Query 000161
Match_columns 1988
No_of_seqs 441 out of 1876
Neff 5.9
Searched_HMMs 46136
Date Thu Mar 28 21:19:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000161.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000161hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1798 DNA polymerase epsilon 100.0 0E+00 0E+00 4400.3 141.2 1901 25-1987 31-2170(2173)
2 cd05535 POLBc_epsilon DNA poly 100.0 2E-170 4E-175 1553.7 52.6 618 501-1120 1-621 (621)
3 PTZ00166 DNA polymerase delta 100.0 9E-121 2E-125 1219.1 72.0 809 61-1155 72-958 (1054)
4 KOG0969 DNA polymerase delta, 100.0 6E-112 1E-116 1021.3 41.4 779 61-1132 94-936 (1066)
5 PRK05762 DNA polymerase II; Re 100.0 4E-108 8E-113 1082.1 73.2 736 41-1121 3-768 (786)
6 COG0417 PolB DNA polymerase el 100.0 1E-107 3E-112 1075.1 68.4 769 62-1154 7-791 (792)
7 PRK05761 DNA polymerase I; Rev 100.0 2E-106 4E-111 1058.1 65.3 725 45-1155 20-786 (787)
8 PHA02528 43 DNA polymerase; Pr 100.0 2.8E-96 6E-101 961.2 62.3 782 70-1155 19-881 (881)
9 KOG0970 DNA polymerase alpha, 100.0 3.9E-94 8.4E-99 892.7 47.0 684 189-1128 462-1208(1429)
10 TIGR00592 pol2 DNA polymerase 100.0 8.4E-91 1.8E-95 944.1 67.1 773 64-1121 323-1171(1172)
11 PHA03036 DNA polymerase; Provi 100.0 1.3E-88 2.8E-93 877.0 55.2 683 203-1109 112-982 (1004)
12 KOG0968 DNA polymerase zeta, c 100.0 2.6E-81 5.7E-86 777.2 36.6 665 236-1139 655-1368(1488)
13 PF08490 DUF1744: Domain of un 100.0 2.9E-79 6.3E-84 744.6 29.8 263 1414-1677 100-396 (396)
14 cd05534 POLBc_zeta DNA polymer 100.0 2.2E-66 4.7E-71 645.1 30.0 432 467-1122 1-444 (451)
15 cd05536 POLBc_B3 DNA polymeras 100.0 4.1E-65 8.9E-70 622.2 31.5 294 721-1121 66-360 (371)
16 cd05533 POLBc_delta DNA polyme 100.0 4.3E-65 9.3E-70 625.7 27.4 302 721-1121 73-389 (393)
17 cd05532 POLBc_alpha DNA polyme 100.0 2.4E-64 5.2E-69 621.0 28.0 308 721-1125 70-385 (400)
18 cd05537 POLBc_Pol_II DNA polym 100.0 9.6E-63 2.1E-67 599.1 30.5 298 719-1121 65-367 (371)
19 PF00136 DNA_pol_B: DNA polyme 100.0 9.8E-63 2.1E-67 621.7 23.2 430 467-1121 1-444 (466)
20 cd05538 POLBc_Pol_II_B DNA pol 100.0 3.2E-61 6.9E-66 581.2 28.1 295 723-1111 46-344 (347)
21 cd05530 POLBc_B1 DNA polymeras 100.0 3.8E-60 8.2E-65 574.7 35.0 293 717-1111 72-369 (372)
22 smart00486 POLBc DNA polymeras 100.0 2E-59 4.4E-64 590.3 42.8 442 237-839 1-470 (471)
23 cd05531 POLBc_B2 DNA polymeras 100.0 2.3E-58 5.1E-63 557.9 29.8 285 716-1110 61-347 (352)
24 cd00145 POLBc DNA polymerase t 100.0 8.2E-59 1.8E-63 558.6 25.2 251 720-1121 65-322 (323)
25 PHA02524 43A DNA polymerase su 100.0 2.9E-51 6.3E-56 504.6 39.6 295 236-618 103-419 (498)
26 PHA03334 putative DNA polymera 100.0 2.2E-50 4.8E-55 517.1 39.4 392 301-841 322-822 (1545)
27 cd05779 DNA_polB_epsilon_exo D 100.0 1.6E-38 3.5E-43 358.5 23.3 204 238-442 1-204 (204)
28 PF03104 DNA_pol_B_exo1: DNA p 100.0 2.3E-36 5.1E-41 364.5 20.2 283 71-398 1-325 (325)
29 cd05777 DNA_polB_delta_exo DED 100.0 1.1E-32 2.4E-37 318.3 22.7 201 234-444 2-223 (230)
30 cd05781 DNA_polB_B3_exo DEDDy 100.0 2.7E-30 5.8E-35 289.4 22.9 176 237-443 1-187 (188)
31 cd05780 DNA_polB_Kod1_like_exo 100.0 3.6E-30 7.8E-35 290.3 22.3 185 237-443 1-194 (195)
32 cd05778 DNA_polB_zeta_exo inac 100.0 2.2E-29 4.8E-34 290.5 21.7 197 237-441 2-230 (231)
33 PHA02523 43B DNA polymerase su 100.0 3.3E-30 7.1E-35 300.0 13.8 276 761-1054 29-327 (391)
34 TIGR00592 pol2 DNA polymerase 100.0 6.5E-32 1.4E-36 369.2 -6.0 367 133-618 128-534 (1172)
35 cd05785 DNA_polB_like2_exo Unc 100.0 1.7E-28 3.6E-33 278.6 21.6 183 234-441 4-206 (207)
36 cd05783 DNA_polB_B1_exo DEDDy 100.0 9.4E-28 2E-32 271.8 21.0 190 235-442 1-202 (204)
37 cd05784 DNA_polB_II_exo DEDDy 99.9 5E-27 1.1E-31 263.6 21.2 182 237-442 1-193 (193)
38 cd05160 DEDDy_DNA_polB_exo DED 99.9 4.3E-27 9.2E-32 265.9 20.2 192 241-441 1-198 (199)
39 cd05776 DNA_polB_alpha_exo ina 99.9 3.1E-24 6.7E-29 248.6 17.3 199 237-449 1-232 (234)
40 cd05782 DNA_polB_like1_exo Unc 99.8 1.6E-20 3.5E-25 213.9 19.1 160 255-443 45-208 (208)
41 PHA02563 DNA polymerase; Provi 99.7 7.6E-16 1.6E-20 196.7 27.4 64 775-840 403-490 (630)
42 PF10108 DNA_pol_B_exo2: Predi 99.6 5.6E-14 1.2E-18 158.2 18.0 162 255-444 3-169 (209)
43 PF13482 RNase_H_2: RNase_H su 99.2 1.6E-11 3.5E-16 134.8 9.6 152 242-444 1-163 (164)
44 COG3359 Predicted exonuclease 99.1 8.3E-10 1.8E-14 124.1 14.8 157 240-443 99-264 (278)
45 TIGR03491 RecB family nuclease 98.2 7.2E-06 1.6E-10 104.9 13.0 162 238-442 283-455 (457)
46 PRK06309 DNA polymerase III su 98.1 3.5E-05 7.7E-10 90.2 14.1 154 239-444 2-162 (232)
47 PRK07942 DNA polymerase III su 97.9 0.00022 4.8E-09 83.6 17.5 177 236-464 3-192 (232)
48 PRK06063 DNA polymerase III su 97.9 0.00013 2.9E-09 89.0 14.8 157 238-444 14-175 (313)
49 PRK08517 DNA polymerase III su 97.9 0.00016 3.4E-09 86.0 14.7 159 236-444 65-227 (257)
50 PRK06310 DNA polymerase III su 97.8 0.00021 4.5E-09 84.8 14.8 160 238-444 6-170 (250)
51 PHA02735 putative DNA polymera 97.8 0.00024 5.3E-09 85.1 14.3 112 394-522 170-285 (716)
52 PRK05601 DNA polymerase III su 97.8 0.00034 7.4E-09 85.6 15.4 189 235-444 42-245 (377)
53 PRK05711 DNA polymerase III su 97.8 0.00023 5E-09 83.7 13.3 161 237-444 2-172 (240)
54 PRK06807 DNA polymerase III su 97.8 0.00028 6.1E-09 86.1 14.4 158 238-444 7-168 (313)
55 cd06136 TREX1_2 DEDDh 3'-5' ex 97.7 0.00053 1.2E-08 77.2 14.1 92 313-443 84-176 (177)
56 PRK07883 hypothetical protein; 97.7 0.00039 8.4E-09 91.0 14.9 163 235-444 11-178 (557)
57 cd06138 ExoI_N N-terminal DEDD 97.7 0.00026 5.7E-09 80.0 11.4 157 242-441 1-182 (183)
58 TIGR01406 dnaQ_proteo DNA poly 97.6 0.00065 1.4E-08 79.4 14.6 157 240-444 1-168 (225)
59 TIGR01405 polC_Gram_pos DNA po 97.6 0.00039 8.5E-09 97.0 14.1 154 237-444 188-351 (1213)
60 cd06130 DNA_pol_III_epsilon_li 97.6 0.00069 1.5E-08 73.9 12.5 150 242-442 2-155 (156)
61 PRK07740 hypothetical protein; 97.5 0.0014 3.1E-08 77.5 15.5 161 236-444 56-222 (244)
62 cd06137 DEDDh_RNase DEDDh 3'-5 97.5 0.00069 1.5E-08 75.1 12.1 146 242-441 1-160 (161)
63 TIGR00573 dnaq exonuclease, DN 97.5 0.00086 1.9E-08 77.9 13.3 160 238-444 6-173 (217)
64 PRK09146 DNA polymerase III su 97.5 0.0016 3.4E-08 76.8 15.2 162 236-444 44-223 (239)
65 PRK06195 DNA polymerase III su 97.5 0.0014 3.1E-08 80.1 15.3 155 240-444 2-160 (309)
66 cd06125 DnaQ_like_exo DnaQ-lik 97.5 0.00039 8.4E-09 70.6 8.7 69 242-352 1-69 (96)
67 COG2176 PolC DNA polymerase II 97.5 0.00045 9.7E-09 92.1 11.3 137 232-406 414-561 (1444)
68 cd06127 DEDDh DEDDh 3'-5' exon 97.5 0.0013 2.9E-08 70.7 13.2 152 242-441 1-158 (159)
69 cd06131 DNA_pol_III_epsilon_Ec 97.5 0.00092 2E-08 74.1 12.0 154 242-444 2-166 (167)
70 PRK08074 bifunctional ATP-depe 97.4 0.0022 4.7E-08 89.1 18.0 151 240-444 4-165 (928)
71 PRK09145 DNA polymerase III su 97.4 0.0018 3.9E-08 74.3 14.6 156 238-444 28-197 (202)
72 smart00479 EXOIII exonuclease 97.4 0.0013 2.9E-08 72.3 12.9 157 241-444 2-163 (169)
73 PRK07247 DNA polymerase III su 97.4 0.0028 6E-08 72.6 15.0 149 239-444 5-165 (195)
74 cd06134 RNaseT DEDDh 3'-5' exo 97.4 0.0021 4.6E-08 73.2 13.8 158 241-444 7-185 (189)
75 TIGR01407 dinG_rel DnaQ family 97.4 0.0039 8.4E-08 86.1 18.7 156 240-444 1-161 (850)
76 PRK05168 ribonuclease T; Provi 97.3 0.0037 8.1E-08 72.4 15.1 163 236-444 14-197 (211)
77 TIGR01298 RNaseT ribonuclease 97.3 0.0046 9.9E-08 71.1 15.7 160 239-444 8-188 (200)
78 PRK11779 sbcB exonuclease I; P 97.2 0.0015 3.3E-08 83.6 10.8 166 237-444 4-194 (476)
79 PRK07748 sporulation inhibitor 97.1 0.0068 1.5E-07 70.0 14.6 169 238-444 3-176 (207)
80 cd06144 REX4_like DEDDh 3'-5' 97.1 0.0024 5.2E-08 70.1 9.9 147 242-441 1-151 (152)
81 cd05532 POLBc_alpha DNA polyme 97.0 0.0051 1.1E-07 77.8 13.2 111 1568-1680 112-222 (400)
82 PRK07246 bifunctional ATP-depe 97.0 0.0065 1.4E-07 83.3 14.4 151 238-444 6-166 (820)
83 cd06145 REX1_like DEDDh 3'-5' 96.8 0.013 2.7E-07 64.5 12.1 144 242-441 1-149 (150)
84 cd06133 ERI-1_3'hExo_like DEDD 96.7 0.026 5.7E-07 62.7 14.4 159 242-444 2-175 (176)
85 cd06149 ISG20 DEDDh 3'-5' exon 96.6 0.011 2.4E-07 65.4 10.7 148 242-441 1-156 (157)
86 COG0417 PolB DNA polymerase el 96.6 0.033 7.1E-07 76.3 16.7 111 1568-1679 510-621 (792)
87 PRK05762 DNA polymerase II; Re 96.3 0.021 4.7E-07 78.1 13.0 113 1567-1679 494-624 (786)
88 PRK09182 DNA polymerase III su 96.3 0.032 6.9E-07 67.9 12.5 152 236-444 34-197 (294)
89 cd05537 POLBc_Pol_II DNA polym 96.2 0.042 9.2E-07 68.9 13.5 135 1545-1679 68-227 (371)
90 cd05536 POLBc_B3 DNA polymeras 96.2 0.024 5.2E-07 71.2 11.4 103 1568-1677 109-213 (371)
91 PRK06722 exonuclease; Provisio 96.2 0.14 3E-06 61.9 17.1 200 240-482 6-219 (281)
92 COG0847 DnaQ DNA polymerase II 96.1 0.073 1.6E-06 62.8 14.1 159 239-444 13-178 (243)
93 PRK00448 polC DNA polymerase I 95.9 0.056 1.2E-06 77.3 13.9 159 238-444 418-580 (1437)
94 PF01612 DNA_pol_A_exo1: 3'-5' 95.7 0.04 8.7E-07 60.9 9.3 146 240-444 21-171 (176)
95 TIGR00354 polC DNA polymerase, 95.7 0.013 2.7E-07 77.8 5.6 72 1904-1975 991-1064(1095)
96 cd00145 POLBc DNA polymerase t 95.6 0.022 4.8E-07 70.3 7.3 108 1569-1679 110-218 (323)
97 PRK04023 DNA polymerase II lar 95.5 0.015 3.3E-07 77.6 5.8 72 1904-1975 1016-1089(1121)
98 PF00136 DNA_pol_B: DNA polyme 95.5 0.05 1.1E-06 70.5 10.4 113 1568-1680 163-277 (466)
99 PRK14714 DNA polymerase II lar 95.2 0.022 4.8E-07 77.9 5.6 72 1904-1975 1232-1305(1337)
100 cd05533 POLBc_delta DNA polyme 95.1 0.076 1.6E-06 67.3 9.7 110 1569-1679 116-234 (393)
101 PRK05359 oligoribonuclease; Pr 95.0 0.069 1.5E-06 60.6 8.2 106 240-352 4-123 (181)
102 PF03175 DNA_pol_B_2: DNA poly 95.0 0.008 1.7E-07 77.5 0.7 24 327-350 6-29 (459)
103 cd05538 POLBc_Pol_II_B DNA pol 94.9 0.083 1.8E-06 65.8 9.2 105 1568-1677 86-192 (347)
104 cd05530 POLBc_B1 DNA polymeras 94.7 0.11 2.4E-06 65.2 9.6 102 1568-1678 120-222 (372)
105 cd06135 Orn DEDDh 3'-5' exonuc 94.6 0.077 1.7E-06 59.7 7.3 102 242-350 2-117 (173)
106 PRK14715 DNA polymerase II lar 94.4 0.044 9.5E-07 74.8 5.4 70 1904-1974 1521-1592(1627)
107 cd06139 DNA_polA_I_Ecoli_like_ 94.2 1.4 3.1E-05 49.6 16.5 154 239-444 5-166 (193)
108 PTZ00166 DNA polymerase delta 93.9 0.17 3.6E-06 71.4 9.7 110 1569-1679 653-772 (1054)
109 cd05534 POLBc_zeta DNA polymer 93.9 0.13 2.7E-06 66.4 7.9 111 1568-1679 171-285 (451)
110 cd05531 POLBc_B2 DNA polymeras 93.2 0.33 7.2E-06 60.7 9.7 99 1569-1678 103-208 (352)
111 PHA03036 DNA polymerase; Provi 93.1 0.27 5.8E-06 67.8 9.2 113 1568-1680 664-814 (1004)
112 PTZ00315 2'-phosphotransferase 92.7 1.8 4E-05 56.8 15.5 166 238-444 55-251 (582)
113 cd06146 mut-7_like_exo DEDDy 3 92.5 1.2 2.7E-05 51.1 12.5 112 312-444 68-191 (193)
114 PRK05755 DNA polymerase I; Pro 91.2 2.5 5.3E-05 59.3 15.5 146 238-444 314-465 (880)
115 PRK05761 DNA polymerase I; Rev 90.2 0.8 1.7E-05 63.0 9.1 101 1569-1678 516-617 (787)
116 PRK07983 exodeoxyribonuclease 88.3 4.5 9.7E-05 47.6 12.3 89 308-444 62-150 (219)
117 cd06129 RNaseD_like DEDDy 3'-5 88.2 4.9 0.00011 44.7 12.0 92 325-444 65-159 (161)
118 cd06141 WRN_exo DEDDy 3'-5' ex 88.1 4.4 9.5E-05 45.1 11.7 103 315-444 63-168 (170)
119 cd00007 35EXOc 3'-5' exonuclea 86.2 19 0.00041 38.5 14.9 105 311-444 40-151 (155)
120 PF03337 Pox_F12L: Poxvirus F1 84.8 19 0.00041 48.1 16.1 146 232-410 185-345 (651)
121 PHA02952 EEV maturation protei 83.1 21 0.00046 47.5 15.5 98 232-346 185-293 (648)
122 COG1933 Archaeal DNA polymeras 81.3 1.2 2.6E-05 51.8 3.2 59 1917-1975 159-219 (253)
123 cd06148 Egl_like_exo DEDDy 3'- 78.3 36 0.00077 39.3 14.0 51 392-444 114-173 (197)
124 PF00929 RNase_T: Exonuclease; 78.0 2.9 6.3E-05 44.9 4.8 99 242-349 1-105 (164)
125 KOG0970 DNA polymerase alpha, 78.0 1E+02 0.0023 43.4 19.4 189 1480-1680 836-1039(1429)
126 PRK10829 ribonuclease D; Provi 72.5 34 0.00073 43.6 12.7 100 314-444 63-166 (373)
127 PF08996 zf-DNA_Pol: DNA Polym 67.2 8.5 0.00018 44.2 5.4 113 1850-1968 7-130 (188)
128 PF08408 DNA_pol_B_3: DNA poly 66.5 5.5 0.00012 43.3 3.4 56 402-457 83-142 (149)
129 COG2251 Predicted nuclease (Re 63.5 10 0.00022 48.2 5.4 117 309-443 337-465 (474)
130 smart00474 35EXOc 3'-5' exonuc 56.9 2.1E+02 0.0046 31.1 14.0 100 315-444 65-167 (172)
131 COG2925 SbcB Exonuclease I [DN 55.1 1.1E+02 0.0023 38.7 11.8 144 236-401 6-172 (475)
132 PHA02523 43B DNA polymerase su 54.2 95 0.0021 39.2 11.2 87 1544-1630 22-119 (391)
133 KOG2249 3'-5' exonuclease [Rep 50.7 80 0.0017 38.1 9.5 38 391-444 225-262 (280)
134 PF08490 DUF1744: Domain of un 47.8 7.5E+02 0.016 32.1 19.2 60 782-841 289-349 (396)
135 PHA03181 helicase-primase prim 46.7 3.4E+02 0.0074 37.4 15.2 186 778-992 460-651 (764)
136 PHA03144 helicase-primase prim 45.2 3E+02 0.0065 37.9 14.4 185 778-992 451-637 (746)
137 PHA02528 43 DNA polymerase; Pr 41.5 96 0.0021 43.8 9.8 111 1568-1678 547-690 (881)
138 TIGR01388 rnd ribonuclease D. 39.7 2E+02 0.0043 36.8 11.5 101 314-444 59-162 (367)
139 KOG3657 Mitochondrial DNA poly 37.4 46 0.001 45.2 5.4 59 393-452 323-386 (1075)
140 PF10058 DUF2296: Predicted in 31.6 23 0.00051 32.7 1.1 30 1866-1899 23-52 (54)
141 PF11635 Med16: Mediator compl 27.5 20 0.00044 49.6 0.0 11 1940-1950 742-752 (753)
142 PHA02754 hypothetical protein; 25.8 1.4E+02 0.0031 27.9 4.9 35 1594-1628 9-52 (67)
143 KOG0968 DNA polymerase zeta, c 24.4 30 0.00065 48.2 0.7 96 1580-1679 1098-1194(1488)
144 KOG4793 Three prime repair exo 24.0 87 0.0019 37.8 4.2 46 307-354 103-148 (318)
145 cd05535 POLBc_epsilon DNA poly 21.5 4.9E+02 0.011 35.3 10.6 108 1568-1677 280-427 (621)
146 PF08747 DUF1788: Domain of un 21.2 1.3E+02 0.0028 32.7 4.6 23 586-609 59-81 (126)
147 PF09538 FYDLN_acid: Protein o 20.6 60 0.0013 34.3 1.8 29 1867-1904 11-39 (108)
No 1
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=100.00 E-value=0 Score=4400.33 Aligned_cols=1901 Identities=58% Similarity=0.961 Sum_probs=1779.1
Q ss_pred HHHHHhcCCccccCCCceEEEEEeeeecccccccCCCCeEEEEEEEEecCCCeEEEEeCCccEEEEEecCCChHHHHHHH
Q 000161 25 EELEAKLGYDLFSEGDKRLGWLLTFASSSLEDEDTRKVYSCIDLYFVSQDGSTFKSKYKFRPYFYAATKEKMEMDVEAYL 104 (1988)
Q Consensus 25 ~~~~~~~~~~~~~~~~~~~g~L~n~~~~~~~d~~~~~~~~~v~ly~~t~dG~~~~v~v~f~PYFyv~~~~~~~~~v~~~l 104 (1988)
|+||+++||.+|.++.++.|||+|||++++.|++.+.+.++|++||+++||.+|+++++|+|||||++.++.+.+|++||
T Consensus 31 d~ld~~~GF~~~~~~~~~~GWLln~~~t~~~d~~t~~~~S~VD~yFi~~dG~~Fk~~~py~PYFyiAt~d~~e~~Ve~yL 110 (2173)
T KOG1798|consen 31 DELDSKLGFERYSEGRERGGWLLNMHPTELEDEDTKKGISAVDLYFIDDDGSSFKVKYPYRPYFYIATRDGMELEVEEYL 110 (2173)
T ss_pred hhHHHhhCceeccCccccceeEEeeccceeeecccCcceeEEEEEEEccCCCeEEEeecccceEEEeeccccHHHHHHHH
Confidence 99999999999999999999999999999999876779999999999999999999999999999999999999999999
Q ss_pred HHhccccceeEEEEEEeeCCCcCcCCCCCeEEEEEEEechhhHHHHHHHHHHHHHhhcccchhHHHHHHhhhcccCCCCc
Q 000161 105 RRRYESQIADIEILEKEDLDLKNHLSGLHKSYLKISFDTVQQLMDVKKDLLHVVERNQAKFDAAEAYESILTGKREQRPQ 184 (1988)
Q Consensus 105 ~~~~~~~i~~ie~v~k~dl~~~nhl~g~~~~~lKl~f~~~~~l~~vr~~l~~~~~~n~~~~~~~~~y~~~~~~~~~~~~~ 184 (1988)
+++|++.+++||+|.|+||+++|||+|.++.|+||+|.+.++|.++|+.|+++|++|+.+..+.++|...++.+.....+
T Consensus 111 ~Kky~g~i~~ie~v~kEDL~lkNHLsGlqk~yiKlsF~t~~~L~~vrK~l~~iV~~N~~q~~a~daY~~~ls~~~~~~~q 190 (2173)
T KOG1798|consen 111 RKKYEGQIADIEIVHKEDLDLKNHLSGLQKTYIKLSFDTVNQLVEVRKDLRPIVKRNKAQFDALDAYTNILSGNLNGRDQ 190 (2173)
T ss_pred HHHHhhhhhheeEecHhhcCchhhhhcccccEEEEEEecHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHHhhhccCCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998776655544
Q ss_pred -ccccccccccccCCCccceeeeecCCccceeEEEeeCCCCceEEEeccccCCCCceEEEEEEEEccCCCCCCCCCCCeE
Q 000161 185 -DFLDCIVDLREYDVPYHIRFAIDNDVRCGQWYDVSISSTGPLLEKRVDLLQRAEVHVCAFDIETTKLPLKFPDADYDII 263 (1988)
Q Consensus 185 -~~~~~i~~i~E~DI~~~~R~~iD~~I~~g~W~~v~~~~~~~~i~~~~~~~~~p~lrvLsfDIEt~s~~~~fPdp~~D~I 263 (1988)
|.++.|+||+|||||||+|++||++||+|.||.|+...+.++++...+++.+|+++||||||||++.|+||||++.|+|
T Consensus 191 ~D~ld~IvDiREYDVPyHvR~sID~~IrvG~WY~V~~~~~~v~i~~r~~~i~radp~VlAFDIETtKlPLKFPDae~DqI 270 (2173)
T KOG1798|consen 191 GDALDSIVDIREYDVPYHVRVSIDLDIRVGQWYNVSYNSGPVEIERRTDLIERADPRVLAFDIETTKLPLKFPDAESDQI 270 (2173)
T ss_pred cchHhhhhhHhhcCCceEEEEeecCCeeeeeeeeeeeeccceEEEecccccccCCceEEEEeeecccCCCCCCCcccceE
Confidence 9999999999999999999999999999999999987777888888899999999999999999999999999999999
Q ss_pred EEEEEEEcCCceEEEcccccccccccccCCCCCCCCCceEEecCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHH
Q 000161 264 MMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLE 343 (1988)
Q Consensus 264 i~IS~~~~~~g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~ 343 (1988)
||||||+||+|++|+||+|||+||+||||||||||+|.|.|++++||.+||++||+||++.+|.||||||||.|||||+.
T Consensus 271 MMISYMiDGqGfLItNREiVs~DIedfEYTPKpE~eG~F~v~Ne~dEv~Ll~RfFeHiq~~kP~iivTyNGDFFDWPFve 350 (2173)
T KOG1798|consen 271 MMISYMIDGQGFLITNREIVSEDIEDFEYTPKPEYEGPFCVFNEPDEVGLLQRFFEHIQEVKPTIIVTYNGDFFDWPFVE 350 (2173)
T ss_pred EEEEEEecCceEEEechhhhccchhhcccCCccccccceEEecCCcHHHHHHHHHHHHHhcCCcEEEEecCccccchhhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhCh
Q 000161 344 TRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKP 423 (1988)
Q Consensus 344 ~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~ 423 (1988)
+||+.||++|..++||. ++++|+|+.+.++|||||+|||||+|||++|++|++|++++||++|++++|++|.+|+.++|
T Consensus 351 ~Ra~~hGi~m~eEiGF~-~D~~gEyks~~c~HmDcfrWVKRDSYLPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkP 429 (2173)
T KOG1798|consen 351 ARAKIHGISMNEEIGFR-RDSQGEYKSPFCIHMDCFRWVKRDSYLPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKP 429 (2173)
T ss_pred HHHHhcCCCcchhcCce-ecccccccccceeehhhhhhhhhcccCCCcccchhHHHHHhhCCCcccCCHHHhhhhhhhCc
Confidence 99999999999999999 88999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhHHHHHHHHHhccchHhhhhhhcCCChHHHhhhhhHHHHHHHHHHHHHHCCeeccCCCCCCchhhhcccc
Q 000161 424 QMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAYKANVICPNKHQSDPEKFYRNHL 503 (1988)
Q Consensus 424 ~~La~Y~l~Da~lt~~L~~Klv~~~i~~La~i~~l~~~~vlr~Gsg~~~E~LLm~~a~~~n~i~Pnk~~~~~~~~~~g~l 503 (1988)
+.|++|+++||++||+||+||||||||+||+||||+||+|||+||||+||+|||+||++.|+|+|||+..+.+++++||+
T Consensus 430 Q~lasYSVSDAVATYyLYMkYVhPFIFsLctIIPl~PDevLRKGSGTLCE~LLmVeA~~~NIv~PNK~~e~~~~f~dGhl 509 (2173)
T KOG1798|consen 430 QTLASYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDEVLRKGSGTLCEALLMVEAYHANIVFPNKHTEDPEKFYDGHL 509 (2173)
T ss_pred hhhhhcchHHHHHHHHHHHHHhhhHHhhhhhccccChHHHHhcCcchHHHHHHHHHHHhcCeecCCcCccchhhhccCee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCcceeeeccCccccCCCCCCccCChhHHHHHhhhhhhhhHHHHhHhcccccccccchHHHHHHHHHHHHhhccC
Q 000161 504 LESETYIGGHVECLESGVFRSDLPTSFKLDPSAYEQLLNNLDRDLQYAIKVEGKMDLESVSNYDEVKNAIMEKLLRLQEE 583 (1988)
Q Consensus 504 ~~setY~GG~V~~p~~GvY~~d~~~~f~~~~~~~~~l~~~~~~~l~~~~~~e~~~~~~~~~n~~~v~~~i~~~l~~l~~~ 583 (1988)
++||||+||||+++++||||+|||+.|++||+||++||++|+++|+|++++|+++++|+|+||||||++|.++|++|+++
T Consensus 510 leSETYVGGHVE~LesGVFRSDip~~F~~dp~a~~eLi~~l~~~L~~~l~vE~k~~vd~v~nfeEv~~~I~~kL~~lrd~ 589 (2173)
T KOG1798|consen 510 LESETYVGGHVECLESGVFRSDIPTEFRMDPSAYEELIDELGETLDFALTVENKVRVDEVTNFEEVKDEILEKLEELRDV 589 (2173)
T ss_pred eeeeeeechhhhhHhcccccccCcccccCCHHHHHHHHHHHHHHHHHHHhhhcccchhhhcCHHHHHHHHHHHHHHhcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccCCeEEEEeccccchHHHHhcCCCCCccccccccccccCCCCCCccccccccccccccccCCcchhhHhhhhcccc
Q 000161 584 PIREECPLIYHLDVAAMYPNIILTNRLQPPSIVTDEVCTACDFNRPGKTCLRKLEWVWRGEIFMGKRSDYYHLKKQIESE 663 (1988)
Q Consensus 584 p~~~~~p~V~~LDf~SLYPsII~t~NL~p~Tiv~~~~c~~c~~n~p~~~c~r~m~w~~~ge~~p~~~~ey~~i~~~l~~e 663 (1988)
|.|.|+|+||||||+|||||||+||+|||.+||+++.|++||||.|+++|.|+|+|+||||++|++++||++|++||++|
T Consensus 590 p~R~E~PlIYHLDVaaMYPNIilTNRLQP~siv~E~~C~~CDfN~P~ktC~Rkm~W~WRGe~~pa~r~EY~~I~~qlesE 669 (2173)
T KOG1798|consen 590 PIREEGPLIYHLDVAAMYPNIILTNRLQPDSIVDEEICAACDFNKPGKTCKRKMEWAWRGEYFPAKRSEYHRIKKQLESE 669 (2173)
T ss_pred CccccCCeEEEEehhhccCceeeecCCCCcccccHhhhccCCCCCCCcchhhhheeeeeeeEecCcchHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCc-ccccccCchHHHHHHHHHHHHHhhhhhcccccccccccccccccccccccchHHHHHHHHHHHHHHHhhh
Q 000161 664 FVDGTNGHL-SKSFLDLPKMEQQSRLKDRLKKYCQKAYKRVLDKPVTELREAGICMRENSFYVDTVRSFRDRRYEYKGLN 742 (1988)
Q Consensus 664 ~f~~~~~g~-~~~~~~L~~~~q~~~lkkrl~~y~~kvy~k~~~~~~~~~r~~~icqre~~f~~~~lr~f~drR~~~K~l~ 742 (1988)
.||+..+-. ++.|++|+.+||++.+|+|+++||+|+|+|++.+++++ |+++||||||||||+|||.||||||+||++.
T Consensus 670 ~f~~~~~~~~~k~F~~L~~~eq~~~~kkRl~~Ysrk~Y~rv~~~~i~e-Ret~ICqRENpFYVdTVrsFRDRRYeyK~L~ 748 (2173)
T KOG1798|consen 670 SFPAGAPFSPSKSFHELSREEQAAKLKKRLKDYSRKVYHRVKDTEIEE-RETTICQRENPFYVDTVRSFRDRRYEYKGLH 748 (2173)
T ss_pred cCCCCCCCCCCcccccCCHHHHHHHHHHHHHHHHHHHHhHhcccchhh-hhcchhhccCchhhhhHHHhhhhhhHHHHHH
Confidence 999877766 89999999999999999999999999999999999998 9999999999999999999999999999999
Q ss_pred hhhhhhhHHHhhcCChhhHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 000161 743 KVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNARLLIEK 822 (1988)
Q Consensus 743 K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~sR~ys~e~A~~VT~~Gr~iI~~a~~lve~ 822 (1988)
|+||+++++|+..||.++++|+++|.++|||+|+|||||+|||||||||||||||||||||+||.||++||++||++||+
T Consensus 749 K~wkg~ls~a~~sg~~a~i~eak~mvVlYdSLQLAHKcILNSFYGYVMRKGsRWYSMEMAGIvc~TGAnIIq~AR~lVEr 828 (2173)
T KOG1798|consen 749 KVWKGKLSAAKASGDLARIKEAKKMVVLYDSLQLAHKCILNSFYGYVMRKGSRWYSMEMAGIVCLTGANIIQMARELVER 828 (2173)
T ss_pred HHHHHHHhhhhccCchhhHHhhhheEEehHhHHHHHHHHHhhhhhhhhccccchheeehhheeeccchHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCeEEEccceeeEEcCCCCCcccccccccccccccccccccccchhhhccccchhhhhccCCccccccccccceeEEee
Q 000161 823 IGKPLELDTDGIWCVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVDVARNNTNDQYQTLVDPVSKTYETHSECSIEFEV 902 (1988)
Q Consensus 823 ~G~~vygDTDSI~~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~V~~~~tN~~y~~l~~~~~~~y~~~s~~~I~fE~ 902 (1988)
+|+|+++|||||||++|++|||||+||+++| |+++|||||+|||++|+++|||||||+|+||.+..|.++|+|||+|||
T Consensus 829 iGrPLELDTDGIWCilP~SFPEnf~Fk~~n~-kkvtiSYPc~mLN~~V~e~fTN~QYq~L~dp~~~~Y~t~SEnSIfFEV 907 (2173)
T KOG1798|consen 829 IGRPLELDTDGIWCILPGSFPENFTFKLKNG-KKVTISYPCVMLNHLVHEGFTNHQYQELVDPVRLTYVTRSENSIFFEV 907 (2173)
T ss_pred hCCCeeccCCceEEeccCCCccceEEEecCC-cEEEEechHHHHHHHHHhccchhhHHHhcCcccceeeecccceEEEEe
Confidence 9999999999999999999999999999999 889999999999999999999999999999999999999999999999
Q ss_pred eceeeeeecccccccCcccccceEEEcCCCCEEEEEeeeeccCChhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 000161 903 DGPYKAMILPASKEEGILIKKRYAVFNDDGTLAELKGFEIKRRGELKLIKVFQAELFDKFLHGSTIEECYSAVAAVANRW 982 (1988)
Q Consensus 903 Dg~Y~~miLp~s~~~~~~~KKRYa~~~~dG~~~e~KG~E~kRRd~~~liK~~q~~v~~~~L~g~~lee~~~~v~~v~~~~ 982 (1988)
||||+|||||+|+||||++|||||+||+||+++|+||||+||||+++|||.||+++|+.||+|.||||||.+|+.|+++|
T Consensus 908 DGPYkAMILPaSkEEGk~lKKRYAVFN~DGsLAELKGFEiKRRGEL~lIK~FQs~lF~~FL~GstLEEcY~aVA~Vad~W 987 (2173)
T KOG1798|consen 908 DGPYKAMILPASKEEGKLLKKRYAVFNEDGSLAELKGFEIKRRGELKLIKVFQSELFKVFLKGSTLEECYSAVAAVADRW 987 (2173)
T ss_pred cCceeEEeeccchhhhhhhhheeEEecCCCchhhhcCceeeecchhhHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCCchhhhhhhhhccccccChhhhCCCCChHHHHHHHHHhhcCCCcccCCCCeeEEEEEcCCCCCCCcccc
Q 000161 983 LDLLDNQGKDIADSELIDYISESSTMSKSLADYGEQKSCAVTTARRLSDFLGDTMVKDKGLRCQYIVACEPQGTPVSERA 1062 (1988)
Q Consensus 983 ~d~L~~~~~~~~~~eLi~~i~~~k~lsK~l~eY~~~k~~~v~~A~rl~e~lG~~~~~~~G~~i~YVI~~~p~g~~v~eRa 1062 (1988)
+|+|+++|.+++|+||++||+++++|||++++|++|||++|+||+||++|||++|++++|++|+|||++.|.|+||+|||
T Consensus 988 LDiL~s~G~~l~D~eL~elISEnrSMSk~L~dYg~QKStsitTAkRLaeFLGd~MvKDkGL~C~yIIs~~P~g~PVtERA 1067 (2173)
T KOG1798|consen 988 LDILDSHGADLTDSELLELISENRSMSKKLEDYGGQKSTSITTAKRLAEFLGDDMVKDKGLACRYIISRKPEGAPVTERA 1067 (2173)
T ss_pred HHHHHhccCCCCcHHHHHHHhhchhhhhhHHHhccccchHHHHHHHHHHHhchhhhhccCceeEEEEEecCCCCCccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhhcchHHHHHHHHHhhhcCCC--CCCCccccCHHHHHHhhhhhhhheeechhhhhhccCCCCCcchhhhhhhhhhc
Q 000161 1063 VPVAIFETDAEIMKFYLRKWCKTSS--DVGIRSIVDWSYYKQRLSSAIQKIITIPAAMQKVSNPVPRVVHPDWLYKKVRE 1140 (1988)
Q Consensus 1063 ~p~~if~~~~~~~~~~l~~w~~~~~--~~d~~~~iD~~YYierl~~~i~ki~~iPa~lq~~~npv~rv~~p~w~~~~~~~ 1140 (1988)
||++||++|+.||+||||||+|+++ |+|||.+|||+||++||+++||||||||||||+|.||||||+|||||++++++
T Consensus 1068 IPVAIF~ae~~vk~~fLRkW~k~~sl~d~dIR~IiDWdYY~eRLgSaIQKiItIPAAlQ~VsNPVpRv~hPdWL~kkv~~ 1147 (2173)
T KOG1798|consen 1068 IPVAIFQAEPPVKKHFLRKWTKDSSLEDTDIRAIIDWDYYRERLGSAIQKIITIPAALQGVSNPVPRVPHPDWLQKKVAE 1147 (2173)
T ss_pred ceeEEEecCcHHHHHHHHHHhccCccccCChheeeehHHHHHHHHHHHHHHhhhHHHHhccCCCCCCCCCcHHHHhhhcc
Confidence 9999999999999999999999999 69999999999999999999999999999999999999999999999999999
Q ss_pred cccccccccHHHhhhccccCcccccccccccccCCCCCCCCCCCcccCCCCCCCCCCccccccccccccccccccccchh
Q 000161 1141 KEDKFRQRKLVDIFSSLKKDDFLNKTCNAETNLMDENVEDLEDFPKKRRNSVNGPRPIVRCFEVNNEQKTVKTTDQVDSL 1220 (1988)
Q Consensus 1141 ~~~~~kq~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~d~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1220 (1988)
++|+|+|++|.++|+..++.|.+ +. .+. .||||++.......+.+.++++++.++..++.
T Consensus 1148 k~dk~rQ~ki~~~Fs~~~~~~~t---~~-----n~~--~DiED~~~~~~~~~~~~~~Var~~~~~~~~~e---------- 1207 (2173)
T KOG1798|consen 1148 KNDKFRQKKIVDIFSLANKPPTT---MD-----NKV--PDIEDFGSETRPDVKGPIPVARKTKKKENQKE---------- 1207 (2173)
T ss_pred chhhhhhhhHHHHHhhcCCCCcc---cc-----cCC--CChHHhhcccCcccCCCcccchhhhhcchhhh----------
Confidence 99999999999999987665542 11 123 39999977665423444355554444433210
Q ss_pred hcccCCCccccCCcCcccccCCCCCCcccchHHHHHHHHHHHHHHHHHHHHhhccccccccccCCccccccccccccccc
Q 000161 1221 RQQLEPSEVSDQQPSSQNAIDTENIDRIVDYKGWLELKKRKWKDNLDRRKKQKLGSLRASHQANGVSESLGDMINHKEAQ 1300 (1988)
Q Consensus 1221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~k~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~ 1300 (1988)
++++.. ..+....++.+++...++|.+||.++|+||+.|++.|+||+...+.. ..
T Consensus 1208 ~q~~s~------~~e~~~i~~q~~~~~~~~y~~WL~~~KkKWk~q~~~k~rr~~~~~~~-------------------~~ 1262 (2173)
T KOG1798|consen 1208 KQQNSG------DVEFPEILLQEPDKVTDGYQGWLRFLKKKWKVQARDKKRRRQLKGNT-------------------SR 1262 (2173)
T ss_pred HHhccC------CCCcchhhccCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHhhccc-------------------cc
Confidence 011111 11123345555566799999999999999999999998888654332 13
Q ss_pred cccchhhHHHHHHHhhccCceeEEEEeeCCCCceEEEEEEEcCeEEEEEEEeceEEEEeccCCCCCCCCccccccccCCC
Q 000161 1301 RRTGVGSYFRRQETAMTRCHWQIIQLVPSSQSGVFLAWVVVEGIMVRIPITVPRLFYLNSKDPIVEKFPGRRVNKTLPHG 1380 (1988)
Q Consensus 1301 ~~~~~~~~~~~~~~~~~~~~w~i~q~~~~~~~g~~~~~~~~~~~~~~~~~~vpr~~y~n~~~~~~~~~~~~~~~~~lP~~ 1380 (1988)
.+..+++.++.+++++++++||||||.+|.+||.|.+||+|+|.||.|+++|||+||||+|.+..|....++++++||||
T Consensus 1263 d~~~~~~~v~g~~ea~~~~~w~Ilqv~~s~~~g~f~~wv~v~g~m~~I~~~Ipr~fyv~~k~~~~~~~~~ek~n~iLPh~ 1342 (2173)
T KOG1798|consen 1263 DSHVVEKVVRGAAEALTNSDWHILQVVESGQAGQFFAWVLVRGLMHKIRLSIPRVFYVNSKAETGENFKIEKSNAILPHG 1342 (2173)
T ss_pred cHHHHHHHHHhHHHhhhcCCceEEEEEEcCCCceEEEEEEeccceEEEEEEcCcEEEEeccccccccccchhhhccCCCC
Confidence 44568899999999999999999999999999999999999999999999999999999999988777789999999999
Q ss_pred -CCCCCeEEEEcChHHHHHHHHHHHhhhCCCCcc----------------------------------------------
Q 000161 1381 -RRSFNLIEVMIDEDQFRKESKKLAALLADPEVE---------------------------------------------- 1413 (1988)
Q Consensus 1381 -~~~~~L~~~~~~e~~~~~~~~~~~~~l~~~~v~---------------------------------------------- 1413 (1988)
..+..||++++||++|+++..+++++|+||+|+
T Consensus 1343 ~~t~~~l~~~~i~E~~f~~e~~~~~~~l~~p~I~GiyEtkvp~~fraIl~lG~~~~~~~~~~lg~~~q~g~~l~~l~~~~ 1422 (2173)
T KOG1798|consen 1343 PKTVNMLYEIRIPEDQFLEEKKKIAAELADPSIEGIYETKVPLEFRAILQLGCVCRFNNKAKLGGGTQDGFELENLHMMS 1422 (2173)
T ss_pred CCcccceEEEEcCHHHHHHHHHHHHHHhcCcccceeecccCChHHHHHHhhcceeeeccccccCCccccceehhhccccc
Confidence 668889999999999999999999999999998
Q ss_pred --------------------------------------------------------------------------------
Q 000161 1414 -------------------------------------------------------------------------------- 1413 (1988)
Q Consensus 1414 -------------------------------------------------------------------------------- 1413 (1988)
T Consensus 1423 ~~e~~yLe~~si~~vylyhf~~~~r~vy~lf~~~~~~~s~~v~~~~~d~~~~~l~~~y~~~~~~~~ee~s~~~~~~~~~~ 1502 (2173)
T KOG1798|consen 1423 TAECSYLEGHSIRLVYLYHFSQSGRAVYSLFIPSSKLASAFVLDPSGDNQMPSLGSLYERLFRDLLEELSPLCLSPDGIK 1502 (2173)
T ss_pred ccccccccCcccceEEEEeeccccceeeEEeccccceeEEEEEecCCccccccHHHHHHHHHHHHHHhcCccccCCCCce
Confidence
Q ss_pred -------------------------------------------------------------------cccccHHHHHHHH
Q 000161 1414 -------------------------------------------------------------------VLGWQQNAAKIGM 1426 (1988)
Q Consensus 1414 -------------------------------------------------------------------~L~WQ~~~akr~i 1426 (1988)
+|+||+++||+|+
T Consensus 1503 f~V~~~~~~~ka~r~l~~~l~~Yree~~~~~l~vlesp~~~~l~~~i~~l~efP~V~i~~~e~~~~~~l~Wq~~~ak~~i 1582 (2173)
T KOG1798|consen 1503 FEVIYSGDPSKAERQLQRALREYREERCGPTLLVLESPDPTRLKEGIPALEEFPCVRIPRNEDDNSYPLSWQRHAAKRMI 1582 (2173)
T ss_pred EEEEEcCCHHHHHHHHHHHHHHHHHhccCceEEEEeCCchHHHHhcCCChhhCCceeeeccccccccccccchHHHHHHH
Confidence 7999999999999
Q ss_pred HHHHhhhHHHHHHHHHhhccce----------------------------eccCCCCCCCCCCcccccccccccc----C
Q 000161 1427 QRCAASSQWFNERISLARYAHI----------------------------LWISDDGVPDLGGTSEEDECFADEV----H 1474 (1988)
Q Consensus 1427 ~hyl~~~~wl~~~i~laRY~~I----------------------------LW~S~~~~PDlGG~E~D~~~~~~~~----~ 1474 (1988)
+||+++++||.+++++|||+|| ||||++++|||||+|+|+..+.+++ +
T Consensus 1583 ~h~~a~~~wl~~~i~~SRY~~VPigNl~~D~~~f~iD~~faR~Lrk~~~vLW~s~~~~PDlGGie~d~~~~s~~~~~~s~ 1662 (2173)
T KOG1798|consen 1583 QHYLASGSWLSHRIKLSRYSHVPIGNLPEDWLTFIIDLFFARKLRKHNHVLWWSKNGVPDLGGIENDEMLLSSELQTTSD 1662 (2173)
T ss_pred HHHHhHHHHHHHHHHHHHhcCCcccCCchHHHHHHHHHHHHHHHHhcCeeEEecCCCCCCCCcccchhhhhhHHhccccc
Confidence 9999999999999999999999 9999999999999999976665443 4
Q ss_pred CceeccCCcceeEEEEEEecchhHHHHHhhhhcccccCCcccc--ccCCCCCC-CCCCCcccccccCCChhHHHHHHHHH
Q 000161 1475 QPVLTYPGAYRKVSVELKIHHLSVNALLKSNQVNEMEGGGLFG--FDQDMNSG-PYNNELCGFDETTSSAPAFRVVKQLI 1551 (1988)
Q Consensus 1475 ~~~in~pG~Y~svcvEl~i~~LaVnaiL~Ss~ine~EG~~~~~--f~~~~~~~-~~~~~~~~~~e~~~~~~af~iLr~mV 1551 (1988)
.+++|+||+|++|||||+++||||||||+|++|||+||++.++ ||.++.+. .+..++..|||.+.|+++|+|||+||
T Consensus 1663 ~~~ln~~G~Y~~v~vel~l~nlavntll~S~lvne~EG~d~~g~~~dv~~~~~~~d~~~~~~~De~a~~~~~f~VLk~ll 1742 (2173)
T KOG1798|consen 1663 TVELNRPGAYSTVCVELKLSNLAVNTLLQSALVNEMEGADFLGVTFDVNDRTAAEDDLTGACYDETALCAQAFRVLKQLL 1742 (2173)
T ss_pred chhhccccccceeEEEEEehHHHHHHHHHHhhhhhhhccccccccccccccchhhccccccccccccchHHHHHHHHHHH
Confidence 5789999999999999999999999999999999999999655 56665432 22334577999999999999999999
Q ss_pred HHHHHHHHhcCCccHHHHHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHhHcCCeEEEEeCCeEEEEcCCCC
Q 000161 1552 QRCLTDAVTSGNVFADAILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFAMLLAEFRKLGATIIFANFSKVIIDTGKFD 1631 (1988)
Q Consensus 1552 ~~w~~da~~~~n~~AD~ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~flqLlaEfkRLGs~VVyAd~~riil~T~K~~ 1631 (1988)
++||+|++++||.+||.+|+||+|||+||+|+|||||||++||+||||+|+||++|||||||.|||||||+|||+|+|.+
T Consensus 1743 k~~~~d~~~~gN~~AD~iv~~l~~Wl~spss~L~dpaL~~~vh~lmkK~fl~L~~e~~rlGa~iIyA~~nkili~T~K~~ 1822 (2173)
T KOG1798|consen 1743 KRWVLDAAKSGNIYADLIVQHLSRWLRSPSSKLHDPALHRHVHVLMKKLFLQLLAELRRLGAIIIYADFNKILINTGKFS 1822 (2173)
T ss_pred HHHHHHHHhhcchhHHHHHHHHHHHHcCCcccccCHHHHHHHHHHHHHHHHHHHHHHHhcCCeEEEecCCEEEEecCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHhHHHHHHHHHHHhhccccccceecchhchheeeeeecCCCccccccccCCCCCCCcccceeeecchhhcCcHHHHHHH
Q 000161 1632 LSAAKAYCDSLLKALQTRELFEWIELEPVHFWHSLLFMDQYNYGGIPARADESLDDDSQVDIVSSWNIAEYLPKEIQDHF 1711 (1988)
Q Consensus 1632 v~~A~ay~~yi~~si~~~~lF~~l~L~~~~yW~~LlwmD~~NygGi~~~~~~~~~~~~~~~i~~~W~I~~fLP~~~q~~F 1711 (1988)
+++|++|++||+++++++++|++|+|++++|||+|+|||++||||..|..+. +.++++.+++.+|+++++||+.+|.+|
T Consensus 1823 ~e~A~~y~e~l~ksi~t~~~f~~l~i~~~r~wd~llwmD~~n~~g~~gi~~~-e~~~~~~~~~~~w~~~~~l~~~~e~e~ 1901 (2173)
T KOG1798|consen 1823 VEAAKAYSEYLLKSISTLPVFHLLDINPVRYWDSLLWMDAHNYGGHAGIRIS-EKTNSEPTIVVKWDVEEHLPPEIEPEA 1901 (2173)
T ss_pred HHHHHHHHHHHHHhhhcccchhheeccHHHHHHHHhhhccccccccceeeeh-hhccCCCccccchhhhhcCCccccccc
Confidence 9999999999999999999999999999999999999999999998887666 666777889999999999999999999
Q ss_pred HHHHHHHHHhHHHHHHHHHhhhhcccCCCCCCCccchhhhh-hhhhhHHHHHHHHhHHHHHHHHHHHHHHHHHhh---hc
Q 000161 1712 VLVVSEFMYIPWKHAQKLAASRASLQEGSSCTPSITVAAAE-NFESHIVQYVKGEISSYFTGKLLSIVRDAIHHM---KK 1787 (1988)
Q Consensus 1712 ~~~v~~~l~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~i~~~fs~~L~~~v~~l~~~~---~~ 1787 (1988)
+.|+..+++++++.+++......+ ..+......++ ...+.........+.+.+++++++.+.+++..+ ..
T Consensus 1902 e~w~~~~~~~~~~~~q~~f~~~v~------~~~~~f~~~nk~~~~es~~~~~~d~~~~~l~~~~~~l~~~~~~~~~~~~~ 1975 (2173)
T KOG1798|consen 1902 EIWKILEEDPTEASKQEYFLIIVG------AYIVKFKEENKDGSFESAEGGMSDYLSEPLGERVYGLIVKIQEFILDNNT 1975 (2173)
T ss_pred ccchhhhhhhhHHhHHHHHHhhhh------heeEEEeeccCcchhhhcccchhHhhhhHHHHHHHHHHHHhhhhhcCccc
Confidence 999999999999999975332111 01111100110 111111111334455556666666666665533 44
Q ss_pred cCCCCCC-CCCCccccccccCCCchhHHHHHHHHHHcCCcccHHHHHHHHHHHHhhcCcccCCCCCcccCCCCceeeCcc
Q 000161 1788 MNNDQHN-SPGVMQTAANIHKVDAPLEFIKHVCAAFALDQNVQHDVLVMRKNLLKYVRVREFAPEAEFRDPCPSFILPNV 1866 (1988)
Q Consensus 1788 ~~~~~FP-lpGs~l~~~~~~~~npaLEfVK~lc~VLsLd~~~~~eV~~LRr~LL~l~~V~EFS~eA~f~~P~~sl~L~~V 1866 (1988)
..+..|| |||||| ..+||+|||||.||+||+||++++.+|+.|||+||++++|+||++||+|+|||.||+||+|
T Consensus 1976 e~~~~~p~lpgs~l-----~~~n~~le~ik~ic~vlsLdq~~q~~v~~lrk~llrll~v~Ef~~ea~f~dp~~sl~lp~v 2050 (2173)
T KOG1798|consen 1976 EIDVSFPVLPGSHL-----NLGNPALEFIKIICAVLSLDQNVQLEVRVLRKNLLRLLHVKEFAEEAEFRDPSRSLVLPNV 2050 (2173)
T ss_pred chhhcccccccccc-----ccCCchHHHHHHHHHHHhccchHHHHHHHHHHHHHHHhhHHHHHhhhccCCCCcceeeCCc
Confidence 5678999 999999 8999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCcccccccCcccCC-CccccCCCCCCCCCChHHHHHHHHHHHHHHHHHHhhcccccCcchHHhhhcccccCCc
Q 000161 1867 ICSYCNDCRDLDLCRDMALLA-QDWHCAMPQCGQPYDREVMENALLQIVRQRERLYHLQDLVCIRCNQVKAAHLAEQCAC 1945 (1988)
Q Consensus 1867 iC~~Cn~~rDLDlCrD~~~~~-~~W~C~~~~C~~~yd~~~IE~~LI~~v~~~~~~YqlQDL~C~KC~~vk~~~ls~~C~C 1945 (1988)
.|++|+++||+|||||+++.. +.|.|.. |+++||+.+||+.||++|++++++||+|||+|+||++||.++|+++|+|
T Consensus 2051 ~C~sC~~~~d~d~crd~~~~~e~~~sC~~--C~k~yd~~~ie~~l~~~l~~~l~~y~lQDl~C~rC~~Vk~~~ls~~C~C 2128 (2173)
T KOG1798|consen 2051 ACSSCGFYRDLDLCRDSALSTEKIFSCAD--CQKPYDKDAIEETLVDMLRQLLTLYQLQDLVCSRCKQVKETSLSEYCEC 2128 (2173)
T ss_pred ccccchhhhhhhhhcccccCccceeehhh--hCCcCCHHHHHHHHHHHHHHHHHHHHhhhhhhhhhCccchhhhhhcccc
Confidence 999999999999999999864 6799999 9999999999999999999999999999999999999999999999999
Q ss_pred CCCceeccChhHHHHHHHHHHHHHHHhCChhHHHHHHHHHhc
Q 000161 1946 AGSFRCKEDASDFRSKMQIFLNIANRQGFQLLQECTSWILEV 1987 (1988)
Q Consensus 1946 sG~~~~t~~~~~~~~~l~v~~~vA~~~~~~~L~e~v~~~l~~ 1987 (1988)
||.|.+++++++|.+++.||.+||++|+|.+|+|+++|+|.+
T Consensus 2129 ~G~f~~~~~~~~f~~~~~if~~va~~~~f~~L~e~i~wil~~ 2170 (2173)
T KOG1798|consen 2129 SGAFRLQISPEEFRKRASIFDDVAKRYGFSLLQECISWILKN 2170 (2173)
T ss_pred ccccccccCHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhc
Confidence 999999999999999999999999999999999999999864
No 2
>cd05535 POLBc_epsilon DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is characteristic of this family with the exception that it contains a large c-terminal domain with an unclear function. Phylogenetic analyses indicate that Pol epsilon is the ortholog to the archaeal Pol B3 rather than to Pol alpha, delta, or zeta. This might be because pol epsilon is ancestral to both archaea and eukaryotes DNA polymerases type B.
Probab=100.00 E-value=1.9e-170 Score=1553.73 Aligned_cols=618 Identities=67% Similarity=1.116 Sum_probs=609.8
Q ss_pred ccccCCCCCCcceeeeccCccccCCCCCCccCChhHHHHHhhhhhhhhHHHHhHhcccccccccchHHHHHHHHHHHHhh
Q 000161 501 NHLLESETYIGGHVECLESGVFRSDLPTSFKLDPSAYEQLLNNLDRDLQYAIKVEGKMDLESVSNYDEVKNAIMEKLLRL 580 (1988)
Q Consensus 501 g~l~~setY~GG~V~~p~~GvY~~d~~~~f~~~~~~~~~l~~~~~~~l~~~~~~e~~~~~~~~~n~~~v~~~i~~~l~~l 580 (1988)
||+++++||+||||+++++||||+|||++|+|+|++||+||+|||++|+||+++|+++++++|+||+||+++|+++|+.|
T Consensus 1 ghll~setyvgg~ve~l~~GvfRsDi~~~F~~~~~~~~~l~~~ld~~l~~~~~~e~~~~~~~~~n~~ev~~~i~~~L~~l 80 (621)
T cd05535 1 GHLLESETYVGGHVEALESGVFRSDIPCRFKLDPDAIQELLQNVDETLRFAIEVEGKIPLDQVENFEEVREEILEKLQSL 80 (621)
T ss_pred CCcccccccccceeeeeeccccccccchhcCcCHHHHHHHHHHHHHHHHHHHHHhcCCChhhccCHHHHHHHHHHHHHHh
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCcccCCeEEEEeccccchHHHHhcCCCCCccccccccccccCCCCCCccccccccccccccccCCcchhhHhhhhc
Q 000161 581 QEEPIREECPLIYHLDVAAMYPNIILTNRLQPPSIVTDEVCTACDFNRPGKTCLRKLEWVWRGEIFMGKRSDYYHLKKQI 660 (1988)
Q Consensus 581 ~~~p~~~~~p~V~~LDf~SLYPsII~t~NL~p~Tiv~~~~c~~c~~n~p~~~c~r~m~w~~~ge~~p~~~~ey~~i~~~l 660 (1988)
+++|+|.++|+||||||+|||||||+||||||++||++.+|+.||||+|++.|+|+|+|+||||++|++++||++|++||
T Consensus 81 ~~~p~~~~~p~IYHlDV~aMYpnIiltnRLQP~a~v~e~~C~~C~fn~~~~~C~r~m~W~wrge~~p~~~~e~~~i~~~l 160 (621)
T cd05535 81 RDNPKRSEKPLIYHLDVAAMYPNIILTNRLQPDAIVDEDVCAACDFNKPGKTCQRRMEWAWRGEYFPASRGEYERIKQQL 160 (621)
T ss_pred hcCCccccCCceeEeehhhccchhhhhccCCCcccCCHHhCCcCCCCCCcccccccceeeeeecccCCCHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccCCCCCc-ccccccCchHHHHHHHHHHHHHhhhhhcccccccccccccccccccccccchHHHHHHHHHHHHHHH
Q 000161 661 ESEFVDGTNGHL-SKSFLDLPKMEQQSRLKDRLKKYCQKAYKRVLDKPVTELREAGICMRENSFYVDTVRSFRDRRYEYK 739 (1988)
Q Consensus 661 ~~e~f~~~~~g~-~~~~~~L~~~~q~~~lkkrl~~y~~kvy~k~~~~~~~~~r~~~icqre~~f~~~~lr~f~drR~~~K 739 (1988)
+++.||+..++. ++.|++|+++||.+.+|+|+++||+|+|+|++.+++++ |+++|||||||||++|||.||||||+||
T Consensus 161 ~~e~f~~~~~~~~~~~~~~l~~~eq~~~l~~rl~~ys~k~y~k~~~~~~~~-~~~~vCqrEn~Fyvdtvr~FrdrRy~yK 239 (621)
T cd05535 161 ESEKFPPLFPGGPPKSFHELSPEEQAEELKKRLKDYSRKVYKKTHVTKEEE-RSTTICQRENPFYVDTVRAFRDRRYEYK 239 (621)
T ss_pred HhcccCCcCCCCCCcchhhCCHHHHHHHHHHHHHHHHHHHhcccccceeEE-EeeeeEeccCCcHHhhHHHHHHHHHHHH
Confidence 999999988888 89999999999999999999999999999999999988 9999999999999999999999999999
Q ss_pred hhhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 000161 740 GLNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNARLL 819 (1988)
Q Consensus 740 ~l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~sR~ys~e~A~~VT~~Gr~iI~~a~~l 819 (1988)
++.|+||+++++|++.+++.+++++++|+++||++|+|||||+||||||+|+++|||||+|||++||++||+||++|+++
T Consensus 240 ~~~k~~k~~~~~~~~~~~~~~~~~a~~~~~lyDs~Q~A~KiIlNSfYGYlG~~gsRwYs~emA~~VT~~GreIIk~tr~l 319 (621)
T cd05535 240 GLHKVWKKKLEAAKAAGDAAEIKEAKKMVVLYDSLQLAHKCILNSFYGYVMRKGSRWYSMEMAGIVCYTGANIIQMAREL 319 (621)
T ss_pred HHHHHHHHHHhhhhccCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCccCcCCcccCCHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHcCCeEEEccceeeEEcCCCCCcccccccccccccccccccccccchhhhccccchhhhhccCCccccccccccceeE
Q 000161 820 IEKIGKPLELDTDGIWCVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVDVARNNTNDQYQTLVDPVSKTYETHSECSIE 899 (1988)
Q Consensus 820 ve~~G~~vygDTDSI~~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~V~~~~tN~~y~~l~~~~~~~y~~~s~~~I~ 899 (1988)
+|++|++||||||||||++|++||++++++.++| +++.+||||+|||.+|+++|||+|||++++|.+..|.+.++++|+
T Consensus 320 vE~~G~~VegDTDsI~~~lp~~~~e~~~~~~k~g-~~~~~~~~~~~LN~~V~~~~tn~qy~~l~~p~~~~y~i~se~~Ie 398 (621)
T cd05535 320 VEQIGRPLELDTDGIWCILPKSFPENFTFKTKNG-KKVTISYPCVMLNHLVHKKFTNDQYQELVDPSTGTYETRSENSIF 398 (621)
T ss_pred HHhcCCEEEEecCeeEEEcCCCChHHHHHHhhcc-chhhhhhhHHHHHHHHHHHHHHHHhhhccCcccccccccccceeE
Confidence 9999999999999999999999999999888888 899999999999999999999999999999999999999999999
Q ss_pred EeeeceeeeeecccccccCcccccceEEEcCCCCEEEEEeeeeccCChhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Q 000161 900 FEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLAELKGFEIKRRGELKLIKVFQAELFDKFLHGSTIEECYSAVAAVA 979 (1988)
Q Consensus 900 fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~~~dG~~~e~KG~E~kRRd~~~liK~~q~~v~~~~L~g~~lee~~~~v~~v~ 979 (1988)
||+||+|++||||+|+|+++++|||||++++||+++|+||||+||||||+|+|+||++||+.||.|+++++||++|++++
T Consensus 399 fEvDG~Yk~mllpask~~~~~~KKRYAv~~~dG~i~elKGfEikRRd~~~LaK~fQ~eV~e~iL~g~~~Eea~~~V~~v~ 478 (621)
T cd05535 399 FEVDGPYKAMILPASKEEGKLLKKRYAVFNEDGSLAELKGFEVKRRGELQLIKIFQSEVFDAFLKGSTLEECYAAVAAVA 478 (621)
T ss_pred EEeccceeeeEcccccccccccccceEEEcCCCCEEEEeCceeeeCCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCCchhhhhhhhhccccccChhhhCCCCChHHHHHHHHHhhcCCCcccCCCCeeEEEEEcCCCCCCCc
Q 000161 980 NRWLDLLDNQGKDIADSELIDYISESSTMSKSLADYGEQKSCAVTTARRLSDFLGDTMVKDKGLRCQYIVACEPQGTPVS 1059 (1988)
Q Consensus 980 ~~~~d~L~~~~~~~~~~eLi~~i~~~k~lsK~l~eY~~~k~~~v~~A~rl~e~lG~~~~~~~G~~i~YVI~~~p~g~~v~ 1059 (1988)
++|+|+|+.+++++++++|+++|+++++|+|++++|++++++||++|+||++++|+++.+++|+.|+|||+++|.|+|++
T Consensus 479 ~~~ld~L~~~~~~~~d~eLi~li~~~k~LsK~l~eY~~~ks~~V~~AkRl~e~lg~~~~~~~G~~i~YII~~~p~~~~vs 558 (621)
T cd05535 479 NYWLDVLDSKGENLDDEELFELISENRSMSKKLEEYGNQKSTSITTAKRLAEFLGDQMVKDKGLSCKYIISKKPEGSPVT 558 (621)
T ss_pred HHHHHHHHhccCCCChHHHHHHHHhhcccCCCHHHcCCCCCcHHHHHHHHHHhhcCCcccCCCCeEEEEEEeCCCCCCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccchhhhcchHHHHHHHHHhhhcCCC--CCCCccccCHHHHHHhhhhhhhheeechhhhhh
Q 000161 1060 ERAVPVAIFETDAEIMKFYLRKWCKTSS--DVGIRSIVDWSYYKQRLSSAIQKIITIPAAMQK 1120 (1988)
Q Consensus 1060 eRa~p~~if~~~~~~~~~~l~~w~~~~~--~~d~~~~iD~~YYierl~~~i~ki~~iPa~lq~ 1120 (1988)
+||+|+.+|+++++|++||||||+|+++ ++|+|.+|||+||++||+++|||||+||||||+
T Consensus 559 eRAiPv~if~~~~~~~~~~lrkW~~~~~~~~~d~r~iiDW~YY~~rl~~~iqKii~iPa~lQ~ 621 (621)
T cd05535 559 ERAIPVAIFQAEPEVRKHYLRKWLKDPSDEDLDIRDIIDWDYYIERLGSTIQKIITIPAALQG 621 (621)
T ss_pred ccccChhhhcCCHHHHHHHHHHHhCCCCcCCCChhhhhchHHHHHHHHHHHHheeeechhhcc
Confidence 9999999999999999999999999976 889999999999999999999999999999995
No 3
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=100.00 E-value=8.8e-121 Score=1219.07 Aligned_cols=809 Identities=22% Similarity=0.270 Sum_probs=632.2
Q ss_pred CCeEEEEEEEEecCCCeEEEEe-CCccEEEEEecCCCh-HH---HHHHHHHh---------ccccceeEEEEEEeeCCCc
Q 000161 61 KVYSCIDLYFVSQDGSTFKSKY-KFRPYFYAATKEKME-MD---VEAYLRRR---------YESQIADIEILEKEDLDLK 126 (1988)
Q Consensus 61 ~~~~~v~ly~~t~dG~~~~v~v-~f~PYFyv~~~~~~~-~~---v~~~l~~~---------~~~~i~~ie~v~k~dl~~~ 126 (1988)
.+.++|++||+|++|.++++.| +|+|||||.++++.. .+ +..+|... ....|.+|++|+|++|+..
T Consensus 72 ~~~pvIRlFGvTe~G~SV~v~V~gF~PYFYV~~p~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~~V~~VeiV~k~sl~gY 151 (1054)
T PTZ00166 72 VEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAPPNFLPEDSQKLKRELNAQLSEQSQFKKYQNTVLDIEIVKKESLMYY 151 (1054)
T ss_pred CCceEEEEEEecCCCCEEEEEEeCCceEEEEecCCCCCHHHHHHHHHHHHHHHhhcccccccCCceEEEEEEEeeeecee
Confidence 3679999999999999999999 899999999998763 22 23333322 2346899999999999966
Q ss_pred CcCCCCCeEEEEEEEechhhHHHHHHHHHHHHHhhcccchhHHHHHHhhhcccCCCCcccccccccccccCCCccceeee
Q 000161 127 NHLSGLHKSYLKISFDTVQQLMDVKKDLLHVVERNQAKFDAAEAYESILTGKREQRPQDFLDCIVDLREYDVPYHIRFAI 206 (1988)
Q Consensus 127 nhl~g~~~~~lKl~f~~~~~l~~vr~~l~~~~~~n~~~~~~~~~y~~~~~~~~~~~~~~~~~~i~~i~E~DI~~~~R~~i 206 (1988)
++ +.+.+|+||+|.+|..+.++|+.|++++..|.... +. .....+||+||||++||+|
T Consensus 152 ~~--~~~~~flKIt~~~P~~v~klR~~Le~g~~~~~~~~-------------------~~-~~~~~vyEsnI~f~lRFmI 209 (1054)
T PTZ00166 152 KG--NGEKDFLKITVQLPKMVPRLRSLIESGVVVCGGGW-------------------DG-IRLFQTYESNVPFVLRFLI 209 (1054)
T ss_pred CC--CCceeEEEEEEcCHHHHHHHHHHHHcCCccccccc-------------------cc-ccccceeecCCCHHHHHHh
Confidence 54 45789999999999999999999985432211100 00 1235689999999999999
Q ss_pred ecCCccceeEEEeeCCC------------CceEEE----------eccccCCCCceEEEEEEEEccCCC-CCCCCCCCeE
Q 000161 207 DNDVRCGQWYDVSISST------------GPLLEK----------RVDLLQRAEVHVCAFDIETTKLPL-KFPDADYDII 263 (1988)
Q Consensus 207 D~~I~~g~W~~v~~~~~------------~~~i~~----------~~~~~~~p~lrvLsfDIEt~s~~~-~fPdp~~D~I 263 (1988)
|+||.||+||+++.... +.++.+ ..++..+||+++|||||||.+.++ .||+|+.|+|
T Consensus 210 D~~I~g~~Wi~i~~~~~~~~~~~~~~s~c~~E~~~~~~~l~~~~~~~~~~~~pplrilSfDIE~~~~~g~~FP~~~~D~I 289 (1054)
T PTZ00166 210 DNNITGGSWLTLPKGKYKIRPPKKKTSTCQIEVDCSYEDLIPLPPEGEYLTIAPLRILSFDIECIKLKGLGFPEAENDPV 289 (1054)
T ss_pred ccCCCceeEEEecCcceeecccccCCCcceEEEEEehhheeecccccccCCCCCcEEEEEEEEECCCCCCCCCCCCCCcE
Confidence 99999999999874321 123332 113446799999999999999877 5999999999
Q ss_pred EEEEEEEcCCceEEEcccccccccccccCCCCC--CCCCceEEecCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHH
Q 000161 264 MMISYMLDGQGYLIINRECVGEDIEDLEYTPKP--EFEGYFKVTNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPF 341 (1988)
Q Consensus 264 i~IS~~~~~~g~li~nreivs~di~~feytp~~--~~~g~f~V~~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPy 341 (1988)
||||+++..+|... .....+.||+++ ...| ..|..+++|++||.+|+++|+++|||||+|||+++|||||
T Consensus 290 IqIs~~~~~~g~~~-------~~~~r~vftl~~c~~i~g-~~V~~f~sE~eLL~~f~~~I~~~DPDII~GYNi~~FDlpY 361 (1054)
T PTZ00166 290 IQISSVVTNQGDEE-------EPLTKFIFTLKECASIAG-ANVLSFETEKELLLAWAEFVIAVDPDFLTGYNIINFDLPY 361 (1054)
T ss_pred EEEEEEEeeCCCcc-------CCcceEEEecCccccCCC-ceEEEeCCHHHHHHHHHHHHHhcCCCEEEecCCcCCcHHH
Confidence 99999876554311 011122233332 2233 4688899999999999999999999999999999999999
Q ss_pred HHHHHHHcCCCCCcccCcccc------------CCCC-----ceeeccceEechHHHHhhccCCCCCCCCHHHHHHHHcC
Q 000161 342 LETRAAHHGFKMSEELGFQCD------------KNQG-----ECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLG 404 (1988)
Q Consensus 342 L~~Ra~~lGi~l~~~iG~~~~------------~~~g-----~~~i~GRihiDl~~~vkrd~~L~~~SysL~~Va~~~LG 404 (1988)
|.+||+.+|++.+..+|+... ...| .+.+.||+++|+|++++++.+| .||+|++||.++||
T Consensus 362 L~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~~iDl~~~~~~~~kl--~sYsL~~Vs~~~Lg 439 (1054)
T PTZ00166 362 LLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKL--KSYSLNYVSFEFLK 439 (1054)
T ss_pred HHHHHHHhCCCchhhcCcccCCCccccccccccccccccccceeEeeeEEEEEHHHHHHHhcCc--CcCCHHHHHHHHhC
Confidence 999999999987665665310 0122 2468999999999999998665 89999999999999
Q ss_pred CCCCCCChHHHHHHHhhC---hHHHHHHHHHhhHHHHHHHHHh-ccchHhhhhhhcCCChHHHhhhhhHHHHHHHHHHHH
Q 000161 405 YDPLEVNPEDMVRFAKEK---PQMMASYSVSDAVATYYLYMTY-VHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQA 480 (1988)
Q Consensus 405 ~~K~dvd~~~i~~~~~~~---~~~La~Y~l~Da~lt~~L~~Kl-v~~~i~~La~i~~l~~~~vlr~Gsg~~~E~LLm~~a 480 (1988)
++|++++++.|.++|.++ +.+++.||++||.++++|+.++ +++..+++|+++|+++++|+++|++.++|++|+++|
T Consensus 440 ~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L~~kl~~~~~~~e~arv~gip~~~v~~rG~q~kv~s~Llr~~ 519 (1054)
T PTZ00166 440 EQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRGQQIKVTSQLLRKC 519 (1054)
T ss_pred CCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhccCCChHHhhcCCcchhHHHHHHHHH
Confidence 999999999999999754 4589999999999999999998 778899999999999999999999999999999999
Q ss_pred HHCCeeccCCCCCCchhhhcccccCCCCCCcceeeeccCccccCCCCCCccCChhHHHHHhhhhhhhhHHHHhHhccccc
Q 000161 481 YKANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFKLDPSAYEQLLNNLDRDLQYAIKVEGKMDL 560 (1988)
Q Consensus 481 ~~~n~i~Pnk~~~~~~~~~~g~l~~setY~GG~V~~p~~GvY~~d~~~~f~~~~~~~~~l~~~~~~~l~~~~~~e~~~~~ 560 (1988)
++.|+++|++..... ...++|+||+|++|++|+|.+
T Consensus 520 ~~~~~viP~~~~~~~--------~~~~~yeGg~VleP~~G~y~~------------------------------------ 555 (1054)
T PTZ00166 520 KKLNYVIPTVKYSGG--------GSEEKYEGATVLEPKKGFYDE------------------------------------ 555 (1054)
T ss_pred HhcCeeccCchhccc--------cccCCCCCceeecCCCCCeeC------------------------------------
Confidence 999999999875311 134689999999999999987
Q ss_pred ccccchHHHHHHHHHHHHhhccCCCcccCCeEEEEeccccchHHHHhcCCCCCccccccccccccCCCCCCccccccccc
Q 000161 561 ESVSNYDEVKNAIMEKLLRLQEEPIREECPLIYHLDVAAMYPNIILTNRLQPPSIVTDEVCTACDFNRPGKTCLRKLEWV 640 (1988)
Q Consensus 561 ~~~~n~~~v~~~i~~~l~~l~~~p~~~~~p~V~~LDf~SLYPsII~t~NL~p~Tiv~~~~c~~c~~n~p~~~c~r~m~w~ 640 (1988)
||++|||+|||||||++|||||+|++++... . .+
T Consensus 556 ------------------------------pV~vLDF~SLYPSIiia~NlcysTl~~~~~~-~------------~~--- 589 (1054)
T PTZ00166 556 ------------------------------PIATLDFASLYPSIMIAHNLCYSTLVPPNDA-N------------NY--- 589 (1054)
T ss_pred ------------------------------ceEEeecCCcccHHHHhcCCCcceeecchhh-c------------cC---
Confidence 6999999999999999999999999865310 0 00
Q ss_pred cccccccCCcchhhHhhhhcccccccCCCCCcccccccCchHHHHHHHHHHHHHhhhhhccccccccccccccccccccc
Q 000161 641 WRGEIFMGKRSDYYHLKKQIESEFVDGTNGHLSKSFLDLPKMEQQSRLKDRLKKYCQKAYKRVLDKPVTELREAGICMRE 720 (1988)
Q Consensus 641 ~~ge~~p~~~~ey~~i~~~l~~e~f~~~~~g~~~~~~~L~~~~q~~~lkkrl~~y~~kvy~k~~~~~~~~~r~~~icqre 720 (1988)
+ .++| .... .|. .| .+.+. |
T Consensus 590 ------~--~~~~-----------~~~p-~g~--~F------------------------v~~~~------r-------- 609 (1054)
T PTZ00166 590 ------P--EDTY-----------VTTP-TGD--KF------------------------VKKEV------R-------- 609 (1054)
T ss_pred ------C--Ccce-----------eecC-CCc--ee------------------------eecCC------C--------
Confidence 0 0000 0000 010 11 11111 2
Q ss_pred ccchHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHHHHHHHHHHhhhccccccccC-CCCCCH
Q 000161 721 NSFYVDTVRSFRDRRYEYKGLNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKG-ARWYSM 799 (1988)
Q Consensus 721 ~~f~~~~lr~f~drR~~~K~l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~-sR~ys~ 799 (1988)
.+++|.+|+.|++.|.++|+.||.. .|+. +..+||++|+|+|++|||+|||+|+.. +||||.
T Consensus 610 ~Gilp~iL~~Ll~~R~~~K~~mk~~----------~d~~-------~~~~ld~rQ~AlKi~aNS~YG~~G~~~~gr~~c~ 672 (1054)
T PTZ00166 610 KGILPLIVEELIAARKKAKKEMKDE----------KDPL-------LKKVLNGRQLALKISANSVYGYTGAQVGGQLPCL 672 (1054)
T ss_pred CcccHHHHHHHHHHHHHHHHHHhhC----------CCHH-------HHHHHHHHHHhhhhhccccccccccccCCccccH
Confidence 3589999999999999999998863 2454 347999999999999999999999998 999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHc---------CCe-EEEccceeeEEcCCCCCcccccccccccccccccccccccchh
Q 000161 800 EMAGVVTYTGAKIIQNARLLIEKI---------GKP-LELDTDGIWCVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVD 869 (1988)
Q Consensus 800 e~A~~VT~~Gr~iI~~a~~lve~~---------G~~-vygDTDSI~~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~ 869 (1988)
++|++||++||++|++|+++||+. |.. |||||||+||.+|+...+ .++ +.| +++ +..
T Consensus 673 ~iA~sIT~~GR~~i~~t~~~ie~~~~~~~g~~~g~~VIYGDTDSvfV~~~~~~~~-ea~--~~g-~e~---------a~~ 739 (1054)
T PTZ00166 673 EVSTSITSFGRQMIDKTKELVEKHYTKANGYKHDATVIYGDTDSVMVKFGTDDIQ-EAM--DLG-KEA---------AER 739 (1054)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccccccCcCCeEEEecCCCceEEEeCCccHH-HHH--HHH-HHH---------HHH
Confidence 999999999999999999999997 766 699999999998864211 121 233 332 233
Q ss_pred hhccccchhhhhccCCccccccccccceeEEeeeceeeeeecccccccCcccccceEEEcC-----CCCEEEEEeeeecc
Q 000161 870 VARNNTNDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFND-----DGTLAELKGFEIKR 944 (1988)
Q Consensus 870 V~~~~tN~~y~~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~~~-----dG~~~e~KG~E~kR 944 (1988)
|++.| +.+|++|+||+|.+++|.+ ||||||+.. .|++ ++||+|++|
T Consensus 740 Is~~~--------------------~~pi~LefEkvy~~~ll~~--------KKrYag~~~~~~~~~~k~-d~KGie~vR 790 (1054)
T PTZ00166 740 ISKKF--------------------LKPIKLEFEKVYCPYLLMN--------KKRYAGLLYTNPEKYDKI-DCKGIETVR 790 (1054)
T ss_pred HHHhc--------------------CCCcEEEEeeeeeeeeecc--------cceEEEEEEecCCCCcee-eeeeeEEEe
Confidence 32221 3456777779999999976 999999733 2445 999999999
Q ss_pred CChhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhhhhhccccccChhhhCCCCChHHH
Q 000161 945 RGELKLIKVFQAELFDKFLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADSELIDYISESSTMSKSLADYGEQKSCAVT 1024 (1988)
Q Consensus 945 Rd~~~liK~~q~~v~~~~L~g~~lee~~~~v~~v~~~~~d~L~~~~~~~~~~eLi~~i~~~k~lsK~l~eY~~~k~~~v~ 1024 (1988)
||+|+++|++++++++.+|.+++++++.+.+.+++.+ +..++++.++|+ ++|+++| ++|.+ ++|||.
T Consensus 791 RD~c~~~k~~~~~vl~~il~~~d~~~a~~~~~~~~~~------l~~~~v~i~~lv----i~k~l~k--~~Y~~-~~phv~ 857 (1054)
T PTZ00166 791 RDNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISD------LLQNRIDISLLV----ITKSLGK--DDYEG-RLAHVE 857 (1054)
T ss_pred ccchHHHHHHHHHHHHHHHccCCHHHHHHHHHHHHHH------HHcCCCCHHHEE----EEEEech--hhCCC-CCcHHH
Confidence 9999999999999999999999999999999876653 456899988888 8999998 88985 789999
Q ss_pred HHHHHHhhcCCCcccCCCCeeEEEEEcCCCCCCCcccccchhhhcchHHHHHHHHHhhhcCCCCCCCccccCHHHHHHhh
Q 000161 1025 TARRLSDFLGDTMVKDKGLRCQYIVACEPQGTPVSERAVPVAIFETDAEIMKFYLRKWCKTSSDVGIRSIVDWSYYKQRL 1104 (1988)
Q Consensus 1025 ~A~rl~e~lG~~~~~~~G~~i~YVI~~~p~g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~~~~~d~~~~iD~~YYierl 1104 (1988)
+|+||+++ +.+..+..|++|+|||+++..|+++++||+++..+.. .+..||++|||++
T Consensus 858 ~A~rl~~r-d~~~~p~~GdrI~YViv~~~~~~~~~~ra~~p~~~~~--------------------~~~~iD~~YYi~q- 915 (1054)
T PTZ00166 858 LAKKLRQR-DPGSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVLE--------------------NNIPIDTQYYLDQ- 915 (1054)
T ss_pred HHHHHHHh-CcCcCCCCCCEEEEEEEECCCCcchhhhccCHHHHHh--------------------cCCCCCHHHHHHH-
Confidence 99999985 4457899999999999999888899999998864431 1468999999996
Q ss_pred hhhhhheeechhhhhhccCCCCCcchhhhhhhhhh--ccccccccccHHHhhh
Q 000161 1105 SSAIQKIITIPAAMQKVSNPVPRVVHPDWLYKKVR--EKEDKFRQRKLVDIFS 1155 (1988)
Q Consensus 1105 ~~~i~ki~~iPa~lq~~~npv~rv~~p~w~~~~~~--~~~~~~kq~~l~~~f~ 1155 (1988)
++|++.|.+ +|| .+..-.|+...-. .......+..|..|+.
T Consensus 916 --------l~~pl~Ri~-~~i-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 958 (1054)
T PTZ00166 916 --------IKNPLLRIF-EGV-MDNPDSLFSGEHTRHITISSSSKGGLSKFVK 958 (1054)
T ss_pred --------HHHHHHHHH-HHh-hcCHHHHhccCccceeeecCCCcccHHHHHh
Confidence 677777755 343 2345578852110 0111223567777774
No 4
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=100.00 E-value=6.4e-112 Score=1021.25 Aligned_cols=779 Identities=23% Similarity=0.306 Sum_probs=626.3
Q ss_pred CCeEEEEEEEEecCCCeEEEEe-CCccEEEEEecCCCh-HHHH---HHHHHhc-cccceeEEEEEEeeCCCcCcCCCCCe
Q 000161 61 KVYSCIDLYFVSQDGSTFKSKY-KFRPYFYAATKEKME-MDVE---AYLRRRY-ESQIADIEILEKEDLDLKNHLSGLHK 134 (1988)
Q Consensus 61 ~~~~~v~ly~~t~dG~~~~v~v-~f~PYFyv~~~~~~~-~~v~---~~l~~~~-~~~i~~ie~v~k~dl~~~nhl~g~~~ 134 (1988)
...++|++||+|.+|.++|+.+ +|.|||||+++.+.. +.+. ..|..+. ...+..+++|+|+.++..++ ..+.
T Consensus 94 ~~~pvvr~fGvT~~G~sv~~~v~gf~pyfYv~ap~g~~~e~i~~~~~~l~~~~~~~av~~ve~~~k~~l~~~~g--~~k~ 171 (1066)
T KOG0969|consen 94 GSVPVVRLFGVTKEGNSVCCHVHGFFPYFYVEAPNGFGPEHIGKFQQALDVKVTAHAVDHVEVVSKESLYGYQG--DTKQ 171 (1066)
T ss_pred CCCceEEEeeeccCCCeEEEEEecccceEEecCCCCCCHHHHHHHHHHHHHHHHHhHHHHHHHHhhhhhheecC--CCCc
Confidence 4679999999999999999999 999999999999873 2333 3333333 24678899999999984432 2467
Q ss_pred EEEEEEEechhhHHHHHHHHHHHHHhhcccchhHHHHHHhhhcccCCCCcccccccccccccCCCccceeeeecCCccce
Q 000161 135 SYLKISFDTVQQLMDVKKDLLHVVERNQAKFDAAEAYESILTGKREQRPQDFLDCIVDLREYDVPYHIRFAIDNDVRCGQ 214 (1988)
Q Consensus 135 ~~lKl~f~~~~~l~~vr~~l~~~~~~n~~~~~~~~~y~~~~~~~~~~~~~~~~~~i~~i~E~DI~~~~R~~iD~~I~~g~ 214 (1988)
+|+||+..+|..+..+|..|..++... .......+..||.+|+|..||++|.+|.++.
T Consensus 172 ~f~kit~~lP~~~~~~r~~lergv~~~----------------------~~~~~~~~~~yEsNi~f~lrfmvd~~iVG~~ 229 (1066)
T KOG0969|consen 172 PFLKITVTLPRMVAAARRLLERGVFIS----------------------GKGEKVGFTTYESNIDFVLRFMVDCDIVGMN 229 (1066)
T ss_pred eeEEEecccHHHHHHhHHHHHhccccc----------------------ccCcceeeeEecCCccEEEEEEecCccccce
Confidence 999999999999999999988642110 0112235678999999999999999999999
Q ss_pred eEEEeeCCC----------CceEEE----------eccccCCCCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEc--C
Q 000161 215 WYDVSISST----------GPLLEK----------RVDLLQRAEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLD--G 272 (1988)
Q Consensus 215 W~~v~~~~~----------~~~i~~----------~~~~~~~p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~--~ 272 (1988)
|+++...+. ++++.. ..++...||+++|||||||.+..+.||.|+.||||+|+-.+. |
T Consensus 230 wi~lp~gk~~~~~~~~s~cqlEv~v~y~~lishp~eG~w~~~APlrvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~G 309 (1066)
T KOG0969|consen 230 WIELPAGKYRIRDNRVSRCQLEVSVNYKDLISHPAEGEWSKIAPLRVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQG 309 (1066)
T ss_pred eEEeccchheeccchhcccceEEEEeecccccccccCcccccccccccceeEEeccCCCCCCccccChHHHHHHHHHHhc
Confidence 999976542 222221 235667999999999999999999999999999999986643 3
Q ss_pred CceEEEcccccccccccccCCCCCCCCCceEEecCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCC
Q 000161 273 QGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFK 352 (1988)
Q Consensus 273 ~g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~ 352 (1988)
.+.. ...+ -|-+.|.....| ..|..+.+|++||..|-++|++.|||||+|||+.+||+|||.+||+.||+.
T Consensus 310 e~~p------f~rn--vf~l~~capI~G-~~V~~~~~e~elL~~W~~firevDPDvI~GYNi~nFDiPYll~RA~~L~Ie 380 (1066)
T KOG0969|consen 310 ENEP------FVRN--VFTLKTCAPIVG-SNVHSYETEKELLESWRKFIREVDPDVIIGYNICNFDIPYLLNRAKTLGIE 380 (1066)
T ss_pred CCch------HHHh--hhcccCcCCCCC-ceeEEeccHHHHHHHHHHHHHhcCCCeEecccccccccceecChHhhcCcc
Confidence 3321 1111 123334434444 468889999999999999999999999999999999999999999999999
Q ss_pred CCcccCccccCC-------------CC-----ceeeccceEechHHHHhhccCCCCCCCCHHHHHHHHcCCCCCCCChHH
Q 000161 353 MSEELGFQCDKN-------------QG-----ECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPED 414 (1988)
Q Consensus 353 l~~~iG~~~~~~-------------~g-----~~~i~GRihiDl~~~vkrd~~L~~~SysL~~Va~~~LG~~K~dvd~~~ 414 (1988)
.+..+|+. ++. .| ...|.||+.+|++.++.||++| .||+|++|+.||||++|+|++++.
T Consensus 381 ~Fp~LGRi-kn~~s~irDttfSSkq~GtRetK~v~I~GRlqfDllqvi~Rd~KL--rSytLNaVs~hFL~EQKEDV~~si 457 (1066)
T KOG0969|consen 381 NFPYLGRI-KNSRSVIRDSTFSSKQYGTRETKEVNIDGRLQFDLLQVILRDYKL--RSYTLNAVSAHFLGEQKEDVHHSI 457 (1066)
T ss_pred ccccccee-cccceeeeccccchhhcCcccceEEeecceeeehHHHHHHHhhhh--hhcchhhhHHHhhhhhcccccccc
Confidence 98878876 321 23 2569999999999999999888 899999999999999999999999
Q ss_pred HHHHHhhC---hHHHHHHHHHhhHHHHHHHHHh-ccchHhhhhhhcCCChHHHhhhhhHHHHHHHHHHHHHHCCeeccCC
Q 000161 415 MVRFAKEK---PQMMASYSVSDAVATYYLYMTY-VHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAYKANVICPNK 490 (1988)
Q Consensus 415 i~~~~~~~---~~~La~Y~l~Da~lt~~L~~Kl-v~~~i~~La~i~~l~~~~vlr~Gsg~~~E~LLm~~a~~~n~i~Pnk 490 (1988)
|.++.+++ +.+||.||++||.|.++|++|+ +.--..+|||++|+|++.+|.+|++..+-++|++.|.+.++++|+-
T Consensus 458 ItdLQng~~~TRRRlA~YCLkDAYLPlRLlekLM~ivNy~EMARVTGVP~syLltRGqqIKVlSqLlRkakq~~~~~P~i 537 (1066)
T KOG0969|consen 458 ITDLQNGNEQTRRRLAVYCLKDAYLPLRLLEKLMVIVNYTEMARVTGVPISYLLTRGQQIKVLSQLLRKAKQKDFVIPNI 537 (1066)
T ss_pred hhhhhcCcHHHHHHHHHHHhhhhcchHHHHHHHHHHHhHHhhhhhhCCcHHHHHhCCcchHHHHHHHHHHhhcCeeeeee
Confidence 99998854 4699999999999999999998 3333469999999999999999999999999999999999999998
Q ss_pred CCCCchhhhcccccCCCCCCcceeeeccCccccCCCCCCccCChhHHHHHhhhhhhhhHHHHhHhcccccccccchHHHH
Q 000161 491 HQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFKLDPSAYEQLLNNLDRDLQYAIKVEGKMDLESVSNYDEVK 570 (1988)
Q Consensus 491 ~~~~~~~~~~g~l~~setY~GG~V~~p~~GvY~~d~~~~f~~~~~~~~~l~~~~~~~l~~~~~~e~~~~~~~~~n~~~v~ 570 (1988)
..... ..++|+||.|.+|..|+|..
T Consensus 538 ~~~~s---------~~e~yEGatVIEp~kGfY~~---------------------------------------------- 562 (1066)
T KOG0969|consen 538 KSQGS---------DDEQYEGATVIEPRKGFYDK---------------------------------------------- 562 (1066)
T ss_pred cccCC---------ccccccccEEeecccccCCC----------------------------------------------
Confidence 76432 34799999999999999876
Q ss_pred HHHHHHHHhhccCCCcccCCeEEEEeccccchHHHHhcCCCCCccccccccccccCCCCCCccccccccccccccccCCc
Q 000161 571 NAIMEKLLRLQEEPIREECPLIYHLDVAAMYPNIILTNRLQPPSIVTDEVCTACDFNRPGKTCLRKLEWVWRGEIFMGKR 650 (1988)
Q Consensus 571 ~~i~~~l~~l~~~p~~~~~p~V~~LDf~SLYPsII~t~NL~p~Tiv~~~~c~~c~~n~p~~~c~r~m~w~~~ge~~p~~~ 650 (1988)
||..|||+|||||||++|||||+|++..+.- ++++ .
T Consensus 563 --------------------PIATLDFaSLYPSIMmahNLCYtTLl~~~t~-------------~~l~-----------~ 598 (1066)
T KOG0969|consen 563 --------------------PIATLDFASLYPSIMMAHNLCYTTLLTKETV-------------EKLG-----------D 598 (1066)
T ss_pred --------------------CceeeehhhhhhHHHHHhhhhheeccccchh-------------hhcC-----------c
Confidence 7999999999999999999999999876421 1111 0
Q ss_pred chhhHhhhhcccccccCCCCCcccccccCchHHHHHHHHHHHHHhhhhhcccccccccccccccccccccccchHHHHHH
Q 000161 651 SDYYHLKKQIESEFVDGTNGHLSKSFLDLPKMEQQSRLKDRLKKYCQKAYKRVLDKPVTELREAGICMRENSFYVDTVRS 730 (1988)
Q Consensus 651 ~ey~~i~~~l~~e~f~~~~~g~~~~~~~L~~~~q~~~lkkrl~~y~~kvy~k~~~~~~~~~r~~~icqre~~f~~~~lr~ 730 (1988)
++| ...|. |. .|. +++. |. +++|.+|.+
T Consensus 599 ~~~---------~~TP~---g~--yFv------------------------~~~~------rk--------GlLP~ILe~ 626 (1066)
T KOG0969|consen 599 EDY---------TRTPT---GD--YFV------------------------KTEV------RK--------GLLPEILED 626 (1066)
T ss_pred cce---------eECCC---CC--eee------------------------ehhh------hc--------cccHHHHHH
Confidence 011 00111 10 111 1111 33 489999999
Q ss_pred HHHHHHHHHhhhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCCCHHHHHHHHHHHH
Q 000161 731 FRDRRYEYKGLNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGA 810 (1988)
Q Consensus 731 f~drR~~~K~l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~sR~ys~e~A~~VT~~Gr 810 (1988)
|+..|+..|.-+|. +.||.++ ..||.+|||+|+.|||.||++|+..+++||.|+..+||+.||
T Consensus 627 ll~aRKraK~dlk~----------ekDp~kr-------~vldGRQLAlKisANSvYGFTGAtvGkLPCleIS~SVT~yGR 689 (1066)
T KOG0969|consen 627 LLTARKRAKADLKK----------EKDPFKR-------AVLDGRQLALKISANSVYGFTGATVGKLPCLEISQSVTAYGR 689 (1066)
T ss_pred HHHHHHHHHHHHHh----------ccCHHHH-------hhhcchhhheeecccccccccccccCccceeeechhhHHHHH
Confidence 99999988866554 4577654 799999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHc-----CCe-----EEEccceeeEEcCCCCCcccccccccccccccccccccccchhhhccccchhhh
Q 000161 811 KIIQNARLLIEKI-----GKP-----LELDTDGIWCVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVDVARNNTNDQYQ 880 (1988)
Q Consensus 811 ~iI~~a~~lve~~-----G~~-----vygDTDSI~~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~V~~~~tN~~y~ 880 (1988)
++|.+++.+||+. |++ |||||||+||.+..+.-++ ++ +.| ++. ++.|+.+|+
T Consensus 690 ~MI~~TK~~Ve~~y~~~ngy~~da~ViYGDTDSVMv~Fgv~~v~~-am--~lg-~ea---------a~~vs~~F~----- 751 (1066)
T KOG0969|consen 690 QMIEKTKKLVEEKYTIKNGYSHDAVVIYGDTDSVMVKFGVSDVEE-AM--KLG-REA---------AEYVSSKFV----- 751 (1066)
T ss_pred HHHHHHHHHHHHHhhhccCCccccEEEecCCceEEEecCchhHHH-HH--HHh-HHH---------HHHHHhcCC-----
Confidence 9999999999975 663 6999999999988653221 22 235 433 455655553
Q ss_pred hccCCccccccccccceeEEeeeceeeeeecccccccCcccccceEEE---cCC-CCEEEEEeeeeccCChhHHHHHHHH
Q 000161 881 TLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVF---NDD-GTLAELKGFEIKRRGELKLIKVFQA 956 (1988)
Q Consensus 881 ~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~---~~d-G~~~e~KG~E~kRRd~~~liK~~q~ 956 (1988)
.+|.+|++++|.+.+|.. ||||||+ |+| +..++.||+|++|||+|+|++++..
T Consensus 752 ---------------~PIkLEFEKvY~PYLLIn--------KKRYAGL~~t~pd~~DkmD~kGietVRRDnc~LV~~v~~ 808 (1066)
T KOG0969|consen 752 ---------------KPIKLEFEKVYFPYLLIN--------KKRYAGLLWTNPDVFDKMDCKGIETVRRDNCPLVANVVN 808 (1066)
T ss_pred ---------------CCceeEeeeeecceEEec--------cceeeeeEeccCCcCccccccccchhccCCchHHHHHHH
Confidence 234555559999999976 9999995 454 4556999999999999999999999
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhhhhhccccccChhhhCCCCChHHHHHHHHHhhcCCC
Q 000161 957 ELFDKFLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADSELIDYISESSTMSKSLADYGEQKSCAVTTARRLSDFLGDT 1036 (1988)
Q Consensus 957 ~v~~~~L~g~~lee~~~~v~~v~~~~~d~L~~~~~~~~~~eLi~~i~~~k~lsK~l~eY~~~k~~~v~~A~rl~e~lG~~ 1036 (1988)
.+++.+|-.+|++.+.+.|+++++ |.| -+.++.+.|| ++|.|+|.-++|.+ |++||.+|.||+++ +++
T Consensus 809 ~~L~kiLi~rdv~gA~~fvk~~Is---DlL---~nriDiS~LV----ItK~Ltkagd~Y~~-kqaHveLAermrkR-D~g 876 (1066)
T KOG0969|consen 809 TVLRKILIERDVEGALAFVKDTIS---DLL---CNRIDISLLV----ITKELTKAGDDYAA-KQAHVELAERMRKR-DAG 876 (1066)
T ss_pred HHHHHHHhhcChHHHHHHHHHHHH---HHH---hcccceeeee----eeehhcccccchhh-hhhhHHHHHHhhhc-CCC
Confidence 999999999999999999999887 333 3556666666 89999999999997 89999999999996 666
Q ss_pred cccCCCCeeEEEEEcCCCCCCCcccccchhhhcchHHHHHHHHHhhhcCCCCCCCccccCHHHHHHhhhhhhhheeechh
Q 000161 1037 MVKDKGLRCQYIVACEPQGTPVSERAVPVAIFETDAEIMKFYLRKWCKTSSDVGIRSIVDWSYYKQRLSSAIQKIITIPA 1116 (1988)
Q Consensus 1037 ~~~~~G~~i~YVI~~~p~g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~~~~~d~~~~iD~~YYierl~~~i~ki~~iPa 1116 (1988)
..|..|||++|||+++..|+|..+|++.|- |-.+ .+.+||..||+++
T Consensus 877 taP~lGDRVpYVIi~~akg~~ay~rsEDP~-fVLe-------------------nNipiD~~yYL~n------------- 923 (1066)
T KOG0969|consen 877 TAPNLGDRVPYVIIAAAKGAPAYERSEDPL-YVLE-------------------NNIPIDTRYYLEN------------- 923 (1066)
T ss_pred CCCccCCcCcEEEEecccCCchhcCCCCCe-EEec-------------------CCCCcchHHHHhh-------------
Confidence 889999999999999999999999999873 4433 2568999999998
Q ss_pred hhhhccCCCCCcchhh
Q 000161 1117 AMQKVSNPVPRVVHPD 1132 (1988)
Q Consensus 1117 ~lq~~~npv~rv~~p~ 1132 (1988)
++.+|+.||..|.
T Consensus 924 ---QlsKPllrIfePI 936 (1066)
T KOG0969|consen 924 ---QLSKPLLRIFEPI 936 (1066)
T ss_pred ---hhhhhHHHHhhhh
Confidence 4567777776664
No 5
>PRK05762 DNA polymerase II; Reviewed
Probab=100.00 E-value=3.8e-108 Score=1082.06 Aligned_cols=736 Identities=25% Similarity=0.362 Sum_probs=571.6
Q ss_pred ceEEEEEeeeecccccccCCCCeEEEEEEEEecCCCeEEEEe-CCccEEEEEecCCChHHHHHHHHHhccccceeEEEEE
Q 000161 41 KRLGWLLTFASSSLEDEDTRKVYSCIDLYFVSQDGSTFKSKY-KFRPYFYAATKEKMEMDVEAYLRRRYESQIADIEILE 119 (1988)
Q Consensus 41 ~~~g~L~n~~~~~~~d~~~~~~~~~v~ly~~t~dG~~~~v~v-~f~PYFyv~~~~~~~~~v~~~l~~~~~~~i~~ie~v~ 119 (1988)
...||||+.++.+.. ++++|++|++|++|.++++.+ +|+||||+...+. .....+.... ...++.+.
T Consensus 3 ~~~~~lL~~~~~~~~------~~~vi~l~g~t~~G~~~~v~~~~~~~yFy~~~~~~---~~~~~~~~~~---~~~~~~~~ 70 (786)
T PRK05762 3 LQQGFILTRHYRDTP------GGPEVELWLATDEGPRVVLLDPQFRPYFIPAEQDE---RAESLLAGEI---GVRLSPLA 70 (786)
T ss_pred ceEEEEEeeEEEEEC------CeEEEEEEEEcCCCCEEEEECCCCcEEEEEeCchh---hhHHHHhhcc---cceeeccc
Confidence 467999999997643 679999999999999999988 8999999976543 2222333221 12222222
Q ss_pred EeeCCCcCcCCCCCeEEEEEEEechhhHHHHHHHHHHHHHhhcccchhHHHHHHhhhcccCCCCcccccccccccccCCC
Q 000161 120 KEDLDLKNHLSGLHKSYLKISFDTVQQLMDVKKDLLHVVERNQAKFDAAEAYESILTGKREQRPQDFLDCIVDLREYDVP 199 (1988)
Q Consensus 120 k~dl~~~nhl~g~~~~~lKl~f~~~~~l~~vr~~l~~~~~~n~~~~~~~~~y~~~~~~~~~~~~~~~~~~i~~i~E~DI~ 199 (1988)
..+ + ..+++..++|.+...+.++++.++. .++++||+||+
T Consensus 71 l~~------~--~~~~~~~~~~~~~~~~~~~~~~~~~--------------------------------~~~~i~EaDI~ 110 (786)
T PRK05762 71 LKD------F--HRRPVLGLYCRQHRQLTRLPKRLRE--------------------------------GGVDVYEADIR 110 (786)
T ss_pred eec------c--cCCeeeEEEeccHHHHHHHHHHHHH--------------------------------cCCeEEECCCC
Confidence 222 2 2357889999999999999988873 46789999999
Q ss_pred ccceeeeecCCccceeEEEeeCCC--CceEEE--ecccc-CCCCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCc
Q 000161 200 YHIRFAIDNDVRCGQWYDVSISST--GPLLEK--RVDLL-QRAEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQG 274 (1988)
Q Consensus 200 ~~~R~~iD~~I~~g~W~~v~~~~~--~~~i~~--~~~~~-~~p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g 274 (1988)
++.||+||++|++|+||.++.... ...+.. ..... ..|+++++||||||++. ++|++|+++..++.
T Consensus 111 ~~~R~lid~~i~~~~w~~~~~~~~~~~~~~~~~~i~~~~~~~p~lrvlsfDIE~~~~---------~~i~sI~~~~~~~~ 181 (786)
T PRK05762 111 FPERYLMERFITPCVWFSGEVEQYTTDGVLRNARLKPAPDYRPPLKVVSLDIETSNK---------GELYSIGLEGCGQR 181 (786)
T ss_pred hhHhheeeCCCCCcEEEEEEeeccccceeEEecceeeCCCCCCCCeEEEEEEEEcCC---------CceEEeeecCCCCC
Confidence 999999999999999999876442 111111 11111 13999999999999873 36888887643333
Q ss_pred eEEEcccccccccccccCCCCCCCCCceEEecCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCC
Q 000161 275 YLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMS 354 (1988)
Q Consensus 275 ~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~ 354 (1988)
.++.. |.. .+. .+.+ |..+.||++||.+|+++|+++|||||+|||+++||||||.+||+.||+++.
T Consensus 182 ~vi~i----g~~--------~~~-~~~~-v~~~~sE~~LL~~F~~~i~~~DPDIIvGyNi~~FDlpyL~~Ra~~lgi~~~ 247 (786)
T PRK05762 182 PVIML----GPP--------NGE-ALDF-LEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIPLR 247 (786)
T ss_pred eEEEE----ECC--------CCC-Ccce-EEEcCCHHHHHHHHHHHHHhcCCCEEEEeCCCCCcHHHHHHHHHHhCCCcc
Confidence 33321 111 010 1233 678999999999999999999999999999999999999999999999853
Q ss_pred cccCcccc-------C---CCCceeeccceEechHHHHhhccCCCCCCCCHHHHHHHHcCCCCCCCCh----HHHHHHHh
Q 000161 355 EELGFQCD-------K---NQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNP----EDMVRFAK 420 (1988)
Q Consensus 355 ~~iG~~~~-------~---~~g~~~i~GRihiDl~~~vkrd~~L~~~SysL~~Va~~~LG~~K~dvd~----~~i~~~~~ 420 (1988)
+|+... . ..+.+.++||+|+|+|.++++..+ +++||+|++||+++||++|.+.++ ++|.++|.
T Consensus 248 --~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~~~~-~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~ 324 (786)
T PRK05762 248 --LGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATW-VFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFA 324 (786)
T ss_pred --cCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHHhhc-cCCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHh
Confidence 333200 0 112467999999999999999764 469999999999999999987666 78899999
Q ss_pred hChHHHHHHHHHhhHHHHHHHHHh-ccchHhhhhhhcCCChHHHhhhhhHHHHHHHHHHHHHHCCeeccCCCCCCchhhh
Q 000161 421 EKPQMMASYSVSDAVATYYLYMTY-VHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAYKANVICPNKHQSDPEKFY 499 (1988)
Q Consensus 421 ~~~~~La~Y~l~Da~lt~~L~~Kl-v~~~i~~La~i~~l~~~~vlr~Gsg~~~E~LLm~~a~~~n~i~Pnk~~~~~~~~~ 499 (1988)
++++++++||++||.+|++|+.++ ++|+++++|+++|+++++|+ |++..+|++||++|+++|+++|++...
T Consensus 325 ~~~~~l~~Y~l~Da~lt~~L~~kl~ll~~~~ela~l~g~~~~~v~--~~~~~~e~lll~~~~~~g~v~P~~~~~------ 396 (786)
T PRK05762 325 EDKPALARYNLKDCELVTRIFEKTKLLPFLLERATVTGLPLDRVG--GSVAAFEHLYLPRAHRAGYVAPNLGER------ 396 (786)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhCcCHHHhC--ccHHhHHHHHHHHHHHCCEeCCCcccc------
Confidence 899999999999999999999988 89999999999999999996 667777999999999999999998653
Q ss_pred cccccCCCCCCcceeeeccCccccCCCCCCccCChhHHHHHhhhhhhhhHHHHhHhcccccccccchHHHHHHHHHHHHh
Q 000161 500 RNHLLESETYIGGHVECLESGVFRSDLPTSFKLDPSAYEQLLNNLDRDLQYAIKVEGKMDLESVSNYDEVKNAIMEKLLR 579 (1988)
Q Consensus 500 ~g~l~~setY~GG~V~~p~~GvY~~d~~~~f~~~~~~~~~l~~~~~~~l~~~~~~e~~~~~~~~~n~~~v~~~i~~~l~~ 579 (1988)
..++|.||+|++|++|+|++
T Consensus 397 -----~~~~y~Gg~V~~p~~G~y~~------------------------------------------------------- 416 (786)
T PRK05762 397 -----PGEASPGGYVMDSKPGLYDS------------------------------------------------------- 416 (786)
T ss_pred -----cccccCccEEecCCCCCcCc-------------------------------------------------------
Confidence 24689999999999999987
Q ss_pred hccCCCcccCCeEEEEeccccchHHHHhcCCCCCccccccccccccCCCCCCccccccccccccccccCCcchhhHhhhh
Q 000161 580 LQEEPIREECPLIYHLDVAAMYPNIILTNRLQPPSIVTDEVCTACDFNRPGKTCLRKLEWVWRGEIFMGKRSDYYHLKKQ 659 (1988)
Q Consensus 580 l~~~p~~~~~p~V~~LDf~SLYPsII~t~NL~p~Tiv~~~~c~~c~~n~p~~~c~r~m~w~~~ge~~p~~~~ey~~i~~~ 659 (1988)
|++|||+|||||||++|||||+|++... |. |..
T Consensus 417 ------------V~~lDF~SLYPSIi~~~Ni~p~T~~~~~----~~---~~~---------------------------- 449 (786)
T PRK05762 417 ------------VLVLDFKSLYPSIIRTFNIDPDGLVEGL----AQ---PPE---------------------------- 449 (786)
T ss_pred ------------eEEEEchhhhHHHHHHhCcCccceecCC----CC---CCc----------------------------
Confidence 9999999999999999999999997432 10 100
Q ss_pred cccccccCCCCCcccccccCchHHHHHHHHHHHHHhhhhhcccccccccccccccccccccccchHHHHHHHHHHHHHHH
Q 000161 660 IESEFVDGTNGHLSKSFLDLPKMEQQSRLKDRLKKYCQKAYKRVLDKPVTELREAGICMRENSFYVDTVRSFRDRRYEYK 739 (1988)
Q Consensus 660 l~~e~f~~~~~g~~~~~~~L~~~~q~~~lkkrl~~y~~kvy~k~~~~~~~~~r~~~icqre~~f~~~~lr~f~drR~~~K 739 (1988)
+.+++.++. . | |. ..+++|.+|+.|++.|.++|
T Consensus 450 ---~~~~~~~~~---~-------------------f---------------------~k-~~gilp~~l~~l~~~R~~~K 482 (786)
T PRK05762 450 ---ESVAGFLGA---R-------------------F---------------------SR-EKHFLPEIVERLWEGRDEAK 482 (786)
T ss_pred ---ccccCCCCc---c-------------------c---------------------cc-cCcchHHHHHHHHHHHHHHH
Confidence 001111110 0 1 11 23699999999999999999
Q ss_pred hhhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 000161 740 GLNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNARLL 819 (1988)
Q Consensus 740 ~l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~sR~ys~e~A~~VT~~Gr~iI~~a~~l 819 (1988)
+.||. .+|+|+|+++||+|||+|++++||||+++|++||++||++|+.|+++
T Consensus 483 ~~~~~----------------------------~~q~a~Ki~~Ns~YG~~g~~~~r~~~~~~A~~it~~Gr~~l~~~~~~ 534 (786)
T PRK05762 483 REMNK----------------------------PLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTREL 534 (786)
T ss_pred HHHHH----------------------------HHHHHHHhhhhhcccccccccccccChHHHHHHHHhHHHHHHHHHHH
Confidence 77652 38999999999999999999999999999999999999999999999
Q ss_pred HHHcCCe-EEEccceeeEEcCCCCCcccccccccccccccccccccccchhhhccccchhhhhccCCcccccccccccee
Q 000161 820 IEKIGKP-LELDTDGIWCVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVDVARNNTNDQYQTLVDPVSKTYETHSECSI 898 (1988)
Q Consensus 820 ve~~G~~-vygDTDSI~~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~V~~~~tN~~y~~l~~~~~~~y~~~s~~~I 898 (1988)
+|+.|+. ||||||||||.++...+.+... +.| +++ ...| |..|+.. ....+.. +.+|
T Consensus 535 ~~~~g~~viYgDTDSifv~~~~~~~~~~~~--~~~-~~l---------~~~i-----n~~~~~~---l~~~~~~--~~~l 592 (786)
T PRK05762 535 IEAQGYQVIYGDTDSTFVWLGGAHDEEDAA--KIG-RAL---------VQEI-----NQWWQEH---LQQEFGL--ESAL 592 (786)
T ss_pred HHHCCCEEEeecCCceEEEcCCCCCHHHHH--HHH-HHH---------HHHH-----HHHHHhh---hhhhccC--CCce
Confidence 9999998 6999999999988432222121 123 222 2333 4334321 1122333 3446
Q ss_pred EEeeeceeeeeecccccccCcccccceEEEc----CCCCEEEEEeeeeccCChhHHHHHHHHHHHHHHhCCCCHHHHHHH
Q 000161 899 EFEVDGPYKAMILPASKEEGILIKKRYAVFN----DDGTLAELKGFEIKRRGELKLIKVFQAELFDKFLHGSTIEECYSA 974 (1988)
Q Consensus 899 ~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~~----~dG~~~e~KG~E~kRRd~~~liK~~q~~v~~~~L~g~~lee~~~~ 974 (1988)
++|+|++|++|+||+.+|++++.||||||+. .+|++ ++||+|++|||||+|+|++|+++++.+|.++++.+.+
T Consensus 593 ~le~E~vy~~~~l~~~rg~~~~~KKrYag~~~~~~~~~~~-~~KGle~vRrD~~~~~k~~~~~vl~~il~~~~~~~~~-- 669 (786)
T PRK05762 593 ELEFEKHYRRFFMPTIRGAEEGSKKRYAGLIQEGDGDGRI-VFKGLETVRTDWTPLAKEFQQELYERIFRGEPYVDYV-- 669 (786)
T ss_pred EEEEeeeeehhccccccccchhhhheEEEEEEccCCCceE-EEEeeEEECCChHHHHHHHHHHHHHHHhcCCCHHHHH--
Confidence 6666699999999999999999999999975 56776 9999999999999999999999999999999985543
Q ss_pred HHHHHHHHHHHHHhcCCCCCchhhhhhhhhccccccChhhhCCCCChHHHHHHHHHhhcCCCc----ccCCCCeeEEEEE
Q 000161 975 VAAVANRWLDLLDNQGKDIADSELIDYISESSTMSKSLADYGEQKSCAVTTARRLSDFLGDTM----VKDKGLRCQYIVA 1050 (1988)
Q Consensus 975 v~~v~~~~~d~L~~~~~~~~~~eLi~~i~~~k~lsK~l~eY~~~k~~~v~~A~rl~e~lG~~~----~~~~G~~i~YVI~ 1050 (1988)
+++++ +++.++++ ++|+ ++|+|+|++++|.+..+|||.+|+++.+. |... ....|++|+|||+
T Consensus 670 -~~~~~------~l~~~~~~-~~lv----~~k~l~k~~~~Y~~~~~phv~aa~~~~~~-~~~~~~~~~~~~g~~I~Yvi~ 736 (786)
T PRK05762 670 -REVID------KLRAGELD-EKLV----YRKRLRRPLDEYQRNVPPHVRAARLADEM-GYKVGRPLQYQNGGKIGYVIT 736 (786)
T ss_pred -HHHHH------HHHcCCCc-hhEE----EEehcCCCHHHcCCCCCHHHHHHHHHHhc-CcccCCcccCCCCCEEEEEEE
Confidence 33333 35678999 9988 89999999999997789999999999985 5321 2357999999996
Q ss_pred cCCCCCCCcccccchhhhcchHHHHHHHHHhhhcCCCCCCCccccCHHHHHHhhhhhhhheeechhhhhhc
Q 000161 1051 CEPQGTPVSERAVPVAIFETDAEIMKFYLRKWCKTSSDVGIRSIVDWSYYKQRLSSAIQKIITIPAAMQKV 1121 (1988)
Q Consensus 1051 ~~p~g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~~~~~d~~~~iD~~YYierl~~~i~ki~~iPa~lq~~ 1121 (1988)
.++.+ |+.+| ...||++|||++ |+.|++.+.+
T Consensus 737 ~~g~~-~~~~~------------------------------~~~iD~~yYi~k--------ql~p~~~ril 768 (786)
T PRK05762 737 VNGPE-PLEYR------------------------------KSPIDYDYYIEK--------QLQPVADRIL 768 (786)
T ss_pred eCCCC-cHHhc------------------------------CCCCCHHHHHHH--------hhHHHHHHHH
Confidence 43222 33221 257999999999 9999998875
No 6
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.3e-107 Score=1075.06 Aligned_cols=769 Identities=30% Similarity=0.467 Sum_probs=616.8
Q ss_pred CeEEEEEEEEecCCCeEEEEe-CCccEEEEEecCCC-hHHHHHHHHHhccccceeEEEEEEeeCCCcCcCCCCCeEEEEE
Q 000161 62 VYSCIDLYFVSQDGSTFKSKY-KFRPYFYAATKEKM-EMDVEAYLRRRYESQIADIEILEKEDLDLKNHLSGLHKSYLKI 139 (1988)
Q Consensus 62 ~~~~v~ly~~t~dG~~~~v~v-~f~PYFyv~~~~~~-~~~v~~~l~~~~~~~i~~ie~v~k~dl~~~nhl~g~~~~~lKl 139 (1988)
+.+.+.+|+.+++|.++...+ +|.||||+..++.. ++.+.........+.....+...+.+. +.+.+....+|
T Consensus 7 ~~~~~~~~~~~~~G~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~i 81 (792)
T COG0417 7 GFPLVRIFGDTDSGKSVVKLVATFRPYFYVTLDNSRPEDYVLKILNRRLDDVLELEEVENVPDP-----YLGREVEVLKI 81 (792)
T ss_pred CceEEEEeeecCCCCEEEEEecCCCCcEEEecCCCcccchhhhhccccccccceeeeeeeeecc-----ccCCcccceee
Confidence 468899999999998888877 99999999988751 122222211111122222233333332 45677889999
Q ss_pred EEechhhHHHHHHHHHHHHHhhcccchhHHHHHHhhhcccCCCCcccccccccccccCCCccceeeeecCCccceeEEEe
Q 000161 140 SFDTVQQLMDVKKDLLHVVERNQAKFDAAEAYESILTGKREQRPQDFLDCIVDLREYDVPYHIRFAIDNDVRCGQWYDVS 219 (1988)
Q Consensus 140 ~f~~~~~l~~vr~~l~~~~~~n~~~~~~~~~y~~~~~~~~~~~~~~~~~~i~~i~E~DI~~~~R~~iD~~I~~g~W~~v~ 219 (1988)
+..+|+.+.++|+.+.. ..+.+.++||+||||++||++|++|+++.|+.++
T Consensus 82 ~~~~p~~v~~~r~~~~~-----------------------------~~~~~~~i~e~dI~~~~r~~~d~~i~~~~~~~~~ 132 (792)
T COG0417 82 YARDPQAVRKLREKVKR-----------------------------ELEGVVDIFEADIPFAMRYLIDKGIRPMVWVSVD 132 (792)
T ss_pred EecCHHHHHHHHHHHhh-----------------------------hhhccceEeecCCCcchheeeecCCCCceEEEee
Confidence 99999999999988873 1235678999999999999999999999999998
Q ss_pred eCCCCce--EEEeccccCCCCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEcccccccccccccCCCCCC
Q 000161 220 ISSTGPL--LEKRVDLLQRAEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPE 297 (1988)
Q Consensus 220 ~~~~~~~--i~~~~~~~~~p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~di~~feytp~~~ 297 (1988)
....... .........+|++++|||||||++.++++|++..|+|++|+++....+..+ ..+.|++.+.
T Consensus 133 ~~~~~~~~~~~~~~~~~~~p~l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~----------~~~~~~~~~~ 202 (792)
T COG0417 133 VEDIGSIHSLFLEHREDVRPPLRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLI----------EVFIYTSGEG 202 (792)
T ss_pred eccccchhhcccccccCcCCCceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCcc----------ccccccCCCC
Confidence 6543211 111223456899999999999999999999999999999999986655432 2334555544
Q ss_pred CCCceEEecCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccC-----CCCceeecc
Q 000161 298 FEGYFKVTNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDK-----NQGECRAKF 372 (1988)
Q Consensus 298 ~~g~f~V~~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~-----~~g~~~i~G 372 (1988)
+ .|+.+.+|.+||.+|..++.++|||||+|||+++||||||.+||+.+|+++. +|+. .. ..|.+...|
T Consensus 203 ~----~v~~~~~e~e~l~~~~~~i~~~dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~--~gr~-~~~~~~~~~~~~~~~G 275 (792)
T COG0417 203 F----SVEVVISEAELLERFVELIREYDPDVIVGYNGDNFDWPYLAERAERLGIPLR--LGRD-GSELRVRKSGFSSQVG 275 (792)
T ss_pred c----eeEEecCHHHHHHHHHHHHHhcCCCEEEeccCCcCChHHHHHHHHHhCCCcc--cccc-ccccceeecccccccc
Confidence 3 3889999999999999999999999999999999999999999999999986 4443 11 122233349
Q ss_pred ceEechHHHHh-hccCCCCCCCCHHHHHHHHcCCCC-CCCChHHHHHHH---hhChHHHHHHHHHhhHHHHHHHHHh-cc
Q 000161 373 ACHLDCFAWVK-RDSYLPQGSQGLKAVTKAKLGYDP-LEVNPEDMVRFA---KEKPQMMASYSVSDAVATYYLYMTY-VH 446 (1988)
Q Consensus 373 RihiDl~~~vk-rd~~L~~~SysL~~Va~~~LG~~K-~dvd~~~i~~~~---~~~~~~La~Y~l~Da~lt~~L~~Kl-v~ 446 (1988)
|+|+|++..++ +...+ .+|+|++|+.++||+.+ .+++...|...| ..+...++.||++|+.++.+++.+. ++
T Consensus 276 r~~iDl~~~~~~~~~~~--~~ysl~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l~~~~~~~~~~l 353 (792)
T COG0417 276 RLHIDLYPALRRRPLNL--KSYSLEAVSEALLGEGKREDIPYDSMEEIWPDWADSKLRLLLYNLSDADLVLRILLKNELL 353 (792)
T ss_pred eEEEecHHHHhhhhccc--ccccHHHHHHHhcccccccccCccchhhccccCccchhHHHHHHHHHHHHHHHHHHHHhHH
Confidence 99999999999 45444 89999999999999988 777777766544 4566799999999999999999987 78
Q ss_pred chHhhhhhhcCCChHHHhhhhhHHHHHHHHHHHHHHCCeeccCCCCCCchhhhcccccCCCCCCcceeeeccCccccCCC
Q 000161 447 PFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAYKANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDL 526 (1988)
Q Consensus 447 ~~i~~La~i~~l~~~~vlr~Gsg~~~E~LLm~~a~~~n~i~Pnk~~~~~~~~~~g~l~~setY~GG~V~~p~~GvY~~d~ 526 (1988)
+++.++++++|++++++++.|+|.++|++|+++|++.|+++||+..... .+.|.||.|++|++|+|.+
T Consensus 354 ~~~~e~s~vsg~~~~~~~~~~~~~~~~~~l~~~a~~~~~~iP~~~~~~~----------~~~~~Gg~V~~P~~Gly~~-- 421 (792)
T COG0417 354 PLLIELSRVSGLPLDDVTRAGSGARVEGLLLREAKRRGELIPNKEERPE----------RKKYKGGLVLEPEPGLYEN-- 421 (792)
T ss_pred HHHHHHHHHhCCCHHHHcccchhHHHHHHHHHHHhhcCEeccCccccch----------hhhcCCCEEccCCccccCc--
Confidence 8999999999999999999999999999999999999999999987532 2579999999999999888
Q ss_pred CCCccCChhHHHHHhhhhhhhhHHHHhHhcccccccccchHHHHHHHHHHHHhhccCCCcccCCeEEEEeccccchHHHH
Q 000161 527 PTSFKLDPSAYEQLLNNLDRDLQYAIKVEGKMDLESVSNYDEVKNAIMEKLLRLQEEPIREECPLIYHLDVAAMYPNIIL 606 (1988)
Q Consensus 527 ~~~f~~~~~~~~~l~~~~~~~l~~~~~~e~~~~~~~~~n~~~v~~~i~~~l~~l~~~p~~~~~p~V~~LDf~SLYPsII~ 606 (1988)
|++|||+|||||||+
T Consensus 422 -----------------------------------------------------------------V~vLDF~SLYPSII~ 436 (792)
T COG0417 422 -----------------------------------------------------------------VLVLDFSSLYPSIII 436 (792)
T ss_pred -----------------------------------------------------------------EEEEEccccChHHHH
Confidence 999999999999999
Q ss_pred hcCCCCCccccccccccccCCCCCCccccccccccccccccCCcchhhHhhhhcccccccCCCCCcccccccCchHHHHH
Q 000161 607 TNRLQPPSIVTDEVCTACDFNRPGKTCLRKLEWVWRGEIFMGKRSDYYHLKKQIESEFVDGTNGHLSKSFLDLPKMEQQS 686 (1988)
Q Consensus 607 t~NL~p~Tiv~~~~c~~c~~n~p~~~c~r~m~w~~~ge~~p~~~~ey~~i~~~l~~e~f~~~~~g~~~~~~~L~~~~q~~ 686 (1988)
+|||||+|++.+. | |+.. .| ++
T Consensus 437 ~~Ni~p~T~~~~~-~--~~~~------------------~~------------------~~------------------- 458 (792)
T COG0417 437 KYNISPDTLVEED-C--SDDY------------------SP------------------PG------------------- 458 (792)
T ss_pred HhCCCcceecCCC-c--cccc------------------cC------------------CC-------------------
Confidence 9999999997553 1 1000 00 00
Q ss_pred HHHHHHHHhhhhhcccccccccccccccccccccccchHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCChhhHHHHHH
Q 000161 687 RLKDRLKKYCQKAYKRVLDKPVTELREAGICMRENSFYVDTVRSFRDRRYEYKGLNKVWKGKLSEAKASGNSIKIQEAQD 766 (1988)
Q Consensus 687 ~lkkrl~~y~~kvy~k~~~~~~~~~r~~~icqre~~f~~~~lr~f~drR~~~K~l~K~~k~~~~~a~~~~d~~~~~e~~~ 766 (1988)
.....|+++.+|+|++|..|+++|.++|+.+|+++. +.
T Consensus 459 -------------------------~~~~~~~~~~G~lp~il~~L~~~R~~~K~~~k~~~~----------~~------- 496 (792)
T COG0417 459 -------------------------VGHGFCKREKGFLPEILEELLDRRDEIKKKMKKEKD----------PS------- 496 (792)
T ss_pred -------------------------CcccccccCCCchHHHHHHHHHHHHHHHHHhcccCC----------hH-------
Confidence 122457888899999999999999999999887542 22
Q ss_pred HHHHHHHHHHHHHHHhhhccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHcCCe-EEEccceeeEEcCCCCCcc
Q 000161 767 MVVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNARLLIEKIGKP-LELDTDGIWCVLPGSFPEN 845 (1988)
Q Consensus 767 ~~~lyds~QlA~K~ilNS~YGy~g~~~sR~ys~e~A~~VT~~Gr~iI~~a~~lve~~G~~-vygDTDSI~~~lp~~~pe~ 845 (1988)
+.++||++|+|||++|||||||+|+++|||||+|||++||++||++|+.|++++|+.|+. |||||||+||.+|+.. .+
T Consensus 497 e~~~~d~rQ~AlKvl~NS~YGy~G~~~~rf~~~e~a~~VT~~gR~ii~~t~~~ae~~G~~ViyGDTDSlfv~~~~~~-~~ 575 (792)
T COG0417 497 ERKLLDGRQLALKVLANSFYGYLGYSNSRFYCIECAESVTAFGREILRETKELAEEMGLRVIYGDTDSLFVTLPGAT-YE 575 (792)
T ss_pred HHHHHHHHHHHHHHHHhhccccccccCCccCCHHHHHHHHHHHHHHHHHHHHHHHHcCCEEEEECCceeEEEcCCCc-hH
Confidence 357999999999999999999999999999999999999999999999999999999976 7999999999999764 11
Q ss_pred cccccccccccccccccccccchhhhccccchhhhhccCCccccccccccceeEEeeeceeeeeecccccccCcccccce
Q 000161 846 FTFKTKDLKKKLTISYPCVMLNVDVARNNTNDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRY 925 (1988)
Q Consensus 846 ~~~k~~~g~k~i~~sy~~~~ln~~V~~~~tN~~y~~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRY 925 (1988)
.++ ++| +++ .+++|.+ .+.+|++|+||+|++|+||++ ||||
T Consensus 576 ea~--~~~-~~l--------------~~~vn~~---------------~~~~i~lE~e~~y~~~ll~~~-------KKRY 616 (792)
T COG0417 576 EAI--KIG-EEL--------------VEEVNER---------------LPSGIELEVEKVYKRFLLPTA-------KKRY 616 (792)
T ss_pred HHH--HHH-HHH--------------HHHHhhc---------------CCCCeEEEeeehhhhhhcccc-------ccce
Confidence 121 123 222 2444433 157899999999999999974 9999
Q ss_pred EEEcCCCCEEEEEeeeeccCChhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhhhhhc
Q 000161 926 AVFNDDGTLAELKGFEIKRRGELKLIKVFQAELFDKFLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADSELIDYISES 1005 (1988)
Q Consensus 926 a~~~~dG~~~e~KG~E~kRRd~~~liK~~q~~v~~~~L~g~~lee~~~~v~~v~~~~~d~L~~~~~~~~~~eLi~~i~~~ 1005 (1988)
||+..+|..+++||+|++|||||+|+|+||.++++.||.++++++|+ +++++.|.+. ++.+.+++++|+ ++
T Consensus 617 ag~~~~g~~~~vKG~e~~RrD~~~l~k~~q~~vl~~il~~~~~e~~~---~~~~~~v~~~--l~~~~~~~~~lv----i~ 687 (792)
T COG0417 617 AGLLEDGDKIEVKGLETVRRDWPELVKEFQREVLEVLLSGRDVEEAL---AKYVRDVIEK--LRNGEVPIEKLV----IS 687 (792)
T ss_pred EEEeccCCEEEEeeeEEEecCccHHHHHHHHHHHHHHHcCCCHHHHH---HHHHHHHHHH--HHcCCcCHHHhe----ee
Confidence 99999995459999999999999999999999999999999999995 3344555554 445688999998 89
Q ss_pred cccccChhhhCCCCChHHHHHHHHHhhcCCCcccCCCCeeEEEEEcCCCCCCCcccccchhhhcchHHHHHHHHHhhhcC
Q 000161 1006 STMSKSLADYGEQKSCAVTTARRLSDFLGDTMVKDKGLRCQYIVACEPQGTPVSERAVPVAIFETDAEIMKFYLRKWCKT 1085 (1988)
Q Consensus 1006 k~lsK~l~eY~~~k~~~v~~A~rl~e~lG~~~~~~~G~~i~YVI~~~p~g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~ 1085 (1988)
++++|.+++|.+ +.||+++|+|+++. | +.+.+|++|+|||++++ .++.+||.|+..+..+
T Consensus 688 k~l~k~~~ey~~-~~p~~~~a~~~~~~-g--~~~~~g~~i~Yvi~~~~--~~~~~ra~~~~~~~~~-------------- 747 (792)
T COG0417 688 KRLTRPLSEYKA-NKPHVVVAARLRKR-G--INVKPGDRIPYVIVKGK--GKLVERAEPPELVDEE-------------- 747 (792)
T ss_pred eeeccChhhhcC-CCcHHHHHHHHHhC-C--CCCCCCCEeEEEEecCC--CcccccccCceecccc--------------
Confidence 999999999997 45777777777764 5 89999999999999988 5899999999887643
Q ss_pred CCCCCCccccCHHHHHHhhhhhhhheeechhhhhhccCCCCCcchhhhhhhhhhccccccccccHHHhh
Q 000161 1086 SSDVGIRSIVDWSYYKQRLSSAIQKIITIPAAMQKVSNPVPRVVHPDWLYKKVREKEDKFRQRKLVDIF 1154 (1988)
Q Consensus 1086 ~~~~d~~~~iD~~YYierl~~~i~ki~~iPa~lq~~~npv~rv~~p~w~~~~~~~~~~~~kq~~l~~~f 1154 (1988)
+.+|||+||+++ |++||+.+.+. .-+..+..|.... |.++.++|
T Consensus 748 ------~~~iD~~YY~~~--------Ql~~~~~ril~--~i~~~~~~~~~~~---------q~~~~~~f 791 (792)
T COG0417 748 ------NSPIDYEYYITK--------QLLPALERILE--PIGGNFAELKGED---------QTGLFDSF 791 (792)
T ss_pred ------cccCCHHHHHhc--------cchHHHHHHHH--HhcccHhhhcccc---------cccHHhhc
Confidence 358999999999 99999888753 1233444444321 77888877
No 7
>PRK05761 DNA polymerase I; Reviewed
Probab=100.00 E-value=1.7e-106 Score=1058.14 Aligned_cols=725 Identities=24% Similarity=0.339 Sum_probs=564.3
Q ss_pred EEEeeeecccccccCCCCeEEEEEEEEecCCCeEEEEe---CCccEEEEEecCCChHHHHHHHHHhccccceeEEEEEEe
Q 000161 45 WLLTFASSSLEDEDTRKVYSCIDLYFVSQDGSTFKSKY---KFRPYFYAATKEKMEMDVEAYLRRRYESQIADIEILEKE 121 (1988)
Q Consensus 45 ~L~n~~~~~~~d~~~~~~~~~v~ly~~t~dG~~~~v~v---~f~PYFyv~~~~~~~~~v~~~l~~~~~~~i~~ie~v~k~ 121 (1988)
|||+..|.+. .++++|.+|+++ +| .+.+.. +|+||||+..+++ ++.+.....-++.+..++++.++
T Consensus 20 ~lld~~Y~~~------~~~~vi~l~~~~-~~-~~~~~~d~~gfkPYfy~~~~~~---~~~~~~~~~~~~~~~~~e~~~~~ 88 (787)
T PRK05761 20 YLLSVDYDGK------LGKAVVKLYDPE-TG-KIYKWYDRTGHKPYFLTDLDPD---EIDKIPKILRHPSFDHLEIVEKY 88 (787)
T ss_pred eEEEEEEecc------CCeeEEEEEecC-CC-eEEEEEcCCCCCCeEEecCChH---HHHhhhhhhcCCCeeeEEEEEEE
Confidence 9999999542 378999999985 55 444444 5999999987765 22221222224668899999999
Q ss_pred eCCCcCcCCCCCeEEEEEEEechhhHHHHHHHHHHHHHhhcccchhHHHHHHhhhcccCCCCcccccccccccccCCCcc
Q 000161 122 DLDLKNHLSGLHKSYLKISFDTVQQLMDVKKDLLHVVERNQAKFDAAEAYESILTGKREQRPQDFLDCIVDLREYDVPYH 201 (1988)
Q Consensus 122 dl~~~nhl~g~~~~~lKl~f~~~~~l~~vr~~l~~~~~~n~~~~~~~~~y~~~~~~~~~~~~~~~~~~i~~i~E~DI~~~ 201 (1988)
++ +.+...+++||++.+|.+++++|+.++.+ .++||+||+|+
T Consensus 89 ~~-----~~~~~~~~~kI~~~~p~~v~~~r~~~~~~---------------------------------~~~~EaDI~f~ 130 (787)
T PRK05761 89 DG-----LRDKKVKVTKIVVKDPLAVRRLRLSVRDI---------------------------------PRAWEADIKYE 130 (787)
T ss_pred ec-----cCCCcceEEEEEECCHHHHHHHHHHHHhh---------------------------------hhheeCCCChH
Confidence 86 55778999999999999999999988731 46899999999
Q ss_pred ceeeeecCCccceeEEEeeCCCC-------ceE--------EEeccc-----cCCCCceEEEEEEEEccCC-CCCCCCCC
Q 000161 202 IRFAIDNDVRCGQWYDVSISSTG-------PLL--------EKRVDL-----LQRAEVHVCAFDIETTKLP-LKFPDADY 260 (1988)
Q Consensus 202 ~R~~iD~~I~~g~W~~v~~~~~~-------~~i--------~~~~~~-----~~~p~lrvLsfDIEt~s~~-~~fPdp~~ 260 (1988)
.|||||++|.||.||.+...... .++ ....++ ...|+++++||||||.+.. ++||+
T Consensus 131 ~RyliD~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~P~lk~lsfDIE~~~~~~g~~P~--- 207 (787)
T PRK05761 131 FRYIYDNGLIPGMPYDVKNGLESVEPEILVEEIKKAFKDERKLAEDWLPIFEAPIPKIKRIAIDIEVYTPAKGRIPD--- 207 (787)
T ss_pred HheEEeCCCCCCceEEecccccccccccccccccccchhhhhhhhhhhhhccCCCCCcceEEEEEEeccCcCCCCCC---
Confidence 99999999999999998653210 000 001111 1579999999999999753 45554
Q ss_pred CeEEEEEEEEcCCceEEEcccccccccccccCCCCCCCCCceEEecCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHH
Q 000161 261 DIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWP 340 (1988)
Q Consensus 261 D~Ii~IS~~~~~~g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlP 340 (1988)
++|++||.+|+++|+++||||+ ||+++||||
T Consensus 208 -----------------------------------------------~~E~eLL~~f~~~i~~~dPdi~--yN~~~FDlP 238 (787)
T PRK05761 208 -----------------------------------------------DSEKELLAELFDIILEYPPVVT--FNGDNFDLP 238 (787)
T ss_pred -----------------------------------------------CCHHHHHHHHHHHHHhcCCEEE--EcCCcchHH
Confidence 4899999999999999999865 999999999
Q ss_pred HHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhc---c-----CCCCCCCCHHHHHHHHcCCCCCCCCh
Q 000161 341 FLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRD---S-----YLPQGSQGLKAVTKAKLGYDPLEVNP 412 (1988)
Q Consensus 341 yL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd---~-----~L~~~SysL~~Va~~~LG~~K~dvd~ 412 (1988)
||.+||+.+|++.. .+++. . ..|+.|+|++.+++.. . ..++.+|+|++||+++||++|++++
T Consensus 239 YL~~Ra~~lgi~~~-~~~~~-~-------~~~~~~iDl~~~~~~~~~~~y~~~~~~~~~~ysL~~Va~~~Lg~~K~~~~- 308 (787)
T PRK05761 239 YLYNRALKLGIPKE-EIPIE-P-------GRAGIHIDLYKFFQNKAVRSYAFYGKYRHREARLDAVGRALLGISKVELE- 308 (787)
T ss_pred HHHHHHHHhCCCch-hcccc-c-------CCCceEEechhheeecceeeeeccceeecccCChHHHHHHHhCCCccccc-
Confidence 99999999999753 22222 1 1256799999987642 1 1234589999999999999999998
Q ss_pred HHHHHHHhhChHHHHHHHHHhhHHHHHHHH--Hh-ccchHhhhhhhcCCChHHHhhhhhHHHHHHHHHHHHHHCCeeccC
Q 000161 413 EDMVRFAKEKPQMMASYSVSDAVATYYLYM--TY-VHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAYKANVICPN 489 (1988)
Q Consensus 413 ~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~--Kl-v~~~i~~La~i~~l~~~~vlr~Gsg~~~E~LLm~~a~~~n~i~Pn 489 (1988)
..|. ..++++|++||++||.+|++|.. +. +++++++||+++|+|+++|.|.|+|+++|++|+++|+++|+++|+
T Consensus 309 ~~i~---~~~~~~l~~Y~l~Da~l~~~L~~f~~~~~l~~~~elarit~lpl~~v~r~~~g~~i~~~l~~~a~~~~~liP~ 385 (787)
T PRK05761 309 TNIS---ELDLEELAEYNFRDAEITLKLTFFNNELVLKLILLLSRISKLPIEELSRATISTWISNLEYWEHRKRGWLIPW 385 (787)
T ss_pred cccc---ccCHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHCcCHHHHhccCHHHHHHHHHHHHHHhCCEeCCC
Confidence 4444 35889999999999999999952 33 789999999999999999999899999999999999999999999
Q ss_pred CCCCC--chhhhcccccCCCCCCcceeeeccCccccCCCCCCccCChhHHHHHhhhhhhhhHHHHhHhcccccccccchH
Q 000161 490 KHQSD--PEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFKLDPSAYEQLLNNLDRDLQYAIKVEGKMDLESVSNYD 567 (1988)
Q Consensus 490 k~~~~--~~~~~~g~l~~setY~GG~V~~p~~GvY~~d~~~~f~~~~~~~~~l~~~~~~~l~~~~~~e~~~~~~~~~n~~ 567 (1988)
+.... ............++|.||+|++|++|+|++
T Consensus 386 ~~~~~~~~~~~~~~~~~~~~~y~Gg~V~~P~~G~y~~------------------------------------------- 422 (787)
T PRK05761 386 KEDILRLDHEVYKKAIIKGKKYRGGLVFQPPPGIFFN------------------------------------------- 422 (787)
T ss_pred CccccccccccccccccccCCcCCcEEeccCCCceee-------------------------------------------
Confidence 87611 001112223345789999999999999988
Q ss_pred HHHHHHHHHHHhhccCCCcccCCeEEEEeccccchHHHHhcCCCCCccccccccccccCCCCCCcccccccccccccccc
Q 000161 568 EVKNAIMEKLLRLQEEPIREECPLIYHLDVAAMYPNIILTNRLQPPSIVTDEVCTACDFNRPGKTCLRKLEWVWRGEIFM 647 (1988)
Q Consensus 568 ~v~~~i~~~l~~l~~~p~~~~~p~V~~LDf~SLYPsII~t~NL~p~Tiv~~~~c~~c~~n~p~~~c~r~m~w~~~ge~~p 647 (1988)
|++|||+|||||||++|||||+|++.+. |. |..+. +
T Consensus 423 ------------------------V~vlDF~SLYPSIi~~~Ni~p~T~~~~~-~~-~~~~~------------------~ 458 (787)
T PRK05761 423 ------------------------VYVLDFASLYPSIIVKWNLSPETVRIPE-CK-CHYDD------------------E 458 (787)
T ss_pred ------------------------EEEeeecccchHHHHHhCCChhhccCcc-cc-ccccC------------------C
Confidence 9999999999999999999999997542 21 00000 0
Q ss_pred CCcchhhHhhhhcccccccCCCCCcccccccCchHHHHHHHHHHHHHhhhhhcccccccccccccccccccccccchHHH
Q 000161 648 GKRSDYYHLKKQIESEFVDGTNGHLSKSFLDLPKMEQQSRLKDRLKKYCQKAYKRVLDKPVTELREAGICMRENSFYVDT 727 (1988)
Q Consensus 648 ~~~~ey~~i~~~l~~e~f~~~~~g~~~~~~~L~~~~q~~~lkkrl~~y~~kvy~k~~~~~~~~~r~~~icqre~~f~~~~ 727 (1988)
++ + ....+|....++++.+
T Consensus 459 ------------------~~---~----------------------------------------~~~~~~~~~~gl~~~i 477 (787)
T PRK05761 459 ------------------VP---E----------------------------------------LGHSVCDDRPGLTSVL 477 (787)
T ss_pred ------------------CC---C----------------------------------------CCceeecCCCCchHHH
Confidence 00 0 0112355556789999
Q ss_pred HHHHHHHHHHHHhhhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCCCHHHHHHHHH
Q 000161 728 VRSFRDRRYEYKGLNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTY 807 (1988)
Q Consensus 728 lr~f~drR~~~K~l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~sR~ys~e~A~~VT~ 807 (1988)
++.+++.|.++|+.|+..+ ..|+. +..+||++|+|+|+++||+|||+|+++|||||+++|++||+
T Consensus 478 l~~l~~~R~~~k~~~~~~~--------~~~~~-------~~~~ld~~Q~AlKi~~NS~YGy~G~~~~r~~~~~~A~~IT~ 542 (787)
T PRK05761 478 VGLLRDFRVKIYKKKAKDP--------NLDEE-------RRAWYDVVQRALKVFLNASYGVFGAENFKLYRIEVAESITA 542 (787)
T ss_pred HHHHHHHHHHHHHHhhccC--------CCCHH-------HHHHHHHHHHhheeeeecccccccccCCCCCCHHHHHHHHH
Confidence 9999999999987766421 12333 45799999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHcCCe-EEEccceeeEEcCCCCCcccccccccccccccccccccccchhhhccccchhhhhccCCc
Q 000161 808 TGAKIIQNARLLIEKIGKP-LELDTDGIWCVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVDVARNNTNDQYQTLVDPV 886 (1988)
Q Consensus 808 ~Gr~iI~~a~~lve~~G~~-vygDTDSI~~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~V~~~~tN~~y~~l~~~~ 886 (1988)
+||++|+.|++++|+.|+. ||||||||||..|.. +. . +++ ...|
T Consensus 543 ~GR~~l~~t~~~ie~~g~~VIYGDTDSvfv~~~~~--~~-------~-~~l---------~~~i---------------- 587 (787)
T PRK05761 543 LGREILLSTKKKAEELGLKVLYGDTDSLFVWGPTK--ES-------L-EEL---------IKEI---------------- 587 (787)
T ss_pred HHHHHHHHHHHHHHHcCCEEEEEeCceEEEECCCH--HH-------H-HHH---------HHHH----------------
Confidence 9999999999999999988 699999999986531 10 0 111 1111
Q ss_pred cccccccccceeEEeeeceeeeeecccccccCcccccceEEEcCCCCEEEEEeeeeccCChhHHHHHHHHHHHHHHhCCC
Q 000161 887 SKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLAELKGFEIKRRGELKLIKVFQAELFDKFLHGS 966 (1988)
Q Consensus 887 ~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~~~dG~~~e~KG~E~kRRd~~~liK~~q~~v~~~~L~g~ 966 (1988)
.+..+|++|+||+|++++|. +.||||||+..||++ ++||+|++|||||+|+|++|+++++.+|.++
T Consensus 588 ------~~~~~i~LE~Ek~y~~~l~~-------~~KKrYag~~~dgki-~~KG~e~vRrD~~~~~k~~~~~vl~~ll~~~ 653 (787)
T PRK05761 588 ------EERTGIDLEVDKTYDWVAFS-------GLKKNYFGVLKDGKV-KIKGIVAKKRNTPEFVKELQREVLEVLKSIR 653 (787)
T ss_pred ------HHhCCCceEEEEEEEEEEEe-------cccceEEEEecCCeE-EEEEEEEEeCCchHHHHHHHHHHHHHHhcCC
Confidence 11235778888999999883 459999999999988 9999999999999999999999999999999
Q ss_pred CHHHHHHH---HHHHHHHHHHHHHhcCCCCCchhhhhhhhhccccccChhhhCCCCChHHHHHHHHHhhcCCCcccCCCC
Q 000161 967 TIEECYSA---VAAVANRWLDLLDNQGKDIADSELIDYISESSTMSKSLADYGEQKSCAVTTARRLSDFLGDTMVKDKGL 1043 (1988)
Q Consensus 967 ~lee~~~~---v~~v~~~~~d~L~~~~~~~~~~eLi~~i~~~k~lsK~l~eY~~~k~~~v~~A~rl~e~lG~~~~~~~G~ 1043 (1988)
+++++.+. +.+.++...+ +++.++++.++|+ ++++|+|++++|.++++|||++|+++++ .| ..+.+|+
T Consensus 654 ~~~~~~~~~~~~~~~v~~~~~--~l~~g~~~~~~lv----i~k~l~k~~~~Y~~~~~~hv~aa~~~~~-~g--~~~~~Gd 724 (787)
T PRK05761 654 SPEDVEKVKDEIEDVLKRYYE--KLRAKDYPLDELA----IRVRLSKPLDEYTKNTPQHVKAALQLRD-YG--VEVSPGD 724 (787)
T ss_pred ChhHHHHHHHHHHHHHHHHHH--HHHcCCCCHHHEE----EEeeecCCHHHhcCCCchHHHHHHHHHh-CC--CCCCCCC
Confidence 99855443 3333333333 4678899988888 8999999999999878999999999987 47 6678999
Q ss_pred eeEEEEEcCCCCCCCcccccchhhhcchHHHHHHHHHhhhcCCCCCCCccccCHHHHHHhhhhhhhheeechhhhhhccC
Q 000161 1044 RCQYIVACEPQGTPVSERAVPVAIFETDAEIMKFYLRKWCKTSSDVGIRSIVDWSYYKQRLSSAIQKIITIPAAMQKVSN 1123 (1988)
Q Consensus 1044 ~i~YVI~~~p~g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~~~~~d~~~~iD~~YYierl~~~i~ki~~iPa~lq~~~n 1123 (1988)
+|+|||++++. ++.|++.+. ...||++||+++ ++|++.|.
T Consensus 725 ~I~YVi~~~~~------~~~p~~~~~----------------------~~~iD~~yYi~~---------l~~~~~~i--- 764 (787)
T PRK05761 725 IISYVKVDDKR------GVKPVQLAK----------------------LSEIDVEKYIEL---------LRSALEQI--- 764 (787)
T ss_pred EEEEEEEcCCC------CCChhhhcc----------------------cCCcCHHHHHHH---------HHHHHHHH---
Confidence 99999998765 366775421 247999999975 66776665
Q ss_pred CCCCcchhhhhhhhhhccccccc-cccHHHhhh
Q 000161 1124 PVPRVVHPDWLYKKVREKEDKFR-QRKLVDIFS 1155 (1988)
Q Consensus 1124 pv~rv~~p~w~~~~~~~~~~~~k-q~~l~~~f~ 1155 (1988)
..-++..++.++ |++|.+||.
T Consensus 765 -----------l~~~g~~~~~l~~~~~l~~~~~ 786 (787)
T PRK05761 765 -----------LSALGVSWDDIRGTTRLDSFLS 786 (787)
T ss_pred -----------HHHhCCCHHHHcCcccHHHHhc
Confidence 334555566555 899999994
No 8
>PHA02528 43 DNA polymerase; Provisional
Probab=100.00 E-value=2.8e-96 Score=961.22 Aligned_cols=782 Identities=18% Similarity=0.236 Sum_probs=560.5
Q ss_pred EEecCCCeEEEEeCCccEEEEEecCCChHHHHHHHHHhccccceeEEEEEEeeCCCcCcCCCCCeEEEEEEEechhhHHH
Q 000161 70 FVSQDGSTFKSKYKFRPYFYAATKEKMEMDVEAYLRRRYESQIADIEILEKEDLDLKNHLSGLHKSYLKISFDTVQQLMD 149 (1988)
Q Consensus 70 ~~t~dG~~~~v~v~f~PYFyv~~~~~~~~~v~~~l~~~~~~~i~~ie~v~k~dl~~~nhl~g~~~~~lKl~f~~~~~l~~ 149 (1988)
++++||......+.|.|+.|+.+.++. . -+|+ ..+++..++|.+..++.+
T Consensus 19 ~~~~~g~~~~~~~~~~ptl~~~~~~~~--~--------------------~~~~--------~~~~~~~~~~~~~~~~~~ 68 (881)
T PHA02528 19 YIDDNGKERSRKVKYEPTLFVHANEES--K--------------------YKDI--------YGKNCRPKKFDSMRDARK 68 (881)
T ss_pred EEcCCCcEEEEeeccCcceEEecCCCc--c--------------------cccc--------CCCEEeEEECCCHHHHHH
Confidence 345689999999999999999887751 0 1121 467899999999999999
Q ss_pred HHHHHHHHHHhhcccchhHHHHHHhhhcccCCCCcccccccccccccCCCccceeeeecCCccceeEEEeeCCCCceEEE
Q 000161 150 VKKDLLHVVERNQAKFDAAEAYESILTGKREQRPQDFLDCIVDLREYDVPYHIRFAIDNDVRCGQWYDVSISSTGPLLEK 229 (1988)
Q Consensus 150 vr~~l~~~~~~n~~~~~~~~~y~~~~~~~~~~~~~~~~~~i~~i~E~DI~~~~R~~iD~~I~~g~W~~v~~~~~~~~i~~ 229 (1988)
+++.+.. ..++++ ++|+.|....|=+ ..
T Consensus 69 ~~~~~~~--------------------------------~~~~~~----------~merfi~~~~~~~--~~-------- 96 (881)
T PHA02528 69 WMKRMKD--------------------------------VGFEAL----------GMDDFKLQYISDT--YP-------- 96 (881)
T ss_pred HHHHHHh--------------------------------cCCcee----------ehhHHhhhhhhhh--cC--------
Confidence 8887773 122333 7788887776611 00
Q ss_pred eccccCCCCceEEEEEEEEccCCCCCCCCC--CCeEEEEEEEEcCCceEEEcccccccccc-cccCCCCC-CCCCceEEe
Q 000161 230 RVDLLQRAEVHVCAFDIETTKLPLKFPDAD--YDIIMMISYMLDGQGYLIINRECVGEDIE-DLEYTPKP-EFEGYFKVT 305 (1988)
Q Consensus 230 ~~~~~~~p~lrvLsfDIEt~s~~~~fPdp~--~D~Ii~IS~~~~~~g~li~nreivs~di~-~feytp~~-~~~g~f~V~ 305 (1988)
.+-....|+++++||||||++. .+||+|+ .|+|++||+..+++...++.. ++.... +..-.+.+ +......+.
T Consensus 97 ~~~~~~~p~lrv~s~DIE~~~~-~gfP~p~~~~d~IisIsl~~~~~~~~~v~~--~~~~~~~~~~~~~~~~~~~~~v~~~ 173 (881)
T PHA02528 97 GEIKYDRSKIRIANLDIEVTAE-DGFPDPEEAKYEIDAITHYDSIDDRFYVFD--LGSVEEWDAKGDEVPQEILDKVVYM 173 (881)
T ss_pred CCCCCCCCCccEEEEEEEECCC-CCCCCcccCCCcEEEEEEecCCCCEEEEEE--ecCcccccccCCcccccccCCeeEE
Confidence 1112345999999999999863 4799999 789999998654433221110 000000 00000000 112234566
Q ss_pred cCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHH-cCCCCC---cccCccc--c--CCCC----ceeeccc
Q 000161 306 NVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAH-HGFKMS---EELGFQC--D--KNQG----ECRAKFA 373 (1988)
Q Consensus 306 ~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~-lGi~l~---~~iG~~~--~--~~~g----~~~i~GR 373 (1988)
.+++|++||.+|+++|+++|||||+|||+++||||||.+||+. +|+... ..+|... . ...| .+.+.||
T Consensus 174 ~~~sE~eLL~~F~~~i~~~DPDII~GyNi~~FDlpYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~GR 253 (881)
T PHA02528 174 PFDTEREMLLEYINFWEENTPVIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISGI 253 (881)
T ss_pred EcCCHHHHHHHHHHHHHHhCCcEEEecCCccCCHHHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcce
Confidence 7999999999999999999999999999999999999999996 587642 2223220 0 1123 2578999
Q ss_pred eEechHHHHhhccCCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh-ccchHhhh
Q 000161 374 CHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY-VHPFIFSL 452 (1988)
Q Consensus 374 ihiDl~~~vkrd~~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl-v~~~i~~L 452 (1988)
+++|++.++++..+..++||+|++||+++||++|+++++++|.++|.++++++++||++||.+|++|+.++ ++++..++
T Consensus 254 v~lD~~dl~k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~kl~ll~~~~e~ 333 (881)
T PHA02528 254 SILDYLDLYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDKRKLIELVLSM 333 (881)
T ss_pred EEEeHHHHHHHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999998656557999999999999999999999999999999999999999999999999999997 78999999
Q ss_pred hhhcCCChHHHhhhhhHHHHHHHHHHHHHHCCeeccCCCCCCchhhhcccccCCCCCCcceeeeccCccccCCCCCCccC
Q 000161 453 ATIIPMSPDEVLRKGSGTLCEMLLMVQAYKANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFKL 532 (1988)
Q Consensus 453 a~i~~l~~~~vlr~Gsg~~~E~LLm~~a~~~n~i~Pnk~~~~~~~~~~g~l~~setY~GG~V~~p~~GvY~~d~~~~f~~ 532 (1988)
|+++|+++++|+ |++..++++++++++++|+++|++... ..++|.||+|++|+||+|++
T Consensus 334 ArltGi~l~~v~--sq~~~~~~lll~~~~r~g~viP~~~~~-----------~~~~y~Gg~V~eP~pGlY~~-------- 392 (881)
T PHA02528 334 AYYAKINFEDVF--SPIKTWDAIIFNSLKEEKIVIPENKSH-----------KKQKYAGAFVKEPVPGAYRW-------- 392 (881)
T ss_pred HHHhCCcHHHhc--chHhHHHHHHHHHHHHcCcccCCcccc-----------CCCCCCCcEEecCCCCcccc--------
Confidence 999999999995 678888999999999999999998653 24679999999999999977
Q ss_pred ChhHHHHHhhhhhhhhHHHHhHhcccccccccchHHHHHHHHHHHHhhccCCCcccCCeEEEEeccccchHHHHhcCCCC
Q 000161 533 DPSAYEQLLNNLDRDLQYAIKVEGKMDLESVSNYDEVKNAIMEKLLRLQEEPIREECPLIYHLDVAAMYPNIILTNRLQP 612 (1988)
Q Consensus 533 ~~~~~~~l~~~~~~~l~~~~~~e~~~~~~~~~n~~~v~~~i~~~l~~l~~~p~~~~~p~V~~LDf~SLYPsII~t~NL~p 612 (1988)
|++|||+|||||||++|||||
T Consensus 393 -----------------------------------------------------------VvVLDF~SLYPSIIiayNIcp 413 (881)
T PHA02528 393 -----------------------------------------------------------VVSFDLTSLYPSIIRQVNISP 413 (881)
T ss_pred -----------------------------------------------------------eEEEeccccChHHHHHhCCCh
Confidence 999999999999999999999
Q ss_pred CccccccccccccCCCCCCccccccccccccccccCCcchhhHhhhhcccccccCCCCCcccccccCchHHHHHHHHHHH
Q 000161 613 PSIVTDEVCTACDFNRPGKTCLRKLEWVWRGEIFMGKRSDYYHLKKQIESEFVDGTNGHLSKSFLDLPKMEQQSRLKDRL 692 (1988)
Q Consensus 613 ~Tiv~~~~c~~c~~n~p~~~c~r~m~w~~~ge~~p~~~~ey~~i~~~l~~e~f~~~~~g~~~~~~~L~~~~q~~~lkkrl 692 (1988)
+|++.... ..+... .+ .+..|.+.++| ..+++++
T Consensus 414 ~Tlv~~~~------~~~~~~---~~-----~~~~~~~~~~~-----------~~~p~G~--------------------- 447 (881)
T PHA02528 414 ETIAGTFH------VAPVHE---YI-----NKTAPRPSDEY-----------SCSPNGW--------------------- 447 (881)
T ss_pred hhcccccc------cccccc---cc-----ccccCCCCCce-----------eEcCCCC---------------------
Confidence 99986531 000000 00 00000000000 0011110
Q ss_pred HHhhhhhcccccccccccccccccccccccchHHHHHHHHHHHHHHHhhhhhhhhhhHHHhh------------------
Q 000161 693 KKYCQKAYKRVLDKPVTELREAGICMRENSFYVDTVRSFRDRRYEYKGLNKVWKGKLSEAKA------------------ 754 (1988)
Q Consensus 693 ~~y~~kvy~k~~~~~~~~~r~~~icqre~~f~~~~lr~f~drR~~~K~l~K~~k~~~~~a~~------------------ 754 (1988)
.| |....+++|.+|+.|++.|.++|+.||+.+.....++.
T Consensus 448 ------~F----------------~k~~~GiLP~iL~~Ll~~R~~~Kk~Mk~~~~~~~~~k~~l~~~~~~~~~~~~~~~~ 505 (881)
T PHA02528 448 ------MY----------------RKDIRGVIPTEIKKVFDQRKIYKKKMLAAERNAELIKTILEDLNDSVDTPIDVDYY 505 (881)
T ss_pred ------eE----------------eCCCCeehHHHHHHHHHHHHHHHHHHHhcccccccccccccccccccccccccccc
Confidence 11 11124699999999999999999999876532110000
Q ss_pred ----------------cCChhhHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCCCHHHHHHHHHHHHHHHHHHH-
Q 000161 755 ----------------SGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNAR- 817 (1988)
Q Consensus 755 ----------------~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~sR~ys~e~A~~VT~~Gr~iI~~a~- 817 (1988)
+.-...+++++.+..+||.+|+|+|+++||+|||+|+.++||||.++|++||++||.+|+.+.
T Consensus 506 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~d~~Q~A~KI~~NS~YG~lG~~~~r~y~~~~A~aiT~~Gr~~I~~i~~ 585 (881)
T PHA02528 506 FDFSDEFKAELKTLTKSSLKALLEECEKEIALCNTIQMARKILINSLYGALGNEHFRYYDLRNAEAITLFGQLAIQWIER 585 (881)
T ss_pred ccchhhhhhhhcccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHhhhhhccCcCccCCCHHHHHHHHHHhHHHHHHHHH
Confidence 000112345667889999999999999999999999999999999999999999999887555
Q ss_pred ---HHHHH----cC--CeEEEccceeeEEcCCCCCcccccccccccccccccccccccchhhhccccchhhhhccCCccc
Q 000161 818 ---LLIEK----IG--KPLELDTDGIWCVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVDVARNNTNDQYQTLVDPVSK 888 (1988)
Q Consensus 818 ---~lve~----~G--~~vygDTDSI~~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~V~~~~tN~~y~~l~~~~~~ 888 (1988)
+++++ .| ..||||||||||.+++.......-+...+ +.+ +++......+.+ +.+.+..|++++
T Consensus 586 ~~~e~l~~~~~~~g~~~VIYGDTDSvfV~~~~~~~~~~~~~~~~~-~~l-v~~~~~~~~~~l-~~~~~~~~~el~----- 657 (881)
T PHA02528 586 KMNEYLNKLCKTEDEDYVIYGDTDSIYVNLDPLVEKVGEDKFKDT-NHW-VDFLDKFCKERM-EPYIDSSYRELC----- 657 (881)
T ss_pred HHHHHHHHhhcccCCcEEEEEcCCeeEEEeCCcchhhhhccchhH-HHH-HHHHHHHHHHhh-hhhhhHHHHHHH-----
Confidence 44443 45 34799999999998754211100000122 221 111111111122 235566666653
Q ss_pred cccccccceeEEeeeceeeeeecccccccCcccccceEEEc--CCC-----CEEEEEeeeeccCChhHHHHHHHHHHHHH
Q 000161 889 TYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFN--DDG-----TLAELKGFEIKRRGELKLIKVFQAELFDK 961 (1988)
Q Consensus 889 ~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~~--~dG-----~~~e~KG~E~kRRd~~~liK~~q~~v~~~ 961 (1988)
+|...-...++++.++.|.+.|+.+ ||||||.. .+| ..+++||+|++|||||+++|++|+++++.
T Consensus 658 e~~~~~~~~~~m~~ek~~~~~~~~s--------KKRYAgl~~~~~g~~~~~~kl~~kGlEtvRsD~~~lak~~q~~vi~~ 729 (881)
T PHA02528 658 EYMNNYEHLMFMDREAIAGPGFWTA--------KKRYALNVWDSEGTRYAEPKLKIMGIETQRSSTPKAVQKALKEAIRR 729 (881)
T ss_pred HHHhhhccccchhHHHHhhHhhhhc--------cccEEEEeccCCCcccCCCeEEEecceeeecchHHHHHHHHHHHHHH
Confidence 2322222235666669999998864 99999964 433 23499999999999999999999999999
Q ss_pred HhCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhhhhhccccccChhhh-------CCCCChHHHHHH---HHHh
Q 000161 962 FLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADSELIDYISESSTMSKSLADY-------GEQKSCAVTTAR---RLSD 1031 (1988)
Q Consensus 962 ~L~g~~lee~~~~v~~v~~~~~d~L~~~~~~~~~~eLi~~i~~~k~lsK~l~eY-------~~~k~~~v~~A~---rl~e 1031 (1988)
+|.+.. +++.+.|++++.+. +. ++.++++ .+++.|++++| .+..||||.+|+ ++.+
T Consensus 730 Il~~~~-e~~~~yvk~~i~~~------~~--~d~~~i~-----~~~~~~~l~~Y~~~~~~y~k~~pphV~aA~~~~~~~~ 795 (881)
T PHA02528 730 ILQEGE-ESLQEYIKEFEKEF------RK--LDYEEIA-----FVSSANNIAKYSDDKGIPGKGCPIHIRGALLYNRAVK 795 (881)
T ss_pred HHhCCc-HhHHHHHHHHHHHH------Hc--CCHHHEE-----eeeccCCHHHhcccccccccCCCHHHHHHHHHHHHHh
Confidence 999866 77888888777642 23 6766665 45899999997 344689999999 7776
Q ss_pred h-cCCCcccCCCCeeEEEEEcCCCCCCCcccccchhhhcchHHHHHHHHHhhhcCCCCCCCcccc--CHHHHHHhhhhhh
Q 000161 1032 F-LGDTMVKDKGLRCQYIVACEPQGTPVSERAVPVAIFETDAEIMKFYLRKWCKTSSDVGIRSIV--DWSYYKQRLSSAI 1108 (1988)
Q Consensus 1032 ~-lG~~~~~~~G~~i~YVI~~~p~g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~~~~~d~~~~i--D~~YYierl~~~i 1108 (1988)
. .|. ...+.|++|.||++++++ |+++||+|...... +...+ |.+|||+. ...+
T Consensus 796 ~~~g~-~~~~~G~kI~~v~lk~~~--~~~~~~~~~~~~~~--------------------~p~~~~~d~~~~iD~-~~~~ 851 (881)
T PHA02528 796 GTLGY-PPIQEGEKVMVLPLKEPN--PIGENCIAWPSGTE--------------------LPKEIRSDLLKWVDY-NLLF 851 (881)
T ss_pred hhcCC-cccCCCCEEEEEEEeCCC--CCCCceEecccccc--------------------CHHHHhhchhheech-hhhh
Confidence 4 563 377899999999999865 99999999865421 12356 99999998 1112
Q ss_pred hheeechhhhhhccCCCCCcchhhhhhhhhhccccccccccHHHhhh
Q 000161 1109 QKIITIPAAMQKVSNPVPRVVHPDWLYKKVREKEDKFRQRKLVDIFS 1155 (1988)
Q Consensus 1109 ~ki~~iPa~lq~~~npv~rv~~p~w~~~~~~~~~~~~kq~~l~~~f~ 1155 (1988)
+|- +||+++++ .+.++..++ +|.+|.+||.
T Consensus 852 ~k~-~~~p~~~i--------------l~~~g~~~~--~~~~l~~~f~ 881 (881)
T PHA02528 852 EKS-FIKPLKNI--------------TEAIGWDYE--KKASLEDLFG 881 (881)
T ss_pred hhh-hhhHHHHH--------------HHHhCCCcc--ccCcHHHhcC
Confidence 221 89999887 445565554 7999999993
No 9
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=100.00 E-value=3.9e-94 Score=892.65 Aligned_cols=684 Identities=22% Similarity=0.272 Sum_probs=545.2
Q ss_pred ccccccccCCCccceeeeecCCccceeEEEeeCCC--------CceEEEe---------ccccCCCCceEEEEEEEEccC
Q 000161 189 CIVDLREYDVPYHIRFAIDNDVRCGQWYDVSISST--------GPLLEKR---------VDLLQRAEVHVCAFDIETTKL 251 (1988)
Q Consensus 189 ~i~~i~E~DI~~~~R~~iD~~I~~g~W~~v~~~~~--------~~~i~~~---------~~~~~~p~lrvLsfDIEt~s~ 251 (1988)
....++-.+.....||++++.|+|+||++|..... .+++... ....++|+++++|+.|+|.-+
T Consensus 462 sfshvfgt~tn~lE~fll~rKimGPCWlkv~~~s~~~~~~SwCk~Ev~v~sP~nI~~~~~~~a~~Ppl~llsL~i~T~~N 541 (1429)
T KOG0970|consen 462 SFSHVFGTNTNPLERFLLSRKIMGPCWLKVKGYSDPPRNASWCKVEVTVKSPQNITVVCSKKAPPPPLTLLSLNIRTSMN 541 (1429)
T ss_pred hHHHHhccCccHHHHHHHhccccCceEEEeecCCCCCCCccceeeEEEecCCcceEEeecCCCCCCCeeEEEeeeeehhc
Confidence 34467788889999999999999999999986442 2233221 122569999999999999986
Q ss_pred CCCCCCCCCCeEEEEEEEEcCCceEEEccccccccc--ccccC--C-CCCCCCCc---------eEEecCCCHHHHHHHH
Q 000161 252 PLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDI--EDLEY--T-PKPEFEGY---------FKVTNVNNEIELLRLW 317 (1988)
Q Consensus 252 ~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~di--~~fey--t-p~~~~~g~---------f~V~~~~dE~eLL~~F 317 (1988)
+ .-+.++|+|||......-.+. +.. .+.. ..|.- . |.-.++++ ..|..+.+|++||..|
T Consensus 542 ~----k~~~~Eiv~is~l~~~~~~id--~p~-p~~~~~~~~c~l~rP~~~~fP~g~~ela~~k~~~v~~~~sErALLs~f 614 (1429)
T KOG0970|consen 542 P----KQNKNEIVMISMLCFHNFSID--KPA-PAPAFPRHFCVLTRPPGTSFPLGLKELAKQKLSKVVLHNSERALLSHF 614 (1429)
T ss_pred c----ccchhhhhhhhhhhccccccc--CCC-CCCcccCcceeEecCCCCcCCchHHHHHHhccCceEEecCHHHHHHHH
Confidence 4 234589999997643211000 000 0000 00000 0 11112221 1377889999999999
Q ss_pred HHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCC----------CCc-eeeccceEechHHHHhhcc
Q 000161 318 FAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKN----------QGE-CRAKFACHLDCFAWVKRDS 386 (1988)
Q Consensus 318 ~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~----------~g~-~~i~GRihiDl~~~vkrd~ 386 (1988)
+..++..|||+|||||+.+|++..|..|+..++++.|++||+. +++ .|+ +.+.||+.||+ ..+.++.
T Consensus 615 la~~~~~dpD~iVgHn~~~~~l~VLl~R~~~~Kip~WS~IgRL-rrS~~~kfg~~s~~~e~~~~aGRl~CD~-~~~a~~l 692 (1429)
T KOG0970|consen 615 LAMLNKEDPDVIVGHNIQGFYLDVLLSRLHALKIPNWSSIGRL-RRSWPPKFGRSSSFGEFFIIAGRLMCDL-NLAAREL 692 (1429)
T ss_pred HHHhhccCCCEEEEeccccchHHHHHHHHHHhcCcchhhhhhh-hhccccccCCcccccccccccceEEeeh-HHHHHhh
Confidence 9999999999999999999999999999999999999999987 443 233 34789999999 6665543
Q ss_pred CCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhh--ChHHHHHHHHHhhHHHHHHHHHh-ccchHhhhhhhcCCChHHH
Q 000161 387 YLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKE--KPQMMASYSVSDAVATYYLYMTY-VHPFIFSLATIIPMSPDEV 463 (1988)
Q Consensus 387 ~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~--~~~~La~Y~l~Da~lt~~L~~Kl-v~~~i~~La~i~~l~~~~v 463 (1988)
.+..||+|.++++..|+..+.+++..++.++|.+ +.-.+++.+++|+.+.++|+.++ ++|+..+|++|.|..+.+.
T Consensus 693 -ik~~S~~LseL~q~~l~~eR~~i~~~~i~~~y~~s~~L~~ll~~~~~d~~~~l~i~~~l~~LpLs~qlTnIaGni~~RT 771 (1429)
T KOG0970|consen 693 -IKAQSYSLSELSQQILKEERKEINANEIPKMYEDSKSLTYLLEHTITDAELILQIMFRLNALPLSKQLTNIAGNIWART 771 (1429)
T ss_pred -hccccccHHHHHHHHHhhhcccCCHhHhhhhccChHHHHHHHHHHhHHHHHHHHHHHHhccchHHHHHHHHHhHHHHHH
Confidence 3568999999999999999999999999999874 35578899999999999999999 8999999999999999999
Q ss_pred hhhhhHHHHHHHHHHHHHHCCeeccCCCCCCchh-----hhcc-----cccCCCCCCcceeeeccCccccCCCCCCccCC
Q 000161 464 LRKGSGTLCEMLLMVQAYKANVICPNKHQSDPEK-----FYRN-----HLLESETYIGGHVECLESGVFRSDLPTSFKLD 533 (1988)
Q Consensus 464 lr~Gsg~~~E~LLm~~a~~~n~i~Pnk~~~~~~~-----~~~g-----~l~~setY~GG~V~~p~~GvY~~d~~~~f~~~ 533 (1988)
|..|...+.|++|+++++++|||+|.|....... .-+| .-....+|.||+|++|+.|+|..
T Consensus 772 L~G~RAeRnEylLLH~F~~~~fIvPDK~~ssk~~~d~d~~~eg~d~~~~~KKk~kYaGGLVlePkkGlYe~--------- 842 (1429)
T KOG0970|consen 772 LQGGRAERNEYLLLHEFYKNGFIVPDKQNSSKAQKDADETEEGADEPSKGKKKAKYAGGLVLEPKKGLYEK--------- 842 (1429)
T ss_pred hhccchhhhhHHHHHHHHHCCccCCCccchhhhhhhhhhhhccccccccccccccccCceeeccccchhhh---------
Confidence 9999999999999999999999999998322110 0111 11134789999999999999887
Q ss_pred hhHHHHHhhhhhhhhHHHHhHhcccccccccchHHHHHHHHHHHHhhccCCCcccCCeEEEEeccccchHHHHhcCCCCC
Q 000161 534 PSAYEQLLNNLDRDLQYAIKVEGKMDLESVSNYDEVKNAIMEKLLRLQEEPIREECPLIYHLDVAAMYPNIILTNRLQPP 613 (1988)
Q Consensus 534 ~~~~~~l~~~~~~~l~~~~~~e~~~~~~~~~n~~~v~~~i~~~l~~l~~~p~~~~~p~V~~LDf~SLYPsII~t~NL~p~ 613 (1988)
+|.+|||+|||||||+.||||++
T Consensus 843 ---------------------------------------------------------~VLllDFNSLYPSIIQEyNICFT 865 (1429)
T KOG0970|consen 843 ---------------------------------------------------------YVLLLDFNSLYPSIIQEYNICFT 865 (1429)
T ss_pred ---------------------------------------------------------eeEEEEccccchHHHHHhhheee
Confidence 69999999999999999999999
Q ss_pred ccccccccccccCCCCCCccccccccccccccccCCcchhhHhhhhcccccccCCCCCcccccccCchHHHHHHHHHHHH
Q 000161 614 SIVTDEVCTACDFNRPGKTCLRKLEWVWRGEIFMGKRSDYYHLKKQIESEFVDGTNGHLSKSFLDLPKMEQQSRLKDRLK 693 (1988)
Q Consensus 614 Tiv~~~~c~~c~~n~p~~~c~r~m~w~~~ge~~p~~~~ey~~i~~~l~~e~f~~~~~g~~~~~~~L~~~~q~~~lkkrl~ 693 (1988)
|+-.. +.. ++..| .||.+.
T Consensus 866 Tv~~~--------~~d-------------~Dqlp------------------------------~lP~s~---------- 884 (1429)
T KOG0970|consen 866 TVDRF--------SVD-------------SDQLP------------------------------RLPSSS---------- 884 (1429)
T ss_pred ecccc--------ccC-------------cccCC------------------------------CCCCcc----------
Confidence 98431 000 11111 112100
Q ss_pred HhhhhhcccccccccccccccccccccccchHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHH
Q 000161 694 KYCQKAYKRVLDKPVTELREAGICMRENSFYVDTVRSFRDRRYEYKGLNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDS 773 (1988)
Q Consensus 694 ~y~~kvy~k~~~~~~~~~r~~~icqre~~f~~~~lr~f~drR~~~K~l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds 773 (1988)
-+.+|+|+.|+.|++||.++|++||+ +.+|.+ ...||.
T Consensus 885 -------------------------~~~GiLPr~l~~LVerRk~VK~lMK~----------~~tp~~-------~~q~DI 922 (1429)
T KOG0970|consen 885 -------------------------SEQGILPRLLENLVERRKEVKKLMKQ----------ELTPEK-------RKQLDI 922 (1429)
T ss_pred -------------------------ccCCccHHHHHHHHHHHHHHHHHHhc----------CCCHHH-------HHhhhH
Confidence 13469999999999999999999986 245654 478999
Q ss_pred HHHHHHHHhhhccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHcCCe-EEEccceeeEEcCCCCCccccccccc
Q 000161 774 LQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNARLLIEKIGKP-LELDTDGIWCVLPGSFPENFTFKTKD 852 (1988)
Q Consensus 774 ~QlA~K~ilNS~YGy~g~~~sR~ys~e~A~~VT~~Gr~iI~~a~~lve~~G~~-vygDTDSI~~~lp~~~pe~~~~k~~~ 852 (1988)
+|.|+|++|||+||++|+.+||||..+||+.||+.||+||++|+++||++|+. |||||||||+.-... .-+.++ +.
T Consensus 923 RQqALKLTANSMYGCLGf~~SRFyAkpLAaLVT~KGReiLm~Tk~Lve~mnl~VIYGDTDSvMInTn~t-d~~~a~--ki 999 (1429)
T KOG0970|consen 923 RQQALKLTANSMYGCLGFVNSRFYAKPLAALVTYKGREILMNTKDLVEKMNLEVIYGDTDSVMINTNST-DYEEAL--KI 999 (1429)
T ss_pred HHHHHhhhhccchhhcccccchhhhhhHHHHHhhhhHHHHHHHHHHHHhcCeEEEEcCCceEEeeCCCc-cHHHHH--HH
Confidence 99999999999999999999999999999999999999999999999999998 699999999975532 222233 34
Q ss_pred ccccccccccccccchhhhccccchhhhhccCCccccccccccceeEEeeeceeeeeecccccccCcccccceEEE--cC
Q 000161 853 LKKKLTISYPCVMLNVDVARNNTNDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVF--ND 930 (1988)
Q Consensus 853 g~k~i~~sy~~~~ln~~V~~~~tN~~y~~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~--~~ 930 (1988)
| .++ ++-+|..|+.| |+++||+|++|+|.+ |||||++ +.
T Consensus 1000 g-~~~--------------k~~VNkrYk~L----------------EIDiDgVfkrlLLlk--------KKKYAAL~l~~ 1040 (1429)
T KOG0970|consen 1000 G-NEF--------------KQAVNKRYKLL----------------EIDIDGVFKRLLLLK--------KKKYAALTLNK 1040 (1429)
T ss_pred H-HHH--------------HHHHHHHhhhh----------------eeehhHHHHHHHHHh--------hhhheeEEecC
Confidence 4 333 23457777665 899999999999965 9999995 78
Q ss_pred CCC---EEEEEeeeeccCChhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhhhhhccc
Q 000161 931 DGT---LAELKGFEIKRRGELKLIKVFQAELFDKFLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADSELIDYISESST 1007 (1988)
Q Consensus 931 dG~---~~e~KG~E~kRRd~~~liK~~q~~v~~~~L~g~~lee~~~~v~~v~~~~~d~L~~~~~~~~~~eLi~~i~~~k~ 1007 (1988)
||+ ..|+||+++||||||+|+|++..-|++.+|.+.+.++++++|.+.++.... ++.+|.+|.++++ |+++
T Consensus 1041 dgkg~~~~E~KGLDmvRRDwc~Lake~g~~vLd~ILs~~~~ee~veaI~d~L~kI~~--k~~~G~vpl~~fv----I~k~ 1114 (1429)
T KOG0970|consen 1041 DGKGVERIEVKGLDMVRRDWCQLAKEIGKAVLDKILSDKSREEIVEAIHDELRKISE--KLENGNVPLEKFV----ITKT 1114 (1429)
T ss_pred CCCCceeeeecccchhHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH--HHhcCccchhhee----eehh
Confidence 886 569999999999999999999999999999999999999999877766554 5678999988877 8999
Q ss_pred cccChhhhCCCC-ChHHHHHHHHHhhcCCCcccCCCCeeEEEEEc-CCCCCCCcccccchhhhcchHHHHHHHHHhhhcC
Q 000161 1008 MSKSLADYGEQK-SCAVTTARRLSDFLGDTMVKDKGLRCQYIVAC-EPQGTPVSERAVPVAIFETDAEIMKFYLRKWCKT 1085 (1988)
Q Consensus 1008 lsK~l~eY~~~k-~~~v~~A~rl~e~lG~~~~~~~G~~i~YVI~~-~p~g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~ 1085 (1988)
|+|+|++|.+.| .|||++|.||.++ | .+.+..|+.|+|||++ .+.+.|.++||+++.....+
T Consensus 1115 LtK~Pe~Yp~~kslPhVqVALrm~~~-G-~~~~k~gDvV~yVI~~~D~~~~~As~RAyh~~e~~~~-------------- 1178 (1429)
T KOG0970|consen 1115 LTKNPEAYPDGKSLPHVQVALRMNKR-G-KRKVKAGDVVPYVICKEDGIDNPASERAYHPDEVMPD-------------- 1178 (1429)
T ss_pred ccCChhhCCCcccCcHHHHHHHHHHh-c-CcccccCCeEEEEEecCCCCCCchhhcccChHhhCcc--------------
Confidence 999999999876 4999999999996 5 3788999999999995 45567888999999876653
Q ss_pred CCCCCCccccCHHHHHHhhhhhhhheeechhhhhhccCCCCCc
Q 000161 1086 SSDVGIRSIVDWSYYKQRLSSAIQKIITIPAAMQKVSNPVPRV 1128 (1988)
Q Consensus 1086 ~~~~d~~~~iD~~YYierl~~~i~ki~~iPa~lq~~~npv~rv 1128 (1988)
+.++.||++||+.+ ||+|++.|.| .||.+.
T Consensus 1179 ----~~~l~iD~~YYLa~--------QIhPvV~Rlv-e~Iegt 1208 (1429)
T KOG0970|consen 1179 ----EDNLAIDYNYYLAQ--------QIHPVVERLV-EPIEGT 1208 (1429)
T ss_pred ----CcceeechhhHhhh--------hcchhHHHHh-hhhccc
Confidence 23589999999999 9999999976 466654
No 10
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=8.4e-91 Score=944.06 Aligned_cols=773 Identities=19% Similarity=0.220 Sum_probs=580.6
Q ss_pred EEEEEEEEecCCCeEEEEe-CC-ccEEEEEecCCC----hH------HHHH----HHHHhc---cccceeEEEEEEe-eC
Q 000161 64 SCIDLYFVSQDGSTFKSKY-KF-RPYFYAATKEKM----EM------DVEA----YLRRRY---ESQIADIEILEKE-DL 123 (1988)
Q Consensus 64 ~~v~ly~~t~dG~~~~v~v-~f-~PYFyv~~~~~~----~~------~v~~----~l~~~~---~~~i~~ie~v~k~-dl 123 (1988)
..+.+||+..+|.++++.+ ++ +..|++...... .. .+.. +....+ ...-.+...|.+. .-
T Consensus 323 G~~~lfGr~~~~~s~~~~v~g~~R~~~~l~~~Grv~~D~~~~~~~~~~l~~y~le~vs~~~lg~~k~dv~~k~I~~~~~~ 402 (1172)
T TIGR00592 323 GVVLLFGRDVDHVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIAKKYEF 402 (1172)
T ss_pred CeEEEecccCCceeEEEEECCeeeeeEEeeccccccccccchhcccccHHHHHHHHHHHHHhhcCcCceeeEEehhhccC
Confidence 4567888766788899988 75 588888665311 00 0111 111111 1111122223221 00
Q ss_pred CCcCcCCCCCeEEEEEEEechhhHHHHHHHHHHHHHhhcccchhHHHHHHhhhcccCCCCcccccccccccccCCCccce
Q 000161 124 DLKNHLSGLHKSYLKISFDTVQQLMDVKKDLLHVVERNQAKFDAAEAYESILTGKREQRPQDFLDCIVDLREYDVPYHIR 203 (1988)
Q Consensus 124 ~~~nhl~g~~~~~lKl~f~~~~~l~~vr~~l~~~~~~n~~~~~~~~~y~~~~~~~~~~~~~~~~~~i~~i~E~DI~~~~R 203 (1988)
..+.-+......++++.+.....+..+......+ ....+..+|+.+.....|
T Consensus 403 ~~~~~~v~y~~~~lkv~y~l~~~~~~l~~l~~~~----------------------------~g~~~~~vf~~n~g~~er 454 (1172)
T TIGR00592 403 EAPDIDAPYSSEYLEVTYELGKEFAPMEALPSDL----------------------------KGQTFWHVFGSNTGNLER 454 (1172)
T ss_pred CCCccCCcCCcceEEEEEccCccchhhhhhhhhc----------------------------cCCcchheeccCHHHHHH
Confidence 0000022234688899888776665554433310 112445789999999999
Q ss_pred eeeecCCccceeEEEeeCCC---------CceEEEe-cc------ccCCCCceEEEEEEEEccCCCCCCCCCCCeEEEEE
Q 000161 204 FAIDNDVRCGQWYDVSISST---------GPLLEKR-VD------LLQRAEVHVCAFDIETTKLPLKFPDADYDIIMMIS 267 (1988)
Q Consensus 204 ~~iD~~I~~g~W~~v~~~~~---------~~~i~~~-~~------~~~~p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS 267 (1988)
|++++++.+.+|+.+..... +.+.... +. ...+||+.+|+|+||+ .||....++|++||
T Consensus 455 fll~rki~gp~WL~i~~p~~~~~~~~S~c~yEga~v~~p~v~~g~~~~~pPl~vLdFsi~S-----lyPsi~~~~nl~iS 529 (1172)
T TIGR00592 455 FLLLRKIKGPCWLAVKGPDELEYPRRSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMKS-----LNPSIIRNEIVSIP 529 (1172)
T ss_pred HHhcCCCCCCceEEeCCCcccCcCCccccceEEEEecCccccccccCCCCCeEEEEeeeEE-----ecCccccCceEEEE
Confidence 99999999999999964321 1222211 11 1247899999999992 47888889999999
Q ss_pred EEEcCCceEEEcccccccccc--ccc--CCCC--C-------CCCC--ceEEecCCCHHHHHHHHHHHHHhhCCCEEEee
Q 000161 268 YMLDGQGYLIINRECVGEDIE--DLE--YTPK--P-------EFEG--YFKVTNVNNEIELLRLWFAHMQEVKPGIYVTY 332 (1988)
Q Consensus 268 ~~~~~~g~li~nreivs~di~--~fe--ytp~--~-------~~~g--~f~V~~~~dE~eLL~~F~~~I~~~DPDIIvGY 332 (1988)
..+...+.+- ..-+.+.. .+. ..|. . ...| +..|..+.+|++||.+|++.++++|||+++||
T Consensus 530 ~~v~~~~~~d---~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~L~~~~sEr~lL~~fl~~~~~~DPDii~g~ 606 (1172)
T TIGR00592 530 DTLHREFALD---KPPPEPPYDVHPCVGTRPKDCSFPLDLKGEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGH 606 (1172)
T ss_pred EEEeeccccc---CCCCCCccceEEEEEEccCCCCCCchhhhhhhccCCcEEEEecCHHHHHHHHHHHHHhcCCCEEEEE
Confidence 8875432100 00000000 000 0010 0 0011 23577899999999999999999999999999
Q ss_pred CcccCCHHHHHHHHHHcCCCCCcccCccccCC--CC---ceeeccceEechHHHHhhccCCCCCCCCHHHHHHHHcCCCC
Q 000161 333 NGDYFDWPFLETRAAHHGFKMSEELGFQCDKN--QG---ECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDP 407 (1988)
Q Consensus 333 Ngd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~--~g---~~~i~GRihiDl~~~vkrd~~L~~~SysL~~Va~~~LG~~K 407 (1988)
|+.+|||+||.+||+.++++.|+++|+. +++ .| ...+.||+++|++..+++... ..||+|++||+++||.+|
T Consensus 607 n~~qfdlkvl~nR~~~l~i~~~~~~Gr~-~~~~~~~~~~~~~~~Grl~~D~~~~~k~~~~--~~sy~L~~v~~~~L~~~k 683 (1172)
T TIGR00592 607 DYQQRALKVLANRINDLKIPTWSKIGRL-RRSPKFGRRFGERTCGRMICDVEISAKELIR--CKSYDLSELVQQILKTER 683 (1172)
T ss_pred cccCccHHHHHHHHHHcCCCcccccCcc-ccCCCccccccceECCEEEEEHHHHHHHHhC--cCCCCHHHHHHHHhCCCC
Confidence 9999999999999999999999999976 332 11 134899999999999988654 589999999999999999
Q ss_pred CCCChHHHHHHHhh--ChHHHHHHHHHhhHHHHHHHHHh-ccchHhhhhhhcCCChHHHhhhhhHHHHHHHHHHHHHHCC
Q 000161 408 LEVNPEDMVRFAKE--KPQMMASYSVSDAVATYYLYMTY-VHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAYKAN 484 (1988)
Q Consensus 408 ~dvd~~~i~~~~~~--~~~~La~Y~l~Da~lt~~L~~Kl-v~~~i~~La~i~~l~~~~vlr~Gsg~~~E~LLm~~a~~~n 484 (1988)
.++++++|..+|.+ ....++.||++||.++++|+.++ ++|+..++|+++|.++..++.+|++.++|++|+++++++|
T Consensus 684 ~~~~~~~i~~~~~~~~~~~~~~~y~~~Da~l~~~L~~~l~~l~l~~~lt~i~G~~~~~~l~~~~~~r~e~lll~~~~~~~ 763 (1172)
T TIGR00592 684 KVIPIDNINNMYSESSSLTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENN 763 (1172)
T ss_pred cccCHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhCCcHHhccCCchHHHHHHHHHHHHHhCC
Confidence 99999999999873 35789999999999999999999 8999999999999999999999999999999999999999
Q ss_pred eeccCCCCCCchh-h------hcccc-cCCCCCCcceeeeccCccccCCCCCCccCChhHHHHHhhhhhhhhHHHHhHhc
Q 000161 485 VICPNKHQSDPEK-F------YRNHL-LESETYIGGHVECLESGVFRSDLPTSFKLDPSAYEQLLNNLDRDLQYAIKVEG 556 (1988)
Q Consensus 485 ~i~Pnk~~~~~~~-~------~~g~l-~~setY~GG~V~~p~~GvY~~d~~~~f~~~~~~~~~l~~~~~~~l~~~~~~e~ 556 (1988)
+++|++....... . .+|.. -...+|.||+|++|++|+|++
T Consensus 764 ~i~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~Gg~V~eP~~G~y~~-------------------------------- 811 (1172)
T TIGR00592 764 YIVPDKQIFRKQQKLGDEDEEIDGYKKGKKAAYAGGLVLEPKVGLYDK-------------------------------- 811 (1172)
T ss_pred EEccCccccccccccccccccccccccccccCcCCCeEecCCCCcccC--------------------------------
Confidence 9999986432100 0 00100 023689999999999999987
Q ss_pred ccccccccchHHHHHHHHHHHHhhccCCCcccCCeEEEEeccccchHHHHhcCCCCCccccccccccccCCCCCCccccc
Q 000161 557 KMDLESVSNYDEVKNAIMEKLLRLQEEPIREECPLIYHLDVAAMYPNIILTNRLQPPSIVTDEVCTACDFNRPGKTCLRK 636 (1988)
Q Consensus 557 ~~~~~~~~n~~~v~~~i~~~l~~l~~~p~~~~~p~V~~LDf~SLYPsII~t~NL~p~Tiv~~~~c~~c~~n~p~~~c~r~ 636 (1988)
+|++|||+|||||||++|||||+|++... +.
T Consensus 812 ----------------------------------~V~~lDF~SLYPSIi~~~Nic~~t~~~~~-~~-------------- 842 (1172)
T TIGR00592 812 ----------------------------------YVLLMDFNSLYPSIIQEFNICFTTVQQKV-DE-------------- 842 (1172)
T ss_pred ----------------------------------CEEEEEcCCccHHHHHHhCcCccccCCCC-cc--------------
Confidence 69999999999999999999999997432 00
Q ss_pred cccccccccccCCcchhhHhhhhcccccccCCCCCcccccccCchHHHHHHHHHHHHHhhhhhccccccccccccccccc
Q 000161 637 LEWVWRGEIFMGKRSDYYHLKKQIESEFVDGTNGHLSKSFLDLPKMEQQSRLKDRLKKYCQKAYKRVLDKPVTELREAGI 716 (1988)
Q Consensus 637 m~w~~~ge~~p~~~~ey~~i~~~l~~e~f~~~~~g~~~~~~~L~~~~q~~~lkkrl~~y~~kvy~k~~~~~~~~~r~~~i 716 (1988)
+.+| .+|..
T Consensus 843 -------~~~~----------------~~~~~------------------------------------------------ 851 (1172)
T TIGR00592 843 -------DELP----------------ELPDS------------------------------------------------ 851 (1172)
T ss_pred -------hhcc----------------cCCcc------------------------------------------------
Confidence 0000 01100
Q ss_pred ccccccchHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCCC
Q 000161 717 CMRENSFYVDTVRSFRDRRYEYKGLNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGARW 796 (1988)
Q Consensus 717 cqre~~f~~~~lr~f~drR~~~K~l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~sR~ 796 (1988)
....+++|.+|+.|+++|.++|++||. +.|+.+ ..+||++|+|+|++|||+|||+|+++|||
T Consensus 852 -~~~~Gilp~il~~L~~~R~~~K~~mk~----------~~~~~~-------~~~~d~~Q~AlKi~aNS~YG~lG~~~~r~ 913 (1172)
T TIGR00592 852 -ELEMGILPRELRKLVERRKEVKKLMKQ----------DLNPDL-------RLQYDIRQKALKLTANSMYGCLGYSKSRF 913 (1172)
T ss_pred -cccCcchHHHHHHHHHHHHHHHHHhhc----------CCCHHH-------HHHHHHHHHHHHHhhhccccccccccccc
Confidence 001358999999999999999999875 234543 47999999999999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHcCCe-EEEccceeeEEcCCCCCcccccccccccccccccccccccchhhhcccc
Q 000161 797 YSMEMAGVVTYTGAKIIQNARLLIEKIGKP-LELDTDGIWCVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVDVARNNT 875 (1988)
Q Consensus 797 ys~e~A~~VT~~Gr~iI~~a~~lve~~G~~-vygDTDSI~~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~V~~~~t 875 (1988)
||+++|++||++||++|+.|++++++.|+. ||||||||||.+|....++. + +.| +++ . +.+
T Consensus 914 ~~~~~A~~iT~~GR~~l~~~~~~~e~~g~~VIYGDTDSv~v~~~~~~~~e~-~--~~~-~~~---------~-----~~i 975 (1172)
T TIGR00592 914 YAKPLAALVTAKGREILEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEV-F--KIG-KEF---------K-----SEV 975 (1172)
T ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHcCCEEEEecCCeEEEEcCCCCHHHH-H--HHH-HHH---------H-----HHH
Confidence 999999999999999999999999999998 69999999999886533321 1 122 222 1 112
Q ss_pred chhhhhccCCccccccccccceeEEeeeceeeeeecccccccCcccccceEEEcCC----CC---EEEEEeeeeccCChh
Q 000161 876 NDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDD----GT---LAELKGFEIKRRGEL 948 (1988)
Q Consensus 876 N~~y~~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~~~d----G~---~~e~KG~E~kRRd~~ 948 (1988)
|.. | + .|++|+||+|++|+|++ |||||++..+ |. .+++||+|++|||||
T Consensus 976 n~~-----------~----~-~l~le~e~vy~~~ll~~--------KKrYa~l~~~~~~~g~~~~k~~~KGle~vRrD~~ 1031 (1172)
T TIGR00592 976 NKL-----------Y----K-LLELDIDGVFKRLLLLK--------KKKYAAIKVEGDSDGNYTTKQEVKGLDIVRRDWS 1031 (1172)
T ss_pred hhc-----------C----C-ceEEeehhhhHhhHhhh--------ccceEEEeeccCcCCCcceeEEeecceEEECCcH
Confidence 222 2 1 47888889999999975 9999998543 43 459999999999999
Q ss_pred HHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhhhhhccccccChhhhCC-CCChHHHHHH
Q 000161 949 KLIKVFQAELFDKFLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADSELIDYISESSTMSKSLADYGE-QKSCAVTTAR 1027 (1988)
Q Consensus 949 ~liK~~q~~v~~~~L~g~~lee~~~~v~~v~~~~~d~L~~~~~~~~~~eLi~~i~~~k~lsK~l~eY~~-~k~~~v~~A~ 1027 (1988)
+|+|++|.++++.+|.+++++++++.++++++...+. +..|.++.++|+ ++|+|+|.+++|.. ..+|||++|+
T Consensus 1032 ~l~k~~~~~vl~~il~~~~~~~~~~~i~~~l~~~~~~--l~~g~~~~~~lv----i~k~l~k~~~~Y~~~~~~phv~~A~ 1105 (1172)
T TIGR00592 1032 PLAKETGKKVLDTILSDKDVEEAVEEVQEVLEKIGKN--VLNGEVPLEKFV----INKQLTRDPKDYPDGASLPHVHVAL 1105 (1172)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH--HhcCCCCHHHee----ehhhccCCHHHcCCCCCChHHHHHH
Confidence 9999999999999999999999999999888877663 457889988888 89999999999984 3689999999
Q ss_pred HHHhhcCCCcccCCCCeeEEEEEcCCCCCCCcccccchhhhcchHHHHHHHHHhhhcCCCCCCCccccCHHHHHHhhhhh
Q 000161 1028 RLSDFLGDTMVKDKGLRCQYIVACEPQGTPVSERAVPVAIFETDAEIMKFYLRKWCKTSSDVGIRSIVDWSYYKQRLSSA 1107 (1988)
Q Consensus 1028 rl~e~lG~~~~~~~G~~i~YVI~~~p~g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~~~~~d~~~~iD~~YYierl~~~ 1107 (1988)
||.++.| ..+.+|++|+|||++++.+....+||.|++.+... +..+.||++|||++
T Consensus 1106 ~~~~~~g--~~~~~G~~I~Yvi~~~~~~~~~~~ra~~~~~~~~~------------------~~~l~iD~~yYi~~---- 1161 (1172)
T TIGR00592 1106 RINARGG--RKVKAGDVVSYVICKDGGNLSARQRAYALEELQRK------------------HNNLIYDTQYYLEH---- 1161 (1172)
T ss_pred HHHHhcC--CCCCCCCEEEEEEEeCCCCcchhhhccChHHhhcc------------------CCCCCcCHHHHHHh----
Confidence 9998646 57889999999999987766777899998654321 11478999999999
Q ss_pred hhheeechhhhhhc
Q 000161 1108 IQKIITIPAAMQKV 1121 (1988)
Q Consensus 1108 i~ki~~iPa~lq~~ 1121 (1988)
||+|++.|.+
T Consensus 1162 ----qi~p~~~Ri~ 1171 (1172)
T TIGR00592 1162 ----QIHPVVLRIL 1171 (1172)
T ss_pred ----hcHHHHHHhh
Confidence 9999998864
No 11
>PHA03036 DNA polymerase; Provisional
Probab=100.00 E-value=1.3e-88 Score=876.99 Aligned_cols=683 Identities=19% Similarity=0.226 Sum_probs=497.1
Q ss_pred eeeeecCCccceeEEEeeCCC-Cce---EEEec------cc--cCCCCceEEEEEEEEccCCCCCCCCCCCeEEEEEE-E
Q 000161 203 RFAIDNDVRCGQWYDVSISST-GPL---LEKRV------DL--LQRAEVHVCAFDIETTKLPLKFPDADYDIIMMISY-M 269 (1988)
Q Consensus 203 R~~iD~~I~~g~W~~v~~~~~-~~~---i~~~~------~~--~~~p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~-~ 269 (1988)
=|.+-++|.|-+-|++....- .+. +-|.. .. ...-+++.|||||||.. .++||+|..|||++||+ .
T Consensus 112 wf~~~n~i~p~gcy~i~~~~~~~~~~~~y~c~~p~~~f~~~i~~~~~~~~~lsfDIEC~~-~g~FPs~~~~pvshIs~~~ 190 (1004)
T PHA03036 112 WFYVLNNISPDGCYRIDIDKLEKINNKCYHCDDPKKCFANKIPRFDIPRSYLFLDIECHF-DKKFPSVFINPVSHISCCY 190 (1004)
T ss_pred EEEEecCcCCccceecCHHHhccccCCceeeCCHHHHhcCcCCCccCcceeEEEEEEecc-CCCCCCcccCcceEEEEEE
Confidence 367888888888888754321 111 11211 11 23567899999999996 88999999999999996 4
Q ss_pred EcCCc----eEEEcccccccc----cccccCCCCC---CCCCceEEecCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCC
Q 000161 270 LDGQG----YLIINRECVGED----IEDLEYTPKP---EFEGYFKVTNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFD 338 (1988)
Q Consensus 270 ~~~~g----~li~nreivs~d----i~~feytp~~---~~~g~f~V~~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FD 338 (1988)
++..| +.++|.++++++ -..+.|+... +..| ..++.+.+|.+|| +|+++|.+.|||+|+||||++||
T Consensus 191 ~~~~~~~~~~~l~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~sE~~ml-~~~~~i~~~d~D~i~~yNg~nFD 268 (1004)
T PHA03036 191 IDLSGKEKRFTLINEDMLSEDEIEEAVKRGYYEIESLLDMDY-SKELILCSEIVLL-RIAKKLLELEFDYVVTFNGHNFD 268 (1004)
T ss_pred EecCCCeeEEEEeccccccccccccceeeeeeccccccccCC-ceeeecCCHHHHH-HHHHHHHhcCCCEEEeccCCCcc
Confidence 55555 345777666532 1223343332 2233 3467889999988 77999999999999999999999
Q ss_pred HHHHHHHHHHcCC---CCC---------cccCcc---cc-CCCC----ce--e-eccceEechHHHHhhccCCCCCCCCH
Q 000161 339 WPFLETRAAHHGF---KMS---------EELGFQ---CD-KNQG----EC--R-AKFACHLDCFAWVKRDSYLPQGSQGL 395 (1988)
Q Consensus 339 lPyL~~Ra~~lGi---~l~---------~~iG~~---~~-~~~g----~~--~-i~GRihiDl~~~vkrd~~L~~~SysL 395 (1988)
||||.+|++.|+. .+. ..+|.+ .+ ...| .| . .+||+++|+|.++++...| .||+|
T Consensus 269 ~~Yi~~R~~~L~~~~~~~~~~~~~~~~~~~v~~r~~~s~~~~gg~~~~t~~i~~~~G~i~fDLy~~i~k~~~L--~sYkL 346 (1004)
T PHA03036 269 LRYISNRLELLTGEKIIFRSPDGKETVHLCIYERNLSSHKGVGGVANTTYHINNNNGTIFFDLYTFIQKTEKL--DSYKL 346 (1004)
T ss_pred hHHHHHHHHHhccCceeeccCCCcccccceeeccccccccccCccccceEEecccCCeEEEEhHHHHhhhcCc--ccccH
Confidence 9999999999844 221 011111 00 1012 12 2 5899999999999998777 89999
Q ss_pred HHHHHHHc-----------------C--------------------------C---------------------------
Q 000161 396 KAVTKAKL-----------------G--------------------------Y--------------------------- 405 (1988)
Q Consensus 396 ~~Va~~~L-----------------G--------------------------~--------------------------- 405 (1988)
++|++++| | .
T Consensus 347 ~~Vsk~~f~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~f~~vl~t~ny~~i~~~~~~k~~~k~~~~~~~~~~~~~~~~~~ 426 (1004)
T PHA03036 347 DSISKNAFNCNAKVLSENNNEVTFIGDNTTDAKGKASIFSEVLSTGNYVTINDDDICKILDKDIIENSFTVKVICKNNYI 426 (1004)
T ss_pred HHHHHHhhccceeeeecCCceeEEccCcccccccchhhhhhhhcccceeeecccchhhhcccccccccceeeeecccccc
Confidence 99999977 4 4
Q ss_pred ---------CCCCCChHHHHHHHh-hChHHHHHHHHHhhHHHHHHHHHh-ccchHhhhhhhcCCChHHHhhhhhHHHHHH
Q 000161 406 ---------DPLEVNPEDMVRFAK-EKPQMMASYSVSDAVATYYLYMTY-VHPFIFSLATIIPMSPDEVLRKGSGTLCEM 474 (1988)
Q Consensus 406 ---------~K~dvd~~~i~~~~~-~~~~~La~Y~l~Da~lt~~L~~Kl-v~~~i~~La~i~~l~~~~vlr~Gsg~~~E~ 474 (1988)
+|.|+++.+|.+.|. +.+.+++.||++||.|+++|+.++ +|.-+.++|..+.+|..+++..|+++++++
T Consensus 427 ~~~~~~~~~~KdDV~~~~i~~~~~~~~r~rla~YClkDa~L~l~L~~~l~~~~~v~~~a~~~~lp~~~~i~~~~s~~i~~ 506 (1004)
T PHA03036 427 PGDTYTLSFGKDDVDLSDMYKNYNLEIALEMARYCIHDACLCKYLWEYYGIETKIDAGASTYLLPQSMVFEYRASTLIKG 506 (1004)
T ss_pred cccceeecccccCCCHHHHHHHhChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhheEeeeecccccc
Confidence 789999999999887 456799999999999999999998 677788999999999999999999999999
Q ss_pred HHHHHHHHCCeeccCCCCCCchhhhcccccCCCCCCcceeeeccCccccCCCCCCccCChhHHHHHhhhhhhhhHHHHhH
Q 000161 475 LLMVQAYKANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFKLDPSAYEQLLNNLDRDLQYAIKV 554 (1988)
Q Consensus 475 LLm~~a~~~n~i~Pnk~~~~~~~~~~g~l~~setY~GG~V~~p~~GvY~~d~~~~f~~~~~~~~~l~~~~~~~l~~~~~~ 554 (1988)
+|++.|.+.|+++|..... ...+|+||+|++|++|+|.+
T Consensus 507 qllr~~~~~~~i~p~~~~~-----------~~~~YeGa~VlEP~~G~Y~~------------------------------ 545 (1004)
T PHA03036 507 PLLKLLLEEKTILVRSETK-----------NKFPYEGGKVFAPKQKMFDN------------------------------ 545 (1004)
T ss_pred HHHHHHHHCCcccccCCCC-----------ccCCcCceEEecCCCCcccC------------------------------
Confidence 9999999999999943211 12379999999999999876
Q ss_pred hcccccccccchHHHHHHHHHHHHhhccCCCcccCCeEEEEeccccchHHHHhcCCCCCccccccccccccCCCCCCccc
Q 000161 555 EGKMDLESVSNYDEVKNAIMEKLLRLQEEPIREECPLIYHLDVAAMYPNIILTNRLQPPSIVTDEVCTACDFNRPGKTCL 634 (1988)
Q Consensus 555 e~~~~~~~~~n~~~v~~~i~~~l~~l~~~p~~~~~p~V~~LDf~SLYPsII~t~NL~p~Tiv~~~~c~~c~~n~p~~~c~ 634 (1988)
+|++|||+|||||||++|||||+|++... |.-+....
T Consensus 546 ------------------------------------pV~vLDFaSLYPSIIia~NLcyeTlv~~~----~~~~~~~~--- 582 (1004)
T PHA03036 546 ------------------------------------NVLIFDYNSLYPNVCIFGNLSPETLVGVV----VNDNRLEA--- 582 (1004)
T ss_pred ------------------------------------CEEEEEccccchHHHHHhCCCcCeEeecc----cccccccc---
Confidence 59999999999999999999999998542 21110000
Q ss_pred cccccccccccccCCcchhhHhhhhcccccccCCCCCcccccccCchHHHHHHHHHHHHHhhhhhccccccccccccccc
Q 000161 635 RKLEWVWRGEIFMGKRSDYYHLKKQIESEFVDGTNGHLSKSFLDLPKMEQQSRLKDRLKKYCQKAYKRVLDKPVTELREA 714 (1988)
Q Consensus 635 r~m~w~~~ge~~p~~~~ey~~i~~~l~~e~f~~~~~g~~~~~~~L~~~~q~~~lkkrl~~y~~kvy~k~~~~~~~~~r~~ 714 (1988)
...-..-.+.+|. .+|..+. +. ++ ..+ +..+.+.
T Consensus 583 -~i~~~~i~~~~p~--~dy~~v~--------~~--~~---~~~-----------------~v~~~~v------------- 616 (1004)
T PHA03036 583 -EINKQELRRKYPY--PRYIYVH--------CE--PR---SPD-----------------LVSEIAV------------- 616 (1004)
T ss_pred -ccccccccccCCC--ccceeee--------cc--CC---ccc-----------------cccccee-------------
Confidence 0000000000110 1110000 00 00 000 0000000
Q ss_pred ccccccccchHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHHHHHHHHHHhhhccccccccCC
Q 000161 715 GICMRENSFYVDTVRSFRDRRYEYKGLNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGA 794 (1988)
Q Consensus 715 ~icqre~~f~~~~lr~f~drR~~~K~l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~s 794 (1988)
-+....+++|.+|+.|++.|.++|++||+. .|+.+ ..+||++|+|+|+++||+|||+|+.+|
T Consensus 617 -f~~~rkGILP~iL~~Ll~~Rk~~Kk~mK~~----------~d~~e-------~~~lD~rQlAlKI~aNS~YG~~G~~~~ 678 (1004)
T PHA03036 617 -FDRRIEGIIPKLLKTFLEERARYKKLLKEA----------TSSVE-------KAIYDSMQYTYKIVANSVYGLMGFRNS 678 (1004)
T ss_pred -ecCCCCcChHHHHHHHHHHHHHHHHHHhhC----------CChHH-------HHHHHHHHHHHHHHHhcccccccccCc
Confidence 011234699999999999999999998763 23432 379999999999999999999999999
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHH--------------------------------------cCCe-EEEccceee
Q 000161 795 RWYSMEMAGVVTYTGAKIIQNARLLIEK--------------------------------------IGKP-LELDTDGIW 835 (1988)
Q Consensus 795 R~ys~e~A~~VT~~Gr~iI~~a~~lve~--------------------------------------~G~~-vygDTDSI~ 835 (1988)
||||.++|++||+.||++|+.++++||. .|+. |||||||||
T Consensus 679 rly~~~iA~sVTa~GR~mI~~tk~~Ve~~~~~~~~~~l~~~p~~~f~~~~r~~~~~~~~~l~~~~~~g~kVIYGDTDSVF 758 (1004)
T PHA03036 679 ALYSYASAKSCTAIGRNMIKYLNSVLNGSKLINGKLILANCPINPFFKDDRSIDTNYDTNLPVEYNFTFRSVYGDTDSVF 758 (1004)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHhhcccccchhhhhhhccccccccccccccccccccccccccCCcEEEEEecCeeE
Confidence 9999999999999999999999988753 3565 699999999
Q ss_pred EEcCCCCCcccccccccccccccccccccccchhhhccccchhhhhccCCccccccccccceeEEeeeceeeeeeccccc
Q 000161 836 CVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVDVARNNTNDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASK 915 (1988)
Q Consensus 836 ~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~V~~~~tN~~y~~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~ 915 (1988)
|.+++...++ ++ +.| +++ +..| |.. .+ +.+|++|+||+|++|+|.+
T Consensus 759 V~~~~~d~ee-a~--~ig-~el---------a~~I-----n~~--lf------------~~pikLEfEKVY~~lLLl~-- 804 (1004)
T PHA03036 759 LEINTKDVDK-SI--KIA-KEL---------ERII-----NEK--VL------------FDNFKIEFEAVYKNLIMQS-- 804 (1004)
T ss_pred EEcCCCCHHH-HH--HHH-HHH---------HHHH-----HHH--hc------------CCCeEEEehhhHHHHHhhh--
Confidence 9988642211 11 223 332 2222 210 01 2346777779999999975
Q ss_pred ccCcccccceEEEcC-----CCC--EEEEEeeeeccCChhHHHHHHHHHHHHHH---hCCCC---HHHHHHHHHHHHHHH
Q 000161 916 EEGILIKKRYAVFND-----DGT--LAELKGFEIKRRGELKLIKVFQAELFDKF---LHGST---IEECYSAVAAVANRW 982 (1988)
Q Consensus 916 ~~~~~~KKRYa~~~~-----dG~--~~e~KG~E~kRRd~~~liK~~q~~v~~~~---L~g~~---lee~~~~v~~v~~~~ 982 (1988)
||||||+.. +|. .+++||+|++|||+|+|+|++++++++.+ |.+.+ .+.|.+.++++....
T Consensus 805 ------KKRYAGl~~~~~~~~~~~~kid~KGie~VRRD~c~fvK~v~~~vi~~L~~iL~~~d~~~~~~~i~~Lk~~i~dL 878 (1004)
T PHA03036 805 ------KKKYTTLKYIASSTDGSVPERVNKGTSETRRDVSKFHKYMIKIYKTRLLDMLSEGNMNSNQVCIDILRSLEKDL 878 (1004)
T ss_pred ------hhheeeEeeccccCCCCceEEEEECceeEeCchHHHHHHHHHHHHHHHHHHhccCCchhHHHHHHHHHHHHHHH
Confidence 999999643 231 35999999999999999999999876654 66664 667888887766544
Q ss_pred HHHHHhcCCCCCchhhhhhhhhccccccChhhhCCCCChHHHHHHHHHhhcCCCcccCCCCeeEEEEEcCCC--------
Q 000161 983 LDLLDNQGKDIADSELIDYISESSTMSKSLADYGEQKSCAVTTARRLSDFLGDTMVKDKGLRCQYIVACEPQ-------- 1054 (1988)
Q Consensus 983 ~d~L~~~~~~~~~~eLi~~i~~~k~lsK~l~eY~~~k~~~v~~A~rl~e~lG~~~~~~~G~~i~YVI~~~p~-------- 1054 (1988)
++ ..+.+.+|.++|+ +++++++. |++...||+.+|+||+++ +++ .|..|+|++||++.+..
T Consensus 879 ~~--n~~~~~vple~Lv----iSk~l~~~---Yk~~~~ph~~la~r~~~r-~~~-~p~iGDRv~YV~i~~~~~~w~~~~~ 947 (1004)
T PHA03036 879 II--EFDSRSAPLEMFL----LSRTHHCN---YKSPDNPNMYLVNEYNKN-NPE-KIEIGERYYFAYICPINLPWQKKLV 947 (1004)
T ss_pred HH--HHhcCCCCHHHHh----hhhccccc---CCCCCCCHHHHHHHHHhh-CCC-CCCCCCEEEEEEEECCCcccccccc
Confidence 33 2456789999988 78888765 988778999999999986 333 89999999999876533
Q ss_pred CCCCcccccchhhhcchHHHHHHHHHhhhcCCCCCCCccccCHHHHHHhhhhhhh
Q 000161 1055 GTPVSERAVPVAIFETDAEIMKFYLRKWCKTSSDVGIRSIVDWSYYKQRLSSAIQ 1109 (1988)
Q Consensus 1055 g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~~~~~d~~~~iD~~YYierl~~~i~ 1109 (1988)
|.+.+|||+++..... -+.+||.+||+++|.+.+-
T Consensus 948 ~~~~ye~aeDp~yvl~--------------------~~~~I~~e~Y~~~l~~~v~ 982 (1004)
T PHA03036 948 NIKTYERIIDRSFKLK--------------------SNERIFYEVYFKRLATEVV 982 (1004)
T ss_pred CcccceeecCcccccc--------------------CCCceeHHHHHHHHHHHHH
Confidence 6789999998864321 2579999999999555443
No 12
>KOG0968 consensus DNA polymerase zeta, catalytic subunit [Replication, recombination and repair]
Probab=100.00 E-value=2.6e-81 Score=777.16 Aligned_cols=665 Identities=19% Similarity=0.204 Sum_probs=513.6
Q ss_pred CCCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCce------------EEEcccccccccccccCCCC-CCCCCce
Q 000161 236 RAEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGY------------LIINRECVGEDIEDLEYTPK-PEFEGYF 302 (1988)
Q Consensus 236 ~p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~------------li~nreivs~di~~feytp~-~~~~g~f 302 (1988)
.--|+++|+.+.+.++...-|||..|+|-+|.++++.+.. .+++. ++.|+..- ++- ..+. +.
T Consensus 655 ~~~Lt~lsiElha~sr~dl~PDP~~D~V~~l~~~vq~dtp~pd~~si~~~gv~Vv~~--~~~ds~~~--t~~~~~~~-~~ 729 (1488)
T KOG0968|consen 655 TQLLTILSIELHATSRGDLEPDPVFDSVASLFLCVQEDTPMPDADSIVSVGVIVVDK--VCPDSHVQ--TTTLGGIY-GC 729 (1488)
T ss_pred cceeeeeeeeccccccCCCCCCcccccchhhhhhhccCCCCCcccceeeeeEEEEec--cCcccccc--ccccCCcC-Cc
Confidence 5678999999999999999999999999999988765521 12211 01111110 111 1122 35
Q ss_pred EEecCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccc----------cCCCCc-----
Q 000161 303 KVTNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQC----------DKNQGE----- 367 (1988)
Q Consensus 303 ~V~~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~----------~~~~g~----- 367 (1988)
+|..+.+|.+|++++.+++.++||||++||.+.++.|+||.+|++.||++..+.+.+.. .+.+|.
T Consensus 730 ~V~~~~sE~elf~ev~~~i~q~DPDIl~GyEi~~~SWGyl~eR~~~l~~di~~~lsRv~~~~~~n~~d~~~ewg~tt~S~ 809 (1488)
T KOG0968|consen 730 RVVVMESELELFEEVAKLIVQYDPDILLGYEIHNLSWGYLIERAKLLGIDISRDLSRVKCYEKTNESDDEREWGYTTISG 809 (1488)
T ss_pred eEEEehhHHHHHHHHHHHHHhcCcceeeeeeecccchHHHHHHHHHhcchHHHHHhcCCChhhhhhhhhhhhccceeecc
Confidence 68889999999999999999999999999999999999999999999998765444431 011232
Q ss_pred eeeccceEechHHHHhhccCCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhCh----HHHHHHHHHhhHHHHHHHHH
Q 000161 368 CRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKP----QMMASYSVSDAVATYYLYMT 443 (1988)
Q Consensus 368 ~~i~GRihiDl~~~vkrd~~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~----~~La~Y~l~Da~lt~~L~~K 443 (1988)
..+.||+++.+|+.+|.+..| .+|+|++|+.++|...-+-++.+.+.++|.+++ ..++.|-++.+.+.++|+.+
T Consensus 810 i~i~GR~~lNiWRilR~eV~L--~nYtlEsv~~nVL~kk~P~~~~~~Lt~~~~s~~~~~r~~~l~y~l~Ra~~NlelLsq 887 (1488)
T KOG0968|consen 810 INIVGRHVLNIWRILRSEVAL--TNYTLESVVFNVLRKKIPMFDFAVLTRWWKSKRSAERNDVLNYLLSRARLNLELLSQ 887 (1488)
T ss_pred ccccchhhhhHHHHHhhhhhh--hhccHHHHHHHHHHhhcCCCcHHHHHHHHhcccHHHHHHHHHHHHHHhhhhHHHHHH
Confidence 347899999999999999777 899999999999999989999999999998654 58999999999999999998
Q ss_pred h-ccchHhhhhhhcCCChHHHhhhhhHHHHHHHHHHHHHHCCeeccCCCCCCchhhhcccccCCCCCCcceeeeccCccc
Q 000161 444 Y-VHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAYKANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVF 522 (1988)
Q Consensus 444 l-v~~~i~~La~i~~l~~~~vlr~Gsg~~~E~LLm~~a~~~n~i~Pnk~~~~~~~~~~g~l~~setY~GG~V~~p~~GvY 522 (1988)
+ ...-+.++||++|+.+-.|+.+||+.++|++|+|-|+..|||+|+....+... .|. --.-.+|++|++.+|
T Consensus 888 ~d~i~k~~E~ARv~GIdF~sV~tRGSQ~rVESmllRiAk~~Nyi~~SPs~kQv~~--q~A-----~EcvPLVMEPeS~fY 960 (1488)
T KOG0968|consen 888 LDWILKNSEMARVIGIDFHSVLTRGSQFRVESMLLRIAKPMNYIAPSPSHKQVAM--QGA-----PECVPLVMEPESAFY 960 (1488)
T ss_pred HHHHHhhHHHHHhhcceeeEEeeccchhhHHHHHHHHhcccccccCCccHHHHhh--cCC-----ccccceeecchhhhc
Confidence 7 44556899999999999999999999999999999999999999865432211 111 124689999999999
Q ss_pred cCCCCCCccCChhHHHHHhhhhhhhhHHHHhHhcccccccccchHHHHHHHHHHHHhhccCCCcccCCeEEEEeccccch
Q 000161 523 RSDLPTSFKLDPSAYEQLLNNLDRDLQYAIKVEGKMDLESVSNYDEVKNAIMEKLLRLQEEPIREECPLIYHLDVAAMYP 602 (1988)
Q Consensus 523 ~~d~~~~f~~~~~~~~~l~~~~~~~l~~~~~~e~~~~~~~~~n~~~v~~~i~~~l~~l~~~p~~~~~p~V~~LDf~SLYP 602 (1988)
.+ ||+||||+||||
T Consensus 961 ~~------------------------------------------------------------------PViVLDFQSLYP 974 (1488)
T KOG0968|consen 961 FD------------------------------------------------------------------PVIVLDFQSLYP 974 (1488)
T ss_pred cC------------------------------------------------------------------ceEEEEchhhcc
Confidence 88 699999999999
Q ss_pred HHHHhcCCCCCccccccccccccCCCCCCccccccccccccccccCCcchhhHhhhhcccccccCCCCCcccccccCchH
Q 000161 603 NIILTNRLQPPSIVTDEVCTACDFNRPGKTCLRKLEWVWRGEIFMGKRSDYYHLKKQIESEFVDGTNGHLSKSFLDLPKM 682 (1988)
Q Consensus 603 sII~t~NL~p~Tiv~~~~c~~c~~n~p~~~c~r~m~w~~~ge~~p~~~~ey~~i~~~l~~e~f~~~~~g~~~~~~~L~~~ 682 (1988)
||||+||+||+|+.+... ..|..... ++. . .+..++.+
T Consensus 975 SivIAYNyCySTcLG~v~----~l~~~~e~---~LG----~-------------------------------s~~s~~~d 1012 (1488)
T KOG0968|consen 975 SIVIAYNYCYSTCLGKVG----NLNQMNEI---KLG----V-------------------------------SKYSLPPD 1012 (1488)
T ss_pred hHHHhHHHHHHHhhhHHH----hhccccce---eee----e-------------------------------eeccCCHH
Confidence 999999999999987531 01100000 000 0 11112211
Q ss_pred HHHHHHHHHHHH--hhhh--hcccccccccccccccccccccccchHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCCh
Q 000161 683 EQQSRLKDRLKK--YCQK--AYKRVLDKPVTELREAGICMRENSFYVDTVRSFRDRRYEYKGLNKVWKGKLSEAKASGNS 758 (1988)
Q Consensus 683 ~q~~~lkkrl~~--y~~k--vy~k~~~~~~~~~r~~~icqre~~f~~~~lr~f~drR~~~K~l~K~~k~~~~~a~~~~d~ 758 (1988)
.|-++..+ .+|+ +|-|..+ |++ ++|.+|+++++.|.++|+.||..+. .
T Consensus 1013 ----il~~~~ndV~isPNgv~yVK~sV------Rkg--------vLpkmLeEIL~tRiMVKkaMK~~~~----------~ 1064 (1488)
T KOG0968|consen 1013 ----ILVLAKNDVTISPNGVMYVKPSV------RKG--------VLPKMLEEILATRIMVKKAMKRTKD----------N 1064 (1488)
T ss_pred ----HHHHHhcceeeCCCceEEechhh------hhh--------hHHHHHHHHHHHHHHHHHHHHHhcc----------h
Confidence 11111111 1222 3433333 554 8999999999999999999997642 1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhhcccccccc-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHc---CCe-EEEccce
Q 000161 759 IKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRK-GARWYSMEMAGVVTYTGAKIIQNARLLIEKI---GKP-LELDTDG 833 (1988)
Q Consensus 759 ~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~-~sR~ys~e~A~~VT~~Gr~iI~~a~~lve~~---G~~-vygDTDS 833 (1988)
+.+..++|++|||+|+|||..|||+.+. .+||||.|+|++|..+||++|++|+++|+.. |.. |||||||
T Consensus 1065 ------~~L~RiLnaRQLALKLiANVTYGYTsA~FSGRMPCaElADsIV~~GRETLEraIe~Vn~~d~w~AkVVYGDTDS 1138 (1488)
T KOG0968|consen 1065 ------KKLKRILNARQLALKLIANVTYGYTSANFSGRMPCAELADSIVQKGRETLERAIEMVNRGDYWGAKVVYGDTDS 1138 (1488)
T ss_pred ------HHHHHHhhhHHHHHHHHhhccccccccccCCCCchHHHHHHHHHhhHHHHHHHHHHHhcCCcCCeEEEEcCCCc
Confidence 1355899999999999999999999999 7999999999999999999999999999986 544 7999999
Q ss_pred eeEEcCCCCCcccccccccccccccccccccccchhhhccccchhhhhccCCccccccccccceeEEeeeceeeeeeccc
Q 000161 834 IWCVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVDVARNNTNDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPA 913 (1988)
Q Consensus 834 I~~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~V~~~~tN~~y~~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~ 913 (1988)
+||.|||.+.| .+| .+| .+| +..|+ | ..|.+|.+.+||+|+++||.+
T Consensus 1139 mFVlL~GaT~e-eAF--~IG-q~i---------Ae~VT----~----------------~NP~PV~LKfEKVY~PCvL~t 1185 (1488)
T KOG0968|consen 1139 MFVLLPGATVE-EAF--EIG-QEI---------AEAVT----N----------------SNPKPVVLKFEKVYHPCVLLT 1185 (1488)
T ss_pred eEEEecCccHH-HHH--HHH-HHH---------HHHHH----h----------------cCCCCeEEEeeeecccceeee
Confidence 99999998643 344 356 444 33332 2 124455555559999999977
Q ss_pred ccccCcccccceEEEcC-----CCCEEEEEeeeeccCChhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHh
Q 000161 914 SKEEGILIKKRYAVFND-----DGTLAELKGFEIKRRGELKLIKVFQAELFDKFLHGSTIEECYSAVAAVANRWLDLLDN 988 (1988)
Q Consensus 914 s~~~~~~~KKRYa~~~~-----dG~~~e~KG~E~kRRd~~~liK~~q~~v~~~~L~g~~lee~~~~v~~v~~~~~d~L~~ 988 (1988)
||||+||.. +-.+++.||+|+||||.||.+.++.++.+++||+.+++.....++.. .|.. .
T Consensus 1186 --------KKRYVG~~YEs~~Qk~PiFDAKGIETVRRDtcPavakilEksL~LlFetkdlS~IK~y~q~---~~~k---i 1251 (1488)
T KOG0968|consen 1186 --------KKRYVGFMYESPNQKEPIFDAKGIETVRRDTCPAVAKILEKSLRLLFETKDLSKIKKYLQN---VCNK---I 1251 (1488)
T ss_pred --------ccceeeeeeccCcccCCccccccceeeeccCcHHHHHHHHHHHHHHhhcccHHHHHHHHHH---HHHH---H
Confidence 999999843 23467999999999999999999999999999999999988877654 4444 3
Q ss_pred cCCCCCchhhhhhhhhccccccChhhhCC--CCChHHHHHHHHHhhcCCCcccCCCCeeEEEEEcCCCCCCCcccccchh
Q 000161 989 QGKDIADSELIDYISESSTMSKSLADYGE--QKSCAVTTARRLSDFLGDTMVKDKGLRCQYIVACEPQGTPVSERAVPVA 1066 (1988)
Q Consensus 989 ~~~~~~~~eLi~~i~~~k~lsK~l~eY~~--~k~~~v~~A~rl~e~lG~~~~~~~G~~i~YVI~~~p~g~~v~eRa~p~~ 1066 (1988)
..|.++..|++ +.|.+. ++.|.. ..+|...+|+|+... ++...|+.|+||||||+++.+|+++.+|++.+.
T Consensus 1252 ~~Gkvs~qDF~----FaKEvR--l~~~~~~~~~pP~avva~r~i~~-DpR~EPqygERVPYvII~G~pG~~L~~~vvsP~ 1324 (1488)
T KOG0968|consen 1252 QEGKVSFQDFC----FAKEVR--LEKYYSASAAPPGAVVARRRITK-DPRHEPQYGERVPYVIIDGVPGSTLYSRVVSPE 1324 (1488)
T ss_pred hhCCcchhhhe----eeeeec--ceeccccccCCchHHHHHHHhcc-CCccCccccccCCeEEEeCCCCCcHHHHhcCHH
Confidence 46888866665 888773 444543 357888888887763 666789999999999999999999999999998
Q ss_pred hhcchHHHHHHHHHhhhcCCCCCCCccccCHHHHHHhhhhhhhheeechhhhhhccCCCCCcchhhhhhhhhh
Q 000161 1067 IFETDAEIMKFYLRKWCKTSSDVGIRSIVDWSYYKQRLSSAIQKIITIPAAMQKVSNPVPRVVHPDWLYKKVR 1139 (1988)
Q Consensus 1067 if~~~~~~~~~~l~~w~~~~~~~d~~~~iD~~YYierl~~~i~ki~~iPa~lq~~~npv~rv~~p~w~~~~~~ 1139 (1988)
.|-.. ....||..|||.+ |||||+-| |+|- -++.+-.|+++-..
T Consensus 1325 efL~~-------------------~~~rLn~~YYINk--------~iiPpL~R-vf~L-iG~~v~~W~~Empk 1368 (1488)
T KOG0968|consen 1325 EFLRN-------------------PTYRLNTFYYINK--------QIIPPLDR-VFNL-IGADVDSWYHEMPK 1368 (1488)
T ss_pred HHhcC-------------------Cceeccceeeehh--------hccchHHH-Hhhh-cccchhhHHHhccc
Confidence 77542 3578999999999 99999655 6664 47888999987555
No 13
>PF08490 DUF1744: Domain of unknown function (DUF1744); InterPro: IPR013697 This domain is found on the catalytic subunit of DNA polymerase epsilon. It is found C-terminal to IPR006133 from INTERPRO and IPR006134 from INTERPRO. ; GO: 0003887 DNA-directed DNA polymerase activity, 0008270 zinc ion binding, 0006260 DNA replication, 0005634 nucleus
Probab=100.00 E-value=2.9e-79 Score=744.65 Aligned_cols=263 Identities=49% Similarity=0.901 Sum_probs=247.9
Q ss_pred cccccHHHHHHHHHHHHhhhHHHHHHHHHhhccce----------------------------eccCCCCCCCCCCcccc
Q 000161 1414 VLGWQQNAAKIGMQRCAASSQWFNERISLARYAHI----------------------------LWISDDGVPDLGGTSEE 1465 (1988)
Q Consensus 1414 ~L~WQ~~~akr~i~hyl~~~~wl~~~i~laRY~~I----------------------------LW~S~~~~PDlGG~E~D 1465 (1988)
+|+||+.++|+|++||++++.||+++|++|||+|| ||||++++|||||+|.|
T Consensus 100 ~L~WQ~~~~r~~i~~~l~~~~wl~~~i~laRY~~IPlgNl~~D~~~f~~Di~yAR~L~~~~~VLW~S~~~~PDlGG~e~D 179 (396)
T PF08490_consen 100 ALGWQRHAARRMIQHYLNLGSWLSERIELARYAHIPLGNLPSDNPLFLIDIFYARRLRKNNHVLWWSPSPRPDLGGKEED 179 (396)
T ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCcchHHHHHHHHHHHHHHHCCeEEeCCCCCCCCCCcchhh
Confidence 99999999999999999999999999999999999 99999999999999999
Q ss_pred ccc---cccccCCceeccCCcceeEEEEEEecchhHHHHHhhhhcccccCCccc--cccCCCCCC-CCCCCcccccccCC
Q 000161 1466 DEC---FADEVHQPVLTYPGAYRKVSVELKIHHLSVNALLKSNQVNEMEGGGLF--GFDQDMNSG-PYNNELCGFDETTS 1539 (1988)
Q Consensus 1466 ~~~---~~~~~~~~~in~pG~Y~svcvEl~i~~LaVnaiL~Ss~ine~EG~~~~--~f~~~~~~~-~~~~~~~~~~e~~~ 1539 (1988)
|.+ ..+++++|+||+||+|++|||||+|+||||||||||++|||+||+++. +|+...++. +...+.+.|+|+++
T Consensus 180 d~~~~~~~~~~~~~~in~pG~Y~~vcvEl~i~~LavnaiL~S~~i~e~EG~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 259 (396)
T PF08490_consen 180 DNRLLWDMDELESPEINNPGAYRSVCVELDISNLAVNAILQSSLINELEGSDSAGFNFDTASDASNGSANSSSSYDESAF 259 (396)
T ss_pred hhcccccccccCceEEECCCccceEEEEEEecceeHHHHHHHhHHhhhcCCccccccccccccccccccccccccccccc
Confidence 443 346778899999999999999999999999999999999999999855 455544432 33456788999999
Q ss_pred ChhHHHHHHHHHHHHHHHHHhcCCccHHHHHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHhHcCCeEEEEe
Q 000161 1540 SAPAFRVVKQLIQRCLTDAVTSGNVFADAILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFAMLLAEFRKLGATIIFAN 1619 (1988)
Q Consensus 1540 ~~~af~iLr~mV~~w~~da~~~~n~~AD~ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~flqLlaEfkRLGs~VVyAd 1619 (1988)
|+++|+|||+||++||+|+ .++|++||.||+||||||+||+|+||||||||+||+||||+|+||++||||||++|||||
T Consensus 260 ~~~~f~iLr~mv~~w~~d~-~~~n~~AD~ll~~f~rWl~sp~S~LyDPaL~~~v~~LmkK~flqLl~Ef~rlG~~VVyA~ 338 (396)
T PF08490_consen 260 CSAAFRILRSMVKSWLRDA-LKGNSFADSLLQHFYRWLSSPSSLLYDPALHRMVHNLMKKVFLQLLAEFRRLGSKVVYAD 338 (396)
T ss_pred cHHHHHHHHHHHHHHHHHH-hcCCccHHHHHHHHHHHHcCCcccccCHHHHHHHHHHHHHHHHHHHHHHHHcCCEEEEEc
Confidence 9999999999999999995 459999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeEEEEcCCCChHhHHHHHHHHHHHhhccccccceecchhchheeeeeecCCCcccc
Q 000161 1620 FSKVIIDTGKFDLSAAKAYCDSLLKALQTRELFEWIELEPVHFWHSLLFMDQYNYGGI 1677 (1988)
Q Consensus 1620 ~~riil~T~K~~v~~A~ay~~yi~~si~~~~lF~~l~L~~~~yW~~LlwmD~~NygGi 1677 (1988)
|+||||+|+|.++++|+||++||+++|+++|||++|+|+|++||++|||||++|||||
T Consensus 339 ~~riil~T~K~~~~~A~ay~~yi~~~i~~~~lF~~l~l~~~~~w~~LlwmD~~NygGi 396 (396)
T PF08490_consen 339 FNRIILCTGKTSLENAYAYVQYILKSIRSRELFSWLDLKPVRYWDSLLWMDPYNYGGI 396 (396)
T ss_pred CCEEEEECCCCCHHHHHHHHHHHHHHHhcccccccEEeEHHHHhhhheEecccccCCC
Confidence 9999999999999999999999999999999999999999999999999999999997
No 14
>cd05534 POLBc_zeta DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol 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.
Probab=100.00 E-value=2.2e-66 Score=645.09 Aligned_cols=432 Identities=20% Similarity=0.228 Sum_probs=319.3
Q ss_pred hhHHHHHHHHHHHHHHCCeeccCCCCCCchhhhcccccCCCCCCcceeeeccCccccCCCCCCccCChhHHHHHhhhhhh
Q 000161 467 GSGTLCEMLLMVQAYKANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFKLDPSAYEQLLNNLDR 546 (1988)
Q Consensus 467 Gsg~~~E~LLm~~a~~~n~i~Pnk~~~~~~~~~~g~l~~setY~GG~V~~p~~GvY~~d~~~~f~~~~~~~~~l~~~~~~ 546 (1988)
|+|.++|++|+++|++.|+++|++...... . ..++|.||+|++|++|+|++
T Consensus 1 g~q~rve~~llr~~~~~g~~~p~~~~~~~~-----~--~~~~~~g~~V~eP~~G~y~~---------------------- 51 (451)
T cd05534 1 GSQFRVESMLLRLAKPENYILPSPSRQQVA-----Q--QRALECLPLVMEPESGFYSD---------------------- 51 (451)
T ss_pred CCeEEeHHHHHHHHHHcCEEeecCchhccc-----c--ccccccCcEeecCCcCcccC----------------------
Confidence 789999999999999999999987532110 0 13468899999999999887
Q ss_pred hhHHHHhHhcccccccccchHHHHHHHHHHHHhhccCCCcccCCeEEEEeccccchHHHHhcCCCCCccccccccccccC
Q 000161 547 DLQYAIKVEGKMDLESVSNYDEVKNAIMEKLLRLQEEPIREECPLIYHLDVAAMYPNIILTNRLQPPSIVTDEVCTACDF 626 (1988)
Q Consensus 547 ~l~~~~~~e~~~~~~~~~n~~~v~~~i~~~l~~l~~~p~~~~~p~V~~LDf~SLYPsII~t~NL~p~Tiv~~~~c~~c~~ 626 (1988)
||++|||+|||||||++|||||+|++.... +.
T Consensus 52 --------------------------------------------~V~vLDF~SLYPSIi~~~Nic~sT~~~~~~----~~ 83 (451)
T cd05534 52 --------------------------------------------PVIVLDFQSLYPSIMIAYNYCYSTCLGRVE----EL 83 (451)
T ss_pred --------------------------------------------ceEEEecccccHHHHHHhCcCccccccccc----cc
Confidence 699999999999999999999999986421 00
Q ss_pred CCCCCccccccccccccccccC-CcchhhHhhhhcccccccCCCCCcccccccCchHHHHHHHHHHHHHhhhhhcccccc
Q 000161 627 NRPGKTCLRKLEWVWRGEIFMG-KRSDYYHLKKQIESEFVDGTNGHLSKSFLDLPKMEQQSRLKDRLKKYCQKAYKRVLD 705 (1988)
Q Consensus 627 n~p~~~c~r~m~w~~~ge~~p~-~~~ey~~i~~~l~~e~f~~~~~g~~~~~~~L~~~~q~~~lkkrl~~y~~kvy~k~~~ 705 (1988)
+.+ | ....|. +.+. +..+. +......+.....++ -.|.+.+.
T Consensus 84 ~~~---~-~~~~~~----~~~~~~~~~~--~~~~~~~~~~~~p~~---------------------------~~f~~~~~ 126 (451)
T cd05534 84 NGG---G-KFGFLG----VKLYLPPPPL--DLLLLKDDVTISPNG---------------------------VMFVKKSV 126 (451)
T ss_pred ccc---c-cccccc----cccccccccc--ccccCCCcEEECCCc---------------------------ceeecCCC
Confidence 000 1 111111 0000 00000 000000000000000 01111110
Q ss_pred cccccccccccccccccchHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHHHHHHHHHHhhhc
Q 000161 706 KPVTELREAGICMRENSFYVDTVRSFRDRRYEYKGLNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSF 785 (1988)
Q Consensus 706 ~~~~~~r~~~icqre~~f~~~~lr~f~drR~~~K~l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~ 785 (1988)
..+++|.+|+.|+++|.++|++||+.+. ++. +..+||.+|+|+|+++||+
T Consensus 127 --------------~~Gilp~iL~~Ll~~R~~~K~~mk~~~~---------~~~-------~~~~ld~~Q~AlKi~~NS~ 176 (451)
T cd05534 127 --------------RKGILPKMLEEILDTRIMVKKAMKKYKD---------DKK-------LQRILDARQLALKLLANVT 176 (451)
T ss_pred --------------CCCchHHHHHHHHHHHHHHHHHHhhCCC---------CHH-------HHHHHHHHHHHHHHHhhcc
Confidence 2369999999999999999999876321 122 3578999999999999999
Q ss_pred cccccccC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHH---cCCe-EEEccceeeEEcCCCCCccccccccccccccccc
Q 000161 786 YGYVMRKG-ARWYSMEMAGVVTYTGAKIIQNARLLIEK---IGKP-LELDTDGIWCVLPGSFPENFTFKTKDLKKKLTIS 860 (1988)
Q Consensus 786 YGy~g~~~-sR~ys~e~A~~VT~~Gr~iI~~a~~lve~---~G~~-vygDTDSI~~~lp~~~pe~~~~k~~~g~k~i~~s 860 (1988)
|||+|++. +||||.++|++||++||++|++|++++|+ .|+. ||||||||||.+++...++ ++ ..| +++
T Consensus 177 YGy~G~~~~gr~~~~~iA~~IT~~GR~~l~~~~~~ie~~~~~g~~VIYGDTDSvfv~~~~~~~~~-~~--~~~-~~i--- 249 (451)
T cd05534 177 YGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLFVLLPGRTKEE-AF--KIG-KEI--- 249 (451)
T ss_pred ccccccccccccccHHHHHHHHHHHHHHHHHHHHHHhhccccCceEEeecccceeEecCCCCHHH-HH--HHH-HHH---
Confidence 99999996 69999999999999999999999999999 7887 6999999999987642111 11 112 222
Q ss_pred ccccccchhhhccccchhhhhccCCccccccccccceeEEeeeceeeeeecccccccCcccccceEEEcC------CCCE
Q 000161 861 YPCVMLNVDVARNNTNDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFND------DGTL 934 (1988)
Q Consensus 861 y~~~~ln~~V~~~~tN~~y~~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~~~------dG~~ 934 (1988)
...| |.. | +.+|++|+|++|++|+|.+ ||||||+.. +|++
T Consensus 250 ------~~~i-----n~~-----------~----~~~i~le~E~vy~~~ll~~--------KKrYag~~~~~~~~~~~ki 295 (451)
T cd05534 250 ------AEAV-----TAA-----------N----PSPIKLKFEKVYHPCVLVT--------KKRYVGYKYESPDQTEPTF 295 (451)
T ss_pred ------HHHH-----HHh-----------C----CCCceeeHHHHHHHHHHHh--------hhhEEEEEEecCCCCCceE
Confidence 1111 211 1 3456777779999999965 999999742 2344
Q ss_pred EEEEeeeeccCChhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhhhhhccccccChhh
Q 000161 935 AELKGFEIKRRGELKLIKVFQAELFDKFLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADSELIDYISESSTMSKSLAD 1014 (1988)
Q Consensus 935 ~e~KG~E~kRRd~~~liK~~q~~v~~~~L~g~~lee~~~~v~~v~~~~~d~L~~~~~~~~~~eLi~~i~~~k~lsK~l~e 1014 (1988)
++||+|++|||||+|+|++|+++++.+|.+++++++.+.+.+.+. +++.+.++.++|+ ++|++++..-.
T Consensus 296 -~~KGle~vRrD~~~~~k~~~~~vl~~il~~~d~~~~~~~l~~~~~------~l~~g~~~~~dli----i~k~l~~~~y~ 364 (451)
T cd05534 296 -DAKGIETVRRDGCPAVQKILEKSLRILFETKDLSTVKSYLQRQWS------KLLQGRVSIQDFI----FAKEVRLGTYK 364 (451)
T ss_pred -EeecceEEecccHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHH------HHHcCCCCHHHeE----EEEEeeccccC
Confidence 999999999999999999999999999999999999888876654 3567889989988 89999886533
Q ss_pred hCCCCChHHHHHHHHHhhcCCCcccCCCCeeEEEEEcCCCCCCCcccccchhhhcchHHHHHHHHHhhhcCCCCCCCccc
Q 000161 1015 YGEQKSCAVTTARRLSDFLGDTMVKDKGLRCQYIVACEPQGTPVSERAVPVAIFETDAEIMKFYLRKWCKTSSDVGIRSI 1094 (1988)
Q Consensus 1015 Y~~~k~~~v~~A~rl~e~lG~~~~~~~G~~i~YVI~~~p~g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~~~~~d~~~~ 1094 (1988)
|.+..+||+.+|+|+++. |.+..+..|++|+|||++++.|.++++||+|+..|..+ ....
T Consensus 365 ~~~~~p~hv~~A~k~~~~-~~~~~~~~G~rI~YViv~~~~~~~~~~ra~~~~~~~~~-------------------~~~~ 424 (451)
T cd05534 365 EGATLPAGAIVALRRMEK-DPRAEPQYGERVPYVVVRGEPGSRLIDLVVSPEEFLAD-------------------PSLR 424 (451)
T ss_pred ccCCCChHHHHHHHHHHh-CCCCCCCCCCEEEEEEEeCCCCCcHHHhccCHHHHhhc-------------------CCCC
Confidence 344568999999888874 55567899999999999998888999999999755322 2468
Q ss_pred cCHHHHHHhhhhhhhheeechhhhhhcc
Q 000161 1095 VDWSYYKQRLSSAIQKIITIPAAMQKVS 1122 (1988)
Q Consensus 1095 iD~~YYierl~~~i~ki~~iPa~lq~~~ 1122 (1988)
||++||+++ |++|++.|.+.
T Consensus 425 iD~~yYi~~--------Qi~~~~~ril~ 444 (451)
T cd05534 425 LDAEYYITK--------QIIPALDRLFN 444 (451)
T ss_pred CChHHHHHh--------cCHHHHHHHHH
Confidence 999999999 99999999753
No 15
>cd05536 POLBc_B3 DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.
Probab=100.00 E-value=4.1e-65 Score=622.21 Aligned_cols=294 Identities=27% Similarity=0.409 Sum_probs=249.1
Q ss_pred ccchHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCCCHH
Q 000161 721 NSFYVDTVRSFRDRRYEYKGLNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGARWYSME 800 (1988)
Q Consensus 721 ~~f~~~~lr~f~drR~~~K~l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~sR~ys~e 800 (1988)
.+++|.+|+.|+++|.++|++||+.+. ++. +..+||++|+|+|+++||+|||+|+++|||||++
T Consensus 66 ~Gilp~il~~ll~~R~~~K~~mk~~~~---------~~~-------~~~~~d~~Q~AlKi~~NS~YG~~g~~~~r~~~~~ 129 (371)
T cd05536 66 PGFIPSVLEDLLEERRRIKEKMKKLDP---------ESE-------EYKLLDERQRAIKILANSFYGYMGWANARWYCKE 129 (371)
T ss_pred CCchHHHHHHHHHHHHHHHHHHhhCCC---------cHH-------HHHHHHHHHHHHHHHHhccccccccccccCCCHH
Confidence 468999999999999999999886321 112 3579999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCe-EEEccceeeEEcCCCCCcccccccccccccccccccccccchhhhccccchhh
Q 000161 801 MAGVVTYTGAKIIQNARLLIEKIGKP-LELDTDGIWCVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVDVARNNTNDQY 879 (1988)
Q Consensus 801 ~A~~VT~~Gr~iI~~a~~lve~~G~~-vygDTDSI~~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~V~~~~tN~~y 879 (1988)
+|++||++||++|+.|++++++.|+. ||||||||||.+|+... .. ..+ +++ + +.
T Consensus 130 ~A~~iT~~GR~~l~~~~~~i~~~g~~VIYgDTDSvfv~~~~~~~---~~--~~~-~~l------------~--~~----- 184 (371)
T cd05536 130 CAEAVTAWGREYIKTTIKIAEEKGFKVIYGDTDSLFVKIDGADA---VK--KKV-KKL------------L--KY----- 184 (371)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCEEEEEcCcccEEeecCchH---HH--HHH-HHH------------H--HH-----
Confidence 99999999999999999999999998 69999999999886421 00 011 111 1 01
Q ss_pred hhccCCccccccccccceeEEeeeceeeeeecccccccCcccccceEEEcCCCCEEEEEeeeeccCChhHHHHHHHHHHH
Q 000161 880 QTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLAELKGFEIKRRGELKLIKVFQAELF 959 (1988)
Q Consensus 880 ~~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~~~dG~~~e~KG~E~kRRd~~~liK~~q~~v~ 959 (1988)
+.+..+|++|+||+|++|++++ ||||||++.||++ ++||+|++|||+|+|+|++|++++
T Consensus 185 ------------i~~~~~i~le~E~vy~~~l~~~--------KKrY~g~~~~g~i-~~KG~e~~RrD~~~~~k~~~~~~l 243 (371)
T cd05536 185 ------------INEELPLELEIEKFYKRGFFVT--------KKRYAGLTEDGKI-DVVGLEVVRRDWSEIAKETQARVL 243 (371)
T ss_pred ------------HHhcCCeeEEEeeeeHHHHHhh--------hceeEEEccCCeE-EEEeeeeEeCccHHHHHHHHHHHH
Confidence 1122348888889999999975 9999999999998 899999999999999999999999
Q ss_pred HHHhCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhhhhhccccccChhhhCCCCChHHHHHHHHHhhcCCCccc
Q 000161 960 DKFLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADSELIDYISESSTMSKSLADYGEQKSCAVTTARRLSDFLGDTMVK 1039 (1988)
Q Consensus 960 ~~~L~g~~lee~~~~v~~v~~~~~d~L~~~~~~~~~~eLi~~i~~~k~lsK~l~eY~~~k~~~v~~A~rl~e~lG~~~~~ 1039 (1988)
+.+|.+++++++++.++++.++ +++++++.++|+ ++|+++|.+++|.+ ++||+++|+||+++ | ..+
T Consensus 244 ~~ll~~~~~~~~~~~~~~~~~~------l~~g~~~~~dli----i~k~l~k~~~~Y~~-~~~hv~~a~~l~~~-g--~~~ 309 (371)
T cd05536 244 EAILKEGDVEEAVKIVKEVIEK------LKRGEVPPEKLV----IWKQLTKDLSEYKA-TGPHVAAAKKLAKR-G--YKV 309 (371)
T ss_pred HHHHcCCCHHHHHHHHHHHHHH------HHcCCCCHHHeE----EeHHhcCCHHHhCC-CCcHHHHHHHHHhc-C--CCC
Confidence 9999999999999888776653 467889988887 79999999999986 68999999999995 7 568
Q ss_pred CCCCeeEEEEEcCCCCCCCcccccchhhhcchHHHHHHHHHhhhcCCCCCCCccccCHHHHHHhhhhhhhheeechhhhh
Q 000161 1040 DKGLRCQYIVACEPQGTPVSERAVPVAIFETDAEIMKFYLRKWCKTSSDVGIRSIVDWSYYKQRLSSAIQKIITIPAAMQ 1119 (1988)
Q Consensus 1040 ~~G~~i~YVI~~~p~g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~~~~~d~~~~iD~~YYierl~~~i~ki~~iPa~lq 1119 (1988)
.+|++|+|||+++++ ++++||+|++.|.. ...+|++||+++ |++|++.|
T Consensus 310 ~~G~rI~Yvi~~~~~--~~~dr~~p~~~~~~---------------------~~~iD~~yYi~~--------qi~~pl~r 358 (371)
T cd05536 310 RPGTKIGYVIVKGSG--KISDRAYPYDMVDE---------------------KHKYDAEYYIDN--------QVLPAVLR 358 (371)
T ss_pred CCCCEEEEEEEECCC--cccccccCHHHhcc---------------------CCCCCHHHHHHH--------hcHHHHHH
Confidence 899999999998753 79999999977641 357999999999 99999888
Q ss_pred hc
Q 000161 1120 KV 1121 (1988)
Q Consensus 1120 ~~ 1121 (1988)
.+
T Consensus 359 il 360 (371)
T cd05536 359 IL 360 (371)
T ss_pred HH
Confidence 74
No 16
>cd05533 POLBc_delta DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand.
Probab=100.00 E-value=4.3e-65 Score=625.69 Aligned_cols=302 Identities=22% Similarity=0.245 Sum_probs=250.9
Q ss_pred ccchHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCCCHH
Q 000161 721 NSFYVDTVRSFRDRRYEYKGLNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGARWYSME 800 (1988)
Q Consensus 721 ~~f~~~~lr~f~drR~~~K~l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~sR~ys~e 800 (1988)
.+++|.+|+.|+++|.++|++||+ +.|+. +..+||++|+|+|+++||+|||+|+++|||||.+
T Consensus 73 ~Gilp~iL~~Ll~~R~~~K~~mk~----------~~d~~-------~~~~ld~~Q~AlKi~~NS~YG~~G~~~~r~~~~~ 135 (393)
T cd05533 73 KGLLPEILEELLAARKRAKKDLKE----------ETDPF-------KKAVLDGRQLALKISANSVYGFTGATVGKLPCLE 135 (393)
T ss_pred CCchHHHHHHHHHHHHHHHHHHhh----------CCCHH-------HHHHHHHHHHhhheeeeecccccccccCCccchH
Confidence 469999999999999999998875 22454 2469999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHc---------CCe-EEEccceeeEEcCCCCCcccccccccccccccccccccccchhh
Q 000161 801 MAGVVTYTGAKIIQNARLLIEKI---------GKP-LELDTDGIWCVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVDV 870 (1988)
Q Consensus 801 ~A~~VT~~Gr~iI~~a~~lve~~---------G~~-vygDTDSI~~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~V 870 (1988)
+|++||++||++|+.|++++|+. |.. ||||||||||.+++...++ ++ ..+ +++ +..|
T Consensus 136 ~A~~iT~~GR~~l~~~~~~ie~~~~~~~g~~~~~~VIYGDTDSvfv~~~~~~~~~-~~--~~~-~ei---------~~~i 202 (393)
T cd05533 136 ISSSVTSFGRQMIEKTKKLVEEKYTKANGYSHDAKVIYGDTDSVMVKFGVSDVEE-AM--KLG-KEA---------AEYV 202 (393)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHhhcccccCCCceEEEecCCCceEEEcCCCCHHH-HH--HHH-HHH---------HHHH
Confidence 99999999999999999999985 555 6999999999987642221 11 122 222 2222
Q ss_pred hccccchhhhhccCCccccccccccceeEEeeeceeeeeecccccccCcccccceEEEcCC-----CCEEEEEeeeeccC
Q 000161 871 ARNNTNDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDD-----GTLAELKGFEIKRR 945 (1988)
Q Consensus 871 ~~~~tN~~y~~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~~~d-----G~~~e~KG~E~kRR 945 (1988)
|.. | +.+|++|+||+|.+||+++ ||||||+..+ |++ ++||+|++||
T Consensus 203 -----~~~-----------~----~~~i~Le~E~vy~~~ll~~--------KKrYag~~~~~~~~~~ki-~~KGle~vRR 253 (393)
T cd05533 203 -----SKK-----------F----IKPIKLEFEKVYFPYLLIN--------KKRYAGLLWTNPDKHDKM-DTKGIETVRR 253 (393)
T ss_pred -----Hhc-----------C----CCCeEEeeHHHHHHHHHHH--------HhhheEEEeecCCCCcee-EEeceEEEcc
Confidence 211 1 3457778889999999986 9999997432 455 9999999999
Q ss_pred ChhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhhhhhccccccChhhhCCCCChHHHH
Q 000161 946 GELKLIKVFQAELFDKFLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADSELIDYISESSTMSKSLADYGEQKSCAVTT 1025 (1988)
Q Consensus 946 d~~~liK~~q~~v~~~~L~g~~lee~~~~v~~v~~~~~d~L~~~~~~~~~~eLi~~i~~~k~lsK~l~eY~~~k~~~v~~ 1025 (1988)
|||+|+|++|+++++.+|.+++++++.+.+++++++ +..+++|.++|+ ++++++|.+++|.. ++||+.+
T Consensus 254 D~~~~~k~~~~~vl~~il~~~~~~~~~~~~~~~~~~------l~~~~~~~~~l~----i~k~l~k~~~~Y~~-~~phv~~ 322 (393)
T cd05533 254 DNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISD------LLQNKIDISLLV----ITKALTKTADDYAG-KQAHVEL 322 (393)
T ss_pred cchHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH------HHcCCCCHHHEE----EEeeecCChhhcCC-CCchHHH
Confidence 999999999999999999999999999988877653 457899988988 89999999999996 5899999
Q ss_pred HHHHHhhcCCCcccCCCCeeEEEEEcCCCCCCCcccccchhhhcchHHHHHHHHHhhhcCCCCCCCccccCHHHHHHhhh
Q 000161 1026 ARRLSDFLGDTMVKDKGLRCQYIVACEPQGTPVSERAVPVAIFETDAEIMKFYLRKWCKTSSDVGIRSIVDWSYYKQRLS 1105 (1988)
Q Consensus 1026 A~rl~e~lG~~~~~~~G~~i~YVI~~~p~g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~~~~~d~~~~iD~~YYierl~ 1105 (1988)
|+||+++ |.+..+.+|++|+|||+++..|.++++||+++..+..+ +..||++|||++
T Consensus 323 A~rl~~~-~~g~~~~~G~rI~Yvi~~~~~~~~~~~~a~~~~~~~~~--------------------~~~iD~~yYi~~-- 379 (393)
T cd05533 323 AERMRKR-DPGSAPNVGDRVPYVIIKGAKGAKAYEKAEDPIYVLEN--------------------NIPIDTQYYLEN-- 379 (393)
T ss_pred HHHHHhc-CCCCCCCCCCEEEEEEEECCCCCcHHhhccCHHHHHhc--------------------CCCCChHHHHHh--
Confidence 9999985 55578999999999999988788999999998654321 357999999999
Q ss_pred hhhhheeechhhhhhc
Q 000161 1106 SAIQKIITIPAAMQKV 1121 (1988)
Q Consensus 1106 ~~i~ki~~iPa~lq~~ 1121 (1988)
|++|++.|.+
T Consensus 380 ------qi~~pl~ri~ 389 (393)
T cd05533 380 ------QLSKPLLRIF 389 (393)
T ss_pred ------cchHHHHHHH
Confidence 9999999875
No 17
>cd05532 POLBc_alpha DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. In most organisms no specific repair role, other than check point control, has been assigned to this enzyme. Pol alpha contains both polymerase and exonuclease domains, but lacks exonuclease activity suggesting that the exonuclease domain may be for structural purposes only.
Probab=100.00 E-value=2.4e-64 Score=620.95 Aligned_cols=308 Identities=24% Similarity=0.314 Sum_probs=255.7
Q ss_pred ccchHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCCCHH
Q 000161 721 NSFYVDTVRSFRDRRYEYKGLNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGARWYSME 800 (1988)
Q Consensus 721 ~~f~~~~lr~f~drR~~~K~l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~sR~ys~e 800 (1988)
.+++|.+|+.|+++|.++|++||..+ |+. +..+||++|+|+|+++||+|||+|+++|||||++
T Consensus 70 ~Gilp~~l~~l~~~R~~~K~~~k~~~----------d~~-------~~~~~d~~Q~alKi~~NS~YG~~g~~~~r~~~~~ 132 (400)
T cd05532 70 KGILPRIIRKLVERRRQVKKLMKSEK----------DPD-------KKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKP 132 (400)
T ss_pred CCchHHHHHHHHHHHHHHHHHHhcCC----------CHH-------HHHHHHHHHHHHHHHHhhcccccccccccccChH
Confidence 46999999999999999999987632 443 3478999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCe-EEEccceeeEEcCCCCCcccccccccccccccccccccccchhhhccccchhh
Q 000161 801 MAGVVTYTGAKIIQNARLLIEKIGKP-LELDTDGIWCVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVDVARNNTNDQY 879 (1988)
Q Consensus 801 ~A~~VT~~Gr~iI~~a~~lve~~G~~-vygDTDSI~~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~V~~~~tN~~y 879 (1988)
+|++||++||++|+.|++++++.|+. ||||||||||.++....++ .+ +.+ +++ .+ .+|..|
T Consensus 133 ~A~~iT~~GR~~l~~~~~~~e~~g~~ViYgDTDSifv~~~~~~~~~-~~--~~~-~~i-------------~~-~in~~~ 194 (400)
T cd05532 133 LAALITSKGREILQKTKDLVEKMNLEVIYGDTDSIMINTGTTDYEE-AK--KLG-NKI-------------KK-EVNKSY 194 (400)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCEEEEeCCCeEEEecCCCCHHH-HH--HHH-HHH-------------HH-HHHHHH
Confidence 99999999999999999999999998 6999999999987532221 11 112 111 11 123222
Q ss_pred hhccCCccccccccccceeEEeeeceeeeeecccccccCcccccceEEEcCC------CCEEEEEeeeeccCChhHHHHH
Q 000161 880 QTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDD------GTLAELKGFEIKRRGELKLIKV 953 (1988)
Q Consensus 880 ~~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~~~d------G~~~e~KG~E~kRRd~~~liK~ 953 (1988)
. +|++|+||+|.+|+|++ ||||||+..+ |++ ++||+|++|||+|+|+|+
T Consensus 195 ~----------------~i~le~e~iy~~~ll~~--------KKrYag~~~~~~~~~~~k~-~~KGie~~RrD~~~~~k~ 249 (400)
T cd05532 195 K----------------KLEIDIDGVFKRLLLLK--------KKKYAALKVVDDDKGKLKK-EVKGLDIVRRDWCPLSKE 249 (400)
T ss_pred H----------------HHHHHHHHHhHHHHhhh--------hhcceEEEeecCCccceee-EEeceeEEecccHHHHHH
Confidence 1 47888889999999975 9999997543 345 999999999999999999
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhhhhhccccccChhhhCCC-CChHHHHHHHHHhh
Q 000161 954 FQAELFDKFLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADSELIDYISESSTMSKSLADYGEQ-KSCAVTTARRLSDF 1032 (1988)
Q Consensus 954 ~q~~v~~~~L~g~~lee~~~~v~~v~~~~~d~L~~~~~~~~~~eLi~~i~~~k~lsK~l~eY~~~-k~~~v~~A~rl~e~ 1032 (1988)
+|+++++.+|.+++.+++++.+.+.++.+.+. +..+.++.++|+ ++++++|.+++|... .+||+.+|+||+++
T Consensus 250 ~~~~vl~~ll~~~~~~~~~~~i~~~~~~~~~~--l~~~~~~~~~li----i~k~l~k~~~~Y~~~~~~~hv~~A~rl~~~ 323 (400)
T cd05532 250 IGNYVLDQILSDKSREDIVENIHEYLRKINED--LRNGKIPLEKFI----ITKQLTKNPEEYPDKKSLPHVQVALRMNKR 323 (400)
T ss_pred HHHHHHHHHHcCCChHHHHHHHHHHHHHHHHH--HHcCCCCHHHEE----EeecccCChHHcCCCCCCcHHHHHHHHHHc
Confidence 99999999999999999998888777766664 456889988887 899999999999975 57999999999984
Q ss_pred cCCCcccCCCCeeEEEEEcCCCCCCCcccccchhhhcchHHHHHHHHHhhhcCCCCCCCccccCHHHHHHhhhhhhhhee
Q 000161 1033 LGDTMVKDKGLRCQYIVACEPQGTPVSERAVPVAIFETDAEIMKFYLRKWCKTSSDVGIRSIVDWSYYKQRLSSAIQKII 1112 (1988)
Q Consensus 1033 lG~~~~~~~G~~i~YVI~~~p~g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~~~~~d~~~~iD~~YYierl~~~i~ki~ 1112 (1988)
| ..+.+|++|+|||++++.+.++++||+|+..|..+ ....||++||+++ |
T Consensus 324 -g--~~~~~G~rI~Yvi~~~~~~~~~~~ra~~~~~~~~~-------------------~~~~iD~~yYi~~--------q 373 (400)
T cd05532 324 -G--RKVKAGDTIPYIICKDGSSKSLADRAYHPDEVKKN-------------------ENLKIDIEYYLSQ--------Q 373 (400)
T ss_pred -C--CCCCCCCEEEEEEEeCCCCCchhhhccCHHHHhhc-------------------cCCCCChHHHHHH--------h
Confidence 7 66889999999999998888899999999876521 1467999999999 9
Q ss_pred echhhhhhccCCC
Q 000161 1113 TIPAAMQKVSNPV 1125 (1988)
Q Consensus 1113 ~iPa~lq~~~npv 1125 (1988)
++||+.|.+ .|+
T Consensus 374 i~~pl~ri~-~~~ 385 (400)
T cd05532 374 ILPPISRLC-EPI 385 (400)
T ss_pred hHHHHHHHH-Hhc
Confidence 999998865 344
No 18
>cd05537 POLBc_Pol_II DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Probab=100.00 E-value=9.6e-63 Score=599.13 Aligned_cols=298 Identities=22% Similarity=0.311 Sum_probs=237.2
Q ss_pred ccccchHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCCC
Q 000161 719 RENSFYVDTVRSFRDRRYEYKGLNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGARWYS 798 (1988)
Q Consensus 719 re~~f~~~~lr~f~drR~~~K~l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~sR~ys 798 (1988)
++.+++|++|+.|+++|.++|+.++. .+|+|+|+++||+|||+|++++||||
T Consensus 65 ~~~Gilp~~l~~l~~~R~~~K~~~~~----------------------------~~q~AlKi~~Ns~YG~~g~~~~r~~~ 116 (371)
T cd05537 65 REKHILPDLIARLWAARDEAKREKNA----------------------------PLSQAIKIIMNSFYGVLGSTGCRFFD 116 (371)
T ss_pred cCCCchHHHHHHHHHHHHHHHHhccH----------------------------HHHHhHhhheecceeecccccccccC
Confidence 34479999999999999998854321 27999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCe-EEEccceeeEEcCCCCCcccccccccccccccccccccccchhhhccccch
Q 000161 799 MEMAGVVTYTGAKIIQNARLLIEKIGKP-LELDTDGIWCVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVDVARNNTND 877 (1988)
Q Consensus 799 ~e~A~~VT~~Gr~iI~~a~~lve~~G~~-vygDTDSI~~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~V~~~~tN~ 877 (1988)
+++|++||++||++|+.|++++|+.|+. ||||||||||.+++..+.+... +.| .++ + . .+|.
T Consensus 117 ~~~A~~iT~~GR~~l~~~~~~~e~~g~~ViYgDTDSvfV~~~~~~~~~~~~--~~~-~~l-----~----~-----~In~ 179 (371)
T cd05537 117 PRLASSITLRGHEIMKQTRAWIEQQGYQVIYGDTDSTFVWLGEELDAAEAQ--AIG-KEL-----A----S-----QINQ 179 (371)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHcCCEEEEecCCceEEecCCCCCHHHHH--HHH-HHH-----H----H-----HHHH
Confidence 9999999999999999999999999998 5999999999988643332222 122 222 1 2 2244
Q ss_pred hhhhccCCccccccccccceeEEeeeceeeeeecccccccCcccccceEEEcC---CCCEEEEEeeeeccCChhHHHHHH
Q 000161 878 QYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFND---DGTLAELKGFEIKRRGELKLIKVF 954 (1988)
Q Consensus 878 ~y~~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~~~---dG~~~e~KG~E~kRRd~~~liK~~ 954 (1988)
.|... .+.++.++++..| |+||+|++||||++++.+.+.||||||+.. +|++ ++||+|++|||||+|+|++
T Consensus 180 ~~~~~---~~~~~~~~~~l~L--e~Ekvy~~~ll~~~~~~~~~~KKrYag~~~~~~~~~i-~~KGle~vRrD~~~l~k~~ 253 (371)
T cd05537 180 WWAQK---LKEEFGLESFLEI--EFETHYSRFFMPTIRGSDEGSKKRYAGLKSTDGGDEL-VFKGLETVRSDWTPLARQF 253 (371)
T ss_pred HHHHh---hhhhhcCCCCceE--EEeeeeeeeeeeccccccccccceEEEEEEECCCcEE-EeecceeEecchHHHHHHH
Confidence 44332 2334544444545 555999999999999988899999999755 5666 9999999999999999999
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhhhhhccccccChhhhCCCCChHHHHHHHHHhhcC
Q 000161 955 QAELFDKFLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADSELIDYISESSTMSKSLADYGEQKSCAVTTARRLSDFLG 1034 (1988)
Q Consensus 955 q~~v~~~~L~g~~lee~~~~v~~v~~~~~d~L~~~~~~~~~~eLi~~i~~~k~lsK~l~eY~~~k~~~v~~A~rl~e~lG 1034 (1988)
|+++++.+|.++++++.++.+. + +++.++++ ++|+ ++++|+|++++|.++++|||++|++|+++ |
T Consensus 254 ~~~vl~~il~~~~~~~~~~~~~---~------~l~~g~~~-~~lv----i~k~L~k~~~~Y~~~~~phv~aa~~~~~~-~ 318 (371)
T cd05537 254 QKELYERVFNDEPYEGFIKETV---E------ELLAGELD-ELLV----YRKRLRRPLSEYTKNVPPHVQAARLADQI-N 318 (371)
T ss_pred HHHHHHHHhcCCCHHHHHHHHH---H------HHHcCCCc-hHhE----EehhcCCCHHHcCCCCCcHHHHHHHHHhc-C
Confidence 9999999999999987655442 2 35678888 8887 89999999999997789999999999985 6
Q ss_pred CC-cccCCCCeeEEEEEcCCCCCCCcccccchhhhcchHHHHHHHHHhhhcCCCCCCCccccCHHHHHHhhhhhhhheee
Q 000161 1035 DT-MVKDKGLRCQYIVACEPQGTPVSERAVPVAIFETDAEIMKFYLRKWCKTSSDVGIRSIVDWSYYKQRLSSAIQKIIT 1113 (1988)
Q Consensus 1035 ~~-~~~~~G~~i~YVI~~~p~g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~~~~~d~~~~iD~~YYierl~~~i~ki~~ 1113 (1988)
.. ..+..|++|+|||+++.. .|++. .+..||++||+++ |+
T Consensus 319 ~~~~~~~~gd~I~YVi~~~g~--------~~~~~-----------------------~~~~iD~~yYi~~--------qi 359 (371)
T cd05537 319 RELGRPRQYQWIEYVITVNGP--------EPLEY-----------------------RTSPLDYQHYIDK--------QL 359 (371)
T ss_pred CccCCCCCCCEEEEEEecCCc--------chHhh-----------------------cCCCCCHHHHHHh--------cc
Confidence 43 346789999999997321 23321 1467999999999 99
Q ss_pred chhhhhhc
Q 000161 1114 IPAAMQKV 1121 (1988)
Q Consensus 1114 iPa~lq~~ 1121 (1988)
+|++.+.+
T Consensus 360 ~p~~~ril 367 (371)
T cd05537 360 KPIADSIL 367 (371)
T ss_pred HHHHHHHH
Confidence 99998865
No 19
>PF00136 DNA_pol_B: DNA polymerase family B Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006134 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 of DNA polymerase B appears to consist of more than one activities, possibly including elongation, DNA-binding and dNTP binding [].; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 1NOY_A 1NOZ_B 2CW7_A 2CW8_A 1WNS_A 2XHB_A 2VWK_A 2VWJ_A 1TGO_A ....
Probab=100.00 E-value=9.8e-63 Score=621.69 Aligned_cols=430 Identities=29% Similarity=0.433 Sum_probs=312.7
Q ss_pred hhHHHHHHHHHHHHHHCCeeccCCCCCCchhhhcccccCCCCCCcceeeeccCccccCCCCCCccCChhHHHHHhhhhhh
Q 000161 467 GSGTLCEMLLMVQAYKANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFKLDPSAYEQLLNNLDR 546 (1988)
Q Consensus 467 Gsg~~~E~LLm~~a~~~n~i~Pnk~~~~~~~~~~g~l~~setY~GG~V~~p~~GvY~~d~~~~f~~~~~~~~~l~~~~~~ 546 (1988)
|++.+||++|+++|+++|+++|++...+.. .++.....++|.||+|++|++|+|++
T Consensus 1 gq~~~v~~~ll~~~~~~~~~~p~~~~~~~~--~~~~~~~~~~y~Gg~V~~P~~G~~~~---------------------- 56 (466)
T PF00136_consen 1 GQQIRVESLLLREAHRRNYIIPSKKERPEG--FTSKSEQKEKYEGGYVLEPKPGLYEN---------------------- 56 (466)
T ss_dssp -CHHHHHHHHHHHHHHTTBE-B-HHHHHHT--HHHHHHHCTCEEEC-BE--HSSEEEE----------------------
T ss_pred CchhhHHHHHHHHHHHCCEEeeCCcccccc--cccccccccccccceeeccccccccC----------------------
Confidence 899999999999999999999987654111 11112246789999999999999888
Q ss_pred hhHHHHhHhcccccccccchHHHHHHHHHHHHhhccCCCcccCCeEEEEeccccchHHHHhcCCCCCccccccccccccC
Q 000161 547 DLQYAIKVEGKMDLESVSNYDEVKNAIMEKLLRLQEEPIREECPLIYHLDVAAMYPNIILTNRLQPPSIVTDEVCTACDF 626 (1988)
Q Consensus 547 ~l~~~~~~e~~~~~~~~~n~~~v~~~i~~~l~~l~~~p~~~~~p~V~~LDf~SLYPsII~t~NL~p~Tiv~~~~c~~c~~ 626 (1988)
+|.+|||+|||||||++|||||+|+++...|..+.+
T Consensus 57 --------------------------------------------v~~~lDF~SLYPsii~~~Ni~~~T~~~~~~~~~~~~ 92 (466)
T PF00136_consen 57 --------------------------------------------VVSVLDFASLYPSIIIAYNICPETIVDDDECKDNEV 92 (466)
T ss_dssp --------------------------------------------EEEEEEETTHHHHHHHHTTHSTTTBTCTTHCSSEEE
T ss_pred --------------------------------------------ceeeeecccccHHHHHhccCCcceEecchhhhcccc
Confidence 243899999999999999999999987642211111
Q ss_pred CCCCCccccccccccccccccCCcchhhHhhhhcccccccCCCCCcccccccCchHHHHHHHHHHHHHhhhhhccccccc
Q 000161 627 NRPGKTCLRKLEWVWRGEIFMGKRSDYYHLKKQIESEFVDGTNGHLSKSFLDLPKMEQQSRLKDRLKKYCQKAYKRVLDK 706 (1988)
Q Consensus 627 n~p~~~c~r~m~w~~~ge~~p~~~~ey~~i~~~l~~e~f~~~~~g~~~~~~~L~~~~q~~~lkkrl~~y~~kvy~k~~~~ 706 (1988)
.... ..++. ..+.....+ ..| .
T Consensus 93 ~~~~-------------------~~~~~--------~~~~~~~~~--~~~------------------------~----- 114 (466)
T PF00136_consen 93 SPDI-------------------KYDYG--------PFIVGSPVG--VRF------------------------V----- 114 (466)
T ss_dssp HTTC-------------------CCCTC--------EEEECSCCS--EEE------------------------E-----
T ss_pred cccc-------------------ccccc--------ceeecCCce--eee------------------------c-----
Confidence 1000 00000 000000000 000 0
Q ss_pred ccccccccccccccccchHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 000161 707 PVTELREAGICMRENSFYVDTVRSFRDRRYEYKGLNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFY 786 (1988)
Q Consensus 707 ~~~~~r~~~icqre~~f~~~~lr~f~drR~~~K~l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~Y 786 (1988)
-|....+++|.+|+.+++.|.++|+.|++.+. +.+ +..+||++|+|+||++||+|
T Consensus 115 ---------~~~~~~gilp~~l~~~l~~R~~~K~~~~~~~~----------~~~------~~~~~d~~Q~a~Ki~~NS~Y 169 (466)
T PF00136_consen 115 ---------KKGVRPGILPEILEELLEKRKEIKKLMKKAKD----------PDE------EYAILDARQLALKIIANSFY 169 (466)
T ss_dssp ---------SSTCSHHHHHHHHHHHHHHHHHHHHHHHHCCH----------HHH------HHHHHHHHHHHHHHHHTTHH
T ss_pred ---------ccCcccccChHHHHHHHHHHHHHhhhhhhhcc----------chh------hHHHHHHHHHhhcccceeeE
Confidence 01122358999999999999999998876422 211 35799999999999999999
Q ss_pred ccccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHc--CCe-EEEccceeeEEcCCCCCcccccccccccccccccccc
Q 000161 787 GYVMRKGARWYSMEMAGVVTYTGAKIIQNARLLIEKI--GKP-LELDTDGIWCVLPGSFPENFTFKTKDLKKKLTISYPC 863 (1988)
Q Consensus 787 Gy~g~~~sR~ys~e~A~~VT~~Gr~iI~~a~~lve~~--G~~-vygDTDSI~~~lp~~~pe~~~~k~~~g~k~i~~sy~~ 863 (1988)
||+|+++|||||+++|++||++||++|+.|++++++. |+. |||||||+||.+|+...+. .+ ..+ +++
T Consensus 170 G~~g~~~~r~~~~~~a~~iT~~GR~~i~~~~~~~~~~~~g~~viYgDTDSv~v~~~~~~~~~-~~--~~~-~~l------ 239 (466)
T PF00136_consen 170 GYLGAKNSRFYCKEIAEAITATGREIIKKAIEIIEEMEFGFEVIYGDTDSVFVQFPDSDKED-AK--KKG-EEL------ 239 (466)
T ss_dssp HHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHHSCTEEEEEEETTEEEEECTTCHHHH-HH--HHH-HHH------
T ss_pred eecCccccchhhhhhhheehhhhHhhHHHHHHHHHhhcccceEEEEcccceEEecCCCcHHH-HH--HHH-HHH------
Confidence 9999999999999999999999999999999999998 887 6999999999998752111 10 011 111
Q ss_pred cccchhhhccccchhhhhccCCccccccccccceeEEeeeceeeeeecccccccCcccccceEEEcCC------CCEEEE
Q 000161 864 VMLNVDVARNNTNDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDD------GTLAEL 937 (1988)
Q Consensus 864 ~~ln~~V~~~~tN~~y~~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~~~d------G~~~e~ 937 (1988)
+..|.+.+ .+.+|++|+|++|++++|.+ |||||++..+ |++ ++
T Consensus 240 ---~~~i~~~~-------------------~~~~i~le~E~~y~~~~l~~--------KKrY~~~~~~~~~~~~~~~-~~ 288 (466)
T PF00136_consen 240 ---AKEINSEL-------------------FPSPIKLEFEKVYRWFILLA--------KKRYAGLKYDNEGKKKGKI-KI 288 (466)
T ss_dssp ---HHHHHHHS-------------------CSTTHEEEEEEEEEEEEEEE--------TTEEEEEETCCCEEETSEE-EE
T ss_pred ---HHHHhhhh-------------------cCCCceeeecccEEEEEEEc--------cCCccceeeeeccccccee-EE
Confidence 22221110 13456667779999999975 9999998654 444 99
Q ss_pred EeeeeccCChhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHH-H-HhcCCCCCchhhhhhhhhccccccChhhh
Q 000161 938 KGFEIKRRGELKLIKVFQAELFDKFLHGSTIEECYSAVAAVANRWLDL-L-DNQGKDIADSELIDYISESSTMSKSLADY 1015 (1988)
Q Consensus 938 KG~E~kRRd~~~liK~~q~~v~~~~L~g~~lee~~~~v~~v~~~~~d~-L-~~~~~~~~~~eLi~~i~~~k~lsK~l~eY 1015 (1988)
||+|++|||+|+++|++|+++++.+|.+.+.+++.+.++..+..+++- . +++.+.++.++|+ ++++++|++++|
T Consensus 289 kG~e~~RrD~~~~~k~~~~~~l~~il~~~~~~~~~~~i~~~~~e~l~~~~~~l~~~~~~~~~li----~~k~l~k~~~~Y 364 (466)
T PF00136_consen 289 KGLELVRRDWCPFVKDIQREVLEIILKGKDPEEAVEKIKEVIIEYLKKYIEKLRNGEVPIEDLI----ISKRLSKDLEEY 364 (466)
T ss_dssp ESSSGGSSSSTHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHTTCSHGGGGH----EEEECCSCGGGC
T ss_pred eccccccCchhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHhhccccccchhHHHHH----HhhhccCCcccc
Confidence 999999999999999999999999999999999877666322222221 1 2456778888887 899999999999
Q ss_pred CCCCChHHHHHHHHHhhcCCCcccCCCCeeEEEEEcC---CCCCCCcccccchhhhcchHHHHHHHHHhhhcCCCCCCCc
Q 000161 1016 GEQKSCAVTTARRLSDFLGDTMVKDKGLRCQYIVACE---PQGTPVSERAVPVAIFETDAEIMKFYLRKWCKTSSDVGIR 1092 (1988)
Q Consensus 1016 ~~~k~~~v~~A~rl~e~lG~~~~~~~G~~i~YVI~~~---p~g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~~~~~d~~ 1092 (1988)
....+||+.+|+||+++ |....+.+|++|+|||+++ +.+..+++++.++..+... +
T Consensus 365 ~~~~~~hv~~a~rl~~~-~~~~~p~~GdrI~Yvi~~~~~~~~~~~~~~~~~~~~~~~~~--------------------~ 423 (466)
T PF00136_consen 365 KKKTPPHVRAAKRLKKR-GPGYKPQKGDRIPYVIVKGPSKKKGPKPSERAEDPEYVKEN--------------------N 423 (466)
T ss_dssp SSSHHHHHHHHHHHHCT-THCTCTGTTSEEEEEEBSSSSTTHCEEESCSEETTTHHHHT--------------------T
T ss_pred cccCCcHHHHHHHHHhh-hcccCCcCCCEeEEEEEcCccccccccchhhccChhhhhcc--------------------C
Confidence 98777799999999985 5457889999999999998 3566788999998755432 3
Q ss_pred cccCHHHHHHhhhhhhhheeechhhhhhc
Q 000161 1093 SIVDWSYYKQRLSSAIQKIITIPAAMQKV 1121 (1988)
Q Consensus 1093 ~~iD~~YYierl~~~i~ki~~iPa~lq~~ 1121 (1988)
..||++||+++ |++|++.|.+
T Consensus 424 ~~iD~~yYi~~--------ql~~pl~ril 444 (466)
T PF00136_consen 424 LPIDYEYYIEK--------QLLPPLERIL 444 (466)
T ss_dssp S-BSHHHHHHT--------THHHHHHHHH
T ss_pred CCcchHHHHhh--------ccHHHHHHHH
Confidence 68999999998 8888888764
No 20
>cd05538 POLBc_Pol_II_B DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Probab=100.00 E-value=3.2e-61 Score=581.22 Aligned_cols=295 Identities=22% Similarity=0.301 Sum_probs=236.6
Q ss_pred chHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCCCHHHH
Q 000161 723 FYVDTVRSFRDRRYEYKGLNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMA 802 (1988)
Q Consensus 723 f~~~~lr~f~drR~~~K~l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~sR~ys~e~A 802 (1988)
++|.+|+.|+++|.++|++||+. .|+. ...+||++|+|+|+++||+|||+|++++||||+++|
T Consensus 46 ilp~il~~Ll~~R~~~K~~~k~~----------~~~~-------~~~~~d~~Q~AlKi~~NS~YG~lG~~~~r~~~~~~A 108 (347)
T cd05538 46 IFLALLKYLVELRLAAKESARAA----------ARPA-------ERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAA 108 (347)
T ss_pred ccHHHHHHHHHHHHHHHHHHhcC----------CChH-------HHHHHHHHHHHHhhhhhhchhhhcCCCCCCCCHHHH
Confidence 67788999999999999988753 2343 246899999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCe-EEEccceeeEEcCCCCCcccccccccccccccccccccccchhhhccccchhhhh
Q 000161 803 GVVTYTGAKIIQNARLLIEKIGKP-LELDTDGIWCVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVDVARNNTNDQYQT 881 (1988)
Q Consensus 803 ~~VT~~Gr~iI~~a~~lve~~G~~-vygDTDSI~~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~V~~~~tN~~y~~ 881 (1988)
++||++||++|+.+++++++.|.. ||||||||||.+|+.++.... . +++ ...|.+ .
T Consensus 109 ~~iT~~GR~~L~~~~~~~e~~g~~VIygDTDSi~v~~~~~~~~~~~-----~-~~~---------~~~i~~--------~ 165 (347)
T cd05538 109 AEVTRLGRELLKLMIRWLRRRGATPVEVDTDGIYFIPPNGVDTEDE-----E-EEL---------VRELSS--------T 165 (347)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCEEEEEcCCeeEEEeCCCCChHHH-----H-HHH---------HHHHHH--------h
Confidence 999999999999999999999987 699999999998864321110 1 111 111110 1
Q ss_pred ccCCccccccccccceeEEeeeceeeeeecccccccCcccccceEEEcCCCCEEEEEeeeeccCChhHHHHHHHHHHHHH
Q 000161 882 LVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLAELKGFEIKRRGELKLIKVFQAELFDK 961 (1988)
Q Consensus 882 l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~~~dG~~~e~KG~E~kRRd~~~liK~~q~~v~~~ 961 (1988)
+ +.+|++|+||+|++|++. .|||||+++.||++ ++||+|++|||||+|+|++|+++++.
T Consensus 166 ~------------~~~i~le~e~~y~~~l~~--------~KKrYa~~~~~gki-~~KG~e~vRrD~~~~~k~~~~~vl~~ 224 (347)
T cd05538 166 L------------PKGITVEFDGRYRAMFSY--------KIKNYALLDYDGKL-IVKGSAFRSRGIEPFLREFLREAVRL 224 (347)
T ss_pred C------------CCCeEEEEhHHHHHHHhh--------cCceEEEEecCCcE-EEECCCcccCCchHHHHHHHHHHHHH
Confidence 1 356888888999999985 49999999999998 89999999999999999999999999
Q ss_pred HhCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhhhhhccccccChhhhCCCC---ChHHHHHHHHHhhcCCCcc
Q 000161 962 FLHGSTIEECYSAVAAVANRWLDLLDNQGKDIADSELIDYISESSTMSKSLADYGEQK---SCAVTTARRLSDFLGDTMV 1038 (1988)
Q Consensus 962 ~L~g~~lee~~~~v~~v~~~~~d~L~~~~~~~~~~eLi~~i~~~k~lsK~l~eY~~~k---~~~v~~A~rl~e~lG~~~~ 1038 (1988)
+|.+. .+++.+.++++++ +++++.++.++|+ ++++|+|++++|.+.. .+|..+|.+++...| ..
T Consensus 225 ll~~~-~~~~~~~~~~~~~------~l~~~~~~~~~l~----i~k~l~k~~~~Y~~~~~~~~~~~~~a~~~a~~~g--~~ 291 (347)
T cd05538 225 LLQGD-GAGVHDLYEDYLR------RLRSHELPISDLA----RTETLKESPEEYLQKVRAGKRNPAAAYEIALARP--RE 291 (347)
T ss_pred HHcCC-hHHHHHHHHHHHH------HHHcCCCCHHHEE----EEeecCCCHHHHhhhhhcccCChhHHHHHHHhcC--CC
Confidence 99765 4555555554443 3567889988877 8999999999996421 134333334444346 67
Q ss_pred cCCCCeeEEEEEcCCCCCCCcccccchhhhcchHHHHHHHHHhhhcCCCCCCCccccCHHHHHHhhhhhhhhe
Q 000161 1039 KDKGLRCQYIVACEPQGTPVSERAVPVAIFETDAEIMKFYLRKWCKTSSDVGIRSIVDWSYYKQRLSSAIQKI 1111 (1988)
Q Consensus 1039 ~~~G~~i~YVI~~~p~g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~~~~~d~~~~iD~~YYierl~~~i~ki 1111 (1988)
+++|++|+|||++++.|.++++||+|+++|..+ ...+|.+||+++|...+++.
T Consensus 292 ~~~G~~I~Yvi~~~~~g~~~~~ra~~~~~~~~~--------------------~~~~d~~yY~~~l~~~~~~~ 344 (347)
T cd05538 292 WRAGDRVTYYVSGTGKGVSVYENCRLVADYDPA--------------------HPDENTGFYAERLLQLAARL 344 (347)
T ss_pred CCCCCEEEEEEEeCCCCCCHHHhhccHHHhCCC--------------------ccccCHHHHHHHHHHHHHhh
Confidence 899999999999999999999999999999753 24689999999998887765
No 21
>cd05530 POLBc_B1 DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Probab=100.00 E-value=3.8e-60 Score=574.69 Aligned_cols=293 Identities=23% Similarity=0.286 Sum_probs=232.7
Q ss_pred ccccccchHHHHHHHHHHHHHHHh-hhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCC
Q 000161 717 CMRENSFYVDTVRSFRDRRYEYKG-LNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGAR 795 (1988)
Q Consensus 717 cqre~~f~~~~lr~f~drR~~~K~-l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~sR 795 (1988)
|+...+++|.+|+.|+++|.+.|+ ++|.. ..|+. +..+||++|+|+|+++||+|||+|+.++|
T Consensus 72 ~~~~~Gilp~il~~L~~~R~~~~k~~~k~~---------~~d~~-------~~~~ld~~Q~alKi~~NS~YG~~g~~~~~ 135 (372)
T cd05530 72 CKKRPGITSQIIGLLRDLRVKIYKKKAKDK---------SLDEE-------MRQWYDVVQSAMKVFINASYGVFGAENFP 135 (372)
T ss_pred EecCCCccHHHHHHHHHHHHHHHHHHhhCC---------CCCHH-------HHHHHHHHHHHHHHHHhccccccccccCC
Confidence 444557999999999999987543 33320 11343 34799999999999999999999999999
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHcCCe-EEEccceeeEEcCCCCCcccccccccccccccccccccccchhhhccc
Q 000161 796 WYSMEMAGVVTYTGAKIIQNARLLIEKIGKP-LELDTDGIWCVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVDVARNN 874 (1988)
Q Consensus 796 ~ys~e~A~~VT~~Gr~iI~~a~~lve~~G~~-vygDTDSI~~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~V~~~~ 874 (1988)
|||.++|++||++||++|+.|++++++.|+. |||||||+||..++. +. . +++ ...|
T Consensus 136 ~~~~~~A~~it~~GR~~l~~~~~~~~~~g~~VIYGDTDSvfv~~~~~---~~------~-~~i---------~~~i---- 192 (372)
T cd05530 136 LYCPPVAESTTALGRYIITSTIKKARELGLKVLYGDTDSLFLWNPPQ---EQ------L-EDL---------VEWV---- 192 (372)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHCCcEEEEEeccceEEecCCh---hH------H-HHH---------HHHH----
Confidence 9999999999999999999999999999987 699999999986531 10 1 121 0111
Q ss_pred cchhhhhccCCccccccccccceeEEeeeceeeeeecccccccCcccccceEEEcCCCCEEEEEeeeeccCChhHHHHHH
Q 000161 875 TNDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLAELKGFEIKRRGELKLIKVF 954 (1988)
Q Consensus 875 tN~~y~~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~~~dG~~~e~KG~E~kRRd~~~liK~~ 954 (1988)
.++.+|++|+|++|++++|. +.||||||+..||++ ++||+|++|||+|+|+|++
T Consensus 193 ------------------~~~~~i~le~E~~y~~~ll~-------~~KKrY~g~~~~gki-~~KGie~~RrD~~~~~k~~ 246 (372)
T cd05530 193 ------------------EKELGLDLELDKEYRYVVFS-------GLKKNYLGVTKDGSV-DIKGLLGKKRNTPEFVKEL 246 (372)
T ss_pred ------------------hhccCceEEEEEEEeeeeec-------cccccEEEEecCCcE-EEEeEEEEeCCchHHHHHH
Confidence 11335677888999987663 349999999889998 9999999999999999999
Q ss_pred HHHHHHHHhCCCCHH---HHHHHHHHHHHHHHHHHHhcCCCCCchhhhhhhhhccccccChhhhCCCCChHHHHHHHHHh
Q 000161 955 QAELFDKFLHGSTIE---ECYSAVAAVANRWLDLLDNQGKDIADSELIDYISESSTMSKSLADYGEQKSCAVTTARRLSD 1031 (1988)
Q Consensus 955 q~~v~~~~L~g~~le---e~~~~v~~v~~~~~d~L~~~~~~~~~~eLi~~i~~~k~lsK~l~eY~~~k~~~v~~A~rl~e 1031 (1988)
|+++++.+|.+++.+ ++.+.+.++++...+ +++.|++|.++|+ ++++|+|.+++|....+|||.+|++|.+
T Consensus 247 ~~~vl~~ll~~~~~~~~~~~~~~i~~~~~~~~~--~l~~g~~~~~~lv----i~k~L~K~~~~Y~~~~~phv~aa~~~~~ 320 (372)
T cd05530 247 FYEVIEILSAVNSPEDFEKAREKIRDIVKGVYK--RLKKKEYTLDQLA----FKVMLSKPPEEYTKNTPQHVKAARQLEK 320 (372)
T ss_pred HHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHH--HHHcCCCCHHHhe----eehhccCCHHHhcCCCCHHHHHHHHHHh
Confidence 999999999987654 455555555554443 4668899999988 8999999999999778899999999887
Q ss_pred hcCCCcccCCCCeeEEEEEcCCCCCCCcccccchhhhcchHHHHHHHHHhhhcCCCCCCCccccCHHHHHHhhhhhhhhe
Q 000161 1032 FLGDTMVKDKGLRCQYIVACEPQGTPVSERAVPVAIFETDAEIMKFYLRKWCKTSSDVGIRSIVDWSYYKQRLSSAIQKI 1111 (1988)
Q Consensus 1032 ~lG~~~~~~~G~~i~YVI~~~p~g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~~~~~d~~~~iD~~YYierl~~~i~ki 1111 (1988)
.| ..+.+|++|+|||+++.+| +.|++... ...||++|||+.|.++..+|
T Consensus 321 -~g--~~~~~G~~I~YVi~~~~~~------~~p~~~~~----------------------~~~iD~~yYi~~l~~a~~~i 369 (372)
T cd05530 321 -YG--RNVEAGDIISYVKVKGKEG------VKPVQLAR----------------------LDEVDVEKYVEIMRSTLEQI 369 (372)
T ss_pred -cC--CCCCCCCEEEEEEEeCCCC------Cchhhhcc----------------------CCCCCHHHHHHHHHHHHHHH
Confidence 46 7789999999999987665 34554322 13699999999988777765
No 22
>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=100.00 E-value=2e-59 Score=590.30 Aligned_cols=442 Identities=26% Similarity=0.312 Sum_probs=349.4
Q ss_pred CCceEEEEEEEEccCCCCCCCCC--CCeEEEEEEEEcCCceEEEcccccccccccccCCCCCCCCCceEEecCCCHHHHH
Q 000161 237 AEVHVCAFDIETTKLPLKFPDAD--YDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELL 314 (1988)
Q Consensus 237 p~lrvLsfDIEt~s~~~~fPdp~--~D~Ii~IS~~~~~~g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~eLL 314 (1988)
|++++++|||||++.+..||++. .|+|++|+++....+.. .......|.+.+..+..+ ..+..+++|++||
T Consensus 1 ~~~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~------~~~~~~~~~~~~~~~~~~-~~~~~~~~E~~lL 73 (471)
T smart00486 1 PPLKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKK------GPEERICFTLGTCKEIDG-VEVYEFNNEKELL 73 (471)
T ss_pred CCceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCC------CCceeEEEEecCcCCCCC-CeEEecCCHHHHH
Confidence 67899999999999877899998 69999999987543321 011112334445555555 3577789999999
Q ss_pred HHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCcccc-----C-----------CCCceeeccceEech
Q 000161 315 RLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCD-----K-----------NQGECRAKFACHLDC 378 (1988)
Q Consensus 315 ~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~-----~-----------~~g~~~i~GRihiDl 378 (1988)
.+|++++++.|||+|+|||+.+||+|||.+|+..++++.+..+|+... . ....+.+.||+|+|+
T Consensus 74 ~~f~~~i~~~dpdii~g~N~~~FD~~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~Dl 153 (471)
T smart00486 74 KAFLEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSKSFGKTIKVKIKGRLVIDL 153 (471)
T ss_pred HHHHHHHHHhCCCEEEeecCCCCCHHHHHHHHHHcCCCCHHHcCcCCCCCCcccccCccccccccccceeEeccEEEEEh
Confidence 999999999999999999999999999999999999977544444310 0 001356889999999
Q ss_pred HHHHhhccCCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhh---ChHHHHHHHHHhhHHHHHHHHHh-ccchHhhhhh
Q 000161 379 FAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKE---KPQMMASYSVSDAVATYYLYMTY-VHPFIFSLAT 454 (1988)
Q Consensus 379 ~~~vkrd~~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~---~~~~La~Y~l~Da~lt~~L~~Kl-v~~~i~~La~ 454 (1988)
+.++++..+ ..+|+|++||+++||.+|.++++.+|.++|.. ....+++||++|+.++++|+.++ ++++.+++|+
T Consensus 154 ~~~~~~~~k--l~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l~~~~~~~~~s~ 231 (471)
T smart00486 154 YNLYKNKLK--LPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKLNVIPLIIELAR 231 (471)
T ss_pred HHHHHHHhC--cccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence 999999765 48999999999999999999999999999885 56799999999999999999998 8899999999
Q ss_pred hcCCChHHHhhhhhHHHHHHHHHHHHHHCCeeccCCCCCCchhhhcccccCCCCCCcceeeeccCccccCCCCCCccCCh
Q 000161 455 IIPMSPDEVLRKGSGTLCEMLLMVQAYKANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFKLDP 534 (1988)
Q Consensus 455 i~~l~~~~vlr~Gsg~~~E~LLm~~a~~~n~i~Pnk~~~~~~~~~~g~l~~setY~GG~V~~p~~GvY~~d~~~~f~~~~ 534 (1988)
+.++++.++++.|++.++|+++++++++.|+++|++........ .........|.||+|++|++|+|.+
T Consensus 232 ~~~~~~~~~~~~g~~~~v~~~l~~~~~~~~~~~P~~~~~~~~~~-~~~~~~~~~y~gg~v~~p~~g~~~~---------- 300 (471)
T smart00486 232 IAGIPQRRTLYYGSQIRVESLLLREAKKNNYILPSKSLIDFKGS-EPELKKKAKYPGGKVLEPKKGFYDN---------- 300 (471)
T ss_pred HHCcCHHHHHhcCcHHHHHHHHHHHHhhCCEEeccchhcccccc-cccccccccccccEEecCCCCcccC----------
Confidence 99999999999999999999999999999999998776432110 0111224679999999999998776
Q ss_pred hHHHHHhhhhhhhhHHHHhHhcccccccccchHHHHHHHHHHHHhhccCCCcccCCeEEEEeccccchHHHHhcCCCCCc
Q 000161 535 SAYEQLLNNLDRDLQYAIKVEGKMDLESVSNYDEVKNAIMEKLLRLQEEPIREECPLIYHLDVAAMYPNIILTNRLQPPS 614 (1988)
Q Consensus 535 ~~~~~l~~~~~~~l~~~~~~e~~~~~~~~~n~~~v~~~i~~~l~~l~~~p~~~~~p~V~~LDf~SLYPsII~t~NL~p~T 614 (1988)
||+++||+|||||||+++||||+|
T Consensus 301 --------------------------------------------------------~v~~lDf~SlYPsii~~~nl~~~t 324 (471)
T smart00486 301 --------------------------------------------------------PVLVLDFNSLYPSIIIAHNLCYST 324 (471)
T ss_pred --------------------------------------------------------ceEEeehhhccHHHHHHhCCCCcc
Confidence 499999999999999999999999
Q ss_pred cccccccccccCCCCCCccccccccccccccccCCcchhhHhhhhcccccccCCCCCcccccccCchHHHHHHHHHHHHH
Q 000161 615 IVTDEVCTACDFNRPGKTCLRKLEWVWRGEIFMGKRSDYYHLKKQIESEFVDGTNGHLSKSFLDLPKMEQQSRLKDRLKK 694 (1988)
Q Consensus 615 iv~~~~c~~c~~n~p~~~c~r~m~w~~~ge~~p~~~~ey~~i~~~l~~e~f~~~~~g~~~~~~~L~~~~q~~~lkkrl~~ 694 (1988)
++.... ... ....|. +.+ ....+....
T Consensus 325 ~~~~~~----~~~-------~~~~~~----------~~~-------~~~~~~~~~------------------------- 351 (471)
T smart00486 325 LVGRGE----NSG-------ELFLDV----------EDL-------LTIKYEKPE------------------------- 351 (471)
T ss_pred cccccc----ccc-------ccCCCh----------hhc-------ceeeecCCC-------------------------
Confidence 986531 000 000000 000 000000000
Q ss_pred hhhhhcccccccccccccccccccc-cccchHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHH
Q 000161 695 YCQKAYKRVLDKPVTELREAGICMR-ENSFYVDTVRSFRDRRYEYKGLNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDS 773 (1988)
Q Consensus 695 y~~kvy~k~~~~~~~~~r~~~icqr-e~~f~~~~lr~f~drR~~~K~l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds 773 (1988)
....+|.. +.++++.+|+.+++.|.++|+.+|+.+ ++. ..+..+||+
T Consensus 352 -----------------~~~~~~~~~~~gil~~~l~~l~~~R~~~K~~~~~~~----------~~~-----~~~~~~~d~ 399 (471)
T smart00486 352 -----------------GYHFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEK----------DES-----EELKKLLDS 399 (471)
T ss_pred -----------------cceeecCCCCCeehHHHHHHHHHHHHHHHHHHhhCC----------CCc-----HHHHHHHHH
Confidence 00111222 237999999999999999999987642 221 124579999
Q ss_pred HHHHHHHHhhhccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHcC----Ce-EEEccceeeEEcC
Q 000161 774 LQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNARLLIEKIG----KP-LELDTDGIWCVLP 839 (1988)
Q Consensus 774 ~QlA~K~ilNS~YGy~g~~~sR~ys~e~A~~VT~~Gr~iI~~a~~lve~~G----~~-vygDTDSI~~~lp 839 (1988)
+|+|+|+++||+|||+|+..+|||+.++|++||++||.+|+.|++++++.| .. ||||||||||..|
T Consensus 400 ~q~a~K~~~Ns~yG~~g~~~~~~~~~~~a~~iT~~gr~~l~~~~~~i~~~~~~~~~~viYgDTDSi~v~~~ 470 (471)
T smart00486 400 RQLALKLTANSVYGYLGFTNSRLYCKPLAASVTALGREILEKTKELIEKNGYPPGFKVIYGDTDSIFVTKP 470 (471)
T ss_pred HHHHHHhhhcccccccccccccCccHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCeEEEEecCceEEEecC
Confidence 999999999999999999999999999999999999999999999999997 45 6999999999876
No 23
>cd05531 POLBc_B2 DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Probab=100.00 E-value=2.3e-58 Score=557.86 Aligned_cols=285 Identities=25% Similarity=0.398 Sum_probs=224.3
Q ss_pred cccccccchHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCC
Q 000161 716 ICMRENSFYVDTVRSFRDRRYEYKGLNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGAR 795 (1988)
Q Consensus 716 icqre~~f~~~~lr~f~drR~~~K~l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~sR 795 (1988)
+|++..+++|.+|+.|+++|.++|+.||.. . .+|++|+|+|+++||+|||+|+++||
T Consensus 61 ~~~~~~gilp~~l~~l~~~R~~~K~~~k~~----------~-------------~~d~~q~AlKi~~NS~YGylG~~~~~ 117 (352)
T cd05531 61 ICLKRRGFLPEVLEPLLERRLEYKRLKKEE----------D-------------PYAGRQKALKWILVTSFGYLGYKNAK 117 (352)
T ss_pred EecCCCCchHHHHHHHHHHHHHHHHHhhcC----------C-------------CchHHHhhheeeeecccccccccccc
Confidence 466677899999999999999999887641 0 13889999999999999999999999
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHcCCe-EEEccceeeEEcCCCCCcccccccccccccccccccccccchhhhccc
Q 000161 796 WYSMEMAGVVTYTGAKIIQNARLLIEKIGKP-LELDTDGIWCVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVDVARNN 874 (1988)
Q Consensus 796 ~ys~e~A~~VT~~Gr~iI~~a~~lve~~G~~-vygDTDSI~~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~V~~~~ 874 (1988)
||++++|++||++||++|++|++++|+.|+. |||||||+||..++. . +++ ...+
T Consensus 118 f~~~~~A~~vT~~GR~~L~~~~~~~e~~g~~VIygDTDSvfv~~~~~-----------~-~~~---------~~~i---- 172 (352)
T cd05531 118 FGRIEVHEAITAYGRKILLRAKEIAEEMGFRVLHGIVDSLWIQGRGD-----------I-EEL---------AREI---- 172 (352)
T ss_pred cCChHHHHHHHHHHHHHHHHHHHHHHHcCCEEEEEccccceeecCch-----------H-HHH---------HHHH----
Confidence 9999999999999999999999999999987 699999999975321 0 111 0011
Q ss_pred cchhhhhccCCccccccccccceeEEeeeceeeeeecccccccCcccccceEEEcCCCCEEEEEeeeeccCChhHHHHHH
Q 000161 875 TNDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLAELKGFEIKRRGELKLIKVF 954 (1988)
Q Consensus 875 tN~~y~~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~~~dG~~~e~KG~E~kRRd~~~liK~~ 954 (1988)
.++.+|++|+||+|++++|+..++. .+.||||+|...||++ ++||+|++|||||+|+|++
T Consensus 173 ------------------~~~~~i~l~le~~y~~~~~~~~~~~-~~~kKrY~g~~~~g~i-~~KG~e~vRrD~~~~~k~~ 232 (352)
T cd05531 173 ------------------EERTGIPLKLEGHYDWIVFLPERDG-LGAPNRYFGRLSDGEM-KVRGIELRRRDTPPFVKKF 232 (352)
T ss_pred ------------------HHhcCCceEEEEEEEEEEeeccccc-cCcceeEEEecCCCcE-EEEeeEEEeCCchHHHHHH
Confidence 1123466777799999876654432 6789999999989998 9999999999999999999
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHH-HhcCCCCCchhhhhhhhhccccccChhhhCCCCChHHHHHHHHHhhc
Q 000161 955 QAELFDKFLHGSTIEECYSAVAAVANRWLDLL-DNQGKDIADSELIDYISESSTMSKSLADYGEQKSCAVTTARRLSDFL 1033 (1988)
Q Consensus 955 q~~v~~~~L~g~~lee~~~~v~~v~~~~~d~L-~~~~~~~~~~eLi~~i~~~k~lsK~l~eY~~~k~~~v~~A~rl~e~l 1033 (1988)
|+++++.+|.+++++++...+.++.+...+.. +++.++ .++|+ ++++|+|.+++|.. .++| +|++|++ .
T Consensus 233 ~~~vl~~ll~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~lv----i~k~l~k~~~~Y~~-~~~~--~a~~l~~-~ 302 (352)
T cd05531 233 QEEALDILASAKTPEELLKLREEALDLFRRYLQRLREGD--LEDLI----IEKKISKRSSEYKV-LAST--ALKALRA-K 302 (352)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHhcCC--hHHEE----EEEEecCCHHHcCC-chHH--HHHHHHh-C
Confidence 99999999999999988766554433322222 234444 56666 89999999999997 4455 8999988 4
Q ss_pred CCCcccCCCCeeEEEEEcCCCCCCCcccccchhhhcchHHHHHHHHHhhhcCCCCCCCccccCHHHHHHhhhhhhhh
Q 000161 1034 GDTMVKDKGLRCQYIVACEPQGTPVSERAVPVAIFETDAEIMKFYLRKWCKTSSDVGIRSIVDWSYYKQRLSSAIQK 1110 (1988)
Q Consensus 1034 G~~~~~~~G~~i~YVI~~~p~g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~~~~~d~~~~iD~~YYierl~~~i~k 1110 (1988)
| ..+.+|++|+|||+.+..+.|. .. ....+|.+||++.|..++.+
T Consensus 303 g--~~~~~G~~I~Yvi~~~~~~~~~---------~~---------------------~~~~~D~~yYi~~l~~~~~~ 347 (352)
T cd05531 303 G--VSVVPGMKIEYIVRDGKRPVPD---------LG---------------------NDEGYDTKYYRELLERAAEE 347 (352)
T ss_pred C--CCCCCCCEEEEEEEECCCCCcc---------cc---------------------ccCCCCHHHHHHHHHHHHHH
Confidence 7 6789999999999988765433 11 13579999999864444433
No 24
>cd00145 POLBc DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is
Probab=100.00 E-value=8.2e-59 Score=558.58 Aligned_cols=251 Identities=30% Similarity=0.412 Sum_probs=201.3
Q ss_pred cccchHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCChhhHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCCCH
Q 000161 720 ENSFYVDTVRSFRDRRYEYKGLNKVWKGKLSEAKASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGARWYSM 799 (1988)
Q Consensus 720 e~~f~~~~lr~f~drR~~~K~l~K~~k~~~~~a~~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~sR~ys~ 799 (1988)
..+++|.+|+.|++.|.++|+.||..+. |+. +..+||++|+|+|+++||+|||+|+++|||||+
T Consensus 65 ~~Gilp~iL~~Ll~~R~~~K~~mk~~~~---------~~~-------~~~~~d~~Q~AlKi~~NS~YG~~G~~~~r~~~~ 128 (323)
T cd00145 65 RKGLLPRILEELLNFRDEAKKRMKAAKL---------APE-------ERVLYDNRQQALKVLANSFYGYLGAKFFRFYDP 128 (323)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHhhCcC---------CHH-------HHHHHHHHhhhhheeeecceeecccccccCCCh
Confidence 3468999999999999999999876321 233 357999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCe-EEEccceeeEEcCCCCCcccccccccccccccccccccccchhhhccccchh
Q 000161 800 EMAGVVTYTGAKIIQNARLLIEKIGKP-LELDTDGIWCVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVDVARNNTNDQ 878 (1988)
Q Consensus 800 e~A~~VT~~Gr~iI~~a~~lve~~G~~-vygDTDSI~~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~V~~~~tN~~ 878 (1988)
++|++||++||++|+.|++++|+.|.. ||||||||||.+|+....+..+ ++.++.
T Consensus 129 ~~A~~IT~~GR~~l~~~~~~ie~~g~~VIYGDTDSifv~~~~~~~~~~~~------------------------~~~~~~ 184 (323)
T cd00145 129 EVAASITSFGREIIQDTIALVEEHGARVIYGDTDSIFVSLPKMGTKEDAI------------------------KEGREI 184 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCEEEEECCCceEEEeCCCCCHHHHH------------------------HHHHHH
Confidence 999999999999999999999999986 7999999999988621111111 111222
Q ss_pred hhhccCCccccccccccceeEEeeeceeeeeecccccccCcccccceEEEcC-----CCCEEEEEeeeeccCChhHHHHH
Q 000161 879 YQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFND-----DGTLAELKGFEIKRRGELKLIKV 953 (1988)
Q Consensus 879 y~~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~~~-----dG~~~e~KG~E~kRRd~~~liK~ 953 (1988)
.+.. ..+.+|++|+||+|.+|++++ ||||||+.. +|++ ++||+|++|||+|+|+|+
T Consensus 185 ~~~i----------~~~~~i~le~E~vy~~~ll~~--------KKrYag~~~~~~~~~~~~-~~KG~e~vRrD~~~~~k~ 245 (323)
T cd00145 185 LQEL----------ADEHLLELEFEKVYLPFFLGK--------KKRYAGLDIWKGQDEGKI-DIKGLETRRRDSPPLVKK 245 (323)
T ss_pred HHHh----------CCCCCeEEEEchhhHHHHHhh--------hhhEEEEEEEcCCCCceE-EEEcceEEecCcHHHHHH
Confidence 2221 235678888899999999985 999999865 4555 999999999999999999
Q ss_pred HHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhhhhhccccccChhhhCCCCChHHHHHHHHHhh
Q 000161 954 FQAELFDKFLHG-STIEECYSAVAAVANRWLDLLDNQGKDIADSELIDYISESSTMSKSLADYGEQKSCAVTTARRLSDF 1032 (1988)
Q Consensus 954 ~q~~v~~~~L~g-~~lee~~~~v~~v~~~~~d~L~~~~~~~~~~eLi~~i~~~k~lsK~l~eY~~~k~~~v~~A~rl~e~ 1032 (1988)
+|+++++.+|.+ ..++.+.+.+.++
T Consensus 246 ~~~~vl~~ll~~~~~~~~v~~~~~~l------------------------------------------------------ 271 (323)
T cd00145 246 FQKEVLELILEEERKVEAVKEYIDEL------------------------------------------------------ 271 (323)
T ss_pred HHHHHHHHHHcCCchHHHHHHHHHHh------------------------------------------------------
Confidence 999999999995 3333322222110
Q ss_pred cCCCcccCCCCeeEEEEEcCCCCCCCcccccchhhhcchHHHHHHHHHhhhcCCCCCCCccccCHHHHHHhhhhhhhhee
Q 000161 1033 LGDTMVKDKGLRCQYIVACEPQGTPVSERAVPVAIFETDAEIMKFYLRKWCKTSSDVGIRSIVDWSYYKQRLSSAIQKII 1112 (1988)
Q Consensus 1033 lG~~~~~~~G~~i~YVI~~~p~g~~v~eRa~p~~if~~~~~~~~~~l~~w~~~~~~~d~~~~iD~~YYierl~~~i~ki~ 1112 (1988)
++|+|||++++.+.+..+||.|+.... +....|||+||+++ |
T Consensus 272 ----------~~i~yvi~~~~~~~~~~~ra~~~~~~~--------------------~~~~~iD~~yY~~~--------~ 313 (323)
T cd00145 272 ----------DKVKYVVTRGGKGVPDYERADPPLEDL--------------------DKRHRIDYEYYLER--------L 313 (323)
T ss_pred ----------ccccEEEEcCCCCCCcccccCChhhhc--------------------ccCCCCChHHHHHh--------c
Confidence 899999999999989999999986433 12578999999999 9
Q ss_pred echhhhhhc
Q 000161 1113 TIPAAMQKV 1121 (1988)
Q Consensus 1113 ~iPa~lq~~ 1121 (1988)
++|++.+.+
T Consensus 314 ~~~~~~ri~ 322 (323)
T cd00145 314 LQPPLERIF 322 (323)
T ss_pred cHhHHHHhc
Confidence 999988753
No 25
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=100.00 E-value=2.9e-51 Score=504.64 Aligned_cols=295 Identities=23% Similarity=0.304 Sum_probs=238.2
Q ss_pred CCCceEEEEEEEEccCCCCCCCCCC--CeEEEEEEEEcC--CceEEEcccccccccccccCCCC------CCCCCceEEe
Q 000161 236 RAEVHVCAFDIETTKLPLKFPDADY--DIIMMISYMLDG--QGYLIINRECVGEDIEDLEYTPK------PEFEGYFKVT 305 (1988)
Q Consensus 236 ~p~lrvLsfDIEt~s~~~~fPdp~~--D~Ii~IS~~~~~--~g~li~nreivs~di~~feytp~------~~~~g~f~V~ 305 (1988)
.-.+++..+||||++. .||+|.. -+|.+|++.... .....+.. ++ .+...+ .|. ...+ ...|.
T Consensus 103 ~~~i~~~~~DIEv~~~--~fp~~~~a~~~i~~i~~~d~~~~~~~~~~~~-~~-~~~~~~--~~~~~~~~~~~~~-~v~v~ 175 (498)
T PHA02524 103 RDDVVIDVVDIEVTAP--EFPEPKYAKYEIDMISHVRLHNGKKTYYIFD-LV-KDVGHW--DPKKSVLEKYILD-NVVYM 175 (498)
T ss_pred hhhceEEEEEEEecCC--CCCChhhcCCceEEEEeeecccCCccEEEEe-cc-ccccCC--CcccccccccccC-CeEEE
Confidence 5678999999999884 6999975 699999985322 32111110 00 001111 111 1122 35688
Q ss_pred cCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHH-cCCCC---CcccCcccc----CCCC---ceeeccce
Q 000161 306 NVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAH-HGFKM---SEELGFQCD----KNQG---ECRAKFAC 374 (1988)
Q Consensus 306 ~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~-lGi~l---~~~iG~~~~----~~~g---~~~i~GRi 374 (1988)
.|++|++||.+|+++|++.|||||+|||+++||||||.+||+. +|+.. +.++|+... ...| .+.+.||+
T Consensus 176 ~f~sE~eLL~~F~~~i~~~DPDIItGYNi~nFDlPYL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~~~G~~~~~~I~GRv 255 (498)
T PHA02524 176 PFEDEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNILGEKAANQLSPYGKITSKTITNLYGEKIIYKIHGIA 255 (498)
T ss_pred EeCCHHHHHHHHHHHHHHhCCCEEEeCCCcccCHHHHHHHHHHHhCCccccccccccccccccceeecCceeEEEEeeEE
Confidence 8999999999999999999999999999999999999999974 89863 234554200 1224 46899999
Q ss_pred EechHHHHhhccCCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh-ccchHhhhh
Q 000161 375 HLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY-VHPFIFSLA 453 (1988)
Q Consensus 375 hiDl~~~vkrd~~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl-v~~~i~~La 453 (1988)
++|++.++++++..++.||+|++||.++||++|++++. .|.++|.++++++++||++||.+|+.|..++ +.+++.++|
T Consensus 256 ~iDl~~l~kk~s~~~l~sYsL~~Vs~~~Lg~~K~d~~~-~I~~l~~~d~~rla~YclkDa~L~~~L~~~~~ll~~~~~la 334 (498)
T PHA02524 256 LMDYMDVFKKFSFTPMPDYKLGNVGYREVKADKLDYEG-PINKFRKADHQRYVDYCVRDTDIILLIDGRRCFIDLILSLS 334 (498)
T ss_pred EeEHHHHHHHhhhccCCCCCHHHHHHHhcCCccccchh-hHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999997444569999999999999999998864 4888999999999999999999999888665 678888999
Q ss_pred hhcCCChHHHhhhhhHHHHHHHHHHHHHHCCeeccCCCCCCchhhhcccccCCCCCCcceeeeccCccccCCCCCCccCC
Q 000161 454 TIIPMSPDEVLRKGSGTLCEMLLMVQAYKANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVFRSDLPTSFKLD 533 (1988)
Q Consensus 454 ~i~~l~~~~vlr~Gsg~~~E~LLm~~a~~~n~i~Pnk~~~~~~~~~~g~l~~setY~GG~V~~p~~GvY~~d~~~~f~~~ 533 (1988)
+++|+|+++|+ |++..++++|+++|+++|+++|+.... ..++|+||+|++|++|+|++
T Consensus 335 rvtglpl~~v~--~qikv~~~lllr~~~~~g~viP~~~~~-----------~~~~Y~GA~V~eP~~GlY~~--------- 392 (498)
T PHA02524 335 YYAKIRFDDVL--GTIKVWDSIIFNSLVESNVVIPAMKAS-----------PKQSFPGAYVKEPVPGGYRY--------- 392 (498)
T ss_pred HHHCCCHHHhc--cHHHHHHHHHHHHHHHCCEecCCCCCC-----------CCCccCCeEEecCCCccccC---------
Confidence 99999999996 689999999999999999999997643 13579999999999999988
Q ss_pred hhHHHHHhhhhhhhhHHHHhHhcccccccccchHHHHHHHHHHHHhhccCCCcccCCeEEEEeccccchHHHHhcCCCCC
Q 000161 534 PSAYEQLLNNLDRDLQYAIKVEGKMDLESVSNYDEVKNAIMEKLLRLQEEPIREECPLIYHLDVAAMYPNIILTNRLQPP 613 (1988)
Q Consensus 534 ~~~~~~l~~~~~~~l~~~~~~e~~~~~~~~~n~~~v~~~i~~~l~~l~~~p~~~~~p~V~~LDf~SLYPsII~t~NL~p~ 613 (1988)
|++|||+|||||||++|||||+
T Consensus 393 ----------------------------------------------------------VivLDFaSLYPSII~a~NIsPe 414 (498)
T PHA02524 393 ----------------------------------------------------------GLSFDLTSLYPSILRLLNISPE 414 (498)
T ss_pred ----------------------------------------------------------eEEEEccccCHHHHHHhCCCHH
Confidence 7789999999999999999999
Q ss_pred ccccc
Q 000161 614 SIVTD 618 (1988)
Q Consensus 614 Tiv~~ 618 (1988)
|+++.
T Consensus 415 Tl~~~ 419 (498)
T PHA02524 415 MIAGM 419 (498)
T ss_pred Hhhcc
Confidence 99765
No 26
>PHA03334 putative DNA polymerase catalytic subunit; Provisional
Probab=100.00 E-value=2.2e-50 Score=517.07 Aligned_cols=392 Identities=17% Similarity=0.179 Sum_probs=271.3
Q ss_pred ceEEecCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCC------------Cc----c--------
Q 000161 301 YFKVTNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKM------------SE----E-------- 356 (1988)
Q Consensus 301 ~f~V~~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l------------~~----~-------- 356 (1988)
...+..|.||.+||.+|+..++++ .||+--||.+ ||+..|..|...+.-.- |. .
T Consensus 322 ~~~~~~c~~e~~~l~~fl~~~~~~-v~vlyv~n~~-fdv~vi~~rl~~y~~~~~~~~~~~~l~~~~~~~~s~~~~~~~~~ 399 (1545)
T PHA03334 322 RIEFVACADELEMLLAFLNRLRKS-VNVLYVYNAE-FDVQVIQSRLNYYAFKQRPHPLTKALMEAWEAFLSKDPQLVPAQ 399 (1545)
T ss_pred eeEEEEeccHHHHHHHHHHHHHhh-ccEEEEeccc-ccHHHHHHHHHHhhccCCCCcHHHHHHHHHHHHhccCCccCCce
Confidence 345678999999999999999984 4899999985 99999999998774221 10 0
Q ss_pred cCcc-------------------------c------cCCC----------------------CceeeccceEechHHHHh
Q 000161 357 LGFQ-------------------------C------DKNQ----------------------GECRAKFACHLDCFAWVK 383 (1988)
Q Consensus 357 iG~~-------------------------~------~~~~----------------------g~~~i~GRihiDl~~~vk 383 (1988)
+-+. + +... ....+.||+++|+|++++
T Consensus 400 ~~f~~~~~~s~y~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~v~~f~~n~~~~~~~kv~~~GrviiDMy~Vc~ 479 (1545)
T PHA03334 400 LLFGSDILNSNYLELLDVIESHKAQFKATCRKAAARKEEIGSYMKTRDTVQDFNDNDKKYLNSTSHGFGAHIIDLMRVCN 479 (1545)
T ss_pred eEehhhHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhHHHHHHHHHhhcccccccccceeeeccEEEEehHHHHh
Confidence 0000 0 0000 124588999999999999
Q ss_pred hc-cCCCCCCCCHHHHHHHHcCCCC-----------CCCChHHHHHHHhhC---hHHHHHHHHHhhHHHHHHHHHh-ccc
Q 000161 384 RD-SYLPQGSQGLKAVTKAKLGYDP-----------LEVNPEDMVRFAKEK---PQMMASYSVSDAVATYYLYMTY-VHP 447 (1988)
Q Consensus 384 rd-~~L~~~SysL~~Va~~~LG~~K-----------~dvd~~~i~~~~~~~---~~~La~Y~l~Da~lt~~L~~Kl-v~~ 447 (1988)
+. ...+..||+|++||+++||++| .|+++++|..++.++ +.+++.||++||+|+++|+.++ .|.
T Consensus 480 ~K~~~~kL~sYkLNTVA~~~LgeqKp~k~~~k~~K~eDV~YkeI~~lf~~g~e~RaRla~YCLkDA~LvlrLlkkl~~h~ 559 (1545)
T PHA03334 480 TKSIKAKCSSRKLDTVARLIISKSKPHKNPPKIGKMDDVKYTEMDGMFTAGGAALARYLIYNLVDSELLIRIAKNLDPVI 559 (1545)
T ss_pred hcccccCccCCcHHHHHHHHHhcccccccccccCcccCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 93 1234489999999999999999 999999999999854 4689999999999999999998 444
Q ss_pred hHhhhhhhcCCChH------HHhhhh--hHHHHHHHHHHHHH-HCCeeccCCCCC-----CchhhhcccccCCCCCCcce
Q 000161 448 FIFSLATIIPMSPD------EVLRKG--SGTLCEMLLMVQAY-KANVICPNKHQS-----DPEKFYRNHLLESETYIGGH 513 (1988)
Q Consensus 448 ~i~~La~i~~l~~~------~vlr~G--sg~~~E~LLm~~a~-~~n~i~Pnk~~~-----~~~~~~~g~l~~setY~GG~ 513 (1988)
-+.++++.++.++. .|+..| +++++-+.++.+|. +.|+++|.-... +.. ...+ -.+..+|.||+
T Consensus 560 e~~eraRvT~~id~~~l~RG~v~fdG~vQQIKV~s~lL~kA~~~~~~~ia~~~i~~s~ilP~~-~~~~-~~~~~~YeGAt 637 (1545)
T PHA03334 560 EFLNRLRATYNIDYVAHGRGVMNFCGFVQSTKSVEVPLLKARLRIGIFVATGRIAESLCMPEK-YARD-CRQKIKLKGGY 637 (1545)
T ss_pred HHHHHHhcccCCceeecccceecccCccchhhHHHHHHHHHHHhcCcccccccccccccCCcc-cccc-cccccccCCeE
Confidence 44577777764432 233445 88877655555554 888887532221 110 0000 01345799999
Q ss_pred eeeccCccccCCCCCCccCChhHHHHHhhhhhhhhHHHHhHhcccccccccchHHHHHHHHHHHHhhccCCCcccCCeEE
Q 000161 514 VECLESGVFRSDLPTSFKLDPSAYEQLLNNLDRDLQYAIKVEGKMDLESVSNYDEVKNAIMEKLLRLQEEPIREECPLIY 593 (1988)
Q Consensus 514 V~~p~~GvY~~d~~~~f~~~~~~~~~l~~~~~~~l~~~~~~e~~~~~~~~~n~~~v~~~i~~~l~~l~~~p~~~~~p~V~ 593 (1988)
|++|++|+|.+ +.+++ +|+
T Consensus 638 VLEP~~Gf~~~------------------------------------------------------~~Y~~-------PVa 656 (1545)
T PHA03334 638 VFAPLTGLTFA------------------------------------------------------GPYQG-------TEL 656 (1545)
T ss_pred eecCCCCcccc------------------------------------------------------ccCCC-------cEE
Confidence 99999998532 01222 599
Q ss_pred EEeccccchHHHHhcCCCCCccccccccccccCCCCCCccccccccccccccccCCcchhhHhhhhcccccccCCCCCcc
Q 000161 594 HLDVAAMYPNIILTNRLQPPSIVTDEVCTACDFNRPGKTCLRKLEWVWRGEIFMGKRSDYYHLKKQIESEFVDGTNGHLS 673 (1988)
Q Consensus 594 ~LDf~SLYPsII~t~NL~p~Tiv~~~~c~~c~~n~p~~~c~r~m~w~~~ge~~p~~~~ey~~i~~~l~~e~f~~~~~g~~ 673 (1988)
+|||+|||||||++|||||+|++.+. | .-+.++. -..+|.. .| .+ ++.
T Consensus 657 VLDFASLYPSIIiahNLCYeTLV~~~-c---~~~~~~~---~~~d~~k----~p---~g------------y~~------ 704 (1545)
T PHA03334 657 TLDFASLYPSNMCDANISPEAIVDPD-C---TARVRGW---VVFDWKK----ID---RG------------FGK------ 704 (1545)
T ss_pred EEEccccchHHHHHhCCCcccccCcc-c---hhhhccc---ccccccc----CC---cc------------cCc------
Confidence 99999999999999999999999652 3 1111100 0001100 00 00 000
Q ss_pred cccccCchHHHHHHHHHHHHHhhhhhcccccccccccccccccccccccchHHHHHHHHHHHHHHHhhhhhhhhhhHHHh
Q 000161 674 KSFLDLPKMEQQSRLKDRLKKYCQKAYKRVLDKPVTELREAGICMRENSFYVDTVRSFRDRRYEYKGLNKVWKGKLSEAK 753 (1988)
Q Consensus 674 ~~~~~L~~~~q~~~lkkrl~~y~~kvy~k~~~~~~~~~r~~~icqre~~f~~~~lr~f~drR~~~K~l~K~~k~~~~~a~ 753 (1988)
+..+. .+ .+. .....+. .+..++++.+|+.+++.|.++|+.||+.
T Consensus 705 --~~~vy----------~V--~~~---~~~~P~~----------~rf~SiLp~LL~eLL~~RK~~Kk~MKk~-------- 749 (1545)
T PHA03334 705 --ATLMY----------TI--LRT---KPEEPSW----------RRFTTYTTSSLNHYLSMRTEYKGAMKQA-------- 749 (1545)
T ss_pred --cccce----------ee--ccc---cCcCCCc----------ceecchHHHHHHHHHHHHHHHHHHHhhC--------
Confidence 00000 00 000 0000000 1122478999999999999999988753
Q ss_pred hcCChhhHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHH-HcCCe-EEEcc
Q 000161 754 ASGNSIKIQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNARLLIE-KIGKP-LELDT 831 (1988)
Q Consensus 754 ~~~d~~~~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~sR~ys~e~A~~VT~~Gr~iI~~a~~lve-~~G~~-vygDT 831 (1988)
.|+. +..+||++|+|+|+++||+|||+|. ++|.+||+.||++|+.+++++| +.|+. |||||
T Consensus 750 --kDp~-------er~iLD~rQlALKVtANSvYGytG~--------~cA~lVTa~GRemI~~t~~~IE~e~G~~VIYGDT 812 (1545)
T PHA03334 750 --KDPK-------LKSYHNQLQNEMKICANSHYGVAPH--------ACQHLITTLGRHKIKLVEEFIKKEPGMTVNYGDT 812 (1545)
T ss_pred --CCHH-------HHHHHHHHHHHHHHHHHhhcCcchh--------HHHHHHHHHHHHHHHHHHHHHHHhCCCEEEEEeC
Confidence 2443 3479999999999999999999875 5789999999999999999999 88987 69999
Q ss_pred ceeeEEcCCC
Q 000161 832 DGIWCVLPGS 841 (1988)
Q Consensus 832 DSI~~~lp~~ 841 (1988)
|||||.+|..
T Consensus 813 DSVfV~~p~~ 822 (1545)
T PHA03334 813 DSVMFQLPPD 822 (1545)
T ss_pred CceEEEeCcc
Confidence 9999999854
No 27
>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=100.00 E-value=1.6e-38 Score=358.47 Aligned_cols=204 Identities=71% Similarity=1.202 Sum_probs=190.2
Q ss_pred CceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEcccccccccccccCCCCCCCCCceEEecCCCHHHHHHHH
Q 000161 238 EVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRLW 317 (1988)
Q Consensus 238 ~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~eLL~~F 317 (1988)
++++|||||||++.+++||+|..|+|+|||+++.+.|..++++.+++.++.+|.|+|.++.+|.+.|+.+.+|++||.+|
T Consensus 1 ~lrilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~f 80 (204)
T cd05779 1 DPRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIVNREIVSEDIEDFEYTPKPEYEGPFKVFNEPDEKALLQRF 80 (204)
T ss_pred CceEEEEEEEecCCCCCCcCCCCCeEEEEEEEEecCCEEEecccccccccccccccCCCCCCCceEEecCCCHHHHHHHH
Confidence 58999999999988889999999999999999888888777888888888899999999999888899999999999999
Q ss_pred HHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCCCCHHH
Q 000161 318 FAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKA 397 (1988)
Q Consensus 318 ~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~SysL~~ 397 (1988)
+++|+++|||+|+|||+++||||||.+||+.||+.....+|+. .+..+.+.++||+|+|+|.+++++++++.+||+|++
T Consensus 81 ~~~i~~~~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~-~~~~~~~~~~gr~~iDl~~~~~~~~~l~~~sysLd~ 159 (204)
T cd05779 81 FEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFR-KDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQGLKA 159 (204)
T ss_pred HHHHHHhCCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeE-ecCCCeEEeccEEEEEhHHHHHHhhcCCCCCccHHH
Confidence 9999999999999999999999999999999999887778876 444567889999999999999998888788999999
Q ss_pred HHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHH
Q 000161 398 VTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYM 442 (1988)
Q Consensus 398 Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~ 442 (1988)
||+++||++|.++++.+|.++|.++++++++||++||.+|+.||+
T Consensus 160 Va~~~Lg~~K~~~~~~~I~~~~~~~~~~l~~Y~~~D~~~T~~l~~ 204 (204)
T cd05779 160 VTKAKLGYDPVELDPEDMVPLAREDPQTLASYSVSDAVATYYLYM 204 (204)
T ss_pred HHHHHhCCCcCcCCHHHHHHHHhCCcHHHHhccHHHHHHHHHHhC
Confidence 999999999999999999999999999999999999999999984
No 28
>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=100.00 E-value=2.3e-36 Score=364.47 Aligned_cols=283 Identities=27% Similarity=0.421 Sum_probs=207.2
Q ss_pred EecCCCeEEEEe-CCccEEEEEecCCCh-HHHHHH----HHHhccccceeEEEEEE-eeCCCcCcCCCCCeEEEEEEEec
Q 000161 71 VSQDGSTFKSKY-KFRPYFYAATKEKME-MDVEAY----LRRRYESQIADIEILEK-EDLDLKNHLSGLHKSYLKISFDT 143 (1988)
Q Consensus 71 ~t~dG~~~~v~v-~f~PYFyv~~~~~~~-~~v~~~----l~~~~~~~i~~ie~v~k-~dl~~~nhl~g~~~~~lKl~f~~ 143 (1988)
+|++|.++|+.| +|+||||+.+++... .++... +.+.....+.+++.|+| ++++. +.+....|+||+|.+
T Consensus 1 ~t~~g~svcv~v~~f~pyfYv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~r~~~~~~---y~~~~~~~lkV~~~~ 77 (325)
T PF03104_consen 1 MTEDGKSVCVRVHGFRPYFYVLPPESDSPKDLEQFIEQLLRKKFKIDVFKIEKVKRKKSFYG---YDGKEEPFLKVYFSS 77 (325)
T ss_dssp -ECTSEEEEEEEST--EEEEEEESSGGGHHHHTTHEEHHEETTEEEEEEEEEEEEEEEESSE---ETTEEEEEEEEEESS
T ss_pred CCCCCCEEEEEEcCCCEEEEEECCCCccHHHHHHHHHHHhhhccCCceEEEEEEEeeeeecc---CCCCCceEEEEEECc
Confidence 479999999999 999999999998743 233333 23344566789999999 88873 445666799999999
Q ss_pred hhhHHHHHHHHHHHHHhhcccchhHHHHHHhhhcccCCCCcccccccccccccCCCccceeeeecCCccceeEEEeeCC-
Q 000161 144 VQQLMDVKKDLLHVVERNQAKFDAAEAYESILTGKREQRPQDFLDCIVDLREYDVPYHIRFAIDNDVRCGQWYDVSISS- 222 (1988)
Q Consensus 144 ~~~l~~vr~~l~~~~~~n~~~~~~~~~y~~~~~~~~~~~~~~~~~~i~~i~E~DI~~~~R~~iD~~I~~g~W~~v~~~~- 222 (1988)
+..++++++.+.. ....+||+||+++.||++|++|++++|+++....
T Consensus 78 ~~~~~~~~~~l~~--------------------------------~~~~~~e~~i~~~~rfl~~~~i~~~~wi~i~~~~~ 125 (325)
T PF03104_consen 78 PRDVRKLRDNLKK--------------------------------TFFKVYEADIPPLERFLIDRNIRGPGWIKIKNPSK 125 (325)
T ss_dssp TTHHHHHHHHHHH--------------------------------TEEEEESTSS-HHHHHHHHTTHCTTEEEEEETTEC
T ss_pred HHHHHHHHHHHHh--------------------------------ccchhhccCCCHHHheeeecCcccceeeecccccc
Confidence 9999999988873 3457899999999999999999999999998761
Q ss_pred --------CCceEEEe-------ccccCCCCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEccccccccc
Q 000161 223 --------TGPLLEKR-------VDLLQRAEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDI 287 (1988)
Q Consensus 223 --------~~~~i~~~-------~~~~~~p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~di 287 (1988)
...++.+. .+....|++++|||||||.+.+.+||++..|+|+|||++++..|.. .+.
T Consensus 126 ~~~~~~s~~~~e~~~~~~~~~~~~~~~~~p~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~--------~~~ 197 (325)
T PF03104_consen 126 PVKDRVSWCDIEFSVDYSNLKPLPDESIPPPLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSS--------EPY 197 (325)
T ss_dssp HHHHHTCTCSCECECCHHHHECHTSSSSGGGSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEE--------ETT
T ss_pred ccccccccccccccccccccccccccccccccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEecccc--------CCC
Confidence 12233221 1111239999999999999988889999999999999987644310 000
Q ss_pred ccccC--CCCCCCCCceEEecCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcc-------cC
Q 000161 288 EDLEY--TPKPEFEGYFKVTNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEE-------LG 358 (1988)
Q Consensus 288 ~~fey--tp~~~~~g~f~V~~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~-------iG 358 (1988)
....+ .+.+...+...|..+++|++||.+|+++|+++|||||+|||+++||||||.+||+.+|+++... +|
T Consensus 198 ~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~f~~~i~~~dPDii~GyN~~~fD~~yl~~R~~~l~~~~~~~~~~~~~~~~ 277 (325)
T PF03104_consen 198 RRKVFTLGSCDSIEDNVEVIYFDSEKELLEAFLDIIQEYDPDIITGYNIDGFDLPYLIERAKKLGIDMFDLNGRRWSRFG 277 (325)
T ss_dssp EEEEEECSCSCCTTCTTEEEEESSHHHHHHHHHHHHHHHS-SEEEESSTTTTHHHHHHHHHHHTTTCTHHSTTSTTTEEE
T ss_pred ceEEEEecCCCCCCCCcEEEEECCHHHHHHHHHHHHHhcCCcEEEEecccCCCHHHHHHHHHHhCcccccccccccccee
Confidence 11111 1112122145688899999999999999999999999999999999999999999999886422 22
Q ss_pred ccccC-----CC-----CceeeccceEechHHHHhhccCCCCCCCCHHHH
Q 000161 359 FQCDK-----NQ-----GECRAKFACHLDCFAWVKRDSYLPQGSQGLKAV 398 (1988)
Q Consensus 359 ~~~~~-----~~-----g~~~i~GRihiDl~~~vkrd~~L~~~SysL~~V 398 (1988)
+.... .. ..+.++||+|+|+|.++++... +.||+|++|
T Consensus 278 ~~~~~~~~~~~~~~~~~~~~~~~Gr~~~D~~~~~~~~~~--l~sY~L~~V 325 (325)
T PF03104_consen 278 RLKRKKWPSSANGSRKFSRIDIPGRLVLDLYRLARKDYK--LDSYSLDNV 325 (325)
T ss_dssp EEEEEESEECTCCCTTEEEEEETTSEEEEHHHHHHHHS----SS-SHHHH
T ss_pred EEeecccccccCCCcceeEEEECCChHhHHHHHHHhhCC--CCCCCCCCC
Confidence 11000 01 1356999999999999999865 499999987
No 29
>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=100.00 E-value=1.1e-32 Score=318.27 Aligned_cols=201 Identities=26% Similarity=0.318 Sum_probs=164.0
Q ss_pred cCCCCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCce-EEEcccccccccccccCCCCCCCCCceEEecCCCHHH
Q 000161 234 LQRAEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGY-LIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIE 312 (1988)
Q Consensus 234 ~~~p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~-li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~e 312 (1988)
.+.|++++|||||||++.+++||+|+.|+|+|||+++..+|. ..+.+.++.- .+ +.| .+ ...|..+++|++
T Consensus 2 ~~~p~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l--~~--~~~---~~-~~~v~~~~~E~e 73 (230)
T cd05777 2 SKIAPLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTL--KT--CAP---IV-GAQVFSFETEEE 73 (230)
T ss_pred CCCCCceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEe--CC--CCC---CC-CCEEEEECCHHH
Confidence 468999999999999998888999999999999999754442 1001111100 00 111 12 246778999999
Q ss_pred HHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCcccc------------CCCC-----ceeeccceE
Q 000161 313 LLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCD------------KNQG-----ECRAKFACH 375 (1988)
Q Consensus 313 LL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~------------~~~g-----~~~i~GRih 375 (1988)
||.+|+++|+++|||||+|||+++||||||.+||+.+|++.+..+|+... ...| .+.+.||+|
T Consensus 74 LL~~f~~~i~~~DPDii~GyN~~~FDl~yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~~ 153 (230)
T cd05777 74 LLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQ 153 (230)
T ss_pred HHHHHHHHHHhcCCCEEEEecCCCCCHHHHHHHHHHhCCccccccccccCCceeEeCCcccccccccccceEEEEcCEEe
Confidence 99999999999999999999999999999999999999998777776411 0112 146899999
Q ss_pred echHHHHhhccCCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhCh---HHHHHHHHHhhHHHHHHHHHh
Q 000161 376 LDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKP---QMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 376 iDl~~~vkrd~~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~---~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
+|+|+++++..++ .||+|++||+++||++|+++++++|.++|.+++ .++++||++||.+|++|+.++
T Consensus 154 iD~~~~~~~~~kl--~sy~L~~Va~~~Lg~~k~d~~~~~i~~~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl 223 (230)
T cd05777 154 FDLLQVIQRDYKL--RSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKL 223 (230)
T ss_pred eeHHHHHHHhcCc--ccCcHHHHHHHHhCCCCCCCCHHHHHHHHccCHhHhHHHHHhhHHHHHHHHHHHHHH
Confidence 9999999998665 899999999999999999999999999997655 589999999999999999997
No 30
>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=99.97 E-value=2.7e-30 Score=289.37 Aligned_cols=176 Identities=24% Similarity=0.388 Sum_probs=148.1
Q ss_pred CCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEcccccccccccccCCCCCCCCCceEEecCCCHHHHHHH
Q 000161 237 AEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRL 316 (1988)
Q Consensus 237 p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~eLL~~ 316 (1988)
|++++|+|||||++ +.+||+|..|+|+|||++... |... +....+.+|++||.+
T Consensus 1 p~l~~l~fDIEt~~-~~gfp~~~~d~Ii~Is~~~~~-g~~~------------------------~~~~~~~~E~~lL~~ 54 (188)
T cd05781 1 PDLKTLAFDIEVYS-KYGTPNPRRDPIIVISLATSN-GDVE------------------------FILAEGLDDRKIIRE 54 (188)
T ss_pred CCceEEEEEEEecC-CCCCCCCCCCCEEEEEEEeCC-CCEE------------------------EEEecCCCHHHHHHH
Confidence 79999999999996 457999999999999998632 2210 011235899999999
Q ss_pred HHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccc-----cCCCCceeeccceEechHHHHhhccCCCCC
Q 000161 317 WFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQC-----DKNQGECRAKFACHLDCFAWVKRDSYLPQG 391 (1988)
Q Consensus 317 F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~-----~~~~g~~~i~GRihiDl~~~vkrd~~L~~~ 391 (1988)
|+++|+++|||+|+|||+++||||||.+||+.+|+++. +|+.. ....|.+.++||+|+|+|.++++..++ +
T Consensus 55 F~~~i~~~dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~~--~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~l--~ 130 (188)
T cd05781 55 FVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKLD--VGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPEV--K 130 (188)
T ss_pred HHHHHHHcCCCEEEecCCCcCcHHHHHHHHHHhCCCcc--cccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCCC--C
Confidence 99999999999999999999999999999999999763 22210 112467889999999999999998765 8
Q ss_pred CCCHHHHHHHHcCC----CCCCCChHHHHHHHhh--ChHHHHHHHHHhhHHHHHHHHH
Q 000161 392 SQGLKAVTKAKLGY----DPLEVNPEDMVRFAKE--KPQMMASYSVSDAVATYYLYMT 443 (1988)
Q Consensus 392 SysL~~Va~~~LG~----~K~dvd~~~i~~~~~~--~~~~La~Y~l~Da~lt~~L~~K 443 (1988)
||+|++||++ ||. +|.++++.+|.++|.+ +++++++||++||.+|+.|+++
T Consensus 131 ~y~L~~Va~~-Lg~~k~~~k~~~~~~~i~~~~~~~~~~~~l~~Y~~~D~~~t~~l~~~ 187 (188)
T cd05781 131 VKTLENVAEY-LGVMKKSERVLIEWYRIYEYWDDEKKRDILLKYNRDDARSTYGLAEK 187 (188)
T ss_pred CCCHHHHHHH-HCCCccccccCCCHHHHHHHHcCcccHHHHHHHHHHHHHHHHHHHhh
Confidence 9999999985 997 4567899999999986 7899999999999999999986
No 31
>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=99.97 E-value=3.6e-30 Score=290.31 Aligned_cols=185 Identities=26% Similarity=0.389 Sum_probs=153.9
Q ss_pred CCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEcccccccccccccCCCCCCCCCceEEecCCCHHHHHHH
Q 000161 237 AEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRL 316 (1988)
Q Consensus 237 p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~eLL~~ 316 (1988)
|++++++|||||++.. +||++..|+|+|||++..+.+.+++.+... + . .|..+.+|++||.+
T Consensus 1 p~l~i~~fDIEt~~~~-g~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~----------~------~-~v~~~~~E~~lL~~ 62 (195)
T cd05780 1 EDLKILSFDIEVLNHE-GEPNPEKDPIIMISFADEGGNKVITWKKFD----------L------P-FVEVVKTEKEMIKR 62 (195)
T ss_pred CCceEEEEEEEecCCC-CCCCCCCCcEEEEEEecCCCceEEEecCCC----------C------C-eEEEeCCHHHHHHH
Confidence 7899999999999854 699999999999999875555544432210 0 1 35678999999999
Q ss_pred HHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccc--c--CCCC---ceeeccceEechHHHHhhccCCC
Q 000161 317 WFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQC--D--KNQG---ECRAKFACHLDCFAWVKRDSYLP 389 (1988)
Q Consensus 317 F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~--~--~~~g---~~~i~GRihiDl~~~vkrd~~L~ 389 (1988)
|+++|+++|||+|+|||+++||||||.+||+.+|++. .+|+.. . ...| ...+.||+|+|+|+++++...
T Consensus 63 F~~~i~~~dpdiivgyN~~~FD~pyL~~R~~~~gi~~--~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~~-- 138 (195)
T cd05780 63 FIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIEL--DLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLN-- 138 (195)
T ss_pred HHHHHHHcCCCEEEecCCCCCcHHHHHHHHHHhCCCC--ccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhCC--
Confidence 9999999999999999999999999999999999984 233320 0 0011 235789999999999998655
Q ss_pred CCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhC--hHHHHHHHHHhhHHHHHHHHH
Q 000161 390 QGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEK--PQMMASYSVSDAVATYYLYMT 443 (1988)
Q Consensus 390 ~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~--~~~La~Y~l~Da~lt~~L~~K 443 (1988)
..||+|++||+++||.+|.++++++|.++|.++ ++++++||++||.+|++|+.+
T Consensus 139 l~sy~L~~v~~~~Lg~~k~d~~~~~i~~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~ 194 (195)
T cd05780 139 LTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTYEIGKE 194 (195)
T ss_pred CCcCcHHHHHHHHhCCCCCcCCHHHHHHHHhCCCchHHHHHHhHHHHHHHHHHHhh
Confidence 489999999999999999999999999999865 899999999999999999875
No 32
>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=99.97 E-value=2.2e-29 Score=290.54 Aligned_cols=197 Identities=16% Similarity=0.196 Sum_probs=158.6
Q ss_pred CCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCce-----------EEEccccccccccccc-CCCCCCCCCceEE
Q 000161 237 AEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGY-----------LIINRECVGEDIEDLE-YTPKPEFEGYFKV 304 (1988)
Q Consensus 237 p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~-----------li~nreivs~di~~fe-ytp~~~~~g~f~V 304 (1988)
..|++|||||||.+++.+||||+.|+|++|++++.+++. +++..+. .+.. +..... .....|
T Consensus 2 ~~l~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~-----~~~~~~~~~~~-~~~~~v 75 (231)
T cd05778 2 QHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELK-----SNASNGRIRSG-LSGIPV 75 (231)
T ss_pred CceEEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCcc-----chhhhhccccC-CCCCeE
Confidence 468999999999999999999999999999999866543 1111110 0000 000001 123568
Q ss_pred ecCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCC-cccCccccC----------CCC-----ce
Q 000161 305 TNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMS-EELGFQCDK----------NQG-----EC 368 (1988)
Q Consensus 305 ~~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~-~~iG~~~~~----------~~g-----~~ 368 (1988)
..+++|++||.+|+++|+.+|||||+|||+++||||||.+||+.+|+..+ .++|+.... ..| .+
T Consensus 76 ~~~~~E~~LL~~f~~~i~~~DPDii~GyNi~~fd~~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~~g~~~~~~~ 155 (231)
T cd05778 76 EVVESELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDEWGYTHTSGI 155 (231)
T ss_pred EEeCCHHHHHHHHHHHHHHhCCCEEEEeccccCcHHHHHHHHHHhCCcchhhhccCCCCCCcccccccccccccccCCce
Confidence 89999999999999999999999999999999999999999999999876 666654110 022 35
Q ss_pred eeccceEechHHHHhhccCCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhh----ChHHHHHHHHHhhHHHHHHH
Q 000161 369 RAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKE----KPQMMASYSVSDAVATYYLY 441 (1988)
Q Consensus 369 ~i~GRihiDl~~~vkrd~~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~----~~~~La~Y~l~Da~lt~~L~ 441 (1988)
.+.||+++|+|+.++++.++ .||+|++||.++||++|+++++.+|.++|.+ .+.++++||++||.++++|+
T Consensus 156 ~i~GRi~lD~~~~~r~~~kl--~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l~l~Ll 230 (231)
T cd05778 156 KIVGRHILNVWRLMRSELAL--TNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEIL 230 (231)
T ss_pred EEeeEEEeEhHHHHHHHcCc--ccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHHHHHhh
Confidence 79999999999999997655 9999999999999999999999999999853 45789999999999999985
No 33
>PHA02523 43B DNA polymerase subunit B; Provisional
Probab=99.96 E-value=3.3e-30 Score=299.98 Aligned_cols=276 Identities=16% Similarity=0.198 Sum_probs=187.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCCCHHHHHHHHHHHHHHHHH--------HHHHHHHcCCe--EEEc
Q 000161 761 IQEAQDMVVLYDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQN--------ARLLIEKIGKP--LELD 830 (1988)
Q Consensus 761 ~~e~~~~~~lyds~QlA~K~ilNS~YGy~g~~~sR~ys~e~A~~VT~~Gr~iI~~--------a~~lve~~G~~--vygD 830 (1988)
+.+++...+..|..|.|+|+++||||||+|+.++|||+.++|++||++||++|+. +.++++..|+. ||||
T Consensus 29 i~~~~r~~a~~~~~q~AiKIlmNSfYGylG~~~~R~yd~e~A~aVT~~Gre~Ik~i~~~~ney~~~l~~t~G~~~VIYgD 108 (391)
T PHA02523 29 IARCEKEEQKRNTNQLNRKILINSLYGALGNNWFRYFDLRNAEAITTYGQLAIRWIERKLNEYINELVKTTGVDYVCYID 108 (391)
T ss_pred HHHHHHHHHHHhcchHHHHHHHHhhhhhhcCCCceecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCcceEEEec
Confidence 4556666788999999999999999999999999999999999999999999993 44466667984 6999
Q ss_pred cceeeEEcCCCCCcccccccccccccccccccccccchhhhccccchhhhhccCCccccccccccceeEEeeeceeeeee
Q 000161 831 TDGIWCVLPGSFPENFTFKTKDLKKKLTISYPCVMLNVDVARNNTNDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMI 910 (1988)
Q Consensus 831 TDSI~~~lp~~~pe~~~~k~~~g~k~i~~sy~~~~ln~~V~~~~tN~~y~~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~mi 910 (1988)
|||||+.+... .+.........+..+ ++|........+ +.++|..|++|.+-. -.-+..+++|.++.|++++
T Consensus 109 TDSifv~~~~~-v~~~~~~~~~d~~~~-vd~ldk~~~~~i-E~~In~sY~el~eym-----na~~h~~~m~rE~ia~~f~ 180 (391)
T PHA02523 109 TDSVYLNMEAV-VNRVGIDKFRDTNHL-IDFLDNLGSKKL-EPFIDDSYKELEEYM-----NHDHHLLLMDREAIFGAPL 180 (391)
T ss_pred CCeeEEEecch-HHHHhhhhhccchhh-hHHHHHHHHHHh-HHHHHHHHHHHHHHh-----cchhhhhhhhHHHhccccc
Confidence 99999998532 111111000000111 233333333444 467899999995421 1223444445558999873
Q ss_pred cccccccCcccccceEE--EcCCCC-----EEEEEeeeeccCChhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHH
Q 000161 911 LPASKEEGILIKKRYAV--FNDDGT-----LAELKGFEIKRRGELKLIKVFQAELFDKFLHGSTIEECYSAVAAVANRWL 983 (1988)
Q Consensus 911 Lp~s~~~~~~~KKRYa~--~~~dG~-----~~e~KG~E~kRRd~~~liK~~q~~v~~~~L~g~~lee~~~~v~~v~~~~~ 983 (1988)
=...-+.=...|||||+ ++.+|+ .+++.|||++|++.++++|+.|+++++.+|.|..- +.-++++++...+.
T Consensus 181 ~s~g~~gfw~~KKRYA~~v~d~EG~r~~epklkI~G~E~qrSstp~~~~~~~ke~i~~Il~~~ee-~iqeyi~~~~~ey~ 259 (391)
T PHA02523 181 GSDGIGGFWTGKKRYALNVYDMEGTRYAEPHLKIMGLETQRSSTPLACQKSLKESIRRLLQEGES-SLQDYFKEFKDEFK 259 (391)
T ss_pred cccccchhhhhhhhhhheeeeccCccccCCccceeeeeecccCchHHHHHHHHHHHHHHHhCChH-HHHHHHHHHHHHHh
Confidence 21111111236999997 566664 24899999999999999999999999999987643 35566666665432
Q ss_pred HHHHhcCCCCCchhhhhhhhhccccccChhhhCC---CCChHHHHHHHHHhhcCCC--c-ccCCCCeeEEEEEcCCC
Q 000161 984 DLLDNQGKDIADSELIDYISESSTMSKSLADYGE---QKSCAVTTARRLSDFLGDT--M-VKDKGLRCQYIVACEPQ 1054 (1988)
Q Consensus 984 d~L~~~~~~~~~~eLi~~i~~~k~lsK~l~eY~~---~k~~~v~~A~rl~e~lG~~--~-~~~~G~~i~YVI~~~p~ 1054 (1988)
+++.+++.. -+....+.|.++.|+. ..|.||..|+--...+|.. + ....|+++..+-.+.+.
T Consensus 260 --------~~~~~~Ia~-~s~~~~I~K~~d~~~~~~kg~p~hvrGal~~N~~~~~~~~~~~i~~GeKvk~l~Lk~~n 327 (391)
T PHA02523 260 --------NIPYQDVAA-VSSANNIGKNGDALGFPIKGTPYHVKGVLAYNRIAKTDTAIPMISEGEKVMVLPLRDRN 327 (391)
T ss_pred --------cCCHHHhcc-cCCCCchhhcccccCCCCCCCchhhHHHHHHHHHhcccCCCccccCCCceEEEeccCCC
Confidence 456555431 0114577788888763 3567998887555444431 2 36899999999887654
No 34
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.96 E-value=6.5e-32 Score=369.16 Aligned_cols=367 Identities=20% Similarity=0.206 Sum_probs=267.8
Q ss_pred CeEEEEEEEechhhHHHHHHHHHHHHHhhcccchhHHHHHHhhhcccCCCCcccccccccccccCCCccceeeeecCCcc
Q 000161 133 HKSYLKISFDTVQQLMDVKKDLLHVVERNQAKFDAAEAYESILTGKREQRPQDFLDCIVDLREYDVPYHIRFAIDNDVRC 212 (1988)
Q Consensus 133 ~~~~lKl~f~~~~~l~~vr~~l~~~~~~n~~~~~~~~~y~~~~~~~~~~~~~~~~~~i~~i~E~DI~~~~R~~iD~~I~~ 212 (1988)
....+|+++.+|.+++.+|..+.. ...+.+++|+|||+..|+++|+.+.+
T Consensus 128 ~~~~~k~~~~~~~~v~~~~~~~~~------------------------------~~~~~~~~e~di~~~~r~~~d~~~~p 177 (1172)
T TIGR00592 128 LVSVPKLKFSSPADVPAINDFSNH------------------------------HPAVVDIVKKAIPVSTRYLLEKILIP 177 (1172)
T ss_pred cccccccccccccchhhccccccc------------------------------cccccccccCCCCccccccccccccC
Confidence 456677777777777666554441 22456789999999999999999999
Q ss_pred cee--EEEeeCCCCceEEEeccccCCCCceEEEEEEEEccCC--CCC--CCCCCCeEEEEEEE----EcCCceEEEcccc
Q 000161 213 GQW--YDVSISSTGPLLEKRVDLLQRAEVHVCAFDIETTKLP--LKF--PDADYDIIMMISYM----LDGQGYLIINREC 282 (1988)
Q Consensus 213 g~W--~~v~~~~~~~~i~~~~~~~~~p~lrvLsfDIEt~s~~--~~f--Pdp~~D~Ii~IS~~----~~~~g~li~nrei 282 (1988)
+.| +.... . .......|+++++||||||.+.. ..| |++..|+|+|||++ ....|.......
T Consensus 178 ~~~~~~~~~~----~----~~~~~~~p~~~~~sfdiE~~~~~g~~~fp~~~~~~D~ii~is~~~~~~~~~~~~~~~~~~- 248 (1172)
T TIGR00592 178 VPLKRAEFAG----G----DVQMEGDPELKLASFDIETYFHDGKDFFPGDENPADEEIMISTTPVIAKQWDYESEPEAR- 248 (1172)
T ss_pred CCCCcccccc----c----cccccCCCcccccccccccccccccccCcccccccccccccccccccccccccCCCccch-
Confidence 765 11110 0 11222469999999999999753 344 55567999999864 111111000000
Q ss_pred cccccccccCCCCCCCCCceEEecCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHH-------------HHHHc
Q 000161 283 VGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLET-------------RAAHH 349 (1988)
Q Consensus 283 vs~di~~feytp~~~~~g~f~V~~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~-------------Ra~~l 349 (1988)
.-|...++...+|. .|..+++|.+||.+|+++|++.|||||+|||+++||||||.+ |++.+
T Consensus 249 -----~~~~~~~~~~~~~~-~v~~~~~E~~~L~~f~~~i~~~dpdii~gYNi~~FD~pyl~~~~~~~~~~da~~dr~~~~ 322 (1172)
T TIGR00592 249 -----VVTWKKPDKPTTGS-YVESVSEEISMIKRFWDVIDQEDTDVEITVNGDNFDLVYLADRQVFQFYWDAYEDPAEKL 322 (1172)
T ss_pred -----hhhccCccccCCCc-cceeccchHHHHhhHHHHHhhcCcchhcccccccCccceecCCceEEeeHHhhhHHhhCC
Confidence 01222233333443 467889999999999999999999999999999999999999 67776
Q ss_pred CCCCCcccCcccc------CCCC----ce--eeccceEechHHHHhhccCCCCCCCCHHHHHHHHcCCCCCCCChHHHHH
Q 000161 350 GFKMSEELGFQCD------KNQG----EC--RAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVR 417 (1988)
Q Consensus 350 Gi~l~~~iG~~~~------~~~g----~~--~i~GRihiDl~~~vkrd~~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~ 417 (1988)
|.-. .+|+... ...| .| .+.||+++|++..+++...+ .+|+|+.|+.++||.+|.++.+..|.+
T Consensus 323 G~~~--lfGr~~~~~s~~~~v~g~~R~~~~l~~~Grv~~D~~~~~~~~~~l--~~y~le~vs~~~lg~~k~dv~~k~I~~ 398 (1172)
T TIGR00592 323 GVVL--LFGRDVDHVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINL--PDYYLEFVSELALGYKKEKFRAKPIAK 398 (1172)
T ss_pred CeEE--EecccCCceeEEEEECCeeeeeEEeeccccccccccchhcccccH--HHHHHHHHHHHHhhcCcCceeeEEehh
Confidence 6532 2332100 0123 12 46899999999999987655 899999999999999999999999999
Q ss_pred HHhhC-hHHHHHHHHHhhHHHHHHHHHhccchHhhhhhhcCCChHHHhhhhhHHHHHHHHHHHHHHCCeeccCCCCCCch
Q 000161 418 FAKEK-PQMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDEVLRKGSGTLCEMLLMVQAYKANVICPNKHQSDPE 496 (1988)
Q Consensus 418 ~~~~~-~~~La~Y~l~Da~lt~~L~~Klv~~~i~~La~i~~l~~~~vlr~Gsg~~~E~LLm~~a~~~n~i~Pnk~~~~~~ 496 (1988)
.|..+ +.+++.||.+|+.++|.|..++ .++.-...++.|.++..|+..++|.+.+.++.+.+...|++-|+.......
T Consensus 399 ~~~~~~~~~~v~y~~~~lkv~y~l~~~~-~~l~~l~~~~~g~~~~~vf~~n~g~~erfll~rki~gp~WL~i~~p~~~~~ 477 (1172)
T TIGR00592 399 KYEFEAPDIDAPYSSEYLEVTYELGKEF-APMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVKGPDELEY 477 (1172)
T ss_pred hccCCCCccCCcCCcceEEEEEccCccc-hhhhhhhhhccCCcchheeccCHHHHHHHHhcCCCCCCceEEeCCCcccCc
Confidence 88744 3468899999999999986654 222222357778888899888999999999999999999998876543211
Q ss_pred hhhcccccCCCCCCcceeeec--cCccccCCCCCCccCChhHHHHHhhhhhhhhHHHHhHhcccccccccchHHHHHHHH
Q 000161 497 KFYRNHLLESETYIGGHVECL--ESGVFRSDLPTSFKLDPSAYEQLLNNLDRDLQYAIKVEGKMDLESVSNYDEVKNAIM 574 (1988)
Q Consensus 497 ~~~~g~l~~setY~GG~V~~p--~~GvY~~d~~~~f~~~~~~~~~l~~~~~~~l~~~~~~e~~~~~~~~~n~~~v~~~i~ 574 (1988)
++ ....+|+|+.|.+| .+|.|.+
T Consensus 478 ----~~-~S~c~yEga~v~~p~v~~g~~~~-------------------------------------------------- 502 (1172)
T TIGR00592 478 ----PR-RSWCKYEGGYVKPPNVEKGLDKT-------------------------------------------------- 502 (1172)
T ss_pred ----CC-ccccceEEEEecCccccccccCC--------------------------------------------------
Confidence 10 12467999999999 9997654
Q ss_pred HHHHhhccCCCcccCCeEEEEecc--ccchHHHHhcCCCCCccccc
Q 000161 575 EKLLRLQEEPIREECPLIYHLDVA--AMYPNIILTNRLQPPSIVTD 618 (1988)
Q Consensus 575 ~~l~~l~~~p~~~~~p~V~~LDf~--SLYPsII~t~NL~p~Tiv~~ 618 (1988)
-|||.+|||+ |||||||+++|||+++++..
T Consensus 503 --------------~pPl~vLdFsi~SlyPsi~~~~nl~iS~~v~~ 534 (1172)
T TIGR00592 503 --------------PPPLVVLDFSMKSLNPSIIRNEIVSIPDTLHR 534 (1172)
T ss_pred --------------CCCeEEEEeeeEEecCccccCceEEEEEEEee
Confidence 3789999999 99999999999998887654
No 35
>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=99.96 E-value=1.7e-28 Score=278.62 Aligned_cols=183 Identities=23% Similarity=0.237 Sum_probs=147.6
Q ss_pred cCCCCceEEEEEEEEccCCCCC-C--CCCCCeEEEEEEEEcCCceEEEcccccccccccccCCCCCCCCCceEEecCCCH
Q 000161 234 LQRAEVHVCAFDIETTKLPLKF-P--DADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNE 310 (1988)
Q Consensus 234 ~~~p~lrvLsfDIEt~s~~~~f-P--dp~~D~Ii~IS~~~~~~g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE 310 (1988)
+.+|++++|||||||++.+..| | ++..|+|+|||++..+ |...+ + ...+.+|
T Consensus 4 ~~~~~lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~-~~~~~----~--------------------~~~~~~E 58 (207)
T cd05785 4 MTFDDLRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNR-GWEEV----L--------------------HAEDAAE 58 (207)
T ss_pred CCCCCceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCC-Cceee----e--------------------ccCCCCH
Confidence 4689999999999999977554 4 5567999999987432 22110 0 1136899
Q ss_pred HHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCC-CcccCcccc--C---C-------CCceeeccceEec
Q 000161 311 IELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKM-SEELGFQCD--K---N-------QGECRAKFACHLD 377 (1988)
Q Consensus 311 ~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l-~~~iG~~~~--~---~-------~g~~~i~GRihiD 377 (1988)
++||.+|+++|+++|||||+|||+++||||||.+||+.+|++. ++++|.... . . ...+.++||+++|
T Consensus 59 ~~lL~~f~~~i~~~dPdii~g~N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iD 138 (207)
T cd05785 59 KELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVID 138 (207)
T ss_pred HHHHHHHHHHHHHhCCCEEeccCCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEE
Confidence 9999999999999999999999999999999999999999987 445443210 0 0 1135689999999
Q ss_pred hHHHHhhcc--CCCCCCCCHHHHHHHH--cCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHH
Q 000161 378 CFAWVKRDS--YLPQGSQGLKAVTKAK--LGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLY 441 (1988)
Q Consensus 378 l~~~vkrd~--~L~~~SysL~~Va~~~--LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~ 441 (1988)
++.++++.. ..++.||+|++||+++ +|.+|.++++++|.++|.++++++++||++||.+|++|.
T Consensus 139 l~~~~~~~~~~~~~l~sysL~~Va~~~g~~~~~k~d~~~~~I~~l~~~~~~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 139 TYFLVQLFDVSSRDLPSYGLKAVAKHFGLASPDRTYIDGRQIAEVWRSDPARLLAYALDDVRETEGLA 206 (207)
T ss_pred cHHHHHhhcccccCCCCCCHHHHHHHhcccCCCcCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHhh
Confidence 999999721 1235899999999986 677899999999999999999999999999999999884
No 36
>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=99.95 E-value=9.4e-28 Score=271.82 Aligned_cols=190 Identities=25% Similarity=0.311 Sum_probs=146.6
Q ss_pred CCCCceEEEEEEEEccCC-CCCCCCCC--CeEEEEEEEEcCCce---EEEcccccccccccccCCCCCCCCCceEEecCC
Q 000161 235 QRAEVHVCAFDIETTKLP-LKFPDADY--DIIMMISYMLDGQGY---LIINRECVGEDIEDLEYTPKPEFEGYFKVTNVN 308 (1988)
Q Consensus 235 ~~p~lrvLsfDIEt~s~~-~~fPdp~~--D~Ii~IS~~~~~~g~---li~nreivs~di~~feytp~~~~~g~f~V~~~~ 308 (1988)
+.|++++|||||||++.+ ++||+|+. |+|++||+.. ++|. +++++... +..++++.+ ...|..+.
T Consensus 1 ~~P~lrilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~~-~~~~~~v~~~~~~~~--~~~~~~~~~------~~~v~~~~ 71 (204)
T cd05783 1 PIPKLKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALAG-SDGLKRVLVLKREGV--EGLEGLLPE------GAEVEFFD 71 (204)
T ss_pred CCCCceEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEcC-CCCCcEEEEEecCCc--ccccccCCC------CCeEEecC
Confidence 479999999999999865 89999987 8999999863 2332 33333211 111222322 34577899
Q ss_pred CHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccC-
Q 000161 309 NEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSY- 387 (1988)
Q Consensus 309 dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~- 387 (1988)
+|++||.+|+++|+++ |+|+|||+++||||||.+||+.+|++... .+.. . ..+.+.++|++|+|+|++++++..
T Consensus 72 ~E~~lL~~F~~~i~~~--~~iig~N~~~FDlpyl~~R~~~~gi~~~~-~~~~-~-~~~~~~~~g~~~iDl~~~~~~~~~~ 146 (204)
T cd05783 72 SEKELIREAFKIISEY--PIVLTFNGDNFDLPYLYNRALKLGIPKEE-IPIY-L-KRDYATLKHGIHIDLYKFFSNRAIQ 146 (204)
T ss_pred CHHHHHHHHHHHHhcC--CEEEEeCCCCcCHHHHHHHHHHhCCChhh-Ccee-e-cCCceeccCcEEeECHHHhhccchh
Confidence 9999999999999988 58999999999999999999999998421 1111 0 113467899999999999886421
Q ss_pred -----CCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHH
Q 000161 388 -----LPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYM 442 (1988)
Q Consensus 388 -----L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~ 442 (1988)
.+..||+|++||+++||++|.+++ .+|.++ +++++++||++||.+|++|..
T Consensus 147 ~~~~~~~~~~~~L~~Va~~~lg~~K~~~~-~~i~~~---~~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 147 VYAFGNKYREYTLDAVAKALLGEGKVELE-KNISEL---NLYELAEYNYRDAELTLELTT 202 (204)
T ss_pred hhhhccccccCcHHHHHHHhcCCCcccCC-chhhhh---cHHHHHHhhHHHHHHHHHHhc
Confidence 134799999999999999999997 557666 889999999999999999854
No 37
>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=99.95 E-value=5e-27 Score=263.59 Aligned_cols=182 Identities=21% Similarity=0.255 Sum_probs=143.5
Q ss_pred CCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEcccccccccccccCCCCCCCCCceEEecCCCHHHHHHH
Q 000161 237 AEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRL 316 (1988)
Q Consensus 237 p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~eLL~~ 316 (1988)
|+++++||||||++.+ +|++|++...+...+++-.. . .+ . +...+..+++|++||.+
T Consensus 1 p~l~~~~fDIE~~~~~---------~i~~i~~~~~~~~~i~~~~~----~------~~---~-~~~~v~~~~~E~~lL~~ 57 (193)
T cd05784 1 PKLKVVSLDIETSMDG---------ELYSIGLYGEGQERVLMVGD----P------ED---D-APDNIEWFADEKSLLLA 57 (193)
T ss_pred CCccEEEEEeecCCCC---------CEEEEEeecCCCCEEEEECC----C------CC---C-CCCEEEEECCHHHHHHH
Confidence 8999999999998632 88888876544443332111 0 00 1 12357789999999999
Q ss_pred HHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCC-CcccCccc-cCCCC-----ceeeccceEechHHHHhhccCCC
Q 000161 317 WFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKM-SEELGFQC-DKNQG-----ECRAKFACHLDCFAWVKRDSYLP 389 (1988)
Q Consensus 317 F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l-~~~iG~~~-~~~~g-----~~~i~GRihiDl~~~vkrd~~L~ 389 (1988)
|+++|+++|||||+|||+++||||||.+||+.+|++. +++.+... ....| .+.+.||+++|+|.++++..+ +
T Consensus 58 f~~~i~~~dPDvi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~~~~-k 136 (193)
T cd05784 58 LIAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTATY-H 136 (193)
T ss_pred HHHHHHhhCCCEEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHHccC-C
Confidence 9999999999999999999999999999999999986 23322210 01112 467999999999999987433 4
Q ss_pred CCCCCHHHHHHHHcCCCCCCCC----hHHHHHHHhhChHHHHHHHHHhhHHHHHHHH
Q 000161 390 QGSQGLKAVTKAKLGYDPLEVN----PEDMVRFAKEKPQMMASYSVSDAVATYYLYM 442 (1988)
Q Consensus 390 ~~SysL~~Va~~~LG~~K~dvd----~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~ 442 (1988)
+.||+|++||+++||.+|.+++ +.+|.++|.++++++++||++||.++++|+.
T Consensus 137 l~sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~~~~~~~~~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 137 FESFSLENVAQELLGEGKLIHDVDDRGAEIERLFREDKLALARYNLQDCELVWRIFE 193 (193)
T ss_pred CCcCCHHHHHHHHhCCCccccCcccCHHHHHHHHhhCHHHHHHHHHHHHHHHHHHhC
Confidence 6999999999999999998765 4589999999999999999999999999973
No 38
>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=99.95 E-value=4.3e-27 Score=265.87 Aligned_cols=192 Identities=29% Similarity=0.329 Sum_probs=151.0
Q ss_pred EEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEcccccccccccccCCCCCCCCCceEEecCCCHHHHHHHHHHH
Q 000161 241 VCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRLWFAH 320 (1988)
Q Consensus 241 vLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~eLL~~F~~~ 320 (1988)
|++|||||++. .+||++..|+|++||++...+|............ .+.........|..+++|++||.+|+++
T Consensus 1 v~~~DIEt~~~-~~~p~~~~d~Ii~I~~~~~~~g~~~~~~~~~~~~------~~~~~~i~~~~v~~~~~E~~lL~~f~~~ 73 (199)
T cd05160 1 VLSFDIETTPP-VGGPEPDRDPIICITYADSFDGVKVVFLLKTSTV------GDDIEFIDGIEVEYFADEKELLKRFFDI 73 (199)
T ss_pred CccEEEeecCC-CCCcCCCCCCEEEEEEEEeeCCceeeEEEeeccc------CCcCCCCCCceEEEeCCHHHHHHHHHHH
Confidence 58999999985 4689999999999999876444422111100000 0000011245688899999999999999
Q ss_pred HHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccc---c--CCCCceeeccceEechHHHHhhccCCCCCCCCH
Q 000161 321 MQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQC---D--KNQGECRAKFACHLDCFAWVKRDSYLPQGSQGL 395 (1988)
Q Consensus 321 I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~---~--~~~g~~~i~GRihiDl~~~vkrd~~L~~~SysL 395 (1988)
++++|||+|+|||+++||||||.+||+.+|++.+...++.. + +....+.+.||+|+|+|.++++..+ ..||+|
T Consensus 74 i~~~dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~~--l~sy~L 151 (199)
T cd05160 74 IREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFK--LKSYTL 151 (199)
T ss_pred HHhcCCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhcC--cccCCH
Confidence 99999999999999999999999999999998752222220 0 0123467899999999999998765 589999
Q ss_pred HHHHHHHcCCCCCCCChHHHHH-HHhhChHHHHHHHHHhhHHHHHHH
Q 000161 396 KAVTKAKLGYDPLEVNPEDMVR-FAKEKPQMMASYSVSDAVATYYLY 441 (1988)
Q Consensus 396 ~~Va~~~LG~~K~dvd~~~i~~-~~~~~~~~La~Y~l~Da~lt~~L~ 441 (1988)
++||+++||.+|++++++.+.+ +|.+++.++++||++||.+|++|+
T Consensus 152 ~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 152 DAVAEELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred HHHHHHHhCCCCCcCCHHHHhhccCcchHHHHHHHHHHHHHHHHHhh
Confidence 9999999999999999999988 567888999999999999999986
No 39
>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=99.91 E-value=3.1e-24 Score=248.60 Aligned_cols=199 Identities=19% Similarity=0.229 Sum_probs=157.4
Q ss_pred CCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCC----ce----------EEEcccccccccccccCCCCCC-----
Q 000161 237 AEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQ----GY----------LIINRECVGEDIEDLEYTPKPE----- 297 (1988)
Q Consensus 237 p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~----g~----------li~nreivs~di~~feytp~~~----- 297 (1988)
||++++|+.|-|.-++ ....++|+|||+.+..+ +. ....|...+. .|.+.
T Consensus 1 Ppl~v~sls~~T~~n~----k~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~-------~~~~~~~~~~ 69 (234)
T cd05776 1 PPLTVMSLSIKTVLNS----KTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRS-------PPPDLFEKNA 69 (234)
T ss_pred CCeEEEEEEeEEEecC----cCCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCC-------CCCchHHHHH
Confidence 8999999999998753 23368999999876431 10 1111111100 01111
Q ss_pred CCCceEEecCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCC-------CC----
Q 000161 298 FEGYFKVTNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKN-------QG---- 366 (1988)
Q Consensus 298 ~~g~f~V~~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~-------~g---- 366 (1988)
..+...|..+++|++||.+|+++|++.|||||+|||+.+||||||.+||+.+|++.|+++|+. ++. .+
T Consensus 70 ~~~~~~v~~~~~E~~LL~~f~~~i~~~DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~-~~~~~~~~~~~~~~~~ 148 (234)
T cd05776 70 KKKKTKVRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRL-KRSVWPKKKGGGKFGE 148 (234)
T ss_pred HhcCCcEEEeCCHHHHHHHHHHHHhhcCCCEEEeeccCCCCHHHHHHHHHHhCCCcccccccc-ccccCccccccccccc
Confidence 012345888999999999999999999999999999999999999999999999999999986 221 01
Q ss_pred ceeeccceEechHHHHhhccCCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHh--hChHHHHHHHHHhhHHHHHHHHHh
Q 000161 367 ECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAK--EKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 367 ~~~i~GRihiDl~~~vkrd~~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~--~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
...+.||+++|+|..+|+... ..||+|++||+++||.+|.++++++|.++|. ++..++++||++||.++++|+.++
T Consensus 149 ~~~~~GRl~~D~~~~~k~~~~--~~sY~L~~va~~~Lg~~k~di~~~~i~~~~~~~~~l~~l~~y~~~Da~l~~~L~~kl 226 (234)
T cd05776 149 RELTAGRLLCDTYLSAKELIR--CKSYDLTELSQQVLGIERQDIDPEEILNMYNDSESLLKLLEHTEKDAYLILQLMFKL 226 (234)
T ss_pred cccccCchhhccHHHHHHHhC--CCCCChHHHHHHHhCcCcccCCHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 245889999999999988644 5999999999999999999999999999998 466799999999999999999998
Q ss_pred -ccchH
Q 000161 445 -VHPFI 449 (1988)
Q Consensus 445 -v~~~i 449 (1988)
+.|++
T Consensus 227 ~il~Lt 232 (234)
T cd05776 227 NILPLT 232 (234)
T ss_pred CCCcCC
Confidence 66654
No 40
>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=99.85 E-value=1.6e-20 Score=213.87 Aligned_cols=160 Identities=24% Similarity=0.344 Sum_probs=122.3
Q ss_pred CCCCCCCeEEEEEEEEc--CCceEEEcccccccccccccCCCCCCCCCceEEecCCCHHHHHHHHHHHHHhhCCCEEEee
Q 000161 255 FPDADYDIIMMISYMLD--GQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRLWFAHMQEVKPGIYVTY 332 (1988)
Q Consensus 255 fPdp~~D~Ii~IS~~~~--~~g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~eLL~~F~~~I~~~DPDIIvGY 332 (1988)
|+.+..++|++||++.. .++.+.+. -..+.+|++||++|+++|++++| +||||
T Consensus 45 ~l~~~~~~Iv~Is~~~~~~~~~~~~~~------------------------~~~~~~E~elL~~F~~~i~~~~p-~lv~y 99 (208)
T cd05782 45 FLPLPFHKVVSISALYRDDDGGFLKVR------------------------TLDGADEKELLEDFFQLIEKKNP-RLVSF 99 (208)
T ss_pred CCccccCceEEEEEEEEecCCCeEEEe------------------------ecCCCCHHHHHHHHHHHHHHhCC-EEEec
Confidence 55566799999998863 22221110 12457999999999999999988 89999
Q ss_pred CcccCCHHHHHHHHHHcCCCCCcccCccc-cCCCCceeeccceEechHHHHhhccCCCCCCCCHHHHHHHHcCCCCCCCC
Q 000161 333 NGDYFDWPFLETRAAHHGFKMSEELGFQC-DKNQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVN 411 (1988)
Q Consensus 333 Ngd~FDlPyL~~Ra~~lGi~l~~~iG~~~-~~~~g~~~i~GRihiDl~~~vkrd~~L~~~SysL~~Va~~~LG~~K~dvd 411 (1988)
||++||||||..||..||++....++... ..+++ ....|+ |+|++.+++...+ ..+++|++||+.+...+|.+++
T Consensus 100 Ng~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~-~r~~~~-h~DL~~~~~~~~~--~~~~~L~~va~~lG~~~K~d~~ 175 (208)
T cd05782 100 NGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYR-NRYSER-HLDLMDLLAFYGA--RARASLDLLAKLLGIPGKMDVD 175 (208)
T ss_pred CCCcCCHHHHHHHHHHhCCCCccccCcccchhhcc-CcCCCC-cccHHHHHhccCc--cCCCCHHHHHHHhCCCCCcCCC
Confidence 99999999999999999997643332210 11111 124577 9999999987433 4799999999864446899999
Q ss_pred hHHHHHHHh-hChHHHHHHHHHhhHHHHHHHHH
Q 000161 412 PEDMVRFAK-EKPQMMASYSVSDAVATYYLYMT 443 (1988)
Q Consensus 412 ~~~i~~~~~-~~~~~La~Y~l~Da~lt~~L~~K 443 (1988)
++++.++|. ++++++++||++||.+|+.||.+
T Consensus 176 G~~v~~~y~~g~~~~I~~Yc~~Dv~~t~~l~lr 208 (208)
T cd05782 176 GSQVWELYAEGKLDEIAEYCETDVLNTYLLYLR 208 (208)
T ss_pred HHHHHHHHHcCChHHHHHHHHHHHHHHHHHHhC
Confidence 999999887 46799999999999999999864
No 41
>PHA02563 DNA polymerase; Provisional
Probab=99.72 E-value=7.6e-16 Score=196.73 Aligned_cols=64 Identities=20% Similarity=0.163 Sum_probs=53.1
Q ss_pred HHHHHHHhhhccccccccCC---CCCC---------------------HHHHHHHHHHHHHHHHHHHHHHHHcCCeEEEc
Q 000161 775 QLAHKCILNSFYGYVMRKGA---RWYS---------------------MEMAGVVTYTGAKIIQNARLLIEKIGKPLELD 830 (1988)
Q Consensus 775 QlA~K~ilNS~YGy~g~~~s---R~ys---------------------~e~A~~VT~~Gr~iI~~a~~lve~~G~~vygD 830 (1988)
++..|++|||.||-+|-+-. +.+. ..+|++||+.||.+|..+...+++. .+|||
T Consensus 403 ~~i~KLlLNSLYGKfg~~p~~~~~~~~l~~~~~l~~~~~~~~~~~~~yv~iAa~ITa~aR~~m~~~~~~~~~~--v~Y~D 480 (630)
T PHA02563 403 NMLAKLMLNSLYGKFALNPDNTGKVPYLDDNGRLDLISNGEENKEPNYIPIAAFITARARSNLLSALQYLYEK--FIYCD 480 (630)
T ss_pred HHHHHHHHhcccchhhcCccccCceeeecccceeeeecCCccccccccchHHHHHHHHHHHHHHHHHHHhhcc--EEEEC
Confidence 46899999999999987632 2321 4699999999999999999988765 67999
Q ss_pred cceeeEEcCC
Q 000161 831 TDGIWCVLPG 840 (1988)
Q Consensus 831 TDSI~~~lp~ 840 (1988)
|||||+..+.
T Consensus 481 TDSi~v~~~~ 490 (630)
T PHA02563 481 TDSIHLEGAE 490 (630)
T ss_pred CceEEEecCc
Confidence 9999997654
No 42
>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=99.57 E-value=5.6e-14 Score=158.24 Aligned_cols=162 Identities=24% Similarity=0.394 Sum_probs=119.6
Q ss_pred CCCCCCCeEEEEEEE-EcCCceEEEcccccccccccccCCCCCCCCCceEEecCCCHHHHHHHHHHHHHhhCCCEEEeeC
Q 000161 255 FPDADYDIIMMISYM-LDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRLWFAHMQEVKPGIYVTYN 333 (1988)
Q Consensus 255 fPdp~~D~Ii~IS~~-~~~~g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~eLL~~F~~~I~~~DPDIIvGYN 333 (1988)
|+-..-..|++||+. .++++.+.+ . .| .....+|++||..|++.+.++.| .+||||
T Consensus 3 Fl~~~f~kIV~Is~~~~~~~~~~~v-~--------s~-------------~~~~~~E~~lL~~F~~~~~~~~p-~LVs~N 59 (209)
T PF10108_consen 3 FLPLPFHKIVCISVVYADDDGQFKV-K--------SL-------------GGPDDDEKELLQDFFDLVEKYNP-QLVSFN 59 (209)
T ss_pred CCcccCCCeEEEEEEEEecCCcEEE-E--------ec-------------cCCCCCHHHHHHHHHHHHHhCCC-eEEecC
Confidence 544556899999988 343333311 1 11 01235799999999999999988 579999
Q ss_pred cccCCHHHHHHHHHHcCCCCCcccCccccCCCCceee--ccceEechHHHHhhccCCCCCCCCHHHHHHHHcCC-CCCCC
Q 000161 334 GDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRA--KFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKLGY-DPLEV 410 (1988)
Q Consensus 334 gd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i--~GRihiDl~~~vkrd~~L~~~SysL~~Va~~~LG~-~K~dv 410 (1988)
|.+||+|||..||..||++....+... ......|.. .-+ |+|++..+...- ...+.+|+.+|. .||. +|.++
T Consensus 60 G~~FDlP~L~~Ral~~gi~~p~~~~~~-~k~WenY~~Ry~~~-H~DLmd~l~~~g--~~~~~sLd~la~-~lgiPgK~~i 134 (209)
T PF10108_consen 60 GRGFDLPVLCRRALIHGISAPRYLDIG-NKPWENYRNRYSER-HLDLMDLLSFYG--AKARTSLDELAA-LLGIPGKDDI 134 (209)
T ss_pred CccCCHHHHHHHHHHhCCCCchhhhcC-CCCccccccccCcc-cccHHHHHhccC--ccccCCHHHHHH-HcCCCCCCCC
Confidence 999999999999999999975322211 011122221 123 999999876521 224678999999 5886 59999
Q ss_pred ChHHHHHHHh-hChHHHHHHHHHhhHHHHHHHHHh
Q 000161 411 NPEDMVRFAK-EKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 411 d~~~i~~~~~-~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
+++++.++|. ++.++++.||.+|+..|+.||.++
T Consensus 135 dGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~ 169 (209)
T PF10108_consen 135 DGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRF 169 (209)
T ss_pred CHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999776 678999999999999999999986
No 43
>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=99.25 E-value=1.6e-11 Score=134.84 Aligned_cols=152 Identities=32% Similarity=0.429 Sum_probs=92.4
Q ss_pred EEEEEEEccCCCCCCCCCCCeEEEEEEEE-cCCceEEEcccccccccccccCCCCCCCCCceEEecCCCHHHHHHHHHHH
Q 000161 242 CAFDIETTKLPLKFPDADYDIIMMISYML-DGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRLWFAH 320 (1988)
Q Consensus 242 LsfDIEt~s~~~~fPdp~~D~Ii~IS~~~-~~~g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~eLL~~F~~~ 320 (1988)
+.|||||++. +|..+.|++|++.. +++..... .. + ....++|.+.+.++++.
T Consensus 1 l~~DIET~Gl-----~~~~~~i~liG~~~~~~~~~~~~-~~--------------------~-~~~~~~ee~~~~~~~~~ 53 (164)
T PF13482_consen 1 LFFDIETTGL-----SPDNDTIYLIGVADFDDDEIITF-IQ--------------------W-FAEDPDEEEIILEFFEL 53 (164)
T ss_dssp --EEEEESS------GG-G---EEEEEEE-ETTTTE-E-EE--------------------E--GGGHHHHHHHHH--HH
T ss_pred CcEEecCCCC-----CCCCCCEEEEEEEEeCCCceEEe-eH--------------------h-hccCcHHHHHHHHHHHH
Confidence 4699999964 34557799999875 32221100 00 0 11123566666666677
Q ss_pred HHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCCCCHHHHHH
Q 000161 321 MQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTK 400 (1988)
Q Consensus 321 I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~SysL~~Va~ 400 (1988)
+.+. +.++||||..||+|+|.+|+..++++. ..-|+|++..+++... .||+|++|++
T Consensus 54 l~~~--~~iv~yng~~FD~p~L~~~~~~~~~~~------------------~~~~iDl~~~~~~~~~---~~~~Lk~ve~ 110 (164)
T PF13482_consen 54 LDEA--DNIVTYNGKNFDIPFLKRRAKRYGLPP------------------PFNHIDLLKIIKKHFL---ESYSLKNVEK 110 (164)
T ss_dssp HHTT----EEESSTTTTHHHHHHHHH-HHHH--------------------GGGEEEHHHHHT-TTS---CCTT--SHHH
T ss_pred HhcC--CeEEEEeCcccCHHHHHHHHHHcCCCc------------------ccchhhHHHHHHhccC---CCCCHHHHhh
Confidence 7776 789999999999999999998887752 2368999999987433 8999999999
Q ss_pred HHcCCCCC--CCChHHHHHHHhh--------ChHHHHHHHHHhhHHHHHHHHHh
Q 000161 401 AKLGYDPL--EVNPEDMVRFAKE--------KPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 401 ~~LG~~K~--dvd~~~i~~~~~~--------~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
. ||..+. ++++.++..+|.. ..+.|+.||..|+..|..|+.++
T Consensus 111 ~-lg~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~i~~yN~~Dv~~~~~L~~~l 163 (164)
T PF13482_consen 111 F-LGIERRDDDISGSESVKLYKEYLETGDPEALEEILEYNEDDVRATRRLYEWL 163 (164)
T ss_dssp ------------HHHHHHHHHH---TTGGTS--HHHHHHHHHHHHHHHHHHHHH
T ss_pred h-cccccccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 7 776554 6788888776652 34799999999999999999875
No 44
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=99.11 E-value=8.3e-10 Score=124.14 Aligned_cols=157 Identities=22% Similarity=0.299 Sum_probs=114.1
Q ss_pred eEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEcccccccccccccCCCCCCCCCceEEecCCCHHHHHHHHHH
Q 000161 240 HVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRLWFA 319 (1988)
Q Consensus 240 rvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~eLL~~F~~ 319 (1988)
.++.|||||++.+ +..+.|++.++.-..++...+... +.|.| ..|.++|+.|..
T Consensus 99 ~~~FFDiETTGL~-----~ag~~I~~~g~a~~~~~~~~Vrq~----------~lp~p-----------~~E~avle~fl~ 152 (278)
T COG3359 99 DVAFFDIETTGLD-----RAGNTITLVGGARGVDDTMHVRQH----------FLPAP-----------EEEVAVLENFLH 152 (278)
T ss_pred ceEEEeeeccccC-----CCCCeEEEEEEEEccCceEEEEee----------cCCCc-----------chhhHHHHHHhc
Confidence 4888999999863 467899998877544444322111 12322 579999999987
Q ss_pred HHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCCCCHHHHH
Q 000161 320 HMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVT 399 (1988)
Q Consensus 320 ~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~SysL~~Va 399 (1988)
.+ |..++|+|||..||||||. |+....+++. .-+.|+|+|.-.||-.+-...+.+|++|-
T Consensus 153 ~~---~~~~lvsfNGkaFD~Pfik-R~v~~~~el~----------------l~~~H~DL~h~~RRlwk~~l~~c~Lk~VE 212 (278)
T COG3359 153 DP---DFNMLVSFNGKAFDIPFIK-RMVRDRLELS----------------LEFGHFDLYHPSRRLWKHLLPRCGLKTVE 212 (278)
T ss_pred CC---CcceEEEecCcccCcHHHH-HHHhcccccC----------------ccccchhhhhhhhhhhhccCCCCChhhHH
Confidence 66 5579999999999999999 8777766542 12479999999998554345789999999
Q ss_pred HHHcCCCCCC-CChHHHHHH---Hh--hCh---HHHHHHHHHhhHHHHHHHHH
Q 000161 400 KAKLGYDPLE-VNPEDMVRF---AK--EKP---QMMASYSVSDAVATYYLYMT 443 (1988)
Q Consensus 400 ~~~LG~~K~d-vd~~~i~~~---~~--~~~---~~La~Y~l~Da~lt~~L~~K 443 (1988)
+ .||..+.+ +++..-.++ |. ++| ..++.||..|+.....|+..
T Consensus 213 r-~LGi~R~edtdG~~~p~lyr~~~~~~dp~ll~~l~~hN~eDvlnL~~i~~h 264 (278)
T COG3359 213 R-ILGIRREEDTDGYDGPELYRLYRRYGDPGLLDGLVLHNREDVLNLPTIIKH 264 (278)
T ss_pred H-HhCccccccCCCcchHHHHHHHHHcCCHHHHHHHHHccHHHHHhHHHHHHH
Confidence 9 89998876 555433332 22 344 47899999999888777664
No 45
>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=98.21 E-value=7.2e-06 Score=104.90 Aligned_cols=162 Identities=22% Similarity=0.280 Sum_probs=113.5
Q ss_pred CceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEcccccccccccccCCCCCCCCCceEEecCCCHHHHHHHH
Q 000161 238 EVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRLW 317 (1988)
Q Consensus 238 ~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~eLL~~F 317 (1988)
....+.|||||+ | ...-.+++|+.....|.. .+ .|.| |-.....+|++.+.+|
T Consensus 283 ~~~~~ffDiEt~------P--~~~~~yL~G~~~~~~~~~----------~~--~~~~-------fla~~~~~E~~~~~~f 335 (457)
T TIGR03491 283 APGELIFDIESD------P--DENLDYLHGFLVVDKGQE----------NE--KYRP-------FLAEDPNTEELAWQQF 335 (457)
T ss_pred CCccEEEEecCC------C--CCCCceEEEEEEecCCCC----------Cc--ceee-------eecCCchHHHHHHHHH
Confidence 356778999998 2 335677888764322210 00 0111 2223446899999999
Q ss_pred HHHHHhhCCC-EEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCCCCHH
Q 000161 318 FAHMQEVKPG-IYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQGLK 396 (1988)
Q Consensus 318 ~~~I~~~DPD-IIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~SysL~ 396 (1988)
+++++.+ |+ -|+.||+ |-.++|.+.|..+|.... .+-.. + +..+|+|.++++..++|.+||||+
T Consensus 336 ~~~l~~~-~~~~i~hY~~--~e~~~l~rla~~~~~~~~-~~~~l---------~--~~~vDL~~~vr~~~~~p~~sysLK 400 (457)
T TIGR03491 336 LQLLQSY-PDAPIYHYGE--TEKDSLRRLAKRYGTPEA-EIEEL---------L--KRFVDIHTIVRRSWILPIESYSLK 400 (457)
T ss_pred HHHHHHC-CCCeEEeeCH--HHHHHHHHHHHHcCCCHH-HHHHH---------H--HHheehHHHHHhhEECCCCCCCHH
Confidence 9999887 77 6899995 669999999999988621 11100 1 157899999999888999999999
Q ss_pred HHHHHHcCCCCC--CCChHHHHHHHh-----hC---hHHHHHHHHHhhHHHHHHHH
Q 000161 397 AVTKAKLGYDPL--EVNPEDMVRFAK-----EK---PQMMASYSVSDAVATYYLYM 442 (1988)
Q Consensus 397 ~Va~~~LG~~K~--dvd~~~i~~~~~-----~~---~~~La~Y~l~Da~lt~~L~~ 442 (1988)
+|+.. ||.... ..++.....+|. ++ .+.|..||..|+.+|..|-.
T Consensus 401 ~v~~~-lg~~~~~~~~~G~~ai~~y~~~~~~~~~~~l~~l~~YN~dD~~At~~l~~ 455 (457)
T TIGR03491 401 SIARW-LGFEWRQKEASGAKSLLWYRQWKKTGDRRLLERILRYNEDDCRATWIVAD 455 (457)
T ss_pred HHHHH-hCcccCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHhHHHHHHHHHHHH
Confidence 99995 787543 366655444332 23 36899999999999998865
No 46
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=98.08 E-value=3.5e-05 Score=90.23 Aligned_cols=154 Identities=20% Similarity=0.327 Sum_probs=101.9
Q ss_pred ceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCC-ceE---EEcccccccccccccCCCCC-CCCC--ceEEecCCCHH
Q 000161 239 VHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQ-GYL---IINRECVGEDIEDLEYTPKP-EFEG--YFKVTNVNNEI 311 (1988)
Q Consensus 239 lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~-g~l---i~nreivs~di~~feytp~~-~~~g--~f~V~~~~dE~ 311 (1988)
++++.||+||++. ++..|+|+.||++ ++. +.. .++.. ..| .|.. ...| +-.|...+...
T Consensus 2 ~~~vv~D~ETTGl-----~~~~d~IIeig~v-~~~~~~~f~~lv~P~---~~I-----~~~a~~IhGIt~e~v~~~p~f~ 67 (232)
T PRK06309 2 PALIFYDTETTGT-----QIDKDRIIEIAAY-NGVTSESFQTLVNPE---IPI-----PAEASKIHGITTDEVADAPKFP 67 (232)
T ss_pred CcEEEEEeeCCCC-----CCCCCEEEEEEEE-cCccccEEEEEeCCC---CCC-----ChhHHhhcCCCHHHHhCCCCHH
Confidence 5688999999985 4677999999985 321 111 11111 000 0000 0111 11244567888
Q ss_pred HHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCC
Q 000161 312 ELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQG 391 (1988)
Q Consensus 312 eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~ 391 (1988)
+.+.+|.+++.. .++++|||+..||+++|.+-++.+|++.. ....+|++.+.++. +-..+
T Consensus 68 ev~~~~~~fi~~--~~~lVaHN~~~FD~~~L~~e~~r~g~~~~-----------------~~~~iDt~~l~~~~-~~~~~ 127 (232)
T PRK06309 68 EAYQKFIEFCGT--DNILVAHNNDAFDFPLLRKECRRHGLEPP-----------------TLRTIDSLKWAQKY-RPDLP 127 (232)
T ss_pred HHHHHHHHHHcC--CCEEEEeCCHHHHHHHHHHHHHHcCCCCC-----------------CCcEEeHHHHHHHH-cCCCC
Confidence 999999999853 36999999989999999998888888642 02357898888763 22246
Q ss_pred CCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 392 SQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 392 SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
+++|+++++. +|..... ++-.+.||.+|+.|+.++
T Consensus 128 ~~~L~~l~~~-~~~~~~~-----------------aH~Al~Da~~t~~vl~~l 162 (232)
T PRK06309 128 KHNLQYLRQV-YGFEENQ-----------------AHRALDDVITLHRVFSAL 162 (232)
T ss_pred CCCHHHHHHH-cCCCCCC-----------------CCCcHHHHHHHHHHHHHH
Confidence 7999999986 5643211 233567999999999886
No 47
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=97.95 E-value=0.00022 Score=83.58 Aligned_cols=177 Identities=21% Similarity=0.249 Sum_probs=107.0
Q ss_pred CCCceEEEEEEEEccCCCCCCCCCCCeEEEEEEE-EcCCceEEEcccccccccccccCCCCCCC-------CCce--EEe
Q 000161 236 RAEVHVCAFDIETTKLPLKFPDADYDIIMMISYM-LDGQGYLIINRECVGEDIEDLEYTPKPEF-------EGYF--KVT 305 (1988)
Q Consensus 236 ~p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~-~~~~g~li~nreivs~di~~feytp~~~~-------~g~f--~V~ 305 (1988)
+.+.++++||+||++. +|..|+|+.|+++ ++.+|..+...+ .-..|..+. .|-. .+.
T Consensus 3 ~~~~~~vv~D~ETTGl-----~p~~d~Iieig~v~v~~~g~~~~~~~--------~lv~P~~~i~~~a~~IhGIt~e~l~ 69 (232)
T PRK07942 3 WHPGPLAAFDLETTGV-----DPETARIVTAALVVVDADGEVVESRE--------WLADPGVEIPEEASAVHGITTEYAR 69 (232)
T ss_pred cccCcEEEEEeccCCC-----CCCCCeeEEEEEEEEeCCCccccceE--------EEECCCCCCCHHHHHHhCCCHHHHH
Confidence 4567889999999985 4678999999976 343343210000 000111111 1200 011
Q ss_pred c-CCCHHHHHHHHHHHHHhh--CCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHH
Q 000161 306 N-VNNEIELLRLWFAHMQEV--KPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWV 382 (1988)
Q Consensus 306 ~-~~dE~eLL~~F~~~I~~~--DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~v 382 (1988)
. ...+.+.+..|...|.+. +..++||||. .||+.||..=++.+|+... .....+|.+.+.
T Consensus 70 ~~g~~~~~vl~e~~~~l~~~~~~~~~lVahNa-~FD~~fL~~~~~r~~~~~~----------------~~~~~iDt~~l~ 132 (232)
T PRK07942 70 AHGRPAAEVLAEIADALREAWARGVPVVVFNA-PYDLTVLDRELRRHGLPSL----------------VPGPVIDPYVID 132 (232)
T ss_pred hhCCCHHHHHHHHHHHHHHHhhcCCEEEEeCc-HhhHHHHHHHHHHcCCCCc----------------cCCcEeeHHHHH
Confidence 1 234567899999998763 4578999999 6999999888888876431 012346777665
Q ss_pred hhccCCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHhccchHhhhhhhcCCChHH
Q 000161 383 KRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDE 462 (1988)
Q Consensus 383 krd~~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Klv~~~i~~La~i~~l~~~~ 462 (1988)
+.-.....++++|++++++ +|..... ++-.+.||.+|..|+.+++. ....+-.+++++
T Consensus 133 ~~~~~~~~~~~~L~~l~~~-~gi~~~~-----------------aH~Al~Da~ata~l~~~l~~----~~~~l~~~~~~~ 190 (232)
T PRK07942 133 KAVDRYRKGKRTLTALCEH-YGVRLDN-----------------AHEATADALAAARVAWALAR----RFPELAALSPAE 190 (232)
T ss_pred hhhhcccCCCCCHHHHHHH-cCCCCCC-----------------CCChHHHHHHHHHHHHHHHH----HHHHhhcCCHHH
Confidence 5421112368999999996 7753321 12356899999999988621 122344555555
Q ss_pred Hh
Q 000161 463 VL 464 (1988)
Q Consensus 463 vl 464 (1988)
+.
T Consensus 191 l~ 192 (232)
T PRK07942 191 LH 192 (232)
T ss_pred HH
Confidence 44
No 48
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=97.89 E-value=0.00013 Score=88.95 Aligned_cols=157 Identities=15% Similarity=0.132 Sum_probs=101.9
Q ss_pred CceEEEEEEEEccCCCCCCCCCCCeEEEEEEEE-cCCceEE-EcccccccccccccCCCCC-CCCC--ceEEecCCCHHH
Q 000161 238 EVHVCAFDIETTKLPLKFPDADYDIIMMISYML-DGQGYLI-INRECVGEDIEDLEYTPKP-EFEG--YFKVTNVNNEIE 312 (1988)
Q Consensus 238 ~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~-~~~g~li-~nreivs~di~~feytp~~-~~~g--~f~V~~~~dE~e 312 (1988)
+...++||+||++. +|..|+|+.|+.+. +.+|.+. .-..++..+. .|.+ ...| +-.+...+.-.+
T Consensus 14 ~~~fvvlD~ETTGl-----~p~~d~IIeIgav~v~~~g~i~~~~~~lv~P~~-----~~~~~~IhGIt~e~l~~ap~f~e 83 (313)
T PRK06063 14 PRGWAVVDVETSGF-----RPGQARIISLAVLGLDADGNVEQSVVTLLNPGV-----DPGPTHVHGLTAEMLEGQPQFAD 83 (313)
T ss_pred CCCEEEEEEECCCC-----CCCCCEEEEEEEEEEECCceeeeEEEEEECcCC-----CCCCeecCCCCHHHHhCCCCHHH
Confidence 45788999999984 36679999999874 4445321 0001111110 0111 1112 011334456778
Q ss_pred HHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCC
Q 000161 313 LLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGS 392 (1988)
Q Consensus 313 LL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~S 392 (1988)
++..|.+++.. +++||||. .||+.||..-+..+|+... ....+|++.+.++- +.+..+
T Consensus 84 v~~~l~~~l~~---~~lVaHNa-~FD~~fL~~~~~r~g~~~~-----------------~~~~ldTl~lar~~-~~~~~~ 141 (313)
T PRK06063 84 IAGEVAELLRG---RTLVAHNV-AFDYSFLAAEAERAGAELP-----------------VDQVMCTVELARRL-GLGLPN 141 (313)
T ss_pred HHHHHHHHcCC---CEEEEeCH-HHHHHHHHHHHHHcCCCCC-----------------CCCEEehHHHHHHh-ccCCCC
Confidence 99999998854 79999998 7999999988888876531 01246888887763 334589
Q ss_pred CCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 393 QGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 393 ysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
|+|++++++ +|.....- +-.+.||.+|..|+.++
T Consensus 142 ~kL~~l~~~-~gi~~~~~-----------------H~Al~DA~ata~l~~~l 175 (313)
T PRK06063 142 LRLETLAAH-WGVPQQRP-----------------HDALDDARVLAGILRPS 175 (313)
T ss_pred CCHHHHHHH-cCCCCCCC-----------------CCcHHHHHHHHHHHHHH
Confidence 999999996 77643211 23467999999998765
No 49
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=97.88 E-value=0.00016 Score=86.00 Aligned_cols=159 Identities=21% Similarity=0.286 Sum_probs=102.5
Q ss_pred CCCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEE-Ecccccc-cccccccCCCCCCCCC--ceEEecCCCHH
Q 000161 236 RAEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLI-INRECVG-EDIEDLEYTPKPEFEG--YFKVTNVNNEI 311 (1988)
Q Consensus 236 ~p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li-~nreivs-~di~~feytp~~~~~g--~f~V~~~~dE~ 311 (1988)
.-+.+.++|||||++. +|..|+|+.|+.+.-..|..+ .-...+. ..+..+ . ....| .-.+...+...
T Consensus 65 ~~~~~~vv~DiETTG~-----~~~~~~IIEIGAv~v~~g~i~~~f~~~v~p~~ip~~--~--~~itGIt~e~l~~ap~~~ 135 (257)
T PRK08517 65 IKDQVFCFVDIETNGS-----KPKKHQIIEIGAVKVKNGEIIDRFESFVKAKEVPEY--I--TELTGITYEDLENAPSLK 135 (257)
T ss_pred CCCCCEEEEEEeCCCC-----CCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCChh--h--hhhcCcCHHHHcCCCCHH
Confidence 4567889999999983 456789999997642233221 0000110 000000 0 01112 11234567899
Q ss_pred HHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCC
Q 000161 312 ELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQG 391 (1988)
Q Consensus 312 eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~ 391 (1988)
+.+.+|.+++.. +++||||. .||+.||.+-+.++|+... . ...+|++++.++. ++..
T Consensus 136 evl~~f~~fl~~---~v~VaHNa-~FD~~fL~~~l~r~g~~~~-----~------------~~~ldtl~la~~~--~~~~ 192 (257)
T PRK08517 136 EVLEEFRLFLGD---SVFVAHNV-NFDYNFISRSLEEIGLGPL-----L------------NRKLCTIDLAKRT--IESP 192 (257)
T ss_pred HHHHHHHHHHCC---CeEEEECH-HHHHHHHHHHHHHcCCCCC-----C------------CCcEehHHHHHHH--ccCC
Confidence 999999999865 68999999 8999999988888877532 0 1135667776653 3457
Q ss_pred CCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 392 SQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 392 SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
+|+|+++++ ++|..... ++-.+.||.+|.+|+.++
T Consensus 193 ~~~L~~L~~-~lgi~~~~-----------------~HrAl~DA~ata~ll~~l 227 (257)
T PRK08517 193 RYGLSFLKE-LLGIEIEV-----------------HHRAYADALAAYEIFKIC 227 (257)
T ss_pred CCCHHHHHH-HcCcCCCC-----------------CCChHHHHHHHHHHHHHH
Confidence 899999998 47864321 133568999999998876
No 50
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=97.84 E-value=0.00021 Score=84.75 Aligned_cols=160 Identities=14% Similarity=0.088 Sum_probs=101.7
Q ss_pred CceEEEEEEEEccCCCCCCCCCCCeEEEEEEEE-cCCceEEEccccccc--ccccccCCCCCCCCC--ceEEecCCCHHH
Q 000161 238 EVHVCAFDIETTKLPLKFPDADYDIIMMISYML-DGQGYLIINRECVGE--DIEDLEYTPKPEFEG--YFKVTNVNNEIE 312 (1988)
Q Consensus 238 ~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~-~~~g~li~nreivs~--di~~feytp~~~~~g--~f~V~~~~dE~e 312 (1988)
+.++++||+||++. +|..|+|+.|+++. ++++..-.-...+.. .|.... -...| +-.|...+...+
T Consensus 6 ~~~~v~~D~ETTGl-----~~~~d~IIEIa~v~v~~~~~~~~~~~li~P~~~I~~~a----~~ihgIt~e~v~~~p~~~e 76 (250)
T PRK06310 6 DTEFVCLDCETTGL-----DVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAES----QRIHHISDAMLRDKPKIAE 76 (250)
T ss_pred CCcEEEEEEeCCCC-----CCCCCeEEEEEEEEEECCeEEEEEEEEECcCCCCCHhh----hhccCcCHHHHhCCCCHHH
Confidence 46789999999985 46779999998763 332211000000100 000000 00111 012345577888
Q ss_pred HHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCC
Q 000161 313 LLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGS 392 (1988)
Q Consensus 313 LL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~S 392 (1988)
++.+|.+++.. .++++|||. .||+++|..-+..+|++... .....+|++.+.+. +-+..+
T Consensus 77 v~~~~~~fl~~--~~~lvghn~-~FD~~~L~~~~~r~g~~~~~---------------~~~~~iDtl~lar~--~~~~~~ 136 (250)
T PRK06310 77 VFPQIKGFFKE--GDYIVGHSV-GFDLQVLSQESERIGETFLS---------------KHYYIIDTLRLAKE--YGDSPN 136 (250)
T ss_pred HHHHHHHHhCC--CCEEEEECH-HHHHHHHHHHHHHcCCCccc---------------cCCcEEehHHHHHh--cccCCC
Confidence 99999998854 379999997 59999999999888876320 01246888888775 223368
Q ss_pred CCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 393 QGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 393 ysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
++|+++++. +|..... ++=.+.||.+|..|+..+
T Consensus 137 ~~L~~l~~~-~g~~~~~-----------------aH~Al~Da~at~~vl~~l 170 (250)
T PRK06310 137 NSLEALAVH-FNVPYDG-----------------NHRAMKDVEINIKVFKHL 170 (250)
T ss_pred CCHHHHHHH-CCCCCCC-----------------CcChHHHHHHHHHHHHHH
Confidence 999999986 5653221 234578999999998875
No 51
>PHA02735 putative DNA polymerase type B; Provisional
Probab=97.80 E-value=0.00024 Score=85.14 Aligned_cols=112 Identities=20% Similarity=0.231 Sum_probs=66.0
Q ss_pred CHHHHHHHHcCCCCC--CCChH--HHHHHHhhChHHHHHHHHHhhHHHHHHHHHhccchHhhhhhhcCCChHHHhhhhhH
Q 000161 394 GLKAVTKAKLGYDPL--EVNPE--DMVRFAKEKPQMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDEVLRKGSG 469 (1988)
Q Consensus 394 sL~~Va~~~LG~~K~--dvd~~--~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Klv~~~i~~La~i~~l~~~~vlr~Gsg 469 (1988)
+|++.+.+.||+.|. -++.. +-..|..++...++.|.-.||.+|..|....+. .+.-..+|..+- -++|
T Consensus 170 sldna~~ewlge~ka~dgid~~~f~~k~yi~~n~~dilkyak~da~l~~dl~~e~~n-----~~e~ldipmgrp--~stg 242 (716)
T PHA02735 170 SLDNAAEEWLGENKAKDGIDAGKFDAKEYIKDNFDDILKYAKIDAELTQDLAIEATN-----EAEELDIPMGRP--FSTG 242 (716)
T ss_pred HHHhHHHHHhccccccccccccccchHHHHhhhHHHHHHHHhhhHHHHHHHHHHHhh-----hHhhcCCccCCC--cccc
Confidence 599999999999873 23332 223466677789999999999999999876521 122222222221 1367
Q ss_pred HHHHHHHHHHHHHCCeeccCCCCCCchhhhcccccCCCCCCcceeeeccCccc
Q 000161 470 TLCEMLLMVQAYKANVICPNKHQSDPEKFYRNHLLESETYIGGHVECLESGVF 522 (1988)
Q Consensus 470 ~~~E~LLm~~a~~~n~i~Pnk~~~~~~~~~~g~l~~setY~GG~V~~p~~GvY 522 (1988)
.+.+..|-..... -|.-...+..++ --+.|-||+++-.++|-+
T Consensus 243 yla~~yl~~~~~e----kp~lg~~~ma~~------~wEsYyGGrfeV~Krgnv 285 (716)
T PHA02735 243 YLAAEYLDANLEE----KPGLGNEAMAKL------AWESYAGGRFEVFKRGNV 285 (716)
T ss_pred hhhHHHHhccccc----CCCCChHHHHHH------HHHhhcCCceEEeccCcc
Confidence 7766655222111 022111111111 236799999999999843
No 52
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=97.78 E-value=0.00034 Score=85.62 Aligned_cols=189 Identities=14% Similarity=0.163 Sum_probs=109.8
Q ss_pred CCCCceEEEEEEEEccCCCCCCCCCCCeEEEEEEE-EcCCceEE-EcccccccccccccCCCCCCCCC--ceEEecCCCH
Q 000161 235 QRAEVHVCAFDIETTKLPLKFPDADYDIIMMISYM-LDGQGYLI-INRECVGEDIEDLEYTPKPEFEG--YFKVTNVNNE 310 (1988)
Q Consensus 235 ~~p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~-~~~~g~li-~nreivs~di~~feytp~~~~~g--~f~V~~~~dE 310 (1988)
...+..+++|||||++. +|..|+||.|+.+ +..+|.+. ....++..+. +. .| ....| +-.+...++-
T Consensus 42 ~~~~~~fVvlDiETTGL-----dp~~drIIeIgAV~i~~~g~ive~f~tLVnP~~-~~--~p-~~LHGIT~e~La~AP~f 112 (377)
T PRK05601 42 AIEAAPFVAVSIQTSGI-----HPSTSRLITIDAVTLTADGEEVEHFHAVLNPGE-DP--GP-FHLHGLSAEEFAQGKRF 112 (377)
T ss_pred CCCCCCEEEEEEECCCC-----CCCCCeEEEEEEEEEEcCCEEEEEEEEEECcCC-CC--CC-ccccCCCHHHHhcCCCH
Confidence 45667899999999985 5778999999876 44444321 0001111100 00 00 01112 0123445678
Q ss_pred HHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCC----------cccCccc-cCCCCceeeccceEechH
Q 000161 311 IELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMS----------EELGFQC-DKNQGECRAKFACHLDCF 379 (1988)
Q Consensus 311 ~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~----------~~iG~~~-~~~~g~~~i~GRihiDl~ 379 (1988)
.+++..|.++|... ++|+||.. |||.||..-++..+.... ++-|+.. +...|.... .-..+|++
T Consensus 113 ~eVl~el~~fL~g~---vLVaHNA~-FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~-p~~~iDTL 187 (377)
T PRK05601 113 SQILKPLDRLIDGR---TLILHNAP-RTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPK-PVVIVDTL 187 (377)
T ss_pred HHHHHHHHHHhCCC---EEEEECcH-HHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCC-CCCEEEhH
Confidence 89999999999864 89999985 999999887766543211 0111110 111122222 23679999
Q ss_pred HHHhhccCCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 380 AWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 380 ~~vkrd~~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
.+.++.. ....+|+|++||++ ||....+ ..-..-....|. .+.+..|+.++..||.+.
T Consensus 188 ~LARrl~-p~l~~~rL~~La~~-lGi~~p~---~~A~~~Ra~~p~--~~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 188 ATARRQG-VALDDIRIRGVAHT-LGLDAPA---AEASVERAQVPH--RQLCREETLLVARLYFAL 245 (377)
T ss_pred HHHHHHc-CCCCCCCHHHHHHH-hCCCCCc---hhhhhhhhcCCh--hhhhhHHHHHHHHHHHHh
Confidence 9999853 34589999999996 7865432 100000001111 133557999999998874
No 53
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=97.76 E-value=0.00023 Score=83.73 Aligned_cols=161 Identities=20% Similarity=0.184 Sum_probs=100.8
Q ss_pred CCceEEEEEEEEccCCCCCCCCC-CCeEEEEEEEEcCCceEEEcccccccccccccCCCCCC-------CCCc--eEEec
Q 000161 237 AEVHVCAFDIETTKLPLKFPDAD-YDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPE-------FEGY--FKVTN 306 (1988)
Q Consensus 237 p~lrvLsfDIEt~s~~~~fPdp~-~D~Ii~IS~~~~~~g~li~nreivs~di~~feytp~~~-------~~g~--f~V~~ 306 (1988)
++++.++||+||++. +|. .|+||.|+++.-.++.+. .+.. ..-..|..+ ..|- -.+..
T Consensus 2 ~~~r~vvlDtETTGl-----dp~~~drIIEIGaV~v~~~~~~-~~~f------~~~i~P~~~i~~~a~~VHGIT~e~l~~ 69 (240)
T PRK05711 2 AIMRQIVLDTETTGL-----NQREGHRIIEIGAVELINRRLT-GRNF------HVYIKPDRLVDPEALAVHGITDEFLAD 69 (240)
T ss_pred CCCeEEEEEeeCCCc-----CCCCCCeEEEEEEEEEECCEEe-ccEE------EEEECcCCcCCHHHhhhcCCCHHHHcC
Confidence 567899999999984 344 799999998632111111 0000 000011100 1110 01334
Q ss_pred CCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhcc
Q 000161 307 VNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDS 386 (1988)
Q Consensus 307 ~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~ 386 (1988)
.+...+++..|.+++.. ..+|+||. .||++||..-+..+|.... .+. .....+|++.+.++..
T Consensus 70 ~p~f~ev~~~f~~fi~~---~~lVaHNa-~FD~~fL~~el~r~g~~~~-~~~------------~~~~~iDTl~lar~~~ 132 (240)
T PRK05711 70 KPTFAEVADEFLDFIRG---AELIIHNA-PFDIGFMDYEFALLGRDIP-KTN------------TFCKVTDTLAMARRMF 132 (240)
T ss_pred CCCHHHHHHHHHHHhCC---CEEEEEcc-HHhHHHHHHHHHHhCCCCC-ccc------------ccCceeeHHHHHHHHc
Confidence 56788899999999865 46899999 6999999988888874321 000 0123789999888742
Q ss_pred CCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 387 YLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 387 ~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
|-.+++|+++++. +|..... +-+.-.+.||.++..+|.++
T Consensus 133 --p~~~~~L~aL~~~-~gi~~~~---------------r~~H~AL~DA~~~A~v~~~l 172 (240)
T PRK05711 133 --PGKRNSLDALCKR-YGIDNSH---------------RTLHGALLDAEILAEVYLAM 172 (240)
T ss_pred --CCCCCCHHHHHHH-CCCCCCC---------------CCCCCHHHHHHHHHHHHHHH
Confidence 3467899999996 6753211 01233577999999998876
No 54
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=97.75 E-value=0.00028 Score=86.07 Aligned_cols=158 Identities=18% Similarity=0.257 Sum_probs=100.9
Q ss_pred CceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEE-cccccccccccccCCCCC-CCCC--ceEEecCCCHHHH
Q 000161 238 EVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLII-NRECVGEDIEDLEYTPKP-EFEG--YFKVTNVNNEIEL 313 (1988)
Q Consensus 238 ~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~-nreivs~di~~feytp~~-~~~g--~f~V~~~~dE~eL 313 (1988)
+..+++||+||++. +|..|+|+.||.+.-..|.++- -...+..+. . -.|.. ...| .-.+...+...++
T Consensus 7 ~~~~Vv~DlETTGl-----~p~~~eIIEIgaV~v~~g~i~~~f~~lVkP~~-~--I~~~a~~ihGIT~e~l~~~~~~~ev 78 (313)
T PRK06807 7 PLDYVVIDFETTGF-----NPYNDKIIQVAAVKYRNHELVDQFVSYVNPER-P--IPDRITSLTGITNYRVSDAPTIEEV 78 (313)
T ss_pred CCCEEEEEEECCCC-----CCCCCeEEEEEEEEEECCEEEEEEEEEECcCC-C--CCHhhhccCCCCHHHHhCCCCHHHH
Confidence 34678899999874 3557899999976422332210 000111000 0 00000 1112 0113345788999
Q ss_pred HHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCCC
Q 000161 314 LRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQ 393 (1988)
Q Consensus 314 L~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~Sy 393 (1988)
+..|.+++.. ++++|||+ .||+++|.+-+..+|++.. . ...+|+....+.- +...+++
T Consensus 79 l~~f~~fl~~---~~lVaHNa-~FD~~fL~~~~~~~gl~~~-------~----------~~~iDtl~la~~~-~~~~~~~ 136 (313)
T PRK06807 79 LPLFLAFLHT---NVIVAHNA-SFDMRFLKSNVNMLGLPEP-------K----------NKVIDTVFLAKKY-MKHAPNH 136 (313)
T ss_pred HHHHHHHHcC---CeEEEEcH-HHHHHHHHHHHHHcCCCCC-------C----------CCEeeHHHHHHHH-hCCCCCC
Confidence 9999999864 57999999 8999999999999988531 0 1257888776653 2234789
Q ss_pred CHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 394 GLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 394 sL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
+|++++.+ ||... + ++=.+.||..|..||.++
T Consensus 137 kL~~L~~~-lgi~~-~-----------------~H~Al~DA~~ta~l~~~l 168 (313)
T PRK06807 137 KLETLKRM-LGIRL-S-----------------SHNAFDDCITCAAVYQKC 168 (313)
T ss_pred CHHHHHHH-cCCCC-C-----------------CcChHHHHHHHHHHHHHH
Confidence 99999985 77543 1 133467999999998875
No 55
>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=97.68 E-value=0.00053 Score=77.17 Aligned_cols=92 Identities=20% Similarity=0.245 Sum_probs=63.1
Q ss_pred HHHHHHHHHHhhC-CCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCC
Q 000161 313 LLRLWFAHMQEVK-PGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQG 391 (1988)
Q Consensus 313 LL~~F~~~I~~~D-PDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~ 391 (1988)
+...+.+++...+ +.++||||+..||++||..-++++|+... . ....+|.+...++- . +
T Consensus 84 ~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~-----~-----------~~~~iDtl~l~r~~--~--~ 143 (177)
T cd06136 84 TANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLP-----D-----------DILCVDSLPAFREL--D--Q 143 (177)
T ss_pred HHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCC-----C-----------CCEEEEeHHHHhhh--H--h
Confidence 4444444544443 46899999999999999999999887531 0 12456888777752 1 1
Q ss_pred CCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHH
Q 000161 392 SQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMT 443 (1988)
Q Consensus 392 SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~K 443 (1988)
+|++++++++|..... ++-.+.||.+|++++.+
T Consensus 144 --~L~~l~~~~~~~~~~~-----------------~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 144 --SLGSLYKRLFGQEPKN-----------------SHTAEGDVLALLKCALH 176 (177)
T ss_pred --hHHHHHHHHhCCCccc-----------------ccchHHHHHHHHHHHhh
Confidence 8999999777754322 13456799999888754
No 56
>PRK07883 hypothetical protein; Validated
Probab=97.67 E-value=0.00039 Score=91.04 Aligned_cols=163 Identities=20% Similarity=0.139 Sum_probs=105.8
Q ss_pred CCCCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEE-EcccccccccccccCCCCC-CCCC--ceEEecCCCH
Q 000161 235 QRAEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLI-INRECVGEDIEDLEYTPKP-EFEG--YFKVTNVNNE 310 (1988)
Q Consensus 235 ~~p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li-~nreivs~di~~feytp~~-~~~g--~f~V~~~~dE 310 (1988)
+..+...++||+||++. +|..|+|+.|+.+.-..|..+ .-...+..+ ....|.. ...| .-.+...+.+
T Consensus 11 ~~~~~~~Vv~D~ETTGl-----~p~~~~IIEIgaV~v~~g~iv~~f~~lV~P~---~~i~~~~~~itGIt~e~l~~ap~~ 82 (557)
T PRK07883 11 PLRDVTFVVVDLETTGG-----SPAGDAITEIGAVKVRGGEVLGEFATLVNPG---RPIPPFITVLTGITTAMVAGAPPI 82 (557)
T ss_pred CCcCCCEEEEEEecCCC-----CCCCCeEEEEEEEEEECCEEEEEEEEEECCC---CCCChhHHhhcCCCHHHHhCCCCH
Confidence 34567899999999985 356799999998743233221 000011000 0000100 1112 0124456788
Q ss_pred HHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccC-CC
Q 000161 311 IELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSY-LP 389 (1988)
Q Consensus 311 ~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~-L~ 389 (1988)
.+.+..|.+++. .+++||||+ .||++||..-++.+|++.. ....+|++.+.++-.. ..
T Consensus 83 ~evl~~f~~fl~---~~~lVaHNa-~FD~~fL~~~~~r~g~~~~-----------------~~~~iDTl~lar~l~~~~~ 141 (557)
T PRK07883 83 EEVLPAFLEFAR---GAVLVAHNA-PFDIGFLRAAAARCGYPWP-----------------GPPVLCTVRLARRVLPRDE 141 (557)
T ss_pred HHHHHHHHHHhc---CCEEEEeCc-HHHHHHHHHHHHHcCCCCC-----------------CCCcEecHHHHHHhcccCC
Confidence 999999999986 379999999 7999999999999988631 1134788888776221 12
Q ss_pred CCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 390 QGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 390 ~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
..+++|++++.. +|..... ++-.+.||.+|..|+.++
T Consensus 142 ~~~~~L~~L~~~-~gi~~~~-----------------~H~Al~DA~ata~l~~~l 178 (557)
T PRK07883 142 APNVRLSTLARL-FGATTTP-----------------THRALDDARATVDVLHGL 178 (557)
T ss_pred CCCCCHHHHHHH-CCcccCC-----------------CCCHHHHHHHHHHHHHHH
Confidence 478999999984 7764321 144678999999998876
No 57
>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=97.66 E-value=0.00026 Score=79.99 Aligned_cols=157 Identities=20% Similarity=0.170 Sum_probs=93.2
Q ss_pred EEEEEEEccCCCCCCCCCCCeEEEEEEEE-cCCceEEEcccccccccccccCCCCCC---------CCC--ceEEec-CC
Q 000161 242 CAFDIETTKLPLKFPDADYDIIMMISYML-DGQGYLIINRECVGEDIEDLEYTPKPE---------FEG--YFKVTN-VN 308 (1988)
Q Consensus 242 LsfDIEt~s~~~~fPdp~~D~Ii~IS~~~-~~~g~li~nreivs~di~~feytp~~~---------~~g--~f~V~~-~~ 308 (1988)
+.||+||++. ++..|+|++|+.+. ++++..+ +...+-..|.++ ..| +-.+.. ..
T Consensus 1 ~~~D~ETTGl-----~~~~d~Iieig~v~v~~~~~~~--------~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~ 67 (183)
T cd06138 1 LFYDYETFGL-----NPSFDQILQFAAIRTDENFNEI--------EPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGL 67 (183)
T ss_pred CEEEeecCCC-----CCCCCceEEEEEEEECCCCCCc--------cceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCC
Confidence 3599999985 35679999999863 4432211 000111112211 011 112334 46
Q ss_pred CHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhcc--
Q 000161 309 NEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDS-- 386 (1988)
Q Consensus 309 dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~-- 386 (1988)
++.++|..|..++.+ ...++||||...||+.||..=+.++|+.... ..+ ..+...+|.+..++...
T Consensus 68 ~~~~~l~~~~~~~~~-~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~-~~~----------~~~~~~~dtl~l~r~~~~~ 135 (183)
T cd06138 68 SEYEFIAKIHRLFNT-PGTCIVGYNNIRFDDEFLRFAFYRNLYDPYT-WEW----------KNGNSRWDLLDVVRAYYAL 135 (183)
T ss_pred CHHHHHHHHHHHHcc-CCCcEEeeCchhhHHHHHHHHHHHCCCcccc-eec----------cCCccccccHHHHHHHHhh
Confidence 788999999999975 3468999998899999998877777775320 000 01223456665554311
Q ss_pred -----CCC-----CCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHH
Q 000161 387 -----YLP-----QGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLY 441 (1988)
Q Consensus 387 -----~L~-----~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~ 441 (1988)
..+ ..+|+|++++++ +|..... ++-.+.||.+|..|.
T Consensus 136 ~~~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~~-----------------~H~Al~Da~~ta~l~ 182 (183)
T cd06138 136 RPDGIVWPKNDDGKPSFKLEDLAQA-NGIEHSN-----------------AHDALSDVEATIALA 182 (183)
T ss_pred ChhhccCccccCCCcchhHHHHHHH-CCCCccc-----------------cccHHHHHHHHHHHh
Confidence 111 358999999996 6753211 234567888887763
No 58
>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=97.64 E-value=0.00065 Score=79.38 Aligned_cols=157 Identities=21% Similarity=0.265 Sum_probs=97.2
Q ss_pred eEEEEEEEEccCCCCCCCCC-CCeEEEEEEE-EcCCc-----e-EEEcccccccccccccCCCCC-CCCC--ceEEecCC
Q 000161 240 HVCAFDIETTKLPLKFPDAD-YDIIMMISYM-LDGQG-----Y-LIINRECVGEDIEDLEYTPKP-EFEG--YFKVTNVN 308 (1988)
Q Consensus 240 rvLsfDIEt~s~~~~fPdp~-~D~Ii~IS~~-~~~~g-----~-li~nreivs~di~~feytp~~-~~~g--~f~V~~~~ 308 (1988)
|.+.||+||++. +|. .|+||.|+++ +.+.. + ..++.. .+| .|.. ...| .-.+...+
T Consensus 1 r~vvlD~ETTGl-----~p~~~d~IIEIgav~~~~~~~~~~~f~~~i~P~---~~i-----~~~a~~vhGIt~e~l~~~p 67 (225)
T TIGR01406 1 RQIILDTETTGL-----DPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPE---RDM-----PAEAAKVHGITDEFLADKP 67 (225)
T ss_pred CEEEEEeeCCCc-----CCCCCCeEEEEEEEEEECCcEecceEEEEECcC---CCC-----CHHHHhccCCCHHHHhCCC
Confidence 468899999984 344 4899999976 32211 1 111110 000 0000 0111 00123446
Q ss_pred CHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCC
Q 000161 309 NEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYL 388 (1988)
Q Consensus 309 dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L 388 (1988)
...+++.+|.+++.. ..+|+||. .||++||..-+..+|.... .+. .....+|++.+.++. .
T Consensus 68 ~f~ev~~~f~~fi~~---~~lVaHNa-~FD~~fL~~el~r~g~~~~-~~~------------~~~~~iDTl~lar~~--~ 128 (225)
T TIGR01406 68 KFKEIADEFLDFIGG---SELVIHNA-AFDVGFLNYELERLGPTIK-KIG------------EFCRVIDTLAMARER--F 128 (225)
T ss_pred CHHHHHHHHHHHhCC---CEEEEEec-HHHHHHHHHHHHHhCCCCc-ccc------------cCCCEEEHHHHHHHH--c
Confidence 778899999999876 47899998 6999999998888874210 000 012368999988874 2
Q ss_pred CCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 389 PQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 389 ~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
|..+++|+++++. +|.....- -++=.+.||.++..+|.++
T Consensus 129 p~~~~~L~~L~~~-~gi~~~~r---------------~~H~Al~DA~~~a~v~~~l 168 (225)
T TIGR01406 129 PGQRNSLDALCKR-FKVDNSHR---------------TLHGALLDAHLLAEVYLAL 168 (225)
T ss_pred CCCCCCHHHHHHh-cCCCCCCC---------------CCcCHHHHHHHHHHHHHHH
Confidence 4468999999996 67543210 0123567999999998875
No 59
>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=97.60 E-value=0.00039 Score=97.04 Aligned_cols=154 Identities=24% Similarity=0.250 Sum_probs=103.7
Q ss_pred CCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEE-cccccccccccccCCCCCCC-------CC--ceEEec
Q 000161 237 AEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLII-NRECVGEDIEDLEYTPKPEF-------EG--YFKVTN 306 (1988)
Q Consensus 237 p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~-nreivs~di~~feytp~~~~-------~g--~f~V~~ 306 (1988)
-+-++++||+||++. +|..|+|+.|+.+.-.+|..+. -...+ .|.... .| +-.+..
T Consensus 188 ~~~~~VVfDiETTGL-----~~~~d~IIEIGAVkv~~g~iid~f~~~V---------~P~~~I~~~~~~ltGIT~e~L~~ 253 (1213)
T TIGR01405 188 DDATYVVFDIETTGL-----SPQYDEIIEFGAVKVKNGRIIDKFQFFI---------KPHEPLSAFVTELTGITQDMLEN 253 (1213)
T ss_pred cCCcEEEEEeEecCC-----CCCCCeEEEEEEEEEECCeEEEEEEEEE---------CCCCCCCHHHHHHhCCCHHHHhC
Confidence 345899999999984 3567999999987433332210 00000 111111 11 012445
Q ss_pred CCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhcc
Q 000161 307 VNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDS 386 (1988)
Q Consensus 307 ~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~ 386 (1988)
.++..++|.+|.+++.. .++|||| ..||++||.+.+.++|++.+ ....+|++.+.+.-
T Consensus 254 ap~~~evl~~f~~fl~~---~iLVaHN-a~FD~~fL~~~~~r~g~~~~-----------------~~~~IDTl~lar~l- 311 (1213)
T TIGR01405 254 APEIEEVLEKFKEFFKD---SILVAHN-ASFDIGFLNTNFEKVGLEPL-----------------ENPVIDTLELARAL- 311 (1213)
T ss_pred CCCHHHHHHHHHHHhCC---CeEEEEC-hHHHHHHHHHHHHHcCCCcc-----------------CCCEeEHHHHHHHH-
Confidence 67899999999999964 6999999 68999999999999888532 11467888887763
Q ss_pred CCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 387 YLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 387 ~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
+....+++|++++++ +|..... .+.++.||.+|..|+.++
T Consensus 312 ~p~~k~~kL~~Lak~-lgi~~~~-----------------~HrAl~DA~aTa~I~~~l 351 (1213)
T TIGR01405 312 NPEYKSHRLGNICKK-LGVDLDD-----------------HHRADYDAEATAKVFKVM 351 (1213)
T ss_pred hccCCCCCHHHHHHH-cCCCCCC-----------------CcCHHHHHHHHHHHHHHH
Confidence 223478999999997 6764432 244567888888877765
No 60
>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=97.56 E-value=0.00069 Score=73.89 Aligned_cols=150 Identities=17% Similarity=0.116 Sum_probs=93.0
Q ss_pred EEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEE-cccccccccccccCCCCC-CCCC--ceEEecCCCHHHHHHHH
Q 000161 242 CAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLII-NRECVGEDIEDLEYTPKP-EFEG--YFKVTNVNNEIELLRLW 317 (1988)
Q Consensus 242 LsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~-nreivs~di~~feytp~~-~~~g--~f~V~~~~dE~eLL~~F 317 (1988)
+++|+||++. ..|+|+.|+++.-..|.++. -...+..+. +..|.. ...| .-.+...+...+.+.+|
T Consensus 2 v~~D~Ettg~-------~~~~ii~ig~v~~~~~~~~~~~~~~i~p~~---~~~~~~~~i~GIt~e~l~~~~~~~~v~~~l 71 (156)
T cd06130 2 VAIDFETANA-------DRASACSIGLVKVRDGQIVDTFYTLIRPPT---RFDPFNIAIHGITPEDVADAPTFPEVWPEI 71 (156)
T ss_pred EEEEEeCCCC-------CCCceEEEEEEEEECCEEEEEEEEEeCcCC---CCChhhccccCcCHHHHhcCCCHHHHHHHH
Confidence 5799999962 25789999987433333210 000111000 000100 1112 00122345677899999
Q ss_pred HHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCCCCHHH
Q 000161 318 FAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKA 397 (1988)
Q Consensus 318 ~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~SysL~~ 397 (1988)
.+++.. ++++|||. .||+++|..-+..+|+... ....+|++.+.+.... ..++++|++
T Consensus 72 ~~~l~~---~~lv~hn~-~fD~~~l~~~~~~~g~~~~-----------------~~~~idt~~~~~~~~~-~~~~~~L~~ 129 (156)
T cd06130 72 KPFLGG---SLVVAHNA-SFDRSVLRAALEAYGLPPP-----------------PYQYLCTVRLARRVWP-LLPNHKLNT 129 (156)
T ss_pred HHHhCC---CEEEEeCh-HHhHHHHHHHHHHcCCCCC-----------------CCCEEEHHHHHHHHhc-cCCCCCHHH
Confidence 999875 68999998 8999999999998887532 0135788887776322 247899999
Q ss_pred HHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHH
Q 000161 398 VTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYM 442 (1988)
Q Consensus 398 Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~ 442 (1988)
+++. +|.... .+-.+.||.+|.+|+.
T Consensus 130 l~~~-~g~~~~------------------~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 130 VAEH-LGIELN------------------HHDALEDARACAEILL 155 (156)
T ss_pred HHHH-cCCCcc------------------CcCchHHHHHHHHHHh
Confidence 9996 675321 2445779999888864
No 61
>PRK07740 hypothetical protein; Provisional
Probab=97.53 E-value=0.0014 Score=77.51 Aligned_cols=161 Identities=18% Similarity=0.131 Sum_probs=98.6
Q ss_pred CCCceEEEEEEEEccCCCCCCCCCC-CeEEEEEEEEcCCceEEEc--ccccccccccccCCCC-CCCCC--ceEEecCCC
Q 000161 236 RAEVHVCAFDIETTKLPLKFPDADY-DIIMMISYMLDGQGYLIIN--RECVGEDIEDLEYTPK-PEFEG--YFKVTNVNN 309 (1988)
Q Consensus 236 ~p~lrvLsfDIEt~s~~~~fPdp~~-D~Ii~IS~~~~~~g~li~n--reivs~di~~feytp~-~~~~g--~f~V~~~~d 309 (1988)
..+.+++.||+||++. +|.. |+|+.|+.+.-..|.+... ...+..+. ...|. -...| +-.+...+.
T Consensus 56 ~~~~~~vv~D~ETTGl-----~p~~~deIIeIgaV~~~~~~i~~~~f~~lv~P~~---~i~~~~~~ltGIt~e~l~~ap~ 127 (244)
T PRK07740 56 LTDLPFVVFDLETTGF-----SPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKR---PIPEHILELTGITAEDVAFAPP 127 (244)
T ss_pred ccCCCEEEEEEeCCCC-----CCCCCCeEEEEEEEEEECCEEEEEEEEEEeCcCC---CCChhheeccCCCHHHHhCCCC
Confidence 4577899999999973 2443 8999999875333332000 00111000 00000 01112 112445678
Q ss_pred HHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCC
Q 000161 310 EIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLP 389 (1988)
Q Consensus 310 E~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~ 389 (1988)
..+.+.+|.+++.. +++||||. .||+.||..-........+ ....+|+....+.- +-.
T Consensus 128 ~~evl~~f~~fi~~---~~lVahna-~fD~~fL~~~~~~~~~~~~-----------------~~~~iDt~~l~r~l-~~~ 185 (244)
T PRK07740 128 LAEVLHRFYAFIGA---GVLVAHHA-GHDKAFLRHALWRTYRQPF-----------------THRLIDTMFLTKLL-AHE 185 (244)
T ss_pred HHHHHHHHHHHhCC---CEEEEeCH-HHHHHHHHHHHHHhcCCCc-----------------CCCeechHHHHHHH-cCC
Confidence 99999999998764 68999997 8999999765443321100 12467888776642 222
Q ss_pred CCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 390 QGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 390 ~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
.++++|++++.+ +|..... .+-.+.||.+|..|+.++
T Consensus 186 ~~~~sL~~l~~~-~gi~~~~-----------------~H~Al~Da~ata~l~~~l 222 (244)
T PRK07740 186 RDFPTLDDALAY-YGIPIPR-----------------RHHALGDALMTAKLWAIL 222 (244)
T ss_pred CCCCCHHHHHHH-CCcCCCC-----------------CCCcHHHHHHHHHHHHHH
Confidence 358999999985 7764322 133578999999999886
No 62
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=97.53 E-value=0.00069 Score=75.09 Aligned_cols=146 Identities=17% Similarity=0.108 Sum_probs=83.3
Q ss_pred EEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEcccccc--cccccccCCCCCCCCCce--EEecCCC-------H
Q 000161 242 CAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVG--EDIEDLEYTPKPEFEGYF--KVTNVNN-------E 310 (1988)
Q Consensus 242 LsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs--~di~~feytp~~~~~g~f--~V~~~~d-------E 310 (1988)
+++|+||++. +|..|.|+.||++.-.+|.++... .+. ..|.++- -...|-. .+...++ -
T Consensus 1 v~lD~EttGl-----~~~~d~ii~Ig~V~v~~g~i~~~~-~v~P~~~i~~~~----~~i~GIt~~~l~~a~~~~~~~~~~ 70 (161)
T cd06137 1 VALDCEMVGL-----ADGDSEVVRISAVDVLTGEVLIDS-LVRPSVRVTDWR----TRFSGVTPADLEEAAKAGKTIFGW 70 (161)
T ss_pred CEEEeeeeeE-----cCCCCEEEEEEEEEcCCCeEEEec-cccCCCCCCccc----eeccCCCHHHHhhhhhcCCccccH
Confidence 4799999975 345799999998854444433211 111 0011100 0011100 0100111 1
Q ss_pred HHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCC
Q 000161 311 IELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQ 390 (1988)
Q Consensus 311 ~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~ 390 (1988)
.+.+.+|.+++... .++||||. .||+.||..- ....+|+..+.++-.....
T Consensus 71 ~~~~~~~~~~i~~~--~vlVgHn~-~fD~~fL~~~--------------------------~~~~iDT~~l~~~~~~~~~ 121 (161)
T cd06137 71 EAARAALWKFIDPD--TILVGHSL-QNDLDALRMI--------------------------HTRVVDTAILTREAVKGPL 121 (161)
T ss_pred HHHHHHHHHhcCCC--cEEEeccH-HHHHHHHhCc--------------------------CCCeeEehhhhhhccCCCc
Confidence 36778888888642 59999999 5999998420 1135688877776321111
Q ss_pred --CCCCHHHHHHHHcCCCCCC-CChHHHHHHHhhChHHHHHHHHHhhHHHHHHH
Q 000161 391 --GSQGLKAVTKAKLGYDPLE-VNPEDMVRFAKEKPQMMASYSVSDAVATYYLY 441 (1988)
Q Consensus 391 --~SysL~~Va~~~LG~~K~d-vd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~ 441 (1988)
.+|+|+++++.++|..... .. ..-++.||.+|.+||
T Consensus 122 ~~~~~~L~~L~~~~~~~~~~~~~~---------------~H~A~~DA~at~~l~ 160 (161)
T cd06137 122 AKRQWSLRTLCRDFLGLKIQGGGE---------------GHDSLEDALAAREVV 160 (161)
T ss_pred CCCCccHHHHHHHHCCchhcCCCC---------------CCCcHHHHHHHHHHh
Confidence 5899999999988853211 00 123567898888875
No 63
>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=97.52 E-value=0.00086 Score=77.93 Aligned_cols=160 Identities=18% Similarity=0.097 Sum_probs=93.4
Q ss_pred CceEEEEEEEEccCCCCCCCCCCCeEEEEEEEE-cCCceEE-EcccccccccccccCCCCC-CCCC--ceEEecCCCHHH
Q 000161 238 EVHVCAFDIETTKLPLKFPDADYDIIMMISYML-DGQGYLI-INRECVGEDIEDLEYTPKP-EFEG--YFKVTNVNNEIE 312 (1988)
Q Consensus 238 ~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~-~~~g~li-~nreivs~di~~feytp~~-~~~g--~f~V~~~~dE~e 312 (1988)
..+.++||+||++. +|..| |+.|+.+. .+.+... .-...+... . ...|.. ...| +-.+...+...+
T Consensus 6 ~~~fvv~D~ETTGl-----~~~~~-IIeIgav~v~~~~~~~~~f~~li~P~-~--~i~~~a~~ihGIt~e~l~~~p~~~e 76 (217)
T TIGR00573 6 LDTETTGDNETTGL-----YAGHD-IIEIGAVEIINRRITGNKFHTYIKPD-R--PIDPDAIKIHGITDDMLKDKPDFKE 76 (217)
T ss_pred ecCEEEEEecCCCC-----CCCCC-EEEEEEEEEECCCEeeeEEEEEECcC-C--CCCHHHHhhcCCCHHHHcCCCCHHH
Confidence 45688899999984 35567 99999775 3322111 000000000 0 000000 0111 011334567889
Q ss_pred HHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHH---HHhhccCCC
Q 000161 313 LLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFA---WVKRDSYLP 389 (1988)
Q Consensus 313 LL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~---~vkrd~~L~ 389 (1988)
++..|.+++.. +++||||. .||++||..-+..++.... . ....+|+.. ++... ++
T Consensus 77 v~~~~~~~~~~---~~lVaHNa-~FD~~fL~~~~~r~~~~~~-------~---------~~~~~dtl~l~~~~~~~--~~ 134 (217)
T TIGR00573 77 IAEDFADYIRG---AELVIHNA-SFDVGFLNYEFSKLYKVEP-------K---------TNDVIDTTDTLQYARPE--FP 134 (217)
T ss_pred HHHHHHHHhCC---CEEEEecc-HHHHHHHHHHHHHhcCCCC-------C---------ccceecHHHHHHHHHHh--CC
Confidence 99999999854 68999998 7999999888776644211 0 112345444 33332 33
Q ss_pred CCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 390 QGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 390 ~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
..+++|.+++.. +|..... +-+.=.+.||.+|..|+.++
T Consensus 135 ~~~~~L~~l~~~-~gl~~~~---------------~~~H~Al~DA~~ta~l~~~l 173 (217)
T TIGR00573 135 GKRNTLDALCKR-YEITNSH---------------RALHGALADAFILAKLYLVM 173 (217)
T ss_pred CCCCCHHHHHHH-cCCCCCC---------------cccCCHHHHHHHHHHHHHHH
Confidence 457899999986 6754220 00233567999999998875
No 64
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=97.49 E-value=0.0016 Score=76.82 Aligned_cols=162 Identities=18% Similarity=0.113 Sum_probs=97.6
Q ss_pred CCCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEcc---cccccccccccCCCCC-CCCC--ceEEecCCC
Q 000161 236 RAEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINR---ECVGEDIEDLEYTPKP-EFEG--YFKVTNVNN 309 (1988)
Q Consensus 236 ~p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nr---eivs~di~~feytp~~-~~~g--~f~V~~~~d 309 (1988)
.-+..+++||+||++. +|..|+|+.|+.+.-..|.+.... .++..+ -++.+.. ...| +-.+...++
T Consensus 44 ~~~~~~vviD~ETTGl-----~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~---~~i~~~~~~IhGIt~e~l~~ap~ 115 (239)
T PRK09146 44 LSEVPFVALDFETTGL-----DAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPR---RPLEEESVVIHGITHSELQDAPD 115 (239)
T ss_pred cccCCEEEEEeECCCC-----CCCCCcEEEEEEEEEECCeEeecceEEEEECCC---CCCChhhhhhcCCCHHHHhCCCC
Confidence 4467899999999985 356899999998742222211000 000000 0000000 0111 001334567
Q ss_pred HHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccC--
Q 000161 310 EIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSY-- 387 (1988)
Q Consensus 310 E~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~-- 387 (1988)
..+++.+|.+++.. +++||||. .||+.||..-++.++.... . ...+|++.+.++-..
T Consensus 116 ~~evl~~l~~~~~~---~~lVaHna-~FD~~fL~~~l~~~~~~~~-----~------------~~~iDTl~Lar~l~~~~ 174 (239)
T PRK09146 116 LERILDELLEALAG---KVVVVHYR-RIERDFLDQALRNRIGEGI-----E------------FPVIDTMEIEARIQRKQ 174 (239)
T ss_pred HHHHHHHHHHHhCC---CEEEEECH-HHHHHHHHHHHHHhcCCCC-----C------------CceechHHHHHHHcccc
Confidence 88899999998754 79999997 6999999888776532110 0 134788877665210
Q ss_pred ----------CCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 388 ----------LPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 388 ----------L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
.+..+++|++++++ +|..... +.-.+.||.+|..|+.++
T Consensus 175 ~~~~~~~~~~~~~~~~~L~~l~~~-~gl~~~~-----------------~H~Al~DA~ata~l~~~~ 223 (239)
T PRK09146 175 AGGLWNRLKGKKPESIRLADSRLR-YGLPAYS-----------------PHHALTDAIATAELLQAQ 223 (239)
T ss_pred cccccchhccCCCCCCCHHHHHHH-cCCCCCC-----------------CCCcHHHHHHHHHHHHHH
Confidence 11268999999996 6754321 133568999999998875
No 65
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=97.49 E-value=0.0014 Score=80.11 Aligned_cols=155 Identities=15% Similarity=0.173 Sum_probs=96.8
Q ss_pred eEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEE-cccccccccccccCCCCC-CCCC--ceEEecCCCHHHHHH
Q 000161 240 HVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLII-NRECVGEDIEDLEYTPKP-EFEG--YFKVTNVNNEIELLR 315 (1988)
Q Consensus 240 rvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~-nreivs~di~~feytp~~-~~~g--~f~V~~~~dE~eLL~ 315 (1988)
+.++||+||++ +..|+|+.|+.+.-.+|.++. -..++..+. ....|.. ...| +-.|...+...+++.
T Consensus 2 ~~vviD~ETTg-------~~~d~IieIgav~v~~g~i~~~f~~lv~P~~--~~~~~~~~~IhGIT~e~v~~ap~f~ev~~ 72 (309)
T PRK06195 2 NFVAIDFETAN-------EKRNSPCSIGIVVVKDGEIVEKVHYLIKPKE--MRFMPINIGIHGIRPHMVEDELEFDKIWE 72 (309)
T ss_pred cEEEEEEeCCC-------CCCCceEEEEEEEEECCEEEEEEEEEECCCC--CCCChhheeccCcCHHHHhCCCCHHHHHH
Confidence 57889999984 356999999976422332210 000110000 0001100 1122 112334567788999
Q ss_pred HHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCCCCH
Q 000161 316 LWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQGL 395 (1988)
Q Consensus 316 ~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~SysL 395 (1988)
.|.+++.. +++||||+ .||+.||..-+..+|++.. . ...+|++.+.++- +....+|+|
T Consensus 73 ~~~~fl~~---~~lVaHNa-~FD~~fL~~~~~r~~~~~~--------~---------~~~idT~~lar~l-~~~~~~~~L 130 (309)
T PRK06195 73 KIKHYFNN---NLVIAHNA-SFDISVLRKTLELYNIPMP--------S---------FEYICTMKLAKNF-YSNIDNARL 130 (309)
T ss_pred HHHHHhCC---CEEEEECc-HHHHHHHHHHHHHhCCCCC--------C---------CCEEEHHHHHHHH-cCCCCcCCH
Confidence 99999864 79999999 6999999988888877531 0 1247888887763 222478999
Q ss_pred HHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 396 KAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 396 ~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
++++.+ +|.. .+ .+-.+.||.+|..|+.++
T Consensus 131 ~~L~~~-~gi~---~~---------------~H~Al~DA~ata~l~~~l 160 (309)
T PRK06195 131 NTVNNF-LGYE---FK---------------HHDALADAMACSNILLNI 160 (309)
T ss_pred HHHHHH-cCCC---Cc---------------ccCCHHHHHHHHHHHHHH
Confidence 999997 6742 11 134578999999988765
No 66
>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=97.48 E-value=0.00039 Score=70.57 Aligned_cols=69 Identities=30% Similarity=0.326 Sum_probs=53.0
Q ss_pred EEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEcccccccccccccCCCCCCCCCceEEecCCCHHHHHHHHHHHH
Q 000161 242 CAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRLWFAHM 321 (1988)
Q Consensus 242 LsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~eLL~~F~~~I 321 (1988)
++|||||++.+ +..++|++|+++....+. .+ + . + |.+++
T Consensus 1 ~~~DiEt~~~~-----~~~~~i~~i~~~~~~~~~-------------------------~~-~-~-~--------f~~~l 39 (96)
T cd06125 1 IAIDTEATGLD-----GAVHEIIEIALADVNPED-------------------------TA-V-I-D--------LKDIL 39 (96)
T ss_pred CEEEEECCCCC-----CCCCcEEEEEEEEccCCC-------------------------EE-E-e-h--------HHHHH
Confidence 47999999843 467899999987531111 01 1 1 1 88888
Q ss_pred HhhCCCEEEeeCcccCCHHHHHHHHHHcCCC
Q 000161 322 QEVKPGIYVTYNGDYFDWPFLETRAAHHGFK 352 (1988)
Q Consensus 322 ~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~ 352 (1988)
++..|.+++|||+ .||++||.++++++|+.
T Consensus 40 ~~~~~~v~V~hn~-~fD~~fL~~~~~~~~~~ 69 (96)
T cd06125 40 RDKPLAILVGHNG-SFDLPFLNNRCAELGLK 69 (96)
T ss_pred hhCCCCEEEEeCc-HHhHHHHHHHHHHcCCC
Confidence 8888899999999 89999999999999875
No 67
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=97.48 E-value=0.00045 Score=92.14 Aligned_cols=137 Identities=25% Similarity=0.296 Sum_probs=97.1
Q ss_pred cccCCCCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEccccccccccccc--CCCCCCC-------CC--
Q 000161 232 DLLQRAEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLE--YTPKPEF-------EG-- 300 (1988)
Q Consensus 232 ~~~~~p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~di~~fe--ytp~~~~-------~g-- 300 (1988)
.....-+-+.+-|||||++.. |..|.||.|+.+--..|.+| +.|+ -.|.... .|
T Consensus 414 ~d~~l~datyVVfDiETTGLs-----~~~d~iIE~aAvKikng~iI----------d~f~~Fi~P~~pl~~~~telTgIT 478 (1444)
T COG2176 414 DDQKLDDATYVVFDIETTGLS-----PVYDEIIEIAAVKIKNGRII----------DKFQFFIKPGRPLSATITELTGIT 478 (1444)
T ss_pred cccccccccEEEEEeecCCcC-----cccchhhhheeeeeeCCcch----------HHHHHhcCCCCcCchhhhhccccC
Confidence 334566777888999999863 66799999987643333322 1111 1121111 11
Q ss_pred ceEEecCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHH
Q 000161 301 YFKVTNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFA 380 (1988)
Q Consensus 301 ~f~V~~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~ 380 (1988)
+-.+.+..+..+.|.+|.+++.+ +|+|.|| -+||++||..+.+++|+..+ -..+||++.
T Consensus 479 deml~~a~~i~~vL~kf~~~~~d---~IlVAHN-asFD~gFl~~~~~k~~~~~~-----------------~~pvIDTL~ 537 (1444)
T COG2176 479 DEMLENAPEIEEVLEKFREFIGD---SILVAHN-ASFDMGFLNTNYEKYGLEPL-----------------TNPVIDTLE 537 (1444)
T ss_pred HHHHcCCccHHHHHHHHHHHhcC---cEEEecc-CccchhHHHHHHHHhCCccc-----------------cCchhhHHH
Confidence 11255778899999999999987 5999999 79999999999999988643 126789998
Q ss_pred HHhhccCCCCCCCCHHHHHHHHcCCC
Q 000161 381 WVKRDSYLPQGSQGLKAVTKAKLGYD 406 (1988)
Q Consensus 381 ~vkrd~~L~~~SysL~~Va~~~LG~~ 406 (1988)
+.+. .+-.+.||+|..+|+. ||..
T Consensus 538 lar~-L~P~~ksh~Lg~l~kk-~~v~ 561 (1444)
T COG2176 538 LARA-LNPEFKSHRLGTLCKK-LGVE 561 (1444)
T ss_pred HHHH-hChhhhhcchHHHHHH-hCcc
Confidence 8876 3435689999999995 7753
No 68
>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=97.47 E-value=0.0013 Score=70.70 Aligned_cols=152 Identities=22% Similarity=0.178 Sum_probs=90.9
Q ss_pred EEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCc-eEE--Ecccccc-cccccccCCCCCCCCC--ceEEecCCCHHHHHH
Q 000161 242 CAFDIETTKLPLKFPDADYDIIMMISYMLDGQG-YLI--INRECVG-EDIEDLEYTPKPEFEG--YFKVTNVNNEIELLR 315 (1988)
Q Consensus 242 LsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g-~li--~nreivs-~di~~feytp~~~~~g--~f~V~~~~dE~eLL~ 315 (1988)
+.+|+||++. +|..++|+.|+++.-..+ ..+ .+.-+-. .++..+. ....| .-.+.......+.+.
T Consensus 1 v~~D~Ettg~-----~~~~~~iiei~~v~~~~~~~~~~~~~~~i~p~~~~~~~~----~~~~gi~~~~~~~~~~~~~~~~ 71 (159)
T cd06127 1 VVFDTETTGL-----DPKKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEA----TAIHGITDEMLADAPPFEEVLP 71 (159)
T ss_pred CeEEeeCCCc-----CCCCCeEEEEEEEEEECCcChhhhhheeeCcCCcCCHhh----eeccCCCHHHHhcCCCHHHHHH
Confidence 3689999984 356799999997753222 110 0000000 0000000 00011 001234566778999
Q ss_pred HHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCCCCH
Q 000161 316 LWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQGL 395 (1988)
Q Consensus 316 ~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~SysL 395 (1988)
+|.+++.. ++++|||+ .||+++|.+.+..+|.+.+ ....+|+...++.-... ..+++|
T Consensus 72 ~~~~~l~~---~~~v~~n~-~fD~~~l~~~~~~~~~~~~-----------------~~~~iDt~~~~~~~~~~-~~~~~l 129 (159)
T cd06127 72 EFLEFLGG---RVLVAHNA-SFDLRFLNRELRRLGGPPL-----------------PNPWIDTLRLARRLLPG-LRSHRL 129 (159)
T ss_pred HHHHHHCC---CEEEEeCc-HhhHHHHHHHHHHhCCCCC-----------------CCCeeEHHHHHHHHcCC-CCcCch
Confidence 99998876 79999999 8999999999999883211 23468888887764332 356888
Q ss_pred HHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHH
Q 000161 396 KAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLY 441 (1988)
Q Consensus 396 ~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~ 441 (1988)
..+....+|..... ++-.+.||.+|..||
T Consensus 130 ~~~~~~~~~~~~~~-----------------~H~Al~Da~~t~~l~ 158 (159)
T cd06127 130 GLLLAERYGIPLEG-----------------AHRALADALATAELL 158 (159)
T ss_pred HHHHHHHcCCCCCC-----------------CCCcHHHHHHHHHHh
Confidence 88833346653221 133467888887775
No 69
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=97.46 E-value=0.00092 Score=74.06 Aligned_cols=154 Identities=20% Similarity=0.242 Sum_probs=94.9
Q ss_pred EEEEEEEccCCCCCCCC-CCCeEEEEEEEE-cCCceEEEcccccccccccccCCCCCC-------CCC--ceEEecCCCH
Q 000161 242 CAFDIETTKLPLKFPDA-DYDIIMMISYML-DGQGYLIINRECVGEDIEDLEYTPKPE-------FEG--YFKVTNVNNE 310 (1988)
Q Consensus 242 LsfDIEt~s~~~~fPdp-~~D~Ii~IS~~~-~~~g~li~nreivs~di~~feytp~~~-------~~g--~f~V~~~~dE 310 (1988)
+.||+||++. +| ..|+|+.|+++. ++ +.... +.. ..-..|... ..| +-.+...+..
T Consensus 2 v~~D~ETTGl-----~~~~~~~iieig~v~v~~-~~~~~------~~~-~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~~ 68 (167)
T cd06131 2 IVLDTETTGL-----DPREGHRIIEIGCVELIN-RRLTG------NTF-HVYINPERDIPEEAFKVHGITDEFLADKPKF 68 (167)
T ss_pred EEEEeeCCCC-----CCCCCCeEEEEEEEEEEC-CcEec------cEE-EEEECCCCCCCHHHHHHhCCCHHHHhcCCCH
Confidence 5799999984 34 568999999763 32 21100 000 000011100 111 0013345678
Q ss_pred HHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCC
Q 000161 311 IELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQ 390 (1988)
Q Consensus 311 ~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~ 390 (1988)
.+.+..|.+++.. .+++|||+ .||+.+|..-+..+|+.... . .....+|++...++. + +.
T Consensus 69 ~~v~~~l~~~l~~---~~lv~hn~-~fD~~~l~~~~~~~~~~~~~----~----------~~~~~idt~~~~~~~-~-~~ 128 (167)
T cd06131 69 AEIADEFLDFIRG---AELVIHNA-SFDVGFLNAELSLLGLGKKI----I----------DFCRVIDTLALARKK-F-PG 128 (167)
T ss_pred HHHHHHHHHHHCC---CeEEEeCh-HHhHHHHHHHHHHhCCCccc----c----------cCCCceEhHHHHHHH-c-CC
Confidence 8999999998765 46899999 69999998888888764210 0 012457888877763 2 33
Q ss_pred CCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 391 GSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 391 ~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
.+++|++++++ +|.....- -++-.+.||.++..||.++
T Consensus 129 ~~~~L~~l~~~-~~i~~~~~---------------~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 129 KPNSLDALCKR-FGIDNSHR---------------TLHGALLDAELLAEVYLEL 166 (167)
T ss_pred CCCCHHHHHHH-CCCCCCCC---------------CCCChHHHHHHHHHHHHHh
Confidence 57899999996 67432110 0234567999999998764
No 70
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=97.44 E-value=0.0022 Score=89.08 Aligned_cols=151 Identities=19% Similarity=0.198 Sum_probs=99.6
Q ss_pred eEEEEEEEEccCCCCCCCCC-CCeEEEEEEEEcCCceEEE-cccccccccccccCCCCCC-------CCC--ceEEecCC
Q 000161 240 HVCAFDIETTKLPLKFPDAD-YDIIMMISYMLDGQGYLII-NRECVGEDIEDLEYTPKPE-------FEG--YFKVTNVN 308 (1988)
Q Consensus 240 rvLsfDIEt~s~~~~fPdp~-~D~Ii~IS~~~~~~g~li~-nreivs~di~~feytp~~~-------~~g--~f~V~~~~ 308 (1988)
+++++|+||++. +|. .|+||.|+++.-.+|.++- -... ..|... ..| +-.+...+
T Consensus 4 ~~vvvD~ETTG~-----~p~~~d~IIeigav~v~~~~i~~~f~~~---------v~P~~~i~~~~~~ltGIt~~~l~~ap 69 (928)
T PRK08074 4 RFVVVDLETTGN-----SPKKGDKIIQIAAVVVEDGEILERFSSF---------VNPERPIPPFITELTGISEEMVKQAP 69 (928)
T ss_pred CEEEEEEeCCCC-----CCCCCCcEEEEEEEEEECCEEEEEEEEE---------ECcCCCCCHHHhhcCCCCHHHHhcCC
Confidence 578899999974 233 4899999987533333220 0000 012111 112 11234567
Q ss_pred CHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCC
Q 000161 309 NEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYL 388 (1988)
Q Consensus 309 dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L 388 (1988)
...+.+..|.+++. ..++||||+ .||++||..-+...|++.. ....+|++.+.+.- +-
T Consensus 70 ~f~ev~~~l~~~l~---~~~~VaHN~-~FD~~fL~~~~~~~g~~~~-----------------~~~~iDt~~la~~~-~p 127 (928)
T PRK08074 70 LFEDVAPEIVELLE---GAYFVAHNV-HFDLNFLNEELERAGYTEI-----------------HCPKLDTVELARIL-LP 127 (928)
T ss_pred CHHHHHHHHHHHhC---CCeEEEECh-HHHHHHHHHHHHHcCCCCC-----------------CCCeeeHHHHHHHh-cC
Confidence 88899999999985 368999998 5999999988888877532 01358888887763 22
Q ss_pred CCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 389 PQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 389 ~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
...+|+|++++++ ||.....- +-.+.||.+|..|+.++
T Consensus 128 ~~~~~~L~~l~~~-l~i~~~~~-----------------H~Al~DA~ata~l~~~l 165 (928)
T PRK08074 128 TAESYKLRDLSEE-LGLEHDQP-----------------HRADSDAEVTAELFLQL 165 (928)
T ss_pred CCCCCCHHHHHHh-CCCCCCCC-----------------CChHHHHHHHHHHHHHH
Confidence 3479999999996 77532211 23468999999998886
No 71
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=97.44 E-value=0.0018 Score=74.35 Aligned_cols=156 Identities=20% Similarity=0.182 Sum_probs=94.5
Q ss_pred CceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEcccccccccccccCCCCCC-------CCC--ceEEecCC
Q 000161 238 EVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPE-------FEG--YFKVTNVN 308 (1988)
Q Consensus 238 ~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~di~~feytp~~~-------~~g--~f~V~~~~ 308 (1988)
+-+++++|+||++. +|..|+|+.|+++.-..+.+..... ..+-..|... ..| +-.+....
T Consensus 28 ~~~~vviD~ETTGl-----~~~~d~IieIgaV~~~~~~~~~~~~------f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~ 96 (202)
T PRK09145 28 PDEWVALDCETTGL-----DPRRAEIVSIAAVKIRGNRILTSER------LELLVRPPQSLSAESIKIHRLRHQDLEDGL 96 (202)
T ss_pred CCCEEEEEeECCCC-----CCCCCceEEEEEEEEECCEEeecCc------eEEEECCCCCCCHhHhhhcCcCHHHHhcCC
Confidence 34788999999984 4567999999976422222111000 0000011110 111 01134567
Q ss_pred CHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHH-cCCCCCcccCccccCCCCceeeccceEechHHHHhhc--
Q 000161 309 NEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAH-HGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRD-- 385 (1988)
Q Consensus 309 dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~-lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd-- 385 (1988)
...+.+.+|.+++.. .+++|||. .||+.||..-++. +|.+.. ..++|+...+...
T Consensus 97 ~~~~vl~~~~~~i~~---~~lv~hn~-~fD~~fL~~~~~~~~~~~~~------------------~~~id~~~l~~~~~~ 154 (202)
T PRK09145 97 SEEEALRQLLAFIGN---RPLVGYYL-EFDVAMLNRYVRPLLGIPLP------------------NPLIEVSALYYDKKE 154 (202)
T ss_pred CHHHHHHHHHHHHcC---CeEEEeCH-HHHHHHHHHHHHHhcCCCCC------------------CCeeeHHHHHHHHhh
Confidence 899999999999964 57999996 6999999888775 344321 1245665443210
Q ss_pred cCCC--CCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 386 SYLP--QGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 386 ~~L~--~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
..++ ..+++|+++++. +|.....- .-.+.||.+|..||.++
T Consensus 155 ~~~~~~~~~~~L~~l~~~-~gi~~~~~-----------------H~Al~DA~ata~l~~~l 197 (202)
T PRK09145 155 RHLPDAYIDLRFDAILKH-LDLPVLGR-----------------HDALNDAIMAALIFLRL 197 (202)
T ss_pred ccCCCcccCCCHHHHHHH-cCCCCCCC-----------------CCcHHHHHHHHHHHHHH
Confidence 1111 247999999985 67533211 23568999999998875
No 72
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=97.43 E-value=0.0013 Score=72.29 Aligned_cols=157 Identities=24% Similarity=0.245 Sum_probs=99.7
Q ss_pred EEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEE--Eccccc-ccccccccCCCCCCCCC--ceEEecCCCHHHHHH
Q 000161 241 VCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLI--INRECV-GEDIEDLEYTPKPEFEG--YFKVTNVNNEIELLR 315 (1988)
Q Consensus 241 vLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li--~nreiv-s~di~~feytp~~~~~g--~f~V~~~~dE~eLL~ 315 (1988)
+++||+||++. ++..++|+.||.+.-..+... .+.-+- ...+.++. -...| .-.+.......+.+.
T Consensus 2 ~v~~D~Ettg~-----~~~~~~Iieig~v~~~~~~~~~~f~~~v~p~~~i~~~~----~~~~Git~~~l~~~~~~~~~~~ 72 (169)
T smart00479 2 LVVIDCETTGL-----DPGKDEIIEIAAVDVDGGRIIVVFDTYVKPDRPITDYA----TEIHGITPEMLDDAPTFEEVLE 72 (169)
T ss_pred EEEEEeeCCCC-----CCCCCeEEEEEEEEEECCEeEEEEEEEECCCCCCCHHH----HHHhCCCHHHHhCCCCHHHHHH
Confidence 67899999984 345789999998752222111 000000 00010000 00111 001334578889999
Q ss_pred HHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCCCCH
Q 000161 316 LWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQGL 395 (1988)
Q Consensus 316 ~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~SysL 395 (1988)
+|.+++.. .++++||+..||+++|..-+..+|+... . ....+|+..+.+.... ..+++|
T Consensus 73 ~~~~~l~~---~~~v~~n~~~fD~~~L~~~~~~~~~~~~--------~--------~~~~iD~~~~~~~~~~--~~~~~L 131 (169)
T smart00479 73 ELLEFLKG---KILVAGNALNFDLRFLKLEHPRLGIKDP--------P--------KNPVIDTLKLARALNP--GRKYSL 131 (169)
T ss_pred HHHHHhcC---CEEEEeCCHHHhHHHHHHHHHHhCCCCC--------c--------CCCeeEHHHHHHHHCC--CCCCCH
Confidence 99999865 4689999999999999999988887531 0 0126788887776432 248999
Q ss_pred HHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 396 KAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 396 ~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
+++++. +|.....- ++..+.||..|++|+.++
T Consensus 132 ~~l~~~-~~~~~~~~----------------~H~A~~Da~~t~~l~~~~ 163 (169)
T smart00479 132 KKLAER-LGLEVIGR----------------AHRALDDARATAKLFKKL 163 (169)
T ss_pred HHHHHH-CCCCCCCC----------------CcCcHHHHHHHHHHHHHH
Confidence 999996 55433210 355678999999998875
No 73
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=97.39 E-value=0.0028 Score=72.61 Aligned_cols=149 Identities=21% Similarity=0.224 Sum_probs=89.6
Q ss_pred ceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEcccccccccccccCCCCCC-------CCC--ceEEecCCC
Q 000161 239 VHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPE-------FEG--YFKVTNVNN 309 (1988)
Q Consensus 239 lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~di~~feytp~~~-------~~g--~f~V~~~~d 309 (1988)
-+.++||+||++.+ ..|+||.|+.+.-.+|..+. . .+.-..|... ..| +-.|...+.
T Consensus 5 ~~~vvlD~EtTGl~------~~~eIIeIgaV~v~~g~~~~-~-------f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap~ 70 (195)
T PRK07247 5 ETYIAFDLEFNTVN------GVSHIIQVSAVKYDDHKEVD-S-------FDSYVYTDVPLQSFINGLTGITADKIADAPK 70 (195)
T ss_pred CeEEEEEeeCCCCC------CCCeEEEEEEEEEECCEEEE-E-------EEEEECCCCCCCccceecCCCCHHHHhCCCC
Confidence 36789999999742 25789999977422232110 0 0000011111 111 012345578
Q ss_pred HHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHH--hhccC
Q 000161 310 EIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWV--KRDSY 387 (1988)
Q Consensus 310 E~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~v--krd~~ 387 (1988)
-.+.|.+|.+++.. .++||||...||+.+|.+ +|++.. ....+|+++.. ++...
T Consensus 71 ~~evl~~f~~f~~~---~~lVaHNa~~fD~~fL~~----~g~~~~-----------------~~~~idt~~~~~~~~~~~ 126 (195)
T PRK07247 71 VEEVLAAFKEFVGE---LPLIGYNAQKSDLPILAE----NGLDLS-----------------DQYQVDLYDEAFERRSSD 126 (195)
T ss_pred HHHHHHHHHHHHCC---CeEEEEeCcHhHHHHHHH----cCCCcC-----------------CCceeehHHHHHHhhccc
Confidence 88999999999965 479999999999999843 344321 11235555443 22111
Q ss_pred C-CCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 388 L-PQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 388 L-~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
+ ...+|+|.++++. ||.... .+-.+.||.+|..|+.++
T Consensus 127 ~~~~~~~~L~~La~~-~gi~~~------------------~HrAl~DA~~ta~v~~~l 165 (195)
T PRK07247 127 LNGIANLKLQTVADF-LGIKGR------------------GHNSLEDARMTARVYESF 165 (195)
T ss_pred cCCCCCCCHHHHHHh-cCCCCC------------------CcCCHHHHHHHHHHHHHH
Confidence 1 2368999999995 775321 133467999999998876
No 74
>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=97.37 E-value=0.0021 Score=73.17 Aligned_cols=158 Identities=22% Similarity=0.225 Sum_probs=94.6
Q ss_pred EEEEEEEEccCCCCCCCCCCCeEEEEEEE-EcC--CceEEEcccccccccccccCCCCCC--C-------CCce--E-Ee
Q 000161 241 VCAFDIETTKLPLKFPDADYDIIMMISYM-LDG--QGYLIINRECVGEDIEDLEYTPKPE--F-------EGYF--K-VT 305 (1988)
Q Consensus 241 vLsfDIEt~s~~~~fPdp~~D~Ii~IS~~-~~~--~g~li~nreivs~di~~feytp~~~--~-------~g~f--~-V~ 305 (1988)
-++||+||++. +|..|+|+.|+.+ +.+ +|.+.+.. ...+-+.|.++ . .|-. . +.
T Consensus 7 ~vv~D~ETTGl-----~~~~d~Iieigav~v~~~~~~~i~~~~------~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~ 75 (189)
T cd06134 7 PVVVDVETGGF-----NPQTDALLEIAAVTLEMDEQGNLYPDE------TFHFHILPFEGANLDPAALEFNGIDPFHPFR 75 (189)
T ss_pred eEEEEecCCCC-----CCCCCeEEEEEEEEEEECCCCceeccc------eEEEEEcCCCCCCCCHHHHhhcCCCchhhhc
Confidence 35799999984 4678999999976 321 23210000 00111122110 1 1100 0 11
Q ss_pred cCCCHHHHHHHHHHHHHhhC------CCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechH
Q 000161 306 NVNNEIELLRLWFAHMQEVK------PGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCF 379 (1988)
Q Consensus 306 ~~~dE~eLL~~F~~~I~~~D------PDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~ 379 (1988)
....+.+.+.+|++++.++- =.++||||. .||+.||..-++.+|+... .+. ....+|++
T Consensus 76 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHna-~FD~~fL~~~~~~~~~~~~---~~~-----------~~~~lDt~ 140 (189)
T cd06134 76 FAVDEKEALKEIFKPIRKALKAQGCTRAILVGHNA-HFDLGFLNAAVARCKIKRN---PFH-----------PFSTFDTA 140 (189)
T ss_pred cccchHHHHHHHHHHHHHHHhhcccCCCeEEEecc-hhhHHHHHHHHHHhCCCCC---CCC-----------CCcEEEHH
Confidence 12345567788888776531 258999998 6999999998888887410 000 12368999
Q ss_pred HHHhhccCCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 380 AWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 380 ~~vkrd~~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
.+.+.- .++++|++++.. +|....... .+-.+.||.+|..|+.++
T Consensus 141 ~la~~~----~~~~~L~~l~~~-~gi~~~~~~---------------~H~Al~DA~ata~lf~~l 185 (189)
T cd06134 141 TLAGLA----YGQTVLAKACQA-AGIEFDNKE---------------AHSALYDTQKTAELFCKI 185 (189)
T ss_pred HHHHHH----hCCCcHHHHHHH-CCCCCCCCC---------------CcChHHHHHHHHHHHHHH
Confidence 888763 256899999985 676421100 133568999999999876
No 75
>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=97.36 E-value=0.0039 Score=86.11 Aligned_cols=156 Identities=22% Similarity=0.253 Sum_probs=99.7
Q ss_pred eEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEE-cccccc--cccccccCCCCCCCCC--ceEEecCCCHHHHH
Q 000161 240 HVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLII-NRECVG--EDIEDLEYTPKPEFEG--YFKVTNVNNEIELL 314 (1988)
Q Consensus 240 rvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~-nreivs--~di~~feytp~~~~~g--~f~V~~~~dE~eLL 314 (1988)
+.+++|+||++. +|..|+|+.|+++.-.+|.++. -...+. ..|..+- ....| +-.+...+...+++
T Consensus 1 ~~vvvD~ETTG~-----~~~~~~IIeig~v~v~~~~i~~~f~~~v~P~~~i~~~~----~~ltGIt~e~l~~ap~~~ev~ 71 (850)
T TIGR01407 1 RYAVVDLETTGT-----QLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFI----QELTGISDNMLQQAPYFSQVA 71 (850)
T ss_pred CEEEEEEECCCC-----CCCCCeEEEEEEEEEECCEEEEEEEEEeCCCCCCChhh----hhhcCcCHHHHhCCCCHHHHH
Confidence 367899999984 3567999999987433333220 000000 0010000 00112 01133457888999
Q ss_pred HHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCCCC
Q 000161 315 RLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQG 394 (1988)
Q Consensus 315 ~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~Sys 394 (1988)
..|.+++.. .++||||. .||++||..-+..+|++.+ ....+|++.+.+.- +....+|+
T Consensus 72 ~~l~~~l~~---~~~VahN~-~fD~~fL~~~~~~~g~~~~-----------------~~~~iDt~~l~~~~-~p~~~~~~ 129 (850)
T TIGR01407 72 QEIYDLLED---GIFVAHNV-HFDLNFLAKALKDCGYEPL-----------------PKPRIDTVELAQIF-FPTEESYQ 129 (850)
T ss_pred HHHHHHhCC---CEEEEeCc-HHHHHHHHHHHHHcCCCCC-----------------CCCeEeHHHHHHHh-cCCCCCCC
Confidence 999999853 68999998 6999999998888887632 11357888777653 22347899
Q ss_pred HHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 395 LKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 395 L~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
|.+++++ +|..... ++-.+.||.+|..|+.++
T Consensus 130 L~~l~~~-~gi~~~~-----------------~H~Al~DA~ata~l~~~l 161 (850)
T TIGR01407 130 LSELSEA-LGLTHEN-----------------PHRADSDAQATAELLLLL 161 (850)
T ss_pred HHHHHHH-CCCCCCC-----------------CCChHHHHHHHHHHHHHH
Confidence 9999997 7754321 133568999999998875
No 76
>PRK05168 ribonuclease T; Provisional
Probab=97.31 E-value=0.0037 Score=72.42 Aligned_cols=163 Identities=22% Similarity=0.237 Sum_probs=99.5
Q ss_pred CCCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEE-cC--CceEEEcccccccccccccCCCC-----C----CCCCce-
Q 000161 236 RAEVHVCAFDIETTKLPLKFPDADYDIIMMISYML-DG--QGYLIINRECVGEDIEDLEYTPK-----P----EFEGYF- 302 (1988)
Q Consensus 236 ~p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~-~~--~g~li~nreivs~di~~feytp~-----~----~~~g~f- 302 (1988)
.-+...++||+||++. +|..|+|+.|+.+. .+ +|.+.+.. .......|. | ...|-.
T Consensus 14 ~~~~~~vv~D~ETTGl-----~~~~d~IieIgaV~v~~d~~g~i~~~~------~f~~lv~P~~~~~i~~~~~~ihGIt~ 82 (211)
T PRK05168 14 FRGFLPVVIDVETAGF-----NAKTDALLEIAAVTLKMDEQGWLYPDE------TLHFHVEPFEGANLEPEALAFNGIDP 82 (211)
T ss_pred hcCCceEEEEeeCCCC-----CCCCCEEEEEeEEEEEecCCCcEeccc------eEEEEECCCCCCCCCHHHHhhcCCCc
Confidence 5577889999999984 45679999999773 21 23221100 001112221 0 011210
Q ss_pred --EEecCCCHHHHHHHHHHHHHhh------CCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccce
Q 000161 303 --KVTNVNNEIELLRLWFAHMQEV------KPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFAC 374 (1988)
Q Consensus 303 --~V~~~~dE~eLL~~F~~~I~~~------DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRi 374 (1988)
.+.....+.+.+..|++++.+. +=.++||||. .||+.||..-++++|+... .+. ..-
T Consensus 83 e~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa-~FD~~fL~~~~~r~~~~~~---~~~-----------~~~ 147 (211)
T PRK05168 83 DNPLRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNA-HFDLSFLMAAAERAGLKRN---PFH-----------PFS 147 (211)
T ss_pred hhhhhcCCChHHHHHHHHHHHHHHHHhcccCCceEEEecc-HHhHHHHHHHHHHhCCCCC---CCC-----------CCc
Confidence 0112245667788888887643 1258999998 6999999999988887410 000 112
Q ss_pred EechHHHHhhccCCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 375 HLDCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 375 hiDl~~~vkrd~~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
.+|+..+.+.- + +.++|++++.. +|...... -.+-.+.||.+|..|+.++
T Consensus 148 ~iDt~~lar~~-~---~~~~L~~l~~~-~gl~~~~~---------------~~H~Al~DA~ata~l~~~l 197 (211)
T PRK05168 148 TFDTATLSGLA-L---GQTVLAKACQA-AGIEFDNK---------------EAHSALYDTEKTAELFCEI 197 (211)
T ss_pred EeeHHHHHHHH-c---CCCCHHHHHHH-CCCCCCCC---------------CCCChHHHHHHHHHHHHHH
Confidence 78999888763 2 45789999985 66532110 0133567999999998876
No 77
>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=97.31 E-value=0.0046 Score=71.12 Aligned_cols=160 Identities=23% Similarity=0.280 Sum_probs=95.8
Q ss_pred ceEEEEEEEEccCCCCCCCCCCCeEEEEEEEE-c--CCceEEEcccccccccccccCCCCCC---------CCCce---E
Q 000161 239 VHVCAFDIETTKLPLKFPDADYDIIMMISYML-D--GQGYLIINRECVGEDIEDLEYTPKPE---------FEGYF---K 303 (1988)
Q Consensus 239 lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~-~--~~g~li~nreivs~di~~feytp~~~---------~~g~f---~ 303 (1988)
..-++||+||++. +|..|+|+.|+.+. . ++|.+.. .+...+-+.|.|. ..|-. .
T Consensus 8 ~~~vv~D~ETTGl-----~~~~d~IieIgav~v~~~~~g~i~~------~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~ 76 (200)
T TIGR01298 8 YLPVVVDVETGGF-----NAKTDALLEIAAITLKMDEQGWLFP------DTTLHFHVEPFEGANIQPEALEFTGIDLDHP 76 (200)
T ss_pred CeeEEEEeeCCCC-----CCCCCeEEEEEEEEEEEcCCCcEee------cceeEEEEcCCCCCCCCHHHHHccCCChhhh
Confidence 4457899999984 46679999999763 2 2232210 0001111222211 11211 0
Q ss_pred EecCCCHHHHHHHHHHHHHhh------CCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEec
Q 000161 304 VTNVNNEIELLRLWFAHMQEV------KPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLD 377 (1988)
Q Consensus 304 V~~~~dE~eLL~~F~~~I~~~------DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiD 377 (1988)
+.....+.+.+.+|+.++.++ +-.++||||.. ||+.||..=++.+|.... ... ....+|
T Consensus 77 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHNa~-FD~~fL~~~~~r~~~~~~---~~~-----------~~~~lD 141 (200)
T TIGR01298 77 LRGAVSEYEALHEIFKVVRKAMKASGCQRAILVGHNAN-FDLGFLNAAVERTSLKRN---PFH-----------PFSTFD 141 (200)
T ss_pred hhcCcchHHHHHHHHHHHHHHHHhcccCCCEEEEECch-hhHHHHHHHHHHhCCCCC---CCC-----------CCcEEE
Confidence 122345556777777777432 23589999985 999999888888776410 000 113689
Q ss_pred hHHHHhhccCCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 378 CFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 378 l~~~vkrd~~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
++.+.+.. + ++++|+++++. +|...... -.+-.+.||.+|..|+.++
T Consensus 142 Tl~lar~~-~---~~~~L~~l~~~-~gi~~~~~---------------~~H~Al~Da~ata~lf~~l 188 (200)
T TIGR01298 142 TATLAGLA-Y---GQTVLAKACQA-AGXDFDST---------------QAHSALYDTEKTAELFCEI 188 (200)
T ss_pred HHHHHHHH-c---CcccHHHHHHH-cCCCcccc---------------chhhhHHhHHHHHHHHHHH
Confidence 99988762 2 56799999995 67542110 1234578999999998876
No 78
>PRK11779 sbcB exonuclease I; Provisional
Probab=97.17 E-value=0.0015 Score=83.59 Aligned_cols=166 Identities=19% Similarity=0.126 Sum_probs=96.4
Q ss_pred CCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEE-cCCceE------EEcccccccccccccCCCCCCC---CCce--EE
Q 000161 237 AEVHVCAFDIETTKLPLKFPDADYDIIMMISYML-DGQGYL------IINRECVGEDIEDLEYTPKPEF---EGYF--KV 304 (1988)
Q Consensus 237 p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~-~~~g~l------i~nreivs~di~~feytp~~~~---~g~f--~V 304 (1988)
.+.+.+.||+||++. +|..|+|+.|+.+. ++++.. ..++.- . .+.|.|+. .|-. .+
T Consensus 4 ~~~~fvv~D~ETTGL-----dP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~--~-----~~lp~p~a~~IhGIT~e~l 71 (476)
T PRK11779 4 MQPTFLWHDYETFGA-----NPALDRPAQFAGIRTDADLNIIGEPLVFYCKPA--D-----DYLPSPEAVLITGITPQEA 71 (476)
T ss_pred CCCcEEEEEEECCCC-----CCCCCeeEEEEEEEEeCCCceecceeEEEEcCC--c-----CcCCCHHHHHHhCCCHHHH
Confidence 467789999999985 57889999999874 332211 111110 0 01111110 1100 11
Q ss_pred e-cCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHh
Q 000161 305 T-NVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVK 383 (1988)
Q Consensus 305 ~-~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vk 383 (1988)
. ...+|.+++..|.+++.. ...++||||...||+.||..-+....++.... .+. .|...+|++..++
T Consensus 72 ~~~g~~e~e~~~~i~~~l~~-~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~-~~~----------~~n~r~D~LDl~r 139 (476)
T PRK11779 72 LEKGLPEAEFAARIHAEFSQ-PGTCILGYNNIRFDDEVTRYIFYRNFYDPYAR-EWQ----------NGNSRWDLLDVVR 139 (476)
T ss_pred HhcCCCHHHHHHHHHHHHhc-CCCEEEEeCchhhcHHHHHHHHHhccchHHHH-Hhc----------CCCCccCHHHHHH
Confidence 1 123688999999998863 23689999999999999988776554442100 000 1222234444444
Q ss_pred hcc-------CCC-----CCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 384 RDS-------YLP-----QGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 384 rd~-------~L~-----~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
... ..| ..||+|++++++ +|..... ++=.+.||.+|..|+.++
T Consensus 140 l~~~lrp~~i~~P~~~~g~~s~rLe~L~~~-~gI~~~~-----------------AHdALsDa~aT~~la~~l 194 (476)
T PRK11779 140 ACYALRPEGINWPENEDGLPSFKLEHLTKA-NGIEHEN-----------------AHDAMSDVYATIAMAKLI 194 (476)
T ss_pred HHHHhccccccCcccccCCCCCcHHHHHHH-cCCCCCC-----------------CCCcHHHHHHHHHHHHHH
Confidence 211 111 378999999997 5653211 133578999999988865
No 79
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=97.12 E-value=0.0068 Score=69.99 Aligned_cols=169 Identities=18% Similarity=0.118 Sum_probs=99.1
Q ss_pred CceEEEEEEEEccCCC-CCCCCCCCeEEEEEEEEcCCceEEE-cccccccccccccCCCC-CCCCC--ceEEecCCCHHH
Q 000161 238 EVHVCAFDIETTKLPL-KFPDADYDIIMMISYMLDGQGYLII-NRECVGEDIEDLEYTPK-PEFEG--YFKVTNVNNEIE 312 (1988)
Q Consensus 238 ~lrvLsfDIEt~s~~~-~fPdp~~D~Ii~IS~~~~~~g~li~-nreivs~di~~feytp~-~~~~g--~f~V~~~~dE~e 312 (1988)
+.+.++||+||++... .-|....|+|+.|+.+.-..|.++. -...|...... ..+|. ....| +-.|...++..+
T Consensus 3 ~~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~~i~~~f~~lV~P~~~~-~i~~~~~~ltGIt~~~l~~ap~~~e 81 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCEVEDTFSSYVKPKTFP-SLTERCKSFLGITQEDVDKGISFEE 81 (207)
T ss_pred cceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecCcChhhhcceECCCccC-ccChhhhhhcCcCHHHHccCCCHHH
Confidence 5678999999997532 3344345899999976422222110 00000000000 00000 01112 112445678899
Q ss_pred HHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCC
Q 000161 313 LLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGS 392 (1988)
Q Consensus 313 LL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~S 392 (1988)
.+.+|.+++... +.++++| + .||+.||..-++.+|++.. + ....+|+....++. +-...+
T Consensus 82 vl~~f~~~~~~~-~~~iv~~-~-~fD~~fL~~~~~~~~~~~~----~------------~~~~~dl~~~~~~~-~~~~~~ 141 (207)
T PRK07748 82 LVEKLAEYDKRC-KPTIVTW-G-NMDMKVLKHNCEKAGVPFP----F------------KGQCRDLSLEYKKF-FGERNQ 141 (207)
T ss_pred HHHHHHHHhCcC-CeEEEEE-C-HHHHHHHHHHHHHcCCCCc----c------------cccceeHHHHHHHH-hCcCCC
Confidence 999999999753 2366766 4 6999999999998887531 0 02346776655542 212356
Q ss_pred CCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 393 QGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 393 ysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
++|+++++. +|.....- .+-.+.||..|..|+.++
T Consensus 142 ~~L~~~~~~-~gi~~~~~----------------~H~Al~DA~~ta~l~~~l 176 (207)
T PRK07748 142 TGLWKAIEE-YGKEGTGK----------------HHCALDDAMTTYNIFKLV 176 (207)
T ss_pred CCHHHHHHH-cCCCCCCC----------------CcChHHHHHHHHHHHHHH
Confidence 899999985 77543210 123578999999999987
No 80
>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=97.08 E-value=0.0024 Score=70.11 Aligned_cols=147 Identities=20% Similarity=0.200 Sum_probs=80.9
Q ss_pred EEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEccccccc-ccccccCCCCCCCCC--ceEEecCCCHHHHHHHHH
Q 000161 242 CAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGE-DIEDLEYTPKPEFEG--YFKVTNVNNEIELLRLWF 318 (1988)
Q Consensus 242 LsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~-di~~feytp~~~~~g--~f~V~~~~dE~eLL~~F~ 318 (1988)
+++|+||++.. |+....+|..|++. +.+|..+.+.-+-.. .+.++ .....| +-.+...++..+.+.+|.
T Consensus 1 v~lD~EttGl~---~~~~~~~i~~v~~v-~~~~~~~~~~~v~P~~~i~~~----~~~ihGIt~~~v~~a~~~~~~~~~l~ 72 (152)
T cd06144 1 VALDCEMVGVG---PDGSESALARVSIV-NEDGNVVYDTYVKPQEPVTDY----RTAVSGIRPEHLKDAPDFEEVQKKVA 72 (152)
T ss_pred CEEEEEeeccc---CCCCEEEEEEEEEE-eCCCCEEEEEEECCCCCCCcc----cccCCCCCHHHHcCCCCHHHHHHHHH
Confidence 47999999853 32223455566655 334432221111000 00000 001122 112456778899999999
Q ss_pred HHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhh-ccCCCCCCCCHHH
Q 000161 319 AHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKR-DSYLPQGSQGLKA 397 (1988)
Q Consensus 319 ~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkr-d~~L~~~SysL~~ 397 (1988)
+++.. .++||||. .||+.+|. .+.+ + ...+|+..+... ..+ +..+|+|++
T Consensus 73 ~~l~~---~vlVgHn~-~fD~~~L~-----~~~~---------~----------~~~~dt~~l~~~~~~~-~~~~~sL~~ 123 (152)
T cd06144 73 ELLKG---RILVGHAL-KNDLKVLK-----LDHP---------K----------KLIRDTSKYKPLRKTA-KGKSPSLKK 123 (152)
T ss_pred HHhCC---CEEEEcCc-HHHHHHhc-----CcCC---------C----------ccEEEeEEeecccccc-CCCChhHHH
Confidence 99863 79999999 69999984 1110 0 012333322111 111 137899999
Q ss_pred HHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHH
Q 000161 398 VTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLY 441 (1988)
Q Consensus 398 Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~ 441 (1988)
+|+.+||..... + ..-.+.||.+|..||
T Consensus 124 l~~~~lgi~~~~-~---------------~H~Al~DA~at~~l~ 151 (152)
T cd06144 124 LAKQLLGLDIQE-G---------------EHSSVEDARAAMRLY 151 (152)
T ss_pred HHHHHcCcccCC-C---------------CcCcHHHHHHHHHHh
Confidence 999888965321 0 022467898888886
No 81
>cd05532 POLBc_alpha DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. In most organisms no specific repair role, other than check point control, has been assigned to this enzyme. Pol alpha contains both polymerase and exonuclease domains, but lacks exonuclease activity suggesting that the exonuclease domain may be for structural purposes only.
Probab=97.01 E-value=0.0051 Score=77.81 Aligned_cols=111 Identities=15% Similarity=0.293 Sum_probs=101.2
Q ss_pred HHHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHhHcCCeEEEEeCCeEEEEcCCCChHhHHHHHHHHHHHhh
Q 000161 1568 AILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFAMLLAEFRKLGATIIFANFSKVIIDTGKFDLSAAKAYCDSLLKALQ 1647 (1988)
Q Consensus 1568 ~ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~flqLlaEfkRLGs~VVyAd~~riil~T~K~~v~~A~ay~~yi~~si~ 1647 (1988)
.+++.+|-++....|.+|++.++..|-..=+..+.+...-++..|.+|||+|-..|.|..+..+.+++...++-+.+.|.
T Consensus 112 i~~NS~YG~~g~~~~r~~~~~~A~~iT~~GR~~l~~~~~~~e~~g~~ViYgDTDSifv~~~~~~~~~~~~~~~~i~~~in 191 (400)
T cd05532 112 LTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKMNLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEVN 191 (400)
T ss_pred HHHhhcccccccccccccChHHHHHHHHHHHHHHHHHHHHHHHcCCEEEEeCCCeEEEecCCCCHHHHHHHHHHHHHHHH
Confidence 45689999999999999999999999999999999999999999999999999999999999999999999888888776
Q ss_pred ccccccceecchhchheeeeeecCCCccccccc
Q 000161 1648 TRELFEWIELEPVHFWHSLLFMDQYNYGGIPAR 1680 (1988)
Q Consensus 1648 ~~~lF~~l~L~~~~yW~~LlwmD~~NygGi~~~ 1680 (1988)
+. |..|.|+....|..++|+-+-+|.|+...
T Consensus 192 ~~--~~~i~le~e~iy~~~ll~~KKrYag~~~~ 222 (400)
T cd05532 192 KS--YKKLEIDIDGVFKRLLLLKKKKYAALKVV 222 (400)
T ss_pred HH--HHHHHHHHHHHhHHHHhhhhhcceEEEee
Confidence 64 55799999999999999999999998653
No 82
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.95 E-value=0.0065 Score=83.26 Aligned_cols=151 Identities=18% Similarity=0.238 Sum_probs=97.3
Q ss_pred CceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEE-cccccccccccccCCCCCC-------CCC--ceEEecC
Q 000161 238 EVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLII-NRECVGEDIEDLEYTPKPE-------FEG--YFKVTNV 307 (1988)
Q Consensus 238 ~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~-nreivs~di~~feytp~~~-------~~g--~f~V~~~ 307 (1988)
.-+.+++|+||++.. + .|+|+.|+++.-.+|.++. -...| .|... ..| +-.+...
T Consensus 6 ~~~~vvvD~ETTGl~-----~-~d~IIeIgaV~v~~g~i~~~f~~lv---------~P~~~i~~~~~~ltGIt~e~l~~a 70 (820)
T PRK07246 6 LRKYAVVDLEATGAG-----P-NASIIQVGIVIIEGGEIIDSYTTDV---------NPHEPLDEHIKHLTGITDQQLAQA 70 (820)
T ss_pred CCCEEEEEEecCCcC-----C-CCeEEEEEEEEEECCEEEEEEEEEe---------CcCCCCCHhHhhcCCCCHHHHhcC
Confidence 346889999999842 2 4899999987433333220 00000 11111 112 1124456
Q ss_pred CCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccC
Q 000161 308 NNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSY 387 (1988)
Q Consensus 308 ~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~ 387 (1988)
+...+++.+|.+++.. .++||||. .||++||.+-+...|.+.. ...+|++.+.+.. +
T Consensus 71 p~~~ev~~~~~~~l~~---~~lVaHN~-~FD~~fL~~~~~~~g~~~~------------------~~~iDT~~la~~~-~ 127 (820)
T PRK07246 71 PDFSQVARHIYDLIED---CIFVAHNV-KFDANLLAEALFLEGYELR------------------TPRVDTVELAQVF-F 127 (820)
T ss_pred CCHHHHHHHHHHHhCC---CEEEEECc-HHHHHHHHHHHHHcCCCCC------------------CCceeHHHHHHHH-h
Confidence 7888999999999864 68999998 6999999776655555421 0237888877763 2
Q ss_pred CCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 388 LPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 388 L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
-..++|+|++++.+ ||..... .+-.+.||.+|..|+.++
T Consensus 128 p~~~~~~L~~L~~~-lgl~~~~-----------------~H~Al~DA~ata~L~~~l 166 (820)
T PRK07246 128 PTLEKYSLSHLSRE-LNIDLAD-----------------AHTAIADARATAELFLKL 166 (820)
T ss_pred CCCCCCCHHHHHHH-cCCCCCC-----------------CCCHHHHHHHHHHHHHHH
Confidence 22478999999996 7764321 133568999999998875
No 83
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=96.75 E-value=0.013 Score=64.48 Aligned_cols=144 Identities=22% Similarity=0.176 Sum_probs=86.4
Q ss_pred EEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEccccccc--ccccccCCCCCCCCCce--EEecC-CCHHHHHHH
Q 000161 242 CAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGE--DIEDLEYTPKPEFEGYF--KVTNV-NNEIELLRL 316 (1988)
Q Consensus 242 LsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~--di~~feytp~~~~~g~f--~V~~~-~dE~eLL~~ 316 (1988)
+++|+||++... .++|+.|+.. +..|..+.. ..+.. .|.++ .-...|-. .+... +.+.+.+.+
T Consensus 1 ~~iD~E~~g~~~------g~ei~~i~~v-~~~~~~~f~-~lv~P~~~i~~~----~t~itGIt~~~l~~a~~~~~~v~~~ 68 (150)
T cd06145 1 FALDCEMCYTTD------GLELTRVTVV-DENGKVVLD-ELVKPDGEIVDY----NTRFSGITEEMLENVTTTLEDVQKK 68 (150)
T ss_pred CEEeeeeeeecC------CCEEEEEEEE-eCCCCEEEE-EeECCCCccchh----ccCcCCCCHHHhccCCCCHHHHHHH
Confidence 479999998532 3999999987 344543221 11110 01110 00122311 24444 489999999
Q ss_pred HHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCCCCHH
Q 000161 317 WFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQGLK 396 (1988)
Q Consensus 317 F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~SysL~ 396 (1988)
|.+++..- .++||||. .||+.||.. . . .-.+|+..+.++.. .+..+|+|+
T Consensus 69 ~~~fl~~~--~vlVgHn~-~fD~~fL~~---------------~-~----------~~~iDT~~l~r~~~-~~~~~~~L~ 118 (150)
T cd06145 69 LLSLISPD--TILVGHSL-ENDLKALKL---------------I-H----------PRVIDTAILFPHPR-GPPYKPSLK 118 (150)
T ss_pred HHHHhCCC--CEEEEcCh-HHHHHHhhc---------------c-C----------CCEEEcHHhccccC-CCCCChhHH
Confidence 99999621 59999999 499999842 0 0 12478887776532 223589999
Q ss_pred HHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHH
Q 000161 397 AVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLY 441 (1988)
Q Consensus 397 ~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~ 441 (1988)
++|+.++|.....- .+ .+-++.||.+|..||
T Consensus 119 ~L~~~~~~~~i~~~----------~~----~H~Al~DA~~t~~l~ 149 (150)
T cd06145 119 NLAKKYLGRDIQQG----------EG----GHDSVEDARAALELV 149 (150)
T ss_pred HHHHHHCCcceeCC----------CC----CCCcHHHHHHHHHHh
Confidence 99999887432110 00 123467888888775
No 84
>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=96.70 E-value=0.026 Score=62.74 Aligned_cols=159 Identities=18% Similarity=0.099 Sum_probs=96.3
Q ss_pred EEEEEEEccCCCCC-CCCCCCeEEEEEEE-EcCCce-EE-EcccccccccccccCCCCC--C-------CCC--ceEEec
Q 000161 242 CAFDIETTKLPLKF-PDADYDIIMMISYM-LDGQGY-LI-INRECVGEDIEDLEYTPKP--E-------FEG--YFKVTN 306 (1988)
Q Consensus 242 LsfDIEt~s~~~~f-Pdp~~D~Ii~IS~~-~~~~g~-li-~nreivs~di~~feytp~~--~-------~~g--~f~V~~ 306 (1988)
+.||+||++....- | ...++|+.||.+ +++++. .+ .....+ .|.. . ..| .-.+..
T Consensus 2 vv~D~Ettg~~~~~~~-~~~~~IieIgav~v~~~~~~~~~~f~~~i---------~P~~~~~i~~~~~~i~gIt~e~l~~ 71 (176)
T cd06133 2 LVIDFEATCWEGNSKP-DYPNEIIEIGAVLVDVKTKEIIDTFSSYV---------KPVINPKLSDFCTELTGITQEDVDN 71 (176)
T ss_pred EEEEeeccccCCCCCC-CCCcceEEEEEEEEEcCCCeEEeeeeeeE---------CCCcCCchhHHHHHhcCcCHHHHhc
Confidence 67999999853110 0 124899999986 344432 11 000000 1111 0 011 001345
Q ss_pred CCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhcc
Q 000161 307 VNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDS 386 (1988)
Q Consensus 307 ~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~ 386 (1988)
.....+.+.+|.+++....+.++++|+ .||+.+|...+...+.... .. ...-.+|+...++...
T Consensus 72 ~~~~~~vl~~~~~~l~~~~~~~~v~~~--~~d~~~l~~~~~~~~~~~~---~~-----------~~~~~~D~~~~~~~~~ 135 (176)
T cd06133 72 APSFPEVLKEFLEWLGKNGKYAFVTWG--DWDLKDLLQNQCKYKIINL---PP-----------FFRQWIDLKKEFAKFY 135 (176)
T ss_pred CCCHHHHHHHHHHHHHhCCCeEEEeec--HhhHHHHHHHHHHhcCCCC---cc-----------cccceEEHHHHHHHHh
Confidence 678999999999999885445677775 6999999988887765310 00 1234578887777632
Q ss_pred CCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 387 YLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 387 ~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
.. ..+++|++++++ +|.....- .+-.+.||.+|..|+.++
T Consensus 136 ~~-~~~~~L~~l~~~-~gi~~~~~----------------~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 136 GL-KKRTGLSKALEY-LGLEFEGR----------------HHRGLDDARNIARILKRL 175 (176)
T ss_pred CC-CCCCCHHHHHHH-CCCCCCCC----------------CcCcHHHHHHHHHHHHHh
Confidence 22 258999999985 67544310 134578999999998764
No 85
>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=96.64 E-value=0.011 Score=65.37 Aligned_cols=148 Identities=19% Similarity=0.151 Sum_probs=84.2
Q ss_pred EEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEccccccc--ccccccCCCCCCCCC--ceEEecCCCHHHHHHHH
Q 000161 242 CAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGE--DIEDLEYTPKPEFEG--YFKVTNVNNEIELLRLW 317 (1988)
Q Consensus 242 LsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~--di~~feytp~~~~~g--~f~V~~~~dE~eLL~~F 317 (1988)
++||+||++.. |....++|+.|+.+.. +|..+.. .+|-. .|.++. ..+.| +-.+...++-.+++.+|
T Consensus 1 v~~D~EttGl~---~~~~~~~i~~i~~v~~-~g~~~~~-~lv~P~~~i~~~~----~~i~GIt~~~l~~a~~~~~v~~~l 71 (157)
T cd06149 1 VAIDCEMVGTG---PGGRESELARCSIVNY-HGDVLYD-KYIRPEGPVTDYR----TRWSGIRRQHLVNATPFAVAQKEI 71 (157)
T ss_pred CEEEeEecccc---CCCCeEEEEEEEEEeC-CCCEEEE-EeECCCCccCccc----eECCCCCHHHHhcCCCHHHHHHHH
Confidence 47999999853 3323588888887753 3433211 11100 010000 01112 11244567888999999
Q ss_pred HHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHH--HHhhccCCC-CCCCC
Q 000161 318 FAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFA--WVKRDSYLP-QGSQG 394 (1988)
Q Consensus 318 ~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~--~vkrd~~L~-~~Sys 394 (1988)
.+++.. .++||||. .||+.+|... . . + -..+|+.. ..++....| ..+|+
T Consensus 72 ~~~l~~---~vlV~Hn~-~~D~~~l~~~-------~------~-~----------~~~~Dt~~l~~~~~~~~~p~~~~~~ 123 (157)
T cd06149 72 LKILKG---KVVVGHAI-HNDFKALKYF-------H------P-K----------HMTRDTSTIPLLNRKAGFPENCRVS 123 (157)
T ss_pred HHHcCC---CEEEEeCc-HHHHHHhccc-------C------C-C----------cCEEECcccccchhhcCCcccCChh
Confidence 999964 59999997 6899998522 0 0 0 01234332 233322122 36799
Q ss_pred HHHHHHHHcCCCCCC-CChHHHHHHHhhChHHHHHHHHHhhHHHHHHH
Q 000161 395 LKAVTKAKLGYDPLE-VNPEDMVRFAKEKPQMMASYSVSDAVATYYLY 441 (1988)
Q Consensus 395 L~~Va~~~LG~~K~d-vd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~ 441 (1988)
|+++++.++|.+-.. .. ..-++.||.+|..||
T Consensus 124 L~~L~~~~~~~~i~~~~~---------------~H~Al~DA~at~~l~ 156 (157)
T cd06149 124 LKVLAKRLLHRDIQVGRQ---------------GHSSVEDARATMELY 156 (157)
T ss_pred HHHHHHHHcChhhcCCCC---------------CcCcHHHHHHHHHHh
Confidence 999999988653221 10 133567999998886
No 86
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=96.57 E-value=0.033 Score=76.34 Aligned_cols=111 Identities=14% Similarity=0.228 Sum_probs=100.8
Q ss_pred HHHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHhHcCCeEEEEeCCeEEEEcCCCChHhHHHHHHHHHHHhh
Q 000161 1568 AILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFAMLLAEFRKLGATIIFANFSKVIIDTGKFDLSAAKAYCDSLLKALQ 1647 (1988)
Q Consensus 1568 ~ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~flqLlaEfkRLGs~VVyAd~~riil~T~K~~v~~A~ay~~yi~~si~ 1647 (1988)
.+++.+|--+-.+.|.+|++.++..|-..-++++.+-..-..++|.+|||.|-..|.+.++....++|..=++=+.+-|.
T Consensus 510 vl~NS~YGy~G~~~~rf~~~e~a~~VT~~gR~ii~~t~~~ae~~G~~ViyGDTDSlfv~~~~~~~~ea~~~~~~l~~~vn 589 (792)
T COG0417 510 VLANSFYGYLGYSNSRFYCIECAESVTAFGREILRETKELAEEMGLRVIYGDTDSLFVTLPGATYEEAIKIGEELVEEVN 589 (792)
T ss_pred HHHhhccccccccCCccCCHHHHHHHHHHHHHHHHHHHHHHHHcCCEEEEECCceeEEEcCCCchHHHHHHHHHHHHHHh
Confidence 45679999999999999999999999999999999999999999999999999999999997778888877777777777
Q ss_pred ccccccceecchhchheeeeeec-CCCcccccc
Q 000161 1648 TRELFEWIELEPVHFWHSLLFMD-QYNYGGIPA 1679 (1988)
Q Consensus 1648 ~~~lF~~l~L~~~~yW~~LlwmD-~~NygGi~~ 1679 (1988)
++ +=+.|+|+....|+.+++.. +-+|+|+..
T Consensus 590 ~~-~~~~i~lE~e~~y~~~ll~~~KKRYag~~~ 621 (792)
T COG0417 590 ER-LPSGIELEVEKVYKRFLLPTAKKRYAGLLE 621 (792)
T ss_pred hc-CCCCeEEEeeehhhhhhccccccceEEEec
Confidence 76 66689999999999999999 999999854
No 87
>PRK05762 DNA polymerase II; Reviewed
Probab=96.35 E-value=0.021 Score=78.12 Aligned_cols=113 Identities=17% Similarity=0.255 Sum_probs=100.5
Q ss_pred HHHHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHhHcCCeEEEEeCCeEEEEcC-CCChHhHHHHHHHHHHH
Q 000161 1567 DAILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFAMLLAEFRKLGATIIFANFSKVIIDTG-KFDLSAAKAYCDSLLKA 1645 (1988)
Q Consensus 1567 D~ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~flqLlaEfkRLGs~VVyAd~~riil~T~-K~~v~~A~ay~~yi~~s 1645 (1988)
=.+++.+|-++-++.|.+|+|.+...|-..=+..+.+...-.+.+|.+|||+|-..|.|.++ ..+.++|...++-|.+.
T Consensus 494 Ki~~Ns~YG~~g~~~~r~~~~~~A~~it~~Gr~~l~~~~~~~~~~g~~viYgDTDSifv~~~~~~~~~~~~~~~~~l~~~ 573 (786)
T PRK05762 494 KIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQGYQVIYGDTDSTFVWLGGAHDEEDAAKIGRALVQE 573 (786)
T ss_pred HhhhhhcccccccccccccChHHHHHHHHhHHHHHHHHHHHHHHCCCEEEeecCCceEEEcCCCCCHHHHHHHHHHHHHH
Confidence 45678999999999999999999999999999999999999999999999999999999998 67899999888888888
Q ss_pred hhcc---------ccccceecchhchheeeeee--------cCCCcccccc
Q 000161 1646 LQTR---------ELFEWIELEPVHFWHSLLFM--------DQYNYGGIPA 1679 (1988)
Q Consensus 1646 i~~~---------~lF~~l~L~~~~yW~~Llwm--------D~~NygGi~~ 1679 (1988)
|.+. .+-..|.|+....|..++|. -+-+|+|+..
T Consensus 574 in~~~~~~l~~~~~~~~~l~le~E~vy~~~~l~~~rg~~~~~KKrYag~~~ 624 (786)
T PRK05762 574 INQWWQEHLQQEFGLESALELEFEKHYRRFFMPTIRGAEEGSKKRYAGLIQ 624 (786)
T ss_pred HHHHHHhhhhhhccCCCceEEEEeeeeehhccccccccchhhhheEEEEEE
Confidence 8763 23456999999999999994 8999999974
No 88
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=96.27 E-value=0.032 Score=67.87 Aligned_cols=152 Identities=20% Similarity=0.163 Sum_probs=78.8
Q ss_pred CCCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEE-c--CCceEEEcccccccccccccCCCCCCC-------CCce--E
Q 000161 236 RAEVHVCAFDIETTKLPLKFPDADYDIIMMISYML-D--GQGYLIINRECVGEDIEDLEYTPKPEF-------EGYF--K 303 (1988)
Q Consensus 236 ~p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~-~--~~g~li~nreivs~di~~feytp~~~~-------~g~f--~ 303 (1988)
.++.+++.+|+||++. ||..|+|+.|+.+. + .+|.+.. +.+. ..+-..|.... .|-. .
T Consensus 34 ~~~~~~vvlD~ETTGL-----d~~~d~IIEIg~V~v~~~~~g~i~~----v~~~-~~~lv~P~~~I~~~~t~IhGIt~e~ 103 (294)
T PRK09182 34 EFVRLGVILDTETTGL-----DPRKDEIIEIGMVAFEYDDDGRIGD----VLDT-FGGLQQPSRPIPPEITRLTGITDEM 103 (294)
T ss_pred CCCCeEEEEEeeCCCC-----CCCCCeEEEEEEEEEEecCCCceee----eeeE-EEEEeCCCCCCCHHHHHhcCCCHHH
Confidence 3455789999999985 46789999999763 2 1332210 0000 00000121111 1100 0
Q ss_pred EecCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHh
Q 000161 304 VTNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVK 383 (1988)
Q Consensus 304 V~~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vk 383 (1988)
+...+... ..|.+++.. -+++|+||. .||++||......+.-.. +. ..+....|..
T Consensus 104 v~~~~~~~---~~l~~fl~~--~~vlVAHNA-~FD~~fL~~~~~~~~~~~--------------~~----ct~~~i~~~~ 159 (294)
T PRK09182 104 VAGQTIDP---AAVDALIAP--ADLIIAHNA-GFDRPFLERFSPVFATKP--------------WA----CSVSEIDWSA 159 (294)
T ss_pred HhcCCCcH---HHHHHHhcC--CCEEEEeCH-HHHHHHHHHHHHhccCCc--------------cc----ccHHHHhhcc
Confidence 11111111 233334433 379999998 799999976543321111 00 0112222321
Q ss_pred hccCCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 384 RDSYLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 384 rd~~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
..+++++|++++.+ +|.. .+ ++-.+.||.+|..|+...
T Consensus 160 ----~~~~~~kL~~La~~-~g~~---~~---------------aHrAl~Da~Ata~ll~~~ 197 (294)
T PRK09182 160 ----RGFEGTKLGYLAGQ-AGFF---HE---------------GHRAVDDCQALLELLARP 197 (294)
T ss_pred ----ccCCCCCHHHHHHH-cCCC---CC---------------CcChHHHHHHHHHHHHHH
Confidence 12478999999996 6621 11 133578999999988753
No 89
>cd05537 POLBc_Pol_II DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Probab=96.21 E-value=0.042 Score=68.92 Aligned_cols=135 Identities=18% Similarity=0.288 Sum_probs=105.6
Q ss_pred HHHHHHHHHHHHHHHhc---CCc---c-HHHHHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHhHcCCeEEE
Q 000161 1545 RVVKQLIQRCLTDAVTS---GNV---F-ADAILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFAMLLAEFRKLGATIIF 1617 (1988)
Q Consensus 1545 ~iLr~mV~~w~~da~~~---~n~---~-AD~ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~flqLlaEfkRLGs~VVy 1617 (1988)
.||..+|+.|+..-... .+. . -=.+++.+|-++..+.+.+|+|.+...|-.+=+..+......+...|.+|||
T Consensus 68 Gilp~~l~~l~~~R~~~K~~~~~~~q~AlKi~~Ns~YG~~g~~~~r~~~~~~A~~iT~~GR~~l~~~~~~~e~~g~~ViY 147 (371)
T cd05537 68 HILPDLIARLWAARDEAKREKNAPLSQAIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQVIY 147 (371)
T ss_pred CchHHHHHHHHHHHHHHHHhccHHHHHhHhhheecceeecccccccccChHHHHHHHHHHHHHHHHHHHHHHHcCCEEEE
Confidence 67777777777543321 111 1 1234567888888889999999999999999999988888889999999999
Q ss_pred EeCCeEEEEcCC-CChHhHHHHHHHHHHHhhcc---------ccccceecchhchheeeeee--------cCCCcccccc
Q 000161 1618 ANFSKVIIDTGK-FDLSAAKAYCDSLLKALQTR---------ELFEWIELEPVHFWHSLLFM--------DQYNYGGIPA 1679 (1988)
Q Consensus 1618 Ad~~riil~T~K-~~v~~A~ay~~yi~~si~~~---------~lF~~l~L~~~~yW~~Llwm--------D~~NygGi~~ 1679 (1988)
+|-..|.|.++. .+.++|...++.|.+.|.++ ++-..++|+....|..++.. -+-+|.|+..
T Consensus 148 gDTDSvfV~~~~~~~~~~~~~~~~~l~~~In~~~~~~~~~~~~~~~~l~Le~Ekvy~~~ll~~~~~~~~~~KKrYag~~~ 227 (371)
T cd05537 148 GDTDSTFVWLGEELDAAEAQAIGKELASQINQWWAQKLKEEFGLESFLEIEFETHYSRFFMPTIRGSDEGSKKRYAGLKS 227 (371)
T ss_pred ecCCceEEecCCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCCceEEEeeeeeeeeeeccccccccccceEEEEEE
Confidence 999999999986 68899998888888888763 12245888888988877665 5889999854
No 90
>cd05536 POLBc_B3 DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.
Probab=96.21 E-value=0.024 Score=71.19 Aligned_cols=103 Identities=12% Similarity=0.231 Sum_probs=88.5
Q ss_pred HHHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHhHcCCeEEEEeCCeEEEEcCCCC--hHhHHHHHHHHHHH
Q 000161 1568 AILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFAMLLAEFRKLGATIIFANFSKVIIDTGKFD--LSAAKAYCDSLLKA 1645 (1988)
Q Consensus 1568 ~ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~flqLlaEfkRLGs~VVyAd~~riil~T~K~~--v~~A~ay~~yi~~s 1645 (1988)
.+++.+|-++....|.+|++.+...|-..=+..+.+...-+.+.|.+|||+|-..|.|.++..+ .+.+...++.|
T Consensus 109 i~~NS~YG~~g~~~~r~~~~~~A~~iT~~GR~~l~~~~~~i~~~g~~VIYgDTDSvfv~~~~~~~~~~~~~~l~~~i--- 185 (371)
T cd05536 109 ILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIAEEKGFKVIYGDTDSLFVKIDGADAVKKKVKKLLKYI--- 185 (371)
T ss_pred HHHhccccccccccccCCCHHHHHHHHHHHHHHHHHHHHHHHHcCCEEEEEcCcccEEeecCchHHHHHHHHHHHHH---
Confidence 3568899999999999999999999999999999999999999999999999999999998765 34455544444
Q ss_pred hhccccccceecchhchheeeeeecCCCcccc
Q 000161 1646 LQTRELFEWIELEPVHFWHSLLFMDQYNYGGI 1677 (1988)
Q Consensus 1646 i~~~~lF~~l~L~~~~yW~~LlwmD~~NygGi 1677 (1988)
.+. |. +.|+....|+.++|+-+-+|+|+
T Consensus 186 -~~~--~~-i~le~E~vy~~~l~~~KKrY~g~ 213 (371)
T cd05536 186 -NEE--LP-LELEIEKFYKRGFFVTKKRYAGL 213 (371)
T ss_pred -Hhc--CC-eeEEEeeeeHHHHHhhhceeEEE
Confidence 332 33 99999999999999999999997
No 91
>PRK06722 exonuclease; Provisional
Probab=96.17 E-value=0.14 Score=61.89 Aligned_cols=200 Identities=16% Similarity=0.129 Sum_probs=107.6
Q ss_pred eEEEEEEEEccCCCCCCCCCCCeEEEEEEEE-cC-CceEEE-ccccccc--ccccccCCCCCCCCC--ceEEecCCCHHH
Q 000161 240 HVCAFDIETTKLPLKFPDADYDIIMMISYML-DG-QGYLII-NRECVGE--DIEDLEYTPKPEFEG--YFKVTNVNNEIE 312 (1988)
Q Consensus 240 rvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~-~~-~g~li~-nreivs~--di~~feytp~~~~~g--~f~V~~~~dE~e 312 (1988)
++++||+||+..|.. ....|+||.|+.+. ++ .+.++- -...|-. .+..| .....| +-.|...+.-.+
T Consensus 6 ~~vViD~ETT~~p~~--~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~~I~~~----i~~LTGIT~emV~~AP~f~e 79 (281)
T PRK06722 6 HFIVFDIERNFRPYK--SEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGARLTRH----TTKLTGITKKDLIGVEKFPQ 79 (281)
T ss_pred EEEEEEeeCCCCCCC--CCCCCeEEEEEEEEEECCceeEEeeEEEEECCCCcCCHh----HhhhcCCCHHHHcCCCCHHH
Confidence 578899999853321 23448999999764 32 222210 0001100 00000 001112 112445677889
Q ss_pred HHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhcc-CCCCC
Q 000161 313 LLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDS-YLPQG 391 (1988)
Q Consensus 313 LL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~-~L~~~ 391 (1988)
++.+|.+++.. +.++.+|+ .||+.||..-+..+|++... . ...-.+|+.+++.... .+...
T Consensus 80 Vl~ef~~fig~---~~lvahna-~FD~~FL~~~l~~~gi~~p~----~----------~~~~~idl~~la~~~~~~l~~~ 141 (281)
T PRK06722 80 IIEKFIQFIGE---DSIFVTWG-KEDYRFLSHDCTLHSVECPC----M----------EKERRIDLQKFVFQAYEELFEH 141 (281)
T ss_pred HHHHHHHHHCC---CcEEEEEe-HHHHHHHHHHHHHcCCCCCc----c----------cccchhHHHHHHHHHhhhhccC
Confidence 99999999964 33455555 69999999988888875310 0 0011467766654311 11124
Q ss_pred CCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHhccchHhhhhhhcCCChHHH------hh
Q 000161 392 SQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTYVHPFIFSLATIIPMSPDEV------LR 465 (1988)
Q Consensus 392 SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Klv~~~i~~La~i~~l~~~~v------lr 465 (1988)
+++|+++++. +|.....- .+-.+.||..|..|+.++...- -+...+++.++-. |.
T Consensus 142 ~~sL~~l~~~-lgL~~~g~----------------~HrAL~DA~~TA~L~l~l~~~~--~l~~~~~~~~~~~~~~~~~~~ 202 (281)
T PRK06722 142 TPSLQSAVEQ-LGLIWEGK----------------QHRALADAENTANILLKAYSER--DITKRYKRHGELELVKNGKLT 202 (281)
T ss_pred CCCHHHHHHH-CCCCCCCC----------------CcCcHHHHHHHHHHHHHHhccc--chHHHhcCCCCHHHHhhhhhh
Confidence 5789999995 77543210 1335689999999998863211 1333333332222 22
Q ss_pred hhhHHHHHHHHHHHHHH
Q 000161 466 KGSGTLCEMLLMVQAYK 482 (1988)
Q Consensus 466 ~Gsg~~~E~LLm~~a~~ 482 (1988)
+-+-..+...|.++..+
T Consensus 203 ~~~~~~~~~~~~~~~~~ 219 (281)
T PRK06722 203 EKAKKKMRKWVFKEMRK 219 (281)
T ss_pred hccHHHHHHHHHHHHhh
Confidence 33444555666666544
No 92
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=96.10 E-value=0.073 Score=62.79 Aligned_cols=159 Identities=21% Similarity=0.261 Sum_probs=100.8
Q ss_pred ceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEcc--cccccc--cccccCCCCCCCCCceE---EecCCCHH
Q 000161 239 VHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINR--ECVGED--IEDLEYTPKPEFEGYFK---VTNVNNEI 311 (1988)
Q Consensus 239 lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nr--eivs~d--i~~feytp~~~~~g~f~---V~~~~dE~ 311 (1988)
.+...||+||++. ++..|.|+.|+.+.-.++.+.... ..+..+ |... .....| ++ +...+.=.
T Consensus 13 ~~~vv~D~ETtg~-----~~~~~~iieIgav~~~~~~i~~~~~~~~v~P~~~i~~~----~~~i~g-it~e~l~~~p~~~ 82 (243)
T COG0847 13 TRFVVIDLETTGL-----NPKKDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPE----IFKIHG-ITDEMLADAPKFA 82 (243)
T ss_pred CcEEEEecccCCC-----CCCCCceEEEEeEEEECCeeecceeEEEECCCCCCChh----hhhhcC-CCHHHHhcCCCHH
Confidence 6889999999985 357899999997743322221000 000000 0000 001111 11 11223337
Q ss_pred HHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCC
Q 000161 312 ELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQG 391 (1988)
Q Consensus 312 eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~ 391 (1988)
+++..|.+++... .++|+|| ..||++||..++..++.... +...+|.+...++... ...
T Consensus 83 ~v~~~~~~~i~~~--~~~Vahn-a~fD~~fl~~~~~~~~~~~~-----------------~~~~~~t~~~~r~~~~-~~~ 141 (243)
T COG0847 83 EVLPEFLDFIGGL--RLLVAHN-AAFDVGFLRVESERLGIEIP-----------------GDPVLDTLALARRHFP-GFD 141 (243)
T ss_pred HHHHHHHHHHCCC--CeEEEEc-hhhcHHHHHHHHHHcCCCcc-----------------cCceehHHHHHHHHcC-CCc
Confidence 7888888888764 7999999 68999999999999887632 4466788888877533 247
Q ss_pred CCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 392 SQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 392 SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
+++|++++. .+|.... .... .=.+.||.++..++.++
T Consensus 142 ~~~L~~l~~-~~gi~~~-~~~~--------------H~Al~Da~~~a~~~~~~ 178 (243)
T COG0847 142 RSSLDALAE-RLGIDRN-PFHP--------------HRALFDALALAELFLLL 178 (243)
T ss_pred cchHHHHHH-HcCCCcC-CcCC--------------cchHHHHHHHHHHHHHH
Confidence 899999999 5887643 1100 22567899988888875
No 93
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=95.90 E-value=0.056 Score=77.35 Aligned_cols=159 Identities=23% Similarity=0.235 Sum_probs=99.6
Q ss_pred CceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEE-EcccccccccccccCCCC-CCCCC--ceEEecCCCHHHH
Q 000161 238 EVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLI-INRECVGEDIEDLEYTPK-PEFEG--YFKVTNVNNEIEL 313 (1988)
Q Consensus 238 ~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li-~nreivs~di~~feytp~-~~~~g--~f~V~~~~dE~eL 313 (1988)
+-+.+.||+||++. ++..|+|+.|+.+.-..|..+ .-...+.... . ..|. .+..| +..+....+..+.
T Consensus 418 ~~~~VVfDLETTGL-----~~~~deIIEIgAV~V~~G~iie~F~~~V~P~~-~--I~~~~~~LTGIT~e~L~~aps~~Ea 489 (1437)
T PRK00448 418 DATYVVFDVETTGL-----SAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGH-P--LSAFTTELTGITDDMVKDAPSIEEV 489 (1437)
T ss_pred cCcEEEEEhhhcCC-----CCchhhhheeeeEEEeCCeEeeeEEEEECCCC-C--CCHHHHHHhCCCHHHHcCCCCHHHH
Confidence 45799999999984 356799999987643344322 0000111000 0 0000 00011 0123345688899
Q ss_pred HHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCCC
Q 000161 314 LRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQ 393 (1988)
Q Consensus 314 L~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~Sy 393 (1988)
|..|.+++.. .++++||+ .||++||...++.+|++.+. ...+|++...+... -...++
T Consensus 490 L~~f~~figg---~vLVAHNa-~FD~~fL~~~l~rlgl~~l~-----------------~~~IDTLelar~l~-p~~k~~ 547 (1437)
T PRK00448 490 LPKFKEFCGD---SILVAHNA-SFDVGFINTNYEKLGLEKIK-----------------NPVIDTLELSRFLY-PELKSH 547 (1437)
T ss_pred HHHHHHHhCC---CEEEEeCc-cccHHHHHHHHHHcCCcccc-----------------ccceeHHHHHHHHc-Cccccc
Confidence 9999998764 69999999 79999999999999885321 12467777666532 134789
Q ss_pred CHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 394 GLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 394 sL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
+|+++|++ +|.....- +-.+.||.+|..|+.++
T Consensus 548 kL~~LAk~-lGL~~~~~-----------------HrAl~DA~aTa~lf~~l 580 (1437)
T PRK00448 548 RLNTLAKK-FGVELEHH-----------------HRADYDAEATAYLLIKF 580 (1437)
T ss_pred cHHHHHHH-cCCCCCCC-----------------cChHHHHHHHHHHHHHH
Confidence 99999996 67543221 34567888888887765
No 94
>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=95.73 E-value=0.04 Score=60.87 Aligned_cols=146 Identities=25% Similarity=0.331 Sum_probs=84.1
Q ss_pred eEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEcccccccccccccCCCCCCCCCceEEecCCCHHH-HHHHHH
Q 000161 240 HVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIE-LLRLWF 318 (1988)
Q Consensus 240 rvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~e-LL~~F~ 318 (1988)
.+++||+|+.+.. +......+..|++... ++..+.. . ...+.. ++..+.
T Consensus 21 ~~~a~D~E~~~~~---~~~~~~~~~~iq~~~~-~~~~i~~-~-------------------------~~~~~~~~~~~l~ 70 (176)
T PF01612_consen 21 KVLAFDTETTGLD---PYSYNPKIALIQLATG-EGCYIID-P-------------------------IDLGDNWILDALK 70 (176)
T ss_dssp SEEEEEEEEETST---STTSSEEEEEEEEEES-CEEEEEC-G-------------------------TTSTTTTHHHHHH
T ss_pred CeEEEEEEECCCC---ccccCCeEEEEEEecC-CCceeee-e-------------------------ccccccchHHHHH
Confidence 3999999999742 2223567777776653 3332210 0 000000 344444
Q ss_pred HHHHhhCCC-EEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCCCCHHH
Q 000161 319 AHMQEVKPG-IYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKA 397 (1988)
Q Consensus 319 ~~I~~~DPD-IIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~SysL~~ 397 (1988)
+++. +|+ +.+|||. .||+..|... +|+.. + -.+|+ .....-.. +..+++|++
T Consensus 71 ~ll~--~~~i~kv~~n~-~~D~~~L~~~---~~i~~------------------~-~~~D~-~l~~~~l~-~~~~~~L~~ 123 (176)
T PF01612_consen 71 ELLE--DPNIIKVGHNA-KFDLKWLYRS---FGIDL------------------K-NVFDT-MLAAYLLD-PTRSYSLKD 123 (176)
T ss_dssp HHHT--TTTSEEEESSH-HHHHHHHHHH---HTS--------------------S-SEEEH-HHHHHHTT-TSTTSSHHH
T ss_pred HHHh--CCCccEEEEEE-echHHHHHHH---hcccc------------------C-Cccch-hhhhhccc-ccccccHHH
Confidence 4554 555 5899999 5899999776 55542 1 13566 33322111 223499999
Q ss_pred HHHHHcCCCCCCCChHHHHHHHh-h--ChHHHHHHHHHhhHHHHHHHHHh
Q 000161 398 VTKAKLGYDPLEVNPEDMVRFAK-E--KPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 398 Va~~~LG~~K~dvd~~~i~~~~~-~--~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
++..+|| +.+.+.+....-|. . .+...+.|+..||..++.|+.++
T Consensus 124 L~~~~l~--~~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l 171 (176)
T PF01612_consen 124 LAEEYLG--NIDLDKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKL 171 (176)
T ss_dssp HHHHHHS--EEE-GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHH
T ss_pred HHHHHhh--hccCcHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999 22222221111122 2 23577899999999999999986
No 95
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=95.66 E-value=0.013 Score=77.80 Aligned_cols=72 Identities=15% Similarity=0.352 Sum_probs=66.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccccCcchH-HhhhcccccC-CcCCCceeccChhHHHHHHHHHHHHHHHhCCh
Q 000161 1904 EVMENALLQIVRQRERLYHLQDLVCIRCNQ-VKAAHLAEQC-ACAGSFRCKEDASDFRSKMQIFLNIANRQGFQ 1975 (1988)
Q Consensus 1904 ~~IE~~LI~~v~~~~~~YqlQDL~C~KC~~-vk~~~ls~~C-~CsG~~~~t~~~~~~~~~l~v~~~vA~~~~~~ 1975 (1988)
..|+.++|--+.--+.+|.-|-+||+||+. -++--|+--| .|+|....|++...+.+.|.+-.++|+.|+..
T Consensus 991 rVi~sHFlPDl~GNLRaFsrQ~fRC~kC~~kYRR~PL~G~C~kCGg~lilTV~~GsV~KYl~~s~~la~~Y~v~ 1064 (1095)
T TIGR00354 991 RVINSHFLPDIIGNLRAFSRQEVRCTKCNTKYRRIPLVGKCLKCGNNLTLTVSKGSVMKYLELSKFLAENYNVS 1064 (1095)
T ss_pred HHHHhccchHhhhhHhhhhccceeecccCCccccCCCCCcccccCCeEEEEEecchhHhhHHHHHHHHHHcCch
Confidence 468888888899999999999999999985 5777899999 59999999999999999999999999999983
No 96
>cd00145 POLBc DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is
Probab=95.62 E-value=0.022 Score=70.26 Aligned_cols=108 Identities=16% Similarity=0.255 Sum_probs=90.6
Q ss_pred HHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHhHcCCeEEEEeCCeEEEEcCC-CChHhHHHHHHHHHHHhh
Q 000161 1569 ILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFAMLLAEFRKLGATIIFANFSKVIIDTGK-FDLSAAKAYCDSLLKALQ 1647 (1988)
Q Consensus 1569 ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~flqLlaEfkRLGs~VVyAd~~riil~T~K-~~v~~A~ay~~yi~~si~ 1647 (1988)
+++.+|-++....|.+|++.+...|-.+=+..+.+...-++..|.+|||+|-..|.|.++. .+.+++...++-+.+.|
T Consensus 110 ~~NS~YG~~G~~~~r~~~~~~A~~IT~~GR~~l~~~~~~ie~~g~~VIYGDTDSifv~~~~~~~~~~~~~~~~~~~~~i- 188 (323)
T cd00145 110 LANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEHGARVIYGDTDSIFVSLPKMGTKEDAIKEGREILQEL- 188 (323)
T ss_pred eeecceeecccccccCCChHHHHHHHHHHHHHHHHHHHHHHHcCCEEEEECCCceEEEeCCCCCHHHHHHHHHHHHHHh-
Confidence 4567888888888899999999999888888888888888888999999999999999887 78888888888888877
Q ss_pred ccccccceecchhchheeeeeecCCCcccccc
Q 000161 1648 TRELFEWIELEPVHFWHSLLFMDQYNYGGIPA 1679 (1988)
Q Consensus 1648 ~~~lF~~l~L~~~~yW~~LlwmD~~NygGi~~ 1679 (1988)
..-..|.|+....|..++|+-+-+|+|...
T Consensus 189 --~~~~~i~le~E~vy~~~ll~~KKrYag~~~ 218 (323)
T cd00145 189 --ADEHLLELEFEKVYLPFFLGKKKRYAGLDI 218 (323)
T ss_pred --CCCCCeEEEEchhhHHHHHhhhhhEEEEEE
Confidence 234668888888888888888889988754
No 97
>PRK04023 DNA polymerase II large subunit; Validated
Probab=95.54 E-value=0.015 Score=77.60 Aligned_cols=72 Identities=17% Similarity=0.413 Sum_probs=66.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccccCcchH-HhhhcccccC-CcCCCceeccChhHHHHHHHHHHHHHHHhCCh
Q 000161 1904 EVMENALLQIVRQRERLYHLQDLVCIRCNQ-VKAAHLAEQC-ACAGSFRCKEDASDFRSKMQIFLNIANRQGFQ 1975 (1988)
Q Consensus 1904 ~~IE~~LI~~v~~~~~~YqlQDL~C~KC~~-vk~~~ls~~C-~CsG~~~~t~~~~~~~~~l~v~~~vA~~~~~~ 1975 (1988)
..|+.+++--+.--+++|.-|-+||+||+. -++--|+--| .|+|....|++...+.+.|.+-.++|+.|+..
T Consensus 1016 rVi~sHFlPDl~GNLRaFsrQ~fRC~kC~~kYRR~PL~G~C~kCGg~lilTVh~GsV~KYl~~s~~la~~Y~v~ 1089 (1121)
T PRK04023 1016 RVISSHFLPDLIGNLRAFSRQEFRCTKCGAKYRRPPLSGKCPKCGGNLILTVHKGSVEKYLEVSKKLAEEYGVS 1089 (1121)
T ss_pred HHHHhccchhhhhhhhhhcccceeecccCcccccCCCCCcCccCCCeEEEEEecchHHHHHHHHHHHHHHcCCh
Confidence 578888888999999999999999999985 6778899999 59999999999999999999999999999983
No 98
>PF00136 DNA_pol_B: DNA polymerase family B Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006134 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 of DNA polymerase B appears to consist of more than one activities, possibly including elongation, DNA-binding and dNTP binding [].; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 1NOY_A 1NOZ_B 2CW7_A 2CW8_A 1WNS_A 2XHB_A 2VWK_A 2VWJ_A 1TGO_A ....
Probab=95.52 E-value=0.05 Score=70.46 Aligned_cols=113 Identities=15% Similarity=0.263 Sum_probs=103.0
Q ss_pred HHHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHhHc--CCeEEEEeCCeEEEEcCCCChHhHHHHHHHHHHH
Q 000161 1568 AILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFAMLLAEFRKL--GATIIFANFSKVIIDTGKFDLSAAKAYCDSLLKA 1645 (1988)
Q Consensus 1568 ~ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~flqLlaEfkRL--Gs~VVyAd~~riil~T~K~~v~~A~ay~~yi~~s 1645 (1988)
.+++.+|-++....|.||++.++..|-..=+..+.+...-++.. |.+|||+|-..+.|..+..+.+++..+++-+.+.
T Consensus 163 i~~NS~YG~~g~~~~r~~~~~~a~~iT~~GR~~i~~~~~~~~~~~~g~~viYgDTDSv~v~~~~~~~~~~~~~~~~l~~~ 242 (466)
T PF00136_consen 163 IIANSFYGYLGAKNSRFYCKEIAEAITATGREIIKKAIEIIEEMEFGFEVIYGDTDSVFVQFPDSDKEDAKKKGEELAKE 242 (466)
T ss_dssp HHHTTHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHHSCTEEEEEEETTEEEEECTTCHHHHHHHHHHHHHHH
T ss_pred ccceeeEeecCccccchhhhhhhheehhhhHhhHHHHHHHHHhhcccceEEEEcccceEEecCCCcHHHHHHHHHHHHHH
Confidence 36779999999999999999999999999999999999999988 9999999999999999999999999999999999
Q ss_pred hhccccccceecchhchheeeeeecCCCccccccc
Q 000161 1646 LQTRELFEWIELEPVHFWHSLLFMDQYNYGGIPAR 1680 (1988)
Q Consensus 1646 i~~~~lF~~l~L~~~~yW~~LlwmD~~NygGi~~~ 1680 (1988)
|.++=..+.+.|+....+..++|+-+-+|.|+...
T Consensus 243 i~~~~~~~~i~le~E~~y~~~~l~~KKrY~~~~~~ 277 (466)
T PF00136_consen 243 INSELFPSPIKLEFEKVYRWFILLAKKRYAGLKYD 277 (466)
T ss_dssp HHHHSCSTTHEEEEEEEEEEEEEEETTEEEEEETC
T ss_pred HhhhhcCCCceeeecccEEEEEEEccCCccceeee
Confidence 98876678899999999999999999999998664
No 99
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=95.18 E-value=0.022 Score=77.92 Aligned_cols=72 Identities=15% Similarity=0.355 Sum_probs=66.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccccCcchH-HhhhcccccC-CcCCCceeccChhHHHHHHHHHHHHHHHhCCh
Q 000161 1904 EVMENALLQIVRQRERLYHLQDLVCIRCNQ-VKAAHLAEQC-ACAGSFRCKEDASDFRSKMQIFLNIANRQGFQ 1975 (1988)
Q Consensus 1904 ~~IE~~LI~~v~~~~~~YqlQDL~C~KC~~-vk~~~ls~~C-~CsG~~~~t~~~~~~~~~l~v~~~vA~~~~~~ 1975 (1988)
..|+.++|--+.--+++|.-|-+||+||+. -++--|+--| .|+|....|++...+.+.|.+-..+|+.|+..
T Consensus 1232 rvi~sHflpDl~GNLraFsrQ~~RC~kC~~kyRR~PL~G~C~kCGg~iilTv~~Gsv~KYl~~a~~~~~~y~~~ 1305 (1337)
T PRK14714 1232 RVINYHFIPDLIGNLRAFSRQEFRCLKCGTKYRRMPLAGKCRKCGGRIILTVHEGSVEKYLDTAKMVATEYNVR 1305 (1337)
T ss_pred HHHHhccchhhhhhhhhhhccceeecccCcccccCCCCCcccccCCeEEEEEecchHHHHHHHHHHHHHHcCch
Confidence 468888888999999999999999999985 6778899999 59999999999999999999999999999983
No 100
>cd05533 POLBc_delta DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand.
Probab=95.06 E-value=0.076 Score=67.29 Aligned_cols=110 Identities=14% Similarity=0.205 Sum_probs=96.9
Q ss_pred HHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHhHc---------CCeEEEEeCCeEEEEcCCCChHhHHHHH
Q 000161 1569 ILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFAMLLAEFRKL---------GATIIFANFSKVIIDTGKFDLSAAKAYC 1639 (1988)
Q Consensus 1569 ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~flqLlaEfkRL---------Gs~VVyAd~~riil~T~K~~v~~A~ay~ 1639 (1988)
+++.+|-++-.+.|.+|+..+...|-..=+..+.+...-+... |++|||+|-..|.|.++..+.+++...+
T Consensus 116 ~~NS~YG~~G~~~~r~~~~~~A~~iT~~GR~~l~~~~~~ie~~~~~~~g~~~~~~VIYGDTDSvfv~~~~~~~~~~~~~~ 195 (393)
T cd05533 116 SANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEKYTKANGYSHDAKVIYGDTDSVMVKFGVSDVEEAMKLG 195 (393)
T ss_pred eeeecccccccccCCccchHHHHHHHHhHHHHHHHHHHHHHHhhcccccCCCceEEEecCCCceEEEcCCCCHHHHHHHH
Confidence 3458899999999999999999999999998888877777653 8999999999999999999999999988
Q ss_pred HHHHHHhhccccccceecchhchheeeeeecCCCcccccc
Q 000161 1640 DSLLKALQTRELFEWIELEPVHFWHSLLFMDQYNYGGIPA 1679 (1988)
Q Consensus 1640 ~yi~~si~~~~lF~~l~L~~~~yW~~LlwmD~~NygGi~~ 1679 (1988)
+-|.+.|.+. +=+.+.|+....|..++|+-+-+|+|+..
T Consensus 196 ~ei~~~i~~~-~~~~i~Le~E~vy~~~ll~~KKrYag~~~ 234 (393)
T cd05533 196 KEAAEYVSKK-FIKPIKLEFEKVYFPYLLINKKRYAGLLW 234 (393)
T ss_pred HHHHHHHHhc-CCCCeEEeeHHHHHHHHHHHHhhheEEEe
Confidence 8888888876 22679999999999999999999999864
No 101
>PRK05359 oligoribonuclease; Provisional
Probab=94.99 E-value=0.069 Score=60.60 Aligned_cols=106 Identities=14% Similarity=0.045 Sum_probs=62.5
Q ss_pred eEEEEEEEEccCCCCCCCCCCCeEEEEEEEEc-CCc------eEEEccc--ccccccccccCCCCCCCCC--ceEEecCC
Q 000161 240 HVCAFDIETTKLPLKFPDADYDIIMMISYMLD-GQG------YLIINRE--CVGEDIEDLEYTPKPEFEG--YFKVTNVN 308 (1988)
Q Consensus 240 rvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~-~~g------~li~nre--ivs~di~~feytp~~~~~g--~f~V~~~~ 308 (1988)
+.+.+|+|||+. ||..|+|+.|+.+.- ++. +.++.+. .+..++..+.. .-....| +-.+....
T Consensus 4 ~~vvlD~ETTGL-----dp~~d~IieIgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~-~ih~~tGIt~~~l~~~~ 77 (181)
T PRK05359 4 NLIWIDLEMTGL-----DPERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNT-RTHTRSGLIDRVRASTV 77 (181)
T ss_pred cEEEEEeecCCC-----CCCCCeEEEEEEEEEcCCceEcccceEEEECCCHHHhhccChHHH-HhcccccCcHHHHhcCC
Confidence 578899999985 577899999998753 321 2111110 00000000000 0000012 01123446
Q ss_pred CHHHHHHHHHHHHHhhC---CCEEEeeCcccCCHHHHHHHHHHcCCC
Q 000161 309 NEIELLRLWFAHMQEVK---PGIYVTYNGDYFDWPFLETRAAHHGFK 352 (1988)
Q Consensus 309 dE~eLL~~F~~~I~~~D---PDIIvGYNgd~FDlPyL~~Ra~~lGi~ 352 (1988)
++.+.+..|.++++..- -.+++|+|. .||+.||.+-+..+|..
T Consensus 78 ~~~e~~~~~l~fl~~~~~~~~~~l~g~~v-~FD~~FL~~~~~~~~~~ 123 (181)
T PRK05359 78 SEAEAEAQTLEFLKQWVPAGKSPLCGNSI-GQDRRFLARYMPELEAY 123 (181)
T ss_pred CHHHHHHHHHHHHHHhcCCCCCceeecch-hhCHHHHHHHHHHhccc
Confidence 88999999999998632 135789886 79999999988776553
No 102
>PF03175 DNA_pol_B_2: DNA polymerase type B, organellar and viral; InterPro: IPR004868 This entry is found in DNA polymerase type B proteins. Proteins in this entry are found in plant and fungal mitochondria, and in viruses.; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication; PDB: 1XI1_B 2EX3_G 1XHZ_D 1XHX_C 2PZS_B 2PY5_A 2PYL_A 2PYJ_A.
Probab=94.97 E-value=0.008 Score=77.54 Aligned_cols=24 Identities=21% Similarity=-0.035 Sum_probs=18.4
Q ss_pred CEEEeeCcccCCHHHHHHHHHHcC
Q 000161 327 GIYVTYNGDYFDWPFLETRAAHHG 350 (1988)
Q Consensus 327 DIIvGYNgd~FDlPyL~~Ra~~lG 350 (1988)
-++.-||+-+||..||..-....+
T Consensus 6 ~~~y~HN~~~fD~~fiL~~l~~~~ 29 (459)
T PF03175_consen 6 FIVYFHNLSGFDGIFILKYLIRSN 29 (459)
T ss_dssp SEEEESS-HHHHHHHHHHHHHH--
T ss_pred EEEEEeCCCCCCEEEecchHhHhc
Confidence 467899999999999998887765
No 103
>cd05538 POLBc_Pol_II_B DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Probab=94.88 E-value=0.083 Score=65.79 Aligned_cols=105 Identities=13% Similarity=0.186 Sum_probs=86.6
Q ss_pred HHHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHhHcCCeEEEEeCCeEEEEcCC--CChHhHHHHHHHHHHH
Q 000161 1568 AILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFAMLLAEFRKLGATIIFANFSKVIIDTGK--FDLSAAKAYCDSLLKA 1645 (1988)
Q Consensus 1568 ~ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~flqLlaEfkRLGs~VVyAd~~riil~T~K--~~v~~A~ay~~yi~~s 1645 (1988)
.+++.+|-++-...|.+|++.++..|-..=+..+.+++..++..|.+|||+|-..|.+.... .+.+.+...++.|.+.
T Consensus 86 i~~NS~YG~lG~~~~r~~~~~~A~~iT~~GR~~L~~~~~~~e~~g~~VIygDTDSi~v~~~~~~~~~~~~~~~~~~i~~~ 165 (347)
T cd05538 86 VLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLRRRGATPVEVDTDGIYFIPPNGVDTEDEEEELVRELSST 165 (347)
T ss_pred hhhhhchhhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEcCCeeEEEeCCCCChHHHHHHHHHHHHHh
Confidence 45689999999999999999999999999999999999999999999999999999998643 2244555555555433
Q ss_pred hhccccccceecchhchheeeeeecCCCcccc
Q 000161 1646 LQTRELFEWIELEPVHFWHSLLFMDQYNYGGI 1677 (1988)
Q Consensus 1646 i~~~~lF~~l~L~~~~yW~~LlwmD~~NygGi 1677 (1988)
+ =..|+|+....+..|+...+-||+|+
T Consensus 166 ~-----~~~i~le~e~~y~~~l~~~KKrYa~~ 192 (347)
T cd05538 166 L-----PKGITVEFDGRYRAMFSYKIKNYALL 192 (347)
T ss_pred C-----CCCeEEEEhHHHHHHHhhcCceEEEE
Confidence 2 25689999988888888999999997
No 104
>cd05530 POLBc_B1 DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Probab=94.68 E-value=0.11 Score=65.17 Aligned_cols=102 Identities=13% Similarity=0.199 Sum_probs=85.1
Q ss_pred HHHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHhHcCCeEEEEeCCeEEEEcCCCChHhHHHHHHHHHHHhh
Q 000161 1568 AILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFAMLLAEFRKLGATIIFANFSKVIIDTGKFDLSAAKAYCDSLLKALQ 1647 (1988)
Q Consensus 1568 ~ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~flqLlaEfkRLGs~VVyAd~~riil~T~K~~v~~A~ay~~yi~~si~ 1647 (1988)
.+++.+|-++..+.+.+|++.++..|-.+=+..+.+.+....+.|.+|||+|-..+.+.++- .+.+...++.+.+.
T Consensus 120 i~~NS~YG~~g~~~~~~~~~~~A~~it~~GR~~l~~~~~~~~~~g~~VIYGDTDSvfv~~~~--~~~~~~i~~~i~~~-- 195 (372)
T cd05530 120 VFINASYGVFGAENFPLYCPPVAESTTALGRYIITSTIKKARELGLKVLYGDTDSLFLWNPP--QEQLEDLVEWVEKE-- 195 (372)
T ss_pred HHHhccccccccccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHCCcEEEEEeccceEEecCC--hhHHHHHHHHHhhc--
Confidence 35678999999999999999999999999999999999999999999999999999998752 34555555554432
Q ss_pred ccccccceecchhchheeeeee-cCCCccccc
Q 000161 1648 TRELFEWIELEPVHFWHSLLFM-DQYNYGGIP 1678 (1988)
Q Consensus 1648 ~~~lF~~l~L~~~~yW~~Llwm-D~~NygGi~ 1678 (1988)
| .++|+....++.+++. ++.||.|+.
T Consensus 196 ----~-~i~le~E~~y~~~ll~~~KKrY~g~~ 222 (372)
T cd05530 196 ----L-GLDLELDKEYRYVVFSGLKKNYLGVT 222 (372)
T ss_pred ----c-CceEEEEEEEeeeeeccccccEEEEe
Confidence 3 4789999999988875 899999974
No 105
>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=94.63 E-value=0.077 Score=59.71 Aligned_cols=102 Identities=16% Similarity=0.136 Sum_probs=59.3
Q ss_pred EEEEEEEccCCCCCCCCCCCeEEEEEEEE-cCCc-eE------EEcccc-cccccccccCCCCCCCCC--ceEEecCCCH
Q 000161 242 CAFDIETTKLPLKFPDADYDIIMMISYML-DGQG-YL------IINREC-VGEDIEDLEYTPKPEFEG--YFKVTNVNNE 310 (1988)
Q Consensus 242 LsfDIEt~s~~~~fPdp~~D~Ii~IS~~~-~~~g-~l------i~nrei-vs~di~~feytp~~~~~g--~f~V~~~~dE 310 (1988)
+.+|+||++. +|..|+|+.|+.+. ++++ .+ .++... ++..+..+-.. --+..| +-.+...+++
T Consensus 2 v~iD~ETTGl-----~p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~-ih~~tgIt~~~l~~~~~~ 75 (173)
T cd06135 2 VWIDLEMTGL-----DPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTE-MHTKSGLTERVRASTVTL 75 (173)
T ss_pred EEEEEecCCC-----CCCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHH-cccccccHHHHHhCCCCH
Confidence 5799999985 36789999999874 3321 11 011000 00000000000 000012 0113346789
Q ss_pred HHHHHHHHHHHHhh---CCCEEEeeCcccCCHHHHHHHHHHcC
Q 000161 311 IELLRLWFAHMQEV---KPGIYVTYNGDYFDWPFLETRAAHHG 350 (1988)
Q Consensus 311 ~eLL~~F~~~I~~~---DPDIIvGYNgd~FDlPyL~~Ra~~lG 350 (1988)
.+.+..|.+++... +-.+++|+|. .||+.||..-+.++|
T Consensus 76 ~~vl~~~~~f~~~~~~~~~~~lvgh~~-~FD~~fL~~~~~~~~ 117 (173)
T cd06135 76 AQAEAELLEFIKKYVPKGKSPLAGNSV-HQDRRFLDKYMPELE 117 (173)
T ss_pred HHHHHHHHHHHHHhcCCCCCceeecch-hhCHHHHHHHHHHHh
Confidence 99999999999863 3357788775 799999988777766
No 106
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=94.40 E-value=0.044 Score=74.80 Aligned_cols=70 Identities=14% Similarity=0.348 Sum_probs=64.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccccCcchH-HhhhcccccC-CcCCCceeccChhHHHHHHHHHHHHHHHhCC
Q 000161 1904 EVMENALLQIVRQRERLYHLQDLVCIRCNQ-VKAAHLAEQC-ACAGSFRCKEDASDFRSKMQIFLNIANRQGF 1974 (1988)
Q Consensus 1904 ~~IE~~LI~~v~~~~~~YqlQDL~C~KC~~-vk~~~ls~~C-~CsG~~~~t~~~~~~~~~l~v~~~vA~~~~~ 1974 (1988)
..|+.++|--+.--+++|.-|-+|| ||+. -++--|+--| .|+|....|++...+.+.|.+-..+|+.|+.
T Consensus 1521 ~vi~sHf~PDl~GNLRaFsrQ~~RC-kC~~kyRR~PL~G~C~kCGg~~ilTV~kGsv~KYl~~a~~~~~~y~v 1592 (1627)
T PRK14715 1521 KVIQSHFVPDLIGNLRAFSRQEFRC-KCGAKYRRVPLKGKCPKCGSKLILTVSKGAVEKYMPVAKMMAEKYNV 1592 (1627)
T ss_pred HHHHhccchhhhhhhhhhhccceee-cCCCccccCCCCCcCcccCCeEEEEEecchHHHHHHHHHHHHHHcCc
Confidence 4678888888999999999999999 9985 5677899999 5999999999999999999999999999997
No 107
>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=94.22 E-value=1.4 Score=49.57 Aligned_cols=154 Identities=24% Similarity=0.245 Sum_probs=90.2
Q ss_pred ceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCC-ceEEEcccccccccccccCCCCCCCCCceEEecCCCHHHHHHHH
Q 000161 239 VHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQ-GYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRLW 317 (1988)
Q Consensus 239 lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~-g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~eLL~~F 317 (1988)
...+++|+|+++. ++..+.|+.+++...+. .+.+. +. +.. .....+..+.+..|
T Consensus 5 ~~~~a~d~e~~~~-----~~~~~~i~~l~~~~~~~~~~~~~--------~~-------~~~-----~~~~~~~~~~~~~l 59 (193)
T cd06139 5 AKVFAFDTETTSL-----DPMQAELVGISFAVEPGEAYYIP--------LG-------HDY-----GGEQLPREEVLAAL 59 (193)
T ss_pred CCeEEEEeecCCC-----CcCCCeEEEEEEEcCCCCEEEEe--------cC-------CCc-----cccCCCHHHHHHHH
Confidence 3568999998763 23457888888764321 22110 00 000 00112566778888
Q ss_pred HHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCCCCHHH
Q 000161 318 FAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKA 397 (1988)
Q Consensus 318 ~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~SysL~~ 397 (1988)
.+++...+ -.++|||. .||+.+|. .+|+.+. + .++|+.-...-- .....+++|++
T Consensus 60 ~~~l~~~~-~~~v~hn~-k~d~~~l~----~~gi~~~-----------------~-~~~Dt~l~a~ll-~p~~~~~~l~~ 114 (193)
T cd06139 60 KPLLEDPS-IKKVGQNL-KFDLHVLA----NHGIELR-----------------G-PAFDTMLASYLL-NPGRRRHGLDD 114 (193)
T ss_pred HHHHhCCC-CcEEeecc-HHHHHHHH----HCCCCCC-----------------C-CcccHHHHHHHh-CCCCCCCCHHH
Confidence 88887542 26899999 69999984 3455421 1 346776544321 11112689999
Q ss_pred HHHHHcCCCCCCCChHHHHHH------Hhh-ChHHHHHHHHHhhHHHHHHHHHh
Q 000161 398 VTKAKLGYDPLEVNPEDMVRF------AKE-KPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 398 Va~~~LG~~K~dvd~~~i~~~------~~~-~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
+++.++|.....+ +.+..- +.. .......|+..|+.+++.|+.++
T Consensus 115 l~~~~l~~~~~~~--~~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l 166 (193)
T cd06139 115 LAERYLGHKTISF--EDLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELL 166 (193)
T ss_pred HHHHHhCCCCccH--HHHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999998754321 111100 111 12456779999999999998876
No 108
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=93.89 E-value=0.17 Score=71.37 Aligned_cols=110 Identities=15% Similarity=0.235 Sum_probs=98.8
Q ss_pred HHHhhhhhhcCCC-CCCccHHHHHHHHHHHHHHHHHHHHHHhHc---------CCeEEEEeCCeEEEEcCCCChHhHHHH
Q 000161 1569 ILQHLYRWLCSPH-SKLHDPVLHRILHKVMQKVFAMLLAEFRKL---------GATIIFANFSKVIIDTGKFDLSAAKAY 1638 (1988)
Q Consensus 1569 ll~~~~RWl~sp~-S~LyDPaL~r~v~~LmkK~flqLlaEfkRL---------Gs~VVyAd~~riil~T~K~~v~~A~ay 1638 (1988)
+++.+|-++.... +.||+..+...|-..=+..+.+........ |++|||+|-..+.|.++..++++|...
T Consensus 653 ~aNS~YG~~G~~~~gr~~c~~iA~sIT~~GR~~i~~t~~~ie~~~~~~~g~~~g~~VIYGDTDSvfV~~~~~~~~ea~~~ 732 (1054)
T PTZ00166 653 SANSVYGYTGAQVGGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTKANGYKHDATVIYGDTDSVMVKFGTDDIQEAMDL 732 (1054)
T ss_pred hccccccccccccCCccccHHHHHHHHHHHHHHHHHHHHHHHHhccccccCcCCeEEEecCCCceEEEeCCccHHHHHHH
Confidence 4578999999998 999999999999999999999888888876 999999999999999998899999999
Q ss_pred HHHHHHHhhccccccceecchhchheeeeeecCCCcccccc
Q 000161 1639 CDSLLKALQTRELFEWIELEPVHFWHSLLFMDQYNYGGIPA 1679 (1988)
Q Consensus 1639 ~~yi~~si~~~~lF~~l~L~~~~yW~~LlwmD~~NygGi~~ 1679 (1988)
+.-+.+.|.+. +-+-|.|+..+.+..+|++-+-+|+|+.-
T Consensus 733 g~e~a~~Is~~-~~~pi~LefEkvy~~~ll~~KKrYag~~~ 772 (1054)
T PTZ00166 733 GKEAAERISKK-FLKPIKLEFEKVYCPYLLMNKKRYAGLLY 772 (1054)
T ss_pred HHHHHHHHHHh-cCCCcEEEEeeeeeeeeecccceEEEEEE
Confidence 98888888766 33678999999999999999999999854
No 109
>cd05534 POLBc_zeta DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol 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.
Probab=93.89 E-value=0.13 Score=66.35 Aligned_cols=111 Identities=10% Similarity=0.134 Sum_probs=96.3
Q ss_pred HHHHhhhhhhcCCCC-CCccHHHHHHHHHHHHHHHHHHHHHHhH---cCCeEEEEeCCeEEEEcCCCChHhHHHHHHHHH
Q 000161 1568 AILQHLYRWLCSPHS-KLHDPVLHRILHKVMQKVFAMLLAEFRK---LGATIIFANFSKVIIDTGKFDLSAAKAYCDSLL 1643 (1988)
Q Consensus 1568 ~ll~~~~RWl~sp~S-~LyDPaL~r~v~~LmkK~flqLlaEfkR---LGs~VVyAd~~riil~T~K~~v~~A~ay~~yi~ 1643 (1988)
.+++.+|-++-.+.| .+|+..+...|-..=+..+.+-..-+.. .|.+|||+|-..|.|.++-.+.++|...++-+.
T Consensus 171 i~~NS~YGy~G~~~~gr~~~~~iA~~IT~~GR~~l~~~~~~ie~~~~~g~~VIYGDTDSvfv~~~~~~~~~~~~~~~~i~ 250 (451)
T cd05534 171 LLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLFVLLPGRTKEEAFKIGKEIA 250 (451)
T ss_pred HHhhccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHhhccccCceEEeecccceeEecCCCCHHHHHHHHHHHH
Confidence 456889999998864 8999999999999999988888777776 999999999999999998888999998888888
Q ss_pred HHhhccccccceecchhchheeeeeecCCCcccccc
Q 000161 1644 KALQTRELFEWIELEPVHFWHSLLFMDQYNYGGIPA 1679 (1988)
Q Consensus 1644 ~si~~~~lF~~l~L~~~~yW~~LlwmD~~NygGi~~ 1679 (1988)
+.|.+. +-+.++|+....+..++|.-+-+|+|+..
T Consensus 251 ~~in~~-~~~~i~le~E~vy~~~ll~~KKrYag~~~ 285 (451)
T cd05534 251 EAVTAA-NPSPIKLKFEKVYHPCVLVTKKRYVGYKY 285 (451)
T ss_pred HHHHHh-CCCCceeeHHHHHHHHHHHhhhhEEEEEE
Confidence 888763 22579999999999999999999999864
No 110
>cd05531 POLBc_B2 DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Probab=93.16 E-value=0.33 Score=60.74 Aligned_cols=99 Identities=13% Similarity=0.167 Sum_probs=76.5
Q ss_pred HHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHhHcCCeEEEEeCCeEEEEcCCCChHhHHHHHHHHHHHhhc
Q 000161 1569 ILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFAMLLAEFRKLGATIIFANFSKVIIDTGKFDLSAAKAYCDSLLKALQT 1648 (1988)
Q Consensus 1569 ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~flqLlaEfkRLGs~VVyAd~~riil~T~K~~v~~A~ay~~yi~~si~~ 1648 (1988)
+++.+|-++-.+.|.+|++..+..|-.+=+..+.+.+......|.+|||+|-..|.+.+. +++...++-|.+.
T Consensus 103 ~~NS~YGylG~~~~~f~~~~~A~~vT~~GR~~L~~~~~~~e~~g~~VIygDTDSvfv~~~----~~~~~~~~~i~~~--- 175 (352)
T cd05531 103 ILVTSFGYLGYKNAKFGRIEVHEAITAYGRKILLRAKEIAEEMGFRVLHGIVDSLWIQGR----GDIEELAREIEER--- 175 (352)
T ss_pred eeecccccccccccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCEEEEEccccceeecC----chHHHHHHHHHHh---
Confidence 356889999999999999999999999999999999999999999999999999999983 3445555444432
Q ss_pred cccccceecchhchheeeeee-------cCCCccccc
Q 000161 1649 RELFEWIELEPVHFWHSLLFM-------DQYNYGGIP 1678 (1988)
Q Consensus 1649 ~~lF~~l~L~~~~yW~~Llwm-------D~~NygGi~ 1678 (1988)
| -+.|+....|+.++++ -+.+|.|..
T Consensus 176 ---~-~i~l~le~~y~~~~~~~~~~~~~~kKrY~g~~ 208 (352)
T cd05531 176 ---T-GIPLKLEGHYDWIVFLPERDGLGAPNRYFGRL 208 (352)
T ss_pred ---c-CCceEEEEEEEEEEeeccccccCcceeEEEec
Confidence 1 2556666666766665 246777763
No 111
>PHA03036 DNA polymerase; Provisional
Probab=93.07 E-value=0.27 Score=67.76 Aligned_cols=113 Identities=11% Similarity=0.192 Sum_probs=95.2
Q ss_pred HHHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHHHHHHH-----------------------------------H---h
Q 000161 1568 AILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFAMLLAE-----------------------------------F---R 1609 (1988)
Q Consensus 1568 ~ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~flqLlaE-----------------------------------f---k 1609 (1988)
.+++.+|-.+-...|.||++.+...|-..=+..+...-.. + .
T Consensus 664 I~aNS~YG~~G~~~~rly~~~iA~sVTa~GR~mI~~tk~~Ve~~~~~~~~~~l~~~p~~~f~~~~r~~~~~~~~~l~~~~ 743 (1004)
T PHA03036 664 IVANSVYGLMGFRNSALYSYASAKSCTAIGRNMIKYLNSVLNGSKLINGKLILANCPINPFFKDDRSIDTNYDTNLPVEY 743 (1004)
T ss_pred HHHhcccccccccCccccCHHHHHHHHHHHHHHHHHHHHHhhcccccchhhhhhhccccccccccccccccccccccccc
Confidence 3457899999999999999999988766666555443211 1 2
Q ss_pred HcCCeEEEEeCCeEEEEcCCCChHhHHHHHHHHHHHhhccccccceecchhchheeeeeecCCCccccccc
Q 000161 1610 KLGATIIFANFSKVIIDTGKFDLSAAKAYCDSLLKALQTRELFEWIELEPVHFWHSLLFMDQYNYGGIPAR 1680 (1988)
Q Consensus 1610 RLGs~VVyAd~~riil~T~K~~v~~A~ay~~yi~~si~~~~lF~~l~L~~~~yW~~LlwmD~~NygGi~~~ 1680 (1988)
++|++|||+|-..|.|.++-.++++|.+.++.+.+.|.++-+++-+.|+..+.+..||.+-+-.|+|+...
T Consensus 744 ~~g~kVIYGDTDSVFV~~~~~d~eea~~ig~ela~~In~~lf~~pikLEfEKVY~~lLLl~KKRYAGl~~~ 814 (1004)
T PHA03036 744 NFTFRSVYGDTDSVFLEINTKDVDKSIKIAKELERIINEKVLFDNFKIEFEAVYKNLIMQSKKKYTTLKYI 814 (1004)
T ss_pred cCCcEEEEEecCeeEEEcCCCCHHHHHHHHHHHHHHHHHHhcCCCeEEEehhhHHHHHhhhhhheeeEeec
Confidence 48999999999999999998899999999999999999876778899999999999999999999998653
No 112
>PTZ00315 2'-phosphotransferase; Provisional
Probab=92.67 E-value=1.8 Score=56.85 Aligned_cols=166 Identities=13% Similarity=0.105 Sum_probs=94.5
Q ss_pred CceEEEEEEEEccCCCCCCCCCCCeEEEEEEEE-c-CCceEEE-----cccccccccccccCCCCCCCCC--ceEEecCC
Q 000161 238 EVHVCAFDIETTKLPLKFPDADYDIIMMISYML-D-GQGYLII-----NRECVGEDIEDLEYTPKPEFEG--YFKVTNVN 308 (1988)
Q Consensus 238 ~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~-~-~~g~li~-----nreivs~di~~feytp~~~~~g--~f~V~~~~ 308 (1988)
--.+++||+||++... +....|+||.|+.+. + .+|.++. -++.....+..|. -+..| .-.|...+
T Consensus 55 ~d~~IV~DlETTgl~~--~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fc----t~LTGITqe~V~~Ap 128 (582)
T PTZ00315 55 FDAYVVLDFEATCEAD--RRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFC----TELTGITQSMVSRAD 128 (582)
T ss_pred CCeEEEEEEecCCCCC--CCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhH----hhhcCcCHHHHhcCC
Confidence 3678899999998421 112468999999875 3 2443220 0110000011100 01112 11245567
Q ss_pred CHHHHHHHHHHHHHhhCC-------CEEEeeCcccCCHH-HHHHHHH---HcCCCCCcccCccccCCCCceeeccceEec
Q 000161 309 NEIELLRLWFAHMQEVKP-------GIYVTYNGDYFDWP-FLETRAA---HHGFKMSEELGFQCDKNQGECRAKFACHLD 377 (1988)
Q Consensus 309 dE~eLL~~F~~~I~~~DP-------DIIvGYNgd~FDlP-yL~~Ra~---~lGi~l~~~iG~~~~~~~g~~~i~GRihiD 377 (1988)
+-.+++..|.+++.+... .+++++|+ .||+. ||..-++ .+|++.. ....+|
T Consensus 129 ~F~eVl~ef~~fL~~~~~~e~~~~~~~~vah~g-~fDl~~fL~~e~~~~~~~g~p~~-----------------f~~wid 190 (582)
T PTZ00315 129 PFPVVYCEALQFLAEAGLGDAPPLRSYCVVTCG-DWDLKTMLPSQMRVSGQQGTPLS-----------------FQRWCN 190 (582)
T ss_pred CHHHHHHHHHHHHhccccccccccCceEEEecc-HHHHHHHHHHHHHHhhhcCCCcc-----------------cceEEE
Confidence 788999999999988641 37889998 69995 7776665 3455421 124556
Q ss_pred hHHHHhhcc-----------CCCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 378 CFAWVKRDS-----------YLPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 378 l~~~vkrd~-----------~L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
+-..+.+-. +-...+|+|+++++. +|.....- .+-.+.||..|.+|+.++
T Consensus 191 Lk~~lar~l~p~~~~~~~~~~~~~~~~~L~~al~~-lgL~~eGr----------------~HrAlDDA~ntA~L~~~L 251 (582)
T PTZ00315 191 LKKYMSQLGFGNGSGCGGGATPPLGPSDMPDMLQM-LGLPLQGR----------------HHSGIDDCRNIAAVLCEL 251 (582)
T ss_pred hHHHHHHHhCccccccccccccccCCcCHHHHHHH-CCCCCCCC----------------CcCcHHHHHHHHHHHHHH
Confidence 532222211 012367999999995 77543210 122467999998888876
No 113
>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=92.54 E-value=1.2 Score=51.07 Aligned_cols=112 Identities=16% Similarity=0.147 Sum_probs=66.3
Q ss_pred HHHHHHHHHHHhhCCCEE-EeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccC---
Q 000161 312 ELLRLWFAHMQEVKPGIY-VTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSY--- 387 (1988)
Q Consensus 312 eLL~~F~~~I~~~DPDII-vGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~--- 387 (1988)
+.+..|+.-+-+ ||+|+ |||++. +|+..|.+. +|+... . ...-.-.+|+..+++.-..
T Consensus 68 ~~~~~~L~~ll~-d~~i~KVg~~~~-~D~~~L~~~---~~~~~~--~-----------~~~~~~v~Dl~~~a~~l~~~~~ 129 (193)
T cd06146 68 EDWDRLLKRLFE-DPDVLKLGFGFK-QDLKALSAS---YPALKC--M-----------FERVQNVLDLQNLAKELQKSDM 129 (193)
T ss_pred HHHHHHHHHHhC-CCCeeEEEechH-HHHHHHHHh---cCcccc--c-----------cccCCceEEHHHHHHHHhhccc
Confidence 334444333322 58876 999996 599998643 333110 0 0011245677665553111
Q ss_pred ------CCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhC--hHHHHHHHHHhhHHHHHHHHHh
Q 000161 388 ------LPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEK--PQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 388 ------L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~--~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
.+...++|.+++..+||..-.. + ..+.. |... ...-+.|+..||...+.||.++
T Consensus 130 ~~~~~~~~~~~~sL~~l~~~~lg~~l~K-~-~q~Sd-W~~rpLs~~Qi~YAA~Da~~l~~l~~~L 191 (193)
T cd06146 130 GRLKGNLPSKTKGLADLVQEVLGKPLDK-S-EQCSN-WERRPLREEQILYAALDAYCLLEVFDKL 191 (193)
T ss_pred cccccccCcccCCHHHHHHHHhCCCcCc-c-cccCC-CCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 1135689999999999964221 1 22222 3332 2577899999999999999986
No 114
>PRK05755 DNA polymerase I; Provisional
Probab=91.24 E-value=2.5 Score=59.34 Aligned_cols=146 Identities=22% Similarity=0.246 Sum_probs=89.6
Q ss_pred CceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCC-ceEEEcccccccccccccCCCCCCCCCceEEecCCCHHHHHHH
Q 000161 238 EVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQ-GYLIINRECVGEDIEDLEYTPKPEFEGYFKVTNVNNEIELLRL 316 (1988)
Q Consensus 238 ~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~-g~li~nreivs~di~~feytp~~~~~g~f~V~~~~dE~eLL~~ 316 (1988)
.-.+++||+||++. ++..+.|+.|++...+. .+.+. -. + + .+ ..+..
T Consensus 314 ~~~~~a~DtEt~~l-----~~~~~~i~~i~ls~~~g~~~~ip----------------~~---~---i----~~-~~l~~ 361 (880)
T PRK05755 314 AAGLFAFDTETTSL-----DPMQAELVGLSFAVEPGEAAYIP----------------LD---Q---L----DR-EVLAA 361 (880)
T ss_pred ccCeEEEEeccCCC-----CcccccEEEEEEEeCCCcEEEEe----------------cc---c---c----cH-HHHHH
Confidence 45689999999874 24567898898765432 22210 00 0 0 11 56777
Q ss_pred HHHHHHhhCCCE-EEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCCCCH
Q 000161 317 WFAHMQEVKPGI-YVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQGL 395 (1988)
Q Consensus 317 F~~~I~~~DPDI-IvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~SysL 395 (1988)
|.+++.+ |++ +|+||. .||+.+|.. +|+... + ..+|+.-...-- . +..+++|
T Consensus 362 l~~~L~d--~~v~kV~HNa-kfDl~~L~~----~gi~~~-----------------~-~~~DT~iAa~Ll-~-~~~~~~L 414 (880)
T PRK05755 362 LKPLLED--PAIKKVGQNL-KYDLHVLAR----YGIELR-----------------G-IAFDTMLASYLL-D-PGRRHGL 414 (880)
T ss_pred HHHHHhC--CCCcEEEecc-HhHHHHHHh----CCCCcC-----------------C-CcccHHHHHHHc-C-CCCCCCH
Confidence 7777775 454 799999 799999973 455421 1 246665543321 1 1124999
Q ss_pred HHHHHHHcCCCCCCCChHHHHH---HHhh-ChHHHHHHHHHhhHHHHHHHHHh
Q 000161 396 KAVTKAKLGYDPLEVNPEDMVR---FAKE-KPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 396 ~~Va~~~LG~~K~dvd~~~i~~---~~~~-~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
+++++.++|...... +.+.. -+.. .++....|+..|+.++..|+.++
T Consensus 415 ~~L~~~ylg~~~~~~--~~~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L 465 (880)
T PRK05755 415 DSLAERYLGHKTISF--EEVAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVL 465 (880)
T ss_pred HHHHHHHhCCCccch--HHhcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999998763221 11100 0000 12357799999999999999986
No 115
>PRK05761 DNA polymerase I; Reviewed
Probab=90.19 E-value=0.8 Score=63.03 Aligned_cols=101 Identities=13% Similarity=0.149 Sum_probs=84.5
Q ss_pred HHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHhHcCCeEEEEeCCeEEEEcCCCChHhHHHHHHHHHHHhhc
Q 000161 1569 ILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFAMLLAEFRKLGATIIFANFSKVIIDTGKFDLSAAKAYCDSLLKALQT 1648 (1988)
Q Consensus 1569 ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~flqLlaEfkRLGs~VVyAd~~riil~T~K~~v~~A~ay~~yi~~si~~ 1648 (1988)
+++.+|-.+-.+.|.+|++.++..|-..=+..+.+.+.....+|.+|||+|-..|.|..+- .+.+...++.|.+..
T Consensus 516 ~~NS~YGy~G~~~~r~~~~~~A~~IT~~GR~~l~~t~~~ie~~g~~VIYGDTDSvfv~~~~--~~~~~~l~~~i~~~~-- 591 (787)
T PRK05761 516 FLNASYGVFGAENFKLYRIEVAESITALGREILLSTKKKAEELGLKVLYGDTDSLFVWGPT--KESLEELIKEIEERT-- 591 (787)
T ss_pred eeecccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHcCCEEEEEeCceEEEECCC--HHHHHHHHHHHHHhC--
Confidence 4578999999999999999999999999999999999999999999999999999999653 344555555554432
Q ss_pred cccccceecchhchheeeee-ecCCCccccc
Q 000161 1649 RELFEWIELEPVHFWHSLLF-MDQYNYGGIP 1678 (1988)
Q Consensus 1649 ~~lF~~l~L~~~~yW~~Llw-mD~~NygGi~ 1678 (1988)
.++|+..+.+..+++ ..+-||.|+.
T Consensus 592 -----~i~LE~Ek~y~~~l~~~~KKrYag~~ 617 (787)
T PRK05761 592 -----GIDLEVDKTYDWVAFSGLKKNYFGVL 617 (787)
T ss_pred -----CCceEEEEEEEEEEEecccceEEEEe
Confidence 388999998988776 4999999985
No 116
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=88.33 E-value=4.5 Score=47.59 Aligned_cols=89 Identities=16% Similarity=0.154 Sum_probs=55.7
Q ss_pred CCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccC
Q 000161 308 NNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSY 387 (1988)
Q Consensus 308 ~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~ 387 (1988)
+.-.+++.+|. .-+++||||. .||+.+|.. . +.-.+|++.+.++- +
T Consensus 62 p~~~ev~~~~~------~~~~lVaHNa-~FD~~~L~~------------~--------------~~~~idTl~lar~l-~ 107 (219)
T PRK07983 62 PWIEDVIPHYY------GSEWYVAHNA-SFDRRVLPE------------M--------------PGEWICTMKLARRL-W 107 (219)
T ss_pred CCHHHHHHHHc------CCCEEEEeCc-HhhHHHHhC------------c--------------CCCcEeHHHHHHHH-c
Confidence 34445555541 3479999998 599999831 0 11247889888873 2
Q ss_pred CCCCCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 388 LPQGSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 388 L~~~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
|...|+|.++++. +|..... +.. .-++-.+.||.+|..|+.++
T Consensus 108 -p~~~~~l~~L~~~-~~l~~~~--~~~----------~~aHrAl~Da~ata~ll~~l 150 (219)
T PRK07983 108 -PGIKYSNMALYKS-RKLNVQT--PPG----------LHHHRALYDCYITAALLIDI 150 (219)
T ss_pred -cCCCCCHHHHHHH-cCCCCCC--CCC----------CCCCcHHHHHHHHHHHHHHH
Confidence 3345999999985 6643100 000 01244578999999998875
No 117
>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=88.21 E-value=4.9 Score=44.65 Aligned_cols=92 Identities=16% Similarity=0.078 Sum_probs=58.1
Q ss_pred CCCEE-EeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCCCCHHHHHHHHc
Q 000161 325 KPGIY-VTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQGLKAVTKAKL 403 (1988)
Q Consensus 325 DPDII-vGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~SysL~~Va~~~L 403 (1988)
||+|+ +|||.. .|+..|.. .+|+.. .| + +|+.....-- . +..+.+|+.++..+|
T Consensus 65 d~~i~Kvg~~~k-~D~~~L~~---~~gi~~-----------------~~-~-~D~~~aa~ll-~-~~~~~~L~~l~~~~l 119 (161)
T cd06129 65 NPSIVKALHGIE-GDLWKLLR---DFGEKL-----------------QR-L-FDTTIAANLK-G-LPERWSLASLVEHFL 119 (161)
T ss_pred CCCEEEEEeccH-HHHHHHHH---HcCCCc-----------------cc-H-hHHHHHHHHh-C-CCCCchHHHHHHHHh
Confidence 67775 899984 57777632 245532 12 2 6776554431 1 123679999999999
Q ss_pred CCCCCCCChHHHHHHHhhCh--HHHHHHHHHhhHHHHHHHHHh
Q 000161 404 GYDPLEVNPEDMVRFAKEKP--QMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 404 G~~K~dvd~~~i~~~~~~~~--~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
|..... ...... |...| +..+.|+..||...+.||.++
T Consensus 120 g~~l~K--~~~~s~-W~~rpLt~~qi~YAa~Da~~l~~l~~~l 159 (161)
T cd06129 120 GKTLDK--SISCAD-WSYRPLTEDQKLYAAADVYALLIIYTKL 159 (161)
T ss_pred CCCCCc--cceecc-CCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 964411 111122 44333 578899999999999999885
No 118
>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=88.14 E-value=4.4 Score=45.14 Aligned_cols=103 Identities=18% Similarity=0.130 Sum_probs=61.6
Q ss_pred HHHHHHHHhhCCCE-EEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCCC
Q 000161 315 RLWFAHMQEVKPGI-YVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGSQ 393 (1988)
Q Consensus 315 ~~F~~~I~~~DPDI-IvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~Sy 393 (1988)
..|.+++. +|+| .+|||. .+|+..|.+ .+|+.. .| + +|+......-... ..+.
T Consensus 63 ~~l~~ll~--~~~i~kv~~~~-k~D~~~L~~---~~g~~~-----------------~~-~-~Dl~~aa~ll~~~-~~~~ 116 (170)
T cd06141 63 PSLKQLLE--DPSILKVGVGI-KGDARKLAR---DFGIEV-----------------RG-V-VDLSHLAKRVGPR-RKLV 116 (170)
T ss_pred HHHHHHhc--CCCeeEEEeee-HHHHHHHHh---HcCCCC-----------------CC-e-eeHHHHHHHhCCC-cCCc
Confidence 34445554 4555 489988 567777633 344431 12 2 6887665442111 1246
Q ss_pred CHHHHHHHHcCCCCCCCChHHHHHHHhhCh--HHHHHHHHHhhHHHHHHHHHh
Q 000161 394 GLKAVTKAKLGYDPLEVNPEDMVRFAKEKP--QMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 394 sL~~Va~~~LG~~K~dvd~~~i~~~~~~~~--~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
+|.+++..+||..-..-....+.. |...| ..-+.|+..||..++.|+.++
T Consensus 117 ~l~~l~~~~l~~~~~k~k~~~~s~-W~~rpLt~~qi~YAa~Da~~~~~l~~~l 168 (170)
T cd06141 117 SLARLVEEVLGLPLSKPKKVRCSN-WEARPLSKEQILYAATDAYASLELYRKL 168 (170)
T ss_pred cHHHHHHHHcCcccCCCCCcccCC-CCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999996432111112222 33332 456799999999999999875
No 119
>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=86.18 E-value=19 Score=38.50 Aligned_cols=105 Identities=20% Similarity=0.189 Sum_probs=62.8
Q ss_pred HHHHHHHHHHHHhhCCC-EEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCC
Q 000161 311 IELLRLWFAHMQEVKPG-IYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLP 389 (1988)
Q Consensus 311 ~eLL~~F~~~I~~~DPD-IIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~ 389 (1988)
..++..|.+++.. ++ .++|||. .||+.+|.. +++.. ...++|+.-...-- . |
T Consensus 40 ~~~~~~l~~~l~~--~~~~~v~~~~-k~d~~~L~~----~~~~~------------------~~~~~D~~~~ayll-~-~ 92 (155)
T cd00007 40 EEDLEALKELLED--EDITKVGHDA-KFDLVVLAR----DGIEL------------------PGNIFDTMLAAYLL-N-P 92 (155)
T ss_pred HHHHHHHHHHHcC--CCCcEEeccH-HHHHHHHHH----CCCCC------------------CCCcccHHHHHHHh-C-C
Confidence 4566666677664 45 3799997 588888743 23211 11346765444331 1 2
Q ss_pred CC-CCCHHHHHHHHcCCCCCCCChHHHHHH---H-hh-ChHHHHHHHHHhhHHHHHHHHHh
Q 000161 390 QG-SQGLKAVTKAKLGYDPLEVNPEDMVRF---A-KE-KPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 390 ~~-SysL~~Va~~~LG~~K~dvd~~~i~~~---~-~~-~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
.. +++|+++++.+||..... .+.+... + .. .......|...|+.+++.|+.++
T Consensus 93 ~~~~~~l~~l~~~~l~~~~~~--~~~~~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~~l 151 (155)
T cd00007 93 GEGSHSLDDLAKEYLGIELDK--DEQIYGKGAKTFARPLSEELLEYAAEDADALLRLYEKL 151 (155)
T ss_pred CCCcCCHHHHHHHHcCCCCcc--HHHHhcCCCCccccCCHHHHHHHHHHhHHHHHHHHHHH
Confidence 23 679999999998865321 1111111 0 11 13467789999999999998875
No 120
>PF03337 Pox_F12L: Poxvirus F12L protein; InterPro: IPR005005 The vaccinia virus F12L gene encodes a 65 kDa protein that is expressed late during infection and is important for plaque formation, EEV production and virulence. The F12L protein is located on intracellular enveloped virus (IEV) particles, but is absent from immature virions, intracellular mature virus and cell-associated enveloped virus. F12L shows co-localization with endosomal compartments and microtubules and appears to play a role in the the transport of IEV particles to the cell surface on microtubules [].; GO: 0016032 viral reproduction
Probab=84.80 E-value=19 Score=48.07 Aligned_cols=146 Identities=17% Similarity=0.257 Sum_probs=88.6
Q ss_pred cccCCCCceEEEEEEEEccCCC----CCC-CCCCCeEEEEEEE--EcCCceEEEcccccccccccccCCCCCCCCCceEE
Q 000161 232 DLLQRAEVHVCAFDIETTKLPL----KFP-DADYDIIMMISYM--LDGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKV 304 (1988)
Q Consensus 232 ~~~~~p~lrvLsfDIEt~s~~~----~fP-dp~~D~Ii~IS~~--~~~~g~li~nreivs~di~~feytp~~~~~g~f~V 304 (1988)
....+|++-++.+|||..+.+. .+| ++....|++|++. +...|..+. +++ -++|.. .
T Consensus 185 ~~Y~RPE~DIl~~di~~ia~~~~W~~~~~~~~~~~~v~ai~v~a~it~~gp~iy---mIs------------tyPG~~-F 248 (651)
T PF03337_consen 185 ENYTRPEIDILPYDIKAIAQKSNWSKLRPYNPRALKVFAISVNAIITPNGPSIY---MIS------------TYPGKC-F 248 (651)
T ss_pred hhccCccceeecccHHhhhchhcccccccCCcccceEEEEEEEEEecCCCceeE---EEE------------ecCCce-E
Confidence 4567999999999999987431 144 5556788888764 233343211 000 123432 3
Q ss_pred ecCCCHHHHHHHHHHHHHh-hC----CCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeecc---ceEe
Q 000161 305 TNVNNEIELLRLWFAHMQE-VK----PGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKF---ACHL 376 (1988)
Q Consensus 305 ~~~~dE~eLL~~F~~~I~~-~D----PDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~G---Rihi 376 (1988)
+++++=+.|+..|+++|++ .. -=+++||=+..||+|.|.+..-.. .||. .-+....-.++ .+.+
T Consensus 249 ~nf~s~~~li~~FL~Wl~e~~~~n~~ti~LvGy~ss~FD~pLLra~wp~~-------sGW~-~~~n~~ivs~~G~kvil~ 320 (651)
T PF03337_consen 249 INFDSNKALISDFLKWLRECIMKNIRTIILVGYFSSFFDFPLLRAYWPKN-------SGWN-FIGNNTIVSKDGLKVILV 320 (651)
T ss_pred EeCCCchHHHHHHHHHHHHHHhccCceEEEeehhhhhhccHHHHhhcccC-------CCce-EecCceEEeCCCcEEEEE
Confidence 4778888899999999999 32 237899999999999998775433 2332 10000111111 2456
Q ss_pred chHHHHhhccCCCCCCCCHHHHHHHHcCCCCCCC
Q 000161 377 DCFAWVKRDSYLPQGSQGLKAVTKAKLGYDPLEV 410 (1988)
Q Consensus 377 Dl~~~vkrd~~L~~~SysL~~Va~~~LG~~K~dv 410 (1988)
|+..+. .+.++.+-+++.-|. ...+
T Consensus 321 D~a~Fs--------~~~~~~eYc~~W~~~-~~~~ 345 (651)
T PF03337_consen 321 DAANFS--------PGMSLSEYCEHWTGK-NVSF 345 (651)
T ss_pred ehhhhc--------cCCCHHHHHHhhccC-CCCC
Confidence 777653 345788888875553 3343
No 121
>PHA02952 EEV maturation protein; Provisional
Probab=83.08 E-value=21 Score=47.51 Aligned_cols=98 Identities=19% Similarity=0.290 Sum_probs=63.2
Q ss_pred cccCCCCceEEEEEEEEccCCCC----CC-CCCCCeEEEEEEEE--cCCceEEEcccccccccccccCCCCCCCCCceEE
Q 000161 232 DLLQRAEVHVCAFDIETTKLPLK----FP-DADYDIIMMISYML--DGQGYLIINRECVGEDIEDLEYTPKPEFEGYFKV 304 (1988)
Q Consensus 232 ~~~~~p~lrvLsfDIEt~s~~~~----fP-dp~~D~Ii~IS~~~--~~~g~li~nreivs~di~~feytp~~~~~g~f~V 304 (1988)
....+|++-|+.+||+..+.+.. +| +++...|+.|++.. ...|..+. +++. ++|.. .
T Consensus 185 ~~Y~RPE~dIl~~di~~~a~~~~W~~~~~~~~~~~k~~~~~v~~~i~~~gp~~y---mI~t------------~pG~~-f 248 (648)
T PHA02952 185 EAYTRPEIDILPYDIKSIASKENWAPLSISLEQLLKIIAISVNATITDTGPSPY---MIST------------YPGKC-F 248 (648)
T ss_pred hhccCcchhcccccHHHhhchhccCccCccchhhheEEEEEEEEEecCCCceeE---EEEe------------cCCce-E
Confidence 45679999999999999875321 12 12225666666432 22332211 1110 12322 2
Q ss_pred ecCCCHHHHHHHHHHHHHh----hCCCEEEeeCcccCCHHHHHHHH
Q 000161 305 TNVNNEIELLRLWFAHMQE----VKPGIYVTYNGDYFDWPFLETRA 346 (1988)
Q Consensus 305 ~~~~dE~eLL~~F~~~I~~----~DPDIIvGYNgd~FDlPyL~~Ra 346 (1988)
+.+++ +.|+..|++++++ .+-=+++||=...||+|.|....
T Consensus 249 ~~~~s-k~li~~FL~Wl~e~~~n~~ti~LvGy~Ss~FD~pLL~~~w 293 (648)
T PHA02952 249 INFDS-KKLILDFLKWLKEVMTNTSTIILVGYLSSFFDFPLLKAYW 293 (648)
T ss_pred ecCCH-HHHHHHHHHHHHHHhcCCceEEEEEhhhhhcchHHHHhhc
Confidence 34555 9999999999988 44458999999999999997765
No 122
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=81.35 E-value=1.2 Score=51.77 Aligned_cols=59 Identities=15% Similarity=0.394 Sum_probs=52.8
Q ss_pred HHHHHhhcccccCcchH-HhhhcccccCC-cCCCceeccChhHHHHHHHHHHHHHHHhCCh
Q 000161 1917 RERLYHLQDLVCIRCNQ-VKAAHLAEQCA-CAGSFRCKEDASDFRSKMQIFLNIANRQGFQ 1975 (1988)
Q Consensus 1917 ~~~~YqlQDL~C~KC~~-vk~~~ls~~C~-CsG~~~~t~~~~~~~~~l~v~~~vA~~~~~~ 1975 (1988)
-+.+|--|-++|.||+. .++--|+--|. |+|..+.|+..+.+.+.|.+-..+|..|+..
T Consensus 159 n~r~f~rq~~rc~~c~~k~rr~pl~g~c~kcg~~~~ltv~~g~v~kyL~~t~~~~~~y~~~ 219 (253)
T COG1933 159 NLRSFTRQEFRCVKCNTKFRRPPLDGKCPICGGKIVLTVSKGAIEKYLGTAKMLVTEYKVK 219 (253)
T ss_pred hhhhhhhheeehHhhhhhhcCCCccccccccCCeEEEEEeccHHHHHHHHHHHHHHHcCCc
Confidence 45678899999999975 56778999995 9999999999999999999999999999983
No 123
>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=78.26 E-value=36 Score=39.33 Aligned_cols=51 Identities=22% Similarity=0.221 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHcCCCCCCCChHHH-------HHHHhhCh--HHHHHHHHHhhHHHHHHHHHh
Q 000161 392 SQGLKAVTKAKLGYDPLEVNPEDM-------VRFAKEKP--QMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 392 SysL~~Va~~~LG~~K~dvd~~~i-------~~~~~~~~--~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
..+|+.+++.+||..-... +.+ ..-|...| +..+.|+..||..++.|+.++
T Consensus 114 ~~~L~~l~~~~l~~~~~k~--~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l 173 (197)
T cd06148 114 VISLVQLLDKYLYISISLK--EDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAM 173 (197)
T ss_pred cccHHHHHHHhhCCChHHH--HHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHH
Confidence 4589999999998643210 111 12344444 678999999999999998876
No 124
>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=78.04 E-value=2.9 Score=44.93 Aligned_cols=99 Identities=21% Similarity=0.208 Sum_probs=55.2
Q ss_pred EEEEEEEccCCCCCCCCCCCeEEEEEEEE-cCCc--eEEEcccccccccccccCCCCC-CCCC--ceEEecCCCHHHHHH
Q 000161 242 CAFDIETTKLPLKFPDADYDIIMMISYML-DGQG--YLIINRECVGEDIEDLEYTPKP-EFEG--YFKVTNVNNEIELLR 315 (1988)
Q Consensus 242 LsfDIEt~s~~~~fPdp~~D~Ii~IS~~~-~~~g--~li~nreivs~di~~feytp~~-~~~g--~f~V~~~~dE~eLL~ 315 (1988)
+.||+||++.. +..+.|+.|+++. +++. ........+.... ....+|.. ...| .-.+...+...+.+.
T Consensus 1 v~~D~Ettg~~-----~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~-~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~ 74 (164)
T PF00929_consen 1 VVFDTETTGLD-----PRQDEIIEIGAVKVDDDENEEVESFNSLIRPEE-PPKISPWATKVHGITQEDLEDAPSFEEALD 74 (164)
T ss_dssp EEEEEEESSST-----TTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSS-HCSSEHHHHHHHHHCHHHHHCHCEHHHHHH
T ss_pred cEEEeEcCCCC-----CCCCeEEEEEEEEeeCCccccceeeeecccccc-cccCCHHHeeecCCcccccccCCcHHHHHH
Confidence 47999999853 4568999999874 3322 1111111110000 00000000 0011 001334456677889
Q ss_pred HHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHc
Q 000161 316 LWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHH 349 (1988)
Q Consensus 316 ~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~l 349 (1988)
.|.+++... .+++||| ..||.+++..=...+
T Consensus 75 ~~~~~~~~~--~~~v~~n-~~fd~~~l~~~~~~~ 105 (164)
T PF00929_consen 75 EFEEFLKKN--DILVGHN-ASFDIGFLRREDKRF 105 (164)
T ss_dssp HHHHHHHHH--TEEEETT-CCHEEESSHHHHHHH
T ss_pred hhhhhhhcc--ccccccc-ccchhhHHHHhhhhc
Confidence 999999865 7999999 789998886655544
No 125
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=77.95 E-value=1e+02 Score=43.40 Aligned_cols=189 Identities=15% Similarity=0.219 Sum_probs=122.1
Q ss_pred cCCcceeEEEEEEecchhHHHHHhhhhcccccCCccccccCCCCCCCCCCCcccccccCCChhH-HHHHHHHHHHH--HH
Q 000161 1480 YPGAYRKVSVELKIHHLSVNALLKSNQVNEMEGGGLFGFDQDMNSGPYNNELCGFDETTSSAPA-FRVVKQLIQRC--LT 1556 (1988)
Q Consensus 1480 ~pG~Y~svcvEl~i~~LaVnaiL~Ss~ine~EG~~~~~f~~~~~~~~~~~~~~~~~e~~~~~~a-f~iLr~mV~~w--~~ 1556 (1988)
.-|.|.++.+=|+++.|= -|.|+|.- +.|-......-+......+-+++.-.+- =|+|+.||..= ++
T Consensus 836 kkGlYe~~VLllDFNSLY------PSIIQEyN----ICFTTv~~~~~d~Dqlp~lP~s~~~~GiLPr~l~~LVerRk~VK 905 (1429)
T KOG0970|consen 836 KKGLYEKYVLLLDFNSLY------PSIIQEYN----ICFTTVDRFSVDSDQLPRLPSSSSEQGILPRLLENLVERRKEVK 905 (1429)
T ss_pred ccchhhheeEEEEccccc------hHHHHHhh----heeeeccccccCcccCCCCCCccccCCccHHHHHHHHHHHHHHH
Confidence 359999999999998872 24454432 2233332211011122222222211111 36666666432 23
Q ss_pred HHHhc-CCcc----------HH-HHHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHhHcCCeEEEEeCCeEE
Q 000161 1557 DAVTS-GNVF----------AD-AILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFAMLLAEFRKLGATIIFANFSKVI 1624 (1988)
Q Consensus 1557 da~~~-~n~~----------AD-~ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~flqLlaEfkRLGs~VVyAd~~rii 1624 (1988)
..++. .|+. |= .--++.|-=|-=..|.+|---|.-+|-.==+-.++.---=..++|-.|||.|-..|.
T Consensus 906 ~lMK~~~tp~~~~q~DIRQqALKLTANSMYGCLGf~~SRFyAkpLAaLVT~KGReiLm~Tk~Lve~mnl~VIYGDTDSvM 985 (1429)
T KOG0970|consen 906 KLMKQELTPEKRKQLDIRQQALKLTANSMYGCLGFVNSRFYAKPLAALVTYKGREILMNTKDLVEKMNLEVIYGDTDSVM 985 (1429)
T ss_pred HHHhcCCCHHHHHhhhHHHHHHhhhhccchhhcccccchhhhhhHHHHHhhhhHHHHHHHHHHHHhcCeEEEEcCCceEE
Confidence 33331 1211 11 112356677777789999888887775433444332222223699999999999999
Q ss_pred EEcCCCChHhHHHHHHHHHHHhhccccccceecchhchheeeeeecCCCccccccc
Q 000161 1625 IDTGKFDLSAAKAYCDSLLKALQTRELFEWIELEPVHFWHSLLFMDQYNYGGIPAR 1680 (1988)
Q Consensus 1625 l~T~K~~v~~A~ay~~yi~~si~~~~lF~~l~L~~~~yW~~LlwmD~~NygGi~~~ 1680 (1988)
|.|++.+.++|+.-.+-+.++|.+ +++-|+|.+..-+.-||-+-+--|+++.-.
T Consensus 986 InTn~td~~~a~kig~~~k~~VNk--rYk~LEIDiDgVfkrlLLlkKKKYAAL~l~ 1039 (1429)
T KOG0970|consen 986 INTNSTDYEEALKIGNEFKQAVNK--RYKLLEIDIDGVFKRLLLLKKKKYAALTLN 1039 (1429)
T ss_pred eeCCCccHHHHHHHHHHHHHHHHH--HhhhheeehhHHHHHHHHHhhhhheeEEec
Confidence 999999999999999999999865 589999999999999999999999998664
No 126
>PRK10829 ribonuclease D; Provisional
Probab=72.46 E-value=34 Score=43.59 Aligned_cols=100 Identities=13% Similarity=0.081 Sum_probs=64.2
Q ss_pred HHHHHHHHHhhCCCEE-EeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCC-
Q 000161 314 LRLWFAHMQEVKPGIY-VTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQG- 391 (1988)
Q Consensus 314 L~~F~~~I~~~DPDII-vGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~- 391 (1988)
+..|.+++. ||+|+ |+|+. .+|+++|.. .+|+.. ...+|+....+. +..+
T Consensus 63 ~~~L~~ll~--~~~ivKV~H~~-~~Dl~~l~~---~~g~~p-------------------~~~fDTqiaa~~---lg~~~ 114 (373)
T PRK10829 63 WSPFKALLR--DPQVTKFLHAG-SEDLEVFLN---AFGELP-------------------QPLIDTQILAAF---CGRPL 114 (373)
T ss_pred hHHHHHHHc--CCCeEEEEeCh-HhHHHHHHH---HcCCCc-------------------CCeeeHHHHHHH---cCCCc
Confidence 344555554 57877 78887 589999844 334421 245688655543 2223
Q ss_pred CCCHHHHHHHHcCCCCCCCChHHHHHHHhhCh--HHHHHHHHHhhHHHHHHHHHh
Q 000161 392 SQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKP--QMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 392 SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~--~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
+.+|..+++++||..-.. + +.... |...| ...++|+..|+...+.||.++
T Consensus 115 ~~gl~~Lv~~~lgv~ldK-~-~~~sD-W~~RPLs~~ql~YAa~Dv~~L~~l~~~L 166 (373)
T PRK10829 115 SCGFASMVEEYTGVTLDK-S-ESRTD-WLARPLSERQCEYAAADVFYLLPIAAKL 166 (373)
T ss_pred cccHHHHHHHHhCCccCc-c-cccCC-CCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 689999999999964211 0 11111 33333 578899999999999999886
No 127
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=67.22 E-value=8.5 Score=44.25 Aligned_cols=113 Identities=22% Similarity=0.450 Sum_probs=70.7
Q ss_pred CCCcccCCCCceeeCccccCCCCCCcccccccCcc---cCCCccccCCCCCCCCCChHHHHHHHHHHHHHHHHHHhhccc
Q 000161 1850 PEAEFRDPCPSFILPNVICSYCNDCRDLDLCRDMA---LLAQDWHCAMPQCGQPYDREVMENALLQIVRQRERLYHLQDL 1926 (1988)
Q Consensus 1850 ~eA~f~~P~~sl~L~~ViC~~Cn~~rDLDlCrD~~---~~~~~W~C~~~~C~~~yd~~~IE~~LI~~v~~~~~~YqlQDL 1926 (1988)
++-.|++ |.+|+| .|.+|.....++=..++. .....|.|++ |++.+....|-.+|.-.+.+.+..|..--|
T Consensus 7 d~erf~~-c~~l~~---~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~--C~~~~~~~~l~Nql~l~iR~~i~~YY~gwl 80 (188)
T PF08996_consen 7 DEERFKD-CEPLKL---TCPSCGTEFEFPGVFEEDGDDVSPSGLQCPN--CSTPLSPASLVNQLELQIREHISRYYEGWL 80 (188)
T ss_dssp -TTTTTT----EEE---E-TTT--EEEE-SSS--SSEEEETTEEEETT--T--B--HHHHHHHHHHHHHHHHHHHHH--C
T ss_pred HHHHhcC-CCceEe---ECCCCCCCccccccccCCccccccCcCcCCC--CCCcCCHHHHHHHHHHHHHHHHHHHHHhCc
Confidence 3445553 566665 488888866655443321 1234599999 999999999999999999999999999999
Q ss_pred ccCc--chHHh-hhccccc-C----CcCCCceeccChhHHHHHHHHHHHH
Q 000161 1927 VCIR--CNQVK-AAHLAEQ-C----ACAGSFRCKEDASDFRSKMQIFLNI 1968 (1988)
Q Consensus 1927 ~C~K--C~~vk-~~~ls~~-C----~CsG~~~~t~~~~~~~~~l~v~~~v 1968 (1988)
+|.. |+... .-.+.-. | .|-|......+.+++-.+|.-|..+
T Consensus 81 ~Cdd~~C~~~TR~~~~~~~rC~~~~~C~G~m~~eyse~~LY~QL~yf~~L 130 (188)
T PF08996_consen 81 VCDDPTCGNRTRQLSLYGKRCPGAPGCKGKMRREYSEKDLYNQLCYFRSL 130 (188)
T ss_dssp CCCTCCCHHCCCSTTSTTTCST-STT-HHCCCCSS-HHHHHHHHHHHHHH
T ss_pred eeCcccccCcccccccCCCCCCCcccccceeeeeecHHHHHHHHHHHHHH
Confidence 9988 97432 2222222 6 3788888899999999999888776
No 128
>PF08408 DNA_pol_B_3: DNA polymerase family B viral insert; InterPro: IPR013617 This viral domain is found between the exonuclease domain of the DNA polymerase family B (IPR006133 from INTERPRO) and the IPR006134 from INTERPRO domain, connecting the two. ; GO: 0003887 DNA-directed DNA polymerase activity
Probab=66.49 E-value=5.5 Score=43.31 Aligned_cols=56 Identities=25% Similarity=0.392 Sum_probs=41.0
Q ss_pred HcCCCCCCCChHHHHHHHh-hChHHHHHHHHHhhHHHHHHHHHh-ccchHhhh--hhhcC
Q 000161 402 KLGYDPLEVNPEDMVRFAK-EKPQMMASYSVSDAVATYYLYMTY-VHPFIFSL--ATIIP 457 (1988)
Q Consensus 402 ~LG~~K~dvd~~~i~~~~~-~~~~~La~Y~l~Da~lt~~L~~Kl-v~~~i~~L--a~i~~ 457 (1988)
.|-.+|.|++..+|..=+. +....+++||+.||.|+.+|+..+ |+.-|-+- ..+.|
T Consensus 83 ~lsfgKDDVdL~dmY~nYnl~~a~em~~YCiHDacLCkyLw~Yy~i~~KidA~astYlLP 142 (149)
T PF08408_consen 83 TLSFGKDDVDLSDMYKNYNLDIALEMARYCIHDACLCKYLWDYYGIETKIDAAASTYLLP 142 (149)
T ss_pred EEEecCCCCCHHHHHHhccHHHHHHHHHHHHhHHHHHHHHHHHcCcceeeeccceeeecc
Confidence 4556789999888776333 455689999999999999999988 66544332 34444
No 129
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=63.55 E-value=10 Score=48.22 Aligned_cols=117 Identities=17% Similarity=0.199 Sum_probs=74.4
Q ss_pred CHHHHHHHHHHHHH-hhCCCEEEeeCcccCCHHHHHHH-HHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhcc
Q 000161 309 NEIELLRLWFAHMQ-EVKPGIYVTYNGDYFDWPFLETR-AAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDS 386 (1988)
Q Consensus 309 dE~eLL~~F~~~I~-~~DPDIIvGYNgd~FDlPyL~~R-a~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~ 386 (1988)
-|...+..|..++. .+.+ -.+||-..++-. .| ++.+|.+.. ....+. +..+|+|.++++..
T Consensus 337 ee~~~~~efl~~v~~~yp~--~~~YH~~~ye~~---~rL~klyg~~~~---------~v~~~l---~~~vDi~~lvr~~v 399 (474)
T COG2251 337 EERKALQEFLGIVVRQYPE--ATIYHYAPYEKT---RRLVKLYGVPQN---------QVSPVL---DSLVDIYALVRSSV 399 (474)
T ss_pred HHHHHHHHHHhhhheecCC--CCccccCchhhh---chhheeeccCcc---------hhhHHH---HHHhHHHHHHHhcc
Confidence 45588999999998 5544 356665433332 22 223344321 101111 12789999999977
Q ss_pred CCCCCCCCHHHHHHHHcCCCCCCCC--hHHHHHHH---h-h-C---hHHHHHHHHHhhHHHHHHHHH
Q 000161 387 YLPQGSQGLKAVTKAKLGYDPLEVN--PEDMVRFA---K-E-K---PQMMASYSVSDAVATYYLYMT 443 (1988)
Q Consensus 387 ~L~~~SysL~~Va~~~LG~~K~dvd--~~~i~~~~---~-~-~---~~~La~Y~l~Da~lt~~L~~K 443 (1988)
-.|.+||+|+.++. .||.+.-|.+ +++...++ . . + .+.+..||-.||.+|..+..-
T Consensus 400 ~~p~es~sLK~la~-~lG~~wrD~~~ag~~~~~~Y~~~~~agdeavl~~Il~YN~dDcRaT~~vrdw 465 (474)
T COG2251 400 VVPVESYSLKALAP-YLGFQWRDVEAAGDESLEMYERWLTAGDEAVLKQILRYNEDDCRATRAVRDW 465 (474)
T ss_pred ccCccchhHHHhhh-hhCCCccccccchHHHHHHHHHHHhhchHHHHHHHHhcCccchHHHHHHHHH
Confidence 77789999999999 7999766543 33333322 1 2 1 357899999999999877553
No 130
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=56.92 E-value=2.1e+02 Score=31.08 Aligned_cols=100 Identities=20% Similarity=0.231 Sum_probs=58.9
Q ss_pred HHHHHHHHhhCCCE-EEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCC-CC
Q 000161 315 RLWFAHMQEVKPGI-YVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQ-GS 392 (1988)
Q Consensus 315 ~~F~~~I~~~DPDI-IvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~-~S 392 (1988)
..+.+++.. +++ .+|||. .+|+..|. .+|+.+ +| + +|+.-...-- .|. .+
T Consensus 65 ~~l~~~l~~--~~~~kv~~d~-k~~~~~L~----~~gi~~-----------------~~-~-~D~~laayll--~p~~~~ 116 (172)
T smart00474 65 EILKDLLED--ETITKVGHNA-KFDLHVLA----RFGIEL-----------------EN-I-FDTMLAAYLL--LGGPSK 116 (172)
T ss_pred HHHHHHhcC--CCceEEEech-HHHHHHHH----HCCCcc-----------------cc-h-hHHHHHHHHH--cCCCCc
Confidence 334444443 454 789998 67888874 266643 12 2 6776443310 122 33
Q ss_pred CCHHHHHHHHcCCCCCCCChHHHHHHHhh-ChHHHHHHHHHhhHHHHHHHHHh
Q 000161 393 QGLKAVTKAKLGYDPLEVNPEDMVRFAKE-KPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 393 ysL~~Va~~~LG~~K~dvd~~~i~~~~~~-~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
++|+.++..+||....++-.. ..+... .......|+..||..+..|+.++
T Consensus 117 ~~l~~l~~~~l~~~~~~~~~~--~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l 167 (172)
T smart00474 117 HGLATLLKEYLGVELDKEEQK--SDWGARPLSEEQLQYAAEDADALLRLYEKL 167 (172)
T ss_pred CCHHHHHHHHhCCCCCcccCc--cccccCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 799999999998753221111 011111 13567789999999999998865
No 131
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=55.15 E-value=1.1e+02 Score=38.67 Aligned_cols=144 Identities=19% Similarity=0.126 Sum_probs=79.0
Q ss_pred CCCceEEEEEEEEccCCCCCCCCCCCeEEEEEEEEcCCceEEEccccccccccc-----ccCCCCCCC---CCc--e-EE
Q 000161 236 RAEVHVCAFDIETTKLPLKFPDADYDIIMMISYMLDGQGYLIINRECVGEDIED-----LEYTPKPEF---EGY--F-KV 304 (1988)
Q Consensus 236 ~p~lrvLsfDIEt~s~~~~fPdp~~D~Ii~IS~~~~~~g~li~nreivs~di~~-----feytp~~~~---~g~--f-~V 304 (1988)
..+++.+.+|-||.+- +|..|+.-+++.+-..... .++++.+.= -+|-|.|+. .|- - .-
T Consensus 6 ~~~~tF~~yDYETfG~-----~Pa~DRPaQFAgiRTD~~~-----NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~ 75 (475)
T COG2925 6 TKQPTFLFYDYETFGV-----HPALDRPAQFAGIRTDIEF-----NIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAR 75 (475)
T ss_pred CCCCcEEEEehhhcCC-----Ccccccchhhheeeccccc-----cccCCCeEEEecCccccCCCCCceeeecCCHHHHH
Confidence 4577889999999984 5777887777654222111 233333321 135565542 110 0 01
Q ss_pred ecCCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhh
Q 000161 305 TNVNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKR 384 (1988)
Q Consensus 305 ~~~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkr 384 (1988)
...-+|.+-..+....+..-+ .+++|||...||=.+...-.=++=++.+ ...|. .|..-.|++..++-
T Consensus 76 ~~G~~E~~F~~~I~~~ls~P~-Tcv~GYNniRFDDEvtRy~fyRNF~DPY-a~sWq----------ngNSRWDLLD~~Ra 143 (475)
T COG2925 76 EKGINEAAFAARIHAELTQPN-TCVLGYNNIRFDDEVTRYIFYRNFYDPY-AWSWQ----------NGNSRWDLLDVVRA 143 (475)
T ss_pred hcCCChHHHHHHHHHHhCCCC-eeeecccccccchHHHHHHHHHhcCchh-hhhhc----------CCCchhHHHHHHHH
Confidence 234588886666655554432 4889999999998766444433434432 11122 12223455555443
Q ss_pred ccCC------------CCCCCCHHHHHHH
Q 000161 385 DSYL------------PQGSQGLKAVTKA 401 (1988)
Q Consensus 385 d~~L------------~~~SysL~~Va~~ 401 (1988)
-..| ..+|++|+.++++
T Consensus 144 cyALRPeGI~Wp~n~dG~pSFkLEhLt~A 172 (475)
T COG2925 144 CYALRPEGINWPENDDGLPSFKLEHLTKA 172 (475)
T ss_pred HHhcCcccCCCCcCCCCCcchhhHHHhhc
Confidence 1111 2368999999886
No 132
>PHA02523 43B DNA polymerase subunit B; Provisional
Probab=54.16 E-value=95 Score=39.15 Aligned_cols=87 Identities=14% Similarity=0.202 Sum_probs=69.0
Q ss_pred HHHHHHHHHHHHHHHHh-cCCcc-HHHHHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHH---H-----HHHHHhHcCC
Q 000161 1544 FRVVKQLIQRCLTDAVT-SGNVF-ADAILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFA---M-----LLAEFRKLGA 1613 (1988)
Q Consensus 1544 f~iLr~mV~~w~~da~~-~~n~~-AD~ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~fl---q-----LlaEfkRLGs 1613 (1988)
-..|+.|+..|=++..+ .+|.. -=.++++||--+-.+.+.+||+.+-..|-..=+.+.. + +....+..|-
T Consensus 22 ~~~L~~~i~~~~r~~a~~~~~q~AiKIlmNSfYGylG~~~~R~yd~e~A~aVT~~Gre~Ik~i~~~~ney~~~l~~t~G~ 101 (391)
T PHA02523 22 TDELQQMIARCEKEEQKRNTNQLNRKILINSLYGALGNNWFRYFDLRNAEAITTYGQLAIRWIERKLNEYINELVKTTGV 101 (391)
T ss_pred HHHHHHHHHHHHHHHHHHhcchHHHHHHHHhhhhhhcCCCceecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCc
Confidence 45679999999887554 23333 4567889999999999999999999988777776666 4 5556677899
Q ss_pred e-EEEEeCCeEEEEcCCC
Q 000161 1614 T-IIFANFSKVIIDTGKF 1630 (1988)
Q Consensus 1614 ~-VVyAd~~riil~T~K~ 1630 (1988)
. |||+|-..|.|+-++.
T Consensus 102 ~~VIYgDTDSifv~~~~~ 119 (391)
T PHA02523 102 DYVCYIDTDSVYLNMEAV 119 (391)
T ss_pred ceEEEecCCeeEEEecch
Confidence 5 9999999999998853
No 133
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=50.73 E-value=80 Score=38.13 Aligned_cols=38 Identities=39% Similarity=0.361 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHHcCCCCCCCChHHHHHHHhhChHHHHHHHHHhhHHHHHHHHHh
Q 000161 391 GSQGLKAVTKAKLGYDPLEVNPEDMVRFAKEKPQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 391 ~SysL~~Va~~~LG~~K~dvd~~~i~~~~~~~~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
.+-||+.+++++||++-.. + ..=++.||.+|.+||.+.
T Consensus 225 ~tpSLK~Lt~~~Lg~~IQ~-----------G-----eHsSvEDA~AtM~LY~~v 262 (280)
T KOG2249|consen 225 ATPSLKKLTEALLGKDIQV-----------G-----EHSSVEDARATMELYKRV 262 (280)
T ss_pred CCccHHHHHHHHhchhhhc-----------c-----ccCcHHHHHHHHHHHHHH
Confidence 5678999999999963311 0 134689999999999864
No 134
>PF08490 DUF1744: Domain of unknown function (DUF1744); InterPro: IPR013697 This domain is found on the catalytic subunit of DNA polymerase epsilon. It is found C-terminal to IPR006133 from INTERPRO and IPR006134 from INTERPRO. ; GO: 0003887 DNA-directed DNA polymerase activity, 0008270 zinc ion binding, 0006260 DNA replication, 0005634 nucleus
Probab=47.78 E-value=7.5e+02 Score=32.09 Aligned_cols=60 Identities=15% Similarity=0.210 Sum_probs=52.3
Q ss_pred hhhccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHcCCe-EEEccceeeEEcCCC
Q 000161 782 LNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNARLLIEKIGKP-LELDTDGIWCVLPGS 841 (1988)
Q Consensus 782 lNS~YGy~g~~~sR~ys~e~A~~VT~~Gr~iI~~a~~lve~~G~~-vygDTDSI~~~lp~~ 841 (1988)
++.||-.+-...|.+|++.+...|-..=+..+.+-..-.++.|.. ||+|-..|.+..+..
T Consensus 289 l~~f~rWl~sp~S~LyDPaL~~~v~~LmkK~flqLl~Ef~rlG~~VVyA~~~riil~T~K~ 349 (396)
T PF08490_consen 289 LQHFYRWLSSPSSLLYDPALHRMVHNLMKKVFLQLLAEFRRLGSKVVYADFNRIILCTGKT 349 (396)
T ss_pred HHHHHHHHcCCcccccCHHHHHHHHHHHHHHHHHHHHHHHHcCCEEEEEcCCEEEEECCCC
Confidence 678999999999999999999999999888887776667899988 699999999875543
No 135
>PHA03181 helicase-primase primase subunit; Provisional
Probab=46.70 E-value=3.4e+02 Score=37.36 Aligned_cols=186 Identities=13% Similarity=0.150 Sum_probs=118.6
Q ss_pred HHHHhhhccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHcCCeE-EEccceeeEEcCCCCCccccccccccccc
Q 000161 778 HKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNARLLIEKIGKPL-ELDTDGIWCVLPGSFPENFTFKTKDLKKK 856 (1988)
Q Consensus 778 ~K~ilNS~YGy~g~~~sR~ys~e~A~~VT~~Gr~iI~~a~~lve~~G~~v-ygDTDSI~~~lp~~~pe~~~~k~~~g~k~ 856 (1988)
+|-.+-+|.|-+-. -+.+...+|-..+..|=....+.+.+.|+-| -..-||.|=.+.+..+....-....+ ..
T Consensus 460 LK~aLv~f~G~Lkh-----~~p~~y~aii~i~N~Is~~vE~~A~~~~FAiCtYvkDGfWG~F~~~~~~~~~~~~~~~-~a 533 (764)
T PHA03181 460 LKRPIVEFGGLLKH-----FREDVYKAIIGIGNHISLEVEATASTLMFAPCTYVKDGMWGTFIDKANNVIVSPEGNE-NI 533 (764)
T ss_pred HHHHHHHHhhhhhh-----cCHHHHHHHHHHHHHHHHHHHHHHhhcCeeEEeecCCceEEecccccccccccchhhH-HH
Confidence 67777888886655 6788999999999988888888889999987 67899999877654222111000000 00
Q ss_pred c-cccccccccchhhhccccchhhhhccCCccccccccccceeEEeeeceeeeeecccccccCcccccceEEEcCCCCEE
Q 000161 857 L-TISYPCVMLNVDVARNNTNDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLA 935 (1988)
Q Consensus 857 i-~~sy~~~~ln~~V~~~~tN~~y~~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~~~dG~~~ 935 (1988)
+ .+.--|+..+ |..-+++ -.....+..+.+.+||+|.--++-+ -..|=.+|.+...-
T Consensus 534 ~~~lR~ac~~aA--------~~~l~~~------GL~~p~~~~l~LRlEGvYThAvsW~--------~n~yWLwN~~~~~~ 591 (764)
T PHA03181 534 FETLRVACNESA--------NRLATSI------GLRFPDGINLQMRLEGVYTHAMSWN--------ANCYWLWNRNTRES 591 (764)
T ss_pred HHHHHHHHHHHH--------HHHHHhc------CCCCCCCCCceEEEeEEeeeeeeec--------CcceeeccCCCCCc
Confidence 0 0001121111 1111111 1122345556666669997776654 57888888765333
Q ss_pred EEEeeeeccCChhHHHHHHHHHHHHHHhCC----CCHHHHHHHHHHHHHHHHHHHHhcCCC
Q 000161 936 ELKGFEIKRRGELKLIKVFQAELFDKFLHG----STIEECYSAVAAVANRWLDLLDNQGKD 992 (1988)
Q Consensus 936 e~KG~E~kRRd~~~liK~~q~~v~~~~L~g----~~lee~~~~v~~v~~~~~d~L~~~~~~ 992 (1988)
++-||- .|..-..-+|+..+.+++.+... .+++.+.+.+++..++++..-..+.++
T Consensus 592 ~~vGFP-~r~~~~~~ak~~Ls~lL~~i~~~~~~~~~l~~~~~~a~~~cd~Lv~~AF~~R~D 651 (764)
T PHA03181 592 DFVGFP-KQPEFATHAKEALSTLLEEICLCNDTDESLLTIQEKVQKVFEELLYMAFKKRGD 651 (764)
T ss_pred ceeecC-CCcHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 678994 55667888999999999887754 357778888888888777655555554
No 136
>PHA03144 helicase-primase primase subunit; Provisional
Probab=45.23 E-value=3e+02 Score=37.89 Aligned_cols=185 Identities=14% Similarity=0.165 Sum_probs=119.8
Q ss_pred HHHHhhhccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHcCCeE-EEccceeeEEcCCCCCccccccccccccc
Q 000161 778 HKCILNSFYGYVMRKGARWYSMEMAGVVTYTGAKIIQNARLLIEKIGKPL-ELDTDGIWCVLPGSFPENFTFKTKDLKKK 856 (1988)
Q Consensus 778 ~K~ilNS~YGy~g~~~sR~ys~e~A~~VT~~Gr~iI~~a~~lve~~G~~v-ygDTDSI~~~lp~~~pe~~~~k~~~g~k~ 856 (1988)
+|-.+-+|.|-+-. -+.+...+|-..+..|=....+.+.+.|+-| -..-||.|=.+++.-.+...-. ..+ .-
T Consensus 451 lK~aLv~f~GgL~h-----~~p~~yr~ii~i~N~Is~~vE~~A~~~~FAiCtYvkDGfWG~f~~~~~~~~~~~-a~~-~a 523 (746)
T PHA03144 451 LKAALVSFFGGLQH-----ICPAAYRALIALANAVSRALERAANAVGFAVCTYVKDGFWGVLGVDPQDAVSAD-ALA-AA 523 (746)
T ss_pred HHHHHHHHhhhhhh-----cCHHHHHHHHHHHHHHHHHHHHHHhhcCeeEEeecCCceEEeccCCcccccccc-hhh-HH
Confidence 67777888886655 6788999999999888888888889999987 6789999987776421111100 000 00
Q ss_pred ccccccccccchhhhccccchhhhhccCCccccccccccceeEEeeeceeeeeecccccccCcccccceEEEcCCCCEEE
Q 000161 857 LTISYPCVMLNVDVARNNTNDQYQTLVDPVSKTYETHSECSIEFEVDGPYKAMILPASKEEGILIKKRYAVFNDDGTLAE 936 (1988)
Q Consensus 857 i~~sy~~~~ln~~V~~~~tN~~y~~l~~~~~~~y~~~s~~~I~fE~Dg~Y~~miLp~s~~~~~~~KKRYa~~~~dG~~~e 936 (1988)
..+.--|+... |..-+++ -.....+.++.+.+||+|.--++-+ -..|=.+|.+-..-+
T Consensus 524 e~lR~ace~aA--------~~~L~~~------GL~~~~~~~l~LRlEGvyThAvsW~--------~~~yWLwN~~~~~~~ 581 (746)
T PHA03144 524 ERARAACQAAA--------EAVLADM------GLLLPEGAPLHLRLEGLYTHAVSWS--------QHGYWLWNRRTDTED 581 (746)
T ss_pred HHHHHHHHHHH--------HHHHHhc------CCCCCCCCCceEEEeEEeeeeeeec--------CcceeeccCCCCccc
Confidence 00111122111 1111111 1112445666777779997777654 678888886443337
Q ss_pred EEeeeeccCChhHHHHHHHHHHHH-HHhCCCCHHHHHHHHHHHHHHHHHHHHhcCCC
Q 000161 937 LKGFEIKRRGELKLIKVFQAELFD-KFLHGSTIEECYSAVAAVANRWLDLLDNQGKD 992 (1988)
Q Consensus 937 ~KG~E~kRRd~~~liK~~q~~v~~-~~L~g~~lee~~~~v~~v~~~~~d~L~~~~~~ 992 (1988)
+-||-. |..-...+|+-.+.++. ..-...+++++.+.+++..+++...-..+.++
T Consensus 582 ~vGFP~-Rs~~a~~ak~aL~~lL~~~~~~~~~~~~~~~~a~~~cd~lv~~AF~~R~D 637 (746)
T PHA03144 582 FVGFPL-RSAAARAAKAALRALLRAAVADSADAETLRQAAREACDRLVLEAFARRLD 637 (746)
T ss_pred eeeccC-chHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 899966 78888899999999996 44455678888888888888776655545554
No 137
>PHA02528 43 DNA polymerase; Provisional
Probab=41.49 E-value=96 Score=43.83 Aligned_cols=111 Identities=14% Similarity=0.163 Sum_probs=74.7
Q ss_pred HHHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHH---HHHHH-----HhHcC-CeEEEEeCCeEEEEcCCCC-------
Q 000161 1568 AILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFA---MLLAE-----FRKLG-ATIIFANFSKVIIDTGKFD------- 1631 (1988)
Q Consensus 1568 ~ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~fl---qLlaE-----fkRLG-s~VVyAd~~riil~T~K~~------- 1631 (1988)
.+++.||--+-++.+.+||+.+-..|-..=+.++. +-++| .+..| ++|||+|-..|.|..+..-
T Consensus 547 I~~NS~YG~lG~~~~r~y~~~~A~aiT~~Gr~~I~~i~~~~~e~l~~~~~~~g~~~VIYGDTDSvfV~~~~~~~~~~~~~ 626 (881)
T PHA02528 547 ILINSLYGALGNEHFRYYDLRNAEAITLFGQLAIQWIERKMNEYLNKLCKTEDEDYVIYGDTDSIYVNLDPLVEKVGEDK 626 (881)
T ss_pred HHHHhhhhhccCcCccCCCHHHHHHHHHHhHHHHHHHHHHHHHHHHHhhcccCCcEEEEEcCCeeEEEeCCcchhhhhcc
Confidence 56779999999999999999998887665554443 22323 23357 6999999999999987541
Q ss_pred hHhHHHHHHHHHHHhh---c-------ccc------c-cceecchhchheeeeeecCCCccccc
Q 000161 1632 LSAAKAYCDSLLKALQ---T-------REL------F-EWIELEPVHFWHSLLFMDQYNYGGIP 1678 (1988)
Q Consensus 1632 v~~A~ay~~yi~~si~---~-------~~l------F-~~l~L~~~~yW~~LlwmD~~NygGi~ 1678 (1988)
..+..+.++++-+-.+ . ++| | +-+.|...+.+...+|+-+-.|+|..
T Consensus 627 ~~~~~~lv~~~~~~~~~~l~~~~~~~~~el~e~~~~~~~~~~m~~ek~~~~~~~~sKKRYAgl~ 690 (881)
T PHA02528 627 FKDTNHWVDFLDKFCKERMEPYIDSSYRELCEYMNNYEHLMFMDREAIAGPGFWTAKKRYALNV 690 (881)
T ss_pred chhHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHhhhccccchhHHHHhhHhhhhccccEEEEe
Confidence 1122333322211111 0 011 1 34778899999999999999999974
No 138
>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=39.68 E-value=2e+02 Score=36.75 Aligned_cols=101 Identities=12% Similarity=-0.050 Sum_probs=58.3
Q ss_pred HHHHHHHHHhhCCCE-EEeeCcccCCHHHHHHHHHHcCCCCCcccCccccCCCCceeeccceEechHHHHhhccCCCCCC
Q 000161 314 LRLWFAHMQEVKPGI-YVTYNGDYFDWPFLETRAAHHGFKMSEELGFQCDKNQGECRAKFACHLDCFAWVKRDSYLPQGS 392 (1988)
Q Consensus 314 L~~F~~~I~~~DPDI-IvGYNgd~FDlPyL~~Ra~~lGi~l~~~iG~~~~~~~g~~~i~GRihiDl~~~vkrd~~L~~~S 392 (1988)
+..|.+++. ||+| .++||. .+|+..|.+ ++.. . + ..++|+.-...-- . +..+
T Consensus 59 ~~~L~~lL~--d~~i~KV~h~~-k~Dl~~L~~----~~~~-------~-~----------~~~fDtqlAa~lL-~-~~~~ 111 (367)
T TIGR01388 59 WSPLKELLR--DESVVKVLHAA-SEDLEVFLN----LFGE-------L-P----------QPLFDTQIAAAFC-G-FGMS 111 (367)
T ss_pred HHHHHHHHC--CCCceEEEeec-HHHHHHHHH----HhCC-------C-C----------CCcccHHHHHHHh-C-CCCC
Confidence 444555555 5676 489987 467777642 2111 1 0 1346765433211 1 1135
Q ss_pred CCHHHHHHHHcCCCCCCCChHHHHHHHhhC--hHHHHHHHHHhhHHHHHHHHHh
Q 000161 393 QGLKAVTKAKLGYDPLEVNPEDMVRFAKEK--PQMMASYSVSDAVATYYLYMTY 444 (1988)
Q Consensus 393 ysL~~Va~~~LG~~K~dvd~~~i~~~~~~~--~~~La~Y~l~Da~lt~~L~~Kl 444 (1988)
++|..+++.+||..-.. .+. ...|... ......|...|+..++.|+.++
T Consensus 112 ~~l~~Lv~~~Lg~~l~K--~~~-~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L 162 (367)
T TIGR01388 112 MGYAKLVQEVLGVELDK--SES-RTDWLARPLTDAQLEYAAADVTYLLPLYAKL 162 (367)
T ss_pred ccHHHHHHHHcCCCCCc--ccc-cccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 79999999999975210 010 1123222 3567899999999998888875
No 139
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=37.37 E-value=46 Score=45.22 Aligned_cols=59 Identities=25% Similarity=0.401 Sum_probs=42.1
Q ss_pred CCHHHHHHHHcCCCCCCCChHHHHH-----HHhhChHHHHHHHHHhhHHHHHHHHHhccchHhhh
Q 000161 393 QGLKAVTKAKLGYDPLEVNPEDMVR-----FAKEKPQMMASYSVSDAVATYYLYMTYVHPFIFSL 452 (1988)
Q Consensus 393 ysL~~Va~~~LG~~K~dvd~~~i~~-----~~~~~~~~La~Y~l~Da~lt~~L~~Klv~~~i~~L 452 (1988)
.||.+|++.+.|....+-++.+... =-.++.+.|.+||.+|+.+|.++|.++ .|...+-
T Consensus 323 NSL~dVhk~~c~~~~LdKt~Rd~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~l-fP~Fler 386 (1075)
T KOG3657|consen 323 NSLVDVHKFHCGIDALDKTPRDSFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRL-FPLFLER 386 (1075)
T ss_pred HHHHHHHHhhCCCCccccchHHhhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHH-hHHHHHh
Confidence 5799999988887765544433321 012456799999999999999999985 5654443
No 140
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=31.62 E-value=23 Score=32.74 Aligned_cols=30 Identities=27% Similarity=0.709 Sum_probs=23.2
Q ss_pred cccCCCCCCcccccccCcccCCCccccCCCCCCC
Q 000161 1866 VICSYCNDCRDLDLCRDMALLAQDWHCAMPQCGQ 1899 (1988)
Q Consensus 1866 ViC~~Cn~~rDLDlCrD~~~~~~~W~C~~~~C~~ 1899 (1988)
+||++|....=+-.-.+.... .|+|+. |+.
T Consensus 23 LIC~~C~~hNGla~~~~~~~i--~y~C~~--Cg~ 52 (54)
T PF10058_consen 23 LICSKCFSHNGLAPKEEFEEI--QYRCPY--CGA 52 (54)
T ss_pred EECcccchhhcccccccCCce--EEEcCC--CCC
Confidence 689999998888875444433 499999 985
No 141
>PF11635 Med16: Mediator complex subunit 16; InterPro: IPR021665 Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med16 is one of the subunits of the Tail portion of the Mediator complex and is required for lipopolysaccharide gene-expression []. Several members including the human protein, Q9Y2X0 from SWISSPROT, have one or more WD40 domains on them, PF00400 from PFAM.
Probab=27.49 E-value=20 Score=49.60 Aligned_cols=11 Identities=27% Similarity=0.921 Sum_probs=9.0
Q ss_pred cccCCcCCCce
Q 000161 1940 AEQCACAGSFR 1950 (1988)
Q Consensus 1940 s~~C~CsG~~~ 1950 (1988)
..+|-|||.|.
T Consensus 742 ~R~C~CGG~W~ 752 (753)
T PF11635_consen 742 QRNCICGGMWV 752 (753)
T ss_pred eeeeccCCeeC
Confidence 45899999986
No 142
>PHA02754 hypothetical protein; Provisional
Probab=25.78 E-value=1.4e+02 Score=27.90 Aligned_cols=35 Identities=23% Similarity=0.338 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHHHh-HcCC--------eEEEEeCCeEEEEcC
Q 000161 1594 HKVMQKVFAMLLAEFR-KLGA--------TIIFANFSKVIIDTG 1628 (1988)
Q Consensus 1594 ~~LmkK~flqLlaEfk-RLGs--------~VVyAd~~riil~T~ 1628 (1988)
+-+|.|-|...+.|+| +|.. ++||.+.+||++-|.
T Consensus 9 k~i~eK~Fke~MRelkD~LSe~GiYi~RIkai~~SGdkIVVi~a 52 (67)
T PHA02754 9 KAIMEKDFKEAMRELKDILSEAGIYIDRIKAITTSGDKIVVITA 52 (67)
T ss_pred HHHHHhHHHHHHHHHHHHHhhCceEEEEEEEEEecCCEEEEEEc
Confidence 5689999999999999 6654 567778888888775
No 143
>KOG0968 consensus DNA polymerase zeta, catalytic subunit [Replication, recombination and repair]
Probab=24.37 E-value=30 Score=48.23 Aligned_cols=96 Identities=11% Similarity=0.195 Sum_probs=74.2
Q ss_pred CCCCCccHHHHHHHHHHHHHHHHHHHHHHhHcCCeEEEEeCCeEEEEcCCCChHhHHHHHHHHHHHhhcc-ccccceecc
Q 000161 1580 PHSKLHDPVLHRILHKVMQKVFAMLLAEFRKLGATIIFANFSKVIIDTGKFDLSAAKAYCDSLLKALQTR-ELFEWIELE 1658 (1988)
Q Consensus 1580 p~S~LyDPaL~r~v~~LmkK~flqLlaEfkRLGs~VVyAd~~riil~T~K~~v~~A~ay~~yi~~si~~~-~lF~~l~L~ 1658 (1988)
|-|-|=|.-++.-=..|-| -.-+++....-||+|||.|-..++|.-.-.++++|..-++-|..+|.++ | +-+-|+
T Consensus 1098 PCaElADsIV~~GRETLEr--aIe~Vn~~d~w~AkVVYGDTDSmFVlL~GaT~eeAF~IGq~iAe~VT~~NP--~PV~LK 1173 (1488)
T KOG0968|consen 1098 PCAELADSIVQKGRETLER--AIEMVNRGDYWGAKVVYGDTDSMFVLLPGATVEEAFEIGQEIAEAVTNSNP--KPVVLK 1173 (1488)
T ss_pred chHHHHHHHHHhhHHHHHH--HHHHHhcCCcCCeEEEEcCCCceEEEecCccHHHHHHHHHHHHHHHHhcCC--CCeEEE
Confidence 3344455544444444443 2467888889999999999999999999999999999999999999886 2 345678
Q ss_pred hhchheeeeeecCCCcccccc
Q 000161 1659 PVHFWHSLLFMDQYNYGGIPA 1679 (1988)
Q Consensus 1659 ~~~yW~~LlwmD~~NygGi~~ 1679 (1988)
..+-|+.-+-+-+--|.|..-
T Consensus 1174 fEKVY~PCvL~tKKRYVG~~Y 1194 (1488)
T KOG0968|consen 1174 FEKVYHPCVLLTKKRYVGFMY 1194 (1488)
T ss_pred eeeecccceeeeccceeeeee
Confidence 888888777778888888854
No 144
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=23.99 E-value=87 Score=37.80 Aligned_cols=46 Identities=26% Similarity=0.569 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHHHHhhCCCEEEeeCcccCCHHHHHHHHHHcCCCCC
Q 000161 307 VNNEIELLRLWFAHMQEVKPGIYVTYNGDYFDWPFLETRAAHHGFKMS 354 (1988)
Q Consensus 307 ~~dE~eLL~~F~~~I~~~DPDIIvGYNgd~FDlPyL~~Ra~~lGi~l~ 354 (1988)
.+|=..||..|+..+- .|-.+|-|||+.||+|.+.+-...+|+.++
T Consensus 103 D~dla~LL~afls~lp--~p~CLVaHng~~~dfpil~qela~lg~~lp 148 (318)
T KOG4793|consen 103 DKDLAKLLTAFLSRLP--TPGCLVAHNGNEYDFPILAQELAGLGYSLP 148 (318)
T ss_pred hHHHHHHHHHHHhcCC--CCceEEeecCCccccHHHHHHHHhcCccch
Confidence 3466678888877543 477899999999999999999999998764
No 145
>cd05535 POLBc_epsilon DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is characteristic of this family with the exception that it contains a large c-terminal domain with an unclear function. Phylogenetic analyses indicate that Pol epsilon is the ortholog to the archaeal Pol B3 rather than to Pol alpha, delta, or zeta. This might be because pol epsilon is ancestral to both archaea and eukaryotes DNA polymerases type B.
Probab=21.51 E-value=4.9e+02 Score=35.35 Aligned_cols=108 Identities=13% Similarity=0.113 Sum_probs=71.7
Q ss_pred HHHHhhhhhhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHh-HcCCeEEEEeCCeEEEEcCCCChHhH---H-------
Q 000161 1568 AILQHLYRWLCSPHSKLHDPVLHRILHKVMQKVFAMLLAEFR-KLGATIIFANFSKVIIDTGKFDLSAA---K------- 1636 (1988)
Q Consensus 1568 ~ll~~~~RWl~sp~S~LyDPaL~r~v~~LmkK~flqLlaEfk-RLGs~VVyAd~~riil~T~K~~v~~A---~------- 1636 (1988)
.++++||--|-.+.|.+||+.+...|-..=+..+. ...++- ++|-.| ++|-..|.+.-+....++. .
T Consensus 280 iIlNSfYGYlG~~gsRwYs~emA~~VT~~GreIIk-~tr~lvE~~G~~V-egDTDsI~~~lp~~~~e~~~~~~k~g~~~~ 357 (621)
T cd05535 280 CILNSFYGYVMRKGSRWYSMEMAGIVCYTGANIIQ-MARELVEQIGRPL-ELDTDGIWCILPKSFPENFTFKTKNGKKVT 357 (621)
T ss_pred HHHhhccCccCcCCcccCCHHHHHHHHHHHHHHHH-HHHHHHHhcCCEE-EEecCeeEEEcCCCChHHHHHHhhccchhh
Confidence 56789999999999999999999999666666555 444444 777766 7999999986433333321 1
Q ss_pred -HHHHHHHHH-------------hhcc-------ccccceecchhchheeeee--------ecCCCcccc
Q 000161 1637 -AYCDSLLKA-------------LQTR-------ELFEWIELEPVHFWHSLLF--------MDQYNYGGI 1677 (1988)
Q Consensus 1637 -ay~~yi~~s-------------i~~~-------~lF~~l~L~~~~yW~~Llw--------mD~~NygGi 1677 (1988)
.|..-+++. +..- .-+..|.|++.-.|..|+. .-+-+|+++
T Consensus 358 ~~~~~~~LN~~V~~~~tn~qy~~l~~p~~~~y~i~se~~IefEvDG~Yk~mllpask~~~~~~KKRYAv~ 427 (621)
T cd05535 358 ISYPCVMLNHLVHKKFTNDQYQELVDPSTGTYETRSENSIFFEVDGPYKAMILPASKEEGKLLKKRYAVF 427 (621)
T ss_pred hhhhHHHHHHHHHHHHHHHHhhhccCcccccccccccceeEEEeccceeeeEcccccccccccccceEEE
Confidence 111111111 1110 1123488889889999999 468889875
No 146
>PF08747 DUF1788: Domain of unknown function (DUF1788); InterPro: IPR014858 This entry represents a putative uncharacterised protein of length around 200 amino acids.
Probab=21.24 E-value=1.3e+02 Score=32.69 Aligned_cols=23 Identities=13% Similarity=0.456 Sum_probs=17.4
Q ss_pred cccCCeEEEEeccccchHHHHhcC
Q 000161 586 REECPLIYHLDVAAMYPNIILTNR 609 (1988)
Q Consensus 586 ~~~~p~V~~LDf~SLYPsII~t~N 609 (1988)
..+...|....++|+||=+ +++.
T Consensus 59 ~~~~~vv~ltGvG~l~P~~-R~h~ 81 (126)
T PF08747_consen 59 DDDRDVVFLTGVGSLFPFI-RSHE 81 (126)
T ss_pred CCCCcEEEEeCcchhcchh-hHHH
Confidence 3455689999999999944 6654
No 147
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=20.57 E-value=60 Score=34.32 Aligned_cols=29 Identities=31% Similarity=0.738 Sum_probs=25.2
Q ss_pred ccCCCCCCcccccccCcccCCCccccCCCCCCCCCChH
Q 000161 1867 ICSYCNDCRDLDLCRDMALLAQDWHCAMPQCGQPYDRE 1904 (1988)
Q Consensus 1867 iC~~Cn~~rDLDlCrD~~~~~~~W~C~~~~C~~~yd~~ 1904 (1988)
+|.+|. .|--||=|+|. .||. |++.|+..
T Consensus 11 ~Cp~CG-~kFYDLnk~Pi------vCP~--CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCG-AKFYDLNKDPI------VCPK--CGTEFPPE 39 (108)
T ss_pred cCCCCc-chhccCCCCCc------cCCC--CCCccCcc
Confidence 688887 78889999876 7999 99999987
Done!