Query 010743
Match_columns 502
No_of_seqs 352 out of 1365
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 04:03:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010743.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010743hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2248 3'-5' exonuclease [Rep 100.0 3.6E-41 7.7E-46 350.3 13.4 303 1-304 70-379 (380)
2 cd06145 REX1_like DEDDh 3'-5' 100.0 1.3E-35 2.9E-40 273.2 15.7 148 145-293 1-149 (150)
3 cd06137 DEDDh_RNase DEDDh 3'-5 100.0 6.1E-35 1.3E-39 271.4 13.3 149 145-294 1-161 (161)
4 cd06143 PAN2_exo DEDDh 3'-5' e 100.0 1.1E-34 2.5E-39 273.1 14.1 147 145-294 1-174 (174)
5 cd06149 ISG20 DEDDh 3'-5' exon 100.0 3.3E-34 7.2E-39 266.0 15.2 148 145-294 1-157 (157)
6 KOG2249 3'-5' exonuclease [Rep 100.0 2.5E-34 5.5E-39 282.4 13.9 151 143-297 106-263 (280)
7 cd06144 REX4_like DEDDh 3'-5' 100.0 8.6E-32 1.9E-36 247.9 14.1 146 145-294 1-152 (152)
8 PRK09146 DNA polymerase III su 100.0 3.4E-28 7.4E-33 240.5 19.5 160 138-303 43-230 (239)
9 PRK05711 DNA polymerase III su 100.0 3.2E-28 7E-33 240.9 18.3 155 141-299 3-175 (240)
10 TIGR01406 dnaQ_proteo DNA poly 100.0 6.8E-28 1.5E-32 236.3 17.4 152 143-298 1-170 (225)
11 PRK07740 hypothetical protein; 100.0 2E-27 4.4E-32 235.5 19.1 157 140-302 57-228 (244)
12 PRK06310 DNA polymerase III su 99.9 4.1E-27 8.9E-32 234.1 18.4 156 139-299 4-173 (250)
13 PRK06309 DNA polymerase III su 99.9 3E-27 6.6E-32 232.3 16.9 153 142-299 2-165 (232)
14 PRK07247 DNA polymerase III su 99.9 5.6E-27 1.2E-31 225.4 18.4 155 141-303 4-172 (195)
15 cd06131 DNA_pol_III_epsilon_Ec 99.9 6.9E-27 1.5E-31 216.3 15.4 149 144-296 1-166 (167)
16 PRK09145 DNA polymerase III su 99.9 2E-26 4.4E-31 221.3 18.2 152 141-298 28-199 (202)
17 PRK06807 DNA polymerase III su 99.9 2.5E-26 5.4E-31 235.4 19.0 154 140-300 6-172 (313)
18 PRK07983 exodeoxyribonuclease 99.9 2.9E-26 6.2E-31 224.2 18.1 147 144-299 2-153 (219)
19 PRK07942 DNA polymerase III su 99.9 1.7E-26 3.7E-31 227.2 16.3 157 141-301 5-181 (232)
20 PRK06063 DNA polymerase III su 99.9 4.2E-26 9.1E-31 233.7 19.6 157 141-305 14-184 (313)
21 TIGR00573 dnaq exonuclease, DN 99.9 3E-26 6.5E-31 222.9 17.6 157 141-302 6-179 (217)
22 smart00479 EXOIII exonuclease 99.9 2.6E-26 5.6E-31 210.3 16.2 153 143-300 1-167 (169)
23 PRK08517 DNA polymerase III su 99.9 7E-26 1.5E-30 226.3 19.2 156 139-301 65-232 (257)
24 cd06130 DNA_pol_III_epsilon_li 99.9 4.9E-26 1.1E-30 207.2 16.3 142 144-294 1-155 (156)
25 cd06136 TREX1_2 DEDDh 3'-5' ex 99.9 1.8E-26 3.9E-31 217.9 11.7 144 144-295 1-176 (177)
26 PRK06195 DNA polymerase III su 99.9 1.5E-25 3.3E-30 229.0 18.6 149 143-300 2-164 (309)
27 PRK07748 sporulation inhibitor 99.9 2.1E-25 4.6E-30 215.3 16.8 155 141-300 3-180 (207)
28 TIGR01298 RNaseT ribonuclease 99.9 7E-25 1.5E-29 211.2 16.8 156 141-301 7-193 (200)
29 cd06134 RNaseT DEDDh 3'-5' exo 99.9 6E-25 1.3E-29 209.7 15.8 153 142-299 5-188 (189)
30 PRK05168 ribonuclease T; Provi 99.9 8.8E-25 1.9E-29 212.1 16.5 156 140-300 15-201 (211)
31 PRK07246 bifunctional ATP-depe 99.9 9.2E-25 2E-29 248.3 19.1 155 141-302 6-172 (820)
32 PRK07883 hypothetical protein; 99.9 1.3E-24 2.8E-29 237.9 18.9 161 139-305 12-187 (557)
33 COG2176 PolC DNA polymerase II 99.9 1.6E-25 3.5E-30 251.9 11.5 162 138-305 417-591 (1444)
34 PRK05601 DNA polymerase III su 99.9 3.5E-24 7.5E-29 221.9 18.4 155 140-299 44-248 (377)
35 PRK06722 exonuclease; Provisio 99.9 4.3E-24 9.4E-29 215.6 17.7 152 141-298 4-179 (281)
36 TIGR01407 dinG_rel DnaQ family 99.9 7.4E-24 1.6E-28 242.1 19.0 153 143-301 1-166 (850)
37 KOG1275 PAB-dependent poly(A) 99.9 8.9E-26 1.9E-30 248.3 3.0 275 28-328 785-1112(1118)
38 PRK08074 bifunctional ATP-depe 99.9 7.4E-24 1.6E-28 244.0 18.8 155 142-302 3-171 (928)
39 TIGR01405 polC_Gram_pos DNA po 99.9 1.6E-23 3.4E-28 244.5 18.5 159 140-304 188-359 (1213)
40 cd06133 ERI-1_3'hExo_like DEDD 99.9 1.7E-23 3.7E-28 193.8 13.7 148 144-296 1-175 (176)
41 cd06127 DEDDh DEDDh 3'-5' exon 99.9 3.1E-23 6.7E-28 185.4 14.6 144 145-293 1-158 (159)
42 cd06138 ExoI_N N-terminal DEDD 99.9 1.6E-23 3.4E-28 198.5 13.1 144 145-293 1-182 (183)
43 COG0847 DnaQ DNA polymerase II 99.9 6.4E-23 1.4E-27 201.0 17.2 154 142-299 13-181 (243)
44 PRK09182 DNA polymerase III su 99.9 1.6E-22 3.5E-27 205.7 18.2 151 140-299 35-200 (294)
45 PF00929 RNase_T: Exonuclease; 99.9 2.7E-24 5.8E-29 192.4 -1.8 145 145-293 1-164 (164)
46 PRK11779 sbcB exonuclease I; P 99.8 1.5E-20 3.2E-25 202.1 16.4 158 140-301 4-199 (476)
47 PRK05359 oligoribonuclease; Pr 99.8 1.4E-20 3.1E-25 178.9 14.4 145 141-299 2-174 (181)
48 cd06135 Orn DEDDh 3'-5' exonuc 99.8 8.4E-21 1.8E-25 178.7 11.4 142 144-298 1-170 (173)
49 PTZ00315 2'-phosphotransferase 99.8 9.7E-20 2.1E-24 198.0 19.2 158 142-303 56-258 (582)
50 PRK00448 polC DNA polymerase I 99.8 1.9E-20 4.1E-25 221.3 14.1 159 139-303 416-587 (1437)
51 KOG3242 Oligoribonuclease (3'- 99.2 9.4E-11 2E-15 110.2 8.6 148 141-302 25-201 (208)
52 COG1949 Orn Oligoribonuclease 99.1 2.3E-10 5E-15 106.7 9.8 147 141-301 5-179 (184)
53 cd05160 DEDDy_DNA_polB_exo DED 99.0 1.8E-09 3.9E-14 103.0 11.3 121 144-272 1-162 (199)
54 cd06139 DNA_polA_I_Ecoli_like_ 98.9 3.6E-08 7.7E-13 92.4 15.0 142 141-300 4-170 (193)
55 KOG0542 Predicted exonuclease 98.9 5E-09 1.1E-13 103.8 9.1 158 143-305 57-247 (280)
56 COG5018 KapD Inhibitor of the 98.9 2.5E-09 5.3E-14 100.5 6.0 153 142-298 4-183 (210)
57 COG2925 SbcB Exonuclease I [DN 98.7 4.3E-08 9.4E-13 101.9 10.1 247 140-394 7-304 (475)
58 PF01612 DNA_pol_A_exo1: 3'-5' 98.6 8.6E-07 1.9E-11 81.4 12.6 131 142-298 20-173 (176)
59 PRK05755 DNA polymerase I; Pro 98.4 1.9E-06 4.1E-11 100.1 13.8 134 141-299 314-468 (880)
60 cd06125 DnaQ_like_exo DnaQ-lik 98.4 7.6E-07 1.6E-11 76.4 7.7 59 145-239 1-62 (96)
61 cd06146 mut-7_like_exo DEDDy 3 98.3 1.5E-05 3.2E-10 76.7 14.8 134 139-297 19-192 (193)
62 cd05780 DNA_polB_Kod1_like_exo 98.1 1.9E-05 4.1E-10 75.9 11.3 116 142-273 3-156 (195)
63 cd00007 35EXOc 3'-5' exonuclea 98.1 0.00012 2.6E-09 65.1 15.2 104 144-273 2-111 (155)
64 cd06141 WRN_exo DEDDy 3'-5' ex 98.0 0.00018 3.9E-09 66.9 13.5 128 141-297 17-169 (170)
65 cd05781 DNA_polB_B3_exo DEDDy 97.9 0.0001 2.3E-09 70.8 11.4 107 141-272 2-144 (188)
66 PF04857 CAF1: CAF1 family rib 97.9 5.9E-05 1.3E-09 75.9 9.7 153 141-295 21-262 (262)
67 cd06129 RNaseD_like DEDDy 3'-5 97.8 0.00045 9.7E-09 64.2 14.3 85 213-297 58-160 (161)
68 PF13482 RNase_H_2: RNase_H su 97.8 6E-05 1.3E-09 69.4 6.8 127 145-301 1-138 (164)
69 PRK10829 ribonuclease D; Provi 97.6 0.0013 2.9E-08 69.7 14.9 131 139-299 19-169 (373)
70 cd05779 DNA_polB_epsilon_exo D 97.6 0.0018 3.9E-08 63.3 14.1 128 142-272 2-168 (204)
71 smart00474 35EXOc 3'-5' exonuc 97.4 0.0091 2E-07 54.1 15.7 130 143-298 22-169 (172)
72 cd06142 RNaseD_exo DEDDy 3'-5' 97.3 0.0072 1.6E-07 55.9 14.7 130 142-299 12-159 (178)
73 COG0349 Rnd Ribonuclease D [Tr 97.3 0.0027 5.7E-08 66.9 12.4 133 141-299 16-165 (361)
74 cd05785 DNA_polB_like2_exo Unc 97.3 0.0014 3.1E-08 64.0 9.7 107 141-272 8-168 (207)
75 cd05777 DNA_polB_delta_exo DED 97.2 0.0083 1.8E-07 59.2 14.1 122 141-273 6-183 (230)
76 cd06148 Egl_like_exo DEDDy 3'- 97.2 0.0037 8E-08 60.3 11.2 88 212-299 55-176 (197)
77 TIGR01388 rnd ribonuclease D. 97.2 0.0078 1.7E-07 63.7 14.3 129 141-299 17-165 (367)
78 cd05784 DNA_polB_II_exo DEDDy 97.1 0.007 1.5E-07 58.6 12.7 114 142-272 3-153 (193)
79 cd05783 DNA_polB_B1_exo DEDDy 96.6 0.025 5.5E-07 55.2 11.6 126 141-272 4-170 (204)
80 cd06140 DNA_polA_I_Bacillus_li 96.5 0.079 1.7E-06 49.3 13.7 105 142-273 3-113 (178)
81 COG0749 PolA DNA polymerase I 96.3 0.017 3.7E-07 64.5 9.7 132 145-300 25-180 (593)
82 cd05782 DNA_polB_like1_exo Unc 96.2 0.045 9.7E-07 53.5 10.8 66 206-272 77-169 (208)
83 cd05778 DNA_polB_zeta_exo inac 95.9 0.21 4.6E-06 49.6 14.4 143 142-287 4-204 (231)
84 PF10108 DNA_pol_B_exo2: Predi 95.8 0.16 3.5E-06 50.1 12.8 92 206-298 36-171 (209)
85 KOG4793 Three prime repair exo 95.6 0.028 6.2E-07 57.1 6.8 162 136-299 7-217 (318)
86 PF00076 RRM_1: RNA recognitio 95.5 0.012 2.6E-07 45.6 3.1 60 321-380 2-63 (70)
87 cd05776 DNA_polB_alpha_exo ina 95.3 0.12 2.7E-06 51.2 10.1 131 142-273 3-187 (234)
88 PRK05762 DNA polymerase II; Re 95.1 0.27 5.8E-06 57.2 13.7 139 140-296 153-348 (786)
89 PTZ00166 DNA polymerase delta 95.1 0.3 6.5E-06 58.6 14.2 149 140-297 262-483 (1054)
90 smart00486 POLBc DNA polymeras 95.0 0.25 5.4E-06 52.3 12.1 145 141-296 2-220 (471)
91 cd09018 DEDDy_polA_RNaseD_like 95.0 0.36 7.8E-06 43.0 11.3 104 144-273 1-110 (150)
92 cd06147 Rrp6p_like_exo DEDDy 3 94.6 0.57 1.2E-05 44.5 12.3 102 143-272 25-131 (192)
93 COG3359 Predicted exonuclease 94.4 0.5 1.1E-05 47.8 11.6 113 139-274 95-220 (278)
94 PF14259 RRM_6: RNA recognitio 94.4 0.086 1.9E-06 41.4 5.1 57 321-378 2-61 (70)
95 PF03104 DNA_pol_B_exo1: DNA p 93.9 0.18 4E-06 51.0 7.6 88 140-238 155-256 (325)
96 TIGR00593 pola DNA polymerase 93.3 0.42 9.1E-06 56.4 10.3 94 206-299 362-476 (887)
97 PLN03134 glycine-rich RNA-bind 92.6 0.19 4.1E-06 46.5 4.9 61 319-379 36-99 (144)
98 TIGR00592 pol2 DNA polymerase 92.1 2.5 5.5E-05 51.5 14.8 105 190-295 568-721 (1172)
99 smart00362 RRM_2 RNA recogniti 92.0 0.25 5.5E-06 37.1 4.2 60 320-379 2-62 (72)
100 PHA02570 dexA exonuclease; Pro 91.6 0.65 1.4E-05 46.2 7.6 93 145-238 4-125 (220)
101 KOG0114 Predicted RNA-binding 91.1 0.29 6.4E-06 43.5 4.1 62 319-380 20-81 (124)
102 cd00590 RRM RRM (RNA recogniti 90.4 0.55 1.2E-05 35.4 4.8 60 320-380 2-64 (74)
103 smart00360 RRM RNA recognition 89.5 0.86 1.9E-05 33.9 5.1 57 323-379 2-61 (71)
104 TIGR01659 sex-lethal sex-letha 89.4 0.37 8E-06 50.9 4.0 61 319-380 195-259 (346)
105 KOG0304 mRNA deadenylase subun 89.3 1.7 3.7E-05 43.2 8.2 105 191-298 109-237 (239)
106 TIGR01661 ELAV_HUD_SF ELAV/HuD 89.2 0.76 1.7E-05 47.3 6.1 90 319-412 5-100 (352)
107 PHA02528 43 DNA polymerase; Pr 89.0 1.7 3.6E-05 51.4 9.3 151 141-295 105-323 (881)
108 KOG1798 DNA polymerase epsilon 87.3 7.1 0.00015 48.2 12.8 151 141-298 245-452 (2173)
109 TIGR01659 sex-lethal sex-letha 86.0 1 2.2E-05 47.6 4.9 62 319-381 109-174 (346)
110 TIGR01661 ELAV_HUD_SF ELAV/HuD 85.3 1 2.3E-05 46.3 4.4 68 320-390 272-342 (352)
111 COG0417 PolB DNA polymerase el 84.6 12 0.00025 44.0 13.0 122 139-273 151-309 (792)
112 PLN03120 nucleic acid binding 84.1 1.3 2.8E-05 45.1 4.4 61 319-380 6-66 (260)
113 KOG0144 RNA-binding protein CU 83.6 1.2 2.6E-05 48.2 3.9 61 315-376 32-96 (510)
114 TIGR03491 RecB family nuclease 82.9 17 0.00037 39.7 12.7 83 208-298 329-429 (457)
115 KOG0107 Alternative splicing f 82.0 1 2.2E-05 43.4 2.5 58 319-380 12-71 (195)
116 TIGR01628 PABP-1234 polyadenyl 80.4 1.9 4.1E-05 47.8 4.4 60 320-379 3-65 (562)
117 TIGR01622 SF-CC1 splicing fact 79.6 2.5 5.3E-05 45.4 4.8 61 319-379 188-251 (457)
118 TIGR01628 PABP-1234 polyadenyl 79.3 2 4.3E-05 47.6 4.1 62 319-380 287-350 (562)
119 PRK05761 DNA polymerase I; Rev 76.2 17 0.00036 42.8 10.5 88 206-293 209-334 (787)
120 TIGR01645 half-pint poly-U bin 76.1 3.2 7E-05 47.1 4.6 62 319-380 206-270 (612)
121 KOG0533 RRM motif-containing p 75.9 3.8 8.2E-05 41.5 4.5 77 319-398 85-163 (243)
122 TIGR01642 U2AF_lg U2 snRNP aux 75.5 3 6.5E-05 45.3 4.0 61 319-380 297-361 (509)
123 TIGR01649 hnRNP-L_PTB hnRNP-L/ 75.5 4.1 9E-05 44.6 5.1 69 319-387 396-467 (481)
124 TIGR01648 hnRNP-R-Q heterogene 75.0 3.3 7.2E-05 46.8 4.3 64 318-381 59-124 (578)
125 TIGR01645 half-pint poly-U bin 73.6 4.1 8.8E-05 46.4 4.5 64 317-380 107-173 (612)
126 cd06128 DNA_polA_exo DEDDy 3'- 73.5 11 0.00024 34.0 6.6 59 214-272 45-109 (151)
127 TIGR01648 hnRNP-R-Q heterogene 73.0 3.1 6.7E-05 47.0 3.4 57 319-380 235-293 (578)
128 TIGR01642 U2AF_lg U2 snRNP aux 72.1 3 6.6E-05 45.3 3.0 62 317-379 175-245 (509)
129 KOG0122 Translation initiation 71.9 5.2 0.00011 40.5 4.3 60 319-379 191-254 (270)
130 PF13893 RRM_5: RNA recognitio 69.6 5.7 0.00012 29.9 3.2 25 356-380 21-45 (56)
131 PLN03213 repressor of silencin 69.0 4.6 9.9E-05 44.6 3.5 60 319-380 12-74 (759)
132 smart00361 RRM_1 RNA recogniti 68.3 11 0.00023 30.1 4.7 26 355-380 36-61 (70)
133 PLN03121 nucleic acid binding 68.2 7.3 0.00016 39.4 4.5 62 320-383 8-70 (243)
134 PHA02524 43A DNA polymerase su 68.2 17 0.00037 40.5 7.7 145 141-293 105-321 (498)
135 TIGR01649 hnRNP-L_PTB hnRNP-L/ 67.7 6.9 0.00015 42.9 4.7 61 319-381 98-159 (481)
136 KOG0969 DNA polymerase delta, 65.6 4.3 9.4E-05 47.0 2.5 134 140-284 272-459 (1066)
137 PF11544 Spc42p: Spindle pole 63.8 8.5 0.00018 32.3 3.3 37 460-496 4-40 (76)
138 COG0724 RNA-binding proteins ( 62.9 9.3 0.0002 35.8 4.0 61 318-379 116-180 (306)
139 KOG3657 Mitochondrial DNA poly 60.2 7 0.00015 45.6 3.0 32 219-250 239-276 (1075)
140 TIGR01622 SF-CC1 splicing fact 58.7 13 0.00027 40.0 4.5 60 319-379 91-153 (457)
141 KOG0117 Heterogeneous nuclear 58.5 14 0.0003 40.4 4.7 71 318-390 84-157 (506)
142 KOG0125 Ataxin 2-binding prote 58.2 6.7 0.00015 41.3 2.2 62 319-380 98-160 (376)
143 PF00843 Arena_nucleocap: Aren 56.4 14 0.00029 40.5 4.2 141 139-288 369-526 (533)
144 PF13423 UCH_1: Ubiquitin carb 56.3 1.5 3.3E-05 44.5 -2.8 48 26-86 247-294 (295)
145 KOG1457 RNA binding protein (c 55.3 20 0.00044 36.1 4.9 64 317-380 34-101 (284)
146 KOG0144 RNA-binding protein CU 54.0 9.4 0.0002 41.6 2.5 63 319-381 126-190 (510)
147 KOG0105 Alternative splicing f 53.6 8.8 0.00019 37.6 2.0 66 319-387 8-73 (241)
148 KOG0146 RNA-binding protein ET 52.5 15 0.00032 37.9 3.6 63 319-381 21-85 (371)
149 KOG0123 Polyadenylate-binding 50.5 16 0.00034 39.2 3.6 98 281-384 45-143 (369)
150 PF08777 RRM_3: RNA binding mo 50.4 16 0.00035 32.1 3.1 54 323-379 7-60 (105)
151 KOG3990 Uncharacterized conser 49.7 9.7 0.00021 38.8 1.7 30 461-490 232-261 (305)
152 KOG0108 mRNA cleavage and poly 49.7 27 0.00059 38.3 5.3 71 318-392 19-93 (435)
153 KOG0110 RNA-binding protein (R 49.1 6.9 0.00015 44.8 0.6 97 280-377 567-676 (725)
154 COG5228 POP2 mRNA deadenylase 47.2 50 0.0011 33.4 6.1 138 161-302 82-255 (299)
155 PF03467 Smg4_UPF3: Smg-4/UPF3 46.2 16 0.00034 35.1 2.5 70 318-387 8-86 (176)
156 KOG1457 RNA binding protein (c 43.5 18 0.0004 36.4 2.5 62 319-381 212-273 (284)
157 KOG1275 PAB-dependent poly(A) 43.0 5.4 0.00012 46.9 -1.3 55 54-109 805-859 (1118)
158 PF13017 Maelstrom: piRNA path 42.6 33 0.00071 33.8 4.2 60 160-219 9-79 (213)
159 KOG0970 DNA polymerase alpha, 42.4 94 0.002 38.0 8.4 128 139-272 526-711 (1429)
160 COG5509 Uncharacterized small 42.2 16 0.00034 29.5 1.5 19 461-479 39-57 (65)
161 KOG4211 Splicing factor hnRNP- 42.0 30 0.00065 38.3 4.1 55 320-376 13-69 (510)
162 KOG4207 Predicted splicing fac 40.6 21 0.00046 35.6 2.5 61 320-380 16-79 (256)
163 KOG4253 Tryptophan-rich basic 40.3 41 0.00089 32.1 4.2 34 459-496 49-84 (175)
164 KOG4307 RNA binding protein RB 40.3 28 0.0006 40.2 3.6 58 320-379 870-932 (944)
165 KOG4212 RNA-binding protein hn 39.2 34 0.00074 37.5 4.0 67 320-390 47-117 (608)
166 KOG1548 Transcription elongati 39.1 31 0.00066 36.8 3.5 61 319-380 136-207 (382)
167 PF08112 ATP-synt_E_2: ATP syn 38.1 27 0.0006 27.3 2.2 17 477-493 6-22 (56)
168 KOG4211 Splicing factor hnRNP- 36.8 39 0.00084 37.5 4.0 53 320-376 106-165 (510)
169 KOG0145 RNA-binding protein EL 35.9 24 0.00053 36.3 2.1 62 319-380 129-193 (360)
170 KOG0131 Splicing factor 3b, su 35.9 43 0.00092 32.9 3.7 99 280-380 58-163 (203)
171 PF05266 DUF724: Protein of un 35.5 46 0.00099 32.5 3.9 43 454-496 103-152 (190)
172 KOG0148 Apoptosis-promoting RN 34.6 65 0.0014 33.4 4.9 68 319-392 166-233 (321)
173 PHA02563 DNA polymerase; Provi 34.4 41 0.00089 38.7 3.8 28 211-238 50-83 (630)
174 PF04201 TPD52: Tumour protein 34.0 42 0.00092 32.1 3.3 36 462-497 30-65 (162)
175 KOG0121 Nuclear cap-binding pr 32.3 39 0.00084 31.5 2.6 65 320-384 39-106 (153)
176 KOG4206 Spliceosomal protein s 31.8 45 0.00097 33.4 3.2 62 319-381 11-77 (221)
177 KOG0132 RNA polymerase II C-te 29.9 61 0.0013 38.0 4.2 68 319-395 423-490 (894)
178 KOG4307 RNA binding protein RB 29.7 32 0.00069 39.7 2.0 55 320-375 5-59 (944)
179 PRK04325 hypothetical protein; 29.6 51 0.0011 27.3 2.7 51 439-495 7-57 (74)
180 PF10309 DUF2414: Protein of u 29.6 53 0.0012 26.5 2.7 42 328-376 15-62 (62)
181 KOG0147 Transcriptional coacti 29.2 98 0.0021 34.8 5.5 73 320-396 281-356 (549)
182 KOG0117 Heterogeneous nuclear 28.7 43 0.00092 36.8 2.6 69 319-396 261-330 (506)
183 KOG0110 RNA-binding protein (R 28.1 52 0.0011 38.0 3.3 68 319-390 387-455 (725)
184 PF06810 Phage_GP20: Phage min 27.6 61 0.0013 30.5 3.2 38 460-497 26-66 (155)
185 PRK00846 hypothetical protein; 26.4 60 0.0013 27.4 2.6 52 438-495 10-61 (77)
186 KOG4010 Coiled-coil protein TP 25.6 72 0.0016 31.3 3.3 34 463-496 46-79 (208)
187 KOG0153 Predicted RNA-binding 25.5 59 0.0013 34.7 2.9 59 317-378 228-286 (377)
188 KOG2591 c-Mpl binding protein, 25.3 56 0.0012 36.9 2.8 57 320-378 178-234 (684)
189 COG2433 Uncharacterized conser 25.2 72 0.0016 36.4 3.7 33 461-493 450-492 (652)
190 KOG0127 Nucleolar protein fibr 24.0 86 0.0019 35.5 3.9 67 319-388 119-187 (678)
191 PF08776 VASP_tetra: VASP tetr 23.7 1.3E+02 0.0028 22.4 3.5 9 462-470 4-12 (40)
192 PF04102 SlyX: SlyX; InterPro 23.2 53 0.0012 26.7 1.7 34 462-495 19-52 (69)
193 PF04420 CHD5: CHD5-like prote 23.0 1.3E+02 0.0027 28.5 4.4 19 460-482 46-64 (161)
194 COG5175 MOT2 Transcriptional r 22.3 73 0.0016 34.0 2.9 90 319-414 116-217 (480)
195 PRK00736 hypothetical protein; 21.4 92 0.002 25.4 2.7 33 462-494 20-52 (68)
196 PRK00295 hypothetical protein; 21.0 96 0.0021 25.3 2.8 34 462-495 20-53 (68)
197 PRK04406 hypothetical protein; 20.1 98 0.0021 25.8 2.7 49 441-495 11-59 (75)
No 1
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=3.6e-41 Score=350.34 Aligned_cols=303 Identities=35% Similarity=0.448 Sum_probs=265.5
Q ss_pred CcchhhhHhHHHHHHHHHHHhhcccCCCCCCcccchhhccccCCC-CCCCCCcC--c-hhhHHHHhhcccccccccchhh
Q 010743 1 MDQKLDTLEKKALVEIVKLIQKRRMEGTAGGWKDFLTSYDKKFGS-SLSDPARR--S-KDALSSFLKTFTKEDDLKFIAK 76 (502)
Q Consensus 1 ~~~~~~~~~~~~lv~~vk~~~~~~~~~~~~~~k~~l~~~~~~~~~-~~~dp~~~--~-~~~l~~f~~~~~~~~~~~~~~~ 76 (502)
|...++.+++.+++..++..|+.++.+.+|.|+.||+.+.+..++ +.++|... . ...+..|..+.+..+...+.++
T Consensus 70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~r~~~~f~~~~~~~~~~~~l~~ 149 (380)
T KOG2248|consen 70 SLVAEGNAPKIVLLSKPELKQKDYLLSFSGLSKAILNLVATNLKDVDRSDKALLPRPCSRCGSEFYVTEKGREFKDLLCK 149 (380)
T ss_pred HHHHhccCceeeeeccchhhhhhheeccCCccHHHhhhhhcccccccccCccccCchhhhhhhhhccccchhhhhhhhcc
Confidence 345677888889999999999999999999999999999999986 77777776 3 5588999999988777666666
Q ss_pred hhHhhhhHHHHHHHHhcCCCCCChhhHHHHhhhcCCCCccccCCCCCCCCceeeccCCC-CCCCCCCcEEEEEEeccCCC
Q 010743 77 VVQSHLNRDLVEQLKKTSPDDESPEQRLVRLTLQHPQYPLCYMFPSSDEGWLVTKLGKS-SKTMTSNIMYAVDCEMVLCE 155 (502)
Q Consensus 77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lv~~t~~~~~~~~~y~~p~~~~~~~~t~~~~~-~~~~~~~~~VaID~ETTGl~ 155 (502)
+.+...++.......+++.+.-++.+.++..+..++.|...+.||++...|++...+.. .....+.+++||||||+.+.
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~v~~~~~i~AlDCEm~~te 229 (380)
T KOG2248|consen 150 YHPGKLIREPRRGFKDKTEDCCTPKEGLVSFLCLGPDYHVEILFPSESLDEFVQTLGAKGKAVSKSPNIFALDCEMVVTE 229 (380)
T ss_pred ccccccccchhccccccCchhhcccccCccceeecccccccccCccccccceecccccCCCCCCCCCCeEEEEeeeeeec
Confidence 66656666666666666666677889999988889999989999998777777765543 34677899999999999999
Q ss_pred CCcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhcCCCEEEEEchhhHHHH
Q 010743 156 DGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSNGTILVGHSLNNDLEV 235 (502)
Q Consensus 156 ~g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~~g~ILVGHnl~fDl~f 235 (502)
.| .+++||++||.+|.++||.||+|..+|.||+|+++|||++|++++++++.+||.+|+.|++.++|||||++++||.+
T Consensus 230 ~g-~el~RVt~VD~~~~vi~D~fVkP~~~VvDy~T~~SGIT~~~~e~~t~tl~dvq~~l~~~~~~~TILVGHSLenDL~a 308 (380)
T KOG2248|consen 230 NG-LELTRVTAVDRDGKVILDTFVKPNKPVVDYNTRYSGITEEDLENSTITLEDVQKELLELISKNTILVGHSLENDLKA 308 (380)
T ss_pred cc-eeeEEeeeeeccCcEEeEEeecCCCcccccccccccccHHHHhcCccCHHHHHHHHHhhcCcCcEEEeechhhHHHH
Confidence 99 67999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HcccCCCccchHHHhhhhcC--CCCCCHHHHHHHHcCCccCCCCCCCCHHHHHHHHHHHHHHHHHhcccCC
Q 010743 236 LKLDHPRVIDTSLIFKYVDE--YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLVLAIIERRVDNA 304 (502)
Q Consensus 236 Lk~~~p~vIDT~~L~r~~~~--~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~Ata~L~~~~l~~g~~~~ 304 (502)
|++.|+.+|||+.+|.+..+ ..+.||+.||+.|||..||.+..+|++.+||.|||+|+...+..+...+
T Consensus 309 LKl~H~~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~~~~HdS~eDA~acm~Lv~~k~~~~~~~g 379 (380)
T KOG2248|consen 309 LKLDHPSVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEGVGGHDSVEDALACMKLVKLKIKNSESQG 379 (380)
T ss_pred HhhhCCceeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhccCCCCccHHHHHHHHHHHHHHHhcccccC
Confidence 99999999999999998887 4677899999999999999544579999999999999999988776543
No 2
>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=100.00 E-value=1.3e-35 Score=273.23 Aligned_cols=148 Identities=48% Similarity=0.751 Sum_probs=136.4
Q ss_pred EEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhcCCCEE
Q 010743 145 YAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSNGTIL 224 (502)
Q Consensus 145 VaID~ETTGl~~g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~~g~IL 224 (502)
|+|||||||+..| ++|++|++|+.+|.++|++||+|..+|++++|++||||++||+++|.++.+|+++|++|++++++|
T Consensus 1 ~~iD~E~~g~~~g-~ei~~i~~v~~~~~~~f~~lv~P~~~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~~~fl~~~~vl 79 (150)
T cd06145 1 FALDCEMCYTTDG-LELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTIL 79 (150)
T ss_pred CEEeeeeeeecCC-CEEEEEEEEeCCCCEEEEEeECCCCccchhccCcCCCCHHHhccCCCCHHHHHHHHHHHhCCCCEE
Confidence 5899999999988 789999999999999999999999999999999999999999999548999999999999448999
Q ss_pred EEEchhhHHHHHcccCCCccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCCCCCCCHHHHHHHHHHHH
Q 010743 225 VGHSLNNDLEVLKLDHPRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLV 293 (502)
Q Consensus 225 VGHnl~fDl~fLk~~~p~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~Ata~L~ 293 (502)
||||+.||++||+..+++++||+.|++...+ ..+++|+.||+.|+|+.++.+..+|+|++||++|++||
T Consensus 80 VgHn~~fD~~fL~~~~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 80 VGHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELV 149 (150)
T ss_pred EEcChHHHHHHhhccCCCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCCCCCcHHHHHHHHHHh
Confidence 9999999999999999999999999998776 56789999998888988764235899999999999998
No 3
>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=100.00 E-value=6.1e-35 Score=271.43 Aligned_cols=149 Identities=40% Similarity=0.627 Sum_probs=135.7
Q ss_pred EEEEEeccCCCCCcccEEEEEEEEc-CCcEEEEEEEcCCCcccccccccCCCChhhhccCCC------CHHHHHHHHHHh
Q 010743 145 YAVDCEMVLCEDGSEGLVRLCVVDR-NLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTC------SLAEIQKRMKKL 217 (502)
Q Consensus 145 VaID~ETTGl~~g~~~I~rVsvVd~-~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~------~~~dV~~~l~~f 217 (502)
|||||||||+++..++|++|++|+. +|+++|++||+|..+|+++++++||||++||+++|. ++.+++++|++|
T Consensus 1 v~lD~EttGl~~~~d~ii~Ig~V~v~~g~i~~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~~~~~~~~~~ 80 (161)
T cd06137 1 VALDCEMVGLADGDSEVVRISAVDVLTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAKAGKTIFGWEAARAALWKF 80 (161)
T ss_pred CEEEeeeeeEcCCCCEEEEEEEEEcCCCeEEEeccccCCCCCCccceeccCCCHHHHhhhhhcCCccccHHHHHHHHHHh
Confidence 6899999999987788999999998 888899999999999999999999999999999871 246999999999
Q ss_pred hcCC-CEEEEEchhhHHHHHcccCCCccchHHHhhhhcC-C---CCCCHHHHHHHHcCCccCCCCCCCCHHHHHHHHHHH
Q 010743 218 LSNG-TILVGHSLNNDLEVLKLDHPRVIDTSLIFKYVDE-Y---RRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKL 292 (502)
Q Consensus 218 l~~g-~ILVGHnl~fDl~fLk~~~p~vIDT~~L~r~~~~-~---~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~Ata~L 292 (502)
+ ++ +||||||+.||++||+..++.++||+.|++...+ . .+++|+.||+.+||++++.+..+|+|++||+|||+|
T Consensus 81 i-~~~~vlVgHn~~fD~~fL~~~~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~~~~H~A~~DA~at~~l 159 (161)
T cd06137 81 I-DPDTILVGHSLQNDLDALRMIHTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGGEGHDSLEDALAAREV 159 (161)
T ss_pred c-CCCcEEEeccHHHHHHHHhCcCCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCCCCCCCcHHHHHHHHHH
Confidence 9 55 9999999999999999999999999999999877 3 589999999888999997533589999999999999
Q ss_pred HH
Q 010743 293 VL 294 (502)
Q Consensus 293 ~~ 294 (502)
|+
T Consensus 160 ~~ 161 (161)
T cd06137 160 VL 161 (161)
T ss_pred hC
Confidence 84
No 4
>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=100.00 E-value=1.1e-34 Score=273.08 Aligned_cols=147 Identities=32% Similarity=0.497 Sum_probs=133.3
Q ss_pred EEEEEeccCCCC--------Ccc--------cEEEEEEEE----cCCcEEEEEEEcCCCcccccccccCCCChhhhccCC
Q 010743 145 YAVDCEMVLCED--------GSE--------GLVRLCVVD----RNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVT 204 (502)
Q Consensus 145 VaID~ETTGl~~--------g~~--------~I~rVsvVd----~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap 204 (502)
|||||||+|+.+ |+. +++||++|| .+|+++||.||+|..+|.||+|++||||+++|.+++
T Consensus 1 ~a~d~e~v~~~~~~~~~~~~g~~~~~~~~~~~LaRVsiVd~~~~~~g~vllD~~VkP~~~V~DYrT~~SGIt~~~L~~a~ 80 (174)
T cd06143 1 VAIDAEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKT 80 (174)
T ss_pred CceeeeEEEecchhceecCCCcEeeeccCCceeEEEEEEcCCCCcCCCEEEeeeECCCCCccCcCccccccCHHHcCccc
Confidence 578999988876 444 699999999 689999999999999999999999999999999875
Q ss_pred -----CCHHHHHHHHHHhhcCCCEEEEEchhhHHHHHcccCC--CccchHHHhhhhcCCCCCCHHHHHHHHcCCccCCCC
Q 010743 205 -----CSLAEIQKRMKKLLSNGTILVGHSLNNDLEVLKLDHP--RVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKG 277 (502)
Q Consensus 205 -----~~~~dV~~~l~~fl~~g~ILVGHnl~fDl~fLk~~~p--~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~~ 277 (502)
+++.+++.+++++++.++|||||++++||++|++.|| .+|||+.+|+... .+++||+.||+.+||++||.+
T Consensus 81 ~~~~~~t~~~v~~~l~~li~~~tILVGHsL~nDL~aL~l~hp~~~viDTa~l~~~~~-~r~~sLk~La~~~L~~~IQ~~- 158 (174)
T cd06143 81 SSKNLTTLKSAYLKLRLLVDLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFHLPG-QRKLSLRFLAWYLLGEKIQSE- 158 (174)
T ss_pred cccccCCHHHHHHHHHHHcCCCCEEEeccchhHHHHhcCcCCCcceEEcHHhccCCC-CCChhHHHHHHHHcCCcccCC-
Confidence 3699999999999988999999999999999999987 5999999998643 368999999999999999974
Q ss_pred CCCCHHHHHHHHHHHHH
Q 010743 278 TPHNCLDDASAAMKLVL 294 (502)
Q Consensus 278 ~~HdAleDA~Ata~L~~ 294 (502)
+|+|++||+|||+||+
T Consensus 159 -~HdSvEDArAam~Ly~ 174 (174)
T cd06143 159 -THDSIEDARTALKLYR 174 (174)
T ss_pred -CcCcHHHHHHHHHHhC
Confidence 8999999999999983
No 5
>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=100.00 E-value=3.3e-34 Score=265.96 Aligned_cols=148 Identities=36% Similarity=0.539 Sum_probs=133.3
Q ss_pred EEEEEeccCCCCC--cccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhcCCC
Q 010743 145 YAVDCEMVLCEDG--SEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSNGT 222 (502)
Q Consensus 145 VaID~ETTGl~~g--~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~~g~ 222 (502)
|||||||||++++ .++|++|++|+.+|.++|++||+|..+|+++++.+||||++||+++| ++++|+++|++|+ +|+
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~~~~~~lv~P~~~i~~~~~~i~GIt~~~l~~a~-~~~~v~~~l~~~l-~~~ 78 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNAT-PFAVAQKEILKIL-KGK 78 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCCEEEEEeECCCCccCccceECCCCCHHHHhcCC-CHHHHHHHHHHHc-CCC
Confidence 6899999999986 46899999999999999999999999999999999999999999999 9999999999999 899
Q ss_pred EEEEEchhhHHHHHcccCCC--ccchHHH--hhhh--cC-CCCCCHHHHHHHHcCCccCCCCCCCCHHHHHHHHHHHHH
Q 010743 223 ILVGHSLNNDLEVLKLDHPR--VIDTSLI--FKYV--DE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLVL 294 (502)
Q Consensus 223 ILVGHnl~fDl~fLk~~~p~--vIDT~~L--~r~~--~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~Ata~L~~ 294 (502)
||||||+.||++||+..|+. ++||+.+ ++.. +| ..+++|+.||+.++|..++.++.+|+|++||+||++||+
T Consensus 79 vlV~Hn~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 79 VVVGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157 (157)
T ss_pred EEEEeCcHHHHHHhcccCCCcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCCCcCcHHHHHHHHHHhC
Confidence 99999999999999998775 7899875 4433 44 567999999998888888764457999999999999984
No 6
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=2.5e-34 Score=282.39 Aligned_cols=151 Identities=37% Similarity=0.583 Sum_probs=139.8
Q ss_pred cEEEEEEeccCCCCC--cccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhcC
Q 010743 143 IMYAVDCEMVLCEDG--SEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSN 220 (502)
Q Consensus 143 ~~VaID~ETTGl~~g--~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~~ 220 (502)
++|||||||+|+.++ .+.++||||||..|.++||+||+|..+|.||+|++|||+|+.+.++. +|+.||.++++|| .
T Consensus 106 r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP~~~VtDyRT~vSGIrpehm~~A~-pf~~aQ~ev~klL-~ 183 (280)
T KOG2249|consen 106 RVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKPTEPVTDYRTRVSGIRPEHMRDAM-PFKVAQKEVLKLL-K 183 (280)
T ss_pred eEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecCCCcccccceeeecccCHHHhccCc-cHHHHHHHHHHHH-h
Confidence 699999999999875 34689999999999999999999999999999999999999999998 9999999999999 9
Q ss_pred CCEEEEEchhhHHHHHcccCCC--ccchHHHhhhhc--C-CCCCCHHHHHHHHcCCccCCCCCCCCHHHHHHHHHHHHHH
Q 010743 221 GTILVGHSLNNDLEVLKLDHPR--VIDTSLIFKYVD--E-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLVLA 295 (502)
Q Consensus 221 g~ILVGHnl~fDl~fLk~~~p~--vIDT~~L~r~~~--~-~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~Ata~L~~~ 295 (502)
|+|||||.+.+||.+|...||+ +.||+.+-+... . ...+||+.|++.+||++||.| .|++++||+|||+||..
T Consensus 184 gRIlVGHaLhnDl~~L~l~hp~s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~G--eHsSvEDA~AtM~LY~~ 261 (280)
T KOG2249|consen 184 GRILVGHALHNDLQALKLEHPRSMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVG--EHSSVEDARATMELYKR 261 (280)
T ss_pred CCEEeccccccHHHHHhhhCchhhhcccccCchHHHHhhccCCccHHHHHHHHhchhhhcc--ccCcHHHHHHHHHHHHH
Confidence 9999999999999999999997 899998655433 3 788999999999999999975 69999999999999976
Q ss_pred HH
Q 010743 296 II 297 (502)
Q Consensus 296 ~l 297 (502)
..
T Consensus 262 vk 263 (280)
T KOG2249|consen 262 VK 263 (280)
T ss_pred HH
Confidence 44
No 7
>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=99.97 E-value=8.6e-32 Score=247.89 Aligned_cols=146 Identities=41% Similarity=0.680 Sum_probs=130.5
Q ss_pred EEEEEeccCCCCC--cccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhcCCC
Q 010743 145 YAVDCEMVLCEDG--SEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSNGT 222 (502)
Q Consensus 145 VaID~ETTGl~~g--~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~~g~ 222 (502)
|+|||||||+++. ..+|++|++++.+|.++|++||+|..+|+++++.+||||++||+++| ++.+++.+|..|+ +++
T Consensus 1 v~lD~EttGl~~~~~~~~i~~v~~v~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~~~v~~a~-~~~~~~~~l~~~l-~~~ 78 (152)
T cd06144 1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAP-DFEEVQKKVAELL-KGR 78 (152)
T ss_pred CEEEEEeecccCCCCEEEEEEEEEEeCCCCEEEEEEECCCCCCCcccccCCCCCHHHHcCCC-CHHHHHHHHHHHh-CCC
Confidence 6899999999986 35788999999999999999999999999999999999999999999 9999999999999 789
Q ss_pred EEEEEchhhHHHHHcccCCC--ccchHHHhhhhcC--CCCCCHHHHHHHHcCCccCCCCCCCCHHHHHHHHHHHHH
Q 010743 223 ILVGHSLNNDLEVLKLDHPR--VIDTSLIFKYVDE--YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLVL 294 (502)
Q Consensus 223 ILVGHnl~fDl~fLk~~~p~--vIDT~~L~r~~~~--~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~Ata~L~~ 294 (502)
+|||||+.||++||+..+++ ++||..+.....+ ..++||..||+.+||++++. .+|+|++||++|++||+
T Consensus 79 vlVgHn~~fD~~~L~~~~~~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~--~~H~Al~DA~at~~l~~ 152 (152)
T cd06144 79 ILVGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQE--GEHSSVEDARAAMRLYR 152 (152)
T ss_pred EEEEcCcHHHHHHhcCcCCCccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCC--CCcCcHHHHHHHHHHhC
Confidence 99999999999999987764 7899876554433 47899999997788998863 38999999999999984
No 8
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=3.4e-28 Score=240.51 Aligned_cols=160 Identities=23% Similarity=0.274 Sum_probs=138.3
Q ss_pred CCCCCcEEEEEEeccCCCCCcccEEEEEEEEcCCc-E----EEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHH
Q 010743 138 TMTSNIMYAVDCEMVLCEDGSEGLVRLCVVDRNLK-V----TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQK 212 (502)
Q Consensus 138 ~~~~~~~VaID~ETTGl~~g~~~I~rVsvVd~~G~-v----i~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~ 212 (502)
.....+|++||+||||+++..++|++|++|..++. + .|++||+|+.+|+..++.+||||++||+++| ++.+|+.
T Consensus 43 ~~~~~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap-~~~evl~ 121 (239)
T PRK09146 43 PLSEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAP-DLERILD 121 (239)
T ss_pred CcccCCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCC-CHHHHHH
Confidence 34456899999999999998889999999987443 2 4789999999999999999999999999999 9999999
Q ss_pred HHHHhhcCCCEEEEEchhhHHHHHcccC---------CCccchHHHhhhhcC-C-------------CCCCHHHHHHHHc
Q 010743 213 RMKKLLSNGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDE-Y-------------RRPSLYNLCKSVL 269 (502)
Q Consensus 213 ~l~~fl~~g~ILVGHnl~fDl~fLk~~~---------p~vIDT~~L~r~~~~-~-------------~~~sL~~La~~~L 269 (502)
+|.+++ ++.++||||+.||++||+... ..+|||+.+++.+.+ . ..++|.+|| .++
T Consensus 122 ~l~~~~-~~~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~-~~~ 199 (239)
T PRK09146 122 ELLEAL-AGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSR-LRY 199 (239)
T ss_pred HHHHHh-CCCEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHH-HHc
Confidence 999999 889999999999999998731 247999999987643 1 567899999 677
Q ss_pred CCccCCCCCCCCHHHHHHHHHHHHHHHHHhcccC
Q 010743 270 GYEIRKKGTPHNCLDDASAAMKLVLAIIERRVDN 303 (502)
Q Consensus 270 gi~iq~~~~~HdAleDA~Ata~L~~~~l~~g~~~ 303 (502)
|++.. .+|+|++||.+|++||++++.+..+.
T Consensus 200 gl~~~---~~H~Al~DA~ata~l~~~~~~~~~~~ 230 (239)
T PRK09146 200 GLPAY---SPHHALTDAIATAELLQAQIAHHFSP 230 (239)
T ss_pred CCCCC---CCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 98864 38999999999999999999776543
No 9
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.96 E-value=3.2e-28 Score=240.86 Aligned_cols=155 Identities=21% Similarity=0.280 Sum_probs=135.2
Q ss_pred CCcEEEEEEeccCCCCC-cccEEEEEEEEc-CCcE---EEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHH
Q 010743 141 SNIMYAVDCEMVLCEDG-SEGLVRLCVVDR-NLKV---TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMK 215 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~g-~~~I~rVsvVd~-~G~v---i~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~ 215 (502)
..++|+||+||||+++. .++|++|++|.. ++.+ .|+.||+|..+|++.++++||||++||+++| +|.+|+.+|.
T Consensus 3 ~~r~vvlDtETTGldp~~~drIIEIGaV~v~~~~~~~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~p-~f~ev~~~f~ 81 (240)
T PRK05711 3 IMRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKP-TFAEVADEFL 81 (240)
T ss_pred CCeEEEEEeeCCCcCCCCCCeEEEEEEEEEECCEEeccEEEEEECcCCcCCHHHhhhcCCCHHHHcCCC-CHHHHHHHHH
Confidence 46899999999999986 678999999976 3332 4899999999999999999999999999999 9999999999
Q ss_pred HhhcCCCEEEEEchhhHHHHHccc-------C------CCccchHHHhhhhcCCCCCCHHHHHHHHcCCccCCCCCCCCH
Q 010743 216 KLLSNGTILVGHSLNNDLEVLKLD-------H------PRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNC 282 (502)
Q Consensus 216 ~fl~~g~ILVGHnl~fDl~fLk~~-------~------p~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~~~~HdA 282 (502)
+|+ ++.+|||||+.||+.||+.. . ..++||..+++..++..+++|..|| .+||++... ...|+|
T Consensus 82 ~fi-~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~aL~-~~~gi~~~~-r~~H~A 158 (240)
T PRK05711 82 DFI-RGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALC-KRYGIDNSH-RTLHGA 158 (240)
T ss_pred HHh-CCCEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCCCCCHHHHH-HHCCCCCCC-CCCCCH
Confidence 999 89999999999999999863 1 2379999999998886678999999 667987542 246999
Q ss_pred HHHHHHHHHHHHHHHHh
Q 010743 283 LDDASAAMKLVLAIIER 299 (502)
Q Consensus 283 leDA~Ata~L~~~~l~~ 299 (502)
+.||++|++||+.+...
T Consensus 159 L~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 159 LLDAEILAEVYLAMTGG 175 (240)
T ss_pred HHHHHHHHHHHHHHHCc
Confidence 99999999999998754
No 10
>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=99.95 E-value=6.8e-28 Score=236.26 Aligned_cols=152 Identities=24% Similarity=0.269 Sum_probs=132.7
Q ss_pred cEEEEEEeccCCCCCc-ccEEEEEEEEc-CCc---EEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHh
Q 010743 143 IMYAVDCEMVLCEDGS-EGLVRLCVVDR-NLK---VTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (502)
Q Consensus 143 ~~VaID~ETTGl~~g~-~~I~rVsvVd~-~G~---vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~f 217 (502)
++|+||+||||+++.. ++|++|++|.. ++. ..|+.||+|+.+|+++++++||||++||+++| +|.+|+.+|.+|
T Consensus 1 r~vvlD~ETTGl~p~~~d~IIEIgav~~~~~~~~~~~f~~~i~P~~~i~~~a~~vhGIt~e~l~~~p-~f~ev~~~f~~f 79 (225)
T TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKP-KFKEIADEFLDF 79 (225)
T ss_pred CEEEEEeeCCCcCCCCCCeEEEEEEEEEECCcEecceEEEEECcCCCCCHHHHhccCCCHHHHhCCC-CHHHHHHHHHHH
Confidence 5899999999999864 68999999865 332 24999999999999999999999999999999 999999999999
Q ss_pred hcCCCEEEEEchhhHHHHHccc-------C------CCccchHHHhhhhcCCCCCCHHHHHHHHcCCccCCCCCCCCHHH
Q 010743 218 LSNGTILVGHSLNNDLEVLKLD-------H------PRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNCLD 284 (502)
Q Consensus 218 l~~g~ILVGHnl~fDl~fLk~~-------~------p~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~~~~HdAle 284 (502)
+ ++.+|||||+.||+.||+.. . .+++||..+++..++..+++|..|| .+||++... ...|+|+.
T Consensus 80 i-~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~L~-~~~gi~~~~-r~~H~Al~ 156 (225)
T TIGR01406 80 I-GGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALC-KRFKVDNSH-RTLHGALL 156 (225)
T ss_pred h-CCCEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCCCCCHHHHH-HhcCCCCCC-CCCcCHHH
Confidence 9 89999999999999999862 1 2479999999998886778999999 667988642 24799999
Q ss_pred HHHHHHHHHHHHHH
Q 010743 285 DASAAMKLVLAIIE 298 (502)
Q Consensus 285 DA~Ata~L~~~~l~ 298 (502)
||++|++||.++..
T Consensus 157 DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 157 DAHLLAEVYLALTG 170 (225)
T ss_pred HHHHHHHHHHHHHc
Confidence 99999999998774
No 11
>PRK07740 hypothetical protein; Provisional
Probab=99.95 E-value=2e-27 Score=235.54 Aligned_cols=157 Identities=24% Similarity=0.322 Sum_probs=138.8
Q ss_pred CCCcEEEEEEeccCCCCCc-ccEEEEEEEEcCCcEE----EEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHH
Q 010743 140 TSNIMYAVDCEMVLCEDGS-EGLVRLCVVDRNLKVT----IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRM 214 (502)
Q Consensus 140 ~~~~~VaID~ETTGl~~g~-~~I~rVsvVd~~G~vi----~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l 214 (502)
...++|+|||||||+++.. ++|++|++|..++..+ |+.||+|..+|+++++++||||+++|+++| ++.+|+.+|
T Consensus 57 ~~~~~vv~D~ETTGl~p~~~deIIeIgaV~~~~~~i~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap-~~~evl~~f 135 (244)
T PRK07740 57 TDLPFVVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAP-PLAEVLHRF 135 (244)
T ss_pred cCCCEEEEEEeCCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEEeCcCCCCChhheeccCCCHHHHhCCC-CHHHHHHHH
Confidence 4568999999999999865 6899999998755433 888999999999999999999999999999 999999999
Q ss_pred HHhhcCCCEEEEEchhhHHHHHccc---------CCCccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCCCCCCCHHH
Q 010743 215 KKLLSNGTILVGHSLNNDLEVLKLD---------HPRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLD 284 (502)
Q Consensus 215 ~~fl~~g~ILVGHnl~fDl~fLk~~---------~p~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAle 284 (502)
.+|+ ++++|||||+.||+.||+.. ..+++||..+++...+ ...++|.+|| .++|+++. ++|+|++
T Consensus 136 ~~fi-~~~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~-~~~gi~~~---~~H~Al~ 210 (244)
T PRK07740 136 YAFI-GAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDAL-AYYGIPIP---RRHHALG 210 (244)
T ss_pred HHHh-CCCEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHHH-HHCCcCCC---CCCCcHH
Confidence 9999 89999999999999999763 1358999999998877 5689999999 78899975 3799999
Q ss_pred HHHHHHHHHHHHHHhccc
Q 010743 285 DASAAMKLVLAIIERRVD 302 (502)
Q Consensus 285 DA~Ata~L~~~~l~~g~~ 302 (502)
||++|++||.+++..-..
T Consensus 211 Da~ata~l~~~ll~~~~~ 228 (244)
T PRK07740 211 DALMTAKLWAILLVEAQQ 228 (244)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 999999999999876443
No 12
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=4.1e-27 Score=234.09 Aligned_cols=156 Identities=21% Similarity=0.335 Sum_probs=136.2
Q ss_pred CCCCcEEEEEEeccCCCCCcccEEEEEEEEcCCcE---EEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHH
Q 010743 139 MTSNIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKV---TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMK 215 (502)
Q Consensus 139 ~~~~~~VaID~ETTGl~~g~~~I~rVsvVd~~G~v---i~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~ 215 (502)
.+..+||+|||||||+++..++|++|++|..++.. .|+.||+|+.+|+.+.+.+||||++||+++| ++.+|+.+|.
T Consensus 4 l~~~~~v~~D~ETTGl~~~~d~IIEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p-~~~ev~~~~~ 82 (250)
T PRK06310 4 LKDTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKP-KIAEVFPQIK 82 (250)
T ss_pred ccCCcEEEEEEeCCCCCCCCCeEEEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCC-CHHHHHHHHH
Confidence 34578999999999999888899999999875432 3889999999999999999999999999999 9999999999
Q ss_pred HhhcCCCEEEEEchhhHHHHHcccC-----------CCccchHHHhhhhcCCCCCCHHHHHHHHcCCccCCCCCCCCHHH
Q 010743 216 KLLSNGTILVGHSLNNDLEVLKLDH-----------PRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNCLD 284 (502)
Q Consensus 216 ~fl~~g~ILVGHnl~fDl~fLk~~~-----------p~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~~~~HdAle 284 (502)
+|++++.+|||||+.||+.||+... ..+|||..+++...+..+++|..|| .++|++.. .+|+|++
T Consensus 83 ~fl~~~~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~~~~~L~~l~-~~~g~~~~---~aH~Al~ 158 (250)
T PRK06310 83 GFFKEGDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDSPNNSLEALA-VHFNVPYD---GNHRAMK 158 (250)
T ss_pred HHhCCCCEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcccCCCCCHHHHH-HHCCCCCC---CCcChHH
Confidence 9995459999999999999998631 3479999999875335679999999 66799865 3899999
Q ss_pred HHHHHHHHHHHHHHh
Q 010743 285 DASAAMKLVLAIIER 299 (502)
Q Consensus 285 DA~Ata~L~~~~l~~ 299 (502)
||.+|++||..++++
T Consensus 159 Da~at~~vl~~l~~~ 173 (250)
T PRK06310 159 DVEINIKVFKHLCKR 173 (250)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999999998865
No 13
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=3e-27 Score=232.29 Aligned_cols=153 Identities=20% Similarity=0.303 Sum_probs=135.9
Q ss_pred CcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhcCC
Q 010743 142 NIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSNG 221 (502)
Q Consensus 142 ~~~VaID~ETTGl~~g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~~g 221 (502)
.++|+||+||||+++..++|++|++|+......|+.||+|+.+|+..++.+||||++||+++| +|.+|+++|.+|++++
T Consensus 2 ~~~vv~D~ETTGl~~~~d~IIeig~v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p-~f~ev~~~~~~fi~~~ 80 (232)
T PRK06309 2 PALIFYDTETTGTQIDKDRIIEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAP-KFPEAYQKFIEFCGTD 80 (232)
T ss_pred CcEEEEEeeCCCCCCCCCEEEEEEEEcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCC-CHHHHHHHHHHHHcCC
Confidence 469999999999998888999999998655567999999999999999999999999999999 9999999999999556
Q ss_pred CEEEEEc-hhhHHHHHcccC---------CCccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCCCCCCCHHHHHHHHH
Q 010743 222 TILVGHS-LNNDLEVLKLDH---------PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAM 290 (502)
Q Consensus 222 ~ILVGHn-l~fDl~fLk~~~---------p~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~Ata 290 (502)
.+||||| ..||+.||+... .+++||..+++...+ ..+++|..|| .++|++.. .+|+|++||.+|+
T Consensus 81 ~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~~~~L~~l~-~~~~~~~~---~aH~Al~Da~~t~ 156 (232)
T PRK06309 81 NILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLR-QVYGFEEN---QAHRALDDVITLH 156 (232)
T ss_pred CEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCCCCCHHHHH-HHcCCCCC---CCCCcHHHHHHHH
Confidence 8999999 589999998632 247999999998877 5678999999 66788764 4899999999999
Q ss_pred HHHHHHHHh
Q 010743 291 KLVLAIIER 299 (502)
Q Consensus 291 ~L~~~~l~~ 299 (502)
+||.+++.+
T Consensus 157 ~vl~~l~~~ 165 (232)
T PRK06309 157 RVFSALVGD 165 (232)
T ss_pred HHHHHHHHH
Confidence 999998864
No 14
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=5.6e-27 Score=225.41 Aligned_cols=155 Identities=19% Similarity=0.283 Sum_probs=130.7
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEc-CCcE--EEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHh
Q 010743 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKV--TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~g~~~I~rVsvVd~-~G~v--i~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~f 217 (502)
...||+|||||||+++ .++|++|++|.. +|.+ .|++||+|..+|+++++.+||||++||+++| ++.+|+.+|.+|
T Consensus 4 ~~~~vvlD~EtTGl~~-~~eIIeIgaV~v~~g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap-~~~evl~~f~~f 81 (195)
T PRK07247 4 LETYIAFDLEFNTVNG-VSHIIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAP-KVEEVLAAFKEF 81 (195)
T ss_pred CCeEEEEEeeCCCCCC-CCeEEEEEEEEEECCEEEEEEEEEECCCCCCCccceecCCCCHHHHhCCC-CHHHHHHHHHHH
Confidence 4589999999999985 457999999987 4543 4999999999999999999999999999999 999999999999
Q ss_pred hcCCCEEEEEchh-hHHHHHcccC-----CCccchHHHh--hhh--cC-CCCCCHHHHHHHHcCCccCCCCCCCCHHHHH
Q 010743 218 LSNGTILVGHSLN-NDLEVLKLDH-----PRVIDTSLIF--KYV--DE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDA 286 (502)
Q Consensus 218 l~~g~ILVGHnl~-fDl~fLk~~~-----p~vIDT~~L~--r~~--~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA 286 (502)
+ ++.++||||+. ||+.||+... +..+||.... +.. .+ ..+++|..|| .+||++.. +|+|++||
T Consensus 82 ~-~~~~lVaHNa~~fD~~fL~~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La-~~~gi~~~----~HrAl~DA 155 (195)
T PRK07247 82 V-GELPLIGYNAQKSDLPILAENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVA-DFLGIKGR----GHNSLEDA 155 (195)
T ss_pred H-CCCeEEEEeCcHhHHHHHHHcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHH-HhcCCCCC----CcCCHHHH
Confidence 9 89999999997 8999998642 2347776433 221 12 4689999999 77899842 79999999
Q ss_pred HHHHHHHHHHHHhcccC
Q 010743 287 SAAMKLVLAIIERRVDN 303 (502)
Q Consensus 287 ~Ata~L~~~~l~~g~~~ 303 (502)
++|+.||+++++.+...
T Consensus 156 ~~ta~v~~~ll~~~~~~ 172 (195)
T PRK07247 156 RMTARVYESFLESDQNK 172 (195)
T ss_pred HHHHHHHHHHHhhccch
Confidence 99999999999877643
No 15
>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=99.95 E-value=6.9e-27 Score=216.26 Aligned_cols=149 Identities=23% Similarity=0.320 Sum_probs=128.9
Q ss_pred EEEEEEeccCCCC-CcccEEEEEEEEc-CCcE---EEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhh
Q 010743 144 MYAVDCEMVLCED-GSEGLVRLCVVDR-NLKV---TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLL 218 (502)
Q Consensus 144 ~VaID~ETTGl~~-g~~~I~rVsvVd~-~G~v---i~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl 218 (502)
||+||+||||+++ ..++|++|++|.. ++.+ .|+.||+|..+|++.++++||||++||+++| ++.+|+.+|.+|+
T Consensus 1 ~v~~D~ETTGl~~~~~~~iieig~v~v~~~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~-~~~~v~~~l~~~l 79 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKP-KFAEIADEFLDFI 79 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEEEEEEEECCcEeccEEEEEECCCCCCCHHHHHHhCCCHHHHhcCC-CHHHHHHHHHHHH
Confidence 5899999999998 5678999999865 3332 4889999999999999999999999999999 9999999999999
Q ss_pred cCCCEEEEEchhhHHHHHcccC------------CCccchHHHhhhhcCCCCCCHHHHHHHHcCCccCCCCCCCCHHHHH
Q 010743 219 SNGTILVGHSLNNDLEVLKLDH------------PRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNCLDDA 286 (502)
Q Consensus 219 ~~g~ILVGHnl~fDl~fLk~~~------------p~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA 286 (502)
++.++||||+.||+.||+... ..++||..+++...+...++|..|| .++|++... ..+|+|+.||
T Consensus 80 -~~~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~~~~L~~l~-~~~~i~~~~-~~~H~Al~Da 156 (167)
T cd06131 80 -RGAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALC-KRFGIDNSH-RTLHGALLDA 156 (167)
T ss_pred -CCCeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCCCCCHHHHH-HHCCCCCCC-CCCCChHHHH
Confidence 889999999999999997631 1369999999987765678999999 777988642 2479999999
Q ss_pred HHHHHHHHHH
Q 010743 287 SAAMKLVLAI 296 (502)
Q Consensus 287 ~Ata~L~~~~ 296 (502)
++|++||..+
T Consensus 157 ~~~a~l~~~l 166 (167)
T cd06131 157 ELLAEVYLEL 166 (167)
T ss_pred HHHHHHHHHh
Confidence 9999999764
No 16
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=2e-26 Score=221.32 Aligned_cols=152 Identities=20% Similarity=0.267 Sum_probs=130.7
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEcCCc-E----EEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHH
Q 010743 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDRNLK-V----TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMK 215 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~g~~~I~rVsvVd~~G~-v----i~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~ 215 (502)
+.+||+||+||||+++..++|++|++|..++. + .|+.||+|..+|+++++.+||||++||+++| ++.+|+.+|.
T Consensus 28 ~~~~vviD~ETTGl~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~-~~~~vl~~~~ 106 (202)
T PRK09145 28 PDEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGL-SEEEALRQLL 106 (202)
T ss_pred CCCEEEEEeECCCCCCCCCceEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCC-CHHHHHHHHH
Confidence 45899999999999988788999999987543 2 3789999999999999999999999999999 9999999999
Q ss_pred HhhcCCCEEEEEchhhHHHHHcccC---------CCccchHHHhhhhc----C--CCCCCHHHHHHHHcCCccCCCCCCC
Q 010743 216 KLLSNGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVD----E--YRRPSLYNLCKSVLGYEIRKKGTPH 280 (502)
Q Consensus 216 ~fl~~g~ILVGHnl~fDl~fLk~~~---------p~vIDT~~L~r~~~----~--~~~~sL~~La~~~Lgi~iq~~~~~H 280 (502)
+|+ ++.++||||+.||+.||+... ..++||+.++.... + ..+++|.+|| .++|++.. .+|
T Consensus 107 ~~i-~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~-~~~gi~~~---~~H 181 (202)
T PRK09145 107 AFI-GNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAIL-KHLDLPVL---GRH 181 (202)
T ss_pred HHH-cCCeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHH-HHcCCCCC---CCC
Confidence 999 899999999999999998531 23799988764321 1 3468999999 77899874 389
Q ss_pred CHHHHHHHHHHHHHHHHH
Q 010743 281 NCLDDASAAMKLVLAIIE 298 (502)
Q Consensus 281 dAleDA~Ata~L~~~~l~ 298 (502)
+|++||++|++||+++++
T Consensus 182 ~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 182 DALNDAIMAALIFLRLRK 199 (202)
T ss_pred CcHHHHHHHHHHHHHHHh
Confidence 999999999999998764
No 17
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=2.5e-26 Score=235.38 Aligned_cols=154 Identities=20% Similarity=0.290 Sum_probs=137.9
Q ss_pred CCCcEEEEEEeccCCCCCcccEEEEEEEEc-CCcEE--EEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHH
Q 010743 140 TSNIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKK 216 (502)
Q Consensus 140 ~~~~~VaID~ETTGl~~g~~~I~rVsvVd~-~G~vi--~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~ 216 (502)
-+.+||+||+||||+++..++|++|++|.. +|.++ |++||+|..+|+++++++||||++||+++| +|.+|+.+|.+
T Consensus 6 ~~~~~Vv~DlETTGl~p~~~eIIEIgaV~v~~g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~-~~~evl~~f~~ 84 (313)
T PRK06807 6 LPLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAP-TIEEVLPLFLA 84 (313)
T ss_pred CCCCEEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCCC-CHHHHHHHHHH
Confidence 357899999999999998888999999987 45443 889999999999999999999999999999 99999999999
Q ss_pred hhcCCCEEEEEchhhHHHHHcccC---------CCccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCCCCCCCHHHHH
Q 010743 217 LLSNGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDA 286 (502)
Q Consensus 217 fl~~g~ILVGHnl~fDl~fLk~~~---------p~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA 286 (502)
|+ ++.+|||||+.||+.||+... ..+|||+.+++...+ ..+++|..|| .+||++. . +|+|+.||
T Consensus 85 fl-~~~~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~~~kL~~L~-~~lgi~~-~---~H~Al~DA 158 (313)
T PRK06807 85 FL-HTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLK-RMLGIRL-S---SHNAFDDC 158 (313)
T ss_pred HH-cCCeEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCCCCCHHHHH-HHcCCCC-C---CcChHHHH
Confidence 99 899999999999999998631 237999999998887 6788999999 7889997 3 89999999
Q ss_pred HHHHHHHHHHHHhc
Q 010743 287 SAAMKLVLAIIERR 300 (502)
Q Consensus 287 ~Ata~L~~~~l~~g 300 (502)
++|++||+.+....
T Consensus 159 ~~ta~l~~~l~~~~ 172 (313)
T PRK06807 159 ITCAAVYQKCASIE 172 (313)
T ss_pred HHHHHHHHHHHHhh
Confidence 99999999888654
No 18
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.94 E-value=2.9e-26 Score=224.17 Aligned_cols=147 Identities=18% Similarity=0.196 Sum_probs=127.8
Q ss_pred EEEEEEeccCCCCCcccEEEEEEEEc-CCcEE--EEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhcC
Q 010743 144 MYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSN 220 (502)
Q Consensus 144 ~VaID~ETTGl~~g~~~I~rVsvVd~-~G~vi--~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~~ 220 (502)
+++||+||||+++ .|++|++|+. +|.++ |++||+|+.+|+..++.+||||++||+++| ++.+|+.. |+ +
T Consensus 2 ~~vlD~ETTGl~~---~IieIg~v~v~~~~i~~~~~~lv~P~~~i~~~~~~ihgIt~e~v~~ap-~~~ev~~~---~~-~ 73 (219)
T PRK07983 2 LRVIDTETCGLQG---GIVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKP-WIEDVIPH---YY-G 73 (219)
T ss_pred eEEEEEECCCCCC---CCEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHcCCC-CHHHHHHH---Hc-C
Confidence 7899999999975 3899999876 56654 899999999999999999999999999999 99999876 56 8
Q ss_pred CCEEEEEchhhHHHHHcccCCCccchHHHhhhhcCCCCCCHHHHHHHHcCCccC--CCCCCCCHHHHHHHHHHHHHHHHH
Q 010743 221 GTILVGHSLNNDLEVLKLDHPRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIR--KKGTPHNCLDDASAAMKLVLAIIE 298 (502)
Q Consensus 221 g~ILVGHnl~fDl~fLk~~~p~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq--~~~~~HdAleDA~Ata~L~~~~l~ 298 (502)
+.+|||||+.||++||......+|||..++|.++|...++|..|| .++|++.. ....+|+|+.||++|+.||.++++
T Consensus 74 ~~~lVaHNa~FD~~~L~~~~~~~idTl~lar~l~p~~~~~l~~L~-~~~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~~ 152 (219)
T PRK07983 74 SEWYVAHNASFDRRVLPEMPGEWICTMKLARRLWPGIKYSNMALY-KSRKLNVQTPPGLHHHRALYDCYITAALLIDIMN 152 (219)
T ss_pred CCEEEEeCcHhhHHHHhCcCCCcEeHHHHHHHHccCCCCCHHHHH-HHcCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHH
Confidence 899999999999999987666799999999999884459999999 67787642 113589999999999999999886
Q ss_pred h
Q 010743 299 R 299 (502)
Q Consensus 299 ~ 299 (502)
.
T Consensus 153 ~ 153 (219)
T PRK07983 153 T 153 (219)
T ss_pred H
Confidence 4
No 19
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.94 E-value=1.7e-26 Score=227.20 Aligned_cols=157 Identities=24% Similarity=0.273 Sum_probs=132.9
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEcC--CcEE--EEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHH
Q 010743 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDRN--LKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKK 216 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~g~~~I~rVsvVd~~--G~vi--~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~ 216 (502)
..+|++||+||||+++..++|++|++|..+ |.++ +++||+|..+|+++++.+||||++|+.+.+.++.+++.+|..
T Consensus 5 ~~~~vv~D~ETTGl~p~~d~Iieig~v~v~~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~e~~~ 84 (232)
T PRK07942 5 PGPLAAFDLETTGVDPETARIVTAALVVVDADGEVVESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLAEIAD 84 (232)
T ss_pred cCcEEEEEeccCCCCCCCCeeEEEEEEEEeCCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHHHHHH
Confidence 457999999999999988899999998764 6654 889999999999999999999999998743378888888887
Q ss_pred hhc----CCCEEEEEchhhHHHHHcccC----------CCccchHHHhhhhcC--CCCCCHHHHHHHHcCCccCCCCCCC
Q 010743 217 LLS----NGTILVGHSLNNDLEVLKLDH----------PRVIDTSLIFKYVDE--YRRPSLYNLCKSVLGYEIRKKGTPH 280 (502)
Q Consensus 217 fl~----~g~ILVGHnl~fDl~fLk~~~----------p~vIDT~~L~r~~~~--~~~~sL~~La~~~Lgi~iq~~~~~H 280 (502)
++. ++.+|||||+.||++||+... ..++||..|.+...+ ..+++|.+|| .++|++.. .+|
T Consensus 85 ~l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~-~~~gi~~~---~aH 160 (232)
T PRK07942 85 ALREAWARGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALC-EHYGVRLD---NAH 160 (232)
T ss_pred HHHHHhhcCCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHH-HHcCCCCC---CCC
Confidence 663 689999999999999998731 137999999887655 3578999999 67899875 389
Q ss_pred CHHHHHHHHHHHHHHHHHhcc
Q 010743 281 NCLDDASAAMKLVLAIIERRV 301 (502)
Q Consensus 281 dAleDA~Ata~L~~~~l~~g~ 301 (502)
+|++||.||++||+.++++.+
T Consensus 161 ~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 161 EATADALAAARVAWALARRFP 181 (232)
T ss_pred ChHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999987654
No 20
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.94 E-value=4.2e-26 Score=233.71 Aligned_cols=157 Identities=25% Similarity=0.347 Sum_probs=136.4
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEc--CCcEE--EEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHH
Q 010743 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDR--NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKK 216 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~g~~~I~rVsvVd~--~G~vi--~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~ 216 (502)
+.+||+||+||||++++.++|++|++|.. +|.++ |++||+|..+ ...+.+||||++||.++| +|.+++++|.+
T Consensus 14 ~~~fvvlD~ETTGl~p~~d~IIeIgav~v~~~g~i~~~~~~lv~P~~~--~~~~~IhGIt~e~l~~ap-~f~ev~~~l~~ 90 (313)
T PRK06063 14 PRGWAVVDVETSGFRPGQARIISLAVLGLDADGNVEQSVVTLLNPGVD--PGPTHVHGLTAEMLEGQP-QFADIAGEVAE 90 (313)
T ss_pred CCCEEEEEEECCCCCCCCCEEEEEEEEEEECCceeeeEEEEEECcCCC--CCCeecCCCCHHHHhCCC-CHHHHHHHHHH
Confidence 57899999999999998889999999965 56654 8899999853 567899999999999999 99999999999
Q ss_pred hhcCCCEEEEEchhhHHHHHcccC-------C--CccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCCCCCCCHHHHH
Q 010743 217 LLSNGTILVGHSLNNDLEVLKLDH-------P--RVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDA 286 (502)
Q Consensus 217 fl~~g~ILVGHnl~fDl~fLk~~~-------p--~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA 286 (502)
|+ ++.+|||||+.||++||+... + .++||+.+++.+.+ ..+++|.+|| .+||++.. .+|+|++||
T Consensus 91 ~l-~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~~kL~~l~-~~~gi~~~---~~H~Al~DA 165 (313)
T PRK06063 91 LL-RGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLA-AHWGVPQQ---RPHDALDDA 165 (313)
T ss_pred Hc-CCCEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCCCCHHHHH-HHcCCCCC---CCCCcHHHH
Confidence 99 899999999999999998632 2 37999999998765 6889999999 77899864 389999999
Q ss_pred HHHHHHHHHHHHhcccCCC
Q 010743 287 SAAMKLVLAIIERRVDNAV 305 (502)
Q Consensus 287 ~Ata~L~~~~l~~g~~~~i 305 (502)
++|++||..++++....++
T Consensus 166 ~ata~l~~~ll~~~~~~~~ 184 (313)
T PRK06063 166 RVLAGILRPSLERARERDV 184 (313)
T ss_pred HHHHHHHHHHHHHHHhcCC
Confidence 9999999998877544433
No 21
>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=99.94 E-value=3e-26 Score=222.88 Aligned_cols=157 Identities=23% Similarity=0.318 Sum_probs=134.8
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEE-cCCc---EEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHH
Q 010743 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVD-RNLK---VTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKK 216 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~g~~~I~rVsvVd-~~G~---vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~ 216 (502)
...||+||+||||++++.+ |++|++|. .++. ..|++||+|..+|+++++.+||||++||.++| ++.+|+++|..
T Consensus 6 ~~~fvv~D~ETTGl~~~~~-IIeIgav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p-~~~ev~~~~~~ 83 (217)
T TIGR00573 6 LDTETTGDNETTGLYAGHD-IIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKP-DFKEIAEDFAD 83 (217)
T ss_pred ecCEEEEEecCCCCCCCCC-EEEEEEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCC-CHHHHHHHHHH
Confidence 4689999999999999887 99999998 4443 25899999999999999999999999999999 99999999999
Q ss_pred hhcCCCEEEEEchhhHHHHHcccC----------CCccchHHHhhhhcC---CCCCCHHHHHHHHcCCccCCCCCCCCHH
Q 010743 217 LLSNGTILVGHSLNNDLEVLKLDH----------PRVIDTSLIFKYVDE---YRRPSLYNLCKSVLGYEIRKKGTPHNCL 283 (502)
Q Consensus 217 fl~~g~ILVGHnl~fDl~fLk~~~----------p~vIDT~~L~r~~~~---~~~~sL~~La~~~Lgi~iq~~~~~HdAl 283 (502)
|+ ++.++||||+.||+.||+... ..++||..+++...+ ..+++|..|| .++|++... ..+|+|+
T Consensus 84 ~~-~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~-~~~gl~~~~-~~~H~Al 160 (217)
T TIGR00573 84 YI-RGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALC-KRYEITNSH-RALHGAL 160 (217)
T ss_pred Hh-CCCEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHH-HHcCCCCCC-cccCCHH
Confidence 99 889999999999999998642 136899888777654 3578999999 677987641 1489999
Q ss_pred HHHHHHHHHHHHHHHhccc
Q 010743 284 DDASAAMKLVLAIIERRVD 302 (502)
Q Consensus 284 eDA~Ata~L~~~~l~~g~~ 302 (502)
+||++|++||+.++.+.+.
T Consensus 161 ~DA~~ta~l~~~l~~~~~~ 179 (217)
T TIGR00573 161 ADAFILAKLYLVMTGKQTK 179 (217)
T ss_pred HHHHHHHHHHHHHHhcchh
Confidence 9999999999999876543
No 22
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.94 E-value=2.6e-26 Score=210.35 Aligned_cols=153 Identities=35% Similarity=0.560 Sum_probs=134.5
Q ss_pred cEEEEEEeccCCCCCcccEEEEEEEEcCC---cEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhc
Q 010743 143 IMYAVDCEMVLCEDGSEGLVRLCVVDRNL---KVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS 219 (502)
Q Consensus 143 ~~VaID~ETTGl~~g~~~I~rVsvVd~~G---~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~ 219 (502)
.||+|||||||++++.++|++|++|..++ ...|+.||+|..+|+++++++||||+++|.+++ ++.+|+.+|..|+
T Consensus 1 ~~v~~D~Ettg~~~~~~~Iieig~v~~~~~~~~~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~-~~~~~~~~~~~~l- 78 (169)
T smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGRIIVVFDTYVKPDRPITDYATEIHGITPEMLDDAP-TFEEVLEELLEFL- 78 (169)
T ss_pred CEEEEEeeCCCCCCCCCeEEEEEEEEEECCEeEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCC-CHHHHHHHHHHHh-
Confidence 48999999999999877899999998754 345999999999999999999999999999998 9999999999999
Q ss_pred CCCEEEEEch-hhHHHHHcccCC----------CccchHHHhhhhcCCCCCCHHHHHHHHcCCccCCCCCCCCHHHHHHH
Q 010743 220 NGTILVGHSL-NNDLEVLKLDHP----------RVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASA 288 (502)
Q Consensus 220 ~g~ILVGHnl-~fDl~fLk~~~p----------~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~A 288 (502)
++.++||||. .||+.+|+..+. +++||..+++...+..+++|..|| .++|++... .+|+|++||++
T Consensus 79 ~~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~~~~L~~l~-~~~~~~~~~--~~H~A~~Da~~ 155 (169)
T smart00479 79 KGKILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGRKYSLKKLA-ERLGLEVIG--RAHRALDDARA 155 (169)
T ss_pred cCCEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCCCCCHHHHH-HHCCCCCCC--CCcCcHHHHHH
Confidence 7888889988 999999997421 269999999988775589999999 677888653 25999999999
Q ss_pred HHHHHHHHHHhc
Q 010743 289 AMKLVLAIIERR 300 (502)
Q Consensus 289 ta~L~~~~l~~g 300 (502)
|++||.+++..+
T Consensus 156 t~~l~~~~~~~~ 167 (169)
T smart00479 156 TAKLFKKLVERL 167 (169)
T ss_pred HHHHHHHHHHHh
Confidence 999999988654
No 23
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.94 E-value=7e-26 Score=226.30 Aligned_cols=156 Identities=25% Similarity=0.329 Sum_probs=138.0
Q ss_pred CCCCcEEEEEEeccCCCCCcccEEEEEEEEc-CCcEE--EEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHH
Q 010743 139 MTSNIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMK 215 (502)
Q Consensus 139 ~~~~~~VaID~ETTGl~~g~~~I~rVsvVd~-~G~vi--~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~ 215 (502)
.....||+||+||||++++.++|++|++|.. +|.++ |+.||+|. +|+.+++++||||++||.++| ++.+|+.+|.
T Consensus 65 ~~~~~~vv~DiETTG~~~~~~~IIEIGAv~v~~g~i~~~f~~~v~p~-~ip~~~~~itGIt~e~l~~ap-~~~evl~~f~ 142 (257)
T PRK08517 65 IKDQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAK-EVPEYITELTGITYEDLENAP-SLKEVLEEFR 142 (257)
T ss_pred CCCCCEEEEEEeCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCC-CCChhhhhhcCcCHHHHcCCC-CHHHHHHHHH
Confidence 3467899999999999988878999999987 55543 88999996 899999999999999999999 9999999999
Q ss_pred HhhcCCCEEEEEchhhHHHHHccc---------CCCccchHHHhhhhcCCCCCCHHHHHHHHcCCccCCCCCCCCHHHHH
Q 010743 216 KLLSNGTILVGHSLNNDLEVLKLD---------HPRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNCLDDA 286 (502)
Q Consensus 216 ~fl~~g~ILVGHnl~fDl~fLk~~---------~p~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA 286 (502)
+|+ +++++||||+.||+.||+.. ..+.+||..+++...+..+++|.+|| .++|++.. .+|+|+.||
T Consensus 143 ~fl-~~~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~~~~~L~~L~-~~lgi~~~---~~HrAl~DA 217 (257)
T PRK08517 143 LFL-GDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRYGLSFLK-ELLGIEIE---VHHRAYADA 217 (257)
T ss_pred HHH-CCCeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccCCCCCHHHHH-HHcCcCCC---CCCChHHHH
Confidence 999 89999999999999999863 23479999999987776789999999 68899874 389999999
Q ss_pred HHHHHHHHHHHHhcc
Q 010743 287 SAAMKLVLAIIERRV 301 (502)
Q Consensus 287 ~Ata~L~~~~l~~g~ 301 (502)
.+|++||..++.+.+
T Consensus 218 ~ata~ll~~ll~~~~ 232 (257)
T PRK08517 218 LAAYEIFKICLLNLP 232 (257)
T ss_pred HHHHHHHHHHHHHhH
Confidence 999999999987654
No 24
>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=99.94 E-value=4.9e-26 Score=207.21 Aligned_cols=142 Identities=23% Similarity=0.403 Sum_probs=125.7
Q ss_pred EEEEEEeccCCCCCcccEEEEEEEEc-CCcE--EEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhcC
Q 010743 144 MYAVDCEMVLCEDGSEGLVRLCVVDR-NLKV--TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSN 220 (502)
Q Consensus 144 ~VaID~ETTGl~~g~~~I~rVsvVd~-~G~v--i~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~~ 220 (502)
||+|||||||..+ ++|++|++|.. .|++ .|+.||+|..+++++++.+||||+++|.+++ ++.+|+.+|.+|+ +
T Consensus 1 ~v~~D~Ettg~~~--~~ii~ig~v~~~~~~~~~~~~~~i~p~~~~~~~~~~i~GIt~e~l~~~~-~~~~v~~~l~~~l-~ 76 (156)
T cd06130 1 FVAIDFETANADR--ASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAP-TFPEVWPEIKPFL-G 76 (156)
T ss_pred CEEEEEeCCCCCC--CceEEEEEEEEECCEEEEEEEEEeCcCCCCChhhccccCcCHHHHhcCC-CHHHHHHHHHHHh-C
Confidence 6899999999763 46999999986 4444 3889999999999999999999999999999 8999999999999 7
Q ss_pred CCEEEEEchhhHHHHHccc-------CC--CccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCCCCCCCHHHHHHHHH
Q 010743 221 GTILVGHSLNNDLEVLKLD-------HP--RVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAM 290 (502)
Q Consensus 221 g~ILVGHnl~fDl~fLk~~-------~p--~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~Ata 290 (502)
+.++||||+.||+.+|+.. .+ .++||..+++...+ ..+++|..|| .++|++.+ +|+|++||++|+
T Consensus 77 ~~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~~~~L~~l~-~~~g~~~~----~H~Al~Da~~ta 151 (156)
T cd06130 77 GSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVA-EHLGIELN----HHDALEDARACA 151 (156)
T ss_pred CCEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCCCCCHHHHH-HHcCCCcc----CcCchHHHHHHH
Confidence 8999999999999999753 12 37999999999887 6889999999 67899874 799999999999
Q ss_pred HHHH
Q 010743 291 KLVL 294 (502)
Q Consensus 291 ~L~~ 294 (502)
+||+
T Consensus 152 ~l~~ 155 (156)
T cd06130 152 EILL 155 (156)
T ss_pred HHHh
Confidence 9985
No 25
>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=99.94 E-value=1.8e-26 Score=217.88 Aligned_cols=144 Identities=26% Similarity=0.336 Sum_probs=119.6
Q ss_pred EEEEEEeccCCC-CCcccEEEEEEEEcCCc--------------E--EEEEEEcCCCcccccccccCCCChhhhccCCCC
Q 010743 144 MYAVDCEMVLCE-DGSEGLVRLCVVDRNLK--------------V--TIDELVKPEKAVADYRSEITGLTADDLVGVTCS 206 (502)
Q Consensus 144 ~VaID~ETTGl~-~g~~~I~rVsvVd~~G~--------------v--i~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~ 206 (502)
||+||+||||++ +..++|++|++|...+. + .|++||+|+.+|++.++.+||||++||.++| +
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a~~IhGIt~e~l~~~~-~ 79 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHKA-P 79 (177)
T ss_pred CeEEeeecCCCCCCCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCCcCChhHHHHhCcCHHHHhcCC-C
Confidence 689999999999 57788999999986321 1 3899999999999999999999999999999 7
Q ss_pred HH-HHHHHHHHhh---cCCCEEEEEch-hhHHHHHcccC----------CCccchHHHhhhhcCCCCCCHHHHHHHHcCC
Q 010743 207 LA-EIQKRMKKLL---SNGTILVGHSL-NNDLEVLKLDH----------PRVIDTSLIFKYVDEYRRPSLYNLCKSVLGY 271 (502)
Q Consensus 207 ~~-dV~~~l~~fl---~~g~ILVGHnl-~fDl~fLk~~~----------p~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi 271 (502)
+. ++++.|.+|+ .++.+|||||+ .||++||+... ..++||+.+++.+.+ +|..||+.++|+
T Consensus 80 ~~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~~----~L~~l~~~~~~~ 155 (177)
T cd06136 80 FDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ----SLGSLYKRLFGQ 155 (177)
T ss_pred ccHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhHh----hHHHHHHHHhCC
Confidence 65 3556565555 33579999998 89999997631 125899999998653 999999777899
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHH
Q 010743 272 EIRKKGTPHNCLDDASAAMKLVLA 295 (502)
Q Consensus 272 ~iq~~~~~HdAleDA~Ata~L~~~ 295 (502)
+.. .+|+|++||.||+++|.+
T Consensus 156 ~~~---~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 156 EPK---NSHTAEGDVLALLKCALH 176 (177)
T ss_pred Ccc---cccchHHHHHHHHHHHhh
Confidence 875 389999999999999964
No 26
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=1.5e-25 Score=228.97 Aligned_cols=149 Identities=21% Similarity=0.298 Sum_probs=130.5
Q ss_pred cEEEEEEeccCCCCCcccEEEEEEEEc-CCcEE--EEEEEcCCC-cccccccccCCCChhhhccCCCCHHHHHHHHHHhh
Q 010743 143 IMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT--IDELVKPEK-AVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLL 218 (502)
Q Consensus 143 ~~VaID~ETTGl~~g~~~I~rVsvVd~-~G~vi--~d~LVkP~~-~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl 218 (502)
+||+||+||||.. .++|++|++|.. +|.++ |++||+|.. .+++.++.+||||++||+++| +|.+|+.+|.+|+
T Consensus 2 ~~vviD~ETTg~~--~d~IieIgav~v~~g~i~~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~~ap-~f~ev~~~~~~fl 78 (309)
T PRK06195 2 NFVAIDFETANEK--RNSPCSIGIVVVKDGEIVEKVHYLIKPKEMRFMPINIGIHGIRPHMVEDEL-EFDKIWEKIKHYF 78 (309)
T ss_pred cEEEEEEeCCCCC--CCceEEEEEEEEECCEEEEEEEEEECCCCCCCChhheeccCcCHHHHhCCC-CHHHHHHHHHHHh
Confidence 6999999999753 457999999987 55544 889999985 578889999999999999999 9999999999999
Q ss_pred cCCCEEEEEchhhHHHHHcccC---------CCccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCCCCCCCHHHHHHH
Q 010743 219 SNGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASA 288 (502)
Q Consensus 219 ~~g~ILVGHnl~fDl~fLk~~~---------p~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~A 288 (502)
++.+|||||+.||++||+... ..++||..+++.+++ ..+++|..|| .+||++.. +|+|++||++
T Consensus 79 -~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~~L~~L~-~~~gi~~~----~H~Al~DA~a 152 (309)
T PRK06195 79 -NNNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVN-NFLGYEFK----HHDALADAMA 152 (309)
T ss_pred -CCCEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcCCHHHHH-HHcCCCCc----ccCCHHHHHH
Confidence 899999999999999997631 247999999999887 6789999999 77898752 8999999999
Q ss_pred HHHHHHHHHHhc
Q 010743 289 AMKLVLAIIERR 300 (502)
Q Consensus 289 ta~L~~~~l~~g 300 (502)
|++||+.++++.
T Consensus 153 ta~l~~~l~~~~ 164 (309)
T PRK06195 153 CSNILLNISKEL 164 (309)
T ss_pred HHHHHHHHHHHh
Confidence 999999988754
No 27
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.93 E-value=2.1e-25 Score=215.33 Aligned_cols=155 Identities=21% Similarity=0.276 Sum_probs=129.8
Q ss_pred CCcEEEEEEeccCCCCC------cccEEEEEEEEc-CCcE--EEEEEEcCCC--cccccccccCCCChhhhccCCCCHHH
Q 010743 141 SNIMYAVDCEMVLCEDG------SEGLVRLCVVDR-NLKV--TIDELVKPEK--AVADYRSEITGLTADDLVGVTCSLAE 209 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~g------~~~I~rVsvVd~-~G~v--i~d~LVkP~~--~I~dy~T~ihGIT~e~L~~ap~~~~d 209 (502)
...||+||+||||++++ .++|++|++|.. +|.+ .|++||+|.. +|+++++++||||++||.++| +|.+
T Consensus 3 ~~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap-~~~e 81 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGI-SFEE 81 (207)
T ss_pred cceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecCcChhhhcceECCCccCccChhhhhhcCcCHHHHccCC-CHHH
Confidence 45799999999997643 257999999986 4443 3999999987 799999999999999999999 9999
Q ss_pred HHHHHHHhhcCC-CEEEEEchhhHHHHHcccC-------C---CccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCCC
Q 010743 210 IQKRMKKLLSNG-TILVGHSLNNDLEVLKLDH-------P---RVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKG 277 (502)
Q Consensus 210 V~~~l~~fl~~g-~ILVGHnl~fDl~fLk~~~-------p---~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~~ 277 (502)
|+++|.+|+ ++ .++|+|+..||++||+... | .++|+..+++...+ ...++|..+| .++|++.. +
T Consensus 82 vl~~f~~~~-~~~~~~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~~~~L~~~~-~~~gi~~~--~ 157 (207)
T PRK07748 82 LVEKLAEYD-KRCKPTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKAI-EEYGKEGT--G 157 (207)
T ss_pred HHHHHHHHh-CcCCeEEEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCCCCCHHHHH-HHcCCCCC--C
Confidence 999999999 56 4566667899999997631 2 36888888887776 5678999999 77899864 2
Q ss_pred CCCCHHHHHHHHHHHHHHHHHhc
Q 010743 278 TPHNCLDDASAAMKLVLAIIERR 300 (502)
Q Consensus 278 ~~HdAleDA~Ata~L~~~~l~~g 300 (502)
.+|+|++||++|++||.++++++
T Consensus 158 ~~H~Al~DA~~ta~l~~~l~~~~ 180 (207)
T PRK07748 158 KHHCALDDAMTTYNIFKLVEKDK 180 (207)
T ss_pred CCcChHHHHHHHHHHHHHHHhCc
Confidence 47999999999999999998775
No 28
>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=99.93 E-value=7e-25 Score=211.20 Aligned_cols=156 Identities=24% Similarity=0.312 Sum_probs=128.8
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEc----CCcE----EEEEEEcC--CCcccccccccCCCChh-hhccCCCCHHH
Q 010743 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDR----NLKV----TIDELVKP--EKAVADYRSEITGLTAD-DLVGVTCSLAE 209 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~g~~~I~rVsvVd~----~G~v----i~d~LVkP--~~~I~dy~T~ihGIT~e-~L~~ap~~~~d 209 (502)
...+|+||+||||+++..++|++|++|.. +|.+ .|+++|+| ..+|+..++.+||||++ |+.+++ ++++
T Consensus 7 ~~~~vv~D~ETTGl~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~-~~~~ 85 (200)
T TIGR01298 7 GYLPVVVDVETGGFNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAV-SEYE 85 (200)
T ss_pred CCeeEEEEeeCCCCCCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCc-chHH
Confidence 45689999999999988788999999964 3443 38899997 47999999999999976 699998 8888
Q ss_pred HHHHHHHhh--------cCCCEEEEEchhhHHHHHcccC--------C----CccchHHHhhhhcCCCCCCHHHHHHHHc
Q 010743 210 IQKRMKKLL--------SNGTILVGHSLNNDLEVLKLDH--------P----RVIDTSLIFKYVDEYRRPSLYNLCKSVL 269 (502)
Q Consensus 210 V~~~l~~fl--------~~g~ILVGHnl~fDl~fLk~~~--------p----~vIDT~~L~r~~~~~~~~sL~~La~~~L 269 (502)
++.+++.++ .++++|||||+.||++||+... + .++||..+++..++ .++|..|| .++
T Consensus 86 ~~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~--~~~L~~l~-~~~ 162 (200)
T TIGR01298 86 ALHEIFKVVRKAMKASGCQRAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG--QTVLAKAC-QAA 162 (200)
T ss_pred HHHHHHHHHHHHHHhcccCCCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC--cccHHHHH-HHc
Confidence 888887776 2678999999999999998631 1 27999999998764 45899999 677
Q ss_pred CCccCCCCCCCCHHHHHHHHHHHHHHHHHhcc
Q 010743 270 GYEIRKKGTPHNCLDDASAAMKLVLAIIERRV 301 (502)
Q Consensus 270 gi~iq~~~~~HdAleDA~Ata~L~~~~l~~g~ 301 (502)
|++... ..+|+|++||.+|++||..++.+..
T Consensus 163 gi~~~~-~~~H~Al~Da~ata~lf~~l~~~~~ 193 (200)
T TIGR01298 163 GXDFDS-TQAHSALYDTEKTAELFCEIVNRWK 193 (200)
T ss_pred CCCccc-cchhhhHHhHHHHHHHHHHHHHHHH
Confidence 998632 1489999999999999999887543
No 29
>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=99.93 E-value=6e-25 Score=209.69 Aligned_cols=153 Identities=22% Similarity=0.261 Sum_probs=122.5
Q ss_pred CcEEEEEEeccCCCCCcccEEEEEEEEc----CCcE----EEEEEEcC--CCcccccccccCCCChhh-hccCCCCHHHH
Q 010743 142 NIMYAVDCEMVLCEDGSEGLVRLCVVDR----NLKV----TIDELVKP--EKAVADYRSEITGLTADD-LVGVTCSLAEI 210 (502)
Q Consensus 142 ~~~VaID~ETTGl~~g~~~I~rVsvVd~----~G~v----i~d~LVkP--~~~I~dy~T~ihGIT~e~-L~~ap~~~~dV 210 (502)
-.+|+||+||||+++..++|++|++|.. +|.+ .|++||+| +.+|++.++.+||||++| +.+++ ...++
T Consensus 5 ~~~vv~D~ETTGl~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~-~~~~~ 83 (189)
T cd06134 5 FLPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAV-DEKEA 83 (189)
T ss_pred ceeEEEEecCCCCCCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhcccc-chHHH
Confidence 4579999999999988888999999965 2432 59999999 578999999999999987 55555 55555
Q ss_pred HHHHHHhh----c----CCCEEEEEchhhHHHHHcccC-----------C-CccchHHHhhhhcCCCCCCHHHHHHHHcC
Q 010743 211 QKRMKKLL----S----NGTILVGHSLNNDLEVLKLDH-----------P-RVIDTSLIFKYVDEYRRPSLYNLCKSVLG 270 (502)
Q Consensus 211 ~~~l~~fl----~----~g~ILVGHnl~fDl~fLk~~~-----------p-~vIDT~~L~r~~~~~~~~sL~~La~~~Lg 270 (502)
+.+|+.++ . ++.+|||||+.||+.||+... + +++||..|++...+ .++|..+| .++|
T Consensus 84 ~~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~--~~~L~~l~-~~~g 160 (189)
T cd06134 84 LKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG--QTVLAKAC-QAAG 160 (189)
T ss_pred HHHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC--CCcHHHHH-HHCC
Confidence 55555544 2 378999999999999998631 1 36999999998865 45899999 6789
Q ss_pred CccCCCCCCCCHHHHHHHHHHHHHHHHHh
Q 010743 271 YEIRKKGTPHNCLDDASAAMKLVLAIIER 299 (502)
Q Consensus 271 i~iq~~~~~HdAleDA~Ata~L~~~~l~~ 299 (502)
+++.. ..+|+|+.||++|++||.+++++
T Consensus 161 i~~~~-~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 161 IEFDN-KEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred CCCCC-CCCcChHHHHHHHHHHHHHHHHh
Confidence 98642 24899999999999999998764
No 30
>PRK05168 ribonuclease T; Provisional
Probab=99.92 E-value=8.8e-25 Score=212.11 Aligned_cols=156 Identities=22% Similarity=0.305 Sum_probs=130.3
Q ss_pred CCCcEEEEEEeccCCCCCcccEEEEEEEEc----CCcE----EEEEEEcC--CCcccccccccCCCChhh-hccCCCCHH
Q 010743 140 TSNIMYAVDCEMVLCEDGSEGLVRLCVVDR----NLKV----TIDELVKP--EKAVADYRSEITGLTADD-LVGVTCSLA 208 (502)
Q Consensus 140 ~~~~~VaID~ETTGl~~g~~~I~rVsvVd~----~G~v----i~d~LVkP--~~~I~dy~T~ihGIT~e~-L~~ap~~~~ 208 (502)
+...+|+||+||||+++..++|++|++|.. +|.+ .|++||+| ..+|+.+++.+||||+++ +++++ ++.
T Consensus 15 ~~~~~vv~D~ETTGl~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~~~-~~~ 93 (211)
T PRK05168 15 RGFLPVVIDVETAGFNAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAV-SEK 93 (211)
T ss_pred cCCceEEEEeeCCCCCCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhcCC-ChH
Confidence 346789999999999988888999999965 3542 58999999 578999999999999986 78887 888
Q ss_pred HHHHHHHHhhc--------CCCEEEEEchhhHHHHHcccC-----------C-CccchHHHhhhhcCCCCCCHHHHHHHH
Q 010743 209 EIQKRMKKLLS--------NGTILVGHSLNNDLEVLKLDH-----------P-RVIDTSLIFKYVDEYRRPSLYNLCKSV 268 (502)
Q Consensus 209 dV~~~l~~fl~--------~g~ILVGHnl~fDl~fLk~~~-----------p-~vIDT~~L~r~~~~~~~~sL~~La~~~ 268 (502)
+++.+++.++. .+++|||||+.||+.||+... + +++||..+++...+ .++|..+| .+
T Consensus 94 ~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~--~~~L~~l~-~~ 170 (211)
T PRK05168 94 EALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALG--QTVLAKAC-QA 170 (211)
T ss_pred HHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC--CCCHHHHH-HH
Confidence 88888888763 378999999999999998631 1 37999999998765 35899999 67
Q ss_pred cCCccCCCCCCCCHHHHHHHHHHHHHHHHHhc
Q 010743 269 LGYEIRKKGTPHNCLDDASAAMKLVLAIIERR 300 (502)
Q Consensus 269 Lgi~iq~~~~~HdAleDA~Ata~L~~~~l~~g 300 (502)
+|+++.. ..+|+|++||.+|++||.+++++.
T Consensus 171 ~gl~~~~-~~~H~Al~DA~ata~l~~~l~~~~ 201 (211)
T PRK05168 171 AGIEFDN-KEAHSALYDTEKTAELFCEIVNRW 201 (211)
T ss_pred CCCCCCC-CCCCChHHHHHHHHHHHHHHHHHH
Confidence 7998742 248999999999999999988754
No 31
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.92 E-value=9.2e-25 Score=248.35 Aligned_cols=155 Identities=18% Similarity=0.275 Sum_probs=137.5
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEc-CCcEE--EEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHh
Q 010743 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~g~~~I~rVsvVd~-~G~vi--~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~f 217 (502)
..+||+||+||||+++. ++|++|++|.. +|.++ |++||+|..+|+++++.+||||++||+++| +|.+|+.+|.+|
T Consensus 6 ~~~~vvvD~ETTGl~~~-d~IIeIgaV~v~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap-~~~ev~~~~~~~ 83 (820)
T PRK07246 6 LRKYAVVDLEATGAGPN-ASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAP-DFSQVARHIYDL 83 (820)
T ss_pred CCCEEEEEEecCCcCCC-CeEEEEEEEEEECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCC-CHHHHHHHHHHH
Confidence 46799999999999874 68999999987 45543 889999999999999999999999999999 999999999999
Q ss_pred hcCCCEEEEEchhhHHHHHccc-----C---CCccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCCCCCCCHHHHHHH
Q 010743 218 LSNGTILVGHSLNNDLEVLKLD-----H---PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASA 288 (502)
Q Consensus 218 l~~g~ILVGHnl~fDl~fLk~~-----~---p~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~A 288 (502)
+ +++++||||+.||+.||+.. . ...+||..+++..++ ..+++|.+|| .+||++.. .+|+|++||+|
T Consensus 84 l-~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L~-~~lgl~~~---~~H~Al~DA~a 158 (820)
T PRK07246 84 I-EDCIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLS-RELNIDLA---DAHTAIADARA 158 (820)
T ss_pred h-CCCEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHHH-HHcCCCCC---CCCCHHHHHHH
Confidence 9 89999999999999999763 1 237999999999888 6789999999 67899875 38999999999
Q ss_pred HHHHHHHHHHhccc
Q 010743 289 AMKLVLAIIERRVD 302 (502)
Q Consensus 289 ta~L~~~~l~~g~~ 302 (502)
|++||..++.+...
T Consensus 159 ta~L~~~l~~~l~~ 172 (820)
T PRK07246 159 TAELFLKLLQKIES 172 (820)
T ss_pred HHHHHHHHHHHHhh
Confidence 99999998876543
No 32
>PRK07883 hypothetical protein; Validated
Probab=99.92 E-value=1.3e-24 Score=237.89 Aligned_cols=161 Identities=22% Similarity=0.335 Sum_probs=141.7
Q ss_pred CCCCcEEEEEEeccCCCCCcccEEEEEEEEc-CCcEE--EEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHH
Q 010743 139 MTSNIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMK 215 (502)
Q Consensus 139 ~~~~~~VaID~ETTGl~~g~~~I~rVsvVd~-~G~vi--~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~ 215 (502)
.....||+||+||||+++..++|++|++|.. +|.++ |++||+|..+|+++++.+||||++||+++| ++.+|+.+|.
T Consensus 12 ~~~~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap-~~~evl~~f~ 90 (557)
T PRK07883 12 LRDVTFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAP-PIEEVLPAFL 90 (557)
T ss_pred CcCCCEEEEEEecCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCC-CHHHHHHHHH
Confidence 3457899999999999998889999999987 45554 899999999999999999999999999999 9999999999
Q ss_pred HhhcCCCEEEEEchhhHHHHHccc-------C--CCccchHHHhhhhcC---CCCCCHHHHHHHHcCCccCCCCCCCCHH
Q 010743 216 KLLSNGTILVGHSLNNDLEVLKLD-------H--PRVIDTSLIFKYVDE---YRRPSLYNLCKSVLGYEIRKKGTPHNCL 283 (502)
Q Consensus 216 ~fl~~g~ILVGHnl~fDl~fLk~~-------~--p~vIDT~~L~r~~~~---~~~~sL~~La~~~Lgi~iq~~~~~HdAl 283 (502)
+|+ ++.+|||||+.||+.||+.. . ..++||..+++.+.+ ..+++|.+|| .++|++.. .+|+|+
T Consensus 91 ~fl-~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L~-~~~gi~~~---~~H~Al 165 (557)
T PRK07883 91 EFA-RGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLA-RLFGATTT---PTHRAL 165 (557)
T ss_pred HHh-cCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHHH-HHCCcccC---CCCCHH
Confidence 999 89999999999999999863 1 247999999988765 5789999999 68899975 389999
Q ss_pred HHHHHHHHHHHHHHHhcccCCC
Q 010743 284 DDASAAMKLVLAIIERRVDNAV 305 (502)
Q Consensus 284 eDA~Ata~L~~~~l~~g~~~~i 305 (502)
+||.+|++||..+++.....++
T Consensus 166 ~DA~ata~l~~~l~~~~~~~~~ 187 (557)
T PRK07883 166 DDARATVDVLHGLIERLGNLGV 187 (557)
T ss_pred HHHHHHHHHHHHHHHHHHhcCC
Confidence 9999999999999987654443
No 33
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.92 E-value=1.6e-25 Score=251.86 Aligned_cols=162 Identities=20% Similarity=0.363 Sum_probs=147.8
Q ss_pred CCCCCcEEEEEEeccCCCCCcccEEEEEEEEc-CCcEE--EEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHH
Q 010743 138 TMTSNIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRM 214 (502)
Q Consensus 138 ~~~~~~~VaID~ETTGl~~g~~~I~rVsvVd~-~G~vi--~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l 214 (502)
......||++|+||||+++..++|+++++|.. +|+++ |+.||+|..||+..+|.+||||.+||++++ ++.+|+.+|
T Consensus 417 ~l~datyVVfDiETTGLs~~~d~iIE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~-~i~~vL~kf 495 (1444)
T COG2176 417 KLDDATYVVFDIETTGLSPVYDEIIEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAP-EIEEVLEKF 495 (1444)
T ss_pred ccccccEEEEEeecCCcCcccchhhhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCc-cHHHHHHHH
Confidence 45567899999999999999999999999987 67776 889999999999999999999999999999 999999999
Q ss_pred HHhhcCCCEEEEEchhhHHHHHcccC---------CCccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCCCCCCCHHH
Q 010743 215 KKLLSNGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLD 284 (502)
Q Consensus 215 ~~fl~~g~ILVGHnl~fDl~fLk~~~---------p~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAle 284 (502)
.+|+ +|+||||||++||++||+... ..+|||+.|+|.++| .++|+|..|| .-||+.+. .+|||..
T Consensus 496 ~~~~-~d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh~Lg~l~-kk~~v~le---~hHRA~y 570 (1444)
T COG2176 496 REFI-GDSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSHRLGTLC-KKLGVELE---RHHRADY 570 (1444)
T ss_pred HHHh-cCcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhcchHHHH-HHhCccHH---Hhhhhhh
Confidence 9999 999999999999999999731 248999999999998 9999999999 56699985 3899999
Q ss_pred HHHHHHHHHHHHHHhcccCCC
Q 010743 285 DASAAMKLVLAIIERRVDNAV 305 (502)
Q Consensus 285 DA~Ata~L~~~~l~~g~~~~i 305 (502)
||.||+.||..+++.-.+.++
T Consensus 571 Daeat~~vf~~f~~~~ke~Gi 591 (1444)
T COG2176 571 DAEATAKVFFVFLKDLKEKGI 591 (1444)
T ss_pred hHHHHHHHHHHHHHHHHHhch
Confidence 999999999999987766665
No 34
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.92 E-value=3.5e-24 Score=221.86 Aligned_cols=155 Identities=15% Similarity=0.237 Sum_probs=132.1
Q ss_pred CCCcEEEEEEeccCCCCCcccEEEEEEEEc--CCcE--EEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHH
Q 010743 140 TSNIMYAVDCEMVLCEDGSEGLVRLCVVDR--NLKV--TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMK 215 (502)
Q Consensus 140 ~~~~~VaID~ETTGl~~g~~~I~rVsvVd~--~G~v--i~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~ 215 (502)
....||+||+||||+++..++|++|++|.. +|.+ .|++||+|..++.. ..+||||++||+++| +|.+|+.+|.
T Consensus 44 ~~~~fVvlDiETTGLdp~~drIIeIgAV~i~~~g~ive~f~tLVnP~~~~~p--~~LHGIT~e~La~AP-~f~eVl~el~ 120 (377)
T PRK05601 44 EAAPFVAVSIQTSGIHPSTSRLITIDAVTLTADGEEVEHFHAVLNPGEDPGP--FHLHGLSAEEFAQGK-RFSQILKPLD 120 (377)
T ss_pred CCCCEEEEEEECCCCCCCCCeEEEEEEEEEEcCCEEEEEEEEEECcCCCCCC--ccccCCCHHHHhcCC-CHHHHHHHHH
Confidence 446899999999999998889999999965 5655 49999999986554 479999999999999 9999999999
Q ss_pred HhhcCCCEEEEEchhhHHHHHcccC------------------------------------CCccchHHHhhhhcC-CCC
Q 010743 216 KLLSNGTILVGHSLNNDLEVLKLDH------------------------------------PRVIDTSLIFKYVDE-YRR 258 (502)
Q Consensus 216 ~fl~~g~ILVGHnl~fDl~fLk~~~------------------------------------p~vIDT~~L~r~~~~-~~~ 258 (502)
+|| +|++|||||+.||++||.... ..++||+.+++.+++ ..+
T Consensus 121 ~fL-~g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l~~ 199 (377)
T PRK05601 121 RLI-DGRTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGVALDD 199 (377)
T ss_pred HHh-CCCEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHcCCCCC
Confidence 999 899999999999999997621 136999999999988 789
Q ss_pred CCHHHHHHHHcCCccCC-------CCCCCCHH--HHHHHHHHHHHHHHHh
Q 010743 259 PSLYNLCKSVLGYEIRK-------KGTPHNCL--DDASAAMKLVLAIIER 299 (502)
Q Consensus 259 ~sL~~La~~~Lgi~iq~-------~~~~HdAl--eDA~Ata~L~~~~l~~ 299 (502)
|+|..|| .+||++... ....|+++ +||+.+++||..+.+.
T Consensus 200 ~rL~~La-~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~~~~ 248 (377)
T PRK05601 200 IRIRGVA-HTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFALRAS 248 (377)
T ss_pred CCHHHHH-HHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHhhcc
Confidence 9999999 678998711 12478988 6999999999886444
No 35
>PRK06722 exonuclease; Provisional
Probab=99.92 E-value=4.3e-24 Score=215.63 Aligned_cols=152 Identities=24% Similarity=0.324 Sum_probs=127.0
Q ss_pred CCcEEEEEEeccCCCCC----cccEEEEEEEEcC-C--cEE--EEEEEcCCCcccccccccCCCChhhhccCCCCHHHHH
Q 010743 141 SNIMYAVDCEMVLCEDG----SEGLVRLCVVDRN-L--KVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQ 211 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~g----~~~I~rVsvVd~~-G--~vi--~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~ 211 (502)
...||+||+|||| ++. .++|++|++|..+ | .++ |++||+|..+|+++++.+||||++||.++| +|.+|+
T Consensus 4 ~~~~vViD~ETT~-~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~~I~~~i~~LTGIT~emV~~AP-~f~eVl 81 (281)
T PRK06722 4 ATHFIVFDIERNF-RPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVE-KFPQII 81 (281)
T ss_pred CCEEEEEEeeCCC-CCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCCcCCHhHhhhcCCCHHHHcCCC-CHHHHH
Confidence 4689999999995 432 2579999999863 3 444 999999999999999999999999999999 999999
Q ss_pred HHHHHhhcCCCEEEEEchhhHHHHHccc-------CCC-----ccchHHHhhhhcC---CCCCCHHHHHHHHcCCccCCC
Q 010743 212 KRMKKLLSNGTILVGHSLNNDLEVLKLD-------HPR-----VIDTSLIFKYVDE---YRRPSLYNLCKSVLGYEIRKK 276 (502)
Q Consensus 212 ~~l~~fl~~g~ILVGHnl~fDl~fLk~~-------~p~-----vIDT~~L~r~~~~---~~~~sL~~La~~~Lgi~iq~~ 276 (502)
.+|.+|+ ++.++|+||..||++||+.. .|. .+|++.++...++ ...++|..|| .++|++..
T Consensus 82 ~ef~~fi-g~~~lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~-~~lgL~~~-- 157 (281)
T PRK06722 82 EKFIQFI-GEDSIFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAV-EQLGLIWE-- 157 (281)
T ss_pred HHHHHHH-CCCcEEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHH-HHCCCCCC--
Confidence 9999999 77778888889999999973 121 3788887655443 3557999999 78899864
Q ss_pred CCCCCHHHHHHHHHHHHHHHHH
Q 010743 277 GTPHNCLDDASAAMKLVLAIIE 298 (502)
Q Consensus 277 ~~~HdAleDA~Ata~L~~~~l~ 298 (502)
+.+|+|++||.+|+.||+.++.
T Consensus 158 g~~HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 158 GKQHRALADAENTANILLKAYS 179 (281)
T ss_pred CCCcCcHHHHHHHHHHHHHHhc
Confidence 3489999999999999999874
No 36
>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=99.91 E-value=7.4e-24 Score=242.10 Aligned_cols=153 Identities=22% Similarity=0.299 Sum_probs=137.8
Q ss_pred cEEEEEEeccCCCCCcccEEEEEEEEc-CCcEE--EEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhc
Q 010743 143 IMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS 219 (502)
Q Consensus 143 ~~VaID~ETTGl~~g~~~I~rVsvVd~-~G~vi--~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~ 219 (502)
+||+||+||||++++.++|++|++|.. +|+++ |++||+|..+|+++++.+||||++||+++| +|.+|+.+|.+|+
T Consensus 1 ~~vvvD~ETTG~~~~~~~IIeig~v~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~ap-~~~ev~~~l~~~l- 78 (850)
T TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAP-YFSQVAQEIYDLL- 78 (850)
T ss_pred CEEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEeCCCCCCChhhhhhcCcCHHHHhCCC-CHHHHHHHHHHHh-
Confidence 489999999999988889999999987 56654 999999999999999999999999999999 9999999999999
Q ss_pred CCCEEEEEchhhHHHHHccc-----C----CCccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCCCCCCCHHHHHHHH
Q 010743 220 NGTILVGHSLNNDLEVLKLD-----H----PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAA 289 (502)
Q Consensus 220 ~g~ILVGHnl~fDl~fLk~~-----~----p~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~At 289 (502)
+++++||||+.||+.||+.. . ..++||..+++...+ ..+++|.+|| .++|++.. .+|+|++||.+|
T Consensus 79 ~~~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~~~~L~~l~-~~~gi~~~---~~H~Al~DA~at 154 (850)
T TIGR01407 79 EDGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELS-EALGLTHE---NPHRADSDAQAT 154 (850)
T ss_pred CCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCCCCCHHHHH-HHCCCCCC---CCCChHHHHHHH
Confidence 89999999999999999863 1 137999999999888 7789999999 67899874 389999999999
Q ss_pred HHHHHHHHHhcc
Q 010743 290 MKLVLAIIERRV 301 (502)
Q Consensus 290 a~L~~~~l~~g~ 301 (502)
++||.+++.+-.
T Consensus 155 a~l~~~l~~~~~ 166 (850)
T TIGR01407 155 AELLLLLFEKME 166 (850)
T ss_pred HHHHHHHHHHHH
Confidence 999999887644
No 37
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=99.91 E-value=8.9e-26 Score=248.27 Aligned_cols=275 Identities=23% Similarity=0.298 Sum_probs=197.1
Q ss_pred CCCCcccchhhccccCCCCC----------------CC-CCcCchhhHHHHhhc-ccccccccchhh---hhHhhhhHHH
Q 010743 28 TAGGWKDFLTSYDKKFGSSL----------------SD-PARRSKDALSSFLKT-FTKEDDLKFIAK---VVQSHLNRDL 86 (502)
Q Consensus 28 ~~~~~k~~l~~~~~~~~~~~----------------~d-p~~~~~~~l~~f~~~-~~~~~~~~~~~~---~~~~~~~~~~ 86 (502)
.++.++|.|.+++..+++.. ++ |+...|..||+||+. ++++|++.|-++ |..++| ++.
T Consensus 785 ~~~~~vYeL~a~V~~I~d~~~e~~lVs~Ikv~~~~~~~~~~dsqWylFNDfLV~~ite~EAl~~~~~WKvP~Il~Y-~d~ 863 (1118)
T KOG1275|consen 785 EPSAVVYELDAMVHAIGDNENEVNLVSPIKVLRPYHVIKPDDSQWYLFNDFLVSEITEEEALHFDGPWKVPAILYY-CDK 863 (1118)
T ss_pred CCceEEEEeeeEEEEeccCCCccceEEEEEccCcccccCcCcceeEEEcceeeeeCChHHheEeccCccCcEEEEE-ecc
Confidence 45578999999988887762 11 555677777777777 677777766555 444444 111
Q ss_pred HHHHHhcCCCCCChhhHHHH-hhhcCCCCccccCCCCCCCC----ceeeccCCCCCCCCCCcEEEEEEeccCCCC-----
Q 010743 87 VEQLKKTSPDDESPEQRLVR-LTLQHPQYPLCYMFPSSDEG----WLVTKLGKSSKTMTSNIMYAVDCEMVLCED----- 156 (502)
Q Consensus 87 ~~~~~~~~~~~~~~~~~lv~-~t~~~~~~~~~y~~p~~~~~----~~~t~~~~~~~~~~~~~~VaID~ETTGl~~----- 156 (502)
+. + ...++.- +..+. .++. +.++..+ ...-.+....+.+.+..+|+||.|++.+..
T Consensus 864 -~s--~-~~~~V~~-~~eiSd~~l~---------~~~~~~n~~~a~~t~~pLt~dEmPk~g~LVgiDAEFVtLq~Ee~Ei 929 (1118)
T KOG1275|consen 864 -KS--K-KNFDVKT-PDEISDYLLL---------EESYALNRDGAMTTLQPLTLDEMPKSGDLVGIDAEFVTLQTEELEI 929 (1118)
T ss_pred -cc--c-cCCCCCC-ccccchHhhh---------hchhhhcCCcccceeeeccccccCCCCceeeeehhheecchHHhcc
Confidence 00 0 0001000 00000 1111 1112111 111112244677889999999999998753
Q ss_pred ---Cc--------ccEEEEEEEEcC----CcEEEEEEEcCCCcccccccccCCCChhhhccCC-----CCHHHHHHHHHH
Q 010743 157 ---GS--------EGLVRLCVVDRN----LKVTIDELVKPEKAVADYRSEITGLTADDLVGVT-----CSLAEIQKRMKK 216 (502)
Q Consensus 157 ---g~--------~~I~rVsvVd~~----G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap-----~~~~dV~~~l~~ 216 (502)
|. -+++||++|+++ |.++.|.||--+..|.||.|+++||-|.||.+.. +++.-++.+++-
T Consensus 930 r~DG~~stIkP~~msvARiScvRGeGp~eGiPFiDDYv~T~d~VvDYLTqySGI~PGDLDp~~S~K~Lt~lK~~Y~Kl~~ 1009 (1118)
T KOG1275|consen 930 RSDGKTSTIKPSRMSVARISCVRGEGPNEGIPFIDDYVSTDDKVVDYLTQYSGIKPGDLDPTTSEKRLTTLKVLYLKLRL 1009 (1118)
T ss_pred ccCCceeEeccccceeEEEEEEcccCCCCCCccccceecchhHHHHHHHHhcCCCccccCCccCcceehhHHHHHHHHHH
Confidence 21 268999999985 5677999999999999999999999999999765 478999999999
Q ss_pred hhcCCCEEEEEchhhHHHHHcccCCC--ccchHHHhhhhcCCCCCCHHHHHHHHcCCccCCCCCCCCHHHHHHHHHHHHH
Q 010743 217 LLSNGTILVGHSLNNDLEVLKLDHPR--VIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLVL 294 (502)
Q Consensus 217 fl~~g~ILVGHnl~fDl~fLk~~~p~--vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~Ata~L~~ 294 (502)
+++.|+++|||++.+|+++|++..|+ +|||+.+|+... .+..||++||+.+||..||.+ +||+++||++|+.||.
T Consensus 1010 Li~~GviFVGHGL~nDFrvINi~Vp~~QiiDTv~lf~~~s-~R~LSLrfLa~~lLg~~IQ~~--~HDSIeDA~taLkLYk 1086 (1118)
T KOG1275|consen 1010 LIQRGVIFVGHGLQNDFRVINIHVPEEQIIDTVTLFRLGS-QRMLSLRFLAWELLGETIQME--AHDSIEDARTALKLYK 1086 (1118)
T ss_pred HHHcCcEEEcccccccceEEEEecChhhheeeeEEEeccc-ccEEEHHHHHHHHhcchhhcc--ccccHHHHHHHHHHHH
Confidence 99999999999999999999998875 899999998543 588999999999999999974 9999999999999999
Q ss_pred HHHHhcccCCCCCcchhhhHHHHhhhhcCCCCCC
Q 010743 295 AIIERRVDNAVPLLQEDVAETERARLFLHRIPTK 328 (502)
Q Consensus 295 ~~l~~g~~~~i~l~~~~~~e~~l~~l~~~~iP~~ 328 (502)
++++ +..++..++.+..++..+-|..
T Consensus 1087 ~Yl~--------lkeq~~~~~~l~niye~gr~~q 1112 (1118)
T KOG1275|consen 1087 KYLK--------LKEQGKLESELRNIYECGRPNQ 1112 (1118)
T ss_pred HHHH--------HHHhhHHHHHHHHHhhcCcccc
Confidence 9986 3334445666666665555543
No 38
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.91 E-value=7.4e-24 Score=243.95 Aligned_cols=155 Identities=20% Similarity=0.332 Sum_probs=138.1
Q ss_pred CcEEEEEEeccCCCCCc-ccEEEEEEEEc-CCcEE--EEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHh
Q 010743 142 NIMYAVDCEMVLCEDGS-EGLVRLCVVDR-NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (502)
Q Consensus 142 ~~~VaID~ETTGl~~g~-~~I~rVsvVd~-~G~vi--~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~f 217 (502)
.+||+||+||||+++.. ++|++|++|.. +|+++ |++||+|..+|+++++.+||||++||+++| +|.+|+.+|..|
T Consensus 3 ~~~vvvD~ETTG~~p~~~d~IIeigav~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap-~f~ev~~~l~~~ 81 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKGDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAP-LFEDVAPEIVEL 81 (928)
T ss_pred CCEEEEEEeCCCCCCCCCCcEEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCC-CHHHHHHHHHHH
Confidence 46999999999998654 68999999987 55554 899999999999999999999999999999 999999999999
Q ss_pred hcCCCEEEEEchhhHHHHHccc-----C----CCccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCCCCCCCHHHHHH
Q 010743 218 LSNGTILVGHSLNNDLEVLKLD-----H----PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDAS 287 (502)
Q Consensus 218 l~~g~ILVGHnl~fDl~fLk~~-----~----p~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~ 287 (502)
+ +++++||||+.||+.||+.. . ..+|||..+++..+| ..+++|..|| .+||++.. .+|+|++||+
T Consensus 82 l-~~~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~~~~L~~l~-~~l~i~~~---~~H~Al~DA~ 156 (928)
T PRK08074 82 L-EGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLS-EELGLEHD---QPHRADSDAE 156 (928)
T ss_pred h-CCCeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCCCCCHHHHH-HhCCCCCC---CCCChHHHHH
Confidence 9 89999999999999999863 1 247999999999888 7889999999 77898864 4899999999
Q ss_pred HHHHHHHHHHHhccc
Q 010743 288 AAMKLVLAIIERRVD 302 (502)
Q Consensus 288 Ata~L~~~~l~~g~~ 302 (502)
+|+.||.+++++...
T Consensus 157 ata~l~~~l~~~~~~ 171 (928)
T PRK08074 157 VTAELFLQLLNKLER 171 (928)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999999886543
No 39
>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=99.91 E-value=1.6e-23 Score=244.45 Aligned_cols=159 Identities=23% Similarity=0.392 Sum_probs=142.2
Q ss_pred CCCcEEEEEEeccCCCCCcccEEEEEEEEc-CCcEE--EEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHH
Q 010743 140 TSNIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKK 216 (502)
Q Consensus 140 ~~~~~VaID~ETTGl~~g~~~I~rVsvVd~-~G~vi--~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~ 216 (502)
....||+||+||||+++..++|++|++|.. +|.++ |++||+|..+|+++++++||||++||+++| ++.+|+++|.+
T Consensus 188 ~~~~~VVfDiETTGL~~~~d~IIEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap-~~~evl~~f~~ 266 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAP-EIEEVLEKFKE 266 (1213)
T ss_pred cCCcEEEEEeEecCCCCCCCeEEEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCC-CHHHHHHHHHH
Confidence 567899999999999998889999999986 55554 899999999999999999999999999999 99999999999
Q ss_pred hhcCCCEEEEEchhhHHHHHcccC---------CCccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCCCCCCCHHHHH
Q 010743 217 LLSNGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDA 286 (502)
Q Consensus 217 fl~~g~ILVGHnl~fDl~fLk~~~---------p~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA 286 (502)
|+ ++++|||||+.||+.||+..+ ..++||+.+++.+.+ ..+++|..|| .++|++... +|+|+.||
T Consensus 267 fl-~~~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k~~kL~~La-k~lgi~~~~---~HrAl~DA 341 (1213)
T TIGR01405 267 FF-KDSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRLGNIC-KKLGVDLDD---HHRADYDA 341 (1213)
T ss_pred Hh-CCCeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCCCCCHHHHH-HHcCCCCCC---CcCHHHHH
Confidence 99 899999999999999998631 247999999999887 7899999999 567999863 89999999
Q ss_pred HHHHHHHHHHHHhcccCC
Q 010743 287 SAAMKLVLAIIERRVDNA 304 (502)
Q Consensus 287 ~Ata~L~~~~l~~g~~~~ 304 (502)
.+|++||..+++...+.+
T Consensus 342 ~aTa~I~~~ll~~l~~~~ 359 (1213)
T TIGR01405 342 EATAKVFKVMVEQLKEKG 359 (1213)
T ss_pred HHHHHHHHHHHHHHHHcC
Confidence 999999999887654433
No 40
>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=99.90 E-value=1.7e-23 Score=193.78 Aligned_cols=148 Identities=25% Similarity=0.309 Sum_probs=125.9
Q ss_pred EEEEEEeccCCCCCc-----ccEEEEEEEEc--CCc---EEEEEEEcCCC--cccccccccCCCChhhhccCCCCHHHHH
Q 010743 144 MYAVDCEMVLCEDGS-----EGLVRLCVVDR--NLK---VTIDELVKPEK--AVADYRSEITGLTADDLVGVTCSLAEIQ 211 (502)
Q Consensus 144 ~VaID~ETTGl~~g~-----~~I~rVsvVd~--~G~---vi~d~LVkP~~--~I~dy~T~ihGIT~e~L~~ap~~~~dV~ 211 (502)
||+|||||||++++. ++|++|++|.. ++. ..|++||+|.. +|+++++.+||||++++.++| ++.+|+
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~-~~~~vl 79 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAP-SFPEVL 79 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCC-CHHHHH
Confidence 689999999999764 68999999965 333 24999999998 999999999999999999998 999999
Q ss_pred HHHHHhhcCCC--EEEEEchhhHHHHHccc------------CCCccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCC
Q 010743 212 KRMKKLLSNGT--ILVGHSLNNDLEVLKLD------------HPRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKK 276 (502)
Q Consensus 212 ~~l~~fl~~g~--ILVGHnl~fDl~fLk~~------------~p~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~ 276 (502)
.+|.+|+ ++. .+++|+..||..+|... ..+++|+..+++...+ ...++|..|| .+||++..
T Consensus 80 ~~~~~~l-~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l~-~~~gi~~~-- 155 (176)
T cd06133 80 KEFLEWL-GKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKAL-EYLGLEFE-- 155 (176)
T ss_pred HHHHHHH-HhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHHH-HHCCCCCC--
Confidence 9999999 565 56666669998877652 1137999999999887 5699999999 77899876
Q ss_pred CCCCCHHHHHHHHHHHHHHH
Q 010743 277 GTPHNCLDDASAAMKLVLAI 296 (502)
Q Consensus 277 ~~~HdAleDA~Ata~L~~~~ 296 (502)
+..|+|+.||++|++||+++
T Consensus 156 ~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 156 GRHHRGLDDARNIARILKRL 175 (176)
T ss_pred CCCcCcHHHHHHHHHHHHHh
Confidence 35899999999999999875
No 41
>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=99.90 E-value=3.1e-23 Score=185.38 Aligned_cols=144 Identities=22% Similarity=0.303 Sum_probs=126.6
Q ss_pred EEEEEeccCCCCCcccEEEEEEEEcCC----cEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhcC
Q 010743 145 YAVDCEMVLCEDGSEGLVRLCVVDRNL----KVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSN 220 (502)
Q Consensus 145 VaID~ETTGl~~g~~~I~rVsvVd~~G----~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~~ 220 (502)
|+|||||||+++...+|++|++|..++ ...|+.||+|+..++++.+.+||||++++.+++ ++.+++.+|.+++ .
T Consensus 1 v~~D~Ettg~~~~~~~iiei~~v~~~~~~~~~~~~~~~i~p~~~~~~~~~~~~gi~~~~~~~~~-~~~~~~~~~~~~l-~ 78 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAP-PFEEVLPEFLEFL-G 78 (159)
T ss_pred CeEEeeCCCcCCCCCeEEEEEEEEEECCcChhhhhheeeCcCCcCCHhheeccCCCHHHHhcCC-CHHHHHHHHHHHH-C
Confidence 579999999998777899999998743 235999999999999999999999999999998 9999999999999 7
Q ss_pred CCEEEEEchhhHHHHHcccC---------CCccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCCCCCCCHHHHHHHHH
Q 010743 221 GTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAM 290 (502)
Q Consensus 221 g~ILVGHnl~fDl~fLk~~~---------p~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~Ata 290 (502)
+.++||||+.||+.+|+... ..++||..+++...+ ...++|..+...++|++.. .+|+|++||++|+
T Consensus 79 ~~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~~---~~H~Al~Da~~t~ 155 (159)
T cd06127 79 GRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLE---GAHRALADALATA 155 (159)
T ss_pred CCEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCCC---CCCCcHHHHHHHH
Confidence 79999999999999998742 247999999999887 6778999983367787654 4899999999999
Q ss_pred HHH
Q 010743 291 KLV 293 (502)
Q Consensus 291 ~L~ 293 (502)
+||
T Consensus 156 ~l~ 158 (159)
T cd06127 156 ELL 158 (159)
T ss_pred HHh
Confidence 997
No 42
>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=99.90 E-value=1.6e-23 Score=198.53 Aligned_cols=144 Identities=18% Similarity=0.203 Sum_probs=118.8
Q ss_pred EEEEEeccCCCCCcccEEEEEEEEcCC--cEE--EEEEEcCCC--cccccccccCCCChhhhcc-CCCCHHHHHHHHHHh
Q 010743 145 YAVDCEMVLCEDGSEGLVRLCVVDRNL--KVT--IDELVKPEK--AVADYRSEITGLTADDLVG-VTCSLAEIQKRMKKL 217 (502)
Q Consensus 145 VaID~ETTGl~~g~~~I~rVsvVd~~G--~vi--~d~LVkP~~--~I~dy~T~ihGIT~e~L~~-ap~~~~dV~~~l~~f 217 (502)
++||+||||+++..++|++|++|..++ .++ |++||+|.. +++...+.+||||++||.+ +| ++.+++.+|..|
T Consensus 1 ~~~D~ETTGl~~~~d~Iieig~v~v~~~~~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~-~~~~~l~~~~~~ 79 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQFAAIRTDENFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGL-SEYEFIAKIHRL 79 (183)
T ss_pred CEEEeecCCCCCCCCceEEEEEEEECCCCCCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCC-CHHHHHHHHHHH
Confidence 479999999999888999999997643 333 889999874 5677889999999999999 78 899999999999
Q ss_pred hc-CCCEEEEEc-hhhHHHHHcccCC---------------CccchHHHhhhhc---C-----------CCCCCHHHHHH
Q 010743 218 LS-NGTILVGHS-LNNDLEVLKLDHP---------------RVIDTSLIFKYVD---E-----------YRRPSLYNLCK 266 (502)
Q Consensus 218 l~-~g~ILVGHn-l~fDl~fLk~~~p---------------~vIDT~~L~r~~~---~-----------~~~~sL~~La~ 266 (502)
+. +++++|||| +.||+.||+.... ..+||..+++... + ..+++|.+||
T Consensus 80 ~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L~~l~- 158 (183)
T cd06138 80 FNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKLEDLA- 158 (183)
T ss_pred HccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhHHHHH-
Confidence 95 468999997 8999999986321 2478887776532 1 2468899999
Q ss_pred HHcCCccCCCCCCCCHHHHHHHHHHHH
Q 010743 267 SVLGYEIRKKGTPHNCLDDASAAMKLV 293 (502)
Q Consensus 267 ~~Lgi~iq~~~~~HdAleDA~Ata~L~ 293 (502)
.++|++.. .+|+|++||++|++|.
T Consensus 159 ~~~gi~~~---~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 159 QANGIEHS---NAHDALSDVEATIALA 182 (183)
T ss_pred HHCCCCcc---ccccHHHHHHHHHHHh
Confidence 67899874 3899999999999985
No 43
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.90 E-value=6.4e-23 Score=201.03 Aligned_cols=154 Identities=23% Similarity=0.318 Sum_probs=136.3
Q ss_pred CcEEEEEEeccCCCCCcccEEEEEEEEc-CCcEE---EEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHh
Q 010743 142 NIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT---IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (502)
Q Consensus 142 ~~~VaID~ETTGl~~g~~~I~rVsvVd~-~G~vi---~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~f 217 (502)
.++++||+||||+++..++|++|++|.. ++.++ |+.||+|+.+|+++++++||||.+||.++| .|.+|++.+.+|
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p-~~~~v~~~~~~~ 91 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAP-KFAEVLPEFLDF 91 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcCC-CHHHHHHHHHHH
Confidence 5899999999999987778999999986 44333 889999999999999999999999999999 999999999999
Q ss_pred hcCC-CEEEEEchhhHHHHHcccC---------CCccchHHHhhhhcCC-CCCCHHHHHHHHcCCccCCCCCCCCHHHHH
Q 010743 218 LSNG-TILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDEY-RRPSLYNLCKSVLGYEIRKKGTPHNCLDDA 286 (502)
Q Consensus 218 l~~g-~ILVGHnl~fDl~fLk~~~---------p~vIDT~~L~r~~~~~-~~~sL~~La~~~Lgi~iq~~~~~HdAleDA 286 (502)
+ ++ +++||||+.||+.||+... ..++||..+.+...+. ..++|+.|| .++|++.. ....|+|+.||
T Consensus 92 i-~~~~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~~~L~~l~-~~~gi~~~-~~~~H~Al~Da 168 (243)
T COG0847 92 I-GGLRLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDALA-ERLGIDRN-PFHPHRALFDA 168 (243)
T ss_pred H-CCCCeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCccchHHHHH-HHcCCCcC-CcCCcchHHHH
Confidence 9 66 9999999999999998631 2368999999999984 899999999 58899954 23479999999
Q ss_pred HHHHHHHHHHHHh
Q 010743 287 SAAMKLVLAIIER 299 (502)
Q Consensus 287 ~Ata~L~~~~l~~ 299 (502)
.+++.+|..++..
T Consensus 169 ~~~a~~~~~~~~~ 181 (243)
T COG0847 169 LALAELFLLLQTG 181 (243)
T ss_pred HHHHHHHHHHHhc
Confidence 9999999998874
No 44
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.89 E-value=1.6e-22 Score=205.68 Aligned_cols=151 Identities=16% Similarity=0.249 Sum_probs=122.3
Q ss_pred CCCcEEEEEEeccCCCCCcccEEEEEEEEc----CCcE-----EEEEEEcCCCcccccccccCCCChhhhccCCCCHHHH
Q 010743 140 TSNIMYAVDCEMVLCEDGSEGLVRLCVVDR----NLKV-----TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEI 210 (502)
Q Consensus 140 ~~~~~VaID~ETTGl~~g~~~I~rVsvVd~----~G~v-----i~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV 210 (502)
.+..+|+||+||||+++..++|++|++|.. +|.+ .|+.||+|..+|+..++.+||||++||.++| ...
T Consensus 35 ~~~~~vvlD~ETTGLd~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~~I~~~~t~IhGIt~e~v~~~~-~~~-- 111 (294)
T PRK09182 35 FVRLGVILDTETTGLDPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQT-IDP-- 111 (294)
T ss_pred CCCeEEEEEeeCCCCCCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCCCCCHHHHHhcCCCHHHHhcCC-CcH--
Confidence 346799999999999998889999999965 3542 3889999999999999999999999999998 432
Q ss_pred HHHHHHhhcCCCEEEEEchhhHHHHHcccCC-----CccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCCCCCCCHHH
Q 010743 211 QKRMKKLLSNGTILVGHSLNNDLEVLKLDHP-----RVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLD 284 (502)
Q Consensus 211 ~~~l~~fl~~g~ILVGHnl~fDl~fLk~~~p-----~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAle 284 (502)
..|..|+..+.+|||||+.||+.||+...+ .+.||........+ ..+++|.+|| .++|.. . .+|+|+.
T Consensus 112 -~~l~~fl~~~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~~~~~~~~~~kL~~La-~~~g~~-~---~aHrAl~ 185 (294)
T PRK09182 112 -AAVDALIAPADLIIAHNAGFDRPFLERFSPVFATKPWACSVSEIDWSARGFEGTKLGYLA-GQAGFF-H---EGHRAVD 185 (294)
T ss_pred -HHHHHHhcCCCEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHhhccccCCCCCHHHHH-HHcCCC-C---CCcChHH
Confidence 356777855679999999999999987432 35787765544333 5789999999 667833 2 3899999
Q ss_pred HHHHHHHHHHHHHHh
Q 010743 285 DASAAMKLVLAIIER 299 (502)
Q Consensus 285 DA~Ata~L~~~~l~~ 299 (502)
||.||++||..++..
T Consensus 186 Da~Ata~ll~~~l~~ 200 (294)
T PRK09182 186 DCQALLELLARPLPE 200 (294)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999977754
No 45
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=99.88 E-value=2.7e-24 Score=192.36 Aligned_cols=145 Identities=25% Similarity=0.414 Sum_probs=122.3
Q ss_pred EEEEEeccCCCCCcccEEEEEEEEcC-----CcEEEEEEEcCCCc--ccccccccCCCChhhhccCCCCHHHHHHHHHHh
Q 010743 145 YAVDCEMVLCEDGSEGLVRLCVVDRN-----LKVTIDELVKPEKA--VADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (502)
Q Consensus 145 VaID~ETTGl~~g~~~I~rVsvVd~~-----G~vi~d~LVkP~~~--I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~f 217 (502)
|+|||||||+++..++|++|++|..+ +...|++||+|..+ |+++++.+||||.++|.+++ ++.+++.+|.++
T Consensus 1 v~~D~Ettg~~~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~-~~~~~~~~~~~~ 79 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAP-SFEEALDEFEEF 79 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHC-EHHHHHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCC-cHHHHHHhhhhh
Confidence 68999999999877789999999762 23469999999998 99999999999999999999 999999999999
Q ss_pred hcCCCEEEEEchhhHHHHHcc--------cCC---CccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCCCCCCCHHHH
Q 010743 218 LSNGTILVGHSLNNDLEVLKL--------DHP---RVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDD 285 (502)
Q Consensus 218 l~~g~ILVGHnl~fDl~fLk~--------~~p---~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAleD 285 (502)
+.++.++||||+.||..++.. .+| .++||..+.+...+ ...++|+.|| .++|++... .+|+|++|
T Consensus 80 ~~~~~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~-~~~~~~~~~--~~H~Al~D 156 (164)
T PF00929_consen 80 LKKNDILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNRKKYSLDDLA-EYFGIPFDG--TAHDALDD 156 (164)
T ss_dssp HHHHTEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHHHHHSHHHHH-HHTTSSSTS--TTTSHHHH
T ss_pred hhcccccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhccccCCHHHHH-HHcCCCCCC--CCcChHHH
Confidence 966899999998888766654 233 36888877776655 4448999999 677888653 27999999
Q ss_pred HHHHHHHH
Q 010743 286 ASAAMKLV 293 (502)
Q Consensus 286 A~Ata~L~ 293 (502)
|++|++||
T Consensus 157 a~~t~~l~ 164 (164)
T PF00929_consen 157 ARATAELF 164 (164)
T ss_dssp HHHHHHHH
T ss_pred HHHHhCcC
Confidence 99999997
No 46
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.85 E-value=1.5e-20 Score=202.13 Aligned_cols=158 Identities=17% Similarity=0.182 Sum_probs=126.8
Q ss_pred CCCcEEEEEEeccCCCCCcccEEEEEEEEcCC--cE---EEEEEEcCCCc--ccccccccCCCChhhhccCCCCHHHHHH
Q 010743 140 TSNIMYAVDCEMVLCEDGSEGLVRLCVVDRNL--KV---TIDELVKPEKA--VADYRSEITGLTADDLVGVTCSLAEIQK 212 (502)
Q Consensus 140 ~~~~~VaID~ETTGl~~g~~~I~rVsvVd~~G--~v---i~d~LVkP~~~--I~dy~T~ihGIT~e~L~~ap~~~~dV~~ 212 (502)
....||++|+||||+++..++|++|++|..++ .+ .++.||+|... +++..+.+||||++||.+++.+..++..
T Consensus 4 ~~~~fvv~D~ETTGLdP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~~ 83 (476)
T PRK11779 4 MQPTFLWHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEFAA 83 (476)
T ss_pred CCCcEEEEEEECCCCCCCCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHHHH
Confidence 34679999999999999889999999997633 23 38899999863 3567899999999999888778999999
Q ss_pred HHHHhhc-CCCEEEEEc-hhhHHHHHcccCC------------------CccchHHHhhhhcC-----------CCCCCH
Q 010743 213 RMKKLLS-NGTILVGHS-LNNDLEVLKLDHP------------------RVIDTSLIFKYVDE-----------YRRPSL 261 (502)
Q Consensus 213 ~l~~fl~-~g~ILVGHn-l~fDl~fLk~~~p------------------~vIDT~~L~r~~~~-----------~~~~sL 261 (502)
.|.+++. +++++|||| +.||..||+.... .++|+++++....+ ..+++|
T Consensus 84 ~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rL 163 (476)
T PRK11779 84 RIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKL 163 (476)
T ss_pred HHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCcH
Confidence 9999993 489999997 7999999877321 12466665544321 256999
Q ss_pred HHHHHHHcCCccCCCCCCCCHHHHHHHHHHHHHHHHHhcc
Q 010743 262 YNLCKSVLGYEIRKKGTPHNCLDDASAAMKLVLAIIERRV 301 (502)
Q Consensus 262 ~~La~~~Lgi~iq~~~~~HdAleDA~Ata~L~~~~l~~g~ 301 (502)
..|| .++|++.. .+|+|++||+||++|+..+.++-|
T Consensus 164 e~L~-~~~gI~~~---~AHdALsDa~aT~~la~~l~~~qP 199 (476)
T PRK11779 164 EHLT-KANGIEHE---NAHDAMSDVYATIAMAKLIKQKQP 199 (476)
T ss_pred HHHH-HHcCCCCC---CCCCcHHHHHHHHHHHHHHHHhCh
Confidence 9999 66799864 489999999999999998886643
No 47
>PRK05359 oligoribonuclease; Provisional
Probab=99.85 E-value=1.4e-20 Score=178.92 Aligned_cols=145 Identities=16% Similarity=0.217 Sum_probs=117.5
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEcCCc--EE---EEEEEcCCCc----ccccccccC---CCChhhhccCCCCHH
Q 010743 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDRNLK--VT---IDELVKPEKA----VADYRSEIT---GLTADDLVGVTCSLA 208 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~g~~~I~rVsvVd~~G~--vi---~d~LVkP~~~----I~dy~T~ih---GIT~e~L~~ap~~~~ 208 (502)
..+||+|||||||+++..++|++|++|..++. ++ |+.+|+|... ++.+++.+| |||+++++++| ++.
T Consensus 2 ~~~~vvlD~ETTGLdp~~d~IieIgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~-~~~ 80 (181)
T PRK05359 2 EDNLIWIDLEMTGLDPERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTV-SEA 80 (181)
T ss_pred CCcEEEEEeecCCCCCCCCeEEEEEEEEEcCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCC-CHH
Confidence 35799999999999998889999999976542 23 8899999875 467788887 99999999999 999
Q ss_pred HHHHHHHHhhc-----CCCEEEEEchhhHHHHHccc--------CCCccc--hH-HHhhhhcCCCCCCHHHHHHHHcCCc
Q 010743 209 EIQKRMKKLLS-----NGTILVGHSLNNDLEVLKLD--------HPRVID--TS-LIFKYVDEYRRPSLYNLCKSVLGYE 272 (502)
Q Consensus 209 dV~~~l~~fl~-----~g~ILVGHnl~fDl~fLk~~--------~p~vID--T~-~L~r~~~~~~~~sL~~La~~~Lgi~ 272 (502)
+|+.+|++|+. ++++|||||+.||+.||+.. +.+++| |. .+++.++|. + +++++
T Consensus 81 e~~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~tl~~l~r~~~P~----~------~~~~~ 150 (181)
T PRK05359 81 EAEAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLDVSTLKELARRWKPE----I------LNGFK 150 (181)
T ss_pred HHHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhcccCCCcccchhHHHHHHHHhChh----h------hhCCC
Confidence 99999999995 36899999999999999974 234677 55 577766651 1 23554
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHHHHHh
Q 010743 273 IRKKGTPHNCLDDASAAMKLVLAIIER 299 (502)
Q Consensus 273 iq~~~~~HdAleDA~Ata~L~~~~l~~ 299 (502)
.. ..|||++||+++.++|.++.+.
T Consensus 151 ~~---~~HRal~D~~~s~~~~~~~~~~ 174 (181)
T PRK05359 151 KQ---GTHRALADIRESIAELKYYREH 174 (181)
T ss_pred Cc---CCcccHHHHHHHHHHHHHHHHH
Confidence 33 3799999999999999988764
No 48
>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=99.84 E-value=8.4e-21 Score=178.68 Aligned_cols=142 Identities=16% Similarity=0.207 Sum_probs=112.2
Q ss_pred EEEEEEeccCCCCCcccEEEEEEEEcCCc--E---EEEEEEcCCCcccc----ccccc---CCCChhhhccCCCCHHHHH
Q 010743 144 MYAVDCEMVLCEDGSEGLVRLCVVDRNLK--V---TIDELVKPEKAVAD----YRSEI---TGLTADDLVGVTCSLAEIQ 211 (502)
Q Consensus 144 ~VaID~ETTGl~~g~~~I~rVsvVd~~G~--v---i~d~LVkP~~~I~d----y~T~i---hGIT~e~L~~ap~~~~dV~ 211 (502)
+++||+||||+++..++|++|++|..++. . .|+.+|+|..+++. +...+ ||||++|++++| ++.+|+
T Consensus 1 lv~iD~ETTGl~p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~-~~~~vl 79 (173)
T cd06135 1 LVWIDLEMTGLDPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTV-TLAQAE 79 (173)
T ss_pred CEEEEEecCCCCCCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCC-CHHHHH
Confidence 58999999999987788999999987552 2 39999999987653 44455 599999999999 999999
Q ss_pred HHHHHhhcC-----CCEEEEEchhhHHHHHcccC--------CCccch---HHHhhhhcCCCCCCHHHHHHHHcCCccCC
Q 010743 212 KRMKKLLSN-----GTILVGHSLNNDLEVLKLDH--------PRVIDT---SLIFKYVDEYRRPSLYNLCKSVLGYEIRK 275 (502)
Q Consensus 212 ~~l~~fl~~-----g~ILVGHnl~fDl~fLk~~~--------p~vIDT---~~L~r~~~~~~~~sL~~La~~~Lgi~iq~ 275 (502)
.+|.+|+.. +.++||||+.||+.||+... .+.+|| ..+++.+.|.. ++ ++++.
T Consensus 80 ~~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~~~l~~l~~~l~p~~-~~--------~~~~~-- 148 (173)
T cd06135 80 AELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDVSSIKELARRWYPEI-YR--------KAPKK-- 148 (173)
T ss_pred HHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHHhccCCcchhhHHHHHHHHHHhCcHh-hh--------cCCCC--
Confidence 999999943 37999999999999998742 346887 44666665511 11 34433
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHH
Q 010743 276 KGTPHNCLDDASAAMKLVLAIIE 298 (502)
Q Consensus 276 ~~~~HdAleDA~Ata~L~~~~l~ 298 (502)
+..|+|++||.+|+.+|.++++
T Consensus 149 -~~~HrAl~Da~~~~~~~~~~~~ 170 (173)
T cd06135 149 -KGTHRALDDIRESIAELKYYRE 170 (173)
T ss_pred -CCCcchHHHHHHHHHHHHHHHH
Confidence 2489999999999999998875
No 49
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.83 E-value=9.7e-20 Score=197.98 Aligned_cols=158 Identities=16% Similarity=0.242 Sum_probs=127.6
Q ss_pred CcEEEEEEeccCCCCC---cccEEEEEEEEc---CCcEE--EEEEEcCCC--cccccccccCCCChhhhccCCCCHHHHH
Q 010743 142 NIMYAVDCEMVLCEDG---SEGLVRLCVVDR---NLKVT--IDELVKPEK--AVADYRSEITGLTADDLVGVTCSLAEIQ 211 (502)
Q Consensus 142 ~~~VaID~ETTGl~~g---~~~I~rVsvVd~---~G~vi--~d~LVkP~~--~I~dy~T~ihGIT~e~L~~ap~~~~dV~ 211 (502)
..||+||+||||+++. .++|++|++|.. +|.++ |++||+|.. +|+++++.+||||++||+++| +|.+|+
T Consensus 56 d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap-~F~eVl 134 (582)
T PTZ00315 56 DAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRAD-PFPVVY 134 (582)
T ss_pred CeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCC-CHHHHH
Confidence 6899999999998753 358999999975 56554 899999987 699999999999999999999 999999
Q ss_pred HHHHHhhcCC---------CEEEEEchhhHHH-HHccc--------CC----CccchH-HHhhhhcC------------C
Q 010743 212 KRMKKLLSNG---------TILVGHSLNNDLE-VLKLD--------HP----RVIDTS-LIFKYVDE------------Y 256 (502)
Q Consensus 212 ~~l~~fl~~g---------~ILVGHnl~fDl~-fLk~~--------~p----~vIDT~-~L~r~~~~------------~ 256 (502)
.+|.+|+.+. ..+|+||..||+. ||... .| .++|.. .+.+..++ .
T Consensus 135 ~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p~~~~~~~~~~~~~ 214 (582)
T PTZ00315 135 CEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFGNGSGCGGGATPPL 214 (582)
T ss_pred HHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCcccccccccccccc
Confidence 9999999322 3699999999995 77431 12 245643 34444332 3
Q ss_pred CCCCHHHHHHHHcCCccCCCCCCCCHHHHHHHHHHHHHHHHHhcccC
Q 010743 257 RRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLVLAIIERRVDN 303 (502)
Q Consensus 257 ~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~Ata~L~~~~l~~g~~~ 303 (502)
..++|.+++ .++|+++. |.+|+|++||++|++||.++++.|.-+
T Consensus 215 ~~~~L~~al-~~lgL~~e--Gr~HrAlDDA~ntA~L~~~Ll~~g~~~ 258 (582)
T PTZ00315 215 GPSDMPDML-QMLGLPLQ--GRHHSGIDDCRNIAAVLCELLRRGLVI 258 (582)
T ss_pred CCcCHHHHH-HHCCCCCC--CCCcCcHHHHHHHHHHHHHHHHcCCEE
Confidence 568999999 77899975 458999999999999999999987643
No 50
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.83 E-value=1.9e-20 Score=221.30 Aligned_cols=159 Identities=20% Similarity=0.334 Sum_probs=139.9
Q ss_pred CCCCcEEEEEEeccCCCCCcccEEEEEEEEc-CCcEE--EEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHH
Q 010743 139 MTSNIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMK 215 (502)
Q Consensus 139 ~~~~~~VaID~ETTGl~~g~~~I~rVsvVd~-~G~vi--~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~ 215 (502)
....++|++|+||||+++..++|++|++|.. +|.++ |+.||+|..+|+++++++||||++||.+++ ++.+|+++|.
T Consensus 416 L~~~~~VVfDLETTGL~~~~deIIEIgAV~V~~G~iie~F~~~V~P~~~I~~~~~~LTGIT~e~L~~ap-s~~EaL~~f~ 494 (1437)
T PRK00448 416 LKDATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAP-SIEEVLPKFK 494 (1437)
T ss_pred hccCcEEEEEhhhcCCCCchhhhheeeeEEEeCCeEeeeEEEEECCCCCCCHHHHHHhCCCHHHHcCCC-CHHHHHHHHH
Confidence 3456899999999999998888999999876 56554 999999999999999999999999999999 9999999999
Q ss_pred HhhcCCCEEEEEchhhHHHHHccc-----C----CCccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCCCCCCCHHHH
Q 010743 216 KLLSNGTILVGHSLNNDLEVLKLD-----H----PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDD 285 (502)
Q Consensus 216 ~fl~~g~ILVGHnl~fDl~fLk~~-----~----p~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAleD 285 (502)
+|+ +|.+|||||+.||+.||+.. . ..++||+.+++...+ ..+++|..|| .++|++... +|+|+.|
T Consensus 495 ~fi-gg~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k~~kL~~LA-k~lGL~~~~---~HrAl~D 569 (1437)
T PRK00448 495 EFC-GDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLA-KKFGVELEH---HHRADYD 569 (1437)
T ss_pred HHh-CCCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccccccHHHHH-HHcCCCCCC---CcChHHH
Confidence 999 89999999999999999642 1 237999999998887 7899999999 668998753 7999999
Q ss_pred HHHHHHHHHHHHHhcccC
Q 010743 286 ASAAMKLVLAIIERRVDN 303 (502)
Q Consensus 286 A~Ata~L~~~~l~~g~~~ 303 (502)
|.+|++||.++++...+.
T Consensus 570 A~aTa~lf~~ll~~l~~~ 587 (1437)
T PRK00448 570 AEATAYLLIKFLKDLKEK 587 (1437)
T ss_pred HHHHHHHHHHHHHHHHHc
Confidence 999999999998765433
No 51
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=99.16 E-value=9.4e-11 Score=110.18 Aligned_cols=148 Identities=22% Similarity=0.318 Sum_probs=109.7
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEE--cCCcEE---EEEEEcCCC----cccccccc---cCCCChhhhccCCCCHH
Q 010743 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVD--RNLKVT---IDELVKPEK----AVADYRSE---ITGLTADDLVGVTCSLA 208 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~g~~~I~rVsvVd--~~G~vi---~d~LVkP~~----~I~dy~T~---ihGIT~e~L~~ap~~~~ 208 (502)
..++|.|||||||++-+.+.|++|+.+- ++.+++ ++..|+-+. .+.+|... -+|+|..-++..- +++
T Consensus 25 ~q~lVWiD~EMTGLdvekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~-tl~ 103 (208)
T KOG3242|consen 25 KQPLVWIDCEMTGLDVEKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKI-TLA 103 (208)
T ss_pred cCceEEEeeeccccccccceeEEEEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhc-cHH
Confidence 3579999999999999999999999884 444443 677777554 34555553 3689999999887 999
Q ss_pred HHHHHHHHhhc-----CCCEEEEEchhhHHHHHccc--------CCCccchHHHhhhhcCCCCCCHHHHHHHHcCCccCC
Q 010743 209 EIQKRMKKLLS-----NGTILVGHSLNNDLEVLKLD--------HPRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRK 275 (502)
Q Consensus 209 dV~~~l~~fl~-----~g~ILVGHnl~fDl~fLk~~--------~p~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~ 275 (502)
++-.++++|+. +.++|-|.++.-|..||... |.++||++. .+.||++++- .++.
T Consensus 104 ~aEnevl~yikk~ip~~~~~laGNSV~~DrlFl~k~mPk~~~~lhyrivDVSt------------IkeL~~Rw~P-~~~~ 170 (208)
T KOG3242|consen 104 DAENEVLEYIKKHIPKGKCPLAGNSVYMDRLFLKKYMPKLIKHLHYRIVDVST------------IKELARRWYP-DIKA 170 (208)
T ss_pred HHHHHHHHHHHHhCCCCCCCccCcchhhHHHHHHHHhHHHHHhcceeeeeHHH------------HHHHHHHhCc-hhhc
Confidence 99999999983 56899999999999999874 456788874 3344444431 1111
Q ss_pred ----CCCCCCHHHHHHHHHHHHHHHHHhccc
Q 010743 276 ----KGTPHNCLDDASAAMKLVLAIIERRVD 302 (502)
Q Consensus 276 ----~~~~HdAleDA~Ata~L~~~~l~~g~~ 302 (502)
....|+|++|.+-+..-++++...-+.
T Consensus 171 ~aPkK~~~HrAldDI~ESI~ELq~Yr~nifk 201 (208)
T KOG3242|consen 171 RAPKKKATHRALDDIRESIKELQYYRENIFK 201 (208)
T ss_pred cCcccccccchHHHHHHHHHHHHHHHHHhcc
Confidence 124799999999988877777765443
No 52
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=99.13 E-value=2.3e-10 Score=106.68 Aligned_cols=147 Identities=22% Similarity=0.299 Sum_probs=105.7
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEE--EcCCcEE---EEEEEcCC----Cccccccccc---CCCChhhhccCCCCHH
Q 010743 141 SNIMYAVDCEMVLCEDGSEGLVRLCVV--DRNLKVT---IDELVKPE----KAVADYRSEI---TGLTADDLVGVTCSLA 208 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~g~~~I~rVsvV--d~~G~vi---~d~LVkP~----~~I~dy~T~i---hGIT~e~L~~ap~~~~ 208 (502)
..++|.|||||||++++.++|++|+.+ |.+.+++ .+.-|.-. ..+.+|+++- +|++..-.+..- +..
T Consensus 5 ~~nLiWIDlEMTGLd~~~drIIEiA~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~-t~~ 83 (184)
T COG1949 5 KNNLIWIDLEMTGLDPERDRIIEIATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTV-TEA 83 (184)
T ss_pred CCceEEEeeeeccCCcCcceEEEEEEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhc-cHH
Confidence 468999999999999999999999987 4455544 33344432 2456777765 477776666665 899
Q ss_pred HHHHHHHHhhc-----CCCEEEEEchhhHHHHHcccCC--------CccchHHHhhhhcCCCCCCHHHHHHHHcCCccCC
Q 010743 209 EIQKRMKKLLS-----NGTILVGHSLNNDLEVLKLDHP--------RVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRK 275 (502)
Q Consensus 209 dV~~~l~~fl~-----~g~ILVGHnl~fDl~fLk~~~p--------~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~ 275 (502)
++-.++++||. +-+++.|.++.-|.+||-...| |.+|++ +|+.||+++ ..+|..
T Consensus 84 ~aE~~~l~flkkwvp~~~spicGNSI~qDRrFl~r~MP~Le~yfHYR~lDVS------------TlKELa~RW-~P~i~~ 150 (184)
T COG1949 84 EAEAQTLDFLKKWVPKGVSPICGNSIAQDRRFLFRYMPKLEAYFHYRYLDVS------------TLKELARRW-NPEILA 150 (184)
T ss_pred HHHHHHHHHHHHhCCCCCCCCccchhhHHHHHHHHHhhhHHHHhhhHhhhHH------------HHHHHHHhh-CcHhhh
Confidence 99999888883 4589999999999999987544 456665 455555433 222221
Q ss_pred ---CCCCCCHHHHHHHHHHHHHHHHHhcc
Q 010743 276 ---KGTPHNCLDDASAAMKLVLAIIERRV 301 (502)
Q Consensus 276 ---~~~~HdAleDA~Ata~L~~~~l~~g~ 301 (502)
.+..|.|++|.+-+..=+.++.++..
T Consensus 151 ~~~K~~~H~Al~DI~ESI~EL~~YR~~f~ 179 (184)
T COG1949 151 GFKKGGTHRALDDIRESIAELRYYREHFL 179 (184)
T ss_pred ccccccchhHHHHHHHHHHHHHHHHHHhc
Confidence 13589999999998887777776543
No 53
>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=99.03 E-value=1.8e-09 Score=102.95 Aligned_cols=121 Identities=17% Similarity=0.125 Sum_probs=94.3
Q ss_pred EEEEEEeccCC----CCCcccEEEEEEEEc-CCcEE-EEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHh
Q 010743 144 MYAVDCEMVLC----EDGSEGLVRLCVVDR-NLKVT-IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (502)
Q Consensus 144 ~VaID~ETTGl----~~g~~~I~rVsvVd~-~G~vi-~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~f 217 (502)
++++|+||+|. ++..++|+.|+++.. +|... +.....|.... .. ||+..++...+ +..+++.+|.++
T Consensus 1 v~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~~~g~~~~~~~~~~~~~~~---~~---~i~~~~v~~~~-~E~~lL~~f~~~ 73 (199)
T cd05160 1 VLSFDIETTPPVGGPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDD---IE---FIDGIEVEYFA-DEKELLKRFFDI 73 (199)
T ss_pred CccEEEeecCCCCCcCCCCCCEEEEEEEEeeCCceeeEEEeecccCCc---CC---CCCCceEEEeC-CHHHHHHHHHHH
Confidence 36899999998 667789999999986 67643 32222332211 11 99999999999 999999999999
Q ss_pred hcCC---CEEEEEch-hhHHHHHccc-------C-----------------------CC-ccchHHHhhhhcCCCCCCHH
Q 010743 218 LSNG---TILVGHSL-NNDLEVLKLD-------H-----------------------PR-VIDTSLIFKYVDEYRRPSLY 262 (502)
Q Consensus 218 l~~g---~ILVGHnl-~fDl~fLk~~-------~-----------------------p~-vIDT~~L~r~~~~~~~~sL~ 262 (502)
+ .. .++||||. .||+.+|... . .+ ++|+..+++...+..+++|+
T Consensus 74 i-~~~dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~~l~sy~L~ 152 (199)
T cd05160 74 I-REYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFKLKSYTLD 152 (199)
T ss_pred H-HhcCCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhcCcccCCHH
Confidence 9 44 59999999 8999999651 1 11 58999999887777889999
Q ss_pred HHHHHHcCCc
Q 010743 263 NLCKSVLGYE 272 (502)
Q Consensus 263 ~La~~~Lgi~ 272 (502)
++|+.+||..
T Consensus 153 ~v~~~~l~~~ 162 (199)
T cd05160 153 AVAEELLGEG 162 (199)
T ss_pred HHHHHHhCCC
Confidence 9998888764
No 54
>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=98.91 E-value=3.6e-08 Score=92.38 Aligned_cols=142 Identities=20% Similarity=0.156 Sum_probs=100.7
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhcC
Q 010743 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSN 220 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~~ 220 (502)
...++++|+|++|+.+....|+.+++....+..+| .-+.+ +.+ .+.+ ++.++...|..++..
T Consensus 4 ~~~~~a~d~e~~~~~~~~~~i~~l~~~~~~~~~~~-~~~~~--------~~~--------~~~~-~~~~~~~~l~~~l~~ 65 (193)
T cd06139 4 KAKVFAFDTETTSLDPMQAELVGISFAVEPGEAYY-IPLGH--------DYG--------GEQL-PREEVLAALKPLLED 65 (193)
T ss_pred cCCeEEEEeecCCCCcCCCeEEEEEEEcCCCCEEE-EecCC--------Ccc--------ccCC-CHHHHHHHHHHHHhC
Confidence 35789999999999876667888988866554322 10111 111 1344 688899999999943
Q ss_pred C-CEEEEEchhhHHHHHcccC----CCccchHHHhhhhcCCC-CCCHHHHHHHHcCCccCC---------------CC--
Q 010743 221 G-TILVGHSLNNDLEVLKLDH----PRVIDTSLIFKYVDEYR-RPSLYNLCKSVLGYEIRK---------------KG-- 277 (502)
Q Consensus 221 g-~ILVGHnl~fDl~fLk~~~----p~vIDT~~L~r~~~~~~-~~sL~~La~~~Lgi~iq~---------------~~-- 277 (502)
. .++||||+.||+.+|.... ..+.||..+++.+.+.. +++|..|++.|+|..+.. ..
T Consensus 66 ~~~~~v~hn~k~d~~~l~~~gi~~~~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~ 145 (193)
T cd06139 66 PSIKKVGQNLKFDLHVLANHGIELRGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPL 145 (193)
T ss_pred CCCcEEeeccHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccCH
Confidence 3 3799999999999997642 24799999999888833 679999999998765210 00
Q ss_pred --CCCCHHHHHHHHHHHHHHHHHhc
Q 010743 278 --TPHNCLDDASAAMKLVLAIIERR 300 (502)
Q Consensus 278 --~~HdAleDA~Ata~L~~~~l~~g 300 (502)
..|.|..||.++..|+..+.+.-
T Consensus 146 ~~~~~ya~~d~~~~~~l~~~l~~~l 170 (193)
T cd06139 146 EKAAEYAAEDADITLRLYELLKPKL 170 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 12358888999999998877643
No 55
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=98.90 E-value=5e-09 Score=103.79 Aligned_cols=158 Identities=16% Similarity=0.299 Sum_probs=119.1
Q ss_pred cEEEEEEeccCCCCCc----ccEEEEEEEEc----CCcE--EEEEEEcCCC--cccccccccCCCChhhhccCCCCHHHH
Q 010743 143 IMYAVDCEMVLCEDGS----EGLVRLCVVDR----NLKV--TIDELVKPEK--AVADYRSEITGLTADDLVGVTCSLAEI 210 (502)
Q Consensus 143 ~~VaID~ETTGl~~g~----~~I~rVsvVd~----~G~v--i~d~LVkP~~--~I~dy~T~ihGIT~e~L~~ap~~~~dV 210 (502)
-+++||+|+|--+... .+|++..+|-. .+.+ .|++||+|.. .+++|.+.+|||..++|..+| +|.+|
T Consensus 57 YLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~-~f~~v 135 (280)
T KOG0542|consen 57 YLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAP-TFPQV 135 (280)
T ss_pred eEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCC-CHHHH
Confidence 4679999999654332 37999998833 3332 4999999975 578999999999999999999 99999
Q ss_pred HHHHHHhhcC--------CCEEEEEchhhHH-HHHccc-------CC----CccchHHHhhhhcC-CCCCCHHHHHHHHc
Q 010743 211 QKRMKKLLSN--------GTILVGHSLNNDL-EVLKLD-------HP----RVIDTSLIFKYVDE-YRRPSLYNLCKSVL 269 (502)
Q Consensus 211 ~~~l~~fl~~--------g~ILVGHnl~fDl-~fLk~~-------~p----~vIDT~~L~r~~~~-~~~~sL~~La~~~L 269 (502)
+.+|..++.. ..-+|--+ .-|| .||... .| .+||.-..|+..+. ...-.+..+- +++
T Consensus 136 l~~f~~Wlr~~~~~~k~~~~Afvtdg-~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it~mL-e~~ 213 (280)
T KOG0542|consen 136 LSEFDSWLRKDSLGDKNGKFAFVTDG-DWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNITGML-EHY 213 (280)
T ss_pred HHHHHHHHHHhhcccccCceEEEeCc-hhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCHHHHH-HHh
Confidence 9999988831 12233222 3454 334332 22 26898888887766 3567888888 788
Q ss_pred CCccCCCCCCCCHHHHHHHHHHHHHHHHHhcccCCC
Q 010743 270 GYEIRKKGTPHNCLDDASAAMKLVLAIIERRVDNAV 305 (502)
Q Consensus 270 gi~iq~~~~~HdAleDA~Ata~L~~~~l~~g~~~~i 305 (502)
|++.. |..|+.++||+..+.|..+++..|....+
T Consensus 214 gL~f~--Gr~HsGiDDa~Nia~I~~kM~~dg~~~~I 247 (280)
T KOG0542|consen 214 GLQFE--GRAHSGIDDARNIARIAQKMIRDGAEFRI 247 (280)
T ss_pred CCccc--CCcccCchhHHHHHHHHHHHHhCCcEEEe
Confidence 99987 57999999999999999999998876555
No 56
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=98.88 E-value=2.5e-09 Score=100.45 Aligned_cols=153 Identities=24% Similarity=0.288 Sum_probs=116.7
Q ss_pred CcEEEEEEeccCCCCC----cccEEEEEEE--Ec-CCcE--EEEEEEcCCC--cccccccccCCCChhhhccCCCCHHHH
Q 010743 142 NIMYAVDCEMVLCEDG----SEGLVRLCVV--DR-NLKV--TIDELVKPEK--AVADYRSEITGLTADDLVGVTCSLAEI 210 (502)
Q Consensus 142 ~~~VaID~ETTGl~~g----~~~I~rVsvV--d~-~G~v--i~d~LVkP~~--~I~dy~T~ihGIT~e~L~~ap~~~~dV 210 (502)
..+++||+|.|--+.+ .-+|++|.+. +. +-.+ .|++||+|.. .+.+|+..+||||...|..+| -|..|
T Consensus 4 ~~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~ap-ifs~v 82 (210)
T COG5018 4 NSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAP-IFSMV 82 (210)
T ss_pred ceEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhccccc-hHHHH
Confidence 4588999999954422 2257666553 32 3333 3899999986 467899999999999999999 99999
Q ss_pred HHHHHHhhcCCCE----EEEEchhhHHHHHccc----C-C------CccchHHHhhhhcC-CCCCCHHHHHHHHcCCccC
Q 010743 211 QKRMKKLLSNGTI----LVGHSLNNDLEVLKLD----H-P------RVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIR 274 (502)
Q Consensus 211 ~~~l~~fl~~g~I----LVGHnl~fDl~fLk~~----~-p------~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq 274 (502)
+++|..++..-.+ -.+-.-..|++.|... | + ..+|...-|...++ ++.-+|.... +.+|..++
T Consensus 83 ~E~f~r~L~~h~Pr~~~~wa~wG~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~pr~tgln~al-e~~G~sf~ 161 (210)
T COG5018 83 FEDFIRKLNEHDPRKNSTWATWGNMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGDPRLTGLNKAL-EEYGDSFT 161 (210)
T ss_pred HHHHHHHHHhcCcccCCccccccchhHHHHHHHHHhcCCCCccccCccchHHHHHHHHhcCCccccHHHHH-HHhccccC
Confidence 9999999954332 2333446899998863 1 1 25899999998888 5557899888 66799887
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHH
Q 010743 275 KKGTPHNCLDDASAAMKLVLAIIE 298 (502)
Q Consensus 275 ~~~~~HdAleDA~Ata~L~~~~l~ 298 (502)
|..|+|++||+.+++|+.....
T Consensus 162 --G~~HraldDArn~~rl~klv~~ 183 (210)
T COG5018 162 --GTHHRALDDARNAYRLFKLVEQ 183 (210)
T ss_pred --CchhhhHHHHHHHHHHHHHHcc
Confidence 5799999999999999987664
No 57
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=98.73 E-value=4.3e-08 Score=101.92 Aligned_cols=247 Identities=16% Similarity=0.164 Sum_probs=156.8
Q ss_pred CCCcEEEEEEeccCCCCCcccEEEEEEEEc--CCcEE---EEEEEcCCCcc-c-ccccccCCCChhhhccCCCCHHHHHH
Q 010743 140 TSNIMYAVDCEMVLCEDGSEGLVRLCVVDR--NLKVT---IDELVKPEKAV-A-DYRSEITGLTADDLVGVTCSLAEIQK 212 (502)
Q Consensus 140 ~~~~~VaID~ETTGl~~g~~~I~rVsvVd~--~G~vi---~d~LVkP~~~I-~-dy~T~ihGIT~e~L~~ap~~~~dV~~ 212 (502)
....|+..|.||.|.++..++.++++.|+- +.+++ ..-|++|.... | +..+-||||||+.....+++-.+...
T Consensus 7 ~~~tF~~yDYETfG~~Pa~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~F~~ 86 (475)
T COG2925 7 KQPTFLFYDYETFGVHPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAAFAA 86 (475)
T ss_pred CCCcEEEEehhhcCCCcccccchhhheeeccccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHHHHH
Confidence 346799999999999999999999999964 44444 66799998643 3 35788999999999988877778777
Q ss_pred HHH-HhhcCCCEEEEEc-hhhHHHHHcccC------C----------C--ccchHHHhhhhcC-----------CCCCCH
Q 010743 213 RMK-KLLSNGTILVGHS-LNNDLEVLKLDH------P----------R--VIDTSLIFKYVDE-----------YRRPSL 261 (502)
Q Consensus 213 ~l~-~fl~~g~ILVGHn-l~fDl~fLk~~~------p----------~--vIDT~~L~r~~~~-----------~~~~sL 261 (502)
.|. +|..+++.+||+| +.||=.+.+..+ | + .+|.++....++| ..+..|
T Consensus 87 ~I~~~ls~P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n~dG~pSFkL 166 (475)
T COG2925 87 RIHAELTQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDDGLPSFKL 166 (475)
T ss_pred HHHHHhCCCCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcCCCCCcchhh
Confidence 776 4556899999996 799987776521 1 1 3666665544433 356789
Q ss_pred HHHHHHHcCCccCCCCCCCCHHHHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHhhhhcCCCCCCCChHhhhccCCCC
Q 010743 262 YNLCKSVLGYEIRKKGTPHNCLDDASAAMKLVLAIIERRVDNAVPLLQEDVAETERARLFLHRIPTKVPSEELHGVIPGD 341 (502)
Q Consensus 262 ~~La~~~Lgi~iq~~~~~HdAleDA~Ata~L~~~~l~~g~~~~i~l~~~~~~e~~l~~l~~~~iP~~~~~eel~~~f~~~ 341 (502)
..|+ .--|++.. .+|+|+.|++||..+.....+.-|.- ..+.+.-..+..+.. .-.++...+.-.+++||+..
T Consensus 167 EhLt-~ANgieH~---nAHdAmsDVyATIamAklvk~~QPrL-fdy~f~~R~K~~~~~--lid~~~~~PlvHVSgm~ga~ 239 (475)
T COG2925 167 EHLT-KANGIEHS---NAHDAMSDVYATIAMAKLVKTAQPRL-FDYLFQLRKKHKLLA--LIDIPNMQPLVHVSGMFGAE 239 (475)
T ss_pred HHHh-hccccccc---hhhHHHHHHHHHHHHHHHHHhhCcHH-HHHHHHhccHHHHHH--HhcccccCceEEeecccchh
Confidence 9999 44577654 49999999999999987655543320 000011111222222 23344445555677788653
Q ss_pred c---eeeeccc--cccCCcceeEEEEeCCHHH-----HHHHHHhhcCCCCCCCCCC---cceEEEE
Q 010743 342 F---TIEAKAV--KRIRGDNYAAFAIFSSPQE-----ANQAFENVKGNQSKDSYGR---PQKLVEF 394 (502)
Q Consensus 342 ~---~i~~k~~--~~~~g~~~~~~~~f~~~~e-----a~~af~~l~g~~~~d~~G~---~qk~v~~ 394 (502)
. +.. -|- ...+.+-.-+|=-+.+++. |+.-+++|=.+....+-|. |-|.|-+
T Consensus 240 r~~~s~V-~PLaWHP~N~NalIv~DL~~Di~~Ll~l~a~~lr~rLyT~~~dL~eg~~~vP~KlvHi 304 (475)
T COG2925 240 RGNTSWV-LPLAWHPTNRNAVIVCDLAGDISPLLELDADTLRERLYTRKADLGEGELAVPVKLVHI 304 (475)
T ss_pred hCCceEE-EeecccCCCCceEEEEEccCChHHHHhhCHHHHHHHhccccccccCCcccCceEEEEe
Confidence 2 222 121 1112222333333456553 5566677766665555444 6676654
No 58
>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=98.57 E-value=8.6e-07 Score=81.35 Aligned_cols=131 Identities=24% Similarity=0.270 Sum_probs=82.6
Q ss_pred CcEEEEEEeccCCCC--CcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhc
Q 010743 142 NIMYAVDCEMVLCED--GSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS 219 (502)
Q Consensus 142 ~~~VaID~ETTGl~~--g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~ 219 (502)
.+++||||||+++.. ....++.|++-..++..++ .|-..-.+. +...|.+++.
T Consensus 20 ~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~----~~~~~~~~~---------------------~~~~l~~ll~ 74 (176)
T PF01612_consen 20 AKVLAFDTETTGLDPYSYNPKIALIQLATGEGCYII----DPIDLGDNW---------------------ILDALKELLE 74 (176)
T ss_dssp TSEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEE----CGTTSTTTT---------------------HHHHHHHHHT
T ss_pred CCeEEEEEEECCCCccccCCeEEEEEEecCCCceee----eeccccccc---------------------hHHHHHHHHh
Confidence 459999999999987 3333444544444322221 221100000 5667777772
Q ss_pred -CCCEEEEEchhhHHHHHccc----CCCccchHHHhhhhcC-CCCCCHHHHHHHHcC-CccCCC---CCCC--C------
Q 010743 220 -NGTILVGHSLNNDLEVLKLD----HPRVIDTSLIFKYVDE-YRRPSLYNLCKSVLG-YEIRKK---GTPH--N------ 281 (502)
Q Consensus 220 -~g~ILVGHnl~fDl~fLk~~----~p~vIDT~~L~r~~~~-~~~~sL~~La~~~Lg-i~iq~~---~~~H--d------ 281 (502)
.+-+.||||+.||+.+|... ...+.|| .++..... ..+++|+.|+..++| .+...+ +... +
T Consensus 75 ~~~i~kv~~n~~~D~~~L~~~~~i~~~~~~D~-~l~~~~l~~~~~~~L~~L~~~~l~~~~~~~~~~~~~~~~~~~l~~~~ 153 (176)
T PF01612_consen 75 DPNIIKVGHNAKFDLKWLYRSFGIDLKNVFDT-MLAAYLLDPTRSYSLKDLAEEYLGNIDLDKKEQMSDWRKARPLSEEQ 153 (176)
T ss_dssp TTTSEEEESSHHHHHHHHHHHHTS--SSEEEH-HHHHHHTTTSTTSSHHHHHHHHHSEEE-GHCCTTSSTTTSSS-HHHH
T ss_pred CCCccEEEEEEechHHHHHHHhccccCCccch-hhhhhcccccccccHHHHHHHHhhhccCcHHHhhccCCcCCCChHHH
Confidence 35689999999999999883 3458999 55544444 444999999999999 433211 1111 2
Q ss_pred ---HHHHHHHHHHHHHHHHH
Q 010743 282 ---CLDDASAAMKLVLAIIE 298 (502)
Q Consensus 282 ---AleDA~Ata~L~~~~l~ 298 (502)
|..||.++.+||..+..
T Consensus 154 ~~YAa~D~~~~~~l~~~l~~ 173 (176)
T PF01612_consen 154 IEYAAQDAVVTFRLYEKLKP 173 (176)
T ss_dssp HHHHHHHHHTHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 45699999999887664
No 59
>PRK05755 DNA polymerase I; Provisional
Probab=98.44 E-value=1.9e-06 Score=100.11 Aligned_cols=134 Identities=23% Similarity=0.243 Sum_probs=97.7
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhcC
Q 010743 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSN 220 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~~ 220 (502)
...++++|+||+|+++....|+.|++-..+|...+ |.+ ++| + . ++...|.+++..
T Consensus 314 ~~~~~a~DtEt~~l~~~~~~i~~i~ls~~~g~~~~---ip~-----------~~i--------~--~-~~l~~l~~~L~d 368 (880)
T PRK05755 314 AAGLFAFDTETTSLDPMQAELVGLSFAVEPGEAAY---IPL-----------DQL--------D--R-EVLAALKPLLED 368 (880)
T ss_pred ccCeEEEEeccCCCCcccccEEEEEEEeCCCcEEE---Eec-----------ccc--------c--H-HHHHHHHHHHhC
Confidence 46799999999999987777888887655564322 211 112 1 1 567788888843
Q ss_pred CC-EEEEEchhhHHHHHcccC----CCccchHHHhhhhcCCCCCCHHHHHHHHcCCccCC-------C---------CCC
Q 010743 221 GT-ILVGHSLNNDLEVLKLDH----PRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRK-------K---------GTP 279 (502)
Q Consensus 221 g~-ILVGHnl~fDl~fLk~~~----p~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~-------~---------~~~ 279 (502)
.. ++||||+.||+.+|.... .+++||..++..+.+...++|+.|++.|+|...-. + ...
T Consensus 369 ~~v~kV~HNakfDl~~L~~~gi~~~~~~~DT~iAa~Ll~~~~~~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~ple~~~ 448 (880)
T PRK05755 369 PAIKKVGQNLKYDLHVLARYGIELRGIAFDTMLASYLLDPGRRHGLDSLAERYLGHKTISFEEVAGKQLTFAQVDLEEAA 448 (880)
T ss_pred CCCcEEEeccHhHHHHHHhCCCCcCCCcccHHHHHHHcCCCCCCCHHHHHHHHhCCCccchHHhcCCCCCccccCHHHHH
Confidence 33 489999999999998632 34899999888877733499999999998876310 0 013
Q ss_pred CCHHHHHHHHHHHHHHHHHh
Q 010743 280 HNCLDDASAAMKLVLAIIER 299 (502)
Q Consensus 280 HdAleDA~Ata~L~~~~l~~ 299 (502)
|.|..||.+++.||..+.+.
T Consensus 449 ~YAa~Dv~~~~~L~~~L~~~ 468 (880)
T PRK05755 449 EYAAEDADVTLRLHEVLKPK 468 (880)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 77999999999999988765
No 60
>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=98.42 E-value=7.6e-07 Score=76.42 Aligned_cols=59 Identities=25% Similarity=0.382 Sum_probs=45.5
Q ss_pred EEEEEeccCCCCCcccEEEEEEEEcC-CcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhcCC--
Q 010743 145 YAVDCEMVLCEDGSEGLVRLCVVDRN-LKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSNG-- 221 (502)
Q Consensus 145 VaID~ETTGl~~g~~~I~rVsvVd~~-G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~~g-- 221 (502)
+++|+||+|+++..++|+.|++.+.+ +...+ .+ |.+++...
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~~~~----~~--------------------------------f~~~l~~~~~ 44 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPEDTAV----ID--------------------------------LKDILRDKPL 44 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCCCEEE----eh--------------------------------HHHHHhhCCC
Confidence 48999999999888889999999873 44221 11 66666332
Q ss_pred CEEEEEchhhHHHHHccc
Q 010743 222 TILVGHSLNNDLEVLKLD 239 (502)
Q Consensus 222 ~ILVGHnl~fDl~fLk~~ 239 (502)
.++||||+.||+.||+..
T Consensus 45 ~v~V~hn~~fD~~fL~~~ 62 (96)
T cd06125 45 AILVGHNGSFDLPFLNNR 62 (96)
T ss_pred CEEEEeCcHHhHHHHHHH
Confidence 599999999999999763
No 61
>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=98.32 E-value=1.5e-05 Score=76.74 Aligned_cols=134 Identities=18% Similarity=0.238 Sum_probs=86.7
Q ss_pred CCCCcEEEEEEeccCCCC----CcccEEEEEEEEcCCcEE-EEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHH
Q 010743 139 MTSNIMYAVDCEMVLCED----GSEGLVRLCVVDRNLKVT-IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKR 213 (502)
Q Consensus 139 ~~~~~~VaID~ETTGl~~----g~~~I~rVsvVd~~G~vi-~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~ 213 (502)
.....+|+||+|+++... +.-++++|+. .+.+. +|.+ . +.. . +-..+...
T Consensus 19 l~~~~vig~D~Ew~~~~~~~~~~~v~LiQiat---~~~~~lid~~-~--------------~~~----~---~~~~~~~~ 73 (193)
T cd06146 19 LEAGRVVGIDSEWKPSFLGDSDPRVAILQLAT---EDEVFLLDLL-A--------------LEN----L---ESEDWDRL 73 (193)
T ss_pred hccCCEEEEECccCCCccCCCCCCceEEEEec---CCCEEEEEch-h--------------ccc----c---chHHHHHH
Confidence 445789999999986643 2224555552 23322 2211 1 110 0 11233345
Q ss_pred HHHhhcCC-CEEEEEchhhHHHHHcccC----------CCccchHHHhhhhcC-----------CCCCCHHHHHHHHcCC
Q 010743 214 MKKLLSNG-TILVGHSLNNDLEVLKLDH----------PRVIDTSLIFKYVDE-----------YRRPSLYNLCKSVLGY 271 (502)
Q Consensus 214 l~~fl~~g-~ILVGHnl~fDl~fLk~~~----------p~vIDT~~L~r~~~~-----------~~~~sL~~La~~~Lgi 271 (502)
|.+++... -+.|||++.+|+.+|...+ ..++||..++..+.+ ...+||..||+.+||.
T Consensus 74 L~~ll~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~ 153 (193)
T cd06146 74 LKRLFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGK 153 (193)
T ss_pred HHHHhCCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCC
Confidence 67777333 4569999999999998643 248999998876542 2568999999999998
Q ss_pred ccCCCC-------------CCCCHHHHHHHHHHHHHHHH
Q 010743 272 EIRKKG-------------TPHNCLDDASAAMKLVLAII 297 (502)
Q Consensus 272 ~iq~~~-------------~~HdAleDA~Ata~L~~~~l 297 (502)
++.+.. .-+=|..||+++..||.++.
T Consensus 154 ~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 154 PLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred CcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 876421 11346789999999998765
No 62
>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=98.15 E-value=1.9e-05 Score=75.89 Aligned_cols=116 Identities=16% Similarity=0.133 Sum_probs=83.1
Q ss_pred CcEEEEEEecc---CC-CCCcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHh
Q 010743 142 NIMYAVDCEMV---LC-EDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (502)
Q Consensus 142 ~~~VaID~ETT---Gl-~~g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~f 217 (502)
-+++++|+||+ |. ++..+.|+.||++...+..++.. ++.. ...+.... +-.+++.+|.++
T Consensus 3 l~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~~--~~~~-------------~~~v~~~~-~E~~lL~~F~~~ 66 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVITW--KKFD-------------LPFVEVVK-TEKEMIKRFIEI 66 (195)
T ss_pred ceEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEEe--cCCC-------------CCeEEEeC-CHHHHHHHHHHH
Confidence 47899999998 44 45667899999988665533311 1111 01233334 667899999999
Q ss_pred hcC--CCEEEEEch-hhHHHHHccc-------CC-----------------------C-ccchHHHhhhhcCCCCCCHHH
Q 010743 218 LSN--GTILVGHSL-NNDLEVLKLD-------HP-----------------------R-VIDTSLIFKYVDEYRRPSLYN 263 (502)
Q Consensus 218 l~~--g~ILVGHnl-~fDl~fLk~~-------~p-----------------------~-vIDT~~L~r~~~~~~~~sL~~ 263 (502)
+.. -.+|||||. .||+.+|... .+ + .+|+..+++......+++|++
T Consensus 67 i~~~dpdiivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~~l~sy~L~~ 146 (195)
T cd05780 67 VKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLNLTRYTLER 146 (195)
T ss_pred HHHcCCCEEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhCCCCcCcHHH
Confidence 954 579999997 5899998641 11 1 588888888766678999999
Q ss_pred HHHHHcCCcc
Q 010743 264 LCKSVLGYEI 273 (502)
Q Consensus 264 La~~~Lgi~i 273 (502)
+|+.+||.+-
T Consensus 147 v~~~~Lg~~k 156 (195)
T cd05780 147 VYEELFGIEK 156 (195)
T ss_pred HHHHHhCCCC
Confidence 9999999863
No 63
>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=98.12 E-value=0.00012 Score=65.15 Aligned_cols=104 Identities=27% Similarity=0.244 Sum_probs=70.4
Q ss_pred EEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhcCC-C
Q 010743 144 MYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSNG-T 222 (502)
Q Consensus 144 ~VaID~ETTGl~~g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~~g-~ 222 (502)
.+++|+|+.+..+....|..+++... +..+| |-. +.. ...+.+.|.+++... .
T Consensus 2 ~l~~d~e~~~~~~~~~~i~~~~l~~~-~~~~~---i~~----~~~------------------~~~~~~~l~~~l~~~~~ 55 (155)
T cd00007 2 EVAFDTETTGLNYHRGKLVGIQIATA-GEAAY---IPD----ELE------------------LEEDLEALKELLEDEDI 55 (155)
T ss_pred ceEEEEecCCCCcCCCeEEEEEEEEC-CcEEE---EEc----CCC------------------HHHHHHHHHHHHcCCCC
Confidence 57999999877632334666666544 32222 110 000 135667777888323 4
Q ss_pred EEEEEchhhHHHHHcccC----CCccchHHHhhhhcCCC-CCCHHHHHHHHcCCcc
Q 010743 223 ILVGHSLNNDLEVLKLDH----PRVIDTSLIFKYVDEYR-RPSLYNLCKSVLGYEI 273 (502)
Q Consensus 223 ILVGHnl~fDl~fLk~~~----p~vIDT~~L~r~~~~~~-~~sL~~La~~~Lgi~i 273 (502)
.+||||+.+|+.+|.... ..+.||..++..+.+.. +++|+.|++.|++..+
T Consensus 56 ~~v~~~~k~d~~~L~~~~~~~~~~~~D~~~~ayll~~~~~~~~l~~l~~~~l~~~~ 111 (155)
T cd00007 56 TKVGHDAKFDLVVLARDGIELPGNIFDTMLAAYLLNPGEGSHSLDDLAKEYLGIEL 111 (155)
T ss_pred cEEeccHHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCCcCCHHHHHHHHcCCCC
Confidence 599999999999997532 24799999999888833 6799999999988774
No 64
>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=97.95 E-value=0.00018 Score=66.88 Aligned_cols=128 Identities=23% Similarity=0.261 Sum_probs=83.7
Q ss_pred CCcEEEEEEeccCCCC----CcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHH
Q 010743 141 SNIMYAVDCEMVLCED----GSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKK 216 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~----g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~ 216 (502)
...+|+||+|+++... +.-++++|+ ..+.+. +|.+.. + ... ...|.+
T Consensus 17 ~~~~ig~D~E~~~~~~~~~~~~~~liQl~---~~~~~~---l~~~~~-----------~-----~~~-------~~~l~~ 67 (170)
T cd06141 17 KEKVVGFDTEWRPSFRKGKRNKVALLQLA---TESRCL---LFQLAH-----------M-----DKL-------PPSLKQ 67 (170)
T ss_pred CCCEEEEeCccCCccCCCCCCCceEEEEe---cCCcEE---EEEhhh-----------h-----hcc-------cHHHHH
Confidence 5689999999998754 222455555 122221 122211 1 111 134556
Q ss_pred hhc-CCCEEEEEchhhHHHHHcccC----CCccchHHHhhhhcCC-CCCCHHHHHHHHcCCccC--CCC-----------
Q 010743 217 LLS-NGTILVGHSLNNDLEVLKLDH----PRVIDTSLIFKYVDEY-RRPSLYNLCKSVLGYEIR--KKG----------- 277 (502)
Q Consensus 217 fl~-~g~ILVGHnl~fDl~fLk~~~----p~vIDT~~L~r~~~~~-~~~sL~~La~~~Lgi~iq--~~~----------- 277 (502)
++. .+.+.|||++.+|+.+|...+ ..++||..++..+.+. ...+|..||..++|..+. ...
T Consensus 68 ll~~~~i~kv~~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt 147 (170)
T cd06141 68 LLEDPSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLS 147 (170)
T ss_pred HhcCCCeeEEEeeeHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCCCCCC
Confidence 663 345679999999999997533 3479999999888773 457999999999999876 210
Q ss_pred --CCCCHHHHHHHHHHHHHHHH
Q 010743 278 --TPHNCLDDASAAMKLVLAII 297 (502)
Q Consensus 278 --~~HdAleDA~Ata~L~~~~l 297 (502)
.-|=|..||..+..||..+.
T Consensus 148 ~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 148 KEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh
Confidence 11446789999999887654
No 65
>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=97.91 E-value=0.0001 Score=70.77 Aligned_cols=107 Identities=18% Similarity=0.111 Sum_probs=77.5
Q ss_pred CCcEEEEEEecc---CC-CCCcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHH
Q 010743 141 SNIMYAVDCEMV---LC-EDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKK 216 (502)
Q Consensus 141 ~~~~VaID~ETT---Gl-~~g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~ 216 (502)
+.+++++|+||+ |. +++.+.|+.||+...+|.+.+-. .... +-.+++.+|.+
T Consensus 2 ~l~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~~-----------------------~~~~-~E~~lL~~F~~ 57 (188)
T cd05781 2 DLKTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFIL-----------------------AEGL-DDRKIIREFVK 57 (188)
T ss_pred CceEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEEEE-----------------------ecCC-CHHHHHHHHHH
Confidence 357899999999 44 45667899999998777532100 0123 67889999999
Q ss_pred hhcCC--CEEEEEch-hhHHHHHccc-------CC---------------------C-ccchHHHhhhhcCCCCCCHHHH
Q 010743 217 LLSNG--TILVGHSL-NNDLEVLKLD-------HP---------------------R-VIDTSLIFKYVDEYRRPSLYNL 264 (502)
Q Consensus 217 fl~~g--~ILVGHnl-~fDl~fLk~~-------~p---------------------~-vIDT~~L~r~~~~~~~~sL~~L 264 (502)
++..- .+|+|||. .||+.+|... .+ + .+|...+.+......+++|+++
T Consensus 58 ~i~~~dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~l~~y~L~~V 137 (188)
T cd05781 58 YVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPEVKVKTLENV 137 (188)
T ss_pred HHHHcCCCEEEecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCCCCCCCHHHH
Confidence 99544 68999996 6999998641 00 0 4777777766555788999999
Q ss_pred HHHHcCCc
Q 010743 265 CKSVLGYE 272 (502)
Q Consensus 265 a~~~Lgi~ 272 (502)
| .+||..
T Consensus 138 a-~~Lg~~ 144 (188)
T cd05781 138 A-EYLGVM 144 (188)
T ss_pred H-HHHCCC
Confidence 9 478863
No 66
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=97.89 E-value=5.9e-05 Score=75.91 Aligned_cols=153 Identities=16% Similarity=0.115 Sum_probs=89.4
Q ss_pred CCcEEEEEEeccCCCCCc---------------------ccEEEEEEEEc---CCcEE-------EEEEEcCCCc-cccc
Q 010743 141 SNIMYAVDCEMVLCEDGS---------------------EGLVRLCVVDR---NLKVT-------IDELVKPEKA-VADY 188 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~g~---------------------~~I~rVsvVd~---~G~vi-------~d~LVkP~~~-I~dy 188 (502)
...|||||+|+||+.... -.|+++++--. ++... |.-++-|... ....
T Consensus 21 ~~~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~~~~~~~~nf~~f~~~~~~~~~ 100 (262)
T PF04857_consen 21 KADFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIPSSYNVWPFNFYLFPLDRDFSQA 100 (262)
T ss_dssp HSSEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEECCEEEEEEEBSTTSTTTCEEEH
T ss_pred hCCEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccccCCceeEEEEeeeeccccccceecc
Confidence 356999999999986321 03777776544 44431 2222223221 1110
Q ss_pred c----cccCCCChhhhccCCCCHHHHHH-----HH------HH-hhcCCCEEEEEchhhHHHHHcc--------------
Q 010743 189 R----SEITGLTADDLVGVTCSLAEIQK-----RM------KK-LLSNGTILVGHSLNNDLEVLKL-------------- 238 (502)
Q Consensus 189 ~----T~ihGIT~e~L~~ap~~~~dV~~-----~l------~~-fl~~g~ILVGHnl~fDl~fLk~-------------- 238 (502)
. -.-+|+.-..+....+++....+ ++ +. +.....++||||.-.|+.+|-.
T Consensus 101 ~sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF~ 180 (262)
T PF04857_consen 101 SSLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHNGLYDLMYLYKKFIGPLPETLEEFK 180 (262)
T ss_dssp HHHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESSTHHHHHHHHHHHTTS--SSHHHHH
T ss_pred hhHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeChHhHHHHHHHHhcCCCCCCHHHHH
Confidence 0 13377777666655544433331 11 11 2234589999999999988743
Q ss_pred -----cCCCccchHHHhhhhcCCCCCCHHHHHHHHcCCcc----------------------CCCCCCCCHHHHHHHHHH
Q 010743 239 -----DHPRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEI----------------------RKKGTPHNCLDDASAAMK 291 (502)
Q Consensus 239 -----~~p~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~i----------------------q~~~~~HdAleDA~Ata~ 291 (502)
..|.++||-.|+.... ....+|..|+ ..++..- ..+...|.|--||+.|+.
T Consensus 181 ~~~~~~FP~i~DtK~la~~~~-~~~~~L~~l~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~HeAGyDA~mTg~ 258 (262)
T PF04857_consen 181 ELLRELFPRIYDTKYLAEECP-GKSTSLQELA-EELGIRRNPSSISSPEGFPSYDEEKNNFPMFGEKAHEAGYDAYMTGC 258 (262)
T ss_dssp HHHHHHSSSEEEHHHHHTSTT-TS-SSHHHHH-HHTTSTT----EEE-TTS-------------SS-TTSHHHHHHHHHH
T ss_pred HHHHHHCcccccHHHHHHhcc-ccccCHHHHH-HHhCCCccccccccccccccccccccccccCCCCCCCcchHHHHHHH
Confidence 2577899999888654 3677999999 6677653 122238999999999999
Q ss_pred HHHH
Q 010743 292 LVLA 295 (502)
Q Consensus 292 L~~~ 295 (502)
+|.+
T Consensus 259 ~F~~ 262 (262)
T PF04857_consen 259 VFIK 262 (262)
T ss_dssp HHHH
T ss_pred HHcC
Confidence 9863
No 67
>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=97.85 E-value=0.00045 Score=64.23 Aligned_cols=85 Identities=24% Similarity=0.214 Sum_probs=60.7
Q ss_pred HHHHhhc-CCCEEEEEchhhHHHHHcccC----CCccchHHHhhhhcCCCCCCHHHHHHHHcCCccCCCC----------
Q 010743 213 RMKKLLS-NGTILVGHSLNNDLEVLKLDH----PRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKG---------- 277 (502)
Q Consensus 213 ~l~~fl~-~g~ILVGHnl~fDl~fLk~~~----p~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~~---------- 277 (502)
.|.+++. .+.+.|||++..|+..|...+ ..++||...+..+.+..+.+|..|+..+||..+.+..
T Consensus 58 ~L~~lL~d~~i~Kvg~~~k~D~~~L~~~~gi~~~~~~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~K~~~~s~W~~rpL 137 (161)
T cd06129 58 GLKMLLENPSIVKALHGIEGDLWKLLRDFGEKLQRLFDTTIAANLKGLPERWSLASLVEHFLGKTLDKSISCADWSYRPL 137 (161)
T ss_pred HHHHHhCCCCEEEEEeccHHHHHHHHHHcCCCcccHhHHHHHHHHhCCCCCchHHHHHHHHhCCCCCccceeccCCCCCC
Confidence 3445562 233569999999999996532 3479999988876654467999999999998764311
Q ss_pred ---CCCCHHHHHHHHHHHHHHHH
Q 010743 278 ---TPHNCLDDASAAMKLVLAII 297 (502)
Q Consensus 278 ---~~HdAleDA~Ata~L~~~~l 297 (502)
.-|=|..||.++..||.++.
T Consensus 138 t~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 138 TEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHh
Confidence 12446789999999887653
No 68
>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=97.76 E-value=6e-05 Score=69.44 Aligned_cols=127 Identities=24% Similarity=0.161 Sum_probs=62.7
Q ss_pred EEEEEeccCCCCCcccEEEEEEEEc-CCc-EEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhcCCC
Q 010743 145 YAVDCEMVLCEDGSEGLVRLCVVDR-NLK-VTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSNGT 222 (502)
Q Consensus 145 VaID~ETTGl~~g~~~I~rVsvVd~-~G~-vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~~g~ 222 (502)
+.||+||+|+++....+.-|+++.. ++. ..|..+.-+.. .-.+...++..++....
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~~~~~~~~~~----------------------~ee~~~~~~~~~l~~~~ 58 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIITFIQWFAEDP----------------------DEEEIILEFFELLDEAD 58 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE-EEEE-GGGH----------------------HHHHHHHH--HHHHTT-
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEEeeHhhccCc----------------------HHHHHHHHHHHHHhcCC
Confidence 5799999999987777888888764 222 22333332211 11122222225565889
Q ss_pred EEEEEc-hhhHHHHHcccC-----C---CccchHHHhhhhcCCCCCCHHHHHHHHcCCccCCCCCCCCHHHHHHHHHHHH
Q 010743 223 ILVGHS-LNNDLEVLKLDH-----P---RVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLV 293 (502)
Q Consensus 223 ILVGHn-l~fDl~fLk~~~-----p---~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~Ata~L~ 293 (502)
.+|+|| ..||+.+|+... + ..+|+..+++.... .++||+.++ .+||+... .--.+...+..+|
T Consensus 59 ~iv~yng~~FD~p~L~~~~~~~~~~~~~~~iDl~~~~~~~~~-~~~~Lk~ve-~~lg~~~~------~~~~~G~~~~~~~ 130 (164)
T PF13482_consen 59 NIVTYNGKNFDIPFLKRRAKRYGLPPPFNHIDLLKIIKKHFL-ESYSLKNVE-KFLGIERR------DDDISGSESVKLY 130 (164)
T ss_dssp -EEESSTTTTHHHHHHHHH-HHHH--GGGEEEHHHHHT-TTS-CCTT--SHH-H-----------------HHHHHHHHH
T ss_pred eEEEEeCcccCHHHHHHHHHHcCCCcccchhhHHHHHHhccC-CCCCHHHHh-hhcccccc------cCCCCHHHHHHHH
Confidence 999999 589999998732 1 26899888765444 788999999 66888753 1223555667778
Q ss_pred HHHHHhcc
Q 010743 294 LAIIERRV 301 (502)
Q Consensus 294 ~~~l~~g~ 301 (502)
..++..+-
T Consensus 131 ~~~~~~~~ 138 (164)
T PF13482_consen 131 KEYLETGD 138 (164)
T ss_dssp H---TTGG
T ss_pred HHHHhcCC
Confidence 77665443
No 69
>PRK10829 ribonuclease D; Provisional
Probab=97.60 E-value=0.0013 Score=69.74 Aligned_cols=131 Identities=19% Similarity=0.242 Sum_probs=84.9
Q ss_pred CCCCcEEEEEEeccCCCCCcc--cEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHH
Q 010743 139 MTSNIMYAVDCEMVLCEDGSE--GLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKK 216 (502)
Q Consensus 139 ~~~~~~VaID~ETTGl~~g~~--~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~ 216 (502)
....++++||+|+.....-.. .+++|+ ..++. .+|.|-. +.+ ...|.+
T Consensus 19 l~~~~~lalDtEf~~~~ty~~~l~LiQl~--~~~~~----~LiD~l~-~~d-----------------------~~~L~~ 68 (373)
T PRK10829 19 ARAFPAIALDTEFVRTRTYYPQLGLIQLY--DGEQL----SLIDPLG-ITD-----------------------WSPFKA 68 (373)
T ss_pred HhcCCeEEEecccccCccCCCceeEEEEe--cCCce----EEEecCC-ccc-----------------------hHHHHH
Confidence 345689999999998764332 234443 22222 2444431 111 133555
Q ss_pred hhcCCCEE-EEEchhhHHHHHccc---C-CCccchHHHhhhhcCCCCCCHHHHHHHHcCCccCCCCCC------------
Q 010743 217 LLSNGTIL-VGHSLNNDLEVLKLD---H-PRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTP------------ 279 (502)
Q Consensus 217 fl~~g~IL-VGHnl~fDl~fLk~~---~-p~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~~~~------------ 279 (502)
++....|+ |+|++.+|+.+|... . ..++||...++.+......+|..|++.+||+.+.++...
T Consensus 69 ll~~~~ivKV~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg~~~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~q 148 (373)
T PRK10829 69 LLRDPQVTKFLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQ 148 (373)
T ss_pred HHcCCCeEEEEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHcCCCccccHHHHHHHHhCCccCcccccCCCCCCCCCHHH
Confidence 56444444 899999999998553 2 348999877765432447899999999999987653111
Q ss_pred -CCHHHHHHHHHHHHHHHHHh
Q 010743 280 -HNCLDDASAAMKLVLAIIER 299 (502)
Q Consensus 280 -HdAleDA~Ata~L~~~~l~~ 299 (502)
+=|..|+.....||..+.+.
T Consensus 149 l~YAa~Dv~~L~~l~~~L~~~ 169 (373)
T PRK10829 149 CEYAAADVFYLLPIAAKLMAE 169 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 22678999999999887754
No 70
>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=97.56 E-value=0.0018 Score=63.25 Aligned_cols=128 Identities=16% Similarity=0.155 Sum_probs=77.0
Q ss_pred CcEEEEEEeccCC-----CCCcccEEEEEEEEc-CCcEEE-EEEEcCCCccccc--ccccCCCChhhhccCCCCHHHHHH
Q 010743 142 NIMYAVDCEMVLC-----EDGSEGLVRLCVVDR-NLKVTI-DELVKPEKAVADY--RSEITGLTADDLVGVTCSLAEIQK 212 (502)
Q Consensus 142 ~~~VaID~ETTGl-----~~g~~~I~rVsvVd~-~G~vi~-d~LVkP~~~I~dy--~T~ihGIT~e~L~~ap~~~~dV~~ 212 (502)
.+++|+|+||.+. ++..+.|+.||++.. .|..+. ..++.+...--.+ .-.+.|. -.+.... +-.+++.
T Consensus 2 lrilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~v~~~~-~E~~lL~ 78 (204)
T cd05779 2 PRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIVNREIVSEDIEDFEYTPKPEYEGP--FKVFNEP-DEKALLQ 78 (204)
T ss_pred ceEEEEEEEecCCCCCCcCCCCCeEEEEEEEEecCCEEEecccccccccccccccCCCCCCCc--eEEecCC-CHHHHHH
Confidence 4789999999863 345578999999865 453221 1111110000000 0011121 0111233 6788999
Q ss_pred HHHHhhcCC--CEEEEEch-hhHHHHHccc---C----C-----------------C-ccchHHHhhhhc--CCCCCCHH
Q 010743 213 RMKKLLSNG--TILVGHSL-NNDLEVLKLD---H----P-----------------R-VIDTSLIFKYVD--EYRRPSLY 262 (502)
Q Consensus 213 ~l~~fl~~g--~ILVGHnl-~fDl~fLk~~---~----p-----------------~-vIDT~~L~r~~~--~~~~~sL~ 262 (502)
+|.+++..- .+++|+|. .||+.+|... + . + .+|...+++... ....++|+
T Consensus 79 ~f~~~i~~~~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~~sysLd 158 (204)
T cd05779 79 RFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQGLK 158 (204)
T ss_pred HHHHHHHHhCCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCCCCccHH
Confidence 999999543 49999997 7999998641 0 0 0 377777766532 24689999
Q ss_pred HHHHHHcCCc
Q 010743 263 NLCKSVLGYE 272 (502)
Q Consensus 263 ~La~~~Lgi~ 272 (502)
++|+.+||..
T Consensus 159 ~Va~~~Lg~~ 168 (204)
T cd05779 159 AVTKAKLGYD 168 (204)
T ss_pred HHHHHHhCCC
Confidence 9998899974
No 71
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=97.39 E-value=0.0091 Score=54.09 Aligned_cols=130 Identities=25% Similarity=0.240 Sum_probs=78.4
Q ss_pred cEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhc-CC
Q 010743 143 IMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS-NG 221 (502)
Q Consensus 143 ~~VaID~ETTGl~~g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~-~g 221 (502)
..+++|+|+.+.......++.+++-.. +..+| ++.+.. ...+...|.+++. .+
T Consensus 22 ~~l~~~~e~~~~~~~~~~~~~l~l~~~-~~~~~--i~~~~~-----------------------~~~~~~~l~~~l~~~~ 75 (172)
T smart00474 22 GEVALDTETTGLNSYSGKLVLIQISVT-GEGAF--IIDPLA-----------------------LGDDLEILKDLLEDET 75 (172)
T ss_pred CeEEEeccccCCccCCCCEEEEEEeEc-CCceE--EEEecc-----------------------chhhHHHHHHHhcCCC
Confidence 588999998776643334555555432 32222 110000 0111344556663 34
Q ss_pred CEEEEEchhhHHHHHcc---cCCCccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCC-CC--------CC----CHHH
Q 010743 222 TILVGHSLNNDLEVLKL---DHPRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKK-GT--------PH----NCLD 284 (502)
Q Consensus 222 ~ILVGHnl~fDl~fLk~---~~p~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~-~~--------~H----dAle 284 (502)
...||||+.+|+.+|+. ..+.+.||...+..+.| ...++|..++..|+|..+... +. .. -|..
T Consensus 76 ~~kv~~d~k~~~~~L~~~gi~~~~~~D~~laayll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~l~~~~~~ya~~ 155 (172)
T smart00474 76 ITKVGHNAKFDLHVLARFGIELENIFDTMLAAYLLLGGPSKHGLATLLKEYLGVELDKEEQKSDWGARPLSEEQLQYAAE 155 (172)
T ss_pred ceEEEechHHHHHHHHHCCCcccchhHHHHHHHHHcCCCCcCCHHHHHHHHhCCCCCcccCccccccCCCCHHHHHHHHH
Confidence 56999999999999964 12235899988887777 443699999999998875310 00 01 1556
Q ss_pred HHHHHHHHHHHHHH
Q 010743 285 DASAAMKLVLAIIE 298 (502)
Q Consensus 285 DA~Ata~L~~~~l~ 298 (502)
||.++..||..+.+
T Consensus 156 ~a~~~~~L~~~l~~ 169 (172)
T smart00474 156 DADALLRLYEKLEK 169 (172)
T ss_pred HHHHHHHHHHHHHH
Confidence 67777777765543
No 72
>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=97.35 E-value=0.0072 Score=55.87 Aligned_cols=130 Identities=24% Similarity=0.252 Sum_probs=80.7
Q ss_pred CcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhc-C
Q 010743 142 NIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS-N 220 (502)
Q Consensus 142 ~~~VaID~ETTGl~~g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~-~ 220 (502)
...+++|+|+.+..+....+..+++-.. +.+. ||.+. .+ . +...|..++. .
T Consensus 12 ~~~l~~~~e~~~~~~~~~~~~~i~l~~~-~~~~---~i~~~----------------~~-~-------~~~~l~~ll~~~ 63 (178)
T cd06142 12 AGVIAVDTEFMRLNTYYPRLCLIQISTG-GEVY---LIDPL----------------AI-G-------DLSPLKELLADP 63 (178)
T ss_pred CCeEEEECCccCCCcCCCceEEEEEeeC-CCEE---EEeCC----------------Cc-c-------cHHHHHHHHcCC
Confidence 3589999998766543334666666544 3222 22211 00 0 2344555562 3
Q ss_pred CCEEEEEchhhHHHHHccc----CCCccchHHHhhhhcCCCCCCHHHHHHHHcCCccCCCC---C-C---------CCHH
Q 010743 221 GTILVGHSLNNDLEVLKLD----HPRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKG---T-P---------HNCL 283 (502)
Q Consensus 221 g~ILVGHnl~fDl~fLk~~----~p~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~~---~-~---------HdAl 283 (502)
+...||||+.+|+.+|... ...+.||...+..+.+..+++|..|++.|+|..+.... . . +-+.
T Consensus 64 ~i~kv~~d~K~~~~~L~~~~gi~~~~~~D~~laayLl~p~~~~~l~~l~~~~l~~~~~~~~~~~~w~~~~l~~~~~~yaa 143 (178)
T cd06142 64 NIVKVFHAAREDLELLKRDFGILPQNLFDTQIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAA 143 (178)
T ss_pred CceEEEeccHHHHHHHHHHcCCCCCCcccHHHHHHHhCCCccccHHHHHHHHhCCCCCcccccccCCCCCCCHHHHHHHH
Confidence 4679999999999999643 23469998777776664446999999999988732110 0 0 1256
Q ss_pred HHHHHHHHHHHHHHHh
Q 010743 284 DDASAAMKLVLAIIER 299 (502)
Q Consensus 284 eDA~Ata~L~~~~l~~ 299 (502)
.||.++..|+..+.+.
T Consensus 144 ~~a~~l~~L~~~l~~~ 159 (178)
T cd06142 144 LDVRYLLPLYEKLKEE 159 (178)
T ss_pred HhHHHHHHHHHHHHHH
Confidence 6777788887766543
No 73
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=97.30 E-value=0.0027 Score=66.93 Aligned_cols=133 Identities=21% Similarity=0.225 Sum_probs=88.2
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhcC
Q 010743 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSN 220 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~~ 220 (502)
...+||||+||.|+..-...++=|=+-+.++ ..+|.|-.++.+ .+ +|..++ .+.
T Consensus 16 ~~~~iAiDTEf~r~~t~~p~LcLIQi~~~e~----~~lIdpl~~~~d---------------~~-~l~~Ll------~d~ 69 (361)
T COG0349 16 GSKAIAIDTEFMRLRTYYPRLCLIQISDGEG----ASLIDPLAGILD---------------LP-PLVALL------ADP 69 (361)
T ss_pred CCCceEEecccccccccCCceEEEEEecCCC----ceEecccccccc---------------cc-hHHHHh------cCC
Confidence 4679999999999987766555555555555 355666443221 22 232222 123
Q ss_pred CCEEEEEchhhHHHHHccc---CC-CccchHHHhhhhcCCCCCCHHHHHHHHcCCccCCCCC----CCC---------HH
Q 010743 221 GTILVGHSLNNDLEVLKLD---HP-RVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGT----PHN---------CL 283 (502)
Q Consensus 221 g~ILVGHnl~fDl~fLk~~---~p-~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~~~----~Hd---------Al 283 (502)
+-+=|-|+++||+.+|... +| .++||...++......+++|++||+.++|+++.++.. .++ |.
T Consensus 70 ~v~KIfHaa~~DL~~l~~~~g~~p~plfdTqiAa~l~g~~~~~gl~~Lv~~ll~v~ldK~~q~SDW~~RPLs~~Ql~YAa 149 (361)
T COG0349 70 NVVKIFHAARFDLEVLLNLFGLLPTPLFDTQIAAKLAGFGTSHGLADLVEELLGVELDKSEQRSDWLARPLSEAQLEYAA 149 (361)
T ss_pred ceeeeeccccccHHHHHHhcCCCCCchhHHHHHHHHhCCcccccHHHHHHHHhCCcccccccccccccCCCCHHHHHHHH
Confidence 3344889999999999875 33 4899998888765444999999999999999976311 233 34
Q ss_pred HHHHHHHHHHHHHHHh
Q 010743 284 DDASAAMKLVLAIIER 299 (502)
Q Consensus 284 eDA~Ata~L~~~~l~~ 299 (502)
.|+.--..||.++.+.
T Consensus 150 ~DV~yL~~l~~~L~~~ 165 (361)
T COG0349 150 ADVEYLLPLYDKLTEE 165 (361)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5666666777665543
No 74
>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=97.29 E-value=0.0014 Score=64.00 Aligned_cols=107 Identities=17% Similarity=0.258 Sum_probs=73.4
Q ss_pred CCcEEEEEEeccCCC--------CCcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHH
Q 010743 141 SNIMYAVDCEMVLCE--------DGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQK 212 (502)
Q Consensus 141 ~~~~VaID~ETTGl~--------~g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~ 212 (502)
+-++++||+|+.... +..+.|+.|++.+..|.... +.. ..+ +-.+++.
T Consensus 8 ~lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~---~~~--------------------~~~-~E~~lL~ 63 (207)
T cd05785 8 DLRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEV---LHA--------------------EDA-AEKELLE 63 (207)
T ss_pred CceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceee---ecc--------------------CCC-CHHHHHH
Confidence 468999999997632 23457999998876652111 100 134 7889999
Q ss_pred HHHHhhcCC--CEEEEEch-hhHHHHHccc-------CC-------------------------------C-ccchHHHh
Q 010743 213 RMKKLLSNG--TILVGHSL-NNDLEVLKLD-------HP-------------------------------R-VIDTSLIF 250 (502)
Q Consensus 213 ~l~~fl~~g--~ILVGHnl-~fDl~fLk~~-------~p-------------------------------~-vIDT~~L~ 250 (502)
+|.+++..- .||||||. .||+.+|... .+ + ++|+..++
T Consensus 64 ~f~~~i~~~dPdii~g~N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~ 143 (207)
T cd05785 64 ELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLV 143 (207)
T ss_pred HHHHHHHHhCCCEEeccCCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHH
Confidence 999999542 79999999 8999998641 10 1 27888777
Q ss_pred hhh----cCCCCCCHHHHHHHHcCCc
Q 010743 251 KYV----DEYRRPSLYNLCKSVLGYE 272 (502)
Q Consensus 251 r~~----~~~~~~sL~~La~~~Lgi~ 272 (502)
+.. ....+++|+++|. ++|..
T Consensus 144 ~~~~~~~~~l~sysL~~Va~-~~g~~ 168 (207)
T cd05785 144 QLFDVSSRDLPSYGLKAVAK-HFGLA 168 (207)
T ss_pred HhhcccccCCCCCCHHHHHH-Hhccc
Confidence 652 1257899999995 55653
No 75
>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=97.19 E-value=0.0083 Score=59.21 Aligned_cols=122 Identities=17% Similarity=0.189 Sum_probs=79.8
Q ss_pred CCcEEEEEEeccCC-----CCCcccEEEEEEEEc-CCc--EEEEE-E-EcCCCcccccccccCCCChhhhccCCCCHHHH
Q 010743 141 SNIMYAVDCEMVLC-----EDGSEGLVRLCVVDR-NLK--VTIDE-L-VKPEKAVADYRSEITGLTADDLVGVTCSLAEI 210 (502)
Q Consensus 141 ~~~~VaID~ETTGl-----~~g~~~I~rVsvVd~-~G~--vi~d~-L-VkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV 210 (502)
+-+.+++|+||..- ++..+.|..|+++.. +|. ..... + +++..+++ | ..+...+ +-.+.
T Consensus 6 ~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~~~~~~~-------~---~~v~~~~-~E~eL 74 (230)
T cd05777 6 PLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIV-------G---AQVFSFE-TEEEL 74 (230)
T ss_pred CceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeCCCCCCC-------C---CEEEEEC-CHHHH
Confidence 46799999999853 345678999999854 442 11111 1 23322222 1 1223334 67889
Q ss_pred HHHHHHhhcC--CCEEEEEch-hhHHHHHccc---C--C-------------------------------------C-cc
Q 010743 211 QKRMKKLLSN--GTILVGHSL-NNDLEVLKLD---H--P-------------------------------------R-VI 244 (502)
Q Consensus 211 ~~~l~~fl~~--g~ILVGHnl-~fDl~fLk~~---~--p-------------------------------------~-vI 244 (502)
+.+|.+++.. -.||+|||+ .||+.+|... + + + ++
T Consensus 75 L~~f~~~i~~~DPDii~GyN~~~FDl~yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~~i 154 (230)
T cd05777 75 LLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQF 154 (230)
T ss_pred HHHHHHHHHhcCCCEEEEecCCCCCHHHHHHHHHHhCCccccccccccCCceeEeCCcccccccccccceEEEEcCEEee
Confidence 9999998843 369999997 5799987430 0 0 0 25
Q ss_pred chHHHhhhhcCCCCCCHHHHHHHHcCCcc
Q 010743 245 DTSLIFKYVDEYRRPSLYNLCKSVLGYEI 273 (502)
Q Consensus 245 DT~~L~r~~~~~~~~sL~~La~~~Lgi~i 273 (502)
|+..+++......+++|+++|+.+||...
T Consensus 155 D~~~~~~~~~kl~sy~L~~Va~~~Lg~~k 183 (230)
T cd05777 155 DLLQVIQRDYKLRSYSLNSVSAHFLGEQK 183 (230)
T ss_pred eHHHHHHHhcCcccCcHHHHHHHHhCCCC
Confidence 66666665544789999999999998754
No 76
>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=97.18 E-value=0.0037 Score=60.28 Aligned_cols=88 Identities=23% Similarity=0.184 Sum_probs=57.8
Q ss_pred HHHHHhhc-CCCEEEEEchhhHHHHHccc----CCCccchHHHhhhhcC-C-------CCCCHHHHHHHHcCCccCC---
Q 010743 212 KRMKKLLS-NGTILVGHSLNNDLEVLKLD----HPRVIDTSLIFKYVDE-Y-------RRPSLYNLCKSVLGYEIRK--- 275 (502)
Q Consensus 212 ~~l~~fl~-~g~ILVGHnl~fDl~fLk~~----~p~vIDT~~L~r~~~~-~-------~~~sL~~La~~~Lgi~iq~--- 275 (502)
..|.+++. .+.+-|||++.+|+.+|... ...+.||...+..+.+ . ...+|..+++.|||.++..
T Consensus 55 ~~L~~iLe~~~i~Kv~h~~k~D~~~L~~~~gi~~~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~ 134 (197)
T cd06148 55 NGLKDILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKED 134 (197)
T ss_pred HHHHHHhcCCCccEEEEechhHHHHHHHhcCccccceeeHHHHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHH
Confidence 34455553 33456999999999999432 2347999876655443 1 2369999999999987621
Q ss_pred ---------CC---------CCCCHHHHHHHHHHHHHHHHHh
Q 010743 276 ---------KG---------TPHNCLDDASAAMKLVLAIIER 299 (502)
Q Consensus 276 ---------~~---------~~HdAleDA~Ata~L~~~~l~~ 299 (502)
.. .-+=|..||..+..||..++..
T Consensus 135 ~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~ 176 (197)
T cd06148 135 VKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDA 176 (197)
T ss_pred HHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 00 0122567888888888877754
No 77
>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=97.15 E-value=0.0078 Score=63.74 Aligned_cols=129 Identities=24% Similarity=0.279 Sum_probs=82.0
Q ss_pred CCcEEEEEEeccCCCCCcc--cEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhh
Q 010743 141 SNIMYAVDCEMVLCEDGSE--GLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLL 218 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~g~~--~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl 218 (502)
...+|+||+|++....-.. ++++|+ +|..+ .+|.|-.. .+ ...|.+++
T Consensus 17 ~~~~ia~DtE~~~~~~y~~~l~LiQia----~~~~~--~liD~~~~-~~-----------------------~~~L~~lL 66 (367)
T TIGR01388 17 TFPFVALDTEFVRERTFWPQLGLIQVA----DGEQL--ALIDPLVI-ID-----------------------WSPLKELL 66 (367)
T ss_pred cCCEEEEeccccCCCCCCCcceEEEEe----eCCeE--EEEeCCCc-cc-----------------------HHHHHHHH
Confidence 4579999999997753222 344444 23322 24544211 00 12344445
Q ss_pred c-CCCEEEEEchhhHHHHHccc---CC-CccchHHHhhhhcCCCCCCHHHHHHHHcCCccCCCCC----CCC--------
Q 010743 219 S-NGTILVGHSLNNDLEVLKLD---HP-RVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGT----PHN-------- 281 (502)
Q Consensus 219 ~-~g~ILVGHnl~fDl~fLk~~---~p-~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~~~----~Hd-------- 281 (502)
. .+.+.|+|++.+|+.+|... .+ .+.||...+..+.+....+|..|++.|||+.+.++.. ..+
T Consensus 67 ~d~~i~KV~h~~k~Dl~~L~~~~~~~~~~~fDtqlAa~lL~~~~~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~ 146 (367)
T TIGR01388 67 RDESVVKVLHAASEDLEVFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLE 146 (367)
T ss_pred CCCCceEEEeecHHHHHHHHHHhCCCCCCcccHHHHHHHhCCCCCccHHHHHHHHcCCCCCcccccccCCCCCCCHHHHH
Confidence 2 34557999999999999753 23 4799988777665544579999999999998754210 122
Q ss_pred -HHHHHHHHHHHHHHHHHh
Q 010743 282 -CLDDASAAMKLVLAIIER 299 (502)
Q Consensus 282 -AleDA~Ata~L~~~~l~~ 299 (502)
|..||.+...||..+.+.
T Consensus 147 YAa~Dv~~L~~L~~~L~~~ 165 (367)
T TIGR01388 147 YAAADVTYLLPLYAKLMER 165 (367)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 677888888888877654
No 78
>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=97.14 E-value=0.007 Score=58.60 Aligned_cols=114 Identities=18% Similarity=0.184 Sum_probs=74.4
Q ss_pred CcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhcCC
Q 010743 142 NIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSNG 221 (502)
Q Consensus 142 ~~~VaID~ETTGl~~g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~~g 221 (502)
-++++||+||+|.. .|..|+..+..-..++ .+=.+ .++. |. .+.-.+ +-.+++..|.+++..-
T Consensus 3 l~~~~fDIE~~~~~----~i~~i~~~~~~~~~i~-~~~~~-~~~~-------~~---~v~~~~-~E~~lL~~f~~~i~~~ 65 (193)
T cd05784 3 LKVVSLDIETSMDG----ELYSIGLYGEGQERVL-MVGDP-EDDA-------PD---NIEWFA-DEKSLLLALIAWFAQY 65 (193)
T ss_pred ccEEEEEeecCCCC----CEEEEEeecCCCCEEE-EECCC-CCCC-------CC---EEEEEC-CHHHHHHHHHHHHHhh
Confidence 47899999998643 5888887765333222 11111 1111 11 122234 6678899999988544
Q ss_pred --CEEEEEch-hhHHHHHcc-------cCC-------------------------C-ccchHHHhhh-hcCCCCCCHHHH
Q 010743 222 --TILVGHSL-NNDLEVLKL-------DHP-------------------------R-VIDTSLIFKY-VDEYRRPSLYNL 264 (502)
Q Consensus 222 --~ILVGHnl-~fDl~fLk~-------~~p-------------------------~-vIDT~~L~r~-~~~~~~~sL~~L 264 (502)
.||+|||. .||+.+|.. .++ + ++|+..+.+. .....+++|+++
T Consensus 66 dPDvi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~~~~kl~sy~L~~V 145 (193)
T cd05784 66 DPDIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTATYHFESFSLENV 145 (193)
T ss_pred CCCEEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHHccCCCCcCCHHHH
Confidence 68999998 689999854 110 1 4777777665 344789999999
Q ss_pred HHHHcCCc
Q 010743 265 CKSVLGYE 272 (502)
Q Consensus 265 a~~~Lgi~ 272 (502)
|+.+||..
T Consensus 146 a~~~Lg~~ 153 (193)
T cd05784 146 AQELLGEG 153 (193)
T ss_pred HHHHhCCC
Confidence 99999864
No 79
>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=96.59 E-value=0.025 Score=55.19 Aligned_cols=126 Identities=19% Similarity=0.133 Sum_probs=76.1
Q ss_pred CCcEEEEEEeccCCC----CC--c--ccEEEEEEEEcCCcEEEEEEEcC-CCcccccccccCCCChhhhccCCCCHHHHH
Q 010743 141 SNIMYAVDCEMVLCE----DG--S--EGLVRLCVVDRNLKVTIDELVKP-EKAVADYRSEITGLTADDLVGVTCSLAEIQ 211 (502)
Q Consensus 141 ~~~~VaID~ETTGl~----~g--~--~~I~rVsvVd~~G~vi~d~LVkP-~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~ 211 (502)
+-++++||+||+.-. |. . +.|+.|++...+|...+ .+++. .....+.-. .-| ..+.... +-.+++
T Consensus 4 ~lrilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~~~~~~~~v-~~~~~~~~~~~~~~~-~~~---~~v~~~~-~E~~lL 77 (204)
T cd05783 4 KLKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALAGSDGLKRV-LVLKREGVEGLEGLL-PEG---AEVEFFD-SEKELI 77 (204)
T ss_pred CceEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEcCCCCCcEE-EEEecCCcccccccC-CCC---CeEEecC-CHHHHH
Confidence 458999999998421 22 2 46999999864453211 11121 111000000 001 1123334 678999
Q ss_pred HHHHHhhcCCCEEEEEch-hhHHHHHccc-----CC-----------------C-ccchHHHhhh-h-----c--CCCCC
Q 010743 212 KRMKKLLSNGTILVGHSL-NNDLEVLKLD-----HP-----------------R-VIDTSLIFKY-V-----D--EYRRP 259 (502)
Q Consensus 212 ~~l~~fl~~g~ILVGHnl-~fDl~fLk~~-----~p-----------------~-vIDT~~L~r~-~-----~--~~~~~ 259 (502)
.+|.+++..-.++||+|. .||+.+|... .+ + .+|....+.. . + ...++
T Consensus 78 ~~F~~~i~~~~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~~~~~~ 157 (204)
T cd05783 78 REAFKIISEYPIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGNKYREY 157 (204)
T ss_pred HHHHHHHhcCCEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhccccccC
Confidence 999999987789999997 6999998641 11 1 3666655432 1 1 24789
Q ss_pred CHHHHHHHHcCCc
Q 010743 260 SLYNLCKSVLGYE 272 (502)
Q Consensus 260 sL~~La~~~Lgi~ 272 (502)
+|+++|+.+||..
T Consensus 158 ~L~~Va~~~lg~~ 170 (204)
T cd05783 158 TLDAVAKALLGEG 170 (204)
T ss_pred cHHHHHHHhcCCC
Confidence 9999998888874
No 80
>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=96.46 E-value=0.079 Score=49.26 Aligned_cols=105 Identities=22% Similarity=0.180 Sum_probs=72.5
Q ss_pred CcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhc-C
Q 010743 142 NIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS-N 220 (502)
Q Consensus 142 ~~~VaID~ETTGl~~g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~-~ 220 (502)
...++||+|++|.++....++.|++-..+ ... ||.+... + .+...|.+++. .
T Consensus 3 ~~~~~~~~~~~~~~~~~~~l~~i~l~~~~-~~~---~i~~~~~----------~-------------~~~~~l~~~l~~~ 55 (178)
T cd06140 3 ADEVALYVELLGENYHTADIIGLALANGG-GAY---YIPLELA----------L-------------LDLAALKEWLEDE 55 (178)
T ss_pred CCceEEEEEEcCCCcceeeEEEEEEEeCC-cEE---EEeccch----------H-------------HHHHHHHHHHhCC
Confidence 45789999999998765668777776543 222 2332211 0 13444556663 3
Q ss_pred CCEEEEEchhhHHHHHccc---CC-CccchHHHhhhhcC-CCCCCHHHHHHHHcCCcc
Q 010743 221 GTILVGHSLNNDLEVLKLD---HP-RVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEI 273 (502)
Q Consensus 221 g~ILVGHnl~fDl~fLk~~---~p-~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~i 273 (502)
+...|+||+.+|+.+|... .+ .+.||...+..+.+ ...++|..|++.|+|.++
T Consensus 56 ~~~ki~~d~K~~~~~l~~~gi~~~~~~fDt~laaYLL~p~~~~~~l~~l~~~yl~~~~ 113 (178)
T cd06140 56 KIPKVGHDAKRAYVALKRHGIELAGVAFDTMLAAYLLDPTRSSYDLADLAKRYLGREL 113 (178)
T ss_pred CCceeccchhHHHHHHHHCCCcCCCcchhHHHHHHHcCCCCCCCCHHHHHHHHcCCCC
Confidence 4579999999999999642 22 35899988888887 344799999999998874
No 81
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=96.32 E-value=0.017 Score=64.48 Aligned_cols=132 Identities=25% Similarity=0.280 Sum_probs=90.2
Q ss_pred EEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhc-CCCE
Q 010743 145 YAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS-NGTI 223 (502)
Q Consensus 145 VaID~ETTGl~~g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~-~g~I 223 (502)
+++|+||+|+++-...++.+++...+ ...| | | -.|+ + ..-++...+..++. .+..
T Consensus 25 ~a~~~et~~l~~~~~~lvg~s~~~~~-~~~y---i-~---------~~~~---------~-~~~~~~~~l~~~l~~~~~~ 80 (593)
T COG0749 25 IAFDTETDGLDPHGADLVGLSVASEE-EAAY---I-P---------LLHG---------P-EQLNVLAALKPLLEDEGIK 80 (593)
T ss_pred ceeeccccccCcccCCeeEEEeeccc-ccee---E-e---------eccc---------h-hhhhhHHHHHHHhhCcccc
Confidence 99999999999854457777776555 2111 1 1 1111 1 11126777888773 2346
Q ss_pred EEEEchhhHHHHHcccC---CCccchHHHhhhhcC-CCCCCHHHHHHHHcCCccCCC------CC-------------CC
Q 010743 224 LVGHSLNNDLEVLKLDH---PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKK------GT-------------PH 280 (502)
Q Consensus 224 LVGHnl~fDl~fLk~~~---p~vIDT~~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~------~~-------------~H 280 (502)
.||||+.+|+.+|...- +..-||+.....+.+ ...+.++.|+++|++...... +. .-
T Consensus 81 kv~~~~K~d~~~l~~~Gi~~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~~~~~~~~~~~~~~~ 160 (593)
T COG0749 81 KVGQNLKYDYKVLANLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQLTFADVKLEKATE 160 (593)
T ss_pred hhccccchhHHHHHHcCCcccchHHHHHHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhccccccCccccchHHHHHH
Confidence 99999999999998754 346788877776665 668999999999988764320 00 12
Q ss_pred CHHHHHHHHHHHHHHHHHhc
Q 010743 281 NCLDDASAAMKLVLAIIERR 300 (502)
Q Consensus 281 dAleDA~Ata~L~~~~l~~g 300 (502)
.+.+||.++.+|+..+....
T Consensus 161 y~a~~a~~~~~L~~~l~~~l 180 (593)
T COG0749 161 YAAEDADATLRLESILEPEL 180 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 35689999999998877543
No 82
>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=96.19 E-value=0.045 Score=53.51 Aligned_cols=66 Identities=27% Similarity=0.343 Sum_probs=49.4
Q ss_pred CHHHHHHHHHHhhcC-CCEEEEEch-hhHHHHHccc-------CC------------------CccchHHHhhhhcCCCC
Q 010743 206 SLAEIQKRMKKLLSN-GTILVGHSL-NNDLEVLKLD-------HP------------------RVIDTSLIFKYVDEYRR 258 (502)
Q Consensus 206 ~~~dV~~~l~~fl~~-g~ILVGHnl-~fDl~fLk~~-------~p------------------~vIDT~~L~r~~~~~~~ 258 (502)
+-.+++.+|++++.. +.+|||||. .||+.+|... .| +.+|+..+.+......+
T Consensus 77 ~E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~~~~~ 156 (208)
T cd05782 77 DEKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYGARAR 156 (208)
T ss_pred CHHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccCccCC
Confidence 346889999999965 678999997 7999999751 11 15787777654322578
Q ss_pred CCHHHHHHHHcCCc
Q 010743 259 PSLYNLCKSVLGYE 272 (502)
Q Consensus 259 ~sL~~La~~~Lgi~ 272 (502)
++|+.+| .+||++
T Consensus 157 ~~L~~va-~~lG~~ 169 (208)
T cd05782 157 ASLDLLA-KLLGIP 169 (208)
T ss_pred CCHHHHH-HHhCCC
Confidence 9999999 678885
No 83
>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=95.93 E-value=0.21 Score=49.58 Aligned_cols=143 Identities=14% Similarity=0.103 Sum_probs=86.8
Q ss_pred CcEEEEEEeccCC-----CCCcccEEEEEEEEc-CCcEE-E------EEEEcCCCcccccccccCCCChhhhccCCCCHH
Q 010743 142 NIMYAVDCEMVLC-----EDGSEGLVRLCVVDR-NLKVT-I------DELVKPEKAVADYRSEITGLTADDLVGVTCSLA 208 (502)
Q Consensus 142 ~~~VaID~ETTGl-----~~g~~~I~rVsvVd~-~G~vi-~------d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~ 208 (502)
..++++|+|+.+- +|..+.|..|+.+-. +.... . --++.+...-........++....+.-.+ +-.
T Consensus 4 l~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~v~~~~-~E~ 82 (231)
T cd05778 4 LTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKSNASNGRIRSGLSGIPVEVVE-SEL 82 (231)
T ss_pred eEEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccchhhhhccccCCCCCeEEEeC-CHH
Confidence 4688999998753 244567998888743 22211 1 12233333111111112233334455555 677
Q ss_pred HHHHHHHHhhc--CCCEEEEEch-hhHHHHHccc------------------------------CC-----------C-c
Q 010743 209 EIQKRMKKLLS--NGTILVGHSL-NNDLEVLKLD------------------------------HP-----------R-V 243 (502)
Q Consensus 209 dV~~~l~~fl~--~g~ILVGHnl-~fDl~fLk~~------------------------------~p-----------~-v 243 (502)
+...+|.+++. .-.||+|||+ .||+.+|-.. .. + +
T Consensus 83 ~LL~~f~~~i~~~DPDii~GyNi~~fd~~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~~g~~~~~~~~i~GRi~ 162 (231)
T cd05778 83 ELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDEWGYTHTSGIKIVGRHI 162 (231)
T ss_pred HHHHHHHHHHHHhCCCEEEEeccccCcHHHHHHHHHHhCCcchhhhccCCCCCCcccccccccccccccCCceEEeeEEE
Confidence 88888888774 4489999998 6898887320 00 0 3
Q ss_pred cchHHHhhhhcCCCCCCHHHHHHHHcCCccCCCCCCCCHHHHHH
Q 010743 244 IDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNCLDDAS 287 (502)
Q Consensus 244 IDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~ 287 (502)
+|+..+.+......+|+|.++|..+||..... ..|..+.+.+
T Consensus 163 lD~~~~~r~~~kl~sYsL~~V~~~~L~~~k~~--~~~~~i~~~~ 204 (231)
T cd05778 163 LNVWRLMRSELALTNYTLENVVYHVLHQRIPL--YSNKTLTEWY 204 (231)
T ss_pred eEhHHHHHHHcCcccCCHHHHHHHHhCCCCCC--CCHHHHHHHH
Confidence 56666776655578999999999999987653 3555555543
No 84
>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=95.84 E-value=0.16 Score=50.11 Aligned_cols=92 Identities=24% Similarity=0.280 Sum_probs=64.7
Q ss_pred CHHHHHHHHHHhhcC-CCEEEEEch-hhHHHHHccc-------CC-------------------CccchHHHhhhhcCCC
Q 010743 206 SLAEIQKRMKKLLSN-GTILVGHSL-NNDLEVLKLD-------HP-------------------RVIDTSLIFKYVDEYR 257 (502)
Q Consensus 206 ~~~dV~~~l~~fl~~-g~ILVGHnl-~fDl~fLk~~-------~p-------------------~vIDT~~L~r~~~~~~ 257 (502)
.-.++...|++++.+ ...|||||- .||+.+|... .| +-+||+.+.....+..
T Consensus 36 ~E~~lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~g~~~ 115 (209)
T PF10108_consen 36 DEKELLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFYGAKA 115 (209)
T ss_pred CHHHHHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhccCccc
Confidence 467889999999954 458999995 8999999751 11 1377776654433367
Q ss_pred CCCHHHHHHHHcCCccCCC--C--------------CCCCHHHHHHHHHHHHHHHHH
Q 010743 258 RPSLYNLCKSVLGYEIRKK--G--------------TPHNCLDDASAAMKLVLAIIE 298 (502)
Q Consensus 258 ~~sL~~La~~~Lgi~iq~~--~--------------~~HdAleDA~Ata~L~~~~l~ 298 (502)
+.||+.|| ..||+|-..+ | -+.=+..|+.+|+.||+++.-
T Consensus 116 ~~sLd~la-~~lgiPgK~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~ 171 (209)
T PF10108_consen 116 RTSLDELA-ALLGIPGKDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFEL 171 (209)
T ss_pred cCCHHHHH-HHcCCCCCCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 89999999 8899984211 0 012245799999999988764
No 85
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=95.63 E-value=0.028 Score=57.07 Aligned_cols=162 Identities=19% Similarity=0.178 Sum_probs=106.6
Q ss_pred CCCCCCCcEEEEEEeccCCCCCcccEEEEEEEEc-----CCc---------------EE---EEEEEcCCCccccccccc
Q 010743 136 SKTMTSNIMYAVDCEMVLCEDGSEGLVRLCVVDR-----NLK---------------VT---IDELVKPEKAVADYRSEI 192 (502)
Q Consensus 136 ~~~~~~~~~VaID~ETTGl~~g~~~I~rVsvVd~-----~G~---------------vi---~d~LVkP~~~I~dy~T~i 192 (502)
++.++-..++.+|.|+||+..-...|+++++.++ +|. .+ ...++.|.........++
T Consensus 7 se~pr~~tf~fldleat~lp~~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~v~~p~aeei 86 (318)
T KOG4793|consen 7 SEVPRLRTFSFLDLEATGLPGWIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVPVTRPIAEEI 86 (318)
T ss_pred CcCCceeEEEeeeeccccCCcccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcCCcChhhhhh
Confidence 4556667899999999999865556888887653 222 12 334677777767778899
Q ss_pred CCCChhhhccCC-CCH-HHHHHHHHHhhc---CCCEEEEEch-hhHHHHHccc-------CCC---ccchHHHhhhhc--
Q 010743 193 TGLTADDLVGVT-CSL-AEIQKRMKKLLS---NGTILVGHSL-NNDLEVLKLD-------HPR---VIDTSLIFKYVD-- 254 (502)
Q Consensus 193 hGIT~e~L~~ap-~~~-~dV~~~l~~fl~---~g~ILVGHnl-~fDl~fLk~~-------~p~---vIDT~~L~r~~~-- 254 (502)
||++..-+.-.. .-| .++.+-|..|+. .---||+||- .||+..|... .+. .+|+...++...
T Consensus 87 tgls~~~~~l~rr~~~D~dla~LL~afls~lp~p~CLVaHng~~~dfpil~qela~lg~~lpq~lvcvdslpa~~ald~a 166 (318)
T KOG4793|consen 87 TGLSQPFLALQRRLAFDKDLAKLLTAFLSRLPTPGCLVAHNGNEYDFPILAQELAGLGYSLPQDLVCVDSLPALNALDRA 166 (318)
T ss_pred cccccHHHHHHHHhhhhHHHHHHHHHHHhcCCCCceEEeecCCccccHHHHHHHHhcCccchhhhcCcchhHHHHHHhhh
Confidence 999986555222 022 244444555552 2345899985 6788877763 232 477776655431
Q ss_pred ------C--CCCCCHHHHHHHHcCCccCCCCCCCCHHHHHHHHHHHHHHHHHh
Q 010743 255 ------E--YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLVLAIIER 299 (502)
Q Consensus 255 ------~--~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~Ata~L~~~~l~~ 299 (502)
+ .+.++|..+-.+|++-.-. ...|.+..|.-+-.-.|+.....
T Consensus 167 ~s~~tr~~~~~~~~l~~If~ry~~q~ep--pa~~~~e~d~~~l~~~fqf~~~e 217 (318)
T KOG4793|consen 167 NSMVTRPEVRRMYSLGSIFLRYVEQREP--PAGHVAEGDVNGLLFIFQFRINE 217 (318)
T ss_pred cCcccCCCCCcccccchHHHhhhcccCC--CcceeeecccchhHHHHHHHHHH
Confidence 2 5788999888777665322 24899999988887777765543
No 86
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=95.54 E-value=0.012 Score=45.55 Aligned_cols=60 Identities=27% Similarity=0.412 Sum_probs=44.9
Q ss_pred hcCCCCCCCChHhhhccCCCCceee-ecccc-ccCCcceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 321 FLHRIPTKVPSEELHGVIPGDFTIE-AKAVK-RIRGDNYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 321 ~~~~iP~~~~~eel~~~f~~~~~i~-~k~~~-~~~g~~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
+..+||++++.++|..+|...-.+. ++-.. ......+.|+|.|.+.++|..|.+.++|..
T Consensus 2 ~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~ 63 (70)
T PF00076_consen 2 YVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKK 63 (70)
T ss_dssp EEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEE
T ss_pred EEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCE
Confidence 4568999999999999887744442 22111 223347899999999999999999998753
No 87
>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=95.30 E-value=0.12 Score=51.22 Aligned_cols=131 Identities=21% Similarity=0.221 Sum_probs=83.0
Q ss_pred CcEEEEEEeccCCCCC-cccEEEEEEEEc-----CCc-------EEEEEEEcCCCc--ccccccccCCCChhhhccCCCC
Q 010743 142 NIMYAVDCEMVLCEDG-SEGLVRLCVVDR-----NLK-------VTIDELVKPEKA--VADYRSEITGLTADDLVGVTCS 206 (502)
Q Consensus 142 ~~~VaID~ETTGl~~g-~~~I~rVsvVd~-----~G~-------vi~d~LVkP~~~--I~dy~T~ihGIT~e~L~~ap~~ 206 (502)
-.+++|-+=|+--... ..+|+.|+++-. ++. ..+-++++|... .+......-......+.-.+ +
T Consensus 3 l~v~sls~~T~~n~k~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~v~~~~-~ 81 (234)
T cd05776 3 LTVMSLSIKTVLNSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKVRIFE-N 81 (234)
T ss_pred eEEEEEEeEEEecCcCCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCCCCCchHHHHHHhcCCcEEEeC-C
Confidence 4567777777644332 467999998733 221 124456677543 22222222122222234444 6
Q ss_pred HHHHHHHHHHhhc--CCCEEEEEch-hhHHHHHcc-------c------------CC----------------C-ccchH
Q 010743 207 LAEIQKRMKKLLS--NGTILVGHSL-NNDLEVLKL-------D------------HP----------------R-VIDTS 247 (502)
Q Consensus 207 ~~dV~~~l~~fl~--~g~ILVGHnl-~fDl~fLk~-------~------------~p----------------~-vIDT~ 247 (502)
-.+.+..|..++. .-.|+||||+ .||+.+|-. . .| | ++|+.
T Consensus 82 E~~LL~~f~~~i~~~DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~ 161 (234)
T cd05776 82 ERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTY 161 (234)
T ss_pred HHHHHHHHHHHHhhcCCCEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCchhhccH
Confidence 6788888888884 3489999999 899998843 0 00 1 47888
Q ss_pred HHhhhhcCCCCCCHHHHHHHHcCCcc
Q 010743 248 LIFKYVDEYRRPSLYNLCKSVLGYEI 273 (502)
Q Consensus 248 ~L~r~~~~~~~~sL~~La~~~Lgi~i 273 (502)
.+++......+|+|.++|..+||..-
T Consensus 162 ~~~k~~~~~~sY~L~~va~~~Lg~~k 187 (234)
T cd05776 162 LSAKELIRCKSYDLTELSQQVLGIER 187 (234)
T ss_pred HHHHHHhCCCCCChHHHHHHHhCcCc
Confidence 88877666789999999999999853
No 88
>PRK05762 DNA polymerase II; Reviewed
Probab=95.14 E-value=0.27 Score=57.19 Aligned_cols=139 Identities=19% Similarity=0.232 Sum_probs=88.4
Q ss_pred CCCcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhc
Q 010743 140 TSNIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS 219 (502)
Q Consensus 140 ~~~~~VaID~ETTGl~~g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~ 219 (502)
.+-++++||+||..- ..|..|++.......++ .|.+..+.+ .+.+...+ +-.+.+..|.+++.
T Consensus 153 p~lrvlsfDIE~~~~----~~i~sI~~~~~~~~~vi--~ig~~~~~~----------~~~v~~~~-sE~~LL~~F~~~i~ 215 (786)
T PRK05762 153 PPLKVVSLDIETSNK----GELYSIGLEGCGQRPVI--MLGPPNGEA----------LDFLEYVA-DEKALLEKFNAWFA 215 (786)
T ss_pred CCCeEEEEEEEEcCC----CceEEeeecCCCCCeEE--EEECCCCCC----------cceEEEcC-CHHHHHHHHHHHHH
Confidence 456899999999753 24777777633222221 122222110 11144445 77889999999984
Q ss_pred C--CCEEEEEch-hhHHHHHccc---------------------CC------------C-ccchHHHhhhhc-CCCCCCH
Q 010743 220 N--GTILVGHSL-NNDLEVLKLD---------------------HP------------R-VIDTSLIFKYVD-EYRRPSL 261 (502)
Q Consensus 220 ~--g~ILVGHnl-~fDl~fLk~~---------------------~p------------~-vIDT~~L~r~~~-~~~~~sL 261 (502)
. -.||||||+ .||+.+|... .+ + ++|+..+.+... ...+++|
T Consensus 216 ~~DPDIIvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~~~~~l~sysL 295 (786)
T PRK05762 216 EHDPDVIIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATWVFDSFSL 295 (786)
T ss_pred hcCCCEEEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHHhhccCCCCCH
Confidence 3 269999997 6899998530 01 0 367777766554 3689999
Q ss_pred HHHHHHHcCCccCCCCCCC-------------------CHHHHHHHHHHHHHHH
Q 010743 262 YNLCKSVLGYEIRKKGTPH-------------------NCLDDASAAMKLVLAI 296 (502)
Q Consensus 262 ~~La~~~Lgi~iq~~~~~H-------------------dAleDA~Ata~L~~~~ 296 (502)
+++|+.+||..-... ..| =++.||..|..||.++
T Consensus 296 ~~Va~~~Lg~~K~~~-d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 296 EYVSQRLLGEGKAID-DPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred HHHHHHHhCCCeecc-CccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999998643210 011 1478999999998743
No 89
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=95.10 E-value=0.3 Score=58.58 Aligned_cols=149 Identities=16% Similarity=0.239 Sum_probs=92.1
Q ss_pred CCCcEEEEEEeccCCC------CCcccEEEEEEE-EcCCcE---EEEEEEcCCCcccccccccCCCChhhhccCCCCHHH
Q 010743 140 TSNIMYAVDCEMVLCE------DGSEGLVRLCVV-DRNLKV---TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAE 209 (502)
Q Consensus 140 ~~~~~VaID~ETTGl~------~g~~~I~rVsvV-d~~G~v---i~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~d 209 (502)
.|.++++||+||++.. +..+.|+.|+.+ ...|.. ....++-+.. ...+.| ..+...+ +-.+
T Consensus 262 pplrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~~~~~r~vftl~~-----c~~i~g---~~V~~f~-sE~e 332 (1054)
T PTZ00166 262 APLRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLTKFIFTLKE-----CASIAG---ANVLSFE-TEKE 332 (1054)
T ss_pred CCcEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCccCCcceEEEecCc-----cccCCC---ceEEEeC-CHHH
Confidence 4668999999998642 234679999987 334431 1222222211 111222 1233334 6678
Q ss_pred HHHHHHHhhc--CCCEEEEEch-hhHHHHHcc-------c----------CC-------------------------C-c
Q 010743 210 IQKRMKKLLS--NGTILVGHSL-NNDLEVLKL-------D----------HP-------------------------R-V 243 (502)
Q Consensus 210 V~~~l~~fl~--~g~ILVGHnl-~fDl~fLk~-------~----------~p-------------------------~-v 243 (502)
.+..|.+++. .-.||+|||+ .||+.+|-. . .+ + +
T Consensus 333 LL~~f~~~I~~~DPDII~GYNi~~FDlpYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~~ 412 (1054)
T PTZ00166 333 LLLAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQ 412 (1054)
T ss_pred HHHHHHHHHHhcCCCEEEecCCcCCcHHHHHHHHHHhCCCchhhcCcccCCCccccccccccccccccccceeEeeeEEE
Confidence 8888888773 3589999998 589988732 0 00 1 3
Q ss_pred cchHHHhhhhcCCCCCCHHHHHHHHcCCccCC----------CCCCC-------CHHHHHHHHHHHHHHHH
Q 010743 244 IDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRK----------KGTPH-------NCLDDASAAMKLVLAII 297 (502)
Q Consensus 244 IDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~----------~~~~H-------dAleDA~Ata~L~~~~l 297 (502)
+|+..+++......+|+|+++|..+||..... .+..+ =++.||..+++|+.++.
T Consensus 413 iDl~~~~~~~~kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L~~kl~ 483 (1054)
T PTZ00166 413 FDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLL 483 (1054)
T ss_pred EEHHHHHHHhcCcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 66666766655578999999999999965321 00111 23678888888887654
No 90
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=95.03 E-value=0.25 Score=52.33 Aligned_cols=145 Identities=19% Similarity=0.224 Sum_probs=88.8
Q ss_pred CCcEEEEEEeccCCCC-----C--cccEEEEEEEEcCCcE----E-EEEEEcCCCcccccccccCCCChhhhccCCCCHH
Q 010743 141 SNIMYAVDCEMVLCED-----G--SEGLVRLCVVDRNLKV----T-IDELVKPEKAVADYRSEITGLTADDLVGVTCSLA 208 (502)
Q Consensus 141 ~~~~VaID~ETTGl~~-----g--~~~I~rVsvVd~~G~v----i-~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~ 208 (502)
+..++++|+||+.-.. . .+.|+.|+++..++.. . ......|...+ .|+. +.... .-.
T Consensus 2 ~~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~---~~~~~-~E~ 70 (471)
T smart00486 2 PLKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCKEI-------DGVE---VYEFN-NEK 70 (471)
T ss_pred CceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcCCC-------CCCe---EEecC-CHH
Confidence 3578999999986431 1 3578999988654321 1 11122333332 2222 22222 456
Q ss_pred HHHHHHHHhhcC--CCEEEEEchh-hHHHHHccc--------C---------------------------------CC-c
Q 010743 209 EIQKRMKKLLSN--GTILVGHSLN-NDLEVLKLD--------H---------------------------------PR-V 243 (502)
Q Consensus 209 dV~~~l~~fl~~--g~ILVGHnl~-fDl~fLk~~--------~---------------------------------p~-v 243 (502)
+...+|.+++.. ..+++|||.. ||+.+|... . .+ .
T Consensus 71 ~lL~~f~~~i~~~dpdii~g~N~~~FD~~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ 150 (471)
T smart00486 71 ELLKAFLEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSKSFGKTIKVKIKGRLV 150 (471)
T ss_pred HHHHHHHHHHHHhCCCEEEeecCCCCCHHHHHHHHHHcCCCCHHHcCcCCCCCCcccccCccccccccccceeEeccEEE
Confidence 778888877742 3699999985 899987531 0 01 3
Q ss_pred cchHHHhhhhcCCCCCCHHHHHHHHcCCccCCC-----------C------CCCCHHHHHHHHHHHHHHH
Q 010743 244 IDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKK-----------G------TPHNCLDDASAAMKLVLAI 296 (502)
Q Consensus 244 IDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~-----------~------~~HdAleDA~Ata~L~~~~ 296 (502)
+|+..+++......+++|+.++..+||..-..- + ...-.+.||..+.+|+.++
T Consensus 151 ~Dl~~~~~~~~kl~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 151 IDLYNLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred EEhHHHHHHHhCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 677777777665789999999988888432210 0 0111256888888888775
No 91
>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=95.00 E-value=0.36 Score=43.04 Aligned_cols=104 Identities=22% Similarity=0.200 Sum_probs=65.9
Q ss_pred EEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhc-CCC
Q 010743 144 MYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS-NGT 222 (502)
Q Consensus 144 ~VaID~ETTGl~~g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~-~g~ 222 (502)
++++|+|+.+..+-...++.+++-..++.+. ||.+.. . .+ . ...|.+++. .+.
T Consensus 1 ~~~~~~e~~~~~~~~~~~~~l~l~~~~~~~~---~i~~~~------~---~~----------~----~~~l~~~l~~~~~ 54 (150)
T cd09018 1 VFAFDTETDSLDNISANLVLIQLAIEPGVAA---LIPVAH------D---YL----------A----LELLKPLLEDEKA 54 (150)
T ss_pred CEEEEeecCCCCCCCceEEEEEEEcCCCcEE---EEEcCC------c---cc----------C----HHHHHHHhcCCCC
Confidence 4789998876664233466666665444322 222110 0 00 1 122445552 346
Q ss_pred EEEEEchhhHHHHHccc---C-CCccchHHHhhhhcCCC-CCCHHHHHHHHcCCcc
Q 010743 223 ILVGHSLNNDLEVLKLD---H-PRVIDTSLIFKYVDEYR-RPSLYNLCKSVLGYEI 273 (502)
Q Consensus 223 ILVGHnl~fDl~fLk~~---~-p~vIDT~~L~r~~~~~~-~~sL~~La~~~Lgi~i 273 (502)
..||||+..|+.+|... . ..+.||...+..+.+.. +.+|..|+++|||.++
T Consensus 55 ~kv~~d~K~~~~~L~~~~~~~~~~~~D~~laayLl~p~~~~~~l~~l~~~~l~~~~ 110 (150)
T cd09018 55 LKVGQNLKYDRGILLNYFIELRGIAFDTMLEAYILNSVAGRWDMDSLVERWLGHKL 110 (150)
T ss_pred ceeeecHHHHHHHHHHcCCccCCcchhHHHHHHHhCCCCCCCCHHHHHHHHhCCCc
Confidence 68999999999999653 2 23689999988887733 4699999999988873
No 92
>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=94.62 E-value=0.57 Score=44.53 Aligned_cols=102 Identities=18% Similarity=0.089 Sum_probs=66.2
Q ss_pred cEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHhhc-CC
Q 010743 143 IMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS-NG 221 (502)
Q Consensus 143 ~~VaID~ETTGl~~g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~-~g 221 (502)
..+++|+|+....+-...++.+++-..++. . ||.+ + . .......|..++. .+
T Consensus 25 ~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~-~---~i~~-------------l-----~-----~~~~~~~L~~~L~~~~ 77 (192)
T cd06147 25 KEIAVDLEHHSYRSYLGFTCLMQISTREED-Y---IVDT-------------L-----K-----LRDDMHILNEVFTDPN 77 (192)
T ss_pred CeEEEEeEecCCccCCCceEEEEEecCCCc-E---EEEe-------------c-----c-----cccchHHHHHHhcCCC
Confidence 488999987655532334777777755542 2 2221 0 1 1111233555563 34
Q ss_pred CEEEEEchhhHHHHHc-cc---CCCccchHHHhhhhcCCCCCCHHHHHHHHcCCc
Q 010743 222 TILVGHSLNNDLEVLK-LD---HPRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYE 272 (502)
Q Consensus 222 ~ILVGHnl~fDl~fLk-~~---~p~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~ 272 (502)
...|||++..|+..|+ .. ...+.||...+..+.+. +++|..|++.|||..
T Consensus 78 i~kv~~d~K~~~~~L~~~~gi~~~~~fD~~laaYLL~p~-~~~l~~l~~~yl~~~ 131 (192)
T cd06147 78 ILKVFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLP-RHSLAYLLQKYCNVD 131 (192)
T ss_pred ceEEEechHHHHHHHHHHhCCCcCchHHHHHHHHHhCCC-cccHHHHHHHHhCCC
Confidence 6789999999999996 21 12248999988888776 569999999998876
No 93
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=94.45 E-value=0.5 Score=47.78 Aligned_cols=113 Identities=11% Similarity=0.027 Sum_probs=74.9
Q ss_pred CCCCcEEEEEEeccCCCCCcccEEEEEEEEcC-CcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHHHHHh
Q 010743 139 MTSNIMYAVDCEMVLCEDGSEGLVRLCVVDRN-LKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (502)
Q Consensus 139 ~~~~~~VaID~ETTGl~~g~~~I~rVsvVd~~-G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~f 217 (502)
....+++.||+||||++.....|+-++.-... +....-.+. .++|-.-..|++.|+..
T Consensus 95 ~~~e~~~FFDiETTGL~~ag~~I~~~g~a~~~~~~~~Vrq~~---------------------lp~p~~E~avle~fl~~ 153 (278)
T COG3359 95 YEAEDVAFFDIETTGLDRAGNTITLVGGARGVDDTMHVRQHF---------------------LPAPEEEVAVLENFLHD 153 (278)
T ss_pred ccccceEEEeeeccccCCCCCeEEEEEEEEccCceEEEEeec---------------------CCCcchhhHHHHHHhcC
Confidence 44678999999999999744445555555543 332222222 22331122466777777
Q ss_pred hcCCCEEEEEc-hhhHHHHHcc---cC-C----C-ccchHHHhhhhcC--CCCCCHHHHHHHHcCCccC
Q 010743 218 LSNGTILVGHS-LNNDLEVLKL---DH-P----R-VIDTSLIFKYVDE--YRRPSLYNLCKSVLGYEIR 274 (502)
Q Consensus 218 l~~g~ILVGHn-l~fDl~fLk~---~~-p----~-vIDT~~L~r~~~~--~~~~sL~~La~~~Lgi~iq 274 (502)
. ....||-.| ..||.-|++. .+ + . -+|.....|++++ ..+.+|+.+=+ +||+.-.
T Consensus 154 ~-~~~~lvsfNGkaFD~PfikR~v~~~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr-~LGi~R~ 220 (278)
T COG3359 154 P-DFNMLVSFNGKAFDIPFIKRMVRDRLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTVER-ILGIRRE 220 (278)
T ss_pred C-CcceEEEecCcccCcHHHHHHHhcccccCccccchhhhhhhhhhhhccCCCCChhhHHH-HhCcccc
Confidence 7 778999998 5899999992 21 1 1 3788888887775 67889999985 8998743
No 94
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=94.38 E-value=0.086 Score=41.37 Aligned_cols=57 Identities=25% Similarity=0.378 Sum_probs=41.7
Q ss_pred hcCCCCCCCChHhhhccCCCCceee-ec--cccccCCcceeEEEEeCCHHHHHHHHHhhcC
Q 010743 321 FLHRIPTKVPSEELHGVIPGDFTIE-AK--AVKRIRGDNYAAFAIFSSPQEANQAFENVKG 378 (502)
Q Consensus 321 ~~~~iP~~~~~eel~~~f~~~~~i~-~k--~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g 378 (502)
+..+||++++.++|..+|.....+. +. ..+. .-..+.|+|.|.|.++|..|.+.+.|
T Consensus 2 ~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~ 61 (70)
T PF14259_consen 2 YISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNG 61 (70)
T ss_dssp EEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred EEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCC
Confidence 4578999999999999998855442 22 1222 22388999999999999999999854
No 95
>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006133 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold [].; GO: 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 4AHC_A 3A2F_A 2JGU_A 4AIL_C 1NOY_A 1NOZ_B 3IAY_A 1WNS_A 3K5O_A ....
Probab=93.87 E-value=0.18 Score=51.04 Aligned_cols=88 Identities=16% Similarity=0.197 Sum_probs=56.6
Q ss_pred CCCcEEEEEEeccCCC-----CCcccEEEEEEE-EcCC-----cEEEEEEEcCCCcccccccccCCCChhhhccCCCCHH
Q 010743 140 TSNIMYAVDCEMVLCE-----DGSEGLVRLCVV-DRNL-----KVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLA 208 (502)
Q Consensus 140 ~~~~~VaID~ETTGl~-----~g~~~I~rVsvV-d~~G-----~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~ 208 (502)
.+.++++||+||..-. +..++|..|+++ ...| ...+-++..+.. +.+ ...+.-.+ +-.
T Consensus 155 p~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~~~~~~-~~~---------~~~v~~~~-~E~ 223 (325)
T PF03104_consen 155 PPLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTLGSCDS-IED---------NVEVIYFD-SEK 223 (325)
T ss_dssp GGSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEECSCSCC-TTC---------TTEEEEES-SHH
T ss_pred cccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEecCCCC-CCC---------CcEEEEEC-CHH
Confidence 4678999999999765 345689999975 3222 222333333332 221 33333444 677
Q ss_pred HHHHHHHHhhc--CCCEEEEEch-hhHHHHHcc
Q 010743 209 EIQKRMKKLLS--NGTILVGHSL-NNDLEVLKL 238 (502)
Q Consensus 209 dV~~~l~~fl~--~g~ILVGHnl-~fDl~fLk~ 238 (502)
+++..|.+++. .-.|++|||+ .||+.+|-.
T Consensus 224 ~lL~~f~~~i~~~dPDii~GyN~~~fD~~yl~~ 256 (325)
T PF03104_consen 224 ELLEAFLDIIQEYDPDIITGYNIDGFDLPYLIE 256 (325)
T ss_dssp HHHHHHHHHHHHHS-SEEEESSTTTTHHHHHHH
T ss_pred HHHHHHHHHHHhcCCcEEEEecccCCCHHHHHH
Confidence 88888888774 3469999998 599999853
No 96
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.35 E-value=0.42 Score=56.36 Aligned_cols=94 Identities=18% Similarity=0.158 Sum_probs=67.0
Q ss_pred CHHHHHHHHHHhhcC-CCEEEEEchhhHHHHHcccC----CCccchHHHhhhhcCCCCCCHHHHHHHHcCCccCC-----
Q 010743 206 SLAEIQKRMKKLLSN-GTILVGHSLNNDLEVLKLDH----PRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRK----- 275 (502)
Q Consensus 206 ~~~dV~~~l~~fl~~-g~ILVGHnl~fDl~fLk~~~----p~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~----- 275 (502)
....+...|..++.. +...||||+.||+.+|.... +.+.||...+..+.+...++|+.|+..||+...-.
T Consensus 362 ~~~~~~~~l~~~l~~~~~~~v~~n~K~d~~~l~~~gi~~~~~~~Dt~la~yll~~~~~~~l~~la~~yl~~~~~~~~~~~ 441 (887)
T TIGR00593 362 LTILTDDKFARWLLNEQIKKIGHDAKFLMHLLKREGIELGGVIFDTMLAAYLLDPAQVSTLDTLARRYLVEELILDEKIG 441 (887)
T ss_pred hhHHHHHHHHHHHhCCCCcEEEeeHHHHHHHHHhCCCCCCCcchhHHHHHHHcCCCCCCCHHHHHHHHcCcccccHHHhc
Confidence 345667778888832 24589999999999997531 24689999888888744569999999998865211
Q ss_pred C-CCC----------CCHHHHHHHHHHHHHHHHHh
Q 010743 276 K-GTP----------HNCLDDASAAMKLVLAIIER 299 (502)
Q Consensus 276 ~-~~~----------HdAleDA~Ata~L~~~~l~~ 299 (502)
+ +.. .-|..||.+++.||..+...
T Consensus 442 ~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~ 476 (887)
T TIGR00593 442 GKLAKFAFPPLEEATEYLARRAAATKRLAEELLKE 476 (887)
T ss_pred cCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 0 000 13677899999999877654
No 97
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=92.61 E-value=0.19 Score=46.46 Aligned_cols=61 Identities=13% Similarity=0.152 Sum_probs=46.6
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceee---eccccccCCcceeEEEEeCCHHHHHHHHHhhcCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIE---AKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGN 379 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~---~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~ 379 (502)
+++..+||..++.++|..+|..--.|. +...+.-.-..++|+|.|.+.++|..|++.+++.
T Consensus 36 ~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~ 99 (144)
T PLN03134 36 KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGK 99 (144)
T ss_pred EEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCC
Confidence 689999999999999999998743442 2222221123679999999999999999999664
No 98
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.13 E-value=2.5 Score=51.49 Aligned_cols=105 Identities=17% Similarity=0.212 Sum_probs=73.2
Q ss_pred cccCCCChhhhccCCCCHHHHHHHHHHhhc--CCCEEEEEch-hhHHHHHccc---------------------------
Q 010743 190 SEITGLTADDLVGVTCSLAEIQKRMKKLLS--NGTILVGHSL-NNDLEVLKLD--------------------------- 239 (502)
Q Consensus 190 T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~--~g~ILVGHnl-~fDl~fLk~~--------------------------- 239 (502)
...-|+.+..|..-. +-.+.+..++.++. .-.+++|||+ .||+.+|-..
T Consensus 568 ~~~~~~~~~~L~~~~-sEr~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~ 646 (1172)
T TIGR00592 568 GEFPGKKPSLVEDLA-TERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGE 646 (1172)
T ss_pred hhhhccCCcEEEEec-CHHHHHHHHHHHHHhcCCCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccCCCccccccc
Confidence 345567777777776 77788888888886 6789999997 6899887430
Q ss_pred --CCC-ccchHHHhhhhcCCCCCCHHHHHHHHcCCccCCC-----------C-----CCCCHHHHHHHHHHHHHH
Q 010743 240 --HPR-VIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKK-----------G-----TPHNCLDDASAAMKLVLA 295 (502)
Q Consensus 240 --~p~-vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~-----------~-----~~HdAleDA~Ata~L~~~ 295 (502)
..+ ++|+..+++......+|+|.++|..+||.+-..- + -.+.++.||..++.|+.+
T Consensus 647 ~~~Grl~~D~~~~~k~~~~~~sy~L~~v~~~~L~~~k~~~~~~~i~~~~~~~~~~~~~~~y~~~Da~l~~~L~~~ 721 (1172)
T TIGR00592 647 RTCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESSSLTYLLEHTWKDAMFILQIMCE 721 (1172)
T ss_pred eECCEEEEEHHHHHHHHhCcCCCCHHHHHHHHhCCCCcccCHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 112 4788888877666789999999999998632210 0 012346677777777653
No 99
>smart00362 RRM_2 RNA recognition motif.
Probab=91.99 E-value=0.25 Score=37.08 Aligned_cols=60 Identities=30% Similarity=0.411 Sum_probs=42.5
Q ss_pred hhcCCCCCCCChHhhhccCCCCceee-eccccccCCcceeEEEEeCCHHHHHHHHHhhcCC
Q 010743 320 LFLHRIPTKVPSEELHGVIPGDFTIE-AKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGN 379 (502)
Q Consensus 320 l~~~~iP~~~~~eel~~~f~~~~~i~-~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~ 379 (502)
++..+||.+++.++|..+|...-.+. +.-........+.+++.|.+.++|..|.+.++|.
T Consensus 2 v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~ 62 (72)
T smart00362 2 LFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGT 62 (72)
T ss_pred EEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCc
Confidence 45678899999999998886543332 2211111233678999999999999999998763
No 100
>PHA02570 dexA exonuclease; Provisional
Probab=91.61 E-value=0.65 Score=46.15 Aligned_cols=93 Identities=17% Similarity=0.126 Sum_probs=57.0
Q ss_pred EEEEEeccCCCCCcccEEEEEEEEc--C-Cc-EEEEEEEcCCCcc------------ccc--ccccCCCChhh---hcc-
Q 010743 145 YAVDCEMVLCEDGSEGLVRLCVVDR--N-LK-VTIDELVKPEKAV------------ADY--RSEITGLTADD---LVG- 202 (502)
Q Consensus 145 VaID~ETTGl~~g~~~I~rVsvVd~--~-G~-vi~d~LVkP~~~I------------~dy--~T~ihGIT~e~---L~~- 202 (502)
+.||+||.|..+.. .|+.|++|-+ + |. ..|+.+|.....| ++. +..+-.-++|- |.+
T Consensus 4 lMIDlETmG~~p~A-aIisIgAV~Fdp~~~~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~L~~s 82 (220)
T PHA02570 4 FIIDFETFGNTPDG-AVIDLAVIAFEHDPHNPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEARKNLKPS 82 (220)
T ss_pred EEEEeeccCCCCCc-eEEEEEEEEecCCCCccccHHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHHHHhccCC
Confidence 57999999998765 6999999944 2 21 2355555432211 111 11222222221 111
Q ss_pred -CCCCHHHHHHHHHHhhcCCC------EEEEEchhhHHHHHcc
Q 010743 203 -VTCSLAEIQKRMKKLLSNGT------ILVGHSLNNDLEVLKL 238 (502)
Q Consensus 203 -ap~~~~dV~~~l~~fl~~g~------ILVGHnl~fDl~fLk~ 238 (502)
..+++.+++.+|.+||.... -+=|-+.+||+..|+.
T Consensus 83 ~~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD~~IL~~ 125 (220)
T PHA02570 83 DEDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDFPILVD 125 (220)
T ss_pred CccccHHHHHHHHHHHHHHcCCCccceeEecCCCccCHHHHHH
Confidence 12479999999999996443 3667788999999964
No 101
>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=91.09 E-value=0.29 Score=43.51 Aligned_cols=62 Identities=21% Similarity=0.354 Sum_probs=49.5
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceeeeccccccCCcceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIEAKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
-|+..++|..+++|++=.+|++.-+|..--.-...+..++|+|++.+...|..|.++|.|..
T Consensus 20 iLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n 81 (124)
T KOG0114|consen 20 ILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYN 81 (124)
T ss_pred eEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccc
Confidence 48889999999999999999987777532111114456799999999999999999997764
No 102
>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
Probab=90.44 E-value=0.55 Score=35.37 Aligned_cols=60 Identities=25% Similarity=0.384 Sum_probs=43.3
Q ss_pred hhcCCCCCCCChHhhhccCCCCceee---eccccccCCcceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 320 LFLHRIPTKVPSEELHGVIPGDFTIE---AKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 320 l~~~~iP~~~~~eel~~~f~~~~~i~---~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
+...++|..++.+++..+|...-.|. +..... ....+.+++.|.+.++|..|.+.+++..
T Consensus 2 i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~-~~~~~~~~v~f~s~~~a~~a~~~~~~~~ 64 (74)
T cd00590 2 LFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKD-TKSKGFAFVEFEDEEDAEKALEALNGKE 64 (74)
T ss_pred EEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCe
Confidence 34678899999999888886533332 222222 1347799999999999999999997754
No 103
>smart00360 RRM RNA recognition motif.
Probab=89.49 E-value=0.86 Score=33.88 Aligned_cols=57 Identities=26% Similarity=0.311 Sum_probs=39.9
Q ss_pred CCCCCCCChHhhhccCCCCcee---eeccccccCCcceeEEEEeCCHHHHHHHHHhhcCC
Q 010743 323 HRIPTKVPSEELHGVIPGDFTI---EAKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGN 379 (502)
Q Consensus 323 ~~iP~~~~~eel~~~f~~~~~i---~~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~ 379 (502)
.+||..++.++|..+|...-.+ .+...+......+.|.|.|.+.++|..|.+.+.+.
T Consensus 2 ~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~ 61 (71)
T smart00360 2 GNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGK 61 (71)
T ss_pred CCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCC
Confidence 4678889999998888653333 22222211223679999999999999999998644
No 104
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=89.40 E-value=0.37 Score=50.87 Aligned_cols=61 Identities=20% Similarity=0.287 Sum_probs=47.0
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceee---eccccccCCc-ceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIE---AKAVKRIRGD-NYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~---~k~~~~~~g~-~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
.|+..+||..++.++|..+|...-.|. +...+. .|. .++++|.|.+.++|..|++.|.+..
T Consensus 195 ~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~-tg~~kG~aFV~F~~~e~A~~Ai~~lng~~ 259 (346)
T TIGR01659 195 NLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKL-TGTPRGVAFVRFNKREEAQEAISALNNVI 259 (346)
T ss_pred eeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCC-CCccceEEEEEECCHHHHHHHHHHhCCCc
Confidence 588999999999999999997644443 222222 222 5799999999999999999998653
No 105
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=89.31 E-value=1.7 Score=43.25 Aligned_cols=105 Identities=17% Similarity=0.243 Sum_probs=78.6
Q ss_pred ccCCCChhhhccCCCCHHHHHHHHH---HhhcCCCEEEEEchhhHHHHHcc--------------------cCCCccchH
Q 010743 191 EITGLTADDLVGVTCSLAEIQKRMK---KLLSNGTILVGHSLNNDLEVLKL--------------------DHPRVIDTS 247 (502)
Q Consensus 191 ~ihGIT~e~L~~ap~~~~dV~~~l~---~fl~~g~ILVGHnl~fDl~fLk~--------------------~~p~vIDT~ 247 (502)
+-+||.-+-.....+...+-.+.+. -.++++-..|-.+..+|+..|=. ..|.+.|+-
T Consensus 109 r~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs~YDfgYLlK~Lt~~~LP~~~~eF~~~v~~~fp~vYDiK 188 (239)
T KOG0304|consen 109 RRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHSGYDFGYLLKILTGKPLPETEEEFFEIVRQLFPFVYDVK 188 (239)
T ss_pred HHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeeccchHHHHHHHHcCCCCcchHHHHHHHHHHHcchhhhHH
Confidence 5689988888877655444433333 33446778899999999988743 135678888
Q ss_pred HHhhhhcC-CCCCCHHHHHHHHcCCccCCCCCCCCHHHHHHHHHHHHHHHHH
Q 010743 248 LIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLVLAIIE 298 (502)
Q Consensus 248 ~L~r~~~~-~~~~sL~~La~~~Lgi~iq~~~~~HdAleDA~Ata~L~~~~l~ 298 (502)
.+++...+ ....+|..|| ..||++-. |..|.|-.|+..|+..|.++.+
T Consensus 189 ~l~~~c~~~~l~~GL~~lA-~~L~~~Rv--G~~HqAGSDSlLT~~~F~kl~~ 237 (239)
T KOG0304|consen 189 YLMKFCEGLSLKGGLQRLA-DLLGLKRV--GIAHQAGSDSLLTARVFFKLKE 237 (239)
T ss_pred HHHHhhhhhhhhcCHHHHH-HHhCCCee--ecccccCcHHHHHHHHHHHHHh
Confidence 88887766 5678999999 77888753 5799999999999999988764
No 106
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=89.25 E-value=0.76 Score=47.26 Aligned_cols=90 Identities=21% Similarity=0.272 Sum_probs=59.5
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceee-ec--cccccCC-cceeEEEEeCCHHHHHHHHHhhcCCCCCCCCCCcceEEEE
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIE-AK--AVKRIRG-DNYAAFAIFSSPQEANQAFENVKGNQSKDSYGRPQKLVEF 394 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~-~k--~~~~~~g-~~~~~~~~f~~~~ea~~af~~l~g~~~~d~~G~~qk~v~~ 394 (502)
.|+..+||..++.++|..+|..--.|. ++ ..+. .| ..++|+|.|.+.++|..|.+.|.|.. -.|++.+.-.-
T Consensus 5 ~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~-~g~s~g~afV~f~~~~~A~~Ai~~l~g~~---l~g~~i~v~~a 80 (352)
T TIGR01661 5 NLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKV-TGQSLGYGFVNYVRPEDAEKAVNSLNGLR---LQNKTIKVSYA 80 (352)
T ss_pred EEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCC-CCccceEEEEEECcHHHHHHHHhhcccEE---ECCeeEEEEee
Confidence 478899999999999999998744442 22 2222 23 36799999999999999999998743 34554432111
Q ss_pred ecCC--CCeEEEEEEeeccC
Q 010743 395 QSNA--GIIASLYVRKMVCD 412 (502)
Q Consensus 395 ~~~~--g~~~~~~vrkm~~~ 412 (502)
++.. ....+|||..+-.+
T Consensus 81 ~~~~~~~~~~~l~v~~l~~~ 100 (352)
T TIGR01661 81 RPSSDSIKGANLYVSGLPKT 100 (352)
T ss_pred cccccccccceEEECCcccc
Confidence 1111 12346777766444
No 107
>PHA02528 43 DNA polymerase; Provisional
Probab=89.03 E-value=1.7 Score=51.42 Aligned_cols=151 Identities=10% Similarity=-0.035 Sum_probs=88.6
Q ss_pred CCcEEEEEEeccCC----CCC--cccEEEEEEEEcCCcEEEEEEEcCCCc---ccccc--cccCCCChhhhccCCCCHHH
Q 010743 141 SNIMYAVDCEMVLC----EDG--SEGLVRLCVVDRNLKVTIDELVKPEKA---VADYR--SEITGLTADDLVGVTCSLAE 209 (502)
Q Consensus 141 ~~~~VaID~ETTGl----~~g--~~~I~rVsvVd~~G~vi~d~LVkP~~~---I~dy~--T~ihGIT~e~L~~ap~~~~d 209 (502)
.-++++||+||+.- ++. .+.|..|++.+..+..++-..+....+ ..+.. ....++ .+...+ +-.+
T Consensus 105 ~lrv~s~DIE~~~~~gfP~p~~~~d~IisIsl~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~v---~~~~~~-sE~e 180 (881)
T PHA02528 105 KIRIANLDIEVTAEDGFPDPEEAKYEIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPQEILDKV---VYMPFD-TERE 180 (881)
T ss_pred CccEEEEEEEECCCCCCCCcccCCCcEEEEEEecCCCCEEEEEEecCcccccccCCcccccccCCe---eEEEcC-CHHH
Confidence 56899999999752 122 457999999877665422222211000 00000 000111 111234 6778
Q ss_pred HHHHHHHhhc--CCCEEEEEch-hhHHHHHccc---C---------C-------------------------C-ccchHH
Q 010743 210 IQKRMKKLLS--NGTILVGHSL-NNDLEVLKLD---H---------P-------------------------R-VIDTSL 248 (502)
Q Consensus 210 V~~~l~~fl~--~g~ILVGHnl-~fDl~fLk~~---~---------p-------------------------~-vIDT~~ 248 (502)
.+.+|.+++. .-.||+|||+ .||+.+|... + . + ++|...
T Consensus 181 LL~~F~~~i~~~DPDII~GyNi~~FDlpYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~GRv~lD~~d 260 (881)
T PHA02528 181 MLLEYINFWEENTPVIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISGISILDYLD 260 (881)
T ss_pred HHHHHHHHHHHhCCcEEEecCCccCCHHHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcceEEEeHHH
Confidence 8999999883 2379999997 6899887420 0 0 0 244555
Q ss_pred Hhhhh-c-CCCCCCHHHHHHHHcCCccCCC-----------C---CCCCHHHHHHHHHHHHHH
Q 010743 249 IFKYV-D-EYRRPSLYNLCKSVLGYEIRKK-----------G---TPHNCLDDASAAMKLVLA 295 (502)
Q Consensus 249 L~r~~-~-~~~~~sL~~La~~~Lgi~iq~~-----------~---~~HdAleDA~Ata~L~~~ 295 (502)
+++.. . ...+++|+++|+.+||..-..- + -.+=++.||..+.+|+.+
T Consensus 261 l~k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 261 LYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred HHHHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 55543 2 2578999999988998753210 0 012246788889998876
No 108
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=87.32 E-value=7.1 Score=48.19 Aligned_cols=151 Identities=17% Similarity=0.194 Sum_probs=90.3
Q ss_pred CCcEEEEEEeccCCC-----CCcccEEEEEE-EEcCCcEEEEE-EEcCC------CcccccccccCCCChhhhccCCCCH
Q 010743 141 SNIMYAVDCEMVLCE-----DGSEGLVRLCV-VDRNLKVTIDE-LVKPE------KAVADYRSEITGLTADDLVGVTCSL 207 (502)
Q Consensus 141 ~~~~VaID~ETTGl~-----~g~~~I~rVsv-Vd~~G~vi~d~-LVkP~------~~I~dy~T~ihGIT~e~L~~ap~~~ 207 (502)
..++.|||+|||-+. ...+.|.-|+. ||+.|--+.+. .|--+ .|-|+|.-.+ -+-+.| .-
T Consensus 245 dp~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREiVs~DIedfEYTPKpE~eG~F------~v~Ne~-dE 317 (2173)
T KOG1798|consen 245 DPRVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREIVSEDIEDFEYTPKPEYEGPF------CVFNEP-DE 317 (2173)
T ss_pred CceEEEEeeecccCCCCCCCcccceEEEEEEEecCceEEEechhhhccchhhcccCCccccccce------EEecCC-cH
Confidence 357899999999874 23456888876 47777644332 11110 0111111111 122334 44
Q ss_pred HHHHHHHHHhhc--CCCEEEEEchh-hHHHHHccc---CC--------Cccc-----------hHHHhhhh-----cCCC
Q 010743 208 AEIQKRMKKLLS--NGTILVGHSLN-NDLEVLKLD---HP--------RVID-----------TSLIFKYV-----DEYR 257 (502)
Q Consensus 208 ~dV~~~l~~fl~--~g~ILVGHnl~-fDl~fLk~~---~p--------~vID-----------T~~L~r~~-----~~~~ 257 (502)
..+++++.+-+. +-.|+|-+|-. ||+-|+... |. ...| -+.-|+.. .|..
T Consensus 318 v~Ll~RfFeHiq~~kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrWVKRDSYLPqG 397 (2173)
T KOG1798|consen 318 VGLLQRFFEHIQEVKPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRWVKRDSYLPQG 397 (2173)
T ss_pred HHHHHHHHHHHHhcCCcEEEEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehhhhhhhhhcccCCCc
Confidence 566666666553 46899999875 699999751 21 0122 12234433 2367
Q ss_pred CCCHHHHHHHHcCCccCC-C-------------CCCCCHHHHHHHHHHHHHHHHH
Q 010743 258 RPSLYNLCKSVLGYEIRK-K-------------GTPHNCLDDASAAMKLVLAIIE 298 (502)
Q Consensus 258 ~~sL~~La~~~Lgi~iq~-~-------------~~~HdAleDA~Ata~L~~~~l~ 298 (502)
+.+|+++++.-||++--+ + .-+-=|+.||.||--||.++..
T Consensus 398 SqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVh 452 (2173)
T KOG1798|consen 398 SQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVH 452 (2173)
T ss_pred ccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhh
Confidence 899999999999985211 0 0234568999999999998884
No 109
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=86.03 E-value=1 Score=47.55 Aligned_cols=62 Identities=21% Similarity=0.241 Sum_probs=47.2
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceee-ec---cccccCCcceeEEEEeCCHHHHHHHHHhhcCCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIE-AK---AVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQS 381 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~-~k---~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~~ 381 (502)
.|+...||..++.++|..+|..--.|. ++ ....+ -..++|+|+|.+.++|..|.+.|.|..-
T Consensus 109 ~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg-~srGyaFVeF~~~e~A~~Ai~~LnG~~l 174 (346)
T TIGR01659 109 NLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTG-YSFGYAFVDFGSEADSQRAIKNLNGITV 174 (346)
T ss_pred EEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCC-ccCcEEEEEEccHHHHHHHHHHcCCCcc
Confidence 588999999999999999998644442 22 11221 2357999999999999999999977543
No 110
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=85.34 E-value=1 Score=46.26 Aligned_cols=68 Identities=13% Similarity=0.073 Sum_probs=50.9
Q ss_pred hhcCCCCCCCChHhhhccCCCCceeee-c--cccccCCcceeEEEEeCCHHHHHHHHHhhcCCCCCCCCCCcce
Q 010743 320 LFLHRIPTKVPSEELHGVIPGDFTIEA-K--AVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQSKDSYGRPQK 390 (502)
Q Consensus 320 l~~~~iP~~~~~eel~~~f~~~~~i~~-k--~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~~~d~~G~~qk 390 (502)
|+..+||..++.++|..+|...-.|+- + ....-+...++++|.|.+.++|..|.+.|+|..- .||+.+
T Consensus 272 lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~---~gr~i~ 342 (352)
T TIGR01661 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTL---GNRVLQ 342 (352)
T ss_pred EEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEE---CCeEEE
Confidence 889999999999999999986444432 1 1111123478999999999999999999988653 466554
No 111
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=84.61 E-value=12 Score=43.96 Aligned_cols=122 Identities=18% Similarity=0.119 Sum_probs=75.9
Q ss_pred CCCCcEEEEEEeccCCCC-----CcccEEEEEEEEcCCcEEEEEEEcCCCcccccccccCCCChhhhccCCCCHHHHHHH
Q 010743 139 MTSNIMYAVDCEMVLCED-----GSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKR 213 (502)
Q Consensus 139 ~~~~~~VaID~ETTGl~~-----g~~~I~rVsvVd~~G~vi~d~LVkP~~~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~ 213 (502)
..+.++++||+|+.+... ..+.+..|+.....+.... . ....+...|.. +.... +-.+++..
T Consensus 151 ~p~l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~---~------~~~~~~~~~~~---v~~~~-~e~e~l~~ 217 (792)
T COG0417 151 RPPLRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLI---E------VFIYTSGEGFS---VEVVI-SEAELLER 217 (792)
T ss_pred CCCceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCcc---c------cccccCCCCce---eEEec-CHHHHHHH
Confidence 456789999999997642 2345777777655322111 0 11111111111 33343 56678888
Q ss_pred HHHhhc--CCCEEEEEchh-hHHHHHccc-------C--------------------CC-ccchHHHhhh-hcCCCCCCH
Q 010743 214 MKKLLS--NGTILVGHSLN-NDLEVLKLD-------H--------------------PR-VIDTSLIFKY-VDEYRRPSL 261 (502)
Q Consensus 214 l~~fl~--~g~ILVGHnl~-fDl~fLk~~-------~--------------------p~-vIDT~~L~r~-~~~~~~~sL 261 (502)
|..++. ...|+||||.. ||+.+|... . .+ .+|....++. ......++|
T Consensus 218 ~~~~i~~~dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~~~~~~~~~~ysl 297 (792)
T COG0417 218 FVELIREYDPDVIVGYNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPALRRRPLNLKSYSL 297 (792)
T ss_pred HHHHHHhcCCCEEEeccCCcCChHHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHHHhhhhcccccccH
Confidence 877763 45799999996 999998641 0 11 3677777663 444789999
Q ss_pred HHHHHHHcCCcc
Q 010743 262 YNLCKSVLGYEI 273 (502)
Q Consensus 262 ~~La~~~Lgi~i 273 (502)
...+..+|+..-
T Consensus 298 ~~v~~~~l~~~k 309 (792)
T COG0417 298 EAVSEALLGEGK 309 (792)
T ss_pred HHHHHHhccccc
Confidence 999988877653
No 112
>PLN03120 nucleic acid binding protein; Provisional
Probab=84.15 E-value=1.3 Score=45.14 Aligned_cols=61 Identities=16% Similarity=0.231 Sum_probs=44.3
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceeeeccccccCCcceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIEAKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
.++..+||+.++.++|..+|+..-.|+-......+...++|+|+|.+++.|..|.. |.|..
T Consensus 6 tVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~ 66 (260)
T PLN03120 6 TVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGAT 66 (260)
T ss_pred EEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCe
Confidence 47889999999999999999775455321111101123699999999999999995 86643
No 113
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=83.57 E-value=1.2 Score=48.19 Aligned_cols=61 Identities=18% Similarity=0.313 Sum_probs=48.0
Q ss_pred HHHhhhhcCCCCCCCChHhhhccCCCCcee-ee---ccccccCCcceeEEEEeCCHHHHHHHHHhh
Q 010743 315 TERARLFLHRIPTKVPSEELHGVIPGDFTI-EA---KAVKRIRGDNYAAFAIFSSPQEANQAFENV 376 (502)
Q Consensus 315 ~~l~~l~~~~iP~~~~~eel~~~f~~~~~i-~~---k~~~~~~g~~~~~~~~f~~~~ea~~af~~l 376 (502)
...-+|+...||..+++.+|..+|.+.-.+ |+ |+... +-..+||+|.|.+.+||++|...|
T Consensus 32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t-~~s~gcCFv~~~trk~a~~a~~Al 96 (510)
T KOG0144|consen 32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKST-GQSKGCCFVKYYTRKEADEAINAL 96 (510)
T ss_pred chhhhheeccCCccccHHHHHHHHHHhCceeEEEeeccccc-CcccceEEEEeccHHHHHHHHHHh
Confidence 345589999999999999999999775533 32 33222 344789999999999999999998
No 114
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=82.94 E-value=17 Score=39.74 Aligned_cols=83 Identities=14% Similarity=0.108 Sum_probs=54.4
Q ss_pred HHHHHHHHHhhc--CCCEEEEEchhhHHHHHccc---CC-----------CccchHHHhhhhc--CCCCCCHHHHHHHHc
Q 010743 208 AEIQKRMKKLLS--NGTILVGHSLNNDLEVLKLD---HP-----------RVIDTSLIFKYVD--EYRRPSLYNLCKSVL 269 (502)
Q Consensus 208 ~dV~~~l~~fl~--~g~ILVGHnl~fDl~fLk~~---~p-----------~vIDT~~L~r~~~--~~~~~sL~~La~~~L 269 (502)
..++.+|++|+. .+..++.+| .+...+|+.. ++ +++|...+.+... |..++||+.++ .++
T Consensus 329 ~~~~~~f~~~l~~~~~~~i~hY~-~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~sysLK~v~-~~l 406 (457)
T TIGR03491 329 ELAWQQFLQLLQSYPDAPIYHYG-ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIESYSLKSIA-RWL 406 (457)
T ss_pred HHHHHHHHHHHHHCCCCeEEeeC-HHHHHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCCCCCHHHHH-HHh
Confidence 455666666663 455788888 8888888762 21 3467665554332 36789999999 778
Q ss_pred CCccCCCCCCCCHHHHHHHHHHHHHHHHH
Q 010743 270 GYEIRKKGTPHNCLDDASAAMKLVLAIIE 298 (502)
Q Consensus 270 gi~iq~~~~~HdAleDA~Ata~L~~~~l~ 298 (502)
|.+.. +...|.-.++..|..++.
T Consensus 407 g~~~~------~~~~~G~~ai~~y~~~~~ 429 (457)
T TIGR03491 407 GFEWR------QKEASGAKSLLWYRQWKK 429 (457)
T ss_pred CcccC------CCCCCHHHHHHHHHHHHH
Confidence 98764 223455566777777664
No 115
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=82.00 E-value=1 Score=43.42 Aligned_cols=58 Identities=17% Similarity=0.273 Sum_probs=47.2
Q ss_pred hhhcCCCCCCCChHhhhccCCCCcee--eeccccccCCcceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTI--EAKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i--~~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
+++.-+|++.....||+..|...-.+ +|..-+. -++|+|+|.++-+|.+|..-|+|..
T Consensus 12 kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP----PGfAFVEFed~RDA~DAvr~LDG~~ 71 (195)
T KOG0107|consen 12 KVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP----PGFAFVEFEDPRDAEDAVRYLDGKD 71 (195)
T ss_pred eEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC----CCceEEeccCcccHHHHHhhcCCcc
Confidence 68899999999999999999875544 3433322 2589999999999999999998876
No 116
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=80.37 E-value=1.9 Score=47.77 Aligned_cols=60 Identities=15% Similarity=0.192 Sum_probs=45.5
Q ss_pred hhcCCCCCCCChHhhhccCCCCceee-ec--cccccCCcceeEEEEeCCHHHHHHHHHhhcCC
Q 010743 320 LFLHRIPTKVPSEELHGVIPGDFTIE-AK--AVKRIRGDNYAAFAIFSSPQEANQAFENVKGN 379 (502)
Q Consensus 320 l~~~~iP~~~~~eel~~~f~~~~~i~-~k--~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~ 379 (502)
|+..+||.+++.++|..+|...-.|. ++ .....+...+.|+|.|.+.++|..|++.+.+.
T Consensus 3 l~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~ 65 (562)
T TIGR01628 3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFK 65 (562)
T ss_pred EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCC
Confidence 67789999999999999997644442 22 11221234679999999999999999999765
No 117
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=79.60 E-value=2.5 Score=45.35 Aligned_cols=61 Identities=20% Similarity=0.273 Sum_probs=46.5
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceee-ec--cccccCCcceeEEEEeCCHHHHHHHHHhhcCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIE-AK--AVKRIRGDNYAAFAIFSSPQEANQAFENVKGN 379 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~-~k--~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~ 379 (502)
.|+..+||..++.++|..+|...-.|. +. ....+.-..++|+|.|.+.++|..|++.|+|.
T Consensus 188 ~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~ 251 (457)
T TIGR01622 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGF 251 (457)
T ss_pred EEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCc
Confidence 588999999999999999997644443 21 11221123678999999999999999999883
No 118
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=79.31 E-value=2 Score=47.63 Aligned_cols=62 Identities=27% Similarity=0.427 Sum_probs=46.4
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceee-eccccccCC-cceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIE-AKAVKRIRG-DNYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~-~k~~~~~~g-~~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
.++..+||..++.++|..+|...-.|. ++-.....| ..++++|+|.|.++|..|++.+.|..
T Consensus 287 ~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~ 350 (562)
T TIGR01628 287 NLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRM 350 (562)
T ss_pred EEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCe
Confidence 478899999999999999998744442 221111122 25799999999999999999998744
No 119
>PRK05761 DNA polymerase I; Reviewed
Probab=76.19 E-value=17 Score=42.76 Aligned_cols=88 Identities=22% Similarity=0.171 Sum_probs=59.5
Q ss_pred CHHHHHHHHHHhhcCCCEEEEEch-hhHHHHHccc---C-------CC-------ccchHHHhhhh-------cC---CC
Q 010743 206 SLAEIQKRMKKLLSNGTILVGHSL-NNDLEVLKLD---H-------PR-------VIDTSLIFKYV-------DE---YR 257 (502)
Q Consensus 206 ~~~dV~~~l~~fl~~g~ILVGHnl-~fDl~fLk~~---~-------p~-------vIDT~~L~r~~-------~~---~~ 257 (502)
+-.+++.+|.+++..-.+.|++|. +||+..|... + +. .+|....+... .+ .+
T Consensus 209 ~E~eLL~~f~~~i~~~dPdi~yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~~~~~y~~~~~~~~~ 288 (787)
T PRK05761 209 SEKELLAELFDIILEYPPVVTFNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNKAVRSYAFYGKYRHR 288 (787)
T ss_pred CHHHHHHHHHHHHHhcCCEEEEcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheeecceeeeeccceeecc
Confidence 778999999999988888999997 6899988541 1 11 14544444321 11 23
Q ss_pred CCCHHHHHHHHcCCccCC-------C---CCCCCHHHHHHHHHHHH
Q 010743 258 RPSLYNLCKSVLGYEIRK-------K---GTPHNCLDDASAAMKLV 293 (502)
Q Consensus 258 ~~sL~~La~~~Lgi~iq~-------~---~~~HdAleDA~Ata~L~ 293 (502)
.++|+..++.+||..-.. . .-..=++.||..|..|+
T Consensus 289 ~ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 289 EARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred cCChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 789999999899875210 0 00123688999999984
No 120
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=76.09 E-value=3.2 Score=47.13 Aligned_cols=62 Identities=13% Similarity=0.187 Sum_probs=47.6
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceee---eccccccCCcceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIE---AKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~---~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
+++..+||..++.++|..+|...-.|. +.....++...++++|.|.+.++|..|.+.++|-.
T Consensus 206 rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~e 270 (612)
T TIGR01645 206 RIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFD 270 (612)
T ss_pred eEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCe
Confidence 688999999999999999997643442 22222222346799999999999999999998663
No 121
>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]
Probab=75.88 E-value=3.8 Score=41.48 Aligned_cols=77 Identities=21% Similarity=0.226 Sum_probs=58.1
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceeeecccccc-CC-cceeEEEEeCCHHHHHHHHHhhcCCCCCCCCCCcceEEEEec
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIEAKAVKRI-RG-DNYAAFAIFSSPQEANQAFENVKGNQSKDSYGRPQKLVEFQS 396 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~~k~~~~~-~g-~~~~~~~~f~~~~ea~~af~~l~g~~~~d~~G~~qk~v~~~~ 396 (502)
++...++|..+..++|..+|...-.+.-....+. .| ..++|.|+|+-.++|..|++.++| ..-+|+|-|...+..
T Consensus 85 ~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~g---v~ldG~~mk~~~i~~ 161 (243)
T KOG0533|consen 85 KVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNG---VALDGRPMKIEIISS 161 (243)
T ss_pred eeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcC---cccCCceeeeEEecC
Confidence 4778889999999999999987433332232322 33 389999999999999999999988 678899977665544
Q ss_pred CC
Q 010743 397 NA 398 (502)
Q Consensus 397 ~~ 398 (502)
.+
T Consensus 162 ~~ 163 (243)
T KOG0533|consen 162 PS 163 (243)
T ss_pred cc
Confidence 43
No 122
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=75.53 E-value=3 Score=45.30 Aligned_cols=61 Identities=15% Similarity=0.305 Sum_probs=46.6
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceeee----ccccccCCcceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIEA----KAVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~~----k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
+|+..+||..++.++|..+|...-.|.. +....| ...+.|+|.|.+.+.|..|++.|.|..
T Consensus 297 ~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g-~~~g~afv~f~~~~~a~~A~~~l~g~~ 361 (509)
T TIGR01642 297 RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATG-LSKGYAFCEYKDPSVTDVAIAALNGKD 361 (509)
T ss_pred EEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCC-CcCeEEEEEECCHHHHHHHHHHcCCCE
Confidence 6899999999999999998876444421 122221 236799999999999999999997654
No 123
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=75.50 E-value=4.1 Score=44.61 Aligned_cols=69 Identities=19% Similarity=0.256 Sum_probs=51.1
Q ss_pred hhhcCCCCCCCChHhhhccCCCCce--e-eeccccccCCcceeEEEEeCCHHHHHHHHHhhcCCCCCCCCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFT--I-EAKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQSKDSYGR 387 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~--i-~~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~~~d~~G~ 387 (502)
.|+..+||..++.++|..+|...-. + .++......+..++++|.|.+.++|..|+..|.|..-.+..|.
T Consensus 396 ~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~~~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~ 467 (481)
T TIGR01649 396 TLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDNERSKMGLLEWESVEDAVEALIALNHHQLNEPNGS 467 (481)
T ss_pred EEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCCCCcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCC
Confidence 4788899999999999999976443 2 1221111123456899999999999999999998877666555
No 124
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=75.02 E-value=3.3 Score=46.77 Aligned_cols=64 Identities=20% Similarity=0.311 Sum_probs=48.3
Q ss_pred hhhhcCCCCCCCChHhhhccCCCCceee-eccccccCC-cceeEEEEeCCHHHHHHHHHhhcCCCC
Q 010743 318 ARLFLHRIPTKVPSEELHGVIPGDFTIE-AKAVKRIRG-DNYAAFAIFSSPQEANQAFENVKGNQS 381 (502)
Q Consensus 318 ~~l~~~~iP~~~~~eel~~~f~~~~~i~-~k~~~~~~g-~~~~~~~~f~~~~ea~~af~~l~g~~~ 381 (502)
..|+..+||.++++++|..+|..--.|. ++-.....| ..+.++|.|.+.++|..|++.|++..-
T Consensus 59 ~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i 124 (578)
T TIGR01648 59 CEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEI 124 (578)
T ss_pred CEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCee
Confidence 4699999999999999999998744332 221111122 367999999999999999999987653
No 125
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=73.57 E-value=4.1 Score=46.37 Aligned_cols=64 Identities=16% Similarity=0.198 Sum_probs=48.1
Q ss_pred HhhhhcCCCCCCCChHhhhccCCCCceee---eccccccCCcceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 317 RARLFLHRIPTKVPSEELHGVIPGDFTIE---AKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 317 l~~l~~~~iP~~~~~eel~~~f~~~~~i~---~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
..+++..+||..++.++|..+|...-.|. +...+.-....++|+|.|.+.++|..|++.++|..
T Consensus 107 ~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~ 173 (612)
T TIGR01645 107 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQM 173 (612)
T ss_pred CCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeE
Confidence 34689999999999999999998744442 21111111236799999999999999999997754
No 126
>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=73.48 E-value=11 Score=33.98 Aligned_cols=59 Identities=24% Similarity=0.218 Sum_probs=43.1
Q ss_pred HHHhhc-CCCEEEEEchhhHHHHHccc---CC-CccchHHHhhhhcCCCC-CCHHHHHHHHcCCc
Q 010743 214 MKKLLS-NGTILVGHSLNNDLEVLKLD---HP-RVIDTSLIFKYVDEYRR-PSLYNLCKSVLGYE 272 (502)
Q Consensus 214 l~~fl~-~g~ILVGHnl~fDl~fLk~~---~p-~vIDT~~L~r~~~~~~~-~sL~~La~~~Lgi~ 272 (502)
|..++. .+...++|++.+++.+|+.. .+ .+.||...+-.+.|..+ .+|..|+.+||+..
T Consensus 45 l~~~l~~~~~~ki~~d~K~~~~~l~~~gi~l~~~~fD~~LAaYLL~p~~~~~~l~~la~~yl~~~ 109 (151)
T cd06128 45 LKPLLEDEKALKVGQNLKYDRVILANYGIELRGIAFDTMLEAYLLDPVAGRHDMDSLAERWLKEK 109 (151)
T ss_pred HHHHHcCCCCCEEeeehHHHHHHHHHCCCCCCCcchhHHHHHHHcCCCCCCCCHHHHHHHHcCCC
Confidence 555563 23458999999999999542 22 35899988777777332 49999999998877
No 127
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=72.96 E-value=3.1 Score=47.04 Aligned_cols=57 Identities=25% Similarity=0.394 Sum_probs=45.2
Q ss_pred hhhcCCCCCCCChHhhhccCCCC--ceeeeccccccCCcceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGD--FTIEAKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~--~~i~~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
.|+..+||..++.++|..+|... -.|+ ..+..+| +++|.|.+.++|..|++.|+|..
T Consensus 235 ~LfVgNL~~~~tee~L~~~F~~f~~G~I~--rV~~~rg---fAFVeF~s~e~A~kAi~~lnG~~ 293 (578)
T TIGR01648 235 ILYVRNLMTTTTEEIIEKSFSEFKPGKVE--RVKKIRD---YAFVHFEDREDAVKAMDELNGKE 293 (578)
T ss_pred EEEEeCCCCCCCHHHHHHHHHhcCCCceE--EEEeecC---eEEEEeCCHHHHHHHHHHhCCCE
Confidence 48899999999999999999874 2343 2222233 89999999999999999997764
No 128
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=72.09 E-value=3 Score=45.27 Aligned_cols=62 Identities=24% Similarity=0.305 Sum_probs=42.3
Q ss_pred HhhhhcCCCCCCCChHhhhccCCCCce------ee-eccc--cccCCcceeEEEEeCCHHHHHHHHHhhcCC
Q 010743 317 RARLFLHRIPTKVPSEELHGVIPGDFT------IE-AKAV--KRIRGDNYAAFAIFSSPQEANQAFENVKGN 379 (502)
Q Consensus 317 l~~l~~~~iP~~~~~eel~~~f~~~~~------i~-~k~~--~~~~g~~~~~~~~f~~~~ea~~af~~l~g~ 379 (502)
..+|+..+||..++.++|..+|..... .. ..+. .......++|+|.|.+.++|..|+. |+|.
T Consensus 175 ~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al~-l~g~ 245 (509)
T TIGR01642 175 ARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAMA-LDSI 245 (509)
T ss_pred ccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhhc-CCCe
Confidence 346999999999999999998864210 00 0010 1112234589999999999999994 7653
No 129
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=71.92 E-value=5.2 Score=40.53 Aligned_cols=60 Identities=17% Similarity=0.212 Sum_probs=42.2
Q ss_pred hhhcCCCCCCCChHhhhccCCCCc---eeeeccccccCCc-ceeEEEEeCCHHHHHHHHHhhcCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDF---TIEAKAVKRIRGD-NYAAFAIFSSPQEANQAFENVKGN 379 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~---~i~~k~~~~~~g~-~~~~~~~f~~~~ea~~af~~l~g~ 379 (502)
-++..+||.+...++|..+|-..- .+-+.-.+. .|. .++|+|.|.|.+.|..|++.|+|.
T Consensus 191 tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~-TG~~kGFAFVtF~sRddA~rAI~~LnG~ 254 (270)
T KOG0122|consen 191 TVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKE-TGLSKGFAFVTFESRDDAARAIADLNGY 254 (270)
T ss_pred eeEEecCccccChhHHHHHhhccCccceeEEEEccc-cCcccceEEEEEecHHHHHHHHHHccCc
Confidence 366778888888888877765432 222222222 333 779999999999999999999653
No 130
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=69.62 E-value=5.7 Score=29.91 Aligned_cols=25 Identities=36% Similarity=0.510 Sum_probs=22.7
Q ss_pred ceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 356 NYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 356 ~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
.++|+|.|.|.++|..|++.|.|..
T Consensus 21 ~~~a~V~f~~~~~A~~a~~~l~~~~ 45 (56)
T PF13893_consen 21 RGFAFVEFASVEDAQKAIEQLNGRQ 45 (56)
T ss_dssp TTEEEEEESSHHHHHHHHHHHTTSE
T ss_pred CCEEEEEECCHHHHHHHHHHhCCCE
Confidence 4799999999999999999997765
No 131
>PLN03213 repressor of silencing 3; Provisional
Probab=69.05 E-value=4.6 Score=44.56 Aligned_cols=60 Identities=22% Similarity=0.314 Sum_probs=47.8
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceee-eccccccCCcceeEEEEeCCH--HHHHHHHHhhcCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIE-AKAVKRIRGDNYAAFAIFSSP--QEANQAFENVKGNQ 380 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~-~k~~~~~~g~~~~~~~~f~~~--~ea~~af~~l~g~~ 380 (502)
+|+..+|+..++.++|..+|...-.+. +.-+ +..| .++++|.|.++ +++..||+.|+|..
T Consensus 12 RIYVGNLSydVTEDDLravFSeFGsVkdVEIp-RETG-RGFAFVEMssdddaEeeKAISaLNGAE 74 (759)
T PLN03213 12 RLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV-RTKG-RSFAYIDFSPSSTNSLTKLFSTYNGCV 74 (759)
T ss_pred EEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe-cccC-CceEEEEecCCcHHHHHHHHHHhcCCe
Confidence 689999999999999999998754442 2222 3355 78999999988 78999999998875
No 132
>smart00361 RRM_1 RNA recognition motif.
Probab=68.35 E-value=11 Score=30.06 Aligned_cols=26 Identities=15% Similarity=0.350 Sum_probs=23.0
Q ss_pred cceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 355 DNYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 355 ~~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
..+.++|.|.+.++|..|++.|+|..
T Consensus 36 ~rG~~fV~f~~~~dA~~A~~~l~g~~ 61 (70)
T smart00361 36 KRGNVYITFERSEDAARAIVDLNGRY 61 (70)
T ss_pred CcEEEEEEECCHHHHHHHHHHhCCCE
Confidence 35789999999999999999998763
No 133
>PLN03121 nucleic acid binding protein; Provisional
Probab=68.17 E-value=7.3 Score=39.43 Aligned_cols=62 Identities=13% Similarity=0.148 Sum_probs=45.5
Q ss_pred hhcCCCCCCCChHhhhccCCCCceeeecc-ccccCCcceeEEEEeCCHHHHHHHHHhhcCCCCCC
Q 010743 320 LFLHRIPTKVPSEELHGVIPGDFTIEAKA-VKRIRGDNYAAFAIFSSPQEANQAFENVKGNQSKD 383 (502)
Q Consensus 320 l~~~~iP~~~~~eel~~~f~~~~~i~~k~-~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~~~d 383 (502)
++..+|++..+.++|.++|+.--.|+-.. .+. ++..++++|+|.+++.|..|. .|.|..-.|
T Consensus 8 V~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D-~et~gfAfVtF~d~~aaetAl-lLnGa~l~d 70 (243)
T PLN03121 8 AEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS-GEYACTAYVTFKDAYALETAV-LLSGATIVD 70 (243)
T ss_pred EEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC-CCcceEEEEEECCHHHHHHHH-hcCCCeeCC
Confidence 56788999999999999998744553221 111 223369999999999999998 687776544
No 134
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=68.16 E-value=17 Score=40.52 Aligned_cols=145 Identities=13% Similarity=0.099 Sum_probs=85.5
Q ss_pred CCcEEEEEEeccCCC-CC----cccEEEEEEEEcC-Cc---EEEEEEEcCCCcccccccccCCCChh-----hhccCCCC
Q 010743 141 SNIMYAVDCEMVLCE-DG----SEGLVRLCVVDRN-LK---VTIDELVKPEKAVADYRSEITGLTAD-----DLVGVTCS 206 (502)
Q Consensus 141 ~~~~VaID~ETTGl~-~g----~~~I~rVsvVd~~-G~---vi~d~LVkP~~~I~dy~T~ihGIT~e-----~L~~ap~~ 206 (502)
.-++..||+|.|+-. |. .-+|..|+..|.. +. .+|+.+ +. ...|-....=...+ .+..-+ +
T Consensus 105 ~i~~~~~DIEv~~~~fp~~~~a~~~i~~i~~~d~~~~~~~~~~~~~~--~~--~~~~~~~~~~~~~~~~~~v~v~~f~-s 179 (498)
T PHA02524 105 DVVIDVVDIEVTAPEFPEPKYAKYEIDMISHVRLHNGKKTYYIFDLV--KD--VGHWDPKKSVLEKYILDNVVYMPFE-D 179 (498)
T ss_pred hceEEEEEEEecCCCCCChhhcCCceEEEEeeecccCCccEEEEecc--cc--ccCCCcccccccccccCCeEEEEeC-C
Confidence 357999999997642 11 1258888887752 22 234333 11 11111111101111 122233 6
Q ss_pred HHHHHHHHHHhhcC--CCEEEEEch-hhHHHHHcc--------c-------CC---------------------C-ccch
Q 010743 207 LAEIQKRMKKLLSN--GTILVGHSL-NNDLEVLKL--------D-------HP---------------------R-VIDT 246 (502)
Q Consensus 207 ~~dV~~~l~~fl~~--g~ILVGHnl-~fDl~fLk~--------~-------~p---------------------~-vIDT 246 (502)
-.+++.+|.+|+.. -.||+|||+ .||+..|-. . .. + ++|.
T Consensus 180 E~eLL~~F~~~i~~~DPDIItGYNi~nFDlPYL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~~~G~~~~~~I~GRv~iDl 259 (498)
T PHA02524 180 EVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNILGEKAANQLSPYGKITSKTITNLYGEKIIYKIHGIALMDY 259 (498)
T ss_pred HHHHHHHHHHHHHHhCCCEEEeCCCcccCHHHHHHHHHHHhCCccccccccccccccccceeecCceeEEEEeeEEEeEH
Confidence 78999999999943 389999997 689977631 0 00 0 3677
Q ss_pred HHHhhhh--cCCCCCCHHHHHHHHcCCccCCCCCCC----------------CHHHHHHHHHHHH
Q 010743 247 SLIFKYV--DEYRRPSLYNLCKSVLGYEIRKKGTPH----------------NCLDDASAAMKLV 293 (502)
Q Consensus 247 ~~L~r~~--~~~~~~sL~~La~~~Lgi~iq~~~~~H----------------dAleDA~Ata~L~ 293 (502)
..+++.. ....+++|++++..+||..--. .| =++.||..+..|+
T Consensus 260 ~~l~kk~s~~~l~sYsL~~Vs~~~Lg~~K~d---~~~~I~~l~~~d~~rla~YclkDa~L~~~L~ 321 (498)
T PHA02524 260 MDVFKKFSFTPMPDYKLGNVGYREVKADKLD---YEGPINKFRKADHQRYVDYCVRDTDIILLID 321 (498)
T ss_pred HHHHHHhhhccCCCCCHHHHHHHhcCCcccc---chhhHHHHhcCchHHHHHHHHHHHHHHHHHH
Confidence 7777764 2378999999998787764221 22 2367888887665
No 135
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=67.72 E-value=6.9 Score=42.87 Aligned_cols=61 Identities=13% Similarity=0.139 Sum_probs=46.1
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceee-eccccccCCcceeEEEEeCCHHHHHHHHHhhcCCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIE-AKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQS 381 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~-~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~~ 381 (502)
.++..+++..++.++|..+|...-.|. ++-.+. +| .++|+|.|.+.++|..|.+.|.|..-
T Consensus 98 ~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~-~~-~~~afVef~~~~~A~~A~~~Lng~~i 159 (481)
T TIGR01649 98 RVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTK-NN-VFQALVEFESVNSAQHAKAALNGADI 159 (481)
T ss_pred EEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEec-CC-ceEEEEEECCHHHHHHHHHHhcCCcc
Confidence 467778899999999999998654443 222222 22 35799999999999999999999864
No 136
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=65.58 E-value=4.3 Score=46.99 Aligned_cols=134 Identities=13% Similarity=0.178 Sum_probs=74.3
Q ss_pred CCCcEEEEEEeccCCCCC-----cccEEEEEE---EEcCCcEEE-EEE-EcCCCcccccccccCCCChhhhccCCCCHHH
Q 010743 140 TSNIMYAVDCEMVLCEDG-----SEGLVRLCV---VDRNLKVTI-DEL-VKPEKAVADYRSEITGLTADDLVGVTCSLAE 209 (502)
Q Consensus 140 ~~~~~VaID~ETTGl~~g-----~~~I~rVsv---Vd~~G~vi~-d~L-VkP~~~I~dy~T~ihGIT~e~L~~ap~~~~d 209 (502)
.|-++..+|+|++|-... .+.+++|+= .-+++..++ +.+ ++|-.+|+.- .-+.-++.+ .+-+
T Consensus 272 APlrvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~Ge~~pf~rnvf~l~~capI~G~-~V~~~~~e~-------elL~ 343 (1066)
T KOG0969|consen 272 APLRVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQGENEPFVRNVFTLKTCAPIVGS-NVHSYETEK-------ELLE 343 (1066)
T ss_pred ccccccceeEEeccCCCCCCccccChHHHHHHHHHHhcCCchHHHhhhcccCcCCCCCc-eeEEeccHH-------HHHH
Confidence 456889999999987532 233444432 223444332 122 2343444431 122233332 2334
Q ss_pred HHHHHHHhhcCCCEEEEEch-hhHHHHHc-------cc-CC----------Cc-------------------------cc
Q 010743 210 IQKRMKKLLSNGTILVGHSL-NNDLEVLK-------LD-HP----------RV-------------------------ID 245 (502)
Q Consensus 210 V~~~l~~fl~~g~ILVGHnl-~fDl~fLk-------~~-~p----------~v-------------------------ID 245 (502)
.|..|..-+ .-.|++|+|+ .||+-.|= +. +| .+ +|
T Consensus 344 ~W~~firev-DPDvI~GYNi~nFDiPYll~RA~~L~Ie~Fp~LGRikn~~s~irDttfSSkq~GtRetK~v~I~GRlqfD 422 (1066)
T KOG0969|consen 344 SWRKFIREV-DPDVIIGYNICNFDIPYLLNRAKTLGIENFPYLGRIKNSRSVIRDSTFSSKQYGTRETKEVNIDGRLQFD 422 (1066)
T ss_pred HHHHHHHhc-CCCeEecccccccccceecChHhhcCcccccccceecccceeeeccccchhhcCcccceEEeecceeeeh
Confidence 567777777 7789999998 68875442 10 11 12 33
Q ss_pred hHHHhhhhcCCCCCCHHHHHHHHcCCccCCCCCCCCHHH
Q 010743 246 TSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNCLD 284 (502)
Q Consensus 246 T~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~~~~HdAle 284 (502)
.+..-.+-+..++|+|..++.+|||..-. +.+|+.+.
T Consensus 423 llqvi~Rd~KLrSytLNaVs~hFL~EQKE--DV~~siIt 459 (1066)
T KOG0969|consen 423 LLQVILRDYKLRSYTLNAVSAHFLGEQKE--DVHHSIIT 459 (1066)
T ss_pred HHHHHHHhhhhhhcchhhhHHHhhhhhcc--cccccchh
Confidence 33333333336899999999999886532 34666553
No 137
>PF11544 Spc42p: Spindle pole body component Spc42p; InterPro: IPR021611 Spc42p is a 42kDa component of the S.cerevisiae spindle body that localises to the electron dense central region of the SPB. Spc42p is a phosphoprotein which forms a polymeric layer at the periphery of the SPB central plaque. This functions during SPB duplication and also facilitates the attachment of the SPB to the nuclear membrane. ; PDB: 2Q6Q_B.
Probab=63.84 E-value=8.5 Score=32.31 Aligned_cols=37 Identities=22% Similarity=0.355 Sum_probs=31.5
Q ss_pred HHHHHHHHHHhhhccccchhhhhhhHHHHHHHHHHHh
Q 010743 460 LKVIERLKRELREKDFQISMQDKNISDLKKKVAEMKD 496 (502)
Q Consensus 460 ~k~ie~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~ 496 (502)
+++=..|+.+|..|+-||-.+-.+|.+|+.||.++..
T Consensus 4 i~qNk~L~~kL~~K~eEI~rLn~lv~sLR~KLiKYt~ 40 (76)
T PF11544_consen 4 IKQNKELKKKLNDKQEEIDRLNILVGSLRGKLIKYTE 40 (76)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455679999999999999999999999999988754
No 138
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=62.89 E-value=9.3 Score=35.78 Aligned_cols=61 Identities=25% Similarity=0.350 Sum_probs=47.4
Q ss_pred hhhhcCCCCCCCChHhhhccCCCCcee---eeccccccCCc-ceeEEEEeCCHHHHHHHHHhhcCC
Q 010743 318 ARLFLHRIPTKVPSEELHGVIPGDFTI---EAKAVKRIRGD-NYAAFAIFSSPQEANQAFENVKGN 379 (502)
Q Consensus 318 ~~l~~~~iP~~~~~eel~~~f~~~~~i---~~k~~~~~~g~-~~~~~~~f~~~~ea~~af~~l~g~ 379 (502)
..++..+||..++.++|..+|.....+ .+.-.+ ..|. .+.+.|.|.+.+.|..|.+.+.|.
T Consensus 116 ~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~-~~~~~~g~~~v~f~~~~~~~~a~~~~~~~ 180 (306)
T COG0724 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDR-ETGKSRGFAFVEFESEESAEKAIEELNGK 180 (306)
T ss_pred ceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeecc-ccCccCceEEEEecCHHHHHHHHHHcCCC
Confidence 458899999999999999999775544 222222 2233 789999999999999999999843
No 139
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=60.20 E-value=7 Score=45.64 Aligned_cols=32 Identities=22% Similarity=0.422 Sum_probs=24.6
Q ss_pred cCCCEEEEEchhhHHHHHccc------CCCccchHHHh
Q 010743 219 SNGTILVGHSLNNDLEVLKLD------HPRVIDTSLIF 250 (502)
Q Consensus 219 ~~g~ILVGHnl~fDl~fLk~~------~p~vIDT~~L~ 250 (502)
+++.++||||+.||..-++-. -.+++||+.|.
T Consensus 239 ~ke~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTMSlH 276 (1075)
T KOG3657|consen 239 GKEQLIVGHNVSFDRARIREEYNINGSKIRFLDTMSLH 276 (1075)
T ss_pred CCCceEEeccccchHHHHHHHHhccccceeeeechhhh
Confidence 378999999999999888753 22478987653
No 140
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=58.66 E-value=13 Score=39.96 Aligned_cols=60 Identities=13% Similarity=0.218 Sum_probs=44.0
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceee-ecc--ccccCCcceeEEEEeCCHHHHHHHHHhhcCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIE-AKA--VKRIRGDNYAAFAIFSSPQEANQAFENVKGN 379 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~-~k~--~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~ 379 (502)
.++..+||..++.++|..+|...-.|. +.- .+...-..+.|+|.|.+.++|..|+. |.|.
T Consensus 91 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~ 153 (457)
T TIGR01622 91 TVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQ 153 (457)
T ss_pred EEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCC
Confidence 589999999999999999997644442 221 11211236899999999999999995 5443
No 141
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=58.46 E-value=14 Score=40.42 Aligned_cols=71 Identities=24% Similarity=0.361 Sum_probs=52.2
Q ss_pred hhhhcCCCCCCCChHhhhccCCCCcee-eeccc-cccCCc-ceeEEEEeCCHHHHHHHHHhhcCCCCCCCCCCcce
Q 010743 318 ARLFLHRIPTKVPSEELHGVIPGDFTI-EAKAV-KRIRGD-NYAAFAIFSSPQEANQAFENVKGNQSKDSYGRPQK 390 (502)
Q Consensus 318 ~~l~~~~iP~~~~~eel~~~f~~~~~i-~~k~~-~~~~g~-~~~~~~~f~~~~ea~~af~~l~g~~~~d~~G~~qk 390 (502)
+.++..+||..+-++||--+|.+--.| |+.-. .++.|. .+-|+|+|.+.++|..|++.|....-. .|++-+
T Consensus 84 ~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir--~GK~ig 157 (506)
T KOG0117|consen 84 CEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIR--PGKLLG 157 (506)
T ss_pred ceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCcccc--CCCEeE
Confidence 358889999999999999998765444 33211 123333 568999999999999999999765443 666655
No 142
>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]
Probab=58.18 E-value=6.7 Score=41.30 Aligned_cols=62 Identities=19% Similarity=0.351 Sum_probs=49.0
Q ss_pred hhhcCCCCCCCChHhhhccCCCCcee-eeccccccCCcceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTI-EAKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i-~~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
+|...+||.....-+|.-||.+.-.| ++.-....+|..++.+|+|.++++|+.|=+.|-|..
T Consensus 98 RLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~ 160 (376)
T KOG0125|consen 98 RLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTV 160 (376)
T ss_pred eeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcce
Confidence 68899999999999999999774443 222233335888899999999999999999997754
No 143
>PF00843 Arena_nucleocap: Arenavirus nucleocapsid protein; InterPro: IPR000229 Arenaviruses are single stranded RNA viruses. The arenavirus S RNAs that have been characterised include conserved terminal sequences, an ambisense arrangement of the coding regions for the precursor glycoprotein (GPC) and nucleocapsid (N) proteins and an intergenic region capable of forming a base-paired "hairpin" structure. The mature glycoproteins that result are G1 and G2 and the N protein []. This family represents the nucleocapsid protein that encapsulates the viral ssRNA [].; GO: 0019013 viral nucleocapsid; PDB: 3MX5_A 3MX2_C 3MWT_C 3Q7C_A 3MWP_B 3Q7B_A 3T5Q_E 3T5N_A 3R3L_B.
Probab=56.35 E-value=14 Score=40.50 Aligned_cols=141 Identities=20% Similarity=0.248 Sum_probs=77.8
Q ss_pred CCCCcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEEEcCCC--cccccccccCCCChhhhccCCCCHHHHHHHHHH
Q 010743 139 MTSNIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEK--AVADYRSEITGLTADDLVGVTCSLAEIQKRMKK 216 (502)
Q Consensus 139 ~~~~~~VaID~ETTGl~~g~~~I~rVsvVd~~G~vi~d~LVkP~~--~I~dy~T~ihGIT~e~L~~ap~~~~dV~~~l~~ 216 (502)
..|..-..||+|-.-.+ .+++++.-.+....++.|=+|.. ...+...--|||--.||.++. | -+...+..
T Consensus 369 Ldp~~ttWiDIEG~p~D-----PVElAiyQP~sg~YiHcyR~P~D~K~FK~~SKysHGillkDl~~aq-P--GL~S~vi~ 440 (533)
T PF00843_consen 369 LDPNATTWIDIEGPPND-----PVELAIYQPSSGNYIHCYREPHDEKQFKNQSKYSHGILLKDLENAQ-P--GLTSAVIE 440 (533)
T ss_dssp S-TTS-EEEEEESETTS-----ESEEEEEETTTTEEEEEE---S-HHHHHHHHHHTT-B-GGGCTTB--T--THHHHHHH
T ss_pred CCCCCCeeEecCCCCCC-----CeEEEEeccCCCcEEEEecCCcchhhhcccccccccccHHHHhhhc-c--chHHHHHH
Confidence 34667789999975433 57899998754447788888975 344556667999999999986 3 56678889
Q ss_pred hhcCCCEEEEEchhhHHHHHcccCCC----ccchHHH---hhhhcCCCCCCHHHHHHHHcCCccCC---CC-----CCCC
Q 010743 217 LLSNGTILVGHSLNNDLEVLKLDHPR----VIDTSLI---FKYVDEYRRPSLYNLCKSVLGYEIRK---KG-----TPHN 281 (502)
Q Consensus 217 fl~~g~ILVGHnl~fDl~fLk~~~p~----vIDT~~L---~r~~~~~~~~sL~~La~~~Lgi~iq~---~~-----~~Hd 281 (502)
.++.+-||-..+.. |.+-|-..|.| +||...- +|.+...-+-....||+.+-|+-+.. ++ .+|.
T Consensus 441 ~LP~~MVlT~QGsD-DIrkLld~hGRrDiKlvDV~lt~eqaR~FEd~VWd~f~~LC~~H~GvVv~KKKkg~~~~~t~PHC 519 (533)
T PF00843_consen 441 LLPKNMVLTCQGSD-DIRKLLDMHGRRDIKLVDVKLTSEQARKFEDQVWDRFGHLCKKHTGVVVKKKKKGKKPESTNPHC 519 (533)
T ss_dssp HS-TT-EEEESSHH-HHHHHHHCTT-TTSEEEE----HHHHTTTHHHHHHHHGGG---B-S-EEE--SSSS-EEE-----
T ss_pred hCCcCcEEEeeChH-HHHHHHHhcCCCcceEEEeecCHHHHHHHHHHHHHHHHHHHHhcCceEEecccCCCCCCCCCchH
Confidence 99788888877754 66666555654 6886432 22111122345567898888886642 11 3899
Q ss_pred HHHHHHH
Q 010743 282 CLDDASA 288 (502)
Q Consensus 282 AleDA~A 288 (502)
||-|+.+
T Consensus 520 ALlDCiM 526 (533)
T PF00843_consen 520 ALLDCIM 526 (533)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 9999875
No 144
>PF13423 UCH_1: Ubiquitin carboxyl-terminal hydrolase
Probab=56.31 E-value=1.5 Score=44.48 Aligned_cols=48 Identities=27% Similarity=0.258 Sum_probs=37.3
Q ss_pred CCCCCCcccchhhccccCCCCCCCCCcCchhhHHHHhhcccccccccchhhhhHhhhhHHH
Q 010743 26 EGTAGGWKDFLTSYDKKFGSSLSDPARRSKDALSSFLKTFTKEDDLKFIAKVVQSHLNRDL 86 (502)
Q Consensus 26 ~~~~~~~k~~l~~~~~~~~~~~~dp~~~~~~~l~~f~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (502)
++..++++|.|.++|..++++. .+..|++|++.....+ .. |++||+.+
T Consensus 247 ~~~~~~~~Y~L~~~V~~i~~~~------~~~HlVs~vrv~~~~~--~~-----W~lFNDfl 294 (295)
T PF13423_consen 247 EGESGIFKYELRSMVCHIGDSI------ESGHLVSLVRVGPSDD--SQ-----WYLFNDFL 294 (295)
T ss_pred cCCCCceEEEEEEEEEEecCCC------CCCceEEEEEcCCCCC--Cc-----EEEECcEe
Confidence 4788999999999999998844 4677999999965212 22 89998854
No 145
>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]
Probab=55.25 E-value=20 Score=36.08 Aligned_cols=64 Identities=27% Similarity=0.258 Sum_probs=49.3
Q ss_pred HhhhhcCCCCCCCChHhhhccCC---CCceeeec-cccccCCcceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 317 RARLFLHRIPTKVPSEELHGVIP---GDFTIEAK-AVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 317 l~~l~~~~iP~~~~~eel~~~f~---~~~~i~~k-~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
.+-|+..++|..+..-||--+|- |.....+| .++.++-+.-.++++|.|-++|..|-..|+|-.
T Consensus 34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvr 101 (284)
T KOG1457|consen 34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVR 101 (284)
T ss_pred cceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCee
Confidence 44589999999999999876664 44455565 344444556788999999999999999998854
No 146
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=53.95 E-value=9.4 Score=41.55 Aligned_cols=63 Identities=22% Similarity=0.259 Sum_probs=49.4
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceeeecccccc--CCcceeEEEEeCCHHHHHHHHHhhcCCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIEAKAVKRI--RGDNYAAFAIFSSPQEANQAFENVKGNQS 381 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~~k~~~~~--~g~~~~~~~~f~~~~ea~~af~~l~g~~~ 381 (502)
+|+..-++...++.|+..+|+..-.||.--.-++ +-+.+|++|+|.+++-|.-|.+.|.|.++
T Consensus 126 KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~t 190 (510)
T KOG0144|consen 126 KLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQT 190 (510)
T ss_pred hhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhcccee
Confidence 5788889999999999999988556653222121 22367999999999999999999988774
No 147
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]
Probab=53.57 E-value=8.8 Score=37.61 Aligned_cols=66 Identities=23% Similarity=0.353 Sum_probs=47.9
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceeeeccccccCCcceeEEEEeCCHHHHHHHHHhhcCCCCCCCCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIEAKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQSKDSYGR 387 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~~~d~~G~ 387 (502)
.++..+||+.+...|++.+|.+.-.|..-+-+.-.|--..|+|.|.++-+|+.|+. |+.+-|=.|.
T Consensus 8 ~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiy---gRdGYdydg~ 73 (241)
T KOG0105|consen 8 RIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIY---GRDGYDYDGC 73 (241)
T ss_pred eEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhh---cccccccCcc
Confidence 57888999999999999999886655332222224556799999999999998875 4444454444
No 148
>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]
Probab=52.47 E-value=15 Score=37.86 Aligned_cols=63 Identities=25% Similarity=0.318 Sum_probs=47.3
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceeeecccccc--CCcceeEEEEeCCHHHHHHHHHhhcCCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIEAKAVKRI--RGDNYAAFAIFSSPQEANQAFENVKGNQS 381 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~~k~~~~~--~g~~~~~~~~f~~~~ea~~af~~l~g~~~ 381 (502)
+|+..-+-..-++|+..++|.-.-.|+....-+| ....+|++|.|.+-.||..|+..|-|.++
T Consensus 21 klfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqT 85 (371)
T KOG0146|consen 21 KLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQT 85 (371)
T ss_pred hhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhccccc
Confidence 4555555666678888888876556665555454 22378999999999999999999988775
No 149
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=50.52 E-value=16 Score=39.17 Aligned_cols=98 Identities=15% Similarity=0.157 Sum_probs=62.2
Q ss_pred CHHHHHHHHHHHHHHHHHhcccCCCCCcchhhhHHHHhhhhcCCCCCCCChHhhhccCCCCceee-eccccccCCcceeE
Q 010743 281 NCLDDASAAMKLVLAIIERRVDNAVPLLQEDVAETERARLFLHRIPTKVPSEELHGVIPGDFTIE-AKAVKRIRGDNYAA 359 (502)
Q Consensus 281 dAleDA~Ata~L~~~~l~~g~~~~i~l~~~~~~e~~l~~l~~~~iP~~~~~eel~~~f~~~~~i~-~k~~~~~~g~~~~~ 359 (502)
...+||..|+.=+-.-.=+|....+ ......+ ..++...+++.++...|...|..--.|. .|-...-+|..|.
T Consensus 45 ~~~~da~~A~~~~n~~~~~~~~~ri--m~s~rd~---~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~- 118 (369)
T KOG0123|consen 45 QQPADAERALDTMNFDVLKGKPIRI--MWSQRDP---SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY- 118 (369)
T ss_pred CCHHHHHHHHHHcCCcccCCcEEEe--ehhccCC---ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-
Confidence 3456888887765433323322222 1111111 1278888999999999998887644332 2222222456666
Q ss_pred EEEeCCHHHHHHHHHhhcCCCCCCC
Q 010743 360 FAIFSSPQEANQAFENVKGNQSKDS 384 (502)
Q Consensus 360 ~~~f~~~~ea~~af~~l~g~~~~d~ 384 (502)
.|.|.|.++|..|.+.+.|..-.|.
T Consensus 119 FV~f~~e~~a~~ai~~~ng~ll~~k 143 (369)
T KOG0123|consen 119 FVQFESEESAKKAIEKLNGMLLNGK 143 (369)
T ss_pred EEEeCCHHHHHHHHHHhcCcccCCC
Confidence 9999999999999999999886654
No 150
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=50.40 E-value=16 Score=32.07 Aligned_cols=54 Identities=15% Similarity=0.231 Sum_probs=32.3
Q ss_pred CCCCCCCChHhhhccCCCCceeeeccccccCCcceeEEEEeCCHHHHHHHHHhhcCC
Q 010743 323 HRIPTKVPSEELHGVIPGDFTIEAKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGN 379 (502)
Q Consensus 323 ~~iP~~~~~eel~~~f~~~~~i~~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~ 379 (502)
-+++..++.++|...|.....|....-.+| -..++|.|++++.|..|++.+.-.
T Consensus 7 ~g~~~~~~re~iK~~f~~~g~V~yVD~~~G---~~~g~VRf~~~~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 7 SGLGEPTSREDIKEAFSQFGEVAYVDFSRG---DTEGYVRFKTPEAAQKALEKLKEA 60 (105)
T ss_dssp EE--SS--HHHHHHHT-SS--EEEEE--TT----SEEEEEESS---HHHHHHHHHHT
T ss_pred ecCCCCcCHHHHHHHHHhcCCcceEEecCC---CCEEEEEECCcchHHHHHHHHHhc
Confidence 346677778999999987666655444443 348999999999999999999665
No 151
>KOG3990 consensus Uncharacterized conserved protein [Function unknown]
Probab=49.68 E-value=9.7 Score=38.75 Aligned_cols=30 Identities=47% Similarity=0.565 Sum_probs=26.9
Q ss_pred HHHHHHHHHhhhccccchhhhhhhHHHHHH
Q 010743 461 KVIERLKRELREKDFQISMQDKNISDLKKK 490 (502)
Q Consensus 461 k~ie~~~~~~~~~~~~~~~~~~~i~~~~~~ 490 (502)
.||-+||.-|.+||..|.--||-||+||-+
T Consensus 232 eeia~Lkk~L~qkdq~ileKdkqisnLKad 261 (305)
T KOG3990|consen 232 EEIARLKKLLHQKDQLILEKDKQISNLKAD 261 (305)
T ss_pred HHHHHHHHHHhhhHHHHHhhhhhhhccCcc
Confidence 378888888899999999999999999976
No 152
>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]
Probab=49.65 E-value=27 Score=38.28 Aligned_cols=71 Identities=21% Similarity=0.359 Sum_probs=53.5
Q ss_pred hhhhcCCCCCCCChHhhhccCCCCcee---eeccccccCCc-ceeEEEEeCCHHHHHHHHHhhcCCCCCCCCCCcceEE
Q 010743 318 ARLFLHRIPTKVPSEELHGVIPGDFTI---EAKAVKRIRGD-NYAAFAIFSSPQEANQAFENVKGNQSKDSYGRPQKLV 392 (502)
Q Consensus 318 ~~l~~~~iP~~~~~eel~~~f~~~~~i---~~k~~~~~~g~-~~~~~~~f~~~~ea~~af~~l~g~~~~d~~G~~qk~v 392 (502)
..++..+||..+++|+|..+|.+.-.+ ..+..+. .|. .+.+++.|.+.+.|..|.++|.|. +.+||+-|.-
T Consensus 19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~-tG~~~G~~f~~~~~~~~~~~a~~~lNg~---~~~gr~l~v~ 93 (435)
T KOG0108|consen 19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRE-TGKPKGFGFCEFTDEETAERAIRNLNGA---EFNGRKLRVN 93 (435)
T ss_pred cceEecCCCCcccHHHHHHHHhccCccceeeeccccc-CCCcCceeeEecCchhhHHHHHHhcCCc---ccCCceEEee
Confidence 347889999999999999999874422 3333343 333 779999999999999999999776 5677766543
No 153
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=49.08 E-value=6.9 Score=44.76 Aligned_cols=97 Identities=16% Similarity=0.282 Sum_probs=63.2
Q ss_pred CCHHHHHHHHHHHHH-HHHHhcccCCCCCcc--------hhhh-HHHHhhhhcCCCCCCCChHhhhccCCCCceee-ec-
Q 010743 280 HNCLDDASAAMKLVL-AIIERRVDNAVPLLQ--------EDVA-ETERARLFLHRIPTKVPSEELHGVIPGDFTIE-AK- 347 (502)
Q Consensus 280 HdAleDA~Ata~L~~-~~l~~g~~~~i~l~~--------~~~~-e~~l~~l~~~~iP~~~~~eel~~~f~~~~~i~-~k- 347 (502)
-+..+||.+|++... ..+ .|..-.+.++. .+.. .....+|...+||-..+..++..+|...-.+- +.
T Consensus 567 F~~~e~A~~a~k~lqgtvl-dGH~l~lk~S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRl 645 (725)
T KOG0110|consen 567 FAKPESAQAALKALQGTVL-DGHKLELKISENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRL 645 (725)
T ss_pred ecCHHHHHHHHHHhcCcee-cCceEEEEeccCccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeecc
Confidence 567899999988765 222 22211111111 1111 11244788889999999999999998743442 22
Q ss_pred cccccCCc-ceeEEEEeCCHHHHHHHHHhhc
Q 010743 348 AVKRIRGD-NYAAFAIFSSPQEANQAFENVK 377 (502)
Q Consensus 348 ~~~~~~g~-~~~~~~~f~~~~ea~~af~~l~ 377 (502)
|.+.++|. .++|.|.|.|++||.-||+.|-
T Consensus 646 PKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~ 676 (725)
T KOG0110|consen 646 PKKIGKGAHRGFGFVDFLTPREAKNAFDALG 676 (725)
T ss_pred chhhcchhhccceeeeccCcHHHHHHHHhhc
Confidence 33445666 7899999999999999999993
No 154
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=47.20 E-value=50 Score=33.35 Aligned_cols=138 Identities=14% Similarity=0.139 Sum_probs=73.8
Q ss_pred EEEEE--EEEcCCcE-----E--EEEEEcCCCccccc----ccccCCCChhhhccCCCCHHHHHHHHH---HhhcCCCEE
Q 010743 161 LVRLC--VVDRNLKV-----T--IDELVKPEKAVADY----RSEITGLTADDLVGVTCSLAEIQKRMK---KLLSNGTIL 224 (502)
Q Consensus 161 I~rVs--vVd~~G~v-----i--~d~LVkP~~~I~dy----~T~ihGIT~e~L~~ap~~~~dV~~~l~---~fl~~g~IL 224 (502)
|++++ +-|.+|+. . |+--.+|...+-.. .-+-+||.-+.-++......|..+-+. -.++..-+.
T Consensus 82 iIQlGlsLSDe~GN~P~~~sTWQFNF~F~l~~dmya~ESieLL~ksgIdFkkHe~~GI~v~eF~elLm~SGLvm~e~VtW 161 (299)
T COG5228 82 IIQLGLSLSDENGNKPNGPSTWQFNFEFDLKKDMYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTW 161 (299)
T ss_pred hhheeeeeccccCCCCCCCceeEEEEEecchhhhcchHHHHHHHHcCCChhhHhhcCCCHHHHHHHHhccCceeccceEE
Confidence 44444 44666642 2 55556666554321 224578877666665543333332222 123456788
Q ss_pred EEEchhhHHHHHccc--------------------CCCccchHHHhhhhcCCCCCCHHHHHHHHcCCccCCCCCCCCHHH
Q 010743 225 VGHSLNNDLEVLKLD--------------------HPRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNCLD 284 (502)
Q Consensus 225 VGHnl~fDl~fLk~~--------------------~p~vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~iq~~~~~HdAle 284 (502)
|-.+..+|+.+|=.. .|...|.-.+++... ..+..|.+.+ .-| .++..|..|.|-.
T Consensus 162 itfHsaYDfgyLikilt~~plP~~~EdFy~~l~~yfP~fYDik~v~ks~~-~~~KglQei~-ndl--ql~r~g~QhQags 237 (299)
T COG5228 162 ITFHSAYDFGYLIKILTNDPLPNNKEDFYWWLHQYFPNFYDIKLVYKSVL-NNSKGLQEIK-NDL--QLQRSGQQHQAGS 237 (299)
T ss_pred EEeecchhHHHHHHHHhcCCCCccHHHHHHHHHHHCccccchHHHHHhhh-hhhhHHHHhc-CcH--hhhccchhhhccc
Confidence 999999999988431 122334333333221 1223344443 112 2333356899999
Q ss_pred HHHHHHHHHHHHHHhccc
Q 010743 285 DASAAMKLVLAIIERRVD 302 (502)
Q Consensus 285 DA~Ata~L~~~~l~~g~~ 302 (502)
||..|+..|-.-...-+.
T Consensus 238 daLlTa~~ff~~R~~~F~ 255 (299)
T COG5228 238 DALLTADEFFLPRFSIFT 255 (299)
T ss_pred hhhhhhHHhcchhhheec
Confidence 999999988654443333
No 155
>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons. Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.
Probab=46.24 E-value=16 Score=35.09 Aligned_cols=70 Identities=20% Similarity=0.372 Sum_probs=43.4
Q ss_pred hhhhcCCCCCCCChHhhhc----cCCCC---ceeeec-ccc-ccCCcceeEEEEeCCHHHHHHHHHhhcCCCCCCCCCC
Q 010743 318 ARLFLHRIPTKVPSEELHG----VIPGD---FTIEAK-AVK-RIRGDNYAAFAIFSSPQEANQAFENVKGNQSKDSYGR 387 (502)
Q Consensus 318 ~~l~~~~iP~~~~~eel~~----~f~~~---~~i~~k-~~~-~~~g~~~~~~~~f~~~~ea~~af~~l~g~~~~d~~G~ 387 (502)
.++-.-+|||+++.+++.. .++.. ....-+ +.. ...+.+.-|++.|++.+.+..=.+.++|..=.|+-|.
T Consensus 8 ~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg~ 86 (176)
T PF03467_consen 8 TKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKGN 86 (176)
T ss_dssp -EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS-
T ss_pred ceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCCC
Confidence 3667788999999999887 34433 122211 111 2255688899999999999988899988877777755
No 156
>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]
Probab=43.48 E-value=18 Score=36.42 Aligned_cols=62 Identities=23% Similarity=0.363 Sum_probs=44.5
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceeeeccccccCCcceeEEEEeCCHHHHHHHHHhhcCCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIEAKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQS 381 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~~ 381 (502)
-|+..++-++.++++|..+|......++--.+. +|+.--+++.|.+.+.|.+|...|+|-+-
T Consensus 212 tlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~-~~g~~vaf~~~~~~~~at~am~~lqg~~~ 273 (284)
T KOG1457|consen 212 TLFIANLGPNCTEDELKQLLSRYPGFHILKIRA-RGGMPVAFADFEEIEQATDAMNHLQGNLL 273 (284)
T ss_pred hHhhhccCCCCCHHHHHHHHHhCCCceEEEEec-CCCcceEeecHHHHHHHHHHHHHhhccee
Confidence 466777788888888887764432222111122 67777888999999999999999999874
No 157
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=43.03 E-value=5.4 Score=46.89 Aligned_cols=55 Identities=13% Similarity=0.024 Sum_probs=37.5
Q ss_pred chhhHHHHhhcccccccccchhhhhHhhhhHHHHHHHHhcCCCCCChhhHHHHhhh
Q 010743 54 SKDALSSFLKTFTKEDDLKFIAKVVQSHLNRDLVEQLKKTSPDDESPEQRLVRLTL 109 (502)
Q Consensus 54 ~~~~l~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lv~~t~ 109 (502)
+.-.|++.++.....+..+ .++--|++||+.++.++.++++.+++.-|++.....
T Consensus 805 ~e~~lVs~Ikv~~~~~~~~-~~dsqWylFNDfLV~~ite~EAl~~~~~WKvP~Il~ 859 (1118)
T KOG1275|consen 805 NEVNLVSPIKVLRPYHVIK-PDDSQWYLFNDFLVSEITEEEALHFDGPWKVPAILY 859 (1118)
T ss_pred CccceEEEEEccCcccccC-cCcceeEEEcceeeeeCChHHheEeccCccCcEEEE
Confidence 4455666665544433333 223359999999999999999988887788776443
No 158
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=42.63 E-value=33 Score=33.80 Aligned_cols=60 Identities=8% Similarity=0.138 Sum_probs=43.9
Q ss_pred cEEEEEEEEc---CCcE-EEEEEEcCCCccccc-------ccccCCCChhhhccCCCCHHHHHHHHHHhhc
Q 010743 160 GLVRLCVVDR---NLKV-TIDELVKPEKAVADY-------RSEITGLTADDLVGVTCSLAEIQKRMKKLLS 219 (502)
Q Consensus 160 ~I~rVsvVd~---~G~v-i~d~LVkP~~~I~dy-------~T~ihGIT~e~L~~ap~~~~dV~~~l~~fl~ 219 (502)
-.+++|++.+ +|.+ .|+++|+|......| ...-|+|...-.+.....+..++.+|..||.
T Consensus 9 ~PaEiai~~fSL~~GI~~~~H~~I~Pg~~p~G~~~~a~~hs~~tH~ip~~~~~~~~~d~~~l~~~l~~fl~ 79 (213)
T PF13017_consen 9 VPAEIAICKFSLKEGIIDSFHTFINPGQIPLGYRYDAQHHSDETHQIPIPPNALGESDYSELYNELLNFLK 79 (213)
T ss_pred EeEEEEEEEEecCCccchhhhcccCCCCCCcHHHHHHHHhhhhhcCCCCCCcccccCCHHHHHHHHHHHhh
Confidence 3688888876 4532 499999999755444 2355888776556555579999999999994
No 159
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=42.39 E-value=94 Score=38.03 Aligned_cols=128 Identities=16% Similarity=0.183 Sum_probs=75.2
Q ss_pred CCCCcEEEEEEeccCCCC-CcccEEEEEEEEcC--------CcE----EEEEEEcCCCccccc------ccccCCCChhh
Q 010743 139 MTSNIMYAVDCEMVLCED-GSEGLVRLCVVDRN--------LKV----TIDELVKPEKAVADY------RSEITGLTADD 199 (502)
Q Consensus 139 ~~~~~~VaID~ETTGl~~-g~~~I~rVsvVd~~--------G~v----i~d~LVkP~~~I~dy------~T~ihGIT~e~ 199 (502)
+.+..+.+|-++|.--.. ...+|+.|++.-+. +.. -+-.+++|..-+-++ ....++
T Consensus 526 ~Ppl~llsL~i~T~~N~k~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~~~fP~g~~ela~~k~~~----- 600 (1429)
T KOG0970|consen 526 PPPLTLLSLNIRTSMNPKQNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPGTSFPLGLKELAKQKLSK----- 600 (1429)
T ss_pred CCCeeEEEeeeeehhccccchhhhhhhhhhhcccccccCCCCCCcccCcceeEecCCCCcCCchHHHHHHhccCc-----
Confidence 445677888888875442 23478888876431 111 266788988655443 111122
Q ss_pred hccCCCCHHHHHHHHHHhhc--CCCEEEEEc-hhhHHHHHcc------------------cC-----------------C
Q 010743 200 LVGVTCSLAEIQKRMKKLLS--NGTILVGHS-LNNDLEVLKL------------------DH-----------------P 241 (502)
Q Consensus 200 L~~ap~~~~dV~~~l~~fl~--~g~ILVGHn-l~fDl~fLk~------------------~~-----------------p 241 (502)
+.-.. +-...+..|+..+. .-.++|||| ..|+|.+|-. .. .
T Consensus 601 v~~~~-sErALLs~fla~~~~~dpD~iVgHn~~~~~l~VLl~R~~~~Kip~WS~IgRLrrS~~~kfg~~s~~~e~~~~aG 679 (1429)
T KOG0970|consen 601 VVLHN-SERALLSHFLAMLNKEDPDVIVGHNIQGFYLDVLLSRLHALKIPNWSSIGRLRRSWPPKFGRSSSFGEFFIIAG 679 (1429)
T ss_pred eEEec-CHHHHHHHHHHHhhccCCCEEEEeccccchHHHHHHHHHHhcCcchhhhhhhhhccccccCCcccccccccccc
Confidence 11111 33445555555553 458999999 6889888821 10 1
Q ss_pred C-ccchHHHhhhhcCCCCCCHHHHHHHHcCCc
Q 010743 242 R-VIDTSLIFKYVDEYRRPSLYNLCKSVLGYE 272 (502)
Q Consensus 242 ~-vIDT~~L~r~~~~~~~~sL~~La~~~Lgi~ 272 (502)
+ +-|+-..++.+.+..+++|..|++..|+.+
T Consensus 680 Rl~CD~~~~a~~lik~~S~~LseL~q~~l~~e 711 (1429)
T KOG0970|consen 680 RLMCDLNLAARELIKAQSYSLSELSQQILKEE 711 (1429)
T ss_pred eEEeehHHHHHhhhccccccHHHHHHHHHhhh
Confidence 1 235533344444568999999999998883
No 160
>COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown]
Probab=42.23 E-value=16 Score=29.46 Aligned_cols=19 Identities=47% Similarity=0.448 Sum_probs=15.2
Q ss_pred HHHHHHHHHhhhccccchh
Q 010743 461 KVIERLKRELREKDFQISM 479 (502)
Q Consensus 461 k~ie~~~~~~~~~~~~~~~ 479 (502)
-||||||.||..|+.-=|+
T Consensus 39 ~EIeRlkAe~~kK~~srsA 57 (65)
T COG5509 39 AEIERLKAELAKKKASRSA 57 (65)
T ss_pred HHHHHHHHHHHhhhccHHH
Confidence 5999999999888765444
No 161
>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]
Probab=42.00 E-value=30 Score=38.31 Aligned_cols=55 Identities=20% Similarity=0.346 Sum_probs=43.9
Q ss_pred hhcCCCCCCCChHhhhccCCCCceee-eccccccCCc-ceeEEEEeCCHHHHHHHHHhh
Q 010743 320 LFLHRIPTKVPSEELHGVIPGDFTIE-AKAVKRIRGD-NYAAFAIFSSPQEANQAFENV 376 (502)
Q Consensus 320 l~~~~iP~~~~~eel~~~f~~~~~i~-~k~~~~~~g~-~~~~~~~f~~~~ea~~af~~l 376 (502)
++..+||-+-+.+|+..+|.. ++|+ .+.++. +|. .+-|+|+|.+.+++++|.++=
T Consensus 13 vr~rGLPwsat~~ei~~Ff~~-~~I~~~~~~r~-~Gr~sGeA~Ve~~seedv~~Alkkd 69 (510)
T KOG4211|consen 13 VRLRGLPWSATEKEILDFFSN-CGIENLEIPRR-NGRPSGEAYVEFTSEEDVEKALKKD 69 (510)
T ss_pred EEecCCCccccHHHHHHHHhc-CceeEEEEecc-CCCcCcceEEEeechHHHHHHHHhh
Confidence 567889999999999998876 6775 333444 344 789999999999999999863
No 162
>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]
Probab=40.59 E-value=21 Score=35.56 Aligned_cols=61 Identities=16% Similarity=0.258 Sum_probs=42.4
Q ss_pred hhcCCCCCCCChHhhhccCCCCcee-eec-c-ccccCCcceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 320 LFLHRIPTKVPSEELHGVIPGDFTI-EAK-A-VKRIRGDNYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 320 l~~~~iP~~~~~eel~~~f~~~~~i-~~k-~-~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
|+.-+|--..+.++|..+|.+.-.+ ++- | .++-+-.-++|+|.|+...+|+.|.+.++|..
T Consensus 16 LkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ 79 (256)
T KOG4207|consen 16 LKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAV 79 (256)
T ss_pred EEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhccee
Confidence 4555666667788899888653333 111 1 12223346799999999999999999998865
No 163
>KOG4253 consensus Tryptophan-rich basic nuclear protein [General function prediction only]
Probab=40.31 E-value=41 Score=32.09 Aligned_cols=34 Identities=29% Similarity=0.531 Sum_probs=26.8
Q ss_pred hHHHHHHHHHHhhhccccchhhhhhh--HHHHHHHHHHHh
Q 010743 459 HLKVIERLKRELREKDFQISMQDKNI--SDLKKKVAEMKD 496 (502)
Q Consensus 459 h~k~ie~~~~~~~~~~~~~~~~~~~i--~~~~~~~~~~~~ 496 (502)
-.+||-.+||+|++ |||||+-- +.|.||+++|-+
T Consensus 49 ~~~ei~dmKqelna----vs~qD~fAkwaRlnRKi~kl~~ 84 (175)
T KOG4253|consen 49 KVAEIQDMKQELNA----VSMQDNFAKWARLNRKINKLDK 84 (175)
T ss_pred HHHHHHHHHHHHhh----hhhHHHHHHHHHHHHHHHHHHH
Confidence 46899999999975 89999864 567788877754
No 164
>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]
Probab=40.26 E-value=28 Score=40.20 Aligned_cols=58 Identities=21% Similarity=0.248 Sum_probs=42.7
Q ss_pred hhcCCCCCCCChHhhhccCCCCce----eeeccccccCCc-ceeEEEEeCCHHHHHHHHHhhcCC
Q 010743 320 LFLHRIPTKVPSEELHGVIPGDFT----IEAKAVKRIRGD-NYAAFAIFSSPQEANQAFENVKGN 379 (502)
Q Consensus 320 l~~~~iP~~~~~eel~~~f~~~~~----i~~k~~~~~~g~-~~~~~~~f~~~~ea~~af~~l~g~ 379 (502)
+...+.|..++.+++-++|.+... |.++-.. .|. ++-|.|-|.|.+||.-||..|.++
T Consensus 870 ~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd--~G~pTGe~mvAfes~~eAr~A~~dl~~~ 932 (944)
T KOG4307|consen 870 LSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRND--DGVPTGECMVAFESQEEARRASMDLDGQ 932 (944)
T ss_pred EEecCCCccccHHHHHHHhcccccCCCceeEeecC--CCCcccceeEeecCHHHHHhhhhccccC
Confidence 445567899999999999977442 2222111 344 789999999999999999988554
No 165
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]
Probab=39.22 E-value=34 Score=37.51 Aligned_cols=67 Identities=18% Similarity=0.235 Sum_probs=44.2
Q ss_pred hhcCCCCCCCChHhhhccCCC----CceeeeccccccCCcceeEEEEeCCHHHHHHHHHhhcCCCCCCCCCCcce
Q 010743 320 LFLHRIPTKVPSEELHGVIPG----DFTIEAKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQSKDSYGRPQK 390 (502)
Q Consensus 320 l~~~~iP~~~~~eel~~~f~~----~~~i~~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~~~d~~G~~qk 390 (502)
.+...||-...-++|..+|-. -.+++.-....| ...+|++|.|++++-+.+|.+.|+.. +-+|||-+
T Consensus 47 vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~G-K~rGcavVEFk~~E~~qKa~E~lnk~---~~~GR~l~ 117 (608)
T KOG4212|consen 47 VFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESG-KARGCAVVEFKDPENVQKALEKLNKY---EVNGRELV 117 (608)
T ss_pred EEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCC-CcCCceEEEeeCHHHHHHHHHHhhhc---cccCceEE
Confidence 567778887777777665532 234443333332 23569999999999999999999654 33455433
No 166
>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]
Probab=39.05 E-value=31 Score=36.76 Aligned_cols=61 Identities=11% Similarity=0.267 Sum_probs=45.0
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceeeecccc----------ccCCc-ceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIEAKAVK----------RIRGD-NYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~~k~~~----------~~~g~-~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
.++..+||..++.+|+..+|++ +.|....++ ..+|. .|-++++|--.+-|++|+.-|++..
T Consensus 136 ~VYVsgLP~DiT~dE~~~~~sK-cGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~ 207 (382)
T KOG1548|consen 136 SVYVSGLPLDITVDEFAEVMSK-CGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDE 207 (382)
T ss_pred eEEecCCCCcccHHHHHHHHHh-cceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCccc
Confidence 4889999999999999988877 544433321 12444 5677777888888999999996654
No 167
>PF08112 ATP-synt_E_2: ATP synthase epsilon subunit; InterPro: IPR012508 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. A-ATPases (or A1A0-ATPase) (3.6.3.14 from EC) are found exclusively in Archaea and display a close resemblance in structure and subunit composition with V-ATPases, although their function in both ATP synthesis and ATP hydrolysis is closer to that of F-ATPases []. A-ATPases are composed of two linked complexes: the A1 complex consisting of seven subunits contains the catalytic core that synthesizes/hydrolyses ATP, while the A0 complex consisting of at least two subunits forms the membrane-spanning pore []. The rotary motor in A-ATPases is composed of only two subunits, the stator subunit I and the rotor subunit C []. A-ATPases may have arisen as an adaptation to the different cellular needs and the more extreme environmental conditions faced by Archaeal species. The epsilon subunit is the smallest (7 kDa) of those found in the A1 complex. Unlike the A, B and C subunits, the epsilon subunit does not have a homologous counterpart in F- or V-ATPases []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0015986 ATP synthesis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain
Probab=38.14 E-value=27 Score=27.34 Aligned_cols=17 Identities=53% Similarity=0.434 Sum_probs=15.3
Q ss_pred chhhhhhhHHHHHHHHH
Q 010743 477 ISMQDKNISDLKKKVAE 493 (502)
Q Consensus 477 ~~~~~~~i~~~~~~~~~ 493 (502)
-|+.|+-|+.||.||++
T Consensus 6 ~~~~d~yI~~Lk~kLd~ 22 (56)
T PF08112_consen 6 KSTIDKYISILKSKLDE 22 (56)
T ss_pred hhhHHHHHHHHHHHHHH
Confidence 37889999999999998
No 168
>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]
Probab=36.79 E-value=39 Score=37.46 Aligned_cols=53 Identities=25% Similarity=0.277 Sum_probs=41.1
Q ss_pred hhcCCCCCCCChHhhhccCCCCceeeeccc-------cccCCcceeEEEEeCCHHHHHHHHHhh
Q 010743 320 LFLHRIPTKVPSEELHGVIPGDFTIEAKAV-------KRIRGDNYAAFAIFSSPQEANQAFENV 376 (502)
Q Consensus 320 l~~~~iP~~~~~eel~~~f~~~~~i~~k~~-------~~~~g~~~~~~~~f~~~~ea~~af~~l 376 (502)
.+..+||-..++++|.++|.+. ++++. .+++ ..+-|.|.|.|++.|+.|...-
T Consensus 106 VRLRGLPfscte~dI~~FFaGL---~Iv~~gi~l~~d~rgR-~tGEAfVqF~sqe~ae~Al~rh 165 (510)
T KOG4211|consen 106 VRLRGLPFSCTEEDIVEFFAGL---EIVPDGILLPMDQRGR-PTGEAFVQFESQESAEIALGRH 165 (510)
T ss_pred EEecCCCccCcHHHHHHHhcCC---cccccceeeeccCCCC-cccceEEEecCHHHHHHHHHHH
Confidence 5567899999999999999873 33222 2333 4889999999999999998654
No 169
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=35.94 E-value=24 Score=36.26 Aligned_cols=62 Identities=21% Similarity=0.356 Sum_probs=46.0
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceeeec--cccccCCc-ceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIEAK--AVKRIRGD-NYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~~k--~~~~~~g~-~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
.|+..+||..++..||+.+|+-.-.|.-- -+..+.|- .+-.++.|.-..||+.|+..|.|..
T Consensus 129 NLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~ 193 (360)
T KOG0145|consen 129 NLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQK 193 (360)
T ss_pred ceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCC
Confidence 58999999999999999999764444210 00111222 4577999999999999999998875
No 170
>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]
Probab=35.86 E-value=43 Score=32.86 Aligned_cols=99 Identities=13% Similarity=0.172 Sum_probs=64.6
Q ss_pred CCHHHHHHHHHHHHHHHHHhcccCCCCCcchhhhH---HHHhhhhcCCCCCCCChHhhhccCCCCceeeeccc----ccc
Q 010743 280 HNCLDDASAAMKLVLAIIERRVDNAVPLLQEDVAE---TERARLFLHRIPTKVPSEELHGVIPGDFTIEAKAV----KRI 352 (502)
Q Consensus 280 HdAleDA~Ata~L~~~~l~~g~~~~i~l~~~~~~e---~~l~~l~~~~iP~~~~~eel~~~f~~~~~i~~k~~----~~~ 352 (502)
-..-+||.-|..++. ++ +....++.++...... ..-++++...+-+.+.+..|-+.|+..-.|...|. ..+
T Consensus 58 f~~eedadYAikiln-~V-kLYgrpIrv~kas~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~t 135 (203)
T KOG0131|consen 58 FRTEEDADYAIKILN-MV-KLYGRPIRVNKASAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDT 135 (203)
T ss_pred EechhhhHHHHHHHH-HH-HhcCceeEEEecccccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccC
Confidence 355689999999987 44 3334444332211000 01135777888888888889999988555543221 122
Q ss_pred CCcceeEEEEeCCHHHHHHHHHhhcCCC
Q 010743 353 RGDNYAAFAIFSSPQEANQAFENVKGNQ 380 (502)
Q Consensus 353 ~g~~~~~~~~f~~~~ea~~af~~l~g~~ 380 (502)
+..-+++++.|.|-+.+..|.+.+.|..
T Consensus 136 g~~~~~g~i~~~sfeasd~ai~s~ngq~ 163 (203)
T KOG0131|consen 136 GNPKGFGFINYASFEASDAAIGSMNGQY 163 (203)
T ss_pred CCCCCCeEEechhHHHHHHHHHHhccch
Confidence 3336799999999999999999997764
No 171
>PF05266 DUF724: Protein of unknown function (DUF724); InterPro: IPR007930 This family contains several uncharacterised proteins found exclusively in Arabidopsis thaliana.
Probab=35.50 E-value=46 Score=32.50 Aligned_cols=43 Identities=23% Similarity=0.404 Sum_probs=24.6
Q ss_pred cchhhhHHHHHHHHHHhhhc-------cccchhhhhhhHHHHHHHHHHHh
Q 010743 454 CKCEDHLKVIERLKRELREK-------DFQISMQDKNISDLKKKVAEMKD 496 (502)
Q Consensus 454 ~~~~~h~k~ie~~~~~~~~~-------~~~~~~~~~~i~~~~~~~~~~~~ 496 (502)
.++..++.+.+.+++++.++ +.+|..+...|..|++..+.|+.
T Consensus 103 ~~~~~~~e~~k~le~~~~~~~~~~~~~e~~i~~Le~ki~el~~~~~~~~~ 152 (190)
T PF05266_consen 103 DDQEKLLEERKKLEKKIEEKEAELKELESEIKELEMKILELQRQAAKLKE 152 (190)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33455555555555555544 66666666666666666544443
No 172
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=34.56 E-value=65 Score=33.42 Aligned_cols=68 Identities=13% Similarity=0.156 Sum_probs=51.1
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceeeeccccccCCcceeEEEEeCCHHHHHHHHHhhcCCCCCCCCCCcceEE
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIEAKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQSKDSYGRPQKLV 392 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~~~d~~G~~qk~v 392 (502)
-.+..+|++.++.++|.+.|+-.-.|-+.-.-+-+ +-++|.|.+.+.|..|+-...+. |-.|.+-|+-
T Consensus 166 sVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q---GYaFVrF~tkEaAahAIv~mNnt---ei~G~~VkCs 233 (321)
T KOG0148|consen 166 SVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ---GYAFVRFETKEAAAHAIVQMNNT---EIGGQLVRCS 233 (321)
T ss_pred eEEeCCcCccccHHHHHHhcccCCcceEEEEeccc---ceEEEEecchhhHHHHHHHhcCc---eeCceEEEEe
Confidence 47889999999999999999876677433222223 48999999999999999998654 4455555543
No 173
>PHA02563 DNA polymerase; Provisional
Probab=34.39 E-value=41 Score=38.65 Aligned_cols=28 Identities=14% Similarity=0.111 Sum_probs=21.6
Q ss_pred HHHHHHhhc------CCCEEEEEchhhHHHHHcc
Q 010743 211 QKRMKKLLS------NGTILVGHSLNNDLEVLKL 238 (502)
Q Consensus 211 ~~~l~~fl~------~g~ILVGHnl~fDl~fLk~ 238 (502)
.++|+.++. .+.++--||+.||..||-.
T Consensus 50 ~~~f~~~i~~~~~k~~~~~vYfHN~~FD~~Fil~ 83 (630)
T PHA02563 50 FDEFLQWIEDTTYKETECIIYFHNLKFDGSFILK 83 (630)
T ss_pred HHHHHHHHhhccccccceEEEEecCCccHHHHHH
Confidence 346666663 3789999999999999865
No 174
>PF04201 TPD52: Tumour protein D52 family; InterPro: IPR007327 The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family []. These proteins have an N-terminal coiled-coil that allows members to form homo- and heterodimers with each other [].
Probab=34.00 E-value=42 Score=32.08 Aligned_cols=36 Identities=22% Similarity=0.311 Sum_probs=26.7
Q ss_pred HHHHHHHHhhhccccchhhhhhhHHHHHHHHHHHhh
Q 010743 462 VIERLKRELREKDFQISMQDKNISDLKKKVAEMKDQ 497 (502)
Q Consensus 462 ~ie~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~ 497 (502)
|=|+|++||.+-+-||.+|...+....|...++|++
T Consensus 30 E~eeLr~EL~KvEeEI~TLrqvL~aKer~~~eLKrk 65 (162)
T PF04201_consen 30 EREELRSELAKVEEEIQTLRQVLAAKERHCAELKRK 65 (162)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence 347788888888888888888877776666666643
No 175
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]
Probab=32.29 E-value=39 Score=31.49 Aligned_cols=65 Identities=14% Similarity=0.229 Sum_probs=47.3
Q ss_pred hhcCCCCCCCChHhhhccCCCCceee--ecccccc-CCcceeEEEEeCCHHHHHHHHHhhcCCCCCCC
Q 010743 320 LFLHRIPTKVPSEELHGVIPGDFTIE--AKAVKRI-RGDNYAAFAIFSSPQEANQAFENVKGNQSKDS 384 (502)
Q Consensus 320 l~~~~iP~~~~~eel~~~f~~~~~i~--~k~~~~~-~g~~~~~~~~f~~~~ea~~af~~l~g~~~~d~ 384 (502)
++..+|....++|+|-.+|+.--.|. +-.-.++ ..--++|.|.|-++++|+.|...|.|...-|.
T Consensus 39 vyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr 106 (153)
T KOG0121|consen 39 VYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDR 106 (153)
T ss_pred EEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCccccc
Confidence 77788888888999999998643332 2121221 23357999999999999999999988765543
No 176
>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]
Probab=31.83 E-value=45 Score=33.43 Aligned_cols=62 Identities=19% Similarity=0.308 Sum_probs=44.5
Q ss_pred hhhcCCCCCCCChHhhhc----cCCCCc-eeeeccccccCCcceeEEEEeCCHHHHHHHHHhhcCCCC
Q 010743 319 RLFLHRIPTKVPSEELHG----VIPGDF-TIEAKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQS 381 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~----~f~~~~-~i~~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~~ 381 (502)
.|+...++..+..++|.+ +|+-.- .+.+..-+. .+-.|.|+|+|++.+.|-.|.+.|+|---
T Consensus 11 TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt-~KmRGQA~VvFk~~~~As~A~r~l~gfpF 77 (221)
T KOG4206|consen 11 TLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKT-PKMRGQAFVVFKETEAASAALRALQGFPF 77 (221)
T ss_pred eEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCC-CCccCceEEEecChhHHHHHHHHhcCCcc
Confidence 356667777778888776 776544 345554443 23356999999999999999999988653
No 177
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=29.88 E-value=61 Score=37.96 Aligned_cols=68 Identities=18% Similarity=0.223 Sum_probs=51.3
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceeeeccccccCCcceeEEEEeCCHHHHHHHHHhhcCCCCCCCCCCcceEEEEe
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIEAKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQSKDSYGRPQKLVEFQ 395 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~~~d~~G~~qk~v~~~ 395 (502)
-|+..+||.++...+|..+|...-.|+-. .- .+..+||+|+-...++|+.|.-.|. ..+-.+|+|.+.
T Consensus 423 TLwvG~i~k~v~e~dL~~~feefGeiqSi--~l-i~~R~cAfI~M~~RqdA~kalqkl~------n~kv~~k~Iki~ 490 (894)
T KOG0132|consen 423 TLWVGGIPKNVTEQDLANLFEEFGEIQSI--IL-IPPRGCAFIKMVRRQDAEKALQKLS------NVKVADKTIKIA 490 (894)
T ss_pred eeeeccccchhhHHHHHHHHHhcccceeE--ee-ccCCceeEEEEeehhHHHHHHHHHh------cccccceeeEEe
Confidence 48999999999999999998764444311 11 3456699999999999999999995 555667777443
No 178
>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]
Probab=29.74 E-value=32 Score=39.73 Aligned_cols=55 Identities=24% Similarity=0.411 Sum_probs=43.2
Q ss_pred hhcCCCCCCCChHhhhccCCCCceeeeccccccCCcceeEEEEeCCHHHHHHHHHh
Q 010743 320 LFLHRIPTKVPSEELHGVIPGDFTIEAKAVKRIRGDNYAAFAIFSSPQEANQAFEN 375 (502)
Q Consensus 320 l~~~~iP~~~~~eel~~~f~~~~~i~~k~~~~~~g~~~~~~~~f~~~~ea~~af~~ 375 (502)
++..+||-....-++.-+|++ -+|-...+.-+.|..+-|+|.|.|+++|.+|.-+
T Consensus 5 IRLqnLP~tAga~DIR~FFSG-L~IPdGgVHIIGGe~GeaFI~FsTDeDARlaM~k 59 (944)
T KOG4307|consen 5 IRLQNLPMTAGASDIRTFFSG-LKIPDGGVHIIGGEEGEAFIGFSTDEDARLAMTK 59 (944)
T ss_pred EEecCCcccccchHHHHhhcc-cccCCCceEEecccccceEEEecccchhhhhhhh
Confidence 456788888888899999998 4444344455578899999999999999999743
No 179
>PRK04325 hypothetical protein; Provisional
Probab=29.65 E-value=51 Score=27.31 Aligned_cols=51 Identities=12% Similarity=0.124 Sum_probs=35.1
Q ss_pred chhhhhHHhhhhccccchhhhHHHHHHHHHHhhhccccchhhhhhhHHHHHHHHHHH
Q 010743 439 IKWINEEEKIADTNQCKCEDHLKVIERLKRELREKDFQISMQDKNISDLKKKVAEMK 495 (502)
Q Consensus 439 ~~~~~~~~~~~~~~~~~~~~h~k~ie~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ 495 (502)
+++.+++..+.-.+|. .-||.||+.+.+-..+|..+.+-+..|..++.++.
T Consensus 7 ~e~Ri~~LE~klAfQE------~tIe~LN~vv~~Qq~~I~~L~~ql~~L~~rl~~~~ 57 (74)
T PRK04325 7 MEDRITELEIQLAFQE------DLIDGLNATVARQQQTLDLLQAQLRLLYQQMRDAN 57 (74)
T ss_pred HHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3444665555555552 24889999988777777777777777777777654
No 180
>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function.
Probab=29.57 E-value=53 Score=26.51 Aligned_cols=42 Identities=14% Similarity=0.260 Sum_probs=28.8
Q ss_pred CCChHhhhccCCCC------ceeeeccccccCCcceeEEEEeCCHHHHHHHHHhh
Q 010743 328 KVPSEELHGVIPGD------FTIEAKAVKRIRGDNYAAFAIFSSPQEANQAFENV 376 (502)
Q Consensus 328 ~~~~eel~~~f~~~------~~i~~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l 376 (502)
+++.+++..+|... ..|||-.. .||.++|.|.+.|..|+..|
T Consensus 15 ~lsT~dI~~y~~~y~~~~~~~~IEWIdD-------tScNvvf~d~~~A~~AL~~L 62 (62)
T PF10309_consen 15 ELSTDDIKAYFSEYFDEEGPFRIEWIDD-------TSCNVVFKDEETAARALVAL 62 (62)
T ss_pred CCCHHHHHHHHHHhcccCCCceEEEecC-------CcEEEEECCHHHHHHHHHcC
Confidence 45566655555433 35555322 58999999999999998765
No 181
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=29.24 E-value=98 Score=34.82 Aligned_cols=73 Identities=22% Similarity=0.338 Sum_probs=56.5
Q ss_pred hhcCCCCCCCChHhhhccCCCCceeeeccccc--cCCc-ceeEEEEeCCHHHHHHHHHhhcCCCCCCCCCCcceEEEEec
Q 010743 320 LFLHRIPTKVPSEELHGVIPGDFTIEAKAVKR--IRGD-NYAAFAIFSSPQEANQAFENVKGNQSKDSYGRPQKLVEFQS 396 (502)
Q Consensus 320 l~~~~iP~~~~~eel~~~f~~~~~i~~k~~~~--~~g~-~~~~~~~f~~~~ea~~af~~l~g~~~~d~~G~~qk~v~~~~ 396 (502)
|+...|=.+++.+.+..+|.-.-.|+...... -+|. .++.+++|.+.+.|..|.+.|.| -+=-||+.| |.+..
T Consensus 281 l~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lng---felAGr~ik-V~~v~ 356 (549)
T KOG0147|consen 281 LYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNG---FELAGRLIK-VSVVT 356 (549)
T ss_pred hhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhcc---ceecCceEE-EEEee
Confidence 67778889999999999997766787543221 1233 67888999999999999999988 677899999 66543
No 182
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=28.74 E-value=43 Score=36.85 Aligned_cols=69 Identities=19% Similarity=0.288 Sum_probs=51.4
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceee-eccccccCCcceeEEEEeCCHHHHHHHHHhhcCCCCCCCCCCcceEEEEec
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIE-AKAVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQSKDSYGRPQKLVEFQS 396 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~-~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~~~d~~G~~qk~v~~~~ 396 (502)
-|+..+||.+++.|.|.+.|...-.++ +|-.+ -.++|-|.+.+.|..|.+.++|. .-.|.+--.++-++
T Consensus 261 vLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~r------DYaFVHf~eR~davkAm~~~ngk---eldG~~iEvtLAKP 330 (506)
T KOG0117|consen 261 VLYVRNLMESTTEETLKKLFNEFGKVERVKKPR------DYAFVHFAEREDAVKAMKETNGK---ELDGSPIEVTLAKP 330 (506)
T ss_pred eeeeeccchhhhHHHHHHHHHhccceEEeeccc------ceeEEeecchHHHHHHHHHhcCc---eecCceEEEEecCC
Confidence 489999999999999999998755554 32222 26889999999999999999764 44566555544444
No 183
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=28.09 E-value=52 Score=37.99 Aligned_cols=68 Identities=21% Similarity=0.116 Sum_probs=53.6
Q ss_pred hhhcCCCCCCCChHhhhccCCCCceeeec-cccccCCcceeEEEEeCCHHHHHHHHHhhcCCCCCCCCCCcce
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDFTIEAK-AVKRIRGDNYAAFAIFSSPQEANQAFENVKGNQSKDSYGRPQK 390 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~~i~~k-~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~~~d~~G~~qk 390 (502)
.+....+|.....+++..+|.....|.-. -+..| ..+.|.|..+.+|++||+.|.....++..+++-+
T Consensus 387 vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~~G----~~aiv~fl~p~eAr~Afrklaysr~k~~plyle~ 455 (725)
T KOG0110|consen 387 VILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPGG----TGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEW 455 (725)
T ss_pred eeeeccCccccccHHHHHHhhcccccceeecCccc----ceeeeeecCccchHHHHHHhchhhhccCcccccc
Confidence 47788899999999999999876666422 12332 4589999999999999999999988888776543
No 184
>PF06810 Phage_GP20: Phage minor structural protein GP20; InterPro: IPR009636 This family consists of several phage minor structural protein Gp20 sequences and prophage sequences of around 180 residues in length. The function of this family is unknown.; GO: 0005198 structural molecule activity
Probab=27.63 E-value=61 Score=30.53 Aligned_cols=38 Identities=32% Similarity=0.441 Sum_probs=31.6
Q ss_pred HHHHHHHHHHhhhccccchhhhh---hhHHHHHHHHHHHhh
Q 010743 460 LKVIERLKRELREKDFQISMQDK---NISDLKKKVAEMKDQ 497 (502)
Q Consensus 460 ~k~ie~~~~~~~~~~~~~~~~~~---~i~~~~~~~~~~~~~ 497 (502)
-.|+..|+.||.+|+-+|..|.+ -+.+|++++++++..
T Consensus 26 ~~e~~~~k~ql~~~d~~i~~Lk~~~~d~eeLk~~i~~lq~~ 66 (155)
T PF06810_consen 26 KEERDNLKTQLKEADKQIKDLKKSAKDNEELKKQIEELQAK 66 (155)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHH
Confidence 45888999999999999998887 788888888887654
No 185
>PRK00846 hypothetical protein; Provisional
Probab=26.44 E-value=60 Score=27.36 Aligned_cols=52 Identities=12% Similarity=0.088 Sum_probs=34.0
Q ss_pred cchhhhhHHhhhhccccchhhhHHHHHHHHHHhhhccccchhhhhhhHHHHHHHHHHH
Q 010743 438 NIKWINEEEKIADTNQCKCEDHLKVIERLKRELREKDFQISMQDKNISDLKKKVAEMK 495 (502)
Q Consensus 438 ~~~~~~~~~~~~~~~~~~~~~h~k~ie~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ 495 (502)
.++.-+++..+.-.+|.+ =||.||+.+.+-.-+|..+..-+.-|+.++.+|.
T Consensus 10 ~le~Ri~~LE~rlAfQe~------tIe~LN~~v~~qq~~I~~L~~ql~~L~~rL~~~~ 61 (77)
T PRK00846 10 ALEARLVELETRLSFQEQ------ALTELSEALADARLTGARNAELIRHLLEDLGKVR 61 (77)
T ss_pred hHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 445556655555555532 3888999887766666666666666666666665
No 186
>KOG4010 consensus Coiled-coil protein TPD52 [General function prediction only]
Probab=25.57 E-value=72 Score=31.29 Aligned_cols=34 Identities=24% Similarity=0.325 Sum_probs=24.1
Q ss_pred HHHHHHHhhhccccchhhhhhhHHHHHHHHHHHh
Q 010743 463 IERLKRELREKDFQISMQDKNISDLKKKVAEMKD 496 (502)
Q Consensus 463 ie~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~ 496 (502)
=|+|+++|.+=+-||++|...++...|...|+|.
T Consensus 46 keelr~EL~kvEeEI~TLrqVLaAKerH~~ELKR 79 (208)
T KOG4010|consen 46 KEELRTELAKVEEEIVTLRQVLAAKERHAAELKR 79 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3577777777777788777777766666666554
No 187
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=25.52 E-value=59 Score=34.72 Aligned_cols=59 Identities=17% Similarity=0.233 Sum_probs=43.3
Q ss_pred HhhhhcCCCCCCCChHhhhccCCCCceeeeccccccCCcceeEEEEeCCHHHHHHHHHhhcC
Q 010743 317 RARLFLHRIPTKVPSEELHGVIPGDFTIEAKAVKRIRGDNYAAFAIFSSPQEANQAFENVKG 378 (502)
Q Consensus 317 l~~l~~~~iP~~~~~eel~~~f~~~~~i~~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g 378 (502)
...|+..++-..+...+|.+.|...--|+-.-+-.++| ||+|.|.|.+.|++|-+.+-.
T Consensus 228 I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~~---CAFv~ftTR~aAE~Aae~~~n 286 (377)
T KOG0153|consen 228 IKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRKG---CAFVTFTTREAAEKAAEKSFN 286 (377)
T ss_pred eeEEEecccccchhHHHHHHHHhhcCCeeeEEeecccc---cceeeehhhHHHHHHHHhhcc
Confidence 44588888888999999998886544443222222233 999999999999999988744
No 188
>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]
Probab=25.26 E-value=56 Score=36.94 Aligned_cols=57 Identities=21% Similarity=0.371 Sum_probs=40.0
Q ss_pred hhcCCCCCCCChHhhhccCCCCceeeeccccccCCcceeEEEEeCCHHHHHHHHHhhcC
Q 010743 320 LFLHRIPTKVPSEELHGVIPGDFTIEAKAVKRIRGDNYAAFAIFSSPQEANQAFENVKG 378 (502)
Q Consensus 320 l~~~~iP~~~~~eel~~~f~~~~~i~~k~~~~~~g~~~~~~~~f~~~~ea~~af~~l~g 378 (502)
+...-||.+.+.|++..+|.+.....+-.-.. +..-.|+|+|.++.+|.+||.-|.-
T Consensus 178 vilREIpettp~e~Vk~lf~~encPk~iscef--a~N~nWyITfesd~DAQqAykylre 234 (684)
T KOG2591|consen 178 VILREIPETTPIEVVKALFKGENCPKVISCEF--AHNDNWYITFESDTDAQQAYKYLRE 234 (684)
T ss_pred EEEeecCCCChHHHHHHHhccCCCCCceeeee--eecCceEEEeecchhHHHHHHHHHH
Confidence 44566899999999999997733221100011 2235799999999999999988754
No 189
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=25.19 E-value=72 Score=36.44 Aligned_cols=33 Identities=39% Similarity=0.604 Sum_probs=25.0
Q ss_pred HHHHHHHHHh----------hhccccchhhhhhhHHHHHHHHH
Q 010743 461 KVIERLKREL----------REKDFQISMQDKNISDLKKKVAE 493 (502)
Q Consensus 461 k~ie~~~~~~----------~~~~~~~~~~~~~i~~~~~~~~~ 493 (502)
+|||.|+.+| -.++-+|.+++.=|..|+++|++
T Consensus 450 ~eie~L~~~l~~~~r~~~~~~~~~rei~~~~~~I~~L~~~L~e 492 (652)
T COG2433 450 REIEKLESELERFRREVRDKVRKDREIRARDRRIERLEKELEE 492 (652)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHH
Confidence 7888888888 34667777777777777777776
No 190
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=24.00 E-value=86 Score=35.47 Aligned_cols=67 Identities=28% Similarity=0.423 Sum_probs=49.9
Q ss_pred hhhcCCCCCCCChHhhhccCCCCc-eeeeccccccCCc-ceeEEEEeCCHHHHHHHHHhhcCCCCCCCCCCc
Q 010743 319 RLFLHRIPTKVPSEELHGVIPGDF-TIEAKAVKRIRGD-NYAAFAIFSSPQEANQAFENVKGNQSKDSYGRP 388 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~~~f~~~~-~i~~k~~~~~~g~-~~~~~~~f~~~~ea~~af~~l~g~~~~d~~G~~ 388 (502)
+|-..++|-.....+|..+|+.-- ..++.-++++-|. -|+++|.|+...+|..|.+.+.|. --.|||
T Consensus 119 rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~---~i~gR~ 187 (678)
T KOG0127|consen 119 RLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGN---KIDGRP 187 (678)
T ss_pred eEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCc---eecCce
Confidence 466677888888889999998743 5577744443333 599999999999999999999654 335555
No 191
>PF08776 VASP_tetra: VASP tetramerisation domain; InterPro: IPR014885 Vasodilator-stimulated phosphoprotein (VASP) is an actin cytoskeletal regulatory protein. This region corresponds to the tetramerisation domain which forms a right handed alpha helical coiled coil structure []. ; PDB: 1USE_A 1USD_A.
Probab=23.67 E-value=1.3e+02 Score=22.44 Aligned_cols=9 Identities=56% Similarity=0.863 Sum_probs=6.5
Q ss_pred HHHHHHHHh
Q 010743 462 VIERLKREL 470 (502)
Q Consensus 462 ~ie~~~~~~ 470 (502)
+.|++||++
T Consensus 4 dle~~KqEI 12 (40)
T PF08776_consen 4 DLERLKQEI 12 (40)
T ss_dssp HHHHHHHHH
T ss_pred hHHHHHHHH
Confidence 567788775
No 192
>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function. It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.
Probab=23.15 E-value=53 Score=26.67 Aligned_cols=34 Identities=24% Similarity=0.405 Sum_probs=22.9
Q ss_pred HHHHHHHHhhhccccchhhhhhhHHHHHHHHHHH
Q 010743 462 VIERLKRELREKDFQISMQDKNISDLKKKVAEMK 495 (502)
Q Consensus 462 ~ie~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ 495 (502)
-||.||+.+.+-.-+|..|...+..|..|+.++.
T Consensus 19 ~ie~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~ 52 (69)
T PF04102_consen 19 TIEELNDVVTEQQRQIDRLQRQLRLLRERLRELE 52 (69)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-----
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4888898887777777777777777777777765
No 193
>PF04420 CHD5: CHD5-like protein; InterPro: IPR007514 Members of this family are probably coiled-coil proteins that are similar to the CHD5 (Congenital heart disease 5) protein. The exact molecular function of these eukaryotic proteins is unknown.; PDB: 3SJA_H 3SJC_D 3SJB_D 3ZS8_D 3VLC_E.
Probab=22.96 E-value=1.3e+02 Score=28.46 Aligned_cols=19 Identities=58% Similarity=0.627 Sum_probs=11.5
Q ss_pred HHHHHHHHHHhhhccccchhhhh
Q 010743 460 LKVIERLKRELREKDFQISMQDK 482 (502)
Q Consensus 460 ~k~ie~~~~~~~~~~~~~~~~~~ 482 (502)
.+||.+|++|++. ||+||.
T Consensus 46 ~~Ei~~l~~E~~~----iS~qDe 64 (161)
T PF04420_consen 46 RKEILQLKRELNA----ISAQDE 64 (161)
T ss_dssp HHHHHHHHHHHTT----S-TTTS
T ss_pred HHHHHHHHHHHHc----CCcHHH
Confidence 4677777777753 566653
No 194
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=22.29 E-value=73 Score=34.00 Aligned_cols=90 Identities=22% Similarity=0.333 Sum_probs=59.3
Q ss_pred hhhcCCCCCCCChHhhh------ccCCCCc---eeee--cc-ccccCCcceeEEEEeCCHHHHHHHHHhhcCCCCCCCCC
Q 010743 319 RLFLHRIPTKVPSEELH------GVIPGDF---TIEA--KA-VKRIRGDNYAAFAIFSSPQEANQAFENVKGNQSKDSYG 386 (502)
Q Consensus 319 ~l~~~~iP~~~~~eel~------~~f~~~~---~i~~--k~-~~~~~g~~~~~~~~f~~~~ea~~af~~l~g~~~~d~~G 386 (502)
..+..+||+.+..|+.. ++|+-.- .|.+ |. +..-..+.+-++++|.+.++|.-++..++|.. .+|
T Consensus 116 LvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~---~DG 192 (480)
T COG5175 116 LVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSL---LDG 192 (480)
T ss_pred eeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccc---ccC
Confidence 46788899999888833 4454322 3333 12 11112225778999999999999999998776 468
Q ss_pred CcceEEEEecCCCCeEEEEEEeeccCCC
Q 010743 387 RPQKLVEFQSNAGIIASLYVRKMVCDEP 414 (502)
Q Consensus 387 ~~qk~v~~~~~~g~~~~~~vrkm~~~~~ 414 (502)
|--|.-+ ++..-++.|.|-.+|..|
T Consensus 193 r~lkatY---GTTKYCtsYLRn~~CpNp 217 (480)
T COG5175 193 RVLKATY---GTTKYCTSYLRNAVCPNP 217 (480)
T ss_pred ceEeeec---CchHHHHHHHcCCCCCCC
Confidence 8766543 333346788898776554
No 195
>PRK00736 hypothetical protein; Provisional
Probab=21.38 E-value=92 Score=25.36 Aligned_cols=33 Identities=21% Similarity=0.319 Sum_probs=21.4
Q ss_pred HHHHHHHHhhhccccchhhhhhhHHHHHHHHHH
Q 010743 462 VIERLKRELREKDFQISMQDKNISDLKKKVAEM 494 (502)
Q Consensus 462 ~ie~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~ 494 (502)
-||.||+.+.+-.-+|..+.+-+.-|..++.++
T Consensus 20 tie~Ln~~v~~Qq~~i~~L~~ql~~L~~rl~~~ 52 (68)
T PRK00736 20 TIEELSDQLAEQWKTVEQMRKKLDALTERFLSL 52 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 488888887665556665555555555555554
No 196
>PRK00295 hypothetical protein; Provisional
Probab=20.99 E-value=96 Score=25.27 Aligned_cols=34 Identities=26% Similarity=0.268 Sum_probs=24.4
Q ss_pred HHHHHHHHhhhccccchhhhhhhHHHHHHHHHHH
Q 010743 462 VIERLKRELREKDFQISMQDKNISDLKKKVAEMK 495 (502)
Q Consensus 462 ~ie~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ 495 (502)
-||.||+.+.+-.-+|..+.+-+..|..++.++.
T Consensus 20 tie~Ln~~v~~Qq~~I~~L~~ql~~L~~rl~~~~ 53 (68)
T PRK00295 20 TIQALNDVLVEQQRVIERLQLQMAALIKRQEEMV 53 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4788888887766677777777777777666654
No 197
>PRK04406 hypothetical protein; Provisional
Probab=20.11 E-value=98 Score=25.78 Aligned_cols=49 Identities=18% Similarity=0.156 Sum_probs=30.2
Q ss_pred hhhhHHhhhhccccchhhhHHHHHHHHHHhhhccccchhhhhhhHHHHHHHHHHH
Q 010743 441 WINEEEKIADTNQCKCEDHLKVIERLKRELREKDFQISMQDKNISDLKKKVAEMK 495 (502)
Q Consensus 441 ~~~~~~~~~~~~~~~~~~h~k~ie~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ 495 (502)
.-+.+..+.-.+|. .-||.||+.+.+-.-+|..+.+-+..|..++.++.
T Consensus 11 ~Ri~~LE~~lAfQE------~tIe~LN~~v~~Qq~~I~~L~~ql~~L~~rl~~~~ 59 (75)
T PRK04406 11 ERINDLECQLAFQE------QTIEELNDALSQQQLLITKMQDQMKYVVGKVKNMD 59 (75)
T ss_pred HHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 33444444444442 24888888887766666666666666666666543
Done!