Query 032149
Match_columns 146
No_of_seqs 121 out of 778
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 10:15:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032149.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032149hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1096 Predicted RNA-binding 100.0 2.2E-33 4.7E-38 214.2 14.2 129 6-145 3-133 (188)
2 KOG3409 Exosomal 3'-5' exoribo 100.0 1.1E-31 2.4E-36 202.3 11.6 132 8-145 5-137 (193)
3 PRK09521 exosome complex RNA-b 100.0 1.1E-30 2.4E-35 201.4 16.2 128 7-145 4-133 (189)
4 PRK04163 exosome complex RNA-b 100.0 4.5E-29 9.7E-34 198.5 15.3 117 8-145 8-126 (235)
5 COG1097 RRP4 RNA-binding prote 100.0 9.3E-28 2E-32 189.7 14.8 120 6-145 6-127 (239)
6 PF10447 EXOSC1: Exosome compo 99.9 1.1E-25 2.3E-30 152.7 8.0 72 73-144 1-82 (82)
7 KOG3013 Exosomal 3'-5' exoribo 99.9 9.3E-26 2E-30 179.4 4.3 123 7-145 28-154 (301)
8 cd05791 S1_CSL4 S1_CSL4: CSL4, 99.9 4.4E-24 9.5E-29 147.7 8.3 74 72-145 2-75 (92)
9 cd04454 S1_Rrp4_like S1_Rrp4_l 99.6 2E-14 4.4E-19 96.5 8.0 65 71-145 1-65 (82)
10 cd05790 S1_Rrp40 S1_Rrp40: Rrp 99.5 2.9E-14 6.3E-19 97.5 7.8 64 71-145 1-64 (86)
11 PF14382 ECR1_N: Exosome compl 99.5 2.5E-14 5.4E-19 84.2 3.4 38 10-49 1-38 (39)
12 KOG1004 Exosomal 3'-5' exoribo 99.4 2.5E-12 5.4E-17 100.3 11.9 118 9-144 2-122 (230)
13 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.4 2.1E-12 4.6E-17 87.2 7.6 67 71-145 1-69 (86)
14 cd05704 S1_Rrp5_repeat_hs13 S1 99.1 3.2E-10 6.9E-15 74.6 7.0 61 75-145 2-63 (72)
15 cd05702 S1_Rrp5_repeat_hs11_sc 99.1 5E-10 1.1E-14 72.9 7.5 61 77-145 1-61 (70)
16 cd05687 S1_RPS1_repeat_ec1_hs1 99.1 5.2E-10 1.1E-14 72.4 7.6 59 77-145 1-59 (70)
17 COG1098 VacB Predicted RNA bin 99.1 2.8E-10 6.1E-15 82.2 5.5 62 74-145 3-64 (129)
18 cd05705 S1_Rrp5_repeat_hs14 S1 99.0 2E-09 4.4E-14 71.3 7.6 63 75-145 2-65 (74)
19 cd04452 S1_IF2_alpha S1_IF2_al 99.0 2.5E-09 5.5E-14 70.0 7.9 64 74-145 1-64 (76)
20 cd05706 S1_Rrp5_repeat_sc10 S1 99.0 4.5E-09 9.7E-14 68.6 8.3 61 75-145 2-62 (73)
21 cd05691 S1_RPS1_repeat_ec6 S1_ 98.9 6.5E-09 1.4E-13 67.3 7.6 59 77-145 1-59 (73)
22 cd05707 S1_Rrp5_repeat_sc11 S1 98.9 6.1E-09 1.3E-13 67.2 7.4 59 77-145 1-59 (68)
23 cd05693 S1_Rrp5_repeat_hs1_sc1 98.9 5.1E-09 1.1E-13 73.3 6.1 63 75-145 2-81 (100)
24 cd05708 S1_Rrp5_repeat_sc12 S1 98.9 1.8E-08 3.9E-13 65.8 7.8 62 75-145 1-62 (77)
25 PF00575 S1: S1 RNA binding do 98.8 3E-08 6.4E-13 64.6 8.6 62 74-145 2-63 (74)
26 cd05692 S1_RPS1_repeat_hs4 S1_ 98.8 2.1E-08 4.5E-13 63.6 7.6 59 77-145 1-59 (69)
27 cd05686 S1_pNO40 S1_pNO40: pNO 98.8 2.4E-08 5.2E-13 65.6 7.9 63 74-145 1-63 (73)
28 PRK08582 hypothetical protein; 98.8 3.5E-08 7.5E-13 73.0 8.5 62 74-145 3-64 (139)
29 cd05703 S1_Rrp5_repeat_hs12_sc 98.8 3.2E-08 7E-13 65.2 7.5 61 77-145 1-61 (73)
30 smart00316 S1 Ribosomal protei 98.8 3.9E-08 8.5E-13 62.2 7.3 61 75-145 1-61 (72)
31 PRK07252 hypothetical protein; 98.8 5.5E-08 1.2E-12 70.3 8.3 61 75-145 2-62 (120)
32 cd05688 S1_RPS1_repeat_ec3 S1_ 98.8 5.6E-08 1.2E-12 61.7 7.4 59 76-145 1-59 (68)
33 cd05698 S1_Rrp5_repeat_hs6_sc5 98.7 5.7E-08 1.2E-12 62.7 7.2 59 77-145 1-59 (70)
34 PRK08059 general stress protei 98.7 6.3E-08 1.4E-12 70.0 7.9 62 74-145 5-66 (123)
35 cd05685 S1_Tex S1_Tex: The C-t 98.7 1E-07 2.2E-12 60.3 7.1 59 77-145 1-59 (68)
36 PTZ00248 eukaryotic translatio 98.7 6.2E-08 1.4E-12 80.4 7.7 65 72-145 13-78 (319)
37 PRK03987 translation initiatio 98.7 9.9E-08 2.1E-12 77.4 8.6 66 72-145 4-69 (262)
38 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.7 1.3E-07 2.9E-12 61.0 7.6 59 77-145 1-59 (69)
39 cd04461 S1_Rrp5_repeat_hs8_sc7 98.7 1.2E-07 2.6E-12 63.5 7.5 62 74-145 12-73 (83)
40 PRK05807 hypothetical protein; 98.7 1.5E-07 3.3E-12 69.3 8.5 61 74-145 3-63 (136)
41 cd04453 S1_RNase_E S1_RNase_E: 98.6 2.4E-07 5.1E-12 63.4 7.7 63 74-144 5-70 (88)
42 cd04472 S1_PNPase S1_PNPase: P 98.6 4.1E-07 8.8E-12 57.8 7.5 59 77-145 1-59 (68)
43 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.6 5.3E-07 1.1E-11 58.2 7.8 57 77-145 1-57 (66)
44 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.6 4.7E-07 1E-11 59.2 7.6 59 77-145 1-61 (71)
45 COG0539 RpsA Ribosomal protein 98.5 3.1E-07 6.8E-12 80.8 7.2 61 74-145 190-250 (541)
46 cd05690 S1_RPS1_repeat_ec5 S1_ 98.5 6.7E-07 1.5E-11 57.3 7.0 59 77-145 1-60 (69)
47 TIGR03591 polynuc_phos polyrib 98.4 1.6E-07 3.4E-12 85.0 4.2 89 35-145 589-677 (684)
48 cd05694 S1_Rrp5_repeat_hs2_sc2 98.4 2.1E-06 4.6E-11 56.8 8.0 55 75-145 3-58 (74)
49 cd00164 S1_like S1_like: Ribos 98.4 1.1E-06 2.3E-11 54.5 6.1 55 80-144 1-55 (65)
50 PRK11824 polynucleotide phosph 98.4 3.1E-07 6.7E-12 83.3 4.4 89 35-145 592-680 (693)
51 PRK07400 30S ribosomal protein 98.3 2.1E-06 4.5E-11 71.3 8.3 62 73-145 193-254 (318)
52 cd05689 S1_RPS1_repeat_ec4 S1_ 98.3 3.8E-06 8.3E-11 54.4 7.7 62 75-145 2-63 (72)
53 PHA02945 interferon resistance 98.3 2.8E-06 6E-11 58.1 7.2 62 72-145 7-71 (88)
54 cd05684 S1_DHX8_helicase S1_DH 98.3 5E-06 1.1E-10 55.0 7.5 61 77-144 1-62 (79)
55 COG1093 SUI2 Translation initi 98.3 1.5E-06 3.3E-11 70.1 5.7 66 71-145 6-72 (269)
56 TIGR02696 pppGpp_PNP guanosine 98.3 3E-06 6.5E-11 76.9 8.0 65 73-145 644-710 (719)
57 cd04455 S1_NusA S1_NusA: N-uti 98.2 9.2E-06 2E-10 52.4 7.4 54 75-145 2-55 (67)
58 cd04473 S1_RecJ_like S1_RecJ_l 98.2 2.2E-05 4.7E-10 52.0 9.0 53 74-144 14-66 (77)
59 PRK07400 30S ribosomal protein 98.2 8.3E-06 1.8E-10 67.8 8.0 63 72-144 27-89 (318)
60 PRK08563 DNA-directed RNA poly 98.1 2.6E-05 5.6E-10 59.9 9.1 65 72-145 77-150 (187)
61 PRK13806 rpsA 30S ribosomal pr 98.1 1.1E-05 2.5E-10 70.4 7.7 62 74-145 200-261 (491)
62 PRK13806 rpsA 30S ribosomal pr 98.1 1.2E-05 2.5E-10 70.4 7.5 62 74-145 377-438 (491)
63 PRK07899 rpsA 30S ribosomal pr 98.0 2.3E-05 5E-10 68.6 7.7 61 74-145 206-266 (486)
64 cd04465 S1_RPS1_repeat_ec2_hs2 98.0 4.8E-05 1E-09 48.7 7.3 56 77-145 1-56 (67)
65 PRK06299 rpsA 30S ribosomal pr 98.0 2.6E-05 5.6E-10 68.9 7.4 62 74-145 458-519 (565)
66 COG1095 RPB7 DNA-directed RNA 97.9 1.9E-05 4.1E-10 60.9 5.5 64 72-144 77-149 (183)
67 PRK06676 rpsA 30S ribosomal pr 97.9 3.5E-05 7.5E-10 65.1 7.8 61 74-145 190-250 (390)
68 TIGR00448 rpoE DNA-directed RN 97.9 4.4E-05 9.6E-10 58.4 7.4 65 72-145 77-150 (179)
69 PRK07899 rpsA 30S ribosomal pr 97.9 4.2E-05 9.1E-10 67.0 7.9 61 74-144 33-93 (486)
70 PRK12269 bifunctional cytidyla 97.9 3.5E-05 7.5E-10 71.5 7.6 63 74-145 576-638 (863)
71 cd04471 S1_RNase_R S1_RNase_R: 97.9 9.4E-05 2E-09 48.7 7.5 62 76-145 1-72 (83)
72 COG0539 RpsA Ribosomal protein 97.9 3.5E-05 7.6E-10 68.0 6.7 62 74-145 275-336 (541)
73 PRK06676 rpsA 30S ribosomal pr 97.8 7.2E-05 1.6E-09 63.2 8.0 62 74-145 275-336 (390)
74 PLN00207 polyribonucleotide nu 97.8 4.4E-05 9.6E-10 70.8 7.1 63 73-145 750-813 (891)
75 PRK06299 rpsA 30S ribosomal pr 97.8 7.8E-05 1.7E-09 65.9 8.1 61 74-145 199-259 (565)
76 TIGR00717 rpsA ribosomal prote 97.8 6.8E-05 1.5E-09 65.4 7.5 62 74-145 444-505 (516)
77 PRK00087 4-hydroxy-3-methylbut 97.8 9.2E-05 2E-09 66.8 7.8 61 74-145 475-535 (647)
78 cd04460 S1_RpoE S1_RpoE: RpoE, 97.8 0.00016 3.4E-09 50.0 7.2 59 78-145 1-68 (99)
79 PRK00087 4-hydroxy-3-methylbut 97.7 0.00015 3.3E-09 65.3 7.9 61 75-145 561-621 (647)
80 TIGR00717 rpsA ribosomal prote 97.6 0.00025 5.4E-09 61.9 7.9 62 73-145 184-245 (516)
81 PRK12269 bifunctional cytidyla 97.6 0.00028 6.1E-09 65.6 7.9 61 74-145 491-551 (863)
82 COG2183 Tex Transcriptional ac 97.5 0.00022 4.7E-09 65.1 6.1 62 74-145 656-717 (780)
83 PTZ00162 DNA-directed RNA poly 97.4 0.00081 1.8E-08 51.6 7.1 64 72-144 77-150 (176)
84 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.3 0.0013 2.9E-08 44.8 7.3 60 76-144 1-69 (88)
85 PRK09202 nusA transcription el 97.3 0.00068 1.5E-08 59.3 6.8 56 72-144 130-185 (470)
86 PRK12327 nusA transcription el 97.1 0.0016 3.5E-08 55.2 6.6 58 71-145 129-186 (362)
87 TIGR00757 RNaseEG ribonuclease 97.1 0.002 4.3E-08 55.5 7.1 62 74-143 23-96 (414)
88 TIGR01953 NusA transcription t 96.9 0.0027 5.9E-08 53.4 6.8 58 71-145 126-184 (341)
89 COG1185 Pnp Polyribonucleotide 96.6 0.0046 9.9E-08 56.0 6.2 63 73-145 616-678 (692)
90 TIGR02063 RNase_R ribonuclease 96.3 0.018 3.9E-07 52.6 7.8 64 74-145 625-698 (709)
91 KOG1070 rRNA processing protei 96.2 0.007 1.5E-07 58.6 5.1 67 70-144 879-945 (1710)
92 PHA02858 EIF2a-like PKR inhibi 96.1 0.022 4.8E-07 38.8 5.8 63 72-145 12-75 (86)
93 PRK12328 nusA transcription el 96.1 0.017 3.7E-07 49.2 6.3 57 71-144 133-190 (374)
94 PRK12329 nusA transcription el 95.8 0.026 5.7E-07 49.0 6.4 62 71-144 147-209 (449)
95 PRK11642 exoribonuclease R; Pr 95.5 0.06 1.3E-06 50.2 7.8 64 74-145 641-714 (813)
96 TIGR00358 3_prime_RNase VacB a 95.3 0.081 1.8E-06 48.0 7.8 64 74-145 570-643 (654)
97 PRK11712 ribonuclease G; Provi 95.0 0.069 1.5E-06 47.1 6.4 62 74-143 36-109 (489)
98 KOG1856 Transcription elongati 94.9 0.053 1.2E-06 51.8 5.7 65 74-145 983-1047(1299)
99 PRK10811 rne ribonuclease E; R 94.9 0.082 1.8E-06 50.0 6.9 62 74-143 36-106 (1068)
100 cd05699 S1_Rrp5_repeat_hs7 S1_ 94.9 0.099 2.1E-06 34.6 5.4 59 77-142 1-60 (72)
101 PF01016 Ribosomal_L27: Riboso 94.5 0.069 1.5E-06 36.1 3.9 47 3-50 22-70 (81)
102 CHL00121 rpl27 ribosomal prote 94.0 0.12 2.7E-06 35.2 4.4 59 4-67 24-84 (86)
103 PRK05435 rpmA 50S ribosomal pr 93.9 0.19 4.2E-06 34.0 5.2 47 3-50 23-71 (82)
104 KOG1070 rRNA processing protei 93.6 0.24 5.3E-06 48.5 7.2 62 74-145 1160-1221(1710)
105 PF13509 S1_2: S1 domain; PDB: 90.9 1.2 2.7E-05 27.9 5.9 48 76-141 1-48 (61)
106 COG2996 Predicted RNA-bindinin 90.9 1 2.2E-05 37.0 6.8 50 77-144 156-205 (287)
107 TIGR00062 L27 ribosomal protei 90.9 0.53 1.2E-05 31.9 4.3 47 3-50 23-71 (83)
108 PF01959 DHQS: 3-dehydroquinat 90.0 3.8 8.3E-05 34.9 9.7 93 10-143 246-338 (354)
109 KOG3298 DNA-directed RNA polym 89.8 1.4 3E-05 33.6 6.2 67 72-144 77-149 (170)
110 KOG1067 Predicted RNA-binding 89.3 0.64 1.4E-05 42.0 4.7 60 74-143 661-725 (760)
111 PRK02290 3-dehydroquinate synt 88.9 5.1 0.00011 34.0 9.6 93 10-143 236-328 (344)
112 KOG4600 Mitochondrial ribosoma 87.9 1.4 3.1E-05 32.5 5.0 63 3-68 50-114 (144)
113 PF08292 RNA_pol_Rbc25: RNA po 86.4 4.2 9.1E-05 29.4 6.7 69 74-144 1-74 (122)
114 COG1530 CafA Ribonucleases G a 85.5 1.4 3.1E-05 38.8 4.7 62 74-143 35-100 (487)
115 KOG2916 Translation initiation 84.1 1.1 2.4E-05 36.7 3.1 66 71-144 11-76 (304)
116 PRK05054 exoribonuclease II; P 83.7 5.3 0.00011 36.4 7.6 65 74-145 557-633 (644)
117 PF10246 MRP-S35: Mitochondria 79.0 13 0.00029 26.2 6.6 54 74-144 21-74 (104)
118 COG0211 RpmA Ribosomal protein 76.6 6.9 0.00015 26.6 4.5 59 4-67 24-84 (87)
119 PF04085 MreC: rod shape-deter 75.2 11 0.00023 27.9 5.8 60 80-139 36-102 (152)
120 cd04454 S1_Rrp4_like S1_Rrp4_l 74.9 6.4 0.00014 25.6 4.0 24 73-96 50-74 (82)
121 PTZ00248 eukaryotic translatio 74.4 5.1 0.00011 33.6 4.2 99 14-144 18-116 (319)
122 TIGR02062 RNase_B exoribonucle 74.4 16 0.00034 33.4 7.6 64 75-145 554-629 (639)
123 COG0557 VacB Exoribonuclease R 74.2 13 0.00028 34.2 7.1 64 75-145 621-693 (706)
124 PF03961 DUF342: Protein of un 70.7 12 0.00025 32.5 5.7 36 22-66 144-180 (451)
125 cd05790 S1_Rrp40 S1_Rrp40: Rrp 70.3 9.9 0.00021 25.8 4.2 29 71-100 47-75 (86)
126 PRK04012 translation initiatio 70.1 14 0.0003 25.8 5.0 55 73-143 17-72 (100)
127 KOG4134 DNA-dependent RNA poly 64.5 5.6 0.00012 32.0 2.3 58 72-144 103-160 (253)
128 smart00652 eIF1a eukaryotic tr 63.2 30 0.00066 23.1 5.4 22 74-96 2-24 (83)
129 PTZ00329 eukaryotic translatio 63.1 13 0.00029 28.0 4.0 40 8-48 24-67 (155)
130 PRK13922 rod shape-determining 63.0 70 0.0015 25.6 8.5 78 59-138 133-222 (276)
131 PF07497 Rho_RNA_bind: Rho ter 62.2 20 0.00043 24.0 4.3 43 60-102 29-74 (78)
132 COG1096 Predicted RNA-binding 61.9 21 0.00045 27.8 4.9 22 74-96 119-140 (188)
133 cd05791 S1_CSL4 S1_CSL4: CSL4, 61.5 12 0.00026 25.3 3.3 23 74-96 61-84 (92)
134 TIGR00219 mreC rod shape-deter 60.4 38 0.00081 27.7 6.6 61 78-138 155-223 (283)
135 PF01336 tRNA_anti-codon: OB-f 60.3 33 0.00071 21.0 5.0 50 79-140 2-54 (75)
136 PF09953 DUF2187: Uncharacteri 59.8 26 0.00056 22.1 4.2 22 80-101 16-37 (57)
137 PRK06763 F0F1 ATP synthase sub 59.3 38 0.00083 26.8 6.0 79 37-140 6-84 (213)
138 PLN00208 translation initiatio 58.4 37 0.00081 25.3 5.6 24 72-96 27-51 (145)
139 PF01938 TRAM: TRAM domain; I 57.3 23 0.0005 21.7 3.8 24 73-96 37-60 (61)
140 PF08810 KapB: Kinase associat 57.2 19 0.00042 25.7 3.8 22 80-101 6-27 (112)
141 PTZ00329 eukaryotic translatio 54.1 48 0.001 25.0 5.7 23 73-96 28-51 (155)
142 PF01176 eIF-1a: Translation i 53.7 48 0.001 20.9 4.9 49 78-141 3-52 (65)
143 cd04322 LysRS_N LysRS_N: N-ter 53.6 63 0.0014 22.0 6.0 55 79-140 3-59 (108)
144 COG1315 Uncharacterized conser 52.9 22 0.00048 31.8 4.2 35 22-67 220-255 (543)
145 COG0361 InfA Translation initi 52.4 38 0.00083 22.5 4.4 54 77-144 6-60 (75)
146 PRK07252 hypothetical protein; 51.3 50 0.0011 23.5 5.2 28 73-100 47-76 (120)
147 COG1107 Archaea-specific RecJ- 50.8 17 0.00037 33.3 3.2 58 72-145 118-175 (715)
148 PF12508 DUF3714: Protein of u 49.5 1.3E+02 0.0027 23.6 7.8 57 35-101 52-112 (200)
149 cd04456 S1_IF1A_like S1_IF1A_l 46.1 64 0.0014 21.3 4.8 17 80-96 2-19 (78)
150 COG1792 MreC Cell shape-determ 45.7 1E+02 0.0022 25.3 6.9 61 75-138 153-220 (284)
151 TIGR00074 hypC_hupF hydrogenas 43.1 80 0.0017 20.9 4.8 16 81-96 6-21 (76)
152 PF10844 DUF2577: Protein of u 41.5 1E+02 0.0023 21.0 5.5 15 125-139 71-85 (100)
153 TIGR00523 eIF-1A eukaryotic/ar 41.4 81 0.0018 21.9 4.9 20 77-96 18-38 (99)
154 TIGR00008 infA translation ini 40.7 86 0.0019 20.3 4.6 17 80-96 7-24 (68)
155 KOG3297 DNA-directed RNA polym 40.1 64 0.0014 25.3 4.5 69 74-144 79-156 (202)
156 PRK00276 infA translation init 39.7 1E+02 0.0022 19.8 5.9 48 80-141 9-57 (72)
157 PLN00208 translation initiatio 39.2 58 0.0013 24.3 4.1 40 8-48 24-67 (145)
158 COG2932 Predicted transcriptio 38.6 1.8E+02 0.0039 22.3 8.4 69 10-89 136-211 (214)
159 COG3269 Predicted RNA-binding 37.6 74 0.0016 21.0 3.9 23 75-97 47-69 (73)
160 cd00210 PTS_IIA_glc PTS_IIA, P 37.1 47 0.001 24.0 3.2 27 23-49 23-49 (124)
161 PRK12442 translation initiatio 36.2 1.4E+02 0.0031 20.4 5.3 17 80-96 9-26 (87)
162 cd05793 S1_IF1A S1_IF1A: Trans 36.2 58 0.0013 21.5 3.3 25 24-48 9-35 (77)
163 PRK09521 exosome complex RNA-b 35.3 75 0.0016 24.1 4.3 22 74-96 119-140 (189)
164 COG2996 Predicted RNA-bindinin 34.2 1.5E+02 0.0033 24.5 6.1 54 74-141 71-125 (287)
165 PRK14872 rod shape-determining 34.0 1.7E+02 0.0037 24.9 6.5 22 80-101 143-164 (337)
166 PF01455 HupF_HypC: HupF/HypC 33.7 1.3E+02 0.0028 19.3 4.9 17 80-96 5-23 (68)
167 COG1465 Predicted alternative 33.5 1.1E+02 0.0024 25.9 5.2 40 10-49 268-307 (376)
168 PF14444 S1-like: S1-like 32.1 51 0.0011 20.8 2.4 16 71-86 31-46 (58)
169 PF15057 DUF4537: Domain of un 31.0 1.8E+02 0.0039 20.7 5.5 16 126-141 51-66 (124)
170 TIGR00830 PTBA PTS system, glu 30.5 74 0.0016 22.9 3.4 27 23-49 23-49 (121)
171 PF11720 Inhibitor_I78: Peptid 30.0 85 0.0019 19.4 3.2 35 8-44 26-60 (60)
172 PRK05585 yajC preprotein trans 29.9 1.2E+02 0.0026 21.2 4.3 23 74-96 53-81 (106)
173 KOG3409 Exosomal 3'-5' exoribo 29.0 50 0.0011 25.6 2.3 15 132-146 67-81 (193)
174 PRK04163 exosome complex RNA-b 27.8 96 0.0021 24.6 3.9 23 74-96 112-135 (235)
175 cd06541 ASCH ASC-1 homology or 27.2 2.1E+02 0.0045 19.5 5.3 41 59-101 16-56 (105)
176 COG2190 NagE Phosphotransferas 26.7 70 0.0015 24.2 2.8 28 22-49 29-56 (156)
177 PRK09439 PTS system glucose-sp 26.7 71 0.0015 24.3 2.8 42 9-50 22-72 (169)
178 TIGR00638 Mop molybdenum-pteri 26.4 1.6E+02 0.0034 17.8 6.3 54 78-143 7-61 (69)
179 COG4714 Uncharacterized membra 25.9 33 0.00071 27.9 0.9 46 80-135 94-139 (303)
180 CHL00010 infA translation init 25.7 2E+02 0.0043 18.8 5.8 48 80-141 9-57 (78)
181 PRK10862 SoxR reducing system 25.5 1.8E+02 0.0038 21.6 4.8 17 81-97 5-21 (154)
182 PRK10409 hydrogenase assembly 23.7 1.9E+02 0.0041 19.8 4.3 16 81-96 6-21 (90)
183 PF00717 Peptidase_S24: Peptid 23.2 62 0.0013 19.7 1.7 15 126-140 6-20 (70)
184 COG1097 RRP4 RNA-binding prote 21.8 86 0.0019 25.4 2.6 26 71-96 110-136 (239)
185 COG4873 Uncharacterized protei 21.5 2.5E+02 0.0054 18.4 4.5 22 80-101 36-57 (81)
186 TIGR00499 lysS_bact lysyl-tRNA 21.5 2.7E+02 0.0059 24.6 5.9 55 79-140 57-113 (496)
187 KOG3416 Predicted nucleic acid 21.5 64 0.0014 23.7 1.6 15 126-140 57-71 (134)
188 PF08865 DUF1830: Domain of un 21.1 44 0.00096 21.7 0.7 20 9-32 25-44 (68)
189 PF13375 RnfC_N: RnfC Barrel s 20.6 95 0.0021 21.5 2.3 12 37-48 68-79 (101)
190 COG0093 RplN Ribosomal protein 20.1 3.5E+02 0.0076 19.6 6.0 28 61-89 21-48 (122)
191 KOG4078 Putative mitochondrial 20.1 3.5E+02 0.0075 20.4 5.3 25 72-96 78-102 (173)
No 1
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.2e-33 Score=214.24 Aligned_cols=129 Identities=32% Similarity=0.471 Sum_probs=121.9
Q ss_pred cCCcEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 032149 6 EEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT 85 (146)
Q Consensus 6 ~~~~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~ 85 (146)
+++++|+|||.|+.+|||++|.|||+. +|.|+|+.+|.+.+ |+++..++|.|.+..+.+|+.||+|+|+|+
T Consensus 3 ~~g~~v~PGd~~a~~EE~~~G~gt~~~--~g~i~Aa~~G~~~~-------d~~n~~~~V~p~~~~~~~~K~GdiV~grV~ 73 (188)
T COG1096 3 KDGTFVLPGDVLAVIEEFLPGEGTYEE--GGEIRAAATGVVRR-------DDKNRVISVKPGKKTPPLPKGGDIVYGRVT 73 (188)
T ss_pred ccCcEEcCcceeeeeeeeecCCCeEeE--CCEEEEeecccEEE-------cccceEEEeccCCCCCCCCCCCCEEEEEEe
Confidence 468999999999999999999999999 99999999999999 567889999999877999999999999999
Q ss_pred EEecceEEEEEEeecc--cccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 86 KVMTRMASADIMCVGA--KSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 86 ~v~~~~~~v~I~~v~~--~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
+++.+.|.|+|.++++ +.+.+++.|.||+|+++..+.. +++++|++||+|+|+|+|++
T Consensus 74 ~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~--~~~d~f~~GDivrA~Vis~~ 133 (188)
T COG1096 74 DVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVE--KLSDAFRIGDIVRARVISTG 133 (188)
T ss_pred eccceEEEEEEEEEecccccCCCCceeeEEEEeccccccc--ccccccccccEEEEEEEecC
Confidence 9999999999999999 4588899999999999999988 89999999999999999975
No 2
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1.1e-31 Score=202.27 Aligned_cols=132 Identities=42% Similarity=0.635 Sum_probs=115.6
Q ss_pred CcEEecCCccCCCC-CeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEE
Q 032149 8 MVLVTPGEVLGKAT-EVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTK 86 (146)
Q Consensus 8 ~~iV~PGd~l~~~~-~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~ 86 (146)
..+++|||++|..+ ++..|.|||+. +|.|+||.+|...++. ..+++++.++........+|..||||+++|++
T Consensus 5 ~~~~lpG~~~c~~e~~~~~g~Gtye~--~~yI~aS~ag~~~~~~----~~~~~~v~~~~~~~~~~~LP~~G~IVtarV~~ 78 (193)
T KOG3409|consen 5 ETLVLPGEVVCRAEGEYRMGEGTYER--NGYIFASVAGVNFRDN----LVQKIEVVSVEKQLFNELLPFVGAIVTARVSR 78 (193)
T ss_pred eEEEcccceeeecccccccccceeec--CCeEEeccccceeecC----CccceeeeeecccchhhcCCccCcEEEEEEEe
Confidence 57999999999876 49999999999 9999999999554421 13334455555443467899999999999999
Q ss_pred EecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 87 VMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 87 v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
++.++|.|+|+++++.+|...|+|+||++|+|++++|++++..+|+|||+|+|+|+|++
T Consensus 79 i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~ 137 (193)
T KOG3409|consen 79 INLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLG 137 (193)
T ss_pred eccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecC
Confidence 99999999999999999999999999999999999999999999999999999999965
No 3
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=99.97 E-value=1.1e-30 Score=201.44 Aligned_cols=128 Identities=30% Similarity=0.439 Sum_probs=117.2
Q ss_pred CCcEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEE
Q 032149 7 EMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTK 86 (146)
Q Consensus 7 ~~~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~ 86 (146)
.+++|+|||.|+..++|++|+|||++ +|.||||++|.+++ |..++.|+|.|.....+.|++||+|+|+|++
T Consensus 4 ~~~~V~PGe~l~~~~e~~~G~Gty~~--~~~i~as~~G~~~i-------d~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~ 74 (189)
T PRK09521 4 QGDLVLPGDYLAVIEEYLPGEGTYED--NGEVYASVVGKVFI-------DDINRKISVIPFKKTPPLLKKGDIVYGRVVD 74 (189)
T ss_pred cCCEECCCCccccccceEcCCCEEee--CCEEEEEeeEEEEE-------cCCCCEEEEecCcCCCCCCCCCCEEEEEEEE
Confidence 46799999999998999999999999 99999999999999 3346799999987668999999999999999
Q ss_pred EecceEEEEEEeec--ccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 87 VMTRMASADIMCVG--AKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 87 v~~~~~~v~I~~v~--~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
+.++.|+|+|.+++ +++++.++.|++|.+|++..+.+ +|.++|++||+|+|+|+++.
T Consensus 75 i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~--~~~~~~~~GD~V~akV~~i~ 133 (189)
T PRK09521 75 VKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVE--SLTDAFKIGDIVRAKVISYT 133 (189)
T ss_pred EcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhh--hHHhccCCCCEEEEEEEecC
Confidence 99999999999887 67788889999999999877666 89999999999999999873
No 4
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=99.96 E-value=4.5e-29 Score=198.55 Aligned_cols=117 Identities=27% Similarity=0.451 Sum_probs=106.5
Q ss_pred CcEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEE
Q 032149 8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKV 87 (146)
Q Consensus 8 ~~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~v 87 (146)
+++|+|||.|+ .++|.+|+|||++ +|.|+||++|.+... ++.++|.|.++ +|+|++||+|+|+|+++
T Consensus 8 ~~~V~PGd~l~-~~~~~~G~Gty~~--~g~i~As~~G~~~~~---------~~~i~V~p~~~-~y~P~vGDiViG~V~~i 74 (235)
T PRK04163 8 RKIVVPGDLLA-EGEFKAGRGTYKE--NGKIYSTVVGLVDIK---------DDKVRVIPLEG-KYIPKVGDLVIGKVTDV 74 (235)
T ss_pred CcEECCCCCcC-cCCeecCCceEEe--CCEEEEEEeEEEEEE---------CCEEEEEECCC-cccCCCCCEEEEEEEEE
Confidence 58999999997 5889999999999 999999999999984 25999999875 59999999999999999
Q ss_pred ecceEEEEEEeecccccccceeeEEeccccccccc--cccccccCCCCCCEEEEEEEEee
Q 032149 88 MTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI--DKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 88 ~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~--d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
+++.|+|+| ..++.|+||.++++..+. |+.+|+++|++||+|+|||+++.
T Consensus 75 ~~~~~~vdI--------~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~ 126 (235)
T PRK04163 75 TFSGWEVDI--------NSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVD 126 (235)
T ss_pred eCceEEEEe--------CCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEEC
Confidence 999999999 678999999999986643 66799999999999999999874
No 5
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=9.3e-28 Score=189.66 Aligned_cols=120 Identities=28% Similarity=0.415 Sum_probs=109.4
Q ss_pred cCCcEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 032149 6 EEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT 85 (146)
Q Consensus 6 ~~~~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~ 85 (146)
..+++|+|||.|...+.+..|+|||.. +++||||++|.+++. ++.+.|.|+++ +|+|++||+|||+|+
T Consensus 6 ~~~~iV~PGd~vl~~~~~~~G~Gty~~--~~~iyssv~G~~~~~---------~~~v~VIpl~g-~YiP~~gD~VIG~I~ 73 (239)
T COG1097 6 SMRKIVLPGDLVLAEGSYKLGHGTYFE--GGKIYSSVVGLLDVK---------GKLVRVIPLEG-RYIPEVGDVVIGKII 73 (239)
T ss_pred cccceecCCCccCCCCCEecCCCcEec--CCEEEEEEEeEEEEe---------CCEEEEEeCCC-cccCCCCCEEEEEEE
Confidence 457999999977777899999999998 999999999999995 46899999975 999999999999999
Q ss_pred EEecceEEEEEEeecccccccceeeEEecccc--ccccccccccccCCCCCCEEEEEEEEee
Q 032149 86 KVMTRMASADIMCVGAKSVREKFSGIIRQQDV--RATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 86 ~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi--~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.+.++.|.||| +++|.++|+.|++ |..+.++.+|+++|++||+|+|||.+++
T Consensus 74 ~v~~~~W~VDI--------~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd 127 (239)
T COG1097 74 EVGPSGWKVDI--------GSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVD 127 (239)
T ss_pred EEcccceEEEc--------CCccceEeehhhhhcccccccccccccccccCCEEEEEEEEcc
Confidence 99999999999 8999999999999 3445557799999999999999999875
No 6
>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=99.93 E-value=1.1e-25 Score=152.74 Aligned_cols=72 Identities=60% Similarity=0.955 Sum_probs=52.6
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEEee----------cccccccceeeEEeccccccccccccccccCCCCCCEEEEEEE
Q 032149 73 VPEPGSVVIARVTKVMTRMASADIMCV----------GAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVV 142 (146)
Q Consensus 73 ~P~~GdiViG~V~~v~~~~~~v~I~~v----------~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vi 142 (146)
+|++||+|+|+|+++++++|.|+|+++ .+.++..+|+|+||++|+|+++.|+++|.+||+|||+|+|+|+
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 599999999999999999999999999 6778889999999999999999999999999999999999999
Q ss_pred Ee
Q 032149 143 SF 144 (146)
Q Consensus 143 s~ 144 (146)
|+
T Consensus 81 Sl 82 (82)
T PF10447_consen 81 SL 82 (82)
T ss_dssp EE
T ss_pred eC
Confidence 96
No 7
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=99.92 E-value=9.3e-26 Score=179.38 Aligned_cols=123 Identities=28% Similarity=0.487 Sum_probs=108.1
Q ss_pred CCcEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEE
Q 032149 7 EMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTK 86 (146)
Q Consensus 7 ~~~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~ 86 (146)
..++|+||+.+...+.|+.|+|||.. ||.|+||++|.+++. |+.++|+|++ .+|.|++||+|.|||+.
T Consensus 28 ~~~ivtPG~~V~~d~~fmRGHGTy~~--d~~i~ssvaG~v~rv---------NkLi~V~plk-~rY~pEvGDvVVgRV~e 95 (301)
T KOG3013|consen 28 HSTIVTPGELVTDDPGFMRGHGTYVR--DGEIYSSVAGVVQRV---------NKLISVKPLK-SRYAPEVGDVVVGRVIE 95 (301)
T ss_pred CceeecCCccccCchhhhhcccceec--CCeEEEeecchhhhh---------cceEEEeehh-hhcCCccCCEEEEEeee
Confidence 46799999999998899999999999 999999999999885 5899999997 78999999999999999
Q ss_pred EecceEEEEEEeeccccccc---cee-eEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 87 VMTRMASADIMCVGAKSVRE---KFS-GIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 87 v~~~~~~v~I~~v~~~~l~~---~~~-g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
|.+++|+|++.+-.++.|.. ... |++| |..+.|+..|+++|+.||+|.|+|++++
T Consensus 96 Vq~KRWkvd~nsk~d~vL~LsSvNLPGg~~R----Rk~~~DEl~MR~fl~egDLi~AEVQ~v~ 154 (301)
T KOG3013|consen 96 VQQKRWKVDLNSKQDAVLMLSSVNLPGGIQR----RKSEEDELQMRSFLKEGDLIVAEVQNVF 154 (301)
T ss_pred eecceeEEecccccceEEEeecccCCchhhh----ccchhhHHHHHHHhhccCeehHHHHHhc
Confidence 99999999998777765543 223 3443 6778899999999999999999998764
No 8
>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=99.91 E-value=4.4e-24 Score=147.73 Aligned_cols=74 Identities=55% Similarity=0.947 Sum_probs=72.3
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
|+|++||+|+|+|++++.++|.|+|+++++++++++|+|+||+||+++++.++.+|++||++||+|+|||+|++
T Consensus 2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~ 75 (92)
T cd05791 2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLG 75 (92)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcC
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999986
No 9
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.56 E-value=2e-14 Score=96.49 Aligned_cols=65 Identities=26% Similarity=0.442 Sum_probs=58.9
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
+|+|++||+|+|+|+++.++.|+|+| ...++|++|.+++...+.. ++.+.|++||+|+|+|+++.
T Consensus 1 ~y~p~~GdiV~G~V~~v~~~~~~V~i--------~~~~~g~l~~~~~~~~~~~--~~~~~~~~GD~i~~~V~~~~ 65 (82)
T cd04454 1 RYLPDVGDIVIGIVTEVNSRFWKVDI--------LSRGTARLEDSSATEKDKK--EIRKSLQPGDLILAKVISLG 65 (82)
T ss_pred CCCCCCCCEEEEEEEEEcCCEEEEEe--------CCCceEEeechhccCcchH--HHHhcCCCCCEEEEEEEEeC
Confidence 48999999999999999999999999 6779999999999765444 89999999999999999874
No 10
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.54 E-value=2.9e-14 Score=97.54 Aligned_cols=64 Identities=22% Similarity=0.181 Sum_probs=55.4
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
+|+|++||+|+|+|+++..+.|+|+| ++++.|+|+.+++... ..++++.|++||+|+|||.++.
T Consensus 1 rY~P~~gD~VIG~V~~~~~~~~~VdI--------~s~~~a~L~~~~f~ga---tk~~rp~L~~GDlV~ArV~~~~ 64 (86)
T cd05790 1 RYVPAKGDHVIGIVVAKAGDFFKVDI--------GGSEPASLSYLAFEGA---TKRNRPNLNVGDLVYARVVKAN 64 (86)
T ss_pred CCcCCCCCEEEEEEEEEcCCeEEEEc--------CCCcceEechHHcccc---cccccccCCCCCEEEEEEEecC
Confidence 59999999999999999999999999 7888999998765321 2267999999999999998863
No 11
>PF14382 ECR1_N: Exosome complex exonuclease RRP4 N-terminal region; PDB: 2NN6_I 3M7N_C 2BA1_A 3M85_C.
Probab=99.48 E-value=2.5e-14 Score=84.21 Aligned_cols=38 Identities=39% Similarity=0.773 Sum_probs=34.1
Q ss_pred EEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEc
Q 032149 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTL 49 (146)
Q Consensus 10 iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~ 49 (146)
+|+|||+|+.+++|++|+|||++ +|+||||++|.+++.
T Consensus 1 iV~PG~~l~~~~e~~~G~GTY~~--~g~I~asv~G~v~~~ 38 (39)
T PF14382_consen 1 IVVPGDRLGSSEEYMPGHGTYVR--DGNIYASVAGTVKID 38 (39)
T ss_dssp EE-TT-EEEETTTSEESTTEEEE--TTEEEESSSEEEEEE
T ss_pred CCCCCCEeecCCCEecCCCEEEe--CCEEEEEeeEEEEEc
Confidence 69999999999999999999999 999999999999873
No 12
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=99.43 E-value=2.5e-12 Score=100.27 Aligned_cols=118 Identities=23% Similarity=0.249 Sum_probs=89.0
Q ss_pred cEEecCCccCC--CCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEE
Q 032149 9 VLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTK 86 (146)
Q Consensus 9 ~iV~PGd~l~~--~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~ 86 (146)
++.+|||.+.. +.+-.+|+|.+.+ ++.+.++.+|.+...++- ....++.+|... +++|+|.+||.|||+|+.
T Consensus 2 ~~~~pg~~~~~~~~~sv~~G~g~~~~--g~~~~~~~~G~~~~~~~g---k~~~~v~~vds~-~kRYiP~~~D~VIGiV~~ 75 (230)
T KOG1004|consen 2 TFYFPGDSIPRPRLCSVVLGPGLRRR--GQERLVTKCGRLRHKEPG---KGGGGVYWVDSQ-QKRYIPVKGDHVIGIVTS 75 (230)
T ss_pred ceecCCcccccCccCceeecCCcccc--CceEEeccccceeeccCC---cccceeEEEecc-cceecCCCCCEEEEEEEe
Confidence 57899998764 3458999999998 999999999988775410 111225677764 689999999999999999
Q ss_pred EecceEEEEEEeecccccc-cceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149 87 VMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 87 v~~~~~~v~I~~v~~~~l~-~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
-..+.++|||..-+-+.|+ ..|+|. +. .-++.|..||+|+|||...
T Consensus 76 ~~gd~ykVDigg~~~a~L~~laFe~A--------tk----rNrPnl~vGdliyakv~~a 122 (230)
T KOG1004|consen 76 KSGDIYKVDIGGSEPASLSYLAFEGA--------TK----RNRPNLQVGDLIYAKVVDA 122 (230)
T ss_pred ccCceEEEecCCCCeeeeeeccccCc--------cc----cCCCccccccEEEEEEEec
Confidence 9999999999543333333 234442 22 4489999999999999864
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=99.38 E-value=2.1e-12 Score=87.17 Aligned_cols=67 Identities=30% Similarity=0.441 Sum_probs=57.6
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccc--cccccccccCCCCCCEEEEEEEEee
Q 032149 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT--EIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~--~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
+|.|++||+|.|+|+++.++.|+|+| ...+.|+||.+|+... .....++.+.|++||.|.|+|+++.
T Consensus 1 ~y~p~~GdiV~g~V~~i~~~g~~v~i--------~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~ 69 (86)
T cd05789 1 RYIPEVGDVVIGRVTEVGFKRWKVDI--------NSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVD 69 (86)
T ss_pred CCcCCCCCEEEEEEEEECCCEEEEEC--------CCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEEC
Confidence 48899999999999999999999999 6789999999998631 1122378899999999999999874
No 14
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.11 E-value=3.2e-10 Score=74.59 Aligned_cols=61 Identities=25% Similarity=0.378 Sum_probs=54.2
Q ss_pred CCCCEEEEEEEEEec-ceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 75 EPGSVVIARVTKVMT-RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 75 ~~GdiViG~V~~v~~-~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
++|++|.|+|+++.+ ..+++++ .....|++|++|++..+.. ++.+.|++||+|+|+|+++.
T Consensus 2 ~~G~iv~G~V~~i~~~~g~~v~l--------~~~~~Glvhis~~s~~~~~--~~~~~~~~Gd~v~~kV~~~~ 63 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQL--------PFGKTGLVSIFHLSDSYTE--NPLEGFKPGKIVRCCILSKK 63 (72)
T ss_pred CCCCEEEEEEEEeeCCcEEEEEC--------CCCCEEEEEHHHhcCcccC--CHHHhCCCCCEEEEEEEEec
Confidence 689999999999987 5899998 6789999999999877666 67899999999999999874
No 15
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.10 E-value=5e-10 Score=72.93 Aligned_cols=61 Identities=21% Similarity=0.263 Sum_probs=53.4
Q ss_pred CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
|++|.|+|+++.++.++|++ ...+.|.+|.++++..+.+..++.++|++||.|+|+|+++.
T Consensus 1 G~iV~g~V~~i~~~gi~v~l--------~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d 61 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQL--------ADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGH 61 (70)
T ss_pred CCEEEEEEEEEECCcEEEEe--------CCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEe
Confidence 89999999999999999998 57799999999998654223378999999999999999874
No 16
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.10 E-value=5.2e-10 Score=72.44 Aligned_cols=59 Identities=25% Similarity=0.271 Sum_probs=53.4
Q ss_pred CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
||+|.|+|+++.++.|+|++ ...+.|++|.+++...+.+ ++.++|++||.++|+|+++.
T Consensus 1 G~iv~g~V~~i~~~~~~v~l--------~~~~~g~l~~~e~~~~~~~--~~~~~~~~Gd~i~~~i~~~~ 59 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDI--------GYKSEGIIPISEFSDDPIE--NGEDEVKVGDEVEVYVLRVE 59 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEe--------CCCceEEEEHHHhCccccC--CHhHcCCCCCEEEEEEEEEE
Confidence 89999999999999999999 4568999999999876666 78999999999999999864
No 17
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.06 E-value=2.8e-10 Score=82.24 Aligned_cols=62 Identities=16% Similarity=0.283 Sum_probs=58.7
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
+++|+++.|+||+|++..|||++ ...-+|++|+|++...++. ++.+.+++||.|.++|+++.
T Consensus 3 ~kvG~~l~GkItgI~~yGAFV~l--------~~g~tGLVHISEIa~~fVk--dI~d~L~vG~eV~vKVl~id 64 (129)
T COG1098 3 MKVGSKLKGKITGITPYGAFVEL--------EGGKTGLVHISEIADGFVK--DIHDHLKVGQEVKVKVLDID 64 (129)
T ss_pred ccccceEEEEEEeeEecceEEEe--------cCCCcceEEehHhhhhhHH--hHHHHhcCCCEEEEEEEeec
Confidence 68999999999999999999999 6778899999999999999 99999999999999999874
No 18
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.01 E-value=2e-09 Score=71.29 Aligned_cols=63 Identities=16% Similarity=0.162 Sum_probs=54.4
Q ss_pred CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccccc-ccccccCCCCCCEEEEEEEEee
Q 032149 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID-KVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d-~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
++||+|.|+|+++++..++|++ .....|++|.+++...... ..++.+.|++||.|.|+|+++.
T Consensus 2 k~G~~V~g~V~~i~~~G~fV~l--------~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id 65 (74)
T cd05705 2 KEGQLLRGYVSSVTKQGVFFRL--------SSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVN 65 (74)
T ss_pred CCCCEEEEEEEEEeCCcEEEEe--------CCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEE
Confidence 6899999999999999999998 6679999999999876533 2236799999999999999874
No 19
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=99.00 E-value=2.5e-09 Score=70.00 Aligned_cols=64 Identities=17% Similarity=0.271 Sum_probs=54.8
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
|+.|+++.|+|+++.+..|++++... ....|++|.++++..... ++.+.|++||.|+|+|+++.
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~------~~~~gll~~s~l~~~~~~--~~~~~~~~Gd~v~vkv~~~d 64 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEY------GNIEGMILLSELSRRRIR--SIRKLVKVGRKEVVKVIRVD 64 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCC------CCeEEEEEhHHcCCcccC--CHHHeeCCCCEEEEEEEEEE
Confidence 67899999999999999999999211 138999999999866555 78999999999999999864
No 20
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.98 E-value=4.5e-09 Score=68.55 Aligned_cols=61 Identities=30% Similarity=0.371 Sum_probs=53.8
Q ss_pred CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
++|++|.|+|+++.+..++|++ ....+|++|.+++...+.. +..+.|++||.|+|+|+++.
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l--------~~~~~g~v~~s~l~~~~~~--~~~~~~~~Gd~v~~~V~~~d 62 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQL--------GNKVTGPSFITDALDDYSE--ALPYKFKKNDIVRACVLSVD 62 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEe--------CCCcEEEEEhhhccCcccc--ccccccCCCCEEEEEEEEEe
Confidence 6899999999999999999998 6679999999999765433 56789999999999999874
No 21
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.93 E-value=6.5e-09 Score=67.33 Aligned_cols=59 Identities=25% Similarity=0.468 Sum_probs=53.1
Q ss_pred CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
|++|.|+|+++.+..|+|++ .....|++|.+++...+.+ ++.+.|++||.++|+|+++.
T Consensus 1 G~~v~g~V~~v~~~g~~v~l--------~~~~~g~i~~~~~~~~~~~--~~~~~~~~Gd~v~~~v~~~d 59 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKL--------GDGVEGFLRAAELSRDRVE--DATERFKVGDEVEAKITNVD 59 (73)
T ss_pred CCEEEEEEEEEECCeEEEEe--------CCCCEEEEEHHHCCCcccc--CHHHccCCCCEEEEEEEEEe
Confidence 79999999999999999999 4678999999999876655 78899999999999999874
No 22
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.93 E-value=6.1e-09 Score=67.19 Aligned_cols=59 Identities=19% Similarity=0.319 Sum_probs=52.8
Q ss_pred CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
|++|.|+|+++.+..++|++ .....|++|.+++...... +..+.|++||.|+|+|+++.
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l--------~~~~~G~v~~s~l~~~~~~--~~~~~~~~Gd~v~~~v~~~d 59 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTL--------GRGVDARVRVSELSDSYLK--DWKKRFKVGQLVKGKIVSID 59 (68)
T ss_pred CCEEEEEEEEEECccEEEEe--------CCCCEEEEEHHHCCchhhc--CHhhccCCCCEEEEEEEEEe
Confidence 79999999999999999999 5569999999999765555 78899999999999999875
No 23
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.88 E-value=5.1e-09 Score=73.32 Aligned_cols=63 Identities=19% Similarity=0.322 Sum_probs=54.0
Q ss_pred CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccc-----------------cccccccCCCCCCEE
Q 032149 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI-----------------DKVDMHLSFRPGDIV 137 (146)
Q Consensus 75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~-----------------d~~~~~~~~~~GDiV 137 (146)
++|++|.|+|+++.+..+++++ .....|++|.+|+...+. +..++.+.|++||+|
T Consensus 2 ~~G~vV~G~V~~v~~~gl~v~L--------~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V 73 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISL--------PNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLV 73 (100)
T ss_pred CCCCEEEEEEEEEcCCCEEEEC--------CCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEE
Confidence 6899999999999999999988 667999999999975431 123588999999999
Q ss_pred EEEEEEee
Q 032149 138 RASVVSFM 145 (146)
Q Consensus 138 ~A~Vis~~ 145 (146)
+|+|+++.
T Consensus 74 ~~kVi~~d 81 (100)
T cd05693 74 RCKVVSLD 81 (100)
T ss_pred EEEEEEcc
Confidence 99999875
No 24
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.85 E-value=1.8e-08 Score=65.76 Aligned_cols=62 Identities=26% Similarity=0.337 Sum_probs=53.1
Q ss_pred CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
++|++|.|+|+++++..|+|++. .....|++|.++++..... ++.+.|++||.|+|+|+++.
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~-------~~~~~g~i~~~~l~~~~~~--~~~~~~~~Gd~v~v~i~~vd 62 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDID-------GTNVSGLCHKSEISDNRVA--DASKLFRVGDKVRAKVLKID 62 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEEC-------CCCeEEEEEHHHCCCCccC--CHhHeecCCCEEEEEEEEEe
Confidence 46999999999999999999992 1368999999999765544 67889999999999999874
No 25
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=98.84 E-value=3e-08 Score=64.63 Aligned_cols=62 Identities=24% Similarity=0.338 Sum_probs=56.4
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
|++|+++.|+|+++.+..++|++ .....|++|.+++.....+ +..+.|++||.|.|+|+++.
T Consensus 2 ~~~G~iv~g~V~~v~~~g~~V~l--------~~~~~g~ip~~~l~~~~~~--~~~~~~~~G~~v~v~v~~vd 63 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDFGVFVDL--------GNGIEGFIPISELSDDRID--DPSEVYKIGQTVRVKVIKVD 63 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEE--------STSSEEEEEGGGSSSSEES--SSHGTCETTCEEEEEEEEEE
T ss_pred CCCCCEEEEEEEEEECCEEEEEE--------CCcEEEEEEeehhcCcccc--ccccccCCCCEEEEEEEEEE
Confidence 68999999999999999999999 6789999999999876555 78999999999999999874
No 26
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.84 E-value=2.1e-08 Score=63.65 Aligned_cols=59 Identities=25% Similarity=0.375 Sum_probs=51.8
Q ss_pred CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
|+++.|+|+++.+..|+|++ ...+.|++|.++++..... ++.+.|++||.|.++|+++.
T Consensus 1 G~~~~g~V~~i~~~g~~v~i--------~~~~~g~l~~~~l~~~~~~--~~~~~~~~Gd~v~v~v~~~~ 59 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVEL--------GGGISGLVHISQIAHKRVK--DVKDVLKEGDKVKVKVLSID 59 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEE--------CCCCEEEEEhHHcCCcccC--CHHHccCCCCEEEEEEEEEC
Confidence 79999999999999999999 5679999999998765544 66788999999999998864
No 27
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=98.83 E-value=2.4e-08 Score=65.58 Aligned_cols=63 Identities=17% Similarity=0.187 Sum_probs=54.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
|+.|+++.|+|+++.+..++|++. .....|++|.+++.....+ +..+.|++||.|+++|+++.
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~-------~~~~eGlvh~sel~~~~~~--~~~~~~~~Gd~v~vkv~~vd 63 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIP-------GCRKQGLVHKSHMSSCRVD--DPSEVVDVGEKVWVKVIGRE 63 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEEC-------CCCeEEEEEchhhCCCccc--CHhhEECCCCEEEEEEEEEC
Confidence 578999999999999999999981 1236899999999876666 88899999999999999874
No 28
>PRK08582 hypothetical protein; Provisional
Probab=98.80 E-value=3.5e-08 Score=73.02 Aligned_cols=62 Identities=23% Similarity=0.310 Sum_probs=55.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
+++|++|.|+|+++++..++|+| .....|++|.+++...+.. ++.+.|++||.|.|+|+++.
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L--------~~~~~GlVhiSels~~~v~--~~~~~l~vGD~VkvkV~~id 64 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVEL--------PEGKTGLVHISEVADNYVK--DINDHLKVGDEVEVKVLNVE 64 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEE--------CCCCEEEEEeeccCccccc--ccccccCCCCEEEEEEEEEC
Confidence 57899999999999999999999 5679999999999866655 67899999999999999874
No 29
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.79 E-value=3.2e-08 Score=65.24 Aligned_cols=61 Identities=21% Similarity=0.170 Sum_probs=52.8
Q ss_pred CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
||+|.|+|+++.+..++|++ .....|++|.+++........+..+.|++||.|.|+|+++.
T Consensus 1 G~~V~g~V~~i~~~g~~V~l--------~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id 61 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTI--------SPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVD 61 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEe--------CCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEe
Confidence 89999999999999999998 66799999999997543223378999999999999999874
No 30
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.78 E-value=3.9e-08 Score=62.17 Aligned_cols=61 Identities=26% Similarity=0.344 Sum_probs=53.1
Q ss_pred CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
++|+++.|+|+++.+..++|++ ...+.|++|.+++...... ++.+.|++||.|+|+|.++.
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i--------~~~~~g~l~~~~~~~~~~~--~~~~~~~~G~~v~~~V~~~~ 61 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDL--------GNGVEGLIPISELSDKRVK--DPEEVLKVGDEVKVKVLSVD 61 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEe--------CCCCEEEEEHHHCCccccC--CHHHeecCCCEEEEEEEEEe
Confidence 4699999999999999999999 5579999999998866544 66788999999999999864
No 31
>PRK07252 hypothetical protein; Provisional
Probab=98.76 E-value=5.5e-08 Score=70.29 Aligned_cols=61 Identities=21% Similarity=0.335 Sum_probs=54.0
Q ss_pred CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
++|+++.|+|+++.+..|+|+| .....|++|.++++..... +..+.|++||.|.|+|+++.
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei--------~~~~~GllhiseLs~~~~~--~~~~~~~vGD~V~VkI~~iD 62 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVAL--------ENGTTGLIHISEIKTGFID--NIHQLLKVGEEVLVQVVDFD 62 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEE--------CCCCEEEEEHHHcCCcccc--ChhhccCCCCEEEEEEEEEe
Confidence 5799999999999999999999 5668999999999865554 67788999999999999874
No 32
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.75 E-value=5.6e-08 Score=61.75 Aligned_cols=59 Identities=20% Similarity=0.234 Sum_probs=51.1
Q ss_pred CCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 76 PGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 76 ~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
+|+++.|+|+++.+..|+|++ . ...|++|.+++...+.. ++.+.|++||.|+|+|+++.
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l--------~-~~~g~l~~~e~~~~~~~--~~~~~~~~Gd~v~v~i~~vd 59 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDL--------G-GVDGLLHISDMSWGRVK--HPSEVVNVGDEVEVKVLKID 59 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEE--------C-CeEEEEEhHHCCCcccc--CHhHEECCCCEEEEEEEEEE
Confidence 489999999999999999998 3 48899999998754444 67788999999999999874
No 33
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.74 E-value=5.7e-08 Score=62.69 Aligned_cols=59 Identities=20% Similarity=0.303 Sum_probs=52.2
Q ss_pred CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
|+++.|+|+++.+..++|++ .....|++|.+++...... +..+.|++||.+.++|+++.
T Consensus 1 g~~~~g~V~~v~~~G~~V~l--------~~~~~gli~~s~l~~~~~~--~~~~~~~~G~~i~v~v~~~d 59 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSF--------YNNVKGFLPKSELSEAFIK--DPEEHFRVGQVVKVKVLSCD 59 (70)
T ss_pred CCEEEEEEEEEecCcEEEEE--------CCCCEEEEEHHHcChhhcC--CHHHcccCCCEEEEEEEEEc
Confidence 89999999999999999999 4568999999999765555 67889999999999999864
No 34
>PRK08059 general stress protein 13; Validated
Probab=98.73 E-value=6.3e-08 Score=69.98 Aligned_cols=62 Identities=27% Similarity=0.345 Sum_probs=55.0
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
+++|++|.|+|+++.+..|+|+| ...+.|++|.++++..... ++.+.|++||.|.|+|+++.
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i--------~~~~~Gli~~sel~~~~~~--~~~~~~~vGD~I~vkI~~id 66 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVAL--------DEETQGLVHISEITHGFVK--DIHDFLSVGDEVKVKVLSVD 66 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEE--------CCCCEEEEEHHHCCccccc--CHHHcCCCCCEEEEEEEEEE
Confidence 57899999999999999999999 5679999999999765554 67889999999999999873
No 35
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=98.69 E-value=1e-07 Score=60.30 Aligned_cols=59 Identities=29% Similarity=0.259 Sum_probs=51.7
Q ss_pred CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
|+++.|+|+++.+..|+|++ .....|++|.++++..... ++.+.|++||.++|+|+++.
T Consensus 1 g~~~~g~V~~i~~~G~fv~l--------~~~~~g~~~~~~l~~~~~~--~~~~~~~~Gd~v~v~i~~vd 59 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDI--------GVKQDGLIHISKMADRFVS--HPSDVVSVGDIVEVKVISID 59 (68)
T ss_pred CCEEEEEEEEEecccEEEEc--------CCCCEEEEEHHHCCCcccc--CHHHhcCCCCEEEEEEEEEE
Confidence 78999999999999999999 5568999999999765555 67788999999999999874
No 36
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=98.69 E-value=6.2e-08 Score=80.41 Aligned_cols=65 Identities=17% Similarity=0.306 Sum_probs=57.6
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEEeecccccc-cceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~-~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
-.|++||+|.|+|++|.+..++|+|. . ....|+||.|++...... ++++.|++||.|.++|+++.
T Consensus 13 ~~P~~GdvV~g~V~~I~d~GafV~L~-------EY~gvEGlIhiSElS~~ri~--~i~d~vkvGd~v~vkVl~VD 78 (319)
T PTZ00248 13 KFPEEDDLVMVKVVRITEMGAYVSLL-------EYDDIEGMILMSELSKRRIR--SINKLIRVGRHEVVVVLRVD 78 (319)
T ss_pred hCCCCCCEEEEEEEEEeCCeEEEEec-------CCCCcEEEEEHHHhcccccC--CHHHhcCCCCEEEEEEEEEe
Confidence 45899999999999999999999992 1 258999999999876666 99999999999999999874
No 37
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.68 E-value=9.9e-08 Score=77.38 Aligned_cols=66 Identities=20% Similarity=0.220 Sum_probs=56.8
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
-.|++||+|.|+|+++.+..|+|++... ....|++|.+++...... ++++.|++||.|.|+|+++.
T Consensus 4 ~~P~~GdiV~G~V~~I~~~G~fV~L~e~------~gieGlI~iSEls~~~i~--~i~~~~kvGd~V~vkVi~VD 69 (262)
T PRK03987 4 EWPEEGELVVGTVKEVKDFGAFVTLDEY------PGKEGFIHISEVASGWVK--NIRDHVKEGQKVVCKVIRVD 69 (262)
T ss_pred CCCCCCCEEEEEEEEEECCEEEEEECCC------CCcEEEEEHHHcCccccc--CHHHhCCCCCEEEEEEEEEe
Confidence 4699999999999999999999999311 157999999999766555 78899999999999999875
No 38
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.68 E-value=1.3e-07 Score=61.03 Aligned_cols=59 Identities=19% Similarity=0.340 Sum_probs=51.9
Q ss_pred CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
|+++.|+|+++.+..++|++ .....|++|.+++...... +..+.|++||.+.++|+++.
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l--------~~~v~g~i~~~~l~~~~~~--~~~~~~~~Gd~i~~~V~~id 59 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKL--------SDHIKGLVPPMHLADVRLK--HPEKKFKPGLKVKCRVLSVE 59 (69)
T ss_pred CCEEEEEEEEEeccEEEEEe--------cCCcEEEEEHHHCCCcccc--CHHHcCCCCCEEEEEEEEEE
Confidence 78999999999999999999 5669999999998765444 67789999999999999874
No 39
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.67 E-value=1.2e-07 Score=63.51 Aligned_cols=62 Identities=21% Similarity=0.285 Sum_probs=55.4
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
+++|+++.|+|+++.+..++|++ .....|++|.++++..... ++.+.|++||.|+++|+++.
T Consensus 12 ~~~G~i~~g~V~~v~~~G~fv~l--------~~~~~g~v~~~el~~~~~~--~~~~~~~~Gd~v~vkV~~id 73 (83)
T cd04461 12 LKPGMVVHGYVRNITPYGVFVEF--------LGGLTGLAPKSYISDEFVT--DPSFGFKKGQSVTAKVTSVD 73 (83)
T ss_pred CCCCCEEEEEEEEEeeceEEEEc--------CCCCEEEEEHHHCCccccc--CHHHhcCCCCEEEEEEEEEc
Confidence 68999999999999999999999 4568999999999765554 78899999999999999864
No 40
>PRK05807 hypothetical protein; Provisional
Probab=98.67 E-value=1.5e-07 Score=69.32 Aligned_cols=61 Identities=20% Similarity=0.316 Sum_probs=54.1
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.++|++|.|+|+++++..|+|++ . ..+|++|++++...+.. +..+.|++||.|.++|+++.
T Consensus 3 ~~vG~vv~G~Vt~i~~~GafV~L--------~-~~~Glvhiseis~~~v~--~~~~~~kvGd~V~VkV~~id 63 (136)
T PRK05807 3 LKAGSILEGTVVNITNFGAFVEV--------E-GKTGLVHISEVADTYVK--DIREHLKEQDKVKVKVISID 63 (136)
T ss_pred ccCCCEEEEEEEEEECCeEEEEE--------C-CEEEEEEhhhccccccc--CccccCCCCCEEEEEEEEEC
Confidence 36899999999999999999998 2 35899999999877766 77899999999999999874
No 41
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=98.61 E-value=2.4e-07 Score=63.39 Aligned_cols=63 Identities=21% Similarity=0.284 Sum_probs=52.0
Q ss_pred CCCCCEEEEEEEEEecc--eEEEEEEeecccccccceeeEEecccccccc-ccccccccCCCCCCEEEEEEEEe
Q 032149 74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATE-IDKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~--~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~-~d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
+++|+++.|+|+++.+. .|+|++ .....|+||.+++.... ....+..+.|++||.|.++|+..
T Consensus 5 ~~~G~iy~g~V~~i~~~~~GaFV~l--------~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~ 70 (88)
T cd04453 5 PIVGNIYLGRVKKIVPGLQAAFVDI--------GLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKE 70 (88)
T ss_pred CCCCCEEEEEEEEeccCCcEEEEEe--------CCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEe
Confidence 58999999999999996 999999 45679999999985411 12226688999999999999874
No 42
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=98.57 E-value=4.1e-07 Score=57.82 Aligned_cols=59 Identities=17% Similarity=0.291 Sum_probs=50.8
Q ss_pred CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
|+++.|+|+++.+..|+|++ .....|++|.++++..... +..+.|++||.|+++|.++.
T Consensus 1 g~~~~g~V~~v~~~G~~v~l--------~~~~~g~l~~~~l~~~~~~--~~~~~~~~Gd~v~v~v~~~d 59 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEI--------LPGKDGLVHISELSDERVE--KVEDVLKVGDEVKVKVIEVD 59 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEe--------CCCCEEEEEhHHcCCcccc--CHHHccCCCCEEEEEEEEEC
Confidence 78999999999999999999 5568999999999755444 55688999999999999864
No 43
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.56 E-value=5.3e-07 Score=58.23 Aligned_cols=57 Identities=25% Similarity=0.387 Sum_probs=49.0
Q ss_pred CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
|++|.|+|+++.++.++|++ ...+.|++|.+++.... . . .+.|++||.|.|+|+.+.
T Consensus 1 G~~V~g~V~~i~~~G~~v~l--------~~~v~g~v~~~~l~~~~-~--~-~~~~~~G~~i~~kVi~id 57 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDF--------LSSFTGTVDFLHLDPEK-S--S-KSTYKEGQKVRARILYVD 57 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEE--------cCCceEEEEHHHcCCcc-C--c-ccCcCCCCEEEEEEEEEe
Confidence 89999999999999999998 45699999999985332 2 2 788999999999999875
No 44
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.56 E-value=4.7e-07 Score=59.21 Aligned_cols=59 Identities=20% Similarity=0.363 Sum_probs=50.8
Q ss_pred CCEEE-EEEEEE-ecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 77 GSVVI-ARVTKV-MTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 77 GdiVi-G~V~~v-~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
|+++- |+|+++ .+..++|++ .....|++|.+++.....+ ...+.|++||.+.|+|+++.
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l--------~~gv~G~i~~s~l~~~~~~--~~~~~~~vG~~v~~kV~~id 61 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFEL--------KDGLLGFVHISHLSDDKVP--SDTGPFKAGTTHKARIIGYS 61 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEe--------CCCCEEEEEHHHCCcchhc--CcccccCCCCEEEEEEEEEe
Confidence 67888 999999 689999999 5568999999999755555 67889999999999999874
No 45
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=98.50 E-value=3.1e-07 Score=80.79 Aligned_cols=61 Identities=25% Similarity=0.310 Sum_probs=57.4
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.++|++|.|.|+++++..|+|+| ..+.|++|++|+.....+ .+++.|++||.|+++|+++.
T Consensus 190 l~~G~vV~G~V~~It~~GafVdi---------gGvdGLlHiseiS~~rv~--~P~~vvkvGd~VkvkVi~~D 250 (541)
T COG0539 190 LEVGEVVEGVVKNITDYGAFVDI---------GGVDGLLHISEISWKRVD--HPSEVVKVGDEVKVKVISLD 250 (541)
T ss_pred CCCCceEEEEEEEeecCcEEEEe---------cCeeeEEehhhccccccC--CHHHhcccCCEEEEEEEEEc
Confidence 68999999999999999999999 449999999999988888 99999999999999999975
No 46
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.50 E-value=6.7e-07 Score=57.29 Aligned_cols=59 Identities=15% Similarity=0.268 Sum_probs=50.0
Q ss_pred CCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccc-ccccccccccCCCCCCEEEEEEEEee
Q 032149 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRA-TEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~-~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
|+++.|+|+++++..++|++ .....|++|.+++.. .... +..+.|++||.|+|+|+++.
T Consensus 1 G~~~~g~V~~i~~~G~fv~l--------~~~~~Glv~~~~l~~~~~~~--~~~~~~~~G~~v~v~v~~id 60 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGL--------DGGIDGLVHISDISWTQRVR--HPSEIYKKGQEVEAVVLNID 60 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEe--------CCCCEEEEEHHHCCCccccC--ChhhEECCCCEEEEEEEEEE
Confidence 78999999999999999999 456899999999873 2223 56788999999999999874
No 47
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=98.45 E-value=1.6e-07 Score=85.01 Aligned_cols=89 Identities=17% Similarity=0.238 Sum_probs=71.0
Q ss_pred CCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEec
Q 032149 35 NGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQ 114 (146)
Q Consensus 35 ~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~ 114 (146)
+|.++++..+..... +.+..|.... ..|++|+++.|+|+++.+..++|+| .....|++|+
T Consensus 589 dG~V~i~~~~~~~~~-------~a~~~I~~~~-----~~~~~G~i~~G~V~~I~~~GafVei--------~~g~~GllHi 648 (684)
T TIGR03591 589 DGTVKIAASDGEAAE-------AAIKMIEGIT-----AEPEVGKIYEGKVVRIMDFGAFVEI--------LPGKDGLVHI 648 (684)
T ss_pred CeEEEEEECcHHHHH-------HHHHHHHhhh-----cccccCcEEEEEEEEEeCCEEEEEE--------CCCcEEEEEH
Confidence 788888887766552 1123444332 2389999999999999999999999 4468999999
Q ss_pred cccccccccccccccCCCCCCEEEEEEEEee
Q 032149 115 QDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 115 sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
|+++....+ +..+.|++||.|+++|+++.
T Consensus 649 Sei~~~~v~--~~~~~~kvGD~V~VkVi~id 677 (684)
T TIGR03591 649 SEIANERVE--KVEDVLKEGDEVKVKVLEID 677 (684)
T ss_pred HHcCCCccc--ChhhccCCCCEEEEEEEEEC
Confidence 999776666 78999999999999999875
No 48
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.42 E-value=2.1e-06 Score=56.78 Aligned_cols=55 Identities=18% Similarity=0.199 Sum_probs=48.4
Q ss_pred CCCCEEEEEEEEEecceEEEEEEeecccccc-cceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~-~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
+.|++|.|.|.++.+..+++++ . ..+.|++|.+++... +.|++||.+.|+|+++.
T Consensus 3 ~~G~~v~g~V~si~d~G~~v~~--------g~~gv~Gfl~~~~~~~~--------~~~~~Gq~v~~~V~~vd 58 (74)
T cd05694 3 VEGMVLSGCVSSVEDHGYILDI--------GIPGTTGFLPKKDAGNF--------SKLKVGQLLLCVVEKVK 58 (74)
T ss_pred CCCCEEEEEEEEEeCCEEEEEe--------CCCCcEEEEEHHHCCcc--------cccCCCCEEEEEEEEEE
Confidence 6799999999999999999998 4 368999999887532 88999999999999874
No 49
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=98.40 E-value=1.1e-06 Score=54.47 Aligned_cols=55 Identities=16% Similarity=0.305 Sum_probs=47.2
Q ss_pred EEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149 80 VIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 80 ViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
+.|+|+++.+..|+|++ .....|++|.+++...... ++.+.|++||.|+|+|+++
T Consensus 1 v~g~V~~v~~~g~~v~l--------~~~~~g~~~~~~~~~~~~~--~~~~~~~~G~~v~~~v~~~ 55 (65)
T cd00164 1 VTGKVVSITKFGVFVEL--------EDGVEGLVHISELSDKFVK--DPSEVFKVGDEVEVKVLEV 55 (65)
T ss_pred CEEEEEEEEeeeEEEEe--------cCCCEEEEEHHHCCCcccc--CHhhEeCCCCEEEEEEEEE
Confidence 47999999999999999 4568999999998755443 5778899999999999986
No 50
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.38 E-value=3.1e-07 Score=83.26 Aligned_cols=89 Identities=17% Similarity=0.249 Sum_probs=71.7
Q ss_pred CCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEec
Q 032149 35 NGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQ 114 (146)
Q Consensus 35 ~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~ 114 (146)
+|.++++..+..... ..+..|+..+. .|++|+++.|+|+++.+..++|+| .....|++|+
T Consensus 592 ~G~v~i~~~~~~~~~-------~a~~~I~~~~~-----~~~vG~v~~G~V~~I~~fGafVei--------~~~~~Gllhi 651 (693)
T PRK11824 592 DGTVKIAATDGEAAE-------AAKERIEGITA-----EPEVGEIYEGKVVRIVDFGAFVEI--------LPGKDGLVHI 651 (693)
T ss_pred CceEEEEcccHHHHH-------HHHHHHHHhcc-----cCcCCeEEEEEEEEEECCeEEEEE--------CCCCEEEEEe
Confidence 788888888877662 12334444432 278999999999999999999999 4568999999
Q ss_pred cccccccccccccccCCCCCCEEEEEEEEee
Q 032149 115 QDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 115 sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
++++..... +..+.|++||.|+++|+++.
T Consensus 652 Sels~~~v~--~~~~v~kvGD~V~VkV~~iD 680 (693)
T PRK11824 652 SEIADERVE--KVEDVLKEGDEVKVKVLEID 680 (693)
T ss_pred eeccCcccc--CccceeCCCCEEEEEEEEEC
Confidence 999866666 77899999999999999874
No 51
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.35 E-value=2.1e-06 Score=71.35 Aligned_cols=62 Identities=23% Similarity=0.329 Sum_probs=54.9
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 73 ~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
-+++|++|.|+|+++++..++|++ ....|++|.+++...... ++.+.|++||.|+|+|+++.
T Consensus 193 ~~k~G~vv~G~V~~I~~~G~fV~i---------~gv~Gllhisels~~~~~--~~~~~~~vGd~VkvkVl~iD 254 (318)
T PRK07400 193 RLEVGEVVVGTVRGIKPYGAFIDI---------GGVSGLLHISEISHEHIE--TPHSVFNVNDEMKVMIIDLD 254 (318)
T ss_pred cCCCCCEEEEEEEEEECCeEEEEE---------CCEEEEEEHHHccccccc--ChhhccCCCCEEEEEEEEEe
Confidence 368999999999999999999998 246799999999876655 78899999999999999874
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=98.34 E-value=3.8e-06 Score=54.39 Aligned_cols=62 Identities=16% Similarity=0.256 Sum_probs=51.3
Q ss_pred CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.+|+++.|+|+++++..++|++ ....+|++|.+++...+ ...+..+.|+.||.|+++|+++.
T Consensus 2 ~~g~~~~g~V~~i~~~G~fv~l--------~~~~~Gl~~~~~l~~~~-~~~~~~~~~~~Gd~v~v~v~~id 63 (72)
T cd05689 2 PEGTRLFGKVTNLTDYGCFVEL--------EEGVEGLVHVSEMDWTN-KNIHPSKVVSLGDEVEVMVLDID 63 (72)
T ss_pred cCCCEEEEEEEEEEeeEEEEEc--------CCCCEEEEEEEeccCcc-cccCcccEeCCCCEEEEEEEEee
Confidence 4699999999999999999999 45689999999986321 12256688999999999999864
No 53
>PHA02945 interferon resistance protein; Provisional
Probab=98.34 E-value=2.8e-06 Score=58.11 Aligned_cols=62 Identities=15% Similarity=0.166 Sum_probs=52.1
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEEeeccccccc-ceeeEEecccc--ccccccccccccCCCCCCEEEEEEEEee
Q 032149 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDV--RATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~sdi--~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
-.|++|++|+|+|+. .+..++|.+. .. ..+|+||.|++ .+.-.. + ++.+ .|..|.|||+.+.
T Consensus 7 ~~P~~GelvigtV~~-~d~ga~v~L~-------EY~g~eg~i~~seveva~~wvK--~-rd~l-~GqkvV~KVirVd 71 (88)
T PHA02945 7 SLPNVGDVLKGKVYE-NGYALYIDLF-------DYPHSEAILAESVQMHMNRYFK--Y-RDKL-VGKTVKVKVIRVD 71 (88)
T ss_pred cCCCCCcEEEEEEEe-cCceEEEEec-------ccCCcEEEEEeehhhhccceEe--e-eeEe-cCCEEEEEEEEEC
Confidence 359999999999999 9999999983 22 47899999955 665555 5 9999 9999999999864
No 54
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=98.29 E-value=5e-06 Score=54.99 Aligned_cols=61 Identities=15% Similarity=0.238 Sum_probs=50.1
Q ss_pred CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccc-cccccccCCCCCCEEEEEEEEe
Q 032149 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI-DKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~-d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
|+++.|+|+++.+..++|+|... .....|++|.+++..... . +..+.|++||.|+++|.++
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~-----~~~~~gll~~s~l~~~~~~~--~~~~~~~~Gd~v~v~v~~v 62 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGL-----KGRKEGLVHISQLSFEGRVA--NPSDVVKRGQKVKVKVISI 62 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCC-----CCCcEEEEEhHhccCCCCcC--ChhheeCCCCEEEEEEEEE
Confidence 78999999999999999999200 025789999999975543 4 6788999999999999886
No 55
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.28 E-value=1.5e-06 Score=70.06 Aligned_cols=66 Identities=21% Similarity=0.265 Sum_probs=58.9
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEEeeccccccc-ceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
+-.|..|++|+|+|.+|.+..|+|.+. -+ ...|++|.|++...-+. +++++++.|..+.|+|+++.
T Consensus 6 ~~~PeeGEiVv~tV~~V~~~GAyv~L~-------EY~g~Eg~ihiSEvas~wVk--nIrd~vkegqkvV~kVlrVd 72 (269)
T COG1093 6 REYPEEGEIVVGTVKQVADYGAYVELD-------EYPGKEGFIHISEVASGWVK--NIRDYVKEGQKVVAKVLRVD 72 (269)
T ss_pred cCCCCCCcEEEEEEEEeeccccEEEee-------ccCCeeeeEEHHHHHHHHHH--HHHHHhhcCCeEEEEEEEEc
Confidence 457999999999999999999999983 23 37899999999888778 99999999999999999874
No 56
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.27 E-value=3e-06 Score=76.89 Aligned_cols=65 Identities=14% Similarity=0.197 Sum_probs=55.1
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccc--ccccccccccCCCCCCEEEEEEEEee
Q 032149 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRA--TEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 73 ~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~--~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.|++|+++.|+|+++.+..++|+| .....|++|+|++.. +.....++.+.|++||.|.++|+++.
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel--------~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID 710 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSL--------LPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADID 710 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEe--------cCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEEC
Confidence 489999999999999999999999 456899999999852 22222388999999999999999874
No 57
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=98.22 E-value=9.2e-06 Score=52.40 Aligned_cols=54 Identities=24% Similarity=0.391 Sum_probs=46.5
Q ss_pred CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
+.|++|.|+|.++..+.++|+| .. ..|+|+.++... .+.|++||.|.+.|.++.
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdi--------g~-~eg~lp~~e~~~--------~~~~~~Gd~v~v~v~~v~ 55 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDL--------GK-VEAILPKKEQIP--------GESYRPGDRIKAYVLEVR 55 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEc--------CC-eEEEeeHHHCCC--------CCcCCCCCEEEEEEEEEe
Confidence 5799999999999999999998 44 899999888742 456899999999998863
No 58
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=98.19 E-value=2.2e-05 Score=51.98 Aligned_cols=53 Identities=21% Similarity=0.324 Sum_probs=47.4
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
++.|+.+.|+|+++++..+++++ .....|++|.+++ .+.|+.||.+.++|.++
T Consensus 14 ~~~G~~~~g~V~~i~~~G~fV~l--------~~~~~Glv~~se~----------~~~~~iGd~v~v~I~~i 66 (77)
T cd04473 14 LEVGKLYKGKVNGVAKYGVFVDL--------NDHVRGLIHRSNL----------LRDYEVGDEVIVQVTDI 66 (77)
T ss_pred CCCCCEEEEEEEeEecceEEEEE--------CCCcEEEEEchhc----------cCcCCCCCEEEEEEEEE
Confidence 68999999999999999999999 5569999998774 45699999999999886
No 59
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.16 E-value=8.3e-06 Score=67.76 Aligned_cols=63 Identities=19% Similarity=0.216 Sum_probs=56.3
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
+-.++|++|.|+|+++..+.++|+| .....|++|.+|+...+.. ++.+.|++||.|.++|++.
T Consensus 27 ~~~~~G~iv~G~V~~i~~~g~~Vdi--------g~k~~g~lp~sEis~~~~~--~~~~~~~~G~~v~~~Vi~~ 89 (318)
T PRK07400 27 YHFKPGDIVNGTVFSLEPRGALIDI--------GAKTAAFMPIQEMSINRVE--GPEEVLQPNETREFFILSD 89 (318)
T ss_pred hhcCCCCEEEEEEEEEECCEEEEEE--------CCCeEEEEEHHHhcccccc--CHHHccCCCCEEEEEEEEE
Confidence 3369999999999999999999999 6678999999999876666 7889999999999999975
No 60
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.11 E-value=2.6e-05 Score=59.86 Aligned_cols=65 Identities=25% Similarity=0.300 Sum_probs=52.2
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccccc--c-------cccccCCCCCCEEEEEEE
Q 032149 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID--K-------VDMHLSFRPGDIVRASVV 142 (146)
Q Consensus 72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d--~-------~~~~~~~~~GDiV~A~Vi 142 (146)
+.|.+|+++.|+|+++....+++++ .+++|+++.+++...... . .+....|+.||.|++||.
T Consensus 77 f~P~~GEVv~g~V~~v~~~Gi~V~l---------g~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~ 147 (187)
T PRK08563 77 FKPELQEVVEGEVVEVVEFGAFVRI---------GPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIV 147 (187)
T ss_pred EeccCCCEEEEEEEEEEccEEEEEE---------eCceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEE
Confidence 4489999999999999999999998 368999999988643211 0 134567899999999998
Q ss_pred Eee
Q 032149 143 SFM 145 (146)
Q Consensus 143 s~~ 145 (146)
++.
T Consensus 148 ~v~ 150 (187)
T PRK08563 148 AVS 150 (187)
T ss_pred EEE
Confidence 864
No 61
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.09 E-value=1.1e-05 Score=70.42 Aligned_cols=62 Identities=19% Similarity=0.296 Sum_probs=55.5
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.++|++|.|+|+++.+..++|+| .....|++|.+++...... ++.+.|++||.|+|+|+++.
T Consensus 200 l~~G~iv~G~V~~v~~~G~fV~l--------~~gv~g~v~~sels~~~~~--~~~~~~~vGd~i~vkVl~id 261 (491)
T PRK13806 200 VKEGDVVEGTVTRLAPFGAFVEL--------APGVEGMVHISELSWSRVQ--KADEAVSVGDTVRVKVLGIE 261 (491)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEc--------CCCcEEEEEHHHCCCcccc--ChhHhcCCCCEEEEEEEEEe
Confidence 68999999999999999999998 4568999999999876656 78899999999999999764
No 62
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.08 E-value=1.2e-05 Score=70.39 Aligned_cols=62 Identities=18% Similarity=0.201 Sum_probs=54.7
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
..+|++|.|+|+++++..++|++ .....|++|.+++...... +..+.|++||.|.|+|+++.
T Consensus 377 ~~vG~~v~G~V~~i~~~G~FV~l--------~~gv~Gli~~se~s~~~~~--~~~~~~~~Gd~v~~~V~~id 438 (491)
T PRK13806 377 FAPGTTVTGTVEKRAQFGLFVNL--------APGVTGLLPASVISRAGKP--ATYEKLKPGDSVTLVVEEID 438 (491)
T ss_pred CCCCCEEEEEEEEEecCceEEEc--------CCCcEEEEEHHHcCccccc--chhhcCCCCCEEEEEEEEEe
Confidence 35799999999999999999999 5579999999999865554 77899999999999999874
No 63
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.99 E-value=2.3e-05 Score=68.60 Aligned_cols=61 Identities=18% Similarity=0.210 Sum_probs=54.3
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.++|++|.|+|+++++..++|+| . ...|++|.+++.....+ ++.+.|++||.|.++|+++.
T Consensus 206 lk~G~iv~G~V~~i~~~G~FVdl--------g-gv~Glv~~Sels~~~v~--~~~~~~kvGd~V~vkVl~iD 266 (486)
T PRK07899 206 LQKGQVRKGVVSSIVNFGAFVDL--------G-GVDGLVHVSELSWKHID--HPSEVVEVGQEVTVEVLDVD 266 (486)
T ss_pred ccCCCEEEEEEEEEECCeEEEEE--------C-CEEEEEEHHHCCCcccC--CHHHhcCCCCEEEEEEEEEE
Confidence 46899999999999999999999 3 48899999999876666 78899999999999999864
No 64
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.99 E-value=4.8e-05 Score=48.67 Aligned_cols=56 Identities=18% Similarity=0.290 Sum_probs=46.1
Q ss_pred CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
|++|.|+|+++.+..++|++ ....|++|.+++...... +..+ .+||.+.|+|+++.
T Consensus 1 G~iv~g~V~~v~~~G~~v~l---------~g~~gfip~s~~~~~~~~--~~~~--~vG~~i~~~i~~vd 56 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI---------EGVRAFLPASQVDLRPVE--DLDE--YVGKELKFKIIEID 56 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE---------CCEEEEEEHHHCCCcccC--ChHH--hCCCEEEEEEEEEe
Confidence 78999999999999999997 358999999998755443 3333 38999999999874
No 65
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.95 E-value=2.6e-05 Score=68.89 Aligned_cols=62 Identities=26% Similarity=0.439 Sum_probs=55.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.++|++|.|+|+++.+..++|.+ .....|++|.+++...... ++.+.|++||.|+|+|+++.
T Consensus 458 ~~~G~vV~G~V~~v~~~G~fV~l--------~~gi~g~i~~se~s~~~~~--~~~~~~~~Gd~v~~~V~~vd 519 (565)
T PRK06299 458 HKKGSIVTGTVTEVKDKGAFVEL--------EDGVEGLIRASELSRDRVE--DATEVLKVGDEVEAKVINID 519 (565)
T ss_pred cCCCCEEEEEEEEEecCceEEec--------CCCcEEEEEHHHhcchhcc--CccccCCCCCEEEEEEEEEc
Confidence 37899999999999999999998 4578999999999877666 88999999999999999864
No 66
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=97.94 E-value=1.9e-05 Score=60.87 Aligned_cols=64 Identities=30% Similarity=0.340 Sum_probs=52.8
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccccc-----ccc----cccCCCCCCEEEEEEE
Q 032149 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID-----KVD----MHLSFRPGDIVRASVV 142 (146)
Q Consensus 72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d-----~~~----~~~~~~~GDiV~A~Vi 142 (146)
+.|..|.+|-|.|+++....++|.| .|+.|++|.+++...+.+ ... -...|+.||.|||||+
T Consensus 77 fkP~~gEVV~GeVv~~~~~G~fV~i---------gp~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv 147 (183)
T COG1095 77 FKPFRGEVVEGEVVEVVEFGAFVRI---------GPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIV 147 (183)
T ss_pred EEeccccEEEEEEEEEeecceEEEe---------ccccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEE
Confidence 4588999999999999999999999 699999999999754321 112 2338999999999999
Q ss_pred Ee
Q 032149 143 SF 144 (146)
Q Consensus 143 s~ 144 (146)
+.
T Consensus 148 ~~ 149 (183)
T COG1095 148 GV 149 (183)
T ss_pred EE
Confidence 75
No 67
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.94 E-value=3.5e-05 Score=65.11 Aligned_cols=61 Identities=20% Similarity=0.250 Sum_probs=53.5
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.++|++|.|+|+++.+..++|++ . ...|++|.+++.....+ ++.+.|++||.|.|+|+++.
T Consensus 190 ~~~G~~v~g~V~~v~~~G~fV~l--------~-~v~g~v~~sels~~~~~--~~~~~~~vGd~i~~~Vl~vd 250 (390)
T PRK06676 190 LKEGDVVEGTVARLTDFGAFVDI--------G-GVDGLVHISELSHERVE--KPSEVVSVGQEVEVKVLSID 250 (390)
T ss_pred CCCCCEEEEEEEEEecceEEEEe--------C-CeEEEEEHHHcCccccC--CHHHhcCCCCEEEEEEEEEe
Confidence 58999999999999999999998 2 47899999999865555 77889999999999999863
No 68
>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=97.93 E-value=4.4e-05 Score=58.35 Aligned_cols=65 Identities=25% Similarity=0.342 Sum_probs=52.2
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccc--ccc-------ccccCCCCCCEEEEEEE
Q 032149 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI--DKV-------DMHLSFRPGDIVRASVV 142 (146)
Q Consensus 72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~--d~~-------~~~~~~~~GDiV~A~Vi 142 (146)
+.|.+|+++.|+|+++++..+++++ .+++|+++.+++...+. |.. +....|+.||.|++||.
T Consensus 77 f~p~~gEvv~G~V~~v~~~GifV~l---------g~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~ 147 (179)
T TIGR00448 77 FKPELGEIVEGEVIEIVEFGAFVSL---------GPFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIV 147 (179)
T ss_pred EeccCCCEEEEEEEEEEeeEEEEEe---------CCceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEE
Confidence 4488999999999999999999998 46999999998863321 111 23468999999999999
Q ss_pred Eee
Q 032149 143 SFM 145 (146)
Q Consensus 143 s~~ 145 (146)
++.
T Consensus 148 ~v~ 150 (179)
T TIGR00448 148 ALS 150 (179)
T ss_pred EEE
Confidence 863
No 69
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.91 E-value=4.2e-05 Score=66.99 Aligned_cols=61 Identities=26% Similarity=0.221 Sum_probs=53.7
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
.+.||+|.|+|+++..+.++|+| .....|+|+.+++...... ++.+.|++||.|.|+|+++
T Consensus 33 ~~~GdiV~G~V~~v~~~gv~VdI--------g~k~eG~Ip~~Els~~~~~--~~~~~~~vGd~Ie~~V~~~ 93 (486)
T PRK07899 33 FNDGDIVEGTVVKVDRDEVLLDI--------GYKTEGVIPSRELSIKHDV--DPNEVVEVGDEVEALVLQK 93 (486)
T ss_pred CCCCCEEEEEEEEEECCcEEEEE--------CCCcEEEEEHHHhcccccC--ChhhcCCCCCEEEEEEEEE
Confidence 58999999999999999999999 6678999999998764433 6788899999999999975
No 70
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=97.90 E-value=3.5e-05 Score=71.55 Aligned_cols=63 Identities=19% Similarity=0.172 Sum_probs=53.8
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
..+|++|.|+|+++.+..++|++ .....|++|.+|+... .+..++.+.|++||.|.|+|+++.
T Consensus 576 ~~vG~iV~G~V~~I~~fG~fVeL--------~~gveGLvhiSEls~~-~~~~~p~~~~kvGd~V~vkVl~iD 638 (863)
T PRK12269 576 FGVNDVVKGRVTKIADFGAFIEL--------AEGIEGLAHISEFSWV-KKTSKPSDMVKIGDEVECMILGYD 638 (863)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEe--------cCCceeeeEHHHhcCc-cccCCHHHcCCCCCEEEEEEEEEe
Confidence 57899999999999999999999 5578999999999742 122277889999999999999874
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=97.88 E-value=9.4e-05 Score=48.69 Aligned_cols=62 Identities=18% Similarity=0.203 Sum_probs=48.6
Q ss_pred CCCEEEEEEEEEecceEEEEEEeeccccccc-ceeeEEeccccccccc--cc-------cccccCCCCCCEEEEEEEEee
Q 032149 76 PGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEI--DK-------VDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 76 ~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~sdi~~~~~--d~-------~~~~~~~~~GDiV~A~Vis~~ 145 (146)
+|+++.|+|+++++..++|++ .. ...|++|.+++..... |. ......|++||.|+++|+++.
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l--------~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd 72 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVEL--------DNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVD 72 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEe--------cCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEec
Confidence 389999999999999999999 33 5889999998863210 10 133578999999999999864
No 72
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=97.87 E-value=3.5e-05 Score=68.05 Aligned_cols=62 Identities=19% Similarity=0.206 Sum_probs=57.1
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
..+|+.+.|+|+++++..|+++| .....|++|+|++...... ...+.++.||.|.++|+++.
T Consensus 275 ~~~g~~v~G~Vt~i~~~GafVei--------~~GvEGlvhvSEisw~~~~--~P~evv~~Gq~V~V~Vl~id 336 (541)
T COG0539 275 YPVGDKVEGKVTNLTDYGAFVEI--------EEGVEGLVHVSEISWTKKN--VPSEVVKVGQEVEVKVLDID 336 (541)
T ss_pred cCCCCEEEEEEEEeecCcEEEEe--------cCCccceeechhhcccccC--CHHHhcccCCEEEEEEEeeC
Confidence 47899999999999999999999 6889999999999988777 59999999999999999864
No 73
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.84 E-value=7.2e-05 Score=63.19 Aligned_cols=62 Identities=15% Similarity=0.212 Sum_probs=53.8
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.++|+++.|+|+++.+..++|++ .....|++|.+++...... +..+.|++||.|.|+|+++.
T Consensus 275 ~~~G~~v~g~V~~i~~~G~fV~l--------~~gi~Glv~~se~~~~~~~--~~~~~~~~Gd~v~v~V~~id 336 (390)
T PRK06676 275 LPEGDVIEGTVKRLTDFGAFVEV--------LPGVEGLVHISQISHKHIA--TPSEVLEEGQEVKVKVLEVN 336 (390)
T ss_pred hcCCcEEEEEEEEEeCceEEEEE--------CCCCeEEEEhHHcCccccC--ChhhccCCCCEEEEEEEEEE
Confidence 57899999999999999999998 4568999999998755444 67788999999999999874
No 74
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.84 E-value=4.4e-05 Score=70.81 Aligned_cols=63 Identities=14% Similarity=0.256 Sum_probs=55.1
Q ss_pred CCCCCCEEE-EEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 73 VPEPGSVVI-ARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 73 ~P~~GdiVi-G~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.|++|+++. |+|++|.+..+||+| ....+|++|+|++...... +..+.|++||.|.++|+++.
T Consensus 750 ~~~vG~iy~~g~V~~I~~FGaFVeL--------~~g~EGLVHISeLs~~rv~--~~~dv~kvGD~V~VkVi~ID 813 (891)
T PLN00207 750 VPTVGDIYRNCEIKSIAPYGAFVEI--------APGREGLCHISELSSNWLA--KPEDAFKVGDRIDVKLIEVN 813 (891)
T ss_pred CcCCCcEEECcEEEEEeccEEEEEe--------CCCCEEEEEhhhcCCcccc--CHHHhcCCCCEEEEEEEEEC
Confidence 389999995 699999999999999 4457999999999866555 77899999999999999874
No 75
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.82 E-value=7.8e-05 Score=65.88 Aligned_cols=61 Identities=23% Similarity=0.301 Sum_probs=54.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.++|+++-|+|+++.+..++|++ . ...|++|.+++...... ++.+.|++||.|.|+|+++.
T Consensus 199 l~~G~iv~g~V~~v~~~G~~V~i--------~-g~~glv~~se~s~~~~~--~~~~~~kvG~~v~v~V~~~d 259 (565)
T PRK06299 199 LEEGQVVEGVVKNITDYGAFVDL--------G-GVDGLLHITDISWKRVN--HPSEVVNVGDEVKVKVLKFD 259 (565)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEE--------C-CEEEEEEHHHhcccccC--CHhhcCCCCCEEEEEEEEEe
Confidence 68999999999999999999999 4 68999999999766555 78899999999999999863
No 76
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=97.81 E-value=6.8e-05 Score=65.39 Aligned_cols=62 Identities=27% Similarity=0.336 Sum_probs=55.1
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.++|++|.|+|+++++..++|.+ ...+.|++|.+++.....+ ++.+.|++||.|.|+|+++.
T Consensus 444 ~~~G~~v~g~V~~v~~~G~fV~l--------~~~~~Glv~~s~l~~~~~~--~~~~~~~~Gd~v~~~V~~id 505 (516)
T TIGR00717 444 YKVGSVVKGKVTEIKDFGAFVEL--------PGGVEGLIRNSELSENRDE--DKTDEIKVGDEVEAKVVDID 505 (516)
T ss_pred cCcceEEEEEEEEEecceEEEEc--------CCCeEEEEEHHHcCccccc--cccccCCCCCEEEEEEEEEe
Confidence 36899999999999999999998 5669999999999876655 78999999999999999863
No 77
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.77 E-value=9.2e-05 Score=66.77 Aligned_cols=61 Identities=18% Similarity=0.281 Sum_probs=53.4
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.++|++|.|+|+++.+..++|++ ....|++|.++++..... ++.+.|++||.|.|+|+++.
T Consensus 475 l~~G~iV~g~V~~v~~~G~fV~l---------~gv~Gll~~sels~~~~~--~~~~~~~vGd~V~vkV~~id 535 (647)
T PRK00087 475 LEEGDVVEGEVKRLTDFGAFVDI---------GGVDGLLHVSEISWGRVE--KPSDVLKVGDEIKVYILDID 535 (647)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEE---------CCEEEEEEHHHcCccccC--CHHHhcCCCCEEEEEEEEEE
Confidence 47899999999999999999998 347899999999865555 77889999999999999874
No 78
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=97.75 E-value=0.00016 Score=49.95 Aligned_cols=59 Identities=24% Similarity=0.305 Sum_probs=46.0
Q ss_pred CEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccccccc---------ccccCCCCCCEEEEEEEEee
Q 032149 78 SVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKV---------DMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 78 diViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~---------~~~~~~~~GDiV~A~Vis~~ 145 (146)
+++.|+|+++.+..++|++ . +..|++|.++++..+.... .....|++||.|+++|.++.
T Consensus 1 ~vv~g~V~~i~~~GifV~l--------~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd 68 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRI--------G-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVS 68 (99)
T ss_pred CEEEEEEEEEEeccEEEEE--------c-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEe
Confidence 4789999999999999999 2 4789999988864432210 12467899999999998874
No 79
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.68 E-value=0.00015 Score=65.33 Aligned_cols=61 Identities=18% Similarity=0.321 Sum_probs=54.2
Q ss_pred CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
++|++|.|+|+++++..++|++ .....|++|.++++..... ++.+.|++||.|+|+|+++.
T Consensus 561 ~~G~~v~g~V~~i~~~G~fV~l--------~~~i~Gli~~sel~~~~~~--~~~~~~kvGd~V~vkV~~id 621 (647)
T PRK00087 561 PVGSIVLGKVVRIAPFGAFVEL--------EPGVDGLVHISQISWKRID--KPEDVLSEGEEVKAKILEVD 621 (647)
T ss_pred cCCeEEEEEEEEEECCeEEEEE--------CCCCEEEEEhhhcCccccC--CHhhcCCCCCEEEEEEEEEe
Confidence 6899999999999999999998 5579999999999865555 77889999999999999874
No 80
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=97.61 E-value=0.00025 Score=61.90 Aligned_cols=62 Identities=19% Similarity=0.247 Sum_probs=53.3
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 73 ~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
-.++|++|.|+|+++.+..++|++ . ...|++|.+++...... ++.+.|++||.|.|+|+++.
T Consensus 184 ~l~~G~~v~g~V~~i~~~G~~V~l--------~-g~~g~lp~~e~s~~~~~--~~~~~~~vG~~v~v~Vl~~d 245 (516)
T TIGR00717 184 NLKEGDVVKGVVKNITDFGAFVDL--------G-GVDGLLHITDMSWKRVK--HPSEYVKVGQEVKVKVIKFD 245 (516)
T ss_pred hccCCCEEEEEEEEEECCeEEEEE--------C-CEEEEEEHHHcCCCCCC--CHHHhccCCCEEEEEEEEEE
Confidence 368999999999999999999998 3 47899999998765555 67888999999999998764
No 81
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=97.55 E-value=0.00028 Score=65.62 Aligned_cols=61 Identities=15% Similarity=0.168 Sum_probs=53.8
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.++|++|.|+|.++.+..++|++ ....|++|.+++...... ++.+.|++|+.|.|+|+++.
T Consensus 491 l~~G~~V~G~Vk~i~~~G~fVdl---------~Gv~Gfvp~SeiS~~~v~--~~~~~~kvGq~v~vkVi~iD 551 (863)
T PRK12269 491 VHIEDSVSGVVKSFTSFGAFIDL---------GGFDGLLHVNDMSWGHVA--RPREFVKKGQTIELKVIRLD 551 (863)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEE---------CCEEEEEEchhccccccC--CHHHhccCCCEEEEEEEEEe
Confidence 57899999999999999999998 357899999999876655 77899999999999999874
No 82
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=97.49 E-value=0.00022 Score=65.14 Aligned_cols=62 Identities=23% Similarity=0.324 Sum_probs=57.3
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.++|.++.|.|+.+.+..++|+| +-...|++|+|+....... +..+.+++||+|.++|+++.
T Consensus 656 Lk~Gm~leg~Vrnv~~fgafVdI--------gv~qDglvHis~ls~~fv~--~P~~vv~vGdiV~v~V~~vD 717 (780)
T COG2183 656 LKPGMILEGTVRNVVDFGAFVDI--------GVHQDGLVHISQLSDKFVK--DPNEVVKVGDIVKVKVIEVD 717 (780)
T ss_pred ccCCCEEEEEEEEeeeccceEEe--------ccccceeeeHHHhhhhhcC--ChHHhcccCCEEEEEEEEEe
Confidence 59999999999999999999999 7788999999999887777 77999999999999999874
No 83
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.37 E-value=0.00081 Score=51.57 Aligned_cols=64 Identities=19% Similarity=0.155 Sum_probs=50.0
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccc-cc---c--c----ccccCCCCCCEEEEEE
Q 032149 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATE-ID---K--V----DMHLSFRPGDIVRASV 141 (146)
Q Consensus 72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~-~d---~--~----~~~~~~~~GDiV~A~V 141 (146)
+.|-.|+++.|+|+++....+++++ .++++.+|.+++.... -| . . +-...++.||.||+||
T Consensus 77 FrPf~gEVv~g~V~~v~~~G~~v~~---------Gp~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV 147 (176)
T PTZ00162 77 FKPFKDEVLDAIVTDVNKLGFFAQA---------GPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRL 147 (176)
T ss_pred EecCCCCEEEEEEEEEecceEEEEe---------eCeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEE
Confidence 4489999999999999999999998 6788888888885211 01 1 1 1245789999999999
Q ss_pred EEe
Q 032149 142 VSF 144 (146)
Q Consensus 142 is~ 144 (146)
.++
T Consensus 148 ~~v 150 (176)
T PTZ00162 148 QGV 150 (176)
T ss_pred EEE
Confidence 875
No 84
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=97.34 E-value=0.0013 Score=44.83 Aligned_cols=60 Identities=20% Similarity=0.156 Sum_probs=41.8
Q ss_pred CCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccc----cc--c---ccccCCCCCCEEEEEEEEe
Q 032149 76 PGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEI----DK--V---DMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 76 ~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~----d~--~---~~~~~~~~GDiV~A~Vis~ 144 (146)
+|+++.|+|+++....+++++. |..++++.+++.+... .. . +-...+++||.||+||+++
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G---------pl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v 69 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG---------PLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGT 69 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc---------CceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEE
Confidence 4899999999999999999994 4444444444431110 00 0 1245689999999999875
No 85
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=97.30 E-value=0.00068 Score=59.25 Aligned_cols=56 Identities=25% Similarity=0.340 Sum_probs=49.2
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
|..+.|++|.|+|.++....++|++ ....|+||.++.. ..+.|++||.|+|.|+++
T Consensus 130 yk~~~GeIV~G~V~ri~~~giiVDL---------ggvea~LP~sE~i--------p~E~~~~GdrIka~I~~V 185 (470)
T PRK09202 130 YKDRVGEIITGVVKRVERGNIIVDL---------GRAEAILPRKEQI--------PRENFRPGDRVRAYVYEV 185 (470)
T ss_pred HHhhcCCEEEEEEEEEecCCEEEEE---------CCeEEEecHHHcC--------CCccCCCCCEEEEEEEEE
Confidence 4567999999999999999999998 4589999988863 477899999999999986
No 86
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.08 E-value=0.0016 Score=55.24 Aligned_cols=58 Identities=16% Similarity=0.251 Sum_probs=48.7
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.|..+.|++|.|+|.++..+.|+|++ . ...|+||.++.. ..+.|++||.|+|.|.++.
T Consensus 129 ef~~k~GeiV~G~V~~~~~~~~~Vdl--------g-~vEa~LP~~E~i--------p~e~~~~Gd~Ika~V~~V~ 186 (362)
T PRK12327 129 EFSEREGDIVTGVVQRRDNRFVYVNL--------G-KIEAVLPPAEQI--------PGETYKHGDRIKVYVVKVE 186 (362)
T ss_pred HHHHhcCCEEEEEEEEEeCCcEEEEe--------C-CeEEEecHHHcC--------CCCCCCCCCEEEEEEEEEe
Confidence 35679999999999999999999998 3 388999965542 2677999999999999864
No 87
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=97.06 E-value=0.002 Score=55.55 Aligned_cols=62 Identities=24% Similarity=0.337 Sum_probs=50.0
Q ss_pred CCCCCEEEEEEEEEecc--eEEEEEEeecccccccceeeEEecccccccc----------ccccccccCCCCCCEEEEEE
Q 032149 74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATE----------IDKVDMHLSFRPGDIVRASV 141 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~--~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~----------~d~~~~~~~~~~GDiV~A~V 141 (146)
+.+|++..|+|+++.+. .|||+| ...-.|+||.+|+.... ...-++.+.+++||.|.++|
T Consensus 23 ~~vGnIY~GrV~~i~p~l~aAFVdi--------G~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV 94 (414)
T TIGR00757 23 QLKGNIYKGRVTRILPSLQAAFVDI--------GLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQV 94 (414)
T ss_pred CCCCCEEEEEEeeecCCCceEEEEc--------CCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEE
Confidence 46899999999999998 899999 66778999999985321 01114567899999999999
Q ss_pred EE
Q 032149 142 VS 143 (146)
Q Consensus 142 is 143 (146)
..
T Consensus 95 ~K 96 (414)
T TIGR00757 95 VK 96 (414)
T ss_pred ee
Confidence 75
No 88
>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=96.94 E-value=0.0027 Score=53.42 Aligned_cols=58 Identities=22% Similarity=0.312 Sum_probs=47.7
Q ss_pred CCCCCCCCEEEEEEEEEecce-EEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 71 GPVPEPGSVVIARVTKVMTRM-ASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 71 ~~~P~~GdiViG~V~~v~~~~-~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.|..+.|++|.|+|.++..+. |+|+| ....|+|+.++... .+.|++||.++|.|.++.
T Consensus 126 ey~~k~GeiV~G~V~~v~~~g~v~Vdi---------G~~ea~LP~~E~ip--------~E~~~~Gd~ik~~V~~V~ 184 (341)
T TIGR01953 126 EFSSKEGEIISGTVKRVNRRGNLYVEL---------GKTEGILPKKEQIP--------GEKFRIGDRIKAYVYEVR 184 (341)
T ss_pred HHHhhcCCEEEEEEEEEecCCcEEEEE---------CCeEEEecHHHcCC--------CcCCCCCCEEEEEEEEEE
Confidence 355689999999999998865 79998 35899999877643 445999999999999864
No 89
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.64 E-value=0.0046 Score=56.01 Aligned_cols=63 Identities=16% Similarity=0.256 Sum_probs=56.4
Q ss_pred CCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 73 ~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
-+++|.+-.|+|+++.+..++|.+ ...-.|++|+|++....++ +..+.++.||.|+.||+++.
T Consensus 616 e~evg~iy~G~V~ri~~fGaFv~l--------~~gkdgl~hiS~~~~~rv~--kv~dvlk~Gd~v~Vkv~~iD 678 (692)
T COG1185 616 EVEVGEVYEGTVVRIVDFGAFVEL--------LPGKDGLVHISQLAKERVE--KVEDVLKEGDEVKVKVIEID 678 (692)
T ss_pred hcccccEEEEEEEEEeecceEEEe--------cCCcceeEEehhhhhhhhh--cccceeecCceEEEEEeeec
Confidence 389999999999999999999999 4667899999999877666 77899999999999999874
No 90
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=96.26 E-value=0.018 Score=52.60 Aligned_cols=64 Identities=17% Similarity=0.215 Sum_probs=50.7
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeeccccccc-ceeeEEeccccccccc--cc-------cccccCCCCCCEEEEEEEE
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEI--DK-------VDMHLSFRPGDIVRASVVS 143 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~sdi~~~~~--d~-------~~~~~~~~~GDiV~A~Vis 143 (146)
.++|.++.|+|+++++..++|++ .. ...|++|.+++...+. +. ......|++||.|.++|.+
T Consensus 625 ~~iG~~~~g~V~~v~~fGifV~L--------~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~ 696 (709)
T TIGR02063 625 EKIGEEFEGVISGVTSFGLFVEL--------ENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVK 696 (709)
T ss_pred ccCCcEEEEEEEEEEeCCEEEEe--------cCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEE
Confidence 67899999999999999999999 33 5899999999863211 10 1224679999999999998
Q ss_pred ee
Q 032149 144 FM 145 (146)
Q Consensus 144 ~~ 145 (146)
+.
T Consensus 697 vd 698 (709)
T TIGR02063 697 AD 698 (709)
T ss_pred Ee
Confidence 74
No 91
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=96.23 E-value=0.007 Score=58.57 Aligned_cols=67 Identities=21% Similarity=0.134 Sum_probs=59.4
Q ss_pred CCCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149 70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 70 ~~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
..+-.++|++|.|.|+++.+++..|.. ...+.|-+|++++......-.++.+.|++||-|.|||+.-
T Consensus 879 ~~~~~~igsiv~a~v~svKp~~L~v~l--------~~~~~gri~isev~d~~~eitDp~~k~~vG~~I~vrviG~ 945 (1710)
T KOG1070|consen 879 STEDLSIGSIVRAYVKSVKPDQLNVLL--------AANHHGRIHISEVLDNLHEITDPLDKFKVGDGIFVRVIGG 945 (1710)
T ss_pred cccceeeeeEEEEEEeeecccceEEec--------cccccCceehHHhhccccccCChhhhcccCCeEEEEEEcC
Confidence 456679999999999999999999997 7789999999999877766668999999999999999853
No 92
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=96.15 E-value=0.022 Score=38.78 Aligned_cols=63 Identities=13% Similarity=0.190 Sum_probs=52.0
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEe-ccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR-QQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~-~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
..|++||+|. .|..+++..+.|.++ ....+|+|- .++++....+ ++...+ +|-.+.++|+.+.
T Consensus 12 ~~P~v~dvv~-~Vv~i~d~~~YV~Ll-------eY~iegmIl~~selsr~rir--si~kll-VGk~e~v~ViRVD 75 (86)
T PHA02858 12 VFPNINEVTK-GIVFVKDNIFYVKLI-------DYGLEALIVNYVNVNADRAE--KLKKKL-VGKTINVQVIRTD 75 (86)
T ss_pred ecCCCCeEEE-EEEEEeccEEEEEEe-------cCccceEEecHHHHhHHHHH--hhhhhh-cCCeeEEEEEEEC
Confidence 3599999999 899999999999994 445778877 7777665555 788888 9999999999764
No 93
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.09 E-value=0.017 Score=49.22 Aligned_cols=57 Identities=18% Similarity=0.289 Sum_probs=46.9
Q ss_pred CCCCCCCCEEEEEEEEEec-ceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149 71 GPVPEPGSVVIARVTKVMT-RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 71 ~~~P~~GdiViG~V~~v~~-~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
.|..++|++|.|+|.++.. ..+++++ ....|+|+.++.- ..+.|++||.|+|-|..+
T Consensus 133 ey~~~~Geiv~g~V~r~~~~~~i~vdl---------g~~ea~LP~~eqi--------p~E~~~~Gdrik~~i~~V 190 (374)
T PRK12328 133 KYKKKVGKIVFGTVVRVDNEENTFIEI---------DEIRAVLPMKNRI--------KGEKFKVGDVVKAVLKRV 190 (374)
T ss_pred HHHHhcCcEEEEEEEEEecCCCEEEEc---------CCeEEEeCHHHcC--------CCCcCCCCCEEEEEEEEE
Confidence 4678999999999999986 4588887 3588999876543 367799999999999876
No 94
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.83 E-value=0.026 Score=49.05 Aligned_cols=62 Identities=8% Similarity=0.075 Sum_probs=48.3
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEEeeccccccc-ceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
.|..++|++|.|+|.++..+.+++++.+ .+.. ...|+|+.++. -..+.|++||.|+|-|..+
T Consensus 147 ef~~~~GeIV~G~V~r~e~~~viv~l~~----~~g~~~~EaiLP~~Eq--------ip~E~y~~Gdrika~i~~V 209 (449)
T PRK12329 147 EFQDLEDTVLTARVLRFERQSVIMAVSS----GFGQPEVEAELPKREQ--------LPNDNYRANATFKVFLKEV 209 (449)
T ss_pred HHHHhcCcEEEEEEEEEcCCCEEEEecc----cCCCcceEEEecHHHc--------CCCCcCCCCCEEEEEEEEe
Confidence 4668999999999999999989988721 0111 37899987654 3367899999999999876
No 95
>PRK11642 exoribonuclease R; Provisional
Probab=95.47 E-value=0.06 Score=50.17 Aligned_cols=64 Identities=17% Similarity=0.231 Sum_probs=50.0
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeeccccccc-ceeeEEeccccccc-c-cccc-------ccccCCCCCCEEEEEEEE
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRQQDVRAT-E-IDKV-------DMHLSFRPGDIVRASVVS 143 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~sdi~~~-~-~d~~-------~~~~~~~~GDiV~A~Vis 143 (146)
.++|+++.|+|++|++..++|++ .. ...|++|.+++... + .+.. .....|+.||.|.++|.+
T Consensus 641 ~~iGe~f~G~Is~V~~fGifVeL--------~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~ 712 (813)
T PRK11642 641 DQVGNVFKGVISSVTGFGFFVRL--------DDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEA 712 (813)
T ss_pred ccCCcEEEEEEEEeecCceEEEE--------CCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEE
Confidence 46899999999999999999999 43 48899999988632 1 1110 234679999999999987
Q ss_pred ee
Q 032149 144 FM 145 (146)
Q Consensus 144 ~~ 145 (146)
+.
T Consensus 713 vD 714 (813)
T PRK11642 713 VN 714 (813)
T ss_pred ee
Confidence 64
No 96
>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=95.27 E-value=0.081 Score=48.04 Aligned_cols=64 Identities=14% Similarity=0.192 Sum_probs=50.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccc-cceeeEEecccccccc--ccc-------cccccCCCCCCEEEEEEEE
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRQQDVRATE--IDK-------VDMHLSFRPGDIVRASVVS 143 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~-~~~~g~l~~sdi~~~~--~d~-------~~~~~~~~~GDiV~A~Vis 143 (146)
.++|...-|+|+++++..++|++ . ....|++|.+++.... -|+ ......|++||.|+.+|++
T Consensus 570 ~~iG~~~~g~I~~v~~~GifV~L--------~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~ 641 (654)
T TIGR00358 570 DKVGTEFSGEISSVTRFGMFVRL--------DDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTE 641 (654)
T ss_pred hCCCcEEEEEEEeEEcCcEEEEe--------cCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEE
Confidence 46799999999999999999999 4 4589999999886431 111 1223679999999999998
Q ss_pred ee
Q 032149 144 FM 145 (146)
Q Consensus 144 ~~ 145 (146)
+.
T Consensus 642 vd 643 (654)
T TIGR00358 642 VN 643 (654)
T ss_pred Ee
Confidence 74
No 97
>PRK11712 ribonuclease G; Provisional
Probab=95.01 E-value=0.069 Score=47.08 Aligned_cols=62 Identities=21% Similarity=0.231 Sum_probs=47.8
Q ss_pred CCCCCEEEEEEEEEecc--eEEEEEEeecccccccceeeEEecccccccc-------c---cccccccCCCCCCEEEEEE
Q 032149 74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRQQDVRATE-------I---DKVDMHLSFRPGDIVRASV 141 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~--~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~-------~---d~~~~~~~~~~GDiV~A~V 141 (146)
..+|+|-.|+|.+|-+. .|||+| ...-.|.||.+|+.+.. . ....+.+.+++||.|..+|
T Consensus 36 ~~vGnIY~G~V~~v~pg~~AAFVdI--------G~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV 107 (489)
T PRK11712 36 GIVGNIYKGRVSRVLPGMQAAFVDI--------GLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQV 107 (489)
T ss_pred cccccEEEEEEeecCCCCceeEEee--------CCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEE
Confidence 46799999999999874 499999 67788999999884210 0 0113566799999999999
Q ss_pred EE
Q 032149 142 VS 143 (146)
Q Consensus 142 is 143 (146)
..
T Consensus 108 ~K 109 (489)
T PRK11712 108 VK 109 (489)
T ss_pred Ee
Confidence 75
No 98
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=94.91 E-value=0.053 Score=51.76 Aligned_cols=65 Identities=18% Similarity=0.241 Sum_probs=53.2
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
-..|.+|.++|++++.+...| + ...+.....|.|+.+++...... .+.+-+++|+.|.|||+++.
T Consensus 983 ~~~g~iV~~~V~~vt~rr~~C-v----~v~ld~G~~g~i~~~~~Sd~~v~--~p~~~v~vgq~v~~kvi~id 1047 (1299)
T KOG1856|consen 983 FYEGAIVPVTVTKVTHRRGIC-V----RVRLDCGVTGFILAKNLSDRDVR--RPENRVKVGQTVYCKVIKID 1047 (1299)
T ss_pred hccCceEEEeeeEEEecccce-e----EEEecCCCceeeeccccChhhcc--CHHHhhccCceEEEEeeeee
Confidence 367999999999999999666 1 11236788999999998875555 88999999999999999874
No 99
>PRK10811 rne ribonuclease E; Reviewed
Probab=94.91 E-value=0.082 Score=49.98 Aligned_cols=62 Identities=11% Similarity=0.215 Sum_probs=48.1
Q ss_pred CCCCCEEEEEEEEEecce--EEEEEEeecccccccceeeEEecccccccc-cc------ccccccCCCCCCEEEEEEEE
Q 032149 74 PEPGSVVIARVTKVMTRM--ASADIMCVGAKSVREKFSGIIRQQDVRATE-ID------KVDMHLSFRPGDIVRASVVS 143 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~--~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~-~d------~~~~~~~~~~GDiV~A~Vis 143 (146)
+.+|+|-.|+|.+|-+.. |||+| ...-.|+|+.+|+.... .. .-...+.+++||.|..+|..
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDI--------G~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~K 106 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDY--------GAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDK 106 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEe--------cCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEee
Confidence 468999999999997754 99999 67788999999884221 11 11346779999999999975
No 100
>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=94.87 E-value=0.099 Score=34.59 Aligned_cols=59 Identities=17% Similarity=0.195 Sum_probs=46.3
Q ss_pred CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEE-EEEEE
Q 032149 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIV-RASVV 142 (146)
Q Consensus 77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV-~A~Vi 142 (146)
|++|.|+|..-+.+...|++. .+...|+|+.....+.......+..++++||.+ .+=|+
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~-------~~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL 60 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAIL-------PEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL 60 (72)
T ss_pred CceEEEEEEEEcCCcEEEEec-------CCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEE
Confidence 789999999999999999993 457888888777665444444688899999988 55444
No 101
>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=94.46 E-value=0.069 Score=36.12 Aligned_cols=47 Identities=17% Similarity=0.321 Sum_probs=38.8
Q ss_pred ccccCCcEEecCCccCC--CCCeeeCCcEEEEcCCCeEEEEEeeeEEEcC
Q 032149 3 VKEEEMVLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLS 50 (146)
Q Consensus 3 ~~~~~~~iV~PGd~l~~--~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~ 50 (146)
+|.-..+.|.||+.|.. -..|-||.++..-. |..|||..-|.+.+..
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 34556789999998863 35799999999865 8999999999998854
No 102
>CHL00121 rpl27 ribosomal protein L27; Reviewed
Probab=94.00 E-value=0.12 Score=35.20 Aligned_cols=59 Identities=20% Similarity=0.268 Sum_probs=43.5
Q ss_pred cccCCcEEecCCccCC--CCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecC
Q 032149 4 KEEEMVLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH 67 (146)
Q Consensus 4 ~~~~~~iV~PGd~l~~--~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~ 67 (146)
|.-..+.|.||+.|.. ...|-||.++-.-. |..|||...|.+.+... ..++..|+|.|.
T Consensus 24 K~~~gq~V~~G~IivRQRGtk~hPG~NVg~Gr-D~TlfAl~~G~V~f~~~----~~~~~~vsv~~~ 84 (86)
T CHL00121 24 KRFGGEKVSAGNILIRQRGTKFKPGLNVGCGK-DFTLYALIDGFVKFKKK----NKKQKSINVINI 84 (86)
T ss_pred EEcCCEEEcCCcEEEEcCCCeECCCCcccccC-CceEEEccceEEEEEEe----CCCCEEEEEeec
Confidence 4456789999998864 34699999887643 99999999999988531 223456777764
No 103
>PRK05435 rpmA 50S ribosomal protein L27; Validated
Probab=93.87 E-value=0.19 Score=33.96 Aligned_cols=47 Identities=19% Similarity=0.288 Sum_probs=37.8
Q ss_pred ccccCCcEEecCCccCC--CCCeeeCCcEEEEcCCCeEEEEEeeeEEEcC
Q 032149 3 VKEEEMVLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLS 50 (146)
Q Consensus 3 ~~~~~~~iV~PGd~l~~--~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~ 50 (146)
+|.-..+.|.||..|.. ...|.||.++-.-. |..|||...|.+.+..
T Consensus 23 vK~~~g~~V~~G~IivRQRGtk~~PG~nVg~Gr-D~TlfA~~~G~V~f~~ 71 (82)
T PRK05435 23 VKRFGGQFVKAGNIIVRQRGTKFHPGVNVGRGK-DHTLFALVDGVVKFER 71 (82)
T ss_pred eEecCCEEEcCCcEEEEeCCCeECCCCCEeecC-CceEEEecceEEEEEE
Confidence 34456789999998863 34699999999853 9999999999998853
No 104
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=93.63 E-value=0.24 Score=48.49 Aligned_cols=62 Identities=16% Similarity=0.165 Sum_probs=55.9
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.+.||+|.|.|..+..+..++.+ ...+.|..++++...+... .-+..|.+|++|.++|.++.
T Consensus 1160 lk~g~iv~G~V~nv~~~glfi~l--------s~~v~a~v~is~~~ds~~k--~w~k~~~~gklv~~rv~~ve 1221 (1710)
T KOG1070|consen 1160 LKIGDIVRGFVKNVETKGLFIAL--------SRKVEAFVPISGLSDSFEK--EWEKHLPVGKLVTGRVLSVE 1221 (1710)
T ss_pred cccCceeEEEEEEecCCcEEEEE--------ccceEEEEEccccccchhh--hhhccCCccceeeeEEEEee
Confidence 48899999999999999999998 7889999999998877766 77889999999999999863
No 105
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=90.91 E-value=1.2 Score=27.92 Aligned_cols=48 Identities=19% Similarity=0.099 Sum_probs=25.3
Q ss_pred CCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEE
Q 032149 76 PGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASV 141 (146)
Q Consensus 76 ~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~V 141 (146)
+|+++..+|++.++..|+++- ...-.-+|+.++. .+-+++||.|.+-|
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~--------~~~~~vlLp~~e~----------~~~~~~Gd~v~VFv 48 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDD--------GEGKEVLLPKSEV----------PEPLKVGDEVEVFV 48 (61)
T ss_dssp --------EEEE-SSEEEEEE--------TT-EEEEEEGGG----------------TTSEEEEEE
T ss_pred CCCCcceEEEEEeCCEEEEEC--------CCCCEEEechHHc----------CCCCCCCCEEEEEE
Confidence 589999999999999999986 4456677776544 34478899887654
No 106
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=90.88 E-value=1 Score=37.01 Aligned_cols=50 Identities=18% Similarity=0.215 Sum_probs=33.6
Q ss_pred CCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149 77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 77 GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
+..|-|.|-+......++-+ ...+.|+||.|++ ....+.|+.+.|||+.+
T Consensus 156 nq~v~~tVYr~~~~G~fv~~--------e~~~~GfIh~sEr----------~~~prlG~~l~~rVi~~ 205 (287)
T COG2996 156 NQEVDATVYRLLESGTFVIT--------ENGYLGFIHKSER----------FAEPRLGERLTARVIGV 205 (287)
T ss_pred cCeeeeEEEEEeccceEEEE--------cCCeEEEEcchhh----------cccccCCceEEEEEEEE
Confidence 44445555554444444433 4678899998765 45569999999999975
No 107
>TIGR00062 L27 ribosomal protein L27. Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.
Probab=90.86 E-value=0.53 Score=31.93 Aligned_cols=47 Identities=19% Similarity=0.326 Sum_probs=37.6
Q ss_pred ccccCCcEEecCCccCC--CCCeeeCCcEEEEcCCCeEEEEEeeeEEEcC
Q 032149 3 VKEEEMVLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLS 50 (146)
Q Consensus 3 ~~~~~~~iV~PGd~l~~--~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~ 50 (146)
+|.-..+.|.||+.|.. ...|-||.++-.-. |..|||...|.+....
T Consensus 23 vK~~~gq~V~~G~IivRQRGtk~hPG~nVg~Gr-D~TlfAl~~G~V~f~~ 71 (83)
T TIGR00062 23 VKRAGGQFVRAGSIIVRQRGTKFHPGNNVGMGK-DHTLFALSDGVVKFEK 71 (83)
T ss_pred eEecCCEEEcCCcEEEEcCCceECCCCcccccC-CCeEEEecceEEEEEE
Confidence 34456789999998864 34699999998753 9999999999998853
No 108
>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=90.02 E-value=3.8 Score=34.85 Aligned_cols=93 Identities=15% Similarity=0.345 Sum_probs=63.7
Q ss_pred EEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEec
Q 032149 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMT 89 (146)
Q Consensus 10 iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~v~~ 89 (146)
+..||+.=...+|+.+|.-+..-..+|+-+....|++++. +++.+.|+-.. +. -++.-+-+
T Consensus 246 v~~pg~kT~YLSEL~sG~~VlvVd~~G~tR~~~VGRvKIE--------~RPLllIeA~~--------~g---~~~svilQ 306 (354)
T PF01959_consen 246 VLMPGGKTRYLSELRSGDEVLVVDADGRTRTAIVGRVKIE--------RRPLLLIEAEA--------DG---KRISVILQ 306 (354)
T ss_pred EEcCCCceeehhhhcCCCEEEEEeCCCCEEEEEeeEEEEe--------ecceEEEEEEe--------CC---eEEEEEEe
Confidence 4678998777788999999887666999999999999995 36677777431 22 23334567
Q ss_pred ceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEE
Q 032149 90 RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVS 143 (146)
Q Consensus 90 ~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis 143 (146)
+-|.+.+..-++.+ ++ --.++|||.|.+++..
T Consensus 307 naetIRlv~p~G~~--------vs--------------Vt~Lk~GD~vL~~~~~ 338 (354)
T PF01959_consen 307 NAETIRLVGPDGEP--------VS--------------VTELKPGDEVLVYLEE 338 (354)
T ss_pred cCcEEEEECCCCCE--------ee--------------eeecCCCCEEEEEecC
Confidence 77888884322211 11 2346889988887653
No 109
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=89.80 E-value=1.4 Score=33.62 Aligned_cols=67 Identities=21% Similarity=0.098 Sum_probs=43.5
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEEeecccccc------cceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR------EKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~------~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
..|-.|++|-|.|+.+....+++++...+-..++ ..|. +-++-.....+ +++ ....|+.||-+|+..
T Consensus 77 FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~---p~~n~P~f~~~--d~s-~I~~~~~VR~kiigt 149 (170)
T KOG3298|consen 77 FKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFD---PGENPPNFQTE--DES-VIQKGVEVRLKIIGT 149 (170)
T ss_pred EeecCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccC---CCCCCCccccc--ccc-eeeeCcEEEEEEEEE
Confidence 4588899999999999999999999655432221 1222 22221111112 333 688999999999864
No 110
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=89.29 E-value=0.64 Score=41.97 Aligned_cols=60 Identities=8% Similarity=0.156 Sum_probs=48.3
Q ss_pred CCCCCEE-----EEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEE
Q 032149 74 PEPGSVV-----IARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVS 143 (146)
Q Consensus 74 P~~GdiV-----iG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis 143 (146)
++++|+. .|+|+.+++..++|++ ....+|++|.+|....... +.++.+.+|+-|-.+-+.
T Consensus 661 ~~~~~l~~g~vy~~tIt~~rd~G~~V~l--------~p~~~~Llh~sqL~~e~ia--kpsd~levGq~I~vk~ie 725 (760)
T KOG1067|consen 661 DQVQDLEFGGVYTATITEIRDTGVMVEL--------YPMQQGLLHNSQLDQEKIA--KPSDLLEVGQEIQVKYIE 725 (760)
T ss_pred ccccceEeeeEEEEEEeeecccceEEEe--------cCCchhhccchhccccccc--ChHHHHhhcceeEEEEEe
Confidence 4555554 6899999999999999 3357799999999877666 788889999999877553
No 111
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=88.92 E-value=5.1 Score=33.99 Aligned_cols=93 Identities=17% Similarity=0.367 Sum_probs=62.3
Q ss_pred EEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEec
Q 032149 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMT 89 (146)
Q Consensus 10 iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~v~~ 89 (146)
+..||+.=...+|+.+|.-+-.-..+|+-+..+.|++++. +++.+-|+-.. -| -++.-+-+
T Consensus 236 v~~pgg~T~YLsEL~sG~eVlvVd~~G~tR~~~VGRvKIE--------~RPL~lIeAe~-------~g----~~~~viLQ 296 (344)
T PRK02290 236 VRVPGDKTRYLSELRSGDEVLVVDADGNTREAIVGRVKIE--------KRPLLLIEAEY-------GG----KRIRTILQ 296 (344)
T ss_pred EEcCCCcchhhHhhcCCCEEEEEeCCCCEEEEEeeEEEEe--------eccEEEEEEEe-------CC----eEEEEEEe
Confidence 4679998877788999998887666999999999999995 35666666421 12 22333456
Q ss_pred ceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEE
Q 032149 90 RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVS 143 (146)
Q Consensus 90 ~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis 143 (146)
+-|.+.+..-+++ .++ --.++|||.|.+++..
T Consensus 297 naetIrlv~~dG~--------~vs--------------Vt~Lk~GD~VL~~~~~ 328 (344)
T PRK02290 297 NAETIRLVTPDGK--------PVS--------------VVDLKPGDEVLGYLEE 328 (344)
T ss_pred cCcEEEEECCCCC--------Eee--------------eeecCCCCEEEEEecC
Confidence 7788887422221 111 2235888888887643
No 112
>KOG4600 consensus Mitochondrial ribosomal protein MRP7 (L2) [Translation, ribosomal structure and biogenesis]
Probab=87.88 E-value=1.4 Score=32.54 Aligned_cols=63 Identities=22% Similarity=0.279 Sum_probs=46.1
Q ss_pred ccccCCcEEecCCccCCC--CCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCC
Q 032149 3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHK 68 (146)
Q Consensus 3 ~~~~~~~iV~PGd~l~~~--~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~ 68 (146)
+|.+.++.|.||+.|... ..|-||.++=.-. |..|||-.-|.++.......- .++.|.|.|..
T Consensus 50 vKk~egq~V~~G~IIvrQRgtkfHPG~nVGiGK-DhtifaL~eG~Vrf~k~~~~~--~Rk~i~V~~~~ 114 (144)
T KOG4600|consen 50 VKKYEGQSVIPGNIIVRQRGTKFHPGDNVGIGK-DHTIFALEEGRVRFEKSKITP--PRKWIGVDPRG 114 (144)
T ss_pred ceecCCeeeecccEEEEecccccCCCcccccCC-cceEEEeeccEEEEEEccCCC--CcceEEEeecC
Confidence 466778999999998753 3577877666543 889999999999986533222 35788888753
No 113
>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=86.37 E-value=4.2 Score=29.36 Aligned_cols=69 Identities=17% Similarity=0.154 Sum_probs=37.7
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccc-----cccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKS-----VREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~-----l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
|-+|.++.|+|.+.+.+...|.+.-.++-- |..+ ...=+.+++=-..- ..+-.-+|..|+.||=||.+.
T Consensus 1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~p-s~fd~~~~~W~W~~-~~~~~l~~d~ge~IRFRV~~~ 74 (122)
T PF08292_consen 1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEP-SRFDEEEQAWVWEY-DEEQELFFDIGEEIRFRVESE 74 (122)
T ss_dssp --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TT-EEEECCCTEEEEEE-SSSEEEEE-TT-EEEEEEEEE
T ss_pred CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCC-CccCccCCEEEEEC-CCCceeEccCCCEEEEEEeEE
Confidence 668999999999999999999985554411 1100 00001111100001 014456679999999999875
No 114
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=85.54 E-value=1.4 Score=38.83 Aligned_cols=62 Identities=21% Similarity=0.299 Sum_probs=49.0
Q ss_pred CCCCCEEEEEEEEEecce--EEEEEEeecccccccceeeEEecccccccccc--ccccccCCCCCCEEEEEEEE
Q 032149 74 PEPGSVVIARVTKVMTRM--ASADIMCVGAKSVREKFSGIIRQQDVRATEID--KVDMHLSFRPGDIVRASVVS 143 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~--~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d--~~~~~~~~~~GDiV~A~Vis 143 (146)
-.+|++-.|+|++|-+.. ||||| ...-.|+||.+++.+.... ..++...++.|+.+..+|..
T Consensus 35 ~~~gniy~grv~~i~p~~~aafvdi--------g~~r~gfl~~~~~~~~~~~~~~~~i~~~lr~~~~~~Vqv~k 100 (487)
T COG1530 35 QIVGNIYKGRVTRVLPSLEAAFVDI--------GLERNGFLHLSEIVPYFRAVLEEKIKVRLRGGQATLVQVVK 100 (487)
T ss_pred eeecCceEEEecccCccchhheeec--------cCCccceEEecccchhhhhcccccceeeecCCceEEEEEEe
Confidence 367999999999998865 99999 5677899999998762222 11356799999999988875
No 115
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=84.08 E-value=1.1 Score=36.74 Aligned_cols=66 Identities=17% Similarity=0.245 Sum_probs=48.2
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149 71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
.-.|+++++|++.|..|..-.|.|.++-.+ ...|++--|+.+..... ++....++|-.=.+-|+.+
T Consensus 11 ~kyPev~e~VmvnV~sIaemGayv~LlEYn------niEGmiLlsELSrRRIR--SI~klirVGr~E~vvVlrV 76 (304)
T KOG2916|consen 11 NKYPEVEEIVMVNVRSIAEMGAYVKLLEYN------NIEGMILLSELSRRRIR--SIQKLIRVGRNEPVVVLRV 76 (304)
T ss_pred ccCCCcccEEEEEeeEehhccceEeeeecC------CcccchhhhHHHHHHHH--HHHHHHhcCCcceEEEEEE
Confidence 346999999999999999999999996443 35677777776655555 6666677776555555544
No 116
>PRK05054 exoribonuclease II; Provisional
Probab=83.68 E-value=5.3 Score=36.44 Aligned_cols=65 Identities=11% Similarity=0.248 Sum_probs=47.3
Q ss_pred CCCCC--EEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccc---cc---c--cccc--ccCCCCCCEEEEEE
Q 032149 74 PEPGS--VVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT---EI---D--KVDM--HLSFRPGDIVRASV 141 (146)
Q Consensus 74 P~~Gd--iViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~---~~---d--~~~~--~~~~~~GDiV~A~V 141 (146)
.++|+ ..-|.|++++....+|+|. .....|++|.+.+... +. + ...+ ...|+.||-|+.+|
T Consensus 557 ~~~G~~~~f~g~I~~v~~~G~fV~l~-------~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v 629 (644)
T PRK05054 557 DKAGTDTRFAAEIIDISRGGMRVRLL-------ENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTL 629 (644)
T ss_pred hccCCCeEEEEEEEeeecCcEEEEEe-------CCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEE
Confidence 35665 9999999999999999993 3457899998877431 10 1 1111 24699999999999
Q ss_pred EEee
Q 032149 142 VSFM 145 (146)
Q Consensus 142 is~~ 145 (146)
.++.
T Consensus 630 ~~vd 633 (644)
T PRK05054 630 AEVR 633 (644)
T ss_pred EEEc
Confidence 9864
No 117
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=78.96 E-value=13 Score=26.20 Aligned_cols=54 Identities=20% Similarity=0.330 Sum_probs=42.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
+-.|-+|+|+|..+-.+-..+|. ...|.++...... + .+.|..|+-|+.++.++
T Consensus 21 ~~~gk~V~G~I~hvv~ddLYIDf--------G~KFhcVc~rp~~-----~----~~~y~~G~rV~lrLkdl 74 (104)
T PF10246_consen 21 DPEGKIVIGKIFHVVDDDLYIDF--------GGKFHCVCKRPAV-----N----GEKYVRGSRVRLRLKDL 74 (104)
T ss_pred CccCCEEEEEEEEEecCceEEEe--------CCceeEEEecccc-----c----ccccccCCEEEEEECCH
Confidence 45689999999999999999998 7788888874322 2 45688899999887654
No 118
>COG0211 RpmA Ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=76.63 E-value=6.9 Score=26.62 Aligned_cols=59 Identities=19% Similarity=0.260 Sum_probs=42.4
Q ss_pred cccCCcEEecCCccCC--CCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecC
Q 032149 4 KEEEMVLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH 67 (146)
Q Consensus 4 ~~~~~~iV~PGd~l~~--~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~ 67 (146)
|.-..++|.+|+.|-. -..|-||.++=.-. |..|||-.-|.++.... ..+++.++|.|.
T Consensus 24 K~~~Gq~v~aG~IivRQRGTk~hpG~NVG~Gk-DhTlFAl~dG~Vkf~~k----~~~rk~vsV~~~ 84 (87)
T COG0211 24 KKFGGQFVKAGSIIVRQRGTKFHPGVNVGRGK-DHTLFALVDGVVKFETK----GKNRKYVSVVPE 84 (87)
T ss_pred eeeCCeEEecccEEEEeccccccCCcccccCC-CceEEEeeccEEEEEEc----cCCccEEEEEee
Confidence 4445778899988753 23578888776543 88999999999987541 244568999875
No 119
>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=75.21 E-value=11 Score=27.85 Aligned_cols=60 Identities=20% Similarity=0.298 Sum_probs=35.1
Q ss_pred EEEEEEEEecceEEEEEEeecccc-----cccceeeEEecccccc--ccccccccccCCCCCCEEEE
Q 032149 80 VIARVTKVMTRMASADIMCVGAKS-----VREKFSGIIRQQDVRA--TEIDKVDMHLSFRPGDIVRA 139 (146)
Q Consensus 80 ViG~V~~v~~~~~~v~I~~v~~~~-----l~~~~~g~l~~sdi~~--~~~d~~~~~~~~~~GDiV~A 139 (146)
++|+|+.+.++.+.|..+.-.+.. ......|+++-..-.. .....+....-+++||.|..
T Consensus 36 lVG~V~~V~~~~S~V~li~d~~~~v~v~i~~~~~~Gi~~G~~~~~~~~~l~~i~~~~~i~~GD~V~T 102 (152)
T PF04085_consen 36 LVGRVTEVGPNTSRVLLITDPNSRVSVKIERSGDRGILRGDGSNTGLLKLEYIPKDADIKKGDIVVT 102 (152)
T ss_dssp EEEEEEEE-SS-EEEEETTSSBCEEEEEEECTTEEEEEEEEETTTTEEEEEEECTTS---TT-EEEE
T ss_pred cEEEEEEECCCEEEEEEEeCCCceEEEEEecCCeeEEEEeCCCCCceEEEEECCCCCCCCCCCEEEE
Confidence 789999999999999886544321 2234568887655433 23344556777889998763
No 120
>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=74.87 E-value=6.4 Score=25.56 Aligned_cols=24 Identities=17% Similarity=0.271 Sum_probs=18.6
Q ss_pred CCCCCCEEEEEEEEEec-ceEEEEE
Q 032149 73 VPEPGSVVIARVTKVMT-RMASADI 96 (146)
Q Consensus 73 ~P~~GdiViG~V~~v~~-~~~~v~I 96 (146)
..++||.+.++|.++.. ....+.+
T Consensus 50 ~~~~GD~i~~~V~~~~~~~~i~LS~ 74 (82)
T cd04454 50 SLQPGDLILAKVISLGDDMNVLLTT 74 (82)
T ss_pred cCCCCCEEEEEEEEeCCCCCEEEEE
Confidence 35999999999999976 3455554
No 121
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=74.41 E-value=5.1 Score=33.63 Aligned_cols=99 Identities=14% Similarity=0.193 Sum_probs=55.9
Q ss_pred CCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecceEE
Q 032149 14 GEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMAS 93 (146)
Q Consensus 14 Gd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~v~~~~~~ 93 (146)
||.+-..-.-..-.|.|+.. .+ |--+=|.+.+++ ++-...++..-+.++||.|.++|.++....-.
T Consensus 18 GdvV~g~V~~I~d~GafV~L-~E--Y~gvEGlIhiSE-----------lS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~ 83 (319)
T PTZ00248 18 DDLVMVKVVRITEMGAYVSL-LE--YDDIEGMILMSE-----------LSKRRIRSINKLIRVGRHEVVVVLRVDKEKGY 83 (319)
T ss_pred CCEEEEEEEEEeCCeEEEEe-cC--CCCcEEEEEHHH-----------hcccccCCHHHhcCCCCEEEEEEEEEeCCCCE
Confidence 66654322234445777662 11 113456666643 11122222333469999999999999766555
Q ss_pred EEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149 94 ADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 94 v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
+++ + ..++...... ...+.|..|++|.++|..+
T Consensus 84 IdL--------S--------~K~v~~~pw~--~~~e~~~~g~~v~~~V~~i 116 (319)
T PTZ00248 84 IDL--------S--------KKRVSPEDIE--ACEEKFSKSKKVHSIMRHI 116 (319)
T ss_pred EEE--------E--------eeecccchHH--HHHHhCcCCCEEEEEEEEc
Confidence 554 1 1111111222 6678889999999998865
No 122
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=74.41 E-value=16 Score=33.41 Aligned_cols=64 Identities=9% Similarity=0.180 Sum_probs=46.8
Q ss_pred CCCC--EEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccc---c---ccc--cccc--cCCCCCCEEEEEEE
Q 032149 75 EPGS--VVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRAT---E---IDK--VDMH--LSFRPGDIVRASVV 142 (146)
Q Consensus 75 ~~Gd--iViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~---~---~d~--~~~~--~~~~~GDiV~A~Vi 142 (146)
++|. .--|.|++++....+|.+. ...+.|++|.++.... + .+. ..+. ..|+.||-|+.+|.
T Consensus 554 ~~g~~~~f~g~I~~v~~~g~~v~l~-------~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~ 626 (639)
T TIGR02062 554 KAAKNTRFAAEIVDISRGGMRVRLL-------ENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLT 626 (639)
T ss_pred ccCCCcEEEEEEEeeeCCcEEEEEe-------cCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEE
Confidence 5554 8899999999999999993 4568899988877541 1 111 1222 25999999999998
Q ss_pred Eee
Q 032149 143 SFM 145 (146)
Q Consensus 143 s~~ 145 (146)
++.
T Consensus 627 ~vd 629 (639)
T TIGR02062 627 EVR 629 (639)
T ss_pred Eec
Confidence 864
No 123
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=74.18 E-value=13 Score=34.25 Aligned_cols=64 Identities=17% Similarity=0.101 Sum_probs=47.6
Q ss_pred CCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEecccccccc-c--------cccccccCCCCCCEEEEEEEEee
Q 032149 75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATE-I--------DKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~-~--------d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
++|..-.|.|+++....++|.+. .....|.+|.+.....+ . .-......|+.||-|+.+|.+..
T Consensus 621 ~vg~~f~g~V~~v~~~g~~V~l~-------~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~ 693 (706)
T COG0557 621 RVGEEFDGVVTGVTSFGFFVELP-------ELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVD 693 (706)
T ss_pred hcCCEEEEEEEEEEeccEEEEec-------ccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEc
Confidence 67899999999999999999992 23367888877765211 0 11134557999999999998763
No 124
>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=70.70 E-value=12 Score=32.47 Aligned_cols=36 Identities=25% Similarity=0.328 Sum_probs=28.3
Q ss_pred CeeeCCcEEEE-cCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEec
Q 032149 22 EVKAGKGAYVA-KHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTG 66 (146)
Q Consensus 22 ~~~~G~Gty~~-~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p 66 (146)
.+.+|+||... ++...++|++.|.+.... ..++|.|
T Consensus 144 ~~~~g~~~~~~~~d~~~~~A~~~G~~~~~~---------~~i~V~~ 180 (451)
T PF03961_consen 144 PLKAGKNTEVSEEDGNKLYAAIDGRPVFEN---------GKISVDP 180 (451)
T ss_pred ceeCCCCEEEEcCCCCEEEEecCCEEEEEC---------CEEEEEE
Confidence 48899999987 435689999999998853 4577665
No 125
>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=70.35 E-value=9.9 Score=25.78 Aligned_cols=29 Identities=34% Similarity=0.550 Sum_probs=20.9
Q ss_pred CCCCCCCCEEEEEEEEEecceEEEEEEeec
Q 032149 71 GPVPEPGSVVIARVTKVMTRMASADIMCVG 100 (146)
Q Consensus 71 ~~~P~~GdiViG~V~~v~~~~~~v~I~~v~ 100 (146)
+...++||.|+|+|..+...+ ..++.|++
T Consensus 47 rp~L~~GDlV~ArV~~~~~~~-~~eLtc~~ 75 (86)
T cd05790 47 RPNLNVGDLVYARVVKANRDM-EPELSCVD 75 (86)
T ss_pred cccCCCCCEEEEEEEecCCCC-CeEEEEeC
Confidence 345699999999999997753 34544444
No 126
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=70.08 E-value=14 Score=25.83 Aligned_cols=55 Identities=22% Similarity=0.301 Sum_probs=29.8
Q ss_pred CCCCCCEEEEEEEEEecc-eEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEE
Q 032149 73 VPEPGSVVIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVS 143 (146)
Q Consensus 73 ~P~~GdiViG~V~~v~~~-~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis 143 (146)
.|..| -++|+|+...++ .+.|.+ -++ ...-+.++- +...+=++++||.|.+....
T Consensus 17 ~p~e~-e~~g~V~~~lG~~~~~V~~--~dG----~~~la~i~G---------K~Rk~IwI~~GD~VlVe~~~ 72 (100)
T PRK04012 17 MPEEG-EVFGVVEQMLGANRVRVRC--MDG----VERMGRIPG---------KMKKRMWIREGDVVIVAPWD 72 (100)
T ss_pred CCCCC-EEEEEEEEEcCCCEEEEEe--CCC----CEEEEEEch---------hhcccEEecCCCEEEEEecc
Confidence 35544 599999999665 455554 121 112222221 01114456789988877544
No 127
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=64.50 E-value=5.6 Score=31.96 Aligned_cols=58 Identities=16% Similarity=0.115 Sum_probs=42.6
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
.-|++||+..|.|--+.....-+-| ..-|.+.|+.-++. .+ .++..+++...++|..+
T Consensus 103 f~Pk~Gd~LeG~Vn~vS~sHIglLI--------hg~FNASIpk~nip---~d----w~fI~md~eee~~v~nt 160 (253)
T KOG4134|consen 103 FRPKAGDILEGVVNHVSRSHIGLLI--------HGVFNASIPKTNIP---AD----WEFIAMDQEEEIRVKNT 160 (253)
T ss_pred ECCCCCCeeeeeeeecchhhhceee--------hhhhhccCCCCCCc---cc----eeeecCCchhhhceeec
Confidence 4499999999999999999988888 45577777665543 23 44667777777777654
No 128
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=63.21 E-value=30 Score=23.15 Aligned_cols=22 Identities=23% Similarity=0.164 Sum_probs=14.7
Q ss_pred CCCCCEEEEEEEEEecc-eEEEEE
Q 032149 74 PEPGSVVIARVTKVMTR-MASADI 96 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~-~~~v~I 96 (146)
|.. +-++|+|+...++ .+.|..
T Consensus 2 p~e-~q~~g~V~~~lG~~~~~V~~ 24 (83)
T smart00652 2 KED-GQEIAQVVKMLGNGRLEVMC 24 (83)
T ss_pred CCC-CcEEEEEEEEcCCCEEEEEE
Confidence 443 3489999998664 455555
No 129
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=63.15 E-value=13 Score=28.01 Aligned_cols=40 Identities=20% Similarity=0.190 Sum_probs=26.7
Q ss_pred CcEEec--CCccCCCCCeeeCCcEEEE--cCCCeEEEEEeeeEEE
Q 032149 8 MVLVTP--GEVLGKATEVKAGKGAYVA--KHNGLVYASLTGLLRT 48 (146)
Q Consensus 8 ~~iV~P--Gd~l~~~~~~~~G~Gty~~--~~~g~i~As~~G~~~~ 48 (146)
..+++| ||.++... -..|.|.|.. ..+..+.|.+.|.++.
T Consensus 24 rel~~~eegq~~g~V~-~~LGn~~f~V~c~dG~~rLa~I~GKmRK 67 (155)
T PTZ00329 24 RELVFKEEGQEYAQVL-RMLGNGRLEAYCFDGVKRLCHIRGKMRK 67 (155)
T ss_pred eeeccCCCCcEEEEEE-EEcCCCEEEEEECCCCEEEEEeecccee
Confidence 456677 66666533 4678888862 2256788999998865
No 130
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=62.99 E-value=70 Score=25.57 Aligned_cols=78 Identities=15% Similarity=0.231 Sum_probs=46.5
Q ss_pred CCeEEEecCCCCCCCCCCCCE------EEEEEEEEecceEEEEEEeecccc----c-ccceeeEEecccccc-ccccccc
Q 032149 59 RPTVEVTGHKAHGPVPEPGSV------VIARVTKVMTRMASADIMCVGAKS----V-REKFSGIIRQQDVRA-TEIDKVD 126 (146)
Q Consensus 59 ~~~i~V~p~~~~~~~P~~Gdi------ViG~V~~v~~~~~~v~I~~v~~~~----l-~~~~~g~l~~sdi~~-~~~d~~~ 126 (146)
.+.+.+... ..--.++|+. ++|+|+++.++.+.|..+.-.+.. + .+...|+++-+.-.. -..+-..
T Consensus 133 ~~~i~Id~G--~~~Gv~~g~~Vv~~~GlVG~V~~v~~~~s~V~li~d~~~~v~v~i~~~~~~gi~~G~g~~~~l~l~~i~ 210 (276)
T PRK13922 133 SQQVTIDKG--SNDGVKKGMPVIDPGGLVGRVIEVSPNTSRVLLLTDPNSRVPVQVGRNGIRGILSGNGSGDNLKLEFIP 210 (276)
T ss_pred eeEEEEccC--cccCCCCCCceEcCCCCeEEEEEECCCeeEEEEEEcCCCceEEEEEcCCceEEEEecCCCCceEEEecC
Confidence 345666532 1222355555 699999999999999887654321 1 234567777653211 1233334
Q ss_pred cccCCCCCCEEE
Q 032149 127 MHLSFRPGDIVR 138 (146)
Q Consensus 127 ~~~~~~~GDiV~ 138 (146)
-...+++||.|.
T Consensus 211 ~~~~i~~GD~Vv 222 (276)
T PRK13922 211 RSADIKVGDLVV 222 (276)
T ss_pred CCCCCCCCCEEE
Confidence 456689999875
No 131
>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=62.18 E-value=20 Score=23.96 Aligned_cols=43 Identities=16% Similarity=0.101 Sum_probs=27.0
Q ss_pred CeEEEecCCCCCCCCCCCCEEEEEEEEEecc---eEEEEEEeeccc
Q 032149 60 PTVEVTGHKAHGPVPEPGSVVIARVTKVMTR---MASADIMCVGAK 102 (146)
Q Consensus 60 ~~i~V~p~~~~~~~P~~GdiViG~V~~v~~~---~~~v~I~~v~~~ 102 (146)
.-|.|-+.-=.++-.+.||.|.|.|..=++. .+.+.|.+|++.
T Consensus 29 ~DvYVs~~qIrrf~LR~GD~V~G~vr~p~~~ek~~aL~~V~~VNg~ 74 (78)
T PF07497_consen 29 DDVYVSPSQIRRFGLRTGDLVEGQVRPPREGEKYFALLRVESVNGR 74 (78)
T ss_dssp TSEEE-CCCCCCTT--TTEEEEEEEE--STTSSSEEECEECEETTE
T ss_pred CCEEECHHHHHHcCCCCCCEEEEEEeCCCCCCcceeeEEEEeECCc
Confidence 3577777544567789999999999986543 367777666654
No 132
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=61.91 E-value=21 Score=27.84 Aligned_cols=22 Identities=23% Similarity=0.110 Sum_probs=18.7
Q ss_pred CCCCCEEEEEEEEEecceEEEEE
Q 032149 74 PEPGSVVIARVTKVMTRMASADI 96 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I 96 (146)
-++||+|.|+|++.. +...+.+
T Consensus 119 f~~GDivrA~Vis~~-~~~~Lst 140 (188)
T COG1096 119 FRIGDIVRARVISTG-DPIQLST 140 (188)
T ss_pred cccccEEEEEEEecC-CCeEEEe
Confidence 389999999999998 6677776
No 133
>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=61.47 E-value=12 Score=25.33 Aligned_cols=23 Identities=22% Similarity=0.215 Sum_probs=18.5
Q ss_pred CCCCCEEEEEEEEEec-ceEEEEE
Q 032149 74 PEPGSVVIARVTKVMT-RMASADI 96 (146)
Q Consensus 74 P~~GdiViG~V~~v~~-~~~~v~I 96 (146)
-++||+|.|+|.+..+ ....+.+
T Consensus 61 f~~GDiV~AkVis~~~~~~~~Lst 84 (92)
T cd05791 61 FRPGDIVRAKVISLGDASSYYLST 84 (92)
T ss_pred cCCCCEEEEEEEEcCCCCCcEEEe
Confidence 3999999999999976 5566655
No 134
>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=60.44 E-value=38 Score=27.73 Aligned_cols=61 Identities=15% Similarity=0.254 Sum_probs=38.5
Q ss_pred CEEEEEEEEEecceEEEEEEeecccc-----cccceeeEEeccccccc---cccccccccCCCCCCEEE
Q 032149 78 SVVIARVTKVMTRMASADIMCVGAKS-----VREKFSGIIRQQDVRAT---EIDKVDMHLSFRPGDIVR 138 (146)
Q Consensus 78 diViG~V~~v~~~~~~v~I~~v~~~~-----l~~~~~g~l~~sdi~~~---~~d~~~~~~~~~~GDiV~ 138 (146)
+=++|+|+++.++...|..+.-.+.. ..+...|+++-.+-... ..........+++||.|.
T Consensus 155 ~GLVG~V~~V~~~~S~V~litd~~~~v~v~v~~t~~~gi~~G~~~g~~~~l~l~~~~~~~~v~~GD~Vv 223 (283)
T TIGR00219 155 KGLVGKVVSVGSNTSRVLLLTDYTNFVPAQILRSDFRGLIEGNGYGKTLEMNLVNRPAEKDIKKGDLIV 223 (283)
T ss_pred CceEEEEEEECCCeEEEEEEEcCCCceEEEEecCCceEEEEecCCCCCcEEEEEECCCCCCCCCCCEEE
Confidence 34889999999999999987654422 22455688876541110 011123356789999875
No 135
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=60.30 E-value=33 Score=21.02 Aligned_cols=50 Identities=22% Similarity=0.249 Sum_probs=27.0
Q ss_pred EEEEEEEEEe---cceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEE
Q 032149 79 VVIARVTKVM---TRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRAS 140 (146)
Q Consensus 79 iViG~V~~v~---~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~ 140 (146)
.|.|+|+++. ...+++.| + ..+|.+.. ..+........+.+++||.|+++
T Consensus 2 ~v~G~V~~~~~~~~~~~~~~l---~------D~tg~i~~---~~~~~~~~~~~~~l~~g~~v~v~ 54 (75)
T PF01336_consen 2 TVEGRVTSIRRSGGKIVFFTL---E------DGTGSIQV---VFFNEEYERFREKLKEGDIVRVR 54 (75)
T ss_dssp EEEEEEEEEEEEETTEEEEEE---E------ETTEEEEE---EEETHHHHHHHHTS-TTSEEEEE
T ss_pred EEEEEEEEEEcCCCCEEEEEE---E------ECCccEEE---EEccHHhhHHhhcCCCCeEEEEE
Confidence 3678888883 34455555 1 11233322 11111223678889999998865
No 136
>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=59.76 E-value=26 Score=22.11 Aligned_cols=22 Identities=23% Similarity=0.184 Sum_probs=19.1
Q ss_pred EEEEEEEEecceEEEEEEeecc
Q 032149 80 VIARVTKVMTRMASADIMCVGA 101 (146)
Q Consensus 80 ViG~V~~v~~~~~~v~I~~v~~ 101 (146)
..|+|..+..+.+.|+|...++
T Consensus 16 ~~G~V~kv~eNSVIVdIT~m~~ 37 (57)
T PF09953_consen 16 FTGIVEKVYENSVIVDITIMEN 37 (57)
T ss_pred cEEEEEEEecCcEEEEEEecCC
Confidence 5899999999999999966554
No 137
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=59.32 E-value=38 Score=26.77 Aligned_cols=79 Identities=22% Similarity=0.230 Sum_probs=43.9
Q ss_pred eEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccc
Q 032149 37 LVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQD 116 (146)
Q Consensus 37 ~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~~~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sd 116 (146)
.|.|..+|...... .+.+-+++.-.+ ...+=..-+.+-|||+.+......++.- .++.+.+-.+
T Consensus 6 ~ila~alg~~~~~g------~n~~~~e~~~as-aa~~e~n~~tiEGrVvEV~~~~i~iesk-----~yn~~v~i~~---- 69 (213)
T PRK06763 6 VILAGALGIAALSG------TNLPGLEITKAS-AASIESNFSTIEGRVVEVDNGVIVIKSK-----QYEEPVSVYI---- 69 (213)
T ss_pred EEEecchhheeeec------cCCCcceechhh-hhhhhcccceeeeEEEEEeCCEEEEEec-----cCCCceEEEe----
Confidence 46677777665532 111123332211 1112234578899999999998888762 2223322111
Q ss_pred cccccccccccccCCCCCCEEEEE
Q 032149 117 VRATEIDKVDMHLSFRPGDIVRAS 140 (146)
Q Consensus 117 i~~~~~d~~~~~~~~~~GDiV~A~ 140 (146)
+....+++||.|+|.
T Consensus 70 ---------d~~~nvKVGD~VKaT 84 (213)
T PRK06763 70 ---------DSLSNVKVGDEVKAT 84 (213)
T ss_pred ---------cCCCCcccCcEEEEc
Confidence 334556999999985
No 138
>PLN00208 translation initiation factor (eIF); Provisional
Probab=58.40 E-value=37 Score=25.35 Aligned_cols=24 Identities=21% Similarity=0.177 Sum_probs=16.3
Q ss_pred CCCCCCCEEEEEEEEEecc-eEEEEE
Q 032149 72 PVPEPGSVVIARVTKVMTR-MASADI 96 (146)
Q Consensus 72 ~~P~~GdiViG~V~~v~~~-~~~v~I 96 (146)
.+|..|. ++|+|++..++ .+.|.+
T Consensus 27 ~~p~egq-~~g~V~~~lGn~~~~V~c 51 (145)
T PLN00208 27 IFKEDGQ-EYAQVLRMLGNGRCEALC 51 (145)
T ss_pred ccCCCCc-EEEEEEEEcCCCEEEEEE
Confidence 3466665 89999999665 455554
No 139
>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=57.25 E-value=23 Score=21.66 Aligned_cols=24 Identities=25% Similarity=0.372 Sum_probs=17.8
Q ss_pred CCCCCCEEEEEEEEEecceEEEEE
Q 032149 73 VPEPGSVVIARVTKVMTRMASADI 96 (146)
Q Consensus 73 ~P~~GdiViG~V~~v~~~~~~v~I 96 (146)
.|.+||.|..+|++...+.++-++
T Consensus 37 ~~~iG~~v~v~I~~~~~~~l~G~~ 60 (61)
T PF01938_consen 37 LPLIGEFVKVRITKAKKNYLFGEL 60 (61)
T ss_dssp -T--TEEEEEEEEEE-SSEEEEEE
T ss_pred CCCCCCEEEEEEEEeeCCcEEEEE
Confidence 356899999999999999887765
No 140
>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=57.24 E-value=19 Score=25.71 Aligned_cols=22 Identities=14% Similarity=0.132 Sum_probs=19.4
Q ss_pred EEEEEEEEecceEEEEEEeecc
Q 032149 80 VIARVTKVMTRMASADIMCVGA 101 (146)
Q Consensus 80 ViG~V~~v~~~~~~v~I~~v~~ 101 (146)
=+|.|+..+++.+.|.|++|--
T Consensus 6 Yigei~e~~~~~~lVkVlaVlK 27 (112)
T PF08810_consen 6 YIGEITEERPQHYLVKVLAVLK 27 (112)
T ss_dssp EEEEEEEEETTEEEEEEEEEEE
T ss_pred eEEEEEeecCCeEEEEEEEEec
Confidence 4799999999999999998853
No 141
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=54.08 E-value=48 Score=25.05 Aligned_cols=23 Identities=22% Similarity=0.192 Sum_probs=15.5
Q ss_pred CCCCCCEEEEEEEEEecce-EEEEE
Q 032149 73 VPEPGSVVIARVTKVMTRM-ASADI 96 (146)
Q Consensus 73 ~P~~GdiViG~V~~v~~~~-~~v~I 96 (146)
+|..|. ++|+|+...++. +.|.+
T Consensus 28 ~~eegq-~~g~V~~~LGn~~f~V~c 51 (155)
T PTZ00329 28 FKEEGQ-EYAQVLRMLGNGRLEAYC 51 (155)
T ss_pred cCCCCc-EEEEEEEEcCCCEEEEEE
Confidence 356565 799999997654 44443
No 142
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=53.72 E-value=48 Score=20.86 Aligned_cols=49 Identities=20% Similarity=0.217 Sum_probs=26.3
Q ss_pred CEEEEEEEEEec-ceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEE
Q 032149 78 SVVIARVTKVMT-RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASV 141 (146)
Q Consensus 78 diViG~V~~v~~-~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~V 141 (146)
+-++|+|++..+ +.+.|.. -+ .....+.|+.. ... +=.+++||.|.+..
T Consensus 3 ~e~~~~V~~~lG~~~~~V~~--~d----g~~~l~~i~gK-----~r~----~iwI~~GD~V~V~~ 52 (65)
T PF01176_consen 3 GEVIGRVTEMLGNNLFEVEC--ED----GEERLARIPGK-----FRK----RIWIKRGDFVLVEP 52 (65)
T ss_dssp TEEEEEEEEEESSSEEEEEE--TT----SEEEEEEE-HH-----HHT----CC---TTEEEEEEE
T ss_pred cEEEEEEEEECCCCEEEEEe--CC----CCEEEEEeccc-----eee----eEecCCCCEEEEEe
Confidence 458999999866 4466665 11 12333444422 222 33578899988765
No 143
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=53.59 E-value=63 Score=21.99 Aligned_cols=55 Identities=18% Similarity=0.254 Sum_probs=31.3
Q ss_pred EEEEEEEEEec--ceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEE
Q 032149 79 VVIARVTKVMT--RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRAS 140 (146)
Q Consensus 79 iViG~V~~v~~--~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~ 140 (146)
.|.|+|..++. +.+|+++-.- ....|.++...+.... .-.+....+..||.|.++
T Consensus 3 ~v~GwV~~~R~~g~~~Fi~lrd~-----~~~lQ~v~~~~~~~~~--~~~~~~~~l~~g~~V~v~ 59 (108)
T cd04322 3 SVAGRIMSKRGSGKLSFADLQDE-----SGKIQVYVNKDDLGEE--EFEDFKKLLDLGDIIGVT 59 (108)
T ss_pred EEEEEEEEEecCCCeEEEEEEEC-----CeEEEEEEECCCCCHH--HHHHHHhcCCCCCEEEEE
Confidence 47799999875 4577777211 1346666654432111 001223348999998764
No 144
>COG1315 Uncharacterized conserved protein [Function unknown]
Probab=52.92 E-value=22 Score=31.81 Aligned_cols=35 Identities=20% Similarity=0.229 Sum_probs=29.7
Q ss_pred CeeeCCcE-EEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecC
Q 032149 22 EVKAGKGA-YVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH 67 (146)
Q Consensus 22 ~~~~G~Gt-y~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~ 67 (146)
.|.+|+|| ..+ ++.+.|+..|.+-++ +++|+|.|.
T Consensus 220 ~l~lG~nt~~kd--~~tlvA~~~G~~~~s---------~~tI~V~~i 255 (543)
T COG1315 220 KLNLGKNTAFKD--NNTLVAKRDGQPIVS---------KNTISVYPI 255 (543)
T ss_pred eeecCCCCccCC--CCEEEEeeCCeEEec---------CCeeEEEEE
Confidence 48999999 566 999999999999884 469999974
No 145
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=52.37 E-value=38 Score=22.49 Aligned_cols=54 Identities=9% Similarity=0.241 Sum_probs=28.9
Q ss_pred CCEEEEEEEEEecc-eEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEe
Q 032149 77 GSVVIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 77 GdiViG~V~~v~~~-~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
.--+.|+|+..-++ ++.|.+ .....-+-|++. ... ..+=...|||+|..+.-.+
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~--------edg~~~~ahI~G----Kmr--~~~i~I~~GD~V~Ve~~~~ 60 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVEL--------ENGHERLAHISG----KMR--KNRIRILPGDVVLVELSPY 60 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEe--------cCCcEEEEEccC----cch--heeEEeCCCCEEEEEeccc
Confidence 34588999998654 455554 222222222211 001 2244668899988776443
No 146
>PRK07252 hypothetical protein; Provisional
Probab=51.34 E-value=50 Score=23.53 Aligned_cols=28 Identities=18% Similarity=0.188 Sum_probs=20.9
Q ss_pred CCCCCCEEEEEEEEEec--ceEEEEEEeec
Q 032149 73 VPEPGSVVIARVTKVMT--RMASADIMCVG 100 (146)
Q Consensus 73 ~P~~GdiViG~V~~v~~--~~~~v~I~~v~ 100 (146)
..++||.|.++|.++.. ..+.+.+..++
T Consensus 47 ~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~ 76 (120)
T PRK07252 47 LLKVGEEVLVQVVDFDEYTGKASLSLRTLE 76 (120)
T ss_pred ccCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence 36999999999999986 44555554443
No 147
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=50.75 E-value=17 Score=33.27 Aligned_cols=58 Identities=17% Similarity=0.244 Sum_probs=48.7
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEEee
Q 032149 72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVSFM 145 (146)
Q Consensus 72 ~~P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis~~ 145 (146)
.--+.|.+=-|.|+++....+++++ ++...|++|.+|... ..-|.+||-+..+|.++.
T Consensus 118 ~Dve~g~~Y~g~v~~v~~~GvFv~L--------n~~v~GL~~~~d~~~--------~~~~~vgdeiiV~v~~vr 175 (715)
T COG1107 118 EDVEAGKYYKGIVSRVEKYGVFVEL--------NSHVRGLIHRRDLGG--------DPDYAVGDEIIVQVSDVR 175 (715)
T ss_pred hhcccceeeeccccchhhhcceeec--------ChhhhccccccccCC--------CCCCCCCCeEEEEeeccC
Confidence 3458899999999999999999998 888999999776542 366899999999988764
No 148
>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=49.48 E-value=1.3e+02 Score=23.63 Aligned_cols=57 Identities=12% Similarity=0.142 Sum_probs=43.0
Q ss_pred CCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCC----CCCCCCCCCCEEEEEEEEEecceEEEEEEeecc
Q 032149 35 NGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHK----AHGPVPEPGSVVIARVTKVMTRMASADIMCVGA 101 (146)
Q Consensus 35 ~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~----~~~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~ 101 (146)
..-|+|.+-|...+.. ...+..+=+. +...+|+ |..++| +.++.+++..+.|.++.-
T Consensus 52 ~n~I~A~V~~~qtv~~--------Gs~vrlRLle~i~i~g~~IPk-gt~l~G-~~~~~~~Rl~i~I~SI~~ 112 (200)
T PF12508_consen 52 KNTIRAVVDGTQTVVD--------GSRVRLRLLEDIQIGGILIPK-GTYLYG-VASFQGQRLLITITSIEY 112 (200)
T ss_pred CCeEEEEEecceEEeC--------CCEEEEEEcCceEECCEEeCC-CCEEEE-EEeeeccEEEEEEEEEEE
Confidence 7889999999887753 3456554211 3456665 999999 999999999999987653
No 149
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=46.07 E-value=64 Score=21.32 Aligned_cols=17 Identities=18% Similarity=0.298 Sum_probs=11.7
Q ss_pred EEEEEEEEecc-eEEEEE
Q 032149 80 VIARVTKVMTR-MASADI 96 (146)
Q Consensus 80 ViG~V~~v~~~-~~~v~I 96 (146)
++|+|++..++ .+.|..
T Consensus 2 ~i~~V~~~lG~~~~~V~~ 19 (78)
T cd04456 2 QIVRVLRMLGNNRHEVEC 19 (78)
T ss_pred eEEEEEEECCCCEEEEEE
Confidence 58899998654 455555
No 150
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=45.73 E-value=1e+02 Score=25.26 Aligned_cols=61 Identities=16% Similarity=0.237 Sum_probs=35.1
Q ss_pred CCCCEEEEEEEEEecceEEEEEEeeccccc-----ccceeeEEecccccccc--ccccccccCCCCCCEEE
Q 032149 75 EPGSVVIARVTKVMTRMASADIMCVGAKSV-----REKFSGIIRQQDVRATE--IDKVDMHLSFRPGDIVR 138 (146)
Q Consensus 75 ~~GdiViG~V~~v~~~~~~v~I~~v~~~~l-----~~~~~g~l~~sdi~~~~--~d~~~~~~~~~~GDiV~ 138 (146)
.-| ++|+|+.|..+...|..++-.+..+ +..+..+... +-.+.. .........+++||+|.
T Consensus 153 ~~G--LVG~V~~V~~~tS~V~Lltd~~~~i~v~i~r~~~~~i~~~-d~~~~~l~~~~~~~~~~i~~GD~vv 220 (284)
T COG1792 153 EGG--LVGKVVEVSKNTSRVLLLTDVNSKIPVKINRGDIGVIVGG-DGENDLLLLVYLPPNSDIKEGDLVV 220 (284)
T ss_pred CCc--eEEEEEEEcCceeEEEEeeccccceeEEeccCceeEEEec-CCCCCceeeeeccCCCCccCCCEEE
Confidence 445 8999999999999999987543221 1122222211 111111 11335677889999775
No 151
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=43.09 E-value=80 Score=20.85 Aligned_cols=16 Identities=13% Similarity=0.229 Sum_probs=13.1
Q ss_pred EEEEEEEecceEEEEE
Q 032149 81 IARVTKVMTRMASADI 96 (146)
Q Consensus 81 iG~V~~v~~~~~~v~I 96 (146)
=|+|+++.++.+.|+.
T Consensus 6 P~~V~~i~~~~A~v~~ 21 (76)
T TIGR00074 6 PGQVVEIDENIALVEF 21 (76)
T ss_pred ceEEEEEcCCEEEEEc
Confidence 3788899888888886
No 152
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=41.54 E-value=1e+02 Score=21.04 Aligned_cols=15 Identities=20% Similarity=0.288 Sum_probs=12.5
Q ss_pred cccccCCCCCCEEEE
Q 032149 125 VDMHLSFRPGDIVRA 139 (146)
Q Consensus 125 ~~~~~~~~~GDiV~A 139 (146)
....+.|++||.|..
T Consensus 71 i~~~~~Lk~GD~V~l 85 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLL 85 (100)
T ss_pred EEEecCCcCCCEEEE
Confidence 567889999999874
No 153
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=41.37 E-value=81 Score=21.87 Aligned_cols=20 Identities=0% Similarity=0.111 Sum_probs=14.6
Q ss_pred CCEEEEEEEEEecc-eEEEEE
Q 032149 77 GSVVIARVTKVMTR-MASADI 96 (146)
Q Consensus 77 GdiViG~V~~v~~~-~~~v~I 96 (146)
-+-++|+|+...++ .+.|.+
T Consensus 18 e~e~~g~V~~~lG~~~~~V~~ 38 (99)
T TIGR00523 18 EGEILGVIEQMLGAGRVKVRC 38 (99)
T ss_pred CCEEEEEEEEEcCCCEEEEEe
Confidence 56699999999664 455554
No 154
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=40.70 E-value=86 Score=20.34 Aligned_cols=17 Identities=12% Similarity=0.272 Sum_probs=11.2
Q ss_pred EEEEEEEEecce-EEEEE
Q 032149 80 VIARVTKVMTRM-ASADI 96 (146)
Q Consensus 80 ViG~V~~v~~~~-~~v~I 96 (146)
+.|.|+..-++. +.|.+
T Consensus 7 ~~G~V~e~L~~~~f~V~l 24 (68)
T TIGR00008 7 MEGKVTESLPNAMFRVEL 24 (68)
T ss_pred EEEEEEEECCCCEEEEEE
Confidence 678888886543 55554
No 155
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=40.13 E-value=64 Score=25.27 Aligned_cols=69 Identities=16% Similarity=0.131 Sum_probs=42.0
Q ss_pred CCCCCEEEEEEEEEecceEEEEEEeecccccccceeeEEec------ccccccc-c--cccccccCCCCCCEEEEEEEEe
Q 032149 74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQ------QDVRATE-I--DKVDMHLSFRPGDIVRASVVSF 144 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~------sdi~~~~-~--d~~~~~~~~~~GDiV~A~Vis~ 144 (146)
|-+|.++.|+|.........|.+.-.++--.. -.++.+. +++=-++ . |--.-.-+|++|..|+=||.+.
T Consensus 79 PF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP--~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e 156 (202)
T KOG3297|consen 79 PFVGEVITGKIKECSEEGLRVTLGFFDDIFIP--KEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDE 156 (202)
T ss_pred cccceEEEEEeecCCccceEEEEEeeeceeec--hhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeee
Confidence 78899999999999999999999655542111 0111111 1110000 0 0012345789999999999864
No 156
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=39.73 E-value=1e+02 Score=19.75 Aligned_cols=48 Identities=21% Similarity=0.378 Sum_probs=26.7
Q ss_pred EEEEEEEEecc-eEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEE
Q 032149 80 VIARVTKVMTR-MASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASV 141 (146)
Q Consensus 80 ViG~V~~v~~~-~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~V 141 (146)
..|+|++..++ .+.|.. -++....-...|-++.+.+ ...+||.|..++
T Consensus 9 ~~G~Vi~~~~~~~y~V~~--~~g~~~~c~~~Gklr~~~i------------~i~vGD~V~ve~ 57 (72)
T PRK00276 9 MEGTVVEALPNAMFRVEL--ENGHEVLAHISGKMRKNYI------------RILPGDKVTVEL 57 (72)
T ss_pred EEEEEEEEcCCCEEEEEe--CCCCEEEEEEccceeeCCc------------ccCCCCEEEEEE
Confidence 45899998766 666642 2222222334454443222 257888887764
No 157
>PLN00208 translation initiation factor (eIF); Provisional
Probab=39.18 E-value=58 Score=24.33 Aligned_cols=40 Identities=18% Similarity=0.212 Sum_probs=25.2
Q ss_pred CcEEec--CCccCCCCCeeeCCcEEEE--cCCCeEEEEEeeeEEE
Q 032149 8 MVLVTP--GEVLGKATEVKAGKGAYVA--KHNGLVYASLTGLLRT 48 (146)
Q Consensus 8 ~~iV~P--Gd~l~~~~~~~~G~Gty~~--~~~g~i~As~~G~~~~ 48 (146)
..+.+| ||.++... -..|.|.|+. .++....|.+.|.++.
T Consensus 24 ~el~~p~egq~~g~V~-~~lGn~~~~V~c~dG~~rLa~IpGKmRK 67 (145)
T PLN00208 24 RELIFKEDGQEYAQVL-RMLGNGRCEALCIDGTKRLCHIRGKMRK 67 (145)
T ss_pred eecccCCCCcEEEEEE-EEcCCCEEEEEECCCCEEEEEEecccee
Confidence 345666 55555422 4678888853 2255788888888765
No 158
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=38.64 E-value=1.8e+02 Score=22.26 Aligned_cols=69 Identities=17% Similarity=0.221 Sum_probs=40.3
Q ss_pred EEecCCccC--CCCCeeeCCcEEEEcCCCeEEEEEeeeEEEcCCCCCCCCCCCeEEEecCCC---CCCCCCCCC-E-EEE
Q 032149 10 LVTPGEVLG--KATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA---HGPVPEPGS-V-VIA 82 (146)
Q Consensus 10 iV~PGd~l~--~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~~~~~~~~~~~~~i~V~p~~~---~~~~P~~Gd-i-ViG 82 (146)
...|||.|. ...+...|.+.|...++|..+.-.+.... +..+.+...+. ....+...+ + +||
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 467888644 34456777777766545566666655432 13454554421 233456666 5 899
Q ss_pred EEEEEec
Q 032149 83 RVTKVMT 89 (146)
Q Consensus 83 ~V~~v~~ 89 (146)
+|..+..
T Consensus 205 rVv~~~~ 211 (214)
T COG2932 205 RVVWVSR 211 (214)
T ss_pred EEEEEee
Confidence 9987643
No 159
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=37.58 E-value=74 Score=21.05 Aligned_cols=23 Identities=35% Similarity=0.483 Sum_probs=21.4
Q ss_pred CCCCEEEEEEEEEecceEEEEEE
Q 032149 75 EPGSVVIARVTKVMTRMASADIM 97 (146)
Q Consensus 75 ~~GdiViG~V~~v~~~~~~v~I~ 97 (146)
++||.|.=+|+++.+++++-++.
T Consensus 47 ~~Gd~V~vkI~~v~~~~afaevv 69 (73)
T COG3269 47 EVGDEVKVKITKVKPNFAFAEVV 69 (73)
T ss_pred CCCCeeeEEEEEeeccceeeEEe
Confidence 78999999999999999998884
No 160
>cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=37.06 E-value=47 Score=23.98 Aligned_cols=27 Identities=22% Similarity=0.369 Sum_probs=23.4
Q ss_pred eeeCCcEEEEcCCCeEEEEEeeeEEEc
Q 032149 23 VKAGKGAYVAKHNGLVYASLTGLLRTL 49 (146)
Q Consensus 23 ~~~G~Gty~~~~~g~i~As~~G~~~~~ 49 (146)
-..|.|+...+.++++||.+.|.+...
T Consensus 23 ~~lG~GvaI~P~~~~v~AP~~G~v~~i 49 (124)
T cd00210 23 KMMGDGFAIKPSDGKVVAPVDGTIVQI 49 (124)
T ss_pred cCccceEEEEccCCeEECcCCeEEEEE
Confidence 467899999888999999999998764
No 161
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=36.21 E-value=1.4e+02 Score=20.38 Aligned_cols=17 Identities=12% Similarity=0.108 Sum_probs=9.3
Q ss_pred EEEEEEEEecc-eEEEEE
Q 032149 80 VIARVTKVMTR-MASADI 96 (146)
Q Consensus 80 ViG~V~~v~~~-~~~v~I 96 (146)
+.|.|+.+.++ .+.|.+
T Consensus 9 ~~G~V~e~Lp~~~frV~L 26 (87)
T PRK12442 9 LDGIVDEVLPDSRFRVTL 26 (87)
T ss_pred EEEEEEEECCCCEEEEEe
Confidence 56777776443 344444
No 162
>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=36.16 E-value=58 Score=21.45 Aligned_cols=25 Identities=16% Similarity=0.219 Sum_probs=16.2
Q ss_pred eeCCcEEEE--cCCCeEEEEEeeeEEE
Q 032149 24 KAGKGAYVA--KHNGLVYASLTGLLRT 48 (146)
Q Consensus 24 ~~G~Gty~~--~~~g~i~As~~G~~~~ 48 (146)
..|.|.|.- +++..+.|.+.|..+.
T Consensus 9 ~~g~~~~~V~~~~g~~~la~i~gK~rk 35 (77)
T cd05793 9 MLGNGRLEVRCFDGKKRLCRIRGKMRK 35 (77)
T ss_pred EcCCCEEEEEECCCCEEEEEEchhhcc
Confidence 457777752 2255788888887643
No 163
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=35.34 E-value=75 Score=24.15 Aligned_cols=22 Identities=18% Similarity=0.113 Sum_probs=18.9
Q ss_pred CCCCCEEEEEEEEEecceEEEEE
Q 032149 74 PEPGSVVIARVTKVMTRMASADI 96 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~~~~v~I 96 (146)
.++||+|.++|.++. +.+.+.+
T Consensus 119 ~~~GD~V~akV~~i~-~~i~LS~ 140 (189)
T PRK09521 119 FKIGDIVRAKVISYT-DPLQLST 140 (189)
T ss_pred cCCCCEEEEEEEecC-CcEEEEE
Confidence 589999999999999 6677666
No 164
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=34.25 E-value=1.5e+02 Score=24.53 Aligned_cols=54 Identities=15% Similarity=0.034 Sum_probs=39.6
Q ss_pred CCCCCEEEEEEEEEe-cceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEE
Q 032149 74 PEPGSVVIARVTKVM-TRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASV 141 (146)
Q Consensus 74 P~~GdiViG~V~~v~-~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~V 141 (146)
.++|..-.++|+.++ ...++++. ..+-.-+++.++.+.-. +-++++||-+.+.+
T Consensus 71 ~tvg~~g~~~Vv~v~~~lGaFlD~--------Gl~KDl~vp~~elp~~~------~~wpq~Gd~l~v~l 125 (287)
T COG2996 71 ATVGEYGWLKVVEVNKDLGAFLDW--------GLPKDLLVPLDELPTLK------SLWPQKGDKLLVYL 125 (287)
T ss_pred EeecceeEEEEEEEcCCcceEEec--------CCCcceeeehhhccccc------ccCCCCCCEEEEEE
Confidence 489999999999999 67799998 55555666666554211 44578888877654
No 165
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=34.02 E-value=1.7e+02 Score=24.85 Aligned_cols=22 Identities=9% Similarity=0.058 Sum_probs=18.7
Q ss_pred EEEEEEEEecceEEEEEEeecc
Q 032149 80 VIARVTKVMTRMASADIMCVGA 101 (146)
Q Consensus 80 ViG~V~~v~~~~~~v~I~~v~~ 101 (146)
++|+|+++.++.+.|..+.-.+
T Consensus 143 LVGrV~~Vs~~sSrVlLITD~~ 164 (337)
T PRK14872 143 LVGLVDYVGEHQSRVRLITDVG 164 (337)
T ss_pred CEEEEEEECCCeEEEEEEEcCC
Confidence 6799999999999999876543
No 166
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=33.66 E-value=1.3e+02 Score=19.26 Aligned_cols=17 Identities=35% Similarity=0.395 Sum_probs=13.6
Q ss_pred EEEEEEEEe--cceEEEEE
Q 032149 80 VIARVTKVM--TRMASADI 96 (146)
Q Consensus 80 ViG~V~~v~--~~~~~v~I 96 (146)
+=++|+++. +..|.|+.
T Consensus 5 iP~~Vv~v~~~~~~A~v~~ 23 (68)
T PF01455_consen 5 IPGRVVEVDEDGGMAVVDF 23 (68)
T ss_dssp EEEEEEEEETTTTEEEEEE
T ss_pred ccEEEEEEeCCCCEEEEEc
Confidence 347899998 78888886
No 167
>COG1465 Predicted alternative 3-dehydroquinate synthase [Amino acid transport and metabolism]
Probab=33.50 E-value=1.1e+02 Score=25.93 Aligned_cols=40 Identities=20% Similarity=0.365 Sum_probs=30.0
Q ss_pred EEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEeeeEEEc
Q 032149 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTL 49 (146)
Q Consensus 10 iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G~~~~~ 49 (146)
+-+||..=-...|+.+|.-+-.-..+|+-++++.|++++.
T Consensus 268 i~vPg~kTkYLaEL~aGDeV~iVD~dGr~R~aiVGRvKIE 307 (376)
T COG1465 268 IRVPGGKTKYLAELKAGDEVLIVDFDGRTRSAIVGRVKIE 307 (376)
T ss_pred EEcCCCceEEhhhhcCCCeEEEEecCCceeEEEEEEEEee
Confidence 4567876554566778876665444999999999999994
No 168
>PF14444 S1-like: S1-like
Probab=32.06 E-value=51 Score=20.83 Aligned_cols=16 Identities=31% Similarity=0.528 Sum_probs=12.8
Q ss_pred CCCCCCCCEEEEEEEE
Q 032149 71 GPVPEPGSVVIARVTK 86 (146)
Q Consensus 71 ~~~P~~GdiViG~V~~ 86 (146)
-++|++||.|++.-+.
T Consensus 31 G~~P~vGdrV~v~A~~ 46 (58)
T PF14444_consen 31 GNVPKVGDRVLVEAIY 46 (58)
T ss_pred cCCCccCCEEEEEEEe
Confidence 3689999999987654
No 169
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=30.97 E-value=1.8e+02 Score=20.74 Aligned_cols=16 Identities=38% Similarity=0.360 Sum_probs=13.7
Q ss_pred ccccCCCCCCEEEEEE
Q 032149 126 DMHLSFRPGDIVRASV 141 (146)
Q Consensus 126 ~~~~~~~~GDiV~A~V 141 (146)
.++..+++||-|.|+.
T Consensus 51 ~~~~~L~~GD~VLA~~ 66 (124)
T PF15057_consen 51 AMRHSLQVGDKVLAPW 66 (124)
T ss_pred cccCcCCCCCEEEEec
Confidence 5588999999999974
No 170
>TIGR00830 PTBA PTS system, glucose subfamily, IIA component. These are part of the The PTS Glucose-Glucoside (Glc) SuperFamily. The Glc family includes permeases specific for glucose, N-acetylglucosamine and a large variety of a- and b-glucosides. However, not all b-glucoside PTS permeases are in this class, as the cellobiose (Cel) b-glucoside PTS permease is in the Lac family (TC #4.A.3). The IIA, IIB and IIC domains of all of the permeases listed below are demonstrably homologous. These permeases show limited sequence similarity with members of the Fru family (TC #4.A.2). Several of the PTS permeases in the Glc family lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). Most of these permeases have the B and C domains linked together in a single polypeptide chain, and a cysteyl residue in the IIB domain is phosphorylated by direct phosphoryl transfer from IIAglc(his~P). Those permeases which lack a IIA domain include the maltose (Mal), arbutin-salicin-c
Probab=30.52 E-value=74 Score=22.86 Aligned_cols=27 Identities=22% Similarity=0.363 Sum_probs=23.3
Q ss_pred eeeCCcEEEEcCCCeEEEEEeeeEEEc
Q 032149 23 VKAGKGAYVAKHNGLVYASLTGLLRTL 49 (146)
Q Consensus 23 ~~~G~Gty~~~~~g~i~As~~G~~~~~ 49 (146)
-..|.|.-..+.+++++|.+.|.+...
T Consensus 23 ~~~G~G~aI~P~~~~v~AP~~G~v~~v 49 (121)
T TIGR00830 23 KIVGDGFAILPTDGKVVAPVDGKIGKI 49 (121)
T ss_pred cCccceEEEEcCCCeEEccCCeEEEEE
Confidence 467899999888999999999988764
No 171
>PF11720 Inhibitor_I78: Peptidase inhibitor I78 family; InterPro: IPR021719 This family includes Aspergillus elastase inhibitor and belongs to MEROPS peptidase inhibitor family I78.
Probab=29.95 E-value=85 Score=19.44 Aligned_cols=35 Identities=11% Similarity=0.362 Sum_probs=24.4
Q ss_pred CcEEecCCccCCCCCeeeCCcEEEEcCCCeEEEEEee
Q 032149 8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTG 44 (146)
Q Consensus 8 ~~iV~PGd~l~~~~~~~~G~Gty~~~~~g~i~As~~G 44 (146)
-+++-||+.+ +.+|.+..=......+|.|.+..+|
T Consensus 26 ~Rvi~Pg~~v--TmDyr~dRLnv~~D~~g~I~~v~CG 60 (60)
T PF11720_consen 26 VRVIRPGDAV--TMDYRPDRLNVEVDDDGVITRVRCG 60 (60)
T ss_pred eEEeCCCCcC--cccCCCCcEEEEECCCCcEEEEecC
Confidence 4678899975 4678888844433237888887776
No 172
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=29.89 E-value=1.2e+02 Score=21.20 Aligned_cols=23 Identities=30% Similarity=0.410 Sum_probs=20.2
Q ss_pred CCCCCEE------EEEEEEEecceEEEEE
Q 032149 74 PEPGSVV------IARVTKVMTRMASADI 96 (146)
Q Consensus 74 P~~GdiV------iG~V~~v~~~~~~v~I 96 (146)
.++||.| +|+|+++.++.+.++|
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 5788888 7999999999888888
No 173
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=28.96 E-value=50 Score=25.64 Aligned_cols=15 Identities=40% Similarity=0.350 Sum_probs=13.2
Q ss_pred CCCCEEEEEEEEeeC
Q 032149 132 RPGDIVRASVVSFML 146 (146)
Q Consensus 132 ~~GDiV~A~Vis~~~ 146 (146)
..||||.|||.++.+
T Consensus 67 ~~G~IVtarV~~i~~ 81 (193)
T KOG3409|consen 67 FVGAIVTARVSRINL 81 (193)
T ss_pred ccCcEEEEEEEeecc
Confidence 789999999998764
No 174
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=27.81 E-value=96 Score=24.57 Aligned_cols=23 Identities=22% Similarity=0.258 Sum_probs=17.9
Q ss_pred CCCCCEEEEEEEEEecc-eEEEEE
Q 032149 74 PEPGSVVIARVTKVMTR-MASADI 96 (146)
Q Consensus 74 P~~GdiViG~V~~v~~~-~~~v~I 96 (146)
.++||+|.|+|.++.+. .+.+.+
T Consensus 112 ~~~GDlV~akV~~i~~~~~~~LS~ 135 (235)
T PRK04163 112 LDIGDYIIAKVKDVDRTRDVVLTL 135 (235)
T ss_pred CCCCCEEEEEEEEECCCCcEEEEE
Confidence 59999999999999764 355554
No 175
>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=27.18 E-value=2.1e+02 Score=19.51 Aligned_cols=41 Identities=22% Similarity=0.321 Sum_probs=24.0
Q ss_pred CCeEEEecCCCCCCCCCCCCEEEEEEEEEecceEEEEEEeecc
Q 032149 59 RPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGA 101 (146)
Q Consensus 59 ~~~i~V~p~~~~~~~P~~GdiViG~V~~v~~~~~~v~I~~v~~ 101 (146)
.+++.+.........|++||.++- .+-....+.+++..+.-
T Consensus 16 ~Ktat~r~~~~~~~~~k~Gd~~i~--~~~~~~~~~i~v~~V~~ 56 (105)
T cd06541 16 RKTIEIRSLDIYEQLPKAGDYLII--LDGQQPLAIAEVVKVEI 56 (105)
T ss_pred CCEEEEEcchhcccCCCCCCEEEE--ecCCCcEEEEEEEEEEE
Confidence 356666654334577999999883 33222245555555543
No 176
>COG2190 NagE Phosphotransferase system IIA components [Carbohydrate transport and metabolism]
Probab=26.75 E-value=70 Score=24.18 Aligned_cols=28 Identities=25% Similarity=0.386 Sum_probs=24.3
Q ss_pred CeeeCCcEEEEcCCCeEEEEEeeeEEEc
Q 032149 22 EVKAGKGAYVAKHNGLVYASLTGLLRTL 49 (146)
Q Consensus 22 ~~~~G~Gty~~~~~g~i~As~~G~~~~~ 49 (146)
+-+.|.|.-..+.+|+++|++.|.+...
T Consensus 29 ~k~mGdGiAI~P~~g~vvAPvdG~v~~i 56 (156)
T COG2190 29 EKMVGDGVAIKPSEGEVVAPVDGTVVLI 56 (156)
T ss_pred cccccCcEEEecCCCeEEeccCcEEEEE
Confidence 4678999999998999999999987653
No 177
>PRK09439 PTS system glucose-specific transporter subunit; Provisional
Probab=26.67 E-value=71 Score=24.31 Aligned_cols=42 Identities=19% Similarity=0.390 Sum_probs=31.9
Q ss_pred cEEec--CCccCCCC-------CeeeCCcEEEEcCCCeEEEEEeeeEEEcC
Q 032149 9 VLVTP--GEVLGKAT-------EVKAGKGAYVAKHNGLVYASLTGLLRTLS 50 (146)
Q Consensus 9 ~iV~P--Gd~l~~~~-------~~~~G~Gty~~~~~g~i~As~~G~~~~~~ 50 (146)
.+..| |..+.-.+ +-..|.|.-..+.+|++||.+.|.+...-
T Consensus 22 ~i~aP~~G~vi~L~~V~D~vFs~k~mGdGvAI~P~~~~v~AP~dG~V~~vf 72 (169)
T PRK09439 22 EIIAPLSGEIVNIEDVPDVVFAEKIVGDGIAIKPTGNKMVAPVDGTIGKIF 72 (169)
T ss_pred EEEecCCeEEEEhHHCCChHhcccCccceEEEEccCCEEEecCCeEEEEEc
Confidence 45566 77665422 35679999999989999999999987654
No 178
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=26.37 E-value=1.6e+02 Score=17.83 Aligned_cols=54 Identities=20% Similarity=0.367 Sum_probs=32.2
Q ss_pred CEEEEEEEEEecceEEEEEEe-ecccccccceeeEEeccccccccccccccccCCCCCCEEEEEEEE
Q 032149 78 SVVIARVTKVMTRMASADIMC-VGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVVS 143 (146)
Q Consensus 78 diViG~V~~v~~~~~~v~I~~-v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~Vis 143 (146)
...-|+|.++......+++.. .++ ...+.+.+..+.+ ..-.|++||-|.|.+-+
T Consensus 7 N~l~g~I~~i~~~g~~~~v~l~~~~---~~~l~a~i~~~~~---------~~l~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 7 NQLKGKVVAIEDGDVNAEVDLLLGG---GTKLTAVITLESV---------AELGLKPGKEVYAVIKA 61 (69)
T ss_pred cEEEEEEEEEEECCCeEEEEEEECC---CCEEEEEecHHHH---------hhCCCCCCCEEEEEEEC
Confidence 467899999966555555521 111 1145555554332 24457899999988754
No 179
>COG4714 Uncharacterized membrane-anchored protein conserved in bacteria [Function unknown]
Probab=25.93 E-value=33 Score=27.94 Aligned_cols=46 Identities=22% Similarity=0.245 Sum_probs=38.6
Q ss_pred EEEEEEEEecceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCC
Q 032149 80 VIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGD 135 (146)
Q Consensus 80 ViG~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GD 135 (146)
-+|.|..-....|+++| ...-+|.+.-.|.+.++.| ++.+.++.|+
T Consensus 94 ~lGlVm~~~~~ew~~~i--------~yddsGYvkDddAk~Wdad--~Lf~~lreGt 139 (303)
T COG4714 94 RLGLVMEDNDSEWIADI--------LYDDSGYVKDDDAKKWDAD--ALFTALREGT 139 (303)
T ss_pred ceeEEeecCCcceEEEE--------EecccCcccccccccCCHH--HHHHHHHhcc
Confidence 57888888888899999 5667899998898888888 8888888776
No 180
>CHL00010 infA translation initiation factor 1
Probab=25.74 E-value=2e+02 Score=18.79 Aligned_cols=48 Identities=25% Similarity=0.336 Sum_probs=26.1
Q ss_pred EEEEEEEEe-cceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEEE
Q 032149 80 VIARVTKVM-TRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASV 141 (146)
Q Consensus 80 ViG~V~~v~-~~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~V 141 (146)
+.|+|++.. ...+.|.. -++....-...|-++.+ .-...+||.|..++
T Consensus 9 ~~G~Vik~lg~~~y~V~~--~~g~~~~c~~rGklr~~------------~i~~~vGD~V~ve~ 57 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRL--DNGCQVLGYISGKIRRN------------SIRILPGDRVKVEL 57 (78)
T ss_pred EEEEEEEEcCCCEEEEEe--CCCCEEEEEeccceecC------------CcccCCCCEEEEEE
Confidence 568999988 46666643 22222222344544422 12246788887663
No 181
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=25.49 E-value=1.8e+02 Score=21.59 Aligned_cols=17 Identities=18% Similarity=-0.036 Sum_probs=15.0
Q ss_pred EEEEEEEecceEEEEEE
Q 032149 81 IARVTKVMTRMASADIM 97 (146)
Q Consensus 81 iG~V~~v~~~~~~v~I~ 97 (146)
.|+|+++.++.++|+..
T Consensus 5 ~~~Vv~v~~~~a~Ve~~ 21 (154)
T PRK10862 5 WATVVSWQNGIALLRCE 21 (154)
T ss_pred EEEEEEEECCEEEEEEe
Confidence 58999999999999984
No 182
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=23.74 E-value=1.9e+02 Score=19.76 Aligned_cols=16 Identities=13% Similarity=0.233 Sum_probs=13.0
Q ss_pred EEEEEEEecceEEEEE
Q 032149 81 IARVTKVMTRMASADI 96 (146)
Q Consensus 81 iG~V~~v~~~~~~v~I 96 (146)
=|+|+++.+..+.|+.
T Consensus 6 P~kVv~i~~~~A~vd~ 21 (90)
T PRK10409 6 PGQIRTIDGNQAKVDV 21 (90)
T ss_pred ceEEEEEcCCeEEEEc
Confidence 3788888888888886
No 183
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=23.16 E-value=62 Score=19.71 Aligned_cols=15 Identities=33% Similarity=0.545 Sum_probs=10.7
Q ss_pred ccccCCCCCCEEEEE
Q 032149 126 DMHLSFRPGDIVRAS 140 (146)
Q Consensus 126 ~~~~~~~~GDiV~A~ 140 (146)
+|.+.|..||+|.+.
T Consensus 6 SM~P~i~~Gd~v~v~ 20 (70)
T PF00717_consen 6 SMEPTIKDGDIVLVD 20 (70)
T ss_dssp TTGGTSSTTEEEEEE
T ss_pred CcccCeeCCCEEEEE
Confidence 677777777777654
No 184
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=21.83 E-value=86 Score=25.36 Aligned_cols=26 Identities=23% Similarity=0.289 Sum_probs=19.8
Q ss_pred CCCCCCCCEEEEEEEEEecce-EEEEE
Q 032149 71 GPVPEPGSVVIARVTKVMTRM-ASADI 96 (146)
Q Consensus 71 ~~~P~~GdiViG~V~~v~~~~-~~v~I 96 (146)
+...++||.|+++|..+.... +.+..
T Consensus 110 r~~l~vGD~v~AkV~~vd~~~~~~L~~ 136 (239)
T COG1097 110 RPFLNVGDLVYAKVVDVDRDGEVELTL 136 (239)
T ss_pred ccccccCCEEEEEEEEccCCCceEEEe
Confidence 344699999999999997654 55554
No 185
>COG4873 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.53 E-value=2.5e+02 Score=18.41 Aligned_cols=22 Identities=18% Similarity=0.167 Sum_probs=18.5
Q ss_pred EEEEEEEEecceEEEEEEeecc
Q 032149 80 VIARVTKVMTRMASADIMCVGA 101 (146)
Q Consensus 80 ViG~V~~v~~~~~~v~I~~v~~ 101 (146)
..|+|..+..+.+.|++.--++
T Consensus 36 l~g~vek~nensvivdlt~men 57 (81)
T COG4873 36 LTGVVEKVNENSVIVDLTIMEN 57 (81)
T ss_pred ceeeeeeecCCcEEEEEEeecc
Confidence 4799999999999999965544
No 186
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.
Probab=21.49 E-value=2.7e+02 Score=24.64 Aligned_cols=55 Identities=9% Similarity=0.108 Sum_probs=32.1
Q ss_pred EEEEEEEEEec--ceEEEEEEeecccccccceeeEEeccccccccccccccccCCCCCCEEEEE
Q 032149 79 VVIARVTKVMT--RMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRAS 140 (146)
Q Consensus 79 iViG~V~~v~~--~~~~v~I~~v~~~~l~~~~~g~l~~sdi~~~~~d~~~~~~~~~~GDiV~A~ 140 (146)
.|-|+|..++. +.++++|-.- ....|.++...++.....+ .....++.||+|.++
T Consensus 57 ~v~Grv~~~R~~gk~~F~~l~D~-----~g~iQ~~~~~~~~~~~~~~--~~~~~l~~gd~V~v~ 113 (496)
T TIGR00499 57 SIAGRIMARRSMGKATFITLQDE-----SGQIQLYVNKDDLPEDFYE--FDEYLLDLGDIIGVT 113 (496)
T ss_pred EEEEEEEEEecCCCeEEEEEEcC-----CccEEEEEECCcCcHHHHH--HHHhcCCCCCEEEEE
Confidence 46799999975 3477777211 2346777765443211101 122358999998764
No 187
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=21.47 E-value=64 Score=23.73 Aligned_cols=15 Identities=33% Similarity=0.649 Sum_probs=12.1
Q ss_pred ccccCCCCCCEEEEE
Q 032149 126 DMHLSFRPGDIVRAS 140 (146)
Q Consensus 126 ~~~~~~~~GDiV~A~ 140 (146)
+..+.|.|||+|+-+
T Consensus 57 e~~~~~~PGDIirLt 71 (134)
T KOG3416|consen 57 EEGCLIQPGDIIRLT 71 (134)
T ss_pred CcCcccCCccEEEec
Confidence 457889999999853
No 188
>PF08865 DUF1830: Domain of unknown function (DUF1830); InterPro: IPR014964 This group of short proteins is functionally uncharacterised.
Probab=21.06 E-value=44 Score=21.71 Aligned_cols=20 Identities=35% Similarity=0.326 Sum_probs=12.6
Q ss_pred cEEecCCccCCCCCeeeCCcEEEE
Q 032149 9 VLVTPGEVLGKATEVKAGKGAYVA 32 (146)
Q Consensus 9 ~iV~PGd~l~~~~~~~~G~Gty~~ 32 (146)
++|+|||.+. |.+.++.+..
T Consensus 25 RVVFP~e~l~----FeAp~~A~LE 44 (68)
T PF08865_consen 25 RVVFPGERLL----FEAPPEARLE 44 (68)
T ss_pred EEEcCCcEEE----EEcCCCCEEE
Confidence 5899999874 3444444433
No 189
>PF13375 RnfC_N: RnfC Barrel sandwich hybrid domain
Probab=20.64 E-value=95 Score=21.47 Aligned_cols=12 Identities=25% Similarity=0.390 Sum_probs=8.6
Q ss_pred eEEEEEeeeEEE
Q 032149 37 LVYASLTGLLRT 48 (146)
Q Consensus 37 ~i~As~~G~~~~ 48 (146)
.|+||+.|.+.-
T Consensus 68 ~iHAsvSG~V~~ 79 (101)
T PF13375_consen 68 PIHASVSGTVTA 79 (101)
T ss_pred eEEcCCCeEEEE
Confidence 567888887754
No 190
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=20.11 E-value=3.5e+02 Score=19.61 Aligned_cols=28 Identities=18% Similarity=0.385 Sum_probs=17.9
Q ss_pred eEEEecCCCCCCCCCCCCEEEEEEEEEec
Q 032149 61 TVEVTGHKAHGPVPEPGSVVIARVTKVMT 89 (146)
Q Consensus 61 ~i~V~p~~~~~~~P~~GdiViG~V~~v~~ 89 (146)
.|.|.... .+..-.+||+|.+.|.+-.+
T Consensus 21 ~I~V~gg~-~r~~A~vGD~ivvsVKka~P 48 (122)
T COG0093 21 CIKVLGGS-RRRYAGVGDIIVVSVKKAIP 48 (122)
T ss_pred EEEEeccc-cccccCCCCEEEEEEeeccC
Confidence 45555332 23356888888888877766
No 191
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=20.09 E-value=3.5e+02 Score=20.39 Aligned_cols=25 Identities=16% Similarity=0.235 Sum_probs=20.3
Q ss_pred CCCCCCCEEEEEEEEEecceEEEEE
Q 032149 72 PVPEPGSVVIARVTKVMTRMASADI 96 (146)
Q Consensus 72 ~~P~~GdiViG~V~~v~~~~~~v~I 96 (146)
.-+..|-+|+|+|-.+-.+-..+|-
T Consensus 78 lg~a~gklV~GkIfhiV~~DlYIDF 102 (173)
T KOG4078|consen 78 LGDAKGKLVIGKIFHIVEEDLYIDF 102 (173)
T ss_pred ccCcCCcEEEeeeeeeeccceEEec
Confidence 3367899999999998877777776
Done!