Query 036883
Match_columns 277
No_of_seqs 234 out of 1157
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 06:24:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036883.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036883hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0542 Predicted exonuclease 100.0 5E-43 1.1E-47 303.6 13.9 192 1-192 55-251 (280)
2 PTZ00315 2'-phosphotransferase 100.0 2E-38 4.4E-43 306.9 23.9 196 1-196 55-268 (582)
3 PRK07748 sporulation inhibitor 100.0 3.7E-38 8E-43 274.5 19.5 174 3-185 5-182 (207)
4 PRK06722 exonuclease; Provisio 100.0 1.3E-35 2.8E-40 267.9 21.1 171 2-181 5-179 (281)
5 cd06133 ERI-1_3'hExo_like DEDD 100.0 4.9E-34 1.1E-38 240.6 20.1 172 4-180 1-176 (176)
6 TIGR01406 dnaQ_proteo DNA poly 100.0 1.8E-32 4E-37 241.5 20.9 170 3-186 1-175 (225)
7 PRK05711 DNA polymerase III su 100.0 2.6E-32 5.7E-37 242.3 21.5 172 3-188 5-181 (240)
8 smart00479 EXOIII exonuclease 100.0 4.8E-32 1E-36 226.4 21.6 167 3-184 1-168 (169)
9 cd06131 DNA_pol_III_epsilon_Ec 100.0 1E-31 2.2E-36 225.5 20.5 162 4-179 1-166 (167)
10 PRK06807 DNA polymerase III su 100.0 1E-31 2.2E-36 247.0 20.8 165 1-183 7-172 (313)
11 PRK06195 DNA polymerase III su 100.0 4E-31 8.6E-36 243.3 22.6 162 3-183 2-164 (309)
12 cd06130 DNA_pol_III_epsilon_li 100.0 2.7E-31 5.9E-36 219.9 18.6 154 4-177 1-155 (156)
13 PRK08517 DNA polymerase III su 100.0 7E-31 1.5E-35 235.5 20.9 163 3-183 69-231 (257)
14 COG5018 KapD Inhibitor of the 100.0 1.5E-32 3.3E-37 225.3 8.3 184 2-187 4-189 (210)
15 PRK07740 hypothetical protein; 100.0 2E-30 4.4E-35 231.1 20.0 164 3-183 60-226 (244)
16 PRK09145 DNA polymerase III su 100.0 2.7E-30 5.9E-35 224.1 19.7 163 2-182 29-200 (202)
17 PRK06310 DNA polymerase III su 100.0 3.8E-30 8.3E-35 230.1 20.7 168 2-183 7-174 (250)
18 PRK06063 DNA polymerase III su 100.0 2.6E-30 5.6E-35 238.0 19.1 163 2-182 15-178 (313)
19 TIGR00573 dnaq exonuclease, DN 100.0 8.9E-30 1.9E-34 223.3 21.4 171 2-187 7-181 (217)
20 PRK09146 DNA polymerase III su 100.0 5.6E-30 1.2E-34 227.5 20.3 164 3-184 48-228 (239)
21 PRK07247 DNA polymerase III su 100.0 5.7E-30 1.2E-34 220.8 19.3 160 2-184 5-170 (195)
22 PRK07942 DNA polymerase III su 100.0 6.5E-30 1.4E-34 226.3 20.0 173 2-184 6-181 (232)
23 PRK05168 ribonuclease T; Provi 100.0 1.1E-29 2.4E-34 221.9 20.8 175 3-183 18-201 (211)
24 cd06134 RNaseT DEDDh 3'-5' exo 100.0 4.5E-29 9.8E-34 214.5 20.0 174 3-182 6-188 (189)
25 cd06136 TREX1_2 DEDDh 3'-5' ex 100.0 2.4E-29 5.2E-34 214.0 17.3 162 4-178 1-176 (177)
26 PRK06309 DNA polymerase III su 100.0 4.1E-29 9E-34 221.2 19.3 163 2-183 2-166 (232)
27 TIGR01298 RNaseT ribonuclease 100.0 1.4E-28 3.1E-33 213.2 19.5 175 3-183 9-192 (200)
28 PRK07883 hypothetical protein; 100.0 1.1E-28 2.5E-33 242.6 21.2 167 3-186 16-185 (557)
29 PRK07246 bifunctional ATP-depe 100.0 2.5E-28 5.3E-33 249.6 21.1 163 2-183 7-170 (820)
30 PRK05601 DNA polymerase III su 100.0 2.2E-27 4.7E-32 219.4 22.9 166 3-183 47-249 (377)
31 COG2176 PolC DNA polymerase II 100.0 3.3E-29 7.1E-34 252.6 10.7 163 3-182 422-585 (1444)
32 cd06138 ExoI_N N-terminal DEDD 100.0 1.1E-27 2.5E-32 204.7 16.9 162 5-176 1-182 (183)
33 PRK08074 bifunctional ATP-depe 100.0 1.9E-27 4.1E-32 246.3 21.3 166 2-184 3-170 (928)
34 TIGR01405 polC_Gram_pos DNA po 100.0 3E-27 6.5E-32 247.3 21.0 167 3-186 191-358 (1213)
35 TIGR01407 dinG_rel DnaQ family 100.0 5.1E-27 1.1E-31 241.6 21.1 163 3-182 1-164 (850)
36 cd06127 DEDDh DEDDh 3'-5' exon 99.9 6.1E-27 1.3E-31 191.8 16.0 156 5-176 1-158 (159)
37 PRK07983 exodeoxyribonuclease 99.9 1.5E-26 3.2E-31 203.0 18.4 148 4-182 2-153 (219)
38 cd06137 DEDDh_RNase DEDDh 3'-5 99.9 1.2E-26 2.6E-31 194.5 9.8 147 5-177 1-161 (161)
39 cd06135 Orn DEDDh 3'-5' exonuc 99.9 2.2E-25 4.7E-30 189.0 16.1 161 4-181 1-170 (173)
40 cd06144 REX4_like DEDDh 3'-5' 99.9 5.5E-26 1.2E-30 188.7 11.7 149 5-177 1-152 (152)
41 COG0847 DnaQ DNA polymerase II 99.9 1E-24 2.3E-29 193.7 19.9 165 3-182 14-181 (243)
42 PF00929 RNase_T: Exonuclease; 99.9 2.3E-26 4.9E-31 188.8 6.6 159 5-176 1-164 (164)
43 cd06145 REX1_like DEDDh 3'-5' 99.9 3.1E-25 6.8E-30 183.9 12.2 145 5-177 1-150 (150)
44 cd06149 ISG20 DEDDh 3'-5' exon 99.9 5.2E-25 1.1E-29 183.9 11.2 149 5-177 1-157 (157)
45 PRK09182 DNA polymerase III su 99.9 4.8E-24 1E-28 194.6 17.7 181 2-204 37-222 (294)
46 PRK00448 polC DNA polymerase I 99.9 3.6E-24 7.8E-29 226.7 18.8 165 3-184 420-585 (1437)
47 PRK05359 oligoribonuclease; Pr 99.9 3.8E-23 8.1E-28 176.6 16.9 162 2-182 3-174 (181)
48 PRK11779 sbcB exonuclease I; P 99.9 2.8E-22 6.2E-27 193.0 21.4 171 3-182 7-197 (476)
49 KOG2249 3'-5' exonuclease [Rep 99.5 9.2E-14 2E-18 122.4 13.9 155 3-182 106-265 (280)
50 PF06839 zf-GRF: GRF zinc fing 99.5 3.2E-14 7E-19 94.1 3.5 44 230-276 1-44 (45)
51 cd06143 PAN2_exo DEDDh 3'-5' e 99.3 2E-11 4.3E-16 103.0 12.6 135 22-177 31-174 (174)
52 cd05160 DEDDy_DNA_polB_exo DED 99.2 8.6E-10 1.9E-14 95.0 14.6 138 5-157 2-161 (199)
53 PHA02570 dexA exonuclease; Pro 99.1 3.9E-10 8.5E-15 97.8 10.8 166 4-183 3-199 (220)
54 COG2925 SbcB Exonuclease I [DN 99.0 2.4E-09 5.2E-14 98.9 12.5 168 3-181 10-199 (475)
55 COG1949 Orn Oligoribonuclease 99.0 2.2E-09 4.8E-14 88.5 10.2 162 1-183 5-178 (184)
56 KOG3242 Oligoribonuclease (3'- 99.0 3.7E-09 8E-14 88.0 9.5 165 1-182 25-198 (208)
57 cd06125 DnaQ_like_exo DnaQ-lik 98.9 1.4E-08 3.1E-13 77.8 10.1 94 5-175 1-94 (96)
58 KOG2248 3'-5' exonuclease [Rep 98.8 1.4E-08 3E-13 95.6 9.0 155 3-186 217-378 (380)
59 cd05781 DNA_polB_B3_exo DEDDy 98.6 8.1E-07 1.8E-11 76.3 13.3 120 3-157 4-144 (188)
60 cd05780 DNA_polB_Kod1_like_exo 98.6 2.3E-06 5E-11 73.8 15.2 129 3-158 4-156 (195)
61 cd05782 DNA_polB_like1_exo Unc 98.5 7.6E-06 1.7E-10 71.4 16.2 76 77-158 79-170 (208)
62 PF13482 RNase_H_2: RNase_H su 98.4 9.9E-07 2.1E-11 73.4 8.1 116 5-159 1-117 (164)
63 KOG1956 DNA topoisomerase III 98.4 1.9E-07 4.1E-12 91.2 4.2 49 221-274 710-758 (758)
64 PF04857 CAF1: CAF1 family rib 98.4 1.6E-05 3.4E-10 71.8 14.8 171 3-178 23-262 (262)
65 KOG0304 mRNA deadenylase subun 98.3 1.3E-05 2.7E-10 69.4 12.1 172 3-181 25-237 (239)
66 PF10108 DNA_pol_B_exo2: Predi 98.3 4E-05 8.6E-10 66.8 15.0 130 20-181 7-171 (209)
67 cd06139 DNA_polA_I_Ecoli_like_ 98.1 8.6E-05 1.9E-09 62.8 13.4 142 3-183 6-170 (193)
68 cd05779 DNA_polB_epsilon_exo D 98.1 0.00017 3.7E-09 62.8 15.4 142 3-158 3-169 (204)
69 PRK05755 DNA polymerase I; Pro 97.9 0.00024 5.2E-09 74.4 14.7 134 3-182 316-468 (880)
70 cd05785 DNA_polB_like2_exo Unc 97.9 0.00042 9.1E-09 60.4 13.6 121 3-158 10-169 (207)
71 TIGR03491 RecB family nuclease 97.6 0.0011 2.4E-08 64.5 12.8 121 4-159 286-411 (457)
72 cd05783 DNA_polB_B1_exo DEDDy 97.6 0.0031 6.8E-08 54.9 14.2 137 3-157 6-170 (204)
73 cd05777 DNA_polB_delta_exo DED 97.5 0.013 2.7E-07 51.8 17.4 135 3-156 8-181 (230)
74 KOG4793 Three prime repair exo 97.4 0.00055 1.2E-08 61.2 7.0 170 2-181 13-216 (318)
75 COG3359 Predicted exonuclease 97.2 0.0066 1.4E-07 53.9 11.9 116 2-157 98-218 (278)
76 cd05784 DNA_polB_II_exo DEDDy 96.9 0.039 8.5E-07 47.6 14.3 121 3-154 4-149 (193)
77 smart00486 POLBc DNA polymeras 96.9 0.084 1.8E-06 50.6 17.3 161 3-179 4-220 (471)
78 cd05778 DNA_polB_zeta_exo inac 96.7 0.2 4.4E-06 44.3 17.1 170 4-182 6-222 (231)
79 PTZ00166 DNA polymerase delta 96.5 0.077 1.7E-06 56.8 15.6 161 3-180 265-483 (1054)
80 PRK05762 DNA polymerase II; Re 96.0 0.31 6.7E-06 50.8 16.3 146 3-179 156-348 (786)
81 PF03104 DNA_pol_B_exo1: DNA p 95.9 0.079 1.7E-06 48.4 10.3 100 3-121 158-264 (325)
82 PF01612 DNA_pol_A_exo1: 3'-5' 95.7 0.61 1.3E-05 38.3 14.3 91 79-182 65-174 (176)
83 PF13017 Maelstrom: piRNA path 95.5 0.69 1.5E-05 40.5 14.3 162 21-187 7-201 (213)
84 cd05776 DNA_polB_alpha_exo ina 94.9 0.82 1.8E-05 40.5 13.2 146 5-157 6-186 (234)
85 COG5228 POP2 mRNA deadenylase 94.9 0.035 7.6E-07 48.5 4.2 171 3-182 43-252 (299)
86 COG0349 Rnd Ribonuclease D [Tr 94.6 1.4 3E-05 41.6 14.2 129 3-181 18-164 (361)
87 KOG1798 DNA polymerase epsilon 94.4 0.49 1.1E-05 51.5 11.9 170 3-192 247-462 (2173)
88 TIGR00592 pol2 DNA polymerase 93.9 3.5 7.7E-05 45.0 17.6 143 4-154 506-678 (1172)
89 KOG4793 Three prime repair exo 93.8 0.086 1.9E-06 47.5 4.4 148 22-181 130-289 (318)
90 cd00007 35EXOc 3'-5' exonuclea 93.2 1 2.2E-05 35.8 9.5 66 77-154 40-106 (155)
91 cd06146 mut-7_like_exo DEDDy 3 93.2 2.5 5.5E-05 36.1 12.5 140 3-180 23-192 (193)
92 PHA02528 43 DNA polymerase; Pr 92.9 6 0.00013 41.9 16.9 165 3-178 107-323 (881)
93 KOG1275 PAB-dependent poly(A) 92.5 0.071 1.5E-06 55.0 2.0 110 54-181 972-1090(1118)
94 TIGR01388 rnd ribonuclease D. 91.0 11 0.00024 35.7 15.0 87 82-181 61-164 (367)
95 cd06141 WRN_exo DEDDy 3'-5' ex 90.5 8.1 0.00018 31.8 12.3 130 3-180 19-169 (170)
96 COG0417 PolB DNA polymerase el 90.2 9.5 0.00021 39.9 14.9 130 3-156 155-306 (792)
97 PHA03036 DNA polymerase; Provi 88.8 8 0.00017 41.3 13.1 178 3-190 161-399 (1004)
98 PRK05761 DNA polymerase I; Rev 88.0 2.7 5.8E-05 43.9 9.1 97 74-176 208-334 (787)
99 smart00474 35EXOc 3'-5' exonuc 87.3 12 0.00025 30.2 11.0 90 80-182 64-170 (172)
100 PHA02524 43A DNA polymerase su 87.1 8.7 0.00019 38.0 11.5 139 3-152 107-281 (498)
101 cd06129 RNaseD_like DEDDy 3'-5 79.7 20 0.00043 29.4 9.3 86 82-180 58-160 (161)
102 TIGR00593 pola DNA polymerase 76.6 10 0.00023 40.2 8.2 95 75-181 362-475 (887)
103 PF11074 DUF2779: Domain of un 71.7 8.1 0.00018 31.1 4.7 61 73-139 54-118 (130)
104 cd06142 RNaseD_exo DEDDy 3'-5' 71.0 55 0.0012 26.6 10.6 91 79-182 52-159 (178)
105 PRK10829 ribonuclease D; Provi 69.0 52 0.0011 31.3 10.3 129 3-182 23-169 (373)
106 PF01396 zf-C4_Topoisom: Topoi 65.8 7.9 0.00017 24.4 2.8 19 253-276 20-38 (39)
107 cd06140 DNA_polA_I_Bacillus_li 60.7 85 0.0019 25.6 9.1 67 79-157 44-112 (178)
108 PF05325 DUF730: Protein of un 52.7 17 0.00036 27.8 3.0 48 226-274 17-65 (122)
109 COG0749 PolA DNA polymerase I 50.0 2.1E+02 0.0046 29.1 11.1 90 79-181 66-178 (593)
110 PHA02563 DNA polymerase; Provi 42.6 1.4E+02 0.003 30.6 8.7 39 80-119 50-89 (630)
111 KOG0969 DNA polymerase delta, 39.7 41 0.00089 35.1 4.4 101 4-121 276-380 (1066)
112 PF12377 DuffyBP_N: Duffy bind 38.3 14 0.0003 25.5 0.6 28 2-29 21-48 (66)
113 PRK06319 DNA topoisomerase I/S 35.3 29 0.00063 36.8 2.7 36 230-275 697-732 (860)
114 cd06147 Rrp6p_like_exo DEDDy 3 33.7 2.5E+02 0.0055 23.4 7.9 61 82-156 68-130 (192)
115 TIGR01056 topB DNA topoisomera 33.3 28 0.0006 35.7 2.1 39 231-275 613-653 (660)
116 cd09018 DEDDy_polA_RNaseD_like 33.1 2.3E+02 0.005 21.9 9.5 63 83-157 45-109 (150)
117 PF06373 CART: Cocaine and amp 32.9 14 0.0003 26.5 -0.1 37 226-272 33-69 (73)
118 PF12860 PAS_7: PAS fold 32.8 1.1E+02 0.0023 23.0 4.9 46 25-84 4-49 (115)
119 PF07846 Metallothio_Cad: Meta 32.2 29 0.00063 18.7 1.1 17 232-251 1-17 (21)
120 KOG1294 Apurinic/apyrimidinic 29.9 29 0.00063 32.6 1.5 27 233-259 293-319 (335)
121 PF00843 Arena_nucleocap: Aren 27.9 93 0.002 30.4 4.4 87 5-112 375-461 (533)
122 PF11079 YqhG: Bacterial prote 25.3 35 0.00076 30.8 1.1 69 7-90 126-195 (260)
123 COG2251 Predicted nuclease (Re 24.9 1.4E+02 0.003 29.3 5.0 85 78-170 340-430 (474)
124 PF11288 DUF3089: Protein of u 24.6 1.6E+02 0.0035 25.7 5.1 32 72-104 73-104 (207)
125 COG1098 VacB Predicted RNA bin 24.3 1.4E+02 0.003 24.1 4.1 80 1-90 19-112 (129)
126 COG3218 ABC-type uncharacteriz 22.8 2.4E+02 0.0052 24.6 5.6 47 4-50 126-174 (205)
127 cd06148 Egl_like_exo DEDDy 3'- 22.6 3.3E+02 0.0071 23.0 6.6 91 82-184 56-178 (197)
128 COG2055 Malate/L-lactate dehyd 22.4 4.5E+02 0.0097 24.9 7.8 56 65-123 273-329 (349)
129 PRK07726 DNA topoisomerase III 22.0 55 0.0012 33.6 1.9 16 253-274 629-644 (658)
130 KOG0970 DNA polymerase alpha, 21.4 6.7E+02 0.015 27.8 9.5 110 4-120 531-648 (1429)
131 PF04606 Ogr_Delta: Ogr/Delta- 21.2 48 0.001 21.6 0.9 27 233-259 4-30 (47)
132 PF06888 Put_Phosphatase: Puta 20.0 1.9E+02 0.0042 25.6 4.7 54 64-121 57-113 (234)
No 1
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=5e-43 Score=303.64 Aligned_cols=192 Identities=42% Similarity=0.764 Sum_probs=177.9
Q ss_pred CCeEEEEEEccCCCCCCC-CCCCcEEEEceEEEECC-CCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHH
Q 036883 1 FEYYVVIDFEATCDKERN-LHPQEIIEFPSVVVSGV-SGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGE 78 (277)
Q Consensus 1 f~~~vviDlETTg~~~~~-~~~~eIIEIgAV~vd~~-~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~e 78 (277)
|+++++||||+||.++.. .+.+||||+.||.+|.. ++.|.++|+.||||..+|.++++|+++|||.|++|+.||+|.+
T Consensus 55 fdYLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~~f~~ 134 (280)
T KOG0542|consen 55 FDYLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAPTFPQ 134 (280)
T ss_pred cceEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCCCHHH
Confidence 799999999999998766 46899999999966544 4555569999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhcCCC--CCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCC-CCCCHHHHHHHhC
Q 036883 79 ALYFHDKWLLQMGLN--NTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGD-VRCNLKEAVELAG 155 (277)
Q Consensus 79 vl~~f~~fl~~~~l~--~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~-~~~~L~~l~~~~g 155 (277)
|+.+|..||....+. ++++++|+||+|||+.||..+|.+.+|..|.|+++|||+++.|+..+.. .+.++..|++++|
T Consensus 135 vl~~f~~Wlr~~~~~~k~~~~Afvtdg~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it~mLe~~g 214 (280)
T KOG0542|consen 135 VLSEFDSWLRKDSLGDKNGKFAFVTDGDWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNITGMLEHYG 214 (280)
T ss_pred HHHHHHHHHHHhhcccccCceEEEeCchhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCHHHHHHHhC
Confidence 999999999887664 3789999999999999999999999999999999999999999999987 5789999999999
Q ss_pred CCCCCCCCchHHHHHHHHHHHHHHHHhcCccCcCccc
Q 036883 156 LIWQGRVHCGLDDAINIARLLSVIMRRGFKFSITKSL 192 (277)
Q Consensus 156 i~~~~~~H~Al~DA~~ta~l~~~l~~~g~~~~i~~~l 192 (277)
|+++|++|+++|||+++|.|..+|++.|..+.||+.-
T Consensus 215 L~f~Gr~HsGiDDa~Nia~I~~kM~~dg~~~~In~~~ 251 (280)
T KOG0542|consen 215 LQFEGRAHSGIDDARNIARIAQKMIRDGAEFRINELC 251 (280)
T ss_pred CcccCCcccCchhHHHHHHHHHHHHhCCcEEEechhh
Confidence 9999999999999999999999999999999999663
No 2
>PTZ00315 2'-phosphotransferase; Provisional
Probab=100.00 E-value=2e-38 Score=306.91 Aligned_cols=196 Identities=38% Similarity=0.661 Sum_probs=166.8
Q ss_pred CCeEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHH
Q 036883 1 FEYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEAL 80 (277)
Q Consensus 1 f~~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl 80 (277)
|++||||||||||.+......+||||||||+||.++++++++|++||||..++.|+++|+++||||++||++||+|.+|+
T Consensus 55 ~d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap~F~eVl 134 (582)
T PTZ00315 55 FDAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFPVVY 134 (582)
T ss_pred CCeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCCCHHHHH
Confidence 78999999999997543334689999999999877999999999999998767799999999999999999999999999
Q ss_pred HHHHHHHhhcCCC----CCcEEEEEeccchHHHHHHHHHHHhC-CCCCCCCcchhhhHHHHhHh-cC------------C
Q 036883 81 YFHDKWLLQMGLN----NTNFSVVTWSDWDCQVMLESECRIKK-IQKPAYFNQWINLRVPFSKV-FG------------D 142 (277)
Q Consensus 81 ~~f~~fl~~~~l~----~~~~~vv~~~~fDl~~~L~~~~~~~g-i~~p~~~~~~iDl~~~~~~~-~~------------~ 142 (277)
.+|.+||++..++ ..+++|+|||+||++.||..+|+..+ ...|..+..|+|++..+.+. ++ .
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 9999999886432 34588999999998679999998543 23344567899987666543 33 2
Q ss_pred CCCCHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHHhcCccCcCccccccc
Q 036883 143 VRCNLKEAVELAGLIWQGRVHCGLDDAINIARLLSVIMRRGFKFSITKSLTPQA 196 (277)
Q Consensus 143 ~~~~L~~l~~~~gi~~~~~~H~Al~DA~~ta~l~~~l~~~g~~~~i~~~l~~~~ 196 (277)
.+++|.+|++.+||+++|++|+|++||++||+||.+|+++|..+.+|..+....
T Consensus 215 ~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~~g~~~~~t~~~~~~~ 268 (582)
T PTZ00315 215 GPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRGLVIDPTFDTAPFR 268 (582)
T ss_pred CCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHcCCEEEecCCCChhh
Confidence 458999999999999999999999999999999999999999999988765443
No 3
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=100.00 E-value=3.7e-38 Score=274.48 Aligned_cols=174 Identities=29% Similarity=0.484 Sum_probs=152.6
Q ss_pred eEEEEEEccCCCCCC-CC--CCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHH
Q 036883 3 YYVVIDFEATCDKER-NL--HPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEA 79 (277)
Q Consensus 3 ~~vviDlETTg~~~~-~~--~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~ev 79 (277)
+|||||+||||+++. ++ ..+||||||||+|+ +|++.++|++||||+..+.|+++++++||||++||++||+|++|
T Consensus 5 ~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~--~~~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~~~ev 82 (207)
T PRK07748 5 QFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVV--GCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFEEL 82 (207)
T ss_pred eEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEe--cCcChhhhcceECCCccCccChhhhhhcCcCHHHHccCCCHHHH
Confidence 699999999997532 22 25899999999997 67888999999999865569999999999999999999999999
Q ss_pred HHHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCC-CCCCHHHHHHHhCCCC
Q 036883 80 LYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGD-VRCNLKEAVELAGLIW 158 (277)
Q Consensus 80 l~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~-~~~~L~~l~~~~gi~~ 158 (277)
+.+|.+|+++. +.+++||+.||+ .||+++|+++|++.| +...|+|++.+++.+++. ..++|++++++|||+.
T Consensus 83 l~~f~~~~~~~-----~~~iv~~~~fD~-~fL~~~~~~~~~~~~-~~~~~~dl~~~~~~~~~~~~~~~L~~~~~~~gi~~ 155 (207)
T PRK07748 83 VEKLAEYDKRC-----KPTIVTWGNMDM-KVLKHNCEKAGVPFP-FKGQCRDLSLEYKKFFGERNQTGLWKAIEEYGKEG 155 (207)
T ss_pred HHHHHHHhCcC-----CeEEEEECHHHH-HHHHHHHHHcCCCCc-ccccceeHHHHHHHHhCcCCCCCHHHHHHHcCCCC
Confidence 99999999863 247889999997 799999999998876 457899999888887764 4689999999999998
Q ss_pred CCCCCchHHHHHHHHHHHHHHHHhcCc
Q 036883 159 QGRVHCGLDDAINIARLLSVIMRRGFK 185 (277)
Q Consensus 159 ~~~~H~Al~DA~~ta~l~~~l~~~g~~ 185 (277)
.+++|+|++||++||+||.+|++++..
T Consensus 156 ~~~~H~Al~DA~~ta~l~~~l~~~~~~ 182 (207)
T PRK07748 156 TGKHHCALDDAMTTYNIFKLVEKDKEY 182 (207)
T ss_pred CCCCcChHHHHHHHHHHHHHHHhCcce
Confidence 778899999999999999999988653
No 4
>PRK06722 exonuclease; Provisional
Probab=100.00 E-value=1.3e-35 Score=267.89 Aligned_cols=171 Identities=25% Similarity=0.391 Sum_probs=145.1
Q ss_pred CeEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHH
Q 036883 2 EYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALY 81 (277)
Q Consensus 2 ~~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~ 81 (277)
+.|||||||||+........+||||||||+|+..+++++++|++||+|.. .|+++++++||||++||++||+|++|+.
T Consensus 5 ~~~vViD~ETT~~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~--~I~~~i~~LTGIT~emV~~AP~f~eVl~ 82 (281)
T PRK06722 5 THFIVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGA--RLTRHTTKLTGITKKDLIGVEKFPQIIE 82 (281)
T ss_pred CEEEEEEeeCCCCCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCC--cCCHhHhhhcCCCHHHHcCCCCHHHHHH
Confidence 57999999999643222356899999999998333488999999999985 6999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCC-cchhhhHHHHhHhcCC---CCCCHHHHHHHhCCC
Q 036883 82 FHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYF-NQWINLRVPFSKVFGD---VRCNLKEAVELAGLI 157 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~-~~~iDl~~~~~~~~~~---~~~~L~~l~~~~gi~ 157 (277)
+|.+|+++. .+|+||+.||+ .||..+|.++|++.|.+. ..++|++.++...++. +.++|+++++++||+
T Consensus 83 ef~~fig~~------~lvahna~FD~-~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~~~lgL~ 155 (281)
T PRK06722 83 KFIQFIGED------SIFVTWGKEDY-RFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAVEQLGLI 155 (281)
T ss_pred HHHHHHCCC------cEEEEEeHHHH-HHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHHHHCCCC
Confidence 999999864 36889999996 799999999998876432 4589998766544432 346899999999999
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHH
Q 036883 158 WQGRVHCGLDDAINIARLLSVIMR 181 (277)
Q Consensus 158 ~~~~~H~Al~DA~~ta~l~~~l~~ 181 (277)
..+++|+|++||++||+||.+|++
T Consensus 156 ~~g~~HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 156 WEGKQHRALADAENTANILLKAYS 179 (281)
T ss_pred CCCCCcCcHHHHHHHHHHHHHHhc
Confidence 888899999999999999999984
No 5
>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=100.00 E-value=4.9e-34 Score=240.64 Aligned_cols=172 Identities=46% Similarity=0.765 Sum_probs=147.6
Q ss_pred EEEEEEccCCCCCCC--CCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHH
Q 036883 4 YVVIDFEATCDKERN--LHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALY 81 (277)
Q Consensus 4 ~vviDlETTg~~~~~--~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~ 81 (277)
|||||+||||..... ...++|||||||+++..+++++++|++||||.....+++++.++||||+++++++++|++|+.
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~~~~~vl~ 80 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCCCHHHHHH
Confidence 699999999875321 235899999999999655568899999999986446999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCC-CCCCCcchhhhHHHHhHhcCC-CCCCHHHHHHHhCCCCC
Q 036883 82 FHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQ-KPAYFNQWINLRVPFSKVFGD-VRCNLKEAVELAGLIWQ 159 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~-~p~~~~~~iDl~~~~~~~~~~-~~~~L~~l~~~~gi~~~ 159 (277)
+|.+|+++.. +..+++|+.||+ .+|..++.+.+.. .+++..+++|++.+++..++. +.++|++++++||++..
T Consensus 81 ~~~~~l~~~~----~~~~v~~~~~d~-~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l~~~~gi~~~ 155 (176)
T cd06133 81 EFLEWLGKNG----KYAFVTWGDWDL-KDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFE 155 (176)
T ss_pred HHHHHHHhCC----CeEEEeecHhhH-HHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHHHHHCCCCCC
Confidence 9999999852 257899999996 5777777777653 355678899999999998886 47999999999999998
Q ss_pred CCCCchHHHHHHHHHHHHHHH
Q 036883 160 GRVHCGLDDAINIARLLSVIM 180 (277)
Q Consensus 160 ~~~H~Al~DA~~ta~l~~~l~ 180 (277)
+++|+||+||++||+|+++|+
T Consensus 156 ~~~H~Al~DA~~~a~l~~~~~ 176 (176)
T cd06133 156 GRHHRGLDDARNIARILKRLL 176 (176)
T ss_pred CCCcCcHHHHHHHHHHHHHhC
Confidence 789999999999999999874
No 6
>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=100.00 E-value=1.8e-32 Score=241.52 Aligned_cols=170 Identities=16% Similarity=0.096 Sum_probs=144.7
Q ss_pred eEEEEEEccCCCCCCCCC-CCcEEEEceEEEECCCCE-EEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHH
Q 036883 3 YYVVIDFEATCDKERNLH-PQEIIEFPSVVVSGVSGE-IIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEAL 80 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~-~~eIIEIgAV~vd~~~g~-i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl 80 (277)
++||||+||||++ +. .++|||||||.++ ++. ..++|++||+|.. .+++.++++||||+++|+++|+|.+|+
T Consensus 1 r~vvlD~ETTGl~---p~~~d~IIEIgav~~~--~~~~~~~~f~~~i~P~~--~i~~~a~~vhGIt~e~l~~~p~f~ev~ 73 (225)
T TIGR01406 1 RQIILDTETTGLD---PKGGHRIVEIGAVELV--NRMLTGDNFHVYVNPER--DMPAEAAKVHGITDEFLADKPKFKEIA 73 (225)
T ss_pred CEEEEEeeCCCcC---CCCCCeEEEEEEEEEE--CCcEecceEEEEECcCC--CCCHHHHhccCCCHHHHhCCCCHHHHH
Confidence 5899999999863 44 3899999999987 333 4579999999985 599999999999999999999999999
Q ss_pred HHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCC--CCCcchhhhHHHHhHhcCCCCCCHHHHHHHhCCCC
Q 036883 81 YFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKP--AYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIW 158 (277)
Q Consensus 81 ~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p--~~~~~~iDl~~~~~~~~~~~~~~L~~l~~~~gi~~ 158 (277)
.+|.+|+++. .+|+||+.||+ .||+.++.+.|...+ ..+.+|+|+..+++..++..+++|++++++|||+.
T Consensus 74 ~~f~~fi~~~------~lVaHNa~FD~-~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~L~~~~gi~~ 146 (225)
T TIGR01406 74 DEFLDFIGGS------ELVIHNAAFDV-GFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDN 146 (225)
T ss_pred HHHHHHhCCC------EEEEEecHHHH-HHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCCCCCHHHHHHhcCCCC
Confidence 9999999875 35778999997 799999999984322 22368999999999888777889999999999987
Q ss_pred CCC-CCchHHHHHHHHHHHHHHHHhcCcc
Q 036883 159 QGR-VHCGLDDAINIARLLSVIMRRGFKF 186 (277)
Q Consensus 159 ~~~-~H~Al~DA~~ta~l~~~l~~~g~~~ 186 (277)
.++ .|+||+||++||+||.+|......+
T Consensus 147 ~~r~~H~Al~DA~~~a~v~~~l~~~~~~~ 175 (225)
T TIGR01406 147 SHRTLHGALLDAHLLAEVYLALTGGQESL 175 (225)
T ss_pred CCCCCcCHHHHHHHHHHHHHHHHcCCcch
Confidence 643 6999999999999999998754443
No 7
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=100.00 E-value=2.6e-32 Score=242.28 Aligned_cols=172 Identities=17% Similarity=0.189 Sum_probs=147.6
Q ss_pred eEEEEEEccCCCCCCCCC-CCcEEEEceEEEECCCCEEE-eEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHH
Q 036883 3 YYVVIDFEATCDKERNLH-PQEIIEFPSVVVSGVSGEII-ACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEAL 80 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~-~~eIIEIgAV~vd~~~g~i~-~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl 80 (277)
+|||||+||||++ +. .++|||||||.++ ++.+. ++|++||+|.. .+++++.++||||+++|.++|+|.+|+
T Consensus 5 r~vvlDtETTGld---p~~~drIIEIGaV~v~--~~~~~~~~f~~~i~P~~--~i~~~a~~VHGIT~e~l~~~p~f~ev~ 77 (240)
T PRK05711 5 RQIVLDTETTGLN---QREGHRIIEIGAVELI--NRRLTGRNFHVYIKPDR--LVDPEALAVHGITDEFLADKPTFAEVA 77 (240)
T ss_pred eEEEEEeeCCCcC---CCCCCeEEEEEEEEEE--CCEEeccEEEEEECcCC--cCCHHHhhhcCCCHHHHcCCCCHHHHH
Confidence 6899999999864 44 7899999999997 55554 68999999975 599999999999999999999999999
Q ss_pred HHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCC--CcchhhhHHHHhHhcCCCCCCHHHHHHHhCCCC
Q 036883 81 YFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAY--FNQWINLRVPFSKVFGDVRCNLKEAVELAGLIW 158 (277)
Q Consensus 81 ~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~--~~~~iDl~~~~~~~~~~~~~~L~~l~~~~gi~~ 158 (277)
.+|.+|+++. .+|+||+.||+ .||+.++++.|...|.+ ...++|+..+.+..++..+++|+.++++|||+.
T Consensus 78 ~~f~~fi~~~------~lVaHNa~FD~-~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~aL~~~~gi~~ 150 (240)
T PRK05711 78 DEFLDFIRGA------ELIIHNAPFDI-GFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDN 150 (240)
T ss_pred HHHHHHhCCC------EEEEEccHHhH-HHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCCCCCHHHHHHHCCCCC
Confidence 9999999875 35778999997 79999999998665533 356899999998888777789999999999987
Q ss_pred CCC-CCchHHHHHHHHHHHHHHHHhcCccCc
Q 036883 159 QGR-VHCGLDDAINIARLLSVIMRRGFKFSI 188 (277)
Q Consensus 159 ~~~-~H~Al~DA~~ta~l~~~l~~~g~~~~i 188 (277)
..+ .|+||.||++||+||.+|......+..
T Consensus 151 ~~r~~H~AL~DA~~~A~v~~~l~~~~~~l~~ 181 (240)
T PRK05711 151 SHRTLHGALLDAEILAEVYLAMTGGQTSLGF 181 (240)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHCccccccc
Confidence 543 699999999999999999876555443
No 8
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=100.00 E-value=4.8e-32 Score=226.41 Aligned_cols=167 Identities=32% Similarity=0.372 Sum_probs=147.3
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYF 82 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~ 82 (277)
.||+||+||||.. +..++|||||||+++ ++++.++|+++|+|. ..++++++++|||++++++++++|.+|+.+
T Consensus 1 ~~v~~D~Ettg~~---~~~~~Iieig~v~~~--~~~~~~~f~~~v~p~--~~i~~~~~~~~Git~~~l~~~~~~~~~~~~ 73 (169)
T smart00479 1 TLVVIDCETTGLD---PGKDEIIEIAAVDVD--GGRIIVVFDTYVKPD--RPITDYATEIHGITPEMLDDAPTFEEVLEE 73 (169)
T ss_pred CEEEEEeeCCCCC---CCCCeEEEEEEEEEE--CCEeEEEEEEEECCC--CCCCHHHHHHhCCCHHHHhCCCCHHHHHHH
Confidence 4899999999863 457899999999998 456889999999995 469999999999999999999999999999
Q ss_pred HHHHHhhcCCCCCcEEEEEec-cchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCCCCCHHHHHHHhCCCCCCC
Q 036883 83 HDKWLLQMGLNNTNFSVVTWS-DWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQGR 161 (277)
Q Consensus 83 f~~fl~~~~l~~~~~~vv~~~-~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~~~~L~~l~~~~gi~~~~~ 161 (277)
|.+|+++. .++++|+ .||+ .+|+.++.+.+++.|. ..+++|+..+++..++...++|++++++||++..++
T Consensus 74 ~~~~l~~~------~~v~~n~~~fD~-~~L~~~~~~~~~~~~~-~~~~iD~~~~~~~~~~~~~~~L~~l~~~~~~~~~~~ 145 (169)
T smart00479 74 LLEFLKGK------ILVAGNALNFDL-RFLKLEHPRLGIKDPP-KNPVIDTLKLARALNPGRKYSLKKLAERLGLEVIGR 145 (169)
T ss_pred HHHHhcCC------EEEEeCCHHHhH-HHHHHHHHHhCCCCCc-CCCeeEHHHHHHHHCCCCCCCHHHHHHHCCCCCCCC
Confidence 99999874 4677888 9997 7999999999988763 356999999988887756899999999999998766
Q ss_pred CCchHHHHHHHHHHHHHHHHhcC
Q 036883 162 VHCGLDDAINIARLLSVIMRRGF 184 (277)
Q Consensus 162 ~H~Al~DA~~ta~l~~~l~~~g~ 184 (277)
+|+|++||++|++||.+|++++.
T Consensus 146 ~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 146 AHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred CcCcHHHHHHHHHHHHHHHHHhh
Confidence 79999999999999999988653
No 9
>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=100.00 E-value=1e-31 Score=225.47 Aligned_cols=162 Identities=19% Similarity=0.167 Sum_probs=139.5
Q ss_pred EEEEEEccCCCCCCCC-CCCcEEEEceEEEECCCCEE-EeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHH
Q 036883 4 YVVIDFEATCDKERNL-HPQEIIEFPSVVVSGVSGEI-IACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALY 81 (277)
Q Consensus 4 ~vviDlETTg~~~~~~-~~~eIIEIgAV~vd~~~g~i-~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~ 81 (277)
||+||+||||+. + ..++|||||||+++ ++.+ .++|+.+|+|.. .++++++++|||++++++++++|.+|+.
T Consensus 1 ~v~~D~ETTGl~---~~~~~~iieig~v~v~--~~~~~~~~~~~~v~P~~--~i~~~~~~ihGIt~e~l~~~~~~~~v~~ 73 (167)
T cd06131 1 QIVLDTETTGLD---PREGHRIIEIGCVELI--NRRLTGNTFHVYINPER--DIPEEAFKVHGITDEFLADKPKFAEIAD 73 (167)
T ss_pred CEEEEeeCCCCC---CCCCCeEEEEEEEEEE--CCcEeccEEEEEECCCC--CCCHHHHHHhCCCHHHHhcCCCHHHHHH
Confidence 699999999863 4 56899999999997 4554 468999999985 4999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCC-CCcchhhhHHHHhHhcCCCCCCHHHHHHHhCCCCCC
Q 036883 82 FHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPA-YFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQG 160 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~-~~~~~iDl~~~~~~~~~~~~~~L~~l~~~~gi~~~~ 160 (277)
+|.+|+++. .+|+||++||+ .||++++.++|+..+. ....|+|+..+++..++..+++|++++++||++.++
T Consensus 74 ~l~~~l~~~------~lv~hn~~fD~-~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~~~~L~~l~~~~~i~~~~ 146 (167)
T cd06131 74 EFLDFIRGA------ELVIHNASFDV-GFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSH 146 (167)
T ss_pred HHHHHHCCC------eEEEeChHHhH-HHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCCCCCHHHHHHHCCCCCCC
Confidence 999999874 35778999996 7999999998765432 235799999888887765678999999999999764
Q ss_pred -CCCchHHHHHHHHHHHHHH
Q 036883 161 -RVHCGLDDAINIARLLSVI 179 (277)
Q Consensus 161 -~~H~Al~DA~~ta~l~~~l 179 (277)
.+|+|++||++||+||.+|
T Consensus 147 ~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 147 RTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred CCCCChHHHHHHHHHHHHHh
Confidence 4799999999999999886
No 10
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=1e-31 Score=247.04 Aligned_cols=165 Identities=25% Similarity=0.296 Sum_probs=147.8
Q ss_pred CCeEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHH
Q 036883 1 FEYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEAL 80 (277)
Q Consensus 1 f~~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl 80 (277)
+++|||||+||||+ ++..++|||||||+++ +++++++|+++|+|.. .++++++++||||++||+++++|.+|+
T Consensus 7 ~~~~Vv~DlETTGl---~p~~~eIIEIgaV~v~--~g~i~~~f~~lVkP~~--~I~~~a~~ihGIT~e~l~~~~~~~evl 79 (313)
T PRK06807 7 PLDYVVIDFETTGF---NPYNDKIIQVAAVKYR--NHELVDQFVSYVNPER--PIPDRITSLTGITNYRVSDAPTIEEVL 79 (313)
T ss_pred CCCEEEEEEECCCC---CCCCCeEEEEEEEEEE--CCEEEEEEEEEECcCC--CCCHhhhccCCCCHHHHhCCCCHHHHH
Confidence 47899999999975 4567999999999997 7899999999999986 599999999999999999999999999
Q ss_pred HHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCC-CCCCHHHHHHHhCCCCC
Q 036883 81 YFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGD-VRCNLKEAVELAGLIWQ 159 (277)
Q Consensus 81 ~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~-~~~~L~~l~~~~gi~~~ 159 (277)
.+|.+|+++. .+|+||+.||+ .||.+++.++|++.| ...++|+..+++.+++. ..++|++|+++||++.
T Consensus 80 ~~f~~fl~~~------~lVaHNa~FD~-~fL~~~~~~~gl~~~--~~~~iDtl~la~~~~~~~~~~kL~~L~~~lgi~~- 149 (313)
T PRK06807 80 PLFLAFLHTN------VIVAHNASFDM-RFLKSNVNMLGLPEP--KNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRL- 149 (313)
T ss_pred HHHHHHHcCC------eEEEEcHHHHH-HHHHHHHHHcCCCCC--CCCEeeHHHHHHHHhCCCCCCCHHHHHHHcCCCC-
Confidence 9999999864 46889999997 799999999998765 35699999988887763 5689999999999997
Q ss_pred CCCCchHHHHHHHHHHHHHHHHhc
Q 036883 160 GRVHCGLDDAINIARLLSVIMRRG 183 (277)
Q Consensus 160 ~~~H~Al~DA~~ta~l~~~l~~~g 183 (277)
++|+|++||++|+.||.++....
T Consensus 150 -~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 150 -SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred -CCcChHHHHHHHHHHHHHHHHhh
Confidence 68999999999999999998754
No 11
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.98 E-value=4e-31 Score=243.28 Aligned_cols=162 Identities=18% Similarity=0.283 Sum_probs=144.2
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYF 82 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~ 82 (277)
.|||||+||||. ..++|||||||+++ +|+++++|++||+|.. ..++++++++||||++||+++|+|.+|+.+
T Consensus 2 ~~vviD~ETTg~-----~~d~IieIgav~v~--~g~i~~~f~~lv~P~~-~~~~~~~~~IhGIT~e~v~~ap~f~ev~~~ 73 (309)
T PRK06195 2 NFVAIDFETANE-----KRNSPCSIGIVVVK--DGEIVEKVHYLIKPKE-MRFMPINIGIHGIRPHMVEDELEFDKIWEK 73 (309)
T ss_pred cEEEEEEeCCCC-----CCCceEEEEEEEEE--CCEEEEEEEEEECCCC-CCCChhheeccCcCHHHHhCCCCHHHHHHH
Confidence 599999999963 46899999999997 7899999999999975 357889999999999999999999999999
Q ss_pred HHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCC-CCCCHHHHHHHhCCCCCCC
Q 036883 83 HDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGD-VRCNLKEAVELAGLIWQGR 161 (277)
Q Consensus 83 f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~-~~~~L~~l~~~~gi~~~~~ 161 (277)
|.+|+++. .+|+||+.||+ .||++++++++++.|. ..|+|+..+++.+++. .+++|++++++||++. +
T Consensus 74 ~~~fl~~~------~lVaHNa~FD~-~fL~~~~~r~~~~~~~--~~~idT~~lar~l~~~~~~~~L~~L~~~~gi~~--~ 142 (309)
T PRK06195 74 IKHYFNNN------LVIAHNASFDI-SVLRKTLELYNIPMPS--FEYICTMKLAKNFYSNIDNARLNTVNNFLGYEF--K 142 (309)
T ss_pred HHHHhCCC------EEEEECcHHHH-HHHHHHHHHhCCCCCC--CCEEEHHHHHHHHcCCCCcCCHHHHHHHcCCCC--c
Confidence 99999864 56788999997 7999999999987763 4799999999888764 5789999999999985 5
Q ss_pred CCchHHHHHHHHHHHHHHHHhc
Q 036883 162 VHCGLDDAINIARLLSVIMRRG 183 (277)
Q Consensus 162 ~H~Al~DA~~ta~l~~~l~~~g 183 (277)
+|+|++||++||+||.+|+++.
T Consensus 143 ~H~Al~DA~ata~l~~~l~~~~ 164 (309)
T PRK06195 143 HHDALADAMACSNILLNISKEL 164 (309)
T ss_pred ccCCHHHHHHHHHHHHHHHHHh
Confidence 8999999999999999998763
No 12
>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=99.98 E-value=2.7e-31 Score=219.86 Aligned_cols=154 Identities=23% Similarity=0.280 Sum_probs=137.4
Q ss_pred EEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHHH
Q 036883 4 YVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFH 83 (277)
Q Consensus 4 ~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~f 83 (277)
||+||+||||. ..++|||||||+++ ++++.++|+.+|+|.. .++++++++|||++++|+++++|.+|+.+|
T Consensus 1 ~v~~D~Ettg~-----~~~~ii~ig~v~~~--~~~~~~~~~~~i~p~~--~~~~~~~~i~GIt~e~l~~~~~~~~v~~~l 71 (156)
T cd06130 1 FVAIDFETANA-----DRASACSIGLVKVR--DGQIVDTFYTLIRPPT--RFDPFNIAIHGITPEDVADAPTFPEVWPEI 71 (156)
T ss_pred CEEEEEeCCCC-----CCCceEEEEEEEEE--CCEEEEEEEEEeCcCC--CCChhhccccCcCHHHHhcCCCHHHHHHHH
Confidence 69999999974 36899999999997 7889999999999985 599999999999999999999999999999
Q ss_pred HHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCC-CCCCHHHHHHHhCCCCCCCC
Q 036883 84 DKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGD-VRCNLKEAVELAGLIWQGRV 162 (277)
Q Consensus 84 ~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~-~~~~L~~l~~~~gi~~~~~~ 162 (277)
.+|+++. .++.||+.||+ .||+++++++|++.|+ ..++|+..+++..++. .+++|+++++++|++.. +
T Consensus 72 ~~~l~~~------~lv~hn~~fD~-~~l~~~~~~~g~~~~~--~~~idt~~~~~~~~~~~~~~~L~~l~~~~g~~~~--~ 140 (156)
T cd06130 72 KPFLGGS------LVVAHNASFDR-SVLRAALEAYGLPPPP--YQYLCTVRLARRVWPLLPNHKLNTVAEHLGIELN--H 140 (156)
T ss_pred HHHhCCC------EEEEeChHHhH-HHHHHHHHHcCCCCCC--CCEEEHHHHHHHHhccCCCCCHHHHHHHcCCCcc--C
Confidence 9999873 45666779996 7999999999988663 5799999999888764 57899999999999986 8
Q ss_pred CchHHHHHHHHHHHH
Q 036883 163 HCGLDDAINIARLLS 177 (277)
Q Consensus 163 H~Al~DA~~ta~l~~ 177 (277)
|+|++||++||+||.
T Consensus 141 H~Al~Da~~ta~l~~ 155 (156)
T cd06130 141 HDALEDARACAEILL 155 (156)
T ss_pred cCchHHHHHHHHHHh
Confidence 999999999999985
No 13
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.98 E-value=7e-31 Score=235.45 Aligned_cols=163 Identities=21% Similarity=0.276 Sum_probs=144.8
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYF 82 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~ 82 (277)
.|||||+||||. .+..++|||||||+++ +|+++++|+++|+|. .++++++++|||+++|+++||++.+|+.+
T Consensus 69 ~~vv~DiETTG~---~~~~~~IIEIGAv~v~--~g~i~~~f~~~v~p~---~ip~~~~~itGIt~e~l~~ap~~~evl~~ 140 (257)
T PRK08517 69 VFCFVDIETNGS---KPKKHQIIEIGAVKVK--NGEIIDRFESFVKAK---EVPEYITELTGITYEDLENAPSLKEVLEE 140 (257)
T ss_pred CEEEEEEeCCCC---CCCCCeEEEEEEEEEE--CCEEEEEEEEEECCC---CCChhhhhhcCcCHHHHcCCCCHHHHHHH
Confidence 599999999985 4567799999999997 789999999999996 48999999999999999999999999999
Q ss_pred HHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCCCCCHHHHHHHhCCCCCCCC
Q 036883 83 HDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQGRV 162 (277)
Q Consensus 83 f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~~~~L~~l~~~~gi~~~~~~ 162 (277)
|.+|+++. ..|+||++||. .||.+++++.|.+. +.++++|+..+++..+...+++|+++++++|++.+ .+
T Consensus 141 f~~fl~~~------v~VaHNa~FD~-~fL~~~l~r~g~~~--~~~~~ldtl~la~~~~~~~~~~L~~L~~~lgi~~~-~~ 210 (257)
T PRK08517 141 FRLFLGDS------VFVAHNVNFDY-NFISRSLEEIGLGP--LLNRKLCTIDLAKRTIESPRYGLSFLKELLGIEIE-VH 210 (257)
T ss_pred HHHHHCCC------eEEEECHHHHH-HHHHHHHHHcCCCC--CCCCcEehHHHHHHHccCCCCCHHHHHHHcCcCCC-CC
Confidence 99999864 46678899996 79999999998753 45678998888888777678999999999999976 68
Q ss_pred CchHHHHHHHHHHHHHHHHhc
Q 036883 163 HCGLDDAINIARLLSVIMRRG 183 (277)
Q Consensus 163 H~Al~DA~~ta~l~~~l~~~g 183 (277)
|+|++||++|++||..++++-
T Consensus 211 HrAl~DA~ata~ll~~ll~~~ 231 (257)
T PRK08517 211 HRAYADALAAYEIFKICLLNL 231 (257)
T ss_pred CChHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999764
No 14
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.97 E-value=1.5e-32 Score=225.35 Aligned_cols=184 Identities=30% Similarity=0.448 Sum_probs=161.3
Q ss_pred CeEEEEEEccCCCCCCC-CCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHH
Q 036883 2 EYYVVIDFEATCDKERN-LHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEAL 80 (277)
Q Consensus 2 ~~~vviDlETTg~~~~~-~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl 80 (277)
..++|||+|+|+.+|.. +.+.|||||+|.+|+.-+.+++++|++||||..+|.++.+|..+|||+|..|+.||-|..|+
T Consensus 4 ~~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~apifs~v~ 83 (210)
T COG5018 4 NSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAPIFSMVF 83 (210)
T ss_pred ceEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhccccchHHHHH
Confidence 46789999999998764 56899999999999877888999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCCC-CCHHHHHHHhCCCCC
Q 036883 81 YFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVR-CNLKEAVELAGLIWQ 159 (277)
Q Consensus 81 ~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~~-~~L~~l~~~~gi~~~ 159 (277)
.+|..||.+.... .+-..++||++|+ ..|..+|..+++..-++-..++|++..|...++..+ .+|..|++++|..+.
T Consensus 84 E~f~r~L~~h~Pr-~~~~wa~wG~~Dm-~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~pr~tgln~ale~~G~sf~ 161 (210)
T COG5018 84 EDFIRKLNEHDPR-KNSTWATWGNMDM-KVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGDPRLTGLNKALEEYGDSFT 161 (210)
T ss_pred HHHHHHHHhcCcc-cCCccccccchhH-HHHHHHHHhcCCCCccccCccchHHHHHHHHhcCCccccHHHHHHHhccccC
Confidence 9999999886431 2236789999997 688999999988722244579999999999998764 899999999999999
Q ss_pred CCCCchHHHHHHHHHHHHHHHHhcCccC
Q 036883 160 GRVHCGLDDAINIARLLSVIMRRGFKFS 187 (277)
Q Consensus 160 ~~~H~Al~DA~~ta~l~~~l~~~g~~~~ 187 (277)
|.+|+||+||+++++||..+....+.+.
T Consensus 162 G~~HraldDArn~~rl~klv~~~~~~~e 189 (210)
T COG5018 162 GTHHRALDDARNAYRLFKLVEQDKQYLE 189 (210)
T ss_pred CchhhhHHHHHHHHHHHHHHcchhhhcc
Confidence 9999999999999999999987666554
No 15
>PRK07740 hypothetical protein; Provisional
Probab=99.97 E-value=2e-30 Score=231.13 Aligned_cols=164 Identities=21% Similarity=0.249 Sum_probs=141.1
Q ss_pred eEEEEEEccCCCCCCCCC-CCcEEEEceEEEECCCCEE-EeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHH
Q 036883 3 YYVVIDFEATCDKERNLH-PQEIIEFPSVVVSGVSGEI-IACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEAL 80 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~-~~eIIEIgAV~vd~~~g~i-~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl 80 (277)
.|||||+||||+. +. .+||||||||+++ ++.+ .++|+++|+|.. .+++++.++||||+++|+++|+|.+|+
T Consensus 60 ~~vv~D~ETTGl~---p~~~deIIeIgaV~~~--~~~i~~~~f~~lv~P~~--~i~~~~~~ltGIt~e~l~~ap~~~evl 132 (244)
T PRK07740 60 PFVVFDLETTGFS---PQQGDEILSIGAVKTK--GGEVETDTFYSLVKPKR--PIPEHILELTGITAEDVAFAPPLAEVL 132 (244)
T ss_pred CEEEEEEeCCCCC---CCCCCeEEEEEEEEEE--CCEEEEEEEEEEeCcCC--CCChhheeccCCCHHHHhCCCCHHHHH
Confidence 5999999999853 44 3899999999998 6676 899999999985 599999999999999999999999999
Q ss_pred HHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCC-CCCCHHHHHHHhCCCCC
Q 036883 81 YFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGD-VRCNLKEAVELAGLIWQ 159 (277)
Q Consensus 81 ~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~-~~~~L~~l~~~~gi~~~ 159 (277)
.+|.+|+++. .+|+||+.||. .||+.++.+.. .. ++..+++|+..+++.+++. +.++|+++++++|++..
T Consensus 133 ~~f~~fi~~~------~lVahna~fD~-~fL~~~~~~~~-~~-~~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~~gi~~~ 203 (244)
T PRK07740 133 HRFYAFIGAG------VLVAHHAGHDK-AFLRHALWRTY-RQ-PFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIP 203 (244)
T ss_pred HHHHHHhCCC------EEEEeCHHHHH-HHHHHHHHHhc-CC-CcCCCeechHHHHHHHcCCCCCCCHHHHHHHCCcCCC
Confidence 9999999874 46678889996 79999887653 22 2456899999998877764 47899999999999987
Q ss_pred CCCCchHHHHHHHHHHHHHHHHhc
Q 036883 160 GRVHCGLDDAINIARLLSVIMRRG 183 (277)
Q Consensus 160 ~~~H~Al~DA~~ta~l~~~l~~~g 183 (277)
+ +|+|++||++||+||.+++.+-
T Consensus 204 ~-~H~Al~Da~ata~l~~~ll~~~ 226 (244)
T PRK07740 204 R-RHHALGDALMTAKLWAILLVEA 226 (244)
T ss_pred C-CCCcHHHHHHHHHHHHHHHHHH
Confidence 5 6999999999999999998763
No 16
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=2.7e-30 Score=224.08 Aligned_cols=163 Identities=20% Similarity=0.249 Sum_probs=135.5
Q ss_pred CeEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEE--eEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHH
Q 036883 2 EYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEII--ACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEA 79 (277)
Q Consensus 2 ~~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~--~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~ev 79 (277)
+.|||||+||||+ ++..++|||||||+++ ++.+. ++|+.+|+|.. .++++++++||||+++|++++++.+|
T Consensus 29 ~~~vviD~ETTGl---~~~~d~IieIgaV~~~--~~~~~~~~~f~~~i~p~~--~i~~~~~~ihGIt~~~l~~~~~~~~v 101 (202)
T PRK09145 29 DEWVALDCETTGL---DPRRAEIVSIAAVKIR--GNRILTSERLELLVRPPQ--SLSAESIKIHRLRHQDLEDGLSEEEA 101 (202)
T ss_pred CCEEEEEeECCCC---CCCCCceEEEEEEEEE--CCEEeecCceEEEECCCC--CCCHhHhhhcCcCHHHHhcCCCHHHH
Confidence 4789999999986 4567899999999998 45543 68999999984 69999999999999999999999999
Q ss_pred HHHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHh-CCCCCCCCcchhhhHHHHhHh----cC--CCCCCHHHHHH
Q 036883 80 LYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIK-KIQKPAYFNQWINLRVPFSKV----FG--DVRCNLKEAVE 152 (277)
Q Consensus 80 l~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~-gi~~p~~~~~~iDl~~~~~~~----~~--~~~~~L~~l~~ 152 (277)
+.+|.+|+++. .+++|++.||+ .||.+++++. +.++| ..++|+..++... +. ..+++|+++++
T Consensus 102 l~~~~~~i~~~------~lv~hn~~fD~-~fL~~~~~~~~~~~~~---~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~ 171 (202)
T PRK09145 102 LRQLLAFIGNR------PLVGYYLEFDV-AMLNRYVRPLLGIPLP---NPLIEVSALYYDKKERHLPDAYIDLRFDAILK 171 (202)
T ss_pred HHHHHHHHcCC------eEEEeCHHHHH-HHHHHHHHHhcCCCCC---CCeeeHHHHHHHHhhccCCCcccCCCHHHHHH
Confidence 99999999864 34566779996 7999999874 55544 4688988776432 11 13589999999
Q ss_pred HhCCCCCCCCCchHHHHHHHHHHHHHHHHh
Q 036883 153 LAGLIWQGRVHCGLDDAINIARLLSVIMRR 182 (277)
Q Consensus 153 ~~gi~~~~~~H~Al~DA~~ta~l~~~l~~~ 182 (277)
+||++.. .+|+|++||++||+||.+|++.
T Consensus 172 ~~gi~~~-~~H~Al~DA~ata~l~~~l~~~ 200 (202)
T PRK09145 172 HLDLPVL-GRHDALNDAIMAALIFLRLRKG 200 (202)
T ss_pred HcCCCCC-CCCCcHHHHHHHHHHHHHHHhc
Confidence 9999986 4799999999999999998764
No 17
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=3.8e-30 Score=230.12 Aligned_cols=168 Identities=13% Similarity=0.127 Sum_probs=145.2
Q ss_pred CeEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHH
Q 036883 2 EYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALY 81 (277)
Q Consensus 2 ~~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~ 81 (277)
..||+||+||||+ ++..++|||||+|+++ .+++.++|+.+|+|.. .|++.++++||||+++|+++|+|.+|+.
T Consensus 7 ~~~v~~D~ETTGl---~~~~d~IIEIa~v~v~--~~~~~~~~~~li~P~~--~I~~~a~~ihgIt~e~v~~~p~~~ev~~ 79 (250)
T PRK06310 7 TEFVCLDCETTGL---DVKKDRIIEFAAIRFT--FDEVIDSVEFLINPER--VVSAESQRIHHISDAMLRDKPKIAEVFP 79 (250)
T ss_pred CcEEEEEEeCCCC---CCCCCeEEEEEEEEEE--CCeEEEEEEEEECcCC--CCCHhhhhccCcCHHHHhCCCCHHHHHH
Confidence 3699999999985 4567999999999997 5678899999999986 4999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCCCCCHHHHHHHhCCCCCCC
Q 036883 82 FHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQGR 161 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~~~~L~~l~~~~gi~~~~~ 161 (277)
+|.+|+++. .+++.|++.||+ .||.+++.+.|++.+....+++|+..+++.+.+..+++|+++++++|++.. .
T Consensus 80 ~~~~fl~~~-----~~lvghn~~FD~-~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~~~~~L~~l~~~~g~~~~-~ 152 (250)
T PRK06310 80 QIKGFFKEG-----DYIVGHSVGFDL-QVLSQESERIGETFLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPYD-G 152 (250)
T ss_pred HHHHHhCCC-----CEEEEECHHHHH-HHHHHHHHHcCCCccccCCcEEehHHHHHhcccCCCCCHHHHHHHCCCCCC-C
Confidence 999999763 245667789996 799999999998775433679999998876543456899999999999976 4
Q ss_pred CCchHHHHHHHHHHHHHHHHhc
Q 036883 162 VHCGLDDAINIARLLSVIMRRG 183 (277)
Q Consensus 162 ~H~Al~DA~~ta~l~~~l~~~g 183 (277)
+|+|++||++|++||.+++++.
T Consensus 153 aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 153 NHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred CcChHHHHHHHHHHHHHHHHhc
Confidence 8999999999999999998764
No 18
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=2.6e-30 Score=238.02 Aligned_cols=163 Identities=17% Similarity=0.134 Sum_probs=141.7
Q ss_pred CeEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHH
Q 036883 2 EYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALY 81 (277)
Q Consensus 2 ~~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~ 81 (277)
+.|||||+||||+ ++..++|||||||+++ .+|++.++|+++|+|.. ++..+.+||||++||.++|+|.+++.
T Consensus 15 ~~fvvlD~ETTGl---~p~~d~IIeIgav~v~-~~g~i~~~~~~lv~P~~----~~~~~~IhGIt~e~l~~ap~f~ev~~ 86 (313)
T PRK06063 15 RGWAVVDVETSGF---RPGQARIISLAVLGLD-ADGNVEQSVVTLLNPGV----DPGPTHVHGLTAEMLEGQPQFADIAG 86 (313)
T ss_pred CCEEEEEEECCCC---CCCCCEEEEEEEEEEE-CCceeeeEEEEEECcCC----CCCCeecCCCCHHHHhCCCCHHHHHH
Confidence 4699999999986 4567999999999998 46889999999999974 34568899999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcC-CCCCCHHHHHHHhCCCCCC
Q 036883 82 FHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFG-DVRCNLKEAVELAGLIWQG 160 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~-~~~~~L~~l~~~~gi~~~~ 160 (277)
+|.+|+++. .+|.||+.||+ .||++++++.+++.| ...++|+..+.+.+.. ..+++|++++++|||+..
T Consensus 87 ~l~~~l~~~------~lVaHNa~FD~-~fL~~~~~r~g~~~~--~~~~ldTl~lar~~~~~~~~~kL~~l~~~~gi~~~- 156 (313)
T PRK06063 87 EVAELLRGR------TLVAHNVAFDY-SFLAAEAERAGAELP--VDQVMCTVELARRLGLGLPNLRLETLAAHWGVPQQ- 156 (313)
T ss_pred HHHHHcCCC------EEEEeCHHHHH-HHHHHHHHHcCCCCC--CCCEEehHHHHHHhccCCCCCCHHHHHHHcCCCCC-
Confidence 999999764 56778899996 799999999998776 3468999988887653 467899999999999864
Q ss_pred CCCchHHHHHHHHHHHHHHHHh
Q 036883 161 RVHCGLDDAINIARLLSVIMRR 182 (277)
Q Consensus 161 ~~H~Al~DA~~ta~l~~~l~~~ 182 (277)
++|+|++||++||+||..++++
T Consensus 157 ~~H~Al~DA~ata~l~~~ll~~ 178 (313)
T PRK06063 157 RPHDALDDARVLAGILRPSLER 178 (313)
T ss_pred CCCCcHHHHHHHHHHHHHHHHH
Confidence 6899999999999999999865
No 19
>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=99.97 E-value=8.9e-30 Score=223.32 Aligned_cols=171 Identities=18% Similarity=0.134 Sum_probs=140.7
Q ss_pred CeEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHH
Q 036883 2 EYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALY 81 (277)
Q Consensus 2 ~~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~ 81 (277)
..|||||+||||+. +..+ |||||||+++ .++.+.++|+++|+|.. .+++.+.++||||++||.++|+|.+|+.
T Consensus 7 ~~fvv~D~ETTGl~---~~~~-IIeIgav~v~-~~~~~~~~f~~li~P~~--~i~~~a~~ihGIt~e~l~~~p~~~ev~~ 79 (217)
T TIGR00573 7 DTETTGDNETTGLY---AGHD-IIEIGAVEII-NRRITGNKFHTYIKPDR--PIDPDAIKIHGITDDMLKDKPDFKEIAE 79 (217)
T ss_pred cCEEEEEecCCCCC---CCCC-EEEEEEEEEE-CCCEeeeEEEEEECcCC--CCCHHHHhhcCCCHHHHcCCCCHHHHHH
Confidence 47999999999863 4456 9999999976 34556799999999985 5999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhc---CCCCCCHHHHHHHhCCCC
Q 036883 82 FHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVF---GDVRCNLKEAVELAGLIW 158 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~---~~~~~~L~~l~~~~gi~~ 158 (277)
+|.+|+++. .+|.||+.||+ .||++++.+.+...+ ....++|+..+++..+ +..+++|.++++++|++.
T Consensus 80 ~~~~~~~~~------~lVaHNa~FD~-~fL~~~~~r~~~~~~-~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~gl~~ 151 (217)
T TIGR00573 80 DFADYIRGA------ELVIHNASFDV-GFLNYEFSKLYKVEP-KTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITN 151 (217)
T ss_pred HHHHHhCCC------EEEEeccHHHH-HHHHHHHHHhcCCCC-CccceecHHHHHHHHHHhCCCCCCCHHHHHHHcCCCC
Confidence 999999764 46778899996 799999998754332 2346788776655443 334679999999999986
Q ss_pred CC-CCCchHHHHHHHHHHHHHHHHhcCccC
Q 036883 159 QG-RVHCGLDDAINIARLLSVIMRRGFKFS 187 (277)
Q Consensus 159 ~~-~~H~Al~DA~~ta~l~~~l~~~g~~~~ 187 (277)
.. .+|+|++||++|++||..|+++.....
T Consensus 152 ~~~~~H~Al~DA~~ta~l~~~l~~~~~~~~ 181 (217)
T TIGR00573 152 SHRALHGALADAFILAKLYLVMTGKQTKYG 181 (217)
T ss_pred CCcccCCHHHHHHHHHHHHHHHHhcchhhc
Confidence 52 479999999999999999998765544
No 20
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=5.6e-30 Score=227.48 Aligned_cols=164 Identities=20% Similarity=0.149 Sum_probs=140.0
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEE--EeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEI--IACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEAL 80 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i--~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl 80 (277)
.|||||+||||+ ++..++|||||+|+++ ++++ .++|+++|+|.. .|++++.++||||+++|++||+|.+|+
T Consensus 48 ~~vviD~ETTGl---~p~~d~IieIg~v~v~--~~~i~~~~~~~~li~P~~--~i~~~~~~IhGIt~e~l~~ap~~~evl 120 (239)
T PRK09146 48 PFVALDFETTGL---DAEQDAIVSIGLVPFT--LQRIRCRQARHWVVKPRR--PLEEESVVIHGITHSELQDAPDLERIL 120 (239)
T ss_pred CEEEEEeECCCC---CCCCCcEEEEEEEEEE--CCeEeecceEEEEECCCC--CCChhhhhhcCCCHHHHhCCCCHHHHH
Confidence 699999999985 4678999999999997 5665 489999999985 599999999999999999999999999
Q ss_pred HHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHh-CCCCCCCCcchhhhHHHHhHhcCC--------------CCC
Q 036883 81 YFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIK-KIQKPAYFNQWINLRVPFSKVFGD--------------VRC 145 (277)
Q Consensus 81 ~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~-gi~~p~~~~~~iDl~~~~~~~~~~--------------~~~ 145 (277)
.+|.+|+++. .+|+|++.||+ .||++++.+. +.+. ...++|+..+++.+++. .++
T Consensus 121 ~~l~~~~~~~------~lVaHna~FD~-~fL~~~l~~~~~~~~---~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~ 190 (239)
T PRK09146 121 DELLEALAGK------VVVVHYRRIER-DFLDQALRNRIGEGI---EFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESI 190 (239)
T ss_pred HHHHHHhCCC------EEEEECHHHHH-HHHHHHHHHhcCCCC---CCceechHHHHHHHcccccccccchhccCCCCCC
Confidence 9999999764 46778899995 8999999875 3333 24689999988776432 357
Q ss_pred CHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHHhcC
Q 036883 146 NLKEAVELAGLIWQGRVHCGLDDAINIARLLSVIMRRGF 184 (277)
Q Consensus 146 ~L~~l~~~~gi~~~~~~H~Al~DA~~ta~l~~~l~~~g~ 184 (277)
+|++++++|||+.. .+|+|++||++||+||..++++..
T Consensus 191 ~L~~l~~~~gl~~~-~~H~Al~DA~ata~l~~~~~~~~~ 228 (239)
T PRK09146 191 RLADSRLRYGLPAY-SPHHALTDAIATAELLQAQIAHHF 228 (239)
T ss_pred CHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHHHHc
Confidence 89999999999975 579999999999999999997654
No 21
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=5.7e-30 Score=220.85 Aligned_cols=160 Identities=20% Similarity=0.285 Sum_probs=129.6
Q ss_pred CeEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHH
Q 036883 2 EYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALY 81 (277)
Q Consensus 2 ~~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~ 81 (277)
++|||||+||||.. ..++|||||||+++ +|+++++|++||+|.. .++++++++||||++||++||+|.+|+.
T Consensus 5 ~~~vvlD~EtTGl~----~~~eIIeIgaV~v~--~g~~~~~f~~lv~P~~--~i~~~~~~lhGIt~~~v~~ap~~~evl~ 76 (195)
T PRK07247 5 ETYIAFDLEFNTVN----GVSHIIQVSAVKYD--DHKEVDSFDSYVYTDV--PLQSFINGLTGITADKIADAPKVEEVLA 76 (195)
T ss_pred CeEEEEEeeCCCCC----CCCeEEEEEEEEEE--CCEEEEEEEEEECCCC--CCCccceecCCCCHHHHhCCCCHHHHHH
Confidence 68999999999863 35899999999997 7888899999999985 5999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEecc-chHHHHHHHHHHHhCCCCCCCCcchhhhHHH-HhHh---c-CCCCCCHHHHHHHhC
Q 036883 82 FHDKWLLQMGLNNTNFSVVTWSD-WDCQVMLESECRIKKIQKPAYFNQWINLRVP-FSKV---F-GDVRCNLKEAVELAG 155 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~~~~-fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~-~~~~---~-~~~~~~L~~l~~~~g 155 (277)
+|.+|+++. ..+.|++. ||+ .||++ .|++.+. ..++|+... +.+. + +.++++|.+++++||
T Consensus 77 ~f~~f~~~~------~lVaHNa~~fD~-~fL~~----~g~~~~~--~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~g 143 (195)
T PRK07247 77 AFKEFVGEL------PLIGYNAQKSDL-PILAE----NGLDLSD--QYQVDLYDEAFERRSSDLNGIANLKLQTVADFLG 143 (195)
T ss_pred HHHHHHCCC------eEEEEeCcHhHH-HHHHH----cCCCcCC--CceeehHHHHHHhhccccCCCCCCCHHHHHHhcC
Confidence 999999875 34566775 897 79864 4555331 234554322 2221 1 335799999999999
Q ss_pred CCCCCCCCchHHHHHHHHHHHHHHHHhcC
Q 036883 156 LIWQGRVHCGLDDAINIARLLSVIMRRGF 184 (277)
Q Consensus 156 i~~~~~~H~Al~DA~~ta~l~~~l~~~g~ 184 (277)
|+. .+|+|++||++||.||.+|++.+.
T Consensus 144 i~~--~~HrAl~DA~~ta~v~~~ll~~~~ 170 (195)
T PRK07247 144 IKG--RGHNSLEDARMTARVYESFLESDQ 170 (195)
T ss_pred CCC--CCcCCHHHHHHHHHHHHHHHhhcc
Confidence 985 479999999999999999998755
No 22
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=6.5e-30 Score=226.31 Aligned_cols=173 Identities=20% Similarity=0.142 Sum_probs=141.8
Q ss_pred CeEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhC-CCCHHHHH
Q 036883 2 EYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDN-GITLGEAL 80 (277)
Q Consensus 2 ~~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~-ap~f~evl 80 (277)
..|||||+||||+ ++..++|||||+|+++ .+|+++++|++||+|.. .|+++++++||||++++.+ ++++.+|+
T Consensus 6 ~~~vv~D~ETTGl---~p~~d~Iieig~v~v~-~~g~~~~~~~~lv~P~~--~i~~~a~~IhGIt~e~l~~~g~~~~~vl 79 (232)
T PRK07942 6 GPLAAFDLETTGV---DPETARIVTAALVVVD-ADGEVVESREWLADPGV--EIPEEASAVHGITTEYARAHGRPAAEVL 79 (232)
T ss_pred CcEEEEEeccCCC---CCCCCeeEEEEEEEEe-CCCccccceEEEECCCC--CCCHHHHHHhCCCHHHHHhhCCCHHHHH
Confidence 3689999999986 4667899999999998 35788899999999985 5999999999999999975 89999999
Q ss_pred HHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcC--CCCCCHHHHHHHhCCCC
Q 036883 81 YFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFG--DVRCNLKEAVELAGLIW 158 (277)
Q Consensus 81 ~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~--~~~~~L~~l~~~~gi~~ 158 (277)
.+|.++|.+.-. +...+|+||+.||+ .||+++++++|++.+ ....++|+..+.+.+.. ..+++|++++++||++.
T Consensus 80 ~e~~~~l~~~~~-~~~~lVahNa~FD~-~fL~~~~~r~~~~~~-~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~gi~~ 156 (232)
T PRK07942 80 AEIADALREAWA-RGVPVVVFNAPYDL-TVLDRELRRHGLPSL-VPGPVIDPYVIDKAVDRYRKGKRTLTALCEHYGVRL 156 (232)
T ss_pred HHHHHHHHHHhh-cCCEEEEeCcHhhH-HHHHHHHHHcCCCCc-cCCcEeeHHHHHhhhhcccCCCCCHHHHHHHcCCCC
Confidence 999999964211 12356788999996 799999999987532 12457887766655433 23679999999999998
Q ss_pred CCCCCchHHHHHHHHHHHHHHHHhcC
Q 036883 159 QGRVHCGLDDAINIARLLSVIMRRGF 184 (277)
Q Consensus 159 ~~~~H~Al~DA~~ta~l~~~l~~~g~ 184 (277)
. .+|+|++||++|++||.+|+++-.
T Consensus 157 ~-~aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 157 D-NAHEATADALAAARVAWALARRFP 181 (232)
T ss_pred C-CCCChHHHHHHHHHHHHHHHHHHH
Confidence 6 489999999999999999987644
No 23
>PRK05168 ribonuclease T; Provisional
Probab=99.97 E-value=1.1e-29 Score=221.89 Aligned_cols=175 Identities=19% Similarity=0.183 Sum_probs=141.6
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECC-CCEE--EeEEEEeecCCCCCCCChhhHhHhCCChHH-HhCCCCHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGV-SGEI--IACFQTYVRPTFEPLLTDFCKELTGIQQHQ-VDNGITLGE 78 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~-~g~i--~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~-l~~ap~f~e 78 (277)
.+||||+||||+ ++..++|||||||++... +|.+ .++|+++|+|.....|+++++++||||+++ +++++++.+
T Consensus 18 ~~vv~D~ETTGl---~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~~~~~~~ 94 (211)
T PRK05168 18 LPVVIDVETAGF---NAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAVSEKE 94 (211)
T ss_pred ceEEEEeeCCCC---CCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhcCCChHH
Confidence 689999999986 456799999999999632 3554 589999999953246999999999999986 789999999
Q ss_pred HHHHHHHHHhhcCC---CCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCC-cchhhhHHHHhHhcCCCCCCHHHHHHHh
Q 036883 79 ALYFHDKWLLQMGL---NNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYF-NQWINLRVPFSKVFGDVRCNLKEAVELA 154 (277)
Q Consensus 79 vl~~f~~fl~~~~l---~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~-~~~iDl~~~~~~~~~~~~~~L~~l~~~~ 154 (277)
++.+|.+|+.+.-. .+....|.|+++||+ .||++++++.++...++. .+++|+..+++..++. .+|+++++++
T Consensus 95 ~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~-~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~~--~~L~~l~~~~ 171 (211)
T PRK05168 95 ALHEIFKMVRKGIKASGCNRAILVAHNAHFDL-SFLMAAAERAGLKRNPFHPFSTFDTATLSGLALGQ--TVLAKACQAA 171 (211)
T ss_pred HHHHHHHHHHHHHHhcccCCceEEEeccHHhH-HHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcCC--CCHHHHHHHC
Confidence 99999999974210 012356677889997 799999999987532222 3589999999887763 5899999999
Q ss_pred CCCCCC-CCCchHHHHHHHHHHHHHHHHhc
Q 036883 155 GLIWQG-RVHCGLDDAINIARLLSVIMRRG 183 (277)
Q Consensus 155 gi~~~~-~~H~Al~DA~~ta~l~~~l~~~g 183 (277)
|++.+. .+|+|++||++||+||.+|+++-
T Consensus 172 gl~~~~~~~H~Al~DA~ata~l~~~l~~~~ 201 (211)
T PRK05168 172 GIEFDNKEAHSALYDTEKTAELFCEIVNRW 201 (211)
T ss_pred CCCCCCCCCCChHHHHHHHHHHHHHHHHHH
Confidence 998743 58999999999999999999864
No 24
>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=99.97 E-value=4.5e-29 Score=214.46 Aligned_cols=174 Identities=21% Similarity=0.174 Sum_probs=138.2
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEEC-CCCE--EEeEEEEeecCCCCCCCChhhHhHhCCChHH-HhCCCCHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSG-VSGE--IIACFQTYVRPTFEPLLTDFCKELTGIQQHQ-VDNGITLGE 78 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~-~~g~--i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~-l~~ap~f~e 78 (277)
.+||||+||||+ ++..++|||||||+|+. .+|. +.++|+++|+|.....|++.+.++|||++++ +++++...+
T Consensus 6 ~~vv~D~ETTGl---~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~~ 82 (189)
T cd06134 6 LPVVVDVETGGF---NPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEKE 82 (189)
T ss_pred eeEEEEecCCCC---CCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchHH
Confidence 368999999985 45679999999999963 2454 3689999999942135999999999999987 678888888
Q ss_pred HHHHHHHHHhhcCC---CCCcEEEEEeccchHHHHHHHHHHHhCCC-CCCCCcchhhhHHHHhHhcCCCCCCHHHHHHHh
Q 036883 79 ALYFHDKWLLQMGL---NNTNFSVVTWSDWDCQVMLESECRIKKIQ-KPAYFNQWINLRVPFSKVFGDVRCNLKEAVELA 154 (277)
Q Consensus 79 vl~~f~~fl~~~~l---~~~~~~vv~~~~fDl~~~L~~~~~~~gi~-~p~~~~~~iDl~~~~~~~~~~~~~~L~~l~~~~ 154 (277)
++.+|.+++.+..- .+...+|.||++||+ .||++++++.|+. .|....+++|+..+.+..++ ..+|++++++|
T Consensus 83 ~~~~~~~~l~~~~~~~~~~~~~lVaHna~FD~-~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~--~~~L~~l~~~~ 159 (189)
T cd06134 83 ALKEIFKPIRKALKAQGCTRAILVGHNAHFDL-GFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG--QTVLAKACQAA 159 (189)
T ss_pred HHHHHHHHHHHHHhhcccCCCeEEEecchhhH-HHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC--CCcHHHHHHHC
Confidence 88888888764210 112356778899997 7999999999883 33112358999999888776 35899999999
Q ss_pred CCCCC-CCCCchHHHHHHHHHHHHHHHHh
Q 036883 155 GLIWQ-GRVHCGLDDAINIARLLSVIMRR 182 (277)
Q Consensus 155 gi~~~-~~~H~Al~DA~~ta~l~~~l~~~ 182 (277)
||++. .++|+|++||++||+||.+|+++
T Consensus 160 gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 160 GIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred CCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 99864 36899999999999999999875
No 25
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=99.97 E-value=2.4e-29 Score=214.02 Aligned_cols=162 Identities=15% Similarity=0.136 Sum_probs=130.6
Q ss_pred EEEEEEccCCCCCCCCCCCcEEEEceEEEECCC---C--------EEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhC
Q 036883 4 YVVIDFEATCDKERNLHPQEIIEFPSVVVSGVS---G--------EIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDN 72 (277)
Q Consensus 4 ~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~---g--------~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ 72 (277)
|||||+||||+.. +..++|||||||+|+... + +++++|+++|+|.. .|++.++++||||++++.+
T Consensus 1 ~vv~D~ETTGl~~--~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~--~I~~~a~~IhGIt~e~l~~ 76 (177)
T cd06136 1 FVFLDLETTGLPK--HNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGR--AISPGASEITGLSNDLLEH 76 (177)
T ss_pred CeEEeeecCCCCC--CCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCC--cCChhHHHHhCcCHHHHhc
Confidence 7999999998631 467999999999997321 1 35689999999985 5999999999999999999
Q ss_pred CCCHHH-HHHHHHHHHhhcCCCCCcEEEEEec-cchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCCCCCHHHH
Q 036883 73 GITLGE-ALYFHDKWLLQMGLNNTNFSVVTWS-DWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEA 150 (277)
Q Consensus 73 ap~f~e-vl~~f~~fl~~~~l~~~~~~vv~~~-~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~~~~L~~l 150 (277)
+++|++ +++.+.+|++... +...+|.||+ .||+ .||++++.+.|++.| ....|+|+..+++...+ +|+++
T Consensus 77 ~~~~~~~~~~~l~~f~~~~~--~~~~lVaHNa~~FD~-~fL~~~~~r~~~~~~-~~~~~iDtl~l~r~~~~----~L~~l 148 (177)
T cd06136 77 KAPFDSDTANLIKLFLRRQP--KPICLVAHNGNRFDF-PILRSELERLGTKLP-DDILCVDSLPAFRELDQ----SLGSL 148 (177)
T ss_pred CCCccHHHHHHHHHHHHhcC--CCCEEEEcCCcccCH-HHHHHHHHHcCCCCC-CCCEEEEeHHHHhhhHh----hHHHH
Confidence 998874 6666777776421 1124667787 8997 799999999998766 34568899888887653 89999
Q ss_pred HHH-hCCCCCCCCCchHHHHHHHHHHHHH
Q 036883 151 VEL-AGLIWQGRVHCGLDDAINIARLLSV 178 (277)
Q Consensus 151 ~~~-~gi~~~~~~H~Al~DA~~ta~l~~~ 178 (277)
+++ ||++.. .+|+|++||.+|++||.+
T Consensus 149 ~~~~~~~~~~-~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 149 YKRLFGQEPK-NSHTAEGDVLALLKCALH 176 (177)
T ss_pred HHHHhCCCcc-cccchHHHHHHHHHHHhh
Confidence 985 899875 579999999999999864
No 26
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=4.1e-29 Score=221.20 Aligned_cols=163 Identities=23% Similarity=0.286 Sum_probs=139.1
Q ss_pred CeEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHH
Q 036883 2 EYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALY 81 (277)
Q Consensus 2 ~~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~ 81 (277)
..+||||+||||+ ++..++|||||++ + +...++|+++|+|.. .|++.++++||||++||+++|+|.+|+.
T Consensus 2 ~~~vv~D~ETTGl---~~~~d~IIeig~v--~---~~~~~~f~~lv~P~~--~I~~~a~~IhGIt~e~v~~~p~f~ev~~ 71 (232)
T PRK06309 2 PALIFYDTETTGT---QIDKDRIIEIAAY--N---GVTSESFQTLVNPEI--PIPAEASKIHGITTDEVADAPKFPEAYQ 71 (232)
T ss_pred CcEEEEEeeCCCC---CCCCCEEEEEEEE--c---CccccEEEEEeCCCC--CCChhHHhhcCCCHHHHhCCCCHHHHHH
Confidence 4689999999986 4567999999995 3 234578999999985 4999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEe-ccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCC-CCCCHHHHHHHhCCCCC
Q 036883 82 FHDKWLLQMGLNNTNFSVVTW-SDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGD-VRCNLKEAVELAGLIWQ 159 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~~-~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~-~~~~L~~l~~~~gi~~~ 159 (277)
+|.+|+++. ..++.|| +.||+ .||.+++.+.|++.|. .+++|+..+++.+.+. .+++|+.++++||++..
T Consensus 72 ~~~~fi~~~-----~~lVaHN~~~FD~-~~L~~e~~r~g~~~~~--~~~iDt~~l~~~~~~~~~~~~L~~l~~~~~~~~~ 143 (232)
T PRK06309 72 KFIEFCGTD-----NILVAHNNDAFDF-PLLRKECRRHGLEPPT--LRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFEEN 143 (232)
T ss_pred HHHHHHcCC-----CEEEEeCCHHHHH-HHHHHHHHHcCCCCCC--CcEEeHHHHHHHHcCCCCCCCHHHHHHHcCCCCC
Confidence 999999753 2455666 47996 7999999999987663 5799999998877654 46899999999999865
Q ss_pred CCCCchHHHHHHHHHHHHHHHHhc
Q 036883 160 GRVHCGLDDAINIARLLSVIMRRG 183 (277)
Q Consensus 160 ~~~H~Al~DA~~ta~l~~~l~~~g 183 (277)
.+|+|++||++|++||.+|+++-
T Consensus 144 -~aH~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 144 -QAHRALDDVITLHRVFSALVGDL 166 (232)
T ss_pred -CCCCcHHHHHHHHHHHHHHHHHH
Confidence 58999999999999999998753
No 27
>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=99.96 E-value=1.4e-28 Score=213.18 Aligned_cols=175 Identities=19% Similarity=0.165 Sum_probs=139.7
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECC-CCEE--EeEEEEeecCCCCCCCChhhHhHhCCChH-HHhCCCCHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGV-SGEI--IACFQTYVRPTFEPLLTDFCKELTGIQQH-QVDNGITLGE 78 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~-~g~i--~~~f~~lVrP~~~~~i~~~~~~ltGIt~~-~l~~ap~f~e 78 (277)
.+||||+||||+ ++..++|||||||+|... +|++ .++|+++|+|.....|++++.++||||++ ++++++++.+
T Consensus 9 ~~vv~D~ETTGl---~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~~~~ 85 (200)
T TIGR01298 9 LPVVVDVETGGF---NAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVSEYE 85 (200)
T ss_pred eeEEEEeeCCCC---CCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcchHH
Confidence 489999999986 456789999999999632 4665 36799999985323599999999999976 6899999999
Q ss_pred HHHHHHHHHhhcCC---CCCcEEEEEeccchHHHHHHHHHHHhCCCC-CCCCcchhhhHHHHhHhcCCCCCCHHHHHHHh
Q 036883 79 ALYFHDKWLLQMGL---NNTNFSVVTWSDWDCQVMLESECRIKKIQK-PAYFNQWINLRVPFSKVFGDVRCNLKEAVELA 154 (277)
Q Consensus 79 vl~~f~~fl~~~~l---~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~-p~~~~~~iDl~~~~~~~~~~~~~~L~~l~~~~ 154 (277)
++.++..|+.+... .+...+|+||++||+ .||+.++++.++.. |.....++|+..+.+..++ ..+|+++++++
T Consensus 86 ~~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~-~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~--~~~L~~l~~~~ 162 (200)
T TIGR01298 86 ALHEIFKVVRKAMKASGCQRAILVGHNANFDL-GFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG--QTVLAKACQAA 162 (200)
T ss_pred HHHHHHHHHHHHHHhcccCCCEEEEECchhhH-HHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC--cccHHHHHHHc
Confidence 99999998853211 123456778999997 79999999988642 2112358999999887775 35899999999
Q ss_pred CCCCC-CCCCchHHHHHHHHHHHHHHHHhc
Q 036883 155 GLIWQ-GRVHCGLDDAINIARLLSVIMRRG 183 (277)
Q Consensus 155 gi~~~-~~~H~Al~DA~~ta~l~~~l~~~g 183 (277)
||+.. ..+|+|++||++||+||..|+++.
T Consensus 163 gi~~~~~~~H~Al~Da~ata~lf~~l~~~~ 192 (200)
T TIGR01298 163 GXDFDSTQAHSALYDTEKTAELFCEIVNRW 192 (200)
T ss_pred CCCccccchhhhHHhHHHHHHHHHHHHHHH
Confidence 99864 368999999999999999999764
No 28
>PRK07883 hypothetical protein; Validated
Probab=99.96 E-value=1.1e-28 Score=242.57 Aligned_cols=167 Identities=23% Similarity=0.213 Sum_probs=147.1
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYF 82 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~ 82 (277)
.|||||+||||+ ++..++|||||||+++ +++++++|+++|+|.. .++++++++||||++||+++++|.+|+.+
T Consensus 16 ~~Vv~D~ETTGl---~p~~~~IIEIgaV~v~--~g~iv~~f~~lV~P~~--~i~~~~~~itGIt~e~l~~ap~~~evl~~ 88 (557)
T PRK07883 16 TFVVVDLETTGG---SPAGDAITEIGAVKVR--GGEVLGEFATLVNPGR--PIPPFITVLTGITTAMVAGAPPIEEVLPA 88 (557)
T ss_pred CEEEEEEecCCC---CCCCCeEEEEEEEEEE--CCEEEEEEEEEECCCC--CCChhHHhhcCCCHHHHhCCCCHHHHHHH
Confidence 699999999985 4567999999999997 7889999999999985 59999999999999999999999999999
Q ss_pred HHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcC---CCCCCHHHHHHHhCCCCC
Q 036883 83 HDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFG---DVRCNLKEAVELAGLIWQ 159 (277)
Q Consensus 83 f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~---~~~~~L~~l~~~~gi~~~ 159 (277)
|.+|+++. .+|+||+.||+ .||+.+|+++|++.| ...++|+..+++.+++ ..+++|+++++++|++..
T Consensus 89 f~~fl~~~------~lVaHNa~FD~-~fL~~~~~r~g~~~~--~~~~iDTl~lar~l~~~~~~~~~~L~~L~~~~gi~~~ 159 (557)
T PRK07883 89 FLEFARGA------VLVAHNAPFDI-GFLRAAAARCGYPWP--GPPVLCTVRLARRVLPRDEAPNVRLSTLARLFGATTT 159 (557)
T ss_pred HHHHhcCC------EEEEeCcHHHH-HHHHHHHHHcCCCCC--CCCcEecHHHHHHhcccCCCCCCCHHHHHHHCCcccC
Confidence 99999864 45667899996 799999999998876 3578999998888775 357899999999999976
Q ss_pred CCCCchHHHHHHHHHHHHHHHHhcCcc
Q 036883 160 GRVHCGLDDAINIARLLSVIMRRGFKF 186 (277)
Q Consensus 160 ~~~H~Al~DA~~ta~l~~~l~~~g~~~ 186 (277)
.+|+|++||++|++||.+++.+-...
T Consensus 160 -~~H~Al~DA~ata~l~~~l~~~~~~~ 185 (557)
T PRK07883 160 -PTHRALDDARATVDVLHGLIERLGNL 185 (557)
T ss_pred -CCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 47999999999999999999865443
No 29
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=2.5e-28 Score=249.57 Aligned_cols=163 Identities=20% Similarity=0.244 Sum_probs=144.6
Q ss_pred CeEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHH
Q 036883 2 EYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALY 81 (277)
Q Consensus 2 ~~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~ 81 (277)
+.|||||+||||.. + .++|||||||+++ +|+++++|+++|+|.. .|+++++.+||||++||++||+|++|+.
T Consensus 7 ~~~vvvD~ETTGl~---~-~d~IIeIgaV~v~--~g~i~~~f~~lv~P~~--~i~~~~~~ltGIt~e~l~~ap~~~ev~~ 78 (820)
T PRK07246 7 RKYAVVDLEATGAG---P-NASIIQVGIVIIE--GGEIIDSYTTDVNPHE--PLDEHIKHLTGITDQQLAQAPDFSQVAR 78 (820)
T ss_pred CCEEEEEEecCCcC---C-CCeEEEEEEEEEE--CCEEEEEEEEEeCcCC--CCCHhHhhcCCCCHHHHhcCCCHHHHHH
Confidence 57999999999863 3 4899999999997 7899999999999985 5999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCC-CCCCHHHHHHHhCCCCCC
Q 036883 82 FHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGD-VRCNLKEAVELAGLIWQG 160 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~-~~~~L~~l~~~~gi~~~~ 160 (277)
+|.+|+++. .+|.||++||+ .||++++.+.|++.+ ..++|+..+.+.+++. .+++|+++++++|++..
T Consensus 79 ~~~~~l~~~------~lVaHN~~FD~-~fL~~~~~~~g~~~~---~~~iDT~~la~~~~p~~~~~~L~~L~~~lgl~~~- 147 (820)
T PRK07246 79 HIYDLIEDC------IFVAHNVKFDA-NLLAEALFLEGYELR---TPRVDTVELAQVFFPTLEKYSLSHLSRELNIDLA- 147 (820)
T ss_pred HHHHHhCCC------EEEEECcHHHH-HHHHHHHHHcCCCCC---CCceeHHHHHHHHhCCCCCCCHHHHHHHcCCCCC-
Confidence 999999874 45678889996 799999988887653 4689999888888874 57999999999999976
Q ss_pred CCCchHHHHHHHHHHHHHHHHhc
Q 036883 161 RVHCGLDDAINIARLLSVIMRRG 183 (277)
Q Consensus 161 ~~H~Al~DA~~ta~l~~~l~~~g 183 (277)
++|+|++||++||+||..|+++-
T Consensus 148 ~~H~Al~DA~ata~L~~~l~~~l 170 (820)
T PRK07246 148 DAHTAIADARATAELFLKLLQKI 170 (820)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHH
Confidence 68999999999999999998764
No 30
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=2.2e-27 Score=219.39 Aligned_cols=166 Identities=13% Similarity=0.123 Sum_probs=136.7
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYF 82 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~ 82 (277)
.|||||+||||+ ++..++|||||||+++ .+|++.++|++||+|... +.+ ..+||||++||++||+|.+++.+
T Consensus 47 ~fVvlDiETTGL---dp~~drIIeIgAV~i~-~~g~ive~f~tLVnP~~~--~~p--~~LHGIT~e~La~AP~f~eVl~e 118 (377)
T PRK05601 47 PFVAVSIQTSGI---HPSTSRLITIDAVTLT-ADGEEVEHFHAVLNPGED--PGP--FHLHGLSAEEFAQGKRFSQILKP 118 (377)
T ss_pred CEEEEEEECCCC---CCCCCeEEEEEEEEEE-cCCEEEEEEEEEECcCCC--CCC--ccccCCCHHHHhcCCCHHHHHHH
Confidence 599999999985 5678999999999997 478899999999999862 233 36999999999999999999999
Q ss_pred HHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCC-------------------------CCCCCCcchhhhHHHHh
Q 036883 83 HDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKI-------------------------QKPAYFNQWINLRVPFS 137 (277)
Q Consensus 83 f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi-------------------------~~p~~~~~~iDl~~~~~ 137 (277)
|.+||++. .+|+||+.||+ .||..++++... ...+....++|+..+.+
T Consensus 119 l~~fL~g~------vLVaHNA~FD~-~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LAR 191 (377)
T PRK05601 119 LDRLIDGR------TLILHNAPRTW-GFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATAR 191 (377)
T ss_pred HHHHhCCC------EEEEECcHHHH-HHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHH
Confidence 99999975 46788999996 799999876411 11112357899999998
Q ss_pred HhcC-CCCCCHHHHHHHhCCCCC---------CCCCchH--HHHHHHHHHHHHHHHhc
Q 036883 138 KVFG-DVRCNLKEAVELAGLIWQ---------GRVHCGL--DDAINIARLLSVIMRRG 183 (277)
Q Consensus 138 ~~~~-~~~~~L~~l~~~~gi~~~---------~~~H~Al--~DA~~ta~l~~~l~~~g 183 (277)
++++ ..+++|+.++++|||+.. ...|+|| +||+.++.||..+.+.|
T Consensus 192 rl~p~l~~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~~~~~ 249 (377)
T PRK05601 192 RQGVALDDIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFALRASG 249 (377)
T ss_pred HHcCCCCCCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHhhccC
Confidence 8875 468999999999999871 2468888 69999999999875444
No 31
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.96 E-value=3.3e-29 Score=252.57 Aligned_cols=163 Identities=24% Similarity=0.260 Sum_probs=148.4
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYF 82 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~ 82 (277)
.|||||+||||+ ++..++|||||||++. +|++++.|+.+|+|.. .|+.+++++||||++||.+|+++.+|+.+
T Consensus 422 tyVVfDiETTGL---s~~~d~iIE~aAvKik--ng~iId~f~~Fi~P~~--pl~~~~telTgITdeml~~a~~i~~vL~k 494 (1444)
T COG2176 422 TYVVFDIETTGL---SPVYDEIIEIAAVKIK--NGRIIDKFQFFIKPGR--PLSATITELTGITDEMLENAPEIEEVLEK 494 (1444)
T ss_pred cEEEEEeecCCc---Ccccchhhhheeeeee--CCcchHHHHHhcCCCC--cCchhhhhccccCHHHHcCCccHHHHHHH
Confidence 599999999976 5678999999999995 9999999999999985 59999999999999999999999999999
Q ss_pred HHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcC-CCCCCHHHHHHHhCCCCCCC
Q 036883 83 HDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFG-DVRCNLKEAVELAGLIWQGR 161 (277)
Q Consensus 83 f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~-~~~~~L~~l~~~~gi~~~~~ 161 (277)
|.+|++++ ..|+||++||+ .||+..+.++++. ++-+..||+..+.+.+++ .++++|..+++.||+..+ +
T Consensus 495 f~~~~~d~------IlVAHNasFD~-gFl~~~~~k~~~~--~~~~pvIDTL~lar~L~P~~ksh~Lg~l~kk~~v~le-~ 564 (1444)
T COG2176 495 FREFIGDS------ILVAHNASFDM-GFLNTNYEKYGLE--PLTNPVIDTLELARALNPEFKSHRLGTLCKKLGVELE-R 564 (1444)
T ss_pred HHHHhcCc------EEEeccCccch-hHHHHHHHHhCCc--cccCchhhHHHHHHHhChhhhhcchHHHHHHhCccHH-H
Confidence 99999986 45678899998 7999999998875 356789999999998886 478999999999999985 7
Q ss_pred CCchHHHHHHHHHHHHHHHHh
Q 036883 162 VHCGLDDAINIARLLSVIMRR 182 (277)
Q Consensus 162 ~H~Al~DA~~ta~l~~~l~~~ 182 (277)
+|||.+||.+|++||..+++.
T Consensus 565 hHRA~yDaeat~~vf~~f~~~ 585 (1444)
T COG2176 565 HHRADYDAEATAKVFFVFLKD 585 (1444)
T ss_pred hhhhhhhHHHHHHHHHHHHHH
Confidence 999999999999999998864
No 32
>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=99.95 E-value=1.1e-27 Score=204.68 Aligned_cols=162 Identities=17% Similarity=0.142 Sum_probs=127.1
Q ss_pred EEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhC-CCCHHHHHHHH
Q 036883 5 VVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDN-GITLGEALYFH 83 (277)
Q Consensus 5 vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~-ap~f~evl~~f 83 (277)
++||+||||+ ++..++|||||||+++. ++.++++|+++|+|.....+++.+.++||||++||.+ ++++.+++.+|
T Consensus 1 ~~~D~ETTGl---~~~~d~Iieig~v~v~~-~~~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~ 76 (183)
T cd06138 1 LFYDYETFGL---NPSFDQILQFAAIRTDE-NFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKI 76 (183)
T ss_pred CEEEeecCCC---CCCCCceEEEEEEEECC-CCCCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHH
Confidence 5899999986 45678999999999973 4456699999999974224788999999999999998 99999999999
Q ss_pred HHHHhhcCCCCCcEEEEEe-ccchHHHHHHHHHHHhCCCCCCC----CcchhhhHHHHhHhc--------------CCCC
Q 036883 84 DKWLLQMGLNNTNFSVVTW-SDWDCQVMLESECRIKKIQKPAY----FNQWINLRVPFSKVF--------------GDVR 144 (277)
Q Consensus 84 ~~fl~~~~l~~~~~~vv~~-~~fDl~~~L~~~~~~~gi~~p~~----~~~~iDl~~~~~~~~--------------~~~~ 144 (277)
.+|+++.+ ..+|+|| ..||+ .||++++.+.++..+.+ .+.++|+..+.+..+ +..+
T Consensus 77 ~~~~~~~~----~~lVahn~~~FD~-~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~ 151 (183)
T cd06138 77 HRLFNTPG----TCIVGYNNIRFDD-EFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPS 151 (183)
T ss_pred HHHHccCC----CcEEeeCchhhHH-HHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcc
Confidence 99997421 2355566 58996 79999999988653211 124566665544322 1246
Q ss_pred CCHHHHHHHhCCCCCCCCCchHHHHHHHHHHH
Q 036883 145 CNLKEAVELAGLIWQGRVHCGLDDAINIARLL 176 (277)
Q Consensus 145 ~~L~~l~~~~gi~~~~~~H~Al~DA~~ta~l~ 176 (277)
++|++++++|||+.. .+|+|++||++||+|+
T Consensus 152 ~~L~~l~~~~gi~~~-~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 152 FKLEDLAQANGIEHS-NAHDALSDVEATIALA 182 (183)
T ss_pred hhHHHHHHHCCCCcc-ccccHHHHHHHHHHHh
Confidence 889999999999974 6899999999999986
No 33
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=1.9e-27 Score=246.33 Aligned_cols=166 Identities=22% Similarity=0.254 Sum_probs=146.3
Q ss_pred CeEEEEEEccCCCCCCCCC-CCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHH
Q 036883 2 EYYVVIDFEATCDKERNLH-PQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEAL 80 (277)
Q Consensus 2 ~~~vviDlETTg~~~~~~~-~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl 80 (277)
+.|||||+||||.. +. .++|||||||+++ +|+++++|+++|+|.. .|+++++++||||++||++||+|.+|+
T Consensus 3 ~~~vvvD~ETTG~~---p~~~d~IIeigav~v~--~~~i~~~f~~~v~P~~--~i~~~~~~ltGIt~~~l~~ap~f~ev~ 75 (928)
T PRK08074 3 KRFVVVDLETTGNS---PKKGDKIIQIAAVVVE--DGEILERFSSFVNPER--PIPPFITELTGISEEMVKQAPLFEDVA 75 (928)
T ss_pred CCEEEEEEeCCCCC---CCCCCcEEEEEEEEEE--CCEEEEEEEEEECcCC--CCCHHHhhcCCCCHHHHhcCCCHHHHH
Confidence 57999999999853 33 4899999999997 8899999999999985 599999999999999999999999999
Q ss_pred HHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCC-CCCCHHHHHHHhCCCCC
Q 036883 81 YFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGD-VRCNLKEAVELAGLIWQ 159 (277)
Q Consensus 81 ~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~-~~~~L~~l~~~~gi~~~ 159 (277)
.+|.+|+++. .+|.||+.||+ .||+++|.+.|++.+ ..+++|+..+.+.+++. .+++|+++++++|++..
T Consensus 76 ~~l~~~l~~~------~~VaHN~~FD~-~fL~~~~~~~g~~~~--~~~~iDt~~la~~~~p~~~~~~L~~l~~~l~i~~~ 146 (928)
T PRK08074 76 PEIVELLEGA------YFVAHNVHFDL-NFLNEELERAGYTEI--HCPKLDTVELARILLPTAESYKLRDLSEELGLEHD 146 (928)
T ss_pred HHHHHHhCCC------eEEEEChHHHH-HHHHHHHHHcCCCCC--CCCeeeHHHHHHHhcCCCCCCCHHHHHHhCCCCCC
Confidence 9999999864 45677889996 799999999987643 46799999998887764 57899999999999875
Q ss_pred CCCCchHHHHHHHHHHHHHHHHhcC
Q 036883 160 GRVHCGLDDAINIARLLSVIMRRGF 184 (277)
Q Consensus 160 ~~~H~Al~DA~~ta~l~~~l~~~g~ 184 (277)
++|+|++||++||+||.+|+++-.
T Consensus 147 -~~H~Al~DA~ata~l~~~l~~~~~ 170 (928)
T PRK08074 147 -QPHRADSDAEVTAELFLQLLNKLE 170 (928)
T ss_pred -CCCChHHHHHHHHHHHHHHHHHHH
Confidence 689999999999999999987643
No 34
>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=99.95 E-value=3e-27 Score=247.28 Aligned_cols=167 Identities=25% Similarity=0.274 Sum_probs=147.8
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYF 82 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~ 82 (277)
.|||||+||||+ ++..++|||||||+++ +|+++++|+++|+|.. .|++.++++||||++||++++++.+|+++
T Consensus 191 ~~VVfDiETTGL---~~~~d~IIEIGAVkv~--~g~iid~f~~~V~P~~--~I~~~~~~ltGIT~e~L~~ap~~~evl~~ 263 (1213)
T TIGR01405 191 TYVVFDIETTGL---SPQYDEIIEFGAVKVK--NGRIIDKFQFFIKPHE--PLSAFVTELTGITQDMLENAPEIEEVLEK 263 (1213)
T ss_pred cEEEEEeEecCC---CCCCCeEEEEEEEEEE--CCeEEEEEEEEECCCC--CCCHHHHHHhCCCHHHHhCCCCHHHHHHH
Confidence 699999999986 4678999999999997 7899999999999984 59999999999999999999999999999
Q ss_pred HHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcC-CCCCCHHHHHHHhCCCCCCC
Q 036883 83 HDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFG-DVRCNLKEAVELAGLIWQGR 161 (277)
Q Consensus 83 f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~-~~~~~L~~l~~~~gi~~~~~ 161 (277)
|.+|+++. .+|.||+.||+ .||+.+++++|++ ++..+++|+..+++.+++ .++++|+++++++|++..+
T Consensus 264 f~~fl~~~------iLVaHNa~FD~-~fL~~~~~r~g~~--~~~~~~IDTl~lar~l~p~~k~~kL~~Lak~lgi~~~~- 333 (1213)
T TIGR01405 264 FKEFFKDS------ILVAHNASFDI-GFLNTNFEKVGLE--PLENPVIDTLELARALNPEYKSHRLGNICKKLGVDLDD- 333 (1213)
T ss_pred HHHHhCCC------eEEEEChHHHH-HHHHHHHHHcCCC--ccCCCEeEHHHHHHHHhccCCCCCHHHHHHHcCCCCCC-
Confidence 99999874 45677889996 7999999999875 245689999999988775 4679999999999999875
Q ss_pred CCchHHHHHHHHHHHHHHHHhcCcc
Q 036883 162 VHCGLDDAINIARLLSVIMRRGFKF 186 (277)
Q Consensus 162 ~H~Al~DA~~ta~l~~~l~~~g~~~ 186 (277)
+|+|++||.+|++||..|+++....
T Consensus 334 ~HrAl~DA~aTa~I~~~ll~~l~~~ 358 (1213)
T TIGR01405 334 HHRADYDAEATAKVFKVMVEQLKEK 358 (1213)
T ss_pred CcCHHHHHHHHHHHHHHHHHHHHHc
Confidence 8999999999999999998765443
No 35
>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=99.95 E-value=5.1e-27 Score=241.59 Aligned_cols=163 Identities=25% Similarity=0.269 Sum_probs=144.3
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYF 82 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~ 82 (277)
+|||||+||||. ++..++|||||||+++ +|+++++|+++|+|.. .|+++++++||||++||+++|+|.+|+.+
T Consensus 1 ~~vvvD~ETTG~---~~~~~~IIeig~v~v~--~~~i~~~f~~~v~P~~--~i~~~~~~ltGIt~e~l~~ap~~~ev~~~ 73 (850)
T TIGR01407 1 RYAVVDLETTGT---QLSFDKIIQIGIVVVE--DGEIVDTFHTDVNPNE--PIPPFIQELTGISDNMLQQAPYFSQVAQE 73 (850)
T ss_pred CEEEEEEECCCC---CCCCCeEEEEEEEEEE--CCEEEEEEEEEeCCCC--CCChhhhhhcCcCHHHHhCCCCHHHHHHH
Confidence 489999999986 3567999999999997 7899999999999984 59999999999999999999999999999
Q ss_pred HHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCC-CCCCHHHHHHHhCCCCCCC
Q 036883 83 HDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGD-VRCNLKEAVELAGLIWQGR 161 (277)
Q Consensus 83 f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~-~~~~L~~l~~~~gi~~~~~ 161 (277)
|.+|+++. .+|.||+.||+ .||++++++.|++. +...++|+..+.+.+++. .+++|+++++++|++.. +
T Consensus 74 l~~~l~~~------~~VahN~~fD~-~fL~~~~~~~g~~~--~~~~~iDt~~l~~~~~p~~~~~~L~~l~~~~gi~~~-~ 143 (850)
T TIGR01407 74 IYDLLEDG------IFVAHNVHFDL-NFLAKALKDCGYEP--LPKPRIDTVELAQIFFPTEESYQLSELSEALGLTHE-N 143 (850)
T ss_pred HHHHhCCC------EEEEeCcHHHH-HHHHHHHHHcCCCC--CCCCeEeHHHHHHHhcCCCCCCCHHHHHHHCCCCCC-C
Confidence 99999764 45667889996 89999999998763 346789998888887764 57999999999999975 5
Q ss_pred CCchHHHHHHHHHHHHHHHHh
Q 036883 162 VHCGLDDAINIARLLSVIMRR 182 (277)
Q Consensus 162 ~H~Al~DA~~ta~l~~~l~~~ 182 (277)
+|+|++||++||+||.+|+++
T Consensus 144 ~H~Al~DA~ata~l~~~l~~~ 164 (850)
T TIGR01407 144 PHRADSDAQATAELLLLLFEK 164 (850)
T ss_pred CCChHHHHHHHHHHHHHHHHH
Confidence 899999999999999999775
No 36
>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=99.95 E-value=6.1e-27 Score=191.78 Aligned_cols=156 Identities=26% Similarity=0.274 Sum_probs=135.5
Q ss_pred EEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHHHH
Q 036883 5 VVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFHD 84 (277)
Q Consensus 5 vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~f~ 84 (277)
|+||+||||+ ++..++|||||+++++. ++++++.|+.+|+|+. .++++++++|||+++++.+++++.+++.+|.
T Consensus 1 v~~D~Ettg~---~~~~~~iiei~~v~~~~-~~~~~~~~~~~i~p~~--~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~ 74 (159)
T cd06127 1 VVFDTETTGL---DPKKDRIIEIGAVKVDG-GIEIVERFETLVNPGR--PIPPEATAIHGITDEMLADAPPFEEVLPEFL 74 (159)
T ss_pred CeEEeeCCCc---CCCCCeEEEEEEEEEEC-CcChhhhhheeeCcCC--cCCHhheeccCCCHHHHhcCCCHHHHHHHHH
Confidence 6899999985 35689999999999984 4678899999999985 5899999999999999999999999999999
Q ss_pred HHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCC-CCCCHHHH-HHHhCCCCCCCC
Q 036883 85 KWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGD-VRCNLKEA-VELAGLIWQGRV 162 (277)
Q Consensus 85 ~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~-~~~~L~~l-~~~~gi~~~~~~ 162 (277)
+|+++. .++.||+.||+ .+|++++.+++. +.+...|+|+..+++..++. ..++|..+ +++++++. ..+
T Consensus 75 ~~l~~~------~~v~~n~~fD~-~~l~~~~~~~~~--~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~-~~~ 144 (159)
T cd06127 75 EFLGGR------VLVAHNASFDL-RFLNRELRRLGG--PPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPL-EGA 144 (159)
T ss_pred HHHCCC------EEEEeCcHhhH-HHHHHHHHHhCC--CCCCCCeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCC-CCC
Confidence 999873 56667789996 799999999983 33457899999999988875 45789888 88999976 478
Q ss_pred CchHHHHHHHHHHH
Q 036883 163 HCGLDDAINIARLL 176 (277)
Q Consensus 163 H~Al~DA~~ta~l~ 176 (277)
|+|++||++|++||
T Consensus 145 H~Al~Da~~t~~l~ 158 (159)
T cd06127 145 HRALADALATAELL 158 (159)
T ss_pred CCcHHHHHHHHHHh
Confidence 99999999999997
No 37
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.95 E-value=1.5e-26 Score=203.00 Aligned_cols=148 Identities=21% Similarity=0.192 Sum_probs=126.5
Q ss_pred EEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHHH
Q 036883 4 YVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFH 83 (277)
Q Consensus 4 ~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~f 83 (277)
++|||+||||++ .+|||||+|.|. +|++.++|+++|+|.. .|++.++++||||++||.++|+|.+++.+|
T Consensus 2 ~~vlD~ETTGl~------~~IieIg~v~v~--~~~i~~~~~~lv~P~~--~i~~~~~~ihgIt~e~v~~ap~~~ev~~~~ 71 (219)
T PRK07983 2 LRVIDTETCGLQ------GGIVEIASVDVI--DGKIVNPMSHLVRPDR--PISPQAMAIHRITEAMVADKPWIEDVIPHY 71 (219)
T ss_pred eEEEEEECCCCC------CCCEEEEEEEEE--CCEEEEEEEEEECcCC--CCCHHHhhcCCCCHHHHcCCCCHHHHHHHH
Confidence 789999999863 349999999996 7899999999999985 599999999999999999999999999885
Q ss_pred HHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCCCCCHHHHHHHhCCCCC----
Q 036883 84 DKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQ---- 159 (277)
Q Consensus 84 ~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~~~~L~~l~~~~gi~~~---- 159 (277)
+++ ..+|.||+.||. .||.. ...+|+|+..+++++++..+++|+.+++++|++..
T Consensus 72 ---~~~------~~lVaHNa~FD~-~~L~~-----------~~~~~idTl~lar~l~p~~~~~l~~L~~~~~l~~~~~~~ 130 (219)
T PRK07983 72 ---YGS------EWYVAHNASFDR-RVLPE-----------MPGEWICTMKLARRLWPGIKYSNMALYKSRKLNVQTPPG 130 (219)
T ss_pred ---cCC------CEEEEeCcHhhH-HHHhC-----------cCCCcEeHHHHHHHHccCCCCCHHHHHHHcCCCCCCCCC
Confidence 333 356778899995 78841 12469999999999888656899999999998642
Q ss_pred CCCCchHHHHHHHHHHHHHHHHh
Q 036883 160 GRVHCGLDDAINIARLLSVIMRR 182 (277)
Q Consensus 160 ~~~H~Al~DA~~ta~l~~~l~~~ 182 (277)
..+|+|++||++||.||.+|+++
T Consensus 131 ~~aHrAl~Da~ata~ll~~l~~~ 153 (219)
T PRK07983 131 LHHHRALYDCYITAALLIDIMNT 153 (219)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHH
Confidence 36899999999999999999975
No 38
>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=99.94 E-value=1.2e-26 Score=194.49 Aligned_cols=147 Identities=19% Similarity=0.219 Sum_probs=121.0
Q ss_pred EEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCC-------HH
Q 036883 5 VVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGIT-------LG 77 (277)
Q Consensus 5 vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~-------f~ 77 (277)
|+||+||||+ ++..++|||||||.+. +|+++ |++||+|.. .++++++++||||++||+++|+ |+
T Consensus 1 v~lD~EttGl---~~~~d~ii~Ig~V~v~--~g~i~--~~~~v~P~~--~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~ 71 (161)
T cd06137 1 VALDCEMVGL---ADGDSEVVRISAVDVL--TGEVL--IDSLVRPSV--RVTDWRTRFSGVTPADLEEAAKAGKTIFGWE 71 (161)
T ss_pred CEEEeeeeeE---cCCCCEEEEEEEEEcC--CCeEE--EeccccCCC--CCCccceeccCCCHHHHhhhhhcCCccccHH
Confidence 6899999986 4567999999999994 77875 999999984 5999999999999999999876 45
Q ss_pred HHHHHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCC----CCCCHHHHHHH
Q 036883 78 EALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGD----VRCNLKEAVEL 153 (277)
Q Consensus 78 evl~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~----~~~~L~~l~~~ 153 (277)
+|+.+|.+|+++. ..+|.|+..||+ .||+.. ..+++|+..+++..++. .+++|++++++
T Consensus 72 ~~~~~~~~~i~~~-----~vlVgHn~~fD~-~fL~~~-----------~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~ 134 (161)
T cd06137 72 AARAALWKFIDPD-----TILVGHSLQNDL-DALRMI-----------HTRVVDTAILTREAVKGPLAKRQWSLRTLCRD 134 (161)
T ss_pred HHHHHHHHhcCCC-----cEEEeccHHHHH-HHHhCc-----------CCCeeEehhhhhhccCCCcCCCCccHHHHHHH
Confidence 8999999999862 245567789997 798631 13589999999887764 47999999986
Q ss_pred -hCCCCC--CCCCchHHHHHHHHHHHH
Q 036883 154 -AGLIWQ--GRVHCGLDDAINIARLLS 177 (277)
Q Consensus 154 -~gi~~~--~~~H~Al~DA~~ta~l~~ 177 (277)
+|++.. ..+|+|++||++||+||+
T Consensus 135 ~~~~~~~~~~~~H~A~~DA~at~~l~~ 161 (161)
T cd06137 135 FLGLKIQGGGEGHDSLEDALAAREVVL 161 (161)
T ss_pred HCCchhcCCCCCCCcHHHHHHHHHHhC
Confidence 788763 257999999999999974
No 39
>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=99.93 E-value=2.2e-25 Score=189.03 Aligned_cols=161 Identities=15% Similarity=0.128 Sum_probs=122.5
Q ss_pred EEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCC--CCCChhhHhH---hCCChHHHhCCCCHHH
Q 036883 4 YVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFE--PLLTDFCKEL---TGIQQHQVDNGITLGE 78 (277)
Q Consensus 4 ~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~--~~i~~~~~~l---tGIt~~~l~~ap~f~e 78 (277)
+|+||+||||+ ++..++|||||||+++...+++.++|+.+|+|... +.+++++..+ |||++++++++|++.+
T Consensus 1 lv~iD~ETTGl---~p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~~ 77 (173)
T cd06135 1 LVWIDLEMTGL---DPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQ 77 (173)
T ss_pred CEEEEEecCCC---CCCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHHH
Confidence 58999999985 46789999999999986566888999999999851 1244666677 5999999999999999
Q ss_pred HHHHHHHHHhhcCCCCCcEEEEEec-cchHHHHHHHHHHHhCCCCCCCCcchhhhHH---HHhHhcCCCCCCHHHHHHHh
Q 036883 79 ALYFHDKWLLQMGLNNTNFSVVTWS-DWDCQVMLESECRIKKIQKPAYFNQWINLRV---PFSKVFGDVRCNLKEAVELA 154 (277)
Q Consensus 79 vl~~f~~fl~~~~l~~~~~~vv~~~-~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~---~~~~~~~~~~~~L~~l~~~~ 154 (277)
|+.+|.+|+++..-.+ ...+++|+ +||+ .||++++.+.+.. +.++.+|+.. +.+.+++. +.. +
T Consensus 78 vl~~~~~f~~~~~~~~-~~~lvgh~~~FD~-~fL~~~~~~~~~~---~~~~~~D~~~l~~l~~~l~p~----~~~----~ 144 (173)
T cd06135 78 AEAELLEFIKKYVPKG-KSPLAGNSVHQDR-RFLDKYMPELEEY---LHYRILDVSSIKELARRWYPE----IYR----K 144 (173)
T ss_pred HHHHHHHHHHHhcCCC-CCceeecchhhCH-HHHHHHHHHHhcc---CCcchhhHHHHHHHHHHhCcH----hhh----c
Confidence 9999999998631111 23456655 9996 8999999988732 4456788743 45554432 111 5
Q ss_pred CCCCCCCCCchHHHHHHHHHHHHHHHH
Q 036883 155 GLIWQGRVHCGLDDAINIARLLSVIMR 181 (277)
Q Consensus 155 gi~~~~~~H~Al~DA~~ta~l~~~l~~ 181 (277)
+++. +..||||+||++++.+|..+++
T Consensus 145 ~~~~-~~~HrAl~Da~~~~~~~~~~~~ 170 (173)
T cd06135 145 APKK-KGTHRALDDIRESIAELKYYRE 170 (173)
T ss_pred CCCC-CCCcchHHHHHHHHHHHHHHHH
Confidence 6654 4679999999999999998875
No 40
>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=99.93 E-value=5.5e-26 Score=188.71 Aligned_cols=149 Identities=19% Similarity=0.198 Sum_probs=113.3
Q ss_pred EEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHHHH
Q 036883 5 VVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFHD 84 (277)
Q Consensus 5 vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~f~ 84 (277)
|+||+||||++ +. ++++||++|.+...+++++ |++||+|.. .++++++++||||++||++||+|.+++.+|.
T Consensus 1 v~lD~EttGl~---~~-~~~~~i~~v~~v~~~~~~~--~~~~v~P~~--~i~~~~~~ihGIt~~~v~~a~~~~~~~~~l~ 72 (152)
T cd06144 1 VALDCEMVGVG---PD-GSESALARVSIVNEDGNVV--YDTYVKPQE--PVTDYRTAVSGIRPEHLKDAPDFEEVQKKVA 72 (152)
T ss_pred CEEEEEeeccc---CC-CCEEEEEEEEEEeCCCCEE--EEEEECCCC--CCCcccccCCCCCHHHHcCCCCHHHHHHHHH
Confidence 68999999863 32 3677776654432355554 999999985 5999999999999999999999999999999
Q ss_pred HHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHh--cCCCCCCHHHHHHH-hCCCCCCC
Q 036883 85 KWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKV--FGDVRCNLKEAVEL-AGLIWQGR 161 (277)
Q Consensus 85 ~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~--~~~~~~~L~~l~~~-~gi~~~~~ 161 (277)
+|+++. .+|.||+.||+ .||+ +..|. ..++|+..+.... +...+++|++++++ +|++....
T Consensus 73 ~~l~~~------vlVgHn~~fD~-~~L~-------~~~~~--~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~ 136 (152)
T cd06144 73 ELLKGR------ILVGHALKNDL-KVLK-------LDHPK--KLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEG 136 (152)
T ss_pred HHhCCC------EEEEcCcHHHH-HHhc-------CcCCC--ccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCC
Confidence 999864 45677889997 7986 23332 3456655432221 11357899999997 69987556
Q ss_pred CCchHHHHHHHHHHHH
Q 036883 162 VHCGLDDAINIARLLS 177 (277)
Q Consensus 162 ~H~Al~DA~~ta~l~~ 177 (277)
+|+|++||++|++||+
T Consensus 137 ~H~Al~DA~at~~l~~ 152 (152)
T cd06144 137 EHSSVEDARAAMRLYR 152 (152)
T ss_pred CcCcHHHHHHHHHHhC
Confidence 8999999999999984
No 41
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.93 E-value=1e-24 Score=193.66 Aligned_cols=165 Identities=23% Similarity=0.272 Sum_probs=144.9
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEe-EEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIA-CFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALY 81 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~-~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~ 81 (277)
.+|+||+||||. ++..++|||||||.+. ++++++ .|+.+|+|+. .|++++.++|||+.++|.++|.|.+++.
T Consensus 14 ~~vv~D~ETtg~---~~~~~~iieIgav~~~--~~~i~~~~~~~~v~P~~--~i~~~~~~i~git~e~l~~~p~~~~v~~ 86 (243)
T COG0847 14 RFVVIDLETTGL---NPKKDRIIEIGAVTLE--DGRIVERSFHTLVNPER--PIPPEIFKIHGITDEMLADAPKFAEVLP 86 (243)
T ss_pred cEEEEecccCCC---CCCCCceEEEEeEEEE--CCeeecceeEEEECCCC--CCChhhhhhcCCCHHHHhcCCCHHHHHH
Confidence 689999999975 4578999999999997 777874 4999999964 4999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCC-CCCCHHHHHHHhCCCCC-
Q 036883 82 FHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGD-VRCNLKEAVELAGLIWQ- 159 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~-~~~~L~~l~~~~gi~~~- 159 (277)
+|.+|+++. ...|.|++.||+ .||..++.+.+.+.+ ...++|+..+.+..++. ..++|+.+++++|++..
T Consensus 87 ~~~~~i~~~-----~~~Vahna~fD~-~fl~~~~~~~~~~~~--~~~~~~t~~~~r~~~~~~~~~~L~~l~~~~gi~~~~ 158 (243)
T COG0847 87 EFLDFIGGL-----RLLVAHNAAFDV-GFLRVESERLGIEIP--GDPVLDTLALARRHFPGFDRSSLDALAERLGIDRNP 158 (243)
T ss_pred HHHHHHCCC-----CeEEEEchhhcH-HHHHHHHHHcCCCcc--cCceehHHHHHHHHcCCCccchHHHHHHHcCCCcCC
Confidence 999999983 246778899996 899999999988765 46788988888888877 78999999999999943
Q ss_pred CCCCchHHHHHHHHHHHHHHHHh
Q 036883 160 GRVHCGLDDAINIARLLSVIMRR 182 (277)
Q Consensus 160 ~~~H~Al~DA~~ta~l~~~l~~~ 182 (277)
...|+|+.||.++|.+|..+...
T Consensus 159 ~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 159 FHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred cCCcchHHHHHHHHHHHHHHHhc
Confidence 24699999999999999999986
No 42
>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=99.93 E-value=2.3e-26 Score=188.78 Aligned_cols=159 Identities=26% Similarity=0.363 Sum_probs=123.7
Q ss_pred EEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHHHH
Q 036883 5 VVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFHD 84 (277)
Q Consensus 5 vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~f~ 84 (277)
||||+||||++ +..++|||||+|+++.....+...|+++|+|...+.++++++++||||+++|++++++.+++.+|.
T Consensus 1 v~~D~Ettg~~---~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~~~ 77 (164)
T PF00929_consen 1 VVFDTETTGLD---PRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDEFE 77 (164)
T ss_dssp EEEEEEESSST---TTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHHHH
T ss_pred cEEEeEcCCCC---CCCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHhhh
Confidence 79999999864 467999999999999554447889999999997546999999999999999999999999999999
Q ss_pred HHHhhcCCCCCcEEEEE-eccchHHHHHHHHHHHh-CCCCC---CCCcchhhhHHHHhHhcCCCCCCHHHHHHHhCCCCC
Q 036883 85 KWLLQMGLNNTNFSVVT-WSDWDCQVMLESECRIK-KIQKP---AYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQ 159 (277)
Q Consensus 85 ~fl~~~~l~~~~~~vv~-~~~fDl~~~L~~~~~~~-gi~~p---~~~~~~iDl~~~~~~~~~~~~~~L~~l~~~~gi~~~ 159 (277)
+|+.+.. .+|. +..||+ .+|...+.+. +...| .+++.+...+..+.... .++|++++++|+++..
T Consensus 78 ~~~~~~~------~~v~~n~~fd~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~l~~l~~~~~~~~~ 147 (164)
T PF00929_consen 78 EFLKKND------ILVGHNASFDI-GFLRREDKRFLGKPIPKPNPFIDTLELARALFPNRK---KYSLDDLAEYFGIPFD 147 (164)
T ss_dssp HHHHHHT------EEEETTCCHEE-ESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHHH---HHSHHHHHHHTTSSST
T ss_pred hhhhccc------ccccccccchh-hHHHHhhhhcccccccccchhhhhhHHHHHHhhccc---cCCHHHHHHHcCCCCC
Confidence 9998542 4555 468886 6777777765 33222 12222222223333222 2689999999999998
Q ss_pred CCCCchHHHHHHHHHHH
Q 036883 160 GRVHCGLDDAINIARLL 176 (277)
Q Consensus 160 ~~~H~Al~DA~~ta~l~ 176 (277)
+.+|+|++||++|++||
T Consensus 148 ~~~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 148 GTAHDALDDARATAELF 164 (164)
T ss_dssp STTTSHHHHHHHHHHHH
T ss_pred CCCcChHHHHHHHhCcC
Confidence 76899999999999987
No 43
>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=99.93 E-value=3.1e-25 Score=183.91 Aligned_cols=145 Identities=19% Similarity=0.182 Sum_probs=116.5
Q ss_pred EEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCC-CHHHHHHHH
Q 036883 5 VVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGI-TLGEALYFH 83 (277)
Q Consensus 5 vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap-~f~evl~~f 83 (277)
|++|+||||... .+||+||++|.+ +|++ .|++||+|.. .++++++++||||++||+++| +|++|+++|
T Consensus 1 ~~iD~E~~g~~~----g~ei~~i~~v~~---~~~~--~f~~lv~P~~--~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~ 69 (150)
T cd06145 1 FALDCEMCYTTD----GLELTRVTVVDE---NGKV--VLDELVKPDG--EIVDYNTRFSGITEEMLENVTTTLEDVQKKL 69 (150)
T ss_pred CEEeeeeeeecC----CCEEEEEEEEeC---CCCE--EEEEeECCCC--ccchhccCcCCCCHHHhccCCCCHHHHHHHH
Confidence 589999998642 299999999976 4454 4999999985 599999999999999999995 999999999
Q ss_pred HHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCC-CCCCHHHHHHHh-CCCCC--
Q 036883 84 DKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGD-VRCNLKEAVELA-GLIWQ-- 159 (277)
Q Consensus 84 ~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~-~~~~L~~l~~~~-gi~~~-- 159 (277)
.+|+++. ..+|.|+.+||+ .||+.. ..+++|+..+++..++. .+++|+.++++| ++...
T Consensus 70 ~~fl~~~-----~vlVgHn~~fD~-~fL~~~-----------~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~ 132 (150)
T cd06145 70 LSLISPD-----TILVGHSLENDL-KALKLI-----------HPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQG 132 (150)
T ss_pred HHHhCCC-----CEEEEcChHHHH-HHhhcc-----------CCCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeCC
Confidence 9999732 245567789998 698631 13589999888876543 468999999876 54332
Q ss_pred CCCCchHHHHHHHHHHHH
Q 036883 160 GRVHCGLDDAINIARLLS 177 (277)
Q Consensus 160 ~~~H~Al~DA~~ta~l~~ 177 (277)
..+|+|++||++|++||.
T Consensus 133 ~~~H~Al~DA~~t~~l~~ 150 (150)
T cd06145 133 EGGHDSVEDARAALELVK 150 (150)
T ss_pred CCCCCcHHHHHHHHHHhC
Confidence 367999999999999973
No 44
>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=99.92 E-value=5.2e-25 Score=183.94 Aligned_cols=149 Identities=20% Similarity=0.211 Sum_probs=116.7
Q ss_pred EEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHHHH
Q 036883 5 VVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFHD 84 (277)
Q Consensus 5 vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~f~ 84 (277)
|+||+||||+.. ....++|++|++|.+ +|+++ |++||+|.. .++++++++|||+++||++||+|++|+.+|.
T Consensus 1 v~~D~EttGl~~-~~~~~~i~~i~~v~~---~g~~~--~~~lv~P~~--~i~~~~~~i~GIt~~~l~~a~~~~~v~~~l~ 72 (157)
T cd06149 1 VAIDCEMVGTGP-GGRESELARCSIVNY---HGDVL--YDKYIRPEG--PVTDYRTRWSGIRRQHLVNATPFAVAQKEIL 72 (157)
T ss_pred CEEEeEeccccC-CCCeEEEEEEEEEeC---CCCEE--EEEeECCCC--ccCccceECCCCCHHHHhcCCCHHHHHHHHH
Confidence 689999998742 113588999988875 56665 999999985 5999999999999999999999999999999
Q ss_pred HHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHH--HhHh--cC-CCCCCHHHHHHHh---CC
Q 036883 85 KWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVP--FSKV--FG-DVRCNLKEAVELA---GL 156 (277)
Q Consensus 85 ~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~--~~~~--~~-~~~~~L~~l~~~~---gi 156 (277)
+|+++. .+|.|+..||+ .||+.. .|. ..++|+..+ +++. ++ .++++|+.++++| ++
T Consensus 73 ~~l~~~------vlV~Hn~~~D~-~~l~~~-------~~~--~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i 136 (157)
T cd06149 73 KILKGK------VVVGHAIHNDF-KALKYF-------HPK--HMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDI 136 (157)
T ss_pred HHcCCC------EEEEeCcHHHH-HHhccc-------CCC--cCEEECcccccchhhcCCcccCChhHHHHHHHHcChhh
Confidence 999874 45667889998 688633 221 235676543 4333 43 2468999999999 67
Q ss_pred CCCCCCCchHHHHHHHHHHHH
Q 036883 157 IWQGRVHCGLDDAINIARLLS 177 (277)
Q Consensus 157 ~~~~~~H~Al~DA~~ta~l~~ 177 (277)
+..++.|+|++||++|++||+
T Consensus 137 ~~~~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 137 QVGRQGHSSVEDARATMELYK 157 (157)
T ss_pred cCCCCCcCcHHHHHHHHHHhC
Confidence 754567999999999999984
No 45
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.92 E-value=4.8e-24 Score=194.57 Aligned_cols=181 Identities=20% Similarity=0.231 Sum_probs=132.7
Q ss_pred CeEEEEEEccCCCCCCCCCCCcEEEEceEEEECC-CC---EEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHH
Q 036883 2 EYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGV-SG---EIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLG 77 (277)
Q Consensus 2 ~~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~-~g---~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~ 77 (277)
..+||||+||||+ ++..++|||||+|+++.. +| ++.++|+.||+|.. .|+++++++||||++||.+++...
T Consensus 37 ~~~vvlD~ETTGL---d~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~--~I~~~~t~IhGIt~e~v~~~~~~~ 111 (294)
T PRK09182 37 RLGVILDTETTGL---DPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSR--PIPPEITRLTGITDEMVAGQTIDP 111 (294)
T ss_pred CeEEEEEeeCCCC---CCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCC--CCCHHHHHhcCCCHHHHhcCCCcH
Confidence 3689999999985 467899999999999742 34 45689999999985 599999999999999999988765
Q ss_pred HHHHHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHh-HhcCCCCCCHHHHHHHhCC
Q 036883 78 EALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFS-KVFGDVRCNLKEAVELAGL 156 (277)
Q Consensus 78 evl~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~-~~~~~~~~~L~~l~~~~gi 156 (277)
++ |.+|++.. .++|+||+.||+ .||++.+.... ..+ |.+...... ...+..+++|++++.+||.
T Consensus 112 ~~---l~~fl~~~-----~vlVAHNA~FD~-~fL~~~~~~~~-~~~-----~~ct~~~i~~~~~~~~~~kL~~La~~~g~ 176 (294)
T PRK09182 112 AA---VDALIAPA-----DLIIAHNAGFDR-PFLERFSPVFA-TKP-----WACSVSEIDWSARGFEGTKLGYLAGQAGF 176 (294)
T ss_pred HH---HHHHhcCC-----CEEEEeCHHHHH-HHHHHHHHhcc-CCc-----ccccHHHHhhccccCCCCCHHHHHHHcCC
Confidence 54 45555543 356778999995 89998765442 112 222222111 1122357899999999994
Q ss_pred CCCCCCCchHHHHHHHHHHHHHHHHhcCccCcCcccccccCCCccccc
Q 036883 157 IWQGRVHCGLDDAINIARLLSVIMRRGFKFSITKSLTPQANPNCLTWN 204 (277)
Q Consensus 157 ~~~~~~H~Al~DA~~ta~l~~~l~~~g~~~~i~~~l~~~~~~~~~~~~ 204 (277)
. ..+|+|++||++|++||.+++.......+.+.+.....|+-.+|.
T Consensus 177 -~-~~aHrAl~Da~Ata~ll~~~l~~~~~~~l~~Ll~~~~~~~~~~~a 222 (294)
T PRK09182 177 -F-HEGHRAVDDCQALLELLARPLPETGQPPLAELLEASRRSRVRIWA 222 (294)
T ss_pred -C-CCCcChHHHHHHHHHHHHHHHhhcCCcCHHHHHHHhccCeeEEEc
Confidence 3 368999999999999999887665444556666666666655554
No 46
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.92 E-value=3.6e-24 Score=226.75 Aligned_cols=165 Identities=24% Similarity=0.253 Sum_probs=146.2
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYF 82 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~ 82 (277)
.|||+|+||||+ ++..++|||||||+++ +|.++++|+.||+|.. .++++++++||||+++|.+++++.+|+.+
T Consensus 420 ~~VVfDLETTGL---~~~~deIIEIgAV~V~--~G~iie~F~~~V~P~~--~I~~~~~~LTGIT~e~L~~aps~~EaL~~ 492 (1437)
T PRK00448 420 TYVVFDVETTGL---SAVYDEIIEIGAVKIK--NGEIIDKFEFFIKPGH--PLSAFTTELTGITDDMVKDAPSIEEVLPK 492 (1437)
T ss_pred cEEEEEhhhcCC---CCchhhhheeeeEEEe--CCeEeeeEEEEECCCC--CCCHHHHHHhCCCHHHHcCCCCHHHHHHH
Confidence 699999999985 4578999999999997 8899999999999985 59999999999999999999999999999
Q ss_pred HHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcC-CCCCCHHHHHHHhCCCCCCC
Q 036883 83 HDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFG-DVRCNLKEAVELAGLIWQGR 161 (277)
Q Consensus 83 f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~-~~~~~L~~l~~~~gi~~~~~ 161 (277)
|.+|+++. .+|+|++.||+ .||+.++++.|++. +...++|+..+++..++ ..+++|+++++++|++..+
T Consensus 493 f~~figg~------vLVAHNa~FD~-~fL~~~l~rlgl~~--l~~~~IDTLelar~l~p~~k~~kL~~LAk~lGL~~~~- 562 (1437)
T PRK00448 493 FKEFCGDS------ILVAHNASFDV-GFINTNYEKLGLEK--IKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVELEH- 562 (1437)
T ss_pred HHHHhCCC------EEEEeCccccH-HHHHHHHHHcCCcc--ccccceeHHHHHHHHcCccccccHHHHHHHcCCCCCC-
Confidence 99999874 56778899996 79999999998753 34678999988887775 4578999999999999864
Q ss_pred CCchHHHHHHHHHHHHHHHHhcC
Q 036883 162 VHCGLDDAINIARLLSVIMRRGF 184 (277)
Q Consensus 162 ~H~Al~DA~~ta~l~~~l~~~g~ 184 (277)
+|+|++||.+||+||.+|+++-.
T Consensus 563 ~HrAl~DA~aTa~lf~~ll~~l~ 585 (1437)
T PRK00448 563 HHRADYDAEATAYLLIKFLKDLK 585 (1437)
T ss_pred CcChHHHHHHHHHHHHHHHHHHH
Confidence 79999999999999999987643
No 47
>PRK05359 oligoribonuclease; Provisional
Probab=99.91 E-value=3.8e-23 Score=176.58 Aligned_cols=162 Identities=15% Similarity=0.074 Sum_probs=124.1
Q ss_pred CeEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEE-eEEEEeecCCCC--CCCChhhHhHh---CCChHHHhCCCC
Q 036883 2 EYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEII-ACFQTYVRPTFE--PLLTDFCKELT---GIQQHQVDNGIT 75 (277)
Q Consensus 2 ~~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~-~~f~~lVrP~~~--~~i~~~~~~lt---GIt~~~l~~ap~ 75 (277)
+.||+||+||||+ ++..++|||||||+++. +..++ +.|+.+|+|... ..++++++.+| ||++++++++++
T Consensus 3 ~~~vvlD~ETTGL---dp~~d~IieIgaV~~~~-~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~ 78 (181)
T PRK05359 3 DNLIWIDLEMTGL---DPERDRIIEIATIVTDA-DLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVS 78 (181)
T ss_pred CcEEEEEeecCCC---CCCCCeEEEEEEEEEcC-CceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCC
Confidence 5799999999985 56789999999999973 33343 679999999752 23578888887 899999999999
Q ss_pred HHHHHHHHHHHHhhcCCCCCcEEEEEe-ccchHHHHHHHHHHHhCCCCCCCCcchhhhH---HHHhHhcCCCCCCHHHHH
Q 036883 76 LGEALYFHDKWLLQMGLNNTNFSVVTW-SDWDCQVMLESECRIKKIQKPAYFNQWINLR---VPFSKVFGDVRCNLKEAV 151 (277)
Q Consensus 76 f~evl~~f~~fl~~~~l~~~~~~vv~~-~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~---~~~~~~~~~~~~~L~~l~ 151 (277)
+.+|+.+|.+|+++.... +...+++| ..||+ .||++.+.+.+..+ .++++|+. .+.+.+++. +
T Consensus 79 ~~e~~~~~l~fl~~~~~~-~~~~l~g~~v~FD~-~FL~~~~~~~~~~l---~~~~~Dv~tl~~l~r~~~P~----~---- 145 (181)
T PRK05359 79 EAEAEAQTLEFLKQWVPA-GKSPLCGNSIGQDR-RFLARYMPELEAYF---HYRNLDVSTLKELARRWKPE----I---- 145 (181)
T ss_pred HHHHHHHHHHHHHHhcCC-CCCceeecchhhCH-HHHHHHHHHhcccC---CCcccchhHHHHHHHHhChh----h----
Confidence 999999999999865332 22345665 49996 89999998776543 35677854 445555442 2
Q ss_pred HHhCCCCCCCCCchHHHHHHHHHHHHHHHHh
Q 036883 152 ELAGLIWQGRVHCGLDDAINIARLLSVIMRR 182 (277)
Q Consensus 152 ~~~gi~~~~~~H~Al~DA~~ta~l~~~l~~~ 182 (277)
+++++.. ..|||++||+.+.+.+..+.+.
T Consensus 146 -~~~~~~~-~~HRal~D~~~s~~~~~~~~~~ 174 (181)
T PRK05359 146 -LNGFKKQ-GTHRALADIRESIAELKYYREH 174 (181)
T ss_pred -hhCCCCc-CCcccHHHHHHHHHHHHHHHHH
Confidence 3577765 4799999999999999988764
No 48
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.90 E-value=2.8e-22 Score=193.04 Aligned_cols=171 Identities=12% Similarity=0.047 Sum_probs=128.8
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHh-CCCCHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVD-NGITLGEALY 81 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~-~ap~f~evl~ 81 (277)
.|||+|+||||+ ++..++|||||||+++.....+.+.|+.+|+|.....+++.+..+||||++|+. .+.+..+++.
T Consensus 7 ~fvv~D~ETTGL---dP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~~ 83 (476)
T PRK11779 7 TFLWHDYETFGA---NPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEFAA 83 (476)
T ss_pred cEEEEEEECCCC---CCCCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHHHH
Confidence 699999999985 567899999999999842234557899999998532357889999999999995 5678999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEe-ccchHHHHHHHHHHHhCCCC-------CCCCcchhhhHHHHhHhc-----------CC
Q 036883 82 FHDKWLLQMGLNNTNFSVVTW-SDWDCQVMLESECRIKKIQK-------PAYFNQWINLRVPFSKVF-----------GD 142 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~~-~~fDl~~~L~~~~~~~gi~~-------p~~~~~~iDl~~~~~~~~-----------~~ 142 (277)
+|.+|+... ..++|.|| ..||+ .||+.++.+..+.. +......+|+..++..+. |.
T Consensus 84 ~i~~~l~~~----~~~lVGhNni~FD~-eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~ 158 (476)
T PRK11779 84 RIHAEFSQP----GTCILGYNNIRFDD-EVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGL 158 (476)
T ss_pred HHHHHHhcC----CCEEEEeCchhhcH-HHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCC
Confidence 999999631 12444454 47996 79999987654321 000113456555443321 23
Q ss_pred CCCCHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHHh
Q 036883 143 VRCNLKEAVELAGLIWQGRVHCGLDDAINIARLLSVIMRR 182 (277)
Q Consensus 143 ~~~~L~~l~~~~gi~~~~~~H~Al~DA~~ta~l~~~l~~~ 182 (277)
.+++|+++++++||+.. ++|+|++||++|+.|+..+.++
T Consensus 159 ~s~rLe~L~~~~gI~~~-~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 159 PSFKLEHLTKANGIEHE-NAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CCCcHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHHh
Confidence 56899999999999875 6899999999999999998876
No 49
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.55 E-value=9.2e-14 Score=122.41 Aligned_cols=155 Identities=20% Similarity=0.241 Sum_probs=113.4
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYF 82 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~ 82 (277)
++|++|+|+.|.. .+...+..--+.+| + ..|.++ |..||||+. .++++.+.++||+++.+.+|++|..|-.+
T Consensus 106 r~vAmDCEMVG~G-p~G~~s~lARvSIV--N-~~G~Vv--yDkyVkP~~--~VtDyRT~vSGIrpehm~~A~pf~~aQ~e 177 (280)
T KOG2249|consen 106 RVVAMDCEMVGVG-PDGRESLLARVSIV--N-YHGHVV--YDKYVKPTE--PVTDYRTRVSGIRPEHMRDAMPFKVAQKE 177 (280)
T ss_pred eEEEEeeeEeccC-CCccceeeeEEEEe--e-ccCcEe--eeeecCCCc--ccccceeeecccCHHHhccCccHHHHHHH
Confidence 6899999999862 22334555555444 4 478886 899999995 59999999999999999999999999999
Q ss_pred HHHHHhhcCCCCCcEEEEEec-cchHHHHHHHHHHHhCCCCCCCCcchhhhHH--HHhHhcC-CCCCCHHHHH-HHhCCC
Q 036883 83 HDKWLLQMGLNNTNFSVVTWS-DWDCQVMLESECRIKKIQKPAYFNQWINLRV--PFSKVFG-DVRCNLKEAV-ELAGLI 157 (277)
Q Consensus 83 f~~fl~~~~l~~~~~~vv~~~-~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~--~~~~~~~-~~~~~L~~l~-~~~gi~ 157 (277)
++++|.+. +||.|+ ..|+ ..|. +..|.. ..-|+.. .|.+.+. ....||..|. +.+|++
T Consensus 178 v~klL~gR-------IlVGHaLhnDl-~~L~-------l~hp~s--~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~ 240 (280)
T KOG2249|consen 178 VLKLLKGR-------ILVGHALHNDL-QALK-------LEHPRS--MIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKD 240 (280)
T ss_pred HHHHHhCC-------EEeccccccHH-HHHh-------hhCchh--hhcccccCchHHHHhhccCCccHHHHHHHHhchh
Confidence 99999986 566665 5676 3553 333421 1123322 2333222 3468999988 568888
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHh
Q 036883 158 WQGRVHCGLDDAINIARLLSVIMRR 182 (277)
Q Consensus 158 ~~~~~H~Al~DA~~ta~l~~~l~~~ 182 (277)
+....|+...||++|.+||.++..+
T Consensus 241 IQ~GeHsSvEDA~AtM~LY~~vk~q 265 (280)
T KOG2249|consen 241 IQVGEHSSVEDARATMELYKRVKVQ 265 (280)
T ss_pred hhccccCcHHHHHHHHHHHHHHHHH
Confidence 7655799999999999999988643
No 50
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=99.47 E-value=3.2e-14 Score=94.11 Aligned_cols=44 Identities=32% Similarity=0.952 Sum_probs=40.0
Q ss_pred eeeecCCccccceeccCCCCCCCcceeCCCCCCCCCCCCCceeeccC
Q 036883 230 RYCYCGAKSIKKVIQRPGPKRGSFFFGCGNWTPNRGACCNYFQWATT 276 (277)
Q Consensus 230 ~~c~c~~~~~~~~~~~~g~~~g~~f~~c~~~~~~~~~~c~~f~w~~~ 276 (277)
|.|.||..+..+|++|.|+|+||.||+|+++ ..+.|+||+|.|+
T Consensus 1 p~C~Cg~~~~~~~s~k~~~N~GR~Fy~C~~~---~~~~C~fF~W~De 44 (45)
T PF06839_consen 1 PKCPCGEPAVRRTSKKTGPNPGRRFYKCPNY---KDKGCNFFQWEDE 44 (45)
T ss_pred CCCCCCCEeEEEEEeCCCCCCCCcceECCCC---CCCCcCCEEeccC
Confidence 5799999999999999999999999999885 3378999999996
No 51
>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=99.33 E-value=2e-11 Score=103.00 Aligned_cols=135 Identities=21% Similarity=0.196 Sum_probs=100.7
Q ss_pred CcEEEEceEEEEC-CCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCC------CHHHHHHHHHHHHhhcCCCC
Q 036883 22 QEIIEFPSVVVSG-VSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGI------TLGEALYFHDKWLLQMGLNN 94 (277)
Q Consensus 22 ~eIIEIgAV~vd~-~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap------~f~evl~~f~~fl~~~~l~~ 94 (277)
.++.-|.+|-.++ .+|+++ +..||+|.. .+.++.++.+|||.++++++. ++++|..++.+++...
T Consensus 31 ~~LaRVsiVd~~~~~~g~vl--lD~~VkP~~--~V~DYrT~~SGIt~~~L~~a~~~~~~~t~~~v~~~l~~li~~~---- 102 (174)
T cd06143 31 MSLARVSVVRGEGELEGVPF--IDDYISTTE--PVVDYLTRFSGIKPGDLDPKTSSKNLTTLKSAYLKLRLLVDLG---- 102 (174)
T ss_pred ceeEEEEEEcCCCCcCCCEE--EeeeECCCC--CccCcCccccccCHHHcCccccccccCCHHHHHHHHHHHcCCC----
Confidence 4566665553211 256665 789999984 599999999999999998775 6899999999988643
Q ss_pred CcEEEEEec-cchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCCCCCHHHHH-HHhCCCCCCCCCchHHHHHHH
Q 036883 95 TNFSVVTWS-DWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAV-ELAGLIWQGRVHCGLDDAINI 172 (277)
Q Consensus 95 ~~~~vv~~~-~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~~~~L~~l~-~~~gi~~~~~~H~Al~DA~~t 172 (277)
.++|.|+ ..|| ..| ++..|. ...+|+..+|+.-. .+..+|..|+ +++|..++...|+.++||+++
T Consensus 103 --tILVGHsL~nDL-~aL-------~l~hp~--~~viDTa~l~~~~~-~r~~sLk~La~~~L~~~IQ~~~HdSvEDArAa 169 (174)
T cd06143 103 --CIFVGHGLAKDF-RVI-------NIQVPK--EQVIDTVELFHLPG-QRKLSLRFLAWYLLGEKIQSETHDSIEDARTA 169 (174)
T ss_pred --CEEEeccchhHH-HHh-------cCcCCC--cceEEcHHhccCCC-CCChhHHHHHHHHcCCcccCCCcCcHHHHHHH
Confidence 3677776 6787 344 455552 46789988775422 2467999988 568888876689999999999
Q ss_pred HHHHH
Q 036883 173 ARLLS 177 (277)
Q Consensus 173 a~l~~ 177 (277)
.+||+
T Consensus 170 m~Ly~ 174 (174)
T cd06143 170 LKLYR 174 (174)
T ss_pred HHHhC
Confidence 99983
No 52
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=99.17 E-value=8.6e-10 Score=94.98 Aligned_cols=138 Identities=14% Similarity=-0.026 Sum_probs=99.5
Q ss_pred EEEEEccCCCCCC-CCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHHH
Q 036883 5 VVIDFEATCDKER-NLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFH 83 (277)
Q Consensus 5 vviDlETTg~~~~-~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~f 83 (277)
++||+|||+..+. ++..++||+||++... +|... .+.....+.. ..+. ||+..++...++..+++.+|
T Consensus 2 ~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~~--~g~~~-~~~~~~~~~~-~~~~-------~i~~~~v~~~~~E~~lL~~f 70 (199)
T cd05160 2 LSFDIETTPPVGGPEPDRDPIICITYADSF--DGVKV-VFLLKTSTVG-DDIE-------FIDGIEVEYFADEKELLKRF 70 (199)
T ss_pred ccEEEeecCCCCCcCCCCCCEEEEEEEEee--CCcee-eEEEeecccC-CcCC-------CCCCceEEEeCCHHHHHHHH
Confidence 6899999986432 4567999999998873 45443 2333333321 1111 88888999999999999999
Q ss_pred HHHHhhcCCCCCcEEEEEec-cchHHHHHHHHHHHhCCCCC-CC-------------------CcchhhhHHHHhHhcCC
Q 036883 84 DKWLLQMGLNNTNFSVVTWS-DWDCQVMLESECRIKKIQKP-AY-------------------FNQWINLRVPFSKVFGD 142 (277)
Q Consensus 84 ~~fl~~~~l~~~~~~vv~~~-~fDl~~~L~~~~~~~gi~~p-~~-------------------~~~~iDl~~~~~~~~~~ 142 (277)
.++++.... +.++.+++ .||+ .+|...+..+|++.. .. ....+|+..+++..+..
T Consensus 71 ~~~i~~~dp---diivg~N~~~FD~-~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~~l 146 (199)
T cd05160 71 FDIIREYDP---DILTGYNIDDFDL-PYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFKL 146 (199)
T ss_pred HHHHHhcCC---CEEEEeccCCCcH-HHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhcCc
Confidence 999988521 23444566 7998 799999999887651 11 12368998888888777
Q ss_pred CCCCHHHHHHHhCCC
Q 036883 143 VRCNLKEAVELAGLI 157 (277)
Q Consensus 143 ~~~~L~~l~~~~gi~ 157 (277)
.+++|++++++++..
T Consensus 147 ~sy~L~~v~~~~l~~ 161 (199)
T cd05160 147 KSYTLDAVAEELLGE 161 (199)
T ss_pred ccCCHHHHHHHHhCC
Confidence 789999999877654
No 53
>PHA02570 dexA exonuclease; Provisional
Probab=99.14 E-value=3.9e-10 Score=97.78 Aligned_cols=166 Identities=14% Similarity=0.068 Sum_probs=106.5
Q ss_pred EEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCC---------C-CCChhhHhHhCCChHH----
Q 036883 4 YVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFE---------P-LLTDFCKELTGIQQHQ---- 69 (277)
Q Consensus 4 ~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~---------~-~i~~~~~~ltGIt~~~---- 69 (277)
=++||+||.|. .....||+||||.+|+..+ +..+|+.+|..... . ...+..+-.....|..
T Consensus 3 dlMIDlETmG~----~p~AaIisIgAV~Fdp~~~-~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~ 77 (220)
T PHA02570 3 DFIIDFETFGN----TPDGAVIDLAVIAFEHDPH-NPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEARK 77 (220)
T ss_pred eEEEEeeccCC----CCCceEEEEEEEEecCCCC-ccccHHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHHHH
Confidence 37899999973 4679999999999998666 67899988863210 1 1222233333333332
Q ss_pred -Hh---CCCCHHHHHHHHHHHHhhcCCCCCcEEEEEec-cchHHHHHHHHHHHh----C--CCCCCCCcchhhhHHHHhH
Q 036883 70 -VD---NGITLGEALYFHDKWLLQMGLNNTNFSVVTWS-DWDCQVMLESECRIK----K--IQKPAYFNQWINLRVPFSK 138 (277)
Q Consensus 70 -l~---~ap~f~evl~~f~~fl~~~~l~~~~~~vv~~~-~fDl~~~L~~~~~~~----g--i~~p~~~~~~iDl~~~~~~ 138 (277)
|. +..++.+++.+|.+||...+...+...+-.+| +||+ .+|+..+++. + ++.|..|..--|++.+...
T Consensus 78 ~L~~s~~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD~-~IL~~a~r~~~~~~~~~~~~Pw~fwN~RDVRT~ie~ 156 (220)
T PHA02570 78 NLKPSDEDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDF-PILVDVIRDIHNTRDTFKLEPVKFWNQRDVRTAIEA 156 (220)
T ss_pred hccCCCccccHHHHHHHHHHHHHHcCCCccceeEecCCCccCH-HHHHHHHHHHhcccCcCcCCCeeecCccchHHHHhh
Confidence 22 45789999999999999864211112233344 7997 8999999988 6 5667555556688876654
Q ss_pred hc-CCC----CCCHHHHHHHhCCCCCC-CCCchHHHHHHHHHHHHHHHHhc
Q 036883 139 VF-GDV----RCNLKEAVELAGLIWQG-RVHCGLDDAINIARLLSVIMRRG 183 (277)
Q Consensus 139 ~~-~~~----~~~L~~l~~~~gi~~~~-~~H~Al~DA~~ta~l~~~l~~~g 183 (277)
.+ .+. +..-..| +| .+|+|+.||..-|..+....+..
T Consensus 157 ~~l~r~~~~cp~~~g~l--------~gfv~H~sihDcakd~lml~y~~rya 199 (220)
T PHA02570 157 TLLTRGMTTCPLPKGTL--------DGFVAHDSIHDCAKDILMLIYAKRYA 199 (220)
T ss_pred hhccCCcccCCCcCccc--------cchhhcccHHHHHHHHHHHHHHHHHh
Confidence 32 211 1111111 22 57999999988887776666543
No 54
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=99.05 E-value=2.4e-09 Score=98.94 Aligned_cols=168 Identities=14% Similarity=0.115 Sum_probs=125.3
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHH-hCCCCHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQV-DNGITLGEALY 81 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l-~~ap~f~evl~ 81 (277)
.|.+.|.||.|. .|..++..+|++|+-|..=+.|.+-...|++|...---.+.+.-+||||+... ++|.+-.+.+.
T Consensus 10 tF~~yDYETfG~---~Pa~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~F~~ 86 (475)
T COG2925 10 TFLFYDYETFGV---HPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAAFAA 86 (475)
T ss_pred cEEEEehhhcCC---CcccccchhhheeeccccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHHHHH
Confidence 588999999975 57889999999999996555667888999999863222467788999999987 58999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEe--ccchHHHHHHHHHHHhCCCCC---CC--CcchhhhHHHHhHhcCC------------
Q 036883 82 FHDKWLLQMGLNNTNFSVVTW--SDWDCQVMLESECRIKKIQKP---AY--FNQWINLRVPFSKVFGD------------ 142 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~~--~~fDl~~~L~~~~~~~gi~~p---~~--~~~~iDl~~~~~~~~~~------------ 142 (277)
++..-+... +.+++.. -.|| -.+-+.-|-|+-++ | +| .+.-+||..+.+..+..
T Consensus 87 ~I~~~ls~P-----~Tcv~GYNniRFD-DEvtRy~fyRNF~D-PYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n~d 159 (475)
T COG2925 87 RIHAELTQP-----NTCVLGYNNIRFD-DEVTRYIFYRNFYD-PYAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDD 159 (475)
T ss_pred HHHHHhCCC-----Ceeeecccccccc-hHHHHHHHHHhcCc-hhhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcCCC
Confidence 998888664 3466653 3788 46777777666444 2 11 23445777766655421
Q ss_pred --CCCCHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHH
Q 036883 143 --VRCNLKEAVELAGLIWQGRVHCGLDDAINIARLLSVIMR 181 (277)
Q Consensus 143 --~~~~L~~l~~~~gi~~~~~~H~Al~DA~~ta~l~~~l~~ 181 (277)
.+.+|+.|...-||+. +++|+||+|+++|..+-+....
T Consensus 160 G~pSFkLEhLt~ANgieH-~nAHdAmsDVyATIamAklvk~ 199 (475)
T COG2925 160 GLPSFKLEHLTKANGIEH-SNAHDAMSDVYATIAMAKLVKT 199 (475)
T ss_pred CCcchhhHHHhhcccccc-chhhHHHHHHHHHHHHHHHHHh
Confidence 2578999999999986 4799999999999876665544
No 55
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=99.03 E-value=2.2e-09 Score=88.54 Aligned_cols=162 Identities=17% Similarity=0.114 Sum_probs=107.6
Q ss_pred CCeEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEE-eEEEEeecCCC--CCCCChhhHhHh---CCChHHHhCCC
Q 036883 1 FEYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEII-ACFQTYVRPTF--EPLLTDFCKELT---GIQQHQVDNGI 74 (277)
Q Consensus 1 f~~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~-~~f~~lVrP~~--~~~i~~~~~~lt---GIt~~~l~~ap 74 (277)
++++|=||+|+||+ ++..++||||++++-|. +.+++ +-+..-|.-.. ...+++.+++.| |+++.-.+...
T Consensus 5 ~~nLiWIDlEMTGL---d~~~drIIEiA~iVTD~-~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~ 80 (184)
T COG1949 5 KNNLIWIDLEMTGL---DPERDRIIEIATIVTDA-NLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTV 80 (184)
T ss_pred CCceEEEeeeeccC---CcCcceEEEEEEEEecC-cccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhc
Confidence 46889999999986 57899999999999984 55554 33333343321 223567787775 57766667899
Q ss_pred CHHHHHHHHHHHHhhcCCCCCcEEEEEec-cchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCCCCCHHHHHHH
Q 036883 75 TLGEALYFHDKWLLQMGLNNTNFSVVTWS-DWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVEL 153 (277)
Q Consensus 75 ~f~evl~~f~~fl~~~~l~~~~~~vv~~~-~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~~~~L~~l~~~ 153 (277)
+..+|-.+.++||+.-...+ ...++.|+ .-| |.||.+.+-+.- ..+..+.+|+. +|++|+.+
T Consensus 81 t~~~aE~~~l~flkkwvp~~-~spicGNSI~qD-RrFl~r~MP~Le---~yfHYR~lDVS------------TlKELa~R 143 (184)
T COG1949 81 TEAEAEAQTLDFLKKWVPKG-VSPICGNSIAQD-RRFLFRYMPKLE---AYFHYRYLDVS------------TLKELARR 143 (184)
T ss_pred cHHHHHHHHHHHHHHhCCCC-CCCCccchhhHH-HHHHHHHhhhHH---HHhhhHhhhHH------------HHHHHHHh
Confidence 99999999999998875432 23455554 358 789876654321 01234667754 45555554
Q ss_pred hCC-----CCCCCCCchHHHHHHHHHHHHHHHHhc
Q 036883 154 AGL-----IWQGRVHCGLDDAINIARLLSVIMRRG 183 (277)
Q Consensus 154 ~gi-----~~~~~~H~Al~DA~~ta~l~~~l~~~g 183 (277)
+.- ...+..|+||+|.+-...=++...+.-
T Consensus 144 W~P~i~~~~~K~~~H~Al~DI~ESI~EL~~YR~~f 178 (184)
T COG1949 144 WNPEILAGFKKGGTHRALDDIRESIAELRYYREHF 178 (184)
T ss_pred hCcHhhhccccccchhHHHHHHHHHHHHHHHHHHh
Confidence 332 234568999999998776666655543
No 56
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=98.97 E-value=3.7e-09 Score=88.03 Aligned_cols=165 Identities=15% Similarity=0.145 Sum_probs=111.0
Q ss_pred CCeEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCC--CCCCChhhHhHhC---CChHHHhCCCC
Q 036883 1 FEYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTF--EPLLTDFCKELTG---IQQHQVDNGIT 75 (277)
Q Consensus 1 f~~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~--~~~i~~~~~~ltG---It~~~l~~ap~ 75 (277)
++.+|=||+|+||++ ...++||||++++-|++-+.+.+-+...|+-.. ...+++.|.+-|| ++..-+....+
T Consensus 25 ~q~lVWiD~EMTGLd---vekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~t 101 (208)
T KOG3242|consen 25 KQPLVWIDCEMTGLD---VEKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKIT 101 (208)
T ss_pred cCceEEEeeeccccc---cccceeEEEEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhcc
Confidence 467899999999874 578999999999998644445566676775532 2346788888765 77777789999
Q ss_pred HHHHHHHHHHHHhhcCCCCCcEEEEEec-cchHHHHHHHHHHHhCCCCCCCCcchhhhHH---HHhHhcCCCCCCHHHHH
Q 036883 76 LGEALYFHDKWLLQMGLNNTNFSVVTWS-DWDCQVMLESECRIKKIQKPAYFNQWINLRV---PFSKVFGDVRCNLKEAV 151 (277)
Q Consensus 76 f~evl~~f~~fl~~~~l~~~~~~vv~~~-~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~---~~~~~~~~~~~~L~~l~ 151 (277)
+.+|-.++++|++.....| ...++.++ .-| +.||.+++-..--- +..+.+|+.. +.++.++...
T Consensus 102 l~~aEnevl~yikk~ip~~-~~~laGNSV~~D-rlFl~k~mPk~~~~---lhyrivDVStIkeL~~Rw~P~~~------- 169 (208)
T KOG3242|consen 102 LADAENEVLEYIKKHIPKG-KCPLAGNSVYMD-RLFLKKYMPKLIKH---LHYRIVDVSTIKELARRWYPDIK------- 169 (208)
T ss_pred HHHHHHHHHHHHHHhCCCC-CCCccCcchhhH-HHHHHHHhHHHHHh---cceeeeeHHHHHHHHHHhCchhh-------
Confidence 9999999999999875533 23455554 458 67988776543111 2356778643 3444443210
Q ss_pred HHhCCCCCCCCCchHHHHHHHHHHHHHHHHh
Q 036883 152 ELAGLIWQGRVHCGLDDAINIARLLSVIMRR 182 (277)
Q Consensus 152 ~~~gi~~~~~~H~Al~DA~~ta~l~~~l~~~ 182 (277)
.+ -|.....|||++|.+-...=++...+.
T Consensus 170 -~~-aPkK~~~HrAldDI~ESI~ELq~Yr~n 198 (208)
T KOG3242|consen 170 -AR-APKKKATHRALDDIRESIKELQYYREN 198 (208)
T ss_pred -cc-CcccccccchHHHHHHHHHHHHHHHHH
Confidence 00 022234699999999887777766554
No 57
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=98.91 E-value=1.4e-08 Score=77.82 Aligned_cols=94 Identities=23% Similarity=0.249 Sum_probs=68.3
Q ss_pred EEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHHHH
Q 036883 5 VVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFHD 84 (277)
Q Consensus 5 vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~f~ 84 (277)
++||+||||++ +..++|++|+....+ .+. .|. + . |.
T Consensus 1 ~~~DiEt~~~~---~~~~~i~~i~~~~~~--~~~---~~~--~-~---------------------------------f~ 36 (96)
T cd06125 1 IAIDTEATGLD---GAVHEIIEIALADVN--PED---TAV--I-D---------------------------------LK 36 (96)
T ss_pred CEEEEECCCCC---CCCCcEEEEEEEEcc--CCC---EEE--e-h---------------------------------HH
Confidence 57999999864 578999999888542 121 111 0 0 88
Q ss_pred HHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCCCCCHHHHHHHhCCCCCCCCCc
Q 036883 85 KWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQGRVHC 164 (277)
Q Consensus 85 ~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~~~~L~~l~~~~gi~~~~~~H~ 164 (277)
+|+++... ...+.|++.||+ .||+++|++++++.|.....++|++.+
T Consensus 37 ~~l~~~~~---~v~V~hn~~fD~-~fL~~~~~~~~~~~p~~~~~~lDT~~l----------------------------- 83 (96)
T cd06125 37 DILRDKPL---AILVGHNGSFDL-PFLNNRCAELGLKYPLLAGSWIDTIKL----------------------------- 83 (96)
T ss_pred HHHhhCCC---CEEEEeCcHHhH-HHHHHHHHHcCCCCCCcCCcEEEehHH-----------------------------
Confidence 88887531 233445569997 799999999998887666789998754
Q ss_pred hHHHHHHHHHH
Q 036883 165 GLDDAINIARL 175 (277)
Q Consensus 165 Al~DA~~ta~l 175 (277)
|+.||+.+++|
T Consensus 84 ~~~~~~~~~~~ 94 (96)
T cd06125 84 AADDVENTLQI 94 (96)
T ss_pred hhhhHHHHHHh
Confidence 88888888765
No 58
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=98.82 E-value=1.4e-08 Score=95.60 Aligned_cols=155 Identities=19% Similarity=0.278 Sum_probs=116.9
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHh-CCCCHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVD-NGITLGEALY 81 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~-~ap~f~evl~ 81 (277)
+++++|+|+...+. .-|+..|++|-. ++++ -+..+|+|.. .|.++.+..+|||.++++ ...+++++-.
T Consensus 217 ~i~AlDCEm~~te~----g~el~RVt~VD~---~~~v--i~D~fVkP~~--~VvDy~T~~SGIT~~~~e~~t~tl~dvq~ 285 (380)
T KOG2248|consen 217 NIFALDCEMVVTEN----GLELTRVTAVDR---DGKV--ILDTFVKPNK--PVVDYNTRYSGITEEDLENSTITLEDVQK 285 (380)
T ss_pred CeEEEEeeeeeecc----ceeeEEeeeeec---cCcE--EeEEeecCCC--cccccccccccccHHHHhcCccCHHHHHH
Confidence 67899999996432 378899988854 4555 3789999984 599999999999999997 5778999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEec-cchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCC--CCCCHHHHHH-HhCCC
Q 036883 82 FHDKWLLQMGLNNTNFSVVTWS-DWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGD--VRCNLKEAVE-LAGLI 157 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~~~-~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~--~~~~L~~l~~-~~gi~ 157 (277)
++..|+... .++|.|+ ..|| ..|+ +.. ...||++.+|....|. ...+|..|++ ++|..
T Consensus 286 ~l~~~~~~~------TILVGHSLenDL-~aLK-------l~H----~~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~ 347 (380)
T KOG2248|consen 286 ELLELISKN------TILVGHSLENDL-KALK-------LDH----PSVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKL 347 (380)
T ss_pred HHHhhcCcC------cEEEeechhhHH-HHHh-------hhC----CceeeeeEEEecCCCCccchHHHHHHHHHHHHHH
Confidence 999999875 5788787 5688 4554 233 3578988777655552 3456888875 45544
Q ss_pred CC--CCCCchHHHHHHHHHHHHHHHHhcCcc
Q 036883 158 WQ--GRVHCGLDDAINIARLLSVIMRRGFKF 186 (277)
Q Consensus 158 ~~--~~~H~Al~DA~~ta~l~~~l~~~g~~~ 186 (277)
+. ...|+...||.++.+|+...+..+..+
T Consensus 348 Iq~~~~~HdS~eDA~acm~Lv~~k~~~~~~~ 378 (380)
T KOG2248|consen 348 IQEGVGGHDSVEDALACMKLVKLKIKNSESQ 378 (380)
T ss_pred HhccCCCCccHHHHHHHHHHHHHHHhccccc
Confidence 43 235999999999999999888776654
No 59
>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=98.63 E-value=8.1e-07 Score=76.34 Aligned_cols=120 Identities=13% Similarity=0.110 Sum_probs=85.7
Q ss_pred eEEEEEEccCCCCCC-CCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHH
Q 036883 3 YYVVIDFEATCDKER-NLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALY 81 (277)
Q Consensus 3 ~~vviDlETTg~~~~-~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~ 81 (277)
+.+.||+||++..+. ++..+.||.||++..+ |.+. -|. .+..+-.+.+.
T Consensus 4 ~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~---g~~~-~~~--------------------------~~~~~E~~lL~ 53 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNPRRDPIIVISLATSN---GDVE-FIL--------------------------AEGLDDRKIIR 53 (188)
T ss_pred eEEEEEEEecCCCCCCCCCCCCEEEEEEEeCC---CCEE-EEE--------------------------ecCCCHHHHHH
Confidence 478999999965543 4567999999987643 3221 011 11356788999
Q ss_pred HHHHHHhhcCCCCCcEEEEEec--cchHHHHHHHHHHHhCCCCCCC--C----------------cchhhhHHHHhHhcC
Q 036883 82 FHDKWLLQMGLNNTNFSVVTWS--DWDCQVMLESECRIKKIQKPAY--F----------------NQWINLRVPFSKVFG 141 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~~~--~fDl~~~L~~~~~~~gi~~p~~--~----------------~~~iDl~~~~~~~~~ 141 (277)
+|.+++..... -++++|. .||+ .+|..-++.+|++.+.. . .-.+|+....++...
T Consensus 54 ~F~~~i~~~dP----d~i~gyN~~~FDl-pyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~ 128 (188)
T cd05781 54 EFVKYVKEYDP----DIIVGYNSNAFDW-PYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPE 128 (188)
T ss_pred HHHHHHHHcCC----CEEEecCCCcCcH-HHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCC
Confidence 99999998631 2566763 6998 79999899998765410 0 016788888877776
Q ss_pred CCCCCHHHHHHHhCCC
Q 036883 142 DVRCNLKEAVELAGLI 157 (277)
Q Consensus 142 ~~~~~L~~l~~~~gi~ 157 (277)
..+++|+++++++|+.
T Consensus 129 l~~y~L~~Va~~Lg~~ 144 (188)
T cd05781 129 VKVKTLENVAEYLGVM 144 (188)
T ss_pred CCCCCHHHHHHHHCCC
Confidence 7789999999999974
No 60
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=98.59 E-value=2.3e-06 Score=73.76 Aligned_cols=129 Identities=16% Similarity=0.097 Sum_probs=87.1
Q ss_pred eEEEEEEccCCCCCC-CCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHH
Q 036883 3 YYVVIDFEATCDKER-NLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALY 81 (277)
Q Consensus 3 ~~vviDlETTg~~~~-~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~ 81 (277)
+.+.||+||++..+. ++..++||.||.+..+ .+.++ .+ ++.. . ..+..-.+-.+.+.
T Consensus 4 ~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~--~~~~~-~~----~~~~---~------------~~v~~~~~E~~lL~ 61 (195)
T cd05780 4 KILSFDIEVLNHEGEPNPEKDPIIMISFADEG--GNKVI-TW----KKFD---L------------PFVEVVKTEKEMIK 61 (195)
T ss_pred eEEEEEEEecCCCCCCCCCCCcEEEEEEecCC--CceEE-Ee----cCCC---C------------CeEEEeCCHHHHHH
Confidence 468899999976544 4678999999986532 33332 11 2211 0 02333456688999
Q ss_pred HHHHHHhhcCCCCCcEEEEEe-c-cchHHHHHHHHHHHhCCCCCCC--------------------CcchhhhHHHHhHh
Q 036883 82 FHDKWLLQMGLNNTNFSVVTW-S-DWDCQVMLESECRIKKIQKPAY--------------------FNQWINLRVPFSKV 139 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~~-~-~fDl~~~L~~~~~~~gi~~p~~--------------------~~~~iDl~~~~~~~ 139 (277)
+|.+++..... + ++++| + .||+ .+|...+..+|++.+.- ....+|+..++++.
T Consensus 62 ~F~~~i~~~dp---d-iivgyN~~~FD~-pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~ 136 (195)
T cd05780 62 RFIEIVKEKDP---D-VIYTYNGDNFDF-PYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRT 136 (195)
T ss_pred HHHHHHHHcCC---C-EEEecCCCCCcH-HHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhh
Confidence 99999987421 2 45655 4 6998 79999898888875410 12377888888887
Q ss_pred cCCCCCCHHHHHH-HhCCCC
Q 036883 140 FGDVRCNLKEAVE-LAGLIW 158 (277)
Q Consensus 140 ~~~~~~~L~~l~~-~~gi~~ 158 (277)
++..+++|+++++ .+|.+.
T Consensus 137 ~~l~sy~L~~v~~~~Lg~~k 156 (195)
T cd05780 137 LNLTRYTLERVYEELFGIEK 156 (195)
T ss_pred CCCCcCcHHHHHHHHhCCCC
Confidence 7778899999876 677753
No 61
>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=98.51 E-value=7.6e-06 Score=71.42 Aligned_cols=76 Identities=20% Similarity=0.233 Sum_probs=58.0
Q ss_pred HHHHHHHHHHHhhcCCCCCcEEEEEe-c-cchHHHHHHHHHHHhCCCCCCCCc--------------chhhhHHHHhHhc
Q 036883 77 GEALYFHDKWLLQMGLNNTNFSVVTW-S-DWDCQVMLESECRIKKIQKPAYFN--------------QWINLRVPFSKVF 140 (277)
Q Consensus 77 ~evl~~f~~fl~~~~l~~~~~~vv~~-~-~fDl~~~L~~~~~~~gi~~p~~~~--------------~~iDl~~~~~~~~ 140 (277)
.+.+.+|.++++... .++|+| | .||+ .+|..-+..+|++.|.++. +.+|+..+++...
T Consensus 79 ~elL~~F~~~i~~~~-----p~lv~yNg~~FDl-P~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~ 152 (208)
T cd05782 79 KELLEDFFQLIEKKN-----PRLVSFNGRGFDL-PVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYG 152 (208)
T ss_pred HHHHHHHHHHHHHhC-----CEEEecCCCcCCH-HHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccC
Confidence 788999999999842 256665 5 7998 7999999999997764432 3678888776543
Q ss_pred CCCCCCHHHHHHHhCCCC
Q 036883 141 GDVRCNLKEAVELAGLIW 158 (277)
Q Consensus 141 ~~~~~~L~~l~~~~gi~~ 158 (277)
...+.+|+.+++.+|++.
T Consensus 153 ~~~~~~L~~va~~lG~~~ 170 (208)
T cd05782 153 ARARASLDLLAKLLGIPG 170 (208)
T ss_pred ccCCCCHHHHHHHhCCCC
Confidence 346789999999999953
No 62
>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=98.42 E-value=9.9e-07 Score=73.36 Aligned_cols=116 Identities=15% Similarity=0.053 Sum_probs=59.6
Q ss_pred EEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHHHH
Q 036883 5 VVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFHD 84 (277)
Q Consensus 5 vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~f~ 84 (277)
++||+||||+ .+....|.-||++.++...... |..+.-.. +.-++.+.++.
T Consensus 1 l~~DIET~Gl---~~~~~~i~liG~~~~~~~~~~~---~~~~~~~~-----------------------~~ee~~~~~~~ 51 (164)
T PF13482_consen 1 LFFDIETTGL---SPDNDTIYLIGVADFDDDEIIT---FIQWFAED-----------------------PDEEEIILEFF 51 (164)
T ss_dssp --EEEEESS----GG-G---EEEEEEE-ETTTTE----EEEE-GGG-----------------------HHHHHHHHH--
T ss_pred CcEEecCCCC---CCCCCCEEEEEEEEeCCCceEE---eeHhhccC-----------------------cHHHHHHHHHH
Confidence 6899999976 4556789999999987322221 33333221 01233444444
Q ss_pred HHHhhcCCCCCcEEEEEec-cchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCCCCCHHHHHHHhCCCCC
Q 036883 85 KWLLQMGLNNTNFSVVTWS-DWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQ 159 (277)
Q Consensus 85 ~fl~~~~l~~~~~~vv~~~-~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~~~~L~~l~~~~gi~~~ 159 (277)
+++.+.. .++..|| .||+ .+|++.+.+++++. ...++|+...+++... .+++|+++.+.+|+...
T Consensus 52 ~~l~~~~-----~iv~yng~~FD~-p~L~~~~~~~~~~~---~~~~iDl~~~~~~~~~-~~~~Lk~ve~~lg~~~~ 117 (164)
T PF13482_consen 52 ELLDEAD-----NIVTYNGKNFDI-PFLKRRAKRYGLPP---PFNHIDLLKIIKKHFL-ESYSLKNVEKFLGIERR 117 (164)
T ss_dssp HHHHTT-------EEESSTTTTHH-HHHHHHH-HHHH-----GGGEEEHHHHHT-TTS-CCTT--SHHH-------
T ss_pred HHHhcCC-----eEEEEeCcccCH-HHHHHHHHHcCCCc---ccchhhHHHHHHhccC-CCCCHHHHhhhcccccc
Confidence 7777652 3444454 8996 89999997777654 3578999888765443 56799999999998763
No 63
>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair]
Probab=98.42 E-value=1.9e-07 Score=91.17 Aligned_cols=49 Identities=29% Similarity=0.750 Sum_probs=41.5
Q ss_pred cccccCCceeeeecCCccccceeccCCCCCCCcceeCCCCCCCCCCCCCceeec
Q 036883 221 SLIHEFEDCRYCYCGAKSIKKVIQRPGPKRGSFFFGCGNWTPNRGACCNYFQWA 274 (277)
Q Consensus 221 ~~~~~~~~~~~c~c~~~~~~~~~~~~g~~~g~~f~~c~~~~~~~~~~c~~f~w~ 274 (277)
|..++....+.|+||.++..++|+|.|||.||.||+|.. . ++|+||.|+
T Consensus 710 p~~a~~~~~~~c~c~~ra~~l~v~k~~~nrGR~f~sc~~----~-k~c~ff~w~ 758 (758)
T KOG1956|consen 710 PTAATEEEEVTCGCGTRAVKLLVAKTEPNRGRKFYSCLP----E-KSCNFFAWE 758 (758)
T ss_pred ccccCCCcccccCCcchhhhhhhhccCccCCCCCcccCC----C-CCcceEeeC
Confidence 344445667999999999999999999999999999954 2 569999996
No 64
>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=98.35 E-value=1.6e-05 Score=71.76 Aligned_cols=171 Identities=18% Similarity=0.114 Sum_probs=97.8
Q ss_pred eEEEEEEccCCCCCCCC------------------CCCcEEEEceEEEECCCCEE-----EeEEEEeecCCCCCCCChhh
Q 036883 3 YYVVIDFEATCDKERNL------------------HPQEIIEFPSVVVSGVSGEI-----IACFQTYVRPTFEPLLTDFC 59 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~------------------~~~eIIEIgAV~vd~~~g~i-----~~~f~~lVrP~~~~~i~~~~ 59 (277)
.||.||+|.||+..... ..-.|||+|...+...++.. ...|..++-|......+..+
T Consensus 23 ~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~~~~~~~~nf~~f~~~~~~~~~~s 102 (262)
T PF04857_consen 23 DFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIPSSYNVWPFNFYLFPLDRDFSQASS 102 (262)
T ss_dssp SEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEECCEEEEEEEBSTTSTTTCEEEHHH
T ss_pred CEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccccCCceeEEEEeeeeccccccceecchh
Confidence 58999999999753221 34689999999993245665 34555554454321112222
Q ss_pred H---hHhCCChHHH-hCCCCHHHHHHH--HHHHHhhcCC-----CCCcEEEEEeccchHHHHHHHHHHHhCCCCCC----
Q 036883 60 K---ELTGIQQHQV-DNGITLGEALYF--HDKWLLQMGL-----NNTNFSVVTWSDWDCQVMLESECRIKKIQKPA---- 124 (277)
Q Consensus 60 ~---~ltGIt~~~l-~~ap~f~evl~~--f~~fl~~~~l-----~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~---- 124 (277)
. .-+|++=+.+ .+|.++....++ +.+.++-..+ ..+..+|.|++-+|+ .+|-+.+.. ++|.
T Consensus 103 l~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn~~~Dl-~~l~~~f~~---~LP~t~~e 178 (262)
T PF04857_consen 103 LQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHNGLYDL-MYLYKKFIG---PLPETLEE 178 (262)
T ss_dssp HHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESSTHHHH-HHHHHHHTT---S--SSHHH
T ss_pred HHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeChHhHH-HHHHHHhcC---CCCCCHHH
Confidence 2 2377776665 567776554421 1133333332 223566667888998 677665543 5553
Q ss_pred -------CCcchhhhHHHHhHhcCCCCCCHHHHHHHhCCCC-----------------------CCC-CCchHHHHHHHH
Q 036883 125 -------YFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIW-----------------------QGR-VHCGLDDAINIA 173 (277)
Q Consensus 125 -------~~~~~iDl~~~~~~~~~~~~~~L~~l~~~~gi~~-----------------------~~~-~H~Al~DA~~ta 173 (277)
+|...+|++.+..... ....+|+.+.+.++... .+. .|.|-.||++|+
T Consensus 179 F~~~~~~~FP~i~DtK~la~~~~-~~~~~L~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~HeAGyDA~mTg 257 (262)
T PF04857_consen 179 FKELLRELFPRIYDTKYLAEECP-GKSTSLQELAEELGIRRNPSSISSPEGFPSYDEEKNNFPMFGEKAHEAGYDAYMTG 257 (262)
T ss_dssp HHHHHHHHSSSEEEHHHHHTSTT-TS-SSHHHHHHHTTSTT----EEE-TTS-------------SS-TTSHHHHHHHHH
T ss_pred HHHHHHHHCcccccHHHHHHhcc-ccccCHHHHHHHhCCCccccccccccccccccccccccccCCCCCCCcchHHHHHH
Confidence 2334556655443221 23568999999999764 344 899999999999
Q ss_pred HHHHH
Q 036883 174 RLLSV 178 (277)
Q Consensus 174 ~l~~~ 178 (277)
.+|.+
T Consensus 258 ~~F~~ 262 (262)
T PF04857_consen 258 CVFIK 262 (262)
T ss_dssp HHHHH
T ss_pred HHHcC
Confidence 99863
No 65
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=98.29 E-value=1.3e-05 Score=69.43 Aligned_cols=172 Identities=20% Similarity=0.235 Sum_probs=111.8
Q ss_pred eEEEEEEccCCCCC----C--------------CCCCCcEEEEceEEEECCCCEEEe----EEEEeec---CCCCCCCCh
Q 036883 3 YYVVIDFEATCDKE----R--------------NLHPQEIIEFPSVVVSGVSGEIIA----CFQTYVR---PTFEPLLTD 57 (277)
Q Consensus 3 ~~vviDlETTg~~~----~--------------~~~~~eIIEIgAV~vd~~~g~i~~----~f~~lVr---P~~~~~i~~ 57 (277)
.||.+|+|.-|.-- . +-..-.+||+|-.+.| ++|++.+ +++.-.+ +.. .-.++
T Consensus 25 ~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQlGlTlsd-~~Gn~p~~g~~tWqfNF~dF~~~~-D~~a~ 102 (239)
T KOG0304|consen 25 PYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQLGLTLSD-EKGNLPDCGTDTWQFNFSDFNLEK-DMYAQ 102 (239)
T ss_pred CeeEecCcCCceeeecCccccCChHHHHHHHHhchhhhhhhheeeeeec-cCCCCCCCCCceeEEecccCCchh-hccch
Confidence 48999999887411 0 0123479999999998 5676654 6665554 222 12334
Q ss_pred hhHhH---hCCChHHHh-CCCCHHHHHHHHHHHHhhcCCC-CCcEEEEE-eccchHHHHHHHHHHHhCCCCC--------
Q 036883 58 FCKEL---TGIQQHQVD-NGITLGEALYFHDKWLLQMGLN-NTNFSVVT-WSDWDCQVMLESECRIKKIQKP-------- 123 (277)
Q Consensus 58 ~~~~l---tGIt~~~l~-~ap~f~evl~~f~~fl~~~~l~-~~~~~vv~-~~~fDl~~~L~~~~~~~gi~~p-------- 123 (277)
.+.++ +||.-+-.. .+....+ |.+.+-..+++ ..+...|+ |+.+|. .+|-+-+....+|..
T Consensus 103 ~SIElLr~~Gidf~K~~e~GI~~~~----F~ellm~sg~v~~~~V~WvTFhs~YDf-gYLlK~Lt~~~LP~~~~eF~~~v 177 (239)
T KOG0304|consen 103 DSIELLRRSGIDFEKHREEGIDIEE----FAELLMTSGLVLDENVTWVTFHSGYDF-GYLLKILTGKPLPETEEEFFEIV 177 (239)
T ss_pred hhHHHHHHcCcCHHHHHHcCCCHHH----HHHHHHHhhhhccCceEEEEeeccchH-HHHHHHHcCCCCcchHHHHHHHH
Confidence 44443 889888774 5776653 44444344332 23455666 688997 577665554433321
Q ss_pred -CCCcchhhhHHHHhHhcCC-CCCCHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHH
Q 036883 124 -AYFNQWINLRVPFSKVFGD-VRCNLKEAVELAGLIWQGRVHCGLDDAINIARLLSVIMR 181 (277)
Q Consensus 124 -~~~~~~iDl~~~~~~~~~~-~~~~L~~l~~~~gi~~~~~~H~Al~DA~~ta~l~~~l~~ 181 (277)
.++....|++.+++..-+. ...+|..+++.++++-.|..|.|-.|+..||.+|.+|.+
T Consensus 178 ~~~fp~vYDiK~l~~~c~~~~l~~GL~~lA~~L~~~RvG~~HqAGSDSlLT~~~F~kl~~ 237 (239)
T KOG0304|consen 178 RQLFPFVYDVKYLMKFCEGLSLKGGLQRLADLLGLKRVGIAHQAGSDSLLTARVFFKLKE 237 (239)
T ss_pred HHHcchhhhHHHHHHhhhhhhhhcCHHHHHHHhCCCeeecccccCcHHHHHHHHHHHHHh
Confidence 1344566777665544332 256899999999999999999999999999999999865
No 66
>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=98.28 E-value=4e-05 Score=66.78 Aligned_cols=130 Identities=18% Similarity=0.159 Sum_probs=90.5
Q ss_pred CCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHHHHHHHhhcCCCCCcEEE
Q 036883 20 HPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFHDKWLLQMGLNNTNFSV 99 (277)
Q Consensus 20 ~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~f~~fl~~~~l~~~~~~v 99 (277)
.-.+||.|+++.++ .++++ ...++-.+. -+-.+.+.+|.+++++.. ..+
T Consensus 7 ~f~kIV~Is~~~~~-~~~~~--~v~s~~~~~-----------------------~~E~~lL~~F~~~~~~~~-----p~L 55 (209)
T PF10108_consen 7 PFHKIVCISVVYAD-DDGQF--KVKSLGGPD-----------------------DDEKELLQDFFDLVEKYN-----PQL 55 (209)
T ss_pred cCCCeEEEEEEEEe-cCCcE--EEEeccCCC-----------------------CCHHHHHHHHHHHHHhCC-----CeE
Confidence 35899999999887 33443 222222111 125788999999998752 356
Q ss_pred EEe-c-cchHHHHHHHHHHHhCCCCCCCCc---------------chhhhHHHHhHhcCCCCCCHHHHHHHhCCCCCCCC
Q 036883 100 VTW-S-DWDCQVMLESECRIKKIQKPAYFN---------------QWINLRVPFSKVFGDVRCNLKEAVELAGLIWQGRV 162 (277)
Q Consensus 100 v~~-~-~fDl~~~L~~~~~~~gi~~p~~~~---------------~~iDl~~~~~~~~~~~~~~L~~l~~~~gi~~~~~~ 162 (277)
|+| | .||+ .+|......+|++.|.++. +-+||.+++...-+....+|+.++..+|||-...-
T Consensus 56 Vs~NG~~FDl-P~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~g~~~~~sLd~la~~lgiPgK~~i 134 (209)
T PF10108_consen 56 VSFNGRGFDL-PVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFYGAKARTSLDELAALLGIPGKDDI 134 (209)
T ss_pred EecCCccCCH-HHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhccCccccCCHHHHHHHcCCCCCCCC
Confidence 765 4 6998 7999988899999886442 34788877544323457899999999999853211
Q ss_pred Cc------------------hHHHHHHHHHHHHHHHH
Q 036883 163 HC------------------GLDDAINIARLLSVIMR 181 (277)
Q Consensus 163 H~------------------Al~DA~~ta~l~~~l~~ 181 (277)
+- -..|+++|+.||.++..
T Consensus 135 dGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~ 171 (209)
T PF10108_consen 135 DGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFEL 171 (209)
T ss_pred CHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 11 16799999999999875
No 67
>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=98.11 E-value=8.6e-05 Score=62.84 Aligned_cols=142 Identities=15% Similarity=0.041 Sum_probs=91.5
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYF 82 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~ 82 (277)
.++++|+|+|+. ++...+|+.++.. . ..++ .|..-+++. .. .+++++.+++..
T Consensus 6 ~~~a~d~e~~~~---~~~~~~i~~l~~~--~-~~~~---~~~~~~~~~---~~---------------~~~~~~~~~~~~ 58 (193)
T cd06139 6 KVFAFDTETTSL---DPMQAELVGISFA--V-EPGE---AYYIPLGHD---YG---------------GEQLPREEVLAA 58 (193)
T ss_pred CeEEEEeecCCC---CcCCCeEEEEEEE--c-CCCC---EEEEecCCC---cc---------------ccCCCHHHHHHH
Confidence 578999999975 3456788887654 2 1221 222112221 01 145678889999
Q ss_pred HHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCC-CCCHHHHHHHh-CCCC--
Q 036883 83 HDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDV-RCNLKEAVELA-GLIW-- 158 (277)
Q Consensus 83 f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~-~~~L~~l~~~~-gi~~-- 158 (277)
|.+++++.. ...++|++.||+ .+|. +.|+..+ ..++|+..+.....+.. .++|+++++.| +...
T Consensus 59 l~~~l~~~~----~~~v~hn~k~d~-~~l~----~~gi~~~---~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~ 126 (193)
T cd06139 59 LKPLLEDPS----IKKVGQNLKFDL-HVLA----NHGIELR---GPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTIS 126 (193)
T ss_pred HHHHHhCCC----CcEEeeccHHHH-HHHH----HCCCCCC---CCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCcc
Confidence 999998742 135677889997 5774 4677654 45789887766665544 67999998765 3320
Q ss_pred --------------CC-----CCCchHHHHHHHHHHHHHHHHhc
Q 036883 159 --------------QG-----RVHCGLDDAINIARLLSVIMRRG 183 (277)
Q Consensus 159 --------------~~-----~~H~Al~DA~~ta~l~~~l~~~g 183 (277)
.. ..|.|..||.++..|+..|..+-
T Consensus 127 ~~~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l 170 (193)
T cd06139 127 FEDLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKL 170 (193)
T ss_pred HHHHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 00 12357888999999999887653
No 68
>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=98.11 E-value=0.00017 Score=62.80 Aligned_cols=142 Identities=15% Similarity=0.105 Sum_probs=85.0
Q ss_pred eEEEEEEccCCCCCC--CCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChh----hHhHhCCChHHHhCCCCH
Q 036883 3 YYVVIDFEATCDKER--NLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDF----CKELTGIQQHQVDNGITL 76 (277)
Q Consensus 3 ~~vviDlETTg~~~~--~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~----~~~ltGIt~~~l~~ap~f 76 (277)
+.+.||+|+.+.+++ ++..++||+|+.+. + .+|..+. ....+.+. +..+ +..+-|. -.+..-.+-
T Consensus 3 rilafDIE~~~~~~~fP~~~~D~Ii~IS~~~-~-~~g~~~~-~~~~~~~~----~~~~~~~~~~~~~~~--~~v~~~~~E 73 (204)
T cd05779 3 RVLAFDIETTKLPLKFPDAETDQIMMISYMI-D-GQGYLIV-NREIVSED----IEDFEYTPKPEYEGP--FKVFNEPDE 73 (204)
T ss_pred eEEEEEEEecCCCCCCcCCCCCeEEEEEEEE-e-cCCEEEe-cccccccc----cccccccCCCCCCCc--eEEecCCCH
Confidence 478999999875443 35789999999775 3 2443220 00111110 0000 0000010 112234678
Q ss_pred HHHHHHHHHHHhhcCCCCCcEEEEEe-c-cchHHHHHHHHHHHhCCCCCC-C---Cc----------chhhhHHHHhHhc
Q 036883 77 GEALYFHDKWLLQMGLNNTNFSVVTW-S-DWDCQVMLESECRIKKIQKPA-Y---FN----------QWINLRVPFSKVF 140 (277)
Q Consensus 77 ~evl~~f~~fl~~~~l~~~~~~vv~~-~-~fDl~~~L~~~~~~~gi~~p~-~---~~----------~~iDl~~~~~~~~ 140 (277)
.+.+.+|.+|+..... -++++| + .||+ .+|.+-+..+|++... . .. -.+|+..++++..
T Consensus 74 ~~lL~~f~~~i~~~~P----d~i~gyN~~~FD~-pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~ 148 (204)
T cd05779 74 KALLQRFFEHIREVKP----HIIVTYNGDFFDW-PFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDS 148 (204)
T ss_pred HHHHHHHHHHHHHhCC----CEEEecCccccCH-HHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhh
Confidence 9999999999998631 245665 3 7998 7998888888876431 0 00 1468877776532
Q ss_pred --CCCCCCHHHHHH-HhCCCC
Q 036883 141 --GDVRCNLKEAVE-LAGLIW 158 (277)
Q Consensus 141 --~~~~~~L~~l~~-~~gi~~ 158 (277)
..++++|+.+++ .+|...
T Consensus 149 ~l~~~sysLd~Va~~~Lg~~K 169 (204)
T cd05779 149 YLPQGSQGLKAVTKAKLGYDP 169 (204)
T ss_pred cCCCCCccHHHHHHHHhCCCc
Confidence 335789999998 488753
No 69
>PRK05755 DNA polymerase I; Provisional
Probab=97.90 E-value=0.00024 Score=74.41 Aligned_cols=134 Identities=18% Similarity=0.099 Sum_probs=90.6
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYF 82 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~ 82 (277)
.+++||+||+++ ++...+|+.|+.. .+ ++.. .+|.+. . +. .+++..
T Consensus 316 ~~~a~DtEt~~l---~~~~~~i~~i~ls-~~--~g~~-----~~ip~~---~----------i~----------~~~l~~ 361 (880)
T PRK05755 316 GLFAFDTETTSL---DPMQAELVGLSFA-VE--PGEA-----AYIPLD---Q----------LD----------REVLAA 361 (880)
T ss_pred CeEEEEeccCCC---CcccccEEEEEEE-eC--CCcE-----EEEecc---c----------cc----------HHHHHH
Confidence 478999999975 4578889998753 32 3422 233221 1 11 167888
Q ss_pred HHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCCCCCHHHHHHHh-CCCCC--
Q 036883 83 HDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELA-GLIWQ-- 159 (277)
Q Consensus 83 f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~~~~L~~l~~~~-gi~~~-- 159 (277)
|.+|+++... ..|.|++.||+ .+|.+ .|+..+ ..++|++.......+...++|++++++| |+...
T Consensus 362 l~~~L~d~~v----~kV~HNakfDl-~~L~~----~gi~~~---~~~~DT~iAa~Ll~~~~~~~L~~L~~~ylg~~~~~~ 429 (880)
T PRK05755 362 LKPLLEDPAI----KKVGQNLKYDL-HVLAR----YGIELR---GIAFDTMLASYLLDPGRRHGLDSLAERYLGHKTISF 429 (880)
T ss_pred HHHHHhCCCC----cEEEeccHhHH-HHHHh----CCCCcC---CCcccHHHHHHHcCCCCCCCHHHHHHHHhCCCccch
Confidence 9999988532 24677889997 68863 477654 4688988765555443348999999876 55410
Q ss_pred ----------------CCCCchHHHHHHHHHHHHHHHHh
Q 036883 160 ----------------GRVHCGLDDAINIARLLSVIMRR 182 (277)
Q Consensus 160 ----------------~~~H~Al~DA~~ta~l~~~l~~~ 182 (277)
...|.|..|+..|+.|+..|.++
T Consensus 430 ~~~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~ 468 (880)
T PRK05755 430 EEVAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPK 468 (880)
T ss_pred HHhcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 12367999999999999988764
No 70
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=97.87 E-value=0.00042 Score=60.45 Aligned_cols=121 Identities=13% Similarity=-0.003 Sum_probs=80.6
Q ss_pred eEEEEEEccCCCCCC-----CCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHH
Q 036883 3 YYVVIDFEATCDKER-----NLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLG 77 (277)
Q Consensus 3 ~~vviDlETTg~~~~-----~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~ 77 (277)
+.+.||+|++...+. .+..++||.||...- ++.. ..+ . ....+-.
T Consensus 10 kilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~---~~~~-----~~~--------~--------------~~~~~E~ 59 (207)
T cd05785 10 RRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDN---RGWE-----EVL--------H--------------AEDAAEK 59 (207)
T ss_pred eEEEEEEEecCCCCccCCCCCCCCCeEEEEecccC---CCce-----eee--------c--------------cCCCCHH
Confidence 467899999886542 235689999987521 2210 000 0 0146789
Q ss_pred HHHHHHHHHHhhcCCCCCcEEEEEe-c-cchHHHHHHHHHHHhCCCCCC-------------C--------------C-c
Q 036883 78 EALYFHDKWLLQMGLNNTNFSVVTW-S-DWDCQVMLESECRIKKIQKPA-------------Y--------------F-N 127 (277)
Q Consensus 78 evl~~f~~fl~~~~l~~~~~~vv~~-~-~fDl~~~L~~~~~~~gi~~p~-------------~--------------~-~ 127 (277)
+.+.+|.+++..... -++++| + .||+ .+|.+.++.+|++.+. + . .
T Consensus 60 ~lL~~f~~~i~~~dP----dii~g~N~~~FD~-pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr 134 (207)
T cd05785 60 ELLEELVAIIRERDP----DVIEGHNIFRFDL-PYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGR 134 (207)
T ss_pred HHHHHHHHHHHHhCC----CEEeccCCcccCH-HHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCE
Confidence 999999999998521 255555 4 7998 7999999999887630 0 0 1
Q ss_pred chhhhHHHHhHh----cCCCCCCHHHHHHHhCCCC
Q 036883 128 QWINLRVPFSKV----FGDVRCNLKEAVELAGLIW 158 (277)
Q Consensus 128 ~~iDl~~~~~~~----~~~~~~~L~~l~~~~gi~~ 158 (277)
-.+|+..++++. +...+++|+++++++|+..
T Consensus 135 ~~iDl~~~~~~~~~~~~~l~sysL~~Va~~~g~~~ 169 (207)
T cd05785 135 HVIDTYFLVQLFDVSSRDLPSYGLKAVAKHFGLAS 169 (207)
T ss_pred EEEEcHHHHHhhcccccCCCCCCHHHHHHHhcccC
Confidence 126887777652 3345789999999998744
No 71
>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=97.57 E-value=0.0011 Score=64.50 Aligned_cols=121 Identities=11% Similarity=0.117 Sum_probs=83.6
Q ss_pred EEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHHH
Q 036883 4 YVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFH 83 (277)
Q Consensus 4 ~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~f 83 (277)
.++||+||+ |...-.-.+|++..+ ++...+.|..++.... ..-.+++.+|
T Consensus 286 ~~ffDiEt~------P~~~~~yL~G~~~~~--~~~~~~~~~~fla~~~----------------------~~E~~~~~~f 335 (457)
T TIGR03491 286 ELIFDIESD------PDENLDYLHGFLVVD--KGQENEKYRPFLAEDP----------------------NTEELAWQQF 335 (457)
T ss_pred cEEEEecCC------CCCCCceEEEEEEec--CCCCCcceeeeecCCc----------------------hHHHHHHHHH
Confidence 578999999 244556789997664 3333233554443321 1246688999
Q ss_pred HHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCC---CCCcchhhhHHHHhHh--cCCCCCCHHHHHHHhCCCC
Q 036883 84 DKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKP---AYFNQWINLRVPFSKV--FGDVRCNLKEAVELAGLIW 158 (277)
Q Consensus 84 ~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p---~~~~~~iDl~~~~~~~--~~~~~~~L~~l~~~~gi~~ 158 (277)
.+|+...+ +..|+|++.+.. ..|++-+.+++.+.. .+..+++||....+.. ++..+++|+.++..+|.++
T Consensus 336 ~~~l~~~~----~~~i~hY~~~e~-~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~sysLK~v~~~lg~~~ 410 (457)
T TIGR03491 336 LQLLQSYP----DAPIYHYGETEK-DSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIESYSLKSIARWLGFEW 410 (457)
T ss_pred HHHHHHCC----CCeEEeeCHHHH-HHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCCCCCHHHHHHHhCccc
Confidence 99998752 236788888994 799999998876531 1334789988776654 3556899999999999976
Q ss_pred C
Q 036883 159 Q 159 (277)
Q Consensus 159 ~ 159 (277)
.
T Consensus 411 ~ 411 (457)
T TIGR03491 411 R 411 (457)
T ss_pred C
Confidence 5
No 72
>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=97.56 E-value=0.0031 Score=54.86 Aligned_cols=137 Identities=18% Similarity=0.093 Sum_probs=79.2
Q ss_pred eEEEEEEccCCCC-CCCCC----CCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHH
Q 036883 3 YYVVIDFEATCDK-ERNLH----PQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLG 77 (277)
Q Consensus 3 ~~vviDlETTg~~-~~~~~----~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~ 77 (277)
+++.||+||++.. +..|. .++||+|+.+ + .++. ..+ .++............. ....+..-.+-.
T Consensus 6 rilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~--~-~~~~--~~v-~~~~~~~~~~~~~~~~-----~~~~v~~~~~E~ 74 (204)
T cd05783 6 KRIAIDIEVYTPIKGRIPDPKTAEYPVISVALA--G-SDGL--KRV-LVLKREGVEGLEGLLP-----EGAEVEFFDSEK 74 (204)
T ss_pred eEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEc--C-CCCC--cEE-EEEecCCcccccccCC-----CCCeEEecCCHH
Confidence 4688999999743 33332 2689999875 3 1221 111 1122110000000000 011233346789
Q ss_pred HHHHHHHHHHhhcCCCCCcEEEEEec--cchHHHHHHHHHHHhCCC---CCCC---------CcchhhhHHHHhH-h---
Q 036883 78 EALYFHDKWLLQMGLNNTNFSVVTWS--DWDCQVMLESECRIKKIQ---KPAY---------FNQWINLRVPFSK-V--- 139 (277)
Q Consensus 78 evl~~f~~fl~~~~l~~~~~~vv~~~--~fDl~~~L~~~~~~~gi~---~p~~---------~~~~iDl~~~~~~-~--- 139 (277)
+.+.+|.+|+.+.+ ++++|. .||+ .+|..-+.++|+. .|.. ....+|+...+.. .
T Consensus 75 ~lL~~F~~~i~~~~------~iig~N~~~FDl-pyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~ 147 (204)
T cd05783 75 ELIREAFKIISEYP------IVLTFNGDNFDL-PYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQV 147 (204)
T ss_pred HHHHHHHHHHhcCC------EEEEeCCCCcCH-HHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhh
Confidence 99999999998752 566763 6998 7999999999887 2211 1235677665543 1
Q ss_pred --c--CCCCCCHHHHHHHh-CCC
Q 036883 140 --F--GDVRCNLKEAVELA-GLI 157 (277)
Q Consensus 140 --~--~~~~~~L~~l~~~~-gi~ 157 (277)
+ ...+++|+++++++ |..
T Consensus 148 ~~~~~~~~~~~L~~Va~~~lg~~ 170 (204)
T cd05783 148 YAFGNKYREYTLDAVAKALLGEG 170 (204)
T ss_pred hhhccccccCcHHHHHHHhcCCC
Confidence 2 23578999999866 543
No 73
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=97.49 E-value=0.013 Score=51.84 Aligned_cols=135 Identities=14% Similarity=0.096 Sum_probs=83.5
Q ss_pred eEEEEEEccCCCCCC--CCCCCcEEEEceEEEECCCCE--EEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHH
Q 036883 3 YYVVIDFEATCDKER--NLHPQEIIEFPSVVVSGVSGE--IIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGE 78 (277)
Q Consensus 3 ~~vviDlETTg~~~~--~~~~~eIIEIgAV~vd~~~g~--i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~e 78 (277)
+.+.||+|++...+. ++..++||.|+.+.-. ++. .....-..+++.. .++ ...+..-.+-.+
T Consensus 8 ~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~--~~~~~~~~~~~~~l~~~~--~~~----------~~~v~~~~~E~e 73 (230)
T cd05777 8 RILSFDIECAGRKGVFPEPEKDPVIQIANVVTR--QGEGEPFIRNIFTLKTCA--PIV----------GAQVFSFETEEE 73 (230)
T ss_pred eEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEe--CCCCCCceeEEEEeCCCC--CCC----------CCEEEEECCHHH
Confidence 367899999986553 3567999999988653 232 1111111122211 121 123334567899
Q ss_pred HHHHHHHHHhhcCCCCCcEEEEEe-c-cchHHHHHHHHHHHhCCCCC-CC------------------------------
Q 036883 79 ALYFHDKWLLQMGLNNTNFSVVTW-S-DWDCQVMLESECRIKKIQKP-AY------------------------------ 125 (277)
Q Consensus 79 vl~~f~~fl~~~~l~~~~~~vv~~-~-~fDl~~~L~~~~~~~gi~~p-~~------------------------------ 125 (277)
.+.+|.+++..... + ++++| + .||+ .+|..-++..|++.- .+
T Consensus 74 LL~~f~~~i~~~DP---D-ii~GyN~~~FDl-~yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i 148 (230)
T cd05777 74 LLLAWRDFVQEVDP---D-IITGYNICNFDL-PYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINI 148 (230)
T ss_pred HHHHHHHHHHhcCC---C-EEEEecCCCCCH-HHHHHHHHHhCCccccccccccCCceeEeCCcccccccccccceEEEE
Confidence 99999999988632 2 45554 4 6998 688888887776521 00
Q ss_pred -CcchhhhHHHHhHhcCCCCCCHHHHHH-HhCC
Q 036883 126 -FNQWINLRVPFSKVFGDVRCNLKEAVE-LAGL 156 (277)
Q Consensus 126 -~~~~iDl~~~~~~~~~~~~~~L~~l~~-~~gi 156 (277)
..-.+|+...+++.+...+++|+++++ .+|.
T Consensus 149 ~GR~~iD~~~~~~~~~kl~sy~L~~Va~~~Lg~ 181 (230)
T cd05777 149 EGRIQFDLLQVIQRDYKLRSYSLNSVSAHFLGE 181 (230)
T ss_pred cCEEeeeHHHHHHHhcCcccCcHHHHHHHHhCC
Confidence 012347777777766667899999987 4553
No 74
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=97.37 E-value=0.00055 Score=61.22 Aligned_cols=170 Identities=12% Similarity=0.081 Sum_probs=106.6
Q ss_pred CeEEEEEEccCCCCCCCCCCCcEEEEce-----EEEECC------C-------CEEEeEEEEeecCCCCCCCChhhHhHh
Q 036883 2 EYYVVIDFEATCDKERNLHPQEIIEFPS-----VVVSGV------S-------GEIIACFQTYVRPTFEPLLTDFCKELT 63 (277)
Q Consensus 2 ~~~vviDlETTg~~~~~~~~~eIIEIgA-----V~vd~~------~-------g~i~~~f~~lVrP~~~~~i~~~~~~lt 63 (277)
+-|+|+|+|+||+.+ ...+|-|+.. ..++.+ + -++.+..+-++.|.. ..++...++|
T Consensus 13 ~tf~fldleat~lp~---~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~--v~~p~aeeit 87 (318)
T KOG4793|consen 13 RTFSFLDLEATGLPG---WIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVP--VTRPIAEEIT 87 (318)
T ss_pred eEEEeeeeccccCCc---ccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcC--CcChhhhhhc
Confidence 458999999998754 3345544432 222211 0 134566777778873 5788899999
Q ss_pred CCChHHH--hCCCCHHH-HHHHHHHHHhhcCCCCCcEEE-EEec-cchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhH
Q 036883 64 GIQQHQV--DNGITLGE-ALYFHDKWLLQMGLNNTNFSV-VTWS-DWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSK 138 (277)
Q Consensus 64 GIt~~~l--~~ap~f~e-vl~~f~~fl~~~~l~~~~~~v-v~~~-~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~ 138 (277)
|+++.-+ ....-|.. +.+-+..|+..-+ ...++ .|+| .+|+ .+|..+++..|+..|.- --++|....+..
T Consensus 88 gls~~~~~l~rr~~~D~dla~LL~afls~lp---~p~CLVaHng~~~df-pil~qela~lg~~lpq~-lvcvdslpa~~a 162 (318)
T KOG4793|consen 88 GLSQPFLALQRRLAFDKDLAKLLTAFLSRLP---TPGCLVAHNGNEYDF-PILAQELAGLGYSLPQD-LVCVDSLPALNA 162 (318)
T ss_pred ccccHHHHHHHHhhhhHHHHHHHHHHHhcCC---CCceEEeecCCcccc-HHHHHHHHhcCccchhh-hcCcchhHHHHH
Confidence 9999654 33344444 5566677777643 22344 5666 5887 79999999999988732 346676555544
Q ss_pred hcC----------CCCCCHHHHHHHhCCC-CCCCCCchHHHHHHHHHHHHHHHH
Q 036883 139 VFG----------DVRCNLKEAVELAGLI-WQGRVHCGLDDAINIARLLSVIMR 181 (277)
Q Consensus 139 ~~~----------~~~~~L~~l~~~~gi~-~~~~~H~Al~DA~~ta~l~~~l~~ 181 (277)
+-. .+.++|..+..+|--. .....|.|+.|.-...-+|+...+
T Consensus 163 ld~a~s~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~~ 216 (318)
T KOG4793|consen 163 LDRANSMVTRPEVRRMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRIN 216 (318)
T ss_pred HhhhcCcccCCCCCcccccchHHHhhhcccCCCcceeeecccchhHHHHHHHHH
Confidence 321 1246777776554322 222469999988887777776554
No 75
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=97.20 E-value=0.0066 Score=53.85 Aligned_cols=116 Identities=17% Similarity=0.138 Sum_probs=66.7
Q ss_pred CeEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCH-HHHH
Q 036883 2 EYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITL-GEAL 80 (277)
Q Consensus 2 ~~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f-~evl 80 (277)
+++++||+||||+. +..+.|+-+|...+. +.. .+||....+ ||.- ..++
T Consensus 98 e~~~FFDiETTGL~---~ag~~I~~~g~a~~~--~~~------~~Vrq~~lp-------------------~p~~E~avl 147 (278)
T COG3359 98 EDVAFFDIETTGLD---RAGNTITLVGGARGV--DDT------MHVRQHFLP-------------------APEEEVAVL 147 (278)
T ss_pred cceEEEeeeccccC---CCCCeEEEEEEEEcc--Cce------EEEEeecCC-------------------CcchhhHHH
Confidence 46899999999874 355667767666553 222 345543211 1111 1234
Q ss_pred HHHHHHHhhcCCCCCcEEEEE-ec-cchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcC--CCCCCHHHHHHHhCC
Q 036883 81 YFHDKWLLQMGLNNTNFSVVT-WS-DWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFG--DVRCNLKEAVELAGL 156 (277)
Q Consensus 81 ~~f~~fl~~~~l~~~~~~vv~-~~-~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~--~~~~~L~~l~~~~gi 156 (277)
..|. ...+. + .+|+ || .||+ .|+++ +.+..+++- +-+.-+||.-..+++.+ ..+.+|+.+-+.+|+
T Consensus 148 e~fl---~~~~~---~-~lvsfNGkaFD~-PfikR-~v~~~~el~-l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr~LGi 217 (278)
T COG3359 148 ENFL---HDPDF---N-MLVSFNGKAFDI-PFIKR-MVRDRLELS-LEFGHFDLYHPSRRLWKHLLPRCGLKTVERILGI 217 (278)
T ss_pred HHHh---cCCCc---c-eEEEecCcccCc-HHHHH-HHhcccccC-ccccchhhhhhhhhhhhccCCCCChhhHHHHhCc
Confidence 4444 33211 2 4565 55 7996 89995 555555542 22345677665555543 246788888888887
Q ss_pred C
Q 036883 157 I 157 (277)
Q Consensus 157 ~ 157 (277)
.
T Consensus 218 ~ 218 (278)
T COG3359 218 R 218 (278)
T ss_pred c
Confidence 5
No 76
>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=96.95 E-value=0.039 Score=47.55 Aligned_cols=121 Identities=11% Similarity=0.123 Sum_probs=76.1
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYF 82 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~ 82 (277)
+++.||+||++. .+|..||-. +.....++ .+=.+.. .. | ..+.--++-.+.+.+
T Consensus 4 ~~~~fDIE~~~~-------~~i~~i~~~--~~~~~~i~----~~~~~~~---~~-------~---~~v~~~~~E~~lL~~ 57 (193)
T cd05784 4 KVVSLDIETSMD-------GELYSIGLY--GEGQERVL----MVGDPED---DA-------P---DNIEWFADEKSLLLA 57 (193)
T ss_pred cEEEEEeecCCC-------CCEEEEEee--cCCCCEEE----EECCCCC---CC-------C---CEEEEECCHHHHHHH
Confidence 468999999952 289999764 33333332 1111211 11 1 123334577889999
Q ss_pred HHHHHhhcCCCCCcEEEEEe-c-cchHHHHHHHHHHHhCCCCC--------CC--------------CcchhhhHHHHhH
Q 036883 83 HDKWLLQMGLNNTNFSVVTW-S-DWDCQVMLESECRIKKIQKP--------AY--------------FNQWINLRVPFSK 138 (277)
Q Consensus 83 f~~fl~~~~l~~~~~~vv~~-~-~fDl~~~L~~~~~~~gi~~p--------~~--------------~~~~iDl~~~~~~ 138 (277)
|.+++..... + ++++| + .||+ .+|..-+..+|++.+ .+ ..-.+|+..+.+.
T Consensus 58 f~~~i~~~dP---D-vi~g~N~~~FD~-~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~ 132 (193)
T cd05784 58 LIAWFAQYDP---D-IIIGWNVINFDL-RLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKT 132 (193)
T ss_pred HHHHHHhhCC---C-EEEECCCcCcCH-HHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHH
Confidence 9999988632 2 45554 3 6998 788888888887642 00 0115677777665
Q ss_pred -hcCCCCCCHHHHHHHh
Q 036883 139 -VFGDVRCNLKEAVELA 154 (277)
Q Consensus 139 -~~~~~~~~L~~l~~~~ 154 (277)
.++..+++|+++++++
T Consensus 133 ~~~kl~sy~L~~Va~~~ 149 (193)
T cd05784 133 ATYHFESFSLENVAQEL 149 (193)
T ss_pred ccCCCCcCCHHHHHHHH
Confidence 4667789999999854
No 77
>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=96.85 E-value=0.084 Score=50.57 Aligned_cols=161 Identities=14% Similarity=0.031 Sum_probs=96.6
Q ss_pred eEEEEEEccCCCCCCCC--C--CCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHH
Q 036883 3 YYVVIDFEATCDKERNL--H--PQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGE 78 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~--~--~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~e 78 (277)
.+++||+||+...+..| . .++||.|+.+.-+...............+.. .+. ++ .+..-....+
T Consensus 4 ~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~--~~~-------~~---~~~~~~~E~~ 71 (471)
T smart00486 4 KILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCK--EID-------GV---EVYEFNNEKE 71 (471)
T ss_pred eEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcC--CCC-------CC---eEEecCCHHH
Confidence 57899999997643222 2 6899999988876332222222233333432 122 21 2222237788
Q ss_pred HHHHHHHHHhhcCCCCCcEEEEEec-cchHHHHHHHHHHHhCCCCCC----------C---------------------C
Q 036883 79 ALYFHDKWLLQMGLNNTNFSVVTWS-DWDCQVMLESECRIKKIQKPA----------Y---------------------F 126 (277)
Q Consensus 79 vl~~f~~fl~~~~l~~~~~~vv~~~-~fDl~~~L~~~~~~~gi~~p~----------~---------------------~ 126 (277)
.+.+|.+++..... +.++.+++ .||+ .+|...+...++.... . .
T Consensus 72 lL~~f~~~i~~~dp---dii~g~N~~~FD~-~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~g 147 (471)
T smart00486 72 LLKAFLEFIKKYDP---DIIYGHNISNFDL-PYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSKSFGKTIKVKIKG 147 (471)
T ss_pred HHHHHHHHHHHhCC---CEEEeecCCCCCH-HHHHHHHHHcCCCCHHHcCcCCCCCCcccccCccccccccccceeEecc
Confidence 99999999987632 33444555 5997 6888777766553310 0 0
Q ss_pred cchhhhHHHHhHhcCCCCCCHHHHHHHhCCCCCCCC-C-------------------chHHHHHHHHHHHHHH
Q 036883 127 NQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQGRV-H-------------------CGLDDAINIARLLSVI 179 (277)
Q Consensus 127 ~~~iDl~~~~~~~~~~~~~~L~~l~~~~gi~~~~~~-H-------------------~Al~DA~~ta~l~~~l 179 (277)
.-.+|+...++..++..+++|+++++++.......- + --+.||..+.+|+.++
T Consensus 148 ~~~~Dl~~~~~~~~kl~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 148 RLVIDLYNLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred EEEEEhHHHHHHHhCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 234577778887777678999998876543211110 0 0156888888888875
No 78
>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=96.68 E-value=0.2 Score=44.30 Aligned_cols=170 Identities=8% Similarity=-0.062 Sum_probs=99.9
Q ss_pred EEEEEEccCCCCCC--CCCCCcEEEEceEEEECCCCEEEe-----EEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCH
Q 036883 4 YVVIDFEATCDKER--NLHPQEIIEFPSVVVSGVSGEIIA-----CFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITL 76 (277)
Q Consensus 4 ~vviDlETTg~~~~--~~~~~eIIEIgAV~vd~~~g~i~~-----~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f 76 (277)
.+.+|+|+.+..+. +|..++|+.|+.++-+ +..... ..-.++.+.... .... .....+....|.--.+-
T Consensus 6 ~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~--~~~~~~~~~~~~~~l~~~~~~~~-~~~~-~~~~~~~~~~v~~~~~E 81 (231)
T cd05778 6 ILSLEVHVNTRGDLLPDPEFDPISAIFYCIDD--DVSPFILDANKVGVIIVDELKSN-ASNG-RIRSGLSGIPVEVVESE 81 (231)
T ss_pred EEEEEEEECCCCCCCcCCCCCCeeEEEEEEec--CCCcccccccceeEEEEcCccch-hhhh-ccccCCCCCeEEEeCCH
Confidence 56799999865443 3567999999988543 222211 122333333210 1000 01123333456667888
Q ss_pred HHHHHHHHHHHhhcCCCCCcEEEEEe-c-cchHHHHHHHHHHHhCCCCC--C------------------CC--------
Q 036883 77 GEALYFHDKWLLQMGLNNTNFSVVTW-S-DWDCQVMLESECRIKKIQKP--A------------------YF-------- 126 (277)
Q Consensus 77 ~evl~~f~~fl~~~~l~~~~~~vv~~-~-~fDl~~~L~~~~~~~gi~~p--~------------------~~-------- 126 (277)
.+.+.+|.+++..... -+++.| . .||+ .+|.+-++..++..- . +.
T Consensus 82 ~~LL~~f~~~i~~~DP----Dii~GyNi~~fd~-~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~~g~~~~~~~~ 156 (231)
T cd05778 82 LELFEELIDLVRRFDP----DILSGYEIQRSSW-GYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDEWGYTHTSGIK 156 (231)
T ss_pred HHHHHHHHHHHHHhCC----CEEEEeccccCcH-HHHHHHHHHhCCcchhhhccCCCCCCcccccccccccccccCCceE
Confidence 9999999999988642 245555 3 7997 677766666554320 0 00
Q ss_pred ---cchhhhHHHHhHhcCCCCCCHHHHHH-HhCCCCCCCCCchHHHHH------HHHHHHHHHHHh
Q 036883 127 ---NQWINLRVPFSKVFGDVRCNLKEAVE-LAGLIWQGRVHCGLDDAI------NIARLLSVIMRR 182 (277)
Q Consensus 127 ---~~~iDl~~~~~~~~~~~~~~L~~l~~-~~gi~~~~~~H~Al~DA~------~ta~l~~~l~~~ 182 (277)
.-.+|+..+++..+...+++|++++. .+|-....-.|..+.+.+ ..++++...+++
T Consensus 157 i~GRi~lD~~~~~r~~~kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d 222 (231)
T cd05778 157 IVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKR 222 (231)
T ss_pred EeeEEEeEhHHHHHHHcCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHH
Confidence 01346777777777777899999886 677655444456666653 345566665544
No 79
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=96.53 E-value=0.077 Score=56.83 Aligned_cols=161 Identities=16% Similarity=0.129 Sum_probs=96.2
Q ss_pred eEEEEEEccCCCCC-C--CCCCCcEEEEceEEEECCCCEEEeEEEEee-cCCCCCCCChhhHhHhCCChHHHhCCCCHHH
Q 036883 3 YYVVIDFEATCDKE-R--NLHPQEIIEFPSVVVSGVSGEIIACFQTYV-RPTFEPLLTDFCKELTGIQQHQVDNGITLGE 78 (277)
Q Consensus 3 ~~vviDlETTg~~~-~--~~~~~eIIEIgAV~vd~~~g~i~~~f~~lV-rP~~~~~i~~~~~~ltGIt~~~l~~ap~f~e 78 (277)
+++.||+||++.++ + .+..++||+|+.+... .|.-.+.+...| -+.. +..+.| ..+..-.+-.+
T Consensus 265 rilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~--~g~~~~~~~r~vftl~~-------c~~i~g---~~V~~f~sE~e 332 (1054)
T PTZ00166 265 RILSFDIECIKLKGLGFPEAENDPVIQISSVVTN--QGDEEEPLTKFIFTLKE-------CASIAG---ANVLSFETEKE 332 (1054)
T ss_pred EEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEee--CCCccCCcceEEEecCc-------cccCCC---ceEEEeCCHHH
Confidence 36789999998654 1 2457999999998653 332211111111 1110 111112 23444568899
Q ss_pred HHHHHHHHHhhcCCCCCcEEEEEe-c-cchHHHHHHHHHHHhCCCC-CC--------------------CC---------
Q 036883 79 ALYFHDKWLLQMGLNNTNFSVVTW-S-DWDCQVMLESECRIKKIQK-PA--------------------YF--------- 126 (277)
Q Consensus 79 vl~~f~~fl~~~~l~~~~~~vv~~-~-~fDl~~~L~~~~~~~gi~~-p~--------------------~~--------- 126 (277)
.+.+|.+++..... + ++++| . .||+ .+|..-++..|+.. +. +.
T Consensus 333 LL~~f~~~I~~~DP---D-II~GYNi~~FDl-pYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i 407 (1054)
T PTZ00166 333 LLLAWAEFVIAVDP---D-FLTGYNIINFDL-PYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINI 407 (1054)
T ss_pred HHHHHHHHHHhcCC---C-EEEecCCcCCcH-HHHHHHHHHhCCCchhhcCcccCCCccccccccccccccccccceeEe
Confidence 99999999987632 2 45554 3 6997 68777776665541 10 00
Q ss_pred --cchhhhHHHHhHhcCCCCCCHHHHHHH-hCCCCCCCC------------Cc-------hHHHHHHHHHHHHHHH
Q 036883 127 --NQWINLRVPFSKVFGDVRCNLKEAVEL-AGLIWQGRV------------HC-------GLDDAINIARLLSVIM 180 (277)
Q Consensus 127 --~~~iDl~~~~~~~~~~~~~~L~~l~~~-~gi~~~~~~------------H~-------Al~DA~~ta~l~~~l~ 180 (277)
.-.+|+..++++.+...+++|++++.+ +|.....-. ++ .+.||..+.+|+.+|.
T Consensus 408 ~GR~~iDl~~~~~~~~kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L~~kl~ 483 (1054)
T PTZ00166 408 EGRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLL 483 (1054)
T ss_pred eeEEEEEHHHHHHHhcCcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 124577777777777778999999874 454321111 11 2678888888887763
No 80
>PRK05762 DNA polymerase II; Reviewed
Probab=95.98 E-value=0.31 Score=50.78 Aligned_cols=146 Identities=11% Similarity=0.049 Sum_probs=89.6
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYF 82 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~ 82 (277)
+.+.||+|+++ ..+|+.|+.. +..+..++ .|-+.. + .. .+.+..-++-.+.+.+
T Consensus 156 rvlsfDIE~~~-------~~~i~sI~~~--~~~~~~vi-----~ig~~~-~-~~----------~~~v~~~~sE~~LL~~ 209 (786)
T PRK05762 156 KVVSLDIETSN-------KGELYSIGLE--GCGQRPVI-----MLGPPN-G-EA----------LDFLEYVADEKALLEK 209 (786)
T ss_pred eEEEEEEEEcC-------CCceEEeeec--CCCCCeEE-----EEECCC-C-CC----------cceEEEcCCHHHHHHH
Confidence 46889999995 2368888764 21122221 122211 1 10 0114456788999999
Q ss_pred HHHHHhhcCCCCCcEEEEEe-c-cchHHHHHHHHHHHhCCCCC-------------CCC----------cchhhhHHHHh
Q 036883 83 HDKWLLQMGLNNTNFSVVTW-S-DWDCQVMLESECRIKKIQKP-------------AYF----------NQWINLRVPFS 137 (277)
Q Consensus 83 f~~fl~~~~l~~~~~~vv~~-~-~fDl~~~L~~~~~~~gi~~p-------------~~~----------~~~iDl~~~~~ 137 (277)
|.+++..... -++++| + .||+ .+|.+-+..+|++.. ... .-.+|+..+.+
T Consensus 210 F~~~i~~~DP----DIIvGyNi~~FDl-pyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k 284 (786)
T PRK05762 210 FNAWFAEHDP----DVIIGWNVVQFDL-RLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALK 284 (786)
T ss_pred HHHHHHhcCC----CEEEEeCCCCCcH-HHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHH
Confidence 9999988632 245555 3 6998 788888888887642 000 01567777776
Q ss_pred Hhc-CCCCCCHHHHHHHhCCCCCC--CCC-------------------chHHHHHHHHHHHHHH
Q 036883 138 KVF-GDVRCNLKEAVELAGLIWQG--RVH-------------------CGLDDAINIARLLSVI 179 (277)
Q Consensus 138 ~~~-~~~~~~L~~l~~~~gi~~~~--~~H-------------------~Al~DA~~ta~l~~~l 179 (277)
... ...+++|+++++++...... ..| =.+.||..|..|+.++
T Consensus 285 ~~~~~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 285 SATWVFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred HhhccCCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHh
Confidence 654 55689999999876543211 110 0378999999988843
No 81
>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=95.85 E-value=0.079 Score=48.43 Aligned_cols=100 Identities=16% Similarity=0.084 Sum_probs=65.0
Q ss_pred eEEEEEEccCCCCCC--CCCCCcEEEEceEEEECCCCE---EEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHH
Q 036883 3 YYVVIDFEATCDKER--NLHPQEIIEFPSVVVSGVSGE---IIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLG 77 (277)
Q Consensus 3 ~~vviDlETTg~~~~--~~~~~eIIEIgAV~vd~~~g~---i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~ 77 (277)
.++.||+||....+. ++..++|+.|+.+.-+ .+. ..+.+.++..+.. ... ...+.--.+-.
T Consensus 158 ~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~--~~~~~~~~~~~~~~~~~~~---~~~---------~~~v~~~~~E~ 223 (325)
T PF03104_consen 158 RILSFDIETYSNDGKFPDPEKDEIIMISYVVYR--NGSSEPYRRKVFTLGSCDS---IED---------NVEVIYFDSEK 223 (325)
T ss_dssp EEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEE--TTEEETTEEEEEECSCSCC---TTC---------TTEEEEESSHH
T ss_pred ceeEEEEEEccccCCCCCCCCCeEEEEEEEEEe--ccccCCCceEEEEecCCCC---CCC---------CcEEEEECCHH
Confidence 468899999986532 3567999999988764 221 1233334443331 111 33445567889
Q ss_pred HHHHHHHHHHhhcCCCCCcEEEEEe-c-cchHHHHHHHHHHHhCCC
Q 036883 78 EALYFHDKWLLQMGLNNTNFSVVTW-S-DWDCQVMLESECRIKKIQ 121 (277)
Q Consensus 78 evl~~f~~fl~~~~l~~~~~~vv~~-~-~fDl~~~L~~~~~~~gi~ 121 (277)
+.+.+|.+++..... + ++++| . .||+ .+|..-+...|+.
T Consensus 224 ~lL~~f~~~i~~~dP---D-ii~GyN~~~fD~-~yl~~R~~~l~~~ 264 (325)
T PF03104_consen 224 ELLEAFLDIIQEYDP---D-IITGYNIDGFDL-PYLIERAKKLGID 264 (325)
T ss_dssp HHHHHHHHHHHHHS----S-EEEESSTTTTHH-HHHHHHHHHTTTC
T ss_pred HHHHHHHHHHHhcCC---c-EEEEecccCCCH-HHHHHHHHHhCcc
Confidence 999999999988642 2 45555 3 6998 6888888877544
No 82
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=95.71 E-value=0.61 Score=38.26 Aligned_cols=91 Identities=15% Similarity=0.111 Sum_probs=55.6
Q ss_pred HHHHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCC-CCCHHHHHH-HhC-
Q 036883 79 ALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDV-RCNLKEAVE-LAG- 155 (277)
Q Consensus 79 vl~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~-~~~L~~l~~-~~g- 155 (277)
++..+.+++++..+ ..+.|+..||+ .+|.+. .|+... .++|+ .+.....+.. +++|+++++ ++|
T Consensus 65 ~~~~l~~ll~~~~i----~kv~~n~~~D~-~~L~~~---~~i~~~----~~~D~-~l~~~~l~~~~~~~L~~L~~~~l~~ 131 (176)
T PF01612_consen 65 ILDALKELLEDPNI----IKVGHNAKFDL-KWLYRS---FGIDLK----NVFDT-MLAAYLLDPTRSYSLKDLAEEYLGN 131 (176)
T ss_dssp HHHHHHHHHTTTTS----EEEESSHHHHH-HHHHHH---HTS--S----SEEEH-HHHHHHTTTSTTSSHHHHHHHHHSE
T ss_pred hHHHHHHHHhCCCc----cEEEEEEechH-HHHHHH---hccccC----Cccch-hhhhhcccccccccHHHHHHHHhhh
Confidence 66777788886532 23445668997 577654 676543 46787 5555555433 389999875 456
Q ss_pred CCC--C---CCCC--c---------hHHHHHHHHHHHHHHHHh
Q 036883 156 LIW--Q---GRVH--C---------GLDDAINIARLLSVIMRR 182 (277)
Q Consensus 156 i~~--~---~~~H--~---------Al~DA~~ta~l~~~l~~~ 182 (277)
+.. . ++.. + |-.||..|.+|+..|..+
T Consensus 132 ~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~ 174 (176)
T PF01612_consen 132 IDLDKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQ 174 (176)
T ss_dssp EE-GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHH
T ss_pred ccCcHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 321 1 1111 2 456999999999988764
No 83
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=95.49 E-value=0.69 Score=40.49 Aligned_cols=162 Identities=17% Similarity=0.044 Sum_probs=93.5
Q ss_pred CCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCC------hhhHhHhCCChHHHhCCC-CHHHHHHHHHHHHhhcCCC
Q 036883 21 PQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLT------DFCKELTGIQQHQVDNGI-TLGEALYFHDKWLLQMGLN 93 (277)
Q Consensus 21 ~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~------~~~~~ltGIt~~~l~~ap-~f~evl~~f~~fl~~~~l~ 93 (277)
..-.+|||++....++| |.+.|+++|+|...+ +- ..+...|+|..+-.+.+. .+..++.++.+||+.....
T Consensus 7 ~y~PaEiai~~fSL~~G-I~~~~H~~I~Pg~~p-~G~~~~a~~hs~~tH~ip~~~~~~~~~d~~~l~~~l~~fl~~~~~~ 84 (213)
T PF13017_consen 7 EYVPAEIAICKFSLKEG-IIDSFHTFINPGQIP-LGYRYDAQHHSDETHQIPIPPNALGESDYSELYNELLNFLKPNKGG 84 (213)
T ss_pred cEEeEEEEEEEEecCCc-cchhhhcccCCCCCC-cHHHHHHHHhhhhhcCCCCCCcccccCCHHHHHHHHHHHhhhcCCC
Confidence 34568999999998887 779999999998421 11 223445777776566555 6999999999999987433
Q ss_pred CCcEEEEEec-cchH-HHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcC----C----C-CCCHHHHHHHhC-------
Q 036883 94 NTNFSVVTWS-DWDC-QVMLESECRIKKIQKPAYFNQWINLRVPFSKVFG----D----V-RCNLKEAVELAG------- 155 (277)
Q Consensus 94 ~~~~~vv~~~-~fDl-~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~----~----~-~~~L~~l~~~~g------- 155 (277)
+....|++.. .... ...|+.-+...+.... -...++..++..+.. . . ..+..-+-..+.
T Consensus 85 ~~~~~i~~~~~~~~~V~~cl~~La~~a~~~~~---~~v~~~~~lf~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 161 (213)
T PF13017_consen 85 EKMPPIFTKRDQIPRVQSCLKWLAKKAGEDND---FKVYDFEYLFFDLKNEKVDYRWDRQDFPSKTIADALFPKDFFEYS 161 (213)
T ss_pred CCcceEEEeHhHHHHHHHHHHHHHHhcCCCcc---eEeecHHHHHHHHHHHHhhcccccccCchHHHHHHHccchhhhcc
Confidence 3333455543 2221 2355555554444322 122334443332221 1 1 112211111111
Q ss_pred --C------CCCCCCCchHHHHHHHHHHHHHHHHhcCccC
Q 036883 156 --L------IWQGRVHCGLDDAINIARLLSVIMRRGFKFS 187 (277)
Q Consensus 156 --i------~~~~~~H~Al~DA~~ta~l~~~l~~~g~~~~ 187 (277)
+ ......++|+..+.-+|..+...+.+...++
T Consensus 162 ~~~~C~~He~~d~~~~Ca~s~v~r~ay~i~d~~c~~~~i~ 201 (213)
T PF13017_consen 162 SNIRCDFHEEIDRSKYCALSTVKRWAYTISDYMCRDLGIK 201 (213)
T ss_pred CCCceeecccCCCcccchhHHHHHHHHHHHHHHHHhcCcc
Confidence 1 1123479999999999998877775544433
No 84
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=94.90 E-value=0.82 Score=40.47 Aligned_cols=146 Identities=14% Similarity=0.107 Sum_probs=88.4
Q ss_pred EEEEEccCCCCCCCCCCCcEEEEceEEEECC--CC-----EEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHH
Q 036883 5 VVIDFEATCDKERNLHPQEIIEFPSVVVSGV--SG-----EIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLG 77 (277)
Q Consensus 5 vviDlETTg~~~~~~~~~eIIEIgAV~vd~~--~g-----~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~ 77 (277)
+.|-+-|..- ......||+.|+++....- ++ .....+.+.++|......+......-......+.--.+-.
T Consensus 6 ~sls~~T~~n--~k~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~v~~~~~E~ 83 (234)
T cd05776 6 MSLSIKTVLN--SKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKVRIFENER 83 (234)
T ss_pred EEEEeEEEec--CcCCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCCCCCchHHHHHHhcCCcEEEeCCHH
Confidence 4455556531 1224699999999885411 11 1235567778887531123322233223333466678889
Q ss_pred HHHHHHHHHHhhcCCCCCcEEEEEe-c-cchHHHHHHHHHHHhCCCC------------CCC-------------Ccchh
Q 036883 78 EALYFHDKWLLQMGLNNTNFSVVTW-S-DWDCQVMLESECRIKKIQK------------PAY-------------FNQWI 130 (277)
Q Consensus 78 evl~~f~~fl~~~~l~~~~~~vv~~-~-~fDl~~~L~~~~~~~gi~~------------p~~-------------~~~~i 130 (277)
+.+..|.+++...+. + ++++| . .||+ .+|..-+...|++. |.. ..-.+
T Consensus 84 ~LL~~f~~~i~~~DP---D-iivG~Ni~~fdl-~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~ 158 (234)
T cd05776 84 ALLNFFLAKLQKIDP---D-VLVGHDLEGFDL-DVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLC 158 (234)
T ss_pred HHHHHHHHHHhhcCC---C-EEEeeccCCCCH-HHHHHHHHHhCCCccccccccccccCccccccccccccccccCchhh
Confidence 999999999988642 2 44544 3 6998 68877777766642 100 01245
Q ss_pred hhHHHHhHhcCCCCCCHHHHHH-HhCCC
Q 036883 131 NLRVPFSKVFGDVRCNLKEAVE-LAGLI 157 (277)
Q Consensus 131 Dl~~~~~~~~~~~~~~L~~l~~-~~gi~ 157 (277)
|+...++.+....+++|+++++ .+|..
T Consensus 159 D~~~~~k~~~~~~sY~L~~va~~~Lg~~ 186 (234)
T cd05776 159 DTYLSAKELIRCKSYDLTELSQQVLGIE 186 (234)
T ss_pred ccHHHHHHHhCCCCCChHHHHHHHhCcC
Confidence 7777777776667899999997 67753
No 85
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=94.89 E-value=0.035 Score=48.54 Aligned_cols=171 Identities=19% Similarity=0.180 Sum_probs=101.2
Q ss_pred eEEEEEEccCCCCCC-----C-------------CCCCcEEEEceEEEECCCCEE----EeEEEEeecCCCCCCCChhhH
Q 036883 3 YYVVIDFEATCDKER-----N-------------LHPQEIIEFPSVVVSGVSGEI----IACFQTYVRPTFEPLLTDFCK 60 (277)
Q Consensus 3 ~~vviDlETTg~~~~-----~-------------~~~~eIIEIgAV~vd~~~g~i----~~~f~~lVrP~~~~~i~~~~~ 60 (277)
++|-+|+|..|.--. + ..--.||++|..+-|..+++- .-.|+.-..|+. .-...+..
T Consensus 43 n~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQlGlsLSDe~GN~P~~~sTWQFNF~F~l~~-dmya~ESi 121 (299)
T COG5228 43 NHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDENGNKPNGPSTWQFNFEFDLKK-DMYATESI 121 (299)
T ss_pred CceeeccccCceeecccccccccchHHHHHHhcccchhhhhheeeeeccccCCCCCCCceeEEEEEecchh-hhcchHHH
Confidence 467889998875211 0 122379999999988433322 345666667764 22344444
Q ss_pred hH---hCCChHHHhC-CCCHHHHHHHHHHHHhhcCCCC-CcEEEEE-eccchHHHHHHHHHHHhCCCCCC----------
Q 036883 61 EL---TGIQQHQVDN-GITLGEALYFHDKWLLQMGLNN-TNFSVVT-WSDWDCQVMLESECRIKKIQKPA---------- 124 (277)
Q Consensus 61 ~l---tGIt~~~l~~-ap~f~evl~~f~~fl~~~~l~~-~~~~vv~-~~~fDl~~~L~~~~~~~gi~~p~---------- 124 (277)
++ .||.-+.-++ +.. ..+|.+.|-+++|+- .....++ |+.+|+ .+|-+.+.. .++|.
T Consensus 122 eLL~ksgIdFkkHe~~GI~----v~eF~elLm~SGLvm~e~VtWitfHsaYDf-gyLikilt~--~plP~~~EdFy~~l~ 194 (299)
T COG5228 122 ELLRKSGIDFKKHENLGID----VFEFSELLMDSGLVMDESVTWITFHSAYDF-GYLIKILTN--DPLPNNKEDFYWWLH 194 (299)
T ss_pred HHHHHcCCChhhHhhcCCC----HHHHHHHHhccCceeccceEEEEeecchhH-HHHHHHHhc--CCCCccHHHHHHHHH
Confidence 43 4555443322 332 245666666776642 2233444 677897 677665553 34442
Q ss_pred -CCcchhhhHHHHhHhcCCCCCCHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHHh
Q 036883 125 -YFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQGRVHCGLDDAINIARLLSVIMRR 182 (277)
Q Consensus 125 -~~~~~iDl~~~~~~~~~~~~~~L~~l~~~~gi~~~~~~H~Al~DA~~ta~l~~~l~~~ 182 (277)
++..+.|+.-+++.... .+..|.+...-++|...+..|.|-.||+.||..|-.....
T Consensus 195 ~yfP~fYDik~v~ks~~~-~~KglQei~ndlql~r~g~QhQagsdaLlTa~~ff~~R~~ 252 (299)
T COG5228 195 QYFPNFYDIKLVYKSVLN-NSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRFS 252 (299)
T ss_pred HHCccccchHHHHHhhhh-hhhHHHHhcCcHhhhccchhhhccchhhhhhHHhcchhhh
Confidence 23334455544443322 1246778888888888888999999999999987654433
No 86
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=94.57 E-value=1.4 Score=41.57 Aligned_cols=129 Identities=16% Similarity=0.139 Sum_probs=76.4
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYF 82 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~ 82 (277)
.+|.||+||.+. .++.++..=| .+.++ ++ -.+|+|.. + + .+.++|
T Consensus 18 ~~iAiDTEf~r~---~t~~p~LcLI--Qi~~~-e~------~~lIdpl~-~-~---------------~d~~~l------ 62 (361)
T COG0349 18 KAIAIDTEFMRL---RTYYPRLCLI--QISDG-EG------ASLIDPLA-G-I---------------LDLPPL------ 62 (361)
T ss_pred CceEEecccccc---cccCCceEEE--EEecC-CC------ceEecccc-c-c---------------cccchH------
Confidence 479999999975 4555544333 22231 22 25777753 1 1 112333
Q ss_pred HHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCC-CCCHHHHH-HHhCCCCCC
Q 036883 83 HDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDV-RCNLKEAV-ELAGLIWQG 160 (277)
Q Consensus 83 f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~-~~~L~~l~-~~~gi~~~~ 160 (277)
..++.+..+ .-|.|.++||+ .+|...| |+. | ...+|++. ..++.|.. +++|++|+ +.+|+..+.
T Consensus 63 -~~Ll~d~~v----~KIfHaa~~DL-~~l~~~~---g~~-p---~plfdTqi-Aa~l~g~~~~~gl~~Lv~~ll~v~ldK 128 (361)
T COG0349 63 -VALLADPNV----VKIFHAARFDL-EVLLNLF---GLL-P---TPLFDTQI-AAKLAGFGTSHGLADLVEELLGVELDK 128 (361)
T ss_pred -HHHhcCCce----eeeeccccccH-HHHHHhc---CCC-C---CchhHHHH-HHHHhCCcccccHHHHHHHHhCCcccc
Confidence 334444321 22668889998 5666444 432 2 23567664 44555644 89999998 567776542
Q ss_pred CCCc----------------hHHHHHHHHHHHHHHHH
Q 036883 161 RVHC----------------GLDDAINIARLLSVIMR 181 (277)
Q Consensus 161 ~~H~----------------Al~DA~~ta~l~~~l~~ 181 (277)
.|. |..|+..+..|+.+|.+
T Consensus 129 -~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~ 164 (361)
T COG0349 129 -SEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTE 164 (361)
T ss_pred -cccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 222 68899999999888865
No 87
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=94.43 E-value=0.49 Score=51.53 Aligned_cols=170 Identities=16% Similarity=0.130 Sum_probs=96.5
Q ss_pred eEEEEEEccCCCCCCC--CCCCcEEEEceEEEECCCCEEE---------eEEEEeecCCCCCCCChhhHhHhCCChHHHh
Q 036883 3 YYVVIDFEATCDKERN--LHPQEIIEFPSVVVSGVSGEII---------ACFQTYVRPTFEPLLTDFCKELTGIQQHQVD 71 (277)
Q Consensus 3 ~~vviDlETTg~~~~~--~~~~eIIEIgAV~vd~~~g~i~---------~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~ 71 (277)
.+++||+|||-+.-.. ...++|.=|.. ++|+.+.-|+ +.|..-=||+. .-+| -+-
T Consensus 247 ~VlAFDIETtKlPLKFPDae~DqIMMISY-MiDGqGfLItNREiVs~DIedfEYTPKpE~---eG~F----------~v~ 312 (2173)
T KOG1798|consen 247 RVLAFDIETTKLPLKFPDAESDQIMMISY-MIDGQGFLITNREIVSEDIEDFEYTPKPEY---EGPF----------CVF 312 (2173)
T ss_pred eEEEEeeecccCCCCCCCcccceEEEEEE-EecCceEEEechhhhccchhhcccCCcccc---ccce----------EEe
Confidence 4678999999864323 35688888854 5575432221 22333333332 1111 134
Q ss_pred CCCCHHHHHHHHHHHHhhcCCCCCcEEEEE-ecc-chHHHHHHHHHHHhCCCCCC---CC--------cch---hhhHHH
Q 036883 72 NGITLGEALYFHDKWLLQMGLNNTNFSVVT-WSD-WDCQVMLESECRIKKIQKPA---YF--------NQW---INLRVP 135 (277)
Q Consensus 72 ~ap~f~evl~~f~~fl~~~~l~~~~~~vv~-~~~-fDl~~~L~~~~~~~gi~~p~---~~--------~~~---iDl~~~ 135 (277)
+-++-...+.+|.+-+.+. +..++|| ||+ || +.|+++....+|+.+-. +. .++ .|.-..
T Consensus 313 Ne~dEv~Ll~RfFeHiq~~----kP~iivTyNGDFFD-WPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrW 387 (2173)
T KOG1798|consen 313 NEPDEVGLLQRFFEHIQEV----KPTIIVTYNGDFFD-WPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRW 387 (2173)
T ss_pred cCCcHHHHHHHHHHHHHhc----CCcEEEEecCcccc-chhhHHHHHhcCCCcchhcCceecccccccccceeehhhhhh
Confidence 5667788889988888764 3456777 675 79 69999999999987531 10 011 121111
Q ss_pred HhH--hcCCCCCCHHHHH-HHhCCCCC-------------CCCCc---hHHHHHHHHHHHHHHHHhcCccCcCccc
Q 036883 136 FSK--VFGDVRCNLKEAV-ELAGLIWQ-------------GRVHC---GLDDAINIARLLSVIMRRGFKFSITKSL 192 (277)
Q Consensus 136 ~~~--~~~~~~~~L~~l~-~~~gi~~~-------------~~~H~---Al~DA~~ta~l~~~l~~~g~~~~i~~~l 192 (277)
.++ +++..+.+|+.+. .++|.... .-.|- ...||.+|..||.+...- +.|.....+
T Consensus 388 VKRDSYLPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVhP-FIFsLctII 462 (2173)
T KOG1798|consen 388 VKRDSYLPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVHP-FIFSLCTII 462 (2173)
T ss_pred hhhcccCCCcccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhhh-HHhhhhhcc
Confidence 111 2344466777655 45664321 11233 378999999999887653 233444443
No 88
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.88 E-value=3.5 Score=44.98 Aligned_cols=143 Identities=15% Similarity=0.101 Sum_probs=88.3
Q ss_pred EEEEEEc--cCCCCCCCCCCCcEEEEceEEEECCC-----C--EEEeEEEEeecCCCCCCCC-hhhHhHhCCChHHHhCC
Q 036883 4 YVVIDFE--ATCDKERNLHPQEIIEFPSVVVSGVS-----G--EIIACFQTYVRPTFEPLLT-DFCKELTGIQQHQVDNG 73 (277)
Q Consensus 4 ~vviDlE--TTg~~~~~~~~~eIIEIgAV~vd~~~-----g--~i~~~f~~lVrP~~~~~i~-~~~~~ltGIt~~~l~~a 73 (277)
++++||- +.-+ +...++||.|..++..... . .....|...++|... .++ .+.....|+....|..-
T Consensus 506 l~vLdFsi~SlyP---si~~~~nl~iS~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~~-~~p~~~~~~~~~~~~~~L~~~ 581 (1172)
T TIGR00592 506 LVVLDFSMKSLNP---SIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKDC-SFPLDLKGEFPGKKPSLVEDL 581 (1172)
T ss_pred eEEEEeeeEEecC---ccccCceEEEEEEEeecccccCCCCCCccceEEEEEEccCCC-CCCchhhhhhhccCCcEEEEe
Confidence 6666665 4421 2346899999888765200 1 122345556677321 122 23335567777778888
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCcEEEEEec-cchHHHHHHHHHHHhCCCC----------CCC---------CcchhhhH
Q 036883 74 ITLGEALYFHDKWLLQMGLNNTNFSVVTWS-DWDCQVMLESECRIKKIQK----------PAY---------FNQWINLR 133 (277)
Q Consensus 74 p~f~evl~~f~~fl~~~~l~~~~~~vv~~~-~fDl~~~L~~~~~~~gi~~----------p~~---------~~~~iDl~ 133 (277)
.+-.+.+..|++++..... +.++.++. +||+ .+|-.-+...+++. +.+ ..-.+|+.
T Consensus 582 ~sEr~lL~~fl~~~~~~DP---Dii~g~n~~qfdl-kvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~ 657 (1172)
T TIGR00592 582 ATERALIKKFMAKVKKIDP---DEIVGHDYQQRAL-KVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVE 657 (1172)
T ss_pred cCHHHHHHHHHHHHHhcCC---CEEEEEcccCccH-HHHHHHHHHcCCCcccccCccccCCCccccccceECCEEEEEHH
Confidence 8899999999999985421 24455554 7998 56666666666642 000 11246777
Q ss_pred HHHhHhcCCCCCCHHHHHHHh
Q 036883 134 VPFSKVFGDVRCNLKEAVELA 154 (277)
Q Consensus 134 ~~~~~~~~~~~~~L~~l~~~~ 154 (277)
..++..+...+++|++++.++
T Consensus 658 ~~~k~~~~~~sy~L~~v~~~~ 678 (1172)
T TIGR00592 658 ISAKELIRCKSYDLSELVQQI 678 (1172)
T ss_pred HHHHHHhCcCCCCHHHHHHHH
Confidence 777777777789999988643
No 89
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=93.83 E-value=0.086 Score=47.51 Aligned_cols=148 Identities=9% Similarity=-0.040 Sum_probs=90.7
Q ss_pred CcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCC--CCHHHHHHHHHHHHhhc-CCCCCcEE
Q 036883 22 QEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNG--ITLGEALYFHDKWLLQM-GLNNTNFS 98 (277)
Q Consensus 22 ~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~a--p~f~evl~~f~~fl~~~-~l~~~~~~ 98 (277)
..+++|.+.-+. .+.+ ..++.+|.+.. ++....-.+ +++++..+ +.-.+...-|..+.+.+ +-.+++.-
T Consensus 130 ~~dfpil~qela--~lg~-~lpq~lvcvds---lpa~~ald~--a~s~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e 201 (318)
T KOG4793|consen 130 EYDFPILAQELA--GLGY-SLPQDLVCVDS---LPALNALDR--ANSMVTRPEVRRMYSLGSIFLRYVEQREPPAGHVAE 201 (318)
T ss_pred ccccHHHHHHHH--hcCc-cchhhhcCcch---hHHHHHHhh--hcCcccCCCCCcccccchHHHhhhcccCCCcceeee
Confidence 445555555442 2222 56788888873 443322222 45555433 33444445566666663 33333333
Q ss_pred EEEec-cchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhH------hcCC--CCCCHHHHHHHhCCCCCCCCCchHHHH
Q 036883 99 VVTWS-DWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSK------VFGD--VRCNLKEAVELAGLIWQGRVHCGLDDA 169 (277)
Q Consensus 99 vv~~~-~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~------~~~~--~~~~L~~l~~~~gi~~~~~~H~Al~DA 169 (277)
.-+++ .|++ .|..+++-+.+-+.+ ..|.-++.+|.. .++. ..++|+.++.++.+..+..+|+|+.|+
T Consensus 202 ~d~~~l~~~f-qf~~~ellR~~deqa---~pw~~ir~l~~~~~~a~~~~P~p~~vs~le~Lat~~~~~p~l~ahra~~Dv 277 (318)
T KOG4793|consen 202 GDVNGLLFIF-QFRINELLRWSDEQA---RPWLLIRPLYLARENAKSVEPTPKLVSSLEALATYYSLTPELDAHRALSDV 277 (318)
T ss_pred cccchhHHHH-HHHHHHHHhhHhhcC---CCcccccchhhhhhhccccCCCCccchhHHHHHHHhhcCcccchhhhcccc
Confidence 33344 5786 788999888775554 235566666631 1221 247899999999998888899999999
Q ss_pred HHHHHHHHHHHH
Q 036883 170 INIARLLSVIMR 181 (277)
Q Consensus 170 ~~ta~l~~~l~~ 181 (277)
..+.++++++-.
T Consensus 278 ~~~~k~~q~~~i 289 (318)
T KOG4793|consen 278 LLLSKVFQKLTI 289 (318)
T ss_pred chhhhHHHHhhh
Confidence 999999998743
No 90
>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=93.21 E-value=1 Score=35.82 Aligned_cols=66 Identities=15% Similarity=0.073 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCC-CCCHHHHHHHh
Q 036883 77 GEALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDV-RCNLKEAVELA 154 (277)
Q Consensus 77 ~evl~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~-~~~L~~l~~~~ 154 (277)
.++...|.+|+++... ..++|+..+|+ .+|. ..++..+ ..++|+......+.+.. +++|+++++.|
T Consensus 40 ~~~~~~l~~~l~~~~~----~~v~~~~k~d~-~~L~----~~~~~~~---~~~~D~~~~ayll~~~~~~~~l~~l~~~~ 106 (155)
T cd00007 40 EEDLEALKELLEDEDI----TKVGHDAKFDL-VVLA----RDGIELP---GNIFDTMLAAYLLNPGEGSHSLDDLAKEY 106 (155)
T ss_pred HHHHHHHHHHHcCCCC----cEEeccHHHHH-HHHH----HCCCCCC---CCcccHHHHHHHhCCCCCcCCHHHHHHHH
Confidence 5677778888886521 24556778996 5764 3344443 35789877666655544 57999999876
No 91
>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=93.20 E-value=2.5 Score=36.12 Aligned_cols=140 Identities=12% Similarity=0.019 Sum_probs=78.2
Q ss_pred eEEEEEEccCCCCCC-CCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHH-
Q 036883 3 YYVVIDFEATCDKER-NLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEAL- 80 (277)
Q Consensus 3 ~~vviDlETTg~~~~-~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl- 80 (277)
.+|.||+|++..... ....-.+|||+. .+.+ .+|.+.. +.. .-.+.+
T Consensus 23 ~vig~D~Ew~~~~~~~~~~~v~LiQiat------~~~~-----~lid~~~---~~~-----------------~~~~~~~ 71 (193)
T cd06146 23 RVVGIDSEWKPSFLGDSDPRVAILQLAT------EDEV-----FLLDLLA---LEN-----------------LESEDWD 71 (193)
T ss_pred CEEEEECccCCCccCCCCCCceEEEEec------CCCE-----EEEEchh---ccc-----------------cchHHHH
Confidence 478999999864321 124567888862 1111 2444431 111 002222
Q ss_pred HHHHHHHhhcCCCCCcEE-EEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcC-----------CCCCCHH
Q 036883 81 YFHDKWLLQMGLNNTNFS-VVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFG-----------DVRCNLK 148 (277)
Q Consensus 81 ~~f~~fl~~~~l~~~~~~-vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~-----------~~~~~L~ 148 (277)
..+.+++++. +++ |.++...|+ ..|.+.+...+- .+......+|++.++..+.+ ....+|.
T Consensus 72 ~~L~~ll~d~-----~i~KVg~~~~~D~-~~L~~~~~~~~~-~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~ 144 (193)
T cd06146 72 RLLKRLFEDP-----DVLKLGFGFKQDL-KALSASYPALKC-MFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLA 144 (193)
T ss_pred HHHHHHhCCC-----CeeEEEechHHHH-HHHHHhcCcccc-ccccCCceEEHHHHHHHHhhccccccccccCcccCCHH
Confidence 3345566654 233 345567897 577654432210 00112568899887765432 2357999
Q ss_pred HHHHHh-CCCCC---------C------CCCchHHHHHHHHHHHHHHH
Q 036883 149 EAVELA-GLIWQ---------G------RVHCGLDDAINIARLLSVIM 180 (277)
Q Consensus 149 ~l~~~~-gi~~~---------~------~~H~Al~DA~~ta~l~~~l~ 180 (277)
++++.+ |.+.. . .-+=|..||+.+..|+.+|.
T Consensus 145 ~l~~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 145 DLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred HHHHHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 999764 54321 1 12447899999999999885
No 92
>PHA02528 43 DNA polymerase; Provisional
Probab=92.94 E-value=6 Score=41.88 Aligned_cols=165 Identities=12% Similarity=0.013 Sum_probs=87.8
Q ss_pred eEEEEEEccCCCCCC-CCC--CCcEEEEceEEEECCCCEEEeEEEEeecCCCCC-CCChhhHhHhCCChHHHhCCCCHHH
Q 036883 3 YYVVIDFEATCDKER-NLH--PQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEP-LLTDFCKELTGIQQHQVDNGITLGE 78 (277)
Q Consensus 3 ~~vviDlETTg~~~~-~~~--~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~-~i~~~~~~ltGIt~~~l~~ap~f~e 78 (277)
+.+.||+||+...+. +|. .++||.||.. +..+.++ ..+.-+...+ ..........-.....+..-.+-.+
T Consensus 107 rv~s~DIE~~~~~gfP~p~~~~d~IisIsl~--~~~~~~~----~v~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~sE~e 180 (881)
T PHA02528 107 RIANLDIEVTAEDGFPDPEEAKYEIDAITHY--DSIDDRF----YVFDLGSVEEWDAKGDEVPQEILDKVVYMPFDTERE 180 (881)
T ss_pred cEEEEEEEECCCCCCCCcccCCCcEEEEEEe--cCCCCEE----EEEEecCcccccccCCcccccccCCeeEEEcCCHHH
Confidence 468899999864332 233 5699999873 4222222 2222111000 0000000000000111122467899
Q ss_pred HHHHHHHHHhhcCCCCCcEEEEEec--cchHHHHHHHHHHH-hCCCC----CCC------------C----------cch
Q 036883 79 ALYFHDKWLLQMGLNNTNFSVVTWS--DWDCQVMLESECRI-KKIQK----PAY------------F----------NQW 129 (277)
Q Consensus 79 vl~~f~~fl~~~~l~~~~~~vv~~~--~fDl~~~L~~~~~~-~gi~~----p~~------------~----------~~~ 129 (277)
.+.+|.+|+..... -+|+.|. .||+ .+|.+-+.+ .|+.. .++ . .-.
T Consensus 181 LL~~F~~~i~~~DP----DII~GyNi~~FDl-pYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~GRv~ 255 (881)
T PHA02528 181 MLLEYINFWEENTP----VIFTGWNVELFDV-PYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISGISI 255 (881)
T ss_pred HHHHHHHHHHHhCC----cEEEecCCccCCH-HHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcceEE
Confidence 99999999977532 2556553 7998 677666664 35331 100 0 013
Q ss_pred hhhHHHHhHh-c-CCCCCCHHHHHHH-hCCCCCCC----------------CCchHHHHHHHHHHHHH
Q 036883 130 INLRVPFSKV-F-GDVRCNLKEAVEL-AGLIWQGR----------------VHCGLDDAINIARLLSV 178 (277)
Q Consensus 130 iDl~~~~~~~-~-~~~~~~L~~l~~~-~gi~~~~~----------------~H~Al~DA~~ta~l~~~ 178 (277)
+|+..+++.+ + ...+++|++++++ +|.....- .+=.+.||..+.+|+.+
T Consensus 256 lD~~dl~k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 256 LDYLDLYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred EeHHHHHHHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 4555566553 2 3467999999984 77643210 01126799999998877
No 93
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=92.47 E-value=0.071 Score=55.01 Aligned_cols=110 Identities=22% Similarity=0.277 Sum_probs=76.5
Q ss_pred CCChhhHhHhCCChHHHhC------CCCHHHHHHHHHHHHhhcCCCCCcEEEEEec-cchHHHHHHHHHHHhCCCCCCCC
Q 036883 54 LLTDFCKELTGIQQHQVDN------GITLGEALYFHDKWLLQMGLNNTNFSVVTWS-DWDCQVMLESECRIKKIQKPAYF 126 (277)
Q Consensus 54 ~i~~~~~~ltGIt~~~l~~------ap~f~evl~~f~~fl~~~~l~~~~~~vv~~~-~fDl~~~L~~~~~~~gi~~p~~~ 126 (277)
.+.++-++..||-+.||+. -.++.-++.++.=.+.- + .++|.|| +-|.+ .| ++-.|+
T Consensus 972 ~VvDYLTqySGI~PGDLDp~~S~K~Lt~lK~~Y~Kl~~Li~~-G-----viFVGHGL~nDFr-vI-------Ni~Vp~-- 1035 (1118)
T KOG1275|consen 972 KVVDYLTQYSGIKPGDLDPTTSEKRLTTLKVLYLKLRLLIQR-G-----VIFVGHGLQNDFR-VI-------NIHVPE-- 1035 (1118)
T ss_pred HHHHHHHHhcCCCccccCCccCcceehhHHHHHHHHHHHHHc-C-----cEEEcccccccce-EE-------EEecCh--
Confidence 5788899999999999963 33466677776655543 2 4788887 55642 33 344442
Q ss_pred cchhhhHHHHhHhcCC-CCCCHHHHH-HHhCCCCCCCCCchHHHHHHHHHHHHHHHH
Q 036883 127 NQWINLRVPFSKVFGD-VRCNLKEAV-ELAGLIWQGRVHCGLDDAINIARLLSVIMR 181 (277)
Q Consensus 127 ~~~iDl~~~~~~~~~~-~~~~L~~l~-~~~gi~~~~~~H~Al~DA~~ta~l~~~l~~ 181 (277)
.+.+|+..+|. .|. +-.+|..|+ +.+|-.+.-.+|+.+.||+.+.+||++.++
T Consensus 1036 ~QiiDTv~lf~--~~s~R~LSLrfLa~~lLg~~IQ~~~HDSIeDA~taLkLYk~Yl~ 1090 (1118)
T KOG1275|consen 1036 EQIIDTVTLFR--LGSQRMLSLRFLAWELLGETIQMEAHDSIEDARTALKLYKKYLK 1090 (1118)
T ss_pred hhheeeeEEEe--cccccEEEHHHHHHHHhcchhhccccccHHHHHHHHHHHHHHHH
Confidence 34667665543 232 346899988 567877766789999999999999988765
No 94
>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=90.97 E-value=11 Score=35.72 Aligned_cols=87 Identities=11% Similarity=0.079 Sum_probs=50.5
Q ss_pred HHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCC-CCCCHHHHHHHh-CCCCC
Q 036883 82 FHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGD-VRCNLKEAVELA-GLIWQ 159 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~-~~~~L~~l~~~~-gi~~~ 159 (277)
.|.+++.+..+ ..+.|+...|+ .+|. +.+...| ...+|++.... +++. ...+|+.+++.| |+...
T Consensus 61 ~L~~lL~d~~i----~KV~h~~k~Dl-~~L~----~~~~~~~---~~~fDtqlAa~-lL~~~~~~~l~~Lv~~~Lg~~l~ 127 (367)
T TIGR01388 61 PLKELLRDESV----VKVLHAASEDL-EVFL----NLFGELP---QPLFDTQIAAA-FCGFGMSMGYAKLVQEVLGVELD 127 (367)
T ss_pred HHHHHHCCCCc----eEEEeecHHHH-HHHH----HHhCCCC---CCcccHHHHHH-HhCCCCCccHHHHHHHHcCCCCC
Confidence 34556665421 23556678887 4664 3333333 34678875433 3442 357999998664 66532
Q ss_pred CC------CCc---------hHHHHHHHHHHHHHHHH
Q 036883 160 GR------VHC---------GLDDAINIARLLSVIMR 181 (277)
Q Consensus 160 ~~------~H~---------Al~DA~~ta~l~~~l~~ 181 (277)
.. ..+ |..||..+..|+..|.+
T Consensus 128 K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~ 164 (367)
T TIGR01388 128 KSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLME 164 (367)
T ss_pred cccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 11 022 67888888888888764
No 95
>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=90.47 E-value=8.1 Score=31.77 Aligned_cols=130 Identities=15% Similarity=0.028 Sum_probs=75.8
Q ss_pred eEEEEEEccCCCCC-CCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHH
Q 036883 3 YYVVIDFEATCDKE-RNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALY 81 (277)
Q Consensus 3 ~~vviDlETTg~~~-~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~ 81 (277)
..|.||+|++.... ....+-.+|+|+. .+ . ..+|++.. + .....
T Consensus 19 ~~ig~D~E~~~~~~~~~~~~~~liQl~~-----~~-~-----~~l~~~~~---~---------------------~~~~~ 63 (170)
T cd06141 19 KVVGFDTEWRPSFRKGKRNKVALLQLAT-----ES-R-----CLLFQLAH---M---------------------DKLPP 63 (170)
T ss_pred CEEEEeCccCCccCCCCCCCceEEEEec-----CC-c-----EEEEEhhh---h---------------------hcccH
Confidence 57899999997431 0123566778761 11 1 23444431 1 11123
Q ss_pred HHHHHHhhcCCCCCcEE-EEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCC-CCCCHHHHHHHh-CCCC
Q 036883 82 FHDKWLLQMGLNNTNFS-VVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGD-VRCNLKEAVELA-GLIW 158 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~-vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~-~~~~L~~l~~~~-gi~~ 158 (277)
.|.+++.+.. .. +.++...|+ ..|. +.+|+... ..+|+...+....+. ...+|+++++.+ |+..
T Consensus 64 ~l~~ll~~~~-----i~kv~~~~k~D~-~~L~---~~~g~~~~----~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~ 130 (170)
T cd06141 64 SLKQLLEDPS-----ILKVGVGIKGDA-RKLA---RDFGIEVR----GVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPL 130 (170)
T ss_pred HHHHHhcCCC-----eeEEEeeeHHHH-HHHH---hHcCCCCC----CeeeHHHHHHHhCCCcCCccHHHHHHHHcCccc
Confidence 4556676542 23 445667886 4653 24566532 347988776665543 246999999775 6543
Q ss_pred C--C---------------CCCchHHHHHHHHHHHHHHH
Q 036883 159 Q--G---------------RVHCGLDDAINIARLLSVIM 180 (277)
Q Consensus 159 ~--~---------------~~H~Al~DA~~ta~l~~~l~ 180 (277)
. . .-|=|-.||+.+..|+..|.
T Consensus 131 ~k~k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 131 SKPKKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCCCCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 2 1 11447889999999998875
No 96
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=90.15 E-value=9.5 Score=39.95 Aligned_cols=130 Identities=14% Similarity=0.053 Sum_probs=81.0
Q ss_pred eEEEEEEccCCCCCCCCC--CCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHH
Q 036883 3 YYVVIDFEATCDKERNLH--PQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEAL 80 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~--~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl 80 (277)
.+++||+|+....+..+. .+.|+.|+...-. .++.. ..+.. ..... . .+....+-.+.+
T Consensus 155 ~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~-~~~~~-------~~~~~-~~~~~-------~---~v~~~~~e~e~l 215 (792)
T COG0417 155 RVLAFDIETLSEPGKFPDGEKDPIIMISYAIEA-EGGLI-------EVFIY-TSGEG-------F---SVEVVISEAELL 215 (792)
T ss_pred eEEEEEEEEecCCCCCCCccCCceEEEEEEecc-CCCcc-------ccccc-cCCCC-------c---eeEEecCHHHHH
Confidence 468999999987654433 6788888666432 22222 11111 00111 0 155566778999
Q ss_pred HHHHHHHhhcCCCCCcEEEEE-ec-cchHHHHHHHHHHHhCCCCCC-------------C----CcchhhhHHHHh-Hhc
Q 036883 81 YFHDKWLLQMGLNNTNFSVVT-WS-DWDCQVMLESECRIKKIQKPA-------------Y----FNQWINLRVPFS-KVF 140 (277)
Q Consensus 81 ~~f~~fl~~~~l~~~~~~vv~-~~-~fDl~~~L~~~~~~~gi~~p~-------------~----~~~~iDl~~~~~-~~~ 140 (277)
.+|.+++..... -++++ ++ .||+ .+|..-+...|++... + ...-+|+...++ +.+
T Consensus 216 ~~~~~~i~~~dP----dVIvgyn~~~fd~-pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~~~~~~ 290 (792)
T COG0417 216 ERFVELIREYDP----DVIVGYNGDNFDW-PYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPALRRRPL 290 (792)
T ss_pred HHHHHHHHhcCC----CEEEeccCCcCCh-HHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHHHhhhhc
Confidence 999999988632 24555 45 5996 7999999988887640 0 123467777766 455
Q ss_pred CCCCCCHHHHHHHhCC
Q 036883 141 GDVRCNLKEAVELAGL 156 (277)
Q Consensus 141 ~~~~~~L~~l~~~~gi 156 (277)
...+++|++.++.+..
T Consensus 291 ~~~~ysl~~v~~~~l~ 306 (792)
T COG0417 291 NLKSYSLEAVSEALLG 306 (792)
T ss_pred ccccccHHHHHHHhcc
Confidence 5567899988765543
No 97
>PHA03036 DNA polymerase; Provisional
Probab=88.80 E-value=8 Score=41.34 Aligned_cols=178 Identities=15% Similarity=0.073 Sum_probs=102.2
Q ss_pred eEEEEEEccCCCCCCC--CCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCC---------ChHHHh
Q 036883 3 YYVVIDFEATCDKERN--LHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGI---------QQHQVD 71 (277)
Q Consensus 3 ~~vviDlETTg~~~~~--~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGI---------t~~~l~ 71 (277)
.|+.||+|.-. ++.. +..+.|+.|+...++ +.|.. .--++++....+.-...-..+-|. .-..+-
T Consensus 161 ~~lsfDIEC~~-~g~FPs~~~~pvshIs~~~~~-~~~~~--~~~~l~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 236 (1004)
T PHA03036 161 SYLFLDIECHF-DKKFPSVFINPVSHISCCYID-LSGKE--KRFTLINEDMLSEDEIEEAVKRGYYEIESLLDMDYSKEL 236 (1004)
T ss_pred eeEEEEEEecc-CCCCCCcccCcceEEEEEEEe-cCCCe--eEEEEeccccccccccccceeeeeeccccccccCCceee
Confidence 58999999995 3433 456899999987777 34432 123566653211111111122222 111111
Q ss_pred CCCCHHHHHHHHHHHHhhcCCCCCcEEEEE-ec-cchHHHHHHHHHHHh---CCCCC-----------------------
Q 036883 72 NGITLGEALYFHDKWLLQMGLNNTNFSVVT-WS-DWDCQVMLESECRIK---KIQKP----------------------- 123 (277)
Q Consensus 72 ~ap~f~evl~~f~~fl~~~~l~~~~~~vv~-~~-~fDl~~~L~~~~~~~---gi~~p----------------------- 123 (277)
.-.+-.+ +.+|.+++.+... ++ |++ |+ .||++ .|..-+... ++.++
T Consensus 237 ~~~sE~~-ml~~~~~i~~~d~---D~-i~~yNg~nFD~~-Yi~~R~~~L~~~~~~~~~~~~~~~~~~~v~~r~~~s~~~~ 310 (1004)
T PHA03036 237 ILCSEIV-LLRIAKKLLELEF---DY-VVTFNGHNFDLR-YISNRLELLTGEKIIFRSPDGKETVHLCIYERNLSSHKGV 310 (1004)
T ss_pred ecCCHHH-HHHHHHHHHhcCC---CE-EEeccCCCcchH-HHHHHHHHhccCceeeccCCCcccccceeecccccccccc
Confidence 2244444 5577888877532 34 444 55 79995 554444332 11100
Q ss_pred ------------CCCcchhhhHHHHhHhcCCCCCCHHHHHHH-hCCC-----CCCC-CC---chHHHHHHHHHHHHHHHH
Q 036883 124 ------------AYFNQWINLRVPFSKVFGDVRCNLKEAVEL-AGLI-----WQGR-VH---CGLDDAINIARLLSVIMR 181 (277)
Q Consensus 124 ------------~~~~~~iDl~~~~~~~~~~~~~~L~~l~~~-~gi~-----~~~~-~H---~Al~DA~~ta~l~~~l~~ 181 (277)
....-++|+....++.+..++++|+++.+. |+.. ...+ -+ .-..||...+.+|...++
T Consensus 311 gg~~~~t~~i~~~~G~i~fDLy~~i~k~~~L~sYkL~~Vsk~~f~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~f~~vl~ 390 (1004)
T PHA03036 311 GGVANTTYHINNNNGTIFFDLYTFIQKTEKLDSYKLDSISKNAFNCNAKVLSENNNEVTFIGDNTTDAKGKASIFSEVLS 390 (1004)
T ss_pred CccccceEEecccCCeEEEEhHHHHhhhcCcccccHHHHHHHhhccceeeeecCCceeEEccCcccccccchhhhhhhhc
Confidence 001235688888888888889999999876 4331 0000 00 113688899999999999
Q ss_pred hcCccCcCc
Q 036883 182 RGFKFSITK 190 (277)
Q Consensus 182 ~g~~~~i~~ 190 (277)
-|.-.+|++
T Consensus 391 t~ny~~i~~ 399 (1004)
T PHA03036 391 TGNYVTIND 399 (1004)
T ss_pred ccceeeecc
Confidence 888888887
No 98
>PRK05761 DNA polymerase I; Reviewed
Probab=87.99 E-value=2.7 Score=43.92 Aligned_cols=97 Identities=19% Similarity=0.067 Sum_probs=61.6
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCcEEEEEec-cchHHHHHHHHHHHhCCCCCCCCcc------hhhhHHHHhHh----c--
Q 036883 74 ITLGEALYFHDKWLLQMGLNNTNFSVVTWS-DWDCQVMLESECRIKKIQKPAYFNQ------WINLRVPFSKV----F-- 140 (277)
Q Consensus 74 p~f~evl~~f~~fl~~~~l~~~~~~vv~~~-~fDl~~~L~~~~~~~gi~~p~~~~~------~iDl~~~~~~~----~-- 140 (277)
.+-.+.+.+|.+|+.... ..|..|+ .||+ .+|..-+..+|++...+... .+|+...+... +
T Consensus 208 ~~E~eLL~~f~~~i~~~d-----Pdi~yN~~~FDl-PYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~~~~~y~~ 281 (787)
T PRK05761 208 DSEKELLAELFDIILEYP-----PVVTFNGDNFDL-PYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNKAVRSYAF 281 (787)
T ss_pred CCHHHHHHHHHHHHHhcC-----CEEEEcCCcchH-HHHHHHHHHhCCCchhcccccCCCceEEechhheeecceeeeec
Confidence 678999999999999864 2344455 6998 78988888888865311111 15554443321 1
Q ss_pred -C---CCCCCHHHHHH-HhCCCCCCCC------------CchHHHHHHHHHHH
Q 036883 141 -G---DVRCNLKEAVE-LAGLIWQGRV------------HCGLDDAINIARLL 176 (277)
Q Consensus 141 -~---~~~~~L~~l~~-~~gi~~~~~~------------H~Al~DA~~ta~l~ 176 (277)
+ .++++|+.+++ .+|....... .=.+.||..|.+|+
T Consensus 282 ~~~~~~~~ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 282 YGKYRHREARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred cceeecccCChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 1 12578999887 6776532110 11378999998874
No 99
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=87.32 E-value=12 Score=30.15 Aligned_cols=90 Identities=14% Similarity=0.120 Sum_probs=53.8
Q ss_pred HHHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCCC-CCHHHHHHHh-CCC
Q 036883 80 LYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVR-CNLKEAVELA-GLI 157 (277)
Q Consensus 80 l~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~~-~~L~~l~~~~-gi~ 157 (277)
+..+.+|+++... ..++++..+|+ .+|. ++|+..+ ..+|++..+..+.+... .+|+++++.+ ++.
T Consensus 64 ~~~l~~~l~~~~~----~kv~~d~k~~~-~~L~----~~gi~~~----~~~D~~laayll~p~~~~~~l~~l~~~~l~~~ 130 (172)
T smart00474 64 LEILKDLLEDETI----TKVGHNAKFDL-HVLA----RFGIELE----NIFDTMLAAYLLLGGPSKHGLATLLKEYLGVE 130 (172)
T ss_pred HHHHHHHhcCCCc----eEEEechHHHH-HHHH----HCCCccc----chhHHHHHHHHHcCCCCcCCHHHHHHHHhCCC
Confidence 4556677776421 23556778886 5664 3677654 24898776655555433 6999998765 554
Q ss_pred CCC---C--------CC----chHHHHHHHHHHHHHHHHh
Q 036883 158 WQG---R--------VH----CGLDDAINIARLLSVIMRR 182 (277)
Q Consensus 158 ~~~---~--------~H----~Al~DA~~ta~l~~~l~~~ 182 (277)
.+. . .. -|..||.++.+|+..|.++
T Consensus 131 ~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~ 170 (172)
T smart00474 131 LDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKE 170 (172)
T ss_pred CCcccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 211 0 01 1556677777777776553
No 100
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=87.10 E-value=8.7 Score=37.97 Aligned_cols=139 Identities=12% Similarity=-0.071 Sum_probs=74.4
Q ss_pred eEEEEEEccCCCCCCCC----CCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChh--hHhHhCCChHHHhCCCCH
Q 036883 3 YYVVIDFEATCDKERNL----HPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDF--CKELTGIQQHQVDNGITL 76 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~----~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~--~~~ltGIt~~~l~~ap~f 76 (277)
++..||+|+|+.+ .| ...+|..|.-.-.. ...++|..+.=........+. .....-+..-.+-.-++-
T Consensus 107 ~~~~~DIEv~~~~--fp~~~~a~~~i~~i~~~d~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~f~sE 180 (498)
T PHA02524 107 VIDVVDIEVTAPE--FPEPKYAKYEIDMISHVRLH----NGKKTYYIFDLVKDVGHWDPKKSVLEKYILDNVVYMPFEDE 180 (498)
T ss_pred eEEEEEEEecCCC--CCChhhcCCceEEEEeeecc----cCCccEEEEeccccccCCCcccccccccccCCeEEEEeCCH
Confidence 4678999999853 23 23567666444221 112334443211100011111 110011222233457788
Q ss_pred HHHHHHHHHHHhhcCCCCCcEEEEEec--cchHHHHHHHHHH-HhCCCC----CCCC---------------------cc
Q 036883 77 GEALYFHDKWLLQMGLNNTNFSVVTWS--DWDCQVMLESECR-IKKIQK----PAYF---------------------NQ 128 (277)
Q Consensus 77 ~evl~~f~~fl~~~~l~~~~~~vv~~~--~fDl~~~L~~~~~-~~gi~~----p~~~---------------------~~ 128 (277)
.+.|.+|.+|+.+... -+|+.|. .||+ .+|.+-++ ..|+.. ..+. .-
T Consensus 181 ~eLL~~F~~~i~~~DP----DIItGYNi~nFDl-PYL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~~~G~~~~~~I~GRv 255 (498)
T PHA02524 181 VDLLLNYIQLWKANTP----DLVFGWNSEGFDI-PYIITRITNILGEKAANQLSPYGKITSKTITNLYGEKIIYKIHGIA 255 (498)
T ss_pred HHHHHHHHHHHHHhCC----CEEEeCCCcccCH-HHHHHHHHHHhCCccccccccccccccccceeecCceeEEEEeeEE
Confidence 9999999999988632 2455553 7998 57766664 356531 1110 01
Q ss_pred hhhhHHHHhHh--cCCCCCCHHHHHH
Q 036883 129 WINLRVPFSKV--FGDVRCNLKEAVE 152 (277)
Q Consensus 129 ~iDl~~~~~~~--~~~~~~~L~~l~~ 152 (277)
.+|+..++++. ...++++|+++++
T Consensus 256 ~iDl~~l~kk~s~~~l~sYsL~~Vs~ 281 (498)
T PHA02524 256 LMDYMDVFKKFSFTPMPDYKLGNVGY 281 (498)
T ss_pred EeEHHHHHHHhhhccCCCCCHHHHHH
Confidence 34667777764 4567899999876
No 101
>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=79.73 E-value=20 Score=29.39 Aligned_cols=86 Identities=10% Similarity=-0.085 Sum_probs=52.5
Q ss_pred HHHHHHhhcCCCCCcEE-EEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCCCCCHHHHHHHh-CCCCC
Q 036883 82 FHDKWLLQMGLNNTNFS-VVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELA-GLIWQ 159 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~-vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~~~~L~~l~~~~-gi~~~ 159 (277)
.+.+++++. +.. +.++...|+ ..|.+ .+|+.. ...+|++..+..+-...+.+|+++++.+ |+..+
T Consensus 58 ~L~~lL~d~-----~i~Kvg~~~k~D~-~~L~~---~~gi~~----~~~~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~ 124 (161)
T cd06129 58 GLKMLLENP-----SIVKALHGIEGDL-WKLLR---DFGEKL----QRLFDTTIAANLKGLPERWSLASLVEHFLGKTLD 124 (161)
T ss_pred HHHHHhCCC-----CEEEEEeccHHHH-HHHHH---HcCCCc----ccHhHHHHHHHHhCCCCCchHHHHHHHHhCCCCC
Confidence 344566654 233 345557786 45532 356653 2358988765543222357999999875 76431
Q ss_pred ---------C------CCCchHHHHHHHHHHHHHHH
Q 036883 160 ---------G------RVHCGLDDAINIARLLSVIM 180 (277)
Q Consensus 160 ---------~------~~H~Al~DA~~ta~l~~~l~ 180 (277)
. .-|=|..||+.+..|+.+|.
T Consensus 125 K~~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 125 KSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred ccceeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 1 12557899999999998875
No 102
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.65 E-value=10 Score=40.18 Aligned_cols=95 Identities=11% Similarity=-0.007 Sum_probs=58.6
Q ss_pred CHHHHHHHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCCCCCHHHHHHHh
Q 036883 75 TLGEALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELA 154 (277)
Q Consensus 75 ~f~evl~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~~~~L~~l~~~~ 154 (277)
+..+++..|..|+++... ..+.|+..||+ .+|. ++|+..+ ..+.|++-....+-+...++|+++++.|
T Consensus 362 ~~~~~~~~l~~~l~~~~~----~~v~~n~K~d~-~~l~----~~gi~~~---~~~~Dt~la~yll~~~~~~~l~~la~~y 429 (887)
T TIGR00593 362 LTILTDDKFARWLLNEQI----KKIGHDAKFLM-HLLK----REGIELG---GVIFDTMLAAYLLDPAQVSTLDTLARRY 429 (887)
T ss_pred hhHHHHHHHHHHHhCCCC----cEEEeeHHHHH-HHHH----hCCCCCC---CcchhHHHHHHHcCCCCCCCHHHHHHHH
Confidence 355677888899987532 24678889997 5764 6787764 2467876554444444456999988665
Q ss_pred -CCCC---C---CC-----C-------CchHHHHHHHHHHHHHHHH
Q 036883 155 -GLIW---Q---GR-----V-------HCGLDDAINIARLLSVIMR 181 (277)
Q Consensus 155 -gi~~---~---~~-----~-------H~Al~DA~~ta~l~~~l~~ 181 (277)
+... . +. . .-|-.||.+|.+|+..+..
T Consensus 430 l~~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~ 475 (887)
T TIGR00593 430 LVEELILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLK 475 (887)
T ss_pred cCcccccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3210 0 00 0 1255678888877776643
No 103
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=71.66 E-value=8.1 Score=31.15 Aligned_cols=61 Identities=15% Similarity=0.088 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHHhhc-CCCCCcEEEEEeccchHHHHHHHHHHHhC-C--CCCCCCcchhhhHHHHhHh
Q 036883 73 GITLGEALYFHDKWLLQM-GLNNTNFSVVTWSDWDCQVMLESECRIKK-I--QKPAYFNQWINLRVPFSKV 139 (277)
Q Consensus 73 ap~f~evl~~f~~fl~~~-~l~~~~~~vv~~~~fDl~~~L~~~~~~~g-i--~~p~~~~~~iDl~~~~~~~ 139 (277)
..+-.+.+..|.+-|+.. + .+||.+.+|. +..|++-+...- + .+-....+.+||..+|+..
T Consensus 54 ~DPr~~~~~~L~~~i~~~~g-----~ivvyN~sfE-~~rL~ela~~~p~~~~~l~~I~~r~vDL~~~f~~~ 118 (130)
T PF11074_consen 54 EDPRRELIEALIKAIGSIYG-----SIVVYNKSFE-KTRLKELAELFPDYAEKLNSIIERTVDLLDPFKNH 118 (130)
T ss_pred CCchHHHHHHHHHHhhhhcC-----eEEEechHHH-HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 445677788888888775 3 4566677798 577776544320 0 0001234677887777663
No 104
>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=71.04 E-value=55 Score=26.61 Aligned_cols=91 Identities=14% Similarity=0.067 Sum_probs=51.1
Q ss_pred HHHHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHh-CCCCCCCCcchhhhHHHHhHhcCCCCCCHHHHHHH-hCC
Q 036883 79 ALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIK-KIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVEL-AGL 156 (277)
Q Consensus 79 vl~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~-gi~~p~~~~~~iDl~~~~~~~~~~~~~~L~~l~~~-~gi 156 (277)
+...|.+++++... ..++++..+|+ ..|. ++ |+. + ....|+.-....+-+..+.+|+++++. +++
T Consensus 52 ~~~~l~~ll~~~~i----~kv~~d~K~~~-~~L~----~~~gi~-~---~~~~D~~laayLl~p~~~~~l~~l~~~~l~~ 118 (178)
T cd06142 52 DLSPLKELLADPNI----VKVFHAAREDL-ELLK----RDFGIL-P---QNLFDTQIAARLLGLGDSVGLAALVEELLGV 118 (178)
T ss_pred cHHHHHHHHcCCCc----eEEEeccHHHH-HHHH----HHcCCC-C---CCcccHHHHHHHhCCCccccHHHHHHHHhCC
Confidence 34446667776421 23455667775 4553 33 766 3 345788654444333344699999875 465
Q ss_pred CCC-----CC---C-------CchHHHHHHHHHHHHHHHHh
Q 036883 157 IWQ-----GR---V-------HCGLDDAINIARLLSVIMRR 182 (277)
Q Consensus 157 ~~~-----~~---~-------H~Al~DA~~ta~l~~~l~~~ 182 (277)
... ++ . +-+-.||.++..|+..|.++
T Consensus 119 ~~~~~~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~ 159 (178)
T cd06142 119 ELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEE 159 (178)
T ss_pred CCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 421 00 0 02556677788887777653
No 105
>PRK10829 ribonuclease D; Provisional
Probab=69.03 E-value=52 Score=31.32 Aligned_cols=129 Identities=14% Similarity=0.168 Sum_probs=76.9
Q ss_pred eEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHH
Q 036883 3 YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYF 82 (277)
Q Consensus 3 ~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~ 82 (277)
..+.||+|+..... ....--+|+|+ + ... ..+|.|.. +.+ +..
T Consensus 23 ~~lalDtEf~~~~t-y~~~l~LiQl~----~--~~~-----~~LiD~l~---~~d----------------------~~~ 65 (373)
T PRK10829 23 PAIALDTEFVRTRT-YYPQLGLIQLY----D--GEQ-----LSLIDPLG---ITD----------------------WSP 65 (373)
T ss_pred CeEEEecccccCcc-CCCceeEEEEe----c--CCc-----eEEEecCC---ccc----------------------hHH
Confidence 46899999996432 11234556664 2 111 24677752 211 233
Q ss_pred HHHHHhhcCCCCCcEE-EEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCC-CCCHHHHHH-HhCCCCC
Q 036883 83 HDKWLLQMGLNNTNFS-VVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDV-RCNLKEAVE-LAGLIWQ 159 (277)
Q Consensus 83 f~~fl~~~~l~~~~~~-vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~-~~~L~~l~~-~~gi~~~ 159 (277)
|.+++.+.. .+ |.|.+.+|+ .+|.+ ..|+. | ...+|++... .+.|.. +.+|..|++ ++|+..+
T Consensus 66 L~~ll~~~~-----ivKV~H~~~~Dl-~~l~~---~~g~~-p---~~~fDTqiaa-~~lg~~~~~gl~~Lv~~~lgv~ld 131 (373)
T PRK10829 66 FKALLRDPQ-----VTKFLHAGSEDL-EVFLN---AFGEL-P---QPLIDTQILA-AFCGRPLSCGFASMVEEYTGVTLD 131 (373)
T ss_pred HHHHHcCCC-----eEEEEeChHhHH-HHHHH---HcCCC-c---CCeeeHHHHH-HHcCCCccccHHHHHHHHhCCccC
Confidence 555666643 33 456678998 56643 44653 2 3477886544 456644 689999885 5777532
Q ss_pred C---------C------CCchHHHHHHHHHHHHHHHHh
Q 036883 160 G---------R------VHCGLDDAINIARLLSVIMRR 182 (277)
Q Consensus 160 ~---------~------~H~Al~DA~~ta~l~~~l~~~ 182 (277)
. + -+=|..|+..+..|+..|.++
T Consensus 132 K~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~ 169 (373)
T PRK10829 132 KSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAE 169 (373)
T ss_pred cccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1 1 123789999999999987753
No 106
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=65.75 E-value=7.9 Score=24.37 Aligned_cols=19 Identities=32% Similarity=0.754 Sum_probs=15.0
Q ss_pred cceeCCCCCCCCCCCCCceeeccC
Q 036883 253 FFFGCGNWTPNRGACCNYFQWATT 276 (277)
Q Consensus 253 ~f~~c~~~~~~~~~~c~~f~w~~~ 276 (277)
.||+|.++ ..|.|..|..+
T Consensus 20 ~F~~Cs~y-----P~C~~~~~~~~ 38 (39)
T PF01396_consen 20 KFLGCSNY-----PECKYTEPLPK 38 (39)
T ss_pred CEEECCCC-----CCcCCeEeCCC
Confidence 99999664 45999998754
No 107
>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=60.71 E-value=85 Score=25.63 Aligned_cols=67 Identities=13% Similarity=0.031 Sum_probs=39.1
Q ss_pred HHHHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCC-CCCHHHHHHHh-CC
Q 036883 79 ALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDV-RCNLKEAVELA-GL 156 (277)
Q Consensus 79 vl~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~-~~~L~~l~~~~-gi 156 (277)
+...|.+|+++... ..++|+..+|+ .+| .+.|+..+ ....|+.-...-+-+.. +++|++++..| +.
T Consensus 44 ~~~~l~~~l~~~~~----~ki~~d~K~~~-~~l----~~~gi~~~---~~~fDt~laaYLL~p~~~~~~l~~l~~~yl~~ 111 (178)
T cd06140 44 DLAALKEWLEDEKI----PKVGHDAKRAY-VAL----KRHGIELA---GVAFDTMLAAYLLDPTRSSYDLADLAKRYLGR 111 (178)
T ss_pred HHHHHHHHHhCCCC----ceeccchhHHH-HHH----HHCCCcCC---CcchhHHHHHHHcCCCCCCCCHHHHHHHHcCC
Confidence 45556777776421 23455667775 454 35687765 23578775544443433 37999998664 44
Q ss_pred C
Q 036883 157 I 157 (277)
Q Consensus 157 ~ 157 (277)
.
T Consensus 112 ~ 112 (178)
T cd06140 112 E 112 (178)
T ss_pred C
Confidence 3
No 108
>PF05325 DUF730: Protein of unknown function (DUF730); InterPro: IPR007989 This family consists of several uncharacterised Arabidopsis thaliana proteins of unknown function.
Probab=52.72 E-value=17 Score=27.79 Aligned_cols=48 Identities=23% Similarity=0.454 Sum_probs=32.5
Q ss_pred CCceeeeecCCccccceeccCCCCCCCcceeCCCC-CCCCCCCCCceeec
Q 036883 226 FEDCRYCYCGAKSIKKVIQRPGPKRGSFFFGCGNW-TPNRGACCNYFQWA 274 (277)
Q Consensus 226 ~~~~~~c~c~~~~~~~~~~~~g~~~g~~f~~c~~~-~~~~~~~c~~f~w~ 274 (277)
.+-++-|.|+..-...|. .+--..|+.||.|+-- .-..+.+|+|=.|-
T Consensus 17 kgv~ie~dcnakvvvats-~dpvts~klyfscpyeisdg~g~~~gfkrww 65 (122)
T PF05325_consen 17 KGVPIECDCNAKVVVATS-RDPVTSGKLYFSCPYEISDGPGRGCGFKRWW 65 (122)
T ss_pred CCcceeccCCceEEEEec-cCCcccceeeecCccccccCCCCCccceeEE
Confidence 445788999866554443 3344679999999542 22457899998884
No 109
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=49.99 E-value=2.1e+02 Score=29.08 Aligned_cols=90 Identities=21% Similarity=0.149 Sum_probs=53.5
Q ss_pred HHHHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHh-cCCCCCCHHHHHHHh-CC
Q 036883 79 ALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKV-FGDVRCNLKEAVELA-GL 156 (277)
Q Consensus 79 vl~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~-~~~~~~~L~~l~~~~-gi 156 (277)
+...+..|+++... ..+.++..+|. .+| .++|+. + ....|++-....+ .+...++|+++++++ +.
T Consensus 66 ~~~~l~~~l~~~~~----~kv~~~~K~d~-~~l----~~~Gi~-~---~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~ 132 (593)
T COG0749 66 VLAALKPLLEDEGI----KKVGQNLKYDY-KVL----ANLGIE-P---GVAFDTMLASYLLNPGAGAHNLDDLAKRYLGL 132 (593)
T ss_pred hHHHHHHHhhCccc----chhccccchhH-HHH----HHcCCc-c---cchHHHHHHHhccCcCcCcCCHHHHHHHhcCC
Confidence 88999999988631 23556778885 455 466754 2 2355765332222 233467898888766 32
Q ss_pred CCC--------CC-------------CCchHHHHHHHHHHHHHHHH
Q 036883 157 IWQ--------GR-------------VHCGLDDAINIARLLSVIMR 181 (277)
Q Consensus 157 ~~~--------~~-------------~H~Al~DA~~ta~l~~~l~~ 181 (277)
... +. .-.+-.||.+|.+|...|..
T Consensus 133 ~~~~~~~i~~kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~ 178 (593)
T COG0749 133 ETITFEDIAGKGKKQLTFADVKLEKATEYAAEDADATLRLESILEP 178 (593)
T ss_pred ccchhHHhhccccccCccccchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 211 00 11246788888888877764
No 110
>PHA02563 DNA polymerase; Provisional
Probab=42.64 E-value=1.4e+02 Score=30.59 Aligned_cols=39 Identities=8% Similarity=-0.011 Sum_probs=25.4
Q ss_pred HHHHHHHHhhcCCCCCcE-EEEEeccchHHHHHHHHHHHhC
Q 036883 80 LYFHDKWLLQMGLNNTNF-SVVTWSDWDCQVMLESECRIKK 119 (277)
Q Consensus 80 l~~f~~fl~~~~l~~~~~-~vv~~~~fDl~~~L~~~~~~~g 119 (277)
+.+|.+|+........++ +.+||+.||. .||-..+.+.+
T Consensus 50 ~~~f~~~i~~~~~k~~~~~vYfHN~~FD~-~Fil~~L~~~~ 89 (630)
T PHA02563 50 FDEFLQWIEDTTYKETECIIYFHNLKFDG-SFILKWLLRNG 89 (630)
T ss_pred HHHHHHHHhhccccccceEEEEecCCccH-HHHHHHHHhhc
Confidence 348888887321122233 4568899995 79999888765
No 111
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=39.73 E-value=41 Score=35.12 Aligned_cols=101 Identities=20% Similarity=0.227 Sum_probs=55.7
Q ss_pred EEEEEEccCCCCCCCC--CCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHH
Q 036883 4 YVVIDFEATCDKERNL--HPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALY 81 (277)
Q Consensus 4 ~vviDlETTg~~~~~~--~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~ 81 (277)
..-||+|+.|-.|..| ..+.||+|+-++.- -|+- . -+|+-.. .+.+ ..+|.-.+|-.-..-++++.
T Consensus 276 vlSfDIECagrkg~FPe~~~DPvIQIan~v~~--~Ge~-~---pf~rnvf--~l~~----capI~G~~V~~~~~e~elL~ 343 (1066)
T KOG0969|consen 276 VLSFDIECAGRKGVFPEAKIDPVIQIANLVTL--QGEN-E---PFVRNVF--TLKT----CAPIVGSNVHSYETEKELLE 343 (1066)
T ss_pred ccceeEEeccCCCCCCccccChHHHHHHHHHH--hcCC-c---hHHHhhh--cccC----cCCCCCceeEEeccHHHHHH
Confidence 4569999999776654 46889999876542 2221 1 1222111 1111 24566666666666777887
Q ss_pred HHHHHHhhcCCCCCcEEEEE-e-ccchHHHHHHHHHHHhCCC
Q 036883 82 FHDKWLLQMGLNNTNFSVVT-W-SDWDCQVMLESECRIKKIQ 121 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~-~-~~fDl~~~L~~~~~~~gi~ 121 (277)
.-..|+.+-.. + +++. + -.||+ ..|-.-....|++
T Consensus 344 ~W~~firevDP---D-vI~GYNi~nFDi-PYll~RA~~L~Ie 380 (1066)
T KOG0969|consen 344 SWRKFIREVDP---D-VIIGYNICNFDI-PYLLNRAKTLGIE 380 (1066)
T ss_pred HHHHHHHhcCC---C-eEeccccccccc-ceecChHhhcCcc
Confidence 77777776421 1 2332 2 26886 4443333334443
No 112
>PF12377 DuffyBP_N: Duffy binding protein N terminal ; InterPro: IPR021032 This entry represents the N terminus of the Duffy-antigen binding protein and is thought to bind to the human erythrocytes Duffy blood group determinant. These domains are found in eukaryotic proteins and are approximately 70 amino acids in length [].
Probab=38.25 E-value=14 Score=25.51 Aligned_cols=28 Identities=14% Similarity=0.394 Sum_probs=18.0
Q ss_pred CeEEEEEEccCCCCCCCCCCCcEEEEce
Q 036883 2 EYYVVIDFEATCDKERNLHPQEIIEFPS 29 (277)
Q Consensus 2 ~~~vviDlETTg~~~~~~~~~eIIEIgA 29 (277)
+++|++|.||++-.....-.+.++|+++
T Consensus 21 ~nlvmldyd~s~nghp~g~~dnvle~~t 48 (66)
T PF12377_consen 21 NNLVMLDYDTSSNGHPAGTIDNVLEFVT 48 (66)
T ss_pred cceEEEEeeccCCCCcCchhhhHHHhhh
Confidence 4789999999974211123466777754
No 113
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=35.33 E-value=29 Score=36.79 Aligned_cols=36 Identities=17% Similarity=0.400 Sum_probs=22.1
Q ss_pred eeeecCCccccceeccCCCCCCCcceeCCCCCCCCCCCCCceeecc
Q 036883 230 RYCYCGAKSIKKVIQRPGPKRGSFFFGCGNWTPNRGACCNYFQWAT 275 (277)
Q Consensus 230 ~~c~c~~~~~~~~~~~~g~~~g~~f~~c~~~~~~~~~~c~~f~w~~ 275 (277)
+-|.||.. .+. +.|. .|+.||+|.++ ..|.|..|.-
T Consensus 697 P~~~C~g~---l~~-r~gr-~G~~f~~Cs~y-----p~C~~~~~~~ 732 (860)
T PRK06319 697 PAIGCTGH---IVK-RRSR-FNKMFYSCSEY-----PACSVIGNSI 732 (860)
T ss_pred CCcCCCCc---EEE-EecC-CCCeeeccCCC-----CCCceeeccC
Confidence 44457743 233 4443 47789999765 4599886653
No 114
>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=33.67 E-value=2.5e+02 Score=23.36 Aligned_cols=61 Identities=11% Similarity=0.021 Sum_probs=34.4
Q ss_pred HHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHH-HhCCCCCCCCcchhhhHHHHhHhcCCCCCCHHHHHHHh-CC
Q 036883 82 FHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECR-IKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELA-GL 156 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~-~~gi~~p~~~~~~iDl~~~~~~~~~~~~~~L~~l~~~~-gi 156 (277)
.|.+|+++... ..++++...|+ ..| . .+|+..+ .. +|+.-....+-+. +.+|+.+++.| +.
T Consensus 68 ~L~~~L~~~~i----~kv~~d~K~~~-~~L----~~~~gi~~~---~~-fD~~laaYLL~p~-~~~l~~l~~~yl~~ 130 (192)
T cd06147 68 ILNEVFTDPNI----LKVFHGADSDI-IWL----QRDFGLYVV---NL-FDTGQAARVLNLP-RHSLAYLLQKYCNV 130 (192)
T ss_pred HHHHHhcCCCc----eEEEechHHHH-HHH----HHHhCCCcC---ch-HHHHHHHHHhCCC-cccHHHHHHHHhCC
Confidence 46667775421 23444455553 333 3 6677654 23 7887655444444 46899998765 44
No 115
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=33.26 E-value=28 Score=35.75 Aligned_cols=39 Identities=15% Similarity=0.350 Sum_probs=24.5
Q ss_pred eeecCCccccceeccCCCCCCCcceeCCCCCCCC--CCCCCceeecc
Q 036883 231 YCYCGAKSIKKVIQRPGPKRGSFFFGCGNWTPNR--GACCNYFQWAT 275 (277)
Q Consensus 231 ~c~c~~~~~~~~~~~~g~~~g~~f~~c~~~~~~~--~~~c~~f~w~~ 275 (277)
.|-||.... .+.|.+ |+ |.+|.+++.-. +.+|+|=.|..
T Consensus 613 ~cpcg~~l~----~~~~~~-g~-f~~c~~~p~C~~~~~~c~~~~~~~ 653 (660)
T TIGR01056 613 PVSCGGIAK----CPAKDN-GR-LIDCKKFPECTEYGNGCEFTIPKK 653 (660)
T ss_pred cCCCCCcee----eeecCC-Ce-eecCCCCCCccCcCCCCeEEccHH
Confidence 355775332 234443 54 99998875533 36899999964
No 116
>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=33.14 E-value=2.3e+02 Score=21.95 Aligned_cols=63 Identities=14% Similarity=-0.036 Sum_probs=35.5
Q ss_pred HHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCC-CCCHHHHHHHh-CCC
Q 036883 83 HDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDV-RCNLKEAVELA-GLI 157 (277)
Q Consensus 83 f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~-~~~L~~l~~~~-gi~ 157 (277)
+.+++++... ..++++...|+ .+| .+.|+..+ ....|+.-....+-+.+ +.+|+++++.| +..
T Consensus 45 l~~~l~~~~~----~kv~~d~K~~~-~~L----~~~~~~~~---~~~~D~~laayLl~p~~~~~~l~~l~~~~l~~~ 109 (150)
T cd09018 45 LKPLLEDEKA----LKVGQNLKYDR-GIL----LNYFIELR---GIAFDTMLEAYILNSVAGRWDMDSLVERWLGHK 109 (150)
T ss_pred HHHHhcCCCC----ceeeecHHHHH-HHH----HHcCCccC---CcchhHHHHHHHhCCCCCCCCHHHHHHHHhCCC
Confidence 5566765421 12344456664 344 45566554 34578876655544433 46899998765 554
No 117
>PF06373 CART: Cocaine and amphetamine regulated transcript protein (CART); InterPro: IPR009106 The cocaine and amphetamine regulated transcript (CART) is a brain-localised peptide that acts as a satiety factor in appetite regulation. CART was found to inhibit both normal and starvation-induced feeding, and completely blocks the feeding response induced by neuropeptide Y. CART is regulated by leptin in the hypothalamus, and can be transcriptionally induced after cocaine or amphetamine administration []. Posttranslational processing of CART produces an N-terminal CART peptide and a C-terminal CART peptide. The C-terminal CART peptide has been isolated from the hypothalamus, nucleus accumbens, and the anterior pituitary lobe in rats. C-terminal CART is the biologically active part of the molecule affecting food intake. The structure of C-terminal CART consists of a disulphide-bound fold containing a beta-hairpin and two adjacent disulphide bridges [].; GO: 0000186 activation of MAPKK activity, 0001678 cellular glucose homeostasis, 0007186 G-protein coupled receptor protein signaling pathway, 0008343 adult feeding behavior, 0009267 cellular response to starvation, 0032099 negative regulation of appetite, 0005615 extracellular space; PDB: 1HY9_A.
Probab=32.88 E-value=14 Score=26.50 Aligned_cols=37 Identities=30% Similarity=0.849 Sum_probs=15.7
Q ss_pred CCceeeeecCCccccceeccCCCCCCCcceeCCCCCCCCCCCCCcee
Q 036883 226 FEDCRYCYCGAKSIKKVIQRPGPKRGSFFFGCGNWTPNRGACCNYFQ 272 (277)
Q Consensus 226 ~~~~~~c~c~~~~~~~~~~~~g~~~g~~f~~c~~~~~~~~~~c~~f~ 272 (277)
-+..++|.=|... .|+ .||.-||.= .| ++|+.|+||+
T Consensus 33 ~g~vP~Cd~GE~C---Avr-kG~RIGklC-dC-----~rG~~CN~fl 69 (73)
T PF06373_consen 33 YGQVPSCDVGEQC---AVR-KGPRIGKLC-DC-----PRGTSCNFFL 69 (73)
T ss_dssp -----B--SSS-S---EEE--SSSEEE---B-------TT--B-TTT
T ss_pred cCcCCCCCCCchh---hhc-ccccccccc-CC-----CCCCchhhhH
Confidence 3446788777653 454 499999763 55 5899999986
No 118
>PF12860 PAS_7: PAS fold
Probab=32.84 E-value=1.1e+02 Score=23.00 Aligned_cols=46 Identities=15% Similarity=0.285 Sum_probs=35.5
Q ss_pred EEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHHHH
Q 036883 25 IEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFHD 84 (277)
Q Consensus 25 IEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~f~ 84 (277)
+..|.+++| .+++++ + .++...++.|+..+++..+.++.+++....
T Consensus 4 l~~Gv~v~D-~~~rl~-----~--------~N~~~~~l~~~~~~~~~~G~~~~~l~~~~~ 49 (115)
T PF12860_consen 4 LPQGVAVFD-SDGRLV-----F--------WNQRFRELFGLPPEMLRPGASFRDLLRRLA 49 (115)
T ss_pred cCceEEEEc-CCCeEE-----e--------EcHHHHHHhCCCHHHhcCCCCHHHHHHHHH
Confidence 446888888 477774 2 455577899999999999999998888663
No 119
>PF07846 Metallothio_Cad: Metallothionein family; InterPro: IPR012484 The sequence making up family 7 of the metallothionein superfamily are found repeated in metallothionein proteins expressed by two Tetrahymena species. Metallothioneins are low molecular mass, cysteine-rich metal-binding proteins that are thought to be involved in the regulation of levels of trace metals, and detoxification of these metals when present in excess []. Some of the metallothioneins found in this family (for example, Q8T6B3 from SWISSPROT) are known to be induced by cadmium and are thought to be involved in the cellular sequestration of toxic metal ions. The high proportion of cysteine residues allows the metal ions to be bound by the formation of clusters of metal-thiolate complexes []. Tetrahymena spp. metallothioneins differ from other eukaryotic metallothioneins mainly in the length of their sequences and in the cysteine-containing motifs they exhibit. ; GO: 0046870 cadmium ion binding
Probab=32.18 E-value=29 Score=18.72 Aligned_cols=17 Identities=29% Similarity=0.782 Sum_probs=11.5
Q ss_pred eecCCccccceeccCCCCCC
Q 036883 232 CYCGAKSIKKVIQRPGPKRG 251 (277)
Q Consensus 232 c~c~~~~~~~~~~~~g~~~g 251 (277)
|-||.+++..-. .||.|
T Consensus 1 CccG~naK~cC~---DPnsG 17 (21)
T PF07846_consen 1 CCCGVNAKPCCT---DPNSG 17 (21)
T ss_pred CccCCCCccccc---CCCCc
Confidence 668888877543 56666
No 120
>KOG1294 consensus Apurinic/apyrimidinic endonuclease and related enzymes [Replication, recombination and repair]
Probab=29.94 E-value=29 Score=32.60 Aligned_cols=27 Identities=26% Similarity=0.615 Sum_probs=21.6
Q ss_pred ecCCccccceeccCCCCCCCcceeCCC
Q 036883 233 YCGAKSIKKVIQRPGPKRGSFFFGCGN 259 (277)
Q Consensus 233 ~c~~~~~~~~~~~~g~~~g~~f~~c~~ 259 (277)
+=|-+-.-.+|+|+|+|.||.||=|+.
T Consensus 293 ~~~~r~dy~~Vsk~~~n~~r~~~Ic~r 319 (335)
T KOG1294|consen 293 GHGERCDYILVSKPGPNNGRRFYICSR 319 (335)
T ss_pred CCCCceeEEEecCcCCCCCceeeeecC
Confidence 334445567999999999999999965
No 121
>PF00843 Arena_nucleocap: Arenavirus nucleocapsid protein; InterPro: IPR000229 Arenaviruses are single stranded RNA viruses. The arenavirus S RNAs that have been characterised include conserved terminal sequences, an ambisense arrangement of the coding regions for the precursor glycoprotein (GPC) and nucleocapsid (N) proteins and an intergenic region capable of forming a base-paired "hairpin" structure. The mature glycoproteins that result are G1 and G2 and the N protein []. This family represents the nucleocapsid protein that encapsulates the viral ssRNA [].; GO: 0019013 viral nucleocapsid; PDB: 3MX5_A 3MX2_C 3MWT_C 3Q7C_A 3MWP_B 3Q7B_A 3T5Q_E 3T5N_A 3R3L_B.
Probab=27.87 E-value=93 Score=30.36 Aligned_cols=87 Identities=21% Similarity=0.229 Sum_probs=48.8
Q ss_pred EEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHHHHHHH
Q 036883 5 VVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFHD 84 (277)
Q Consensus 5 vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~f~ 84 (277)
.=||+|.. +..-+||+.. -+.+|+-+ +.|=+|......-..+.--|||...||.+|.| -.+..+.
T Consensus 375 tWiDIEG~--------p~DPVElAiy--QP~sg~Yi---HcyR~P~D~K~FK~~SKysHGillkDl~~aqP--GL~S~vi 439 (533)
T PF00843_consen 375 TWIDIEGP--------PNDPVELAIY--QPSSGNYI---HCYREPHDEKQFKNQSKYSHGILLKDLENAQP--GLTSAVI 439 (533)
T ss_dssp EEEEEESE--------TTSESEEEEE--ETTTTEEE---EEE---S-HHHHHHHHHHTT-B-GGGCTTB-T--THHHHHH
T ss_pred eeEecCCC--------CCCCeEEEEe--ccCCCcEE---EEecCCcchhhhcccccccccccHHHHhhhcc--chHHHHH
Confidence 45788877 3556888544 67789886 45667864222334455569999999998776 3444444
Q ss_pred HHHhhcCCCCCcEEEEEeccchHHHHHH
Q 036883 85 KWLLQMGLNNTNFSVVTWSDWDCQVMLE 112 (277)
Q Consensus 85 ~fl~~~~l~~~~~~vv~~~~fDl~~~L~ 112 (277)
..|-.. .++-+-|+-|++..|.
T Consensus 440 ~~LP~~------MVlT~QGsDDIrkLld 461 (533)
T PF00843_consen 440 ELLPKN------MVLTCQGSDDIRKLLD 461 (533)
T ss_dssp HHS-TT-------EEEESSHHHHHHHHH
T ss_pred HhCCcC------cEEEeeChHHHHHHHH
Confidence 445443 3444468888865443
No 122
>PF11079 YqhG: Bacterial protein YqhG of unknown function; InterPro: IPR024562 This family of putative proteins appears to be restricted to Firmicutes. Their function is not known.
Probab=25.25 E-value=35 Score=30.79 Aligned_cols=69 Identities=23% Similarity=0.417 Sum_probs=50.7
Q ss_pred EEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEeEEEEeecCCC-CCCCChhhHhHhCCChHHHhCCCCHHHHHHHHHH
Q 036883 7 IDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTF-EPLLTDFCKELTGIQQHQVDNGITLGEALYFHDK 85 (277)
Q Consensus 7 iDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~-~~~i~~~~~~ltGIt~~~l~~ap~f~evl~~f~~ 85 (277)
+-++..|. -.++++..+|.-++ +|+++..|+..+.... .|.|++++--++- ..++..++.++.+
T Consensus 126 ~KVsy~cD----~KkDel~SlGi~Li---~G~ive~F~~~L~~~~LtpkiPdy~ftlsp--------~i~~~sa~~rlE~ 190 (260)
T PF11079_consen 126 VKVSYQCD----RKKDELLSLGINLI---SGQIVENFHERLQGRQLTPKIPDYCFTLSP--------IIKPKSALKRLEQ 190 (260)
T ss_pred EEEEEeec----cchHHHhhheeecc---CCcchhhHHHHHhcCCCCCCCCcceeecCC--------cCCHHHHHHHHHH
Confidence 34455542 35799999999988 7999999999998754 3567776644433 3467899999999
Q ss_pred HHhhc
Q 036883 86 WLLQM 90 (277)
Q Consensus 86 fl~~~ 90 (277)
+|...
T Consensus 191 ~l~~~ 195 (260)
T PF11079_consen 191 YLEQY 195 (260)
T ss_pred HHHHH
Confidence 99874
No 123
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=24.87 E-value=1.4e+02 Score=29.29 Aligned_cols=85 Identities=11% Similarity=0.221 Sum_probs=53.0
Q ss_pred HHHHHHHHHHh-hcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCC---CCCcchhhhHHHHhHhc--CCCCCCHHHHH
Q 036883 78 EALYFHDKWLL-QMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKP---AYFNQWINLRVPFSKVF--GDVRCNLKEAV 151 (277)
Q Consensus 78 evl~~f~~fl~-~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p---~~~~~~iDl~~~~~~~~--~~~~~~L~~l~ 151 (277)
.++.+|+.++. ..+ +-.+.|+...+ +. .+-...+|++.. ++...|+|+..+.+..+ |..+++|+.+.
T Consensus 340 ~~~~efl~~v~~~yp----~~~~YH~~~ye-~~--~rL~klyg~~~~~v~~~l~~~vDi~~lvr~~v~~p~es~sLK~la 412 (474)
T COG2251 340 KALQEFLGIVVRQYP----EATIYHYAPYE-KT--RRLVKLYGVPQNQVSPVLDSLVDIYALVRSSVVVPVESYSLKALA 412 (474)
T ss_pred HHHHHHHhhhheecC----CCCccccCchh-hh--chhheeeccCcchhhHHHHHHhHHHHHHHhccccCccchhHHHhh
Confidence 58899999987 221 12466777667 32 222344555432 23446888887776654 45689999999
Q ss_pred HHhCCCCCCCCCchHHHHH
Q 036883 152 ELAGLIWQGRVHCGLDDAI 170 (277)
Q Consensus 152 ~~~gi~~~~~~H~Al~DA~ 170 (277)
.++|.++.+ .--|.++.+
T Consensus 413 ~~lG~~wrD-~~~ag~~~~ 430 (474)
T COG2251 413 PYLGFQWRD-VEAAGDESL 430 (474)
T ss_pred hhhCCCccc-cccchHHHH
Confidence 999998763 233444443
No 124
>PF11288 DUF3089: Protein of unknown function (DUF3089); InterPro: IPR021440 This family of proteins has no known function.
Probab=24.60 E-value=1.6e+02 Score=25.67 Aligned_cols=32 Identities=16% Similarity=0.196 Sum_probs=25.7
Q ss_pred CCCCHHHHHHHHHHHHhhcCCCCCcEEEEEecc
Q 036883 72 NGITLGEALYFHDKWLLQMGLNNTNFSVVTWSD 104 (277)
Q Consensus 72 ~ap~f~evl~~f~~fl~~~~l~~~~~~vv~~~~ 104 (277)
-...+.+|...|..||+... .|+.++|+.|++
T Consensus 73 ~~~ay~DV~~AF~~yL~~~n-~GRPfILaGHSQ 104 (207)
T PF11288_consen 73 FDLAYSDVRAAFDYYLANYN-NGRPFILAGHSQ 104 (207)
T ss_pred HHhhHHHHHHHHHHHHHhcC-CCCCEEEEEeCh
Confidence 35679999999999998763 467899998864
No 125
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=24.31 E-value=1.4e+02 Score=24.06 Aligned_cols=80 Identities=13% Similarity=0.115 Sum_probs=47.0
Q ss_pred CCeEEEEEEccCCCCCCC-------------CCCCcEEEEceEEEECCCCEEEeEEEEee-cCCCCCCCChhhHhHhCCC
Q 036883 1 FEYYVVIDFEATCDKERN-------------LHPQEIIEFPSVVVSGVSGEIIACFQTYV-RPTFEPLLTDFCKELTGIQ 66 (277)
Q Consensus 1 f~~~vviDlETTg~~~~~-------------~~~~eIIEIgAV~vd~~~g~i~~~f~~lV-rP~~~~~i~~~~~~ltGIt 66 (277)
|.-||-||-.+||+-..+ -...+-+++=.+-+| ++|++.=+...+. +|+..+.-+.+ +
T Consensus 19 yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~id-e~GKisLSIr~~~e~pe~~~~kp~~------~- 90 (129)
T COG1098 19 YGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDID-ENGKISLSIRKLEEEPEKQHRKPRF------S- 90 (129)
T ss_pred cceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeec-cCCCcceehHHhhhCcccccccccc------C-
Confidence 567888888888862211 123445566556666 4777743333333 23321101111 1
Q ss_pred hHHHhCCCCHHHHHHHHHHHHhhc
Q 036883 67 QHQVDNGITLGEALYFHDKWLLQM 90 (277)
Q Consensus 67 ~~~l~~ap~f~evl~~f~~fl~~~ 90 (277)
....++.|+.-+.+|..|++++
T Consensus 91 --~~r~~~gFe~~~~~~~~w~ee~ 112 (129)
T COG1098 91 --KSRPKEGFETLLSRLLKWIEES 112 (129)
T ss_pred --CcccCcChHHHHHHHHHHHHHH
Confidence 1467899999999999999985
No 126
>COG3218 ABC-type uncharacterized transport system, auxiliary component [General function prediction only]
Probab=22.77 E-value=2.4e+02 Score=24.56 Aligned_cols=47 Identities=15% Similarity=0.203 Sum_probs=30.3
Q ss_pred EEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEE--eEEEEeecCC
Q 036883 4 YVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEII--ACFQTYVRPT 50 (277)
Q Consensus 4 ~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~--~~f~~lVrP~ 50 (277)
-+..|+-+=..+..++.+...|||.+.+++.++|+++ ..|..-++-+
T Consensus 126 ~l~~dlr~FE~~y~~~~~~A~Iei~v~Ll~~~n~~v~A~r~F~a~~pv~ 174 (205)
T COG3218 126 QLILDLRAFEIQYVTGAPTAVIEISVRLLNDRNGTVRASRVFRASQPVD 174 (205)
T ss_pred eeeehhhhhhhhccCCCceEEEEEEEEEeccCCCcEEEEEEEEEeeccc
Confidence 3444444333322245678899999999998899986 5565555444
No 127
>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=22.65 E-value=3.3e+02 Score=23.01 Aligned_cols=91 Identities=12% Similarity=-0.011 Sum_probs=50.5
Q ss_pred HHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcC--------CCCCCHHHHHHH
Q 036883 82 FHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFG--------DVRCNLKEAVEL 153 (277)
Q Consensus 82 ~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~--------~~~~~L~~l~~~ 153 (277)
.+.+++++..+ .-+.|+...|+ .+|. ...|+... ..+|++..+..+.. ....+|+++++.
T Consensus 56 ~L~~iLe~~~i----~Kv~h~~k~D~-~~L~---~~~gi~~~----~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~ 123 (197)
T cd06148 56 GLKDILESKKI----LKVIHDCRRDS-DALY---HQYGIKLN----NVFDTQVADALLQEQETGGFNPDRVISLVQLLDK 123 (197)
T ss_pred HHHHHhcCCCc----cEEEEechhHH-HHHH---HhcCcccc----ceeeHHHHHHHHHHHhcCCccccccccHHHHHHH
Confidence 34455665421 23556677886 4553 34566532 23677654332211 113588888866
Q ss_pred h-CCCCC-----------------CCC------CchHHHHHHHHHHHHHHHHhcC
Q 036883 154 A-GLIWQ-----------------GRV------HCGLDDAINIARLLSVIMRRGF 184 (277)
Q Consensus 154 ~-gi~~~-----------------~~~------H~Al~DA~~ta~l~~~l~~~g~ 184 (277)
+ |++.. .+. +=|..||..+..|+..|++.-.
T Consensus 124 ~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~ 178 (197)
T cd06148 124 YLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALI 178 (197)
T ss_pred hhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhh
Confidence 4 55431 111 2367899999999999887543
No 128
>COG2055 Malate/L-lactate dehydrogenases [Energy production and conversion]
Probab=22.45 E-value=4.5e+02 Score=24.92 Aligned_cols=56 Identities=13% Similarity=0.009 Sum_probs=36.6
Q ss_pred CChHHHhCCCCHHHHHHHHHHHHhhcCC-CCCcEEEEEeccchHHHHHHHHHHHhCCCCC
Q 036883 65 IQQHQVDNGITLGEALYFHDKWLLQMGL-NNTNFSVVTWSDWDCQVMLESECRIKKIQKP 123 (277)
Q Consensus 65 It~~~l~~ap~f~evl~~f~~fl~~~~l-~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p 123 (277)
|+++.+.++..|.+.+.++.++++...- .+.. -|...|..- ...+++.++.||+.+
T Consensus 273 Idp~~f~~~~~f~~~~~~~~~~~~~~~~a~~~~-~V~lPG~~~--~~~~~~~~~~GI~i~ 329 (349)
T COG2055 273 IDPEAFGDGDEFDERLSAYLDELRASEPADGFQ-GVRLPGERE--FAAREKRQKEGIPID 329 (349)
T ss_pred ECHHHcCCchhhhHHHHHHHHHHhccCCCCCCC-eeecCCcHH--HHHHHHHHhcCCccC
Confidence 7778888889999999999999988742 1111 233344322 233455666788875
No 129
>PRK07726 DNA topoisomerase III; Provisional
Probab=21.98 E-value=55 Score=33.59 Aligned_cols=16 Identities=13% Similarity=0.204 Sum_probs=10.8
Q ss_pred cceeCCCCCCCCCCCCCceeec
Q 036883 253 FFFGCGNWTPNRGACCNYFQWA 274 (277)
Q Consensus 253 ~f~~c~~~~~~~~~~c~~f~w~ 274 (277)
.||+|.++ .|.++.|-
T Consensus 629 ~f~~Cs~~------~~~~~~~~ 644 (658)
T PRK07726 629 KMLVCQDR------ECGKRKNV 644 (658)
T ss_pred eeEecCCC------cccccccc
Confidence 49999653 36666774
No 130
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=21.36 E-value=6.7e+02 Score=27.83 Aligned_cols=110 Identities=15% Similarity=0.049 Sum_probs=60.7
Q ss_pred EEEEEEccCCCCCCCCCCCcEEEEceEEEECCCC-------EEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCH
Q 036883 4 YVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSG-------EIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITL 76 (277)
Q Consensus 4 ~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g-------~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f 76 (277)
+..|-++|+-- ......||+-|++........ .....|..++||.. ...+-...++-.-...-|.-..+-
T Consensus 531 llsL~i~T~~N--~k~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~-~~fP~g~~ela~~k~~~v~~~~sE 607 (1429)
T KOG0970|consen 531 LLSLNIRTSMN--PKQNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPG-TSFPLGLKELAKQKLSKVVLHNSE 607 (1429)
T ss_pred EEEeeeeehhc--cccchhhhhhhhhhhcccccccCCCCCCcccCcceeEecCCC-CcCCchHHHHHHhccCceEEecCH
Confidence 34567777741 123468999998776531111 12367888999985 334443333321111114445556
Q ss_pred HHHHHHHHHHHhhcCCCCCcEEEEEe-ccchHHHHHHHHHHHhCC
Q 036883 77 GEALYFHDKWLLQMGLNNTNFSVVTW-SDWDCQVMLESECRIKKI 120 (277)
Q Consensus 77 ~evl~~f~~fl~~~~l~~~~~~vv~~-~~fDl~~~L~~~~~~~gi 120 (277)
...+..|++.+...+ -+.+|.|+ -.|++ ..|-..+...++
T Consensus 608 rALLs~fla~~~~~d---pD~iVgHn~~~~~l-~VLl~R~~~~Ki 648 (1429)
T KOG0970|consen 608 RALLSHFLAMLNKED---PDVIVGHNIQGFYL-DVLLSRLHALKI 648 (1429)
T ss_pred HHHHHHHHHHhhccC---CCEEEEeccccchH-HHHHHHHHHhcC
Confidence 667788888887653 24555555 46777 566444444333
No 131
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=21.24 E-value=48 Score=21.55 Aligned_cols=27 Identities=22% Similarity=0.529 Sum_probs=23.4
Q ss_pred ecCCccccceeccCCCCCCCcceeCCC
Q 036883 233 YCGAKSIKKVIQRPGPKRGSFFFGCGN 259 (277)
Q Consensus 233 ~c~~~~~~~~~~~~g~~~g~~f~~c~~ 259 (277)
.||..++.++..+--+.--+.+|.|.|
T Consensus 4 ~Cg~~a~ir~S~~~s~~~~~~Y~qC~N 30 (47)
T PF04606_consen 4 HCGSKARIRTSRQLSPLTRELYCQCTN 30 (47)
T ss_pred CCCCeeEEEEchhhCcceEEEEEEECC
Confidence 688999888888888899999999955
No 132
>PF06888 Put_Phosphatase: Putative Phosphatase; InterPro: IPR016965 This group represents phosphatases related to PHOSPHO1 and PHOSPHO2 []. It includes plant phosphatases with homology to the haloacid dehalogenase (HAD) superfamily [, ]. PHOSPHO1 is a phosphoethanolamine/phosphocholine phosphatase [], while PHOSPHO2 has high activity toward pyridoxal 5'-phosphate (PLP), and it is active at much lower level toward pyrophosphate, phosphoethanolamine (PEA)and phosphocholine (PCho) []. ; GO: 0016791 phosphatase activity
Probab=20.04 E-value=1.9e+02 Score=25.61 Aligned_cols=54 Identities=7% Similarity=0.213 Sum_probs=40.6
Q ss_pred CCChHHHh---CCCCHHHHHHHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCC
Q 036883 64 GIQQHQVD---NGITLGEALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQ 121 (277)
Q Consensus 64 GIt~~~l~---~ap~f~evl~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~ 121 (277)
|++.+++. ...++...+.++.+++.... .+.+++|+++|. + -|++.-++.+|+.
T Consensus 57 gvt~~~I~~~l~~ip~~pgm~~~l~~l~~~~-~~~~~~IiSDaN-s--~fI~~iL~~~gl~ 113 (234)
T PF06888_consen 57 GVTPEDIRDALRSIPIDPGMKELLRFLAKNQ-RGFDLIIISDAN-S--FFIETILEHHGLR 113 (234)
T ss_pred CCCHHHHHHHHHcCCCCccHHHHHHHHHhcC-CCceEEEEeCCc-H--hHHHHHHHhCCCc
Confidence 89999985 57888999999999995421 145678888883 4 3777778888875
Done!