 (144)
T KOG4600|consen 50 VKKYEGQSVIPGNIIVRQRGTKFHPGDNVGIGK-DHTIFALEEGRVRFEKSKITP--PRKWIGVDPRGG-LPLPP 120 (144)
T ss_pred ceecCCeeeecccEEEEecccccCCCcccccCC-cceEEEeeccEEEEEEccCCC--CcceEEEeecCC-ccCCC
Confidence 56678889999999976543 66666554332 367999999999996532222 367899998763 33343
No 82
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=80.96 E-value=2.8 Score=38.15 Aligned_cols=40 Identities=20% Similarity=0.197 Sum_probs=33.8
Q ss_pred CCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.-.++|++|.|+|+++..+.+.|++ .....|+|+..++..
T Consensus 298 ~~l~~G~iV~G~V~~v~~~gv~Vdi--------g~~~~G~lp~~els~ 337 (647)
T PRK00087 298 KQIRRGDIVKGTVVSVNENEVFVDV--------GYKSEGVIPLRELTL 337 (647)
T ss_pred hhccCCCEEEEEEEEEECCEEEEEE--------CCCeEEEEEHHHhcc
Confidence 3469999999999999999999998 556788888887763
No 83
>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=80.70 E-value=2.9 Score=36.52 Aligned_cols=37 Identities=19% Similarity=0.229 Sum_probs=31.9
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccc
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY 118 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr 118 (141)
-++|+++.|+|+++.+..+.|++ .....|+++.+++.
T Consensus 270 ~~~G~i~~g~V~~v~~~G~fV~l--------~~~v~g~v~~sels 306 (516)
T TIGR00717 270 FPVGDKITGRVTNLTDYGVFVEI--------EEGIEGLVHVSEMS 306 (516)
T ss_pred ccCCCEEEEEEEEeeCCcEEEEe--------CCCCEEEEEHHHcC
Confidence 36899999999999999999998 55678888887764
No 84
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=80.20 E-value=3.3 Score=37.71 Aligned_cols=37 Identities=16% Similarity=0.292 Sum_probs=33.7
Q ss_pred CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
++|++|.|+|+++++..+.|++ .....|+++.+++..
T Consensus 561 ~~G~~v~g~V~~i~~~G~fV~l--------~~~i~Gli~~sel~~ 597 (647)
T PRK00087 561 PVGSIVLGKVVRIAPFGAFVEL--------EPGVDGLVHISQISW 597 (647)
T ss_pred cCCeEEEEEEEEEECCeEEEEE--------CCCCEEEEEhhhcCc
Confidence 6899999999999999999998 567999999999876
No 85
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=80.17 E-value=4 Score=34.41 Aligned_cols=37 Identities=22% Similarity=0.222 Sum_probs=32.1
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.++|++|.|+|+++.+..+.|++ . ...|+||.+++..
T Consensus 190 ~~~G~~v~g~V~~v~~~G~fV~l--------~-~v~g~v~~sels~ 226 (390)
T PRK06676 190 LKEGDVVEGTVARLTDFGAFVDI--------G-GVDGLVHISELSH 226 (390)
T ss_pred CCCCCEEEEEEEEEecceEEEEe--------C-CeEEEEEHHHcCc
Confidence 58999999999999999999998 2 3679999988864
No 86
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=80.10 E-value=3.8 Score=31.36 Aligned_cols=40 Identities=18% Similarity=-0.089 Sum_probs=34.3
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
..-|-.|.+|.|+|++++...+.+++ .+|.+.|+.+.+.+
T Consensus 76 vFrPf~gEVv~g~V~~v~~~G~~v~~---------Gp~~ifI~~~~l~~ 115 (176)
T PTZ00162 76 VFKPFKDEVLDAIVTDVNKLGFFAQA---------GPLKAFVSRSAIPP 115 (176)
T ss_pred EEecCCCCEEEEEEEEEecceEEEEe---------eCeEEEEcHHHCCC
Confidence 35599999999999999999999999 36778888887764
No 87
>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=80.01 E-value=9.8 Score=32.54 Aligned_cols=40 Identities=18% Similarity=0.370 Sum_probs=34.3
Q ss_pred EEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEee
Q 032397 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTL 49 (141)
Q Consensus 10 iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~ 49 (141)
+.+||++=.--+|..+|.-+.+-+.+|.-+..++|++++.
T Consensus 246 v~~pg~kT~YLSEL~sG~~VlvVd~~G~tR~~~VGRvKIE 285 (354)
T PF01959_consen 246 VLMPGGKTRYLSELRSGDEVLVVDADGRTRTAIVGRVKIE 285 (354)
T ss_pred EEcCCCceeehhhhcCCCEEEEEeCCCCEEEEEeeEEEEe
Confidence 4678988776678999999887777799999999999995
No 88
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=79.15 E-value=7.6 Score=26.68 Aligned_cols=40 Identities=10% Similarity=0.077 Sum_probs=31.0
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEe-ccccc
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR-FFIFY 118 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir-~~dvr 118 (141)
-..|++||+|. .|..+....+.|.++- ...+|+|- -.+++
T Consensus 11 y~~P~v~dvv~-~Vv~i~d~~~YV~Lle-------Y~iegmIl~~sels 51 (86)
T PHA02858 11 YVFPNINEVTK-GIVFVKDNIFYVKLID-------YGLEALIVNYVNVN 51 (86)
T ss_pred EecCCCCeEEE-EEEEEeccEEEEEEec-------CccceEEecHHHHh
Confidence 35799999999 8999999999999943 23677765 55554
No 89
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=78.21 E-value=4.5 Score=34.13 Aligned_cols=38 Identities=13% Similarity=0.150 Sum_probs=32.3
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.++|+++.|+|+++.+..+.|++ .....|++|.+++..
T Consensus 275 ~~~G~~v~g~V~~i~~~G~fV~l--------~~gi~Glv~~se~~~ 312 (390)
T PRK06676 275 LPEGDVIEGTVKRLTDFGAFVEV--------LPGVEGLVHISQISH 312 (390)
T ss_pred hcCCcEEEEEEEEEeCceEEEEE--------CCCCeEEEEhHHcCc
Confidence 46899999999999999999998 446788888888754
No 90
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=77.49 E-value=13 Score=31.70 Aligned_cols=41 Identities=17% Similarity=0.353 Sum_probs=34.9
Q ss_pred EEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeC
Q 032397 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLS 50 (141)
Q Consensus 10 iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~ 50 (141)
+.+||++=.--+|..+|.-+.+-+.+|.-+..++|++++..
T Consensus 236 v~~pgg~T~YLsEL~sG~eVlvVd~~G~tR~~~VGRvKIE~ 276 (344)
T PRK02290 236 VRVPGDKTRYLSELRSGDEVLVVDADGNTREAIVGRVKIEK 276 (344)
T ss_pred EEcCCCcchhhHhhcCCCEEEEEeCCCCEEEEEeeEEEEee
Confidence 57899987777889999998877777999999999999953
No 91
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=77.08 E-value=5.1 Score=35.53 Aligned_cols=37 Identities=22% Similarity=0.205 Sum_probs=33.0
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.++|++|-|+|+++.+..+.|+| . ...|++|.+++..
T Consensus 199 l~~G~iv~g~V~~v~~~G~~V~i--------~-g~~glv~~se~s~ 235 (565)
T PRK06299 199 LEEGQVVEGVVKNITDYGAFVDL--------G-GVDGLLHITDISW 235 (565)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEE--------C-CEEEEEEHHHhcc
Confidence 58999999999999999999999 4 6889999888764
No 92
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=76.68 E-value=3.9 Score=34.94 Aligned_cols=38 Identities=11% Similarity=0.107 Sum_probs=30.7
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEecccc
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIF 117 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dv 117 (141)
.|..+.|++|.|+|.++....+.++| .. ..|+|+.++.
T Consensus 129 ef~~k~GeiV~G~V~~~~~~~~~Vdl--------g~-vEa~LP~~E~ 166 (362)
T PRK12327 129 EFSEREGDIVTGVVQRRDNRFVYVNL--------GK-IEAVLPPAEQ 166 (362)
T ss_pred HHHHhcCCEEEEEEEEEeCCcEEEEe--------CC-eEEEecHHHc
Confidence 57789999999999999999999998 22 5667765444
No 93
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=73.43 E-value=4.8 Score=35.54 Aligned_cols=39 Identities=13% Similarity=0.053 Sum_probs=32.0
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccc
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY 118 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr 118 (141)
.|-.+.|++|.|+|.++....+.|++ . ...|+|++++.-
T Consensus 129 eyk~~~GeIV~G~V~ri~~~giiVDL--------g-gvea~LP~sE~i 167 (470)
T PRK09202 129 EYKDRVGEIITGVVKRVERGNIIVDL--------G-RAEAILPRKEQI 167 (470)
T ss_pred HHHhhcCCEEEEEEEEEecCCEEEEE--------C-CeEEEecHHHcC
Confidence 46678999999999999999999998 2 367778777763
No 94
>PRK11712 ribonuclease G; Provisional
Probab=72.89 E-value=5.2 Score=35.53 Aligned_cols=37 Identities=22% Similarity=0.205 Sum_probs=33.1
Q ss_pred CCCCCEEEEEEEEeccce--EEEEEEEecCeecccceeEEEeccccc
Q 032397 74 PEPGSVVIARVTKVMTRM--ASADIMCVGAKSVREKFSGIIRFFIFY 118 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~--a~v~I~~v~~~~l~~~~~G~Ir~~dvr 118 (141)
..+|+|-.|+|.+|.+.. |+|+| ...-.|.|+..|+.
T Consensus 36 ~~vGnIY~G~V~~v~pg~~AAFVdI--------G~~k~gFL~~~d~~ 74 (489)
T PRK11712 36 GIVGNIYKGRVSRVLPGMQAAFVDI--------GLDKAAFLHASDIV 74 (489)
T ss_pred cccccEEEEEEeecCCCCceeEEee--------CCCccEEEEhhhcc
Confidence 468999999999998876 99999 88899999999985
No 95
>COG1465 Predicted alternative 3-dehydroquinate synthase [Amino acid transport and metabolism]
Probab=72.61 E-value=17 Score=30.78 Aligned_cols=77 Identities=17% Similarity=0.329 Sum_probs=46.2
Q ss_pred EEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCC-----CCCCC--------CCCeEEEecCCCCC---CC
Q 032397 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPP-----PDSPD--------QRPTVEVTGHKAHG---PV 73 (141)
Q Consensus 10 iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~-----~~~~~--------~~~~i~V~~~~~~~---~~ 73 (141)
+-+||.+=--..|..+|.-+-+-+.+|.-+++++|++++..-+ ..-+. +..+|.+...++.+ .-
T Consensus 268 i~vPg~kTkYLaEL~aGDeV~iVD~dGr~R~aiVGRvKIErRPl~lIeAey~g~~i~tiLQNAETIkLv~~dG~pvSV~e 347 (376)
T COG1465 268 IRVPGGKTKYLAELKAGDEVLIVDFDGRTRSAIVGRVKIERRPLMLIEAEYEGVEISTILQNAETIKLVNPDGEPVSVAE 347 (376)
T ss_pred EEcCCCceEEhhhhcCCCeEEEEecCCceeEEEEEEEEeecCceEEEEEEecCcEEEEEeccceeEEEEcCCCcEeeeEe
Confidence 4568877544456778887765555699999999999995311 00000 01233333333221 22
Q ss_pred CCCCCEEEEEEEE
Q 032397 74 PEPGSVVIARVTK 86 (141)
Q Consensus 74 P~~GdiVig~V~~ 86 (141)
.++||-|+..+..
T Consensus 348 Lk~GD~vlv~~ee 360 (376)
T COG1465 348 LKPGDEVLVYLEE 360 (376)
T ss_pred cCCCCEEEEEehh
Confidence 4789998888776
No 96
>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=72.56 E-value=5.3 Score=27.23 Aligned_cols=22 Identities=23% Similarity=0.282 Sum_probs=18.6
Q ss_pred CCCCEEEEEEEEecc-ceEEEEE
Q 032397 75 EPGSVVIARVTKVMT-RMASADI 96 (141)
Q Consensus 75 ~~GdiVig~V~~v~~-~~a~v~I 96 (141)
++||+|.|+|.++.. +...+.+
T Consensus 62 ~~GDiV~AkVis~~~~~~~~Lst 84 (92)
T cd05791 62 RPGDIVRAKVISLGDASSYYLST 84 (92)
T ss_pred CCCCEEEEEEEEcCCCCCcEEEe
Confidence 899999999999986 5566666
No 97
>COG0211 RpmA Ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=70.67 E-value=11 Score=25.85 Aligned_cols=61 Identities=18% Similarity=0.250 Sum_probs=43.0
Q ss_pred ccccCCcEEecCCccCCC--CCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCC
Q 032397 3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHK 68 (141)
Q Consensus 3 ~~~~~~~iVlPGd~L~~~--~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~ 68 (141)
+|..++++|.+|+.|-.. ..+-||.++=.- .|..++|-+-|.++.... ..+++.++|.|..
T Consensus 23 vK~~~Gq~v~aG~IivRQRGTk~hpG~NVG~G-kDhTlFAl~dG~Vkf~~k----~~~rk~vsV~~~~ 85 (87)
T COG0211 23 VKKFGGQFVKAGSIIVRQRGTKFHPGVNVGRG-KDHTLFALVDGVVKFETK----GKNRKYVSVVPEA 85 (87)
T ss_pred eeeeCCeEEecccEEEEeccccccCCcccccC-CCceEEEeeccEEEEEEc----cCCccEEEEEeec
Confidence 577788999999998543 236777766433 237899999999988530 1345788888753
No 98
>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=70.39 E-value=12 Score=25.16 Aligned_cols=45 Identities=16% Similarity=0.086 Sum_probs=31.2
Q ss_pred CeEEEecCCCCCCCCCCCCEEEEEEEEeccc---eEEEEEEEecCeec
Q 032397 60 PTVEVTGHKAHGPVPEPGSVVIARVTKVMTR---MASADIMCVGAKSV 104 (141)
Q Consensus 60 ~~i~V~~~~~~~~~P~~GdiVig~V~~v~~~---~a~v~I~~v~~~~l 104 (141)
.-|.|.+..-+.+-.+.||.|.|.|..=... .+.+.|..||+.+.
T Consensus 29 ~DvYVs~~qIrrf~LR~GD~V~G~vr~p~~~ek~~aL~~V~~VNg~~p 76 (78)
T PF07497_consen 29 DDVYVSPSQIRRFGLRTGDLVEGQVRPPREGEKYFALLRVESVNGRPP 76 (78)
T ss_dssp TSEEE-CCCCCCTT--TTEEEEEEEE--STTSSSEEECEECEETTECT
T ss_pred CCEEECHHHHHHcCCCCCCEEEEEEeCCCCCCcceeeEEEEeECCcCC
Confidence 4677877666678889999999999986433 38889989988754
No 99
>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=70.34 E-value=9.3 Score=23.58 Aligned_cols=25 Identities=24% Similarity=0.379 Sum_probs=18.7
Q ss_pred CCCCCCEEEEEEEEeccceEEEEEE
Q 032397 73 VPEPGSVVIARVTKVMTRMASADIM 97 (141)
Q Consensus 73 ~P~~GdiVig~V~~v~~~~a~v~I~ 97 (141)
.|.+||+|-.+|++.....++-+++
T Consensus 37 ~~~iG~~v~v~I~~~~~~~l~G~~v 61 (61)
T PF01938_consen 37 LPLIGEFVKVRITKAKKNYLFGELV 61 (61)
T ss_dssp -T--TEEEEEEEEEE-SSEEEEEEE
T ss_pred CCCCCCEEEEEEEEeeCCcEEEEEC
Confidence 4668999999999999999887763
No 100
>PRK10811 rne ribonuclease E; Reviewed
Probab=67.85 E-value=7.6 Score=37.44 Aligned_cols=37 Identities=11% Similarity=0.198 Sum_probs=32.4
Q ss_pred CCCCCEEEEEEEEeccce--EEEEEEEecCeecccceeEEEeccccc
Q 032397 74 PEPGSVVIARVTKVMTRM--ASADIMCVGAKSVREKFSGIIRFFIFY 118 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~--a~v~I~~v~~~~l~~~~~G~Ir~~dvr 118 (141)
+.+|+|-.|+|.+|.+.+ |+|+| ...-.|+|+..|+.
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDI--------G~gknGFL~L~Di~ 74 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDY--------GAERHGFLPLKEIA 74 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEe--------cCCcceEEEhhhcc
Confidence 468999999999997776 99999 77788999998885
No 101
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=67.60 E-value=16 Score=25.66 Aligned_cols=64 Identities=25% Similarity=0.311 Sum_probs=39.0
Q ss_pred cEEec--CCccCCCCCeeecCcEEEe---CCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEE
Q 032397 9 VLVTP--GEVLGKATEVKAGKGAYVA---KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIAR 83 (141)
Q Consensus 9 ~iVlP--Gd~L~~~~e~~~G~GtY~~---~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~ 83 (141)
.+.+| ||.++.. .-..|.|.|.- | +-.+.|.+.|..+ +.||+. +||.|+..
T Consensus 14 ~~~~p~e~e~~g~V-~~~lG~~~~~V~~~d-G~~~la~i~GK~R------------k~IwI~----------~GD~VlVe 69 (100)
T PRK04012 14 RLPMPEEGEVFGVV-EQMLGANRVRVRCMD-GVERMGRIPGKMK------------KRMWIR----------EGDVVIVA 69 (100)
T ss_pred EccCCCCCEEEEEE-EEEcCCCEEEEEeCC-CCEEEEEEchhhc------------ccEEec----------CCCEEEEE
Confidence 45666 5666652 34667787752 3 1468888888774 356665 48888777
Q ss_pred EEEeccceEEEEEEE
Q 032397 84 VTKVMTRMASADIMC 98 (141)
Q Consensus 84 V~~v~~~~a~v~I~~ 98 (141)
...-.. -+++|.-
T Consensus 70 ~~~~~~--~kg~Iv~ 82 (100)
T PRK04012 70 PWDFQD--EKADIIW 82 (100)
T ss_pred ecccCC--CEEEEEE
Confidence 655542 3455543
No 102
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=67.50 E-value=7.6 Score=30.27 Aligned_cols=40 Identities=23% Similarity=0.157 Sum_probs=35.9
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.+.|..|.+|-|.|+++..-.+.|.| .|+.|+||++.+-+
T Consensus 76 ~fkP~~gEVV~GeVv~~~~~G~fV~i---------gp~dglvh~sqi~d 115 (183)
T COG1095 76 VFKPFRGEVVEGEVVEVVEFGAFVRI---------GPLDGLVHVSQIMD 115 (183)
T ss_pred EEEeccccEEEEEEEEEeecceEEEe---------ccccccccHhhccC
Confidence 35689999999999999999999999 38999999998875
No 103
>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=66.23 E-value=19 Score=24.30 Aligned_cols=22 Identities=36% Similarity=0.190 Sum_probs=20.6
Q ss_pred CCCEEEEEEEEeccceEEEEEE
Q 032397 76 PGSVVIARVTKVMTRMASADIM 97 (141)
Q Consensus 76 ~GdiVig~V~~v~~~~a~v~I~ 97 (141)
+|.++.|+|++++...+.+++-
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G 22 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG 22 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc
Confidence 4899999999999999999996
No 104
>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=65.84 E-value=9.2 Score=32.39 Aligned_cols=39 Identities=18% Similarity=0.156 Sum_probs=29.7
Q ss_pred CCCCCCCCEEEEEEEEeccce-EEEEEEEecCeecccceeEEEeccccc
Q 032397 71 GPVPEPGSVVIARVTKVMTRM-ASADIMCVGAKSVREKFSGIIRFFIFY 118 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~-a~v~I~~v~~~~l~~~~~G~Ir~~dvr 118 (141)
.|..+.|++|.|+|.++..+. +.++| . ...|+|+.++.-
T Consensus 126 ey~~k~GeiV~G~V~~v~~~g~v~Vdi--------G-~~ea~LP~~E~i 165 (341)
T TIGR01953 126 EFSSKEGEIISGTVKRVNRRGNLYVEL--------G-KTEGILPKKEQI 165 (341)
T ss_pred HHHhhcCCEEEEEEEEEecCCcEEEEE--------C-CeEEEecHHHcC
Confidence 466789999999999998865 78988 2 356666665554
No 105
>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=65.55 E-value=6.3 Score=26.68 Aligned_cols=13 Identities=46% Similarity=0.795 Sum_probs=10.8
Q ss_pred CCCCEEEEEEEEe
Q 032397 75 EPGSVVIARVTKV 87 (141)
Q Consensus 75 ~~GdiVig~V~~v 87 (141)
++||+|.|+|.++
T Consensus 70 rpGDIVrA~ViSl 82 (82)
T PF10447_consen 70 RPGDIVRARVISL 82 (82)
T ss_dssp -SSSEEEEEEEEE
T ss_pred CCCCEEEEEEeeC
Confidence 7899999999864
No 106
>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=62.38 E-value=15 Score=23.84 Aligned_cols=25 Identities=16% Similarity=0.252 Sum_probs=19.4
Q ss_pred CCCCCCCEEEEEEEEecc-ceEEEEE
Q 032397 72 PVPEPGSVVIARVTKVMT-RMASADI 96 (141)
Q Consensus 72 ~~P~~GdiVig~V~~v~~-~~a~v~I 96 (141)
...++||++.|+|.++.. +...+.+
T Consensus 49 ~~~~~GD~i~~~V~~~~~~~~i~LS~ 74 (82)
T cd04454 49 KSLQPGDLILAKVISLGDDMNVLLTT 74 (82)
T ss_pred hcCCCCCEEEEEEEEeCCCCCEEEEE
Confidence 345999999999999976 4555555
No 107
>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=59.10 E-value=49 Score=21.90 Aligned_cols=36 Identities=22% Similarity=0.195 Sum_probs=29.6
Q ss_pred CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
|++|-|+|..-+.+...+++. .+...|+|+...+.+
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~-------~~~l~a~l~~~HLsD 36 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAIL-------PEEIRAFLPTMHLSD 36 (72)
T ss_pred CceEEEEEEEEcCCcEEEEec-------CCCcEEEEEccccCC
Confidence 789999999999999999992 246888887766654
No 108
>COG1315 Uncharacterized conserved protein [Function unknown]
Probab=58.98 E-value=16 Score=32.78 Aligned_cols=48 Identities=15% Similarity=0.147 Sum_probs=34.7
Q ss_pred CeeecCcE-EEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCC--CCCCCCCCCCEE
Q 032397 22 EVKAGKGA-YVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHK--AHGPVPEPGSVV 80 (141)
Q Consensus 22 e~~~G~Gt-Y~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~--~~~~~P~~GdiV 80 (141)
.+.+|+|| ..++ +.+.|+.-|..-++ +.+|+|.|.- ....-++.|+|.
T Consensus 220 ~l~lG~nt~~kd~--~tlvA~~~G~~~~s---------~~tI~V~~iyeV~gdV~~kTGnI~ 270 (543)
T COG1315 220 KLNLGKNTAFKDN--NTLVAKRDGQPIVS---------KNTISVYPIYEVNGDVDVKTGNIK 270 (543)
T ss_pred eeecCCCCccCCC--CEEEEeeCCeEEec---------CCeeEEEEEEEecCCcccccccee
Confidence 48999999 5666 89999999999884 6899999731 113345666553
No 109
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=56.79 E-value=10 Score=33.61 Aligned_cols=38 Identities=24% Similarity=0.297 Sum_probs=33.3
Q ss_pred CCCCCEEEEEEEEeccce--EEEEEEEecCeecccceeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRM--ASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~--a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
-.+|+|-.|+|++|.+.+ |+||| ...-.|+|+..|+-.
T Consensus 35 ~~~gniy~grv~~i~p~~~aafvdi--------g~~r~gfl~~~~~~~ 74 (487)
T COG1530 35 QIVGNIYKGRVTRVLPSLEAAFVDI--------GLERNGFLHLSEIVP 74 (487)
T ss_pred eeecCceEEEecccCccchhheeec--------cCCccceEEecccch
Confidence 357999999999998876 99999 778899999998865
No 110
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=54.27 E-value=26 Score=26.74 Aligned_cols=22 Identities=18% Similarity=0.113 Sum_probs=19.3
Q ss_pred CCCCCEEEEEEEEeccceEEEEE
Q 032397 74 PEPGSVVIARVTKVMTRMASADI 96 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I 96 (141)
-++||+|.++|.++. +.+.+.+
T Consensus 119 ~~~GD~V~akV~~i~-~~i~LS~ 140 (189)
T PRK09521 119 FKIGDIVRAKVISYT-DPLQLST 140 (189)
T ss_pred cCCCCEEEEEEEecC-CcEEEEE
Confidence 489999999999999 7777776
No 111
>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=52.75 E-value=61 Score=23.34 Aligned_cols=40 Identities=13% Similarity=0.017 Sum_probs=28.7
Q ss_pred EEEEEEEeccceEEEEEEEecC---------------------eecccceeEEEeccccch
Q 032397 80 VIARVTKVMTRMASADIMCVGA---------------------KSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 80 Vig~V~~v~~~~a~v~I~~v~~---------------------~~l~~~~~G~Ir~~dvr~ 119 (141)
=||.|+.++++.+.|.|++|-- +.|+..-+..+..+.+++
T Consensus 6 Yigei~e~~~~~~lVkVlaVlKHP~QGDLHnP~q~dvpfFHERkALs~~Ek~~ip~~~vk~ 66 (112)
T PF08810_consen 6 YIGEITEERPQHYLVKVLAVLKHPKQGDLHNPKQTDVPFFHERKALSYREKTNIPKSMVKP 66 (112)
T ss_dssp EEEEEEEEETTEEEEEEEEEEE-------------------------TT-EEEEEGGGEEE
T ss_pred eEEEEEeecCCeEEEEEEEEecCCCccCCCCCCcCCCcceehhhhcchHHHhcCCHHhccc
Confidence 4899999999999999999832 345555667777777775
No 112
>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=51.04 E-value=28 Score=22.61 Aligned_cols=23 Identities=22% Similarity=0.326 Sum_probs=18.4
Q ss_pred CCCCCEEEEEEEEeccc-eEEEEE
Q 032397 74 PEPGSVVIARVTKVMTR-MASADI 96 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~-~a~v~I 96 (141)
.++||.+.|+|.++... ...+.+
T Consensus 55 l~vGd~i~~~V~~~~~~~~i~LS~ 78 (86)
T cd05789 55 LDEGDLIVAEVQSVDSDGSVSLHT 78 (86)
T ss_pred CCCCCEEEEEEEEECCCCCEEEEe
Confidence 59999999999999763 455555
No 113
>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=50.83 E-value=32 Score=31.69 Aligned_cols=40 Identities=8% Similarity=0.066 Sum_probs=34.6
Q ss_pred CCCCCCCEEEEEEEEeccceEEEEEEEecCeeccc-ceeEEEeccccch
Q 032397 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRFFIFYI 119 (141)
Q Consensus 72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~-~~~G~Ir~~dvr~ 119 (141)
.-+++|.++.|+|++|+...+.|++ .. ...|++|.+++..
T Consensus 623 l~~~iG~~~~g~V~~v~~fGifV~L--------~~~~~eGlvhis~l~~ 663 (709)
T TIGR02063 623 MSEKIGEEFEGVISGVTSFGLFVEL--------ENNTIEGLVHISTLKD 663 (709)
T ss_pred hhccCCcEEEEEEEEEEeCCEEEEe--------cCCceEEEEEeeecCC
Confidence 4467899999999999999999999 44 5899999998874
No 114
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=49.13 E-value=17 Score=36.61 Aligned_cols=59 Identities=14% Similarity=-0.103 Sum_probs=46.6
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch----hhhHHHHhh-------hhccccccc
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI----ELLMHLLYG-------YLGSCKMQL 137 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~----~v~~~~~f~-------~vis~gd~~ 137 (141)
.+--.+|+||.|.|++|.+.+..+.. ...+.|-|+.+++.+ -.++.+-|+ ++|.-+|..
T Consensus 880 ~~~~~igsiv~a~v~svKp~~L~v~l--------~~~~~gri~isev~d~~~eitDp~~k~~vG~~I~vrviG~~D~k 949 (1710)
T KOG1070|consen 880 TEDLSIGSIVRAYVKSVKPDQLNVLL--------AANHHGRIHISEVLDNLHEITDPLDKFKVGDGIFVRVIGGHDVK 949 (1710)
T ss_pred ccceeeeeEEEEEEeeecccceEEec--------cccccCceehHHhhccccccCChhhhcccCCeEEEEEEcCCccc
Confidence 34468999999999999999999998 889999999999986 244555553 666666654
No 115
>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=48.84 E-value=38 Score=21.49 Aligned_cols=23 Identities=13% Similarity=0.156 Sum_probs=18.1
Q ss_pred CCCCCEEEEEEEEeccceEEEEE
Q 032397 74 PEPGSVVIARVTKVMTRMASADI 96 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I 96 (141)
-++||+|-++|.++...+..+.+
T Consensus 49 ~~~Gd~v~~kV~~~~~~~i~LSl 71 (72)
T cd05704 49 FKPGKIVRCCILSKKDGKYQLSL 71 (72)
T ss_pred CCCCCEEEEEEEEecCCEEEEEe
Confidence 37899999999999766665544
No 116
>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=48.60 E-value=46 Score=28.82 Aligned_cols=28 Identities=29% Similarity=0.368 Sum_probs=22.4
Q ss_pred CeeecCcEEEe-CCCCeEEEEEeeEEEee
Q 032397 22 EVKAGKGAYVA-KHNGLVYASLTGLLRTL 49 (141)
Q Consensus 22 e~~~G~GtY~~-~~~g~I~Asv~G~~~~~ 49 (141)
.+.+|+||... +-...++|++-|.+.+.
T Consensus 144 ~~~~g~~~~~~~~d~~~~~A~~~G~~~~~ 172 (451)
T PF03961_consen 144 PLKAGKNTEVSEEDGNKLYAAIDGRPVFE 172 (451)
T ss_pred ceeCCCCEEEEcCCCCEEEEecCCEEEEE
Confidence 48889999987 21258999999999984
No 117
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=48.59 E-value=31 Score=26.19 Aligned_cols=66 Identities=18% Similarity=0.271 Sum_probs=39.8
Q ss_pred CcEEec--CCccCCCCCeeecCcEEEe---CCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEE
Q 032397 8 MVLVTP--GEVLGKATEVKAGKGAYVA---KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIA 82 (141)
Q Consensus 8 ~~iVlP--Gd~L~~~~e~~~G~GtY~~---~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig 82 (141)
..+++| ||.++... -..|.|.|.. + +-.+.|.+.|..+. .|||. +||+|+.
T Consensus 24 rel~~~eegq~~g~V~-~~LGn~~f~V~c~d-G~~rLa~I~GKmRK------------~IWI~----------~GD~VlV 79 (155)
T PTZ00329 24 RELVFKEEGQEYAQVL-RMLGNGRLEAYCFD-GVKRLCHIRGKMRK------------RVWIN----------IGDIILV 79 (155)
T ss_pred eeeccCCCCcEEEEEE-EEcCCCEEEEEECC-CCEEEEEeecccee------------eEEec----------CCCEEEE
Confidence 346666 66776633 4667777652 3 14688888888753 36765 4788877
Q ss_pred EEEEeccceEEEEEEEe
Q 032397 83 RVTKVMTRMASADIMCV 99 (141)
Q Consensus 83 ~V~~v~~~~a~v~I~~v 99 (141)
....- +..+++|+..
T Consensus 80 el~~y--d~~KgdIi~R 94 (155)
T PTZ00329 80 SLRDF--QDSKADVILK 94 (155)
T ss_pred eccCC--CCCEEEEEEE
Confidence 55322 2356666554
No 118
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=48.36 E-value=36 Score=26.68 Aligned_cols=22 Identities=23% Similarity=0.110 Sum_probs=18.9
Q ss_pred CCCCCEEEEEEEEeccceEEEEE
Q 032397 74 PEPGSVVIARVTKVMTRMASADI 96 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I 96 (141)
-++||||-|+|.+.. ....+.+
T Consensus 119 f~~GDivrA~Vis~~-~~~~Lst 140 (188)
T COG1096 119 FRIGDIVRARVISTG-DPIQLST 140 (188)
T ss_pred cccccEEEEEEEecC-CCeEEEe
Confidence 389999999999998 6677777
No 119
>PRK12696 flgH flagellar basal body L-ring protein; Reviewed
Probab=47.37 E-value=1.5e+02 Score=23.87 Aligned_cols=12 Identities=25% Similarity=0.088 Sum_probs=10.9
Q ss_pred eeEEEeccccch
Q 032397 108 FSGIIRFFIFYI 119 (141)
Q Consensus 108 ~~G~Ir~~dvr~ 119 (141)
++|++|.+||..
T Consensus 184 lsGvVRP~DI~~ 195 (236)
T PRK12696 184 VSGLVRPRDIGP 195 (236)
T ss_pred EEEEECHHHCCC
Confidence 699999999985
No 120
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=46.26 E-value=28 Score=28.97 Aligned_cols=30 Identities=17% Similarity=0.220 Sum_probs=27.3
Q ss_pred CCCCCCCEEEEEEEEeccceEEEEEEEecC
Q 032397 72 PVPEPGSVVIARVTKVMTRMASADIMCVGA 101 (141)
Q Consensus 72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~ 101 (141)
-.|.++++|++.|..|..-.|.|.++--|+
T Consensus 12 kyPev~e~VmvnV~sIaemGayv~LlEYnn 41 (304)
T KOG2916|consen 12 KYPEVEEIVMVNVRSIAEMGAYVKLLEYNN 41 (304)
T ss_pred cCCCcccEEEEEeeEehhccceEeeeecCC
Confidence 459999999999999999999999987666
No 121
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=45.94 E-value=44 Score=22.25 Aligned_cols=24 Identities=33% Similarity=0.422 Sum_probs=22.0
Q ss_pred CCCCEEEEEEEEeccceEEEEEEE
Q 032397 75 EPGSVVIARVTKVMTRMASADIMC 98 (141)
Q Consensus 75 ~~GdiVig~V~~v~~~~a~v~I~~ 98 (141)
++||.|.-+|+++.+++|..++..
T Consensus 47 ~~Gd~V~vkI~~v~~~~afaevve 70 (73)
T COG3269 47 EVGDEVKVKITKVKPNFAFAEVVE 70 (73)
T ss_pred CCCCeeeEEEEEeeccceeeEEee
Confidence 789999999999999999998854
No 122
>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=43.88 E-value=42 Score=24.24 Aligned_cols=28 Identities=11% Similarity=0.165 Sum_probs=21.8
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecC
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGA 101 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~ 101 (141)
|-+|.|+.|+|++-+....+|.+-.-++
T Consensus 1 PF~gEvl~g~I~~~~~~Gi~vslgFFdd 28 (122)
T PF08292_consen 1 PFVGEVLTGKIKSSTAEGIRVSLGFFDD 28 (122)
T ss_dssp --TT-EEEEEEEEEETTEEEEEECCEEE
T ss_pred CCCCCEEEEEEEecCCCcEEEEeccccc
Confidence 6789999999999999999998855544
No 123
>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=43.41 E-value=64 Score=20.48 Aligned_cols=22 Identities=23% Similarity=0.184 Sum_probs=19.1
Q ss_pred EEEEEEEeccceEEEEEEEecC
Q 032397 80 VIARVTKVMTRMASADIMCVGA 101 (141)
Q Consensus 80 Vig~V~~v~~~~a~v~I~~v~~ 101 (141)
..|+|..+..+.+.|+|-..++
T Consensus 16 ~~G~V~kv~eNSVIVdIT~m~~ 37 (57)
T PF09953_consen 16 FTGIVEKVYENSVIVDITIMEN 37 (57)
T ss_pred cEEEEEEEecCcEEEEEEecCC
Confidence 5899999999999999966554
No 124
>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=43.19 E-value=44 Score=22.98 Aligned_cols=23 Identities=13% Similarity=0.138 Sum_probs=18.9
Q ss_pred CCCCCEEEEEEEEeccc-----eEEEEE
Q 032397 74 PEPGSVVIARVTKVMTR-----MASADI 96 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~-----~a~v~I 96 (141)
-++||+|.|+|.++... +..|.+
T Consensus 67 f~vGd~V~~kVi~~d~~~~~~~~i~LSl 94 (100)
T cd05693 67 FSVGQLVRCKVVSLDKSKSGKKRIELSL 94 (100)
T ss_pred ccCCCEEEEEEEEccCCcCCCcEEEEEe
Confidence 38999999999999875 566665
No 125
>PRK11642 exoribonuclease R; Provisional
Probab=43.05 E-value=47 Score=31.36 Aligned_cols=38 Identities=11% Similarity=0.095 Sum_probs=33.3
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccc-eeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREK-FSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~-~~G~Ir~~dvr~ 119 (141)
.++|+++.|+|++|+...+.|++ ... ..|++|.+++..
T Consensus 641 ~~iGe~f~G~Is~V~~fGifVeL--------~~~~vEGlV~vs~L~~ 679 (813)
T PRK11642 641 DQVGNVFKGVISSVTGFGFFVRL--------DDLFIDGLVHVSSLDN 679 (813)
T ss_pred ccCCcEEEEEEEEeecCceEEEE--------CCCCeeeeEEEeecCC
Confidence 47899999999999999999999 543 899999998864
No 126
>PF02107 FlgH: Flagellar L-ring protein; InterPro: IPR000527 The flgH, flgI and fliF genes of Salmonella typhimurium encode the major proteins for the L, P and M rings of the flagellar basal body []. In fact, the basal body consists of four rings (L,P,S and M) surrounding the flagellar rod, which is believed to transmit motor rotation to the filament []. The M ring is integral to the inner membrane of the cell, and may be connected to the rod via the S (supramembrane) ring, which lies just distal to it. The L and P rings reside in the outer membrane and periplasmic space, respectively. FlgH and FlgI, which are exported across the cell membrane to their destinations in the outer membrane and periplasmic space, have typical N-terminal cleaved signal-peptide sequences. FlgH is predicted to have an extensive beta-sheet structure, in keeping with other outer membrane proteins [].; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0009427 bacterial-type flagellum basal body, distal rod, L ring
Probab=42.72 E-value=49 Score=25.28 Aligned_cols=41 Identities=22% Similarity=0.154 Sum_probs=24.1
Q ss_pred EEEEEEEEeccceEEEE----EEEecCeecccceeEEEeccccch
Q 032397 79 VVIARVTKVMTRMASAD----IMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 79 iVig~V~~v~~~~a~v~----I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.+.++|++|.++.-.+- -+.+++..-.-.++|++|.+||..
T Consensus 95 ~ita~Vv~VlpNGnL~I~G~k~i~vn~e~~~i~lsGiVRp~DI~~ 139 (179)
T PF02107_consen 95 TITARVVEVLPNGNLVIEGEKQIRVNGEEQYIRLSGIVRPEDIDP 139 (179)
T ss_pred EEEEEEEEECCCCcEEEEEEEEEEECCCEEEEEEEEEECHHHCCC
Confidence 56777777777642211 112222222225899999999985
No 127
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=41.35 E-value=32 Score=29.71 Aligned_cols=26 Identities=19% Similarity=0.211 Sum_probs=22.2
Q ss_pred CCCCCCCCEEEEEEEEecc-ceEEEEE
Q 032397 71 GPVPEPGSVVIARVTKVMT-RMASADI 96 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~-~~a~v~I 96 (141)
.|.+++|++|.|.|.++.. ..+.+++
T Consensus 133 ey~~~~Geiv~g~V~r~~~~~~i~vdl 159 (374)
T PRK12328 133 KYKKKVGKIVFGTVVRVDNEENTFIEI 159 (374)
T ss_pred HHHHhcCcEEEEEEEEEecCCCEEEEc
Confidence 5789999999999999986 4577777
No 128
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=41.30 E-value=19 Score=29.13 Aligned_cols=41 Identities=17% Similarity=0.064 Sum_probs=33.1
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
..-|++||+.-|.|.-++....-|-| ..-|.+-|++.++..
T Consensus 102 Vf~Pk~Gd~LeG~Vn~vS~sHIglLI--------hg~FNASIpk~nip~ 142 (253)
T KOG4134|consen 102 VFRPKAGDILEGVVNHVSRSHIGLLI--------HGVFNASIPKTNIPA 142 (253)
T ss_pred EECCCCCCeeeeeeeecchhhhceee--------hhhhhccCCCCCCcc
Confidence 45699999999999999999999999 445666666666553
No 129
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=40.49 E-value=35 Score=33.66 Aligned_cols=41 Identities=22% Similarity=0.074 Sum_probs=32.4
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
-..|.+|.|.|++|+.+++.| -...+.+...|+|..+++.+
T Consensus 983 ~~~g~iV~~~V~~vt~rr~~C-----v~v~ld~G~~g~i~~~~~Sd 1023 (1299)
T KOG1856|consen 983 FYEGAIVPVTVTKVTHRRGIC-----VRVRLDCGVTGFILAKNLSD 1023 (1299)
T ss_pred hccCceEEEeeeEEEecccce-----eEEEecCCCceeeeccccCh
Confidence 368999999999999999777 11234778889999888875
No 130
>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=40.03 E-value=1.8e+02 Score=22.80 Aligned_cols=55 Identities=13% Similarity=0.155 Sum_probs=40.6
Q ss_pred CeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCC----CCCCCCCCCCEEEEEEEEeccceEEEEEEEec
Q 032397 36 GLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHK----AHGPVPEPGSVVIARVTKVMTRMASADIMCVG 100 (141)
Q Consensus 36 g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~----~~~~~P~~GdiVig~V~~v~~~~a~v~I~~v~ 100 (141)
..|+|-+-|...+.. ...+..+=.. ....+|+ |.+++| +.++.+++..+.|-++.
T Consensus 53 n~I~A~V~~~qtv~~--------Gs~vrlRLle~i~i~g~~IPk-gt~l~G-~~~~~~~Rl~i~I~SI~ 111 (200)
T PF12508_consen 53 NTIRAVVDGTQTVVD--------GSRVRLRLLEDIQIGGILIPK-GTYLYG-VASFQGQRLLITITSIE 111 (200)
T ss_pred CeEEEEEecceEEeC--------CCEEEEEEcCceEECCEEeCC-CCEEEE-EEeeeccEEEEEEEEEE
Confidence 789999999887742 3333333221 1356676 999999 99999999999998763
No 131
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=39.16 E-value=37 Score=32.01 Aligned_cols=38 Identities=21% Similarity=0.232 Sum_probs=34.0
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.++|.++.|.|++|..-.|.|+| .-.--|++|++...+
T Consensus 656 Lk~Gm~leg~Vrnv~~fgafVdI--------gv~qDglvHis~ls~ 693 (780)
T COG2183 656 LKPGMILEGTVRNVVDFGAFVDI--------GVHQDGLVHISQLSD 693 (780)
T ss_pred ccCCCEEEEEEEEeeeccceEEe--------ccccceeeeHHHhhh
Confidence 58999999999999999999999 666778999888765
No 132
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=38.31 E-value=48 Score=26.35 Aligned_cols=23 Identities=22% Similarity=0.258 Sum_probs=18.2
Q ss_pred CCCCCEEEEEEEEeccc-eEEEEE
Q 032397 74 PEPGSVVIARVTKVMTR-MASADI 96 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~-~a~v~I 96 (141)
-++||+|.|+|.++... ...+.+
T Consensus 112 ~~~GDlV~akV~~i~~~~~~~LS~ 135 (235)
T PRK04163 112 LDIGDYIIAKVKDVDRTRDVVLTL 135 (235)
T ss_pred CCCCCEEEEEEEEECCCCcEEEEE
Confidence 49999999999999764 355555
No 133
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=37.56 E-value=32 Score=30.40 Aligned_cols=26 Identities=15% Similarity=0.084 Sum_probs=23.5
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEE
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADI 96 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I 96 (141)
.|..++|++|.|+|.++..+.+.+++
T Consensus 147 ef~~~~GeIV~G~V~r~e~~~viv~l 172 (449)
T PRK12329 147 EFQDLEDTVLTARVLRFERQSVIMAV 172 (449)
T ss_pred HHHHhcCcEEEEEEEEEcCCCEEEEe
Confidence 47789999999999999999888877
No 134
>cd06541 ASCH ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery.
Probab=36.86 E-value=1.4e+02 Score=20.47 Aligned_cols=24 Identities=25% Similarity=0.461 Sum_probs=16.8
Q ss_pred CCeEEEecCCCCCCCCCCCCEEEE
Q 032397 59 RPTVEVTGHKAHGPVPEPGSVVIA 82 (141)
Q Consensus 59 ~~~i~V~~~~~~~~~P~~GdiVig 82 (141)
++++.+.........|++||.++-
T Consensus 16 ~Ktat~r~~~~~~~~~k~Gd~~i~ 39 (105)
T cd06541 16 RKTIEIRSLDIYEQLPKAGDYLII 39 (105)
T ss_pred CCEEEEEcchhcccCCCCCCEEEE
Confidence 466666655433578999999983
No 135
>CHL00010 infA translation initiation factor 1
Probab=35.45 E-value=1.3e+02 Score=19.77 Aligned_cols=21 Identities=14% Similarity=0.014 Sum_probs=13.9
Q ss_pred CCCCCCCEEEEEEEEeccceE
Q 032397 72 PVPEPGSVVIARVTKVMTRMA 92 (141)
Q Consensus 72 ~~P~~GdiVig~V~~v~~~~a 92 (141)
..|.+||.|.-.++......+
T Consensus 45 i~~~vGD~V~ve~~~~~~~~g 65 (78)
T CHL00010 45 IRILPGDRVKVELSPYDLTKG 65 (78)
T ss_pred cccCCCCEEEEEEcccCCCeE
Confidence 447899999777655544443
No 136
>PLN00208 translation initiation factor (eIF); Provisional
Probab=34.40 E-value=90 Score=23.44 Aligned_cols=42 Identities=17% Similarity=0.251 Sum_probs=27.7
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEec
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRF 114 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~ 114 (141)
..+|..|. ++|+|++..+.. .+.+.|-++...-..+.|=+|+
T Consensus 26 l~~p~egq-~~g~V~~~lGn~-~~~V~c~dG~~rLa~IpGKmRK 67 (145)
T PLN00208 26 LIFKEDGQ-EYAQVLRMLGNG-RCEALCIDGTKRLCHIRGKMRK 67 (145)
T ss_pred cccCCCCc-EEEEEEEEcCCC-EEEEEECCCCEEEEEEecccee
Confidence 45577665 899999987664 4455555666555556666665
No 137
>PF14444 S1-like: S1-like
Probab=34.22 E-value=45 Score=21.25 Aligned_cols=16 Identities=31% Similarity=0.528 Sum_probs=12.8
Q ss_pred CCCCCCCCEEEEEEEE
Q 032397 71 GPVPEPGSVVIARVTK 86 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~ 86 (141)
-++|++||.|++.-+.
T Consensus 31 G~~P~vGdrV~v~A~~ 46 (58)
T PF14444_consen 31 GNVPKVGDRVLVEAIY 46 (58)
T ss_pred cCCCccCCEEEEEEEe
Confidence 4689999999987554
No 138
>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=31.81 E-value=98 Score=28.35 Aligned_cols=38 Identities=11% Similarity=0.120 Sum_probs=33.4
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecc-cceeEEEeccccch
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRFFIFYI 119 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~-~~~~G~Ir~~dvr~ 119 (141)
.++|.++-|+|+.++...+.|+| . ....|++|.+++..
T Consensus 570 ~~iG~~~~g~I~~v~~~GifV~L--------~~~~veGlV~~s~l~~ 608 (654)
T TIGR00358 570 DKVGTEFSGEISSVTRFGMFVRL--------DDNGIDGLIHISTLHN 608 (654)
T ss_pred hCCCcEEEEEEEeEEcCcEEEEe--------cCCceEEEEEeEeCCC
Confidence 46799999999999999999999 5 45899999998864
No 139
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=30.35 E-value=76 Score=21.30 Aligned_cols=61 Identities=21% Similarity=0.320 Sum_probs=33.1
Q ss_pred cCCccCCCCCeeecCcEEEeC-CCC-eEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEeccc
Q 032397 13 PGEVLGKATEVKAGKGAYVAK-HNG-LVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTR 90 (141)
Q Consensus 13 PGd~L~~~~e~~~G~GtY~~~-~~g-~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V~~v~~~ 90 (141)
+||.++... -..|.|.|.-. .|| .+.|.+.|..+ +.|++. .||+|+.....-.
T Consensus 4 e~q~~g~V~-~~lG~~~~~V~~~dG~~~la~ipgK~R------------k~iwI~----------~GD~VlVe~~~~~-- 58 (83)
T smart00652 4 DGQEIAQVV-KMLGNGRLEVMCADGKERLARIPGKMR------------KKVWIR----------RGDIVLVDPWDFQ-- 58 (83)
T ss_pred CCcEEEEEE-EEcCCCEEEEEECCCCEEEEEEchhhc------------ccEEEc----------CCCEEEEEecCCC--
Confidence 455555422 45667776521 124 57788888763 355654 4777776554332
Q ss_pred eEEEEEEE
Q 032397 91 MASADIMC 98 (141)
Q Consensus 91 ~a~v~I~~ 98 (141)
.-+.+|..
T Consensus 59 ~~kg~Iv~ 66 (83)
T smart00652 59 DVKADIIY 66 (83)
T ss_pred CCEEEEEE
Confidence 34445533
No 140
>COG2928 Uncharacterized conserved protein [Function unknown]
Probab=29.38 E-value=73 Score=25.61 Aligned_cols=60 Identities=15% Similarity=0.033 Sum_probs=42.6
Q ss_pred CCCCCCEEEEEEEEeccceEEEEEEEecCee----------c-ccceeEEEeccccch-hhhHHHHhhhhcccccc
Q 032397 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKS----------V-REKFSGIIRFFIFYI-ELLMHLLYGYLGSCKMQ 136 (141)
Q Consensus 73 ~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~----------l-~~~~~G~Ir~~dvr~-~v~~~~~f~~vis~gd~ 136 (141)
.|..|--.+|-|++....-..= ..+++ . .+.|--..+++|+.. --.+.+.|+.+||+|--
T Consensus 127 fP~~G~~~i~fvtg~~~~e~~~----~~~~~~v~VfvPTTPNPTsGfl~~Vpkedi~~ldmtvEda~k~iIS~G~v 198 (222)
T COG2928 127 FPRRGIWAIAFVTGEKAGELKE----KEGRPMVAVFVPTTPNPTSGFLLLVPKEDIVPLDMTVEDALKYIISGGVV 198 (222)
T ss_pred CCCCCcEEEEEeccCCCcchhc----ccCCceEEEEcCCCCCCCcceEEEEEHHHceeccccHHHHhheeeecccc
Confidence 3788988999988765433222 23322 2 245777899999997 67778999999999953
No 141
>PF11720 Inhibitor_I78: Peptidase inhibitor I78 family; InterPro: IPR021719 This family includes Aspergillus elastase inhibitor and belongs to MEROPS peptidase inhibitor family I78.
Probab=28.76 E-value=97 Score=19.28 Aligned_cols=35 Identities=11% Similarity=0.346 Sum_probs=24.0
Q ss_pred CcEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEee
Q 032397 8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTG 44 (141)
Q Consensus 8 ~~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G 44 (141)
-.++-||+.+. .+|.+..=+...+.+|.|.+.-+|
T Consensus 26 ~Rvi~Pg~~vT--mDyr~dRLnv~~D~~g~I~~v~CG 60 (60)
T PF11720_consen 26 VRVIRPGDAVT--MDYRPDRLNVEVDDDGVITRVRCG 60 (60)
T ss_pred eEEeCCCCcCc--ccCCCCcEEEEECCCCcEEEEecC
Confidence 35788999844 678988855444445788776555
No 142
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=28.51 E-value=39 Score=21.10 Aligned_cols=12 Identities=33% Similarity=0.695 Sum_probs=10.4
Q ss_pred CCCCEEEEEEEE
Q 032397 75 EPGSVVIARVTK 86 (141)
Q Consensus 75 ~~GdiVig~V~~ 86 (141)
++||+|.|++..
T Consensus 2 ~~GdlVwaK~~G 13 (63)
T smart00293 2 KPGDLVWAKMKG 13 (63)
T ss_pred CCCCEEEEECCC
Confidence 579999999975
No 143
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=28.48 E-value=1.5e+02 Score=18.31 Aligned_cols=21 Identities=14% Similarity=-0.094 Sum_probs=11.0
Q ss_pred CCCEEEEEEEEeccceEEEEE
Q 032397 76 PGSVVIARVTKVMTRMASADI 96 (141)
Q Consensus 76 ~GdiVig~V~~v~~~~a~v~I 96 (141)
+|+++..+|.+++...|.++-
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~ 21 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDD 21 (61)
T ss_dssp --------EEEE-SSEEEEEE
T ss_pred CCCCcceEEEEEeCCEEEEEC
Confidence 589999999999999999875
No 144
>PRK12700 flgH flagellar basal body L-ring protein; Reviewed
Probab=28.03 E-value=1.2e+02 Score=24.35 Aligned_cols=38 Identities=18% Similarity=0.189 Sum_probs=23.6
Q ss_pred EEEEEEEEeccceEEEEEEEecCeecc-------cceeEEEeccccch
Q 032397 79 VVIARVTKVMTRMASADIMCVGAKSVR-------EKFSGIIRFFIFYI 119 (141)
Q Consensus 79 iVig~V~~v~~~~a~v~I~~v~~~~l~-------~~~~G~Ir~~dvr~ 119 (141)
.+.++|++|.++--.+-- +.+.+. -.++|++|.+||..
T Consensus 145 tIta~V~~VlpNGNLvI~---GeK~i~vN~~~e~irlsGiVRP~DI~~ 189 (230)
T PRK12700 145 TITTTVIGVLPNGNLQIA---GEKQIAINRGSEYVRFSGVVDPRSITG 189 (230)
T ss_pred EEEEEEEEECCCCCEEEE---EEEEEEECCCEEEEEEEEEECHHHCCC
Confidence 466777777776533211 222221 24999999999985
No 145
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=27.99 E-value=84 Score=24.19 Aligned_cols=29 Identities=31% Similarity=0.035 Sum_probs=25.1
Q ss_pred CCCCCCCCEEEEEEEEeccceEEEEEEEe
Q 032397 71 GPVPEPGSVVIARVTKVMTRMASADIMCV 99 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v 99 (141)
...|-.|++|-|.|+.++...+.+++--.
T Consensus 76 ~FkpfKGEVvdgvV~~Vnk~G~F~~~GPl 104 (170)
T KOG3298|consen 76 TFKPFKGEVVDGVVTKVNKMGVFARSGPL 104 (170)
T ss_pred EEeecCCcEEEEEEEEEeeeeEEEeccce
Confidence 45688999999999999999999998543
No 146
>cd05838 WHSC1_related The PWWP domain was first identified in the WHSC1 (Wolf-Hirschhorn syndrome candidate 1) protein, a protein implicated in Wolf-Hirschhorn syndrome (WHS). When translocated, WHSC1 plays a role in lymphoid multiple myeloma (MM) disease, also known as plasmacytoma. WHCS1 proteins typically contain two copies of the PWWP 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=27.13 E-value=43 Score=22.90 Aligned_cols=23 Identities=30% Similarity=0.247 Sum_probs=18.1
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEE
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMC 98 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~ 98 (141)
|.+||+|-|++.+ -..|=+.|+.
T Consensus 1 ~~~GdlVWaK~~g--~pwWPa~V~~ 23 (95)
T cd05838 1 PLYGDIVWAKLGN--FRWWPAIICD 23 (95)
T ss_pred CCcCCEEEEECCC--CCCCCeEEcC
Confidence 6789999999987 5567777754
No 147
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=26.42 E-value=53 Score=25.41 Aligned_cols=19 Identities=26% Similarity=0.314 Sum_probs=13.6
Q ss_pred ecCCCCCCCCCCCCEEEEE
Q 032397 65 TGHKAHGPVPEPGSVVIAR 83 (141)
Q Consensus 65 ~~~~~~~~~P~~GdiVig~ 83 (141)
+..+.+..-|++||||+++
T Consensus 57 Ekls~~f~~~~~gDIVi~~ 75 (176)
T KOG0171|consen 57 EKLSYRFRKPQVGDIVIAK 75 (176)
T ss_pred hhhhHhhcCCCCCCEEEEe
Confidence 4444456668999999985
No 148
>PRK00249 flgH flagellar basal body L-ring protein; Reviewed
Probab=26.41 E-value=1.2e+02 Score=24.03 Aligned_cols=41 Identities=17% Similarity=0.053 Sum_probs=23.8
Q ss_pred EEEEEEEEeccceEEEEE----EEecCeecccceeEEEeccccch
Q 032397 79 VVIARVTKVMTRMASADI----MCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 79 iVig~V~~v~~~~a~v~I----~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.+.++|++|.++.-.+-- +.|++..=.-.++|++|.+||..
T Consensus 137 ~Ita~V~~VlpNGnLvI~G~K~i~vN~e~~~i~lsGiVRP~DI~~ 181 (222)
T PRK00249 137 TITVTVTQVLPNGNLVIRGEKEVRVNQGTEFLRVSGVVRPRDISG 181 (222)
T ss_pred EEEEEEEEECCCCcEEEEEEEEEEECCCEEEEEEEEEECHHHCCC
Confidence 467777777776432211 11121111125999999999985
No 149
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=25.20 E-value=1.8e+02 Score=18.69 Aligned_cols=37 Identities=16% Similarity=0.171 Sum_probs=25.3
Q ss_pred EEEEEEEeccc-eEEEEEEEecCeecccceeEEEeccccc
Q 032397 80 VIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRFFIFY 118 (141)
Q Consensus 80 Vig~V~~v~~~-~a~v~I~~v~~~~l~~~~~G~Ir~~dvr 118 (141)
..|+|++..+. ++.|. +-++..+.....|-+|.++++
T Consensus 9 ~~G~Vi~~~~~~~y~V~--~~~g~~~~c~~~Gklr~~~i~ 46 (72)
T PRK00276 9 MEGTVVEALPNAMFRVE--LENGHEVLAHISGKMRKNYIR 46 (72)
T ss_pred EEEEEEEEcCCCEEEEE--eCCCCEEEEEEccceeeCCcc
Confidence 45888887755 56553 456666666788888877765
No 150
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=24.95 E-value=2.4e+02 Score=22.88 Aligned_cols=26 Identities=23% Similarity=0.289 Sum_probs=21.0
Q ss_pred CCCCCCCCEEEEEEEEeccce-EEEEE
Q 032397 71 GPVPEPGSVVIARVTKVMTRM-ASADI 96 (141)
Q Consensus 71 ~~~P~~GdiVig~V~~v~~~~-a~v~I 96 (141)
+...++||.|+|+|.++.... +.+..
T Consensus 110 r~~l~vGD~v~AkV~~vd~~~~~~L~~ 136 (239)
T COG1097 110 RPFLNVGDLVYAKVVDVDRDGEVELTL 136 (239)
T ss_pred ccccccCCEEEEEEEEccCCCceEEEe
Confidence 455699999999999997776 66666
No 151
>PRK12701 flgH flagellar basal body L-ring protein; Reviewed
Probab=24.45 E-value=1.5e+02 Score=23.73 Aligned_cols=38 Identities=29% Similarity=0.269 Sum_probs=23.7
Q ss_pred EEEEEEEEeccceEEEEEEEecCeecc-------cceeEEEeccccch
Q 032397 79 VVIARVTKVMTRMASADIMCVGAKSVR-------EKFSGIIRFFIFYI 119 (141)
Q Consensus 79 iVig~V~~v~~~~a~v~I~~v~~~~l~-------~~~~G~Ir~~dvr~ 119 (141)
.+.++|++|.++--.+-- +.+.+. -.++|++|.+||..
T Consensus 144 tItv~V~~VlpNGnL~I~---GeK~v~vN~e~e~i~lsGvVRP~DI~~ 188 (230)
T PRK12701 144 SISVTVAKVLANGNMVVQ---GEKWVRINQGNEFVRLSGIVRPQDIKA 188 (230)
T ss_pred EEEEEEEEECCCCCEEEE---EEEEEEECCCeEEEEEEEEECHHHCCC
Confidence 467777777776532211 222221 24999999999985
No 152
>PF13375 RnfC_N: RnfC Barrel sandwich hybrid domain
Probab=24.19 E-value=89 Score=21.69 Aligned_cols=13 Identities=23% Similarity=0.373 Sum_probs=9.6
Q ss_pred CeEEEEEeeEEEe
Q 032397 36 GLVYASLTGLLRT 48 (141)
Q Consensus 36 g~I~Asv~G~~~~ 48 (141)
-.|+||+.|++.-
T Consensus 67 a~iHAsvSG~V~~ 79 (101)
T PF13375_consen 67 APIHASVSGTVTA 79 (101)
T ss_pred eeEEcCCCeEEEE
Confidence 3588888888765
No 153
>PRK12788 flgH flagellar basal body L-ring protein; Reviewed
Probab=23.71 E-value=1.4e+02 Score=24.02 Aligned_cols=38 Identities=26% Similarity=0.220 Sum_probs=23.8
Q ss_pred EEEEEEEEeccceEEEEEEEecCeecc-------cceeEEEeccccch
Q 032397 79 VVIARVTKVMTRMASADIMCVGAKSVR-------EKFSGIIRFFIFYI 119 (141)
Q Consensus 79 iVig~V~~v~~~~a~v~I~~v~~~~l~-------~~~~G~Ir~~dvr~ 119 (141)
.|.++|++|.++--.+-- +.+.+. -.++|++|.+||..
T Consensus 149 tIaa~V~~VLPNGNLvI~---G~kev~vN~e~~~i~vsGvVRP~DI~~ 193 (234)
T PRK12788 149 SVAAIVVDVLPNGNLLIS---GSQEVRVNYEMRVLNVGGIVRPLDITR 193 (234)
T ss_pred EEEEEEEEEcCCCCEEEE---EEEEEEECCCEEEEEEEEEECHHHCCC
Confidence 467777777776533211 222221 24999999999985
No 154
>PF12059 DUF3540: Protein of unknown function (DUF3540); InterPro: IPR021927 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 212 to 238 amino acids in length. This protein has a conserved SCL sequence motif.
Probab=23.50 E-value=3.2e+02 Score=21.32 Aligned_cols=35 Identities=14% Similarity=0.123 Sum_probs=23.8
Q ss_pred EEEecCCCCCCCCCCCCEEEEEEEEecc--ceEEEEEEE
Q 032397 62 VEVTGHKAHGPVPEPGSVVIARVTKVMT--RMASADIMC 98 (141)
Q Consensus 62 i~V~~~~~~~~~P~~GdiVig~V~~v~~--~~a~v~I~~ 98 (141)
+...+..++.+.|.+||.|+- ..+.+ +.|.+-|+.
T Consensus 23 ~~arrAaSCLl~P~~GD~VLv--~~~~d~~~~yILAVL~ 59 (202)
T PF12059_consen 23 WRARRAASCLLEPAVGDTVLV--SGVADEERVYILAVLE 59 (202)
T ss_pred EEEEeccccccCCCCCCEEEE--eecCCCCcEEEEEEEe
Confidence 777777778999999999964 44322 235555544
No 155
>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=23.41 E-value=1.8e+02 Score=23.79 Aligned_cols=38 Identities=16% Similarity=0.162 Sum_probs=28.2
Q ss_pred EEEEEEEEeccceEEEEEEEecCee-----cccceeEEEeccc
Q 032397 79 VVIARVTKVMTRMASADIMCVGAKS-----VREKFSGIIRFFI 116 (141)
Q Consensus 79 iVig~V~~v~~~~a~v~I~~v~~~~-----l~~~~~G~Ir~~d 116 (141)
=++|+|++|.+..++|..+.-.+.. ..+..+|+++-.+
T Consensus 156 GLVG~V~~V~~~~S~V~litd~~~~v~v~v~~t~~~gi~~G~~ 198 (283)
T TIGR00219 156 GLVGKVVSVGSNTSRVLLLTDYTNFVPAQILRSDFRGLIEGNG 198 (283)
T ss_pred ceEEEEEEECCCeEEEEEEEcCCCceEEEEecCCceEEEEecC
Confidence 3899999999999999988743322 2356678887765
No 156
>PRK12698 flgH flagellar basal body L-ring protein; Reviewed
Probab=23.28 E-value=1.7e+02 Score=23.36 Aligned_cols=41 Identities=15% Similarity=0.093 Sum_probs=23.7
Q ss_pred EEEEEEEEeccceEEEEE----EEecCeecccceeEEEeccccch
Q 032397 79 VVIARVTKVMTRMASADI----MCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 79 iVig~V~~v~~~~a~v~I----~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.+.++|++|.++--.+-- +.+++-.=--.++|++|.+||..
T Consensus 138 tIta~V~~VlpNGnL~I~GeK~i~vN~~~e~I~lsGvVRP~DI~~ 182 (224)
T PRK12698 138 SISANVMQVLPNGNLVIRGEKWISINNGDEFIRLTGIVRSQDITP 182 (224)
T ss_pred EEEEEEEEECCCCCEEEEEEEEEEECCCEEEEEEEEEECHHHCCC
Confidence 467777777776532211 11121111124999999999985
No 157
>PRK12697 flgH flagellar basal body L-ring protein; Reviewed
Probab=22.89 E-value=1.6e+02 Score=23.67 Aligned_cols=38 Identities=21% Similarity=0.219 Sum_probs=24.5
Q ss_pred EEEEEEEEeccceEEEEEEEecCeecc-------cceeEEEeccccch
Q 032397 79 VVIARVTKVMTRMASADIMCVGAKSVR-------EKFSGIIRFFIFYI 119 (141)
Q Consensus 79 iVig~V~~v~~~~a~v~I~~v~~~~l~-------~~~~G~Ir~~dvr~ 119 (141)
.+.++|++|.++--.+-- +.+.+. -.++|++|.+||..
T Consensus 141 tItv~V~~VlpNGnL~I~---GeK~i~vN~e~e~IrlsGvVRP~DI~~ 185 (226)
T PRK12697 141 TITVTVTNVLPNGNLVVS---GEKQMLINQGNEFVRFSGVVNPNTISG 185 (226)
T ss_pred EEEEEEEEECCCCCEEEE---EEEEEEECCCEEEEEEEEEECHHHCCC
Confidence 466688888777643321 222221 24999999999985
No 158
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=22.83 E-value=2.1e+02 Score=29.34 Aligned_cols=45 Identities=13% Similarity=-0.065 Sum_probs=38.7
Q ss_pred CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch-hhhHHHH
Q 032397 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI-ELLMHLL 126 (141)
Q Consensus 74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~-~v~~~~~ 126 (141)
-++||+|.|.|-.+..+...+.+ ...+.|..|+++..+ ..+.++-
T Consensus 1160 lk~g~iv~G~V~nv~~~glfi~l--------s~~v~a~v~is~~~ds~~k~w~k 1205 (1710)
T KOG1070|consen 1160 LKIGDIVRGFVKNVETKGLFIAL--------SRKVEAFVPISGLSDSFEKEWEK 1205 (1710)
T ss_pred cccCceeEEEEEEecCCcEEEEE--------ccceEEEEEccccccchhhhhhc
Confidence 37899999999999999999998 889999999888887 5555543
No 159
>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=22.48 E-value=1.6e+02 Score=19.46 Aligned_cols=49 Identities=20% Similarity=0.311 Sum_probs=27.1
Q ss_pred eecCcEEEeC-CC-CeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEeccceEEEEE
Q 032397 24 KAGKGAYVAK-HN-GLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADI 96 (141)
Q Consensus 24 ~~G~GtY~~~-~~-g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V~~v~~~~a~v~I 96 (141)
..|.|.|.-. .| -.+.|.+.|..+ +.||+. +||.|+.....- +.-+++|
T Consensus 9 ~~g~~~~~V~~~~g~~~la~i~gK~r------------k~iwI~----------~GD~V~Ve~~~~--d~~kg~I 59 (77)
T cd05793 9 MLGNGRLEVRCFDGKKRLCRIRGKMR------------KRVWIN----------EGDIVLVAPWDF--QDDKADI 59 (77)
T ss_pred EcCCCEEEEEECCCCEEEEEEchhhc------------ccEEEc----------CCCEEEEEeccc--cCCEEEE
Confidence 4466666421 11 467888888764 246665 366666654433 2344444
No 160
>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=22.38 E-value=1.5e+02 Score=21.66 Aligned_cols=39 Identities=21% Similarity=0.094 Sum_probs=24.9
Q ss_pred EEEEEEEeccceEEEEEEEecCee-----cccceeEEEeccccc
Q 032397 80 VIARVTKVMTRMASADIMCVGAKS-----VREKFSGIIRFFIFY 118 (141)
Q Consensus 80 Vig~V~~v~~~~a~v~I~~v~~~~-----l~~~~~G~Ir~~dvr 118 (141)
++|+|+++.++.++|..+.-.+.. ..+...|+++-.+-.
T Consensus 36 lVG~V~~V~~~~S~V~li~d~~~~v~v~i~~~~~~Gi~~G~~~~ 79 (152)
T PF04085_consen 36 LVGRVTEVGPNTSRVLLITDPNSRVSVKIERSGDRGILRGDGSN 79 (152)
T ss_dssp EEEEEEEE-SS-EEEEETTSSBCEEEEEEECTTEEEEEEEEETT
T ss_pred cEEEEEEECCCEEEEEEEeCCCceEEEEEecCCeeEEEEeCCCC
Confidence 789999999999998875433321 234566887665543
No 161
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=22.26 E-value=1.2e+02 Score=21.02 Aligned_cols=19 Identities=42% Similarity=0.793 Sum_probs=11.1
Q ss_pred CCCCCCCCEEE------------EEEEEecc
Q 032397 71 GPVPEPGSVVI------------ARVTKVMT 89 (141)
Q Consensus 71 ~~~P~~GdiVi------------g~V~~v~~ 89 (141)
...|++||||+ |.|+.+..
T Consensus 60 ~~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~ 90 (124)
T PF05257_consen 60 GSTPQPGDIVVWDSGSGGGYGHVAIVESVND 90 (124)
T ss_dssp CS---TTEEEEEEECTTTTT-EEEEEEEE-T
T ss_pred CcccccceEEEeccCCCCCCCeEEEEEEECC
Confidence 45699999995 57777733
No 162
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=22.09 E-value=1.8e+02 Score=20.38 Aligned_cols=23 Identities=30% Similarity=0.410 Sum_probs=19.7
Q ss_pred CCCCCEE------EEEEEEeccceEEEEE
Q 032397 74 PEPGSVV------IARVTKVMTRMASADI 96 (141)
Q Consensus 74 P~~GdiV------ig~V~~v~~~~a~v~I 96 (141)
.++||-| +|+|..+..+.+.++|
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 5788887 7999999998888888
No 163
>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=22.04 E-value=57 Score=22.27 Aligned_cols=20 Identities=30% Similarity=0.341 Sum_probs=13.2
Q ss_pred CCCCEEEEEEEEeccceEEEEE
Q 032397 75 EPGSVVIARVTKVMTRMASADI 96 (141)
Q Consensus 75 ~~GdiVig~V~~v~~~~a~v~I 96 (141)
++||+|.|++- .-.-|=+.|
T Consensus 2 ~~GDlVwaK~~--GyPwWPA~V 21 (93)
T cd05840 2 QPGDRVLAKVK--GFPAWPAIV 21 (93)
T ss_pred CCCCEEEEeCC--CCCCCCEEE
Confidence 57999999987 233344444
No 164
>PRK12407 flgH flagellar basal body L-ring protein; Reviewed
Probab=21.99 E-value=1.7e+02 Score=23.34 Aligned_cols=41 Identities=10% Similarity=0.050 Sum_probs=24.3
Q ss_pred EEEEEEEEeccceEEEEE----EEecCeecccceeEEEeccccch
Q 032397 79 VVIARVTKVMTRMASADI----MCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 79 iVig~V~~v~~~~a~v~I----~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
.+.++|++|.++--.+-- +.+++-.=--.++|++|.+||..
T Consensus 135 tIta~V~~VlpNGnL~I~GeK~i~vN~e~e~i~~sGvVRP~DI~~ 179 (221)
T PRK12407 135 SITVAVHQVLPNGVLVIRGEKWLTLNQGDEYMRVTGLVRADDIAR 179 (221)
T ss_pred EEEEEEEEECCCCCEEEEEEEEEEECCCEEEEEEEEEECHHHCCC
Confidence 467778888777533211 11111111124999999999985
No 165
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=21.00 E-value=3.8e+02 Score=20.39 Aligned_cols=69 Identities=17% Similarity=0.221 Sum_probs=40.2
Q ss_pred EEecCCccC--CCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCC---CCCCCCCCC-E-EEE
Q 032397 10 LVTPGEVLG--KATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA---HGPVPEPGS-V-VIA 82 (141)
Q Consensus 10 iVlPGd~L~--~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~---~~~~P~~Gd-i-Vig 82 (141)
...|||.|. +..+...|.+.|+...+|..|.-.+.... ...+.+.+.+. ..-.+...+ + +||
T Consensus 136 ~~~~Gd~ilVd~~~~~~~gd~v~v~~~g~~~~VK~l~~~~-----------~~~~~l~S~N~~~~~~~~~~~~~~v~iIg 204 (214)
T COG2932 136 TYEDGDTLLVDPGVNTRRGDRVYVETDGGELYVKKLQREP-----------GGLLRLVSLNPDYYPDEIFSEDDDVEIIG 204 (214)
T ss_pred cccCCCEEEECCCCceeeCCEEEEEEeCCeEEEEEEEEec-----------CCeEEEEeCCCCCCcccccCccceEEEEE
Confidence 456788653 33446666667766433566666555442 35555666542 234556666 5 899
Q ss_pred EEEEecc
Q 032397 83 RVTKVMT 89 (141)
Q Consensus 83 ~V~~v~~ 89 (141)
||..+..
T Consensus 205 rVv~~~~ 211 (214)
T COG2932 205 RVVWVSR 211 (214)
T ss_pred EEEEEee
Confidence 9987643
No 166
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=20.99 E-value=1.5e+02 Score=27.67 Aligned_cols=40 Identities=15% Similarity=0.116 Sum_probs=34.4
Q ss_pred CCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI 119 (141)
Q Consensus 72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~ 119 (141)
--|++|.+=.|+|+++..-.|++.+ ...-.|++|++.+..
T Consensus 615 ~e~evg~iy~G~V~ri~~fGaFv~l--------~~gkdgl~hiS~~~~ 654 (692)
T COG1185 615 REVEVGEVYEGTVVRIVDFGAFVEL--------LPGKDGLVHISQLAK 654 (692)
T ss_pred hhcccccEEEEEEEEEeecceEEEe--------cCCcceeEEehhhhh
Confidence 3489999999999999998899999 667788888887764
No 167
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=20.19 E-value=2.3e+02 Score=22.55 Aligned_cols=37 Identities=19% Similarity=0.202 Sum_probs=26.4
Q ss_pred EEEEEEEeccceEEEEEEEecCeec-----ccceeEEEeccc
Q 032397 80 VIARVTKVMTRMASADIMCVGAKSV-----REKFSGIIRFFI 116 (141)
Q Consensus 80 Vig~V~~v~~~~a~v~I~~v~~~~l-----~~~~~G~Ir~~d 116 (141)
++|+|+++.++.+.|..+.-.+..+ .+...|+++-++
T Consensus 158 lVG~V~~v~~~~s~V~li~d~~~~v~v~i~~~~~~gi~~G~g 199 (276)
T PRK13922 158 LVGRVIEVSPNTSRVLLLTDPNSRVPVQVGRNGIRGILSGNG 199 (276)
T ss_pred CeEEEEEECCCeeEEEEEEcCCCceEEEEEcCCceEEEEecC
Confidence 7999999999999998877443221 345567776663
Done!