Query 008340
Match_columns 569
No_of_seqs 278 out of 1238
Neff 5.4
Searched_HMMs 46136
Date Thu Mar 28 22:35:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008340.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008340hhsearch_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 7.9E-47 1.7E-51 398.6 21.1 335 25-375 34-380 (380)
2 cd06143 PAN2_exo DEDDh 3'-5' e 100.0 1.3E-42 2.8E-47 331.9 14.3 146 215-364 1-174 (174)
3 KOG2249 3'-5' exonuclease [Rep 100.0 2.5E-39 5.5E-44 322.1 13.8 150 213-366 106-262 (280)
4 cd06145 REX1_like DEDDh 3'-5' 100.0 6.9E-36 1.5E-40 279.6 15.6 150 215-364 1-150 (150)
5 cd06149 ISG20 DEDDh 3'-5' exon 100.0 1.9E-33 4.1E-38 265.1 15.1 148 215-364 1-157 (157)
6 cd06137 DEDDh_RNase DEDDh 3'-5 100.0 3.5E-33 7.5E-38 263.9 13.4 150 215-364 1-161 (161)
7 cd06144 REX4_like DEDDh 3'-5' 100.0 2.3E-29 5E-34 235.6 14.6 146 215-364 1-152 (152)
8 PRK07247 DNA polymerase III su 99.9 6.1E-23 1.3E-27 200.7 17.8 153 212-371 5-170 (195)
9 PRK07740 hypothetical protein; 99.9 3.7E-22 7.9E-27 201.3 18.1 169 212-389 59-242 (244)
10 cd06130 DNA_pol_III_epsilon_li 99.9 5E-22 1.1E-26 183.9 15.3 143 214-364 1-155 (156)
11 smart00479 EXOIII exonuclease 99.9 3.8E-22 8.3E-27 185.8 14.1 150 214-369 2-166 (169)
12 PRK06310 DNA polymerase III su 99.9 1.6E-21 3.4E-26 197.4 16.6 165 212-390 7-186 (250)
13 KOG1275 PAB-dependent poly(A) 99.9 1E-22 2.2E-27 227.5 8.1 175 210-394 908-1110(1118)
14 PRK06309 DNA polymerase III su 99.9 1.3E-21 2.9E-26 195.5 15.3 153 212-369 2-165 (232)
15 PRK05711 DNA polymerase III su 99.9 1.9E-21 4.2E-26 195.8 16.2 158 212-374 4-180 (240)
16 PRK06807 DNA polymerase III su 99.9 2.1E-21 4.6E-26 202.3 16.9 154 210-370 6-172 (313)
17 PRK09145 DNA polymerase III su 99.9 2.9E-21 6.2E-26 188.8 16.5 151 212-368 29-199 (202)
18 PRK09146 DNA polymerase III su 99.9 3.1E-21 6.8E-26 194.1 16.2 153 212-370 47-227 (239)
19 PRK06063 DNA polymerase III su 99.9 7.4E-21 1.6E-25 198.3 18.3 152 211-370 14-179 (313)
20 TIGR01406 dnaQ_proteo DNA poly 99.9 3.8E-21 8.2E-26 191.7 14.8 151 213-368 1-170 (225)
21 PRK07942 DNA polymerase III su 99.9 5.3E-21 1.2E-25 191.4 15.7 184 212-399 6-221 (232)
22 PRK07983 exodeoxyribonuclease 99.9 5.6E-21 1.2E-25 190.0 15.7 147 214-369 2-153 (219)
23 PRK06195 DNA polymerase III su 99.9 9.8E-21 2.1E-25 196.9 17.0 150 213-370 2-164 (309)
24 TIGR00573 dnaq exonuclease, DN 99.9 8.4E-21 1.8E-25 187.8 15.1 159 212-374 7-181 (217)
25 PRK08517 DNA polymerase III su 99.8 2.7E-20 5.8E-25 189.2 18.6 183 181-371 35-232 (257)
26 cd06131 DNA_pol_III_epsilon_Ec 99.8 1.3E-20 2.9E-25 177.2 14.4 147 214-365 1-165 (167)
27 cd06136 TREX1_2 DEDDh 3'-5' ex 99.8 4.9E-21 1.1E-25 183.9 11.6 143 214-365 1-176 (177)
28 PRK07246 bifunctional ATP-depe 99.8 2E-20 4.3E-25 216.6 17.2 158 211-374 6-174 (820)
29 PRK07748 sporulation inhibitor 99.8 1.8E-20 4E-25 184.0 13.3 160 212-375 4-185 (207)
30 PRK07883 hypothetical protein; 99.8 9.8E-20 2.1E-24 202.9 17.6 159 212-376 15-188 (557)
31 cd06127 DEDDh DEDDh 3'-5' exon 99.8 1.3E-19 2.7E-24 164.8 13.3 144 215-363 1-158 (159)
32 TIGR01298 RNaseT ribonuclease 99.8 1.7E-19 3.6E-24 176.8 13.5 155 212-372 8-194 (200)
33 PRK08074 bifunctional ATP-depe 99.8 2.8E-19 6.1E-24 209.7 17.1 155 212-372 3-171 (928)
34 TIGR01407 dinG_rel DnaQ family 99.8 3.5E-19 7.7E-24 207.2 17.7 153 213-371 1-166 (850)
35 cd06134 RNaseT DEDDh 3'-5' exo 99.8 3.9E-19 8.4E-24 172.5 14.4 151 213-369 6-188 (189)
36 PRK05168 ribonuclease T; Provi 99.8 5.5E-19 1.2E-23 174.5 14.4 157 212-374 17-205 (211)
37 PRK06722 exonuclease; Provisio 99.8 1.3E-18 2.8E-23 178.8 15.6 152 212-368 5-179 (281)
38 cd06133 ERI-1_3'hExo_like DEDD 99.8 4.9E-19 1.1E-23 166.8 11.0 148 214-366 1-175 (176)
39 TIGR01405 polC_Gram_pos DNA po 99.8 8.1E-19 1.8E-23 208.5 14.9 157 212-374 190-359 (1213)
40 COG2176 PolC DNA polymerase II 99.8 1.9E-19 4E-24 206.3 7.8 154 212-371 421-587 (1444)
41 PF00929 RNase_T: Exonuclease; 99.8 6.6E-21 1.4E-25 173.4 -3.5 145 215-363 1-164 (164)
42 PRK05601 DNA polymerase III su 99.8 6.8E-18 1.5E-22 177.9 18.0 150 212-366 46-245 (377)
43 PRK09182 DNA polymerase III su 99.8 4.3E-18 9.3E-23 176.2 16.2 151 210-369 35-200 (294)
44 COG0847 DnaQ DNA polymerase II 99.8 6.6E-18 1.4E-22 168.5 15.7 155 212-369 13-181 (243)
45 cd06138 ExoI_N N-terminal DEDD 99.7 7.4E-18 1.6E-22 162.5 11.4 145 215-363 1-182 (183)
46 PRK11779 sbcB exonuclease I; P 99.6 1.1E-15 2.4E-20 167.3 14.1 157 212-372 6-200 (476)
47 PRK00448 polC DNA polymerase I 99.6 6.6E-16 1.4E-20 186.0 12.9 157 212-374 419-588 (1437)
48 cd06135 Orn DEDDh 3'-5' exonuc 99.6 7.7E-16 1.7E-20 147.4 10.9 141 214-368 1-170 (173)
49 PTZ00315 2'-phosphotransferase 99.6 2.3E-15 5E-20 166.6 15.9 160 212-375 56-260 (582)
50 PRK05359 oligoribonuclease; Pr 99.6 1.6E-15 3.4E-20 146.8 12.2 143 212-369 3-174 (181)
51 cd05160 DEDDy_DNA_polB_exo DED 98.5 7.9E-07 1.7E-11 86.3 10.3 122 214-343 1-163 (199)
52 PF01612 DNA_pol_A_exo1: 3'-5' 98.4 2.6E-06 5.7E-11 79.5 10.8 129 213-367 21-172 (176)
53 COG5018 KapD Inhibitor of the 98.4 2.2E-07 4.8E-12 88.8 3.1 159 213-375 5-190 (210)
54 cd06139 DNA_polA_I_Ecoli_like_ 98.4 4.2E-06 9.1E-11 79.8 11.9 140 212-369 5-169 (193)
55 KOG0542 Predicted exonuclease 98.3 3.3E-07 7.1E-12 92.5 2.6 157 214-375 58-247 (280)
56 KOG3242 Oligoribonuclease (3'- 98.2 3.9E-06 8.4E-11 80.7 6.9 142 212-368 26-197 (208)
57 cd06146 mut-7_like_exo DEDDy 3 98.1 1E-05 2.2E-10 79.1 9.1 87 280-366 71-191 (193)
58 COG1949 Orn Oligoribonuclease 97.9 3.4E-05 7.4E-10 73.7 8.5 152 211-369 5-177 (184)
59 PRK05755 DNA polymerase I; Pro 97.9 7.5E-05 1.6E-09 88.5 11.9 132 212-369 315-468 (880)
60 cd06141 WRN_exo DEDDy 3'-5' ex 97.8 0.00018 3.9E-09 68.0 11.4 126 212-366 18-168 (170)
61 cd06125 DnaQ_like_exo DnaQ-lik 97.7 0.00016 3.4E-09 63.1 8.2 57 215-307 1-61 (96)
62 cd00007 35EXOc 3'-5' exonuclea 97.7 0.00086 1.9E-08 60.7 12.8 104 214-343 2-111 (155)
63 cd06129 RNaseD_like DEDDy 3'-5 97.6 0.00033 7.2E-09 66.2 10.1 82 283-365 59-158 (161)
64 PRK10829 ribonuclease D; Provi 97.6 0.00085 1.8E-08 72.4 13.0 126 212-368 22-168 (373)
65 COG2925 SbcB Exonuclease I [DN 97.5 0.00093 2E-08 71.4 11.5 156 212-371 9-202 (475)
66 cd05780 DNA_polB_Kod1_like_exo 97.4 0.00099 2.1E-08 65.2 10.4 115 212-343 3-156 (195)
67 smart00474 35EXOc 3'-5' exonuc 97.0 0.018 4E-07 53.1 13.2 64 281-344 65-132 (172)
68 TIGR01696 deoB phosphopentomut 96.9 0.0061 1.3E-07 66.0 10.6 117 372-523 209-325 (381)
69 TIGR01388 rnd ribonuclease D. 96.9 0.0092 2E-07 64.3 12.0 123 213-366 19-162 (367)
70 cd05784 DNA_polB_II_exo DEDDy 96.6 0.046 9.9E-07 53.9 13.7 116 211-342 2-153 (193)
71 cd05779 DNA_polB_epsilon_exo D 96.6 0.03 6.6E-07 55.7 12.4 128 212-342 2-168 (204)
72 cd06142 RNaseD_exo DEDDy 3'-5' 96.6 0.051 1.1E-06 51.1 13.2 85 281-366 54-156 (178)
73 cd06148 Egl_like_exo DEDDy 3'- 96.5 0.0053 1.2E-07 60.2 6.6 62 282-343 56-129 (197)
74 COG0349 Rnd Ribonuclease D [Tr 96.4 0.011 2.5E-07 63.3 8.5 124 212-362 17-152 (361)
75 cd05785 DNA_polB_like2_exo Unc 96.4 0.017 3.7E-07 57.4 9.3 71 212-306 9-91 (207)
76 cd05781 DNA_polB_B3_exo DEDDy 96.3 0.037 8E-07 54.2 10.9 104 212-341 3-143 (188)
77 PRK05362 phosphopentomutase; P 96.3 0.03 6.5E-07 61.0 10.9 118 371-523 215-333 (394)
78 COG1015 DeoB Phosphopentomutas 96.0 0.056 1.2E-06 58.1 11.2 109 382-523 227-336 (397)
79 cd05783 DNA_polB_B1_exo DEDDy 95.9 0.13 2.8E-06 51.1 12.5 124 211-342 4-170 (204)
80 cd05777 DNA_polB_delta_exo DED 95.8 0.27 5.8E-06 49.4 14.6 122 211-344 6-184 (230)
81 PF13482 RNase_H_2: RNase_H su 95.4 0.035 7.5E-07 52.0 6.4 125 215-370 1-137 (164)
82 PRK12383 putative mutase; Prov 95.3 0.13 2.8E-06 56.4 11.1 110 382-525 234-343 (406)
83 cd06140 DNA_polA_I_Bacillus_li 94.8 0.57 1.2E-05 44.3 12.8 104 213-343 4-113 (178)
84 smart00486 POLBc DNA polymeras 93.4 0.53 1.2E-05 50.8 10.7 143 212-366 3-220 (471)
85 PRK05762 DNA polymerase II; Re 93.3 0.74 1.6E-05 54.5 12.3 137 210-364 153-346 (786)
86 cd09018 DEDDy_polA_RNaseD_like 93.0 0.88 1.9E-05 41.3 9.9 60 283-343 45-110 (150)
87 PF01676 Metalloenzyme: Metall 92.4 0.17 3.7E-06 51.6 4.8 78 419-529 124-202 (252)
88 KOG2126 Glycosylphosphatidylin 92.4 0.25 5.5E-06 58.0 6.6 123 370-524 133-264 (895)
89 cd06147 Rrp6p_like_exo DEDDy 3 92.1 1.2 2.5E-05 43.2 10.0 102 213-343 25-132 (192)
90 COG0749 PolA DNA polymerase I 92.0 0.66 1.4E-05 53.1 9.2 132 214-369 24-179 (593)
91 PF03104 DNA_pol_B_exo1: DNA p 91.0 0.66 1.4E-05 47.9 7.4 86 210-306 155-255 (325)
92 cd05778 DNA_polB_zeta_exo inac 90.9 2.4 5.3E-05 42.8 11.1 140 213-356 5-203 (231)
93 cd05782 DNA_polB_like1_exo Unc 90.6 0.51 1.1E-05 47.0 5.8 64 277-342 79-169 (208)
94 TIGR00593 pola DNA polymerase 89.9 1.1 2.3E-05 54.0 8.7 93 276-369 363-476 (887)
95 PF04857 CAF1: CAF1 family rib 89.4 0.8 1.7E-05 47.0 6.3 74 288-364 147-261 (262)
96 cd05776 DNA_polB_alpha_exo ina 87.9 0.83 1.8E-05 46.2 5.2 131 212-344 3-188 (234)
97 PF01663 Phosphodiest: Type I 86.9 1.7 3.7E-05 45.1 7.0 67 429-526 177-248 (365)
98 PF10108 DNA_pol_B_exo2: Predi 83.2 5.8 0.00013 40.0 8.5 93 275-369 36-172 (209)
99 PLN02538 2,3-bisphosphoglycera 80.3 5 0.00011 45.8 7.6 81 416-529 401-482 (558)
100 PHA02528 43 DNA polymerase; Pr 79.3 8.1 0.00018 46.6 9.3 151 211-365 105-323 (881)
101 TIGR01307 pgm_bpd_ind 2,3-bisp 77.4 7.3 0.00016 44.1 7.7 81 415-528 361-442 (501)
102 TIGR00592 pol2 DNA polymerase 77.3 14 0.0003 46.1 10.7 100 263-364 572-720 (1172)
103 COG0417 PolB DNA polymerase el 71.9 32 0.0007 41.1 11.6 121 210-343 152-309 (792)
104 PTZ00166 DNA polymerase delta 70.7 14 0.0003 45.6 8.5 145 210-366 262-482 (1054)
105 KOG0969 DNA polymerase delta, 68.8 2.3 5E-05 49.8 1.3 149 210-369 272-479 (1066)
106 PHA02570 dexA exonuclease; Pro 66.3 23 0.00049 36.1 7.5 92 215-306 4-124 (220)
107 PRK05434 phosphoglyceromutase; 65.4 16 0.00035 41.4 7.1 79 416-527 368-447 (507)
108 COG4566 TtrR Response regulato 64.9 11 0.00023 37.8 4.8 26 507-534 71-96 (202)
109 cd06128 DNA_polA_exo DEDDy 3'- 64.3 14 0.0003 34.0 5.3 59 283-342 45-109 (151)
110 PRK05761 DNA polymerase I; Rev 59.6 18 0.00039 43.2 6.4 90 274-363 208-334 (787)
111 TIGR02335 hydr_PhnA phosphonoa 58.9 76 0.0017 35.0 10.7 34 488-524 208-241 (408)
112 KOG4793 Three prime repair exo 53.4 14 0.00031 38.7 3.7 161 212-374 13-222 (318)
113 PRK04024 cofactor-independent 51.2 55 0.0012 36.2 8.0 74 419-527 279-353 (412)
114 PHA02524 43A DNA polymerase su 49.5 62 0.0014 36.8 8.2 129 211-343 105-288 (498)
115 PRK11598 putative metal depend 49.0 37 0.0008 38.9 6.5 129 381-524 305-458 (545)
116 KOG3657 Mitochondrial DNA poly 41.1 23 0.00049 42.3 3.2 31 288-318 239-275 (1075)
117 KOG1798 DNA polymerase epsilon 38.9 1.9E+02 0.0042 37.2 10.4 152 212-368 246-452 (2173)
118 cd05015 SIS_PGI_1 Phosphogluco 38.5 55 0.0012 30.9 5.0 30 503-532 64-94 (158)
119 COG3359 Predicted exonuclease 37.1 1.8E+02 0.0039 30.5 8.5 113 211-345 97-221 (278)
120 PRK09598 lipid A phosphoethano 35.8 79 0.0017 36.1 6.4 130 382-524 293-442 (522)
121 PF07819 PGAP1: PGAP1-like pro 27.8 35 0.00075 34.3 1.7 44 257-300 47-96 (225)
122 PRK11560 phosphoethanolamine t 26.8 1.6E+02 0.0034 34.1 6.9 33 492-524 435-468 (558)
123 TIGR00306 apgM 2,3-bisphosphog 25.4 2.4E+02 0.0053 31.1 7.8 36 490-525 309-345 (396)
124 PF01380 SIS: SIS domain SIS d 24.6 1.2E+02 0.0027 26.5 4.5 32 502-533 44-75 (131)
125 KOG0304 mRNA deadenylase subun 24.4 78 0.0017 32.5 3.4 54 310-366 182-235 (239)
126 KOG0100 Molecular chaperones G 23.0 1.8E+02 0.0038 32.7 6.0 53 511-563 245-307 (663)
127 TIGR03491 RecB family nuclease 22.9 7.2E+02 0.016 27.7 11.0 83 279-369 331-430 (457)
128 KOG4513 Phosphoglycerate mutas 22.6 2.4E+02 0.0053 31.3 6.8 83 413-528 382-465 (531)
129 cd05017 SIS_PGI_PMI_1 The memb 21.4 1.4E+02 0.003 26.6 4.2 27 508-534 40-66 (119)
130 PF01964 ThiC: ThiC family; I 20.4 2.5E+02 0.0055 31.3 6.6 68 497-567 74-158 (420)
131 PRK04200 cofactor-independent 20.3 2.5E+02 0.0055 30.9 6.7 36 490-525 305-343 (395)
132 smart00266 CAD Domains present 20.1 79 0.0017 27.0 2.1 17 505-521 55-71 (74)
133 PF10752 DUF2533: Protein of u 20.1 1.3E+02 0.0027 26.3 3.3 21 545-565 26-46 (84)
No 1
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=7.9e-47 Score=398.56 Aligned_cols=335 Identities=39% Similarity=0.500 Sum_probs=248.6
Q ss_pred CceeEeeeCCCcceEEEEecC-Cc--cchhhHHHHHHHHhcCCCCCceEEeccCCCcceEEEEEecCcChhhhhcccccc
Q 008340 25 GNNFYDIYGPQGKAEVIFKNE-ST--LNLTDVQGLVTWVLADGIMPSWVFIKNKPLIQKVVMLYVPGLDAALYLSQSKTL 101 (569)
Q Consensus 25 ~~~~~~i~g~~ak~ev~f~~~-~~--i~l~dlq~L~l~~~~~~~~P~W~~v~~~~~i~kvVvl~vpGl~~~~~~~~~~~~ 101 (569)
..-+++.+|+-.+.. .+... ++ +..+..+....+..+.+.+|.|..+.+....++...++.+|+..+.+......+
T Consensus 34 ~~~~~~~~~~~~~~~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 112 (380)
T KOG2248|consen 34 LQLFPDLEGALLKTC-SSIAPNSPLCLNSKGREGTRISLVAEGNAPKIVLLSKPELKQKDYLLSFSGLSKAILNLVATNL 112 (380)
T ss_pred ccccccccccccccc-cccccccchhccccccccchhHHHHhccCceeeeeccchhhhhhheeccCCccHHHhhhhhccc
Confidence 678899999988888 66555 44 677778888888889999999999999999999999999999999886554333
Q ss_pred ccccccCCCCcccccccccc-----cccchhhhhhhccccccccccccCCCCCCCCCcCCCCccCCCCchhhhcCCCCCC
Q 008340 102 AGFKECCDKPRALLALSCLS-----DTMLTIDGLLTCKLKRKRNAVDSMTKSTQPSQKENCSTVSENSSSAELLKDIPFP 176 (569)
Q Consensus 102 ~~~~~~~~~p~~~~~~~~~~-----~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 176 (569)
.........+.+-....|.. ....-+. -+.|..+..+........... .+..+ .......
T Consensus 113 ~~~~~~~~~~~~~~~~r~~~~f~~~~~~~~~~-~~l~~~~~~~~~~~~~~~~~~--~~~~~-----------~~~~~~~- 177 (380)
T KOG2248|consen 113 KDVDRSDKALLPRPCSRCGSEFYVTEKGREFK-DLLCKYHPGKLIREPRRGFKD--KTEDC-----------CTPKEGL- 177 (380)
T ss_pred ccccccCccccCchhhhhhhhhccccchhhhh-hhhccccccccccchhccccc--cCchh-----------hcccccC-
Confidence 32222211111000000000 0000011 112322211111100000000 00001 1111112
Q ss_pred cccccCCHHHHhhCCccc-CCCCceeccCCC--CCCCCCcEEEEEeceecCCCCceEEEEEEEEeeCeEEEEEEEecCCC
Q 008340 177 ITYYTLTEKQLEDNNYCY-NQPGFLSTVPAP--FGSSPYEILALDCEMCYTNEGLELTRVTLVDIKGQVLLDKLVKPSNA 253 (569)
Q Consensus 177 ~~~~~l~~~~l~~~~~~~-~~~~~~~t~~~~--~~~~~~~~vAiDcEm~~t~~g~eL~rVsvVd~~G~vv~D~lVkP~~~ 253 (569)
+..+.+..+...+..|+. ...+|+++...+ ..+.+.+++|||||||.+..|.|++||++||.+|+++||+||+|..|
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 222334445555555554 456777776553 23445789999999999999999999999999999999999999999
Q ss_pred CCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcCCCEEEEeCchhhHHHHcccCCCccchhhhccccCCC-CCCchHH
Q 008340 254 IVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKETILVGHSLENDLLALKISHGLVIDTAVLYKHPQGG-SHKTSLR 332 (569)
Q Consensus 254 I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~~tILVGHsL~~DL~aLki~hp~viDT~~L~~~~~g~-~~k~sLk 332 (569)
|+||+|+|||||++|++++++++.|||.+|+++++.+||||||||++||++||+.||.||||+.+|.++.|+ +++.||+
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 999999999999999999999999999999999999999999999999999999999999999999999885 8999999
Q ss_pred HHHHHhcCcccccCCCCCChHHHHHHHHHHHHHHHHcCCCCCC
Q 008340 333 VLAKKFLSREIQQSGFGHDSTEDARAAMELALLKIRNGPDFGS 375 (569)
Q Consensus 333 ~La~~~Lg~~Iq~~~~~HdS~EDA~Atl~L~~~kl~~g~~fg~ 375 (569)
+||+.|||+.||++..||||+|||.|||+|++++++++..||.
T Consensus 338 ~L~~~~L~~~Iq~~~~~HdS~eDA~acm~Lv~~k~~~~~~~g~ 380 (380)
T KOG2248|consen 338 NLAKSYLGKLIQEGVGGHDSVEDALACMKLVKLKIKNSESQGS 380 (380)
T ss_pred HHHHHHHHHHHhccCCCCccHHHHHHHHHHHHHHHhcccccCC
Confidence 9999999999996567899999999999999999999998873
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=1.3e-42 Score=331.85 Aligned_cols=146 Identities=38% Similarity=0.530 Sum_probs=135.0
Q ss_pred EEEEeceecCCC--------C---------ceEEEEEEEE----eeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCC
Q 008340 215 LALDCEMCYTNE--------G---------LELTRVTLVD----IKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVT 273 (569)
Q Consensus 215 vAiDcEm~~t~~--------g---------~eL~rVsvVd----~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~ 273 (569)
|||||||+++++ | .+|+|||+|| ++|+++||+||+|..+|.||+|+|||||+++|++++
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 589999999876 3 2699999999 689999999999999999999999999999999874
Q ss_pred -----CCHHHHHHHHHHhhcCCCEEEEeCchhhHHHHcccCC--CccchhhhccccCCCCCCchHHHHHHHhcCcccccC
Q 008340 274 -----TSLKDIQEEFLKLVYKETILVGHSLENDLLALKISHG--LVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQS 346 (569)
Q Consensus 274 -----~tl~dVq~~l~~ll~~~tILVGHsL~~DL~aLki~hp--~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~ 346 (569)
++++++|+++++++++++|||||+|+|||++|++.|| .+|||+.+|+++.+ +++||++||+.|||++||.
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 79999999998754 5899999999999999997
Q ss_pred CCCCChHHHHHHHHHHHH
Q 008340 347 GFGHDSTEDARAAMELAL 364 (569)
Q Consensus 347 ~~~HdS~EDA~Atl~L~~ 364 (569)
++|||+|||+|||+||+
T Consensus 158 -~~HdSvEDArAam~Ly~ 174 (174)
T cd06143 158 -ETHDSIEDARTALKLYR 174 (174)
T ss_pred -CCcCcHHHHHHHHHHhC
Confidence 69999999999999984
No 3
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=2.5e-39 Score=322.13 Aligned_cols=150 Identities=41% Similarity=0.585 Sum_probs=137.4
Q ss_pred cEEEEEeceecCCCC---ceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcC
Q 008340 213 EILALDCEMCYTNEG---LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYK 289 (569)
Q Consensus 213 ~~vAiDcEm~~t~~g---~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~ 289 (569)
++|||||||+|++++ +.|+||||||..|.||||+||||..+|+||+|++|||+++.|.++ ++|+.||.++.+|| .
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 579999999999999999999999999999999999999999999 79999999999999 8
Q ss_pred CCEEEEeCchhhHHHHcccCC--CccchhhhccccC--CCCCCchHHHHHHHhcCcccccCCCCCChHHHHHHHHHHHHH
Q 008340 290 ETILVGHSLENDLLALKISHG--LVIDTAVLYKHPQ--GGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMELALL 365 (569)
Q Consensus 290 ~tILVGHsL~~DL~aLki~hp--~viDT~~L~~~~~--g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~Atl~L~~~ 365 (569)
+.|||||.|.|||++|++.|| .+.||+..-+..+ .....+||+.|++.+||++||. +-|+|+|||+|||+||..
T Consensus 184 gRIlVGHaLhnDl~~L~l~hp~s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~--GeHsSvEDA~AtM~LY~~ 261 (280)
T KOG2249|consen 184 GRILVGHALHNDLQALKLEHPRSMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQV--GEHSSVEDARATMELYKR 261 (280)
T ss_pred CCEEeccccccHHHHHhhhCchhhhcccccCchHHHHhhccCCccHHHHHHHHhchhhhc--cccCcHHHHHHHHHHHHH
Confidence 899999999999999999999 5999997543322 3456799999999999999998 469999999999999965
Q ss_pred H
Q 008340 366 K 366 (569)
Q Consensus 366 k 366 (569)
.
T Consensus 262 v 262 (280)
T KOG2249|consen 262 V 262 (280)
T ss_pred H
Confidence 3
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=6.9e-36 Score=279.58 Aligned_cols=150 Identities=65% Similarity=0.983 Sum_probs=139.5
Q ss_pred EEEEeceecCCCCceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcCCCEEE
Q 008340 215 LALDCEMCYTNEGLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKETILV 294 (569)
Q Consensus 215 vAiDcEm~~t~~g~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~~tILV 294 (569)
|||||||+|++.|+||++|++|+.+|+++|++||+|..+|++|+|++||||++||+++++++++|++++++|+.++++||
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 58999999999899999999999999999999999999999999999999999999986699999999999996689999
Q ss_pred EeCchhhHHHHcccCCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHHHHHHHHHH
Q 008340 295 GHSLENDLLALKISHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMELAL 364 (569)
Q Consensus 295 GHsL~~DL~aLki~hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~Atl~L~~ 364 (569)
|||+.||+.+|+..|++++||+.|++...+...+++|+.||++|+|+.||...+.|+|++||++|++||+
T Consensus 81 gHn~~fD~~fL~~~~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~~t~~l~~ 150 (150)
T cd06145 81 GHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELVK 150 (150)
T ss_pred EcChHHHHHHhhccCCCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCCCCCcHHHHHHHHHHhC
Confidence 9999999999999999999999999876655567899999999999999853468999999999999973
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=1.9e-33 Score=265.14 Aligned_cols=148 Identities=43% Similarity=0.650 Sum_probs=132.6
Q ss_pred EEEEeceecCCCC---ceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcCCC
Q 008340 215 LALDCEMCYTNEG---LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKET 291 (569)
Q Consensus 215 vAiDcEm~~t~~g---~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~~t 291 (569)
|||||||||++++ .+|++|++|+.+|+++|++||+|..+|++|+|++||||++||+++ ++++++++++++++ +++
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 5899999999875 699999999999999999999999999999999999999999998 79999999999999 899
Q ss_pred EEEEeCchhhHHHHcccCCC--ccchhhhc--ccc--CCCCCCchHHHHHHHhcCcccccCCCCCChHHHHHHHHHHHH
Q 008340 292 ILVGHSLENDLLALKISHGL--VIDTAVLY--KHP--QGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMELAL 364 (569)
Q Consensus 292 ILVGHsL~~DL~aLki~hp~--viDT~~L~--~~~--~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~Atl~L~~ 364 (569)
||||||+.||+++|++.|+. ++||+.++ ++. .+...+++|+.||++|+|..||.+..+|+|++||+||++||+
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 99999999999999999874 89998763 222 112255899999999999999975568999999999999984
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=3.5e-33 Score=263.89 Aligned_cols=150 Identities=44% Similarity=0.671 Sum_probs=134.1
Q ss_pred EEEEeceecCCC-CceEEEEEEEEe-eCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCC------CHHHHHHHHHHh
Q 008340 215 LALDCEMCYTNE-GLELTRVTLVDI-KGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTT------SLKDIQEEFLKL 286 (569)
Q Consensus 215 vAiDcEm~~t~~-g~eL~rVsvVd~-~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~------tl~dVq~~l~~l 286 (569)
|||||||||+++ +++|++|++|+. +|+++|++||+|..+|++|+|++||||++||+++++ ++++++++|+++
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 579999999998 899999999999999999999999999999998731 256999999999
Q ss_pred hcCCCEEEEeCchhhHHHHcccCCCccchhhhccccCCCC---CCchHHHHHHHhcCcccccCCCCCChHHHHHHHHHHH
Q 008340 287 VYKETILVGHSLENDLLALKISHGLVIDTAVLYKHPQGGS---HKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMELA 363 (569)
Q Consensus 287 l~~~tILVGHsL~~DL~aLki~hp~viDT~~L~~~~~g~~---~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~Atl~L~ 363 (569)
+..++||||||+.||+++|++.|+.++||+.|+++..+.. .+++|+.||++|||+++|.+..+|+|++||+||++||
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 9444999999999999999999999999999998765433 4689999999999999986446899999999999998
Q ss_pred H
Q 008340 364 L 364 (569)
Q Consensus 364 ~ 364 (569)
+
T Consensus 161 ~ 161 (161)
T cd06137 161 L 161 (161)
T ss_pred C
Confidence 4
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=2.3e-29 Score=235.55 Aligned_cols=146 Identities=41% Similarity=0.598 Sum_probs=129.4
Q ss_pred EEEEeceecCCCC---ceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcCCC
Q 008340 215 LALDCEMCYTNEG---LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKET 291 (569)
Q Consensus 215 vAiDcEm~~t~~g---~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~~t 291 (569)
|+|||||||+.++ .+|++|++++.+|.++|++||+|..+|+++++++||||++||+++ +++++++++|++++ .++
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--CccchhhhccccCCC-CCCchHHHHHHHhcCcccccCCCCCChHHHHHHHHHHHH
Q 008340 292 ILVGHSLENDLLALKISHG--LVIDTAVLYKHPQGG-SHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMELAL 364 (569)
Q Consensus 292 ILVGHsL~~DL~aLki~hp--~viDT~~L~~~~~g~-~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~Atl~L~~ 364 (569)
+|||||+.||+++|++.++ .++||..+....... ..++||+.||++|||++++. +.|+|++||+||++||+
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 9999999999999998776 588998764432211 35789999999989999874 48999999999999984
No 8
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.90 E-value=6.1e-23 Score=200.70 Aligned_cols=153 Identities=20% Similarity=0.253 Sum_probs=126.8
Q ss_pred CcEEEEEeceecCCCCceEEEEEEEEee-CeE--EEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhc
Q 008340 212 YEILALDCEMCYTNEGLELTRVTLVDIK-GQV--LLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVY 288 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g~eL~rVsvVd~~-G~v--v~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~ 288 (569)
.++++|||||+|....++|++|++|..+ |.+ .|++||+|..+|+.+.+++||||++||+++ +++.+|.++|.+++
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 443 399999999999999999999999999998 79999999999999
Q ss_pred CCCEEEEeCch-hhHHHHccc-----CCCccchhhh-cccc---CCCCCCchHHHHHHHhcCcccccCCCCCChHHHHHH
Q 008340 289 KETILVGHSLE-NDLLALKIS-----HGLVIDTAVL-YKHP---QGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARA 358 (569)
Q Consensus 289 ~~tILVGHsL~-~DL~aLki~-----hp~viDT~~L-~~~~---~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~A 358 (569)
++.+|||||+. ||+.+|+.. .+..+||... +... ......++|..||++ ||++. .+|+|++||++
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 899999852 2356787532 2111 111245789999985 68874 37999999999
Q ss_pred HHHHHHHHHHcCC
Q 008340 359 AMELALLKIRNGP 371 (569)
Q Consensus 359 tl~L~~~kl~~g~ 371 (569)
|+.||+..++.++
T Consensus 158 ta~v~~~ll~~~~ 170 (195)
T PRK07247 158 TARVYESFLESDQ 170 (195)
T ss_pred HHHHHHHHHhhcc
Confidence 9999999888765
No 9
>PRK07740 hypothetical protein; Provisional
Probab=99.89 E-value=3.7e-22 Score=201.27 Aligned_cols=169 Identities=21% Similarity=0.217 Sum_probs=137.9
Q ss_pred CcEEEEEeceecCCCC--ceEEEEEEEEeeCeEE----EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHH
Q 008340 212 YEILALDCEMCYTNEG--LELTRVTLVDIKGQVL----LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLK 285 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g--~eL~rVsvVd~~G~vv----~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ 285 (569)
.++|+|||||+|..+. ++|++|++|..++..+ |+.||+|..+|+++.+++||||+++|+++ +++.+|..+|.+
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 4699999999998864 6999999999866544 77799999999999999999999999998 799999999999
Q ss_pred hhcCCCEEEEeCchhhHHHHccc---------CCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHH
Q 008340 286 LVYKETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDA 356 (569)
Q Consensus 286 ll~~~tILVGHsL~~DL~aLki~---------hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA 356 (569)
++ .+.+|||||+.||+.+|+.. ...++||..+++........++|..||. ++|+++. +.|+|++||
T Consensus 138 fi-~~~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~~-~~gi~~~---~~H~Al~Da 212 (244)
T PRK07740 138 FI-GAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALA-YYGIPIP---RRHHALGDA 212 (244)
T ss_pred Hh-CCCEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHHHH-HCCcCCC---CCCCcHHHH
Confidence 99 78899999999999999731 2369999998875543334678999997 5799886 379999999
Q ss_pred HHHHHHHHHHHHcCCCCCCCCchhHHHHHHHHH
Q 008340 357 RAAMELALLKIRNGPDFGSPPSVMRTKLLKVLF 389 (569)
Q Consensus 357 ~Atl~L~~~kl~~g~~fg~~~~~~~~~l~~~l~ 389 (569)
+||++|+...+..-..-|.. +...|...|+
T Consensus 213 ~ata~l~~~ll~~~~~~~~~---~~~dl~~~~~ 242 (244)
T PRK07740 213 LMTAKLWAILLVEAQQRGIT---TLHDLYAALS 242 (244)
T ss_pred HHHHHHHHHHHHHHHHcCCc---CHHHHHHHHh
Confidence 99999998887664443432 2334444443
No 10
>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=5e-22 Score=183.87 Aligned_cols=143 Identities=24% Similarity=0.347 Sum_probs=121.9
Q ss_pred EEEEEeceecCCCCceEEEEEEEEee-CeEE--EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcCC
Q 008340 214 ILALDCEMCYTNEGLELTRVTLVDIK-GQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKE 290 (569)
Q Consensus 214 ~vAiDcEm~~t~~g~eL~rVsvVd~~-G~vv--~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~~ 290 (569)
+|+|||||++.. ..+|++|++|..+ |+++ ++.||+|..+++.+.+++||||+++|+++ +++.++.++|.+++ .+
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 589999999865 3589999999874 4443 67899999999999999999999999998 68999999999999 67
Q ss_pred CEEEEeCchhhHHHHcc-------c--CCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHHHHHHH
Q 008340 291 TILVGHSLENDLLALKI-------S--HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAME 361 (569)
Q Consensus 291 tILVGHsL~~DL~aLki-------~--hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~Atl~ 361 (569)
.++||||+.||+.+|+. . ...++||..+++...+....++|..|++. +|++.+ .|+|+.||++|++
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 22689999988776444456789999985 688875 7999999999999
Q ss_pred HHH
Q 008340 362 LAL 364 (569)
Q Consensus 362 L~~ 364 (569)
|++
T Consensus 153 l~~ 155 (156)
T cd06130 153 ILL 155 (156)
T ss_pred HHh
Confidence 985
No 11
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.88 E-value=3.8e-22 Score=185.83 Aligned_cols=150 Identities=36% Similarity=0.531 Sum_probs=127.1
Q ss_pred EEEEEeceecCCCC-ceEEEEEEEEeeC---eEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcC
Q 008340 214 ILALDCEMCYTNEG-LELTRVTLVDIKG---QVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYK 289 (569)
Q Consensus 214 ~vAiDcEm~~t~~g-~eL~rVsvVd~~G---~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~ 289 (569)
+|+|||||+|..++ .+|++|++|..++ ...|+.||+|..+|.++.+++||||+++|+++ +++.++.++|.+++ .
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 35599999999999999999999999999997 79999999999999 5
Q ss_pred CCEEEEeCc-hhhHHHHcccC-------C---CccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHHHH
Q 008340 290 ETILVGHSL-ENDLLALKISH-------G---LVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARA 358 (569)
Q Consensus 290 ~tILVGHsL-~~DL~aLki~h-------p---~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~A 358 (569)
+.++||||. .||+.+|+... | .++||..+++...+. ..++|..||+. +|.+... ..|+|++||++
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 567777776 99999999521 1 379999988766543 37899999986 5777653 25999999999
Q ss_pred HHHHHHHHHHc
Q 008340 359 AMELALLKIRN 369 (569)
Q Consensus 359 tl~L~~~kl~~ 369 (569)
|++||+..+++
T Consensus 156 t~~l~~~~~~~ 166 (169)
T smart00479 156 TAKLFKKLVER 166 (169)
T ss_pred HHHHHHHHHHH
Confidence 99999887665
No 12
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.87 E-value=1.6e-21 Score=197.36 Aligned_cols=165 Identities=21% Similarity=0.262 Sum_probs=136.8
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEeeCeEE---EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDIKGQVL---LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~~G~vv---~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll 287 (569)
..+|+|||||+|..+. ++|++|++|..++..+ ++.||+|..+|+.+.+++||||++||+++ +++.+|..++.+++
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 4699999999999865 6899999999865433 77899999999999999999999999999 79999999999999
Q ss_pred cCCCEEEEeCchhhHHHHccc-----------CCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHH
Q 008340 288 YKETILVGHSLENDLLALKIS-----------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDA 356 (569)
Q Consensus 288 ~~~tILVGHsL~~DL~aLki~-----------hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA 356 (569)
.+..+|||||+.||+.+|+.. +..+|||..+++.. +...+++|..|++. +|++.. +.|+|++||
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 656999999999999999731 24689999988754 33345789999986 488765 489999999
Q ss_pred HHHHHHHHHHHHcCCCCCCCCchhHHHHHHHHHh
Q 008340 357 RAAMELALLKIRNGPDFGSPPSVMRTKLLKVLFE 390 (569)
Q Consensus 357 ~Atl~L~~~kl~~g~~fg~~~~~~~~~l~~~l~~ 390 (569)
.||++|++..+++- + ..+++.+.+.+
T Consensus 161 ~at~~vl~~l~~~~---~-----~~~~l~~~~~~ 186 (250)
T PRK06310 161 EINIKVFKHLCKRF---R-----TLEQLKQILSK 186 (250)
T ss_pred HHHHHHHHHHHHhc---c-----cHHHHHHHhhc
Confidence 99999998887652 2 23667776663
No 13
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=99.87 E-value=1e-22 Score=227.51 Aligned_cols=175 Identities=31% Similarity=0.455 Sum_probs=146.3
Q ss_pred CCCcEEEEEeceecCCC--------C---------ceEEEEEEEEee----CeEEEEEEEecCCCCCCCcEeecCCChhh
Q 008340 210 SPYEILALDCEMCYTNE--------G---------LELTRVTLVDIK----GQVLLDKLVKPSNAIVDYNTRYSGITHEM 268 (569)
Q Consensus 210 ~~~~~vAiDcEm~~t~~--------g---------~eL~rVsvVd~~----G~vv~D~lVkP~~~I~dy~T~~SGIT~e~ 268 (569)
.+++.||||-|++.+.. | ..|+|||+|+++ |-..+|.||--++.|+||+|+||||-|.|
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 35689999999998752 2 269999999975 45779999999999999999999999999
Q ss_pred hcCCC-----CCHHHHHHHHHHhhcCCCEEEEeCchhhHHHHcccCC--CccchhhhccccCCCCCCchHHHHHHHhcCc
Q 008340 269 LSGVT-----TSLKDIQEEFLKLVYKETILVGHSLENDLLALKISHG--LVIDTAVLYKHPQGGSHKTSLRVLAKKFLSR 341 (569)
Q Consensus 269 L~~~~-----~tl~dVq~~l~~ll~~~tILVGHsL~~DL~aLki~hp--~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~ 341 (569)
|++.. ++++-++.+++-+++-++|+|||+|++|++++++.-| +||||+.+|... ..+..||++||+++||.
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 LDPTTSEKRLTTLKVLYLKLRLLIQRGVIFVGHGLQNDFRVINIHVPEEQIIDTVTLFRLG--SQRMLSLRFLAWELLGE 1065 (1118)
T ss_pred cCCccCcceehhHHHHHHHHHHHHHcCcEEEcccccccceEEEEecChhhheeeeEEEecc--cccEEEHHHHHHHHhcc
Confidence 99743 6899999999999999999999999999999998654 799999999865 34678999999999999
Q ss_pred ccccCCCCCChHHHHHHHHHHHHHHHHcCCCCCCCCchhHHHHHHHHHhcCCe
Q 008340 342 EIQQSGFGHDSTEDARAAMELALLKIRNGPDFGSPPSVMRTKLLKVLFEYGKT 394 (569)
Q Consensus 342 ~Iq~~~~~HdS~EDA~Atl~L~~~kl~~g~~fg~~~~~~~~~l~~~l~~~g~~ 394 (569)
+||. ..|||+|||++|+.||+..++-..+ ..+++.++-+.+.|+.
T Consensus 1066 ~IQ~--~~HDSIeDA~taLkLYk~Yl~lkeq------~~~~~~l~niye~gr~ 1110 (1118)
T KOG1275|consen 1066 TIQM--EAHDSIEDARTALKLYKKYLKLKEQ------GKLESELRNIYECGRP 1110 (1118)
T ss_pred hhhc--cccccHHHHHHHHHHHHHHHHHHHh------hHHHHHHHHHhhcCcc
Confidence 9997 5999999999999999876553110 1244555566666653
No 14
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.87 E-value=1.3e-21 Score=195.54 Aligned_cols=153 Identities=16% Similarity=0.178 Sum_probs=130.5
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcCC
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKE 290 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~~ 290 (569)
.++++||+||||.... ++|++|++++......|+.||+|..+|+...+++||||++||+++ +++.+|.+++.+++.++
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 3589999999999865 699999999865556799999999999999999999999999999 69999999999999767
Q ss_pred CEEEEeC-chhhHHHHccc---------CCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHHHHHH
Q 008340 291 TILVGHS-LENDLLALKIS---------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAM 360 (569)
Q Consensus 291 tILVGHs-L~~DL~aLki~---------hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~Atl 360 (569)
.+||||| ..||+.+|+-. ...++||..+++..++...+++|..|++.| |++.. .+|+|++||.+|+
T Consensus 81 ~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~~~~L~~l~~~~-~~~~~---~aH~Al~Da~~t~ 156 (232)
T PRK06309 81 NILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLRQVY-GFEEN---QAHRALDDVITLH 156 (232)
T ss_pred CEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCCCCCHHHHHHHc-CCCCC---CCCCcHHHHHHHH
Confidence 8999999 58999999731 126899999887654433457899999865 77754 4899999999999
Q ss_pred HHHHHHHHc
Q 008340 361 ELALLKIRN 369 (569)
Q Consensus 361 ~L~~~kl~~ 369 (569)
+|++..+++
T Consensus 157 ~vl~~l~~~ 165 (232)
T PRK06309 157 RVFSALVGD 165 (232)
T ss_pred HHHHHHHHH
Confidence 999887764
No 15
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.87 E-value=1.9e-21 Score=195.76 Aligned_cols=158 Identities=20% Similarity=0.287 Sum_probs=129.7
Q ss_pred CcEEEEEeceecCCC--CceEEEEEEEEee-CeE---EEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHH
Q 008340 212 YEILALDCEMCYTNE--GLELTRVTLVDIK-GQV---LLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLK 285 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~--g~eL~rVsvVd~~-G~v---v~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ 285 (569)
.++++||+||+|..+ +++|++|++|... +.+ -|+.||+|..+|+...+++||||++||+++ ++|++|..+|.+
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 469999999999985 5789999998863 332 378999999999999999999999999998 799999999999
Q ss_pred hhcCCCEEEEeCchhhHHHHccc-------------CCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCCh
Q 008340 286 LVYKETILVGHSLENDLLALKIS-------------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDS 352 (569)
Q Consensus 286 ll~~~tILVGHsL~~DL~aLki~-------------hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS 352 (569)
|+ .+.+|||||+.||+.+|+.. ...++||..+++...+ ..+++|..||++| |++... ...|+|
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-GKRNSLDALCKRY-GIDNSH-RTLHGA 158 (240)
T ss_pred Hh-CCCEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcC-CCCCCHHHHHHHC-CCCCCC-CCCCCH
Confidence 99 88899999999999999731 1258999988766532 2457899999965 876432 246999
Q ss_pred HHHHHHHHHHHHHHHHcCCCCC
Q 008340 353 TEDARAAMELALLKIRNGPDFG 374 (569)
Q Consensus 353 ~EDA~Atl~L~~~kl~~g~~fg 374 (569)
+.||.++++||+..+.....|+
T Consensus 159 L~DA~~~A~v~~~l~~~~~~l~ 180 (240)
T PRK05711 159 LLDAEILAEVYLAMTGGQTSLG 180 (240)
T ss_pred HHHHHHHHHHHHHHHCcccccc
Confidence 9999999999988765544443
No 16
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.87 E-value=2.1e-21 Score=202.32 Aligned_cols=154 Identities=21% Similarity=0.291 Sum_probs=130.5
Q ss_pred CCCcEEEEEeceecCCCC-ceEEEEEEEEee-CeEE--EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHH
Q 008340 210 SPYEILALDCEMCYTNEG-LELTRVTLVDIK-GQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLK 285 (569)
Q Consensus 210 ~~~~~vAiDcEm~~t~~g-~eL~rVsvVd~~-G~vv--~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ 285 (569)
-|.++|+||+||+|..+. .+|++|++|..+ |+++ |+.||+|..+|+.+.+++||||++||+++ +++.+|+++|.+
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 78899999999999999999999999998 699999999999
Q ss_pred hhcCCCEEEEeCchhhHHHHccc-------C--CCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHH
Q 008340 286 LVYKETILVGHSLENDLLALKIS-------H--GLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDA 356 (569)
Q Consensus 286 ll~~~tILVGHsL~~DL~aLki~-------h--p~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA 356 (569)
++ .+.+|||||+.||+.+|+-. . ..++||..+++...+....++|..||+ +||++. . +|+|+.||
T Consensus 85 fl-~~~~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~~~kL~~L~~-~lgi~~-~---~H~Al~DA 158 (313)
T PRK06807 85 FL-HTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKR-MLGIRL-S---SHNAFDDC 158 (313)
T ss_pred HH-cCCeEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCCCCCHHHHHH-HcCCCC-C---CcChHHHH
Confidence 99 78899999999999999831 2 258999988765443334568999997 569887 3 89999999
Q ss_pred HHHHHHHHHHHHcC
Q 008340 357 RAAMELALLKIRNG 370 (569)
Q Consensus 357 ~Atl~L~~~kl~~g 370 (569)
++|++||+.++...
T Consensus 159 ~~ta~l~~~l~~~~ 172 (313)
T PRK06807 159 ITCAAVYQKCASIE 172 (313)
T ss_pred HHHHHHHHHHHHhh
Confidence 99999998777653
No 17
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.87 E-value=2.9e-21 Score=188.76 Aligned_cols=151 Identities=25% Similarity=0.324 Sum_probs=125.1
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEeeCe-EE----EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHH
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDIKGQ-VL----LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLK 285 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~~G~-vv----~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ 285 (569)
.++|+|||||+|+.+. ++|++|++|..++. ++ |+.||+|..+|..+.+++||||++||+++ +++.+|.++|.+
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 4699999999999865 79999999998654 32 67899999999999999999999999998 799999999999
Q ss_pred hhcCCCEEEEeCchhhHHHHccc---------CCCccchhhhcccc-----CCCCCCchHHHHHHHhcCcccccCCCCCC
Q 008340 286 LVYKETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHP-----QGGSHKTSLRVLAKKFLSREIQQSGFGHD 351 (569)
Q Consensus 286 ll~~~tILVGHsL~~DL~aLki~---------hp~viDT~~L~~~~-----~g~~~k~sLk~La~~~Lg~~Iq~~~~~Hd 351 (569)
++ .+.+|||||+.||+.+|+.. +..++||+.+|... .+...+++|..||+. +|++.. +.|+
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 12588998776421 111235789999985 588764 4799
Q ss_pred hHHHHHHHHHHHHHHHH
Q 008340 352 STEDARAAMELALLKIR 368 (569)
Q Consensus 352 S~EDA~Atl~L~~~kl~ 368 (569)
|++||+||++||+..++
T Consensus 183 Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 183 ALNDAIMAALIFLRLRK 199 (202)
T ss_pred cHHHHHHHHHHHHHHHh
Confidence 99999999999975543
No 18
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.86 E-value=3.1e-21 Score=194.08 Aligned_cols=153 Identities=23% Similarity=0.193 Sum_probs=128.0
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEeeCe-E----EEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHH
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDIKGQ-V----LLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLK 285 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~~G~-v----v~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ 285 (569)
..+++||+||+|..+. ++|++|++|..++. + .+..||+|+.+|+...+++||||++||+++ +++.+|..+|.+
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 79999999997543 2 367899999999999999999999999998 799999999999
Q ss_pred hhcCCCEEEEeCchhhHHHHccc---------CCCccchhhhccccCCC-------------CCCchHHHHHHHhcCccc
Q 008340 286 LVYKETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQGG-------------SHKTSLRVLAKKFLSREI 343 (569)
Q Consensus 286 ll~~~tILVGHsL~~DL~aLki~---------hp~viDT~~L~~~~~g~-------------~~k~sLk~La~~~Lg~~I 343 (569)
++ .+.+|||||+.||+.+|+.. ...++||..++++.... ...++|..||+. +|++.
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 78999999999999999741 13689999987653110 134579999996 58775
Q ss_pred ccCCCCCChHHHHHHHHHHHHHHHHcC
Q 008340 344 QQSGFGHDSTEDARAAMELALLKIRNG 370 (569)
Q Consensus 344 q~~~~~HdS~EDA~Atl~L~~~kl~~g 370 (569)
. ..|+|++||.||++|++..+.+.
T Consensus 204 ~---~~H~Al~DA~ata~l~~~~~~~~ 227 (239)
T PRK09146 204 Y---SPHHALTDAIATAELLQAQIAHH 227 (239)
T ss_pred C---CCCCcHHHHHHHHHHHHHHHHHH
Confidence 4 48999999999999999887664
No 19
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.86 E-value=7.4e-21 Score=198.29 Aligned_cols=152 Identities=24% Similarity=0.283 Sum_probs=127.5
Q ss_pred CCcEEEEEeceecCCCC-ceEEEEEEEEe--eCeEE--EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHH
Q 008340 211 PYEILALDCEMCYTNEG-LELTRVTLVDI--KGQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLK 285 (569)
Q Consensus 211 ~~~~vAiDcEm~~t~~g-~eL~rVsvVd~--~G~vv--~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ 285 (569)
+.+|++||+||+|..++ ++|++|++|.. +|+++ |.+||+|.. ....+++||||++||+++ ++|.++.++|.+
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 79999999975 46655 889999975 356799999999999999 699999999999
Q ss_pred hhcCCCEEEEeCchhhHHHHccc---------CCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHH
Q 008340 286 LVYKETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDA 356 (569)
Q Consensus 286 ll~~~tILVGHsL~~DL~aLki~---------hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA 356 (569)
++ .+.+|||||+.||+.+|+-. ...++||..+++.......+++|..||++ +|++.. ..|+|++||
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 88999999999999999831 12589999988765333356789999985 688754 489999999
Q ss_pred HHHHHHHHHHHHcC
Q 008340 357 RAAMELALLKIRNG 370 (569)
Q Consensus 357 ~Atl~L~~~kl~~g 370 (569)
+||++|+...+++-
T Consensus 166 ~ata~l~~~ll~~~ 179 (313)
T PRK06063 166 RVLAGILRPSLERA 179 (313)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999998776653
No 20
>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=99.86 E-value=3.8e-21 Score=191.74 Aligned_cols=151 Identities=23% Similarity=0.278 Sum_probs=125.5
Q ss_pred cEEEEEeceecCCCC--ceEEEEEEEEee-CeE---EEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHh
Q 008340 213 EILALDCEMCYTNEG--LELTRVTLVDIK-GQV---LLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKL 286 (569)
Q Consensus 213 ~~vAiDcEm~~t~~g--~eL~rVsvVd~~-G~v---v~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~l 286 (569)
++++||+||+|..+. ++|++|++|... +.. -|+.||+|..+|+.+.+++||||++||+++ ++|++|..+|.++
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 689999988653 222 389999999999999999999999999999 7999999999999
Q ss_pred hcCCCEEEEeCchhhHHHHccc-----------C--CCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChH
Q 008340 287 VYKETILVGHSLENDLLALKIS-----------H--GLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDST 353 (569)
Q Consensus 287 l~~~tILVGHsL~~DL~aLki~-----------h--p~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~ 353 (569)
+ .+.+|||||+.||+.+|+.. + ..++||..+++...+ ..+++|..||++| |++... ...|+|+
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-GQRNSLDALCKRF-KVDNSH-RTLHGAL 155 (225)
T ss_pred h-CCCEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcC-CCCCCHHHHHHhc-CCCCCC-CCCcCHH
Confidence 9 78899999999999999831 1 258999998876532 3467999999965 877542 2479999
Q ss_pred HHHHHHHHHHHHHHH
Q 008340 354 EDARAAMELALLKIR 368 (569)
Q Consensus 354 EDA~Atl~L~~~kl~ 368 (569)
.||+++++||+....
T Consensus 156 ~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 156 LDAHLLAEVYLALTG 170 (225)
T ss_pred HHHHHHHHHHHHHHc
Confidence 999999999976644
No 21
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.86 E-value=5.3e-21 Score=191.36 Aligned_cols=184 Identities=22% Similarity=0.275 Sum_probs=138.7
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEee--CeEE--EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHh
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDIK--GQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKL 286 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~~--G~vv--~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~l 286 (569)
.++++||+||+|..+. .+|++|++|..+ |.++ +..||+|..+|+.+.+++||||++||...+++++++..++..+
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 4699999999999865 689999998765 7655 7889999999999999999999999987556777777777766
Q ss_pred h----cCCCEEEEeCchhhHHHHccc---C-------CCccchhhhccccCC-CCCCchHHHHHHHhcCcccccCCCCCC
Q 008340 287 V----YKETILVGHSLENDLLALKIS---H-------GLVIDTAVLYKHPQG-GSHKTSLRVLAKKFLSREIQQSGFGHD 351 (569)
Q Consensus 287 l----~~~tILVGHsL~~DL~aLki~---h-------p~viDT~~L~~~~~g-~~~k~sLk~La~~~Lg~~Iq~~~~~Hd 351 (569)
| ..+.+|||||+.||+.+|+.. | ..++||..|.+.... ...+++|..||++ +|++.. +.|+
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 368899999999999999741 1 247899987654311 1235689999986 588865 4899
Q ss_pred hHHHHHHHHHHHHHHHHcCCCCCCCCch------------hHHHHHHHHHhcCCeeeeec
Q 008340 352 STEDARAAMELALLKIRNGPDFGSPPSV------------MRTKLLKVLFEYGKTSTLID 399 (569)
Q Consensus 352 S~EDA~Atl~L~~~kl~~g~~fg~~~~~------------~~~~l~~~l~~~g~~~~~~d 399 (569)
|++||+||++|++..+++-+..+..... ...++.+.|.+.|+....++
T Consensus 162 Al~Da~ata~l~~~l~~~~~~l~~~~~~~l~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (232)
T PRK07942 162 ATADALAAARVAWALARRFPELAALSPAELHELQAVWYAEQAASFQAYLRRKGRPAAVVD 221 (232)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCccC
Confidence 9999999999998887765544433211 11245555666666554444
No 22
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.86 E-value=5.6e-21 Score=189.98 Aligned_cols=147 Identities=22% Similarity=0.245 Sum_probs=123.0
Q ss_pred EEEEEeceecCCCCceEEEEEEEEe-eCeEE--EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcCC
Q 008340 214 ILALDCEMCYTNEGLELTRVTLVDI-KGQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKE 290 (569)
Q Consensus 214 ~vAiDcEm~~t~~g~eL~rVsvVd~-~G~vv--~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~~ 290 (569)
+++||+||+|...+ |++|++|+. +|+++ |++||+|..+|+.+.+++||||++||+++ +++.+|..+ ++ .+
T Consensus 2 ~~vlD~ETTGl~~~--IieIg~v~v~~~~i~~~~~~lv~P~~~i~~~~~~ihgIt~e~v~~a-p~~~ev~~~---~~-~~ 74 (219)
T PRK07983 2 LRVIDTETCGLQGG--IVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADK-PWIEDVIPH---YY-GS 74 (219)
T ss_pred eEEEEEECCCCCCC--CEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHcCC-CCHHHHHHH---Hc-CC
Confidence 68999999998643 788887775 45655 89999999999999999999999999999 689998776 45 78
Q ss_pred CEEEEeCchhhHHHHcccCCCccchhhhccccCCCCCCchHHHHHHHhcCcccc--cCCCCCChHHHHHHHHHHHHHHHH
Q 008340 291 TILVGHSLENDLLALKISHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQ--QSGFGHDSTEDARAAMELALLKIR 368 (569)
Q Consensus 291 tILVGHsL~~DL~aLki~hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq--~~~~~HdS~EDA~Atl~L~~~kl~ 368 (569)
.+|||||+.||+++|+.....++||..+++...+. .+++|..||+. +|++.. ....+|+|+.||.+|++||+..++
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 89999999999999987777899999998765433 45889999985 587653 123589999999999999988876
Q ss_pred c
Q 008340 369 N 369 (569)
Q Consensus 369 ~ 369 (569)
+
T Consensus 153 ~ 153 (219)
T PRK07983 153 T 153 (219)
T ss_pred H
Confidence 5
No 23
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.85 E-value=9.8e-21 Score=196.86 Aligned_cols=150 Identities=20% Similarity=0.254 Sum_probs=125.7
Q ss_pred cEEEEEeceecCCCCceEEEEEEEEe-eCeEE--EEEEEecCC-CCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhc
Q 008340 213 EILALDCEMCYTNEGLELTRVTLVDI-KGQVL--LDKLVKPSN-AIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVY 288 (569)
Q Consensus 213 ~~vAiDcEm~~t~~g~eL~rVsvVd~-~G~vv--~D~lVkP~~-~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~ 288 (569)
+|++||+||++. ..++|++|++|.. +|+++ +++||+|.. .+..+.+++||||++||+++ ++|.+|.++|.+++
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 589999999964 3468999999986 45555 789999985 57888999999999999998 69999999999999
Q ss_pred CCCEEEEeCchhhHHHHccc---------CCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHHHHH
Q 008340 289 KETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAA 359 (569)
Q Consensus 289 ~~tILVGHsL~~DL~aLki~---------hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~At 359 (569)
.+.+|||||+.||+.+|+.. +..++||..+++...+....++|..||+. +|++. ..|+|++||+||
T Consensus 79 ~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~~L~~L~~~-~gi~~----~~H~Al~DA~at 153 (309)
T PRK06195 79 NNNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNF-LGYEF----KHHDALADAMAC 153 (309)
T ss_pred CCCEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcCCHHHHHHH-cCCCC----cccCCHHHHHHH
Confidence 78999999999999999731 23689999888765433346789999986 58875 379999999999
Q ss_pred HHHHHHHHHcC
Q 008340 360 MELALLKIRNG 370 (569)
Q Consensus 360 l~L~~~kl~~g 370 (569)
++||...+++-
T Consensus 154 a~l~~~l~~~~ 164 (309)
T PRK06195 154 SNILLNISKEL 164 (309)
T ss_pred HHHHHHHHHHh
Confidence 99998887763
No 24
>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=8.4e-21 Score=187.79 Aligned_cols=159 Identities=22% Similarity=0.252 Sum_probs=128.9
Q ss_pred CcEEEEEeceecCCCCceEEEEEEEE-eeCe-E--EEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008340 212 YEILALDCEMCYTNEGLELTRVTLVD-IKGQ-V--LLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g~eL~rVsvVd-~~G~-v--v~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll 287 (569)
..||+||+||+|..++..|++|++|. .+|. + .|..||+|..+|+.+.+++||||++||+++ +++.+|.++|.+++
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 46999999999998764499999888 4443 2 478999999999999999999999999998 79999999999999
Q ss_pred cCCCEEEEeCchhhHHHHccc----------CCCccchhhhccccC--CCCCCchHHHHHHHhcCcccccCCCCCChHHH
Q 008340 288 YKETILVGHSLENDLLALKIS----------HGLVIDTAVLYKHPQ--GGSHKTSLRVLAKKFLSREIQQSGFGHDSTED 355 (569)
Q Consensus 288 ~~~tILVGHsL~~DL~aLki~----------hp~viDT~~L~~~~~--g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~ED 355 (569)
++.++||||+.||+.+|+.. ...++||..+++..+ .+..+++|..|++. +|.+... ...|||+.|
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 125788876554321 12356789999986 5876542 147999999
Q ss_pred HHHHHHHHHHHHHcCCCCC
Q 008340 356 ARAAMELALLKIRNGPDFG 374 (569)
Q Consensus 356 A~Atl~L~~~kl~~g~~fg 374 (569)
|++|++|++..+.+.+..+
T Consensus 163 A~~ta~l~~~l~~~~~~~~ 181 (217)
T TIGR00573 163 AFILAKLYLVMTGKQTKYG 181 (217)
T ss_pred HHHHHHHHHHHHhcchhhc
Confidence 9999999998888765544
No 25
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.85 E-value=2.7e-20 Score=189.24 Aligned_cols=183 Identities=22% Similarity=0.273 Sum_probs=142.9
Q ss_pred cCCHHHHhhCCccc--CCCCceeccCCCCCCCCCcEEEEEeceecCCCC-ceEEEEEEEEe-eCeEE--EEEEEecCCCC
Q 008340 181 TLTEKQLEDNNYCY--NQPGFLSTVPAPFGSSPYEILALDCEMCYTNEG-LELTRVTLVDI-KGQVL--LDKLVKPSNAI 254 (569)
Q Consensus 181 ~l~~~~l~~~~~~~--~~~~~~~t~~~~~~~~~~~~vAiDcEm~~t~~g-~eL~rVsvVd~-~G~vv--~D~lVkP~~~I 254 (569)
....+-+...|+|+ ...+.+........-....++++|+||+|..++ .+|++|++|.. +|+++ |..||+|. +|
T Consensus 35 ~~~~~~~~~~g~~~~~~~~~~~~l~~~~~~~~~~~~vv~DiETTG~~~~~~~IIEIGAv~v~~g~i~~~f~~~v~p~-~i 113 (257)
T PRK08517 35 DIDLELLKALGLPLVENKENLITLKTRFTPIKDQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAK-EV 113 (257)
T ss_pred HHHHHHHHHCCCceEEcCCCeEEeccCCCCCCCCCEEEEEEeCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCC-CC
Confidence 34455667788887 223322211111112235799999999999876 49999999997 45554 77899997 89
Q ss_pred CCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcCCCEEEEeCchhhHHHHcc---------cCCCccchhhhccccCCC
Q 008340 255 VDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKETILVGHSLENDLLALKI---------SHGLVIDTAVLYKHPQGG 325 (569)
Q Consensus 255 ~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~~tILVGHsL~~DL~aLki---------~hp~viDT~~L~~~~~g~ 325 (569)
+.+.+++||||++||+++ +++.+|.++|..++ .+.++||||+.||+.+|+. .++..+||..+++... +
T Consensus 114 p~~~~~itGIt~e~l~~a-p~~~evl~~f~~fl-~~~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~-~ 190 (257)
T PRK08517 114 PEYITELTGITYEDLENA-PSLKEVLEEFRLFL-GDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTI-E 190 (257)
T ss_pred ChhhhhhcCcCHHHHcCC-CCHHHHHHHHHHHH-CCCeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHc-c
Confidence 999999999999999998 79999999999999 7899999999999999973 1346789998876542 2
Q ss_pred CCCchHHHHHHHhcCcccccCCCCCChHHHHHHHHHHHHHHHHcCC
Q 008340 326 SHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMELALLKIRNGP 371 (569)
Q Consensus 326 ~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~Atl~L~~~kl~~g~ 371 (569)
..+++|..|++ ++|++.. ..|+|+.||.||++|+..++.+-+
T Consensus 191 ~~~~~L~~L~~-~lgi~~~---~~HrAl~DA~ata~ll~~ll~~~~ 232 (257)
T PRK08517 191 SPRYGLSFLKE-LLGIEIE---VHHRAYADALAAYEIFKICLLNLP 232 (257)
T ss_pred CCCCCHHHHHH-HcCcCCC---CCCChHHHHHHHHHHHHHHHHHhH
Confidence 35678999998 5798865 489999999999999999887754
No 26
>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=99.85 E-value=1.3e-20 Score=177.22 Aligned_cols=147 Identities=24% Similarity=0.304 Sum_probs=121.4
Q ss_pred EEEEEeceecCCC--CceEEEEEEEEee-CeE---EEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008340 214 ILALDCEMCYTNE--GLELTRVTLVDIK-GQV---LLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (569)
Q Consensus 214 ~vAiDcEm~~t~~--g~eL~rVsvVd~~-G~v---v~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll 287 (569)
+++||+||+|..+ +.+|++|++|... |.+ -|+.||+|..+|+.+.+++||||++||+++ +++.+|.++|.+++
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 5899999999986 3689999988753 332 478899999999999999999999999998 68999999999999
Q ss_pred cCCCEEEEeCchhhHHHHccc-----------C-CCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHH
Q 008340 288 YKETILVGHSLENDLLALKIS-----------H-GLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTED 355 (569)
Q Consensus 288 ~~~tILVGHsL~~DL~aLki~-----------h-p~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~ED 355 (569)
.+.++||||+.||+.+|+-. . ..++||..+++...+ ...++|..||++ +|++... ...|+|+.|
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 1 257999988765432 245689999986 5877542 247999999
Q ss_pred HHHHHHHHHH
Q 008340 356 ARAAMELALL 365 (569)
Q Consensus 356 A~Atl~L~~~ 365 (569)
|++|++||+.
T Consensus 156 a~~~a~l~~~ 165 (167)
T cd06131 156 AELLAEVYLE 165 (167)
T ss_pred HHHHHHHHHH
Confidence 9999999964
No 27
>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=4.9e-21 Score=183.88 Aligned_cols=143 Identities=23% Similarity=0.287 Sum_probs=116.3
Q ss_pred EEEEEeceecCC-C-CceEEEEEEEEeeCe--------------E--EEEEEEecCCCCCCCcEeecCCChhhhcCCCCC
Q 008340 214 ILALDCEMCYTN-E-GLELTRVTLVDIKGQ--------------V--LLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTS 275 (569)
Q Consensus 214 ~vAiDcEm~~t~-~-g~eL~rVsvVd~~G~--------------v--v~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~t 275 (569)
|++||+||+|+. . .++|++|++|...+. + -|+.||+|..+|+...+++||||++||.+++ +
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a~~IhGIt~e~l~~~~-~ 79 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHKA-P 79 (177)
T ss_pred CeEEeeecCCCCCCCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCCcCChhHHHHhCcCHHHHhcCC-C
Confidence 589999999998 3 479999999986432 1 2788999999999999999999999999984 5
Q ss_pred HH-HHHHHHHHhh---cCCCEEEEeCc-hhhHHHHccc----------CCCccchhhhccccCCCCCCchHHHHHHHhcC
Q 008340 276 LK-DIQEEFLKLV---YKETILVGHSL-ENDLLALKIS----------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLS 340 (569)
Q Consensus 276 l~-dVq~~l~~ll---~~~tILVGHsL-~~DL~aLki~----------hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg 340 (569)
+. ++.+.|.+|+ +++.+|||||+ .||+.+|+-. ...++||..+++... ++|..||++++|
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 54 4666666665 34579999998 8999999731 135789999998652 189999998789
Q ss_pred cccccCCCCCChHHHHHHHHHHHHH
Q 008340 341 REIQQSGFGHDSTEDARAAMELALL 365 (569)
Q Consensus 341 ~~Iq~~~~~HdS~EDA~Atl~L~~~ 365 (569)
++.. +.|+|+.||.||+++++.
T Consensus 155 ~~~~---~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 155 QEPK---NSHTAEGDVLALLKCALH 176 (177)
T ss_pred CCcc---cccchHHHHHHHHHHHhh
Confidence 8876 489999999999999875
No 28
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.84 E-value=2e-20 Score=216.59 Aligned_cols=158 Identities=22% Similarity=0.275 Sum_probs=133.5
Q ss_pred CCcEEEEEeceecCCCCceEEEEEEEEee-CeEE--EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008340 211 PYEILALDCEMCYTNEGLELTRVTLVDIK-GQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (569)
Q Consensus 211 ~~~~vAiDcEm~~t~~g~eL~rVsvVd~~-G~vv--~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll 287 (569)
..++++||+||+|..+.++|++|++|... |+++ |.+||+|..+|+++++++||||++||+++ +++++|..+|.+++
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 35799999999999877899999999974 5544 77889999999999999999999999998 79999999999999
Q ss_pred cCCCEEEEeCchhhHHHHccc--------CCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHHHHH
Q 008340 288 YKETILVGHSLENDLLALKIS--------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAA 359 (569)
Q Consensus 288 ~~~tILVGHsL~~DL~aLki~--------hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~At 359 (569)
.++++||||+.||+.+|+.. ...++||..+++...+...+++|..||+. ||++.. ..|+|++||+||
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 88999999999999999741 12579999887654433346889999985 688865 489999999999
Q ss_pred HHHHHHHHHcCCCCC
Q 008340 360 MELALLKIRNGPDFG 374 (569)
Q Consensus 360 l~L~~~kl~~g~~fg 374 (569)
++|+...+++-...+
T Consensus 160 a~L~~~l~~~l~~l~ 174 (820)
T PRK07246 160 AELFLKLLQKIESLP 174 (820)
T ss_pred HHHHHHHHHHHhhcC
Confidence 999988877654433
No 29
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.84 E-value=1.8e-20 Score=183.98 Aligned_cols=160 Identities=20% Similarity=0.204 Sum_probs=126.0
Q ss_pred CcEEEEEeceecCCCC-------ceEEEEEEEEee-CeEE--EEEEEecCC--CCCCCcEeecCCChhhhcCCCCCHHHH
Q 008340 212 YEILALDCEMCYTNEG-------LELTRVTLVDIK-GQVL--LDKLVKPSN--AIVDYNTRYSGITHEMLSGVTTSLKDI 279 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-------~eL~rVsvVd~~-G~vv--~D~lVkP~~--~I~dy~T~~SGIT~e~L~~~~~tl~dV 279 (569)
.+|++||+||++...+ .||++|++|..+ |+++ |++||+|.. +|+.+.+++||||++||+++ +++.+|
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 589999999864 4443 889999987 79999999999999999998 799999
Q ss_pred HHHHHHhhcCCCEEEEeCchhhHHHHccc-------CC---CccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCC
Q 008340 280 QEEFLKLVYKETILVGHSLENDLLALKIS-------HG---LVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFG 349 (569)
Q Consensus 280 q~~l~~ll~~~tILVGHsL~~DL~aLki~-------hp---~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~ 349 (569)
.++|.+++.....+|.|+..||+.+|+.. .| .++|+..+|+...+....++|..+++. +|++... ..
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 12 578888877655444445789999985 5887532 47
Q ss_pred CChHHHHHHHHHHHHHHHHcCCCCCC
Q 008340 350 HDSTEDARAAMELALLKIRNGPDFGS 375 (569)
Q Consensus 350 HdS~EDA~Atl~L~~~kl~~g~~fg~ 375 (569)
|+|+.||++|++|++..++++..++.
T Consensus 160 H~Al~DA~~ta~l~~~l~~~~~~~~~ 185 (207)
T PRK07748 160 HCALDDAMTTYNIFKLVEKDKEYLVK 185 (207)
T ss_pred cChHHHHHHHHHHHHHHHhCcceeec
Confidence 99999999999999988887654444
No 30
>PRK07883 hypothetical protein; Validated
Probab=99.83 E-value=9.8e-20 Score=202.90 Aligned_cols=159 Identities=23% Similarity=0.351 Sum_probs=135.5
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEee-CeEE--EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDIK-GQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~~-G~vv--~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll 287 (569)
..+|+||+||+|..+. .+|++|++|..+ |+++ |+.||+|..+|+.+.+++||||.+||+++ ++++++..+|.+++
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 799999999974 5555 88899999999999999999999999998 79999999999999
Q ss_pred cCCCEEEEeCchhhHHHHccc-------C--CCccchhhhccccCC--CCCCchHHHHHHHhcCcccccCCCCCChHHHH
Q 008340 288 YKETILVGHSLENDLLALKIS-------H--GLVIDTAVLYKHPQG--GSHKTSLRVLAKKFLSREIQQSGFGHDSTEDA 356 (569)
Q Consensus 288 ~~~tILVGHsL~~DL~aLki~-------h--p~viDT~~L~~~~~g--~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA 356 (569)
.+.+|||||+.||+.+|+.. . ..++||..+++.... ...+++|..||+ ++|+++. +.|+|+.||
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 1 258999988765432 335678999998 5799875 489999999
Q ss_pred HHHHHHHHHHHHcCCCCCCC
Q 008340 357 RAAMELALLKIRNGPDFGSP 376 (569)
Q Consensus 357 ~Atl~L~~~kl~~g~~fg~~ 376 (569)
+||++|+...+.+-...|..
T Consensus 169 ~ata~l~~~l~~~~~~~~~~ 188 (557)
T PRK07883 169 RATVDVLHGLIERLGNLGVH 188 (557)
T ss_pred HHHHHHHHHHHHHHHhcCCC
Confidence 99999999888876655543
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=99.82 E-value=1.3e-19 Score=164.83 Aligned_cols=144 Identities=26% Similarity=0.317 Sum_probs=122.7
Q ss_pred EEEEeceecCCC-CceEEEEEEEEeeCe----EEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcC
Q 008340 215 LALDCEMCYTNE-GLELTRVTLVDIKGQ----VLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYK 289 (569)
Q Consensus 215 vAiDcEm~~t~~-g~eL~rVsvVd~~G~----vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~ 289 (569)
|++||||+|..+ ..+|++|++|..++. ..++.||+|...+..+.++++|||++++++. +++.++..+|.+++ .
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 479999999998643 4489999999999999999999999999988 79999999999999 5
Q ss_pred CCEEEEeCchhhHHHHccc---------CCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHHHHHH
Q 008340 290 ETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAM 360 (569)
Q Consensus 290 ~tILVGHsL~~DL~aLki~---------hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~Atl 360 (569)
+.++||||..||+.+|+.. +..++||..+++...+....++|+.+...++|.+.. ..|+|++||++++
T Consensus 79 ~~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~~---~~H~Al~Da~~t~ 155 (159)
T cd06127 79 GRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLE---GAHRALADALATA 155 (159)
T ss_pred CCEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCCC---CCCCcHHHHHHHH
Confidence 5999999999999999842 347899999987765555667899983335677654 5899999999999
Q ss_pred HHH
Q 008340 361 ELA 363 (569)
Q Consensus 361 ~L~ 363 (569)
+||
T Consensus 156 ~l~ 158 (159)
T cd06127 156 ELL 158 (159)
T ss_pred HHh
Confidence 997
No 32
>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=99.81 E-value=1.7e-19 Score=176.79 Aligned_cols=155 Identities=25% Similarity=0.287 Sum_probs=121.9
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEe----eCeEE----EEEEEec--CCCCCCCcEeecCCChh-hhcCCCCCHHHH
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDI----KGQVL----LDKLVKP--SNAIVDYNTRYSGITHE-MLSGVTTSLKDI 279 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~----~G~vv----~D~lVkP--~~~I~dy~T~~SGIT~e-~L~~~~~tl~dV 279 (569)
..+++||+||+|.++. ++|++|++|.. +|.+. |+++|+| ..+|+...+++||||++ |++++ ++.+++
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 4589999999999874 68999998874 34442 7899997 47999999999999975 68887 677777
Q ss_pred HHHHHHhh--------cCCCEEEEeCchhhHHHHccc-----------CC-CccchhhhccccCCCCCCchHHHHHHHhc
Q 008340 280 QEEFLKLV--------YKETILVGHSLENDLLALKIS-----------HG-LVIDTAVLYKHPQGGSHKTSLRVLAKKFL 339 (569)
Q Consensus 280 q~~l~~ll--------~~~tILVGHsL~~DL~aLki~-----------hp-~viDT~~L~~~~~g~~~k~sLk~La~~~L 339 (569)
..++.+++ .++.+|||||+.||+++|+.. ++ .++||..|++...+ ..+|..||+. +
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 77766665 267899999999999999831 11 38999999876543 3469999995 5
Q ss_pred CcccccCCCCCChHHHHHHHHHHHHHHHHcCCC
Q 008340 340 SREIQQSGFGHDSTEDARAAMELALLKIRNGPD 372 (569)
Q Consensus 340 g~~Iq~~~~~HdS~EDA~Atl~L~~~kl~~g~~ 372 (569)
|+++.. ...|+|+.||.+|++|+...+.+-..
T Consensus 163 gi~~~~-~~~H~Al~Da~ata~lf~~l~~~~~~ 194 (200)
T TIGR01298 163 GXDFDS-TQAHSALYDTEKTAELFCEIVNRWKR 194 (200)
T ss_pred CCCccc-cchhhhHHhHHHHHHHHHHHHHHHHH
Confidence 888642 14899999999999999888766443
No 33
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.81 E-value=2.8e-19 Score=209.67 Aligned_cols=155 Identities=24% Similarity=0.340 Sum_probs=131.6
Q ss_pred CcEEEEEeceecCCC--CceEEEEEEEEe-eCeEE--EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHh
Q 008340 212 YEILALDCEMCYTNE--GLELTRVTLVDI-KGQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKL 286 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~--g~eL~rVsvVd~-~G~vv--~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~l 286 (569)
.+|++|||||+|..+ +++|++|++|.. +|+++ |++||+|..+|+.+++++||||++||+++ +++++|..+|..+
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 359999999999874 469999999997 56665 88899999999999999999999999999 6999999999999
Q ss_pred hcCCCEEEEeCchhhHHHHccc---------CCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHHH
Q 008340 287 VYKETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDAR 357 (569)
Q Consensus 287 l~~~tILVGHsL~~DL~aLki~---------hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~ 357 (569)
+ .++++||||+.||+.+|+-. +..+|||..+++...+....++|..||+. ||++.. ..|+|+.||+
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 78999999999999999841 22689999876654333356789999985 687754 5899999999
Q ss_pred HHHHHHHHHHHcCCC
Q 008340 358 AAMELALLKIRNGPD 372 (569)
Q Consensus 358 Atl~L~~~kl~~g~~ 372 (569)
||++||...+++-..
T Consensus 157 ata~l~~~l~~~~~~ 171 (928)
T PRK08074 157 VTAELFLQLLNKLER 171 (928)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999988876543
No 34
>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=99.81 E-value=3.5e-19 Score=207.24 Aligned_cols=153 Identities=23% Similarity=0.292 Sum_probs=131.7
Q ss_pred cEEEEEeceecCCCC-ceEEEEEEEEe-eCeEE--EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhc
Q 008340 213 EILALDCEMCYTNEG-LELTRVTLVDI-KGQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVY 288 (569)
Q Consensus 213 ~~vAiDcEm~~t~~g-~eL~rVsvVd~-~G~vv--~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~ 288 (569)
+|+++|+||+|+.++ ++|++|++|.. +|+++ |++||+|..+|+.+.+++||||++||+++ +.+++|..+|.+++
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 79999999987 56665 89999999999999999999999999998 79999999999999
Q ss_pred CCCEEEEeCchhhHHHHccc---------CCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHHHHH
Q 008340 289 KETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAA 359 (569)
Q Consensus 289 ~~tILVGHsL~~DL~aLki~---------hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~At 359 (569)
.++++||||+.||+.+|+.. ...++||..+++...+...+++|..||+. +|++.. +.|+|++||+||
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 78999999999999999741 12589999887665444456789999986 688865 489999999999
Q ss_pred HHHHHHHHHcCC
Q 008340 360 MELALLKIRNGP 371 (569)
Q Consensus 360 l~L~~~kl~~g~ 371 (569)
++|++..+.+-+
T Consensus 155 a~l~~~l~~~~~ 166 (850)
T TIGR01407 155 AELLLLLFEKME 166 (850)
T ss_pred HHHHHHHHHHHH
Confidence 999988776643
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=3.9e-19 Score=172.55 Aligned_cols=151 Identities=23% Similarity=0.225 Sum_probs=116.1
Q ss_pred cEEEEEeceecCCCC-ceEEEEEEEEee----CeE----EEEEEEec--CCCCCCCcEeecCCChhh-hcCCCCC----H
Q 008340 213 EILALDCEMCYTNEG-LELTRVTLVDIK----GQV----LLDKLVKP--SNAIVDYNTRYSGITHEM-LSGVTTS----L 276 (569)
Q Consensus 213 ~~vAiDcEm~~t~~g-~eL~rVsvVd~~----G~v----v~D~lVkP--~~~I~dy~T~~SGIT~e~-L~~~~~t----l 276 (569)
..|+||+||+|..+. ++|++|++|... |.+ .|++||+| ..+|+...+++||||+++ ++.. +. +
T Consensus 6 ~~vv~D~ETTGl~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~-~~~~~~~ 84 (189)
T cd06134 6 LPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFA-VDEKEAL 84 (189)
T ss_pred eeEEEEecCCCCCCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccc-cchHHHH
Confidence 468999999999864 689999988753 332 48999999 578999999999999987 4443 44 4
Q ss_pred HHHHHHHHHhhc----CCCEEEEeCchhhHHHHccc-----------CC-CccchhhhccccCCCCCCchHHHHHHHhcC
Q 008340 277 KDIQEEFLKLVY----KETILVGHSLENDLLALKIS-----------HG-LVIDTAVLYKHPQGGSHKTSLRVLAKKFLS 340 (569)
Q Consensus 277 ~dVq~~l~~ll~----~~tILVGHsL~~DL~aLki~-----------hp-~viDT~~L~~~~~g~~~k~sLk~La~~~Lg 340 (569)
.++.+.|.+++. .+.+|||||+.||+.+|+.. ++ +++||..|++...+ .++|..||++ +|
T Consensus 85 ~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~---~~~L~~l~~~-~g 160 (189)
T cd06134 85 KEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG---QTVLAKACQA-AG 160 (189)
T ss_pred HHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC---CCcHHHHHHH-CC
Confidence 445555555552 36899999999999999831 12 47999999876543 3479999996 58
Q ss_pred cccccCCCCCChHHHHHHHHHHHHHHHHc
Q 008340 341 REIQQSGFGHDSTEDARAAMELALLKIRN 369 (569)
Q Consensus 341 ~~Iq~~~~~HdS~EDA~Atl~L~~~kl~~ 369 (569)
+++.. ...|+|+.||.||++||...+++
T Consensus 161 i~~~~-~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 161 IEFDN-KEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred CCCCC-CCCcChHHHHHHHHHHHHHHHHh
Confidence 88652 25899999999999999877653
No 36
>PRK05168 ribonuclease T; Provisional
Probab=99.80 E-value=5.5e-19 Score=174.48 Aligned_cols=157 Identities=25% Similarity=0.288 Sum_probs=123.3
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEee----CeE----EEEEEEec--CCCCCCCcEeecCCChhh-hcCCCCCHHHH
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDIK----GQV----LLDKLVKP--SNAIVDYNTRYSGITHEM-LSGVTTSLKDI 279 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~~----G~v----v~D~lVkP--~~~I~dy~T~~SGIT~e~-L~~~~~tl~dV 279 (569)
..+++||+||+|..+. ++|++|++|... |.+ .|+.||+| ..+|+.+.+++||||+++ +++. +.+.++
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 3589999999999865 689999999753 542 38899999 578999999999999986 6766 677777
Q ss_pred HHHHHHhhc--------CCCEEEEeCchhhHHHHccc-----------CC-CccchhhhccccCCCCCCchHHHHHHHhc
Q 008340 280 QEEFLKLVY--------KETILVGHSLENDLLALKIS-----------HG-LVIDTAVLYKHPQGGSHKTSLRVLAKKFL 339 (569)
Q Consensus 280 q~~l~~ll~--------~~tILVGHsL~~DL~aLki~-----------hp-~viDT~~L~~~~~g~~~k~sLk~La~~~L 339 (569)
..++.+++. .+.+|||||+.||+.+|+.. ++ +++||..|++...+ ..+|..+|++ +
T Consensus 96 l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~---~~~L~~l~~~-~ 171 (211)
T PRK05168 96 LHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALG---QTVLAKACQA-A 171 (211)
T ss_pred HHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC---CCCHHHHHHH-C
Confidence 777766653 37899999999999999741 22 58999999876543 2469999986 5
Q ss_pred CcccccCCCCCChHHHHHHHHHHHHHHHHcCCCCC
Q 008340 340 SREIQQSGFGHDSTEDARAAMELALLKIRNGPDFG 374 (569)
Q Consensus 340 g~~Iq~~~~~HdS~EDA~Atl~L~~~kl~~g~~fg 374 (569)
|++++. ...|+|++||.||++||...+++-...|
T Consensus 172 gl~~~~-~~~H~Al~DA~ata~l~~~l~~~~~~~~ 205 (211)
T PRK05168 172 GIEFDN-KEAHSALYDTEKTAELFCEIVNRWKRLG 205 (211)
T ss_pred CCCCCC-CCCCChHHHHHHHHHHHHHHHHHHHHcc
Confidence 888742 2589999999999999988776644333
No 37
>PRK06722 exonuclease; Provisional
Probab=99.79 E-value=1.3e-18 Score=178.83 Aligned_cols=152 Identities=22% Similarity=0.280 Sum_probs=120.2
Q ss_pred CcEEEEEeceecCCC----CceEEEEEEEEee-C--eEE--EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHH
Q 008340 212 YEILALDCEMCYTNE----GLELTRVTLVDIK-G--QVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEE 282 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~----g~eL~rVsvVd~~-G--~vv--~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~ 282 (569)
..+++||+||++... +++|++|++|..+ | +++ |++||+|..+|+.+++++||||++||+++ +++.+|..+
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 469999999985321 2689999999874 4 555 99999999999999999999999999999 699999999
Q ss_pred HHHhhcCCCEEEEeCchhhHHHHccc-------CC-----Cccchhhhcccc--CCCCCCchHHHHHHHhcCcccccCCC
Q 008340 283 FLKLVYKETILVGHSLENDLLALKIS-------HG-----LVIDTAVLYKHP--QGGSHKTSLRVLAKKFLSREIQQSGF 348 (569)
Q Consensus 283 l~~ll~~~tILVGHsL~~DL~aLki~-------hp-----~viDT~~L~~~~--~g~~~k~sLk~La~~~Lg~~Iq~~~~ 348 (569)
|.+++ ++..+|+|+..||+++|+.. .| .++|+..++... +..+..++|..|++. +|++.. +.
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 55566666679999999851 22 247888654321 112234689999985 688763 24
Q ss_pred CCChHHHHHHHHHHHHHHHH
Q 008340 349 GHDSTEDARAAMELALLKIR 368 (569)
Q Consensus 349 ~HdS~EDA~Atl~L~~~kl~ 368 (569)
.|+|++||.+|+.|++..+.
T Consensus 160 ~HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 160 QHRALADAENTANILLKAYS 179 (281)
T ss_pred CcCcHHHHHHHHHHHHHHhc
Confidence 89999999999999987764
No 38
>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=99.79 E-value=4.9e-19 Score=166.81 Aligned_cols=148 Identities=24% Similarity=0.262 Sum_probs=121.0
Q ss_pred EEEEEeceecCCCC------ceEEEEEEEEee--Ce-E--EEEEEEecCC--CCCCCcEeecCCChhhhcCCCCCHHHHH
Q 008340 214 ILALDCEMCYTNEG------LELTRVTLVDIK--GQ-V--LLDKLVKPSN--AIVDYNTRYSGITHEMLSGVTTSLKDIQ 280 (569)
Q Consensus 214 ~vAiDcEm~~t~~g------~eL~rVsvVd~~--G~-v--v~D~lVkP~~--~I~dy~T~~SGIT~e~L~~~~~tl~dVq 280 (569)
|+++||||+|...+ .+|++|++|..+ +. + .|+.||+|.. +|.++.+++||||.++|+++ +++.+|.
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 699999999754 32 2 3899999998 99999999999999999998 8999999
Q ss_pred HHHHHhhcCC--CEEEEeCchhhHHHHcc------------cCCCccchhhhccccCCCCCCchHHHHHHHhcCcccccC
Q 008340 281 EEFLKLVYKE--TILVGHSLENDLLALKI------------SHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQS 346 (569)
Q Consensus 281 ~~l~~ll~~~--tILVGHsL~~DL~aLki------------~hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~ 346 (569)
++|.+++... .++|+| ..+|+.+|.. .+..++|+..+|+...+...+++|..|++. +|++..
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 5899877653 122689999998876655467899999985 688876
Q ss_pred CCCCChHHHHHHHHHHHHHH
Q 008340 347 GFGHDSTEDARAAMELALLK 366 (569)
Q Consensus 347 ~~~HdS~EDA~Atl~L~~~k 366 (569)
+..|+|+.||++|++|++..
T Consensus 156 ~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 156 GRHHRGLDDARNIARILKRL 175 (176)
T ss_pred CCCcCcHHHHHHHHHHHHHh
Confidence 25899999999999999754
No 39
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=99.78 E-value=8.1e-19 Score=208.50 Aligned_cols=157 Identities=23% Similarity=0.359 Sum_probs=134.7
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEe-eCeEE--EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDI-KGQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~-~G~vv--~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll 287 (569)
..+|++||||+|..+. ++|++|++|.. +|+++ |+.||+|..+|+++.+++||||++||+++ +++++|.++|.+++
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 69999999996 46655 89999999999999999999999999998 79999999999999
Q ss_pred cCCCEEEEeCchhhHHHHccc---------CCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHHHH
Q 008340 288 YKETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARA 358 (569)
Q Consensus 288 ~~~tILVGHsL~~DL~aLki~---------hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~A 358 (569)
++++|||||+.||+.+|+.. +..++||..+++.......+++|..||++ +|++... +|+|+.||.|
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 78999999999999999842 23689999988765433457889999986 5888764 8999999999
Q ss_pred HHHHHHHHHHcCCCCC
Q 008340 359 AMELALLKIRNGPDFG 374 (569)
Q Consensus 359 tl~L~~~kl~~g~~fg 374 (569)
|++||...+++....|
T Consensus 344 Ta~I~~~ll~~l~~~~ 359 (1213)
T TIGR01405 344 TAKVFKVMVEQLKEKG 359 (1213)
T ss_pred HHHHHHHHHHHHHHcC
Confidence 9999988776544333
No 40
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.78 E-value=1.9e-19 Score=206.32 Aligned_cols=154 Identities=24% Similarity=0.348 Sum_probs=136.6
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEe-eCeEE--EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDI-KGQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~-~G~vv--~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll 287 (569)
..||++|+||+|+++. ++|+++++|.. +|+++ |+.|++|..||+...|.+||||.+||+++ +.+.+|..++++++
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 4699999999999886 79999999996 67777 77899999999999999999999999999 79999999999999
Q ss_pred cCCCEEEEeCchhhHHHHccc---------CCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHHHH
Q 008340 288 YKETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARA 358 (569)
Q Consensus 288 ~~~tILVGHsL~~DL~aLki~---------hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~A 358 (569)
.|+|||+||+.||+.+|+.. -..+|||..|.+...+...+++|..||++| |+... .+|+|.-||.|
T Consensus 500 -~d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh~Lg~l~kk~-~v~le---~hHRA~yDaea 574 (1444)
T COG2176 500 -GDSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSHRLGTLCKKL-GVELE---RHHRADYDAEA 574 (1444)
T ss_pred -cCcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhcchHHHHHHh-CccHH---HhhhhhhhHHH
Confidence 99999999999999999952 236999999887766555678999999974 99985 49999999999
Q ss_pred HHHHHHHHHHcCC
Q 008340 359 AMELALLKIRNGP 371 (569)
Q Consensus 359 tl~L~~~kl~~g~ 371 (569)
+..||...+++-.
T Consensus 575 t~~vf~~f~~~~k 587 (1444)
T COG2176 575 TAKVFFVFLKDLK 587 (1444)
T ss_pred HHHHHHHHHHHHH
Confidence 9999988776543
No 41
>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=99.78 E-value=6.6e-21 Score=173.35 Aligned_cols=145 Identities=29% Similarity=0.368 Sum_probs=116.3
Q ss_pred EEEEeceecCCC-CceEEEEEEEEeeC-----eEEEEEEEecCCC--CCCCcEeecCCChhhhcCCCCCHHHHHHHHHHh
Q 008340 215 LALDCEMCYTNE-GLELTRVTLVDIKG-----QVLLDKLVKPSNA--IVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKL 286 (569)
Q Consensus 215 vAiDcEm~~t~~-g~eL~rVsvVd~~G-----~vv~D~lVkP~~~--I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~l 286 (569)
|+|||||+|... ..+|++|++|..++ ...++.||+|..+ |.++.+++||||.++|+++ +++.++..++.++
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 689999999987 46888888888632 3469999999998 9999999999999999999 6999999999999
Q ss_pred hcCCCEEEEeCchhhHHHHc--------ccCC---CccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHH
Q 008340 287 VYKETILVGHSLENDLLALK--------ISHG---LVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTED 355 (569)
Q Consensus 287 l~~~tILVGHsL~~DL~aLk--------i~hp---~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~ED 355 (569)
+.+..++||||..||..+++ ..+| .++||..+.+...+...+++|+.|++.| |.+... .+|+|++|
T Consensus 80 ~~~~~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~-~~~~~~--~~H~Al~D 156 (164)
T PF00929_consen 80 LKKNDILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNRKKYSLDDLAEYF-GIPFDG--TAHDALDD 156 (164)
T ss_dssp HHHHTEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHHHHHSHHHHHHHT-TSSSTS--TTTSHHHH
T ss_pred hhcccccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhccccCCHHHHHHHc-CCCCCC--CCcChHHH
Confidence 97789999999888875554 2233 4788876654432222237899999965 666553 27999999
Q ss_pred HHHHHHHH
Q 008340 356 ARAAMELA 363 (569)
Q Consensus 356 A~Atl~L~ 363 (569)
|++|++||
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 42
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.77 E-value=6.8e-18 Score=177.93 Aligned_cols=150 Identities=13% Similarity=0.184 Sum_probs=122.8
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEe--eCeEE--EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHh
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDI--KGQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKL 286 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~--~G~vv--~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~l 286 (569)
..|++||+||+|..+. ++|+.|++|.. +|+++ |.+||+|..++.. +.+||||++||+++ ++|.+|.++|.+|
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 68999988875 46654 8999999986554 47999999999998 7999999999999
Q ss_pred hcCCCEEEEeCchhhHHHHccc--------------------------------C----CCccchhhhccccCCCCCCch
Q 008340 287 VYKETILVGHSLENDLLALKIS--------------------------------H----GLVIDTAVLYKHPQGGSHKTS 330 (569)
Q Consensus 287 l~~~tILVGHsL~~DL~aLki~--------------------------------h----p~viDT~~L~~~~~g~~~k~s 330 (569)
| .+.+|||||+.||+.||... | ..++||..|.+.......+++
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 89999999999999998641 1 258999998776543335688
Q ss_pred HHHHHHHhcCcccc-------cCCCCCChH--HHHHHHHHHHHHH
Q 008340 331 LRVLAKKFLSREIQ-------QSGFGHDST--EDARAAMELALLK 366 (569)
Q Consensus 331 Lk~La~~~Lg~~Iq-------~~~~~HdS~--EDA~Atl~L~~~k 366 (569)
|..||++ ||++.. .....|+++ +||+...+||...
T Consensus 202 L~~La~~-lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 202 IRGVAHT-LGLDAPAAEASVERAQVPHRQLCREETLLVARLYFAL 245 (377)
T ss_pred HHHHHHH-hCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHh
Confidence 9999996 598871 112478888 7999999999764
No 43
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.77 E-value=4.3e-18 Score=176.20 Aligned_cols=151 Identities=23% Similarity=0.213 Sum_probs=117.1
Q ss_pred CCCcEEEEEeceecCCCC-ceEEEEEEEEee----CeE-----EEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHH
Q 008340 210 SPYEILALDCEMCYTNEG-LELTRVTLVDIK----GQV-----LLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDI 279 (569)
Q Consensus 210 ~~~~~vAiDcEm~~t~~g-~eL~rVsvVd~~----G~v-----v~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dV 279 (569)
.+..+++||+||+|+.+. ++|++|++|..+ |.+ .|+.||+|..+|+...|++||||++||++++...
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 456799999999999875 799999999864 542 2888999999999999999999999999985433
Q ss_pred HHHHHHhhcCCCEEEEeCchhhHHHHccc-----CCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHH
Q 008340 280 QEEFLKLVYKETILVGHSLENDLLALKIS-----HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTE 354 (569)
Q Consensus 280 q~~l~~ll~~~tILVGHsL~~DL~aLki~-----hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~E 354 (569)
+++..++....+|||||+.||+.+|+.. ...+.+|............+++|.+||.. +|.. . .+|+|+.
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 3466777666899999999999999842 22456666543322112246789999986 4732 2 4899999
Q ss_pred HHHHHHHHHHHHHHc
Q 008340 355 DARAAMELALLKIRN 369 (569)
Q Consensus 355 DA~Atl~L~~~kl~~ 369 (569)
||.||++|+..++..
T Consensus 186 Da~Ata~ll~~~l~~ 200 (294)
T PRK09182 186 DCQALLELLARPLPE 200 (294)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999877765
No 44
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.77 E-value=6.6e-18 Score=168.45 Aligned_cols=155 Identities=26% Similarity=0.321 Sum_probs=130.1
Q ss_pred CcEEEEEeceecCCC-CceEEEEEEEEe-eCeEE---EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHh
Q 008340 212 YEILALDCEMCYTNE-GLELTRVTLVDI-KGQVL---LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKL 286 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~-g~eL~rVsvVd~-~G~vv---~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~l 286 (569)
.++++||+||+|... +.++++|++|.. ++.++ |+.||+|+.+|+.+.+++||||.+||.++ +.+.+|.+++.++
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 468999999999986 678999999986 44444 88999999999999999999999999999 8999999999999
Q ss_pred hcCCCEEEEeCchhhHHHHccc---------CCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHHH
Q 008340 287 VYKETILVGHSLENDLLALKIS---------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDAR 357 (569)
Q Consensus 287 l~~~tILVGHsL~~DL~aLki~---------hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~ 357 (569)
+.+..++||||+.||+.+|+.. -..++||..+.+...+...+++|++||. ++|++.. ....|+++.||.
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 1257799888766543335788999999 5688844 224799999999
Q ss_pred HHHHHHHHHHHc
Q 008340 358 AAMELALLKIRN 369 (569)
Q Consensus 358 Atl~L~~~kl~~ 369 (569)
+++++|......
T Consensus 170 ~~a~~~~~~~~~ 181 (243)
T COG0847 170 ALAELFLLLQTG 181 (243)
T ss_pred HHHHHHHHHHhc
Confidence 999999887764
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=7.4e-18 Score=162.47 Aligned_cols=145 Identities=19% Similarity=0.137 Sum_probs=113.7
Q ss_pred EEEEeceecCCCC-ceEEEEEEEEeeC--eEE--EEEEEecCC--CCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008340 215 LALDCEMCYTNEG-LELTRVTLVDIKG--QVL--LDKLVKPSN--AIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (569)
Q Consensus 215 vAiDcEm~~t~~g-~eL~rVsvVd~~G--~vv--~D~lVkP~~--~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll 287 (569)
+.+|+||+|+... ++|++|++|..++ .++ |+.||+|.. ++....+++||||++||.+..+++.++.+++.+++
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 6899999998643 444 888999974 56667889999999999993378999999999999
Q ss_pred c-CCCEEEEeC-chhhHHHHccc---C------------CCccchhhhcccc---------C----CCCCCchHHHHHHH
Q 008340 288 Y-KETILVGHS-LENDLLALKIS---H------------GLVIDTAVLYKHP---------Q----GGSHKTSLRVLAKK 337 (569)
Q Consensus 288 ~-~~tILVGHs-L~~DL~aLki~---h------------p~viDT~~L~~~~---------~----g~~~k~sLk~La~~ 337 (569)
. ++++||||| +.||+.+|+.. + ..++||..+++.. . +....++|..||++
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 478999997 89999999741 1 1247887544321 0 01235789999986
Q ss_pred hcCcccccCCCCCChHHHHHHHHHHH
Q 008340 338 FLSREIQQSGFGHDSTEDARAAMELA 363 (569)
Q Consensus 338 ~Lg~~Iq~~~~~HdS~EDA~Atl~L~ 363 (569)
+|++.. ..|+|+.||+||++|+
T Consensus 161 -~gi~~~---~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 161 -NGIEHS---NAHDALSDVEATIALA 182 (183)
T ss_pred -CCCCcc---ccccHHHHHHHHHHHh
Confidence 588875 4899999999999986
No 46
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.65 E-value=1.1e-15 Score=167.32 Aligned_cols=157 Identities=17% Similarity=0.121 Sum_probs=121.9
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEeeCe--EE---EEEEEecCCC--CCCCcEeecCCChhhhcCCCCCHHHHHHHH
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDIKGQ--VL---LDKLVKPSNA--IVDYNTRYSGITHEMLSGVTTSLKDIQEEF 283 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~~G~--vv---~D~lVkP~~~--I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l 283 (569)
..++++|+||+|+.+. ++|++|+.|..++. ++ +..||+|... +....+.+||||++||.+.+.+..++.++|
T Consensus 6 ~~fvv~D~ETTGLdP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~~~i 85 (476)
T PRK11779 6 PTFLWHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEFAARI 85 (476)
T ss_pred CcEEEEEEECCCCCCCCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHH
Confidence 4699999999999975 79999999987542 33 7899999863 345688999999999988767899999999
Q ss_pred HHhhc-CCCEEEEeC-chhhHHHHcccC------C------------CccchhhhccccC--C--------CCCCchHHH
Q 008340 284 LKLVY-KETILVGHS-LENDLLALKISH------G------------LVIDTAVLYKHPQ--G--------GSHKTSLRV 333 (569)
Q Consensus 284 ~~ll~-~~tILVGHs-L~~DL~aLki~h------p------------~viDT~~L~~~~~--g--------~~~k~sLk~ 333 (569)
.+++. +++++|||| +.||+.+|+... + .++|++.++...+ + ....++|..
T Consensus 86 ~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rLe~ 165 (476)
T PRK11779 86 HAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKLEH 165 (476)
T ss_pred HHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCcHHH
Confidence 99994 589999997 899999887421 1 2356666543211 1 123478999
Q ss_pred HHHHhcCcccccCCCCCChHHHHHHHHHHHHHHHHcCCC
Q 008340 334 LAKKFLSREIQQSGFGHDSTEDARAAMELALLKIRNGPD 372 (569)
Q Consensus 334 La~~~Lg~~Iq~~~~~HdS~EDA~Atl~L~~~kl~~g~~ 372 (569)
||+.| |++.. ++|||+.||.||++|++...++.|.
T Consensus 166 L~~~~-gI~~~---~AHdALsDa~aT~~la~~l~~~qP~ 200 (476)
T PRK11779 166 LTKAN-GIEHE---NAHDAMSDVYATIAMAKLIKQKQPK 200 (476)
T ss_pred HHHHc-CCCCC---CCCCcHHHHHHHHHHHHHHHHhChH
Confidence 99964 87765 4899999999999999887776553
No 47
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.64 E-value=6.6e-16 Score=186.03 Aligned_cols=157 Identities=24% Similarity=0.359 Sum_probs=131.7
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEe-eCeEE--EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhh
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDI-KGQVL--LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLV 287 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~-~G~vv--~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll 287 (569)
.++|++|+||+|.... .+|++|++|.. +|.++ |+.||+|..+|+.+.+++||||++||.++ +++.+|.++|.+++
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 4699999999998875 57888877775 56665 89999999999999999999999999987 79999999999999
Q ss_pred cCCCEEEEeCchhhHHHHcc---------cCCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHHHH
Q 008340 288 YKETILVGHSLENDLLALKI---------SHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARA 358 (569)
Q Consensus 288 ~~~tILVGHsL~~DL~aLki---------~hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~A 358 (569)
++.+|||||..||+.+|+- ....++||..+++...+...+++|..||++ +|.... ++|+|+.||.|
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 123689999987665444467889999996 588876 47999999999
Q ss_pred HHHHHHHHHHcCCCCC
Q 008340 359 AMELALLKIRNGPDFG 374 (569)
Q Consensus 359 tl~L~~~kl~~g~~fg 374 (569)
|++|+...+++....|
T Consensus 573 Ta~lf~~ll~~l~~~g 588 (1437)
T PRK00448 573 TAYLLIKFLKDLKEKG 588 (1437)
T ss_pred HHHHHHHHHHHHHHcC
Confidence 9999988876544333
No 48
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=99.64 E-value=7.7e-16 Score=147.44 Aligned_cols=141 Identities=16% Similarity=0.246 Sum_probs=106.3
Q ss_pred EEEEEeceecCCC-CceEEEEEEEEeeCe--EE---EEEEEecCCCCC----CCcEee---cCCChhhhcCCCCCHHHHH
Q 008340 214 ILALDCEMCYTNE-GLELTRVTLVDIKGQ--VL---LDKLVKPSNAIV----DYNTRY---SGITHEMLSGVTTSLKDIQ 280 (569)
Q Consensus 214 ~vAiDcEm~~t~~-g~eL~rVsvVd~~G~--vv---~D~lVkP~~~I~----dy~T~~---SGIT~e~L~~~~~tl~dVq 280 (569)
+++||+||+|+.+ .++|++|++|..++. .+ |+.+|+|..++. .+..++ ||||++|++++ +++.++.
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 578999999988663 22 899999998665 343444 69999999998 7999999
Q ss_pred HHHHHhhcC-----CCEEEEeCchhhHHHHcc--------cCCCccchhh---hccccCCCCCCchHHHHHHHhcCcccc
Q 008340 281 EEFLKLVYK-----ETILVGHSLENDLLALKI--------SHGLVIDTAV---LYKHPQGGSHKTSLRVLAKKFLSREIQ 344 (569)
Q Consensus 281 ~~l~~ll~~-----~tILVGHsL~~DL~aLki--------~hp~viDT~~---L~~~~~g~~~k~sLk~La~~~Lg~~Iq 344 (569)
++|.+++.. ..+|||||+.||+.+|+. .+..++||.. +++.... .++. ++..-
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 008340 345 QSGFGHDSTEDARAAMELALLKIR 368 (569)
Q Consensus 345 ~~~~~HdS~EDA~Atl~L~~~kl~ 368 (569)
+..|+|+.||+||+.+|+..+.
T Consensus 149 --~~~HrAl~Da~~~~~~~~~~~~ 170 (173)
T cd06135 149 --KGTHRALDDIRESIAELKYYRE 170 (173)
T ss_pred --CCCcchHHHHHHHHHHHHHHHH
Confidence 2579999999999999987764
No 49
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.64 E-value=2.3e-15 Score=166.60 Aligned_cols=160 Identities=16% Similarity=0.198 Sum_probs=124.5
Q ss_pred CcEEEEEeceecCCC----CceEEEEEEEEe---eCeEE--EEEEEecCC--CCCCCcEeecCCChhhhcCCCCCHHHHH
Q 008340 212 YEILALDCEMCYTNE----GLELTRVTLVDI---KGQVL--LDKLVKPSN--AIVDYNTRYSGITHEMLSGVTTSLKDIQ 280 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~----g~eL~rVsvVd~---~G~vv--~D~lVkP~~--~I~dy~T~~SGIT~e~L~~~~~tl~dVq 280 (569)
..|++||+||++... ..||++|++|-. +|+++ |.+||+|.. +|+.++|++||||.+||+++ ++|.+|.
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 56555 889999987 79999999999999999998 7999999
Q ss_pred HHHHHhhcCC---------CEEEEeCchhhHH-HHcc--------c----CCCccchhhh-----cccc-------CCCC
Q 008340 281 EEFLKLVYKE---------TILVGHSLENDLL-ALKI--------S----HGLVIDTAVL-----YKHP-------QGGS 326 (569)
Q Consensus 281 ~~l~~ll~~~---------tILVGHsL~~DL~-aLki--------~----hp~viDT~~L-----~~~~-------~g~~ 326 (569)
.+|.+++... ..+|+|+..||+. +|.- . ...++|.... |+.. ....
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 2246664322 2210 0012
Q ss_pred CCchHHHHHHHhcCcccccCCCCCChHHHHHHHHHHHHHHHHcCCCCCC
Q 008340 327 HKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMELALLKIRNGPDFGS 375 (569)
Q Consensus 327 ~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~Atl~L~~~kl~~g~~fg~ 375 (569)
..++|..+++. +|+++.. ..|+++.||++++.|+..++++|--|-.
T Consensus 215 ~~~~L~~al~~-lgL~~eG--r~HrAlDDA~ntA~L~~~Ll~~g~~~~~ 260 (582)
T PTZ00315 215 GPSDMPDMLQM-LGLPLQG--RHHSGIDDCRNIAAVLCELLRRGLVIDP 260 (582)
T ss_pred CCcCHHHHHHH-CCCCCCC--CCcCcHHHHHHHHHHHHHHHHcCCEEEe
Confidence 45789999985 6888753 5799999999999999999998875543
No 50
>PRK05359 oligoribonuclease; Provisional
Probab=99.63 E-value=1.6e-15 Score=146.77 Aligned_cols=143 Identities=16% Similarity=0.180 Sum_probs=109.5
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEeeC--eEE---EEEEEecCCC----CCCCcEeec---CCChhhhcCCCCCHHH
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDIKG--QVL---LDKLVKPSNA----IVDYNTRYS---GITHEMLSGVTTSLKD 278 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~~G--~vv---~D~lVkP~~~----I~dy~T~~S---GIT~e~L~~~~~tl~d 278 (569)
.++|+|||||+|+++. ++|++|++|-.++ +++ +..+|+|... +..+.+++| |||+++++++ +++.+
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 4699999999999875 6899999998754 334 7889999865 466777776 9999999998 79999
Q ss_pred HHHHHHHhhc-----CCCEEEEeCchhhHHHHcc--------cCCCccchhh---hccccCCCCCCchHHHHHHHhcCcc
Q 008340 279 IQEEFLKLVY-----KETILVGHSLENDLLALKI--------SHGLVIDTAV---LYKHPQGGSHKTSLRVLAKKFLSRE 342 (569)
Q Consensus 279 Vq~~l~~ll~-----~~tILVGHsL~~DL~aLki--------~hp~viDT~~---L~~~~~g~~~k~sLk~La~~~Lg~~ 342 (569)
+..+|++|+. .+.+|||||+.||+.+|+. .|.+++|++. +.+... |.+ ++++.
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 2446777442 443321 112 22333
Q ss_pred cccCCCCCChHHHHHHHHHHHHHHHHc
Q 008340 343 IQQSGFGHDSTEDARAAMELALLKIRN 369 (569)
Q Consensus 343 Iq~~~~~HdS~EDA~Atl~L~~~kl~~ 369 (569)
-. +.|+|++||+++.++++.+.+.
T Consensus 151 ~~---~~HRal~D~~~s~~~~~~~~~~ 174 (181)
T PRK05359 151 KQ---GTHRALADIRESIAELKYYREH 174 (181)
T ss_pred Cc---CCcccHHHHHHHHHHHHHHHHH
Confidence 22 4799999999999999876553
No 51
>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=98.48 E-value=7.9e-07 Score=86.32 Aligned_cols=122 Identities=18% Similarity=0.197 Sum_probs=88.8
Q ss_pred EEEEEeceecC----CC-CceEEEEEEEEe-eCeEE-EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHh
Q 008340 214 ILALDCEMCYT----NE-GLELTRVTLVDI-KGQVL-LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKL 286 (569)
Q Consensus 214 ~vAiDcEm~~t----~~-g~eL~rVsvVd~-~G~vv-~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~l 286 (569)
++++|+||++. .. +++|+.|+++.. +|... +.....+...... ||+..++..+ ++-.++..++.++
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 32 479999999997 66643 2222223222111 8999999998 6999999999999
Q ss_pred hcCC--CEEEEeCc-hhhHHHHcc-------cC------------------------CCccchhhhccccCCCCCCchHH
Q 008340 287 VYKE--TILVGHSL-ENDLLALKI-------SH------------------------GLVIDTAVLYKHPQGGSHKTSLR 332 (569)
Q Consensus 287 l~~~--tILVGHsL-~~DL~aLki-------~h------------------------p~viDT~~L~~~~~g~~~k~sLk 332 (569)
+..- .||||||. .||+.+|.- .+ ..++|+..+++... +...++|.
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 69999999 899988873 12 12678888876543 24568899
Q ss_pred HHHHHhcCccc
Q 008340 333 VLAKKFLSREI 343 (569)
Q Consensus 333 ~La~~~Lg~~I 343 (569)
.+|+.+||..-
T Consensus 153 ~v~~~~l~~~k 163 (199)
T cd05160 153 AVAEELLGEGK 163 (199)
T ss_pred HHHHHHhCCCC
Confidence 99999998743
No 52
>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=98.38 E-value=2.6e-06 Score=79.54 Aligned_cols=129 Identities=22% Similarity=0.228 Sum_probs=80.1
Q ss_pred cEEEEEeceecCCC--C-ceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhc-
Q 008340 213 EILALDCEMCYTNE--G-LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVY- 288 (569)
Q Consensus 213 ~~vAiDcEm~~t~~--g-~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~- 288 (569)
+++|+|||+++... . ..++-|++-..++..++ .|...-.+. +...|.+++.
T Consensus 21 ~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~----~~~~~~~~~---------------------~~~~l~~ll~~ 75 (176)
T PF01612_consen 21 KVLAFDTETTGLDPYSYNPKIALIQLATGEGCYII----DPIDLGDNW---------------------ILDALKELLED 75 (176)
T ss_dssp SEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEE----CGTTSTTTT---------------------HHHHHHHHHTT
T ss_pred CeEEEEEEECCCCccccCCeEEEEEEecCCCceee----eeccccccc---------------------hHHHHHHHHhC
Confidence 38999999999877 2 34555555554332222 222111101 5556666663
Q ss_pred CCCEEEEeCchhhHHHHccc----CCCccchhhhccccCCCCCCchHHHHHHHhcC-cccccC---CCCC--C-------
Q 008340 289 KETILVGHSLENDLLALKIS----HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLS-REIQQS---GFGH--D------- 351 (569)
Q Consensus 289 ~~tILVGHsL~~DL~aLki~----hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg-~~Iq~~---~~~H--d------- 351 (569)
++.+.||||+.||+.+|.-. ...++|| .+..+..++..+++|+.|+..||| .....+ +... +
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 46689999999999999852 3478999 444444344444899999999999 444321 1222 2
Q ss_pred --hHHHHHHHHHHHHHHH
Q 008340 352 --STEDARAAMELALLKI 367 (569)
Q Consensus 352 --S~EDA~Atl~L~~~kl 367 (569)
|..||.++.+|+....
T Consensus 155 ~YAa~D~~~~~~l~~~l~ 172 (176)
T PF01612_consen 155 EYAAQDAVVTFRLYEKLK 172 (176)
T ss_dssp HHHHHHHHTHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 3458888888876543
No 53
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=98.36 E-value=2.2e-07 Score=88.76 Aligned_cols=159 Identities=19% Similarity=0.278 Sum_probs=117.5
Q ss_pred cEEEEEeceecCCCC-----ceEEEEE--EEEe-eCeEE--EEEEEecCC--CCCCCcEeecCCChhhhcCCCCCHHHHH
Q 008340 213 EILALDCEMCYTNEG-----LELTRVT--LVDI-KGQVL--LDKLVKPSN--AIVDYNTRYSGITHEMLSGVTTSLKDIQ 280 (569)
Q Consensus 213 ~~vAiDcEm~~t~~g-----~eL~rVs--vVd~-~G~vv--~D~lVkP~~--~I~dy~T~~SGIT~e~L~~~~~tl~dVq 280 (569)
..++||.|.+.-..+ .||+.|. +|+. +-+++ |.+||+|.. ..++|+..++|||...++.+ +-|.+|.
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 478999999876543 3565553 4443 33333 778999976 57799999999999999999 6999999
Q ss_pred HHHHHhhcCCCE----EEEeCchhhHHHHccc----C--C-----CccchhhhccccCCCCCCchHHHHHHHhcCccccc
Q 008340 281 EEFLKLVYKETI----LVGHSLENDLLALKIS----H--G-----LVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQ 345 (569)
Q Consensus 281 ~~l~~ll~~~tI----LVGHsL~~DL~aLki~----h--p-----~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~ 345 (569)
+++..++.+... -..---+-|.+.|+.. | | ..+|-+.-|...++.++-.+|....+.| |-.++.
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 999888843221 1222336788988841 1 2 3689888888887776667788888876 877764
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHcCCCCCC
Q 008340 346 SGFGHDSTEDARAAMELALLKIRNGPDFGS 375 (569)
Q Consensus 346 ~~~~HdS~EDA~Atl~L~~~kl~~g~~fg~ 375 (569)
..|++++||+.+.+|+++.+...-.|..
T Consensus 163 --~~HraldDArn~~rl~klv~~~~~~~e~ 190 (210)
T COG5018 163 --THHRALDDARNAYRLFKLVEQDKQYLEK 190 (210)
T ss_pred --chhhhHHHHHHHHHHHHHHcchhhhccC
Confidence 6899999999999999888776555544
No 54
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=98.36 E-value=4.2e-06 Score=79.76 Aligned_cols=140 Identities=19% Similarity=0.186 Sum_probs=92.3
Q ss_pred CcEEEEEeceecCCC-CceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcCC
Q 008340 212 YEILALDCEMCYTNE-GLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKE 290 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~-g~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~~ 290 (569)
..++|+|+|+++... ...++.+++....+..+|- -+++ +.+ .+. ..+.++...|.+++...
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 357999999988765 3578888887655544320 0111 111 122 46788888999988443
Q ss_pred -CEEEEeCchhhHHHHccc----CCCccchhhhccccCCCCCCchHHHHHHHhcCccccc-----C--------------
Q 008340 291 -TILVGHSLENDLLALKIS----HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQ-----S-------------- 346 (569)
Q Consensus 291 -tILVGHsL~~DL~aLki~----hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~-----~-------------- 346 (569)
..+||||+.+|+.+|+.. ...++||..++....+...+++|..|++.|+|.++.. +
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 2367999987654432221469999999998866210 0
Q ss_pred CCCCChHHHHHHHHHHHHHHHHc
Q 008340 347 GFGHDSTEDARAAMELALLKIRN 369 (569)
Q Consensus 347 ~~~HdS~EDA~Atl~L~~~kl~~ 369 (569)
...|.+..||.++.+|+....++
T Consensus 147 ~~~~ya~~d~~~~~~l~~~l~~~ 169 (193)
T cd06139 147 KAAEYAAEDADITLRLYELLKPK 169 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 01234778888888888666554
No 55
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=98.29 E-value=3.3e-07 Score=92.46 Aligned_cols=157 Identities=22% Similarity=0.352 Sum_probs=113.0
Q ss_pred EEEEEeceecCCCC-----ceEEEEEEEEe----eCeE--EEEEEEecCC--CCCCCcEeecCCChhhhcCCCCCHHHHH
Q 008340 214 ILALDCEMCYTNEG-----LELTRVTLVDI----KGQV--LLDKLVKPSN--AIVDYNTRYSGITHEMLSGVTTSLKDIQ 280 (569)
Q Consensus 214 ~vAiDcEm~~t~~g-----~eL~rVsvVd~----~G~v--v~D~lVkP~~--~I~dy~T~~SGIT~e~L~~~~~tl~dVq 280 (569)
+++||+|.+--... .||++.-+|-. .+.+ -|++||+|.. ...+|++.+|||..++++.+ ++|.+|.
T Consensus 58 LliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a-~~f~~vl 136 (280)
T KOG0542|consen 58 LLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEA-PTFPQVL 136 (280)
T ss_pred EEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccC-CCHHHHH
Confidence 78999998765432 48988888732 2332 3889999965 56799999999999999999 7999999
Q ss_pred HHHHHhhcC--------CCEEEEeCchhhHH-HHc-------ccCC----CccchhhhccccCCCCCCchHHHHHHHhcC
Q 008340 281 EEFLKLVYK--------ETILVGHSLENDLL-ALK-------ISHG----LVIDTAVLYKHPQGGSHKTSLRVLAKKFLS 340 (569)
Q Consensus 281 ~~l~~ll~~--------~tILVGHsL~~DL~-aLk-------i~hp----~viDT~~L~~~~~g~~~k~sLk~La~~~Lg 340 (569)
+++...|-. ..-+|--+ .-||. +|. |.-| .+||.-.+|......+.+.++..+-++| |
T Consensus 137 ~~f~~Wlr~~~~~~k~~~~Afvtdg-~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it~mLe~~-g 214 (280)
T KOG0542|consen 137 SEFDSWLRKDSLGDKNGKFAFVTDG-DWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNITGMLEHY-G 214 (280)
T ss_pred HHHHHHHHHhhcccccCceEEEeCc-hhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCHHHHHHHh-C
Confidence 998887721 22233332 34553 332 2223 6899888887653333445677777654 6
Q ss_pred cccccCCCCCChHHHHHHHHHHHHHHHHcCCCCCC
Q 008340 341 REIQQSGFGHDSTEDARAAMELALLKIRNGPDFGS 375 (569)
Q Consensus 341 ~~Iq~~~~~HdS~EDA~Atl~L~~~kl~~g~~fg~ 375 (569)
.+.+ |..|+.++||+-...++.++++.|-.|-.
T Consensus 215 L~f~--Gr~HsGiDDa~Nia~I~~kM~~dg~~~~I 247 (280)
T KOG0542|consen 215 LQFE--GRAHSGIDDARNIARIAQKMIRDGAEFRI 247 (280)
T ss_pred Cccc--CCcccCchhHHHHHHHHHHHHhCCcEEEe
Confidence 6665 47899999999999999999999877653
No 56
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=98.17 E-value=3.9e-06 Score=80.69 Aligned_cols=142 Identities=20% Similarity=0.324 Sum_probs=102.5
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEeeCe--EE---EEEEEecCCC----CCCCcE---eecCCChhhhcCCCCCHHH
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDIKGQ--VL---LDKLVKPSNA----IVDYNT---RYSGITHEMLSGVTTSLKD 278 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~~G~--vv---~D~lVkP~~~----I~dy~T---~~SGIT~e~L~~~~~tl~d 278 (569)
.++|=|||||+|++-+ +.|++|+.+=.+|. ++ +|..|+-... +.+|.. --||+|+.-++.. .|++|
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 4599999999999876 68888887765553 33 6777775443 334543 4578999988887 69999
Q ss_pred HHHHHHHhh-----cCCCEEEEeCchhhHHHHccc--------CCCccchhhhccccCCCCCCchHHHHHHHhcCccccc
Q 008340 279 IQEEFLKLV-----YKETILVGHSLENDLLALKIS--------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQ 345 (569)
Q Consensus 279 Vq~~l~~ll-----~~~tILVGHsL~~DL~aLki~--------hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~ 345 (569)
+-.++++|+ ...+.|-|-|+.-|..||+-. |-++||.+. .+.||+++ .-+++.
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 356889999999999999843 446778764 44455544 222332
Q ss_pred ----CCCCCChHHHHHHHHHHHHHHHH
Q 008340 346 ----SGFGHDSTEDARAAMELALLKIR 368 (569)
Q Consensus 346 ----~~~~HdS~EDA~Atl~L~~~kl~ 368 (569)
....|+|+.|.+-+..=+++...
T Consensus 171 ~aPkK~~~HrAldDI~ESI~ELq~Yr~ 197 (208)
T KOG3242|consen 171 RAPKKKATHRALDDIRESIKELQYYRE 197 (208)
T ss_pred cCcccccccchHHHHHHHHHHHHHHHH
Confidence 23689999999998877666543
No 57
>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=98.12 E-value=1e-05 Score=79.14 Aligned_cols=87 Identities=23% Similarity=0.197 Sum_probs=61.0
Q ss_pred HHHHHHhhcC-CCEEEEeCchhhHHHHcccC----------CCccchhhhccccCC----------CCCCchHHHHHHHh
Q 008340 280 QEEFLKLVYK-ETILVGHSLENDLLALKISH----------GLVIDTAVLYKHPQG----------GSHKTSLRVLAKKF 338 (569)
Q Consensus 280 q~~l~~ll~~-~tILVGHsL~~DL~aLki~h----------p~viDT~~L~~~~~g----------~~~k~sLk~La~~~ 338 (569)
-+.|.+++.. +.+-|||+..+|++.|+-.+ ..++||..++....+ ...+.||+.||+.+
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 3446667643 44569999999999998421 268999987654321 13567999999999
Q ss_pred cCcccccCC-------------CCCChHHHHHHHHHHHHHH
Q 008340 339 LSREIQQSG-------------FGHDSTEDARAAMELALLK 366 (569)
Q Consensus 339 Lg~~Iq~~~-------------~~HdS~EDA~Atl~L~~~k 366 (569)
||..+.... .-+=|..||.+++.||...
T Consensus 151 lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L 191 (193)
T cd06146 151 LGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKL 191 (193)
T ss_pred hCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 999887521 1133568888888888654
No 58
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=97.94 E-value=3.4e-05 Score=73.66 Aligned_cols=152 Identities=16% Similarity=0.211 Sum_probs=104.3
Q ss_pred CCcEEEEEeceecCCCC-ceEEEEEEEEeeC--eEE---EEEEEecCC----CCCCCcEee---cCCChhhhcCCCCCHH
Q 008340 211 PYEILALDCEMCYTNEG-LELTRVTLVDIKG--QVL---LDKLVKPSN----AIVDYNTRY---SGITHEMLSGVTTSLK 277 (569)
Q Consensus 211 ~~~~vAiDcEm~~t~~g-~eL~rVsvVd~~G--~vv---~D~lVkP~~----~I~dy~T~~---SGIT~e~L~~~~~tl~ 277 (569)
..+.+=|||||+|++++ +.|++|+.+=.++ +++ .+.-|.-.. .+.+|+++- ||+++.-.+.. .+.+
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 35689999999999988 5889988776543 444 333444322 556787755 56666655554 7999
Q ss_pred HHHHHHHHhhc-----CCCEEEEeCchhhHHHHcccCCCccchhhhccccCCCCCCchHHHHHHHhcCccccc---CCCC
Q 008340 278 DIQEEFLKLVY-----KETILVGHSLENDLLALKISHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQ---SGFG 349 (569)
Q Consensus 278 dVq~~l~~ll~-----~~tILVGHsL~~DL~aLki~hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~---~~~~ 349 (569)
++-.+++.||. ....+-|-|+..|-+||--.-|.+.+ ..-|+.. --.+||.||+++ .-+|.. .++.
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 99988888883 56789999999999999754443332 1112211 123578888776 555554 2478
Q ss_pred CChHHHHHHHHHHHHHHHHc
Q 008340 350 HDSTEDARAAMELALLKIRN 369 (569)
Q Consensus 350 HdS~EDA~Atl~L~~~kl~~ 369 (569)
|.|++|.+-+..=+.++.++
T Consensus 158 H~Al~DI~ESI~EL~~YR~~ 177 (184)
T COG1949 158 HRALDDIRESIAELRYYREH 177 (184)
T ss_pred hhHHHHHHHHHHHHHHHHHH
Confidence 99999999887776776665
No 59
>PRK05755 DNA polymerase I; Provisional
Probab=97.88 E-value=7.5e-05 Score=88.48 Aligned_cols=132 Identities=19% Similarity=0.254 Sum_probs=90.4
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcCC
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKE 290 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~~ 290 (569)
..++|+|+|+++.... ..++.|++-..+|.+.+ |.+ . ++.. ++...|.+++...
T Consensus 315 ~~~~a~DtEt~~l~~~~~~i~~i~ls~~~g~~~~---ip~-~----------~i~~-----------~~l~~l~~~L~d~ 369 (880)
T PRK05755 315 AGLFAFDTETTSLDPMQAELVGLSFAVEPGEAAY---IPL-D----------QLDR-----------EVLAALKPLLEDP 369 (880)
T ss_pred cCeEEEEeccCCCCcccccEEEEEEEeCCCcEEE---Eec-c----------cccH-----------HHHHHHHHHHhCC
Confidence 4589999999998764 46888887555564432 211 1 1110 4667788888543
Q ss_pred C-EEEEeCchhhHHHHccc----CCCccchhhhccccCCCCCCchHHHHHHHhcCccccc----------------CCCC
Q 008340 291 T-ILVGHSLENDLLALKIS----HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQ----------------SGFG 349 (569)
Q Consensus 291 t-ILVGHsL~~DL~aLki~----hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~----------------~~~~ 349 (569)
. ++||||+.||+.+|+.. ...++||.+++...... ..++|+.|++.|+|.++-. ....
T Consensus 370 ~v~kV~HNakfDl~~L~~~gi~~~~~~~DT~iAa~Ll~~~-~~~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~ple~~~ 448 (880)
T PRK05755 370 AIKKVGQNLKYDLHVLARYGIELRGIAFDTMLASYLLDPG-RRHGLDSLAERYLGHKTISFEEVAGKQLTFAQVDLEEAA 448 (880)
T ss_pred CCcEEEeccHhHHHHHHhCCCCcCCCcccHHHHHHHcCCC-CCCCHHHHHHHHhCCCccchHHhcCCCCCccccCHHHHH
Confidence 4 48999999999999742 23689999876544322 2389999999999877310 0023
Q ss_pred CChHHHHHHHHHHHHHHHHc
Q 008340 350 HDSTEDARAAMELALLKIRN 369 (569)
Q Consensus 350 HdS~EDA~Atl~L~~~kl~~ 369 (569)
|-+..|+.+++.|+....++
T Consensus 449 ~YAa~Dv~~~~~L~~~L~~~ 468 (880)
T PRK05755 449 EYAAEDADVTLRLHEVLKPK 468 (880)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 67899999999999766554
No 60
>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=97.83 E-value=0.00018 Score=68.02 Aligned_cols=126 Identities=18% Similarity=0.175 Sum_probs=79.7
Q ss_pred CcEEEEEeceecCCC-----CceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHh
Q 008340 212 YEILALDCEMCYTNE-----GLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKL 286 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~-----g~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~l 286 (569)
..++++|||.+.... ...|.+|+ ..+.+. +|.+... .. +-+.|.++
T Consensus 18 ~~~ig~D~E~~~~~~~~~~~~~~liQl~---~~~~~~---l~~~~~~----------------~~-------~~~~l~~l 68 (170)
T cd06141 18 EKVVGFDTEWRPSFRKGKRNKVALLQLA---TESRCL---LFQLAHM----------------DK-------LPPSLKQL 68 (170)
T ss_pred CCEEEEeCccCCccCCCCCCCceEEEEe---cCCcEE---EEEhhhh----------------hc-------ccHHHHHH
Confidence 469999999998643 23566666 122332 1222111 11 12345556
Q ss_pred hc-CCCEEEEeCchhhHHHHcccC----CCccchhhhccccCCCCCCchHHHHHHHhcCcccc--cC----C--------
Q 008340 287 VY-KETILVGHSLENDLLALKISH----GLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQ--QS----G-------- 347 (569)
Q Consensus 287 l~-~~tILVGHsL~~DL~aLki~h----p~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq--~~----~-------- 347 (569)
+. ++.+.|||++.+|+..|...+ ..++||..++....+...+.+|+.|++.|||.++. .. .
T Consensus 69 l~~~~i~kv~~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt~ 148 (170)
T cd06141 69 LEDPSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSK 148 (170)
T ss_pred hcCCCeeEEEeeeHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCCCCCCH
Confidence 63 445679999999999997332 35799998876654332346999999999999887 21 0
Q ss_pred -CCCChHHHHHHHHHHHHHH
Q 008340 348 -FGHDSTEDARAAMELALLK 366 (569)
Q Consensus 348 -~~HdS~EDA~Atl~L~~~k 366 (569)
.-|=|..||..+++||...
T Consensus 149 ~qi~YAa~Da~~~~~l~~~l 168 (170)
T cd06141 149 EQILYAATDAYASLELYRKL 168 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 1234567888888887543
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=97.70 E-value=0.00016 Score=63.14 Aligned_cols=57 Identities=26% Similarity=0.356 Sum_probs=41.6
Q ss_pred EEEEeceecCCCC-ceEEEEEEEEee-CeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcCC--
Q 008340 215 LALDCEMCYTNEG-LELTRVTLVDIK-GQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKE-- 290 (569)
Q Consensus 215 vAiDcEm~~t~~g-~eL~rVsvVd~~-G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~~-- 290 (569)
+++|+|+++.... .+|+.|++.+.+ +... +.+ +.+++...
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~~~----~~~--------------------------------f~~~l~~~~~ 44 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPEDTA----VID--------------------------------LKDILRDKPL 44 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCCCEE----Eeh--------------------------------HHHHHhhCCC
Confidence 4799999998765 589999999873 3322 111 55555333
Q ss_pred CEEEEeCchhhHHHHcc
Q 008340 291 TILVGHSLENDLLALKI 307 (569)
Q Consensus 291 tILVGHsL~~DL~aLki 307 (569)
.++||||..||+.+|+.
T Consensus 45 ~v~V~hn~~fD~~fL~~ 61 (96)
T cd06125 45 AILVGHNGSFDLPFLNN 61 (96)
T ss_pred CEEEEeCcHHhHHHHHH
Confidence 69999999999998874
No 62
>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=97.67 E-value=0.00086 Score=60.74 Aligned_cols=104 Identities=26% Similarity=0.289 Sum_probs=66.3
Q ss_pred EEEEEeceecCCC-CceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcCC-C
Q 008340 214 ILALDCEMCYTNE-GLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKE-T 291 (569)
Q Consensus 214 ~vAiDcEm~~t~~-g~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~~-t 291 (569)
.+++|||+..... ...+.-+++... ++++| +-.... ...+.+.+.+++... .
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 5799999766542 235666666543 33332 110000 145666677877433 4
Q ss_pred EEEEeCchhhHHHHccc----CCCccchhhhccccCCCCCCchHHHHHHHhcCccc
Q 008340 292 ILVGHSLENDLLALKIS----HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREI 343 (569)
Q Consensus 292 ILVGHsL~~DL~aLki~----hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~I 343 (569)
.+||||+.+|+.+|+.. ...++||..++........+++|+.|+++||+..+
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 59999999999999632 23578998876544322214699999999998874
No 63
>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=97.65 E-value=0.00033 Score=66.24 Aligned_cols=82 Identities=21% Similarity=0.215 Sum_probs=56.5
Q ss_pred HHHhhc-CCCEEEEeCchhhHHHHcccC----CCccchhhhccccCCCCCCchHHHHHHHhcCcccccC----C------
Q 008340 283 FLKLVY-KETILVGHSLENDLLALKISH----GLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQS----G------ 347 (569)
Q Consensus 283 l~~ll~-~~tILVGHsL~~DL~aLki~h----p~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~----~------ 347 (569)
|.+++. ++.+.|||++..|+..|...+ ..++||...+... ++..+.+|+.|+++|||..+... .
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 445553 444569999999999986422 2579999876644 33345699999999999987542 1
Q ss_pred ---CCCChHHHHHHHHHHHHH
Q 008340 348 ---FGHDSTEDARAAMELALL 365 (569)
Q Consensus 348 ---~~HdS~EDA~Atl~L~~~ 365 (569)
.-|=|..||.++..||..
T Consensus 138 t~~qi~YAa~Da~~l~~l~~~ 158 (161)
T cd06129 138 TEDQKLYAAADVYALLIIYTK 158 (161)
T ss_pred CHHHHHHHHHHHHHHHHHHHH
Confidence 123356788888888754
No 64
>PRK10829 ribonuclease D; Provisional
Probab=97.56 E-value=0.00085 Score=72.41 Aligned_cols=126 Identities=21% Similarity=0.221 Sum_probs=81.1
Q ss_pred CcEEEEEeceecCCCC---ceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhc
Q 008340 212 YEILALDCEMCYTNEG---LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVY 288 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g---~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~ 288 (569)
..++|||+|+...... ..|++|+ +..+..++| |-. +.| ...|.+++.
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 3589999999887543 2444444 433333333 331 111 123566665
Q ss_pred CCCEE-EEeCchhhHHHHcc----cCCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCC----CCC--------
Q 008340 289 KETIL-VGHSLENDLLALKI----SHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGF----GHD-------- 351 (569)
Q Consensus 289 ~~tIL-VGHsL~~DL~aLki----~hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~----~Hd-------- 351 (569)
...|+ |+|+..+|+.+|.. ....++||.+.+... |...+.+|+.|++.|||+.+.++.. ..+
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 55555 89999999999843 234799998877644 4445679999999999999876321 122
Q ss_pred -hHHHHHHHHHHHHHHHH
Q 008340 352 -STEDARAAMELALLKIR 368 (569)
Q Consensus 352 -S~EDA~Atl~L~~~kl~ 368 (569)
|..|+...++||.....
T Consensus 151 YAa~Dv~~L~~l~~~L~~ 168 (373)
T PRK10829 151 YAAADVFYLLPIAAKLMA 168 (373)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 35788888888765443
No 65
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=97.47 E-value=0.00093 Score=71.39 Aligned_cols=156 Identities=19% Similarity=0.186 Sum_probs=107.5
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEee--CeEE---EEEEEecCCCCC--CCcEeecCCChhhhcCCCCCHHHHHHHH
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDIK--GQVL---LDKLVKPSNAIV--DYNTRYSGITHEMLSGVTTSLKDIQEEF 283 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~~--G~vv---~D~lVkP~~~I~--dy~T~~SGIT~e~L~~~~~tl~dVq~~l 283 (569)
..|+..|-||-|..+. +..++++-|..+ -+++ +.-|+||.+-.. ...+=+|||||......+..-.+....|
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 688888888853 2233 567899976332 3367899999998887666666665555
Q ss_pred H-HhhcCCCEEEEeC-chhhHHHHccc--------------CC----Cccchhhh-c-cccCC--------CCCCchHHH
Q 008340 284 L-KLVYKETILVGHS-LENDLLALKIS--------------HG----LVIDTAVL-Y-KHPQG--------GSHKTSLRV 333 (569)
Q Consensus 284 ~-~ll~~~tILVGHs-L~~DL~aLki~--------------hp----~viDT~~L-~-~~~~g--------~~~k~sLk~ 333 (569)
. .+-.++|++||+| +.||=.+-+.. |. ..+|.... | -++.| .....+|..
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 5 4557999999996 89998887731 21 13454432 1 11212 123456999
Q ss_pred HHHHhcCcccccCCCCCChHHHHHHHHHHHHHHHHcCC
Q 008340 334 LAKKFLSREIQQSGFGHDSTEDARAAMELALLKIRNGP 371 (569)
Q Consensus 334 La~~~Lg~~Iq~~~~~HdS~EDA~Atl~L~~~kl~~g~ 371 (569)
|++.= |++-. .+|||+.|.+||..+.++.-+..|
T Consensus 169 Lt~AN-gieH~---nAHdAmsDVyATIamAklvk~~QP 202 (475)
T COG2925 169 LTKAN-GIEHS---NAHDAMSDVYATIAMAKLVKTAQP 202 (475)
T ss_pred Hhhcc-ccccc---hhhHHHHHHHHHHHHHHHHHhhCc
Confidence 99863 55543 689999999999999876555443
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=97.42 E-value=0.00099 Score=65.17 Aligned_cols=115 Identities=16% Similarity=0.205 Sum_probs=76.1
Q ss_pred CcEEEEEeceecC-----CCCceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHh
Q 008340 212 YEILALDCEMCYT-----NEGLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKL 286 (569)
Q Consensus 212 ~~~vAiDcEm~~t-----~~g~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~l 286 (569)
-+++++|+||..- ...++|..||++...++.++.. ++.. ...+... .+-.++..++.++
T Consensus 3 l~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~~--~~~~-------------~~~v~~~-~~E~~lL~~F~~~ 66 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVITW--KKFD-------------LPFVEVV-KTEKEMIKRFIEI 66 (195)
T ss_pred ceEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEEe--cCCC-------------CCeEEEe-CCHHHHHHHHHHH
Confidence 4689999999842 1236899999998666544311 1111 1123333 3567788888888
Q ss_pred hcC--CCEEEEeCc-hhhHHHHcc-------cCC------------------------CccchhhhccccCCCCCCchHH
Q 008340 287 VYK--ETILVGHSL-ENDLLALKI-------SHG------------------------LVIDTAVLYKHPQGGSHKTSLR 332 (569)
Q Consensus 287 l~~--~tILVGHsL-~~DL~aLki-------~hp------------------------~viDT~~L~~~~~g~~~k~sLk 332 (569)
+.. -.+|||||. .||+..|.- ..+ .++|+..+++... ....++|+
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 864 479999997 579988762 111 1567776665532 23578899
Q ss_pred HHHHHhcCccc
Q 008340 333 VLAKKFLSREI 343 (569)
Q Consensus 333 ~La~~~Lg~~I 343 (569)
++|+++||..-
T Consensus 146 ~v~~~~Lg~~k 156 (195)
T cd05780 146 RVYEELFGIEK 156 (195)
T ss_pred HHHHHHhCCCC
Confidence 99999999863
No 67
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=96.96 E-value=0.018 Score=53.05 Aligned_cols=64 Identities=28% Similarity=0.323 Sum_probs=44.0
Q ss_pred HHHHHhhc-CCCEEEEeCchhhHHHHcc---cCCCccchhhhccccCCCCCCchHHHHHHHhcCcccc
Q 008340 281 EEFLKLVY-KETILVGHSLENDLLALKI---SHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQ 344 (569)
Q Consensus 281 ~~l~~ll~-~~tILVGHsL~~DL~aLki---~hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq 344 (569)
..|.+++. .+...||||+.+|+.+|+. .-+.++||+..+.-..+.....+|+.|++.|||..+.
T Consensus 65 ~~l~~~l~~~~~~kv~~d~k~~~~~L~~~gi~~~~~~D~~laayll~p~~~~~~l~~l~~~~l~~~~~ 132 (172)
T smart00474 65 EILKDLLEDETITKVGHNAKFDLHVLARFGIELENIFDTMLAAYLLLGGPSKHGLATLLKEYLGVELD 132 (172)
T ss_pred HHHHHHhcCCCceEEEechHHHHHHHHHCCCcccchhHHHHHHHHHcCCCCcCCHHHHHHHHhCCCCC
Confidence 34555553 3456899999999999963 1124599998765332222325899999999998763
No 68
>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=96.89 E-value=0.0061 Score=65.99 Aligned_cols=117 Identities=20% Similarity=0.308 Sum_probs=87.9
Q ss_pred CCCCCCchhHHHHHHHHHhcCCeeeeeccccccccccCCCcceeecCChHHHHHHHHHhccCCCccEEEEeccccchhhh
Q 008340 372 DFGSPPSVMRTKLLKVLFEYGKTSTLIDNVSIIKRYASESSHAIPVSSDDEVLSKARKEVKNDRIHFVWTQFSELNLHFK 451 (569)
Q Consensus 372 ~fg~~~~~~~~~l~~~l~~~g~~~~~~d~~~~~~~~~~~~~~~i~~~~D~ev~~~~~~~v~~~~~~f~~~~~~~l~~~~~ 451 (569)
.|+..+. ...++++|.+.|.....|........ +++-+.+++..++++.++++++++++...+|+++.|.++...+.
T Consensus 209 dy~~~p~--~pTvld~l~~aG~~V~~VGki~DiF~-g~Glt~a~~~~~~~~~~~~~l~aL~~~~~~lif~nl~d~D~~~G 285 (381)
T TIGR01696 209 DYALKPF--APTVLQKLKDEGHDVISIGKIADIYD-GEGITKKVRTTSNMDGMDATIKEMKEDFTGISFTNLVDFDALWG 285 (381)
T ss_pred CCCCCCC--CCCHHHHHHHCCCeEEEEccHHhEec-CCCcccccCCCCHHHHHHHHHHHHhcCCCCEEEEEeCCCccccC
Confidence 5666652 24799999999998887765432221 33455667889999999999999987667899999988752112
Q ss_pred hhhHhHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHHHHHHHHHHHHHhhCCCCcEEEEEeCCCC
Q 008340 452 KQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPEIKEILARTDARVNSLYTALPTNTMLIICTGHGD 523 (569)
Q Consensus 452 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~iy~~lP~~t~liv~sg~gd 523 (569)
+. .......++++.+|++|.+|.+.|++++++||.+=||.
T Consensus 286 H~--------------------------------~d~~~y~~ale~vD~~Lg~ll~~L~~~tllIITADHG~ 325 (381)
T TIGR01696 286 HR--------------------------------RDVAGYAAALELFDRRLPELFSLLREDDLLIITADHGN 325 (381)
T ss_pred CC--------------------------------CCHHHHHHHHHHHHHHHHHHHHHhccCCEEEEECCCCC
Confidence 11 01123566789999999999999999999999999998
No 69
>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=96.88 E-value=0.0092 Score=64.30 Aligned_cols=123 Identities=20% Similarity=0.179 Sum_probs=74.6
Q ss_pred cEEEEEeceecCCCC---ceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhc-
Q 008340 213 EILALDCEMCYTNEG---LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVY- 288 (569)
Q Consensus 213 ~~vAiDcEm~~t~~g---~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~- 288 (569)
.++|||+|+...... ..|++|+- .++.. +|.|-.. .+ + ..|.+++.
T Consensus 19 ~~ia~DtE~~~~~~y~~~l~LiQia~--~~~~~----liD~~~~-~~-------------------~----~~L~~lL~d 68 (367)
T TIGR01388 19 PFVALDTEFVRERTFWPQLGLIQVAD--GEQLA----LIDPLVI-ID-------------------W----SPLKELLRD 68 (367)
T ss_pred CEEEEeccccCCCCCCCcceEEEEee--CCeEE----EEeCCCc-cc-------------------H----HHHHHHHCC
Confidence 599999999876432 34555552 22222 4444221 00 1 12344443
Q ss_pred CCCEEEEeCchhhHHHHcc---cC-CCccchhhhccccCCCCCCchHHHHHHHhcCcccccCC----CCCC---------
Q 008340 289 KETILVGHSLENDLLALKI---SH-GLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSG----FGHD--------- 351 (569)
Q Consensus 289 ~~tILVGHsL~~DL~aLki---~h-p~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~----~~Hd--------- 351 (569)
++.+.|+|++.+|+.+|+. .. ..++||.+.+... |+..+.+|..|++.|||+.+..+. -..+
T Consensus 69 ~~i~KV~h~~k~Dl~~L~~~~~~~~~~~fDtqlAa~lL-~~~~~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~Y 147 (367)
T TIGR01388 69 ESVVKVLHAASEDLEVFLNLFGELPQPLFDTQIAAAFC-GFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEY 147 (367)
T ss_pred CCceEEEeecHHHHHHHHHHhCCCCCCcccHHHHHHHh-CCCCCccHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHH
Confidence 4455799999999999863 22 3679998764433 333456999999999999886421 0122
Q ss_pred hHHHHHHHHHHHHHH
Q 008340 352 STEDARAAMELALLK 366 (569)
Q Consensus 352 S~EDA~Atl~L~~~k 366 (569)
+..||.+...|+...
T Consensus 148 Aa~Dv~~L~~L~~~L 162 (367)
T TIGR01388 148 AAADVTYLLPLYAKL 162 (367)
T ss_pred HHHHHHHHHHHHHHH
Confidence 456676677776544
No 70
>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=96.61 E-value=0.046 Score=53.90 Aligned_cols=116 Identities=18% Similarity=0.195 Sum_probs=68.8
Q ss_pred CCcEEEEEeceecCCCCceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcCC
Q 008340 211 PYEILALDCEMCYTNEGLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKE 290 (569)
Q Consensus 211 ~~~~vAiDcEm~~t~~g~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~~ 290 (569)
+-+++++|+|+.+-+ +|.-|+..+..-+.++ .+.-..++. |. .+.-. .+-.++...+.+++..-
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 347999999996533 7888887775333322 111111111 11 11112 35556677777777444
Q ss_pred --CEEEEeCc-hhhHHHHc-------ccCC--------------------------CccchhhhccccCCCCCCchHHHH
Q 008340 291 --TILVGHSL-ENDLLALK-------ISHG--------------------------LVIDTAVLYKHPQGGSHKTSLRVL 334 (569)
Q Consensus 291 --tILVGHsL-~~DL~aLk-------i~hp--------------------------~viDT~~L~~~~~g~~~k~sLk~L 334 (569)
.||+|||. .||+..|. +.++ -++|+..+.+...-....++|.++
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 69999997 56998865 2111 056766655432112457889999
Q ss_pred HHHhcCcc
Q 008340 335 AKKFLSRE 342 (569)
Q Consensus 335 a~~~Lg~~ 342 (569)
|+++||..
T Consensus 146 a~~~Lg~~ 153 (193)
T cd05784 146 AQELLGEG 153 (193)
T ss_pred HHHHhCCC
Confidence 99999974
No 71
>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=96.58 E-value=0.03 Score=55.66 Aligned_cols=128 Identities=16% Similarity=0.173 Sum_probs=71.7
Q ss_pred CcEEEEEeceecCCC------CceEEEEEEEEe-eCeEEE-EEEEecCCCCCCCc--EeecCCChhhhcCCCCCHHHHHH
Q 008340 212 YEILALDCEMCYTNE------GLELTRVTLVDI-KGQVLL-DKLVKPSNAIVDYN--TRYSGITHEMLSGVTTSLKDIQE 281 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~------g~eL~rVsvVd~-~G~vv~-D~lVkP~~~I~dy~--T~~SGIT~e~L~~~~~tl~dVq~ 281 (569)
.+++|+|+|+..... .+.|..||++.. .|..+. ..++.+...-..|. -.+.|. -.+... .+-.++..
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 268999999975 353321 11111100000000 011111 011112 36677888
Q ss_pred HHHHhhcCC--CEEEEeCc-hhhHHHHccc---CC----------------------Cccchhhhcccc-CCCCCCchHH
Q 008340 282 EFLKLVYKE--TILVGHSL-ENDLLALKIS---HG----------------------LVIDTAVLYKHP-QGGSHKTSLR 332 (569)
Q Consensus 282 ~l~~ll~~~--tILVGHsL-~~DL~aLki~---hp----------------------~viDT~~L~~~~-~g~~~k~sLk 332 (569)
++.+++..- .+++|+|. .||+.+|.-. |. -.+|...+++.. ......++|.
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 49999996 7899887621 10 045665555431 1122367899
Q ss_pred HHHHHhcCcc
Q 008340 333 VLAKKFLSRE 342 (569)
Q Consensus 333 ~La~~~Lg~~ 342 (569)
++|+.+||.+
T Consensus 159 ~Va~~~Lg~~ 168 (204)
T cd05779 159 AVTKAKLGYD 168 (204)
T ss_pred HHHHHHhCCC
Confidence 9999999963
No 72
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=96.56 E-value=0.051 Score=51.07 Aligned_cols=85 Identities=20% Similarity=0.185 Sum_probs=53.7
Q ss_pred HHHHHhhc-CCCEEEEeCchhhHHHHcc----cCCCccchhhhccccCCCCCCchHHHHHHHhcCcccccC---CC-CCC
Q 008340 281 EEFLKLVY-KETILVGHSLENDLLALKI----SHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQS---GF-GHD 351 (569)
Q Consensus 281 ~~l~~ll~-~~tILVGHsL~~DL~aLki----~hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~---~~-~Hd 351 (569)
..|..++. ++...|||++.+|+.+|+. ....+.||...+.-. ++..+.+|+.|++.|||..+-.. +. +.+
T Consensus 54 ~~l~~ll~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~~D~~laayLl-~p~~~~~l~~l~~~~l~~~~~~~~~~~~w~~~ 132 (178)
T cd06142 54 SPLKELLADPNIVKVFHAAREDLELLKRDFGILPQNLFDTQIAARLL-GLGDSVGLAALVEELLGVELDKGEQRSDWSKR 132 (178)
T ss_pred HHHHHHHcCCCceEEEeccHHHHHHHHHHcCCCCCCcccHHHHHHHh-CCCccccHHHHHHHHhCCCCCcccccccCCCC
Confidence 33555553 4567899999999999953 223578998654332 33234599999999999873211 01 112
Q ss_pred ---------hHHHHHHHHHHHHHH
Q 008340 352 ---------STEDARAAMELALLK 366 (569)
Q Consensus 352 ---------S~EDA~Atl~L~~~k 366 (569)
+..||.++.+|+...
T Consensus 133 ~l~~~~~~yaa~~a~~l~~L~~~l 156 (178)
T cd06142 133 PLTDEQLEYAALDVRYLLPLYEKL 156 (178)
T ss_pred CCCHHHHHHHHHhHHHHHHHHHHH
Confidence 455676777776543
No 73
>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=96.53 E-value=0.0053 Score=60.22 Aligned_cols=62 Identities=27% Similarity=0.191 Sum_probs=41.3
Q ss_pred HHHHhhc-CCCEEEEeCchhhHHHHcc----cCCCccchhhhcccc----CC---CCCCchHHHHHHHhcCccc
Q 008340 282 EFLKLVY-KETILVGHSLENDLLALKI----SHGLVIDTAVLYKHP----QG---GSHKTSLRVLAKKFLSREI 343 (569)
Q Consensus 282 ~l~~ll~-~~tILVGHsL~~DL~aLki----~hp~viDT~~L~~~~----~g---~~~k~sLk~La~~~Lg~~I 343 (569)
.|.+++. ++.+-|||++.+|+.+|.. .-..+.||.+.+... .| ..+..+|..|++.|||..+
T Consensus 56 ~L~~iLe~~~i~Kv~h~~k~D~~~L~~~~gi~~~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~ 129 (197)
T cd06148 56 GLKDILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISI 129 (197)
T ss_pred HHHHHhcCCCccEEEEechhHHHHHHHhcCccccceeeHHHHHHHHHHHhcCCccccccccHHHHHHHhhCCCh
Confidence 3555553 3445699999999999942 223579998753221 11 1223589999999999887
No 74
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=96.40 E-value=0.011 Score=63.27 Aligned_cols=124 Identities=22% Similarity=0.245 Sum_probs=80.3
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcCC
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKE 290 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~~ 290 (569)
..+||||.|+.+...- ..++=|-|-+.++.. +|.|-.++.|. +.|..+. -+++
T Consensus 17 ~~~iAiDTEf~r~~t~~p~LcLIQi~~~e~~~----lIdpl~~~~d~----------------~~l~~Ll------~d~~ 70 (361)
T COG0349 17 SKAIAIDTEFMRLRTYYPRLCLIQISDGEGAS----LIDPLAGILDL----------------PPLVALL------ADPN 70 (361)
T ss_pred CCceEEecccccccccCCceEEEEEecCCCce----Eeccccccccc----------------chHHHHh------cCCc
Confidence 3589999999998775 466666666666633 55554432221 1222111 1233
Q ss_pred CEEEEeCchhhHHHHcc---cCC-CccchhhhccccCCCCCCchHHHHHHHhcCcccccCC----CCCChHHHHH---HH
Q 008340 291 TILVGHSLENDLLALKI---SHG-LVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSG----FGHDSTEDAR---AA 359 (569)
Q Consensus 291 tILVGHsL~~DL~aLki---~hp-~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~----~~HdS~EDA~---At 359 (569)
-+=|=|+..+||.+|.- .+| .++||.+..+.. |..-+++|+.|+++++|++|.++. =+++++.++. |+
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 33377999999999874 244 689999877655 333489999999999999998742 2466666653 44
Q ss_pred HHH
Q 008340 360 MEL 362 (569)
Q Consensus 360 l~L 362 (569)
.++
T Consensus 150 ~DV 152 (361)
T COG0349 150 ADV 152 (361)
T ss_pred HHH
Confidence 444
No 75
>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=96.39 E-value=0.017 Score=57.40 Aligned_cols=71 Identities=23% Similarity=0.309 Sum_probs=49.6
Q ss_pred CcEEEEEeceecCC---------CCceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHH
Q 008340 212 YEILALDCEMCYTN---------EGLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEE 282 (569)
Q Consensus 212 ~~~vAiDcEm~~t~---------~g~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~ 282 (569)
-++++||+|+.... .++.|..|++.+..|.... +. ... .+-.++..+
T Consensus 9 lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~---~~--------------------~~~-~~E~~lL~~ 64 (207)
T cd05785 9 LRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEV---LH--------------------AED-AAEKELLEE 64 (207)
T ss_pred ceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceee---ec--------------------cCC-CCHHHHHHH
Confidence 47999999996642 1257999998876552111 10 012 477788888
Q ss_pred HHHhhcCC--CEEEEeCc-hhhHHHHc
Q 008340 283 FLKLVYKE--TILVGHSL-ENDLLALK 306 (569)
Q Consensus 283 l~~ll~~~--tILVGHsL-~~DL~aLk 306 (569)
+.+++..- .||||||. .||+..|.
T Consensus 65 f~~~i~~~dPdii~g~N~~~FD~pyl~ 91 (207)
T cd05785 65 LVAIIRERDPDVIEGHNIFRFDLPYLR 91 (207)
T ss_pred HHHHHHHhCCCEEeccCCcccCHHHHH
Confidence 88888543 79999999 89998866
No 76
>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=96.29 E-value=0.037 Score=54.16 Aligned_cols=104 Identities=22% Similarity=0.222 Sum_probs=68.4
Q ss_pred CcEEEEEeceecC----CC-CceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHh
Q 008340 212 YEILALDCEMCYT----NE-GLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKL 286 (569)
Q Consensus 212 ~~~vAiDcEm~~t----~~-g~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~l 286 (569)
-+++++|+||..- ++ .+.|+.||+...+|.+.+ +. .+. .+-.++...+.++
T Consensus 3 l~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~---~~--------------------~~~-~~E~~lL~~F~~~ 58 (188)
T cd05781 3 LKTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEF---IL--------------------AEG-LDDRKIIREFVKY 58 (188)
T ss_pred ceEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEE---EE--------------------ecC-CCHHHHHHHHHHH
Confidence 4689999999832 12 258999999987665321 00 012 4666777788888
Q ss_pred hcCC--CEEEEeCc-hhhHHHHccc---C----C----------------------CccchhhhccccCCCCCCchHHHH
Q 008340 287 VYKE--TILVGHSL-ENDLLALKIS---H----G----------------------LVIDTAVLYKHPQGGSHKTSLRVL 334 (569)
Q Consensus 287 l~~~--tILVGHsL-~~DL~aLki~---h----p----------------------~viDT~~L~~~~~g~~~k~sLk~L 334 (569)
+..- .+|+|+|. .||+.+|.-. | + .++|...+.+... ....++|..+
T Consensus 59 i~~~dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~-~l~~y~L~~V 137 (188)
T cd05781 59 VKEYDPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIP-EVKVKTLENV 137 (188)
T ss_pred HHHcCCCEEEecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhC-CCCCCCHHHH
Confidence 8544 69999996 6899887620 1 0 1566665554432 2456889999
Q ss_pred HHHhcCc
Q 008340 335 AKKFLSR 341 (569)
Q Consensus 335 a~~~Lg~ 341 (569)
|+ +||.
T Consensus 138 a~-~Lg~ 143 (188)
T cd05781 138 AE-YLGV 143 (188)
T ss_pred HH-HHCC
Confidence 98 5886
No 77
>PRK05362 phosphopentomutase; Provisional
Probab=96.25 E-value=0.03 Score=61.04 Aligned_cols=118 Identities=20% Similarity=0.307 Sum_probs=85.6
Q ss_pred CCCCCCCchhHHHHHHHHHhcCCeeeeeccccccccccCCCcceeecCChHHHHHHHHHhcc-CCCccEEEEeccccchh
Q 008340 371 PDFGSPPSVMRTKLLKVLFEYGKTSTLIDNVSIIKRYASESSHAIPVSSDDEVLSKARKEVK-NDRIHFVWTQFSELNLH 449 (569)
Q Consensus 371 ~~fg~~~~~~~~~l~~~l~~~g~~~~~~d~~~~~~~~~~~~~~~i~~~~D~ev~~~~~~~v~-~~~~~f~~~~~~~l~~~ 449 (569)
..|+..+. ...++++|.+.|.....|........ ..+-+.+++..++.++++++++.++ ....+|++++|.++...
T Consensus 215 ~d~~~~p~--~~Tl~d~L~~aG~~v~~VGki~DiFa-~~G~t~~~~~~~~~~~~~~ale~L~~~~~~~fvfvn~~~~D~~ 291 (394)
T PRK05362 215 HDYALKPP--APTVLDKLKEAGGEVIAVGKIADIFA-GQGITEKVKTKSNMDGMDATIEEMKEAGDNGLVFTNLVDFDSL 291 (394)
T ss_pred CCcCcCCC--CCCHHHHHHHCCCeEEEEEehhhccc-CCCcccccCCCCHHHHHHHHHHHHHhCCCCcEEEEecccCccc
Confidence 35666552 35799999999988888775332211 2233445678889999999999998 55678999999876421
Q ss_pred hhhhhHhHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHHHHHHHHHHHHHhhCCCCcEEEEEeCCCC
Q 008340 450 FKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPEIKEILARTDARVNSLYTALPTNTMLIICTGHGD 523 (569)
Q Consensus 450 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~iy~~lP~~t~liv~sg~gd 523 (569)
+.+. ...+...++++.+|++|.+|.+.|++++++||.+=||.
T Consensus 292 ~GH~--------------------------------~~~~~y~~ale~~D~~lg~ll~~L~~~tlliiTaDHG~ 333 (394)
T PRK05362 292 YGHR--------------------------------RDVAGYAAALEEFDARLPELLAALKEDDLLIITADHGN 333 (394)
T ss_pred cCCc--------------------------------CCHHHHHHHHHHHHHHHHHHHHHhccCCEEEEeCCCCC
Confidence 1110 01124567799999999999999999999999999995
No 78
>COG1015 DeoB Phosphopentomutase [Carbohydrate transport and metabolism]
Probab=96.02 E-value=0.056 Score=58.07 Aligned_cols=109 Identities=20% Similarity=0.329 Sum_probs=82.8
Q ss_pred HHHHHHHHhcCCeeeeeccccccccccCCCcceeecCChHHHHHHHHHhccCCCc-cEEEEeccccchhhhhhhHhHHHH
Q 008340 382 TKLLKVLFEYGKTSTLIDNVSIIKRYASESSHAIPVSSDDEVLSKARKEVKNDRI-HFVWTQFSELNLHFKKQAKDEAKL 460 (569)
Q Consensus 382 ~~l~~~l~~~g~~~~~~d~~~~~~~~~~~~~~~i~~~~D~ev~~~~~~~v~~~~~-~f~~~~~~~l~~~~~~~~~~~~~~ 460 (569)
+.+++.|.+.|+....|......-. +.+-+..+.-.++.+.++..+++++.... .|+|..|-+....+.++ +++
T Consensus 227 ~tvl~~L~e~g~~vi~IGKI~DI~~-~~Git~~~~~~~n~~~~d~tl~~~~~~~~~~~vFtNlVdfD~~yGHR-rDv--- 301 (397)
T COG1015 227 PTVLDKLKEAGRPVIAIGKIADIYA-GQGITEKVKAVSNMDGMDVTLEEMKTAEFNGLVFTNLVDFDSLYGHR-RDV--- 301 (397)
T ss_pred hhHHHHHHHcCCceEEEeeHHhhhc-cccccccccCCCcHHHHHHHHHHHhcCCCCcEEEEeeeecccccccc-cch---
Confidence 6899999999987777765433322 23456677889999999999999985433 49999987776444432 122
Q ss_pred HHHHHHHhhhhhcccccccccccCCCCcHHHHHHHHHHHHHHHHHHhhCCCCcEEEEEeCCCC
Q 008340 461 NEKLAELISLATCDKKLSDSKRFKSFVTPEIKEILARTDARVNSLYTALPTNTMLIICTGHGD 523 (569)
Q Consensus 461 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~iy~~lP~~t~liv~sg~gd 523 (569)
.--.++|+.+|+||-.|.++|.++.+|||..-||+
T Consensus 302 ----------------------------~gYa~aLe~FD~rL~e~~~~l~edDlLiiTADHGn 336 (397)
T COG1015 302 ----------------------------AGYAAALEEFDRRLPELIENLREDDLLIITADHGN 336 (397)
T ss_pred ----------------------------HHHHHHHHHHHHHHHHHHHhcCCCCEEEEecCCCC
Confidence 13567799999999999999999999999999986
No 79
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=95.86 E-value=0.13 Score=51.11 Aligned_cols=124 Identities=19% Similarity=0.174 Sum_probs=72.4
Q ss_pred CCcEEEEEeceecCC----C-----CceEEEEEEEEeeCeEEEEEEEec-CCCCC--CCcEeecCCChhhhcCCCCCHHH
Q 008340 211 PYEILALDCEMCYTN----E-----GLELTRVTLVDIKGQVLLDKLVKP-SNAIV--DYNTRYSGITHEMLSGVTTSLKD 278 (569)
Q Consensus 211 ~~~~vAiDcEm~~t~----~-----g~eL~rVsvVd~~G~vv~D~lVkP-~~~I~--dy~T~~SGIT~e~L~~~~~tl~d 278 (569)
+-+++|+|+|+..-. + +++|+.|++.+.+|..-+ -++.. ..... ++. -| ..+... .+-.+
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 357999999997522 1 258999999864442111 11111 10000 000 00 112233 46778
Q ss_pred HHHHHHHhhcCCCEEEEeCc-hhhHHHHccc---C--------------------CCccchhhhcccc------C-CCCC
Q 008340 279 IQEEFLKLVYKETILVGHSL-ENDLLALKIS---H--------------------GLVIDTAVLYKHP------Q-GGSH 327 (569)
Q Consensus 279 Vq~~l~~ll~~~tILVGHsL-~~DL~aLki~---h--------------------p~viDT~~L~~~~------~-g~~~ 327 (569)
+..++.+++..-.+|||+|. .||+..|.-. | ...+|....+... . ....
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 88889999987789999996 7899887621 1 1235554433321 0 1224
Q ss_pred CchHHHHHHHhcCcc
Q 008340 328 KTSLRVLAKKFLSRE 342 (569)
Q Consensus 328 k~sLk~La~~~Lg~~ 342 (569)
.++|+.+|+.+||..
T Consensus 156 ~~~L~~Va~~~lg~~ 170 (204)
T cd05783 156 EYTLDAVAKALLGEG 170 (204)
T ss_pred cCcHHHHHHHhcCCC
Confidence 678999999999874
No 80
>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=95.79 E-value=0.27 Score=49.45 Aligned_cols=122 Identities=18% Similarity=0.258 Sum_probs=71.8
Q ss_pred CCcEEEEEeceecCCC------CceEEEEEEEEe-eCe--EEEEE-E-EecCCCCCCCcEeecCCChhhhcCCCCCHHHH
Q 008340 211 PYEILALDCEMCYTNE------GLELTRVTLVDI-KGQ--VLLDK-L-VKPSNAIVDYNTRYSGITHEMLSGVTTSLKDI 279 (569)
Q Consensus 211 ~~~~vAiDcEm~~t~~------g~eL~rVsvVd~-~G~--vv~D~-l-VkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dV 279 (569)
+-+++|+|+|+..... .++|..||++.. +|. ..... + +++..++. | ..+... .+-.++
T Consensus 6 ~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~~~~~~~-------~---~~v~~~-~~E~eL 74 (230)
T cd05777 6 PLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIV-------G---AQVFSF-ETEEEL 74 (230)
T ss_pred CceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeCCCCCCC-------C---CEEEEE-CCHHHH
Confidence 4579999999975321 268999999965 443 11111 1 22333322 1 112222 356677
Q ss_pred HHHHHHhhcC--CCEEEEeCc-hhhHHHHcc-------cC----------C--------------------------Ccc
Q 008340 280 QEEFLKLVYK--ETILVGHSL-ENDLLALKI-------SH----------G--------------------------LVI 313 (569)
Q Consensus 280 q~~l~~ll~~--~tILVGHsL-~~DL~aLki-------~h----------p--------------------------~vi 313 (569)
..++.+++.. -.||+|||. .||+..|.- .+ + .++
T Consensus 75 L~~f~~~i~~~DPDii~GyN~~~FDl~yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~~i 154 (230)
T cd05777 75 LLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQF 154 (230)
T ss_pred HHHHHHHHHhcCCCEEEEecCCCCCHHHHHHHHHHhCCccccccccccCCceeEeCCcccccccccccceEEEEcCEEee
Confidence 7777777743 269999997 569987651 10 0 123
Q ss_pred chhhhccccCCCCCCchHHHHHHHhcCcccc
Q 008340 314 DTAVLYKHPQGGSHKTSLRVLAKKFLSREIQ 344 (569)
Q Consensus 314 DT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq 344 (569)
|+..+++.. .....++|..+|+++||....
T Consensus 155 D~~~~~~~~-~kl~sy~L~~Va~~~Lg~~k~ 184 (230)
T cd05777 155 DLLQVIQRD-YKLRSYSLNSVSAHFLGEQKE 184 (230)
T ss_pred eHHHHHHHh-cCcccCcHHHHHHHHhCCCCC
Confidence 444444332 124578899999999997654
No 81
>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=95.44 E-value=0.035 Score=51.97 Aligned_cols=125 Identities=18% Similarity=0.110 Sum_probs=58.2
Q ss_pred EEEEeceecCCCC-ceEEEEEEEEee-CeEE-EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcCCC
Q 008340 215 LALDCEMCYTNEG-LELTRVTLVDIK-GQVL-LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYKET 291 (569)
Q Consensus 215 vAiDcEm~~t~~g-~eL~rVsvVd~~-G~vv-~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~~t 291 (569)
+.+|+||+|..++ ..+.-|+++..+ ++.. +..+. .-.++ .-+.+.+.+ .++....
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~~~~~~--------------~~~~~-------ee~~~~~~~-~~l~~~~ 58 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIITFIQWF--------------AEDPD-------EEEIILEFF-ELLDEAD 58 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE-EEEE---------------GGGHH-------HHHHHHH---HHHHTT-
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEEeeHhh--------------ccCcH-------HHHHHHHHH-HHHhcCC
Confidence 4699999999775 456777777642 2221 22221 11110 111222223 5566889
Q ss_pred EEEEeC-chhhHHHHccc--------CCCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHHHHHHHH
Q 008340 292 ILVGHS-LENDLLALKIS--------HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMEL 362 (569)
Q Consensus 292 ILVGHs-L~~DL~aLki~--------hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~Atl~L 362 (569)
.+|+|| -.||+.+|+-. ....+|.....++... .++||+.+++. ||++-+. .--+...+..+
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 58899999842 2257898877754422 55689999985 6777531 22345566777
Q ss_pred HHHHHHcC
Q 008340 363 ALLKIRNG 370 (569)
Q Consensus 363 ~~~kl~~g 370 (569)
|+..++.|
T Consensus 130 ~~~~~~~~ 137 (164)
T PF13482_consen 130 YKEYLETG 137 (164)
T ss_dssp HH---TTG
T ss_pred HHHHHhcC
Confidence 76554443
No 82
>PRK12383 putative mutase; Provisional
Probab=95.32 E-value=0.13 Score=56.35 Aligned_cols=110 Identities=17% Similarity=0.245 Sum_probs=80.6
Q ss_pred HHHHHHHHhcCCeeeeeccccccccccCCCcceeecCChHHHHHHHHHhccCCCccEEEEeccccchhhhhhhHhHHHHH
Q 008340 382 TKLLKVLFEYGKTSTLIDNVSIIKRYASESSHAIPVSSDDEVLSKARKEVKNDRIHFVWTQFSELNLHFKKQAKDEAKLN 461 (569)
Q Consensus 382 ~~l~~~l~~~g~~~~~~d~~~~~~~~~~~~~~~i~~~~D~ev~~~~~~~v~~~~~~f~~~~~~~l~~~~~~~~~~~~~~~ 461 (569)
..+.+.+.+.|.+...|........ ..+.+..++..+.++.++++++.++....+|+++.|.+.. .+.+..
T Consensus 234 ~~v~~~l~~~G~~v~~VGKi~Di~s-~~G~t~~~~~~~t~~~~~~~l~aL~~~~~dlvfvnl~~~D-~~GH~~------- 304 (406)
T PRK12383 234 VQVPQKLYEAGVPVVLVGKVADIVN-NPYGVSWQNLVDTQRVMDITLDEFNTHPTAFICTNIQETD-LAGHAE------- 304 (406)
T ss_pred chhhhHHHHcCCCEEEEEEhHHeec-cCCcccccccCCHHHHHHHHHHHHhcCCCCEEEEeccCCc-cccccC-------
Confidence 4678888889988888854321111 2234455667777899999999998766799999998875 222210
Q ss_pred HHHHHHhhhhhcccccccccccCCCCcHHHHHHHHHHHHHHHHHHhhCCCCcEEEEEeCCCChH
Q 008340 462 EKLAELISLATCDKKLSDSKRFKSFVTPEIKEILARTDARVNSLYTALPTNTMLIICTGHGDTA 525 (569)
Q Consensus 462 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~iy~~lP~~t~liv~sg~gd~~ 525 (569)
..+...++++.+|++|.+|.+.|++++++||.+=||++-
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 112356678999999999999999999999999999853
No 83
>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=94.82 E-value=0.57 Score=44.27 Aligned_cols=104 Identities=21% Similarity=0.204 Sum_probs=67.0
Q ss_pred cEEEEEeceecCCCC-ceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhc-CC
Q 008340 213 EILALDCEMCYTNEG-LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVY-KE 290 (569)
Q Consensus 213 ~~vAiDcEm~~t~~g-~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~-~~ 290 (569)
+..++|.|+.+.... ..+..+++-..+ ++. ||.+... + .+.+.+.+++. ++
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 568999999998863 467777776543 332 2322211 0 13444556663 34
Q ss_pred CEEEEeCchhhHHHHccc----CCCccchhhhccccCCCCCCchHHHHHHHhcCccc
Q 008340 291 TILVGHSLENDLLALKIS----HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREI 343 (569)
Q Consensus 291 tILVGHsL~~DL~aLki~----hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~I 343 (569)
...||||+.+|+.+|+.. ...+.||.+..--.......++|..|+++||+.++
T Consensus 57 ~~ki~~d~K~~~~~l~~~gi~~~~~~fDt~laaYLL~p~~~~~~l~~l~~~yl~~~~ 113 (178)
T cd06140 57 IPKVGHDAKRAYVALKRHGIELAGVAFDTMLAAYLLDPTRSSYDLADLAKRYLGREL 113 (178)
T ss_pred CceeccchhHHHHHHHHCCCcCCCcchhHHHHHHHcCCCCCCCCHHHHHHHHcCCCC
Confidence 569999999999999631 12468998765433221223689999999999884
No 84
>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=93.45 E-value=0.53 Score=50.77 Aligned_cols=143 Identities=22% Similarity=0.249 Sum_probs=82.1
Q ss_pred CcEEEEEeceecCCC--------CceEEEEEEEEeeCeE--E---EEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHH
Q 008340 212 YEILALDCEMCYTNE--------GLELTRVTLVDIKGQV--L---LDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKD 278 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~--------g~eL~rVsvVd~~G~v--v---~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~d 278 (569)
..++++|+||..... .++++.|+++..++.. . .-....|...+.+ +. +... .+-.+
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 468999999976532 3689999988865432 1 1112233333332 11 2222 13445
Q ss_pred HHHHHHHhhcC--CCEEEEeCch-hhHHHHccc-------C-----------------------------------CCcc
Q 008340 279 IQEEFLKLVYK--ETILVGHSLE-NDLLALKIS-------H-----------------------------------GLVI 313 (569)
Q Consensus 279 Vq~~l~~ll~~--~tILVGHsL~-~DL~aLki~-------h-----------------------------------p~vi 313 (569)
...++.+++.. ..|++|||.. ||+..|.-. . ..++
T Consensus 72 lL~~f~~~i~~~dpdii~g~N~~~FD~~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~ 151 (471)
T smart00486 72 LLKAFLEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSKSFGKTIKVKIKGRLVI 151 (471)
T ss_pred HHHHHHHHHHHhCCCEEEeecCCCCCHHHHHHHHHHcCCCCHHHcCcCCCCCCcccccCccccccccccceeEeccEEEE
Confidence 55555555532 2699999985 899876510 0 0134
Q ss_pred chhhhccccCCCCCCchHHHHHHHhcCccccc-C---------C-------CCCChHHHHHHHHHHHHHH
Q 008340 314 DTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQ-S---------G-------FGHDSTEDARAAMELALLK 366 (569)
Q Consensus 314 DT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~-~---------~-------~~HdS~EDA~Atl~L~~~k 366 (569)
|+..+++.... ...++|..+|+++||..-.. . . -..-.+.||..+.+|+...
T Consensus 152 Dl~~~~~~~~k-l~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 152 DLYNLYKNKLK-LPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred EhHHHHHHHhC-cccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55555554432 35678999999999833221 0 0 0111257899999988653
No 85
>PRK05762 DNA polymerase II; Reviewed
Probab=93.28 E-value=0.74 Score=54.55 Aligned_cols=137 Identities=20% Similarity=0.244 Sum_probs=80.6
Q ss_pred CCCcEEEEEeceecCCCCceEEEEEEEEeeC-eEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhc
Q 008340 210 SPYEILALDCEMCYTNEGLELTRVTLVDIKG-QVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVY 288 (569)
Q Consensus 210 ~~~~~vAiDcEm~~t~~g~eL~rVsvVd~~G-~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~ 288 (569)
++.+++++|+|+... + +|..|++.+... .+++ |-+..+.. .+.+... .+-.++...+.+++.
T Consensus 153 p~lrvlsfDIE~~~~--~-~i~sI~~~~~~~~~vi~---ig~~~~~~----------~~~v~~~-~sE~~LL~~F~~~i~ 215 (786)
T PRK05762 153 PPLKVVSLDIETSNK--G-ELYSIGLEGCGQRPVIM---LGPPNGEA----------LDFLEYV-ADEKALLEKFNAWFA 215 (786)
T ss_pred CCCeEEEEEEEEcCC--C-ceEEeeecCCCCCeEEE---EECCCCCC----------cceEEEc-CCHHHHHHHHHHHHH
Confidence 356899999999653 2 677777654322 2221 22222210 0113333 466777777777774
Q ss_pred C--CCEEEEeCc-hhhHHHHcc-------cC--------------C-------------CccchhhhccccCCCCCCchH
Q 008340 289 K--ETILVGHSL-ENDLLALKI-------SH--------------G-------------LVIDTAVLYKHPQGGSHKTSL 331 (569)
Q Consensus 289 ~--~tILVGHsL-~~DL~aLki-------~h--------------p-------------~viDT~~L~~~~~g~~~k~sL 331 (569)
. -.||||||. .|||..|.- .. + -++|+..+.+........++|
T Consensus 216 ~~DPDIIvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~~~~~l~sysL 295 (786)
T PRK05762 216 EHDPDVIIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATWVFDSFSL 295 (786)
T ss_pred hcCCCEEEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHHhhccCCCCCH
Confidence 3 269999997 579988652 10 1 034554444332112346789
Q ss_pred HHHHHHhcCcccccCCCCC-------------------ChHHHHHHHHHHHH
Q 008340 332 RVLAKKFLSREIQQSGFGH-------------------DSTEDARAAMELAL 364 (569)
Q Consensus 332 k~La~~~Lg~~Iq~~~~~H-------------------dS~EDA~Atl~L~~ 364 (569)
.++|+++||..-... ..| =++.||..+++|+.
T Consensus 296 ~~Va~~~Lg~~K~~~-d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~ 346 (786)
T PRK05762 296 EYVSQRLLGEGKAID-DPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFE 346 (786)
T ss_pred HHHHHHHhCCCeecc-CccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHH
Confidence 999999998653210 111 14789999999986
No 86
>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=93.01 E-value=0.88 Score=41.27 Aligned_cols=60 Identities=18% Similarity=0.253 Sum_probs=42.0
Q ss_pred HHHhhc-CCCEEEEeCchhhHHHHcc----cCCCccchhhhccccCCCCC-CchHHHHHHHhcCccc
Q 008340 283 FLKLVY-KETILVGHSLENDLLALKI----SHGLVIDTAVLYKHPQGGSH-KTSLRVLAKKFLSREI 343 (569)
Q Consensus 283 l~~ll~-~~tILVGHsL~~DL~aLki----~hp~viDT~~L~~~~~g~~~-k~sLk~La~~~Lg~~I 343 (569)
|.+++. ++...|||++..|+.+|+. ....+.||.+.+-... +.. +.+|+.|+++|||.++
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 1235689987654332 222 3589999999998873
No 87
>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=92.43 E-value=0.17 Score=51.61 Aligned_cols=78 Identities=23% Similarity=0.341 Sum_probs=59.9
Q ss_pred ChHHHHHHHHHhccCCCccEEEEeccccchhhhhhhHhHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHHHHH
Q 008340 419 SDDEVLSKARKEVKNDRIHFVWTQFSELNLHFKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPEIKEILART 498 (569)
Q Consensus 419 ~D~ev~~~~~~~v~~~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 498 (569)
++.++++++++.+....+||+++++-+.. ...+. ...+...++++.+
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 46888999999996667799999986543 11110 0123467789999
Q ss_pred HHHHHHHHhhC-CCCcEEEEEeCCCChHHHHH
Q 008340 499 DARVNSLYTAL-PTNTMLIICTGHGDTAIVHR 529 (569)
Q Consensus 499 ~~~i~~iy~~l-P~~t~liv~sg~gd~~~m~~ 529 (569)
|+.|.+|+++| +++++|||.+=||++..|..
T Consensus 171 D~~l~~l~~~~~~~~~~liiTaDHg~~~~~~~ 202 (252)
T PF01676_consen 171 DRFLGRLLEALDKEDDLLIITADHGNDETMGH 202 (252)
T ss_dssp HHHHHHHHHHHHHTTEEEEEEESSBSTTTSBS
T ss_pred HHHHHHHHHHHhcCCCEEEEECCCCCccccCC
Confidence 99999999999 99999999999999876543
No 88
>KOG2126 consensus Glycosylphosphatidylinositol anchor synthesis protein [Signal transduction mechanisms]
Probab=92.38 E-value=0.25 Score=58.03 Aligned_cols=123 Identities=20% Similarity=0.409 Sum_probs=81.2
Q ss_pred CCCCCCCCchhHHHHHHHHHhcCCeeeeeccccccccccC---C--Ccceeec----CChHHHHHHHHHhccCCCccEEE
Q 008340 370 GPDFGSPPSVMRTKLLKVLFEYGKTSTLIDNVSIIKRYAS---E--SSHAIPV----SSDDEVLSKARKEVKNDRIHFVW 440 (569)
Q Consensus 370 g~~fg~~~~~~~~~l~~~l~~~g~~~~~~d~~~~~~~~~~---~--~~~~i~~----~~D~ev~~~~~~~v~~~~~~f~~ 440 (569)
|-.|+.. ...-+++.+-+...||+..+..|......+-. + +...+.+ +-|++|+++.-+.+.++..|-.+
T Consensus 133 GsNF~g~-~I~EDNfv~Ql~~~gk~vvflGDdTW~~LFp~~f~~s~s~pSfnv~DLdtVDn~v~~~if~~l~s~dwdVlI 211 (895)
T KOG2126|consen 133 GSNFAGP-AIAEDNFVRQLVLNGKSVVFLGDDTWTSLFPNQFNKSYSFPSFNVHDLDTVDNGVIEKIFKSLNSKDWDVLI 211 (895)
T ss_pred cccCCCc-ccchhHHHHHHHHCCCeEEEecCccHHHhChHhhcCCCCCCCCCCccccccchHHHHHhhhhhccCchHHHH
Confidence 3345532 23457999999999999999987544322211 1 1112222 34899999988888876555555
Q ss_pred EeccccchhhhhhhHhHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHHHHHHHHHHHHHhhCCCCcEEEEEeC
Q 008340 441 TQFSELNLHFKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPEIKEILARTDARVNSLYTALPTNTMLIICTG 520 (569)
Q Consensus 441 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~iy~~lP~~t~liv~sg 520 (569)
++|=+.. .|-.+-. +..++-.+-+.++|+-|+++++.|..+|++||+.-
T Consensus 212 AHfLGVD------------------------H~GHk~G-------PdH~~M~~KL~qmD~vI~~ii~~mdedTlLvVmGD 260 (895)
T KOG2126|consen 212 AHFLGVD------------------------HCGHKHG-------PDHPEMADKLVQMDRVINEIIKKMDEDTLLVVMGD 260 (895)
T ss_pred HHHhCcc------------------------cccccCC-------CCCHHHHHHHHHHHHHHHHHHHHhccCeeEEEecC
Confidence 5554432 2333321 23346677799999999999999999999999998
Q ss_pred CCCh
Q 008340 521 HGDT 524 (569)
Q Consensus 521 ~gd~ 524 (569)
||=+
T Consensus 261 HGMt 264 (895)
T KOG2126|consen 261 HGMT 264 (895)
T ss_pred CCCC
Confidence 7644
No 89
>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=92.14 E-value=1.2 Score=43.21 Aligned_cols=102 Identities=17% Similarity=0.096 Sum_probs=61.0
Q ss_pred cEEEEEeceecCCC-CceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhc-CC
Q 008340 213 EILALDCEMCYTNE-GLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVY-KE 290 (569)
Q Consensus 213 ~~vAiDcEm~~t~~-g~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~-~~ 290 (569)
..+++|+|+..... ..+++.+++...++ +. ||.+ +. .......|.+++. .+
T Consensus 25 ~~l~~~~e~~~~~~~~~~~~~l~l~~~~~-~~---~i~~------------------l~-----~~~~~~~L~~~L~~~~ 77 (192)
T cd06147 25 KEIAVDLEHHSYRSYLGFTCLMQISTREE-DY---IVDT------------------LK-----LRDDMHILNEVFTDPN 77 (192)
T ss_pred CeEEEEeEecCCccCCCceEEEEEecCCC-cE---EEEe------------------cc-----cccchHHHHHHhcCCC
Confidence 47899997644332 23566677775444 22 2221 11 1111223455553 44
Q ss_pred CEEEEeCchhhHHHHc-c---cCCCccchhhhccccCCCCCCchHHHHHHHhcCccc
Q 008340 291 TILVGHSLENDLLALK-I---SHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREI 343 (569)
Q Consensus 291 tILVGHsL~~DL~aLk-i---~hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~I 343 (569)
...|||++..|+.+|+ . .-+.+.||.+.+--.. +. +.+|+.|++.|||..+
T Consensus 78 i~kv~~d~K~~~~~L~~~~gi~~~~~fD~~laaYLL~-p~-~~~l~~l~~~yl~~~~ 132 (192)
T cd06147 78 ILKVFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLN-LP-RHSLAYLLQKYCNVDA 132 (192)
T ss_pred ceEEEechHHHHHHHHHHhCCCcCchHHHHHHHHHhC-CC-cccHHHHHHHHhCCCc
Confidence 6789999999999996 2 1112399987654332 32 3489999999998764
No 90
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=92.00 E-value=0.66 Score=53.09 Aligned_cols=132 Identities=23% Similarity=0.243 Sum_probs=84.5
Q ss_pred EEEEEeceecCCC-CceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhc-CCC
Q 008340 214 ILALDCEMCYTNE-GLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVY-KET 291 (569)
Q Consensus 214 ~vAiDcEm~~t~~-g~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~-~~t 291 (569)
.+|+|+|+.+... +..++.+++.... +..|--+-.. ++.+. +...+..++. ++.
T Consensus 24 ~~a~~~et~~l~~~~~~lvg~s~~~~~-~~~yi~~~~~---------------~~~~~--------~~~~l~~~l~~~~~ 79 (593)
T COG0749 24 NIAFDTETDGLDPHGADLVGLSVASEE-EAAYIPLLHG---------------PEQLN--------VLAALKPLLEDEGI 79 (593)
T ss_pred cceeeccccccCcccCCeeEEEeeccc-cceeEeeccc---------------hhhhh--------hHHHHHHHhhCccc
Confidence 3899999999886 3467777776554 2222111110 11111 5666777772 344
Q ss_pred EEEEeCchhhHHHHccc--C-CCccchhhhccccCCCCCCchHHHHHHHhcCcccccC----CC---------------C
Q 008340 292 ILVGHSLENDLLALKIS--H-GLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQS----GF---------------G 349 (569)
Q Consensus 292 ILVGHsL~~DL~aLki~--h-p~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~----~~---------------~ 349 (569)
-.||||+.+|+.+|... + +...||++..--......++.+..|+++||+.+.... +. .
T Consensus 80 ~kv~~~~K~d~~~l~~~Gi~~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~~~~~~~~~~~~~~ 159 (593)
T COG0749 80 KKVGQNLKYDYKVLANLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQLTFADVKLEKAT 159 (593)
T ss_pred chhccccchhHHHHHHcCCcccchHHHHHHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhccccccCccccchHHHHH
Confidence 59999999999999863 2 3567888653322222346889999999998876541 11 2
Q ss_pred CChHHHHHHHHHHHHHHHHc
Q 008340 350 HDSTEDARAAMELALLKIRN 369 (569)
Q Consensus 350 HdS~EDA~Atl~L~~~kl~~ 369 (569)
-.+.+||.++++|+.....+
T Consensus 160 ~y~a~~a~~~~~L~~~l~~~ 179 (593)
T COG0749 160 EYAAEDADATLRLESILEPE 179 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 23568999999998766543
No 91
>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=90.99 E-value=0.66 Score=47.89 Aligned_cols=86 Identities=21% Similarity=0.194 Sum_probs=50.9
Q ss_pred CCCcEEEEEeceecCCC------CceEEEEEEEE------eeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHH
Q 008340 210 SPYEILALDCEMCYTNE------GLELTRVTLVD------IKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLK 277 (569)
Q Consensus 210 ~~~~~vAiDcEm~~t~~------g~eL~rVsvVd------~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~ 277 (569)
.+..++++|+|+..... .++|..|+++= ......+-.+..+..... ...+.-. .+-.
T Consensus 155 p~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~v~~~-~~E~ 223 (325)
T PF03104_consen 155 PPLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTLGSCDSIED----------NVEVIYF-DSEK 223 (325)
T ss_dssp GGSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEECSCSCCTTC----------TTEEEEE-SSHH
T ss_pred cccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEecCCCCCCC----------CcEEEEE-CCHH
Confidence 45689999999988762 46999999742 223333334443333221 1122222 2445
Q ss_pred HHHHHHHHhhc--CCCEEEEeCch-hhHHHHc
Q 008340 278 DIQEEFLKLVY--KETILVGHSLE-NDLLALK 306 (569)
Q Consensus 278 dVq~~l~~ll~--~~tILVGHsL~-~DL~aLk 306 (569)
++...+.+++. .-.||+|||+. ||+..|-
T Consensus 224 ~lL~~f~~~i~~~dPDii~GyN~~~fD~~yl~ 255 (325)
T PF03104_consen 224 ELLEAFLDIIQEYDPDIITGYNIDGFDLPYLI 255 (325)
T ss_dssp HHHHHHHHHHHHHS-SEEEESSTTTTHHHHHH
T ss_pred HHHHHHHHHHHhcCCcEEEEecccCCCHHHHH
Confidence 55555555543 33599999985 8998876
No 92
>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=90.88 E-value=2.4 Score=42.80 Aligned_cols=140 Identities=15% Similarity=0.141 Sum_probs=73.2
Q ss_pred cEEEEEeceecCCCC------ceEEEEEEEEeeCeEEEE-------EE-EecCCCCCCCcEeecCCChhhhcCCCCCHHH
Q 008340 213 EILALDCEMCYTNEG------LELTRVTLVDIKGQVLLD-------KL-VKPSNAIVDYNTRYSGITHEMLSGVTTSLKD 278 (569)
Q Consensus 213 ~~vAiDcEm~~t~~g------~eL~rVsvVd~~G~vv~D-------~l-VkP~~~I~dy~T~~SGIT~e~L~~~~~tl~d 278 (569)
.++++|+|+...+.. ++|..|+.+-.+...... -+ +.+...-.+......++....+.-. .+-.+
T Consensus 5 ~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~v~~~-~~E~~ 83 (231)
T cd05778 5 TILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKSNASNGRIRSGLSGIPVEVV-ESELE 83 (231)
T ss_pred EEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccchhhhhccccCCCCCeEEEe-CCHHH
Confidence 588999999654432 468888776432211111 12 2222211111111223333333333 35566
Q ss_pred HHHHHHHhhc--CCCEEEEeCc-hhhHHHHcc-------cC-------------C----------------------Ccc
Q 008340 279 IQEEFLKLVY--KETILVGHSL-ENDLLALKI-------SH-------------G----------------------LVI 313 (569)
Q Consensus 279 Vq~~l~~ll~--~~tILVGHsL-~~DL~aLki-------~h-------------p----------------------~vi 313 (569)
...++.+++. .-.||+|||+ .||+..|-- .. + -++
T Consensus 84 LL~~f~~~i~~~DPDii~GyNi~~fd~~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~~g~~~~~~~~i~GRi~l 163 (231)
T cd05778 84 LFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDEWGYTHTSGIKIVGRHIL 163 (231)
T ss_pred HHHHHHHHHHHhCCCEEEEeccccCcHHHHHHHHHHhCCcchhhhccCCCCCCcccccccccccccccCCceEEeeEEEe
Confidence 6666665552 2369999998 678876531 00 0 023
Q ss_pred chhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHH
Q 008340 314 DTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDA 356 (569)
Q Consensus 314 DT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA 356 (569)
|...+.++.. ....|+|..+|+++||..... -.|..+-+.
T Consensus 164 D~~~~~r~~~-kl~sYsL~~V~~~~L~~~k~~--~~~~~i~~~ 203 (231)
T cd05778 164 NVWRLMRSEL-ALTNYTLENVVYHVLHQRIPL--YSNKTLTEW 203 (231)
T ss_pred EhHHHHHHHc-CcccCCHHHHHHHHhCCCCCC--CCHHHHHHH
Confidence 4333333321 345789999999999997654 334444443
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=90.56 E-value=0.51 Score=46.97 Aligned_cols=64 Identities=31% Similarity=0.405 Sum_probs=45.6
Q ss_pred HHHHHHHHHhhcC-CCEEEEeCc-hhhHHHHccc---C----C------------------CccchhhhccccCCCCCCc
Q 008340 277 KDIQEEFLKLVYK-ETILVGHSL-ENDLLALKIS---H----G------------------LVIDTAVLYKHPQGGSHKT 329 (569)
Q Consensus 277 ~dVq~~l~~ll~~-~tILVGHsL-~~DL~aLki~---h----p------------------~viDT~~L~~~~~g~~~k~ 329 (569)
.++.+++.+++.. +.+|||||. .||+.+|... | | ..+|+..+.+.. +....+
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 5677778888865 669999997 8999888731 1 1 267887766533 334577
Q ss_pred hHHHHHHHhcCcc
Q 008340 330 SLRVLAKKFLSRE 342 (569)
Q Consensus 330 sLk~La~~~Lg~~ 342 (569)
+|+.+|+ +||.+
T Consensus 158 ~L~~va~-~lG~~ 169 (208)
T cd05782 158 SLDLLAK-LLGIP 169 (208)
T ss_pred CHHHHHH-HhCCC
Confidence 8999997 57874
No 94
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.92 E-value=1.1 Score=54.02 Aligned_cols=93 Identities=19% Similarity=0.219 Sum_probs=61.3
Q ss_pred HHHHHHHHHHhhcC-CCEEEEeCchhhHHHHccc----CCCccchhhhccccCCCCCCchHHHHHHHhcCccccc----C
Q 008340 276 LKDIQEEFLKLVYK-ETILVGHSLENDLLALKIS----HGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQ----S 346 (569)
Q Consensus 276 l~dVq~~l~~ll~~-~tILVGHsL~~DL~aLki~----hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~----~ 346 (569)
...+...|..++.. ....||||+.+|+.+|+.. .+.+.||++..--.. +..+.+|+.|+.+||+.+... .
T Consensus 363 ~~~~~~~l~~~l~~~~~~~v~~n~K~d~~~l~~~gi~~~~~~~Dt~la~yll~-~~~~~~l~~la~~yl~~~~~~~~~~~ 441 (887)
T TIGR00593 363 TILTDDKFARWLLNEQIKKIGHDAKFLMHLLKREGIELGGVIFDTMLAAYLLD-PAQVSTLDTLARRYLVEELILDEKIG 441 (887)
T ss_pred hHHHHHHHHHHHhCCCCcEEEeeHHHHHHHHHhCCCCCCCcchhHHHHHHHcC-CCCCCCHHHHHHHHcCcccccHHHhc
Confidence 44566777777743 3458999999999999731 235789997644332 223458999999999965321 0
Q ss_pred CCCC------------ChHHHHHHHHHHHHHHHHc
Q 008340 347 GFGH------------DSTEDARAAMELALLKIRN 369 (569)
Q Consensus 347 ~~~H------------dS~EDA~Atl~L~~~kl~~ 369 (569)
+.+- -+.+||.+++.|+.....+
T Consensus 442 ~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~ 476 (887)
T TIGR00593 442 GKLAKFAFPPLEEATEYLARRAAATKRLAEELLKE 476 (887)
T ss_pred cCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1111 2567888999998765443
No 95
>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=89.38 E-value=0.8 Score=47.04 Aligned_cols=74 Identities=24% Similarity=0.172 Sum_probs=53.6
Q ss_pred cCCCEEEEeCchhhHHHHcc-------------------cCCCccchhhhccccCCCCCCchHHHHHHHhcCccc-----
Q 008340 288 YKETILVGHSLENDLLALKI-------------------SHGLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREI----- 343 (569)
Q Consensus 288 ~~~tILVGHsL~~DL~aLki-------------------~hp~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~I----- 343 (569)
....++||||.-.||-.|-- .-|.++||-.|+.... ....+|..|+.. |+..-
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 45689999999999976431 1378999999988653 245689999985 56543
Q ss_pred -----------------ccCCCCCChHHHHHHHHHHHH
Q 008340 344 -----------------QQSGFGHDSTEDARAAMELAL 364 (569)
Q Consensus 344 -----------------q~~~~~HdS~EDA~Atl~L~~ 364 (569)
..+...|.|--||..|..+|.
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 122348999999999999885
No 96
>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=87.88 E-value=0.83 Score=46.15 Aligned_cols=131 Identities=19% Similarity=0.215 Sum_probs=73.9
Q ss_pred CcEEEEEeceecCCCC--ceEEEEEEEEeeCe------------EEEEEEEecCCC--CCCCcEeecCCChhhhcCCCCC
Q 008340 212 YEILALDCEMCYTNEG--LELTRVTLVDIKGQ------------VLLDKLVKPSNA--IVDYNTRYSGITHEMLSGVTTS 275 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g--~eL~rVsvVd~~G~------------vv~D~lVkP~~~--I~dy~T~~SGIT~e~L~~~~~t 275 (569)
-.+.+|-.-|+..... .||+-||++=.+.- .-+-.+++|... .+....+.-......+.-. .+
T Consensus 3 l~v~sls~~T~~n~k~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~v~~~-~~ 81 (234)
T cd05776 3 LTVMSLSIKTVLNSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKVRIF-EN 81 (234)
T ss_pred eEEEEEEeEEEecCcCCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCCCCCchHHHHHHhcCCcEEEe-CC
Confidence 4577787778766554 68999988754211 112334555432 1111111111111112222 35
Q ss_pred HHHHHHHHHHhhc--CCCEEEEeCc-hhhHHHHc-------ccC------------C-----------------Cccchh
Q 008340 276 LKDIQEEFLKLVY--KETILVGHSL-ENDLLALK-------ISH------------G-----------------LVIDTA 316 (569)
Q Consensus 276 l~dVq~~l~~ll~--~~tILVGHsL-~~DL~aLk-------i~h------------p-----------------~viDT~ 316 (569)
-.+....+..++. .-.||||||+ .|||..|- +.+ | -++|+.
T Consensus 82 E~~LL~~f~~~i~~~DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~ 161 (234)
T cd05776 82 ERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTY 161 (234)
T ss_pred HHHHHHHHHHHHhhcCCCEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCchhhccH
Confidence 5566666666653 2269999999 78997754 211 0 145666
Q ss_pred hhccccCCCCCCchHHHHHHHhcCcccc
Q 008340 317 VLYKHPQGGSHKTSLRVLAKKFLSREIQ 344 (569)
Q Consensus 317 ~L~~~~~g~~~k~sLk~La~~~Lg~~Iq 344 (569)
.+++... ....|+|.++|+.+||.+-.
T Consensus 162 ~~~k~~~-~~~sY~L~~va~~~Lg~~k~ 188 (234)
T cd05776 162 LSAKELI-RCKSYDLTELSQQVLGIERQ 188 (234)
T ss_pred HHHHHHh-CCCCCChHHHHHHHhCcCcc
Confidence 6665442 24678899999999998543
No 97
>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=86.94 E-value=1.7 Score=45.06 Aligned_cols=67 Identities=25% Similarity=0.394 Sum_probs=47.4
Q ss_pred HhccCCCccEEEEeccccchhhhhhhHhHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHHHHHHHHHHHHHhh
Q 008340 429 KEVKNDRIHFVWTQFSELNLHFKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPEIKEILARTDARVNSLYTA 508 (569)
Q Consensus 429 ~~v~~~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~iy~~ 508 (569)
..+.....||+++.|.++.. ..+ ..+ ...++..+++..+|+.|.+|++.
T Consensus 177 ~l~~~~~pdl~~~~~~~~D~-~~H-----~~g-------------------------~~s~~~~~~~~~~D~~ig~l~~~ 225 (365)
T PF01663_consen 177 YLIQKERPDLIFVYFPEPDH-IGH-----RYG-------------------------PDSPEIEDAYRRIDQAIGRLLEA 225 (365)
T ss_dssp HHHHTTTESEEEEEEECCHH-HHH-----HH--------------------------TTSHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHhhCCCCEEEEEecCCCc-ccc-----CCC-------------------------CCCHHHHHHHHHHHHHHHHHHHH
Confidence 33666678999999988753 211 100 11235788999999999999999
Q ss_pred CCCC-----cEEEEEeCCCChHH
Q 008340 509 LPTN-----TMLIICTGHGDTAI 526 (569)
Q Consensus 509 lP~~-----t~liv~sg~gd~~~ 526 (569)
|+++ +.+||+|-||=..-
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 98
>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=83.24 E-value=5.8 Score=39.98 Aligned_cols=93 Identities=26% Similarity=0.173 Sum_probs=61.5
Q ss_pred CHHHHHHHHHHhhcC-CCEEEEeC-chhhHHHHcc---cC----C-------------------CccchhhhccccCCCC
Q 008340 275 SLKDIQEEFLKLVYK-ETILVGHS-LENDLLALKI---SH----G-------------------LVIDTAVLYKHPQGGS 326 (569)
Q Consensus 275 tl~dVq~~l~~ll~~-~tILVGHs-L~~DL~aLki---~h----p-------------------~viDT~~L~~~~~g~~ 326 (569)
.-+++.+.+++++.+ ...||||| -.||+-+|.. .| | .-+||+.+.... |..
T Consensus 36 ~E~~lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~-g~~ 114 (209)
T PF10108_consen 36 DEKELLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFY-GAK 114 (209)
T ss_pred CHHHHHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhcc-Ccc
Confidence 466788889999864 34899999 6899998873 12 1 236777665432 345
Q ss_pred CCchHHHHHHHhcCcccccCCCC----------------CChHHHHHHHHHHHHHHHHc
Q 008340 327 HKTSLRVLAKKFLSREIQQSGFG----------------HDSTEDARAAMELALLKIRN 369 (569)
Q Consensus 327 ~k~sLk~La~~~Lg~~Iq~~~~~----------------HdS~EDA~Atl~L~~~kl~~ 369 (569)
.+.||..||. .||++=..+-.| .=...|+.+|..||++...-
T Consensus 115 ~~~sLd~la~-~lgiPgK~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~~ 172 (209)
T PF10108_consen 115 ARTSLDELAA-LLGIPGKDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFELL 172 (209)
T ss_pred ccCCHHHHHH-HcCCCCCCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 6789999998 579873211001 11247888888888765543
No 99
>PLN02538 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Probab=80.29 E-value=5 Score=45.82 Aligned_cols=81 Identities=15% Similarity=0.198 Sum_probs=61.6
Q ss_pred ecCChHHHHHHHHHhccCCCccEEEEeccccchhhhhhhHhHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHH
Q 008340 416 PVSSDDEVLSKARKEVKNDRIHFVWTQFSELNLHFKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPEIKEIL 495 (569)
Q Consensus 416 ~~~~D~ev~~~~~~~v~~~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 (569)
|--|-.||.+++++++....+||+++.|-.-.- .. + . ...+...+++
T Consensus 401 PeMSA~eVtd~~i~~i~~~~ydfi~vNfan~Dm-vG----------------------H---------t-G~~ea~ikAI 447 (558)
T PLN02538 401 PKMKALEIAEKARDALLSGKFDQVRVNLANGDM-VG----------------------H---------T-GDLEATIVAC 447 (558)
T ss_pred CCCCHHHHHHHHHHHHhcCCCCEEEEeccCccc-cc----------------------C---------C-CCHHHHHHHH
Confidence 334557899999999998889999988854320 00 0 0 1123467889
Q ss_pred HHHHHHHHHHHhhC-CCCcEEEEEeCCCChHHHHH
Q 008340 496 ARTDARVNSLYTAL-PTNTMLIICTGHGDTAIVHR 529 (569)
Q Consensus 496 ~~~~~~i~~iy~~l-P~~t~liv~sg~gd~~~m~~ 529 (569)
+.+|+.|.+|++++ +.+..+||.+=||+-.+|..
T Consensus 448 E~vD~~Lg~Il~al~~~g~~liITADHGNaE~M~d 482 (558)
T PLN02538 448 EAVDAAVKEILDAVEQVGGIYLVTADHGNAEDMVK 482 (558)
T ss_pred HHHHHHHHHHHHHHHhcCCEEEEeCCCCCchhhcc
Confidence 99999999999999 66889999999999887763
No 100
>PHA02528 43 DNA polymerase; Provisional
Probab=79.29 E-value=8.1 Score=46.64 Aligned_cols=151 Identities=17% Similarity=0.123 Sum_probs=80.9
Q ss_pred CCcEEEEEeceecCCC-------CceEEEEEEEEeeCeE--EEEE-EEecCCCCCCCc--EeecCCChhhhcCCCCCHHH
Q 008340 211 PYEILALDCEMCYTNE-------GLELTRVTLVDIKGQV--LLDK-LVKPSNAIVDYN--TRYSGITHEMLSGVTTSLKD 278 (569)
Q Consensus 211 ~~~~vAiDcEm~~t~~-------g~eL~rVsvVd~~G~v--v~D~-lVkP~~~I~dy~--T~~SGIT~e~L~~~~~tl~d 278 (569)
.-+++++|+|+..... ..+|..|++.+..+.. +|.. =+.|.....+.. .-..++ .+... .+-.+
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 4579999999965221 2479999998876553 3322 000100000000 000000 01112 35567
Q ss_pred HHHHHHHhhc--CCCEEEEeCc-hhhHHHHccc-------------CCC-------------------------ccchhh
Q 008340 279 IQEEFLKLVY--KETILVGHSL-ENDLLALKIS-------------HGL-------------------------VIDTAV 317 (569)
Q Consensus 279 Vq~~l~~ll~--~~tILVGHsL-~~DL~aLki~-------------hp~-------------------------viDT~~ 317 (569)
...++.+++. .-.||+|||+ .|||..|.-. .+. ++|...
T Consensus 181 LL~~F~~~i~~~DPDII~GyNi~~FDlpYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~GRv~lD~~d 260 (881)
T PHA02528 181 MLLEYINFWEENTPVIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISGISILDYLD 260 (881)
T ss_pred HHHHHHHHHHHhCCcEEEecCCccCCHHHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcceEEEeHHH
Confidence 7777777772 2269999996 6799776410 000 122222
Q ss_pred hcccc-CCCCCCchHHHHHHHhcCccccc-C-------------CCCCChHHHHHHHHHHHHH
Q 008340 318 LYKHP-QGGSHKTSLRVLAKKFLSREIQQ-S-------------GFGHDSTEDARAAMELALL 365 (569)
Q Consensus 318 L~~~~-~g~~~k~sLk~La~~~Lg~~Iq~-~-------------~~~HdS~EDA~Atl~L~~~ 365 (569)
+++.. ......++|.++|+++||..-.. . .-.+=++.||+.+++|+.+
T Consensus 261 l~k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 261 LYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred HHHHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 33321 00124678999999999965432 0 0112246899999999865
No 101
>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=77.39 E-value=7.3 Score=44.08 Aligned_cols=81 Identities=11% Similarity=0.153 Sum_probs=60.9
Q ss_pred eecCChHHHHHHHHHhccCCCccEEEEeccccchhhhhhhHhHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHH
Q 008340 415 IPVSSDDEVLSKARKEVKNDRIHFVWTQFSELNLHFKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPEIKEI 494 (569)
Q Consensus 415 i~~~~D~ev~~~~~~~v~~~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 (569)
.|.-+..||.+++++.+....+||++..|.... ... . . ...+...++
T Consensus 361 ~PeMsa~evtd~~i~~I~~~k~dfi~vnfan~D-mvG----------------------H---------t-g~~~a~v~A 407 (501)
T TIGR01307 361 QPEMSAKAVTDAVLEAIAQGKFDLIVVNFANPD-MVG----------------------H---------T-GNFEAAIKA 407 (501)
T ss_pred CCccCHHHHHHHHHHHHhccCCCEEEEECCCcc-ccc----------------------C---------C-CCHHHHHHH
Confidence 577789999999999998888899999884331 100 0 0 112246788
Q ss_pred HHHHHHHHHHHHhhCCC-CcEEEEEeCCCChHHHH
Q 008340 495 LARTDARVNSLYTALPT-NTMLIICTGHGDTAIVH 528 (569)
Q Consensus 495 ~~~~~~~i~~iy~~lP~-~t~liv~sg~gd~~~m~ 528 (569)
++.+|..|.+|.++|-. +.++|+.|=||+...|.
T Consensus 408 IE~vD~~LGrIl~aLke~G~~VIiTADHGnae~m~ 442 (501)
T TIGR01307 408 VEALDVCLGRIVEACKKVGGTLFLTADHGNAEEMI 442 (501)
T ss_pred HHHHHHHHHHHHHHHHhCCCEEEEEcCCCChhhcc
Confidence 99999999999999964 55888899999876553
No 102
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=77.28 E-value=14 Score=46.14 Aligned_cols=100 Identities=17% Similarity=0.249 Sum_probs=61.6
Q ss_pred CCChhhhcCCCCCHHHHHHHHHHhhc--CCCEEEEeCc-hhhHHHHcc-------cC----------------------C
Q 008340 263 GITHEMLSGVTTSLKDIQEEFLKLVY--KETILVGHSL-ENDLLALKI-------SH----------------------G 310 (569)
Q Consensus 263 GIT~e~L~~~~~tl~dVq~~l~~ll~--~~tILVGHsL-~~DL~aLki-------~h----------------------p 310 (569)
|+-+..|... .+-.+....+++.+. .-.+++|||. .|||.+|-- .+ .
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 4444445444 355556666666664 5579999996 679987542 11 1
Q ss_pred -CccchhhhccccCCCCCCchHHHHHHHhcCccccc-----------C-----CCCCChHHHHHHHHHHHH
Q 008340 311 -LVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQ-----------S-----GFGHDSTEDARAAMELAL 364 (569)
Q Consensus 311 -~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~-----------~-----~~~HdS~EDA~Atl~L~~ 364 (569)
.++|+..+++... ....|+|..+|+++||.+-.. . .-.+..+.||..++.|+.
T Consensus 651 rl~~D~~~~~k~~~-~~~sy~L~~v~~~~L~~~k~~~~~~~i~~~~~~~~~~~~~~~y~~~Da~l~~~L~~ 720 (1172)
T TIGR00592 651 RMICDVEISAKELI-RCKSYDLSELVQQILKTERKVIPIDNINNMYSESSSLTYLLEHTWKDAMFILQIMC 720 (1172)
T ss_pred EEEEEHHHHHHHHh-CcCCCCHHHHHHHHhCCCCcccCHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHHHH
Confidence 2467776665442 245788999999999853221 0 012345678888887764
No 103
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=71.90 E-value=32 Score=41.14 Aligned_cols=121 Identities=19% Similarity=0.168 Sum_probs=67.7
Q ss_pred CCCcEEEEEeceecCCCC------ceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHH
Q 008340 210 SPYEILALDCEMCYTNEG------LELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEF 283 (569)
Q Consensus 210 ~~~~~vAiDcEm~~t~~g------~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l 283 (569)
.+.+++|+|+|+...... +.+..|+.....+.-.. .+ .-.+...|.. +..+ .+=.++...+
T Consensus 152 p~l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~----~~-----~~~~~~~~~~---v~~~-~~e~e~l~~~ 218 (792)
T COG0417 152 PPLRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLI----EV-----FIYTSGEGFS---VEVV-ISEAELLERF 218 (792)
T ss_pred CCceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCcc----cc-----ccccCCCCce---eEEe-cCHHHHHHHH
Confidence 346799999999987532 35777777765332111 00 0001111111 2222 2334455555
Q ss_pred HHhhc--CCCEEEEeCch-hhHHHHccc-------CC---------------------CccchhhhccccCCCCCCchHH
Q 008340 284 LKLVY--KETILVGHSLE-NDLLALKIS-------HG---------------------LVIDTAVLYKHPQGGSHKTSLR 332 (569)
Q Consensus 284 ~~ll~--~~tILVGHsL~-~DL~aLki~-------hp---------------------~viDT~~L~~~~~g~~~k~sLk 332 (569)
..++- .-+|+||||.+ ||+..|.-. .. ..+|...++....-....++|.
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 44442 44699999987 899887621 11 2456655555211124578899
Q ss_pred HHHHHhcCccc
Q 008340 333 VLAKKFLSREI 343 (569)
Q Consensus 333 ~La~~~Lg~~I 343 (569)
..+..+|+..-
T Consensus 299 ~v~~~~l~~~k 309 (792)
T COG0417 299 AVSEALLGEGK 309 (792)
T ss_pred HHHHHhccccc
Confidence 99999988765
No 104
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=70.74 E-value=14 Score=45.56 Aligned_cols=145 Identities=19% Similarity=0.218 Sum_probs=81.4
Q ss_pred CCCcEEEEEeceecCCC-------CceEEEEEEEE-eeCeE---EEEEEEec--CCCCCCCcEeecCCChhhhcCCCCCH
Q 008340 210 SPYEILALDCEMCYTNE-------GLELTRVTLVD-IKGQV---LLDKLVKP--SNAIVDYNTRYSGITHEMLSGVTTSL 276 (569)
Q Consensus 210 ~~~~~vAiDcEm~~t~~-------g~eL~rVsvVd-~~G~v---v~D~lVkP--~~~I~dy~T~~SGIT~e~L~~~~~tl 276 (569)
.|.+++++|+|+.+... .++|+.||.+- ..|.. +...++-+ ..++. |. .+... .+-
T Consensus 262 pplrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~~~~~r~vftl~~c~~i~-------g~---~V~~f-~sE 330 (1054)
T PTZ00166 262 APLRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLTKFIFTLKECASIA-------GA---NVLSF-ETE 330 (1054)
T ss_pred CCcEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCccCCcceEEEecCccccCC-------Cc---eEEEe-CCH
Confidence 35689999999986432 26899999874 44432 11222211 11222 21 11112 244
Q ss_pred HHHHHHHHHhhc--CCCEEEEeCc-hhhHHHHc-------ccC----------C--------------------------
Q 008340 277 KDIQEEFLKLVY--KETILVGHSL-ENDLLALK-------ISH----------G-------------------------- 310 (569)
Q Consensus 277 ~dVq~~l~~ll~--~~tILVGHsL-~~DL~aLk-------i~h----------p-------------------------- 310 (569)
.+...++.+++. .-.||+|||. .|||..|- +.. +
T Consensus 331 ~eLL~~f~~~I~~~DPDII~GYNi~~FDlpYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR 410 (1054)
T PTZ00166 331 KELLLAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGR 410 (1054)
T ss_pred HHHHHHHHHHHHhcCCCEEEecCCcCCcHHHHHHHHHHhCCCchhhcCcccCCCccccccccccccccccccceeEeeeE
Confidence 555555555442 2379999997 57997654 110 0
Q ss_pred CccchhhhccccCCCCCCchHHHHHHHhcCccccc----------CCCCC-------ChHHHHHHHHHHHHHH
Q 008340 311 LVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQ----------SGFGH-------DSTEDARAAMELALLK 366 (569)
Q Consensus 311 ~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~----------~~~~H-------dS~EDA~Atl~L~~~k 366 (569)
-++|+..+++... ....++|.++|.+|||..... .+..+ =++.||+.+++|+...
T Consensus 411 ~~iDl~~~~~~~~-kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L~~kl 482 (1054)
T PTZ00166 411 IQFDVMDLIRRDY-KLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKL 482 (1054)
T ss_pred EEEEHHHHHHHhc-CcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 1234444443322 235788999999999965431 01112 2368999999988654
No 105
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=68.79 E-value=2.3 Score=49.81 Aligned_cols=149 Identities=18% Similarity=0.280 Sum_probs=81.9
Q ss_pred CCCcEEEEEeceecCCCC------ceEEEEE-EEE--eeCeEEE-EEE-EecCCCCCCCcEeecCCChhhhcCCCCCHHH
Q 008340 210 SPYEILALDCEMCYTNEG------LELTRVT-LVD--IKGQVLL-DKL-VKPSNAIVDYNTRYSGITHEMLSGVTTSLKD 278 (569)
Q Consensus 210 ~~~~~vAiDcEm~~t~~g------~eL~rVs-vVd--~~G~vv~-D~l-VkP~~~I~dy~T~~SGIT~e~L~~~~~tl~d 278 (569)
.|.++..+|+|++|.... +-+++|+ +|. ++++.++ +-+ ++|-.+|..-.. ++-+|++ .+-+
T Consensus 272 APlrvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~Ge~~pf~rnvf~l~~capI~G~~V-~~~~~e~-------elL~ 343 (1066)
T KOG0969|consen 272 APLRVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQGENEPFVRNVFTLKTCAPIVGSNV-HSYETEK-------ELLE 343 (1066)
T ss_pred ccccccceeEEeccCCCCCCccccChHHHHHHHHHHhcCCchHHHhhhcccCcCCCCCcee-EEeccHH-------HHHH
Confidence 467899999999998654 2233332 222 2333321 222 334444443222 2223332 2334
Q ss_pred HHHHHHHhhcCCCEEEEeCc-hhhHH-------HHccc--------CC---Cccchhhhcccc-----------------
Q 008340 279 IQEEFLKLVYKETILVGHSL-ENDLL-------ALKIS--------HG---LVIDTAVLYKHP----------------- 322 (569)
Q Consensus 279 Vq~~l~~ll~~~tILVGHsL-~~DL~-------aLki~--------hp---~viDT~~L~~~~----------------- 322 (569)
.|..+..-+++ +|++|+|+ +||+- .|++. +. .+.||+.=.+..
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 57778888866 59999997 77983 34431 21 355765211110
Q ss_pred ------C-CCCCCchHHHHHHHhcCcccccCCCCCChHH-----HHHHHHHHHHHHHHc
Q 008340 323 ------Q-GGSHKTSLRVLAKKFLSREIQQSGFGHDSTE-----DARAAMELALLKIRN 369 (569)
Q Consensus 323 ------~-g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~E-----DA~Atl~L~~~kl~~ 369 (569)
| -..+.|+|..++.+|||..-.. .+|+.+. |+.+-.+|+.+|++.
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 0 0235789999999999976443 4666653 344555565556554
No 106
>PHA02570 dexA exonuclease; Provisional
Probab=66.26 E-value=23 Score=36.08 Aligned_cols=92 Identities=12% Similarity=0.068 Sum_probs=55.6
Q ss_pred EEEEeceecCCCCceEEEEEEEEee--CeEE--EEEEEecCCCCCCCcEeecC---CChhh--------------hcC--
Q 008340 215 LALDCEMCYTNEGLELTRVTLVDIK--GQVL--LDKLVKPSNAIVDYNTRYSG---ITHEM--------------LSG-- 271 (569)
Q Consensus 215 vAiDcEm~~t~~g~eL~rVsvVd~~--G~vv--~D~lVkP~~~I~dy~T~~SG---IT~e~--------------L~~-- 271 (569)
+.||.||-|+.+.-.|+.|++|-++ .... |.++|.....|.--...-.| ++... |.+
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 5799999999988889999999653 2111 33344321111100000012 11122 211
Q ss_pred CCCCHHHHHHHHHHhhcCCC------EEEEeCchhhHHHHc
Q 008340 272 VTTSLKDIQEEFLKLVYKET------ILVGHSLENDLLALK 306 (569)
Q Consensus 272 ~~~tl~dVq~~l~~ll~~~t------ILVGHsL~~DL~aLk 306 (569)
...++.++..+|.++|.... .+=|-+.+||+-.|+
T Consensus 84 ~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD~~IL~ 124 (220)
T PHA02570 84 EDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDFPILV 124 (220)
T ss_pred ccccHHHHHHHHHHHHHHcCCCccceeEecCCCccCHHHHH
Confidence 12578999999999996444 467888999999886
No 107
>PRK05434 phosphoglyceromutase; Provisional
Probab=65.39 E-value=16 Score=41.43 Aligned_cols=79 Identities=16% Similarity=0.259 Sum_probs=58.0
Q ss_pred ecCChHHHHHHHHHhccCCCccEEEEeccccchhhhhhhHhHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHH
Q 008340 416 PVSSDDEVLSKARKEVKNDRIHFVWTQFSELNLHFKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPEIKEIL 495 (569)
Q Consensus 416 ~~~~D~ev~~~~~~~v~~~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 (569)
+--+..|+.+++++.++...+||+++.|.... ...+ .. ..+...+++
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 44578889999999998777899999986542 1110 00 123467789
Q ss_pred HHHHHHHHHHHhhCC-CCcEEEEEeCCCChHHH
Q 008340 496 ARTDARVNSLYTALP-TNTMLIICTGHGDTAIV 527 (569)
Q Consensus 496 ~~~~~~i~~iy~~lP-~~t~liv~sg~gd~~~m 527 (569)
+.+|+.|.+|+++|- .+-++||.+=||+...|
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 108
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=64.89 E-value=11 Score=37.81 Aligned_cols=26 Identities=27% Similarity=0.358 Sum_probs=18.7
Q ss_pred hhCCCCcEEEEEeCCCChHHHHHHHHHH
Q 008340 507 TALPTNTMLIICTGHGDTAIVHRLREML 534 (569)
Q Consensus 507 ~~lP~~t~liv~sg~gd~~~m~~l~~~~ 534 (569)
...-..--+|++|||||.. ...|+|+
T Consensus 71 ~~~~~~~PVIfiTGhgDIp--maV~AmK 96 (202)
T COG4566 71 AERGIRLPVIFLTGHGDIP--MAVQAMK 96 (202)
T ss_pred HhcCCCCCEEEEeCCCChH--HHHHHHH
Confidence 3455666799999999986 3456664
No 109
>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=64.27 E-value=14 Score=33.99 Aligned_cols=59 Identities=20% Similarity=0.293 Sum_probs=39.5
Q ss_pred HHHhhc-CCCEEEEeCchhhHHHHcc---c-CCCccchhhhccccCCCCCC-chHHHHHHHhcCcc
Q 008340 283 FLKLVY-KETILVGHSLENDLLALKI---S-HGLVIDTAVLYKHPQGGSHK-TSLRVLAKKFLSRE 342 (569)
Q Consensus 283 l~~ll~-~~tILVGHsL~~DL~aLki---~-hp~viDT~~L~~~~~g~~~k-~sLk~La~~~Lg~~ 342 (569)
|.+++. .+...+||++.+++.+|+. . ...+.||++..--. .+..+ .+|..|+++||+..
T Consensus 45 l~~~l~~~~~~ki~~d~K~~~~~l~~~gi~l~~~~fD~~LAaYLL-~p~~~~~~l~~la~~yl~~~ 109 (151)
T cd06128 45 LKPLLEDEKALKVGQNLKYDRVILANYGIELRGIAFDTMLEAYLL-DPVAGRHDMDSLAERWLKEK 109 (151)
T ss_pred HHHHHcCCCCCEEeeehHHHHHHHHHCCCCCCCcchhHHHHHHHc-CCCCCCCCHHHHHHHHcCCC
Confidence 445553 3345899999999999953 1 23468998653222 23222 48999999999887
No 110
>PRK05761 DNA polymerase I; Reviewed
Probab=59.58 E-value=18 Score=43.24 Aligned_cols=90 Identities=18% Similarity=0.250 Sum_probs=56.8
Q ss_pred CCHHHHHHHHHHhhcCCCEEEEeCc-hhhHHHHccc---CC-------C-------ccchhhhcccc-------CCC--C
Q 008340 274 TSLKDIQEEFLKLVYKETILVGHSL-ENDLLALKIS---HG-------L-------VIDTAVLYKHP-------QGG--S 326 (569)
Q Consensus 274 ~tl~dVq~~l~~ll~~~tILVGHsL-~~DL~aLki~---hp-------~-------viDT~~L~~~~-------~g~--~ 326 (569)
.+-.++..++.+++....+.|+.|. +||+..|.-. +. . .+|....+... .|. .
T Consensus 208 ~~E~eLL~~f~~~i~~~dPdi~yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~~~~~y~~~~~~~~ 287 (787)
T PRK05761 208 DSEKELLAELFDIILEYPPVVTFNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNKAVRSYAFYGKYRH 287 (787)
T ss_pred CCHHHHHHHHHHHHHhcCCEEEEcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheeecceeeeeccceeec
Confidence 3567788888888887788888986 5799776521 10 0 14544443321 011 1
Q ss_pred CCchHHHHHHHhcCccccc-C---------CCCCChHHHHHHHHHHH
Q 008340 327 HKTSLRVLAKKFLSREIQQ-S---------GFGHDSTEDARAAMELA 363 (569)
Q Consensus 327 ~k~sLk~La~~~Lg~~Iq~-~---------~~~HdS~EDA~Atl~L~ 363 (569)
..++|...++.+||..=.. . .-+.=++.||..+++|.
T Consensus 288 ~~ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 288 REARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred ccCChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 1578999999999975211 0 01233589999999984
No 111
>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=58.87 E-value=76 Score=34.96 Aligned_cols=34 Identities=24% Similarity=0.391 Sum_probs=29.5
Q ss_pred cHHHHHHHHHHHHHHHHHHhhCCCCcEEEEEeCCCCh
Q 008340 488 TPEIKEILARTDARVNSLYTALPTNTMLIICTGHGDT 524 (569)
Q Consensus 488 ~~~~~~~~~~~~~~i~~iy~~lP~~t~liv~sg~gd~ 524 (569)
+.+..+++.++|+.|.+|.+. ++.|||.|-||=.
T Consensus 208 S~e~~~~~~~lD~~l~~L~~~---~~~vvvtaDHG~~ 241 (408)
T TIGR02335 208 EPESNAFYAAMDSRFKRYHEQ---GAIVAITADHGMN 241 (408)
T ss_pred CHHHHHHHHHHHHHHHHHHHC---CCEEEEECCCCCc
Confidence 457889999999999999985 8999999988854
No 112
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=53.41 E-value=14 Score=38.68 Aligned_cols=161 Identities=18% Similarity=0.205 Sum_probs=95.7
Q ss_pred CcEEEEEeceecCCCC-ceEEEEEEEEe-----eCe---------------EEEE---EEEecCCCCCCCcEeecCCChh
Q 008340 212 YEILALDCEMCYTNEG-LELTRVTLVDI-----KGQ---------------VLLD---KLVKPSNAIVDYNTRYSGITHE 267 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~g-~eL~rVsvVd~-----~G~---------------vv~D---~lVkP~~~I~dy~T~~SGIT~e 267 (569)
..++.+|.|+++...- .+++++++.++ +|. -+.| -++.|......-..+++|.+..
T Consensus 13 ~tf~fldleat~lp~~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~v~~p~aeeitgls~~ 92 (318)
T KOG4793|consen 13 RTFSFLDLEATGLPGWIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVPVTRPIAEEITGLSQP 92 (318)
T ss_pred eEEEeeeeccccCCcccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcCCcChhhhhhcccccH
Confidence 4688899999998543 46777766653 232 2333 3566776666667788998875
Q ss_pred hhcCC-----CCCHHHHHHHHHHhhcCCCEEEEeCc-hhhHHHHcc-------cCC---Cccchhhhcccc--------C
Q 008340 268 MLSGV-----TTSLKDIQEEFLKLVYKETILVGHSL-ENDLLALKI-------SHG---LVIDTAVLYKHP--------Q 323 (569)
Q Consensus 268 ~L~~~-----~~tl~dVq~~l~~ll~~~tILVGHsL-~~DL~aLki-------~hp---~viDT~~L~~~~--------~ 323 (569)
-+.-. ...+......|++-++.---||.||- ++|+-.|.. .-| .++|+...+... +
T Consensus 93 ~~~l~rr~~~D~dla~LL~afls~lp~p~CLVaHng~~~dfpil~qela~lg~~lpq~lvcvdslpa~~ald~a~s~~tr 172 (318)
T KOG4793|consen 93 FLALQRRLAFDKDLAKLLTAFLSRLPTPGCLVAHNGNEYDFPILAQELAGLGYSLPQDLVCVDSLPALNALDRANSMVTR 172 (318)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHhcCCCCceEEeecCCccccHHHHHHHHhcCccchhhhcCcchhHHHHHHhhhcCcccC
Confidence 44321 12233333444444434345999984 678877663 333 478877654311 2
Q ss_pred CC-CCCchHHHHHHHhcCcccccCCCCCChHHHHHHHHHHHHHHHHcCCCCC
Q 008340 324 GG-SHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMELALLKIRNGPDFG 374 (569)
Q Consensus 324 g~-~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~Atl~L~~~kl~~g~~fg 374 (569)
+. +..++|..+-..|.+-. +-.++|.+..|--+-+-.+++...+-..|+
T Consensus 173 ~~~~~~~~l~~If~ry~~q~--eppa~~~~e~d~~~l~~~fqf~~~ellR~~ 222 (318)
T KOG4793|consen 173 PEVRRMYSLGSIFLRYVEQR--EPPAGHVAEGDVNGLLFIFQFRINELLRWS 222 (318)
T ss_pred CCCCcccccchHHHhhhccc--CCCcceeeecccchhHHHHHHHHHHHHhhH
Confidence 22 45678888877665543 223689988877766666665555444443
No 113
>PRK04024 cofactor-independent phosphoglycerate mutase; Provisional
Probab=51.20 E-value=55 Score=36.25 Aligned_cols=74 Identities=12% Similarity=0.083 Sum_probs=53.9
Q ss_pred ChHHHHHHHHHhccCCCccEEEEeccccchhhhhhhHhHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHHHHH
Q 008340 419 SDDEVLSKARKEVKNDRIHFVWTQFSELNLHFKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPEIKEILART 498 (569)
Q Consensus 419 ~D~ev~~~~~~~v~~~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 498 (569)
+-.+-.+.+++.++. +|||++++..... ..+ . ...+...++++++
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 556677788888873 6999998865431 110 0 1123466789999
Q ss_pred HHHHHHHHhhCC-CCcEEEEEeCCCChHHH
Q 008340 499 DARVNSLYTALP-TNTMLIICTGHGDTAIV 527 (569)
Q Consensus 499 ~~~i~~iy~~lP-~~t~liv~sg~gd~~~m 527 (569)
|+.|.+|++.+. +..++||.+=||+|-.+
T Consensus 324 D~~l~~il~~l~~~~~~liITaDHgtp~~~ 353 (412)
T PRK04024 324 DKMLGYILDNLDLDEVYIAVTGDHSTPVEV 353 (412)
T ss_pred HHHHHHHHHHhhcCCCEEEEecCCCCCccc
Confidence 999999999995 78899999999998543
No 114
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=49.46 E-value=62 Score=36.79 Aligned_cols=129 Identities=14% Similarity=0.182 Sum_probs=73.5
Q ss_pred CCcEEEEEeceecCC-C-----CceEEEEEEEEee-C---eEEEEEEEecCCCCCCCcEeecCCChhhhcCCC----CCH
Q 008340 211 PYEILALDCEMCYTN-E-----GLELTRVTLVDIK-G---QVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVT----TSL 276 (569)
Q Consensus 211 ~~~~vAiDcEm~~t~-~-----g~eL~rVsvVd~~-G---~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~----~tl 276 (569)
.-++..||+|.+.-+ + .-+|..|+..|.. + -.+|+.+ + ....|-...+=.-.+.+.++. .+-
T Consensus 105 ~i~~~~~DIEv~~~~fp~~~~a~~~i~~i~~~d~~~~~~~~~~~~~~--~--~~~~~~~~~~~~~~~~~~~v~v~~f~sE 180 (498)
T PHA02524 105 DVVIDVVDIEVTAPEFPEPKYAKYEIDMISHVRLHNGKKTYYIFDLV--K--DVGHWDPKKSVLEKYILDNVVYMPFEDE 180 (498)
T ss_pred hceEEEEEEEecCCCCCChhhcCCceEEEEeeecccCCccEEEEecc--c--cccCCCcccccccccccCCeEEEEeCCH
Confidence 347899999996532 1 2478899998853 1 1345543 1 111122111112222244431 356
Q ss_pred HHHHHHHHHhhcC--CCEEEEeCc-hhhHHHHc--------cc-----------C-----------------C-Cccchh
Q 008340 277 KDIQEEFLKLVYK--ETILVGHSL-ENDLLALK--------IS-----------H-----------------G-LVIDTA 316 (569)
Q Consensus 277 ~dVq~~l~~ll~~--~tILVGHsL-~~DL~aLk--------i~-----------h-----------------p-~viDT~ 316 (569)
.++..++.+++.. -.||+|||. +|||..|. +. + . -++|..
T Consensus 181 ~eLL~~F~~~i~~~DPDIItGYNi~nFDlPYL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~~~G~~~~~~I~GRv~iDl~ 260 (498)
T PHA02524 181 VDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNILGEKAANQLSPYGKITSKTITNLYGEKIIYKIHGIALMDYM 260 (498)
T ss_pred HHHHHHHHHHHHHhCCCEEEeCCCcccCHHHHHHHHHHHhCCccccccccccccccccceeecCceeEEEEeeEEEeEHH
Confidence 7788888888843 389999997 67996543 10 0 0 023444
Q ss_pred hhcccc-CCCCCCchHHHHHHHhcCccc
Q 008340 317 VLYKHP-QGGSHKTSLRVLAKKFLSREI 343 (569)
Q Consensus 317 ~L~~~~-~g~~~k~sLk~La~~~Lg~~I 343 (569)
.+++.. ......++|.+++..+||..-
T Consensus 261 ~l~kk~s~~~l~sYsL~~Vs~~~Lg~~K 288 (498)
T PHA02524 261 DVFKKFSFTPMPDYKLGNVGYREVKADK 288 (498)
T ss_pred HHHHHhhhccCCCCCHHHHHHHhcCCcc
Confidence 454432 112356889999999998653
No 115
>PRK11598 putative metal dependent hydrolase; Provisional
Probab=49.04 E-value=37 Score=38.94 Aligned_cols=129 Identities=15% Similarity=0.164 Sum_probs=67.0
Q ss_pred HHHHHHHHHhcCCeeeeecccc----ccccc-----c----CCCcceeecCChHHHHHHHHHhccCC-CccEEEEecccc
Q 008340 381 RTKLLKVLFEYGKTSTLIDNVS----IIKRY-----A----SESSHAIPVSSDDEVLSKARKEVKND-RIHFVWTQFSEL 446 (569)
Q Consensus 381 ~~~l~~~l~~~g~~~~~~d~~~----~~~~~-----~----~~~~~~i~~~~D~ev~~~~~~~v~~~-~~~f~~~~~~~l 446 (569)
.++|.+.+.+.|-....++... ...+. . ...|..-.| .|+..+..+.+.+.+. +-.|++.++.+-
T Consensus 305 ~~~l~d~l~~aG~~t~W~~Nq~g~~g~~~r~~~~~~~~~~~~~~~~~~~~-~De~LL~~l~~~L~~~~~~~fivLH~~GS 383 (545)
T PRK11598 305 QEGLLDIIQRAGINVLWNDNDGGCKGACDRVPHQDVTALNLPGQCIDGEC-YDEVLFHGLENYINNLQGDGVIVLHTIGS 383 (545)
T ss_pred cccHHHHHHHcCCeEEeecCCCCCcchhcccchhhhhhhccccccCCCCc-cHHHHHHHHHHHHHhcCCCeEEEEeCCCC
Confidence 3679999999998887776211 00000 0 001111122 4777776655544321 125899888774
Q ss_pred ch--hhhhhhHhHHHHHHHHHHHhhhhhcccccccccccCCCCcHH----HHHHHHHHHHHHHHHHhhCCC-----CcEE
Q 008340 447 NL--HFKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPE----IKEILARTDARVNSLYTALPT-----NTML 515 (569)
Q Consensus 447 ~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~i~~iy~~lP~-----~t~l 515 (569)
.. |+... +..... . ...|...... ++. .++ -...+..+|..|.+|++.|.. ||++
T Consensus 384 H~P~Y~~Ry---P~~~~~-F-----~p~~~~~~~~----~~~-~~~~~n~YdnsI~ytD~~lg~ii~~Lk~~~~~~nT~i 449 (545)
T PRK11598 384 HGPTYYNRY---PPQFRK-F-----TPTCDTNEIQ----TCT-QQQLVNTYDNTILYVDYIVDKAINLLKQHQDKFNTSL 449 (545)
T ss_pred CCcchhhcC---Chhhcc-C-----CCCCCccccc----ccc-HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcCCeEE
Confidence 32 22111 111100 0 0112211110 111 112 245567788899999988754 7899
Q ss_pred EEEeCCCCh
Q 008340 516 IICTGHGDT 524 (569)
Q Consensus 516 iv~sg~gd~ 524 (569)
|.+|=||..
T Consensus 450 Iy~SDHGe~ 458 (545)
T PRK11598 450 VYLSDHGES 458 (545)
T ss_pred EEECcCCCc
Confidence 999999985
No 116
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=41.12 E-value=23 Score=42.31 Aligned_cols=31 Identities=29% Similarity=0.348 Sum_probs=23.5
Q ss_pred cCCCEEEEeCchhhHHHHcc---c---CCCccchhhh
Q 008340 288 YKETILVGHSLENDLLALKI---S---HGLVIDTAVL 318 (569)
Q Consensus 288 ~~~tILVGHsL~~DL~aLki---~---hp~viDT~~L 318 (569)
.++.++||||+.||-.-++= + ..+.+||+.|
T Consensus 239 ~ke~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTMSl 275 (1075)
T KOG3657|consen 239 GKEQLIVGHNVSFDRARIREEYNINGSKIRFLDTMSL 275 (1075)
T ss_pred CCCceEEeccccchHHHHHHHHhccccceeeeechhh
Confidence 57899999999999987772 1 2357888754
No 117
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=38.86 E-value=1.9e+02 Score=37.25 Aligned_cols=152 Identities=20% Similarity=0.254 Sum_probs=84.9
Q ss_pred CcEEEEEeceecCCC------CceEEEEE-EEEeeCeEEEEE-EEecCCCCCCCc----EeecCCChhhhcCCCCCHHHH
Q 008340 212 YEILALDCEMCYTNE------GLELTRVT-LVDIKGQVLLDK-LVKPSNAIVDYN----TRYSGITHEMLSGVTTSLKDI 279 (569)
Q Consensus 212 ~~~vAiDcEm~~t~~------g~eL~rVs-vVd~~G~vv~D~-lVkP~~~I~dy~----T~~SGIT~e~L~~~~~tl~dV 279 (569)
..+.|+|+||+...- .++|.-|| +||+.|..+.+. .|- +.|.|+- -.|-|- =.+-|. +.-..+
T Consensus 246 p~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREiVs--~DIedfEYTPKpE~eG~--F~v~Ne-~dEv~L 320 (2173)
T KOG1798|consen 246 PRVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREIVS--EDIEDFEYTPKPEYEGP--FCVFNE-PDEVGL 320 (2173)
T ss_pred ceEEEEeeecccCCCCCCCcccceEEEEEEEecCceEEEechhhhc--cchhhcccCCccccccc--eEEecC-CcHHHH
Confidence 469999999999752 25676666 355666655442 221 1111110 011110 001122 233334
Q ss_pred HHHHHHhhc--CCCEEEEeCchh-hHHHHcc---cCC--------Cccchhhhcccc---------------CCCCCCch
Q 008340 280 QEEFLKLVY--KETILVGHSLEN-DLLALKI---SHG--------LVIDTAVLYKHP---------------QGGSHKTS 330 (569)
Q Consensus 280 q~~l~~ll~--~~tILVGHsL~~-DL~aLki---~hp--------~viDT~~L~~~~---------------~g~~~k~s 330 (569)
.+.+.+.+. .-+|+|-+|-.| |+-++.. .|. ...|...-|+.+ +-|....+
T Consensus 321 l~RfFeHiq~~kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrWVKRDSYLPqGSqg 400 (2173)
T KOG1798|consen 321 LQRFFEHIQEVKPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRWVKRDSYLPQGSQG 400 (2173)
T ss_pred HHHHHHHHHhcCCcEEEEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehhhhhhhhhcccCCCcccc
Confidence 444444442 568999999764 9988873 232 234433222111 12344678
Q ss_pred HHHHHHHhcCccccc-C-------------CCCCChHHHHHHHHHHHHHHHH
Q 008340 331 LRVLAKKFLSREIQQ-S-------------GFGHDSTEDARAAMELALLKIR 368 (569)
Q Consensus 331 Lk~La~~~Lg~~Iq~-~-------------~~~HdS~EDA~Atl~L~~~kl~ 368 (569)
||.+++..||.+--+ + .-+-=|+.||.||.-||...+.
T Consensus 401 LKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVh 452 (2173)
T KOG1798|consen 401 LKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVH 452 (2173)
T ss_pred hhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhh
Confidence 999999999976322 1 1356679999999999977654
No 118
>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=38.52 E-value=55 Score=30.93 Aligned_cols=30 Identities=23% Similarity=0.319 Sum_probs=22.6
Q ss_pred HHHHhhC-CCCcEEEEEeCCCChHHHHHHHH
Q 008340 503 NSLYTAL-PTNTMLIICTGHGDTAIVHRLRE 532 (569)
Q Consensus 503 ~~iy~~l-P~~t~liv~sg~gd~~~m~~l~~ 532 (569)
+++...+ |++|++|++|-+|++.|....-+
T Consensus 64 ~~~~~~~~~~~tlvi~iSkSG~T~Et~~~~~ 94 (158)
T cd05015 64 AELLKKLDPETTLFIVISKSGTTLETLANAR 94 (158)
T ss_pred HHHHHhCCcccEEEEEEECCcCCHHHHHHHH
Confidence 4444444 79999999999999988765433
No 119
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=37.15 E-value=1.8e+02 Score=30.49 Aligned_cols=113 Identities=14% Similarity=0.085 Sum_probs=64.8
Q ss_pred CCcEEEEEeceecCCC-CceEEEEEEEEeeCeEEEEEEEecCCCCCCCcEeecCCChhhhcCCCCCHHHHHHHHHHhhcC
Q 008340 211 PYEILALDCEMCYTNE-GLELTRVTLVDIKGQVLLDKLVKPSNAIVDYNTRYSGITHEMLSGVTTSLKDIQEEFLKLVYK 289 (569)
Q Consensus 211 ~~~~vAiDcEm~~t~~-g~eL~rVsvVd~~G~vv~D~lVkP~~~I~dy~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll~~ 289 (569)
..+++-+|+||+|.+. |+-|+-++.-...+.++ +||-. +.+++-.-..|.+.++... .
T Consensus 97 ~e~~~FFDiETTGL~~ag~~I~~~g~a~~~~~~~---~Vrq~-----------------~lp~p~~E~avle~fl~~~-~ 155 (278)
T COG3359 97 AEDVAFFDIETTGLDRAGNTITLVGGARGVDDTM---HVRQH-----------------FLPAPEEEVAVLENFLHDP-D 155 (278)
T ss_pred ccceEEEeeeccccCCCCCeEEEEEEEEccCceE---EEEee-----------------cCCCcchhhHHHHHHhcCC-C
Confidence 3569999999999985 45566555555433322 22211 1112111223667777777 7
Q ss_pred CCEEEEeC-chhhHHHHc-ccCC--------CccchhhhccccCC-CCCCchHHHHHHHhcCccccc
Q 008340 290 ETILVGHS-LENDLLALK-ISHG--------LVIDTAVLYKHPQG-GSHKTSLRVLAKKFLSREIQQ 345 (569)
Q Consensus 290 ~tILVGHs-L~~DL~aLk-i~hp--------~viDT~~L~~~~~g-~~~k~sLk~La~~~Lg~~Iq~ 345 (569)
.+.||-.| ..||.-+++ +.+. --+|-....+...+ ...+-+|+.+=+ +||+.=..
T Consensus 156 ~~~lvsfNGkaFD~PfikR~v~~~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr-~LGi~R~e 221 (278)
T COG3359 156 FNMLVSFNGKAFDIPFIKRMVRDRLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTVER-ILGIRREE 221 (278)
T ss_pred cceEEEecCcccCcHHHHHHHhcccccCccccchhhhhhhhhhhhccCCCCChhhHHH-HhCccccc
Confidence 78999998 589999998 2111 12443322222111 124557999887 88887443
No 120
>PRK09598 lipid A phosphoethanolamine transferase; Reviewed
Probab=35.78 E-value=79 Score=36.07 Aligned_cols=130 Identities=11% Similarity=0.093 Sum_probs=66.2
Q ss_pred HHHHHHHHhcCCeeeeeccc--ccc---ccc-c----CCCcceeecCChHHHHHHHHHhccCC--CccEEEEeccccch-
Q 008340 382 TKLLKVLFEYGKTSTLIDNV--SII---KRY-A----SESSHAIPVSSDDEVLSKARKEVKND--RIHFVWTQFSELNL- 448 (569)
Q Consensus 382 ~~l~~~l~~~g~~~~~~d~~--~~~---~~~-~----~~~~~~i~~~~D~ev~~~~~~~v~~~--~~~f~~~~~~~l~~- 448 (569)
+++.+.+.+.|-++..++.. ... ..+ . ...+....|.-|++.+..+.+.+++. +.-|++.++.+-..
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 46777788888777766632 110 000 0 01122334567888888777666432 23588988877432
Q ss_pred -hhhhhhHhHHHHHHHHHHHhhhhhcccccccccccCCCCc---HHHHHHHHHHHHHHHHHHhhC---CCCcEEEEEeCC
Q 008340 449 -HFKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVT---PEIKEILARTDARVNSLYTAL---PTNTMLIICTGH 521 (569)
Q Consensus 449 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~i~~iy~~l---P~~t~liv~sg~ 521 (569)
|..++ +... .... ..|..... .++... ..-...+.-+|..|.++++.| +.+|++|.+|=|
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-RVFK-----PVCSSVEL----SSCSKESLINAYDNTIFYNDYLLDKIISMLKNLKQPALMIYLSDH 439 (522)
T ss_pred cccccC---Chhh-cccC-----CCCcchhh----hhccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeEEEEEccC
Confidence 22211 1111 0000 11211100 000010 112345566777787777766 448999999988
Q ss_pred CCh
Q 008340 522 GDT 524 (569)
Q Consensus 522 gd~ 524 (569)
|..
T Consensus 440 Ge~ 442 (522)
T PRK09598 440 GES 442 (522)
T ss_pred ccc
Confidence 864
No 121
>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=27.83 E-value=35 Score=34.33 Aligned_cols=44 Identities=27% Similarity=0.380 Sum_probs=26.7
Q ss_pred CcEeecCCChhhhcCCCCCHHHHHHHHHHhh------cCCCEEEEeCchh
Q 008340 257 YNTRYSGITHEMLSGVTTSLKDIQEEFLKLV------YKETILVGHSLEN 300 (569)
Q Consensus 257 y~T~~SGIT~e~L~~~~~tl~dVq~~l~~ll------~~~tILVGHsL~~ 300 (569)
|...+++..-..|......+.+..+.|++.. +..-||||||.--
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 3333333333334433345667777777777 5778999999755
No 122
>PRK11560 phosphoethanolamine transferase; Provisional
Probab=26.78 E-value=1.6e+02 Score=34.07 Aligned_cols=33 Identities=15% Similarity=0.339 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHhhCC-CCcEEEEEeCCCCh
Q 008340 492 KEILARTDARVNSLYTALP-TNTMLIICTGHGDT 524 (569)
Q Consensus 492 ~~~~~~~~~~i~~iy~~lP-~~t~liv~sg~gd~ 524 (569)
...+..+|..|.+|.+.|- .||++|.+|=||..
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 123
>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=25.39 E-value=2.4e+02 Score=31.09 Aligned_cols=36 Identities=19% Similarity=0.259 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHHHhhCCC-CcEEEEEeCCCChH
Q 008340 490 EIKEILARTDARVNSLYTALPT-NTMLIICTGHGDTA 525 (569)
Q Consensus 490 ~~~~~~~~~~~~i~~iy~~lP~-~t~liv~sg~gd~~ 525 (569)
...++++++|+.+.+++++|.. ...+||.+=||+|-
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 124
>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=24.63 E-value=1.2e+02 Score=26.46 Aligned_cols=32 Identities=19% Similarity=0.269 Sum_probs=25.3
Q ss_pred HHHHHhhCCCCcEEEEEeCCCChHHHHHHHHH
Q 008340 502 VNSLYTALPTNTMLIICTGHGDTAIVHRLREM 533 (569)
Q Consensus 502 i~~iy~~lP~~t~liv~sg~gd~~~m~~l~~~ 533 (569)
.......+.+++++|++|.+|.++++.++=+.
T Consensus 44 ~~~~~~~~~~~d~vi~is~sg~~~~~~~~~~~ 75 (131)
T PF01380_consen 44 FHGPLENLDPDDLVIIISYSGETRELIELLRF 75 (131)
T ss_dssp HTTGGGGCSTTEEEEEEESSSTTHHHHHHHHH
T ss_pred hhhhcccccccceeEeeeccccchhhhhhhHH
Confidence 34445778899999999999999988765443
No 125
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=24.42 E-value=78 Score=32.45 Aligned_cols=54 Identities=26% Similarity=0.247 Sum_probs=41.3
Q ss_pred CCccchhhhccccCCCCCCchHHHHHHHhcCcccccCCCCCChHHHHHHHHHHHHHH
Q 008340 310 GLVIDTAVLYKHPQGGSHKTSLRVLAKKFLSREIQQSGFGHDSTEDARAAMELALLK 366 (569)
Q Consensus 310 p~viDT~~L~~~~~g~~~k~sLk~La~~~Lg~~Iq~~~~~HdS~EDA~Atl~L~~~k 366 (569)
|.+-|+-.++....+...+.+|..||.. |+.+=. |..|.|-.|+..|+..|.+.
T Consensus 182 p~vYDiK~l~~~c~~~~l~~GL~~lA~~-L~~~Rv--G~~HqAGSDSlLT~~~F~kl 235 (239)
T KOG0304|consen 182 PFVYDVKYLMKFCEGLSLKGGLQRLADL-LGLKRV--GIAHQAGSDSLLTARVFFKL 235 (239)
T ss_pred chhhhHHHHHHhhhhhhhhcCHHHHHHH-hCCCee--ecccccCcHHHHHHHHHHHH
Confidence 6778888888776565567889999985 565532 36799999999999998543
No 126
>KOG0100 consensus Molecular chaperones GRP78/BiP/KAR2, HSP70 superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=22.95 E-value=1.8e+02 Score=32.68 Aligned_cols=53 Identities=17% Similarity=0.298 Sum_probs=38.4
Q ss_pred CCcEEEEEeCCCCh---------HHHHHHHHHHHHHhhhcccHH-HHHHHHHHHHHHHhhcee
Q 008340 511 TNTMLIICTGHGDT---------AIVHRLREMLREQSKNSMSRK-MIVKVLEELQAQAEVALC 563 (569)
Q Consensus 511 ~~t~liv~sg~gd~---------~~m~~l~~~~~~~~~~~~~~~-~~~~~l~~~~~~Ar~g~~ 563 (569)
.|.+|=|++-+||+ |-|.-|-++.+.......+++ +-.+.|++.|++|+++|.
T Consensus 245 dnGVFeVlaTnGDThLGGEDFD~rvm~~fiklykkK~gkDv~kdnkA~~KLrRe~EkAKRaLS 307 (663)
T KOG0100|consen 245 DNGVFEVLATNGDTHLGGEDFDQRVMEYFIKLYKKKHGKDVRKDNKAVQKLRREVEKAKRALS 307 (663)
T ss_pred cCceEEEEecCCCcccCccchHHHHHHHHHHHHhhhcCCccchhhHHHHHHHHHHHHHHhhhc
Confidence 47899999999998 777777777544333223333 356889999999999875
No 127
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=22.94 E-value=7.2e+02 Score=27.73 Aligned_cols=83 Identities=16% Similarity=0.148 Sum_probs=49.5
Q ss_pred HHHHHHHhhc--CCCEEEEeCchhhHHHHcc---cCC-----------Cccchhhhcc-ccCCCCCCchHHHHHHHhcCc
Q 008340 279 IQEEFLKLVY--KETILVGHSLENDLLALKI---SHG-----------LVIDTAVLYK-HPQGGSHKTSLRVLAKKFLSR 341 (569)
Q Consensus 279 Vq~~l~~ll~--~~tILVGHsL~~DL~aLki---~hp-----------~viDT~~L~~-~~~g~~~k~sLk~La~~~Lg~ 341 (569)
+..+|++++. ++..|+-+| .+-..+|+- .|+ ++||...+.+ +.+.+..++|||.++. +||.
T Consensus 331 ~~~~f~~~l~~~~~~~i~hY~-~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~sysLK~v~~-~lg~ 408 (457)
T TIGR03491 331 AWQQFLQLLQSYPDAPIYHYG-ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIESYSLKSIAR-WLGF 408 (457)
T ss_pred HHHHHHHHHHHCCCCeEEeeC-HHHHHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCCCCCHHHHHH-HhCc
Confidence 4444444443 566788888 787877772 122 4566543322 2233445789999998 5688
Q ss_pred ccccCCCCCChHHHHHHHHHHHHHHHHc
Q 008340 342 EIQQSGFGHDSTEDARAAMELALLKIRN 369 (569)
Q Consensus 342 ~Iq~~~~~HdS~EDA~Atl~L~~~kl~~ 369 (569)
+... ..-|...++..|...+..
T Consensus 409 ~~~~------~~~~G~~ai~~y~~~~~~ 430 (457)
T TIGR03491 409 EWRQ------KEASGAKSLLWYRQWKKT 430 (457)
T ss_pred ccCC------CCCCHHHHHHHHHHHHHh
Confidence 7542 234555667777665553
No 128
>KOG4513 consensus Phosphoglycerate mutase [Carbohydrate transport and metabolism]
Probab=22.57 E-value=2.4e+02 Score=31.31 Aligned_cols=83 Identities=16% Similarity=0.242 Sum_probs=56.9
Q ss_pred ceeecCChHHHHHHHHHhccCCCccEEEEeccccchhhhhhhHhHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHH
Q 008340 413 HAIPVSSDDEVLSKARKEVKNDRIHFVWTQFSELNLHFKKQAKDEAKLNEKLAELISLATCDKKLSDSKRFKSFVTPEIK 492 (569)
Q Consensus 413 ~~i~~~~D~ev~~~~~~~v~~~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 492 (569)
+..|--.-.||-++++.++..+.++||.+.|--- .|.. . +... +...
T Consensus 382 d~qP~M~a~eva~ka~~~ie~G~~p~v~vNlapp------------DMVG-----------H---------TG~~-EAtv 428 (531)
T KOG4513|consen 382 DVQPKMKALEVAEKARDAIESGKFPQVRVNLAPP------------DMVG-----------H---------TGDI-EATV 428 (531)
T ss_pred ecChhhhHHHHHHHHHHHHHcCCCCeEEEcCCCc------------cccC-----------c---------ccch-hhhh
Confidence 3445556789999999999988899997776321 1101 0 0011 1345
Q ss_pred HHHHHHHHHHHHHHhhCCCCcEEEE-EeCCCChHHHH
Q 008340 493 EILARTDARVNSLYTALPTNTMLII-CTGHGDTAIVH 528 (569)
Q Consensus 493 ~~~~~~~~~i~~iy~~lP~~t~liv-~sg~gd~~~m~ 528 (569)
.+.+.++..|.+||++...+.-+.| ..-||+-..|.
T Consensus 429 ~AcEatD~aig~Iy~A~~~~~y~lvvTADHGNAEkMv 465 (531)
T KOG4513|consen 429 VACEATDEAIGKIYDAIEQVGYILVVTADHGNAEKMV 465 (531)
T ss_pred hHHHHHHHHHHHHHHHHHhcCcEEEEEcCCCCHHHhc
Confidence 6788999999999999988766555 45689988775
No 129
>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=21.36 E-value=1.4e+02 Score=26.55 Aligned_cols=27 Identities=19% Similarity=0.146 Sum_probs=22.6
Q ss_pred hCCCCcEEEEEeCCCChHHHHHHHHHH
Q 008340 508 ALPTNTMLIICTGHGDTAIVHRLREML 534 (569)
Q Consensus 508 ~lP~~t~liv~sg~gd~~~m~~l~~~~ 534 (569)
.+.+++++|++|.+|.+.++.+.=+.-
T Consensus 40 ~~~~~dl~I~iS~SG~t~e~i~~~~~a 66 (119)
T cd05017 40 FVDRKTLVIAVSYSGNTEETLSAVEQA 66 (119)
T ss_pred CCCCCCEEEEEECCCCCHHHHHHHHHH
Confidence 678999999999999999887754443
No 130
>PF01964 ThiC: ThiC family; InterPro: IPR002817 ThiC is found within the thiamin biosynthesis operon. ThiC is involved in thiamin biosynthesis []. The precise catalytic function of ThiC is still not known. ThiC participates in the formation of 4-Amino-5-hydroxymethyl-2-methylpyrimidine from AIR, an intermediate in the de novo pyrimidine biosynthesis.; GO: 0009228 thiamine biosynthetic process; PDB: 3EPO_A 3EPN_B 3EPM_B.
Probab=20.39 E-value=2.5e+02 Score=31.25 Aligned_cols=68 Identities=16% Similarity=0.225 Sum_probs=34.0
Q ss_pred HHHHHHHHHHhhCCCC-cEEEEEeCCCChHHHHHH---------------HHHHHHH-hhhcccHHHHHHHHHHHHHHHh
Q 008340 497 RTDARVNSLYTALPTN-TMLIICTGHGDTAIVHRL---------------REMLREQ-SKNSMSRKMIVKVLEELQAQAE 559 (569)
Q Consensus 497 ~~~~~i~~iy~~lP~~-t~liv~sg~gd~~~m~~l---------------~~~~~~~-~~~~~~~~~~~~~l~~~~~~Ar 559 (569)
.++.-++|+-.+.--+ ..++=+|-.||..++++. |+..+.+ .-...+ ++..++..-++|+
T Consensus 74 d~~~E~~K~~~A~~~GADtvMDLStggdl~~iR~~il~~~~vpvGTVPiYqa~~~~~~~~~~~t---~d~~~~~ie~qa~ 150 (420)
T PF01964_consen 74 DIEEELEKLKIAEKAGADTVMDLSTGGDLDEIRRAILENSPVPVGTVPIYQAAIRKGGSIVDMT---EDDFFDVIEKQAK 150 (420)
T ss_dssp -HHHHHHHHHHHHHTT-SEEEE---STTHHHHHHHHHHT-SS-EEE-HHHHHHHHTTT-GGG-----HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHhCCCccccchHHHHHHHhCCChhhCC---HHHHHHHHHHHHH
Confidence 4444455555554444 567788888999988762 2221111 112222 3344444447899
Q ss_pred hceeEEEe
Q 008340 560 VALCFVGV 567 (569)
Q Consensus 560 ~g~~fi~v 567 (569)
+|+-||+|
T Consensus 151 ~GVDfmti 158 (420)
T PF01964_consen 151 DGVDFMTI 158 (420)
T ss_dssp HT--EEEE
T ss_pred cCCCEEEE
Confidence 99999987
No 131
>PRK04200 cofactor-independent phosphoglycerate mutase; Provisional
Probab=20.27 E-value=2.5e+02 Score=30.92 Aligned_cols=36 Identities=17% Similarity=0.278 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHH-HHHHHhhCC--CCcEEEEEeCCCChH
Q 008340 490 EIKEILARTDAR-VNSLYTALP--TNTMLIICTGHGDTA 525 (569)
Q Consensus 490 ~~~~~~~~~~~~-i~~iy~~lP--~~t~liv~sg~gd~~ 525 (569)
...++++++++. +..|+++|. .+..++|.+=||+|-
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 456779999998 457999997 477899999999864
No 132
>smart00266 CAD Domains present in proteins implicated in post-mortem DNA fragmentation.
Probab=20.13 E-value=79 Score=26.98 Aligned_cols=17 Identities=29% Similarity=0.456 Sum_probs=14.5
Q ss_pred HHhhCCCCcEEEEEeCC
Q 008340 505 LYTALPTNTMLIICTGH 521 (569)
Q Consensus 505 iy~~lP~~t~liv~sg~ 521 (569)
-|..||+||.|||+...
T Consensus 55 yF~tLp~nt~l~~L~~g 71 (74)
T smart00266 55 YFQTLPDNTELMALEKG 71 (74)
T ss_pred HHhcCCCCcEEEEEcCC
Confidence 47899999999998753
No 133
>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=20.10 E-value=1.3e+02 Score=26.28 Aligned_cols=21 Identities=14% Similarity=0.058 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHhhceeEE
Q 008340 545 KMIVKVLEELQAQAEVALCFV 565 (569)
Q Consensus 545 ~~~~~~l~~~~~~Ar~g~~fi 565 (569)
.++|+++++||.++++|.-|-
T Consensus 26 ~~RE~aIeeav~~c~~g~pFs 46 (84)
T PF10752_consen 26 QQREAAIEEAVSLCKQGEPFS 46 (84)
T ss_pred HHHHHHHHHHHHHHHCCCCCc
Confidence 457899999999999998873
Done!