Query psy6276
Match_columns 271
No_of_seqs 167 out of 725
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 22:14:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6276.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6276hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1096 Predicted RNA-binding 100.0 1E-44 2.3E-49 315.5 16.2 179 3-192 4-186 (188)
2 KOG3409|consensus 100.0 5.2E-44 1.1E-48 307.3 15.2 184 2-188 3-189 (193)
3 PRK09521 exosome complex RNA-b 100.0 7.4E-42 1.6E-46 299.1 19.6 179 3-192 4-187 (189)
4 PRK04163 exosome complex RNA-b 100.0 8.4E-33 1.8E-37 250.0 17.8 218 1-249 5-227 (235)
5 COG1097 RRP4 RNA-binding prote 100.0 2.8E-32 6E-37 245.9 18.7 184 3-212 7-193 (239)
6 cd05791 S1_CSL4 S1_CSL4: CSL4, 99.9 2.8E-27 6E-32 186.0 9.7 91 65-155 1-92 (92)
7 KOG3013|consensus 99.9 7E-27 1.5E-31 212.2 10.3 178 5-210 30-212 (301)
8 PF10447 EXOSC1: Exosome compo 99.9 1.8E-22 3.8E-27 156.3 7.3 71 67-137 1-82 (82)
9 KOG1004|consensus 99.8 1.6E-18 3.4E-23 154.0 13.6 179 5-212 2-194 (230)
10 cd04454 S1_Rrp4_like S1_Rrp4_l 99.6 9.4E-16 2E-20 116.6 9.5 81 65-155 1-82 (82)
11 cd05790 S1_Rrp40 S1_Rrp40: Rrp 99.5 7.8E-14 1.7E-18 109.0 8.1 74 65-149 1-75 (86)
12 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.4 6.4E-13 1.4E-17 101.5 9.0 83 65-155 1-86 (86)
13 PF14382 ECR1_N: Exosome compl 99.3 9.1E-13 2E-17 88.8 4.1 39 6-45 1-39 (39)
14 cd05704 S1_Rrp5_repeat_hs13 S1 98.7 8.2E-08 1.8E-12 71.7 7.2 69 69-148 2-72 (72)
15 cd05687 S1_RPS1_repeat_ec1_hs1 98.6 1.8E-07 4E-12 68.4 7.8 67 71-147 1-69 (70)
16 cd05702 S1_Rrp5_repeat_hs11_sc 98.5 3.6E-07 7.7E-12 67.4 6.8 64 71-142 1-65 (70)
17 cd04452 S1_IF2_alpha S1_IF2_al 98.5 6.8E-07 1.5E-11 66.0 8.0 73 68-148 1-75 (76)
18 cd05693 S1_Rrp5_repeat_hs1_sc1 98.5 7.1E-07 1.5E-11 71.2 7.6 73 69-149 2-96 (100)
19 cd05691 S1_RPS1_repeat_ec6 S1_ 98.4 1.2E-06 2.6E-11 64.0 7.8 70 71-150 1-72 (73)
20 cd05706 S1_Rrp5_repeat_sc10 S1 98.4 2.3E-06 5.1E-11 63.0 8.3 70 69-148 2-73 (73)
21 cd05705 S1_Rrp5_repeat_hs14 S1 98.3 3E-06 6.6E-11 63.8 7.6 70 69-146 2-74 (74)
22 cd05692 S1_RPS1_repeat_hs4 S1_ 98.3 4.1E-06 9E-11 59.7 7.9 68 71-148 1-69 (69)
23 COG1098 VacB Predicted RNA bin 98.3 1.4E-06 3E-11 72.4 6.1 74 68-151 3-77 (129)
24 cd05708 S1_Rrp5_repeat_sc12 S1 98.2 5.5E-06 1.2E-10 60.9 7.8 72 69-149 1-74 (77)
25 cd05707 S1_Rrp5_repeat_sc11 S1 98.2 6E-06 1.3E-10 60.2 7.4 66 71-146 1-68 (68)
26 smart00316 S1 Ribosomal protei 98.2 7.8E-06 1.7E-10 57.9 7.6 69 69-147 1-71 (72)
27 PRK08582 hypothetical protein; 98.2 9.5E-06 2.1E-10 68.5 8.9 73 68-150 3-76 (139)
28 cd05703 S1_Rrp5_repeat_hs12_sc 98.2 1.1E-05 2.3E-10 60.5 7.9 70 71-148 1-72 (73)
29 PF00575 S1: S1 RNA binding do 98.1 1.3E-05 2.9E-10 58.9 8.0 71 68-148 2-74 (74)
30 cd05686 S1_pNO40 S1_pNO40: pNO 98.1 2.1E-05 4.5E-10 58.5 8.5 71 68-147 1-72 (73)
31 PRK08059 general stress protei 98.1 1.7E-05 3.7E-10 65.2 8.5 74 68-151 5-80 (123)
32 PRK07252 hypothetical protein; 98.0 2.4E-05 5.1E-10 64.6 8.5 71 69-149 2-74 (120)
33 PRK03987 translation initiatio 98.0 2.1E-05 4.6E-10 72.9 8.2 77 65-149 3-81 (262)
34 PRK08563 DNA-directed RNA poly 98.0 1.5E-05 3.3E-10 69.5 6.9 83 65-156 76-174 (187)
35 PRK05807 hypothetical protein; 98.0 3.8E-05 8.3E-10 64.5 8.9 70 69-149 4-74 (136)
36 cd05698 S1_Rrp5_repeat_hs6_sc5 98.0 3.6E-05 7.8E-10 56.1 7.7 67 71-147 1-69 (70)
37 cd05688 S1_RPS1_repeat_ec3 S1_ 97.9 3.9E-05 8.5E-10 54.8 6.7 58 70-138 1-59 (68)
38 cd04461 S1_Rrp5_repeat_hs8_sc7 97.8 0.00011 2.4E-09 55.7 7.7 71 67-147 11-83 (83)
39 TIGR00448 rpoE DNA-directed RN 97.8 7.1E-05 1.5E-09 65.2 7.5 83 65-156 76-174 (179)
40 cd04472 S1_PNPase S1_PNPase: P 97.8 0.00014 3E-09 52.0 7.7 66 71-146 1-67 (68)
41 cd05685 S1_Tex S1_Tex: The C-t 97.8 0.00011 2.3E-09 52.3 6.8 66 71-146 1-68 (68)
42 PTZ00248 eukaryotic translatio 97.8 9.4E-05 2E-09 70.5 8.1 77 65-149 12-90 (319)
43 PRK11824 polynucleotide phosph 97.7 2.9E-05 6.2E-10 80.6 4.9 101 28-149 590-691 (693)
44 cd05695 S1_Rrp5_repeat_hs3 S1_ 97.7 0.00015 3.2E-09 53.2 7.3 64 71-146 1-66 (66)
45 cd05697 S1_Rrp5_repeat_hs5 S1_ 97.7 0.00016 3.5E-09 52.7 7.4 66 71-146 1-68 (69)
46 cd05694 S1_Rrp5_repeat_hs2_sc2 97.7 0.00037 8.1E-09 52.5 8.5 67 69-150 3-71 (74)
47 cd04460 S1_RpoE S1_RpoE: RpoE, 97.6 0.00019 4.2E-09 56.4 6.4 76 72-156 1-92 (99)
48 cd04453 S1_RNase_E S1_RNase_E: 97.6 0.00039 8.6E-09 54.1 8.0 72 68-147 5-81 (88)
49 PRK07400 30S ribosomal protein 97.5 0.00037 7.9E-09 66.2 8.9 73 67-150 193-267 (318)
50 TIGR03591 polynuc_phos polyrib 97.5 7.4E-05 1.6E-09 77.5 4.3 91 28-139 587-678 (684)
51 COG0539 RpsA Ribosomal protein 97.5 0.00032 7E-09 71.0 7.8 74 67-151 189-264 (541)
52 cd05696 S1_Rrp5_repeat_hs4 S1_ 97.4 0.00074 1.6E-08 50.1 7.3 67 71-147 1-71 (71)
53 COG1095 RPB7 DNA-directed RNA 97.4 0.00041 8.9E-09 61.3 6.4 83 65-156 76-174 (183)
54 cd00164 S1_like S1_like: Ribos 97.4 0.00056 1.2E-08 47.4 6.0 55 74-138 1-56 (65)
55 COG1093 SUI2 Translation initi 97.4 0.00048 1E-08 63.9 7.1 133 64-205 5-149 (269)
56 cd04455 S1_NusA S1_NusA: N-uti 97.4 0.0012 2.5E-08 48.4 7.7 53 69-138 2-55 (67)
57 PHA02945 interferon resistance 97.3 0.0011 2.4E-08 52.2 7.0 72 67-149 8-83 (88)
58 TIGR02696 pppGpp_PNP guanosine 97.2 0.0011 2.4E-08 69.1 8.0 72 67-146 644-718 (719)
59 cd05690 S1_RPS1_repeat_ec5 S1_ 97.2 0.0014 3.1E-08 47.2 6.3 59 71-138 1-60 (69)
60 cd04473 S1_RecJ_like S1_RecJ_l 97.1 0.0059 1.3E-07 45.9 9.6 63 67-147 13-76 (77)
61 cd05684 S1_DHX8_helicase S1_DH 97.1 0.0032 6.8E-08 47.1 7.9 72 71-149 1-73 (79)
62 PRK07400 30S ribosomal protein 97.1 0.0019 4E-08 61.4 7.9 75 66-150 27-103 (318)
63 cd05689 S1_RPS1_repeat_ec4 S1_ 96.9 0.0042 9.1E-08 45.4 7.0 61 69-138 2-63 (72)
64 cd04465 S1_RPS1_repeat_ec2_hs2 96.8 0.01 2.2E-07 42.9 8.2 64 71-147 1-66 (67)
65 PTZ00162 DNA-directed RNA poly 96.8 0.0044 9.5E-08 54.3 7.3 84 65-157 76-173 (176)
66 PRK06299 rpsA 30S ribosomal pr 96.8 0.0094 2E-07 60.1 10.6 72 69-150 459-532 (565)
67 PRK13806 rpsA 30S ribosomal pr 96.8 0.0041 8.8E-08 62.3 7.8 73 67-149 199-277 (491)
68 PRK06676 rpsA 30S ribosomal pr 96.7 0.021 4.6E-07 54.9 11.7 72 68-149 275-348 (390)
69 PRK07899 rpsA 30S ribosomal pr 96.7 0.0053 1.1E-07 61.7 7.7 73 68-150 33-107 (486)
70 PRK06676 rpsA 30S ribosomal pr 96.6 0.0083 1.8E-07 57.7 8.6 71 68-149 190-262 (390)
71 PRK13806 rpsA 30S ribosomal pr 96.6 0.0077 1.7E-07 60.3 7.9 72 69-150 378-451 (491)
72 PRK06299 rpsA 30S ribosomal pr 96.5 0.0074 1.6E-07 60.9 7.6 72 69-149 372-445 (565)
73 PRK09202 nusA transcription el 96.4 0.0068 1.5E-07 60.7 6.7 71 64-151 128-202 (470)
74 PRK07899 rpsA 30S ribosomal pr 96.4 0.012 2.6E-07 59.2 8.3 144 68-232 206-370 (486)
75 PRK12269 bifunctional cytidyla 96.3 0.027 6E-07 60.2 10.8 73 68-149 576-650 (863)
76 PRK00087 4-hydroxy-3-methylbut 96.3 0.034 7.4E-07 57.5 11.3 72 69-150 561-634 (647)
77 TIGR00717 rpsA ribosomal prote 96.3 0.04 8.7E-07 54.8 11.0 70 69-148 445-516 (516)
78 PLN00207 polyribonucleotide nu 96.2 0.013 2.8E-07 62.7 7.7 73 67-149 750-824 (891)
79 PRK00087 4-hydroxy-3-methylbut 96.2 0.018 3.9E-07 59.5 8.4 71 68-149 475-547 (647)
80 PRK12327 nusA transcription el 96.1 0.013 2.7E-07 57.0 6.6 109 64-189 128-265 (362)
81 cd04471 S1_RNase_R S1_RNase_R: 96.1 0.032 6.9E-07 41.4 7.4 70 70-146 1-81 (83)
82 TIGR00717 rpsA ribosomal prote 96.1 0.048 1E-06 54.3 10.5 73 68-149 270-344 (516)
83 COG0539 RpsA Ribosomal protein 96.0 0.019 4.1E-07 58.5 7.2 71 69-149 276-348 (541)
84 PRK12269 bifunctional cytidyla 95.9 0.06 1.3E-06 57.7 10.9 75 68-150 750-827 (863)
85 TIGR01953 NusA transcription t 95.8 0.021 4.6E-07 55.0 6.6 109 64-189 125-263 (341)
86 cd04462 S1_RNAPII_Rpb7 S1_RNAP 94.6 0.21 4.5E-06 38.9 7.6 78 70-153 1-88 (88)
87 PRK12329 nusA transcription el 94.3 0.11 2.4E-06 51.8 6.7 76 64-151 146-227 (449)
88 PRK12328 nusA transcription el 94.2 0.12 2.5E-06 50.6 6.5 71 64-151 132-208 (374)
89 PF01016 Ribosomal_L27: Riboso 93.3 0.23 4.9E-06 38.7 5.4 53 3-58 26-80 (81)
90 TIGR00757 RNaseEG ribonuclease 92.9 0.35 7.5E-06 47.8 7.5 69 55-134 13-93 (414)
91 KOG1070|consensus 92.5 0.15 3.3E-06 56.8 4.7 77 63-147 878-955 (1710)
92 CHL00121 rpl27 ribosomal prote 92.5 0.27 5.9E-06 38.7 4.9 56 3-61 27-84 (86)
93 COG2183 Tex Transcriptional ac 92.3 0.29 6.4E-06 51.7 6.4 75 68-152 656-732 (780)
94 PRK05435 rpmA 50S ribosomal pr 92.3 0.38 8.2E-06 37.6 5.4 43 3-45 27-71 (82)
95 COG1185 Pnp Polyribonucleotide 89.5 0.86 1.9E-05 47.7 6.6 73 67-149 616-689 (692)
96 cd05699 S1_Rrp5_repeat_hs7 S1_ 89.1 2.2 4.7E-05 32.6 6.9 58 71-135 1-60 (72)
97 KOG1070|consensus 88.4 2 4.2E-05 48.5 8.6 71 69-149 1161-1233(1710)
98 TIGR00062 L27 ribosomal protei 85.6 1.9 4.1E-05 33.8 4.9 43 3-45 27-71 (83)
99 KOG1856|consensus 83.3 1 2.2E-05 49.5 3.4 78 68-152 983-1062(1299)
100 TIGR02063 RNase_R ribonuclease 82.4 4.9 0.00011 42.2 7.9 72 68-146 625-707 (709)
101 PRK11712 ribonuclease G; Provi 82.1 3.7 8.1E-05 41.6 6.7 60 67-134 35-106 (489)
102 PF09297 zf-NADH-PPase: NADH p 81.8 0.63 1.4E-05 29.5 0.7 23 158-180 5-30 (32)
103 PRK11642 exoribonuclease R; Pr 81.7 5.3 0.00011 42.9 7.9 72 69-147 642-724 (813)
104 PF07754 DUF1610: Domain of un 80.3 0.69 1.5E-05 28.2 0.5 20 160-179 3-24 (24)
105 PF15616 TerY-C: TerY-C metal 79.5 1.3 2.8E-05 37.4 2.1 41 156-202 89-130 (131)
106 PRK10811 rne ribonuclease E; R 79.3 4.9 0.00011 44.0 6.7 59 68-134 36-103 (1068)
107 KOG4600|consensus 78.9 5.2 0.00011 34.2 5.4 65 3-69 54-120 (144)
108 TIGR01384 TFS_arch transcripti 77.5 0.69 1.5E-05 36.6 -0.2 29 158-186 2-31 (104)
109 PHA02858 EIF2a-like PKR inhibi 77.0 18 0.00038 28.6 7.5 69 67-146 13-84 (86)
110 PF01959 DHQS: 3-dehydroquinat 76.4 19 0.00042 35.2 9.3 89 6-135 246-336 (354)
111 PF01336 tRNA_anti-codon: OB-f 73.9 27 0.00059 24.6 7.5 62 74-147 3-69 (75)
112 PRK02290 3-dehydroquinate synt 72.5 27 0.00058 34.1 9.2 88 6-134 236-325 (344)
113 PLN00208 translation initiatio 72.0 8.1 0.00018 33.3 4.9 55 66-136 27-82 (145)
114 PRK08402 replication factor A; 71.9 27 0.00058 34.1 9.1 54 153-213 209-265 (355)
115 COG0211 RpmA Ribosomal protein 71.5 9.3 0.0002 30.1 4.7 56 3-61 27-84 (87)
116 PF13509 S1_2: S1 domain; PDB: 71.0 25 0.00053 25.3 6.7 60 70-147 1-60 (61)
117 TIGR00358 3_prime_RNase VacB a 69.5 18 0.0004 37.7 7.9 72 68-146 570-652 (654)
118 COG1645 Uncharacterized Zn-fin 69.4 1.8 4E-05 36.6 0.5 25 158-182 30-55 (131)
119 PF02150 RNA_POL_M_15KD: RNA p 67.5 2.4 5.2E-05 27.7 0.7 25 158-182 3-31 (35)
120 COG1571 Predicted DNA-binding 66.1 17 0.00038 36.3 6.6 62 120-182 311-378 (421)
121 KOG3298|consensus 64.9 20 0.00044 31.5 6.0 85 65-155 76-170 (170)
122 PTZ00329 eukaryotic translatio 64.8 13 0.00029 32.3 4.8 54 66-135 27-81 (155)
123 COG1315 Uncharacterized conser 63.4 11 0.00023 38.6 4.6 48 19-74 220-270 (543)
124 cd05790 S1_Rrp40 S1_Rrp40: Rrp 62.2 11 0.00024 29.5 3.5 30 64-94 46-75 (86)
125 PRK12366 replication factor A; 60.8 7.9 0.00017 40.4 3.3 49 157-212 533-582 (637)
126 PF03961 DUF342: Protein of un 60.3 20 0.00044 35.5 5.9 35 19-61 144-181 (451)
127 PRK00420 hypothetical protein; 58.3 4.7 0.0001 33.2 0.9 28 157-184 24-53 (112)
128 COG1594 RPB9 DNA-directed RNA 57.3 5.7 0.00012 32.5 1.3 28 157-184 3-35 (113)
129 PF09723 Zn-ribbon_8: Zinc rib 56.5 5.7 0.00012 26.7 0.9 27 158-184 7-39 (42)
130 COG2996 Predicted RNA-bindinin 56.4 44 0.00096 31.8 7.1 57 100-166 177-242 (287)
131 COG1110 Reverse gyrase [DNA re 55.7 18 0.00038 40.2 4.9 74 126-205 653-746 (1187)
132 smart00652 eIF1a eukaryotic tr 54.0 28 0.00062 26.9 4.6 54 68-137 2-57 (83)
133 PRK04012 translation initiatio 53.9 30 0.00066 27.8 4.9 57 66-138 16-74 (100)
134 PRK04012 translation initiatio 53.6 25 0.00054 28.3 4.4 54 6-82 15-74 (100)
135 PRK13922 rod shape-determining 53.4 82 0.0018 28.9 8.4 97 31-136 118-227 (276)
136 smart00834 CxxC_CXXC_SSSS Puta 53.2 8.2 0.00018 24.9 1.3 26 158-183 7-38 (41)
137 PF04085 MreC: rod shape-deter 52.9 22 0.00048 30.1 4.2 64 73-136 35-106 (152)
138 smart00661 RPOL9 RNA polymeras 47.9 7.4 0.00016 26.5 0.4 25 158-182 2-31 (52)
139 cd05791 S1_CSL4 S1_CSL4: CSL4, 46.8 23 0.00051 27.5 3.2 23 69-91 62-85 (92)
140 cd04456 S1_IF1A_like S1_IF1A_l 46.1 34 0.00075 26.2 3.9 49 74-137 2-52 (78)
141 COG1545 Predicted nucleic-acid 46.0 8.4 0.00018 32.5 0.6 36 151-188 24-63 (140)
142 COG2816 NPY1 NTP pyrophosphohy 45.3 8 0.00017 36.6 0.4 27 158-184 113-142 (279)
143 PRK14351 ligA NAD-dependent DN 45.2 68 0.0015 34.0 7.2 63 121-185 386-456 (689)
144 TIGR00523 eIF-1A eukaryotic/ar 45.2 41 0.00089 27.0 4.4 57 67-138 13-72 (99)
145 PF10246 MRP-S35: Mitochondria 44.7 1.1E+02 0.0023 25.1 6.6 50 68-134 21-70 (104)
146 TIGR00100 hypA hydrogenase nic 43.6 17 0.00038 29.5 2.1 27 155-181 69-96 (115)
147 COG2888 Predicted Zn-ribbon RN 42.9 18 0.00039 26.8 1.8 20 160-179 32-58 (61)
148 PRK14890 putative Zn-ribbon RN 42.8 10 0.00022 28.0 0.5 21 160-180 12-34 (59)
149 PF03604 DNA_RNApol_7kD: DNA d 41.9 15 0.00032 23.7 1.1 22 159-180 3-26 (32)
150 smart00293 PWWP domain with co 41.9 18 0.0004 26.0 1.7 11 125-135 1-11 (63)
151 PRK12380 hydrogenase nickel in 41.5 19 0.00042 29.2 2.0 26 155-180 69-95 (113)
152 TIGR02605 CxxC_CxxC_SSSS putat 41.1 15 0.00034 25.1 1.2 27 158-184 7-39 (52)
153 PF06677 Auto_anti-p27: Sjogre 40.1 16 0.00035 24.8 1.1 23 156-178 17-41 (41)
154 PF01927 Mut7-C: Mut7-C RNAse 39.7 10 0.00023 31.9 0.2 17 153-169 88-105 (147)
155 PF07497 Rho_RNA_bind: Rho ter 39.4 59 0.0013 25.1 4.3 44 54-97 29-75 (78)
156 PF01176 eIF-1a: Translation i 39.4 71 0.0015 23.2 4.6 51 72-137 3-54 (65)
157 PRK00432 30S ribosomal protein 39.4 9.9 0.00021 26.8 -0.0 26 156-181 20-47 (50)
158 cd05793 S1_IF1A S1_IF1A: Trans 39.3 46 0.00099 25.4 3.7 47 74-135 2-49 (77)
159 cd04482 RPA2_OBF_like RPA2_OBF 39.1 1.5E+02 0.0033 22.8 6.7 20 120-139 43-64 (91)
160 PRK14350 ligA NAD-dependent DN 38.8 90 0.002 33.0 6.9 63 121-185 361-430 (669)
161 TIGR00219 mreC rod shape-deter 38.8 68 0.0015 30.1 5.5 64 73-136 156-228 (283)
162 PF12508 DUF3714: Protein of u 38.4 1.9E+02 0.004 26.1 8.0 58 28-94 50-111 (200)
163 PRK00398 rpoP DNA-directed RNA 38.2 23 0.0005 23.9 1.7 25 157-181 4-31 (46)
164 COG1656 Uncharacterized conser 37.8 13 0.00028 32.7 0.5 27 154-180 95-139 (165)
165 PF14446 Prok-RING_1: Prokaryo 37.8 12 0.00025 27.2 0.2 33 157-189 6-39 (54)
166 KOG1067|consensus 37.6 55 0.0012 34.3 4.9 72 67-148 660-737 (760)
167 COG1530 CafA Ribonucleases G a 37.5 51 0.0011 33.4 4.7 59 68-134 35-97 (487)
168 PTZ00329 eukaryotic translatio 37.3 74 0.0016 27.7 5.0 63 5-92 25-93 (155)
169 smart00659 RPOLCX RNA polymera 37.0 22 0.00048 24.4 1.4 25 158-182 4-30 (44)
170 PF10447 EXOSC1: Exosome compo 36.9 31 0.00068 26.7 2.4 13 69-81 70-82 (82)
171 KOG2916|consensus 36.8 56 0.0012 31.1 4.5 77 65-149 11-89 (304)
172 PRK00276 infA translation init 36.8 1.1E+02 0.0025 22.6 5.4 49 74-136 9-58 (72)
173 KOG1885|consensus 36.1 1.1E+02 0.0023 31.5 6.6 144 66-219 101-258 (560)
174 PF07334 IFP_35_N: Interferon- 35.8 15 0.00033 28.3 0.6 16 241-256 2-17 (76)
175 PF01155 HypA: Hydrogenase exp 35.7 16 0.00034 29.7 0.6 27 155-181 69-96 (113)
176 CHL00010 infA translation init 35.4 1.1E+02 0.0024 23.1 5.3 49 74-136 9-58 (78)
177 cd05840 SPBC215_ISWI_like The 35.2 26 0.00055 27.6 1.8 11 125-135 1-11 (93)
178 COG0361 InfA Translation initi 35.1 67 0.0014 24.7 3.9 52 71-136 6-58 (75)
179 PF09845 DUF2072: Zn-ribbon co 34.9 14 0.00031 31.3 0.3 23 158-180 3-28 (131)
180 PRK12495 hypothetical protein; 34.8 13 0.00029 34.1 0.1 30 153-182 39-69 (226)
181 PF04805 Pox_E10: E10-like pro 34.7 5.9 0.00013 30.0 -1.8 28 161-188 5-32 (70)
182 cd05841 BS69_related The PWWP 34.7 27 0.0006 27.2 1.8 16 122-137 4-20 (83)
183 cd04497 hPOT1_OB1_like hPOT1_O 34.4 2.1E+02 0.0045 23.6 7.2 16 122-137 66-82 (138)
184 cd05834 HDGF_related The PWWP 34.3 27 0.00059 26.8 1.7 14 124-137 2-16 (83)
185 PF01938 TRAM: TRAM domain; I 34.3 67 0.0015 22.5 3.7 24 67-90 37-60 (61)
186 PRK11032 hypothetical protein; 34.1 23 0.00049 30.9 1.4 29 152-182 122-153 (160)
187 PRK03681 hypA hydrogenase nick 33.9 29 0.00063 28.2 2.0 27 155-181 69-97 (114)
188 cd05836 N_Pac_NP60 The PWWP do 33.3 28 0.00061 26.9 1.7 11 125-135 1-11 (86)
189 KOG3416|consensus 33.1 54 0.0012 27.8 3.4 43 120-163 57-109 (134)
190 COG2932 Predicted transcriptio 33.1 2.3E+02 0.0049 24.9 7.6 68 6-83 136-211 (214)
191 PF08810 KapB: Kinase associat 32.5 1.1E+02 0.0024 25.3 5.0 30 74-107 6-35 (112)
192 PRK03824 hypA hydrogenase nick 32.1 37 0.00081 28.4 2.4 27 155-181 69-117 (135)
193 PRK12442 translation initiatio 32.0 1.2E+02 0.0026 24.0 5.0 50 74-137 9-59 (87)
194 cd04476 RPA1_DBD_C RPA1_DBD_C: 32.0 86 0.0019 26.4 4.6 54 153-212 31-87 (166)
195 PHA03005 sulfhydryl oxidase; P 30.5 10 0.00022 30.4 -1.2 29 160-188 29-57 (96)
196 TIGR00008 infA translation ini 30.4 1.4E+02 0.0029 22.5 4.9 49 74-136 7-56 (68)
197 PF08292 RNA_pol_Rbc25: RNA po 30.3 82 0.0018 26.1 4.1 63 68-134 1-70 (122)
198 PF14803 Nudix_N_2: Nudix N-te 30.1 18 0.00039 23.6 0.1 23 158-180 2-31 (34)
199 PF07295 DUF1451: Protein of u 29.1 35 0.00077 29.2 1.8 29 152-182 110-141 (146)
200 smart00532 LIGANc Ligase N fam 28.8 1.6E+02 0.0035 29.5 6.6 65 121-186 359-434 (441)
201 cd05162 PWWP The PWWP domain, 28.5 39 0.00084 25.5 1.7 11 125-135 1-11 (87)
202 PRK00564 hypA hydrogenase nick 28.2 32 0.0007 28.1 1.3 27 155-181 70-98 (117)
203 PF09953 DUF2187: Uncharacteri 27.7 1.3E+02 0.0028 22.0 4.2 22 74-95 16-37 (57)
204 KOG4134|consensus 27.3 45 0.00098 31.0 2.2 61 64-139 101-162 (253)
205 COG0375 HybF Zn finger protein 27.2 32 0.0007 28.5 1.1 25 156-180 70-95 (115)
206 PTZ00248 eukaryotic translatio 27.1 1.5E+02 0.0032 28.7 5.7 98 10-137 18-116 (319)
207 PF12172 DUF35_N: Rubredoxin-l 26.5 57 0.0012 20.9 2.0 28 151-180 6-34 (37)
208 cd05835 Dnmt3b_related The PWW 26.2 44 0.00095 25.7 1.7 11 125-135 1-11 (87)
209 PF07282 OrfB_Zn_ribbon: Putat 25.9 23 0.00051 25.5 0.1 30 158-187 30-62 (69)
210 KOG3297|consensus 25.8 1.7E+02 0.0037 26.5 5.4 29 67-95 78-106 (202)
211 PF00855 PWWP: PWWP domain; I 25.5 41 0.00089 24.9 1.4 11 125-135 1-11 (86)
212 PF07494 Reg_prop: Two compone 24.2 56 0.0012 19.1 1.5 15 195-209 7-21 (24)
213 COG3364 Zn-ribbon containing p 24.2 21 0.00046 29.2 -0.5 58 158-215 4-81 (112)
214 PF10844 DUF2577: Protein of u 23.7 1E+02 0.0022 24.3 3.4 62 69-134 15-86 (100)
215 PF13240 zinc_ribbon_2: zinc-r 23.7 30 0.00066 20.5 0.3 18 160-179 4-21 (23)
216 PRK07956 ligA NAD-dependent DN 23.5 2.6E+02 0.0056 29.6 7.2 66 121-187 364-441 (665)
217 PF09538 FYDLN_acid: Protein o 23.1 35 0.00076 27.8 0.6 36 148-184 2-39 (108)
218 COG0272 Lig NAD-dependent DNA 22.9 2.6E+02 0.0055 29.9 6.9 54 122-176 365-427 (667)
219 PF04319 NifZ: NifZ domain; I 22.5 1.9E+02 0.0041 22.3 4.4 38 121-159 1-45 (75)
220 COG3357 Predicted transcriptio 22.3 38 0.00083 27.2 0.6 30 149-178 51-83 (97)
221 PF13375 RnfC_N: RnfC Barrel s 22.2 67 0.0015 25.7 2.1 15 31-45 67-81 (101)
222 TIGR00074 hypC_hupF hydrogenas 22.0 1.6E+02 0.0034 22.6 3.9 39 76-134 7-45 (76)
223 COG0777 AccD Acetyl-CoA carbox 22.0 40 0.00087 32.1 0.8 29 155-183 27-59 (294)
224 PRK14810 formamidopyrimidine-D 21.7 44 0.00095 31.1 1.1 22 158-179 246-272 (272)
225 PF09926 DUF2158: Uncharacteri 20.8 65 0.0014 23.0 1.5 24 125-151 1-24 (53)
226 PF01455 HupF_HypC: HupF/HypC 20.7 2.3E+02 0.0051 21.0 4.6 41 74-134 5-47 (68)
227 PF13742 tRNA_anti_2: OB-fold 20.6 4.1E+02 0.009 20.6 6.6 65 72-148 24-95 (99)
228 PRK05054 exoribonuclease II; P 20.3 2.3E+02 0.0049 29.8 6.0 64 68-138 557-633 (644)
No 1
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1e-44 Score=315.53 Aligned_cols=179 Identities=24% Similarity=0.356 Sum_probs=167.1
Q ss_pred CCCeEecCCcccCCCCCeeeCCCEEEeCCEEEEEEeeEEEEeccccCCCcceEEEEeeCCCccccCCCCCEEEEEEEEEe
Q psy6276 3 NPPICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQ 82 (271)
Q Consensus 3 ~~~iVlPGD~L~~~eE~~~~G~GtY~~~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~~~yiP~vGDIVIGrVt~V~ 82 (271)
++.+|+|||.|+..|| |++|.|||+++|.|+|+.+|.+.+|. ++++++|.|.+..+.+|+.||+|+|+|+++.
T Consensus 4 ~g~~v~PGd~~a~~EE-~~~G~gt~~~~g~i~Aa~~G~~~~d~------~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~ 76 (188)
T COG1096 4 DGTFVLPGDVLAVIEE-FLPGEGTYEEGGEIRAAATGVVRRDD------KNRVISVKPGKKTPPLPKGGDIVYGRVTDVR 76 (188)
T ss_pred cCcEEcCcceeeeeee-eecCCCeEeECCEEEEeecccEEEcc------cceEEEeccCCCCCCCCCCCCEEEEEEeecc
Confidence 3589999999999999 99999999999999999999999998 7899999998666999999999999999999
Q ss_pred cceEEEEEeeecCc--ccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCceeeeeccCCCeeEEEEc
Q psy6276 83 QHLCKAHVISVGNT--ALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQLSTAENELGVVIALS 159 (271)
Q Consensus 83 ~~~a~VdI~~v~~~--~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~LST~~~eLGVV~A~c 159 (271)
.+.|.|+|.++++. .+..++.|.||+|+++... ..+++++|+|||||+|+ +|++ .+|.|||++++||||+|+|
T Consensus 77 ~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~--~~~~~d~f~~GDivrA~Vis~~--~~~~Lst~~~dlGVI~A~C 152 (188)
T COG1096 77 EQRALVRIVGVEGKERELATSGAADIHVSQVRDGY--VEKLSDAFRIGDIVRARVISTG--DPIQLSTKGNDLGVIYARC 152 (188)
T ss_pred ceEEEEEEEEEecccccCCCCceeeEEEEeccccc--ccccccccccccEEEEEEEecC--CCeEEEecCCcceEEEEEc
Confidence 99999999999994 4889999999999998754 45788999999999999 9987 5799999999999999999
Q ss_pred -cCCCeeEeccCccCchhhhhhhhhhhHHHhccc
Q psy6276 160 -EAASLFRSSEKLTNDIEFLKQEKLKLYEELSSS 192 (271)
Q Consensus 160 -~cG~~Mvp~s~~~~c~~~~~~e~rKla~~~~s~ 192 (271)
+||.+|++.+..++||+|+.+|+||+|.++.+.
T Consensus 153 srC~~~L~~~~~~l~Cp~Cg~tEkRKia~~y~~~ 186 (188)
T COG1096 153 SRCRAPLVKKGNMLKCPNCGNTEKRKIAKDYGKV 186 (188)
T ss_pred cCCCcceEEcCcEEECCCCCCEEeeeeccccccc
Confidence 999999998899999999999999999997553
No 2
>KOG3409|consensus
Probab=100.00 E-value=5.2e-44 Score=307.31 Aligned_cols=184 Identities=34% Similarity=0.587 Sum_probs=167.2
Q ss_pred CCCCeEecCCcccCCCCCeeeCCCEEEeCCEEEEEEeeEEEEeccccCCCcceEEEEeeCCCccccCCCCCEEEEEEEEE
Q psy6276 2 SNPPICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAV 81 (271)
Q Consensus 2 ~~~~iVlPGD~L~~~eE~~~~G~GtY~~~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~~~yiP~vGDIVIGrVt~V 81 (271)
..-.+|+|||+++..++.+..|.|||..+++|+||.+|..-+++ ..+...++++........+|.+||||++||+++
T Consensus 3 ~a~~~~lpG~~~c~~e~~~~~g~Gtye~~~yI~aS~ag~~~~~~---~~~~~~v~~~~~~~~~~~LP~~G~IVtarV~~i 79 (193)
T KOG3409|consen 3 LAETLVLPGEVVCRAEGEYRMGEGTYERNGYIFASVAGVNFRDN---LVQKIEVVSVEKQLFNELLPFVGAIVTARVSRI 79 (193)
T ss_pred cceEEEcccceeeecccccccccceeecCCeEEeccccceeecC---CccceeeeeecccchhhcCCccCcEEEEEEEee
Confidence 34468999999998775599999999999999999999655543 233455666665455789999999999999999
Q ss_pred ecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCceeeeeccCCCeeEEEEc-
Q psy6276 82 QQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQLSTAENELGVVIALS- 159 (271)
Q Consensus 82 ~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~LST~~~eLGVV~A~c- 159 (271)
+.++|+|+|+++++.+|..+|+|+||.+|+|++++|+++.+++|+|||||+|+ ||++++.+|+|||++++||||+|++
T Consensus 80 ~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LTtAeneLGVV~a~as 159 (193)
T KOG3409|consen 80 NLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLTTAENELGVVFARAS 159 (193)
T ss_pred ccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcEEEEEecccceEEEEecc
Confidence 99999999999999999999999999999999999999999999999999999 9999999999999999999999999
Q ss_pred cCCCeeEeccC-ccCchhhhhhhhhhhHHH
Q psy6276 160 EAASLFRSSEK-LTNDIEFLKQEKLKLYEE 188 (271)
Q Consensus 160 ~cG~~Mvp~s~-~~~c~~~~~~e~rKla~~ 188 (271)
+.|.+|+|++| .+.||.++++|.||.||=
T Consensus 160 ~~g~~M~pvdw~~mqsp~Tg~tE~RK~AKv 189 (193)
T KOG3409|consen 160 ETGEPMVPVDWQEMQSPKTGKTEPRKCAKV 189 (193)
T ss_pred ccCCceeeccceeEEcCccCcccchhhccC
Confidence 99999999998 899999999999999984
No 3
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=100.00 E-value=7.4e-42 Score=299.13 Aligned_cols=179 Identities=22% Similarity=0.344 Sum_probs=163.8
Q ss_pred CCCeEecCCcccCCCCCeeeCCCEEEeCCEEEEEEeeEEEEeccccCCCcceEEEEeeCCCccccCCCCCEEEEEEEEEe
Q psy6276 3 NPPICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQ 82 (271)
Q Consensus 3 ~~~iVlPGD~L~~~eE~~~~G~GtY~~~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~~~yiP~vGDIVIGrVt~V~ 82 (271)
++.+|+|||.|++.++ |++|+|||+++|+|||+++|.+++|. .++.|+|.|.....|.|++||+|+|+|+++.
T Consensus 4 ~~~~V~PGe~l~~~~e-~~~G~Gty~~~~~i~as~~G~~~id~------~~~~Isv~P~~~~~~~~~~GdiV~GkV~~i~ 76 (189)
T PRK09521 4 QGDLVLPGDYLAVIEE-YLPGEGTYEDNGEVYASVVGKVFIDD------INRKISVIPFKKTPPLLKKGDIVYGRVVDVK 76 (189)
T ss_pred cCCEECCCCccccccc-eEcCCCEEeeCCEEEEEeeEEEEEcC------CCCEEEEecCcCCCCCCCCCCEEEEEEEEEc
Confidence 4579999999999888 99999999999999999999999986 5689999998555899999999999999999
Q ss_pred cceEEEEEeeec--CcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCceeeeeccCCCeeEEEEc
Q psy6276 83 QHLCKAHVISVG--NTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQLSTAENELGVVIALS 159 (271)
Q Consensus 83 ~~~a~VdI~~v~--~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~LST~~~eLGVV~A~c 159 (271)
++.|.|+|.+++ ++++..++.|++|.++++..+ ..+|+++|++||+|+|+ ++++ +.+.|||++++||||+|.|
T Consensus 77 ~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~--~~~~~~~~~~GD~V~akV~~i~--~~i~LS~k~~~lGvv~a~~ 152 (189)
T PRK09521 77 EQRALVRIVSIEGSERELATSKLAYIHISQVSDGY--VESLTDAFKIGDIVRAKVISYT--DPLQLSTKGKDLGVIYAMC 152 (189)
T ss_pred CCeEEEEEEEecccccccCCCceeeEEhhHcChhh--hhhHHhccCCCCEEEEEEEecC--CcEEEEEecCCceEEEEEc
Confidence 999999999887 677888899999999987643 34799999999999999 8887 6899999999999999999
Q ss_pred -cCCCeeEecc-CccCchhhhhhhhhhhHHHhccc
Q psy6276 160 -EAASLFRSSE-KLTNDIEFLKQEKLKLYEELSSS 192 (271)
Q Consensus 160 -~cG~~Mvp~s-~~~~c~~~~~~e~rKla~~~~s~ 192 (271)
+||.+|+|.+ ..+.||+|++.|+||+|++++..
T Consensus 153 ~~~g~~~~~~~~~~~~c~~~~~~e~rkva~~~~~~ 187 (189)
T PRK09521 153 SRCRTPLVKKGENELKCPNCGNIETRKLSSYYGKG 187 (189)
T ss_pred cccCCceEECCCCEEECCCCCCEEeeccchhhccc
Confidence 7999999999 59999999999999999998644
No 4
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=100.00 E-value=8.4e-33 Score=249.99 Aligned_cols=218 Identities=21% Similarity=0.341 Sum_probs=165.9
Q ss_pred CCCCCeEecCCcccCCCCCeeeCCCEEEeCCEEEEEEeeEEEEeccccCCCcceEEEEeeCCCccccCCCCCEEEEEEEE
Q psy6276 1 MSNPPICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMA 80 (271)
Q Consensus 1 M~~~~iVlPGD~L~~~eE~~~~G~GtY~~~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~~~yiP~vGDIVIGrVt~ 80 (271)
|.++.+|+|||.|+ .++ |.+|+|||.++|.|+||++|.+.+++ +.++|+|. +.+|+|++||+|+|+|++
T Consensus 5 ~~~~~~V~PGd~l~-~~~-~~~G~Gty~~~g~i~As~~G~~~~~~--------~~i~V~p~-~~~y~P~vGDiViG~V~~ 73 (235)
T PRK04163 5 VEDRKIVVPGDLLA-EGE-FKAGRGTYKENGKIYSTVVGLVDIKD--------DKVRVIPL-EGKYIPKVGDLVIGKVTD 73 (235)
T ss_pred eeCCcEECCCCCcC-cCC-eecCCceEEeCCEEEEEEeEEEEEEC--------CEEEEEEC-CCcccCCCCCEEEEEEEE
Confidence 56778999999997 456 99999999999999999999999986 59999997 567999999999999999
Q ss_pred EecceEEEEEeeecCcccCCceeeEEeccccccc--hhhhHhhhcCCCCCCEEEEE-EecCCCCceeeeeccCCCeeEEE
Q psy6276 81 VQQHLCKAHVISVGNTALSRTFRALLRRENVRAT--EIDRIEMYKCYRPGDIILAR-LPLKELHSYQLSTAENELGVVIA 157 (271)
Q Consensus 81 V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~t--e~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~LST~~~eLGVV~A 157 (271)
+.++.|+|+|. .+|.|+||.++++.. +.|..+|+++|++||+|+|| +++++...+.|||++++||++.
T Consensus 74 i~~~~~~vdI~--------~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~~~lG~L~- 144 (235)
T PRK04163 74 VTFSGWEVDIN--------SPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGKGLGKIE- 144 (235)
T ss_pred EeCceEEEEeC--------CCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcCCCCCccC-
Confidence 99999999994 578999999999764 34678999999999999999 9987666799999999999996
Q ss_pred EccCCCeeEeccCccCchhhhhh--hhhhhHHHhcccccceeeeeeccCceEEEeEeeccccceeeeeehhhhccccCch
Q psy6276 158 LSEAASLFRSSEKLTNDIEFLKQ--EKLKLYEELSSSQKENEILRQTTGDLEVRLMQMNEVKGEMEFKIKELNKKNQSES 235 (271)
Q Consensus 158 ~c~cG~~Mvp~s~~~~c~~~~~~--e~rKla~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 (271)
++.++.+.... +++. ..-++-+.+. ...-++|+.|.||++||.+-....+.-- .-.|+.+..+ ..-+
T Consensus 145 ----~G~~~~V~~~~----i~~lig~~g~~i~~l~-~~~~~~I~ig~NG~VwI~~~~~~~~~~a-~~~I~~~e~~-~~~~ 213 (235)
T PRK04163 145 ----GGTIVEIKPVK----VPRVIGKKGSMINMLK-EETGCDIIVGQNGRIWIKGPDEEDEEIA-IEAIKKIERE-AHTS 213 (235)
T ss_pred ----CCEEEEECHHH----HHhhcCCCChhHhhhh-hhhCcEEEEcCCcEEEEeeCCHHHHHHH-HHHHHHHHhh-hhcc
Confidence 34444443100 0000 0112334442 2457889999999999998765433221 1124444332 2345
Q ss_pred hhhhHHHhhhcccc
Q psy6276 236 KLSDTIRELNEENI 249 (271)
Q Consensus 236 ~~~~~~~~~~~~~~ 249 (271)
-|.|.++++-|+-.
T Consensus 214 ~l~~~v~~~~~~~~ 227 (235)
T PRK04163 214 GLTDRIKEFLEEEL 227 (235)
T ss_pred ChHHHHHHHHHHhh
Confidence 77888887766543
No 5
>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=2.8e-32 Score=245.89 Aligned_cols=184 Identities=21% Similarity=0.290 Sum_probs=151.9
Q ss_pred CCCeEecCCcccCCCCCeeeCCCEEEeCCEEEEEEeeEEEEeccccCCCcceEEEEeeCCCccccCCCCCEEEEEEEEEe
Q psy6276 3 NPPICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQ 82 (271)
Q Consensus 3 ~~~iVlPGD~L~~~eE~~~~G~GtY~~~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~~~yiP~vGDIVIGrVt~V~ 82 (271)
.+++|+|||.|.+.+. +..|+|||.++++|||+++|.+.+.+ +.+.|+|+ +++|+|++||+|||+|++|.
T Consensus 7 ~~~iV~PGd~vl~~~~-~~~G~Gty~~~~~iyssv~G~~~~~~--------~~v~VIpl-~g~YiP~~gD~VIG~I~~v~ 76 (239)
T COG1097 7 MRKIVLPGDLVLAEGS-YKLGHGTYFEGGKIYSSVVGLLDVKG--------KLVRVIPL-EGRYIPEVGDVVIGKIIEVG 76 (239)
T ss_pred ccceecCCCccCCCCC-EecCCCcEecCCEEEEEEEeEEEEeC--------CEEEEEeC-CCcccCCCCCEEEEEEEEEc
Confidence 4579999998777676 99999999999999999999999987 78999997 67999999999999999999
Q ss_pred cceEEEEEeeecCcccCCceeeEEecccc--ccchhhhHhhhcCCCCCCEEEEE-EecCCCCceeeeeccCCCeeEEEEc
Q psy6276 83 QHLCKAHVISVGNTALSRTFRALLRRENV--RATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQLSTAENELGVVIALS 159 (271)
Q Consensus 83 ~~~a~VdI~~v~~~~L~~~f~GiLr~sdv--r~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~LST~~~eLGVV~A~c 159 (271)
++.|+|||. ++|.|.|+.+++ |..+.++.+|+++|++||+|+|| .+++....+.|++++..||.+.
T Consensus 77 ~~~W~VDI~--------sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~~GkL~--- 145 (239)
T COG1097 77 PSGWKVDIG--------SPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLGKLK--- 145 (239)
T ss_pred ccceEEEcC--------CccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCceEEEeecCCCcccc---
Confidence 999999997 688999999888 45566788999999999999999 8887778899999999999986
Q ss_pred cCCCeeEeccCccCchhhhhhhhhhhHHHhcccccceeeeeeccCceEEEeEe
Q psy6276 160 EAASLFRSSEKLTNDIEFLKQEKLKLYEELSSSQKENEILRQTTGDLEVRLMQ 212 (271)
Q Consensus 160 ~cG~~Mvp~s~~~~c~~~~~~e~rKla~~~~s~~~~~~~~~~~~~~~~~~~~~ 212 (271)
++.|+.+.+...+.--++.-. +.+-| -....++|+.|.||++||++-.
T Consensus 146 --~G~iv~i~p~kVpRvig~~~s--m~~~l-~~~~~~~I~VG~NG~IWV~~~~ 193 (239)
T COG1097 146 --NGQIVKIPPSKVPRVIGKKGS--MLNML-KEKTGCEIIVGQNGRIWVDGEN 193 (239)
T ss_pred --CCEEEEEchhhcceEecCCCc--HHHHh-hhhcCeEEEEecCCEEEecCCC
Confidence 566666665444332222211 11222 2346899999999999998753
No 6
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.94 E-value=2.8e-27 Score=185.96 Aligned_cols=91 Identities=47% Similarity=0.902 Sum_probs=88.1
Q ss_pred cccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCce
Q psy6276 65 VIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSY 143 (271)
Q Consensus 65 ~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~ 143 (271)
.|+|++||+|+|+|++++.++|.|+|.+++++++.++|.|+||.+|+++++.|+.+|+++|+|||+|+|| +|++++++|
T Consensus 1 ~~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~~ 80 (92)
T cd05791 1 LVLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSY 80 (92)
T ss_pred CCCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCCc
Confidence 3789999999999999999999999999999999999999999999999999999999999999999999 999988899
Q ss_pred eeeeccCCCeeE
Q psy6276 144 QLSTAENELGVV 155 (271)
Q Consensus 144 ~LST~~~eLGVV 155 (271)
+|||++++||||
T Consensus 81 ~Lst~~~~lGVv 92 (92)
T cd05791 81 YLSTAENELGVV 92 (92)
T ss_pred EEEecCCCCccC
Confidence 999999999996
No 7
>KOG3013|consensus
Probab=99.94 E-value=7e-27 Score=212.18 Aligned_cols=178 Identities=26% Similarity=0.354 Sum_probs=143.2
Q ss_pred CeEecCCcccCCCCCeeeCCCEEEeCCEEEEEEeeEEEEeccccCCCcceEEEEeeCCCccccCCCCCEEEEEEEEEecc
Q psy6276 5 PICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQQH 84 (271)
Q Consensus 5 ~iVlPGD~L~~~eE~~~~G~GtY~~~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~~~yiP~vGDIVIGrVt~V~~~ 84 (271)
.+|+||+.+...+. |+.|||||+.||.|+||++|.+...+ ++|+|+|+ +.+|.|++||+|+|||+.|.++
T Consensus 30 ~ivtPG~~V~~d~~-fmRGHGTy~~d~~i~ssvaG~v~rvN--------kLi~V~pl-k~rY~pEvGDvVVgRV~eVq~K 99 (301)
T KOG3013|consen 30 TIVTPGELVTDDPG-FMRGHGTYVRDGEIYSSVAGVVQRVN--------KLISVKPL-KSRYAPEVGDVVVGRVIEVQQK 99 (301)
T ss_pred eeecCCccccCchh-hhhcccceecCCeEEEeecchhhhhc--------ceEEEeeh-hhhcCCccCCEEEEEeeeeecc
Confidence 59999999999887 99999999999999999999999886 89999997 6999999999999999999999
Q ss_pred eEEEEEeeecCcccCCc----eeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCceeeeeccCCCeeEEEEc
Q psy6276 85 LCKAHVISVGNTALSRT----FRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQLSTAENELGVVIALS 159 (271)
Q Consensus 85 ~a~VdI~~v~~~~L~~~----f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~LST~~~eLGVV~A~c 159 (271)
.|+||+++-.++.|..+ .-|++|+ .++.|+..|+.+|+.||+|.|+ .++....+..|+|+...+|.+.
T Consensus 100 RWkvd~nsk~d~vL~LsSvNLPGg~~RR----k~~~DEl~MR~fl~egDLi~AEVQ~v~~dGs~sLhTRS~KYGKL~--- 172 (301)
T KOG3013|consen 100 RWKVDLNSKQDAVLMLSSVNLPGGIQRR----KSEEDELQMRSFLKEGDLIVAEVQNVFHDGSLSLHTRSLKYGKLG--- 172 (301)
T ss_pred eeEEecccccceEEEeecccCCchhhhc----cchhhHHHHHHHhhccCeehHHHHHhccCCeEEEEecchhccccc---
Confidence 99999999888775532 3466554 6788999999999999999999 6664446899999999999985
Q ss_pred cCCCeeEeccCccCchhhhhhhhhhhHHHhcccccceeeeeeccCceEEEe
Q psy6276 160 EAASLFRSSEKLTNDIEFLKQEKLKLYEELSSSQKENEILRQTTGDLEVRL 210 (271)
Q Consensus 160 ~cG~~Mvp~s~~~~c~~~~~~e~rKla~~~~s~~~~~~~~~~~~~~~~~~~ 210 (271)
-+.++.+.+.+. .+.| ..+-+..+--.+..|-||-+||.-
T Consensus 173 --~G~lvkVpp~Lv-------kr~K--~hfh~lp~g~~vIlG~NGyIWv~~ 212 (301)
T KOG3013|consen 173 --QGILVKVPPALV-------KRSK--THFHNLPGGVDVILGCNGYIWVGP 212 (301)
T ss_pred --CceEEEeCHHHh-------hhhh--hhhccCCCCeEEEEecCceEEecC
Confidence 234444442211 1112 112233344566789999999976
No 8
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=99.87 E-value=1.8e-22 Score=156.26 Aligned_cols=71 Identities=42% Similarity=0.882 Sum_probs=51.3
Q ss_pred cCCCCCEEEEEEEEEecceEEEEEeee----------cCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-E
Q psy6276 67 VPTPGDVVTARIMAVQQHLCKAHVISV----------GNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-L 135 (271)
Q Consensus 67 iP~vGDIVIGrVt~V~~~~a~VdI~~v----------~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-i 135 (271)
+|++||+|+|+|+++++++|.|+|+++ ++.++..+|+|+||.+|+|+++.|+++|++||+|||||+|+ +
T Consensus 1 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~Vi 80 (82)
T PF10447_consen 1 LPKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVI 80 (82)
T ss_dssp ---TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEE
T ss_pred CCCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEe
Confidence 599999999999999999999999999 77788899999999999999999999999999999999999 9
Q ss_pred ec
Q psy6276 136 PL 137 (271)
Q Consensus 136 S~ 137 (271)
|+
T Consensus 81 Sl 82 (82)
T PF10447_consen 81 SL 82 (82)
T ss_dssp EE
T ss_pred eC
Confidence 85
No 9
>KOG1004|consensus
Probab=99.79 E-value=1.6e-18 Score=154.03 Aligned_cols=179 Identities=19% Similarity=0.203 Sum_probs=125.4
Q ss_pred CeEecCCcccCC--CCCeeeCCCEEEeCCEEEEEEeeEEEEeccccCCCcceEEEEeeCCCccccCCCCCEEEEEEEEEe
Q psy6276 5 PICIPGQRICQL--DSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQ 82 (271)
Q Consensus 5 ~iVlPGD~L~~~--eE~~~~G~GtY~~~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~~~yiP~vGDIVIGrVt~V~ 82 (271)
.+.+|||.+... .+ ..+|+|.|..++.+.++..|.+....+ ......+.+|... +.+|+|.+||.|||+|++-.
T Consensus 2 ~~~~pg~~~~~~~~~s-v~~G~g~~~~g~~~~~~~~G~~~~~~~--gk~~~~v~~vds~-~kRYiP~~~D~VIGiV~~~~ 77 (230)
T KOG1004|consen 2 TFYFPGDSIPRPRLCS-VVLGPGLRRRGQERLVTKCGRLRHKEP--GKGGGGVYWVDSQ-QKRYIPVKGDHVIGIVTSKS 77 (230)
T ss_pred ceecCCcccccCccCc-eeecCCccccCceEEeccccceeeccC--CcccceeEEEecc-cceecCCCCCEEEEEEEecc
Confidence 467999988643 23 889999999999999999998776541 0001225577763 78999999999999999999
Q ss_pred cceEEEEEeeecCcccC-CceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC-CCCc---eeeee-ccCCCeeE
Q psy6276 83 QHLCKAHVISVGNTALS-RTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK-ELHS---YQLST-AENELGVV 155 (271)
Q Consensus 83 ~~~a~VdI~~v~~~~L~-~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~-d~~~---~~LST-~~~eLGVV 155 (271)
.++++|||...+-+.|+ .+|+|.-+ ..|+.|..||+|||| +..+ |..+ +.-|| +..++|++
T Consensus 78 gd~ykVDigg~~~a~L~~laFe~Atk------------rNrPnl~vGdliyakv~~a~~~~Epel~Cids~graaGfG~L 145 (230)
T KOG1004|consen 78 GDIYKVDIGGSEPASLSYLAFEGATK------------RNRPNLQVGDLIYAKVVDANKDMEPELTCIDSTGRAAGFGVL 145 (230)
T ss_pred CceEEEecCCCCeeeeeeccccCccc------------cCCCccccccEEEEEEEecCCCcCcceEEEcccCcccCcccc
Confidence 99999999875555566 56777432 579999999999999 6543 2221 22233 33466665
Q ss_pred EEEccCCCeeEecc-C----ccCchhhhhhhhhhhHHHhcccccceeeeeeccCceEEEeEe
Q psy6276 156 IALSEAASLFRSSE-K----LTNDIEFLKQEKLKLYEELSSSQKENEILRQTTGDLEVRLMQ 212 (271)
Q Consensus 156 ~A~c~cG~~Mvp~s-~----~~~c~~~~~~e~rKla~~~~s~~~~~~~~~~~~~~~~~~~~~ 212 (271)
. +..|.+.| | ++. |.| .+.+.++ ++--||||.|-||++||++-.
T Consensus 146 k-----dG~if~vs~~~~R~Ll~-p~~------~iLq~vG-k~~~FEia~GlNGriWV~ae~ 194 (230)
T KOG1004|consen 146 K-----DGMIFKVSLGLCRKLLL-PDC------PILQTVG-KKYPFEIAFGLNGRIWVKAET 194 (230)
T ss_pred c-----CceEEEecHHHHHHHHc-CCC------cHHHHhh-cccceEEEEecCceEEEeccC
Confidence 3 45555555 1 111 212 1445553 455799999999999998743
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=99.65 E-value=9.4e-16 Score=116.57 Aligned_cols=81 Identities=32% Similarity=0.511 Sum_probs=72.0
Q ss_pred cccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCce
Q psy6276 65 VIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSY 143 (271)
Q Consensus 65 ~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~ 143 (271)
+|+|++||+|+|+|+++..+.|.|+|. ..+.|+||.+++.. .+..++.+.|++||+|.|+ +++++.+.+
T Consensus 1 ~y~p~~GdiV~G~V~~v~~~~~~V~i~--------~~~~g~l~~~~~~~--~~~~~~~~~~~~GD~i~~~V~~~~~~~~i 70 (82)
T cd04454 1 RYLPDVGDIVIGIVTEVNSRFWKVDIL--------SRGTARLEDSSATE--KDKKEIRKSLQPGDLILAKVISLGDDMNV 70 (82)
T ss_pred CCCCCCCCEEEEEEEEEcCCEEEEEeC--------CCceEEeechhccC--cchHHHHhcCCCCCEEEEEEEEeCCCCCE
Confidence 589999999999999999999999996 46899999998854 2356899999999999999 888765789
Q ss_pred eeeeccCCCeeE
Q psy6276 144 QLSTAENELGVV 155 (271)
Q Consensus 144 ~LST~~~eLGVV 155 (271)
.||+++++||||
T Consensus 71 ~LS~~~~~~Gvi 82 (82)
T cd04454 71 LLTTADNELGVI 82 (82)
T ss_pred EEEECCCCCccC
Confidence 999999999986
No 11
>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=99.50 E-value=7.8e-14 Score=108.96 Aligned_cols=74 Identities=20% Similarity=0.165 Sum_probs=59.1
Q ss_pred cccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCce
Q psy6276 65 VIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSY 143 (271)
Q Consensus 65 ~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~ 143 (271)
+|+|++||+|||+|+++..+.|+|||.+ ++.|+|+..++. ....++++.|++||+|+|| .+++....+
T Consensus 1 rY~P~~gD~VIG~V~~~~~~~~~VdI~s--------~~~a~L~~~~f~---gatk~~rp~L~~GDlV~ArV~~~~~~~~~ 69 (86)
T cd05790 1 RYVPAKGDHVIGIVVAKAGDFFKVDIGG--------SEPASLSYLAFE---GATKRNRPNLNVGDLVYARVVKANRDMEP 69 (86)
T ss_pred CCcCCCCCEEEEEEEEEcCCeEEEEcCC--------CcceEechHHcc---cccccccccCCCCCEEEEEEEecCCCCCe
Confidence 6999999999999999999999999974 566777765432 1234689999999999999 777654567
Q ss_pred eeeecc
Q psy6276 144 QLSTAE 149 (271)
Q Consensus 144 ~LST~~ 149 (271)
.||..+
T Consensus 70 eLtc~~ 75 (86)
T cd05790 70 ELSCVD 75 (86)
T ss_pred EEEEeC
Confidence 777754
No 12
>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=99.43 E-value=6.4e-13 Score=101.51 Aligned_cols=83 Identities=27% Similarity=0.360 Sum_probs=71.4
Q ss_pred cccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEecccccc--chhhhHhhhcCCCCCCEEEEE-EecCCCC
Q psy6276 65 VIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRA--TEIDRIEMYKCYRPGDIILAR-LPLKELH 141 (271)
Q Consensus 65 ~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~--te~d~~~m~~~f~~GDIV~Ak-iS~~d~~ 141 (271)
+|.|++||+|.|+|+++.+..|.|+|. ..+.|+||.+++.. ++....++.+.|++||.|.|+ +++++.+
T Consensus 1 ~y~p~~GdiV~g~V~~i~~~g~~v~i~--------~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~ 72 (86)
T cd05789 1 RYIPEVGDVVIGRVTEVGFKRWKVDIN--------SPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDG 72 (86)
T ss_pred CCcCCCCCEEEEEEEEECCCEEEEECC--------CCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCCC
Confidence 589999999999999999999999984 56999999999853 123345788999999999999 8886546
Q ss_pred ceeeeeccCCCeeE
Q psy6276 142 SYQLSTAENELGVV 155 (271)
Q Consensus 142 ~~~LST~~~eLGVV 155 (271)
.+.||++.++||++
T Consensus 73 ~i~LS~~~~~~g~~ 86 (86)
T cd05789 73 SVSLHTRSLKYGKL 86 (86)
T ss_pred CEEEEeCcccccCC
Confidence 79999999999985
No 13
>PF14382 ECR1_N: Exosome complex exonuclease RRP4 N-terminal region; PDB: 2NN6_I 3M7N_C 2BA1_A 3M85_C.
Probab=99.34 E-value=9.1e-13 Score=88.77 Aligned_cols=39 Identities=44% Similarity=0.882 Sum_probs=34.8
Q ss_pred eEecCCcccCCCCCeeeCCCEEEeCCEEEEEEeeEEEEec
Q psy6276 6 ICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINK 45 (271)
Q Consensus 6 iVlPGD~L~~~eE~~~~G~GtY~~~g~I~ASv~G~v~i~~ 45 (271)
+|+|||+|++.++ |++|+|||+++|+||||++|.+++++
T Consensus 1 iV~PG~~l~~~~e-~~~G~GTY~~~g~I~asv~G~v~~~n 39 (39)
T PF14382_consen 1 IVVPGDRLGSSEE-YMPGHGTYVRDGNIYASVAGTVKIDN 39 (39)
T ss_dssp EE-TT-EEEETTT-SEESTTEEEETTEEEESSSEEEEEET
T ss_pred CCCCCCEeecCCC-EecCCCEEEeCCEEEEEeeEEEEEcC
Confidence 6999999999988 99999999999999999999998763
No 14
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.67 E-value=8.2e-08 Score=71.66 Aligned_cols=69 Identities=19% Similarity=0.210 Sum_probs=56.1
Q ss_pred CCCCEEEEEEEEEec-ceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCceeee
Q psy6276 69 TPGDVVTARIMAVQQ-HLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQLS 146 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~-~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~LS 146 (271)
++||+|.|+|+++.+ ..+.+++ .....|++|.+++.... ...+.+.|++||+|+|+ ++.++ ..+.||
T Consensus 2 ~~G~iv~G~V~~i~~~~g~~v~l--------~~~~~Glvhis~~s~~~--~~~~~~~~~~Gd~v~~kV~~~~~-~~i~LS 70 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQL--------PFGKTGLVSIFHLSDSY--TENPLEGFKPGKIVRCCILSKKD-GKYQLS 70 (72)
T ss_pred CCCCEEEEEEEEeeCCcEEEEEC--------CCCCEEEEEHHHhcCcc--cCCHHHhCCCCCEEEEEEEEecC-CEEEEE
Confidence 589999999999987 4688876 35689999999986532 33567889999999999 88865 679998
Q ss_pred ec
Q psy6276 147 TA 148 (271)
Q Consensus 147 T~ 148 (271)
++
T Consensus 71 l~ 72 (72)
T cd05704 71 LR 72 (72)
T ss_pred eC
Confidence 74
No 15
>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=98.62 E-value=1.8e-07 Score=68.39 Aligned_cols=67 Identities=15% Similarity=0.136 Sum_probs=54.7
Q ss_pred CCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC-CCCceeeee
Q psy6276 71 GDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK-ELHSYQLST 147 (271)
Q Consensus 71 GDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~-d~~~~~LST 147 (271)
||+|.|+|+++.+..|.|++. ..+.|+||.+++.... ..++.+.|++||.|.|+ ++++ +...+.||.
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~--------~~~~g~l~~~e~~~~~--~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~ 69 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIG--------YKSEGIIPISEFSDDP--IENGEDEVKVGDEVEVYVLRVEDEEGNVVLSK 69 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeC--------CCceEEEEHHHhCccc--cCCHhHcCCCCCEEEEEEEEEECCCCeEEEEe
Confidence 899999999999999999995 3579999999886432 33578889999999999 8875 334577775
No 16
>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=98.51 E-value=3.6e-07 Score=67.40 Aligned_cols=64 Identities=17% Similarity=0.218 Sum_probs=53.0
Q ss_pred CCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCc
Q psy6276 71 GDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHS 142 (271)
Q Consensus 71 GDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~ 142 (271)
|++|.|+|+++.+..+.|++. ..+.|.+|.+++.....+..++.+.|++||+|.|+ +++++...
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~--------~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~ 65 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLA--------DNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT 65 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeC--------CCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence 899999999999999999984 56999999999865322344678899999999999 99876543
No 17
>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=98.49 E-value=6.8e-07 Score=66.02 Aligned_cols=73 Identities=11% Similarity=0.211 Sum_probs=58.1
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCceee
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSYQL 145 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~~L 145 (271)
|++|++|.|.|+++.+..|.|++.... .+.|++|.++++.. ...++.+.|++||.|.|+ ++.+. ...+.|
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~------~~~gll~~s~l~~~--~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~l 72 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYG------NIEGMILLSELSRR--RIRSIRKLVKVGRKEVVKVIRVDKEKGYIDL 72 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCCC------CeEEEEEhHHcCCc--ccCCHHHeeCCCCEEEEEEEEEECCCCEEEE
Confidence 689999999999999999999995321 37999999998642 233678889999999999 87653 245788
Q ss_pred eec
Q psy6276 146 STA 148 (271)
Q Consensus 146 ST~ 148 (271)
|++
T Consensus 73 s~k 75 (76)
T cd04452 73 SKK 75 (76)
T ss_pred EEc
Confidence 875
No 18
>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=98.45 E-value=7.1e-07 Score=71.18 Aligned_cols=73 Identities=10% Similarity=0.190 Sum_probs=58.5
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchh-----------------hhHhhhcCCCCCCEE
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEI-----------------DRIEMYKCYRPGDII 131 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~-----------------d~~~m~~~f~~GDIV 131 (271)
++|++|.|+|++|.+..+.|++ +....|++|.+++..... +..++.+.|++||+|
T Consensus 2 ~~G~vV~G~V~~v~~~gl~v~L--------~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V 73 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISL--------PNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLV 73 (100)
T ss_pred CCCCEEEEEEEEEcCCCEEEEC--------CCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEE
Confidence 6899999999999999999976 356899999999864211 122478999999999
Q ss_pred EEE-EecCCC----Cceeeeecc
Q psy6276 132 LAR-LPLKEL----HSYQLSTAE 149 (271)
Q Consensus 132 ~Ak-iS~~d~----~~~~LST~~ 149 (271)
+|+ +++++. +.+.||.+-
T Consensus 74 ~~kVi~~d~~~~~~~~i~LSlr~ 96 (100)
T cd05693 74 RCKVVSLDKSKSGKKRIELSLEP 96 (100)
T ss_pred EEEEEEccCCcCCCcEEEEEecH
Confidence 999 999763 468888864
No 19
>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=98.43 E-value=1.2e-06 Score=63.96 Aligned_cols=70 Identities=16% Similarity=0.248 Sum_probs=57.1
Q ss_pred CCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCC-Cceeeeec
Q psy6276 71 GDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKEL-HSYQLSTA 148 (271)
Q Consensus 71 GDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~-~~~~LST~ 148 (271)
|++|.|+|+++.+..|.|+|. ..+.|.+|.+++.... ..++.+.|++||.|.|+ ++.+.. ..+.||++
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 GSIVTGKVTEVDAKGATVKLG--------DGVEGFLRAAELSRDR--VEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeC--------CCCEEEEEHHHCCCcc--ccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEE
Confidence 899999999999999999996 3589999999876432 23578889999999999 777533 46888887
Q ss_pred cC
Q psy6276 149 EN 150 (271)
Q Consensus 149 ~~ 150 (271)
..
T Consensus 71 ~~ 72 (73)
T cd05691 71 AK 72 (73)
T ss_pred Ec
Confidence 64
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=98.38 E-value=2.3e-06 Score=62.99 Aligned_cols=70 Identities=14% Similarity=0.131 Sum_probs=56.4
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCceeee
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSYQLS 146 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~~LS 146 (271)
++|++|.|+|+++.+..+.|++. ...+|.+|.+++.... ..+..+.|++||.|.|+ ++.+. ...+.||
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 KVGDILPGRVTKVNDRYVLVQLG--------NKVTGPSFITDALDDY--SEALPYKFKKNDIVRACVLSVDVPNKKIALS 71 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEeC--------CCcEEEEEhhhccCcc--ccccccccCCCCEEEEEEEEEeCCCCEEEEE
Confidence 58999999999999999999973 4689999999886422 22457889999999999 88753 3568888
Q ss_pred ec
Q psy6276 147 TA 148 (271)
Q Consensus 147 T~ 148 (271)
++
T Consensus 72 ~~ 73 (73)
T cd05706 72 LR 73 (73)
T ss_pred EC
Confidence 63
No 21
>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=98.31 E-value=3e-06 Score=63.80 Aligned_cols=70 Identities=16% Similarity=0.145 Sum_probs=54.8
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccch-hhhHhhhcCCCCCCEEEEE-EecCCC-Cceee
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATE-IDRIEMYKCYRPGDIILAR-LPLKEL-HSYQL 145 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te-~d~~~m~~~f~~GDIV~Ak-iS~~d~-~~~~L 145 (271)
++||+|.|+|+++.+..++|++. ....|.+|.+++.... .+..++.+.|++||.|.|+ ++.+.. ..+.|
T Consensus 2 k~G~~V~g~V~~i~~~G~fV~l~--------~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~L 73 (74)
T cd05705 2 KEGQLLRGYVSSVTKQGVFFRLS--------SSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVEL 73 (74)
T ss_pred CCCCEEEEEEEEEeCCcEEEEeC--------CCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEec
Confidence 68999999999999999999983 4689999998886533 1223467899999999999 888543 33555
Q ss_pred e
Q psy6276 146 S 146 (271)
Q Consensus 146 S 146 (271)
|
T Consensus 74 S 74 (74)
T cd05705 74 S 74 (74)
T ss_pred C
Confidence 4
No 22
>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=98.30 E-value=4.1e-06 Score=59.71 Aligned_cols=68 Identities=13% Similarity=0.190 Sum_probs=54.2
Q ss_pred CCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCceeeeec
Q psy6276 71 GDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQLSTA 148 (271)
Q Consensus 71 GDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~LST~ 148 (271)
||+|.|+|+++.+..|+|+|. ..+.|+||.++++... ..+....|++||.|.++ ++.+....+.||++
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~--------~~~~g~l~~~~l~~~~--~~~~~~~~~~Gd~v~v~v~~~~~~~~i~ls~k 69 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELG--------GGISGLVHISQIAHKR--VKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEEC--------CCCEEEEEhHHcCCcc--cCCHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence 899999999999999999995 4589999999876322 23456789999999999 77754356777763
No 23
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=98.30 E-value=1.4e-06 Score=72.44 Aligned_cols=74 Identities=12% Similarity=0.076 Sum_probs=65.3
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCceeee
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQLS 146 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~LS 146 (271)
+++||+|-|+||.|.+-.|+|++- ..-+|++|+|+|.. .+..++.+.+.+||-|.++ ++.++...+.||
T Consensus 3 ~kvG~~l~GkItgI~~yGAFV~l~--------~g~tGLVHISEIa~--~fVkdI~d~L~vG~eV~vKVl~ide~GKisLS 72 (129)
T COG1098 3 MKVGSKLKGKITGITPYGAFVELE--------GGKTGLVHISEIAD--GFVKDIHDHLKVGQEVKVKVLDIDENGKISLS 72 (129)
T ss_pred ccccceEEEEEEeeEecceEEEec--------CCCcceEEehHhhh--hhHHhHHHHhcCCCEEEEEEEeeccCCCccee
Confidence 689999999999999999999984 45689999999976 4577999999999999999 999887789999
Q ss_pred eccCC
Q psy6276 147 TAENE 151 (271)
Q Consensus 147 T~~~e 151 (271)
++..+
T Consensus 73 Ir~~~ 77 (129)
T COG1098 73 IRKLE 77 (129)
T ss_pred hHHhh
Confidence 97643
No 24
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.25 E-value=5.5e-06 Score=60.94 Aligned_cols=72 Identities=14% Similarity=0.206 Sum_probs=57.3
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCceeee
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSYQLS 146 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~~LS 146 (271)
++|++|.|+|+++.+..|.|++.. ....|++|.+++.... ..++.+.|++||.|.|+ ++.+. ...+.||
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~~-------~~~~g~i~~~~l~~~~--~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 71 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDG-------TNVSGLCHKSEISDNR--VADASKLFRVGDKVRAKVLKIDAEKKRISLG 71 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECC-------CCeEEEEEHHHCCCCc--cCCHhHeecCCCEEEEEEEEEeCCCCEEEEE
Confidence 469999999999999999999952 3579999999886422 23567889999999999 77753 3567788
Q ss_pred ecc
Q psy6276 147 TAE 149 (271)
Q Consensus 147 T~~ 149 (271)
++.
T Consensus 72 ~k~ 74 (77)
T cd05708 72 LKA 74 (77)
T ss_pred EEe
Confidence 764
No 25
>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=98.22 E-value=6e-06 Score=60.19 Aligned_cols=66 Identities=14% Similarity=0.216 Sum_probs=52.5
Q ss_pred CCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCceeee
Q psy6276 71 GDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSYQLS 146 (271)
Q Consensus 71 GDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~~LS 146 (271)
|++|.|+|+++.+..+.|++. ..+.|++|.+++... ...+..+.|++||.|.|+ ++++. .+.+.||
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~--------~~~~G~v~~s~l~~~--~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls 68 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLG--------RGVDARVRVSELSDS--YLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeC--------CCCEEEEEHHHCCch--hhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 899999999999999999985 358999999988542 233678889999999999 88764 2345443
No 26
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.20 E-value=7.8e-06 Score=57.92 Aligned_cols=69 Identities=16% Similarity=0.172 Sum_probs=54.2
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCC-Cceeee
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKEL-HSYQLS 146 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~-~~~~LS 146 (271)
++|++|.|+|+++.+..|.|++. ..+.|++|.+++.... ..++...|++||.|.|+ ++.... ..+.||
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~--------~~~~g~l~~~~~~~~~--~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls 70 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLG--------NGVEGLIPISELSDKR--VKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeC--------CCCEEEEEHHHCCccc--cCCHHHeecCCCEEEEEEEEEeCCCCEEEEE
Confidence 46999999999999999999995 3688999998876532 23456789999999999 776432 556666
Q ss_pred e
Q psy6276 147 T 147 (271)
Q Consensus 147 T 147 (271)
+
T Consensus 71 ~ 71 (72)
T smart00316 71 L 71 (72)
T ss_pred e
Confidence 5
No 27
>PRK08582 hypothetical protein; Provisional
Probab=98.19 E-value=9.5e-06 Score=68.47 Aligned_cols=73 Identities=11% Similarity=0.122 Sum_probs=59.8
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCceeee
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQLS 146 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~LS 146 (271)
+++|++|.|+|+.|.+..++|+|. ....|++|.+++.... ..++.+.|.+||.|.|+ +++++...+.||
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L~--------~~~~GlVhiSels~~~--v~~~~~~l~vGD~VkvkV~~id~~gkI~LS 72 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVELP--------EGKTGLVHISEVADNY--VKDINDHLKVGDEVEVKVLNVEDDGKIGLS 72 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEEC--------CCCEEEEEeeccCccc--ccccccccCCCCEEEEEEEEECCCCcEEEE
Confidence 478999999999999999999984 3589999999986432 34567899999999999 888644678888
Q ss_pred eccC
Q psy6276 147 TAEN 150 (271)
Q Consensus 147 T~~~ 150 (271)
++..
T Consensus 73 lk~~ 76 (139)
T PRK08582 73 IKKA 76 (139)
T ss_pred EEec
Confidence 7654
No 28
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.17 E-value=1.1e-05 Score=60.50 Aligned_cols=70 Identities=13% Similarity=0.098 Sum_probs=56.5
Q ss_pred CCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCceeeeec
Q psy6276 71 GDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSYQLSTA 148 (271)
Q Consensus 71 GDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~~LST~ 148 (271)
||+|.|+|+++.+..++|.+. ..+.|.+|.+++........+....|++||.|.|+ ++++. .+.+.||.+
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~--------~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTIS--------PDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeC--------CCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 899999999999999999983 45899999999864322234678899999999999 88753 356888864
No 29
>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=98.15 E-value=1.3e-05 Score=58.91 Aligned_cols=71 Identities=11% Similarity=0.198 Sum_probs=57.7
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCC-Cceee
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKEL-HSYQL 145 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~-~~~~L 145 (271)
|++|++|.|+|+++.+..+.|++. ....|++|.+++.... .......|++||-|.|+ ++.+.. ..+.|
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 LKEGDIVEGKVTSVEDFGVFVDLG--------NGIEGFIPISELSDDR--IDDPSEVYKIGQTVRVKVIKVDKEKGRIRL 71 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEES--------TSSEEEEEGGGSSSSE--ESSSHGTCETTCEEEEEEEEEETTTTEEEE
T ss_pred CCCCCEEEEEEEEEECCEEEEEEC--------CcEEEEEEeehhcCcc--ccccccccCCCCEEEEEEEEEECCCCeEEE
Confidence 689999999999999999999995 4689999999886532 23578899999999999 777433 44777
Q ss_pred eec
Q psy6276 146 STA 148 (271)
Q Consensus 146 ST~ 148 (271)
|++
T Consensus 72 S~k 74 (74)
T PF00575_consen 72 SLK 74 (74)
T ss_dssp EST
T ss_pred EEC
Confidence 764
No 30
>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=98.11 E-value=2.1e-05 Score=58.54 Aligned_cols=71 Identities=8% Similarity=0.109 Sum_probs=56.5
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCceeee
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQLS 146 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~LS 146 (271)
|+.|+++.|+|+++.+..++|++.. ....|++|.+++.... ..+..+.|++||.|.++ ++.+....+.||
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~~-------~~~eGlvh~sel~~~~--~~~~~~~~~~Gd~v~vkv~~vd~~~ki~ls 71 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPG-------CRKQGLVHKSHMSSCR--VDDPSEVVDVGEKVWVKVIGREMKDKMKLS 71 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEECC-------CCeEEEEEchhhCCCc--ccCHhhEECCCCEEEEEEEEECCCCcEEEE
Confidence 6799999999999999999999842 1258999999986533 23677889999999999 887653356666
Q ss_pred e
Q psy6276 147 T 147 (271)
Q Consensus 147 T 147 (271)
+
T Consensus 72 ~ 72 (73)
T cd05686 72 L 72 (73)
T ss_pred e
Confidence 4
No 31
>PRK08059 general stress protein 13; Validated
Probab=98.10 E-value=1.7e-05 Score=65.24 Aligned_cols=74 Identities=18% Similarity=0.173 Sum_probs=59.4
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC-CCCceee
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK-ELHSYQL 145 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~-d~~~~~L 145 (271)
+++|++|.|+|+++.+..|.|+|. ..+.|++|.+++.... ..++...|++||.|.|+ ++.+ ..+.+.|
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 YEVGSVVTGKVTGIQPYGAFVALD--------EETQGLVHISEITHGF--VKDIHDFLSVGDEVKVKVLSVDEEKGKISL 74 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEEC--------CCCEEEEEHHHCCccc--ccCHHHcCCCCCEEEEEEEEEECCCCeEEE
Confidence 578999999999999999999994 3589999999886422 23567789999999999 8874 2356888
Q ss_pred eeccCC
Q psy6276 146 STAENE 151 (271)
Q Consensus 146 ST~~~e 151 (271)
|++..+
T Consensus 75 slk~~~ 80 (123)
T PRK08059 75 SIRATE 80 (123)
T ss_pred EEEEcc
Confidence 886543
No 32
>PRK07252 hypothetical protein; Provisional
Probab=98.05 E-value=2.4e-05 Score=64.57 Aligned_cols=71 Identities=13% Similarity=0.140 Sum_probs=56.5
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCceeee
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSYQLS 146 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~~LS 146 (271)
++|++|.|+|++|.+..|.|+|. ....|++|.++++... .......|++||.|.|+ ++++. .+.+.||
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~--------~~~~GllhiseLs~~~--~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lS 71 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALE--------NGTTGLIHISEIKTGF--IDNIHQLLKVGEEVLVQVVDFDEYTGKASLS 71 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEEC--------CCCEEEEEHHHcCCcc--ccChhhccCCCCEEEEEEEEEeCCCCEEEEE
Confidence 57999999999999999999994 3579999999986422 23466789999999999 88753 3557777
Q ss_pred ecc
Q psy6276 147 TAE 149 (271)
Q Consensus 147 T~~ 149 (271)
++.
T Consensus 72 lk~ 74 (120)
T PRK07252 72 LRT 74 (120)
T ss_pred Eee
Confidence 654
No 33
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.01 E-value=2.1e-05 Score=72.89 Aligned_cols=77 Identities=10% Similarity=0.113 Sum_probs=61.9
Q ss_pred cccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCC-Cc
Q psy6276 65 VIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKEL-HS 142 (271)
Q Consensus 65 ~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~-~~ 142 (271)
.-+|++||+|.|+|++|.+..|+|++...+ ...|+||.+++.... ...+++.|++||.|.|+ ++++.. +.
T Consensus 3 ~~~P~~GdiV~G~V~~I~~~G~fV~L~e~~------gieGlI~iSEls~~~--i~~i~~~~kvGd~V~vkVi~VD~~k~~ 74 (262)
T PRK03987 3 KEWPEEGELVVGTVKEVKDFGAFVTLDEYP------GKEGFIHISEVASGW--VKNIRDHVKEGQKVVCKVIRVDPRKGH 74 (262)
T ss_pred CCCCCCCCEEEEEEEEEECCEEEEEECCCC------CcEEEEEHHHcCccc--ccCHHHhCCCCCEEEEEEEEEecccCe
Confidence 347999999999999999999999996321 369999999986422 33578899999999999 887633 46
Q ss_pred eeeeecc
Q psy6276 143 YQLSTAE 149 (271)
Q Consensus 143 ~~LST~~ 149 (271)
+.||++.
T Consensus 75 I~LSlK~ 81 (262)
T PRK03987 75 IDLSLKR 81 (262)
T ss_pred EEEEEEe
Confidence 8999874
No 34
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.01 E-value=1.5e-05 Score=69.53 Aligned_cols=83 Identities=22% Similarity=0.287 Sum_probs=63.4
Q ss_pred cccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchh--hh-------HhhhcCCCCCCEEEEE-
Q psy6276 65 VIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEI--DR-------IEMYKCYRPGDIILAR- 134 (271)
Q Consensus 65 ~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~--d~-------~~m~~~f~~GDIV~Ak- 134 (271)
.+-|.+|++|.|+|+++....+.|++. ++.|+++.+++..... |. .+....|++||.|++|
T Consensus 76 vf~P~~GEVv~g~V~~v~~~Gi~V~lg---------~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV 146 (187)
T PRK08563 76 VFKPELQEVVEGEVVEVVEFGAFVRIG---------PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARI 146 (187)
T ss_pred EEeccCCCEEEEEEEEEEccEEEEEEe---------CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEE
Confidence 456899999999999999999999983 5788888887753210 10 1245678999999999
Q ss_pred EecC--CC----CceeeeeccCCCeeEE
Q psy6276 135 LPLK--EL----HSYQLSTAENELGVVI 156 (271)
Q Consensus 135 iS~~--d~----~~~~LST~~~eLGVV~ 156 (271)
++.. +. ..+.||++++.||.+.
T Consensus 147 ~~v~~~~~~~~~~~I~ls~~~~~LG~~~ 174 (187)
T PRK08563 147 VAVSLKERRPRGSKIGLTMRQPGLGKLE 174 (187)
T ss_pred EEEEcccCCCCCCEEEEEecCCCCCcHH
Confidence 6653 22 3588899999999873
No 35
>PRK05807 hypothetical protein; Provisional
Probab=98.00 E-value=3.8e-05 Score=64.54 Aligned_cols=70 Identities=11% Similarity=0.174 Sum_probs=57.9
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCceeeee
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQLST 147 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~LST 147 (271)
++|++|.|+|+.+.+..++|++. ...|++|++++.... ..+....|++||.|.++ ++++....+.||+
T Consensus 4 ~vG~vv~G~Vt~i~~~GafV~L~---------~~~Glvhiseis~~~--v~~~~~~~kvGd~V~VkV~~id~~gkI~LSl 72 (136)
T PRK05807 4 KAGSILEGTVVNITNFGAFVEVE---------GKTGLVHISEVADTY--VKDIREHLKEQDKVKVKVISIDDNGKISLSI 72 (136)
T ss_pred cCCCEEEEEEEEEECCeEEEEEC---------CEEEEEEhhhccccc--ccCccccCCCCCEEEEEEEEECCCCcEEEEE
Confidence 68999999999999999999992 248999999986532 33567889999999999 8876545788888
Q ss_pred cc
Q psy6276 148 AE 149 (271)
Q Consensus 148 ~~ 149 (271)
+.
T Consensus 73 k~ 74 (136)
T PRK05807 73 KQ 74 (136)
T ss_pred Ee
Confidence 65
No 36
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.99 E-value=3.6e-05 Score=56.06 Aligned_cols=67 Identities=15% Similarity=0.247 Sum_probs=53.9
Q ss_pred CCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCceeeee
Q psy6276 71 GDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSYQLST 147 (271)
Q Consensus 71 GDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~~LST 147 (271)
|++|.|+|+++.+..+.|++. ....|++|.+++.... ..+....|++||.|.++ ++.+. .+.+.||.
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~--------~~~~gli~~s~l~~~~--~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~ 69 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFY--------NNVKGFLPKSELSEAF--IKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSC 69 (70)
T ss_pred CCEEEEEEEEEecCcEEEEEC--------CCCEEEEEHHHcChhh--cCCHHHcccCCCEEEEEEEEEcCCCCEEEEEe
Confidence 899999999999999999995 2479999999986422 33567789999999999 88754 24577775
No 37
>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=97.92 E-value=3.9e-05 Score=54.80 Aligned_cols=58 Identities=16% Similarity=0.169 Sum_probs=47.4
Q ss_pred CCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC
Q psy6276 70 PGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK 138 (271)
Q Consensus 70 vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~ 138 (271)
+|++|.|+|+++.+..|.|++. ...|++|.+++.... ...+...|++||.|+|+ ++.+
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~---------~~~g~l~~~e~~~~~--~~~~~~~~~~Gd~v~v~i~~vd 59 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLG---------GVDGLLHISDMSWGR--VKHPSEVVNVGDEVEVKVLKID 59 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC---------CeEEEEEhHHCCCcc--ccCHhHEECCCCEEEEEEEEEE
Confidence 5999999999999999999984 368999998876322 23466789999999999 7764
No 38
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.80 E-value=0.00011 Score=55.68 Aligned_cols=71 Identities=14% Similarity=0.160 Sum_probs=56.9
Q ss_pred cCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCcee
Q psy6276 67 VPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSYQ 144 (271)
Q Consensus 67 iP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~~ 144 (271)
-+++|+++.|+|+++.+..+.|++. ....|++|.+++.... ..++.+.|++||.|.++ ++.+. ...+.
T Consensus 11 ~~~~G~i~~g~V~~v~~~G~fv~l~--------~~~~g~v~~~el~~~~--~~~~~~~~~~Gd~v~vkV~~id~~~~~i~ 80 (83)
T cd04461 11 DLKPGMVVHGYVRNITPYGVFVEFL--------GGLTGLAPKSYISDEF--VTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80 (83)
T ss_pred hCCCCCEEEEEEEEEeeceEEEEcC--------CCCEEEEEHHHCCccc--ccCHHHhcCCCCEEEEEEEEEcCCCCEEE
Confidence 3689999999999999999999995 3478999999886422 33678999999999999 77753 24566
Q ss_pred eee
Q psy6276 145 LST 147 (271)
Q Consensus 145 LST 147 (271)
||+
T Consensus 81 lsl 83 (83)
T cd04461 81 LSL 83 (83)
T ss_pred EeC
Confidence 663
No 39
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=97.80 E-value=7.1e-05 Score=65.21 Aligned_cols=83 Identities=23% Similarity=0.288 Sum_probs=63.5
Q ss_pred cccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchh--hhH-------hhhcCCCCCCEEEEE-
Q psy6276 65 VIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEI--DRI-------EMYKCYRPGDIILAR- 134 (271)
Q Consensus 65 ~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~--d~~-------~m~~~f~~GDIV~Ak- 134 (271)
.+-|.+|+++.|+|++++...+.|++. ++.|+++.++...... |.. +....|+.||.|++|
T Consensus 76 ~f~p~~gEvv~G~V~~v~~~GifV~lg---------~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV 146 (179)
T TIGR00448 76 VFKPELGEIVEGEVIEIVEFGAFVSLG---------PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARI 146 (179)
T ss_pred EEeccCCCEEEEEEEEEEeeEEEEEeC---------CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEE
Confidence 356889999999999999999999983 5788888887753110 111 234679999999999
Q ss_pred EecC------CCCceeeeeccCCCeeEE
Q psy6276 135 LPLK------ELHSYQLSTAENELGVVI 156 (271)
Q Consensus 135 iS~~------d~~~~~LST~~~eLGVV~ 156 (271)
++.+ +...+.||++++.||.+.
T Consensus 147 ~~v~~~~~~~~~~~I~lt~k~~~LG~~~ 174 (179)
T TIGR00448 147 VALSLKDRRPEGSKIGLTMRQPLLGKLE 174 (179)
T ss_pred EEEEccCCCCCcceEEEEeccCcCCccc
Confidence 6553 234589999999999874
No 40
>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=97.79 E-value=0.00014 Score=52.01 Aligned_cols=66 Identities=9% Similarity=0.209 Sum_probs=51.3
Q ss_pred CCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCceeee
Q psy6276 71 GDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQLS 146 (271)
Q Consensus 71 GDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~LS 146 (271)
|+++.|+|+++.+..|+|+|. ....|++|.++++... .......|++||.|.++ ++.+....+.||
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 GKIYEGKVVKIKDFGAFVEIL--------PGKDGLVHISELSDER--VEKVEDVLKVGDEVKVKVIEVDDRGRISLS 67 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeC--------CCCEEEEEhHHcCCcc--ccCHHHccCCCCEEEEEEEEECCCCcEEee
Confidence 789999999999999999995 2478999998886422 12445789999999999 777543456665
No 41
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=97.77 E-value=0.00011 Score=52.27 Aligned_cols=66 Identities=15% Similarity=0.123 Sum_probs=50.4
Q ss_pred CCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCceeee
Q psy6276 71 GDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSYQLS 146 (271)
Q Consensus 71 GDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~~LS 146 (271)
|+++.|+|+++.+..|+|++. ....|++|.++++... ..+....|++||.|.|+ ++.+. ...+.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~--------~~~~g~~~~~~l~~~~--~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIG--------VKQDGLIHISKMADRF--VSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcC--------CCCEEEEEHHHCCCcc--ccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 789999999999999999985 3478999998876422 22556789999999999 77643 2334443
No 42
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=97.75 E-value=9.4e-05 Score=70.46 Aligned_cols=77 Identities=13% Similarity=0.169 Sum_probs=62.7
Q ss_pred cccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC-CCCc
Q psy6276 65 VIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK-ELHS 142 (271)
Q Consensus 65 ~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~-d~~~ 142 (271)
.-+|.+||+|.|+|++|.+..++|+|... ....|+||.|++.... ..++++.|++||-|.++ +.++ +.+.
T Consensus 12 ~~~P~~GdvV~g~V~~I~d~GafV~L~EY------~gvEGlIhiSElS~~r--i~~i~d~vkvGd~v~vkVl~VD~ekg~ 83 (319)
T PTZ00248 12 QKFPEEDDLVMVKVVRITEMGAYVSLLEY------DDIEGMILMSELSKRR--IRSINKLIRVGRHEVVVVLRVDKEKGY 83 (319)
T ss_pred hhCCCCCCEEEEEEEEEeCCeEEEEecCC------CCcEEEEEHHHhcccc--cCCHHHhcCCCCEEEEEEEEEeCCCCE
Confidence 45799999999999999999999999521 1479999999986422 35789999999999999 8874 3356
Q ss_pred eeeeecc
Q psy6276 143 YQLSTAE 149 (271)
Q Consensus 143 ~~LST~~ 149 (271)
+.||.+.
T Consensus 84 IdLS~K~ 90 (319)
T PTZ00248 84 IDLSKKR 90 (319)
T ss_pred EEEEeee
Confidence 8999975
No 43
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.75 E-value=2.9e-05 Score=80.64 Aligned_cols=101 Identities=11% Similarity=0.151 Sum_probs=80.5
Q ss_pred EeCCEEEEEEeeEEEEeccccCCCcceEEEEeeCCCccccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEe
Q psy6276 28 VRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLR 107 (271)
Q Consensus 28 ~~~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~~~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr 107 (271)
.++|.++++..|...++. .+..|...+. .|++|+++.|+|+++.+..++|+|. ....|++|
T Consensus 590 ~d~G~v~i~~~~~~~~~~------a~~~I~~~~~-----~~~vG~v~~G~V~~I~~fGafVei~--------~~~~Gllh 650 (693)
T PRK11824 590 EDDGTVKIAATDGEAAEA------AKERIEGITA-----EPEVGEIYEGKVVRIVDFGAFVEIL--------PGKDGLVH 650 (693)
T ss_pred CCCceEEEEcccHHHHHH------HHHHHHHhcc-----cCcCCeEEEEEEEEEECCeEEEEEC--------CCCEEEEE
Confidence 447999999999888775 4456665552 3789999999999999999999996 34799999
Q ss_pred ccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCceeeeecc
Q psy6276 108 RENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQLSTAE 149 (271)
Q Consensus 108 ~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~LST~~ 149 (271)
.+++.... ..+..+.|++||.|.++ ++.+..+.+.||++.
T Consensus 651 iSels~~~--v~~~~~v~kvGD~V~VkV~~iD~~grI~LS~k~ 691 (693)
T PRK11824 651 ISEIADER--VEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRKA 691 (693)
T ss_pred eeeccCcc--ccCccceeCCCCEEEEEEEEECCCCcEEEEEEe
Confidence 99986422 23567889999999999 888654678999864
No 44
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.74 E-value=0.00015 Score=53.19 Aligned_cols=64 Identities=20% Similarity=0.243 Sum_probs=50.2
Q ss_pred CCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCceeee
Q psy6276 71 GDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSYQLS 146 (271)
Q Consensus 71 GDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~~LS 146 (271)
||+|.|+|+++.+..+.|++. ..+.|.+|.+++.... .. .+.|++||.|.|| ++++. .+.+.||
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 GMLVNARVKKVLSNGLILDFL--------SSFTGTVDFLHLDPEK---SS-KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEc--------CCceEEEEHHHcCCcc---Cc-ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 899999999999999999985 3489999998874321 12 7789999999999 88753 2345554
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=97.73 E-value=0.00016 Score=52.71 Aligned_cols=66 Identities=17% Similarity=0.214 Sum_probs=52.3
Q ss_pred CCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCceeee
Q psy6276 71 GDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSYQLS 146 (271)
Q Consensus 71 GDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~~LS 146 (271)
|++|.|+|++|.+..+.|++. ....|++|.+++.... ..+....|++||.|.++ ++++. .+.+.||
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 GQVVKGTIRKLRPSGIFVKLS--------DHIKGLVPPMHLADVR--LKHPEKKFKPGLKVKCRVLSVEPERKRLVLT 68 (69)
T ss_pred CCEEEEEEEEEeccEEEEEec--------CCcEEEEEHHHCCCcc--ccCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence 799999999999999999984 3479999998875422 22466789999999999 88753 3556666
No 46
>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=97.66 E-value=0.00037 Score=52.50 Aligned_cols=67 Identities=15% Similarity=0.203 Sum_probs=53.8
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCC-Cceeee
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKEL-HSYQLS 146 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~-~~~~LS 146 (271)
+.|++|.|.|.+|.+..+.+++. + ..+.|++|.+++... ..|++||.+.|+ ++++.. +.+.||
T Consensus 3 ~~G~~v~g~V~si~d~G~~v~~g-~------~gv~Gfl~~~~~~~~--------~~~~~Gq~v~~~V~~vd~~~~~v~ls 67 (74)
T cd05694 3 VEGMVLSGCVSSVEDHGYILDIG-I------PGTTGFLPKKDAGNF--------SKLKVGQLLLCVVEKVKDDGRVVSLS 67 (74)
T ss_pred CCCCEEEEEEEEEeCCEEEEEeC-C------CCcEEEEEHHHCCcc--------cccCCCCEEEEEEEEEECCCCEEEEE
Confidence 67999999999999999999983 1 247999999876431 789999999999 877533 567888
Q ss_pred eccC
Q psy6276 147 TAEN 150 (271)
Q Consensus 147 T~~~ 150 (271)
++..
T Consensus 68 ~k~~ 71 (74)
T cd05694 68 ADPS 71 (74)
T ss_pred Eeec
Confidence 8643
No 47
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=97.59 E-value=0.00019 Score=56.36 Aligned_cols=76 Identities=18% Similarity=0.223 Sum_probs=57.0
Q ss_pred CEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhH---------hhhcCCCCCCEEEEE-EecCC--
Q psy6276 72 DVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRI---------EMYKCYRPGDIILAR-LPLKE-- 139 (271)
Q Consensus 72 DIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~---------~m~~~f~~GDIV~Ak-iS~~d-- 139 (271)
++|.|+|+++....++|++. +..|++|.+++........ .....|++||.|.++ ++.+.
T Consensus 1 ~vv~g~V~~i~~~GifV~l~---------~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~ 71 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIG---------PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKE 71 (99)
T ss_pred CEEEEEEEEEEeccEEEEEc---------CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHH
Confidence 47999999999999999994 2588888887753211100 123678999999999 77752
Q ss_pred ----CCceeeeeccCCCeeEE
Q psy6276 140 ----LHSYQLSTAENELGVVI 156 (271)
Q Consensus 140 ----~~~~~LST~~~eLGVV~ 156 (271)
...+.||++++.||.+.
T Consensus 72 ~~~~~~~i~ls~k~~~~g~~~ 92 (99)
T cd04460 72 RRPRESKIGLTMRQPGLGKLE 92 (99)
T ss_pred CcCCCceEEEEEecCCCCcHH
Confidence 14699999999999763
No 48
>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=97.58 E-value=0.00039 Score=54.12 Aligned_cols=72 Identities=14% Similarity=0.170 Sum_probs=52.1
Q ss_pred CCCCCEEEEEEEEEecc--eEEEEEeeecCcccCCceeeEEeccccccch-hhhHhhhcCCCCCCEEEEE-EecC-CCCc
Q psy6276 68 PTPGDVVTARIMAVQQH--LCKAHVISVGNTALSRTFRALLRRENVRATE-IDRIEMYKCYRPGDIILAR-LPLK-ELHS 142 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~--~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te-~d~~~m~~~f~~GDIV~Ak-iS~~-d~~~ 142 (271)
|++|+++.|+|+++.+. .|+|+|. ....|+||.+++.... ....+..+.|++||.|.++ +..+ +...
T Consensus 5 ~~~G~iy~g~V~~i~~~~~GaFV~l~--------~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~ 76 (88)
T cd04453 5 PIVGNIYLGRVKKIVPGLQAAFVDIG--------LGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKG 76 (88)
T ss_pred CCCCCEEEEEEEEeccCCcEEEEEeC--------CCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCC
Confidence 57999999999999996 8999995 2468999999874311 1122457789999999999 6543 1233
Q ss_pred eeeee
Q psy6276 143 YQLST 147 (271)
Q Consensus 143 ~~LST 147 (271)
..||+
T Consensus 77 ~~lt~ 81 (88)
T cd04453 77 PRLTT 81 (88)
T ss_pred ceEEE
Confidence 44554
No 49
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=97.55 E-value=0.00037 Score=66.20 Aligned_cols=73 Identities=14% Similarity=0.088 Sum_probs=59.2
Q ss_pred cCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCcee
Q psy6276 67 VPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSYQ 144 (271)
Q Consensus 67 iP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~~ 144 (271)
-+++|++|.|.|+++.+..++|++. ...|++|.+++.... ..+..+.|++||.|.|+ ++.+. ...+.
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---------GVSGLLHISEISHEH--IETPHSVFNVNDEMKVMIIDLDAERGRIS 261 (318)
T ss_pred cCCCCCEEEEEEEEEECCeEEEEEC---------CEEEEEEHHHccccc--ccChhhccCCCCEEEEEEEEEeCCCCEEE
Confidence 3688999999999999999999984 257999999987532 23578899999999999 88753 35688
Q ss_pred eeeccC
Q psy6276 145 LSTAEN 150 (271)
Q Consensus 145 LST~~~ 150 (271)
||++..
T Consensus 262 LS~K~l 267 (318)
T PRK07400 262 LSTKQL 267 (318)
T ss_pred EEEecc
Confidence 888753
No 50
>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=97.53 E-value=7.4e-05 Score=77.53 Aligned_cols=91 Identities=10% Similarity=0.181 Sum_probs=71.8
Q ss_pred EeCCEEEEEEeeEEEEeccccCCCcceEEEEeeCCCccccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEe
Q psy6276 28 VRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLR 107 (271)
Q Consensus 28 ~~~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~~~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr 107 (271)
.++|.++++..+...++. .+..|.+... .|++|+++.|+|+++.+..++|+|. ....|++|
T Consensus 587 ~ddG~V~i~~~~~~~~~~------a~~~I~~~~~-----~~~~G~i~~G~V~~I~~~GafVei~--------~g~~GllH 647 (684)
T TIGR03591 587 EDDGTVKIAASDGEAAEA------AIKMIEGITA-----EPEVGKIYEGKVVRIMDFGAFVEIL--------PGKDGLVH 647 (684)
T ss_pred ecCeEEEEEECcHHHHHH------HHHHHHhhhc-----ccccCcEEEEEEEEEeCCEEEEEEC--------CCcEEEEE
Confidence 347889988888777665 3445555542 4899999999999999999999996 25799999
Q ss_pred ccccccchhhhHhhhcCCCCCCEEEEE-EecCC
Q psy6276 108 RENVRATEIDRIEMYKCYRPGDIILAR-LPLKE 139 (271)
Q Consensus 108 ~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d 139 (271)
++++... ...+..+.|++||.|+++ ++.+.
T Consensus 648 iSei~~~--~v~~~~~~~kvGD~V~VkVi~id~ 678 (684)
T TIGR03591 648 ISEIANE--RVEKVEDVLKEGDEVKVKVLEIDK 678 (684)
T ss_pred HHHcCCC--cccChhhccCCCCEEEEEEEEECC
Confidence 9998542 223678899999999999 88764
No 51
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=97.48 E-value=0.00032 Score=70.95 Aligned_cols=74 Identities=16% Similarity=0.124 Sum_probs=62.7
Q ss_pred cCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC-CCCcee
Q psy6276 67 VPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK-ELHSYQ 144 (271)
Q Consensus 67 iP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~-d~~~~~ 144 (271)
-.++|++|-|.|+++++..++|||. .+.|++|++++.... .....+.|++||-|.++ ++++ +...+.
T Consensus 189 ~l~~G~vV~G~V~~It~~GafVdig---------GvdGLlHiseiS~~r--v~~P~~vvkvGd~VkvkVi~~D~e~~RVs 257 (541)
T COG0539 189 KLEVGEVVEGVVKNITDYGAFVDIG---------GVDGLLHISEISWKR--VDHPSEVVKVGDEVKVKVISLDEERGRVS 257 (541)
T ss_pred cCCCCceEEEEEEEeecCcEEEEec---------CeeeEEehhhccccc--cCCHHHhcccCCEEEEEEEEEccCCCeEE
Confidence 3589999999999999999999995 489999999987543 34789999999999999 9997 445699
Q ss_pred eeeccCC
Q psy6276 145 LSTAENE 151 (271)
Q Consensus 145 LST~~~e 151 (271)
||++...
T Consensus 258 LSlK~l~ 264 (541)
T COG0539 258 LSLKQLE 264 (541)
T ss_pred EEehhcc
Confidence 9998643
No 52
>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=97.42 E-value=0.00074 Score=50.12 Aligned_cols=67 Identities=15% Similarity=0.143 Sum_probs=51.4
Q ss_pred CCEEE-EEEEEE-ecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCC-Cceeee
Q psy6276 71 GDVVT-ARIMAV-QQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKEL-HSYQLS 146 (271)
Q Consensus 71 GDIVI-GrVt~V-~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~-~~~~LS 146 (271)
|+++- |+|+++ .+..+.|++. ....|.+|.+++.... .....+.|++||.|.|+ ++++.. +.+.||
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 GAVVDSVKVTKVEPDLGAVFELK--------DGLLGFVHISHLSDDK--VPSDTGPFKAGTTHKARIIGYSPMDGLLQLS 70 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeC--------CCCEEEEEHHHCCcch--hcCcccccCCCCEEEEEEEEEeCCCCEEEEe
Confidence 77888 999999 6888999984 3478999999885422 23467889999999999 877532 457776
Q ss_pred e
Q psy6276 147 T 147 (271)
Q Consensus 147 T 147 (271)
+
T Consensus 71 ~ 71 (71)
T cd05696 71 L 71 (71)
T ss_pred C
Confidence 4
No 53
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=97.39 E-value=0.00041 Score=61.33 Aligned_cols=83 Identities=23% Similarity=0.341 Sum_probs=64.3
Q ss_pred cccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhh-----hH----hhhcCCCCCCEEEEE-
Q psy6276 65 VIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEID-----RI----EMYKCYRPGDIILAR- 134 (271)
Q Consensus 65 ~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d-----~~----~m~~~f~~GDIV~Ak- 134 (271)
.+.|..|.+|-|.|+++..-.++|.|. |+.|++|.+++..-+.+ .. .-...|+.||.||||
T Consensus 76 ~fkP~~gEVV~GeVv~~~~~G~fV~ig---------p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RI 146 (183)
T COG1095 76 VFKPFRGEVVEGEVVEVVEFGAFVRIG---------PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARI 146 (183)
T ss_pred EEEeccccEEEEEEEEEeecceEEEec---------cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEE
Confidence 567889999999999999999999994 88999999888642111 01 233489999999999
Q ss_pred E--ecCCC----CceeeeeccCCCeeEE
Q psy6276 135 L--PLKEL----HSYQLSTAENELGVVI 156 (271)
Q Consensus 135 i--S~~d~----~~~~LST~~~eLGVV~ 156 (271)
+ |+.+. ..+.||++++.||++.
T Consensus 147 v~~s~~~~~~~~~~I~lTmrq~~LGkle 174 (183)
T COG1095 147 VGVSLKSRRPRESKIGLTMRQPGLGKLE 174 (183)
T ss_pred EEEecccCccccceEEEEeccccCCcch
Confidence 5 45443 3478999999999874
No 54
>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=97.38 E-value=0.00056 Score=47.38 Aligned_cols=55 Identities=11% Similarity=0.199 Sum_probs=44.2
Q ss_pred EEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC
Q psy6276 74 VTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK 138 (271)
Q Consensus 74 VIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~ 138 (271)
|.|+|+++.+..+.|++. ....|++|.+++.... ..++.+.|++||.|+|+ ++.+
T Consensus 1 v~g~V~~v~~~g~~v~l~--------~~~~g~~~~~~~~~~~--~~~~~~~~~~G~~v~~~v~~~d 56 (65)
T cd00164 1 VTGKVVSITKFGVFVELE--------DGVEGLVHISELSDKF--VKDPSEVFKVGDEVEVKVLEVD 56 (65)
T ss_pred CEEEEEEEEeeeEEEEec--------CCCEEEEEHHHCCCcc--ccCHhhEeCCCCEEEEEEEEEc
Confidence 579999999999999985 3578999998875422 12467889999999999 8775
No 55
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=97.38 E-value=0.00048 Score=63.90 Aligned_cols=133 Identities=17% Similarity=0.127 Sum_probs=87.6
Q ss_pred ccccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCC-C
Q psy6276 64 EVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKEL-H 141 (271)
Q Consensus 64 ~~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~-~ 141 (271)
.+-.|..|++|+|+|.+|.+-.+.|.+.-..| .+|++|.|++.. .-..++++.++.|--|.|+ |..+.. +
T Consensus 5 ~~~~PeeGEiVv~tV~~V~~~GAyv~L~EY~g------~Eg~ihiSEvas--~wVknIrd~vkegqkvV~kVlrVd~~rg 76 (269)
T COG1093 5 RREYPEEGEIVVGTVKQVADYGAYVELDEYPG------KEGFIHISEVAS--GWVKNIRDYVKEGQKVVAKVLRVDPKRG 76 (269)
T ss_pred ccCCCCCCcEEEEEEEEeeccccEEEeeccCC------eeeeEEHHHHHH--HHHHHHHHHhhcCCeEEEEEEEEcCCCC
Confidence 45689999999999999999999999864332 589999999864 2356899999999999999 988654 3
Q ss_pred ceeeeeccCCCeeEEEEc--------cCCCeeEeccC-ccCc-hhhhhhhhhhhHHHhcccccceeeeeeccCc
Q psy6276 142 SYQLSTAENELGVVIALS--------EAASLFRSSEK-LTND-IEFLKQEKLKLYEELSSSQKENEILRQTTGD 205 (271)
Q Consensus 142 ~~~LST~~~eLGVV~A~c--------~cG~~Mvp~s~-~~~c-~~~~~~e~rKla~~~~s~~~~~~~~~~~~~~ 205 (271)
.+.||.+.-.--=.. .| +.-..|..... +... -+|=..-..+|..+++|.+.+||-+...+++
T Consensus 77 ~IDLSlkrV~~~q~~-~k~~~wk~~qka~klle~aaekl~~~~ee~~~~vg~~L~e~fG~~y~aFE~aa~~g~~ 149 (269)
T COG1093 77 HIDLSLKRVTEHQRR-KKIQEWKKEQKADKLLELAAEKLGKDLEEAYEEVGWKLEEEFGSLYDAFEAAAKEGGE 149 (269)
T ss_pred eEeeehhhCCHHHHH-HHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHhHHHHHHhCCHHHHHHHHHhcCCc
Confidence 478888642100000 00 01111111110 1111 1234455578889999999999955544443
No 56
>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=97.36 E-value=0.0012 Score=48.44 Aligned_cols=53 Identities=26% Similarity=0.384 Sum_probs=44.4
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK 138 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~ 138 (271)
..|++|.|+|.++....+.|+|. ...|+||.+++.. .+.|++||-|.+. .+..
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig---------~~eg~lp~~e~~~--------~~~~~~Gd~v~v~v~~v~ 55 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLG---------KVEAILPKKEQIP--------GESYRPGDRIKAYVLEVR 55 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcC---------CeEEEeeHHHCCC--------CCcCCCCCEEEEEEEEEe
Confidence 57999999999999999999984 2689999877642 3568999999999 7764
No 57
>PHA02945 interferon resistance protein; Provisional
Probab=97.28 E-value=0.0011 Score=52.24 Aligned_cols=72 Identities=10% Similarity=0.065 Sum_probs=55.5
Q ss_pred cCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEecccc--ccchhhhHhhhcCCCCCCEEEEE-EecCCC-Cc
Q psy6276 67 VPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENV--RATEIDRIEMYKCYRPGDIILAR-LPLKEL-HS 142 (271)
Q Consensus 67 iP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdv--r~te~d~~~m~~~f~~GDIV~Ak-iS~~d~-~~ 142 (271)
+|.+|++|+|+|+. .+..+.|.+.-.+ ..+|+||.+.+ .. .-... ++.+ .|..|.|| |..+.. ..
T Consensus 8 ~P~~GelvigtV~~-~d~ga~v~L~EY~------g~eg~i~~seveva~--~wvK~-rd~l-~GqkvV~KVirVd~~kg~ 76 (88)
T PHA02945 8 LPNVGDVLKGKVYE-NGYALYIDLFDYP------HSEAILAESVQMHMN--RYFKY-RDKL-VGKTVKVKVIRVDYTKGY 76 (88)
T ss_pred CCCCCcEEEEEEEe-cCceEEEEecccC------CcEEEEEeehhhhcc--ceEee-eeEe-cCCEEEEEEEEECCCCCE
Confidence 69999999999999 9999999985322 35899999855 32 11223 8999 99999999 888644 45
Q ss_pred eeeeecc
Q psy6276 143 YQLSTAE 149 (271)
Q Consensus 143 ~~LST~~ 149 (271)
+.||.+.
T Consensus 77 IDlSlK~ 83 (88)
T PHA02945 77 IDVNYKR 83 (88)
T ss_pred EEeEeeE
Confidence 7888764
No 58
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.18 E-value=0.0011 Score=69.13 Aligned_cols=72 Identities=11% Similarity=0.122 Sum_probs=57.3
Q ss_pred cCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEecccccc--chhhhHhhhcCCCCCCEEEEE-EecCCCCce
Q psy6276 67 VPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRA--TEIDRIEMYKCYRPGDIILAR-LPLKELHSY 143 (271)
Q Consensus 67 iP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~--te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~ 143 (271)
.|++|++|.|+|++|.+-.++|+|. ....|++|+|++.. +.....+..+.|++||.|.++ +++++...+
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~--------~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~~gKI 715 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLL--------PGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDDRGKL 715 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEec--------CCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECCCCCe
Confidence 4899999999999999999999995 34799999998742 112234789999999999999 888754455
Q ss_pred eee
Q psy6276 144 QLS 146 (271)
Q Consensus 144 ~LS 146 (271)
.|+
T Consensus 716 ~L~ 718 (719)
T TIGR02696 716 SLV 718 (719)
T ss_pred eec
Confidence 554
No 59
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.17 E-value=0.0014 Score=47.21 Aligned_cols=59 Identities=17% Similarity=0.205 Sum_probs=47.2
Q ss_pred CCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC
Q psy6276 71 GDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK 138 (271)
Q Consensus 71 GDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~ 138 (271)
|+++.|.|+++.+..++|++. ....|++|.+++.... ...+....|++||.|.|+ ++.+
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~--------~~~~Glv~~~~l~~~~-~~~~~~~~~~~G~~v~v~v~~id 60 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLD--------GGIDGLVHISDISWTQ-RVRHPSEIYKKGQEVEAVVLNID 60 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeC--------CCCEEEEEHHHCCCcc-ccCChhhEECCCCEEEEEEEEEE
Confidence 789999999999999999995 2478999999886211 122456789999999999 7764
No 60
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=97.14 E-value=0.0059 Score=45.87 Aligned_cols=63 Identities=17% Similarity=0.251 Sum_probs=50.5
Q ss_pred cCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCceee
Q psy6276 67 VPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQL 145 (271)
Q Consensus 67 iP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~L 145 (271)
-+++|+++.|+|+++.+..++|++. ....|++|.+++ ...|++||.+.++ .+..+.+.+.|
T Consensus 13 ~~~~G~~~~g~V~~i~~~G~fV~l~--------~~~~Glv~~se~----------~~~~~iGd~v~v~I~~i~e~~~i~l 74 (77)
T cd04473 13 DLEVGKLYKGKVNGVAKYGVFVDLN--------DHVRGLIHRSNL----------LRDYEVGDEVIVQVTDIPENGNIDL 74 (77)
T ss_pred hCCCCCEEEEEEEeEecceEEEEEC--------CCcEEEEEchhc----------cCcCCCCCEEEEEEEEECCCCcEEE
Confidence 3689999999999999999999985 358999998653 4569999999999 77644355666
Q ss_pred ee
Q psy6276 146 ST 147 (271)
Q Consensus 146 ST 147 (271)
|.
T Consensus 75 ~~ 76 (77)
T cd04473 75 IP 76 (77)
T ss_pred EE
Confidence 53
No 61
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=97.11 E-value=0.0032 Score=47.13 Aligned_cols=72 Identities=8% Similarity=0.175 Sum_probs=54.6
Q ss_pred CCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCceeeeecc
Q psy6276 71 GDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQLSTAE 149 (271)
Q Consensus 71 GDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~LST~~ 149 (271)
|+++.|+|+++.+..++|+|... .....|++|.+++..... ..+....|++||.|.++ ++.+ ...+.||.+.
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~-----~~~~~gll~~s~l~~~~~-~~~~~~~~~~Gd~v~v~v~~vd-~~~i~~s~k~ 73 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGL-----KGRKEGLVHISQLSFEGR-VANPSDVVKRGQKVKVKVISIQ-NGKISLSMKD 73 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCC-----CCCcEEEEEhHhccCCCC-cCChhheeCCCCEEEEEEEEEe-CCEEEEEEEe
Confidence 78999999999999999999521 024689999998864221 12567889999999999 7776 5567777753
No 62
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=97.09 E-value=0.0019 Score=61.41 Aligned_cols=75 Identities=12% Similarity=0.081 Sum_probs=59.6
Q ss_pred ccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCce
Q psy6276 66 IVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSY 143 (271)
Q Consensus 66 yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~ 143 (271)
+-.++||+|.|+|+++..+.+.|+|. ....|+||.+++.... ..+..+.|++||.|.++ ++..+ ...+
T Consensus 27 ~~~~~G~iv~G~V~~i~~~g~~Vdig--------~k~~g~lp~sEis~~~--~~~~~~~~~~G~~v~~~Vi~~~~~~~~i 96 (318)
T PRK07400 27 YHFKPGDIVNGTVFSLEPRGALIDIG--------AKTAAFMPIQEMSINR--VEGPEEVLQPNETREFFILSDENEDGQL 96 (318)
T ss_pred hhcCCCCEEEEEEEEEECCEEEEEEC--------CCeEEEEEHHHhcccc--ccCHHHccCCCCEEEEEEEEEeCCCCeE
Confidence 34699999999999999999999994 3468999999886432 23567889999999999 87643 3568
Q ss_pred eeeeccC
Q psy6276 144 QLSTAEN 150 (271)
Q Consensus 144 ~LST~~~ 150 (271)
.||.+..
T Consensus 97 ~lS~k~~ 103 (318)
T PRK07400 97 TLSIRRI 103 (318)
T ss_pred EEehhhh
Confidence 8998753
No 63
>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=96.94 E-value=0.0042 Score=45.38 Aligned_cols=61 Identities=15% Similarity=0.190 Sum_probs=48.6
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK 138 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~ 138 (271)
.+|+++.|+|+++.+..++|++. ....|++|.+++...+ ...+....|++||.|.++ ++.+
T Consensus 2 ~~g~~~~g~V~~i~~~G~fv~l~--------~~~~Gl~~~~~l~~~~-~~~~~~~~~~~Gd~v~v~v~~id 63 (72)
T cd05689 2 PEGTRLFGKVTNLTDYGCFVELE--------EGVEGLVHVSEMDWTN-KNIHPSKVVSLGDEVEVMVLDID 63 (72)
T ss_pred cCCCEEEEEEEEEEeeEEEEEcC--------CCCEEEEEEEeccCcc-cccCcccEeCCCCEEEEEEEEee
Confidence 46999999999999999999995 2478999999885321 122455789999999999 7765
No 64
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=96.81 E-value=0.01 Score=42.94 Aligned_cols=64 Identities=14% Similarity=0.237 Sum_probs=47.7
Q ss_pred CCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCceeeee
Q psy6276 71 GDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSYQLST 147 (271)
Q Consensus 71 GDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~~LST 147 (271)
|++|.|+|+++....+.|++. .+.|.+|.+++...... +... .+||.+.|+ ++++. .+.+.||.
T Consensus 1 G~iv~g~V~~v~~~G~~v~l~---------g~~gfip~s~~~~~~~~--~~~~--~vG~~i~~~i~~vd~~~~~i~lS~ 66 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDIE---------GVRAFLPASQVDLRPVE--DLDE--YVGKELKFKIIEIDRERNNIVLSR 66 (67)
T ss_pred CCEEEEEEEEEECCeEEEEEC---------CEEEEEEHHHCCCcccC--ChHH--hCCCEEEEEEEEEeCCCCEEEEEc
Confidence 789999999999999999982 47999999887542211 1222 389999999 88763 35577764
No 65
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=96.80 E-value=0.0044 Score=54.35 Aligned_cols=84 Identities=15% Similarity=0.128 Sum_probs=60.3
Q ss_pred cccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEecccccc---chhh-h------HhhhcCCCCCCEEEEE
Q psy6276 65 VIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRA---TEID-R------IEMYKCYRPGDIILAR 134 (271)
Q Consensus 65 ~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~---te~d-~------~~m~~~f~~GDIV~Ak 134 (271)
.+-|..|.+|.|+|+++....+.+++. +|.+.+|.+++.. .+.+ . .+-...++.||.||+|
T Consensus 76 vFrPf~gEVv~g~V~~v~~~G~~v~~G---------p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~r 146 (176)
T PTZ00162 76 VFKPFKDEVLDAIVTDVNKLGFFAQAG---------PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLR 146 (176)
T ss_pred EEecCCCCEEEEEEEEEecceEEEEee---------CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEE
Confidence 466889999999999999999999995 5667777666641 1110 0 0124578999999999
Q ss_pred -Ee--cCCC-CceeeeeccCCCeeEEE
Q psy6276 135 -LP--LKEL-HSYQLSTAENELGVVIA 157 (271)
Q Consensus 135 -iS--~~d~-~~~~LST~~~eLGVV~A 157 (271)
++ +... .....|++++.||.+.|
T Consensus 147 V~~v~~~~~~~~~i~T~~~~~LG~~~~ 173 (176)
T PTZ00162 147 LQGVRYDASNLFAIATINSDYLGPIES 173 (176)
T ss_pred EEEEEecCCCcEEEEEecCCCcCcccc
Confidence 54 3322 23567889999999855
No 66
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.80 E-value=0.0094 Score=60.15 Aligned_cols=72 Identities=15% Similarity=0.213 Sum_probs=58.0
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCceeee
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSYQLS 146 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~~LS 146 (271)
++||+|.|.|+++.+..++|.+. ..+.|++|.+++... ...+..+.|++||.|.|+ ++++. ...+.||
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 KKGSIVTGTVTEVKDKGAFVELE--------DGVEGLIRASELSRD--RVEDATEVLKVGDEVEAKVINIDRKNRRISLS 528 (565)
T ss_pred CCCCEEEEEEEEEecCceEEecC--------CCcEEEEEHHHhcch--hccCccccCCCCCEEEEEEEEEccccCEEEEE
Confidence 78999999999999999999985 357999999887542 234678899999999999 88752 3568888
Q ss_pred eccC
Q psy6276 147 TAEN 150 (271)
Q Consensus 147 T~~~ 150 (271)
++..
T Consensus 529 ~k~~ 532 (565)
T PRK06299 529 IKAL 532 (565)
T ss_pred eeeh
Confidence 8643
No 67
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=96.78 E-value=0.0041 Score=62.26 Aligned_cols=73 Identities=12% Similarity=0.153 Sum_probs=58.0
Q ss_pred cCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCC-----
Q psy6276 67 VPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKEL----- 140 (271)
Q Consensus 67 iP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~----- 140 (271)
-.++|++|.|+|+++.+..++|+|. ....|++|.+++.... ..++...|++||.|.|+ ++++..
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 TVKEGDVVEGTVTRLAPFGAFVELA--------PGVEGMVHISELSWSR--VQKADEAVSVGDTVRVKVLGIERAKKGKG 268 (491)
T ss_pred hCCCCCEEEEEEEEEeCCeEEEEcC--------CCcEEEEEHHHCCCcc--ccChhHhcCCCCEEEEEEEEEecccCCcc
Confidence 3689999999999999999999984 2468999999986432 23577889999999999 877532
Q ss_pred Cceeeeecc
Q psy6276 141 HSYQLSTAE 149 (271)
Q Consensus 141 ~~~~LST~~ 149 (271)
..+.||++.
T Consensus 269 ~ri~lS~K~ 277 (491)
T PRK13806 269 LRISLSIKQ 277 (491)
T ss_pred eEEEEEehh
Confidence 247888754
No 68
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.69 E-value=0.021 Score=54.91 Aligned_cols=72 Identities=14% Similarity=0.183 Sum_probs=55.9
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC-CCCceee
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK-ELHSYQL 145 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~-d~~~~~L 145 (271)
.++|++|.|.|+++.+..++|++. ..+.|++|.+++.... ..+....|++||.|.|+ ++++ +.+.+.|
T Consensus 275 ~~~G~~v~g~V~~i~~~G~fV~l~--------~gi~Glv~~se~~~~~--~~~~~~~~~~Gd~v~v~V~~id~e~~~i~l 344 (390)
T PRK06676 275 LPEGDVIEGTVKRLTDFGAFVEVL--------PGVEGLVHISQISHKH--IATPSEVLEEGQEVKVKVLEVNEEEKRISL 344 (390)
T ss_pred hcCCcEEEEEEEEEeCceEEEEEC--------CCCeEEEEhHHcCccc--cCChhhccCCCCEEEEEEEEEECCCCEEEE
Confidence 468999999999999999999984 2479999999875422 22456789999999999 7775 2355777
Q ss_pred eecc
Q psy6276 146 STAE 149 (271)
Q Consensus 146 ST~~ 149 (271)
|++.
T Consensus 345 s~k~ 348 (390)
T PRK06676 345 SIKA 348 (390)
T ss_pred EEEe
Confidence 7654
No 69
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.68 E-value=0.0053 Score=61.68 Aligned_cols=73 Identities=14% Similarity=0.166 Sum_probs=58.0
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCC-Cceee
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKEL-HSYQL 145 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~-~~~~L 145 (271)
.++||+|.|+|+++..+.+.|+|. ..+.|+||.+++.... ..+....|.+||-|.|. ++..+. +.+.|
T Consensus 33 ~~~GdiV~G~V~~v~~~gv~VdIg--------~k~eG~Ip~~Els~~~--~~~~~~~~~vGd~Ie~~V~~~~~~~g~liL 102 (486)
T PRK07899 33 FNDGDIVEGTVVKVDRDEVLLDIG--------YKTEGVIPSRELSIKH--DVDPNEVVEVGDEVEALVLQKEDKEGRLIL 102 (486)
T ss_pred CCCCCEEEEEEEEEECCcEEEEEC--------CCcEEEEEHHHhcccc--cCChhhcCCCCCEEEEEEEEEECCCCeEEE
Confidence 589999999999999999999994 3579999998875421 12456679999999999 877543 46889
Q ss_pred eeccC
Q psy6276 146 STAEN 150 (271)
Q Consensus 146 ST~~~ 150 (271)
|.+..
T Consensus 103 S~k~~ 107 (486)
T PRK07899 103 SKKRA 107 (486)
T ss_pred Eehhh
Confidence 98743
No 70
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.65 E-value=0.0083 Score=57.74 Aligned_cols=71 Identities=13% Similarity=0.117 Sum_probs=56.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCceee
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSYQL 145 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~~L 145 (271)
.++|++|.|+|+++.+..++|++. ...|++|.+++.... ..++.+.|++||.|.|+ ++++. ...+.|
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---------GVDGLVHISELSHER--VEKPSEVVSVGQEVEVKVLSIDWETERISL 258 (390)
T ss_pred CCCCCEEEEEEEEEecceEEEEeC---------CeEEEEEHHHcCccc--cCCHHHhcCCCCEEEEEEEEEeCCCCEEEE
Confidence 589999999999999999999984 367999999876422 23567789999999999 88743 356788
Q ss_pred eecc
Q psy6276 146 STAE 149 (271)
Q Consensus 146 ST~~ 149 (271)
|.+.
T Consensus 259 S~k~ 262 (390)
T PRK06676 259 SLKD 262 (390)
T ss_pred EEee
Confidence 8763
No 71
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=96.55 E-value=0.0077 Score=60.30 Aligned_cols=72 Identities=18% Similarity=0.206 Sum_probs=57.6
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC-CCCceeee
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK-ELHSYQLS 146 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~-d~~~~~LS 146 (271)
.+|++|.|+|+++.+..++|++. ....|++|.+++..... .+..+.|++||.|.|+ ++++ +.+.+.||
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 APGTTVTGTVEKRAQFGLFVNLA--------PGVTGLLPASVISRAGK--PATYEKLKPGDSVTLVVEEIDTAKRKISLA 447 (491)
T ss_pred CCCCEEEEEEEEEecCceEEEcC--------CCcEEEEEHHHcCcccc--cchhhcCCCCCEEEEEEEEEeCCCCEEEEE
Confidence 47999999999999999999984 35899999998864322 3567889999999999 7774 33568888
Q ss_pred eccC
Q psy6276 147 TAEN 150 (271)
Q Consensus 147 T~~~ 150 (271)
++..
T Consensus 448 ~~~~ 451 (491)
T PRK13806 448 PAGA 451 (491)
T ss_pred eehh
Confidence 8743
No 72
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.51 E-value=0.0074 Score=60.90 Aligned_cols=72 Identities=18% Similarity=0.226 Sum_probs=57.3
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC-CCCceeee
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK-ELHSYQLS 146 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~-d~~~~~LS 146 (271)
.+|++|.|+|+++.+..++|+|. ....|++|.+++..... ..+....|++||.|.|+ ++++ +.+.+.||
T Consensus 372 ~~G~~v~g~V~~v~~~G~fV~l~--------~~v~g~i~~s~l~~~~~-~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls 442 (565)
T PRK06299 372 PVGDVVEGKVKNITDFGAFVGLE--------GGIDGLVHLSDISWDKK-GEEAVELYKKGDEVEAVVLKVDVEKERISLG 442 (565)
T ss_pred CCCCEEEEEEEEEecceEEEECC--------CCCEEEEEHHHcCcccc-ccChHhhCCCCCEEEEEEEEEeCCCCEEEEE
Confidence 58999999999999999999984 35789999999864221 13567889999999999 8775 23568888
Q ss_pred ecc
Q psy6276 147 TAE 149 (271)
Q Consensus 147 T~~ 149 (271)
++.
T Consensus 443 ~k~ 445 (565)
T PRK06299 443 IKQ 445 (565)
T ss_pred Eeh
Confidence 753
No 73
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.44 E-value=0.0068 Score=60.66 Aligned_cols=71 Identities=21% Similarity=0.237 Sum_probs=58.1
Q ss_pred ccccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC---
Q psy6276 64 EVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE--- 139 (271)
Q Consensus 64 ~~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d--- 139 (271)
..|-.+.|++|.|+|.++....+.|++. ...|+||.++.- .++.|++||-|+|. +.+..
T Consensus 128 ~eyk~~~GeIV~G~V~ri~~~giiVDLg---------gvea~LP~sE~i--------p~E~~~~GdrIka~I~~Vd~~~k 190 (470)
T PRK09202 128 EEYKDRVGEIITGVVKRVERGNIIVDLG---------RAEAILPRKEQI--------PRENFRPGDRVRAYVYEVRKEAR 190 (470)
T ss_pred HHHHhhcCCEEEEEEEEEecCCEEEEEC---------CeEEEecHHHcC--------CCccCCCCCEEEEEEEEEecCCC
Confidence 3577789999999999999999999983 368999987753 46779999999999 77643
Q ss_pred CCceeeeeccCC
Q psy6276 140 LHSYQLSTAENE 151 (271)
Q Consensus 140 ~~~~~LST~~~e 151 (271)
++++.||-+.++
T Consensus 191 g~qIilSRt~p~ 202 (470)
T PRK09202 191 GPQIILSRTHPE 202 (470)
T ss_pred CCeEEEEeCcHH
Confidence 357899988765
No 74
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.41 E-value=0.012 Score=59.18 Aligned_cols=144 Identities=13% Similarity=0.102 Sum_probs=89.6
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCceee
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSYQL 145 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~~L 145 (271)
-++|++|-|+|+++.+..++|+|. ...|++|.+++.... ..+..+.|++||.|.++ ++++. ...+.|
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---------GVDGLVHVSELSWKH--IDHPSEVVEVGQEVTVEVLDVDMDRERVSL 274 (486)
T ss_pred ccCCCEEEEEEEEEECCeEEEEEC---------CEEEEEEHHHCCCcc--cCCHHHhcCCCCEEEEEEEEEECCCCEEEE
Confidence 368999999999999999999993 368999999986432 23567889999999999 87742 356888
Q ss_pred eeccCC-----------------CeeEEEEccCCCeeEec-cCccCchhhhhhhhhhhHHHhcccccc-eeeeeeccCce
Q psy6276 146 STAENE-----------------LGVVIALSEAASLFRSS-EKLTNDIEFLKQEKLKLYEELSSSQKE-NEILRQTTGDL 206 (271)
Q Consensus 146 ST~~~e-----------------LGVV~A~c~cG~~Mvp~-s~~~~c~~~~~~e~rKla~~~~s~~~~-~~~~~~~~~~~ 206 (271)
|++... -|.|..+...|..+... +....|+. .+++...-. ..-.....=.+
T Consensus 275 SlK~~~~dPw~~~~~~~~vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~----------SeLs~~~v~~~~~~~kvGd~V 344 (486)
T PRK07899 275 SLKATQEDPWQQFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHI----------SELAERHVEVPEQVVQVGDEV 344 (486)
T ss_pred EEeeccccchhhhHHhcCCCCEEEEEEEEEeccEEEEEeCCCcEEEEEH----------HHcCcccccCccceeCCCCEE
Confidence 876322 13333333333332211 11111111 111110000 01112333467
Q ss_pred EEEeEeeccccceeeeeehhhhcccc
Q psy6276 207 EVRLMQMNEVKGEMEFKIKELNKKNQ 232 (271)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 232 (271)
.|+....+.-++.+.|.+|+++..-.
T Consensus 345 ~VkIi~ID~e~rrI~LSlK~~~~~~~ 370 (486)
T PRK07899 345 FVKVIDIDLERRRISLSLKQANEGVT 370 (486)
T ss_pred EEEEEEEECCCCEEEEEEEEcccCCC
Confidence 88888888889999999998865543
No 75
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=96.32 E-value=0.027 Score=60.22 Aligned_cols=73 Identities=12% Similarity=0.047 Sum_probs=58.2
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCceee
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSYQL 145 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~~L 145 (271)
..+||+|-|+|+++.+..++|++. ..+.|++|.+++... ....+..+.|++||.|.|+ ++++. .+.+.|
T Consensus 576 ~~vG~iV~G~V~~I~~fG~fVeL~--------~gveGLvhiSEls~~-~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsL 646 (863)
T PRK12269 576 FGVNDVVKGRVTKIADFGAFIELA--------EGIEGLAHISEFSWV-KKTSKPSDMVKIGDEVECMILGYDIQAGRVSL 646 (863)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEec--------CCceeeeEHHHhcCc-cccCCHHHcCCCCCEEEEEEEEEecccCceEE
Confidence 468999999999999999999984 357899999988632 1223567889999999999 88753 356888
Q ss_pred eecc
Q psy6276 146 STAE 149 (271)
Q Consensus 146 ST~~ 149 (271)
|++.
T Consensus 647 S~K~ 650 (863)
T PRK12269 647 GLKQ 650 (863)
T ss_pred Eehh
Confidence 8864
No 76
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=96.32 E-value=0.034 Score=57.47 Aligned_cols=72 Identities=14% Similarity=0.153 Sum_probs=57.9
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC-CCCceeee
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK-ELHSYQLS 146 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~-d~~~~~LS 146 (271)
++|++|.|.|+++.+..++|++. ..+.|++|.+++.... .......|++||.|.|+ ++.+ +.+.+.||
T Consensus 561 ~~G~~v~g~V~~i~~~G~fV~l~--------~~i~Gli~~sel~~~~--~~~~~~~~kvGd~V~vkV~~id~e~~rI~ls 630 (647)
T PRK00087 561 PVGSIVLGKVVRIAPFGAFVELE--------PGVDGLVHISQISWKR--IDKPEDVLSEGEEVKAKILEVDPEEKRIRLS 630 (647)
T ss_pred cCCeEEEEEEEEEECCeEEEEEC--------CCCEEEEEhhhcCccc--cCCHhhcCCCCCEEEEEEEEEeCCCCEEEEE
Confidence 68999999999999999999984 3579999999876422 23567789999999999 8775 33668888
Q ss_pred eccC
Q psy6276 147 TAEN 150 (271)
Q Consensus 147 T~~~ 150 (271)
++..
T Consensus 631 lk~~ 634 (647)
T PRK00087 631 IKEV 634 (647)
T ss_pred Eeec
Confidence 8653
No 77
>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=96.26 E-value=0.04 Score=54.83 Aligned_cols=70 Identities=14% Similarity=0.223 Sum_probs=55.9
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC-CCCceeee
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK-ELHSYQLS 146 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~-d~~~~~LS 146 (271)
.+|++|.|+|+++++..++|.+. ..+.|++|.+++.... ..+..+.|++||.|.|+ ++++ +...+.||
T Consensus 445 ~~G~~v~g~V~~v~~~G~fV~l~--------~~~~Glv~~s~l~~~~--~~~~~~~~~~Gd~v~~~V~~id~~~~~i~ls 514 (516)
T TIGR00717 445 KVGSVVKGKVTEIKDFGAFVELP--------GGVEGLIRNSELSENR--DEDKTDEIKVGDEVEAKVVDIDKKNRKVSLS 514 (516)
T ss_pred CcceEEEEEEEEEecceEEEEcC--------CCeEEEEEHHHcCccc--cccccccCCCCCEEEEEEEEEeCCCCEEEEE
Confidence 67999999999999999999984 3489999999876422 23688999999999999 7774 23457777
Q ss_pred ec
Q psy6276 147 TA 148 (271)
Q Consensus 147 T~ 148 (271)
.+
T Consensus 515 ~k 516 (516)
T TIGR00717 515 VK 516 (516)
T ss_pred EC
Confidence 53
No 78
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.23 E-value=0.013 Score=62.70 Aligned_cols=73 Identities=16% Similarity=0.207 Sum_probs=58.2
Q ss_pred cCCCCCEEE-EEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCcee
Q psy6276 67 VPTPGDVVT-ARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQ 144 (271)
Q Consensus 67 iP~vGDIVI-GrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~ 144 (271)
.|++|+++. |+|++|.+-.++|+|. ....|++|++++.... .....+.|++||.|.++ ++.+..+.+.
T Consensus 750 ~~~vG~iy~~g~V~~I~~FGaFVeL~--------~g~EGLVHISeLs~~r--v~~~~dv~kvGD~V~VkVi~ID~~grI~ 819 (891)
T PLN00207 750 VPTVGDIYRNCEIKSIAPYGAFVEIA--------PGREGLCHISELSSNW--LAKPEDAFKVGDRIDVKLIEVNDKGQLR 819 (891)
T ss_pred CcCCCcEEECcEEEEEeccEEEEEeC--------CCCEEEEEhhhcCCcc--ccCHHHhcCCCCEEEEEEEEECCCCcEE
Confidence 489999995 6999999999999995 2369999999986422 23556889999999999 8886545677
Q ss_pred eeecc
Q psy6276 145 LSTAE 149 (271)
Q Consensus 145 LST~~ 149 (271)
||++.
T Consensus 820 LSlK~ 824 (891)
T PLN00207 820 LSRRA 824 (891)
T ss_pred EEEec
Confidence 77653
No 79
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=96.18 E-value=0.018 Score=59.48 Aligned_cols=71 Identities=18% Similarity=0.158 Sum_probs=56.5
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC-CCCceee
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK-ELHSYQL 145 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~-d~~~~~L 145 (271)
.++|++|.|+|+++.+..++|++. ...|++|.+++.... ..++.+.|++||.|.|+ ++++ +.+.+.|
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 LEEGDVVEGEVKRLTDFGAFVDIG---------GVDGLLHVSEISWGR--VEKPSDVLKVGDEIKVYILDIDKENKKLSL 543 (647)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEEC---------CEEEEEEHHHcCccc--cCCHHHhcCCCCEEEEEEEEEECCCCEEEE
Confidence 468999999999999999999983 357999999876422 23567789999999999 8874 2356888
Q ss_pred eecc
Q psy6276 146 STAE 149 (271)
Q Consensus 146 ST~~ 149 (271)
|++.
T Consensus 544 S~K~ 547 (647)
T PRK00087 544 SLKK 547 (647)
T ss_pred Eeec
Confidence 8864
No 80
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.15 E-value=0.013 Score=57.00 Aligned_cols=109 Identities=17% Similarity=0.125 Sum_probs=75.0
Q ss_pred ccccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC---C
Q psy6276 64 EVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK---E 139 (271)
Q Consensus 64 ~~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~---d 139 (271)
..|.++.|++|.|+|.++....|.|+|. ...|+||.++..+ .+.|++||-|+|. .++. .
T Consensus 128 ~ef~~k~GeiV~G~V~~~~~~~~~Vdlg---------~vEa~LP~~E~ip--------~e~~~~Gd~Ika~V~~V~~~~k 190 (362)
T PRK12327 128 NEFSEREGDIVTGVVQRRDNRFVYVNLG---------KIEAVLPPAEQIP--------GETYKHGDRIKVYVVKVEKTTK 190 (362)
T ss_pred HHHHHhcCCEEEEEEEEEeCCcEEEEeC---------CeEEEecHHHcCC--------CCCCCCCCEEEEEEEEEecCCC
Confidence 4688899999999999999999999984 3688999754322 5679999999999 7664 3
Q ss_pred CCceeeeeccCC--------------CeeEEEEc---cCCCee---Ee-----ccCccCchhhhhhhhhhhHHHh
Q psy6276 140 LHSYQLSTAENE--------------LGVVIALS---EAASLF---RS-----SEKLTNDIEFLKQEKLKLYEEL 189 (271)
Q Consensus 140 ~~~~~LST~~~e--------------LGVV~A~c---~cG~~M---vp-----~s~~~~c~~~~~~e~rKla~~~ 189 (271)
++.+.||-..++ -|.|.=+. ..|..- +. +.+...|..-+-.--..+.++|
T Consensus 191 gp~IivSRt~p~~v~~Lfe~EVPEI~~G~VeIk~iaR~pG~RtKVAV~s~~~~iDpvGa~iG~~G~rI~~i~~el 265 (362)
T PRK12327 191 GPQIFVSRTHPGLVKRLFELEVPEIYDGTVEIKSIAREAGDRTKIAVRSNNPNVDAKGACVGPKGQRVQNIVSEL 265 (362)
T ss_pred CCeEEEEeCCHHHHHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCchheeECCCChhHHHHHHHh
Confidence 356888888765 27665544 333322 11 1135555555544445566777
No 81
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=96.13 E-value=0.032 Score=41.36 Aligned_cols=70 Identities=16% Similarity=0.152 Sum_probs=49.4
Q ss_pred CCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccch--hhh-------HhhhcCCCCCCEEEEE-EecCC
Q psy6276 70 PGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATE--IDR-------IEMYKCYRPGDIILAR-LPLKE 139 (271)
Q Consensus 70 vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te--~d~-------~~m~~~f~~GDIV~Ak-iS~~d 139 (271)
+|+++-|.|+++.+..+.|++. .....|.+|.++..... .|. ......|++||.|+++ ++.+.
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~-------~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~ 73 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELD-------NLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDL 73 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEec-------CCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEecc
Confidence 4899999999999999999994 12478999988765211 010 1234788999999999 77643
Q ss_pred -CCceeee
Q psy6276 140 -LHSYQLS 146 (271)
Q Consensus 140 -~~~~~LS 146 (271)
...+.++
T Consensus 74 ~~~~i~~~ 81 (83)
T cd04471 74 DRRKIDFE 81 (83)
T ss_pred ccCEEEEE
Confidence 2345444
No 82
>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=96.07 E-value=0.048 Score=54.30 Aligned_cols=73 Identities=14% Similarity=0.133 Sum_probs=55.9
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC-CCceee
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-LHSYQL 145 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-~~~~~L 145 (271)
-++|+++.|+|+++.+..+.|++. ....|.+|.+++... ....+..+.|.+||.|.|+ ++++. .+.+.|
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 FPVGDKITGRVTNLTDYGVFVEIE--------EGIEGLVHVSEMSWV-KKNSHPSKVVKKGDEVEVMILDIDPERRRLSL 340 (516)
T ss_pred ccCCCEEEEEEEEeeCCcEEEEeC--------CCCEEEEEHHHcCCc-cccCCHHHhccCCCEEEEEEEEEcCCCCEEEE
Confidence 368999999999999999999984 357899999887521 1122345679999999999 77753 356888
Q ss_pred eecc
Q psy6276 146 STAE 149 (271)
Q Consensus 146 ST~~ 149 (271)
|++.
T Consensus 341 S~k~ 344 (516)
T TIGR00717 341 GLKQ 344 (516)
T ss_pred Eehh
Confidence 8764
No 83
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=95.99 E-value=0.019 Score=58.46 Aligned_cols=71 Identities=13% Similarity=0.165 Sum_probs=60.4
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC-CCCceeee
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK-ELHSYQLS 146 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~-d~~~~~LS 146 (271)
.+||.+.|+|+++.+..++|+|. ...+|++|+|++..+... ...+.+..||.|.++ ++.+ +.+.+.||
T Consensus 276 ~~g~~v~G~Vt~i~~~GafVei~--------~GvEGlvhvSEisw~~~~--~P~evv~~Gq~V~V~Vl~id~e~rRIsL~ 345 (541)
T COG0539 276 PVGDKVEGKVTNLTDYGAFVEIE--------EGVEGLVHVSEISWTKKN--VPSEVVKVGQEVEVKVLDIDPERRRISLG 345 (541)
T ss_pred CCCCEEEEEEEEeecCcEEEEec--------CCccceeechhhcccccC--CHHHhcccCCEEEEEEEeeCchhceEEee
Confidence 67999999999999999999996 578999999998765543 289999999999999 8875 23568888
Q ss_pred ecc
Q psy6276 147 TAE 149 (271)
Q Consensus 147 T~~ 149 (271)
++.
T Consensus 346 iKq 348 (541)
T COG0539 346 LKQ 348 (541)
T ss_pred ehh
Confidence 874
No 84
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=95.90 E-value=0.06 Score=57.70 Aligned_cols=75 Identities=17% Similarity=0.184 Sum_probs=57.3
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchh-hhHhhhcCCCCCCEEEEE-EecC-CCCcee
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEI-DRIEMYKCYRPGDIILAR-LPLK-ELHSYQ 144 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~-d~~~m~~~f~~GDIV~Ak-iS~~-d~~~~~ 144 (271)
.++||+|.|+|+++.+..++|++. ....|++|.+++..... +..++...|++||.|.++ ++++ +.+.+.
T Consensus 750 ~~vG~iV~GkV~~v~~~GvFVeL~--------~gVeGlI~~s~lsdd~~~~~~~~~~~f~vGD~V~v~Vl~iD~~~rkI~ 821 (863)
T PRK12269 750 YGVGSTVEGEVSSVTDFGIFVRVP--------GGVEGLVRKQHLVENRDGDPGEALRKYAVGDRVKAVIVDMNVKDRKVA 821 (863)
T ss_pred CCCCCEEEEEEEEEecCeEEEEcC--------CCeEEEEEHHHcCCcccccchhhccccCCCCEEEEEEEEEEcCCCEEE
Confidence 468999999999999999999984 35899999998754211 112345679999999999 8774 335688
Q ss_pred eeeccC
Q psy6276 145 LSTAEN 150 (271)
Q Consensus 145 LST~~~ 150 (271)
||++..
T Consensus 822 LSlk~~ 827 (863)
T PRK12269 822 FSVRDY 827 (863)
T ss_pred EEEech
Confidence 888743
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=95.83 E-value=0.021 Score=54.97 Aligned_cols=109 Identities=14% Similarity=0.142 Sum_probs=73.9
Q ss_pred ccccCCCCCEEEEEEEEEecce-EEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC--
Q psy6276 64 EVIVPTPGDVVTARIMAVQQHL-CKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE-- 139 (271)
Q Consensus 64 ~~yiP~vGDIVIGrVt~V~~~~-a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d-- 139 (271)
..|..+.|++|.|+|.++..+. |.|+|. ...|+||.++.-. .+.|++||-|.|. .++.+
T Consensus 125 ~ey~~k~GeiV~G~V~~v~~~g~v~VdiG---------~~ea~LP~~E~ip--------~E~~~~Gd~ik~~V~~V~~~~ 187 (341)
T TIGR01953 125 DEFSSKEGEIISGTVKRVNRRGNLYVELG---------KTEGILPKKEQIP--------GEKFRIGDRIKAYVYEVRKTA 187 (341)
T ss_pred HHHHhhcCCEEEEEEEEEecCCcEEEEEC---------CeEEEecHHHcCC--------CcCCCCCCEEEEEEEEEEcCC
Confidence 4577889999999999998855 799983 3689999876543 3449999999999 76643
Q ss_pred -CCceeeeeccCCC--------------eeEEEEc---cCCCee---Ee-----ccCccCchhhhhhhhhhhHHHh
Q psy6276 140 -LHSYQLSTAENEL--------------GVVIALS---EAASLF---RS-----SEKLTNDIEFLKQEKLKLYEEL 189 (271)
Q Consensus 140 -~~~~~LST~~~eL--------------GVV~A~c---~cG~~M---vp-----~s~~~~c~~~~~~e~rKla~~~ 189 (271)
++.+.||...++| |.|.-+. ..|..- +. +.+...|..-+-.--..+.++|
T Consensus 188 kg~qIivSRt~~~~v~~Lfe~EVPEI~dG~VeI~~iaR~pG~RtKvAV~s~~~~iDpvga~vG~~G~ri~~i~~el 263 (341)
T TIGR01953 188 KGPQIILSRTHPEFVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVESNDENIDPVGACVGPKGSRIQAISKEL 263 (341)
T ss_pred CCCeEEEEeCcHHHHHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCcceeeECCCCchHHHHHHHh
Confidence 3568999987763 7766554 344332 11 1134555554444445566666
No 86
>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=94.64 E-value=0.21 Score=38.93 Aligned_cols=78 Identities=12% Similarity=0.090 Sum_probs=45.4
Q ss_pred CCCEEEEEEEEEecceEEEEEee----ecCcccCCceeeEEecc--ccccchhhhHhhhcCCCCCCEEEEE-EecC-CCC
Q psy6276 70 PGDVVTARIMAVQQHLCKAHVIS----VGNTALSRTFRALLRRE--NVRATEIDRIEMYKCYRPGDIILAR-LPLK-ELH 141 (271)
Q Consensus 70 vGDIVIGrVt~V~~~~a~VdI~~----v~~~~L~~~f~GiLr~s--dvr~te~d~~~m~~~f~~GDIV~Ak-iS~~-d~~ 141 (271)
+|.||.|+|+++....++|.+.. +....++.. ++... +.-.+. + +-...+++||.||+| ++.. +.+
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~~---~~~~~~~~~~~~~-~--~~~~~i~~g~~VR~rV~~v~~~~~ 74 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSD---MEFDPNASPPCFT-S--NEDIVIKKDTEVRLKIIGTRVDAT 74 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCcc---ceECCcCCCCeEe-C--CCcEEECCCCEEEEEEEEEEEccC
Confidence 48999999999999999999973 222222211 11110 100111 1 125668999999999 5431 222
Q ss_pred c--eeeeeccCCCe
Q psy6276 142 S--YQLSTAENELG 153 (271)
Q Consensus 142 ~--~~LST~~~eLG 153 (271)
. ..-|++++.||
T Consensus 75 ~~~~igt~~~~~LG 88 (88)
T cd04462 75 DIFAIGTIKDDYLG 88 (88)
T ss_pred ceEEEEEccCCCCC
Confidence 2 22355666665
No 87
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.34 E-value=0.11 Score=51.83 Aligned_cols=76 Identities=17% Similarity=0.118 Sum_probs=56.8
Q ss_pred ccccCCCCCEEEEEEEEEecceEEEEEeeecCcccCC-ceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC---
Q psy6276 64 EVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSR-TFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK--- 138 (271)
Q Consensus 64 ~~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~-~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~--- 138 (271)
..|.+++|++|.|+|.++..+.+.|++.+- +.. ...|+|+..+.- ..+.|++||-|+|- ..+.
T Consensus 146 ~ef~~~~GeIV~G~V~r~e~~~viv~l~~~----~g~~~~EaiLP~~Eqi--------p~E~y~~Gdrika~i~~V~~~~ 213 (449)
T PRK12329 146 EEFQDLEDTVLTARVLRFERQSVIMAVSSG----FGQPEVEAELPKREQL--------PNDNYRANATFKVFLKEVSEGP 213 (449)
T ss_pred HHHHHhcCcEEEEEEEEEcCCCEEEEeccc----CCCcceEEEecHHHcC--------CCCcCCCCCEEEEEEEEeecCC
Confidence 468899999999999999999898888421 111 368999986543 35679999999998 5442
Q ss_pred -CCCceeeeeccCC
Q psy6276 139 -ELHSYQLSTAENE 151 (271)
Q Consensus 139 -d~~~~~LST~~~e 151 (271)
.++.+.||-..++
T Consensus 214 ~kGpqIilSRt~p~ 227 (449)
T PRK12329 214 RRGPQLFVSRANAG 227 (449)
T ss_pred CCCCEEEEEcCCHH
Confidence 3456888887765
No 88
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=94.18 E-value=0.12 Score=50.61 Aligned_cols=71 Identities=20% Similarity=0.187 Sum_probs=54.4
Q ss_pred ccccCCCCCEEEEEEEEEec-ceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC---
Q psy6276 64 EVIVPTPGDVVTARIMAVQQ-HLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK--- 138 (271)
Q Consensus 64 ~~yiP~vGDIVIGrVt~V~~-~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~--- 138 (271)
..|.+++|++|.|.|.++.. ..+.|++. ...|+||.++.- ..+.|++||-|+|- ....
T Consensus 132 ~ey~~~~Geiv~g~V~r~~~~~~i~vdlg---------~~ea~LP~~eqi--------p~E~~~~Gdrik~~i~~V~~~~ 194 (374)
T PRK12328 132 EKYKKKVGKIVFGTVVRVDNEENTFIEID---------EIRAVLPMKNRI--------KGEKFKVGDVVKAVLKRVKIDK 194 (374)
T ss_pred HHHHHhcCcEEEEEEEEEecCCCEEEEcC---------CeEEEeCHHHcC--------CCCcCCCCCEEEEEEEEEecCC
Confidence 46889999999999999986 45778873 368898876543 36679999999998 5442
Q ss_pred C-CCceeeeeccCC
Q psy6276 139 E-LHSYQLSTAENE 151 (271)
Q Consensus 139 d-~~~~~LST~~~e 151 (271)
. ++.+.||-..++
T Consensus 195 k~gp~IilSRt~p~ 208 (374)
T PRK12328 195 NNGILIELSRTSPK 208 (374)
T ss_pred CCCCEEEEEcCCHH
Confidence 2 456888888765
No 89
>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=93.25 E-value=0.23 Score=38.72 Aligned_cols=53 Identities=15% Similarity=0.258 Sum_probs=40.1
Q ss_pred CCCeEecCCcccCCC-CCeeeCCCEEEe-CCEEEEEEeeEEEEeccccCCCcceEEEE
Q psy6276 3 NPPICIPGQRICQLD-SDIVGGRGTYVR-QGYLYSTLAGTVSINKHVEDNKEVSVIEV 58 (271)
Q Consensus 3 ~~~iVlPGD~L~~~e-E~~~~G~GtY~~-~g~I~ASv~G~v~i~~~~~~~~~~~~I~V 58 (271)
++++|.||+.|..-- -.|.||.++..- |..|||.+-|.|.+... ...++.|+|
T Consensus 26 ~G~~V~~G~IivRQRgtk~hPG~NVg~GrD~TLfAl~~G~V~f~~~---~~~rk~v~V 80 (81)
T PF01016_consen 26 GGQFVKAGNIIVRQRGTKFHPGENVGMGRDHTLFALVDGRVKFTKE---KRNRKYVSV 80 (81)
T ss_dssp TTCEESSTSEEEEBSSSSSEEBTTEEEETTSEEEESSSCEEEEEEE---TTTEEEEEE
T ss_pred CCEEEcCCCEEEEeCCCcCcCCCCEEECCCCcEEEecCEEEEEEEe---CCCCEEEEe
Confidence 467999999986432 139999999876 88999999999998751 123456666
No 90
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=92.90 E-value=0.35 Score=47.85 Aligned_cols=69 Identities=10% Similarity=0.138 Sum_probs=49.9
Q ss_pred EEEEeeCCCccccCCCCCEEEEEEEEEecc--eEEEEEeeecCcccCCceeeEEeccccccch----------hhhHhhh
Q psy6276 55 VIEVSSYKKEVIVPTPGDVVTARIMAVQQH--LCKAHVISVGNTALSRTFRALLRRENVRATE----------IDRIEMY 122 (271)
Q Consensus 55 ~I~V~P~~~~~yiP~vGDIVIGrVt~V~~~--~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te----------~d~~~m~ 122 (271)
-+.+.+. ..-+.+|+|..|+|+++.+. .|+|||. ..-.|.||.+|+.... ....++.
T Consensus 13 e~~ie~~---~~~~~vGnIY~GrV~~i~p~l~aAFVdiG--------~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~ 81 (414)
T TIGR00757 13 DLIIERP---KSRQLKGNIYKGRVTRILPSLQAAFVDIG--------LEKNGFLHASDIGPNYECLAPAEAKREAGPSIS 81 (414)
T ss_pred EEEEecC---cCcCCCCCEEEEEEeeecCCCceEEEEcC--------CCceEEEEHHHcCchhhccccccccccccCCHH
Confidence 3445543 22346899999999999999 7999995 3457999999875310 0012456
Q ss_pred cCCCCCCEEEEE
Q psy6276 123 KCYRPGDIILAR 134 (271)
Q Consensus 123 ~~f~~GDIV~Ak 134 (271)
+.+++||.|.+.
T Consensus 82 ~~l~~G~~IlVQ 93 (414)
T TIGR00757 82 ELLRPGQSVLVQ 93 (414)
T ss_pred HhCcCCCEEEEE
Confidence 679999999999
No 91
>KOG1070|consensus
Probab=92.54 E-value=0.15 Score=56.78 Aligned_cols=77 Identities=13% Similarity=0.169 Sum_probs=62.6
Q ss_pred CccccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCC
Q psy6276 63 KEVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELH 141 (271)
Q Consensus 63 ~~~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~ 141 (271)
+..+--.+|++|.|.|++|.++...|... ..+.|-||++++........+....|+.||-|.|| +.-.|..
T Consensus 878 k~~~~~~igsiv~a~v~svKp~~L~v~l~--------~~~~gri~isev~d~~~eitDp~~k~~vG~~I~vrviG~~D~k 949 (1710)
T KOG1070|consen 878 KSTEDLSIGSIVRAYVKSVKPDQLNVLLA--------ANHHGRIHISEVLDNLHEITDPLDKFKVGDGIFVRVIGGHDVK 949 (1710)
T ss_pred ccccceeeeeEEEEEEeeecccceEEecc--------ccccCceehHHhhccccccCChhhhcccCCeEEEEEEcCCccc
Confidence 34566789999999999999999999864 57899999999987665566789999999999999 8776655
Q ss_pred ceeeee
Q psy6276 142 SYQLST 147 (271)
Q Consensus 142 ~~~LST 147 (271)
+.-.|+
T Consensus 950 ~lpith 955 (1710)
T KOG1070|consen 950 DLPITH 955 (1710)
T ss_pred cCcccc
Confidence 544444
No 92
>CHL00121 rpl27 ribosomal protein L27; Reviewed
Probab=92.51 E-value=0.27 Score=38.68 Aligned_cols=56 Identities=20% Similarity=0.221 Sum_probs=41.6
Q ss_pred CCCeEecCCcccCCCC-CeeeCCCEEE-eCCEEEEEEeeEEEEeccccCCCcceEEEEeeC
Q psy6276 3 NPPICIPGQRICQLDS-DIVGGRGTYV-RQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSY 61 (271)
Q Consensus 3 ~~~iVlPGD~L~~~eE-~~~~G~GtY~-~~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~ 61 (271)
++++|.||+.|...-. .|.||.++-. .|..|||.+.|.|.+... ...+..|+|.|.
T Consensus 27 ~gq~V~~G~IivRQRGtk~hPG~NVg~GrD~TlfAl~~G~V~f~~~---~~~~~~vsv~~~ 84 (86)
T CHL00121 27 GGEKVSAGNILIRQRGTKFKPGLNVGCGKDFTLYALIDGFVKFKKK---NKKQKSINVINI 84 (86)
T ss_pred CCEEEcCCcEEEEcCCCeECCCCcccccCCceEEEccceEEEEEEe---CCCCEEEEEeec
Confidence 3578999999865322 4889998865 488999999999998651 123467888874
No 93
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=92.34 E-value=0.29 Score=51.73 Aligned_cols=75 Identities=13% Similarity=0.139 Sum_probs=59.0
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCC-Cceee
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKEL-HSYQL 145 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~-~~~~L 145 (271)
.++|-++.|.|++|....++|||.. .-.|++|+|..... -..+..+.+++||+|.++ +.++-. ..+-|
T Consensus 656 Lk~Gm~leg~Vrnv~~fgafVdIgv--------~qDglvHis~ls~~--fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~L 725 (780)
T COG2183 656 LKPGMILEGTVRNVVDFGAFVDIGV--------HQDGLVHISQLSDK--FVKDPNEVVKVGDIVKVKVIEVDTARKRIAL 725 (780)
T ss_pred ccCCCEEEEEEEEeeeccceEEecc--------ccceeeeHHHhhhh--hcCChHHhcccCCEEEEEEEEEecccCeeee
Confidence 4899999999999999999999963 55799999876532 223458899999999999 776422 45888
Q ss_pred eeccCCC
Q psy6276 146 STAENEL 152 (271)
Q Consensus 146 ST~~~eL 152 (271)
|++..+.
T Consensus 726 smr~~~~ 732 (780)
T COG2183 726 SMRLDEE 732 (780)
T ss_pred EeeccCC
Confidence 9876553
No 94
>PRK05435 rpmA 50S ribosomal protein L27; Validated
Probab=92.30 E-value=0.38 Score=37.56 Aligned_cols=43 Identities=14% Similarity=0.198 Sum_probs=35.0
Q ss_pred CCCeEecCCcccCCCC-CeeeCCCEEEe-CCEEEEEEeeEEEEec
Q psy6276 3 NPPICIPGQRICQLDS-DIVGGRGTYVR-QGYLYSTLAGTVSINK 45 (271)
Q Consensus 3 ~~~iVlPGD~L~~~eE-~~~~G~GtY~~-~g~I~ASv~G~v~i~~ 45 (271)
+++.|.||..|...-. .|.||.++..- |..|||.+.|.|.+..
T Consensus 27 ~g~~V~~G~IivRQRGtk~~PG~nVg~GrD~TlfA~~~G~V~f~~ 71 (82)
T PRK05435 27 GGQFVKAGNIIVRQRGTKFHPGVNVGRGKDHTLFALVDGVVKFER 71 (82)
T ss_pred CCEEEcCCcEEEEeCCCeECCCCCEeecCCceEEEecceEEEEEE
Confidence 3578999999865322 49999999874 8899999999999875
No 95
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=89.52 E-value=0.86 Score=47.71 Aligned_cols=73 Identities=10% Similarity=0.146 Sum_probs=60.0
Q ss_pred cCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCceee
Q psy6276 67 VPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQL 145 (271)
Q Consensus 67 iP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~L 145 (271)
-|++|.+-.|+|+++.+-.++|.++ ..-.|++|++++.... ..+..+.++.||.|+.| +.+++...+.|
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 EVEVGEVYEGTVVRIVDFGAFVELL--------PGKDGLVHISQLAKER--VEKVEDVLKEGDEVKVKVIEIDKQGRIRL 685 (692)
T ss_pred hcccccEEEEEEEEEeecceEEEec--------CCcceeEEehhhhhhh--hhcccceeecCceEEEEEeeecccCCccc
Confidence 4799999999999999999999986 3458999999875432 23566999999999999 99987667888
Q ss_pred eecc
Q psy6276 146 STAE 149 (271)
Q Consensus 146 ST~~ 149 (271)
|+..
T Consensus 686 s~~~ 689 (692)
T COG1185 686 SIKA 689 (692)
T ss_pred eehh
Confidence 8764
No 96
>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=89.14 E-value=2.2 Score=32.56 Aligned_cols=58 Identities=21% Similarity=0.351 Sum_probs=45.0
Q ss_pred CCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEE-EEE-E
Q psy6276 71 GDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDII-LAR-L 135 (271)
Q Consensus 71 GDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV-~Ak-i 135 (271)
|++|-|+|...+.+...|++. .....|+|+.............+..++++||-+ .+= +
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~-------~~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL 60 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAIL-------PEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL 60 (72)
T ss_pred CceEEEEEEEEcCCcEEEEec-------CCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEE
Confidence 789999999999999999996 356788887766554333345688899999987 555 5
No 97
>KOG1070|consensus
Probab=88.42 E-value=2 Score=48.48 Aligned_cols=71 Identities=18% Similarity=0.215 Sum_probs=57.8
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC-CCCceeee
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK-ELHSYQLS 146 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~-d~~~~~LS 146 (271)
++||+|.|.|..+..+..++.+. ..+.|..|+++...+. +..-.+.|.+|++|.+| +++. +...+.||
T Consensus 1161 k~g~iv~G~V~nv~~~glfi~ls--------~~v~a~v~is~~~ds~--~k~w~k~~~~gklv~~rv~~ve~~s~riel~ 1230 (1710)
T KOG1070|consen 1161 KIGDIVRGFVKNVETKGLFIALS--------RKVEAFVPISGLSDSF--EKEWEKHLPVGKLVTGRVLSVEEDSKRIELS 1230 (1710)
T ss_pred ccCceeEEEEEEecCCcEEEEEc--------cceEEEEEccccccch--hhhhhccCCccceeeeEEEEeeccCceEEEE
Confidence 78999999999999999999874 6789999988876543 55778899999999999 8875 33457777
Q ss_pred ecc
Q psy6276 147 TAE 149 (271)
Q Consensus 147 T~~ 149 (271)
.+.
T Consensus 1231 Lk~ 1233 (1710)
T KOG1070|consen 1231 LKN 1233 (1710)
T ss_pred Eec
Confidence 653
No 98
>TIGR00062 L27 ribosomal protein L27. Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.
Probab=85.65 E-value=1.9 Score=33.80 Aligned_cols=43 Identities=16% Similarity=0.240 Sum_probs=34.6
Q ss_pred CCCeEecCCcccCCCC-CeeeCCCEEE-eCCEEEEEEeeEEEEec
Q psy6276 3 NPPICIPGQRICQLDS-DIVGGRGTYV-RQGYLYSTLAGTVSINK 45 (271)
Q Consensus 3 ~~~iVlPGD~L~~~eE-~~~~G~GtY~-~~g~I~ASv~G~v~i~~ 45 (271)
+++.|.||..|..--. .|.||.++-. .|..|||.+.|.|.+..
T Consensus 27 ~gq~V~~G~IivRQRGtk~hPG~nVg~GrD~TlfAl~~G~V~f~~ 71 (83)
T TIGR00062 27 GGQFVRAGSIIVRQRGTKFHPGNNVGMGKDHTLFALSDGVVKFEK 71 (83)
T ss_pred CCEEEcCCcEEEEcCCceECCCCcccccCCCeEEEecceEEEEEE
Confidence 3468999999865322 4999999976 48899999999999875
No 99
>KOG1856|consensus
Probab=83.29 E-value=1 Score=49.55 Aligned_cols=78 Identities=15% Similarity=0.195 Sum_probs=57.0
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCC-Cceee
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKEL-HSYQL 145 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~-~~~~L 145 (271)
-..|.+|.|.|++|..+...| + ...|....+|+|+.+++.. .+.....+.+++|+.|.|| ++++-. -...|
T Consensus 983 ~~~g~iV~~~V~~vt~rr~~C-v----~v~ld~G~~g~i~~~~~Sd--~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~L 1055 (1299)
T KOG1856|consen 983 FYEGAIVPVTVTKVTHRRGIC-V----RVRLDCGVTGFILAKNLSD--RDVRRPENRVKVGQTVYCKVIKIDKERFSVEL 1055 (1299)
T ss_pred hccCceEEEeeeEEEecccce-e----EEEecCCCceeeeccccCh--hhccCHHHhhccCceEEEEeeeeeHhhhhhhh
Confidence 368999999999999998555 1 1123457899999988654 5667788889999999999 887422 23556
Q ss_pred eeccCCC
Q psy6276 146 STAENEL 152 (271)
Q Consensus 146 ST~~~eL 152 (271)
|++..+|
T Consensus 1056 s~r~sdl 1062 (1299)
T KOG1856|consen 1056 SCRTSDL 1062 (1299)
T ss_pred hhhhHHh
Confidence 6665444
No 100
>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=82.39 E-value=4.9 Score=42.19 Aligned_cols=72 Identities=15% Similarity=0.158 Sum_probs=51.4
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccch--hhh-------HhhhcCCCCCCEEEEE-Eec
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATE--IDR-------IEMYKCYRPGDIILAR-LPL 137 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te--~d~-------~~m~~~f~~GDIV~Ak-iS~ 137 (271)
+.+|.++-|+|++|.+..++|.+.. ....|++|.+++.... -|. ......|++||.|.++ ++.
T Consensus 625 ~~iG~~~~g~V~~v~~fGifV~L~~-------~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~v 697 (709)
T TIGR02063 625 EKIGEEFEGVISGVTSFGLFVELEN-------NTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKA 697 (709)
T ss_pred ccCCcEEEEEEEEEEeCCEEEEecC-------CceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEE
Confidence 5789999999999999999999841 2478999998875210 010 1123579999999999 776
Q ss_pred CC-CCceeee
Q psy6276 138 KE-LHSYQLS 146 (271)
Q Consensus 138 ~d-~~~~~LS 146 (271)
+. .+.+.++
T Consensus 698 d~~~~~I~~~ 707 (709)
T TIGR02063 698 DLDTGKIDFE 707 (709)
T ss_pred ecccCeEEEE
Confidence 42 2445554
No 101
>PRK11712 ribonuclease G; Provisional
Probab=82.09 E-value=3.7 Score=41.60 Aligned_cols=60 Identities=13% Similarity=0.139 Sum_probs=44.1
Q ss_pred cCCCCCEEEEEEEEEecce--EEEEEeeecCcccCCceeeEEeccccccch------h----hhHhhhcCCCCCCEEEEE
Q psy6276 67 VPTPGDVVTARIMAVQQHL--CKAHVISVGNTALSRTFRALLRRENVRATE------I----DRIEMYKCYRPGDIILAR 134 (271)
Q Consensus 67 iP~vGDIVIGrVt~V~~~~--a~VdI~~v~~~~L~~~f~GiLr~sdvr~te------~----d~~~m~~~f~~GDIV~Ak 134 (271)
-..+|+|..|+|.+|-+.. |+|||. ..-.|.||.+|+.+.. . ....+.+.+++||.|...
T Consensus 35 ~~~vGnIY~G~V~~v~pg~~AAFVdIG--------~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQ 106 (489)
T PRK11712 35 RGIVGNIYKGRVSRVLPGMQAAFVDIG--------LDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQ 106 (489)
T ss_pred ccccccEEEEEEeecCCCCceeEEeeC--------CCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEE
Confidence 3468999999999997776 999996 4557888888874210 0 011345669999999999
No 102
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=81.83 E-value=0.63 Score=29.51 Aligned_cols=23 Identities=0% Similarity=-0.136 Sum_probs=14.2
Q ss_pred Ec-cCCCeeEec--cCccCchhhhhh
Q psy6276 158 LS-EAASLFRSS--EKLTNDIEFLKQ 180 (271)
Q Consensus 158 ~c-~cG~~Mvp~--s~~~~c~~~~~~ 180 (271)
.| .||.+|.+. +|...||.|+..
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred ccCcCCccccCCCCcCEeECCCCcCE
Confidence 46 899999886 489999999864
No 103
>PRK11642 exoribonuclease R; Provisional
Probab=81.69 E-value=5.3 Score=42.90 Aligned_cols=72 Identities=17% Similarity=0.205 Sum_probs=51.1
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccc--hhhhH-------hhhcCCCCCCEEEEE-EecC
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRAT--EIDRI-------EMYKCYRPGDIILAR-LPLK 138 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~t--e~d~~-------~m~~~f~~GDIV~Ak-iS~~ 138 (271)
.+|+++-|+|++|....++|.+. .....|++|.+++..- .-|.. .....|++||.|..+ ++++
T Consensus 642 ~iGe~f~G~Is~V~~fGifVeL~-------~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD 714 (813)
T PRK11642 642 QVGNVFKGVISSVTGFGFFVRLD-------DLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVN 714 (813)
T ss_pred cCCcEEEEEEEEeecCceEEEEC-------CCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEee
Confidence 68999999999999999999984 1237899998876421 11111 234679999999999 6653
Q ss_pred -CCCceeeee
Q psy6276 139 -ELHSYQLST 147 (271)
Q Consensus 139 -d~~~~~LST 147 (271)
+.+.+.+++
T Consensus 715 ~~~rkI~f~l 724 (813)
T PRK11642 715 MDERKIDFSL 724 (813)
T ss_pred cCCCeEEEEE
Confidence 224566654
No 104
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=80.34 E-value=0.69 Score=28.15 Aligned_cols=20 Identities=5% Similarity=-0.290 Sum_probs=17.0
Q ss_pred cCCCeeEecc--CccCchhhhh
Q psy6276 160 EAASLFRSSE--KLTNDIEFLK 179 (271)
Q Consensus 160 ~cG~~Mvp~s--~~~~c~~~~~ 179 (271)
.||..|.|.. ..+.||+||+
T Consensus 3 sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 3 SCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred cCCCcccCcccCceEeCCCCCC
Confidence 6899998874 7899999985
No 105
>PF15616 TerY-C: TerY-C metal binding domain
Probab=79.53 E-value=1.3 Score=37.44 Aligned_cols=41 Identities=12% Similarity=0.055 Sum_probs=30.3
Q ss_pred EEEccCCCee-EeccCccCchhhhhhhhhhhHHHhcccccceeeeeec
Q psy6276 156 IALSEAASLF-RSSEKLTNDIEFLKQEKLKLYEELSSSQKENEILRQT 202 (271)
Q Consensus 156 ~A~c~cG~~M-vp~s~~~~c~~~~~~e~rKla~~~~s~~~~~~~~~~~ 202 (271)
+|.|.||..| +-.+....||||++....- +....|+|.||+
T Consensus 89 fa~C~CGkl~Ci~g~~~~~CPwCg~~g~~~------~~~~~fdv~Rg~ 130 (131)
T PF15616_consen 89 FAVCGCGKLFCIDGEGEVTCPWCGNEGSFG------AGDGGFDVNRGR 130 (131)
T ss_pred EEEecCCCEEEeCCCCCEECCCCCCeeeec------ccCCceEecCCC
Confidence 5567999999 5667899999999987654 233667777664
No 106
>PRK10811 rne ribonuclease E; Reviewed
Probab=79.25 E-value=4.9 Score=43.98 Aligned_cols=59 Identities=10% Similarity=0.151 Sum_probs=43.0
Q ss_pred CCCCCEEEEEEEEEecce--EEEEEeeecCcccCCceeeEEecccccc-chhh------hHhhhcCCCCCCEEEEE
Q psy6276 68 PTPGDVVTARIMAVQQHL--CKAHVISVGNTALSRTFRALLRRENVRA-TEID------RIEMYKCYRPGDIILAR 134 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~--a~VdI~~v~~~~L~~~f~GiLr~sdvr~-te~d------~~~m~~~f~~GDIV~Ak 134 (271)
+.+|+|.+|+|.+|-+.+ ++|||. ..-.|+|+..|+.. .... ...+...+++||.|...
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDIG--------~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQ 103 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDYG--------AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQ 103 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEec--------CCcceEEEhhhccccccccccccccccccccccCCCCEEEEE
Confidence 468999999999997766 999996 34578888887742 1000 11245569999999998
No 107
>KOG4600|consensus
Probab=78.92 E-value=5.2 Score=34.18 Aligned_cols=65 Identities=17% Similarity=0.224 Sum_probs=44.8
Q ss_pred CCCeEecCCcccCCCC-CeeeCCCEEE-eCCEEEEEEeeEEEEeccccCCCcceEEEEeeCCCccccCC
Q psy6276 3 NPPICIPGQRICQLDS-DIVGGRGTYV-RQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPT 69 (271)
Q Consensus 3 ~~~iVlPGD~L~~~eE-~~~~G~GtY~-~~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~~~yiP~ 69 (271)
+++.|.||+.|...-. .|-||.++=. .|..|||-.-|.|++....-.. .++.|.|.|. ....+|.
T Consensus 54 egq~V~~G~IIvrQRgtkfHPG~nVGiGKDhtifaL~eG~Vrf~k~~~~~-~Rk~i~V~~~-~~~~l~~ 120 (144)
T KOG4600|consen 54 EGQSVIPGNIIVRQRGTKFHPGDNVGIGKDHTIFALEEGRVRFEKSKITP-PRKWIGVDPR-GGLPLPP 120 (144)
T ss_pred CCeeeecccEEEEecccccCCCcccccCCcceEEEeeccEEEEEEccCCC-CcceEEEeec-CCccCCC
Confidence 4579999999976432 3777777654 3778999999999987522122 4678888885 3344443
No 108
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=77.47 E-value=0.69 Score=36.55 Aligned_cols=29 Identities=10% Similarity=-0.030 Sum_probs=25.0
Q ss_pred Ec-cCCCeeEeccCccCchhhhhhhhhhhH
Q psy6276 158 LS-EAASLFRSSEKLTNDIEFLKQEKLKLY 186 (271)
Q Consensus 158 ~c-~cG~~Mvp~s~~~~c~~~~~~e~rKla 186 (271)
.| .||++|.|.+..+.|+.|+..+.++.+
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~~~~~~~~~ 31 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCGYEKEKKPE 31 (104)
T ss_pred CCcccCcccccCCCeEECcCCCCccccccc
Confidence 47 899999998889999999998877643
No 109
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=77.03 E-value=18 Score=28.59 Aligned_cols=69 Identities=20% Similarity=0.253 Sum_probs=49.6
Q ss_pred cCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEe-ccccccchhhhHhhhcCCCCCCEEEEE-EecCCC-Cce
Q psy6276 67 VPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLR-RENVRATEIDRIEMYKCYRPGDIILAR-LPLKEL-HSY 143 (271)
Q Consensus 67 iP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr-~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~-~~~ 143 (271)
+|++||+|. .|..+....+.|.++- ...+|+|- .++++.. --..+.+.+ +|-.+.++ +-.+.. .-+
T Consensus 13 ~P~v~dvv~-~Vv~i~d~~~YV~Lle-------Y~iegmIl~~selsr~--rirsi~kll-VGk~e~v~ViRVDk~KGYI 81 (86)
T PHA02858 13 FPNINEVTK-GIVFVKDNIFYVKLID-------YGLEALIVNYVNVNAD--RAEKLKKKL-VGKTINVQVIRTDKLKGYI 81 (86)
T ss_pred cCCCCeEEE-EEEEEeccEEEEEEec-------CccceEEecHHHHhHH--HHHhhhhhh-cCCeeEEEEEEECCCCCEE
Confidence 699999999 8889999999999864 33677776 6655431 123567777 99999999 876422 334
Q ss_pred eee
Q psy6276 144 QLS 146 (271)
Q Consensus 144 ~LS 146 (271)
.||
T Consensus 82 DLs 84 (86)
T PHA02858 82 DVR 84 (86)
T ss_pred EeE
Confidence 555
No 110
>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=76.39 E-value=19 Score=35.18 Aligned_cols=89 Identities=20% Similarity=0.358 Sum_probs=64.6
Q ss_pred eEecCCcccCCCCCeeeCCCEEEe--CCEEEEEEeeEEEEeccccCCCcceEEEEeeCCCccccCCCCCEEEEEEEEEec
Q psy6276 6 ICIPGQRICQLDSDIVGGRGTYVR--QGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQQ 83 (271)
Q Consensus 6 iVlPGD~L~~~eE~~~~G~GtY~~--~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~~~yiP~vGDIVIGrVt~V~~ 83 (271)
+.+||+.=....| +.+|.-+... +|+-+..++|.+++.. ++.+.|+.. + ++ -++.-+.+
T Consensus 246 v~~pg~kT~YLSE-L~sG~~VlvVd~~G~tR~~~VGRvKIE~-------RPLllIeA~----~----~g---~~~svilQ 306 (354)
T PF01959_consen 246 VLMPGGKTRYLSE-LRSGDEVLVVDADGRTRTAIVGRVKIER-------RPLLLIEAE----A----DG---KRISVILQ 306 (354)
T ss_pred EEcCCCceeehhh-hcCCCEEEEEeCCCCEEEEEeeEEEEee-------cceEEEEEE----e----CC---eEEEEEEe
Confidence 4678888777777 8888887654 7999999999999985 678888763 1 22 33444577
Q ss_pred ceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEEE
Q psy6276 84 HLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARL 135 (271)
Q Consensus 84 ~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Aki 135 (271)
+.|.|.+...++.+++ --.++|||-|+..+
T Consensus 307 naetIRlv~p~G~~vs----------------------Vt~Lk~GD~vL~~~ 336 (354)
T PF01959_consen 307 NAETIRLVGPDGEPVS----------------------VTELKPGDEVLVYL 336 (354)
T ss_pred cCcEEEEECCCCCEee----------------------eeecCCCCEEEEEe
Confidence 8899999865554332 11279999999983
No 111
>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=73.93 E-value=27 Score=24.57 Aligned_cols=62 Identities=11% Similarity=0.075 Sum_probs=35.0
Q ss_pred EEEEEEEE---ecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE--EecCCCCceeeee
Q psy6276 74 VTARIMAV---QQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR--LPLKELHSYQLST 147 (271)
Q Consensus 74 VIGrVt~V---~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak--iS~~d~~~~~LST 147 (271)
|.|+|+++ ....+.+.|.. .+|.+..- .+..+.....+.+++||+|+.+ +...+...+.|+.
T Consensus 3 v~G~V~~~~~~~~~~~~~~l~D---------~tg~i~~~---~~~~~~~~~~~~l~~g~~v~v~G~v~~~~~~~~~l~~ 69 (75)
T PF01336_consen 3 VEGRVTSIRRSGGKIVFFTLED---------GTGSIQVV---FFNEEYERFREKLKEGDIVRVRGKVKRYNGGELELIV 69 (75)
T ss_dssp EEEEEEEEEEEETTEEEEEEEE---------TTEEEEEE---EETHHHHHHHHTS-TTSEEEEEEEEEEETTSSEEEEE
T ss_pred EEEEEEEEEcCCCCEEEEEEEE---------CCccEEEE---EccHHhhHHhhcCCCCeEEEEEEEEEEECCccEEEEE
Confidence 67888888 33345555532 22433321 1223345788999999999999 6554333355443
No 112
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=72.48 E-value=27 Score=34.07 Aligned_cols=88 Identities=22% Similarity=0.367 Sum_probs=63.3
Q ss_pred eEecCCcccCCCCCeeeCCCEEEe--CCEEEEEEeeEEEEeccccCCCcceEEEEeeCCCccccCCCCCEEEEEEEEEec
Q psy6276 6 ICIPGQRICQLDSDIVGGRGTYVR--QGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQQ 83 (271)
Q Consensus 6 iVlPGD~L~~~eE~~~~G~GtY~~--~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~~~yiP~vGDIVIGrVt~V~~ 83 (271)
+.+||+.=....| +.+|.-+-.. +|.-+..++|.+++.. ++.+-|+.. + -| -++.-+.+
T Consensus 236 v~~pgg~T~YLsE-L~sG~eVlvVd~~G~tR~~~VGRvKIE~-------RPL~lIeAe----~---~g----~~~~viLQ 296 (344)
T PRK02290 236 VRVPGDKTRYLSE-LRSGDEVLVVDADGNTREAIVGRVKIEK-------RPLLLIEAE----Y---GG----KRIRTILQ 296 (344)
T ss_pred EEcCCCcchhhHh-hcCCCEEEEEeCCCCEEEEEeeEEEEee-------ccEEEEEEE----e---CC----eEEEEEEe
Confidence 4678998877777 8888877543 7999999999999985 578888762 1 23 23344567
Q ss_pred ceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE
Q psy6276 84 HLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR 134 (271)
Q Consensus 84 ~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak 134 (271)
+.|.+.+...++++++ + -.++|||-|+.+
T Consensus 297 naetIrlv~~dG~~vs--------V--------------t~Lk~GD~VL~~ 325 (344)
T PRK02290 297 NAETIRLVTPDGKPVS--------V--------------VDLKPGDEVLGY 325 (344)
T ss_pred cCcEEEEECCCCCEee--------e--------------eecCCCCEEEEE
Confidence 8899998765544222 1 127999999998
No 113
>PLN00208 translation initiation factor (eIF); Provisional
Probab=71.96 E-value=8.1 Score=33.25 Aligned_cols=55 Identities=27% Similarity=0.344 Sum_probs=33.0
Q ss_pred ccCCCCCEEEEEEEEEecc-eEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEEEe
Q psy6276 66 IVPTPGDVVTARIMAVQQH-LCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARLP 136 (271)
Q Consensus 66 yiP~vGDIVIGrVt~V~~~-~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~AkiS 136 (271)
.+|..|. ++|+|+...+. .+.|.+. ++...-..++|=+| .+-.+++||+|.+.++
T Consensus 27 ~~p~egq-~~g~V~~~lGn~~~~V~c~--dG~~rLa~IpGKmR-------------KrIWI~~GD~VlVel~ 82 (145)
T PLN00208 27 IFKEDGQ-EYAQVLRMLGNGRCEALCI--DGTKRLCHIRGKMR-------------KKVWIAAGDIILVGLR 82 (145)
T ss_pred ccCCCCc-EEEEEEEEcCCCEEEEEEC--CCCEEEEEEeccce-------------eeEEecCCCEEEEEcc
Confidence 4577666 78999998655 4555543 33322222333222 2456799999999843
No 114
>PRK08402 replication factor A; Reviewed
Probab=71.95 E-value=27 Score=34.07 Aligned_cols=54 Identities=19% Similarity=0.001 Sum_probs=37.1
Q ss_pred eeEEEEc-cCCCeeEe--ccCccCchhhhhhhhhhhHHHhcccccceeeeeeccCceEEEeEee
Q psy6276 153 GVVIALS-EAASLFRS--SEKLTNDIEFLKQEKLKLYEELSSSQKENEILRQTTGDLEVRLMQM 213 (271)
Q Consensus 153 GVV~A~c-~cG~~Mvp--~s~~~~c~~~~~~e~rKla~~~~s~~~~~~~~~~~~~~~~~~~~~~ 213 (271)
+.++..| .|...|.. .+....|+.|++.+... -+--......-||.+||.+.+-
T Consensus 209 ~~~y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p~~-------ryil~~~l~D~TG~~~vt~f~e 265 (355)
T PRK08402 209 VLVYDACPECRRKVDYDPATDTWICPEHGEVEPIK-------ITILDFGLDDGTGYIRVTLFGD 265 (355)
T ss_pred CeeEecCCCCCeEEEEecCCCCEeCCCCCCcCcce-------eEEEEEEEEcCCCcEEEEEecH
Confidence 5578889 89999973 33567899998643311 1233445677899999999863
No 115
>COG0211 RpmA Ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=71.48 E-value=9.3 Score=30.10 Aligned_cols=56 Identities=14% Similarity=0.188 Sum_probs=40.5
Q ss_pred CCCeEecCCcccCCCC-CeeeCCCEEE-eCCEEEEEEeeEEEEeccccCCCcceEEEEeeC
Q psy6276 3 NPPICIPGQRICQLDS-DIVGGRGTYV-RQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSY 61 (271)
Q Consensus 3 ~~~iVlPGD~L~~~eE-~~~~G~GtY~-~~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~ 61 (271)
++++|.+|..|...-. .|-||.++=. .|..|+|.+-|.|++.. ....++.|+|.|.
T Consensus 27 ~Gq~v~aG~IivRQRGTk~hpG~NVG~GkDhTlFAl~dG~Vkf~~---k~~~rk~vsV~~~ 84 (87)
T COG0211 27 GGQFVKAGSIIVRQRGTKFHPGVNVGRGKDHTLFALVDGVVKFET---KGKNRKYVSVVPE 84 (87)
T ss_pred CCeEEecccEEEEeccccccCCcccccCCCceEEEeeccEEEEEE---ccCCccEEEEEee
Confidence 4578999998864321 3788888754 47899999999998765 1124578999884
No 116
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=71.02 E-value=25 Score=25.27 Aligned_cols=60 Identities=13% Similarity=0.060 Sum_probs=28.0
Q ss_pred CCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEEEecCCCCceeeee
Q psy6276 70 PGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARLPLKELHSYQLST 147 (271)
Q Consensus 70 vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~AkiS~~d~~~~~LST 147 (271)
+|+++..+|.+++...|.++.. ..-.-.||.++ +...+.+||-|.+-+-.+.......||
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~--------~~~~vlLp~~e----------~~~~~~~Gd~v~VFvY~D~~~rl~AT~ 60 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDG--------EGKEVLLPKSE----------VPEPLKVGDEVEVFVYLDKEGRLVATT 60 (61)
T ss_dssp --------EEEE-SSEEEEEET--------T-EEEEEEGGG----------------TTSEEEEEEEE-TTS-EEEE-
T ss_pred CCCCcceEEEEEeCCEEEEECC--------CCCEEEechHH----------cCCCCCCCCEEEEEEEECCCCCEEEec
Confidence 5899999999999999999853 23345556543 334589999999884433223455555
No 117
>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=69.50 E-value=18 Score=37.72 Aligned_cols=72 Identities=15% Similarity=0.167 Sum_probs=50.4
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccch--hhh-------HhhhcCCCCCCEEEEE-Eec
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATE--IDR-------IEMYKCYRPGDIILAR-LPL 137 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te--~d~-------~~m~~~f~~GDIV~Ak-iS~ 137 (271)
.++|.++-|+|++|+...++|.|- .....|++|.+++.... -|. ......|++||.|..+ ++.
T Consensus 570 ~~iG~~~~g~I~~v~~~GifV~L~-------~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~v 642 (654)
T TIGR00358 570 DKVGTEFSGEISSVTRFGMFVRLD-------DNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEV 642 (654)
T ss_pred hCCCcEEEEEEEeEEcCcEEEEec-------CCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEE
Confidence 367999999999999999999983 13478999998875310 111 1223679999999999 766
Q ss_pred CC-CCceeee
Q psy6276 138 KE-LHSYQLS 146 (271)
Q Consensus 138 ~d-~~~~~LS 146 (271)
+. .+.+.++
T Consensus 643 d~~~~~I~f~ 652 (654)
T TIGR00358 643 NMETRSIIFE 652 (654)
T ss_pred ecccCeEEEE
Confidence 42 2344444
No 118
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=69.40 E-value=1.8 Score=36.57 Aligned_cols=25 Identities=4% Similarity=-0.231 Sum_probs=21.1
Q ss_pred Ec-cCCCeeEeccCccCchhhhhhhh
Q psy6276 158 LS-EAASLFRSSEKLTNDIEFLKQEK 182 (271)
Q Consensus 158 ~c-~cG~~Mvp~s~~~~c~~~~~~e~ 182 (271)
.| .||.||+.-.....||.|+..+.
T Consensus 30 hCp~Cg~PLF~KdG~v~CPvC~~~~~ 55 (131)
T COG1645 30 HCPKCGTPLFRKDGEVFCPVCGYREV 55 (131)
T ss_pred hCcccCCcceeeCCeEECCCCCceEE
Confidence 46 89999999888999999995443
No 119
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=67.52 E-value=2.4 Score=27.68 Aligned_cols=25 Identities=16% Similarity=0.091 Sum_probs=18.1
Q ss_pred Ec-cCCCeeEeccCccC---chhhhhhhh
Q psy6276 158 LS-EAASLFRSSEKLTN---DIEFLKQEK 182 (271)
Q Consensus 158 ~c-~cG~~Mvp~s~~~~---c~~~~~~e~ 182 (271)
.| +||+.|+|...... |+.|+..+.
T Consensus 3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~ 31 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRVACRTCGYEEP 31 (35)
T ss_dssp BETTTTSBEEEEEETTTTEEESSSS-EEE
T ss_pred eCCCCCccceEcCCCccCcCCCCCCCccC
Confidence 47 89999999874444 888887654
No 120
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=66.08 E-value=17 Score=36.27 Aligned_cols=62 Identities=15% Similarity=0.140 Sum_probs=39.7
Q ss_pred hhhcCCCCCCEEEEE--EecCC--CCceeeeeccCCCeeEEEEc-cCCCeeEeccC-ccCchhhhhhhh
Q psy6276 120 EMYKCYRPGDIILAR--LPLKE--LHSYQLSTAENELGVVIALS-EAASLFRSSEK-LTNDIEFLKQEK 182 (271)
Q Consensus 120 ~m~~~f~~GDIV~Ak--iS~~d--~~~~~LST~~~eLGVV~A~c-~cG~~Mvp~s~-~~~c~~~~~~e~ 182 (271)
+.-..+.|||.|.+- +--+. -..+++..-.. +-...-+| .||..|.-.+. -++|+.||....
T Consensus 311 ~~a~~L~pGD~i~~~G~~~~~~~n~ek~~v~~l~~-~~~~~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~ 378 (421)
T COG1571 311 ELARKLIPGDEITVYGSVKPGTLNLEKFQVLKLAR-YERVNPVCPRCGGRMKSAGRNGFRCKKCGTRAR 378 (421)
T ss_pred HHHHhcCCCCEEEEecCccccceeEEEEEEEEeee-eEEcCCCCCccCCchhhcCCCCcccccccccCC
Confidence 456678999999776 32110 01122211122 55555578 89999988774 899999998765
No 121
>KOG3298|consensus
Probab=64.93 E-value=20 Score=31.53 Aligned_cols=85 Identities=16% Similarity=0.150 Sum_probs=51.4
Q ss_pred cccCCCCCEEEEEEEEEecceEEEEEeeecCcccC------CceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-Eec
Q psy6276 65 VIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALS------RTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPL 137 (271)
Q Consensus 65 ~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~------~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~ 137 (271)
...|-.|+||-|.|+.|....+++++...+-..++ ..|. +-+|=.... ..++. .+..|+-||-+ +..
T Consensus 76 ~FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~---p~~n~P~f~--~~d~s-~I~~~~~VR~kiigt 149 (170)
T KOG3298|consen 76 TFKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFD---PGENPPNFQ--TEDES-VIQKGVEVRLKIIGT 149 (170)
T ss_pred EEeecCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccC---CCCCCCccc--ccccc-eeeeCcEEEEEEEEE
Confidence 45678899999999999999999998654432221 1222 222211000 01222 67899999999 654
Q ss_pred C-CCCc-eee-eeccCCCeeE
Q psy6276 138 K-ELHS-YQL-STAENELGVV 155 (271)
Q Consensus 138 ~-d~~~-~~L-ST~~~eLGVV 155 (271)
- |... +.| |+.++-||++
T Consensus 150 r~~~~~i~algtl~~D~LG~i 170 (170)
T KOG3298|consen 150 RVDETEIFALGTLKGDYLGPI 170 (170)
T ss_pred EEeeeeEEEEEEecCcccccC
Confidence 1 2223 334 6677888864
No 122
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=64.76 E-value=13 Score=32.30 Aligned_cols=54 Identities=20% Similarity=0.211 Sum_probs=32.4
Q ss_pred ccCCCCCEEEEEEEEEecce-EEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEEE
Q psy6276 66 IVPTPGDVVTARIMAVQQHL-CKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARL 135 (271)
Q Consensus 66 yiP~vGDIVIGrVt~V~~~~-a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Aki 135 (271)
.+|..|. +||+|+...++. +.|.+ .++...-..++|=+| .+-.+.+||+|...+
T Consensus 27 ~~~eegq-~~g~V~~~LGn~~f~V~c--~dG~~rLa~I~GKmR-------------K~IWI~~GD~VlVel 81 (155)
T PTZ00329 27 VFKEEGQ-EYAQVLRMLGNGRLEAYC--FDGVKRLCHIRGKMR-------------KRVWINIGDIILVSL 81 (155)
T ss_pred ccCCCCc-EEEEEEEEcCCCEEEEEE--CCCCEEEEEeeccce-------------eeEEecCCCEEEEec
Confidence 3567676 689999996554 55554 334322222333222 245579999999884
No 123
>COG1315 Uncharacterized conserved protein [Function unknown]
Probab=63.42 E-value=11 Score=38.63 Aligned_cols=48 Identities=17% Similarity=0.232 Sum_probs=36.2
Q ss_pred CeeeCCCE-EEeCCEEEEEEeeEEEEeccccCCCcceEEEEeeCC--CccccCCCCCEE
Q psy6276 19 DIVGGRGT-YVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYK--KEVIVPTPGDVV 74 (271)
Q Consensus 19 ~~~~G~Gt-Y~~~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~--~~~yiP~vGDIV 74 (271)
.+.+|.|| +.+++.+.|+.-|.+-+++ ++|+|.|.. .+..-++.|+|.
T Consensus 220 ~l~lG~nt~~kd~~tlvA~~~G~~~~s~--------~tI~V~~iyeV~gdV~~kTGnI~ 270 (543)
T COG1315 220 KLNLGKNTAFKDNNTLVAKRDGQPIVSK--------NTISVYPIYEVNGDVDVKTGNIK 270 (543)
T ss_pred eeecCCCCccCCCCEEEEeeCCeEEecC--------CeeEEEEEEEecCCcccccccee
Confidence 37889999 7778999999999999987 899999862 123344555543
No 124
>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=62.16 E-value=11 Score=29.50 Aligned_cols=30 Identities=20% Similarity=0.307 Sum_probs=21.5
Q ss_pred ccccCCCCCEEEEEEEEEecceEEEEEeeec
Q psy6276 64 EVIVPTPGDVVTARIMAVQQHLCKAHVISVG 94 (271)
Q Consensus 64 ~~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~ 94 (271)
.+...++||+|+|||.++...+ .+.+-|++
T Consensus 46 ~rp~L~~GDlV~ArV~~~~~~~-~~eLtc~~ 75 (86)
T cd05790 46 NRPNLNVGDLVYARVVKANRDM-EPELSCVD 75 (86)
T ss_pred ccccCCCCCEEEEEEEecCCCC-CeEEEEeC
Confidence 3555699999999999997763 34444444
No 125
>PRK12366 replication factor A; Reviewed
Probab=60.81 E-value=7.9 Score=40.37 Aligned_cols=49 Identities=14% Similarity=-0.042 Sum_probs=34.0
Q ss_pred EEc-cCCCeeEeccCccCchhhhhhhhhhhHHHhcccccceeeeeeccCceEEEeEe
Q psy6276 157 ALS-EAASLFRSSEKLTNDIEFLKQEKLKLYEELSSSQKENEILRQTTGDLEVRLMQ 212 (271)
Q Consensus 157 A~c-~cG~~Mvp~s~~~~c~~~~~~e~rKla~~~~s~~~~~~~~~~~~~~~~~~~~~ 212 (271)
..| .|...|........|+.|++.+... -+--......-+|.+|+.+.+
T Consensus 533 ~aCp~CnkKv~~~~g~~~C~~c~~~~p~~-------~~~l~~~i~D~TG~~~~t~f~ 582 (637)
T PRK12366 533 YLCPNCRKRVEEVDGEYICEFCGEVEPNE-------LLMLNFTLDDGTGTINCRFYG 582 (637)
T ss_pred ecccccCeEeEcCCCcEECCCCCCCCCcE-------EEEEEEEEEcCCCCEEEEEEh
Confidence 346 6888887655677899999873221 233345666789999999875
No 126
>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=60.28 E-value=20 Score=35.47 Aligned_cols=35 Identities=23% Similarity=0.394 Sum_probs=29.1
Q ss_pred CeeeCCCEEEe--C-CEEEEEEeeEEEEeccccCCCcceEEEEeeC
Q psy6276 19 DIVGGRGTYVR--Q-GYLYSTLAGTVSINKHVEDNKEVSVIEVSSY 61 (271)
Q Consensus 19 ~~~~G~GtY~~--~-g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~ 61 (271)
++.+|+||... | ..+||++-|.+.+.+ ..++|.|.
T Consensus 144 ~~~~g~~~~~~~~d~~~~~A~~~G~~~~~~--------~~i~V~~~ 181 (451)
T PF03961_consen 144 PLKAGKNTEVSEEDGNKLYAAIDGRPVFEN--------GKISVDPV 181 (451)
T ss_pred ceeCCCCEEEEcCCCCEEEEecCCEEEEEC--------CEEEEEEe
Confidence 47889999986 3 589999999999987 56888875
No 127
>PRK00420 hypothetical protein; Validated
Probab=58.32 E-value=4.7 Score=33.22 Aligned_cols=28 Identities=7% Similarity=-0.260 Sum_probs=22.8
Q ss_pred EEc-cCCCeeEe-ccCccCchhhhhhhhhh
Q psy6276 157 ALS-EAASLFRS-SEKLTNDIEFLKQEKLK 184 (271)
Q Consensus 157 A~c-~cG~~Mvp-~s~~~~c~~~~~~e~rK 184 (271)
..| .||.||+. ......||.|+.....+
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVYIVK 53 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCeeeec
Confidence 567 89999988 56799999999865544
No 128
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=57.32 E-value=5.7 Score=32.49 Aligned_cols=28 Identities=11% Similarity=-0.034 Sum_probs=23.0
Q ss_pred EEc-cCCCeeEe----ccCccCchhhhhhhhhh
Q psy6276 157 ALS-EAASLFRS----SEKLTNDIEFLKQEKLK 184 (271)
Q Consensus 157 A~c-~cG~~Mvp----~s~~~~c~~~~~~e~rK 184 (271)
-.| +||+.|+| .+..+.|+.|+......
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECCCCCcchhcc
Confidence 357 89999999 55799999999887754
No 129
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=56.53 E-value=5.7 Score=26.73 Aligned_cols=27 Identities=15% Similarity=0.015 Sum_probs=18.6
Q ss_pred Ec-cCC---CeeEecc--CccCchhhhhhhhhh
Q psy6276 158 LS-EAA---SLFRSSE--KLTNDIEFLKQEKLK 184 (271)
Q Consensus 158 ~c-~cG---~~Mvp~s--~~~~c~~~~~~e~rK 184 (271)
+| .|| ..+.+++ ....||.|+..+-++
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISEDDPVPCPECGSTEVRR 39 (42)
T ss_pred EeCCCCCEEEEEEEcCCCCCCcCCCCCCCceEE
Confidence 35 788 4456666 489999999944433
No 130
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=56.41 E-value=44 Score=31.77 Aligned_cols=57 Identities=12% Similarity=0.247 Sum_probs=38.7
Q ss_pred CceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCceeeeeccCCC-------eeEEEEc-cCCCeeE
Q psy6276 100 RTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQLSTAENEL-------GVVIALS-EAASLFR 166 (271)
Q Consensus 100 ~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~LST~~~eL-------GVV~A~c-~cG~~Mv 166 (271)
..+.|.||.++ .....+.|+.+-|| +.+.+-+.+.||++.-.. -+|+++= ..|+.|-
T Consensus 177 ~~~~GfIh~sE----------r~~~prlG~~l~~rVi~~reDg~lnLSl~p~~~E~l~~daq~Il~yL~~~gG~mp 242 (287)
T COG2996 177 NGYLGFIHKSE----------RFAEPRLGERLTARVIGVREDGKLNLSLRPRAHEMLDEDAQMILTYLESNGGFMP 242 (287)
T ss_pred CCeEEEEcchh----------hcccccCCceEEEEEEEEccCCeeecccccccHHhhhhhHHHHHHHHHHcCCccc
Confidence 35788888764 45567999999999 888655789999965332 2333332 4566663
No 131
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=55.67 E-value=18 Score=40.16 Aligned_cols=74 Identities=24% Similarity=0.298 Sum_probs=50.0
Q ss_pred CCCCEEEEE-EecCCCCceeeeeccCCCeeEEE------------Ec-cCCCeeEeccCccCchhhhhhh------hhhh
Q psy6276 126 RPGDIILAR-LPLKELHSYQLSTAENELGVVIA------------LS-EAASLFRSSEKLTNDIEFLKQE------KLKL 185 (271)
Q Consensus 126 ~~GDIV~Ak-iS~~d~~~~~LST~~~eLGVV~A------------~c-~cG~~Mvp~s~~~~c~~~~~~e------~rKl 185 (271)
-.||.|.-= .|.| +-+.|.|...=.||+.- +| .||...+-.+ -.||.|+-.. -.+.
T Consensus 653 ~~gD~vL~ItAS~G--Hv~DLvt~~g~hGvl~~~~~~vPvY~tIKrC~dcg~q~~~~~--~~cP~Cgs~~v~d~~~~ve~ 728 (1187)
T COG1110 653 AIGDLVLTITASGG--HVFDLVTEPGVHGVLVKDGKYVPVYDTIKRCRDCGEQFVDSE--DKCPRCGSRNVEDKTETVEA 728 (1187)
T ss_pred ecCCeEEEEEecCC--eeEEeecccccceeeccCCceEehHHHHHHHhhcCceecccc--ccCCCCCCccccccHHHHHH
Confidence 567877666 5654 67899998888886654 46 7888776553 3899999722 2455
Q ss_pred HHHhcccccceeeeeeccCc
Q psy6276 186 YEELSSSQKENEILRQTTGD 205 (271)
Q Consensus 186 a~~~~s~~~~~~~~~~~~~~ 205 (271)
..++ +.-.++|.+||+=|
T Consensus 729 lRel--A~EvDeVlIgTDPD 746 (1187)
T COG1110 729 LREL--ALEVDEILIGTDPD 746 (1187)
T ss_pred HHHH--HhhcCEEEEcCCCC
Confidence 5555 33457788887654
No 132
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=54.00 E-value=28 Score=26.89 Aligned_cols=54 Identities=15% Similarity=0.157 Sum_probs=31.2
Q ss_pred CCCCCEEEEEEEEEecc-eEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-Eec
Q psy6276 68 PTPGDVVTARIMAVQQH-LCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPL 137 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~-~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~ 137 (271)
|..| -++|+|+...++ .+.|.+. ++. .+.+.|+.. ...+-.++.||+|... ..+
T Consensus 2 p~e~-q~~g~V~~~lG~~~~~V~~~--dG~----~~la~ipgK---------~Rk~iwI~~GD~VlVe~~~~ 57 (83)
T smart00652 2 KEDG-QEIAQVVKMLGNGRLEVMCA--DGK----ERLARIPGK---------MRKKVWIRRGDIVLVDPWDF 57 (83)
T ss_pred CCCC-cEEEEEEEEcCCCEEEEEEC--CCC----EEEEEEchh---------hcccEEEcCCCEEEEEecCC
Confidence 5544 478999998554 4666553 332 223333321 1124557999999999 443
No 133
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=53.91 E-value=30 Score=27.82 Aligned_cols=57 Identities=11% Similarity=0.202 Sum_probs=33.0
Q ss_pred ccCCCCCEEEEEEEEEecc-eEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC
Q psy6276 66 IVPTPGDVVTARIMAVQQH-LCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK 138 (271)
Q Consensus 66 yiP~vGDIVIGrVt~V~~~-~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~ 138 (271)
..|..| -++|+|+...++ .+.|.+. ++.. ..+.|+. +...+-.+++||+|.+. ..++
T Consensus 16 ~~p~e~-e~~g~V~~~lG~~~~~V~~~--dG~~----~la~i~G---------K~Rk~IwI~~GD~VlVe~~~~~ 74 (100)
T PRK04012 16 PMPEEG-EVFGVVEQMLGANRVRVRCM--DGVE----RMGRIPG---------KMKKRMWIREGDVVIVAPWDFQ 74 (100)
T ss_pred cCCCCC-EEEEEEEEEcCCCEEEEEeC--CCCE----EEEEEch---------hhcccEEecCCCEEEEEecccC
Confidence 345544 588999998555 4555553 3322 2233222 11125567999999999 4443
No 134
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=53.64 E-value=25 Score=28.29 Aligned_cols=54 Identities=17% Similarity=0.208 Sum_probs=33.1
Q ss_pred eEec--CCcccCCCCCeeeCCCEEEe---C-CEEEEEEeeEEEEeccccCCCcceEEEEeeCCCccccCCCCCEEEEEEE
Q psy6276 6 ICIP--GQRICQLDSDIVGGRGTYVR---Q-GYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIM 79 (271)
Q Consensus 6 iVlP--GD~L~~~eE~~~~G~GtY~~---~-g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~~~yiP~vGDIVIGrVt 79 (271)
++.| |+.++... -..|.|.|.. | ..+.|.+.|..+ +.|+|. +||.|+....
T Consensus 15 ~~~p~e~e~~g~V~--~~lG~~~~~V~~~dG~~~la~i~GK~R-----------k~IwI~----------~GD~VlVe~~ 71 (100)
T PRK04012 15 LPMPEEGEVFGVVE--QMLGANRVRVRCMDGVERMGRIPGKMK-----------KRMWIR----------EGDVVIVAPW 71 (100)
T ss_pred ccCCCCCEEEEEEE--EEcCCCEEEEEeCCCCEEEEEEchhhc-----------ccEEec----------CCCEEEEEec
Confidence 4555 55555543 3567777752 3 468888888664 246664 4888877665
Q ss_pred EEe
Q psy6276 80 AVQ 82 (271)
Q Consensus 80 ~V~ 82 (271)
.-.
T Consensus 72 ~~~ 74 (100)
T PRK04012 72 DFQ 74 (100)
T ss_pred ccC
Confidence 554
No 135
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=53.44 E-value=82 Score=28.85 Aligned_cols=97 Identities=10% Similarity=0.162 Sum_probs=53.2
Q ss_pred CEEEEEEeeEEEEeccccCCCcceEEEEeeCCCccccCCCCCE------EEEEEEEEecceEEEEEeeecCccc-----C
Q psy6276 31 GYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDV------VTARIMAVQQHLCKAHVISVGNTAL-----S 99 (271)
Q Consensus 31 g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~~~yiP~vGDI------VIGrVt~V~~~~a~VdI~~v~~~~L-----~ 99 (271)
..+.|.+.+.-.-. -.+.+.+.. ....--++|+. ++|+|+++.++.+.|..+.-.+..+ .
T Consensus 118 ~~i~A~Vi~~~~~~-------~~~~i~Id~--G~~~Gv~~g~~Vv~~~GlVG~V~~v~~~~s~V~li~d~~~~v~v~i~~ 188 (276)
T PRK13922 118 QFITARVISRSPDP-------WSQQVTIDK--GSNDGVKKGMPVIDPGGLVGRVIEVSPNTSRVLLLTDPNSRVPVQVGR 188 (276)
T ss_pred ceEEEEEEEeCCCC-------ceeEEEEcc--CcccCCCCCCceEcCCCCeEEEEEECCCeeEEEEEEcCCCceEEEEEc
Confidence 55667666644211 234454432 11222344555 6899999999999998765333211 2
Q ss_pred CceeeEEecccccc-chhhhHhhhcCCCCCCEEEEE-Ee
Q psy6276 100 RTFRALLRRENVRA-TEIDRIEMYKCYRPGDIILAR-LP 136 (271)
Q Consensus 100 ~~f~GiLr~sdvr~-te~d~~~m~~~f~~GDIV~Ak-iS 136 (271)
....|+++-..... ..-+-..-...+++||.|.-- ++
T Consensus 189 ~~~~gi~~G~g~~~~l~l~~i~~~~~i~~GD~VvTSGl~ 227 (276)
T PRK13922 189 NGIRGILSGNGSGDNLKLEFIPRSADIKVGDLVVTSGLG 227 (276)
T ss_pred CCceEEEEecCCCCceEEEecCCCCCCCCCCEEEECCCC
Confidence 34567777653211 011112334558999998776 63
No 136
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=53.25 E-value=8.2 Score=24.94 Aligned_cols=26 Identities=12% Similarity=0.036 Sum_probs=17.5
Q ss_pred Ec-cCCCee---Eecc--CccCchhhhhhhhh
Q psy6276 158 LS-EAASLF---RSSE--KLTNDIEFLKQEKL 183 (271)
Q Consensus 158 ~c-~cG~~M---vp~s--~~~~c~~~~~~e~r 183 (271)
+| .||... .+.+ ....||.|+...+|
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~r 38 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGGDVRR 38 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCCccee
Confidence 57 788844 3332 47889999994444
No 137
>PF04085 MreC: rod shape-determining protein MreC; InterPro: IPR007221 MreC (murein formation C) is involved in the rod shape determination in Escherichia coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped.; GO: 0008360 regulation of cell shape; PDB: 2J5U_B 2QF4_B 2QF5_A.
Probab=52.85 E-value=22 Score=30.06 Aligned_cols=64 Identities=19% Similarity=0.264 Sum_probs=34.9
Q ss_pred EEEEEEEEEecceEEEEEeeecCcc-----cCCceeeEEecccccc--chhhhHhhhcCCCCCCEEEEE-Ee
Q psy6276 73 VVTARIMAVQQHLCKAHVISVGNTA-----LSRTFRALLRRENVRA--TEIDRIEMYKCYRPGDIILAR-LP 136 (271)
Q Consensus 73 IVIGrVt~V~~~~a~VdI~~v~~~~-----L~~~f~GiLr~sdvr~--te~d~~~m~~~f~~GDIV~Ak-iS 136 (271)
-++|+|+.+.++.+.|..+.-.... ......|+++-..-.. ...........+++||.|.-. ++
T Consensus 35 glVG~V~~V~~~~S~V~li~d~~~~v~v~i~~~~~~Gi~~G~~~~~~~~~l~~i~~~~~i~~GD~V~TSG~~ 106 (152)
T PF04085_consen 35 GLVGRVTEVGPNTSRVLLITDPNSRVSVKIERSGDRGILRGDGSNTGLLKLEYIPKDADIKKGDIVVTSGLG 106 (152)
T ss_dssp EEEEEEEEE-SS-EEEEETTSSBCEEEEEEECTTEEEEEEEEETTTTEEEEEEECTTS---TT-EEEEE-TT
T ss_pred CcEEEEEEECCCEEEEEEEeCCCceEEEEEecCCeeEEEEeCCCCCceEEEEECCCCCCCCCCCEEEECCCC
Confidence 3789999999999999876433321 1244568876544322 111223456667889988876 54
No 138
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=47.92 E-value=7.4 Score=26.54 Aligned_cols=25 Identities=8% Similarity=0.013 Sum_probs=19.0
Q ss_pred Ec-cCCCeeEecc----CccCchhhhhhhh
Q psy6276 158 LS-EAASLFRSSE----KLTNDIEFLKQEK 182 (271)
Q Consensus 158 ~c-~cG~~Mvp~s----~~~~c~~~~~~e~ 182 (271)
.| .||+.|.+.. +.+.||.|+....
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEE
Confidence 46 7999998864 3688999997654
No 139
>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=46.84 E-value=23 Score=27.53 Aligned_cols=23 Identities=22% Similarity=0.456 Sum_probs=18.8
Q ss_pred CCCCEEEEEEEEEec-ceEEEEEe
Q psy6276 69 TPGDVVTARIMAVQQ-HLCKAHVI 91 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~-~~a~VdI~ 91 (271)
++||+|.|+|.++.+ +.+.+.+.
T Consensus 62 ~~GDiV~AkVis~~~~~~~~Lst~ 85 (92)
T cd05791 62 RPGDIVRAKVISLGDASSYYLSTA 85 (92)
T ss_pred CCCCEEEEEEEEcCCCCCcEEEec
Confidence 899999999999976 55666653
No 140
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=46.12 E-value=34 Score=26.16 Aligned_cols=49 Identities=6% Similarity=0.122 Sum_probs=28.9
Q ss_pred EEEEEEEEecc-eEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-Eec
Q psy6276 74 VTARIMAVQQH-LCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPL 137 (271)
Q Consensus 74 VIGrVt~V~~~-~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~ 137 (271)
++|+|+...++ .+.|.+. ++. ...+-++. +...+-.+++||+|.+. ...
T Consensus 2 ~i~~V~~~lG~~~~~V~~~--dg~----~~l~~i~g---------K~Rk~iwI~~GD~VlV~~~~~ 52 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECA--DGQ----RRLVSIPG---------KLRKNIWIKRGDFLIVDPIEE 52 (78)
T ss_pred eEEEEEEECCCCEEEEEEC--CCC----EEEEEEch---------hhccCEEEcCCCEEEEEeccc
Confidence 68999998554 4666653 332 22233322 11123457999999999 655
No 141
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=46.05 E-value=8.4 Score=32.52 Aligned_cols=36 Identities=11% Similarity=0.020 Sum_probs=26.4
Q ss_pred CCeeEEEEc-cCCCeeEeccCccCchhhhhh---hhhhhHHH
Q psy6276 151 ELGVVIALS-EAASLFRSSEKLTNDIEFLKQ---EKLKLYEE 188 (271)
Q Consensus 151 eLGVV~A~c-~cG~~Mvp~s~~~~c~~~~~~---e~rKla~~ 188 (271)
+...+-++| +||...+|-. ..||.|+.. |-+.++.+
T Consensus 24 ~~kl~g~kC~~CG~v~~PPr--~~Cp~C~~~~~~E~vels~~ 63 (140)
T COG1545 24 EGKLLGTKCKKCGRVYFPPR--AYCPKCGSETELEWVELSGE 63 (140)
T ss_pred hCcEEEEEcCCCCeEEcCCc--ccCCCCCCCCceEEEEeCCC
Confidence 356677789 9999999974 479999988 44555443
No 142
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=45.34 E-value=8 Score=36.60 Aligned_cols=27 Identities=0% Similarity=-0.229 Sum_probs=22.0
Q ss_pred Ec-cCCCeeEec--cCccCchhhhhhhhhh
Q psy6276 158 LS-EAASLFRSS--EKLTNDIEFLKQEKLK 184 (271)
Q Consensus 158 ~c-~cG~~Mvp~--s~~~~c~~~~~~e~rK 184 (271)
.| .||.+|.+. +|...||.|+..--..
T Consensus 113 FCg~CG~~~~~~~~g~~~~C~~cg~~~fPR 142 (279)
T COG2816 113 FCGRCGTKTYPREGGWARVCPKCGHEHFPR 142 (279)
T ss_pred CCCCCCCcCccccCceeeeCCCCCCccCCC
Confidence 46 899999886 4999999999876544
No 143
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=45.25 E-value=68 Score=34.05 Aligned_cols=63 Identities=11% Similarity=-0.005 Sum_probs=38.9
Q ss_pred hhcCCCCCCEEEEEEecCCCCceeeeec----cCCCeeEEEEc-cCCCeeEeccCccCchh---hhhhhhhhh
Q psy6276 121 MYKCYRPGDIILARLPLKELHSYQLSTA----ENELGVVIALS-EAASLFRSSEKLTNDIE---FLKQEKLKL 185 (271)
Q Consensus 121 m~~~f~~GDIV~AkiS~~d~~~~~LST~----~~eLGVV~A~c-~cG~~Mvp~s~~~~c~~---~~~~e~rKl 185 (271)
-+..+++||.|.-.-+ ||.-|...... ...+ .+-..| .||++++..+....|++ |...-.++|
T Consensus 386 ~~~di~iGD~V~V~ra-GdVIPkI~~vv~~~~~~~~-~~P~~CP~C~~~l~~~~~~~~C~n~~~Cpaq~~~~l 456 (689)
T PRK14351 386 EELGVNVGDRVRVKRA-GDVIPYVEEVVEKDSEGTF-EFPDTCPVCDSAVERDGPLAFCTGGLACPAQLERSI 456 (689)
T ss_pred HHcCCCCCCEEEEEec-CCccceeeeeecccCCCCC-cCCCCCCCCCCEeeeCCceEEcCCCCCCHHHHHHHH
Confidence 4667899999998722 34444443321 1222 334578 89999987655666863 766655553
No 144
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=45.25 E-value=41 Score=26.99 Aligned_cols=57 Identities=12% Similarity=0.219 Sum_probs=33.0
Q ss_pred cCC-CCCEEEEEEEEEecc-eEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecC
Q psy6276 67 VPT-PGDVVTARIMAVQQH-LCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLK 138 (271)
Q Consensus 67 iP~-vGDIVIGrVt~V~~~-~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~ 138 (271)
+|. .-+-++|+|+...++ .+.|.+. ++. .+.+.|+. +...+-.+++||+|... ..+.
T Consensus 13 ~p~~~e~e~~g~V~~~lG~~~~~V~~~--dG~----~~la~i~G---------K~Rk~iwI~~GD~VlVsp~d~~ 72 (99)
T TIGR00523 13 LPRKEEGEILGVIEQMLGAGRVKVRCL--DGK----TRLGRIPG---------KLKKRIWIREGDVVIVKPWEFQ 72 (99)
T ss_pred CCCCCCCEEEEEEEEEcCCCEEEEEeC--CCC----EEEEEEch---------hhcccEEecCCCEEEEEEccCC
Confidence 453 356699999999554 4555553 332 22333332 11125567999999986 4443
No 145
>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=44.72 E-value=1.1e+02 Score=25.13 Aligned_cols=50 Identities=20% Similarity=0.231 Sum_probs=39.9
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR 134 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak 134 (271)
|..|-+|+|+|..+-.+-..+|+. .-|.+++++... ..+.|..|+-|+-+
T Consensus 21 ~~~gk~V~G~I~hvv~ddLYIDfG--------~KFhcVc~rp~~---------~~~~y~~G~rV~lr 70 (104)
T PF10246_consen 21 DPEGKIVIGKIFHVVDDDLYIDFG--------GKFHCVCKRPAV---------NGEKYVRGSRVRLR 70 (104)
T ss_pred CccCCEEEEEEEEEecCceEEEeC--------CceeEEEecccc---------cccccccCCEEEEE
Confidence 347899999999999998888875 578999886432 23458889999998
No 146
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=43.57 E-value=17 Score=29.54 Aligned_cols=27 Identities=7% Similarity=-0.138 Sum_probs=20.3
Q ss_pred EEEEc-cCCCeeEeccCccCchhhhhhh
Q psy6276 155 VIALS-EAASLFRSSEKLTNDIEFLKQE 181 (271)
Q Consensus 155 V~A~c-~cG~~Mvp~s~~~~c~~~~~~e 181 (271)
+.++| .||...-+......||.|+-..
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 69 VECECEDCSEEVSPEIDLYRCPKCHGIM 96 (115)
T ss_pred cEEEcccCCCEEecCCcCccCcCCcCCC
Confidence 35789 8997776666678899998643
No 147
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=42.90 E-value=18 Score=26.77 Aligned_cols=20 Identities=0% Similarity=-0.391 Sum_probs=11.2
Q ss_pred cCCCeeEecc-------CccCchhhhh
Q psy6276 160 EAASLFRSSE-------KLTNDIEFLK 179 (271)
Q Consensus 160 ~cG~~Mvp~s-------~~~~c~~~~~ 179 (271)
.||+.++-.. ..+.||+||.
T Consensus 32 nCGe~~I~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 32 NCGEVEIYRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred CCCceeeehhhhHHHcCCceECCCcCc
Confidence 6665554432 4666666664
No 148
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=42.77 E-value=10 Score=27.98 Aligned_cols=21 Identities=5% Similarity=-0.292 Sum_probs=11.1
Q ss_pred cCCCeeEecc--CccCchhhhhh
Q psy6276 160 EAASLFRSSE--KLTNDIEFLKQ 180 (271)
Q Consensus 160 ~cG~~Mvp~s--~~~~c~~~~~~ 180 (271)
.||..|.|.+ ..+.||+||+.
T Consensus 12 SCg~~i~~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 12 SCGIEIAPREKAVKFLCPNCGEV 34 (59)
T ss_pred CCCCcccCCCccCEeeCCCCCCe
Confidence 4555555543 35555555554
No 149
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=41.94 E-value=15 Score=23.71 Aligned_cols=22 Identities=9% Similarity=-0.061 Sum_probs=14.9
Q ss_pred c-cCCCeeE-eccCccCchhhhhh
Q psy6276 159 S-EAASLFR-SSEKLTNDIEFLKQ 180 (271)
Q Consensus 159 c-~cG~~Mv-p~s~~~~c~~~~~~ 180 (271)
| .||.... .......|++||-.
T Consensus 3 C~~Cg~~~~~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 3 CGECGAEVELKPGDPIRCPECGHR 26 (32)
T ss_dssp ESSSSSSE-BSTSSTSSBSSSS-S
T ss_pred CCcCCCeeEcCCCCcEECCcCCCe
Confidence 5 7887774 33467899999864
No 150
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=41.87 E-value=18 Score=26.04 Aligned_cols=11 Identities=36% Similarity=1.204 Sum_probs=9.8
Q ss_pred CCCCCEEEEEE
Q psy6276 125 YRPGDIILARL 135 (271)
Q Consensus 125 f~~GDIV~Aki 135 (271)
|++||+|.||+
T Consensus 1 f~~GdlVwaK~ 11 (63)
T smart00293 1 FKPGDLVWAKM 11 (63)
T ss_pred CCCCCEEEEEC
Confidence 78999999993
No 151
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=41.46 E-value=19 Score=29.20 Aligned_cols=26 Identities=4% Similarity=-0.037 Sum_probs=19.4
Q ss_pred EEEEc-cCCCeeEeccCccCchhhhhh
Q psy6276 155 VIALS-EAASLFRSSEKLTNDIEFLKQ 180 (271)
Q Consensus 155 V~A~c-~cG~~Mvp~s~~~~c~~~~~~ 180 (271)
+.++| .||...-+......||.|+..
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred cEEEcccCCCEEecCCcCccCcCCCCC
Confidence 35678 899777665667779999954
No 152
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=41.14 E-value=15 Score=25.13 Aligned_cols=27 Identities=7% Similarity=0.005 Sum_probs=18.3
Q ss_pred Ec-cCCC---eeEecc--CccCchhhhhhhhhh
Q psy6276 158 LS-EAAS---LFRSSE--KLTNDIEFLKQEKLK 184 (271)
Q Consensus 158 ~c-~cG~---~Mvp~s--~~~~c~~~~~~e~rK 184 (271)
+| +||. .+.+.+ ....||.|+..+-++
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r 39 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGGEKLRR 39 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCCCceeE
Confidence 46 7887 555554 467899999855444
No 153
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=40.06 E-value=16 Score=24.83 Aligned_cols=23 Identities=0% Similarity=-0.143 Sum_probs=17.9
Q ss_pred EEEc-cCCCeeEe-ccCccCchhhh
Q psy6276 156 IALS-EAASLFRS-SEKLTNDIEFL 178 (271)
Q Consensus 156 ~A~c-~cG~~Mvp-~s~~~~c~~~~ 178 (271)
-..| .||.||.+ ......|+.|+
T Consensus 17 ~~~Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred cCccCCCCCeeEEecCCCEECCCCC
Confidence 3467 89999988 55688898884
No 154
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=39.72 E-value=10 Score=31.87 Aligned_cols=17 Identities=6% Similarity=0.143 Sum_probs=13.2
Q ss_pred eeEEEEc-cCCCeeEecc
Q psy6276 153 GVVIALS-EAASLFRSSE 169 (271)
Q Consensus 153 GVV~A~c-~cG~~Mvp~s 169 (271)
.-++++| .|++++.+++
T Consensus 88 ~~~~sRC~~CN~~L~~v~ 105 (147)
T PF01927_consen 88 DPIFSRCPKCNGPLRPVS 105 (147)
T ss_pred CCCCCccCCCCcEeeech
Confidence 4456788 8999998876
No 155
>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=39.41 E-value=59 Score=25.07 Aligned_cols=44 Identities=18% Similarity=0.171 Sum_probs=28.1
Q ss_pred eEEEEeeCCCccccCCCCCEEEEEEEEEecc---eEEEEEeeecCcc
Q psy6276 54 SVIEVSSYKKEVIVPTPGDVVTARIMAVQQH---LCKAHVISVGNTA 97 (271)
Q Consensus 54 ~~I~V~P~~~~~yiP~vGDIVIGrVt~V~~~---~a~VdI~~v~~~~ 97 (271)
.-|+|-|..=.++-.+.||.|.|.|..-... .+.+.|..|++.+
T Consensus 29 ~DvYVs~~qIrrf~LR~GD~V~G~vr~p~~~ek~~aL~~V~~VNg~~ 75 (78)
T PF07497_consen 29 DDVYVSPSQIRRFGLRTGDLVEGQVRPPREGEKYFALLRVESVNGRP 75 (78)
T ss_dssp TSEEE-CCCCCCTT--TTEEEEEEEE--STTSSSEEECEECEETTEC
T ss_pred CCEEECHHHHHHcCCCCCCEEEEEEeCCCCCCcceeeEEEEeECCcC
Confidence 3578877644778889999999999986433 2666777777643
No 156
>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=39.41 E-value=71 Score=23.21 Aligned_cols=51 Identities=12% Similarity=0.088 Sum_probs=28.8
Q ss_pred CEEEEEEEEEecce-EEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEEEec
Q psy6276 72 DVVTARIMAVQQHL-CKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARLPL 137 (271)
Q Consensus 72 DIVIGrVt~V~~~~-a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~AkiS~ 137 (271)
+-++|+|+...++. +.|.+. ++. ...+.|+.. ..-+-.+++||+|...++.
T Consensus 3 ~e~~~~V~~~lG~~~~~V~~~--dg~----~~l~~i~gK---------~r~~iwI~~GD~V~V~~~~ 54 (65)
T PF01176_consen 3 GEVIGRVTEMLGNNLFEVECE--DGE----ERLARIPGK---------FRKRIWIKRGDFVLVEPSP 54 (65)
T ss_dssp TEEEEEEEEEESSSEEEEEET--TSE----EEEEEE-HH---------HHTCC---TTEEEEEEEST
T ss_pred cEEEEEEEEECCCCEEEEEeC--CCC----EEEEEeccc---------eeeeEecCCCCEEEEEecc
Confidence 45889999986554 666652 332 234444431 1234568999999998653
No 157
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=39.39 E-value=9.9 Score=26.80 Aligned_cols=26 Identities=8% Similarity=-0.144 Sum_probs=21.3
Q ss_pred EEEc-cCCC-eeEeccCccCchhhhhhh
Q psy6276 156 IALS-EAAS-LFRSSEKLTNDIEFLKQE 181 (271)
Q Consensus 156 ~A~c-~cG~-~Mvp~s~~~~c~~~~~~e 181 (271)
+..| +||+ .|.+....+.|..|+.++
T Consensus 20 ~~fCP~Cg~~~m~~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSGFMAEHLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCcchheccCCcEECCCcCCEE
Confidence 3357 8999 888888899999999765
No 158
>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=39.25 E-value=46 Score=25.38 Aligned_cols=47 Identities=11% Similarity=0.121 Sum_probs=27.9
Q ss_pred EEEEEEEEecc-eEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEEE
Q psy6276 74 VTARIMAVQQH-LCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARL 135 (271)
Q Consensus 74 VIGrVt~V~~~-~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Aki 135 (271)
++|+|+...++ .+.|.+. ++. ...+.++. +...+-.+++||+|..+.
T Consensus 2 ~~g~V~~~~g~~~~~V~~~--~g~----~~la~i~g---------K~rk~iwI~~GD~V~Ve~ 49 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCF--DGK----KRLCRIRG---------KMRKRVWINEGDIVLVAP 49 (77)
T ss_pred EEEEEEEEcCCCEEEEEEC--CCC----EEEEEEch---------hhcccEEEcCCCEEEEEe
Confidence 68999998554 4666553 332 22333332 111245679999999993
No 159
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-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). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=39.15 E-value=1.5e+02 Score=22.84 Aligned_cols=20 Identities=15% Similarity=0.263 Sum_probs=15.6
Q ss_pred hhhcCCCCCCEEEEE--EecCC
Q psy6276 120 EMYKCYRPGDIILAR--LPLKE 139 (271)
Q Consensus 120 ~m~~~f~~GDIV~Ak--iS~~d 139 (271)
.+...+++||.|.+. ++...
T Consensus 43 ~~~~~l~~Gd~V~v~G~v~~y~ 64 (91)
T cd04482 43 DVVRLLIPGDEVTVYGSVRPGT 64 (91)
T ss_pred cccCCCCCCCEEEEEEEEecCC
Confidence 355678999999999 77653
No 160
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=38.81 E-value=90 Score=33.05 Aligned_cols=63 Identities=3% Similarity=-0.133 Sum_probs=38.1
Q ss_pred hhcCCCCCCEEEEEEecCCCCceeeee----ccCCCeeEEEEc-cCCCeeEeccCccCch--hhhhhhhhhh
Q psy6276 121 MYKCYRPGDIILARLPLKELHSYQLST----AENELGVVIALS-EAASLFRSSEKLTNDI--EFLKQEKLKL 185 (271)
Q Consensus 121 m~~~f~~GDIV~AkiS~~d~~~~~LST----~~~eLGVV~A~c-~cG~~Mvp~s~~~~c~--~~~~~e~rKl 185 (271)
-+.-+++||.|.-.-+ ||.-|..+.. +...+ ++-..| .||.+++..+..+.|+ .|..+..++|
T Consensus 361 ~~~di~iGD~V~V~ra-GdVIP~I~~v~~~~r~~~~-~~P~~CP~C~s~l~~~~~~~~C~n~~C~aq~~~~i 430 (669)
T PRK14350 361 DSIGLNVGDVVKISRR-GDVIPAVELVIEKLSVGFF-KIPDNCPSCKTALIKEGAHLFCVNNHCPSVIVERI 430 (669)
T ss_pred HHcCCCCCCEEEEEec-CCCCCceeeecccccCCCC-CCCCCCCCCCCEeeeCCEEEEECCCCCHHHHHhhh
Confidence 3566899999988722 3444443332 22221 234468 8999998766667776 4766555543
No 161
>TIGR00219 mreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.
Probab=38.78 E-value=68 Score=30.07 Aligned_cols=64 Identities=16% Similarity=0.237 Sum_probs=39.6
Q ss_pred EEEEEEEEEecceEEEEEeeecCccc-----CCceeeEEeccccccch---hhhHhhhcCCCCCCEEEEE-Ee
Q psy6276 73 VVTARIMAVQQHLCKAHVISVGNTAL-----SRTFRALLRRENVRATE---IDRIEMYKCYRPGDIILAR-LP 136 (271)
Q Consensus 73 IVIGrVt~V~~~~a~VdI~~v~~~~L-----~~~f~GiLr~sdvr~te---~d~~~m~~~f~~GDIV~Ak-iS 136 (271)
=++|+|++|.+....|..+.-.+..+ .....|+++-.+-.... -........+++||.|.-- ++
T Consensus 156 GLVG~V~~V~~~~S~V~litd~~~~v~v~v~~t~~~gi~~G~~~g~~~~l~l~~~~~~~~v~~GD~VvTSGlg 228 (283)
T TIGR00219 156 GLVGKVVSVGSNTSRVLLLTDYTNFVPAQILRSDFRGLIEGNGYGKTLEMNLVNRPAEKDIKKGDLIVTSGLG 228 (283)
T ss_pred ceEEEEEEECCCeEEEEEEEcCCCceEEEEecCCceEEEEecCCCCCcEEEEEECCCCCCCCCCCEEEECCCC
Confidence 48899999999999998765433222 24567887765311100 0011224568999998776 64
No 162
>PF12508 DUF3714: Protein of unknown function (DUF3714) ; InterPro: IPR022187 Proteins in this entry are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage.
Probab=38.37 E-value=1.9e+02 Score=26.11 Aligned_cols=58 Identities=12% Similarity=0.229 Sum_probs=42.8
Q ss_pred EeCCEEEEEEeeEEEEeccccCCCcceEEEEeeC----CCccccCCCCCEEEEEEEEEecceEEEEEeeec
Q psy6276 28 VRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSY----KKEVIVPTPGDVVTARIMAVQQHLCKAHVISVG 94 (271)
Q Consensus 28 ~~~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~----~~~~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~ 94 (271)
.....|+|.+-|...+.+ -..|..+=+ -.+..+|+ |.+++| +.++.+.+..+.|.++.
T Consensus 50 ~~~n~I~A~V~~~qtv~~-------Gs~vrlRLle~i~i~g~~IPk-gt~l~G-~~~~~~~Rl~i~I~SI~ 111 (200)
T PF12508_consen 50 TEKNTIRAVVDGTQTVVD-------GSRVRLRLLEDIQIGGILIPK-GTYLYG-VASFQGQRLLITITSIE 111 (200)
T ss_pred CCCCeEEEEEecceEEeC-------CCEEEEEEcCceEECCEEeCC-CCEEEE-EEeeeccEEEEEEEEEE
Confidence 357889999999887764 133333311 13567776 999999 99999999999998754
No 163
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=38.17 E-value=23 Score=23.95 Aligned_cols=25 Identities=4% Similarity=-0.320 Sum_probs=16.6
Q ss_pred EEc-cCCCeeEecc--CccCchhhhhhh
Q psy6276 157 ALS-EAASLFRSSE--KLTNDIEFLKQE 181 (271)
Q Consensus 157 A~c-~cG~~Mvp~s--~~~~c~~~~~~e 181 (271)
-+| .||..+.-.. ....||.||...
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeE
Confidence 356 7888774433 268888888543
No 164
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=37.81 E-value=13 Score=32.71 Aligned_cols=27 Identities=7% Similarity=-0.071 Sum_probs=20.7
Q ss_pred eEEEEc-cCCCeeEeccC-----------------ccCchhhhhh
Q psy6276 154 VVIALS-EAASLFRSSEK-----------------LTNDIEFLKQ 180 (271)
Q Consensus 154 VV~A~c-~cG~~Mvp~s~-----------------~~~c~~~~~~ 180 (271)
--+++| .|++++.+++. -..||.||+.
T Consensus 95 ~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cgki 139 (165)
T COG1656 95 PEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKI 139 (165)
T ss_pred cccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccc
Confidence 347889 99999999872 2349999874
No 165
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=37.77 E-value=12 Score=27.15 Aligned_cols=33 Identities=9% Similarity=0.047 Sum_probs=27.4
Q ss_pred EEc-cCCCeeEeccCccCchhhhhhhhhhhHHHh
Q psy6276 157 ALS-EAASLFRSSEKLTNDIEFLKQEKLKLYEEL 189 (271)
Q Consensus 157 A~c-~cG~~Mvp~s~~~~c~~~~~~e~rKla~~~ 189 (271)
.+| .||.++.+......||+|++.=.|-=....
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 357 799999999999999999998887755543
No 166
>KOG1067|consensus
Probab=37.61 E-value=55 Score=34.34 Aligned_cols=72 Identities=15% Similarity=0.137 Sum_probs=51.4
Q ss_pred cCCCCCEE-----EEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCC
Q psy6276 67 VPTPGDVV-----TARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKEL 140 (271)
Q Consensus 67 iP~vGDIV-----IGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~ 140 (271)
.|+++|++ .|.|+++.+..++|.+.. -..|+||.++...-... ...+.+.+||-|-.+ +-.+..
T Consensus 660 ~~~~~~l~~g~vy~~tIt~~rd~G~~V~l~p--------~~~~Llh~sqL~~e~ia--kpsd~levGq~I~vk~ie~d~~ 729 (760)
T KOG1067|consen 660 DDQVQDLEFGGVYTATITEIRDTGVMVELYP--------MQQGLLHNSQLDQEKIA--KPSDLLEVGQEIQVKYIERDPR 729 (760)
T ss_pred CccccceEeeeEEEEEEeeecccceEEEecC--------Cchhhccchhccccccc--ChHHHHhhcceeEEEEEeecCc
Confidence 45566665 589999999999999862 35788998877543222 455669999999999 877654
Q ss_pred Cceeeeec
Q psy6276 141 HSYQLSTA 148 (271)
Q Consensus 141 ~~~~LST~ 148 (271)
..+.||-+
T Consensus 730 g~~~ls~r 737 (760)
T KOG1067|consen 730 GGIMLSSR 737 (760)
T ss_pred cceeehhh
Confidence 55656554
No 167
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=37.46 E-value=51 Score=33.43 Aligned_cols=59 Identities=14% Similarity=0.139 Sum_probs=43.8
Q ss_pred CCCCCEEEEEEEEEecce--EEEEEeeecCcccCCceeeEEeccccccchhhhH--hhhcCCCCCCEEEEE
Q psy6276 68 PTPGDVVTARIMAVQQHL--CKAHVISVGNTALSRTFRALLRRENVRATEIDRI--EMYKCYRPGDIILAR 134 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~--a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~--~m~~~f~~GDIV~Ak 134 (271)
-.+|+|-.|+|++|-+.+ |+|||.. .=.|+||.+++.+...... .+...++.|+.+.-.
T Consensus 35 ~~~gniy~grv~~i~p~~~aafvdig~--------~r~gfl~~~~~~~~~~~~~~~~i~~~lr~~~~~~Vq 97 (487)
T COG1530 35 QIVGNIYKGRVTRVLPSLEAAFVDIGL--------ERNGFLHLSEIVPYFRAVLEEKIKVRLRGGQATLVQ 97 (487)
T ss_pred eeecCceEEEecccCccchhheeeccC--------CccceEEecccchhhhhcccccceeeecCCceEEEE
Confidence 357999999999998877 9999963 4578888888765111111 346788999988877
No 168
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=37.28 E-value=74 Score=27.71 Aligned_cols=63 Identities=19% Similarity=0.247 Sum_probs=38.0
Q ss_pred CeEec--CCcccCCCCCeeeCCCEEEe---C-CEEEEEEeeEEEEeccccCCCcceEEEEeeCCCccccCCCCCEEEEEE
Q psy6276 5 PICIP--GQRICQLDSDIVGGRGTYVR---Q-GYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARI 78 (271)
Q Consensus 5 ~iVlP--GD~L~~~eE~~~~G~GtY~~---~-g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~~~yiP~vGDIVIGrV 78 (271)
.+++| ||.++... -..|.|.|.. + ..+.|.+.|.++ +.|+|.+ ||+|+-..
T Consensus 25 el~~~eegq~~g~V~--~~LGn~~f~V~c~dG~~rLa~I~GKmR-----------K~IWI~~----------GD~VlVel 81 (155)
T PTZ00329 25 ELVFKEEGQEYAQVL--RMLGNGRLEAYCFDGVKRLCHIRGKMR-----------KRVWINI----------GDIILVSL 81 (155)
T ss_pred eeccCCCCcEEEEEE--EEcCCCEEEEEECCCCEEEEEeeccce-----------eeEEecC----------CCEEEEec
Confidence 46666 66666654 3567777652 4 468888888664 2377754 88887755
Q ss_pred EEEecceEEEEEee
Q psy6276 79 MAVQQHLCKAHVIS 92 (271)
Q Consensus 79 t~V~~~~a~VdI~~ 92 (271)
..- ..-+.+|..
T Consensus 82 ~~y--d~~KgdIi~ 93 (155)
T PTZ00329 82 RDF--QDSKADVIL 93 (155)
T ss_pred cCC--CCCEEEEEE
Confidence 333 224455544
No 169
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=36.97 E-value=22 Score=24.38 Aligned_cols=25 Identities=8% Similarity=-0.113 Sum_probs=17.8
Q ss_pred Ec-cCCCeeEec-cCccCchhhhhhhh
Q psy6276 158 LS-EAASLFRSS-EKLTNDIEFLKQEK 182 (271)
Q Consensus 158 ~c-~cG~~Mvp~-s~~~~c~~~~~~e~ 182 (271)
.| .||...... .....||+||-.--
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG~rIl 30 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECGYRIL 30 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCCceEE
Confidence 46 888876443 47899999986543
No 170
>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=36.90 E-value=31 Score=26.73 Aligned_cols=13 Identities=46% Similarity=1.040 Sum_probs=10.8
Q ss_pred CCCCEEEEEEEEE
Q psy6276 69 TPGDVVTARIMAV 81 (271)
Q Consensus 69 ~vGDIVIGrVt~V 81 (271)
++||+|.|+|.+.
T Consensus 70 rpGDIVrA~ViSl 82 (82)
T PF10447_consen 70 RPGDIVRARVISL 82 (82)
T ss_dssp -SSSEEEEEEEEE
T ss_pred CCCCEEEEEEeeC
Confidence 8899999999874
No 171
>KOG2916|consensus
Probab=36.82 E-value=56 Score=31.08 Aligned_cols=77 Identities=12% Similarity=0.101 Sum_probs=49.7
Q ss_pred cccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCC-Cc
Q psy6276 65 VIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKEL-HS 142 (271)
Q Consensus 65 ~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~-~~ 142 (271)
.-.|.++|+|++.|..|..-.+.|.++-.++ .+|++--++... .-...+....++|-.=.+- +-++.. +-
T Consensus 11 ~kyPev~e~VmvnV~sIaemGayv~LlEYnn------iEGmiLlsELSr--RRIRSI~klirVGr~E~vvVlrVDkekGY 82 (304)
T KOG2916|consen 11 NKYPEVEEIVMVNVRSIAEMGAYVKLLEYNN------IEGMILLSELSR--RRIRSIQKLIRVGRNEPVVVLRVDKEKGY 82 (304)
T ss_pred ccCCCcccEEEEEeeEehhccceEeeeecCC------cccchhhhHHHH--HHHHHHHHHHhcCCcceEEEEEEcCCCCc
Confidence 3469999999999999999999999875443 355554444322 1123566677787655555 444322 34
Q ss_pred eeeeecc
Q psy6276 143 YQLSTAE 149 (271)
Q Consensus 143 ~~LST~~ 149 (271)
+.||.+.
T Consensus 83 IDLSkrr 89 (304)
T KOG2916|consen 83 IDLSKRR 89 (304)
T ss_pred eechhcc
Confidence 5677653
No 172
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=36.75 E-value=1.1e+02 Score=22.59 Aligned_cols=49 Identities=10% Similarity=0.279 Sum_probs=29.2
Q ss_pred EEEEEEEEecc-eEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEEEe
Q psy6276 74 VTARIMAVQQH-LCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARLP 136 (271)
Q Consensus 74 VIGrVt~V~~~-~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~AkiS 136 (271)
..|+|++..+. ++.|.. .++........|-++.+.+ ...+||+|.-+++
T Consensus 9 ~~G~Vi~~~~~~~y~V~~--~~g~~~~c~~~Gklr~~~i------------~i~vGD~V~ve~~ 58 (72)
T PRK00276 9 MEGTVVEALPNAMFRVEL--ENGHEVLAHISGKMRKNYI------------RILPGDKVTVELS 58 (72)
T ss_pred EEEEEEEEcCCCEEEEEe--CCCCEEEEEEccceeeCCc------------ccCCCCEEEEEEc
Confidence 45899988766 677643 2333333344555553221 2589999998843
No 173
>KOG1885|consensus
Probab=36.06 E-value=1.1e+02 Score=31.51 Aligned_cols=144 Identities=19% Similarity=0.152 Sum_probs=81.4
Q ss_pred ccCCCCCEEEEEEEEEecce---EEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEEEecCCCCc
Q psy6276 66 IVPTPGDVVTARIMAVQQHL---CKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARLPLKELHS 142 (271)
Q Consensus 66 yiP~vGDIVIGrVt~V~~~~---a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~AkiS~~d~~~ 142 (271)
-++.+-=-|-|||.+++... ++.|+..- + . ..+-+...+++ ..+.+-..+.+.++-||||-|.=..|.+.+
T Consensus 101 ~~~n~~~svaGRI~s~R~sGsKL~Fydl~~~-g--~--klQvm~~~~~~-~~~~~F~~~~~~lkrGDiig~~G~pgrt~~ 174 (560)
T KOG1885|consen 101 HLDNEIVSVAGRIHSKRESGSKLVFYDLHGD-G--V--KLQVMANAKKI-TSEEDFEQLHKFLKRGDIIGVSGYPGRTKS 174 (560)
T ss_pred ccccceeeeeeeEeeeeccCCceEEEEEecC-C--e--EEEEEEehhhc-CCHHHHHHHHhhhhccCEEeeecCCCcCCC
Confidence 33444445778998885554 45555421 1 1 12333333333 334456688999999999999833344445
Q ss_pred eeeeeccCCCeeEEEEccCCCeeEeccCccCchhhhhhhhhhhHHHhcccccceeeee-----------eccCceEEEeE
Q psy6276 143 YQLSTAENELGVVIALSEAASLFRSSEKLTNDIEFLKQEKLKLYEELSSSQKENEILR-----------QTTGDLEVRLM 211 (271)
Q Consensus 143 ~~LST~~~eLGVV~A~c~cG~~Mvp~s~~~~c~~~~~~e~rKla~~~~s~~~~~~~~~-----------~~~~~~~~~~~ 211 (271)
=-||+--+++ .+.+.| =.+|-..--.++..|.|.. +|.|.--++....+....| ..-|-|+|.--
T Consensus 175 gELSi~~~~~-~lLspc--Lh~lP~~~~gLkD~EtRyr-qRylDlilN~~~r~~f~~RakII~~iRkfld~rgFlEVETP 250 (560)
T KOG1885|consen 175 GELSIIPNEI-ILLSPC--LHMLPHEHFGLKDKETRYR-KRYLDLILNPEVRDRFRIRAKIISYIRKFLDSRGFLEVETP 250 (560)
T ss_pred ceEEEeecch-heecch--hccCChhhcCCCcHHHHHH-HHHHHHHcCHHHHHHHHHHHHHHHHHHHHhhhcCceEecch
Confidence 5788877777 666555 3333222245677777766 6665444433333333222 23467777776
Q ss_pred eeccccce
Q psy6276 212 QMNEVKGE 219 (271)
Q Consensus 212 ~~~~~~~~ 219 (271)
-||-.-|-
T Consensus 251 mmn~iaGG 258 (560)
T KOG1885|consen 251 MMNMIAGG 258 (560)
T ss_pred hhccccCc
Confidence 66666554
No 174
>PF07334 IFP_35_N: Interferon-induced 35 kDa protein (IFP 35) N-terminus; InterPro: IPR009938 This entry represents the N terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration []. This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.
Probab=35.79 E-value=15 Score=28.29 Aligned_cols=16 Identities=44% Similarity=0.746 Sum_probs=13.0
Q ss_pred HHhhhccccccchhhh
Q psy6276 241 IRELNEENIGLKQKVE 256 (271)
Q Consensus 241 ~~~~~~~~~~~~~~~~ 256 (271)
|.+|++||+.||....
T Consensus 2 i~ei~eEn~~Lk~eiq 17 (76)
T PF07334_consen 2 IHEIQEENARLKEEIQ 17 (76)
T ss_pred hHHHHHHHHHHHHHHH
Confidence 6789999999987544
No 175
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=35.75 E-value=16 Score=29.66 Aligned_cols=27 Identities=11% Similarity=-0.071 Sum_probs=19.4
Q ss_pred EEEEc-cCCCeeEeccCccCchhhhhhh
Q psy6276 155 VIALS-EAASLFRSSEKLTNDIEFLKQE 181 (271)
Q Consensus 155 V~A~c-~cG~~Mvp~s~~~~c~~~~~~e 181 (271)
+.++| .||...-+......||.|+...
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDEFDFSCPRCGSPD 96 (113)
T ss_dssp -EEEETTTS-EEECHHCCHH-SSSSSS-
T ss_pred CcEECCCCCCEEecCCCCCCCcCCcCCC
Confidence 45678 8999998887778999998764
No 176
>CHL00010 infA translation initiation factor 1
Probab=35.39 E-value=1.1e+02 Score=23.15 Aligned_cols=49 Identities=12% Similarity=0.177 Sum_probs=29.3
Q ss_pred EEEEEEEEe-cceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEEEe
Q psy6276 74 VTARIMAVQ-QHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARLP 136 (271)
Q Consensus 74 VIGrVt~V~-~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~AkiS 136 (271)
+.|+|+++. ..++.|.. -++........|-++.+ .-...+||.|..+++
T Consensus 9 ~~G~Vik~lg~~~y~V~~--~~g~~~~c~~rGklr~~------------~i~~~vGD~V~ve~~ 58 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRL--DNGCQVLGYISGKIRRN------------SIRILPGDRVKVELS 58 (78)
T ss_pred EEEEEEEEcCCCEEEEEe--CCCCEEEEEeccceecC------------CcccCCCCEEEEEEc
Confidence 568999988 47777753 23332233345554432 122578999998843
No 177
>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=35.21 E-value=26 Score=27.59 Aligned_cols=11 Identities=45% Similarity=1.123 Sum_probs=9.9
Q ss_pred CCCCCEEEEEE
Q psy6276 125 YRPGDIILARL 135 (271)
Q Consensus 125 f~~GDIV~Aki 135 (271)
|+|||+|.||+
T Consensus 1 f~~GDlVwaK~ 11 (93)
T cd05840 1 FQPGDRVLAKV 11 (93)
T ss_pred CCCCCEEEEeC
Confidence 78999999994
No 178
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=35.13 E-value=67 Score=24.73 Aligned_cols=52 Identities=12% Similarity=0.176 Sum_probs=29.8
Q ss_pred CCEEEEEEEEEecc-eEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEEEe
Q psy6276 71 GDVVTARIMAVQQH-LCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARLP 136 (271)
Q Consensus 71 GDIVIGrVt~V~~~-~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~AkiS 136 (271)
...+.|.|+.+-+. .+.|.+- ++........|=+| .++-.+.|||+|..+++
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~e--dg~~~~ahI~GKmr------------~~~i~I~~GD~V~Ve~~ 58 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELE--NGHERLAHISGKMR------------KNRIRILPGDVVLVELS 58 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEec--CCcEEEEEccCcch------------heeEEeCCCCEEEEEec
Confidence 44678999998554 4666642 22221111222111 23567899999999944
No 179
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=34.94 E-value=14 Score=31.28 Aligned_cols=23 Identities=13% Similarity=0.101 Sum_probs=17.4
Q ss_pred Ec-cCCCeeEecc--CccCchhhhhh
Q psy6276 158 LS-EAASLFRSSE--KLTNDIEFLKQ 180 (271)
Q Consensus 158 ~c-~cG~~Mvp~s--~~~~c~~~~~~ 180 (271)
+| +||...--.+ ....||+||+-
T Consensus 3 ~Ct~Cg~~f~dgs~eil~GCP~CGg~ 28 (131)
T PF09845_consen 3 QCTKCGRVFEDGSKEILSGCPECGGN 28 (131)
T ss_pred ccCcCCCCcCCCcHHHHccCcccCCc
Confidence 46 8988776655 57889999874
No 180
>PRK12495 hypothetical protein; Provisional
Probab=34.77 E-value=13 Score=34.06 Aligned_cols=30 Identities=7% Similarity=-0.147 Sum_probs=24.0
Q ss_pred eeEEEEc-cCCCeeEeccCccCchhhhhhhh
Q psy6276 153 GVVIALS-EAASLFRSSEKLTNDIEFLKQEK 182 (271)
Q Consensus 153 GVV~A~c-~cG~~Mvp~s~~~~c~~~~~~e~ 182 (271)
++....| .||.|+........||.|....-
T Consensus 39 tmsa~hC~~CG~PIpa~pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 39 TMTNAHCDECGDPIFRHDGQEFCPTCQQPVT 69 (226)
T ss_pred ccchhhcccccCcccCCCCeeECCCCCCccc
Confidence 3445568 89999998888999999997654
No 181
>PF04805 Pox_E10: E10-like protein conserved region; InterPro: IPR006890 This entry represents a family of probable FAD-linked sulphydryl oxidases found in poxviruses.; GO: 0016972 thiol oxidase activity, 0055114 oxidation-reduction process
Probab=34.73 E-value=5.9 Score=29.99 Aligned_cols=28 Identities=7% Similarity=-0.135 Sum_probs=21.0
Q ss_pred CCCeeEeccCccCchhhhhhhhhhhHHH
Q psy6276 161 AASLFRSSEKLTNDIEFLKQEKLKLYEE 188 (271)
Q Consensus 161 cG~~Mvp~s~~~~c~~~~~~e~rKla~~ 188 (271)
|...++-+..++.||+||..++..+-+-
T Consensus 5 cKr~ly~I~~tLPC~~Cr~HA~~ai~kN 32 (70)
T PF04805_consen 5 CKRKLYTICSTLPCPECRIHAKEAIQKN 32 (70)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHhc
Confidence 3344445556899999999999887766
No 182
>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=34.69 E-value=27 Score=27.18 Aligned_cols=16 Identities=19% Similarity=0.480 Sum_probs=13.4
Q ss_pred hcCCCCCCEEEEE-Eec
Q psy6276 122 YKCYRPGDIILAR-LPL 137 (271)
Q Consensus 122 ~~~f~~GDIV~Ak-iS~ 137 (271)
++|+.|||||-|| -..
T Consensus 4 ~pc~~p~dLVwAK~kGy 20 (83)
T cd05841 4 EPCRPPHELVWAKLKGF 20 (83)
T ss_pred cccCCCCCEEEEeCCCC
Confidence 5799999999999 443
No 183
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=34.36 E-value=2.1e+02 Score=23.65 Aligned_cols=16 Identities=38% Similarity=0.602 Sum_probs=12.0
Q ss_pred hcCCCCCCEEEEE-Eec
Q psy6276 122 YKCYRPGDIILAR-LPL 137 (271)
Q Consensus 122 ~~~f~~GDIV~Ak-iS~ 137 (271)
-+...+||+|+.+ +.+
T Consensus 66 LP~v~~GDVIll~~~kv 82 (138)
T cd04497 66 LPIVKVGDIILLRRVKI 82 (138)
T ss_pred CCCCCCCCEEEEEEEEE
Confidence 4445999999999 543
No 184
>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=34.30 E-value=27 Score=26.84 Aligned_cols=14 Identities=21% Similarity=0.627 Sum_probs=11.5
Q ss_pred CCCCCCEEEEE-Eec
Q psy6276 124 CYRPGDIILAR-LPL 137 (271)
Q Consensus 124 ~f~~GDIV~Ak-iS~ 137 (271)
.|.+||||.|| -..
T Consensus 2 ~f~~GdlVwaK~kGy 16 (83)
T cd05834 2 QFKAGDLVFAKVKGY 16 (83)
T ss_pred CCCCCCEEEEecCCC
Confidence 58999999999 443
No 185
>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain. The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets []. Secondary structure prediction indicates that the TRAM domain adopts a simple beta-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five beta-strands in the predicted secondary structure [].; PDB: 1YEZ_A 2BH2_A 1UWV_A 1YVC_A.
Probab=34.29 E-value=67 Score=22.53 Aligned_cols=24 Identities=21% Similarity=0.396 Sum_probs=17.5
Q ss_pred cCCCCCEEEEEEEEEecceEEEEE
Q psy6276 67 VPTPGDVVTARIMAVQQHLCKAHV 90 (271)
Q Consensus 67 iP~vGDIVIGrVt~V~~~~a~VdI 90 (271)
.|.+||.|-.+|++.....+.-++
T Consensus 37 ~~~iG~~v~v~I~~~~~~~l~G~~ 60 (61)
T PF01938_consen 37 LPLIGEFVKVRITKAKKNYLFGEL 60 (61)
T ss_dssp -T--TEEEEEEEEEE-SSEEEEEE
T ss_pred CCCCCCEEEEEEEEeeCCcEEEEE
Confidence 566899999999999998887655
No 186
>PRK11032 hypothetical protein; Provisional
Probab=34.08 E-value=23 Score=30.95 Aligned_cols=29 Identities=14% Similarity=0.037 Sum_probs=21.4
Q ss_pred CeeEEEEc-cCCCeeEe--ccCccCchhhhhhhh
Q psy6276 152 LGVVIALS-EAASLFRS--SEKLTNDIEFLKQEK 182 (271)
Q Consensus 152 LGVV~A~c-~cG~~Mvp--~s~~~~c~~~~~~e~ 182 (271)
+|++ +| +||..|.- .+....||+|+..+=
T Consensus 122 ~G~L--vC~~Cg~~~~~~~p~~i~pCp~C~~~~F 153 (160)
T PRK11032 122 LGNL--VCEKCHHHLAFYTPEVLPLCPKCGHDQF 153 (160)
T ss_pred cceE--EecCCCCEEEecCCCcCCCCCCCCCCee
Confidence 4555 48 89999944 356889999998754
No 187
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=33.89 E-value=29 Score=28.21 Aligned_cols=27 Identities=0% Similarity=-0.198 Sum_probs=18.3
Q ss_pred EEEEc-cCCCeeEeccCc-cCchhhhhhh
Q psy6276 155 VIALS-EAASLFRSSEKL-TNDIEFLKQE 181 (271)
Q Consensus 155 V~A~c-~cG~~Mvp~s~~-~~c~~~~~~e 181 (271)
..++| .||...-...+. ..||.|+...
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 69 AECWCETCQQYVTLLTQRVRRCPQCHGDM 97 (114)
T ss_pred cEEEcccCCCeeecCCccCCcCcCcCCCC
Confidence 35678 899755444454 7799999543
No 188
>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=33.26 E-value=28 Score=26.88 Aligned_cols=11 Identities=27% Similarity=0.752 Sum_probs=9.9
Q ss_pred CCCCCEEEEEE
Q psy6276 125 YRPGDIILARL 135 (271)
Q Consensus 125 f~~GDIV~Aki 135 (271)
|++||||-||+
T Consensus 1 f~~GDlVwaK~ 11 (86)
T cd05836 1 LKLGDLVWAKM 11 (86)
T ss_pred CCCCCEEEEeC
Confidence 78999999994
No 189
>KOG3416|consensus
Probab=33.05 E-value=54 Score=27.82 Aligned_cols=43 Identities=23% Similarity=0.240 Sum_probs=30.1
Q ss_pred hhhcCCCCCCEEEEE---EecCCCCceeeeeccC-------CCeeEEEEccCCC
Q psy6276 120 EMYKCYRPGDIILAR---LPLKELHSYQLSTAEN-------ELGVVIALSEAAS 163 (271)
Q Consensus 120 ~m~~~f~~GDIV~Ak---iS~~d~~~~~LST~~~-------eLGVV~A~c~cG~ 163 (271)
+..+.|.|||||+-+ .|+-. ....|.+.+. ++.++|+-+.|-.
T Consensus 57 e~~~~~~PGDIirLt~Gy~Si~q-g~LtL~~GK~Ge~~KiGef~~vf~etpn~S 109 (134)
T KOG3416|consen 57 EEGCLIQPGDIIRLTGGYASIFQ-GCLTLYVGKGGEVQKIGEFCMVFSETPNIS 109 (134)
T ss_pred CcCcccCCccEEEecccchhhhc-CceEEEecCCceEeEeeeeEEeeecCCCcc
Confidence 456789999999998 46654 3677877543 4677777665544
No 190
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=33.05 E-value=2.3e+02 Score=24.90 Aligned_cols=68 Identities=18% Similarity=0.207 Sum_probs=35.8
Q ss_pred eEecCCcccCCC-CCeeeCCCEEEe--CCEEEEEEeeEEEEeccccCCCcceEEEEeeCCC---ccccCCCCC-E-EEEE
Q psy6276 6 ICIPGQRICQLD-SDIVGGRGTYVR--QGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKK---EVIVPTPGD-V-VTAR 77 (271)
Q Consensus 6 iVlPGD~L~~~e-E~~~~G~GtY~~--~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~---~~yiP~vGD-I-VIGr 77 (271)
...|||.|.... .....|.++|+. +|..|.-.+.... ...+.+...+. ...++...+ + +||+
T Consensus 136 ~~~~Gd~ilVd~~~~~~~gd~v~v~~~g~~~~VK~l~~~~----------~~~~~l~S~N~~~~~~~~~~~~~~v~iIgr 205 (214)
T COG2932 136 TYEDGDTLLVDPGVNTRRGDRVYVETDGGELYVKKLQREP----------GGLLRLVSLNPDYYPDEIFSEDDDVEIIGR 205 (214)
T ss_pred cccCCCEEEECCCCceeeCCEEEEEEeCCeEEEEEEEEec----------CCeEEEEeCCCCCCcccccCccceEEEEEE
Confidence 456788654322 124555555544 3455555444221 13444554321 234556667 5 8999
Q ss_pred EEEEec
Q psy6276 78 IMAVQQ 83 (271)
Q Consensus 78 Vt~V~~ 83 (271)
|..+..
T Consensus 206 Vv~~~~ 211 (214)
T COG2932 206 VVWVSR 211 (214)
T ss_pred EEEEee
Confidence 987653
No 191
>PF08810 KapB: Kinase associated protein B; InterPro: IPR014916 This bacterial protein forms an anti-parallel beta sheet with an extending alpha helical region. ; PDB: 1Y71_B.
Probab=32.52 E-value=1.1e+02 Score=25.33 Aligned_cols=30 Identities=13% Similarity=0.067 Sum_probs=18.7
Q ss_pred EEEEEEEEecceEEEEEeeecCcccCCceeeEEe
Q psy6276 74 VTARIMAVQQHLCKAHVISVGNTALSRTFRALLR 107 (271)
Q Consensus 74 VIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr 107 (271)
=||.|+.++++.+.|.|.+|- +.|-+|-||
T Consensus 6 Yigei~e~~~~~~lVkVlaVl----KHP~QGDLH 35 (112)
T PF08810_consen 6 YIGEITEERPQHYLVKVLAVL----KHPKQGDLH 35 (112)
T ss_dssp EEEEEEEEETTEEEEEEEEEE----E--------
T ss_pred eEEEEEeecCCeEEEEEEEEe----cCCCccCCC
Confidence 469999999999999999763 344445444
No 192
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.09 E-value=37 Score=28.40 Aligned_cols=27 Identities=0% Similarity=-0.029 Sum_probs=18.9
Q ss_pred EEEEc-cCCCeeEec---------------------cCccCchhhhhhh
Q psy6276 155 VIALS-EAASLFRSS---------------------EKLTNDIEFLKQE 181 (271)
Q Consensus 155 V~A~c-~cG~~Mvp~---------------------s~~~~c~~~~~~e 181 (271)
..+.| .||...-+. .....||.||...
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRD 117 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCC
Confidence 56788 899766443 3567799999653
No 193
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=32.04 E-value=1.2e+02 Score=24.02 Aligned_cols=50 Identities=10% Similarity=0.074 Sum_probs=30.7
Q ss_pred EEEEEEEEecc-eEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEEEec
Q psy6276 74 VTARIMAVQQH-LCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARLPL 137 (271)
Q Consensus 74 VIGrVt~V~~~-~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~AkiS~ 137 (271)
+.|.|+.+.++ .+.|.+. ++........|=+|.. +-.+.+||.|..++|.
T Consensus 9 ~~G~V~e~Lp~~~frV~Le--nG~~vla~isGKmR~~------------rIrIl~GD~V~VE~sp 59 (87)
T PRK12442 9 LDGIVDEVLPDSRFRVTLE--NGVEVGAYASGRMRKH------------RIRILAGDRVTLELSP 59 (87)
T ss_pred EEEEEEEECCCCEEEEEeC--CCCEEEEEeccceeee------------eEEecCCCEEEEEECc
Confidence 67888888554 3666652 3433333455544442 3346899999999653
No 194
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=32.01 E-value=86 Score=26.42 Aligned_cols=54 Identities=7% Similarity=-0.119 Sum_probs=40.6
Q ss_pred eeEEEEc-cCCCeeEecc-CccCchhhhhhh-hhhhHHHhcccccceeeeeeccCceEEEeEe
Q psy6276 153 GVVIALS-EAASLFRSSE-KLTNDIEFLKQE-KLKLYEELSSSQKENEILRQTTGDLEVRLMQ 212 (271)
Q Consensus 153 GVV~A~c-~cG~~Mvp~s-~~~~c~~~~~~e-~rKla~~~~s~~~~~~~~~~~~~~~~~~~~~ 212 (271)
+-.+.-| .|+..|.+.. ..+.|+.|++.- ..+ ..+.-+.....-+|.+|+.+..
T Consensus 31 ~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~~~------~ry~l~~~i~D~Tg~~~~~~F~ 87 (166)
T cd04476 31 NWWYPACPGCNKKVVEEGNGTYRCEKCNKSVPNPE------YRYILSLNVADHTGEAWLTLFD 87 (166)
T ss_pred CeEEccccccCcccEeCCCCcEECCCCCCcCCCcc------EEEEEEEEEEeCCCCEEEEEeh
Confidence 5677778 8999999887 789999999864 121 3455566667778999999873
No 195
>PHA03005 sulfhydryl oxidase; Provisional
Probab=30.50 E-value=10 Score=30.43 Aligned_cols=29 Identities=3% Similarity=-0.128 Sum_probs=23.8
Q ss_pred cCCCeeEeccCccCchhhhhhhhhhhHHH
Q psy6276 160 EAASLFRSSEKLTNDIEFLKQEKLKLYEE 188 (271)
Q Consensus 160 ~cG~~Mvp~s~~~~c~~~~~~e~rKla~~ 188 (271)
.|...|+-+..++.||+|+..++-.+-+.
T Consensus 29 ~cK~~lytI~~tLPC~~Cr~HA~~ai~kn 57 (96)
T PHA03005 29 ACKRKLYTICSTLPCPACRRHAKEAIEKN 57 (96)
T ss_pred HHHHHHHHhhhcCCCHHHHHHHHHHHhhc
Confidence 36677777778999999999999887765
No 196
>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=30.35 E-value=1.4e+02 Score=22.54 Aligned_cols=49 Identities=12% Similarity=0.221 Sum_probs=28.9
Q ss_pred EEEEEEEEecce-EEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEEEe
Q psy6276 74 VTARIMAVQQHL-CKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARLP 136 (271)
Q Consensus 74 VIGrVt~V~~~~-a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~AkiS 136 (271)
+.|.|+...++. +.|.+. ++........|=+|. .+-.+.+||.|..++|
T Consensus 7 ~~G~V~e~L~~~~f~V~l~--ng~~vla~i~GKmr~------------~rI~I~~GD~V~Ve~s 56 (68)
T TIGR00008 7 MEGKVTESLPNAMFRVELE--NGHEVLAHISGKIRM------------HYIRILPGDKVKVELS 56 (68)
T ss_pred EEEEEEEECCCCEEEEEEC--CCCEEEEEecCcchh------------ccEEECCCCEEEEEEC
Confidence 678999986554 555552 333322233443332 2445789999999955
No 197
>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=30.33 E-value=82 Score=26.10 Aligned_cols=63 Identities=21% Similarity=0.207 Sum_probs=34.7
Q ss_pred CCCCCEEEEEEEEEecceEEEEEeeecCcc-----cCC--ceeeEEeccccccchhhhHhhhcCCCCCCEEEEE
Q psy6276 68 PTPGDVVTARIMAVQQHLCKAHVISVGNTA-----LSR--TFRALLRRENVRATEIDRIEMYKCYRPGDIILAR 134 (271)
Q Consensus 68 P~vGDIVIGrVt~V~~~~a~VdI~~v~~~~-----L~~--~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak 134 (271)
|-+|.|+.|+|.+.......|.+.-.++-- |.. .|.- .+++=-.+- ..+..-+|..|+-||=|
T Consensus 1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~---~~~~W~W~~-~~~~~l~~d~ge~IRFR 70 (122)
T PF08292_consen 1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDE---EEQAWVWEY-DEEQELFFDIGEEIRFR 70 (122)
T ss_dssp --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEEC---CCTEEEEEE-SSSEEEEE-TT-EEEEE
T ss_pred CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCc---cCCEEEEEC-CCCceeEccCCCEEEEE
Confidence 678999999999999999999886555522 221 1210 010000000 02345567999999999
No 198
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=30.07 E-value=18 Score=23.60 Aligned_cols=23 Identities=0% Similarity=-0.223 Sum_probs=11.4
Q ss_pred Ec-cCCCeeE---ecc---CccCchhhhhh
Q psy6276 158 LS-EAASLFR---SSE---KLTNDIEFLKQ 180 (271)
Q Consensus 158 ~c-~cG~~Mv---p~s---~~~~c~~~~~~ 180 (271)
.| .||.+|. |.+ .-..|+.|+++
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCE
Confidence 35 7888873 333 46788888764
No 199
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=29.15 E-value=35 Score=29.21 Aligned_cols=29 Identities=14% Similarity=0.087 Sum_probs=20.7
Q ss_pred CeeEEEEc-cCCCeeEec--cCccCchhhhhhhh
Q psy6276 152 LGVVIALS-EAASLFRSS--EKLTNDIEFLKQEK 182 (271)
Q Consensus 152 LGVV~A~c-~cG~~Mvp~--s~~~~c~~~~~~e~ 182 (271)
+|.. +| .||..+.-. +....||.|+...=
T Consensus 110 ~G~l--~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F 141 (146)
T PF07295_consen 110 PGTL--VCENCGHEVELTHPERLPPCPKCGHTEF 141 (146)
T ss_pred CceE--ecccCCCEEEecCCCcCCCCCCCCCCee
Confidence 4444 48 899988543 46889999997653
No 200
>smart00532 LIGANc Ligase N family.
Probab=28.82 E-value=1.6e+02 Score=29.53 Aligned_cols=65 Identities=14% Similarity=0.042 Sum_probs=38.8
Q ss_pred hhcCCCCCCEEEEEEecCCCCceeeeecc-CCCe-----eEEEEc-cCCCeeEecc--CccCchh--hhhhhhhhhH
Q psy6276 121 MYKCYRPGDIILARLPLKELHSYQLSTAE-NELG-----VVIALS-EAASLFRSSE--KLTNDIE--FLKQEKLKLY 186 (271)
Q Consensus 121 m~~~f~~GDIV~AkiS~~d~~~~~LST~~-~eLG-----VV~A~c-~cG~~Mvp~s--~~~~c~~--~~~~e~rKla 186 (271)
.+..+++||.|.-+-+ ||.-+..+.... ..-| .+-..| .||..++... ..+.|++ |...-..+|.
T Consensus 359 ~~~~i~iGd~V~V~ra-GdVIP~I~~vv~~~r~~~~~~~~~P~~CP~C~s~l~~~~~~~~~~C~n~~C~aq~~~~l~ 434 (441)
T smart00532 359 EEKDIRIGDTVVVRKA-GDVIPKVVGVVKEKRPGDEREIEMPTHCPSCGSELVREEGEVDIRCPNPLCPAQLIERII 434 (441)
T ss_pred HHcCCCCCCEEEEEEC-CCcCcceeecccccCCCCCccCcCCCCCCCCCCEeEecCCceEEEeCCCCCHHHHHHHHH
Confidence 4667899999998832 344444444322 1111 234578 8999998643 3566764 7666555543
No 201
>cd05162 PWWP The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.
Probab=28.54 E-value=39 Score=25.51 Aligned_cols=11 Identities=45% Similarity=1.265 Sum_probs=9.8
Q ss_pred CCCCCEEEEEE
Q psy6276 125 YRPGDIILARL 135 (271)
Q Consensus 125 f~~GDIV~Aki 135 (271)
|++||+|-||+
T Consensus 1 f~~GdlVwaK~ 11 (87)
T cd05162 1 FRPGDLVWAKM 11 (87)
T ss_pred CCCCCEEEEeC
Confidence 78999999993
No 202
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.17 E-value=32 Score=28.09 Aligned_cols=27 Identities=7% Similarity=-0.005 Sum_probs=17.9
Q ss_pred EEEEc-cCCCeeEeccCc-cCchhhhhhh
Q psy6276 155 VIALS-EAASLFRSSEKL-TNDIEFLKQE 181 (271)
Q Consensus 155 V~A~c-~cG~~Mvp~s~~-~~c~~~~~~e 181 (271)
+.+.| .||...-+.... ..||.|+-..
T Consensus 70 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 70 VELECKDCSHVFKPNALDYGVCEKCHSKN 98 (117)
T ss_pred CEEEhhhCCCccccCCccCCcCcCCCCCc
Confidence 35678 899766554443 4599998643
No 203
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=27.72 E-value=1.3e+02 Score=22.02 Aligned_cols=22 Identities=14% Similarity=0.117 Sum_probs=18.8
Q ss_pred EEEEEEEEecceEEEEEeeecC
Q psy6276 74 VTARIMAVQQHLCKAHVISVGN 95 (271)
Q Consensus 74 VIGrVt~V~~~~a~VdI~~v~~ 95 (271)
..|+|..+..+++.|+|-..++
T Consensus 16 ~~G~V~kv~eNSVIVdIT~m~~ 37 (57)
T PF09953_consen 16 FTGIVEKVYENSVIVDITIMEN 37 (57)
T ss_pred cEEEEEEEecCcEEEEEEecCC
Confidence 5899999999999999975444
No 204
>KOG4134|consensus
Probab=27.34 E-value=45 Score=30.96 Aligned_cols=61 Identities=16% Similarity=0.165 Sum_probs=45.0
Q ss_pred ccccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCC
Q psy6276 64 EVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKE 139 (271)
Q Consensus 64 ~~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d 139 (271)
-..-|++||+.-|.|--|+++..-+-|.. .|.+-||..++.+ -+.++.+++-..++ ..+++
T Consensus 101 yVf~Pk~Gd~LeG~Vn~vS~sHIglLIhg--------~FNASIpk~nip~-------dw~fI~md~eee~~v~ntD~ 162 (253)
T KOG4134|consen 101 YVFRPKAGDILEGVVNHVSRSHIGLLIHG--------VFNASIPKTNIPA-------DWEFIAMDQEEEIRVKNTDI 162 (253)
T ss_pred EEECCCCCCeeeeeeeecchhhhceeehh--------hhhccCCCCCCcc-------ceeeecCCchhhhceeeccc
Confidence 35679999999999999999998888863 4666666655432 24467888888888 76654
No 205
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=27.17 E-value=32 Score=28.50 Aligned_cols=25 Identities=4% Similarity=-0.247 Sum_probs=20.4
Q ss_pred EEEc-cCCCeeEeccCccCchhhhhh
Q psy6276 156 IALS-EAASLFRSSEKLTNDIEFLKQ 180 (271)
Q Consensus 156 ~A~c-~cG~~Mvp~s~~~~c~~~~~~ 180 (271)
.+.| .|+.+..+.-+.+.||.|+-.
T Consensus 70 ~~~C~~C~~~~~~e~~~~~CP~C~s~ 95 (115)
T COG0375 70 ECWCLDCGQEVELEELDYRCPKCGSI 95 (115)
T ss_pred EEEeccCCCeecchhheeECCCCCCC
Confidence 4567 789999998888889999843
No 206
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=27.08 E-value=1.5e+02 Score=28.72 Aligned_cols=98 Identities=8% Similarity=0.061 Sum_probs=55.2
Q ss_pred CCcccCCCCCeeeCCCEEEeCCEEEEEEeeEEEEeccccCCCcceEEEEeeCCCccccCCCCCEEEEEEEEEecceEEEE
Q psy6276 10 GQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQQHLCKAH 89 (271)
Q Consensus 10 GD~L~~~eE~~~~G~GtY~~~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~~~yiP~vGDIVIGrVt~V~~~~a~Vd 89 (271)
||.+-..-. -..-.|.|++=+. |--+=|++.+.. ++-.+..+..-+-++||.|.++|.+|....=.++
T Consensus 18 GdvV~g~V~-~I~d~GafV~L~E-Y~gvEGlIhiSE----------lS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~Id 85 (319)
T PTZ00248 18 DDLVMVKVV-RITEMGAYVSLLE-YDDIEGMILMSE----------LSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYID 85 (319)
T ss_pred CCEEEEEEE-EEeCCeEEEEecC-CCCcEEEEEHHH----------hcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEE
Confidence 666543222 3344567755211 223566776654 1112212334456999999999999976654444
Q ss_pred EeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-Eec
Q psy6276 90 VISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPL 137 (271)
Q Consensus 90 I~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~ 137 (271)
+. ..-+ ++......-..|..|++|.++ ..+
T Consensus 86 LS----------~K~v--------~~~pw~~~~e~~~~g~~v~~~V~~i 116 (319)
T PTZ00248 86 LS----------KKRV--------SPEDIEACEEKFSKSKKVHSIMRHI 116 (319)
T ss_pred EE----------eeec--------ccchHHHHHHhCcCCCEEEEEEEEc
Confidence 42 1111 112334677889999999999 444
No 207
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=26.46 E-value=57 Score=20.90 Aligned_cols=28 Identities=4% Similarity=-0.187 Sum_probs=15.4
Q ss_pred CCeeEEEEc-cCCCeeEeccCccCchhhhhh
Q psy6276 151 ELGVVIALS-EAASLFRSSEKLTNDIEFLKQ 180 (271)
Q Consensus 151 eLGVV~A~c-~cG~~Mvp~s~~~~c~~~~~~ 180 (271)
+.-.+..+| .||....|-. ..||.|+..
T Consensus 6 ~~~l~~~rC~~Cg~~~~pPr--~~Cp~C~s~ 34 (37)
T PF12172_consen 6 EGRLLGQRCRDCGRVQFPPR--PVCPHCGSD 34 (37)
T ss_dssp TT-EEEEE-TTT--EEES----SEETTTT--
T ss_pred CCEEEEEEcCCCCCEecCCC--cCCCCcCcc
Confidence 345677788 8999988764 578888754
No 208
>cd05835 Dnmt3b_related The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of Dnmt3b has been identified in patients with ICF syndrome (immunodeficiency, centromeric instability, and facial anomalies), a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=26.21 E-value=44 Score=25.74 Aligned_cols=11 Identities=18% Similarity=0.791 Sum_probs=9.8
Q ss_pred CCCCCEEEEEE
Q psy6276 125 YRPGDIILARL 135 (271)
Q Consensus 125 f~~GDIV~Aki 135 (271)
|.+||||-||+
T Consensus 1 f~vGDlVWaK~ 11 (87)
T cd05835 1 FNVGDLVWGKI 11 (87)
T ss_pred CCCCCEEEEec
Confidence 68999999994
No 209
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=25.87 E-value=23 Score=25.54 Aligned_cols=30 Identities=3% Similarity=-0.139 Sum_probs=23.1
Q ss_pred Ec-cCCCeeEe--ccCccCchhhhhhhhhhhHH
Q psy6276 158 LS-EAASLFRS--SEKLTNDIEFLKQEKLKLYE 187 (271)
Q Consensus 158 ~c-~cG~~Mvp--~s~~~~c~~~~~~e~rKla~ 187 (271)
.| .||..+.. ......||.||....|.+..
T Consensus 30 ~C~~CG~~~~~~~~~r~~~C~~Cg~~~~rD~na 62 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSGRVFTCPNCGFEMDRDVNA 62 (69)
T ss_pred CccCcccccccccccceEEcCCCCCEECcHHHH
Confidence 35 79988866 45789999999988777543
No 210
>KOG3297|consensus
Probab=25.82 E-value=1.7e+02 Score=26.45 Aligned_cols=29 Identities=17% Similarity=0.249 Sum_probs=25.2
Q ss_pred cCCCCCEEEEEEEEEecceEEEEEeeecC
Q psy6276 67 VPTPGDVVTARIMAVQQHLCKAHVISVGN 95 (271)
Q Consensus 67 iP~vGDIVIGrVt~V~~~~a~VdI~~v~~ 95 (271)
-|-+|.+++|+|..-+.....|.|.-.++
T Consensus 78 rPF~gEVi~gki~~cs~eG~rvtl~FFdD 106 (202)
T KOG3297|consen 78 RPFVGEVITGKIKECSEEGLRVTLGFFDD 106 (202)
T ss_pred ecccceEEEEEeecCCccceEEEEEeeec
Confidence 36789999999999999999999876665
No 211
>PF00855 PWWP: PWWP domain; InterPro: IPR000313 Upon characterisation of WHSC1, a gene mapping to the Wolf-Hirschhornsyndrome critical region and at its C terminus similar to the Drosophila melanogaster ASH1/trithorax group proteins, a novel protein domain designated PWWP domain was identified []. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. It is present in proteins of nuclear origin and plays a role in cell growth and differentiation. Due to its position, the composition of amino acids close to the PWWP motif and the pattern of other domains present it has been suggested that the domain is involved in protein-protein interactions [].; PDB: 3LYI_B 2L89_A 2NLU_A 1RI0_A 1KHC_A 3QKJ_C 2DAQ_A 1N27_A 3PFS_B 3QJ6_A ....
Probab=25.50 E-value=41 Score=24.86 Aligned_cols=11 Identities=55% Similarity=1.301 Sum_probs=9.2
Q ss_pred CCCCCEEEEEE
Q psy6276 125 YRPGDIILARL 135 (271)
Q Consensus 125 f~~GDIV~Aki 135 (271)
|.+||||-||+
T Consensus 1 f~~GdlVWaK~ 11 (86)
T PF00855_consen 1 FRPGDLVWAKL 11 (86)
T ss_dssp -STTEEEEEEE
T ss_pred CCCCCEEEEEe
Confidence 78999999996
No 212
>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=24.18 E-value=56 Score=19.12 Aligned_cols=15 Identities=20% Similarity=0.302 Sum_probs=10.9
Q ss_pred ceeeeeeccCceEEE
Q psy6276 195 ENEILRQTTGDLEVR 209 (271)
Q Consensus 195 ~~~~~~~~~~~~~~~ 209 (271)
-.-|....+|.|||-
T Consensus 7 I~~i~~D~~G~lWig 21 (24)
T PF07494_consen 7 IYSIYEDSDGNLWIG 21 (24)
T ss_dssp EEEEEE-TTSCEEEE
T ss_pred EEEEEEcCCcCEEEE
Confidence 345778899999984
No 213
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=24.16 E-value=21 Score=29.24 Aligned_cols=58 Identities=17% Similarity=0.120 Sum_probs=34.2
Q ss_pred Ec-cCCCeeEecc--CccCchhhhhhhhhhhHHHh----------------ccccccee-eeeeccCceEEEeEeecc
Q psy6276 158 LS-EAASLFRSSE--KLTNDIEFLKQEKLKLYEEL----------------SSSQKENE-ILRQTTGDLEVRLMQMNE 215 (271)
Q Consensus 158 ~c-~cG~~Mvp~s--~~~~c~~~~~~e~rKla~~~----------------~s~~~~~~-~~~~~~~~~~~~~~~~~~ 215 (271)
.| +||...-..+ ....||+||+--=+.++++- +..+..+| |-+-++|.-+++++..-+
T Consensus 4 ~CtrCG~vf~~g~~~il~GCp~CG~nkF~yv~~e~rpa~~e~~d~~vrde~~a~ge~ietIrI~~pG~YeiNl~~Lld 81 (112)
T COG3364 4 QCTRCGEVFDDGSEEILSGCPKCGCNKFLYVPEEKRPAVAEAADPEVRDEDGAQGEPIETIRILRPGVYEINLESLLD 81 (112)
T ss_pred eecccccccccccHHHHccCccccchheEecccccccchhhhcCCcccchhhcccCcceEEEEecCceEEEehhhhcc
Confidence 46 8887775555 46789999875333333322 12222333 445677888888776655
No 214
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=23.72 E-value=1e+02 Score=24.33 Aligned_cols=62 Identities=19% Similarity=0.263 Sum_probs=32.5
Q ss_pred CCCCEEEEEEEEEecceEEEEEeeecCcccCC----------ceeeEEeccccccchhhhHhhhcCCCCCCEEEEE
Q psy6276 69 TPGDVVTARIMAVQQHLCKAHVISVGNTALSR----------TFRALLRRENVRATEIDRIEMYKCYRPGDIILAR 134 (271)
Q Consensus 69 ~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~----------~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak 134 (271)
++=++++|.|+++.| .++.|.. .-.|.. .+.--+.......+.......++.|++||-|..-
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--LKIKIDQ--KLILDKDFLIIPELLKDYTRDITIEHNSETDNITITFTDGLKVGDKVLLL 86 (100)
T ss_pred CCceeEEEEEEeccc--EEEEECC--eEEEchHHEEeehhccceEEEEEEeccccccceeEEEecCCcCCCEEEEE
Confidence 445669999999999 6666543 011111 1111111111111111113567899999998876
No 215
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=23.71 E-value=30 Score=20.47 Aligned_cols=18 Identities=0% Similarity=-0.212 Sum_probs=12.4
Q ss_pred cCCCeeEeccCccCchhhhh
Q psy6276 160 EAASLFRSSEKLTNDIEFLK 179 (271)
Q Consensus 160 ~cG~~Mvp~s~~~~c~~~~~ 179 (271)
.||+.+-+. ...|+.||.
T Consensus 4 ~CG~~~~~~--~~fC~~CG~ 21 (23)
T PF13240_consen 4 NCGAEIEDD--AKFCPNCGT 21 (23)
T ss_pred ccCCCCCCc--CcchhhhCC
Confidence 688777543 456888875
No 216
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=23.54 E-value=2.6e+02 Score=29.64 Aligned_cols=66 Identities=18% Similarity=0.093 Sum_probs=38.7
Q ss_pred hhcCCCCCCEEEEEEecCCCCceeeeec-c---CCC--eeEEEEc-cCCCeeEecc--CccCchh---hhhhhhhhhHH
Q psy6276 121 MYKCYRPGDIILARLPLKELHSYQLSTA-E---NEL--GVVIALS-EAASLFRSSE--KLTNDIE---FLKQEKLKLYE 187 (271)
Q Consensus 121 m~~~f~~GDIV~AkiS~~d~~~~~LST~-~---~eL--GVV~A~c-~cG~~Mvp~s--~~~~c~~---~~~~e~rKla~ 187 (271)
-+..+++||.|.-+-+ ||.-|..+... + .+. =.+-..| .||.+++... -.+.|++ |...-.++|..
T Consensus 364 ~~~~i~iGD~V~V~ra-GdVIP~i~~vv~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~C~n~~~C~aq~~~~l~h 441 (665)
T PRK07956 364 ERKDIRIGDTVVVRRA-GDVIPEVVGVVLEKRPGDEREIVMPTHCPVCGSELVRVEGEAVLRCTNGLSCPAQLKERLIH 441 (665)
T ss_pred HHcCCCCCCEEEEEEC-CCccceeeeeecccCCCCCccCcCCCCCCCCCCEeEecCCCeEEECCCCCCCHHHHHHHHHH
Confidence 4667899999998822 34434333321 1 111 1133468 8999997632 4677763 77776666543
No 217
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=23.13 E-value=35 Score=27.79 Aligned_cols=36 Identities=14% Similarity=0.002 Sum_probs=25.9
Q ss_pred ccCCCeeEEEEc-cCCCeeEecc-CccCchhhhhhhhhh
Q psy6276 148 AENELGVVIALS-EAASLFRSSE-KLTNDIEFLKQEKLK 184 (271)
Q Consensus 148 ~~~eLGVV~A~c-~cG~~Mvp~s-~~~~c~~~~~~e~rK 184 (271)
+.++||.= -+| .||...+-.. .-..||.||..-..-
T Consensus 2 akpelGtK-R~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 2 AKPELGTK-RTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CccccCCc-ccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 46777753 358 8999998776 346699999876544
No 218
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=22.85 E-value=2.6e+02 Score=29.86 Aligned_cols=54 Identities=15% Similarity=0.051 Sum_probs=31.2
Q ss_pred hcCCCCCCEEEEEEecCCCCc----eeeeeccCCC--eeEEEEc-cCCCeeEec--cCccCchh
Q psy6276 122 YKCYRPGDIILARLPLKELHS----YQLSTAENEL--GVVIALS-EAASLFRSS--EKLTNDIE 176 (271)
Q Consensus 122 ~~~f~~GDIV~AkiS~~d~~~----~~LST~~~eL--GVV~A~c-~cG~~Mvp~--s~~~~c~~ 176 (271)
+..+++||-|.-+-+ ||.-| +.+..+..+- -..-..| .||..+++. .-...|++
T Consensus 365 rkdIrIGDtV~V~kA-GdVIP~V~~Vv~e~R~~~~~~~~~P~~CP~C~s~l~r~~~e~~~rC~n 427 (667)
T COG0272 365 RKDIRIGDTVVVRKA-GDVIPQVVGVVLEKRPGNEKPIPFPTHCPVCGSELVREEGEVVIRCTN 427 (667)
T ss_pred hcCCCCCCEEEEEec-CCCCcceeeeecccCCCCCCCCCCCCCCCCCCCeeEeccCceeEecCC
Confidence 688999999998822 23322 2222222111 1245568 899999883 34555655
No 219
>PF04319 NifZ: NifZ domain; InterPro: IPR007415 NifZ is a short protein is found in the nif (nitrogen fixation) operon. It is required for the maturation of the nitrogenase MoFe protein. In the absence of NifZ, only one of the two P-clusters of the MoFe protein is matured to the ultimate [8Fe-7S] structure. The other P-cluster site in the protein contains a [4Fe-4S] cluster pair, suggesting that NifZ is specifically required for the formation of the second P-cluster [, , ].; GO: 0009399 nitrogen fixation
Probab=22.46 E-value=1.9e+02 Score=22.25 Aligned_cols=38 Identities=21% Similarity=0.338 Sum_probs=22.4
Q ss_pred hhcCCCCCCEEEEE-EecCCCCce------eeeeccCCCeeEEEEc
Q psy6276 121 MYKCYRPGDIILAR-LPLKELHSY------QLSTAENELGVVIALS 159 (271)
Q Consensus 121 m~~~f~~GDIV~Ak-iS~~d~~~~------~LST~~~eLGVV~A~c 159 (271)
|.+.|.+||.|+|. --.+|+ +| .|=.+.-+.|.|....
T Consensus 1 ~~p~f~~G~~V~a~~~irNDG-t~Pg~~~g~lLv~~G~~G~V~~iG 45 (75)
T PF04319_consen 1 MPPRFEWGDKVRARKDIRNDG-TFPGKEIGELLVRKGDVGYVVSIG 45 (75)
T ss_pred CCCccCCCCEEEEEEEeEcCC-CCCCCCCCCEEEcCCCcEEEEEee
Confidence 45789999999999 333444 22 1222344556666544
No 220
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=22.30 E-value=38 Score=27.19 Aligned_cols=30 Identities=20% Similarity=0.030 Sum_probs=24.1
Q ss_pred cCCCeeEEEEc-cCCCeeEe--ccCccCchhhh
Q psy6276 149 ENELGVVIALS-EAASLFRS--SEKLTNDIEFL 178 (271)
Q Consensus 149 ~~eLGVV~A~c-~cG~~Mvp--~s~~~~c~~~~ 178 (271)
+..|=|.-|.| +||-...+ +..-..||.|.
T Consensus 51 g~~Llv~Pa~CkkCGfef~~~~ik~pSRCP~CK 83 (97)
T COG3357 51 GKRLLVRPARCKKCGFEFRDDKIKKPSRCPKCK 83 (97)
T ss_pred CceEEecChhhcccCccccccccCCcccCCcch
Confidence 55677888999 89988866 55678899996
No 221
>PF13375 RnfC_N: RnfC Barrel sandwich hybrid domain
Probab=22.22 E-value=67 Score=25.65 Aligned_cols=15 Identities=20% Similarity=0.337 Sum_probs=11.4
Q ss_pred CEEEEEEeeEEEEec
Q psy6276 31 GYLYSTLAGTVSINK 45 (271)
Q Consensus 31 g~I~ASv~G~v~i~~ 45 (271)
-.|+||+.|+|.-..
T Consensus 67 a~iHAsvSG~V~~I~ 81 (101)
T PF13375_consen 67 APIHASVSGTVTAIE 81 (101)
T ss_pred eeEEcCCCeEEEEEe
Confidence 379999999886543
No 222
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=22.05 E-value=1.6e+02 Score=22.57 Aligned_cols=39 Identities=10% Similarity=0.336 Sum_probs=24.7
Q ss_pred EEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE
Q psy6276 76 ARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR 134 (271)
Q Consensus 76 GrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak 134 (271)
|+|.++.+..+.|+.. |..+.-++ .+-+...|||+|..-
T Consensus 7 ~~V~~i~~~~A~v~~~------------G~~~~v~l--------~lv~~~~vGD~VLVH 45 (76)
T TIGR00074 7 GQVVEIDENIALVEFC------------GIKRDVSL--------DLVGEVKVGDYVLVH 45 (76)
T ss_pred eEEEEEcCCEEEEEcC------------CeEEEEEE--------EeeCCCCCCCEEEEe
Confidence 7888898888888863 33222111 122457899998765
No 223
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=21.96 E-value=40 Score=32.14 Aligned_cols=29 Identities=7% Similarity=0.056 Sum_probs=22.5
Q ss_pred EEEEc-cCCCeeEecc---CccCchhhhhhhhh
Q psy6276 155 VIALS-EAASLFRSSE---KLTNDIEFLKQEKL 183 (271)
Q Consensus 155 V~A~c-~cG~~Mvp~s---~~~~c~~~~~~e~r 183 (271)
+..+| .||..|+... +...||.|+..-+.
T Consensus 27 lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri 59 (294)
T COG0777 27 LWTKCPSCGEMLYRKELESNLKVCPKCGHHMRI 59 (294)
T ss_pred ceeECCCccceeeHHHHHhhhhcccccCccccc
Confidence 46789 8999998764 68899999865443
No 224
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.72 E-value=44 Score=31.06 Aligned_cols=22 Identities=9% Similarity=-0.114 Sum_probs=17.0
Q ss_pred Ec-cCCCeeEecc----CccCchhhhh
Q psy6276 158 LS-EAASLFRSSE----KLTNDIEFLK 179 (271)
Q Consensus 158 ~c-~cG~~Mvp~s----~~~~c~~~~~ 179 (271)
.| .||.++.... .++.||.|.+
T Consensus 246 pCprCG~~I~~~~~~gR~t~~CP~CQ~ 272 (272)
T PRK14810 246 PCLNCKTPIRRVVVAGRSSHYCPHCQK 272 (272)
T ss_pred cCCCCCCeeEEEEECCCccEECcCCcC
Confidence 47 8999996643 6899999963
No 225
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=20.77 E-value=65 Score=23.01 Aligned_cols=24 Identities=8% Similarity=0.217 Sum_probs=15.0
Q ss_pred CCCCCEEEEEEecCCCCceeeeeccCC
Q psy6276 125 YRPGDIILARLPLKELHSYQLSTAENE 151 (271)
Q Consensus 125 f~~GDIV~AkiS~~d~~~~~LST~~~e 151 (271)
|++||+|+-|-. ++.+.++..++.
T Consensus 1 f~~GDvV~LKSG---Gp~MTV~~v~~~ 24 (53)
T PF09926_consen 1 FKIGDVVQLKSG---GPRMTVTEVGPN 24 (53)
T ss_pred CCCCCEEEEccC---CCCeEEEEcccc
Confidence 789999987621 345666554443
No 226
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=20.65 E-value=2.3e+02 Score=20.98 Aligned_cols=41 Identities=15% Similarity=0.284 Sum_probs=24.7
Q ss_pred EEEEEEEEe--cceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE
Q psy6276 74 VTARIMAVQ--QHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR 134 (271)
Q Consensus 74 VIGrVt~V~--~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak 134 (271)
|=++|+++. +..+.|+.. |..+.-++ .+-+...|||+|..-
T Consensus 5 iP~~Vv~v~~~~~~A~v~~~------------G~~~~V~~--------~lv~~v~~Gd~VLVH 47 (68)
T PF01455_consen 5 IPGRVVEVDEDGGMAVVDFG------------GVRREVSL--------ALVPDVKVGDYVLVH 47 (68)
T ss_dssp EEEEEEEEETTTTEEEEEET------------TEEEEEEG--------TTCTSB-TT-EEEEE
T ss_pred ccEEEEEEeCCCCEEEEEcC------------CcEEEEEE--------EEeCCCCCCCEEEEe
Confidence 347899998 888998863 43332211 234447999999765
No 227
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=20.61 E-value=4.1e+02 Score=20.64 Aligned_cols=65 Identities=17% Similarity=0.195 Sum_probs=39.4
Q ss_pred CEEEEEEEEEec-ce--EEEEEeeecCcccCCceeeEEeccccccchhhhHhhh-cCCCCCCEEEEE--EecCCC-Ccee
Q psy6276 72 DVVTARIMAVQQ-HL--CKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMY-KCYRPGDIILAR--LPLKEL-HSYQ 144 (271)
Q Consensus 72 DIVIGrVt~V~~-~~--a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~-~~f~~GDIV~Ak--iS~~d~-~~~~ 144 (271)
=-|.|.|++++. +. +..++.. +. ....+++-.+... .+. ..++.||-|.+. +++... ..|.
T Consensus 24 vwV~GEIs~~~~~~~gh~YftLkD--~~---a~i~~~~~~~~~~-------~i~~~~l~~G~~V~v~g~~~~y~~~G~~s 91 (99)
T PF13742_consen 24 VWVEGEISNLKRHSSGHVYFTLKD--EE---ASISCVIFRSRAR-------RIRGFDLKDGDKVLVRGRVSFYEPRGSLS 91 (99)
T ss_pred EEEEEEEeecEECCCceEEEEEEc--CC---cEEEEEEEHHHHh-------hCCCCCCCCCCEEEEEEEEEEECCCcEEE
Confidence 358899988876 33 4445432 21 4456665553322 344 678999999999 777433 3366
Q ss_pred eeec
Q psy6276 145 LSTA 148 (271)
Q Consensus 145 LST~ 148 (271)
|...
T Consensus 92 l~v~ 95 (99)
T PF13742_consen 92 LIVE 95 (99)
T ss_pred EEEE
Confidence 6543
No 228
>PRK05054 exoribonuclease II; Provisional
Probab=20.30 E-value=2.3e+02 Score=29.78 Aligned_cols=64 Identities=14% Similarity=0.258 Sum_probs=43.5
Q ss_pred CCCCC--EEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccc-hh-----hh--H--hhhcCCCCCCEEEEE-
Q psy6276 68 PTPGD--VVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRAT-EI-----DR--I--EMYKCYRPGDIILAR- 134 (271)
Q Consensus 68 P~vGD--IVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~t-e~-----d~--~--~m~~~f~~GDIV~Ak- 134 (271)
..+|+ ..-|.|++|+....+|.|. .....|++|.+....- +. +. . .-...|++||-|..+
T Consensus 557 ~~~G~~~~f~g~I~~v~~~G~fV~l~-------~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v 629 (644)
T PRK05054 557 DKAGTDTRFAAEIIDISRGGMRVRLL-------ENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTL 629 (644)
T ss_pred hccCCCeEEEEEEEeeecCcEEEEEe-------CCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEE
Confidence 35665 9999999999999999985 2346788887765321 00 00 0 112469999999999
Q ss_pred EecC
Q psy6276 135 LPLK 138 (271)
Q Consensus 135 iS~~ 138 (271)
.+.+
T Consensus 630 ~~vd 633 (644)
T PRK05054 630 AEVR 633 (644)
T ss_pred EEEc
Confidence 6653
Done!