Query 013817
Match_columns 436
No_of_seqs 366 out of 1380
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 07:41:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013817.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013817hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10829 ribonuclease D; Provi 100.0 1.9E-33 4.2E-38 286.2 21.7 238 10-299 2-250 (373)
2 COG0349 Rnd Ribonuclease D [Tr 100.0 7.2E-32 1.6E-36 269.0 15.9 216 19-274 4-224 (361)
3 cd06146 mut-7_like_exo DEDDy 3 100.0 2.1E-30 4.6E-35 242.6 20.1 184 11-213 1-192 (193)
4 cd06129 RNaseD_like DEDDy 3'-5 100.0 1.2E-29 2.5E-34 230.7 18.3 158 22-213 2-160 (161)
5 TIGR01388 rnd ribonuclease D. 100.0 2.8E-29 6.1E-34 256.4 21.0 235 14-300 2-247 (367)
6 cd06141 WRN_exo DEDDy 3'-5' ex 100.0 2.2E-27 4.7E-32 216.9 18.8 163 19-213 4-169 (170)
7 cd06148 Egl_like_exo DEDDy 3'- 100.0 1.6E-27 3.5E-32 223.8 17.1 170 25-220 3-181 (197)
8 PF01612 DNA_pol_A_exo1: 3'-5' 99.9 9E-26 1.9E-30 205.1 19.5 174 11-217 1-176 (176)
9 cd06142 RNaseD_exo DEDDy 3'-5' 99.8 9.5E-20 2.1E-24 166.6 19.1 170 23-228 3-175 (178)
10 COG1656 Uncharacterized conser 99.8 8.1E-21 1.8E-25 169.7 6.9 81 353-436 3-83 (165)
11 PF01927 Mut7-C: Mut7-C RNAse 99.8 3.2E-20 7E-25 166.6 8.6 77 357-436 1-77 (147)
12 smart00474 35EXOc 3'-5' exonuc 99.8 1.1E-17 2.3E-22 150.8 19.8 169 12-216 2-171 (172)
13 KOG2206 Exosome 3'-5' exoribon 99.8 1.7E-18 3.8E-23 179.2 9.4 224 11-276 193-423 (687)
14 cd06147 Rrp6p_like_exo DEDDy 3 99.7 2.2E-16 4.9E-21 147.3 20.5 175 8-220 2-176 (192)
15 KOG2207 Predicted 3'-5' exonuc 99.7 1.7E-17 3.7E-22 173.0 9.4 196 4-217 385-586 (617)
16 cd00007 35EXOc 3'-5' exonuclea 99.7 3.3E-15 7.3E-20 132.0 16.6 149 34-215 2-154 (155)
17 cd09018 DEDDy_polA_RNaseD_like 99.7 3.8E-15 8.2E-20 132.1 15.5 147 34-213 1-149 (150)
18 PRK05755 DNA polymerase I; Pro 99.6 1.2E-14 2.6E-19 164.1 20.9 181 6-222 291-475 (880)
19 cd06140 DNA_polA_I_Bacillus_li 99.5 1.2E-13 2.7E-18 126.6 15.5 157 32-222 3-162 (178)
20 cd06139 DNA_polA_I_Ecoli_like_ 99.5 3.2E-12 6.8E-17 118.1 17.4 159 30-220 3-175 (193)
21 PRK14975 bifunctional 3'-5' ex 99.4 1.8E-12 3.9E-17 139.6 12.7 146 10-219 2-147 (553)
22 KOG2207 Predicted 3'-5' exonuc 99.1 1.7E-12 3.7E-17 135.9 -4.2 275 135-414 154-456 (617)
23 COG0749 PolA DNA polymerase I 99.1 3.3E-10 7.1E-15 120.7 12.7 170 19-222 9-186 (593)
24 TIGR00593 pola DNA polymerase 99.1 2.8E-09 6.1E-14 120.1 19.9 172 11-221 304-482 (887)
25 KOG4373 Predicted 3'-5' exonuc 98.8 1.6E-08 3.5E-13 99.8 10.6 148 33-209 128-281 (319)
26 cd06128 DNA_polA_exo DEDDy 3'- 98.6 8.3E-07 1.8E-11 79.2 13.6 117 78-213 30-150 (151)
27 COG4634 Uncharacterized protei 98.5 4.8E-07 1.1E-11 75.8 6.9 71 357-427 1-77 (113)
28 cd06137 DEDDh_RNase DEDDh 3'-5 97.4 0.0022 4.9E-08 58.2 12.3 86 94-209 75-160 (161)
29 PRK06063 DNA polymerase III su 97.4 0.0053 1.2E-07 62.0 15.6 102 91-221 83-184 (313)
30 PRK07942 DNA polymerase III su 97.4 0.0092 2E-07 57.6 16.4 89 105-218 94-182 (232)
31 cd06149 ISG20 DEDDh 3'-5' exon 97.2 0.0026 5.7E-08 57.6 9.9 89 91-210 66-157 (157)
32 PRK08517 DNA polymerase III su 97.1 0.025 5.4E-07 55.6 16.8 98 91-218 136-233 (257)
33 PRK07740 hypothetical protein; 97.1 0.027 5.9E-07 54.8 16.8 100 92-221 131-231 (244)
34 cd06131 DNA_pol_III_epsilon_Ec 97.1 0.015 3.3E-07 52.5 14.0 95 92-212 71-166 (167)
35 PRK06309 DNA polymerase III su 97.0 0.041 8.8E-07 53.1 16.8 144 33-217 3-167 (232)
36 PRK06310 DNA polymerase III su 97.0 0.025 5.4E-07 55.3 15.0 150 29-216 4-174 (250)
37 PRK06807 DNA polymerase III su 97.0 0.026 5.6E-07 57.0 15.5 97 91-217 77-173 (313)
38 KOG2249 3'-5' exonuclease [Rep 97.0 0.0093 2E-07 58.0 11.4 95 93-219 175-269 (280)
39 PRK05711 DNA polymerase III su 96.9 0.023 5.1E-07 55.2 14.0 97 92-213 76-173 (240)
40 TIGR01406 dnaQ_proteo DNA poly 96.9 0.036 7.8E-07 53.3 15.0 98 91-213 71-169 (225)
41 TIGR01405 polC_Gram_pos DNA po 96.9 0.024 5.2E-07 66.6 16.2 103 91-222 259-361 (1213)
42 PRK07883 hypothetical protein; 96.9 0.032 6.9E-07 60.7 16.2 159 27-222 10-188 (557)
43 TIGR01298 RNaseT ribonuclease 96.8 0.069 1.5E-06 50.3 16.4 92 105-222 106-198 (200)
44 PRK05168 ribonuclease T; Provi 96.8 0.091 2E-06 49.9 17.2 93 104-222 114-207 (211)
45 smart00479 EXOIII exonuclease 96.8 0.043 9.3E-07 49.1 14.3 98 91-216 69-167 (169)
46 cd06144 REX4_like DEDDh 3'-5' 96.8 0.0049 1.1E-07 55.4 8.0 86 91-210 66-152 (152)
47 PRK09145 DNA polymerase III su 96.7 0.082 1.8E-06 49.7 15.9 159 22-213 19-198 (202)
48 cd06145 REX1_like DEDDh 3'-5' 96.7 0.0066 1.4E-07 54.6 7.9 86 91-209 64-149 (150)
49 TIGR00573 dnaq exonuclease, DN 96.7 0.037 8.1E-07 52.7 13.4 105 91-219 76-180 (217)
50 cd06125 DnaQ_like_exo DnaQ-lik 96.7 0.012 2.6E-07 48.8 8.6 82 35-145 1-83 (96)
51 TIGR01407 dinG_rel DnaQ family 96.6 0.044 9.6E-07 62.6 15.9 99 91-218 69-167 (850)
52 PRK07246 bifunctional ATP-depe 96.6 0.033 7.3E-07 63.3 14.6 101 91-221 75-175 (820)
53 PRK09146 DNA polymerase III su 96.6 0.1 2.2E-06 50.7 15.9 103 92-217 119-228 (239)
54 cd06130 DNA_pol_III_epsilon_li 96.6 0.083 1.8E-06 46.8 14.3 89 91-209 66-154 (156)
55 cd05780 DNA_polB_Kod1_like_exo 96.6 0.061 1.3E-06 50.4 13.7 160 33-212 4-195 (195)
56 cd05160 DEDDy_DNA_polB_exo DED 96.4 0.052 1.1E-06 50.6 12.2 110 91-209 65-198 (199)
57 cd06143 PAN2_exo DEDDh 3'-5' e 96.4 0.011 2.5E-07 54.5 7.3 80 95-209 94-173 (174)
58 PRK08074 bifunctional ATP-depe 96.1 0.2 4.4E-06 57.8 17.6 99 91-218 73-171 (928)
59 cd06127 DEDDh DEDDh 3'-5' exon 96.0 0.23 4.9E-06 43.3 13.7 91 91-209 68-158 (159)
60 COG2176 PolC DNA polymerase II 95.7 0.037 8.1E-07 63.4 8.9 109 91-228 490-599 (1444)
61 PRK05601 DNA polymerase III su 95.4 0.31 6.7E-06 50.2 13.6 161 29-212 43-245 (377)
62 cd05781 DNA_polB_B3_exo DEDDy 95.4 0.43 9.2E-06 44.6 13.5 158 33-212 4-188 (188)
63 PRK07247 DNA polymerase III su 95.4 0.27 5.8E-06 46.3 12.1 105 91-228 73-181 (195)
64 cd06134 RNaseT DEDDh 3'-5' exo 94.5 0.45 9.8E-06 44.3 11.0 84 105-214 103-187 (189)
65 KOG2405 Predicted 3'-5' exonuc 94.4 0.0054 1.2E-07 62.3 -2.1 140 37-204 63-215 (458)
66 KOG2405 Predicted 3'-5' exonuc 94.4 0.01 2.2E-07 60.4 -0.3 136 53-214 212-359 (458)
67 cd05784 DNA_polB_II_exo DEDDy 94.3 1.4 3E-05 41.4 13.8 109 91-210 53-193 (193)
68 PRK06195 DNA polymerase III su 94.2 0.37 8E-06 48.5 10.5 99 91-219 69-167 (309)
69 PRK00448 polC DNA polymerase I 94.1 0.74 1.6E-05 55.3 14.2 107 92-227 489-596 (1437)
70 cd05777 DNA_polB_delta_exo DED 92.4 4.4 9.5E-05 38.9 14.3 54 160-213 167-224 (230)
71 cd05785 DNA_polB_like2_exo Unc 92.4 2.1 4.6E-05 40.5 11.9 159 33-209 10-206 (207)
72 PRK07983 exodeoxyribonuclease 92.3 4.1 8.9E-05 39.0 13.9 104 95-235 67-170 (219)
73 cd05783 DNA_polB_B1_exo DEDDy 91.6 8.9 0.00019 36.3 15.2 161 33-210 6-202 (204)
74 cd06136 TREX1_2 DEDDh 3'-5' ex 91.4 0.89 1.9E-05 41.9 8.0 88 93-210 85-175 (177)
75 PF13482 RNase_H_2: RNase_H su 90.7 0.35 7.6E-06 43.4 4.4 148 35-212 1-163 (164)
76 cd05779 DNA_polB_epsilon_exo D 90.1 5.3 0.00011 37.9 12.1 111 91-210 75-204 (204)
77 PRK09182 DNA polymerase III su 89.4 12 0.00025 37.7 14.5 88 93-213 111-198 (294)
78 PRK11779 sbcB exonuclease I; P 89.4 10 0.00022 40.7 14.7 106 92-215 81-197 (476)
79 PRK07748 sporulation inhibitor 88.2 5.1 0.00011 37.8 10.5 99 91-215 81-179 (207)
80 cd05782 DNA_polB_like1_exo Unc 85.3 8.9 0.00019 36.3 10.5 110 90-210 79-207 (208)
81 PF09281 Taq-exonuc: Taq polym 84.5 5.1 0.00011 35.2 7.5 55 135-216 84-138 (138)
82 KOG2248 3'-5' exonuclease [Rep 84.2 1 2.2E-05 46.7 3.8 91 91-213 282-372 (380)
83 cd06138 ExoI_N N-terminal DEDD 83.5 7.5 0.00016 35.8 8.9 99 92-208 72-181 (183)
84 cd05776 DNA_polB_alpha_exo ina 83.4 2.4 5.2E-05 40.9 5.8 112 92-213 85-227 (234)
85 KOG1275 PAB-dependent poly(A) 82.9 0.37 8E-06 54.1 -0.1 97 99-230 1009-1105(1118)
86 COG0847 DnaQ DNA polymerase II 81.7 12 0.00026 35.7 10.0 97 92-214 84-180 (243)
87 KOG3657 Mitochondrial DNA poly 80.1 3.6 7.7E-05 46.3 6.1 109 104-219 241-386 (1075)
88 cd06133 ERI-1_3'hExo_like DEDD 79.4 16 0.00034 32.7 9.4 97 91-212 77-175 (176)
89 PRK05762 DNA polymerase II; Re 78.4 44 0.00094 38.2 14.4 112 91-212 205-348 (786)
90 TIGR03447 mycothiol_MshC cyste 77.2 1.4 3.1E-05 46.2 2.0 56 342-402 42-98 (411)
91 COG1412 Uncharacterized protei 75.7 6.9 0.00015 34.8 5.6 55 371-427 71-126 (136)
92 PRK06722 exonuclease; Provisio 75.2 22 0.00047 35.5 9.7 98 91-213 79-178 (281)
93 cd00672 CysRS_core catalytic c 74.9 2.6 5.6E-05 40.3 3.0 34 367-400 47-80 (213)
94 PRK12418 cysteinyl-tRNA synthe 68.3 4.7 0.0001 42.0 3.3 36 367-402 36-71 (384)
95 PRK14535 cysS cysteinyl-tRNA s 63.8 3.8 8.3E-05 45.6 1.7 56 342-402 254-310 (699)
96 PRK00260 cysS cysteinyl-tRNA s 61.3 8.3 0.00018 41.1 3.7 35 367-401 50-84 (463)
97 cd00814 MetRS_core catalytic c 60.9 7.6 0.00017 39.1 3.2 34 368-401 29-62 (319)
98 TIGR00435 cysS cysteinyl-tRNA 59.0 8.3 0.00018 41.2 3.2 35 367-401 48-82 (465)
99 PLN02946 cysteine-tRNA ligase 58.6 8.3 0.00018 42.1 3.1 55 342-401 86-141 (557)
100 TIGR00305 probable toxin-antit 57.6 13 0.00028 31.3 3.6 28 385-412 85-113 (114)
101 PTZ00399 cysteinyl-tRNA-synthe 54.7 7.2 0.00016 43.5 1.9 56 342-402 66-123 (651)
102 PF05991 NYN_YacP: YacP-like N 54.6 17 0.00037 33.2 4.1 59 373-433 64-127 (166)
103 COG0215 CysS Cysteinyl-tRNA sy 52.4 15 0.00032 39.2 3.7 54 342-401 28-83 (464)
104 PRK02261 methylaspartate mutas 52.3 20 0.00043 31.7 4.0 33 368-401 23-55 (137)
105 PRK13764 ATPase; Provisional 51.6 30 0.00065 38.3 6.0 40 388-427 91-130 (602)
106 TIGR00398 metG methionyl-tRNA 51.4 14 0.00031 39.8 3.5 34 368-401 28-61 (530)
107 PLN02224 methionine-tRNA ligas 51.0 17 0.00037 40.3 4.0 50 352-401 81-131 (616)
108 cd00812 LeuRS_core catalytic c 50.5 15 0.00033 36.9 3.4 40 362-401 22-62 (314)
109 PRK05359 oligoribonuclease; Pr 50.5 2.1E+02 0.0045 26.4 12.9 21 197-217 156-176 (181)
110 PF04900 Fcf1: Fcf1; InterPro 50.4 30 0.00065 28.6 4.6 40 387-426 52-93 (101)
111 PRK12268 methionyl-tRNA synthe 48.6 27 0.00058 38.0 5.1 34 368-401 33-66 (556)
112 PRK11893 methionyl-tRNA synthe 48.4 19 0.00041 38.5 3.9 34 368-401 30-63 (511)
113 PRK14534 cysS cysteinyl-tRNA s 48.4 15 0.00032 39.5 3.0 56 342-402 27-93 (481)
114 cd05778 DNA_polB_zeta_exo inac 45.6 29 0.00062 33.4 4.3 50 160-209 176-230 (231)
115 PF12813 XPG_I_2: XPG domain c 45.0 24 0.00051 34.5 3.6 46 368-415 9-57 (246)
116 PRK12267 methionyl-tRNA synthe 44.7 23 0.00049 39.4 3.8 34 368-401 33-66 (648)
117 cd02067 B12-binding B12 bindin 44.3 37 0.00081 28.5 4.4 39 368-407 19-59 (119)
118 PF01406 tRNA-synt_1e: tRNA sy 43.9 14 0.00031 37.1 1.9 34 368-402 36-70 (300)
119 TIGR01501 MthylAspMutase methy 42.8 37 0.0008 30.1 4.2 35 368-403 21-55 (134)
120 cd00802 class_I_aaRS_core cata 42.3 26 0.00057 30.6 3.2 37 363-399 20-57 (143)
121 PRK14536 cysS cysteinyl-tRNA s 41.7 25 0.00053 37.9 3.4 56 342-402 29-95 (490)
122 PRK00133 metG methionyl-tRNA s 41.1 26 0.00056 39.2 3.6 33 368-400 31-63 (673)
123 COG0143 MetG Methionyl-tRNA sy 40.4 23 0.0005 38.8 3.0 38 363-401 27-67 (558)
124 cd02072 Glm_B12_BD B12 binding 39.3 48 0.001 29.2 4.3 35 368-403 19-53 (128)
125 cd00758 MoCF_BD MoCF_BD: molyb 39.2 74 0.0016 27.6 5.6 49 359-407 15-66 (133)
126 TIGR00592 pol2 DNA polymerase 39.0 1.2E+02 0.0027 36.3 8.9 102 102-213 599-723 (1172)
127 cd00668 Ile_Leu_Val_MetRS_core 38.2 28 0.0006 34.8 3.0 39 368-406 29-67 (312)
128 TIGR00640 acid_CoA_mut_C methy 36.4 49 0.0011 29.0 3.9 33 368-401 22-54 (132)
129 PF10108 DNA_pol_B_exo2: Predi 36.0 1.8E+02 0.004 27.7 8.0 113 90-213 38-170 (209)
130 PHA02119 hypothetical protein 35.4 38 0.00083 26.6 2.7 18 366-383 57-74 (87)
131 cd02071 MM_CoA_mut_B12_BD meth 35.0 62 0.0013 27.6 4.3 33 368-401 19-51 (122)
132 cd00671 ArgRS_core catalytic c 35.0 28 0.00061 32.8 2.4 37 363-399 23-60 (212)
133 COG1487 VapC Predicted nucleic 35.0 61 0.0013 27.9 4.3 44 365-414 79-123 (133)
134 PF09334 tRNA-synt_1g: tRNA sy 33.9 23 0.00051 36.9 1.7 35 368-402 28-62 (391)
135 cd02070 corrinoid_protein_B12- 33.7 61 0.0013 30.3 4.4 38 365-403 97-136 (201)
136 PRK03670 competence damage-ind 32.4 81 0.0018 30.9 5.1 48 359-407 16-68 (252)
137 COG0525 ValS Valyl-tRNA synthe 30.3 27 0.00059 40.1 1.6 47 344-395 40-87 (877)
138 COG2185 Sbm Methylmalonyl-CoA 29.3 85 0.0018 28.2 4.2 41 366-407 30-71 (143)
139 cd00885 cinA Competence-damage 29.3 99 0.0021 28.3 4.9 49 359-407 15-66 (170)
140 PRK03094 hypothetical protein; 28.8 2E+02 0.0043 23.3 5.8 61 357-426 2-63 (80)
141 cd02069 methionine_synthase_B1 26.9 99 0.0021 29.4 4.6 39 364-403 102-142 (213)
142 COG1058 CinA Predicted nucleot 26.4 1.2E+02 0.0026 29.9 5.1 48 360-407 18-68 (255)
143 PRK03673 hypothetical protein; 25.9 1E+02 0.0022 32.3 4.9 50 358-407 16-68 (396)
144 TIGR02370 pyl_corrinoid methyl 24.6 1.1E+02 0.0023 28.6 4.3 38 365-403 99-138 (197)
145 PF02639 DUF188: Uncharacteriz 24.5 1.1E+02 0.0023 27.0 4.0 30 388-418 41-70 (130)
146 cd06135 Orn DEDDh 3'-5' exonuc 24.4 3.4E+02 0.0073 24.5 7.5 32 92-123 78-113 (173)
147 TIGR03599 YloV DAK2 domain fus 24.4 3.6E+02 0.0079 29.4 8.8 79 356-434 314-401 (530)
148 PF13986 DUF4224: Domain of un 24.2 82 0.0018 22.6 2.7 26 367-407 19-44 (47)
149 PTZ00315 2'-phosphotransferase 24.2 6.7E+02 0.014 27.8 10.7 103 91-213 132-252 (582)
150 PRK01215 competence damage-ind 22.2 1.5E+02 0.0032 29.2 5.0 50 358-407 18-70 (264)
151 cd00886 MogA_MoaB MogA_MoaB fa 21.8 1.4E+02 0.0031 26.5 4.4 48 360-407 17-69 (152)
152 PLN02610 probable methionyl-tR 21.8 91 0.002 35.8 3.8 33 368-400 47-79 (801)
153 PF03698 UPF0180: Uncharacteri 21.1 1.4E+02 0.003 24.2 3.6 49 357-413 2-51 (80)
154 PF08845 SymE_toxin: Toxin Sym 20.2 27 0.00058 26.3 -0.6 27 369-405 30-56 (57)
No 1
>PRK10829 ribonuclease D; Provisional
Probab=100.00 E-value=1.9e-33 Score=286.25 Aligned_cols=238 Identities=21% Similarity=0.295 Sum_probs=196.0
Q ss_pred cEEEEcCCChHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCc
Q 013817 10 KIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPL 89 (436)
Q Consensus 10 ~i~~V~t~~~~el~~l~~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~ 89 (436)
.|++|++ ++++..+++.+..+++||||+|+.+... |++++|||||++. +++|+||+..+.
T Consensus 2 ~~~~I~t--~~~L~~~~~~l~~~~~lalDtEf~~~~t---y~~~l~LiQl~~~--------------~~~~LiD~l~~~- 61 (373)
T PRK10829 2 NYQMITT--DDALASVCEAARAFPAIALDTEFVRTRT---YYPQLGLIQLYDG--------------EQLSLIDPLGIT- 61 (373)
T ss_pred CcEEeCC--HHHHHHHHHHHhcCCeEEEecccccCcc---CCCceeEEEEecC--------------CceEEEecCCcc-
Confidence 4788999 8999999999999999999999988764 8899999999974 679999998774
Q ss_pred hhHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHH
Q 013817 90 PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (436)
Q Consensus 90 ~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~ 169 (436)
.+..|.++|+|++|+||+|++++|+..|.+.||+ . +.++|| |++|+.+++.+ ..+||+.|++
T Consensus 62 --d~~~L~~ll~~~~ivKV~H~~~~Dl~~l~~~~g~---~-----p~~~fD-Tqiaa~~lg~~-------~~~gl~~Lv~ 123 (373)
T PRK10829 62 --DWSPFKALLRDPQVTKFLHAGSEDLEVFLNAFGE---L-----PQPLID-TQILAAFCGRP-------LSCGFASMVE 123 (373)
T ss_pred --chHHHHHHHcCCCeEEEEeChHhHHHHHHHHcCC---C-----cCCeee-HHHHHHHcCCC-------ccccHHHHHH
Confidence 2678999999999999999999999999877765 2 589999 99999999864 3689999999
Q ss_pred HHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---cchhhhcccCCC--cCCCCCCccC
Q 013817 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS---CSSISELDSSNL--DLGLKGILEK 244 (436)
Q Consensus 170 ~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l---~~~~~~~~~~~~--~~~~~~~~~~ 244 (436)
++||+.++|+++++||+.||||++|+.|||.||++|+.||+.|.++|.+.|++ .+||..+..... ..+-..|++
T Consensus 124 ~~lgv~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g~~~w~~ee~~~l~~~~~~~~~~~~~~~~- 202 (373)
T PRK10829 124 EYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGWLPAALDECRLLCQRRQEVLAPEEAYRD- 202 (373)
T ss_pred HHhCCccCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHhccccCCChHHHHHH-
Confidence 99999999999999999999999999999999999999999999999999987 889988754321 111122333
Q ss_pred CCCCCCcccccchhHHHHHHHhhhcccC------CCCCcccccccCCCCCCchHHHHHHHh
Q 013817 245 PDIGNKTVRFKLCEALDIIRATSYYSQC------LPEGVVSRVSYLNTMPMDESLVKIVRK 299 (436)
Q Consensus 245 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~------i~~~~~~~~~~~~~~~~~~~~~~~~~~ 299 (436)
.++..+++ +++|+++|+|+.-... +|++- +--|+.+..|+++
T Consensus 203 ---ik~~~~L~-~~~lavl~~L~~WRe~~Ar~~d~p~~~---------Vl~d~~L~~lA~~ 250 (373)
T PRK10829 203 ---ITNAWQLR-TRQLACLQLLADWRLRKARERDLAVNF---------VVREEHLWQVARY 250 (373)
T ss_pred ---hccccCCC-HHHHHHHHHHHHHHHHHHHHhCCCcce---------ecChHHHHHHHHh
Confidence 34444555 9999999999554444 44431 2236777777764
No 2
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.98 E-value=7.2e-32 Score=269.00 Aligned_cols=216 Identities=24% Similarity=0.293 Sum_probs=186.1
Q ss_pred hHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhHHHHHHH
Q 013817 19 SPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKE 98 (436)
Q Consensus 19 ~~el~~l~~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~ 98 (436)
.+.++.++..+.+++.|++|||+...++ +++++|||||+.. +++++||+.... .-+..|..
T Consensus 4 ~~~l~~~~~~~~~~~~iAiDTEf~r~~t---~~p~LcLIQi~~~--------------e~~~lIdpl~~~--~d~~~l~~ 64 (361)
T COG0349 4 GDLLAAACALLRGSKAIAIDTEFMRLRT---YYPRLCLIQISDG--------------EGASLIDPLAGI--LDLPPLVA 64 (361)
T ss_pred hhHHHHHHHHhcCCCceEEecccccccc---cCCceEEEEEecC--------------CCceEecccccc--cccchHHH
Confidence 5678888999999999999999998885 8899999999985 449999988732 23678999
Q ss_pred hhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcCCcccc
Q 013817 99 LFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSK 178 (436)
Q Consensus 99 lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~K 178 (436)
+|.|++|+||+|.+++|+.+|.+.||. .+.++|| |++|+.+++.+ .++||++||++++|+.++|
T Consensus 65 Ll~d~~v~KIfHaa~~DL~~l~~~~g~--------~p~plfd-TqiAa~l~g~~-------~~~gl~~Lv~~ll~v~ldK 128 (361)
T COG0349 65 LLADPNVVKIFHAARFDLEVLLNLFGL--------LPTPLFD-TQIAAKLAGFG-------TSHGLADLVEELLGVELDK 128 (361)
T ss_pred HhcCCceeeeeccccccHHHHHHhcCC--------CCCchhH-HHHHHHHhCCc-------ccccHHHHHHHHhCCcccc
Confidence 999999999999999999999998766 2689999 99999999975 3899999999999999999
Q ss_pred cccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---cchhhhcccC--CCcCCCCCCccCCCCCCCccc
Q 013817 179 ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS---CSSISELDSS--NLDLGLKGILEKPDIGNKTVR 253 (436)
Q Consensus 179 ~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l---~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~ 253 (436)
++|.|||.+||||++|++|||.||.||+.||+.|.++|.++|++ .+||+.+.+. ........|.+ .+. ..
T Consensus 129 ~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r~~~a~~ef~~l~~r~~~~~~~~~~w~~----i~~-a~ 203 (361)
T COG0349 129 SEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAREGRLEWAEDEFRLLPTRRTYKVLPEDAWRE----IKI-AH 203 (361)
T ss_pred cccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHhhhccccccChHhHHHH----hhh-hh
Confidence 99999999999999999999999999999999999999999998 8999999776 33355556544 333 45
Q ss_pred ccchhHHHHHHHhhhcccCCC
Q 013817 254 FKLCEALDIIRATSYYSQCLP 274 (436)
Q Consensus 254 ~~~~~~~~~~~~~~~~~~~i~ 274 (436)
.+.+++++++|+|..-.++++
T Consensus 204 ~~~p~~la~l~~La~wRe~~A 224 (361)
T COG0349 204 SLDPRELAVLRELAAWREREA 224 (361)
T ss_pred cCChHHHHHHHHHHHHHHHHH
Confidence 677999999999955444444
No 3
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=99.97 E-value=2.1e-30 Score=242.60 Aligned_cols=184 Identities=46% Similarity=0.765 Sum_probs=150.8
Q ss_pred EEEEcCCChHHHHHHHHH--hcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCC
Q 013817 11 IHLVTSTESPEFTHLARA--LSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIP 88 (436)
Q Consensus 11 i~~V~t~~~~el~~l~~~--L~~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~ 88 (436)
||+|++ ++++.+++.. +...++||||+||.+.+.. ...+++++||||+. +.+|+||+..++
T Consensus 1 ~~~i~~--~~el~~~~~~~~l~~~~vig~D~Ew~~~~~~-~~~~~v~LiQiat~--------------~~~~lid~~~~~ 63 (193)
T cd06146 1 IHIVDS--EEELEALLLALSLEAGRVVGIDSEWKPSFLG-DSDPRVAILQLATE--------------DEVFLLDLLALE 63 (193)
T ss_pred CeEecC--HHHHHHHHHHHhhccCCEEEEECccCCCccC-CCCCCceEEEEecC--------------CCEEEEEchhcc
Confidence 688999 8999999999 8899999999999987742 12579999999985 789999998765
Q ss_pred ---chhHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCC---CCCcCcc
Q 013817 89 ---LPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGR---KLPKETK 162 (436)
Q Consensus 89 ---~~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~---~~~~~~~ 162 (436)
...+...|+++|+|++|+||||++++|+..|.+.||+.+.. +..+.+++|+..++..+.....++ ..+....
T Consensus 64 ~~~~~~~~~~L~~ll~d~~i~KVg~~~~~D~~~L~~~~~~~~~~--~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~ 141 (193)
T cd06146 64 NLESEDWDRLLKRLFEDPDVLKLGFGFKQDLKALSASYPALKCM--FERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTK 141 (193)
T ss_pred ccchHHHHHHHHHHhCCCCeeEEEechHHHHHHHHHhcCccccc--cccCCceEEHHHHHHHHhhccccccccccCcccC
Confidence 23467889999999999999999999999999988762210 012579999555555554332111 1112478
Q ss_pred cHHHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 013817 163 SLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (436)
Q Consensus 163 gL~~Lv~~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~ 213 (436)
||++||+++||.+++|..++|||..|||+++|+.|||.||+++++||+.|.
T Consensus 142 sL~~l~~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 142 GLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred CHHHHHHHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999999999999999999999985
No 4
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=99.97 E-value=1.2e-29 Score=230.73 Aligned_cols=158 Identities=34% Similarity=0.581 Sum_probs=140.8
Q ss_pred HHHHHHHhc-CCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhHHHHHHHhh
Q 013817 22 FTHLARALS-QSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELF 100 (436)
Q Consensus 22 l~~l~~~L~-~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL 100 (436)
++++++.|. .+++||||+||.+.+. +.+++|+||||+. ++.+||||+..++. .+..|+++|
T Consensus 2 l~~~~~~l~~~~~~ig~D~E~~~~~~---~~~~~~liQl~~~-------------~~~~~l~d~~~~~~--~~~~L~~lL 63 (161)
T cd06129 2 LSSLCEDLSMDGDVIAFDMEWPPGRR---YYGEVALIQLCVS-------------EEKCYLFDPLSLSV--DWQGLKMLL 63 (161)
T ss_pred HHHHHHHHhcCCCEEEEECCccCCCC---CCCceEEEEEEEC-------------CCCEEEEecccCcc--CHHHHHHHh
Confidence 567888898 9999999999998874 5689999999995 37899999987652 567899999
Q ss_pred CCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcCCcccccc
Q 013817 101 VSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKEL 180 (436)
Q Consensus 101 e~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~K~~ 180 (436)
++++|+||||++++|+..|.+.||+ .+.++|| +++++|++++. .+.||+++++++||.+++|..
T Consensus 64 ~d~~i~Kvg~~~k~D~~~L~~~~gi--------~~~~~~D-~~~aa~ll~~~-------~~~~L~~l~~~~lg~~l~K~~ 127 (161)
T cd06129 64 ENPSIVKALHGIEGDLWKLLRDFGE--------KLQRLFD-TTIAANLKGLP-------ERWSLASLVEHFLGKTLDKSI 127 (161)
T ss_pred CCCCEEEEEeccHHHHHHHHHHcCC--------CcccHhH-HHHHHHHhCCC-------CCchHHHHHHHHhCCCCCccc
Confidence 9999999999999999999876766 1467899 89999999874 357999999999999999999
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 013817 181 QCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (436)
Q Consensus 181 q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~ 213 (436)
++|||..|||+++|+.|||.||++++.||+.|.
T Consensus 128 ~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 128 SCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred eeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999885
No 5
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=99.97 E-value=2.8e-29 Score=256.40 Aligned_cols=235 Identities=23% Similarity=0.358 Sum_probs=189.9
Q ss_pred EcCCChHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhHH
Q 013817 14 VTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIW 93 (436)
Q Consensus 14 V~t~~~~el~~l~~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~ 93 (436)
|++ .+++.++++.+...++||||+||..... |++++|||||++. +.+|+||+..+. .+
T Consensus 2 I~t--~~~l~~~~~~l~~~~~ia~DtE~~~~~~---y~~~l~LiQia~~--------------~~~~liD~~~~~---~~ 59 (367)
T TIGR01388 2 ITT--DDELATVCEAVRTFPFVALDTEFVRERT---FWPQLGLIQVADG--------------EQLALIDPLVII---DW 59 (367)
T ss_pred cCC--HHHHHHHHHHHhcCCEEEEeccccCCCC---CCCcceEEEEeeC--------------CeEEEEeCCCcc---cH
Confidence 566 7999999999999999999999988763 7899999999984 789999998763 36
Q ss_pred HHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcC
Q 013817 94 ELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLD 173 (436)
Q Consensus 94 ~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg 173 (436)
+.|+++|+|++|.||+|++++|+..|.+.++. .+.++|| |++|+|+++++ ..+||+.|+++|||
T Consensus 60 ~~L~~lL~d~~i~KV~h~~k~Dl~~L~~~~~~--------~~~~~fD-tqlAa~lL~~~-------~~~~l~~Lv~~~Lg 123 (367)
T TIGR01388 60 SPLKELLRDESVVKVLHAASEDLEVFLNLFGE--------LPQPLFD-TQIAAAFCGFG-------MSMGYAKLVQEVLG 123 (367)
T ss_pred HHHHHHHCCCCceEEEeecHHHHHHHHHHhCC--------CCCCccc-HHHHHHHhCCC-------CCccHHHHHHHHcC
Confidence 78999999999999999999999999876443 2478999 99999999975 35799999999999
Q ss_pred CcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---cchhhhcccCC-CcC-CCCCCccCCCCC
Q 013817 174 ISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS---CSSISELDSSN-LDL-GLKGILEKPDIG 248 (436)
Q Consensus 174 ~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l---~~~~~~~~~~~-~~~-~~~~~~~~~~~~ 248 (436)
+.++|+++.++|..|||+.+|+.|||.||++++.||+.|.++|++.|++ .+||..+.... ... +-..|.+ .
T Consensus 124 ~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~~~g~~~w~~ee~~~l~~~~~~~~~~~~~~~~----i 199 (367)
T TIGR01388 124 VELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLEESGRLAWLEEECTLLTDRRTYVVNPEDAWRD----I 199 (367)
T ss_pred CCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHhccccCCCChHHHHHH----h
Confidence 9999998999999999999999999999999999999999999999987 88999876532 111 1122322 3
Q ss_pred CCcccccchhHHHHHHHhhhccc------CCCCCcccccccCCCCCCchHHHHHHHhh
Q 013817 249 NKTVRFKLCEALDIIRATSYYSQ------CLPEGVVSRVSYLNTMPMDESLVKIVRKY 300 (436)
Q Consensus 249 ~~~~~~~~~~~~~~~~~~~~~~~------~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ 300 (436)
++..++ .+++|+++|+|+.-.. ++|++-| --|+.+..|+++-
T Consensus 200 ~~~~~l-~~~~l~~l~~L~~wRe~~A~~~d~p~~~i---------l~d~~l~~lA~~~ 247 (367)
T TIGR01388 200 KNAWQL-RPQQLAVLQALAAWREREARERDLPRNFV---------LKEEALWELARQA 247 (367)
T ss_pred cccccC-CHHHHHHHHHHHHHHHHHHHHcCCCccee---------eCHHHHHHHHHhC
Confidence 333334 4899999999944333 4444422 2367777777754
No 6
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=99.95 E-value=2.2e-27 Score=216.86 Aligned_cols=163 Identities=33% Similarity=0.531 Sum_probs=143.1
Q ss_pred hHHHHHHHHHhc-CCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhHHHHHH
Q 013817 19 SPEFTHLARALS-QSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLK 97 (436)
Q Consensus 19 ~~el~~l~~~L~-~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~ 97 (436)
..+++.+++.+. ...+||||+||.+.+.. ++.+++++||||+. +.+|+||+..+. .+...|+
T Consensus 4 ~~~~~~~~~~~~~~~~~ig~D~E~~~~~~~-~~~~~~~liQl~~~--------------~~~~l~~~~~~~--~~~~~l~ 66 (170)
T cd06141 4 AQDAEEAVKELLGKEKVVGFDTEWRPSFRK-GKRNKVALLQLATE--------------SRCLLFQLAHMD--KLPPSLK 66 (170)
T ss_pred HHHHHHHHHHHhcCCCEEEEeCccCCccCC-CCCCCceEEEEecC--------------CcEEEEEhhhhh--cccHHHH
Confidence 678899999998 99999999999987642 24679999999984 789999988753 3667899
Q ss_pred HhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcCCccc
Q 013817 98 ELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS 177 (436)
Q Consensus 98 ~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~ 177 (436)
++|+++++.||||++++|+..|.+.||+ . +.++|| +++++|++++. ....||++|++.+||..++
T Consensus 67 ~ll~~~~i~kv~~~~k~D~~~L~~~~g~---~-----~~~~~D-l~~aa~ll~~~------~~~~~l~~l~~~~l~~~~~ 131 (170)
T cd06141 67 QLLEDPSILKVGVGIKGDARKLARDFGI---E-----VRGVVD-LSHLAKRVGPR------RKLVSLARLVEEVLGLPLS 131 (170)
T ss_pred HHhcCCCeeEEEeeeHHHHHHHHhHcCC---C-----CCCeee-HHHHHHHhCCC------cCCccHHHHHHHHcCcccC
Confidence 9999999999999999999999877776 1 467899 89999999874 2347999999999999998
Q ss_pred --ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 013817 178 --KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (436)
Q Consensus 178 --K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~ 213 (436)
|..++|||..|||+++|+.|||.||++++.||+.|.
T Consensus 132 k~k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 132 KPKKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCCCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 788999999999999999999999999999999885
No 7
>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins. The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.
Probab=99.95 E-value=1.6e-27 Score=223.78 Aligned_cols=170 Identities=25% Similarity=0.327 Sum_probs=142.9
Q ss_pred HHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhHHHHHHHhhCCCC
Q 013817 25 LARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPD 104 (436)
Q Consensus 25 l~~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lLe~~~ 104 (436)
+++.|..+++||||+||.+.+. .+++||||||+. ++.+||||+..++...+...|+++|++++
T Consensus 3 ~~~~l~~~~~i~~D~E~~~~~~----~~~~~LiQia~~-------------~~~v~l~D~~~~~~~~~~~~L~~iLe~~~ 65 (197)
T cd06148 3 AIIHLKKQKVIGLDCEGVNLGR----KGKLCLVQIATR-------------TGQIYLFDILKLGSIVFINGLKDILESKK 65 (197)
T ss_pred hhhhhhhCCEEEEEcccccCCC----CCCEEEEEEeeC-------------CCcEEEEEhhhccchhHHHHHHHHhcCCC
Confidence 4567778999999999987653 468999999995 38999999998754346788999999999
Q ss_pred ceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCC-CCCCcCcccHHHHHHHHcCCcccc-----
Q 013817 105 ILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLG-RKLPKETKSLANICKELLDISLSK----- 178 (436)
Q Consensus 105 i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~-~~~~~~~~gL~~Lv~~~Lg~~l~K----- 178 (436)
|.||||++++|+..|.+.||+ . +.++|| |++|+|++++..+ ...+....||+++++++||.+++|
T Consensus 66 i~Kv~h~~k~D~~~L~~~~gi---~-----~~~~fD-t~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~ 136 (197)
T cd06148 66 ILKVIHDCRRDSDALYHQYGI---K-----LNNVFD-TQVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVK 136 (197)
T ss_pred ccEEEEechhHHHHHHHhcCc---c-----ccceee-HHHHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHH
Confidence 999999999999999776776 1 467899 9999999987521 111223479999999999999865
Q ss_pred ---cccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 013817 179 ---ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKG 220 (436)
Q Consensus 179 ---~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g 220 (436)
..+++||..|||+++|+.|||.||++++.||+.|...|.+..
T Consensus 137 ~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~~~~ 181 (197)
T cd06148 137 KLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALISKF 181 (197)
T ss_pred HHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhhhhH
Confidence 467899999999999999999999999999999999998763
No 8
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=99.94 E-value=9e-26 Score=205.14 Aligned_cols=174 Identities=29% Similarity=0.451 Sum_probs=150.7
Q ss_pred EEEEcCCChHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCch
Q 013817 11 IHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLP 90 (436)
Q Consensus 11 i~~V~t~~~~el~~l~~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~ 90 (436)
|++|++ .+++.+++..+...+++|||+||.+.... ....+++++|+++. ..+|+++.......
T Consensus 1 y~~v~~--~~~l~~~~~~l~~~~~~a~D~E~~~~~~~-~~~~~~~~iq~~~~--------------~~~~i~~~~~~~~~ 63 (176)
T PF01612_consen 1 YQIVDT--EEELEEAIKKLKNAKVLAFDTETTGLDPY-SYNPKIALIQLATG--------------EGCYIIDPIDLGDN 63 (176)
T ss_dssp SEEEHS--HHHHHHHHHHHTTTSEEEEEEEEETSTST-TSSEEEEEEEEEES--------------CEEEEECGTTSTTT
T ss_pred CEecCC--HHHHHHHHHHHcCCCeEEEEEEECCCCcc-ccCCeEEEEEEecC--------------CCceeeeecccccc
Confidence 578998 89999999999999999999999988753 24678999999984 78899887765532
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
.++..|+++|+++++.|||||+++|+..|.+.+|+ .+.+++| ++++++++++. ..+||++|+.+
T Consensus 64 ~~~~~l~~ll~~~~i~kv~~n~~~D~~~L~~~~~i--------~~~~~~D-~~l~~~~l~~~-------~~~~L~~L~~~ 127 (176)
T PF01612_consen 64 WILDALKELLEDPNIIKVGHNAKFDLKWLYRSFGI--------DLKNVFD-TMLAAYLLDPT-------RSYSLKDLAEE 127 (176)
T ss_dssp THHHHHHHHHTTTTSEEEESSHHHHHHHHHHHHTS----------SSEEE-HHHHHHHTTTS-------TTSSHHHHHHH
T ss_pred chHHHHHHHHhCCCccEEEEEEechHHHHHHHhcc--------ccCCccc-hhhhhhccccc-------ccccHHHHHHH
Confidence 36889999999999999999999999999987666 2578999 79999999975 23999999999
Q ss_pred HcC-CcccccccccCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 013817 171 LLD-ISLSKELQCSDWS-NRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (436)
Q Consensus 171 ~Lg-~~l~K~~q~sdW~-~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~ 217 (436)
++| ..++|..++++|. .+||+++|+.|||.||+++++||+.|.++|+
T Consensus 128 ~l~~~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l~ 176 (176)
T PF01612_consen 128 YLGNIDLDKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQLE 176 (176)
T ss_dssp HHSEEE-GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHHC
T ss_pred HhhhccCcHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 999 7788899999999 8999999999999999999999999998874
No 9
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=99.84 E-value=9.5e-20 Score=166.55 Aligned_cols=170 Identities=30% Similarity=0.483 Sum_probs=138.5
Q ss_pred HHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhHHHHHHHhhCC
Q 013817 23 THLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVS 102 (436)
Q Consensus 23 ~~l~~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lLe~ 102 (436)
..+++.+...+.+++|+|+.+..+ ..++++++|+++. +.+|+||+... .....|+++|++
T Consensus 3 ~~~~~~l~~~~~l~~~~e~~~~~~---~~~~~~~i~l~~~--------------~~~~~i~~~~~---~~~~~l~~ll~~ 62 (178)
T cd06142 3 EDLCERLASAGVIAVDTEFMRLNT---YYPRLCLIQISTG--------------GEVYLIDPLAI---GDLSPLKELLAD 62 (178)
T ss_pred HHHHHHHhcCCeEEEECCccCCCc---CCCceEEEEEeeC--------------CCEEEEeCCCc---ccHHHHHHHHcC
Confidence 444555555669999999865542 3467899999983 44888886532 256678999999
Q ss_pred CCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcCCcccccccc
Q 013817 103 PDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQC 182 (436)
Q Consensus 103 ~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~K~~q~ 182 (436)
+++.|||||+|.|++.|.+.||+ . .+++|| +++++|++++. .+++|++++++|||..+.+...+
T Consensus 63 ~~i~kv~~d~K~~~~~L~~~~gi-------~-~~~~~D-~~laayLl~p~-------~~~~l~~l~~~~l~~~~~~~~~~ 126 (178)
T cd06142 63 PNIVKVFHAAREDLELLKRDFGI-------L-PQNLFD-TQIAARLLGLG-------DSVGLAALVEELLGVELDKGEQR 126 (178)
T ss_pred CCceEEEeccHHHHHHHHHHcCC-------C-CCCccc-HHHHHHHhCCC-------ccccHHHHHHHHhCCCCCccccc
Confidence 99999999999999999887676 1 357899 99999999985 24699999999999987666678
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---cchhhh
Q 013817 183 SDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS---CSSISE 228 (436)
Q Consensus 183 sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l---~~~~~~ 228 (436)
++|..+|++.+|+.|||.||+++++|++.|.++|++.|.. ..||+.
T Consensus 127 ~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~e~~l~~L~~~~~~~ 175 (178)
T cd06142 127 SDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEEEGRLEWAEEECEL 175 (178)
T ss_pred ccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCcHHHHHHHHHH
Confidence 8999999999999999999999999999999999988765 555554
No 10
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=99.82 E-value=8.1e-21 Score=169.70 Aligned_cols=81 Identities=32% Similarity=0.400 Sum_probs=74.9
Q ss_pred CCCCCeEEEeCccHHHHHHHHhcCCceeecCCCCCChHHHHHHHhcCCcEEEecChhHHhhhcccCCcEEEEcCCChhhh
Q 013817 353 GDGYPKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQ 432 (436)
Q Consensus 353 ~~~~~~fl~D~~l~~la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ri~lT~d~~l~~~~~~~~~~~~~v~~~~~~~Q 432 (436)
.++.|+|+||.|||+||||||++||||+|.. ..+|.+++.+|.+|||||||||+.|++|+ +.|.++++|+++++.+|
T Consensus 3 ~~~~~kF~vD~mLG~LARwLRllGydt~~~~--~~~d~~i~~i~~~e~rIllTRDr~L~~r~-k~g~~~i~i~~~s~~~Q 79 (165)
T COG1656 3 PMGEMKFVVDAMLGKLARWLRLLGYDTVYSS--NESDDEIILIAKKEGRILLTRDRELYKRA-KLGIKAILIRSDSIEEQ 79 (165)
T ss_pred CccceeeeHHHhHHHHHHHHHHcCCceeeec--cCCcHHHHHHHhcCCeEEEeccHHHHHHh-hccCceEEEeCCCHHHH
Confidence 3678999999999999999999999999986 35888999999999999999999999998 66789999999999999
Q ss_pred hhcC
Q 013817 433 LLEV 436 (436)
Q Consensus 433 l~ev 436 (436)
+.|+
T Consensus 80 l~e~ 83 (165)
T COG1656 80 LAEF 83 (165)
T ss_pred HHHH
Confidence 9885
No 11
>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=99.81 E-value=3.2e-20 Score=166.63 Aligned_cols=77 Identities=34% Similarity=0.505 Sum_probs=71.8
Q ss_pred CeEEEeCccHHHHHHHHhcCCceeecCCCCCChHHHHHHHhcCCcEEEecChhHHhhhcccCCcEEEEcCCChhhhhhcC
Q 013817 357 PKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQLLEV 436 (436)
Q Consensus 357 ~~fl~D~~l~~la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ri~lT~d~~l~~~~~~~~~~~~~v~~~~~~~Ql~ev 436 (436)
||||||.|||+||||||++||||+|.. +.+|.+|+..|++|+|||||+|++|+++....++ ++++.++++.+||.||
T Consensus 1 ~rfl~D~~L~~Lar~LR~lG~Dt~~~~--~~~D~~il~~A~~e~RillTrd~~l~~~~~~~~~-~~li~~~~~~~QL~ev 77 (147)
T PF01927_consen 1 MRFLVDAMLGRLARWLRLLGYDTLYSR--DIDDDEILELAREEGRILLTRDRDLLKRRRVSGG-VILIRSDDPEEQLREV 77 (147)
T ss_pred CEEEEeCCHHHHHHHHHHCCCcEEEeC--CCChHHHHHHhhhCCeEEEECCHHHHHHhhccCC-EEEEcCCCHHHHHHHH
Confidence 799999999999999999999999997 5699999999999999999999999999887654 7899999999999985
No 12
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.79 E-value=1.1e-17 Score=150.80 Aligned_cols=169 Identities=32% Similarity=0.434 Sum_probs=132.8
Q ss_pred EEEcCCChHHHHHHHHHhc-CCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCch
Q 013817 12 HLVTSTESPEFTHLARALS-QSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLP 90 (436)
Q Consensus 12 ~~V~t~~~~el~~l~~~L~-~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~ 90 (436)
.+|++ .+++..++..+. ....+++|+|+.+... +.+.++++|++.. ++.+|+++.... .
T Consensus 2 ~~i~~--~~~~~~~~~~~~~~~~~l~~~~e~~~~~~---~~~~~~~l~l~~~-------------~~~~~i~~~~~~--~ 61 (172)
T smart00474 2 RVVTD--SETLEELLEKLRAAGGEVALDTETTGLNS---YSGKLVLIQISVT-------------GEGAFIIDPLAL--G 61 (172)
T ss_pred EEecC--HHHHHHHHHHHHhcCCeEEEeccccCCcc---CCCCEEEEEEeEc-------------CCceEEEEeccc--h
Confidence 56777 677777666665 5669999999876653 3467889999963 245676654322 2
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
.....|+++|+++++.|||||+|.|+..|.+ +|+ . +.++|| +++++|++++. ...++|+.+++.
T Consensus 62 ~~~~~l~~~l~~~~~~kv~~d~k~~~~~L~~-~gi-~-------~~~~~D-~~laayll~p~------~~~~~l~~l~~~ 125 (172)
T smart00474 62 DDLEILKDLLEDETITKVGHNAKFDLHVLAR-FGI-E-------LENIFD-TMLAAYLLLGG------PSKHGLATLLKE 125 (172)
T ss_pred hhHHHHHHHhcCCCceEEEechHHHHHHHHH-CCC-c-------ccchhH-HHHHHHHHcCC------CCcCCHHHHHHH
Confidence 3356789999999999999999999999986 666 1 345699 99999999875 233699999999
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKV 216 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L 216 (436)
++|..+++..+.++|..+|+..+|+.||+.||+++++|++.|.++|
T Consensus 126 ~l~~~~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 126 YLGVELDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred HhCCCCCcccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 9998876544556897788999999999999999999999998776
No 13
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=99.75 E-value=1.7e-18 Score=179.24 Aligned_cols=224 Identities=24% Similarity=0.333 Sum_probs=176.3
Q ss_pred EEEEcCCChHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCch
Q 013817 11 IHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLP 90 (436)
Q Consensus 11 i~~V~t~~~~el~~l~~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~ 90 (436)
.++|.+ ..++.++.+.+.....+|+|.|..+.. ++.+-.|||||+|. ..-|+||...+.
T Consensus 193 ~~~I~t--~~el~~l~~~l~~~~Efavdlehhsyr---sf~gltclmqISTr--------------~ed~iIDt~~l~-- 251 (687)
T KOG2206|consen 193 KVWICT--LGELEALPEILDSVIEFAVDLEHHSYR---SFLGLTCLMQISTR--------------TEDFIIDTFKLR-- 251 (687)
T ss_pred ceeeec--hHHHHHHHHHHhhhhhhhhhccccchh---hhcCceeEEEeecc--------------chhheehhHHHH--
Confidence 567887 788899999998888999999987665 37789999999996 567999987664
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
+....|.+.|.+|.|+||+|++..|+.+|++.||+ .+.++|| |--|..+++.+ .++|+.|.+.
T Consensus 252 ~~i~~l~e~fsdp~ivkvfhgaD~diiwlqrdfgi--------yvvnLfd-t~~a~r~L~~~--------r~sL~~ll~~ 314 (687)
T KOG2206|consen 252 DHIGILNEVFSDPGIVKVFHGADTDIIWLQRDFGI--------YVVNLFD-TIQASRLLGLP--------RPSLAYLLEC 314 (687)
T ss_pred HHHHHhhhhccCCCeEEEEecCccchhhhhccceE--------EEEechh-hHHHHHHhCCC--------cccHHHHHHH
Confidence 35668999999999999999999999999999988 2578999 99999999864 8999999999
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC----cchhhhcccCC---CcCCCCCCcc
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS----CSSISELDSSN---LDLGLKGILE 243 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l----~~~~~~~~~~~---~~~~~~~~~~ 243 (436)
+.|+..+|..|..+|..|||+++++.||-.|.++++.||+.|+..|.+.+.- -.|-..+.... ..+..+..++
T Consensus 315 ~~~v~~nk~yqladwR~rpLp~~Mv~yar~dthyllyiyD~lr~el~~~a~~~~~~~~~~~d~c~~~~~k~~~~~~sy~~ 394 (687)
T KOG2206|consen 315 VCGVLTNKKYQLADWRIRPLPEEMVRYAREDTHYLLYIYDVLRKELKRLAKGRAVTYSESRDMCTNGYKKKTFCTKSYLE 394 (687)
T ss_pred HHhhhhhhhhhhchhccccCcHHHHHHHhhcchhHHHHHHHHHHHHHHHhcccccccchhhhhhhcceecccCCCcchHh
Confidence 9999999999999999999999999999999999999999999888876632 11111111111 1122222222
Q ss_pred CCCCCCCcccccchhHHHHHHHhhhcccCCCCC
Q 013817 244 KPDIGNKTVRFKLCEALDIIRATSYYSQCLPEG 276 (436)
Q Consensus 244 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~ 276 (436)
..+.-.. =-++|+.++|+|=.-.+.|+.+
T Consensus 395 v~~~q~~----ln~~q~~~l~~L~~wRd~iARa 423 (687)
T KOG2206|consen 395 VEDIQSR----LNSSQLDVLRALLRWRDFIARA 423 (687)
T ss_pred HHHHHhc----cchhHHHHHHHHHHHHHHHHhh
Confidence 2222122 2378999999996666666655
No 14
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=99.74 E-value=2.2e-16 Score=147.28 Aligned_cols=175 Identities=25% Similarity=0.398 Sum_probs=134.1
Q ss_pred CccEEEEcCCChHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCC
Q 013817 8 PLKIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSI 87 (436)
Q Consensus 8 ~~~i~~V~t~~~~el~~l~~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l 87 (436)
..+|.+|++ ++++..+++.+...+.+++++|+.+..+ ..+.+..+|++.. +++|+|++..
T Consensus 2 ~~~~~~i~~--~~~l~~~~~~l~~~~~l~~~~e~~~~~~---~~~~~~~l~l~~~--------------~~~~~i~~l~- 61 (192)
T cd06147 2 ETPLTFVDT--EEKLEELVEKLKNCKEIAVDLEHHSYRS---YLGFTCLMQISTR--------------EEDYIVDTLK- 61 (192)
T ss_pred CCCcEEECC--HHHHHHHHHHHhcCCeEEEEeEecCCcc---CCCceEEEEEecC--------------CCcEEEEecc-
Confidence 356788866 5667776666655568999998754432 2457788888874 3477777422
Q ss_pred CchhHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHH
Q 013817 88 PLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANI 167 (436)
Q Consensus 88 ~~~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~L 167 (436)
.......|+++|+++++.||+||+|.++..|.+.+|+ . ..++|| ++|++||++++ +++|+.+
T Consensus 62 -~~~~~~~L~~~L~~~~i~kv~~d~K~~~~~L~~~~gi---~-----~~~~fD-~~laaYLL~p~--------~~~l~~l 123 (192)
T cd06147 62 -LRDDMHILNEVFTDPNILKVFHGADSDIIWLQRDFGL---Y-----VVNLFD-TGQAARVLNLP--------RHSLAYL 123 (192)
T ss_pred -cccchHHHHHHhcCCCceEEEechHHHHHHHHHHhCC---C-----cCchHH-HHHHHHHhCCC--------cccHHHH
Confidence 2234566899999999999999999999999734555 1 233499 99999999984 3599999
Q ss_pred HHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 013817 168 CKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKG 220 (436)
Q Consensus 168 v~~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g 220 (436)
+++||+..+.|..+.++|+.+||..+|..||+.+|.++++|++.|.++|+++.
T Consensus 124 ~~~yl~~~~~k~~~~~~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~L~e~~ 176 (192)
T cd06147 124 LQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELLERA 176 (192)
T ss_pred HHHHhCCCcchhhhccccccCCCCHHHHHHHHhhHHHHHHHHHHHHHHHHHhc
Confidence 99999987545456678988888999999999999999999999999998763
No 15
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.71 E-value=1.7e-17 Score=172.97 Aligned_cols=196 Identities=31% Similarity=0.489 Sum_probs=149.3
Q ss_pred CCCCCccEEEEcCCChHHHHHHH-HHhcCC-CeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEE
Q 013817 4 TYRKPLKIHLVTSTESPEFTHLA-RALSQS-SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFL 81 (436)
Q Consensus 4 ~~~~~~~i~~V~t~~~~el~~l~-~~L~~~-~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~l 81 (436)
.|+....|++|.+ +.++..++ +.+... ..||+|+||.+.-. ....+++++|+++ ++.+||
T Consensus 385 ~~~~~~~i~~V~~--e~El~~l~l~~l~~e~~yVGiDsEwkps~~--v~dsk~~IlQif~--------------~~~v~L 446 (617)
T KOG2207|consen 385 EPPWVESIGMVGN--EKELRDLLLESLSEELRYVGIDSEWKPSKK--VSDSKLAILQIFF--------------KDCVYL 446 (617)
T ss_pred CCCcccceeeeCC--HHHHHHHHHHHhhhcCEEEEEccccCcccC--CChhHHHHHHHHh--------------cCeEEE
Confidence 3566677899998 88888876 456655 78999999998722 2457899999999 489999
Q ss_pred EeCCCCCc--hhHHH-HHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccC-CCCC
Q 013817 82 LDLSSIPL--PSIWE-LLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQL-GRKL 157 (436)
Q Consensus 82 iD~~~l~~--~~~~~-~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~-~~~~ 157 (436)
||+..+.. .+.|. .+..+|+++++.|||+++.+|+..|.++.+.+...-.++.+++++++..++..+.+-.. ....
T Consensus 447 idc~~l~~~~se~w~~~~s~if~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~ 526 (617)
T KOG2207|consen 447 IDCVKLENLASEIWHLLLSQIFESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENL 526 (617)
T ss_pred eehHHhhhchHHHHHHHHHHHccCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhh
Confidence 99876542 34444 45679999999999999999999998533310000011234566666777777665321 1122
Q ss_pred CcCcccHHHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 013817 158 PKETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (436)
Q Consensus 158 ~~~~~gL~~Lv~~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~ 217 (436)
+....+|+.|...+||..++|.++||||..|||+..|+.|||.||.++..+|..+....+
T Consensus 527 ~~~~~~L~~Lt~~llg~~lnKteqcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv~ 586 (617)
T KOG2207|consen 527 NEATKGLADLTDCLLGKKLNKTEQCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVVE 586 (617)
T ss_pred cchhhhhhhhhHHHhhhhcccccccchhhcCCchhhHHHHHHhcchhhHHHHHHHHhhcc
Confidence 344789999999999999999999999999999999999999999999999999986554
No 16
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=99.66 E-value=3.3e-15 Score=132.03 Aligned_cols=149 Identities=28% Similarity=0.310 Sum_probs=113.6
Q ss_pred eEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhHHHHHHHhhCCCCceEEEEehH
Q 013817 34 LVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFK 113 (436)
Q Consensus 34 ~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lLe~~~i~KVgh~~k 113 (436)
.+++|+|+.+... ..++++++|+++. +.+++++... ....+.+.|+++|+++.+.|||||++
T Consensus 2 ~l~~d~e~~~~~~---~~~~i~~~~l~~~--------------~~~~~i~~~~-~~~~~~~~l~~~l~~~~~~~v~~~~k 63 (155)
T cd00007 2 EVAFDTETTGLNY---HRGKLVGIQIATA--------------GEAAYIPDEL-ELEEDLEALKELLEDEDITKVGHDAK 63 (155)
T ss_pred ceEEEEecCCCCc---CCCeEEEEEEEEC--------------CcEEEEEcCC-CHHHHHHHHHHHHcCCCCcEEeccHH
Confidence 5799999866552 3468899999983 2244443221 12346677999999999999999999
Q ss_pred HhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcCCcccccccccCCC----CCC
Q 013817 114 QDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWS----NRP 189 (436)
Q Consensus 114 ~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~K~~q~sdW~----~RP 189 (436)
+|+..|.+. ++ ....+++| |++++|++++. ..+++|++|+++|++..+.+..+..+|. .+|
T Consensus 64 ~d~~~L~~~-~~-------~~~~~~~D-~~~~ayll~~~------~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~ 128 (155)
T cd00007 64 FDLVVLARD-GI-------ELPGNIFD-TMLAAYLLNPG------EGSHSLDDLAKEYLGIELDKDEQIYGKGAKTFARP 128 (155)
T ss_pred HHHHHHHHC-CC-------CCCCCccc-HHHHHHHhCCC------CCcCCHHHHHHHHcCCCCccHHHHhcCCCCccccC
Confidence 999999875 22 12467899 99999999986 2156999999999998865433345552 578
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHH
Q 013817 190 LTEEQKNYAAIDAHCLIEIFNIFQVK 215 (436)
Q Consensus 190 L~~~ql~YAA~DA~~Ll~L~~~L~~~ 215 (436)
++.+|..||+.||.++++|++.|.++
T Consensus 129 ~~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 129 LSEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 89999999999999999999999754
No 17
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=99.65 E-value=3.8e-15 Score=132.05 Aligned_cols=147 Identities=27% Similarity=0.265 Sum_probs=112.7
Q ss_pred eEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhHHHHHHHhhCCCCceEEEEehH
Q 013817 34 LVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFK 113 (436)
Q Consensus 34 ~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lLe~~~i~KVgh~~k 113 (436)
++++|+|+.+..+ ...+++++|++.. ++.+|+|++.... -....|+++|+++++.|++||+|
T Consensus 1 ~~~~~~e~~~~~~---~~~~~~~l~l~~~-------------~~~~~~i~~~~~~--~~~~~l~~~l~~~~~~kv~~d~K 62 (150)
T cd09018 1 VFAFDTETDSLDN---ISANLVLIQLAIE-------------PGVAALIPVAHDY--LALELLKPLLEDEKALKVGQNLK 62 (150)
T ss_pred CEEEEeecCCCCC---CCceEEEEEEEcC-------------CCcEEEEEcCCcc--cCHHHHHHHhcCCCCceeeecHH
Confidence 4789998866553 3468899999984 2447888754311 12556899999999999999999
Q ss_pred HhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcCCcccc-cc-cccCCCCCCCC
Q 013817 114 QDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSK-EL-QCSDWSNRPLT 191 (436)
Q Consensus 114 ~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~K-~~-q~sdW~~RPL~ 191 (436)
.|+..|.+. |+ ...+++|| +++|+||+++. ..+.+|+.|+++||+..+.+ .. ..++|..++++
T Consensus 63 ~~~~~L~~~-~~-------~~~~~~~D-~~laayLl~p~------~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~ 127 (150)
T cd09018 63 YDRGILLNY-FI-------ELRGIAFD-TMLEAYILNSV------AGRWDMDSLVERWLGHKLIKFESIAGKLWFNQPLT 127 (150)
T ss_pred HHHHHHHHc-CC-------ccCCcchh-HHHHHHHhCCC------CCCCCHHHHHHHHhCCCcccHHHhcCCCCcccCCH
Confidence 999999764 43 12467899 99999999985 21459999999999988654 21 12248557889
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 013817 192 EEQKNYAAIDAHCLIEIFNIFQ 213 (436)
Q Consensus 192 ~~ql~YAA~DA~~Ll~L~~~L~ 213 (436)
.+|+.||+.||+++++|++.|.
T Consensus 128 ~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 128 EEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999875
No 18
>PRK05755 DNA polymerase I; Provisional
Probab=99.63 E-value=1.2e-14 Score=164.11 Aligned_cols=181 Identities=18% Similarity=0.214 Sum_probs=144.1
Q ss_pred CCCccEEEEcCCChHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCC
Q 013817 6 RKPLKIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLS 85 (436)
Q Consensus 6 ~~~~~i~~V~t~~~~el~~l~~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~ 85 (436)
.+.+.|.+|++ .+++..+++.+.....++||+|+.+..+ +.++++++|++.. ++.+|+|++.
T Consensus 291 ~~~~~~~~I~~--~~~L~~~l~~l~~~~~~a~DtEt~~l~~---~~~~i~~i~ls~~-------------~g~~~~ip~~ 352 (880)
T PRK05755 291 LDEEDYETILD--EEELEAWLAKLKAAGLFAFDTETTSLDP---MQAELVGLSFAVE-------------PGEAAYIPLD 352 (880)
T ss_pred CCCCceEEeCC--HHHHHHHHHHhhccCeEEEEeccCCCCc---ccccEEEEEEEeC-------------CCcEEEEecc
Confidence 34456788887 7889999988888899999999988774 5688999999875 3558888875
Q ss_pred CCCchhHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHH
Q 013817 86 SIPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLA 165 (436)
Q Consensus 86 ~l~~~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~ 165 (436)
.++. ..+..|.++|+++.+.||+||+++|+..|.+ +|+ . ...++|| |++++|+++++ . .++|+
T Consensus 353 ~i~~-~~l~~l~~~L~d~~v~kV~HNakfDl~~L~~-~gi---~----~~~~~~D-T~iAa~Ll~~~------~-~~~L~ 415 (880)
T PRK05755 353 QLDR-EVLAALKPLLEDPAIKKVGQNLKYDLHVLAR-YGI---E----LRGIAFD-TMLASYLLDPG------R-RHGLD 415 (880)
T ss_pred cccH-HHHHHHHHHHhCCCCcEEEeccHhHHHHHHh-CCC---C----cCCCccc-HHHHHHHcCCC------C-CCCHH
Confidence 4432 4678899999999999999999999999987 454 1 1367999 99999999986 2 38999
Q ss_pred HHHHHHcCCcccccc----cccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 013817 166 NICKELLDISLSKEL----QCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (436)
Q Consensus 166 ~Lv~~~Lg~~l~K~~----q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l 222 (436)
+|+++|+|.++.... ...+|+..|+ +.+..||+.||.++++||..|.++|.+.+.+
T Consensus 416 ~L~~~ylg~~~~~~~~~~gk~~~~~~~pl-e~~~~YAa~Dv~~~~~L~~~L~~~L~~~~~l 475 (880)
T PRK05755 416 SLAERYLGHKTISFEEVAGKQLTFAQVDL-EEAAEYAAEDADVTLRLHEVLKPKLLEEPGL 475 (880)
T ss_pred HHHHHHhCCCccchHHhcCCCCCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHHhcccH
Confidence 999999998853211 2234555577 5789999999999999999999999876443
No 19
>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases. Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Probab=99.55 E-value=1.2e-13 Score=126.57 Aligned_cols=157 Identities=17% Similarity=0.131 Sum_probs=118.1
Q ss_pred CCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhHHHHHHHhhCCCCceEEEEe
Q 013817 32 SSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFK 111 (436)
Q Consensus 32 ~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lLe~~~i~KVgh~ 111 (436)
...+++++|.....+ ..++++.++++.. +++|+|++... ......|+++|+++++.|++||
T Consensus 3 ~~~~~~~~~~~~~~~---~~~~l~~i~l~~~--------------~~~~~i~~~~~--~~~~~~l~~~l~~~~~~ki~~d 63 (178)
T cd06140 3 ADEVALYVELLGENY---HTADIIGLALANG--------------GGAYYIPLELA--LLDLAALKEWLEDEKIPKVGHD 63 (178)
T ss_pred CCceEEEEEEcCCCc---ceeeEEEEEEEeC--------------CcEEEEeccch--HHHHHHHHHHHhCCCCceeccc
Confidence 356788998876553 3467777778763 35777774321 0135568899999999999999
Q ss_pred hHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcCCcccccccccCCC---CC
Q 013817 112 FKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWS---NR 188 (436)
Q Consensus 112 ~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~K~~q~sdW~---~R 188 (436)
+|.|++.|.+ +|+ . ....+|| |+||+||++++ ...+++++++.+||+..+.+..+.+.|. .+
T Consensus 64 ~K~~~~~l~~-~gi---~----~~~~~fD-t~laaYLL~p~------~~~~~l~~l~~~yl~~~~~~~~~~~~~~~~~~~ 128 (178)
T cd06140 64 AKRAYVALKR-HGI---E----LAGVAFD-TMLAAYLLDPT------RSSYDLADLAKRYLGRELPSDEEVYGKGAKFAV 128 (178)
T ss_pred hhHHHHHHHH-CCC---c----CCCcchh-HHHHHHHcCCC------CCCCCHHHHHHHHcCCCCcchHHhcCCCCCccc
Confidence 9999999976 454 1 2356799 99999999986 2347999999999998875533344442 24
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 013817 189 PLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (436)
Q Consensus 189 PL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l 222 (436)
+....+..|++.||.++++|++.|.++|++++.+
T Consensus 129 ~~~~~~~~y~~~~a~~l~~l~~~l~~~L~~~~l~ 162 (178)
T cd06140 129 PDEEVLAEHLARKAAAIARLAPKLEEELEENEQL 162 (178)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHH
Confidence 4467788999999999999999999999987654
No 20
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=99.46 E-value=3.2e-12 Score=118.15 Aligned_cols=159 Identities=21% Similarity=0.337 Sum_probs=116.6
Q ss_pred cCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC------CCchhHHHHHHHhhCCC
Q 013817 30 SQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS------IPLPSIWELLKELFVSP 103 (436)
Q Consensus 30 ~~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~------l~~~~~~~~L~~lLe~~ 103 (436)
.+.+.+++|+|..+..+ +..++..++++.. .+.+|+++... .........|+++|++.
T Consensus 3 ~~~~~~a~d~e~~~~~~---~~~~i~~l~~~~~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~ 66 (193)
T cd06139 3 EKAKVFAFDTETTSLDP---MQAELVGISFAVE-------------PGEAYYIPLGHDYGGEQLPREEVLAALKPLLEDP 66 (193)
T ss_pred ccCCeEEEEeecCCCCc---CCCeEEEEEEEcC-------------CCCEEEEecCCCccccCCCHHHHHHHHHHHHhCC
Confidence 35678999998766553 3457777777764 23366665432 12234566688999998
Q ss_pred CceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcCCccc------
Q 013817 104 DILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS------ 177 (436)
Q Consensus 104 ~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~------ 177 (436)
.+.+|+||+++|+..|.+ +|+ . ....++| |++++|+++++ ...++|.+++++++|....
T Consensus 67 ~~~~v~hn~k~d~~~l~~-~gi---~----~~~~~~D-t~l~a~ll~p~------~~~~~l~~l~~~~l~~~~~~~~~~~ 131 (193)
T cd06139 67 SIKKVGQNLKFDLHVLAN-HGI---E----LRGPAFD-TMLASYLLNPG------RRRHGLDDLAERYLGHKTISFEDLV 131 (193)
T ss_pred CCcEEeeccHHHHHHHHH-CCC---C----CCCCccc-HHHHHHHhCCC------CCCCCHHHHHHHHhCCCCccHHHHc
Confidence 889999999999999987 454 1 2356899 99999999986 2257999999999987621
Q ss_pred -ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh-cC
Q 013817 178 -KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ-KG 220 (436)
Q Consensus 178 -K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~-~g 220 (436)
|+.+..+|...|+ ..+..||+.||.++++|++.|.++|++ .+
T Consensus 132 ~k~~~~~~~~~~~~-~~~~~ya~~d~~~~~~l~~~l~~~l~~~~~ 175 (193)
T cd06139 132 GKGKKQITFDQVPL-EKAAEYAAEDADITLRLYELLKPKLKEEPG 175 (193)
T ss_pred CCCcCcCCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 2223445654444 668999999999999999999999987 54
No 21
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.39 E-value=1.8e-12 Score=139.56 Aligned_cols=146 Identities=22% Similarity=0.211 Sum_probs=119.6
Q ss_pred cEEEEcCCChHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCc
Q 013817 10 KIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPL 89 (436)
Q Consensus 10 ~i~~V~t~~~~el~~l~~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~ 89 (436)
.+.+|.+ .+++..++..+...+.+++|+|+....+ .++++|++. ++.+|+||+...
T Consensus 2 ~~~~I~~--~~~l~~~~~~l~~~~~~a~DtEf~r~~t------~l~liQ~~~--------------~~~~~liDpl~~-- 57 (553)
T PRK14975 2 DMKVILA--PEELGAALERLSPAGVVAGDTETTGDDA------AAAAAQEGE--------------EEPRWVWASTAA-- 57 (553)
T ss_pred CceEEec--cchhHHHHHHhccCCceeCCccccCCcc------hhheeeecC--------------CCceEEECchHH--
Confidence 4567887 7889999999999999999999876552 789999987 378999997531
Q ss_pred hhHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHH
Q 013817 90 PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (436)
Q Consensus 90 ~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~ 169 (436)
+.+ + |.+ +|+ . +.++|| |+||+|+++++.+ ...+|++.+++
T Consensus 58 ---l~~---~-------------------L~~-~Gv---~-----~~~~fD-T~LAa~lL~~~~~----~~~~~l~~la~ 98 (553)
T PRK14975 58 ---LYP---R-------------------LLA-AGV---R-----VERCHD-LMLASQLLLGSEG----RAGSSLSAAAA 98 (553)
T ss_pred ---hHH---H-------------------HHH-CCC---c-----cCCCch-HHHHHHHcCCCCC----cCCCCHHHHHH
Confidence 111 1 434 344 2 456999 9999999998511 01589999999
Q ss_pred HHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 013817 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (436)
Q Consensus 170 ~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~ 219 (436)
.+|++.++|..+.++|. ||++++|+.||+.||.+++.||+.|.++|++.
T Consensus 99 ~~l~~~l~k~~~~sdw~-rpls~~q~~YAa~Dv~~l~~L~~~L~~qL~~~ 147 (553)
T PRK14975 99 RALGEGLDKPPQTSALS-DPPDEEQLLYAAADADVLLELYAVLADQLNRI 147 (553)
T ss_pred HHhCCCCCChhhhcccc-ccchHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Confidence 99999999988889997 99999999999999999999999999999876
No 22
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.14 E-value=1.7e-12 Score=135.91 Aligned_cols=275 Identities=29% Similarity=0.317 Sum_probs=195.9
Q ss_pred CCceeeHHH--HHHHhhcccCCCCCCcC-cc---cHHHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHH-
Q 013817 135 VEPYLDITS--IYNHLHHKQLGRKLPKE-TK---SLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIE- 207 (436)
Q Consensus 135 ~~~v~Dlt~--La~yLl~~~~~~~~~~~-~~---gL~~Lv~~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~- 207 (436)
...++|++. +..||-+..++...+.. .. +--++.+..+..-+.+..++++|..+++++.|..|+...+.++..
T Consensus 154 ~~~~~Di~l~~i~e~lq~~~f~e~a~~~ik~~l~~~~~~e~~~ldlIls~k~q~a~~ll~~~~~~q~p~v~fld~~v~~~ 233 (617)
T KOG2207|consen 154 LKQTLDITLCKIDEYLQNQRFGEAAPKAIKSLLLSDNAFEQLMLDLILSKKLQIADELLRHLTELQKPYVEFLDQMVLDN 233 (617)
T ss_pred hhhhHhHhcchhHHHHHhHHHHHHHHHHHHhhhhhhhhHHHHhccHhhccchhHHHHHHhhhhhhhhhHHHHHHHHHHHH
Confidence 346788776 77777665443222211 11 112345555666667888999999999999999999999999999
Q ss_pred -HHHHHHHHHHhc-----CCCcchhhhcc-cCCCcCCCCCCccCCCCCCCcccccchhHHHHHHHhhhcccCCCCCcccc
Q 013817 208 -IFNIFQVKVAQK-----GNSCSSISELD-SSNLDLGLKGILEKPDIGNKTVRFKLCEALDIIRATSYYSQCLPEGVVSR 280 (436)
Q Consensus 208 -L~~~L~~~L~~~-----g~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~ 280 (436)
..+.+.+.+.+. -.+..-+..+- .+..-.+-.. ...+++.+...++++...+...+.++++....++.
T Consensus 234 ~~v~e~~~~~~e~~~~~~~tl~~~v~~i~~rn~~~~~f~~-----~~~~n~v~~~~~kal~~~~~~~e~~~~~~~~f~~~ 308 (617)
T KOG2207|consen 234 FIVDERCAHLLERTINLPKTLTILVQEIINRNQKKYTFSD-----EYAKNYVQNKNCKALHYIRSEREKGQMADKGFVQH 308 (617)
T ss_pred HHHHHHHHHHHhhccCCCchhhhhHHHHHhccchhhhhhh-----hhhhhHhhcccHHHHHHHHHHhhhhhhHHHhhchh
Confidence 777777666654 11111111111 1111111111 35677788899999999999999999988888888
Q ss_pred cccCCCCCCchHHHHHHHhhc---cccccccccCCC-Cc----ccccccCCCCc-----chhhhhcccccCCCCCCCCCC
Q 013817 281 VSYLNTMPMDESLVKIVRKYG---EKILLRECDKAP-KT----SKKKGRKRSSV-----IVDSREKRLDDIGDWQGPPPW 347 (436)
Q Consensus 281 ~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~-~~----~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~p~ 347 (436)
.-+-.|.|+|+++++++.+.| |+|.+...+.-+ |. -+++-.++... .....+.++.++..|+.+|||
T Consensus 309 ~~~~~t~~~d~~~lkyLw~~~~~iEai~~~~~~~i~~~d~~~el~~~~s~~~~~k~~~~~~~~~~~pl~~~~~~~~~~~~ 388 (617)
T KOG2207|consen 309 VVETKTKPDDENLLKYLWSFGEHIEAIYLATYDNIDPKDDAKELEKRTSRRGAGKTLFNQRMTTNVPLVCEDLFLFEPPW 388 (617)
T ss_pred heeecccccchhHHHHHHHHHHhhhhhhhhhhhcCCCchhHHHHhchhhhcccChhhhhcccccccCccchhhhccCCCc
Confidence 889999999999999999999 888888876442 21 11111111112 225567789999999999999
Q ss_pred CCCCCCCCCCeEEEeCccHHHHHHHHhcCCceeecCCCCCCh-HHHHHHHhcCCcEEEecChhHHhhh
Q 013817 348 DLSLGGDGYPKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEP-RELIDQTSKEKRVLLTRDAKLLRHQ 414 (436)
Q Consensus 348 ~~~~~~~~~~~fl~D~~l~~la~~LR~~G~d~~~~~~~~~~~-~~~~~~a~~e~ri~lT~d~~l~~~~ 414 (436)
+.+.+..+..+++-|.|+++|.+.+|..|||+.|..+.+..| +..+-++-.+++|.|+...++.+.+
T Consensus 389 ~~~i~~V~~e~El~~l~l~~l~~e~~yVGiDsEwkps~~v~dsk~~IlQif~~~~v~Lidc~~l~~~~ 456 (617)
T KOG2207|consen 389 VESIGMVGNEKELRDLLLESLSEELRYVGIDSEWKPSKKVSDSKLAILQIFFKDCVYLIDCVKLENLA 456 (617)
T ss_pred ccceeeeCCHHHHHHHHHHHhhhcCEEEEEccccCcccCCChhHHHHHHHHhcCeEEEeehHHhhhch
Confidence 999999999999999999999999999999999988633333 3344455579999999998887643
No 23
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=99.14 E-value=3.3e-10 Score=120.67 Aligned_cols=170 Identities=18% Similarity=0.190 Sum_probs=124.0
Q ss_pred hHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCC-chhHHHHHH
Q 013817 19 SPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIP-LPSIWELLK 97 (436)
Q Consensus 19 ~~el~~l~~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~-~~~~~~~L~ 97 (436)
.+.+..+...+...+.+++|+|..+..+ ...+++.++... +..++++....-+ .-.....|+
T Consensus 9 ~~~~~~~~~~~~~~~~~a~~~et~~l~~-----~~~~lvg~s~~~------------~~~~~yi~~~~~~~~~~~~~~l~ 71 (593)
T COG0749 9 LAVLNAWLTKLNAAANIAFDTETDGLDP-----HGADLVGLSVAS------------EEEAAYIPLLHGPEQLNVLAALK 71 (593)
T ss_pred HHHHHHHHHHHhhcccceeeccccccCc-----ccCCeeEEEeec------------cccceeEeeccchhhhhhHHHHH
Confidence 4555666666665555999999988875 355677776651 2245555443211 113678899
Q ss_pred HhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcCCccc
Q 013817 98 ELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS 177 (436)
Q Consensus 98 ~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~ 177 (436)
+||+++.+.|+|||.|.|.+.|.+. |+ . ....|| |||++|+++++ ...+++++|++++++....
T Consensus 72 ~~l~~~~~~kv~~~~K~d~~~l~~~-Gi-------~-~~~~~D-tmlasYll~~~------~~~~~~~~l~~r~l~~~~~ 135 (593)
T COG0749 72 PLLEDEGIKKVGQNLKYDYKVLANL-GI-------E-PGVAFD-TMLASYLLNPG------AGAHNLDDLAKRYLGLETI 135 (593)
T ss_pred HHhhCcccchhccccchhHHHHHHc-CC-------c-ccchHH-HHHHHhccCcC------cCcCCHHHHHHHhcCCccc
Confidence 9999999999999999999999985 43 1 367899 99999999987 3579999999999998764
Q ss_pred ccc-------cccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 013817 178 KEL-------QCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (436)
Q Consensus 178 K~~-------q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l 222 (436)
... +.-+...-++ +....|+|.||.++++|+..|.+++.+...+
T Consensus 136 ~~~~i~~kg~~~~~~~~~~~-~~~~~y~a~~a~~~~~L~~~l~~~l~~~~~L 186 (593)
T COG0749 136 TFEDIAGKGKKQLTFADVKL-EKATEYAAEDADATLRLESILEPELLKTPVL 186 (593)
T ss_pred hhHHhhccccccCccccchH-HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhH
Confidence 322 1112222222 4568999999999999999999988877653
No 24
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.12 E-value=2.8e-09 Score=120.06 Aligned_cols=172 Identities=13% Similarity=0.047 Sum_probs=115.2
Q ss_pred EEEEcCCChHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCC-CEEEEEeCC---C
Q 013817 11 IHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNA-SVVFLLDLS---S 86 (436)
Q Consensus 11 i~~V~t~~~~el~~l~~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~-~~v~liD~~---~ 86 (436)
+..|.+ .+++..+++. ...+.+++ .+..+ ....+..+.+++. . +.+|+++.. .
T Consensus 304 ~~~~~~--~~~~~~~~~~-~~~~~~~~----~~~~~---~~~~~~~~~~~~~-------------~~~~~~~~~~~~~~~ 360 (887)
T TIGR00593 304 AKESEE--AAPLANPAEK-AEVGGFVL----ERLLD---QLKKALALAFATE-------------NQSYVAYASEADGIP 360 (887)
T ss_pred ceEeCC--HHHHHHHHHh-CcCCeEEE----cCccc---ccCceeEEEEEec-------------CCCceEEEecccchh
Confidence 445655 5667776655 44556777 22221 1234444445543 2 336666532 1
Q ss_pred CCchhHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHH
Q 013817 87 IPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLAN 166 (436)
Q Consensus 87 l~~~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~ 166 (436)
+......+.|+++|+++.+.|||||+|+|+..|.+ +|+ . ....+|| |||++||++++ ..++|++
T Consensus 361 ~~~~~~~~~l~~~l~~~~~~~v~~n~K~d~~~l~~-~gi---~----~~~~~~D-t~la~yll~~~-------~~~~l~~ 424 (887)
T TIGR00593 361 LLTILTDDKFARWLLNEQIKKIGHDAKFLMHLLKR-EGI---E----LGGVIFD-TMLAAYLLDPA-------QVSTLDT 424 (887)
T ss_pred hhhHHHHHHHHHHHhCCCCcEEEeeHHHHHHHHHh-CCC---C----CCCcchh-HHHHHHHcCCC-------CCCCHHH
Confidence 12234566799999999999999999999999987 455 2 1346899 99999999985 2469999
Q ss_pred HHHHHcCCcccccccccCC--CCCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 013817 167 ICKELLDISLSKELQCSDW--SNRPLT-EEQKNYAAIDAHCLIEIFNIFQVKVAQKGN 221 (436)
Q Consensus 167 Lv~~~Lg~~l~K~~q~sdW--~~RPL~-~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~ 221 (436)
++.+||+..+.+......| ....++ +.+..||+.||.++++||..|.++|.+.+.
T Consensus 425 la~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~~~~l 482 (887)
T TIGR00593 425 LARRYLVEELILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKELDENKL 482 (887)
T ss_pred HHHHHcCcccccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhccH
Confidence 9999999775442222111 111343 456789999999999999999999987654
No 25
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=98.84 E-value=1.6e-08 Score=99.83 Aligned_cols=148 Identities=24% Similarity=0.255 Sum_probs=112.6
Q ss_pred CeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhHHHHHHHhhCCCCceEEEEeh
Q 013817 33 SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKF 112 (436)
Q Consensus 33 ~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lLe~~~i~KVgh~~ 112 (436)
..+..+.||.+...+++..+.+..+||+.. ++.++|+.+.... .++..|+.+|+|++.++||.+.
T Consensus 128 ~~~~~~~e~~~~~d~~~~~P~~~~lqlcV~-------------en~C~I~ql~~~~--~IP~~LR~fl~D~~~~~vgv~~ 192 (319)
T KOG4373|consen 128 PFVCYRREAQPYLDMGRSDPPPDTLQLCVG-------------ENRCLIIQLIHCK--RIPHELRSFLEDPDHTFVGVWN 192 (319)
T ss_pred cceeecccccccccccccCCCcchhhhhhc-------------ccceeeEEeeccc--cchHHHHHhhcCCCceEEeccc
Confidence 456677777777655555677899999995 4788888665443 3678888899999999999999
Q ss_pred HHhHHHHHh-hcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcC-----CcccccccccCCC
Q 013817 113 KQDLIYLSS-TFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLD-----ISLSKELQCSDWS 186 (436)
Q Consensus 113 k~Dl~~L~~-~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg-----~~l~K~~q~sdW~ 186 (436)
++|...|.+ .|+. .+..+.||..+..-.++.+ ..+-+...|++..+| +.+++..+++||+
T Consensus 193 d~D~~KL~r~~hql--------~I~~~~dlr~~~~d~~g~~------~~~~s~e~i~~~~~~~~~~~v~l~~~i~msdw~ 258 (319)
T KOG4373|consen 193 DQDAGKLERKEHQL--------EIGELEDLRLLVNDSLGGS------MPNDSFEEIVSETLGYYGKDVRLDKEIRMSDWS 258 (319)
T ss_pred cccHHHHhhhhhcc--------cHHhhhhHHhhcchhhccC------ccCccHHHHHHHHhhccccccccChhcccccce
Confidence 999999987 4433 1456677666665555542 234566666666655 3456778999999
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHH
Q 013817 187 NRPLTEEQKNYAAIDAHCLIEIF 209 (436)
Q Consensus 187 ~RPL~~~ql~YAA~DA~~Ll~L~ 209 (436)
..||+.+|+.||+.|||+...|+
T Consensus 259 ~~~Ls~~Ql~~asidvy~c~~lg 281 (319)
T KOG4373|consen 259 VYPLSDDQLLQASIDVYVCHKLG 281 (319)
T ss_pred eeeccHHHHHHHHhHHHHHHHHH
Confidence 99999999999999999999999
No 26
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
Probab=98.62 E-value=8.3e-07 Score=79.24 Aligned_cols=117 Identities=21% Similarity=0.207 Sum_probs=78.8
Q ss_pred EEEEEeCCCCCchhHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCC
Q 013817 78 VVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKL 157 (436)
Q Consensus 78 ~v~liD~~~l~~~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~ 157 (436)
++|+|++.. .. ....|+++|++..+.|++||+|.+++.|.+ +|+ . ....+|| ++||+||++|.
T Consensus 30 ~~~yi~~~~-~~--~~~~l~~~l~~~~~~ki~~d~K~~~~~l~~-~gi-~------l~~~~fD-~~LAaYLL~p~----- 92 (151)
T cd06128 30 VAAYIPVAH-DY--ALELLKPLLEDEKALKVGQNLKYDRVILAN-YGI-E------LRGIAFD-TMLEAYLLDPV----- 92 (151)
T ss_pred CeEEEeCCC-Cc--CHHHHHHHHcCCCCCEEeeehHHHHHHHHH-CCC-C------CCCcchh-HHHHHHHcCCC-----
Confidence 367775321 00 144588999999999999999999999976 455 1 2356799 99999999996
Q ss_pred CcCcccHHHHHHHHcCCcccc-cccccCCCC--CCC-CHHHHHHHHHHHHHHHHHHHHHH
Q 013817 158 PKETKSLANICKELLDISLSK-ELQCSDWSN--RPL-TEEQKNYAAIDAHCLIEIFNIFQ 213 (436)
Q Consensus 158 ~~~~~gL~~Lv~~~Lg~~l~K-~~q~sdW~~--RPL-~~~ql~YAA~DA~~Ll~L~~~L~ 213 (436)
....++++++++||+..+.. .. ...... .++ ..+...|++..|.++++|++.|.
T Consensus 93 -~~~~~l~~la~~yl~~~~~~~~~-~~gkg~~~~~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 93 -AGRHDMDSLAERWLKEKTITFEE-IAGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred -CCCCCHHHHHHHHcCCCCccHHH-HcCCCCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 23149999999999877321 11 111100 012 12234488888999999988874
No 27
>COG4634 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.45 E-value=4.8e-07 Score=75.84 Aligned_cols=71 Identities=21% Similarity=0.314 Sum_probs=60.2
Q ss_pred CeEEEeCccH-HHHHHHHhcCCceeecCC---CCCChHHHHHHHhcCCcEEEecChhHHhhhcccC--CcEEEEcCC
Q 013817 357 PKFLCDVMVE-GLAKHLRCVGIDAATPRS---KKPEPRELIDQTSKEKRVLLTRDAKLLRHQYLIK--NQIYRVKSL 427 (436)
Q Consensus 357 ~~fl~D~~l~-~la~~LR~~G~d~~~~~~---~~~~~~~~~~~a~~e~ri~lT~d~~l~~~~~~~~--~~~~~v~~~ 427 (436)
|||++|..|. +||+||-+-||++++.++ ++..|.||...|+.++|||+|.|.+|...+...| -++++++-.
T Consensus 1 MkilvD~~Lp~rlad~l~~~g~e~~h~r~lg~~da~D~EI~a~A~~~~~iivTkDsDF~~la~~~G~Ppki~wLr~g 77 (113)
T COG4634 1 MKILVDAQLPPRLADWLPMAGIEAVHWRDLGLRDATDIEIWAYARRNNRIIVTKDSDFADLALTLGSPPKIVWLRCG 77 (113)
T ss_pred CcEeeecCCChHHHHHhhhcccceeeecccCcCCCccHHHHHHHHhcCcEEEEcCccHHHHHHHcCCCCeEEEEEec
Confidence 8999999999 799999999999988875 2456899999999999999999999998654444 367888753
No 28
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=97.44 E-value=0.0022 Score=58.21 Aligned_cols=86 Identities=20% Similarity=0.247 Sum_probs=56.5
Q ss_pred HHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcC
Q 013817 94 ELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLD 173 (436)
Q Consensus 94 ~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg 173 (436)
..|.+++.+.. +-||||+.+|+.+|... ...++|+..++..+. +.. ....+++|..|+++++|
T Consensus 75 ~~~~~~i~~~~-vlVgHn~~fD~~fL~~~------------~~~~iDT~~l~~~~~-~~~---~~~~~~~L~~L~~~~~~ 137 (161)
T cd06137 75 AALWKFIDPDT-ILVGHSLQNDLDALRMI------------HTRVVDTAILTREAV-KGP---LAKRQWSLRTLCRDFLG 137 (161)
T ss_pred HHHHHhcCCCc-EEEeccHHHHHHHHhCc------------CCCeeEehhhhhhcc-CCC---cCCCCccHHHHHHHHCC
Confidence 45566666533 45999999999999753 135789555555543 320 00137999999999999
Q ss_pred CcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 013817 174 ISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (436)
Q Consensus 174 ~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~ 209 (436)
+++..+....+ |..||.++.+||
T Consensus 138 ~~~~~~~~~H~-------------A~~DA~at~~l~ 160 (161)
T cd06137 138 LKIQGGGEGHD-------------SLEDALAAREVV 160 (161)
T ss_pred chhcCCCCCCC-------------cHHHHHHHHHHh
Confidence 87743222222 778999888876
No 29
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=97.40 E-value=0.0053 Score=61.96 Aligned_cols=102 Identities=14% Similarity=0.128 Sum_probs=68.6
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
+++..|.+++.+. +.|+||+.+|+..|.+.|.-.|.. + ....++|+..++..+ .+. ..++.|.+|++.
T Consensus 83 ev~~~l~~~l~~~--~lVaHNa~FD~~fL~~~~~r~g~~--~-~~~~~ldTl~lar~~-~~~------~~~~kL~~l~~~ 150 (313)
T PRK06063 83 DIAGEVAELLRGR--TLVAHNVAFDYSFLAAEAERAGAE--L-PVDQVMCTVELARRL-GLG------LPNLRLETLAAH 150 (313)
T ss_pred HHHHHHHHHcCCC--EEEEeCHHHHHHHHHHHHHHcCCC--C-CCCCEEehHHHHHHh-ccC------CCCCCHHHHHHH
Confidence 4556677777664 459999999999997654332321 1 124588943444443 332 247889999976
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGN 221 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~ 221 (436)
+|++....+ -|..||.++.+|+..+..++.+.+.
T Consensus 151 -~gi~~~~~H----------------~Al~DA~ata~l~~~ll~~~~~~~~ 184 (313)
T PRK06063 151 -WGVPQQRPH----------------DALDDARVLAGILRPSLERARERDV 184 (313)
T ss_pred -cCCCCCCCC----------------CcHHHHHHHHHHHHHHHHHHHhcCC
Confidence 576543222 2789999999999999988887754
No 30
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=97.38 E-value=0.0092 Score=57.60 Aligned_cols=89 Identities=17% Similarity=0.267 Sum_probs=57.4
Q ss_pred ceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcCCcccccccccC
Q 013817 105 ILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSD 184 (436)
Q Consensus 105 i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~K~~q~sd 184 (436)
.+.|+||+.+|+..|.+.+.-.|..+ + ...+++| +......+.+. + ..+++|.+|++. +|++....+
T Consensus 94 ~~lVahNa~FD~~fL~~~~~r~~~~~-~-~~~~~iD-t~~l~~~~~~~--~---~~~~~L~~l~~~-~gi~~~~aH---- 160 (232)
T PRK07942 94 VPVVVFNAPYDLTVLDRELRRHGLPS-L-VPGPVID-PYVIDKAVDRY--R---KGKRTLTALCEH-YGVRLDNAH---- 160 (232)
T ss_pred CEEEEeCcHhhHHHHHHHHHHcCCCC-c-cCCcEee-HHHHHhhhhcc--c---CCCCCHHHHHHH-cCCCCCCCC----
Confidence 34599999999998876543323210 0 1246889 55444333221 0 125789999977 577654333
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 013817 185 WSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ 218 (436)
Q Consensus 185 W~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~ 218 (436)
-|..||.++.+|+..|..+..+
T Consensus 161 ------------~Al~Da~ata~l~~~l~~~~~~ 182 (232)
T PRK07942 161 ------------EATADALAAARVAWALARRFPE 182 (232)
T ss_pred ------------ChHHHHHHHHHHHHHHHHHHHH
Confidence 1889999999999999876653
No 31
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=97.21 E-value=0.0026 Score=57.62 Aligned_cols=89 Identities=17% Similarity=0.168 Sum_probs=56.6
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHH--HHHh-hcccCCCCCCcCcccHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSI--YNHL-HHKQLGRKLPKETKSLANI 167 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~L--a~yL-l~~~~~~~~~~~~~gL~~L 167 (436)
++...|.+++.+ -+-||||+++|+..|...+. ..++.|+..+ +... ..+. ...++|..|
T Consensus 66 ~v~~~l~~~l~~--~vlV~Hn~~~D~~~l~~~~~----------~~~~~Dt~~l~~~~~~~~~p~------~~~~~L~~L 127 (157)
T cd06149 66 VAQKEILKILKG--KVVVGHAIHNDFKALKYFHP----------KHMTRDTSTIPLLNRKAGFPE------NCRVSLKVL 127 (157)
T ss_pred HHHHHHHHHcCC--CEEEEeCcHHHHHHhcccCC----------CcCEEECcccccchhhcCCcc------cCChhHHHH
Confidence 456667777764 34599999999998864311 2356783222 2211 1222 246999999
Q ss_pred HHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 013817 168 CKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (436)
Q Consensus 168 v~~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~ 210 (436)
+++++|..+..+.+..+ |..||.++.+||+
T Consensus 128 ~~~~~~~~i~~~~~~H~-------------Al~DA~at~~l~~ 157 (157)
T cd06149 128 AKRLLHRDIQVGRQGHS-------------SVEDARATMELYK 157 (157)
T ss_pred HHHHcChhhcCCCCCcC-------------cHHHHHHHHHHhC
Confidence 99999876654222222 6789999988873
No 32
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=97.14 E-value=0.025 Score=55.59 Aligned_cols=98 Identities=16% Similarity=0.181 Sum_probs=65.6
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
+++..+..++.+. +.|+||+.+|...|.+.+.-.|+.+ .....+|+..++..+... .+++|++|++
T Consensus 136 evl~~f~~fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~---~~~~~ldtl~la~~~~~~--------~~~~L~~L~~- 201 (257)
T PRK08517 136 EVLEEFRLFLGDS--VFVAHNVNFDYNFISRSLEEIGLGP---LLNRKLCTIDLAKRTIES--------PRYGLSFLKE- 201 (257)
T ss_pred HHHHHHHHHHCCC--eEEEECHHHHHHHHHHHHHHcCCCC---CCCCcEehHHHHHHHccC--------CCCCHHHHHH-
Confidence 4566677777654 4599999999999875432223221 134578855566655432 3689999987
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ 218 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~ 218 (436)
++|++....+ -|..||.++.+|+..+..++..
T Consensus 202 ~lgi~~~~~H----------------rAl~DA~ata~ll~~ll~~~~~ 233 (257)
T PRK08517 202 LLGIEIEVHH----------------RAYADALAAYEIFKICLLNLPS 233 (257)
T ss_pred HcCcCCCCCC----------------ChHHHHHHHHHHHHHHHHHhHH
Confidence 4687654322 2788999999999999876643
No 33
>PRK07740 hypothetical protein; Provisional
Probab=97.13 E-value=0.027 Score=54.82 Aligned_cols=100 Identities=13% Similarity=0.160 Sum_probs=66.3
Q ss_pred HHHHHHHhhCCCCceEEEEehHHhHHHHHhhc-ccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTF-CSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 92 ~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~-gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
++..+.+++.+. .-||||+..|...|.+.+ ...+. .....++|+..++..+ .+. ...++|.+++..
T Consensus 131 vl~~f~~fi~~~--~lVahna~fD~~fL~~~~~~~~~~----~~~~~~iDt~~l~r~l-~~~------~~~~sL~~l~~~ 197 (244)
T PRK07740 131 VLHRFYAFIGAG--VLVAHHAGHDKAFLRHALWRTYRQ----PFTHRLIDTMFLTKLL-AHE------RDFPTLDDALAY 197 (244)
T ss_pred HHHHHHHHhCCC--EEEEeCHHHHHHHHHHHHHHhcCC----CcCCCeechHHHHHHH-cCC------CCCCCHHHHHHH
Confidence 445555566553 458999999999886532 11111 1235789955555444 332 247899999965
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGN 221 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~ 221 (436)
+|++....+ -|..||.++.+|+..+..++.+.|.
T Consensus 198 -~gi~~~~~H----------------~Al~Da~ata~l~~~ll~~~~~~~~ 231 (244)
T PRK07740 198 -YGIPIPRRH----------------HALGDALMTAKLWAILLVEAQQRGI 231 (244)
T ss_pred -CCcCCCCCC----------------CcHHHHHHHHHHHHHHHHHHHHcCC
Confidence 687664322 2789999999999999998887653
No 34
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=97.11 E-value=0.015 Score=52.47 Aligned_cols=95 Identities=18% Similarity=0.206 Sum_probs=58.4
Q ss_pred HHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHH-HHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITS-IYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 92 ~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~-La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
+...|.+++.+.- .|+||+.+|+..|.+.+.-.|..+.+.....++| |+ ++..+ .+. ...+|+++++.
T Consensus 71 v~~~l~~~l~~~~--lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~id-t~~~~~~~-~~~-------~~~~L~~l~~~ 139 (167)
T cd06131 71 IADEFLDFIRGAE--LVIHNASFDVGFLNAELSLLGLGKKIIDFCRVID-TLALARKK-FPG-------KPNSLDALCKR 139 (167)
T ss_pred HHHHHHHHHCCCe--EEEeChHHhHHHHHHHHHHhCCCcccccCCCceE-hHHHHHHH-cCC-------CCCCHHHHHHH
Confidence 4556667776643 4999999999988654332221110111246799 55 44443 332 35799999988
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L 212 (436)
+ |++.... +.+-|..||..+.+|+..|
T Consensus 140 ~-~i~~~~~--------------~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 140 F-GIDNSHR--------------TLHGALLDAELLAEVYLEL 166 (167)
T ss_pred C-CCCCCCC--------------CCCChHHHHHHHHHHHHHh
Confidence 6 6554211 1123889999999998765
No 35
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=97.03 E-value=0.041 Score=53.09 Aligned_cols=144 Identities=13% Similarity=0.119 Sum_probs=85.1
Q ss_pred CeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-----------CCc---------hhH
Q 013817 33 SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-----------IPL---------PSI 92 (436)
Q Consensus 33 ~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~-----------l~~---------~~~ 92 (436)
..+.||+|+++..+ . +-.+|+|+.-. .. ..+.-..++.+.. +.. .++
T Consensus 3 ~~vv~D~ETTGl~~---~--~d~IIeig~v~--~~------~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev 69 (232)
T PRK06309 3 ALIFYDTETTGTQI---D--KDRIIEIAAYN--GV------TSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEA 69 (232)
T ss_pred cEEEEEeeCCCCCC---C--CCEEEEEEEEc--Cc------cccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHH
Confidence 46899999998774 1 23478886531 00 0012222444321 111 123
Q ss_pred HHHHHHhhCCCCceEEEEe-hHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHH
Q 013817 93 WELLKELFVSPDILKLGFK-FKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKEL 171 (436)
Q Consensus 93 ~~~L~~lLe~~~i~KVgh~-~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~ 171 (436)
...+.+++.+. ..-|||| ..+|+..|.+.+.-.|+.+ ....++|+..++..+ .++ ...++|..+++.|
T Consensus 70 ~~~~~~fi~~~-~~lVaHN~~~FD~~~L~~e~~r~g~~~---~~~~~iDt~~l~~~~-~~~------~~~~~L~~l~~~~ 138 (232)
T PRK06309 70 YQKFIEFCGTD-NILVAHNNDAFDFPLLRKECRRHGLEP---PTLRTIDSLKWAQKY-RPD------LPKHNLQYLRQVY 138 (232)
T ss_pred HHHHHHHHcCC-CEEEEeCCHHHHHHHHHHHHHHcCCCC---CCCcEEeHHHHHHHH-cCC------CCCCCHHHHHHHc
Confidence 44556666543 3459999 5899999876543223221 124689955555444 332 1367899998776
Q ss_pred cCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 013817 172 LDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (436)
Q Consensus 172 Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~ 217 (436)
|++....+ -|..||.++.+|+..+..++.
T Consensus 139 -~~~~~~aH----------------~Al~Da~~t~~vl~~l~~~~~ 167 (232)
T PRK06309 139 -GFEENQAH----------------RALDDVITLHRVFSALVGDLS 167 (232)
T ss_pred -CCCCCCCC----------------CcHHHHHHHHHHHHHHHHHHH
Confidence 65543222 288999999999999887765
No 36
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=96.98 E-value=0.025 Score=55.27 Aligned_cols=150 Identities=19% Similarity=0.222 Sum_probs=86.0
Q ss_pred hcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-----------CCc--------
Q 013817 29 LSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-----------IPL-------- 89 (436)
Q Consensus 29 L~~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~-----------l~~-------- 89 (436)
+.....|.||+|+++..+ .+-.+||||.-. -+. ... .+.-..++.+.. +..
T Consensus 4 l~~~~~v~~D~ETTGl~~-----~~d~IIEIa~v~-v~~--~~~--~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~ 73 (250)
T PRK06310 4 LKDTEFVCLDCETTGLDV-----KKDRIIEFAAIR-FTF--DEV--IDSVEFLINPERVVSAESQRIHHISDAMLRDKPK 73 (250)
T ss_pred ccCCcEEEEEEeCCCCCC-----CCCeEEEEEEEE-EEC--CeE--EEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCC
Confidence 345678999999998764 133477775531 000 000 011223444321 111
Q ss_pred -hhHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCcc-CCCceeeHHHHHHHhhcccCCCCCCcCcccHHHH
Q 013817 90 -PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFD-RVEPYLDITSIYNHLHHKQLGRKLPKETKSLANI 167 (436)
Q Consensus 90 -~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~-~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~L 167 (436)
.++...+.+++.+.. .-||||+.+|...|...+.-.|.. +. ....++|+..++. .... ..+++|+.|
T Consensus 74 ~~ev~~~~~~fl~~~~-~lvghn~~FD~~~L~~~~~r~g~~--~~~~~~~~iDtl~lar-~~~~-------~~~~~L~~l 142 (250)
T PRK06310 74 IAEVFPQIKGFFKEGD-YIVGHSVGFDLQVLSQESERIGET--FLSKHYYIIDTLRLAK-EYGD-------SPNNSLEAL 142 (250)
T ss_pred HHHHHHHHHHHhCCCC-EEEEECHHHHHHHHHHHHHHcCCC--ccccCCcEEehHHHHH-hccc-------CCCCCHHHH
Confidence 134556666776544 459999999999987653222211 11 1146899444443 3322 136899999
Q ss_pred HHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 013817 168 CKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKV 216 (436)
Q Consensus 168 v~~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L 216 (436)
++.+ |++....+ -|..||.++..|+..+..++
T Consensus 143 ~~~~-g~~~~~aH----------------~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 143 AVHF-NVPYDGNH----------------RAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred HHHC-CCCCCCCc----------------ChHHHHHHHHHHHHHHHHhc
Confidence 8775 76553222 28899999999999887554
No 37
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=96.97 E-value=0.026 Score=57.05 Aligned_cols=97 Identities=13% Similarity=0.147 Sum_probs=65.3
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
+++..+.+++.+..+ ||||+.+|+..|.+.+.-.|+. .....++|+..++..+.. . ...++|.+|++.
T Consensus 77 evl~~f~~fl~~~~l--VaHNa~FD~~fL~~~~~~~gl~---~~~~~~iDtl~la~~~~~-~------~~~~kL~~L~~~ 144 (313)
T PRK06807 77 EVLPLFLAFLHTNVI--VAHNASFDMRFLKSNVNMLGLP---EPKNKVIDTVFLAKKYMK-H------APNHKLETLKRM 144 (313)
T ss_pred HHHHHHHHHHcCCeE--EEEcHHHHHHHHHHHHHHcCCC---CCCCCEeeHHHHHHHHhC-C------CCCCCHHHHHHH
Confidence 345566667765433 9999999999998765433421 013468996666665543 2 136799999855
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~ 217 (436)
+|++. +.+ =|..||.++..|+..+.....
T Consensus 145 -lgi~~-~~H----------------~Al~DA~~ta~l~~~l~~~~~ 173 (313)
T PRK06807 145 -LGIRL-SSH----------------NAFDDCITCAAVYQKCASIEE 173 (313)
T ss_pred -cCCCC-CCc----------------ChHHHHHHHHHHHHHHHHhhh
Confidence 67665 222 278999999999999987664
No 38
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=96.95 E-value=0.0093 Score=58.03 Aligned_cols=95 Identities=22% Similarity=0.222 Sum_probs=63.5
Q ss_pred HHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHc
Q 013817 93 WELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELL 172 (436)
Q Consensus 93 ~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~L 172 (436)
-..+.++|.+. +.|||++++|+.+|.-.+.- ..+-| |.-+.-|... .....+.||..|++.+|
T Consensus 175 Q~ev~klL~gR--IlVGHaLhnDl~~L~l~hp~----------s~iRD-Ts~~~pl~k~----~~~~~tpSLK~Lt~~~L 237 (280)
T KOG2249|consen 175 QKEVLKLLKGR--ILVGHALHNDLQALKLEHPR----------SMIRD-TSKYPPLMKL----LSKKATPSLKKLTEALL 237 (280)
T ss_pred HHHHHHHHhCC--EEeccccccHHHHHhhhCch----------hhhcc-cccCchHHHH----hhccCCccHHHHHHHHh
Confidence 34566788774 34999999999998754321 23446 4322111110 00124789999999999
Q ss_pred CCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 013817 173 DISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (436)
Q Consensus 173 g~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~ 219 (436)
|+.+--++..| .+||.++.+||.....+-++.
T Consensus 238 g~~IQ~GeHsS---------------vEDA~AtM~LY~~vk~qwe~~ 269 (280)
T KOG2249|consen 238 GKDIQVGEHSS---------------VEDARATMELYKRVKVQWEKI 269 (280)
T ss_pred chhhhccccCc---------------HHHHHHHHHHHHHHHHHHHHH
Confidence 99886655433 489999999999998666654
No 39
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.91 E-value=0.023 Score=55.21 Aligned_cols=97 Identities=16% Similarity=0.225 Sum_probs=59.7
Q ss_pred HHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCc-cCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCD-IGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 92 ~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~-~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
+...+.+++.+.. .|+||+.+|+..|.+.+.-.|.. |.+.....++|+..++.++ .++ ...+|.+||++
T Consensus 76 v~~~f~~fi~~~~--lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~-~p~-------~~~~L~aL~~~ 145 (240)
T PRK05711 76 VADEFLDFIRGAE--LIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRM-FPG-------KRNSLDALCKR 145 (240)
T ss_pred HHHHHHHHhCCCE--EEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHH-cCC-------CCCCHHHHHHH
Confidence 4555666666643 49999999999987554322210 1011124589944455444 343 35799999987
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~ 213 (436)
| |++.... + .+-|..||+.+.++|..|.
T Consensus 146 ~-gi~~~~r-~-------------~H~AL~DA~~~A~v~~~l~ 173 (240)
T PRK05711 146 Y-GIDNSHR-T-------------LHGALLDAEILAEVYLAMT 173 (240)
T ss_pred C-CCCCCCC-C-------------CCCHHHHHHHHHHHHHHHH
Confidence 5 6542211 1 1228899999999998886
No 40
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=96.89 E-value=0.036 Score=53.29 Aligned_cols=98 Identities=16% Similarity=0.209 Sum_probs=61.2
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCc-cCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCD-IGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~-~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~ 169 (436)
+++..|.+++.+.. .|+||+.+|+.+|...+.-.|.. +.+.....++|+..++..+ .++ .+++|.+||+
T Consensus 71 ev~~~f~~fi~~~~--lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~-~p~-------~~~~L~~L~~ 140 (225)
T TIGR01406 71 EIADEFLDFIGGSE--LVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARER-FPG-------QRNSLDALCK 140 (225)
T ss_pred HHHHHHHHHhCCCE--EEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHH-cCC-------CCCCHHHHHH
Confidence 34556667776643 39999999999987554322310 0011124689944444444 343 3689999999
Q ss_pred HHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 013817 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (436)
Q Consensus 170 ~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~ 213 (436)
+| |++.... . .+=|..||..+.+||..|.
T Consensus 141 ~~-gi~~~~r-~-------------~H~Al~DA~~~a~v~~~l~ 169 (225)
T TIGR01406 141 RF-KVDNSHR-T-------------LHGALLDAHLLAEVYLALT 169 (225)
T ss_pred hc-CCCCCCC-C-------------CcCHHHHHHHHHHHHHHHH
Confidence 86 6543211 0 1228899999999998885
No 41
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=96.88 E-value=0.024 Score=66.59 Aligned_cols=103 Identities=22% Similarity=0.415 Sum_probs=72.3
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
+++..+..++.+. +.|+||+.+|+..|...+.-.|..+ ....++|+..++.. +.+. ...++|++|+++
T Consensus 259 evl~~f~~fl~~~--iLVaHNa~FD~~fL~~~~~r~g~~~---~~~~~IDTl~lar~-l~p~------~k~~kL~~Lak~ 326 (1213)
T TIGR01405 259 EVLEKFKEFFKDS--ILVAHNASFDIGFLNTNFEKVGLEP---LENPVIDTLELARA-LNPE------YKSHRLGNICKK 326 (1213)
T ss_pred HHHHHHHHHhCCC--eEEEEChHHHHHHHHHHHHHcCCCc---cCCCEeEHHHHHHH-Hhcc------CCCCCHHHHHHH
Confidence 4566777777653 4599999999999876533223221 13578995455544 4443 247899999987
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l 222 (436)
+|+++... +.|..||.++.+|+..+..++++.|..
T Consensus 327 -lgi~~~~~----------------HrAl~DA~aTa~I~~~ll~~l~~~~i~ 361 (1213)
T TIGR01405 327 -LGVDLDDH----------------HRADYDAEATAKVFKVMVEQLKEKGIT 361 (1213)
T ss_pred -cCCCCCCC----------------cCHHHHHHHHHHHHHHHHHHHHHcCCc
Confidence 47765321 348899999999999999999887654
No 42
>PRK07883 hypothetical protein; Validated
Probab=96.87 E-value=0.032 Score=60.70 Aligned_cols=159 Identities=12% Similarity=0.138 Sum_probs=95.4
Q ss_pred HHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-----------CCc------
Q 013817 27 RALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-----------IPL------ 89 (436)
Q Consensus 27 ~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~-----------l~~------ 89 (436)
..+.....|.||+|+++..+ . ...+++|+.-. -+.+-.. +.-..+|.+.. +..
T Consensus 10 ~~~~~~~~Vv~D~ETTGl~p---~--~~~IIEIgaV~-v~~g~iv----~~f~~lV~P~~~i~~~~~~itGIt~e~l~~a 79 (557)
T PRK07883 10 TPLRDVTFVVVDLETTGGSP---A--GDAITEIGAVK-VRGGEVL----GEFATLVNPGRPIPPFITVLTGITTAMVAGA 79 (557)
T ss_pred CCCcCCCEEEEEEecCCCCC---C--CCeEEEEEEEE-EECCEEE----EEEEEEECCCCCCChhHHhhcCCCHHHHhCC
Confidence 34556789999999998774 1 24566665421 0000000 00112333321 111
Q ss_pred ---hhHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHH
Q 013817 90 ---PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLAN 166 (436)
Q Consensus 90 ---~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~ 166 (436)
.+++..+..++.+ -+.|+||+.+|+..|...+.-.|.. + .....+|+..++..+..+. ....++|++
T Consensus 80 p~~~evl~~f~~fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~--~-~~~~~iDTl~lar~l~~~~-----~~~~~~L~~ 149 (557)
T PRK07883 80 PPIEEVLPAFLEFARG--AVLVAHNAPFDIGFLRAAAARCGYP--W-PGPPVLCTVRLARRVLPRD-----EAPNVRLST 149 (557)
T ss_pred CCHHHHHHHHHHHhcC--CEEEEeCcHHHHHHHHHHHHHcCCC--C-CCCCcEecHHHHHHhcccC-----CCCCCCHHH
Confidence 1345566667765 3458999999999997654333322 1 1245789556666655421 024789999
Q ss_pred HHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 013817 167 ICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (436)
Q Consensus 167 Lv~~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l 222 (436)
|++ ++|++....+ -|..||.++.+|+..+..++.+.|..
T Consensus 150 L~~-~~gi~~~~~H----------------~Al~DA~ata~l~~~l~~~~~~~~~~ 188 (557)
T PRK07883 150 LAR-LFGATTTPTH----------------RALDDARATVDVLHGLIERLGNLGVH 188 (557)
T ss_pred HHH-HCCcccCCCC----------------CHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 987 5687653222 28899999999999999999876653
No 43
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=96.85 E-value=0.069 Score=50.33 Aligned_cols=92 Identities=15% Similarity=0.140 Sum_probs=59.4
Q ss_pred ceEEEEehHHhHHHHHhhcccCCCccCcc-CCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcCCccccccccc
Q 013817 105 ILKLGFKFKQDLIYLSSTFCSQGCDIGFD-RVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCS 183 (436)
Q Consensus 105 i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~-~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~K~~q~s 183 (436)
.+.||||+.+|+..|...+.-.|... .. ....++|+..++..+ .+ ..+|..+++.+ |++...
T Consensus 106 ~~lVaHNa~FD~~fL~~~~~r~~~~~-~~~~~~~~lDTl~lar~~-~~---------~~~L~~l~~~~-gi~~~~----- 168 (200)
T TIGR01298 106 AILVGHNANFDLGFLNAAVERTSLKR-NPFHPFSTFDTATLAGLA-YG---------QTVLAKACQAA-GXDFDS----- 168 (200)
T ss_pred CEEEEECchhhHHHHHHHHHHhCCCC-CCCCCCcEEEHHHHHHHH-cC---------cccHHHHHHHc-CCCccc-----
Confidence 45699999999999875432112110 00 012479955555443 32 35799999864 655320
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 013817 184 DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (436)
Q Consensus 184 dW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l 222 (436)
.+.+-|..||.++.+|+..+..++.+.+.|
T Consensus 169 ---------~~~H~Al~Da~ata~lf~~l~~~~~~~~~~ 198 (200)
T TIGR01298 169 ---------TQAHSALYDTEKTAELFCEIVNRWKRLGGW 198 (200)
T ss_pred ---------cchhhhHHhHHHHHHHHHHHHHHHHHccCC
Confidence 123448899999999999999999877654
No 44
>PRK05168 ribonuclease T; Provisional
Probab=96.84 E-value=0.091 Score=49.94 Aligned_cols=93 Identities=15% Similarity=0.156 Sum_probs=60.3
Q ss_pred CceEEEEehHHhHHHHHhhcccCCCccCcc-CCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcCCcccccccc
Q 013817 104 DILKLGFKFKQDLIYLSSTFCSQGCDIGFD-RVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQC 182 (436)
Q Consensus 104 ~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~-~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~K~~q~ 182 (436)
+.+.||||+.+|+..|.+.+.-.|+.. .. ....++|+..++..+. + ..+|..+++. +|+++... ..
T Consensus 114 ~~~lVaHNa~FD~~fL~~~~~r~~~~~-~~~~~~~~iDt~~lar~~~-~---------~~~L~~l~~~-~gl~~~~~-~~ 180 (211)
T PRK05168 114 RAILVAHNAHFDLSFLMAAAERAGLKR-NPFHPFSTFDTATLSGLAL-G---------QTVLAKACQA-AGIEFDNK-EA 180 (211)
T ss_pred CceEEEeccHHhHHHHHHHHHHhCCCC-CCCCCCcEeeHHHHHHHHc-C---------CCCHHHHHHH-CCCCCCCC-CC
Confidence 456799999999998875532222110 00 0124799556665543 2 3579999987 47664311 11
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 013817 183 SDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (436)
Q Consensus 183 sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l 222 (436)
+-|..||.++.+|+..+..++.+.|.+
T Consensus 181 -------------H~Al~DA~ata~l~~~l~~~~~~~~~~ 207 (211)
T PRK05168 181 -------------HSALYDTEKTAELFCEIVNRWKRLGGW 207 (211)
T ss_pred -------------CChHHHHHHHHHHHHHHHHHHHHccCC
Confidence 228899999999999999999877653
No 45
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=96.83 E-value=0.043 Score=49.11 Aligned_cols=98 Identities=17% Similarity=0.185 Sum_probs=63.1
Q ss_pred hHHHHHHHhhCCCCceEEEEeh-HHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKF-KQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~-k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~ 169 (436)
++...+..++.+.. .|+|+. ++|+..|...+...|+. +.....++|+..++..+. +. ...+|.++++
T Consensus 69 ~~~~~~~~~l~~~~--~v~~n~~~fD~~~L~~~~~~~~~~--~~~~~~~iD~~~~~~~~~-~~-------~~~~L~~l~~ 136 (169)
T smart00479 69 EVLEELLEFLKGKI--LVAGNALNFDLRFLKLEHPRLGIK--DPPKNPVIDTLKLARALN-PG-------RKYSLKKLAE 136 (169)
T ss_pred HHHHHHHHHhcCCE--EEEeCCHHHhHHHHHHHHHHhCCC--CCcCCCeeEHHHHHHHHC-CC-------CCCCHHHHHH
Confidence 45667777887643 377777 99999987654432321 111234799545544443 32 2789999998
Q ss_pred HHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 013817 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKV 216 (436)
Q Consensus 170 ~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L 216 (436)
.+ |++.... .+.|..||..+.+|+..+..++
T Consensus 137 ~~-~~~~~~~---------------~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 137 RL-GLEVIGR---------------AHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred HC-CCCCCCC---------------CcCcHHHHHHHHHHHHHHHHHh
Confidence 76 4433211 2458899999999999987654
No 46
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=96.82 E-value=0.0049 Score=55.37 Aligned_cols=86 Identities=24% Similarity=0.354 Sum_probs=57.1
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
+++..|..++.+ .+ -||||+.+|+..|... . + ...++| |........+. +..+++|++|++.
T Consensus 66 ~~~~~l~~~l~~-~v-lVgHn~~fD~~~L~~~--~----~----~~~~~d-t~~l~~~~~~~-----~~~~~sL~~l~~~ 127 (152)
T cd06144 66 EVQKKVAELLKG-RI-LVGHALKNDLKVLKLD--H----P----KKLIRD-TSKYKPLRKTA-----KGKSPSLKKLAKQ 127 (152)
T ss_pred HHHHHHHHHhCC-CE-EEEcCcHHHHHHhcCc--C----C----CccEEE-eEEeecccccc-----CCCChhHHHHHHH
Confidence 456677788876 44 4999999999998642 1 0 235678 44332222211 0247999999999
Q ss_pred HcCCcccc-cccccCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 013817 171 LLDISLSK-ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (436)
Q Consensus 171 ~Lg~~l~K-~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~ 210 (436)
+||+++.. .+ -|..||.++.+||+
T Consensus 128 ~lgi~~~~~~H----------------~Al~DA~at~~l~~ 152 (152)
T cd06144 128 LLGLDIQEGEH----------------SSVEDARAAMRLYR 152 (152)
T ss_pred HcCcccCCCCc----------------CcHHHHHHHHHHhC
Confidence 99987642 22 17789999988873
No 47
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=96.73 E-value=0.082 Score=49.70 Aligned_cols=159 Identities=18% Similarity=0.200 Sum_probs=86.6
Q ss_pred HHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-----------CC--
Q 013817 22 FTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-----------IP-- 88 (436)
Q Consensus 22 l~~l~~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~-----------l~-- 88 (436)
+..+.+.......|.+|+|+++..+ . .-.+++|+.-. -+.+- ....+.-.++|.+.. +.
T Consensus 19 ~~~~~~~~~~~~~vviD~ETTGl~~---~--~d~IieIgaV~-~~~~~--~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~ 90 (202)
T PRK09145 19 YAFLFEPPPPDEWVALDCETTGLDP---R--RAEIVSIAAVK-IRGNR--ILTSERLELLVRPPQSLSAESIKIHRLRHQ 90 (202)
T ss_pred HHHHhcCCCCCCEEEEEeECCCCCC---C--CCceEEEEEEE-EECCE--EeecCceEEEECCCCCCCHhHhhhcCcCHH
Confidence 3334444445688999999998764 2 22466665421 00000 000001123344321 11
Q ss_pred -------chhHHHHHHHhhCCCCceEEEEehHHhHHHHHhhccc-CCCccCccCCCceeeHHHHHHHhhcccCCCCCCcC
Q 013817 89 -------LPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCS-QGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKE 160 (436)
Q Consensus 89 -------~~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi-~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~ 160 (436)
..+++..+.+++.+. ..||||+.+|+..|.+.+.- .|. ......+|+..++........ .....
T Consensus 91 ~l~~~~~~~~vl~~~~~~i~~~--~lv~hn~~fD~~fL~~~~~~~~~~----~~~~~~id~~~l~~~~~~~~~--~~~~~ 162 (202)
T PRK09145 91 DLEDGLSEEEALRQLLAFIGNR--PLVGYYLEFDVAMLNRYVRPLLGI----PLPNPLIEVSALYYDKKERHL--PDAYI 162 (202)
T ss_pred HHhcCCCHHHHHHHHHHHHcCC--eEEEeCHHHHHHHHHHHHHHhcCC----CCCCCeeeHHHHHHHHhhccC--CCccc
Confidence 123556667777764 35999999999998754321 121 123567895555433222110 00123
Q ss_pred cccHHHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 013817 161 TKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (436)
Q Consensus 161 ~~gL~~Lv~~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~ 213 (436)
+++|+++++.+ |++....+ + |..||.++..||..|.
T Consensus 163 ~~~L~~l~~~~-gi~~~~~H---~-------------Al~DA~ata~l~~~l~ 198 (202)
T PRK09145 163 DLRFDAILKHL-DLPVLGRH---D-------------ALNDAIMAALIFLRLR 198 (202)
T ss_pred CCCHHHHHHHc-CCCCCCCC---C-------------cHHHHHHHHHHHHHHH
Confidence 68999999764 76653222 2 7899999999998875
No 48
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=96.70 E-value=0.0066 Score=54.57 Aligned_cols=86 Identities=20% Similarity=0.255 Sum_probs=55.8
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
+++..+.+++.. +.+-||||+.+|+..|... ...++|+..++..+..+ ..+++|..||++
T Consensus 64 ~v~~~~~~fl~~-~~vlVgHn~~fD~~fL~~~------------~~~~iDT~~l~r~~~~~-------~~~~~L~~L~~~ 123 (150)
T cd06145 64 DVQKKLLSLISP-DTILVGHSLENDLKALKLI------------HPRVIDTAILFPHPRGP-------PYKPSLKNLAKK 123 (150)
T ss_pred HHHHHHHHHhCC-CCEEEEcChHHHHHHhhcc------------CCCEEEcHHhccccCCC-------CCChhHHHHHHH
Confidence 345566677752 2356999999999998753 13578944443333322 236899999999
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~ 209 (436)
+++..+....+.. -|..||.++.+||
T Consensus 124 ~~~~~i~~~~~~H-------------~Al~DA~~t~~l~ 149 (150)
T cd06145 124 YLGRDIQQGEGGH-------------DSVEDARAALELV 149 (150)
T ss_pred HCCcceeCCCCCC-------------CcHHHHHHHHHHh
Confidence 9986553211111 1778999998886
No 49
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.69 E-value=0.037 Score=52.73 Aligned_cols=105 Identities=17% Similarity=0.189 Sum_probs=64.4
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
+++..|..++.+. ..||||+.+|+..|.+.|.-.+.. ......++|+..++.++.. . .+..+.+|..+++.
T Consensus 76 ev~~~~~~~~~~~--~lVaHNa~FD~~fL~~~~~r~~~~--~~~~~~~~dtl~l~~~~~~-~----~~~~~~~L~~l~~~ 146 (217)
T TIGR00573 76 EIAEDFADYIRGA--ELVIHNASFDVGFLNYEFSKLYKV--EPKTNDVIDTTDTLQYARP-E----FPGKRNTLDALCKR 146 (217)
T ss_pred HHHHHHHHHhCCC--EEEEeccHHHHHHHHHHHHHhcCC--CCCccceecHHHHHHHHHH-h----CCCCCCCHHHHHHH
Confidence 3455666777653 458999999999998664321100 0112467884445554432 2 11236789999977
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~ 219 (436)
+ |++.... .. .=|..||.++.+|+..+..+..+.
T Consensus 147 ~-gl~~~~~-~~-------------H~Al~DA~~ta~l~~~l~~~~~~~ 180 (217)
T TIGR00573 147 Y-EITNSHR-AL-------------HGALADAFILAKLYLVMTGKQTKY 180 (217)
T ss_pred c-CCCCCCc-cc-------------CCHHHHHHHHHHHHHHHHhcchhh
Confidence 5 6543200 11 128899999999999998766544
No 50
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=96.67 E-value=0.012 Score=48.85 Aligned_cols=82 Identities=17% Similarity=0.228 Sum_probs=55.7
Q ss_pred EEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhHHHHHHHhhCCCC-ceEEEEehH
Q 013817 35 VGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPD-ILKLGFKFK 113 (436)
Q Consensus 35 Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lLe~~~-i~KVgh~~k 113 (436)
+++|+|+.+..+ +.+.++++|++... ++..|++| +.+++.+.. ...|+||+.
T Consensus 1 ~~~DiEt~~~~~---~~~~i~~i~~~~~~------------~~~~~~~~------------f~~~l~~~~~~v~V~hn~~ 53 (96)
T cd06125 1 IAIDTEATGLDG---AVHEIIEIALADVN------------PEDTAVID------------LKDILRDKPLAILVGHNGS 53 (96)
T ss_pred CEEEEECCCCCC---CCCcEEEEEEEEcc------------CCCEEEeh------------HHHHHhhCCCCEEEEeCcH
Confidence 479999988764 66889999998741 25667766 556776665 678999999
Q ss_pred HhHHHHHhhcccCCCccCccCCCceeeHHHHH
Q 013817 114 QDLIYLSSTFCSQGCDIGFDRVEPYLDITSIY 145 (436)
Q Consensus 114 ~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La 145 (436)
.|+..|.+.+...|...-+ .....+| |+.+
T Consensus 54 fD~~fL~~~~~~~~~~~p~-~~~~~lD-T~~l 83 (96)
T cd06125 54 FDLPFLNNRCAELGLKYPL-LAGSWID-TIKL 83 (96)
T ss_pred HhHHHHHHHHHHcCCCCCC-cCCcEEE-ehHH
Confidence 9999887665443322100 1356889 6544
No 51
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=96.64 E-value=0.044 Score=62.56 Aligned_cols=99 Identities=15% Similarity=0.259 Sum_probs=64.4
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
++...|.+++.+. ..||||+.+|+..|.+.+.-.|+.+ .....+|+..++..+. +. ..+++|.+|++.
T Consensus 69 ev~~~l~~~l~~~--~~VahN~~fD~~fL~~~~~~~g~~~---~~~~~iDt~~l~~~~~-p~------~~~~~L~~l~~~ 136 (850)
T TIGR01407 69 QVAQEIYDLLEDG--IFVAHNVHFDLNFLAKALKDCGYEP---LPKPRIDTVELAQIFF-PT------EESYQLSELSEA 136 (850)
T ss_pred HHHHHHHHHhCCC--EEEEeCcHHHHHHHHHHHHHcCCCC---CCCCeEeHHHHHHHhc-CC------CCCCCHHHHHHH
Confidence 3456667777653 4599999999999976543323221 1356899545555543 33 247899999888
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ 218 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~ 218 (436)
+|++....|. |..||.++.+|+..+..++.+
T Consensus 137 -~gi~~~~~H~----------------Al~DA~ata~l~~~l~~~~~~ 167 (850)
T TIGR01407 137 -LGLTHENPHR----------------ADSDAQATAELLLLLFEKMEK 167 (850)
T ss_pred -CCCCCCCCCC----------------hHHHHHHHHHHHHHHHHHHHh
Confidence 5776543322 677788877777777766654
No 52
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.62 E-value=0.033 Score=63.26 Aligned_cols=101 Identities=20% Similarity=0.256 Sum_probs=68.2
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
++...+.+++.+. +.||||+.+|+..|.+.+...|.. ...+.+|+..++..+ .+. ..+++|.+|++.
T Consensus 75 ev~~~~~~~l~~~--~lVaHN~~FD~~fL~~~~~~~g~~----~~~~~iDT~~la~~~-~p~------~~~~~L~~L~~~ 141 (820)
T PRK07246 75 QVARHIYDLIEDC--IFVAHNVKFDANLLAEALFLEGYE----LRTPRVDTVELAQVF-FPT------LEKYSLSHLSRE 141 (820)
T ss_pred HHHHHHHHHhCCC--EEEEECcHHHHHHHHHHHHHcCCC----CCCCceeHHHHHHHH-hCC------CCCCCHHHHHHH
Confidence 4556667777763 459999999999997653221322 235678944455444 443 247899999986
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGN 221 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~ 221 (436)
+|++....+ -|..||.++..|+..|..++...+.
T Consensus 142 -lgl~~~~~H----------------~Al~DA~ata~L~~~l~~~l~~l~~ 175 (820)
T PRK07246 142 -LNIDLADAH----------------TAIADARATAELFLKLLQKIESLPK 175 (820)
T ss_pred -cCCCCCCCC----------------CHHHHHHHHHHHHHHHHHHHhhcCc
Confidence 687654322 2889999999999999888866443
No 53
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=96.61 E-value=0.1 Score=50.74 Aligned_cols=103 Identities=17% Similarity=0.117 Sum_probs=62.5
Q ss_pred HHHHHHHhhCCCCceEEEEehHHhHHHHHhhccc-CCCccCccCCCceeeHHHHHHHhhcccCCC------CCCcCcccH
Q 013817 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTFCS-QGCDIGFDRVEPYLDITSIYNHLHHKQLGR------KLPKETKSL 164 (436)
Q Consensus 92 ~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi-~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~------~~~~~~~gL 164 (436)
++..|..++.+. +-|+||+..|...|.+.+.- .|. .....++|+..++..+.....+. ......++|
T Consensus 119 vl~~l~~~~~~~--~lVaHna~FD~~fL~~~l~~~~~~----~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L 192 (239)
T PRK09146 119 ILDELLEALAGK--VVVVHYRRIERDFLDQALRNRIGE----GIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRL 192 (239)
T ss_pred HHHHHHHHhCCC--EEEEECHHHHHHHHHHHHHHhcCC----CCCCceechHHHHHHHcccccccccchhccCCCCCCCH
Confidence 445555555543 45999999999998654221 010 11356899666666664321000 000136789
Q ss_pred HHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 013817 165 ANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (436)
Q Consensus 165 ~~Lv~~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~ 217 (436)
.+++++ +|++....+ -|..||.++.+|+..+..+.-
T Consensus 193 ~~l~~~-~gl~~~~~H----------------~Al~DA~ata~l~~~~~~~~~ 228 (239)
T PRK09146 193 ADSRLR-YGLPAYSPH----------------HALTDAIATAELLQAQIAHHF 228 (239)
T ss_pred HHHHHH-cCCCCCCCC----------------CcHHHHHHHHHHHHHHHHHHc
Confidence 999987 466543222 288999999999988876653
No 54
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=96.60 E-value=0.083 Score=46.83 Aligned_cols=89 Identities=19% Similarity=0.242 Sum_probs=57.9
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
+.+..|..++.+. ..||||+.+|+..|...+.-.|..+ .....+|+..++..+. +. ...++|..+++.
T Consensus 66 ~v~~~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~g~~~---~~~~~idt~~~~~~~~-~~------~~~~~L~~l~~~ 133 (156)
T cd06130 66 EVWPEIKPFLGGS--LVVAHNASFDRSVLRAALEAYGLPP---PPYQYLCTVRLARRVW-PL------LPNHKLNTVAEH 133 (156)
T ss_pred HHHHHHHHHhCCC--EEEEeChHHhHHHHHHHHHHcCCCC---CCCCEEEHHHHHHHHh-cc------CCCCCHHHHHHH
Confidence 3566777788763 4599999999999875543323221 1346889444554443 32 247899999986
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~ 209 (436)
+|++.. .+. |..||..+.+|+
T Consensus 134 -~g~~~~-~H~----------------Al~Da~~ta~l~ 154 (156)
T cd06130 134 -LGIELN-HHD----------------ALEDARACAEIL 154 (156)
T ss_pred -cCCCcc-CcC----------------chHHHHHHHHHH
Confidence 576654 222 678898888876
No 55
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=96.56 E-value=0.061 Score=50.37 Aligned_cols=160 Identities=16% Similarity=0.218 Sum_probs=89.9
Q ss_pred CeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC------CC-chhHHHHHHHhhCC--C
Q 013817 33 SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS------IP-LPSIWELLKELFVS--P 103 (436)
Q Consensus 33 ~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~------l~-~~~~~~~L~~lLe~--~ 103 (436)
.+++||.|..+.... .....-.++||+... . +++.++.+.... .. ..+++..+..++.. |
T Consensus 4 ~i~~fDIEt~~~~g~-p~~~~d~Ii~Is~~~--------~--~~~~~~~~~~~~~~~v~~~~~E~~lL~~F~~~i~~~dp 72 (195)
T cd05780 4 KILSFDIEVLNHEGE-PNPEKDPIIMISFAD--------E--GGNKVITWKKFDLPFVEVVKTEKEMIKRFIEIVKEKDP 72 (195)
T ss_pred eEEEEEEEecCCCCC-CCCCCCcEEEEEEec--------C--CCceEEEecCCCCCeEEEeCCHHHHHHHHHHHHHHcCC
Confidence 478999999743210 011233466776641 0 123333221110 11 12456666666665 7
Q ss_pred CceEEEEehH-HhHHHHHhhcccCCCccCccC-------------------CCceeeHHHHHHHhhcccCCCCCCcCccc
Q 013817 104 DILKLGFKFK-QDLIYLSSTFCSQGCDIGFDR-------------------VEPYLDITSIYNHLHHKQLGRKLPKETKS 163 (436)
Q Consensus 104 ~i~KVgh~~k-~Dl~~L~~~~gi~g~~~~~~~-------------------~~~v~Dlt~La~yLl~~~~~~~~~~~~~g 163 (436)
++ .+|||.. +|+..|......+|+...+.. -...+|+-.++..... ..+++
T Consensus 73 di-ivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~~--------l~sy~ 143 (195)
T cd05780 73 DV-IYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLN--------LTRYT 143 (195)
T ss_pred CE-EEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhCC--------CCcCc
Confidence 75 4999986 699998644322232211100 0236785555444322 24899
Q ss_pred HHHHHHHHcCCcccc--ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 013817 164 LANICKELLDISLSK--ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (436)
Q Consensus 164 L~~Lv~~~Lg~~l~K--~~q~s-dW~~RPL~~~ql~YAA~DA~~Ll~L~~~L 212 (436)
|.++++++||.+... ..+.. -|...+-...-++|+..||..+++|.+.|
T Consensus 144 L~~v~~~~Lg~~k~d~~~~~i~~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 144 LERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred HHHHHHHHhCCCCCcCCHHHHHHHHhCCCchHHHHHHhHHHHHHHHHHHhhC
Confidence 999999999986422 12222 24444444678999999999999998653
No 56
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=96.41 E-value=0.052 Score=50.59 Aligned_cols=110 Identities=22% Similarity=0.282 Sum_probs=65.4
Q ss_pred hHHHHHHHhhCC--CCceEEEEeh-HHhHHHHHhhcccCCCcc--CccC-----------------CCceeeHHHHHHHh
Q 013817 91 SIWELLKELFVS--PDILKLGFKF-KQDLIYLSSTFCSQGCDI--GFDR-----------------VEPYLDITSIYNHL 148 (436)
Q Consensus 91 ~~~~~L~~lLe~--~~i~KVgh~~-k~Dl~~L~~~~gi~g~~~--~~~~-----------------~~~v~Dlt~La~yL 148 (436)
+++..+.+++.+ |++ .+|||. .+|+..|......+|+.. ++.. -..++|+-.++...
T Consensus 65 ~lL~~f~~~i~~~dpdi-ivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~ 143 (199)
T cd05160 65 ELLKRFFDIIREYDPDI-LTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRD 143 (199)
T ss_pred HHHHHHHHHHHhcCCCE-EEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHh
Confidence 455555565554 554 499999 689999864432223221 0000 12367854444443
Q ss_pred hcccCCCCCCcCcccHHHHHHHHcCCcccc--cccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 013817 149 HHKQLGRKLPKETKSLANICKELLDISLSK--ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (436)
Q Consensus 149 l~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~K--~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~ 209 (436)
.. ..+++|.++++.+||..-.. .....+|....-...-++|.-.||..+++|+
T Consensus 144 ~~--------l~sy~L~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 144 FK--------LKSYTLDAVAEELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred cC--------cccCCHHHHHHHHhCCCCCcCCHHHHhhccCcchHHHHHHHHHHHHHHHHHhh
Confidence 32 24799999999999864322 1222332111223567999999999999886
No 57
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=96.36 E-value=0.011 Score=54.49 Aligned_cols=80 Identities=20% Similarity=0.203 Sum_probs=54.0
Q ss_pred HHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcCC
Q 013817 95 LLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDI 174 (436)
Q Consensus 95 ~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~ 174 (436)
.|..++. ++.+-|||++.+|+.+|.-.++ -..+.| |.+... .+. ....+|..|++++||.
T Consensus 94 ~l~~li~-~~tILVGHsL~nDL~aL~l~hp----------~~~viD-Ta~l~~--~~~------~r~~sLk~La~~~L~~ 153 (174)
T cd06143 94 KLRLLVD-LGCIFVGHGLAKDFRVINIQVP----------KEQVID-TVELFH--LPG------QRKLSLRFLAWYLLGE 153 (174)
T ss_pred HHHHHcC-CCCEEEeccchhHHHHhcCcCC----------CcceEE-cHHhcc--CCC------CCChhHHHHHHHHcCC
Confidence 4555553 4456699999999999864311 146889 643321 121 2368999999999999
Q ss_pred cccccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 013817 175 SLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (436)
Q Consensus 175 ~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~ 209 (436)
.+..+. .| ..+||.++++||
T Consensus 154 ~IQ~~~--Hd-------------SvEDArAam~Ly 173 (174)
T cd06143 154 KIQSET--HD-------------SIEDARTALKLY 173 (174)
T ss_pred cccCCC--cC-------------cHHHHHHHHHHh
Confidence 885421 11 458999999998
No 58
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.14 E-value=0.2 Score=57.79 Aligned_cols=99 Identities=20% Similarity=0.237 Sum_probs=66.0
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
++...|..++.+. ..|+||+.+|+..|.+.|.-.|..+ ....++|+..++..+. |. ...++|.+|++.
T Consensus 73 ev~~~l~~~l~~~--~~VaHN~~FD~~fL~~~~~~~g~~~---~~~~~iDt~~la~~~~-p~------~~~~~L~~l~~~ 140 (928)
T PRK08074 73 DVAPEIVELLEGA--YFVAHNVHFDLNFLNEELERAGYTE---IHCPKLDTVELARILL-PT------AESYKLRDLSEE 140 (928)
T ss_pred HHHHHHHHHhCCC--eEEEEChHHHHHHHHHHHHHcCCCC---CCCCeeeHHHHHHHhc-CC------CCCCCHHHHHHh
Confidence 3556677778753 4599999999999976543323221 1346899555665544 43 247899999987
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ 218 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~ 218 (436)
||++....++ |-.||.++..|+..|..++.+
T Consensus 141 -l~i~~~~~H~----------------Al~DA~ata~l~~~l~~~~~~ 171 (928)
T PRK08074 141 -LGLEHDQPHR----------------ADSDAEVTAELFLQLLNKLER 171 (928)
T ss_pred -CCCCCCCCCC----------------hHHHHHHHHHHHHHHHHHHHh
Confidence 5765543332 678888888888888777764
No 59
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=96.04 E-value=0.23 Score=43.25 Aligned_cols=91 Identities=18% Similarity=0.198 Sum_probs=58.2
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
+....+..++.+ ...||||+..|...|.+.+...|..+ .....+|+..++..+... ...+++..+...
T Consensus 68 ~~~~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~---~~~~~iDt~~~~~~~~~~-------~~~~~l~~~~~~ 135 (159)
T cd06127 68 EVLPEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPP---LPNPWIDTLRLARRLLPG-------LRSHRLGLLLAE 135 (159)
T ss_pred HHHHHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCC---CCCCeeEHHHHHHHHcCC-------CCcCchHHHHHH
Confidence 356677778877 45699999999999877644322110 135689955566555543 235778887555
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~ 209 (436)
++|....+. +-|..||.++.+|+
T Consensus 136 ~~~~~~~~~----------------H~Al~Da~~t~~l~ 158 (159)
T cd06127 136 RYGIPLEGA----------------HRALADALATAELL 158 (159)
T ss_pred HcCCCCCCC----------------CCcHHHHHHHHHHh
Confidence 566543222 23888999998876
No 60
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=95.74 E-value=0.037 Score=63.40 Aligned_cols=109 Identities=19% Similarity=0.386 Sum_probs=77.7
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
+++..+++++.+. +-|.||+.+|+..|...|--.|..+ .-.+++|+.+++ +.+.|. ..+|+|..||..
T Consensus 490 ~vL~kf~~~~~d~--IlVAHNasFD~gFl~~~~~k~~~~~---~~~pvIDTL~la-r~L~P~------~ksh~Lg~l~kk 557 (1444)
T COG2176 490 EVLEKFREFIGDS--ILVAHNASFDMGFLNTNYEKYGLEP---LTNPVIDTLELA-RALNPE------FKSHRLGTLCKK 557 (1444)
T ss_pred HHHHHHHHHhcCc--EEEeccCccchhHHHHHHHHhCCcc---ccCchhhHHHHH-HHhChh------hhhcchHHHHHH
Confidence 5677788888764 4499999999999875543223222 236899944554 555555 358999999988
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-cchhhh
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS-CSSISE 228 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l-~~~~~~ 228 (436)
+ |+.+ ++.+-|-.||.++-.++-.+...+++.|.. ..|+..
T Consensus 558 ~-~v~l----------------e~hHRA~yDaeat~~vf~~f~~~~ke~Gi~~l~eln~ 599 (1444)
T COG2176 558 L-GVEL----------------ERHHRADYDAEATAKVFFVFLKDLKEKGITNLSELND 599 (1444)
T ss_pred h-CccH----------------HHhhhhhhhHHHHHHHHHHHHHHHHHhchhhHHHHhH
Confidence 6 4443 345568889999999999999999999865 444443
No 61
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=95.43 E-value=0.31 Score=50.23 Aligned_cols=161 Identities=7% Similarity=0.031 Sum_probs=85.5
Q ss_pred hcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC---------CC---------ch
Q 013817 29 LSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS---------IP---------LP 90 (436)
Q Consensus 29 L~~~~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~---------l~---------~~ 90 (436)
+.....++||+|+++..+ . ...+|+|+.-.-...|-. .+.-..+|.+.. +. ..
T Consensus 43 ~~~~~fVvlDiETTGLdp---~--~drIIeIgAV~i~~~g~i----ve~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~ 113 (377)
T PRK05601 43 IEAAPFVAVSIQTSGIHP---S--TSRLITIDAVTLTADGEE----VEHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFS 113 (377)
T ss_pred CCCCCEEEEEEECCCCCC---C--CCeEEEEEEEEEEcCCEE----EEEEEEEECcCCCCCCccccCCCHHHHhcCCCHH
Confidence 445789999999998875 2 234666632100000000 011222333221 11 12
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCC------------------------ccCccCCCceeeHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGC------------------------DIGFDRVEPYLDITSIYN 146 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~------------------------~~~~~~~~~v~Dlt~La~ 146 (436)
+++..|.+++.+. +.|+||+.+|+.+|.+.+.-.+. ..+......++|+..++.
T Consensus 114 eVl~el~~fL~g~--vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LAR 191 (377)
T PRK05601 114 QILKPLDRLIDGR--TLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATAR 191 (377)
T ss_pred HHHHHHHHHhCCC--EEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHH
Confidence 5677788888764 45999999999988654311000 000112346899445555
Q ss_pred HhhcccCCCCCCcCcccHHHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 013817 147 HLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (436)
Q Consensus 147 yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L 212 (436)
.+. +. ..++.|..|+++ +|++.+... .|. .+..-+..++ +-.||..+.+||..+
T Consensus 192 rl~-p~------l~~~rL~~La~~-lGi~~p~~~-A~~-~Ra~~p~~~l--~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 192 RQG-VA------LDDIRIRGVAHT-LGLDAPAAE-ASV-ERAQVPHRQL--CREETLLVARLYFAL 245 (377)
T ss_pred HHc-CC------CCCCCHHHHHHH-hCCCCCchh-hhh-hhhcCChhhh--hhHHHHHHHHHHHHh
Confidence 554 33 247999999987 577653211 110 0111112211 225899999998776
No 62
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=95.39 E-value=0.43 Score=44.57 Aligned_cols=158 Identities=15% Similarity=0.196 Sum_probs=83.0
Q ss_pred CeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhHHHHHHHhhCC--CCceEEEE
Q 013817 33 SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVS--PDILKLGF 110 (436)
Q Consensus 33 ~~Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lLe~--~~i~KVgh 110 (436)
.+++||.|+.+... ......-.+++|+... . .+.+.++-.......+++..+.+++.. |++ .+||
T Consensus 4 ~~l~fDIEt~~~~g-fp~~~~d~Ii~Is~~~---------~--~g~~~~~~~~~~~E~~lL~~F~~~i~~~dPd~-i~gy 70 (188)
T cd05781 4 KTLAFDIEVYSKYG-TPNPRRDPIIVISLAT---------S--NGDVEFILAEGLDDRKIIREFVKYVKEYDPDI-IVGY 70 (188)
T ss_pred eEEEEEEEecCCCC-CCCCCCCCEEEEEEEe---------C--CCCEEEEEecCCCHHHHHHHHHHHHHHcCCCE-EEec
Confidence 46899999974221 0011223455555531 0 122333322112223456666665554 564 3799
Q ss_pred ehH-HhHHHHHhhcccCCCccCccCCC-----------------ceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHc
Q 013817 111 KFK-QDLIYLSSTFCSQGCDIGFDRVE-----------------PYLDITSIYNHLHHKQLGRKLPKETKSLANICKELL 172 (436)
Q Consensus 111 ~~k-~Dl~~L~~~~gi~g~~~~~~~~~-----------------~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~L 172 (436)
|.. +|+..|......+|+...+.... ..+|+-.+...... ..+++|.++++ +|
T Consensus 71 N~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~--------l~~y~L~~Va~-~L 141 (188)
T cd05781 71 NSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPE--------VKVKTLENVAE-YL 141 (188)
T ss_pred CCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCC--------CCCCCHHHHHH-HH
Confidence 966 79998753322223221110000 26784444333222 24799999997 58
Q ss_pred CCc--ccc----ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 013817 173 DIS--LSK----ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (436)
Q Consensus 173 g~~--l~K----~~q~s-dW~~RPL~~~ql~YAA~DA~~Ll~L~~~L 212 (436)
|.. ..| ..+.. -|....-...-..|...|+..++.|+..+
T Consensus 142 g~~k~~~k~~~~~~~i~~~~~~~~~~~~l~~Y~~~D~~~t~~l~~~~ 188 (188)
T cd05781 142 GVMKKSERVLIEWYRIYEYWDDEKKRDILLKYNRDDARSTYGLAEKL 188 (188)
T ss_pred CCCccccccCCCHHHHHHHHcCcccHHHHHHHHHHHHHHHHHHHhhC
Confidence 863 122 11111 35432244678999999999999998753
No 63
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=95.37 E-value=0.27 Score=46.33 Aligned_cols=105 Identities=14% Similarity=0.123 Sum_probs=61.8
Q ss_pred hHHHHHHHhhCCCCceEEEEehH-HhHHHHHhhcccCCCccCccCCCceeeHH--HHHHHhh-cccCCCCCCcCcccHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFK-QDLIYLSSTFCSQGCDIGFDRVEPYLDIT--SIYNHLH-HKQLGRKLPKETKSLAN 166 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k-~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt--~La~yLl-~~~~~~~~~~~~~gL~~ 166 (436)
+++..+..++.+.. .||||+. .|+..|... |. . +. ....+|+- .....+. .++ ..+++|.+
T Consensus 73 evl~~f~~f~~~~~--lVaHNa~~fD~~fL~~~-g~---~--~~-~~~~idt~~~~~~~~~~~~~~------~~~~~L~~ 137 (195)
T PRK07247 73 EVLAAFKEFVGELP--LIGYNAQKSDLPILAEN-GL---D--LS-DQYQVDLYDEAFERRSSDLNG------IANLKLQT 137 (195)
T ss_pred HHHHHHHHHHCCCe--EEEEeCcHhHHHHHHHc-CC---C--cC-CCceeehHHHHHHhhccccCC------CCCCCHHH
Confidence 45666777777653 4999996 799999874 33 1 10 11234521 1111111 111 24689999
Q ss_pred HHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcchhhh
Q 013817 167 ICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNSCSSISE 228 (436)
Q Consensus 167 Lv~~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l~~~~~~ 228 (436)
|++. ||++. .. . -|..||.++..|+..|...-+....++||=++
T Consensus 138 La~~-~gi~~-~~---H-------------rAl~DA~~ta~v~~~ll~~~~~~~~~~~~~~~ 181 (195)
T PRK07247 138 VADF-LGIKG-RG---H-------------NSLEDARMTARVYESFLESDQNKEYLEQQEEV 181 (195)
T ss_pred HHHh-cCCCC-CC---c-------------CCHHHHHHHHHHHHHHHhhccchhhhhcchhh
Confidence 9986 57653 11 2 27789999999999987655544444443333
No 64
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=94.49 E-value=0.45 Score=44.32 Aligned_cols=84 Identities=17% Similarity=0.202 Sum_probs=53.0
Q ss_pred ceEEEEehHHhHHHHHhhcccCCC-ccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcCCccccccccc
Q 013817 105 ILKLGFKFKQDLIYLSSTFCSQGC-DIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCS 183 (436)
Q Consensus 105 i~KVgh~~k~Dl~~L~~~~gi~g~-~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~K~~q~s 183 (436)
.+.||||+.+|+..|.+.+.-.|+ ...+ ....++|+..++..+. + ...|.+++++ +|+++... +
T Consensus 103 ~~lVaHna~FD~~fL~~~~~~~~~~~~~~-~~~~~lDt~~la~~~~-~---------~~~L~~l~~~-~gi~~~~~-~-- 167 (189)
T cd06134 103 AILVGHNAHFDLGFLNAAVARCKIKRNPF-HPFSTFDTATLAGLAY-G---------QTVLAKACQA-AGIEFDNK-E-- 167 (189)
T ss_pred CeEEEecchhhHHHHHHHHHHhCCCCCCC-CCCcEEEHHHHHHHHh-C---------CCcHHHHHHH-CCCCCCCC-C--
Confidence 456999999999998755332232 1000 1235799556665553 2 3579999887 47664211 1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 013817 184 DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (436)
Q Consensus 184 dW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~ 214 (436)
.+-|..||.++.+|+..|.+
T Consensus 168 -----------~H~Al~DA~ata~lf~~l~~ 187 (189)
T cd06134 168 -----------AHSALYDTQKTAELFCKIVN 187 (189)
T ss_pred -----------CcChHHHHHHHHHHHHHHHH
Confidence 12288999999999988764
No 65
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=94.45 E-value=0.0054 Score=62.30 Aligned_cols=140 Identities=21% Similarity=0.246 Sum_probs=94.3
Q ss_pred EEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhHHHHHHHhhCCCCceEEEEehHHhH
Q 013817 37 LDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFKQDL 116 (436)
Q Consensus 37 ~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lLe~~~i~KVgh~~k~Dl 116 (436)
+-.|.+..-. .+++|.+|.++. ..+|++|+..++...+-..++.++++.+|.|+-|++..-+
T Consensus 63 ~~~e~a~~~~----~~~l~~~q~~~~--------------~~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~~~~d~~~~~ 124 (458)
T KOG2405|consen 63 VAAEGANVCR----HGKLCWLQVATN--------------CRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLS 124 (458)
T ss_pred ccccCccccc----cCcchhHHHHHH--------------HHHHHHHHHHhhhHHHHHHHHHHhhhhhHhhhHHHHHHHH
Confidence 4455544432 358999999984 6789999877766667788999999999999999999999
Q ss_pred HHHHhhcccCCCccCccCCCceeeHHHHHHHhhcc-cCCCCCCcCcccHH-HHHHHHcCCcc------cc-----ccccc
Q 013817 117 IYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHK-QLGRKLPKETKSLA-NICKELLDISL------SK-----ELQCS 183 (436)
Q Consensus 117 ~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~-~~~~~~~~~~~gL~-~Lv~~~Lg~~l------~K-----~~q~s 183 (436)
.+++..||| ..+++|| |+++.-+... +.|...|.....+. .|.+ .|.+.+ .| .+...
T Consensus 125 ~~~~~~~~i--------~~n~v~~-~q~~d~~q~~~e~g~~~~n~~~~~q~sl~k-h~~~a~k~~~~l~~r~~~~~~n~e 194 (458)
T KOG2405|consen 125 DCLSHQYGI--------LLNNVFD-TQVADVLQFSMETGGYLPNCITTLQESLIK-HLQVAPKYLSFLEKRQKLIQENPE 194 (458)
T ss_pred HHhccccee--------eecchhh-hhhhhhhhhcccccccCCccccchHHHHHH-HHHhcccHHHHHHHHHHHHhhCcc
Confidence 999999988 3689999 8887666442 22444443323332 3333 222211 11 12344
Q ss_pred CCCCCCCCHHHHHHHHHHHHH
Q 013817 184 DWSNRPLTEEQKNYAAIDAHC 204 (436)
Q Consensus 184 dW~~RPL~~~ql~YAA~DA~~ 204 (436)
-|-.||.++.-+.--|..|.+
T Consensus 195 ~~~i~~~~~s~~~~~~~e~~~ 215 (458)
T KOG2405|consen 195 VWFIRPVSPSLLKILALEATY 215 (458)
T ss_pred eeEeecCchhHHHhhhhhhhh
Confidence 588899888766655555544
No 66
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=94.40 E-value=0.01 Score=60.36 Aligned_cols=136 Identities=21% Similarity=0.222 Sum_probs=85.9
Q ss_pred ceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCc
Q 013817 53 RVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGF 132 (436)
Q Consensus 53 ~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~ 132 (436)
.+.++++|+. +..|++|...-+.--.....+..|++..+ +. |.+.+...|...|++
T Consensus 212 e~~~m~ia~~--------------n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~------- 267 (458)
T KOG2405|consen 212 EATYMNIADG--------------NEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHS------- 267 (458)
T ss_pred hhhhhhhccc--------------chhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHH-------
Confidence 3445677773 78899986543321123335666776655 44 899999999888876
Q ss_pred cCCCceeeHHHHHHHhhcccC-CCCCCcC-cccHHHHHH--HHcCCcc------ccc-cccc-CCCCCCCCHHHHHHHHH
Q 013817 133 DRVEPYLDITSIYNHLHHKQL-GRKLPKE-TKSLANICK--ELLDISL------SKE-LQCS-DWSNRPLTEEQKNYAAI 200 (436)
Q Consensus 133 ~~~~~v~Dlt~La~yLl~~~~-~~~~~~~-~~gL~~Lv~--~~Lg~~l------~K~-~q~s-dW~~RPL~~~ql~YAA~ 200 (436)
.+.+++| |++++.+..+.. |+..|.. -.+...|-. .|.+.+. .+. .++- +|..||.++...+-++.
T Consensus 268 -~L~nVkD-tQia~sLve~~e~grr~p~~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~ 345 (458)
T KOG2405|consen 268 -ALKNVKD-TQIASSLVEPSEYGRRHPTSILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHR 345 (458)
T ss_pred -HHHhhHH-HHHHHHHhhhHHhcccCCccceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHHH
Confidence 2689999 999999988763 4443321 111111111 0111111 111 1233 79999999999999999
Q ss_pred HHHHHHHHHHHHHH
Q 013817 201 DAHCLIEIFNIFQV 214 (436)
Q Consensus 201 DA~~Ll~L~~~L~~ 214 (436)
||.+|+.....|.+
T Consensus 346 dv~~Ll~~~~~l~a 359 (458)
T KOG2405|consen 346 DVISLLGIFDTLVA 359 (458)
T ss_pred HHHHHHHHHhhHhh
Confidence 99999997766653
No 67
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=94.30 E-value=1.4 Score=41.45 Aligned_cols=109 Identities=24% Similarity=0.285 Sum_probs=62.8
Q ss_pred hHHHHHHHhhC--CCCceEEEEehHH-hHHHHHhhcccCCCccCccC--------------------C-CceeeHHHHHH
Q 013817 91 SIWELLKELFV--SPDILKLGFKFKQ-DLIYLSSTFCSQGCDIGFDR--------------------V-EPYLDITSIYN 146 (436)
Q Consensus 91 ~~~~~L~~lLe--~~~i~KVgh~~k~-Dl~~L~~~~gi~g~~~~~~~--------------------~-~~v~Dlt~La~ 146 (436)
+++..+..++. +|++ .+|||... |+..|.+....+|+.+.+.+ . ..++|+-.+..
T Consensus 53 ~lL~~f~~~i~~~dPDv-i~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k 131 (193)
T cd05784 53 SLLLALIAWFAQYDPDI-IIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALK 131 (193)
T ss_pred HHHHHHHHHHHhhCCCE-EEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHH
Confidence 45555555544 4564 48999885 99887543332233211110 0 12677433332
Q ss_pred H-hhcccCCCCCCcCcccHHHHHHHHcCCcccc-c-----cccc-CCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 013817 147 H-LHHKQLGRKLPKETKSLANICKELLDISLSK-E-----LQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (436)
Q Consensus 147 y-Ll~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~K-~-----~q~s-dW~~RPL~~~ql~YAA~DA~~Ll~L~~ 210 (436)
. ... ..+++|.++++++||..-.. . .... -|...+ ..-++|+..||..+++|++
T Consensus 132 ~~~~k--------l~sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~~~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 132 TATYH--------FESFSLENVAQELLGEGKLIHDVDDRGAEIERLFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred HccCC--------CCcCCHHHHHHHHhCCCccccCcccCHHHHHHHHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 2 111 24899999999999964221 1 1122 244333 5679999999999999873
No 68
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=94.24 E-value=0.37 Score=48.54 Aligned_cols=99 Identities=17% Similarity=0.201 Sum_probs=64.6
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
+++..|.+++.+. +-|+||+.+|+..|.+.+.-.|.. + ....++|+..++..+.. . ...++|..|++.
T Consensus 69 ev~~~~~~fl~~~--~lVaHNa~FD~~fL~~~~~r~~~~--~-~~~~~idT~~lar~l~~-~------~~~~~L~~L~~~ 136 (309)
T PRK06195 69 KIWEKIKHYFNNN--LVIAHNASFDISVLRKTLELYNIP--M-PSFEYICTMKLAKNFYS-N------IDNARLNTVNNF 136 (309)
T ss_pred HHHHHHHHHhCCC--EEEEECcHHHHHHHHHHHHHhCCC--C-CCCCEEEHHHHHHHHcC-C------CCcCCHHHHHHH
Confidence 3556677777653 459999999999986543322211 1 12368894456665543 2 236899999988
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~ 219 (436)
+ |++.. . +-|..||.++.+|+..|..++...
T Consensus 137 ~-gi~~~-~----------------H~Al~DA~ata~l~~~l~~~~~~~ 167 (309)
T PRK06195 137 L-GYEFK-H----------------HDALADAMACSNILLNISKELNSK 167 (309)
T ss_pred c-CCCCc-c----------------cCCHHHHHHHHHHHHHHHHHhccC
Confidence 5 65421 1 238899999999998888776543
No 69
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=94.14 E-value=0.74 Score=55.34 Aligned_cols=107 Identities=14% Similarity=0.240 Sum_probs=70.9
Q ss_pred HHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHH
Q 013817 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKEL 171 (436)
Q Consensus 92 ~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~ 171 (436)
++..+..++.+ ...|+|++.+|...|...+.-+|+.+ ....++|+..+++. +.+. ...++|.+|+++
T Consensus 489 aL~~f~~figg--~vLVAHNa~FD~~fL~~~l~rlgl~~---l~~~~IDTLelar~-l~p~------~k~~kL~~LAk~- 555 (1437)
T PRK00448 489 VLPKFKEFCGD--SILVAHNASFDVGFINTNYEKLGLEK---IKNPVIDTLELSRF-LYPE------LKSHRLNTLAKK- 555 (1437)
T ss_pred HHHHHHHHhCC--CEEEEeCccccHHHHHHHHHHcCCcc---ccccceeHHHHHHH-HcCc------cccccHHHHHHH-
Confidence 44455555544 56699999999988754433223221 13567894445444 4443 357899999987
Q ss_pred cCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-cchhh
Q 013817 172 LDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS-CSSIS 227 (436)
Q Consensus 172 Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l-~~~~~ 227 (436)
+|+.+... +-|..||.++..|+..|..++.+.|.. .+++.
T Consensus 556 lGL~~~~~----------------HrAl~DA~aTa~lf~~ll~~l~~~gi~~~~~L~ 596 (1437)
T PRK00448 556 FGVELEHH----------------HRADYDAEATAYLLIKFLKDLKEKGITNLDELN 596 (1437)
T ss_pred cCCCCCCC----------------cChHHHHHHHHHHHHHHHHHHHHcCCCCHHHHH
Confidence 57765432 338899999999999999999887765 33333
No 70
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=92.40 E-value=4.4 Score=38.87 Aligned_cols=54 Identities=17% Similarity=0.177 Sum_probs=38.9
Q ss_pred CcccHHHHHHHHcCCcccc--cccccC-CCCCCCC-HHHHHHHHHHHHHHHHHHHHHH
Q 013817 160 ETKSLANICKELLDISLSK--ELQCSD-WSNRPLT-EEQKNYAAIDAHCLIEIFNIFQ 213 (436)
Q Consensus 160 ~~~gL~~Lv~~~Lg~~l~K--~~q~sd-W~~RPL~-~~ql~YAA~DA~~Ll~L~~~L~ 213 (436)
.+++|.++++++||..... ...... |...|-. ..-++|...||..+++|+..|.
T Consensus 167 ~sy~L~~Va~~~Lg~~k~d~~~~~i~~~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl~ 224 (230)
T cd05777 167 RSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLM 224 (230)
T ss_pred ccCcHHHHHHHHhCCCCCCCCHHHHHHHHccCHhHhHHHHHhhHHHHHHHHHHHHHHh
Confidence 4899999999999965321 122232 4333322 5679999999999999999885
No 71
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=92.38 E-value=2.1 Score=40.53 Aligned_cols=159 Identities=16% Similarity=0.168 Sum_probs=80.7
Q ss_pred CeEEEEEeEeCCCCCC---CCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhHHHHHHHhhCC--CCceE
Q 013817 33 SLVGLDAEWKPQRSHQ---SNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVS--PDILK 107 (436)
Q Consensus 33 ~~Va~D~E~~~~~~~~---~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lLe~--~~i~K 107 (436)
.+++||.|..+..... .....-.++||+... . .+...++........+++..+..++.. |++ .
T Consensus 10 kilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~---------~--~~~~~~~~~~~~~E~~lL~~f~~~i~~~dPdi-i 77 (207)
T cd05785 10 RRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRD---------N--RGWEEVLHAEDAAEKELLEELVAIIRERDPDV-I 77 (207)
T ss_pred eEEEEEEEecCCCCccCCCCCCCCCeEEEEeccc---------C--CCceeeeccCCCCHHHHHHHHHHHHHHhCCCE-E
Confidence 5789999986543110 012335688888752 0 111122221112223455555555554 665 3
Q ss_pred EEEeh-HHhHHHHHhhcccCCCccCccC--------------------------C-CceeeHHHHHHHhhcccCCCCCCc
Q 013817 108 LGFKF-KQDLIYLSSTFCSQGCDIGFDR--------------------------V-EPYLDITSIYNHLHHKQLGRKLPK 159 (436)
Q Consensus 108 Vgh~~-k~Dl~~L~~~~gi~g~~~~~~~--------------------------~-~~v~Dlt~La~yLl~~~~~~~~~~ 159 (436)
+|||. .+|+..|......+|+...+.+ . ..++|+-.++....... +. .
T Consensus 78 ~g~N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~--~~--l 153 (207)
T cd05785 78 EGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSS--RD--L 153 (207)
T ss_pred eccCCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccc--cC--C
Confidence 79999 6799987543222232211100 0 12368323222211110 11 2
Q ss_pred CcccHHHHHHHH--cCCc-cc-ccccc-cCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 013817 160 ETKSLANICKEL--LDIS-LS-KELQC-SDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (436)
Q Consensus 160 ~~~gL~~Lv~~~--Lg~~-l~-K~~q~-sdW~~RPL~~~ql~YAA~DA~~Ll~L~ 209 (436)
.+++|.++++.+ ++.. .+ ...+. .-|...+ +.-+.|+..||..++.|.
T Consensus 154 ~sysL~~Va~~~g~~~~~k~d~~~~~I~~l~~~~~--~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 154 PSYGLKAVAKHFGLASPDRTYIDGRQIAEVWRSDP--ARLLAYALDDVRETEGLA 206 (207)
T ss_pred CCCCHHHHHHHhcccCCCcCCCCHHHHHHHHhcCH--HHHHHHHHHHHHHHHHhh
Confidence 478999999986 2321 11 01111 1354442 678999999999998875
No 72
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=92.34 E-value=4.1 Score=39.01 Aligned_cols=104 Identities=9% Similarity=0.027 Sum_probs=60.5
Q ss_pred HHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcCC
Q 013817 95 LLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDI 174 (436)
Q Consensus 95 ~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~ 174 (436)
.+..+..+ -.-||||+.+|...|... ....+|+..++..+ .++ ..+++..|++. +|+
T Consensus 67 v~~~~~~~--~~lVaHNa~FD~~~L~~~------------~~~~idTl~lar~l-~p~-------~~~~l~~L~~~-~~l 123 (219)
T PRK07983 67 VIPHYYGS--EWYVAHNASFDRRVLPEM------------PGEWICTMKLARRL-WPG-------IKYSNMALYKS-RKL 123 (219)
T ss_pred HHHHHcCC--CEEEEeCcHhhHHHHhCc------------CCCcEeHHHHHHHH-ccC-------CCCCHHHHHHH-cCC
Confidence 34444332 355999999999988642 24678944455444 443 24888888865 465
Q ss_pred cccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcchhhhcccCCCc
Q 013817 175 SLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNSCSSISELDSSNLD 235 (436)
Q Consensus 175 ~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l~~~~~~~~~~~~~ 235 (436)
...... . ...+-|..||+++..|+..+.. ..|...+|+-.+...|..
T Consensus 124 ~~~~~~-~----------~~aHrAl~Da~ata~ll~~l~~---~~~~~~~~l~~~~~~~~~ 170 (219)
T PRK07983 124 NVQTPP-G----------LHHHRALYDCYITAALLIDIMN---TSGWTAEEMADITGRPSL 170 (219)
T ss_pred CCCCCC-C----------CCCCcHHHHHHHHHHHHHHHHH---HcCCCHHHHHHHhcCCcc
Confidence 431100 0 0123388999999999888763 233223445555444433
No 73
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=91.61 E-value=8.9 Score=36.25 Aligned_cols=161 Identities=16% Similarity=0.125 Sum_probs=84.4
Q ss_pred CeEEEEEeEeCCC----CCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC----------------CC-chh
Q 013817 33 SLVGLDAEWKPQR----SHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS----------------IP-LPS 91 (436)
Q Consensus 33 ~~Va~D~E~~~~~----~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~----------------l~-~~~ 91 (436)
.+++||.|..+.. +.. ....-.++||+.... ++...++++.... .. ..+
T Consensus 6 rilsfDIE~~~~~~~~fP~~-~~~~d~IisI~~~~~---------~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~~~E~~ 75 (204)
T cd05783 6 KRIAIDIEVYTPIKGRIPDP-KTAEYPVISVALAGS---------DGLKRVLVLKREGVEGLEGLLPEGAEVEFFDSEKE 75 (204)
T ss_pred eEEEEEEEECCCCCCCCcCC-CCCCCeEEEEEEcCC---------CCCcEEEEEecCCcccccccCCCCCeEEecCCHHH
Confidence 5789999997422 210 112235788888510 0123455443100 11 134
Q ss_pred HHHHHHHhhCCCCceEEEEehH-HhHHHHHhhcccCCCc-----cCcc------CCCceeeHHHHHHH-hhc-ccCCCCC
Q 013817 92 IWELLKELFVSPDILKLGFKFK-QDLIYLSSTFCSQGCD-----IGFD------RVEPYLDITSIYNH-LHH-KQLGRKL 157 (436)
Q Consensus 92 ~~~~L~~lLe~~~i~KVgh~~k-~Dl~~L~~~~gi~g~~-----~~~~------~~~~v~Dlt~La~y-Ll~-~~~~~~~ 157 (436)
++..+.+++.+.. ..||||.. +|+..|......+|+. ..+. .....+|+-..... .+. -.++.
T Consensus 76 lL~~F~~~i~~~~-~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~-- 152 (204)
T cd05783 76 LIREAFKIISEYP-IVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGN-- 152 (204)
T ss_pred HHHHHHHHHhcCC-EEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhcc--
Confidence 6666666776654 45899987 6999885432222322 0000 01235674332221 110 00000
Q ss_pred CcCcccHHHHHHHHcCCccc-ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 013817 158 PKETKSLANICKELLDISLS-KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (436)
Q Consensus 158 ~~~~~gL~~Lv~~~Lg~~l~-K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~ 210 (436)
...+++|.++++.+||..-. -..+ -|.. =.+.-+.|+..||..++.|..
T Consensus 153 ~~~~~~L~~Va~~~lg~~K~~~~~~--i~~~--~~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 153 KYREYTLDAVAKALLGEGKVELEKN--ISEL--NLYELAEYNYRDAELTLELTT 202 (204)
T ss_pred ccccCcHHHHHHHhcCCCcccCCch--hhhh--cHHHHHHhhHHHHHHHHHHhc
Confidence 12489999999999996321 1111 1222 126678999999999988864
No 74
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=91.42 E-value=0.89 Score=41.85 Aligned_cols=88 Identities=17% Similarity=0.075 Sum_probs=54.2
Q ss_pred HHHHHHhhCC--CCceEEEEeh-HHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHH
Q 013817 93 WELLKELFVS--PDILKLGFKF-KQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (436)
Q Consensus 93 ~~~L~~lLe~--~~i~KVgh~~-k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~ 169 (436)
.+.|..++.. ...+-||||+ .+|+..|.+.+.-.|+. +.....++| |.-.+..+. . +|++|++
T Consensus 85 ~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~--~~~~~~~iD-tl~l~r~~~----------~-~L~~l~~ 150 (177)
T cd06136 85 ANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTK--LPDDILCVD-SLPAFRELD----------Q-SLGSLYK 150 (177)
T ss_pred HHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCC--CCCCCEEEE-eHHHHhhhH----------h-hHHHHHH
Confidence 3556666543 2356799998 89999986554322322 111134579 543222221 2 8999999
Q ss_pred HHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 013817 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (436)
Q Consensus 170 ~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~ 210 (436)
+++|++....+ -|..||.++.+++.
T Consensus 151 ~~~~~~~~~~H----------------~A~~Da~at~~v~~ 175 (177)
T cd06136 151 RLFGQEPKNSH----------------TAEGDVLALLKCAL 175 (177)
T ss_pred HHhCCCccccc----------------chHHHHHHHHHHHh
Confidence 98887764333 28889999877753
No 75
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=90.66 E-value=0.35 Score=43.35 Aligned_cols=148 Identities=17% Similarity=0.171 Sum_probs=67.7
Q ss_pred EEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCc---hhHHHHHHHhhCCCCceEEEEe
Q 013817 35 VGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPL---PSIWELLKELFVSPDILKLGFK 111 (436)
Q Consensus 35 Va~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~---~~~~~~L~~lLe~~~i~KVgh~ 111 (436)
+.||.|+.+..+ ....+.+++++... .+...++........ ..+.+.+ ..+.+...+ |+||
T Consensus 1 l~~DIET~Gl~~---~~~~i~liG~~~~~-----------~~~~~~~~~~~~~~~~ee~~~~~~~-~~l~~~~~i-v~yn 64 (164)
T PF13482_consen 1 LFFDIETTGLSP---DNDTIYLIGVADFD-----------DDEIITFIQWFAEDPDEEEIILEFF-ELLDEADNI-VTYN 64 (164)
T ss_dssp --EEEEESS-GG----G---EEEEEEE-E-----------TTTTE-EEEE-GGGHHHHHHHHH---HHHHTT--E-EESS
T ss_pred CcEEecCCCCCC---CCCCEEEEEEEEeC-----------CCceEEeeHhhccCcHHHHHHHHHH-HHHhcCCeE-EEEe
Confidence 468999997765 23567888887531 012222222111111 1233333 344444433 7777
Q ss_pred h-HHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcCCcccc----ccccc---
Q 013817 112 F-KQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSK----ELQCS--- 183 (436)
Q Consensus 112 ~-k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~K----~~q~s--- 183 (436)
. .+|...|.+.+.-.++. .....+||-.++..... .+.+|+.++.. ||..-.+ +.+..
T Consensus 65 g~~FD~p~L~~~~~~~~~~----~~~~~iDl~~~~~~~~~---------~~~~Lk~ve~~-lg~~~~~~~~~G~~~~~~~ 130 (164)
T PF13482_consen 65 GKNFDIPFLKRRAKRYGLP----PPFNHIDLLKIIKKHFL---------ESYSLKNVEKF-LGIERRDDDISGSESVKLY 130 (164)
T ss_dssp TTTTHHHHHHHHH-HHHH------GGGEEEHHHHHT-TTS---------CCTT--SHHH------------HHHHHHHHH
T ss_pred CcccCHHHHHHHHHHcCCC----cccchhhHHHHHHhccC---------CCCCHHHHhhh-cccccccCCCCHHHHHHHH
Confidence 5 56999987654221221 24678895444422111 36788888776 6765441 11111
Q ss_pred -CCCC---CCCCHHHHHHHHHHHHHHHHHHHHH
Q 013817 184 -DWSN---RPLTEEQKNYAAIDAHCLIEIFNIF 212 (436)
Q Consensus 184 -dW~~---RPL~~~ql~YAA~DA~~Ll~L~~~L 212 (436)
.|.. ...-+..+.|.-.|+..+.+|++.|
T Consensus 131 ~~~~~~~~~~~~~~i~~yN~~Dv~~~~~L~~~l 163 (164)
T PF13482_consen 131 KEYLETGDPEALEEILEYNEDDVRATRRLYEWL 163 (164)
T ss_dssp H---TTGGTS--HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 1211 2355788999999999999999876
No 76
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=90.14 E-value=5.3 Score=37.86 Aligned_cols=111 Identities=15% Similarity=0.197 Sum_probs=62.6
Q ss_pred hHHHHHHHhhCC--CCceEEEEehH-HhHHHHHhhcccCCCcc----CccC---------CCceeeHHHHHHHhhcccCC
Q 013817 91 SIWELLKELFVS--PDILKLGFKFK-QDLIYLSSTFCSQGCDI----GFDR---------VEPYLDITSIYNHLHHKQLG 154 (436)
Q Consensus 91 ~~~~~L~~lLe~--~~i~KVgh~~k-~Dl~~L~~~~gi~g~~~----~~~~---------~~~v~Dlt~La~yLl~~~~~ 154 (436)
+++..+.+++.+ |++ .+|||.. +|+..|......+|+.+ ++.. ....+|+-.+...-..
T Consensus 75 ~lL~~f~~~i~~~~Pd~-i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~---- 149 (204)
T cd05779 75 ALLQRFFEHIREVKPHI-IVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSY---- 149 (204)
T ss_pred HHHHHHHHHHHHhCCCE-EEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhc----
Confidence 455555555554 555 4899876 69988753322223221 1110 0125674333321101
Q ss_pred CCCCcCcccHHHHHHHHcCCccccc--cc-ccCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 013817 155 RKLPKETKSLANICKELLDISLSKE--LQ-CSDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (436)
Q Consensus 155 ~~~~~~~~gL~~Lv~~~Lg~~l~K~--~q-~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~ 210 (436)
++..+++|..+++.+||..-..- .. ..-|...+ +.-++|...||..++.||.
T Consensus 150 --l~~~sysLd~Va~~~Lg~~K~~~~~~~I~~~~~~~~--~~l~~Y~~~D~~~T~~l~~ 204 (204)
T cd05779 150 --LPQGSQGLKAVTKAKLGYDPVELDPEDMVPLAREDP--QTLASYSVSDAVATYYLYM 204 (204)
T ss_pred --CCCCCccHHHHHHHHhCCCcCcCCHHHHHHHHhCCc--HHHHhccHHHHHHHHHHhC
Confidence 11237899999999999742111 11 11465544 5679999999999999983
No 77
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=89.44 E-value=12 Score=37.65 Aligned_cols=88 Identities=15% Similarity=0.138 Sum_probs=51.1
Q ss_pred HHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHc
Q 013817 93 WELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELL 172 (436)
Q Consensus 93 ~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~L 172 (436)
.+.+..++.... +.|+||+.+|...|.+.+.. +. .....+ ++.......+. ..+++|.+|+..+
T Consensus 111 ~~~l~~fl~~~~-vlVAHNA~FD~~fL~~~~~~------~~-~~~~~c-t~~~i~~~~~~------~~~~kL~~La~~~- 174 (294)
T PRK09182 111 PAAVDALIAPAD-LIIAHNAGFDRPFLERFSPV------FA-TKPWAC-SVSEIDWSARG------FEGTKLGYLAGQA- 174 (294)
T ss_pred HHHHHHHhcCCC-EEEEeCHHHHHHHHHHHHHh------cc-CCcccc-cHHHHhhcccc------CCCCCHHHHHHHc-
Confidence 456677777643 55999999999999764221 10 112233 33211111111 2478999999875
Q ss_pred CCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 013817 173 DISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (436)
Q Consensus 173 g~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~ 213 (436)
|. .. . .+=|..||.++.+|+....
T Consensus 175 g~-~~---~-------------aHrAl~Da~Ata~ll~~~l 198 (294)
T PRK09182 175 GF-FH---E-------------GHRAVDDCQALLELLARPL 198 (294)
T ss_pred CC-CC---C-------------CcChHHHHHHHHHHHHHHH
Confidence 42 11 1 1228899999988877543
No 78
>PRK11779 sbcB exonuclease I; Provisional
Probab=89.35 E-value=10 Score=40.71 Aligned_cols=106 Identities=16% Similarity=0.155 Sum_probs=57.3
Q ss_pred HHHHHHHhhCCCCceEEEEe-hHHhHHHHHhhcccCCCccC---ccCCCceeeHHHHHH--HhhcccCCCCCC-----cC
Q 013817 92 IWELLKELFVSPDILKLGFK-FKQDLIYLSSTFCSQGCDIG---FDRVEPYLDITSIYN--HLHHKQLGRKLP-----KE 160 (436)
Q Consensus 92 ~~~~L~~lLe~~~i~KVgh~-~k~Dl~~L~~~~gi~g~~~~---~~~~~~v~Dlt~La~--yLl~~~~~~~~~-----~~ 160 (436)
+...+..++..+..+.|||| +.+|...|...|....+.+. +......+|+..++. +.+.+. +-.-| ..
T Consensus 81 ~~~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~-~i~~P~~~~g~~ 159 (476)
T PRK11779 81 FAARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPE-GINWPENEDGLP 159 (476)
T ss_pred HHHHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccc-cccCcccccCCC
Confidence 45566667765555679997 78999887654311000000 000011234322222 222221 00000 23
Q ss_pred cccHHHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 013817 161 TKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVK 215 (436)
Q Consensus 161 ~~gL~~Lv~~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~ 215 (436)
++.|++|++.+ |++....+ =|..||+++.+|+..+..+
T Consensus 160 s~rLe~L~~~~-gI~~~~AH----------------dALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 160 SFKLEHLTKAN-GIEHENAH----------------DAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CCcHHHHHHHc-CCCCCCCC----------------CcHHHHHHHHHHHHHHHHh
Confidence 68999999875 66543222 2788999999999988865
No 79
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=88.17 E-value=5.1 Score=37.75 Aligned_cols=99 Identities=16% Similarity=0.104 Sum_probs=60.3
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
+++..|.+++.+...+ +.|+...|+..|.+.+...|+. +.....++|+..++..+... ...++|.++++.
T Consensus 81 evl~~f~~~~~~~~~~-iv~~~~fD~~fL~~~~~~~~~~--~~~~~~~~dl~~~~~~~~~~-------~~~~~L~~~~~~ 150 (207)
T PRK07748 81 ELVEKLAEYDKRCKPT-IVTWGNMDMKVLKHNCEKAGVP--FPFKGQCRDLSLEYKKFFGE-------RNQTGLWKAIEE 150 (207)
T ss_pred HHHHHHHHHhCcCCeE-EEEECHHHHHHHHHHHHHcCCC--CcccccceeHHHHHHHHhCc-------CCCCCHHHHHHH
Confidence 4566777788763333 4456789999997654322322 11124577855444434322 236899998877
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVK 215 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~ 215 (436)
+|++... + -+-|..||.++.+|+..|...
T Consensus 151 -~gi~~~~--~-------------~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 151 -YGKEGTG--K-------------HHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred -cCCCCCC--C-------------CcChHHHHHHHHHHHHHHHhC
Confidence 4654321 1 122889999999999988643
No 80
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=85.35 E-value=8.9 Score=36.33 Aligned_cols=110 Identities=21% Similarity=0.196 Sum_probs=62.8
Q ss_pred hhHHHHHHHhhCCCCceEEEEehH-HhHHHHHhhcccCCCc-c-CccCC-----------CceeeHHHHHHHhhcccCCC
Q 013817 90 PSIWELLKELFVSPDILKLGFKFK-QDLIYLSSTFCSQGCD-I-GFDRV-----------EPYLDITSIYNHLHHKQLGR 155 (436)
Q Consensus 90 ~~~~~~L~~lLe~~~i~KVgh~~k-~Dl~~L~~~~gi~g~~-~-~~~~~-----------~~v~Dlt~La~yLl~~~~~~ 155 (436)
.+++..+..++++.....||||.+ +|+..|....-.+|+. | .+... ...+||-.+.+ ..+
T Consensus 79 ~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~---~~~--- 152 (208)
T cd05782 79 KELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLA---FYG--- 152 (208)
T ss_pred HHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHh---ccC---
Confidence 356666666666523345999996 6999986442223331 0 01000 12678433322 211
Q ss_pred CCCcCcccHHHHHHHHcCCccccc----ccc-cCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 013817 156 KLPKETKSLANICKELLDISLSKE----LQC-SDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (436)
Q Consensus 156 ~~~~~~~gL~~Lv~~~Lg~~l~K~----~q~-sdW~~RPL~~~ql~YAA~DA~~Ll~L~~ 210 (436)
...+.+|..+++ +||.+ .|. .+. .-|.... .+.-.+|+..||..+..||.
T Consensus 153 --~~~~~~L~~va~-~lG~~-~K~d~~G~~v~~~y~~g~-~~~I~~Yc~~Dv~~t~~l~l 207 (208)
T cd05782 153 --ARARASLDLLAK-LLGIP-GKMDVDGSQVWELYAEGK-LDEIAEYCETDVLNTYLLYL 207 (208)
T ss_pred --ccCCCCHHHHHH-HhCCC-CCcCCCHHHHHHHHHcCC-hHHHHHHHHHHHHHHHHHHh
Confidence 124789999986 67773 221 111 2355444 45678999999999999874
No 81
>PF09281 Taq-exonuc: Taq polymerase, exonuclease; InterPro: IPR015361 This domain is found in prokaryotic Taq DNA polymerase (thermostable), where it assumes a ribonuclease H-like motif. The domain confers 5'-3' exonuclease activity to the polymerase []. ; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 4DF4_A 3T3F_A 1QSY_A 3OJS_A 3PO5_A 3OJU_A 1QTM_A 1QSS_A 3PY8_A 4DFJ_A ....
Probab=84.48 E-value=5.1 Score=35.24 Aligned_cols=55 Identities=18% Similarity=0.319 Sum_probs=35.5
Q ss_pred CCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 013817 135 VEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (436)
Q Consensus 135 ~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~ 214 (436)
+.+--| -+|.+||+++. +.+...++++|+| .+|... |+..|.+..+|+..|.+
T Consensus 84 v~PGDD-PlLlAYLlDPs--------Nt~p~~varRY~~---------~~W~~d---------A~~RA~~t~~L~~~L~p 136 (138)
T PF09281_consen 84 VEPGDD-PLLLAYLLDPS--------NTNPEGVARRYLG---------GEWPED---------AATRALATARLLRALPP 136 (138)
T ss_dssp --B----HHHHHHHH-TT----------SHHHHHHHH-T---------S---SS---------HHHHHHHHHHHHHHHHH
T ss_pred cCCCCC-cchhhhhcCcc--------CCChHHHHHHhcC---------CCCCcc---------HHHHHHHHHHHHHHhhh
Confidence 455568 99999999986 6789999999987 345432 77888888899988876
Q ss_pred HH
Q 013817 215 KV 216 (436)
Q Consensus 215 ~L 216 (436)
+|
T Consensus 137 rL 138 (138)
T PF09281_consen 137 RL 138 (138)
T ss_dssp HT
T ss_pred cC
Confidence 64
No 82
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=84.18 E-value=1 Score=46.67 Aligned_cols=91 Identities=19% Similarity=0.264 Sum_probs=58.6
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (436)
++-..|..++.. +-+-|||+.-.||.+|+-.+ ..+.|+.++..+-.++ . ....+|..|++.
T Consensus 282 dvq~~l~~~~~~-~TILVGHSLenDL~aLKl~H------------~~ViDTa~lf~~~~g~-----~-~~k~sLk~L~~~ 342 (380)
T KOG2248|consen 282 DVQKELLELISK-NTILVGHSLENDLKALKLDH------------PSVIDTAVLFKHPTGP-----Y-PFKSSLKNLAKS 342 (380)
T ss_pred HHHHHHHhhcCc-CcEEEeechhhHHHHHhhhC------------CceeeeeEEEecCCCC-----c-cchHHHHHHHHH
Confidence 445667775554 44569999999999998642 3467832233333221 0 136789999999
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 013817 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (436)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~ 213 (436)
|||..+.-+..-.+ .+.||.+.++|.....
T Consensus 343 ~L~~~Iq~~~~~Hd-------------S~eDA~acm~Lv~~k~ 372 (380)
T KOG2248|consen 343 YLGKLIQEGVGGHD-------------SVEDALACMKLVKLKI 372 (380)
T ss_pred HHHHHHhccCCCCc-------------cHHHHHHHHHHHHHHH
Confidence 99987751111111 5689999988876654
No 83
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=83.50 E-value=7.5 Score=35.79 Aligned_cols=99 Identities=16% Similarity=0.221 Sum_probs=52.8
Q ss_pred HHHHHHHhhCCCCceEEEEe-hHHhHHHHHhhcccCCCccCcc----CCCceeeHHHHHHHhh--ccc---CCC-CCCcC
Q 013817 92 IWELLKELFVSPDILKLGFK-FKQDLIYLSSTFCSQGCDIGFD----RVEPYLDITSIYNHLH--HKQ---LGR-KLPKE 160 (436)
Q Consensus 92 ~~~~L~~lLe~~~i~KVgh~-~k~Dl~~L~~~~gi~g~~~~~~----~~~~v~Dlt~La~yLl--~~~---~~~-~~~~~ 160 (436)
++..+..++..+...-|||| +.+|+..|.+.+.-.|..+ +. .....+|+..++..+. .+. ... .....
T Consensus 72 ~l~~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~-~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~ 150 (183)
T cd06138 72 FIAKIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDP-YTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKP 150 (183)
T ss_pred HHHHHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcc-cceeccCCccccccHHHHHHHHhhChhhccCccccCCCc
Confidence 34556666754443458996 7999999976543212110 00 0112457444555432 121 000 00013
Q ss_pred cccHHHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHH
Q 013817 161 TKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEI 208 (436)
Q Consensus 161 ~~gL~~Lv~~~Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L 208 (436)
+++|++++++ +|++... .+-|..||.++.+|
T Consensus 151 ~~~L~~l~~~-~gi~~~~----------------~H~Al~Da~~ta~l 181 (183)
T cd06138 151 SFKLEDLAQA-NGIEHSN----------------AHDALSDVEATIAL 181 (183)
T ss_pred chhHHHHHHH-CCCCccc----------------cccHHHHHHHHHHH
Confidence 6889999987 5765422 23388899888766
No 84
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=83.43 E-value=2.4 Score=40.91 Aligned_cols=112 Identities=14% Similarity=0.176 Sum_probs=63.7
Q ss_pred HHHHHHHhhC--CCCceEEEEeh-HHhHHHHHhhcccCCCccCccCC-------------------------CceeeHHH
Q 013817 92 IWELLKELFV--SPDILKLGFKF-KQDLIYLSSTFCSQGCDIGFDRV-------------------------EPYLDITS 143 (436)
Q Consensus 92 ~~~~L~~lLe--~~~i~KVgh~~-k~Dl~~L~~~~gi~g~~~~~~~~-------------------------~~v~Dlt~ 143 (436)
++..+...+. ||+|+ +|||+ .+|+..|.+....+|+. .+... .-++|+-.
T Consensus 85 LL~~f~~~i~~~DPDii-vG~Ni~~fdl~~L~~R~~~l~i~-~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~~ 162 (234)
T cd05776 85 LLNFFLAKLQKIDPDVL-VGHDLEGFDLDVLLSRIQELKVP-HWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYL 162 (234)
T ss_pred HHHHHHHHHhhcCCCEE-EeeccCCCCHHHHHHHHHHhCCC-ccccccccccccCccccccccccccccccCchhhccHH
Confidence 4444444333 68865 89999 57998874332211211 00000 12456444
Q ss_pred HHHHhhcccCCCCCCcCcccHHHHHHHHcCCcccc--ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 013817 144 IYNHLHHKQLGRKLPKETKSLANICKELLDISLSK--ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (436)
Q Consensus 144 La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~K--~~q~s-dW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~ 213 (436)
++..+.. ..+++|.++++.+||..-.. ..... -|....--..-+.|...||+..++|...|.
T Consensus 163 ~~k~~~~--------~~sY~L~~va~~~Lg~~k~di~~~~i~~~~~~~~~l~~l~~y~~~Da~l~~~L~~kl~ 227 (234)
T cd05776 163 SAKELIR--------CKSYDLTELSQQVLGIERQDIDPEEILNMYNDSESLLKLLEHTEKDAYLILQLMFKLN 227 (234)
T ss_pred HHHHHhC--------CCCCChHHHHHHHhCcCcccCCHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence 4444432 24899999999999973211 11111 244311124568899999999999988774
No 85
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=82.87 E-value=0.37 Score=54.13 Aligned_cols=97 Identities=19% Similarity=0.282 Sum_probs=68.1
Q ss_pred hhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHHcCCcccc
Q 013817 99 LFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSK 178 (436)
Q Consensus 99 lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~K 178 (436)
+|-+-.++.|||+.++|..++--. + | ...++| |... .+++. .+..+|.-||-.+||..+--
T Consensus 1009 ~Li~~GviFVGHGL~nDFrvINi~--V----p----~~QiiD-Tv~l-f~~~s-------~R~LSLrfLa~~lLg~~IQ~ 1069 (1118)
T KOG1275|consen 1009 LLIQRGVIFVGHGLQNDFRVINIH--V----P----EEQIID-TVTL-FRLGS-------QRMLSLRFLAWELLGETIQM 1069 (1118)
T ss_pred HHHHcCcEEEcccccccceEEEEe--c----C----hhhhee-eeEE-Eeccc-------ccEEEHHHHHHHHhcchhhc
Confidence 566788999999999998764211 0 0 134788 5332 22222 25789999999999987632
Q ss_pred cccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcchhhhcc
Q 013817 179 ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNSCSSISELD 230 (436)
Q Consensus 179 ~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l~~~~~~~~ 230 (436)
+. .| ..+||..++.||+... +|+++|++++|+..+-
T Consensus 1070 ~~--HD-------------SIeDA~taLkLYk~Yl-~lkeq~~~~~~l~niy 1105 (1118)
T KOG1275|consen 1070 EA--HD-------------SIEDARTALKLYKKYL-KLKEQGKLESELRNIY 1105 (1118)
T ss_pred cc--cc-------------cHHHHHHHHHHHHHHH-HHHHhhHHHHHHHHHh
Confidence 21 11 4589999999999986 7889999888888653
No 86
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=81.66 E-value=12 Score=35.73 Aligned_cols=97 Identities=20% Similarity=0.223 Sum_probs=61.5
Q ss_pred HHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHHHH
Q 013817 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKEL 171 (436)
Q Consensus 92 ~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~ 171 (436)
+...+..++.+. -.-|+||+..|+..|...+...+..+ ....++|.-.++.... ++ ....+|..|+. .
T Consensus 84 v~~~~~~~i~~~-~~~Vahna~fD~~fl~~~~~~~~~~~---~~~~~~~t~~~~r~~~-~~------~~~~~L~~l~~-~ 151 (243)
T COG0847 84 VLPEFLDFIGGL-RLLVAHNAAFDVGFLRVESERLGIEI---PGDPVLDTLALARRHF-PG------FDRSSLDALAE-R 151 (243)
T ss_pred HHHHHHHHHCCC-CeEEEEchhhcHHHHHHHHHHcCCCc---ccCceehHHHHHHHHc-CC------CccchHHHHHH-H
Confidence 445555666663 34499999999999875544323111 1246778444444443 32 24789999999 5
Q ss_pred cCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 013817 172 LDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (436)
Q Consensus 172 Lg~~l~K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~~ 214 (436)
+|+... .... .=|..||.++..+|..+..
T Consensus 152 ~gi~~~-~~~~-------------H~Al~Da~~~a~~~~~~~~ 180 (243)
T COG0847 152 LGIDRN-PFHP-------------HRALFDALALAELFLLLQT 180 (243)
T ss_pred cCCCcC-CcCC-------------cchHHHHHHHHHHHHHHHh
Confidence 676632 1111 2288999999999998875
No 87
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=80.10 E-value=3.6 Score=46.28 Aligned_cols=109 Identities=19% Similarity=0.179 Sum_probs=67.3
Q ss_pred CceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhc-c-cCCC-----------------CCC------
Q 013817 104 DILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHH-K-QLGR-----------------KLP------ 158 (436)
Q Consensus 104 ~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~-~-~~~~-----------------~~~------ 158 (436)
.-+.||||..+|-..++..|.+.|. -..++| ||-.+.-.. - ..+| ..|
T Consensus 241 e~liVGHNVsfDRaRirEeY~i~~S------k~rFlD-TMSlHia~~Gm~S~Qrplw~ka~k~k~a~~d~~~~ps~~d~~ 313 (1075)
T KOG3657|consen 241 EQLIVGHNVSFDRARIREEYNINGS------KIRFLD-TMSLHIAMSGMCSRQRPLWFKARKAKSAMYDSETNPSISDYD 313 (1075)
T ss_pred CceEEeccccchHHHHHHHHhcccc------ceeeee-chhhhhhhhccccccchhHhhhhhhhhhhhhcccCCchhhhh
Confidence 4567999999999999988887441 135778 764322111 0 0011 001
Q ss_pred ------cCcccHHHHHHHHcCCc-ccccccccC--CCCCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 013817 159 ------KETKSLANICKELLDIS-LSKELQCSD--WSNRPLT---EEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (436)
Q Consensus 159 ------~~~~gL~~Lv~~~Lg~~-l~K~~q~sd--W~~RPL~---~~ql~YAA~DA~~Ll~L~~~L~~~L~~~ 219 (436)
....||.++...+.|.. ++|+...+- -...++. .+-+.|.|.|++++.++|..+-+..-+.
T Consensus 314 ~pWL~~SS~NSL~dVhk~~c~~~~LdKt~Rd~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Fler 386 (1075)
T KOG3657|consen 314 NPWLGRSSLNSLVDVHKFHCGIDALDKTPRDSFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLER 386 (1075)
T ss_pred hhhhhhhhhHHHHHHHHhhCCCCccccchHHhhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHHh
Confidence 01246777888888887 777543221 0111111 2457899999999999999988877665
No 88
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=79.37 E-value=16 Score=32.72 Aligned_cols=97 Identities=12% Similarity=0.065 Sum_probs=57.6
Q ss_pred hHHHHHHHhhCCC-CceEEEEehHHhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHH
Q 013817 91 SIWELLKELFVSP-DILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (436)
Q Consensus 91 ~~~~~L~~lLe~~-~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~ 169 (436)
+++..+.+++.+. ... +.|+...|...+...+...+..+........+|+..++..+.+. ....+|.++++
T Consensus 77 ~vl~~~~~~l~~~~~~~-~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~-------~~~~~L~~l~~ 148 (176)
T cd06133 77 EVLKEFLEWLGKNGKYA-FVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGL-------KKRTGLSKALE 148 (176)
T ss_pred HHHHHHHHHHHhCCCeE-EEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCC-------CCCCCHHHHHH
Confidence 4566777788774 133 45556888776543211111110001235789977777766543 13789999986
Q ss_pred HHcCCccc-ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 013817 170 ELLDISLS-KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (436)
Q Consensus 170 ~~Lg~~l~-K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L 212 (436)
. +|++.. ..+ -|-.||.++.+|+..|
T Consensus 149 ~-~gi~~~~~~H----------------~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 149 Y-LGLEFEGRHH----------------RGLDDARNIARILKRL 175 (176)
T ss_pred H-CCCCCCCCCc----------------CcHHHHHHHHHHHHHh
Confidence 6 476654 122 2778999998888765
No 89
>PRK05762 DNA polymerase II; Reviewed
Probab=78.40 E-value=44 Score=38.21 Aligned_cols=112 Identities=18% Similarity=0.241 Sum_probs=63.3
Q ss_pred hHHHHHHHhhC--CCCceEEEEehH-HhHHHHHhhcccCCCccCccC----------C------------CceeeHHHHH
Q 013817 91 SIWELLKELFV--SPDILKLGFKFK-QDLIYLSSTFCSQGCDIGFDR----------V------------EPYLDITSIY 145 (436)
Q Consensus 91 ~~~~~L~~lLe--~~~i~KVgh~~k-~Dl~~L~~~~gi~g~~~~~~~----------~------------~~v~Dlt~La 145 (436)
+++..+..++. ||+|+ +|||.. +|+..|.+....+|+...+.+ . ..++|+-.++
T Consensus 205 ~LL~~F~~~i~~~DPDII-vGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~ 283 (786)
T PRK05762 205 ALLEKFNAWFAEHDPDVI-IGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDAL 283 (786)
T ss_pred HHHHHHHHHHHhcCCCEE-EEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHH
Confidence 45555555544 47754 899976 699987543222232210000 0 1256743333
Q ss_pred HHhhcccCCCCCCcCcccHHHHHHHHcCCcccc--c----ccc-cCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 013817 146 NHLHHKQLGRKLPKETKSLANICKELLDISLSK--E----LQC-SDWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (436)
Q Consensus 146 ~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~l~K--~----~q~-sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L 212 (436)
...... ..+++|..+++++||..-.. . .+. ..|... .+..+.|...||..++.|+..+
T Consensus 284 k~~~~~-------l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~--~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 284 KSATWV-------FDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAED--KPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred HHhhcc-------CCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhh--HHHHHHHHHHHHHHHHHHHHHh
Confidence 332211 24789999999999854211 0 111 124321 2567899999999999998843
No 90
>TIGR03447 mycothiol_MshC cysteine--1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase. Members of this protein family are MshC, l-cysteine:1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase, an enzyme that uses ATP to ligate a Cys residue to a mycothiol precursor molecule, in the second to last step in mycothiol biosynthesis. This enzyme shows considerable homology to Cys--tRNA ligases, and many instances are misannotated as such. Mycothiol is found in Mycobacterium tuberculosis, Corynebacterium glutamicum, Streptomyces coelicolor, and various other members of the Actinobacteria. Mycothiol is an analog to glutathione.
Probab=77.20 E-value=1.4 Score=46.15 Aligned_cols=56 Identities=14% Similarity=0.194 Sum_probs=36.7
Q ss_pred CCCCCC-CCCCCCCCCCeEEEeCccHHHHHHHHhcCCceeecCCCCCChHHHHHHHhcCCcE
Q 013817 342 QGPPPW-DLSLGGDGYPKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRV 402 (436)
Q Consensus 342 ~~~~p~-~~~~~~~~~~~fl~D~~l~~la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ri 402 (436)
+||-|. +++.|-... -+++|. |+||||..||++.|+.+-..-|..|+..|+++|.-
T Consensus 42 CGpTvY~~~HIGhart-~V~~Dv----l~R~lr~~G~~V~fV~nitD~dDKIi~~A~~~g~t 98 (411)
T TIGR03447 42 CGITPYDATHLGHAAT-YLTFDL----VNRVWRDAGHRVHYVQNVTDVDDPLFERAERDGVD 98 (411)
T ss_pred eCCccCCCcccccchH-HHHHHH----HHHHHHhcCCceEEeeCCCchhHHHHHHHHHcCCC
Confidence 455555 345544333 244443 79999999999999985322244589999888853
No 91
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=75.75 E-value=6.9 Score=34.81 Aligned_cols=55 Identities=11% Similarity=0.067 Sum_probs=43.3
Q ss_pred HHHhcCCceeecCCCCCChHHHHHHHhcCC-cEEEecChhHHhhhcccCCcEEEEcCC
Q 013817 371 HLRCVGIDAATPRSKKPEPRELIDQTSKEK-RVLLTRDAKLLRHQYLIKNQIYRVKSL 427 (436)
Q Consensus 371 ~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~-ri~lT~d~~l~~~~~~~~~~~~~v~~~ 427 (436)
.....++.+.+.. +..|+-|++.|.+.+ -|+.|.|++|-+|....|+.++++++.
T Consensus 71 ~~~~er~~~~~~~--~~aDe~i~~~a~~~~~~iVaTnD~eLk~rlr~~GIPvi~lr~r 126 (136)
T COG1412 71 LKYAERLECIHKG--RYADECLLEAALKHGRYIVATNDKELKRRLRENGIPVITLRQR 126 (136)
T ss_pred HHHhhccCccccC--CChHHHHHHHHHHcCCEEEEeCCHHHHHHHHHcCCCEEEEeCC
Confidence 3456677777763 345777999999999 677799999999977778889998753
No 92
>PRK06722 exonuclease; Provisional
Probab=75.23 E-value=22 Score=35.49 Aligned_cols=98 Identities=18% Similarity=0.126 Sum_probs=57.3
Q ss_pred hHHHHHHHhhCCCCceEEEEehHHhHHHHHhhcccCCCc-cCccCCCceeeHHHHHHHhhcccCCCCCCcCcccHHHHHH
Q 013817 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCD-IGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (436)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~-~~~~~~~~v~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~ 169 (436)
+++..+..++.+..+ |+|+...|+..|...+...|+. |.+. ....+|+..++..+...- .....+|.++++
T Consensus 79 eVl~ef~~fig~~~l--vahna~FD~~FL~~~l~~~gi~~p~~~-~~~~idl~~la~~~~~~l-----~~~~~sL~~l~~ 150 (281)
T PRK06722 79 QIIEKFIQFIGEDSI--FVTWGKEDYRFLSHDCTLHSVECPCME-KERRIDLQKFVFQAYEEL-----FEHTPSLQSAVE 150 (281)
T ss_pred HHHHHHHHHHCCCcE--EEEEeHHHHHHHHHHHHHcCCCCCccc-ccchhHHHHHHHHHhhhh-----ccCCCCHHHHHH
Confidence 456667777766444 6777899999987754432321 1000 122467554443322110 012468999998
Q ss_pred HHcCCccc-ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 013817 170 ELLDISLS-KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (436)
Q Consensus 170 ~~Lg~~l~-K~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~ 213 (436)
.+ |++.. ..+ -|-.||.++..|+..|.
T Consensus 151 ~l-gL~~~g~~H----------------rAL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 151 QL-GLIWEGKQH----------------RALADAENTANILLKAY 178 (281)
T ss_pred HC-CCCCCCCCc----------------CcHHHHHHHHHHHHHHh
Confidence 75 66542 112 27789999999998886
No 93
>cd00672 CysRS_core catalytic core domain of cysteinyl tRNA synthetase. Cysteinyl tRNA synthetase (CysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.
Probab=74.94 E-value=2.6 Score=40.25 Aligned_cols=34 Identities=15% Similarity=0.158 Sum_probs=26.4
Q ss_pred HHHHHHHhcCCceeecCCCCCChHHHHHHHhcCC
Q 013817 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 400 (436)
Q Consensus 367 ~la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ 400 (436)
=++||||+.||++.++.+.+.-+..|+..|.++|
T Consensus 47 vl~R~lr~~G~~V~~~~g~dd~g~ki~~~A~~~g 80 (213)
T cd00672 47 VLRRYLEDLGYKVRYVQNITDIDDKIIKRAREEG 80 (213)
T ss_pred HHHHHHHhcCCeeEEEeecCCCCCHHHHHHHHcC
Confidence 3799999999999999854333445888888776
No 94
>PRK12418 cysteinyl-tRNA synthetase; Provisional
Probab=68.32 E-value=4.7 Score=42.00 Aligned_cols=36 Identities=11% Similarity=0.115 Sum_probs=28.4
Q ss_pred HHHHHHHhcCCceeecCCCCCChHHHHHHHhcCCcE
Q 013817 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRV 402 (436)
Q Consensus 367 ~la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ri 402 (436)
=|+||||.+||++.|+.+-..-|..|+..|.++|.-
T Consensus 36 vl~R~lr~~G~~V~~V~nitD~ddKIi~~A~~~G~~ 71 (384)
T PRK12418 36 LVNRVWRDAGHDVHYVQNVTDVDDPLLERAARDGVD 71 (384)
T ss_pred HHHHHHHHcCCceEEEEecCCcchHHHHHHHHcCCC
Confidence 379999999999999986333344589999888864
No 95
>PRK14535 cysS cysteinyl-tRNA synthetase; Provisional
Probab=63.81 E-value=3.8 Score=45.55 Aligned_cols=56 Identities=18% Similarity=0.196 Sum_probs=37.7
Q ss_pred CCCCCC-CCCCCCCCCCeEEEeCccHHHHHHHHhcCCceeecCCCCCChHHHHHHHhcCCcE
Q 013817 342 QGPPPW-DLSLGGDGYPKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRV 402 (436)
Q Consensus 342 ~~~~p~-~~~~~~~~~~~fl~D~~l~~la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ri 402 (436)
+||-+. .++.|-... -++.| =|+||||.+||++.|+.+-..-|..|+..|+++|.-
T Consensus 254 CGPTVYd~~HIGHaRt-~V~~D----VL~R~Lr~~Gy~V~fV~NiTD~DDKII~~A~e~G~s 310 (699)
T PRK14535 254 CGMTVYDYCHLGHARV-MVVFD----MIARWLRECGYPLTYVRNITDIDDKIIARAAENGET 310 (699)
T ss_pred cCCcCCCCCcccchhH-HHHHH----HHHHHHHHcCCceEEEeCCcccchHHHHHHHHcCCC
Confidence 677776 445543322 24444 389999999999999985332344588889888743
No 96
>PRK00260 cysS cysteinyl-tRNA synthetase; Validated
Probab=61.28 E-value=8.3 Score=41.11 Aligned_cols=35 Identities=20% Similarity=0.276 Sum_probs=27.2
Q ss_pred HHHHHHHhcCCceeecCCCCCChHHHHHHHhcCCc
Q 013817 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (436)
Q Consensus 367 ~la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~r 401 (436)
=++|+||+.||++.|+.+...-+..|+..|+++|.
T Consensus 50 vl~R~lr~~G~~V~~v~~~tD~ddki~~~A~~~g~ 84 (463)
T PRK00260 50 VLRRYLRYLGYKVTYVRNITDIDDKIIKRANEEGE 84 (463)
T ss_pred HHHHHHHhcCCceEEeecCCCCcHHHHHHHHHcCC
Confidence 37999999999999998633334558888888773
No 97
>cd00814 MetRS_core catalytic core domain of methioninyl-tRNA synthetases. Methionine tRNA synthetase (MetRS) catalytic core domain. This class I enzyme aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. MetRS, which consists of the core domain and an anti-codon binding domain, functions as a monomer. However, in some species the anti-codon binding domain is followed by an EMAP domain. In this case, MetRS functions as a homodimer. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. As a result of a deletion event, MetRS has a significantly shorter core domain insertion than IleRS, ValRS, and LeuR. Consequently, the MetRS insertion lacks the editing function.
Probab=60.92 E-value=7.6 Score=39.10 Aligned_cols=34 Identities=15% Similarity=0.150 Sum_probs=26.3
Q ss_pred HHHHHHhcCCceeecCCCCCChHHHHHHHhcCCc
Q 013817 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (436)
Q Consensus 368 la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~r 401 (436)
++||||+.|+++.++.+.+.-+..|...|.++|.
T Consensus 29 ~~R~~r~~G~~V~~~~g~Dd~g~~i~~~a~~~g~ 62 (319)
T cd00814 29 FARYQRLRGYDVLFVTGTDEHGTKIEQKAEEEGV 62 (319)
T ss_pred HHHHHHhCCCcccccCccCCCCcHHHHHHHHcCC
Confidence 6999999999999998543334457888877774
No 98
>TIGR00435 cysS cysteinyl-tRNA synthetase. This model finds the cysteinyl-tRNA synthetase from most but not from all species. The enzyme from one archaeal species, Archaeoglobus fulgidus, is found but the equivalent enzymes from some other Archaea, including Methanococcus jannaschii, are not found, although biochemical evidence suggests that tRNA(Cys) in these species are charged directly with Cys rather than through a misacylation and correction pathway as for tRNA(Gln).
Probab=59.00 E-value=8.3 Score=41.19 Aligned_cols=35 Identities=14% Similarity=0.202 Sum_probs=27.3
Q ss_pred HHHHHHHhcCCceeecCCCCCChHHHHHHHhcCCc
Q 013817 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (436)
Q Consensus 367 ~la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~r 401 (436)
-++||||..||++.|+.+-..-|..|+..|+++|.
T Consensus 48 vl~R~lr~~G~~V~~v~n~tD~ddkIi~~A~~~g~ 82 (465)
T TIGR00435 48 VLRRYLRYLGYKVQYVQNITDIDDKIIKRARENGE 82 (465)
T ss_pred HHHHHHHHcCCcEEEEEeeCCccHHHHHHHHHcCC
Confidence 37999999999999998533334468888888876
No 99
>PLN02946 cysteine-tRNA ligase
Probab=58.62 E-value=8.3 Score=42.14 Aligned_cols=55 Identities=15% Similarity=0.151 Sum_probs=36.4
Q ss_pred CCCCCC-CCCCCCCCCCeEEEeCccHHHHHHHHhcCCceeecCCCCCChHHHHHHHhcCCc
Q 013817 342 QGPPPW-DLSLGGDGYPKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (436)
Q Consensus 342 ~~~~p~-~~~~~~~~~~~fl~D~~l~~la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~r 401 (436)
+||-+. .++.|-... -++.| =|+||||..||++.|+.+-..-|..|+..|.++|.
T Consensus 86 CGpTvYd~~HIGhaR~-~V~~D----vl~R~Lr~~Gy~V~~V~niTDiDDKIi~~A~~~g~ 141 (557)
T PLN02946 86 CGVTAYDLSHIGHARV-YVTFD----VLYRYLKHLGYEVRYVRNFTDVDDKIIARANELGE 141 (557)
T ss_pred eCCccCCCCccccchh-hHHHH----HHHHHHHhcCCcEEEEECCCCccCHHHHHHHHcCC
Confidence 677666 445544322 13333 37999999999999998533224458888988775
No 100
>TIGR00305 probable toxin-antitoxin system toxin component, PIN family. This uncharacterized protein family, part of the PIN domain superfamily, is restricted to bacteria and archaea. A comprehensive in silico study of toxin-antitoxin systems by Makarova, et al. (2009) finds evidence this family represents the toxin-like component of one class of type 2 toxin-antitoxin systems.
Probab=57.60 E-value=13 Score=31.29 Aligned_cols=28 Identities=21% Similarity=0.393 Sum_probs=23.3
Q ss_pred CCCChHHHHHHHhcCCc-EEEecChhHHh
Q 013817 385 KKPEPRELIDQTSKEKR-VLLTRDAKLLR 412 (436)
Q Consensus 385 ~~~~~~~~~~~a~~e~r-i~lT~d~~l~~ 412 (436)
.+++|..+++.|..-+- +|+|+|++|+.
T Consensus 85 ~D~~D~~~l~~A~~~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 85 RDKKDNKFLNTAYASKANALITGDTDLLV 113 (114)
T ss_pred CCchhHHHHHHHHhcCCCEEEECCHHHhh
Confidence 36788889999987665 99999999864
No 101
>PTZ00399 cysteinyl-tRNA-synthetase; Provisional
Probab=54.73 E-value=7.2 Score=43.48 Aligned_cols=56 Identities=20% Similarity=0.271 Sum_probs=37.0
Q ss_pred CCCCCC-CCCCCCCCCCeEEEeCccHHHHHHHH-hcCCceeecCCCCCChHHHHHHHhcCCcE
Q 013817 342 QGPPPW-DLSLGGDGYPKFLCDVMVEGLAKHLR-CVGIDAATPRSKKPEPRELIDQTSKEKRV 402 (436)
Q Consensus 342 ~~~~p~-~~~~~~~~~~~fl~D~~l~~la~~LR-~~G~d~~~~~~~~~~~~~~~~~a~~e~ri 402 (436)
+||-+. .++.| ....-++.|. |+|||| .+||++.|+.+-..-|..|+..|+++|.-
T Consensus 66 CGPTvYd~~HiG-hart~v~~Di----l~R~l~~~~Gy~V~~v~nitDidDKIi~~A~~~g~~ 123 (651)
T PTZ00399 66 CGPTVYDSSHLG-HARTYVTFDI----IRRILEDYFGYDVFYVMNITDIDDKIIKRAREEKLS 123 (651)
T ss_pred eCCCccCCcccc-cchHHHHHHH----HHHHHHHhcCCceEEEeCCCCcchHHHHHHHHhCCC
Confidence 566655 33443 2332344443 799999 89999999986332344599999988873
No 102
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=54.58 E-value=17 Score=33.17 Aligned_cols=59 Identities=15% Similarity=0.094 Sum_probs=37.8
Q ss_pred HhcCCceeecCCCCCChHHHHHHHhcCCc-----EEEecChhHHhhhcccCCcEEEEcCCChhhhh
Q 013817 373 RCVGIDAATPRSKKPEPRELIDQTSKEKR-----VLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQL 433 (436)
Q Consensus 373 R~~G~d~~~~~~~~~~~~~~~~~a~~e~r-----i~lT~d~~l~~~~~~~~~~~~~v~~~~~~~Ql 433 (436)
+.-|+.++|..+....|..|...+..... +++|.|+.+.......| ++.+.+....+++
T Consensus 64 ~~~gi~Vvft~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~~~~~G--A~~iss~ef~~~l 127 (166)
T PF05991_consen 64 EYGGIEVVFTKEGETADDYIERLVRELKNRPRQVTVVTSDREIQRAARGRG--AKRISSEEFLREL 127 (166)
T ss_pred eeCceEEEECCCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHHHHhhCC--CEEEcHHHHHHHH
Confidence 33577888876534456667766655554 77788888887765543 6666665444444
No 103
>COG0215 CysS Cysteinyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=52.44 E-value=15 Score=39.17 Aligned_cols=54 Identities=24% Similarity=0.399 Sum_probs=37.3
Q ss_pred CCCCCCC-CCCCCCCCCeEEEeCccHHHHHHHHhcCCceeecCCC-CCChHHHHHHHhcCCc
Q 013817 342 QGPPPWD-LSLGGDGYPKFLCDVMVEGLAKHLRCVGIDAATPRSK-KPEPRELIDQTSKEKR 401 (436)
Q Consensus 342 ~~~~p~~-~~~~~~~~~~fl~D~~l~~la~~LR~~G~d~~~~~~~-~~~~~~~~~~a~~e~r 401 (436)
|||-+.| .+.| ...+-++.|. |.||||.+||++.|+.+- ++ |+.|+..|+++|-
T Consensus 28 CGpTVYd~~HIG-haRt~V~fDv----l~R~L~~~Gy~V~yV~NiTDI-DDKIi~rA~~~g~ 83 (464)
T COG0215 28 CGPTVYDYAHIG-HARTYVVFDV----LRRYLRYLGYKVTYVRNITDI-DDKIINRAREEGL 83 (464)
T ss_pred cCCccCCccccc-cCcceehHHH----HHHHHHHhCCeEEEEeccccc-cHHHHHHHHHhCC
Confidence 5666663 3444 3444444443 699999999999999863 34 4468999998885
No 104
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=52.29 E-value=20 Score=31.71 Aligned_cols=33 Identities=18% Similarity=0.257 Sum_probs=28.4
Q ss_pred HHHHHHhcCCceeecCCCCCChHHHHHHHhcCCc
Q 013817 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (436)
Q Consensus 368 la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~r 401 (436)
++..||..||++.|++. ....+++++.|.+++-
T Consensus 23 v~~~lr~~G~eVi~LG~-~vp~e~i~~~a~~~~~ 55 (137)
T PRK02261 23 LDRALTEAGFEVINLGV-MTSQEEFIDAAIETDA 55 (137)
T ss_pred HHHHHHHCCCEEEECCC-CCCHHHHHHHHHHcCC
Confidence 69999999999999985 5677889999887765
No 105
>PRK13764 ATPase; Provisional
Probab=51.61 E-value=30 Score=38.28 Aligned_cols=40 Identities=10% Similarity=-0.054 Sum_probs=36.1
Q ss_pred ChHHHHHHHhcCCcEEEecChhHHhhhcccCCcEEEEcCC
Q 013817 388 EPRELIDQTSKEKRVLLTRDAKLLRHQYLIKNQIYRVKSL 427 (436)
Q Consensus 388 ~~~~~~~~a~~e~ri~lT~d~~l~~~~~~~~~~~~~v~~~ 427 (436)
-|..|++.|++.+-+|||.|.-+.+.+...|..+.+++..
T Consensus 91 vD~~I~~~A~~~~~~lvT~D~~l~~~A~~~GI~V~~l~~~ 130 (602)
T PRK13764 91 IDALIREVAKELGATLVTSDRVQAEVARAKGIDVIYLKPE 130 (602)
T ss_pred HHHHHHHHHHHcCCEEEeCCHHHHHHHHHcCCEEEEeCCC
Confidence 4667999999999999999999999999999999999764
No 106
>TIGR00398 metG methionyl-tRNA synthetase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma
Probab=51.35 E-value=14 Score=39.80 Aligned_cols=34 Identities=12% Similarity=0.040 Sum_probs=26.5
Q ss_pred HHHHHHhcCCceeecCCCCCChHHHHHHHhcCCc
Q 013817 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (436)
Q Consensus 368 la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~r 401 (436)
++||||+.|+||.++.+.+.-+..+...|.++|.
T Consensus 28 l~R~~r~~G~~V~~v~g~D~~g~~i~~~a~~~g~ 61 (530)
T TIGR00398 28 YARYKRLRGYEVLFVCGTDEHGTKIELKAEQEGL 61 (530)
T ss_pred HHHHHHhcCCeEEEecccCCCCcHHHHHHHHcCC
Confidence 7999999999999998543334458888888764
No 107
>PLN02224 methionine-tRNA ligase
Probab=50.98 E-value=17 Score=40.31 Aligned_cols=50 Identities=8% Similarity=0.074 Sum_probs=31.0
Q ss_pred CCCCCCeEEEeCccH-HHHHHHHhcCCceeecCCCCCChHHHHHHHhcCCc
Q 013817 352 GGDGYPKFLCDVMVE-GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (436)
Q Consensus 352 ~~~~~~~fl~D~~l~-~la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~r 401 (436)
.+.-.+.=+.-..+. =++||+|+.||+|.|+...+.-...|...|.++|.
T Consensus 81 NG~~HiGHa~~~~~aDviaR~~r~~G~~V~fv~G~DehG~kI~~~A~~~g~ 131 (616)
T PLN02224 81 NAPPHMGSAYTTIAADSIARFQRLLGKKVIFITGTDEHGEKIATSAAANGR 131 (616)
T ss_pred CCCCchhccHHHHHHHHHHHHHHhcCCceEEecCcCCcchHHHHHHHHcCC
Confidence 333333333333333 27999999999999997532222337777877774
No 108
>cd00812 LeuRS_core catalytic core domain of leucyl-tRNA synthetases. Leucyl tRNA synthetase (LeuRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. In Aquifex aeolicus, the gene encoding LeuRS is split in two, just before the KMSKS motif. Consequently, LeuRS is a heterodimer, which likely superimposes with the LeuRS monomer found in most other organisms. LeuRS has an insertion in the core domain, which is subject to both deletions and rearrangements and thus differs between prokaryotic LeuRS and archaeal/eukaryotic LeuRS. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
Probab=50.52 E-value=15 Score=36.86 Aligned_cols=40 Identities=15% Similarity=0.069 Sum_probs=27.2
Q ss_pred eCccHH-HHHHHHhcCCceeecCCCCCChHHHHHHHhcCCc
Q 013817 362 DVMVEG-LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (436)
Q Consensus 362 D~~l~~-la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~r 401 (436)
-..+.- ++|+||+.|++|.++.+-+.-+..+...|.++|.
T Consensus 22 ~~v~~Dv~~R~lr~~G~~V~~v~g~Dd~g~~i~~~a~~~g~ 62 (314)
T cd00812 22 TYTIGDIIARYKRMQGYNVLFPMGFDAFGLPAENAAIKIGR 62 (314)
T ss_pred HHHHHHHHHHHHHHcCCCcCCCCCcCCCCCHHHHHHHHcCC
Confidence 334443 7999999999999997532223346667777764
No 109
>PRK05359 oligoribonuclease; Provisional
Probab=50.46 E-value=2.1e+02 Score=26.37 Aligned_cols=21 Identities=14% Similarity=0.074 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 013817 197 YAAIDAHCLIEIFNIFQVKVA 217 (436)
Q Consensus 197 YAA~DA~~Ll~L~~~L~~~L~ 217 (436)
-|-.|+...++.+..+...+.
T Consensus 156 Ral~D~~~s~~~~~~~~~~~~ 176 (181)
T PRK05359 156 RALADIRESIAELKYYREHFF 176 (181)
T ss_pred ccHHHHHHHHHHHHHHHHHhc
Confidence 366788888888888876654
No 110
>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins.
Probab=50.36 E-value=30 Score=28.64 Aligned_cols=40 Identities=15% Similarity=0.233 Sum_probs=32.6
Q ss_pred CChHHHHHHHhcCC-cEEEecChhHHhhhc-ccCCcEEEEcC
Q 013817 387 PEPRELIDQTSKEK-RVLLTRDAKLLRHQY-LIKNQIYRVKS 426 (436)
Q Consensus 387 ~~~~~~~~~a~~e~-ri~lT~d~~l~~~~~-~~~~~~~~v~~ 426 (436)
..|+-|++.|.+.+ -|+.|.|++|-++.. .+|+..++++.
T Consensus 52 ~addci~~~~~~~~~~~VaT~D~~Lr~~lr~~~GvPvi~l~~ 93 (101)
T PF04900_consen 52 SADDCILDLAGKNNKYIVATQDKELRRRLRKIPGVPVIYLRR 93 (101)
T ss_pred CHHHHHHHHhccCCeEEEEecCHHHHHHHhcCCCCCEEEEEC
Confidence 35667999997766 677799999999866 78888999874
No 111
>PRK12268 methionyl-tRNA synthetase; Reviewed
Probab=48.64 E-value=27 Score=37.99 Aligned_cols=34 Identities=15% Similarity=0.050 Sum_probs=25.1
Q ss_pred HHHHHHhcCCceeecCCCCCChHHHHHHHhcCCc
Q 013817 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (436)
Q Consensus 368 la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~r 401 (436)
++||+|+.|++|.|+.+.+.-+..+...|.++|.
T Consensus 33 ~~R~~r~~G~~v~~~~g~d~~g~~i~~~a~~~g~ 66 (556)
T PRK12268 33 FARYQRLKGNEVLFVSGSDEHGTPIELAAKKEGV 66 (556)
T ss_pred HHHHHHhcCCceEecCcCCCcccHHHHHHHHcCC
Confidence 6999999999999998533223347777776655
No 112
>PRK11893 methionyl-tRNA synthetase; Reviewed
Probab=48.40 E-value=19 Score=38.54 Aligned_cols=34 Identities=15% Similarity=0.143 Sum_probs=25.7
Q ss_pred HHHHHHhcCCceeecCCCCCChHHHHHHHhcCCc
Q 013817 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (436)
Q Consensus 368 la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~r 401 (436)
++||||+.|++|.++.+.+.-+..|...|.++|.
T Consensus 30 ~~R~~r~~G~~v~~v~g~dd~g~~i~~~a~~~g~ 63 (511)
T PRK11893 30 LARFKRLRGYDVFFLTGTDEHGQKIQRKAEEAGI 63 (511)
T ss_pred HHHHHHhcCCcEEecCCCCCCChHHHHHHHHcCC
Confidence 6999999999999998543233457777877764
No 113
>PRK14534 cysS cysteinyl-tRNA synthetase; Provisional
Probab=48.39 E-value=15 Score=39.50 Aligned_cols=56 Identities=14% Similarity=0.138 Sum_probs=35.2
Q ss_pred CCCCCC-CCCCCCCCCCeEEEeCccHHHHHHHHhcCCceeecCCC-CC---------ChHHHHHHHhcCCcE
Q 013817 342 QGPPPW-DLSLGGDGYPKFLCDVMVEGLAKHLRCVGIDAATPRSK-KP---------EPRELIDQTSKEKRV 402 (436)
Q Consensus 342 ~~~~p~-~~~~~~~~~~~fl~D~~l~~la~~LR~~G~d~~~~~~~-~~---------~~~~~~~~a~~e~ri 402 (436)
+||-+. .++.|-... -++.| =|+||||.+||++.|+.+- ++ .|..|+..|.++|.-
T Consensus 27 CGpTVYd~~HiGh~r~-~v~~D----vl~R~l~~~G~~V~~v~NiTDIghltg~~D~gddKIi~~A~~~g~~ 93 (481)
T PRK14534 27 CGPTVYNYAHIGNFRT-YIFED----LLIKSLRLLKYNVNYAMNITDIGHLTGDFDDGEDKVVKAARERGLT 93 (481)
T ss_pred CCCCCCCCCCccchhH-HHHHH----HHHHHHHHcCCceEEEEeccccccccCCccCCCcHHHHHHHHcCCC
Confidence 666655 445543322 12223 3799999999999995421 22 245588889888864
No 114
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=45.62 E-value=29 Score=33.41 Aligned_cols=50 Identities=14% Similarity=0.216 Sum_probs=36.5
Q ss_pred CcccHHHHHHHHcCCcccc--cccccCC-CC-C-CCCHHHHHHHHHHHHHHHHHH
Q 013817 160 ETKSLANICKELLDISLSK--ELQCSDW-SN-R-PLTEEQKNYAAIDAHCLIEIF 209 (436)
Q Consensus 160 ~~~gL~~Lv~~~Lg~~l~K--~~q~sdW-~~-R-PL~~~ql~YAA~DA~~Ll~L~ 209 (436)
.+++|.+++.++||...+. ....+.| .. . .-...-+.|...||...++|.
T Consensus 176 ~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l~l~Ll 230 (231)
T cd05778 176 TNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEIL 230 (231)
T ss_pred ccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHHHHHhh
Confidence 4899999999999986543 2344555 22 2 234667999999999998875
No 115
>PF12813 XPG_I_2: XPG domain containing
Probab=45.04 E-value=24 Score=34.47 Aligned_cols=46 Identities=24% Similarity=0.240 Sum_probs=38.1
Q ss_pred HHHHHHhc---CCceeecCCCCCChHHHHHHHhcCCcEEEecChhHHhhhc
Q 013817 368 LAKHLRCV---GIDAATPRSKKPEPRELIDQTSKEKRVLLTRDAKLLRHQY 415 (436)
Q Consensus 368 la~~LR~~---G~d~~~~~~~~~~~~~~~~~a~~e~ri~lT~d~~l~~~~~ 415 (436)
+..-||.+ |..+..+. +..|.+++..|++-|..+||.|.+|+=...
T Consensus 9 ~~e~L~~~~~~~~~~~~~~--~EAD~~~A~~A~~~~~~VLt~DSDf~I~dl 57 (246)
T PF12813_consen 9 FIEALRESWRYGVPVVQCP--GEADRECAALARKWGCPVLTNDSDFLIHDL 57 (246)
T ss_pred HHHHHHHHhhcCCcEEEcC--ccchHHHHHHHHHcCCeEEccCCCEEEecc
Confidence 34557777 99999886 458999999999999999999999986543
No 116
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=44.66 E-value=23 Score=39.44 Aligned_cols=34 Identities=18% Similarity=0.192 Sum_probs=26.0
Q ss_pred HHHHHHhcCCceeecCCCCCChHHHHHHHhcCCc
Q 013817 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (436)
Q Consensus 368 la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~r 401 (436)
++||+|+.|+||.|+...+.-+..|...|.++|.
T Consensus 33 ~~R~~r~~G~~v~~~~g~D~~g~~i~~~A~~~g~ 66 (648)
T PRK12267 33 LARYKRLQGYDVFFLTGTDEHGQKIQQAAEKAGK 66 (648)
T ss_pred HHHHHHhcCCceEeecCCCCcchHHHHHHHHcCC
Confidence 6999999999999998543223457778877774
No 117
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=44.32 E-value=37 Score=28.55 Aligned_cols=39 Identities=21% Similarity=0.342 Sum_probs=29.8
Q ss_pred HHHHHHhcCCceeecCCCCCChHHHHHHHhcCC--cEEEecC
Q 013817 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK--RVLLTRD 407 (436)
Q Consensus 368 la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~--ri~lT~d 407 (436)
++.+||..||++.|... ....+++++.+.+++ -|.|+..
T Consensus 19 ~~~~l~~~G~~V~~lg~-~~~~~~l~~~~~~~~pdvV~iS~~ 59 (119)
T cd02067 19 VARALRDAGFEVIDLGV-DVPPEEIVEAAKEEDADAIGLSGL 59 (119)
T ss_pred HHHHHHHCCCEEEECCC-CCCHHHHHHHHHHcCCCEEEEecc
Confidence 69999999999999875 567888888887664 3445543
No 118
>PF01406 tRNA-synt_1e: tRNA synthetases class I (C) catalytic domain; InterPro: IPR015803 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Cysteinyl-tRNA synthetase (6.1.1.16 from EC) is an alpha monomer and belongs to class Ia.; GO: 0000166 nucleotide binding, 0004817 cysteine-tRNA ligase activity, 0005524 ATP binding, 0006423 cysteinyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3SP1_B 3TQO_A 3C8Z_B 1LI5_B 1LI7_B 1U0B_B.
Probab=43.86 E-value=14 Score=37.15 Aligned_cols=34 Identities=18% Similarity=0.254 Sum_probs=25.3
Q ss_pred HHHHHHhcCCceeecCCC-CCChHHHHHHHhcCCcE
Q 013817 368 LAKHLRCVGIDAATPRSK-KPEPRELIDQTSKEKRV 402 (436)
Q Consensus 368 la~~LR~~G~d~~~~~~~-~~~~~~~~~~a~~e~ri 402 (436)
|.|+|+.+||++.|+.+- ++| +.|+..|+++|.-
T Consensus 36 l~R~L~~~g~~V~~V~NiTDiD-DKii~~A~~~g~~ 70 (300)
T PF01406_consen 36 LRRYLEYLGYDVTYVMNITDID-DKIIKRAREEGVS 70 (300)
T ss_dssp HHHHHHHTT-EEEEEEEEB-SS-HHHHHHHHHTTS-
T ss_pred HHHHHHHcCCeEEEEEeccccc-hHHHHHHHhccCC
Confidence 689999999999999752 444 4688899888854
No 119
>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.
Probab=42.79 E-value=37 Score=30.09 Aligned_cols=35 Identities=14% Similarity=0.155 Sum_probs=30.0
Q ss_pred HHHHHHhcCCceeecCCCCCChHHHHHHHhcCCcEE
Q 013817 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVL 403 (436)
Q Consensus 368 la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ri~ 403 (436)
++..||..||++.+++- +...+++++.|++++-=+
T Consensus 21 v~~~l~~~GfeVi~LG~-~v~~e~~v~aa~~~~adi 55 (134)
T TIGR01501 21 LDHAFTNAGFNVVNLGV-LSPQEEFIKAAIETKADA 55 (134)
T ss_pred HHHHHHHCCCEEEECCC-CCCHHHHHHHHHHcCCCE
Confidence 69999999999999984 678888999999887633
No 120
>cd00802 class_I_aaRS_core catalytic core domain of class I amino acyl-tRNA synthetase. Class I amino acyl-tRNA synthetase (aaRS) catalytic core domain. These enzymes are mostly monomers which aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.
Probab=42.29 E-value=26 Score=30.60 Aligned_cols=37 Identities=16% Similarity=0.070 Sum_probs=23.8
Q ss_pred CccH-HHHHHHHhcCCceeecCCCCCChHHHHHHHhcC
Q 013817 363 VMVE-GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKE 399 (436)
Q Consensus 363 ~~l~-~la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e 399 (436)
.+++ -++|+||.+||++.++...+.-+..+...|.+.
T Consensus 20 ~~~~d~~~r~lr~~G~~v~~~~~~dd~~~~~~~~a~~~ 57 (143)
T cd00802 20 IVTFDFLAQAYRKLGYKVRCIALIDDAGGLIGDPANKK 57 (143)
T ss_pred HHHHHHHHHHHHHcCCCeEEEeeeCCCchHHHHHHHhc
Confidence 4444 379999999999999874322233355555443
No 121
>PRK14536 cysS cysteinyl-tRNA synthetase; Provisional
Probab=41.72 E-value=25 Score=37.95 Aligned_cols=56 Identities=13% Similarity=0.215 Sum_probs=35.3
Q ss_pred CCCCCC-CCCCCCCCCCeEEEeCccHHHHHHHHhcCCceeecCCC-CC---------ChHHHHHHHhcCCcE
Q 013817 342 QGPPPW-DLSLGGDGYPKFLCDVMVEGLAKHLRCVGIDAATPRSK-KP---------EPRELIDQTSKEKRV 402 (436)
Q Consensus 342 ~~~~p~-~~~~~~~~~~~fl~D~~l~~la~~LR~~G~d~~~~~~~-~~---------~~~~~~~~a~~e~ri 402 (436)
+||-+. +++.|-. ..-+.+| =|+||||.+||++.|+.+- ++ .+..|+..|.++|.-
T Consensus 29 CGpTvy~~~HiGha-r~~v~~D----vl~R~l~~~G~~V~~v~NiTDv~hl~~~~De~ddKii~~A~~~g~~ 95 (490)
T PRK14536 29 CGPTVYNYAHIGNL-RTYVFQD----TLRRTLHFLGYRVTHVMNITDVGHLTDDADSGEDKMVKSAQEHGKS 95 (490)
T ss_pred eCCccCCCcccchh-HHHHHHH----HHHHHHHhcCCceEEEEeeccccccccCCcCCChHHHHHHHHcCCC
Confidence 677665 3444432 2223333 3799999999999998521 22 255688888887754
No 122
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=41.08 E-value=26 Score=39.23 Aligned_cols=33 Identities=12% Similarity=0.100 Sum_probs=24.6
Q ss_pred HHHHHHhcCCceeecCCCCCChHHHHHHHhcCC
Q 013817 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 400 (436)
Q Consensus 368 la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ 400 (436)
++||||+.||+|.|+.+.+.-...|...|.++|
T Consensus 31 ~aR~~r~~G~~V~~~~g~D~hG~~i~~~A~~~g 63 (673)
T PRK00133 31 WVRYQRMRGHEVLFVCADDAHGTPIMLKAEKEG 63 (673)
T ss_pred HHHHHHhcCCeeEEeCccCCCChHHHHHHHHcC
Confidence 799999999999999853222234777777766
No 123
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=40.36 E-value=23 Score=38.76 Aligned_cols=38 Identities=18% Similarity=0.132 Sum_probs=27.0
Q ss_pred CccHH--HHHHHHhcCCceeecCCCCCChHH-HHHHHhcCCc
Q 013817 363 VMVEG--LAKHLRCVGIDAATPRSKKPEPRE-LIDQTSKEKR 401 (436)
Q Consensus 363 ~~l~~--la~~LR~~G~d~~~~~~~~~~~~~-~~~~a~~e~r 401 (436)
..|.. +||++|+.|+||.|+... .++.. |...|.++|.
T Consensus 27 ~~l~ADv~aRy~Rl~G~~v~fvtGt-DeHGt~I~~~A~~~g~ 67 (558)
T COG0143 27 TYLAADVYARYLRLRGYEVFFLTGT-DEHGTKIELKAEKEGI 67 (558)
T ss_pred HHHHHHHHHHHHHhcCCeEEEEecc-CCCCCHHHHHHHHcCC
Confidence 44442 699999999999999852 23333 7777777774
No 124
>cd02072 Glm_B12_BD B12 binding domain of glutamate mutase (Glm). Glutamate mutase catalysis the conversion of (S)-glutamate with (2S,3S)-3-methylaspartate. The rearrangement reaction is initiated by the extraction of a hydrogen from the protein-bound substrate by a 5'-desoxyadenosyl radical, which is generated by the homolytic cleavage of the organometallic bond of the cofactor B12. Glm is a heterotetrameric molecule consisting of two alpha and two epsilon polypeptide chains.
Probab=39.28 E-value=48 Score=29.16 Aligned_cols=35 Identities=14% Similarity=0.158 Sum_probs=29.8
Q ss_pred HHHHHHhcCCceeecCCCCCChHHHHHHHhcCCcEE
Q 013817 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVL 403 (436)
Q Consensus 368 la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ri~ 403 (436)
++..||..||++.+++- +...+++++.|.+++-=+
T Consensus 19 v~~~L~~~GfeVidLG~-~v~~e~~v~aa~~~~adi 53 (128)
T cd02072 19 LDHAFTEAGFNVVNLGV-LSPQEEFIDAAIETDADA 53 (128)
T ss_pred HHHHHHHCCCEEEECCC-CCCHHHHHHHHHHcCCCE
Confidence 68999999999999984 678888999998887633
No 125
>cd00758 MoCF_BD MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin.
Probab=39.24 E-value=74 Score=27.56 Aligned_cols=49 Identities=16% Similarity=0.157 Sum_probs=33.2
Q ss_pred EEEeCccHHHHHHHHhcCCceeecCCCCCChHH---HHHHHhcCCcEEEecC
Q 013817 359 FLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRE---LIDQTSKEKRVLLTRD 407 (436)
Q Consensus 359 fl~D~~l~~la~~LR~~G~d~~~~~~~~~~~~~---~~~~a~~e~ri~lT~d 407 (436)
-+.|.+-.-|+.+|+..|+++.+..--..+..+ .+..|.++-.++||..
T Consensus 15 ~i~d~n~~~l~~~l~~~G~~v~~~~~v~Dd~~~i~~~i~~~~~~~DlvittG 66 (133)
T cd00758 15 QIEDTNGPALEALLEDLGCEVIYAGVVPDDADSIRAALIEASREADLVLTTG 66 (133)
T ss_pred ceEEchHHHHHHHHHHCCCEEEEeeecCCCHHHHHHHHHHHHhcCCEEEECC
Confidence 467888888999999999999876422223232 3344555678888864
No 126
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.98 E-value=1.2e+02 Score=36.30 Aligned_cols=102 Identities=14% Similarity=0.142 Sum_probs=60.1
Q ss_pred CCCceEEEEehHH-hHHHHHhhcccCCCccCccC-------------------CCceeeHHHHHHHhhcccCCCCCCcCc
Q 013817 102 SPDILKLGFKFKQ-DLIYLSSTFCSQGCDIGFDR-------------------VEPYLDITSIYNHLHHKQLGRKLPKET 161 (436)
Q Consensus 102 ~~~i~KVgh~~k~-Dl~~L~~~~gi~g~~~~~~~-------------------~~~v~Dlt~La~yLl~~~~~~~~~~~~ 161 (436)
||++ .+|||..+ |+..|.+....+++. .+.. -..++|+-.++...+.. .+
T Consensus 599 DPDi-i~g~n~~qfdlkvl~nR~~~l~i~-~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~~~~k~~~~~--------~s 668 (1172)
T TIGR00592 599 DPDE-IVGHDYQQRALKVLANRINDLKIP-TWSKIGRLRRSPKFGRRFGERTCGRMICDVEISAKELIRC--------KS 668 (1172)
T ss_pred CCCE-EEEEcccCccHHHHHHHHHHcCCC-cccccCccccCCCccccccceECCEEEEEHHHHHHHHhCc--------CC
Confidence 7875 57999875 777765432111111 0000 12367866666555543 38
Q ss_pred ccHHHHHHHHcCCcccc--ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 013817 162 KSLANICKELLDISLSK--ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (436)
Q Consensus 162 ~gL~~Lv~~~Lg~~l~K--~~q~s-dW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~ 213 (436)
++|.++++.+||..-.. ..... -|....--..-+.|...||..+++|...+.
T Consensus 669 y~L~~v~~~~L~~~k~~~~~~~i~~~~~~~~~~~~~~~y~~~Da~l~~~L~~~l~ 723 (1172)
T TIGR00592 669 YDLSELVQQILKTERKVIPIDNINNMYSESSSLTYLLEHTWKDAMFILQIMCELN 723 (1172)
T ss_pred CCHHHHHHHHhCCCCcccCHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999853211 01111 243222225568899999999999887553
No 127
>cd00668 Ile_Leu_Val_MetRS_core catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases. Catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases. These class I enzymes are all monomers. However, in some species, MetRS functions as a homodimer, as a result of an additional C-terminal domain. These enzymes aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. Enzymes in this subfamily share an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. MetRS has a significantly shorter insertion, which lacks the editing function.
Probab=38.22 E-value=28 Score=34.83 Aligned_cols=39 Identities=8% Similarity=-0.027 Sum_probs=27.2
Q ss_pred HHHHHHhcCCceeecCCCCCChHHHHHHHhcCCcEEEec
Q 013817 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTR 406 (436)
Q Consensus 368 la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ri~lT~ 406 (436)
++|+||+.||+|.++.+.+.-+..|...|.+++.+-.++
T Consensus 29 i~R~~r~~G~~v~~~~g~D~~g~~i~~~a~~~~~~~~~~ 67 (312)
T cd00668 29 IARYKRMRGYEVPFLPGWDTHGLPIELKAERKGGRKKKT 67 (312)
T ss_pred HHHHHHhCCCCCCCCCccCCCCHHHHHHHHHhcCccccc
Confidence 699999999999999754332334777777766544333
No 128
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=36.38 E-value=49 Score=29.04 Aligned_cols=33 Identities=18% Similarity=0.221 Sum_probs=27.8
Q ss_pred HHHHHHhcCCceeecCCCCCChHHHHHHHhcCCc
Q 013817 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (436)
Q Consensus 368 la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~r 401 (436)
++..||..||++.+... ..+.+++++.|.+++-
T Consensus 22 v~~~l~~~GfeVi~lg~-~~s~e~~v~aa~e~~a 54 (132)
T TIGR00640 22 IATAYADLGFDVDVGPL-FQTPEEIARQAVEADV 54 (132)
T ss_pred HHHHHHhCCcEEEECCC-CCCHHHHHHHHHHcCC
Confidence 68999999999999974 4577789999888775
No 129
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=36.01 E-value=1.8e+02 Score=27.73 Aligned_cols=113 Identities=20% Similarity=0.217 Sum_probs=65.1
Q ss_pred hhHHHHHHHhhCCCCceEEEEehH-HhHHHHHhhcccCCCcc--CccCC------------CceeeHHHHHHHhhcccCC
Q 013817 90 PSIWELLKELFVSPDILKLGFKFK-QDLIYLSSTFCSQGCDI--GFDRV------------EPYLDITSIYNHLHHKQLG 154 (436)
Q Consensus 90 ~~~~~~L~~lLe~~~i~KVgh~~k-~Dl~~L~~~~gi~g~~~--~~~~~------------~~v~Dlt~La~yLl~~~~~ 154 (436)
.+++..+...++.....-|+||.+ +|+..|...-=++|+.+ -++.. ..-+|| +..+.+.+
T Consensus 38 ~~lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DL---md~l~~~g-- 112 (209)
T PF10108_consen 38 KELLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDL---MDLLSFYG-- 112 (209)
T ss_pred HHHHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccH---HHHHhccC--
Confidence 457777777887655566999987 69998753211123220 00000 013562 23333322
Q ss_pred CCCCcCcccHHHHHHHHcCCccccc----cccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 013817 155 RKLPKETKSLANICKELLDISLSKE----LQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (436)
Q Consensus 155 ~~~~~~~~gL~~Lv~~~Lg~~l~K~----~q~s-dW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~ 213 (436)
.+...+|..||. .||++= |. .+.. -|....+ ++-..|.-.||..+..||-.+.
T Consensus 113 ---~~~~~sLd~la~-~lgiPg-K~~idGs~V~~~y~~g~i-~~I~~YCe~DVl~T~~lylR~~ 170 (209)
T PF10108_consen 113 ---AKARTSLDELAA-LLGIPG-KDDIDGSQVAELYQEGDI-DEIREYCEKDVLNTYLLYLRFE 170 (209)
T ss_pred ---ccccCCHHHHHH-HcCCCC-CCCCCHHHHHHHHHcCCH-HHHHHHHHHHHHHHHHHHHHHH
Confidence 134788998875 568764 42 1111 2433333 3467899999999999998885
No 130
>PHA02119 hypothetical protein
Probab=35.40 E-value=38 Score=26.55 Aligned_cols=18 Identities=28% Similarity=0.488 Sum_probs=14.7
Q ss_pred HHHHHHHHhcCCceeecC
Q 013817 366 EGLAKHLRCVGIDAATPR 383 (436)
Q Consensus 366 ~~la~~LR~~G~d~~~~~ 383 (436)
..+..|||.+|||+.+-+
T Consensus 57 ~divdylr~lgy~~~~~s 74 (87)
T PHA02119 57 KDIVDYLRSLGYDAKSDS 74 (87)
T ss_pred HHHHHHHHHccchhcccc
Confidence 357899999999998653
No 131
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=35.02 E-value=62 Score=27.65 Aligned_cols=33 Identities=21% Similarity=0.427 Sum_probs=26.7
Q ss_pred HHHHHHhcCCceeecCCCCCChHHHHHHHhcCCc
Q 013817 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (436)
Q Consensus 368 la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~r 401 (436)
++..||..||++.|.+. ....+++++.|.+.+-
T Consensus 19 ~~~~l~~~G~~vi~lG~-~vp~e~~~~~a~~~~~ 51 (122)
T cd02071 19 IARALRDAGFEVIYTGL-RQTPEEIVEAAIQEDV 51 (122)
T ss_pred HHHHHHHCCCEEEECCC-CCCHHHHHHHHHHcCC
Confidence 58999999999999985 4667788888766654
No 132
>cd00671 ArgRS_core catalytic core domain of arginyl-tRNA synthetases. Arginyl tRNA synthetase (ArgRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. There are at least three subgroups of ArgRS. One type contains both characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The second subtype lacks the KMSKS motif; however, it has a lysine N-terminal to the HIGH motif, which serves as the functional counterpart to the second lysine of the KMSKS motif. A third group, which is found primarily in archaea and a few bacteria, lacks both the KMSKS motif and the HIGH loop lysine.
Probab=35.01 E-value=28 Score=32.83 Aligned_cols=37 Identities=16% Similarity=0.095 Sum_probs=24.2
Q ss_pred CccH-HHHHHHHhcCCceeecCCCCCChHHHHHHHhcC
Q 013817 363 VMVE-GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKE 399 (436)
Q Consensus 363 ~~l~-~la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e 399 (436)
..+| -|+|+||.+||++.+...-+.-+..|...|...
T Consensus 23 ~vigD~l~R~l~~~G~~V~~~~~~~D~G~qi~~~a~~~ 60 (212)
T cd00671 23 AIIGDSLARILEFLGYDVTREYYINDWGRQIGLLILSL 60 (212)
T ss_pred HHHHHHHHHHHHHCCCcEEEEeccCCcHHHHHHHHHHH
Confidence 3555 389999999999997753222234466666443
No 133
>COG1487 VapC Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=34.97 E-value=61 Score=27.88 Aligned_cols=44 Identities=23% Similarity=0.246 Sum_probs=34.9
Q ss_pred cHHHHHHHHhcCCceeecCCCCCChHHHHHHHhcCCcEEEecC-hhHHhhh
Q 013817 365 VEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRD-AKLLRHQ 414 (436)
Q Consensus 365 l~~la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ri~lT~d-~~l~~~~ 414 (436)
-+.+.+-|+..|. . .+..|--|...|...|-+++|+| ++|..-.
T Consensus 79 ~~~i~~~l~~~G~----~--~~~~D~lIAa~A~~~~~~LvT~d~~df~~i~ 123 (133)
T COG1487 79 AAEIQARLRKEGI----P--IGLNDLLIAATAIAHGLLLVTRDVKDFERIP 123 (133)
T ss_pred HHHHHHHHHhcCC----C--CChHHHHHHHHHHHcCCEEEEcCHHhccccc
Confidence 4678899999999 2 24577789999999999999999 6665443
No 134
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=33.86 E-value=23 Score=36.86 Aligned_cols=35 Identities=20% Similarity=0.149 Sum_probs=24.7
Q ss_pred HHHHHHhcCCceeecCCCCCChHHHHHHHhcCCcE
Q 013817 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRV 402 (436)
Q Consensus 368 la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ri 402 (436)
+|||+|+.|+||.++...+.--..|...|.++|.-
T Consensus 28 ~aR~~r~~G~~v~~~tGtDehG~~i~~~A~~~g~~ 62 (391)
T PF09334_consen 28 LARYLRLRGHDVLFVTGTDEHGSKIETAAEKQGID 62 (391)
T ss_dssp HHHHHHHTT-EEEEEEEEE-SSHHHHHHHHHTTS-
T ss_pred HHHHHhhcccceeeEEecchhhHHHHHHHHHcCCC
Confidence 69999999999999875332233478888888774
No 135
>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.
Probab=33.67 E-value=61 Score=30.29 Aligned_cols=38 Identities=16% Similarity=0.302 Sum_probs=30.6
Q ss_pred cHH--HHHHHHhcCCceeecCCCCCChHHHHHHHhcCCcEE
Q 013817 365 VEG--LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVL 403 (436)
Q Consensus 365 l~~--la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ri~ 403 (436)
+|. ++..||..||++.|++. +...+++++.+.+++--+
T Consensus 97 lG~~~v~~~l~~~G~~vi~lG~-~~p~~~l~~~~~~~~~d~ 136 (201)
T cd02070 97 IGKNLVATMLEANGFEVIDLGR-DVPPEEFVEAVKEHKPDI 136 (201)
T ss_pred HHHHHHHHHHHHCCCEEEECCC-CCCHHHHHHHHHHcCCCE
Confidence 553 69999999999999984 667888999888776544
No 136
>PRK03670 competence damage-inducible protein A; Provisional
Probab=32.37 E-value=81 Score=30.92 Aligned_cols=48 Identities=15% Similarity=0.045 Sum_probs=31.4
Q ss_pred EEEeCccHHHHHHHHhcCCceeecCCCCCChHH-HHH---HHhc-CCcEEEecC
Q 013817 359 FLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRE-LID---QTSK-EKRVLLTRD 407 (436)
Q Consensus 359 fl~D~~l~~la~~LR~~G~d~~~~~~~~~~~~~-~~~---~a~~-e~ri~lT~d 407 (436)
-+.|.+..-|+++|+.+|+++.+..-- .||.+ |.+ .|.. ...++||.+
T Consensus 16 ~i~dtN~~~la~~L~~~G~~v~~~~iV-~Dd~~~I~~~l~~a~~~~~DlVIttG 68 (252)
T PRK03670 16 NTVDSNSAFIAQKLTEKGYWVRRITTV-GDDVEEIKSVVLEILSRKPEVLVISG 68 (252)
T ss_pred eEEehhHHHHHHHHHHCCCEEEEEEEc-CCCHHHHHHHHHHHhhCCCCEEEECC
Confidence 578999999999999999998765421 23333 332 2333 236666655
No 137
>COG0525 ValS Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=30.33 E-value=27 Score=40.07 Aligned_cols=47 Identities=21% Similarity=0.277 Sum_probs=34.1
Q ss_pred CCCCCCCCCCCCCCeEEEeCccH-HHHHHHHhcCCceeecCCCCCChHHHHHH
Q 013817 344 PPPWDLSLGGDGYPKFLCDVMVE-GLAKHLRCVGIDAATPRSKKPEPRELIDQ 395 (436)
Q Consensus 344 ~~p~~~~~~~~~~~~fl~D~~l~-~la~~LR~~G~d~~~~~~~~~~~~~~~~~ 395 (436)
||| -+.|.=.|.=-.+.+|. -|+||-||.||+|+|+. +.||.=|...
T Consensus 40 PPP---NVTG~LHmGHAl~~tl~D~l~RykRM~G~~vl~~p--G~DhAGIaTq 87 (877)
T COG0525 40 PPP---NVTGSLHMGHALNYTLQDILARYKRMRGYNVLWPP--GTDHAGIATQ 87 (877)
T ss_pred CCC---CCCCcccchhhhhHHHHHHHHHHHHcCCCeeecCC--CCCCCCchHH
Confidence 455 35566667777788888 48999999999999997 4455444433
No 138
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=29.31 E-value=85 Score=28.21 Aligned_cols=41 Identities=17% Similarity=0.214 Sum_probs=29.8
Q ss_pred HHHHHHHHhcCCceeecCCCCCChHHHHHHHhcCC-cEEEecC
Q 013817 366 EGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK-RVLLTRD 407 (436)
Q Consensus 366 ~~la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~-ri~lT~d 407 (436)
.=+++-||..||++.|..- .....|++..|.+|+ -++.-+.
T Consensus 30 kvia~~l~d~GfeVi~~g~-~~tp~e~v~aA~~~dv~vIgvSs 71 (143)
T COG2185 30 KVIARALADAGFEVINLGL-FQTPEEAVRAAVEEDVDVIGVSS 71 (143)
T ss_pred HHHHHHHHhCCceEEecCC-cCCHHHHHHHHHhcCCCEEEEEe
Confidence 3479999999999999985 346678899885554 3444333
No 139
>cd00885 cinA Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, where the domain is presumed to bind molybdopterin.
Probab=29.28 E-value=99 Score=28.29 Aligned_cols=49 Identities=18% Similarity=0.219 Sum_probs=32.3
Q ss_pred EEEeCccHHHHHHHHhcCCceeecCCCCCChHH---HHHHHhcCCcEEEecC
Q 013817 359 FLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRE---LIDQTSKEKRVLLTRD 407 (436)
Q Consensus 359 fl~D~~l~~la~~LR~~G~d~~~~~~~~~~~~~---~~~~a~~e~ri~lT~d 407 (436)
-+.|.+..-|+++|+.+|+++.+..--..+..+ .+..+.++-.++||.+
T Consensus 15 ~i~d~n~~~l~~~L~~~G~~v~~~~~v~Dd~~~I~~~l~~~~~~~dlVIttG 66 (170)
T cd00885 15 QIVDTNAAFLAKELAELGIEVYRVTVVGDDEDRIAEALRRASERADLVITTG 66 (170)
T ss_pred eEEEhHHHHHHHHHHHCCCEEEEEEEeCCCHHHHHHHHHHHHhCCCEEEECC
Confidence 578999999999999999998764321222222 2333444566777765
No 140
>PRK03094 hypothetical protein; Provisional
Probab=28.79 E-value=2e+02 Score=23.31 Aligned_cols=61 Identities=11% Similarity=0.137 Sum_probs=41.6
Q ss_pred CeEEEeCccHHHHHHHHhcCCceeecCCCCCChHHHHHHHhcCCcEEEe-cChhHHhhhcccCCcEEEEcC
Q 013817 357 PKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLT-RDAKLLRHQYLIKNQIYRVKS 426 (436)
Q Consensus 357 ~~fl~D~~l~~la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ri~lT-~d~~l~~~~~~~~~~~~~v~~ 426 (436)
.|+=+...|..+..+|+..||+++-+.+. .+ ++.=+.+++| .|..++.-.... .++..|..
T Consensus 2 ~kIaVE~~Ls~i~~~L~~~GYeVv~l~~~--~~------~~~~Da~VitG~d~n~mgi~d~~-t~~pVI~A 63 (80)
T PRK03094 2 AKIGVEQSLTDVQQALKQKGYEVVQLRSE--QD------AQGCDCCVVTGQDSNVMGIADTS-TKGSVITA 63 (80)
T ss_pred CeEEeecCcHHHHHHHHHCCCEEEecCcc--cc------cCCcCEEEEeCCCcceecccccc-cCCcEEEc
Confidence 35678889999999999999999977531 22 2344788898 677777544332 23555543
No 141
>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).
Probab=26.91 E-value=99 Score=29.41 Aligned_cols=39 Identities=8% Similarity=0.072 Sum_probs=30.9
Q ss_pred ccHH--HHHHHHhcCCceeecCCCCCChHHHHHHHhcCCcEE
Q 013817 364 MVEG--LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVL 403 (436)
Q Consensus 364 ~l~~--la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ri~ 403 (436)
.||+ ++-.||..||++.|++. +...+++++.+.+.+--+
T Consensus 102 diG~~iv~~~l~~~G~~Vi~LG~-~vp~e~~v~~~~~~~~~~ 142 (213)
T cd02069 102 DIGKNLVGVILSNNGYEVIDLGV-MVPIEKILEAAKEHKADI 142 (213)
T ss_pred HHHHHHHHHHHHhCCCEEEECCC-CCCHHHHHHHHHHcCCCE
Confidence 3564 59999999999999985 677888999887766533
No 142
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=26.43 E-value=1.2e+02 Score=29.86 Aligned_cols=48 Identities=23% Similarity=0.324 Sum_probs=34.2
Q ss_pred EEeCccHHHHHHHHhcCCceeecCCCCCChHH---HHHHHhcCCcEEEecC
Q 013817 360 LCDVMVEGLAKHLRCVGIDAATPRSKKPEPRE---LIDQTSKEKRVLLTRD 407 (436)
Q Consensus 360 l~D~~l~~la~~LR~~G~d~~~~~~~~~~~~~---~~~~a~~e~ri~lT~d 407 (436)
++|.+...||+.|..+||+..+..--+.+..+ .+..|.+.-.++||.+
T Consensus 18 ivdtNa~~la~~L~~~G~~v~~~~~VgD~~~~I~~~l~~a~~r~D~vI~tG 68 (255)
T COG1058 18 IVDTNAAFLADELTELGVDLARITTVGDNPDRIVEALREASERADVVITTG 68 (255)
T ss_pred eecchHHHHHHHHHhcCceEEEEEecCCCHHHHHHHHHHHHhCCCEEEECC
Confidence 68999999999999999999776532223222 4566666677777654
No 143
>PRK03673 hypothetical protein; Provisional
Probab=25.90 E-value=1e+02 Score=32.30 Aligned_cols=50 Identities=16% Similarity=0.181 Sum_probs=33.9
Q ss_pred eEEEeCccHHHHHHHHhcCCceeecCCCCCChHHHHH---HHhcCCcEEEecC
Q 013817 358 KFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELID---QTSKEKRVLLTRD 407 (436)
Q Consensus 358 ~fl~D~~l~~la~~LR~~G~d~~~~~~~~~~~~~~~~---~a~~e~ri~lT~d 407 (436)
.-+.|.+-.-|+++|+.+|+++.+..--+.+.++|.+ .|..+..++||.+
T Consensus 16 G~i~dtN~~~la~~L~~~G~~v~~~~~v~D~~~~i~~~l~~a~~~~DlVI~tG 68 (396)
T PRK03673 16 GQIVDTNAAWLADFFFHQGLPLSRRNTVGDNLDALVAILRERSQHADVLIVNG 68 (396)
T ss_pred CeEEEhHHHHHHHHHHHCCCEEEEEEEcCCCHHHHHHHHHHHhccCCEEEEcC
Confidence 3678999999999999999998765432323333433 3555566666654
No 144
>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family. This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.
Probab=24.62 E-value=1.1e+02 Score=28.64 Aligned_cols=38 Identities=18% Similarity=0.309 Sum_probs=30.9
Q ss_pred cHH--HHHHHHhcCCceeecCCCCCChHHHHHHHhcCCcEE
Q 013817 365 VEG--LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVL 403 (436)
Q Consensus 365 l~~--la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ri~ 403 (436)
+|. ++..||..||++.|++. +...+++++.+++++--+
T Consensus 99 lG~~~v~~~l~~~G~~vi~LG~-~vp~e~~v~~~~~~~pd~ 138 (197)
T TIGR02370 99 IGKNIVVTMLRANGFDVIDLGR-DVPIDTVVEKVKKEKPLM 138 (197)
T ss_pred HHHHHHHHHHHhCCcEEEECCC-CCCHHHHHHHHHHcCCCE
Confidence 453 69999999999999985 677888999988777633
No 145
>PF02639 DUF188: Uncharacterized BCR, YaiI/YqxD family COG1671; InterPro: IPR003791 This entry describes proteins of unknown function.
Probab=24.49 E-value=1.1e+02 Score=26.95 Aligned_cols=30 Identities=13% Similarity=0.155 Sum_probs=24.5
Q ss_pred ChHHHHHHHhcCCcEEEecChhHHhhhcccC
Q 013817 388 EPRELIDQTSKEKRVLLTRDAKLLRHQYLIK 418 (436)
Q Consensus 388 ~~~~~~~~a~~e~ri~lT~d~~l~~~~~~~~ 418 (436)
-|..|++.+ +.|-|+||.|-.|+.+....|
T Consensus 41 aD~~I~~~~-~~gDiVITqDigLA~~~l~Kg 70 (130)
T PF02639_consen 41 ADFYIVNHA-KPGDIVITQDIGLASLLLAKG 70 (130)
T ss_pred HHHHHHHcC-CCCCEEEECCHHHHHHHHHCC
Confidence 466788887 689999999999998866654
No 146
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=24.45 E-value=3.4e+02 Score=24.53 Aligned_cols=32 Identities=19% Similarity=0.075 Sum_probs=21.9
Q ss_pred HHHHHHHhhCC----CCceEEEEehHHhHHHHHhhc
Q 013817 92 IWELLKELFVS----PDILKLGFKFKQDLIYLSSTF 123 (436)
Q Consensus 92 ~~~~L~~lLe~----~~i~KVgh~~k~Dl~~L~~~~ 123 (436)
++..+..++.+ ....-+||++.+|+..|.+.+
T Consensus 78 vl~~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~ 113 (173)
T cd06135 78 AEAELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYM 113 (173)
T ss_pred HHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHH
Confidence 34455555543 345668999999999987654
No 147
>TIGR03599 YloV DAK2 domain fusion protein YloV. This model describes a protein family that contains an N-terminal DAK2 domain (pfam02734), so named because of similarity to the dihydroxyacetone kinase family family. The GTP-binding protein CgtA (a member of the obg family) is a bacterial GTPase associated with ribosome biogenesis, and it has a characteristic extension (TIGR03595) in certain lineages. This protein family described here was found, by the method of partial phylognetic profiling, to have a phylogenetic distribution strongly correlated to that of TIGR03595. This correlation implies some form of functional coupling.
Probab=24.39 E-value=3.6e+02 Score=29.43 Aligned_cols=79 Identities=13% Similarity=0.221 Sum_probs=56.3
Q ss_pred CCeEEEeCccHHHHHHHHhcCCceeecCCC--CCChHHHHHHHh---cCCcEEEecChhHHhh----hcccCCcEEEEcC
Q 013817 356 YPKFLCDVMVEGLAKHLRCVGIDAATPRSK--KPEPRELIDQTS---KEKRVLLTRDAKLLRH----QYLIKNQIYRVKS 426 (436)
Q Consensus 356 ~~~fl~D~~l~~la~~LR~~G~d~~~~~~~--~~~~~~~~~~a~---~e~ri~lT~d~~l~~~----~~~~~~~~~~v~~ 426 (436)
...||.-+.=.++++.++.+|.|++..... .++-.+|+.... .++=|||..++....- +...+.+++.|.+
T Consensus 314 ~~~ivAv~~g~g~~~~f~~~Ga~~vi~ggqt~nPS~~dll~ai~~~~a~~V~iLPNn~nii~aA~qa~~~~~~~v~vvpT 393 (530)
T TIGR03599 314 EYAIVAVAPGEGIAELFKSLGADVVIEGGQTMNPSTEDILKAIEKVNAKNVFVLPNNKNIILAAEQAAELADKNVVVIPT 393 (530)
T ss_pred CeEEEEEcCCchHHHHHHHCCCCEEEeCCCCCCCCHHHHHHHHHhCCCCeEEEecCCccHHHHHHHHHHHhCCcEEEEeC
Confidence 346899998889999999999999987753 456667775443 3445777888766421 2233457899998
Q ss_pred CChhhhhh
Q 013817 427 LLKNQQLL 434 (436)
Q Consensus 427 ~~~~~Ql~ 434 (436)
.++.+.|.
T Consensus 394 ~s~~qgia 401 (530)
T TIGR03599 394 KTIVQGLA 401 (530)
T ss_pred CCHHHHHH
Confidence 88877664
No 148
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=24.23 E-value=82 Score=22.65 Aligned_cols=26 Identities=27% Similarity=0.331 Sum_probs=19.3
Q ss_pred HHHHHHHhcCCceeecCCCCCChHHHHHHHhcCCcEEEecC
Q 013817 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRD 407 (436)
Q Consensus 367 ~la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ri~lT~d 407 (436)
+-++||+..|+.-..-. .||.++||+
T Consensus 19 ~Q~~~L~~~Gi~~~~~~---------------~G~p~V~r~ 44 (47)
T PF13986_consen 19 KQIRWLRRNGIPFVVRA---------------DGRPIVTRS 44 (47)
T ss_pred HHHHHHHHCCCeeEECC---------------CCCEEeeHH
Confidence 35899999999877532 377777764
No 149
>PTZ00315 2'-phosphotransferase; Provisional
Probab=24.20 E-value=6.7e+02 Score=27.82 Aligned_cols=103 Identities=12% Similarity=0.134 Sum_probs=57.5
Q ss_pred hHHHHHHHhhCCCC--------ceEEEEehHHhHH-HHHhhcc---cCCCccCccCCCceeeHHHHHHHhhcccC-----
Q 013817 91 SIWELLKELFVSPD--------ILKLGFKFKQDLI-YLSSTFC---SQGCDIGFDRVEPYLDITSIYNHLHHKQL----- 153 (436)
Q Consensus 91 ~~~~~L~~lLe~~~--------i~KVgh~~k~Dl~-~L~~~~g---i~g~~~~~~~~~~v~Dlt~La~yLl~~~~----- 153 (436)
+++..+..+|.+.. -..++|+...|+. .|...+. ..|+.. .....+|+....+..+.+..
T Consensus 132 eVl~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~---~f~~widLk~~lar~l~p~~~~~~~ 208 (582)
T PTZ00315 132 VVYCEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPL---SFQRWCNLKKYMSQLGFGNGSGCGG 208 (582)
T ss_pred HHHHHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCc---ccceEEEhHHHHHHHhCcccccccc
Confidence 45666777776542 1358999999995 5644322 112111 12346675433333333210
Q ss_pred CCCCCcCcccHHHHHHHHcCCcccc-cccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 013817 154 GRKLPKETKSLANICKELLDISLSK-ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (436)
Q Consensus 154 ~~~~~~~~~gL~~Lv~~~Lg~~l~K-~~q~sdW~~RPL~~~ql~YAA~DA~~Ll~L~~~L~ 213 (436)
+..-....++|.+|++. +|++..- .+ -|-.||..+.+|+..|.
T Consensus 209 ~~~~~~~~~~L~~al~~-lgL~~eGr~H----------------rAlDDA~ntA~L~~~Ll 252 (582)
T PTZ00315 209 GATPPLGPSDMPDMLQM-LGLPLQGRHH----------------SGIDDCRNIAAVLCELL 252 (582)
T ss_pred ccccccCCcCHHHHHHH-CCCCCCCCCc----------------CcHHHHHHHHHHHHHHH
Confidence 00001246899999986 6766421 12 16679999988888775
No 150
>PRK01215 competence damage-inducible protein A; Provisional
Probab=22.20 E-value=1.5e+02 Score=29.22 Aligned_cols=50 Identities=8% Similarity=0.077 Sum_probs=33.7
Q ss_pred eEEEeCccHHHHHHHHhcCCceeecCCCCCChH---HHHHHHhcCCcEEEecC
Q 013817 358 KFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPR---ELIDQTSKEKRVLLTRD 407 (436)
Q Consensus 358 ~fl~D~~l~~la~~LR~~G~d~~~~~~~~~~~~---~~~~~a~~e~ri~lT~d 407 (436)
.-+.|.+-.-|+++|+.+|+++.+..--..+.. +.+..|.....++||.+
T Consensus 18 G~i~dtn~~~l~~~L~~~G~~v~~~~~v~Dd~~~I~~~l~~a~~~~DlVIttG 70 (264)
T PRK01215 18 GRTVNTNASWIARRLTYLGYTVRRITVVMDDIEEIVSAFREAIDRADVVVSTG 70 (264)
T ss_pred CeEEEhhHHHHHHHHHHCCCeEEEEEEeCCCHHHHHHHHHHHhcCCCEEEEeC
Confidence 368899999999999999999976542121222 23444555567777765
No 151
>cd00886 MogA_MoaB MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea, and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT). MogA, together with MoeA, is responsible for the metal incorporation into MPT, the third step in MoCF biosynthesis. The plant homolog Cnx1 is a MoeA-MogA fusion protein. The mammalian homolog gephyrin is a MogA-MoeA fusion protein, that plays a critical role in postsynaptic anchoring of inhibitory glycine receptors and major GABAa receptor subtypes. In contrast, MoaB shows high similarity to MogA, but little is known about its physiological role. All well studied members of this family form highly stable trimers.
Probab=21.82 E-value=1.4e+02 Score=26.49 Aligned_cols=48 Identities=15% Similarity=0.066 Sum_probs=30.9
Q ss_pred EEeCccHHHHHHHHhcCCceeecCCCCCChHHHH---HHHhc--CCcEEEecC
Q 013817 360 LCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELI---DQTSK--EKRVLLTRD 407 (436)
Q Consensus 360 l~D~~l~~la~~LR~~G~d~~~~~~~~~~~~~~~---~~a~~--e~ri~lT~d 407 (436)
+.|.+-.-|+.+|+..|+++....--..+.++|. ..+.+ +..++||..
T Consensus 17 i~d~n~~~l~~~l~~~G~~v~~~~~v~Dd~~~i~~~l~~~~~~~~~DlVittG 69 (152)
T cd00886 17 AEDRSGPALVELLEEAGHEVVAYEIVPDDKDEIREALIEWADEDGVDLILTTG 69 (152)
T ss_pred CccchHHHHHHHHHHcCCeeeeEEEcCCCHHHHHHHHHHHHhcCCCCEEEECC
Confidence 4577777899999999999876542122333332 33334 567888765
No 152
>PLN02610 probable methionyl-tRNA synthetase
Probab=21.76 E-value=91 Score=35.82 Aligned_cols=33 Identities=15% Similarity=0.055 Sum_probs=22.7
Q ss_pred HHHHHHhcCCceeecCCCCCChHHHHHHHhcCC
Q 013817 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 400 (436)
Q Consensus 368 la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ 400 (436)
+|||+|+.|+||.|+...+.--..+...|.++|
T Consensus 47 ~aRy~r~~G~~v~f~~GtDehG~~i~~~A~~~g 79 (801)
T PLN02610 47 FARYCRLRGYNAIYICGTDEYGTATETKALEEN 79 (801)
T ss_pred HHHHHHhCCCceEecccccCCcHHHHHHHHHcC
Confidence 699999999999999853211222555565555
No 153
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=21.14 E-value=1.4e+02 Score=24.15 Aligned_cols=49 Identities=12% Similarity=0.238 Sum_probs=35.6
Q ss_pred CeEEEeCccHHHHHHHHhcCCceeecCCCCCChHHHHHHHhcCCcEEEe-cChhHHhh
Q 013817 357 PKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLT-RDAKLLRH 413 (436)
Q Consensus 357 ~~fl~D~~l~~la~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ri~lT-~d~~l~~~ 413 (436)
.|+=+...|..+..+|+..||+++-+.+. +| ++.=+.|++| .|..+..-
T Consensus 2 kkIAVE~~Ls~v~~~L~~~GyeVv~l~~~--~~------~~~~daiVvtG~~~n~mg~ 51 (80)
T PF03698_consen 2 KKIAVEEGLSNVKEALREKGYEVVDLENE--QD------LQNVDAIVVTGQDTNMMGI 51 (80)
T ss_pred CeEEecCCchHHHHHHHHCCCEEEecCCc--cc------cCCcCEEEEECCCcccccc
Confidence 35778889999999999999999988642 21 2234778888 55556543
No 154
>PF08845 SymE_toxin: Toxin SymE, type I toxin-antitoxin system; InterPro: IPR014944 This entry represents a SOS-induced gene whose product shows homology to the antitoxin MazE (SymE), the coding region contains a cis-encoded antisense RNA. The small antisense RNA and the gene have the all the hallmarks of a toxin-antitoxin module. The synthesis of the SymE is tightly repressed at multiple levels; at the transcriptional level by the LexA repressor, at the level of mRNA stability and translation by the SymR RNA and at the level of protein stability by the Lon protease. SymE co-purifies with ribosomes and overproduction of the protein leads to cell growth inhibition, decreased protein synthesis and increased RNA degradation. These properties are shared with several RNA endonuclease toxins of toxin-antitoxin modules. It seems probable that the SymE protein represents an evolutionary derivative of a toxin containing the AbrB fold, whose representatives are typically antitoxins. The SymE promoted cleavage of RNA cleavage may be important for the recycling of RNAs damaged under SOS-inducing conditions []. ; GO: 0003723 RNA binding, 0016788 hydrolase activity, acting on ester bonds, 0016070 RNA metabolic process, 0005737 cytoplasm
Probab=20.17 E-value=27 Score=26.31 Aligned_cols=27 Identities=19% Similarity=0.297 Sum_probs=18.8
Q ss_pred HHHHHhcCCceeecCCCCCChHHHHHHHhcCCcEEEe
Q 013817 369 AKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLT 405 (436)
Q Consensus 369 a~~LR~~G~d~~~~~~~~~~~~~~~~~a~~e~ri~lT 405 (436)
++||..+||++=.. +.+-..+|+|+||
T Consensus 30 G~WL~~aGF~~G~~----------v~V~v~~g~lvIt 56 (57)
T PF08845_consen 30 GKWLEEAGFTIGDP----------VKVRVMPGCLVIT 56 (57)
T ss_pred hhhhHHhCCCCCCE----------EEEEEECCEEEEe
Confidence 79999999976422 1222467888887
Done!