Query 008596
Match_columns 560
No_of_seqs 279 out of 1286
Neff 5.4
Searched_HMMs 46136
Date Thu Mar 28 14:09:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008596.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008596hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2248 3'-5' exonuclease [Rep 100.0 1.8E-46 4E-51 395.0 20.7 329 25-369 34-374 (380)
2 cd06143 PAN2_exo DEDDh 3'-5' e 100.0 1.8E-42 3.8E-47 330.3 13.8 146 215-364 1-174 (174)
3 KOG2249 3'-5' exonuclease [Rep 100.0 8.6E-39 1.9E-43 317.9 14.0 148 213-364 106-260 (280)
4 cd06145 REX1_like DEDDh 3'-5' 100.0 1.8E-35 3.9E-40 276.2 15.6 149 215-363 1-149 (150)
5 cd06149 ISG20 DEDDh 3'-5' exon 100.0 2.7E-33 5.8E-38 263.6 15.5 148 215-364 1-157 (157)
6 cd06137 DEDDh_RNase DEDDh 3'-5 100.0 3.3E-33 7.1E-38 263.5 13.0 150 215-364 1-161 (161)
7 cd06144 REX4_like DEDDh 3'-5' 100.0 4.3E-29 9.2E-34 233.2 15.2 146 215-364 1-152 (152)
8 PRK07247 DNA polymerase III su 99.9 5E-23 1.1E-27 200.8 17.5 159 212-377 5-176 (195)
9 PRK07740 hypothetical protein; 99.9 3.4E-22 7.3E-27 201.1 17.9 152 212-369 59-225 (244)
10 KOG1275 PAB-dependent poly(A) 99.9 3.8E-23 8.2E-28 230.5 10.5 172 210-385 908-1110(1118)
11 cd06130 DNA_pol_III_epsilon_li 99.9 3.7E-22 8.1E-27 184.3 14.7 143 214-364 1-155 (156)
12 PRK06309 DNA polymerase III su 99.9 7.4E-22 1.6E-26 196.9 16.6 166 212-382 2-178 (232)
13 PRK06310 DNA polymerase III su 99.9 8.6E-22 1.9E-26 198.8 17.1 163 212-380 7-185 (250)
14 smart00479 EXOIII exonuclease 99.9 4.7E-22 1E-26 184.8 13.7 150 214-369 2-166 (169)
15 PRK06807 DNA polymerase III su 99.9 1.8E-21 3.9E-26 202.5 18.5 153 210-369 6-171 (313)
16 PRK09145 DNA polymerase III su 99.9 2.9E-21 6.2E-26 188.3 15.8 150 212-367 29-198 (202)
17 PRK06195 DNA polymerase III su 99.9 4.4E-21 9.6E-26 199.0 17.4 157 213-377 2-171 (309)
18 PRK09146 DNA polymerase III su 99.9 3.3E-21 7.1E-26 193.5 15.9 152 212-369 47-226 (239)
19 PRK07942 DNA polymerase III su 99.9 4.4E-21 9.5E-26 191.6 16.1 154 212-369 6-179 (232)
20 PRK06063 DNA polymerase III su 99.9 7.3E-21 1.6E-25 197.9 18.1 151 211-369 14-178 (313)
21 PRK05711 DNA polymerase III su 99.9 4E-21 8.7E-26 193.1 15.5 151 212-367 4-173 (240)
22 PRK07983 exodeoxyribonuclease 99.9 5.2E-21 1.1E-25 189.8 15.7 156 214-378 2-164 (219)
23 TIGR01406 dnaQ_proteo DNA poly 99.9 4.9E-21 1.1E-25 190.6 14.2 149 213-366 1-168 (225)
24 cd06136 TREX1_2 DEDDh 3'-5' ex 99.8 3.6E-21 7.8E-26 184.4 10.9 143 214-365 1-176 (177)
25 PRK08517 DNA polymerase III su 99.8 3.3E-20 7.1E-25 188.2 18.4 181 182-370 36-231 (257)
26 TIGR00573 dnaq exonuclease, DN 99.8 1.4E-20 3E-25 185.8 15.0 154 212-369 7-176 (217)
27 cd06131 DNA_pol_III_epsilon_Ec 99.8 1.6E-20 3.5E-25 176.2 13.9 147 214-365 1-165 (167)
28 PRK07246 bifunctional ATP-depe 99.8 3.5E-20 7.5E-25 214.1 17.7 153 211-369 6-169 (820)
29 PRK07748 sporulation inhibitor 99.8 5.3E-20 1.1E-24 180.3 13.4 154 212-369 4-179 (207)
30 PRK07883 hypothetical protein; 99.8 1.3E-19 2.8E-24 201.5 17.2 153 212-370 15-182 (557)
31 cd06127 DEDDh DEDDh 3'-5' exon 99.8 1.6E-19 3.5E-24 163.7 12.8 143 215-363 1-158 (159)
32 TIGR01407 dinG_rel DnaQ family 99.8 3.6E-19 7.8E-24 206.7 16.3 151 213-369 1-164 (850)
33 PRK08074 bifunctional ATP-depe 99.8 3.3E-19 7.1E-24 208.6 15.9 152 212-369 3-168 (928)
34 TIGR01298 RNaseT ribonuclease 99.8 3.8E-19 8.3E-24 173.8 13.5 152 212-369 8-191 (200)
35 cd06134 RNaseT DEDDh 3'-5' exo 99.8 5.9E-19 1.3E-23 170.9 14.1 151 213-368 6-187 (189)
36 PRK06722 exonuclease; Provisio 99.8 8E-19 1.7E-23 179.9 14.9 153 212-369 5-180 (281)
37 PRK09182 DNA polymerase III su 99.8 1.6E-18 3.6E-23 178.9 17.0 164 210-382 35-213 (294)
38 PRK05168 ribonuclease T; Provi 99.8 1.2E-18 2.6E-23 171.6 14.5 152 212-369 17-200 (211)
39 PF00929 RNase_T: Exonuclease; 99.8 5.6E-21 1.2E-25 173.4 -2.1 145 215-363 1-164 (164)
40 cd06133 ERI-1_3'hExo_like DEDD 99.8 5.1E-19 1.1E-23 166.2 10.4 147 214-365 1-174 (176)
41 TIGR01405 polC_Gram_pos DNA po 99.8 9.4E-19 2E-23 207.5 15.1 152 212-369 190-354 (1213)
42 COG2176 PolC DNA polymerase II 99.8 1.5E-19 3.2E-24 206.8 7.4 152 212-369 421-585 (1444)
43 PRK05601 DNA polymerase III su 99.8 7.7E-18 1.7E-22 177.2 16.9 149 212-365 46-244 (377)
44 COG0847 DnaQ DNA polymerase II 99.8 6.2E-18 1.4E-22 168.2 15.1 155 212-369 13-181 (243)
45 cd06138 ExoI_N N-terminal DEDD 99.7 7.2E-18 1.6E-22 162.2 10.2 145 215-363 1-182 (183)
46 PRK00448 polC DNA polymerase I 99.6 9.3E-16 2E-20 184.4 13.6 152 212-369 419-583 (1437)
47 PRK11779 sbcB exonuclease I; P 99.6 1.5E-15 3.3E-20 165.9 13.8 155 211-369 5-197 (476)
48 PRK05359 oligoribonuclease; Pr 99.6 1.4E-15 3E-20 146.8 11.7 142 212-368 3-173 (181)
49 cd06135 Orn DEDDh 3'-5' exonuc 99.6 9E-16 2E-20 146.7 10.2 141 214-368 1-170 (173)
50 PTZ00315 2'-phosphotransferase 99.6 6.5E-15 1.4E-19 162.8 15.3 154 212-369 56-254 (582)
51 cd06139 DNA_polA_I_Ecoli_like_ 98.5 2.5E-06 5.4E-11 81.1 13.0 149 212-378 5-179 (193)
52 COG5018 KapD Inhibitor of the 98.4 9.8E-08 2.1E-12 91.0 2.5 153 213-369 5-184 (210)
53 cd05160 DEDDy_DNA_polB_exo DED 98.4 1.1E-06 2.4E-11 85.0 9.7 122 214-343 1-163 (199)
54 PF01612 DNA_pol_A_exo1: 3'-5' 98.3 3E-06 6.5E-11 78.9 9.6 127 213-365 21-170 (176)
55 KOG3242 Oligoribonuclease (3'- 98.1 6.1E-06 1.3E-10 79.2 6.7 143 212-369 26-198 (208)
56 cd06146 mut-7_like_exo DEDDy 3 98.1 1.2E-05 2.5E-10 78.6 8.5 86 280-365 71-190 (193)
57 KOG0542 Predicted exonuclease 98.0 2.7E-06 5.8E-11 85.9 3.2 153 213-370 57-242 (280)
58 COG1949 Orn Oligoribonuclease 98.0 1E-05 2.3E-10 77.0 6.8 152 211-369 5-177 (184)
59 PRK05755 DNA polymerase I; Pro 97.9 9.7E-05 2.1E-09 87.3 12.6 132 212-369 315-468 (880)
60 COG2925 SbcB Exonuclease I [DN 97.7 0.00034 7.3E-09 74.5 11.7 154 212-369 9-200 (475)
61 cd06125 DnaQ_like_exo DnaQ-lik 97.7 0.00018 4E-09 62.6 8.0 57 215-307 1-61 (96)
62 cd06141 WRN_exo DEDDy 3'-5' ex 97.7 0.0002 4.4E-09 67.5 8.8 83 282-364 64-166 (170)
63 cd00007 35EXOc 3'-5' exonuclea 97.6 0.0011 2.4E-08 59.8 12.2 104 214-343 2-111 (155)
64 cd06129 RNaseD_like DEDDy 3'-5 97.5 0.00048 1E-08 65.0 9.2 81 283-364 59-157 (161)
65 PRK10829 ribonuclease D; Provi 97.5 0.0013 2.7E-08 71.0 13.3 124 212-366 22-166 (373)
66 cd05780 DNA_polB_Kod1_like_exo 97.3 0.0015 3.2E-08 63.8 9.7 115 212-343 3-156 (195)
67 TIGR01388 rnd ribonuclease D. 96.9 0.011 2.4E-07 63.5 12.4 62 283-345 62-128 (367)
68 COG0349 Rnd Ribonuclease D [Tr 96.8 0.011 2.5E-07 63.2 11.9 125 212-363 17-153 (361)
69 TIGR01696 deoB phosphopentomut 96.8 0.0071 1.5E-07 65.4 10.4 110 372-514 216-325 (381)
70 smart00474 35EXOc 3'-5' exonuc 96.6 0.043 9.4E-07 50.4 13.1 65 280-344 64-132 (172)
71 cd06142 RNaseD_exo DEDDy 3'-5' 96.6 0.055 1.2E-06 50.8 13.7 63 280-343 53-120 (178)
72 cd06148 Egl_like_exo DEDDy 3'- 96.4 0.0068 1.5E-07 59.3 6.3 63 281-343 55-129 (197)
73 cd05779 DNA_polB_epsilon_exo D 96.2 0.052 1.1E-06 53.9 11.7 128 212-342 2-168 (204)
74 cd05784 DNA_polB_II_exo DEDDy 96.1 0.12 2.5E-06 51.0 13.2 116 211-342 2-153 (193)
75 PRK05362 phosphopentomutase; P 96.0 0.039 8.5E-07 60.0 10.5 110 372-514 223-333 (394)
76 cd05785 DNA_polB_like2_exo Unc 95.9 0.034 7.4E-07 55.2 8.7 72 211-306 8-91 (207)
77 cd05781 DNA_polB_B3_exo DEDDy 95.8 0.072 1.6E-06 52.0 10.2 105 211-341 2-143 (188)
78 PF13482 RNase_H_2: RNase_H su 95.7 0.025 5.5E-07 52.8 6.5 124 215-369 1-136 (164)
79 COG1015 DeoB Phosphopentomutas 95.7 0.077 1.7E-06 56.9 10.5 110 372-514 226-336 (397)
80 cd06140 DNA_polA_I_Bacillus_li 95.5 0.41 8.9E-06 45.2 13.9 103 213-343 4-113 (178)
81 cd05783 DNA_polB_B1_exo DEDDy 95.4 0.22 4.7E-06 49.4 12.2 124 211-342 4-170 (204)
82 PRK12383 putative mutase; Prov 94.9 0.17 3.6E-06 55.4 10.3 109 373-516 234-343 (406)
83 COG0749 PolA DNA polymerase I 94.2 0.28 6E-06 56.0 10.5 131 215-369 25-179 (593)
84 TIGR00593 pola DNA polymerase 92.0 0.64 1.4E-05 55.7 9.4 94 275-369 362-476 (887)
85 cd06147 Rrp6p_like_exo DEDDy 3 91.9 1 2.2E-05 43.6 9.2 58 283-343 69-132 (192)
86 PF01676 Metalloenzyme: Metall 90.9 0.29 6.3E-06 49.8 4.5 77 410-519 124-201 (252)
87 PRK05762 DNA polymerase II; Re 90.7 1.7 3.7E-05 51.5 11.2 136 210-364 153-346 (786)
88 PF04857 CAF1: CAF1 family rib 89.6 0.58 1.3E-05 47.9 5.5 74 288-364 147-261 (262)
89 PF03104 DNA_pol_B_exo1: DNA p 89.3 1.7 3.7E-05 44.7 8.7 86 210-306 155-255 (325)
90 cd05778 DNA_polB_zeta_exo inac 88.4 5.1 0.00011 40.4 11.2 94 212-306 4-114 (231)
91 cd05777 DNA_polB_delta_exo DED 88.1 3.6 7.9E-05 41.2 9.9 85 211-306 6-104 (230)
92 PF01663 Phosphodiest: Type I 87.9 1.4 3.1E-05 45.4 7.1 67 420-517 177-248 (365)
93 cd05782 DNA_polB_like1_exo Unc 86.5 1.1 2.5E-05 44.4 5.2 64 277-342 79-169 (208)
94 KOG2126 Glycosylphosphatidylin 85.9 1.3 2.8E-05 52.3 5.9 112 373-515 144-264 (895)
95 cd05776 DNA_polB_alpha_exo ina 84.3 3.7 8.1E-05 41.4 7.8 132 211-344 2-188 (234)
96 cd09018 DEDDy_polA_RNaseD_like 84.1 1.5 3.2E-05 39.7 4.4 60 283-343 45-110 (150)
97 smart00486 POLBc DNA polymeras 81.3 3.4 7.3E-05 44.5 6.6 84 212-306 3-102 (471)
98 PTZ00166 DNA polymerase delta 78.9 7.9 0.00017 47.6 9.2 86 210-306 262-363 (1054)
99 PHA02528 43 DNA polymerase; Pr 78.3 9.5 0.00021 46.0 9.4 92 211-306 105-211 (881)
100 PRK04024 cofactor-independent 74.2 17 0.00038 40.0 9.5 74 410-518 279-353 (412)
101 TIGR00592 pol2 DNA polymerase 73.9 14 0.00031 45.8 9.7 99 263-363 572-719 (1172)
102 PLN02538 2,3-bisphosphoglycera 73.3 11 0.00024 43.1 7.8 81 406-519 400-481 (558)
103 TIGR01307 pgm_bpd_ind 2,3-bisp 72.2 13 0.00028 42.1 8.0 81 405-518 360-441 (501)
104 COG4566 TtrR Response regulato 68.1 8.1 0.00018 38.5 4.7 26 498-525 71-96 (202)
105 PF10108 DNA_pol_B_exo2: Predi 66.4 9.9 0.00021 38.3 5.0 65 276-342 37-129 (209)
106 PHA02570 dexA exonuclease; Pro 64.8 31 0.00067 35.1 8.2 92 215-306 4-124 (220)
107 cd06128 DNA_polA_exo DEDDy 3'- 64.0 11 0.00024 34.5 4.6 59 283-342 45-109 (151)
108 TIGR00306 apgM 2,3-bisphosphog 63.6 50 0.0011 36.3 10.2 36 481-516 309-345 (396)
109 TIGR02335 hydr_PhnA phosphonoa 63.6 58 0.0013 35.8 10.7 35 478-515 207-241 (408)
110 COG0417 PolB DNA polymerase el 62.6 54 0.0012 39.2 11.0 121 210-343 152-309 (792)
111 PRK05434 phosphoglyceromutase; 58.8 25 0.00054 39.9 7.0 79 407-518 368-447 (507)
112 KOG0969 DNA polymerase delta, 57.0 8.7 0.00019 45.2 3.0 149 210-369 272-479 (1066)
113 COG3359 Predicted exonuclease 56.0 1.4E+02 0.003 31.2 11.0 112 211-344 97-220 (278)
114 PRK05761 DNA polymerase I; Rev 53.1 30 0.00065 41.3 6.8 89 275-363 209-334 (787)
115 PRK11598 putative metal depend 47.5 43 0.00092 38.4 6.6 129 373-515 306-458 (545)
116 PRK09598 lipid A phosphoethano 42.9 63 0.0014 36.8 7.1 130 373-515 293-442 (522)
117 cd05015 SIS_PGI_1 Phosphogluco 40.2 51 0.0011 31.1 5.0 30 494-523 64-94 (158)
118 KOG3657 Mitochondrial DNA poly 39.9 23 0.00049 42.3 2.9 31 288-318 239-275 (1075)
119 KOG4793 Three prime repair exo 39.7 42 0.00092 35.3 4.6 156 211-368 12-216 (318)
120 KOG1798 DNA polymerase epsilon 39.5 2.3E+02 0.005 36.6 11.1 148 212-369 246-453 (2173)
121 PHA02524 43A DNA polymerase su 38.5 1.1E+02 0.0023 34.9 7.9 92 211-306 105-213 (498)
122 PF07819 PGAP1: PGAP1-like pro 31.3 27 0.00058 35.0 1.6 44 257-300 47-96 (225)
123 PRK11560 phosphoethanolamine t 29.0 1.5E+02 0.0033 34.1 7.3 33 483-515 435-468 (558)
124 PRK04135 cofactor-independent 28.6 2.4E+02 0.0052 31.2 8.4 100 380-516 233-334 (395)
125 PF01380 SIS: SIS domain SIS d 24.6 1.2E+02 0.0027 26.4 4.5 33 493-525 44-76 (131)
126 PF10239 DUF2465: Protein of u 23.4 2.9E+02 0.0064 29.6 7.7 51 481-533 152-205 (318)
127 cd05017 SIS_PGI_PMI_1 The memb 22.1 1.3E+02 0.0028 26.6 4.2 28 499-526 40-67 (119)
128 PRK04200 cofactor-independent 20.5 2.5E+02 0.0055 30.9 6.7 36 481-516 305-343 (395)
129 PF10752 DUF2533: Protein of u 20.1 1.2E+02 0.0026 26.4 3.2 21 536-556 26-46 (84)
No 1
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=1.8e-46 Score=395.03 Aligned_cols=329 Identities=38% Similarity=0.483 Sum_probs=244.4
Q ss_pred CceeEeeeCCCcceEEEEecC-Cc--cchhhHHHHHHHHhcCCCCCceEEeccCCCcceEEEEEecCcChhhhhcccccc
Q 008596 25 GNNFYDIYGPQGKAEVIFKNE-ST--LNLTDVQGLVTWVLADGIMPSWVFIKNKPLIQKVVMLYVPGLDAALYLSQSKTL 101 (560)
Q Consensus 25 ~~~~~~i~g~~ak~ev~f~~~-~~--i~l~dlq~Lll~~~~~~~~P~W~~v~~~~~i~kvVvl~vpGl~~~~~~~~~~~~ 101 (560)
...+++.+|+-.+.. .+..+ ++ +..+..+....+..+.+.+|.|+.+.+....++...++.+|+..+.+......+
T Consensus 34 ~~~~~~~~~~~~~~~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 112 (380)
T KOG2248|consen 34 LQLFPDLEGALLKTC-SSIAPNSPLCLNSKGREGTRISLVAEGNAPKIVLLSKPELKQKDYLLSFSGLSKAILNLVATNL 112 (380)
T ss_pred ccccccccccccccc-cccccccchhccccccccchhHHHHhccCceeeeeccchhhhhhheeccCCccHHHhhhhhccc
Confidence 778999999988888 76665 44 677778888888889999999999999999999999999999999886554433
Q ss_pred ccccccCCCCcccccccccc-----CccchhhhhhhccccccccccccCCCCCCCCCcCCCCccCCCCchhhhcCCCCCC
Q 008596 102 AGFKECCDKPRALLALSCLS-----DTMLTIDGLLTCKLKRKRNAVDSMTKSTQPSQKENCSTVSENSSSAELLKDIPFP 176 (560)
Q Consensus 102 ~~~~~~~~~p~~~~~~~~~~-----~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 176 (560)
.........+.+-....|.. ....-+. -+.|..+..+.......... +.+..+.......
T Consensus 113 ~~~~~~~~~~~~~~~~r~~~~f~~~~~~~~~~-~~l~~~~~~~~~~~~~~~~~-------------~~~~~~~~~~~~~- 177 (380)
T KOG2248|consen 113 KDVDRSDKALLPRPCSRCGSEFYVTEKGREFK-DLLCKYHPGKLIREPRRGFK-------------DKTEDCCTPKEGL- 177 (380)
T ss_pred ccccccCccccCchhhhhhhhhccccchhhhh-hhhccccccccccchhcccc-------------ccCchhhcccccC-
Confidence 32222221111100000100 0000011 11222221111110000000 0000111111112
Q ss_pred cccccCCHHHHhhCCccc-cCCCceeccCCC--CCCCCCcEEEEEeccccCCCCceEEEEEEEEecCcEEEEEEEeCCCC
Q 008596 177 ITYYTLTEKQLEDNNYCY-NQPGFLSTVPAP--FGSSPYEILALDCEMCYTNEGLELTRVTLVDIKGQVLLDKLVKPSNA 253 (560)
Q Consensus 177 ~~~~~l~~~~l~~~~~p~-~~~~~~~t~~~~--~~~~~~~~valDcEm~~t~~g~eL~rVsvVd~~G~vvlD~LVkP~~~ 253 (560)
+..+.+.++...+..|+. ...+|+++...+ ..+.+.+++|||||||.|..|.|++||++||.+|+++||+||+|.+|
T Consensus 178 ~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~v~~~~~i~AlDCEm~~te~g~el~RVt~VD~~~~vi~D~fVkP~~~ 257 (380)
T KOG2248|consen 178 VSFLCLGPDYHVEILFPSESLDEFVQTLGAKGKAVSKSPNIFALDCEMVVTENGLELTRVTAVDRDGKVILDTFVKPNKP 257 (380)
T ss_pred ccceeecccccccccCccccccceecccccCCCCCCCCCCeEEEEeeeeeeccceeeEEeeeeeccCcEEeEEeecCCCc
Confidence 222334445555555555 456777776553 23445689999999999999999999999999999999999999999
Q ss_pred CCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcCCCEEEEeCchhhHHHHccccCcccccccccccccCC-CCCccHH
Q 008596 254 IVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKETILVGHSLENDLLALKISHGLVIDTAVLYKHPQGG-SHKTSLR 332 (560)
Q Consensus 254 I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~~~ILVGHsL~~DL~aLki~Hp~viDT~~Ly~~~~g~-~~k~sLk 332 (560)
|+||+|+|||||++|+++++++++|||.+|+++++.+||||||||++||++||+.||.||||+.+|.++.|+ +++.||+
T Consensus 258 VvDy~T~~SGIT~~~~e~~t~tl~dvq~~l~~~~~~~TILVGHSLenDL~aLKl~H~~ViDTa~lf~~~~g~~~~k~sLk 337 (380)
T KOG2248|consen 258 VVDYNTRYSGITEEDLENSTITLEDVQKELLELISKNTILVGHSLENDLKALKLDHPSVIDTAVLFKHPTGPYPFKSSLK 337 (380)
T ss_pred ccccccccccccHHHHhcCccCHHHHHHHHHhhcCcCcEEEeechhhHHHHHhhhCCceeeeeEEEecCCCCccchHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999999986 8999999
Q ss_pred HHHHHhcCcccccCCCCCChHHHHHHHHHHHHHHHHh
Q 008596 333 VLAKKFLSREIQQSGFGHDSTEDARAAMELALLKIRN 369 (560)
Q Consensus 333 ~La~~~Lg~~IQ~~~~~HdSlEDA~Atl~L~~~kl~~ 369 (560)
+||+.|||+.||++..||||+|||.|||+|+++++++
T Consensus 338 ~L~~~~L~~~Iq~~~~~HdS~eDA~acm~Lv~~k~~~ 374 (380)
T KOG2248|consen 338 NLAKSYLGKLIQEGVGGHDSVEDALACMKLVKLKIKN 374 (380)
T ss_pred HHHHHHHHHHHhccCCCCccHHHHHHHHHHHHHHHhc
Confidence 9999999999996557899999999999999998877
No 2
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=100.00 E-value=1.8e-42 Score=330.32 Aligned_cols=146 Identities=38% Similarity=0.530 Sum_probs=134.5
Q ss_pred EEEEeccccCCC--------C---------ceEEEEEEEE----ecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCC
Q 008596 215 LALDCEMCYTNE--------G---------LELTRVTLVD----IKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVT 273 (560)
Q Consensus 215 valDcEm~~t~~--------g---------~eL~rVsvVd----~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~ 273 (560)
|||||||++++. | .+|+|||+|| .+|+++||+||+|..+|.||+|+|||||+++|++++
T Consensus 1 ~a~d~e~v~~~~~~~~~~~~g~~~~~~~~~~~LaRVsiVd~~~~~~g~vllD~~VkP~~~V~DYrT~~SGIt~~~L~~a~ 80 (174)
T cd06143 1 VAIDAEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKT 80 (174)
T ss_pred CceeeeEEEecchhceecCCCcEeeeccCCceeEEEEEEcCCCCcCCCEEEeeeECCCCCccCcCccccccCHHHcCccc
Confidence 589999998865 4 2699999999 689999999999999999999999999999999874
Q ss_pred -----CCHHHHHHHHHHhhcCCCEEEEeCchhhHHHHccccC--cccccccccccccCCCCCccHHHHHHHhcCcccccC
Q 008596 274 -----TSLKDIQEEFLKLVYKETILVGHSLENDLLALKISHG--LVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQS 346 (560)
Q Consensus 274 -----~tl~dVq~~L~~~i~~~~ILVGHsL~~DL~aLki~Hp--~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~ 346 (560)
++++++|+++++++++++|||||+|+|||++|++.|| .+|||+.+|+++.+ +++||++||++|||++||.
T Consensus 81 ~~~~~~t~~~v~~~l~~li~~~tILVGHsL~nDL~aL~l~hp~~~viDTa~l~~~~~~--r~~sLk~La~~~L~~~IQ~- 157 (174)
T cd06143 81 SSKNLTTLKSAYLKLRLLVDLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFHLPGQ--RKLSLRFLAWYLLGEKIQS- 157 (174)
T ss_pred cccccCCHHHHHHHHHHHcCCCCEEEeccchhHHHHhcCcCCCcceEEcHHhccCCCC--CChhHHHHHHHHcCCcccC-
Confidence 4799999999999999999999999999999999987 79999999988754 5899999999999999997
Q ss_pred CCCCChHHHHHHHHHHHH
Q 008596 347 GFGHDSTEDARAAMELAL 364 (560)
Q Consensus 347 ~~~HdSlEDA~Atl~L~~ 364 (560)
++|||+|||+|||+||+
T Consensus 158 -~~HdSvEDArAam~Ly~ 174 (174)
T cd06143 158 -ETHDSIEDARTALKLYR 174 (174)
T ss_pred -CCcCcHHHHHHHHHHhC
Confidence 59999999999999983
No 3
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=8.6e-39 Score=317.85 Aligned_cols=148 Identities=42% Similarity=0.594 Sum_probs=135.8
Q ss_pred cEEEEEeccccCCCC---ceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcC
Q 008596 213 EILALDCEMCYTNEG---LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYK 289 (560)
Q Consensus 213 ~~valDcEm~~t~~g---~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~ 289 (560)
++|||||||+|++++ +.|+||||||..|.||||+||||..+|+||+|++|||+++.|.++ ++|+.+|.++.+|| .
T Consensus 106 r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP~~~VtDyRT~vSGIrpehm~~A-~pf~~aQ~ev~klL-~ 183 (280)
T KOG2249|consen 106 RVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKPTEPVTDYRTRVSGIRPEHMRDA-MPFKVAQKEVLKLL-K 183 (280)
T ss_pred eEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecCCCcccccceeeecccCHHHhccC-ccHHHHHHHHHHHH-h
Confidence 599999999999874 589999999999999999999999999999999999999999999 79999999999999 8
Q ss_pred CCEEEEeCchhhHHHHccccC--cccccccccccc--cCCCCCccHHHHHHHhcCcccccCCCCCChHHHHHHHHHHHH
Q 008596 290 ETILVGHSLENDLLALKISHG--LVIDTAVLYKHP--QGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMELAL 364 (560)
Q Consensus 290 ~~ILVGHsL~~DL~aLki~Hp--~viDT~~Ly~~~--~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~Atl~L~~ 364 (560)
+.|||||.|.|||.+|++.|| .+.||+..-+.. ......+||+.|++.+||++||. +-|+|+|||+|||+||.
T Consensus 184 gRIlVGHaLhnDl~~L~l~hp~s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~--GeHsSvEDA~AtM~LY~ 260 (280)
T KOG2249|consen 184 GRILVGHALHNDLQALKLEHPRSMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQV--GEHSSVEDARATMELYK 260 (280)
T ss_pred CCEEeccccccHHHHHhhhCchhhhcccccCchHHHHhhccCCccHHHHHHHHhchhhhc--cccCcHHHHHHHHHHHH
Confidence 999999999999999999999 489999753322 23456899999999999999998 46999999999999984
No 4
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=100.00 E-value=1.8e-35 Score=276.18 Aligned_cols=149 Identities=66% Similarity=0.994 Sum_probs=138.8
Q ss_pred EEEEeccccCCCCceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcCCCEEE
Q 008596 215 LALDCEMCYTNEGLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKETILV 294 (560)
Q Consensus 215 valDcEm~~t~~g~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~~~ILV 294 (560)
|||||||+|+..|+||++|++|+.+|+++|++||+|..+|++|+|++||||++||++++++++++++++++|+.++++||
T Consensus 1 ~~iD~E~~g~~~g~ei~~i~~v~~~~~~~f~~lv~P~~~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~~~fl~~~~vlV 80 (150)
T cd06145 1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80 (150)
T ss_pred CEEeeeeeeecCCCEEEEEEEEeCCCCEEEEEeECCCCccchhccCcCCCCHHHhccCCCCHHHHHHHHHHHhCCCCEEE
Confidence 68999999999899999999999999999999999999999999999999999999995699999999999996589999
Q ss_pred EeCchhhHHHHccccCcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHHHHHHHHHH
Q 008596 295 GHSLENDLLALKISHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMELA 363 (560)
Q Consensus 295 GHsL~~DL~aLki~Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~Atl~L~ 363 (560)
|||+.||+++|+..|++++||+.|++...++..+++|+.||++|+|+.||.+++.|+|++||++|++||
T Consensus 81 gHn~~fD~~fL~~~~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 81 GHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELV 149 (150)
T ss_pred EcChHHHHHHhhccCCCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCCCCCcHHHHHHHHHHh
Confidence 999999999999999999999999988766555789999999999999985346899999999999997
No 5
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=100.00 E-value=2.7e-33 Score=263.56 Aligned_cols=148 Identities=43% Similarity=0.650 Sum_probs=132.5
Q ss_pred EEEEeccccCCCC---ceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcCCC
Q 008596 215 LALDCEMCYTNEG---LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKET 291 (560)
Q Consensus 215 valDcEm~~t~~g---~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~~~ 291 (560)
|||||||||++++ .+|++|++|+.+|.++|++||+|..+|++|.|++||||++||+++ ++++++++++++|+ +++
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~~~~~~lv~P~~~i~~~~~~i~GIt~~~l~~a-~~~~~v~~~l~~~l-~~~ 78 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNA-TPFAVAQKEILKIL-KGK 78 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCCEEEEEeECCCCccCccceECCCCCHHHHhcC-CCHHHHHHHHHHHc-CCC
Confidence 5899999999975 699999999999999999999999999999999999999999999 79999999999999 799
Q ss_pred EEEEeCchhhHHHHccccCc--cccccccc--ccc--cCCCCCccHHHHHHHhcCcccccCCCCCChHHHHHHHHHHHH
Q 008596 292 ILVGHSLENDLLALKISHGL--VIDTAVLY--KHP--QGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMELAL 364 (560)
Q Consensus 292 ILVGHsL~~DL~aLki~Hp~--viDT~~Ly--~~~--~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~Atl~L~~ 364 (560)
||||||+.||+++|++.|+. ++||+.++ ++. .+...+++|+.||++|+|..||.++.+|+|++||+||++||+
T Consensus 79 vlV~Hn~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 79 VVVGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157 (157)
T ss_pred EEEEeCcHHHHHHhcccCCCcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCCCcCcHHHHHHHHHHhC
Confidence 99999999999999999875 89998763 222 122245899999999999999875568999999999999973
No 6
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=100.00 E-value=3.3e-33 Score=263.47 Aligned_cols=150 Identities=44% Similarity=0.671 Sum_probs=134.0
Q ss_pred EEEEeccccCCC-CceEEEEEEEEe-cCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCC------CHHHHHHHHHHh
Q 008596 215 LALDCEMCYTNE-GLELTRVTLVDI-KGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTT------SLKDIQEEFLKL 286 (560)
Q Consensus 215 valDcEm~~t~~-g~eL~rVsvVd~-~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~------tl~dVq~~L~~~ 286 (560)
|||||||||+++ +++|++|++|+. +|+++|++||+|..+|++|.|++||||++||+++++ ++++++++|++|
T Consensus 1 v~lD~EttGl~~~~d~ii~Ig~V~v~~g~i~~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~~~~~~~~~~ 80 (161)
T cd06137 1 VALDCEMVGLADGDSEVVRISAVDVLTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAKAGKTIFGWEAARAALWKF 80 (161)
T ss_pred CEEEeeeeeEcCCCCEEEEEEEEEcCCCeEEEeccccCCCCCCccceeccCCCHHHHhhhhhcCCccccHHHHHHHHHHh
Confidence 589999999986 589999999998 899999999999999999999999999999998731 356999999999
Q ss_pred hcCCCEEEEeCchhhHHHHccccCcccccccccccccCCC---CCccHHHHHHHhcCcccccCCCCCChHHHHHHHHHHH
Q 008596 287 VYKETILVGHSLENDLLALKISHGLVIDTAVLYKHPQGGS---HKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMELA 363 (560)
Q Consensus 287 i~~~~ILVGHsL~~DL~aLki~Hp~viDT~~Ly~~~~g~~---~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~Atl~L~ 363 (560)
+.++++|||||+.||+++|+..|+.++||+.|+++..+.. .+++|+.||++|||++||.+..+|+|++||+||++||
T Consensus 81 i~~~~vlVgHn~~fD~~fL~~~~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~~~~H~A~~DA~at~~l~ 160 (161)
T cd06137 81 IDPDTILVGHSLQNDLDALRMIHTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGGEGHDSLEDALAAREVV 160 (161)
T ss_pred cCCCcEEEeccHHHHHHHHhCcCCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCCCCCCCcHHHHHHHHHHh
Confidence 9444999999999999999999999999999998865433 4689999999999999986446899999999999997
Q ss_pred H
Q 008596 364 L 364 (560)
Q Consensus 364 ~ 364 (560)
+
T Consensus 161 ~ 161 (161)
T cd06137 161 L 161 (161)
T ss_pred C
Confidence 3
No 7
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=99.96 E-value=4.3e-29 Score=233.25 Aligned_cols=146 Identities=41% Similarity=0.598 Sum_probs=129.0
Q ss_pred EEEEeccccCCCC---ceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcCCC
Q 008596 215 LALDCEMCYTNEG---LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKET 291 (560)
Q Consensus 215 valDcEm~~t~~g---~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~~~ 291 (560)
|+|||||||++++ .+|++|++|+.+|.++|++||+|..+|.++++++||||++||+++ +++.+++.+|++++ .++
T Consensus 1 v~lD~EttGl~~~~~~~~i~~v~~v~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~~~v~~a-~~~~~~~~~l~~~l-~~~ 78 (152)
T cd06144 1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDA-PDFEEVQKKVAELL-KGR 78 (152)
T ss_pred CEEEEEeecccCCCCEEEEEEEEEEeCCCCEEEEEEECCCCCCCcccccCCCCCHHHHcCC-CCHHHHHHHHHHHh-CCC
Confidence 5899999999875 589999999999999999999999999999999999999999998 79999999999999 679
Q ss_pred EEEEeCchhhHHHHccccC--cccccccccccccCC-CCCccHHHHHHHhcCcccccCCCCCChHHHHHHHHHHHH
Q 008596 292 ILVGHSLENDLLALKISHG--LVIDTAVLYKHPQGG-SHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMELAL 364 (560)
Q Consensus 292 ILVGHsL~~DL~aLki~Hp--~viDT~~Ly~~~~g~-~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~Atl~L~~ 364 (560)
+|||||+.||+++|++.++ .++||..+....... ..+++|..||++|||++++. +.|+|++||+||++||+
T Consensus 79 vlVgHn~~fD~~~L~~~~~~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~--~~H~Al~DA~at~~l~~ 152 (152)
T cd06144 79 ILVGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQE--GEHSSVEDARAAMRLYR 152 (152)
T ss_pred EEEEcCcHHHHHHhcCcCCCccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCC--CCcCcHHHHHHHHHHhC
Confidence 9999999999999998765 588998764332111 35689999999889999874 47999999999999973
No 8
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.90 E-value=5e-23 Score=200.84 Aligned_cols=159 Identities=20% Similarity=0.258 Sum_probs=129.7
Q ss_pred CcEEEEEeccccCCCCceEEEEEEEEec-CcEE--EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhc
Q 008596 212 YEILALDCEMCYTNEGLELTRVTLVDIK-GQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVY 288 (560)
Q Consensus 212 ~~~valDcEm~~t~~g~eL~rVsvVd~~-G~vv--lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~ 288 (560)
.++++|||||+|+...++|++|++|..+ |.++ |++||+|..+|+++.+++||||++||+++ +++.+|+.++.+++
T Consensus 5 ~~~vvlD~EtTGl~~~~eIIeIgaV~v~~g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~a-p~~~evl~~f~~f~- 82 (195)
T PRK07247 5 ETYIAFDLEFNTVNGVSHIIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADA-PKVEEVLAAFKEFV- 82 (195)
T ss_pred CeEEEEEeeCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCCCccceecCCCCHHHHhCC-CCHHHHHHHHHHHH-
Confidence 4799999999999877899999999974 4433 89999999999999999999999999999 79999999999999
Q ss_pred CCCEEEEeCch-hhHHHHccc-----cCcccccccc-cccc---cCCCCCccHHHHHHHhcCcccccCCCCCChHHHHHH
Q 008596 289 KETILVGHSLE-NDLLALKIS-----HGLVIDTAVL-YKHP---QGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARA 358 (560)
Q Consensus 289 ~~~ILVGHsL~-~DL~aLki~-----Hp~viDT~~L-y~~~---~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~A 358 (560)
++.++||||+. ||+.+|+.. .+..+||... +... .+....++|..||++ ||++. ..|+|++||++
T Consensus 83 ~~~~lVaHNa~~fD~~fL~~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~-~gi~~----~~HrAl~DA~~ 157 (195)
T PRK07247 83 GELPLIGYNAQKSDLPILAENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVADF-LGIKG----RGHNSLEDARM 157 (195)
T ss_pred CCCeEEEEeCcHhHHHHHHHcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHHHh-cCCCC----CCcCCHHHHHH
Confidence 88999999997 899999842 3355777532 2111 111245789999985 79874 27999999999
Q ss_pred HHHHHHHHHHhhhhHHHHH
Q 008596 359 AMELALLKIRNVMRTKLLK 377 (560)
Q Consensus 359 tl~L~~~kl~~~~~~~i~~ 377 (560)
|+.|++..++.....+.++
T Consensus 158 ta~v~~~ll~~~~~~~~~~ 176 (195)
T PRK07247 158 TARVYESFLESDQNKEYLE 176 (195)
T ss_pred HHHHHHHHHhhccchhhhh
Confidence 9999988888865555554
No 9
>PRK07740 hypothetical protein; Provisional
Probab=99.89 E-value=3.4e-22 Score=201.08 Aligned_cols=152 Identities=22% Similarity=0.224 Sum_probs=130.0
Q ss_pred CcEEEEEeccccCCCC--ceEEEEEEEEecCcEE----EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHH
Q 008596 212 YEILALDCEMCYTNEG--LELTRVTLVDIKGQVL----LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLK 285 (560)
Q Consensus 212 ~~~valDcEm~~t~~g--~eL~rVsvVd~~G~vv----lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~ 285 (560)
.++|+|||||+|.++. ++|++|++|..++..+ |+.||+|..+|+++.+++||||+++|+++ +++.++..+|.+
T Consensus 59 ~~~vv~D~ETTGl~p~~~deIIeIgaV~~~~~~i~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~a-p~~~evl~~f~~ 137 (244)
T PRK07740 59 LPFVVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFA-PPLAEVLHRFYA 137 (244)
T ss_pred CCEEEEEEeCCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEEeCcCCCCChhheeccCCCHHHHhCC-CCHHHHHHHHHH
Confidence 4699999999999864 6999999999866554 67799999999999999999999999998 799999999999
Q ss_pred hhcCCCEEEEeCchhhHHHHccc---------cCcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHHH
Q 008596 286 LVYKETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDA 356 (560)
Q Consensus 286 ~i~~~~ILVGHsL~~DL~aLki~---------Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA 356 (560)
++ ++.+|||||+.||+.+|+-. ...++||..+++...+....++|..||.+ +|+++.. .|+|++||
T Consensus 138 fi-~~~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~-~gi~~~~---~H~Al~Da 212 (244)
T PRK07740 138 FI-GAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAY-YGIPIPR---RHHALGDA 212 (244)
T ss_pred Hh-CCCEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHHHHH-CCcCCCC---CCCcHHHH
Confidence 99 78899999999999999731 24789999887655433346789999974 7998763 79999999
Q ss_pred HHHHHHHHHHHHh
Q 008596 357 RAAMELALLKIRN 369 (560)
Q Consensus 357 ~Atl~L~~~kl~~ 369 (560)
+||++|+...+..
T Consensus 213 ~ata~l~~~ll~~ 225 (244)
T PRK07740 213 LMTAKLWAILLVE 225 (244)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999766554
No 10
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=99.88 E-value=3.8e-23 Score=230.52 Aligned_cols=172 Identities=31% Similarity=0.464 Sum_probs=146.5
Q ss_pred CCCcEEEEEeccccCCC--------C---------ceEEEEEEEEec----CcEEEEEEEeCCCCCCCCcEEecCCChhh
Q 008596 210 SPYEILALDCEMCYTNE--------G---------LELTRVTLVDIK----GQVLLDKLVKPSNAIVDYNTRYSGITHEM 268 (560)
Q Consensus 210 ~~~~~valDcEm~~t~~--------g---------~eL~rVsvVd~~----G~vvlD~LVkP~~~I~dy~T~~SGIT~e~ 268 (560)
.++++||||-|++.+.. | ..|+|||+|+++ |-+.+|.||--+++|+||+|+||||-+.|
T Consensus 908 k~g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msvARiScvRGeGp~eGiPFiDDYv~T~d~VvDYLTqySGI~PGD 987 (1118)
T KOG1275|consen 908 KSGDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSVARISCVRGEGPNEGIPFIDDYVSTDDKVVDYLTQYSGIKPGD 987 (1118)
T ss_pred CCCceeeeehhheecchHHhccccCCceeEeccccceeEEEEEEcccCCCCCCccccceecchhHHHHHHHHhcCCCccc
Confidence 45689999999998742 3 268999999975 45779999999999999999999999999
Q ss_pred hcCCC-----CCHHHHHHHHHHhhcCCCEEEEeCchhhHHHHccccC--cccccccccccccCCCCCccHHHHHHHhcCc
Q 008596 269 LSGVT-----TSLKDIQEEFLKLVYKETILVGHSLENDLLALKISHG--LVIDTAVLYKHPQGGSHKTSLRVLAKKFLSR 341 (560)
Q Consensus 269 L~~~~-----~tl~dVq~~L~~~i~~~~ILVGHsL~~DL~aLki~Hp--~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~ 341 (560)
|++.+ ++++-++.+++=+++.+.|+|||+|++|++++++.-| +||||+.||.... .++.||++||+++||.
T Consensus 988 LDp~~S~K~Lt~lK~~Y~Kl~~Li~~GviFVGHGL~nDFrvINi~Vp~~QiiDTv~lf~~~s--~R~LSLrfLa~~lLg~ 1065 (1118)
T KOG1275|consen 988 LDPTTSEKRLTTLKVLYLKLRLLIQRGVIFVGHGLQNDFRVINIHVPEEQIIDTVTLFRLGS--QRMLSLRFLAWELLGE 1065 (1118)
T ss_pred cCCccCcceehhHHHHHHHHHHHHHcCcEEEcccccccceEEEEecChhhheeeeEEEeccc--ccEEEHHHHHHHHhcc
Confidence 99753 5899999999999999999999999999999998644 6999999997753 4788999999999999
Q ss_pred ccccCCCCCChHHHHHHHHHHHHHHHHh---hhhHHHHHHHHHcCCe
Q 008596 342 EIQQSGFGHDSTEDARAAMELALLKIRN---VMRTKLLKVLFEYGKT 385 (560)
Q Consensus 342 ~IQ~~~~~HdSlEDA~Atl~L~~~kl~~---~~~~~i~~~l~~~g~~ 385 (560)
+||. ..|||+|||++|+.||+..++- ...++.++-+.+.|+.
T Consensus 1066 ~IQ~--~~HDSIeDA~taLkLYk~Yl~lkeq~~~~~~l~niye~gr~ 1110 (1118)
T KOG1275|consen 1066 TIQM--EAHDSIEDARTALKLYKKYLKLKEQGKLESELRNIYECGRP 1110 (1118)
T ss_pred hhhc--cccccHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhhcCcc
Confidence 9998 5899999999999999766554 3455555666666653
No 11
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=99.88 E-value=3.7e-22 Score=184.28 Aligned_cols=143 Identities=24% Similarity=0.347 Sum_probs=121.9
Q ss_pred EEEEEeccccCCCCceEEEEEEEEec-CcEE--EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcCC
Q 008596 214 ILALDCEMCYTNEGLELTRVTLVDIK-GQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKE 290 (560)
Q Consensus 214 ~valDcEm~~t~~g~eL~rVsvVd~~-G~vv--lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~~ 290 (560)
+|+|||||++.. .+++++|++|..+ |+++ ++.||+|..+++.+.+++||||+++|+++ +++.+++++|.+++ .+
T Consensus 1 ~v~~D~Ettg~~-~~~ii~ig~v~~~~~~~~~~~~~~i~p~~~~~~~~~~i~GIt~e~l~~~-~~~~~v~~~l~~~l-~~ 77 (156)
T cd06130 1 FVAIDFETANAD-RASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADA-PTFPEVWPEIKPFL-GG 77 (156)
T ss_pred CEEEEEeCCCCC-CCceEEEEEEEEECCEEEEEEEEEeCcCCCCChhhccccCcCHHHHhcC-CCHHHHHHHHHHHh-CC
Confidence 589999999866 3589999999974 4443 66899999999999999999999999998 68999999999999 67
Q ss_pred CEEEEeCchhhHHHHcc-------c--cCcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHHHHHHHH
Q 008596 291 TILVGHSLENDLLALKI-------S--HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAME 361 (560)
Q Consensus 291 ~ILVGHsL~~DL~aLki-------~--Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~Atl~ 361 (560)
.++||||+.||+.+|+. . ...++||..+++...+....++|..|+++ +|++.+ .|+|+.||++|++
T Consensus 78 ~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~~~~L~~l~~~-~g~~~~----~H~Al~Da~~ta~ 152 (156)
T cd06130 78 SLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEH-LGIELN----HHDALEDARACAE 152 (156)
T ss_pred CEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCCCCCHHHHHHH-cCCCcc----CcCchHHHHHHHH
Confidence 99999999999999973 1 22689999888776544456789999985 798875 6999999999999
Q ss_pred HHH
Q 008596 362 LAL 364 (560)
Q Consensus 362 L~~ 364 (560)
|+.
T Consensus 153 l~~ 155 (156)
T cd06130 153 ILL 155 (156)
T ss_pred HHh
Confidence 974
No 12
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.88 E-value=7.4e-22 Score=196.91 Aligned_cols=166 Identities=16% Similarity=0.170 Sum_probs=137.5
Q ss_pred CcEEEEEeccccCCCC-ceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcCC
Q 008596 212 YEILALDCEMCYTNEG-LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKE 290 (560)
Q Consensus 212 ~~~valDcEm~~t~~g-~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~~ 290 (560)
.++++||+||||++.. ++|++|++|+......++.||+|..+|+...+++||||++||+++ +++.+|.+++.+|+.++
T Consensus 2 ~~~vv~D~ETTGl~~~~d~IIeig~v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~-p~f~ev~~~~~~fi~~~ 80 (232)
T PRK06309 2 PALIFYDTETTGTQIDKDRIIEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADA-PKFPEAYQKFIEFCGTD 80 (232)
T ss_pred CcEEEEEeeCCCCCCCCCEEEEEEEEcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCC-CCHHHHHHHHHHHHcCC
Confidence 3589999999999864 799999999865556699999999999999999999999999999 78999999999999667
Q ss_pred CEEEEeC-chhhHHHHccc---------cCcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHHHHHHH
Q 008596 291 TILVGHS-LENDLLALKIS---------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAM 360 (560)
Q Consensus 291 ~ILVGHs-L~~DL~aLki~---------Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~Atl 360 (560)
.+||||| ..||+.+|+.. ...++||..+++..++...+++|..|++. +|++.. .+|+|++||.+|+
T Consensus 81 ~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~~~~L~~l~~~-~~~~~~---~aH~Al~Da~~t~ 156 (232)
T PRK06309 81 NILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLRQV-YGFEEN---QAHRALDDVITLH 156 (232)
T ss_pred CEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCCCCCHHHHHHH-cCCCCC---CCCCcHHHHHHHH
Confidence 8999999 58999999831 13689999888765443335689999986 587754 4899999999999
Q ss_pred HHHHHHHHhhhhHHHHHHHHHc
Q 008596 361 ELALLKIRNVMRTKLLKVLFEY 382 (560)
Q Consensus 361 ~L~~~kl~~~~~~~i~~~l~~~ 382 (560)
+|+...+++...+.+..+....
T Consensus 157 ~vl~~l~~~~~~~~l~~l~~~~ 178 (232)
T PRK06309 157 RVFSALVGDLSPQQVYDLLNES 178 (232)
T ss_pred HHHHHHHHHHHHhhHHHHHHhh
Confidence 9998888775555566555443
No 13
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.88 E-value=8.6e-22 Score=198.79 Aligned_cols=163 Identities=21% Similarity=0.271 Sum_probs=136.1
Q ss_pred CcEEEEEeccccCCCC-ceEEEEEEEEecCcEE---EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008596 212 YEILALDCEMCYTNEG-LELTRVTLVDIKGQVL---LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (560)
Q Consensus 212 ~~~valDcEm~~t~~g-~eL~rVsvVd~~G~vv---lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i 287 (560)
..+|+|||||+|+... ++|++|++|...+..+ ++.||+|..+|+.+.+.+||||+++|+++ +++.+|..++.+++
T Consensus 7 ~~~v~~D~ETTGl~~~~d~IIEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~-p~~~ev~~~~~~fl 85 (250)
T PRK06310 7 TEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDK-PKIAEVFPQIKGFF 85 (250)
T ss_pred CcEEEEEEeCCCCCCCCCeEEEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCC-CCHHHHHHHHHHHh
Confidence 4699999999999864 7999999999865443 67899999999999999999999999999 79999999999999
Q ss_pred cCCCEEEEeCchhhHHHHcc-----------ccCcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHHH
Q 008596 288 YKETILVGHSLENDLLALKI-----------SHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDA 356 (560)
Q Consensus 288 ~~~~ILVGHsL~~DL~aLki-----------~Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA 356 (560)
.+..+|||||+.||+.+|+. .+..+|||..+++.. ++...++|..|+++ +|++.. +.|+|++||
T Consensus 86 ~~~~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~-~~~~~~~L~~l~~~-~g~~~~---~aH~Al~Da 160 (250)
T PRK06310 86 KEGDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEY-GDSPNNSLEALAVH-FNVPYD---GNHRAMKDV 160 (250)
T ss_pred CCCCEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhc-ccCCCCCHHHHHHH-CCCCCC---CCcChHHHH
Confidence 55599999999999999973 134689999887753 33235789999986 588865 489999999
Q ss_pred HHHHHHHHHHHHh-hhhHHHHHHHH
Q 008596 357 RAAMELALLKIRN-VMRTKLLKVLF 380 (560)
Q Consensus 357 ~Atl~L~~~kl~~-~~~~~i~~~l~ 380 (560)
.||++|++..+++ ...+.+.+.++
T Consensus 161 ~at~~vl~~l~~~~~~~~~l~~~~~ 185 (250)
T PRK06310 161 EINIKVFKHLCKRFRTLEQLKQILS 185 (250)
T ss_pred HHHHHHHHHHHHhcccHHHHHHHhh
Confidence 9999999887766 34466666655
No 14
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.88 E-value=4.7e-22 Score=184.76 Aligned_cols=150 Identities=36% Similarity=0.531 Sum_probs=126.2
Q ss_pred EEEEEeccccCCCC-ceEEEEEEEEecC---cEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcC
Q 008596 214 ILALDCEMCYTNEG-LELTRVTLVDIKG---QVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYK 289 (560)
Q Consensus 214 ~valDcEm~~t~~g-~eL~rVsvVd~~G---~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~ 289 (560)
+|+|||||+|+.++ .+|++|++|..++ ...|+.||+|..+|.++.+++||||+++|+++ +++.+++.+|.+++ .
T Consensus 2 ~v~~D~Ettg~~~~~~~Iieig~v~~~~~~~~~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~-~~~~~~~~~~~~~l-~ 79 (169)
T smart00479 2 LVVIDCETTGLDPGKDEIIEIAAVDVDGGRIIVVFDTYVKPDRPITDYATEIHGITPEMLDDA-PTFEEVLEELLEFL-K 79 (169)
T ss_pred EEEEEeeCCCCCCCCCeEEEEEEEEEECCEeEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCC-CCHHHHHHHHHHHh-c
Confidence 79999999999887 7999999999765 34489999999999999999999999999997 79999999999999 5
Q ss_pred CCEEEEeCc-hhhHHHHcccc-------C---cccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHHHHH
Q 008596 290 ETILVGHSL-ENDLLALKISH-------G---LVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARA 358 (560)
Q Consensus 290 ~~ILVGHsL-~~DL~aLki~H-------p---~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~A 358 (560)
+.++||||. .||+.+|+... | .++||..+++...+. ..++|..||+. +|.+... ..|+|++||++
T Consensus 80 ~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~-~~~~L~~l~~~-~~~~~~~--~~H~A~~Da~~ 155 (169)
T smart00479 80 GKILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPG-RKYSLKKLAER-LGLEVIG--RAHRALDDARA 155 (169)
T ss_pred CCEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCC-CCCCHHHHHHH-CCCCCCC--CCcCcHHHHHH
Confidence 667777777 99999999521 1 379999888766543 37899999986 5777653 25999999999
Q ss_pred HHHHHHHHHHh
Q 008596 359 AMELALLKIRN 369 (560)
Q Consensus 359 tl~L~~~kl~~ 369 (560)
|++|++..++.
T Consensus 156 t~~l~~~~~~~ 166 (169)
T smart00479 156 TAKLFKKLVER 166 (169)
T ss_pred HHHHHHHHHHH
Confidence 99999765543
No 15
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.87 E-value=1.8e-21 Score=202.46 Aligned_cols=153 Identities=22% Similarity=0.287 Sum_probs=129.8
Q ss_pred CCCcEEEEEeccccCCCC-ceEEEEEEEEec-CcEE--EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHH
Q 008596 210 SPYEILALDCEMCYTNEG-LELTRVTLVDIK-GQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLK 285 (560)
Q Consensus 210 ~~~~~valDcEm~~t~~g-~eL~rVsvVd~~-G~vv--lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~ 285 (560)
-|.++|+||+||+|+++. ++|++|++|... |+++ |+.||+|..+|+.+.+++||||.+||+++ +++.+|+.+|.+
T Consensus 6 ~~~~~Vv~DlETTGl~p~~~eIIEIgaV~v~~g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~-~~~~evl~~f~~ 84 (313)
T PRK06807 6 LPLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDA-PTIEEVLPLFLA 84 (313)
T ss_pred CCCCEEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCC-CCHHHHHHHHHH
Confidence 356799999999999875 699999999974 5544 67899999999999999999999999998 799999999999
Q ss_pred hhcCCCEEEEeCchhhHHHHcc-------cc--CcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHHH
Q 008596 286 LVYKETILVGHSLENDLLALKI-------SH--GLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDA 356 (560)
Q Consensus 286 ~i~~~~ILVGHsL~~DL~aLki-------~H--p~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA 356 (560)
|+ ++.+|||||+.||+++|+- .. ..++||..+++...+....++|..||++ ||++. . +|+|+.||
T Consensus 85 fl-~~~~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~~~kL~~L~~~-lgi~~-~---~H~Al~DA 158 (313)
T PRK06807 85 FL-HTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRM-LGIRL-S---SHNAFDDC 158 (313)
T ss_pred HH-cCCeEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCCCCCHHHHHHH-cCCCC-C---CcChHHHH
Confidence 99 7889999999999999983 12 2589999877655433345689999975 79987 3 79999999
Q ss_pred HHHHHHHHHHHHh
Q 008596 357 RAAMELALLKIRN 369 (560)
Q Consensus 357 ~Atl~L~~~kl~~ 369 (560)
++|++|++..+..
T Consensus 159 ~~ta~l~~~l~~~ 171 (313)
T PRK06807 159 ITCAAVYQKCASI 171 (313)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999776665
No 16
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.86 E-value=2.9e-21 Score=188.32 Aligned_cols=150 Identities=25% Similarity=0.320 Sum_probs=124.3
Q ss_pred CcEEEEEeccccCCCC-ceEEEEEEEEecCc-EE----EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHH
Q 008596 212 YEILALDCEMCYTNEG-LELTRVTLVDIKGQ-VL----LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLK 285 (560)
Q Consensus 212 ~~~valDcEm~~t~~g-~eL~rVsvVd~~G~-vv----lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~ 285 (560)
..+|+|||||+|+++. ++|++|++|..+|. ++ ++.||+|..+|..+.+++||||+++|+++ +++.+|..++.+
T Consensus 29 ~~~vviD~ETTGl~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~-~~~~~vl~~~~~ 107 (202)
T PRK09145 29 DEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDG-LSEEEALRQLLA 107 (202)
T ss_pred CCEEEEEeECCCCCCCCCceEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcC-CCHHHHHHHHHH
Confidence 4699999999999875 79999999998654 32 67899999999999999999999999998 799999999999
Q ss_pred hhcCCCEEEEeCchhhHHHHccc---------cCcccccccccccc-----cCCCCCccHHHHHHHhcCcccccCCCCCC
Q 008596 286 LVYKETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHP-----QGGSHKTSLRVLAKKFLSREIQQSGFGHD 351 (560)
Q Consensus 286 ~i~~~~ILVGHsL~~DL~aLki~---------Hp~viDT~~Ly~~~-----~g~~~k~sLk~La~~~Lg~~IQ~~~~~Hd 351 (560)
++ .+.+|||||+.||+.+|+.. +..++||+.+|... .+...+++|..||+. +|++.. +.|+
T Consensus 108 ~i-~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~---~~H~ 182 (202)
T PRK09145 108 FI-GNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILKH-LDLPVL---GRHD 182 (202)
T ss_pred HH-cCCeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHHHH-cCCCCC---CCCC
Confidence 99 78999999999999999731 23578998776321 111235789999986 688864 4799
Q ss_pred hHHHHHHHHHHHHHHH
Q 008596 352 STEDARAAMELALLKI 367 (560)
Q Consensus 352 SlEDA~Atl~L~~~kl 367 (560)
|++||++|++||+..+
T Consensus 183 Al~DA~ata~l~~~l~ 198 (202)
T PRK09145 183 ALNDAIMAALIFLRLR 198 (202)
T ss_pred cHHHHHHHHHHHHHHH
Confidence 9999999999986443
No 17
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.86 E-value=4.4e-21 Score=198.98 Aligned_cols=157 Identities=19% Similarity=0.262 Sum_probs=129.4
Q ss_pred cEEEEEeccccCCCCceEEEEEEEEe-cCcEE--EEEEEeCCC-CCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhc
Q 008596 213 EILALDCEMCYTNEGLELTRVTLVDI-KGQVL--LDKLVKPSN-AIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVY 288 (560)
Q Consensus 213 ~~valDcEm~~t~~g~eL~rVsvVd~-~G~vv--lD~LVkP~~-~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~ 288 (560)
+|++||+||++. .+++|++|++|.. +|+++ +++||+|.. .+.++.+++||||++||+++ ++|.+|+.+|.+|+
T Consensus 2 ~~vviD~ETTg~-~~d~IieIgav~v~~g~i~~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~~a-p~f~ev~~~~~~fl- 78 (309)
T PRK06195 2 NFVAIDFETANE-KRNSPCSIGIVVVKDGEIVEKVHYLIKPKEMRFMPINIGIHGIRPHMVEDE-LEFDKIWEKIKHYF- 78 (309)
T ss_pred cEEEEEEeCCCC-CCCceEEEEEEEEECCEEEEEEEEEECCCCCCCChhheeccCcCHHHHhCC-CCHHHHHHHHHHHh-
Confidence 589999999974 3468999999997 55555 778999985 57888999999999999999 68999999999999
Q ss_pred CCCEEEEeCchhhHHHHcc---------ccCcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHHHHHH
Q 008596 289 KETILVGHSLENDLLALKI---------SHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAA 359 (560)
Q Consensus 289 ~~~ILVGHsL~~DL~aLki---------~Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~At 359 (560)
.+.+|||||+.||+.+|+. .+..++||..+++...+....++|..||++ ||++.+ .|+|++||+||
T Consensus 79 ~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~~L~~L~~~-~gi~~~----~H~Al~DA~at 153 (309)
T PRK06195 79 NNNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNF-LGYEFK----HHDALADAMAC 153 (309)
T ss_pred CCCEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcCCHHHHHHH-cCCCCc----ccCCHHHHHHH
Confidence 7899999999999999973 123689999887765433345789999986 688753 79999999999
Q ss_pred HHHHHHHHHhhhhHHHHH
Q 008596 360 MELALLKIRNVMRTKLLK 377 (560)
Q Consensus 360 l~L~~~kl~~~~~~~i~~ 377 (560)
++|+...+++.....+..
T Consensus 154 a~l~~~l~~~~~~~~~~~ 171 (309)
T PRK06195 154 SNILLNISKELNSKDINE 171 (309)
T ss_pred HHHHHHHHHHhccCCHHH
Confidence 999988887754444433
No 18
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.86 E-value=3.3e-21 Score=193.54 Aligned_cols=152 Identities=23% Similarity=0.197 Sum_probs=127.0
Q ss_pred CcEEEEEeccccCCCC-ceEEEEEEEEecCc-E----EEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHH
Q 008596 212 YEILALDCEMCYTNEG-LELTRVTLVDIKGQ-V----LLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLK 285 (560)
Q Consensus 212 ~~~valDcEm~~t~~g-~eL~rVsvVd~~G~-v----vlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~ 285 (560)
..+++||+||+|+++. ++|++|++|..++. + .+..||+|+.+|+...+++||||+++|+++ +++.+|..++.+
T Consensus 47 ~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~a-p~~~evl~~l~~ 125 (239)
T PRK09146 47 VPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDA-PDLERILDELLE 125 (239)
T ss_pred CCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCC-CCHHHHHHHHHH
Confidence 4699999999999864 79999999998543 2 267899999999999999999999999998 799999999999
Q ss_pred hhcCCCEEEEeCchhhHHHHccc---------cCcccccccccccccCC-------------CCCccHHHHHHHhcCccc
Q 008596 286 LVYKETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQGG-------------SHKTSLRVLAKKFLSREI 343 (560)
Q Consensus 286 ~i~~~~ILVGHsL~~DL~aLki~---------Hp~viDT~~Ly~~~~g~-------------~~k~sLk~La~~~Lg~~I 343 (560)
++ .+.++||||+.||+.+|+.. ...+|||..|+++.... ...++|..||++ +|++.
T Consensus 126 ~~-~~~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~-~gl~~ 203 (239)
T PRK09146 126 AL-AGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLR-YGLPA 203 (239)
T ss_pred Hh-CCCEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHH-cCCCC
Confidence 99 78899999999999999741 23689999986553110 134579999986 68875
Q ss_pred ccCCCCCChHHHHHHHHHHHHHHHHh
Q 008596 344 QQSGFGHDSTEDARAAMELALLKIRN 369 (560)
Q Consensus 344 Q~~~~~HdSlEDA~Atl~L~~~kl~~ 369 (560)
. ..|+|++||+||++|++..+++
T Consensus 204 ~---~~H~Al~DA~ata~l~~~~~~~ 226 (239)
T PRK09146 204 Y---SPHHALTDAIATAELLQAQIAH 226 (239)
T ss_pred C---CCCCcHHHHHHHHHHHHHHHHH
Confidence 4 4799999999999999776665
No 19
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.86 E-value=4.4e-21 Score=191.56 Aligned_cols=154 Identities=24% Similarity=0.274 Sum_probs=123.7
Q ss_pred CcEEEEEeccccCCCC-ceEEEEEEEEec--CcEE--EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHh
Q 008596 212 YEILALDCEMCYTNEG-LELTRVTLVDIK--GQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKL 286 (560)
Q Consensus 212 ~~~valDcEm~~t~~g-~eL~rVsvVd~~--G~vv--lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~ 286 (560)
..+++||+||+|.+.. ++|++|++|..+ |.++ +..||+|..+|+.+.+++||||.+||.....+++++..++..+
T Consensus 6 ~~~vv~D~ETTGl~p~~d~Iieig~v~v~~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~e~~~~ 85 (232)
T PRK07942 6 GPLAAFDLETTGVDPETARIVTAALVVVDADGEVVESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLAEIADA 85 (232)
T ss_pred CcEEEEEeccCCCCCCCCeeEEEEEEEEeCCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHHHHHHH
Confidence 4699999999999875 689999998875 7665 6789999999999999999999999986446777777777766
Q ss_pred h----cCCCEEEEeCchhhHHHHccc---c-------CcccccccccccccC-CCCCccHHHHHHHhcCcccccCCCCCC
Q 008596 287 V----YKETILVGHSLENDLLALKIS---H-------GLVIDTAVLYKHPQG-GSHKTSLRVLAKKFLSREIQQSGFGHD 351 (560)
Q Consensus 287 i----~~~~ILVGHsL~~DL~aLki~---H-------p~viDT~~Ly~~~~g-~~~k~sLk~La~~~Lg~~IQ~~~~~Hd 351 (560)
| ..+.+|||||+.||+++|+.. | ..++||..|.+.... ...+++|..||++ +|++.. +.|+
T Consensus 86 l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~-~gi~~~---~aH~ 161 (232)
T PRK07942 86 LREAWARGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALCEH-YGVRLD---NAHE 161 (232)
T ss_pred HHHHhhcCCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHHHH-cCCCCC---CCCC
Confidence 5 368899999999999999731 1 257899877543211 1124689999986 698865 4899
Q ss_pred hHHHHHHHHHHHHHHHHh
Q 008596 352 STEDARAAMELALLKIRN 369 (560)
Q Consensus 352 SlEDA~Atl~L~~~kl~~ 369 (560)
|++||+||++|+...+++
T Consensus 162 Al~Da~ata~l~~~l~~~ 179 (232)
T PRK07942 162 ATADALAAARVAWALARR 179 (232)
T ss_pred hHHHHHHHHHHHHHHHHH
Confidence 999999999999777665
No 20
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.86 E-value=7.3e-21 Score=197.87 Aligned_cols=151 Identities=25% Similarity=0.283 Sum_probs=126.2
Q ss_pred CCcEEEEEeccccCCCC-ceEEEEEEEEe--cCcEE--EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHH
Q 008596 211 PYEILALDCEMCYTNEG-LELTRVTLVDI--KGQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLK 285 (560)
Q Consensus 211 ~~~~valDcEm~~t~~g-~eL~rVsvVd~--~G~vv--lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~ 285 (560)
+.+|++||+||+|...+ ++|++|++|.. +|+++ |.+||+|.. ....+.+||||++||+++ ++|.++..+|.+
T Consensus 14 ~~~fvvlD~ETTGl~p~~d~IIeIgav~v~~~g~i~~~~~~lv~P~~--~~~~~~IhGIt~e~l~~a-p~f~ev~~~l~~ 90 (313)
T PRK06063 14 PRGWAVVDVETSGFRPGQARIISLAVLGLDADGNVEQSVVTLLNPGV--DPGPTHVHGLTAEMLEGQ-PQFADIAGEVAE 90 (313)
T ss_pred CCCEEEEEEECCCCCCCCCEEEEEEEEEEECCceeeeEEEEEECcCC--CCCCeecCCCCHHHHhCC-CCHHHHHHHHHH
Confidence 46799999999999876 79999999976 46665 788999985 356799999999999999 789999999999
Q ss_pred hhcCCCEEEEeCchhhHHHHccc---------cCcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHHH
Q 008596 286 LVYKETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDA 356 (560)
Q Consensus 286 ~i~~~~ILVGHsL~~DL~aLki~---------Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA 356 (560)
|+ ++.+|||||+.||+.+|+-. ...++||..+++....+...++|..||++ ||++.. ..|+|++||
T Consensus 91 ~l-~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~~kL~~l~~~-~gi~~~---~~H~Al~DA 165 (313)
T PRK06063 91 LL-RGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLAAH-WGVPQQ---RPHDALDDA 165 (313)
T ss_pred Hc-CCCEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCCCCHHHHHHH-cCCCCC---CCCCcHHHH
Confidence 99 78999999999999999831 23589999887664333346779999985 698854 489999999
Q ss_pred HHHHHHHHHHHHh
Q 008596 357 RAAMELALLKIRN 369 (560)
Q Consensus 357 ~Atl~L~~~kl~~ 369 (560)
+||++|+...+++
T Consensus 166 ~ata~l~~~ll~~ 178 (313)
T PRK06063 166 RVLAGILRPSLER 178 (313)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999655555
No 21
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.86 E-value=4e-21 Score=193.07 Aligned_cols=151 Identities=21% Similarity=0.272 Sum_probs=125.2
Q ss_pred CcEEEEEeccccCCC--CceEEEEEEEEec-CcE---EEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHH
Q 008596 212 YEILALDCEMCYTNE--GLELTRVTLVDIK-GQV---LLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLK 285 (560)
Q Consensus 212 ~~~valDcEm~~t~~--g~eL~rVsvVd~~-G~v---vlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~ 285 (560)
.++++||+||||+++ +++|++|++|... +.+ -|..||+|..+|+...+++||||+++|+++ ++|++|..++.+
T Consensus 4 ~r~vvlDtETTGldp~~~drIIEIGaV~v~~~~~~~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~-p~f~ev~~~f~~ 82 (240)
T PRK05711 4 MRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADK-PTFAEVADEFLD 82 (240)
T ss_pred CeEEEEEeeCCCcCCCCCCeEEEEEEEEEECCEEeccEEEEEECcCCcCCHHHhhhcCCCHHHHcCC-CCHHHHHHHHHH
Confidence 579999999999986 5799999999864 332 278999999999999999999999999999 799999999999
Q ss_pred hhcCCCEEEEeCchhhHHHHccc-------------cCcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCCh
Q 008596 286 LVYKETILVGHSLENDLLALKIS-------------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDS 352 (560)
Q Consensus 286 ~i~~~~ILVGHsL~~DL~aLki~-------------Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdS 352 (560)
|+ .+.+|||||+.||+.+|+.. ...++||..+++...+ ..+++|..||++ +|++... ...|+|
T Consensus 83 fi-~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p-~~~~~L~aL~~~-~gi~~~~-r~~H~A 158 (240)
T PRK05711 83 FI-RGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFP-GKRNSLDALCKR-YGIDNSH-RTLHGA 158 (240)
T ss_pred Hh-CCCEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcC-CCCCCHHHHHHH-CCCCCCC-CCCCCH
Confidence 99 78899999999999999831 1358999988766532 245689999986 5876432 246999
Q ss_pred HHHHHHHHHHHHHHH
Q 008596 353 TEDARAAMELALLKI 367 (560)
Q Consensus 353 lEDA~Atl~L~~~kl 367 (560)
+.||+++++||+..+
T Consensus 159 L~DA~~~A~v~~~l~ 173 (240)
T PRK05711 159 LLDAEILAEVYLAMT 173 (240)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999985443
No 22
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.86 E-value=5.2e-21 Score=189.83 Aligned_cols=156 Identities=20% Similarity=0.224 Sum_probs=127.4
Q ss_pred EEEEEeccccCCCCceEEEEEEEEe-cCcEE--EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcCC
Q 008596 214 ILALDCEMCYTNEGLELTRVTLVDI-KGQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKE 290 (560)
Q Consensus 214 ~valDcEm~~t~~g~eL~rVsvVd~-~G~vv--lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~~ 290 (560)
+++||+||+|+.. +|++|++|+. +|+++ +++||+|..+|+.+.+++||||++||+++ +++.++..+ |+ ++
T Consensus 2 ~~vlD~ETTGl~~--~IieIg~v~v~~~~i~~~~~~lv~P~~~i~~~~~~ihgIt~e~v~~a-p~~~ev~~~---~~-~~ 74 (219)
T PRK07983 2 LRVIDTETCGLQG--GIVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADK-PWIEDVIPH---YY-GS 74 (219)
T ss_pred eEEEEEECCCCCC--CCEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHcCC-CCHHHHHHH---Hc-CC
Confidence 6899999999864 3889988886 55655 88999999999999999999999999999 789998776 45 78
Q ss_pred CEEEEeCchhhHHHHccccCcccccccccccccCCCCCccHHHHHHHhcCcccc--cCCCCCChHHHHHHHHHHHHHHHH
Q 008596 291 TILVGHSLENDLLALKISHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQ--QSGFGHDSTEDARAAMELALLKIR 368 (560)
Q Consensus 291 ~ILVGHsL~~DL~aLki~Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ--~~~~~HdSlEDA~Atl~L~~~kl~ 368 (560)
.+|||||+.||+++|+.....++||..++++..+. .+++|..||+. +|++.. ....+|+|+.||.+|++|++..++
T Consensus 75 ~~lVaHNa~FD~~~L~~~~~~~idTl~lar~l~p~-~~~~l~~L~~~-~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~~ 152 (219)
T PRK07983 75 EWYVAHNASFDRRVLPEMPGEWICTMKLARRLWPG-IKYSNMALYKS-RKLNVQTPPGLHHHRALYDCYITAALLIDIMN 152 (219)
T ss_pred CEEEEeCcHhhHHHHhCcCCCcEeHHHHHHHHccC-CCCCHHHHHHH-cCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHH
Confidence 89999999999999997777899999988775433 34789999975 687653 123589999999999999988776
Q ss_pred hh--hhHHHHHH
Q 008596 369 NV--MRTKLLKV 378 (560)
Q Consensus 369 ~~--~~~~i~~~ 378 (560)
+. ..+.+++.
T Consensus 153 ~~~~~~~~l~~~ 164 (219)
T PRK07983 153 TSGWTAEEMADI 164 (219)
T ss_pred HcCCCHHHHHHH
Confidence 53 33444443
No 23
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=99.85 E-value=4.9e-21 Score=190.57 Aligned_cols=149 Identities=23% Similarity=0.274 Sum_probs=124.1
Q ss_pred cEEEEEeccccCCCC--ceEEEEEEEEec-CcE---EEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHh
Q 008596 213 EILALDCEMCYTNEG--LELTRVTLVDIK-GQV---LLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKL 286 (560)
Q Consensus 213 ~~valDcEm~~t~~g--~eL~rVsvVd~~-G~v---vlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~ 286 (560)
++|+||+||+|+++. ++|++|++|... +.. -|..||+|..+|+.+.+++||||.+||+++ +++++|..+|.+|
T Consensus 1 r~vvlD~ETTGl~p~~~d~IIEIgav~~~~~~~~~~~f~~~i~P~~~i~~~a~~vhGIt~e~l~~~-p~f~ev~~~f~~f 79 (225)
T TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADK-PKFKEIADEFLDF 79 (225)
T ss_pred CEEEEEeeCCCcCCCCCCeEEEEEEEEEECCcEecceEEEEECcCCCCCHHHHhccCCCHHHHhCC-CCHHHHHHHHHHH
Confidence 479999999999864 799999998753 222 388999999999999999999999999999 7999999999999
Q ss_pred hcCCCEEEEeCchhhHHHHccc-----------c--CcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChH
Q 008596 287 VYKETILVGHSLENDLLALKIS-----------H--GLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDST 353 (560)
Q Consensus 287 i~~~~ILVGHsL~~DL~aLki~-----------H--p~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSl 353 (560)
+ ++.+|||||+.||+.+|+.. + ..++||..+++...+ ..+++|..||++ ||++... ...|+|+
T Consensus 80 i-~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p-~~~~~L~~L~~~-~gi~~~~-r~~H~Al 155 (225)
T TIGR01406 80 I-GGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFP-GQRNSLDALCKR-FKVDNSH-RTLHGAL 155 (225)
T ss_pred h-CCCEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcC-CCCCCHHHHHHh-cCCCCCC-CCCcCHH
Confidence 9 78899999999999999831 1 258999988776542 346789999987 5877542 2479999
Q ss_pred HHHHHHHHHHHHH
Q 008596 354 EDARAAMELALLK 366 (560)
Q Consensus 354 EDA~Atl~L~~~k 366 (560)
.||+++++||...
T Consensus 156 ~DA~~~a~v~~~l 168 (225)
T TIGR01406 156 LDAHLLAEVYLAL 168 (225)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999998533
No 24
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=99.85 E-value=3.6e-21 Score=184.40 Aligned_cols=143 Identities=24% Similarity=0.310 Sum_probs=116.5
Q ss_pred EEEEEeccccCC-C-CceEEEEEEEEecCc--------------EE--EEEEEeCCCCCCCCcEEecCCChhhhcCCCCC
Q 008596 214 ILALDCEMCYTN-E-GLELTRVTLVDIKGQ--------------VL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTS 275 (560)
Q Consensus 214 ~valDcEm~~t~-~-g~eL~rVsvVd~~G~--------------vv--lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~t 275 (560)
|++||+||+|++ . .++|++|++|...+. ++ |+.||+|..+|+...+++||||.+||.++ ++
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a~~IhGIt~e~l~~~-~~ 79 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHK-AP 79 (177)
T ss_pred CeEEeeecCCCCCCCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCCcCChhHHHHhCcCHHHHhcC-CC
Confidence 589999999998 3 479999999987432 22 68899999999999999999999999998 45
Q ss_pred HH-HHHHHHHHhh---cCCCEEEEeCc-hhhHHHHccc----------cCcccccccccccccCCCCCccHHHHHHHhcC
Q 008596 276 LK-DIQEEFLKLV---YKETILVGHSL-ENDLLALKIS----------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLS 340 (560)
Q Consensus 276 l~-dVq~~L~~~i---~~~~ILVGHsL-~~DL~aLki~----------Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg 340 (560)
+. ++.+.|.+|+ +++.+|||||+ .||+++|+-. ...++||..+++... ++|..||++++|
T Consensus 80 ~~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~-----~~L~~l~~~~~~ 154 (177)
T cd06136 80 FDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELD-----QSLGSLYKRLFG 154 (177)
T ss_pred ccHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhH-----hhHHHHHHHHhC
Confidence 55 4666666665 34579999998 8999999731 235789999888753 179999998789
Q ss_pred cccccCCCCCChHHHHHHHHHHHHH
Q 008596 341 REIQQSGFGHDSTEDARAAMELALL 365 (560)
Q Consensus 341 ~~IQ~~~~~HdSlEDA~Atl~L~~~ 365 (560)
++... .|+|+.||.||+++++.
T Consensus 155 ~~~~~---~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 155 QEPKN---SHTAEGDVLALLKCALH 176 (177)
T ss_pred CCccc---ccchHHHHHHHHHHHhh
Confidence 88763 89999999999999864
No 25
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.85 E-value=3.3e-20 Score=188.21 Aligned_cols=181 Identities=22% Similarity=0.274 Sum_probs=141.1
Q ss_pred CCHHHHhhCCccc--cCCCceeccCCCCCCCCCcEEEEEeccccCCCC-ceEEEEEEEEe-cCcEE--EEEEEeCCCCCC
Q 008596 182 LTEKQLEDNNYCY--NQPGFLSTVPAPFGSSPYEILALDCEMCYTNEG-LELTRVTLVDI-KGQVL--LDKLVKPSNAIV 255 (560)
Q Consensus 182 l~~~~l~~~~~p~--~~~~~~~t~~~~~~~~~~~~valDcEm~~t~~g-~eL~rVsvVd~-~G~vv--lD~LVkP~~~I~ 255 (560)
...+-+...|+|+ ...+..........-....++++|+||+|..++ ++|++|++|.. +|+++ |..||+|. +|+
T Consensus 36 ~~~~~~~~~g~~~~~~~~~~~~l~~~~~~~~~~~~vv~DiETTG~~~~~~~IIEIGAv~v~~g~i~~~f~~~v~p~-~ip 114 (257)
T PRK08517 36 IDLELLKALGLPLVENKENLITLKTRFTPIKDQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAK-EVP 114 (257)
T ss_pred HHHHHHHHCCCceEEcCCCeEEeccCCCCCCCCCEEEEEEeCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCC-CCC
Confidence 3345567778887 233332211111111234699999999999876 59999999997 45554 67899997 899
Q ss_pred CCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcCCCEEEEeCchhhHHHHcc---------ccCcccccccccccccCCC
Q 008596 256 DYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKETILVGHSLENDLLALKI---------SHGLVIDTAVLYKHPQGGS 326 (560)
Q Consensus 256 dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~~~ILVGHsL~~DL~aLki---------~Hp~viDT~~Ly~~~~g~~ 326 (560)
.+.+++||||++||+++ +++.+|..+|.+++ ++.++||||+.||+.+|+. .++..+||..+++... +.
T Consensus 115 ~~~~~itGIt~e~l~~a-p~~~evl~~f~~fl-~~~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~-~~ 191 (257)
T PRK08517 115 EYITELTGITYEDLENA-PSLKEVLEEFRLFL-GDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTI-ES 191 (257)
T ss_pred hhhhhhcCcCHHHHcCC-CCHHHHHHHHHHHH-CCCeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHc-cC
Confidence 99999999999999998 79999999999999 7899999999999999973 1346789988876542 23
Q ss_pred CCccHHHHHHHhcCcccccCCCCCChHHHHHHHHHHHHHHHHhh
Q 008596 327 HKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMELALLKIRNV 370 (560)
Q Consensus 327 ~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~Atl~L~~~kl~~~ 370 (560)
.+++|..|++ ++|++.. ..|+|+.||.||++|+...+.+.
T Consensus 192 ~~~~L~~L~~-~lgi~~~---~~HrAl~DA~ata~ll~~ll~~~ 231 (257)
T PRK08517 192 PRYGLSFLKE-LLGIEIE---VHHRAYADALAAYEIFKICLLNL 231 (257)
T ss_pred CCCCHHHHHH-HcCcCCC---CCCChHHHHHHHHHHHHHHHHHh
Confidence 4678999998 5798865 48999999999999998887663
No 26
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.85 E-value=1.4e-20 Score=185.82 Aligned_cols=154 Identities=22% Similarity=0.243 Sum_probs=125.4
Q ss_pred CcEEEEEeccccCCCCceEEEEEEEE-ecCcE---EEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008596 212 YEILALDCEMCYTNEGLELTRVTLVD-IKGQV---LLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (560)
Q Consensus 212 ~~~valDcEm~~t~~g~eL~rVsvVd-~~G~v---vlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i 287 (560)
..||+||+||+|.+++..|++|++|. .+|.. .|..||+|..+|..+.+.+||||++||.++ +++.+|.++|.+++
T Consensus 7 ~~fvv~D~ETTGl~~~~~IIeIgav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~-p~~~ev~~~~~~~~ 85 (217)
T TIGR00573 7 DTETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDK-PDFKEIAEDFADYI 85 (217)
T ss_pred cCEEEEEecCCCCCCCCCEEEEEEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCC-CCHHHHHHHHHHHh
Confidence 46999999999998764599999998 44432 378999999999999999999999999998 79999999999999
Q ss_pred cCCCEEEEeCchhhHHHHccc----------cCccccccccccccc--CCCCCccHHHHHHHhcCcccccCCCCCChHHH
Q 008596 288 YKETILVGHSLENDLLALKIS----------HGLVIDTAVLYKHPQ--GGSHKTSLRVLAKKFLSREIQQSGFGHDSTED 355 (560)
Q Consensus 288 ~~~~ILVGHsL~~DL~aLki~----------Hp~viDT~~Ly~~~~--g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlED 355 (560)
++.++||||+.||+.+|+.. ...++||..+++... .+..+++|..|+++ +|++... ...|||++|
T Consensus 86 -~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~-~gl~~~~-~~~H~Al~D 162 (217)
T TIGR00573 86 -RGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKR-YEITNSH-RALHGALAD 162 (217)
T ss_pred -CCCEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHHH-cCCCCCC-cccCCHHHH
Confidence 77999999999999999831 125788876544321 13356789999986 5877541 147999999
Q ss_pred HHHHHHHHHHHHHh
Q 008596 356 ARAAMELALLKIRN 369 (560)
Q Consensus 356 A~Atl~L~~~kl~~ 369 (560)
|++|++|++..+.+
T Consensus 163 A~~ta~l~~~l~~~ 176 (217)
T TIGR00573 163 AFILAKLYLVMTGK 176 (217)
T ss_pred HHHHHHHHHHHHhc
Confidence 99999999766555
No 27
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=99.84 E-value=1.6e-20 Score=176.20 Aligned_cols=147 Identities=24% Similarity=0.303 Sum_probs=121.2
Q ss_pred EEEEEeccccCCC--CceEEEEEEEEec-CcE---EEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008596 214 ILALDCEMCYTNE--GLELTRVTLVDIK-GQV---LLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (560)
Q Consensus 214 ~valDcEm~~t~~--g~eL~rVsvVd~~-G~v---vlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i 287 (560)
+|+||+||+|.+. +++|++|++|... |.+ -++.||+|..+|..+.+++||||+++|+++ ++++++..+|.+++
T Consensus 1 ~v~~D~ETTGl~~~~~~~iieig~v~v~~~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~-~~~~~v~~~l~~~l 79 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADK-PKFAEIADEFLDFI 79 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEEEEEEEECCcEeccEEEEEECCCCCCCHHHHHHhCCCHHHHhcC-CCHHHHHHHHHHHH
Confidence 4899999999986 3699999998753 332 368899999999999999999999999999 68999999999999
Q ss_pred cCCCEEEEeCchhhHHHHccc------------cCcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHH
Q 008596 288 YKETILVGHSLENDLLALKIS------------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTED 355 (560)
Q Consensus 288 ~~~~ILVGHsL~~DL~aLki~------------Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlED 355 (560)
.+.++||||..||+.+|+-. +..++||..+++...+ ...++|..||++ +|++... ...|+|+.|
T Consensus 80 -~~~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~-~~~~~L~~l~~~-~~i~~~~-~~~H~Al~D 155 (167)
T cd06131 80 -RGAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFP-GKPNSLDALCKR-FGIDNSH-RTLHGALLD 155 (167)
T ss_pred -CCCeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcC-CCCCCHHHHHHH-CCCCCCC-CCCCChHHH
Confidence 77889999999999999731 1257999887765432 245689999986 6877542 247999999
Q ss_pred HHHHHHHHHH
Q 008596 356 ARAAMELALL 365 (560)
Q Consensus 356 A~Atl~L~~~ 365 (560)
|++|++|++.
T Consensus 156 a~~~a~l~~~ 165 (167)
T cd06131 156 AELLAEVYLE 165 (167)
T ss_pred HHHHHHHHHH
Confidence 9999999853
No 28
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.84 E-value=3.5e-20 Score=214.08 Aligned_cols=153 Identities=22% Similarity=0.293 Sum_probs=130.6
Q ss_pred CCcEEEEEeccccCCCCceEEEEEEEEec-CcEE--EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008596 211 PYEILALDCEMCYTNEGLELTRVTLVDIK-GQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (560)
Q Consensus 211 ~~~~valDcEm~~t~~g~eL~rVsvVd~~-G~vv--lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i 287 (560)
..++++||+||||++..++|++|++|... |+++ |.+||+|..+|+++.+++||||++||+++ +++++|..+|.+++
T Consensus 6 ~~~~vvvD~ETTGl~~~d~IIeIgaV~v~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~a-p~~~ev~~~~~~~l 84 (820)
T PRK07246 6 LRKYAVVDLEATGAGPNASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQA-PDFSQVARHIYDLI 84 (820)
T ss_pred CCCEEEEEEecCCcCCCCeEEEEEEEEEECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcC-CCHHHHHHHHHHHh
Confidence 35799999999999877899999999975 4444 67789999999999999999999999999 79999999999999
Q ss_pred cCCCEEEEeCchhhHHHHccc--------cCcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHHHHHH
Q 008596 288 YKETILVGHSLENDLLALKIS--------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAA 359 (560)
Q Consensus 288 ~~~~ILVGHsL~~DL~aLki~--------Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~At 359 (560)
.++++||||+.||+.+|+.. ....+||..+++...+...+++|..||+. ||++.. ..|+|++||+||
T Consensus 85 -~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L~~~-lgl~~~---~~H~Al~DA~at 159 (820)
T PRK07246 85 -EDCIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLSRE-LNIDLA---DAHTAIADARAT 159 (820)
T ss_pred -CCCEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHHHHH-cCCCCC---CCCCHHHHHHHH
Confidence 78999999999999999731 12579999876654433346789999985 798865 489999999999
Q ss_pred HHHHHHHHHh
Q 008596 360 MELALLKIRN 369 (560)
Q Consensus 360 l~L~~~kl~~ 369 (560)
++|+...+++
T Consensus 160 a~L~~~l~~~ 169 (820)
T PRK07246 160 AELFLKLLQK 169 (820)
T ss_pred HHHHHHHHHH
Confidence 9999777766
No 29
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.82 E-value=5.3e-20 Score=180.34 Aligned_cols=154 Identities=21% Similarity=0.242 Sum_probs=121.3
Q ss_pred CcEEEEEeccccCCCC-------ceEEEEEEEEec-CcEE--EEEEEeCCC--CCCCCcEEecCCChhhhcCCCCCHHHH
Q 008596 212 YEILALDCEMCYTNEG-------LELTRVTLVDIK-GQVL--LDKLVKPSN--AIVDYNTRYSGITHEMLSGVTTSLKDI 279 (560)
Q Consensus 212 ~~~valDcEm~~t~~g-------~eL~rVsvVd~~-G~vv--lD~LVkP~~--~I~dy~T~~SGIT~e~L~~~~~tl~dV 279 (560)
.++++||+||++...+ +||++|++|..+ |+++ |.+||+|.. +|+.+.+++||||++||+++ +++++|
T Consensus 4 ~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~a-p~~~ev 82 (207)
T PRK07748 4 QQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKG-ISFEEL 82 (207)
T ss_pred ceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecCcChhhhcceECCCccCccChhhhhhcCcCHHHHccC-CCHHHH
Confidence 4699999999986532 589999999874 5443 889999987 79999999999999999998 899999
Q ss_pred HHHHHHhhcCCCEEEEeCchhhHHHHccc-------c---CcccccccccccccCCCCCccHHHHHHHhcCcccccCCCC
Q 008596 280 QEEFLKLVYKETILVGHSLENDLLALKIS-------H---GLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFG 349 (560)
Q Consensus 280 q~~L~~~i~~~~ILVGHsL~~DL~aLki~-------H---p~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~ 349 (560)
.++|.+++.....+|.|+..||+++|+.. . ..++|+..+|+...+....++|..++++ +|++.-. ..
T Consensus 83 l~~f~~~~~~~~~~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~~~~L~~~~~~-~gi~~~~--~~ 159 (207)
T PRK07748 83 VEKLAEYDKRCKPTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKAIEE-YGKEGTG--KH 159 (207)
T ss_pred HHHHHHHhCcCCeEEEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCCCCCHHHHHHH-cCCCCCC--CC
Confidence 99999999442444445569999999731 1 2478888777655444445789999986 6888532 47
Q ss_pred CChHHHHHHHHHHHHHHHHh
Q 008596 350 HDSTEDARAAMELALLKIRN 369 (560)
Q Consensus 350 HdSlEDA~Atl~L~~~kl~~ 369 (560)
|+|+.||++|++|+...+++
T Consensus 160 H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 160 HCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred cChHHHHHHHHHHHHHHHhC
Confidence 99999999999999765544
No 30
>PRK07883 hypothetical protein; Validated
Probab=99.82 E-value=1.3e-19 Score=201.45 Aligned_cols=153 Identities=24% Similarity=0.353 Sum_probs=131.7
Q ss_pred CcEEEEEeccccCCCC-ceEEEEEEEEe-cCcEE--EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008596 212 YEILALDCEMCYTNEG-LELTRVTLVDI-KGQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (560)
Q Consensus 212 ~~~valDcEm~~t~~g-~eL~rVsvVd~-~G~vv--lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i 287 (560)
..+|+||+||+|+++. ++|++|++|.. .|+++ |+.||+|..+|+++.+++||||.+||+++ +++.++..+|.+|+
T Consensus 15 ~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~a-p~~~evl~~f~~fl 93 (557)
T PRK07883 15 VTFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGA-PPIEEVLPAFLEFA 93 (557)
T ss_pred CCEEEEEEecCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCC-CCHHHHHHHHHHHh
Confidence 4699999999999875 79999999998 45555 78899999999999999999999999999 79999999999999
Q ss_pred cCCCEEEEeCchhhHHHHccc---------cCcccccccccccccC--CCCCccHHHHHHHhcCcccccCCCCCChHHHH
Q 008596 288 YKETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQG--GSHKTSLRVLAKKFLSREIQQSGFGHDSTEDA 356 (560)
Q Consensus 288 ~~~~ILVGHsL~~DL~aLki~---------Hp~viDT~~Ly~~~~g--~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA 356 (560)
.+.++||||+.||+.+|+.. ...++||..++++..+ ....++|..||+ ++|+++. +.|+|+.||
T Consensus 94 -~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L~~-~~gi~~~---~~H~Al~DA 168 (557)
T PRK07883 94 -RGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLAR-LFGATTT---PTHRALDDA 168 (557)
T ss_pred -cCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHHHH-HCCcccC---CCCCHHHHH
Confidence 78999999999999999841 1357999887765432 335678999998 5799875 479999999
Q ss_pred HHHHHHHHHHHHhh
Q 008596 357 RAAMELALLKIRNV 370 (560)
Q Consensus 357 ~Atl~L~~~kl~~~ 370 (560)
+||++|+...+++.
T Consensus 169 ~ata~l~~~l~~~~ 182 (557)
T PRK07883 169 RATVDVLHGLIERL 182 (557)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999998888773
No 31
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=99.81 E-value=1.6e-19 Score=163.70 Aligned_cols=143 Identities=27% Similarity=0.328 Sum_probs=122.5
Q ss_pred EEEEeccccCCC-CceEEEEEEEEecCc----EEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcC
Q 008596 215 LALDCEMCYTNE-GLELTRVTLVDIKGQ----VLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYK 289 (560)
Q Consensus 215 valDcEm~~t~~-g~eL~rVsvVd~~G~----vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~ 289 (560)
|++||||+|... ..+|++|++|..++. ..++.||+|...+..+.++++|||++++++. .++.++..++.+++ .
T Consensus 1 v~~D~Ettg~~~~~~~iiei~~v~~~~~~~~~~~~~~~i~p~~~~~~~~~~~~gi~~~~~~~~-~~~~~~~~~~~~~l-~ 78 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADA-PPFEEVLPEFLEFL-G 78 (159)
T ss_pred CeEEeeCCCcCCCCCeEEEEEEEEEECCcChhhhhheeeCcCCcCCHhheeccCCCHHHHhcC-CCHHHHHHHHHHHH-C
Confidence 579999999987 479999999998542 3389999999999999999999999999988 79999999999999 5
Q ss_pred CCEEEEeCchhhHHHHccc---------cCcccccccccccccCCCCCccHHHH-HHHhcCcccccCCCCCChHHHHHHH
Q 008596 290 ETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQGGSHKTSLRVL-AKKFLSREIQQSGFGHDSTEDARAA 359 (560)
Q Consensus 290 ~~ILVGHsL~~DL~aLki~---------Hp~viDT~~Ly~~~~g~~~k~sLk~L-a~~~Lg~~IQ~~~~~HdSlEDA~At 359 (560)
+.++||||..||+.+|+.. +..++||..+|+...+....++|+.+ ++ ++|.+.. ..|+|++||+++
T Consensus 79 ~~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~---~~H~Al~Da~~t 154 (159)
T cd06127 79 GRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAE-RYGIPLE---GAHRALADALAT 154 (159)
T ss_pred CCEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCCCcCchHHHHHH-HcCCCCC---CCCCcHHHHHHH
Confidence 6999999999999999842 34789999988776655556789998 55 5687654 489999999999
Q ss_pred HHHH
Q 008596 360 MELA 363 (560)
Q Consensus 360 l~L~ 363 (560)
++|+
T Consensus 155 ~~l~ 158 (159)
T cd06127 155 AELL 158 (159)
T ss_pred HHHh
Confidence 9987
No 32
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=99.80 E-value=3.6e-19 Score=206.67 Aligned_cols=151 Identities=23% Similarity=0.305 Sum_probs=130.6
Q ss_pred cEEEEEeccccCCCC-ceEEEEEEEEe-cCcEE--EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhc
Q 008596 213 EILALDCEMCYTNEG-LELTRVTLVDI-KGQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVY 288 (560)
Q Consensus 213 ~~valDcEm~~t~~g-~eL~rVsvVd~-~G~vv--lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~ 288 (560)
+||++|+||+|++++ ++|++|++|.. +|+++ |+.||+|..+|+++.+++||||++||+++ +++++|..+|.+++
T Consensus 1 ~~vvvD~ETTG~~~~~~~IIeig~v~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~a-p~~~ev~~~l~~~l- 78 (850)
T TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQA-PYFSQVAQEIYDLL- 78 (850)
T ss_pred CEEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEeCCCCCCChhhhhhcCcCHHHHhCC-CCHHHHHHHHHHHh-
Confidence 389999999999865 79999999997 56665 88999999999999999999999999998 79999999999999
Q ss_pred CCCEEEEeCchhhHHHHccc---------cCcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHHHHHH
Q 008596 289 KETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAA 359 (560)
Q Consensus 289 ~~~ILVGHsL~~DL~aLki~---------Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~At 359 (560)
.++++||||+.||+.+|+-. ...++||..+++...+...+++|..||++ ||++.. ++|+|++||+||
T Consensus 79 ~~~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~~~~L~~l~~~-~gi~~~---~~H~Al~DA~at 154 (850)
T TIGR01407 79 EDGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEA-LGLTHE---NPHRADSDAQAT 154 (850)
T ss_pred CCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCCCCCHHHHHHH-CCCCCC---CCCChHHHHHHH
Confidence 78999999999999999831 12579999887665444456789999986 688865 489999999999
Q ss_pred HHHHHHHHHh
Q 008596 360 MELALLKIRN 369 (560)
Q Consensus 360 l~L~~~kl~~ 369 (560)
++|+...+++
T Consensus 155 a~l~~~l~~~ 164 (850)
T TIGR01407 155 AELLLLLFEK 164 (850)
T ss_pred HHHHHHHHHH
Confidence 9999777666
No 33
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.80 E-value=3.3e-19 Score=208.64 Aligned_cols=152 Identities=24% Similarity=0.354 Sum_probs=130.0
Q ss_pred CcEEEEEeccccCCC--CceEEEEEEEEe-cCcEE--EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHh
Q 008596 212 YEILALDCEMCYTNE--GLELTRVTLVDI-KGQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKL 286 (560)
Q Consensus 212 ~~~valDcEm~~t~~--g~eL~rVsvVd~-~G~vv--lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~ 286 (560)
.+||+|||||+|+.+ +++|++|++|.. +|+++ |+.||+|..+|+.+.+++||||++||+++ +++++|..+|.++
T Consensus 3 ~~~vvvD~ETTG~~p~~~d~IIeigav~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~a-p~f~ev~~~l~~~ 81 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKGDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQA-PLFEDVAPEIVEL 81 (928)
T ss_pred CCEEEEEEeCCCCCCCCCCcEEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcC-CCHHHHHHHHHHH
Confidence 369999999999874 479999999997 56565 78899999999999999999999999999 7999999999999
Q ss_pred hcCCCEEEEeCchhhHHHHcc---------ccCcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHHHH
Q 008596 287 VYKETILVGHSLENDLLALKI---------SHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDAR 357 (560)
Q Consensus 287 i~~~~ILVGHsL~~DL~aLki---------~Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~ 357 (560)
+ .++++||||+.||+.+|+- .+..+|||..|++...+....++|..||++ ||++.. ..|+|++||+
T Consensus 82 l-~~~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~~~~L~~l~~~-l~i~~~---~~H~Al~DA~ 156 (928)
T PRK08074 82 L-EGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEE-LGLEHD---QPHRADSDAE 156 (928)
T ss_pred h-CCCeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCCCCCHHHHHHh-CCCCCC---CCCChHHHHH
Confidence 9 7999999999999999983 123689998876554333345789999985 688754 4899999999
Q ss_pred HHHHHHHHHHHh
Q 008596 358 AAMELALLKIRN 369 (560)
Q Consensus 358 Atl~L~~~kl~~ 369 (560)
||++|+...+++
T Consensus 157 ata~l~~~l~~~ 168 (928)
T PRK08074 157 VTAELFLQLLNK 168 (928)
T ss_pred HHHHHHHHHHHH
Confidence 999999887776
No 34
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=99.80 E-value=3.8e-19 Score=173.82 Aligned_cols=152 Identities=25% Similarity=0.296 Sum_probs=119.2
Q ss_pred CcEEEEEeccccCCCC-ceEEEEEEEEe----cCcEE----EEEEEeC--CCCCCCCcEEecCCChh-hhcCCCCCHHHH
Q 008596 212 YEILALDCEMCYTNEG-LELTRVTLVDI----KGQVL----LDKLVKP--SNAIVDYNTRYSGITHE-MLSGVTTSLKDI 279 (560)
Q Consensus 212 ~~~valDcEm~~t~~g-~eL~rVsvVd~----~G~vv----lD~LVkP--~~~I~dy~T~~SGIT~e-~L~~~~~tl~dV 279 (560)
..+++||+||+|+++. ++|++|++|.. .|.+. |.++|+| ..+|+...+++||||++ |++++ ++.+++
T Consensus 8 ~~~vv~D~ETTGl~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~-~~~~~~ 86 (200)
T TIGR01298 8 YLPVVVDVETGGFNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGA-VSEYEA 86 (200)
T ss_pred CeeEEEEeeCCCCCCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcC-cchHHH
Confidence 3579999999999874 68999999975 24443 7899998 47999999999999975 68887 677777
Q ss_pred HHHHHHhh--------cCCCEEEEeCchhhHHHHccc-----------c-CcccccccccccccCCCCCccHHHHHHHhc
Q 008596 280 QEEFLKLV--------YKETILVGHSLENDLLALKIS-----------H-GLVIDTAVLYKHPQGGSHKTSLRVLAKKFL 339 (560)
Q Consensus 280 q~~L~~~i--------~~~~ILVGHsL~~DL~aLki~-----------H-p~viDT~~Ly~~~~g~~~k~sLk~La~~~L 339 (560)
..++.+++ .++.+|||||+.||+++|+.. + ..++||..|++...+ ..+|..||++ +
T Consensus 87 ~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~---~~~L~~l~~~-~ 162 (200)
T TIGR01298 87 LHEIFKVVRKAMKASGCQRAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG---QTVLAKACQA-A 162 (200)
T ss_pred HHHHHHHHHHHHHhcccCCCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC---cccHHHHHHH-c
Confidence 66666665 257899999999999999831 1 137999998876543 2469999985 6
Q ss_pred CcccccCCCCCChHHHHHHHHHHHHHHHHh
Q 008596 340 SREIQQSGFGHDSTEDARAAMELALLKIRN 369 (560)
Q Consensus 340 g~~IQ~~~~~HdSlEDA~Atl~L~~~kl~~ 369 (560)
|+++.. ...|+|+.||.+|++|+...+++
T Consensus 163 gi~~~~-~~~H~Al~Da~ata~lf~~l~~~ 191 (200)
T TIGR01298 163 GXDFDS-TQAHSALYDTEKTAELFCEIVNR 191 (200)
T ss_pred CCCccc-cchhhhHHhHHHHHHHHHHHHHH
Confidence 988642 14899999999999999766554
No 35
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=99.80 E-value=5.9e-19 Score=170.89 Aligned_cols=151 Identities=23% Similarity=0.226 Sum_probs=115.8
Q ss_pred cEEEEEeccccCCCC-ceEEEEEEEEec----CcE----EEEEEEeC--CCCCCCCcEEecCCChhh-hcCCC---CCHH
Q 008596 213 EILALDCEMCYTNEG-LELTRVTLVDIK----GQV----LLDKLVKP--SNAIVDYNTRYSGITHEM-LSGVT---TSLK 277 (560)
Q Consensus 213 ~~valDcEm~~t~~g-~eL~rVsvVd~~----G~v----vlD~LVkP--~~~I~dy~T~~SGIT~e~-L~~~~---~tl~ 277 (560)
..|+||+||+|+++. ++|++|++|... |.+ -|++||+| ..+|+...+++||||+++ ++... +.+.
T Consensus 6 ~~vv~D~ETTGl~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~~~~~ 85 (189)
T cd06134 6 LPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEKEALK 85 (189)
T ss_pred eeEEEEecCCCCCCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchHHHHH
Confidence 468999999999864 799999999863 332 38899999 578999999999999987 44431 2445
Q ss_pred HHHHHHHHhhc----CCCEEEEeCchhhHHHHccc-----------cC-cccccccccccccCCCCCccHHHHHHHhcCc
Q 008596 278 DIQEEFLKLVY----KETILVGHSLENDLLALKIS-----------HG-LVIDTAVLYKHPQGGSHKTSLRVLAKKFLSR 341 (560)
Q Consensus 278 dVq~~L~~~i~----~~~ILVGHsL~~DL~aLki~-----------Hp-~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~ 341 (560)
++...|.+++. .+.+|||||+.||+.+|+.. ++ +++||..|++...+ ..+|..||++ +|+
T Consensus 86 ~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~---~~~L~~l~~~-~gi 161 (189)
T cd06134 86 EIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG---QTVLAKACQA-AGI 161 (189)
T ss_pred HHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC---CCcHHHHHHH-CCC
Confidence 55555555552 36899999999999999831 12 47999998876543 3469999986 699
Q ss_pred ccccCCCCCChHHHHHHHHHHHHHHHH
Q 008596 342 EIQQSGFGHDSTEDARAAMELALLKIR 368 (560)
Q Consensus 342 ~IQ~~~~~HdSlEDA~Atl~L~~~kl~ 368 (560)
++.. ...|+|+.||.||++|+...++
T Consensus 162 ~~~~-~~~H~Al~DA~ata~lf~~l~~ 187 (189)
T cd06134 162 EFDN-KEAHSALYDTQKTAELFCKIVN 187 (189)
T ss_pred CCCC-CCCcChHHHHHHHHHHHHHHHH
Confidence 8752 2479999999999999976654
No 36
>PRK06722 exonuclease; Provisional
Probab=99.79 E-value=8e-19 Score=179.94 Aligned_cols=153 Identities=22% Similarity=0.280 Sum_probs=120.3
Q ss_pred CcEEEEEeccccCCC----CceEEEEEEEEec-C--cEE--EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHH
Q 008596 212 YEILALDCEMCYTNE----GLELTRVTLVDIK-G--QVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEE 282 (560)
Q Consensus 212 ~~~valDcEm~~t~~----g~eL~rVsvVd~~-G--~vv--lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~ 282 (560)
..+++||+||++... +++|++|++|... | +++ |.+||+|..+|+++++++||||++||+++ +++++|..+
T Consensus 5 ~~~vViD~ETT~~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~~I~~~i~~LTGIT~emV~~A-P~f~eVl~e 83 (281)
T PRK06722 5 THFIVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGV-EKFPQIIEK 83 (281)
T ss_pred CEEEEEEeeCCCCCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCCcCCHhHhhhcCCCHHHHcCC-CCHHHHHHH
Confidence 569999999985331 2699999999974 4 555 88999999999999999999999999999 799999999
Q ss_pred HHHhhcCCCEEEEeCchhhHHHHccc-------cC-----cccccccccccc--cCCCCCccHHHHHHHhcCcccccCCC
Q 008596 283 FLKLVYKETILVGHSLENDLLALKIS-------HG-----LVIDTAVLYKHP--QGGSHKTSLRVLAKKFLSREIQQSGF 348 (560)
Q Consensus 283 L~~~i~~~~ILVGHsL~~DL~aLki~-------Hp-----~viDT~~Ly~~~--~g~~~k~sLk~La~~~Lg~~IQ~~~~ 348 (560)
+.+|+ ++..+|+|+..||+++|+.. .| +.+|+..++... +..+..++|..|+++ +|++.. +.
T Consensus 84 f~~fi-g~~~lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~~~-lgL~~~--g~ 159 (281)
T PRK06722 84 FIQFI-GEDSIFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAVEQ-LGLIWE--GK 159 (281)
T ss_pred HHHHH-CCCcEEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHHHH-CCCCCC--CC
Confidence 99999 55666667779999999951 22 247887654221 111234689999985 688863 24
Q ss_pred CCChHHHHHHHHHHHHHHHHh
Q 008596 349 GHDSTEDARAAMELALLKIRN 369 (560)
Q Consensus 349 ~HdSlEDA~Atl~L~~~kl~~ 369 (560)
.|+|++||++|+.|+...+.+
T Consensus 160 ~HrAL~DA~~TA~L~l~l~~~ 180 (281)
T PRK06722 160 QHRALADAENTANILLKAYSE 180 (281)
T ss_pred CcCcHHHHHHHHHHHHHHhcc
Confidence 799999999999999766543
No 37
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.79 E-value=1.6e-18 Score=178.92 Aligned_cols=164 Identities=22% Similarity=0.199 Sum_probs=123.4
Q ss_pred CCCcEEEEEeccccCCCC-ceEEEEEEEEec----CcE-----EEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHH
Q 008596 210 SPYEILALDCEMCYTNEG-LELTRVTLVDIK----GQV-----LLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDI 279 (560)
Q Consensus 210 ~~~~~valDcEm~~t~~g-~eL~rVsvVd~~----G~v-----vlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dV 279 (560)
.+..+++||+||||++.. ++|++|++|..+ |.+ .++.||+|..+|+...|++||||++||++++...
T Consensus 35 ~~~~~vvlD~ETTGLd~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~~I~~~~t~IhGIt~e~v~~~~~~~--- 111 (294)
T PRK09182 35 FVRLGVILDTETTGLDPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDP--- 111 (294)
T ss_pred CCCeEEEEEeeCCCCCCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCCCCCHHHHHhcCCCHHHHhcCCCcH---
Confidence 456799999999999874 799999999864 543 2788999999999999999999999999985433
Q ss_pred HHHHHHhhcCCCEEEEeCchhhHHHHccc-----cCcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHH
Q 008596 280 QEEFLKLVYKETILVGHSLENDLLALKIS-----HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTE 354 (560)
Q Consensus 280 q~~L~~~i~~~~ILVGHsL~~DL~aLki~-----Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlE 354 (560)
..+..|+....+|||||+.||+.+|+.. ...+.||............+++|.+||.+ +|.. . .+|+|+.
T Consensus 112 -~~l~~fl~~~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~~~~~~~~~~kL~~La~~-~g~~--~--~aHrAl~ 185 (294)
T PRK09182 112 -AAVDALIAPADLIIAHNAGFDRPFLERFSPVFATKPWACSVSEIDWSARGFEGTKLGYLAGQ-AGFF--H--EGHRAVD 185 (294)
T ss_pred -HHHHHHhcCCCEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHhhccccCCCCCHHHHHHH-cCCC--C--CCcChHH
Confidence 3467777666799999999999999842 22456665433222112246789999986 5832 2 4899999
Q ss_pred HHHHHHHHHHHHHHhhhhHHHHHHHHHc
Q 008596 355 DARAAMELALLKIRNVMRTKLLKVLFEY 382 (560)
Q Consensus 355 DA~Atl~L~~~kl~~~~~~~i~~~l~~~ 382 (560)
||.||++|+...+.+.+...+-+++...
T Consensus 186 Da~Ata~ll~~~l~~~~~~~l~~Ll~~~ 213 (294)
T PRK09182 186 DCQALLELLARPLPETGQPPLAELLEAS 213 (294)
T ss_pred HHHHHHHHHHHHHhhcCCcCHHHHHHHh
Confidence 9999999998888775444554444443
No 38
>PRK05168 ribonuclease T; Provisional
Probab=99.79 E-value=1.2e-18 Score=171.64 Aligned_cols=152 Identities=26% Similarity=0.284 Sum_probs=120.1
Q ss_pred CcEEEEEeccccCCCC-ceEEEEEEEEec----CcE----EEEEEEeC--CCCCCCCcEEecCCChhh-hcCCCCCHHHH
Q 008596 212 YEILALDCEMCYTNEG-LELTRVTLVDIK----GQV----LLDKLVKP--SNAIVDYNTRYSGITHEM-LSGVTTSLKDI 279 (560)
Q Consensus 212 ~~~valDcEm~~t~~g-~eL~rVsvVd~~----G~v----vlD~LVkP--~~~I~dy~T~~SGIT~e~-L~~~~~tl~dV 279 (560)
..+++||+||+|.++. ++|++|++|... |.+ -|+.||+| ..+|+.+.+++||||+++ +++. +...++
T Consensus 17 ~~~vv~D~ETTGl~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~~-~~~~~~ 95 (211)
T PRK05168 17 FLPVVIDVETAGFNAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGA-VSEKEA 95 (211)
T ss_pred CceEEEEeeCCCCCCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhcC-CChHHH
Confidence 3589999999999864 799999999853 543 37889999 578999999999999986 6666 677777
Q ss_pred HHHHHHhhc--------CCCEEEEeCchhhHHHHccc-----------cC-cccccccccccccCCCCCccHHHHHHHhc
Q 008596 280 QEEFLKLVY--------KETILVGHSLENDLLALKIS-----------HG-LVIDTAVLYKHPQGGSHKTSLRVLAKKFL 339 (560)
Q Consensus 280 q~~L~~~i~--------~~~ILVGHsL~~DL~aLki~-----------Hp-~viDT~~Ly~~~~g~~~k~sLk~La~~~L 339 (560)
..++.+++. .+.+|||||+.||+.+|+.. ++ +++||..|++...+. .+|..+|++ +
T Consensus 96 l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~~---~~L~~l~~~-~ 171 (211)
T PRK05168 96 LHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALGQ---TVLAKACQA-A 171 (211)
T ss_pred HHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcCC---CCHHHHHHH-C
Confidence 777666653 37899999999999999831 22 589999988765432 469999986 6
Q ss_pred CcccccCCCCCChHHHHHHHHHHHHHHHHh
Q 008596 340 SREIQQSGFGHDSTEDARAAMELALLKIRN 369 (560)
Q Consensus 340 g~~IQ~~~~~HdSlEDA~Atl~L~~~kl~~ 369 (560)
|++++. ...|+|++||.||++|+...+++
T Consensus 172 gl~~~~-~~~H~Al~DA~ata~l~~~l~~~ 200 (211)
T PRK05168 172 GIEFDN-KEAHSALYDTEKTAELFCEIVNR 200 (211)
T ss_pred CCCCCC-CCCCChHHHHHHHHHHHHHHHHH
Confidence 988752 25899999999999999755544
No 39
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=99.79 E-value=5.6e-21 Score=173.39 Aligned_cols=145 Identities=28% Similarity=0.357 Sum_probs=118.4
Q ss_pred EEEEeccccCCC-CceEEEEEEEEecC-----cEEEEEEEeCCCC--CCCCcEEecCCChhhhcCCCCCHHHHHHHHHHh
Q 008596 215 LALDCEMCYTNE-GLELTRVTLVDIKG-----QVLLDKLVKPSNA--IVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKL 286 (560)
Q Consensus 215 valDcEm~~t~~-g~eL~rVsvVd~~G-----~vvlD~LVkP~~~--I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~ 286 (560)
|+|||||+|+.. ..++++|++|...+ ...++.||+|..+ |.++.+++||||.++|+++ +++.++..++.++
T Consensus 1 v~~D~Ettg~~~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~-~~~~~~~~~~~~~ 79 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDA-PSFEEALDEFEEF 79 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCH-CEHHHHHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccC-CcHHHHHHhhhhh
Confidence 689999999998 47899999988632 2459999999998 9999999999999999999 6899999999999
Q ss_pred hcCCCEEEEeCchhhHHHHc--------cccC---cccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHH
Q 008596 287 VYKETILVGHSLENDLLALK--------ISHG---LVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTED 355 (560)
Q Consensus 287 i~~~~ILVGHsL~~DL~aLk--------i~Hp---~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlED 355 (560)
+.+..++||||..||..+++ ..+| .++||..+.+...+...+++|+.|++. +|.+... .+|+|++|
T Consensus 80 ~~~~~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~-~~~~~~~--~~H~Al~D 156 (164)
T PF00929_consen 80 LKKNDILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNRKKYSLDDLAEY-FGIPFDG--TAHDALDD 156 (164)
T ss_dssp HHHHTEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHHHHHSHHHHHHH-TTSSSTS--TTTSHHHH
T ss_pred hhcccccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhccccCCHHHHHHH-cCCCCCC--CCcChHHH
Confidence 97689999999888876654 2233 578888775554332233789999986 5776553 26999999
Q ss_pred HHHHHHHH
Q 008596 356 ARAAMELA 363 (560)
Q Consensus 356 A~Atl~L~ 363 (560)
|++|++||
T Consensus 157 a~~t~~l~ 164 (164)
T PF00929_consen 157 ARATAELF 164 (164)
T ss_dssp HHHHHHHH
T ss_pred HHHHhCcC
Confidence 99999986
No 40
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=99.78 E-value=5.1e-19 Score=166.23 Aligned_cols=147 Identities=24% Similarity=0.269 Sum_probs=120.4
Q ss_pred EEEEEeccccCCCC------ceEEEEEEEEec--Cc-E--EEEEEEeCCC--CCCCCcEEecCCChhhhcCCCCCHHHHH
Q 008596 214 ILALDCEMCYTNEG------LELTRVTLVDIK--GQ-V--LLDKLVKPSN--AIVDYNTRYSGITHEMLSGVTTSLKDIQ 280 (560)
Q Consensus 214 ~valDcEm~~t~~g------~eL~rVsvVd~~--G~-v--vlD~LVkP~~--~I~dy~T~~SGIT~e~L~~~~~tl~dVq 280 (560)
+|++||||+|...+ .+|++|++|..+ +. + .|+.||+|.. +|.++.+++||||.++|+++ +++++|.
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~-~~~~~vl 79 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNA-PSFPEVL 79 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcC-CCHHHHH
Confidence 58999999999863 699999999753 33 3 2889999998 99999999999999999999 8999999
Q ss_pred HHHHHhhcCC--CEEEEeCchhhHHHHcc------------ccCcccccccccccccCCCCCccHHHHHHHhcCcccccC
Q 008596 281 EEFLKLVYKE--TILVGHSLENDLLALKI------------SHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQS 346 (560)
Q Consensus 281 ~~L~~~i~~~--~ILVGHsL~~DL~aLki------------~Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~ 346 (560)
.++.+++.+. .++|+| ..+|+++|.. .+..++|+..+|+...+....++|..|+++ ||++..
T Consensus 80 ~~~~~~l~~~~~~~~v~~-~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~-- 155 (176)
T cd06133 80 KEFLEWLGKNGKYAFVTW-GDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEY-LGLEFE-- 155 (176)
T ss_pred HHHHHHHHhCCCeEEEee-cHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHHHHH-CCCCCC--
Confidence 9999999443 355555 5999887663 123679999998877655457899999975 688876
Q ss_pred CCCCChHHHHHHHHHHHHH
Q 008596 347 GFGHDSTEDARAAMELALL 365 (560)
Q Consensus 347 ~~~HdSlEDA~Atl~L~~~ 365 (560)
+..|+|+.||++|++|++.
T Consensus 156 ~~~H~Al~DA~~~a~l~~~ 174 (176)
T cd06133 156 GRHHRGLDDARNIARILKR 174 (176)
T ss_pred CCCcCcHHHHHHHHHHHHH
Confidence 2589999999999999864
No 41
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=99.78 E-value=9.4e-19 Score=207.51 Aligned_cols=152 Identities=23% Similarity=0.369 Sum_probs=132.9
Q ss_pred CcEEEEEeccccCCCC-ceEEEEEEEEe-cCcEE--EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008596 212 YEILALDCEMCYTNEG-LELTRVTLVDI-KGQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (560)
Q Consensus 212 ~~~valDcEm~~t~~g-~eL~rVsvVd~-~G~vv--lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i 287 (560)
..+|+|||||||++.. ++|++|++|.. +|+++ |+.||+|..+|+++.+++||||.+||+++ +++++|+++|.+++
T Consensus 190 ~~~VVfDiETTGL~~~~d~IIEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~a-p~~~evl~~f~~fl 268 (1213)
T TIGR01405 190 ATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENA-PEIEEVLEKFKEFF 268 (1213)
T ss_pred CcEEEEEeEecCCCCCCCeEEEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCC-CCHHHHHHHHHHHh
Confidence 4799999999999875 69999999997 56665 88999999999999999999999999998 79999999999999
Q ss_pred cCCCEEEEeCchhhHHHHccc---------cCcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHHHHH
Q 008596 288 YKETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARA 358 (560)
Q Consensus 288 ~~~~ILVGHsL~~DL~aLki~---------Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~A 358 (560)
++++|||||+.||+.+|+.. +..++||..+++...+...+++|..||++ ||++... .|+|++||.|
T Consensus 269 -~~~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k~~kL~~Lak~-lgi~~~~---~HrAl~DA~a 343 (1213)
T TIGR01405 269 -KDSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRLGNICKK-LGVDLDD---HHRADYDAEA 343 (1213)
T ss_pred -CCCeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCCCCCHHHHHHH-cCCCCCC---CcCHHHHHHH
Confidence 78999999999999999841 23689999887765444457889999986 6988764 8999999999
Q ss_pred HHHHHHHHHHh
Q 008596 359 AMELALLKIRN 369 (560)
Q Consensus 359 tl~L~~~kl~~ 369 (560)
|++++...+++
T Consensus 344 Ta~I~~~ll~~ 354 (1213)
T TIGR01405 344 TAKVFKVMVEQ 354 (1213)
T ss_pred HHHHHHHHHHH
Confidence 99999877765
No 42
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.78 E-value=1.5e-19 Score=206.81 Aligned_cols=152 Identities=25% Similarity=0.368 Sum_probs=137.0
Q ss_pred CcEEEEEeccccCCCC-ceEEEEEEEEe-cCcEE--EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008596 212 YEILALDCEMCYTNEG-LELTRVTLVDI-KGQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (560)
Q Consensus 212 ~~~valDcEm~~t~~g-~eL~rVsvVd~-~G~vv--lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i 287 (560)
..||++|+||||+++. ++|+++++|.. +|++| |+.|++|..||+...|.+||||.+||+++ +.+.+|..++++|+
T Consensus 421 atyVVfDiETTGLs~~~d~iIE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a-~~i~~vL~kf~~~~ 499 (1444)
T COG2176 421 ATYVVFDIETTGLSPVYDEIIEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENA-PEIEEVLEKFREFI 499 (1444)
T ss_pred ccEEEEEeecCCcCcccchhhhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCC-ccHHHHHHHHHHHh
Confidence 4699999999999987 79999999997 67777 77899999999999999999999999999 79999999999999
Q ss_pred cCCCEEEEeCchhhHHHHccc---------cCcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHHHHH
Q 008596 288 YKETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARA 358 (560)
Q Consensus 288 ~~~~ILVGHsL~~DL~aLki~---------Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~A 358 (560)
+|+|||+||+.||+.+|+.. ...+|||..|.+..++...+++|..||++ ||+... .+|+|.-||.|
T Consensus 500 -~d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh~Lg~l~kk-~~v~le---~hHRA~yDaea 574 (1444)
T COG2176 500 -GDSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSHRLGTLCKK-LGVELE---RHHRADYDAEA 574 (1444)
T ss_pred -cCcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhcchHHHHHH-hCccHH---HhhhhhhhHHH
Confidence 99999999999999999952 23689999987777666677899999997 699985 48999999999
Q ss_pred HHHHHHHHHHh
Q 008596 359 AMELALLKIRN 369 (560)
Q Consensus 359 tl~L~~~kl~~ 369 (560)
+..|+..++++
T Consensus 575 t~~vf~~f~~~ 585 (1444)
T COG2176 575 TAKVFFVFLKD 585 (1444)
T ss_pred HHHHHHHHHHH
Confidence 99999888877
No 43
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.77 E-value=7.7e-18 Score=177.24 Aligned_cols=149 Identities=13% Similarity=0.190 Sum_probs=122.1
Q ss_pred CcEEEEEeccccCCCC-ceEEEEEEEEe--cCcEE--EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHh
Q 008596 212 YEILALDCEMCYTNEG-LELTRVTLVDI--KGQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKL 286 (560)
Q Consensus 212 ~~~valDcEm~~t~~g-~eL~rVsvVd~--~G~vv--lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~ 286 (560)
..|++||+||+|+++. ++|+.|++|.. +|+++ |.+||+|..++.. ..+||||++||+++ ++|.+|+.+|.+|
T Consensus 46 ~~fVvlDiETTGLdp~~drIIeIgAV~i~~~g~ive~f~tLVnP~~~~~p--~~LHGIT~e~La~A-P~f~eVl~el~~f 122 (377)
T PRK05601 46 APFVAVSIQTSGIHPSTSRLITIDAVTLTADGEEVEHFHAVLNPGEDPGP--FHLHGLSAEEFAQG-KRFSQILKPLDRL 122 (377)
T ss_pred CCEEEEEEECCCCCCCCCeEEEEEEEEEEcCCEEEEEEEEEECcCCCCCC--ccccCCCHHHHhcC-CCHHHHHHHHHHH
Confidence 4699999999999875 69999999975 46654 8889999986554 47999999999998 8999999999999
Q ss_pred hcCCCEEEEeCchhhHHHHccc--------------------------------c----CcccccccccccccCCCCCcc
Q 008596 287 VYKETILVGHSLENDLLALKIS--------------------------------H----GLVIDTAVLYKHPQGGSHKTS 330 (560)
Q Consensus 287 i~~~~ILVGHsL~~DL~aLki~--------------------------------H----p~viDT~~Ly~~~~g~~~k~s 330 (560)
| .+.+|||||+.||+.||... | ..++||..|.+.......+++
T Consensus 123 L-~g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l~~~r 201 (377)
T PRK05601 123 I-DGRTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGVALDDIR 201 (377)
T ss_pred h-CCCEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHcCCCCCCC
Confidence 9 89999999999999998631 1 257999988776644345678
Q ss_pred HHHHHHHhcCcccc-------cCCCCCChH--HHHHHHHHHHHH
Q 008596 331 LRVLAKKFLSREIQ-------QSGFGHDST--EDARAAMELALL 365 (560)
Q Consensus 331 Lk~La~~~Lg~~IQ-------~~~~~HdSl--EDA~Atl~L~~~ 365 (560)
|..||++ ||++.. .....|+++ +||+...+|+..
T Consensus 202 L~~La~~-lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~ 244 (377)
T PRK05601 202 IRGVAHT-LGLDAPAAEASVERAQVPHRQLCREETLLVARLYFA 244 (377)
T ss_pred HHHHHHH-hCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHH
Confidence 9999986 699871 112478888 799999999853
No 44
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.76 E-value=6.2e-18 Score=168.21 Aligned_cols=155 Identities=26% Similarity=0.321 Sum_probs=129.1
Q ss_pred CcEEEEEeccccCCC-CceEEEEEEEEe-cCcEE---EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHh
Q 008596 212 YEILALDCEMCYTNE-GLELTRVTLVDI-KGQVL---LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKL 286 (560)
Q Consensus 212 ~~~valDcEm~~t~~-g~eL~rVsvVd~-~G~vv---lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~ 286 (560)
.++++||+||+|... ++++++|++|.. ++.++ |+.||+|+.+|+++.+++||||.+||.++ +.+.+|.+++.++
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~-p~~~~v~~~~~~~ 91 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADA-PKFAEVLPEFLDF 91 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcC-CCHHHHHHHHHHH
Confidence 468999999999996 689999999997 45444 78999999999999999999999999999 8999999999999
Q ss_pred hcCCCEEEEeCchhhHHHHccc---------cCcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHHHH
Q 008596 287 VYKETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDAR 357 (560)
Q Consensus 287 i~~~~ILVGHsL~~DL~aLki~---------Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~ 357 (560)
+.+..++||||+.||+.+|+.. -..++||..+.+...+...+++|.+||. ++|++.. ....|+++.||.
T Consensus 92 i~~~~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~~~L~~l~~-~~gi~~~-~~~~H~Al~Da~ 169 (243)
T COG0847 92 IGGLRLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDALAE-RLGIDRN-PFHPHRALFDAL 169 (243)
T ss_pred HCCCCeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCccchHHHHHH-HcCCCcC-CcCCcchHHHHH
Confidence 9444999999999999999842 1256799887666543335788999998 5798844 224799999999
Q ss_pred HHHHHHHHHHHh
Q 008596 358 AAMELALLKIRN 369 (560)
Q Consensus 358 Atl~L~~~kl~~ 369 (560)
++++++......
T Consensus 170 ~~a~~~~~~~~~ 181 (243)
T COG0847 170 ALAELFLLLQTG 181 (243)
T ss_pred HHHHHHHHHHhc
Confidence 999998655543
No 45
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=99.74 E-value=7.2e-18 Score=162.20 Aligned_cols=145 Identities=19% Similarity=0.133 Sum_probs=113.5
Q ss_pred EEEEeccccCCCC-ceEEEEEEEEecC--cEE--EEEEEeCCC--CCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008596 215 LALDCEMCYTNEG-LELTRVTLVDIKG--QVL--LDKLVKPSN--AIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (560)
Q Consensus 215 valDcEm~~t~~g-~eL~rVsvVd~~G--~vv--lD~LVkP~~--~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i 287 (560)
+.+|+||+|++.. ++|++|++|..++ .++ ++.||+|.. ++....+.+||||++||++..+++.++..++.+|+
T Consensus 1 ~~~D~ETTGl~~~~d~Iieig~v~v~~~~~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~~~~~ 80 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQFAAIRTDENFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKIHRLF 80 (183)
T ss_pred CEEEeecCCCCCCCCceEEEEEEEECCCCCCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHHHHHH
Confidence 3699999999875 6999999998743 444 788999975 56667889999999999993378999999999999
Q ss_pred c-CCCEEEEeC-chhhHHHHccc---c------------Ccccccccccccc---------cC----CCCCccHHHHHHH
Q 008596 288 Y-KETILVGHS-LENDLLALKIS---H------------GLVIDTAVLYKHP---------QG----GSHKTSLRVLAKK 337 (560)
Q Consensus 288 ~-~~~ILVGHs-L~~DL~aLki~---H------------p~viDT~~Ly~~~---------~g----~~~k~sLk~La~~ 337 (560)
. ++.++|||| +.||+.+|+.. + ..++||..+.+.. .+ ....++|..||++
T Consensus 81 ~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L~~l~~~ 160 (183)
T cd06138 81 NTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKLEDLAQA 160 (183)
T ss_pred ccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhHHHHHHH
Confidence 5 467999997 89999999831 1 1247887543321 00 1235779999986
Q ss_pred hcCcccccCCCCCChHHHHHHHHHHH
Q 008596 338 FLSREIQQSGFGHDSTEDARAAMELA 363 (560)
Q Consensus 338 ~Lg~~IQ~~~~~HdSlEDA~Atl~L~ 363 (560)
+|++.. ..|+|++||+||++|+
T Consensus 161 -~gi~~~---~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 161 -NGIEHS---NAHDALSDVEATIALA 182 (183)
T ss_pred -CCCCcc---ccccHHHHHHHHHHHh
Confidence 698875 4899999999999986
No 46
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.64 E-value=9.3e-16 Score=184.38 Aligned_cols=152 Identities=24% Similarity=0.369 Sum_probs=130.6
Q ss_pred CcEEEEEeccccCCCC-ceEEEEEEEEe-cCcEE--EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008596 212 YEILALDCEMCYTNEG-LELTRVTLVDI-KGQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (560)
Q Consensus 212 ~~~valDcEm~~t~~g-~eL~rVsvVd~-~G~vv--lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i 287 (560)
.++|++|+||+|.+.. ++|+++++|.. +|.++ |+.||+|..+|+.+.+++||||++||.++ +++.++.+++.+|+
T Consensus 419 ~~~VVfDLETTGL~~~~deIIEIgAV~V~~G~iie~F~~~V~P~~~I~~~~~~LTGIT~e~L~~a-ps~~EaL~~f~~fi 497 (1437)
T PRK00448 419 ATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDA-PSIEEVLPKFKEFC 497 (1437)
T ss_pred CcEEEEEhhhcCCCCchhhhheeeeEEEeCCeEeeeEEEEECCCCCCCHHHHHHhCCCHHHHcCC-CCHHHHHHHHHHHh
Confidence 4699999999999875 68888988886 56665 88999999999999999999999999988 79999999999999
Q ss_pred cCCCEEEEeCchhhHHHHcc---------ccCcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHHHHH
Q 008596 288 YKETILVGHSLENDLLALKI---------SHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARA 358 (560)
Q Consensus 288 ~~~~ILVGHsL~~DL~aLki---------~Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~A 358 (560)
++.+|||||..||+.+|+- ....++||..+++...+...+++|..||++ +|+... ++|+|+.||.|
T Consensus 498 -gg~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k~~kL~~LAk~-lGL~~~---~~HrAl~DA~a 572 (1437)
T PRK00448 498 -GDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKK-FGVELE---HHHRADYDAEA 572 (1437)
T ss_pred -CCCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccccccHHHHHHH-cCCCCC---CCcChHHHHHH
Confidence 8899999999999998852 123689999887665444457789999986 688875 37999999999
Q ss_pred HHHHHHHHHHh
Q 008596 359 AMELALLKIRN 369 (560)
Q Consensus 359 tl~L~~~kl~~ 369 (560)
|++|+...+++
T Consensus 573 Ta~lf~~ll~~ 583 (1437)
T PRK00448 573 TAYLLIKFLKD 583 (1437)
T ss_pred HHHHHHHHHHH
Confidence 99999887766
No 47
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.64 E-value=1.5e-15 Score=165.88 Aligned_cols=155 Identities=17% Similarity=0.106 Sum_probs=119.7
Q ss_pred CCcEEEEEeccccCCCC-ceEEEEEEEEecC--cEE---EEEEEeCCCC--CCCCcEEecCCChhhhcCCCCCHHHHHHH
Q 008596 211 PYEILALDCEMCYTNEG-LELTRVTLVDIKG--QVL---LDKLVKPSNA--IVDYNTRYSGITHEMLSGVTTSLKDIQEE 282 (560)
Q Consensus 211 ~~~~valDcEm~~t~~g-~eL~rVsvVd~~G--~vv---lD~LVkP~~~--I~dy~T~~SGIT~e~L~~~~~tl~dVq~~ 282 (560)
...+|++|+||+|+++. ++|++|++|..++ .++ +..||+|... +....+.+||||++||...+.+..++..+
T Consensus 5 ~~~fvv~D~ETTGLdP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~~~ 84 (476)
T PRK11779 5 QPTFLWHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEFAAR 84 (476)
T ss_pred CCcEEEEEEECCCCCCCCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHHHHH
Confidence 34699999999999975 7999999998743 233 7899999863 34567899999999998876789999999
Q ss_pred HHHhhc-CCCEEEEeC-chhhHHHHcccc------C------------ccccccccccccc--C--------CCCCccHH
Q 008596 283 FLKLVY-KETILVGHS-LENDLLALKISH------G------------LVIDTAVLYKHPQ--G--------GSHKTSLR 332 (560)
Q Consensus 283 L~~~i~-~~~ILVGHs-L~~DL~aLki~H------p------------~viDT~~Ly~~~~--g--------~~~k~sLk 332 (560)
|.+++. +++++|||| +.||+.+|+... + .++|++.++...+ + ....++|.
T Consensus 85 i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rLe 164 (476)
T PRK11779 85 IHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKLE 164 (476)
T ss_pred HHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCcHH
Confidence 999994 589999996 899999887421 1 2356666543211 1 11347799
Q ss_pred HHHHHhcCcccccCCCCCChHHHHHHHHHHHHHHHHh
Q 008596 333 VLAKKFLSREIQQSGFGHDSTEDARAAMELALLKIRN 369 (560)
Q Consensus 333 ~La~~~Lg~~IQ~~~~~HdSlEDA~Atl~L~~~kl~~ 369 (560)
.||+. +|++.. .+|||+.||.||++|++...++
T Consensus 165 ~L~~~-~gI~~~---~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 165 HLTKA-NGIEHE---NAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred HHHHH-cCCCCC---CCCCcHHHHHHHHHHHHHHHHh
Confidence 99997 588765 4899999999999998766655
No 48
>PRK05359 oligoribonuclease; Provisional
Probab=99.63 E-value=1.4e-15 Score=146.83 Aligned_cols=142 Identities=16% Similarity=0.179 Sum_probs=108.6
Q ss_pred CcEEEEEeccccCCCC-ceEEEEEEEEecCc--EE---EEEEEeCCCC----CCCCcEEec---CCChhhhcCCCCCHHH
Q 008596 212 YEILALDCEMCYTNEG-LELTRVTLVDIKGQ--VL---LDKLVKPSNA----IVDYNTRYS---GITHEMLSGVTTSLKD 278 (560)
Q Consensus 212 ~~~valDcEm~~t~~g-~eL~rVsvVd~~G~--vv---lD~LVkP~~~----I~dy~T~~S---GIT~e~L~~~~~tl~d 278 (560)
.++|+|||||||+++. ++|++|++|..++. ++ +..+|+|... +..+.+++| |||.++++++ +++.+
T Consensus 3 ~~~vvlD~ETTGLdp~~d~IieIgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~-~~~~e 81 (181)
T PRK05359 3 DNLIWIDLEMTGLDPERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRAST-VSEAE 81 (181)
T ss_pred CcEEEEEeecCCCCCCCCeEEEEEEEEEcCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcC-CCHHH
Confidence 4699999999999975 79999999987553 33 6789999875 466787877 9999999998 79999
Q ss_pred HHHHHHHhhc-----CCCEEEEeCchhhHHHHcc--------ccCcccccccc---cccccCCCCCccHHHHHHHhcCcc
Q 008596 279 IQEEFLKLVY-----KETILVGHSLENDLLALKI--------SHGLVIDTAVL---YKHPQGGSHKTSLRVLAKKFLSRE 342 (560)
Q Consensus 279 Vq~~L~~~i~-----~~~ILVGHsL~~DL~aLki--------~Hp~viDT~~L---y~~~~g~~~k~sLk~La~~~Lg~~ 342 (560)
+..+|++|+. .+.+|||||+.||+.+|+. .|.+++|++.+ .+... |.+ +++++
T Consensus 82 ~~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~tl~~l~r~~~-----P~~------~~~~~ 150 (181)
T PRK05359 82 AEAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLDVSTLKELARRWK-----PEI------LNGFK 150 (181)
T ss_pred HHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhcccCCCcccchhHHHHHHHHhC-----hhh------hhCCC
Confidence 9999999995 3689999999999999984 24467775433 32221 111 22333
Q ss_pred cccCCCCCChHHHHHHHHHHHHHHHH
Q 008596 343 IQQSGFGHDSTEDARAAMELALLKIR 368 (560)
Q Consensus 343 IQ~~~~~HdSlEDA~Atl~L~~~kl~ 368 (560)
-. +.|++++||+++.+.++...+
T Consensus 151 ~~---~~HRal~D~~~s~~~~~~~~~ 173 (181)
T PRK05359 151 KQ---GTHRALADIRESIAELKYYRE 173 (181)
T ss_pred Cc---CCcccHHHHHHHHHHHHHHHH
Confidence 22 479999999999999865554
No 49
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=99.63 E-value=9e-16 Score=146.66 Aligned_cols=141 Identities=16% Similarity=0.246 Sum_probs=105.6
Q ss_pred EEEEEeccccCCC-CceEEEEEEEEecCc--EE---EEEEEeCCCCCC----CCcEEe---cCCChhhhcCCCCCHHHHH
Q 008596 214 ILALDCEMCYTNE-GLELTRVTLVDIKGQ--VL---LDKLVKPSNAIV----DYNTRY---SGITHEMLSGVTTSLKDIQ 280 (560)
Q Consensus 214 ~valDcEm~~t~~-g~eL~rVsvVd~~G~--vv---lD~LVkP~~~I~----dy~T~~---SGIT~e~L~~~~~tl~dVq 280 (560)
+++||+||+|+++ .++|++|++|..++. .+ |+.+|+|..++. .+..++ ||||+++++++ +++.++.
T Consensus 1 lv~iD~ETTGl~p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~-~~~~~vl 79 (173)
T cd06135 1 LVWIDLEMTGLDPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRAST-VTLAQAE 79 (173)
T ss_pred CEEEEEecCCCCCCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCC-CCHHHHH
Confidence 4789999999996 579999999988653 33 889999998655 344445 69999999998 7999999
Q ss_pred HHHHHhhcC-----CCEEEEeCchhhHHHHcc--------ccCccccccc---ccccccCCCCCccHHHHHHHhcCcccc
Q 008596 281 EEFLKLVYK-----ETILVGHSLENDLLALKI--------SHGLVIDTAV---LYKHPQGGSHKTSLRVLAKKFLSREIQ 344 (560)
Q Consensus 281 ~~L~~~i~~-----~~ILVGHsL~~DL~aLki--------~Hp~viDT~~---Ly~~~~g~~~k~sLk~La~~~Lg~~IQ 344 (560)
.++.+|+.. ..+|||||+.||+.+|+. .+.+++||.. |++...+ .++. ++..-
T Consensus 80 ~~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~~~l~~l~~~l~p-----~~~~-----~~~~~- 148 (173)
T cd06135 80 AELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDVSSIKELARRWYP-----EIYR-----KAPKK- 148 (173)
T ss_pred HHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHHhccCCcchhhHHHHHHHHHHhCc-----Hhhh-----cCCCC-
Confidence 999999953 479999999999999984 2345688743 3332211 1111 23332
Q ss_pred cCCCCCChHHHHHHHHHHHHHHHH
Q 008596 345 QSGFGHDSTEDARAAMELALLKIR 368 (560)
Q Consensus 345 ~~~~~HdSlEDA~Atl~L~~~kl~ 368 (560)
+..|+|+.||++|+.+|+..++
T Consensus 149 --~~~HrAl~Da~~~~~~~~~~~~ 170 (173)
T cd06135 149 --KGTHRALDDIRESIAELKYYRE 170 (173)
T ss_pred --CCCcchHHHHHHHHHHHHHHHH
Confidence 2579999999999999976554
No 50
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.61 E-value=6.5e-15 Score=162.78 Aligned_cols=154 Identities=16% Similarity=0.199 Sum_probs=120.1
Q ss_pred CcEEEEEeccccCCC----CceEEEEEEEEe---cCcEE--EEEEEeCCC--CCCCCcEEecCCChhhhcCCCCCHHHHH
Q 008596 212 YEILALDCEMCYTNE----GLELTRVTLVDI---KGQVL--LDKLVKPSN--AIVDYNTRYSGITHEMLSGVTTSLKDIQ 280 (560)
Q Consensus 212 ~~~valDcEm~~t~~----g~eL~rVsvVd~---~G~vv--lD~LVkP~~--~I~dy~T~~SGIT~e~L~~~~~tl~dVq 280 (560)
..|++||+|||+.+. .+||++|++|-. +|+++ |.+||+|.. +|+.|+|++||||.+||+++ ++|.+|+
T Consensus 56 d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~A-p~F~eVl 134 (582)
T PTZ00315 56 DAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRA-DPFPVVY 134 (582)
T ss_pred CeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcC-CCHHHHH
Confidence 469999999999764 369999999986 56655 788999987 79999999999999999999 7999999
Q ss_pred HHHHHhhcCC---------CEEEEeCchhhHH-HHcc--------c----cCcccccccc-----cccc-------cCCC
Q 008596 281 EEFLKLVYKE---------TILVGHSLENDLL-ALKI--------S----HGLVIDTAVL-----YKHP-------QGGS 326 (560)
Q Consensus 281 ~~L~~~i~~~---------~ILVGHsL~~DL~-aLki--------~----Hp~viDT~~L-----y~~~-------~g~~ 326 (560)
.+|.+++... ..+|+|+..||++ +|.- . ...++|.... |+.. ....
T Consensus 135 ~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p~~~~~~~~~~~~~ 214 (582)
T PTZ00315 135 CEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFGNGSGCGGGATPPL 214 (582)
T ss_pred HHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCcccccccccccccc
Confidence 9999999432 3699999999995 6631 1 2245564222 2210 0012
Q ss_pred CCccHHHHHHHhcCcccccCCCCCChHHHHHHHHHHHHHHHHh
Q 008596 327 HKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMELALLKIRN 369 (560)
Q Consensus 327 ~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~Atl~L~~~kl~~ 369 (560)
..++|..+++. +|++... ..|+++.||+++++|+...+++
T Consensus 215 ~~~~L~~al~~-lgL~~eG--r~HrAlDDA~ntA~L~~~Ll~~ 254 (582)
T PTZ00315 215 GPSDMPDMLQM-LGLPLQG--RHHSGIDDCRNIAAVLCELLRR 254 (582)
T ss_pred CCcCHHHHHHH-CCCCCCC--CCcCcHHHHHHHHHHHHHHHHc
Confidence 44689999985 7988753 5799999999999999888877
No 51
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=98.46 E-value=2.5e-06 Score=81.08 Aligned_cols=149 Identities=19% Similarity=0.199 Sum_probs=95.3
Q ss_pred CcEEEEEeccccCCC-CceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcCC
Q 008596 212 YEILALDCEMCYTNE-GLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKE 290 (560)
Q Consensus 212 ~~~valDcEm~~t~~-g~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~~ 290 (560)
..++|+|+|+++... ...++.+++....+..++= -+++ +.+ .+. ..+.++...|.+++...
T Consensus 5 ~~~~a~d~e~~~~~~~~~~i~~l~~~~~~~~~~~~-~~~~--------~~~--------~~~-~~~~~~~~~l~~~l~~~ 66 (193)
T cd06139 5 AKVFAFDTETTSLDPMQAELVGISFAVEPGEAYYI-PLGH--------DYG--------GEQ-LPREEVLAALKPLLEDP 66 (193)
T ss_pred CCeEEEEeecCCCCcCCCeEEEEEEEcCCCCEEEE-ecCC--------Ccc--------ccC-CCHHHHHHHHHHHHhCC
Confidence 357999999988775 3578888887655544320 0111 111 122 46888889999998544
Q ss_pred -CEEEEeCchhhHHHHccc----cCcccccccccccccCCCCCccHHHHHHHhcCccccc-----CC-------------
Q 008596 291 -TILVGHSLENDLLALKIS----HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQ-----SG------------- 347 (560)
Q Consensus 291 -~ILVGHsL~~DL~aLki~----Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~-----~~------------- 347 (560)
..+||||+.+|+.+|+.. ...++||..++....+...+.+|..|++.|+|..+.. +.
T Consensus 67 ~~~~v~hn~k~d~~~l~~~gi~~~~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~~ 146 (193)
T cd06139 67 SIKKVGQNLKFDLHVLANHGIELRGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPLE 146 (193)
T ss_pred CCcEEeeccHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccCHH
Confidence 379999999999999742 2367999887554432221468999999998876210 00
Q ss_pred -CCCChHHHHHHHHHHHHHHHHhhhh-HHHHHH
Q 008596 348 -FGHDSTEDARAAMELALLKIRNVMR-TKLLKV 378 (560)
Q Consensus 348 -~~HdSlEDA~Atl~L~~~kl~~~~~-~~i~~~ 378 (560)
..|.+..||.++++|+....++-.. +++.+.
T Consensus 147 ~~~~ya~~d~~~~~~l~~~l~~~l~~~~~~~~l 179 (193)
T cd06139 147 KAAEYAAEDADITLRLYELLKPKLKEEPGLLEL 179 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHH
Confidence 1134677888888887655555433 334433
No 52
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=98.43 E-value=9.8e-08 Score=91.01 Aligned_cols=153 Identities=20% Similarity=0.295 Sum_probs=115.3
Q ss_pred cEEEEEeccccCCCC-----ceEEEEE--EEEe-cCcEE--EEEEEeCCC--CCCCCcEEecCCChhhhcCCCCCHHHHH
Q 008596 213 EILALDCEMCYTNEG-----LELTRVT--LVDI-KGQVL--LDKLVKPSN--AIVDYNTRYSGITHEMLSGVTTSLKDIQ 280 (560)
Q Consensus 213 ~~valDcEm~~t~~g-----~eL~rVs--vVd~-~G~vv--lD~LVkP~~--~I~dy~T~~SGIT~e~L~~~~~tl~dVq 280 (560)
..++||.|.+.-+.+ .|++.|. +|+. +.++| |.+||+|.. ..++|+..++|||...++.+ +-|++|+
T Consensus 5 ~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~a-pifs~v~ 83 (210)
T COG5018 5 SLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEA-PIFSMVF 83 (210)
T ss_pred eEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhcccc-chHHHHH
Confidence 478999999876554 3666554 4543 33443 678999987 67799999999999999999 7899999
Q ss_pred HHHHHhhcCCCE----EEEeCchhhHHHHccc----c--C-----cccccccccccccCCCCCccHHHHHHHhcCccccc
Q 008596 281 EEFLKLVYKETI----LVGHSLENDLLALKIS----H--G-----LVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQ 345 (560)
Q Consensus 281 ~~L~~~i~~~~I----LVGHsL~~DL~aLki~----H--p-----~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~ 345 (560)
+++..++..... -..---.-|++.|+.. | | ..+|.+.-|...++.++-.+|....+.| |...+.
T Consensus 84 E~f~r~L~~h~Pr~~~~wa~wG~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~pr~tgln~ale~~-G~sf~G 162 (210)
T COG5018 84 EDFIRKLNEHDPRKNSTWATWGNMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGDPRLTGLNKALEEY-GDSFTG 162 (210)
T ss_pred HHHHHHHHhcCcccCCccccccchhHHHHHHHHHhcCCCCccccCccchHHHHHHHHhcCCccccHHHHHHHh-ccccCC
Confidence 998888843221 1222346799999841 2 1 4689888888887777667898888875 888874
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHh
Q 008596 346 SGFGHDSTEDARAAMELALLKIRN 369 (560)
Q Consensus 346 ~~~~HdSlEDA~Atl~L~~~kl~~ 369 (560)
..|++++|||.+.+|+++.+..
T Consensus 163 --~~HraldDArn~~rl~klv~~~ 184 (210)
T COG5018 163 --THHRALDDARNAYRLFKLVEQD 184 (210)
T ss_pred --chhhhHHHHHHHHHHHHHHcch
Confidence 6899999999999999776655
No 53
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=98.42 E-value=1.1e-06 Score=85.04 Aligned_cols=122 Identities=18% Similarity=0.197 Sum_probs=88.0
Q ss_pred EEEEEeccccC----CC-CceEEEEEEEEe-cCcEE-EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHh
Q 008596 214 ILALDCEMCYT----NE-GLELTRVTLVDI-KGQVL-LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKL 286 (560)
Q Consensus 214 ~valDcEm~~t----~~-g~eL~rVsvVd~-~G~vv-lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~ 286 (560)
++++|+||++. +. +++|+.||++.. .|... +.....|...... ||+..++..+ .+-.++...+.++
T Consensus 1 v~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~~~g~~~~~~~~~~~~~~~~~------~i~~~~v~~~-~~E~~lL~~f~~~ 73 (199)
T cd05160 1 VLSFDIETTPPVGGPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDDIE------FIDGIEVEYF-ADEKELLKRFFDI 73 (199)
T ss_pred CccEEEeecCCCCCcCCCCCCEEEEEEEEeeCCceeeEEEeecccCCcCC------CCCCceEEEe-CCHHHHHHHHHHH
Confidence 46899999997 33 479999999997 67643 2222223222111 8898899988 6899999999999
Q ss_pred hcCC--CEEEEeCc-hhhHHHHcc-------cc------------------------CcccccccccccccCCCCCccHH
Q 008596 287 VYKE--TILVGHSL-ENDLLALKI-------SH------------------------GLVIDTAVLYKHPQGGSHKTSLR 332 (560)
Q Consensus 287 i~~~--~ILVGHsL-~~DL~aLki-------~H------------------------p~viDT~~Ly~~~~g~~~k~sLk 332 (560)
+..- .+|||||. .||+.+|.- .+ ..++|+..+++... +...++|.
T Consensus 74 i~~~dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~-~l~sy~L~ 152 (199)
T cd05160 74 IREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDF-KLKSYTLD 152 (199)
T ss_pred HHhcCCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhc-CcccCCHH
Confidence 9432 59999999 899999873 12 12578877765543 24567899
Q ss_pred HHHHHhcCccc
Q 008596 333 VLAKKFLSREI 343 (560)
Q Consensus 333 ~La~~~Lg~~I 343 (560)
.+|+++||...
T Consensus 153 ~v~~~~l~~~k 163 (199)
T cd05160 153 AVAEELLGEGK 163 (199)
T ss_pred HHHHHHhCCCC
Confidence 99999988743
No 54
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=98.32 E-value=3e-06 Score=78.95 Aligned_cols=127 Identities=24% Similarity=0.253 Sum_probs=78.0
Q ss_pred cEEEEEeccccCCCC---ceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhc-
Q 008596 213 EILALDCEMCYTNEG---LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVY- 288 (560)
Q Consensus 213 ~~valDcEm~~t~~g---~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~- 288 (560)
+++|+|||+++.... ..++-|++-...+..+++ |-..-.+. +...|.+++.
T Consensus 21 ~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~~----~~~~~~~~---------------------~~~~l~~ll~~ 75 (176)
T PF01612_consen 21 KVLAFDTETTGLDPYSYNPKIALIQLATGEGCYIID----PIDLGDNW---------------------ILDALKELLED 75 (176)
T ss_dssp SEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEEC----GTTSTTTT---------------------HHHHHHHHHTT
T ss_pred CeEEEEEEECCCCccccCCeEEEEEEecCCCceeee----eccccccc---------------------hHHHHHHHHhC
Confidence 389999999998772 244444444432222222 21110000 5666777773
Q ss_pred CCCEEEEeCchhhHHHHccc----cCcccccccccccccCCCCCccHHHHHHHhcC-cccccC---CCCC--C-------
Q 008596 289 KETILVGHSLENDLLALKIS----HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLS-REIQQS---GFGH--D------- 351 (560)
Q Consensus 289 ~~~ILVGHsL~~DL~aLki~----Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg-~~IQ~~---~~~H--d------- 351 (560)
++.+.||||+.+|+.+|... ...++|| .+..+..++..+++|+.|+..|+| ...... +... +
T Consensus 76 ~~i~kv~~n~~~D~~~L~~~~~i~~~~~~D~-~l~~~~l~~~~~~~L~~L~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~ 154 (176)
T PF01612_consen 76 PNIIKVGHNAKFDLKWLYRSFGIDLKNVFDT-MLAAYLLDPTRSYSLKDLAEEYLGNIDLDKKEQMSDWRKARPLSEEQI 154 (176)
T ss_dssp TTSEEEESSHHHHHHHHHHHHTS--SSEEEH-HHHHHHTTTSTTSSHHHHHHHHHSEEE-GHCCTTSSTTTSSS-HHHHH
T ss_pred CCccEEEEEEechHHHHHHHhccccCCccch-hhhhhcccccccccHHHHHHHHhhhccCcHHHhhccCCcCCCChHHHH
Confidence 45689999999999999852 3478999 555444444444899999999999 443221 1122 2
Q ss_pred --hHHHHHHHHHHHHH
Q 008596 352 --STEDARAAMELALL 365 (560)
Q Consensus 352 --SlEDA~Atl~L~~~ 365 (560)
|..||.++.+|+..
T Consensus 155 ~YAa~D~~~~~~l~~~ 170 (176)
T PF01612_consen 155 EYAAQDAVVTFRLYEK 170 (176)
T ss_dssp HHHHHHHHTHHHHHHH
T ss_pred HHHHHHHHHHHHHHHH
Confidence 34578888887743
No 55
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=98.10 E-value=6.1e-06 Score=79.24 Aligned_cols=143 Identities=21% Similarity=0.329 Sum_probs=102.9
Q ss_pred CcEEEEEeccccCCCC-ceEEEEEEEEecCc--EE---EEEEEeCCC----CCCCCcE---EecCCChhhhcCCCCCHHH
Q 008596 212 YEILALDCEMCYTNEG-LELTRVTLVDIKGQ--VL---LDKLVKPSN----AIVDYNT---RYSGITHEMLSGVTTSLKD 278 (560)
Q Consensus 212 ~~~valDcEm~~t~~g-~eL~rVsvVd~~G~--vv---lD~LVkP~~----~I~dy~T---~~SGIT~e~L~~~~~tl~d 278 (560)
.++|=|||||+|++-+ +.|++|+.+=.+|. ++ +|.-|+-.. ...+|+. .-||+|+.-++.. .+++|
T Consensus 26 q~lVWiD~EMTGLdvekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~-~tl~~ 104 (208)
T KOG3242|consen 26 QPLVWIDCEMTGLDVEKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASK-ITLAD 104 (208)
T ss_pred CceEEEeeeccccccccceeEEEEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhh-ccHHH
Confidence 3589999999999976 68999987755443 33 566666433 4456653 4578999988887 79999
Q ss_pred HHHHHHHhh-----cCCCEEEEeCchhhHHHHccc--------cCcccccccccccccCCCCCccHHHHHHHhcCccccc
Q 008596 279 IQEEFLKLV-----YKETILVGHSLENDLLALKIS--------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQ 345 (560)
Q Consensus 279 Vq~~L~~~i-----~~~~ILVGHsL~~DL~aLki~--------Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~ 345 (560)
+-.++++|+ ++.++|-|-|+.-|..||+-. |-++||.+. .+.||+++ .-+++.
T Consensus 105 aEnevl~yikk~ip~~~~~laGNSV~~DrlFl~k~mPk~~~~lhyrivDVSt-------------IkeL~~Rw-~P~~~~ 170 (208)
T KOG3242|consen 105 AENEVLEYIKKHIPKGKCPLAGNSVYMDRLFLKKYMPKLIKHLHYRIVDVST-------------IKELARRW-YPDIKA 170 (208)
T ss_pred HHHHHHHHHHHhCCCCCCCccCcchhhHHHHHHHHhHHHHHhcceeeeeHHH-------------HHHHHHHh-Cchhhc
Confidence 999999888 356789999999999999842 457788764 45555555 233332
Q ss_pred ----CCCCCChHHHHHHHHHHHHHHHHh
Q 008596 346 ----SGFGHDSTEDARAAMELALLKIRN 369 (560)
Q Consensus 346 ----~~~~HdSlEDA~Atl~L~~~kl~~ 369 (560)
....|+|+.|-+-+..=+++..++
T Consensus 171 ~aPkK~~~HrAldDI~ESI~ELq~Yr~n 198 (208)
T KOG3242|consen 171 RAPKKKATHRALDDIRESIKELQYYREN 198 (208)
T ss_pred cCcccccccchHHHHHHHHHHHHHHHHH
Confidence 125799999999887665555443
No 56
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=98.08 E-value=1.2e-05 Score=78.56 Aligned_cols=86 Identities=23% Similarity=0.195 Sum_probs=60.6
Q ss_pred HHHHHHhhcCCC-EEEEeCchhhHHHHcccc----------CcccccccccccccC----------CCCCccHHHHHHHh
Q 008596 280 QEEFLKLVYKET-ILVGHSLENDLLALKISH----------GLVIDTAVLYKHPQG----------GSHKTSLRVLAKKF 338 (560)
Q Consensus 280 q~~L~~~i~~~~-ILVGHsL~~DL~aLki~H----------p~viDT~~Ly~~~~g----------~~~k~sLk~La~~~ 338 (560)
-..|++++.... +-|||++.+|++.|+-.+ ..++||..++....+ .....||..||+.+
T Consensus 71 ~~~L~~ll~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~ 150 (193)
T cd06146 71 DRLLKRLFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEV 150 (193)
T ss_pred HHHHHHHhCCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHH
Confidence 345777774434 459999999999998421 368999887654321 13567999999999
Q ss_pred cCcccccCC-------------CCCChHHHHHHHHHHHHH
Q 008596 339 LSREIQQSG-------------FGHDSTEDARAAMELALL 365 (560)
Q Consensus 339 Lg~~IQ~~~-------------~~HdSlEDA~Atl~L~~~ 365 (560)
||..+.... .-+=|..||.++++|+..
T Consensus 151 lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~ 190 (193)
T cd06146 151 LGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDK 190 (193)
T ss_pred hCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 999887521 123356888888888753
No 57
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=98.04 E-value=2.7e-06 Score=85.86 Aligned_cols=153 Identities=22% Similarity=0.312 Sum_probs=108.3
Q ss_pred cEEEEEeccccCCCC-----ceEEEEEEEEe----cCcE--EEEEEEeCCC--CCCCCcEEecCCChhhhcCCCCCHHHH
Q 008596 213 EILALDCEMCYTNEG-----LELTRVTLVDI----KGQV--LLDKLVKPSN--AIVDYNTRYSGITHEMLSGVTTSLKDI 279 (560)
Q Consensus 213 ~~valDcEm~~t~~g-----~eL~rVsvVd~----~G~v--vlD~LVkP~~--~I~dy~T~~SGIT~e~L~~~~~tl~dV 279 (560)
-+++||.|.|--+.+ .||++.-+|-. .+.+ -|..||+|.. ...+|++.+|||..++++.+ ++|.+|
T Consensus 57 YLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a-~~f~~v 135 (280)
T KOG0542|consen 57 YLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEA-PTFPQV 135 (280)
T ss_pred eEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccC-CCHHHH
Confidence 478999998765543 48998888832 2332 2778999986 66799999999999999999 799999
Q ss_pred HHHHHHhhcC--------CCEEEEeCchhhHHH-Hc-------cccC----cccccccccccccCCCCCccHHHHHHHhc
Q 008596 280 QEEFLKLVYK--------ETILVGHSLENDLLA-LK-------ISHG----LVIDTAVLYKHPQGGSHKTSLRVLAKKFL 339 (560)
Q Consensus 280 q~~L~~~i~~--------~~ILVGHsL~~DL~a-Lk-------i~Hp----~viDT~~Ly~~~~g~~~k~sLk~La~~~L 339 (560)
..++...+-. ..-+|--+ .-||.. |. |.-| .+||.-..|......+...++..+-++ +
T Consensus 136 l~~f~~Wlr~~~~~~k~~~~Afvtdg-~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it~mLe~-~ 213 (280)
T KOG0542|consen 136 LSEFDSWLRKDSLGDKNGKFAFVTDG-DWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNITGMLEH-Y 213 (280)
T ss_pred HHHHHHHHHHhhcccccCceEEEeCc-hhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCHHHHHHH-h
Confidence 9988877721 12233322 445533 22 1222 578987777655333345568777765 5
Q ss_pred CcccccCCCCCChHHHHHHHHHHHHHHHHhh
Q 008596 340 SREIQQSGFGHDSTEDARAAMELALLKIRNV 370 (560)
Q Consensus 340 g~~IQ~~~~~HdSlEDA~Atl~L~~~kl~~~ 370 (560)
|.+.+ |..|+.+.||+-.+.++..+++..
T Consensus 214 gL~f~--Gr~HsGiDDa~Nia~I~~kM~~dg 242 (280)
T KOG0542|consen 214 GLQFE--GRAHSGIDDARNIARIAQKMIRDG 242 (280)
T ss_pred CCccc--CCcccCchhHHHHHHHHHHHHhCC
Confidence 77776 368999999999999997777663
No 58
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=98.03 E-value=1e-05 Score=77.00 Aligned_cols=152 Identities=16% Similarity=0.193 Sum_probs=101.9
Q ss_pred CCcEEEEEeccccCCCC-ceEEEEEEEEe--cCcEE---EEEEEe-CC---CCCCCCcEEe---cCCChhhhcCCCCCHH
Q 008596 211 PYEILALDCEMCYTNEG-LELTRVTLVDI--KGQVL---LDKLVK-PS---NAIVDYNTRY---SGITHEMLSGVTTSLK 277 (560)
Q Consensus 211 ~~~~valDcEm~~t~~g-~eL~rVsvVd~--~G~vv---lD~LVk-P~---~~I~dy~T~~---SGIT~e~L~~~~~tl~ 277 (560)
..++|=|||||||++.+ +.|++|+.+-- +-+++ .+.-|. |+ ....+|+++- ||+++.-.+.. .+..
T Consensus 5 ~~nLiWIDlEMTGLd~~~drIIEiA~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~-~t~~ 83 (184)
T COG1949 5 KNNLIWIDLEMTGLDPERDRIIEIATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKAST-VTEA 83 (184)
T ss_pred CCceEEEeeeeccCCcCcceEEEEEEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhh-ccHH
Confidence 34689999999999988 68999987644 33444 233333 22 2566888755 46777666655 6898
Q ss_pred HHHHHHHHhhc-----CCCEEEEeCchhhHHHHccccCcccccccccccccCCCCCccHHHHHHHhcCcccccC---CCC
Q 008596 278 DIQEEFLKLVY-----KETILVGHSLENDLLALKISHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQS---GFG 349 (560)
Q Consensus 278 dVq~~L~~~i~-----~~~ILVGHsL~~DL~aLki~Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~---~~~ 349 (560)
++-.+++.||. +.+++-|-|+.-|-+||--.-|.+.+ ..-|+.. --.+|+.||+.+ .-+|+.+ ++.
T Consensus 84 ~aE~~~l~flkkwvp~~~spicGNSI~qDRrFl~r~MP~Le~-yfHYR~l----DVSTlKELa~RW-~P~i~~~~~K~~~ 157 (184)
T COG1949 84 EAEAQTLDFLKKWVPKGVSPICGNSIAQDRRFLFRYMPKLEA-YFHYRYL----DVSTLKELARRW-NPEILAGFKKGGT 157 (184)
T ss_pred HHHHHHHHHHHHhCCCCCCCCccchhhHHHHHHHHHhhhHHH-HhhhHhh----hHHHHHHHHHhh-CcHhhhccccccc
Confidence 88888888883 55789999999999999854343332 1111111 113578888776 5556542 367
Q ss_pred CChHHHHHHHHHHHHHHHHh
Q 008596 350 HDSTEDARAAMELALLKIRN 369 (560)
Q Consensus 350 HdSlEDA~Atl~L~~~kl~~ 369 (560)
|.|++|-+-+..=+.+..++
T Consensus 158 H~Al~DI~ESI~EL~~YR~~ 177 (184)
T COG1949 158 HRALDDIRESIAELRYYREH 177 (184)
T ss_pred hhHHHHHHHHHHHHHHHHHH
Confidence 99999999887655555544
No 59
>PRK05755 DNA polymerase I; Provisional
Probab=97.87 E-value=9.7e-05 Score=87.34 Aligned_cols=132 Identities=19% Similarity=0.248 Sum_probs=89.8
Q ss_pred CcEEEEEeccccCCCC-ceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcCC
Q 008596 212 YEILALDCEMCYTNEG-LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKE 290 (560)
Q Consensus 212 ~~~valDcEm~~t~~g-~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~~ 290 (560)
..++|+|+|+++.... ..++.|++-..+|.+.+ |.+ +++.. ++...|.+++...
T Consensus 315 ~~~~a~DtEt~~l~~~~~~i~~i~ls~~~g~~~~---ip~-----------~~i~~-----------~~l~~l~~~L~d~ 369 (880)
T PRK05755 315 AGLFAFDTETTSLDPMQAELVGLSFAVEPGEAAY---IPL-----------DQLDR-----------EVLAALKPLLEDP 369 (880)
T ss_pred cCeEEEEeccCCCCcccccEEEEEEEeCCCcEEE---Eec-----------ccccH-----------HHHHHHHHHHhCC
Confidence 4589999999998764 46888887554554432 211 11110 4677788888543
Q ss_pred C-EEEEeCchhhHHHHccc----cCcccccccccccccCCCCCccHHHHHHHhcCccccc-------C---------CCC
Q 008596 291 T-ILVGHSLENDLLALKIS----HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQ-------S---------GFG 349 (560)
Q Consensus 291 ~-ILVGHsL~~DL~aLki~----Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~-------~---------~~~ 349 (560)
. ++||||+.||+.+|+.. ...++||.+++....+.. .++|+.|++.|+|.++-. + ...
T Consensus 370 ~v~kV~HNakfDl~~L~~~gi~~~~~~~DT~iAa~Ll~~~~-~~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~ple~~~ 448 (880)
T PRK05755 370 AIKKVGQNLKYDLHVLARYGIELRGIAFDTMLASYLLDPGR-RHGLDSLAERYLGHKTISFEEVAGKQLTFAQVDLEEAA 448 (880)
T ss_pred CCcEEEeccHhHHHHHHhCCCCcCCCcccHHHHHHHcCCCC-CCCHHHHHHHHhCCCccchHHhcCCCCCccccCHHHHH
Confidence 4 48999999999999842 246899988654443222 379999999999877310 0 013
Q ss_pred CChHHHHHHHHHHHHHHHHh
Q 008596 350 HDSTEDARAAMELALLKIRN 369 (560)
Q Consensus 350 HdSlEDA~Atl~L~~~kl~~ 369 (560)
|-+..|+.+++.|+....++
T Consensus 449 ~YAa~Dv~~~~~L~~~L~~~ 468 (880)
T PRK05755 449 EYAAEDADVTLRLHEVLKPK 468 (880)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 67899999999998666655
No 60
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=97.69 E-value=0.00034 Score=74.55 Aligned_cols=154 Identities=18% Similarity=0.157 Sum_probs=104.4
Q ss_pred CcEEEEEeccccCCCC-ceEEEEEEEEec--CcEE---EEEEEeCCCCCC--CCcEEecCCChhhhcCCCCCHHHHHHHH
Q 008596 212 YEILALDCEMCYTNEG-LELTRVTLVDIK--GQVL---LDKLVKPSNAIV--DYNTRYSGITHEMLSGVTTSLKDIQEEF 283 (560)
Q Consensus 212 ~~~valDcEm~~t~~g-~eL~rVsvVd~~--G~vv---lD~LVkP~~~I~--dy~T~~SGIT~e~L~~~~~tl~dVq~~L 283 (560)
..|+..|-||.|..+. +..++.+-|+-+ -++| +--|+||.+-.. ...+-++|||++........=.+....|
T Consensus 9 ~tF~~yDYETfG~~Pa~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~F~~~I 88 (475)
T COG2925 9 PTFLFYDYETFGVHPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAAFAARI 88 (475)
T ss_pred CcEEEEehhhcCCCcccccchhhheeeccccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHHHHHHH
Confidence 4699999999999886 688899888753 2333 567999987332 3468999999988876544444444444
Q ss_pred -HHhhcCCCEEEEeC-chhhHHHHccc------cC------------cccccccc-c-ccccC--------CCCCccHHH
Q 008596 284 -LKLVYKETILVGHS-LENDLLALKIS------HG------------LVIDTAVL-Y-KHPQG--------GSHKTSLRV 333 (560)
Q Consensus 284 -~~~i~~~~ILVGHs-L~~DL~aLki~------Hp------------~viDT~~L-y-~~~~g--------~~~k~sLk~ 333 (560)
.+|-.++|.+||+| +.||=.+-+.. .| .++|.... | -+|-| +.-..+|..
T Consensus 89 ~~~ls~P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n~dG~pSFkLEh 168 (475)
T COG2925 89 HAELTQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDDGLPSFKLEH 168 (475)
T ss_pred HHHhCCCCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcCCCCCcchhhHH
Confidence 45667999999995 89998888731 12 13555432 1 11211 112345999
Q ss_pred HHHHhcCcccccCCCCCChHHHHHHHHHHHHHHHHh
Q 008596 334 LAKKFLSREIQQSGFGHDSTEDARAAMELALLKIRN 369 (560)
Q Consensus 334 La~~~Lg~~IQ~~~~~HdSlEDA~Atl~L~~~kl~~ 369 (560)
|++.- |++-. .+|||+.|.+||..+.++.-+.
T Consensus 169 Lt~AN-gieH~---nAHdAmsDVyATIamAklvk~~ 200 (475)
T COG2925 169 LTKAN-GIEHS---NAHDAMSDVYATIAMAKLVKTA 200 (475)
T ss_pred Hhhcc-ccccc---hhhHHHHHHHHHHHHHHHHHhh
Confidence 99863 54432 5899999999999997544333
No 61
>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=97.66 E-value=0.00018 Score=62.60 Aligned_cols=57 Identities=26% Similarity=0.356 Sum_probs=41.5
Q ss_pred EEEEeccccCCCC-ceEEEEEEEEec-CcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcCC--
Q 008596 215 LALDCEMCYTNEG-LELTRVTLVDIK-GQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKE-- 290 (560)
Q Consensus 215 valDcEm~~t~~g-~eL~rVsvVd~~-G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~~-- 290 (560)
+++|.|+++.... .+|+.|++.+.. +.. ++.+ +.+++...
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~~----~~~~--------------------------------f~~~l~~~~~ 44 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPEDT----AVID--------------------------------LKDILRDKPL 44 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCCCE----EEeh--------------------------------HHHHHhhCCC
Confidence 4799999998765 589999999873 332 1211 55555333
Q ss_pred CEEEEeCchhhHHHHcc
Q 008596 291 TILVGHSLENDLLALKI 307 (560)
Q Consensus 291 ~ILVGHsL~~DL~aLki 307 (560)
.++||||..+|+.+|+.
T Consensus 45 ~v~V~hn~~fD~~fL~~ 61 (96)
T cd06125 45 AILVGHNGSFDLPFLNN 61 (96)
T ss_pred CEEEEeCcHHhHHHHHH
Confidence 69999999999999884
No 62
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=97.65 E-value=0.0002 Score=67.52 Aligned_cols=83 Identities=22% Similarity=0.176 Sum_probs=58.5
Q ss_pred HHHHhhc-CCCEEEEeCchhhHHHHcccc----CcccccccccccccCCCCCccHHHHHHHhcCcccc--cC----C---
Q 008596 282 EFLKLVY-KETILVGHSLENDLLALKISH----GLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQ--QS----G--- 347 (560)
Q Consensus 282 ~L~~~i~-~~~ILVGHsL~~DL~aLki~H----p~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ--~~----~--- 347 (560)
.|.+++. ++.+.|||++.+|+..|...+ ..++||..++....+.....+|..|++.|||..+. .. .
T Consensus 64 ~l~~ll~~~~i~kv~~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~ 143 (170)
T cd06141 64 SLKQLLEDPSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEA 143 (170)
T ss_pred HHHHHhcCCCeeEEEeeeHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCC
Confidence 4666664 345579999999999997322 35799998776654432346999999999999887 21 0
Q ss_pred ------CCCChHHHHHHHHHHHH
Q 008596 348 ------FGHDSTEDARAAMELAL 364 (560)
Q Consensus 348 ------~~HdSlEDA~Atl~L~~ 364 (560)
.-|=|..||..+++|+.
T Consensus 144 rpLt~~qi~YAa~Da~~~~~l~~ 166 (170)
T cd06141 144 RPLSKEQILYAATDAYASLELYR 166 (170)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHH
Confidence 12445678888888874
No 63
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=97.58 E-value=0.0011 Score=59.82 Aligned_cols=104 Identities=26% Similarity=0.289 Sum_probs=65.7
Q ss_pred EEEEEeccccCCC-CceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcCC-C
Q 008596 214 ILALDCEMCYTNE-GLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKE-T 291 (560)
Q Consensus 214 ~valDcEm~~t~~-g~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~~-~ 291 (560)
.+++|||...... ...++.+++... +++++ +-.... ...+.+.|.+++... .
T Consensus 2 ~l~~d~e~~~~~~~~~~i~~~~l~~~-~~~~~---i~~~~~----------------------~~~~~~~l~~~l~~~~~ 55 (155)
T cd00007 2 EVAFDTETTGLNYHRGKLVGIQIATA-GEAAY---IPDELE----------------------LEEDLEALKELLEDEDI 55 (155)
T ss_pred ceEEEEecCCCCcCCCeEEEEEEEEC-CcEEE---EEcCCC----------------------HHHHHHHHHHHHcCCCC
Confidence 5799999866552 235555555543 33322 110000 145666788888433 4
Q ss_pred EEEEeCchhhHHHHccc----cCcccccccccccccCCCCCccHHHHHHHhcCccc
Q 008596 292 ILVGHSLENDLLALKIS----HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREI 343 (560)
Q Consensus 292 ILVGHsL~~DL~aLki~----Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~I 343 (560)
.+||||+.+|+.+|+-. ...++||..++....+...+.+|+.|+++||+..+
T Consensus 56 ~~v~~~~k~d~~~L~~~~~~~~~~~~D~~~~ayll~~~~~~~~l~~l~~~~l~~~~ 111 (155)
T cd00007 56 TKVGHDAKFDLVVLARDGIELPGNIFDTMLAAYLLNPGEGSHSLDDLAKEYLGIEL 111 (155)
T ss_pred cEEeccHHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCCcCCHHHHHHHHcCCCC
Confidence 59999999999999732 23578998765444322214699999999998874
No 64
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=97.52 E-value=0.00048 Score=65.02 Aligned_cols=81 Identities=21% Similarity=0.226 Sum_probs=55.9
Q ss_pred HHHhhc-CCCEEEEeCchhhHHHHcccc----CcccccccccccccCCCCCccHHHHHHHhcCcccccC----C------
Q 008596 283 FLKLVY-KETILVGHSLENDLLALKISH----GLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQS----G------ 347 (560)
Q Consensus 283 L~~~i~-~~~ILVGHsL~~DL~aLki~H----p~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~----~------ 347 (560)
|.+++. ++.+.|||++..|+..|...+ ..++||...+... ++..+.+|+.|+++|||..+... .
T Consensus 59 L~~lL~d~~i~Kvg~~~k~D~~~L~~~~gi~~~~~~D~~~aa~ll-~~~~~~~L~~l~~~~lg~~l~K~~~~s~W~~rpL 137 (161)
T cd06129 59 LKMLLENPSIVKALHGIEGDLWKLLRDFGEKLQRLFDTTIAANLK-GLPERWSLASLVEHFLGKTLDKSISCADWSYRPL 137 (161)
T ss_pred HHHHhCCCCEEEEEeccHHHHHHHHHHcCCCcccHhHHHHHHHHh-CCCCCchHHHHHHHHhCCCCCccceeccCCCCCC
Confidence 455553 334569999999999996422 3579998866543 33345699999999999987432 1
Q ss_pred ---CCCChHHHHHHHHHHHH
Q 008596 348 ---FGHDSTEDARAAMELAL 364 (560)
Q Consensus 348 ---~~HdSlEDA~Atl~L~~ 364 (560)
.-|=|..||.++.+|+.
T Consensus 138 t~~qi~YAa~Da~~l~~l~~ 157 (161)
T cd06129 138 TEDQKLYAAADVYALLIIYT 157 (161)
T ss_pred CHHHHHHHHHHHHHHHHHHH
Confidence 12345678888888873
No 65
>PRK10829 ribonuclease D; Provisional
Probab=97.50 E-value=0.0013 Score=70.96 Aligned_cols=124 Identities=21% Similarity=0.219 Sum_probs=78.5
Q ss_pred CcEEEEEeccccCCCC---ceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhc
Q 008596 212 YEILALDCEMCYTNEG---LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVY 288 (560)
Q Consensus 212 ~~~valDcEm~~t~~g---~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~ 288 (560)
..++|||+|+...... -.|++|+ +..+..++| |-. +.| ...|.+++.
T Consensus 22 ~~~lalDtEf~~~~ty~~~l~LiQl~--~~~~~~LiD----~l~-~~d-----------------------~~~L~~ll~ 71 (373)
T PRK10829 22 FPAIALDTEFVRTRTYYPQLGLIQLY--DGEQLSLID----PLG-ITD-----------------------WSPFKALLR 71 (373)
T ss_pred CCeEEEecccccCccCCCceeEEEEe--cCCceEEEe----cCC-ccc-----------------------hHHHHHHHc
Confidence 3589999999886653 2344444 333333333 331 111 123666665
Q ss_pred CCCEE-EEeCchhhHHHHcc----ccCcccccccccccccCCCCCccHHHHHHHhcCcccccCCC----CCC--------
Q 008596 289 KETIL-VGHSLENDLLALKI----SHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGF----GHD-------- 351 (560)
Q Consensus 289 ~~~IL-VGHsL~~DL~aLki----~Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~----~Hd-------- 351 (560)
...|+ |+|+..+|+.+|.. ....++||.+.+... |.+...+|+.|+++|||+.+..+.. ..+
T Consensus 72 ~~~ivKV~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~l-g~~~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~ql~ 150 (373)
T PRK10829 72 DPQVTKFLHAGSEDLEVFLNAFGELPQPLIDTQILAAFC-GRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCE 150 (373)
T ss_pred CCCeEEEEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHc-CCCccccHHHHHHHHhCCccCcccccCCCCCCCCCHHHHH
Confidence 55665 89999999999843 234789998766543 4444679999999999999876321 122
Q ss_pred -hHHHHHHHHHHHHHH
Q 008596 352 -STEDARAAMELALLK 366 (560)
Q Consensus 352 -SlEDA~Atl~L~~~k 366 (560)
|..|+...++|+...
T Consensus 151 YAa~Dv~~L~~l~~~L 166 (373)
T PRK10829 151 YAAADVFYLLPIAAKL 166 (373)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 346777777776433
No 66
>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=97.28 E-value=0.0015 Score=63.82 Aligned_cols=115 Identities=16% Similarity=0.207 Sum_probs=73.4
Q ss_pred CcEEEEEeccccC-----CCCceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHh
Q 008596 212 YEILALDCEMCYT-----NEGLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKL 286 (560)
Q Consensus 212 ~~~valDcEm~~t-----~~g~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~ 286 (560)
-+++++|+|++.- ...++|+.||++...++.++.. ++... ..+... .+=.++..++.++
T Consensus 3 l~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~~--~~~~~-------------~~v~~~-~~E~~lL~~F~~~ 66 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVITW--KKFDL-------------PFVEVV-KTEKEMIKRFIEI 66 (195)
T ss_pred ceEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEEe--cCCCC-------------CeEEEe-CCHHHHHHHHHHH
Confidence 4689999999842 1236899999998666544311 11111 112222 3446677788888
Q ss_pred hcC--CCEEEEeCc-hhhHHHHcc-------ccC------------------------cccccccccccccCCCCCccHH
Q 008596 287 VYK--ETILVGHSL-ENDLLALKI-------SHG------------------------LVIDTAVLYKHPQGGSHKTSLR 332 (560)
Q Consensus 287 i~~--~~ILVGHsL-~~DL~aLki-------~Hp------------------------~viDT~~Ly~~~~g~~~k~sLk 332 (560)
+.. -.+|||||. .||+..|.- ..+ .++|+..+++... ....++|.
T Consensus 67 i~~~dpdiivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~-~l~sy~L~ 145 (195)
T cd05780 67 VKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTL-NLTRYTLE 145 (195)
T ss_pred HHHcCCCEEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhC-CCCcCcHH
Confidence 854 579999997 589998872 111 1456655554432 23467899
Q ss_pred HHHHHhcCccc
Q 008596 333 VLAKKFLSREI 343 (560)
Q Consensus 333 ~La~~~Lg~~I 343 (560)
++|+++||..-
T Consensus 146 ~v~~~~Lg~~k 156 (195)
T cd05780 146 RVYEELFGIEK 156 (195)
T ss_pred HHHHHHhCCCC
Confidence 99999999863
No 67
>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=96.86 E-value=0.011 Score=63.53 Aligned_cols=62 Identities=18% Similarity=0.174 Sum_probs=43.8
Q ss_pred HHHhhc-CCCEEEEeCchhhHHHHccc---c-CcccccccccccccCCCCCccHHHHHHHhcCccccc
Q 008596 283 FLKLVY-KETILVGHSLENDLLALKIS---H-GLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQ 345 (560)
Q Consensus 283 L~~~i~-~~~ILVGHsL~~DL~aLki~---H-p~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~ 345 (560)
|.+++. ++.+.|+|++.+|+.+|+.. . ..++||.+.+.- .|+..+.+|..|++.|||..+..
T Consensus 62 L~~lL~d~~i~KV~h~~k~Dl~~L~~~~~~~~~~~fDtqlAa~l-L~~~~~~~l~~Lv~~~Lg~~l~K 128 (367)
T TIGR01388 62 LKELLRDESVVKVLHAASEDLEVFLNLFGELPQPLFDTQIAAAF-CGFGMSMGYAKLVQEVLGVELDK 128 (367)
T ss_pred HHHHHCCCCceEEEeecHHHHHHHHHHhCCCCCCcccHHHHHHH-hCCCCCccHHHHHHHHcCCCCCc
Confidence 444553 34457999999999999732 2 367999875433 23334569999999999998764
No 68
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=96.82 E-value=0.011 Score=63.15 Aligned_cols=125 Identities=22% Similarity=0.237 Sum_probs=78.9
Q ss_pred CcEEEEEeccccCCCC-ceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcCC
Q 008596 212 YEILALDCEMCYTNEG-LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKE 290 (560)
Q Consensus 212 ~~~valDcEm~~t~~g-~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~~ 290 (560)
..+||||.|+.+...- ..|+=|-+-+.+|. .+|.|-.++.|. +.|..+.. +++
T Consensus 17 ~~~iAiDTEf~r~~t~~p~LcLIQi~~~e~~----~lIdpl~~~~d~----------------~~l~~Ll~------d~~ 70 (361)
T COG0349 17 SKAIAIDTEFMRLRTYYPRLCLIQISDGEGA----SLIDPLAGILDL----------------PPLVALLA------DPN 70 (361)
T ss_pred CCceEEecccccccccCCceEEEEEecCCCc----eEeccccccccc----------------chHHHHhc------CCc
Confidence 3589999999998875 45655555565553 355554432221 12221111 122
Q ss_pred CEEEEeCchhhHHHHccc---cC-cccccccccccccCCCCCccHHHHHHHhcCcccccCC----CCCChHHHH---HHH
Q 008596 291 TILVGHSLENDLLALKIS---HG-LVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSG----FGHDSTEDA---RAA 359 (560)
Q Consensus 291 ~ILVGHsL~~DL~aLki~---Hp-~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~----~~HdSlEDA---~At 359 (560)
-+=|=|+..+||.+|... +| .++||.+..+.. |.+-+++|+.|+++++|++|..+. =+++++.++ +|+
T Consensus 71 v~KIfHaa~~DL~~l~~~~g~~p~plfdTqiAa~l~-g~~~~~gl~~Lv~~ll~v~ldK~~q~SDW~~RPLs~~Ql~YAa 149 (361)
T COG0349 71 VVKIFHAARFDLEVLLNLFGLLPTPLFDTQIAAKLA-GFGTSHGLADLVEELLGVELDKSEQRSDWLARPLSEAQLEYAA 149 (361)
T ss_pred eeeeeccccccHHHHHHhcCCCCCchhHHHHHHHHh-CCcccccHHHHHHHHhCCcccccccccccccCCCCHHHHHHHH
Confidence 222559999999999842 44 689998765554 333378999999999999998642 256666664 345
Q ss_pred HHHH
Q 008596 360 MELA 363 (560)
Q Consensus 360 l~L~ 363 (560)
.++.
T Consensus 150 ~DV~ 153 (361)
T COG0349 150 ADVE 153 (361)
T ss_pred HHHH
Confidence 5543
No 69
>TIGR01696 deoB phosphopentomutase. This protein is involved in the purine and pyrimidine salvage pathway. It catalyzes the conversion of D-ribose 1-phosphate to D-ribose 5-phosphate and the conversion of 2-deoxy-D-ribose 1-phosphate to 2-deoxy-D-ribose 5-phosphate. The seed members of this protein are characterized deoB proteins from E.Coli and Bacillus. This model matches pfam01676 for Metalloenzyme superfamily.
Probab=96.81 E-value=0.0071 Score=65.36 Aligned_cols=110 Identities=19% Similarity=0.298 Sum_probs=84.2
Q ss_pred hHHHHHHHHHcCCeeeeecccccccccCCCCcceecCCChHHHHHHHHHhccCCCccEEEEecccchhhhhhhhhhHHHH
Q 008596 372 RTKLLKVLFEYGKTSTLIDNVSIIKRYASESSHAIPVSSDDEVLSKARKEVKNDRIHFVWTQFSELNLHFKKQAKDEAKL 451 (560)
Q Consensus 372 ~~~i~~~l~~~g~~~~~id~~~~~~~~~~~~~~~i~c~~D~ev~~~~~~~v~~~~~~f~~~~~~~l~~~~~~~~~~~~~~ 451 (560)
...++++|.+.|.....|........ +++-+.+++..++++.++++++.++....+|+++.+.++...+.+..
T Consensus 216 ~pTvld~l~~aG~~V~~VGki~DiF~-g~Glt~a~~~~~~~~~~~~~l~aL~~~~~~lif~nl~d~D~~~GH~~------ 288 (381)
T TIGR01696 216 APTVLQKLKDEGHDVISIGKIADIYD-GEGITKKVRTTSNMDGMDATIKEMKEDFTGISFTNLVDFDALWGHRR------ 288 (381)
T ss_pred CCCHHHHHHHCCCeEEEEccHHhEec-CCCcccccCCCCHHHHHHHHHHHHhcCCCCEEEEEeCCCccccCCCC------
Confidence 45799999999998888865432221 34455667899999999999999987667899999988752111110
Q ss_pred HHHHHHHhhhhccccccccccccCCCCChHHHHHHHHHHHHHHHHHhhCCCCcEEEEEeCCCC
Q 008596 452 NEKLAELISLATCDKKLSDSKRFKSFVTPEIKEILARTDARVNSLYTALPTNTMLIICTGHGD 514 (560)
Q Consensus 452 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~iy~~lP~~t~liv~sg~gd 514 (560)
......++++.+|++|.+|.+.|++++++||.+=||.
T Consensus 289 --------------------------d~~~y~~ale~vD~~Lg~ll~~L~~~tllIITADHG~ 325 (381)
T TIGR01696 289 --------------------------DVAGYAAALELFDRRLPELFSLLREDDLLIITADHGN 325 (381)
T ss_pred --------------------------CHHHHHHHHHHHHHHHHHHHHHhccCCEEEEECCCCC
Confidence 1123467789999999999999999999999999998
No 70
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=96.64 E-value=0.043 Score=50.42 Aligned_cols=65 Identities=28% Similarity=0.310 Sum_probs=44.3
Q ss_pred HHHHHHhhc-CCCEEEEeCchhhHHHHcc---ccCcccccccccccccCCCCCccHHHHHHHhcCcccc
Q 008596 280 QEEFLKLVY-KETILVGHSLENDLLALKI---SHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQ 344 (560)
Q Consensus 280 q~~L~~~i~-~~~ILVGHsL~~DL~aLki---~Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ 344 (560)
...|.+++. .+...||||+.+|+.+|+. .-+.+.||...+.-..+.....+|..|++.|||..+.
T Consensus 64 ~~~l~~~l~~~~~~kv~~d~k~~~~~L~~~gi~~~~~~D~~laayll~p~~~~~~l~~l~~~~l~~~~~ 132 (172)
T smart00474 64 LEILKDLLEDETITKVGHNAKFDLHVLARFGIELENIFDTMLAAYLLLGGPSKHGLATLLKEYLGVELD 132 (172)
T ss_pred HHHHHHHhcCCCceEEEechHHHHHHHHHCCCcccchhHHHHHHHHHcCCCCcCCHHHHHHHHhCCCCC
Confidence 344556663 3456899999999999963 1123589987654332222225899999999998763
No 71
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=96.60 E-value=0.055 Score=50.75 Aligned_cols=63 Identities=22% Similarity=0.249 Sum_probs=43.6
Q ss_pred HHHHHHhhc-CCCEEEEeCchhhHHHHccc----cCcccccccccccccCCCCCccHHHHHHHhcCccc
Q 008596 280 QEEFLKLVY-KETILVGHSLENDLLALKIS----HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREI 343 (560)
Q Consensus 280 q~~L~~~i~-~~~ILVGHsL~~DL~aLki~----Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~I 343 (560)
...|.+++. ++...|||++.+|+.+|+.. ...+.||.....- .++..+.+|+.|++.|||..+
T Consensus 53 ~~~l~~ll~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~~D~~laayL-l~p~~~~~l~~l~~~~l~~~~ 120 (178)
T cd06142 53 LSPLKELLADPNIVKVFHAAREDLELLKRDFGILPQNLFDTQIAARL-LGLGDSVGLAALVEELLGVEL 120 (178)
T ss_pred HHHHHHHHcCCCceEEEeccHHHHHHHHHHcCCCCCCcccHHHHHHH-hCCCccccHHHHHHHHhCCCC
Confidence 344555563 44678999999999999532 2357899764332 233334599999999999873
No 72
>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=96.38 E-value=0.0068 Score=59.32 Aligned_cols=63 Identities=25% Similarity=0.176 Sum_probs=41.7
Q ss_pred HHHHHhhcC-CCEEEEeCchhhHHHHcc----ccCcccccccccccc----cC---CCCCccHHHHHHHhcCccc
Q 008596 281 EEFLKLVYK-ETILVGHSLENDLLALKI----SHGLVIDTAVLYKHP----QG---GSHKTSLRVLAKKFLSREI 343 (560)
Q Consensus 281 ~~L~~~i~~-~~ILVGHsL~~DL~aLki----~Hp~viDT~~Ly~~~----~g---~~~k~sLk~La~~~Lg~~I 343 (560)
..|.+++.. +.+-|||++.+|+.+|.. .-..+.||.+.+... .| +.+..+|..|++.|||.++
T Consensus 55 ~~L~~iLe~~~i~Kv~h~~k~D~~~L~~~~gi~~~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~ 129 (197)
T cd06148 55 NGLKDILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISI 129 (197)
T ss_pred HHHHHHhcCCCccEEEEechhHHHHHHHhcCccccceeeHHHHHHHHHHHhcCCccccccccHHHHHHHhhCCCh
Confidence 345556643 344599999999999942 123578998753221 11 1223589999999999887
No 73
>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=96.25 E-value=0.052 Score=53.92 Aligned_cols=128 Identities=16% Similarity=0.165 Sum_probs=69.5
Q ss_pred CcEEEEEeccccCCC------CceEEEEEEEEe-cCcEEEE-EEEeCCCCCCCCc--EEecCCChhhhcCCCCCHHHHHH
Q 008596 212 YEILALDCEMCYTNE------GLELTRVTLVDI-KGQVLLD-KLVKPSNAIVDYN--TRYSGITHEMLSGVTTSLKDIQE 281 (560)
Q Consensus 212 ~~~valDcEm~~t~~------g~eL~rVsvVd~-~G~vvlD-~LVkP~~~I~dy~--T~~SGIT~e~L~~~~~tl~dVq~ 281 (560)
.+++|+|+|+..... .+.++.||++.. .|..+.. .++.+...-..|. -.+.|. -.+... .+=.++..
T Consensus 2 lrilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~v~~~-~~E~~lL~ 78 (204)
T cd05779 2 PRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIVNREIVSEDIEDFEYTPKPEYEGP--FKVFNE-PDEKALLQ 78 (204)
T ss_pred ceEEEEEEEecCCCCCCcCCCCCeEEEEEEEEecCCEEEecccccccccccccccCCCCCCCc--eEEecC-CCHHHHHH
Confidence 468999999975322 268999999865 3533211 1111100000000 011111 011112 35567777
Q ss_pred HHHHhhcCC--CEEEEeCc-hhhHHHHccc---cC---c-------------------ccccccccccc-cCCCCCccHH
Q 008596 282 EFLKLVYKE--TILVGHSL-ENDLLALKIS---HG---L-------------------VIDTAVLYKHP-QGGSHKTSLR 332 (560)
Q Consensus 282 ~L~~~i~~~--~ILVGHsL-~~DL~aLki~---Hp---~-------------------viDT~~Ly~~~-~g~~~k~sLk 332 (560)
++.+++..- .+++|+|. .||+.+|.-. |. . .+|...+++.. ......++|.
T Consensus 79 ~f~~~i~~~~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~~sysLd 158 (204)
T cd05779 79 RFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQGLK 158 (204)
T ss_pred HHHHHHHHhCCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCCCCccHH
Confidence 888888543 49999986 7899988721 10 0 34444443321 1122357899
Q ss_pred HHHHHhcCcc
Q 008596 333 VLAKKFLSRE 342 (560)
Q Consensus 333 ~La~~~Lg~~ 342 (560)
.+|+++||..
T Consensus 159 ~Va~~~Lg~~ 168 (204)
T cd05779 159 AVTKAKLGYD 168 (204)
T ss_pred HHHHHHhCCC
Confidence 9999999973
No 74
>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=96.08 E-value=0.12 Score=50.95 Aligned_cols=116 Identities=18% Similarity=0.169 Sum_probs=65.9
Q ss_pred CCcEEEEEeccccCCCCceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcCC
Q 008596 211 PYEILALDCEMCYTNEGLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKE 290 (560)
Q Consensus 211 ~~~~valDcEm~~t~~g~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~~ 290 (560)
+-++++||+|+.+-+ +|.-|+..+..-+.++ .+.-..++. |. .+.-. .+=.++...+.+++..-
T Consensus 2 ~l~~~~fDIE~~~~~---~i~~i~~~~~~~~~i~--~~~~~~~~~-------~~---~v~~~-~~E~~lL~~f~~~i~~~ 65 (193)
T cd05784 2 KLKVVSLDIETSMDG---ELYSIGLYGEGQERVL--MVGDPEDDA-------PD---NIEWF-ADEKSLLLALIAWFAQY 65 (193)
T ss_pred CccEEEEEeecCCCC---CEEEEEeecCCCCEEE--EECCCCCCC-------CC---EEEEE-CCHHHHHHHHHHHHHhh
Confidence 357999999996532 7888887775333332 111111111 11 11111 23344566666666433
Q ss_pred --CEEEEeCc-hhhHHHHcc-------ccC-------------------------c-ccccccccccccCCCCCccHHHH
Q 008596 291 --TILVGHSL-ENDLLALKI-------SHG-------------------------L-VIDTAVLYKHPQGGSHKTSLRVL 334 (560)
Q Consensus 291 --~ILVGHsL-~~DL~aLki-------~Hp-------------------------~-viDT~~Ly~~~~g~~~k~sLk~L 334 (560)
.||+|||. .||+..|.- .++ + ++|+..+++...-....++|.++
T Consensus 66 dPDvi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~~~~kl~sy~L~~V 145 (193)
T cd05784 66 DPDIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTATYHFESFSLENV 145 (193)
T ss_pred CCCEEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHHccCCCCcCCHHHH
Confidence 59999997 569988862 111 0 45655444431112356789999
Q ss_pred HHHhcCcc
Q 008596 335 AKKFLSRE 342 (560)
Q Consensus 335 a~~~Lg~~ 342 (560)
|+++||..
T Consensus 146 a~~~Lg~~ 153 (193)
T cd05784 146 AQELLGEG 153 (193)
T ss_pred HHHHhCCC
Confidence 99999874
No 75
>PRK05362 phosphopentomutase; Provisional
Probab=96.04 E-value=0.039 Score=60.02 Aligned_cols=110 Identities=20% Similarity=0.279 Sum_probs=81.4
Q ss_pred hHHHHHHHHHcCCeeeeecccccccccCCCCcceecCCChHHHHHHHHHhcc-CCCccEEEEecccchhhhhhhhhhHHH
Q 008596 372 RTKLLKVLFEYGKTSTLIDNVSIIKRYASESSHAIPVSSDDEVLSKARKEVK-NDRIHFVWTQFSELNLHFKKQAKDEAK 450 (560)
Q Consensus 372 ~~~i~~~l~~~g~~~~~id~~~~~~~~~~~~~~~i~c~~D~ev~~~~~~~v~-~~~~~f~~~~~~~l~~~~~~~~~~~~~ 450 (560)
...++++|.+.|.+...|........ ..+-+..++..++.++++++++.++ ....+|+++.|.++...+.+ .
T Consensus 223 ~~Tl~d~L~~aG~~v~~VGki~DiFa-~~G~t~~~~~~~~~~~~~~ale~L~~~~~~~fvfvn~~~~D~~~GH-~----- 295 (394)
T PRK05362 223 APTVLDKLKEAGGEVIAVGKIADIFA-GQGITEKVKTKSNMDGMDATIEEMKEAGDNGLVFTNLVDFDSLYGH-R----- 295 (394)
T ss_pred CCCHHHHHHHCCCeEEEEEehhhccc-CCCcccccCCCCHHHHHHHHHHHHHhCCCCcEEEEecccCccccCC-c-----
Confidence 46899999999998888875332111 2233445678899999999999998 55578999999877421111 0
Q ss_pred HHHHHHHHhhhhccccccccccccCCCCChHHHHHHHHHHHHHHHHHhhCCCCcEEEEEeCCCC
Q 008596 451 LNEKLAELISLATCDKKLSDSKRFKSFVTPEIKEILARTDARVNSLYTALPTNTMLIICTGHGD 514 (560)
Q Consensus 451 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~iy~~lP~~t~liv~sg~gd 514 (560)
.....-.++++.+|++|.+|.+.|++++++||.+=||.
T Consensus 296 --------------------------~~~~~y~~ale~~D~~lg~ll~~L~~~tlliiTaDHG~ 333 (394)
T PRK05362 296 --------------------------RDVAGYAAALEEFDARLPELLAALKEDDLLIITADHGN 333 (394)
T ss_pred --------------------------CCHHHHHHHHHHHHHHHHHHHHHhccCCEEEEeCCCCC
Confidence 01123467789999999999999999999999999995
No 76
>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=95.93 E-value=0.034 Score=55.18 Aligned_cols=72 Identities=22% Similarity=0.298 Sum_probs=49.2
Q ss_pred CCcEEEEEeccccCC---------CCceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHH
Q 008596 211 PYEILALDCEMCYTN---------EGLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQE 281 (560)
Q Consensus 211 ~~~~valDcEm~~t~---------~g~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~ 281 (560)
+-++++||+|+.... .++.|+.|++.+..|...+ +.. .. .+=.++..
T Consensus 8 ~lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~---~~~--------------------~~-~~E~~lL~ 63 (207)
T cd05785 8 DLRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEV---LHA--------------------ED-AAEKELLE 63 (207)
T ss_pred CceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceee---ecc--------------------CC-CCHHHHHH
Confidence 357999999996532 1257899998876552111 100 12 45667777
Q ss_pred HHHHhhcCC--CEEEEeCc-hhhHHHHc
Q 008596 282 EFLKLVYKE--TILVGHSL-ENDLLALK 306 (560)
Q Consensus 282 ~L~~~i~~~--~ILVGHsL-~~DL~aLk 306 (560)
++.+++..- .||||||. .||+.+|.
T Consensus 64 ~f~~~i~~~dPdii~g~N~~~FD~pyl~ 91 (207)
T cd05785 64 ELVAIIRERDPDVIEGHNIFRFDLPYLR 91 (207)
T ss_pred HHHHHHHHhCCCEEeccCCcccCHHHHH
Confidence 888888442 79999998 89999887
No 77
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=95.78 E-value=0.072 Score=52.02 Aligned_cols=105 Identities=24% Similarity=0.262 Sum_probs=66.1
Q ss_pred CCcEEEEEeccccC----CC-CceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHH
Q 008596 211 PYEILALDCEMCYT----NE-GLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLK 285 (560)
Q Consensus 211 ~~~~valDcEm~~t----~~-g~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~ 285 (560)
+.+++++|+|+..- +. .+.|+.||+...+|.+.+ +. .++ .+=.++...+.+
T Consensus 2 ~l~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~---~~-----------~~~----------~~E~~lL~~F~~ 57 (188)
T cd05781 2 DLKTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEF---IL-----------AEG----------LDDRKIIREFVK 57 (188)
T ss_pred CceEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEE---EE-----------ecC----------CCHHHHHHHHHH
Confidence 34789999999832 12 258999999887665321 00 112 345566777777
Q ss_pred hhcCC--CEEEEeCc-hhhHHHHccc---cC--------------------------cccccccccccccCCCCCccHHH
Q 008596 286 LVYKE--TILVGHSL-ENDLLALKIS---HG--------------------------LVIDTAVLYKHPQGGSHKTSLRV 333 (560)
Q Consensus 286 ~i~~~--~ILVGHsL-~~DL~aLki~---Hp--------------------------~viDT~~Ly~~~~g~~~k~sLk~ 333 (560)
++..- .+|+|||. .||+.+|.-. |. .++|...+.++.. ....++|..
T Consensus 58 ~i~~~dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~-~l~~y~L~~ 136 (188)
T cd05781 58 YVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIP-EVKVKTLEN 136 (188)
T ss_pred HHHHcCCCEEEecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhC-CCCCCCHHH
Confidence 77433 68999995 6899988721 10 0455544443332 234688999
Q ss_pred HHHHhcCc
Q 008596 334 LAKKFLSR 341 (560)
Q Consensus 334 La~~~Lg~ 341 (560)
+|+ +||.
T Consensus 137 Va~-~Lg~ 143 (188)
T cd05781 137 VAE-YLGV 143 (188)
T ss_pred HHH-HHCC
Confidence 997 5886
No 78
>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=95.71 E-value=0.025 Score=52.78 Aligned_cols=124 Identities=17% Similarity=0.086 Sum_probs=55.7
Q ss_pred EEEEeccccCCCC-ceEEEEEEEEec-CcEE-EEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcCCC
Q 008596 215 LALDCEMCYTNEG-LELTRVTLVDIK-GQVL-LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKET 291 (560)
Q Consensus 215 valDcEm~~t~~g-~eL~rVsvVd~~-G~vv-lD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~~~ 291 (560)
+.||+||+|..++ ..+.-|+++..+ ++.. +-.+ ..-.++ --+.+.+.+ .++....
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~~~~~--------------~~~~~~-------ee~~~~~~~-~~l~~~~ 58 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIITFIQW--------------FAEDPD-------EEEIILEFF-ELLDEAD 58 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE-EEEE---------------GGGHH-------HHHHHHH---HHHHTT-
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEEeeHh--------------hccCcH-------HHHHHHHHH-HHHhcCC
Confidence 4699999999775 356666666532 2221 2222 111111 011122222 5566889
Q ss_pred EEEEeC-chhhHHHHccc--------cCcccccccccccccCCCCCccHHHHHHHhcCcccccCCCCCChHHHHHHHHHH
Q 008596 292 ILVGHS-LENDLLALKIS--------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMEL 362 (560)
Q Consensus 292 ILVGHs-L~~DL~aLki~--------Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~Atl~L 362 (560)
.+|+|| ..||+.+|+-. ....+|+.....+... ..++|+.+++. ||++-+. .--+...+..+
T Consensus 59 ~iv~yng~~FD~p~L~~~~~~~~~~~~~~~iDl~~~~~~~~~--~~~~Lk~ve~~-lg~~~~~------~~~~G~~~~~~ 129 (164)
T PF13482_consen 59 NIVTYNGKNFDIPFLKRRAKRYGLPPPFNHIDLLKIIKKHFL--ESYSLKNVEKF-LGIERRD------DDISGSESVKL 129 (164)
T ss_dssp -EEESSTTTTHHHHHHHHH-HHHH--GGGEEEHHHHHT-TTS--CCTT--SHHH------------------HHHHHHHH
T ss_pred eEEEEeCcccCHHHHHHHHHHcCCCcccchhhHHHHHHhccC--CCCCHHHHhhh-ccccccc------CCCCHHHHHHH
Confidence 999999 58899999932 2256888766654332 45689999986 7887542 12344556666
Q ss_pred HHHHHHh
Q 008596 363 ALLKIRN 369 (560)
Q Consensus 363 ~~~kl~~ 369 (560)
+...++.
T Consensus 130 ~~~~~~~ 136 (164)
T PF13482_consen 130 YKEYLET 136 (164)
T ss_dssp HH---TT
T ss_pred HHHHHhc
Confidence 6554444
No 79
>COG1015 DeoB Phosphopentomutase [Carbohydrate transport and metabolism]
Probab=95.66 E-value=0.077 Score=56.92 Aligned_cols=110 Identities=21% Similarity=0.321 Sum_probs=82.4
Q ss_pred hHHHHHHHHHcCCeeeeecccccccccCCCCcceecCCChHHHHHHHHHhccCCCc-cEEEEecccchhhhhhhhhhHHH
Q 008596 372 RTKLLKVLFEYGKTSTLIDNVSIIKRYASESSHAIPVSSDDEVLSKARKEVKNDRI-HFVWTQFSELNLHFKKQAKDEAK 450 (560)
Q Consensus 372 ~~~i~~~l~~~g~~~~~id~~~~~~~~~~~~~~~i~c~~D~ev~~~~~~~v~~~~~-~f~~~~~~~l~~~~~~~~~~~~~ 450 (560)
.+.+++.|.+.|+....|......-. +.+-++.+.-.++.+.++..+++++.... .|+++.|-+....+.++. ++.
T Consensus 226 ~~tvl~~L~e~g~~vi~IGKI~DI~~-~~Git~~~~~~~n~~~~d~tl~~~~~~~~~~~vFtNlVdfD~~yGHRr-Dv~- 302 (397)
T COG1015 226 APTVLDKLKEAGRPVIAIGKIADIYA-GQGITEKVKAVSNMDGMDVTLEEMKTAEFNGLVFTNLVDFDSLYGHRR-DVA- 302 (397)
T ss_pred hhhHHHHHHHcCCceEEEeeHHhhhc-cccccccccCCCcHHHHHHHHHHHhcCCCCcEEEEeeeeccccccccc-chH-
Confidence 46788899999987776665333222 33456677889999999999999985433 499999877754443321 221
Q ss_pred HHHHHHHHhhhhccccccccccccCCCCChHHHHHHHHHHHHHHHHHhhCCCCcEEEEEeCCCC
Q 008596 451 LNEKLAELISLATCDKKLSDSKRFKSFVTPEIKEILARTDARVNSLYTALPTNTMLIICTGHGD 514 (560)
Q Consensus 451 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~iy~~lP~~t~liv~sg~gd 514 (560)
--.++|+.+|+||-+|.++|.++.+|||..-||+
T Consensus 303 ------------------------------gYa~aLe~FD~rL~e~~~~l~edDlLiiTADHGn 336 (397)
T COG1015 303 ------------------------------GYAAALEEFDRRLPELIENLREDDLLIITADHGN 336 (397)
T ss_pred ------------------------------HHHHHHHHHHHHHHHHHHhcCCCCEEEEecCCCC
Confidence 2467799999999999999999999999998885
No 80
>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases. Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Probab=95.48 E-value=0.41 Score=45.16 Aligned_cols=103 Identities=21% Similarity=0.215 Sum_probs=66.2
Q ss_pred cEEEEEeccccCCCC-ceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhc-CC
Q 008596 213 EILALDCEMCYTNEG-LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVY-KE 290 (560)
Q Consensus 213 ~~valDcEm~~t~~g-~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~-~~ 290 (560)
+.+++|.|+.+.+.. ..+..+++-..+ +++ ||.+... + .+...+.+++. .+
T Consensus 4 ~~~~~~~~~~~~~~~~~~l~~i~l~~~~-~~~---~i~~~~~----------~-------------~~~~~l~~~l~~~~ 56 (178)
T cd06140 4 DEVALYVELLGENYHTADIIGLALANGG-GAY---YIPLELA----------L-------------LDLAALKEWLEDEK 56 (178)
T ss_pred CceEEEEEEcCCCcceeeEEEEEEEeCC-cEE---EEeccch----------H-------------HHHHHHHHHHhCCC
Confidence 468999999998853 467777776542 332 2222211 0 13444666663 34
Q ss_pred CEEEEeCchhhHHHHccc----cCcccccccccccccCCCC-CccHHHHHHHhcCccc
Q 008596 291 TILVGHSLENDLLALKIS----HGLVIDTAVLYKHPQGGSH-KTSLRVLAKKFLSREI 343 (560)
Q Consensus 291 ~ILVGHsL~~DL~aLki~----Hp~viDT~~Ly~~~~g~~~-k~sLk~La~~~Lg~~I 343 (560)
...||||+.+|+.+|+.. ...+.||.+..--. ++.. .++|..|+++||+.++
T Consensus 57 ~~ki~~d~K~~~~~l~~~gi~~~~~~fDt~laaYLL-~p~~~~~~l~~l~~~yl~~~~ 113 (178)
T cd06140 57 IPKVGHDAKRAYVALKRHGIELAGVAFDTMLAAYLL-DPTRSSYDLADLAKRYLGREL 113 (178)
T ss_pred CceeccchhHHHHHHHHCCCcCCCcchhHHHHHHHc-CCCCCCCCHHHHHHHHcCCCC
Confidence 569999999999999631 22468998754333 2322 3689999999999884
No 81
>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=95.42 E-value=0.22 Score=49.43 Aligned_cols=124 Identities=19% Similarity=0.193 Sum_probs=70.1
Q ss_pred CCcEEEEEeccccCC---------CCceEEEEEEEEecCcEEEEEEEeC-CCCCCC--CcEEecCCChhhhcCCCCCHHH
Q 008596 211 PYEILALDCEMCYTN---------EGLELTRVTLVDIKGQVLLDKLVKP-SNAIVD--YNTRYSGITHEMLSGVTTSLKD 278 (560)
Q Consensus 211 ~~~~valDcEm~~t~---------~g~eL~rVsvVd~~G~vvlD~LVkP-~~~I~d--y~T~~SGIT~e~L~~~~~tl~d 278 (560)
+-+++|+|+|+..-. .+++|+.|++.+.+|..-+ -++.. .....+ +. -| ..+... .+=.+
T Consensus 4 ~lrilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~~~~~~~~v-~~~~~~~~~~~~~~~~---~~---~~v~~~-~~E~~ 75 (204)
T cd05783 4 KLKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALAGSDGLKRV-LVLKREGVEGLEGLLP---EG---AEVEFF-DSEKE 75 (204)
T ss_pred CceEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEcCCCCCcEE-EEEecCCcccccccCC---CC---CeEEec-CCHHH
Confidence 457999999997522 1258999999864442110 11111 100000 00 00 012222 35567
Q ss_pred HHHHHHHhhcCCCEEEEeCc-hhhHHHHccc---c--------------------Ccccccccccccc------c-CCCC
Q 008596 279 IQEEFLKLVYKETILVGHSL-ENDLLALKIS---H--------------------GLVIDTAVLYKHP------Q-GGSH 327 (560)
Q Consensus 279 Vq~~L~~~i~~~~ILVGHsL-~~DL~aLki~---H--------------------p~viDT~~Ly~~~------~-g~~~ 327 (560)
+..++.+++..-.+|||+|. .||+..|.-. | ...+|....+... . ....
T Consensus 76 lL~~F~~~i~~~~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~~~~ 155 (204)
T cd05783 76 LIREAFKIISEYPIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGNKYR 155 (204)
T ss_pred HHHHHHHHHhcCCEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhccccc
Confidence 78888888877789999986 7899988721 1 0134543322221 0 1224
Q ss_pred CccHHHHHHHhcCcc
Q 008596 328 KTSLRVLAKKFLSRE 342 (560)
Q Consensus 328 k~sLk~La~~~Lg~~ 342 (560)
.++|+.+|+.+||..
T Consensus 156 ~~~L~~Va~~~lg~~ 170 (204)
T cd05783 156 EYTLDAVAKALLGEG 170 (204)
T ss_pred cCcHHHHHHHhcCCC
Confidence 678999999998874
No 82
>PRK12383 putative mutase; Provisional
Probab=94.85 E-value=0.17 Score=55.43 Aligned_cols=109 Identities=17% Similarity=0.242 Sum_probs=79.9
Q ss_pred HHHHHHHHHcCCeeeeeccccccccc-CCCCcceecCCChHHHHHHHHHhccCCCccEEEEecccchhhhhhhhhhHHHH
Q 008596 373 TKLLKVLFEYGKTSTLIDNVSIIKRY-ASESSHAIPVSSDDEVLSKARKEVKNDRIHFVWTQFSELNLHFKKQAKDEAKL 451 (560)
Q Consensus 373 ~~i~~~l~~~g~~~~~id~~~~~~~~-~~~~~~~i~c~~D~ev~~~~~~~v~~~~~~f~~~~~~~l~~~~~~~~~~~~~~ 451 (560)
..++.++.+.|.+...|.... .-+ ..+.+..++..+.++.++++++.++....||+++.|.+.. .+.+..
T Consensus 234 ~~v~~~l~~~G~~v~~VGKi~--Di~s~~G~t~~~~~~~t~~~~~~~l~aL~~~~~dlvfvnl~~~D-~~GH~~------ 304 (406)
T PRK12383 234 VQVPQKLYEAGVPVVLVGKVA--DIVNNPYGVSWQNLVDTQRVMDITLDEFNTHPTAFICTNIQETD-LAGHAE------ 304 (406)
T ss_pred chhhhHHHHcCCCEEEEEEhH--HeeccCCcccccccCCHHHHHHHHHHHHhcCCCCEEEEeccCCc-cccccC------
Confidence 356677788898888885332 111 2234555677777899999999998766799999998875 222110
Q ss_pred HHHHHHHhhhhccccccccccccCCCCChHHHHHHHHHHHHHHHHHhhCCCCcEEEEEeCCCChH
Q 008596 452 NEKLAELISLATCDKKLSDSKRFKSFVTPEIKEILARTDARVNSLYTALPTNTMLIICTGHGDTA 516 (560)
Q Consensus 452 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~iy~~lP~~t~liv~sg~gd~~ 516 (560)
..+...++++.+|++|.+|.+.|++++++||.+=||++-
T Consensus 305 --------------------------d~~~y~~aiE~iD~~lg~ll~~L~~~~lliITaDHG~d~ 343 (406)
T PRK12383 305 --------------------------DVARYAERLEVVDRNLARLLEAMTPDDCLVVMADHGNDP 343 (406)
T ss_pred --------------------------CHHHHHHHHHHHHHHHHHHHHHhccCCEEEEEcCCCCCC
Confidence 112346778999999999999999999999999999853
No 83
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=94.24 E-value=0.28 Score=55.95 Aligned_cols=131 Identities=23% Similarity=0.257 Sum_probs=82.9
Q ss_pred EEEEeccccCCC-CceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhc-CCCE
Q 008596 215 LALDCEMCYTNE-GLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVY-KETI 292 (560)
Q Consensus 215 valDcEm~~t~~-g~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~-~~~I 292 (560)
+++|+|+.+... +..++.+++.... +..| | |.. ++ ++.+. +...+..++. ++..
T Consensus 25 ~a~~~et~~l~~~~~~lvg~s~~~~~-~~~y---i-~~~---------~~--~~~~~--------~~~~l~~~l~~~~~~ 80 (593)
T COG0749 25 IAFDTETDGLDPHGADLVGLSVASEE-EAAY---I-PLL---------HG--PEQLN--------VLAALKPLLEDEGIK 80 (593)
T ss_pred ceeeccccccCcccCCeeEEEeeccc-ccee---E-eec---------cc--hhhhh--------hHHHHHHHhhCcccc
Confidence 899999999887 3467777776544 2211 1 111 11 11111 5666777772 3446
Q ss_pred EEEeCchhhHHHHccc--c-CcccccccccccccCCCCCccHHHHHHHhcCcccccC-----CC--------------CC
Q 008596 293 LVGHSLENDLLALKIS--H-GLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQS-----GF--------------GH 350 (560)
Q Consensus 293 LVGHsL~~DL~aLki~--H-p~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~~-----~~--------------~H 350 (560)
.||||+.+|+.+|... + +...||.+..--......++.+..|++.||+...... .+ .-
T Consensus 81 kv~~~~K~d~~~l~~~Gi~~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~~~~~~~~~~~~~~~ 160 (593)
T COG0749 81 KVGQNLKYDYKVLANLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQLTFADVKLEKATE 160 (593)
T ss_pred hhccccchhHHHHHHcCCcccchHHHHHHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhccccccCccccchHHHHHH
Confidence 9999999999999863 2 3567887653222222346889999999998876431 11 12
Q ss_pred ChHHHHHHHHHHHHHHHHh
Q 008596 351 DSTEDARAAMELALLKIRN 369 (560)
Q Consensus 351 dSlEDA~Atl~L~~~kl~~ 369 (560)
.+.+||.++++|+.....+
T Consensus 161 y~a~~a~~~~~L~~~l~~~ 179 (593)
T COG0749 161 YAAEDADATLRLESILEPE 179 (593)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3468999999998555543
No 84
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.95 E-value=0.64 Score=55.72 Aligned_cols=94 Identities=20% Similarity=0.216 Sum_probs=61.4
Q ss_pred CHHHHHHHHHHhhcCC-CEEEEeCchhhHHHHccc----cCcccccccccccccCCCCCccHHHHHHHhcCccccc----
Q 008596 275 SLKDIQEEFLKLVYKE-TILVGHSLENDLLALKIS----HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQ---- 345 (560)
Q Consensus 275 tl~dVq~~L~~~i~~~-~ILVGHsL~~DL~aLki~----Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~---- 345 (560)
....+...|..++... ...||||+.+|+.+|+.. .+.+.||.+...-.. +..+.+|..|+.+||+..+-.
T Consensus 362 ~~~~~~~~l~~~l~~~~~~~v~~n~K~d~~~l~~~gi~~~~~~~Dt~la~yll~-~~~~~~l~~la~~yl~~~~~~~~~~ 440 (887)
T TIGR00593 362 LTILTDDKFARWLLNEQIKKIGHDAKFLMHLLKREGIELGGVIFDTMLAAYLLD-PAQVSTLDTLARRYLVEELILDEKI 440 (887)
T ss_pred hhHHHHHHHHHHHhCCCCcEEEeeHHHHHHHHHhCCCCCCCcchhHHHHHHHcC-CCCCCCHHHHHHHHcCcccccHHHh
Confidence 3455677788877433 458999999999999731 235689987543322 223458999999999865321
Q ss_pred CCCCC------------ChHHHHHHHHHHHHHHHHh
Q 008596 346 SGFGH------------DSTEDARAAMELALLKIRN 369 (560)
Q Consensus 346 ~~~~H------------dSlEDA~Atl~L~~~kl~~ 369 (560)
.+.+- -+.+||.+++.|+....++
T Consensus 441 ~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~ 476 (887)
T TIGR00593 441 GGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKE 476 (887)
T ss_pred ccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 01111 2567888899988655444
No 85
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=91.89 E-value=1 Score=43.57 Aligned_cols=58 Identities=19% Similarity=0.204 Sum_probs=40.7
Q ss_pred HHHhhc-CCCEEEEeCchhhHHHHc-c----ccCcccccccccccccCCCCCccHHHHHHHhcCccc
Q 008596 283 FLKLVY-KETILVGHSLENDLLALK-I----SHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREI 343 (560)
Q Consensus 283 L~~~i~-~~~ILVGHsL~~DL~aLk-i----~Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~I 343 (560)
|.+++. .+...|||++..|+.+|+ . .++. .||.+...-.. +. +.+|..|++.|||..+
T Consensus 69 L~~~L~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~-fD~~laaYLL~-p~-~~~l~~l~~~yl~~~~ 132 (192)
T cd06147 69 LNEVFTDPNILKVFHGADSDIIWLQRDFGLYVVNL-FDTGQAARVLN-LP-RHSLAYLLQKYCNVDA 132 (192)
T ss_pred HHHHhcCCCceEEEechHHHHHHHHHHhCCCcCch-HHHHHHHHHhC-CC-cccHHHHHHHHhCCCc
Confidence 555553 346789999999999996 2 1233 89987544332 33 3489999999998764
No 86
>PF01676 Metalloenzyme: Metalloenzyme superfamily; InterPro: IPR006124 This domain unites alkaline phosphatase, N-acetylgalactosamine-4-sulphatase, and cerebroside sulphatase, enzymes with known three-dimensional structures, with phosphopentomutase, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, phosphoglycerol transferase, phosphonate monoesterase, streptomycin-6-phosphate phosphatase, alkaline phosphodiesterase/nucleotide pyrophosphatase PC-1, and several closely related sulphatases. This domain is also related to alkaline phosphatase IPR001952 from INTERPRO []. The most conserved residues are probably involved in metal binding and catalysis.; GO: 0003824 catalytic activity, 0046872 metal ion binding; PDB: 1EQJ_A 1EJJ_A 1O99_A 1O98_A 3UN5_F 3UN3_B 3M8Y_C 3UO0_B 3UN2_B 3UNY_E ....
Probab=90.86 E-value=0.29 Score=49.79 Aligned_cols=77 Identities=23% Similarity=0.343 Sum_probs=59.1
Q ss_pred ChHHHHHHHHHhccCCCccEEEEecccchhhhhhhhhhHHHHHHHHHHHhhhhccccccccccccCCCCChHHHHHHHHH
Q 008596 410 SDDEVLSKARKEVKNDRIHFVWTQFSELNLHFKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPEIKEILART 489 (560)
Q Consensus 410 ~D~ev~~~~~~~v~~~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 489 (560)
++.++++++++.+.....||+++.+-+.. ...+. ...+...++++.+
T Consensus 124 ~~~~~~~~~~~~l~~~~~~~v~~~~~~~D-~~GH~--------------------------------~~~~~~~~~ie~~ 170 (252)
T PF01676_consen 124 SAKEIAEAAIEALKKDKYDFVFVHVKGTD-EAGHR--------------------------------GDPEAYIEAIERI 170 (252)
T ss_dssp THHHHHHHHHHHHHHTTSSEEEEEEEHHH-HHHTT--------------------------------T-HHHHHHHHHHH
T ss_pred hhHHHHHHHHHhhhcccCCeEEEeecCcc-hhhcc--------------------------------CCHHHHHHHHHHH
Confidence 56888999999995566789999886543 11110 0112457889999
Q ss_pred HHHHHHHHhhC-CCCcEEEEEeCCCChHHHH
Q 008596 490 DARVNSLYTAL-PTNTMLIICTGHGDTAIVH 519 (560)
Q Consensus 490 ~~~i~~iy~~l-P~~t~liv~sg~gd~~~~~ 519 (560)
|+.|.+|+++| +++++|||.+=||++..|.
T Consensus 171 D~~l~~l~~~~~~~~~~liiTaDHg~~~~~~ 201 (252)
T PF01676_consen 171 DRFLGRLLEALDKEDDLLIITADHGNDETMG 201 (252)
T ss_dssp HHHHHHHHHHHHHTTEEEEEEESSBSTTTSB
T ss_pred HHHHHHHHHHHhcCCCEEEEECCCCCccccC
Confidence 99999999999 9999999999999987654
No 87
>PRK05762 DNA polymerase II; Reviewed
Probab=90.66 E-value=1.7 Score=51.45 Aligned_cols=136 Identities=21% Similarity=0.266 Sum_probs=76.9
Q ss_pred CCCcEEEEEeccccCCCCceEEEEEEEEecC-cEEEEEEEeCCCCC-CCCcEEecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008596 210 SPYEILALDCEMCYTNEGLELTRVTLVDIKG-QVLLDKLVKPSNAI-VDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (560)
Q Consensus 210 ~~~~~valDcEm~~t~~g~eL~rVsvVd~~G-~vvlD~LVkP~~~I-~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i 287 (560)
++.++++||+|+..- + +|..|++.+... .+++ +-+..+. .++ +... .+=.++...+.+++
T Consensus 153 p~lrvlsfDIE~~~~--~-~i~sI~~~~~~~~~vi~---ig~~~~~~~~~-----------v~~~-~sE~~LL~~F~~~i 214 (786)
T PRK05762 153 PPLKVVSLDIETSNK--G-ELYSIGLEGCGQRPVIM---LGPPNGEALDF-----------LEYV-ADEKALLEKFNAWF 214 (786)
T ss_pred CCCeEEEEEEEEcCC--C-ceEEeeecCCCCCeEEE---EECCCCCCcce-----------EEEc-CCHHHHHHHHHHHH
Confidence 456899999999652 2 677777654322 2322 2222221 111 2222 34556666677776
Q ss_pred cC--CCEEEEeCc-hhhHHHHccc---c------------------C-------------cccccccccccccCCCCCcc
Q 008596 288 YK--ETILVGHSL-ENDLLALKIS---H------------------G-------------LVIDTAVLYKHPQGGSHKTS 330 (560)
Q Consensus 288 ~~--~~ILVGHsL-~~DL~aLki~---H------------------p-------------~viDT~~Ly~~~~g~~~k~s 330 (560)
.. -.||||||. .|||..|.-. | + -++|+-.+.+........++
T Consensus 215 ~~~DPDIIvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~~~~~l~sys 294 (786)
T PRK05762 215 AEHDPDVIIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATWVFDSFS 294 (786)
T ss_pred HhcCCCEEEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHHhhccCCCCC
Confidence 43 369999996 5799888620 1 1 02333333222111224678
Q ss_pred HHHHHHHhcCcccccCCCCC-------------------ChHHHHHHHHHHHH
Q 008596 331 LRVLAKKFLSREIQQSGFGH-------------------DSTEDARAAMELAL 364 (560)
Q Consensus 331 Lk~La~~~Lg~~IQ~~~~~H-------------------dSlEDA~Atl~L~~ 364 (560)
|.++|+++||...... ..| =++.||..+++|+.
T Consensus 295 L~~Va~~~Lg~~K~~~-d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~ 346 (786)
T PRK05762 295 LEYVSQRLLGEGKAID-DPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFE 346 (786)
T ss_pred HHHHHHHHhCCCeecc-CccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHH
Confidence 9999999998653210 111 14678999998875
No 88
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=89.60 E-value=0.58 Score=47.91 Aligned_cols=74 Identities=24% Similarity=0.172 Sum_probs=53.6
Q ss_pred cCCCEEEEeCchhhHHHHcc-------------------ccCcccccccccccccCCCCCccHHHHHHHhcCccc-----
Q 008596 288 YKETILVGHSLENDLLALKI-------------------SHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREI----- 343 (560)
Q Consensus 288 ~~~~ILVGHsL~~DL~aLki-------------------~Hp~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~I----- 343 (560)
....++||||.-.||..|-- .-|.++||-.|+.... ....+|..|+.. |+..-
T Consensus 147 ~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~--~~~~~L~~l~~~-l~~~~~~~~~ 223 (262)
T PF04857_consen 147 SSKKPIVGHNGLYDLMYLYKKFIGPLPETLEEFKELLRELFPRIYDTKYLAEECP--GKSTSLQELAEE-LGIRRNPSSI 223 (262)
T ss_dssp CC-SEEEESSTHHHHHHHHHHHTTS--SSHHHHHHHHHHHSSSEEEHHHHHTSTT--TS-SSHHHHHHH-TTSTT----E
T ss_pred ccCCcEEEeChHhHHHHHHHHhcCCCCCCHHHHHHHHHHHCcccccHHHHHHhcc--ccccCHHHHHHH-hCCCcccccc
Confidence 45689999999999987641 1378999998887653 245679999985 66543
Q ss_pred -----------------ccCCCCCChHHHHHHHHHHHH
Q 008596 344 -----------------QQSGFGHDSTEDARAAMELAL 364 (560)
Q Consensus 344 -----------------Q~~~~~HdSlEDA~Atl~L~~ 364 (560)
..+...|.|--||.+|..++.
T Consensus 224 ~~~~~~~~~~~~~~~~~~~~~~~HeAGyDA~mTg~~F~ 261 (262)
T PF04857_consen 224 SSPEGFPSYDEEKNNFPMFGEKAHEAGYDAYMTGCVFI 261 (262)
T ss_dssp EE-TTS-------------SS-TTSHHHHHHHHHHHHH
T ss_pred ccccccccccccccccccCCCCCCCcchHHHHHHHHHc
Confidence 122348999999999998874
No 89
>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=89.28 E-value=1.7 Score=44.74 Aligned_cols=86 Identities=20% Similarity=0.207 Sum_probs=49.2
Q ss_pred CCCcEEEEEeccccCCC------CceEEEEEEE-E-----ecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHH
Q 008596 210 SPYEILALDCEMCYTNE------GLELTRVTLV-D-----IKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLK 277 (560)
Q Consensus 210 ~~~~~valDcEm~~t~~------g~eL~rVsvV-d-----~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~ 277 (560)
.+.++++||+|+..... .++|+.||++ . ......+-.+..++....+-...+. -++..
T Consensus 155 p~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~-~~E~~--------- 224 (325)
T PF03104_consen 155 PPLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTLGSCDSIEDNVEVIYF-DSEKE--------- 224 (325)
T ss_dssp GGSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEECSCSCCTTCTTEEEEE-SSHHH---------
T ss_pred cccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEecCCCCCCCCcEEEEE-CCHHH---------
Confidence 45689999999988752 3799999964 2 2233333344444432212222221 24433
Q ss_pred HHHHHHHHhhc--CCCEEEEeCch-hhHHHHc
Q 008596 278 DIQEEFLKLVY--KETILVGHSLE-NDLLALK 306 (560)
Q Consensus 278 dVq~~L~~~i~--~~~ILVGHsL~-~DL~aLk 306 (560)
+...+.++|. .-.||+|||+. ||+..|.
T Consensus 225 -lL~~f~~~i~~~dPDii~GyN~~~fD~~yl~ 255 (325)
T PF03104_consen 225 -LLEAFLDIIQEYDPDIITGYNIDGFDLPYLI 255 (325)
T ss_dssp -HHHHHHHHHHHHS-SEEEESSTTTTHHHHHH
T ss_pred -HHHHHHHHHHhcCCcEEEEecccCCCHHHHH
Confidence 3333333332 34599999974 8999886
No 90
>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=88.45 E-value=5.1 Score=40.43 Aligned_cols=94 Identities=17% Similarity=0.119 Sum_probs=47.1
Q ss_pred CcEEEEEeccccCCCC------ceEEEEEEEEecCcEEEE--------EEEeCCCCCCCCcEEecCCChhhhcCCCCCHH
Q 008596 212 YEILALDCEMCYTNEG------LELTRVTLVDIKGQVLLD--------KLVKPSNAIVDYNTRYSGITHEMLSGVTTSLK 277 (560)
Q Consensus 212 ~~~valDcEm~~t~~g------~eL~rVsvVd~~G~vvlD--------~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~ 277 (560)
..++++|+|+...+.. ++|..|+.+-.+...... -++.+...-.+......++....+.-. .+=.
T Consensus 4 l~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~v~~~-~~E~ 82 (231)
T cd05778 4 LTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKSNASNGRIRSGLSGIPVEVV-ESEL 82 (231)
T ss_pred eEEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccchhhhhccccCCCCCeEEEe-CCHH
Confidence 3588999999654332 578888876432111111 122222211111011122222223333 3444
Q ss_pred HHHHHHHHhhc--CCCEEEEeCc-hhhHHHHc
Q 008596 278 DIQEEFLKLVY--KETILVGHSL-ENDLLALK 306 (560)
Q Consensus 278 dVq~~L~~~i~--~~~ILVGHsL-~~DL~aLk 306 (560)
+...++.+++. .-.||+|||+ .||+..|-
T Consensus 83 ~LL~~f~~~i~~~DPDii~GyNi~~fd~~YL~ 114 (231)
T cd05778 83 ELFEELIDLVRRFDPDILSGYEIQRSSWGYLI 114 (231)
T ss_pred HHHHHHHHHHHHhCCCEEEEeccccCcHHHHH
Confidence 55555555542 3369999998 67987765
No 91
>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=88.09 E-value=3.6 Score=41.21 Aligned_cols=85 Identities=19% Similarity=0.275 Sum_probs=49.8
Q ss_pred CCcEEEEEeccccCCC------CceEEEEEEEEe-cCc--EEEEE-E-EeCCCCCCCCcEEecCCChhhhcCCCCCHHHH
Q 008596 211 PYEILALDCEMCYTNE------GLELTRVTLVDI-KGQ--VLLDK-L-VKPSNAIVDYNTRYSGITHEMLSGVTTSLKDI 279 (560)
Q Consensus 211 ~~~~valDcEm~~t~~------g~eL~rVsvVd~-~G~--vvlD~-L-VkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dV 279 (560)
+-+++|+|+|+..... .++|+.||++.. .|. +.... + +++..++.+- .+... .+=.++
T Consensus 6 ~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~v~~~-~~E~eL 74 (230)
T cd05777 6 PLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIVGA----------QVFSF-ETEEEL 74 (230)
T ss_pred CceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeCCCCCCCCC----------EEEEE-CCHHHH
Confidence 4679999999975321 268999999864 443 11111 1 2233333211 11112 244556
Q ss_pred HHHHHHhhcC--CCEEEEeCc-hhhHHHHc
Q 008596 280 QEEFLKLVYK--ETILVGHSL-ENDLLALK 306 (560)
Q Consensus 280 q~~L~~~i~~--~~ILVGHsL-~~DL~aLk 306 (560)
...+.+++.. -.||+|||. .|||..|.
T Consensus 75 L~~f~~~i~~~DPDii~GyN~~~FDl~yL~ 104 (230)
T cd05777 75 LLAWRDFVQEVDPDIITGYNICNFDLPYLL 104 (230)
T ss_pred HHHHHHHHHhcCCCEEEEecCCCCCHHHHH
Confidence 6666666633 369999997 56999876
No 92
>PF01663 Phosphodiest: Type I phosphodiesterase / nucleotide pyrophosphatase; InterPro: IPR002591 This family consists of phosphodiesterases, including human plasma-cell membrane glycoprotein PC-1 / alkaline phosphodiesterase I / nucleotide pyrophosphatase (nppase). These enzymes catalyse the cleavage of phosphodiester and phosphosulphate bonds in NAD, deoxynucleotides and nucleotide sugars []. Another member of this family is ATX an autotaxin, tumor cell motility-stimulating protein which exhibits type I phosphodiesterases activity []. The alignment encompasses the active site [, ]. Also present within this family is 60 kDa Ca2+-ATPase from Myroides odoratus []. This signature also hits a number of ethanolamine phosphate transferase involved in glycosylphosphatidylinositol-anchor biosynthesis.; GO: 0003824 catalytic activity; PDB: 2XRG_A 2XR9_A 3T02_A 3T01_A 3SZZ_A 3SZY_A 3T00_A 3NKM_A 3NKN_A 3NKR_A ....
Probab=87.90 E-value=1.4 Score=45.45 Aligned_cols=67 Identities=25% Similarity=0.378 Sum_probs=47.4
Q ss_pred HhccCCCccEEEEecccchhhhhhhhhhHHHHHHHHHHHhhhhccccccccccccCCCCChHHHHHHHHHHHHHHHHHhh
Q 008596 420 KEVKNDRIHFVWTQFSELNLHFKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPEIKEILARTDARVNSLYTA 499 (560)
Q Consensus 420 ~~v~~~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~iy~~ 499 (560)
..+.....||+++.|.++... .+ ..+ ..+++..+++..+|+.|.+|++.
T Consensus 177 ~l~~~~~pdl~~~~~~~~D~~-~H-----~~g-------------------------~~s~~~~~~~~~~D~~ig~l~~~ 225 (365)
T PF01663_consen 177 YLIQKERPDLIFVYFPEPDHI-GH-----RYG-------------------------PDSPEIEDAYRRIDQAIGRLLEA 225 (365)
T ss_dssp HHHHTTTESEEEEEEECCHHH-HH-----HH--------------------------TTSHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHhhCCCCEEEEEecCCCcc-cc-----CCC-------------------------CCCHHHHHHHHHHHHHHHHHHHH
Confidence 335566679999999887531 11 101 11345788999999999999999
Q ss_pred CCCC-----cEEEEEeCCCChHH
Q 008596 500 LPTN-----TMLIICTGHGDTAI 517 (560)
Q Consensus 500 lP~~-----t~liv~sg~gd~~~ 517 (560)
|+++ |.+||+|-||=..-
T Consensus 226 l~~~~~~~~~~iiv~SDHG~~~~ 248 (365)
T PF01663_consen 226 LDENGLLEDTNIIVTSDHGMTPV 248 (365)
T ss_dssp HHHTT-TTTEEEEEEES---EEE
T ss_pred HHhhCCCCceEEEEEccCccccc
Confidence 9988 99999999997654
No 93
>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=86.48 E-value=1.1 Score=44.42 Aligned_cols=64 Identities=31% Similarity=0.405 Sum_probs=43.7
Q ss_pred HHHHHHHHHhhcC-CCEEEEeCc-hhhHHHHccc---c----C------------------cccccccccccccCCCCCc
Q 008596 277 KDIQEEFLKLVYK-ETILVGHSL-ENDLLALKIS---H----G------------------LVIDTAVLYKHPQGGSHKT 329 (560)
Q Consensus 277 ~dVq~~L~~~i~~-~~ILVGHsL-~~DL~aLki~---H----p------------------~viDT~~Ly~~~~g~~~k~ 329 (560)
.++.+++.+++.. +.+|||||. .||+.+|... | | +.+|+..+.+.. +.....
T Consensus 79 ~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~-~~~~~~ 157 (208)
T cd05782 79 KELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFY-GARARA 157 (208)
T ss_pred HHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhcc-CccCCC
Confidence 4567777777754 568999996 8899999831 1 1 156766655432 233567
Q ss_pred cHHHHHHHhcCcc
Q 008596 330 SLRVLAKKFLSRE 342 (560)
Q Consensus 330 sLk~La~~~Lg~~ 342 (560)
+|+.+|+ +||.+
T Consensus 158 ~L~~va~-~lG~~ 169 (208)
T cd05782 158 SLDLLAK-LLGIP 169 (208)
T ss_pred CHHHHHH-HhCCC
Confidence 8999997 57884
No 94
>KOG2126 consensus Glycosylphosphatidylinositol anchor synthesis protein [Signal transduction mechanisms]
Probab=85.94 E-value=1.3 Score=52.32 Aligned_cols=112 Identities=20% Similarity=0.357 Sum_probs=72.7
Q ss_pred HHHHHHHHHcCCeeeeecccccccccCC---C--CcceecC----CChHHHHHHHHHhccCCCccEEEEecccchhhhhh
Q 008596 373 TKLLKVLFEYGKTSTLIDNVSIIKRYAS---E--SSHAIPV----SSDDEVLSKARKEVKNDRIHFVWTQFSELNLHFKK 443 (560)
Q Consensus 373 ~~i~~~l~~~g~~~~~id~~~~~~~~~~---~--~~~~i~c----~~D~ev~~~~~~~v~~~~~~f~~~~~~~l~~~~~~ 443 (560)
+++...+...||+..++.|..-...+.. + +...+.+ +-|++|+++.-+.+.++.-|..+++|=+.
T Consensus 144 DNfv~Ql~~~gk~vvflGDdTW~~LFp~~f~~s~s~pSfnv~DLdtVDn~v~~~if~~l~s~dwdVlIAHfLGV------ 217 (895)
T KOG2126|consen 144 DNFVRQLVLNGKSVVFLGDDTWTSLFPNQFNKSYSFPSFNVHDLDTVDNGVIEKIFKSLNSKDWDVLIAHFLGV------ 217 (895)
T ss_pred hHHHHHHHHCCCeEEEecCccHHHhChHhhcCCCCCCCCCCccccccchHHHHHhhhhhccCchHHHHHHHhCc------
Confidence 4666777888999999876432111111 1 1112222 45899999888888765544444444333
Q ss_pred hhhhHHHHHHHHHHHhhhhccccccccccccCCCCChHHHHHHHHHHHHHHHHHhhCCCCcEEEEEeCCCCh
Q 008596 444 QAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPEIKEILARTDARVNSLYTALPTNTMLIICTGHGDT 515 (560)
Q Consensus 444 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~iy~~lP~~t~liv~sg~gd~ 515 (560)
..|-.+-. +..++-++-+.++|+-|+++++.|-.+|++||+.-||=+
T Consensus 218 ------------------DH~GHk~G-------PdH~~M~~KL~qmD~vI~~ii~~mdedTlLvVmGDHGMt 264 (895)
T KOG2126|consen 218 ------------------DHCGHKHG-------PDHPEMADKLVQMDRVINEIIKKMDEDTLLVVMGDHGMT 264 (895)
T ss_pred ------------------ccccccCC-------CCCHHHHHHHHHHHHHHHHHHHHhccCeeEEEecCCCCC
Confidence 23333321 234466777999999999999999999999999988744
No 95
>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=84.25 E-value=3.7 Score=41.36 Aligned_cols=132 Identities=20% Similarity=0.232 Sum_probs=70.2
Q ss_pred CCcEEEEEeccccCCCC--ceEEEEEEEEecCc------------EEEEEEEeCCCC--CCCCcEEecCCChhhhcCCCC
Q 008596 211 PYEILALDCEMCYTNEG--LELTRVTLVDIKGQ------------VLLDKLVKPSNA--IVDYNTRYSGITHEMLSGVTT 274 (560)
Q Consensus 211 ~~~~valDcEm~~t~~g--~eL~rVsvVd~~G~------------vvlD~LVkP~~~--I~dy~T~~SGIT~e~L~~~~~ 274 (560)
|-.+.+|-.=|+.-... .||+-||++=...- .-+-.+++|... .++...+.-......+.-. .
T Consensus 2 pl~v~sls~~T~~n~k~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~v~~~-~ 80 (234)
T cd05776 2 PLTVMSLSIKTVLNSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKVRIF-E 80 (234)
T ss_pred CeEEEEEEeEEEecCcCCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCCCCCchHHHHHHhcCCcEEEe-C
Confidence 34567777777655543 68988887743211 112234455432 1111111111111111112 2
Q ss_pred CHHHHHHHHHHhhc--CCCEEEEeCc-hhhHHHHc-------ccc------------C-----------------ccccc
Q 008596 275 SLKDIQEEFLKLVY--KETILVGHSL-ENDLLALK-------ISH------------G-----------------LVIDT 315 (560)
Q Consensus 275 tl~dVq~~L~~~i~--~~~ILVGHsL-~~DL~aLk-------i~H------------p-----------------~viDT 315 (560)
+=.+....+..++. .-.|+||||+ .|||..|- +.+ | -++|+
T Consensus 81 ~E~~LL~~f~~~i~~~DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~ 160 (234)
T cd05776 81 NERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDT 160 (234)
T ss_pred CHHHHHHHHHHHHhhcCCCEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCchhhcc
Confidence 33455555555553 3369999999 78998875 111 0 03555
Q ss_pred ccccccccCCCCCccHHHHHHHhcCcccc
Q 008596 316 AVLYKHPQGGSHKTSLRVLAKKFLSREIQ 344 (560)
Q Consensus 316 ~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ 344 (560)
..+++... ....|+|..+|+.+||.+-.
T Consensus 161 ~~~~k~~~-~~~sY~L~~va~~~Lg~~k~ 188 (234)
T cd05776 161 YLSAKELI-RCKSYDLTELSQQVLGIERQ 188 (234)
T ss_pred HHHHHHHh-CCCCCChHHHHHHHhCcCcc
Confidence 55544332 24568899999999998543
No 96
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=84.07 E-value=1.5 Score=39.69 Aligned_cols=60 Identities=18% Similarity=0.253 Sum_probs=41.9
Q ss_pred HHHhhc-CCCEEEEeCchhhHHHHcc----ccCcccccccccccccCCCC-CccHHHHHHHhcCccc
Q 008596 283 FLKLVY-KETILVGHSLENDLLALKI----SHGLVIDTAVLYKHPQGGSH-KTSLRVLAKKFLSREI 343 (560)
Q Consensus 283 L~~~i~-~~~ILVGHsL~~DL~aLki----~Hp~viDT~~Ly~~~~g~~~-k~sLk~La~~~Lg~~I 343 (560)
|.+++. ++...|||++..|+.+|+. ....+.||.+.+--.. +.. +.+|..|+++|||.++
T Consensus 45 l~~~l~~~~~~kv~~d~K~~~~~L~~~~~~~~~~~~D~~laayLl~-p~~~~~~l~~l~~~~l~~~~ 110 (150)
T cd09018 45 LKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAFDTMLEAYILN-SVAGRWDMDSLVERWLGHKL 110 (150)
T ss_pred HHHHhcCCCCceeeecHHHHHHHHHHcCCccCCcchhHHHHHHHhC-CCCCCCCHHHHHHHHhCCCc
Confidence 445553 4566899999999999963 1235689987643332 222 3589999999998873
No 97
>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=81.30 E-value=3.4 Score=44.47 Aligned_cols=84 Identities=20% Similarity=0.271 Sum_probs=48.2
Q ss_pred CcEEEEEeccccCCC--------CceEEEEEEEEecCcE--EE--E-EEEeCCCCCCCCcEEecCCChhhhcCCCCCHHH
Q 008596 212 YEILALDCEMCYTNE--------GLELTRVTLVDIKGQV--LL--D-KLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKD 278 (560)
Q Consensus 212 ~~~valDcEm~~t~~--------g~eL~rVsvVd~~G~v--vl--D-~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~d 278 (560)
..++++|+||..-.. .++++.|+++...+.. .. . ....|..++.+ +. +... .+-.+
T Consensus 3 ~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~---~~~~-~~E~~ 71 (471)
T smart00486 3 LKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCKEIDG-------VE---VYEF-NNEKE 71 (471)
T ss_pred ceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcCCCCC-------Ce---EEec-CCHHH
Confidence 468999999976432 3689999988864431 11 1 12233333332 11 1111 13334
Q ss_pred HHHHHHHhhc--CCCEEEEeCch-hhHHHHc
Q 008596 279 IQEEFLKLVY--KETILVGHSLE-NDLLALK 306 (560)
Q Consensus 279 Vq~~L~~~i~--~~~ILVGHsL~-~DL~aLk 306 (560)
...++.+++. ...+++|||.. ||+..|.
T Consensus 72 lL~~f~~~i~~~dpdii~g~N~~~FD~~~i~ 102 (471)
T smart00486 72 LLKAFLEFIKKYDPDIIYGHNISNFDLPYII 102 (471)
T ss_pred HHHHHHHHHHHhCCCEEEeecCCCCCHHHHH
Confidence 4555555552 22699999985 8998876
No 98
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=78.89 E-value=7.9 Score=47.55 Aligned_cols=86 Identities=20% Similarity=0.232 Sum_probs=47.8
Q ss_pred CCCcEEEEEeccccCCC-------CceEEEEEEEE-ecCcE---EEEEEEeC--CCCCCCCcEEecCCChhhhcCCCCCH
Q 008596 210 SPYEILALDCEMCYTNE-------GLELTRVTLVD-IKGQV---LLDKLVKP--SNAIVDYNTRYSGITHEMLSGVTTSL 276 (560)
Q Consensus 210 ~~~~~valDcEm~~t~~-------g~eL~rVsvVd-~~G~v---vlD~LVkP--~~~I~dy~T~~SGIT~e~L~~~~~tl 276 (560)
+|.++++||+|+.+... .++++.||.+- ..|.. +...++-+ ..++.+..... . .+=
T Consensus 262 pplrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~~~~~r~vftl~~c~~i~g~~V~~----------f-~sE 330 (1054)
T PTZ00166 262 APLRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLTKFIFTLKECASIAGANVLS----------F-ETE 330 (1054)
T ss_pred CCcEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCccCCcceEEEecCccccCCCceEEE----------e-CCH
Confidence 46689999999986432 26899999864 44532 12222211 12332221111 1 233
Q ss_pred HHHHHHHHHhhc--CCCEEEEeCc-hhhHHHHc
Q 008596 277 KDIQEEFLKLVY--KETILVGHSL-ENDLLALK 306 (560)
Q Consensus 277 ~dVq~~L~~~i~--~~~ILVGHsL-~~DL~aLk 306 (560)
.+....+.+++. .-.||+|||+ .|||..|-
T Consensus 331 ~eLL~~f~~~I~~~DPDII~GYNi~~FDlpYL~ 363 (1054)
T PTZ00166 331 KELLLAWAEFVIAVDPDFLTGYNIINFDLPYLL 363 (1054)
T ss_pred HHHHHHHHHHHHhcCCCEEEecCCcCCcHHHHH
Confidence 344444444441 3469999997 57998765
No 99
>PHA02528 43 DNA polymerase; Provisional
Probab=78.26 E-value=9.5 Score=45.98 Aligned_cols=92 Identities=14% Similarity=0.106 Sum_probs=48.9
Q ss_pred CCcEEEEEeccccCCC-------CceEEEEEEEEecCcEEEEEEEe---CCCCCCCCc--EEecCCChhhhcCCCCCHHH
Q 008596 211 PYEILALDCEMCYTNE-------GLELTRVTLVDIKGQVLLDKLVK---PSNAIVDYN--TRYSGITHEMLSGVTTSLKD 278 (560)
Q Consensus 211 ~~~~valDcEm~~t~~-------g~eL~rVsvVd~~G~vvlD~LVk---P~~~I~dy~--T~~SGIT~e~L~~~~~tl~d 278 (560)
.-++++||+|+..... ..+|+.|++.+..+..++=..+. |.....+.. .-..++ .+... .+=.+
T Consensus 105 ~lrv~s~DIE~~~~~gfP~p~~~~d~IisIsl~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~v---~~~~~-~sE~e 180 (881)
T PHA02528 105 KIRIANLDIEVTAEDGFPDPEEAKYEIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPQEILDKV---VYMPF-DTERE 180 (881)
T ss_pred CccEEEEEEEECCCCCCCCcccCCCcEEEEEEecCCCCEEEEEEecCcccccccCCcccccccCCe---eEEEc-CCHHH
Confidence 4689999999964221 24799999987665532111111 000000000 000000 00011 24455
Q ss_pred HHHHHHHhhc--CCCEEEEeCc-hhhHHHHc
Q 008596 279 IQEEFLKLVY--KETILVGHSL-ENDLLALK 306 (560)
Q Consensus 279 Vq~~L~~~i~--~~~ILVGHsL-~~DL~aLk 306 (560)
....+.+++. .-.||+|||+ .|||..|.
T Consensus 181 LL~~F~~~i~~~DPDII~GyNi~~FDlpYL~ 211 (881)
T PHA02528 181 MLLEYINFWEENTPVIFTGWNVELFDVPYII 211 (881)
T ss_pred HHHHHHHHHHHhCCcEEEecCCccCCHHHHH
Confidence 6666666662 2369999996 67998876
No 100
>PRK04024 cofactor-independent phosphoglycerate mutase; Provisional
Probab=74.20 E-value=17 Score=40.03 Aligned_cols=74 Identities=12% Similarity=0.083 Sum_probs=52.8
Q ss_pred ChHHHHHHHHHhccCCCccEEEEecccchhhhhhhhhhHHHHHHHHHHHhhhhccccccccccccCCCCChHHHHHHHHH
Q 008596 410 SDDEVLSKARKEVKNDRIHFVWTQFSELNLHFKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPEIKEILART 489 (560)
Q Consensus 410 ~D~ev~~~~~~~v~~~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 489 (560)
+-.+-.+.+++.++. .|||++.+..... ..+ . ...+...++++++
T Consensus 279 ~~~~k~~~~~~~l~~--~Dfv~vh~~~~D~-~GH----------------------~----------gd~~~k~~aiE~i 323 (412)
T PRK04024 279 NYMAKAKAAVELLKE--YDFVLLNIKGTDE-AGH----------------------D----------GDFEGKVEVIEKI 323 (412)
T ss_pred CHHHHHHHHHHHhcc--CCEEEEeccCcch-hhc----------------------C----------CCHHHHHHHHHHH
Confidence 446666777887763 6899988865431 000 0 0122456789999
Q ss_pred HHHHHHHHhhCC-CCcEEEEEeCCCChHHH
Q 008596 490 DARVNSLYTALP-TNTMLIICTGHGDTAIV 518 (560)
Q Consensus 490 ~~~i~~iy~~lP-~~t~liv~sg~gd~~~~ 518 (560)
|+.|.+|+++|. +..++||.+=||.|-.+
T Consensus 324 D~~l~~il~~l~~~~~~liITaDHgtp~~~ 353 (412)
T PRK04024 324 DKMLGYILDNLDLDEVYIAVTGDHSTPVEV 353 (412)
T ss_pred HHHHHHHHHHhhcCCCEEEEecCCCCCccc
Confidence 999999999995 78899999999998543
No 101
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=73.90 E-value=14 Score=45.83 Aligned_cols=99 Identities=17% Similarity=0.257 Sum_probs=58.4
Q ss_pred CCChhhhcCCCCCHHHHHHHHHHhhc--CCCEEEEeCc-hhhHHHHcc-------cc----------------------C
Q 008596 263 GITHEMLSGVTTSLKDIQEEFLKLVY--KETILVGHSL-ENDLLALKI-------SH----------------------G 310 (560)
Q Consensus 263 GIT~e~L~~~~~tl~dVq~~L~~~i~--~~~ILVGHsL-~~DL~aLki-------~H----------------------p 310 (560)
|+-+..|... .+=.+....+++++. .-.+++|||+ .+||.+|-- .+ .
T Consensus 572 ~~~~~~L~~~-~sEr~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~G 650 (1172)
T TIGR00592 572 GKKPSLVEDL-ATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERTCG 650 (1172)
T ss_pred ccCCcEEEEe-cCHHHHHHHHHHHHHhcCCCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccCCCccccccceECC
Confidence 4444444444 344555556666664 5679999996 679987752 11 1
Q ss_pred -cccccccccccccCCCCCccHHHHHHHhcCccccc-----------C-----CCCCChHHHHHHHHHHH
Q 008596 311 -LVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQ-----------S-----GFGHDSTEDARAAMELA 363 (560)
Q Consensus 311 -~viDT~~Ly~~~~g~~~k~sLk~La~~~Lg~~IQ~-----------~-----~~~HdSlEDA~Atl~L~ 363 (560)
-++|+..+++... ....++|..+|+++||.+-.. . .-.+..+.||..+++|+
T Consensus 651 rl~~D~~~~~k~~~-~~~sy~L~~v~~~~L~~~k~~~~~~~i~~~~~~~~~~~~~~~y~~~Da~l~~~L~ 719 (1172)
T TIGR00592 651 RMICDVEISAKELI-RCKSYDLSELVQQILKTERKVIPIDNINNMYSESSSLTYLLEHTWKDAMFILQIM 719 (1172)
T ss_pred EEEEEHHHHHHHHh-CcCCCCHHHHHHHHhCCCCcccCHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHHH
Confidence 1356555554432 234688999999999853211 0 01234567787777775
No 102
>PLN02538 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Probab=73.32 E-value=11 Score=43.13 Aligned_cols=81 Identities=15% Similarity=0.179 Sum_probs=61.7
Q ss_pred ecCCChHHHHHHHHHhccCCCccEEEEecccchhhhhhhhhhHHHHHHHHHHHhhhhccccccccccccCCCCChHHHHH
Q 008596 406 IPVSSDDEVLSKARKEVKNDRIHFVWTQFSELNLHFKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPEIKEI 485 (560)
Q Consensus 406 i~c~~D~ev~~~~~~~v~~~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 485 (560)
-|--|-.||.+++++.+.....||+++.|..-.- .. + . ...+...++
T Consensus 400 ~PeMSA~eVtd~~i~~i~~~~ydfi~vNfan~Dm-vG----------------------H---------t-G~~ea~ikA 446 (558)
T PLN02538 400 QPKMKALEIAEKARDALLSGKFDQVRVNLANGDM-VG----------------------H---------T-GDLEATIVA 446 (558)
T ss_pred CCCCCHHHHHHHHHHHHhcCCCCEEEEeccCccc-cc----------------------C---------C-CCHHHHHHH
Confidence 3445668899999999998889999988854320 00 0 0 012346788
Q ss_pred HHHHHHHHHHHHhhC-CCCcEEEEEeCCCChHHHH
Q 008596 486 LARTDARVNSLYTAL-PTNTMLIICTGHGDTAIVH 519 (560)
Q Consensus 486 ~~~~~~~i~~iy~~l-P~~t~liv~sg~gd~~~~~ 519 (560)
++.+|+.|.+|++++ +.+..+||.+=||+-.+|.
T Consensus 447 IE~vD~~Lg~Il~al~~~g~~liITADHGNaE~M~ 481 (558)
T PLN02538 447 CEAVDAAVKEILDAVEQVGGIYLVTADHGNAEDMV 481 (558)
T ss_pred HHHHHHHHHHHHHHHHhcCCEEEEeCCCCCchhhc
Confidence 999999999999999 6688999999999988776
No 103
>TIGR01307 pgm_bpd_ind 2,3-bisphosphoglycerate-independent phosphoglycerate mutase. This protein is about double in length of, and devoid of homology to the form of phosphoglycerate mutase that uses 2,3-bisphosphoglycerate as a cofactor.
Probab=72.21 E-value=13 Score=42.12 Aligned_cols=81 Identities=11% Similarity=0.158 Sum_probs=60.9
Q ss_pred eecCCChHHHHHHHHHhccCCCccEEEEecccchhhhhhhhhhHHHHHHHHHHHhhhhccccccccccccCCCCChHHHH
Q 008596 405 AIPVSSDDEVLSKARKEVKNDRIHFVWTQFSELNLHFKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPEIKE 484 (560)
Q Consensus 405 ~i~c~~D~ev~~~~~~~v~~~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 484 (560)
-.|.-+..||.+++++.+..+..||++..|.... +..+ . ...+...+
T Consensus 360 ~~PeMsa~evtd~~i~~I~~~k~dfi~vnfan~D-mvGH-------------------------------t-g~~~a~v~ 406 (501)
T TIGR01307 360 LQPEMSAKAVTDAVLEAIAQGKFDLIVVNFANPD-MVGH-------------------------------T-GNFEAAIK 406 (501)
T ss_pred cCCccCHHHHHHHHHHHHhccCCCEEEEECCCcc-cccC-------------------------------C-CCHHHHHH
Confidence 3677899999999999998877899998884321 1000 0 11224578
Q ss_pred HHHHHHHHHHHHHhhCC-CCcEEEEEeCCCChHHH
Q 008596 485 ILARTDARVNSLYTALP-TNTMLIICTGHGDTAIV 518 (560)
Q Consensus 485 ~~~~~~~~i~~iy~~lP-~~t~liv~sg~gd~~~~ 518 (560)
+++.+|+.|.+|.++|- .+.++||.|=||+..+|
T Consensus 407 AIE~vD~~LGrIl~aLke~G~~VIiTADHGnae~m 441 (501)
T TIGR01307 407 AVEALDVCLGRIVEACKKVGGTLFLTADHGNAEEM 441 (501)
T ss_pred HHHHHHHHHHHHHHHHHhCCCEEEEEcCCCChhhc
Confidence 89999999999999995 45588889999987655
No 104
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=68.12 E-value=8.1 Score=38.50 Aligned_cols=26 Identities=27% Similarity=0.358 Sum_probs=18.7
Q ss_pred hhCCCCcEEEEEeCCCChHHHHHHHHHH
Q 008596 498 TALPTNTMLIICTGHGDTAIVHRLREML 525 (560)
Q Consensus 498 ~~lP~~t~liv~sg~gd~~~~~rl~~~~ 525 (560)
...-..--+|++|||||.. ...|+|+
T Consensus 71 ~~~~~~~PVIfiTGhgDIp--maV~AmK 96 (202)
T COG4566 71 AERGIRLPVIFLTGHGDIP--MAVQAMK 96 (202)
T ss_pred HhcCCCCCEEEEeCCCChH--HHHHHHH
Confidence 3455666799999999986 3456664
No 105
>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=66.38 E-value=9.9 Score=38.26 Aligned_cols=65 Identities=31% Similarity=0.309 Sum_probs=44.6
Q ss_pred HHHHHHHHHHhhcC-CCEEEEeC-chhhHHHHcc---cc----Cc-------------------ccccccccccccCCCC
Q 008596 276 LKDIQEEFLKLVYK-ETILVGHS-LENDLLALKI---SH----GL-------------------VIDTAVLYKHPQGGSH 327 (560)
Q Consensus 276 l~dVq~~L~~~i~~-~~ILVGHs-L~~DL~aLki---~H----p~-------------------viDT~~Ly~~~~g~~~ 327 (560)
=+++.+++++++.+ ...||||| -+||+.+|.. .| |. -+|+..+.... |...
T Consensus 37 E~~lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~-g~~~ 115 (209)
T PF10108_consen 37 EKELLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFY-GAKA 115 (209)
T ss_pred HHHHHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhcc-Cccc
Confidence 55677888888864 34799998 5899999983 22 22 25555443332 3345
Q ss_pred CccHHHHHHHhcCcc
Q 008596 328 KTSLRVLAKKFLSRE 342 (560)
Q Consensus 328 k~sLk~La~~~Lg~~ 342 (560)
+.||..||. .||++
T Consensus 116 ~~sLd~la~-~lgiP 129 (209)
T PF10108_consen 116 RTSLDELAA-LLGIP 129 (209)
T ss_pred cCCHHHHHH-HcCCC
Confidence 789999997 58987
No 106
>PHA02570 dexA exonuclease; Provisional
Probab=64.77 E-value=31 Score=35.07 Aligned_cols=92 Identities=11% Similarity=0.043 Sum_probs=55.7
Q ss_pred EEEEeccccCCCCceEEEEEEEEec--CcEE--EEEEEe------CCCCCCCC------cE--EecCCCh---hhhcC--
Q 008596 215 LALDCEMCYTNEGLELTRVTLVDIK--GQVL--LDKLVK------PSNAIVDY------NT--RYSGITH---EMLSG-- 271 (560)
Q Consensus 215 valDcEm~~t~~g~eL~rVsvVd~~--G~vv--lD~LVk------P~~~I~dy------~T--~~SGIT~---e~L~~-- 271 (560)
+.||.||-|+.+.-.|+.|++|-++ .... |.++|. -+.....+ -| -+-.=++ ..|.+
T Consensus 4 lMIDlETmG~~p~AaIisIgAV~Fdp~~~~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~L~~s~ 83 (220)
T PHA02570 4 FIIDFETFGNTPDGAVIDLAVIAFEHDPHNPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEARKNLKPSD 83 (220)
T ss_pred EEEEeeccCCCCCceEEEEEEEEecCCCCccccHHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHHHHhccCCC
Confidence 6799999999998899999999552 2111 333443 22111111 00 0101111 11211
Q ss_pred CCCCHHHHHHHHHHhhcCCC------EEEEeCchhhHHHHc
Q 008596 272 VTTSLKDIQEEFLKLVYKET------ILVGHSLENDLLALK 306 (560)
Q Consensus 272 ~~~tl~dVq~~L~~~i~~~~------ILVGHsL~~DL~aLk 306 (560)
...++.++..+|.+||.... .+=|-+.+||+..|+
T Consensus 84 ~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD~~IL~ 124 (220)
T PHA02570 84 EDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDFPILV 124 (220)
T ss_pred ccccHHHHHHHHHHHHHHcCCCccceeEecCCCccCHHHHH
Confidence 12578999999999996444 467888999999996
No 107
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
Probab=63.97 E-value=11 Score=34.53 Aligned_cols=59 Identities=20% Similarity=0.281 Sum_probs=39.8
Q ss_pred HHHhhc-CCCEEEEeCchhhHHHHcc----ccCcccccccccccccCCCCC-ccHHHHHHHhcCcc
Q 008596 283 FLKLVY-KETILVGHSLENDLLALKI----SHGLVIDTAVLYKHPQGGSHK-TSLRVLAKKFLSRE 342 (560)
Q Consensus 283 L~~~i~-~~~ILVGHsL~~DL~aLki----~Hp~viDT~~Ly~~~~g~~~k-~sLk~La~~~Lg~~ 342 (560)
|.+++. .+...|||++.+++.+|+. ....+.||.+..- ...|..+ .+|..|+++||+..
T Consensus 45 l~~~l~~~~~~ki~~d~K~~~~~l~~~gi~l~~~~fD~~LAaY-LL~p~~~~~~l~~la~~yl~~~ 109 (151)
T cd06128 45 LKPLLEDEKALKVGQNLKYDRVILANYGIELRGIAFDTMLEAY-LLDPVAGRHDMDSLAERWLKEK 109 (151)
T ss_pred HHHHHcCCCCCEEeeehHHHHHHHHHCCCCCCCcchhHHHHHH-HcCCCCCCCCHHHHHHHHcCCC
Confidence 455553 3345899999999999963 1234689886432 2233222 48999999999887
No 108
>TIGR00306 apgM 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, archaeal form. This model describes a set of proteins in the Archaea (two each in Methanococcus jannaschii, Methanobacterium thermoautotrophicum, and Archaeoglobus fulgidus) and in Aquifex aeolicus (1 member).
Probab=63.63 E-value=50 Score=36.32 Aligned_cols=36 Identities=19% Similarity=0.259 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHHHhhCCC-CcEEEEEeCCCChH
Q 008596 481 EIKEILARTDARVNSLYTALPT-NTMLIICTGHGDTA 516 (560)
Q Consensus 481 ~~~~~~~~~~~~i~~iy~~lP~-~t~liv~sg~gd~~ 516 (560)
...++++++|+.+.+++++|.. ...+||.+=||+|-
T Consensus 309 ~k~~aIE~iD~~l~~~l~~l~~~~~~liiTaDHgtp~ 345 (396)
T TIGR00306 309 LKVRAIEKIDSKIVGPLLALDLDETRLILTADHSTPV 345 (396)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhCCCEEEEeCCCCCCC
Confidence 4567899999999999999976 55899999999983
No 109
>TIGR02335 hydr_PhnA phosphonoacetate hydrolase. This family consists of examples of phosphonoacetate hydrolase, an enzyme specific for the cleavage of the C-P bond in phosphonoacetate. Phosphonates are organic compounds with a direct C-P bond that is far less labile that the C-O-P bonds of phosphate attachment sites. Phosphonates may be degraded for phosphorus and energy by broad spectrum C-P lyase encoded by large operon or by specific enzymes for some of the more common phosphonates in nature. This family represents an enzyme from the latter category. It may be found encoded near genes for phosphonate transport and for pther specific phosphonatases.
Probab=63.56 E-value=58 Score=35.81 Aligned_cols=35 Identities=23% Similarity=0.349 Sum_probs=30.1
Q ss_pred CChHHHHHHHHHHHHHHHHHhhCCCCcEEEEEeCCCCh
Q 008596 478 VTPEIKEILARTDARVNSLYTALPTNTMLIICTGHGDT 515 (560)
Q Consensus 478 ~~~~~~~~~~~~~~~i~~iy~~lP~~t~liv~sg~gd~ 515 (560)
.+++..+++.++|+.|.+|.+. ++.|||.|-||=.
T Consensus 207 ~S~e~~~~~~~lD~~l~~L~~~---~~~vvvtaDHG~~ 241 (408)
T TIGR02335 207 GEPESNAFYAAMDSRFKRYHEQ---GAIVAITADHGMN 241 (408)
T ss_pred CCHHHHHHHHHHHHHHHHHHHC---CCEEEEECCCCCc
Confidence 3467899999999999999985 8999999988854
No 110
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=62.60 E-value=54 Score=39.16 Aligned_cols=121 Identities=19% Similarity=0.159 Sum_probs=66.0
Q ss_pred CCCcEEEEEeccccCCCC------ceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHH
Q 008596 210 SPYEILALDCEMCYTNEG------LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEF 283 (560)
Q Consensus 210 ~~~~~valDcEm~~t~~g------~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L 283 (560)
.+.+++|+|+|+...... +.+..|+.....+.-.. ..+. .+...|.. +..+ .+=.++...+
T Consensus 152 p~l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~---~~~~------~~~~~~~~---v~~~-~~e~e~l~~~ 218 (792)
T COG0417 152 PPLRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLI---EVFI------YTSGEGFS---VEVV-ISEAELLERF 218 (792)
T ss_pred CCceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCcc---cccc------ccCCCCce---eEEe-cCHHHHHHHH
Confidence 356899999999986532 35777777665322111 0000 01111111 2222 2233444444
Q ss_pred HHhhc--CCCEEEEeCch-hhHHHHccc-------cC---------------------cccccccccccccCCCCCccHH
Q 008596 284 LKLVY--KETILVGHSLE-NDLLALKIS-------HG---------------------LVIDTAVLYKHPQGGSHKTSLR 332 (560)
Q Consensus 284 ~~~i~--~~~ILVGHsL~-~DL~aLki~-------Hp---------------------~viDT~~Ly~~~~g~~~k~sLk 332 (560)
..++- .-.|+||||.+ ||+..|.-. .. ..+|...++....-....++|.
T Consensus 219 ~~~i~~~dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~~~~~~~~~~ysl~ 298 (792)
T COG0417 219 VELIREYDPDVIVGYNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPALRRRPLNLKSYSLE 298 (792)
T ss_pred HHHHHhcCCCEEEeccCCcCChHHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHHHhhhhcccccccHH
Confidence 44441 45699999987 899988731 11 2345444444111123567899
Q ss_pred HHHHHhcCccc
Q 008596 333 VLAKKFLSREI 343 (560)
Q Consensus 333 ~La~~~Lg~~I 343 (560)
..+..+|+..-
T Consensus 299 ~v~~~~l~~~k 309 (792)
T COG0417 299 AVSEALLGEGK 309 (792)
T ss_pred HHHHHhccccc
Confidence 99999888764
No 111
>PRK05434 phosphoglyceromutase; Provisional
Probab=58.82 E-value=25 Score=39.88 Aligned_cols=79 Identities=16% Similarity=0.259 Sum_probs=57.9
Q ss_pred cCCChHHHHHHHHHhccCCCccEEEEecccchhhhhhhhhhHHHHHHHHHHHhhhhccccccccccccCCCCChHHHHHH
Q 008596 407 PVSSDDEVLSKARKEVKNDRIHFVWTQFSELNLHFKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPEIKEIL 486 (560)
Q Consensus 407 ~c~~D~ev~~~~~~~v~~~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 486 (560)
+--+..|+.+++++.++....||++..|.... ...+ .. ..+...+++
T Consensus 368 p~Ms~~e~~d~~i~~l~~~~~Dfv~vnf~~~D-~vGH-------------------------------tg-~~~a~~~AI 414 (507)
T PRK05434 368 PEMSAYEVTDKLVEAIESGKYDFIILNFANPD-MVGH-------------------------------TG-NLEAAVKAV 414 (507)
T ss_pred CCCcHHHHHHHHHHHHhccCCCEEEEEecCcc-hhhc-------------------------------CC-CHHHHHHHH
Confidence 44588889999999998777899998886542 1100 00 123467789
Q ss_pred HHHHHHHHHHHhhCC-CCcEEEEEeCCCChHHH
Q 008596 487 ARTDARVNSLYTALP-TNTMLIICTGHGDTAIV 518 (560)
Q Consensus 487 ~~~~~~i~~iy~~lP-~~t~liv~sg~gd~~~~ 518 (560)
+.+|+.|.+|+++|- .+-++||.|=||+...|
T Consensus 415 e~vD~~LGrll~aLk~~g~ivIITADHGn~e~m 447 (507)
T PRK05434 415 EAVDECLGRVVDAVLKVGGTLLITADHGNAEQM 447 (507)
T ss_pred HHHHHHHHHHHHHHHhCCCEEEEEcCCCccccc
Confidence 999999999999994 46688888889976544
No 112
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=57.01 E-value=8.7 Score=45.24 Aligned_cols=149 Identities=19% Similarity=0.299 Sum_probs=83.3
Q ss_pred CCCcEEEEEeccccCCCC------ceEEEEE-EEEe--cCcEEE-EEEE-eCCCCCCCCcEEecCCChhhhcCCCCCHHH
Q 008596 210 SPYEILALDCEMCYTNEG------LELTRVT-LVDI--KGQVLL-DKLV-KPSNAIVDYNTRYSGITHEMLSGVTTSLKD 278 (560)
Q Consensus 210 ~~~~~valDcEm~~t~~g------~eL~rVs-vVd~--~G~vvl-D~LV-kP~~~I~dy~T~~SGIT~e~L~~~~~tl~d 278 (560)
.|.++.++|+|+++.... +-+++|+ +|.. +++..+ +-+. +|-.+|..-. -++-+|++.|. +
T Consensus 272 APlrvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~Ge~~pf~rnvf~l~~capI~G~~-V~~~~~e~elL-------~ 343 (1066)
T KOG0969|consen 272 APLRVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQGENEPFVRNVFTLKTCAPIVGSN-VHSYETEKELL-------E 343 (1066)
T ss_pred ccccccceeEEeccCCCCCCccccChHHHHHHHHHHhcCCchHHHhhhcccCcCCCCCce-eEEeccHHHHH-------H
Confidence 467899999999998764 2344443 2232 333332 2222 3444554322 23334554433 3
Q ss_pred HHHHHHHhhcCCCEEEEeCc-hhhHHHH-------ccc--------cC---cccccccccccc----------cC-----
Q 008596 279 IQEEFLKLVYKETILVGHSL-ENDLLAL-------KIS--------HG---LVIDTAVLYKHP----------QG----- 324 (560)
Q Consensus 279 Vq~~L~~~i~~~~ILVGHsL-~~DL~aL-------ki~--------Hp---~viDT~~Ly~~~----------~g----- 324 (560)
.|..+..-+++ +|++|+|+ .||+-.| ++. +. .+.||+.-.+.. .|
T Consensus 344 ~W~~firevDP-DvI~GYNi~nFDiPYll~RA~~L~Ie~Fp~LGRikn~~s~irDttfSSkq~GtRetK~v~I~GRlqfD 422 (1066)
T KOG0969|consen 344 SWRKFIREVDP-DVIIGYNICNFDIPYLLNRAKTLGIENFPYLGRIKNSRSVIRDSTFSSKQYGTRETKEVNIDGRLQFD 422 (1066)
T ss_pred HHHHHHHhcCC-CeEecccccccccceecChHhhcCcccccccceecccceeeeccccchhhcCcccceEEeecceeeeh
Confidence 47778888855 59999997 6788433 331 11 356776322111 01
Q ss_pred ---------CCCCccHHHHHHHhcCcccccCCCCCChHH-----HHHHHHHHHHHHHHh
Q 008596 325 ---------GSHKTSLRVLAKKFLSREIQQSGFGHDSTE-----DARAAMELALLKIRN 369 (560)
Q Consensus 325 ---------~~~k~sLk~La~~~Lg~~IQ~~~~~HdSlE-----DA~Atl~L~~~kl~~ 369 (560)
.-+.++|..++.+|||..-.. .+|+.+. |+.+-.+|..+|++.
T Consensus 423 llqvi~Rd~KLrSytLNaVs~hFL~EQKED--V~~siItdLQng~~~TRRRlA~YCLkD 479 (1066)
T KOG0969|consen 423 LLQVILRDYKLRSYTLNAVSAHFLGEQKED--VHHSIITDLQNGNEQTRRRLAVYCLKD 479 (1066)
T ss_pred HHHHHHHhhhhhhcchhhhHHHhhhhhccc--ccccchhhhhcCcHHHHHHHHHHHhhh
Confidence 235688999999999876432 3555543 344445555555555
No 113
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=55.96 E-value=1.4e+02 Score=31.22 Aligned_cols=112 Identities=14% Similarity=0.078 Sum_probs=63.0
Q ss_pred CCcEEEEEeccccCCC-CceEEEEEEEEecCcEEEEEEEeCCCCCCCCcEEecCCChhhhcCCCCCHHHHHHHHHHhhcC
Q 008596 211 PYEILALDCEMCYTNE-GLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYK 289 (560)
Q Consensus 211 ~~~~valDcEm~~t~~-g~eL~rVsvVd~~G~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i~~ 289 (560)
..+++.+|+||+|++. |+-|+-++.-...+.++ +||- .+.+++-.=..|.+.++... .
T Consensus 97 ~e~~~FFDiETTGL~~ag~~I~~~g~a~~~~~~~---~Vrq-----------------~~lp~p~~E~avle~fl~~~-~ 155 (278)
T COG3359 97 AEDVAFFDIETTGLDRAGNTITLVGGARGVDDTM---HVRQ-----------------HFLPAPEEEVAVLENFLHDP-D 155 (278)
T ss_pred ccceEEEeeeccccCCCCCeEEEEEEEEccCceE---EEEe-----------------ecCCCcchhhHHHHHHhcCC-C
Confidence 3579999999999986 34555555554433322 2221 11111111122566777777 7
Q ss_pred CCEEEEeC-chhhHHHHc-cccC--------cccccccccccccC-CCCCccHHHHHHHhcCcccc
Q 008596 290 ETILVGHS-LENDLLALK-ISHG--------LVIDTAVLYKHPQG-GSHKTSLRVLAKKFLSREIQ 344 (560)
Q Consensus 290 ~~ILVGHs-L~~DL~aLk-i~Hp--------~viDT~~Ly~~~~g-~~~k~sLk~La~~~Lg~~IQ 344 (560)
.++||-+| ..||.-+++ +.+. .=+|-....++..+ ...+-+|+.+=+ +||+.=.
T Consensus 156 ~~~lvsfNGkaFD~PfikR~v~~~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr-~LGi~R~ 220 (278)
T COG3359 156 FNMLVSFNGKAFDIPFIKRMVRDRLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTVER-ILGIRRE 220 (278)
T ss_pred cceEEEecCcccCcHHHHHHHhcccccCccccchhhhhhhhhhhhccCCCCChhhHHH-HhCcccc
Confidence 78999997 589999998 2111 11443221111111 123456999887 7888743
No 114
>PRK05761 DNA polymerase I; Reviewed
Probab=53.08 E-value=30 Score=41.31 Aligned_cols=89 Identities=18% Similarity=0.253 Sum_probs=55.2
Q ss_pred CHHHHHHHHHHhhcCCCEEEEeCc-hhhHHHHccc---cC-------c-------ccccccccccc-------cCC--CC
Q 008596 275 SLKDIQEEFLKLVYKETILVGHSL-ENDLLALKIS---HG-------L-------VIDTAVLYKHP-------QGG--SH 327 (560)
Q Consensus 275 tl~dVq~~L~~~i~~~~ILVGHsL-~~DL~aLki~---Hp-------~-------viDT~~Ly~~~-------~g~--~~ 327 (560)
+=.++..++.+++....+.|++|. .||+..|.-. +. . .+|....+... .|. ..
T Consensus 209 ~E~eLL~~f~~~i~~~dPdi~yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~~~~~y~~~~~~~~~ 288 (787)
T PRK05761 209 SEKELLAELFDIILEYPPVVTFNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNKAVRSYAFYGKYRHR 288 (787)
T ss_pred CHHHHHHHHHHHHHhcCCEEEEcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheeecceeeeeccceeecc
Confidence 456677788888877788888986 6799887621 10 0 14443333211 011 11
Q ss_pred CccHHHHHHHhcCccccc-C---------CCCCChHHHHHHHHHHH
Q 008596 328 KTSLRVLAKKFLSREIQQ-S---------GFGHDSTEDARAAMELA 363 (560)
Q Consensus 328 k~sLk~La~~~Lg~~IQ~-~---------~~~HdSlEDA~Atl~L~ 363 (560)
.++|...++.+||..=.. . .-+.=++.||..+++|.
T Consensus 289 ~ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 289 EARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred cCChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 478999999999975210 0 01233589999999985
No 115
>PRK11598 putative metal dependent hydrolase; Provisional
Probab=47.52 E-value=43 Score=38.37 Aligned_cols=129 Identities=15% Similarity=0.146 Sum_probs=66.4
Q ss_pred HHHHHHHHHcCCeeeeecc-cc---ccccc-----C----CCCcceecCCChHHHHHHHHHhccCC-CccEEEEecccch
Q 008596 373 TKLLKVLFEYGKTSTLIDN-VS---IIKRY-----A----SESSHAIPVSSDDEVLSKARKEVKND-RIHFVWTQFSELN 438 (560)
Q Consensus 373 ~~i~~~l~~~g~~~~~id~-~~---~~~~~-----~----~~~~~~i~c~~D~ev~~~~~~~v~~~-~~~f~~~~~~~l~ 438 (560)
+++++.+.+.|.+..+++. +. ...+. . ...|..-.| .|+..+..+.+.+.+. +-.|++.++.+--
T Consensus 306 ~~l~d~l~~aG~~t~W~~Nq~g~~g~~~r~~~~~~~~~~~~~~~~~~~~-~De~LL~~l~~~L~~~~~~~fivLH~~GSH 384 (545)
T PRK11598 306 EGLLDIIQRAGINVLWNDNDGGCKGACDRVPHQDVTALNLPGQCIDGEC-YDEVLFHGLENYINNLQGDGVIVLHTIGSH 384 (545)
T ss_pred ccHHHHHHHcCCeEEeecCCCCCcchhcccchhhhhhhccccccCCCCc-cHHHHHHHHHHHHHhcCCCeEEEEeCCCCC
Confidence 5799999999999988862 11 00000 0 001111122 4666666555444321 1248888887632
Q ss_pred h-hhhhhhhhHHHHHHHHHHHhhhhccccccccccccCCCCChH----HHHHHHHHHHHHHHHHhhCCC-----CcEEEE
Q 008596 439 L-HFKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPE----IKEILARTDARVNSLYTALPT-----NTMLII 508 (560)
Q Consensus 439 ~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~i~~iy~~lP~-----~t~liv 508 (560)
. ++..+- +...... ...|...... ++ ..++ -..++..+|..|.+|.+.|.. ||++|.
T Consensus 385 ~P~Y~~Ry--P~~~~~F------~p~~~~~~~~----~~-~~~~~~n~YdnsI~ytD~~lg~ii~~Lk~~~~~~nT~iIy 451 (545)
T PRK11598 385 GPTYYNRY--PPQFRKF------TPTCDTNEIQ----TC-TQQQLVNTYDNTILYVDYIVDKAINLLKQHQDKFNTSLVY 451 (545)
T ss_pred CcchhhcC--ChhhccC------CCCCCccccc----cc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcCCeEEEE
Confidence 1 111111 1111000 0123222110 01 1112 245566788899999988754 789999
Q ss_pred EeCCCCh
Q 008596 509 CTGHGDT 515 (560)
Q Consensus 509 ~sg~gd~ 515 (560)
+|=||..
T Consensus 452 ~SDHGe~ 458 (545)
T PRK11598 452 LSDHGES 458 (545)
T ss_pred ECcCCCc
Confidence 9999985
No 116
>PRK09598 lipid A phosphoethanolamine transferase; Reviewed
Probab=42.91 E-value=63 Score=36.77 Aligned_cols=130 Identities=11% Similarity=0.088 Sum_probs=67.4
Q ss_pred HHHHHHHHHcCCeeeeeccc--ccc---ccc-C----CCCcceecCCChHHHHHHHHHhccCC--CccEEEEecccchh-
Q 008596 373 TKLLKVLFEYGKTSTLIDNV--SII---KRY-A----SESSHAIPVSSDDEVLSKARKEVKND--RIHFVWTQFSELNL- 439 (560)
Q Consensus 373 ~~i~~~l~~~g~~~~~id~~--~~~---~~~-~----~~~~~~i~c~~D~ev~~~~~~~v~~~--~~~f~~~~~~~l~~- 439 (560)
+++++.+.+.|.+..+++.. ... ..+ . ...|....|.-|++.+..+.+.+++. +.-|+|..+.+--.
T Consensus 293 ~nl~~ilk~aGy~T~W~snq~g~~~~~~~~~~~~~~~~~~~~~~~~~~De~LL~~l~~~l~~~~~~p~fivlH~~GSH~P 372 (522)
T PRK09598 293 ENLPTYLTRAGIKVFWRSANDGEPNVKVTSYLKNYELIQKCPNCEAPYDESLLYNLPELIKASSNENVLLILHLAGSHGP 372 (522)
T ss_pred CCHHHHHHHCCCeEEEEECCCCCCCccceeeccchhccccCCCCCCCCHHHHHHHHHHHHHhcCCCCeEEEEeCcCCCCC
Confidence 46788889999999888742 110 000 0 01122335567888888776666432 23588888876321
Q ss_pred -hhhhhhhhHHHHHHHHHHHhhhhccccccccccccCCCCC---hHHHHHHHHHHHHHHHHHhhC---CCCcEEEEEeCC
Q 008596 440 -HFKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVT---PEIKEILARTDARVNSLYTAL---PTNTMLIICTGH 512 (560)
Q Consensus 440 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~i~~iy~~l---P~~t~liv~sg~ 512 (560)
|..++ +..+ ... ...|..... .++... ..-..++.-+|..|.++++.| +.+|++|++|=|
T Consensus 373 ~Y~~Ry---P~~f-~~F-----~p~~~~~~l----~~~~~~~~~n~YdnsI~ytD~~l~~ii~~Lk~~~~~t~iIy~SDH 439 (522)
T PRK09598 373 NYDNKY---PLNF-RVF-----KPVCSSVEL----SSCSKESLINAYDNTIFYNDYLLDKIISMLKNLKQPALMIYLSDH 439 (522)
T ss_pred cccccC---Chhh-ccc-----CCCCcchhh----hhccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeEEEEEccC
Confidence 22111 1111 000 011221110 000010 112344566777787777766 448999999988
Q ss_pred CCh
Q 008596 513 GDT 515 (560)
Q Consensus 513 gd~ 515 (560)
|..
T Consensus 440 Ge~ 442 (522)
T PRK09598 440 GES 442 (522)
T ss_pred ccc
Confidence 864
No 117
>cd05015 SIS_PGI_1 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the first SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of glucose 6-phosphate to fructose 6-phosphate. As an extracellular protein, PGI also has functions equivalent to neuroleukin (NLK), autocrine motility factor (AMF), and maturation factor (MF). Evidence suggests that PGI, NLK, AMF, and MF are closely related or identical. NLK is a neurotrophic growth factor that promotes regeneration and survival of neurons. The dimeric form of NLK has isomerase function, whereas its monomeric form carries out neurotrophic activity. AMF is a cytokine that stimulates cell migration and metastasis. MF mediates the differentiation of human myeloid leukemic HL-60 cells to terminal monocytic cells.
Probab=40.17 E-value=51 Score=31.10 Aligned_cols=30 Identities=23% Similarity=0.319 Sum_probs=22.5
Q ss_pred HHHHhhC-CCCcEEEEEeCCCChHHHHHHHH
Q 008596 494 NSLYTAL-PTNTMLIICTGHGDTAIVHRLRE 523 (560)
Q Consensus 494 ~~iy~~l-P~~t~liv~sg~gd~~~~~rl~~ 523 (560)
.++...+ |++|++|++|-+|+|.|....-+
T Consensus 64 ~~~~~~~~~~~tlvi~iSkSG~T~Et~~~~~ 94 (158)
T cd05015 64 AELLKKLDPETTLFIVISKSGTTLETLANAR 94 (158)
T ss_pred HHHHHhCCcccEEEEEEECCcCCHHHHHHHH
Confidence 3444443 79999999999999988765433
No 118
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=39.87 E-value=23 Score=42.27 Aligned_cols=31 Identities=29% Similarity=0.348 Sum_probs=23.7
Q ss_pred cCCCEEEEeCchhhHHHHcc---c---cCcccccccc
Q 008596 288 YKETILVGHSLENDLLALKI---S---HGLVIDTAVL 318 (560)
Q Consensus 288 ~~~~ILVGHsL~~DL~aLki---~---Hp~viDT~~L 318 (560)
+.+.++||||+.||-.-++- + ..+.+||..|
T Consensus 239 ~ke~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTMSl 275 (1075)
T KOG3657|consen 239 GKEQLIVGHNVSFDRARIREEYNINGSKIRFLDTMSL 275 (1075)
T ss_pred CCCceEEeccccchHHHHHHHHhccccceeeeechhh
Confidence 57789999999999988872 1 2367888754
No 119
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=39.66 E-value=42 Score=35.28 Aligned_cols=156 Identities=18% Similarity=0.186 Sum_probs=89.7
Q ss_pred CCcEEEEEeccccCCCC-ceEEEEEEEEe-----cCc---------------EEEE---EEEeCCCCCCCCcEEecCCCh
Q 008596 211 PYEILALDCEMCYTNEG-LELTRVTLVDI-----KGQ---------------VLLD---KLVKPSNAIVDYNTRYSGITH 266 (560)
Q Consensus 211 ~~~~valDcEm~~t~~g-~eL~rVsvVd~-----~G~---------------vvlD---~LVkP~~~I~dy~T~~SGIT~ 266 (560)
-..++.+|.|++++..- .+++++++.+. +|. -++| -++.|......-..+++|.+.
T Consensus 12 ~~tf~fldleat~lp~~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~v~~p~aeeitgls~ 91 (318)
T KOG4793|consen 12 LRTFSFLDLEATGLPGWIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVPVTRPIAEEITGLSQ 91 (318)
T ss_pred eeEEEeeeeccccCCcccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcCCcChhhhhhccccc
Confidence 35688999999998643 35666665543 222 2333 356677666666788999888
Q ss_pred hhhcC--CCCCHHHHHHHHHHhh---cCCCEEEEeCc-hhhHHHHcc-------ccC---cccccccccccc--------
Q 008596 267 EMLSG--VTTSLKDIQEEFLKLV---YKETILVGHSL-ENDLLALKI-------SHG---LVIDTAVLYKHP-------- 322 (560)
Q Consensus 267 e~L~~--~~~tl~dVq~~L~~~i---~~~~ILVGHsL-~~DL~aLki-------~Hp---~viDT~~Ly~~~-------- 322 (560)
+-+.- ..---.|+.+-|..|+ +.---||.||- ++|+-.|.. .-| .++|+...+...
T Consensus 92 ~~~~l~rr~~~D~dla~LL~afls~lp~p~CLVaHng~~~dfpil~qela~lg~~lpq~lvcvdslpa~~ald~a~s~~t 171 (318)
T KOG4793|consen 92 PFLALQRRLAFDKDLAKLLTAFLSRLPTPGCLVAHNGNEYDFPILAQELAGLGYSLPQDLVCVDSLPALNALDRANSMVT 171 (318)
T ss_pred HHHHHHHHhhhhHHHHHHHHHHHhcCCCCceEEeecCCccccHHHHHHHHhcCccchhhhcCcchhHHHHHHhhhcCccc
Confidence 54432 1111123333344444 33335999984 778877773 223 467776543211
Q ss_pred cCC-CCCccHHHHHHHhcCcccccCCCCCChHHHHHHHHHHHHHHHH
Q 008596 323 QGG-SHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMELALLKIR 368 (560)
Q Consensus 323 ~g~-~~k~sLk~La~~~Lg~~IQ~~~~~HdSlEDA~Atl~L~~~kl~ 368 (560)
++. +..++|..+-..|.+-. + -.++|.+..|--+-+-.+++...
T Consensus 172 r~~~~~~~~l~~If~ry~~q~-e-ppa~~~~e~d~~~l~~~fqf~~~ 216 (318)
T KOG4793|consen 172 RPEVRRMYSLGSIFLRYVEQR-E-PPAGHVAEGDVNGLLFIFQFRIN 216 (318)
T ss_pred CCCCCcccccchHHHhhhccc-C-CCcceeeecccchhHHHHHHHHH
Confidence 222 45678888877775543 1 23688888876655555444433
No 120
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=39.48 E-value=2.3e+02 Score=36.58 Aligned_cols=148 Identities=19% Similarity=0.230 Sum_probs=86.0
Q ss_pred CcEEEEEeccccCCC------CceEEEEE-EEEecCcEEEEE-EEe---------CCCCCCCCcEEecCCChhhhcCCCC
Q 008596 212 YEILALDCEMCYTNE------GLELTRVT-LVDIKGQVLLDK-LVK---------PSNAIVDYNTRYSGITHEMLSGVTT 274 (560)
Q Consensus 212 ~~~valDcEm~~t~~------g~eL~rVs-vVd~~G~vvlD~-LVk---------P~~~I~dy~T~~SGIT~e~L~~~~~ 274 (560)
..+.|+|+||+...- .++|.-|| .||+.|-.|.+. .|- |.....-+-+-+ |. +
T Consensus 246 p~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREiVs~DIedfEYTPKpE~eG~F~v~---------Ne-~ 315 (2173)
T KOG1798|consen 246 PRVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREIVSEDIEDFEYTPKPEYEGPFCVF---------NE-P 315 (2173)
T ss_pred ceEEEEeeecccCCCCCCCcccceEEEEEEEecCceEEEechhhhccchhhcccCCccccccceEEe---------cC-C
Confidence 479999999998752 25787787 467777665442 221 222222222222 22 1
Q ss_pred CHHHHHHHHHHhh--cCCCEEEEeCchh-hHHHHcc---ccC--------cccccccccccc---------------cCC
Q 008596 275 SLKDIQEEFLKLV--YKETILVGHSLEN-DLLALKI---SHG--------LVIDTAVLYKHP---------------QGG 325 (560)
Q Consensus 275 tl~dVq~~L~~~i--~~~~ILVGHsL~~-DL~aLki---~Hp--------~viDT~~Ly~~~---------------~g~ 325 (560)
.=..+.+++.+-+ -.-+|+|-+|-.| |+-++.- .|. ...|..--|+-+ +-|
T Consensus 316 dEv~Ll~RfFeHiq~~kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrWVKRDSYLP 395 (2173)
T KOG1798|consen 316 DEVGLLQRFFEHIQEVKPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRWVKRDSYLP 395 (2173)
T ss_pred cHHHHHHHHHHHHHhcCCcEEEEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehhhhhhhhhcccCC
Confidence 2222333333322 1568999999765 9998873 232 234433222211 124
Q ss_pred CCCccHHHHHHHhcCcc-cccC-------------CCCCChHHHHHHHHHHHHHHHHh
Q 008596 326 SHKTSLRVLAKKFLSRE-IQQS-------------GFGHDSTEDARAAMELALLKIRN 369 (560)
Q Consensus 326 ~~k~sLk~La~~~Lg~~-IQ~~-------------~~~HdSlEDA~Atl~L~~~kl~~ 369 (560)
....+||..++..||.+ +..+ .-+-=|+.||.||--||.+.+.-
T Consensus 396 qGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVhP 453 (2173)
T KOG1798|consen 396 QGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVHP 453 (2173)
T ss_pred CcccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhhh
Confidence 45678999999999985 3221 13566899999999998766654
No 121
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=38.47 E-value=1.1e+02 Score=34.87 Aligned_cols=92 Identities=15% Similarity=0.237 Sum_probs=52.5
Q ss_pred CCcEEEEEeccccCC-C-----CceEEEEEEEEec-C---cEEEEEEEeCCCCCCCCcEEecCCChhhhcCCC----CCH
Q 008596 211 PYEILALDCEMCYTN-E-----GLELTRVTLVDIK-G---QVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVT----TSL 276 (560)
Q Consensus 211 ~~~~valDcEm~~t~-~-----g~eL~rVsvVd~~-G---~vvlD~LVkP~~~I~dy~T~~SGIT~e~L~~~~----~tl 276 (560)
.-++..||+|.+.-. + ..+|..|+..|.. + -.+++.+ +. ...|....+=.-.+.++++. .+=
T Consensus 105 ~i~~~~~DIEv~~~~fp~~~~a~~~i~~i~~~d~~~~~~~~~~~~~~--~~--~~~~~~~~~~~~~~~~~~v~v~~f~sE 180 (498)
T PHA02524 105 DVVIDVVDIEVTAPEFPEPKYAKYEIDMISHVRLHNGKKTYYIFDLV--KD--VGHWDPKKSVLEKYILDNVVYMPFEDE 180 (498)
T ss_pred hceEEEEEEEecCCCCCChhhcCCceEEEEeeecccCCccEEEEecc--cc--ccCCCcccccccccccCCeEEEEeCCH
Confidence 347999999996532 1 2478888887752 1 2345543 11 11122111111222244431 355
Q ss_pred HHHHHHHHHhhcC--CCEEEEeCc-hhhHHHHc
Q 008596 277 KDIQEEFLKLVYK--ETILVGHSL-ENDLLALK 306 (560)
Q Consensus 277 ~dVq~~L~~~i~~--~~ILVGHsL-~~DL~aLk 306 (560)
.++..++.+++.. -.||+|||. .|||..|.
T Consensus 181 ~eLL~~F~~~i~~~DPDIItGYNi~nFDlPYL~ 213 (498)
T PHA02524 181 VDLLLNYIQLWKANTPDLVFGWNSEGFDIPYII 213 (498)
T ss_pred HHHHHHHHHHHHHhCCCEEEeCCCcccCHHHHH
Confidence 6777788888843 379999996 68997654
No 122
>PF07819 PGAP1: PGAP1-like protein; InterPro: IPR012908 The sequences found in this family are similar to PGAP1 (Q765A7 from SWISSPROT). This is an endoplasmic reticulum membrane protein with a catalytic serine-containing motif that is conserved in a number of lipases. PGAP1 functions as a GPI inositol-deacylase; this deacylation is important for the efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi body [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006505 GPI anchor metabolic process, 0006886 intracellular protein transport, 0031227 intrinsic to endoplasmic reticulum membrane
Probab=31.27 E-value=27 Score=35.03 Aligned_cols=44 Identities=27% Similarity=0.380 Sum_probs=27.1
Q ss_pred CcEEecCCChhhhcCCCCCHHHHHHHHHHhh------cCCCEEEEeCchh
Q 008596 257 YNTRYSGITHEMLSGVTTSLKDIQEEFLKLV------YKETILVGHSLEN 300 (560)
Q Consensus 257 y~T~~SGIT~e~L~~~~~tl~dVq~~L~~~i------~~~~ILVGHsL~~ 300 (560)
|...+++..-..|......+.+..+.|++.. +..-+|||||.--
T Consensus 47 f~~~~s~~~g~~l~~q~~~~~~~i~~i~~~~~~~~~~~~~vilVgHSmGG 96 (225)
T PF07819_consen 47 FNEELSAFHGRTLQRQAEFLAEAIKYILELYKSNRPPPRSVILVGHSMGG 96 (225)
T ss_pred cCccccccccccHHHHHHHHHHHHHHHHHhhhhccCCCCceEEEEEchhh
Confidence 4444444444444444345666777777766 4667999999765
No 123
>PRK11560 phosphoethanolamine transferase; Provisional
Probab=29.03 E-value=1.5e+02 Score=34.09 Aligned_cols=33 Identities=15% Similarity=0.339 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHhhCC-CCcEEEEEeCCCCh
Q 008596 483 KEILARTDARVNSLYTALP-TNTMLIICTGHGDT 515 (560)
Q Consensus 483 ~~~~~~~~~~i~~iy~~lP-~~t~liv~sg~gd~ 515 (560)
...+..+|..|.+|.+.|- .||++|.+|=||..
T Consensus 435 dnsI~ytD~~lg~ii~~Lk~~nTivIy~SDHGe~ 468 (558)
T PRK11560 435 DNSVLYVDHFISSVIDQLRDKKAIVFYAADHGES 468 (558)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCeEEEEEcCCCCc
Confidence 3445567777777777764 58999999999985
No 124
>PRK04135 cofactor-independent phosphoglycerate mutase; Provisional
Probab=28.64 E-value=2.4e+02 Score=31.20 Aligned_cols=100 Identities=14% Similarity=0.235 Sum_probs=59.7
Q ss_pred HHcCCeeeeecccccccccCCC-Ccceec-CCChHHHHHHHHHhccCCCccEEEEecccchhhhhhhhhhHHHHHHHHHH
Q 008596 380 FEYGKTSTLIDNVSIIKRYASE-SSHAIP-VSSDDEVLSKARKEVKNDRIHFVWTQFSELNLHFKKQAKDEAKLNEKLAE 457 (560)
Q Consensus 380 ~~~g~~~~~id~~~~~~~~~~~-~~~~i~-c~~D~ev~~~~~~~v~~~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~~~~ 457 (560)
.+.|.+.++|......++.+.. .-..|. -.+=.+-.+.+++..+. +|||+..+..... ..
T Consensus 233 e~~Glkga~Ia~~~l~kGi~~~~Gm~~i~~ga~~~~k~~~a~~~l~~--~DfV~vhvk~~De-aG--------------- 294 (395)
T PRK04135 233 EVYKLKAAAIASYPMYRGLAKLVGMDVLPTGQTLEDEIKTLKENWND--YDFFFLHVKKTDS-YG--------------- 294 (395)
T ss_pred HHhCCceEEEehhHHHHHHHHHcCCeecCCCCCHHHHHHHHHHHHhc--CCEEEEEeccCch-hh---------------
Confidence 4557777777665554443321 112222 11444555566666654 6899887744321 00
Q ss_pred HhhhhccccccccccccCCCCChHHHHHHHHHHHHHHHHHhhCCCCcEEEEEeCCCChH
Q 008596 458 LISLATCDKKLSDSKRFKSFVTPEIKEILARTDARVNSLYTALPTNTMLIICTGHGDTA 516 (560)
Q Consensus 458 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~iy~~lP~~t~liv~sg~gd~~ 516 (560)
+. ...+.-.++++++|+.|..|. .++ .+.++|.+=|+.|-
T Consensus 295 -------H~----------gd~~~Kv~~IE~iD~~l~~ll-~l~-~~~ivVT~DH~TP~ 334 (395)
T PRK04135 295 -------ED----------GNFEEKVKVIEEVDALLPEIL-ALK-PDVLVITGDHSTPA 334 (395)
T ss_pred -------cc----------CCHHHHHHHHHHHHHHHHHHh-cCC-CcEEEEeCCCCCcc
Confidence 00 012245678999999999999 774 44899999999997
No 125
>PF01380 SIS: SIS domain SIS domain web page.; InterPro: IPR001347 The SIS (Sugar ISomerase) domain is a phosphosugar-binding domain [] found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars possibly by binding to the end-product of the pathway.; GO: 0005529 sugar binding, 0005975 carbohydrate metabolic process; PDB: 3TBF_C 2V4M_A 2ZJ4_A 2ZJ3_A 3FKJ_A 3ODP_A 3EUA_H 1VIV_A 1M3S_B 1TZB_A ....
Probab=24.56 E-value=1.2e+02 Score=26.38 Aligned_cols=33 Identities=18% Similarity=0.249 Sum_probs=25.6
Q ss_pred HHHHHhhCCCCcEEEEEeCCCChHHHHHHHHHH
Q 008596 493 VNSLYTALPTNTMLIICTGHGDTAIVHRLREML 525 (560)
Q Consensus 493 i~~iy~~lP~~t~liv~sg~gd~~~~~rl~~~~ 525 (560)
.......+.+++++|++|.+|.++++.++=+..
T Consensus 44 ~~~~~~~~~~~d~vi~is~sg~~~~~~~~~~~a 76 (131)
T PF01380_consen 44 FHGPLENLDPDDLVIIISYSGETRELIELLRFA 76 (131)
T ss_dssp HTTGGGGCSTTEEEEEEESSSTTHHHHHHHHHH
T ss_pred hhhhcccccccceeEeeeccccchhhhhhhHHH
Confidence 344456788999999999999999887654443
No 126
>PF10239 DUF2465: Protein of unknown function (DUF2465); InterPro: IPR018797 FAM98A, B and C are glycine-rich proteins found from worms to humans whose function is unknown.
Probab=23.37 E-value=2.9e+02 Score=29.58 Aligned_cols=51 Identities=18% Similarity=0.324 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCcE---EEEEeCCCChHHHHHHHHHHHHHhhhcc
Q 008596 481 EIKEILARTDARVNSLYTALPTNTM---LIICTGHGDTAIVHRLREMLREQSKNSM 533 (560)
Q Consensus 481 ~~~~~~~~~~~~i~~iy~~lP~~t~---liv~sg~gd~~~~~rl~~~~~~~~~~~~ 533 (560)
...+.+.++..+|+.+...+|++.+ |+ ..+=++..+.+|.++++.-.++|.
T Consensus 152 ~~~~lf~~i~~ki~~~L~~lp~~~~~~PLl--~~~L~~~Qw~~Le~i~~~L~~EY~ 205 (318)
T PF10239_consen 152 TASQLFSKIEAKIEELLSKLPPGHMGKPLL--KKSLTDEQWEKLEKINQALSKEYE 205 (318)
T ss_pred CHHHHHHHHHHHHHHHHHhcCccccCCCCc--CCCCCHHHHHHHHHHHHHHHHHHH
Confidence 4678899999999999999999988 44 888999999999888766444443
No 127
>cd05017 SIS_PGI_PMI_1 The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the first SIS domain.
Probab=22.10 E-value=1.3e+02 Score=26.62 Aligned_cols=28 Identities=18% Similarity=0.173 Sum_probs=23.0
Q ss_pred hCCCCcEEEEEeCCCChHHHHHHHHHHH
Q 008596 499 ALPTNTMLIICTGHGDTAIVHRLREMLR 526 (560)
Q Consensus 499 ~lP~~t~liv~sg~gd~~~~~rl~~~~~ 526 (560)
.+.+++++|++|.+|.+.++.+.=+.-+
T Consensus 40 ~~~~~dl~I~iS~SG~t~e~i~~~~~a~ 67 (119)
T cd05017 40 FVDRKTLVIAVSYSGNTEETLSAVEQAK 67 (119)
T ss_pred CCCCCCEEEEEECCCCCHHHHHHHHHHH
Confidence 6789999999999999998877544433
No 128
>PRK04200 cofactor-independent phosphoglycerate mutase; Provisional
Probab=20.52 E-value=2.5e+02 Score=30.86 Aligned_cols=36 Identities=17% Similarity=0.278 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHH-HHHHHhhCC--CCcEEEEEeCCCChH
Q 008596 481 EIKEILARTDAR-VNSLYTALP--TNTMLIICTGHGDTA 516 (560)
Q Consensus 481 ~~~~~~~~~~~~-i~~iy~~lP--~~t~liv~sg~gd~~ 516 (560)
.-.++++++++. +..|+++|+ .+..++|.+=||+|-
T Consensus 305 ~kv~aiE~lD~~~~~~ll~al~~~~~~~l~it~DH~tp~ 343 (395)
T PRK04200 305 AKIKAIEDIDERVVGPILEALKKYEDYRILVLPDHPTPI 343 (395)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHhcCCCEEEEeccCCcCC
Confidence 346779999998 447999997 477899999999864
No 129
>PF10752 DUF2533: Protein of unknown function (DUF2533) ; InterPro: IPR019688 This entry represents proteins with unknown function, and appear to be restricted to Bacillus spp.
Probab=20.12 E-value=1.2e+02 Score=26.37 Aligned_cols=21 Identities=14% Similarity=0.058 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHhhceeEE
Q 008596 536 KMIVKVLEELQAQAEVALCFV 556 (560)
Q Consensus 536 ~~~~~~l~~~~~~Ar~g~~f~ 556 (560)
.++|+++++||..++.|.-|-
T Consensus 26 ~~RE~aIeeav~~c~~g~pFs 46 (84)
T PF10752_consen 26 QQREAAIEEAVSLCKQGEPFS 46 (84)
T ss_pred HHHHHHHHHHHHHHHCCCCCc
Confidence 357899999999999998873
Done!