Query psy10116
Match_columns 298
No_of_seqs 256 out of 1112
Neff 5.6
Searched_HMMs 46136
Date Fri Aug 16 18:20:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10116.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10116hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3013|consensus 100.0 7.9E-81 1.7E-85 566.4 19.8 271 25-295 24-300 (301)
2 COG1097 RRP4 RNA-binding prote 100.0 6.4E-50 1.4E-54 363.4 21.6 216 28-250 6-233 (239)
3 PRK04163 exosome complex RNA-b 100.0 7.6E-44 1.6E-48 326.3 23.0 200 28-252 6-211 (235)
4 KOG1004|consensus 100.0 1.4E-32 3.1E-37 244.8 20.7 175 31-216 2-195 (230)
5 PRK09521 exosome complex RNA-b 100.0 3.2E-28 6.9E-33 216.1 17.9 137 29-182 4-153 (189)
6 COG1096 Predicted RNA-binding 99.9 5.3E-26 1.2E-30 200.1 16.2 157 28-216 3-172 (188)
7 cd05790 S1_Rrp40 S1_Rrp40: Rrp 99.9 3.2E-21 6.9E-26 151.8 9.6 75 81-166 1-75 (86)
8 KOG3409|consensus 99.8 7.6E-20 1.7E-24 159.1 13.2 136 29-172 4-154 (193)
9 cd05791 S1_CSL4 S1_CSL4: CSL4, 99.8 8.6E-20 1.9E-24 145.1 9.6 83 82-172 2-92 (92)
10 cd04454 S1_Rrp4_like S1_Rrp4_l 99.8 6.4E-18 1.4E-22 130.2 10.5 82 81-172 1-82 (82)
11 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.7 1E-15 2.3E-20 118.6 10.4 86 81-172 1-86 (86)
12 PF10447 EXOSC1: Exosome compo 99.4 4.2E-13 9E-18 104.9 6.6 64 83-154 1-82 (82)
13 PF14382 ECR1_N: Exosome compl 99.3 1.9E-12 4E-17 87.8 3.5 39 32-70 1-39 (39)
14 COG1098 VacB Predicted RNA bin 99.0 4.3E-10 9.4E-15 93.7 7.0 76 83-168 2-77 (129)
15 cd05704 S1_Rrp5_repeat_hs13 S1 99.0 1.7E-09 3.7E-14 81.8 8.4 70 85-165 2-72 (72)
16 cd05687 S1_RPS1_repeat_ec1_hs1 98.9 4.7E-09 1E-13 78.0 8.4 69 87-165 1-70 (70)
17 cd05691 S1_RPS1_repeat_ec6 S1_ 98.8 2.5E-08 5.3E-13 74.1 8.8 71 87-167 1-72 (73)
18 cd04452 S1_IF2_alpha S1_IF2_al 98.8 2.6E-08 5.6E-13 74.7 8.9 72 84-165 1-75 (76)
19 cd05692 S1_RPS1_repeat_hs4 S1_ 98.8 3.4E-08 7.5E-13 71.7 8.9 69 87-165 1-69 (69)
20 cd05706 S1_Rrp5_repeat_sc10 S1 98.8 4.7E-08 1E-12 73.1 9.3 71 85-165 2-73 (73)
21 PF00575 S1: S1 RNA binding do 98.8 3.5E-08 7.7E-13 73.8 8.5 72 84-165 2-74 (74)
22 cd05705 S1_Rrp5_repeat_hs14 S1 98.8 3.8E-08 8.2E-13 75.0 8.1 72 85-163 2-74 (74)
23 smart00316 S1 Ribosomal protei 98.7 7.1E-08 1.5E-12 69.7 8.6 71 85-165 1-72 (72)
24 PRK08582 hypothetical protein; 98.7 8.2E-08 1.8E-12 81.9 9.8 75 84-168 3-77 (139)
25 cd05708 S1_Rrp5_repeat_sc12 S1 98.7 1.2E-07 2.5E-12 71.0 8.8 74 85-168 1-76 (77)
26 cd05686 S1_pNO40 S1_pNO40: pNO 98.7 2.2E-07 4.8E-12 70.1 9.2 71 84-164 1-72 (73)
27 cd05707 S1_Rrp5_repeat_sc11 S1 98.6 1.5E-07 3.2E-12 69.7 7.9 67 87-163 1-68 (68)
28 cd05698 S1_Rrp5_repeat_hs6_sc5 98.6 3.3E-07 7.2E-12 67.8 8.7 69 87-165 1-70 (70)
29 COG1093 SUI2 Translation initi 98.6 1.4E-07 2.9E-12 87.8 8.0 78 78-165 3-83 (269)
30 PTZ00248 eukaryotic translatio 98.6 1.7E-07 3.7E-12 89.9 8.7 75 82-166 13-90 (319)
31 PRK07252 hypothetical protein; 98.6 3.7E-07 8E-12 76.1 9.3 73 85-167 2-75 (120)
32 cd05693 S1_Rrp5_repeat_hs1_sc1 98.6 3.3E-07 7.1E-12 74.0 8.6 81 85-166 2-96 (100)
33 cd05702 S1_Rrp5_repeat_hs11_sc 98.6 2.7E-07 5.9E-12 68.9 7.5 63 87-157 1-63 (70)
34 PRK08059 general stress protei 98.6 4E-07 8.7E-12 75.9 9.1 75 84-168 5-80 (123)
35 PRK05807 hypothetical protein; 98.5 4.4E-07 9.5E-12 77.2 9.3 72 85-167 4-75 (136)
36 PRK03987 translation initiatio 98.5 2.9E-07 6.4E-12 86.2 9.0 77 81-167 3-82 (262)
37 TIGR00448 rpoE DNA-directed RN 98.5 1.3E-06 2.8E-11 77.1 11.8 86 81-173 76-174 (179)
38 cd05703 S1_Rrp5_repeat_hs12_sc 98.5 7.2E-07 1.6E-11 67.7 8.8 71 87-165 1-72 (73)
39 PRK08563 DNA-directed RNA poly 98.5 4.5E-07 9.7E-12 80.3 8.5 88 81-173 76-174 (187)
40 cd04461 S1_Rrp5_repeat_hs8_sc7 98.5 8.1E-07 1.8E-11 68.4 8.5 73 82-164 10-83 (83)
41 cd05694 S1_Rrp5_repeat_hs2_sc2 98.5 1.3E-06 2.8E-11 66.7 9.1 67 85-167 3-71 (74)
42 COG1095 RPB7 DNA-directed RNA 98.4 6.8E-07 1.5E-11 79.4 7.8 91 81-173 76-174 (183)
43 cd05685 S1_Tex S1_Tex: The C-t 98.4 9.4E-07 2E-11 64.0 7.2 67 87-163 1-68 (68)
44 PHA02945 interferon resistance 98.4 1.2E-06 2.5E-11 69.3 8.1 72 83-165 8-82 (88)
45 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.4 1.6E-06 3.4E-11 64.3 8.3 67 87-163 1-68 (69)
46 cd04472 S1_PNPase S1_PNPase: P 98.4 1.9E-06 4.1E-11 62.8 8.6 67 87-163 1-67 (68)
47 cd04453 S1_RNase_E S1_RNase_E: 98.4 1.7E-06 3.7E-11 68.2 8.6 74 84-164 5-81 (88)
48 cd05688 S1_RPS1_repeat_ec3 S1_ 98.4 1.4E-06 3.1E-11 63.2 7.4 66 86-162 1-67 (68)
49 COG0539 RpsA Ribosomal protein 98.4 1.4E-06 3E-11 88.7 9.7 74 84-168 190-264 (541)
50 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.3 3.6E-06 7.8E-11 63.3 8.1 68 87-164 1-71 (71)
51 PRK07400 30S ribosomal protein 98.3 3.9E-06 8.4E-11 80.6 10.3 76 82-167 27-103 (318)
52 cd04455 S1_NusA S1_NusA: N-uti 98.3 4.5E-06 9.8E-11 62.0 8.3 55 85-156 2-56 (67)
53 cd00164 S1_like S1_like: Ribos 98.2 3.8E-06 8.3E-11 59.4 6.6 64 90-163 1-65 (65)
54 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.2 7.1E-06 1.5E-10 61.0 7.3 65 87-163 1-66 (66)
55 PRK07899 rpsA 30S ribosomal pr 98.2 9.3E-06 2E-10 82.2 10.3 74 84-167 33-107 (486)
56 cd05684 S1_DHX8_helicase S1_DH 98.2 1.3E-05 2.9E-10 60.9 8.6 70 87-166 1-73 (79)
57 PTZ00162 DNA-directed RNA poly 98.2 1.5E-05 3.3E-10 70.6 10.0 91 81-174 76-173 (176)
58 cd04460 S1_RpoE S1_RpoE: RpoE, 98.1 1.1E-05 2.4E-10 64.3 7.7 83 88-172 1-91 (99)
59 cd04473 S1_RecJ_like S1_RecJ_l 98.1 3.4E-05 7.3E-10 58.9 9.5 64 82-163 12-75 (77)
60 cd05690 S1_RPS1_repeat_ec5 S1_ 98.1 1.5E-05 3.3E-10 58.5 7.2 67 87-162 1-68 (69)
61 PRK07400 30S ribosomal protein 98.0 2E-05 4.3E-10 75.8 9.2 74 83-167 193-267 (318)
62 TIGR02696 pppGpp_PNP guanosine 98.0 1.4E-05 3E-10 84.0 8.6 75 83-163 644-718 (719)
63 PRK11824 polynucleotide phosph 98.0 2E-05 4.3E-10 83.0 9.4 99 54-166 591-691 (693)
64 PRK13806 rpsA 30S ribosomal pr 98.0 3.1E-05 6.6E-10 78.4 10.1 75 83-167 199-278 (491)
65 PRK06676 rpsA 30S ribosomal pr 98.0 3.4E-05 7.3E-10 75.4 10.0 74 83-166 14-89 (390)
66 cd04465 S1_RPS1_repeat_ec2_hs2 98.0 4.5E-05 9.7E-10 56.2 8.1 66 87-165 1-67 (67)
67 PRK07899 rpsA 30S ribosomal pr 98.0 4.3E-05 9.4E-10 77.4 10.1 72 84-166 206-278 (486)
68 PRK06299 rpsA 30S ribosomal pr 97.9 5.8E-05 1.2E-09 77.2 10.5 72 84-166 199-271 (565)
69 cd05689 S1_RPS1_repeat_ec4 S1_ 97.9 6.6E-05 1.4E-09 55.8 7.8 64 85-157 2-65 (72)
70 PRK06676 rpsA 30S ribosomal pr 97.9 8.5E-05 1.9E-09 72.5 10.6 72 84-166 190-262 (390)
71 TIGR03591 polynuc_phos polyrib 97.8 3.8E-05 8.2E-10 80.8 7.5 94 54-161 588-683 (684)
72 TIGR00717 rpsA ribosomal prote 97.8 0.00034 7.3E-09 70.7 13.1 74 84-166 270-344 (516)
73 PRK12269 bifunctional cytidyla 97.8 0.00042 9E-09 74.7 14.0 104 53-166 625-737 (863)
74 PRK06299 rpsA 30S ribosomal pr 97.8 0.00029 6.2E-09 72.2 12.3 73 85-167 459-532 (565)
75 PRK12269 bifunctional cytidyla 97.7 0.00016 3.5E-09 77.8 10.4 74 84-166 576-650 (863)
76 PLN00207 polyribonucleotide nu 97.7 9.7E-05 2.1E-09 79.3 8.6 75 83-167 750-825 (891)
77 PRK00087 4-hydroxy-3-methylbut 97.7 0.00018 3.8E-09 75.3 10.2 72 84-166 475-547 (647)
78 TIGR00717 rpsA ribosomal prote 97.7 0.00025 5.3E-09 71.7 10.6 73 83-166 184-257 (516)
79 PRK00087 4-hydroxy-3-methylbut 97.6 0.00028 6.1E-09 73.8 10.5 77 82-168 298-375 (647)
80 COG2183 Tex Transcriptional ac 97.6 0.00011 2.4E-09 77.3 7.4 76 83-168 655-731 (780)
81 PRK13806 rpsA 30S ribosomal pr 97.6 0.00067 1.4E-08 68.8 12.3 73 85-167 378-451 (491)
82 cd04471 S1_RNase_R S1_RNase_R: 97.6 0.00055 1.2E-08 51.7 8.6 72 86-163 1-81 (83)
83 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.5 0.00075 1.6E-08 53.3 8.9 82 86-170 1-88 (88)
84 COG0539 RpsA Ribosomal protein 97.4 0.00039 8.5E-09 71.1 7.6 73 85-167 276-349 (541)
85 TIGR01953 NusA transcription t 97.4 0.00048 1E-08 67.0 7.4 71 81-168 126-200 (341)
86 PRK12327 nusA transcription el 97.4 0.00052 1.1E-08 67.3 7.4 70 81-167 129-201 (362)
87 PRK09202 nusA transcription el 97.3 0.00051 1.1E-08 69.5 7.5 71 81-168 129-202 (470)
88 TIGR00757 RNaseEG ribonuclease 96.9 0.0072 1.6E-07 60.3 10.4 88 73-165 14-109 (414)
89 COG1185 Pnp Polyribonucleotide 96.4 0.0095 2.1E-07 62.3 7.4 74 83-166 616-689 (692)
90 PRK12328 nusA transcription el 96.3 0.011 2.4E-07 58.3 7.0 59 81-156 133-192 (374)
91 PRK12329 nusA transcription el 96.1 0.015 3.2E-07 58.5 7.0 70 81-166 147-225 (449)
92 KOG1070|consensus 96.1 0.019 4.1E-07 64.1 8.1 75 84-168 1160-1235(1710)
93 PHA02858 EIF2a-like PKR inhibi 95.7 0.061 1.3E-06 42.5 7.6 69 83-163 13-84 (86)
94 TIGR02063 RNase_R ribonuclease 95.0 0.087 1.9E-06 55.8 8.4 74 84-163 625-707 (709)
95 PF13509 S1_2: S1 domain; PDB: 94.8 0.19 4.2E-06 36.8 7.5 60 86-164 1-60 (61)
96 PRK11712 ribonuclease G; Provi 94.6 0.22 4.7E-06 51.0 9.8 83 82-165 34-122 (489)
97 PRK11642 exoribonuclease R; Pr 94.4 0.18 4E-06 54.4 9.1 75 84-164 641-724 (813)
98 KOG2916|consensus 94.0 0.077 1.7E-06 50.1 4.7 74 82-165 12-88 (304)
99 PRK10811 rne ribonuclease E; R 94.0 0.28 6.1E-06 53.7 9.3 81 84-165 36-119 (1068)
100 TIGR00358 3_prime_RNase VacB a 93.6 0.3 6.4E-06 51.5 8.6 74 84-163 570-652 (654)
101 COG2996 Predicted RNA-bindinin 92.8 0.39 8.4E-06 45.6 7.3 65 86-168 155-219 (287)
102 cd05699 S1_Rrp5_repeat_hs7 S1_ 92.6 0.73 1.6E-05 35.4 7.2 68 87-163 1-70 (72)
103 KOG1856|consensus 92.3 0.19 4.1E-06 55.5 5.2 77 83-169 982-1062(1299)
104 COG2088 SpoVG Uncharacterized 88.9 1.3 2.8E-05 35.4 5.7 41 197-238 32-73 (95)
105 KOG1070|consensus 88.1 0.65 1.4E-05 52.5 4.8 69 79-155 878-946 (1710)
106 PF10246 MRP-S35: Mitochondria 85.4 4.2 9E-05 33.4 7.0 54 84-154 21-74 (104)
107 KOG3298|consensus 85.4 6.7 0.00015 34.7 8.7 87 81-171 76-169 (170)
108 KOG1067|consensus 85.3 1.6 3.5E-05 45.5 5.5 76 82-167 659-739 (760)
109 PF08292 RNA_pol_Rbc25: RNA po 84.8 3.7 7.9E-05 34.5 6.7 70 84-155 1-75 (122)
110 CHL00121 rpl27 ribosomal prote 83.0 2.5 5.4E-05 33.5 4.6 52 27-78 25-84 (86)
111 COG2996 Predicted RNA-bindinin 81.9 31 0.00067 33.1 12.2 64 83-161 70-134 (287)
112 PF04026 SpoVG: SpoVG; InterP 80.8 3.5 7.7E-05 32.4 4.8 41 197-238 32-73 (84)
113 PRK13259 regulatory protein Sp 79.8 6.4 0.00014 31.8 6.0 52 197-267 32-84 (94)
114 COG1530 CafA Ribonucleases G a 79.7 3.1 6.8E-05 42.5 5.3 75 84-164 35-112 (487)
115 cd02393 PNPase_KH Polynucleoti 76.4 1.8 4E-05 31.5 1.9 40 177-216 5-50 (61)
116 PRK05435 rpmA 50S ribosomal pr 74.7 7.4 0.00016 30.6 4.9 43 27-69 25-70 (82)
117 PF01016 Ribosomal_L27: Riboso 74.7 3.9 8.4E-05 32.2 3.3 43 27-69 24-69 (81)
118 PRK05054 exoribonuclease II; P 72.5 18 0.00038 38.4 8.7 70 82-155 554-633 (644)
119 COG0073 ARC1 EMAP domain [Gene 68.9 36 0.00078 28.3 8.2 76 85-181 17-99 (123)
120 cd05839 BR140_related The PWWP 60.5 19 0.0004 29.9 4.8 74 141-216 1-75 (111)
121 TIGR00062 L27 ribosomal protei 59.7 12 0.00026 29.5 3.4 43 27-69 25-70 (83)
122 KOG3297|consensus 58.8 41 0.00089 30.5 7.0 72 81-154 76-156 (202)
123 smart00652 eIF1a eukaryotic tr 57.7 55 0.0012 25.5 6.8 55 84-154 2-57 (83)
124 cd05791 S1_CSL4 S1_CSL4: CSL4, 56.5 9 0.0002 30.2 2.2 29 84-112 61-90 (92)
125 PF03961 DUF342: Protein of un 55.6 24 0.00052 35.4 5.6 35 45-79 145-182 (451)
126 PF01336 tRNA_anti-codon: OB-f 53.3 56 0.0012 23.2 6.0 62 90-164 3-69 (75)
127 KOG4078|consensus 52.8 23 0.00051 30.8 4.3 59 84-165 80-138 (173)
128 KOG4134|consensus 51.8 16 0.00035 34.1 3.4 69 72-155 93-161 (253)
129 PF15057 DUF4537: Domain of un 50.2 98 0.0021 25.8 7.6 49 92-151 17-66 (124)
130 PF01176 eIF-1a: Translation i 49.6 39 0.00085 24.9 4.6 50 88-152 3-53 (65)
131 COG0211 RpmA Ribosomal protein 49.2 44 0.00096 26.5 5.0 53 27-79 25-85 (87)
132 PLN00208 translation initiatio 48.6 71 0.0015 27.8 6.6 56 83-154 28-84 (145)
133 cd04456 S1_IF1A_like S1_IF1A_l 48.5 1.2E+02 0.0027 23.3 7.8 50 90-154 2-52 (78)
134 COG0557 VacB Exoribonuclease R 48.1 78 0.0017 33.9 8.3 78 85-163 621-702 (706)
135 PTZ00248 eukaryotic translatio 46.3 35 0.00075 33.3 4.9 101 35-156 17-118 (319)
136 TIGR02062 RNase_B exoribonucle 45.6 73 0.0016 33.8 7.6 72 82-155 550-629 (639)
137 PRK06763 F0F1 ATP synthase sub 44.8 54 0.0012 30.1 5.5 23 86-108 38-60 (213)
138 COG1107 Archaea-specific RecJ- 44.5 24 0.00052 37.3 3.6 78 70-163 105-184 (715)
139 COG2932 Predicted transcriptio 43.6 1.3E+02 0.0027 26.9 7.8 73 25-99 129-211 (214)
140 PF07494 Reg_prop: Two compone 42.7 27 0.00057 20.7 2.3 16 199-214 8-23 (24)
141 KOG4600|consensus 42.5 54 0.0012 28.3 4.9 54 28-81 53-116 (144)
142 PTZ00329 eukaryotic translatio 41.7 60 0.0013 28.5 5.2 45 28-76 22-72 (155)
143 cd02394 vigilin_like_KH K homo 41.3 20 0.00043 25.4 1.9 38 178-215 4-51 (62)
144 cd06850 biotinyl_domain The bi 39.9 1.2E+02 0.0027 20.8 6.6 51 58-119 2-52 (67)
145 cd05793 S1_IF1A S1_IF1A: Trans 39.8 1.3E+02 0.0028 23.1 6.3 50 90-154 2-52 (77)
146 COG1096 Predicted RNA-binding 39.8 63 0.0014 29.3 5.2 21 138-158 59-79 (188)
147 PF10844 DUF2577: Protein of u 36.9 67 0.0015 25.7 4.5 62 85-150 15-86 (100)
148 PF01959 DHQS: 3-dehydroquinat 36.7 3.5E+02 0.0076 26.9 10.2 94 30-155 244-340 (354)
149 PRK04012 translation initiatio 36.1 2.3E+02 0.0051 22.9 8.3 58 82-155 16-74 (100)
150 COG1315 Uncharacterized conser 35.4 87 0.0019 32.6 5.9 47 44-90 220-270 (543)
151 PRK04163 exosome complex RNA-b 35.3 51 0.0011 30.4 4.0 31 84-114 112-143 (235)
152 PLN00208 translation initiatio 34.4 93 0.002 27.1 5.2 54 28-94 22-81 (145)
153 PRK02290 3-dehydroquinate synt 33.4 4.9E+02 0.011 25.8 10.5 93 31-155 235-330 (344)
154 cd05705 S1_Rrp5_repeat_hs14 S1 33.3 51 0.0011 24.6 3.1 18 141-158 1-18 (74)
155 TIGR00638 Mop molybdenum-pteri 33.1 1.3E+02 0.0028 21.3 5.2 16 138-153 46-61 (69)
156 PF10447 EXOSC1: Exosome compo 32.9 41 0.00089 26.3 2.5 16 142-157 3-18 (82)
157 PTZ00329 eukaryotic translatio 31.8 1.9E+02 0.004 25.5 6.7 54 83-152 28-82 (155)
158 PF07497 Rho_RNA_bind: Rho ter 31.4 65 0.0014 25.1 3.4 43 71-120 29-72 (78)
159 PRK00215 LexA repressor; Valid 31.0 2.2E+02 0.0047 25.0 7.3 36 64-99 164-203 (205)
160 PF08970 Sda: Sporulation inhi 30.6 72 0.0016 22.5 3.2 33 254-290 4-36 (46)
161 cd03524 RPA2_OBF_family RPA2_O 30.4 1.7E+02 0.0038 19.7 7.7 64 90-164 2-70 (75)
162 KOG3038|consensus 29.3 1.6E+02 0.0034 28.1 6.1 71 70-183 114-187 (264)
163 PRK06763 F0F1 ATP synthase sub 28.5 1.5E+02 0.0032 27.3 5.7 17 138-154 162-178 (213)
164 cd04454 S1_Rrp4_like S1_Rrp4_l 28.2 89 0.0019 23.3 3.7 31 82-112 49-80 (82)
165 smart00293 PWWP domain with co 28.1 38 0.00082 24.6 1.6 15 141-155 1-15 (63)
166 PF01436 NHL: NHL repeat; Int 28.1 79 0.0017 19.2 2.8 18 197-214 3-20 (28)
167 PF14398 ATPgrasp_YheCD: YheC/ 28.0 37 0.00081 31.6 1.8 19 196-214 211-229 (262)
168 COG2106 Uncharacterized conser 27.8 1.3E+02 0.0029 28.7 5.5 49 83-154 102-150 (272)
169 PF13375 RnfC_N: RnfC Barrel s 27.8 80 0.0017 25.5 3.5 39 30-70 43-81 (101)
170 PF08406 CbbQ_C: CbbQ/NirQ/Nor 27.7 2.8E+02 0.006 21.7 6.5 29 228-256 10-38 (86)
171 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 27.4 65 0.0014 24.2 2.8 18 141-158 4-21 (86)
172 cd05790 S1_Rrp40 S1_Rrp40: Rrp 26.5 61 0.0013 25.5 2.6 20 81-100 47-66 (86)
173 COG1158 Rho Transcription term 26.4 60 0.0013 32.4 3.0 44 71-121 80-124 (422)
174 PF03459 TOBE: TOBE domain; I 25.9 2.1E+02 0.0046 20.0 5.2 47 90-153 7-59 (64)
175 TIGR00739 yajC preprotein tran 25.7 1.5E+02 0.0033 23.0 4.7 33 131-164 28-66 (84)
176 cd05834 HDGF_related The PWWP 25.2 45 0.00098 25.8 1.6 16 140-155 2-17 (83)
177 PF00364 Biotin_lipoyl: Biotin 24.7 2.2E+02 0.0048 21.0 5.3 54 57-115 2-55 (74)
178 cd05841 BS69_related The PWWP 24.6 47 0.001 26.1 1.6 18 138-155 4-21 (83)
179 cd05836 N_Pac_NP60 The PWWP do 24.1 47 0.001 25.9 1.5 18 199-216 39-56 (86)
180 cd05840 SPBC215_ISWI_like The 22.8 51 0.0011 26.1 1.5 15 141-155 1-15 (93)
181 PF00877 NLPC_P60: NlpC/P60 fa 22.4 83 0.0018 24.5 2.6 45 31-82 50-95 (105)
182 cd03693 EF1_alpha_II EF1_alpha 22.2 3.3E+02 0.0072 20.8 6.0 61 62-149 22-87 (91)
183 COG1792 MreC Cell shape-determ 21.8 1.3E+02 0.0028 28.6 4.3 19 90-108 156-174 (284)
184 TIGR00008 infA translation ini 21.8 3.6E+02 0.0078 20.4 6.7 52 90-155 7-59 (68)
185 PRK15095 FKBP-type peptidyl-pr 21.5 1.2E+02 0.0027 26.1 3.8 28 86-113 105-132 (156)
186 cd05693 S1_Rrp5_repeat_hs1_sc1 20.4 1.1E+02 0.0024 24.3 3.0 22 141-163 1-22 (100)
187 PRK05054 exoribonuclease II; P 20.2 4.3E+02 0.0093 28.1 8.1 16 140-155 121-136 (644)
188 cd02796 tRNA_bind_bactPheRS tR 20.2 3E+02 0.0064 21.5 5.4 37 141-178 40-76 (103)
No 1
>KOG3013|consensus
Probab=100.00 E-value=7.9e-81 Score=566.44 Aligned_cols=271 Identities=51% Similarity=0.808 Sum_probs=259.3
Q ss_pred ccccCCCeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEeCcEEEEEecCccccccCCCEEEEEEEEEecceEEE
Q psy10116 25 IHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVV 104 (298)
Q Consensus 25 ~~~~~~~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~nk~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~V 104 (298)
.......+|+||+.++.++.||+|||||+.|+.|+||++|.++++||+++|+|++.||.|++||+|+|||++|++++|+|
T Consensus 24 ~~~~~~~ivtPG~~V~~d~~fmRGHGTy~~d~~i~ssvaG~v~rvNkLi~V~plk~rY~pEvGDvVVgRV~eVq~KRWkv 103 (301)
T KOG3013|consen 24 DTSDHSTIVTPGELVTDDPGFMRGHGTYVRDGEIYSSVAGVVQRVNKLISVKPLKSRYAPEVGDVVVGRVIEVQQKRWKV 103 (301)
T ss_pred ccccCceeecCCccccCchhhhhcccceecCCeEEEeecchhhhhcceEEEeehhhhcCCccCCEEEEEeeeeecceeEE
Confidence 34456789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEeccCCCccCCCceEEEeCchh
Q psy10116 105 DTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSL 184 (298)
Q Consensus 105 DI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~~~lGkL~~G~lv~v~~~l 184 (298)
|+|+.++|+|++|++|+|||++|||+++||.+||+||++||+|.|+||+++.||+++||||+.+||||.+|++++|||+|
T Consensus 104 d~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~dGs~sLhTRS~KYGKL~~G~lvkVpp~L 183 (301)
T KOG3013|consen 104 DLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFHDGSLSLHTRSLKYGKLGQGILVKVPPAL 183 (301)
T ss_pred ecccccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhccCCeEEEEecchhcccccCceEEEeCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccccCcceeccccEEEEEeeCceEEEecCCCC-----CCCcccccc-ccCCHHHHHHHHHHHHHHHHHhhCCcccCHHH
Q psy10116 185 IRRSKSHFCNLACGAQVILGCNGYVWVSAIDEN-----KSGGFIQNM-EVVKLSDRETITRLNNVIKALAESKVMLFDTS 258 (298)
Q Consensus 185 i~r~~~~~~~l~~~~eiivG~NG~IWI~~~~~~-----~~~~~~~~~-~~i~~~~r~~i~rv~n~i~~l~~~~~~i~~~~ 258 (298)
++|+|+|||.++||+++|+|+|||||+.+.++. ..++|++.+ +.+|.++|++|||++|||++|+.++++||+++
T Consensus 184 vkr~K~hfh~lp~g~~vIlG~NGyIWv~~s~~~~~ee~~~~~~~~~~~~~v~~~~R~~i~Rl~n~i~~La~~~~~i~~~s 263 (301)
T KOG3013|consen 184 VKRSKTHFHNLPGGVDVILGCNGYIWVGPSIKDQEEEESIGSYSSENDEHVSLNTRVNICRLANCIRALANCSIMITLTS 263 (301)
T ss_pred hhhhhhhhccCCCCeEEEEecCceEEecCCCCcchhhhcccccccCcccCCCHHHHHHHHHHHHHHHHHHhcCeeeeHHH
Confidence 999999999999999999999999999997662 134566666 67999999999999999999999999999999
Q ss_pred HHHHHHHHhCCCCcccCChhHHHHHHHHHHHHHHHcc
Q psy10116 259 IQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQTLG 295 (298)
Q Consensus 259 i~~~~~~s~~~~~~~~l~~~~~~~~~~~~~~~~~~~~ 295 (298)
|+++||+|+.|+++||+.|++|+.+|+++++||.++.
T Consensus 264 I~~~ye~S~~~~i~ell~~~~~~~ia~~~~~rl~~~~ 300 (301)
T KOG3013|consen 264 ITYCYEASLPYEIHELLEQEFMEVIAMEIAARLRTKR 300 (301)
T ss_pred HHHHHHhcCcchHHHHhhhhHHHHHHHHHHHHHHhhc
Confidence 9999999999999999999999999999999998763
No 2
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.4e-50 Score=363.36 Aligned_cols=216 Identities=29% Similarity=0.481 Sum_probs=190.9
Q ss_pred cCCCeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEeCcEEEEEecCccccccCCCEEEEEEEEEecceEEEEeC
Q psy10116 28 FTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTN 107 (298)
Q Consensus 28 ~~~~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~nk~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~ 107 (298)
..+++|+|||.+...+++++|||||.+++++|||++|.++.+++.+.|+|++++|.|++||+|||+|+++..++|+|||+
T Consensus 6 ~~~~iV~PGd~vl~~~~~~~G~Gty~~~~~iyssv~G~~~~~~~~v~VIpl~g~YiP~~gD~VIG~I~~v~~~~W~VDI~ 85 (239)
T COG1097 6 SMRKIVLPGDLVLAEGSYKLGHGTYFEGGKIYSSVVGLLDVKGKLVRVIPLEGRYIPEVGDVVIGKIIEVGPSGWKVDIG 85 (239)
T ss_pred cccceecCCCccCCCCCEecCCCcEecCCEEEEEEEeEEEEeCCEEEEEeCCCcccCCCCCEEEEEEEEEcccceEEEcC
Confidence 35789999998888889999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEeccCCCccCCCceEEEeCchhhcc
Q psy10116 108 SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRR 187 (298)
Q Consensus 108 s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~~~lGkL~~G~lv~v~~~li~r 187 (298)
|++.|.||+|++ +||+.+.++.+||++|++||+|+|||++++.+++++||||+.+||+|++|+++.++|+++.|
T Consensus 86 sp~~A~L~ls~~------~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p~kVpR 159 (239)
T COG1097 86 SPYPALLSLSDF------LRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPPSKVPR 159 (239)
T ss_pred CccceEeehhhh------hcccccccccccccccccCCEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEchhhcce
Confidence 999999999997 48988999999999999999999999999999999999999999999999999999999988
Q ss_pred ccCcceec------cccEEEEEeeCceEEEecCCCCC-CCcc----cccc-ccCCHHHHHHHHHHHHHHHHHhhC
Q psy10116 188 SKSHFCNL------ACGAQVILGCNGYVWVSAIDENK-SGGF----IQNM-EVVKLSDRETITRLNNVIKALAES 250 (298)
Q Consensus 188 ~~~~~~~l------~~~~eiivG~NG~IWI~~~~~~~-~~~~----~~~~-~~i~~~~r~~i~rv~n~i~~l~~~ 250 (298)
..+|...+ .++|+|++|+|||||+++++... +... .-.. .+++--+++.++++.+++ .+++.
T Consensus 160 vig~~~sm~~~l~~~~~~~I~VG~NG~IWV~~~~~~~e~~~~~aI~~ie~ea~~~gltdr~~~~i~~~~-~~~~~ 233 (239)
T COG1097 160 VIGKKGSMLNMLKEKTGCEIIVGQNGRIWVDGENESLEELAIEAIRKIEREAHTSGLTDRIKEFLKKLL-RLKES 233 (239)
T ss_pred EecCCCcHHHHhhhhcCeEEEEecCCEEEecCCCcchHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHH-hcccc
Confidence 87766653 38999999999999999998732 1111 1112 246667778888877777 44443
No 3
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=100.00 E-value=7.6e-44 Score=326.30 Aligned_cols=200 Identities=26% Similarity=0.468 Sum_probs=177.9
Q ss_pred cCCCeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEeCcEEEEEecCccccccCCCEEEEEEEEEecceEEEEeC
Q psy10116 28 FTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTN 107 (298)
Q Consensus 28 ~~~~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~nk~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~ 107 (298)
.++.+|+|||.|+. ++|++|+|||.++|+++||++|.+...++.++|+|++++|.|++||+|+|+|+++.+++|+|||+
T Consensus 6 ~~~~~V~PGd~l~~-~~~~~G~Gty~~~g~i~As~~G~~~~~~~~i~V~p~~~~y~P~vGDiViG~V~~i~~~~~~vdI~ 84 (235)
T PRK04163 6 EDRKIVVPGDLLAE-GEFKAGRGTYKENGKIYSTVVGLVDIKDDKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGWEVDIN 84 (235)
T ss_pred eCCcEECCCCCcCc-CCeecCCceEEeCCEEEEEEeEEEEEECCEEEEEECCCcccCCCCCEEEEEEEEEeCceEEEEeC
Confidence 35689999999974 68999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEeccCCCccCCCceEEEeCchhhcc
Q psy10116 108 SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRR 187 (298)
Q Consensus 108 s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~~~lGkL~~G~lv~v~~~li~r 187 (298)
++++|+||++++. +++.+.|+.+|+++|++||+|+|||++++.++.+.|||++.+||+|.+|++++|+|.+++|
T Consensus 85 ~~~~g~L~~s~i~------~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~~~lG~L~~G~~~~V~~~~i~~ 158 (235)
T PRK04163 85 SPYKAYLPVSEVL------GRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGKGLGKIEGGTIVEIKPVKVPR 158 (235)
T ss_pred CCceeEEEHHHcC------CCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcCCCCCccCCCEEEEECHHHHHh
Confidence 9999999999984 3445568899999999999999999999988889999999999999999999999999988
Q ss_pred ccC----cceec--cccEEEEEeeCceEEEecCCCCCCCccccccccCCHHHHHHHHHHHHHHHHHhhCCc
Q psy10116 188 SKS----HFCNL--ACGAQVILGCNGYVWVSAIDENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKV 252 (298)
Q Consensus 188 ~~~----~~~~l--~~~~eiivG~NG~IWI~~~~~~~~~~~~~~~~~i~~~~r~~i~rv~n~i~~l~~~~~ 252 (298)
+.. ++..| .++|+|++|+||+|||++++. +.+....++|+.+++..-
T Consensus 159 lig~~g~~i~~l~~~~~~~I~ig~NG~VwI~~~~~------------------~~~~~a~~~I~~~e~~~~ 211 (235)
T PRK04163 159 VIGKKGSMINMLKEETGCDIIVGQNGRIWIKGPDE------------------EDEEIAIEAIKKIEREAH 211 (235)
T ss_pred hcCCCChhHhhhhhhhCcEEEEcCCcEEEEeeCCH------------------HHHHHHHHHHHHHHhhhh
Confidence 843 33334 489999999999999999875 455566777777665543
No 4
>KOG1004|consensus
Probab=100.00 E-value=1.4e-32 Score=244.80 Aligned_cols=175 Identities=24% Similarity=0.365 Sum_probs=156.0
Q ss_pred CeEecCCccCCC--CCeeccCCeEecCCeEEEEEeeEEEEe--Cc----EEEEEecCccccccCCCEEEEEEEEEecceE
Q psy10116 31 PILTPGETVEYL--EGYMTGHGTFPDDEEIKASVGGVVEKV--NQ----LVSVRAMNSRYIGEIGEVVVGRVTGLQSQKW 102 (298)
Q Consensus 31 ~iV~PGD~I~~~--~~~~~G~Gty~~~g~i~Asv~G~v~~~--nk----~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~ 102 (298)
...+|||.+... .+..+|+|.+..++.+..+.+|.+... ++ ..||...++||+|.+||.|||+|++..++.|
T Consensus 2 ~~~~pg~~~~~~~~~sv~~G~g~~~~g~~~~~~~~G~~~~~~~gk~~~~v~~vds~~kRYiP~~~D~VIGiV~~~~gd~y 81 (230)
T KOG1004|consen 2 TFYFPGDSIPRPRLCSVVLGPGLRRRGQERLVTKCGRLRHKEPGKGGGGVYWVDSQQKRYIPVKGDHVIGIVTSKSGDIY 81 (230)
T ss_pred ceecCCcccccCccCceeecCCccccCceEEeccccceeeccCCcccceeEEEecccceecCCCCCEEEEEEEeccCceE
Confidence 467899988763 357799999999999999999977753 33 5799999999999999999999999999999
Q ss_pred EEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEe-----ccCCCccCCCceE
Q psy10116 103 VVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHT-----RSLKYGKLGQGIL 177 (298)
Q Consensus 103 ~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lst-----r~~~lGkL~~G~l 177 (298)
+|||+++..|.|+..+ |||+++|+ ||.|++||+|||+|...++|.+++|++ |..+||+|++|++
T Consensus 82 kVDigg~~~a~L~~la--Fe~AtkrN---------rPnl~vGdliyakv~~a~~~~Epel~Cids~graaGfG~LkdG~i 150 (230)
T KOG1004|consen 82 KVDIGGSEPASLSYLA--FEGATKRN---------RPNLQVGDLIYAKVVDANKDMEPELTCIDSTGRAAGFGVLKDGMI 150 (230)
T ss_pred EEecCCCCeeeeeecc--ccCccccC---------CCccccccEEEEEEEecCCCcCcceEEEcccCcccCcccccCceE
Confidence 9999999999998666 58999888 799999999999999999999999996 5569999999999
Q ss_pred EEeCchhhccccCcceec------cccEEEEEeeCceEEEecCCC
Q psy10116 178 LTVPPSLIRRSKSHFCNL------ACGAQVILGCNGYVWVSAIDE 216 (298)
Q Consensus 178 v~v~~~li~r~~~~~~~l------~~~~eiivG~NG~IWI~~~~~ 216 (298)
++++++++|++..+-+.+ .++|||++|+||||||++...
T Consensus 151 f~vs~~~~R~Ll~p~~~iLq~vGk~~~FEia~GlNGriWV~ae~~ 195 (230)
T KOG1004|consen 151 FKVSLGLCRKLLLPDCPILQTVGKKYPFEIAFGLNGRIWVKAETL 195 (230)
T ss_pred EEecHHHHHHHHcCCCcHHHHhhcccceEEEEecCceEEEeccCc
Confidence 999999999998866653 389999999999999999875
No 5
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=99.96 E-value=3.2e-28 Score=216.08 Aligned_cols=137 Identities=26% Similarity=0.403 Sum_probs=122.9
Q ss_pred CCCeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEe--CcEEEEEecCc-cccccCCCEEEEEEEEEecceEEEE
Q psy10116 29 TDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKV--NQLVSVRAMNS-RYIGEIGEVVVGRVTGLQSQKWVVD 105 (298)
Q Consensus 29 ~~~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~--nk~v~V~p~~~-rY~P~vGDiVIG~V~~V~~~~~~VD 105 (298)
++++|+|||.|++.++|++|+|||+++|+|+||++|.++.. ++.++|.|.+. .|.|++||+|+|+|+++.+++|+||
T Consensus 4 ~~~~V~PGe~l~~~~e~~~G~Gty~~~~~i~as~~G~~~id~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~ 83 (189)
T PRK09521 4 QGDLVLPGDYLAVIEEYLPGEGTYEDNGEVYASVVGKVFIDDINRKISVIPFKKTPPLLKKGDIVYGRVVDVKEQRALVR 83 (189)
T ss_pred cCCEECCCCccccccceEcCCCEEeeCCEEEEEeeEEEEEcCCCCEEEEecCcCCCCCCCCCCEEEEEEEEEcCCeEEEE
Confidence 56899999999998899999999999999999999999964 66899999987 9999999999999999999999999
Q ss_pred eC----------CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEeccCCCccCCCc
Q psy10116 106 TN----------SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQG 175 (298)
Q Consensus 106 I~----------s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~~~lGkL~~G 175 (298)
|. ++.+|+||.++++ +....+|+++|++||+|.|+|++++ +.+.||+++.+||+
T Consensus 84 I~~~~~~~~~l~~~~~G~l~~s~i~----------~~~~~~~~~~~~~GD~V~akV~~i~--~~i~LS~k~~~lGv---- 147 (189)
T PRK09521 84 IVSIEGSERELATSKLAYIHISQVS----------DGYVESLTDAFKIGDIVRAKVISYT--DPLQLSTKGKDLGV---- 147 (189)
T ss_pred EEEecccccccCCCceeeEEhhHcC----------hhhhhhHHhccCCCCEEEEEEEecC--CcEEEEEecCCceE----
Confidence 95 3678999999874 2234578999999999999999997 78999999999999
Q ss_pred eEEEeCc
Q psy10116 176 ILLTVPP 182 (298)
Q Consensus 176 ~lv~v~~ 182 (298)
+++.|+
T Consensus 148 -v~a~~~ 153 (189)
T PRK09521 148 -IYAMCS 153 (189)
T ss_pred -EEEEcc
Confidence 677664
No 6
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=5.3e-26 Score=200.11 Aligned_cols=157 Identities=22% Similarity=0.405 Sum_probs=137.8
Q ss_pred cCCCeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEE--eCcEEEEEecCc-cccccCCCEEEEEEEEEecceEEE
Q psy10116 28 FTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEK--VNQLVSVRAMNS-RYIGEIGEVVVGRVTGLQSQKWVV 104 (298)
Q Consensus 28 ~~~~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~--~nk~v~V~p~~~-rY~P~vGDiVIG~V~~V~~~~~~V 104 (298)
..+.+|+|||.|+..|+|++|.|||+++|+|+|+.+|.+.. +|..++|+|.+. ..+|+.||+|+|+|+++..+.+.|
T Consensus 3 ~~g~~v~PGd~~a~~EE~~~G~gt~~~~g~i~Aa~~G~~~~d~~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~~~~a~V 82 (188)
T COG1096 3 KDGTFVLPGDVLAVIEEFLPGEGTYEEGGEIRAAATGVVRRDDKNRVISVKPGKKTPPLPKGGDIVYGRVTDVREQRALV 82 (188)
T ss_pred ccCcEEcCcceeeeeeeeecCCCeEeECCEEEEeecccEEEcccceEEEeccCCCCCCCCCCCCEEEEEEeeccceEEEE
Confidence 35789999999999999999999999999999999999997 578999999998 899999999999999999999999
Q ss_pred Ee----------CCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEeccCCCccCCC
Q psy10116 105 DT----------NSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQ 174 (298)
Q Consensus 105 DI----------~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~~~lGkL~~ 174 (298)
.| .++..|.+|+|++. +....+.+++|++||+|+|+|++.. ..+.|||+.+.||+
T Consensus 83 ~i~~ve~~~r~~~~~~~~~ihvs~~~----------~~~~~~~~d~f~~GDivrA~Vis~~--~~~~Lst~~~dlGV--- 147 (188)
T COG1096 83 RIVGVEGKERELATSGAADIHVSQVR----------DGYVEKLSDAFRIGDIVRARVISTG--DPIQLSTKGNDLGV--- 147 (188)
T ss_pred EEEEEecccccCCCCceeeEEEEecc----------cccccccccccccccEEEEEEEecC--CCeEEEecCCcceE---
Confidence 88 23578999999983 3344567899999999999999986 67999999999999
Q ss_pred ceEEEeCchhhccccCcceeccccEEEEEeeCceEEEecCCC
Q psy10116 175 GILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWVSAIDE 216 (298)
Q Consensus 175 G~lv~v~~~li~r~~~~~~~l~~~~eiivG~NG~IWI~~~~~ 216 (298)
+++.|+ .|+..+.. -|+..-|+.|.
T Consensus 148 --I~A~Cs-------------rC~~~L~~--~~~~l~Cp~Cg 172 (188)
T COG1096 148 --IYARCS-------------RCRAPLVK--KGNMLKCPNCG 172 (188)
T ss_pred --EEEEcc-------------CCCcceEE--cCcEEECCCCC
Confidence 899884 57777776 56677777775
No 7
>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=99.85 E-value=3.2e-21 Score=151.84 Aligned_cols=75 Identities=24% Similarity=0.337 Sum_probs=68.9
Q ss_pred cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcE
Q psy10116 81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSL 160 (298)
Q Consensus 81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~ 160 (298)
||+|++||+|||+|+++..+.|+|||++++.|+||.++| ||+++| +|++|++||+|+|||++++.++++
T Consensus 1 rY~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f--~gatk~---------~rp~L~~GDlV~ArV~~~~~~~~~ 69 (86)
T cd05790 1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAF--EGATKR---------NRPNLNVGDLVYARVVKANRDMEP 69 (86)
T ss_pred CCcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHc--cccccc---------ccccCCCCCEEEEEEEecCCCCCe
Confidence 699999999999999999999999999999999998774 788654 389999999999999999999999
Q ss_pred EEEecc
Q psy10116 161 TLHTRS 166 (298)
Q Consensus 161 ~Lstr~ 166 (298)
+|++..
T Consensus 70 eLtc~~ 75 (86)
T cd05790 70 ELSCVD 75 (86)
T ss_pred EEEEeC
Confidence 999854
No 8
>KOG3409|consensus
Probab=99.83 E-value=7.6e-20 Score=159.11 Aligned_cols=136 Identities=24% Similarity=0.342 Sum_probs=114.5
Q ss_pred CCCeEecCCccCCCC-CeeccCCeEecCCeEEEEEeeEEEEe--CcEEEEEec----CccccccCCCEEEEEEEEEecce
Q psy10116 29 TDPILTPGETVEYLE-GYMTGHGTFPDDEEIKASVGGVVEKV--NQLVSVRAM----NSRYIGEIGEVVVGRVTGLQSQK 101 (298)
Q Consensus 29 ~~~iV~PGD~I~~~~-~~~~G~Gty~~~g~i~Asv~G~v~~~--nk~v~V~p~----~~rY~P~vGDiVIG~V~~V~~~~ 101 (298)
...+++|||.++..+ ++..|.|||..++.|+||.+|+..+. ++.+.|... ...-+|.+||||..+|..++..+
T Consensus 4 a~~~~lpG~~~c~~e~~~~~g~Gtye~~~yI~aS~ag~~~~~~~~~~~~v~~~~~~~~~~~LP~~G~IVtarV~~i~~rf 83 (193)
T KOG3409|consen 4 AETLVLPGEVVCRAEGEYRMGEGTYERNGYIFASVAGVNFRDNLVQKIEVVSVEKQLFNELLPFVGAIVTARVSRINLRF 83 (193)
T ss_pred ceEEEcccceeeecccccccccceeecCCeEEeccccceeecCCccceeeeeecccchhhcCCccCcEEEEEEEeeccce
Confidence 346899999999864 48899999999999999999955443 344444333 34688999999999999999999
Q ss_pred EEEEe--------CCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEeccCCCccC
Q psy10116 102 WVVDT--------NSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKL 172 (298)
Q Consensus 102 ~~VDI--------~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~~~lGkL 172 (298)
++||| ...+.|+|+..++ |.++.|..+...+|+|||+|+|+|++.+...++.|||.++.||++
T Consensus 84 Akv~I~~V~d~~lk~~Frglirkqdv--------R~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LTtAeneLGVV 154 (193)
T KOG3409|consen 84 AKVDILSVGDKPLKKSFRGLIRKQDV--------RATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLTTAENELGVV 154 (193)
T ss_pred eeEEEEEEcCEEhhhhhcceeehhhc--------cccccchhhhhhccCCCcEEEEEEeecCCCCcEEEEEecccceEE
Confidence 99999 3467888888777 678899999999999999999999997655679999999999993
No 9
>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=99.81 E-value=8.6e-20 Score=145.10 Aligned_cols=83 Identities=20% Similarity=0.374 Sum_probs=76.6
Q ss_pred ccccCCCEEEEEEEEEecceEEEEe--------CCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEE
Q psy10116 82 YIGEIGEVVVGRVTGLQSQKWVVDT--------NSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQ 153 (298)
Q Consensus 82 Y~P~vGDiVIG~V~~V~~~~~~VDI--------~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~s 153 (298)
|.|++||+|+|+|+++..++|.||| ++++.|+||.+++ |.++.|+.+|+++|++||+|+|||++
T Consensus 2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv--------~~~~~d~~~~~~~f~~GDiV~AkVis 73 (92)
T cd05791 2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDI--------RATEKDKVEMYKCFRPGDIVRAKVIS 73 (92)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHc--------cccccchHHHHhhcCCCCEEEEEEEE
Confidence 8999999999999999999999999 8899999999997 34567788999999999999999999
Q ss_pred eCCCCcEEEEeccCCCccC
Q psy10116 154 ISTEGSLTLHTRSLKYGKL 172 (298)
Q Consensus 154 v~~dg~~~Lstr~~~lGkL 172 (298)
++....+.|||++++||++
T Consensus 74 ~~~~~~~~Lst~~~~lGVv 92 (92)
T cd05791 74 LGDASSYYLSTAENELGVV 92 (92)
T ss_pred cCCCCCcEEEecCCCCccC
Confidence 9766789999999999984
No 10
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.76 E-value=6.4e-18 Score=130.23 Aligned_cols=82 Identities=30% Similarity=0.490 Sum_probs=75.4
Q ss_pred cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcE
Q psy10116 81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSL 160 (298)
Q Consensus 81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~ 160 (298)
+|.|++||+|+|+|+++.++.|+|||++..+|+||.++++. .+..++++.|++||+|.|+|++++.++.+
T Consensus 1 ~y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~----------~~~~~~~~~~~~GD~i~~~V~~~~~~~~i 70 (82)
T cd04454 1 RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATE----------KDKKEIRKSLQPGDLILAKVISLGDDMNV 70 (82)
T ss_pred CCCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccC----------cchHHHHhcCCCCCEEEEEEEEeCCCCCE
Confidence 69999999999999999999999999999999999999852 23567899999999999999999877889
Q ss_pred EEEeccCCCccC
Q psy10116 161 TLHTRSLKYGKL 172 (298)
Q Consensus 161 ~Lstr~~~lGkL 172 (298)
.||+++.+||+|
T Consensus 71 ~LS~~~~~~Gvi 82 (82)
T cd04454 71 LLTTADNELGVI 82 (82)
T ss_pred EEEECCCCCccC
Confidence 999999999985
No 11
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.65 E-value=1e-15 Score=118.61 Aligned_cols=86 Identities=55% Similarity=0.903 Sum_probs=76.4
Q ss_pred cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcE
Q psy10116 81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSL 160 (298)
Q Consensus 81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~ 160 (298)
+|.|++||+|.|+|+++.+++|+|+|++..+|+||++++.. .+++....++.+.|++||.|.|+|+++++++.+
T Consensus 1 ~y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~------~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~~i 74 (86)
T cd05789 1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNL------PRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSV 74 (86)
T ss_pred CCcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccC------CCCccchHHHHhhCCCCCEEEEEEEEECCCCCE
Confidence 69999999999999999999999999999999999999841 112334567889999999999999999878899
Q ss_pred EEEeccCCCccC
Q psy10116 161 TLHTRSLKYGKL 172 (298)
Q Consensus 161 ~Lstr~~~lGkL 172 (298)
.||++..+||+|
T Consensus 75 ~LS~~~~~~g~~ 86 (86)
T cd05789 75 SLHTRSLKYGKL 86 (86)
T ss_pred EEEeCcccccCC
Confidence 999999999986
No 12
>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=99.41 E-value=4.2e-13 Score=104.94 Aligned_cols=64 Identities=20% Similarity=0.437 Sum_probs=43.6
Q ss_pred cccCCCEEEEEEEEEecceEEEEeCC------------------CceeeEecccccCCCCcccccchhhhhhhhcccCCC
Q psy10116 83 IGEIGEVVVGRVTGLQSQKWVVDTNS------------------ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEG 144 (298)
Q Consensus 83 ~P~vGDiVIG~V~~V~~~~~~VDI~s------------------~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~G 144 (298)
+|++||+|+|+|+++++++++|+|-+ ++.|+|+.+++ |.++.|+.+|.++|+||
T Consensus 1 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DV--------R~te~Dkv~~~~~FrpG 72 (82)
T PF10447_consen 1 LPKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDV--------RATEKDKVKMYDCFRPG 72 (82)
T ss_dssp ---TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGG--------GT-SS----GGGT--SS
T ss_pred CCCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeee--------cccccchhhHHhccCCC
Confidence 59999999999999999999999832 45667776666 67889999999999999
Q ss_pred CEEEEEEEEe
Q psy10116 145 DLISAEIHQI 154 (298)
Q Consensus 145 DlV~A~V~sv 154 (298)
|+|+|+|+|+
T Consensus 73 DIVrA~ViSl 82 (82)
T PF10447_consen 73 DIVRARVISL 82 (82)
T ss_dssp SEEEEEEEEE
T ss_pred CEEEEEEeeC
Confidence 9999999984
No 13
>PF14382 ECR1_N: Exosome complex exonuclease RRP4 N-terminal region; PDB: 2NN6_I 3M7N_C 2BA1_A 3M85_C.
Probab=99.30 E-value=1.9e-12 Score=87.80 Aligned_cols=39 Identities=46% Similarity=0.721 Sum_probs=35.1
Q ss_pred eEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEeC
Q psy10116 32 ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVN 70 (298)
Q Consensus 32 iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~n 70 (298)
+|+|||.|+..++|++|+|||+++|+|+||++|.+++.|
T Consensus 1 iV~PG~~l~~~~e~~~G~GTY~~~g~I~asv~G~v~~~n 39 (39)
T PF14382_consen 1 IVVPGDRLGSSEEYMPGHGTYVRDGNIYASVAGTVKIDN 39 (39)
T ss_dssp EE-TT-EEEETTTSEESTTEEEETTEEEESSSEEEEEET
T ss_pred CCCCCCEeecCCCEecCCCEEEeCCEEEEEeeEEEEEcC
Confidence 699999999999999999999999999999999998765
No 14
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.05 E-value=4.3e-10 Score=93.74 Aligned_cols=76 Identities=18% Similarity=0.335 Sum_probs=70.6
Q ss_pred cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEE
Q psy10116 83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTL 162 (298)
Q Consensus 83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~L 162 (298)
.+++||+|-|+|+++++.++||++....+|++|+|++. +....++.++|++||.|.++|++++.+|.++|
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa----------~~fVkdI~d~L~vG~eV~vKVl~ide~GKisL 71 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIA----------DGFVKDIHDHLKVGQEVKVKVLDIDENGKISL 71 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecCCCcceEEehHhh----------hhhHHhHHHHhcCCCEEEEEEEeeccCCCcce
Confidence 36899999999999999999999998899999999994 66789999999999999999999999999999
Q ss_pred EeccCC
Q psy10116 163 HTRSLK 168 (298)
Q Consensus 163 str~~~ 168 (298)
|.|...
T Consensus 72 SIr~~~ 77 (129)
T COG1098 72 SIRKLE 77 (129)
T ss_pred ehHHhh
Confidence 998754
No 15
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.01 E-value=1.7e-09 Score=81.76 Aligned_cols=70 Identities=21% Similarity=0.170 Sum_probs=59.9
Q ss_pred cCCCEEEEEEEEEec-ceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEE
Q psy10116 85 EIGEVVVGRVTGLQS-QKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLH 163 (298)
Q Consensus 85 ~vGDiVIG~V~~V~~-~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Ls 163 (298)
++||+|.|+|+++.+ .+++|++....+|++|+|++.- ....+..+.|++||.|.|+|.+++. +.+.||
T Consensus 2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~----------~~~~~~~~~~~~Gd~v~~kV~~~~~-~~i~LS 70 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSD----------SYTENPLEGFKPGKIVRCCILSKKD-GKYQLS 70 (72)
T ss_pred CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcC----------cccCCHHHhCCCCCEEEEEEEEecC-CEEEEE
Confidence 589999999999986 6999999999999999999851 1233456889999999999999975 889998
Q ss_pred ec
Q psy10116 164 TR 165 (298)
Q Consensus 164 tr 165 (298)
+|
T Consensus 71 l~ 72 (72)
T cd05704 71 LR 72 (72)
T ss_pred eC
Confidence 75
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=98.94 E-value=4.7e-09 Score=77.96 Aligned_cols=69 Identities=22% Similarity=0.338 Sum_probs=58.0
Q ss_pred CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCCcEEEEec
Q psy10116 87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEGSLTLHTR 165 (298)
Q Consensus 87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg~~~Lstr 165 (298)
||+|.|+|+++.+++|+||+++..+|+||.+++..+ ...++.+.|++||.+.|+|.+++ .++.+.||.+
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~----------~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDD----------PIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCcc----------ccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 899999999999999999999899999999988421 12346788999999999999998 4466777753
No 17
>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=98.83 E-value=2.5e-08 Score=74.07 Aligned_cols=71 Identities=23% Similarity=0.332 Sum_probs=60.0
Q ss_pred CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcEEEEec
Q psy10116 87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSLTLHTR 165 (298)
Q Consensus 87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~~Lstr 165 (298)
||+|.|+|+++.+++|+|++....+|++|.+++.. ....+..+.|++||.|.|+|.+++.. +.+.|+.+
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~----------~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k 70 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSR----------DRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCC----------ccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEE
Confidence 89999999999999999999989999999998741 11234578899999999999999854 67899887
Q ss_pred cC
Q psy10116 166 SL 167 (298)
Q Consensus 166 ~~ 167 (298)
..
T Consensus 71 ~~ 72 (73)
T cd05691 71 AK 72 (73)
T ss_pred Ec
Confidence 53
No 18
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=98.83 E-value=2.6e-08 Score=74.74 Aligned_cols=72 Identities=19% Similarity=0.276 Sum_probs=60.1
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCC--CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcE
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNS--ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSL 160 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s--~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~ 160 (298)
|+.|++|.|+|+++...+|+|++.. ..+|++|.+++.. ....++.+.|++||.|.|+|.+++. .+.+
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~----------~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i 70 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSR----------RRIRSIRKLVKVGRKEVVKVIRVDKEKGYI 70 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCC----------cccCCHHHeeCCCCEEEEEEEEEECCCCEE
Confidence 6899999999999999999999974 3799999999741 1123457889999999999999985 4678
Q ss_pred EEEec
Q psy10116 161 TLHTR 165 (298)
Q Consensus 161 ~Lstr 165 (298)
.|+++
T Consensus 71 ~ls~k 75 (76)
T cd04452 71 DLSKK 75 (76)
T ss_pred EEEEc
Confidence 88876
No 19
>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=98.81 E-value=3.4e-08 Score=71.70 Aligned_cols=69 Identities=26% Similarity=0.472 Sum_probs=58.4
Q ss_pred CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEec
Q psy10116 87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTR 165 (298)
Q Consensus 87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr 165 (298)
||+|.|+|+++.+.+|+|+|+...+|+||.+++. . ++ ..+..+.|++||.|.++|.+++.++.+.||++
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~--~---~~-----~~~~~~~~~~Gd~v~v~v~~~~~~~~i~ls~k 69 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIA--H---KR-----VKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcC--C---cc-----cCCHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence 8999999999999999999999999999999873 1 11 12345789999999999999987778888874
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=98.79 E-value=4.7e-08 Score=73.13 Aligned_cols=71 Identities=18% Similarity=0.306 Sum_probs=59.9
Q ss_pred cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116 85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH 163 (298)
Q Consensus 85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls 163 (298)
++|++|.|+|+++.+++++|++.+..+|++|++++.- ....+..+.|++||.|.|+|.+++. .+.+.||
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~----------~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls 71 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALD----------DYSEALPYKFKKNDIVRACVLSVDVPNKKIALS 71 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccC----------ccccccccccCCCCEEEEEEEEEeCCCCEEEEE
Confidence 5899999999999999999999999999999998741 1122346889999999999999985 4678888
Q ss_pred ec
Q psy10116 164 TR 165 (298)
Q Consensus 164 tr 165 (298)
+|
T Consensus 72 ~~ 73 (73)
T cd05706 72 LR 73 (73)
T ss_pred EC
Confidence 74
No 21
>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=98.79 E-value=3.5e-08 Score=73.76 Aligned_cols=72 Identities=19% Similarity=0.308 Sum_probs=61.5
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcEEE
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSLTL 162 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~~L 162 (298)
|++||+|-|+|+++.+++++||++...+|++|.+++... ........|++||.|.|+|.+++.+ +.+.|
T Consensus 2 ~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~----------~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~l 71 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDD----------RIDDPSEVYKIGQTVRVKVIKVDKEKGRIRL 71 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSS----------EESSSHGTCETTCEEEEEEEEEETTTTEEEE
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCc----------cccccccccCCCCEEEEEEEEEECCCCeEEE
Confidence 689999999999999999999999999999999998521 1234478999999999999999955 45888
Q ss_pred Eec
Q psy10116 163 HTR 165 (298)
Q Consensus 163 str 165 (298)
|.|
T Consensus 72 S~k 74 (74)
T PF00575_consen 72 SLK 74 (74)
T ss_dssp EST
T ss_pred EEC
Confidence 865
No 22
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.76 E-value=3.8e-08 Score=75.04 Aligned_cols=72 Identities=19% Similarity=0.347 Sum_probs=58.3
Q ss_pred cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116 85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH 163 (298)
Q Consensus 85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls 163 (298)
++||+|.|+|+++++.+++|+++...+|.+|+++++. ++ -.+..++.+.|++||.|.|+|++++. ++.+.||
T Consensus 2 k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~-----~~--~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS 74 (74)
T cd05705 2 KEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTK-----YF--VSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccC-----cc--ccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 6899999999999999999999989999999999852 11 01123467899999999999999985 3556654
No 23
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.74 E-value=7.1e-08 Score=69.71 Aligned_cols=71 Identities=25% Similarity=0.373 Sum_probs=59.3
Q ss_pred cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcEEEE
Q psy10116 85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSLTLH 163 (298)
Q Consensus 85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~~Ls 163 (298)
++|++|.|+|+++.+.+|+|+++....|++|.+++..+ ...+....|++||.|.|+|.+++.+ +.+.|+
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~----------~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls 70 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDK----------RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCcc----------ccCCHHHeecCCCEEEEEEEEEeCCCCEEEEE
Confidence 47999999999999999999999889999999987421 0233457799999999999999865 778887
Q ss_pred ec
Q psy10116 164 TR 165 (298)
Q Consensus 164 tr 165 (298)
++
T Consensus 71 ~~ 72 (72)
T smart00316 71 LK 72 (72)
T ss_pred eC
Confidence 64
No 24
>PRK08582 hypothetical protein; Provisional
Probab=98.72 E-value=8.2e-08 Score=81.92 Aligned_cols=75 Identities=21% Similarity=0.340 Sum_probs=64.6
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEE
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLH 163 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Ls 163 (298)
.++|++|.|+|+++.+.+++|+|+...+|++|++++.. ....++.+.|++||.|.|+|++++.++.+.|+
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~----------~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LS 72 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVAD----------NYVKDINDHLKVGDEVEVKVLNVEDDGKIGLS 72 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCc----------ccccccccccCCCCEEEEEEEEECCCCcEEEE
Confidence 47899999999999999999999999999999999841 11234568899999999999999877899999
Q ss_pred eccCC
Q psy10116 164 TRSLK 168 (298)
Q Consensus 164 tr~~~ 168 (298)
++...
T Consensus 73 lk~~~ 77 (139)
T PRK08582 73 IKKAK 77 (139)
T ss_pred EEecc
Confidence 87654
No 25
>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=98.69 E-value=1.2e-07 Score=70.97 Aligned_cols=74 Identities=15% Similarity=0.293 Sum_probs=61.0
Q ss_pred cCCCEEEEEEEEEecceEEEEeCC-CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEE
Q psy10116 85 EIGEVVVGRVTGLQSQKWVVDTNS-ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTL 162 (298)
Q Consensus 85 ~vGDiVIG~V~~V~~~~~~VDI~s-~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~L 162 (298)
++|++|.|+|+++.+.+|+|++.. ..+|++|.+++.. . + ..++.+.|++||.|.|+|.+++. .+.+.|
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~-~----~-----~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~l 70 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISD-N----R-----VADASKLFRVGDKVRAKVLKIDAEKKRISL 70 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCC-C----c-----cCCHhHeecCCCEEEEEEEEEeCCCCEEEE
Confidence 469999999999999999999984 7899999998741 1 1 12356889999999999999985 578999
Q ss_pred EeccCC
Q psy10116 163 HTRSLK 168 (298)
Q Consensus 163 str~~~ 168 (298)
+.|...
T Consensus 71 s~k~~~ 76 (77)
T cd05708 71 GLKASY 76 (77)
T ss_pred EEEeec
Confidence 887653
No 26
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=98.65 E-value=2.2e-07 Score=70.12 Aligned_cols=71 Identities=10% Similarity=0.111 Sum_probs=58.7
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCC-CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEE
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNS-ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTL 162 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s-~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~L 162 (298)
|+.|+++.|+|+++.+.+++|++.. ..+|++|++++.- . ...+..+.|++||.|.++|.+++..+.+.|
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~-----~-----~~~~~~~~~~~Gd~v~vkv~~vd~~~ki~l 70 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSS-----C-----RVDDPSEVVDVGEKVWVKVIGREMKDKMKL 70 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCC-----C-----cccCHhhEECCCCEEEEEEEEECCCCcEEE
Confidence 6799999999999999999999954 3699999999841 1 123557889999999999999987667777
Q ss_pred Ee
Q psy10116 163 HT 164 (298)
Q Consensus 163 st 164 (298)
|+
T Consensus 71 s~ 72 (73)
T cd05686 71 SL 72 (73)
T ss_pred Ee
Confidence 64
No 27
>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=98.64 E-value=1.5e-07 Score=69.69 Aligned_cols=67 Identities=18% Similarity=0.310 Sum_probs=55.8
Q ss_pred CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116 87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH 163 (298)
Q Consensus 87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls 163 (298)
|++|.|+|+++.+++++|++....+|++|++++. +....+..+.|++||.|.|+|.+++. .+.+.||
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~----------~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls 68 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELS----------DSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCC----------chhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 7999999999999999999998899999999874 11233557889999999999999985 4556553
No 28
>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=98.59 E-value=3.3e-07 Score=67.84 Aligned_cols=69 Identities=12% Similarity=0.170 Sum_probs=57.7
Q ss_pred CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEEec
Q psy10116 87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLHTR 165 (298)
Q Consensus 87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Lstr 165 (298)
||++.|+|+++.+.+++|++....+|++|.+++.- ....+....|++||.|.++|.+++. .+.+.||.+
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~----------~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k 70 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSE----------AFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcCh----------hhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 89999999999999999999878999999999841 1122346789999999999999985 567888864
No 29
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.59 E-value=1.4e-07 Score=87.77 Aligned_cols=78 Identities=26% Similarity=0.401 Sum_probs=67.6
Q ss_pred cCccccccCCCEEEEEEEEEecceEEEEeCC--CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC
Q psy10116 78 MNSRYIGEIGEVVVGRVTGLQSQKWVVDTNS--ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS 155 (298)
Q Consensus 78 ~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~s--~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~ 155 (298)
+..+-.|++||+|+|+|.+|.+.+++|.+.- ...|++|+|++. ..+..++|+++++|..+.|+|++++
T Consensus 3 ~~~~~~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEva----------s~wVknIrd~vkegqkvV~kVlrVd 72 (269)
T COG1093 3 MKRREYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVA----------SGWVKNIRDYVKEGQKVVAKVLRVD 72 (269)
T ss_pred ccccCCCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHH----------HHHHHHHHHHhhcCCeEEEEEEEEc
Confidence 3456679999999999999999999999953 368999999994 4568999999999999999999999
Q ss_pred C-CCcEEEEec
Q psy10116 156 T-EGSLTLHTR 165 (298)
Q Consensus 156 ~-dg~~~Lstr 165 (298)
+ .|.+.||.|
T Consensus 73 ~~rg~IDLSlk 83 (269)
T COG1093 73 PKRGHIDLSLK 83 (269)
T ss_pred CCCCeEeeehh
Confidence 4 577889864
No 30
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=98.59 E-value=1.7e-07 Score=89.95 Aligned_cols=75 Identities=13% Similarity=0.244 Sum_probs=64.2
Q ss_pred ccccCCCEEEEEEEEEecceEEEEeC--CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCC
Q psy10116 82 YIGEIGEVVVGRVTGLQSQKWVVDTN--SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEG 158 (298)
Q Consensus 82 Y~P~vGDiVIG~V~~V~~~~~~VDI~--s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg 158 (298)
-.|++||+|.|+|+.+.+.+++|+|. ...+|++|+|+++ +++ ..++++.|++||.|.++|++++ ..+
T Consensus 13 ~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS------~~r----i~~i~d~vkvGd~v~vkVl~VD~ekg 82 (319)
T PTZ00248 13 KFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELS------KRR----IRSINKLIRVGRHEVVVVLRVDKEKG 82 (319)
T ss_pred hCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhc------ccc----cCCHHHhcCCCCEEEEEEEEEeCCCC
Confidence 45899999999999999999999995 3689999999985 222 3567999999999999999998 457
Q ss_pred cEEEEecc
Q psy10116 159 SLTLHTRS 166 (298)
Q Consensus 159 ~~~Lstr~ 166 (298)
.+.||.|.
T Consensus 83 ~IdLS~K~ 90 (319)
T PTZ00248 83 YIDLSKKR 90 (319)
T ss_pred EEEEEeee
Confidence 79999764
No 31
>PRK07252 hypothetical protein; Provisional
Probab=98.57 E-value=3.7e-07 Score=76.12 Aligned_cols=73 Identities=19% Similarity=0.370 Sum_probs=61.0
Q ss_pred cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116 85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH 163 (298)
Q Consensus 85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls 163 (298)
++||+|.|+|+++.+.+|+|+|.....|++|++++.. .+ ..+..+.|++||.|.++|.+++. .+.+.|+
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~-----~~-----~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lS 71 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKT-----GF-----IDNIHQLLKVGEEVLVQVVDFDEYTGKASLS 71 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCC-----cc-----ccChhhccCCCCEEEEEEEEEeCCCCEEEEE
Confidence 5799999999999999999999988999999998741 11 12346789999999999999985 6778888
Q ss_pred eccC
Q psy10116 164 TRSL 167 (298)
Q Consensus 164 tr~~ 167 (298)
++..
T Consensus 72 lk~~ 75 (120)
T PRK07252 72 LRTL 75 (120)
T ss_pred Eeec
Confidence 7654
No 32
>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=98.57 E-value=3.3e-07 Score=73.96 Aligned_cols=81 Identities=14% Similarity=0.267 Sum_probs=63.2
Q ss_pred cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCccc----------ccchhhhhhhhcccCCCCEEEEEEEEe
Q psy10116 85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQR----------RRSVQDEEMMREFLKEGDLISAEIHQI 154 (298)
Q Consensus 85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~R----------r~~~~d~~~mr~~~~~GDlV~A~V~sv 154 (298)
++|++|.|+|+++.+...+|++.....|++|++++.-. .+.+ +..+.+..++.+.|++||+|.|+|+++
T Consensus 2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~ 80 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDA-YTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL 80 (100)
T ss_pred CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHH-HHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence 68999999999999999999999889999999998410 0000 012223345789999999999999999
Q ss_pred CCC----CcEEEEecc
Q psy10116 155 STE----GSLTLHTRS 166 (298)
Q Consensus 155 ~~d----g~~~Lstr~ 166 (298)
+.. ..+.||.|.
T Consensus 81 d~~~~~~~~i~LSlr~ 96 (100)
T cd05693 81 DKSKSGKKRIELSLEP 96 (100)
T ss_pred cCCcCCCcEEEEEecH
Confidence 864 578888764
No 33
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.56 E-value=2.7e-07 Score=68.89 Aligned_cols=63 Identities=17% Similarity=0.188 Sum_probs=53.1
Q ss_pred CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC
Q psy10116 87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE 157 (298)
Q Consensus 87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d 157 (298)
||+|.|+|+++.+++++|++.+..+|.+|++++.-. .....++.+.|++||.|.|+|++++..
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~--------~~~~~~~~~~~~~Gd~i~~kVl~~d~~ 63 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDE--------WPDGKNPLSKFKIGQKIKARVIGGHDA 63 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccc--------cccccChhHhCCCCCEEEEEEEEEeCc
Confidence 899999999999999999999999999999998410 002345678899999999999999754
No 34
>PRK08059 general stress protein 13; Validated
Probab=98.56 E-value=4e-07 Score=75.86 Aligned_cols=75 Identities=24% Similarity=0.441 Sum_probs=63.2
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCCcEEE
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEGSLTL 162 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg~~~L 162 (298)
.++|++|.|+|+++.+.+|+|+|....+|++|.+++.. ++ ..+..+.|++||.|.|+|.+++ .++.+.|
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~-----~~-----~~~~~~~~~vGD~I~vkI~~id~~~~~i~l 74 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITH-----GF-----VKDIHDFLSVGDEVKVKVLSVDEEKGKISL 74 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCc-----cc-----ccCHHHcCCCCCEEEEEEEEEECCCCeEEE
Confidence 46899999999999999999999999999999998741 11 2344678999999999999997 4678999
Q ss_pred EeccCC
Q psy10116 163 HTRSLK 168 (298)
Q Consensus 163 str~~~ 168 (298)
+++...
T Consensus 75 slk~~~ 80 (123)
T PRK08059 75 SIRATE 80 (123)
T ss_pred EEEEcc
Confidence 987764
No 35
>PRK05807 hypothetical protein; Provisional
Probab=98.55 E-value=4.4e-07 Score=77.17 Aligned_cols=72 Identities=21% Similarity=0.332 Sum_probs=61.4
Q ss_pred cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEe
Q psy10116 85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHT 164 (298)
Q Consensus 85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lst 164 (298)
++|++|.|+|+++++.+++|++. ...|++|++++.. ....+...+|++||.|.++|.+++.++.+.||+
T Consensus 4 ~vG~vv~G~Vt~i~~~GafV~L~-~~~Glvhiseis~----------~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSl 72 (136)
T PRK05807 4 KAGSILEGTVVNITNFGAFVEVE-GKTGLVHISEVAD----------TYVKDIREHLKEQDKVKVKVISIDDNGKISLSI 72 (136)
T ss_pred cCCCEEEEEEEEEECCeEEEEEC-CEEEEEEhhhccc----------ccccCccccCCCCCEEEEEEEEECCCCcEEEEE
Confidence 58999999999999999999994 5789999999841 122345678999999999999998888999998
Q ss_pred ccC
Q psy10116 165 RSL 167 (298)
Q Consensus 165 r~~ 167 (298)
+..
T Consensus 73 k~~ 75 (136)
T PRK05807 73 KQA 75 (136)
T ss_pred Eec
Confidence 764
No 36
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.55 E-value=2.9e-07 Score=86.22 Aligned_cols=77 Identities=22% Similarity=0.338 Sum_probs=63.9
Q ss_pred cccccCCCEEEEEEEEEecceEEEEeCC--CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-C
Q psy10116 81 RYIGEIGEVVVGRVTGLQSQKWVVDTNS--ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-E 157 (298)
Q Consensus 81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s--~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-d 157 (298)
.-.|++||+|.|+|+++.+.+|+|++.. ..+|+||+|++.- + ...++++.|++||.|.|+|.+++. .
T Consensus 3 ~~~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~------~----~i~~i~~~~kvGd~V~vkVi~VD~~k 72 (262)
T PRK03987 3 KEWPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVAS------G----WVKNIRDHVKEGQKVVCKVIRVDPRK 72 (262)
T ss_pred CCCCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCc------c----cccCHHHhCCCCCEEEEEEEEEeccc
Confidence 3469999999999999999999999975 5799999999841 1 123567899999999999999985 4
Q ss_pred CcEEEEeccC
Q psy10116 158 GSLTLHTRSL 167 (298)
Q Consensus 158 g~~~Lstr~~ 167 (298)
+.+.||.+..
T Consensus 73 ~~I~LSlK~v 82 (262)
T PRK03987 73 GHIDLSLKRV 82 (262)
T ss_pred CeEEEEEEec
Confidence 6799997643
No 37
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=98.52 E-value=1.3e-06 Score=77.13 Aligned_cols=86 Identities=26% Similarity=0.341 Sum_probs=69.1
Q ss_pred cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhh-------hhhhcccCCCCEEEEEEEE
Q psy10116 81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDE-------EMMREFLKEGDLISAEIHQ 153 (298)
Q Consensus 81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~-------~~mr~~~~~GDlV~A~V~s 153 (298)
-|.|.+|+++.|+|+++++.+++|+++ +.+|+++.+++. |... ..|+ .+....|+.||.|+++|.+
T Consensus 76 ~f~p~~gEvv~G~V~~v~~~GifV~lg-~~~gi~~~~~l~-~~~~-----~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~ 148 (179)
T TIGR00448 76 VFKPELGEIVEGEVIEIVEFGAFVSLG-PFDGLFHVSQVT-DDYC-----YYDPKESALIGKETKKVLDEGDKVRARIVA 148 (179)
T ss_pred EEeccCCCEEEEEEEEEEeeEEEEEeC-CceEEEEcHHhC-CCce-----EEccccceEEEccCCeEEcCCCEEEEEEEE
Confidence 367999999999999999999999996 799999999873 2211 1111 1335789999999999999
Q ss_pred eC------CCCcEEEEeccCCCccCC
Q psy10116 154 IS------TEGSLTLHTRSLKYGKLG 173 (298)
Q Consensus 154 v~------~dg~~~Lstr~~~lGkL~ 173 (298)
++ ....+.||+|++.||+++
T Consensus 149 v~~~~~~~~~~~I~lt~k~~~LG~~~ 174 (179)
T TIGR00448 149 LSLKDRRPEGSKIGLTMRQPLLGKLE 174 (179)
T ss_pred EEccCCCCCcceEEEEeccCcCCccc
Confidence 96 235699999999999974
No 38
>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=98.51 E-value=7.2e-07 Score=67.66 Aligned_cols=71 Identities=15% Similarity=0.152 Sum_probs=58.6
Q ss_pred CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEEec
Q psy10116 87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLHTR 165 (298)
Q Consensus 87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Lstr 165 (298)
||+|.|+|+++.+++++|.+....+|.+|+++++... ....+....|++||.|.|+|++++. ...+.||.+
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~--------~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDV--------SVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCcc--------ccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 8999999999999999999988899999999984210 1123457889999999999999985 456888864
No 39
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.50 E-value=4.5e-07 Score=80.33 Aligned_cols=88 Identities=24% Similarity=0.286 Sum_probs=68.6
Q ss_pred cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhh-----hhhhhcccCCCCEEEEEEEEeC
Q psy10116 81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQD-----EEMMREFLKEGDLISAEIHQIS 155 (298)
Q Consensus 81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d-----~~~mr~~~~~GDlV~A~V~sv~ 155 (298)
-|.|.+|++|.|+|+++...+|+|+++ +.+++++.+++. +.... .+.. ..+....++.||.|+++|.+++
T Consensus 76 vf~P~~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~~l~-~~~~~---~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~ 150 (187)
T PRK08563 76 VFKPELQEVVEGEVVEVVEFGAFVRIG-PVDGLLHISQIM-DDYIS---YDPKNGRLIGKESKRVLKVGDVVRARIVAVS 150 (187)
T ss_pred EEeccCCCEEEEEEEEEEccEEEEEEe-CceEEEEcHHcC-CCceE---EccccceEEEccCCeEEcCCCEEEEEEEEEE
Confidence 467999999999999999999999998 799999998873 21100 0000 0234678999999999999998
Q ss_pred CC------CcEEEEeccCCCccCC
Q psy10116 156 TE------GSLTLHTRSLKYGKLG 173 (298)
Q Consensus 156 ~d------g~~~Lstr~~~lGkL~ 173 (298)
.+ ..+.||+++++||+++
T Consensus 151 ~~~~~~~~~~I~ls~~~~~LG~~~ 174 (187)
T PRK08563 151 LKERRPRGSKIGLTMRQPGLGKLE 174 (187)
T ss_pred cccCCCCCCEEEEEecCCCCCcHH
Confidence 43 3688999999999863
No 40
>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=98.48 E-value=8.1e-07 Score=68.38 Aligned_cols=73 Identities=15% Similarity=0.046 Sum_probs=61.2
Q ss_pred ccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcE
Q psy10116 82 YIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSL 160 (298)
Q Consensus 82 Y~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~ 160 (298)
..+++|+++.|+|+.+.+.+.+|+++...+|++|.+++.. ++ ..++.+.|++||.|.++|.+++. .+.+
T Consensus 10 ~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~-----~~-----~~~~~~~~~~Gd~v~vkV~~id~~~~~i 79 (83)
T cd04461 10 SDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISD-----EF-----VTDPSFGFKKGQSVTAKVTSVDEEKQRF 79 (83)
T ss_pred HhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCc-----cc-----ccCHHHhcCCCCEEEEEEEEEcCCCCEE
Confidence 3478999999999999999999999888999999999842 11 23457899999999999999985 4677
Q ss_pred EEEe
Q psy10116 161 TLHT 164 (298)
Q Consensus 161 ~Lst 164 (298)
.||+
T Consensus 80 ~lsl 83 (83)
T cd04461 80 LLSL 83 (83)
T ss_pred EEeC
Confidence 7763
No 41
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.47 E-value=1.3e-06 Score=66.71 Aligned_cols=67 Identities=16% Similarity=0.238 Sum_probs=57.3
Q ss_pred cCCCEEEEEEEEEecceEEEEeC-CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcEEE
Q psy10116 85 EIGEVVVGRVTGLQSQKWVVDTN-SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSLTL 162 (298)
Q Consensus 85 ~vGDiVIG~V~~V~~~~~~VDI~-s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~~L 162 (298)
+.|++|.|.|.++.+.+++||++ ...+|+||.++++. ...|++||.+.|+|.+++.. ..+.|
T Consensus 3 ~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~----------------~~~~~~Gq~v~~~V~~vd~~~~~v~l 66 (74)
T cd05694 3 VEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGN----------------FSKLKVGQLLLCVVEKVKDDGRVVSL 66 (74)
T ss_pred CCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCc----------------ccccCCCCEEEEEEEEEECCCCEEEE
Confidence 58999999999999999999997 46899999998741 17899999999999999844 56888
Q ss_pred EeccC
Q psy10116 163 HTRSL 167 (298)
Q Consensus 163 str~~ 167 (298)
|.+..
T Consensus 67 s~k~~ 71 (74)
T cd05694 67 SADPS 71 (74)
T ss_pred EEeec
Confidence 88754
No 42
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.43 E-value=6.8e-07 Score=79.42 Aligned_cols=91 Identities=25% Similarity=0.302 Sum_probs=70.4
Q ss_pred cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCC--CCcccccchhhhhhhhcccCCCCEEEEEEEEeCC--
Q psy10116 81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLP--GGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-- 156 (298)
Q Consensus 81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~p--gg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-- 156 (298)
-|.|..|++|-|.|+++...+++|.|+ |.+|++|.+++..+ ....++..=. ...-...|++||.|+|||.+++.
T Consensus 76 ~fkP~~gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~dd~~~~d~~~~~~~-g~~tk~~i~~gd~VR~RIv~~s~~~ 153 (183)
T COG1095 76 VFKPFRGEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIMDDYIDYDEKNKVLI-GEETKRVLKVGDKVRARIVGVSLKS 153 (183)
T ss_pred EEEeccccEEEEEEEEEeecceEEEec-cccccccHhhccCcccccCcccceee-ecccceEEecCCEEEEEEEEEeccc
Confidence 578999999999999999999999999 99999999998532 0001111000 12235589999999999999882
Q ss_pred ----CCcEEEEeccCCCccCC
Q psy10116 157 ----EGSLTLHTRSLKYGKLG 173 (298)
Q Consensus 157 ----dg~~~Lstr~~~lGkL~ 173 (298)
+..+.||+|++.||+++
T Consensus 154 ~~~~~~~I~lTmrq~~LGkle 174 (183)
T COG1095 154 RRPRESKIGLTMRQPGLGKLE 174 (183)
T ss_pred CccccceEEEEeccccCCcch
Confidence 24588999999999975
No 43
>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=98.43 E-value=9.4e-07 Score=63.99 Aligned_cols=67 Identities=21% Similarity=0.336 Sum_probs=54.6
Q ss_pred CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116 87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH 163 (298)
Q Consensus 87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls 163 (298)
|+++.|+|+++.+.+|+|+++....|++|.+++.. .+ ..+....|++||.|.|+|.+++. ++.+.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~-----~~-----~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMAD-----RF-----VSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCC-----cc-----ccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 78999999999999999999988999999998741 11 12346789999999999999985 4566553
No 44
>PHA02945 interferon resistance protein; Provisional
Probab=98.43 E-value=1.2e-06 Score=69.25 Aligned_cols=72 Identities=15% Similarity=0.230 Sum_probs=58.8
Q ss_pred cccCCCEEEEEEEEEecceEEEEeCC--CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCc
Q psy10116 83 IGEIGEVVVGRVTGLQSQKWVVDTNS--ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGS 159 (298)
Q Consensus 83 ~P~vGDiVIG~V~~V~~~~~~VDI~s--~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~ 159 (298)
.|++||+|+|+|.+ .+.+++|++.. ..+|++|+|.+.. ++.+.++ |+++ +|..|.|+|+.+++ .|.
T Consensus 8 ~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~sevev--------a~~wvK~-rd~l-~GqkvV~KVirVd~~kg~ 76 (88)
T PHA02945 8 LPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMH--------MNRYFKY-RDKL-VGKTVKVKVIRVDYTKGY 76 (88)
T ss_pred CCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhh--------ccceEee-eeEe-cCCEEEEEEEEECCCCCE
Confidence 59999999999999 99999999953 4789999995510 1234456 9999 99999999999994 467
Q ss_pred EEEEec
Q psy10116 160 LTLHTR 165 (298)
Q Consensus 160 ~~Lstr 165 (298)
+-||.+
T Consensus 77 IDlSlK 82 (88)
T PHA02945 77 IDVNYK 82 (88)
T ss_pred EEeEee
Confidence 888765
No 45
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.42 E-value=1.6e-06 Score=64.29 Aligned_cols=67 Identities=15% Similarity=0.185 Sum_probs=55.5
Q ss_pred CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116 87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH 163 (298)
Q Consensus 87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls 163 (298)
|++|.|+|+++.+.+++|++....+|++|.++++.. ...+..+.|++||.+.++|.+++. .+.+.|+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~----------~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls 68 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADV----------RLKHPEKKFKPGLKVKCRVLSVEPERKRLVLT 68 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCc----------cccCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence 799999999999999999998789999999987411 112346789999999999999985 4667776
No 46
>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=98.42 E-value=1.9e-06 Score=62.77 Aligned_cols=67 Identities=19% Similarity=0.379 Sum_probs=55.2
Q ss_pred CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEE
Q psy10116 87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLH 163 (298)
Q Consensus 87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Ls 163 (298)
|+++.|+|+++.+.+|+|+|+....|+||++++.. ++ .......|++||.|.++|.+++..+.+.||
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~-----~~-----~~~~~~~~~~Gd~v~v~v~~~d~~~~i~ls 67 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSD-----ER-----VEKVEDVLKVGDEVKVKVIEVDDRGRISLS 67 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCC-----cc-----ccCHHHccCCCCEEEEEEEEECCCCcEEee
Confidence 78999999999999999999988999999998741 11 112346899999999999999876677776
No 47
>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=98.40 E-value=1.7e-06 Score=68.17 Aligned_cols=74 Identities=22% Similarity=0.260 Sum_probs=57.5
Q ss_pred ccCCCEEEEEEEEEecc--eEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCc-E
Q psy10116 84 GEIGEVVVGRVTGLQSQ--KWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGS-L 160 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~--~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~-~ 160 (298)
|++|+++.|+|+++.+. .++||++...+|+||++++.-. .++ ...+..+.|++||.|.++|.....+++ +
T Consensus 5 ~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~---~~~----~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~ 77 (88)
T cd04453 5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPA---YFK----KHKKIAKLLKEGQEILVQVVKEPIGTKGP 77 (88)
T ss_pred CCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCch---hcc----ccCCHHHcCCCCCEEEEEEEEecCCCCCc
Confidence 57999999999999996 9999999889999999998420 001 123446789999999999999874433 5
Q ss_pred EEEe
Q psy10116 161 TLHT 164 (298)
Q Consensus 161 ~Lst 164 (298)
.||+
T Consensus 78 ~lt~ 81 (88)
T cd04453 78 RLTT 81 (88)
T ss_pred eEEE
Confidence 5654
No 48
>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=98.39 E-value=1.4e-06 Score=63.25 Aligned_cols=66 Identities=23% Similarity=0.366 Sum_probs=53.2
Q ss_pred CCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEE
Q psy10116 86 IGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTL 162 (298)
Q Consensus 86 vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~L 162 (298)
+|++|.|+|+++.+.+|+|+++ ..+|+||.+++.. ++ ...+...|++||.|.|+|.+++. .+.+.|
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~-~~~g~l~~~e~~~-----~~-----~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~l 67 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSW-----GR-----VKHPSEVVNVGDEVEVKVLKIDKERKRISL 67 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCC-----cc-----ccCHhHEECCCCEEEEEEEEEECCCCEEec
Confidence 5999999999999999999998 5899999998741 11 12346789999999999999985 345554
No 49
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=98.38 E-value=1.4e-06 Score=88.70 Aligned_cols=74 Identities=24% Similarity=0.432 Sum_probs=64.5
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCCcEEE
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEGSLTL 162 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg~~~L 162 (298)
.++||+|.|+|+++++.+++|||+. .+|+||+++++. .......++|++||-|.++|++++ ..+.++|
T Consensus 190 l~~G~vV~G~V~~It~~GafVdigG-vdGLlHiseiS~----------~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsL 258 (541)
T COG0539 190 LEVGEVVEGVVKNITDYGAFVDIGG-VDGLLHISEISW----------KRVDHPSEVVKVGDEVKVKVISLDEERGRVSL 258 (541)
T ss_pred CCCCceEEEEEEEeecCcEEEEecC-eeeEEehhhccc----------cccCCHHHhcccCCEEEEEEEEEccCCCeEEE
Confidence 5899999999999999999999997 999999999963 113455899999999999999999 4567999
Q ss_pred EeccCC
Q psy10116 163 HTRSLK 168 (298)
Q Consensus 163 str~~~ 168 (298)
|++...
T Consensus 259 SlK~l~ 264 (541)
T COG0539 259 SLKQLE 264 (541)
T ss_pred Eehhcc
Confidence 998754
No 50
>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=98.31 E-value=3.6e-06 Score=63.35 Aligned_cols=68 Identities=24% Similarity=0.194 Sum_probs=55.5
Q ss_pred CCEEE-EEEEEE-ecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116 87 GEVVV-GRVTGL-QSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH 163 (298)
Q Consensus 87 GDiVI-G~V~~V-~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls 163 (298)
|+++- |+|+++ .+.+++|++....+|++|.|++.- ....+..+.|++||.+.|+|+++++ ++.+.||
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~----------~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS 70 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSD----------DKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLS 70 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCc----------chhcCcccccCCCCEEEEEEEEEeCCCCEEEEe
Confidence 78888 999999 699999999878999999999841 1123346789999999999999984 5578777
Q ss_pred e
Q psy10116 164 T 164 (298)
Q Consensus 164 t 164 (298)
+
T Consensus 71 ~ 71 (71)
T cd05696 71 L 71 (71)
T ss_pred C
Confidence 3
No 51
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.31 E-value=3.9e-06 Score=80.61 Aligned_cols=76 Identities=21% Similarity=0.281 Sum_probs=64.2
Q ss_pred ccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcE
Q psy10116 82 YIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSL 160 (298)
Q Consensus 82 Y~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~ 160 (298)
|..++||+|-|+|+.+..++.+|||+....|+||++++.. ....+..+.|++||.|.+.|++++. ++.+
T Consensus 27 ~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~----------~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i 96 (318)
T PRK07400 27 YHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSI----------NRVEGPEEVLQPNETREFFILSDENEDGQL 96 (318)
T ss_pred hhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcc----------ccccCHHHccCCCCEEEEEEEEEeCCCCeE
Confidence 4579999999999999999999999988999999999852 1123446789999999999999874 5789
Q ss_pred EEEeccC
Q psy10116 161 TLHTRSL 167 (298)
Q Consensus 161 ~Lstr~~ 167 (298)
.||.|..
T Consensus 97 ~lS~k~~ 103 (318)
T PRK07400 97 TLSIRRI 103 (318)
T ss_pred EEehhhh
Confidence 9998754
No 52
>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=98.30 E-value=4.5e-06 Score=62.04 Aligned_cols=55 Identities=27% Similarity=0.378 Sum_probs=48.9
Q ss_pred cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC
Q psy10116 85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST 156 (298)
Q Consensus 85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~ 156 (298)
..|++|.|+|.++..+.++|||+. .+|+||.+++. | .+.|++||.|.+.|.+++.
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~-~eg~lp~~e~~-~---------------~~~~~~Gd~v~v~v~~v~~ 56 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGK-VEAILPKKEQI-P---------------GESYRPGDRIKAYVLEVRK 56 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCC-eEEEeeHHHCC-C---------------CCcCCCCCEEEEEEEEEec
Confidence 579999999999999999999986 89999998874 2 3568999999999999974
No 53
>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=98.24 E-value=3.8e-06 Score=59.45 Aligned_cols=64 Identities=19% Similarity=0.339 Sum_probs=51.1
Q ss_pred EEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116 90 VVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH 163 (298)
Q Consensus 90 VIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls 163 (298)
|.|+|+++.+.+|+|+++...+|++|.+++.. + ...+++..|++||.|.|+|.+++. ++.+.||
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~------~----~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSD------K----FVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCC------c----cccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 47999999999999999988999999998741 1 113457889999999999999974 4555543
No 54
>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=98.19 E-value=7.1e-06 Score=60.95 Aligned_cols=65 Identities=20% Similarity=0.275 Sum_probs=52.8
Q ss_pred CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcEEEE
Q psy10116 87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSLTLH 163 (298)
Q Consensus 87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~~Ls 163 (298)
||+|-|+|+++.+++++|++....+|++|.+++..+ ... .+.|++||.|.|+|++++++ ..+.||
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~-----------~~~-~~~~~~G~~i~~kVi~id~~~~~i~LS 66 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPE-----------KSS-KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCc-----------cCc-ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 899999999999999999997679999999987411 011 56799999999999999853 445553
No 55
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.18 E-value=9.3e-06 Score=82.22 Aligned_cols=74 Identities=20% Similarity=0.285 Sum_probs=61.9
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCCcEEE
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEGSLTL 162 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg~~~L 162 (298)
.+.||+|.|+|+.+..+.++|||+...+|+||.+++.. ....+....|++||.|.|.|++++ ..+.+.|
T Consensus 33 ~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~----------~~~~~~~~~~~vGd~Ie~~V~~~~~~~g~liL 102 (486)
T PRK07899 33 FNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSI----------KHDVDPNEVVEVGDEVEALVLQKEDKEGRLIL 102 (486)
T ss_pred CCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhcc----------cccCChhhcCCCCCEEEEEEEEEECCCCeEEE
Confidence 58999999999999999999999988999999998852 111234567999999999999987 4567999
Q ss_pred EeccC
Q psy10116 163 HTRSL 167 (298)
Q Consensus 163 str~~ 167 (298)
|.|..
T Consensus 103 S~k~~ 107 (486)
T PRK07899 103 SKKRA 107 (486)
T ss_pred Eehhh
Confidence 98754
No 56
>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=98.17 E-value=1.3e-05 Score=60.93 Aligned_cols=70 Identities=19% Similarity=0.377 Sum_probs=57.6
Q ss_pred CCEEEEEEEEEecceEEEEeC---CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEE
Q psy10116 87 GEVVVGRVTGLQSQKWVVDTN---SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLH 163 (298)
Q Consensus 87 GDiVIG~V~~V~~~~~~VDI~---s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Ls 163 (298)
|+++.|+|+++.+.+++|+|. ...+|++|++++.. . +. ..+....|++||.|.++|.+++ .+.+.|+
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~-~----~~----~~~~~~~~~~Gd~v~v~v~~vd-~~~i~~s 70 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSF-E----GR----VANPSDVVKRGQKVKVKVISIQ-NGKISLS 70 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccC-C----CC----cCChhheeCCCCEEEEEEEEEe-CCEEEEE
Confidence 789999999999999999998 45899999999841 1 10 1244678999999999999998 7888888
Q ss_pred ecc
Q psy10116 164 TRS 166 (298)
Q Consensus 164 tr~ 166 (298)
.+.
T Consensus 71 ~k~ 73 (79)
T cd05684 71 MKD 73 (79)
T ss_pred EEe
Confidence 765
No 57
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=98.16 E-value=1.5e-05 Score=70.58 Aligned_cols=91 Identities=11% Similarity=0.032 Sum_probs=68.5
Q ss_pred cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCccc-ccch--hh-hhhhhcccCCCCEEEEEEEEeC-
Q psy10116 81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQR-RRSV--QD-EEMMREFLKEGDLISAEIHQIS- 155 (298)
Q Consensus 81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~R-r~~~--~d-~~~mr~~~~~GDlV~A~V~sv~- 155 (298)
-|.|-.|++|.|+|+++...+++|++| +.++++|.+++ |....= .... .+ ..+-+..++.||.|++||.++.
T Consensus 76 vFrPf~gEVv~g~V~~v~~~G~~v~~G-p~~ifI~~~~l--~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~ 152 (176)
T PTZ00162 76 VFKPFKDEVLDAIVTDVNKLGFFAQAG-PLKAFVSRSAI--PPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRY 152 (176)
T ss_pred EEecCCCCEEEEEEEEEecceEEEEee-CeEEEEcHHHC--CCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEe
Confidence 588999999999999999999999997 78899998887 322110 0000 00 1122678999999999999887
Q ss_pred --CCCcEEEEeccCCCccCCC
Q psy10116 156 --TEGSLTLHTRSLKYGKLGQ 174 (298)
Q Consensus 156 --~dg~~~Lstr~~~lGkL~~ 174 (298)
.+.....|+|++.||+++.
T Consensus 153 ~~~~~~~i~T~~~~~LG~~~~ 173 (176)
T PTZ00162 153 DASNLFAIATINSDYLGPIES 173 (176)
T ss_pred cCCCcEEEEEecCCCcCcccc
Confidence 3345677899999999843
No 58
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=98.12 E-value=1.1e-05 Score=64.28 Aligned_cols=83 Identities=25% Similarity=0.282 Sum_probs=60.9
Q ss_pred CEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCccc--ccchhhhhhhhcccCCCCEEEEEEEEeCCC------Cc
Q psy10116 88 EVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQR--RRSVQDEEMMREFLKEGDLISAEIHQISTE------GS 159 (298)
Q Consensus 88 DiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~R--r~~~~d~~~mr~~~~~GDlV~A~V~sv~~d------g~ 159 (298)
++|.|+|+++...+++|++. +.+|++|++++.- .-... +............|++||.|.++|.+++.+ ..
T Consensus 1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~ 78 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMD-DYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESK 78 (99)
T ss_pred CEEEEEEEEEEeccEEEEEc-CeEEEEEEEEccC-CceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCce
Confidence 47899999999999999998 5899999988731 10000 000000011246799999999999999843 57
Q ss_pred EEEEeccCCCccC
Q psy10116 160 LTLHTRSLKYGKL 172 (298)
Q Consensus 160 ~~Lstr~~~lGkL 172 (298)
+.||+++..+|.+
T Consensus 79 i~ls~k~~~~g~~ 91 (99)
T cd04460 79 IGLTMRQPGLGKL 91 (99)
T ss_pred EEEEEecCCCCcH
Confidence 9999999999986
No 59
>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=98.09 E-value=3.4e-05 Score=58.88 Aligned_cols=64 Identities=22% Similarity=0.343 Sum_probs=56.0
Q ss_pred ccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEE
Q psy10116 82 YIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLT 161 (298)
Q Consensus 82 Y~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~ 161 (298)
--.++|+.+.|+|+++++.+++|++....+|++|.+++ .+.++.||.+.++|.++..++.+.
T Consensus 12 ~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~------------------~~~~~iGd~v~v~I~~i~e~~~i~ 73 (77)
T cd04473 12 EDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNL------------------LRDYEVGDEVIVQVTDIPENGNID 73 (77)
T ss_pred hhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhc------------------cCcCCCCCEEEEEEEEECCCCcEE
Confidence 33689999999999999999999999889999998875 245999999999999996667777
Q ss_pred EE
Q psy10116 162 LH 163 (298)
Q Consensus 162 Ls 163 (298)
|+
T Consensus 74 l~ 75 (77)
T cd04473 74 LI 75 (77)
T ss_pred EE
Confidence 76
No 60
>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=98.08 E-value=1.5e-05 Score=58.51 Aligned_cols=67 Identities=22% Similarity=0.404 Sum_probs=53.3
Q ss_pred CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcEEE
Q psy10116 87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSLTL 162 (298)
Q Consensus 87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~~L 162 (298)
|+++.|+|+++.+.+++|++....+|++|.+++..+ .+ ..+.++.|++||.|.|+|.+++.+ +.+.|
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~---~~------~~~~~~~~~~G~~v~v~v~~id~~~~~i~l 68 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWT---QR------VRHPSEIYKKGQEVEAVVLNIDVERERISL 68 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCc---cc------cCChhhEECCCCEEEEEEEEEECCcCEEeC
Confidence 789999999999999999999889999999987411 01 123357899999999999999743 44544
No 61
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.05 E-value=2e-05 Score=75.78 Aligned_cols=74 Identities=26% Similarity=0.408 Sum_probs=62.1
Q ss_pred cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEE
Q psy10116 83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLT 161 (298)
Q Consensus 83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~ 161 (298)
..++|++|.|+|+.+.+.+++|+++ ...|++|++++.. .+ ..+..+.|++||.|.|+|.+++. .+.+.
T Consensus 193 ~~k~G~vv~G~V~~I~~~G~fV~i~-gv~Gllhisels~-----~~-----~~~~~~~~~vGd~VkvkVl~iD~e~~rI~ 261 (318)
T PRK07400 193 RLEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISH-----EH-----IETPHSVFNVNDEMKVMIIDLDAERGRIS 261 (318)
T ss_pred cCCCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHccc-----cc-----ccChhhccCCCCEEEEEEEEEeCCCCEEE
Confidence 3688999999999999999999996 5789999999852 11 23457889999999999999984 57899
Q ss_pred EEeccC
Q psy10116 162 LHTRSL 167 (298)
Q Consensus 162 Lstr~~ 167 (298)
|+++..
T Consensus 262 LS~K~l 267 (318)
T PRK07400 262 LSTKQL 267 (318)
T ss_pred EEEecc
Confidence 998764
No 62
>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=98.04 E-value=1.4e-05 Score=84.00 Aligned_cols=75 Identities=27% Similarity=0.376 Sum_probs=61.6
Q ss_pred cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEE
Q psy10116 83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTL 162 (298)
Q Consensus 83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~L 162 (298)
.|++|++|.|+|+++.+.+++|+|....+|++|+|++.-=.. .+| ..+.++.|++||.|.++|++++..+.+.|
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~-~~r-----v~~~~dv~kvGd~V~VKVl~ID~~gKI~L 717 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAG-GKR-----VENVEDVLSVGQKIQVEIADIDDRGKLSL 717 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhcccccc-ccC-----cCCHHHcCCCCCEEEEEEEEECCCCCeee
Confidence 589999999999999999999999878999999998730000 011 24668999999999999999997778877
Q ss_pred E
Q psy10116 163 H 163 (298)
Q Consensus 163 s 163 (298)
+
T Consensus 718 ~ 718 (719)
T TIGR02696 718 V 718 (719)
T ss_pred c
Confidence 5
No 63
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.02 E-value=2e-05 Score=82.95 Aligned_cols=99 Identities=20% Similarity=0.308 Sum_probs=77.5
Q ss_pred cCCeEEEEEeeEEEEe--CcEEEEEecCccccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccch
Q psy10116 54 DDEEIKASVGGVVEKV--NQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSV 131 (298)
Q Consensus 54 ~~g~i~Asv~G~v~~~--nk~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~ 131 (298)
++|.++++..|..... +..+...+. .|++|+++.|+|+++.+.+++|+|....+|++|+|++.- +|
T Consensus 591 d~G~v~i~~~~~~~~~~a~~~I~~~~~----~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~-----~~--- 658 (693)
T PRK11824 591 DDGTVKIAATDGEAAEAAKERIEGITA----EPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIAD-----ER--- 658 (693)
T ss_pred CCceEEEEcccHHHHHHHHHHHHHhcc----cCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccC-----cc---
Confidence 4688888888776642 222332222 378999999999999999999999988999999999741 11
Q ss_pred hhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEecc
Q psy10116 132 QDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRS 166 (298)
Q Consensus 132 ~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~ 166 (298)
..+..+.|++||.|.++|.+++..+.+.||+|.
T Consensus 659 --v~~~~~v~kvGD~V~VkV~~iD~~grI~LS~k~ 691 (693)
T PRK11824 659 --VEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRKA 691 (693)
T ss_pred --ccCccceeCCCCEEEEEEEEECCCCcEEEEEEe
Confidence 234568899999999999999876899999875
No 64
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.01 E-value=3.1e-05 Score=78.43 Aligned_cols=75 Identities=20% Similarity=0.276 Sum_probs=62.1
Q ss_pred cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCC----
Q psy10116 83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEG---- 158 (298)
Q Consensus 83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg---- 158 (298)
..++|++|.|+|+++.+.+++|||+...+|++|++++.. ....++...|++||.|.|+|.+++.+.
T Consensus 199 ~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~----------~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~ 268 (491)
T PRK13806 199 TVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSW----------SRVQKADEAVSVGDTVRVKVLGIERAKKGKG 268 (491)
T ss_pred hCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCC----------ccccChhHhcCCCCEEEEEEEEEecccCCcc
Confidence 368999999999999999999999878999999999852 112345678999999999999998543
Q ss_pred -cEEEEeccC
Q psy10116 159 -SLTLHTRSL 167 (298)
Q Consensus 159 -~~~Lstr~~ 167 (298)
.+.||.|..
T Consensus 269 ~ri~lS~K~~ 278 (491)
T PRK13806 269 LRISLSIKQA 278 (491)
T ss_pred eEEEEEehhh
Confidence 588887643
No 65
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.00 E-value=3.4e-05 Score=75.38 Aligned_cols=74 Identities=22% Similarity=0.368 Sum_probs=60.8
Q ss_pred cccCCCEEEEEEEEEecceEEEEe-CCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcE
Q psy10116 83 IGEIGEVVVGRVTGLQSQKWVVDT-NSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSL 160 (298)
Q Consensus 83 ~P~vGDiVIG~V~~V~~~~~~VDI-~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~ 160 (298)
-.++||+|.|+|+.+.++++.||| +...+|+||.+++... ...+....|++||.|.|+|.+++.+ +.+
T Consensus 14 ~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~----------~~~~~~~~~~vGd~v~~~V~~v~~~~~~i 83 (390)
T PRK06676 14 EVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSND----------HIEDINDVVKVGDELEVYVLKVEDGEGNL 83 (390)
T ss_pred cccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhccc----------cccCcccccCCCCEEEEEEEEEECCCCCE
Confidence 468999999999999999999999 8789999999988421 1123356799999999999999844 469
Q ss_pred EEEecc
Q psy10116 161 TLHTRS 166 (298)
Q Consensus 161 ~Lstr~ 166 (298)
.||.+.
T Consensus 84 ~lS~k~ 89 (390)
T PRK06676 84 LLSKRR 89 (390)
T ss_pred EEEHHH
Confidence 999875
No 66
>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=97.98 E-value=4.5e-05 Score=56.20 Aligned_cols=66 Identities=29% Similarity=0.377 Sum_probs=51.6
Q ss_pred CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEEec
Q psy10116 87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLHTR 165 (298)
Q Consensus 87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Lstr 165 (298)
|++|.|+|+++.+.+++|++ ....|++|.+++.. ++. .+..+ .+||.+.|+|.+++. .+.+.||.|
T Consensus 1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~~~-----~~~-----~~~~~--~vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDL-----RPV-----EDLDE--YVGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCC-----ccc-----CChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence 78999999999999999999 57999999998842 110 11111 389999999999995 567888753
No 67
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.95 E-value=4.3e-05 Score=77.43 Aligned_cols=72 Identities=15% Similarity=0.275 Sum_probs=60.2
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEE
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTL 162 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~L 162 (298)
-++||+|-|+|+++.+.+++|||+ ..+|++|++++.. ++ ..+..+.|++||.|.++|++++. ++.+.|
T Consensus 206 lk~G~iv~G~V~~i~~~G~FVdlg-gv~Glv~~Sels~-----~~-----v~~~~~~~kvGd~V~vkVl~iD~e~~rI~L 274 (486)
T PRK07899 206 LQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSW-----KH-----IDHPSEVVEVGQEVTVEVLDVDMDRERVSL 274 (486)
T ss_pred ccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHCCC-----cc-----cCCHHHhcCCCCEEEEEEEEEECCCCEEEE
Confidence 469999999999999999999997 5899999999852 11 23456789999999999999985 477899
Q ss_pred Eecc
Q psy10116 163 HTRS 166 (298)
Q Consensus 163 str~ 166 (298)
|.|.
T Consensus 275 SlK~ 278 (486)
T PRK07899 275 SLKA 278 (486)
T ss_pred EEee
Confidence 9764
No 68
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.92 E-value=5.8e-05 Score=77.23 Aligned_cols=72 Identities=21% Similarity=0.308 Sum_probs=61.4
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEE
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTL 162 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~L 162 (298)
.++|++|-|+|+.+.+.+++||++ ..+|++|++++.. ....+..+.|++||.|.|+|.+++. ++.+.|
T Consensus 199 l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~----------~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~l 267 (565)
T PRK06299 199 LEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISW----------KRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSL 267 (565)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhcc----------cccCCHhhcCCCCCEEEEEEEEEeCCCCeEEE
Confidence 579999999999999999999998 8999999999852 1123457789999999999999985 578999
Q ss_pred Eecc
Q psy10116 163 HTRS 166 (298)
Q Consensus 163 str~ 166 (298)
|.+.
T Consensus 268 S~k~ 271 (565)
T PRK06299 268 GLKQ 271 (565)
T ss_pred EEEe
Confidence 9874
No 69
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.90 E-value=6.6e-05 Score=55.80 Aligned_cols=64 Identities=19% Similarity=0.303 Sum_probs=52.2
Q ss_pred cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC
Q psy10116 85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE 157 (298)
Q Consensus 85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d 157 (298)
.+|+++.|+|+++.+.+++|++....+|++|.+++.-+ ++ ..+....|+.||.|.++|.+++.+
T Consensus 2 ~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~----~~-----~~~~~~~~~~Gd~v~v~v~~id~~ 65 (72)
T cd05689 2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWT----NK-----NIHPSKVVSLGDEVEVMVLDIDEE 65 (72)
T ss_pred cCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCc----cc-----ccCcccEeCCCCEEEEEEEEeeCC
Confidence 37999999999999999999998889999999987311 01 123457899999999999999743
No 70
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.89 E-value=8.5e-05 Score=72.54 Aligned_cols=72 Identities=19% Similarity=0.267 Sum_probs=60.5
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEE
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTL 162 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~L 162 (298)
.++||+|.|+|+++.+.+++|+++ ..+|++|.+++.. + ...++.+.|++||.|.|+|.+++. ++.+.|
T Consensus 190 ~~~G~~v~g~V~~v~~~G~fV~l~-~v~g~v~~sels~-----~-----~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~l 258 (390)
T PRK06676 190 LKEGDVVEGTVARLTDFGAFVDIG-GVDGLVHISELSH-----E-----RVEKPSEVVSVGQEVEVKVLSIDWETERISL 258 (390)
T ss_pred CCCCCEEEEEEEEEecceEEEEeC-CeEEEEEHHHcCc-----c-----ccCCHHHhcCCCCEEEEEEEEEeCCCCEEEE
Confidence 589999999999999999999997 4899999999852 1 123456789999999999999984 577999
Q ss_pred Eecc
Q psy10116 163 HTRS 166 (298)
Q Consensus 163 str~ 166 (298)
|.|.
T Consensus 259 S~k~ 262 (390)
T PRK06676 259 SLKD 262 (390)
T ss_pred EEee
Confidence 9874
No 71
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.83 E-value=3.8e-05 Score=80.77 Aligned_cols=94 Identities=18% Similarity=0.287 Sum_probs=69.7
Q ss_pred cCCeEEEEEeeEEEEe--CcEEEEEecCccccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccch
Q psy10116 54 DDEEIKASVGGVVEKV--NQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSV 131 (298)
Q Consensus 54 ~~g~i~Asv~G~v~~~--nk~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~ 131 (298)
++|.++....+..... ...+.... ..|++|+++.|+|+++.+.+++|+|....+|+||+|++.- +
T Consensus 588 ddG~V~i~~~~~~~~~~a~~~I~~~~----~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~-----~---- 654 (684)
T TIGR03591 588 DDGTVKIAASDGEAAEAAIKMIEGIT----AEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIAN-----E---- 654 (684)
T ss_pred cCeEEEEEECcHHHHHHHHHHHHhhh----cccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCC-----C----
Confidence 3677776666654422 22333322 2489999999999999999999999888999999999841 1
Q ss_pred hhhhhhhcccCCCCEEEEEEEEeCCCCcEE
Q psy10116 132 QDEEMMREFLKEGDLISAEIHQISTEGSLT 161 (298)
Q Consensus 132 ~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~ 161 (298)
...+..+.|++||.|.++|.+++..+.+.
T Consensus 655 -~v~~~~~~~kvGD~V~VkVi~id~~gki~ 683 (684)
T TIGR03591 655 -RVEKVEDVLKEGDEVKVKVLEIDKQGRIK 683 (684)
T ss_pred -cccChhhccCCCCEEEEEEEEECCCCCcc
Confidence 12356789999999999999998655544
No 72
>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=97.78 E-value=0.00034 Score=70.66 Aligned_cols=74 Identities=22% Similarity=0.354 Sum_probs=60.4
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEE
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTL 162 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~L 162 (298)
-++|+++.|+|+++.+.+++|+++....|++|++++... + ...+..+.|++||.|.|+|.+++. ++.+.|
T Consensus 270 ~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~----~-----~~~~~~~~~~vG~~v~v~V~~id~~~~~i~l 340 (516)
T TIGR00717 270 FPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWV----K-----KNSHPSKVVKKGDEVEVMILDIDPERRRLSL 340 (516)
T ss_pred ccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCc----c-----ccCCHHHhccCCCEEEEEEEEEcCCCCEEEE
Confidence 368999999999999999999999889999999987421 0 112234679999999999999985 467999
Q ss_pred Eecc
Q psy10116 163 HTRS 166 (298)
Q Consensus 163 str~ 166 (298)
|+|.
T Consensus 341 S~k~ 344 (516)
T TIGR00717 341 GLKQ 344 (516)
T ss_pred Eehh
Confidence 9875
No 73
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=97.76 E-value=0.00042 Score=74.71 Aligned_cols=104 Identities=13% Similarity=0.191 Sum_probs=72.6
Q ss_pred ecCCeEEEEEeeEEEEeCcEEE--EEecCc-c---cc--ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCC
Q psy10116 53 PDDEEIKASVGGVVEKVNQLVS--VRAMNS-R---YI--GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGG 124 (298)
Q Consensus 53 ~~~g~i~Asv~G~v~~~nk~v~--V~p~~~-r---Y~--P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg 124 (298)
..++++.+.+.+. ...++.++ ++-+.. + +. -.+|++|.|+|+.+.+.+++|++....+|+||.++++..
T Consensus 625 kvGd~V~vkVl~i-D~e~~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~sels~~-- 701 (863)
T PRK12269 625 KIGDEVECMILGY-DIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWV-- 701 (863)
T ss_pred CCCCEEEEEEEEE-ecccCceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEecceEEEEeCCCcEEEEEhHHhhcc--
Confidence 3455666666665 22233333 332221 1 11 257999999999999999999998889999999987521
Q ss_pred cccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEEecc
Q psy10116 125 EQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLHTRS 166 (298)
Q Consensus 125 ~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Lstr~ 166 (298)
++ .......|++||.|.|+|++++. ...+.||.|.
T Consensus 702 --~~-----~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~ 737 (863)
T PRK12269 702 --KR-----TRPADHELEVGKEIECMVIECDPQARRIRLGVKQ 737 (863)
T ss_pred --cc-----ccchhhccCCCCEEEEEEEEEeccCCEEEEEecc
Confidence 11 12234579999999999999985 4679999874
No 74
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.75 E-value=0.00029 Score=72.16 Aligned_cols=73 Identities=23% Similarity=0.363 Sum_probs=62.2
Q ss_pred cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116 85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH 163 (298)
Q Consensus 85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls 163 (298)
++||+|.|+|+++.+.+++|.+.....|++|.+++. .....+..+.|++||.|.|+|++++. ++.+.||
T Consensus 459 ~~G~vV~G~V~~v~~~G~fV~l~~gi~g~i~~se~s----------~~~~~~~~~~~~~Gd~v~~~V~~vd~~~~~i~LS 528 (565)
T PRK06299 459 KKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELS----------RDRVEDATEVLKVGDEVEAKVINIDRKNRRISLS 528 (565)
T ss_pred CCCCEEEEEEEEEecCceEEecCCCcEEEEEHHHhc----------chhccCccccCCCCCEEEEEEEEEccccCEEEEE
Confidence 689999999999999999999987899999999874 11234567889999999999999985 5789999
Q ss_pred eccC
Q psy10116 164 TRSL 167 (298)
Q Consensus 164 tr~~ 167 (298)
++..
T Consensus 529 ~k~~ 532 (565)
T PRK06299 529 IKAL 532 (565)
T ss_pred eeeh
Confidence 8643
No 75
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=97.73 E-value=0.00016 Score=77.82 Aligned_cols=74 Identities=19% Similarity=0.276 Sum_probs=61.7
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEE
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTL 162 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~L 162 (298)
..+||+|-|+|+++.+.+++|+++...+|++|+|++... + ...+..+.|++||.|.|+|++++. .+.++|
T Consensus 576 ~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~----~-----~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsL 646 (863)
T PRK12269 576 FGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWV----K-----KTSKPSDMVKIGDEVECMILGYDIQAGRVSL 646 (863)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCc----c-----ccCCHHHcCCCCCEEEEEEEEEecccCceEE
Confidence 469999999999999999999999889999999998521 1 123446789999999999999984 467899
Q ss_pred Eecc
Q psy10116 163 HTRS 166 (298)
Q Consensus 163 str~ 166 (298)
|.+.
T Consensus 647 S~K~ 650 (863)
T PRK12269 647 GLKQ 650 (863)
T ss_pred Eehh
Confidence 9764
No 76
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.73 E-value=9.7e-05 Score=79.30 Aligned_cols=75 Identities=17% Similarity=0.297 Sum_probs=63.2
Q ss_pred cccCCCEEE-EEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEE
Q psy10116 83 IGEIGEVVV-GRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLT 161 (298)
Q Consensus 83 ~P~vGDiVI-G~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~ 161 (298)
.|++|+++. |+|++|.+.+++|+|....+|++|+|++.- +| ..+..+.|++||.|.++|.+++..+.+.
T Consensus 750 ~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~-----~r-----v~~~~dv~kvGD~V~VkVi~ID~~grI~ 819 (891)
T PLN00207 750 VPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSS-----NW-----LAKPEDAFKVGDRIDVKLIEVNDKGQLR 819 (891)
T ss_pred CcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCC-----cc-----ccCHHHhcCCCCEEEEEEEEECCCCcEE
Confidence 389999995 699999999999999877999999999841 11 2334688999999999999999778899
Q ss_pred EEeccC
Q psy10116 162 LHTRSL 167 (298)
Q Consensus 162 Lstr~~ 167 (298)
|+.+..
T Consensus 820 LSlK~l 825 (891)
T PLN00207 820 LSRRAL 825 (891)
T ss_pred EEEecc
Confidence 998753
No 77
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.71 E-value=0.00018 Score=75.25 Aligned_cols=72 Identities=31% Similarity=0.365 Sum_probs=60.1
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEE
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTL 162 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~L 162 (298)
.++||+|.|+|+++.+.+++|++ ...+|++|.+++... + ..++.+.|++||.|.|+|.+++. ++.+.|
T Consensus 475 l~~G~iV~g~V~~v~~~G~fV~l-~gv~Gll~~sels~~-----~-----~~~~~~~~~vGd~V~vkV~~id~~~~~I~l 543 (647)
T PRK00087 475 LEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWG-----R-----VEKPSDVLKVGDEIKVYILDIDKENKKLSL 543 (647)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEHHHcCcc-----c-----cCCHHHhcCCCCEEEEEEEEEECCCCEEEE
Confidence 46899999999999999999999 578999999987521 1 12356789999999999999974 578999
Q ss_pred Eecc
Q psy10116 163 HTRS 166 (298)
Q Consensus 163 str~ 166 (298)
|+|.
T Consensus 544 S~K~ 547 (647)
T PRK00087 544 SLKK 547 (647)
T ss_pred Eeec
Confidence 9874
No 78
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=97.69 E-value=0.00025 Score=71.66 Aligned_cols=73 Identities=21% Similarity=0.326 Sum_probs=60.3
Q ss_pred cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEE
Q psy10116 83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLT 161 (298)
Q Consensus 83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~ 161 (298)
..++||+|.|+|+++.+.+++||++ ..+|++|.++++.. ...+..+.|++||.|.|+|.+++. ++.+.
T Consensus 184 ~l~~G~~v~g~V~~i~~~G~~V~l~-g~~g~lp~~e~s~~----------~~~~~~~~~~vG~~v~v~Vl~~d~~~~~i~ 252 (516)
T TIGR00717 184 NLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWK----------RVKHPSEYVKVGQEVKVKVIKFDKEKGRIS 252 (516)
T ss_pred hccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCCC----------CCCCHHHhccCCCEEEEEEEEEECCCCcEE
Confidence 4689999999999999999999997 48999999998521 113346789999999999999985 46799
Q ss_pred EEecc
Q psy10116 162 LHTRS 166 (298)
Q Consensus 162 Lstr~ 166 (298)
||.|.
T Consensus 253 lS~k~ 257 (516)
T TIGR00717 253 LSLKQ 257 (516)
T ss_pred EEEEe
Confidence 98774
No 79
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.65 E-value=0.00028 Score=73.75 Aligned_cols=77 Identities=21% Similarity=0.334 Sum_probs=64.5
Q ss_pred ccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCCcE
Q psy10116 82 YIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEGSL 160 (298)
Q Consensus 82 Y~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg~~ 160 (298)
+..++|++|.|+|+++..++++||++...+|+||.+++... ...+....|++||.|.++|.+++ .++.+
T Consensus 298 ~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~----------~~~~~~~~~~vGd~V~v~V~~vd~~~g~i 367 (647)
T PRK00087 298 KQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLD----------EISSLKESVKVGDEIEVKVLKLEDEDGYV 367 (647)
T ss_pred hhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccc----------ccCChhhccCCCCEEEEEEEEEECCCCcE
Confidence 45799999999999999999999999889999999988521 12344678999999999999996 56789
Q ss_pred EEEeccCC
Q psy10116 161 TLHTRSLK 168 (298)
Q Consensus 161 ~Lstr~~~ 168 (298)
.||.+...
T Consensus 368 ~LS~k~~~ 375 (647)
T PRK00087 368 VLSKKEAD 375 (647)
T ss_pred EEEeehhc
Confidence 99987653
No 80
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=97.64 E-value=0.00011 Score=77.32 Aligned_cols=76 Identities=16% Similarity=0.211 Sum_probs=65.5
Q ss_pred cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCCcEE
Q psy10116 83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEGSLT 161 (298)
Q Consensus 83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg~~~ 161 (298)
-.++|.++.|+|+.|...+++||||..++|.+|+|+.+ +....+..+.+++||+|.++|.+++ ....+.
T Consensus 655 dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls----------~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~ 724 (780)
T COG2183 655 DLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLS----------DKFVKDPNEVVKVGDIVKVKVIEVDTARKRIA 724 (780)
T ss_pred hccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhh----------hhhcCChHHhcccCCEEEEEEEEEecccCeee
Confidence 35899999999999999999999999999999999974 3334445899999999999999999 456799
Q ss_pred EEeccCC
Q psy10116 162 LHTRSLK 168 (298)
Q Consensus 162 Lstr~~~ 168 (298)
||+|...
T Consensus 725 Lsmr~~~ 731 (780)
T COG2183 725 LSMRLDE 731 (780)
T ss_pred eEeeccC
Confidence 9987643
No 81
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=97.61 E-value=0.00067 Score=68.81 Aligned_cols=73 Identities=19% Similarity=0.211 Sum_probs=60.9
Q ss_pred cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcEEEE
Q psy10116 85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSLTLH 163 (298)
Q Consensus 85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~~Ls 163 (298)
.+|++|.|+|+++.+.+++|++....+|++|.+++.. .| ..+..+.|++||.|.|+|++++.+ ..++|+
T Consensus 378 ~vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~----~~------~~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls 447 (491)
T PRK13806 378 APGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISR----AG------KPATYEKLKPGDSVTLVVEEIDTAKRKISLA 447 (491)
T ss_pred CCCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCc----cc------ccchhhcCCCCCEEEEEEEEEeCCCCEEEEE
Confidence 4799999999999999999999888999999999842 11 134467899999999999999854 569999
Q ss_pred eccC
Q psy10116 164 TRSL 167 (298)
Q Consensus 164 tr~~ 167 (298)
.+..
T Consensus 448 ~~~~ 451 (491)
T PRK13806 448 PAGA 451 (491)
T ss_pred eehh
Confidence 8743
No 82
>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=97.57 E-value=0.00055 Score=51.73 Aligned_cols=72 Identities=18% Similarity=0.354 Sum_probs=54.3
Q ss_pred CCCEEEEEEEEEecceEEEEeCC-CceeeEecccccCCCCcccccchhhh-------hhhhcccCCCCEEEEEEEEeCC-
Q psy10116 86 IGEVVVGRVTGLQSQKWVVDTNS-ILESALHLTSVNLPGGEQRRRSVQDE-------EMMREFLKEGDLISAEIHQIST- 156 (298)
Q Consensus 86 vGDiVIG~V~~V~~~~~~VDI~s-~~~a~L~~s~v~~pgg~~Rr~~~~d~-------~~mr~~~~~GDlV~A~V~sv~~- 156 (298)
+|+++.|.|+++.+.+++|++.. ..+|++|++++. ... ...|+ ......|++||.|.++|.+++.
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~--~~~----~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~ 74 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLG--DDY----YEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLD 74 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecC--CCc----EEEcccceEEEeccCCCEEcCCCEEEEEEEEeccc
Confidence 48999999999999999999986 589999999863 111 01111 1235789999999999999985
Q ss_pred CCcEEEE
Q psy10116 157 EGSLTLH 163 (298)
Q Consensus 157 dg~~~Ls 163 (298)
.+.+.|+
T Consensus 75 ~~~i~~~ 81 (83)
T cd04471 75 RRKIDFE 81 (83)
T ss_pred cCEEEEE
Confidence 3556554
No 83
>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=97.52 E-value=0.00075 Score=53.29 Aligned_cols=82 Identities=13% Similarity=0.053 Sum_probs=55.2
Q ss_pred CCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCccccc-ch--hhhhhhhcccCCCCEEEEEEEEeCCC---Cc
Q psy10116 86 IGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRR-SV--QDEEMMREFLKEGDLISAEIHQISTE---GS 159 (298)
Q Consensus 86 vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~-~~--~d~~~mr~~~~~GDlV~A~V~sv~~d---g~ 159 (298)
+|++|.|+|+++...+++|+++ |.+++++.+.+ |...+-.. .. .+..+-..+++.||.|++||.++.-+ ..
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G-pl~~f~~~~~i--p~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~ 77 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG-PLSIFISRHLI--PSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDATDIF 77 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc-CceEEEEeeec--CccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccCceE
Confidence 5899999999999999999997 77788876665 32211110 00 11112367899999999999998622 11
Q ss_pred EEEEeccCCCc
Q psy10116 160 LTLHTRSLKYG 170 (298)
Q Consensus 160 ~~Lstr~~~lG 170 (298)
..-|.+++.||
T Consensus 78 ~igt~~~~~LG 88 (88)
T cd04462 78 AIGTIKDDYLG 88 (88)
T ss_pred EEEEccCCCCC
Confidence 22255777766
No 84
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=97.41 E-value=0.00039 Score=71.14 Aligned_cols=73 Identities=21% Similarity=0.389 Sum_probs=62.3
Q ss_pred cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116 85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH 163 (298)
Q Consensus 85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls 163 (298)
.+||.+.|+|+.+.+.+++|+|....+|++|+|+++- .+ ....++.+++||.|.++|++++. +..++|+
T Consensus 276 ~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw-----~~-----~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~ 345 (541)
T COG0539 276 PVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISW-----TK-----KNVPSEVVKVGQEVEVKVLDIDPERRRISLG 345 (541)
T ss_pred CCCCEEEEEEEEeecCcEEEEecCCccceeechhhcc-----cc-----cCCHHHhcccCCEEEEEEEeeCchhceEEee
Confidence 5899999999999999999999999999999999862 11 11257899999999999999995 4679999
Q ss_pred eccC
Q psy10116 164 TRSL 167 (298)
Q Consensus 164 tr~~ 167 (298)
+|..
T Consensus 346 iKq~ 349 (541)
T COG0539 346 LKQL 349 (541)
T ss_pred ehhh
Confidence 8753
No 85
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=97.37 E-value=0.00048 Score=67.01 Aligned_cols=71 Identities=20% Similarity=0.282 Sum_probs=58.5
Q ss_pred cccccCCCEEEEEEEEEecce-EEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC--
Q psy10116 81 RYIGEIGEVVVGRVTGLQSQK-WVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-- 157 (298)
Q Consensus 81 rY~P~vGDiVIG~V~~V~~~~-~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-- 157 (298)
.|..+.|++|.|+|.++..++ |+|||+ ..+|+||.++.. | ++.|++||.|.|.|.++..+
T Consensus 126 ey~~k~GeiV~G~V~~v~~~g~v~VdiG-~~ea~LP~~E~i-p---------------~E~~~~Gd~ik~~V~~V~~~~k 188 (341)
T TIGR01953 126 EFSSKEGEIISGTVKRVNRRGNLYVELG-KTEGILPKKEQI-P---------------GEKFRIGDRIKAYVYEVRKTAK 188 (341)
T ss_pred HHHhhcCCEEEEEEEEEecCCcEEEEEC-CeEEEecHHHcC-C---------------CcCCCCCCEEEEEEEEEEcCCC
Confidence 488899999999999999866 799997 689999988763 3 35599999999999999833
Q ss_pred -CcEEEEeccCC
Q psy10116 158 -GSLTLHTRSLK 168 (298)
Q Consensus 158 -g~~~Lstr~~~ 168 (298)
+.+.||.+.++
T Consensus 189 g~qIivSRt~~~ 200 (341)
T TIGR01953 189 GPQIILSRTHPE 200 (341)
T ss_pred CCeEEEEeCcHH
Confidence 45788866544
No 86
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.35 E-value=0.00052 Score=67.28 Aligned_cols=70 Identities=19% Similarity=0.254 Sum_probs=57.9
Q ss_pred cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC---
Q psy10116 81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE--- 157 (298)
Q Consensus 81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d--- 157 (298)
.|..+.|++|.|+|.++..+.|+||++. .+|+||.++.. | ++.|++||.|.|.|.++..+
T Consensus 129 ef~~k~GeiV~G~V~~~~~~~~~Vdlg~-vEa~LP~~E~i-p---------------~e~~~~Gd~Ika~V~~V~~~~kg 191 (362)
T PRK12327 129 EFSEREGDIVTGVVQRRDNRFVYVNLGK-IEAVLPPAEQI-P---------------GETYKHGDRIKVYVVKVEKTTKG 191 (362)
T ss_pred HHHHhcCCEEEEEEEEEeCCcEEEEeCC-eEEEecHHHcC-C---------------CCCCCCCCEEEEEEEEEecCCCC
Confidence 3999999999999999999999999986 89999977652 3 56799999999999999833
Q ss_pred CcEEEEeccC
Q psy10116 158 GSLTLHTRSL 167 (298)
Q Consensus 158 g~~~Lstr~~ 167 (298)
..+.||..++
T Consensus 192 p~IivSRt~p 201 (362)
T PRK12327 192 PQIFVSRTHP 201 (362)
T ss_pred CeEEEEeCCH
Confidence 2477774443
No 87
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=97.35 E-value=0.00051 Score=69.48 Aligned_cols=71 Identities=24% Similarity=0.389 Sum_probs=60.2
Q ss_pred cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC---
Q psy10116 81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE--- 157 (298)
Q Consensus 81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d--- 157 (298)
.|..+.|++|.|+|..+...+++||++ ..+|+||.++.. | ++.|++||.|.|.|..++..
T Consensus 129 eyk~~~GeIV~G~V~ri~~~giiVDLg-gvea~LP~sE~i-p---------------~E~~~~GdrIka~I~~Vd~~~kg 191 (470)
T PRK09202 129 EYKDRVGEIITGVVKRVERGNIIVDLG-RAEAILPRKEQI-P---------------RENFRPGDRVRAYVYEVRKEARG 191 (470)
T ss_pred HHHhhcCCEEEEEEEEEecCCEEEEEC-CeEEEecHHHcC-C---------------CccCCCCCEEEEEEEEEecCCCC
Confidence 488899999999999999999999996 579999988873 3 57899999999999999853
Q ss_pred CcEEEEeccCC
Q psy10116 158 GSLTLHTRSLK 168 (298)
Q Consensus 158 g~~~Lstr~~~ 168 (298)
..+.||-+++.
T Consensus 192 ~qIilSRt~p~ 202 (470)
T PRK09202 192 PQIILSRTHPE 202 (470)
T ss_pred CeEEEEeCcHH
Confidence 35888865544
No 88
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=96.88 E-value=0.0072 Score=60.31 Aligned_cols=88 Identities=20% Similarity=0.260 Sum_probs=61.2
Q ss_pred EEEEecCccccccCCCEEEEEEEEEecc--eEEEEeCCCceeeEecccccCCCCcc-----cccchhhhhhhhcccCCCC
Q psy10116 73 VSVRAMNSRYIGEIGEVVVGRVTGLQSQ--KWVVDTNSILESALHLTSVNLPGGEQ-----RRRSVQDEEMMREFLKEGD 145 (298)
Q Consensus 73 v~V~p~~~rY~P~vGDiVIG~V~~V~~~--~~~VDI~s~~~a~L~~s~v~~pgg~~-----Rr~~~~d~~~mr~~~~~GD 145 (298)
+.+++... .+.+|++..|+|+.+.+. .+||||+....|+||++++. |.... .++ ....+..+.+++||
T Consensus 14 ~~ie~~~~--~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~-~~~~~~~~~~~~~--~~~~~i~~~l~~G~ 88 (414)
T TIGR00757 14 LIIERPKS--RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIG-PNYECLAPAEAKR--EAGPSISELLRPGQ 88 (414)
T ss_pred EEEecCcC--cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcC-chhhccccccccc--cccCCHHHhCcCCC
Confidence 34444433 345899999999999998 99999999999999999973 21100 000 00124566899999
Q ss_pred EEEEEEEEeC-CCCcEEEEec
Q psy10116 146 LISAEIHQIS-TEGSLTLHTR 165 (298)
Q Consensus 146 lV~A~V~sv~-~dg~~~Lstr 165 (298)
.|.++|..-. ....+.||+.
T Consensus 89 ~IlVQV~Ke~~~~Kgp~lT~~ 109 (414)
T TIGR00757 89 SVLVQVVKEPRGNKGARLTTD 109 (414)
T ss_pred EEEEEEeeCCcCCCCCeEEEE
Confidence 9999999843 2234667763
No 89
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.36 E-value=0.0095 Score=62.34 Aligned_cols=74 Identities=24% Similarity=0.395 Sum_probs=64.5
Q ss_pred cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEE
Q psy10116 83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTL 162 (298)
Q Consensus 83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~L 162 (298)
-+++|.+-.|+|+.+.+.+++|.+-...+|.+|+|++. .+| ..+..+.+++||.|+.||..+++.|.+.|
T Consensus 616 e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~----~~r------v~kv~dvlk~Gd~v~Vkv~~iD~~Gri~l 685 (692)
T COG1185 616 EVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLA----KER------VEKVEDVLKEGDEVKVKVIEIDKQGRIRL 685 (692)
T ss_pred hcccccEEEEEEEEEeecceEEEecCCcceeEEehhhh----hhh------hhcccceeecCceEEEEEeeecccCCccc
Confidence 47999999999999999999999999999999999974 122 24456999999999999999999899999
Q ss_pred Eecc
Q psy10116 163 HTRS 166 (298)
Q Consensus 163 str~ 166 (298)
+.+.
T Consensus 686 s~~~ 689 (692)
T COG1185 686 SIKA 689 (692)
T ss_pred eehh
Confidence 8754
No 90
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.28 E-value=0.011 Score=58.25 Aligned_cols=59 Identities=19% Similarity=0.455 Sum_probs=50.6
Q ss_pred cccccCCCEEEEEEEEEec-ceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC
Q psy10116 81 RYIGEIGEVVVGRVTGLQS-QKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST 156 (298)
Q Consensus 81 rY~P~vGDiVIG~V~~V~~-~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~ 156 (298)
.|.+++|++|.|+|..+.. ..+.||++ ...|+||..+. .| ++.|++||.|.|-|..+..
T Consensus 133 ey~~~~Geiv~g~V~r~~~~~~i~vdlg-~~ea~LP~~eq-ip---------------~E~~~~Gdrik~~i~~V~~ 192 (374)
T PRK12328 133 KYKKKVGKIVFGTVVRVDNEENTFIEID-EIRAVLPMKNR-IK---------------GEKFKVGDVVKAVLKRVKI 192 (374)
T ss_pred HHHHhcCcEEEEEEEEEecCCCEEEEcC-CeEEEeCHHHc-CC---------------CCcCCCCCEEEEEEEEEec
Confidence 5999999999999999986 46889998 57899997765 23 5779999999999999973
No 91
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.11 E-value=0.015 Score=58.49 Aligned_cols=70 Identities=16% Similarity=0.220 Sum_probs=56.6
Q ss_pred cccccCCCEEEEEEEEEecceEEEEeCC-----CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC
Q psy10116 81 RYIGEIGEVVVGRVTGLQSQKWVVDTNS-----ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS 155 (298)
Q Consensus 81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s-----~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~ 155 (298)
.|.+++|++|.|+|..+..+.+.||+++ ...|+||..+. +| ++.|++||.|+|-|..+.
T Consensus 147 ef~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eq-ip---------------~E~y~~Gdrika~i~~V~ 210 (449)
T PRK12329 147 EFQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQ-LP---------------NDNYRANATFKVFLKEVS 210 (449)
T ss_pred HHHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHc-CC---------------CCcCCCCCEEEEEEEEee
Confidence 4999999999999999999999999943 27899997765 34 577999999999999996
Q ss_pred CC----CcEEEEecc
Q psy10116 156 TE----GSLTLHTRS 166 (298)
Q Consensus 156 ~d----g~~~Lstr~ 166 (298)
.+ ..+.||-..
T Consensus 211 ~~~~kGpqIilSRt~ 225 (449)
T PRK12329 211 EGPRRGPQLFVSRAN 225 (449)
T ss_pred cCCCCCCEEEEEcCC
Confidence 43 246777443
No 92
>KOG1070|consensus
Probab=96.06 E-value=0.019 Score=64.13 Aligned_cols=75 Identities=15% Similarity=0.304 Sum_probs=65.3
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCC-cEEE
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEG-SLTL 162 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg-~~~L 162 (298)
-+.||+|-|+|..+..++.++-++...+|++++++.. +..+..-++.|.+|++|.++|.+++.+. .++|
T Consensus 1160 lk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~----------ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel 1229 (1710)
T KOG1070|consen 1160 LKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLS----------DSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIEL 1229 (1710)
T ss_pred cccCceeEEEEEEecCCcEEEEEccceEEEEEccccc----------cchhhhhhccCCccceeeeEEEEeeccCceEEE
Confidence 4789999999999999999999999999999999873 4556777899999999999999999664 6888
Q ss_pred EeccCC
Q psy10116 163 HTRSLK 168 (298)
Q Consensus 163 str~~~ 168 (298)
+.+..+
T Consensus 1230 ~Lk~s~ 1235 (1710)
T KOG1070|consen 1230 SLKNSD 1235 (1710)
T ss_pred EEeccc
Confidence 876544
No 93
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=95.75 E-value=0.061 Score=42.48 Aligned_cols=69 Identities=20% Similarity=0.268 Sum_probs=53.5
Q ss_pred cccCCCEEEEEEEEEecceEEEEeC-CCceeeEe-cccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-Cc
Q psy10116 83 IGEIGEVVVGRVTGLQSQKWVVDTN-SILESALH-LTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GS 159 (298)
Q Consensus 83 ~P~vGDiVIG~V~~V~~~~~~VDI~-s~~~a~L~-~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~ 159 (298)
.|++||+|. .|+.+++..+.|.+- ...+|.+. .++++ ||+ -.+++..+ +|-.+.++|+.++.+ |-
T Consensus 13 ~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~sels------r~r----irsi~kll-VGk~e~v~ViRVDk~KGY 80 (86)
T PHA02858 13 FPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVN------ADR----AEKLKKKL-VGKTINVQVIRTDKLKGY 80 (86)
T ss_pred cCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHh------HHH----HHhhhhhh-cCCeeEEEEEEECCCCCE
Confidence 499999999 788899999999873 33667666 88875 333 35567788 999999999999854 55
Q ss_pred EEEE
Q psy10116 160 LTLH 163 (298)
Q Consensus 160 ~~Ls 163 (298)
+-||
T Consensus 81 IDLs 84 (86)
T PHA02858 81 IDVR 84 (86)
T ss_pred EEeE
Confidence 6665
No 94
>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=94.99 E-value=0.087 Score=55.84 Aligned_cols=74 Identities=22% Similarity=0.398 Sum_probs=56.5
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCC-CceeeEecccccCCCCcccccchhhh-------hhhhcccCCCCEEEEEEEEeC
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNS-ILESALHLTSVNLPGGEQRRRSVQDE-------EMMREFLKEGDLISAEIHQIS 155 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s-~~~a~L~~s~v~~pgg~~Rr~~~~d~-------~~mr~~~~~GDlV~A~V~sv~ 155 (298)
.++|+++-|+|+++.+.+++|++.. ..+|++|++++. +.. ...|+ ......|++||.|.++|.+++
T Consensus 625 ~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~--~d~----~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd 698 (709)
T TIGR02063 625 EKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLK--DDY----YVFDEKGLALVGERTGKVFRLGDRVKVRVVKAD 698 (709)
T ss_pred ccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecC--CCc----EEEcccceEEEeccCCcEECCCCEEEEEEEEEe
Confidence 6889999999999999999999976 689999999873 110 00011 112467999999999999998
Q ss_pred C-CCcEEEE
Q psy10116 156 T-EGSLTLH 163 (298)
Q Consensus 156 ~-dg~~~Ls 163 (298)
. .+.+.++
T Consensus 699 ~~~~~I~~~ 707 (709)
T TIGR02063 699 LDTGKIDFE 707 (709)
T ss_pred cccCeEEEE
Confidence 4 4666665
No 95
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=94.85 E-value=0.19 Score=36.78 Aligned_cols=60 Identities=27% Similarity=0.275 Sum_probs=34.9
Q ss_pred CCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEe
Q psy10116 86 IGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHT 164 (298)
Q Consensus 86 vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lst 164 (298)
+|+++..+|+++...+|++|.+...+-.||.+++ ...+++||.|.+-|=. +.++.+..||
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~------------------~~~~~~Gd~v~VFvY~-D~~~rl~AT~ 60 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEV------------------PEPLKVGDEVEVFVYL-DKEGRLVATT 60 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG------------------------TTSEEEEEEEE--TTS-EEEE-
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHc------------------CCCCCCCCEEEEEEEE-CCCCCEEEec
Confidence 5899999999999999999998888889997775 2448999999988865 3455666665
No 96
>PRK11712 ribonuclease G; Provisional
Probab=94.64 E-value=0.22 Score=50.95 Aligned_cols=83 Identities=20% Similarity=0.227 Sum_probs=56.9
Q ss_pred ccccCCCEEEEEEEEEe--cceEEEEeCCCceeeEecccccCCCCcc-cc--cchhhhhhhhcccCCCCEEEEEEEEeC-
Q psy10116 82 YIGEIGEVVVGRVTGLQ--SQKWVVDTNSILESALHLTSVNLPGGEQ-RR--RSVQDEEMMREFLKEGDLISAEIHQIS- 155 (298)
Q Consensus 82 Y~P~vGDiVIG~V~~V~--~~~~~VDI~s~~~a~L~~s~v~~pgg~~-Rr--~~~~d~~~mr~~~~~GDlV~A~V~sv~- 155 (298)
....+|+|-.|+|..|. -+.+|||||....|+||++++ .|.... +. +.......+.+.+++||.|...|..-.
T Consensus 34 ~~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~-~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~ 112 (489)
T PRK11712 34 KRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDI-VPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPL 112 (489)
T ss_pred cccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhc-cchhhhcccccccccccccHHHhccCCCEEEEEEEeCCc
Confidence 34569999999999995 467999999999999999987 231100 00 000001134567999999999999854
Q ss_pred CCCcEEEEec
Q psy10116 156 TEGSLTLHTR 165 (298)
Q Consensus 156 ~dg~~~Lstr 165 (298)
....+.||+.
T Consensus 113 ~~KG~~lT~~ 122 (489)
T PRK11712 113 GTKGARLTTD 122 (489)
T ss_pred CCCCCeEEEE
Confidence 2234667663
No 97
>PRK11642 exoribonuclease R; Provisional
Probab=94.39 E-value=0.18 Score=54.42 Aligned_cols=75 Identities=15% Similarity=0.351 Sum_probs=56.3
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCCC-ceeeEecccccCCCCcccccchhhh-------hhhhcccCCCCEEEEEEEEeC
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNSI-LESALHLTSVNLPGGEQRRRSVQDE-------EMMREFLKEGDLISAEIHQIS 155 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s~-~~a~L~~s~v~~pgg~~Rr~~~~d~-------~~mr~~~~~GDlV~A~V~sv~ 155 (298)
.++|+++-|+|++|.+.+++|.+... .+|++|++++. .. ....|+ ......|+.||.|.++|.+++
T Consensus 641 ~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~--~d----~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD 714 (813)
T PRK11642 641 DQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLD--ND----YYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVN 714 (813)
T ss_pred ccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecC--Cc----ceEecchheEEecccCCcEECCCCEEEEEEEEee
Confidence 47999999999999999999999754 89999999863 11 000111 123477999999999999998
Q ss_pred C-CCcEEEEe
Q psy10116 156 T-EGSLTLHT 164 (298)
Q Consensus 156 ~-dg~~~Lst 164 (298)
. .+.+.++.
T Consensus 715 ~~~rkI~f~l 724 (813)
T PRK11642 715 MDERKIDFSL 724 (813)
T ss_pred cCCCeEEEEE
Confidence 3 45666653
No 98
>KOG2916|consensus
Probab=94.02 E-value=0.077 Score=50.08 Aligned_cols=74 Identities=19% Similarity=0.300 Sum_probs=61.4
Q ss_pred ccccCCCEEEEEEEEEecceEEEEeCC--CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CC
Q psy10116 82 YIGEIGEVVVGRVTGLQSQKWVVDTNS--ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EG 158 (298)
Q Consensus 82 Y~P~vGDiVIG~V~~V~~~~~~VDI~s--~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg 158 (298)
-.|+++|+|++.|..+..-++.|.+-- ...|.+.+|+.+ ||| ...+...+++|-.=.+-|+.++. .|
T Consensus 12 kyPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELS------rRR----IRSI~klirVGr~E~vvVlrVDkekG 81 (304)
T KOG2916|consen 12 KYPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELS------RRR----IRSIQKLIRVGRNEPVVVLRVDKEKG 81 (304)
T ss_pred cCCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHH------HHH----HHHHHHHHhcCCcceEEEEEEcCCCC
Confidence 359999999999999999999998842 456888888875 554 35668889999999999999994 57
Q ss_pred cEEEEec
Q psy10116 159 SLTLHTR 165 (298)
Q Consensus 159 ~~~Lstr 165 (298)
-+-||.|
T Consensus 82 YIDLSkr 88 (304)
T KOG2916|consen 82 YIDLSKR 88 (304)
T ss_pred ceechhc
Confidence 7889975
No 99
>PRK10811 rne ribonuclease E; Reviewed
Probab=93.97 E-value=0.28 Score=53.66 Aligned_cols=81 Identities=16% Similarity=0.171 Sum_probs=55.2
Q ss_pred ccCCCEEEEEEEEE--ecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcE
Q psy10116 84 GEIGEVVVGRVTGL--QSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSL 160 (298)
Q Consensus 84 P~vGDiVIG~V~~V--~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~ 160 (298)
+.+|+|-+|+|..| +-+.+|||||....|+|+++++.-|.-.... ......+....+++||.|...|..-... ...
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~-~~~~~~~i~~~Lk~GqeILVQV~KEa~gtKGp 114 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANY-SAHGRPNIKDVLREGQEVIVQIDKEERGNKGA 114 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEecCCcceEEEhhhcccccccccc-ccccccccccccCCCCEEEEEEeecccCCCCC
Confidence 35899999999999 4678999999999999999987411100000 0000113456799999999999985422 235
Q ss_pred EEEec
Q psy10116 161 TLHTR 165 (298)
Q Consensus 161 ~Lstr 165 (298)
.||++
T Consensus 115 ~LTt~ 119 (1068)
T PRK10811 115 ALTTF 119 (1068)
T ss_pred ceeee
Confidence 66654
No 100
>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=93.58 E-value=0.3 Score=51.51 Aligned_cols=74 Identities=12% Similarity=0.317 Sum_probs=55.6
Q ss_pred ccCCCEEEEEEEEEecceEEEEeC-CCceeeEecccccCCCCcccccchhhh-------hhhhcccCCCCEEEEEEEEeC
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTN-SILESALHLTSVNLPGGEQRRRSVQDE-------EMMREFLKEGDLISAEIHQIS 155 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~-s~~~a~L~~s~v~~pgg~~Rr~~~~d~-------~~mr~~~~~GDlV~A~V~sv~ 155 (298)
.++|+.+-|+|+++...+++|.+. ...+|++|++++. +. ....|+ ......|++||.|..+|.+++
T Consensus 570 ~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~--~d----~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd 643 (654)
T TIGR00358 570 DKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLH--ND----YYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVN 643 (654)
T ss_pred hCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCC--Cc----ceEEeccccEEEeccCCcEECCCCEEEEEEEEEe
Confidence 478999999999999999999997 5689999999873 21 011111 122467999999999999998
Q ss_pred -CCCcEEEE
Q psy10116 156 -TEGSLTLH 163 (298)
Q Consensus 156 -~dg~~~Ls 163 (298)
..+.+.++
T Consensus 644 ~~~~~I~f~ 652 (654)
T TIGR00358 644 METRSIIFE 652 (654)
T ss_pred cccCeEEEE
Confidence 34455554
No 101
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=92.85 E-value=0.39 Score=45.64 Aligned_cols=65 Identities=18% Similarity=0.131 Sum_probs=55.9
Q ss_pred CCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEec
Q psy10116 86 IGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTR 165 (298)
Q Consensus 86 vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr 165 (298)
.++.|-|+|.+....+.+|=+...+-|++|-|+. ....+.|+.+.|+|+.+..||++-||++
T Consensus 155 ~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr------------------~~~prlG~~l~~rVi~~reDg~lnLSl~ 216 (287)
T COG2996 155 KNQEVDATVYRLLESGTFVITENGYLGFIHKSER------------------FAEPRLGERLTARVIGVREDGKLNLSLR 216 (287)
T ss_pred hcCeeeeEEEEEeccceEEEEcCCeEEEEcchhh------------------cccccCCceEEEEEEEEccCCeeecccc
Confidence 3788889999999999999888899999998875 3557899999999999999999999987
Q ss_pred cCC
Q psy10116 166 SLK 168 (298)
Q Consensus 166 ~~~ 168 (298)
...
T Consensus 217 p~~ 219 (287)
T COG2996 217 PRA 219 (287)
T ss_pred ccc
Confidence 543
No 102
>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=92.57 E-value=0.73 Score=35.40 Aligned_cols=68 Identities=19% Similarity=0.157 Sum_probs=49.1
Q ss_pred CCEEEEEEEEEecceEEEEeCC-CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEE-EEEEEEeCCCCcEEEE
Q psy10116 87 GEVVVGRVTGLQSQKWVVDTNS-ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLI-SAEIHQISTEGSLTLH 163 (298)
Q Consensus 87 GDiVIG~V~~V~~~~~~VDI~s-~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV-~A~V~sv~~dg~~~Ls 163 (298)
|++|-|+|.+...+...|++.. ...|+|+...... ...+. ..+...+++||.+ .+-|.+. ....+.||
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD-~~~k~-------~~~~~klrvG~~L~~~lvL~~-~~r~i~lt 70 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSD-HVSNC-------PLLWHCLQEGDTIPNLMCLSN-YKGRIILT 70 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC-chhhC-------HHHHhhhhcCCCccceEEEec-cccEEEEe
Confidence 7899999999999999999965 7789998777642 22222 3346789999999 7777722 23344454
No 103
>KOG1856|consensus
Probab=92.35 E-value=0.19 Score=55.47 Aligned_cols=77 Identities=17% Similarity=0.135 Sum_probs=61.1
Q ss_pred cccCCCEEEEEEEEEecce---EEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-C
Q psy10116 83 IGEIGEVVVGRVTGLQSQK---WVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-G 158 (298)
Q Consensus 83 ~P~vGDiVIG~V~~V~~~~---~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g 158 (298)
+-.+|-+|.++|++|+..+ ..|-..+..+|+++..+++ +.+.....+-+++|+.|+|+|++++.. =
T Consensus 982 t~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~S----------d~~v~~p~~~v~vgq~v~~kvi~id~e~f 1051 (1299)
T KOG1856|consen 982 TFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLS----------DRDVRRPENRVKVGQTVYCKVIKIDKERF 1051 (1299)
T ss_pred HhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccC----------hhhccCHHHhhccCceEEEEeeeeeHhhh
Confidence 3468999999999999998 6668999999999988774 233444567789999999999999843 3
Q ss_pred cEEEEeccCCC
Q psy10116 159 SLTLHTRSLKY 169 (298)
Q Consensus 159 ~~~Lstr~~~l 169 (298)
.+.||+|...|
T Consensus 1052 ~v~Ls~r~sdl 1062 (1299)
T KOG1856|consen 1052 SVELSCRTSDL 1062 (1299)
T ss_pred hhhhhhhhHHh
Confidence 57788876543
No 104
>COG2088 SpoVG Uncharacterized protein, involved in the regulation of septum location [Cell envelope biogenesis, outer membrane]
Probab=88.91 E-value=1.3 Score=35.41 Aligned_cols=41 Identities=27% Similarity=0.392 Sum_probs=34.3
Q ss_pred ccEEEEEeeCceEEEecCCCC-CCCccccccccCCHHHHHHHH
Q psy10116 197 CGAQVILGCNGYVWVSAIDEN-KSGGFIQNMEVVKLSDRETIT 238 (298)
Q Consensus 197 ~~~eiivG~NG~IWI~~~~~~-~~~~~~~~~~~i~~~~r~~i~ 238 (298)
-+..++=|.|| +||..++.. .++.|-+...||+.++|+.|.
T Consensus 32 hdirVi~G~~G-lfVAMPSrrt~dgEFrDI~HPI~~~~R~kIq 73 (95)
T COG2088 32 HDIRVIEGNNG-LFVAMPSRRTPDGEFRDIAHPINSDTREKIQ 73 (95)
T ss_pred eccEEEeCCcc-eEEEccCccCCCcchhhccCcCCHHHHHHHH
Confidence 47899999999 999988873 356677778899999999994
No 105
>KOG1070|consensus
Probab=88.12 E-value=0.65 Score=52.53 Aligned_cols=69 Identities=17% Similarity=0.090 Sum_probs=56.7
Q ss_pred CccccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC
Q psy10116 79 NSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS 155 (298)
Q Consensus 79 ~~rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~ 155 (298)
++.|.-++|++|-+.|+++.++...|+..+...|-+|+|++..- .....+.-..|++||-|.|+|+.-.
T Consensus 878 k~~~~~~igsiv~a~v~svKp~~L~v~l~~~~~gri~isev~d~--------~~eitDp~~k~~vG~~I~vrviG~~ 946 (1710)
T KOG1070|consen 878 KSTEDLSIGSIVRAYVKSVKPDQLNVLLAANHHGRIHISEVLDN--------LHEITDPLDKFKVGDGIFVRVIGGH 946 (1710)
T ss_pred ccccceeeeeEEEEEEeeecccceEEeccccccCceehHHhhcc--------ccccCChhhhcccCCeEEEEEEcCC
Confidence 34688899999999999999999999999999999999987421 0111225678999999999999864
No 106
>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=85.41 E-value=4.2 Score=33.37 Aligned_cols=54 Identities=15% Similarity=0.297 Sum_probs=45.0
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEe
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQI 154 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv 154 (298)
+-.|-+|+|+|..+-++-.++|.|..+.++.+-.+.+ .+.+..|+.|+.++...
T Consensus 21 ~~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~-----------------~~~y~~G~rV~lrLkdl 74 (104)
T PF10246_consen 21 DPEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVN-----------------GEKYVRGSRVRLRLKDL 74 (104)
T ss_pred CccCCEEEEEEEEEecCceEEEeCCceeEEEeccccc-----------------ccccccCCEEEEEECCH
Confidence 3478899999999999999999999999998755543 34588899999998753
No 107
>KOG3298|consensus
Probab=85.38 E-value=6.7 Score=34.71 Aligned_cols=87 Identities=16% Similarity=0.124 Sum_probs=52.9
Q ss_pred cccccCCCEEEEEEEEEecceEEEEeCCCceeeEec---cccc-CCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC
Q psy10116 81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHL---TSVN-LPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST 156 (298)
Q Consensus 81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~---s~v~-~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~ 156 (298)
-+.|-.||+|=|.|+.+...++++++|--.-.+++- .++. .||.-.-. -...++. .++.|+.|+.+|+..--
T Consensus 76 ~FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~p~~n~P~---f~~~d~s-~I~~~~~VR~kiigtr~ 151 (170)
T KOG3298|consen 76 TFKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPGENPPN---FQTEDES-VIQKGVEVRLKIIGTRV 151 (170)
T ss_pred EEeecCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccCCCCCCCc---ccccccc-eeeeCcEEEEEEEEEEE
Confidence 578999999999999999999999998432222221 1111 13211000 0011222 68999999999998752
Q ss_pred C--CcEEE-EeccCCCcc
Q psy10116 157 E--GSLTL-HTRSLKYGK 171 (298)
Q Consensus 157 d--g~~~L-str~~~lGk 171 (298)
| .-+.| |..++.||.
T Consensus 152 ~~~~i~algtl~~D~LG~ 169 (170)
T KOG3298|consen 152 DETEIFALGTLKGDYLGP 169 (170)
T ss_pred eeeeEEEEEEecCccccc
Confidence 2 12334 346667775
No 108
>KOG1067|consensus
Probab=85.26 E-value=1.6 Score=45.49 Aligned_cols=76 Identities=16% Similarity=0.281 Sum_probs=61.9
Q ss_pred ccccCCCEEE-----EEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC
Q psy10116 82 YIGEIGEVVV-----GRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST 156 (298)
Q Consensus 82 Y~P~vGDiVI-----G~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~ 156 (298)
-.|+++|++. ++|+++.+.+++|.+-....|.||.|+.. +| ...+..+.+++||.|..+-...+.
T Consensus 659 ~~~~~~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~-----~e-----~iakpsd~levGq~I~vk~ie~d~ 728 (760)
T KOG1067|consen 659 KDDQVQDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLD-----QE-----KIAKPSDLLEVGQEIQVKYIERDP 728 (760)
T ss_pred cCccccceEeeeEEEEEEeeecccceEEEecCCchhhccchhcc-----cc-----cccChHHHHhhcceeEEEEEeecC
Confidence 3477888876 78999999999999988889999999974 22 234446779999999999999998
Q ss_pred CCcEEEEeccC
Q psy10116 157 EGSLTLHTRSL 167 (298)
Q Consensus 157 dg~~~Lstr~~ 167 (298)
.+.+.|+.|..
T Consensus 729 ~g~~~ls~ral 739 (760)
T KOG1067|consen 729 RGGIMLSSRAL 739 (760)
T ss_pred ccceeehhhhh
Confidence 88888887653
No 109
>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=84.77 E-value=3.7 Score=34.47 Aligned_cols=70 Identities=14% Similarity=0.171 Sum_probs=44.1
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCccc-ccch----hhhhhhhcccCCCCEEEEEEEEeC
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQR-RRSV----QDEEMMREFLKEGDLISAEIHQIS 155 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~R-r~~~----~d~~~mr~~~~~GDlV~A~V~sv~ 155 (298)
|-+|+++.|+|.+-..++.+|.++--.+-++|.+.+ |....- .... ......+-++..|+.|+-||.++.
T Consensus 1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L--~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~ 75 (122)
T PF08292_consen 1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLL--PEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEI 75 (122)
T ss_dssp --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC---TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEE
T ss_pred CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHC--CCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEE
Confidence 678999999999999999999997656666665543 322110 0000 001344678999999999999975
No 110
>CHL00121 rpl27 ribosomal protein L27; Reviewed
Probab=83.01 E-value=2.5 Score=33.53 Aligned_cols=52 Identities=15% Similarity=0.184 Sum_probs=39.4
Q ss_pred ccCCCeEecCCccCCC--CCeeccCCeEe-cCCeEEEEEeeEEEEe-----CcEEEEEec
Q psy10116 27 EFTDPILTPGETVEYL--EGYMTGHGTFP-DDEEIKASVGGVVEKV-----NQLVSVRAM 78 (298)
Q Consensus 27 ~~~~~iV~PGD~I~~~--~~~~~G~Gty~-~~g~i~Asv~G~v~~~-----nk~v~V~p~ 78 (298)
....+.|.||+.|.-. ..|-||.++-. .|..|+|.+.|.|... .+.|+|.|.
T Consensus 25 ~~~gq~V~~G~IivRQRGtk~hPG~NVg~GrD~TlfAl~~G~V~f~~~~~~~~~vsv~~~ 84 (86)
T CHL00121 25 RFGGEKVSAGNILIRQRGTKFKPGLNVGCGKDFTLYALIDGFVKFKKKNKKQKSINVINI 84 (86)
T ss_pred EcCCEEEcCCcEEEEcCCCeECCCCcccccCCceEEEccceEEEEEEeCCCCEEEEEeec
Confidence 3466899999999764 35778887655 4899999999999963 245777664
No 111
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=81.94 E-value=31 Score=33.06 Aligned_cols=64 Identities=14% Similarity=0.147 Sum_probs=49.2
Q ss_pred cccCCCEEEEEEEEEe-cceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEE
Q psy10116 83 IGEIGEVVVGRVTGLQ-SQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLT 161 (298)
Q Consensus 83 ~P~vGDiVIG~V~~V~-~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~ 161 (298)
.-.+|+.=-++|+++. .-+++||.|=+.+.++|+++. |- .-+-..++||-+++.+-- ++.+-+.
T Consensus 70 ~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~el--p~------------~~~~wpq~Gd~l~v~l~~-Dkk~Ri~ 134 (287)
T COG2996 70 KATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDEL--PT------------LKSLWPQKGDKLLVYLYV-DKKGRIW 134 (287)
T ss_pred eEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhc--cc------------ccccCCCCCCEEEEEEEE-ccCCcEE
Confidence 3489999999999999 999999999999999998875 20 003458999999988764 3333343
No 112
>PF04026 SpoVG: SpoVG; InterPro: IPR007170 This is a stage V sporulation protein G. It is essential for sporulation and specific to stage V sporulation in Bacillus megaterium and Bacillus subtilis []. In B. subtilis, expression decreases after 30-60 minutes of cold shock [].; GO: 0030435 sporulation resulting in formation of a cellular spore; PDB: 2IA9_F 2I9X_B 2I9Z_A.
Probab=80.84 E-value=3.5 Score=32.42 Aligned_cols=41 Identities=24% Similarity=0.333 Sum_probs=31.7
Q ss_pred ccEEEEEeeCceEEEecCCC-CCCCccccccccCCHHHHHHHH
Q psy10116 197 CGAQVILGCNGYVWVSAIDE-NKSGGFIQNMEVVKLSDRETIT 238 (298)
Q Consensus 197 ~~~eiivG~NG~IWI~~~~~-~~~~~~~~~~~~i~~~~r~~i~ 238 (298)
-++.|+=|.|| .||.-++. ..++.|.+...|++.+.|+.|.
T Consensus 32 ~~ikVieg~~G-lFVaMPs~k~~~g~y~Di~~Pitke~Re~i~ 73 (84)
T PF04026_consen 32 HDIKVIEGEKG-LFVAMPSRKSKDGEYKDICHPITKEFREQIE 73 (84)
T ss_dssp EEEEEEEETTE-EEEE--EEE-TTS-EEESEEESSHHHHHHHH
T ss_pred EeEEEEECCCC-cEEECCCcCCCCCCEEEEEEECCHHHHHHHH
Confidence 47899999999 99998876 3456777888999999999985
No 113
>PRK13259 regulatory protein SpoVG; Reviewed
Probab=79.85 E-value=6.4 Score=31.78 Aligned_cols=52 Identities=25% Similarity=0.363 Sum_probs=42.4
Q ss_pred ccEEEEEeeCceEEEecCCCC-CCCccccccccCCHHHHHHHHHHHHHHHHHhhCCcccCHHHHHHHHHHHh
Q psy10116 197 CGAQVILGCNGYVWVSAIDEN-KSGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESL 267 (298)
Q Consensus 197 ~~~eiivG~NG~IWI~~~~~~-~~~~~~~~~~~i~~~~r~~i~rv~n~i~~l~~~~~~i~~~~i~~~~~~s~ 267 (298)
-++.|+=|.|| +||.-++.. .++.|.+...+++.+.|+.|. ..|+.+|+..+
T Consensus 32 ~~ikVieg~~G-lFVaMPs~k~~~g~y~DI~~Pit~e~Re~i~------------------~aVl~aY~~~~ 84 (94)
T PRK13259 32 HDIRVIEGNNG-LFIAMPSKRTPDGEFRDIAHPINSDTREKIQ------------------DAILKEYERVG 84 (94)
T ss_pred eeeEEEECCCC-eEEECcCcCCCCCcEEEEEccCCHHHHHHHH------------------HHHHHHHHHHH
Confidence 48999999999 999988764 345688888999999999984 56777887775
No 114
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=79.67 E-value=3.1 Score=42.53 Aligned_cols=75 Identities=24% Similarity=0.258 Sum_probs=55.3
Q ss_pred ccCCCEEEEEEEEEe--cceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcE
Q psy10116 84 GEIGEVVVGRVTGLQ--SQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSL 160 (298)
Q Consensus 84 P~vGDiVIG~V~~V~--~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~ 160 (298)
-.+|++-.|+|++|- -..+||||+..-.|+||++++. | ..+. ....+++..++.|+.+...|..-... .-.
T Consensus 35 ~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~-~---~~~~--~~~~~i~~~lr~~~~~~Vqv~ke~~G~Kga 108 (487)
T COG1530 35 QIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIV-P---YFRA--VLEEKIKVRLRGGQATLVQVVKEPRGTKGA 108 (487)
T ss_pred eeecCceEEEecccCccchhheeeccCCccceEEecccc-h---hhhh--cccccceeeecCCceEEEEEEeecCccccc
Confidence 358999999999985 5679999999999999999984 2 1121 11225678999999999999986521 124
Q ss_pred EEEe
Q psy10116 161 TLHT 164 (298)
Q Consensus 161 ~Lst 164 (298)
.|||
T Consensus 109 ~lT~ 112 (487)
T COG1530 109 RLTT 112 (487)
T ss_pred ccee
Confidence 5554
No 115
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=76.45 E-value=1.8 Score=31.51 Aligned_cols=40 Identities=20% Similarity=0.468 Sum_probs=30.5
Q ss_pred EEEeCch----hhccccCcceec--cccEEEEEeeCceEEEecCCC
Q psy10116 177 LLTVPPS----LIRRSKSHFCNL--ACGAQVILGCNGYVWVSAIDE 216 (298)
Q Consensus 177 lv~v~~~----li~r~~~~~~~l--~~~~eiivG~NG~IWI~~~~~ 216 (298)
.+.|++. +|+|.++.+..| ++|+.|-+..||.|||.+.++
T Consensus 5 ~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~g~v~I~G~~~ 50 (61)
T cd02393 5 TMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDDGTVYIAASDK 50 (61)
T ss_pred EEEeChhheeeeECCCchHHHHHHHHHCCEEEeCCCCEEEEEeCCH
Confidence 4677776 455556666666 499999999999999999743
No 116
>PRK05435 rpmA 50S ribosomal protein L27; Validated
Probab=74.74 E-value=7.4 Score=30.65 Aligned_cols=43 Identities=21% Similarity=0.264 Sum_probs=35.2
Q ss_pred ccCCCeEecCCccCCC--CCeeccCCeEe-cCCeEEEEEeeEEEEe
Q psy10116 27 EFTDPILTPGETVEYL--EGYMTGHGTFP-DDEEIKASVGGVVEKV 69 (298)
Q Consensus 27 ~~~~~iV~PGD~I~~~--~~~~~G~Gty~-~~g~i~Asv~G~v~~~ 69 (298)
....+.|.||..|.-. ..|-||.++-. .|..|+|.+.|.|...
T Consensus 25 ~~~g~~V~~G~IivRQRGtk~~PG~nVg~GrD~TlfA~~~G~V~f~ 70 (82)
T PRK05435 25 RFGGQFVKAGNIIVRQRGTKFHPGVNVGRGKDHTLFALVDGVVKFE 70 (82)
T ss_pred ecCCEEEcCCcEEEEeCCCeECCCCCEeecCCceEEEecceEEEEE
Confidence 3567899999999764 35889999877 4899999999999964
No 117
>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=74.71 E-value=3.9 Score=32.16 Aligned_cols=43 Identities=19% Similarity=0.247 Sum_probs=36.1
Q ss_pred ccCCCeEecCCccCCC--CCeeccCCeEec-CCeEEEEEeeEEEEe
Q psy10116 27 EFTDPILTPGETVEYL--EGYMTGHGTFPD-DEEIKASVGGVVEKV 69 (298)
Q Consensus 27 ~~~~~iV~PGD~I~~~--~~~~~G~Gty~~-~g~i~Asv~G~v~~~ 69 (298)
....+.|.||+.|.-. ..|.||.++..- |..|+|.+.|.|...
T Consensus 24 ~~~G~~V~~G~IivRQRgtk~hPG~NVg~GrD~TLfAl~~G~V~f~ 69 (81)
T PF01016_consen 24 KFGGQFVKAGNIIVRQRGTKFHPGENVGMGRDHTLFALVDGRVKFT 69 (81)
T ss_dssp SSTTCEESSTSEEEEBSSSSSEEBTTEEEETTSEEEESSSCEEEEE
T ss_pred EeCCEEEcCCCEEEEeCCCcCcCCCCEEECCCCcEEEecCEEEEEE
Confidence 4567899999999763 468899999875 899999999999964
No 118
>PRK05054 exoribonuclease II; Provisional
Probab=72.47 E-value=18 Score=38.39 Aligned_cols=70 Identities=13% Similarity=0.136 Sum_probs=49.8
Q ss_pred cc-ccCCC--EEEEEEEEEecceEEEEeCC-CceeeEecccccCCCC--cccccchhhh----hhhhcccCCCCEEEEEE
Q psy10116 82 YI-GEIGE--VVVGRVTGLQSQKWVVDTNS-ILESALHLTSVNLPGG--EQRRRSVQDE----EMMREFLKEGDLISAEI 151 (298)
Q Consensus 82 Y~-P~vGD--iVIG~V~~V~~~~~~VDI~s-~~~a~L~~s~v~~pgg--~~Rr~~~~d~----~~mr~~~~~GDlV~A~V 151 (298)
|. .++|+ ..-|.|++++..+++|.|.. ...|++|++++. +. ..+ .+.++ ..-+..|+.||-|..+|
T Consensus 554 y~~~~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~--~~~~~y~--~~~~~~~~~~~~~~~~~lGd~V~V~v 629 (644)
T PRK05054 554 YLKDKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLH--AVRDELV--CNQENGTVQIKGETVYKLGDVIDVTL 629 (644)
T ss_pred HHhhccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccC--CCccceE--EccccceEEEeCCEEEcCCCEEEEEE
Confidence 44 46765 99999999999999999954 578999998863 21 000 00010 11125799999999999
Q ss_pred EEeC
Q psy10116 152 HQIS 155 (298)
Q Consensus 152 ~sv~ 155 (298)
.+++
T Consensus 630 ~~vd 633 (644)
T PRK05054 630 AEVR 633 (644)
T ss_pred EEEc
Confidence 9997
No 119
>COG0073 ARC1 EMAP domain [General function prediction only]
Probab=68.93 E-value=36 Score=28.26 Aligned_cols=76 Identities=21% Similarity=0.347 Sum_probs=49.8
Q ss_pred cCCCEEEEEEEEEec-------ceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC
Q psy10116 85 EIGEVVVGRVTGLQS-------QKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE 157 (298)
Q Consensus 85 ~vGDiVIG~V~~V~~-------~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d 157 (298)
...|+|+|+|.++.. ...+||++... ..+.+.. |+ .++...-+++.|+|..+-++
T Consensus 17 ~~~~l~vg~V~~~~~~p~adkL~~~~Vd~G~~~-~~~qiv~----G~-------------~n~~~~~~vv~a~v~~v~~~ 78 (123)
T COG0073 17 AKVDLRVGKVVEAEPHPNADKLLVLKVDLGDEK-EPRQIVC----GA-------------PNFYAGEKLVGAKVGAVLNG 78 (123)
T ss_pred ccCCeEEEEEEEeEECCCCCeeEEEEEEcCCCC-cEEEEEc----CC-------------ccccCCceeeeeeEEEEeCC
Confidence 478999999999842 23455666422 1222211 21 23333448888999988776
Q ss_pred CcEEEEeccCCCccCCCceEEEeC
Q psy10116 158 GSLTLHTRSLKYGKLGQGILLTVP 181 (298)
Q Consensus 158 g~~~Lstr~~~lGkL~~G~lv~v~ 181 (298)
+ .|..+..+ |..+.|++....
T Consensus 79 ~--~ikp~klr-G~~S~GMics~~ 99 (123)
T COG0073 79 G--KLKPAKLR-GVESEGMLLSAE 99 (123)
T ss_pred C--cccceeec-CcccceEEEEcc
Confidence 6 67777777 999999998765
No 120
>cd05839 BR140_related The PWWP domain is found in the BR140 family, which includes peregrin and BR140-like proteins 1 and 2. BR140 is the only family to contain the PWWP domain at the C terminus, with PHD and bromo domains in the N-terminal region. In myeloid leukemias, BR140 is disrupted by chromosomal translocations, similar to translocations of WHSC1 in lymphoid multiple myeloma. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding proteins, that function as transcription factors regulating a variety of developmental processes.
Probab=60.45 E-value=19 Score=29.90 Aligned_cols=74 Identities=12% Similarity=0.089 Sum_probs=36.4
Q ss_pred cCCCCEEEEEEEEeCCCCcEEEEeccCCCccCCCceEEEeCchhhccccCcceeccccEEEEEee-CceEEEecCCC
Q psy10116 141 LKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGC-NGYVWVSAIDE 216 (298)
Q Consensus 141 ~~~GDlV~A~V~sv~~dg~~~Lstr~~~lGkL~~G~lv~v~~~li~r~~~~~~~l~~~~eiivG~-NG~IWI~~~~~ 216 (298)
+.+||+|-|++...---..+.+.-.....|.+.+|.-.++.-.-..+.+..-. .+=+--.++. +.+.||....-
T Consensus 1 ~~pg~lVwaK~~g~P~wPa~iidp~~~~~~~~~~~~p~~~l~~~~~~~~~~~~--~~~lV~FFd~~~s~~Wv~~~~l 75 (111)
T cd05839 1 LEPLTLVWAKCRGYPSYPALIIDPKMPRDGVFHNGVPPDVLTLGEARAQNADE--RLYLVLFFDNKRTWQWLPGDKL 75 (111)
T ss_pred CCCcCEeeeeecCCCCCCeEeeCCCCCCcccccCCCCchhhhHHHHHhccCCC--cEEEEEEecCCCcceecCHHHC
Confidence 46899999999665333333333233344666665532221110111111000 0111225665 89999998653
No 121
>TIGR00062 L27 ribosomal protein L27. Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.
Probab=59.67 E-value=12 Score=29.54 Aligned_cols=43 Identities=16% Similarity=0.164 Sum_probs=34.7
Q ss_pred ccCCCeEecCCccCCC--CCeeccCCeEe-cCCeEEEEEeeEEEEe
Q psy10116 27 EFTDPILTPGETVEYL--EGYMTGHGTFP-DDEEIKASVGGVVEKV 69 (298)
Q Consensus 27 ~~~~~iV~PGD~I~~~--~~~~~G~Gty~-~~g~i~Asv~G~v~~~ 69 (298)
....+.|.||..|.-. ..|-||.++-. .|..|+|.+.|.|...
T Consensus 25 ~~~gq~V~~G~IivRQRGtk~hPG~nVg~GrD~TlfAl~~G~V~f~ 70 (83)
T TIGR00062 25 RAGGQFVRAGSIIVRQRGTKFHPGNNVGMGKDHTLFALSDGVVKFE 70 (83)
T ss_pred ecCCEEEcCCcEEEEcCCceECCCCcccccCCCeEEEecceEEEEE
Confidence 3456899999999764 35778888766 4899999999999864
No 122
>KOG3297|consensus
Probab=58.78 E-value=41 Score=30.52 Aligned_cols=72 Identities=13% Similarity=0.153 Sum_probs=48.3
Q ss_pred cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCc-cc--------ccchhhhhhhhcccCCCCEEEEEE
Q psy10116 81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGE-QR--------RRSVQDEEMMREFLKEGDLISAEI 151 (298)
Q Consensus 81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~-~R--------r~~~~d~~~mr~~~~~GDlV~A~V 151 (298)
-+.|-+|+++.|+|.+-...+.+|-++--.+-++|...+ |-+. .+ ..-.+|-..-.-+|++|..|+-||
T Consensus 76 VFrPF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L--~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV 153 (202)
T KOG3297|consen 76 VFRPFVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEML--PEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRV 153 (202)
T ss_pred EEecccceEEEEEeecCCccceEEEEEeeeceeechhhC--CCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEE
Confidence 366889999999999999999999887434444554433 2221 11 000011123456899999999999
Q ss_pred EEe
Q psy10116 152 HQI 154 (298)
Q Consensus 152 ~sv 154 (298)
.+.
T Consensus 154 ~~e 156 (202)
T KOG3297|consen 154 EDE 156 (202)
T ss_pred eee
Confidence 986
No 123
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=57.75 E-value=55 Score=25.52 Aligned_cols=55 Identities=18% Similarity=0.355 Sum_probs=35.6
Q ss_pred ccCCCEEEEEEEEE-ecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEe
Q psy10116 84 GEIGEVVVGRVTGL-QSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQI 154 (298)
Q Consensus 84 P~vGDiVIG~V~~V-~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv 154 (298)
|+.|+ ++|+|++. .++.+.|.......-..++ ||- .|+ +=.++.||.|.++....
T Consensus 2 p~e~q-~~g~V~~~lG~~~~~V~~~dG~~~la~i-----pgK-~Rk---------~iwI~~GD~VlVe~~~~ 57 (83)
T smart00652 2 KEDGQ-EIAQVVKMLGNGRLEVMCADGKERLARI-----PGK-MRK---------KVWIRRGDIVLVDPWDF 57 (83)
T ss_pred CCCCc-EEEEEEEEcCCCEEEEEECCCCEEEEEE-----chh-hcc---------cEEEcCCCEEEEEecCC
Confidence 55555 77999997 4677778776544433332 332 233 46799999999987643
No 124
>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=56.47 E-value=9 Score=30.19 Aligned_cols=29 Identities=17% Similarity=0.189 Sum_probs=21.7
Q ss_pred ccCCCEEEEEEEEEec-ceEEEEeCCCcee
Q psy10116 84 GEIGEVVVGRVTGLQS-QKWVVDTNSILES 112 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~-~~~~VDI~s~~~a 112 (298)
-++||+|.++|.+..+ ..+.+.+.....|
T Consensus 61 f~~GDiV~AkVis~~~~~~~~Lst~~~~lG 90 (92)
T cd05791 61 FRPGDIVRAKVISLGDASSYYLSTAENELG 90 (92)
T ss_pred cCCCCEEEEEEEEcCCCCCcEEEecCCCCc
Confidence 3899999999999975 5677766544433
No 125
>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=55.60 E-value=24 Score=35.44 Aligned_cols=35 Identities=20% Similarity=0.168 Sum_probs=30.1
Q ss_pred eeccCCeEec---CCeEEEEEeeEEEEeCcEEEEEecC
Q psy10116 45 YMTGHGTFPD---DEEIKASVGGVVEKVNQLVSVRAMN 79 (298)
Q Consensus 45 ~~~G~Gty~~---~g~i~Asv~G~v~~~nk~v~V~p~~ 79 (298)
+..|.||... ...++|++.|.+...++.++|.|.-
T Consensus 145 ~~~g~~~~~~~~d~~~~~A~~~G~~~~~~~~i~V~~~l 182 (451)
T PF03961_consen 145 LKAGKNTEVSEEDGNKLYAAIDGRPVFENGKISVDPVL 182 (451)
T ss_pred eeCCCCEEEEcCCCCEEEEecCCEEEEECCEEEEEEee
Confidence 6679999875 3589999999999999999998874
No 126
>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=53.27 E-value=56 Score=23.23 Aligned_cols=62 Identities=27% Similarity=0.411 Sum_probs=37.5
Q ss_pred EEEEEEEE---ecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEE--EEEeCCCCcEEEEe
Q psy10116 90 VVGRVTGL---QSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAE--IHQISTEGSLTLHT 164 (298)
Q Consensus 90 VIG~V~~V---~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~--V~sv~~dg~~~Lst 164 (298)
|.|+|+.+ .....++.|.... |.+.+.-++ .+-....+.+++||.|.++ |... ++++++|+.
T Consensus 3 v~G~V~~~~~~~~~~~~~~l~D~t-g~i~~~~~~-----------~~~~~~~~~l~~g~~v~v~G~v~~~-~~~~~~l~~ 69 (75)
T PF01336_consen 3 VEGRVTSIRRSGGKIVFFTLEDGT-GSIQVVFFN-----------EEYERFREKLKEGDIVRVRGKVKRY-NGGELELIV 69 (75)
T ss_dssp EEEEEEEEEEEETTEEEEEEEETT-EEEEEEEET-----------HHHHHHHHTS-TTSEEEEEEEEEEE-TTSSEEEEE
T ss_pred EEEEEEEEEcCCCCEEEEEEEECC-ccEEEEEcc-----------HHhhHHhhcCCCCeEEEEEEEEEEE-CCccEEEEE
Confidence 67888887 4666777775444 555544331 2345668889999998754 4443 223366653
No 127
>KOG4078|consensus
Probab=52.81 E-value=23 Score=30.81 Aligned_cols=59 Identities=17% Similarity=0.331 Sum_probs=46.3
Q ss_pred ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEE
Q psy10116 84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLH 163 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Ls 163 (298)
|..|-+|+|+|-.+-++-.++|-|..+.++-..-..| .+.++-|--|+-+++. ++||
T Consensus 80 ~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n-----------------~e~Y~~GaRVrlRl~D------lELs 136 (173)
T KOG4078|consen 80 DAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALN-----------------GEAYQKGARVRLRLID------LELS 136 (173)
T ss_pred CcCCcEEEeeeeeeeccceEEecCCeEEEEEcCcCcC-----------------HHHhhcCceEEEEEcC------hhHh
Confidence 6789999999999999999999998888776544443 3457788888888875 3566
Q ss_pred ec
Q psy10116 164 TR 165 (298)
Q Consensus 164 tr 165 (298)
+|
T Consensus 137 ~r 138 (173)
T KOG4078|consen 137 ER 138 (173)
T ss_pred hh
Confidence 55
No 128
>KOG4134|consensus
Probab=51.81 E-value=16 Score=34.06 Aligned_cols=69 Identities=12% Similarity=0.178 Sum_probs=52.2
Q ss_pred EEEEEecCccccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEE
Q psy10116 72 LVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151 (298)
Q Consensus 72 ~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V 151 (298)
.+|+..---.|.|++||+..|.|--+..+..-+=|-.-+.|.++..++. .| +.++..++...++|
T Consensus 93 hlwi~adfyVf~Pk~Gd~LeG~Vn~vS~sHIglLIhg~FNASIpk~nip-----------~d----w~fI~md~eee~~v 157 (253)
T KOG4134|consen 93 HLWINADFYVFRPKAGDILEGVVNHVSRSHIGLLIHGVFNASIPKTNIP-----------AD----WEFIAMDQEEEIRV 157 (253)
T ss_pred EEEEeeeEEEECCCCCCeeeeeeeecchhhhceeehhhhhccCCCCCCc-----------cc----eeeecCCchhhhce
Confidence 3566555557889999999999999988887666665666666654431 11 66899999999999
Q ss_pred EEeC
Q psy10116 152 HQIS 155 (298)
Q Consensus 152 ~sv~ 155 (298)
...+
T Consensus 158 ~ntD 161 (253)
T KOG4134|consen 158 KNTD 161 (253)
T ss_pred eecc
Confidence 9987
No 129
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=50.16 E-value=98 Score=25.78 Aligned_cols=49 Identities=20% Similarity=0.264 Sum_probs=29.5
Q ss_pred EEEEEE-ecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEE
Q psy10116 92 GRVTGL-QSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151 (298)
Q Consensus 92 G~V~~V-~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V 151 (298)
|+|.+. ....+.|+-.+...-..+...+- + ....|+..|++||.|.|..
T Consensus 17 GtV~~~~~~~~~lV~f~~~~~~~v~~~~iI-~----------~~~~~~~~L~~GD~VLA~~ 66 (124)
T PF15057_consen 17 GTVKKCVSSGQFLVEFDDGDTQEVPISDII-A----------LSDAMRHSLQVGDKVLAPW 66 (124)
T ss_pred EEEEEccCCCEEEEEECCCCEEEeChHHeE-E----------ccCcccCcCCCCCEEEEec
Confidence 455543 56667777654444444444431 1 1133478899999999994
No 130
>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=49.64 E-value=39 Score=24.85 Aligned_cols=50 Identities=30% Similarity=0.484 Sum_probs=30.2
Q ss_pred CEEEEEEEEE-ecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEE
Q psy10116 88 EVVVGRVTGL-QSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIH 152 (298)
Q Consensus 88 DiVIG~V~~V-~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~ 152 (298)
+-++|+|++. .++.+.|.......-.-+ +||- .|+ +=.+++||.|.+++-
T Consensus 3 ~e~~~~V~~~lG~~~~~V~~~dg~~~l~~-----i~gK-~r~---------~iwI~~GD~V~V~~~ 53 (65)
T PF01176_consen 3 GEVIGRVTEMLGNNLFEVECEDGEERLAR-----IPGK-FRK---------RIWIKRGDFVLVEPS 53 (65)
T ss_dssp TEEEEEEEEEESSSEEEEEETTSEEEEEE-----E-HH-HHT---------CC---TTEEEEEEES
T ss_pred cEEEEEEEEECCCCEEEEEeCCCCEEEEE-----eccc-eee---------eEecCCCCEEEEEec
Confidence 4578999997 467788888655443333 2332 222 457999999988873
No 131
>COG0211 RpmA Ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=49.17 E-value=44 Score=26.50 Aligned_cols=53 Identities=23% Similarity=0.258 Sum_probs=38.3
Q ss_pred ccCCCeEecCCccCCC--CCeeccCCeEe-cCCeEEEEEeeEEEEe-----CcEEEEEecC
Q psy10116 27 EFTDPILTPGETVEYL--EGYMTGHGTFP-DDEEIKASVGGVVEKV-----NQLVSVRAMN 79 (298)
Q Consensus 27 ~~~~~iV~PGD~I~~~--~~~~~G~Gty~-~~g~i~Asv~G~v~~~-----nk~v~V~p~~ 79 (298)
.+..+.|.+|..|.-. ..|-||.++=. .|..|+|.+.|.|+.. .+.++|.|..
T Consensus 25 ~~~Gq~v~aG~IivRQRGTk~hpG~NVG~GkDhTlFAl~dG~Vkf~~k~~~rk~vsV~~~~ 85 (87)
T COG0211 25 KFGGQFVKAGSIIVRQRGTKFHPGVNVGRGKDHTLFALVDGVVKFETKGKNRKYVSVVPEA 85 (87)
T ss_pred eeCCeEEecccEEEEeccccccCCcccccCCCceEEEeeccEEEEEEccCCccEEEEEeec
Confidence 4567899999998653 23556665433 4789999999999853 2478888764
No 132
>PLN00208 translation initiation factor (eIF); Provisional
Probab=48.61 E-value=71 Score=27.77 Aligned_cols=56 Identities=16% Similarity=0.245 Sum_probs=36.6
Q ss_pred cccCCCEEEEEEEEE-ecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEe
Q psy10116 83 IGEIGEVVVGRVTGL-QSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQI 154 (298)
Q Consensus 83 ~P~vGDiVIG~V~~V-~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv 154 (298)
.|..|+ ++|+|++. .+..+.|.......-+-++ ||- .|+ +-.+++||+|.++.-..
T Consensus 28 ~p~egq-~~g~V~~~lGn~~~~V~c~dG~~rLa~I-----pGK-mRK---------rIWI~~GD~VlVel~~~ 84 (145)
T PLN00208 28 FKEDGQ-EYAQVLRMLGNGRCEALCIDGTKRLCHI-----RGK-MRK---------KVWIAAGDIILVGLRDY 84 (145)
T ss_pred cCCCCc-EEEEEEEEcCCCEEEEEECCCCEEEEEE-----ecc-cee---------eEEecCCCEEEEEccCC
Confidence 477777 77999997 4667777765444333332 332 233 46799999999995543
No 133
>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=48.48 E-value=1.2e+02 Score=23.28 Aligned_cols=50 Identities=18% Similarity=0.339 Sum_probs=33.5
Q ss_pred EEEEEEEE-ecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEe
Q psy10116 90 VVGRVTGL-QSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQI 154 (298)
Q Consensus 90 VIG~V~~V-~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv 154 (298)
++|+|++. .++.+.|.......-..++ || ..|+ +=.+++||.|.++....
T Consensus 2 ~i~~V~~~lG~~~~~V~~~dg~~~l~~i-----~g-K~Rk---------~iwI~~GD~VlV~~~~~ 52 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECADGQRRLVSI-----PG-KLRK---------NIWIKRGDFLIVDPIEE 52 (78)
T ss_pred eEEEEEEECCCCEEEEEECCCCEEEEEE-----ch-hhcc---------CEEEcCCCEEEEEeccc
Confidence 68999997 4677888876544433332 33 2233 45699999999987665
No 134
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=48.10 E-value=78 Score=33.89 Aligned_cols=78 Identities=22% Similarity=0.324 Sum_probs=54.0
Q ss_pred cCCCEEEEEEEEEecceEEEEeCCC-ceeeEecccccCCC--CcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcE
Q psy10116 85 EIGEVVVGRVTGLQSQKWVVDTNSI-LESALHLTSVNLPG--GEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSL 160 (298)
Q Consensus 85 ~vGDiVIG~V~~V~~~~~~VDI~s~-~~a~L~~s~v~~pg--g~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~ 160 (298)
++|+.--|.|++|...+.+|.+... .+|.+|++.+...= ...++ ...........++.||-|..+|.+++. .+.+
T Consensus 621 ~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~-~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~i 699 (706)
T COG0557 621 RVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERG-QALVGEKSGKVYRLGDEVKVKVTSVDLDERKI 699 (706)
T ss_pred hcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeecccc-ceeeccccccccccCCEEEEEEEEEcccccce
Confidence 7899999999999999999999765 78999998864100 00000 001123335679999999999999973 3344
Q ss_pred EEE
Q psy10116 161 TLH 163 (298)
Q Consensus 161 ~Ls 163 (298)
.++
T Consensus 700 ~~~ 702 (706)
T COG0557 700 DFE 702 (706)
T ss_pred EEE
Confidence 443
No 135
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=46.27 E-value=35 Score=33.29 Aligned_cols=101 Identities=19% Similarity=0.179 Sum_probs=60.1
Q ss_pred cCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEeCcEEEEEecCc-cccccCCCEEEEEEEEEecceEEEEeCCCceee
Q psy10116 35 PGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNS-RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESA 113 (298)
Q Consensus 35 PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~nk~v~V~p~~~-rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~ 113 (298)
+||.+...-..+.-.|.|++=+. |--+-|.+.... ++-...+. +-.-++||.|..+|.++..+.=++|+
T Consensus 17 ~GdvV~g~V~~I~d~GafV~L~E-Y~gvEGlIhiSE--lS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdL------- 86 (319)
T PTZ00248 17 EDDLVMVKVVRITEMGAYVSLLE-YDDIEGMILMSE--LSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDL------- 86 (319)
T ss_pred CCCEEEEEEEEEeCCeEEEEecC-CCCcEEEEEHHH--hcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEE-------
Confidence 47776543233445677765211 123556766542 22222222 23358999999999999766533333
Q ss_pred EecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC
Q psy10116 114 LHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST 156 (298)
Q Consensus 114 L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~ 156 (298)
++-.+ ++.+-......|+.|+.|.++|..+..
T Consensus 87 -S~K~v----------~~~pw~~~~e~~~~g~~v~~~V~~ia~ 118 (319)
T PTZ00248 87 -SKKRV----------SPEDIEACEEKFSKSKKVHSIMRHIAQ 118 (319)
T ss_pred -Eeeec----------ccchHHHHHHhCcCCCEEEEEEEEchh
Confidence 22222 233445667889999999999999853
No 136
>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=45.63 E-value=73 Score=33.78 Aligned_cols=72 Identities=8% Similarity=0.156 Sum_probs=49.1
Q ss_pred cc-ccCCC--EEEEEEEEEecceEEEEe-CCCceeeEecccccCCCCcccccchhhhh--hh--hcccCCCCEEEEEEEE
Q psy10116 82 YI-GEIGE--VVVGRVTGLQSQKWVVDT-NSILESALHLTSVNLPGGEQRRRSVQDEE--MM--REFLKEGDLISAEIHQ 153 (298)
Q Consensus 82 Y~-P~vGD--iVIG~V~~V~~~~~~VDI-~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~--~m--r~~~~~GDlV~A~V~s 153 (298)
|+ .++|+ .--|.|+++...+++|.+ .....|++|.+++. +....-..+.++. .+ +..|+.||-|..+|.+
T Consensus 550 yl~~~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~--~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~ 627 (639)
T TIGR02062 550 FLADKAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLH--ANREELVCNQENGTVQIKGETVYKIGDVIDVVLTE 627 (639)
T ss_pred HHhhccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcC--CCCcceEEcccccEEEEeccEEEecCCEEEEEEEE
Confidence 44 35654 789999999999999999 55689999988762 2100000011110 11 1379999999999999
Q ss_pred eC
Q psy10116 154 IS 155 (298)
Q Consensus 154 v~ 155 (298)
++
T Consensus 628 vd 629 (639)
T TIGR02062 628 VR 629 (639)
T ss_pred ec
Confidence 97
No 137
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=44.79 E-value=54 Score=30.12 Aligned_cols=23 Identities=17% Similarity=0.232 Sum_probs=17.3
Q ss_pred CCCEEEEEEEEEecceEEEEeCC
Q psy10116 86 IGEVVVGRVTGLQSQKWVVDTNS 108 (298)
Q Consensus 86 vGDiVIG~V~~V~~~~~~VDI~s 108 (298)
.-+.+-|||++|....+.+....
T Consensus 38 n~~tiEGrVvEV~~~~i~iesk~ 60 (213)
T PRK06763 38 NFSTIEGRVVEVDNGVIVIKSKQ 60 (213)
T ss_pred ccceeeeEEEEEeCCEEEEEecc
Confidence 45678888888888888777643
No 138
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=44.45 E-value=24 Score=37.29 Aligned_cols=78 Identities=21% Similarity=0.249 Sum_probs=61.3
Q ss_pred CcEEEEEec-CccccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEE
Q psy10116 70 NQLVSVRAM-NSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLIS 148 (298)
Q Consensus 70 nk~v~V~p~-~~rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~ 148 (298)
.+.+++-.. -.-+--+.|.+=-|.|.++...+++|++|+...|.+|-+++. + .+.|.+||-+.
T Consensus 105 ~~~vy~l~~~c~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~---~-------------~~~~~vgdeii 168 (715)
T COG1107 105 PKIVYVLDNSCTMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLG---G-------------DPDYAVGDEII 168 (715)
T ss_pred CceeEEeccccchhhcccceeeeccccchhhhcceeecChhhhccccccccC---C-------------CCCCCCCCeEE
Confidence 344555333 345556899999999999999999999999999999977662 1 36699999999
Q ss_pred EEEEEeCCC-CcEEEE
Q psy10116 149 AEIHQISTE-GSLTLH 163 (298)
Q Consensus 149 A~V~sv~~d-g~~~Ls 163 (298)
..|..+... +++.+.
T Consensus 169 V~v~~vr~~~geidf~ 184 (715)
T COG1107 169 VQVSDVRPEKGEIDFE 184 (715)
T ss_pred EEeeccCCCCCcccee
Confidence 999999855 676665
No 139
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=43.58 E-value=1.3e+02 Score=26.90 Aligned_cols=73 Identities=18% Similarity=0.242 Sum_probs=43.0
Q ss_pred ccccCCCeEecCCccCCCC--CeeccCCeEec--CCeEEEEEeeEEEEeCcEEEEEecCccc----cccCCC-E-EEEEE
Q psy10116 25 IHEFTDPILTPGETVEYLE--GYMTGHGTFPD--DEEIKASVGGVVEKVNQLVSVRAMNSRY----IGEIGE-V-VVGRV 94 (298)
Q Consensus 25 ~~~~~~~iV~PGD~I~~~~--~~~~G~Gty~~--~g~i~Asv~G~v~~~nk~v~V~p~~~rY----~P~vGD-i-VIG~V 94 (298)
..+++-....|||.|..+. ....|.+.|+. +|..+....... .++.+.+..+...| .+...| + +||+|
T Consensus 129 ~GDSMeP~~~~Gd~ilVd~~~~~~~gd~v~v~~~g~~~~VK~l~~~--~~~~~~l~S~N~~~~~~~~~~~~~~v~iIgrV 206 (214)
T COG2932 129 TGDSMEPTYEDGDTLLVDPGVNTRRGDRVYVETDGGELYVKKLQRE--PGGLLRLVSLNPDYYPDEIFSEDDDVEIIGRV 206 (214)
T ss_pred eCCcccccccCCCEEEECCCCceeeCCEEEEEEeCCeEEEEEEEEe--cCCeEEEEeCCCCCCcccccCccceEEEEEEE
Confidence 4567778899999776542 23344444443 234443322221 25566687777655 345666 5 89999
Q ss_pred EEEec
Q psy10116 95 TGLQS 99 (298)
Q Consensus 95 ~~V~~ 99 (298)
+.+..
T Consensus 207 v~~~~ 211 (214)
T COG2932 207 VWVSR 211 (214)
T ss_pred EEEee
Confidence 97653
No 140
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=42.73 E-value=27 Score=20.70 Aligned_cols=16 Identities=13% Similarity=0.513 Sum_probs=12.2
Q ss_pred EEEEEeeCceEEEecC
Q psy10116 199 AQVILGCNGYVWVSAI 214 (298)
Q Consensus 199 ~eiivG~NG~IWI~~~ 214 (298)
..|....||++||...
T Consensus 8 ~~i~~D~~G~lWigT~ 23 (24)
T PF07494_consen 8 YSIYEDSDGNLWIGTY 23 (24)
T ss_dssp EEEEE-TTSCEEEEET
T ss_pred EEEEEcCCcCEEEEeC
Confidence 4678899999999864
No 141
>KOG4600|consensus
Probab=42.46 E-value=54 Score=28.31 Aligned_cols=54 Identities=19% Similarity=0.242 Sum_probs=37.4
Q ss_pred cCCCeEecCCccCCCCC--eeccCCeEe-cCCeEEEEEeeEEEEe-------CcEEEEEecCcc
Q psy10116 28 FTDPILTPGETVEYLEG--YMTGHGTFP-DDEEIKASVGGVVEKV-------NQLVSVRAMNSR 81 (298)
Q Consensus 28 ~~~~iV~PGD~I~~~~~--~~~G~Gty~-~~g~i~Asv~G~v~~~-------nk~v~V~p~~~r 81 (298)
...+.|.||+.|...-. |-||..+=. .|-.|||-.-|.|+.. .|.+.|.|...-
T Consensus 53 ~egq~V~~G~IIvrQRgtkfHPG~nVGiGKDhtifaL~eG~Vrf~k~~~~~~Rk~i~V~~~~~~ 116 (144)
T KOG4600|consen 53 YEGQSVIPGNIIVRQRGTKFHPGDNVGIGKDHTIFALEEGRVRFEKSKITPPRKWIGVDPRGGL 116 (144)
T ss_pred cCCeeeecccEEEEecccccCCCcccccCCcceEEEeeccEEEEEEccCCCCcceEEEeecCCc
Confidence 44579999999987533 445543322 3678999999999963 256777776653
No 142
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=41.65 E-value=60 Score=28.55 Aligned_cols=45 Identities=18% Similarity=0.238 Sum_probs=32.0
Q ss_pred cCCCeEec--CCccCCCCCeeccCCeEe----cCCeEEEEEeeEEEEeCcEEEEE
Q psy10116 28 FTDPILTP--GETVEYLEGYMTGHGTFP----DDEEIKASVGGVVEKVNQLVSVR 76 (298)
Q Consensus 28 ~~~~iV~P--GD~I~~~~~~~~G~Gty~----~~g~i~Asv~G~v~~~nk~v~V~ 76 (298)
....+++| |+.++... -+.|.|.|. ++-.+.|.+.|.+++ .|||.
T Consensus 22 ~~rel~~~eegq~~g~V~-~~LGn~~f~V~c~dG~~rLa~I~GKmRK---~IWI~ 72 (155)
T PTZ00329 22 EKRELVFKEEGQEYAQVL-RMLGNGRLEAYCFDGVKRLCHIRGKMRK---RVWIN 72 (155)
T ss_pred ceeeeccCCCCcEEEEEE-EEcCCCEEEEEECCCCEEEEEeecccee---eEEec
Confidence 44678887 67776643 467888876 346789999999986 37764
No 143
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=41.32 E-value=20 Score=25.44 Aligned_cols=38 Identities=11% Similarity=0.287 Sum_probs=28.3
Q ss_pred EEeCch----hhccccCcceec--cccEEEEEee----CceEEEecCC
Q psy10116 178 LTVPPS----LIRRSKSHFCNL--ACGAQVILGC----NGYVWVSAID 215 (298)
Q Consensus 178 v~v~~~----li~r~~~~~~~l--~~~~eiivG~----NG~IWI~~~~ 215 (298)
+.|++. +++|.+.++..| .+|+.|.+.. ++.|||.++.
T Consensus 4 i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~~ 51 (62)
T cd02394 4 VEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPK 51 (62)
T ss_pred EEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcCH
Confidence 455555 566666777666 4999999988 7999999874
No 144
>cd06850 biotinyl_domain The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase, oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, transcarboxylase and urea amidolyase. This domain functions in transferring CO2 from one subsite to another, allowing carboxylation, decarboxylation, or transcarboxylation. During this process, biotin is covalently attached to a specific lysine.
Probab=39.93 E-value=1.2e+02 Score=20.81 Aligned_cols=51 Identities=20% Similarity=0.266 Sum_probs=30.3
Q ss_pred EEEEEeeEEEEeCcEEEEEecCccccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccc
Q psy10116 58 IKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSV 119 (298)
Q Consensus 58 i~Asv~G~v~~~nk~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v 119 (298)
++|+..|++.. +.|. .+.++ +.||.+ +.+. ......+|.++.+|.+.-..+
T Consensus 2 v~a~~~G~v~~----~~v~--~G~~v-~~g~~l-~~i~---~~~~~~~i~ap~~G~v~~~~~ 52 (67)
T cd06850 2 VTAPMPGTVVK----VLVK--EGDKV-EAGQPL-AVLE---AMKMENEVTAPVAGVVKEILV 52 (67)
T ss_pred ccCCccEEEEE----EEeC--CCCEE-CCCCEE-EEEE---cccEEEEEeCCCCEEEEEEEE
Confidence 56777787753 1121 12333 566665 4543 334578899999999874443
No 145
>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=39.84 E-value=1.3e+02 Score=23.10 Aligned_cols=50 Identities=18% Similarity=0.278 Sum_probs=32.9
Q ss_pred EEEEEEEE-ecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEe
Q psy10116 90 VVGRVTGL-QSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQI 154 (298)
Q Consensus 90 VIG~V~~V-~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv 154 (298)
++|+|++. .++.+.|.......-.-+ +||-- |+ +=.+++||.|.++....
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g~~~la~-----i~gK~-rk---------~iwI~~GD~V~Ve~~~~ 52 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDGKKRLCR-----IRGKM-RK---------RVWINEGDIVLVAPWDF 52 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEE-----Echhh-cc---------cEEEcCCCEEEEEeccc
Confidence 68999998 466777877654443333 23322 22 46799999999996654
No 146
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=39.80 E-value=63 Score=29.26 Aligned_cols=21 Identities=14% Similarity=0.384 Sum_probs=17.5
Q ss_pred hcccCCCCEEEEEEEEeCCCC
Q psy10116 138 REFLKEGDLISAEIHQISTEG 158 (298)
Q Consensus 138 r~~~~~GDlV~A~V~sv~~dg 158 (298)
.+..++||+|+++|+++..+.
T Consensus 59 ~~~~K~GdiV~grV~~v~~~~ 79 (188)
T COG1096 59 PPLPKGGDIVYGRVTDVREQR 79 (188)
T ss_pred CCCCCCCCEEEEEEeeccceE
Confidence 467899999999999997543
No 147
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=36.92 E-value=67 Score=25.68 Aligned_cols=62 Identities=15% Similarity=0.101 Sum_probs=35.4
Q ss_pred cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccch----------hhhhhhhcccCCCCEEEEE
Q psy10116 85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSV----------QDEEMMREFLKEGDLISAE 150 (298)
Q Consensus 85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~----------~d~~~mr~~~~~GDlV~A~ 150 (298)
++=++++|+|+++.+ .+|.++.. -+|+-..+.+|....+...+ ...-..++.|++||.|..-
T Consensus 15 ~p~~i~~G~V~s~~P--L~I~i~~~--liL~~~~L~i~~~l~~~~~~~~~~~~~~~~~~~i~~~~~Lk~GD~V~ll 86 (100)
T PF10844_consen 15 NPVDIVIGTVVSVPP--LKIKIDQK--LILDKDFLIIPELLKDYTRDITIEHNSETDNITITFTDGLKVGDKVLLL 86 (100)
T ss_pred CCceeEEEEEEeccc--EEEEECCe--EEEchHHEEeehhccceEEEEEEeccccccceeEEEecCCcCCCEEEEE
Confidence 445678999999988 77877753 44444444444322221100 0003456788999987643
No 148
>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=36.74 E-value=3.5e+02 Score=26.92 Aligned_cols=94 Identities=18% Similarity=0.238 Sum_probs=62.0
Q ss_pred CCeEecCCccCCCCCeeccCCeEec--CCeEEEEEeeEEEEeC-cEEEEEecCccccccCCCEEEEEEEEEecceEEEEe
Q psy10116 30 DPILTPGETVEYLEGYMTGHGTFPD--DEEIKASVGGVVEKVN-QLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDT 106 (298)
Q Consensus 30 ~~iV~PGD~I~~~~~~~~G~Gty~~--~g~i~Asv~G~v~~~n-k~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI 106 (298)
.-+.+||+.=..-.+...|.-+... +|+-+..+.|.++... -++.|+... ++ -++.-+-++-|.|-+
T Consensus 244 aYv~~pg~kT~YLSEL~sG~~VlvVd~~G~tR~~~VGRvKIE~RPLllIeA~~-------~g---~~~svilQnaetIRl 313 (354)
T PF01959_consen 244 AYVLMPGGKTRYLSELRSGDEVLVVDADGRTRTAIVGRVKIERRPLLLIEAEA-------DG---KRISVILQNAETIRL 313 (354)
T ss_pred eEEEcCCCceeehhhhcCCCEEEEEeCCCCEEEEEeeEEEEeecceEEEEEEe-------CC---eEEEEEEecCcEEEE
Confidence 3467888876555566677766553 6999999999998753 355554432 22 233335678888888
Q ss_pred CCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC
Q psy10116 107 NSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS 155 (298)
Q Consensus 107 ~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~ 155 (298)
-.+.-..+++. .|++||.|.+.+..-.
T Consensus 314 v~p~G~~vsVt----------------------~Lk~GD~vL~~~~~~~ 340 (354)
T PF01959_consen 314 VGPDGEPVSVT----------------------ELKPGDEVLVYLEEAG 340 (354)
T ss_pred ECCCCCEeeee----------------------ecCCCCEEEEEecCCC
Confidence 66544344432 3889999999988743
No 149
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=36.14 E-value=2.3e+02 Score=22.91 Aligned_cols=58 Identities=24% Similarity=0.386 Sum_probs=37.8
Q ss_pred ccccCCCEEEEEEEEE-ecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC
Q psy10116 82 YIGEIGEVVVGRVTGL-QSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS 155 (298)
Q Consensus 82 Y~P~vGDiVIG~V~~V-~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~ 155 (298)
..|..|+ ++|+|++. .++.+.|.......-.-++ ||- .|+ +=.+++||.|.++....+
T Consensus 16 ~~p~e~e-~~g~V~~~lG~~~~~V~~~dG~~~la~i-----~GK-~Rk---------~IwI~~GD~VlVe~~~~~ 74 (100)
T PRK04012 16 PMPEEGE-VFGVVEQMLGANRVRVRCMDGVERMGRI-----PGK-MKK---------RMWIREGDVVIVAPWDFQ 74 (100)
T ss_pred cCCCCCE-EEEEEEEEcCCCEEEEEeCCCCEEEEEE-----chh-hcc---------cEEecCCCEEEEEecccC
Confidence 3455555 78999998 4667777776544333332 332 232 467999999999987664
No 150
>COG1315 Uncharacterized conserved protein [Function unknown]
Probab=35.37 E-value=87 Score=32.57 Aligned_cols=47 Identities=19% Similarity=0.208 Sum_probs=36.9
Q ss_pred CeeccCCe-EecCCeEEEEEeeEEEEeCcEEEEEecC---ccccccCCCEE
Q psy10116 44 GYMTGHGT-FPDDEEIKASVGGVVEKVNQLVSVRAMN---SRYIGEIGEVV 90 (298)
Q Consensus 44 ~~~~G~Gt-y~~~g~i~Asv~G~v~~~nk~v~V~p~~---~rY~P~vGDiV 90 (298)
.+.+|.|| +.+++.+.|+..|.....+++|+|.|.- +---++.|+|.
T Consensus 220 ~l~lG~nt~~kd~~tlvA~~~G~~~~s~~tI~V~~iyeV~gdV~~kTGnI~ 270 (543)
T COG1315 220 KLNLGKNTAFKDNNTLVAKRDGQPIVSKNTISVYPIYEVNGDVDVKTGNIK 270 (543)
T ss_pred eeecCCCCccCCCCEEEEeeCCeEEecCCeeEEEEEEEecCCcccccccee
Confidence 37789999 7778999999999999999999999874 23445555553
No 151
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=35.28 E-value=51 Score=30.38 Aligned_cols=31 Identities=13% Similarity=0.244 Sum_probs=22.0
Q ss_pred ccCCCEEEEEEEEEecc-eEEEEeCCCceeeE
Q psy10116 84 GEIGEVVVGRVTGLQSQ-KWVVDTNSILESAL 114 (298)
Q Consensus 84 P~vGDiVIG~V~~V~~~-~~~VDI~s~~~a~L 114 (298)
-++||+|.++|.++..+ .+.+.+..+..|.|
T Consensus 112 ~~~GDlV~akV~~i~~~~~~~LS~k~~~lG~L 143 (235)
T PRK04163 112 LDIGDYIIAKVKDVDRTRDVVLTLKGKGLGKI 143 (235)
T ss_pred CCCCCEEEEEEEEECCCCcEEEEEcCCCCCcc
Confidence 48899999999999754 46666655544443
No 152
>PLN00208 translation initiation factor (eIF); Provisional
Probab=34.38 E-value=93 Score=27.05 Aligned_cols=54 Identities=17% Similarity=0.270 Sum_probs=35.9
Q ss_pred cCCCeEec--CCccCCCCCeeccCCeEe----cCCeEEEEEeeEEEEeCcEEEEEecCccccccCCCEEEEEE
Q psy10116 28 FTDPILTP--GETVEYLEGYMTGHGTFP----DDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRV 94 (298)
Q Consensus 28 ~~~~iV~P--GD~I~~~~~~~~G~Gty~----~~g~i~Asv~G~v~~~nk~v~V~p~~~rY~P~vGDiVIG~V 94 (298)
....+++| |+.++.. .-+.|.|.|. ++-...+.+.|.+++ .+||. .||+|+-..
T Consensus 22 ~~~el~~p~egq~~g~V-~~~lGn~~~~V~c~dG~~rLa~IpGKmRK---rIWI~---------~GD~VlVel 81 (145)
T PLN00208 22 EKRELIFKEDGQEYAQV-LRMLGNGRCEALCIDGTKRLCHIRGKMRK---KVWIA---------AGDIILVGL 81 (145)
T ss_pred ceeecccCCCCcEEEEE-EEEcCCCEEEEEECCCCEEEEEEecccee---eEEec---------CCCEEEEEc
Confidence 34567777 5566553 3467888876 346788999999986 37764 566665543
No 153
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=33.37 E-value=4.9e+02 Score=25.80 Aligned_cols=93 Identities=17% Similarity=0.242 Sum_probs=60.0
Q ss_pred CeEecCCccCCCCCeeccCCeEe--cCCeEEEEEeeEEEEeC-cEEEEEecCccccccCCCEEEEEEEEEecceEEEEeC
Q psy10116 31 PILTPGETVEYLEGYMTGHGTFP--DDEEIKASVGGVVEKVN-QLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTN 107 (298)
Q Consensus 31 ~iV~PGD~I~~~~~~~~G~Gty~--~~g~i~Asv~G~v~~~n-k~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~ 107 (298)
-+.+||+.-..-.+...|.-+.. .+|+-+..+.|.++... -++-|+... -| -++.-+-++-|.|.+-
T Consensus 235 Yv~~pgg~T~YLsEL~sG~eVlvVd~~G~tR~~~VGRvKIE~RPL~lIeAe~------~g----~~~~viLQnaetIrlv 304 (344)
T PRK02290 235 YVRVPGDKTRYLSELRSGDEVLVVDADGNTREAIVGRVKIEKRPLLLIEAEY------GG----KRIRTILQNAETIRLV 304 (344)
T ss_pred EEEcCCCcchhhHhhcCCCEEEEEeCCCCEEEEEeeEEEEeeccEEEEEEEe------CC----eEEEEEEecCcEEEEE
Confidence 47788987665555666766544 37999999999998653 344444332 12 2233345788888886
Q ss_pred CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC
Q psy10116 108 SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS 155 (298)
Q Consensus 108 s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~ 155 (298)
.+....+++ -.|++||.|.+++....
T Consensus 305 ~~dG~~vsV----------------------t~Lk~GD~VL~~~~~~~ 330 (344)
T PRK02290 305 TPDGKPVSV----------------------VDLKPGDEVLGYLEEAA 330 (344)
T ss_pred CCCCCEeee----------------------eecCCCCEEEEEecCCc
Confidence 554333332 23899999999998643
No 154
>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=33.26 E-value=51 Score=24.61 Aligned_cols=18 Identities=28% Similarity=0.697 Sum_probs=15.2
Q ss_pred cCCCCEEEEEEEEeCCCC
Q psy10116 141 LKEGDLISAEIHQISTEG 158 (298)
Q Consensus 141 ~~~GDlV~A~V~sv~~dg 158 (298)
|++||+|.++|.++...|
T Consensus 1 ~k~G~~V~g~V~~i~~~G 18 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQG 18 (74)
T ss_pred CCCCCEEEEEEEEEeCCc
Confidence 589999999999986444
No 155
>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=33.11 E-value=1.3e+02 Score=21.31 Aligned_cols=16 Identities=31% Similarity=0.200 Sum_probs=13.2
Q ss_pred hcccCCCCEEEEEEEE
Q psy10116 138 REFLKEGDLISAEIHQ 153 (298)
Q Consensus 138 r~~~~~GDlV~A~V~s 153 (298)
+-.|++||-|+|.+.+
T Consensus 46 ~l~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 46 ELGLKPGKEVYAVIKA 61 (69)
T ss_pred hCCCCCCCEEEEEEEC
Confidence 3458999999999876
No 156
>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=32.94 E-value=41 Score=26.31 Aligned_cols=16 Identities=25% Similarity=0.590 Sum_probs=11.5
Q ss_pred CCCCEEEEEEEEeCCC
Q psy10116 142 KEGDLISAEIHQISTE 157 (298)
Q Consensus 142 ~~GDlV~A~V~sv~~d 157 (298)
++||+|.|+|.++...
T Consensus 3 ~vGdiV~~rVtrv~~~ 18 (82)
T PF10447_consen 3 KVGDIVIARVTRVNPR 18 (82)
T ss_dssp -TT-EEEEEEEEE-SS
T ss_pred CCCCEEEEEEEEEecc
Confidence 5899999999999743
No 157
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=31.82 E-value=1.9e+02 Score=25.50 Aligned_cols=54 Identities=19% Similarity=0.292 Sum_probs=34.5
Q ss_pred cccCCCEEEEEEEEEe-cceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEE
Q psy10116 83 IGEIGEVVVGRVTGLQ-SQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIH 152 (298)
Q Consensus 83 ~P~vGDiVIG~V~~V~-~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~ 152 (298)
.|+.|+ ++|+|++.. +..+.|-......-+-|+ ||- .|+ +=.+++||+|..+.-
T Consensus 28 ~~eegq-~~g~V~~~LGn~~f~V~c~dG~~rLa~I-----~GK-mRK---------~IWI~~GD~VlVel~ 82 (155)
T PTZ00329 28 FKEEGQ-EYAQVLRMLGNGRLEAYCFDGVKRLCHI-----RGK-MRK---------RVWINIGDIILVSLR 82 (155)
T ss_pred cCCCCc-EEEEEEEEcCCCEEEEEECCCCEEEEEe-----ecc-cee---------eEEecCCCEEEEecc
Confidence 367777 679999984 566777765443333332 332 233 456999999999763
No 158
>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=31.39 E-value=65 Score=25.05 Aligned_cols=43 Identities=26% Similarity=0.251 Sum_probs=27.8
Q ss_pred cEEEEEecC-ccccccCCCEEEEEEEEEecceEEEEeCCCceeeEeccccc
Q psy10116 71 QLVSVRAMN-SRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVN 120 (298)
Q Consensus 71 k~v~V~p~~-~rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~ 120 (298)
.-++|-|.. ++|-.+.||.|.|.|..-... ..+.|++.+..+|
T Consensus 29 ~DvYVs~~qIrrf~LR~GD~V~G~vr~p~~~-------ek~~aL~~V~~VN 72 (78)
T PF07497_consen 29 DDVYVSPSQIRRFGLRTGDLVEGQVRPPREG-------EKYFALLRVESVN 72 (78)
T ss_dssp TSEEE-CCCCCCTT--TTEEEEEEEE--STT-------SSSEEECEECEET
T ss_pred CCEEECHHHHHHcCCCCCCEEEEEEeCCCCC-------CcceeeEEEEeEC
Confidence 356776665 589999999999999886543 2456777777775
No 159
>PRK00215 LexA repressor; Validated
Probab=31.03 E-value=2.2e+02 Score=25.02 Aligned_cols=36 Identities=19% Similarity=0.252 Sum_probs=24.7
Q ss_pred eEEEEeCcEEEEEecCccccccC----CCEEEEEEEEEec
Q psy10116 64 GVVEKVNQLVSVRAMNSRYIGEI----GEVVVGRVTGLQS 99 (298)
Q Consensus 64 G~v~~~nk~v~V~p~~~rY~P~v----GDiVIG~V~~V~~ 99 (298)
-.+...++.+++.|....|-|.. .-.|+|+|+.+-.
T Consensus 164 Krl~~~~~~~~L~s~Np~y~~~~~~~~~~~IiG~Vv~~~r 203 (205)
T PRK00215 164 KRFRREGGHIRLEPENPAYEPIIVDPDRVTIEGKVVGLIR 203 (205)
T ss_pred EEEEEeCCEEEEEcCCCCCCCEEeCCCcEEEEEEEEEEEE
Confidence 34444567889999887776522 3588999987643
No 160
>PF08970 Sda: Sporulation inhibitor A; InterPro: IPR015064 Members of this protein group contain two antiparallel alpha helices that are linked by a highly structured inter-helix loop to form a helical hairpin; the structure is stabilised by numerous hydrophobic and electrostatic interactions. These sporulation inhibitors are antikinases that bind to the histidine kinase KinA phosphotransfer domain and act as a molecular barricade that inhibit productive interaction between the ATP binding site and the phosphorylatable KinA His residue. This results in the inhibition of sporulation (by preventing phosphorylation of spo0A) []. ; PDB: 3FYR_B 1PV0_A.
Probab=30.56 E-value=72 Score=22.48 Aligned_cols=33 Identities=18% Similarity=0.222 Sum_probs=25.2
Q ss_pred cCHHHHHHHHHHHhCCCCcccCChhHHHHHHHHHHHH
Q psy10116 254 LFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQK 290 (298)
Q Consensus 254 i~~~~i~~~~~~s~~~~~~~~l~~~~~~~~~~~~~~~ 290 (298)
++++.+..+|..+.++. |+++|+..+.++.+.|
T Consensus 4 LSDe~LiesY~~A~el~----L~~dFI~Ll~~Ei~rR 36 (46)
T PF08970_consen 4 LSDELLIESYHKAIELN----LDPDFIRLLEEEIQRR 36 (46)
T ss_dssp S-HHHHHHHHHHHHHTT------HHHHHHHHHHHHHC
T ss_pred ccHHHHHHHHHHHHHhC----CCHHHHHHHHHHHHHc
Confidence 68899999999997664 6789999888877655
No 161
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=30.39 E-value=1.7e+02 Score=19.68 Aligned_cols=64 Identities=19% Similarity=0.249 Sum_probs=33.9
Q ss_pred EEEEEEEEecc-----eEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEe
Q psy10116 90 VVGRVTGLQSQ-----KWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHT 164 (298)
Q Consensus 90 VIG~V~~V~~~-----~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lst 164 (298)
|.|.|.++... .+.+.|.....+.+.+.-+. .........+++|+.+..+..--..++.+.|+.
T Consensus 2 v~g~v~~~~~~~~~~~~~~~~l~D~~~~~i~~~~~~-----------~~~~~~~~~~~~g~~v~v~g~v~~~~~~~~l~~ 70 (75)
T cd03524 2 IVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFG-----------ELAEELENLLKEGQVVYIKGKVKKFRGRLQLIV 70 (75)
T ss_pred eEEEEEeecccccCCeEEEEEEEcCCCCEEEEEEEc-----------hHHHHHHhhccCCCEEEEEEEEEecCCeEEEEe
Confidence 56888888654 46666654332444433221 011223567999999887733221234455543
No 162
>KOG3038|consensus
Probab=29.33 E-value=1.6e+02 Score=28.11 Aligned_cols=71 Identities=24% Similarity=0.316 Sum_probs=47.0
Q ss_pred CcEEEEEecCccccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEE
Q psy10116 70 NQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISA 149 (298)
Q Consensus 70 nk~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A 149 (298)
+....-.|.++-|.+..||-|-.+|+.+..+ ||.|.|
T Consensus 114 p~~~gaip~~~~~~~~~gd~VAa~v~~~~~d-------------------------------------------g~WIla 150 (264)
T KOG3038|consen 114 PPLCGAIPAQGDYVLLKGDEVAARVKAVSED-------------------------------------------GDWILA 150 (264)
T ss_pred CcccccccccCCccccCCceeeeeeeeccCC-------------------------------------------CCEEEE
Confidence 4455556666677888888887777654322 578888
Q ss_pred EEEEeCCCCcEEEEeccCCCccC---CCceEEEeCch
Q psy10116 150 EIHQISTEGSLTLHTRSLKYGKL---GQGILLTVPPS 183 (298)
Q Consensus 150 ~V~sv~~dg~~~Lstr~~~lGkL---~~G~lv~v~~~ 183 (298)
+|+++..++.++.--....-+++ ..|.+++.+-+
T Consensus 151 eVv~~~~~~~ye~ev~D~Epk~d~~g~r~~~yklp~~ 187 (264)
T KOG3038|consen 151 EVVKVSSETRYEFEVVDPEPKKDEVGNRGQLYKLPRW 187 (264)
T ss_pred EEEEEecCCceEeEecCCCccccccccccceecccHh
Confidence 88888776666666665554444 46778877744
No 163
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=28.55 E-value=1.5e+02 Score=27.31 Aligned_cols=17 Identities=12% Similarity=0.417 Sum_probs=13.8
Q ss_pred hcccCCCCEEEEEEEEe
Q psy10116 138 REFLKEGDLISAEIHQI 154 (298)
Q Consensus 138 r~~~~~GDlV~A~V~sv 154 (298)
...|++||.|+..-..+
T Consensus 162 GQkFnVGDkVKV~~~~~ 178 (213)
T PRK06763 162 GQVFHVGDKVKVDMKYV 178 (213)
T ss_pred CCEEecCCEEEEEeeec
Confidence 57799999999886654
No 164
>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=28.24 E-value=89 Score=23.30 Aligned_cols=31 Identities=13% Similarity=0.133 Sum_probs=21.9
Q ss_pred ccccCCCEEEEEEEEEec-ceEEEEeCCCcee
Q psy10116 82 YIGEIGEVVVGRVTGLQS-QKWVVDTNSILES 112 (298)
Q Consensus 82 Y~P~vGDiVIG~V~~V~~-~~~~VDI~s~~~a 112 (298)
...++||.+.++|.++.. ....+.+..+..|
T Consensus 49 ~~~~~GD~i~~~V~~~~~~~~i~LS~~~~~~G 80 (82)
T cd04454 49 KSLQPGDLILAKVISLGDDMNVLLTTADNELG 80 (82)
T ss_pred hcCCCCCEEEEEEEEeCCCCCEEEEECCCCCc
Confidence 445999999999999976 4555555544333
No 165
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=28.10 E-value=38 Score=24.59 Aligned_cols=15 Identities=33% Similarity=0.598 Sum_probs=12.9
Q ss_pred cCCCCEEEEEEEEeC
Q psy10116 141 LKEGDLISAEIHQIS 155 (298)
Q Consensus 141 ~~~GDlV~A~V~sv~ 155 (298)
|++||+|-||+....
T Consensus 1 f~~GdlVwaK~~G~p 15 (63)
T smart00293 1 FKPGDLVWAKMKGFP 15 (63)
T ss_pred CCCCCEEEEECCCCC
Confidence 689999999998754
No 166
>PF01436 NHL: NHL repeat; InterPro: IPR001258 The NHL repeat, named after NCL-1, HT2A and Lin-41, is found largely in a large number of eukaryotic and prokaryotic proteins. For example, the repeat is found in a variety of enzymes of the copper type II, ascorbate-dependent monooxygenase family which catalyse the C terminus alpha-amidation of biological peptides []. In many it occurs in tandem arrays, for example in the ringfinger beta-box, coiled-coil (RBCC) eukaryotic growth regulators []. The 'Brain Tumor' protein (Brat) is one such growth regulator that contains a 6-bladed NHL-repeat beta-propeller [, ]. The NHL repeats are also found in serine/threonine protein kinase (STPK) in diverse range of pathogenic bacteria. These STPK are transmembrane receptors with a intracellular N-terminal kinase domain and extracellular C-terminal sensor domain. In the STPK, PknD, from Mycobacterium tuberculosis, the sensor domain forms a rigid, six-bladed b-propeller composed of NHL repeats with a flexible tether to the transmembrane domain.; GO: 0005515 protein binding; PDB: 3FVZ_A 3FW0_A 1RWL_A 1RWI_A 1Q7F_A.
Probab=28.09 E-value=79 Score=19.18 Aligned_cols=18 Identities=17% Similarity=0.329 Sum_probs=14.6
Q ss_pred ccEEEEEeeCceEEEecC
Q psy10116 197 CGAQVILGCNGYVWVSAI 214 (298)
Q Consensus 197 ~~~eiivG~NG~IWI~~~ 214 (298)
.+-.|++..||.|||.-.
T Consensus 3 ~P~gvav~~~g~i~VaD~ 20 (28)
T PF01436_consen 3 YPHGVAVDSDGNIYVADS 20 (28)
T ss_dssp SEEEEEEETTSEEEEEEC
T ss_pred CCcEEEEeCCCCEEEEEC
Confidence 456788889999999763
No 167
>PF14398 ATPgrasp_YheCD: YheC/D like ATP-grasp
Probab=27.95 E-value=37 Score=31.62 Aligned_cols=19 Identities=21% Similarity=0.550 Sum_probs=16.5
Q ss_pred cccEEEEEeeCceEEEecC
Q psy10116 196 ACGAQVILGCNGYVWVSAI 214 (298)
Q Consensus 196 ~~~~eiivG~NG~IWI~~~ 214 (298)
+.|+|+++..||.+|+=--
T Consensus 211 ElGiDl~iD~~g~iWliEv 229 (262)
T PF14398_consen 211 ELGIDLGIDKNGKIWLIEV 229 (262)
T ss_pred EEEEEEEEcCCCCEEEEEE
Confidence 5799999999999998543
No 168
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=27.81 E-value=1.3e+02 Score=28.72 Aligned_cols=49 Identities=18% Similarity=0.062 Sum_probs=41.1
Q ss_pred cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEe
Q psy10116 83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQI 154 (298)
Q Consensus 83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv 154 (298)
.|..|.+=.|.|+....+...||||....+.|+ .-+.+|+.|..++.+.
T Consensus 102 ~~~~Ge~ReG~v~~~~~~~~~v~iG~~~~~~l~-----------------------~~~~~~~RvTvri~~~ 150 (272)
T COG2106 102 SPKEGEYREGLVIRRGKKGNLVDIGKDKLAKLS-----------------------SPAPPGARVTVRIISR 150 (272)
T ss_pred CccceeecceEEEEecCCceEEEecCCcceecc-----------------------CCCCCCceEEEEEEec
Confidence 689999999999999999999999988777664 1167788888888876
No 169
>PF13375 RnfC_N: RnfC Barrel sandwich hybrid domain
Probab=27.76 E-value=80 Score=25.46 Aligned_cols=39 Identities=23% Similarity=0.318 Sum_probs=22.6
Q ss_pred CCeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEeC
Q psy10116 30 DPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVN 70 (298)
Q Consensus 30 ~~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~n 70 (298)
.-+|-+||.+..- + +.|...=...-.++||+.|+|....
T Consensus 43 ~p~V~~Gd~V~~G-Q-~Ia~~~~~~sa~iHAsvSG~V~~I~ 81 (101)
T PF13375_consen 43 EPVVKVGDKVKKG-Q-LIAEAEGFLSAPIHASVSGTVTAIE 81 (101)
T ss_pred eEEEcCCCEEcCC-C-EEEecCCCcEeeEEcCCCeEEEEEe
Confidence 3577777776552 1 1121110123479999999998653
No 170
>PF08406 CbbQ_C: CbbQ/NirQ/NorQ C-terminal ; InterPro: IPR013615 This domain is found at the C terminus of proteins of the CbbQ/NirQ/NorQ family of proteins which play a role in the post-translational activation of Rubisco []. It is also found in the Thauera aromaticaTutH protein which is similar to the CbbQ/NirQ/NorQ family [], as well as in putative chaperones. The ATPase domain associated with various cellular activities (AAA) IPR011704 from INTERPRO is found in the same bacterial and archaeal proteins as the domain described here.
Probab=27.68 E-value=2.8e+02 Score=21.71 Aligned_cols=29 Identities=17% Similarity=0.114 Sum_probs=24.8
Q ss_pred cCCHHHHHHHHHHHHHHHHHhhCCcccCH
Q psy10116 228 VVKLSDRETITRLNNVIKALAESKVMLFD 256 (298)
Q Consensus 228 ~i~~~~r~~i~rv~n~i~~l~~~~~~i~~ 256 (298)
-++.++.+.+.+++|.++.|..+++....
T Consensus 10 gl~~~~a~~LV~~A~~iR~l~~~~L~e~~ 38 (86)
T PF08406_consen 10 GLDPEIAEKLVKLANAIRNLKGGGLEETV 38 (86)
T ss_pred CCCHHHHHHHHHHHHHHHhccCCCCCCCC
Confidence 57889999999999999999888887433
No 171
>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=27.38 E-value=65 Score=24.18 Aligned_cols=18 Identities=11% Similarity=0.340 Sum_probs=15.4
Q ss_pred cCCCCEEEEEEEEeCCCC
Q psy10116 141 LKEGDLISAEIHQISTEG 158 (298)
Q Consensus 141 ~~~GDlV~A~V~sv~~dg 158 (298)
.++||+|.|+|.++..++
T Consensus 4 p~~GdiV~g~V~~i~~~g 21 (86)
T cd05789 4 PEVGDVVIGRVTEVGFKR 21 (86)
T ss_pred CCCCCEEEEEEEEECCCE
Confidence 479999999999997554
No 172
>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=26.50 E-value=61 Score=25.52 Aligned_cols=20 Identities=25% Similarity=0.326 Sum_probs=16.9
Q ss_pred cccccCCCEEEEEEEEEecc
Q psy10116 81 RYIGEIGEVVVGRVTGLQSQ 100 (298)
Q Consensus 81 rY~P~vGDiVIG~V~~V~~~ 100 (298)
|...++||+|+++|..+...
T Consensus 47 rp~L~~GDlV~ArV~~~~~~ 66 (86)
T cd05790 47 RPNLNVGDLVYARVVKANRD 66 (86)
T ss_pred cccCCCCCEEEEEEEecCCC
Confidence 55679999999999998764
No 173
>COG1158 Rho Transcription termination factor [Transcription]
Probab=26.44 E-value=60 Score=32.42 Aligned_cols=44 Identities=20% Similarity=0.208 Sum_probs=34.9
Q ss_pred cEEEEEecC-ccccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccC
Q psy10116 71 QLVSVRAMN-SRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNL 121 (298)
Q Consensus 71 k~v~V~p~~-~rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~ 121 (298)
+-|+|.|.. .||-.+.||.|.|+|-.=+.. ..|.|.+.+..+|+
T Consensus 80 ~DiYvSpSQIRrf~LrtGD~v~G~vR~Pke~-------Ery~aLl~ve~vN~ 124 (422)
T COG1158 80 DDIYVSPSQIRRFNLRTGDTVEGKVRPPKEG-------ERYFALLKVEAVNG 124 (422)
T ss_pred CceEECHHHHhhccCccCCEEeeeecCCCcc-------cceeeeEEEeecCC
Confidence 568898887 589999999999999765443 35668888888874
No 174
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=25.91 E-value=2.1e+02 Score=19.99 Aligned_cols=47 Identities=26% Similarity=0.270 Sum_probs=27.2
Q ss_pred EEEEEEEEecce----EEEEeCCC--ceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEE
Q psy10116 90 VVGRVTGLQSQK----WVVDTNSI--LESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQ 153 (298)
Q Consensus 90 VIG~V~~V~~~~----~~VDI~s~--~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~s 153 (298)
.-|+|..+.... +.++++.. ..|.++..++ . +=.|++||-|++.+..
T Consensus 7 l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~---------------~--~L~L~~G~~V~~~ik~ 59 (64)
T PF03459_consen 7 LPGTVESIENLGSEVEVTLDLGGGETLTARITPESA---------------E--ELGLKPGDEVYASIKA 59 (64)
T ss_dssp EEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHH---------------H--HCT-STT-EEEEEE-G
T ss_pred EEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHH---------------H--HcCCCCCCEEEEEEeh
Confidence 568888887776 55566543 3344432222 1 3348899999998754
No 175
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=25.73 E-value=1.5e+02 Score=23.03 Aligned_cols=33 Identities=18% Similarity=0.360 Sum_probs=24.4
Q ss_pred hhhhhhhhcccCCCCEEE------EEEEEeCCCCcEEEEe
Q psy10116 131 VQDEEMMREFLKEGDLIS------AEIHQISTEGSLTLHT 164 (298)
Q Consensus 131 ~~d~~~mr~~~~~GDlV~------A~V~sv~~dg~~~Lst 164 (298)
.....+|.+.+++||.|. ++|.++++ ..+.|..
T Consensus 28 ~k~~~~m~~~L~~Gd~VvT~gGi~G~V~~i~d-~~v~vei 66 (84)
T TIGR00739 28 RKAHKKLIESLKKGDKVLTIGGIIGTVTKIAE-NTIVIEL 66 (84)
T ss_pred HHHHHHHHHhCCCCCEEEECCCeEEEEEEEeC-CEEEEEE
Confidence 445579999999999964 88998864 3455543
No 176
>cd05834 HDGF_related The PWWP domain is an essential part of the Hepatoma Derived Growth Factor (HDGF) family of proteins, and is necessary for DNA binding by HDGF. This family of endogenous nuclear-targeted mitogens includes HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, HPR2, HPR3, HPR4, respectively) and lens epithelium-derived growth factor, LEDGF. Members of the HDGF family have been linked to human diseases, and HDGF is a prognostic factor in several types of cancer. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=25.15 E-value=45 Score=25.85 Aligned_cols=16 Identities=31% Similarity=0.505 Sum_probs=13.5
Q ss_pred ccCCCCEEEEEEEEeC
Q psy10116 140 FLKEGDLISAEIHQIS 155 (298)
Q Consensus 140 ~~~~GDlV~A~V~sv~ 155 (298)
.|++||+|.||+....
T Consensus 2 ~f~~GdlVwaK~kGyp 17 (83)
T cd05834 2 QFKAGDLVFAKVKGYP 17 (83)
T ss_pred CCCCCCEEEEecCCCC
Confidence 4899999999997654
No 177
>PF00364 Biotin_lipoyl: Biotin-requiring enzyme; InterPro: IPR000089 The biotin / lipoyl attachment domain has a conserved lysine residue that binds biotin or lipoic acid. Biotin plays a catalytic role in some carboxyl transfer reactions and is covalently attached, via an amide bond, to a lysine residue in enzymes requiring this coenzyme []. E2 acyltransferases have an essential cofactor, lipoic acid, which is covalently bound via an amide linkage to a lysine group []. The lipoic acid cofactor is found in a variety of proteins that include, H-protein of the glycine cleavage system (GCS), mammalian and yeast pyruvate dehydrogenases and fast migrating protein (FMP) (gene acoC) from Ralstonia eutropha (Alcaligenes eutrophus).; PDB: 2EJG_D 2D5D_A 2EJF_C 2EVB_A 1IYV_A 1IYU_A 1LAC_A 1LAB_A 1DCZ_A 1DD2_A ....
Probab=24.70 E-value=2.2e+02 Score=21.00 Aligned_cols=54 Identities=15% Similarity=0.230 Sum_probs=32.1
Q ss_pred eEEEEEeeEEEEeCcEEEEEecCccccccCCCEEEEEEEEEecceEEEEeCCCceeeEe
Q psy10116 57 EIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALH 115 (298)
Q Consensus 57 ~i~Asv~G~v~~~nk~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~ 115 (298)
.++++..|..........+.-..+.++ +.||.+ -.+.......+|.|+.+|.+.
T Consensus 2 ~i~~P~~G~~~~~~~i~~~~v~~G~~V-~~G~~l----~~iet~K~~~~v~a~~~G~i~ 55 (74)
T PF00364_consen 2 EIKAPMLGEVMEEGTITKWLVEEGDKV-KKGDPL----AEIETMKMEMEVEAPVSGIIK 55 (74)
T ss_dssp EEEESSSSEEEEEEEEEEESSSTTEEE-STTSEE----EEEESSSEEEEEEBSSSEEEE
T ss_pred EEECCCCccEEEecceeEEEECCCCEE-EcCceE----EEEEcCccceEEECCCCEEEE
Confidence 466677777665443322222222233 556554 345667788899999999986
No 178
>cd05841 BS69_related The PWWP domain is part of BS69 protein, a nuclear protein that specifically binds adenoviral E1A and Epstein-Barr viral EBNA2 proteins, suppressing their transactivation functions. BS69 is a multi-domain protein, containing bromo, PHD, PWWP, and MYND domains. The specific role of the PWWP domain within BS69 is not clearly identified, but BS69 functions in chromatin remodeling, consistent with other PWWP-containing proteins. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=24.65 E-value=47 Score=26.09 Aligned_cols=18 Identities=11% Similarity=0.156 Sum_probs=15.8
Q ss_pred hcccCCCCEEEEEEEEeC
Q psy10116 138 REFLKEGDLISAEIHQIS 155 (298)
Q Consensus 138 r~~~~~GDlV~A~V~sv~ 155 (298)
++|.++||||.||+....
T Consensus 4 ~pc~~p~dLVwAK~kGyp 21 (83)
T cd05841 4 EPCRPPHELVWAKLKGFP 21 (83)
T ss_pred cccCCCCCEEEEeCCCCC
Confidence 689999999999998754
No 179
>cd05836 N_Pac_NP60 The PWWP domain is an essential part of the cytokine-like nuclear factor n-pac protein, or NP60, which enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In a variety of cell lines, NP60 has been shown to localize to the nucleus. In addition to the PWWP domain, NP60 also contains an AT-hook and a C-terminal NAD-binding domain. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding proteins, that function as transcription factors regulating a variety of developmental processes.
Probab=24.09 E-value=47 Score=25.90 Aligned_cols=18 Identities=11% Similarity=0.361 Sum_probs=13.9
Q ss_pred EEEEEeeCceEEEecCCC
Q psy10116 199 AQVILGCNGYVWVSAIDE 216 (298)
Q Consensus 199 ~eiivG~NG~IWI~~~~~ 216 (298)
+-...|.+-+-|++...-
T Consensus 39 ~V~FFG~~~~~wv~~~~l 56 (86)
T cd05836 39 FVFFFGSENHAWIKEENI 56 (86)
T ss_pred EEEEeCCCCEEEECHHhC
Confidence 445778999999988654
No 180
>cd05840 SPBC215_ISWI_like The PWWP domain is a component of the S. pombe hypothetical protein SPBC215, as well as ISWI complex protein 4. The ISWI (imitation switch) proteins are ATPases responsible for chromatin remodeling in eukaryotes, and SPBC215 is proposed to also bind chromatin. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=22.76 E-value=51 Score=26.13 Aligned_cols=15 Identities=20% Similarity=0.463 Sum_probs=12.9
Q ss_pred cCCCCEEEEEEEEeC
Q psy10116 141 LKEGDLISAEIHQIS 155 (298)
Q Consensus 141 ~~~GDlV~A~V~sv~ 155 (298)
|++||+|.|||-...
T Consensus 1 f~~GDlVwaK~~GyP 15 (93)
T cd05840 1 FQPGDRVLAKVKGFP 15 (93)
T ss_pred CCCCCEEEEeCCCCC
Confidence 689999999998754
No 181
>PF00877 NLPC_P60: NlpC/P60 family; InterPro: IPR000064 The Escherichia coli NLPC/Listeria P60 domain occurs at the C terminus of a number of different bacterial and viral proteins. The viral proteins are either described as tail assembly proteins or Gp19. In bacteria, the proteins are variously described as being putative tail component of prophage, invasin, invasion associated protein, putative lipoprotein, cell wall hydrolase, or putative endopeptidase. The E. coli NLPC/Listeria P60 domain is contained within the boundaries of the cysteine peptidase domain that defines the MEROPS peptidase family C40 (clan C-). A type example being dipeptidyl-peptidase VI from Bacillus sphaericus and gamma-glutamyl-diamino acid-endopeptidase precursor from Lactococcus lactis 3.4.19.11 from EC. This group also contains proteins classified as non-peptidase homologues in that they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the C40 family. ; PDB: 3PVQ_B 3GT2_A 3NPF_B 2K1G_A 3I86_A 3S0Q_A 2XIV_A 3PBC_A 3NE0_A 3M1U_B ....
Probab=22.39 E-value=83 Score=24.51 Aligned_cols=45 Identities=24% Similarity=0.389 Sum_probs=27.7
Q ss_pred CeEecCCccCCCCCeeccC-CeEecCCeEEEEEeeEEEEeCcEEEEEecCccc
Q psy10116 31 PILTPGETVEYLEGYMTGH-GTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRY 82 (298)
Q Consensus 31 ~iV~PGD~I~~~~~~~~G~-Gty~~~g~i~Asv~G~v~~~nk~v~V~p~~~rY 82 (298)
.-..|||+|.-...-...| |+|..+++++-+- .+.+.+.+++..|
T Consensus 50 ~~~~pGDlif~~~~~~~~Hvgiy~g~~~~iha~-------~~~v~v~~~~~~~ 95 (105)
T PF00877_consen 50 SELQPGDLIFFKGGGGISHVGIYLGDGKFIHAS-------GGGVSVSSLSGSY 95 (105)
T ss_dssp GG-TTTEEEEEEGTGGEEEEEEEEETTEEEEEE-------TTEEEEEESTSTT
T ss_pred hcCCcccEEEEeCCccCCEeEEEEeCCeEEEeC-------CCcEEEEECCChH
Confidence 3456888886643223345 7788877765544 5566777777643
No 182
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=22.18 E-value=3.3e+02 Score=20.81 Aligned_cols=61 Identities=18% Similarity=0.246 Sum_probs=33.3
Q ss_pred EeeEEEE----eCcEEEEEecCccccccCCCEEEEEEEEEecceEEEEe-CCCceeeEecccccCCCCcccccchhhhhh
Q psy10116 62 VGGVVEK----VNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDT-NSILESALHLTSVNLPGGEQRRRSVQDEEM 136 (298)
Q Consensus 62 v~G~v~~----~nk~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI-~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~ 136 (298)
++|+++. .+..+.+.|.. ..++|.++.-..-.++- .+....-|.+.+++
T Consensus 22 v~G~v~~G~i~~gd~v~i~P~~----------~~~~V~sI~~~~~~~~~a~aG~~v~i~l~~i~---------------- 75 (91)
T cd03693 22 PVGRVETGVLKPGMVVTFAPAG----------VTGEVKSVEMHHEPLEEALPGDNVGFNVKNVS---------------- 75 (91)
T ss_pred EEEEEecceeecCCEEEECCCC----------cEEEEEEEEECCcCcCEECCCCEEEEEECCCC----------------
Confidence 3455552 35566666643 45777777654433332 23444555555442
Q ss_pred hhcccCCCCEEEE
Q psy10116 137 MREFLKEGDLISA 149 (298)
Q Consensus 137 mr~~~~~GDlV~A 149 (298)
.+.++.||++..
T Consensus 76 -~~~v~~G~vl~~ 87 (91)
T cd03693 76 -KKDIKRGDVAGD 87 (91)
T ss_pred -HHHcCCcCEEcc
Confidence 345777887653
No 183
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=21.77 E-value=1.3e+02 Score=28.62 Aligned_cols=19 Identities=21% Similarity=0.200 Sum_probs=15.6
Q ss_pred EEEEEEEEecceEEEEeCC
Q psy10116 90 VVGRVTGLQSQKWVVDTNS 108 (298)
Q Consensus 90 VIG~V~~V~~~~~~VDI~s 108 (298)
++|+|+.|.....+|.+-+
T Consensus 156 LVG~V~~V~~~tS~V~Llt 174 (284)
T COG1792 156 LVGKVVEVSKNTSRVLLLT 174 (284)
T ss_pred eEEEEEEEcCceeEEEEee
Confidence 8899999999998886533
No 184
>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=21.76 E-value=3.6e+02 Score=20.40 Aligned_cols=52 Identities=19% Similarity=0.226 Sum_probs=33.3
Q ss_pred EEEEEEEEe-cceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC
Q psy10116 90 VVGRVTGLQ-SQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS 155 (298)
Q Consensus 90 VIG~V~~V~-~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~ 155 (298)
+.|.|++.- +..+.|.+.....-.-++ ||-..++ +-.+.+||.|..+....+
T Consensus 7 ~~G~V~e~L~~~~f~V~l~ng~~vla~i-----~GKmr~~---------rI~I~~GD~V~Ve~spyd 59 (68)
T TIGR00008 7 MEGKVTESLPNAMFRVELENGHEVLAHI-----SGKIRMH---------YIRILPGDKVKVELSPYD 59 (68)
T ss_pred EEEEEEEECCCCEEEEEECCCCEEEEEe-----cCcchhc---------cEEECCCCEEEEEECccc
Confidence 679999984 566777776544433332 2322222 566899999999876654
No 185
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=21.55 E-value=1.2e+02 Score=26.07 Aligned_cols=28 Identities=21% Similarity=0.261 Sum_probs=23.6
Q ss_pred CCCEEEEEEEEEecceEEEEeCCCceee
Q psy10116 86 IGEVVVGRVTGLQSQKWVVDTNSILESA 113 (298)
Q Consensus 86 vGDiVIG~V~~V~~~~~~VDI~s~~~a~ 113 (298)
.|+.+.++|+++.++...||-|.|.-|.
T Consensus 105 ~G~~~~~~V~~i~~~~v~vD~NHPLAGk 132 (156)
T PRK15095 105 DGSEMPGVIREINGDSITVDFNHPLAGQ 132 (156)
T ss_pred CCCEEEEEEEEEcCCEEEEECCCcCCCC
Confidence 4556688999999999999999987663
No 186
>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=20.39 E-value=1.1e+02 Score=24.32 Aligned_cols=22 Identities=27% Similarity=0.513 Sum_probs=16.7
Q ss_pred cCCCCEEEEEEEEeCCCCcEEEE
Q psy10116 141 LKEGDLISAEIHQISTEGSLTLH 163 (298)
Q Consensus 141 ~~~GDlV~A~V~sv~~dg~~~Ls 163 (298)
|++||+|.|+|.++... .+.++
T Consensus 1 L~~G~vV~G~V~~v~~~-gl~v~ 22 (100)
T cd05693 1 LSEGMLVLGQVKEITKL-DLVIS 22 (100)
T ss_pred CCCCCEEEEEEEEEcCC-CEEEE
Confidence 57899999999999644 34443
No 187
>PRK05054 exoribonuclease II; Provisional
Probab=20.19 E-value=4.3e+02 Score=28.12 Aligned_cols=16 Identities=38% Similarity=0.557 Sum_probs=13.3
Q ss_pred ccCCCCEEEEEEEEeC
Q psy10116 140 FLKEGDLISAEIHQIS 155 (298)
Q Consensus 140 ~~~~GDlV~A~V~sv~ 155 (298)
.++.||+|.++|....
T Consensus 121 ~~~~gd~V~v~i~~~p 136 (644)
T PRK05054 121 EFKEGDWVVAELRRHP 136 (644)
T ss_pred CCCCCCEEEEEEecCC
Confidence 4788999999999753
No 188
>cd02796 tRNA_bind_bactPheRS tRNA-binding-domain-containing prokaryotic phenylalanly tRNA synthetase (PheRS) beta chain. PheRS aminoacylate phenylalanine transfer RNAs (tRNAphe). PheRSs belong structurally to class II aminoacyl tRNA synthetases (aaRSs) but, as they aminoacylate the 2'OH of the terminal ribose of tRNA they belong functionally to class 1 aaRSs. This domain has general tRNA binding properties and is believed to direct tRNAphe to the active site of the enzyme.
Probab=20.16 E-value=3e+02 Score=21.54 Aligned_cols=37 Identities=22% Similarity=0.400 Sum_probs=18.4
Q ss_pred cCCCCEEEEEEEEeCCCCcEEEEeccCCCccCCCceEE
Q psy10116 141 LKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILL 178 (298)
Q Consensus 141 ~~~GDlV~A~V~sv~~dg~~~Lstr~~~lGkL~~G~lv 178 (298)
+..|+.|.+-.....-.+...+..|. -.|..++|++.
T Consensus 40 ~~~g~~vvv~~~gs~l~~~~~i~~~~-~~G~~S~GMl~ 76 (103)
T cd02796 40 VRAGDKVVVALPGAVLPGGLKIKKRK-LRGVESEGMLC 76 (103)
T ss_pred hhcCCEEEEEecCCCcCCCceEccee-eCCcccchhCc
Confidence 46788665543222111112344333 34788888874
Done!