Query gi|254780818|ref|YP_003065231.1| DNA polymerase III subunit epsilon [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 245
No_of_seqs 190 out of 3233
Neff 7.0
Searched_HMMs 39220
Date Sun May 29 18:05:00 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780818.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06022 consensus 100.0 0 0 495.8 15.8 233 7-242 1-234 (234)
2 TIGR01406 dnaQ_proteo DNA poly 100.0 0 0 500.4 11.0 226 8-239 1-246 (246)
3 PRK06859 consensus 100.0 0 0 475.8 15.5 237 4-244 2-250 (253)
4 PRK05711 DNA polymerase III su 100.0 0 0 474.5 15.5 233 4-242 1-240 (240)
5 PRK07982 consensus 100.0 0 0 465.8 15.2 230 3-238 2-242 (243)
6 PRK07009 consensus 100.0 0 0 464.8 15.1 231 7-243 1-238 (241)
7 PRK08816 consensus 100.0 0 0 464.2 15.2 231 7-242 1-238 (244)
8 PRK08858 consensus 100.0 0 0 459.6 15.2 230 3-239 6-246 (246)
9 PRK06631 consensus 100.0 0 0 451.3 16.3 224 5-235 2-229 (229)
10 PRK06807 DNA polymerase III su 100.0 0 0 342.2 11.5 166 4-177 5-171 (313)
11 PRK07740 hypothetical protein; 100.0 0 0 338.4 11.2 172 6-184 56-228 (240)
12 PRK08517 DNA polymerase III su 100.0 0 0 335.0 11.7 163 7-177 70-232 (259)
13 PRK07883 hypothetical protein; 100.0 0 0 335.5 11.1 163 8-177 25-190 (575)
14 cd06131 DNA_pol_III_epsilon_Ec 100.0 0 0 335.1 10.8 164 9-175 1-167 (167)
15 TIGR01405 polC_Gram_pos DNA po 100.0 0 0 337.7 8.4 218 9-231 206-435 (1264)
16 PRK06310 DNA polymerase III su 100.0 0 0 330.6 12.5 207 6-223 6-213 (250)
17 PRK07246 bifunctional ATP-depe 100.0 0 0 323.4 11.6 172 1-181 1-173 (820)
18 TIGR00573 dnaq exonuclease, DN 100.0 0 0 327.3 6.8 180 8-190 8-191 (228)
19 PRK05168 ribonuclease T; Provi 100.0 0 0 322.7 10.4 177 4-182 14-205 (213)
20 PRK08074 bifunctional ATP-depe 100.0 0 0 321.4 10.6 166 8-180 4-171 (932)
21 PRK06309 DNA polymerase III su 100.0 0 0 315.5 11.4 161 8-177 3-165 (232)
22 TIGR01407 dinG_rel DnaQ family 100.0 0 0 317.3 9.1 167 8-181 1-169 (944)
23 PRK00448 polC DNA polymerase I 100.0 0 0 314.7 8.2 169 8-183 419-588 (1436)
24 PRK09145 DNA polymerase III su 100.0 0 0 309.0 11.9 164 8-178 30-201 (203)
25 PRK06195 DNA polymerase III su 100.0 0 0 308.1 10.9 164 7-179 1-165 (309)
26 cd06134 RNaseT RNase T is a DE 100.0 1.4E-45 0 304.9 11.6 173 3-177 1-188 (189)
27 PRK07942 DNA polymerase III su 100.0 2.8E-45 0 303.3 10.4 171 4-178 3-180 (234)
28 PRK06063 DNA polymerase III su 100.0 5.6E-45 0 301.2 11.8 171 7-185 15-186 (313)
29 COG2176 PolC DNA polymerase II 100.0 0 0 309.8 3.4 170 9-185 423-593 (1444)
30 cd06130 DNA_pol_III_epsilon_li 100.0 2.9E-43 0 290.3 9.6 155 9-173 1-156 (156)
31 PRK09146 DNA polymerase III su 100.0 1.2E-42 0 286.5 10.5 164 7-176 47-225 (239)
32 PRK07247 DNA polymerase III su 100.0 2.8E-42 0 284.1 11.6 165 5-179 3-170 (195)
33 COG0847 DnaQ DNA polymerase II 100.0 1E-41 0 280.7 11.5 224 7-239 13-242 (243)
34 cd06136 TREX1_2 Three prime re 100.0 6.2E-42 0 282.0 9.4 158 9-173 1-176 (177)
35 PRK07983 exodeoxyribonuclease 100.0 3.7E-41 1.4E-45 277.1 9.9 198 9-231 2-205 (219)
36 smart00479 EXOIII exonuclease 100.0 2E-39 5E-44 266.3 11.1 165 8-177 1-166 (169)
37 pfam00929 Exonuc_X-T Exonuclea 100.0 1.5E-38 3.9E-43 260.8 9.4 160 9-171 1-162 (162)
38 cd06133 ERI-1_3'hExo_like This 100.0 2.7E-38 7E-43 259.2 10.3 166 9-175 1-176 (176)
39 cd06127 DEDDh DEDDh exonucleas 100.0 6.8E-36 1.7E-40 244.2 8.8 157 10-172 1-159 (159)
40 cd06138 ExoI_N This subfamily 100.0 3E-33 7.6E-38 227.7 8.2 160 10-171 1-182 (183)
41 PRK09182 DNA polymerase III su 100.0 8.7E-32 2.2E-36 218.6 12.4 209 7-230 36-269 (293)
42 cd06125 DnaQ_like_exo The DnaQ 100.0 1E-30 2.6E-35 211.9 4.4 118 10-132 1-120 (130)
43 PRK07748 sporulation inhibitor 99.9 6.7E-28 1.7E-32 194.3 9.6 168 6-176 3-178 (205)
44 cd06144 REX4_like This subfami 99.9 7.6E-27 1.9E-31 187.7 9.7 148 10-172 1-152 (152)
45 PRK06722 exonuclease; Provisio 99.9 6.2E-28 1.6E-32 194.5 2.3 128 42-174 5-138 (242)
46 TIGR01298 RNaseT ribonuclease 99.9 2.1E-25 5.3E-30 178.7 5.1 170 10-181 11-196 (201)
47 PRK05601 DNA polymerase III su 99.9 2.8E-23 7.1E-28 165.4 7.1 155 8-169 47-228 (377)
48 PRK11779 sbcB exonuclease I; P 99.8 1.6E-20 4.1E-25 148.2 9.8 170 1-172 1-193 (477)
49 cd06137 DEDDh_RNase This group 99.8 2.3E-19 6E-24 140.9 7.8 148 10-172 1-161 (161)
50 cd06149 ISG20 Interferon (IFN) 99.7 3.4E-17 8.7E-22 127.4 8.9 149 10-172 1-157 (157)
51 cd06135 Orn Oligoribonuclease 99.7 1.3E-17 3.2E-22 130.1 5.1 147 10-170 2-164 (173)
52 KOG0542 consensus 99.7 8.2E-17 2.1E-21 125.0 4.5 172 10-183 59-247 (280)
53 PTZ00315 2'-phosphotransferase 99.5 1.5E-13 3.9E-18 104.6 7.6 169 9-178 58-254 (570)
54 KOG2249 consensus 99.5 3.9E-13 9.8E-18 102.1 8.7 153 8-175 106-263 (280)
55 COG2925 SbcB Exonuclease I [DN 99.4 2.3E-13 5.9E-18 103.5 6.8 174 6-183 8-204 (475)
56 cd06145 REX1_like This subfami 99.4 5.5E-13 1.4E-17 101.1 7.3 145 10-172 1-150 (150)
57 cd06139 DNA_polA_I_Ecoli_like_ 99.4 1.3E-12 3.3E-17 98.8 9.2 143 6-176 4-168 (193)
58 COG5018 KapD Inhibitor of the 99.4 1E-13 2.6E-18 105.7 0.7 167 7-176 3-183 (210)
59 PRK05359 oligoribonuclease; Pr 99.3 6.6E-12 1.7E-16 94.4 6.9 147 8-167 4-164 (181)
60 cd06143 PAN2_exo PAN2 is the c 99.3 9.8E-12 2.5E-16 93.3 7.5 150 10-172 1-174 (174)
61 cd06128 DNA_polA_exo The 3'-5' 99.2 1E-10 2.6E-15 86.9 8.3 115 9-149 3-118 (166)
62 cd00007 35EXOc 3'-5' exonuclea 99.1 1.4E-09 3.6E-14 79.8 9.5 133 8-176 1-153 (155)
63 cd06142 RNaseD_exo Ribonucleas 99.0 1.6E-09 4.2E-14 79.4 7.3 130 8-177 13-159 (178)
64 pfam01612 3_5_exonuc 3'-5' exo 99.0 1.1E-09 2.8E-14 80.5 5.8 133 8-175 21-168 (172)
65 KOG2248 consensus 98.9 1.1E-08 2.8E-13 74.2 8.7 151 9-176 218-373 (380)
66 PRK07456 consensus 98.9 6.8E-09 1.7E-13 75.5 6.7 141 9-175 384-542 (975)
67 PRK06887 consensus 98.8 1.8E-08 4.5E-13 73.0 6.5 154 8-175 357-540 (954)
68 smart00474 35EXOc 3'-5' exonuc 98.8 3.3E-08 8.4E-13 71.2 7.3 132 7-176 21-169 (172)
69 PRK07556 consensus 98.8 1.5E-08 3.8E-13 73.4 5.5 149 7-175 387-558 (977)
70 KOG4793 consensus 98.7 3.2E-09 8.3E-14 77.6 1.5 173 1-174 6-214 (318)
71 PRK05755 DNA polymerase I; Pro 98.7 4.8E-08 1.2E-12 70.3 7.0 137 8-175 320-477 (889)
72 cd06126 DEDDy DEDDy exonucleas 98.7 5.1E-08 1.3E-12 70.1 6.7 121 10-150 2-141 (181)
73 PRK07625 consensus 98.7 6.3E-08 1.6E-12 69.5 6.8 142 8-175 345-507 (922)
74 COG3359 Predicted exonuclease 98.6 1.5E-07 3.7E-12 67.2 8.0 136 8-173 99-237 (278)
75 COG1949 Orn Oligoribonuclease 98.6 2.3E-08 5.9E-13 72.2 3.8 152 5-169 4-170 (184)
76 cd06140 DNA_polA_I_Bacillus_li 98.6 1.4E-07 3.6E-12 67.3 7.5 132 8-176 4-154 (178)
77 cd05782 DNA_polB_like1_exo A s 98.6 2.1E-07 5.4E-12 66.2 8.3 95 77-172 79-207 (208)
78 PRK08434 consensus 98.6 1.4E-07 3.6E-12 67.3 6.1 140 8-175 319-476 (887)
79 cd05779 DNA_polB_epsilon_exo T 98.6 5.5E-07 1.4E-11 63.6 8.9 136 8-151 3-168 (204)
80 cd05781 DNA_polB_B3_exo The 3' 98.5 4.9E-07 1.2E-11 64.0 7.6 117 7-151 3-144 (188)
81 PRK05797 consensus 98.5 5E-07 1.3E-11 63.9 6.9 136 8-176 320-457 (869)
82 PRK07997 consensus 98.5 3.1E-07 7.9E-12 65.2 5.3 142 8-175 350-513 (928)
83 cd05160 DNA_polB_exo The 3'-5' 98.4 7E-07 1.8E-11 63.0 6.9 132 10-148 2-159 (200)
84 KOG3242 consensus 98.4 9.8E-08 2.5E-12 68.3 2.2 146 8-165 27-186 (208)
85 PRK08835 consensus 98.4 6.1E-07 1.6E-11 63.3 5.7 141 8-175 352-515 (931)
86 cd05785 DNA_polB_like2_exo A s 98.3 1.4E-06 3.5E-11 61.1 6.5 84 4-115 6-99 (207)
87 COG0349 Rnd Ribonuclease D [Tr 98.3 1.5E-06 3.8E-11 60.9 6.7 134 9-181 19-169 (361)
88 cd05777 DNA_polB_delta_exo The 98.3 9E-06 2.3E-10 56.0 10.4 98 6-115 6-112 (230)
89 PRK08786 consensus 98.3 5.3E-07 1.4E-11 63.7 3.9 142 8-175 349-512 (927)
90 cd06147 Rrp6p_like_exo Yeast R 98.3 1.9E-06 4.9E-11 60.2 6.8 131 6-176 23-170 (192)
91 cd06129 RNaseD_like The RNase 98.3 2.2E-06 5.5E-11 59.9 7.0 125 9-172 17-159 (159)
92 PTZ00166 DNA polymerase delta 98.3 1.3E-06 3.3E-11 61.3 5.6 156 7-174 290-508 (1081)
93 pfam04857 CAF1 CAF1 family rib 98.2 2.3E-06 5.9E-11 59.7 5.5 166 7-173 22-235 (235)
94 pfam03104 DNA_pol_B_exo DNA po 98.2 3E-06 7.6E-11 59.0 5.9 101 5-115 84-192 (254)
95 cd05780 DNA_polB_Kod1_like_exo 98.1 5.8E-06 1.5E-10 57.2 6.0 122 7-148 3-151 (195)
96 PRK05762 DNA polymerase II; Re 97.9 3.4E-05 8.5E-10 52.5 6.4 145 6-173 154-345 (785)
97 PRK07898 consensus 97.9 7.7E-05 2E-09 50.2 8.1 132 8-175 338-487 (902)
98 cd05776 DNA_polB_alpha_exo The 97.8 4.4E-05 1.1E-09 51.7 5.9 139 9-148 5-182 (234)
99 COG0749 PolA DNA polymerase I 97.8 7.1E-05 1.8E-09 50.4 6.8 132 9-175 24-177 (593)
100 cd06146 mut-7_like_exo The mut 97.8 0.00011 2.8E-09 49.3 7.1 89 86-174 77-191 (191)
101 cd06141 WRN_exo WRN is a uniqu 97.7 7.7E-05 2E-09 50.2 5.6 86 83-174 65-168 (168)
102 PRK05929 consensus 97.7 0.0002 5.1E-09 47.6 7.5 106 8-149 311-416 (870)
103 smart00486 POLBc DNA polymeras 97.7 0.00027 7E-09 46.8 8.0 157 7-174 3-220 (471)
104 PRK08076 consensus 97.6 0.00018 4.7E-09 47.9 6.2 128 10-175 317-463 (877)
105 cd05778 DNA_polB_zeta_exo The 97.6 0.00037 9.5E-09 45.9 7.2 105 5-111 2-118 (231)
106 cd06148 Egl_like_exo The Egali 97.6 0.00063 1.6E-08 44.5 8.3 133 7-176 10-175 (197)
107 pfam10108 Exon_PolB Predicted 97.5 0.001 2.6E-08 43.2 8.6 128 22-174 7-171 (211)
108 COG0417 PolB DNA polymerase el 97.4 0.00074 1.9E-08 44.1 7.0 151 6-173 153-349 (792)
109 cd05784 DNA_polB_II_exo The 3' 97.3 0.0009 2.3E-08 43.5 6.5 89 6-115 2-92 (193)
110 KOG1798 consensus 97.3 0.0027 6.9E-08 40.5 8.6 156 7-174 246-450 (2173)
111 KOG1275 consensus 96.6 0.013 3.3E-07 36.3 7.5 124 47-183 966-1097(1118)
112 PRK10829 ribonuclease D; Provi 96.5 0.021 5.4E-07 35.0 8.0 136 8-183 23-175 (373)
113 cd05783 DNA_polB_B1_exo The 3' 96.4 0.0085 2.2E-07 37.5 5.7 101 6-116 4-113 (204)
114 KOG0304 consensus 96.4 0.0084 2.1E-07 37.5 5.6 163 8-175 25-236 (239)
115 PRK07300 consensus 95.8 0.012 3.2E-07 36.4 4.0 125 10-175 322-464 (880)
116 TIGR03491 RecB family nuclease 94.7 0.22 5.5E-06 28.7 7.5 77 77-153 329-411 (457)
117 PRK08928 consensus 93.1 0.11 2.8E-06 30.5 3.6 79 84-174 367-446 (861)
118 KOG0970 consensus 92.0 0.096 2.4E-06 30.9 2.0 163 8-174 530-751 (1429)
119 KOG0969 consensus 89.9 0.02 5E-07 35.2 -3.1 129 8-149 275-446 (1066)
120 KOG3657 consensus 87.9 0.12 3.2E-06 30.2 -0.2 36 90-129 240-275 (1075)
121 TIGR01388 rnd ribonuclease D; 84.0 1.7 4.2E-05 23.1 4.0 135 9-183 20-172 (374)
122 pfam00843 Arena_nucleocap Aren 79.5 3 7.7E-05 21.5 4.0 141 10-169 375-529 (534)
123 COG5228 POP2 mRNA deadenylase 78.8 1.8 4.5E-05 23.0 2.6 158 8-173 43-248 (299)
124 TIGR00593 pola DNA polymerase 57.1 2.9 7.4E-05 21.6 -0.1 85 91-179 465-572 (1005)
125 PRK05761 DNA polymerase I; Rev 54.0 4.8 0.00012 20.3 0.6 95 75-170 197-325 (777)
126 TIGR02373 photo_yellow photoac 50.7 6.2 0.00016 19.5 0.8 67 26-105 26-97 (126)
127 TIGR01284 alt_nitrog_alph nitr 42.4 7.2 0.00018 19.1 0.1 96 8-118 139-240 (468)
128 TIGR00658 orni_carb_tr ornithi 39.2 19 0.00048 16.5 1.8 27 140-171 113-143 (341)
129 PRK13582 thrH phosphoserine ph 36.4 18 0.00045 16.7 1.3 13 7-19 1-13 (205)
130 TIGR02386 rpoC_TIGR DNA-direct 34.8 11 0.00029 17.9 0.1 19 68-86 596-614 (1552)
131 COG2251 Predicted nuclease (Re 34.0 35 0.00088 14.9 4.3 80 71-153 332-420 (474)
132 TIGR01363 strep_his_triad stre 32.1 37 0.00095 14.7 2.7 57 31-101 74-137 (376)
133 PRK05406 LamB/YcsF family prot 31.5 25 0.00065 15.7 1.4 86 78-175 44-133 (246)
134 PRK12569 hypothetical protein; 29.4 27 0.00069 15.5 1.3 85 78-175 47-136 (245)
135 pfam05288 Pox_A3L Poxvirus A3L 27.7 18 0.00045 16.7 0.1 36 69-113 33-68 (70)
136 pfam03746 LamB_YcsF LamB/YcsF 25.8 36 0.00092 14.8 1.4 39 137-175 89-131 (242)
137 KOG3543 consensus 25.6 13 0.00034 17.5 -0.9 70 98-171 603-683 (1218)
138 COG2433 Uncharacterized conser 25.4 49 0.0012 14.0 3.6 27 147-175 335-361 (652)
139 TIGR00326 eubact_ribD riboflav 25.1 49 0.0013 13.9 2.3 140 16-181 14-168 (393)
140 pfam10776 DUF2600 Protein of u 23.9 18 0.00045 16.7 -0.5 17 71-87 128-144 (330)
141 pfam11074 DUF2779 Domain of un 22.7 27 0.00069 15.6 0.3 54 77-132 55-114 (127)
142 pfam04382 SAB SAB domain. This 22.5 38 0.00098 14.6 1.0 29 216-244 7-45 (48)
143 PHA02458 A protein A*; Reviewe 21.3 27 0.00069 15.6 0.0 17 160-176 222-238 (341)
144 TIGR01367 pyrE_Therm orotate p 20.7 60 0.0015 13.4 1.8 32 71-106 122-153 (205)
145 TIGR01851 argC_other N-acetyl- 20.6 47 0.0012 14.1 1.1 64 10-75 4-95 (314)
146 COG3219 Uncharacterized protei 20.1 29 0.00074 15.3 -0.0 54 60-113 60-119 (237)
No 1
>PRK06022 consensus
Probab=100.00 E-value=0 Score=495.81 Aligned_cols=233 Identities=47% Similarity=0.862 Sum_probs=209.5
Q ss_pred CCEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 75899984678888888889999999999998803137989858882288657242021012322485210023447775
Q gi|254780818|r 7 MRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDF 86 (245)
Q Consensus 7 mr~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~f 86 (245)
||+||||||||||+|.+|||||||||++.++..++++||+||||++++||+++++|||||++||+++|.|.+|+++|++|
T Consensus 1 mR~IvlDtETTGl~~~~dRIIEIg~vel~~~~~t~~~f~~~inP~~r~I~~~a~~IHGIt~e~L~~~P~F~eva~~fl~F 80 (234)
T PRK06022 1 MREIIFDTETTGLERREDRVIEIGGVELVNRFPTGRTFHKFINPQGRQVHPDALAVHGISDEQLLDKPVFAEILDEFLEF 80 (234)
T ss_pred CCEEEEEEECCCCCCCCCCEEEEEEEEEECCCCCCCEEEEEECCCCCCCCHHHHHHHCCCHHHHCCCCCHHHHHHHHHHH
T ss_conf 97699982279989989707999999997786336578999899998689889988560899870599799999999998
Q ss_pred HHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHH
Q ss_conf 30023202310232243112100000112222100001100000001776422237899971875455566640269999
Q gi|254780818|r 87 FNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHL 166 (245)
Q Consensus 87 i~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~r~~H~Al~Da~~ 166 (245)
++ |+++|||||+||++||++||.|+|.+++...+++|||.+||++|||+++|||+||+||+|++++|..|+||.||++
T Consensus 81 i~--~a~LVaHNA~FD~gFLn~El~r~G~~~~~~~~viDTL~LAR~~~Pg~~~sLdaLc~r~~Id~~~R~~HgAL~Da~l 158 (234)
T PRK06022 81 FD--GARLVAHNATFDLGFINAEFARLGQPEITSERVVDTLALARRKHPMGPNSLDALCRRYGIDNSHRTKHGALLDSEL 158 (234)
T ss_pred HC--CCEEEEECHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCHHHHHH
T ss_conf 18--9859995578729999999998599877788874699999986889988989999983999777353762888999
Q ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHCC
Q ss_conf 999999997305766665444321111011122-2344321123563457899999999999987087811456305
Q gi|254780818|r 167 LSDVYIKMMVGGSQINFGFKTNEDRFFKEEKKT-VPNISLLKRDKPLFTRITKEELDEHDKTIQTLGKNAIWDRYIS 242 (245)
Q Consensus 167 ~a~v~~~ll~g~~q~~l~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~e~~~H~~~l~~l~k~~lW~k~~~ 242 (245)
||+||++|+ ||+|++|.+.............. ........|+++...+++++|..+|.+||++|+++|||+||||
T Consensus 159 La~VyleL~-GG~q~~l~l~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~s~~E~~~H~~~l~~~~~~~iW~k~l~ 234 (234)
T PRK06022 159 LAEVYIELI-GGKQTALGLTMESGSAGGDSRGNGSAPVVLAARPRPLPPRLSDAERAAHAALVAKMGDKAVWKKYLS 234 (234)
T ss_pred HHHHHHHHC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHC
T ss_conf 999999972-8886751246565654433334454321224576656788999999999999985389818878649
No 2
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit; InterPro: IPR006309 These represent DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease region as described in IPR006055 from INTERPRO. 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 not included in this set of sequences, as they are smaller proteins.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication.
Probab=100.00 E-value=0 Score=500.41 Aligned_cols=226 Identities=42% Similarity=0.698 Sum_probs=191.9
Q ss_pred CEEEEECCCCCCCC-C-----CCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCC--CCCCHH
Q ss_conf 58999846788888-8-----888999999999999880313798985888228865724202101232248--521002
Q gi|254780818|r 8 RKIVFDIETTGLDS-K-----NDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDK--PSFSSI 79 (245)
Q Consensus 8 r~iv~D~ETTGl~~-~-----~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~--p~f~ev 79 (245)
|+|||||||||||| . +|||||||||+|+|+..||+.||.||+|+ |+||.+|.+|||||.++|.++ |.|++|
T Consensus 1 R~IiLDTETTGl~~~~G~~~~GhRivEIGavE~vnr~~tG~~fH~Y~~P~-Rd~p~eA~kVHGiT~efL~dKnaP~Fk~I 79 (246)
T TIGR01406 1 REIILDTETTGLDPKGGLPYIGHRIVEIGAVELVNRMLTGKNFHVYVKPE-RDIPAEAAKVHGITDEFLKDKNAPKFKEI 79 (246)
T ss_pred CEEEECCCCCCCCCCCCCCCCCCEEEEEEEEEEECCCCCCCCEEEEECCC-CCCHHHCEECCCCCHHHHCCCCCCCHHHH
T ss_conf 92671155568776677685686268882185673503887312433688-87730021013764688468898952578
Q ss_pred HHHHHHHHHCCCCEEEEECCCCCCCEEEECHHCCC---CCC-CCCCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf 34477753002320231023224311210000011---222-21000011000000017764222378999718754555
Q gi|254780818|r 80 FSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRIN---KDP-LDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHR 155 (245)
Q Consensus 80 ~~~f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~---~~~-~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~r 155 (245)
+++|++||+ |+.||+|||+||++|||.||.|+| ... .+.++++|||.|||++|||+++|||+||+|||||+++|
T Consensus 80 a~~Fl~Fi~--~~~LvIHNA~FD~gFlN~EL~~Lg~~~~~~~~~~~~~~DTL~mAR~~FPG~~~sLDALCkRf~vDns~R 157 (246)
T TIGR01406 80 ADEFLDFIK--GSELVIHNAAFDVGFLNYELERLGLKEIKKISDFCRVIDTLAMARERFPGKRNSLDALCKRFKVDNSHR 157 (246)
T ss_pred HHHHHHHHC--CCEEEEECCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCC
T ss_conf 999999845--988999757021678999998728732100013667865689997237898664678774304250002
Q ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-----HHHHHHHHHHHHH
Q ss_conf 66640269999999999997305766665444321111011122234432112356345789-----9999999999987
Q gi|254780818|r 156 SKHGALLDSHLLSDVYIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRIT-----KEELDEHDKTIQT 230 (245)
Q Consensus 156 ~~H~Al~Da~~~a~v~~~ll~g~~q~~l~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~e~~~H~~~l~~ 230 (245)
+.|+||.||++||+||++|++||......+...+........ ... ......+..+..++ ++|.++|.+||+.
T Consensus 158 ~LHGAL~DA~LLAeVYl~ltGGq~~~~~~~~~~~~~~~~~~~-~~~--~~~~~~~~~~~~p~dWq~~~~E~~~H~~~L~~ 234 (246)
T TIGR01406 158 QLHGALLDAELLAEVYLALTGGQESLLEMLVASESGEAAKAS-KKA--EQKKAKRLKVLAPRDWQVSEEELQAHEAYLDK 234 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHH-HHH--HHHCCCCCCCEECCCCCCCHHHHHHHHHHHHH
T ss_conf 134789999999999998628805777753122013456677-754--55302368704047441238899999999999
Q ss_pred CCC---CHHHHH
Q ss_conf 087---811456
Q gi|254780818|r 231 LGK---NAIWDR 239 (245)
Q Consensus 231 l~k---~~lW~k 239 (245)
+.+ .+||++
T Consensus 235 ~~~~~g~~lW~~ 246 (246)
T TIGR01406 235 LKKEAGTCLWRK 246 (246)
T ss_pred HHHHCCCEECCC
T ss_conf 875168022269
No 3
>PRK06859 consensus
Probab=100.00 E-value=0 Score=475.77 Aligned_cols=237 Identities=39% Similarity=0.657 Sum_probs=199.8
Q ss_pred CCCCCEEEEECCCCCCCC-----CCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCH
Q ss_conf 677758999846788888-----888899999999999988031379898588822886572420210123224852100
Q gi|254780818|r 4 KNKMRKIVFDIETTGLDS-----KNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSS 78 (245)
Q Consensus 4 ~~~mr~iv~D~ETTGl~~-----~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~e 78 (245)
-+.||+||||||||||+| .+|||||||||++.++..++++||+||||+ ++||+++++|||||++||+++|.|.+
T Consensus 2 ~n~~R~VvlDtETTGl~p~~~~~~g~RIIEIgaVel~~~~~t~~~f~~yinP~-r~I~~~a~~vhGIT~e~L~~kP~F~e 80 (253)
T PRK06859 2 INPNRQIVLDTETTGMNQFGAHYEGHCIIEIGAVELINRRYTGNNFHIYIKPD-RPVDPDAIKVHGITDEMLADKPEFKE 80 (253)
T ss_pred CCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCC-CCCCHHHHHHHCCCHHHHHCCCCHHH
T ss_conf 88883799972179999876666898689999999999978240467887869-94998899874508999836997999
Q ss_pred HHHHHHHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCC--CCCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCCCC
Q ss_conf 2344777530023202310232243112100000112222--10000110000000177642223789997187545556
Q gi|254780818|r 79 IFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPL--DPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRS 156 (245)
Q Consensus 79 v~~~f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~--~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~r~ 156 (245)
|+++|++||+ |++||||||+||++||++||+|+|.++. +.|+++|||.+||++|||+++|||+||+||+|++++|.
T Consensus 81 ia~efl~Fi~--~a~LVaHNa~FD~~FLn~El~r~g~~~~~~~~~~viDTL~lAR~~~Pg~~~sLdaLc~r~~id~~~R~ 158 (253)
T PRK06859 81 VAQEFIDYIK--GAELLIHNAPFDVGFMDYEFRKLNLNVKTDDICLVTDTLQMARQMYPGKRNNLDALCDRLGIDNSKRT 158 (253)
T ss_pred HHHHHHHHHC--CCEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCCEEEHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCC
T ss_conf 9999999967--99799957188899999999974999653220011339999998787997799999997399876633
Q ss_pred CCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC--
Q ss_conf 664026999999999999730576666544432111101112223-44321123563457899999999999987087--
Q gi|254780818|r 157 KHGALLDSHLLSDVYIKMMVGGSQINFGFKTNEDRFFKEEKKTVP-NISLLKRDKPLFTRITKEELDEHDKTIQTLGK-- 233 (245)
Q Consensus 157 ~H~Al~Da~~~a~v~~~ll~g~~q~~l~l~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~e~~~H~~~l~~l~k-- 233 (245)
.|+||.||++||+||++|++||. ..+.................. ......+.++.++.++++|+.+|.+||+.|.|
T Consensus 159 ~HgAllDa~lLa~VYl~mtGGQ~-~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~i~~s~eE~~~H~~~L~~i~kk~ 237 (253)
T PRK06859 159 LHGALLDAEILADVYLMMTGGQT-SLFDEEESEVIHVMQEKTAEEIKSAVDFSHNLKLLQPTNDELQAHLEYLKLLNKKS 237 (253)
T ss_pred CCCHHHHHHHHHHHHHHHCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHC
T ss_conf 01328889999999998726754-45334576434443332210002233344577504799999999999999998762
Q ss_pred --CHHHHHHCCCC
Q ss_conf --81145630557
Q gi|254780818|r 234 --NAIWDRYISSN 244 (245)
Q Consensus 234 --~~lW~k~~~~~ 244 (245)
+++|+||+.++
T Consensus 238 g~~~lW~k~~~~~ 250 (253)
T PRK06859 238 KNNCLWEKRLGNN 250 (253)
T ss_pred CCCCCEEECCCCC
T ss_conf 9995403311346
No 4
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=100.00 E-value=0 Score=474.55 Aligned_cols=233 Identities=44% Similarity=0.772 Sum_probs=201.7
Q ss_pred CCCCCEEEEECCCCCCCCCC-CEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHH
Q ss_conf 67775899984678888888-88999999999999880313798985888228865724202101232248521002344
Q gi|254780818|r 4 KNKMRKIVFDIETTGLDSKN-DRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSE 82 (245)
Q Consensus 4 ~~~mr~iv~D~ETTGl~~~~-d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~ 82 (245)
.+.||+||||||||||+|.. |||||||||++.++..++++||+||||+ ++||+++++|||||++||+++|.|.+++++
T Consensus 1 ~~~MR~VvlDtETTGl~~~~gdRIIEIgav~~~~~~~t~~~f~~~inP~-r~i~~~a~~IhGIT~e~L~~~P~F~ei~~e 79 (240)
T PRK05711 1 TAIMRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPD-RDVDPEALAVHGITDEFLADKPTFAEVADE 79 (240)
T ss_pred CCCCCEEEEEEECCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCC-CCCCHHHHHHCCCCHHHHCCCCCHHHHHHH
T ss_conf 9766289998668996999998789999999999988143578998968-959977875408688996458759999999
Q ss_pred HHHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCC---CCCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCC
Q ss_conf 777530023202310232243112100000112222---10000110000000177642223789997187545556664
Q gi|254780818|r 83 FWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPL---DPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHG 159 (245)
Q Consensus 83 f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~---~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~r~~H~ 159 (245)
|++||+ |+++|||||+||++||++||+|+|.+.. ..|+++|||.+||++|||+++|||+||++|+|++++|+.|+
T Consensus 80 fl~Fi~--~s~lVaHNa~FD~~FLn~El~r~g~~~~~~~~~~~viDTL~lAR~~~Pg~~~sLdaLc~r~~I~~s~R~~Hg 157 (240)
T PRK05711 80 FLDFIR--GAELIIHNAPFDIGFMDYEFALLGRDIPKTTTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLHG 157 (240)
T ss_pred HHHHHC--CCEEEEECCHHHHHHHHHHHHHHCCCCCCHHHHCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCC
T ss_conf 999818--997999661998999999999868998764452121019999998789998899999998098988756576
Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC---CHH
Q ss_conf 02699999999999973057666654443211110111222344321123563457899999999999987087---811
Q gi|254780818|r 160 ALLDSHLLSDVYIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEHDKTIQTLGK---NAI 236 (245)
Q Consensus 160 Al~Da~~~a~v~~~ll~g~~q~~l~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~H~~~l~~l~k---~~l 236 (245)
||.||++||+||++|++| |.++.+.................. ...++++....++++|+.+|.+||+.|.| +|+
T Consensus 158 AL~Da~llA~Vyl~l~gG--Q~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~s~eE~~~H~~~l~~i~k~~~~~i 234 (240)
T PRK05711 158 ALLDAEILAEVYLAMTGG--QTSLGFAMEGETQQQQGEATIQRI-VRQASRLPVVRATDEELAAHEARLDLLDKKGGSCL 234 (240)
T ss_pred HHHHHHHHHHHHHHHCCC--CCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 488899999999997178--756655755432112454433434-45556777488999999999999999985589864
Q ss_pred HHHHCC
Q ss_conf 456305
Q gi|254780818|r 237 WDRYIS 242 (245)
Q Consensus 237 W~k~~~ 242 (245)
|+||++
T Consensus 235 W~k~~~ 240 (240)
T PRK05711 235 WRKPLE 240 (240)
T ss_pred CCCCCC
T ss_conf 267079
No 5
>PRK07982 consensus
Probab=100.00 E-value=0 Score=465.78 Aligned_cols=230 Identities=37% Similarity=0.682 Sum_probs=194.5
Q ss_pred CCCCCCEEEEECCCCCCCC-----CCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCC
Q ss_conf 6677758999846788888-----88889999999999998803137989858882288657242021012322485210
Q gi|254780818|r 3 RKNKMRKIVFDIETTGLDS-----KNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFS 77 (245)
Q Consensus 3 ~~~~mr~iv~D~ETTGl~~-----~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ 77 (245)
.+.+||+||||||||||+| .+|||||||||++.|+..++++||+||||+ ++||+++++|||||++||+++|.|.
T Consensus 2 ~~~~~R~ivlDtETTGL~p~~~~~~gdRIIEIgaVei~~~~~t~~~fh~yiNP~-r~I~~~a~~VHGIT~e~L~dkP~F~ 80 (243)
T PRK07982 2 STAITRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVINRRLTGNNFHVYLKPD-RLVDPEAFGVHGIADEFLLDKPTFA 80 (243)
T ss_pred CCCCCEEEEEEEECCCCCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCC-CCCCHHHHHHEEECHHHHHCCCCHH
T ss_conf 864025899971179999877677898799999999999988252343788889-9799889852115778871699899
Q ss_pred HHHHHHHHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCC---CCCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCC
Q ss_conf 02344777530023202310232243112100000112222---100001100000001776422237899971875455
Q gi|254780818|r 78 SIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPL---DPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISH 154 (245)
Q Consensus 78 ev~~~f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~---~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~ 154 (245)
+|+++|++||+ |++||||||+||++||++||.|+|...+ ..|+++|||.+||.+|||+++|||+||+||+|++++
T Consensus 81 eI~~efl~Fi~--~a~LVaHNA~FD~~FLn~El~r~g~~~~~~~~~~~v~DTL~lAR~~~Pg~~~sLDaLc~R~~Id~s~ 158 (243)
T PRK07982 81 DVADEFLDYIR--GAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLALARKMFPGKRNSLDALCDRYEIDNSK 158 (243)
T ss_pred HHHHHHHHHHC--CCEEEEECCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEHHHHHHHHCCCCCCCHHHHHHHCCCCCCC
T ss_conf 99999999967--9989997338889999999997088988610124313499998887889868999998754877656
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCC--
Q ss_conf 566640269999999999997305766665444321111011122234432112356345789999999999998708--
Q gi|254780818|r 155 RSKHGALLDSHLLSDVYIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEHDKTIQTLG-- 232 (245)
Q Consensus 155 r~~H~Al~Da~~~a~v~~~ll~g~~q~~l~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~H~~~l~~l~-- 232 (245)
|+.|+||.||++||+||++|++|| .++.+.................. ...+.++.+..++++|+.+|.+||+.+.
T Consensus 159 R~~HgALlDa~lLAeVYl~ltgGQ--~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~~~~s~eE~~~H~~~L~~i~k~ 235 (243)
T PRK07982 159 RTLHGALLDAQILAEVYLAMTGGQ--TSMAFAMEGETQQQQGEATIQRI-VRQASKLRVVYATDEELAAHESRLDLVQKK 235 (243)
T ss_pred CCCCCHHHHHHHHHHHHHHHCCCC--CCCCCCCCCCCCCCCCCCCHHHC-CCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 552333774889999999972898--66555656542223453211102-344567760579999999999999999851
Q ss_pred -CCHHHH
Q ss_conf -781145
Q gi|254780818|r 233 -KNAIWD 238 (245)
Q Consensus 233 -k~~lW~ 238 (245)
.+|+|+
T Consensus 236 ~~~~lW~ 242 (243)
T PRK07982 236 GGSCLWR 242 (243)
T ss_pred CCCCCCC
T ss_conf 8988578
No 6
>PRK07009 consensus
Probab=100.00 E-value=0 Score=464.81 Aligned_cols=231 Identities=38% Similarity=0.692 Sum_probs=197.6
Q ss_pred CCEEEEECCCCCCCCC-CCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 7589998467888888-888999999999999880313798985888228865724202101232248521002344777
Q gi|254780818|r 7 MRKIVFDIETTGLDSK-NDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWD 85 (245)
Q Consensus 7 mr~iv~D~ETTGl~~~-~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~ 85 (245)
||+||||||||||+|. +|||||||||++.++..++++||+||||+ ++||+++++|||||++||+++|.|.+|+++|++
T Consensus 1 Mr~VvlDtETTGl~~~~gdRIIEIg~v~l~~~~~t~~~~~~yiNP~-r~I~~~a~~IHGIt~e~L~~kP~F~eia~efl~ 79 (241)
T PRK07009 1 MRQIILDTETTGLNARTGDRIIEIGCVELLNRRLTGNNLHFYVNPE-RDSDPGALAVHGLTTEFLSDKPKFAEVVDQIRD 79 (241)
T ss_pred CCEEEEEEECCCCCCCCCCEEEEEEEEEEECCEEECEEEEEEECCC-CCCCHHHHHHHCCCHHHHHCCCCHHHHHHHHHH
T ss_conf 9879998257997999998789999999999978040689987889-979975765122579987258559999999999
Q ss_pred HHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCC--CHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHH
Q ss_conf 53002320231023224311210000011222210--0001100000001776422237899971875455566640269
Q gi|254780818|r 86 FFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDP--SRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLD 163 (245)
Q Consensus 86 fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~--~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~r~~H~Al~D 163 (245)
||+ |++||||||+||++||++||+|+|++++.. ++++|||.+||.+|||+++|||+||+||+|++++|..|+||.|
T Consensus 80 Fi~--~a~LVaHNA~FD~~FLn~EL~r~G~~~~~~~~~~viDTL~lAR~~~Pg~~~sLdaLc~R~~I~~~~r~~HgAL~D 157 (241)
T PRK07009 80 FVQ--DAELIIHNAPFDLGFLDAEFALLGLPPFTEHCAGVIDTLVQAKQMFPGKRNSLDALCDRFGISNAHRTLHGALLD 157 (241)
T ss_pred HHC--CCEEEEECHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCHHH
T ss_conf 966--992788676999999999999839973102444476799999997899987889999982869887330242877
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC----CHHHHH
Q ss_conf 9999999999973057666654443211110111222344321123563457899999999999987087----811456
Q gi|254780818|r 164 SHLLSDVYIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEHDKTIQTLGK----NAIWDR 239 (245)
Q Consensus 164 a~~~a~v~~~ll~g~~q~~l~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~H~~~l~~l~k----~~lW~k 239 (245)
|++||+||++|++||....+....... ............ ..+....+..++++|+.+|.+||+.|+| ++||+|
T Consensus 158 a~lLa~vyl~mtgGq~~l~~~~~~~~~--~~~~~~~~~~~~-~~~~~~~~~~~s~~E~~~H~~~l~~i~k~s~~~~lW~~ 234 (241)
T PRK07009 158 SELLAEVYLAMTRGQDSLVIDMLDEAG--AAGGNGDAPRMA-FSALDLPVLAATDAELAAHEAQLDALDKSVKGACVWRK 234 (241)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCC--CCCCCCCCCCCC-CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 999999999983897433345566433--223456543135-65567873679999999999999999764189851278
Q ss_pred HCCC
Q ss_conf 3055
Q gi|254780818|r 240 YISS 243 (245)
Q Consensus 240 ~~~~ 243 (245)
....
T Consensus 235 ~~~~ 238 (241)
T PRK07009 235 EPVA 238 (241)
T ss_pred CCCC
T ss_conf 9876
No 7
>PRK08816 consensus
Probab=100.00 E-value=0 Score=464.17 Aligned_cols=231 Identities=38% Similarity=0.658 Sum_probs=194.7
Q ss_pred CCEEEEECCCCCCCC-CCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 758999846788888-8888999999999999880313798985888228865724202101232248521002344777
Q gi|254780818|r 7 MRKIVFDIETTGLDS-KNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWD 85 (245)
Q Consensus 7 mr~iv~D~ETTGl~~-~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~ 85 (245)
||+||||||||||+| .+|||||||||++.++..++++||+||||+ ++||+++++|||||++||+++|.|.+|+++|++
T Consensus 1 mR~VVlDtETTGl~~~~gdRIIEIgaV~~~~~~~~~~~f~~~inP~-r~I~~~a~~vhGIT~e~L~dkP~F~eV~~efl~ 79 (244)
T PRK08816 1 MRQIILDTETTGLEWRKGNRVVEIGAVELLERRPSGNNFHRYLKPD-CDFEPGAQEVTGLTLEFLADKPLFGEVVDEFLA 79 (244)
T ss_pred CCEEEEEEECCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCC-CCCCHHHHHHHCCCHHHHHCCCCHHHHHHHHHH
T ss_conf 9879997227998998998899999999999968143789986889-969988987525178998409989999999999
Q ss_pred HHHCCCCEEEEECCCCCCCEEEECHHCCCCCC---CCCCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHH
Q ss_conf 53002320231023224311210000011222---210000110000000177642223789997187545556664026
Q gi|254780818|r 86 FFNEQNAEWIAHNAKFDVGFINAELQRINKDP---LDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALL 162 (245)
Q Consensus 86 fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~---~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~r~~H~Al~ 162 (245)
|++ |++||||||+||++||++||.|+|.++ ...+.++|||.+||.+|||+++|||+||+||+|++++|+.|+||.
T Consensus 80 Fi~--ds~LVaHNa~FDi~FLn~El~r~g~~~~~~~~~~~v~DTl~lAr~~~Pg~~nsLDaLc~r~~id~~~R~~HgALl 157 (244)
T PRK08816 80 YID--GAELIIHNAAFDLGFLDNELSLLGDQYGRIVDRATVVDTLMMARERYPGQRNSLDALCKRLGVDNSHRQLHGALL 157 (244)
T ss_pred HHC--CCEEEEECCHHHHHHHHHHHHHHCCCCCCCCCCCCEEEHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCHHH
T ss_conf 828--998999663652989999999848875676431010438999998787997789999997497887735014888
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC---CHHHHH
Q ss_conf 99999999999973057666654443211110111222344321123563457899999999999987087---811456
Q gi|254780818|r 163 DSHLLSDVYIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEHDKTIQTLGK---NAIWDR 239 (245)
Q Consensus 163 Da~~~a~v~~~ll~g~~q~~l~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~H~~~l~~l~k---~~lW~k 239 (245)
||++||+||++|++||.+.+|........ ..............+.+...+.++++|+.+|.+||+.|.| +|+|+.
T Consensus 158 Da~lLa~VYl~mtgGq~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~i~~s~~El~aH~~~L~~i~k~~g~~lW~~ 235 (244)
T PRK08816 158 DAQILADVYIALTSGQEEIGFASADAGQQ--ADAASGMIAFDPALLLPRPRVVVTASELQAHEARLAQLRKKAGRALWDA 235 (244)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCC--CCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 79999999999747865554566664433--4454441001532125555678999999999999999876448771689
Q ss_pred HCC
Q ss_conf 305
Q gi|254780818|r 240 YIS 242 (245)
Q Consensus 240 ~~~ 242 (245)
++.
T Consensus 236 ~~~ 238 (244)
T PRK08816 236 PVE 238 (244)
T ss_pred CCC
T ss_conf 775
No 8
>PRK08858 consensus
Probab=100.00 E-value=0 Score=459.58 Aligned_cols=230 Identities=42% Similarity=0.730 Sum_probs=195.3
Q ss_pred CCCCCCEEEEECCCCCCCCC------CCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCC
Q ss_conf 66777589998467888888------888999999999999880313798985888228865724202101232248521
Q gi|254780818|r 3 RKNKMRKIVFDIETTGLDSK------NDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSF 76 (245)
Q Consensus 3 ~~~~mr~iv~D~ETTGl~~~------~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f 76 (245)
.++.+|+||||||||||+|. +|||||||||++.++..++++||+||||+ ++||+++++|||||++||+++|.|
T Consensus 6 ~~~~~R~VVlDtETTGl~~~~~~~~~gdRIIEIgaV~i~~~~~t~~~f~~~InP~-r~Ip~~a~~ihGIT~e~L~daP~F 84 (246)
T PRK08858 6 NSEYQRIVVLDTETTGMNREGGPHYEGHRIIEIGAVEIINRKLTGRHFHVYLKPD-REIQPEAIDVHGITDEFLVDKPEY 84 (246)
T ss_pred CCCCCEEEEEEEECCCCCCCCCCCCCCCEEEEEEEEEEECCEEECCEEEEEECCC-CCCCHHHHHHCCCCHHHHHCCCCH
T ss_conf 8760479999857899997656777898799999999999998221478888979-969988997739289998359758
Q ss_pred CHHHHHHHHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCC---CCCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCC
Q ss_conf 002344777530023202310232243112100000112222---10000110000000177642223789997187545
Q gi|254780818|r 77 SSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPL---DPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITIS 153 (245)
Q Consensus 77 ~ev~~~f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~---~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~ 153 (245)
.+|+++|++||+ |++||||||+||++||++||.|+|.... ..|+++|||.+||.+|||+++|||+||+||+|+++
T Consensus 85 ~eI~~efl~FI~--d~~LVaHNa~FD~~FLn~El~r~~~~~~~~~~~~~viDTL~lAR~~~Pg~~~sLdaLc~r~~Id~s 162 (246)
T PRK08858 85 KDVHQEFLEFIK--GAELVAHNAPFDVGFMDYEFEKLNPAIGKTDDYCKVTDTLAMAKKIFPGKRNNLDVLCERYGIDNS 162 (246)
T ss_pred HHHHHHHHHHHC--CCEEEEECCHHHHHHHHHHHHHHCCCCCCHHHHCCCEEHHHHHHHHCCCCCCCHHHHHHHCCCCCC
T ss_conf 999999999958--998999722888999999999828776751342010029999998689998888999998198988
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf 55666402699999999999973057666654443211110111222344321123563457899999999999987087
Q gi|254780818|r 154 HRSKHGALLDSHLLSDVYIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEHDKTIQTLGK 233 (245)
Q Consensus 154 ~r~~H~Al~Da~~~a~v~~~ll~g~~q~~l~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~H~~~l~~l~k 233 (245)
+|+.|+||.||++||+||++|++||....+............... .....+..+.+++++++|+.+|.+||+.|+|
T Consensus 163 ~R~~HgALlDa~lLa~Vyl~mtgGQ~~l~~~~~~~~~~~~~~~~~----~~~~~~~~~~vi~~s~eE~~~H~~~L~~i~k 238 (246)
T PRK08858 163 HRTLHGALLDAEILADVYLLMTGGQTSLEFSANKQEGGLSAETIK----RVRSGRKALKVLRATADELEAHQKRLDIVNK 238 (246)
T ss_pred CCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHH----HHCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf 834023088899999999997289876444667654444421012----1003466775157999999999999999732
Q ss_pred --CHHHHH
Q ss_conf --811456
Q gi|254780818|r 234 --NAIWDR 239 (245)
Q Consensus 234 --~~lW~k 239 (245)
+|||+|
T Consensus 239 ~~~~lWrk 246 (246)
T PRK08858 239 SGTCLWRQ 246 (246)
T ss_pred HCCCCCCC
T ss_conf 06786589
No 9
>PRK06631 consensus
Probab=100.00 E-value=0 Score=451.26 Aligned_cols=224 Identities=37% Similarity=0.664 Sum_probs=194.9
Q ss_pred CCCCEEEEECCCCCCCCC-CCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHH
Q ss_conf 777589998467888888-8889999999999998803137989858882288657242021012322485210023447
Q gi|254780818|r 5 NKMRKIVFDIETTGLDSK-NDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEF 83 (245)
Q Consensus 5 ~~mr~iv~D~ETTGl~~~-~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f 83 (245)
.-||+||||||||||+|. +|||||||||++.|+..++++||+||||+ ++||+.+++|||||++||+++|.|.+|+++|
T Consensus 2 ~~mr~VvlD~ETTGl~~~~gdrIIEIgav~~~~~~~t~~~f~~~inP~-r~i~~~~~~ihGIt~e~l~~~P~f~ev~~~f 80 (229)
T PRK06631 2 SSLREIILDTETTGLDPQQGHRIVEIGAIEMVNKVLTGRNFHFYINPE-RDMPFEAYRIHGISGEFLKDKPLFHTIADDF 80 (229)
T ss_pred CCCCEEEEEEECCCCCCCCCCEEEEEEEEEEECCEEECCEEEEEECCC-CCCCHHHHHCCCCCHHHHHHCCCHHHHHHHH
T ss_conf 878889998257998999998799999999999988043799998989-9797615120186789985387799999999
Q ss_pred HHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCC---CCCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCC
Q ss_conf 77530023202310232243112100000112222---100001100000001776422237899971875455566640
Q gi|254780818|r 84 WDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPL---DPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGA 160 (245)
Q Consensus 84 ~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~---~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~r~~H~A 160 (245)
++||+ |++||||||+||++||++||.++|...+ ..++++|||.+||.+|||++++|++||++|||++++|.+|+|
T Consensus 81 l~Fi~--~s~LVaHNA~FD~~FLn~El~~l~~~~~~~~~~~~viDTL~lAR~~~Pg~~~sLdaLc~r~~I~~s~r~~H~A 158 (229)
T PRK06631 81 LEFIS--DSKLIIHNAPFDIKFLNHELSLLKRTEIKLLELANTIDTLVMARSMFPGSKYNLDALCKRFKVDNSGRQLHGA 158 (229)
T ss_pred HHHCC--CCEEEEECCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCC
T ss_conf 99829--9979997638759899999998278888843201101269999986899888999999984999998555686
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCH
Q ss_conf 269999999999997305766665444321111011122234432112356345789999999999998708781
Q gi|254780818|r 161 LLDSHLLSDVYIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEHDKTIQTLGKNA 235 (245)
Q Consensus 161 l~Da~~~a~v~~~ll~g~~q~~l~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~H~~~l~~l~k~~ 235 (245)
|.||++||+||++|+ ||+|++|++........... ........+....++.++++|+.+|.+||+++.|++
T Consensus 159 L~DA~llA~Vyl~l~-gG~q~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~s~~E~~~H~~~l~~i~K~~ 229 (229)
T PRK06631 159 LKDAALLAEVYVELT-GGRQSAFKMVDKSAEINNLA---TNQVNNKTEQTTIVIKPTKEELQKHKEFLSRILKTA 229 (229)
T ss_pred HHHHHHHHHHHHHHH-CCCCCCCCCCCCCCCCCCCC---HHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCC
T ss_conf 899999999999971-78866655666642124310---110111113477646799999999999998865479
No 10
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=0 Score=342.18 Aligned_cols=166 Identities=27% Similarity=0.446 Sum_probs=153.2
Q ss_pred CCCCCEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHH
Q ss_conf 67775899984678888888889999999999998803137989858882288657242021012322485210023447
Q gi|254780818|r 4 KNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEF 83 (245)
Q Consensus 4 ~~~mr~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f 83 (245)
-.-|.+||||+||||++|.+|+|||||||++.++.++ ++|++||||+ ++||+.+++|||||++||++||+|.+||++|
T Consensus 5 ~lp~~fVV~DiETTGl~p~~D~IIEIgAVkv~ng~Iv-d~f~tLInP~-~~Ip~~It~ItGIT~emV~dAP~f~EVl~~f 82 (313)
T PRK06807 5 SLPLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELV-DQFVSYVNPE-RPIPDRITSLTGITNYRVSDAPTIEEVLPLF 82 (313)
T ss_pred CCCCCEEEEEEECCCCCCCCCEEEEEEEEEEECCEEE-EEEEEEECCC-CCCCHHHHHHCCCCHHHHHCCCCHHHHHHHH
T ss_conf 8998789999788997999987899999999999798-9999998948-9799667653397999982699899999999
Q ss_pred HHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHHCCCCCCCCCCCCHH
Q ss_conf 775300232023102322431121000001122221000011000000017764-2223789997187545556664026
Q gi|254780818|r 84 WDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRYGITISHRSKHGALL 162 (245)
Q Consensus 84 ~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~~i~~~~r~~H~Al~ 162 (245)
++|++ |+++|||||+||++||++++.|+|++.+ .++++||+.+||.++|+. +++|+++|++|||++. +|+|+.
T Consensus 83 ~~Fi~--d~iLVAHNA~FD~~FL~~~L~r~gl~~~-~n~~IDTL~LAR~l~P~L~NhKLnTVa~~LgI~l~---HHrAld 156 (313)
T PRK06807 83 LAFLH--TNVIVAHNASFDMRFLKSNVNMLGLPEP-KNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLS---SHNAFD 156 (313)
T ss_pred HHHCC--CCEEEEECCHHHHHHHHHHHHHCCCCCC-CCCEEEHHHHHHHHCCCCCCCCHHHHHHHHCCCCC---CCCCHH
T ss_conf 98738--9989995536619999999997499888-99877659999986478765667899998399834---367177
Q ss_pred HHHHHHHHHHHHHHC
Q ss_conf 999999999999730
Q gi|254780818|r 163 DSHLLSDVYIKMMVG 177 (245)
Q Consensus 163 Da~~~a~v~~~ll~g 177 (245)
||.+||++|+++..-
T Consensus 157 DA~acAeI~~k~~~~ 171 (313)
T PRK06807 157 DCITCAAVYQKCASI 171 (313)
T ss_pred HHHHHHHHHHHHHHH
T ss_conf 899999999999998
No 11
>PRK07740 hypothetical protein; Provisional
Probab=100.00 E-value=0 Score=338.36 Aligned_cols=172 Identities=23% Similarity=0.381 Sum_probs=155.0
Q ss_pred CCCEEEEECCCCCCCCC-CCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHH
Q ss_conf 77589998467888888-88899999999999988031379898588822886572420210123224852100234477
Q gi|254780818|r 6 KMRKIVFDIETTGLDSK-NDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFW 84 (245)
Q Consensus 6 ~mr~iv~D~ETTGl~~~-~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~ 84 (245)
-+.+||||+|||||+|. +|+|||||||++.++.++ ++|+++|||+ ++||+.+++|||||++||+++|+|.+|+++|+
T Consensus 56 ~~~fvV~D~ETTGl~p~~gD~IIeIgAVkv~~g~i~-d~F~tLVnP~-~~Ip~~i~~ltGIT~emV~~aP~~~eVl~~fl 133 (240)
T PRK07740 56 DLPFVVFDLETTGFSPDQGDEILSIAAVKTVGGEVT-DLYYSLVKPK-KPIPEHILTLTGISAKDVVFAPPLAEVLRTFY 133 (240)
T ss_pred CCEEEEEEEECCCCCCCCCCEEEEEEEEEEECCEEE-EEEEEEECCC-CCCCHHHHHHCCCCHHHHHCCCCHHHHHHHHH
T ss_conf 383899980589989888987899989999999996-8877550887-98998899860989999837999999999999
Q ss_pred HHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHH
Q ss_conf 75300232023102322431121000001122221000011000000017764222378999718754555666402699
Q gi|254780818|r 85 DFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDS 164 (245)
Q Consensus 85 ~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~r~~H~Al~Da 164 (245)
+|++ |+++|||||+||++||++++.|.+..++ .++++||+.++|.++|..+++|++||++|||+..+ +|+|++||
T Consensus 134 ~Fi~--~~vlVaHNa~FD~~FL~~~l~r~~~~~~-~~~~iDT~~Lar~l~~~~~~sL~~l~~~fgI~~~~--rHrAl~DA 208 (240)
T PRK07740 134 PFIN--ASTLVGYHIGHDLAFLRHALWRHYRQKF-SHRFIDTQFLTEIIAHQSFPTLDDALACYGITCPR--RHTADGDV 208 (240)
T ss_pred HHHC--CCEEEEECCHHHHHHHHHHHHHHCCCCC-CCCEEEHHHHHHHHCCCCCCCHHHHHHHCCCCCCC--CCCCHHHH
T ss_conf 9838--9989996828639999999998459987-88763699999986589987899999976999999--98829999
Q ss_pred HHHHHHHHHHHHCCCCCCCC
Q ss_conf 99999999997305766665
Q gi|254780818|r 165 HLLSDVYIKMMVGGSQINFG 184 (245)
Q Consensus 165 ~~~a~v~~~ll~g~~q~~l~ 184 (245)
++||+||++|+...++.++.
T Consensus 209 ~aTA~lf~~ll~~l~~~Gi~ 228 (240)
T PRK07740 209 EMTAKLWAILIIEARQAGIE 228 (240)
T ss_pred HHHHHHHHHHHHHHHHCCCC
T ss_conf 99999999999999976999
No 12
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=100.00 E-value=0 Score=334.98 Aligned_cols=163 Identities=30% Similarity=0.442 Sum_probs=151.7
Q ss_pred CCEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 75899984678888888889999999999998803137989858882288657242021012322485210023447775
Q gi|254780818|r 7 MRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDF 86 (245)
Q Consensus 7 mr~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~f 86 (245)
-.+||||+||||++|..|+|||||||++.++.++ ++|+++|||. +||+.++++||||++||+++|+|.+|+++|.+|
T Consensus 70 ~~fvvvDlETTGl~~~~d~IIEIgavkv~~g~ii-d~f~tlVnp~--~Ip~~It~lTGIt~emv~~aP~~~evl~~f~~F 146 (259)
T PRK08517 70 QVFCFVDIETNGSKPKKGQIIEIGAVKVKGGEII-DRFESFVKAK--EVPEYITELTGITYEDLENAPSLKEVLEDFRLF 146 (259)
T ss_pred CCEEEEEEECCCCCCCCCEEEEEEEEEEECCEEE-EEEEEEECCC--CCCHHHHHHCCCCHHHHHCCCCHHHHHHHHHHH
T ss_conf 8389999658998999982499999999999999-9874323989--899888221389989982799889999999999
Q ss_pred HHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHH
Q ss_conf 30023202310232243112100000112222100001100000001776422237899971875455566640269999
Q gi|254780818|r 87 FNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHL 166 (245)
Q Consensus 87 i~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~r~~H~Al~Da~~ 166 (245)
++ |+++|||||+||++||++++.++|.+++ .++++||+.+||..+|+.+++|++||++|||+..+ +|+|++||.+
T Consensus 147 i~--d~ilVaHNa~FD~~FL~~~l~r~g~~~l-~n~~lDTl~LAR~~~p~~~ykL~~La~~~~I~~~~--~HRAl~DA~a 221 (259)
T PRK08517 147 LG--DSVFVAHNVNFDYNFISRSLEEIGLGPL-LNRKLCTIDLAKRTIESPRYGLSFLKELLGIETEV--HHRAYADALA 221 (259)
T ss_pred HC--CCEEEEECCHHHHHHHHHHHHHCCCCCC-CCCEEEEHHHHHHHCCCCCCCHHHHHHHCCCCCCC--CCCCHHHHHH
T ss_conf 68--8959993727609999999998399976-89856608999987587787889999975989999--9784588999
Q ss_pred HHHHHHHHHHC
Q ss_conf 99999999730
Q gi|254780818|r 167 LSDVYIKMMVG 177 (245)
Q Consensus 167 ~a~v~~~ll~g 177 (245)
||+||..++..
T Consensus 222 TaevF~~~L~~ 232 (259)
T PRK08517 222 AYEIFEICLLN 232 (259)
T ss_pred HHHHHHHHHHH
T ss_conf 99999999985
No 13
>PRK07883 hypothetical protein; Validated
Probab=100.00 E-value=0 Score=335.50 Aligned_cols=163 Identities=29% Similarity=0.455 Sum_probs=151.0
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 58999846788888888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
-+||||+||||++|..|+|||||||++.++.+++ .|++||||+ ++||++++++||||++||.++|+|.+|+++|++|+
T Consensus 25 tfVVvDlETTG~s~~~d~IiEIgAVkv~~g~vv~-~f~tLVnP~-~~Ip~~I~~LTGIt~~mV~~AP~~~~vl~~f~~F~ 102 (575)
T PRK07883 25 TFVVVDLETTGGSPTGDAITEIGAVKVRGGEVLG-EFATLVNPG-RSIPPFIVVLTGITTAMVADAPPIDAVLPAFLEFA 102 (575)
T ss_pred EEEEEEEECCCCCCCCCEEEEEEEEEEECCEEEE-EEECCCCCC-CCCCHHHHCCCCCCHHHHCCCCCHHHHHHHHHHHH
T ss_conf 4899995079999889705999999998999999-971001938-98985440036969899807999999999999996
Q ss_pred HCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCC---CCCCHHHHHHHHCCCCCCCCCCCCHHHH
Q ss_conf 0023202310232243112100000112222100001100000001776---4222378999718754555666402699
Q gi|254780818|r 88 NEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPS---SRNDLNSLCKRYGITISHRSKHGALLDS 164 (245)
Q Consensus 88 ~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~---~~~~L~~l~~~~~i~~~~r~~H~Al~Da 164 (245)
+ |++||||||.||++||++++.++|++|+ .++++||+.|||.++|+ .+++|++||++||+.... .|+||+||
T Consensus 103 ~--~~vlVAHNa~FD~~FL~~~~~r~g~~~~-~~~~ldTl~LARrl~p~~e~~~~kL~tLa~~~g~~~~~--~HRAl~DA 177 (575)
T PRK07883 103 R--GSVLVAHNAPFDIGFLRAAAERCGYPWP-QPEVLCTVRLARRVLSRDEAPNVRLSALARLFGAATTP--THRALDDA 177 (575)
T ss_pred C--CCEEEEECCHHHHHHHHHHHHHCCCCCC-CCCEEEHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCC--CCCHHHHH
T ss_conf 8--9989990834529999999997599987-89786489999986692114689989999975999999--86604529
Q ss_pred HHHHHHHHHHHHC
Q ss_conf 9999999999730
Q gi|254780818|r 165 HLLSDVYIKMMVG 177 (245)
Q Consensus 165 ~~~a~v~~~ll~g 177 (245)
++|++||..|+..
T Consensus 178 ~AT~~vl~~l~~~ 190 (575)
T PRK07883 178 RATVDVLHGLIER 190 (575)
T ss_pred HHHHHHHHHHHHH
T ss_conf 9999999999998
No 14
>cd06131 DNA_pol_III_epsilon_Ecoli_like This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (polIII) and similar proteins. PolIII 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 polIII 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 subunit of polIII also functions as a stabilizer of the holoenzyme complex.
Probab=100.00 E-value=0 Score=335.06 Aligned_cols=164 Identities=54% Similarity=0.888 Sum_probs=153.0
Q ss_pred EEEEECCCCCCCCCC-CEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 899984678888888-8899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 9 KIVFDIETTGLDSKN-DRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 9 ~iv~D~ETTGl~~~~-d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
+||||+|||||+|.. |||||||||++.++..++++|++||||+ +++++++++|||||++||+++|+|.+++++|++|+
T Consensus 1 ~Vv~D~ETTGl~p~~~d~Iieigav~~~~~~~~~~~~~~lv~P~-~~i~~~~~~ihGIt~e~l~~~p~~~ev~~~f~~~l 79 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPE-RDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFI 79 (167)
T ss_pred CEEEECCCCCCCCCCCCEEEEEEEEEEECCEEECCEEEEEECCC-CCCCHHHHHHHCCCHHHHCCCCCHHHHHHHHHHHC
T ss_conf 98997606988988998379999999999999244789998978-98998899780968589835975899999998635
Q ss_pred HCCCCEEEEECCCCCCCEEEECHHCCCCCCCC--CCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHH
Q ss_conf 00232023102322431121000001122221--0000110000000177642223789997187545556664026999
Q gi|254780818|r 88 NEQNAEWIAHNAKFDVGFINAELQRINKDPLD--PSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSH 165 (245)
Q Consensus 88 ~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~--~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~r~~H~Al~Da~ 165 (245)
+ |+++||||++||++||++++.|+|.+... .+.++||+.++|.++|+.+++|+++|++|||+..++++|+||+||+
T Consensus 80 ~--~~~lVaHN~~FD~~fL~~~~~r~~~~~~~~~~~~~~Dtl~l~r~~~p~~~~~L~~l~~~~gi~~~~~~~H~Al~Da~ 157 (167)
T cd06131 80 R--GAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLDAE 157 (167)
T ss_pred C--CCEEEEECHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCHHHHHH
T ss_conf 6--99999837187899999999981899777765541139999999849998889999987697999998758899999
Q ss_pred HHHHHHHHHH
Q ss_conf 9999999997
Q gi|254780818|r 166 LLSDVYIKMM 175 (245)
Q Consensus 166 ~~a~v~~~ll 175 (245)
+||+||++|+
T Consensus 158 ~ta~vf~~lt 167 (167)
T cd06131 158 LLAEVYLELT 167 (167)
T ss_pred HHHHHHHHHC
T ss_conf 9999999769
No 15
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-positive type; InterPro: IPR006308 These are the polypeptide chains of DNA polymerase III. Full-length homologs of this protein are restricted to the Gram-positive lineages, including the Mycoplasmas. This protein is designated alpha chain and given the gene symbol polC, but is not a full-length homolog of other polC genes. The N-terminal region of about 200 amino acids is rich in low-complexity sequence and poorly alignable. ; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0005737 cytoplasm.
Probab=100.00 E-value=0 Score=337.72 Aligned_cols=218 Identities=28% Similarity=0.450 Sum_probs=178.3
Q ss_pred EEEEECCCCCCCCCCCEEEEEEEEEEECC-EECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 89998467888888888999999999999-88031379898588822886572420210123224852100234477753
Q gi|254780818|r 9 KIVFDIETTGLDSKNDRIIEIGAVELLDY-SKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 9 ~iv~D~ETTGl~~~~d~Iieigav~i~~~-~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
|||||+|||||+|.-|.|||||||+|.++ .++ +.|+.+|||. .+++..+++|||||++||++++..++|+++|.+|+
T Consensus 206 yVVfD~ETTGLsp~~d~iIE~gA~k~~nGk~ii-~~~~~FikP~-~~l~~~~~elT~ITq~ml~n~~~~~~vL~k~~~f~ 283 (1264)
T TIGR01405 206 YVVFDIETTGLSPQYDEIIEFGAVKVKNGKRII-DKFQFFIKPK-EPLSAFVTELTGITQDMLENAPEIEEVLEKFKEFL 283 (1264)
T ss_pred EEEEEEEECCCCCCCCCEEEEEEEEEECCCEEE-EEHHHHCCCC-CCCCCCEEEECCCCHHHHCCCCCHHHHHHHHHHHH
T ss_conf 799603515888861424678758874685762-3123232887-54675426624664797379841789999999976
Q ss_pred HCCCCEEEEEC-CCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCC-CCCCHHHHHHHHCCCCCCCCCCCCHHHHH
Q ss_conf 00232023102-32243112100000112222100001100000001776-42223789997187545556664026999
Q gi|254780818|r 88 NEQNAEWIAHN-AKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPS-SRNDLNSLCKRYGITISHRSKHGALLDSH 165 (245)
Q Consensus 88 ~~~~~~lVaHN-a~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~-~~~~L~~l~~~~~i~~~~r~~H~Al~Da~ 165 (245)
+ |+++|||| |+||++||+..|.+.++.++ .+++||||.|||.++|. ++|+|+.+|++|+|++....+|||++||+
T Consensus 284 ~--d~ilVAHNGasFD~~Fl~~~~~k~~~~~~-~~p~IDTL~Lar~lnP~y~sh~Lg~~~~Kl~v~~~~e~~HRA~YDa~ 360 (1264)
T TIGR01405 284 K--DSILVAHNGASFDIGFLNTNFEKVGLEPL-ENPVIDTLELARALNPEYKSHRLGEIAKKLGVDLDDERHHRADYDAE 360 (1264)
T ss_pred C--CEEEEECCCCCCCHHHHHHHHHHCCCCCC-CCCCHHHHHHHHHHCCCCCCCCCCHHHHHCCCCCCCCCCCCHHHHHH
T ss_conf 9--75888627610366889889876277423-36511388999983731134454223332055215330124334799
Q ss_pred HHHHHHHHHHHCCCCCC-CCC-CCCC-------CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHC
Q ss_conf 99999999973057666-654-4432-------111101112223443211235634578999999999999870
Q gi|254780818|r 166 LLSDVYIKMMVGGSQIN-FGF-KTNE-------DRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEHDKTIQTL 231 (245)
Q Consensus 166 ~~a~v~~~ll~g~~q~~-l~l-~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~H~~~l~~l 231 (245)
+|++||..|+.--++.+ ... ...+ +....-..........+.++...++.+.+--..+|.+|--.-
T Consensus 361 ~t~~vF~~~~~~~~e~gGi~~l~~lni~e~~~l~~~~~y~r~~~~~~~i~~kNq~GLKnLykLvS~s~~~Yfy~~ 435 (1264)
T TIGR01405 361 ATAKVFIVMVEQLKEKGGITNLEELNIQELDKLSSEELYKRLRPNHIIILVKNQAGLKNLYKLVSISLTKYFYTR 435 (1264)
T ss_pred HHHHHHHHHHHHHHHHCCCCCHHHCCHHHHHHHCCHHHHHHCCCCEEEEEEECCHHHHHHHHHHHHHHHHHHCCC
T ss_conf 999999999999875037211234057889842052345423745157877630347889999879986531468
No 16
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=0 Score=330.58 Aligned_cols=207 Identities=28% Similarity=0.418 Sum_probs=170.5
Q ss_pred CCCEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 77589998467888888888999999999999880313798985888228865724202101232248521002344777
Q gi|254780818|r 6 KMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWD 85 (245)
Q Consensus 6 ~mr~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~ 85 (245)
--++||||+||||+++.+|||||||||++.++..+ ++|+++|||+ ++||+++++|||||++||+++|+|++++++|.+
T Consensus 6 ~~~yvv~D~ETTGl~~~~DrIIEI~~vkv~~~~i~-~~~~~linP~-~~I~~~~~~ihGIt~emV~d~P~f~ev~~~~~~ 83 (250)
T PRK06310 6 DTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVI-DSMEFLINPE-RVVSAESQRIHHISDAMLRDKPKIAEVFPQIKG 83 (250)
T ss_pred CCCEEEEEEECCCCCCCCCEEEEEEEEEEECCEEE-EEEEEEECCC-CCCCHHHHHHHCCCHHHHHCCCCHHHHHHHHHH
T ss_conf 89889997337997999962799999999999886-8899998928-979988987615489998469999999999999
Q ss_pred HHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCC-CCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHH
Q ss_conf 5300232023102322431121000001122221-000011000000017764222378999718754555666402699
Q gi|254780818|r 86 FFNEQNAEWIAHNAKFDVGFINAELQRINKDPLD-PSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDS 164 (245)
Q Consensus 86 fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~-~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~r~~H~Al~Da 164 (245)
|++. +.++||||+.||++||+.|+.|+|.++.. ..+++||+.+||.+.|..+++|++||++|||++.+ +|+|++||
T Consensus 84 fi~~-~~ilVaHNa~FD~~fL~~e~~r~g~~~~~~~~~~IDTl~lAr~~~~~~~~~L~~L~~~~~i~~~~--aHrAl~Da 160 (250)
T PRK06310 84 FFKE-GDYIVGHSVGFDLQVLAQEAERIGETFLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPYDG--NHRAMKDV 160 (250)
T ss_pred HHCC-CCEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCEECHHHHHHHCCCCCCCHHHHHHHHCCCCCCC--CCCHHHHH
T ss_conf 9679-99999938455799999999976998665679578499999756765456099999970999986--66819999
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf 99999999997305766665444321111011122234432112356345789999999
Q gi|254780818|r 165 HLLSDVYIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDE 223 (245)
Q Consensus 165 ~~~a~v~~~ll~g~~q~~l~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 223 (245)
++||+||.+|+...+. + .+-......+.....+++.|.....+..+..+.+.+
T Consensus 161 ~aTa~vf~~l~~r~~~--~----e~~~~i~~~p~~~~~f~FGKhKGk~v~ev~~~Y~~W 213 (250)
T PRK06310 161 EININVFKHLCKRFRT--L----EQLKQVLSKPIKMKYMPLGKHKGRLFSEIPLEYLQW 213 (250)
T ss_pred HHHHHHHHHHHHHCCC--H----HHHHHHHCCCCCCCEECCCCCCCEEHHHHHHHHHHH
T ss_conf 9999999999985537--9----999998619463420057784988899817999999
No 17
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=0 Score=323.44 Aligned_cols=172 Identities=22% Similarity=0.403 Sum_probs=156.4
Q ss_pred CCCCCCCCEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHH
Q ss_conf 98667775899984678888888889999999999998803137989858882288657242021012322485210023
Q gi|254780818|r 1 MIRKNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIF 80 (245)
Q Consensus 1 ~~~~~~mr~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~ 80 (245)
|.++++.|+||+|+||||++++ +||||||||.+.|+.++ ++|.++|||. ++||++++++||||++||++||.|++|+
T Consensus 1 ~~~~~~~~~~vvDlETTG~~~~-~~Iiqi~~v~~~~~~i~-~~f~t~vnP~-~~ip~~I~~LTgI~~~~v~~ap~f~~v~ 77 (820)
T PRK07246 1 MTQKKLRKYAVVDLEATGAGPN-ASIIQVGIVIIQGNKII-DSYETDVNPH-ESLDEHIVHLTGITDKQLAQAPDFSQVA 77 (820)
T ss_pred CCCCCCCCEEEEEEECCCCCCC-CCEEEEEEEEEECCEEE-EEEEECCCCC-CCCCHHHHHHCCCCHHHHHCCCCHHHHH
T ss_conf 9624467189999887898999-87799999999999998-9987311889-9799788864698989985299989999
Q ss_pred HHHHHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHHCCCCCCCCCCC
Q ss_conf 447775300232023102322431121000001122221000011000000017764-2223789997187545556664
Q gi|254780818|r 81 SEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRYGITISHRSKHG 159 (245)
Q Consensus 81 ~~f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~~i~~~~r~~H~ 159 (245)
+++++|++ |+++||||+.||++||+++|.+.|.+. .++.+||+.|||..+|.. +|+|.+||++||++.. ++|+
T Consensus 78 ~~~~~~l~--~~~~VaHNv~FD~~fl~~~~~~~g~~~--~~~~~DTv~La~i~~P~~~~y~L~~L~~~l~~~~~--~~Hr 151 (820)
T PRK07246 78 HHIYQLIE--DCIFVAHNVKFDANLLAEALFLEGYEL--RTPRVDTVELAQVFFPRLEKYSLSHLSRQLNIDLA--EAHT 151 (820)
T ss_pred HHHHHHHC--CCEEEEECCCCCHHHHHHHHHHCCCCC--CCCCCCHHHHHHHHCCCCCCCCHHHHHHHCCCCCC--CCCC
T ss_conf 99999967--985998372016999999999758988--99826099999997798788888999997399999--8876
Q ss_pred CHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 0269999999999997305766
Q gi|254780818|r 160 ALLDSHLLSDVYIKMMVGGSQI 181 (245)
Q Consensus 160 Al~Da~~~a~v~~~ll~g~~q~ 181 (245)
|++||++||++|+.++.+..+.
T Consensus 152 A~~Da~ata~l~~~l~~~l~~l 173 (820)
T PRK07246 152 AIADARATAILFLRLLQKIESL 173 (820)
T ss_pred HHHHHHHHHHHHHHHHHHHHCC
T ss_conf 1889999999999999998619
No 18
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family; InterPro: IPR006054 All proteins in this entry 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. ; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication.
Probab=100.00 E-value=0 Score=327.31 Aligned_cols=180 Identities=42% Similarity=0.677 Sum_probs=160.6
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 58999846788888888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
-++++|+||||++...++|||||||++++++.++..|++|++|+ |+++|++.+||||||+||.++|.|.||+.+|.+||
T Consensus 8 t~t~~d~e~tgl~~~~~~II~IGAv~~i~rr~~~~~~~~~~~P~-R~~~~~~~k~hGItDd~L~dkP~F~eia~dF~~~I 86 (228)
T TIGR00573 8 TFTTGDNETTGLYAKHDEIIEIGAVEIINRRIIGNKFHTYIKPD-RLIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYI 86 (228)
T ss_pred EEEEEECCCCCCCCCCCCEEEEEEEEEECCCEEECCEEEEECCC-CCCCCCEEEECCCCHHHHCCCCCHHHHHHHHHHHH
T ss_conf 26875211067632243045453376644614401005776188-88896425524888288468985137889999983
Q ss_pred HCCCCEEEEECCCCCCCEEEECHHCCCCC-CCCCCHH---CCCHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHH
Q ss_conf 00232023102322431121000001122-2210000---1100000001776422237899971875455566640269
Q gi|254780818|r 88 NEQNAEWIAHNAKFDVGFINAELQRINKD-PLDPSRI---IDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLD 163 (245)
Q Consensus 88 ~~~~~~lVaHNa~FD~~fL~~el~r~~~~-~~~~~~~---iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~r~~H~Al~D 163 (245)
+ |++||||||+||++||++||++.|.. ......+ +|++.+++..||+++++|++||.+|+|+.++|..|+|++|
T Consensus 87 ~--g~~Lv~HNA~FD~GFl~~e~~~LG~~~~~~~~~v~~~~~~~~~~~~~~p~~~~~Ld~L~~~~~~~~s~R~~H~A~~D 164 (228)
T TIGR00573 87 K--GAVLVIHNASFDVGFLNYEFSKLGLKKEPKTNDVIDTTDTLQAARPEFPGKRNTLDALALRYEITNSHRALHGALLD 164 (228)
T ss_pred C--CCEEEEEHHHCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 7--94787520030577899999851450110011444499999999720588430277778780544037777317788
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 999999999997305766665444321
Q gi|254780818|r 164 SHLLSDVYIKMMVGGSQINFGFKTNED 190 (245)
Q Consensus 164 a~~~a~v~~~ll~g~~q~~l~l~~~~~ 190 (245)
|.+|++||+.|+.|+.+...++.....
T Consensus 165 A~~l~~~~~~~~~~~~~~~de~~~~~g 191 (228)
T TIGR00573 165 AFILAKLYLVMTGKQTKYNDELNENEG 191 (228)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999998612203244788766
No 19
>PRK05168 ribonuclease T; Provisional
Probab=100.00 E-value=0 Score=322.68 Aligned_cols=177 Identities=27% Similarity=0.450 Sum_probs=151.4
Q ss_pred CCCCCEEEEECCCCCCCCCCCEEEEEEEEEEE---C-CEECCCEEEEEECCC-CCCCCHHHEEECCCC-CCCCCCCCCCC
Q ss_conf 67775899984678888888889999999999---9-988031379898588-822886572420210-12322485210
Q gi|254780818|r 4 KNKMRKIVFDIETTGLDSKNDRIIEIGAVELL---D-YSKTNRTFQVFLCPN-GRKNSPEALKLHGIT-DEFLKDKPSFS 77 (245)
Q Consensus 4 ~~~mr~iv~D~ETTGl~~~~d~Iieigav~i~---~-~~~~~~~f~~~i~P~-~~~i~~~~~~ihGIt-~~~l~~~p~f~ 77 (245)
.+.|..||||+|||||+|.+|+|||||||++. + .+.++++|++||||+ +++||++++++|||| +.+++++|+..
T Consensus 14 fr~~~pVV~D~ETTGl~p~~D~IIEIGAV~v~~~e~g~i~~~~~f~~~V~P~~g~~I~~~~~~ltGI~~~~~l~~a~~~~ 93 (213)
T PRK05168 14 FRGFLPVVIDVETAGFNAQTDALLEIAAITLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAVSEK 93 (213)
T ss_pred HCCCCCEEEEEECCCCCCCCCCEEEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCCCHHHHHHCCCCCCCCCCCCCCHH
T ss_conf 55888759983079988778855888889988637886724754889878887887886675112678653222366678
Q ss_pred HHHHHHHHHHHC-------CCCEEEEECCCCCCCEEEECHHCCCCCCC--CCCHHCCCHHCCCCCCCCCCCCHHHHHHHH
Q ss_conf 023447775300-------23202310232243112100000112222--100001100000001776422237899971
Q gi|254780818|r 78 SIFSEFWDFFNE-------QNAEWIAHNAKFDVGFINAELQRINKDPL--DPSRIIDTLSIARRKHPSSRNDLNSLCKRY 148 (245)
Q Consensus 78 ev~~~f~~fi~~-------~~~~lVaHNa~FD~~fL~~el~r~~~~~~--~~~~~iDTl~lar~~~p~~~~~L~~l~~~~ 148 (245)
++..+|.+|++. .++++|||||.||++||+++++|+|+.+. .+.+++||+.|||.+++ +.+|+.+|++|
T Consensus 94 ~al~~~~~~i~~~~~~~~c~~avLVaHNA~FD~~FLn~~~~r~g~~~~P~~~~~viDTl~Lar~~~~--~~~L~~lc~~~ 171 (213)
T PRK05168 94 EALHEIFKPVRKGIKAAGCQRAILVAHNAHFDLGFLNAAAERTGLKRNPFHPFSTFDTATLAGLAYG--QTVLAKACQAA 171 (213)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCCEEEHHHHHHHHHC--CCCHHHHHHHC
T ss_conf 8789999999999875046756377634187499999999984997788887763358998688748--74099999986
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 8754555666402699999999999973057666
Q gi|254780818|r 149 GITISHRSKHGALLDSHLLSDVYIKMMVGGSQIN 182 (245)
Q Consensus 149 ~i~~~~r~~H~Al~Da~~~a~v~~~ll~g~~q~~ 182 (245)
||+++++++|+||.||++||+||++|+...++.+
T Consensus 172 gi~~~~~~~HrAl~DA~~tA~vFl~ll~~l~~~g 205 (213)
T PRK05168 172 GIEFDNKEAHSALYDTEKTAELFCEIVNRWKRLG 205 (213)
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 9999997777738999999999999999999738
No 20
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=0 Score=321.43 Aligned_cols=166 Identities=29% Similarity=0.494 Sum_probs=152.4
Q ss_pred CEEEEECCCCCCCCC-CCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 589998467888888-8889999999999998803137989858882288657242021012322485210023447775
Q gi|254780818|r 8 RKIVFDIETTGLDSK-NDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDF 86 (245)
Q Consensus 8 r~iv~D~ETTGl~~~-~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~f 86 (245)
||||+|+||||++|. +|||||||||.|.|+.++ ++|+++|||. ++||+++.++||||++||++||.|++|++++++|
T Consensus 4 ~~~vvDlETTG~~~~~~d~IIqig~v~i~~~~i~-~~f~t~vnP~-~~iP~~I~~LTgI~~~~v~~AP~f~eva~~i~~~ 81 (932)
T PRK08074 4 RFVVVDLETTGNSPKKGDKIIQIAAVVVEDGEIL-ERFSTFVNPE-RPIPPFITELTGISEEMVKNAPLFEDVAPMIVEL 81 (932)
T ss_pred EEEEEEEECCCCCCCCCCEEEEEEEEEEECCEEE-EEEECCCCCC-CCCCHHHHHHCCCCHHHHCCCCCHHHHHHHHHHH
T ss_conf 0899998888989777988999979999999998-9985325899-9899778860698989980599989999999999
Q ss_pred HHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHHCCCCCCCCCCCCHHHHH
Q ss_conf 300232023102322431121000001122221000011000000017764-2223789997187545556664026999
Q gi|254780818|r 87 FNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRYGITISHRSKHGALLDSH 165 (245)
Q Consensus 87 i~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~~i~~~~r~~H~Al~Da~ 165 (245)
++ |.++||||++||.+||+++|.++|.+.+ .++++||+.|||..+|.. +|+|.+|+++||++.. ++|+|++||+
T Consensus 82 l~--~~~~VaHNv~FD~~FL~~~l~~~G~~~~-~~~~~DTveLa~i~~P~~~sy~L~~L~~~l~i~~~--~~HrA~sDa~ 156 (932)
T PRK08074 82 LE--GAYFVAHNVHFDLNFLNEELERAGYTEI-HCPKLDTVELARILLPTADSYKLSDLSEELELEHD--QPHRADSDAE 156 (932)
T ss_pred HC--CCEEEECCHHHHHHHHHHHHHHCCCCCC-CCCEECHHHHHHHHCCCCCCCCHHHHHHHCCCCCC--CCCCCHHHHH
T ss_conf 66--9959947805409999999997399866-68765199999997788788888999986499999--9875178899
Q ss_pred HHHHHHHHHHHCCCC
Q ss_conf 999999999730576
Q gi|254780818|r 166 LLSDVYIKMMVGGSQ 180 (245)
Q Consensus 166 ~~a~v~~~ll~g~~q 180 (245)
+||++|+.|+.+-.+
T Consensus 157 aTa~l~~~l~~~l~~ 171 (932)
T PRK08074 157 VTAELFLQLLHKLER 171 (932)
T ss_pred HHHHHHHHHHHHHHH
T ss_conf 999999999999983
No 21
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=0 Score=315.47 Aligned_cols=161 Identities=33% Similarity=0.510 Sum_probs=144.9
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 58999846788888888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
.+||||+||||+++.+|||||||+|. + .+++.|+++|||+ ++||+++.+|||||++||+++|+|.+++++|.+|+
T Consensus 3 ~~V~fD~ETTGl~~~~DrIIEiaav~---~-~~~e~f~~linP~-~pIp~~a~~ihGIt~e~v~~~P~~~ev~~~~~~f~ 77 (232)
T PRK06309 3 ALIFYDTETTGTQIDKDRIIEIAAYN---G-VTSESFQTYVNPE-IPIPAEATKIHGITTSEVASAPKFPEAYQKFREFC 77 (232)
T ss_pred CEEEEEEECCCCCCCCCEEEEEEEEE---C-CCCCEEEEEECCC-CCCCHHHHCCCCCCHHHHHCCCCHHHHHHHHHHHH
T ss_conf 68999711799599994589999892---7-5676899997998-96996562103839999805998999999999985
Q ss_pred HCCCCEEEEECC-CCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHHCCCCCCCCCCCCHHHHH
Q ss_conf 002320231023-22431121000001122221000011000000017764-2223789997187545556664026999
Q gi|254780818|r 88 NEQNAEWIAHNA-KFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRYGITISHRSKHGALLDSH 165 (245)
Q Consensus 88 ~~~~~~lVaHNa-~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~~i~~~~r~~H~Al~Da~ 165 (245)
+. ++++||||+ +||++||+.||.|+|.+++ ..+++||+.+||.++|+. +++|++||++||+... ++|+|++||.
T Consensus 78 ~~-~~ilVaHN~~~FD~~fL~~e~~r~g~~~~-~~~~iDTl~lar~l~P~l~~h~L~~L~~~~gi~~~--~aHrAl~Da~ 153 (232)
T PRK06309 78 GT-DNILVAHNNDGFDFPLLVKECRRHSLEPL-TLRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFAEN--QAHRALDDVI 153 (232)
T ss_pred CC-CCEEEEECCHHHHHHHHHHHHHHCCCCCC-CCCHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCC--CCCCHHHHHH
T ss_conf 79-98899848965679999999998599867-74053799999997589776889999998099998--8888599999
Q ss_pred HHHHHHHHHHHC
Q ss_conf 999999999730
Q gi|254780818|r 166 LLSDVYIKMMVG 177 (245)
Q Consensus 166 ~~a~v~~~ll~g 177 (245)
+|++||.+|+..
T Consensus 154 at~~vf~~ll~~ 165 (232)
T PRK06309 154 TLHRVFSALVGD 165 (232)
T ss_pred HHHHHHHHHHHH
T ss_conf 999999998721
No 22
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative; InterPro: IPR006310 These are 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 Escherichia coli. .
Probab=100.00 E-value=0 Score=317.25 Aligned_cols=167 Identities=33% Similarity=0.503 Sum_probs=152.1
Q ss_pred CEEEEECCCCCCCCCC-CEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 5899984678888888-889999999999998803137989858882288657242021012322485210023447775
Q gi|254780818|r 8 RKIVFDIETTGLDSKN-DRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDF 86 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~-d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~f 86 (245)
||+|+|+||||-++.. |||||||||.|.|+.++ ++|+|.|||+ ++|||.+.++|||++.||..||.|.+|+.+++++
T Consensus 1 rYaVVDLEtTg~~~~~~d~IIqiGiV~v~DgeIv-~~f~T~VNP~-~~~pp~I~eLTGisd~~l~~AP~F~qVA~~i~~~ 78 (944)
T TIGR01407 1 RYAVVDLETTGTDSSEFDKIIQIGIVLVEDGEIV-DTFATDVNPN-EPIPPFIQELTGISDEQLKQAPYFSQVAQEIYDL 78 (944)
T ss_pred CEEEEEEEECCCCCCCCCCEEEEEEEEEECCCEE-EECCCCCCCC-CCCCCHHHHHCCCCHHHHCCCCCHHHHHHHHHHH
T ss_conf 9689987416888645576689988998558143-2012677889-8776114542287768640488887999999987
Q ss_pred HHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCC-CCCCHHHHHHHHCCCCCCCCCCCCHHHHH
Q ss_conf 30023202310232243112100000112222100001100000001776-42223789997187545556664026999
Q gi|254780818|r 87 FNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPS-SRNDLNSLCKRYGITISHRSKHGALLDSH 165 (245)
Q Consensus 87 i~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~-~~~~L~~l~~~~~i~~~~r~~H~Al~Da~ 165 (245)
+ +|+++||||+.||++||..+|.++|.++. ..++|||+.|||.+||. ++|+|..||+.+||...| +|+|++||.
T Consensus 79 l--~D~iFVAHNV~FD~nfL~k~l~~~G~~~~-~~~~iDTVELa~if~PT~esY~Ls~L~E~LGl~h~n--pH~AdSDA~ 153 (944)
T TIGR01407 79 L--EDGIFVAHNVHFDLNFLAKELVDEGYEPL-EVPRIDTVELARIFFPTEESYKLSELSEELGLEHEN--PHRADSDAQ 153 (944)
T ss_pred H--CCCEEEEECHHCCHHHHHHHHHHCCCCCC-CCCCCHHHHHHHHHCCCCCCCCCHHHHHHHCCCCCC--CCCCCHHHH
T ss_conf 4--29727761015067899999985689743-435200567998746744355614899971987146--676105789
Q ss_pred HHHHHHHHHHHCCCCC
Q ss_conf 9999999997305766
Q gi|254780818|r 166 LLSDVYIKMMVGGSQI 181 (245)
Q Consensus 166 ~~a~v~~~ll~g~~q~ 181 (245)
+||++.+.+..+-++.
T Consensus 154 ~TAeLLLl~~~K~~~L 169 (944)
T TIGR01407 154 VTAELLLLLEEKMKKL 169 (944)
T ss_pred HHHHHHHHHHHHHHHH
T ss_conf 9999999999998751
No 23
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=100.00 E-value=0 Score=314.74 Aligned_cols=169 Identities=35% Similarity=0.599 Sum_probs=155.2
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 58999846788888888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
.+||||+|||||++..|+|||||||++.++.++ ++|+++|||+ +++|+.++++||||++||+++|++++|+++|++|+
T Consensus 419 ~yVvFDiETTGls~~~d~IiEigAvki~~g~ii-d~f~~fi~P~-~~i~~~i~~lT~Itd~mv~~~~~~~evl~~f~~f~ 496 (1436)
T PRK00448 419 TYVVFDVETTGLSAVYDEIIEIGAVKIKNGEII-DKFEEFIKPG-HPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFC 496 (1436)
T ss_pred CEEEEEECCCCCCCCCCCEEEEEEEEEECCEEE-EEEHHHCCCC-CCCCHHHHHCCCCCHHHHCCCCCHHHHHHHHHHHH
T ss_conf 379986006888866672368757986378175-4102103899-97975453214788478638987899999999982
Q ss_pred HCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCC-CCCCHHHHHHHHCCCCCCCCCCCCHHHHHH
Q ss_conf 0023202310232243112100000112222100001100000001776-422237899971875455566640269999
Q gi|254780818|r 88 NEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPS-SRNDLNSLCKRYGITISHRSKHGALLDSHL 166 (245)
Q Consensus 88 ~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~-~~~~L~~l~~~~~i~~~~r~~H~Al~Da~~ 166 (245)
+ |+++|||||.||++||+..++++|++.+ .++++|||.+||.++|. .+++|+++|++|+|.+.+ +|+|..||++
T Consensus 497 ~--d~vlVAHNa~FD~~Fi~~~~~~~~~~~~-~~p~iDTl~lsr~l~p~~k~~~L~~l~k~~~v~~~~--hHRA~~Da~~ 571 (1436)
T PRK00448 497 G--DSVLVAHNASFDVGFINTNYEKLGLEKI-KNPVIDTLELSRFLYPEYKSHRLNTLAKKFGVELEH--HHRADYDAEA 571 (1436)
T ss_pred C--CCEEEEECCCCCHHHHHHHHHHCCCCCC-CCCEECHHHHHHHHCCCCCCCCHHHHHHHHCCCCCC--CCCCCCCHHH
T ss_conf 8--9779984586568899999998089866-797230299898755101114478899884888654--5443223888
Q ss_pred HHHHHHHHHHCCCCCCC
Q ss_conf 99999999730576666
Q gi|254780818|r 167 LSDVYIKMMVGGSQINF 183 (245)
Q Consensus 167 ~a~v~~~ll~g~~q~~l 183 (245)
||+||..|+...++.++
T Consensus 572 t~~i~~~~l~~~~~~~i 588 (1436)
T PRK00448 572 TAYLLIKFLKDLKEKGI 588 (1436)
T ss_pred HHHHHHHHHHHHHHCCC
T ss_conf 99999999999987487
No 24
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=0 Score=309.01 Aligned_cols=164 Identities=22% Similarity=0.387 Sum_probs=141.7
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEE-CCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 58999846788888888899999999999988-03137989858882288657242021012322485210023447775
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSK-TNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDF 86 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~-~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~f 86 (245)
.+||||+|||||||++|+|||||||++.++.+ .+++|+++|||+ ++|++.+++|||||++||+++|+|.+|+++|.+|
T Consensus 30 ~fVv~D~ETTGL~~~~D~IieIgav~v~~~~i~~~~~f~~lV~P~-~~i~~~~~~IhGIt~~~l~~ap~~~evl~~f~~f 108 (203)
T PRK09145 30 EWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPP-QSLSAESIKIHRLRHQDLEHGLSEEEALRQLLAF 108 (203)
T ss_pred CEEEEEEECCCCCCCCCEEEEEEEEEEECCEEECCCEEEEEECCC-CCCCHHHHCCCCCCHHHHCCCCCHHHHHHHHHHH
T ss_conf 899998568999999970699999999999993175289998979-9598645201387879981399999999999988
Q ss_pred HHCCCCEEEEECCCCCCCEEEECHHCC-CCCCCCCCHHCCCHHC-----CCCCCCC-CCCCHHHHHHHHCCCCCCCCCCC
Q ss_conf 300232023102322431121000001-1222210000110000-----0001776-42223789997187545556664
Q gi|254780818|r 87 FNEQNAEWIAHNAKFDVGFINAELQRI-NKDPLDPSRIIDTLSI-----ARRKHPS-SRNDLNSLCKRYGITISHRSKHG 159 (245)
Q Consensus 87 i~~~~~~lVaHNa~FD~~fL~~el~r~-~~~~~~~~~~iDTl~l-----ar~~~p~-~~~~L~~l~~~~~i~~~~r~~H~ 159 (245)
++ |+++||||++||++||++++.++ |.+. +++++|+..+ .+...++ .+++|++||++|||+..+ +|+
T Consensus 109 i~--~~~lVgHNa~FD~~fL~~~~~r~~g~~l--~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~gi~~~~--~Hr 182 (203)
T PRK09145 109 IG--NRPLVGYYLEFDVAMLNRYVRPLLGIGL--PNPLIEVSSLYHDKKERHLPDAYIDLRFDAILKHLDLPVLG--RHD 182 (203)
T ss_pred CC--CCEEEEECHHHHHHHHHHHHHHHCCCCC--CCCEEEHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCCCCCC--CCC
T ss_conf 29--9989998789999999999999629999--99877609879999996676987788999999857987899--979
Q ss_pred CHHHHHHHHHHHHHHHHCC
Q ss_conf 0269999999999997305
Q gi|254780818|r 160 ALLDSHLLSDVYIKMMVGG 178 (245)
Q Consensus 160 Al~Da~~~a~v~~~ll~g~ 178 (245)
||+||.+||+||++|+.|+
T Consensus 183 AL~DA~aTa~lfl~L~k~~ 201 (203)
T PRK09145 183 ALNDAIMTALIYLRLRKGD 201 (203)
T ss_pred HHHHHHHHHHHHHHHHCCC
T ss_conf 8999999999999986789
No 25
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=0 Score=308.11 Aligned_cols=164 Identities=24% Similarity=0.354 Sum_probs=147.7
Q ss_pred CCEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 75899984678888888889999999999998803137989858882288657242021012322485210023447775
Q gi|254780818|r 7 MRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDF 86 (245)
Q Consensus 7 mr~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~f 86 (245)
|.|||||+|||| +..|+|||||+|++.|+.++ ++|++||||....++|..++|||||++||+++|+|.+|+++|.+|
T Consensus 1 m~fvviD~ETt~--~~~d~iieIg~v~v~~g~iv-~~~~~Li~P~~~~~~p~~i~ihGIt~~~v~~aP~f~ev~~~~~~f 77 (309)
T PRK06195 1 MDFVAIDFETAN--EKRNSPCSIGIVVVKDGEIV-EKVHYLIKPKEMRFMPINIGIHGIRPHMVQDELEFDKIWEKIKDY 77 (309)
T ss_pred CCEEEEEEECCC--CCCCEEEEEEEEEEECCEEE-EEEEEEECCCCCCCCCCEEEECCCCHHHHHCCCCHHHHHHHHHHH
T ss_conf 929999978999--99980599999999999999-999999899998888744640377999996599999999999998
Q ss_pred HHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHHCCCCCCCCCCCCHHHHH
Q ss_conf 300232023102322431121000001122221000011000000017764-2223789997187545556664026999
Q gi|254780818|r 87 FNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRYGITISHRSKHGALLDSH 165 (245)
Q Consensus 87 i~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~~i~~~~r~~H~Al~Da~ 165 (245)
++ |+++|||||.||++||++++.++|++++ .+.++||+.|||..+|+. +++|.+||++|||++. +|+|++||+
T Consensus 78 i~--~~vlVaHNa~FD~~fL~~~~~r~gl~~~-~~~~~cTl~LAR~~~p~l~~~kL~~La~~~gi~~~---hH~Al~DA~ 151 (309)
T PRK06195 78 FN--DNLVIAHNASFDISVLRKTLELYNIPMP-DFEYICTMKLAKNFYSNIPNARLNTVNNFLGYEFK---HHDALEDAM 151 (309)
T ss_pred HC--CCEEEEECCHHHHHHHHHHHHHCCCCCC-CCCEEEHHHHHHHHCCCCCCCCHHHHHHHHCCCCC---CCCCCCCHH
T ss_conf 57--9979995628889999999998499999-99777479999986557765788899998598801---168510199
Q ss_pred HHHHHHHHHHHCCC
Q ss_conf 99999999973057
Q gi|254780818|r 166 LLSDVYIKMMVGGS 179 (245)
Q Consensus 166 ~~a~v~~~ll~g~~ 179 (245)
+||+||+.+.....
T Consensus 152 A~a~I~~~~~~~~~ 165 (309)
T PRK06195 152 ACSNILLNISKELN 165 (309)
T ss_pred HHHHHHHHHHHHHC
T ss_conf 99999999999818
No 26
>cd06134 RNaseT 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=100.00 E-value=1.4e-45 Score=304.92 Aligned_cols=173 Identities=27% Similarity=0.433 Sum_probs=148.1
Q ss_pred CCCCCCEEEEECCCCCCCCCCCEEEEEEEEEEE-C---CEECCCEEEEEECCC-CCCCCHHHEEECCCC-CCCCCCCCCC
Q ss_conf 667775899984678888888889999999999-9---988031379898588-822886572420210-1232248521
Q gi|254780818|r 3 RKNKMRKIVFDIETTGLDSKNDRIIEIGAVELL-D---YSKTNRTFQVFLCPN-GRKNSPEALKLHGIT-DEFLKDKPSF 76 (245)
Q Consensus 3 ~~~~mr~iv~D~ETTGl~~~~d~Iieigav~i~-~---~~~~~~~f~~~i~P~-~~~i~~~~~~ihGIt-~~~l~~~p~f 76 (245)
+.+-|+.||||+|||||+|.+|+|||||||++. | ....+++|+++|+|. ++++|+.++++|||| +++++++|..
T Consensus 1 ~~~~~~~VV~D~ETTGL~p~~d~IIEIgav~v~~d~~g~i~~~~~~~~~v~P~~~~~i~~~~~~itGIt~~~~~~~~~~~ 80 (189)
T cd06134 1 RFRGFLPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDE 80 (189)
T ss_pred CCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCCCHHHHHHCCCCCHHHHCCCCCH
T ss_conf 98898507999528999988980799999999976878532451689977898899898556655077700110016757
Q ss_pred CHHHHHHHHHHHC-------CCCEEEEECCCCCCCEEEECHHCCCCCCCC--CCHHCCCHHCCCCCCCCCCCCHHHHHHH
Q ss_conf 0023447775300-------232023102322431121000001122221--0000110000000177642223789997
Q gi|254780818|r 77 SSIFSEFWDFFNE-------QNAEWIAHNAKFDVGFINAELQRINKDPLD--PSRIIDTLSIARRKHPSSRNDLNSLCKR 147 (245)
Q Consensus 77 ~ev~~~f~~fi~~-------~~~~lVaHNa~FD~~fL~~el~r~~~~~~~--~~~~iDTl~lar~~~p~~~~~L~~l~~~ 147 (245)
.++++++++|++. .++++|||||+||++||++++.|+|..+.+ +..++||+.+||..+| +.+|+.+|++
T Consensus 81 ~~~~~~~~~~i~~~~~~~~~~~avlVaHNa~FD~~FL~~~~~r~g~~~~p~~~~~~~DTl~La~~~~~--~~~L~~l~~~ 158 (189)
T cd06134 81 KEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG--QTVLAKACQA 158 (189)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCCEEEHHHHHHHHHC--CCCHHHHHHH
T ss_conf 78899999999999875167555687517777299999999984998888877765669999867738--0019999998
Q ss_pred HCCCCCCCCCCCCHHHHHHHHHHHHHHHHC
Q ss_conf 187545556664026999999999999730
Q gi|254780818|r 148 YGITISHRSKHGALLDSHLLSDVYIKMMVG 177 (245)
Q Consensus 148 ~~i~~~~r~~H~Al~Da~~~a~v~~~ll~g 177 (245)
|||+++++.+|+||+||++||+||++|+..
T Consensus 159 ~gi~~~~~~~HrAl~DA~~ta~lf~~l~~k 188 (189)
T cd06134 159 AGIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 799999987887299999999999999964
No 27
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=100.00 E-value=2.8e-45 Score=303.28 Aligned_cols=171 Identities=23% Similarity=0.339 Sum_probs=148.1
Q ss_pred CCCCCEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCC-----CCCCCH
Q ss_conf 677758999846788888888899999999999988031379898588822886572420210123224-----852100
Q gi|254780818|r 4 KNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKD-----KPSFSS 78 (245)
Q Consensus 4 ~~~mr~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~-----~p~f~e 78 (245)
+..-..+|||+||||++|..|||||+|+|.+.+...+.++|++|||| +++||+++++|||||++|++. +|.|.+
T Consensus 3 w~~~~lvvfD~ETTG~d~~~dRIIeia~V~~~~~g~~~~~~~~LvnP-g~~IP~~a~~vhGIT~e~~~~~G~p~a~v~~e 81 (234)
T PRK07942 3 WHDGPLAAFDLETTGVDPETARIVTAAIVVVDAHGEVVERREWLADP-GVEIPEEASAVHGITTERARAHGRPAAEVLAE 81 (234)
T ss_pred CCCCCEEEEEEECCCCCCCCCEEEEEEEEEEECCCCEEEEEEEEECC-CCCCCHHHHHHHCCCHHHHHHCCCCCHHHHHH
T ss_conf 75697899980169989889838999999998898546889998695-89499889778488999997428983079999
Q ss_pred HHHHHHHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCC--CCCCCHHHHHHHHCCCCCCCC
Q ss_conf 234477753002320231023224311210000011222210000110000000177--642223789997187545556
Q gi|254780818|r 79 IFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHP--SSRNDLNSLCKRYGITISHRS 156 (245)
Q Consensus 79 v~~~f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p--~~~~~L~~l~~~~~i~~~~r~ 156 (245)
+++.|.+++. .|.++|||||+||++||++||.|+|++++...+++||+.++|.+.| ..+++|++||++|||++.+
T Consensus 82 ia~~l~~~~~-~g~~lVahNA~FDl~fL~~El~R~g~~~l~~~~viDtl~l~r~l~~~r~gkr~L~aL~~~ygv~l~~-- 158 (234)
T PRK07942 82 IAEALRAVWR-AGVPVVVYNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKHVDRYRKGKRTLTALCEHYGVRLDN-- 158 (234)
T ss_pred HHHHHHHHHH-CCCEEEEECCHHHHHHHHHHHHHCCCCCCCCCCEEEHHHHHHHHCCCCCCCCCHHHHHHHCCCCCCC--
T ss_conf 9999999972-7987999670764999999999859996777755619998877514777888899999984998877--
Q ss_pred CCCCHHHHHHHHHHHHHHHHCC
Q ss_conf 6640269999999999997305
Q gi|254780818|r 157 KHGALLDSHLLSDVYIKMMVGG 178 (245)
Q Consensus 157 ~H~Al~Da~~~a~v~~~ll~g~ 178 (245)
+|+|++||.+||+|+..|....
T Consensus 159 aH~A~aDA~Ata~l~~~l~~r~ 180 (234)
T PRK07942 159 AHDATADALAAARLAWALARRF 180 (234)
T ss_pred CCCCHHHHHHHHHHHHHHHHHH
T ss_conf 5564152899999999999876
No 28
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=100.00 E-value=5.6e-45 Score=301.19 Aligned_cols=171 Identities=23% Similarity=0.397 Sum_probs=149.4
Q ss_pred CCEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 75899984678888888889999999999998803137989858882288657242021012322485210023447775
Q gi|254780818|r 7 MRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDF 86 (245)
Q Consensus 7 mr~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~f 86 (245)
-.|+|+|+||||++|..|||||||+|.+.++..+.++|+++|||+ . ++..++|||||++||.++|.|.+|+++|.+|
T Consensus 15 ~~fvvvD~ETTGl~p~~drIieig~v~~~~~g~i~~~~~tlvnP~-~--dp~~~~IhGIt~~~v~~aP~f~ev~~~l~~~ 91 (313)
T PRK06063 15 QGWAVVDVETSGFRPGQARIISVAVLGLDADGNVEQSVVSLLNPG-V--DPGPTHVHGLTAAMLEGQPQFADIAGELAEV 91 (313)
T ss_pred CCEEEEEEECCCCCCCCCEEEEEEEEEEECCCEEEEEEEEEECCC-C--CCCCEEEECCCHHHHCCCCCHHHHHHHHHHH
T ss_conf 997999976899999897069999999989978889999975919-9--9898434187999981799899999999999
Q ss_pred HHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHHCCCCCCCCCCCCHHHHH
Q ss_conf 300232023102322431121000001122221000011000000017764-2223789997187545556664026999
Q gi|254780818|r 87 FNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRYGITISHRSKHGALLDSH 165 (245)
Q Consensus 87 i~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~~i~~~~r~~H~Al~Da~ 165 (245)
++ |++|||||+.||++||++|++|+|.+++ ...++||+.+||+.+|+. +++|.+||++|||.+.+ +|+|+.||+
T Consensus 92 l~--g~vlVAHNa~FD~~FL~~e~~r~g~~~p-~~~~lcTl~lARr~~~~l~~~kL~tla~~~Gi~~~~--~H~Al~DAr 166 (313)
T PRK06063 92 LR--GRTLVAHNVAFDYSFLAAEAELAGAELP-VDQVMCTVELARRLDLGLPNLRLETLAAHWGVVQQR--PHDALDDAR 166 (313)
T ss_pred HC--CCEEEEECCHHHHHHHHHHHHHCCCCCC-CCCEEEHHHHHHHHCCCCCCCCHHHHHHHCCCCCCC--CCCCHHHHH
T ss_conf 78--9979996856529999999997399889-996676899886544899997478899980999887--655067789
Q ss_pred HHHHHHHHHHHCCCCCCCCC
Q ss_conf 99999999973057666654
Q gi|254780818|r 166 LLSDVYIKMMVGGSQINFGF 185 (245)
Q Consensus 166 ~~a~v~~~ll~g~~q~~l~l 185 (245)
+||+++...+....+..+.+
T Consensus 167 a~a~il~~~l~~a~~~~~~l 186 (313)
T PRK06063 167 VLAGILAPALERARERDVWL 186 (313)
T ss_pred HHHHHHHHHHHHHHCCCCCC
T ss_conf 99999899998600246656
No 29
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=100.00 E-value=0 Score=309.83 Aligned_cols=170 Identities=35% Similarity=0.624 Sum_probs=157.1
Q ss_pred EEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 89998467888888888999999999999880313798985888228865724202101232248521002344777530
Q gi|254780818|r 9 KIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFN 88 (245)
Q Consensus 9 ~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi~ 88 (245)
|||||+|||||+|..|.|||||||++.++.++ +.|+.+||| ++++|..++++||||++||+++|...+|+.+|.+|++
T Consensus 423 yVVfDiETTGLs~~~d~iIE~aAvKikng~iI-d~f~~Fi~P-~~pl~~~~telTgITdeml~~a~~i~~vL~kf~~~~~ 500 (1444)
T COG2176 423 YVVFDIETTGLSPVYDEIIEIAAVKIKNGRII-DKFQFFIKP-GRPLSATITELTGITDEMLENAPEIEEVLEKFREFIG 500 (1444)
T ss_pred EEEEEEECCCCCCCCCHHHHHEEEEEECCCCH-HHHHHHCCC-CCCCCHHHHHCCCCCHHHHCCCCCHHHHHHHHHHHHC
T ss_conf 89998553776754201562000443388043-778975089-9967644542035679987488339999999999844
Q ss_pred CCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCC-CCCCHHHHHHHHCCCCCCCCCCCCHHHHHHH
Q ss_conf 023202310232243112100000112222100001100000001776-4222378999718754555666402699999
Q gi|254780818|r 89 EQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPS-SRNDLNSLCKRYGITISHRSKHGALLDSHLL 167 (245)
Q Consensus 89 ~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~-~~~~L~~l~~~~~i~~~~r~~H~Al~Da~~~ 167 (245)
|+++|||||+||++||+..+.+.|.+++ .+++||||.+||.++|. .+++|+.+|+.|++.+++ +|+|..||++|
T Consensus 501 --d~IlVAHNasFD~gFl~~~~~k~~~~~~-~~pvIDTL~lar~L~P~~ksh~Lg~l~kk~~v~le~--hHRA~yDaeat 575 (1444)
T COG2176 501 --DSILVAHNASFDMGFLNTNYEKYGLEPL-TNPVIDTLELARALNPEFKSHRLGTLCKKLGVELER--HHRADYDAEAT 575 (1444)
T ss_pred --CCEEEECCCCCCHHHHHHHHHHHCCCCC-CCCHHHHHHHHHHHCHHHHHCCHHHHHHHHCCCHHH--HHHHHHHHHHH
T ss_conf --8589961675564578888998388510-275011999998757454324667788874863787--53101008999
Q ss_pred HHHHHHHHHCCCCCCCCC
Q ss_conf 999999973057666654
Q gi|254780818|r 168 SDVYIKMMVGGSQINFGF 185 (245)
Q Consensus 168 a~v~~~ll~g~~q~~l~l 185 (245)
|.||..|+...++.++..
T Consensus 576 ~~vf~~f~~~~ke~Gi~~ 593 (1444)
T COG2176 576 AKVFFVFLKDLKEKGITN 593 (1444)
T ss_pred HHHHHHHHHHHHHHCHHH
T ss_conf 999999999998845565
No 30
>cd06130 DNA_pol_III_epsilon_like This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (polIII), 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 polIII 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 subunit of polIII also functions as a stabilizer of the holoenzyme complex
Probab=100.00 E-value=2.9e-43 Score=290.29 Aligned_cols=155 Identities=28% Similarity=0.481 Sum_probs=141.2
Q ss_pred EEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 89998467888888888999999999999880313798985888228865724202101232248521002344777530
Q gi|254780818|r 9 KIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFN 88 (245)
Q Consensus 9 ~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi~ 88 (245)
+||||+|||| +..|+|||||||++.++.++ ++|++||||+ +++++.+.+|||||++||.++|+|.+++++|.+|++
T Consensus 1 fvv~D~ETT~--~~~d~IieIgav~i~~g~i~-~~f~~lv~P~-~~i~~~~~~ihGIt~~~v~~~p~~~~v~~~l~~~l~ 76 (156)
T cd06130 1 FVAIDFETAN--ADRASACSIGLVKVRDGQIV-DTFYTLIRPP-TRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLG 76 (156)
T ss_pred CEEEEEECCC--CCCCEEEEEEEEEEECCEEE-EEEEEEECCC-CCCCHHHHHHHCCCHHHHHCCCCHHHHHHHHHHHCC
T ss_conf 9899977898--99996999999999999998-9999987789-879988932208887998409999999999998558
Q ss_pred CCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHHCCCCCCCCCCCCHHHHHHH
Q ss_conf 0232023102322431121000001122221000011000000017764-222378999718754555666402699999
Q gi|254780818|r 89 EQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRYGITISHRSKHGALLDSHLL 167 (245)
Q Consensus 89 ~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~~i~~~~r~~H~Al~Da~~~ 167 (245)
|+++||||+.||++||+++++|+|.++. ..+++||+.++|..+|+. +++|++||++||++.. +|+|++||++|
T Consensus 77 --~~~lVaHn~~FD~~fL~~~~~~~~~~~~-~~~~iDtl~l~r~~~~~~~~~~L~~l~~~~gi~~~---~H~Al~DA~at 150 (156)
T cd06130 77 --GSLVVAHNASFDRSVLRAALEAYGLPPP-PYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIELN---HHDALEDARAC 150 (156)
T ss_pred --CCEEEEECHHHHHHHHHHHHHHCCCCCC-CCCEECHHHHHHHHCCCCCCCCHHHHHHHCCCCCC---CCCCHHHHHHH
T ss_conf --9889995778899999999998199998-98588189999997388888999999998599987---87968999999
Q ss_pred HHHHHH
Q ss_conf 999999
Q gi|254780818|r 168 SDVYIK 173 (245)
Q Consensus 168 a~v~~~ 173 (245)
|+||++
T Consensus 151 a~l~la 156 (156)
T cd06130 151 AEILLA 156 (156)
T ss_pred HHHHCC
T ss_conf 999819
No 31
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=1.2e-42 Score=286.48 Aligned_cols=164 Identities=24% Similarity=0.380 Sum_probs=143.1
Q ss_pred CCEEEEECCCCCCCCCCCEEEEEEEEEEECC-EECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 7589998467888888888999999999999-880313798985888228865724202101232248521002344777
Q gi|254780818|r 7 MRKIVFDIETTGLDSKNDRIIEIGAVELLDY-SKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWD 85 (245)
Q Consensus 7 mr~iv~D~ETTGl~~~~d~Iieigav~i~~~-~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~ 85 (245)
-.+||||+|||||||++|+|||||+|++.++ +..+++||.+|||+ ++++++++.|||||+++|.++|++++|+++|++
T Consensus 47 ~~fvalD~ETTGLdp~~D~IiSIGaV~i~~~~I~l~~a~~~lV~p~-~~i~~~s~~IHGIt~~~l~~ap~l~evl~~ll~ 125 (239)
T PRK09146 47 VPFVALDFETTGLDPEQDAIVSIGLVPFTLQRIRCRQARHWVVKPR-RPLNEESVVIHGITHSDLQDAPDLERILDELLE 125 (239)
T ss_pred CCEEEEECCCCCCCCCCCCEEEEEEEEEECCEEEECCEEEEEECCC-CCCCCCCEEECCCCHHHHHCCCCHHHHHHHHHH
T ss_conf 8789996415788878885489989998788886534158998899-978764511069698998569999999999999
Q ss_pred HHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCC-----------C---CCCCHHHHHHHHCCC
Q ss_conf 53002320231023224311210000011222210000110000000177-----------6---422237899971875
Q gi|254780818|r 86 FFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHP-----------S---SRNDLNSLCKRYGIT 151 (245)
Q Consensus 86 fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p-----------~---~~~~L~~l~~~~~i~ 151 (245)
|++ |+++||||+.||++||++.++++....+ ..+++||+.+++.... + .+.+|++++++||++
T Consensus 126 ~l~--g~VLVaH~a~~D~~FL~~a~~~~~g~~l-~~P~IDTl~Le~~~~~~~~~~~~~r~~~~~~~slrL~~~r~rYgLP 202 (239)
T PRK09146 126 ALA--GKVVVVHYRRIERDFLDQALRNRIGEGI-EFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLRYGLP 202 (239)
T ss_pred HHC--CCEEEEECCHHHHHHHHHHHHHHHCCCC-CCCEEEHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCCC
T ss_conf 818--9989996839999999999999628898-8746448999999988542004443135898676389999981989
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 4555666402699999999999973
Q gi|254780818|r 152 ISHRSKHGALLDSHLLSDVYIKMMV 176 (245)
Q Consensus 152 ~~~r~~H~Al~Da~~~a~v~~~ll~ 176 (245)
.+. +|+||.||.+||++|++.+.
T Consensus 203 ~y~--aH~AL~DAlATAELflAQi~ 225 (239)
T PRK09146 203 AYP--PHHALTDAIATAELLQAQIA 225 (239)
T ss_pred CCC--CCCCHHHHHHHHHHHHHHHH
T ss_conf 888--76719999999999999999
No 32
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=2.8e-42 Score=284.13 Aligned_cols=165 Identities=18% Similarity=0.261 Sum_probs=141.0
Q ss_pred CCCCEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHH
Q ss_conf 77758999846788888888899999999999988031379898588822886572420210123224852100234477
Q gi|254780818|r 5 NKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFW 84 (245)
Q Consensus 5 ~~mr~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~ 84 (245)
+.--|||||+||||+++ .++|||||||++.++.++ ++|+++|||+ .+||+++.++||||++||+++|+|.+|+++|+
T Consensus 3 ~~~~yvv~DlETTg~~~-~~~IIEIgAVk~~~g~iv-d~F~slVnP~-~~I~~~i~~lTGIt~~~v~~aP~~~eVl~~f~ 79 (195)
T PRK07247 3 HLETYIAFDLEFNTVND-VSHIIQVSAVKYDHHKEV-DSFDTYVYTD-VPLQSFINGLTGITADKIAAAPKVEEVLAAFK 79 (195)
T ss_pred CCCEEEEEEEECCCCCC-CCEEEEEEEEEEECCEEE-EEEEEEECCC-CCCCHHHHHCCCCCHHHHHCCCCHHHHHHHHH
T ss_conf 68849999977899999-980699999999899899-9998356698-99995554135989999835999999999999
Q ss_pred HHHHCCCCEEEEECC-CCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCC-CCCC-CCCHHHHHHHHCCCCCCCCCCCCH
Q ss_conf 753002320231023-2243112100000112222100001100000001-7764-222378999718754555666402
Q gi|254780818|r 85 DFFNEQNAEWIAHNA-KFDVGFINAELQRINKDPLDPSRIIDTLSIARRK-HPSS-RNDLNSLCKRYGITISHRSKHGAL 161 (245)
Q Consensus 85 ~fi~~~~~~lVaHNa-~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~-~p~~-~~~L~~l~~~~~i~~~~r~~H~Al 161 (245)
+|+| |+++||||| .||++||..+..+.+.++. ...+||..++|.. +|+. +++|++||++|||+. ++|+|+
T Consensus 80 ~Fig--d~~lVaHNa~~FD~~fL~~~~~~~~~~~~--~~~~~~~~~~r~~~~p~l~n~kL~tLa~~f~I~~---~~HRAl 152 (195)
T PRK07247 80 NFVG--ELPLIGYNAQKSDLPILAENGLDLRDQYQ--VDLFDEAFDRRSSDLNGIANLKLQTVATFLGIKG---RGHNSL 152 (195)
T ss_pred HHHC--CCEEEEECCCHHHHHHHHHHHHHHCCCCC--CCHHHHHHHHHHHCCCCCCCCCHHHHHHHCCCCC---CCCCCH
T ss_conf 9968--99189908845149999998774157766--8569999999886058876777899999749999---890818
Q ss_pred HHHHHHHHHHHHHHHCCC
Q ss_conf 699999999999973057
Q gi|254780818|r 162 LDSHLLSDVYIKMMVGGS 179 (245)
Q Consensus 162 ~Da~~~a~v~~~ll~g~~ 179 (245)
+||++||+||.+|+...+
T Consensus 153 ~DA~aTa~If~klLe~~~ 170 (195)
T PRK07247 153 EDARMTARIYESFLETDT 170 (195)
T ss_pred HHHHHHHHHHHHHHHHHH
T ss_conf 999999999999999766
No 33
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=100.00 E-value=1e-41 Score=280.65 Aligned_cols=224 Identities=35% Similarity=0.564 Sum_probs=175.2
Q ss_pred CCEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 75899984678888888889999999999998803137989858882288657242021012322485210023447775
Q gi|254780818|r 7 MRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDF 86 (245)
Q Consensus 7 mr~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~f 86 (245)
||+||||+||||+++.+|+|||||+|.+.++.++++.|+.|++| .+++++++.++||||++||.++|.|.+++++|.+|
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~~i~~~~~~~~v~P-~~~i~~~~~~i~git~e~l~~~p~~~~v~~~~~~~ 91 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFHTLVNP-ERPIPPEIFKIHGITDEMLADAPKFAEVLPEFLDF 91 (243)
T ss_pred CCEEEEECCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCEEECC-CCCCCCCCCCCCCCCHHHHHCCCCHHHHHHHHHHH
T ss_conf 75799966148988778854899659967784024311146688-98787543114773889974786389999999998
Q ss_pred HHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCC-CCCCHHHHHHHHCCCCCCCCCCCCHHHHH
Q ss_conf 30023202310232243112100000112222100001100000001776-42223789997187545556664026999
Q gi|254780818|r 87 FNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPS-SRNDLNSLCKRYGITISHRSKHGALLDSH 165 (245)
Q Consensus 87 i~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~-~~~~L~~l~~~~~i~~~~r~~H~Al~Da~ 165 (245)
++. ++.+||||+.||++||+.++.+++.++. .+.++||+.++|..+|+ .+++|++||.+|||+...+..|+|+.||.
T Consensus 92 i~~-~~~~Vahna~fD~~fl~~~~~~~~~~~~-~~~~~~t~~~~r~~~~~~~~~~L~~l~~~~gi~~~~~~~H~Al~Da~ 169 (243)
T COG0847 92 IGG-LRLLVAHNAAFDVGFLRVESERLGIEIP-GDPVLDTLALARRHFPGFDRSSLDALAERLGIDRNPFHPHRALFDAL 169 (243)
T ss_pred HCC-CCEEEEEEHHHCHHHHHHHHHHHCCCCC-CCCCHHHHHHHHHHCCCCCCCCHHHHHHHCCCCCCCCCCCCHHHHHH
T ss_conf 478-8869995053088999989997089875-76420079999987699761348999996298877777661678899
Q ss_pred HHHHHHHHHHHC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC----CHHHHH
Q ss_conf 999999999730-57666654443211110111222344321123563457899999999999987087----811456
Q gi|254780818|r 166 LLSDVYIKMMVG-GSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEHDKTIQTLGK----NAIWDR 239 (245)
Q Consensus 166 ~~a~v~~~ll~g-~~q~~l~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~H~~~l~~l~k----~~lW~k 239 (245)
+||++|+.++.+ ............. ...... .....+...........+...|......+.+ +.+|.+
T Consensus 170 ~~a~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 242 (243)
T COG0847 170 ALAELFLLLQTGLLLKAPLTAILDLD-----KLAHKA-LYDTLKTAARLFCGIENELKAHGSWLDALAKELLEKKLWKE 242 (243)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHH-----HHHHHH-CCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 99999999862000101133322120-----010011-04123334455205521778755444366765210046412
No 34
>cd06136 TREX1_2 Three prime repair exonuclease (TREX) 1 and 2 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 2 that point to different biological roles for these proteins. The main difference is the presence of about 7
Probab=100.00 E-value=6.2e-42 Score=281.98 Aligned_cols=158 Identities=26% Similarity=0.373 Sum_probs=130.9
Q ss_pred EEEEECCCCCCCCC-CCEEEEEEEEEEECCE------------ECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCC
Q ss_conf 89998467888888-8889999999999998------------8031379898588822886572420210123224852
Q gi|254780818|r 9 KIVFDIETTGLDSK-NDRIIEIGAVELLDYS------------KTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPS 75 (245)
Q Consensus 9 ~iv~D~ETTGl~~~-~d~Iieigav~i~~~~------------~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~ 75 (245)
|||||+|||||++. +|||||||||++.++. .+-++|+++|||+ ++||+++++|||||++||+++|+
T Consensus 1 fvv~D~ETTGL~~~~~~rIiEI~av~v~~~~~~~~~~~~~~~~~i~d~~~~lvnP~-~~Ip~~it~itGIt~emv~~~~~ 79 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPG-RAISPGASEITGLSNDLLEHKAP 79 (177)
T ss_pred CEEEEEECCCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEEECCC-CCCCHHHHHHCCCCHHHHHCCCC
T ss_conf 98998678997988998558999999977874443111245662142256764879-93887688751889999815998
Q ss_pred CC-HHHHHHHHHHHC--CCCEEEEECC-CCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHHH-CC
Q ss_conf 10-023447775300--2320231023-2243112100000112222100001100000001776422237899971-87
Q gi|254780818|r 76 FS-SIFSEFWDFFNE--QNAEWIAHNA-KFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRY-GI 150 (245)
Q Consensus 76 f~-ev~~~f~~fi~~--~~~~lVaHNa-~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~-~i 150 (245)
|. ++.+.|.+|++. .+.+|||||| +||++||++||.|+|.+++....++||+.++|.+++ +|++||++| |+
T Consensus 80 ~~~~~~~~~~~F~~~~~~~~~LVAHNa~~FD~~fL~~e~~r~g~~~p~~~~~iDtL~l~r~~~~----~L~~l~~~~~gi 155 (177)
T cd06136 80 FDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ----SLGSLYKRLFGQ 155 (177)
T ss_pred HHHHHHHHHHHHHHHCCCCCEEEECCCHHCCHHHHHHHHHHCCCCCCCCCEEEEEHHHHHHHCC----CHHHHHHHHCCC
T ss_conf 1799999999999626778679964851237999999999869989989889986076455069----999999997599
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 54555666402699999999999
Q gi|254780818|r 151 TISHRSKHGALLDSHLLSDVYIK 173 (245)
Q Consensus 151 ~~~~r~~H~Al~Da~~~a~v~~~ 173 (245)
+.. ++|+|++||++|++||+.
T Consensus 156 ~~~--~aHRAl~Da~at~~vflh 176 (177)
T cd06136 156 EPK--NSHTAEGDVLALLKCALH 176 (177)
T ss_pred CCC--CCCCCHHHHHHHHHHHCC
T ss_conf 998--777848999999999757
No 35
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=100.00 E-value=3.7e-41 Score=277.11 Aligned_cols=198 Identities=23% Similarity=0.371 Sum_probs=152.5
Q ss_pred EEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 89998467888888888999999999999880313798985888228865724202101232248521002344777530
Q gi|254780818|r 9 KIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFN 88 (245)
Q Consensus 9 ~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi~ 88 (245)
.+||||||||++ ++|||||+|++.++..+ +.|+++|||+ ++||+++++|||||++||+++|+|++|+++|. +
T Consensus 2 ~~VlDtETTGl~---~~IiEia~v~v~~g~i~-~~~~~linP~-~pI~~~a~~ihgIT~emv~~aP~f~ev~~~~~---~ 73 (219)
T PRK07983 2 LRIIDTETCGLQ---GGIVEIASVDVIDGKIV-NPMSHLVRPD-RPISPQAMAIHRITEAMVADKPWIEDVIPHYY---G 73 (219)
T ss_pred EEEEEEECCCCC---CCCEEEEEEEEECCEEE-EEEEEEECCC-CCCCHHHHHHCCCCHHHHCCCCCHHHHHHHHC---C
T ss_conf 599963479999---98489999999999997-6689998968-96988899872989999868998899999862---8
Q ss_pred CCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCC---CCCCCCHHHHH
Q ss_conf 023202310232243112100000112222100001100000001776422237899971875455---56664026999
Q gi|254780818|r 89 EQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISH---RSKHGALLDSH 165 (245)
Q Consensus 89 ~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~---r~~H~Al~Da~ 165 (245)
+.++|||||+||++||.. . ..++|||+.+||.+||+.+++|.+||.+++++... .++|+|++||.
T Consensus 74 --~~~lVaHNa~FD~~~L~~---------~-~~~~IcTl~lAR~l~p~~~~~l~~Lry~~~~~~~~~~~~~AHrAl~Dv~ 141 (219)
T PRK07983 74 --SEWYVAHNASFDRRVLPE---------M-PGEWICTMKLARRLWPGIKYSNMALYKSRKLNVQTPPGLHHHRALYDCY 141 (219)
T ss_pred --CCEEEECCCCCCHHHHCC---------C-CCCEEEHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHH
T ss_conf --987875365103866415---------5-8756657899998767742418999998427613324433343078799
Q ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHH---HHHHHHHHHHHC
Q ss_conf 999999999730576666544432111101112223443211235634578999---999999999870
Q gi|254780818|r 166 LLSDVYIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKE---ELDEHDKTIQTL 231 (245)
Q Consensus 166 ~~a~v~~~ll~g~~q~~l~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---e~~~H~~~l~~l 231 (245)
+|+.||.+|+.... . ...+-......+......++.|.....+..+..+ ++.+-.+.++.+
T Consensus 142 v~~~ll~~l~~~~~-~----~~e~l~~~s~~p~~~~~~~FGKyKG~~i~ev~~~dp~Yl~WlL~~~~dl 205 (219)
T PRK07983 142 ITAALLIDIMRTSG-W----TAEEMADITGRPSLLTTFTFGKYRGKAVSDVAERDPGYLRWLFNNLDSM 205 (219)
T ss_pred HHHHHHHHHHHHCC-C----CHHHHHHHHCCCCCCCCCCCCCCCCEEHHHHHCCCCCHHHHHHHCCCCC
T ss_conf 99999999998626-8----9999999863876123025677488099986125832999987362027
No 36
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=100.00 E-value=2e-39 Score=266.35 Aligned_cols=165 Identities=32% Similarity=0.522 Sum_probs=147.3
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 58999846788888888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
..||||+||||++|..|+|||||||.+.++.. .++|++||+|. .++++++.++||||++++.++|+|.+|+.+|.+|+
T Consensus 1 ~~v~~D~ETTGl~~~~~~Iieigav~~~~~~~-~~~~~~~i~P~-~~i~~~~~~i~GIt~~~l~~~~~~~~v~~~~~~~l 78 (169)
T smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGRI-IVVFDTYVKPD-RPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL 78 (169)
T ss_pred CEEEEEEECCCCCCCCCEEEEEEEEEEECCEE-EEEEEEEECCC-CCCCHHHHHHCCCCCHHCCCCCCHHHHHHHHHHHH
T ss_conf 99999985279999998699999999999988-78889887999-99998998631847212045866999999999860
Q ss_pred HCCCCEEEE-ECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHH
Q ss_conf 002320231-0232243112100000112222100001100000001776422237899971875455566640269999
Q gi|254780818|r 88 NEQNAEWIA-HNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHL 166 (245)
Q Consensus 88 ~~~~~~lVa-HNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~r~~H~Al~Da~~ 166 (245)
+ ++.+|+ ||++||++||++++.+.+........++||+.+++..+|+.+++|+++|++||++... ++|+|++||++
T Consensus 79 ~--~~~~v~~~~~~fD~~~L~~~~~~~~~~~~~~~~~~dt~~~~~~~~~~~~~~L~~l~~~~~i~~~~-~~H~Al~Da~~ 155 (169)
T smart00479 79 K--GKILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGRKYSLKKLAERLGLEVIG-RAHRALDDARA 155 (169)
T ss_pred C--CCCCHHCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCC-CCCCHHHHHHH
T ss_conf 4--87451036799999999999998189988665246299999997588545899999985999899-99297999999
Q ss_pred HHHHHHHHHHC
Q ss_conf 99999999730
Q gi|254780818|r 167 LSDVYIKMMVG 177 (245)
Q Consensus 167 ~a~v~~~ll~g 177 (245)
|++||.+|+..
T Consensus 156 t~~v~~~l~~~ 166 (169)
T smart00479 156 TAKLFKKLVER 166 (169)
T ss_pred HHHHHHHHHHH
T ss_conf 99999999977
No 37
>pfam00929 Exonuc_X-T Exonuclease. This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;
Probab=100.00 E-value=1.5e-38 Score=260.80 Aligned_cols=160 Identities=35% Similarity=0.578 Sum_probs=143.2
Q ss_pred EEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 89998467888888888999999999999880313798985888228865724202101232248521002344777530
Q gi|254780818|r 9 KIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFN 88 (245)
Q Consensus 9 ~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi~ 88 (245)
.||||+|||||+|..++|||||||++.++..+.++|++||+|+ .++++++.++||||+++++++|+|.+++.+|.+|++
T Consensus 1 ~v~~D~ETTGl~~~~~~Iieigav~~~~~~~~~~~~~~~v~P~-~~i~~~~~~i~GIt~~~l~~~~~~~~~~~~~~~~l~ 79 (162)
T pfam00929 1 LVVIDCETTGLDPEKDRIIEIAAVSIVGGENIGPVFDTYVKPE-RLITDEATKFHGITPEMLRNAPSFEEVLEAFLEFLK 79 (162)
T ss_pred CEEEEEECCCCCCCCCEEEEEEEEEEECCEEEEEEEEEEECCC-CCCCHHHHHHCCCCHHHHHHCCCHHHHHHHHHHHHC
T ss_conf 9899986899989997589999999999977655567877788-888999998739787775415311779999999842
Q ss_pred CCCCEEEEECCCCCCCEEEECHHCCCCCC-CCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHHCCCCCCCCCCCCHHHHHH
Q ss_conf 02320231023224311210000011222-21000011000000017764-22237899971875455566640269999
Q gi|254780818|r 89 EQNAEWIAHNAKFDVGFINAELQRINKDP-LDPSRIIDTLSIARRKHPSS-RNDLNSLCKRYGITISHRSKHGALLDSHL 166 (245)
Q Consensus 89 ~~~~~lVaHNa~FD~~fL~~el~r~~~~~-~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~~i~~~~r~~H~Al~Da~~ 166 (245)
.+.++|+||+.||.+||++++.+.+... .....++||+.+++..+|+. +.+|+++|++||++... ++|+||+||++
T Consensus 80 -~~~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~~~~dt~~~~~~~~~~~~~~~L~~l~~~~~i~~~~-~aH~Al~Da~~ 157 (162)
T pfam00929 80 -KLKILVGHNASFDVGFLLYDDLRFLKLPHPKLNDVIDTLILDKATYKGFKRRSLDALAEKLGLEKIQ-RAHRALDDARA 157 (162)
T ss_pred -CCCEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCC-CCCCHHHHHHH
T ss_conf -5857777887789999999999858633663333044899999975044679989999885999988-86782999999
Q ss_pred HHHHH
Q ss_conf 99999
Q gi|254780818|r 167 LSDVY 171 (245)
Q Consensus 167 ~a~v~ 171 (245)
|++||
T Consensus 158 t~~lf 162 (162)
T pfam00929 158 TAELF 162 (162)
T ss_pred HHHHC
T ss_conf 99879
No 38
>cd06133 ERI-1_3'hExo_like 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 homolog of either ERI-1 or 3'hExo.
Probab=100.00 E-value=2.7e-38 Score=259.22 Aligned_cols=166 Identities=22% Similarity=0.256 Sum_probs=139.5
Q ss_pred EEEEECCCCCCCCCCC-----EEEEEEEEEEECC-EECCCEEEEEECCCC-CCCCHHHEEECCCCCCCCCCCCCCCHHHH
Q ss_conf 8999846788888888-----8999999999999-880313798985888-22886572420210123224852100234
Q gi|254780818|r 9 KIVFDIETTGLDSKND-----RIIEIGAVELLDY-SKTNRTFQVFLCPNG-RKNSPEALKLHGITDEFLKDKPSFSSIFS 81 (245)
Q Consensus 9 ~iv~D~ETTGl~~~~d-----~Iieigav~i~~~-~~~~~~f~~~i~P~~-~~i~~~~~~ihGIt~~~l~~~p~f~ev~~ 81 (245)
|||||+||||+++..+ +|||||||+++++ ..+.++|++||||+. .++++++.++||||++||+++|+|.+|++
T Consensus 1 yvv~D~EtTg~~~~~~~~~~~eIIeIgav~vd~~~~~i~~~f~~lI~P~~~~~i~~~i~~itGIt~~~l~~ap~~~~v~~ 80 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80 (176)
T ss_pred CEEEEEECCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEEEEEEEECCCCCCCCCHHHHHHHCCCHHHHHCCCCHHHHHH
T ss_conf 98999726899878898999707999999998799979899999975876887898899773818878707863999999
Q ss_pred HHHHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCC--CCCHHCCCHHCCCCCCCC-CCCCHHHHHHHHCCCCCCCCCC
Q ss_conf 4777530023202310232243112100000112222--100001100000001776-4222378999718754555666
Q gi|254780818|r 82 EFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPL--DPSRIIDTLSIARRKHPS-SRNDLNSLCKRYGITISHRSKH 158 (245)
Q Consensus 82 ~f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~--~~~~~iDTl~lar~~~p~-~~~~L~~l~~~~~i~~~~r~~H 158 (245)
+|.+|++.......+||+.||.+|+..++.+.+.... ....++||..++++.+|. .+.+|++||++|||+.+. ++|
T Consensus 81 ~f~~~i~~~~~~~~~~~~~fD~~~l~~~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~~~~sL~~l~~~~gi~~~~-~~H 159 (176)
T cd06133 81 EFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEG-RHH 159 (176)
T ss_pred HHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCC-CCC
T ss_conf 9999972698579996060029999999999789988730111204999999981888898999999986999999-885
Q ss_pred CCHHHHHHHHHHHHHHH
Q ss_conf 40269999999999997
Q gi|254780818|r 159 GALLDSHLLSDVYIKMM 175 (245)
Q Consensus 159 ~Al~Da~~~a~v~~~ll 175 (245)
+||.||++||+||++|+
T Consensus 160 ~AL~DA~~ta~v~~~ll 176 (176)
T cd06133 160 RGLDDARNIARILKRLL 176 (176)
T ss_pred CCHHHHHHHHHHHHHHC
T ss_conf 85999999999999879
No 39
>cd06127 DEDDh 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. DEDDy 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=100.00 E-value=6.8e-36 Score=244.24 Aligned_cols=157 Identities=45% Similarity=0.738 Sum_probs=137.9
Q ss_pred EEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHHHC
Q ss_conf 99984678888888889999999999998803137989858882288657242021012322485210023447775300
Q gi|254780818|r 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNE 89 (245)
Q Consensus 10 iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi~~ 89 (245)
|+||||||||+|.+|+|||||||.+.++....++|+.+|+|. .++++.+.++|||+.+++.++|.|.+++.+|.+|++
T Consensus 1 v~~D~ETTGl~~~~~~Iieia~v~~~~~~~~~~~~~~~i~P~-~~~~~~~~~i~gi~~~~~~~~~~~~~~~~~~~~~l~- 78 (159)
T cd06127 1 VVLDTETTGLDPKGDRIIEIGAVKVDGGIEIVERFETLVNPG-RPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLG- 78 (159)
T ss_pred CEEEEECCCCCCCCCCEEEEEEEEEECCEEEEEEEEEEECCC-CCCCHHHHHHHCCCHHHHCCCCCHHHHHHHHHHHCC-
T ss_conf 989826799999998469999999999956520079998899-999988987606778995899968999999987315-
Q ss_pred CCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCC-CCHH-HHHHHHCCCCCCCCCCCCHHHHHHH
Q ss_conf 2320231023224311210000011222210000110000000177642-2237-8999718754555666402699999
Q gi|254780818|r 90 QNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSR-NDLN-SLCKRYGITISHRSKHGALLDSHLL 167 (245)
Q Consensus 90 ~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~-~~L~-~l~~~~~i~~~~r~~H~Al~Da~~~ 167 (245)
+.++||||++||++||++++.+++.++. ..+++||+.++|..+|..+ ..+. ..|.+||++.. ++|+||+||.+|
T Consensus 79 -~~~lv~hN~~FD~~~L~~~~~~~~~~~~-~~~~iDt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~aH~Al~D~~at 154 (159)
T cd06127 79 -GRVLVAHNASFDLRFLNRELRRLGGPPL-PNPWIDTLRLARRLLPGLRSHRLGLLLAARYGIPLE--GAHRALADALAT 154 (159)
T ss_pred -CCEEEECCHHHHHHHHHHHHHHCCCCCC-CCCEEEHHHHHHHHCCCCCCCCHHHHHHHHCCCCCC--CCCCHHHHHHHH
T ss_conf -6346515888999999999998399988-996664799999973888899999999997698879--895989999999
Q ss_pred HHHHH
Q ss_conf 99999
Q gi|254780818|r 168 SDVYI 172 (245)
Q Consensus 168 a~v~~ 172 (245)
++||.
T Consensus 155 ~~l~~ 159 (159)
T cd06127 155 AELLL 159 (159)
T ss_pred HHHHC
T ss_conf 99969
No 40
>cd06138 ExoI_N This subfamily is composed of the N-terminal domain of E. 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=100.00 E-value=3e-33 Score=227.74 Aligned_cols=160 Identities=27% Similarity=0.358 Sum_probs=129.0
Q ss_pred EEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCC-CCCCCHHHEEECCCCCCCC-CCCCCCCHHHHHHHHHH
Q ss_conf 999846788888888899999999999988031379898588-8228865724202101232-24852100234477753
Q gi|254780818|r 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPN-GRKNSPEALKLHGITDEFL-KDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 10 iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~-~~~i~~~~~~ihGIt~~~l-~~~p~f~ev~~~f~~fi 87 (245)
|+||+|||||+|..|+|||||||.+.+...+.++|+.+++|. +..++|+|.+|||||++++ ..+|++.+++.++.+|+
T Consensus 1 i~fD~ETTGl~~~~d~Iiqiaai~~d~~~~~~~~~~~~i~p~~~~~p~p~a~~v~git~~~~~~~~~s~~e~~~~i~~~~ 80 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQFAAIRTDENFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKIHRLF 80 (183)
T ss_pred CEEEECCCCCCCCCCCEEEEEEEEECCCCCCCCEEEEEECCCCCCCCCHHHHHHCCCCHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 98970389979998760699999998998786446887404899998847998718899997531887789999999986
Q ss_pred HCCCCEEEEEC-CCCCCCEEEECHHCCCCCCC-----CCCHHCCCHHCCCC---CCCC-----------CCCCHHHHHHH
Q ss_conf 00232023102-32243112100000112222-----10000110000000---1776-----------42223789997
Q gi|254780818|r 88 NEQNAEWIAHN-AKFDVGFINAELQRINKDPL-----DPSRIIDTLSIARR---KHPS-----------SRNDLNSLCKR 147 (245)
Q Consensus 88 ~~~~~~lVaHN-a~FD~~fL~~el~r~~~~~~-----~~~~~iDTl~lar~---~~p~-----------~~~~L~~l~~~ 147 (245)
+..++++|||| ++||..||+++|.|.+.++. ..+..+|++.++|. +.|+ .+++|++||++
T Consensus 81 ~~~~~i~vg~N~~~FD~~fL~~~~~r~~~~p~~~~~~~~~~~~D~l~~~r~~~~~~p~~i~~~~~~~g~~s~kL~~l~~~ 160 (183)
T cd06138 81 NTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKLEDLAQA 160 (183)
T ss_pred CCCCCEEEEECCHHHHHHHHHHHHHHHCCCCHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHH
T ss_conf 16997799845355689999999998278715667527871230788999999978201447655689741129999998
Q ss_pred HCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 187545556664026999999999
Q gi|254780818|r 148 YGITISHRSKHGALLDSHLLSDVY 171 (245)
Q Consensus 148 ~~i~~~~r~~H~Al~Da~~~a~v~ 171 (245)
|||+.. ++|+|++||++|++|.
T Consensus 161 ~gi~~~--~aH~Al~Dv~aT~~l~ 182 (183)
T cd06138 161 NGIEHS--NAHDALSDVEATIALA 182 (183)
T ss_pred CCCCCC--CCCCCHHHHHHHHHHH
T ss_conf 499998--8868289999999986
No 41
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.98 E-value=8.7e-32 Score=218.60 Aligned_cols=209 Identities=24% Similarity=0.318 Sum_probs=152.3
Q ss_pred CC-EEEEECCCCCCCCCCCEEEEEEEEEEE---CCE--ECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHH
Q ss_conf 75-899984678888888889999999999---998--803137989858882288657242021012322485210023
Q gi|254780818|r 7 MR-KIVFDIETTGLDSKNDRIIEIGAVELL---DYS--KTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIF 80 (245)
Q Consensus 7 mr-~iv~D~ETTGl~~~~d~Iieigav~i~---~~~--~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~ 80 (245)
+| -||+||||||||+..|+|||||+|.+. ++. .+.++|+.|..| +++||+++++|||||++||+++--=.
T Consensus 36 ~r~g~~lD~ETTGl~~~~d~IIElg~v~f~~~~~G~i~~i~~~~~~~~dP-~~pIp~~it~lTGItd~mV~Gq~id~--- 111 (293)
T PRK09182 36 VRLGVILDTETTGLDPRKDEIIEIGMVAFEYDDDGRIGDVVDTFGGLQQP-SRPIPPEITRLTGITDEMVAGQTIDP--- 111 (293)
T ss_pred EEEEEEEECCCCCCCCCCCEEEEEEEEEEEECCCCCEEEEECCEECCCCC-CCCCCHHHHHHCCCCHHHHCCCCCCH---
T ss_conf 06899995305788977877999768999986998587764323110389-99899879875188889968882799---
Q ss_pred HHHHHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHH---CCCCCCCCCCCCHHHHHHHHCCCCCCCCC
Q ss_conf 447775300232023102322431121000001122221000011000---00001776422237899971875455566
Q gi|254780818|r 81 SEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLS---IARRKHPSSRNDLNSLCKRYGITISHRSK 157 (245)
Q Consensus 81 ~~f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~---lar~~~p~~~~~L~~l~~~~~i~~~~r~~ 157 (245)
.++..|+.. -..+|||||.||.+|+.+-+.- +...++-||+. ....-+ .+.+|+.||..+|.-. ++
T Consensus 112 ~~V~~~~~~-adliiAHNA~FDR~F~E~~~p~-----f~~k~WaCS~~~IdW~~~Gf--~s~kLeyL~~~~G~F~---~a 180 (293)
T PRK09182 112 AEVDALIAP-ADLIIAHNAGFDRPFLERFSPV-----FANKPWACSVSEIDWSARGF--EGTKLGYLAGQAGFFH---DG 180 (293)
T ss_pred HHHHHHHCC-CCEEEECCCCCCHHHHHHHCCC-----CCCCCEEEECCCCCHHHCCC--CCCCHHHHHHHCCCCC---CC
T ss_conf 999998644-9899981775467789850953-----25875053163797032287--7415999998609454---56
Q ss_pred CCCHHHHHHHHHHHH------------HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCCHHHH
Q ss_conf 640269999999999------------997305766665444321111011122234432----1123563457899999
Q gi|254780818|r 158 HGALLDSHLLSDVYI------------KMMVGGSQINFGFKTNEDRFFKEEKKTVPNISL----LKRDKPLFTRITKEEL 221 (245)
Q Consensus 158 H~Al~Da~~~a~v~~------------~ll~g~~q~~l~l~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~e~ 221 (245)
|+|+.||.++..|+. .|+....++.+.....+..+...+..+...+.. ..+++.|.+.+.++++
T Consensus 181 HRA~~Dc~All~LL~~~l~~s~~~~l~~Ll~~a~~~~~rI~A~~aPfd~KD~LK~RGYRW~~~~~~~~k~W~~~v~e~~l 260 (293)
T PRK09182 181 HRAVDDCQALLELLARPLPETGQPPLAELLEASRRPRMRIWAENSPFELKDHLKARGYRWSDGSDGRPKSWWIEVGEDDL 260 (293)
T ss_pred CCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCEEEEEEECCCCHHHHHHHHCCCCCCCCCCCCCCEEEEECCHHHH
T ss_conf 53488999999997677864455499999997278849999707981348999876997799999987517998476368
Q ss_pred HHHHHHHHH
Q ss_conf 999999987
Q gi|254780818|r 222 DEHDKTIQT 230 (245)
Q Consensus 222 ~~H~~~l~~ 230 (245)
+...+||..
T Consensus 261 ~~E~~wL~~ 269 (293)
T PRK09182 261 EAELAFLRT 269 (293)
T ss_pred HHHHHHHHH
T ss_conf 999999998
No 42
>cd06125 DnaQ_like_exo 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 or DEDDh exonucleases depending on the variation of motif
Probab=99.96 E-value=1e-30 Score=211.88 Aligned_cols=118 Identities=28% Similarity=0.437 Sum_probs=105.8
Q ss_pred EEEECCCCCCCC-CCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 999846788888-8888999999999999880313798985888228865724202101232248521002344777530
Q gi|254780818|r 10 IVFDIETTGLDS-KNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFN 88 (245)
Q Consensus 10 iv~D~ETTGl~~-~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi~ 88 (245)
||||+|||||++ .+|+|||||+|.+.. ++.|++++||. +++++.+.++||||++|++++|+|.+++++|.+|++
T Consensus 1 Vv~D~ETTGl~~~~~d~Iiei~~v~~~~----~~~~~~~v~p~-~~i~~~~~~i~gi~~~~v~~~p~~~~~~~~~~~f~~ 75 (130)
T cd06125 1 VAFDIETTGLNGNARDEIIEIALVVVHI----GEKFVFDVKPD-DLIDPYAFTISGITDEVVERAATEAELLIELLAFLR 75 (130)
T ss_pred CEEEEECCCCCCCCCCEEEEEEEEEEEC----CCEEEEEECCC-CCCCHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 9898018996999998589999999718----98899997999-989977941037599998330608999999999976
Q ss_pred CCCCEEEEECCCCCCCEEEECHHCCCCCCCC-CCHHCCCHHCCCC
Q ss_conf 0232023102322431121000001122221-0000110000000
Q gi|254780818|r 89 EQNAEWIAHNAKFDVGFINAELQRINKDPLD-PSRIIDTLSIARR 132 (245)
Q Consensus 89 ~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~-~~~~iDTl~lar~ 132 (245)
..+.++||||++||++||++++.|+|+++.. .++++||+.+||+
T Consensus 76 ~~~~ilVgHN~~FD~~fL~~~~~r~g~~~~~~~~~~iDTl~lar~ 120 (130)
T cd06125 76 DKDDILVGHNISFDLPYLLNRAAELGIPYPILGRIVFDTLALALE 120 (130)
T ss_pred CCCCEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCEEECHHHHHH
T ss_conf 999999991947749999999998499998789968686098421
No 43
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.95 E-value=6.7e-28 Score=194.30 Aligned_cols=168 Identities=18% Similarity=0.201 Sum_probs=142.5
Q ss_pred CCCEEEEECCCCCCCC----CC--CEEEEEEEEEEECCEECCCEEEEEECCCC-CCCCHHHEEECCCCCCCCCCCCCCCH
Q ss_conf 7758999846788888----88--88999999999999880313798985888-22886572420210123224852100
Q gi|254780818|r 6 KMRKIVFDIETTGLDS----KN--DRIIEIGAVELLDYSKTNRTFQVFLCPNG-RKNSPEALKLHGITDEFLKDKPSFSS 78 (245)
Q Consensus 6 ~mr~iv~D~ETTGl~~----~~--d~Iieigav~i~~~~~~~~~f~~~i~P~~-~~i~~~~~~ihGIt~~~l~~~p~f~e 78 (245)
.|++||+|+|.|--+. .+ .+|||||||.+.++.. .++|++||+|.. ..++++..++||||.++|.+||+|.+
T Consensus 3 ~~~yiViDfEaTc~~~~~~p~~~~~EIIEiGaV~l~~~~i-~d~F~~~VkP~~~p~Ls~fc~~LTGItq~~vd~a~~F~e 81 (205)
T PRK07748 3 EQRFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCKV-EDTFSSYVKPKTFPSLTDRCKKFLGITQEDVDKGISFEE 81 (205)
T ss_pred CCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEECCEE-EEEHEEEECCCCCCCCCHHHHHHCCCCHHHHHCCCCHHH
T ss_conf 6669999985478887888777887517997899817815-210000479854785137899752949999625898899
Q ss_pred HHHHHHHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHHCCCCCCCCC
Q ss_conf 23447775300232023102322431121000001122221000011000000017764-22237899971875455566
Q gi|254780818|r 79 IFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRYGITISHRSK 157 (245)
Q Consensus 79 v~~~f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~~i~~~~r~~ 157 (245)
+++.|.+|++..+ .++++...+|+++|.+++++.|++.+....++|....++..++.. +.+|..+.+.+|++..++ +
T Consensus 82 vl~~f~~~~~~~~-~~~~tWG~~D~~~L~~~c~~~~i~~p~~~~~idlk~~f~~~~~~~~~~gL~~aL~~lgl~~eG~-~ 159 (205)
T PRK07748 82 LVEKLAEYDKRCK-PTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKAIEEYGKEGTGK-H 159 (205)
T ss_pred HHHHHHHHHCCCC-EEEEEECHHHHHHHHHHHHHHCCCCCCCCCEEEHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCC-C
T ss_conf 9999999817787-2898717889999999999938999853100639999999968888768999999769988898-6
Q ss_pred CCCHHHHHHHHHHHHHHHH
Q ss_conf 6402699999999999973
Q gi|254780818|r 158 HGALLDSHLLSDVYIKMMV 176 (245)
Q Consensus 158 H~Al~Da~~~a~v~~~ll~ 176 (245)
|+|+.||+.||+||..|..
T Consensus 160 H~glDDA~NtAkI~kk~~~ 178 (205)
T PRK07748 160 HCALDDAMTTYNIFKLVEK 178 (205)
T ss_pred CCHHHHHHHHHHHHHHHHC
T ss_conf 3758999999999999761
No 44
>cd06144 REX4_like 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 clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required fo
Probab=99.94 E-value=7.6e-27 Score=187.70 Aligned_cols=148 Identities=19% Similarity=0.359 Sum_probs=113.4
Q ss_pred EEEECCCCCCCCCCCEEEEEEEEEEECCEECCC-EEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 999846788888888899999999999988031-3798985888228865724202101232248521002344777530
Q gi|254780818|r 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNR-TFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFN 88 (245)
Q Consensus 10 iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~-~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi~ 88 (245)
|++|+||||+.+.+.+ .+++.|.++|. .|+ .|++||+|+ .+|++..+++||||++||+++|+|+++.+++.+|+.
T Consensus 1 valDcEm~g~~~~~~~-~~larv~vvd~--~g~~v~d~~V~P~-~~V~d~~T~~sGIt~~~l~~a~~~~~v~~~~~~~l~ 76 (152)
T cd06144 1 VALDCEMVGVGPDGSE-SALARVSIVNE--DGNVVYDTYVKPQ-EPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLK 76 (152)
T ss_pred CEEEEEECCCCCCCCE-EEEEEEEEEEC--CCCEEEEEEECCC-CCCCCCCEEECCCCHHHHCCCCCHHHHHHHHHHHHC
T ss_conf 9898760335289987-89999999967--8999988723699-767876356248579997389999999999999853
Q ss_pred CCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCC--CCCCCCCCCCHHHHHHHH-CCCCCCCCCCCCHHHHH
Q ss_conf 023202310232243112100000112222100001100000--001776422237899971-87545556664026999
Q gi|254780818|r 89 EQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIA--RRKHPSSRNDLNSLCKRY-GITISHRSKHGALLDSH 165 (245)
Q Consensus 89 ~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~la--r~~~p~~~~~L~~l~~~~-~i~~~~r~~H~Al~Da~ 165 (245)
+.++||||+.||+++|+.... ...++||..+. +...+..+.+|..||++| |++... ..|+|+.||.
T Consensus 77 --~~ilVGH~l~~Dl~~L~l~~~--------~~~i~DT~~~~~~~~~~~~~~~sLk~L~~~~Lg~~Iq~-~~H~s~eDA~ 145 (152)
T cd06144 77 --GRILVGHALKNDLKVLKLDHP--------KKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQE-GEHSSVEDAR 145 (152)
T ss_pred --CCEEEECCHHHHHHHHHCCCC--------CCEEEEEEEEHHHHHCCCCCCCCHHHHHHHHCCCCCCC-CCCCCHHHHH
T ss_conf --887986064646999624388--------76068855642245416889927999999985885899-7969699999
Q ss_pred HHHHHHH
Q ss_conf 9999999
Q gi|254780818|r 166 LLSDVYI 172 (245)
Q Consensus 166 ~~a~v~~ 172 (245)
+|+++|.
T Consensus 146 at~~Lfk 152 (152)
T cd06144 146 AAMRLYR 152 (152)
T ss_pred HHHHHHC
T ss_conf 9999859
No 45
>PRK06722 exonuclease; Provisional
Probab=99.94 E-value=6.2e-28 Score=194.52 Aligned_cols=128 Identities=18% Similarity=0.244 Sum_probs=111.4
Q ss_pred CEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCC
Q ss_conf 13798985888228865724202101232248521002344777530023202310232243112100000112222100
Q gi|254780818|r 42 RTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPS 121 (245)
Q Consensus 42 ~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~ 121 (245)
..|+++|||. .+||+.++++||||++||.++|+|++|+++|++||| |+.+|||||.||++||++.+..+|.+++. .
T Consensus 5 ~rFstLVNPg-~pIp~~It~LTGITdeMV~~aP~ieeVLp~FleFIG--d~~LVAHNAsFD~gFL~~~C~~hg~e~P~-~ 80 (242)
T PRK06722 5 GEFSELVKPG-ARLTRHTTKLTGITKKDLIGVEKFPQIIEKFIQFIG--EDSIFVTWGKEDYRFLSHDCTLHGVECPC-M 80 (242)
T ss_pred HHHHHHCCCC-CCCCHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHHC--CCEEEEECCHHHHHHHHHHHHHCCCCCCC-C
T ss_conf 8888651989-999833565338688998279978999999999827--88389734402277999775242899999-8
Q ss_pred HHCCCHHCCCCCC-C-----CCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 0011000000017-7-----642223789997187545556664026999999999999
Q gi|254780818|r 122 RIIDTLSIARRKH-P-----SSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKM 174 (245)
Q Consensus 122 ~~iDTl~lar~~~-p-----~~~~~L~~l~~~~~i~~~~r~~H~Al~Da~~~a~v~~~l 174 (245)
+..||..++|..+ + ...-||.....+|+...+. ..|+||+||+.|+.||+..
T Consensus 81 ~~~~~~dl~k~v~~~~~el~~h~ps~~~A~~q~~~t~~~-~~HRAlaDA~~T~ni~l~v 138 (242)
T PRK06722 81 EKERRIDLQKFVFQAYEELFEHTPSLQSAVEQLGLIWEG-KQHRALADAENTANILLKA 138 (242)
T ss_pred CCHHHHHHHHHHHHCCHHHHCCCCHHHHHHHHHHCCCCC-HHHHHHHHHHHHHHHHHHH
T ss_conf 421088899998631244321380299999998502567-0367787688889999997
No 46
>TIGR01298 RNaseT ribonuclease T; InterPro: IPR005987 Ribonuclease T (3.1.13 from EC) is an enzyme found so far only 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.; GO: 0004540 ribonuclease activity, 0006396 RNA processing.
Probab=99.91 E-value=2.1e-25 Score=178.74 Aligned_cols=170 Identities=28% Similarity=0.495 Sum_probs=138.6
Q ss_pred EEEECCCCCCCCCCCEEEEEEEEEEE--C-C-EECCCEEEEEECC-CCCCCCHHHEEECCCCCCC-CCCCCCCCHHHHHH
Q ss_conf 99984678888888889999999999--9-9-8803137989858-8822886572420210123-22485210023447
Q gi|254780818|r 10 IVFDIETTGLDSKNDRIIEIGAVELL--D-Y-SKTNRTFQVFLCP-NGRKNSPEALKLHGITDEF-LKDKPSFSSIFSEF 83 (245)
Q Consensus 10 iv~D~ETTGl~~~~d~Iieigav~i~--~-~-~~~~~~f~~~i~P-~~~~i~~~~~~ihGIt~~~-l~~~p~f~ev~~~f 83 (245)
||+|+||.|+|...|-++||+|+.|. + + ...+.+++.-|.| +|..|.|++.+++||..+. ++.+..-..++.++
T Consensus 11 VVvDVET~GfN~~~dALLEiAait~~MDe~G~L~P~~~~~~~~~P~~Gani~P~~L~~~GI~~d~P~R~A~~E~~Al~~i 90 (201)
T TIGR01298 11 VVVDVETAGFNAKTDALLEIAAITLKMDEQGYLVPDETLHFHVEPFEGANIEPEALEFTGIDLDHPLRGAVEEKLALEEI 90 (201)
T ss_pred EEEEECCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCEEEEEEECCCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHHHH
T ss_conf 48861067766013455555420001167300147852578852267998871200220654488752246688999999
Q ss_pred HHHH-------HCCCCEEEEECCCCCCCEEE-ECHHCCCCC--CCCCCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCC
Q ss_conf 7753-------00232023102322431121-000001122--2210000110000000177642223789997187545
Q gi|254780818|r 84 WDFF-------NEQNAEWIAHNAKFDVGFIN-AELQRINKD--PLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITIS 153 (245)
Q Consensus 84 ~~fi-------~~~~~~lVaHNa~FD~~fL~-~el~r~~~~--~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~ 153 (245)
...+ +.+-+++||||+.||.+||+ ++..|.+.+ |+.+...+||..||...| ||.. |...|+.-|++..
T Consensus 91 F~~vR~~~K~~gC~RailV~HNa~fD~~Fl~~AA~~R~~~KRnPFH~F~~FDTatLAGl~y-GQTV-L~kA~Q~Ag~~fd 168 (201)
T TIGR01298 91 FKVVRKALKASGCQRAILVAHNASFDLGFLNRAAVKRTALKRNPFHPFSVFDTATLAGLAY-GQTV-LAKACQAAGLDFD 168 (201)
T ss_pred HHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHH-HHHH-HHHHHHHCCCCCC
T ss_conf 9999999975579603676003204666899999998611578987652246899988864-1799-9988864278867
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 5566640269999999999997305766
Q gi|254780818|r 154 HRSKHGALLDSHLLSDVYIKMMVGGSQI 181 (245)
Q Consensus 154 ~r~~H~Al~Da~~~a~v~~~ll~g~~q~ 181 (245)
.+++|+|++|++-||++|-.+++..++.
T Consensus 169 ~~~AHSA~YDtE~TA~LFC~ivN~wk~~ 196 (201)
T TIGR01298 169 AKQAHSALYDTEKTAELFCEIVNRWKEL 196 (201)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 5443101200356899999886304550
No 47
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.89 E-value=2.8e-23 Score=165.43 Aligned_cols=155 Identities=24% Similarity=0.395 Sum_probs=126.9
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 58999846788888888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
-+|.+-+-|||+-|...|++.|.||.+......++.||+.+||. .+|.-+.|||+|.++|+++|.|.+++.+|.+.|
T Consensus 47 p~va~~~~ttgihpst~r~v~~da~~~da~Ge~~~~f~~~lNPg---~DPGP~HiHGLT~e~L~gAP~F~~ia~~l~~lL 123 (377)
T PRK05601 47 PFVAVSIQSSGIHPSTSRMVTIDAVTLSADGEPVETFHAVLNPK---TDPGPFHLHGVTEEEFASAKRFGQILKSLDRLI 123 (377)
T ss_pred CEEEEEEEECCCCCCCCEEEEEEEEEECCCCCCCCEEEEECCCC---CCCCCCCCCCCCHHHHCCCCCHHHHHHHHHHHH
T ss_conf 72799988557577755058887888647897223457712799---999981013789999706842899999999984
Q ss_pred HCCCCEEEEECCCCCCCEEEECHHCCCCC--------------------------CCCCCHHCCCHHCCCCCCCCC-CCC
Q ss_conf 00232023102322431121000001122--------------------------221000011000000017764-222
Q gi|254780818|r 88 NEQNAEWIAHNAKFDVGFINAELQRINKD--------------------------PLDPSRIIDTLSIARRKHPSS-RND 140 (245)
Q Consensus 88 ~~~~~~lVaHNa~FD~~fL~~el~r~~~~--------------------------~~~~~~~iDTl~lar~~~p~~-~~~ 140 (245)
.|.+||+||+.|||+||-+|++|.... .+.+..++||+.++|..-... ...
T Consensus 124 --dGRtLVaHNa~fdw~Fia~Ea~RA~~~a~~~~R~~~r~~~~~~r~rrrqr~gh~P~P~~iv~TLAlaRR~~l~~~d~R 201 (377)
T PRK05601 124 --DGRTLLLHNAPRTWGFIVSEAKRAMNDAARANRNRNRGNRRGGRGRRRQRVGHIPKPLVIVDTLASARRQAIALDDVR 201 (377)
T ss_pred --CCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHCCCCCCCCCCEEEHHHHHHHCCCCCCCHH
T ss_conf --586799835602088999999986554234432100134444443101003677887521007777764189987435
Q ss_pred HHHHHHHHCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 37899971875455566640269999999
Q gi|254780818|r 141 LNSLCKRYGITISHRSKHGALLDSHLLSD 169 (245)
Q Consensus 141 L~~l~~~~~i~~~~r~~H~Al~Da~~~a~ 169 (245)
|.+++.+||++-.. +|.++.++.+.+.
T Consensus 202 L~~vA~~~g~~a~~--a~a~~~ra~~~~~ 228 (377)
T PRK05601 202 IRGVAHTLGLDAPA--AEASVERAQVPHR 228 (377)
T ss_pred HHHHHHHCCCCCCC--HHHHHHHHCCCHH
T ss_conf 56667660888630--1321656335567
No 48
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.84 E-value=1.6e-20 Score=148.20 Aligned_cols=170 Identities=20% Similarity=0.186 Sum_probs=118.9
Q ss_pred CCCCCCCCEEEEECCCCCCCCCCCEEEEEEEEEEECC-EECCCEEEEEECCC-CCCCCHHHEEECCCCCCCCCC-CCCCC
Q ss_conf 9866777589998467888888888999999999999-88031379898588-822886572420210123224-85210
Q gi|254780818|r 1 MIRKNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDY-SKTNRTFQVFLCPN-GRKNSPEALKLHGITDEFLKD-KPSFS 77 (245)
Q Consensus 1 ~~~~~~mr~iv~D~ETTGl~~~~d~Iieigav~i~~~-~~~~~~f~~~i~P~-~~~i~~~~~~ihGIt~~~l~~-~p~f~ 77 (245)
|.+.-...+|..|+||||++|..|+|+|+|+|..+.. .++++.+..+++|. +.--.|.|.-|||||++++.. +-+-.
T Consensus 1 ~~~~~~~~f~fyD~ETtG~~~~~dqi~Qfa~i~td~~ln~i~~~~~~~c~~~~~~lP~p~A~lvt~itp~~~~~~~~~~~ 80 (477)
T PRK11779 1 MDKNMQPTFLWHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEA 80 (477)
T ss_pred CCCCCCCCEEEEECCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCHHHCCCCCHHHHHHCCCCHH
T ss_conf 97667785799945368999877650125778987753725774105644799989993043114889999986699879
Q ss_pred HHHHHHHHHHHCCCCEEEEECC-CCCCCEEEECHHCCCCCC-----CCCCHHCCCHHCCCC---C------CC----CC-
Q ss_conf 0234477753002320231023-224311210000011222-----210000110000000---1------77----64-
Q gi|254780818|r 78 SIFSEFWDFFNEQNAEWIAHNA-KFDVGFINAELQRINKDP-----LDPSRIIDTLSIARR---K------HP----SS- 137 (245)
Q Consensus 78 ev~~~f~~fi~~~~~~lVaHNa-~FD~~fL~~el~r~~~~~-----~~~~~~iDTl~lar~---~------~p----~~- 137 (245)
+.+.++...+...++.+||+|. .||--|+++.|.|-=.++ -..+.-.|.+.++|. + +| |.
T Consensus 81 ~~~~~i~~~~~~~~t~~iGyNsi~FDee~~R~~fy~nl~dPY~~~~~ngNsR~Dll~~~r~~~~~~p~~i~~p~~~~G~~ 160 (477)
T PRK11779 81 EFAARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLP 160 (477)
T ss_pred HHHHHHHHHHCCCCCEEEECCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCE
T ss_conf 99999999966898489822775448999999999861345766424897057999999999874836611673799985
Q ss_pred CCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 22237899971875455566640269999999999
Q gi|254780818|r 138 RNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYI 172 (245)
Q Consensus 138 ~~~L~~l~~~~~i~~~~r~~H~Al~Da~~~a~v~~ 172 (245)
+.+|+.|+..-||+. .+||+|++|+++|-++-.
T Consensus 161 sfKLe~la~aNgi~h--~~AHDAl~Dv~aTi~lak 193 (477)
T PRK11779 161 SFKLEHLTKANGIEH--ENAHDAMSDVYATIAMAK 193 (477)
T ss_pred EEEHHHHHHHCCCCC--CCCCHHHHHHHHHHHHHH
T ss_conf 444999998559876--554106889999999999
No 49
>cd06137 DEDDh_RNase 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 preference for single-stranded RNA.
Probab=99.79 E-value=2.3e-19 Score=140.92 Aligned_cols=148 Identities=20% Similarity=0.416 Sum_probs=115.8
Q ss_pred EEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCC-------CCCHHHHH
Q ss_conf 99984678888888889999999999998803137989858882288657242021012322485-------21002344
Q gi|254780818|r 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKP-------SFSSIFSE 82 (245)
Q Consensus 10 iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p-------~f~ev~~~ 82 (245)
|++|+|++|..+.++.+++|++|...++... |.+||+|. .+|....++++|||++++++++ .+.++..+
T Consensus 1 VAlDCEMv~~~~~~~el~rvs~Vd~~~g~vl---~d~~VkP~-~~V~Dy~T~~SGIt~~~l~~a~~~~~~~~~~~~a~~~ 76 (161)
T cd06137 1 VALDCEMVGLADGDSEVVRISAVDVLTGEVL---IDSLVRPS-VRVTDWRTRFSGVTPADLEEAAKAGKTIFGWEAARAA 76 (161)
T ss_pred CEEEEEEECCCCCCCEEEEEEEEECCCCEEE---EEECCCCC-CCCCCCEEECCCCCHHHHHHHHHCCCCCCCHHHHHHH
T ss_conf 9796452332299725899999972799199---98633598-4323014332579999985434215333319999999
Q ss_pred HHHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCC----CCCCCCCHHHHHHH-HCCCCCC-CC
Q ss_conf 777530023202310232243112100000112222100001100000001----77642223789997-1875455-56
Q gi|254780818|r 83 FWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRK----HPSSRNDLNSLCKR-YGITISH-RS 156 (245)
Q Consensus 83 f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~----~p~~~~~L~~l~~~-~~i~~~~-r~ 156 (245)
+.+||+ ++.++|||+..+|++.|+- . ..+++||..+.+.. .+..+.+|..||+. +|.+... .+
T Consensus 77 l~~~i~-~~tIlVGH~L~nDL~aL~~---------~-H~~viDTa~l~~~~~~~~~~~~~~sLk~La~~~L~~~IQ~g~~ 145 (161)
T cd06137 77 LWKFID-PDTILVGHSLQNDLDALRM---------I-HTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGGE 145 (161)
T ss_pred HHHHCC-CCCEEEECCHHHHHHHHCC---------C-CCCEEECEEECCHHCCCCCCCCCHHHHHHHHHHHCHHHCCCCC
T ss_conf 997458-9967985101310878627---------7-9835432033200115788888866999999982877528998
Q ss_pred CCCCHHHHHHHHHHHH
Q ss_conf 6640269999999999
Q gi|254780818|r 157 KHGALLDSHLLSDVYI 172 (245)
Q Consensus 157 ~H~Al~Da~~~a~v~~ 172 (245)
.|++..||+++.++|+
T Consensus 146 gHds~EDA~aam~L~l 161 (161)
T cd06137 146 GHDSLEDALAAREVVL 161 (161)
T ss_pred CCCCHHHHHHHHHHHC
T ss_conf 8491999999999859
No 50
>cd06149 ISG20 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 replication. It may carry out its function by degrading viral RNAs as part of the IFN-regulated antiviral r
Probab=99.72 E-value=3.4e-17 Score=127.41 Aligned_cols=149 Identities=19% Similarity=0.292 Sum_probs=108.9
Q ss_pred EEEECCCCCCCCCCCEEEEEEEEEEECCEECCC-EEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 999846788888888899999999999988031-3798985888228865724202101232248521002344777530
Q gi|254780818|r 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNR-TFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFN 88 (245)
Q Consensus 10 iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~-~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi~ 88 (245)
|++|+|..|..+.+. .-|++=|.++|. .|+ -+.+||+|. .+|.+..++++|||++++.++++|.++..++++++.
T Consensus 1 vAlDCEMv~t~~g~~-~~~LaRvsvVd~--~G~vl~D~~VkP~-~~V~dy~T~~SGIt~~~l~~a~~~~~~~~~l~~~l~ 76 (157)
T cd06149 1 VAIDCEMVGTGPGGR-ESELARCSIVNY--HGDVLYDKYIRPE-GPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKILK 76 (157)
T ss_pred CEEECEEEEECCCCC-EEEEEEEEEEEC--CCCEEEEEEECCC-CCCCCCEEECCCCCHHHHCCCCCHHHHHHHHHHHHC
T ss_conf 979365342748998-468999999927--8989867433889-877863656267888895799849999999999716
Q ss_pred CCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHC---CC-CCCCC-CCCCHHHHHHHH-CCCCC-CCCCCCCH
Q ss_conf 02320231023224311210000011222210000110000---00-01776-422237899971-87545-55666402
Q gi|254780818|r 89 EQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSI---AR-RKHPS-SRNDLNSLCKRY-GITIS-HRSKHGAL 161 (245)
Q Consensus 89 ~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~l---ar-~~~p~-~~~~L~~l~~~~-~i~~~-~r~~H~Al 161 (245)
|.++|||+..+|++.|+- ..+ ...++||-.+ .+ .-+|. .+.+|..||+.| |.+.. ....|+++
T Consensus 77 --~~IlVGH~L~nDL~aL~l-----~h~---~~~i~DT~~~~~~~~~~~~p~~~~~sLk~L~~~~L~~~IQ~~~~gHds~ 146 (157)
T cd06149 77 --GKVVVGHAIHNDFKALKY-----FHP---KHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSV 146 (157)
T ss_pred --CCEEEEECCHHHHHHHHC-----CCC---CCCEEECCCCEEHHHHCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHH
T ss_conf --988998260766988603-----389---8726777111001332489876687599999998485025999880809
Q ss_pred HHHHHHHHHHH
Q ss_conf 69999999999
Q gi|254780818|r 162 LDSHLLSDVYI 172 (245)
Q Consensus 162 ~Da~~~a~v~~ 172 (245)
.||.++.++|.
T Consensus 147 EDA~aa~~L~k 157 (157)
T cd06149 147 EDARATMELYK 157 (157)
T ss_pred HHHHHHHHHHC
T ss_conf 99999999859
No 51
>cd06135 Orn 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 E.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=99.70 E-value=1.3e-17 Score=130.11 Aligned_cols=147 Identities=20% Similarity=0.301 Sum_probs=104.2
Q ss_pred EEEECCCCCCCCCCCEEEEEEEEEEEC-CEECCCEEEEEECCCCC---CCCHHHEEEC---CCCCCCCCCCCCCCHHHHH
Q ss_conf 999846788888888899999999999-98803137989858882---2886572420---2101232248521002344
Q gi|254780818|r 10 IVFDIETTGLDSKNDRIIEIGAVELLD-YSKTNRTFQVFLCPNGR---KNSPEALKLH---GITDEFLKDKPSFSSIFSE 82 (245)
Q Consensus 10 iv~D~ETTGl~~~~d~Iieigav~i~~-~~~~~~~f~~~i~P~~~---~i~~~~~~ih---GIt~~~l~~~p~f~ev~~~ 82 (245)
|-+|+|||||||..|+|||||||..+. ...+.+.++..|+|+.. .+++-..+.| |++++++..+++.+++..+
T Consensus 2 vWiDlEmTGLd~~~d~IiEIA~ivTD~~L~~~~eg~~~vI~~~~~~L~~M~~w~~~~H~~sGL~~~v~~s~~t~~~ae~~ 81 (173)
T cd06135 2 VWIDLEMTGLDPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQAEAE 81 (173)
T ss_pred EEEECCCCCCCCCCCEEEEEEEEEECCCCCEECCCCEEEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHH
T ss_conf 59933036888888648999999988998770356318882887998776568775033244167887369999999999
Q ss_pred HHHHHHC----CCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCC-----CC
Q ss_conf 7775300----23202310232243112100000112222100001100000001776422237899971875-----45
Q gi|254780818|r 83 FWDFFNE----QNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGIT-----IS 153 (245)
Q Consensus 83 f~~fi~~----~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~-----~~ 153 (245)
+++|+.. ..+++.|+++.||.+||..++.+.. ..+ ..+.+|.-. +..||++..=+ ..
T Consensus 82 ~l~Fi~~~~~~~~~pLaGNSV~~Dr~FL~k~mP~l~-~~l-hYR~iDVSs------------ikel~~rw~p~~~~~~~~ 147 (173)
T cd06135 82 LLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPELE-EYL-HYRILDVSS------------IKELARRWYPEIYRKAPK 147 (173)
T ss_pred HHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCHHH-HHC-CCEEEEHHH------------HHHHHHHHCCHHHHCCCC
T ss_conf 999999976799853157648770999998580679-759-870466777------------999999869163400699
Q ss_pred CCCCCCCHHHHHHHHHH
Q ss_conf 55666402699999999
Q gi|254780818|r 154 HRSKHGALLDSHLLSDV 170 (245)
Q Consensus 154 ~r~~H~Al~Da~~~a~v 170 (245)
++..|+||+|-+-.-+-
T Consensus 148 K~~~HrAl~DI~eSI~E 164 (173)
T cd06135 148 KKGTHRALDDIRESIAE 164 (173)
T ss_pred CCCCCCHHHHHHHHHHH
T ss_conf 87774349899999999
No 52
>KOG0542 consensus
Probab=99.65 E-value=8.2e-17 Score=125.01 Aligned_cols=172 Identities=20% Similarity=0.358 Sum_probs=132.5
Q ss_pred EEEECCCCCCCCC----CCEEEEEEEEEEEC--CEECCCEEEEEECCC-CCCCCHHHEEECCCCCCCCCCCCCCCHHHHH
Q ss_conf 9998467888888----88899999999999--988031379898588-8228865724202101232248521002344
Q gi|254780818|r 10 IVFDIETTGLDSK----NDRIIEIGAVELLD--YSKTNRTFQVFLCPN-GRKNSPEALKLHGITDEFLKDKPSFSSIFSE 82 (245)
Q Consensus 10 iv~D~ETTGl~~~----~d~Iieigav~i~~--~~~~~~~f~~~i~P~-~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~ 82 (245)
+|+|+|+|--+-. -++|||+.||.+.+ ..++.++||+||+|. ....+...+.+|||..++|-.||+|.+|+.+
T Consensus 59 liiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~~f~~vl~~ 138 (280)
T KOG0542 59 LILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAPTFPQVLSE 138 (280)
T ss_pred EEEEEEEECCCCCCCCCCHHHEECCEEEEECCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHCCHHHHHCCCCCHHHHHHH
T ss_conf 99863003003588886123026344567344301367888865265348538888988628507651457867999999
Q ss_pred HHHHHHCCCC-------EEEEECCCCCC-CEEEECHHCCCCCCCC-CCHHCCCHHCCCCCCCC-CCCCHHHHHHHHCCCC
Q ss_conf 7775300232-------02310232243-1121000001122221-00001100000001776-4222378999718754
Q gi|254780818|r 83 FWDFFNEQNA-------EWIAHNAKFDV-GFINAELQRINKDPLD-PSRIIDTLSIARRKHPS-SRNDLNSLCKRYGITI 152 (245)
Q Consensus 83 f~~fi~~~~~-------~lVaHNa~FD~-~fL~~el~r~~~~~~~-~~~~iDTl~lar~~~p~-~~~~L~~l~~~~~i~~ 152 (245)
|..|+...+. -+| --.+-|+ .||..++++-++..+. .+.+||..+.++..+.. .+-++..+-.+||++.
T Consensus 139 f~~Wlr~~~~~~k~~~~Afv-tdg~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it~mLe~~gL~f 217 (280)
T KOG0542 139 FDSWLRKDSLGDKNGKFAFV-TDGDWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNITGMLEHYGLQF 217 (280)
T ss_pred HHHHHHHHHCCCCCCCEEEE-ECCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCC
T ss_conf 99999986312334766899-67542499999999777278884899878679999999956766567788999719765
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 5556664026999999999999730576666
Q gi|254780818|r 153 SHRSKHGALLDSHLLSDVYIKMMVGGSQINF 183 (245)
Q Consensus 153 ~~r~~H~Al~Da~~~a~v~~~ll~g~~q~~l 183 (245)
.+| +|+++.||.-+|.+-..|+..|-+..+
T Consensus 218 ~Gr-~HsGiDDa~Nia~I~~kM~~dg~~~~I 247 (280)
T KOG0542 218 EGR-AHSGIDDARNIARIAQKMIRDGAEFRI 247 (280)
T ss_pred CCC-CCCCCHHHHHHHHHHHHHHHCCCEEEE
T ss_conf 687-566724477899999999757958996
No 53
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.47 E-value=1.5e-13 Score=104.61 Aligned_cols=169 Identities=18% Similarity=0.288 Sum_probs=117.2
Q ss_pred EEEEECCCCCCCC-C--CCEEEEEEEEEEECCEE-CCCEEEEEECCCCCCC-CHHHEEECCCCCCCCCCCCCCCHHHHHH
Q ss_conf 8999846788888-8--88899999999999988-0313798985888228-8657242021012322485210023447
Q gi|254780818|r 9 KIVFDIETTGLDS-K--NDRIIEIGAVELLDYSK-TNRTFQVFLCPNGRKN-SPEALKLHGITDEFLKDKPSFSSIFSEF 83 (245)
Q Consensus 9 ~iv~D~ETTGl~~-~--~d~Iieigav~i~~~~~-~~~~f~~~i~P~~~~i-~~~~~~ihGIt~~~l~~~p~f~ev~~~f 83 (245)
|+|+|+|.|-..- + ..+|||+-.|.|..+.. +...||+||+|..+++ +.+.+++||||.++|.++|+|.+|+..|
T Consensus 58 y~VLDFEATCe~~~r~~~~EIIEFPvv~Vdart~~~~aEFh~YVRPv~nPvLS~FCTELTGItQs~VD~aptFP~Vl~~f 137 (570)
T PTZ00315 58 YVVLDFEATCERDRRLEDPEVIEFPMVLVDARTATPVAEFQRYVRPVVNPVLSRFCTELTGITQSVVDRADTFPVVFCAA 137 (570)
T ss_pred EEEEEECCCCCCCCCCCCCCEEEEEEEEEECCCCHHHHHHHHHCCCCCCCCHHHHHHHHHCCCHHHHCCCCCCHHHHHHH
T ss_conf 79973002001255678864256027998535340023445414776477278777773175888763788508999999
Q ss_pred HHHHHCCC--------CEEEEECCCCCCC-EEEECHHCCC-----CCCC-CCCHHCCCHHCCCCC-------CCC-CCCC
Q ss_conf 77530023--------2023102322431-1210000011-----2222-100001100000001-------776-4222
Q gi|254780818|r 84 WDFFNEQN--------AEWIAHNAKFDVG-FINAELQRIN-----KDPL-DPSRIIDTLSIARRK-------HPS-SRND 140 (245)
Q Consensus 84 ~~fi~~~~--------~~lVaHNa~FD~~-fL~~el~r~~-----~~~~-~~~~~iDTl~lar~~-------~p~-~~~~ 140 (245)
..|+...| +..+.--.+||+. ||-.-++.++ .... ...+|+..-...... .|. .+.+
T Consensus 138 ~~fL~engLgd~~p~~~f~~VTcGdwDLKtmlp~Qc~~~~~~g~~i~vP~~f~rW~NlKk~~~~~~~~~~~~~ps~~p~~ 217 (570)
T PTZ00315 138 LQFLAEAGLGEAPPMRSYLVVTCGDWDLKTMLPAQMRVSGQQGTTVNVPLSFRRWCNLKKYMSQLSGCGLGATPPLGISD 217 (570)
T ss_pred HHHHHHCCCCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf 99998748776776405999961760687775999888650476423768999998899999872266666676668755
Q ss_pred HHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCC
Q ss_conf 37899971875455566640269999999999997305
Q gi|254780818|r 141 LNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGG 178 (245)
Q Consensus 141 L~~l~~~~~i~~~~r~~H~Al~Da~~~a~v~~~ll~g~ 178 (245)
|.+.-..+|++...| +|+-..||+-.|.+..+|+..|
T Consensus 218 m~dML~~L~Lp~~GR-hHSGIDDcRNIA~IL~ELlRRG 254 (570)
T PTZ00315 218 LPDMLQMLGLPLKGR-HHSGIDDCRNIAAVLCELLRRG 254 (570)
T ss_pred HHHHHHHCCCCCCCC-CCCCCHHHHHHHHHHHHHHHCC
T ss_conf 799998669986787-5788513688999999999668
No 54
>KOG2249 consensus
Probab=99.45 E-value=3.9e-13 Score=102.07 Aligned_cols=153 Identities=17% Similarity=0.291 Sum_probs=112.3
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECC-CEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 5899984678888888889999999999998803-137989858882288657242021012322485210023447775
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTN-RTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDF 86 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~-~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~f 86 (245)
|.|.+|+|.-|.-|.+. .=.+|=|.|+|.. | -.|+.||+|. .+|...-+.+.||+++.+.+|++|+.+-.+++++
T Consensus 106 r~vAmDCEMVG~Gp~G~-~s~lARvSIVN~~--G~VvyDkyVkP~-~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~kl 181 (280)
T KOG2249 106 RVVAMDCEMVGVGPDGR-ESLLARVSIVNYH--GHVVYDKYVKPT-EPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLKL 181 (280)
T ss_pred EEEEEEEEEECCCCCCC-CEEEEEEEEEECC--CCEEEEEECCCC-CCCCCCEEEECCCCHHHHCCCCCHHHHHHHHHHH
T ss_conf 38997404751479976-0003478886146--867655503788-6633103322365877851575389999999999
Q ss_pred HHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCC--CCC-CCCCCCCHHHHHHH-HCCCCCCCCCCCCHH
Q ss_conf 30023202310232243112100000112222100001100000--001-77642223789997-187545556664026
Q gi|254780818|r 87 FNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIA--RRK-HPSSRNDLNSLCKR-YGITISHRSKHGALL 162 (245)
Q Consensus 87 i~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~la--r~~-~p~~~~~L~~l~~~-~~i~~~~r~~H~Al~ 162 (245)
+ +|.+||||-..=|+..|.. .-+ ...+-||-... ++. ..+.+.||..|.+. +|++.-.. .|+.-.
T Consensus 182 L--~gRIlVGHaLhnDl~~L~l-------~hp-~s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~G-eHsSvE 250 (280)
T KOG2249 182 L--KGRILVGHALHNDLQALKL-------EHP-RSMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVG-EHSSVE 250 (280)
T ss_pred H--HCCEEECCCCCCHHHHHHH-------HCC-HHHHCCCCCCCHHHHHHHCCCCCCHHHHHHHHHCHHHHCC-CCCCHH
T ss_conf 7--0877751220007999855-------374-3553143127548777521598319999999845254315-668588
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 9999999999997
Q gi|254780818|r 163 DSHLLSDVYIKMM 175 (245)
Q Consensus 163 Da~~~a~v~~~ll 175 (245)
||++|-++|..+-
T Consensus 251 DA~AtM~LY~~vk 263 (280)
T KOG2249 251 DARATMELYKRVK 263 (280)
T ss_pred HHHHHHHHHHHHH
T ss_conf 9999999999999
No 55
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=99.44 E-value=2.3e-13 Score=103.46 Aligned_cols=174 Identities=19% Similarity=0.219 Sum_probs=113.4
Q ss_pred CCCEEEEECCCCCCCCCCCEEEEEEEEEEE-CCEECCCEEEEEECCCC-CCCCHHHEEECCCCCCCCC-CCCCCCHHHHH
Q ss_conf 775899984678888888889999999999-99880313798985888-2288657242021012322-48521002344
Q gi|254780818|r 6 KMRKIVFDIETTGLDSKNDRIIEIGAVELL-DYSKTNRTFQVFLCPNG-RKNSPEALKLHGITDEFLK-DKPSFSSIFSE 82 (245)
Q Consensus 6 ~mr~iv~D~ETTGl~~~~d~Iieigav~i~-~~~~~~~~f~~~i~P~~-~~i~~~~~~ihGIt~~~l~-~~p~f~ev~~~ 82 (245)
.-.+.+.|.||.|.+|..||.-|+|+|+-+ +-.++|+--..|++|.. .--.|.|+-|||||+.... .+-.-.+-...
T Consensus 8 ~~tF~~yDYETfG~~Pa~DRPaQFAgIRTD~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~Gi~E~~F~~~ 87 (475)
T COG2925 8 QPTFLFYDYETFGVHPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAAFAAR 87 (475)
T ss_pred CCCEEEEECHHCCCCCCCCCCHHHHEEECCCCCCCCCCCEEEEECCCCCCCCCCCCEEEECCCHHHHHHCCCCHHHHHHH
T ss_conf 98679975033177856666135411210343432478727985475456899873666257878897648985899999
Q ss_pred HHHHHHCCCCEEEEEC-CCCCCCEEEECHHCCCCC-----CCCCCHHCCCHHCCCC---------CCC----C-CCCCHH
Q ss_conf 7775300232023102-322431121000001122-----2210000110000000---------177----6-422237
Q gi|254780818|r 83 FWDFFNEQNAEWIAHN-AKFDVGFINAELQRINKD-----PLDPSRIIDTLSIARR---------KHP----S-SRNDLN 142 (245)
Q Consensus 83 f~~fi~~~~~~lVaHN-a~FD~~fL~~el~r~~~~-----~~~~~~~iDTl~lar~---------~~p----~-~~~~L~ 142 (245)
+..-+..-+..++|+| +.||=-+.++-|.|.-.+ |-..+.--|-+.+-|. -|| | .|.+|+
T Consensus 88 I~~~ls~P~Tcv~GYNniRfDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n~dG~pSFkLE 167 (475)
T COG2925 88 IHAELTQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDDGLPSFKLE 167 (475)
T ss_pred HHHHHCCCCEEEECCCCCCCCHHHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHH
T ss_conf 99985799815623555333268898889872276666761389842579999999975285568788678897511068
Q ss_pred HHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 89997187545556664026999999999999730576666
Q gi|254780818|r 143 SLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGGSQINF 183 (245)
Q Consensus 143 ~l~~~~~i~~~~r~~H~Al~Da~~~a~v~~~ll~g~~q~~l 183 (245)
.|.+.=||. |.++|+|++|.++|-.+-. +..++|+.+
T Consensus 168 hLtkANgie--H~nAHdAmsDVyATIamAk--lvk~~QPrL 204 (475)
T COG2925 168 HLTKANGIE--HSNAHDAMSDVYATIAMAK--LVKTAQPRL 204 (475)
T ss_pred HHHHCCCCC--CCHHHHHHHHHHHHHHHHH--HHHHHCCHH
T ss_conf 776425611--0005678899999999999--987618479
No 56
>cd06145 REX1_like 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 E.coli RNase T.
Probab=99.42 E-value=5.5e-13 Score=101.13 Aligned_cols=145 Identities=18% Similarity=0.314 Sum_probs=105.1
Q ss_pred EEEECCCCCCCCCCCEEEEEEEEEEECCEECCCE-EEEEECCCCCCCCHHHEEECCCCCCCCCCCC-CCCHHHHHHHHHH
Q ss_conf 9998467888888888999999999999880313-7989858882288657242021012322485-2100234477753
Q gi|254780818|r 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRT-FQVFLCPNGRKNSPEALKLHGITDEFLKDKP-SFSSIFSEFWDFF 87 (245)
Q Consensus 10 iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~-f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p-~f~ev~~~f~~fi 87 (245)
+.+|+|.-|... +. |+|-|.++|. .|+. |.+||+|. .++....++++|||++++.+++ +|+++-.++.++|
T Consensus 1 ~AlDCEMv~t~~-g~---~LaRvsvVd~--~g~vl~D~~V~P~-~~V~DyrT~~SGIt~~~l~~a~~~~~~~~~~l~~li 73 (150)
T cd06145 1 FALDCEMCYTTD-GL---ELTRVTVVDE--NGKVVLDELVKPD-GEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLI 73 (150)
T ss_pred CCCCCEEEEECC-CC---EEEEEEEECC--CCCEEEEEEECCC-CCCEECCCCCCCCCHHHHHCCCCCHHHHHHHHHHHC
T ss_conf 956136775279-98---8999999938--9989877433499-772132010457898898546588999999999875
Q ss_pred HCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCC-CCCCCCCHHHHHHHH-CCCCCC-CCCCCCHHHH
Q ss_conf 0023202310232243112100000112222100001100000001-776422237899971-875455-5666402699
Q gi|254780818|r 88 NEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRK-HPSSRNDLNSLCKRY-GITISH-RSKHGALLDS 164 (245)
Q Consensus 88 ~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~-~p~~~~~L~~l~~~~-~i~~~~-r~~H~Al~Da 164 (245)
. +|.++|||....|+..|+ +. ..+++||-.+.+.. .+..+.+|..||+.| |.+... ...|++..||
T Consensus 74 ~-~~~IlVGH~L~nDL~aL~-------i~---H~~v~DTa~l~~~~~~~~~~~sLk~L~~~~L~~~IQ~~~~gHdsvEDA 142 (150)
T cd06145 74 S-PDTILVGHSLENDLKALK-------LI---HPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGGHDSVEDA 142 (150)
T ss_pred C-CCCEEEECCCCCCHHHHH-------CC---CCCEEEHHHHHHHCCCCCCCHHHHHHHHHHHCHHHCCCCCCCCCHHHH
T ss_conf 9-998899626434777761-------55---876157166211037999897899999998287743999881839999
Q ss_pred HHHHHHHH
Q ss_conf 99999999
Q gi|254780818|r 165 HLLSDVYI 172 (245)
Q Consensus 165 ~~~a~v~~ 172 (245)
.++-++|.
T Consensus 143 ~aam~L~k 150 (150)
T cd06145 143 RAALELVK 150 (150)
T ss_pred HHHHHHHC
T ss_conf 99999759
No 57
>cd06139 DNA_polA_I_Ecoli_like_exo The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E.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. 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=99.42 E-value=1.3e-12 Score=98.76 Aligned_cols=143 Identities=19% Similarity=0.333 Sum_probs=93.9
Q ss_pred CCCEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 77589998467888888888999999999999880313798985888228865724202101232248521002344777
Q gi|254780818|r 6 KMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWD 85 (245)
Q Consensus 6 ~mr~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~ 85 (245)
+-+.|+||||||||||..++|+-|+.- .. .++.| || |-. .-. ....-...+|+..+.+
T Consensus 4 ~~~~ia~DtETtgl~~~~~~ivGisls-~~----~~~~~--Yi-P~~-h~~-------------~~~~l~~~~v~~~lk~ 61 (193)
T cd06139 4 KAKVFAFDTETTSLDPMQAELVGISFA-VE----PGEAY--YI-PLG-HDY-------------GGEQLPREEVLAALKP 61 (193)
T ss_pred CCCEEEEECCCCCCCCCCCEEEEEEEE-EC----CCCEE--EE-EEC-CCC-------------CCCCCCHHHHHHHHHH
T ss_conf 598789978369998688849999998-07----99689--98-723-656-------------5446799999999999
Q ss_pred HHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHH-CCCCCC---------
Q ss_conf 5300232023102322431121000001122221000011000000017764-22237899971-875455---------
Q gi|254780818|r 86 FFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRY-GITISH--------- 154 (245)
Q Consensus 86 fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~-~i~~~~--------- 154 (245)
++...+...|+||+.||+.+| .+.|... ...+.||+..|...-|+. +++|+.||++| |.+...
T Consensus 62 ~led~~i~Kv~hn~k~D~~~L----~~~gi~~--~~~~~DTmiaa~ll~~~~~~~~L~~La~~~l~~~~~~~~~l~gkg~ 135 (193)
T cd06139 62 LLEDPSIKKVGQNLKFDLHVL----ANHGIEL--RGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGK 135 (193)
T ss_pred HHCCCCCCEEEECCHHHHHHH----HHCCCCC--CCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCHHHHHCCCC
T ss_conf 973999868875479789999----9839866--7830218999987279988889999999981887663899837785
Q ss_pred -----------CCCCCCHHHHHHHHHHHHHHHH
Q ss_conf -----------5666402699999999999973
Q gi|254780818|r 155 -----------RSKHGALLDSHLLSDVYIKMMV 176 (245)
Q Consensus 155 -----------r~~H~Al~Da~~~a~v~~~ll~ 176 (245)
...+-|..||.+|.++|..|..
T Consensus 136 ~~~~~~~~~~~~~~~YAa~Da~~t~~L~~~l~~ 168 (193)
T cd06139 136 KQITFDQVPLEKAAEYAAEDADITLRLYELLKP 168 (193)
T ss_pred CCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 537831332999999999999999999999999
No 58
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.36 E-value=1e-13 Score=105.71 Aligned_cols=167 Identities=21% Similarity=0.250 Sum_probs=124.7
Q ss_pred CCE-EEEECCCCC----CCCCCCEEEEEEEEEE--ECCEECCCEEEEEECCCCCC-CCHHHEEECCCCCCCCCCCCCCCH
Q ss_conf 758-999846788----8888888999999999--99988031379898588822-886572420210123224852100
Q gi|254780818|r 7 MRK-IVFDIETTG----LDSKNDRIIEIGAVEL--LDYSKTNRTFQVFLCPNGRK-NSPEALKLHGITDEFLKDKPSFSS 78 (245)
Q Consensus 7 mr~-iv~D~ETTG----l~~~~d~Iieigav~i--~~~~~~~~~f~~~i~P~~~~-i~~~~~~ihGIt~~~l~~~p~f~e 78 (245)
|+. +|+|+|.|- -.+..-.||||+|..+ ++..+ -++|++||+|..+| .....-.++|||...|-+||.|..
T Consensus 3 ~~~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~v-vd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~apifs~ 81 (210)
T COG5018 3 TNSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEV-VDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAPIFSM 81 (210)
T ss_pred CCEEEEEEEEEECCCCCCCCHHCEEEEEHHHHHHHHHHHH-HHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHH
T ss_conf 7548999756535677877033433442236888756889-999997427543732889998862034640365504888
Q ss_pred HHHHHHHHHHCCCCE----EEEECCCCCCCEEEECHHCCCCCC-CCCCHHCCCHHCCCCCCCCCC-CCHHHHHHHHCCCC
Q ss_conf 234477753002320----231023224311210000011222-210000110000000177642-22378999718754
Q gi|254780818|r 79 IFSEFWDFFNEQNAE----WIAHNAKFDVGFINAELQRINKDP-LDPSRIIDTLSIARRKHPSSR-NDLNSLCKRYGITI 152 (245)
Q Consensus 79 v~~~f~~fi~~~~~~----lVaHNa~FD~~fL~~el~r~~~~~-~~~~~~iDTl~lar~~~p~~~-~~L~~l~~~~~i~~ 152 (245)
|+++|.-|+... ++ -.|--.+.|++.|.++....++++ +...+.+|--.-++..+...+ .+|......||...
T Consensus 82 v~E~f~r~L~~h-~Pr~~~~wa~wG~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~pr~tgln~ale~~G~sf 160 (210)
T COG5018 82 VFEDFIRKLNEH-DPRKNSTWATWGNMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGDPRLTGLNKALEEYGDSF 160 (210)
T ss_pred HHHHHHHHHHHC-CCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHCCCC
T ss_conf 999999999854-9553775020260419999999986179985345751008999878735985213789999842456
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 555666402699999999999973
Q gi|254780818|r 153 SHRSKHGALLDSHLLSDVYIKMMV 176 (245)
Q Consensus 153 ~~r~~H~Al~Da~~~a~v~~~ll~ 176 (245)
.. +.|+||.||+-++++|..+..
T Consensus 161 ~G-~~HraldDArn~~rl~klv~~ 183 (210)
T COG5018 161 TG-THHRALDDARNAYRLFKLVEQ 183 (210)
T ss_pred CC-CHHHHHHHHHHHHHHHHHHCC
T ss_conf 77-301447778889999998712
No 59
>PRK05359 oligoribonuclease; Provisional
Probab=99.30 E-value=6.6e-12 Score=94.36 Aligned_cols=147 Identities=20% Similarity=0.240 Sum_probs=93.7
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEEC-CEECCCEEEEEECCCCC---CCCHHHEEEC---CCCCCCCCCCCCCCHHH
Q ss_conf 58999846788888888899999999999-98803137989858882---2886572420---21012322485210023
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLD-YSKTNRTFQVFLCPNGR---KNSPEALKLH---GITDEFLKDKPSFSSIF 80 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~-~~~~~~~f~~~i~P~~~---~i~~~~~~ih---GIt~~~l~~~p~f~ev~ 80 (245)
|.|=+|+|+|||||..|+||||||+.-+. ..++++.++..|.++.. .+++-..+-| |++.+-....-+..++-
T Consensus 4 ~lvWiDlEMTGLd~~~d~IlEiA~ivTD~~Ln~~~eg~~~vI~~~~e~L~~M~~w~~~~H~~sGL~~~v~~S~~s~~~AE 83 (181)
T PRK05359 4 NLIWIDLEMTGLDPERDRIIEIATIVTDADLNILAEGPVIAIHQSDEVLAAMDEWNTRTHTRSGLIDRVRASTVTEAEAE 83 (181)
T ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEECCCCCCCCCCCEEEEECCHHHHHHHHHHHHCCCCCCCCHHHHHCCCCCHHHHH
T ss_conf 65899761348987877689999999988776702376178858989997521787505743320667862898899999
Q ss_pred HHHHHHHHC----CCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCH---HCCCCCCCCCCCCHHHHHHHHCCCCC
Q ss_conf 447775300----23202310232243112100000112222100001100---00000177642223789997187545
Q gi|254780818|r 81 SEFWDFFNE----QNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTL---SIARRKHPSSRNDLNSLCKRYGITIS 153 (245)
Q Consensus 81 ~~f~~fi~~----~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl---~lar~~~p~~~~~L~~l~~~~~i~~~ 153 (245)
.++++|+.. +.++|.|-.+.||.+||...+.++.. .+ ..+.+|.- .++|+-+|.. +.- ..
T Consensus 84 ~~~l~fi~~~~~~~~~pLaGNSV~~DR~FL~k~MP~l~~-~l-hYR~iDVSSikEl~~rW~p~~----------~~~-p~ 150 (181)
T PRK05359 84 AQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEA-YF-HYRNLDVSTLKELARRWKPEI----------LNG-FK 150 (181)
T ss_pred HHHHHHHHHHCCCCCCCCCCCCEEHHHHHHHHHCHHHHH-HC-CEEEEECCCHHHHHHHHCHHH----------CCC-CC
T ss_conf 999999999679999751687200328899984806797-58-856785125999998848322----------016-99
Q ss_pred CCCCCCCHHHHHHH
Q ss_conf 55666402699999
Q gi|254780818|r 154 HRSKHGALLDSHLL 167 (245)
Q Consensus 154 ~r~~H~Al~Da~~~ 167 (245)
....|+||+|.+--
T Consensus 151 K~~~HrAl~DI~eS 164 (181)
T PRK05359 151 KQGTHRALADIRES 164 (181)
T ss_pred CCCCCCHHHHHHHH
T ss_conf 88874418899999
No 60
>cd06143 PAN2_exo 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=99.29 E-value=9.8e-12 Score=93.29 Aligned_cols=150 Identities=16% Similarity=0.240 Sum_probs=108.6
Q ss_pred EEEECCCCCCCCCCC-------EE------EEEEEEEEECC--EECCC-EEEEEECCCCCCCCHHHEEECCCCCCCCCCC
Q ss_conf 999846788888888-------89------99999999999--88031-3798985888228865724202101232248
Q gi|254780818|r 10 IVFDIETTGLDSKND-------RI------IEIGAVELLDY--SKTNR-TFQVFLCPNGRKNSPEALKLHGITDEFLKDK 73 (245)
Q Consensus 10 iv~D~ETTGl~~~~d-------~I------ieigav~i~~~--~~~~~-~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~ 73 (245)
|.+|+|--|+.|++- +- ..+|=|.++|. -.-|+ -|..||+|. .+|...-+++.|||+++|..+
T Consensus 1 valDcE~Vg~g~~~~~~~~~g~~~~~~~~~~aLARvSiV~~~g~~~G~vl~D~yVkP~-~~VtDYrT~~SGIt~~~L~~~ 79 (174)
T cd06143 1 VAIDAEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVPFIDDYISTT-EPVVDYLTRFSGIKPGDLDPK 79 (174)
T ss_pred CCCCCEEEEECCCCCCCCCCCCEEECCCCCCCCEEEEEECCCCCCCCCEEEEEEECCC-CCCCCCCCCCCCCCHHHCCCC
T ss_conf 9152214664464120257884411035676430278984458716888855517899-974625871635688895855
Q ss_pred C------CCCHHHHHHHHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHH
Q ss_conf 5------210023447775300232023102322431121000001122221000011000000017764-222378999
Q gi|254780818|r 74 P------SFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCK 146 (245)
Q Consensus 74 p------~f~ev~~~f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~ 146 (245)
+ ++.++..++..++. ++.+||||-...|+..|+ +.. +...++||..+.+ .|+. +.+|..||+
T Consensus 80 ~s~~~~~~~~~~~~~l~~li~-~~~ILVGHsL~nDL~aL~-------l~h-P~~~i~DTs~l~~--~~~~r~~sLk~La~ 148 (174)
T cd06143 80 TSSKNLTTLKSAYLKLRLLVD-LGCIFVGHGLAKDFRVIN-------IQV-PKEQVIDTVELFH--LPGQRKLSLRFLAW 148 (174)
T ss_pred CCCCCCCCHHHHHHHHHHHCC-CCCEEECCCCHHHHHHHC-------CCC-CCCCEEECHHHCC--CCCCCCCCHHHHHH
T ss_conf 564443409999999998547-996897896366798850-------669-9866577788526--89988708999999
Q ss_pred HH-CCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 71-875455566640269999999999
Q gi|254780818|r 147 RY-GITISHRSKHGALLDSHLLSDVYI 172 (245)
Q Consensus 147 ~~-~i~~~~r~~H~Al~Da~~~a~v~~ 172 (245)
.| |.+... ..|+...||+++-++|.
T Consensus 149 ~~Lg~~IQ~-g~HdSvEDArAam~LYr 174 (174)
T cd06143 149 YLLGEKIQS-ETHDSIEDARTALKLYR 174 (174)
T ss_pred HHCCCCCCC-CCCCCHHHHHHHHHHHC
T ss_conf 980810469-89593999999999629
No 61
>cd06128 DNA_polA_exo The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli pol I, the Thermus aquaticus (Taq) pol I, and Bacillus stearothermophilus (BF) pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF pol I and Taq pol I resemble the fold of the 3'-5' exonuclease domain of KF
Probab=99.19 E-value=1e-10 Score=86.90 Aligned_cols=115 Identities=17% Similarity=0.243 Sum_probs=78.8
Q ss_pred EEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 89998467888888888999999999999880313798985888228865724202101232248521002344777530
Q gi|254780818|r 9 KIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFN 88 (245)
Q Consensus 9 ~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi~ 88 (245)
.+.|||||||+||...+||-|+.. +. .++.| ||-+.. .... ..+.-....|++.|..++.
T Consensus 3 ~~a~DtETt~ld~~~a~iVGis~s-~~----~~~a~--YiP~~h-~~~~------------~~~~l~~~~vl~~L~p~le 62 (166)
T cd06128 3 VFAFDTETDSLDNISANLVGLSFA-IE----PGVAA--YIPVAH-DYLD------------APDQISRERALELLKPLLE 62 (166)
T ss_pred EEEEECCCCCCCCCCCEEEEEEEE-CC----CCEEE--EEECCC-CCCC------------CHHHHHHHHHHHHHHHHHC
T ss_conf 899978879989043549999998-00----89699--995267-7667------------5257789999999999973
Q ss_pred CCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHHC
Q ss_conf 0232023102322431121000001122221000011000000017764-222378999718
Q gi|254780818|r 89 EQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRYG 149 (245)
Q Consensus 89 ~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~~ 149 (245)
.....-|+||+.||+..| +++|... .....|||-.+...-|++ +++|++|+..|-
T Consensus 63 d~~i~KighNlK~D~~vL----~~~Gi~l--~g~~fDTMlaaylldp~~~~h~Ld~La~~~L 118 (166)
T cd06128 63 DEKALKVGQNLKYDRGIL----ANYGIEL--RGIAFDTMLESYILNSVAGRHDMDSLAERWL 118 (166)
T ss_pred CCCCCEEEECHHHHHHHH----HHCCCCC--CCCCCCHHHHHHHCCCCCCCCCHHHHHHHHC
T ss_conf 999764531156679999----6199668--9998457679876289998899699999983
No 62
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=99.06 E-value=1.4e-09 Score=79.79 Aligned_cols=133 Identities=22% Similarity=0.354 Sum_probs=85.0
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 58999846788888888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
+.|.|||||||+++...+|+-|+.. .. ++.+ |+.... .. ..+.+.+..++
T Consensus 1 ~~ia~D~Et~~l~~~~~~i~~iql~-~~-----~~~~--yi~~~~-~~---------------------~~~~~~l~~~l 50 (155)
T cd00007 1 KEVAFDTETTGLNYHRGKLVGIQIA-TA-----GEAA--YIPDEL-EL---------------------EEDLEALKELL 50 (155)
T ss_pred CEEEEECCCCCCCCCCCCEEEEEEE-EC-----CCEE--EEEECC-CC---------------------HHHHHHHHHHH
T ss_conf 9899989879997788809999999-89-----9359--998147-55---------------------24699999998
Q ss_pred HCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHHC-CCCCC-----------
Q ss_conf 00232023102322431121000001122221000011000000017764-222378999718-75455-----------
Q gi|254780818|r 88 NEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRYG-ITISH----------- 154 (245)
Q Consensus 88 ~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~~-i~~~~----------- 154 (245)
...+-+.|+||+.||+.+|.+ .|... ...+.||+..++..-|++ +++|++++++|. ++...
T Consensus 51 ~~~~i~Kv~hn~k~D~~~L~~----~~~~~--~~~~~Dt~iaa~ll~~~~~~~~L~~l~~~~l~~~~~k~~~~~~~~~~~ 124 (155)
T cd00007 51 EDEDITKVGHDAKFDLVVLAR----DGIEL--PGNIFDTMLAAYLLNPGEGSHSLDDLAKEYLGIELDKDEQIYGKGAKT 124 (155)
T ss_pred HCCCCCEEEECCCHHHHHHHH----CCCCC--CCCEEHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCHHHHHCCCCCCC
T ss_conf 299973898734000999986----28601--350114999999847785523699999998398767488861776544
Q ss_pred -------CCCCCCHHHHHHHHHHHHHHHH
Q ss_conf -------5666402699999999999973
Q gi|254780818|r 155 -------RSKHGALLDSHLLSDVYIKMMV 176 (245)
Q Consensus 155 -------r~~H~Al~Da~~~a~v~~~ll~ 176 (245)
....-|..||.+|.++|..|+.
T Consensus 125 ~~~~l~~~~~~YAa~D~~~~~~l~~~l~~ 153 (155)
T cd00007 125 FARPLSEELLEYAAEDADALLRLYEKLLE 153 (155)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 44799899999999999999999999996
No 63
>cd06142 RNaseD_exo 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=98.99 E-value=1.6e-09 Score=79.41 Aligned_cols=130 Identities=20% Similarity=0.249 Sum_probs=85.3
Q ss_pred CEEEEECCCCCCCCCCCE--EEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 589998467888888888--999999999999880313798985888228865724202101232248521002344777
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDR--IIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWD 85 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~--Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~ 85 (245)
..|.|||||||+++..++ +|||+. + +..| ++.|. .++ .++.+.+
T Consensus 13 ~~i~~DtE~~~~~~~~~~l~LiQia~-----~---~~~y--lid~~--~~~----------------------~~~~L~~ 58 (178)
T cd06142 13 GVIAVDTEFMRLRTYYPRLCLIQIST-----G---GQAY--LIDPL--AIG----------------------DLSPLKE 58 (178)
T ss_pred CEEEEECCCCCCCCCCCEEEEEEEEE-----C---CCEE--EEECC--CCC----------------------CHHHHHH
T ss_conf 94899898678855887289999986-----8---9069--99531--234----------------------4699999
Q ss_pred HHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHH-HCCCCCC----------
Q ss_conf 53002320231023224311210000011222210000110000000177642223789997-1875455----------
Q gi|254780818|r 86 FFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKR-YGITISH---------- 154 (245)
Q Consensus 86 fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~-~~i~~~~---------- 154 (245)
++...+.+-|+||+.||+.+|.+.+ +.. ...++||+..++..-++.+++|++||.+ +|+.++.
T Consensus 59 lL~d~~i~KVgh~~~~Dl~~L~~~~---~~~---~~~v~Dt~ia~~~l~~~~~~~L~~L~~~~lg~~l~K~~q~s~W~~r 132 (178)
T cd06142 59 LLADPNIVKVFHAAREDLELLKRDF---GIL---PVNLFDTQIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWLKR 132 (178)
T ss_pred HHCCCCCEEEEEEHHHHHHHHHHHH---CCC---CCCEEEHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf 9759994399962799999999973---967---6545308999998288673789999999929877777364664336
Q ss_pred ----CCCCCCHHHHHHHHHHHHHHHHC
Q ss_conf ----56664026999999999999730
Q gi|254780818|r 155 ----RSKHGALLDSHLLSDVYIKMMVG 177 (245)
Q Consensus 155 ----r~~H~Al~Da~~~a~v~~~ll~g 177 (245)
.+-+-|..||..|-++|..|...
T Consensus 133 PLs~~qi~YAa~Da~~l~~l~~~l~~~ 159 (178)
T cd06142 133 PLTDEQLEYAANDVRYLLPLYEKLKEE 159 (178)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 782899999999799999999999999
No 64
>pfam01612 3_5_exonuc 3'-5' exonuclease. This domain is responsible for the 3'-5' exonuclease proofreading activity of E. 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). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homologue of the WRN protein. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.
Probab=98.97 E-value=1.1e-09 Score=80.53 Aligned_cols=133 Identities=19% Similarity=0.270 Sum_probs=84.2
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 58999846788888888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
..|.|||||||+++.+.++. +..+.+.. ++.+. ++.+- .. .++.+.+.+++
T Consensus 21 ~~ia~DtEt~~~~~~~~~~~-~~llq~~~----~~~~y-li~~~--~~---------------------~~~~~~L~~ll 71 (172)
T pfam01612 21 KVVAVDTETTSLDTYSYTLV-GCLIQIST----GEGAY-IIDPL--AL---------------------GDDLEGLKRLL 71 (172)
T ss_pred CCEEEEEECCCCCCCCCCCC-EEEEEEEC----CCCCE-EEECC--CC---------------------HHHHHHHHHHH
T ss_conf 90899806289886761343-36999967----98607-76434--75---------------------66799999997
Q ss_pred HCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHH-HCCCCCC------------
Q ss_conf 002320231023224311210000011222210000110000000177642223789997-1875455------------
Q gi|254780818|r 88 NEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKR-YGITISH------------ 154 (245)
Q Consensus 88 ~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~-~~i~~~~------------ 154 (245)
...+-..|+||+.||+.+|.+. .|.. ...++||+..++..-|+.+++|+.||++ +|++.+.
T Consensus 72 ~~~~i~Kvghn~k~D~~~L~~~---~~~~---~~~~~Dt~~a~~~l~~~~~~gL~~L~~~~lg~~~~K~~~~s~w~~rpL 145 (172)
T pfam01612 72 EDPNITKVGHNAKFDLEVLARD---FGIK---LENLFDTMLAAYLLGYPRSHSLDDLAEKYLGVELDKSEQCADWRARPL 145 (172)
T ss_pred CCCCCCEEEEEHHHHHHHHHHH---CCCC---CCCCHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCHHHEECCCCCCCC
T ss_conf 5999879997589999999885---4766---687327899998819964356999999980987874415667887898
Q ss_pred --CCCCCCHHHHHHHHHHHHHHH
Q ss_conf --566640269999999999997
Q gi|254780818|r 155 --RSKHGALLDSHLLSDVYIKMM 175 (245)
Q Consensus 155 --r~~H~Al~Da~~~a~v~~~ll 175 (245)
.+-+-|..||.+|-++|..|.
T Consensus 146 ~~~qi~YAa~Da~~~~~l~~~l~ 168 (172)
T pfam01612 146 SEEQLRYAAEDADYLLRLYDKLR 168 (172)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 29999999999999999999999
No 65
>KOG2248 consensus
Probab=98.89 E-value=1.1e-08 Score=74.24 Aligned_cols=151 Identities=19% Similarity=0.268 Sum_probs=108.7
Q ss_pred EEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCC-CCCHHHHHHHHHH
Q ss_conf 899984678888888889999999999998803137989858882288657242021012322485-2100234477753
Q gi|254780818|r 9 KIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKP-SFSSIFSEFWDFF 87 (245)
Q Consensus 9 ~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p-~f~ev~~~f~~fi 87 (245)
-+++|+|.-...-. -.+..+++|.+.... .|..+|+|. .+|-.......|||.+++++++ +..+|-.++..|+
T Consensus 218 i~AlDCEm~~te~g-~el~RVt~VD~~~~v----i~D~fVkP~-~~VvDy~T~~SGIT~~~~e~~t~tl~dvq~~l~~~~ 291 (380)
T KOG2248 218 IFALDCEMVVTENG-LELTRVTAVDRDGKV----ILDTFVKPN-KPVVDYNTRYSGITEEDLENSTITLEDVQKELLELI 291 (380)
T ss_pred EEEEEEEEEEECCC-EEEEEEEEEECCCCE----EEEEEECCC-CCCCCCCCCCCCCCHHHHHCCCCCHHHHHHHHHHHC
T ss_conf 47887565430565-036786465046847----867863478-861301256554209987258627999999999646
Q ss_pred HCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCC--CCCCHHHHHHHH-CCCCC-CCCCCCCHHH
Q ss_conf 0023202310232243112100000112222100001100000001776--422237899971-87545-5566640269
Q gi|254780818|r 88 NEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPS--SRNDLNSLCKRY-GITIS-HRSKHGALLD 163 (245)
Q Consensus 88 ~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~--~~~~L~~l~~~~-~i~~~-~r~~H~Al~D 163 (245)
. .+.++|||-..=|+.-|+ . ....++||-.+..-.... .+.+|..||+-| |.... .-.-|++-.|
T Consensus 292 ~-~~TILVGHSLenDL~aLK---------l-~H~~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~~~~HdS~eD 360 (380)
T KOG2248 292 S-KNTILVGHSLENDLKALK---------L-DHPSVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEGVGGHDSVED 360 (380)
T ss_pred C-CCCEEEEECHHHHHHHHH---------H-HCCCEEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHH
T ss_conf 8-671799510030788976---------4-2774220058886488985425999999999988998616778760888
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 9999999999973
Q gi|254780818|r 164 SHLLSDVYIKMMV 176 (245)
Q Consensus 164 a~~~a~v~~~ll~ 176 (245)
|.++-++....+.
T Consensus 361 A~acm~Lv~~k~~ 373 (380)
T KOG2248 361 ALACMKLVKLKIK 373 (380)
T ss_pred HHHHHHHHHHHHH
T ss_conf 9999999999985
No 66
>PRK07456 consensus
Probab=98.86 E-value=6.8e-09 Score=75.53 Aligned_cols=141 Identities=19% Similarity=0.295 Sum_probs=90.5
Q ss_pred EEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 89998467888888888999999999999880313798985888228865724202101232248521002344777530
Q gi|254780818|r 9 KIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFN 88 (245)
Q Consensus 9 ~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi~ 88 (245)
.|++|||||||||...+++-||.. .. ...++.| || |-+.. -..+. -...+++..+..|+.
T Consensus 384 ~vA~DtETtsLdp~~A~lVGis~s-~~--~~~~~a~--YI-Pl~h~----------~~~~~----l~~~~vl~~LkpiLe 443 (975)
T PRK07456 384 PVAWDTETTSLNPRDAELVGIGCC-WG--EELDDLA--YI-PLGHQ----------QAGEQ----LPLETVLEALRPWLE 443 (975)
T ss_pred EEEEECCCCCCCHHHCCEEEEEEE-CC--CCCCCEE--EE-ECCCC----------CCHHH----CCHHHHHHHHHHHHC
T ss_conf 589980468877423210266641-15--5787269--97-73455----------61310----579999999999862
Q ss_pred CCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHHH-CCCCC--------CC----
Q ss_conf 023202310232243112100000112222100001100000001776422237899971-87545--------55----
Q gi|254780818|r 89 EQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRY-GITIS--------HR---- 155 (245)
Q Consensus 89 ~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~-~i~~~--------~r---- 155 (245)
......|+||+.||+.+| .++|... .....||+..+-.+-|+.+++|++|+.+| |+... .+
T Consensus 444 d~~i~KighNlKyD~~vL----~~~GI~l--~g~~fDTmLAsYLLnP~~~h~Ld~La~~yL~~~~i~~edl~gkgk~~~~ 517 (975)
T PRK07456 444 SPEHPKALQNAKFDRLIL----LRHGIAL--KGVVFDTLLADYLLNPEAKHNLDDLAQRELGFTPTSYKDLVGKGQTFAD 517 (975)
T ss_pred CCCCCCHHHHHHHHHHHH----HHCCCCC--CCCCCCHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCHHHHCCCCCCCCC
T ss_conf 887531021114679999----9769510--6755139999987687655898999999718887749986288876020
Q ss_pred -----CCCCCHHHHHHHHHHHHHHH
Q ss_conf -----66640269999999999997
Q gi|254780818|r 156 -----SKHGALLDSHLLSDVYIKMM 175 (245)
Q Consensus 156 -----~~H~Al~Da~~~a~v~~~ll 175 (245)
..+-|-.||.++.++|..|.
T Consensus 518 v~~~~~~~ya~~dA~~~~~L~~~l~ 542 (975)
T PRK07456 518 VDIATASQYCGMDVYLTYRLAPILR 542 (975)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 8978999999999999999999999
No 67
>PRK06887 consensus
Probab=98.78 E-value=1.8e-08 Score=72.97 Aligned_cols=154 Identities=17% Similarity=0.226 Sum_probs=93.8
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCC--------CCCHHHEEECCCCCCC-CCCCCCCCH
Q ss_conf 5899984678888888889999999999998803137989858882--------2886572420210123-224852100
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGR--------KNSPEALKLHGITDEF-LKDKPSFSS 78 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~--------~i~~~~~~ihGIt~~~-l~~~p~f~e 78 (245)
..++|||||||++|...+++-|+.. +.++ +.| || |-.. ..+..+....+.+... ..+.-...+
T Consensus 357 ~~va~DtEt~~ld~~~a~lVGis~s-~~~g----~a~--Yi-Pl~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~~~~ 428 (954)
T PRK06887 357 KLIAVDTETDSLDYMSANLVGISFA-LENG----EAC--YI-PLAHKQQVAEQPQSDLFAEEAETQTDYLLAPKQLNKST 428 (954)
T ss_pred CEEEEEEECCCCCCCCCCEEEEEEE-ECCC----CEE--EE-ECCCCCCCCCCCCHHHHHHCCCCHHHHHCCHHHCCHHH
T ss_conf 9279996359987132665789998-3589----789--98-64442100013200233200100122210232127999
Q ss_pred HHHHHHHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHHH-CCCCC----
Q ss_conf 2344777530023202310232243112100000112222100001100000001776422237899971-87545----
Q gi|254780818|r 79 IFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRY-GITIS---- 153 (245)
Q Consensus 79 v~~~f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~-~i~~~---- 153 (245)
++..+..++...+...|+||+.||+.+| .++|... .....||+..+-.+-|+.+++|+.|+.+| |....
T Consensus 429 vl~~Lkplled~~i~KIghNlK~dl~vL----~~~Gi~l--~g~~fDTmLAaYLLdp~~r~~Ld~LA~~yL~~~~i~~ed 502 (954)
T PRK06887 429 CLAALKPLLENPDIHKIGQNIKYDLTIF----ANHGIEL--QGVAFDTMLESYTLNSTGRHNMDDLAERYLGHETIAFES 502 (954)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHHHH----HHCCCCC--CCCCCCHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCHHH
T ss_conf 9999899852975022211478899999----9779624--776516989987518755578899999963886533464
Q ss_pred --C--------------CCCCCCHHHHHHHHHHHHHHH
Q ss_conf --5--------------566640269999999999997
Q gi|254780818|r 154 --H--------------RSKHGALLDSHLLSDVYIKMM 175 (245)
Q Consensus 154 --~--------------r~~H~Al~Da~~~a~v~~~ll 175 (245)
. ....-|..||.+|.++|..|.
T Consensus 503 l~gkGk~ql~f~~v~l~~~~~YAaedA~itl~L~~~L~ 540 (954)
T PRK06887 503 IAGKGKNQLTFDQIPLEQATEYAAEDADVTMKLHQVLW 540 (954)
T ss_pred HCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 22544333784434467999999999999999999999
No 68
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=98.75 E-value=3.3e-08 Score=71.25 Aligned_cols=132 Identities=24% Similarity=0.357 Sum_probs=82.3
Q ss_pred CCEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEE-CCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 758999846788888888899999999999988031379898-5888228865724202101232248521002344777
Q gi|254780818|r 7 MRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFL-CPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWD 85 (245)
Q Consensus 7 mr~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i-~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~ 85 (245)
...|.|||||||+++..++++-|..- . . +. ..|+ .+. ... +..+.+.+
T Consensus 21 ~~~i~~DtE~~~~~~~~~~l~~iql~-~-~----~~--~~yi~~~~--~~~---------------------~~~~~l~~ 69 (172)
T smart00474 21 GGEVALDTETTGLNSYSGKLVLIQIS-V-T----GE--GAFIIDPL--ALG---------------------DDLEILKD 69 (172)
T ss_pred CCEEEEECCCCCCCCCCCEEEEEEEE-E-C----CC--EEEEEECC--CCH---------------------HHHHHHHH
T ss_conf 99599988306885378758999999-6-8----98--48997012--242---------------------17999999
Q ss_pred HHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHH-CCCCCC---------
Q ss_conf 5300232023102322431121000001122221000011000000017764-22237899971-875455---------
Q gi|254780818|r 86 FFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRY-GITISH--------- 154 (245)
Q Consensus 86 fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~-~i~~~~--------- 154 (245)
++...+.+.|+||+.||+.+|. +.|... ..+.||+..+....|+. +++|+.++.+| |++++.
T Consensus 70 ll~~~~i~kv~hn~k~D~~~L~----~~gi~l---~~v~Dt~ia~~l~~~~~~~~~L~~l~~~~~~~~l~k~~~~~~w~~ 142 (172)
T smart00474 70 LLEDETITKVGHNAKFDLHVLA----RFGIEL---ENIFDTMLAAYLLLGGPSKHGLATLLKEYLGVELDKEEQKSDWGA 142 (172)
T ss_pred HHCCCCCCEEEECHHHHHHHHH----HCCCCC---CCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCEECCCCCCCCCCCC
T ss_conf 9809998599974599999999----779856---752467998775057986489999999974923155556466678
Q ss_pred -----CCCCCCHHHHHHHHHHHHHHHH
Q ss_conf -----5666402699999999999973
Q gi|254780818|r 155 -----RSKHGALLDSHLLSDVYIKMMV 176 (245)
Q Consensus 155 -----r~~H~Al~Da~~~a~v~~~ll~ 176 (245)
.+..-|..||.+|.++|..|..
T Consensus 143 rpl~~~~~~YAa~Da~~~~~l~~~l~~ 169 (172)
T smart00474 143 RPLSEEQLQYAAEDADALLRLYEKLEK 169 (172)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999099999999999999999999999
No 69
>PRK07556 consensus
Probab=98.75 E-value=1.5e-08 Score=73.44 Aligned_cols=149 Identities=17% Similarity=0.273 Sum_probs=91.4
Q ss_pred CCEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCC-CCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 7589998467888888888999999999999880313798985888-228865724202101232248521002344777
Q gi|254780818|r 7 MRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNG-RKNSPEALKLHGITDEFLKDKPSFSSIFSEFWD 85 (245)
Q Consensus 7 mr~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~-~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~ 85 (245)
...++||+||||+||....|+-|+.. +.. ++.| || |-. +...... .......++-...+++..+..
T Consensus 387 ~~~~a~DtETtsld~~~a~lVGisls-~~~----~~a~--YI-Pl~h~~~~~~~-----~~~~~~~~ql~~~~vL~~Lkp 453 (977)
T PRK07556 387 TGIVAFDTETTSLDPMQAELVGFSLA-LAP----GRAC--YI-PLGHKSGDGDL-----FGGGLAEGQIPLRDALAALKP 453 (977)
T ss_pred CCEEEEEEECCCCCHHHCCEEEEEEE-ECC----CCEE--EE-ECCCCCCCCCH-----HCCCCCHHHCCHHHHHHHHHH
T ss_conf 79589997318878301553579998-068----9789--99-61444564201-----102222323059999999898
Q ss_pred HHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHH-CCCC---C-----CC
Q ss_conf 5300232023102322431121000001122221000011000000017764-22237899971-8754---5-----55
Q gi|254780818|r 86 FFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRY-GITI---S-----HR 155 (245)
Q Consensus 86 fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~-~i~~---~-----~r 155 (245)
++......-|+||+.||+.+| +++|... .++.||+..|-.+-|+. +++|+.|+.+| |... . .+
T Consensus 454 lLed~~i~KighnlK~d~~vL----~~~gi~l---~~i~DtmLaaYLLdp~~~~~~Ld~La~~yL~~~~~~~~dl~g~gk 526 (977)
T PRK07556 454 VLEDPSVLKIGQNMKYDALVL----ARHGITV---APFDDTMLISYALDAGRGGHGMDALSERWLGHTPIAYKDLTGSGK 526 (977)
T ss_pred HHCCCCHHHHHHHHHHHHHHH----HHCCCCC---CCCCCHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCHHCCCCCC
T ss_conf 853873114441256889999----9769602---685318888888348866478799999964887621000034550
Q ss_pred ------------CCCCCHHHHHHHHHHHHHHH
Q ss_conf ------------66640269999999999997
Q gi|254780818|r 156 ------------SKHGALLDSHLLSDVYIKMM 175 (245)
Q Consensus 156 ------------~~H~Al~Da~~~a~v~~~ll 175 (245)
...-|..||.+|.++|..|.
T Consensus 527 ~~~~f~~v~~~~~~~YaaedA~~t~~L~~~L~ 558 (977)
T PRK07556 527 SAITFDQVDIDRATAYAAEDADVTLRLWQVLK 558 (977)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 10476552068999999999999999999999
No 70
>KOG4793 consensus
Probab=98.73 E-value=3.2e-09 Score=77.55 Aligned_cols=173 Identities=21% Similarity=0.261 Sum_probs=108.6
Q ss_pred CCCCCCCCE-EEEECCCCCCCCCCCEEEEEEEE-----EEECC-EECC----------C---EEEEEECCCCCCCCHHHE
Q ss_conf 986677758-99984678888888889999999-----99999-8803----------1---379898588822886572
Q gi|254780818|r 1 MIRKNKMRK-IVFDIETTGLDSKNDRIIEIGAV-----ELLDY-SKTN----------R---TFQVFLCPNGRKNSPEAL 60 (245)
Q Consensus 1 ~~~~~~mr~-iv~D~ETTGl~~~~d~Iieigav-----~i~~~-~~~~----------~---~f~~~i~P~~~~i~~~~~ 60 (245)
|.+.-+||. +++|.|+|||..-.-.|.|+-.. .+.+. +.+. + ....+..| ++...+.+.
T Consensus 6 ~se~pr~~tf~fldleat~lp~~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p-~~v~~p~ae 84 (318)
T KOG4793 6 ISEVPRLRTFSFLDLEATGLPGWIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGP-VPVTRPIAE 84 (318)
T ss_pred CCCCCCEEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHCCCC-CCCCCHHHH
T ss_conf 5767750378754100256875566403566888898762387652125887547862022120110578-677671555
Q ss_pred EECCCCCCCCC--CCCCCC-HHHHHHHHHHHCCCCE--EEEECC-CCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCC-
Q ss_conf 42021012322--485210-0234477753002320--231023-2243112100000112222100001100000001-
Q gi|254780818|r 61 KLHGITDEFLK--DKPSFS-SIFSEFWDFFNEQNAE--WIAHNA-KFDVGFINAELQRINKDPLDPSRIIDTLSIARRK- 133 (245)
Q Consensus 61 ~ihGIt~~~l~--~~p~f~-ev~~~f~~fi~~~~~~--lVaHNa-~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~- 133 (245)
+|+|++..++. ..--|. ++..-+..|+...-.+ +||||. .||+..|.++|++.|...+...-.+|++...+..
T Consensus 85 eitgls~~~~~l~rr~~~D~dla~LL~afls~lp~p~CLVaHng~~~dfpil~qela~lg~~lpq~lvcvdslpa~~ald 164 (318)
T KOG4793 85 EITGLSQPFLALQRRLAFDKDLAKLLTAFLSRLPTPGCLVAHNGNEYDFPILAQELAGLGYSLPQDLVCVDSLPALNALD 164 (318)
T ss_pred HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHCCCCCHHHHCCCCHHHHHHHHH
T ss_conf 41023418888888862038799999999963899716885248765428899999724756604420744158888776
Q ss_pred -------CC-C-CCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf -------77-6-42223789997187545556664026999999999999
Q gi|254780818|r 134 -------HP-S-SRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKM 174 (245)
Q Consensus 134 -------~p-~-~~~~L~~l~~~~~i~~~~r~~H~Al~Da~~~a~v~~~l 174 (245)
.| + +.++|..+-.+|--..+....|.|+.|...+.-.|+..
T Consensus 165 ~a~s~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~ 214 (318)
T KOG4793 165 RANSMVTRPEVRRMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFR 214 (318)
T ss_pred HHCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHH
T ss_conf 50475447777765300237876411359986435442431157789988
No 71
>PRK05755 DNA polymerase I; Provisional
Probab=98.71 E-value=4.8e-08 Score=70.25 Aligned_cols=137 Identities=19% Similarity=0.303 Sum_probs=91.1
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 58999846788888888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
..++||+||||+++....++-|+.. ..+ ++.| || |-. |. +.....++...+.+++
T Consensus 320 ~~va~dtEttsld~~~a~lVGis~s-~~~----g~a~--YI-Pl~----------~~-------~~~~~~~vl~~Lk~lL 374 (889)
T PRK05755 320 GLVAFDTETTSLDPMSANLVGLSFA-VEE----GEAA--YI-PLA----------HD-------DQLDRDDALAALKPLL 374 (889)
T ss_pred CEEEEEEECCCCCCCCCCEEEEEEE-CCC----CCEE--EE-ECC----------CC-------CCCCHHHHHHHHHHHH
T ss_conf 8499998417887565762599998-279----9689--98-444----------31-------3368899999999997
Q ss_pred HCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHH-CCCCCC-----------
Q ss_conf 00232023102322431121000001122221000011000000017764-22237899971-875455-----------
Q gi|254780818|r 88 NEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRY-GITISH----------- 154 (245)
Q Consensus 88 ~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~-~i~~~~----------- 154 (245)
.+.+...|+||+.||+.+| .++|... ...+.||+..|..+-|+. +++|+.||.+| |.....
T Consensus 375 ed~~i~KIghNlK~dl~vL----~~~GI~l--~g~~fDTmLAaYLLdP~~~~~~Ld~La~~yL~~~~~~~eel~gkg~~~ 448 (889)
T PRK05755 375 EDPAIPKVGQNLKYDRHIL----ANYGIEL--RGIAFDTMLASYLLDPGAGRHDLDSLAERYLGHKTISFEEVAGKGNQL 448 (889)
T ss_pred CCCCCCEEEECHHHHHHHH----HHCCEEC--CCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCHHHHCCCCCCC
T ss_conf 0988724320318999999----9779235--776301999998747887767789999986323442034313656556
Q ss_pred --------CCCCCCHHHHHHHHHHHHHHH
Q ss_conf --------566640269999999999997
Q gi|254780818|r 155 --------RSKHGALLDSHLLSDVYIKMM 175 (245)
Q Consensus 155 --------r~~H~Al~Da~~~a~v~~~ll 175 (245)
....-|..||.+|.++|..|.
T Consensus 449 ~~~~v~~e~~~~YaaedA~~~~~L~~~L~ 477 (889)
T PRK05755 449 TFAQVALEEAAEYAAEDADVTLRLHQVLK 477 (889)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 61007878999999998868999999999
No 72
>cd06126 DEDDy 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. DEDDy exonucleases include the proofreading domains of DNA polymerases (families A and B), as well as RNases such as RNase D and 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, Bacillus-like DNA polymerases contain inactive 3'-5' exonuclease domains which do not possess the metal-binding residues necessary for activity.
Probab=98.69 E-value=5.1e-08 Score=70.09 Aligned_cols=121 Identities=20% Similarity=0.222 Sum_probs=77.6
Q ss_pred EEEECCCCCCCC--CCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 999846788888--888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 10 IVFDIETTGLDS--KNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 10 iv~D~ETTGl~~--~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
+.||+||++... ..|.|+.|+.. +.+ |..+ ++.+..... .+ ...+.-.+.+..|.+++
T Consensus 2 l~fDiE~~~~~~~~~~~pI~~i~~~-~~~----g~~~--~~~~~~~~~--~~-----------~~~~~E~~ll~~f~~~i 61 (181)
T cd06126 2 VAFDIETTPLVGGGGKGPIILIQLA-VSA----GEKF--LLDVLTLTL--DA-----------VDSADEKELLGELKAIL 61 (181)
T ss_pred EEEEEECCCCCCCCCCCCEEEEEEE-ECC----CCEE--EEEECCCCC--CC-----------CCCCCHHHHHHHHHHHH
T ss_conf 2898623798999899988999999-659----9789--998624346--75-----------56789999999999998
Q ss_pred HCCCCEEEEECC-CCCCCEEEECHHCCCCCC---------------CCCCHHCCCHHCCCCCC-CCCCCCHHHHHHHHCC
Q ss_conf 002320231023-224311210000011222---------------21000011000000017-7642223789997187
Q gi|254780818|r 88 NEQNAEWIAHNA-KFDVGFINAELQRINKDP---------------LDPSRIIDTLSIARRKH-PSSRNDLNSLCKRYGI 150 (245)
Q Consensus 88 ~~~~~~lVaHNa-~FD~~fL~~el~r~~~~~---------------~~~~~~iDTl~lar~~~-p~~~~~L~~l~~~~~i 150 (245)
...+.+++|||. .||+.+|..-+.+++.+. +.....+|++.+++... +-.+++|+++|+.+.-
T Consensus 62 ~~~~dii~GyN~~~FDlpyL~~R~~~l~~~~~~~~~~~~~~~~~~~~~gr~~~D~~~~~~~~~~~~~~~~L~~va~~~lg 141 (181)
T cd06126 62 EDYDDIKVGYNIDSFDLPYLLNRAGELGIPLRRGRDRSSGSREEINIKGRILFDLLLAAKRLGVALPSYSLDALAEQLLG 141 (181)
T ss_pred HCCCCEEEEECCCCCCHHHHHHHHHHHCCCCHHCCCCCCCCCCEEEECCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHCC
T ss_conf 30899899979977879999999999589701022666565504863485232199999984136465359999999749
No 73
>PRK07625 consensus
Probab=98.68 E-value=6.3e-08 Score=69.51 Aligned_cols=142 Identities=14% Similarity=0.189 Sum_probs=90.6
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 58999846788888888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
..++||+||||++|....++-|+.- +.. +..|..-+...+ ++ ..+.....+++..+..|+
T Consensus 345 ~~~a~dtEttsld~~~a~lvGis~s-~~~----g~a~YiPl~h~~---~d------------~~~~l~~~~vl~~Lk~~L 404 (922)
T PRK07625 345 ELTAFDTETTSLDPMLAQLVGLSFS-VEP----GHAAYIPVAHRG---PD------------MPAQLPRDEVLARLRPWL 404 (922)
T ss_pred CEEEEEEECCCCCHHHCEEEEEEEE-ECC----CCEEEEEECCCC---CC------------HHHHCCHHHHHHHHHHHH
T ss_conf 8489995227765001305657977-438----867999702158---65------------232158999999879987
Q ss_pred HCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHHH-CCCCC------C------
Q ss_conf 0023202310232243112100000112222100001100000001776422237899971-87545------5------
Q gi|254780818|r 88 NEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRY-GITIS------H------ 154 (245)
Q Consensus 88 ~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~-~i~~~------~------ 154 (245)
...+...|+||+.||+.+| .+.|... .....||+..+-.+-|..+++|++|+.+| |.... .
T Consensus 405 ed~~i~KIghNlK~d~~vL----~~~GI~l--~g~~fDTmLAaYLL~~~r~~~Ld~La~~yL~~~~i~~edl~Gkg~~q~ 478 (922)
T PRK07625 405 EDAGRKKLGQHLKYDAQVL----ANYGIAL--NGIEHDTLLESYVLESHRTHDMDSLALRHLGVKTIKYEDVAGKGAKQI 478 (922)
T ss_pred HCCCCHHHHHHHHHHHHHH----HHCCCCC--CCCCHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCHHHHCCCCCCCC
T ss_conf 4344035542577899999----9779645--875403999988754676788799999872556554132123333337
Q ss_pred --------CCCCCCHHHHHHHHHHHHHHH
Q ss_conf --------566640269999999999997
Q gi|254780818|r 155 --------RSKHGALLDSHLLSDVYIKMM 175 (245)
Q Consensus 155 --------r~~H~Al~Da~~~a~v~~~ll 175 (245)
+..+-|..||.+|.++|..|.
T Consensus 479 ~~~~v~~~~~~~Ya~eda~~t~~L~~~L~ 507 (922)
T PRK07625 479 GFDEVALAQASEYAAEDADITLQLHHALY 507 (922)
T ss_pred CHHHCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 83224679999999999999999999999
No 74
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=98.65 E-value=1.5e-07 Score=67.21 Aligned_cols=136 Identities=22% Similarity=0.250 Sum_probs=85.3
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 58999846788888888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
+..+||+|||||++.++.|+-.|.-.+.+.. + +|+.-.-+-|..- .-|++.|+...
T Consensus 99 ~~~FFDiETTGL~~ag~~I~~~g~a~~~~~~-----~--~Vrq~~lp~p~~E-----------------~avle~fl~~~ 154 (278)
T COG3359 99 DVAFFDIETTGLDRAGNTITLVGGARGVDDT-----M--HVRQHFLPAPEEE-----------------VAVLENFLHDP 154 (278)
T ss_pred CEEEEEEECCCCCCCCCEEEEEEEEECCCCE-----E--EEEEECCCCCCHH-----------------HHHHHHHHCCC
T ss_conf 2589963314668889859999888735756-----9--9975127984135-----------------68999975389
Q ss_pred HCCCCEEEEECC-CCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCC--CCCCHHHHHHHHCCCCCCCCCCCCHHHH
Q ss_conf 002320231023-2243112100000112222100001100000001776--4222378999718754555666402699
Q gi|254780818|r 88 NEQNAEWIAHNA-KFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPS--SRNDLNSLCKRYGITISHRSKHGALLDS 164 (245)
Q Consensus 88 ~~~~~~lVaHNa-~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~--~~~~L~~l~~~~~i~~~~r~~H~Al~Da 164 (245)
....+|-+|. .||+.|+++ +.+...+......-+|-+-.+|+++.. .+.+|.+.-+.+||..+. ----.|+
T Consensus 155 --~~~~lvsfNGkaFD~PfikR-~v~~~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr~LGi~R~e---dtdG~~~ 228 (278)
T COG3359 155 --DFNMLVSFNGKAFDIPFIKR-MVRDRLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTVERILGIRREE---DTDGYDG 228 (278)
T ss_pred --CCCEEEEECCCCCCCHHHHH-HHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCC---CCCCCCH
T ss_conf --84559974683267089999-87516444766663122103445312028788813678885755011---5898501
Q ss_pred HHHHHHHHH
Q ss_conf 999999999
Q gi|254780818|r 165 HLLSDVYIK 173 (245)
Q Consensus 165 ~~~a~v~~~ 173 (245)
..+-..|+.
T Consensus 229 p~lyr~~~~ 237 (278)
T COG3359 229 PELYRLYRR 237 (278)
T ss_pred HHHHHHHHH
T ss_conf 999999987
No 75
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=98.65 E-value=2.3e-08 Score=72.21 Aligned_cols=152 Identities=22% Similarity=0.275 Sum_probs=88.2
Q ss_pred CCCCEEEEECCCCCCCCCCCEEEEEEEEEEEC-CEECCCEEEEEEC-CC--CCCCCHHHEEECC---CCCCCCCCCCCCC
Q ss_conf 77758999846788888888899999999999-9880313798985-88--8228865724202---1012322485210
Q gi|254780818|r 5 NKMRKIVFDIETTGLDSKNDRIIEIGAVELLD-YSKTNRTFQVFLC-PN--GRKNSPEALKLHG---ITDEFLKDKPSFS 77 (245)
Q Consensus 5 ~~mr~iv~D~ETTGl~~~~d~Iieigav~i~~-~~~~~~~f~~~i~-P~--~~~i~~~~~~ihG---It~~~l~~~p~f~ 77 (245)
.+-+.|-+|+|.|||||..||||||+++.-+. ..+.++-+..-|. |+ -..+++-..+.|| ++..-....-+..
T Consensus 4 ~~~nLiWIDlEMTGLd~~~drIIEiA~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~t~~ 83 (184)
T COG1949 4 NKNNLIWIDLEMTGLDPERDRIIEIATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTVTEA 83 (184)
T ss_pred CCCCEEEEEEEECCCCCCCCEEEEEEEEEECCCCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCHH
T ss_conf 77862899632026886764278888877547632103585578867999999889999971454318999997223399
Q ss_pred HHHHHHHHHHH----CCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCH---HCCCCCCCCCCCCHHHHHHHHCC
Q ss_conf 02344777530----023202310232243112100000112222100001100---00000177642223789997187
Q gi|254780818|r 78 SIFSEFWDFFN----EQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTL---SIARRKHPSSRNDLNSLCKRYGI 150 (245)
Q Consensus 78 ev~~~f~~fi~----~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl---~lar~~~p~~~~~L~~l~~~~~i 150 (245)
++-.+.++|+. ..-+++.|-.+.=|.+||-+++.++-- .+ ..+.+|.- .+||+-.|. + .+|
T Consensus 84 ~aE~~~L~flkkwvp~~~spicGNSI~qDRrFl~r~MP~Le~-yf-HYR~lDVSTlKELa~RW~P~-------i--~~~- 151 (184)
T COG1949 84 EAEAQTLDFLKKWVPKGVSPICGNSIAQDRRFLFRYMPKLEA-YF-HYRYLDVSTLKELARRWNPE-------I--LAG- 151 (184)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH-HH-HHHHHHHHHHHHHHHHHCCH-------H--HHH-
T ss_conf 999999999998678998877565065789999997655898-74-46662078799999862937-------7--652-
Q ss_pred CCCCCCCCCCHHHHH-HHHH
Q ss_conf 545556664026999-9999
Q gi|254780818|r 151 TISHRSKHGALLDSH-LLSD 169 (245)
Q Consensus 151 ~~~~r~~H~Al~Da~-~~a~ 169 (245)
...+..|.||+|-+ ..++
T Consensus 152 -~~K~~~H~Al~DI~ESI~E 170 (184)
T COG1949 152 -FKKGGTHRALDDIRESIAE 170 (184)
T ss_pred -HCCCCCHHHHHHHHHHHHH
T ss_conf -1036523469999999999
No 76
>cd06140 DNA_polA_I_Bacillus_like_exo 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=98.63 E-value=1.4e-07 Score=67.28 Aligned_cols=132 Identities=14% Similarity=0.174 Sum_probs=87.7
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 58999846788888888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
..+.+|+||||++|..++|+-||... + ++.| ||.-+. .. .....+..|+
T Consensus 4 ~~~av~~e~~~~~~~~~~i~gi~l~~--~----~~~~--yi~~~~--~~---------------------~~~~~lk~~l 52 (178)
T cd06140 4 DEVALYVELLGENYHTADIIGLALAN--G----GGAY--YIPLEL--AL---------------------LDLAALKEWL 52 (178)
T ss_pred CCEEEEEECCCCCCCCCEEEEEEEEE--C----CEEE--EEECCC--CH---------------------HHHHHHHHHH
T ss_conf 86699973799984535499999988--9----9799--995667--36---------------------4699999997
Q ss_pred HCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHHC-CCCCCC----------
Q ss_conf 00232023102322431121000001122221000011000000017764-222378999718-754555----------
Q gi|254780818|r 88 NEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRYG-ITISHR---------- 155 (245)
Q Consensus 88 ~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~~-i~~~~r---------- 155 (245)
.+.+..-|+||+.||+.+| .+.|... .+...||+-.+...-|+. +++|++|+.+|. .+....
T Consensus 53 ~d~~i~Ki~hn~K~~~~~L----~~~Gi~l--~g~~fDtmiaayLl~p~~~~~~L~~L~~~yl~~~~~~~~~~~gk~~~~ 126 (178)
T cd06140 53 EDEKIPKVGHDAKRAYVAL----KRHGIEL--AGVAFDTMLAAYLLDPTRSSYDLADLAKRYLGRELPSDEEVYGKGAKF 126 (178)
T ss_pred CCCCCCEEEECHHHHHHHH----HHCCCCC--CCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCHHHHHCCCCCC
T ss_conf 2999988986579999999----9889806--883036888988754897779999999998286665478861766562
Q ss_pred -------CCCCCHHHHHHHHHHHHHHHH
Q ss_conf -------666402699999999999973
Q gi|254780818|r 156 -------SKHGALLDSHLLSDVYIKMMV 176 (245)
Q Consensus 156 -------~~H~Al~Da~~~a~v~~~ll~ 176 (245)
.+.-|..||.++.++|..+..
T Consensus 127 ~~~~~~~~~~ya~~~a~~~~~L~~~l~~ 154 (178)
T cd06140 127 AVPDEEVLAEHLARKAAAILRLAPKLEE 154 (178)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 4399799999999999999999999999
No 77
>cd05782 DNA_polB_like1_exo 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=98.62 E-value=2.1e-07 Score=66.19 Aligned_cols=95 Identities=16% Similarity=0.230 Sum_probs=64.0
Q ss_pred CHHHHHHHHHHHCCCCEEEEECC-CCCCCEEEECHHCCCCCCCC---------------CCHHCCCHHCCCCCCCCCCCC
Q ss_conf 00234477753002320231023-22431121000001122221---------------000011000000017764222
Q gi|254780818|r 77 SSIFSEFWDFFNEQNAEWIAHNA-KFDVGFINAELQRINKDPLD---------------PSRIIDTLSIARRKHPSSRND 140 (245)
Q Consensus 77 ~ev~~~f~~fi~~~~~~lVaHNa-~FD~~fL~~el~r~~~~~~~---------------~~~~iDTl~lar~~~p~~~~~ 140 (245)
.+++..|.+++...+..+|+||. .||+.||..-..++|++.+. ..+.+||+.+-...-...+.+
T Consensus 79 ~~ll~~F~~~i~~~~p~lv~~Ng~~FD~P~l~~Ral~~gi~~p~~~~~~~~~~~y~~r~~~~H~Dl~d~l~~~~~~~~~s 158 (208)
T cd05782 79 KELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYGARARAS 158 (208)
T ss_pred HHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCC
T ss_conf 99999999999865997996368757589999999991989755540488741124888763132999985548757788
Q ss_pred HHHHHHHHCCCCCCCCC------------------CCCHHHHHHHHHHHH
Q ss_conf 37899971875455566------------------640269999999999
Q gi|254780818|r 141 LNSLCKRYGITISHRSK------------------HGALLDSHLLSDVYI 172 (245)
Q Consensus 141 L~~l~~~~~i~~~~r~~------------------H~Al~Da~~~a~v~~ 172 (245)
|+.+|+.+|++-.. .- +-...|+..|+.||+
T Consensus 159 Ld~la~llG~pgK~-~~~Gs~V~~~~~~g~l~~I~~YCe~DVl~T~~v~l 207 (208)
T cd05782 159 LDLLAKLLGIPGKM-DVDGSQVWELYAEGKLDEIAEYCETDVLNTYLLYL 207 (208)
T ss_pred HHHHHHHHCCCCCC-CCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999983899757-88889999999819988999999999999999980
No 78
>PRK08434 consensus
Probab=98.57 E-value=1.4e-07 Score=67.29 Aligned_cols=140 Identities=29% Similarity=0.433 Sum_probs=84.0
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 58999846788888888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
..++||+||||+++...+++-++.. +.+ +..| || |-+. ... | .++. -...++...+..+.
T Consensus 319 ~~~a~d~Ett~ld~~~a~lvGis~~-~~~----~~a~--Yi-Pi~h----~~l---~-~~~~----~~~~~~~~~l~~~~ 378 (887)
T PRK08434 319 SIIAFDTETTGLDTKEAKLVGFSFC-FNE----EEAY--YV-PLAH----SYL---G-VGEQ----ISLESAKKAIEKIF 378 (887)
T ss_pred CEEEEEEECCCCCCCCCCEEEEEEE-ECC----CCEE--EE-ECCC----CCC---C-CHHH----CCHHHHHHHHHHHH
T ss_conf 7699995127866133430589999-559----8589--99-7521----125---7-7333----59999999978763
Q ss_pred HCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHHH-CCCCC--------C----
Q ss_conf 0023202310232243112100000112222100001100000001776422237899971-87545--------5----
Q gi|254780818|r 88 NEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRY-GITIS--------H---- 154 (245)
Q Consensus 88 ~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~-~i~~~--------~---- 154 (245)
...+|+||+.||+.+|. ..+|... ...+.||+..|-..-|+.+++|+.|+.+| +.... .
T Consensus 379 ---~~~~IghNlKyDl~vL~---~~~gi~l--~g~~fDTmLAaYLLdp~~r~~Ld~La~~yL~~~~i~~e~l~~kg~~f~ 450 (887)
T PRK08434 379 ---NHFVIGHNLKYDFKIIQ---NNFGLEL--PQKYADTMILAWLKDPSSRVGLDDLAKRLFNYEMIHFESVVKKGENFS 450 (887)
T ss_pred ---HCCCHHHHHHHHHHHHH---HHCCCCC--CCCHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCHHHHHCCCCCCC
T ss_conf ---37403647799999999---8569877--773148999998669866666678999970878774899854677702
Q ss_pred -----CCCCCCHHHHHHHHHHHHHHH
Q ss_conf -----566640269999999999997
Q gi|254780818|r 155 -----RSKHGALLDSHLLSDVYIKMM 175 (245)
Q Consensus 155 -----r~~H~Al~Da~~~a~v~~~ll 175 (245)
...+-|..||.+|.++|..+.
T Consensus 451 ~v~i~~a~~YAaedA~it~~L~~~l~ 476 (887)
T PRK08434 451 SVDLEKACKYAAEDAWITLRFYKKFL 476 (887)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 07889999999999999999999999
No 79
>cd05779 DNA_polB_epsilon_exo 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 large C-terminal domain with an unknown function. Phylogenetic analyses indicate that it is ort
Probab=98.56 E-value=5.5e-07 Score=63.60 Aligned_cols=136 Identities=23% Similarity=0.296 Sum_probs=73.4
Q ss_pred CEEEEECCCCCC-----CCCCCEEEEEEEEEEECCEE-CCCEEEEEECCCCCCCCHHHE----EECCCCCCCCCCCCCCC
Q ss_conf 589998467888-----88888899999999999988-031379898588822886572----42021012322485210
Q gi|254780818|r 8 RKIVFDIETTGL-----DSKNDRIIEIGAVELLDYSK-TNRTFQVFLCPNGRKNSPEAL----KLHGITDEFLKDKPSFS 77 (245)
Q Consensus 8 r~iv~D~ETTGl-----~~~~d~Iieigav~i~~~~~-~~~~f~~~i~P~~~~i~~~~~----~ihGIt~~~l~~~p~f~ 77 (245)
|...||+||++. +|+.|.||+|+.+.-..+.. +.+. .+. ..+...-. .+.| .-.+-.-+.-.
T Consensus 3 rilsfDIE~~~~~~~fP~~~~D~Ii~Is~~~~~~g~~i~~~~---~~~---~~i~~~~~~~~~~~~g--~~~v~~~~~E~ 74 (204)
T cd05779 3 RVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIVNRE---IVS---EDIEDFEYTPKPEYEG--PFKVFNEPDEK 74 (204)
T ss_pred EEEEEEEEEECCCCCCCCCCCCEEEEEEEEEECCCEEEEECC---CCC---CCCCCCCCCCCCCCCC--CEEEEECCCHH
T ss_conf 799999995079999989888908999999916877987434---013---5330001467856657--64898369999
Q ss_pred HHHHHHHHHHHCCC-CEEEEECC-CCCCCEEEECHHCCCCCCCCC------------CH---HCCCHHCCCC--CCCCCC
Q ss_conf 02344777530023-20231023-224311210000011222210------------00---0110000000--177642
Q gi|254780818|r 78 SIFSEFWDFFNEQN-AEWIAHNA-KFDVGFINAELQRINKDPLDP------------SR---IIDTLSIARR--KHPSSR 138 (245)
Q Consensus 78 ev~~~f~~fi~~~~-~~lVaHNa-~FD~~fL~~el~r~~~~~~~~------------~~---~iDTl~lar~--~~p~~~ 138 (245)
+.+.+|.+|+...+ .+++++|. .||+.+|..-..++|.+.... .+ .+|-+...++ +.+..+
T Consensus 75 ~ll~~f~~~i~~~~pdii~gyN~~~FD~pyl~~Ra~~~~~~~~~~~~~~~~~~~~~~~~~~vhiDly~~v~rd~~l~~~s 154 (204)
T cd05779 75 ALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGS 154 (204)
T ss_pred HHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCCCHHHHCCCCCCCCCCEECCCCEEEECHHHHHHHCCCCCCC
T ss_conf 99999999998649999985587677679999999995998255318000677727626725630077651012175568
Q ss_pred CCHHHHHHH-HCCC
Q ss_conf 223789997-1875
Q gi|254780818|r 139 NDLNSLCKR-YGIT 151 (245)
Q Consensus 139 ~~L~~l~~~-~~i~ 151 (245)
++|++.|++ +|..
T Consensus 155 y~Ln~Vs~~~Lg~~ 168 (204)
T cd05779 155 QGLKAVTKAKLGYD 168 (204)
T ss_pred CCHHHHHHHHHCCC
T ss_conf 77899999996899
No 80
>cd05781 DNA_polB_B3_exo 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 replication are similar to those from eukaryotes. Some archaea possess multiple family-B DNA polymerases. B3 is mainly found in crenarch
Probab=98.51 E-value=4.9e-07 Score=63.95 Aligned_cols=117 Identities=17% Similarity=0.257 Sum_probs=74.5
Q ss_pred CCEEEEECCCCC----CCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHH
Q ss_conf 758999846788----8888888999999999999880313798985888228865724202101232248521002344
Q gi|254780818|r 7 MRKIVFDIETTG----LDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSE 82 (245)
Q Consensus 7 mr~iv~D~ETTG----l~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~ 82 (245)
.|.+.||+||++ .+|+.|.||+||.. ..++.. ...+.. ...-.+.+..
T Consensus 3 lk~lsfDIE~~~~~gfp~~~~d~Ii~Is~~-~~~g~~-----~~~~~~----------------------~~~E~~ll~~ 54 (188)
T cd05781 3 LKTLAFDIEVYSKYGTPNPRRDPIIVISLA-TSNGDV-----EFILAE----------------------GLDDRKIIRE 54 (188)
T ss_pred CEEEEEEEEECCCCCCCCCCCCCEEEEEEE-ECCCCE-----EEEEEC----------------------CCCHHHHHHH
T ss_conf 419999988768999899888978999999-689976-----999847----------------------9998999999
Q ss_pred HHHHHHCCC-CEEEEECC-CCCCCEEEECHHCCCCCC-------------------CCCCHHCCCHHCCCCCCCCCCCCH
Q ss_conf 777530023-20231023-224311210000011222-------------------210000110000000177642223
Q gi|254780818|r 83 FWDFFNEQN-AEWIAHNA-KFDVGFINAELQRINKDP-------------------LDPSRIIDTLSIARRKHPSSRNDL 141 (245)
Q Consensus 83 f~~fi~~~~-~~lVaHNa-~FD~~fL~~el~r~~~~~-------------------~~~~~~iDTl~lar~~~p~~~~~L 141 (245)
|.+++...+ .+++|||. .||+.+|..-..++|.+. +..--.+|.+.+.+..+.-++++|
T Consensus 55 f~~~i~~~~Pdii~gyN~~~FD~pyl~~Ra~~~~i~l~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~l~sysL 134 (188)
T cd05781 55 FVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPEVKVKTL 134 (188)
T ss_pred HHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEECHHHHHHHCCCCCCCH
T ss_conf 99999872999999669867578999999999699850155677651225420699878999977899976247564579
Q ss_pred HHHHHHHCCC
Q ss_conf 7899971875
Q gi|254780818|r 142 NSLCKRYGIT 151 (245)
Q Consensus 142 ~~l~~~~~i~ 151 (245)
+++++++|..
T Consensus 135 ~~Va~~lg~~ 144 (188)
T cd05781 135 ENVAEYLGVM 144 (188)
T ss_pred HHHHHHHCCC
T ss_conf 9999985412
No 81
>PRK05797 consensus
Probab=98.48 E-value=5e-07 Score=63.90 Aligned_cols=136 Identities=13% Similarity=0.213 Sum_probs=91.3
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 58999846788888888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
..+++|+|||++++....++.+++.... ++.| || |-....+ ..+++..+..++
T Consensus 320 ~~~~~~~ett~~~~~~~~~vg~s~~~~~-----~~a~--yi-p~~~~~~-------------------~~~~L~~Lk~lL 372 (869)
T PRK05797 320 NQVYINFTLEDENLYSKIEIKKIFINFG-----EKTY--YI-DFKELID-------------------EEEFIEDLKEIF 372 (869)
T ss_pred CCEEEEEECCCCCHHHHHHEEEEEEECC-----CEEE--EE-ECHHHCC-------------------HHHHHHHHHHHH
T ss_conf 9879999738976120304189999619-----9799--98-3145167-------------------789999999998
Q ss_pred HCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHH-CCCCCCCCCCCCHHHHH
Q ss_conf 00232023102322431121000001122221000011000000017764-22237899971-87545556664026999
Q gi|254780818|r 88 NEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRY-GITISHRSKHGALLDSH 165 (245)
Q Consensus 88 ~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~-~i~~~~r~~H~Al~Da~ 165 (245)
.......|+||+.||+.+| .+.|... .+..+||+..+-.+-|+. +++|+.|+.+| |.+....+..-|..||.
T Consensus 373 ed~~i~KIGhNlK~dl~vL----~~~GI~l--~gi~FDTMLAsYLLnP~~~~h~Ld~La~~yL~~~~~~~e~~ya~~dA~ 446 (869)
T PRK05797 373 ENEEIKKIGHDIKNFLTIL----KKLGIEF--KGLAFDTAIAAYLIDPSKSEYDLSDLAKEYLSKDVNSEEEEYKIKEVS 446 (869)
T ss_pred HCCCCCEEEECCHHHHHHH----HHCCCCC--CCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf 4899878984306999999----9759855--661668999999728998888999999998087775147899999999
Q ss_pred HHHHHHHHHHH
Q ss_conf 99999999973
Q gi|254780818|r 166 LLSDVYIKMMV 176 (245)
Q Consensus 166 ~~a~v~~~ll~ 176 (245)
++.++|..|..
T Consensus 447 ~~~~L~~~L~~ 457 (869)
T PRK05797 447 VMKELYEKLKE 457 (869)
T ss_pred HHHHHHHHHHH
T ss_conf 99999999999
No 82
>PRK07997 consensus
Probab=98.45 E-value=3.1e-07 Score=65.19 Aligned_cols=142 Identities=20% Similarity=0.278 Sum_probs=86.8
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 58999846788888888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
..++||+||||+++....++-|+.. +.. ++.| |+ |-+... . . ..+.-....++..+..++
T Consensus 350 ~~~a~DtEt~sld~~~a~lvGiS~s-~~~----g~a~--Yi-Pl~h~~----l-----~---~~~ql~~~~vl~~LkplL 409 (928)
T PRK07997 350 PVFAFDTETDSLDNISANLVGLSFA-IEP----GVAA--YL-PVAHDY----L-----D---APDQISRERVLELLKPLL 409 (928)
T ss_pred CEEEEEEECCCCCCCCCCCCCEEEE-ECC----CCEE--EE-ECCCCC----C-----C---CHHHCCHHHHHHHHHHHH
T ss_conf 8699995127866000244433898-627----7468--74-022123----4-----7---600124999999989875
Q ss_pred HCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCC-CCCCHHHHHHHH-CCCC------CC-----
Q ss_conf 0023202310232243112100000112222100001100000001776-422237899971-8754------55-----
Q gi|254780818|r 88 NEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPS-SRNDLNSLCKRY-GITI------SH----- 154 (245)
Q Consensus 88 ~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~-~~~~L~~l~~~~-~i~~------~~----- 154 (245)
.......|+||+.||+.+| .++|... .....||+..|-.+-|+ .+++|++||.+| +... ..
T Consensus 410 ed~~i~KIghnlK~d~~vL----~~~GI~l--~gi~fDTmLAaYLLnp~~~~~~Ld~La~~yL~~~~i~~~el~gkgk~q 483 (928)
T PRK07997 410 EDEKALKVGQNLKFDRGIL----ANYGIEL--RGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQ 483 (928)
T ss_pred CCCCCCHHCCHHHHHHHHH----HHCCCEE--CCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCHHHHCCCCCCC
T ss_conf 2865303212168899999----9779410--564303455322224433447889999997134664335432446454
Q ss_pred ---------CCCCCCHHHHHHHHHHHHHHH
Q ss_conf ---------566640269999999999997
Q gi|254780818|r 155 ---------RSKHGALLDSHLLSDVYIKMM 175 (245)
Q Consensus 155 ---------r~~H~Al~Da~~~a~v~~~ll 175 (245)
....-|..||.+|.++|..|.
T Consensus 484 ~~f~~v~~~~~~~Ya~edA~~t~~L~~~L~ 513 (928)
T PRK07997 484 LTFNQIALEEAGRYAAEDADVTLQLHLKMW 513 (928)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 774353599999999999999999999999
No 83
>cd05160 DNA_polB_exo 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 E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon and zeta), and eukaryotic viral and
Probab=98.44 E-value=7e-07 Score=62.95 Aligned_cols=132 Identities=20% Similarity=0.245 Sum_probs=75.8
Q ss_pred EEEECCCCCC----CCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 9998467888----888888999999999999880313798985888228865724202101232248521002344777
Q gi|254780818|r 10 IVFDIETTGL----DSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWD 85 (245)
Q Consensus 10 iv~D~ETTGl----~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~ 85 (245)
+.||+||..- +|..|.|++|+++--.++... .+. ..+...........+.| ..+....+-.+.+..|.+
T Consensus 2 lsfDIE~~~~~gfP~p~~d~Ii~Is~~~~~~~~~~--~~~--~~~~~~~~~~~~~~~~~---~~v~~~~~E~eLL~~F~~ 74 (200)
T cd05160 2 LSFDIETLPNVGGPEPSRDPIICISYADSFQGHKV--VFL--LKVSTHGDDIEAGFIDG---IEVEYFDDEKELLKRFFD 74 (200)
T ss_pred EEEEEEECCCCCCCCCCCCEEEEEEEEEECCCEEE--EEE--EECCCCCCCCCCCCCCC---EEEEEECCHHHHHHHHHH
T ss_conf 79998327999978999880899999993599999--988--64355676765467799---699996999999999999
Q ss_pred HHHCCC-CEEEEECC-CCCCCEEEECHHCCCCCCCCCC--------------------HHCCCHHCCCCCCCCCCCCHHH
Q ss_conf 530023-20231023-2243112100000112222100--------------------0011000000017764222378
Q gi|254780818|r 86 FFNEQN-AEWIAHNA-KFDVGFINAELQRINKDPLDPS--------------------RIIDTLSIARRKHPSSRNDLNS 143 (245)
Q Consensus 86 fi~~~~-~~lVaHNa-~FD~~fL~~el~r~~~~~~~~~--------------------~~iDTl~lar~~~p~~~~~L~~ 143 (245)
++...+ .+++|||. .||+.+|..-..++|.+..... -.+|.+.+.|+..--.+++|++
T Consensus 75 ~i~~~dPDii~GyN~~~FD~pyL~~R~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~lD~~~~~k~~~~l~sy~Ld~ 154 (200)
T cd05160 75 IIREYDPDILTGYNIDDFDLPYLLERAKALGIKLDDIGRRSGQEKSSGETERAAVKGRVVFDLLRAVKRDFKLKSYTLDA 154 (200)
T ss_pred HHHHCCCCEEEECCCCCCCHHHHHHHHHHHCCCHHHCCCCCCCCCCCCCEEEEEECCEEEEHHHHHHHHHHCCCCCCHHH
T ss_conf 99970999999726777848899999999698855546734545435750599736778602899999753246653999
Q ss_pred HHHHH
Q ss_conf 99971
Q gi|254780818|r 144 LCKRY 148 (245)
Q Consensus 144 l~~~~ 148 (245)
+|+.+
T Consensus 155 Va~~~ 159 (200)
T cd05160 155 VAEEL 159 (200)
T ss_pred HHHHH
T ss_conf 99998
No 84
>KOG3242 consensus
Probab=98.43 E-value=9.8e-08 Score=68.30 Aligned_cols=146 Identities=24% Similarity=0.313 Sum_probs=90.1
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECC-EECCCEEEEEECCCC---CCCCHHHEEE---CCCCCCCCCCCCCCCHHH
Q ss_conf 589998467888888888999999999999-880313798985888---2288657242---021012322485210023
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDY-SKTNRTFQVFLCPNG---RKNSPEALKL---HGITDEFLKDKPSFSSIF 80 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~-~~~~~~f~~~i~P~~---~~i~~~~~~i---hGIt~~~l~~~p~f~ev~ 80 (245)
+.|-+|+|.||||..+|+|+||+|+.-++. .++.+-+...|+-+. -.+.+-..+- .|+|..-+...-+..++-
T Consensus 27 ~lVWiD~EMTGLdvekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~tl~~aE 106 (208)
T KOG3242 27 PLVWIDCEMTGLDVEKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKITLADAE 106 (208)
T ss_pred CEEEEEEECCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCHHCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCHHHHH
T ss_conf 64899610125532313168788887658755003386404229899998888999983141147999997314399999
Q ss_pred HHHHHHHHC---CCCEEEEEC-CCCCCCEEEECHHCCCCCCCCCCHHCCC---HHCCCCCCCCCCCCHHHHHHHHCCCCC
Q ss_conf 447775300---232023102-3224311210000011222210000110---000000177642223789997187545
Q gi|254780818|r 81 SEFWDFFNE---QNAEWIAHN-AKFDVGFINAELQRINKDPLDPSRIIDT---LSIARRKHPSSRNDLNSLCKRYGITIS 153 (245)
Q Consensus 81 ~~f~~fi~~---~~~~lVaHN-a~FD~~fL~~el~r~~~~~~~~~~~iDT---l~lar~~~p~~~~~L~~l~~~~~i~~~ 153 (245)
+++++|+.. +|..++|-| +--|..||..++...-. .+ ..+++|. ..++|+-+|..+. +. + .
T Consensus 107 nevl~yikk~ip~~~~~laGNSV~~DrlFl~k~mPk~~~-~l-hyrivDVStIkeL~~Rw~P~~~~--------~a-P-k 174 (208)
T KOG3242 107 NEVLEYIKKHIPKGKCPLAGNSVYMDRLFLKKYMPKLIK-HL-HYRIVDVSTIKELARRWYPDIKA--------RA-P-K 174 (208)
T ss_pred HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHH-HC-CEEEEEHHHHHHHHHHHCCHHHC--------CC-C-C
T ss_conf 999999998678988875686034679999998588997-52-54566478799999985903220--------07-2-1
Q ss_pred CCCCCCCHHHHH
Q ss_conf 556664026999
Q gi|254780818|r 154 HRSKHGALLDSH 165 (245)
Q Consensus 154 ~r~~H~Al~Da~ 165 (245)
....|+|+.|-.
T Consensus 175 K~~~HrAldDI~ 186 (208)
T KOG3242 175 KKATHRALDDIR 186 (208)
T ss_pred CCCCCCHHHHHH
T ss_conf 001401088999
No 85
>PRK08835 consensus
Probab=98.40 E-value=6.1e-07 Score=63.34 Aligned_cols=141 Identities=13% Similarity=0.228 Sum_probs=86.2
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCC-CCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 5899984678888888889999999999998803137989858882-288657242021012322485210023447775
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGR-KNSPEALKLHGITDEFLKDKPSFSSIFSEFWDF 86 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~-~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~f 86 (245)
..++||+||||+++....++-|+.. +.. +..| |+ |-.. .+.. ........++..+..+
T Consensus 352 ~~~a~dtEt~~ld~~~a~lvGis~~-~~~----g~a~--Yi-Pl~h~~l~~-------------~~ql~~d~vl~~Lkpl 410 (931)
T PRK08835 352 ELFAFDTETDSLDYMVANLVGLSFA-VAE----GEAA--YV-PVAHDYLDA-------------PEQLDRDWVLAQLKPL 410 (931)
T ss_pred CEEEEEEECCCCCHHHCCCCCEEEE-ECC----CCEE--EE-EECCCCCCC-------------HHHCCHHHHHHHHHHH
T ss_conf 8599995048743222133542687-647----8579--99-712333455-------------1013699999997998
Q ss_pred HHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCC-CCCCHHHHHHHH-CCCC------C-----
Q ss_conf 30023202310232243112100000112222100001100000001776-422237899971-8754------5-----
Q gi|254780818|r 87 FNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPS-SRNDLNSLCKRY-GITI------S----- 153 (245)
Q Consensus 87 i~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~-~~~~L~~l~~~~-~i~~------~----- 153 (245)
+.......|+||+.||+.+| .++|... .....||+..+...-|+ .+++|+.|+.+| +... .
T Consensus 411 Led~~i~KIghNlK~d~~vL----~~~gI~l--~gi~fDTmLAaYLLnp~~~~~~Ld~La~~~L~~~~i~~e~l~gkgk~ 484 (931)
T PRK08835 411 LEDDAKAKVGQNLKYDASVL----ARYGIEM--KGIKHDTMLASYVYNSVGGKHDMDSLALRFLQHSCISFEQVAGKGKN 484 (931)
T ss_pred HCCCCHHHHHCCHHHHHHHH----HHCCCCC--CCCCCCHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCHHHHCCCCCC
T ss_conf 42842436622115789999----9779776--78661243575300477787898999998648776347765144534
Q ss_pred ---------CCCCCCCHHHHHHHHHHHHHHH
Q ss_conf ---------5566640269999999999997
Q gi|254780818|r 154 ---------HRSKHGALLDSHLLSDVYIKMM 175 (245)
Q Consensus 154 ---------~r~~H~Al~Da~~~a~v~~~ll 175 (245)
....+-|..||.++.++|..|.
T Consensus 485 q~~f~~v~~~~~~~YaaedA~~t~~L~~~L~ 515 (931)
T PRK08835 485 QLTFNQIDLEEAAPYAAEDADVTLRLHNRLF 515 (931)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 4783343288999999999999999999999
No 86
>cd05785 DNA_polB_like2_exo 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=98.35 E-value=1.4e-06 Score=61.15 Aligned_cols=84 Identities=21% Similarity=0.361 Sum_probs=53.6
Q ss_pred CCCCCEEEEECCCCCCC------C--CCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCC
Q ss_conf 67775899984678888------8--888899999999999988031379898588822886572420210123224852
Q gi|254780818|r 4 KNKMRKIVFDIETTGLD------S--KNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPS 75 (245)
Q Consensus 4 ~~~mr~iv~D~ETTGl~------~--~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~ 75 (245)
-..+|.+.||+||++.+ | ..|+||+||.. .++ .+...+.-. + ..
T Consensus 6 ~~~lr~lsfDIE~~~~~g~~~p~p~~~~d~Ii~I~~~--~~~-----~~~~v~~~~------------~---------~~ 57 (207)
T cd05785 6 FDDLRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALR--DNR-----GWEEVLHAE------------D---------AA 57 (207)
T ss_pred HHHEEEEEEEEEECCCCCCCCCCCCCCCCCEEEEEEE--ECC-----CCEEEEEEC------------C---------CC
T ss_conf 2040599999974788997799988899978999988--589-----977987626------------9---------99
Q ss_pred CCHHHHHHHHHHHCCC-CEEEEECC-CCCCCEEEECHHCCCC
Q ss_conf 1002344777530023-20231023-2243112100000112
Q gi|254780818|r 76 FSSIFSEFWDFFNEQN-AEWIAHNA-KFDVGFINAELQRINK 115 (245)
Q Consensus 76 f~ev~~~f~~fi~~~~-~~lVaHNa-~FD~~fL~~el~r~~~ 115 (245)
-.+.+.+|.+|+...+ .+++|+|. .||+.+|..-+.++|.
T Consensus 58 E~~lL~~F~~~i~~~dPDIItGyNi~~FD~pYL~~Ra~~~~i 99 (207)
T cd05785 58 EKELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGV 99 (207)
T ss_pred HHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCC
T ss_conf 999999999999873999998679877588999999999599
No 87
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=98.35 E-value=1.5e-06 Score=60.91 Aligned_cols=134 Identities=22% Similarity=0.259 Sum_probs=84.1
Q ss_pred EEEEECCCCCCCCCCCE--EEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 89998467888888888--9999999999998803137989858882288657242021012322485210023447775
Q gi|254780818|r 9 KIVFDIETTGLDSKNDR--IIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDF 86 (245)
Q Consensus 9 ~iv~D~ETTGl~~~~d~--Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~f 86 (245)
.|.+||||.|+.+..++ +||| .+ ++. ..+|.|.. .+ .+.|+| ...
T Consensus 19 ~iAIDTEf~r~~t~~p~LcLIQi-----~~----~e~-~~lIdp~~-~~---------------~d~~~l-------~~L 65 (361)
T COG0349 19 AIAIDTEFMRLRTYYPRLCLIQI-----SD----GEG-ASLIDPLA-GI---------------LDLPPL-------VAL 65 (361)
T ss_pred EEEEECCCCCCCCCCCCEEEEEE-----EC----CCC-CEEECCCC-CC---------------CCCCHH-------HHH
T ss_conf 07983222466436883379998-----44----888-66862265-54---------------666369-------998
Q ss_pred HHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHHH-CCCCCCC----------
Q ss_conf 30023202310232243112100000112222100001100000001776422237899971-8754555----------
Q gi|254780818|r 87 FNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRY-GITISHR---------- 155 (245)
Q Consensus 87 i~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~-~i~~~~r---------- 155 (245)
+...+-+=|-|+++||+.++.+.| |.- +.+++||-..++-.--+.+++|++||+.| ||++++.
T Consensus 66 l~d~~v~KIfHaa~~DL~~l~~~~---g~~---p~plfdTqiAa~l~g~~~~~gl~~Lv~~ll~v~ldK~~q~SDW~~RP 139 (361)
T COG0349 66 LADPNVVKIFHAARFDLEVLLNLF---GLL---PTPLFDTQIAAKLAGFGTSHGLADLVEELLGVELDKSEQRSDWLARP 139 (361)
T ss_pred HCCCCEEEEECCCCCCHHHHHHHC---CCC---CCCHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf 628760255025635199999861---888---77346899999980986323299999999688536444546555579
Q ss_pred ----CCCCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf ----66640269999999999997305766
Q gi|254780818|r 156 ----SKHGALLDSHLLSDVYIKMMVGGSQI 181 (245)
Q Consensus 156 ----~~H~Al~Da~~~a~v~~~ll~g~~q~ 181 (245)
+.--|.+|+..+..+|..|..-..+.
T Consensus 140 Ls~~Ql~YAa~DV~yL~~l~~~L~~~L~~~ 169 (361)
T COG0349 140 LSEAQLEYAAADVEYLLPLYDKLTEELARE 169 (361)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 999999999999999999999999999874
No 88
>cd05777 DNA_polB_delta_exo 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 residues necessary for metal binding and catalysis. The exonuclease domain of family B polyme
Probab=98.33 E-value=9e-06 Score=56.05 Aligned_cols=98 Identities=18% Similarity=0.244 Sum_probs=59.0
Q ss_pred CCCEEEEECCCC---CC--CCCCCEEEEEEEEEEECCEEC--CCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCH
Q ss_conf 775899984678---88--888888999999999999880--31379898588822886572420210123224852100
Q gi|254780818|r 6 KMRKIVFDIETT---GL--DSKNDRIIEIGAVELLDYSKT--NRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSS 78 (245)
Q Consensus 6 ~mr~iv~D~ETT---Gl--~~~~d~Iieigav~i~~~~~~--~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~e 78 (245)
.+|.+.||+||. |. +|+.|.|++|+++...++... .+..-+ ++|. .+++. ..+.-..+-.+
T Consensus 6 plki~sfDIE~~s~~g~fP~p~~D~Ii~I~~~~~~~~~~~~~~~~v~~-l~~~-~~i~~----------~~V~~~~tE~e 73 (230)
T cd05777 6 PLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFT-LKTC-APIVG----------AQVFSFETEEE 73 (230)
T ss_pred CCEEEEEEEEECCCCCCCCCCCCCCEEEEEEEEEECCCCCCEEEEEEE-ECCC-CCCCC----------CEEEECCCHHH
T ss_conf 804999999952699999898888348999999827977604787898-2687-88899----------87998499999
Q ss_pred HHHHHHHHHHCCC-CEEEEECC-CCCCCEEEECHHCCCC
Q ss_conf 2344777530023-20231023-2243112100000112
Q gi|254780818|r 79 IFSEFWDFFNEQN-AEWIAHNA-KFDVGFINAELQRINK 115 (245)
Q Consensus 79 v~~~f~~fi~~~~-~~lVaHNa-~FD~~fL~~el~r~~~ 115 (245)
.+..|.+++...+ .+++|+|. .||+++|..-...++.
T Consensus 74 LL~~F~~~i~~~dPDiitGyN~~~FD~pYL~~Ra~~l~~ 112 (230)
T cd05777 74 LLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKL 112 (230)
T ss_pred HHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCC
T ss_conf 999999999980999999636667887899999999688
No 89
>PRK08786 consensus
Probab=98.32 E-value=5.3e-07 Score=63.72 Aligned_cols=142 Identities=20% Similarity=0.285 Sum_probs=86.0
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 58999846788888888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
..++||+||||++|....++.|+.. .. .+..| |+ |-+...+ |. +..+ ...+++..+..++
T Consensus 349 ~~~afdtET~sld~~~a~lVGiS~s-~~----~g~a~--Yi-P~~h~~~-------g~-~~ql----d~~~~l~~LkplL 408 (927)
T PRK08786 349 GQFAFDTETDSLDPLQADLIGLSVA-AE----PGQAA--YL-PFGHDFP-------GA-PVQL----DRTQALAQLAPLL 408 (927)
T ss_pred CEEEEEEECCCCCHHHHHHHCEEEE-CC----CCCEE--EE-ECCCCCC-------CC-CHHH----HHHHHHHHHHHHH
T ss_conf 8389997238866555312122454-26----78667--75-3244567-------86-0341----3999999989986
Q ss_pred HCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHH-CCCCCC-----------
Q ss_conf 00232023102322431121000001122221000011000000017764-22237899971-875455-----------
Q gi|254780818|r 88 NEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRY-GITISH----------- 154 (245)
Q Consensus 88 ~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~-~i~~~~----------- 154 (245)
.+....-|+||+.||+.+| .++|... ...+.||+..+..+-|+. +++|++|+.+| |.+...
T Consensus 409 ed~~I~KIghnlK~Dl~vL----~~~GI~l--~g~~~DTmLAaYLL~p~~~~~~Ld~La~~yLg~~~~~~~~l~gkg~k~ 482 (927)
T PRK08786 409 TDPAVRKVGQHGKYDLHVM----RRHGIAL--AGYADDTLLESFVLNSGSARHDMDSLAKRYLGYDTVKYEDVCGKGAKQ 482 (927)
T ss_pred CCCCCCHHHHHHHHHHHHH----HHCCCCC--CCCCCCHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCHHHHCCCCCCC
T ss_conf 0865112321178889999----9679711--676642588886237764547889999996697754267542443222
Q ss_pred ---------CCCCCCHHHHHHHHHHHHHHH
Q ss_conf ---------566640269999999999997
Q gi|254780818|r 155 ---------RSKHGALLDSHLLSDVYIKMM 175 (245)
Q Consensus 155 ---------r~~H~Al~Da~~~a~v~~~ll 175 (245)
....-|..||.+|.++|..|.
T Consensus 483 ~~~~~v~~~~~~~Ya~eda~~tl~L~~~l~ 512 (927)
T PRK08786 483 IPFAQVSLEDATRYAAEDADITLRLHCVLG 512 (927)
T ss_pred CCHHHCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 883332599999999999999999999999
No 90
>cd06147 Rrp6p_like_exo 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=98.32 E-value=1.9e-06 Score=60.23 Aligned_cols=131 Identities=18% Similarity=0.210 Sum_probs=82.4
Q ss_pred CCCEEEEECCCCCCCCCCCE--EEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHH
Q ss_conf 77589998467888888888--9999999999998803137989858882288657242021012322485210023447
Q gi|254780818|r 6 KMRKIVFDIETTGLDSKNDR--IIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEF 83 (245)
Q Consensus 6 ~mr~iv~D~ETTGl~~~~d~--Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f 83 (245)
+...|.+|||++|.+...++ +|||+. .+ ..| +|.|- .+. +.++.+
T Consensus 23 ~~~~ialDtE~~~~~~~~~~l~LiQiat---~~-----~~y--liD~l--~l~---------------------~~~~~L 69 (192)
T cd06147 23 NCKEIAVDLEHHSYRSYLGFTCLMQIST---RE-----EDY--IVDTL--KLR---------------------DDMHIL 69 (192)
T ss_pred CCCEEEEECCCCCCCCCCCEEEEEEEEC---CC-----CCE--EEEEC--CCC---------------------CCHHHH
T ss_conf 6996999797378856998279999950---99-----887--98743--430---------------------037999
Q ss_pred HHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHH-HCCCCCC--------
Q ss_conf 7753002320231023224311210000011222210000110000000177642223789997-1875455--------
Q gi|254780818|r 84 WDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKR-YGITISH-------- 154 (245)
Q Consensus 84 ~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~-~~i~~~~-------- 154 (245)
...+...+-.-|+|++.||+.+|.+. .|.. ...++||...++..- ..+.+|.+|++. +|++++.
T Consensus 70 ~~ll~~~~I~KV~H~~~~Dl~~L~~~---~gi~---~~n~fDT~iaa~~l~-~~~~sL~~Lv~~~lg~~l~K~~q~SdW~ 142 (192)
T cd06147 70 NEVFTDPNILKVFHGADSDIIWLQRD---FGLY---VVNLFDTGQAARVLN-LPRHSLAYLLQKYCNVDADKKYQLADWR 142 (192)
T ss_pred HHHHCCCCEEEEEECHHHHHHHHHHH---HCCC---CCCCHHHHHHHHHHC-CCCHHHHHHHHHHHCCCCCCCCEECCCC
T ss_conf 99975988379985578779999998---5898---766042899999848-8811199999999395887323114379
Q ss_pred ------CCCCCCHHHHHHHHHHHHHHHH
Q ss_conf ------5666402699999999999973
Q gi|254780818|r 155 ------RSKHGALLDSHLLSDVYIKMMV 176 (245)
Q Consensus 155 ------r~~H~Al~Da~~~a~v~~~ll~ 176 (245)
.+-+-|..|+..+-.+|..|..
T Consensus 143 ~RPLs~~Ql~YAA~Dv~~Ll~ly~~L~~ 170 (192)
T cd06147 143 IRPLPEEMIKYAREDTHYLLYIYDRLRN 170 (192)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9989999999999999999999999999
No 91
>cd06129 RNaseD_like 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-associated proteins involved in the degradation and processing of prec
Probab=98.32 E-value=2.2e-06 Score=59.89 Aligned_cols=125 Identities=18% Similarity=0.214 Sum_probs=77.5
Q ss_pred EEEEECCCCCCCCCCCE--EEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 89998467888888888--9999999999998803137989858882288657242021012322485210023447775
Q gi|254780818|r 9 KIVFDIETTGLDSKNDR--IIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDF 86 (245)
Q Consensus 9 ~iv~D~ETTGl~~~~d~--Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~f 86 (245)
.|.||||++|+....++ +|||+. .+ . ..++.+.. ++. +.+.+.+ +
T Consensus 17 vig~DtE~~~~~~~~~~v~LiQlat---~~-----~--~~lid~~~--~~~------------------~~~~L~~---l 63 (159)
T cd06129 17 VVALDCEWIPLRLYYGEVTLIQIGT---TE-----H--AFLFDVLS--LSA------------------FDGGLKT---V 63 (159)
T ss_pred EEEEECCCCCCCCCCCCEEEEEEEE---CC-----E--EEEEECCC--CCC------------------CHHHHHH---H
T ss_conf 8999797689879989789999945---99-----6--89995488--876------------------7799999---9
Q ss_pred HHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCC-CCCCCCCHHHHHHHH-CCCCCC----------
Q ss_conf 30023202310232243112100000112222100001100000001-776422237899971-875455----------
Q gi|254780818|r 87 FNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRK-HPSSRNDLNSLCKRY-GITISH---------- 154 (245)
Q Consensus 87 i~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~-~p~~~~~L~~l~~~~-~i~~~~---------- 154 (245)
+...+.+-|+|++.+|...|.+ .+|.. ...++||...++.. +|..+.+|.++|++| |+.++.
T Consensus 64 L~~~~i~Kvgh~~~~D~~~L~~---~~g~~---~~~~~Dt~~~~~~l~~~~~~~sL~~l~~~~lg~~ldK~~q~SnW~~r 137 (159)
T cd06129 64 LENPSITKVGHGCRGDLAKLLR---DFGIL---LRNLFDTQAAHAILGYPEEYWSLNSLVEQYLGPCLDKSRQLSDWAKR 137 (159)
T ss_pred HHCCCCEEEEECHHHHHHHHHH---HCCCC---CCCCHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf 8299924999566999999967---50843---24303699999995888431659999999808787710245888999
Q ss_pred ----CCCCCCHHHHHHHHHHHH
Q ss_conf ----566640269999999999
Q gi|254780818|r 155 ----RSKHGALLDSHLLSDVYI 172 (245)
Q Consensus 155 ----r~~H~Al~Da~~~a~v~~ 172 (245)
++-+-|..||.++-++|+
T Consensus 138 pLt~~Qi~YAA~Da~~ll~lyl 159 (159)
T cd06129 138 PLTEEQMLYAAADVYVLLHIYL 159 (159)
T ss_pred CCCHHHHHHHHHHHHHHHHHHC
T ss_conf 9999999999999999999769
No 92
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=98.30 E-value=1.3e-06 Score=61.30 Aligned_cols=156 Identities=19% Similarity=0.221 Sum_probs=91.7
Q ss_pred CCEEEEECCCCCC------CCCCCEEEEEEEEEEECCEE--CCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCH
Q ss_conf 7589998467888------88888899999999999988--031379898588822886572420210123224852100
Q gi|254780818|r 7 MRKIVFDIETTGL------DSKNDRIIEIGAVELLDYSK--TNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSS 78 (245)
Q Consensus 7 mr~iv~D~ETTGl------~~~~d~Iieigav~i~~~~~--~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~e 78 (245)
.|.+.||+|..|. +|..|.||||++|...-+.. ..+..-..++. .-+|+ ...|..-|+-.+
T Consensus 290 lrilSfDIEC~~~~G~gFP~~~~DpVIqIs~~~~~~g~~~~~~~~~~ftl~~-C~~I~----------g~~V~~F~tE~e 358 (1081)
T PTZ00166 290 IRILSFDIECIKLDGKGFPEANNDPVIQISSVLHTHGDPLDSCKNFIFTLKE-CASLA----------GANVLWFDNEKT 358 (1081)
T ss_pred CEEEEEEEEECCCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCEEEECCC-CCCCC----------CCEEEEECCHHH
T ss_conf 1699986784588899898999995799857988147888764644667478-77889----------977997099999
Q ss_pred HHHHHHHHHHCCC-CEEEEECC-CCCCCEEEECHHCCCCCC-------------------------------CC-CCH-H
Q ss_conf 2344777530023-20231023-224311210000011222-------------------------------21-000-0
Q gi|254780818|r 79 IFSEFWDFFNEQN-AEWIAHNA-KFDVGFINAELQRINKDP-------------------------------LD-PSR-I 123 (245)
Q Consensus 79 v~~~f~~fi~~~~-~~lVaHNa-~FD~~fL~~el~r~~~~~-------------------------------~~-~~~-~ 123 (245)
.+..|.+|+..-| .+++|||+ .||+.+|-.-...++.+. +. ..+ .
T Consensus 359 LL~aF~~fi~~~DPDIITGYNI~nFDlpYLl~Ra~~L~i~~f~~lgRlk~~~~~~~~~~~~s~a~G~~~~k~i~i~GRv~ 438 (1081)
T PTZ00166 359 LLLAWNDFIIAVDPDFLTGYNIINFDLPYLLNRATALNLKKFKFLTRIKSVKSTVKDSIFSSNQFGTHENKEINIEGRIL 438 (1081)
T ss_pred HHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCEEEEECCEEE
T ss_conf 99999999987099899966878888899999999958864332361157765220265665555666550686757899
Q ss_pred CCCHHCCCCCCCCCCCCHHHHHHHH-CCCCCCCCCCC-------------------CHHHHHHHHHHHHHH
Q ss_conf 1100000001776422237899971-87545556664-------------------026999999999999
Q gi|254780818|r 124 IDTLSIARRKHPSSRNDLNSLCKRY-GITISHRSKHG-------------------ALLDSHLLSDVYIKM 174 (245)
Q Consensus 124 iDTl~lar~~~p~~~~~L~~l~~~~-~i~~~~r~~H~-------------------Al~Da~~~a~v~~~l 174 (245)
+|.+.+.++.+.-.+++|+++|.+| |-.... -.|. .+-||.+.-+++.+|
T Consensus 439 ~Dl~~~v~r~~kL~SYkLntVs~~fLgeqKeD-V~~~~I~~l~~~~~e~r~rla~YClkDa~L~lrL~~KL 508 (1081)
T PTZ00166 439 FDVYDLIRRDYKLKSYSLNYVSFEFLKEQKED-VHYSTINKLQNGNPEDRKRIASYCLKDSILPLRLIDKL 508 (1081)
T ss_pred EEHHHHHHHHCCCCCCCHHHHHHHHHCCCCCC-CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 64699998755878576888999981887533-79999999981493788999999899899999999999
No 93
>pfam04857 CAF1 CAF1 family ribonuclease. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localizes to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom#resolution.
Probab=98.23 E-value=2.3e-06 Score=59.74 Aligned_cols=166 Identities=20% Similarity=0.261 Sum_probs=92.5
Q ss_pred CCEEEEECCCCCCCCC-----C--------------C--EEEEEEEEEEE-CCEECC--CE--EEEE-ECCCCCCCCHHH
Q ss_conf 7589998467888888-----8--------------8--89999999999-998803--13--7989-858882288657
Q gi|254780818|r 7 MRKIVFDIETTGLDSK-----N--------------D--RIIEIGAVELL-DYSKTN--RT--FQVF-LCPNGRKNSPEA 59 (245)
Q Consensus 7 mr~iv~D~ETTGl~~~-----~--------------d--~Iieigav~i~-~~~~~~--~~--f~~~-i~P~~~~i~~~~ 59 (245)
-.+|.+|||=+|+-.+ . | .|||+|.--.. ++.... .+ |..+ -++......+++
T Consensus 22 ~~fVaiDtEFpG~v~~p~~~~~~t~~~~Y~~lk~nVd~l~iiQlGlt~~~~~g~~p~~~~~wqfNf~~F~~~~d~~~~~S 101 (235)
T pfam04857 22 YDFIAIDTEFPGVVARPIGSFRSTSDYRYQALRKNVDRLKIIQLGLTLFDEKGNLPDSYYTWQFNFSLFNLEEDFYAPSS 101 (235)
T ss_pred CCEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCCCHHH
T ss_conf 99899951427524689888889878999999843001231468988874688789874378501556797322116889
Q ss_pred E---EECCCCCCCC-CCCCC---CCHHHHHHHH-HHHCCCCEEEEECCCCCCCEEEECHHCCCCCC----------CCCC
Q ss_conf 2---4202101232-24852---1002344777-53002320231023224311210000011222----------2100
Q gi|254780818|r 60 L---KLHGITDEFL-KDKPS---FSSIFSEFWD-FFNEQNAEWIAHNAKFDVGFINAELQRINKDP----------LDPS 121 (245)
Q Consensus 60 ~---~ihGIt~~~l-~~~p~---f~ev~~~f~~-fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~----------~~~~ 121 (245)
+ +-+||.=..+ +.+-+ |.+.+-. .. +....+.++|+||..+|+++|-.-|.--.+|. ....
T Consensus 102 i~fL~~~G~DF~~~~~~GI~~~~f~e~l~~-S~lv~~~~~~~wv~f~g~yD~~yl~k~l~g~~LP~~~~eF~~~l~~~FP 180 (235)
T pfam04857 102 IEFLAKQGFDFNKHRREGIPYLRFAELLGS-SGLFLNISSVTWVTFHGLYDFGYLLKLLTGGPLPETLDDFLELLRELFP 180 (235)
T ss_pred HHHHHHCCCCHHHHHHHCCCHHHHHHHHHH-HHHEECCCCCEEEEECCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCC
T ss_conf 999998598889998709998999989987-0302057998799817277899999997499899989999999999777
Q ss_pred HHCCCHHCCCCCC---CCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 0011000000017---764222378999718754555666402699999999999
Q gi|254780818|r 122 RIIDTLSIARRKH---PSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIK 173 (245)
Q Consensus 122 ~~iDTl~lar~~~---p~~~~~L~~l~~~~~i~~~~r~~H~Al~Da~~~a~v~~~ 173 (245)
.++||--+++... .+.+.+|+.+++.+|++..-...|.|-+|+.+|+.||.+
T Consensus 181 ~vyD~K~la~~~~~~~~~~~~gL~~lA~~L~v~r~~g~~HqAGsDSllT~~~F~k 235 (235)
T pfam04857 181 RVYDTKYLAKFCFELDGGSNGGLQELADLLGVNRRVGRLHQAGSDSLLTALVFFK 235 (235)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHC
T ss_conf 1750999998522135875578999999749978889866655299999987619
No 94
>pfam03104 DNA_pol_B_exo DNA polymerase family B, exonuclease domain. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold.
Probab=98.22 E-value=3e-06 Score=59.04 Aligned_cols=101 Identities=20% Similarity=0.229 Sum_probs=62.5
Q ss_pred CCCCEEEEECCCCCC-----CCCCCEEEEEEEEEEECCEECC-CEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCH
Q ss_conf 777589998467888-----8888889999999999998803-1379898588822886572420210123224852100
Q gi|254780818|r 5 NKMRKIVFDIETTGL-----DSKNDRIIEIGAVELLDYSKTN-RTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSS 78 (245)
Q Consensus 5 ~~mr~iv~D~ETTGl-----~~~~d~Iieigav~i~~~~~~~-~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~e 78 (245)
--+|...||+||+|. ++..|.||+||++.-..+.... ..+...+++. -+++. .-.+..-++-.+
T Consensus 84 pplrilsfDIEc~~~~g~FP~~~~d~IiqIs~~~~~~g~~~~~~~~~~tl~~~-~~i~~---------~~~V~~f~~E~~ 153 (254)
T pfam03104 84 PPLRVLSFDIECTSLKGKFPENEKDPIIQISCMLYREGEPDPIEDKLFTLKSC-ALIEI---------GGEVYIFPSEKE 153 (254)
T ss_pred CCCEEEEEEEEECCCCCCCCCCCCCEEEEEEEEEEECCCCCCCCEEEEEECCC-CCCCC---------CCEEEEECCHHH
T ss_conf 88539999889588899999878983899998988567898632069980787-76778---------977999599999
Q ss_pred HHHHHHHHHHCCC-CEEEEECC-CCCCCEEEECHHCCCC
Q ss_conf 2344777530023-20231023-2243112100000112
Q gi|254780818|r 79 IFSEFWDFFNEQN-AEWIAHNA-KFDVGFINAELQRINK 115 (245)
Q Consensus 79 v~~~f~~fi~~~~-~~lVaHNa-~FD~~fL~~el~r~~~ 115 (245)
.+..|.+|+...+ .+++|||. .||+.+|-.-...++.
T Consensus 154 ll~~f~~~i~~~dpdii~gyNi~~FD~~yl~~Ra~~l~~ 192 (254)
T pfam03104 154 LLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKILGL 192 (254)
T ss_pred HHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCC
T ss_conf 999999998751998999667877888999999999689
No 95
>cd05780 DNA_polB_Kod1_like_exo 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 similarity to eukaryotic DNA polymerases involved in DNA replication. Some archaea possess multiple family-B D
Probab=98.14 E-value=5.8e-06 Score=57.21 Aligned_cols=122 Identities=17% Similarity=0.253 Sum_probs=71.0
Q ss_pred CCEEEEECCCC---CC-CCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHH
Q ss_conf 75899984678---88-888888999999999999880313798985888228865724202101232248521002344
Q gi|254780818|r 7 MRKIVFDIETT---GL-DSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSE 82 (245)
Q Consensus 7 mr~iv~D~ETT---Gl-~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~ 82 (245)
.|...||+||. |+ +|..|.||+|++. ..+. ....+. ++ .+. ..+..-.+-.+.+..
T Consensus 3 lkilsfDIE~~~~~g~P~p~~d~Ii~Is~~-~~~~----~~vi~~-~~----~~~----------~~v~~~~tE~eLL~~ 62 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFA-DEGG----NKVITW-KK----FDL----------PFVEVVKTEKEMIKR 62 (195)
T ss_pred CCEEEEEEEECCCCCCCCCCCCCEEEEEEE-ECCC----CEEEEE-CC----CCC----------CCEEEECCHHHHHHH
T ss_conf 429999999758999989888828999999-6899----789981-79----887----------745673899999999
Q ss_pred HHHHHHCCC-CEEEEECC-CCCCCEEEECHHCCCCCCC---------------------CCCHHCCCHHCCCCCCCCCCC
Q ss_conf 777530023-20231023-2243112100000112222---------------------100001100000001776422
Q gi|254780818|r 83 FWDFFNEQN-AEWIAHNA-KFDVGFINAELQRINKDPL---------------------DPSRIIDTLSIARRKHPSSRN 139 (245)
Q Consensus 83 f~~fi~~~~-~~lVaHNa-~FD~~fL~~el~r~~~~~~---------------------~~~~~iDTl~lar~~~p~~~~ 139 (245)
|.+++...+ .+++|||. .||+++|..-+.++|.+.. ..--++|.+.+.|+.+.-.++
T Consensus 63 F~~~i~~~dPDii~GyN~~~FD~pYl~~R~~~~~~~~~~gr~~~~~~~~~~g~~~~~~i~Gr~~lD~~~~~~~~~~l~sy 142 (195)
T cd05780 63 FIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLNLTRY 142 (195)
T ss_pred HHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCEEEEECCEEEEEHHHHHHHHCCCCCC
T ss_conf 99999872999999579878768999999999589864578886047997785079987686885549999752562401
Q ss_pred CHHHHHHHH
Q ss_conf 237899971
Q gi|254780818|r 140 DLNSLCKRY 148 (245)
Q Consensus 140 ~L~~l~~~~ 148 (245)
+|+++++++
T Consensus 143 ~L~~Va~~~ 151 (195)
T cd05780 143 TLERVYEEL 151 (195)
T ss_pred CHHHHHHHH
T ss_conf 599999998
No 96
>PRK05762 DNA polymerase II; Reviewed
Probab=97.91 E-value=3.4e-05 Score=52.47 Aligned_cols=145 Identities=18% Similarity=0.282 Sum_probs=85.2
Q ss_pred CCCEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 77589998467888888888999999999999880313798985888228865724202101232248521002344777
Q gi|254780818|r 6 KMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWD 85 (245)
Q Consensus 6 ~mr~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~ 85 (245)
..|.+.||+||+ ..+.|++||... .+.. ..|. +.+ +.+ ...+...++-.+.+..|.+
T Consensus 154 ~lrvlSfDIEc~----~~g~ii~I~l~~-~~~~---~v~~--~g~---~~~----------~~~v~~~~~E~eLL~~F~~ 210 (785)
T PRK05762 154 PLKVVSLDIETS----NKGELYSIGLEG-CGQR---QVYM--LGE---ANG----------DAELEYVADEKALLERFNA 210 (785)
T ss_pred CCEEEEEEEEEC----CCCCEEEEEECC-CCCC---EEEE--ECC---CCC----------CCEEEEECCHHHHHHHHHH
T ss_conf 886999998977----999889999517-9984---6899--668---899----------8538990999999999999
Q ss_pred HHHCCC-CEEEEECC-CCCCCEEEECHHCCCCCC------------------------CCCCHHCCCHHCCCCC-CCCCC
Q ss_conf 530023-20231023-224311210000011222------------------------2100001100000001-77642
Q gi|254780818|r 86 FFNEQN-AEWIAHNA-KFDVGFINAELQRINKDP------------------------LDPSRIIDTLSIARRK-HPSSR 138 (245)
Q Consensus 86 fi~~~~-~~lVaHNa-~FD~~fL~~el~r~~~~~------------------------~~~~~~iDTl~lar~~-~p~~~ 138 (245)
|+...| .+++|||+ .||+.+|..-..++|.+. ++.--++|++.+.|.. +.-.+
T Consensus 211 ~i~~~DPDII~GyNi~~FDlpyL~~Ra~~~gi~l~lgR~~~~~~~~~~~~~~~~~~~~i~GRv~iD~~~~~k~~~~~l~s 290 (785)
T PRK05762 211 WFAEFDPDVIIGWNVVQFDLRLLQERAERYGIPLRLGRGGSELSWRVHGHKRGHFFASVPGRLVLDGIDALKSAFYEFKS 290 (785)
T ss_pred HHHHHCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCEEEEEEEEEEEEEEHHHHHHHHHCCCC
T ss_conf 99985999899627478777999999999499854687888653331565566059998428999709999875203676
Q ss_pred CCHHHHHHHH-CC----CCC-CC--------------CCCCCHHHHHHHHHHHHH
Q ss_conf 2237899971-87----545-55--------------666402699999999999
Q gi|254780818|r 139 NDLNSLCKRY-GI----TIS-HR--------------SKHGALLDSHLLSDVYIK 173 (245)
Q Consensus 139 ~~L~~l~~~~-~i----~~~-~r--------------~~H~Al~Da~~~a~v~~~ 173 (245)
++|+++++.+ |- ... .| -+.-.+-||.++.++|.+
T Consensus 291 YsL~~Va~~~Lge~K~~~~~~~r~~eI~~~~~~~r~~l~~Y~l~Da~L~~~L~~k 345 (785)
T PRK05762 291 FSLENVAQELLGEGKAIDNPYDRMDEIDRYFADDKPALAKYNLKDCELVTRIFEK 345 (785)
T ss_pred CCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 6299999998544555566666688889988546899999999999999999998
No 97
>PRK07898 consensus
Probab=97.91 E-value=7.7e-05 Score=50.20 Aligned_cols=132 Identities=14% Similarity=0.141 Sum_probs=82.2
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 58999846788888888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
..+.+|+|||+++. ..+++.++.. ..+ ++ ..|+.+. ...+.. ...+..|+
T Consensus 338 ~~~a~~~~~t~~~~-~a~lvgisl~-~~~----g~--a~yip~~--~~~~~~--------------------~~~L~~~L 387 (902)
T PRK07898 338 RRLGLAVVGTHLPG-DGDATALAIA-AAD----GH--AAYIDTA--DLTPDD--------------------EAALAAWL 387 (902)
T ss_pred CEEEEEEECCCCCC-CCCEEEEEEE-EEC----CE--EEEECCC--CCCHHH--------------------HHHHHHHH
T ss_conf 86999985367866-5738999999-538----80--8997220--179789--------------------99999986
Q ss_pred HCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHH-CCCCCC-----------
Q ss_conf 00232023102322431121000001122221000011000000017764-22237899971-875455-----------
Q gi|254780818|r 88 NEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRY-GITISH----------- 154 (245)
Q Consensus 88 ~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~-~i~~~~----------- 154 (245)
...+...++||+.||+.+| .+.|... .....||+..|-.+-|+. +++|++|+.+| |.....
T Consensus 388 ed~~i~KIghNlK~d~~vL----~~~Gi~l--~g~~fDTmLAaYLLdp~~~~~~Ld~La~~yL~~~~~~~~~~~~~~~~~ 461 (902)
T PRK07898 388 ADPARPKALHEAKGAMHAL----AGRGWTL--AGVTSDTALAAYLVRPGQRSFTLDDLSLRYLRRELRAEAPAQQQLSLD 461 (902)
T ss_pred HCCCCCEEEECHHHHHHHH----HHCCCCC--CCCCHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCC
T ss_conf 0877654554048999999----9669865--775322899998756887878799999997497665156535434713
Q ss_pred -----CCCCCCHHHHHHHHHHHHHHH
Q ss_conf -----566640269999999999997
Q gi|254780818|r 155 -----RSKHGALLDSHLLSDVYIKMM 175 (245)
Q Consensus 155 -----r~~H~Al~Da~~~a~v~~~ll 175 (245)
....-|..||.++.++|..+.
T Consensus 462 ~~~~~~~~~yaa~dA~~~~~L~~~l~ 487 (902)
T PRK07898 462 DAVDAAAAQTLILRARAVLDLADALD 487 (902)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 26768999999999999999999999
No 98
>cd05776 DNA_polB_alpha_exo 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 crucial for metal binding and catalysis. This explains why in most organisms, that no specific repair r
Probab=97.84 E-value=4.4e-05 Score=51.74 Aligned_cols=139 Identities=18% Similarity=0.246 Sum_probs=81.3
Q ss_pred EEEEECCCCCCCCCC--CEEEEEEEEEEECCE---EC-----CCEEEEEECCCCCCCCHHHEE-ECCCCCCCCCCCCCCC
Q ss_conf 899984678888888--889999999999998---80-----313798985888228865724-2021012322485210
Q gi|254780818|r 9 KIVFDIETTGLDSKN--DRIIEIGAVELLDYS---KT-----NRTFQVFLCPNGRKNSPEALK-LHGITDEFLKDKPSFS 77 (245)
Q Consensus 9 ~iv~D~ETTGl~~~~--d~Iieigav~i~~~~---~~-----~~~f~~~i~P~~~~i~~~~~~-ihGIt~~~l~~~p~f~ 77 (245)
...+.+.|. +|++. ++|+.|+++...+-. .+ ...+.+.++|.+...|+.... .-.....-+.-.++-.
T Consensus 5 v~Sisi~T~-~n~k~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~v~~f~sEr 83 (234)
T cd05776 5 VMSLSIKTV-LNSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKVRIFENER 83 (234)
T ss_pred EEEEEEEEE-ECCCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHCCCCCEEECCCHH
T ss_conf 999998997-1688885438898851416847789999754566089998489987997569999862698489848899
Q ss_pred HHHHHHHHHHHCCC-CEEEEECC-CCCCCEEEECHHCCCCCCC-------------------------CCCH-HCCCHHC
Q ss_conf 02344777530023-20231023-2243112100000112222-------------------------1000-0110000
Q gi|254780818|r 78 SIFSEFWDFFNEQN-AEWIAHNA-KFDVGFINAELQRINKDPL-------------------------DPSR-IIDTLSI 129 (245)
Q Consensus 78 ev~~~f~~fi~~~~-~~lVaHNa-~FD~~fL~~el~r~~~~~~-------------------------~~~~-~iDTl~l 129 (245)
+.+..|++++..-| .++||||. +||+.+|-.-+..++.+-+ ...+ ++|+...
T Consensus 84 ~LL~~f~~~i~~~DPDii~Ghni~~fdl~~L~~R~~~lki~~wsriGRlkr~~~p~~~~~~~~~~~~~~~GRl~~D~~~~ 163 (234)
T cd05776 84 ALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYLS 163 (234)
T ss_pred HHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCEEEEECHHH
T ss_conf 99999999998509989985063777599999999980998533135500143764456565344203523588760999
Q ss_pred CCCCCCCCCCCHHHHHHHH
Q ss_conf 0001776422237899971
Q gi|254780818|r 130 ARRKHPSSRNDLNSLCKRY 148 (245)
Q Consensus 130 ar~~~p~~~~~L~~l~~~~ 148 (245)
+|..+.-.+++|+++|..+
T Consensus 164 ~ke~~k~~sy~L~~v~~~~ 182 (234)
T cd05776 164 AKELIRCKSYDLTELSQQV 182 (234)
T ss_pred HHHHHCCCCCCHHHHHHHH
T ss_conf 9987466778889999999
No 99
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=97.82 E-value=7.1e-05 Score=50.43 Aligned_cols=132 Identities=20% Similarity=0.353 Sum_probs=83.4
Q ss_pred EEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 89998467888888888999999999999880313798985888228865724202101232248521002344777530
Q gi|254780818|r 9 KIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFN 88 (245)
Q Consensus 9 ~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi~ 88 (245)
.+.+|+||+|+++....++.++.. ... + ..|| |-. |+ |..-++...+..|+.
T Consensus 24 ~~a~~~et~~l~~~~~~lvg~s~~-~~~-----~--~~yi-~~~----------~~---------~~~~~~~~~l~~~l~ 75 (593)
T COG0749 24 NIAFDTETDGLDPHGADLVGLSVA-SEE-----E--AAYI-PLL----------HG---------PEQLNVLAALKPLLE 75 (593)
T ss_pred CCCEECCCCCCCCCCCCEEEEEEE-CCC-----C--CEEE-EEC----------CC---------HHHHHHHHHHHHHHH
T ss_conf 310100014567555874678862-365-----4--2367-513----------66---------555514899999863
Q ss_pred CCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHHC-CCCCCC-----------
Q ss_conf 0232023102322431121000001122221000011000000017764-222378999718-754555-----------
Q gi|254780818|r 89 EQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRYG-ITISHR----------- 155 (245)
Q Consensus 89 ~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~~-i~~~~r----------- 155 (245)
..+...|+||+.||+.+| .+.|.. .+...||+..+-.+-|+. +++++.|+.+|. ......
T Consensus 76 ~~~~~kv~~~~K~d~~~l----~~~Gi~---~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~~~ 148 (593)
T COG0749 76 DEGIKKVGQNLKYDYKVL----ANLGIE---PGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQL 148 (593)
T ss_pred CCCCCHHCCCCCHHHHHH----HHCCCC---CCCHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCCCHHHHHHCCCCCCC
T ss_conf 754103213413669999----973976---5651789999961486767577789999825877402487632544567
Q ss_pred ---------CCCCCHHHHHHHHHHHHHHH
Q ss_conf ---------66640269999999999997
Q gi|254780818|r 156 ---------SKHGALLDSHLLSDVYIKMM 175 (245)
Q Consensus 156 ---------~~H~Al~Da~~~a~v~~~ll 175 (245)
..-.|-.||.++.+++..|.
T Consensus 149 ~~~~~~~~~~~~y~a~~a~~~~~L~~~l~ 177 (593)
T COG0749 149 TFADVKLEKATEYAAEDADATLRLESILE 177 (593)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 61001477888878888899999999999
No 100
>cd06146 mut-7_like_exo 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=97.78 E-value=0.00011 Score=49.26 Aligned_cols=89 Identities=18% Similarity=0.225 Sum_probs=58.6
Q ss_pred HHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCC-----------CCCCCHHHHHHH-HCCCCC
Q ss_conf 53002320231023224311210000011222210000110000000177-----------642223789997-187545
Q gi|254780818|r 86 FFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHP-----------SSRNDLNSLCKR-YGITIS 153 (245)
Q Consensus 86 fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p-----------~~~~~L~~l~~~-~~i~~~ 153 (245)
++...+-+.|+|++..|+.+|.+.+...+........++|+..+++.... ....+|.+||+. +|+.++
T Consensus 77 ll~~~~i~Kvg~~~~~D~~~L~~~~~~~~~~~~~~~~~~Dl~~~a~~~~~~~~~~~~~~~~~~~~gL~~L~~~~lg~~l~ 156 (191)
T cd06146 77 LFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQAVLGKPLD 156 (191)
T ss_pred HHCCCCEEEEEECHHHHHHHHHHHCCCCCCCCCCCCEEEEHHHHHHHHHCCCCCCHHHCCCCCCCCHHHHHHHHHCCCCC
T ss_conf 94799968999443868999998658643233364403579999999731122101100355675699999999098788
Q ss_pred C--------------CCCCCCHHHHHHHHHHHHHH
Q ss_conf 5--------------56664026999999999999
Q gi|254780818|r 154 H--------------RSKHGALLDSHLLSDVYIKM 174 (245)
Q Consensus 154 ~--------------r~~H~Al~Da~~~a~v~~~l 174 (245)
. .+-|-|..||.++-++|.+|
T Consensus 157 K~~q~SnW~~rPLt~~Qi~YAA~Da~~ll~iy~~L 191 (191)
T cd06146 157 KSEQCSNWERRPLREEQILYAALDAYCLLEVFDKL 191 (191)
T ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 56513899999899999999999899999999739
No 101
>cd06141 WRN_exo WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=97.72 E-value=7.7e-05 Score=50.22 Aligned_cols=86 Identities=16% Similarity=0.222 Sum_probs=59.2
Q ss_pred HHHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCC-CCCCHHHHHHH-HCCCCCC------
Q ss_conf 777530023202310232243112100000112222100001100000001776-42223789997-1875455------
Q gi|254780818|r 83 FWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPS-SRNDLNSLCKR-YGITISH------ 154 (245)
Q Consensus 83 f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~-~~~~L~~l~~~-~~i~~~~------ 154 (245)
+.+++...+-+-|+|++.+|+.+|.+.+ |.. ...++|+..+++...+. .+.+|.+||.. +|..+..
T Consensus 65 L~~lL~~~~i~Kvg~~~~~D~~~L~~~~---g~~---~~~~~Dl~~~a~~~~~~~~~~sL~~l~~~~lg~~l~K~k~~q~ 138 (168)
T cd06141 65 LKQLLEDPSILKVGVGIKGDARKLRRDF---GIE---VRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKDKKVRC 138 (168)
T ss_pred HHHHHCCCCEEEEEEEEHHHHHHHHHHC---CCC---CCCEEEHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCC
T ss_conf 9999759980799963188999998744---502---4876569999998577777632999999983962154665203
Q ss_pred ----------CCCCCCHHHHHHHHHHHHHH
Q ss_conf ----------56664026999999999999
Q gi|254780818|r 155 ----------RSKHGALLDSHLLSDVYIKM 174 (245)
Q Consensus 155 ----------r~~H~Al~Da~~~a~v~~~l 174 (245)
.+-+-|..||.++.++|.+|
T Consensus 139 SdW~~rpLs~~Qi~YAA~Da~~~~~l~~~L 168 (168)
T cd06141 139 SNWEARPLSKEQILYAATDAYASLELYRKL 168 (168)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 888999999999999999999999999739
No 102
>PRK05929 consensus
Probab=97.70 E-value=0.0002 Score=47.61 Aligned_cols=106 Identities=13% Similarity=0.149 Sum_probs=69.7
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 58999846788888888899999999999988031379898588822886572420210123224852100234477753
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi 87 (245)
..+.||+||||.++...+++-++.. .. ++.| ||.... . ..++...+.+|+
T Consensus 311 ~~~a~~~~~~~~~~~~~~lvGisls---~~---~~a~--yip~~~-~---------------------~~~vl~~Lk~~l 360 (870)
T PRK05929 311 GEVAFCVAYTGNHLPSLKLHGVALA---GG---SQVF--YIEVEE-S---------------------GDQEIALLKDFF 360 (870)
T ss_pred CCEEEEEEECCCCCCCCCEEEEEEE---CC---CEEE--EEECCC-C---------------------CHHHHHHHHHHH
T ss_conf 9747999745887677728899997---69---8089--997655-5---------------------523899999986
Q ss_pred HCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHHHC
Q ss_conf 00232023102322431121000001122221000011000000017764222378999718
Q gi|254780818|r 88 NEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYG 149 (245)
Q Consensus 88 ~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~ 149 (245)
...+...|+||+.||+..| .++|... .....||+..+...-|+.+++++.++..++
T Consensus 361 ed~~i~kig~NlK~d~~vL----~~~GI~l--~g~~fDtmLAsYLLn~~~~~~~~~ll~~~~ 416 (870)
T PRK05929 361 ARKDTTFYGYNLKRDNHAL----KNAGIDV--HEITADLALAEHLVNGGAKISFQTLLVEHG 416 (870)
T ss_pred CCCCCCEEECCHHHHHHHH----HHCCCCC--CCCHHHHHHHHHHHCCCCCCCHHHHHHHCC
T ss_conf 0987745322377799999----9689856--872779999998629999888399997666
No 103
>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=97.68 E-value=0.00027 Score=46.78 Aligned_cols=157 Identities=20% Similarity=0.268 Sum_probs=88.1
Q ss_pred CCEEEEECCCCCC-----CCC--CCEEEEEEEEEEECCEECCCEEEE-EECCCCCCCCHHHEEECCCCCCCCCCCCCCCH
Q ss_conf 7589998467888-----888--888999999999999880313798-98588822886572420210123224852100
Q gi|254780818|r 7 MRKIVFDIETTGL-----DSK--NDRIIEIGAVELLDYSKTNRTFQV-FLCPNGRKNSPEALKLHGITDEFLKDKPSFSS 78 (245)
Q Consensus 7 mr~iv~D~ETTGl-----~~~--~d~Iieigav~i~~~~~~~~~f~~-~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~e 78 (245)
.+.+.||+||+.- +|. .|.|++|+++.-.+.......-.. .+.|. .++ .|+. +..-....+
T Consensus 3 ~~i~s~DIEt~~~~~~~p~~~~~~d~i~~i~~~~~~~~~~~~~~~~~~~~~~~-~~~-------~~~~---~~~~~~E~~ 71 (471)
T smart00486 3 LKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTC-KEI-------DGVE---VYEFNNEKE 71 (471)
T ss_pred CEEEEEEEEECCCCCCCCCCCCCCCEEEEEEEEEEECCEEEEEEEEEECCCCC-CCC-------CCCE---EEECCCHHH
T ss_conf 46999998966799999998889984999999982198787887754303676-778-------9988---998099999
Q ss_pred HHHHHHHHHHCCC-CEEEEECC-CCCCCEEEECHHCCCCCCC--------------------------------CCCHHC
Q ss_conf 2344777530023-20231023-2243112100000112222--------------------------------100001
Q gi|254780818|r 79 IFSEFWDFFNEQN-AEWIAHNA-KFDVGFINAELQRINKDPL--------------------------------DPSRII 124 (245)
Q Consensus 79 v~~~f~~fi~~~~-~~lVaHNa-~FD~~fL~~el~r~~~~~~--------------------------------~~~~~i 124 (245)
.+..|.+++...+ .++++||. .||+.||..-+.+++.... ...-.+
T Consensus 72 ll~~f~~~i~~~dpdii~g~N~~~FD~~yi~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~ 151 (471)
T smart00486 72 LLKAFLEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSKSFGKTIKVKIKGRLVI 151 (471)
T ss_pred HHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCEECCCCCCCCCCCEEEEEEEEEEEE
T ss_conf 99999999987199999965887876899999999848964776373577876432033210125663148998559997
Q ss_pred CCHHCCCCCCCCCCCCHHHHHHHHCCC----CCC---------------CCCCCCHHHHHHHHHHHHHH
Q ss_conf 100000001776422237899971875----455---------------56664026999999999999
Q gi|254780818|r 125 DTLSIARRKHPSSRNDLNSLCKRYGIT----ISH---------------RSKHGALLDSHLLSDVYIKM 174 (245)
Q Consensus 125 DTl~lar~~~p~~~~~L~~l~~~~~i~----~~~---------------r~~H~Al~Da~~~a~v~~~l 174 (245)
|++.+.+..+.-.+++|++.+.++.-. ... +-.+-.+.|+.++.+++..+
T Consensus 152 D~~~~~~~~~~l~sy~L~~v~~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~~ 220 (471)
T smart00486 152 DLYNLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred EHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 889999886044668889999999577888899899999985393679999999999999999999986
No 104
>PRK08076 consensus
Probab=97.61 E-value=0.00018 Score=47.87 Aligned_cols=128 Identities=15% Similarity=0.149 Sum_probs=79.4
Q ss_pred EEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHHHC
Q ss_conf 99984678888888889999999999998803137989858882288657242021012322485210023447775300
Q gi|254780818|r 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNE 89 (245)
Q Consensus 10 iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi~~ 89 (245)
..+|+|||++++....++-|+.. +. ...| || |..... ..+.+..++.+
T Consensus 317 ~a~~~Et~~~~~~~a~lvGis~s---~~---~~a~--yi-P~~~~~-----------------------~~~~lk~~Led 364 (877)
T PRK08076 317 SALVVEVLEDNYHKADIQGFAIV---NE---NGCY--FI-PTEIAL-----------------------KSDAFKEWLED 364 (877)
T ss_pred CEEEEEECCCCCCCCCEEEEEEE---CC---CCEE--EE-CCCHHH-----------------------HHHHHHHHHCC
T ss_conf 54999964788563778999998---58---9459--95-500442-----------------------15899998539
Q ss_pred CCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHHCCC-CCC-------------
Q ss_conf 232023102322431121000001122221000011000000017764-22237899971875-455-------------
Q gi|254780818|r 90 QNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRYGIT-ISH------------- 154 (245)
Q Consensus 90 ~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~~i~-~~~------------- 154 (245)
.....++||+.||+..| .++|... ...++||+..|-..-|+. +++|+.|+.+|... ...
T Consensus 365 ~~i~KighNlK~dl~vL----~~~GI~l--~gi~FDTMLAAYLLdP~~~~~~Ld~La~~yl~~~~~~~e~v~Gkg~k~~~ 438 (877)
T PRK08076 365 EEKKKWVFDAKRAIVAL----KWNGIDL--QGIDFDLLLAAYLLNPADSDDDFASVAKMKETHAVKSDEAVYGKGAKRAV 438 (877)
T ss_pred CCCCEEEECHHHHHHHH----HHCCCCC--CCCCCCHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCHHHHCCCCCCCCC
T ss_conf 76540265479999999----9689644--77640299999871887676669999998557777634765376522248
Q ss_pred ----CCCCCCHHHHHHHHHHHHHHH
Q ss_conf ----566640269999999999997
Q gi|254780818|r 155 ----RSKHGALLDSHLLSDVYIKMM 175 (245)
Q Consensus 155 ----r~~H~Al~Da~~~a~v~~~ll 175 (245)
.-..-|..||.+|.++|..|.
T Consensus 439 p~~~~~~eYaaedA~~t~~L~~~L~ 463 (877)
T PRK08076 439 PEEEILAEHLARKAHAIYDLKQTFV 463 (877)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 7789999999999999999999999
No 105
>cd05778 DNA_polB_zeta_exo 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=97.55 E-value=0.00037 Score=45.93 Aligned_cols=105 Identities=12% Similarity=0.074 Sum_probs=62.5
Q ss_pred CCCCEEEEECCCCC-----CCCCCCEEEEEEEEEEECCEE-CC---CEEEE-EECCCCCCCCHHHEEECCCCCCCCCCCC
Q ss_conf 77758999846788-----888888899999999999988-03---13798-9858882288657242021012322485
Q gi|254780818|r 5 NKMRKIVFDIETTG-----LDSKNDRIIEIGAVELLDYSK-TN---RTFQV-FLCPNGRKNSPEALKLHGITDEFLKDKP 74 (245)
Q Consensus 5 ~~mr~iv~D~ETTG-----l~~~~d~Iieigav~i~~~~~-~~---~~f~~-~i~P~~~~i~~~~~~ihGIt~~~l~~~p 74 (245)
+.||.+.||+|+.+ -||..|.|++|+. .+.+... .+ ..-.. ++.+...+.. ......++....+.--+
T Consensus 2 q~LtiLSfDIe~~sr~~~fPdP~~D~I~~I~~-~~~~~~~~~~~~~~~~g~i~~~~~~~~~~-~~~~~~~~~~~~v~~~~ 79 (231)
T cd05778 2 QHLTILSLEVHVNTRGDLLPDPEFDPISAIFY-CIDDDVSPFILDANKVGVIIVDELKSNAS-NGRIRSGLSGIPVEVVE 79 (231)
T ss_pred CCEEEEEEEEEECCCCCCCCCCCCCCEEEEEE-EECCCCCCCCCCCCCEEEEEECCCCCCHH-HCCCCCCCCCCEEEEEC
T ss_conf 82289999999888899996989785789999-96268765445665200799558654112-10222578996499979
Q ss_pred CCCHHHHHHHHHHHCCC-CEEEEECC-CCCCCEEEECHH
Q ss_conf 21002344777530023-20231023-224311210000
Q gi|254780818|r 75 SFSSIFSEFWDFFNEQN-AEWIAHNA-KFDVGFINAELQ 111 (245)
Q Consensus 75 ~f~ev~~~f~~fi~~~~-~~lVaHNa-~FD~~fL~~el~ 111 (245)
+-.+.+.+|.+|+..-| .+++|+|+ .||+++|-.-.+
T Consensus 80 ~E~eLl~~f~~~v~~~DPDii~Gyni~~fd~~Yl~~Ra~ 118 (231)
T cd05778 80 SELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAA 118 (231)
T ss_pred CHHHHHHHHHHHHHHHCCCEEEECCCCCCCCHHHHHHHH
T ss_conf 999999999999997099989622556686189999999
No 106
>cd06148 Egl_like_exo 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.
Probab=97.55 E-value=0.00063 Score=44.49 Aligned_cols=133 Identities=18% Similarity=0.224 Sum_probs=73.6
Q ss_pred CCEEEEECCCCCCCCCCCE--EEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHH
Q ss_conf 7589998467888888888--99999999999988031379898588822886572420210123224852100234477
Q gi|254780818|r 7 MRKIVFDIETTGLDSKNDR--IIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFW 84 (245)
Q Consensus 7 mr~iv~D~ETTGl~~~~d~--Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~ 84 (245)
.+.|.+|||+++++.. ++ +|||+. . .++.| ++.|- .++. ..|...+..++
T Consensus 10 ~~vi~iD~E~~~~~~~-g~l~LiQiat---~----~~~vy--l~D~~--~~~~----------------~~~~~~Lk~iL 61 (197)
T cd06148 10 QKVIGLDCEGVNLGRK-GKLCLVQIAT---R----TGQIY--LFDIL--KLGS----------------IVFINGLKDIL 61 (197)
T ss_pred CCEEEEECCCCCCCCC-CCEEEEEEEE---C----CCCEE--EEECC--CCCC----------------HHHHHHHHHHH
T ss_conf 9999998886788989-9887999964---8----99889--99616--6763----------------44568999995
Q ss_pred HHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCC--------CCCCCCCCCHHHHHHHH-CCC----
Q ss_conf 75300232023102322431121000001122221000011000000--------01776422237899971-875----
Q gi|254780818|r 85 DFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIAR--------RKHPSSRNDLNSLCKRY-GIT---- 151 (245)
Q Consensus 85 ~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar--------~~~p~~~~~L~~l~~~~-~i~---- 151 (245)
+ ..+-+=|.|++.+|..+|.+. .|.. ..+++||...+. ...|+...+|..||..| ++.
T Consensus 62 e---~~~I~KV~H~~r~D~~~L~~~---~gi~---~~nvfDTqiA~~ll~~~~~~~~~~~~~~sl~~l~~~~l~~~~~~~ 132 (197)
T cd06148 62 E---SKKILKVIHDCRRDSDALYHQ---YGIK---LNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLK 132 (197)
T ss_pred C---CCCCEEEEECHHHHHHHHHHH---HCCC---CCCCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCHHH
T ss_conf 6---998239996109999999997---0997---067031999999975313147677564159999999957640177
Q ss_pred ------------------CCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf ------------------4555666402699999999999973
Q gi|254780818|r 152 ------------------ISHRSKHGALLDSHLLSDVYIKMMV 176 (245)
Q Consensus 152 ------------------~~~r~~H~Al~Da~~~a~v~~~ll~ 176 (245)
++.++-.-|..|+..+-.+|..|+.
T Consensus 133 ~~~~~~~~~~~s~W~~RPLt~~ql~YAa~DV~yL~~L~~~L~~ 175 (197)
T cd06148 133 EDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLD 175 (197)
T ss_pred HHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 8778887506554467999999999999989999999999999
No 107
>pfam10108 Exon_PolB Predicted 3'-5' exonuclease related to the exonuclease domain of PolB. This domain is found in various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=97.48 E-value=0.001 Score=43.22 Aligned_cols=128 Identities=16% Similarity=0.205 Sum_probs=75.5
Q ss_pred CCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEECC-C
Q ss_conf 888899999999999988031379898588822886572420210123224852100234477753002320231023-2
Q gi|254780818|r 22 KNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNA-K 100 (245)
Q Consensus 22 ~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi~~~~~~lVaHNa-~ 100 (245)
--+|||.|+||...+.... + ..++=.| .-.-++++..|.+++......||.+|. .
T Consensus 7 ~lhriVaIs~v~~~~~~~~-~-v~slg~~----------------------~~~E~~ll~~F~~~i~~~~P~LVs~NG~g 62 (211)
T pfam10108 7 PLHRIVAISAVIADDDGGF-K-VWSLGDP----------------------ESSEKELIQRFFDGIEKYTPQLVSFNGRG 62 (211)
T ss_pred CCEEEEEEEEEEEECCCCE-E-EEECCCC----------------------CCCHHHHHHHHHHHHHHCCCEEEEECCCC
T ss_conf 6501699999999669927-9-9878899----------------------98999999999999984398288656865
Q ss_pred CCCCEEEECHHCCCCCCCC------------------CCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCC---
Q ss_conf 2431121000001122221------------------0000110000000177642223789997187545556664---
Q gi|254780818|r 101 FDVGFINAELQRINKDPLD------------------PSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHG--- 159 (245)
Q Consensus 101 FD~~fL~~el~r~~~~~~~------------------~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~r~~H~--- 159 (245)
||+.+|..-.-++|+..+. ..+.+|++..-...-+....+|+.+|.-+|++..- .-|+
T Consensus 63 FDlPvL~~RAl~~gi~ap~~~~~~~~~~kw~nY~~Ry~~~H~DLmd~l~~~g~~~~~~Ld~~a~l~G~PGK~-~~~G~~V 141 (211)
T pfam10108 63 FDLPVLHYRALKHGVSAPRYFDTGDRDFKWNNYFNRYSTRHLDLMDLLSGYGARANAPLDEVAALLGLPGKM-GVDGSQV 141 (211)
T ss_pred CCHHHHHHHHHHCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCHHHHHHHCCCCCCC-CCCHHHH
T ss_conf 548999999998188850787567876654441123565445489998732886778989999981999878-7764589
Q ss_pred ---------------CHHHHHHHHHHHHHH
Q ss_conf ---------------026999999999999
Q gi|254780818|r 160 ---------------ALLDSHLLSDVYIKM 174 (245)
Q Consensus 160 ---------------Al~Da~~~a~v~~~l 174 (245)
...|+.-|--||++.
T Consensus 142 ~~~~~~G~l~~I~~YCe~DvlnTylv~LR~ 171 (211)
T pfam10108 142 WELYQAGKIEEIRDYCETDVLNTYLVYLRF 171 (211)
T ss_pred HHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999985988899999887689999999999
No 108
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=97.39 E-value=0.00074 Score=44.06 Aligned_cols=151 Identities=19% Similarity=0.162 Sum_probs=84.9
Q ss_pred CCCEEEEECCCCCCC-----CCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHH
Q ss_conf 775899984678888-----888889999999999998803137989858882288657242021012322485210023
Q gi|254780818|r 6 KMRKIVFDIETTGLD-----SKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIF 80 (245)
Q Consensus 6 ~mr~iv~D~ETTGl~-----~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~ 80 (245)
.+|.++||+||.+.. +..|-++.|+...-.+.... ..+...+ ..|.. +....+-.+++
T Consensus 153 ~l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~-------~~~~~~~-------~~~~~---v~~~~~e~e~l 215 (792)
T COG0417 153 PLRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLI-------EVFIYTS-------GEGFS---VEVVISEAELL 215 (792)
T ss_pred CCCEEEEEEEECCCCCCCCCCCCCCEEEEEEEECCCCCCC-------CCCCCCC-------CCCCC---EEEECCHHHHH
T ss_conf 8754799503105777889877786269999704677764-------4432235-------67763---48725879999
Q ss_pred HHHHHHHHCCC-CEEEEECCC-CCCCEEEECHHCCCCCCC---------------CC--C-HHCCCHHCCC-CCCCCCCC
Q ss_conf 44777530023-202310232-243112100000112222---------------10--0-0011000000-01776422
Q gi|254780818|r 81 SEFWDFFNEQN-AEWIAHNAK-FDVGFINAELQRINKDPL---------------DP--S-RIIDTLSIAR-RKHPSSRN 139 (245)
Q Consensus 81 ~~f~~fi~~~~-~~lVaHNa~-FD~~fL~~el~r~~~~~~---------------~~--~-~~iDTl~lar-~~~p~~~~ 139 (245)
..|.+++...| .++|+||.. ||+.+|..-..++|.+.. .. . ..+|.....+ +.+.-.++
T Consensus 216 ~~~~~~i~~~dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~~~~~~~~~~y 295 (792)
T COG0417 216 ERFVELIREYDPDVIVGYNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPALRRRPLNLKSY 295 (792)
T ss_pred HHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCEEECCCCCCCCEEEEEHHHHHHHCCCCCCCE
T ss_conf 99999985029899998367777738999999981998511356653200212544557716741066542032355632
Q ss_pred CHHHHHHHHC-CCC-C------------------CCCCCCCHHHHHHHHHHHHH
Q ss_conf 2378999718-754-5------------------55666402699999999999
Q gi|254780818|r 140 DLNSLCKRYG-ITI-S------------------HRSKHGALLDSHLLSDVYIK 173 (245)
Q Consensus 140 ~L~~l~~~~~-i~~-~------------------~r~~H~Al~Da~~~a~v~~~ 173 (245)
+|...+..+. ... . .+.+..-+.|+.++++++..
T Consensus 296 sl~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l~~~~~~~ 349 (792)
T COG0417 296 SLEAVSEALLGEGKREDIPYDSMEEIWPDWADSKLRLLLYNLSDADLVLRILLK 349 (792)
T ss_pred EHHHHHHHHCCCCCHHCCCCCHHHHCCCCCCCCHHHHHHHCCCHHHHHHHHHHH
T ss_conf 434677664133522005620133304235510768888341078899999866
No 109
>cd05784 DNA_polB_II_exo The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (PolII) and similar bacterial proteins. PolII 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. PolII is involved in a variety of cellular activities, such as the repair of DNA damaged by UV irradiation or oxidation. It plays a pivotal role in replication-restart, a process that bypasses DNA damage in a
Probab=97.29 E-value=0.0009 Score=43.52 Aligned_cols=89 Identities=16% Similarity=0.220 Sum_probs=51.9
Q ss_pred CCCEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 77589998467888888888999999999999880313798985888228865724202101232248521002344777
Q gi|254780818|r 6 KMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWD 85 (245)
Q Consensus 6 ~mr~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~ 85 (245)
+.|.+.||+||+ ...+|+.||.. -.+. ...| .+.... .. .|. .+.-..+-.+.+..|++
T Consensus 2 ~lki~s~DIE~~----~~~~i~~I~~~-~~~~---~~v~--~~~~~~-~~-------~~~---~v~~~~sE~eLL~~F~~ 60 (193)
T cd05784 2 KLKVVSLDIETS----MDGELYSIGLY-GEGQ---ERVL--MVGDPE-DD-------APD---NIEWFADEKSLLLALIA 60 (193)
T ss_pred CCEEEEEEECCC----CCCCEEEEEEE-CCCC---CEEE--EEECCC-CC-------CCC---EEEEECCHHHHHHHHHH
T ss_conf 830999996327----98888899998-6999---9899--997898-88-------997---79998999999999999
Q ss_pred HHHCCCC-EEEEECC-CCCCCEEEECHHCCCC
Q ss_conf 5300232-0231023-2243112100000112
Q gi|254780818|r 86 FFNEQNA-EWIAHNA-KFDVGFINAELQRINK 115 (245)
Q Consensus 86 fi~~~~~-~lVaHNa-~FD~~fL~~el~r~~~ 115 (245)
++...+- ++.|||. .||+.+|-.-++++|.
T Consensus 61 ~i~~~dPDiItG~N~~~FDiPYL~~R~~~~~i 92 (193)
T cd05784 61 WFAQYDPDIIIGWNVINFDLRLLQRRAEAHGL 92 (193)
T ss_pred HHHHCCCCEEEECCCCCCCHHHHHHHHHHHCC
T ss_conf 99862999999779877767899999998588
No 110
>KOG1798 consensus
Probab=97.26 E-value=0.0027 Score=40.54 Aligned_cols=156 Identities=18% Similarity=0.259 Sum_probs=86.2
Q ss_pred CCEEEEECCCCCCC-----CCCCEEEEEEEE------EEECCEECCC---EEEEEECCCCCCCCHHHEEECCCCCCCCCC
Q ss_conf 75899984678888-----888889999999------9999988031---379898588822886572420210123224
Q gi|254780818|r 7 MRKIVFDIETTGLD-----SKNDRIIEIGAV------ELLDYSKTNR---TFQVFLCPNGRKNSPEALKLHGITDEFLKD 72 (245)
Q Consensus 7 mr~iv~D~ETTGl~-----~~~d~Iieigav------~i~~~~~~~~---~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~ 72 (245)
-|...||+|||-|+ ...|.|.=|.-. -+.|+.++++ -|+-.-+|+. + .-.. +-+
T Consensus 246 p~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREiVs~DIedfEYTPKpE~-e---G~F~--------v~N 313 (2173)
T KOG1798 246 PRVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREIVSEDIEDFEYTPKPEY-E---GPFC--------VFN 313 (2173)
T ss_pred CEEEEEEEECCCCCCCCCCCCCCEEEEEEEEECCCEEEEECHHHHCCCHHHCCCCCCCCC-C---CCEE--------EEC
T ss_conf 558998510355787799866560789999964746899622343052122236886325-2---5458--------866
Q ss_pred CCCCCHHHHHHHHHHH-CCCCEEEEECCC-CCCCEEEECHHCCCCCCCC------------CCHHCCCHHCC---C--CC
Q ss_conf 8521002344777530-023202310232-2431121000001122221------------00001100000---0--01
Q gi|254780818|r 73 KPSFSSIFSEFWDFFN-EQNAEWIAHNAK-FDVGFINAELQRINKDPLD------------PSRIIDTLSIA---R--RK 133 (245)
Q Consensus 73 ~p~f~ev~~~f~~fi~-~~~~~lVaHNa~-FD~~fL~~el~r~~~~~~~------------~~~~iDTl~la---r--~~ 133 (245)
.|.-...+..|.+-+. .+-.++|-+|.+ ||+.|+.+-.+.+|+.... ..++.+-|.-. | ..
T Consensus 314 e~dEv~Ll~RfFeHiq~~kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrWVKRDSY 393 (2173)
T KOG1798 314 EPDEVGLLQRFFEHIQEVKPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRWVKRDSY 393 (2173)
T ss_pred CCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHCCCCCCHHCCCEECCCCCCCCCCEEEHHHHHHHHHCCC
T ss_conf 87688999999999986189679973686446666677887507771121085206533312563211266666520465
Q ss_pred CCCCCCCHHHHHHH-HCCC-CC--------------CCCCCCCHHHHHHHHHHHHHH
Q ss_conf 77642223789997-1875-45--------------556664026999999999999
Q gi|254780818|r 134 HPSSRNDLNSLCKR-YGIT-IS--------------HRSKHGALLDSHLLSDVYIKM 174 (245)
Q Consensus 134 ~p~~~~~L~~l~~~-~~i~-~~--------------~r~~H~Al~Da~~~a~v~~~l 174 (245)
+|..+.+|.+..+. +|.+ .+ .+-+--.-+||.+|--+|.+.
T Consensus 394 LPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkY 450 (2173)
T KOG1798 394 LPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKY 450 (2173)
T ss_pred CCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHCCHHHHHCCHHHHHHHHHHHHHH
T ss_conf 777663126888875078944379888546665082565300057778888898987
No 111
>KOG1275 consensus
Probab=96.61 E-value=0.013 Score=36.34 Aligned_cols=124 Identities=19% Similarity=0.266 Sum_probs=81.2
Q ss_pred EECCCCCCCCHHHEEECCCCCCCCCCCC------CCCHHHHHHHHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCC
Q ss_conf 9858882288657242021012322485------2100234477753002320231023224311210000011222210
Q gi|254780818|r 47 FLCPNGRKNSPEALKLHGITDEFLKDKP------SFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDP 120 (245)
Q Consensus 47 ~i~P~~~~i~~~~~~ihGIt~~~l~~~p------~f~ev~~~f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~ 120 (245)
||--+. .+...-++--||-+.+|--.. +.+-++.++ .++-..|.++|||-.+=|.+.|| +- .+.
T Consensus 966 Yv~T~d-~VvDYLTqySGI~PGDLDp~~S~K~Lt~lK~~Y~Kl-~~Li~~GviFVGHGL~nDFrvIN-------i~-Vp~ 1035 (1118)
T KOG1275 966 YVSTDD-KVVDYLTQYSGIKPGDLDPTTSEKRLTTLKVLYLKL-RLLIQRGVIFVGHGLQNDFRVIN-------IH-VPE 1035 (1118)
T ss_pred EECCHH-HHHHHHHHHCCCCCCCCCCCCCCCEEHHHHHHHHHH-HHHHHCCCEEECCCCCCCCEEEE-------EE-CCH
T ss_conf 331405-888888874487766669765731002678899999-99997382897224466615999-------83-484
Q ss_pred CHHCCCHHCCCCCCCCCC-CCHHHHHHHH-CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 000110000000177642-2237899971-87545556664026999999999999730576666
Q gi|254780818|r 121 SRIIDTLSIARRKHPSSR-NDLNSLCKRY-GITISHRSKHGALLDSHLLSDVYIKMMVGGSQINF 183 (245)
Q Consensus 121 ~~~iDTl~lar~~~p~~~-~~L~~l~~~~-~i~~~~r~~H~Al~Da~~~a~v~~~ll~g~~q~~l 183 (245)
..++||+.+.+ .|.++ -+|..|+.++ |-. -..++|+...||+.+-.+|...+.-..|..|
T Consensus 1036 ~QiiDTv~lf~--~~s~R~LSLrfLa~~lLg~~-IQ~~~HDSIeDA~taLkLYk~Yl~lkeq~~~ 1097 (1118)
T KOG1275 1036 EQIIDTVTLFR--LGSQRMLSLRFLAWELLGET-IQMEAHDSIEDARTALKLYKKYLKLKEQGKL 1097 (1118)
T ss_pred HHHEEEEEEEE--CCCCCEEEHHHHHHHHHCCH-HHCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 56010357786--16662787799999981413-2013455378799999999999988876689
No 112
>PRK10829 ribonuclease D; Provisional
Probab=96.50 E-value=0.021 Score=34.96 Aligned_cols=136 Identities=18% Similarity=0.203 Sum_probs=81.5
Q ss_pred CEEEEECCCCCCCCCCCE--EEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 589998467888888888--999999999999880313798985888228865724202101232248521002344777
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDR--IIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWD 85 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~--Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~ 85 (245)
..|.+|||--..+....+ .|||+ + ++. ..+|.|- .+.. +..|.+
T Consensus 23 ~~iavDTEf~r~~ty~p~l~LiQi~-----~----~~~-~~lIDpl--~~~d----------------------l~~l~~ 68 (373)
T PRK10829 23 PAIALDTEFVRTRTYYPQLGLIQLF-----D----GEQ-LALIDPL--GITD----------------------WSPFKA 68 (373)
T ss_pred CCEEEECCCCCCCCCCCEEEEEEEE-----E----CCC-EEEEECC--CCCC----------------------HHHHHH
T ss_conf 9189857745677789845899985-----1----896-7999478--7777----------------------699999
Q ss_pred HHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHH-HCCCCCC----------
Q ss_conf 53002320231023224311210000011222210000110000000177642223789997-1875455----------
Q gi|254780818|r 86 FFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKR-YGITISH---------- 154 (245)
Q Consensus 86 fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~-~~i~~~~---------- 154 (245)
.+...+-+-|-|-++.|+.++.+ ..|.. +.+++||..-|.-.--+.+.++..|++. +||.++.
T Consensus 69 ll~~~~i~kv~Haa~qDle~l~~---~~g~~---p~~iFDTQiAa~~lg~~~~~gy~~Lv~~~l~v~l~K~~~~sDW~~R 142 (373)
T PRK10829 69 LLRDPSITKFLHAGSEDLEVFLN---AFGEL---PQPLIDTQILAAFCGRPLSWGFASMVEEYSGVALDKSESRTDWLAR 142 (373)
T ss_pred HHCCCCCEEEEECCCCHHHHHHH---HCCCC---CCHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf 97098841652064215999999---81988---7407764889986578655589999999939665666462757889
Q ss_pred ----CCCCCCHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf ----56664026999999999999730576666
Q gi|254780818|r 155 ----RSKHGALLDSHLLSDVYIKMMVGGSQINF 183 (245)
Q Consensus 155 ----r~~H~Al~Da~~~a~v~~~ll~g~~q~~l 183 (245)
.+.+-|..|+..+..+|-.|.....+.+.
T Consensus 143 PLs~~ql~YA~~DV~yL~~l~~~L~~~l~~~~r 175 (373)
T PRK10829 143 PLSERQCEYAAADVWYLLPIAAKLMVETEAAGW 175 (373)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 999899999999999999999999999983575
No 113
>cd05783 DNA_polB_B1_exo 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 unique in that they are able to recognize the presence of uracil in the template strand, leading to the stalling of DNA synthes
Probab=96.43 E-value=0.0085 Score=37.46 Aligned_cols=101 Identities=17% Similarity=0.208 Sum_probs=57.2
Q ss_pred CCCEEEEECCCC-----CC-CCCC--CEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCC
Q ss_conf 775899984678-----88-8888--889999999999998803137989858882288657242021012322485210
Q gi|254780818|r 6 KMRKIVFDIETT-----GL-DSKN--DRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFS 77 (245)
Q Consensus 6 ~mr~iv~D~ETT-----Gl-~~~~--d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ 77 (245)
++|.+.||+||. |+ +|.. +.||+|+.+. .++ .+.+..+-.|. ....+.. ..-|. .+..-.+-.
T Consensus 4 ~lrvlsfDIEv~s~~~~~FP~p~~~~~~iisI~~~~-~~~---~~~~~~~~~~~-~~~~~~~-~~~~~---~v~~f~~E~ 74 (204)
T cd05783 4 KLKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALAG-SDG---LKRVLVLKREG-VEGLEGL-LPEGA---EVEFFDSEK 74 (204)
T ss_pred CCEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEEC-CCC---CEEEEEEEECC-CCCCCCC-CCCCC---EEEEECCHH
T ss_conf 874999998878899997979555886199999992-799---88999995087-1257655-78998---999959999
Q ss_pred HHHHHHHHHHHCCCCEEEEECC-CCCCCEEEECHHCCCCC
Q ss_conf 0234477753002320231023-22431121000001122
Q gi|254780818|r 78 SIFSEFWDFFNEQNAEWIAHNA-KFDVGFINAELQRINKD 116 (245)
Q Consensus 78 ev~~~f~~fi~~~~~~lVaHNa-~FD~~fL~~el~r~~~~ 116 (245)
+.+..|++++..- ..+|++|. .||+.+|-.-..++|..
T Consensus 75 ~LL~~F~~~i~~~-p~Ii~wN~~~FDiPYL~~R~~~Lg~~ 113 (204)
T cd05783 75 ELIREAFKIISEY-PIVLTFNGDNFDLPYLYNRALKLGIP 113 (204)
T ss_pred HHHHHHHHHHHCC-CEEEECCCCCCCHHHHHHHHHHHCCC
T ss_conf 9999999997439-97998178677889999999985998
No 114
>KOG0304 consensus
Probab=96.43 E-value=0.0084 Score=37.48 Aligned_cols=163 Identities=19% Similarity=0.251 Sum_probs=91.0
Q ss_pred CEEEEECCCCCCC--C------C-------------CCEEEEEEEEEEEC-C-EE--CCCEEEEEEC---CCCCCCCHHH
Q ss_conf 5899984678888--8------8-------------88899999999999-9-88--0313798985---8882288657
Q gi|254780818|r 8 RKIVFDIETTGLD--S------K-------------NDRIIEIGAVELLD-Y-SK--TNRTFQVFLC---PNGRKNSPEA 59 (245)
Q Consensus 8 r~iv~D~ETTGl~--~------~-------------~d~Iieigav~i~~-~-~~--~~~~f~~~i~---P~~~~i~~~~ 59 (245)
.+|..|||=-|.= | . .-.+||+|.--... + .+ ...+|+.-.+ +..-...+++
T Consensus 25 ~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQlGlTlsd~~Gn~p~~g~~tWqfNF~dF~~~~D~~a~~S 104 (239)
T KOG0304 25 PYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQLGLTLSDEKGNLPDCGTDTWQFNFSDFNLEKDMYAQDS 104 (239)
T ss_pred CEEEECCCCCCEEEECCCCCCCCHHHHHHHHHHCHHHHHHHHEEEEEECCCCCCCCCCCCEEEEECCCCCCHHHCCCHHH
T ss_conf 91475376785466247665677478899997222331243022256536899999988656886402784332136666
Q ss_pred E---EECCCCCCCCCC-CCCCCHHHHHHHHHH------HCCCCEEEEECCCCCCCEEEECHHCCCCCCCC----------
Q ss_conf 2---420210123224-852100234477753------00232023102322431121000001122221----------
Q gi|254780818|r 60 L---KLHGITDEFLKD-KPSFSSIFSEFWDFF------NEQNAEWIAHNAKFDVGFINAELQRINKDPLD---------- 119 (245)
Q Consensus 60 ~---~ihGIt~~~l~~-~p~f~ev~~~f~~fi------~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~---------- 119 (245)
+ +=+||.-+..++ +-.. .+|.+.+ -..+-.+|-....+|.++|-.-|.+-.+|.-.
T Consensus 105 IElLr~~Gidf~K~~e~GI~~----~~F~ellm~sg~v~~~~V~WvTFhs~YDfgYLlK~Lt~~~LP~~~~eF~~~v~~~ 180 (239)
T KOG0304 105 IELLRRSGIDFEKHREEGIDI----EEFAELLMTSGLVLDENVTWVTFHSGYDFGYLLKILTGKPLPETEEEFFEIVRQL 180 (239)
T ss_pred HHHHHHCCCCHHHHHHCCCCH----HHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf 999998496777798739789----9999999873250068657998322102999999971798860188999999997
Q ss_pred CCHHCCCHHCCCCCC-CCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 000011000000017-76422237899971875455566640269999999999997
Q gi|254780818|r 120 PSRIIDTLSIARRKH-PSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMM 175 (245)
Q Consensus 120 ~~~~iDTl~lar~~~-p~~~~~L~~l~~~~~i~~~~r~~H~Al~Da~~~a~v~~~ll 175 (245)
...+.|.-.+++.-- ...+..|..+++-+++..-. .+|.|-+|+.+||.+|.+|.
T Consensus 181 fp~vYDiK~l~~~c~~~~l~~GL~~lA~~L~~~RvG-~~HqAGSDSlLT~~~F~kl~ 236 (239)
T KOG0304 181 FPFVYDVKYLMKFCEGLSLKGGLQRLADLLGLKRVG-IAHQAGSDSLLTARVFFKLK 236 (239)
T ss_pred CCHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCEEE-CCCCCCCHHHHHHHHHHHHH
T ss_conf 402661999997603335303799999985887111-03236758999999999887
No 115
>PRK07300 consensus
Probab=95.79 E-value=0.012 Score=36.42 Aligned_cols=125 Identities=14% Similarity=0.157 Sum_probs=71.6
Q ss_pred EEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHHHC
Q ss_conf 99984678888888889999999999998803137989858882288657242021012322485210023447775300
Q gi|254780818|r 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNE 89 (245)
Q Consensus 10 iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi~~ 89 (245)
-++++||+|+++....++-++. .+ ++.+ |+..+ .. +...| .|.++.
T Consensus 322 ~~~~~et~~~~~~~a~lvG~s~---~~----~~~~--y~~~~---~~-------------~l~~~-------~~~~~~-- 367 (880)
T PRK07300 322 DFFYFETLGDNYHREAIIGFAW---GN----GEQI--YASTD---LS-------------LLATD-------SFKQVL-- 367 (880)
T ss_pred CEEEEEECCCCCCCCCEEEEEE---EC----CCEE--EECCC---HH-------------HHHCH-------HHHHHH--
T ss_conf 0257653379813077799998---55----9758--95581---33-------------21176-------888876--
Q ss_pred CCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHHHCC-CCCC------CC------
Q ss_conf 2320231023224311210000011222210000110000000177642223789997187-5455------56------
Q gi|254780818|r 90 QNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGI-TISH------RS------ 156 (245)
Q Consensus 90 ~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i-~~~~------r~------ 156 (245)
..+++.||+.+|..+| .++|... .....||+..+-..-|+.+++|+.|+..|.- .... ..
T Consensus 368 -~~~i~~~nlK~~~~vL----~~~GI~l--~~~~fDTmLAsYLL~p~~~~~Ld~La~~yl~~~~~~~e~l~Gkg~k~~~~ 440 (880)
T PRK07300 368 -QKPIATYDFKRSKVLL----SHLGIEL--PAPSFDARLAKYLLSTVEDNELSTIARLYTDISLETDDTVYGKGAKRAIP 440 (880)
T ss_pred -HHHHHHHHHHHHHHHH----HHCCCCC--CCCHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCHHHHCCCCCCCCCC
T ss_conf -5356550378689999----9779866--77403489998536876558778999994688887337663665210366
Q ss_pred -----CCCCHHHHHHHHHHHHHHH
Q ss_conf -----6640269999999999997
Q gi|254780818|r 157 -----KHGALLDSHLLSDVYIKMM 175 (245)
Q Consensus 157 -----~H~Al~Da~~~a~v~~~ll 175 (245)
...|..||.++.+++..|.
T Consensus 441 ~~~~~~~yaa~da~~~~~L~~~L~ 464 (880)
T PRK07300 441 EKEVLLEHLARKVKVLLDSKEQML 464 (880)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 277999999999999999999989
No 116
>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=94.68 E-value=0.22 Score=28.67 Aligned_cols=77 Identities=17% Similarity=0.251 Sum_probs=45.1
Q ss_pred CHHHHHHHHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCC----CCHHCCCHHCCCC--CCCCCCCCHHHHHHHHCC
Q ss_conf 0023447775300232023102322431121000001122221----0000110000000--177642223789997187
Q gi|254780818|r 77 SSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLD----PSRIIDTLSIARR--KHPSSRNDLNSLCKRYGI 150 (245)
Q Consensus 77 ~ev~~~f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~----~~~~iDTl~lar~--~~p~~~~~L~~l~~~~~i 150 (245)
++++.+|++|+.....--|-|-+.+...-|++-..++|.+... ..+++|...+.|. .+|..++||..++.+||.
T Consensus 329 ~~~~~~f~~~l~~~p~~~IyHY~~yE~~al~rLa~~~~~~e~evd~ll~r~VDL~~vvr~~~~~p~~sysLK~ve~~~gf 408 (457)
T TIGR03491 329 ELAWQQFLQLLQSYPDAPIYHYGETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIESYSLKSIARWLGF 408 (457)
T ss_pred HHHHHHHHHHHHHCCCCEEEEECHHHHHHHHHHHHHCCCCHHHHHHHHHHHEEHHHHHHCEEECCCCCCCHHHHHHHCCC
T ss_conf 99999999999868996599845487999999998719986999999987610699760158837998759999987197
Q ss_pred CCC
Q ss_conf 545
Q gi|254780818|r 151 TIS 153 (245)
Q Consensus 151 ~~~ 153 (245)
...
T Consensus 409 ~w~ 411 (457)
T TIGR03491 409 EWR 411 (457)
T ss_pred CCC
T ss_conf 445
No 117
>PRK08928 consensus
Probab=93.11 E-value=0.11 Score=30.45 Aligned_cols=79 Identities=11% Similarity=0.078 Sum_probs=50.8
Q ss_pred HHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCC-CCCHHHHHHHHCCCCCCCCCCCCHH
Q ss_conf 775300232023102322431121000001122221000011000000017764-2223789997187545556664026
Q gi|254780818|r 84 WDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSS-RNDLNSLCKRYGITISHRSKHGALL 162 (245)
Q Consensus 84 ~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~-~~~L~~l~~~~~i~~~~r~~H~Al~ 162 (245)
..++.+....-|+||+.||+.+| .+.|... ..+.||+..+-.+-|+. +++|+.++.+|.... --|..
T Consensus 367 ~~lLed~~i~KIghNlK~dl~vL----~~~gi~l---~~i~DTmLasYLLnp~~~~h~Ld~La~~~~~~~-----~~aa~ 434 (861)
T PRK08928 367 FNLLTDKSILKITYDLKPLLKFY----ANQSHDI---TAIDDLMLMSYSLSAGLHDHSLFNIILKNTNII-----NESAK 434 (861)
T ss_pred HHHHCCCCCCEEECCHHHHHHHH----HHCCCCC---CCCCCHHHHHHHCCCCCCCCCHHHHHHHHCCCC-----CHHHH
T ss_conf 99843999754454579999999----8569675---763718899986499987689899997622200-----14799
Q ss_pred HHHHHHHHHHHH
Q ss_conf 999999999999
Q gi|254780818|r 163 DSHLLSDVYIKM 174 (245)
Q Consensus 163 Da~~~a~v~~~l 174 (245)
||..+..+|..|
T Consensus 435 ~a~~~~~L~~~L 446 (861)
T PRK08928 435 IVCTLISLHKQL 446 (861)
T ss_pred HHHHHHHHHHHH
T ss_conf 999999999999
No 118
>KOG0970 consensus
Probab=91.96 E-value=0.096 Score=30.87 Aligned_cols=163 Identities=18% Similarity=0.292 Sum_probs=78.5
Q ss_pred CEEEEECCCCCCCCCCC--EEEEEEEEEEECC--------EECCCEEEEEECCCCCCCCHHHEEEC--CCCCCCCCCCCC
Q ss_conf 58999846788888888--8999999999999--------88031379898588822886572420--210123224852
Q gi|254780818|r 8 RKIVFDIETTGLDSKND--RIIEIGAVELLDY--------SKTNRTFQVFLCPNGRKNSPEALKLH--GITDEFLKDKPS 75 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d--~Iieigav~i~~~--------~~~~~~f~~~i~P~~~~i~~~~~~ih--GIt~~~l~~~p~ 75 (245)
+...|-++|+ .|++.+ +|+.|++..-.+. -.-.+.|..+++|++...|-.-.++- ..+. +.-.-+
T Consensus 530 ~llsL~i~T~-~N~k~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~~~fP~g~~ela~~k~~~--v~~~~s 606 (1429)
T KOG0970 530 TLLSLNIRTS-MNPKQNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPGTSFPLGLKELAKQKLSK--VVLHNS 606 (1429)
T ss_pred EEEEEEEEEH-HCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHCCCC--EEEECC
T ss_conf 6887653002-1630042152245556434543457899974567532675688776873589998730673--488348
Q ss_pred CCHHHHHHHHHHHCCC-CEEEEECC-CCCCCEEEECHHCCCC-----------CCC--------------CCCHHCCCHH
Q ss_conf 1002344777530023-20231023-2243112100000112-----------222--------------1000011000
Q gi|254780818|r 76 FSSIFSEFWDFFNEQN-AEWIAHNA-KFDVGFINAELQRINK-----------DPL--------------DPSRIIDTLS 128 (245)
Q Consensus 76 f~ev~~~f~~fi~~~~-~~lVaHNa-~FD~~fL~~el~r~~~-----------~~~--------------~~~~~iDTl~ 128 (245)
-.-.+.-|+.-+...| .++|+||+ .|++..|-.-+..+.. .|+ .-.+.+|-+.
T Consensus 607 ErALLs~fla~~~~~dpD~iVgHn~~~~~l~VLl~R~~~~Kip~WS~IgRLrrS~~~kfg~~s~~~e~~~~aGRl~CD~~ 686 (1429)
T KOG0970 607 ERALLSHFLAMLNKEDPDVIVGHNIQGFYLDVLLSRLHALKIPNWSSIGRLRRSWPPKFGRSSSFGEFFIIAGRLMCDLN 686 (1429)
T ss_pred HHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEHH
T ss_conf 89999999999634299879971411020999999998734864434322210464001776654421102115785057
Q ss_pred C-CCCCCCCCCCCHHHHHHHHCCCCCCC-------------CC------CCCHHHHHHHHHHHHHH
Q ss_conf 0-00017764222378999718754555-------------66------64026999999999999
Q gi|254780818|r 129 I-ARRKHPSSRNDLNSLCKRYGITISHR-------------SK------HGALLDSHLLSDVYIKM 174 (245)
Q Consensus 129 l-ar~~~p~~~~~L~~l~~~~~i~~~~r-------------~~------H~Al~Da~~~a~v~~~l 174 (245)
+ ++.+.+.++++|..|+....- .+++ .. -.-..||.+.++|+.++
T Consensus 687 ~~a~~lik~~S~~LseL~q~~l~-~eR~~i~~~~i~~~y~~s~~L~~ll~~~~~d~~~~l~i~~~l 751 (1429)
T KOG0970 687 LAARELIKAQSYSLSELSQQILK-EERKEINANEIPKMYEDSKSLTYLLEHTITDAELILQIMFRL 751 (1429)
T ss_pred HHHHHHHCCCCCCHHHHHHHHHH-HHCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 77776451356659999999986-541557875754523670779999998767799999999995
No 119
>KOG0969 consensus
Probab=89.88 E-value=0.02 Score=35.17 Aligned_cols=129 Identities=21% Similarity=0.296 Sum_probs=63.2
Q ss_pred CEEEEECCCCCC-----CCCCCEEEEEEEEEEECCEECCCEEEE---EECCCCCCCCHHHEEECCCCCCCCCCCCCCCHH
Q ss_conf 589998467888-----888888999999999999880313798---985888228865724202101232248521002
Q gi|254780818|r 8 RKIVFDIETTGL-----DSKNDRIIEIGAVELLDYSKTNRTFQV---FLCPNGRKNSPEALKLHGITDEFLKDKPSFSSI 79 (245)
Q Consensus 8 r~iv~D~ETTGl-----~~~~d~Iieigav~i~~~~~~~~~f~~---~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev 79 (245)
|-..||+|+-|- .|+.|-|||||-+...-+. ++.|.. -++| ..+|+.. +||-- -+-++.
T Consensus 275 rvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~Ge--~~pfvrnvf~l~~-capI~G~--~V~~~--------~~E~el 341 (1066)
T KOG0969 275 RVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQGE--NEPFVRNVFTLKT-CAPIVGS--NVHSY--------ETEKEL 341 (1066)
T ss_pred CCCCEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCC--CCHHHHHHHCCCC-CCCCCCC--EEEEE--------CCHHHH
T ss_conf 015413785257788886011749999888887168--8467876204667-6887775--25771--------338899
Q ss_pred HHHHHHHHHC-CCCEEEEECC-CCCCCEEEECHHCCCCCCCC--------CCHHCCCH----------------------
Q ss_conf 3447775300-2320231023-22431121000001122221--------00001100----------------------
Q gi|254780818|r 80 FSEFWDFFNE-QNAEWIAHNA-KFDVGFINAELQRINKDPLD--------PSRIIDTL---------------------- 127 (245)
Q Consensus 80 ~~~f~~fi~~-~~~~lVaHNa-~FD~~fL~~el~r~~~~~~~--------~~~~iDTl---------------------- 127 (245)
++....|+.. .-.+++|+|+ .||+..|-.-.+-+|...++ ...+-||.
T Consensus 342 L~~W~~firevDPDvI~GYNi~nFDiPYll~RA~tL~Ie~Fp~LGRikn~~s~irDttfSSkq~GtRetK~v~I~GRlqf 421 (1066)
T KOG0969 342 LESWRKFIREVDPDVIIGYNICNFDIPYLLNRAKTLGIENFPYLGRIKNSRSVIRDSTFSSKQYGTRETKEVNIDGRLQF 421 (1066)
T ss_pred HHHHHHHHHHCCCCEEECCCCCCCCCCEECCHHHHCCCCCCCCCCEECCCCEEEECCCCCHHHCCCCCCEEEEECCEEEE
T ss_conf 99999999862988671335445563213076764680666501000354124410321232137510138866565652
Q ss_pred ---HCCCCCCCCCCCCHHHHHHHHC
Q ss_conf ---0000017764222378999718
Q gi|254780818|r 128 ---SIARRKHPSSRNDLNSLCKRYG 149 (245)
Q Consensus 128 ---~lar~~~p~~~~~L~~l~~~~~ 149 (245)
..-++-|.-.+++|.+.+.+|-
T Consensus 422 Dllqvi~RdyKLrSytLNaVs~hFL 446 (1066)
T KOG0969 422 DLLQVILRDYKLRSYTLNAVSAHFL 446 (1066)
T ss_pred HHHHHHHHHHHHHHCCHHHHHHHHH
T ss_conf 2799987764331110114578765
No 120
>KOG3657 consensus
Probab=87.88 E-value=0.12 Score=30.16 Aligned_cols=36 Identities=28% Similarity=0.435 Sum_probs=25.3
Q ss_pred CCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHC
Q ss_conf 2320231023224311210000011222210000110000
Q gi|254780818|r 90 QNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSI 129 (245)
Q Consensus 90 ~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~l 129 (245)
++..+||||+.||..-++.+.. ..- ...+++||+.|
T Consensus 240 ke~liVGHNVsfDRaRirEeY~---i~~-Sk~rFlDTMSl 275 (1075)
T KOG3657 240 KEQLIVGHNVSFDRARIREEYN---ING-SKIRFLDTMSL 275 (1075)
T ss_pred CCCEEEECCCCCHHHHHHHHHH---CCC-CCEEEEECHHH
T ss_conf 7756873355400899999870---266-54066431122
No 121
>TIGR01388 rnd ribonuclease D; InterPro: IPR006292 These proteins represent ribonuclease D, a 3-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Members of this family are restricted to the Proteobacteria; Aquifex, Mycobacteria and eukaryotes. Ribonuclease D is not essential in Escherichia coli but is deleterious when overexpressed. The precise biological role of ribonuclease D is still unknown. ; GO: 0004540 ribonuclease activity, 0008033 tRNA processing, 0005737 cytoplasm.
Probab=83.95 E-value=1.7 Score=23.13 Aligned_cols=135 Identities=16% Similarity=0.172 Sum_probs=82.1
Q ss_pred EEEEECC---CCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 8999846---7888888888999999999999880313798985888228865724202101232248521002344777
Q gi|254780818|r 9 KIVFDIE---TTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWD 85 (245)
Q Consensus 9 ~iv~D~E---TTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~ 85 (245)
+|.+||| ||=+-|.=. +||+| + |+. ..+|.|-. ++ .-+..|..
T Consensus 20 ~valDTEF~R~~TFwP~Lg-LiQ~a-----~----g~~-~~LIDPL~--~~---------------------~~~~Pl~~ 65 (374)
T TIGR01388 20 FVALDTEFVRERTFWPQLG-LIQVA-----D----GEQ-LALIDPLV--ID---------------------IDLSPLLE 65 (374)
T ss_pred EEECCCCEECCCCCCHHHC-CEECC-----C----CCE-EEEECCCC--CC---------------------CCHHHHHH
T ss_conf 3741554112653202040-03113-----7----875-68765888--75---------------------23479999
Q ss_pred HHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHH-HCCCCCC----------
Q ss_conf 53002320231023224311210000011222210000110000000177642223789997-1875455----------
Q gi|254780818|r 86 FFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKR-YGITISH---------- 154 (245)
Q Consensus 86 fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~-~~i~~~~---------- 154 (245)
++.+..-+=|-|-++=|+-. |.+++. .+ +.|.+||.-.|--.--|.+.+-+.|.+. .+|.+++
T Consensus 66 lL~d~~v~KvlHAaseDlEv----F~~l~g-~l-P~PLfDTQi~Aa~~G~g~s~gY~~LV~~~~~v~LdKse~rtDW~~R 139 (374)
T TIGR01388 66 LLADESVVKVLHAASEDLEV----FLNLFG-VL-PKPLFDTQIAAAFLGFGESMGYDKLVQEVLGVELDKSETRTDWLAR 139 (374)
T ss_pred HHHCCCCEEEECCCCHHHHH----HHHHHC-CC-CCCCHHHHHHHHHHCCCCCHHHHHHHHHHHCEECCCCCCCCHHHCC
T ss_conf 97389815853045047999----998705-79-8883058899998367852108999999737031788872221047
Q ss_pred ----CCCCCCHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf ----56664026999999999999730576666
Q gi|254780818|r 155 ----RSKHGALLDSHLLSDVYIKMMVGGSQINF 183 (245)
Q Consensus 155 ----r~~H~Al~Da~~~a~v~~~ll~g~~q~~l 183 (245)
++.--|++|...|+.||..|...-.+.+.
T Consensus 140 PLtd~Ql~YAaaDV~yL~~~y~~L~~~l~~~~R 172 (374)
T TIGR01388 140 PLTDKQLEYAAADVTYLLPLYEKLTERLAEEGR 172 (374)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 898778999999999999999999999988645
No 122
>pfam00843 Arena_nucleocap Arenavirus nucleocapsid protein.
Probab=79.49 E-value=3 Score=21.51 Aligned_cols=141 Identities=21% Similarity=0.322 Sum_probs=71.2
Q ss_pred EEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCC-CCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 9998467888888888999999999999880313798985888-228865724202101232248521002344777530
Q gi|254780818|r 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNG-RKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFN 88 (245)
Q Consensus 10 iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~-~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~fi~ 88 (245)
.-+|+|-+ ..| -+|+|...=. ++...|+|-+|.. +.+-..+---|||--.+|+++.+ -....++..+-
T Consensus 375 tWiDIEG~----p~D-PVE~AiyQP~----~g~yiHcyR~P~D~K~FK~~SkysHGillkDl~~aqP--GL~S~ii~~LP 443 (534)
T pfam00843 375 TWIDIEGP----PND-PVELAIYQPE----SGNYIHCYREPHDEKQFKDQSKYSHGILLKDLENAQP--GLTSAVIGLLP 443 (534)
T ss_pred EEEECCCC----CCC-CEEEEEECCC----CCCEEEEECCCCCHHHHCCCCCCCCCEEHHHHHHCCC--CHHHHHHHHCC
T ss_conf 47825789----999-7578886168----8857988547863433114564445303666643076--54999997678
Q ss_pred CCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCC---HHCCCCCCCCCCCCHHHHHHHH-CCCCC---------CC
Q ss_conf 02320231023224311210000011222210000110---0000001776422237899971-87545---------55
Q gi|254780818|r 89 EQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDT---LSIARRKHPSSRNDLNSLCKRY-GITIS---------HR 155 (245)
Q Consensus 89 ~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDT---l~lar~~~p~~~~~L~~l~~~~-~i~~~---------~r 155 (245)
++-++-+.-+ =|++-| |.-+|..-+ .++|. -.-||.+--.-.-+.+.||+.- ||=.. -.
T Consensus 444 -~~mV~T~QGs-DDIrkL---ld~hgR~Di---k~vDv~ls~eqaR~fE~~VW~~f~~LC~~H~GiVi~kKKkg~~~~~t 515 (534)
T pfam00843 444 -KNMVLTAQGS-DDIRKL---LDMHGRRDI---KLVDVKLTSEQARKFEDKVWDKFGHLCKKHTGIVIKKKKKGGKPEST 515 (534)
T ss_pred -CCCEEEEECH-HHHHHH---HHHCCCCCC---EEEEEEECHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCC
T ss_conf -6738983073-889999---984388663---58876406888888799999998888986485685335579999888
Q ss_pred CCCCCHHHHHHHHH
Q ss_conf 66640269999999
Q gi|254780818|r 156 SKHGALLDSHLLSD 169 (245)
Q Consensus 156 ~~H~Al~Da~~~a~ 169 (245)
++|-||.||.+-..
T Consensus 516 ~pHCALlDCiMF~a 529 (534)
T pfam00843 516 NPHCALLDCIMFDA 529 (534)
T ss_pred CCHHHHHHHHHHHH
T ss_conf 83379987786755
No 123
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=78.85 E-value=1.8 Score=22.97 Aligned_cols=158 Identities=20% Similarity=0.289 Sum_probs=78.4
Q ss_pred CEEEEECCCCCCCCC-------------------CC--EEEEEEEEEEE--CCEECC-CE--EEEEECCCCCCCCHHHEE
Q ss_conf 589998467888888-------------------88--89999999999--998803-13--798985888228865724
Q gi|254780818|r 8 RKIVFDIETTGLDSK-------------------ND--RIIEIGAVELL--DYSKTN-RT--FQVFLCPNGRKNSPEALK 61 (245)
Q Consensus 8 r~iv~D~ETTGl~~~-------------------~d--~Iieigav~i~--~~~~~~-~~--f~~~i~P~~~~i~~~~~~ 61 (245)
..|..|||--|.-++ -| .|||+|.-.-+ +..+.+ .+ |..-.+|+.--..+++++
T Consensus 43 n~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQlGlsLSDe~GN~P~~~sTWQFNF~F~l~~dmya~ESie 122 (299)
T COG5228 43 NHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDENGNKPNGPSTWQFNFEFDLKKDMYATESIE 122 (299)
T ss_pred CCEEECCCCCCEEECCCCCCCCCCHHHHHHHHCCCCHHHHHHEEEEECCCCCCCCCCCCEEEEEEEECCHHHHCCHHHHH
T ss_conf 80043155674030243334354227889886051032020000041030299999973268888755012003568899
Q ss_pred E---CCCCCCCCCCCCCCCHHHHHHHHHHH------CCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCC
Q ss_conf 2---02101232248521002344777530------02320231023224311210000011222210000110000000
Q gi|254780818|r 62 L---HGITDEFLKDKPSFSSIFSEFWDFFN------EQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARR 132 (245)
Q Consensus 62 i---hGIt~~~l~~~p~f~ev~~~f~~fi~------~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~ 132 (245)
+ .||.-+.-++ ..--..+|.+.+- .++-++|-+++.+|.++|-..+... +++ ++.-|-..+-..
T Consensus 123 LL~ksgIdFkkHe~---~GI~v~eF~elLm~SGLvm~e~VtWitfHsaYDfgyLikilt~~---plP-~~~EdFy~~l~~ 195 (299)
T COG5228 123 LLRKSGIDFKKHEN---LGIDVFEFSELLMDSGLVMDESVTWITFHSAYDFGYLIKILTND---PLP-NNKEDFYWWLHQ 195 (299)
T ss_pred HHHHCCCCHHHHHH---CCCCHHHHHHHHHCCCCEECCCEEEEEEECCHHHHHHHHHHHCC---CCC-CCHHHHHHHHHH
T ss_conf 99980887556766---39789999999862672321415799952100089999998369---887-538999999999
Q ss_pred CCCC--------CC-----CCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 1776--------42-----22378999718754555666402699999999999
Q gi|254780818|r 133 KHPS--------SR-----NDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIK 173 (245)
Q Consensus 133 ~~p~--------~~-----~~L~~l~~~~~i~~~~r~~H~Al~Da~~~a~v~~~ 173 (245)
.+|. ++ ..|.....-+++-... ..|.|-.||.+||+.|..
T Consensus 196 yfP~fYDik~v~ks~~~~~KglQei~ndlql~r~g-~QhQagsdaLlTa~~ff~ 248 (299)
T COG5228 196 YFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSG-QQHQAGSDALLTADEFFL 248 (299)
T ss_pred HCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHCCC-HHHHCCCHHHHHHHHHCC
T ss_conf 77653125889876541556798853727651055-655414304443677545
No 124
>TIGR00593 pola DNA polymerase I; InterPro: IPR002298 DNA carries 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 cell life cycle. This function is mediated by DNA-directed DNA polymerases, which add nucleotide triphosphate (dNTP) residues to the 5'-end of the growing DNA chain, using a complementary DNA as template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used. DNA-dependent DNA polymerases have been grouped into families, denoted A, B and X, on the basis of sequence similarities , . Members of family A, which includes bacterial and bacteriophage polymerases, share significant similarity to Escherichia coli polymerase I; hence family A is also known as the pol I family. The bacterial polymerases also contain an exonuclease activity, which is coded for in the N-terminal portion. Three motifs, A, B and C , are seen to be conserved across all DNA polymerases, with motifs A and C also seen in RNA polymerases. They are centred on invariant residues, and their structural significance was implied from the Klenow (E. coli) structure. Motif A contains a strictly-conserved aspartate at the junction of a beta-strand and an alpha-helix; motif B contains an alpha-helix with positive charges; and motif C has a doublet of negative charges, located in a beta-turn-beta secondary structure .; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication.
Probab=57.12 E-value=2.9 Score=21.62 Aligned_cols=85 Identities=20% Similarity=0.246 Sum_probs=57.5
Q ss_pred CCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCC-CHHHHHHHHCCCC---C----C----C---
Q ss_conf 3202310232243112100000112222100001100000001776422-2378999718754---5----5----5---
Q gi|254780818|r 91 NAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRN-DLNSLCKRYGITI---S----H----R--- 155 (245)
Q Consensus 91 ~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~-~L~~l~~~~~i~~---~----~----r--- 155 (245)
-.+.++||+.|+..+| ++.|........+.||+-.|-.+-|++.. .|+.+|.+|.... + + .
T Consensus 465 ~~~~~~~~~K~~~~~L----~~~g~~~~~~~~~~D~~laaYll~~~~~~~~l~~~~~~y~~~~~~~d~~~~~~~~~~~~~ 540 (1005)
T TIGR00593 465 SKVKVAHDAKFLMHLL----KRKGIELIEIGVIFDTMLAAYLLDPAQVSKDLDTLAKRYLVEELILDDDRKEEGIKKLAK 540 (1005)
T ss_pred CCCCCHHHHHHHHHHH----HHCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHH
T ss_conf 1012288999999999----743773344211454899999843035640278999871343467787313455443344
Q ss_pred --------CCCCCHHHHHHHHHHHHHHHHCCC
Q ss_conf --------666402699999999999973057
Q gi|254780818|r 156 --------SKHGALLDSHLLSDVYIKMMVGGS 179 (245)
Q Consensus 156 --------~~H~Al~Da~~~a~v~~~ll~g~~ 179 (245)
..-.+-.+|.++..++-+|+....
T Consensus 541 ~a~~~~~~~~~~~~~~~~~~~~L~~~l~~~L~ 572 (1005)
T TIGR00593 541 FADPDLEEAIEYLARKAAATARLAEELLKELD 572 (1005)
T ss_pred HHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 41121778899999999999999999888731
No 125
>PRK05761 DNA polymerase I; Reviewed
Probab=53.97 E-value=4.8 Score=20.28 Aligned_cols=95 Identities=14% Similarity=0.208 Sum_probs=53.7
Q ss_pred CCCHHHHHHHHHHHCCCCEEEEECC-CCCCCEEEECHHCCCCCCCCC-----------CHHCCCHHCC-----C-----C
Q ss_conf 2100234477753002320231023-224311210000011222210-----------0001100000-----0-----0
Q gi|254780818|r 75 SFSSIFSEFWDFFNEQNAEWIAHNA-KFDVGFINAELQRINKDPLDP-----------SRIIDTLSIA-----R-----R 132 (245)
Q Consensus 75 ~f~ev~~~f~~fi~~~~~~lVaHNa-~FD~~fL~~el~r~~~~~~~~-----------~~~iDTl~la-----r-----~ 132 (245)
+-.+.+.+|.+|+...| +-|.+|. +||+..|..-..++|.+.... ...+|..... + .
T Consensus 197 sE~elL~~f~~~i~~~D-PDIiyN~d~FD~PYL~~Ra~~lgi~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~y~~~~ 275 (777)
T PRK05761 197 SEKELLAELFKIIEDYP-PVITFNGDNFDLPYLYNRALKLGIPKEELPFNVKYASLKTGIHIDLYKFFQNRAIRSYAFYG 275 (777)
T ss_pred CHHHHHHHHHHHHHHCC-CCEEECCCCCCHHHHHHHHHHHCCCCHHCCCCCCCCCCCCCEEEECCCCCCHHHHHHEEECC
T ss_conf 99999999999997469-82998078764899999999838990006651566540244465044531211355301054
Q ss_pred CCCCCCCCHHHHHHHH-CCCCCC-----------CCCCCCHHHHHHHHHH
Q ss_conf 1776422237899971-875455-----------5666402699999999
Q gi|254780818|r 133 KHPSSRNDLNSLCKRY-GITISH-----------RSKHGALLDSHLLSDV 170 (245)
Q Consensus 133 ~~p~~~~~L~~l~~~~-~i~~~~-----------r~~H~Al~Da~~~a~v 170 (245)
++.-.+++|++.++.+ |..... +-+.-.+-||.+|-++
T Consensus 276 ~~~~~~y~Ld~Va~~lLg~~K~~~~~~~~~~~~~~l~~Y~l~Da~l~~~L 325 (777)
T PRK05761 276 KYRHREAALDAVARALLGESKVELEKNISELNYWELAEYNYRDAEITLKL 325 (777)
T ss_pred EECCCCEEHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 74247455478899975997410312466334788999989999999998
No 126
>TIGR02373 photo_yellow photoactive yellow protein; InterPro: IPR012130 Members of this family are photoactive yellow protein, a cytosolic, 14-kDa light-sensing protein which has a 4-hydroxycinnamyl (p-coumaric acid) chromophore covalently linked to a Cys residue. The enzyme 4-coumarate--CoA ligase as described by IPR012743 from INTERPRO is required for its biosynthesis. The modified Cys is in a PAS domain, frequently found in signal transducing proteins. Members are known in alpha and gamma Proteobacteria that include Rhodobacter capsulatus, Halorhodospira halophila, Rhodospirillum centenum, etc.; GO: 0009881 photoreceptor activity, 0007602 phototransduction, 0018298 protein-chromophore linkage.
Probab=50.65 E-value=6.2 Score=19.54 Aligned_cols=67 Identities=24% Similarity=0.318 Sum_probs=40.9
Q ss_pred EEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHH--HHHHHHHCCCCEEEE---ECCC
Q ss_conf 99999999999988031379898588822886572420210123224852100234--477753002320231---0232
Q gi|254780818|r 26 IIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFS--EFWDFFNEQNAEWIA---HNAK 100 (245)
Q Consensus 26 Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~--~f~~fi~~~~~~lVa---HNa~ 100 (245)
=+-+|||.|+....+ +.|=+-|+ .|+|=.|+.|-++--|.||+| +.-+|-|. =..-|+ -|+.
T Consensus 26 ~LpfGAiqlD~~G~I----~~YN~aEg--------~l~GR~P~~VIGrnFF~evAPCt~~~~F~G~-F~~gv~~G~ln~m 92 (126)
T TIGR02373 26 SLPFGAIQLDGSGRI----LKYNAAEG--------ELTGRDPERVIGRNFFKEVAPCTDIPEFSGR-FLEGVASGQLNAM 92 (126)
T ss_pred CCCCCEEEECCCCCH----HHHHCCCC--------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE-ECCCCCCCCCCEE
T ss_conf 554104886698830----21101100--------0138797732274342332788888443232-4011024652136
Q ss_pred CCCCE
Q ss_conf 24311
Q gi|254780818|r 101 FDVGF 105 (245)
Q Consensus 101 FD~~f 105 (245)
||+.|
T Consensus 93 fdy~F 97 (126)
T TIGR02373 93 FDYVF 97 (126)
T ss_pred EEEEE
T ss_conf 76665
No 127
>TIGR01284 alt_nitrog_alph nitrogenase alpha chain; InterPro: IPR005974 The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene. Two operons, nifDK and nifEN, encode a tetrameric (alpha2beta2 and N2E2) enzymatic complex. Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of nifNE and of some other nif genes. It has been proposed that NifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I. This model represents the alpha chains of various forms of the nitrogen-fixing enzyme nitrogenase: vanadium-iron, iron-iron, and molybdenum-iron. Most examples of NifD, the molybdenum-iron type nitrogenase alpha chain, are excluded from this model and described instead by equivalog model IPR005972 from INTERPRO.; GO: 0016163 nitrogenase activity, 0051536 iron-sulfur cluster binding, 0009399 nitrogen fixation.
Probab=42.39 E-value=7.2 Score=19.14 Aligned_cols=96 Identities=20% Similarity=0.260 Sum_probs=49.9
Q ss_pred CEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEE--ECCCC--CCCCCCCCCCCHHHHHH
Q ss_conf 589998467888888888999999999999880313798985888228865724--20210--12322485210023447
Q gi|254780818|r 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALK--LHGIT--DEFLKDKPSFSSIFSEF 83 (245)
Q Consensus 8 r~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~--ihGIt--~~~l~~~p~f~ev~~~f 83 (245)
|-++.-|=|||| =+|.|=.|+- +|.......+.| .||-+|..=|..+-= +-+|+ ++.|...- .++-.+.
T Consensus 139 r~~~Y~TC~TaL--IGDDI~Aia~-eV~ee~p~vDvf--~~n~PGFaGpsQSkGH~v~Ni~win~kVgT~E--peiT~ey 211 (468)
T TIGR01284 139 RMIVYATCATAL--IGDDIDAIAK-EVMEEIPDVDVF--AVNAPGFAGPSQSKGHHVLNIAWINDKVGTVE--PEITTEY 211 (468)
T ss_pred EEEEECCCCCCC--CCCCHHHHHH-HHHHHCCCCCEE--EEECCCCCCCCCCCCHHHHHHHHHHHHCCCCC--CCCCCCC
T ss_conf 377841678743--2444789999-987527994289--98177898987577601223453442112348--8768750
Q ss_pred -HHHHHCCCCEEEE-ECCCCCCCEEEECHHCCCCCCC
Q ss_conf -7753002320231-0232243112100000112222
Q gi|254780818|r 84 -WDFFNEQNAEWIA-HNAKFDVGFINAELQRINKDPL 118 (245)
Q Consensus 84 -~~fi~~~~~~lVa-HNa~FD~~fL~~el~r~~~~~~ 118 (245)
++ +|| +|++=|...|...|.|.|...+
T Consensus 212 ~~N--------~iGeyNIqGD~~vl~~Yf~rmGI~Vl 240 (468)
T TIGR01284 212 DVN--------LIGEYNIQGDLEVLKKYFERMGIQVL 240 (468)
T ss_pred CEE--------EEECCCCHHHHHHHHHHHHHCCCEEE
T ss_conf 065--------55333340008999999986394588
No 128
>TIGR00658 orni_carb_tr ornithine carbamoyltransferase; InterPro: IPR002292 The ornithine carbamoyltransferases are a family of enzymes that catalyse the production of citrulline from carbamoyl-phosphate and ornithine . This reaction is part of the arginine biosynthetic pathway, and in some organisms the reaction is also part of the arginine deaminase pathway . In most prokaryotes, and some lower eukaryotes, the enzyme is found in the cytoplasm, but in higher eukaryotes, such as mammals, the enzyme is found in the mitochondrial matrix and functions as part of the urea cycle. In most organisms analysed to date, the enzyme has been shown to consist of a trimer of identical or nonidentical subunits . Extensive similarity has been found within the ornithine carbamoyltransferase family, some of the conserved areas being important in catalysis . The C-terminal region of these enzymes shows a degree of similarity to the aspartate carbamoyltransferases, which are also known to bind carbamoyl- phosphate . This region contains a highly conserved Cys residue (in a His-Cys-Lys-Pro motif) implicated in ornithine binding . ; GO: 0004585 ornithine carbamoyltransferase activity, 0006520 amino acid metabolic process, 0009348 ornithine carbamoyltransferase complex.
Probab=39.24 E-value=19 Score=16.53 Aligned_cols=27 Identities=26% Similarity=0.448 Sum_probs=21.9
Q ss_pred CHHHHHHHHCCCCCCCCCCCCHHH----HHHHHHHH
Q ss_conf 237899971875455566640269----99999999
Q gi|254780818|r 140 DLNSLCKRYGITISHRSKHGALLD----SHLLSDVY 171 (245)
Q Consensus 140 ~L~~l~~~~~i~~~~r~~H~Al~D----a~~~a~v~ 171 (245)
.+..+|+|=+||.- |||.| |+++|.++
T Consensus 113 ~v~~lA~yasVPVI-----NgLtD~~HPcQ~LADll 143 (341)
T TIGR00658 113 DVEELAKYASVPVI-----NGLTDLFHPCQALADLL 143 (341)
T ss_pred HHHHHHHHCCCCEE-----CCCCCCCCHHHHHHHHH
T ss_conf 89999854898546-----05568552379999988
No 129
>PRK13582 thrH phosphoserine phosphatase; Provisional
Probab=36.40 E-value=18 Score=16.71 Aligned_cols=13 Identities=23% Similarity=0.289 Sum_probs=11.6
Q ss_pred CCEEEEECCCCCC
Q ss_conf 7589998467888
Q gi|254780818|r 7 MRKIVFDIETTGL 19 (245)
Q Consensus 7 mr~iv~D~ETTGl 19 (245)
||.||||.|.|=.
T Consensus 1 mrLv~fDmDstLI 13 (205)
T PRK13582 1 MEIACLDLEGVLV 13 (205)
T ss_pred CEEEEECCCCCCH
T ss_conf 9189976877738
No 130
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit; InterPro: IPR012754 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry represents the beta-prime subunit, RpoC, found in most bacteria. It excludes some, mainly cyanobacterial, species where RpoC is replaced by two homologous proteins that include an additional domain. One arm of the "claw" is predominantly formed by this subunit, the other being predominantly formed by the beta subunit. The active site of the enzyme is defined by three invariant aspartate residues within the beta-prime subunit .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=34.79 E-value=11 Score=17.94 Aligned_cols=19 Identities=21% Similarity=0.384 Sum_probs=7.8
Q ss_pred CCCCCCCCCCHHHHHHHHH
Q ss_conf 2322485210023447775
Q gi|254780818|r 68 EFLKDKPSFSSIFSEFWDF 86 (245)
Q Consensus 68 ~~l~~~p~f~ev~~~f~~f 86 (245)
+++.+-..|.++.+.++++
T Consensus 596 efinnf~~Fs~~~Ev~~Ay 614 (1552)
T TIGR02386 596 EFINNFKIFSDLEEVIRAY 614 (1552)
T ss_pred HHHHHHHCCCCHHHHHHHH
T ss_conf 6554210035889999998
No 131
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=34.01 E-value=35 Score=14.89 Aligned_cols=80 Identities=19% Similarity=0.256 Sum_probs=36.9
Q ss_pred CCCCCCC-HHHHHHHHHHHCCCCEEEE-ECCCCCC-CEEEECHHCCCCCCCCCCHH----CCCHHCCCC--CCCCCCCCH
Q ss_conf 2485210-0234477753002320231-0232243-11210000011222210000----110000000--177642223
Q gi|254780818|r 71 KDKPSFS-SIFSEFWDFFNEQNAEWIA-HNAKFDV-GFINAELQRINKDPLDPSRI----IDTLSIARR--KHPSSRNDL 141 (245)
Q Consensus 71 ~~~p~f~-ev~~~f~~fi~~~~~~lVa-HNa~FD~-~fL~~el~r~~~~~~~~~~~----iDTl~lar~--~~p~~~~~L 141 (245)
...|+-+ .++.+|+.++..+-..-.+ |-+.++. ++| .+++|.+.-...++ +|-..+.|. ..|+.+++|
T Consensus 332 a~~~~ee~~~~~efl~~v~~~yp~~~~YH~~~ye~~~rL---~klyg~~~~~v~~~l~~~vDi~~lvr~~v~~p~es~sL 408 (474)
T COG2251 332 AEDPSEERKALQEFLGIVVRQYPEATIYHYAPYEKTRRL---VKLYGVPQNQVSPVLDSLVDIYALVRSSVVVPVESYSL 408 (474)
T ss_pred HCCCHHHHHHHHHHHHHHHEECCCCCCCCCCCHHHHCHH---HEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHH
T ss_conf 448167789999987556412688774446754441403---40446571103179998867999987511257430218
Q ss_pred HHHHHHHCCCCC
Q ss_conf 789997187545
Q gi|254780818|r 142 NSLCKRYGITIS 153 (245)
Q Consensus 142 ~~l~~~~~i~~~ 153 (245)
..+..+.|....
T Consensus 409 K~la~~lG~~wr 420 (474)
T COG2251 409 KALAPYLGFQWR 420 (474)
T ss_pred HHHHHHHCCCCC
T ss_conf 775554078845
No 132
>TIGR01363 strep_his_triad streptococcal histidine triad protein; InterPro: IPR006270 The sequences represented in this group are identified by a domain which consists of the N-terminal half of a family of Streptococcal proteins that contain a signal peptide and then up to five repeats of a region that includes a His-X-X-His-X-His (histidine triad) motif. Additional copies of the repeats are found in more poorly conserved regions. Members of this family from Streptococcus pneumoniae are suggested to cleave human C3, and the member PhpA has been shown in vaccine studies to be a protective antigen in mice . .
Probab=32.13 E-value=37 Score=14.70 Aligned_cols=57 Identities=26% Similarity=0.445 Sum_probs=36.8
Q ss_pred EEEEEC-CEEC--CCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCC----CHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf 999999-9880--313798985888228865724202101232248521----0023447775300232023102322
Q gi|254780818|r 31 AVELLD-YSKT--NRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSF----SSIFSEFWDFFNEQNAEWIAHNAKF 101 (245)
Q Consensus 31 av~i~~-~~~~--~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f----~ev~~~f~~fi~~~~~~lVaHNa~F 101 (245)
.|+|-| +-+| |+.||.| | | .+|..|+ ||.|.|..-|.+ .||+.++.+ .-+|==|..|
T Consensus 74 ViKITDQGYVTSHGDHYHyY-N--G-KVPYDAI----ISEELLM~DPNY~lK~~DivNEi~~------GYVIKV~G~Y 137 (376)
T TIGR01363 74 VIKITDQGYVTSHGDHYHYY-N--G-KVPYDAI----ISEELLMKDPNYRLKDSDIVNEIKG------GYVIKVNGKY 137 (376)
T ss_pred EEEEECCCEECCCCCEEEEE-C--C-CCCCHHH----HHHHHHCCCCCCCCCCCCCEEEECC------CEEEEECCEE
T ss_conf 89970576031368601432-7--8-5563132----2136643788734464320022038------6689885818
No 133
>PRK05406 LamB/YcsF family protein; Provisional
Probab=31.50 E-value=25 Score=15.72 Aligned_cols=86 Identities=21% Similarity=0.276 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCC
Q ss_conf 02344777530023202310232243112100000112222100001100000001776422237899971875455566
Q gi|254780818|r 78 SIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSK 157 (245)
Q Consensus 78 ev~~~f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~r~~ 157 (245)
++..+.+......|-.+-||=.=-|. .-|.|-.++ ++.....+.+. .|-..|..+|+..|.++.|=+.
T Consensus 44 ~~m~~tv~lA~~~~V~iGAHPsypD~----~gFGRr~~~-~s~~el~~~i~-------~Qi~~l~~~a~~~g~~l~hvKp 111 (246)
T PRK05406 44 AVMRRTVRLAKENGVAIGAHPGYPDL----EGFGRRNMD-LSPEELYALVL-------YQIGALQAIARAAGGRVRHVKP 111 (246)
T ss_pred HHHHHHHHHHHHCCCEEECCCCCCCC----CCCCCCCCC-CCHHHHHHHHH-------HHHHHHHHHHHHCCCCCCEECC
T ss_conf 99999999999849988478999876----789988898-99999999999-------9999999999984996313240
Q ss_pred CCCHHHH----HHHHHHHHHHH
Q ss_conf 6402699----99999999997
Q gi|254780818|r 158 HGALLDS----HLLSDVYIKMM 175 (245)
Q Consensus 158 H~Al~Da----~~~a~v~~~ll 175 (245)
|+||+-. ..+|+.++..+
T Consensus 112 HGALYn~~~~d~~~a~~i~~~i 133 (246)
T PRK05406 112 HGALYNMAAKDPELADAIAEAV 133 (246)
T ss_pred CHHHHHHHHCCHHHHHHHHHHH
T ss_conf 1899998845999999999999
No 134
>PRK12569 hypothetical protein; Provisional
Probab=29.38 E-value=27 Score=15.55 Aligned_cols=85 Identities=16% Similarity=0.285 Sum_probs=42.9
Q ss_pred HHHHHHHHHHHCCCCEEE-EECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCCCC
Q ss_conf 023447775300232023-1023224311210000011222210000110000000177642223789997187545556
Q gi|254780818|r 78 SIFSEFWDFFNEQNAEWI-AHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRS 156 (245)
Q Consensus 78 ev~~~f~~fi~~~~~~lV-aHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~r~ 156 (245)
++..+.+......| +-| ||=.=-|. .-|.|-.+.. +...+.+.+. -|-..|.++|+..|..+.|=+
T Consensus 47 ~~m~~tv~lA~~~~-V~IGAHPsypD~----~gFGRr~~~~-s~~el~~~v~-------~Qi~al~~~a~~~g~~l~hVK 113 (245)
T PRK12569 47 NIMRRTVELAKAHG-VGIGAHPGFRDL----VGFGRRHIAA-SAQELVNDIL-------YQLGALREFARAQGVRLQHVK 113 (245)
T ss_pred HHHHHHHHHHHHCC-CEEECCCCCCCC----CCCCCCCCCC-CHHHHHHHHH-------HHHHHHHHHHHHCCCCEEECC
T ss_conf 99999999999859-988188999976----7899898889-9899999999-------999999999998399301114
Q ss_pred CCCCHHH-HH---HHHHHHHHHH
Q ss_conf 6640269-99---9999999997
Q gi|254780818|r 157 KHGALLD-SH---LLSDVYIKMM 175 (245)
Q Consensus 157 ~H~Al~D-a~---~~a~v~~~ll 175 (245)
.|+||+- +. .+|+++.+.+
T Consensus 114 PHGALYn~~~~d~~la~~i~~ai 136 (245)
T PRK12569 114 PHGALYMHAARDEALARLLVEAL 136 (245)
T ss_pred HHHHHHHHHHCCHHHHHHHHHHH
T ss_conf 21999999856999999999999
No 135
>pfam05288 Pox_A3L Poxvirus A3L Protein. This family consists of several poxvirus A3L or A2_5L proteins.
Probab=27.71 E-value=18 Score=16.69 Aligned_cols=36 Identities=25% Similarity=0.538 Sum_probs=27.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCCCCCEEEECHHCC
Q ss_conf 322485210023447775300232023102322431121000001
Q gi|254780818|r 69 FLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRI 113 (245)
Q Consensus 69 ~l~~~p~f~ev~~~f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~ 113 (245)
++...|.=..++.+|+.|. -|-.||...|..|++|.
T Consensus 33 ~L~sqP~k~~iLk~FL~~~---------RNK~~~~kiLD~EirRv 68 (70)
T pfam05288 33 MLLSQPNKLKILKRFLRFC---------RNKTLDYKILDPEIRRV 68 (70)
T ss_pred HHHCCHHHHHHHHHHHHHH---------HCCCHHHHHCCHHHHHH
T ss_conf 9983915899999999997---------32101055059999976
No 136
>pfam03746 LamB_YcsF LamB/YcsF family. This family includes LamB. The lam locus of Aspergillus nidulans consists of two divergently transcribed genes, lamA and lamB, involved in the utilisation of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive regulatory gene amdR and are subject to carbon and nitrogen metabolite repression. The exact molecular function of the proteins in this family is unknown.
Probab=25.83 E-value=36 Score=14.77 Aligned_cols=39 Identities=21% Similarity=0.409 Sum_probs=27.4
Q ss_pred CCCCHHHHHHHHCCCCCCCCCCCCHHH-HH---HHHHHHHHHH
Q ss_conf 422237899971875455566640269-99---9999999997
Q gi|254780818|r 137 SRNDLNSLCKRYGITISHRSKHGALLD-SH---LLSDVYIKMM 175 (245)
Q Consensus 137 ~~~~L~~l~~~~~i~~~~r~~H~Al~D-a~---~~a~v~~~ll 175 (245)
|-..|..+|+..|..+.|=+.|+||+- +. .+|+++...+
T Consensus 89 Qi~al~~~a~~~g~~l~hVKPHGALYn~~~~d~~la~~i~~ai 131 (242)
T pfam03746 89 QIGALQAFARAQGLRLQHVKPHGALYNMAAKDRALARAVAEAV 131 (242)
T ss_pred HHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHH
T ss_conf 9999999999829963113531999999965999999999999
No 137
>KOG3543 consensus
Probab=25.55 E-value=13 Score=17.46 Aligned_cols=70 Identities=29% Similarity=0.471 Sum_probs=41.0
Q ss_pred CCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCCC-----------CCCCCHHHHHH
Q ss_conf 2322431121000001122221000011000000017764222378999718754555-----------66640269999
Q gi|254780818|r 98 NAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHR-----------SKHGALLDSHL 166 (245)
Q Consensus 98 Na~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~r-----------~~H~Al~Da~~ 166 (245)
-..||-.+|-.-+.|..++...+.+ +|.+-+ +-||+-.-|+..|.+||+..-+| ...+|+.|-.+
T Consensus 603 pcnfdha~lf~~vqrltldhrlnds-ysclgw---fspgqvfvldeycarygvrgchrhlcyl~~lle~aenga~idptl 678 (1218)
T KOG3543 603 PCNFDHAHLFSDVQRLTLDHRLNDS-YSCLGW---FSPGQVFVLDEYCARYGVRGCHRHLCYLSNLLEKAENGALIDPTL 678 (1218)
T ss_pred CCCCCHHHHHHHHHHHHHHHHCCCC-CHHCCC---CCCCCEEEEHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHH
T ss_conf 8787469999999987431114785-201035---688716650777777412068888999999987511785037478
Q ss_pred HHHHH
Q ss_conf 99999
Q gi|254780818|r 167 LSDVY 171 (245)
Q Consensus 167 ~a~v~ 171 (245)
+---|
T Consensus 679 lhysf 683 (1218)
T KOG3543 679 LHYSF 683 (1218)
T ss_pred HHHHH
T ss_conf 88889
No 138
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=25.42 E-value=49 Score=13.97 Aligned_cols=27 Identities=15% Similarity=0.160 Sum_probs=15.5
Q ss_pred HHCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 71875455566640269999999999997
Q gi|254780818|r 147 RYGITISHRSKHGALLDSHLLSDVYIKMM 175 (245)
Q Consensus 147 ~~~i~~~~r~~H~Al~Da~~~a~v~~~ll 175 (245)
.++++.+| --+||+-|.-...-|..-+
T Consensus 335 ~~~~~ddH--~RDALAAA~kAY~~yk~kl 361 (652)
T COG2433 335 KISVSDDH--ERDALAAAYKAYLAYKPKL 361 (652)
T ss_pred CCCCCCCH--HHHHHHHHHHHHHHHHHHH
T ss_conf 88889944--7789999999999989999
No 139
>TIGR00326 eubact_ribD riboflavin biosynthesis protein RibD; InterPro: IPR004794 This entry describes the riboflavin biosynthesis protein (ribD) as found in Escherichia coli. The N-terminal domain includes the conserved zinc-binding site region that is shared by proteins such as cytosine deaminase, mammalian apolipoprotein B mRNA editing protein, blasticidin-S deaminase, and Bacillus subtilis competence protein comEB. The C-terminal domain is homologous to the full length of yeast HTP reductase, a protein required for riboflavin biosynthesis. A number of archaeal proteins that may be related to the riboflavin biosynthesis protein contain only the C-terminal domain.; GO: 0008703 5-amino-6-(5-phosphoribosylamino)uracil reductase activity, 0008835 diaminohydroxyphosphoribosylaminopyrimidine deaminase activity, 0009231 riboflavin biosynthetic process.
Probab=25.13 E-value=49 Score=13.94 Aligned_cols=140 Identities=21% Similarity=0.325 Sum_probs=72.3
Q ss_pred CCCCCCCCCEEEEEEEEEEE-CCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCC-C--CCCHHHHHHHHHHHCCC
Q ss_conf 78888888889999999999-99880313798985888228865724202101232248-5--21002344777530023
Q gi|254780818|r 16 TTGLDSKNDRIIEIGAVELL-DYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDK-P--SFSSIFSEFWDFFNEQN 91 (245)
Q Consensus 16 TTGl~~~~d~Iieigav~i~-~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~-p--~f~ev~~~f~~fi~~~~ 91 (245)
||--||. +|||.|. |+.++|+-||. ++ | .-+.|..+|+ ... +.+ | ++..-++.+-+||- ++
T Consensus 14 ~T~PNP~------VGcViv~~ng~IVG~G~H~--ka-G-~~HAE~~Al~---~AG-~~aRPeisLPkeanaLhefiC-kn 78 (393)
T TIGR00326 14 TTHPNPL------VGCVIVKKNGEIVGEGFHQ--KA-G-EPHAEIHALR---QAG-ENARPEISLPKEANALHEFIC-KN 78 (393)
T ss_pred CCCCCCC------EEEEEEECCCEEEEECCCC--CC-C-CCHHHHHHHH---HHH-HHCCCCCCCCHHHHHHHHHHH-HC
T ss_conf 0057986------0048983387587524669--77-8-8708999999---976-636886568513567888765-22
Q ss_pred CEEEEECCCCCCCEEEECHH---CCCCCCCCCCHHCCCHHCCCCCC----CCC--C-CCHHHHHHHHCCCCCCCCCCCCH
Q ss_conf 20231023224311210000---01122221000011000000017----764--2-22378999718754555666402
Q gi|254780818|r 92 AEWIAHNAKFDVGFINAELQ---RINKDPLDPSRIIDTLSIARRKH----PSS--R-NDLNSLCKRYGITISHRSKHGAL 161 (245)
Q Consensus 92 ~~lVaHNa~FD~~fL~~el~---r~~~~~~~~~~~iDTl~lar~~~----p~~--~-~~L~~l~~~~~i~~~~r~~H~Al 161 (245)
|..-|-=+-+--.|. .+|+.+++-.-++. .-+.|... |+. . ..+.-| +.-||+.. ++-|
T Consensus 79 -----hqGvfKGat~yVTLEPCsH~GrTPPCa~aii~-~Gi~kVv~~M~DpNplvaGkG~~~L-~~aGIeV~----~~~l 147 (393)
T TIGR00326 79 -----HQGVFKGATAYVTLEPCSHYGRTPPCAEAIIE-AGIKKVVVSMQDPNPLVAGKGIERL-KQAGIEVT----FGIL 147 (393)
T ss_pred -----CCCEEECCEEEECCCCCCCCCCCHHHHHHHHH-CCCEEEEEEEECCCCCCCCHHHHHH-HHCCCEEE----ECHH
T ss_conf -----67412077679815766888887156899973-8614898886508722234147999-86697254----4015
Q ss_pred HH-HHHHHHHHHHHHHCCCCC
Q ss_conf 69-999999999997305766
Q gi|254780818|r 162 LD-SHLLSDVYIKMMVGGSQI 181 (245)
Q Consensus 162 ~D-a~~~a~v~~~ll~g~~q~ 181 (245)
.| |+-+-+-|++-++.|-+.
T Consensus 148 ~~~a~~lnk~Fl~~~~~G~Pf 168 (393)
T TIGR00326 148 KEEAEKLNKGFLKRMRTGLPF 168 (393)
T ss_pred HHHHHHCCHHHHHHHCCCCCH
T ss_conf 898640005678886068853
No 140
>pfam10776 DUF2600 Protein of unknown function (DUF2600). This is a bacterial family of proteins. Some members in the family are annotated as YtpB however currently no function is known.
Probab=23.95 E-value=18 Score=16.72 Aligned_cols=17 Identities=12% Similarity=0.256 Sum_probs=7.7
Q ss_pred CCCCCCCHHHHHHHHHH
Q ss_conf 24852100234477753
Q gi|254780818|r 71 KDKPSFSSIFSEFWDFF 87 (245)
Q Consensus 71 ~~~p~f~ev~~~f~~fi 87 (245)
..=|.+..|-+.+.+++
T Consensus 128 ~~lP~y~~V~~~l~~l~ 144 (330)
T pfam10776 128 AKLPSYNLVRPYLLELA 144 (330)
T ss_pred HHCCCHHHHHHHHHHHH
T ss_conf 85886788999999999
No 141
>pfam11074 DUF2779 Domain of unknown function(DUF2779). This domain is conserved in bacteria. The function is not known.
Probab=22.70 E-value=27 Score=15.56 Aligned_cols=54 Identities=11% Similarity=0.235 Sum_probs=31.3
Q ss_pred CHHHHHHHHHHHCCCCEEEEECCCCCCCEEEECHHCCC------CCCCCCCHHCCCHHCCCC
Q ss_conf 00234477753002320231023224311210000011------222210000110000000
Q gi|254780818|r 77 SSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRIN------KDPLDPSRIIDTLSIARR 132 (245)
Q Consensus 77 ~ev~~~f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~------~~~~~~~~~iDTl~lar~ 132 (245)
.+.+..+++-|+.....+|+||++|..+.|+. ++..- +..+ ..+++|.+.+.+.
T Consensus 55 ~~~~~~L~~~i~~~~Gsi~~yn~sfEk~~l~e-la~~~p~~~~~l~~I-~~r~vDL~~~f~~ 114 (127)
T pfam11074 55 RAFIEALKKAIGKDYGSIVVYNKSFEKTRLKE-LAQLFPELADKIKAI-IERTVDLLDLFKK 114 (127)
T ss_pred HHHHHHHHHHHCCCCCEEEEEHHHHHHHHHHH-HHHHHHHHHHHHHHH-HHHHHHHHHHHHH
T ss_conf 99999999984767870999624889999999-999869999999999-9986878999950
No 142
>pfam04382 SAB SAB domain. This presumed domain is found in proteins containing FERM domains pfam00373. This domain is found to bind to both spectrin and actin, hence the name SAB (Spectrin and Actin Binding) domain.
Probab=22.53 E-value=38 Score=14.60 Aligned_cols=29 Identities=28% Similarity=0.573 Sum_probs=18.8
Q ss_pred CCHHHHHHHHHHHHHCCCC----------HHHHHHCCCC
Q ss_conf 8999999999999870878----------1145630557
Q gi|254780818|r 216 ITKEELDEHDKTIQTLGKN----------AIWDRYISSN 244 (245)
Q Consensus 216 ~~~~e~~~H~~~l~~l~k~----------~lW~k~~~~~ 244 (245)
.+.+++-.|...|..|+++ .=|+|+|+++
T Consensus 7 k~qe~~lKHqasIsELKRtFmEs~~~~~~~eWeKRLstS 45 (48)
T pfam04382 7 KTQDELLKHQASISELKRTFMESTPEPRPNEWEKRLSTS 45 (48)
T ss_pred CCHHHHHHHHCCHHHHHHHHHHCCCCCCCCHHHHHHCCC
T ss_conf 189999987523999999998439999953777750268
No 143
>PHA02458 A protein A*; Reviewed
Probab=21.32 E-value=27 Score=15.57 Aligned_cols=17 Identities=18% Similarity=0.294 Sum_probs=12.3
Q ss_pred CHHHHHHHHHHHHHHHH
Q ss_conf 02699999999999973
Q gi|254780818|r 160 ALLDSHLLSDVYIKMMV 176 (245)
Q Consensus 160 Al~Da~~~a~v~~~ll~ 176 (245)
-+.=|.+.+++.++|+.
T Consensus 222 l~smahls~e~l~elt~ 238 (341)
T PHA02458 222 LLSMAHLSAETLMELTQ 238 (341)
T ss_pred HHHHHHHHHHHHHHHHH
T ss_conf 12466544899999987
No 144
>TIGR01367 pyrE_Therm orotate phosphoribosyltransferase; InterPro: IPR006273 This group of sequences are a distinct clade of orotate phosphoribosyltransferases. Members include the experimentally determined example from Thermus aquaticus and additional examples from Caulobacter crescentus, Helicobacter pylori (Campylobacter pylori), Mesorhizobium loti, and related species. ; GO: 0004588 orotate phosphoribosyltransferase activity, 0019856 pyrimidine base biosynthetic process.
Probab=20.66 E-value=60 Score=13.38 Aligned_cols=32 Identities=13% Similarity=0.146 Sum_probs=13.9
Q ss_pred CCCCCCCHHHHHHHHHHHCCCCEEEEECCCCCCCEE
Q ss_conf 248521002344777530023202310232243112
Q gi|254780818|r 71 KDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFI 106 (245)
Q Consensus 71 ~~~p~f~ev~~~f~~fi~~~~~~lVaHNa~FD~~fL 106 (245)
.++=+..+++..+-+ .|..+||--+=-|.+|-
T Consensus 122 TTGGS~~e~~~~i~~----~GG~vvg~a~iidRGfC 153 (205)
T TIGR01367 122 TTGGSLLEAIKAIEE----LGGQVVGLACIIDRGFC 153 (205)
T ss_pred CCCHHHHHHHHHHHH----CCCCEEEEEEHHCCCHH
T ss_conf 047448999999985----79827984211204111
No 145
>TIGR01851 argC_other N-acetyl-gamma-glutamyl-phosphate reductase; InterPro: IPR010136 N -Acetylglutamate (NAG) fulfils distinct biological roles in lower and higher organisms. In prokaryotes, lower eukaryotes and plants it is the first intermediate in the biosynthesis of arginine, whereas in ureotelic (excreting nitrogen mostly in the form of urea) vertebrates, it is an essential allosteric cofactor for carbamyl phosphate synthetase I (CPSI), the first enzyme of the urea cycle. The pathway that leads from glutamate to arginine in lower organisms employs eight steps, starting with the acetylation of glutamate to form NAG. In these species, NAG can be produced by two enzymatic reactions: one catalysed by NAG synthase (NAGS) and the other by ornithine acetyltransferase (OAT). In ureotelic species, NAG is produced exclusively by NAGS. In lower organisms, NAGS is feedback-inhibited by L-arginine, whereas mammalian NAGS activity is significantly enhanced by this amino acid. The NAGS genes of bacteria, fungi and mammals are more diverse than other arginine-biosynthesis and urea-cycle genes. The evolutionary relationship between the distinctly different roles of NAG and its metabolism in lower and higher organisms remains to be determined . The pathway from glutamate to arginine is: NAGS; N-acetylglutamate synthase (2.3.1.1 from EC) (glutamate to N-acetylglutamate) NAGK; N-acetylglutamate kinase (2.7.2.8 from EC) (N-acetylglutamate to N-acetylglutamate-5P) NAGSA; N-acetyl-gamma-glutamyl-phosphate reductase (1.2.1.38 from EC) (N-acetylglutamate-5P to N-acetylglumate semialdehyde) Acetylornithine aminotransferase (2.6.1.11 from EC) (N-acetylglumate semialdehyde to N-acetylornithine) Acetylornithine deacetylase (3.5.1.16 from EC) (N-acetylornithine to ornithine) Arginase (3.5.3.1 from EC) (ornithine to arginine) This entry represents bacterial N-acetyl-gamma-glutamyl-phosphate reductases, an enzyme catalysing the third step of arginine biosynthesis from glutamate.; GO: 0003942 N-acetyl-gamma-glutamyl-phosphate reductase activity, 0006526 arginine biosynthetic process, 0005737 cytoplasm.
Probab=20.65 E-value=47 Score=14.08 Aligned_cols=64 Identities=22% Similarity=0.329 Sum_probs=33.3
Q ss_pred EEEECC--CCCCC------CCCC-EEEEEEEEEEECC---------EEC---------CCEEEEEEC-CCCCCCCHHHEE
Q ss_conf 999846--78888------8888-8999999999999---------880---------313798985-888228865724
Q gi|254780818|r 10 IVFDIE--TTGLD------SKND-RIIEIGAVELLDY---------SKT---------NRTFQVFLC-PNGRKNSPEALK 61 (245)
Q Consensus 10 iv~D~E--TTGl~------~~~d-~Iieigav~i~~~---------~~~---------~~~f~~~i~-P~~~~i~~~~~~ 61 (245)
|++|=| ||||- -+.| ++|+|+.++-+|- ..+ .++=-+||+ |+.+-|+ .+++
T Consensus 4 vFiDGeaGTTGLqi~~rL~~R~DleLlsI~~~rRKDa~~RA~lLNaaDvaiLCLPDdAarEAVSLv~np~~~ilD-ASTA 82 (314)
T TIGR01851 4 VFIDGEAGTTGLQIRERLSGRDDLELLSIAPDRRKDAAERAKLLNAADVAILCLPDDAAREAVSLVDNPNTKILD-ASTA 82 (314)
T ss_pred EEECCCCCCHHHHHHHHHCCCCCHHEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHCEECCCCCCCEEEE-CCCC
T ss_conf 364178886267898862477620003106332679799887754673233348624554300002687724751-5400
Q ss_pred ECCCCCCCCCCCCC
Q ss_conf 20210123224852
Q gi|254780818|r 62 LHGITDEFLKDKPS 75 (245)
Q Consensus 62 ihGIt~~~l~~~p~ 75 (245)
|.+.++.+=+-|.
T Consensus 83 -yRt~~dW~YGfpE 95 (314)
T TIGR01851 83 -YRTADDWVYGFPE 95 (314)
T ss_pred -CCCCCCCCCCCCC
T ss_conf -0048774114645
No 146
>COG3219 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.12 E-value=29 Score=15.35 Aligned_cols=54 Identities=20% Similarity=0.319 Sum_probs=32.8
Q ss_pred EEECCCCCCCCCCC----CCCCHHHHHHHHHHHCCCCEE--EEECCCCCCCEEEECHHCC
Q ss_conf 24202101232248----521002344777530023202--3102322431121000001
Q gi|254780818|r 60 LKLHGITDEFLKDK----PSFSSIFSEFWDFFNEQNAEW--IAHNAKFDVGFINAELQRI 113 (245)
Q Consensus 60 ~~ihGIt~~~l~~~----p~f~ev~~~f~~fi~~~~~~l--VaHNa~FD~~fL~~el~r~ 113 (245)
..=|+....++.++ |.|.++..+|+.||......= +.-=+.|.+.-|..+++..
T Consensus 60 ~~W~~lke~Fvre~ra~tPyFq~IageFl~~cq~~~~~~~~ilaLmdFE~tqllaevae~ 119 (237)
T COG3219 60 ERWHRLKEGFVREGRAHTPYFQDIAGEFLQYCQSLPLFDGAILALMDFEYTQLLAEVAEA 119 (237)
T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf 999999999987245689328871699999987123355789999855899999998538
Done!