Query 037014
Match_columns 198
No_of_seqs 152 out of 1063
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 07:42:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037014.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037014hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06146 mut-7_like_exo DEDDy 3 100.0 5.2E-41 1.1E-45 265.2 18.1 171 17-194 2-193 (193)
2 cd06141 WRN_exo DEDDy 3'-5' ex 100.0 1.1E-39 2.4E-44 252.3 19.5 168 20-194 2-170 (170)
3 cd06129 RNaseD_like DEDDy 3'-5 100.0 1E-38 2.3E-43 245.3 17.2 157 25-193 2-160 (161)
4 PRK10829 ribonuclease D; Provi 100.0 6.3E-33 1.4E-37 237.5 18.9 165 17-194 4-168 (373)
5 PF01612 DNA_pol_A_exo1: 3'-5' 100.0 9.2E-33 2E-37 213.2 14.6 168 18-194 3-173 (176)
6 cd06148 Egl_like_exo DEDDy 3'- 100.0 3.6E-32 7.9E-37 215.4 12.3 152 40-195 10-176 (197)
7 COG0349 Rnd Ribonuclease D [Tr 100.0 2.6E-30 5.7E-35 217.1 15.3 162 21-194 3-164 (361)
8 TIGR01388 rnd ribonuclease D. 100.0 4.5E-29 9.8E-34 214.3 18.3 163 19-194 2-164 (367)
9 KOG4373 Predicted 3'-5' exonuc 99.9 4.8E-27 1E-31 193.3 12.0 187 4-191 16-283 (319)
10 cd06142 RNaseD_exo DEDDy 3'-5' 99.9 1.1E-22 2.3E-27 157.7 17.3 157 25-194 2-158 (178)
11 smart00474 35EXOc 3'-5' exonuc 99.9 1.2E-22 2.7E-27 155.5 17.1 166 18-195 3-170 (172)
12 KOG2207 Predicted 3'-5' exonuc 99.9 3.6E-23 7.8E-28 181.4 8.8 174 14-194 390-583 (617)
13 cd09018 DEDDy_polA_RNaseD_like 99.9 2E-20 4.4E-25 140.8 13.6 147 42-193 1-149 (150)
14 cd06147 Rrp6p_like_exo DEDDy 3 99.8 8.2E-19 1.8E-23 138.2 17.6 163 19-194 8-170 (192)
15 cd00007 35EXOc 3'-5' exonuclea 99.8 3E-19 6.5E-24 134.3 13.2 148 42-195 2-154 (155)
16 KOG2206 Exosome 3'-5' exoribon 99.7 2.9E-18 6.3E-23 150.2 8.0 164 18-195 195-359 (687)
17 PRK05755 DNA polymerase I; Pro 99.7 5.4E-16 1.2E-20 146.6 16.2 166 18-195 298-468 (880)
18 cd06140 DNA_polA_I_Bacillus_li 99.6 1.7E-14 3.7E-19 111.9 13.0 148 41-194 4-154 (178)
19 cd06139 DNA_polA_I_Ecoli_like_ 99.6 1.4E-13 2.9E-18 107.7 14.2 150 40-194 5-168 (193)
20 PRK14975 bifunctional 3'-5' ex 99.4 9.3E-13 2E-17 119.0 10.1 137 18-195 5-143 (553)
21 COG0749 PolA DNA polymerase I 99.4 3.8E-12 8.3E-17 113.9 11.3 162 21-194 8-178 (593)
22 TIGR00593 pola DNA polymerase 99.1 2.4E-09 5.1E-14 101.3 15.2 159 21-194 309-475 (887)
23 cd06128 DNA_polA_exo DEDDy 3'- 98.9 7E-08 1.5E-12 72.8 13.8 130 58-193 17-150 (151)
24 cd06125 DnaQ_like_exo DnaQ-lik 98.1 1.9E-05 4.1E-10 55.3 8.3 60 43-114 1-63 (96)
25 KOG2249 3'-5' exonuclease [Rep 97.9 0.00011 2.3E-09 60.0 10.0 130 41-194 106-264 (280)
26 cd05780 DNA_polB_Kod1_like_exo 97.9 0.00027 5.8E-09 55.8 12.2 149 40-192 3-195 (195)
27 cd06149 ISG20 DEDDh 3'-5' exon 97.8 0.00022 4.7E-09 54.4 9.9 87 85-190 69-157 (157)
28 cd05160 DEDDy_DNA_polB_exo DED 97.8 0.00074 1.6E-08 53.1 12.5 144 42-189 1-198 (199)
29 cd06144 REX4_like DEDDh 3'-5' 97.7 0.00025 5.4E-09 53.7 8.6 84 85-190 69-152 (152)
30 PRK05711 DNA polymerase III su 97.5 0.0037 8.1E-08 51.0 13.6 90 85-196 78-176 (240)
31 cd06143 PAN2_exo DEDDh 3'-5' e 97.5 0.00037 8E-09 54.0 6.5 80 87-190 95-174 (174)
32 PRK06310 DNA polymerase III su 97.4 0.0047 1E-07 50.7 12.9 87 85-194 79-172 (250)
33 cd06137 DEDDh_RNase DEDDh 3'-5 97.4 0.0035 7.6E-08 47.9 11.1 84 86-189 76-160 (161)
34 cd06145 REX1_like DEDDh 3'-5' 97.3 0.0034 7.3E-08 47.5 9.9 82 86-189 68-149 (150)
35 PRK06807 DNA polymerase III su 97.3 0.0076 1.6E-07 51.1 12.7 87 85-195 80-171 (313)
36 PRK07883 hypothetical protein; 97.3 0.008 1.7E-07 54.9 13.5 90 85-195 87-181 (557)
37 PRK07740 hypothetical protein; 97.2 0.033 7.1E-07 45.6 15.4 147 23-195 33-225 (244)
38 cd06134 RNaseT DEDDh 3'-5' exo 97.2 0.023 5E-07 44.5 14.0 79 95-195 102-188 (189)
39 TIGR01406 dnaQ_proteo DNA poly 97.2 0.013 2.9E-07 47.3 12.8 90 85-196 74-172 (225)
40 PRK06063 DNA polymerase III su 97.1 0.0064 1.4E-07 51.6 10.7 88 85-195 86-178 (313)
41 PRK08517 DNA polymerase III su 97.1 0.016 3.4E-07 47.9 12.6 86 85-194 139-229 (257)
42 PRK07942 DNA polymerase III su 97.1 0.014 3.1E-07 47.3 12.1 80 95-194 93-178 (232)
43 TIGR00573 dnaq exonuclease, DN 97.1 0.012 2.7E-07 47.1 11.4 93 85-197 79-178 (217)
44 PRK06309 DNA polymerase III su 97.1 0.019 4E-07 46.6 12.5 130 40-195 2-165 (232)
45 cd05777 DNA_polB_delta_exo DED 97.0 0.019 4.2E-07 46.4 12.2 69 122-193 154-224 (230)
46 cd06131 DNA_pol_III_epsilon_Ec 97.0 0.008 1.7E-07 45.8 9.1 86 85-192 73-166 (167)
47 smart00479 EXOIII exonuclease 96.9 0.03 6.6E-07 42.2 11.7 88 85-195 72-166 (169)
48 PRK07246 bifunctional ATP-depe 96.9 0.02 4.3E-07 54.7 12.6 88 85-195 78-169 (820)
49 cd06127 DEDDh DEDDh 3'-5' exon 96.8 0.02 4.4E-07 42.2 10.3 83 85-189 71-158 (159)
50 TIGR01407 dinG_rel DnaQ family 96.8 0.024 5.3E-07 54.3 13.1 87 85-194 72-163 (850)
51 PRK05168 ribonuclease T; Provi 96.8 0.086 1.9E-06 42.1 14.3 79 95-195 114-200 (211)
52 KOG3657 Mitochondrial DNA poly 96.8 0.0072 1.6E-07 56.5 8.5 107 82-193 226-380 (1075)
53 PRK08074 bifunctional ATP-depe 96.7 0.036 7.9E-07 53.6 13.4 88 85-195 76-168 (928)
54 cd05784 DNA_polB_II_exo DEDDy 96.7 0.022 4.7E-07 45.0 9.9 99 85-190 56-193 (193)
55 cd05781 DNA_polB_B3_exo DEDDy 96.7 0.049 1.1E-06 42.7 11.7 146 41-192 4-188 (188)
56 PRK09145 DNA polymerase III su 96.7 0.077 1.7E-06 41.9 12.9 91 85-196 103-201 (202)
57 KOG2248 3'-5' exonuclease [Rep 96.5 0.013 2.7E-07 50.9 7.7 90 83-193 283-372 (380)
58 PRK07983 exodeoxyribonuclease 96.4 0.17 3.8E-06 40.7 13.5 87 85-194 66-152 (219)
59 cd06136 TREX1_2 DEDDh 3'-5' ex 96.4 0.072 1.6E-06 41.3 10.8 82 85-191 86-176 (177)
60 PRK06195 DNA polymerase III su 96.4 0.1 2.2E-06 44.2 12.4 87 85-195 72-163 (309)
61 PRK07247 DNA polymerase III su 96.3 0.14 3.1E-06 40.4 12.4 88 85-195 76-168 (195)
62 TIGR01405 polC_Gram_pos DNA po 96.3 0.07 1.5E-06 52.9 12.4 87 85-194 262-353 (1213)
63 cd05783 DNA_polB_B1_exo DEDDy 96.3 0.27 5.8E-06 39.1 13.8 141 41-190 6-202 (204)
64 PRK09146 DNA polymerase III su 96.2 0.21 4.6E-06 40.7 13.1 89 86-195 122-226 (239)
65 PRK05601 DNA polymerase III su 96.2 0.13 2.8E-06 44.6 12.1 94 85-192 117-245 (377)
66 PRK07748 sporulation inhibitor 96.0 0.24 5.1E-06 39.3 12.3 90 85-195 84-179 (207)
67 PHA02528 43 DNA polymerase; Pr 96.0 0.42 9.1E-06 46.1 15.7 181 8-192 49-324 (881)
68 cd05785 DNA_polB_like2_exo Unc 95.7 0.33 7.2E-06 38.7 11.8 145 40-189 9-206 (207)
69 cd05779 DNA_polB_epsilon_exo D 95.7 0.26 5.7E-06 39.2 11.2 92 93-189 88-203 (204)
70 cd06133 ERI-1_3'hExo_like DEDD 95.5 0.63 1.4E-05 35.3 12.6 88 85-193 80-176 (176)
71 PF13482 RNase_H_2: RNase_H su 95.0 0.12 2.6E-06 39.0 7.1 141 43-192 1-163 (164)
72 KOG1275 PAB-dependent poly(A) 94.9 0.0096 2.1E-07 56.1 0.9 82 89-193 1008-1089(1118)
73 TIGR01298 RNaseT ribonuclease 94.2 0.4 8.7E-06 37.9 8.5 79 95-195 105-191 (200)
74 cd06130 DNA_pol_III_epsilon_li 93.8 0.74 1.6E-05 34.2 8.9 81 85-189 69-154 (156)
75 COG0847 DnaQ DNA polymerase II 93.4 2.5 5.4E-05 34.0 12.0 91 85-195 86-181 (243)
76 PRK09182 DNA polymerase III su 93.2 2.7 5.8E-05 35.4 12.2 86 85-193 112-198 (294)
77 cd05782 DNA_polB_like1_exo Unc 93.2 0.71 1.5E-05 36.7 8.4 129 55-190 47-207 (208)
78 PRK05762 DNA polymerase II; Re 93.0 1.9 4.1E-05 41.3 12.2 145 40-192 155-348 (786)
79 PRK06722 exonuclease; Provisio 92.6 2.3 5E-05 35.6 10.9 91 85-195 82-180 (281)
80 PRK11779 sbcB exonuclease I; P 92.6 1.2 2.5E-05 40.1 9.6 91 86-195 84-197 (476)
81 COG2176 PolC DNA polymerase II 92.5 0.54 1.2E-05 46.2 7.8 87 85-194 493-584 (1444)
82 PTZ00166 DNA polymerase delta 92.0 2.8 6.1E-05 41.4 12.2 69 122-193 413-483 (1054)
83 PRK00448 polC DNA polymerase I 91.6 1.6 3.6E-05 44.3 10.2 89 86-195 489-583 (1437)
84 KOG2405 Predicted 3'-5' exonuc 90.6 0.0039 8.4E-08 53.5 -7.7 71 57-127 72-144 (458)
85 KOG2405 Predicted 3'-5' exonuc 89.7 0.18 4E-06 43.5 1.6 145 40-194 195-359 (458)
86 PF10108 DNA_pol_B_exo2: Predi 88.7 7.7 0.00017 31.0 10.1 101 85-193 42-170 (209)
87 smart00486 POLBc DNA polymeras 86.2 16 0.00035 31.9 11.8 69 121-192 150-220 (471)
88 cd05778 DNA_polB_zeta_exo inac 84.6 1.6 3.5E-05 35.3 4.3 65 122-189 163-230 (231)
89 cd06138 ExoI_N N-terminal DEDD 80.1 4.7 0.0001 31.1 5.3 84 86-188 75-181 (183)
90 COG3359 Predicted exonuclease 77.9 38 0.00082 28.0 9.8 149 41-194 99-267 (278)
91 TIGR00592 pol2 DNA polymerase 72.2 16 0.00036 36.6 7.8 96 93-193 599-723 (1172)
92 cd05776 DNA_polB_alpha_exo ina 69.6 5.4 0.00012 32.2 3.3 97 92-193 96-227 (234)
93 PF04857 CAF1: CAF1 family rib 66.3 12 0.00027 30.7 4.8 92 93-190 147-261 (262)
94 PTZ00315 2'-phosphotransferase 65.2 1.2E+02 0.0026 28.2 13.7 95 85-197 135-256 (582)
95 COG4328 Predicted nuclease (RN 64.8 10 0.00022 30.7 3.8 34 41-80 2-35 (266)
96 PF00843 Arena_nucleocap: Aren 50.1 9.3 0.0002 33.9 1.4 112 40-158 372-507 (533)
97 PF00169 PH: PH domain; Inter 49.4 56 0.0012 21.3 5.1 33 3-35 70-102 (104)
98 PRK05761 DNA polymerase I; Rev 48.6 1.4E+02 0.003 28.8 9.2 99 83-189 213-334 (787)
99 cd01246 PH_oxysterol_bp Oxyste 47.8 45 0.00098 21.7 4.4 32 3-34 59-90 (91)
100 COG5233 GRH1 Peripheral Golgi 47.6 12 0.00027 31.9 1.8 44 1-52 137-180 (417)
101 PHA03334 putative DNA polymera 41.5 93 0.002 32.0 6.8 72 121-193 471-556 (1545)
102 cd00821 PH Pleckstrin homology 37.0 81 0.0018 19.7 4.3 32 3-34 64-95 (96)
103 cd01260 PH_CNK Connector enhan 36.4 75 0.0016 21.3 4.1 32 3-34 64-95 (96)
104 COG0417 PolB DNA polymerase el 36.1 4.1E+02 0.0089 25.7 13.8 148 40-191 154-349 (792)
105 PHA02563 DNA polymerase; Provi 34.8 4E+02 0.0086 25.2 10.7 147 40-193 12-192 (630)
106 PHA02524 43A DNA polymerase su 34.5 1.4E+02 0.003 27.2 6.4 166 20-190 61-322 (498)
107 PF04857 CAF1: CAF1 family rib 33.7 1.2E+02 0.0026 24.8 5.6 27 22-53 9-35 (262)
108 smart00233 PH Pleckstrin homol 33.3 1.2E+02 0.0027 19.1 4.8 33 3-35 68-100 (102)
109 cd01253 PH_beta_spectrin Beta- 31.1 1.2E+02 0.0027 20.5 4.6 32 3-34 72-103 (104)
110 cd01251 PH_centaurin_alpha Cen 30.8 1.4E+02 0.0031 20.5 4.8 31 4-35 69-99 (103)
111 PF03633 Glyco_hydro_65C: Glyc 30.4 97 0.0021 18.6 3.5 18 2-19 9-26 (54)
112 PF13289 SIR2_2: SIR2-like dom 30.2 44 0.00095 23.9 2.2 30 82-111 75-105 (143)
113 KOG0685 Flavin-containing amin 30.0 43 0.00094 30.2 2.4 34 140-173 392-426 (498)
114 cd01247 PH_GPBP Goodpasture an 29.4 1.7E+02 0.0037 19.7 4.9 31 4-34 60-90 (91)
115 KOG1798 DNA polymerase epsilon 29.1 4.7E+02 0.01 27.8 9.3 145 39-191 245-449 (2173)
116 KOG1097 Adenine deaminase/aden 28.0 2E+02 0.0043 25.4 6.1 146 21-173 189-341 (399)
117 cd07027 RNAP_RPB11_like RPB11 27.3 1.6E+02 0.0035 19.7 4.4 35 70-104 8-44 (83)
118 TIGR03491 RecB family nuclease 27.1 4.5E+02 0.0098 23.4 9.4 146 40-192 284-457 (457)
119 cd01257 PH_IRS Insulin recepto 27.0 1.9E+02 0.0041 20.1 4.9 31 3-34 70-100 (101)
120 cd01244 PH_RasGAP_CG9209 RAS_G 26.2 1.7E+02 0.0037 20.2 4.5 31 3-34 67-97 (98)
121 PF07808 RED_N: RED-like prote 26.0 21 0.00047 29.1 -0.1 27 1-27 172-200 (238)
122 PF10364 NKWYS: Putative capsu 25.6 1.6E+02 0.0035 22.0 4.5 61 26-98 34-96 (141)
123 PF10584 Proteasome_A_N: Prote 24.6 42 0.00091 17.0 0.8 7 173-179 15-21 (23)
124 cd01265 PH_PARIS-1 PARIS-1 ple 23.7 2E+02 0.0044 19.4 4.5 31 4-35 63-93 (95)
125 PF00929 RNase_T: Exonuclease; 22.2 1.1E+02 0.0023 21.8 3.1 84 85-189 74-164 (164)
126 cd06927 RNAP_L L subunit of Ar 22.0 2.4E+02 0.0052 18.9 4.5 34 71-104 9-44 (83)
127 cd07029 RNAP_I_III_AC19 AC19 s 21.9 67 0.0014 21.7 1.7 32 72-103 10-43 (85)
128 KOG0095 GTPase Rab30, small G 21.6 1.3E+02 0.0028 23.1 3.3 37 72-108 84-125 (213)
129 cd01266 PH_Gab Gab (Grb2-assoc 21.5 2.2E+02 0.0047 19.7 4.4 24 11-34 83-106 (108)
130 PF13656 RNA_pol_L_2: RNA poly 21.4 85 0.0018 20.7 2.1 20 85-104 16-36 (77)
131 PRK01146 DNA-directed RNA poly 21.3 2.5E+02 0.0054 18.9 4.4 33 72-104 12-46 (85)
132 PF00982 Glyco_transf_20: Glyc 20.6 1E+02 0.0022 27.8 3.1 66 6-71 230-322 (474)
No 1
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=100.00 E-value=5.2e-41 Score=265.19 Aligned_cols=171 Identities=25% Similarity=0.347 Sum_probs=149.5
Q ss_pred EEcCCHHHHHHHHHH--HHhhccCCCeEEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEccccC-----cccHHHHH
Q 037014 17 TVTSTTSVAENWLLK--IRSLHSAQILIVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYMD-----CIPLSIKN 89 (198)
Q Consensus 17 ~v~~~~~~~~~~i~~--~~~~~~~~~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~~-----~~~~~L~~ 89 (198)
.++++++++++++.. +.. .++||||+||.+.+..+..+++|+||||+++.|||||+...+ .+|+.|++
T Consensus 2 ~~i~~~~el~~~~~~~~l~~-----~~vig~D~Ew~~~~~~~~~~~v~LiQiat~~~~~lid~~~~~~~~~~~~~~~L~~ 76 (193)
T cd06146 2 HIVDSEEELEALLLALSLEA-----GRVVGIDSEWKPSFLGDSDPRVAILQLATEDEVFLLDLLALENLESEDWDRLLKR 76 (193)
T ss_pred eEecCHHHHHHHHHHHhhcc-----CCEEEEECccCCCccCCCCCCceEEEEecCCCEEEEEchhccccchHHHHHHHHH
Confidence 356799999999999 444 599999999999865556899999999999999999998754 47789999
Q ss_pred hhcCCCeEEEEEeecchHHHHhhhcCC------ccCceeehHHHHHHhCCCC--------CCCCchHHHHHHHHcCCcCC
Q 037014 90 FLSDPNVVFVGIEVEEIMSKLKNEYGL------CIKKKIDVRTLAKLHFPIS--------CLGKPGLKVLAYQLLRLRPW 155 (198)
Q Consensus 90 lL~d~~i~kvG~~~~~D~~~L~~~~gi------~~~~~~Dl~~l~~~~l~~~--------~~~~~~L~~l~~~~l~~~l~ 155 (198)
+|+||+|+||||++++|++.|++.||+ .++|++|++.++....+.. .....||++||+++||.+++
T Consensus 77 ll~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~~l~ 156 (193)
T cd06146 77 LFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLD 156 (193)
T ss_pred HhCCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCCCcC
Confidence 999999999999999999999999987 4789999999887543210 02378999999999999999
Q ss_pred CCCceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 037014 156 KPKKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLL 194 (198)
Q Consensus 156 K~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~ 194 (198)
|. .++|||++||||++|+.|||.|||+++.||++|.+
T Consensus 157 K~--~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~~ 193 (193)
T cd06146 157 KS--EQCSNWERRPLREEQILYAALDAYCLLEVFDKLLE 193 (193)
T ss_pred cc--cccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 95 58999999999999999999999999999999974
No 2
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=100.00 E-value=1.1e-39 Score=252.26 Aligned_cols=168 Identities=32% Similarity=0.478 Sum_probs=151.6
Q ss_pred CCHHHHHHHHHHHH-hhccCCCeEEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEccccCcccHHHHHhhcCCCeEE
Q 037014 20 STTSVAENWLLKIR-SLHSAQILIVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYMDCIPLSIKNFLSDPNVVF 98 (198)
Q Consensus 20 ~~~~~~~~~i~~~~-~~~~~~~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~~~~~~~L~~lL~d~~i~k 98 (198)
+++++++++++.+. . ..+||||+||.+.+..+..+++++||||+++.|+|||+.+.+.+|+.|+++|++++|.|
T Consensus 2 ~~~~~~~~~~~~~~~~-----~~~ig~D~E~~~~~~~~~~~~~~liQl~~~~~~~l~~~~~~~~~~~~l~~ll~~~~i~k 76 (170)
T cd06141 2 DSAQDAEEAVKELLGK-----EKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQLAHMDKLPPSLKQLLEDPSILK 76 (170)
T ss_pred CCHHHHHHHHHHHhcC-----CCEEEEeCccCCccCCCCCCCceEEEEecCCcEEEEEhhhhhcccHHHHHHhcCCCeeE
Confidence 57889999999988 5 59999999999986445789999999999999999999987789999999999999999
Q ss_pred EEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCCCCCCCHHHHHHH
Q 037014 99 VGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLESGFLDTELIKFA 178 (198)
Q Consensus 99 vG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~~Qi~YA 178 (198)
|||++++|++.|.+.+|+.+++++|++.++. .++ +..++.||++|++.++|.+++|++.+++|||++||||++||+||
T Consensus 77 v~~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~-ll~-~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt~~qi~YA 154 (170)
T cd06141 77 VGVGIKGDARKLARDFGIEVRGVVDLSHLAK-RVG-PRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYA 154 (170)
T ss_pred EEeeeHHHHHHHHhHcCCCCCCeeeHHHHHH-HhC-CCcCCccHHHHHHHHcCcccCCCCCcccCCCCCCCCCHHHHHHH
Confidence 9999999999998899999999999987665 555 32234699999999999999988899999999999999999999
Q ss_pred HHhHHHHHHHHHHHhc
Q 037014 179 CIDAYVSCAIGTKLLL 194 (198)
Q Consensus 179 A~Da~~~~~l~~~L~~ 194 (198)
|.|||+++.||++|..
T Consensus 155 a~Da~~~~~l~~~l~~ 170 (170)
T cd06141 155 ATDAYASLELYRKLLA 170 (170)
T ss_pred HHHHHHHHHHHHHHhC
Confidence 9999999999999863
No 3
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=100.00 E-value=1e-38 Score=245.27 Aligned_cols=157 Identities=21% Similarity=0.271 Sum_probs=139.4
Q ss_pred HHHHHHHHH-hhccCCCeEEEEeeeecCCCCCCCCCceeEEEeeeC-CeEEEEEccccCcccHHHHHhhcCCCeEEEEEe
Q 037014 25 AENWLLKIR-SLHSAQILIVGLNCKWKPHPIPSLSGKIATLQLCVD-TKCLILQLLYMDCIPLSIKNFLSDPNVVFVGIE 102 (198)
Q Consensus 25 ~~~~i~~~~-~~~~~~~~~vg~D~Ew~~~~~~~~~~~~~liQla~~-~~~~i~~l~~~~~~~~~L~~lL~d~~i~kvG~~ 102 (198)
++++++.+. . .++||||+||.+.+ ...+++|+||||++ +.|+|||+...+..|+.|+++|+|++|+||||+
T Consensus 2 l~~~~~~l~~~-----~~~ig~D~E~~~~~--~~~~~~~liQl~~~~~~~~l~d~~~~~~~~~~L~~lL~d~~i~Kvg~~ 74 (161)
T cd06129 2 LSSLCEDLSMD-----GDVIAFDMEWPPGR--RYYGEVALIQLCVSEEKCYLFDPLSLSVDWQGLKMLLENPSIVKALHG 74 (161)
T ss_pred HHHHHHHHhcC-----CCEEEEECCccCCC--CCCCceEEEEEEECCCCEEEEecccCccCHHHHHHHhCCCCEEEEEec
Confidence 456677777 4 59999999999984 35689999999999 899999999876678999999999999999999
Q ss_pred ecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCCCCCCCHHHHHHHHHhH
Q 037014 103 VEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLESGFLDTELIKFACIDA 182 (198)
Q Consensus 103 ~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~~Qi~YAA~Da 182 (198)
+++|++.|.+.+|+.+.|++|++.++ +.++.+ .+.||++++++++|.+++| .+++|||++||||++|++|||.||
T Consensus 75 ~k~D~~~L~~~~gi~~~~~~D~~~aa-~ll~~~--~~~~L~~l~~~~lg~~l~K--~~~~s~W~~rpLt~~qi~YAa~Da 149 (161)
T cd06129 75 IEGDLWKLLRDFGEKLQRLFDTTIAA-NLKGLP--ERWSLASLVEHFLGKTLDK--SISCADWSYRPLTEDQKLYAAADV 149 (161)
T ss_pred cHHHHHHHHHHcCCCcccHhHHHHHH-HHhCCC--CCchHHHHHHHHhCCCCCc--cceeccCCCCCCCHHHHHHHHHHH
Confidence 99999999878999999999997755 567643 3579999999999999987 679999999999999999999999
Q ss_pred HHHHHHHHHHh
Q 037014 183 YVSCAIGTKLL 193 (198)
Q Consensus 183 ~~~~~l~~~L~ 193 (198)
++++.||++|.
T Consensus 150 ~~l~~l~~~l~ 160 (161)
T cd06129 150 YALLIIYTKLR 160 (161)
T ss_pred HHHHHHHHHHh
Confidence 99999999985
No 4
>PRK10829 ribonuclease D; Provisional
Probab=100.00 E-value=6.3e-33 Score=237.55 Aligned_cols=165 Identities=16% Similarity=0.146 Sum_probs=147.8
Q ss_pred EEcCCHHHHHHHHHHHHhhccCCCeEEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEccccCcccHHHHHhhcCCCe
Q 037014 17 TVTSTTSVAENWLLKIRSLHSAQILIVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYMDCIPLSIKNFLSDPNV 96 (198)
Q Consensus 17 ~v~~~~~~~~~~i~~~~~~~~~~~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~~~~~~~L~~lL~d~~i 96 (198)
.++++++++.++++.+.. .+++|+||||... .++.+++|||||++++.++|||+.....+ ++|.++|+|++|
T Consensus 4 ~~I~t~~~L~~~~~~l~~-----~~~lalDtEf~~~--~ty~~~l~LiQl~~~~~~~LiD~l~~~d~-~~L~~ll~~~~i 75 (373)
T PRK10829 4 QMITTDDALASVCEAARA-----FPAIALDTEFVRT--RTYYPQLGLIQLYDGEQLSLIDPLGITDW-SPFKALLRDPQV 75 (373)
T ss_pred EEeCCHHHHHHHHHHHhc-----CCeEEEecccccC--ccCCCceeEEEEecCCceEEEecCCccch-HHHHHHHcCCCe
Confidence 356699999999999876 4999999999987 56788999999999999999999876443 689999999999
Q ss_pred EEEEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCCCCCCCHHHHH
Q 037014 97 VFVGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLESGFLDTELIK 176 (198)
Q Consensus 97 ~kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~~Qi~ 176 (198)
+||+|++++|+..|.+.+|+.+.++||++..+. .+|.+ .+.||+.|++++||..++|.. +.|||.+||||++|+.
T Consensus 76 vKV~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~-~lg~~--~~~gl~~Lv~~~lgv~ldK~~--~~sDW~~RPLs~~ql~ 150 (373)
T PRK10829 76 TKFLHAGSEDLEVFLNAFGELPQPLIDTQILAA-FCGRP--LSCGFASMVEEYTGVTLDKSE--SRTDWLARPLSERQCE 150 (373)
T ss_pred EEEEeChHhHHHHHHHHcCCCcCCeeeHHHHHH-HcCCC--ccccHHHHHHHHhCCccCccc--ccCCCCCCCCCHHHHH
Confidence 999999999999998899999999999966654 77754 268999999999999999954 7899999999999999
Q ss_pred HHHHhHHHHHHHHHHHhc
Q 037014 177 FACIDAYVSCAIGTKLLL 194 (198)
Q Consensus 177 YAA~Da~~~~~l~~~L~~ 194 (198)
|||.||++++.||.+|.+
T Consensus 151 YAa~Dv~~L~~l~~~L~~ 168 (373)
T PRK10829 151 YAAADVFYLLPIAAKLMA 168 (373)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 999999999999999875
No 5
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=100.00 E-value=9.2e-33 Score=213.17 Aligned_cols=168 Identities=25% Similarity=0.271 Sum_probs=144.4
Q ss_pred EcCCHHHHHHHHHHHHhhccCCCeEEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEccccCc--ccHHHHHhhcCCC
Q 037014 18 VTSTTSVAENWLLKIRSLHSAQILIVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYMDC--IPLSIKNFLSDPN 95 (198)
Q Consensus 18 v~~~~~~~~~~i~~~~~~~~~~~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~~~--~~~~L~~lL~d~~ 95 (198)
+++++++++++++.+... +++|||+||.+........++++||+|+++.|++++...... +++.|+++|+||+
T Consensus 3 ~v~~~~~l~~~~~~l~~~-----~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~~~~~~~~~~~~~~l~~ll~~~~ 77 (176)
T PF01612_consen 3 IVDTEEELEEAIKKLKNA-----KVLAFDTETTGLDPYSYNPKIALIQLATGEGCYIIDPIDLGDNWILDALKELLEDPN 77 (176)
T ss_dssp EEHSHHHHHHHHHHHTTT-----SEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEECGTTSTTTTHHHHHHHHHTTTT
T ss_pred ecCCHHHHHHHHHHHcCC-----CeEEEEEEECCCCccccCCeEEEEEEecCCCceeeeeccccccchHHHHHHHHhCCC
Confidence 445999999999999984 799999999998654578999999999999999988876544 4789999999999
Q ss_pred eEEEEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCC-CCCCCHHH
Q 037014 96 VVFVGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLE-SGFLDTEL 174 (198)
Q Consensus 96 i~kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~-~~~L~~~Q 174 (198)
|+||||++++|+..|.+.+|+.+.+++|+ +++.+.++.. . +.||++|+.+++| ...++++.++++|. ++||+++|
T Consensus 78 i~kv~~n~~~D~~~L~~~~~i~~~~~~D~-~l~~~~l~~~-~-~~~L~~L~~~~l~-~~~~~~~~~~~~~~~~~~l~~~~ 153 (176)
T PF01612_consen 78 IIKVGHNAKFDLKWLYRSFGIDLKNVFDT-MLAAYLLDPT-R-SYSLKDLAEEYLG-NIDLDKKEQMSDWRKARPLSEEQ 153 (176)
T ss_dssp SEEEESSHHHHHHHHHHHHTS--SSEEEH-HHHHHHTTTS-T-TSSHHHHHHHHHS-EEE-GHCCTTSSTTTSSS-HHHH
T ss_pred ccEEEEEEechHHHHHHHhccccCCccch-hhhhhccccc-c-cccHHHHHHHHhh-hccCcHHHhhccCCcCCCChHHH
Confidence 99999999999999988899999999999 8888888743 2 3899999999999 44434466899999 89999999
Q ss_pred HHHHHHhHHHHHHHHHHHhc
Q 037014 175 IKFACIDAYVSCAIGTKLLL 194 (198)
Q Consensus 175 i~YAA~Da~~~~~l~~~L~~ 194 (198)
++|||.||+++++||++|..
T Consensus 154 ~~YAa~D~~~~~~l~~~l~~ 173 (176)
T PF01612_consen 154 IEYAAQDAVVTFRLYEKLKP 173 (176)
T ss_dssp HHHHHHHHHTHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999975
No 6
>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins. The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.
Probab=99.98 E-value=3.6e-32 Score=215.37 Aligned_cols=152 Identities=15% Similarity=0.182 Sum_probs=129.5
Q ss_pred CeEEEEeeeecCCCCCCCCCceeEEEeeeC-CeEEEEEccccC--cccHHHHHhhcCCCeEEEEEeecchHHHHhhhcCC
Q 037014 40 ILIVGLNCKWKPHPIPSLSGKIATLQLCVD-TKCLILQLLYMD--CIPLSIKNFLSDPNVVFVGIEVEEIMSKLKNEYGL 116 (198)
Q Consensus 40 ~~~vg~D~Ew~~~~~~~~~~~~~liQla~~-~~~~i~~l~~~~--~~~~~L~~lL~d~~i~kvG~~~~~D~~~L~~~~gi 116 (198)
.++||||+||.+.+ ..+++|+||+|++ +.+||||+...+ .++..|+++|+|++|.||||++++|...|.+.||+
T Consensus 10 ~~~i~~D~E~~~~~---~~~~~~LiQia~~~~~v~l~D~~~~~~~~~~~~L~~iLe~~~i~Kv~h~~k~D~~~L~~~~gi 86 (197)
T cd06148 10 QKVIGLDCEGVNLG---RKGKLCLVQIATRTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHDCRRDSDALYHQYGI 86 (197)
T ss_pred CCEEEEEcccccCC---CCCCEEEEEEeeCCCcEEEEEhhhccchhHHHHHHHHhcCCCccEEEEechhHHHHHHHhcCc
Confidence 48999999998753 3679999999999 899999999764 35688999999999999999999999999889999
Q ss_pred ccCceeehHHHHHHhCCCCC------CCCchHHHHHHHHcCCcCCCC------CceeccCCCCCCCCHHHHHHHHHhHHH
Q 037014 117 CIKKKIDVRTLAKLHFPISC------LGKPGLKVLAYQLLRLRPWKP------KKVCMNNLESGFLDTELIKFACIDAYV 184 (198)
Q Consensus 117 ~~~~~~Dl~~l~~~~l~~~~------~~~~~L~~l~~~~l~~~l~K~------~~~~~s~W~~~~L~~~Qi~YAA~Da~~ 184 (198)
.+.|++|++ ++.+.++... ....||+++++++||.+++|. +..++|||.+||||++|+.|||.||++
T Consensus 87 ~~~~~fDt~-iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~ 165 (197)
T cd06148 87 KLNNVFDTQ-VADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLC 165 (197)
T ss_pred cccceeeHH-HHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHh
Confidence 999999986 5555554211 124699999999999998652 235789999999999999999999999
Q ss_pred HHHHHHHHhcc
Q 037014 185 SCAIGTKLLLE 195 (198)
Q Consensus 185 ~~~l~~~L~~~ 195 (198)
++.||..|..+
T Consensus 166 Ll~l~~~l~~~ 176 (197)
T cd06148 166 LLPLYYAMLDA 176 (197)
T ss_pred HHHHHHHHHHH
Confidence 99999998754
No 7
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=2.6e-30 Score=217.12 Aligned_cols=162 Identities=17% Similarity=0.111 Sum_probs=143.9
Q ss_pred CHHHHHHHHHHHHhhccCCCeEEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEccccCcccHHHHHhhcCCCeEEEE
Q 037014 21 TTSVAENWLLKIRSLHSAQILIVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYMDCIPLSIKNFLSDPNVVFVG 100 (198)
Q Consensus 21 ~~~~~~~~i~~~~~~~~~~~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~~~~~~~L~~lL~d~~i~kvG 100 (198)
+...+++++..... .+.|++|||+... .++.+++||||+|.++++.+||+.....-.++|..+|.|++|+||.
T Consensus 3 ~~~~l~~~~~~~~~-----~~~iAiDTEf~r~--~t~~p~LcLIQi~~~e~~~lIdpl~~~~d~~~l~~Ll~d~~v~KIf 75 (361)
T COG0349 3 TGDLLAAACALLRG-----SKAIAIDTEFMRL--RTYYPRLCLIQISDGEGASLIDPLAGILDLPPLVALLADPNVVKIF 75 (361)
T ss_pred chhHHHHHHHHhcC-----CCceEEecccccc--cccCCceEEEEEecCCCceEecccccccccchHHHHhcCCceeeee
Confidence 55667777777776 4899999999988 6799999999999999999999987323336899999999999999
Q ss_pred EeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCCCCCCCHHHHHHHHH
Q 037014 101 IEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLESGFLDTELIKFACI 180 (198)
Q Consensus 101 ~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~~Qi~YAA~ 180 (198)
|..++|+..|.+.||+.+.++||++..++ ..|.+. ++||++||++++|++++|+ .+.|||.+||||++|+.|||.
T Consensus 76 Haa~~DL~~l~~~~g~~p~plfdTqiAa~-l~g~~~--~~gl~~Lv~~ll~v~ldK~--~q~SDW~~RPLs~~Ql~YAa~ 150 (361)
T COG0349 76 HAARFDLEVLLNLFGLLPTPLFDTQIAAK-LAGFGT--SHGLADLVEELLGVELDKS--EQRSDWLARPLSEAQLEYAAA 150 (361)
T ss_pred ccccccHHHHHHhcCCCCCchhHHHHHHH-HhCCcc--cccHHHHHHHHhCCccccc--ccccccccCCCCHHHHHHHHH
Confidence 99999999999999999999999977665 667543 8999999999999999995 589999999999999999999
Q ss_pred hHHHHHHHHHHHhc
Q 037014 181 DAYVSCAIGTKLLL 194 (198)
Q Consensus 181 Da~~~~~l~~~L~~ 194 (198)
|+.+++.||.+|.+
T Consensus 151 DV~yL~~l~~~L~~ 164 (361)
T COG0349 151 DVEYLLPLYDKLTE 164 (361)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999999875
No 8
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=99.97 E-value=4.5e-29 Score=214.32 Aligned_cols=163 Identities=16% Similarity=0.133 Sum_probs=143.3
Q ss_pred cCCHHHHHHHHHHHHhhccCCCeEEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEccccCcccHHHHHhhcCCCeEE
Q 037014 19 TSTTSVAENWLLKIRSLHSAQILIVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYMDCIPLSIKNFLSDPNVVF 98 (198)
Q Consensus 19 ~~~~~~~~~~i~~~~~~~~~~~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~~~~~~~L~~lL~d~~i~k 98 (198)
+.+++++.++++.+... .+|||||||... .++.+++|+||||+++.++|||+..... .++|+++|+|++|+|
T Consensus 2 I~t~~~l~~~~~~l~~~-----~~ia~DtE~~~~--~~y~~~l~LiQia~~~~~~liD~~~~~~-~~~L~~lL~d~~i~K 73 (367)
T TIGR01388 2 ITTDDELATVCEAVRTF-----PFVALDTEFVRE--RTFWPQLGLIQVADGEQLALIDPLVIID-WSPLKELLRDESVVK 73 (367)
T ss_pred cCCHHHHHHHHHHHhcC-----CEEEEeccccCC--CCCCCcceEEEEeeCCeEEEEeCCCccc-HHHHHHHHCCCCceE
Confidence 46899999999999874 899999999987 5678899999999999999999976544 468999999999999
Q ss_pred EEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCCCCCCCHHHHHHH
Q 037014 99 VGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLESGFLDTELIKFA 178 (198)
Q Consensus 99 vG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~~Qi~YA 178 (198)
|||++++|+..|.+.++..+.+++|++. +.+.+|.. .+.||++|++++||..++|. .+.|||..+||+.+|+.||
T Consensus 74 V~h~~k~Dl~~L~~~~~~~~~~~fDtql-Aa~lL~~~--~~~~l~~Lv~~~Lg~~l~K~--~~~sdW~~rPL~~~q~~YA 148 (367)
T TIGR01388 74 VLHAASEDLEVFLNLFGELPQPLFDTQI-AAAFCGFG--MSMGYAKLVQEVLGVELDKS--ESRTDWLARPLTDAQLEYA 148 (367)
T ss_pred EEeecHHHHHHHHHHhCCCCCCcccHHH-HHHHhCCC--CCccHHHHHHHHcCCCCCcc--cccccCCCCCCCHHHHHHH
Confidence 9999999999998777888888899855 66788743 25699999999999999985 4789999999999999999
Q ss_pred HHhHHHHHHHHHHHhc
Q 037014 179 CIDAYVSCAIGTKLLL 194 (198)
Q Consensus 179 A~Da~~~~~l~~~L~~ 194 (198)
|.||++++.||.+|.+
T Consensus 149 a~Dv~~L~~L~~~L~~ 164 (367)
T TIGR01388 149 AADVTYLLPLYAKLME 164 (367)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999999999864
No 9
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=99.94 E-value=4.8e-27 Score=193.29 Aligned_cols=187 Identities=30% Similarity=0.458 Sum_probs=163.8
Q ss_pred eEEEEEcCeEEEEEEcCCHHHHHHHHHHHHhh---ccCCCeEEEEeeeecCCCC--------------------------
Q 037014 4 AQSISFCGKIIETTVTSTTSVAENWLLKIRSL---HSAQILIVGLNCKWKPHPI-------------------------- 54 (198)
Q Consensus 4 ~~~v~f~~~~i~~~v~~~~~~~~~~i~~~~~~---~~~~~~~vg~D~Ew~~~~~-------------------------- 54 (198)
.|.|+|+|+...++++.+++.+..|+...+.. +..++.+||++++|+|...
T Consensus 16 ~~~vd~~~~~~~Vtvt~~~svi~~~i~d~~~~~~~~~s~p~vvg~~vqw~p~~~~~~~~~~~~~~~~~~~a~~~~~~~~~ 95 (319)
T KOG4373|consen 16 KYSVDFFGEELIVTVTPDSSVISRWIHDVRFLSRNFSSDPLVVGRGVQWTPPTLTPDQTIYAARDLQISVARFLHLLGSS 95 (319)
T ss_pred ceeeeecccceEEEEccCcccchhhhhhhhhcccCcccCCcccCcCcccCCCCCCccccccccchhccccccccccccCc
Confidence 58999999999999999999999999988854 2355899999999998720
Q ss_pred ----------------------------CC-------------------CCCceeEEEeeeC-CeEEEEEccccCcccHH
Q 037014 55 ----------------------------PS-------------------LSGKIATLQLCVD-TKCLILQLLYMDCIPLS 86 (198)
Q Consensus 55 ----------------------------~~-------------------~~~~~~liQla~~-~~~~i~~l~~~~~~~~~ 86 (198)
.+ ..++++.+|||++ +.|+|+++.+.+.+|..
T Consensus 96 ~~~~~~kl~~~~d~~a~~~~~~~~~~~~~s~~~~~~~~~e~~~~~d~~~~~P~~~~lqlcV~en~C~I~ql~~~~~IP~~ 175 (319)
T KOG4373|consen 96 FKHKRQKLGYGSDARASPYIDNSLEIADDSDPPFVCYRREAQPYLDMGRSDPPPDTLQLCVGENRCLIIQLIHCKRIPHE 175 (319)
T ss_pred ccccccccccccccccccccccccccccccCCcceeecccccccccccccCCCcchhhhhhcccceeeEEeeccccchHH
Confidence 01 3567899999999 66999999999999999
Q ss_pred HHHhhcCCCeEEEEEeecchHHHHhh-hcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCC---cCCCCCceec
Q 037014 87 IKNFLSDPNVVFVGIEVEEIMSKLKN-EYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRL---RPWKPKKVCM 162 (198)
Q Consensus 87 L~~lL~d~~i~kvG~~~~~D~~~L~~-~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~---~l~K~~~~~~ 162 (198)
|+.||+||++++||.++++|..+|++ .|+++|....|++.+++..+|. .+...+...++...+|. .+.+++++++
T Consensus 176 LR~fl~D~~~~~vgv~~d~D~~KL~r~~hql~I~~~~dlr~~~~d~~g~-~~~~~s~e~i~~~~~~~~~~~v~l~~~i~m 254 (319)
T KOG4373|consen 176 LRSFLEDPDHTFVGVWNDQDAGKLERKEHQLEIGELEDLRLLVNDSLGG-SMPNDSFEEIVSETLGYYGKDVRLDKEIRM 254 (319)
T ss_pred HHHhhcCCCceEEeccccccHHHHhhhhhcccHHhhhhHHhhcchhhcc-CccCccHHHHHHHHhhccccccccChhccc
Confidence 99999999999999999999999998 8999999999999999888885 45567777777777763 4778889999
Q ss_pred cCCCCCCCCHHHHHHHHHhHHHHHHHHHH
Q 037014 163 NNLESGFLDTELIKFACIDAYVSCAIGTK 191 (198)
Q Consensus 163 s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~ 191 (198)
|||.-.+|+.+|+.||++|||++..+|.+
T Consensus 255 sdw~~~~Ls~~Ql~~asidvy~c~~lg~~ 283 (319)
T KOG4373|consen 255 SDWSVYPLSDDQLLQASIDVYVCHKLGVL 283 (319)
T ss_pred ccceeeeccHHHHHHHHhHHHHHHHHHHH
Confidence 99999999999999999999999999853
No 10
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=99.91 E-value=1.1e-22 Score=157.67 Aligned_cols=157 Identities=18% Similarity=0.218 Sum_probs=127.5
Q ss_pred HHHHHHHHHhhccCCCeEEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEccccCcccHHHHHhhcCCCeEEEEEeec
Q 037014 25 AENWLLKIRSLHSAQILIVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYMDCIPLSIKNFLSDPNVVFVGIEVE 104 (198)
Q Consensus 25 ~~~~i~~~~~~~~~~~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~~~~~~~L~~lL~d~~i~kvG~~~~ 104 (198)
+.++++.+.. ...+|+|+||.+. .+..++++++|+|+++.+++|++... ..++.|+++|+|+++.||||++|
T Consensus 2 ~~~~~~~l~~-----~~~l~~~~e~~~~--~~~~~~~~~i~l~~~~~~~~i~~~~~-~~~~~l~~ll~~~~i~kv~~d~K 73 (178)
T cd06142 2 LEDLCERLAS-----AGVIAVDTEFMRL--NTYYPRLCLIQISTGGEVYLIDPLAI-GDLSPLKELLADPNIVKVFHAAR 73 (178)
T ss_pred HHHHHHHHhc-----CCeEEEECCccCC--CcCCCceEEEEEeeCCCEEEEeCCCc-ccHHHHHHHHcCCCceEEEeccH
Confidence 3455544432 3599999998765 23467899999999955888887644 45677999999999999999999
Q ss_pred chHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCCCCCCCHHHHHHHHHhHHH
Q 037014 105 EIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLESGFLDTELIKFACIDAYV 184 (198)
Q Consensus 105 ~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~~Qi~YAA~Da~~ 184 (198)
.|++.|.+.||+..++++|+ +++.++++ |.. +.+|++++++++|..+.|.+ ..++|+++||+.+|+.|||.||++
T Consensus 74 ~~~~~L~~~~gi~~~~~~D~-~laayLl~-p~~-~~~l~~l~~~~l~~~~~~~~--~~~~w~~~~l~~~~~~yaa~~a~~ 148 (178)
T cd06142 74 EDLELLKRDFGILPQNLFDT-QIAARLLG-LGD-SVGLAALVEELLGVELDKGE--QRSDWSKRPLTDEQLEYAALDVRY 148 (178)
T ss_pred HHHHHHHHHcCCCCCCcccH-HHHHHHhC-CCc-cccHHHHHHHHhCCCCCccc--ccccCCCCCCCHHHHHHHHHhHHH
Confidence 99999977779985566777 67788887 533 35999999999999876643 678999999999999999999999
Q ss_pred HHHHHHHHhc
Q 037014 185 SCAIGTKLLL 194 (198)
Q Consensus 185 ~~~l~~~L~~ 194 (198)
+++++.+|.+
T Consensus 149 l~~L~~~l~~ 158 (178)
T cd06142 149 LLPLYEKLKE 158 (178)
T ss_pred HHHHHHHHHH
Confidence 9999998864
No 11
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.90 E-value=1.2e-22 Score=155.50 Aligned_cols=166 Identities=23% Similarity=0.229 Sum_probs=131.4
Q ss_pred EcCCHHHHHHHHHHHH-hhccCCCeEEEEeeeecCCCCCCCCCceeEEEeeeCC-eEEEEEccccCcccHHHHHhhcCCC
Q 037014 18 VTSTTSVAENWLLKIR-SLHSAQILIVGLNCKWKPHPIPSLSGKIATLQLCVDT-KCLILQLLYMDCIPLSIKNFLSDPN 95 (198)
Q Consensus 18 v~~~~~~~~~~i~~~~-~~~~~~~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~-~~~i~~l~~~~~~~~~L~~lL~d~~ 95 (198)
++.+++++.+|++.+. . ...+|+|+||.+.. ...++++++|+|.++ .+||++....+..++.|+++|++++
T Consensus 3 ~i~~~~~~~~~~~~~~~~-----~~~l~~~~e~~~~~--~~~~~~~~l~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~ 75 (172)
T smart00474 3 VVTDSETLEELLEKLRAA-----GGEVALDTETTGLN--SYSGKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDET 75 (172)
T ss_pred EecCHHHHHHHHHHHHhc-----CCeEEEeccccCCc--cCCCCEEEEEEeEcCCceEEEEeccchhhHHHHHHHhcCCC
Confidence 3446788899887664 3 36999999998762 346789999999644 6787654333344567999999999
Q ss_pred eEEEEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCCCCCCCHHHH
Q 037014 96 VVFVGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLESGFLDTELI 175 (198)
Q Consensus 96 i~kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~~Qi 175 (198)
+.||||+++.|+..|. .+|+++.+++|+ +++.+++. |..+..+|+.+++.++|..+.+ ....++|..+||..+|+
T Consensus 76 ~~kv~~d~k~~~~~L~-~~gi~~~~~~D~-~laayll~-p~~~~~~l~~l~~~~l~~~~~~--~~~~~~~~~~~l~~~~~ 150 (172)
T smart00474 76 ITKVGHNAKFDLHVLA-RFGIELENIFDT-MLAAYLLL-GGPSKHGLATLLKEYLGVELDK--EEQKSDWGARPLSEEQL 150 (172)
T ss_pred ceEEEechHHHHHHHH-HCCCcccchhHH-HHHHHHHc-CCCCcCCHHHHHHHHhCCCCCc--ccCccccccCCCCHHHH
Confidence 9999999999999996 499999998777 55666554 4333369999999999988754 34557998889999999
Q ss_pred HHHHHhHHHHHHHHHHHhcc
Q 037014 176 KFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 176 ~YAA~Da~~~~~l~~~L~~~ 195 (198)
.|||.||+++++|++.|.++
T Consensus 151 ~ya~~~a~~~~~L~~~l~~~ 170 (172)
T smart00474 151 QYAAEDADALLRLYEKLEKE 170 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999998753
No 12
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.89 E-value=3.6e-23 Score=181.42 Aligned_cols=174 Identities=20% Similarity=0.256 Sum_probs=140.3
Q ss_pred EEEEEcCCHHHHHHHH-HHHHhhccCCCeEEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEccccCccc-----HHH
Q 037014 14 IETTVTSTTSVAENWL-LKIRSLHSAQILIVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYMDCIP-----LSI 87 (198)
Q Consensus 14 i~~~v~~~~~~~~~~i-~~~~~~~~~~~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~~~~~-----~~L 87 (198)
-.+.++.++.+++..+ ..+.+ +..+||+|.||.|. ......+++++|++.++++||+|+...+..+ ..+
T Consensus 390 ~~i~~V~~e~El~~l~l~~l~~----e~~yVGiDsEwkps-~~v~dsk~~IlQif~~~~v~Lidc~~l~~~~se~w~~~~ 464 (617)
T KOG2207|consen 390 ESIGMVGNEKELRDLLLESLSE----ELRYVGIDSEWKPS-KKVSDSKLAILQIFFKDCVYLIDCVKLENLASEIWHLLL 464 (617)
T ss_pred cceeeeCCHHHHHHHHHHHhhh----cCEEEEEccccCcc-cCCChhHHHHHHHHhcCeEEEeehHHhhhchHHHHHHHH
Confidence 3345677999998887 22332 36999999999998 4567899999999999999999998765444 468
Q ss_pred HHhhcCCCeEEEEEeecchHHHHhh-----hcCCcc---CceeehHHHHHHhCCCC------CCCCchHHHHHHHHcCCc
Q 037014 88 KNFLSDPNVVFVGIEVEEIMSKLKN-----EYGLCI---KKKIDVRTLAKLHFPIS------CLGKPGLKVLAYQLLRLR 153 (198)
Q Consensus 88 ~~lL~d~~i~kvG~~~~~D~~~L~~-----~~gi~~---~~~~Dl~~l~~~~l~~~------~~~~~~L~~l~~~~l~~~ 153 (198)
..+|+++.|.|||+++.+|+..|++ .+..++ .+++++..++....+.+ .....+|..|...++|..
T Consensus 465 s~if~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~Lt~~llg~~ 544 (617)
T KOG2207|consen 465 SQIFESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADLTDCLLGKK 544 (617)
T ss_pred HHHccCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhhhhhhHHHhhhh
Confidence 8999999999999999999999975 333333 45566666665433321 123678999999999999
Q ss_pred CCCCCceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 037014 154 PWKPKKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLL 194 (198)
Q Consensus 154 l~K~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~ 194 (198)
++|++ ++|||..|||+.+||.|||+||.++..+|.++.+
T Consensus 545 lnKte--qcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~ 583 (617)
T KOG2207|consen 545 LNKTE--QCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCS 583 (617)
T ss_pred ccccc--ccchhhcCCchhhHHHHHHhcchhhHHHHHHHHh
Confidence 99964 8999999999999999999999999999999875
No 13
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=99.85 E-value=2e-20 Score=140.79 Aligned_cols=147 Identities=18% Similarity=0.162 Sum_probs=115.1
Q ss_pred EEEEeeeecCCCCCCCCCceeEEEeeeCCe-EEEEEccccCcccHHHHHhhcCCCeEEEEEeecchHHHHhhhcCCccCc
Q 037014 42 IVGLNCKWKPHPIPSLSGKIATLQLCVDTK-CLILQLLYMDCIPLSIKNFLSDPNVVFVGIEVEEIMSKLKNEYGLCIKK 120 (198)
Q Consensus 42 ~vg~D~Ew~~~~~~~~~~~~~liQla~~~~-~~i~~l~~~~~~~~~L~~lL~d~~i~kvG~~~~~D~~~L~~~~gi~~~~ 120 (198)
++++|+||.+. .+...+++++|+|++++ ++++++.+.+..+..|+++|+|+++.|+||++|.|...| ...|+...+
T Consensus 1 ~~~~~~e~~~~--~~~~~~~~~l~l~~~~~~~~~i~~~~~~~~~~~l~~~l~~~~~~kv~~d~K~~~~~L-~~~~~~~~~ 77 (150)
T cd09018 1 VFAFDTETDSL--DNISANLVLIQLAIEPGVAALIPVAHDYLALELLKPLLEDEKALKVGQNLKYDRGIL-LNYFIELRG 77 (150)
T ss_pred CEEEEeecCCC--CCCCceEEEEEEEcCCCcEEEEEcCCcccCHHHHHHHhcCCCCceeeecHHHHHHHH-HHcCCccCC
Confidence 57999998775 23467899999999855 877787643213567999999999999999999999999 456766655
Q ss_pred e-eehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 037014 121 K-IDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKLL 193 (198)
Q Consensus 121 ~-~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~ 193 (198)
. +|+ ++++++++ |...+.+|++|++++|+..+.+.+++..++|..++++.+|+.||+.||+++++|++.|.
T Consensus 78 ~~~D~-~laayLl~-p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 78 IAFDT-MLEAYILN-SVAGRWDMDSLVERWLGHKLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred cchhH-HHHHHHhC-CCCCCCCHHHHHHHHhCCCcccHHHhcCCCCcccCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 5 565 67788887 54313599999999999886552234445686678899999999999999999999875
No 14
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=99.83 E-value=8.2e-19 Score=138.22 Aligned_cols=163 Identities=18% Similarity=0.146 Sum_probs=129.0
Q ss_pred cCCHHHHHHHHHHHHhhccCCCeEEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEccccCcccHHHHHhhcCCCeEE
Q 037014 19 TSTTSVAENWLLKIRSLHSAQILIVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYMDCIPLSIKNFLSDPNVVF 98 (198)
Q Consensus 19 ~~~~~~~~~~i~~~~~~~~~~~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~~~~~~~L~~lL~d~~i~k 98 (198)
+.++++++.|++.+.. ...+++|+|..+. .+...+++++|+|+++++++|++...+...+.|+++|+++++.|
T Consensus 8 i~~~~~l~~~~~~l~~-----~~~l~~~~e~~~~--~~~~~~~~~l~l~~~~~~~~i~~l~~~~~~~~L~~~L~~~~i~k 80 (192)
T cd06147 8 VDTEEKLEELVEKLKN-----CKEIAVDLEHHSY--RSYLGFTCLMQISTREEDYIVDTLKLRDDMHILNEVFTDPNILK 80 (192)
T ss_pred ECCHHHHHHHHHHHhc-----CCeEEEEeEecCC--ccCCCceEEEEEecCCCcEEEEecccccchHHHHHHhcCCCceE
Confidence 3355778888866632 2589999987554 23467899999999887777664223333456999999999999
Q ss_pred EEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCCCCCCCHHHHHHH
Q 037014 99 VGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLESGFLDTELIKFA 178 (198)
Q Consensus 99 vG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~~Qi~YA 178 (198)
|||++|.|...|.+.+|+.+.+++|+ +++.|+++ |. + .+|+.|++++|+..+.| +.+.+||+.+||+.+|..||
T Consensus 81 v~~d~K~~~~~L~~~~gi~~~~~fD~-~laaYLL~-p~-~-~~l~~l~~~yl~~~~~k--~~~~~~~~~~~l~~~~~~y~ 154 (192)
T cd06147 81 VFHGADSDIIWLQRDFGLYVVNLFDT-GQAARVLN-LP-R-HSLAYLLQKYCNVDADK--KYQLADWRIRPLPEEMIKYA 154 (192)
T ss_pred EEechHHHHHHHHHHhCCCcCchHHH-HHHHHHhC-CC-c-ccHHHHHHHHhCCCcch--hhhccccccCCCCHHHHHHH
Confidence 99999999999954889998888555 77888888 55 4 49999999999987544 34667898888899999999
Q ss_pred HHhHHHHHHHHHHHhc
Q 037014 179 CIDAYVSCAIGTKLLL 194 (198)
Q Consensus 179 A~Da~~~~~l~~~L~~ 194 (198)
+.||.++++|+..|.+
T Consensus 155 a~~a~~l~~L~~~L~~ 170 (192)
T cd06147 155 REDTHYLLYIYDRLRN 170 (192)
T ss_pred HhhHHHHHHHHHHHHH
Confidence 9999999999998864
No 15
>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=99.82 E-value=3e-19 Score=134.27 Aligned_cols=148 Identities=20% Similarity=0.141 Sum_probs=112.3
Q ss_pred EEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEcccc-CcccHHHHHhhcCCCeEEEEEeecchHHHHhhhcCCccCc
Q 037014 42 IVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYM-DCIPLSIKNFLSDPNVVFVGIEVEEIMSKLKNEYGLCIKK 120 (198)
Q Consensus 42 ~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~-~~~~~~L~~lL~d~~i~kvG~~~~~D~~~L~~~~gi~~~~ 120 (198)
.+|+|+||.+. ....++++++|+|+++.++.++..+. ..+++.|+++|+++.+.||||+++.|+..|.+.++....+
T Consensus 2 ~l~~d~e~~~~--~~~~~~i~~~~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~~~~~~~~~~ 79 (155)
T cd00007 2 EVAFDTETTGL--NYHRGKLVGIQIATAGEAAYIPDELELEEDLEALKELLEDEDITKVGHDAKFDLVVLARDGIELPGN 79 (155)
T ss_pred ceEEEEecCCC--CcCCCeEEEEEEEECCcEEEEEcCCCHHHHHHHHHHHHcCCCCcEEeccHHHHHHHHHHCCCCCCCC
Confidence 58999999776 23468899999999743444454431 3456679999999999999999999999996555444566
Q ss_pred eeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCC----CCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 121 KIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLE----SGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 121 ~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~----~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
++|+ +++.+.++ |...+++|+++++++++..+.+..+ .++|+ .++++.+|+.||+.||+++++++.+|.++
T Consensus 80 ~~D~-~~~ayll~-~~~~~~~l~~l~~~~l~~~~~~~~~--~~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 80 IFDT-MLAAYLLN-PGEGSHSLDDLAKEYLGIELDKDEQ--IYGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred cccH-HHHHHHhC-CCCCcCCHHHHHHHHcCCCCccHHH--HhcCCCCccccCCHHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 7886 56667776 4332469999999999988554222 33442 57889999999999999999999998764
No 16
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=99.74 E-value=2.9e-18 Score=150.23 Aligned_cols=164 Identities=18% Similarity=0.193 Sum_probs=143.2
Q ss_pred EcCCHHHHHHHHHHHHhhccCCCeEEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEcccc-CcccHHHHHhhcCCCe
Q 037014 18 VTSTTSVAENWLLKIRSLHSAQILIVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYM-DCIPLSIKNFLSDPNV 96 (198)
Q Consensus 18 v~~~~~~~~~~i~~~~~~~~~~~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~-~~~~~~L~~lL~d~~i 96 (198)
.+.+..++++....+... ..+++|.|.... +.+.+-.|++||+|.+.-||||.... +.+ ..|.+.++||+|
T Consensus 195 ~I~t~~el~~l~~~l~~~-----~Efavdlehhsy--rsf~gltclmqISTr~ed~iIDt~~l~~~i-~~l~e~fsdp~i 266 (687)
T KOG2206|consen 195 WICTLGELEALPEILDSV-----IEFAVDLEHHSY--RSFLGLTCLMQISTRTEDFIIDTFKLRDHI-GILNEVFSDPGI 266 (687)
T ss_pred eeechHHHHHHHHHHhhh-----hhhhhhccccch--hhhcCceeEEEeeccchhheehhHHHHHHH-HHhhhhccCCCe
Confidence 455677777777766653 778999998776 67889999999999999999998765 334 589999999999
Q ss_pred EEEEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCCCCCCCHHHHH
Q 037014 97 VFVGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLESGFLDTELIK 176 (198)
Q Consensus 97 ~kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~~Qi~ 176 (198)
+||.||...|+.+|.++||+.+-|.+|+....+ ++|.| .+||.-|.+.+.|...+| +.|..+|..|||+.+++.
T Consensus 267 vkvfhgaD~diiwlqrdfgiyvvnLfdt~~a~r-~L~~~---r~sL~~ll~~~~~v~~nk--~yqladwR~rpLp~~Mv~ 340 (687)
T KOG2206|consen 267 VKVFHGADTDIIWLQRDFGIYVVNLFDTIQASR-LLGLP---RPSLAYLLECVCGVLTNK--KYQLADWRIRPLPEEMVR 340 (687)
T ss_pred EEEEecCccchhhhhccceEEEEechhhHHHHH-HhCCC---cccHHHHHHHHHhhhhhh--hhhhchhccccCcHHHHH
Confidence 999999999999999999999999999977654 78866 899999999999998888 678999999999999999
Q ss_pred HHHHhHHHHHHHHHHHhcc
Q 037014 177 FACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 177 YAA~Da~~~~~l~~~L~~~ 195 (198)
||=.|..+++.||+.|..+
T Consensus 341 yar~dthyllyiyD~lr~e 359 (687)
T KOG2206|consen 341 YAREDTHYLLYIYDVLRKE 359 (687)
T ss_pred HHhhcchhHHHHHHHHHHH
Confidence 9999999999999999754
No 17
>PRK05755 DNA polymerase I; Provisional
Probab=99.69 E-value=5.4e-16 Score=146.62 Aligned_cols=166 Identities=20% Similarity=0.265 Sum_probs=128.7
Q ss_pred EcCCHHHHHHHHHHHHhhccCCCeEEEEeeeecCCCCCCCCCceeEEEeeeCCe-EEEEEccccC-cccHHHHHhhcCCC
Q 037014 18 VTSTTSVAENWLLKIRSLHSAQILIVGLNCKWKPHPIPSLSGKIATLQLCVDTK-CLILQLLYMD-CIPLSIKNFLSDPN 95 (198)
Q Consensus 18 v~~~~~~~~~~i~~~~~~~~~~~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~-~~i~~l~~~~-~~~~~L~~lL~d~~ 95 (198)
++.+++++.+|++.+.. ..++++|+|+++. +...+++++||+|.+++ ++++++.+.. ...+.|.++|+|+.
T Consensus 298 ~I~~~~~L~~~l~~l~~-----~~~~a~DtEt~~l--~~~~~~i~~i~ls~~~g~~~~ip~~~i~~~~l~~l~~~L~d~~ 370 (880)
T PRK05755 298 TILDEEELEAWLAKLKA-----AGLFAFDTETTSL--DPMQAELVGLSFAVEPGEAAYIPLDQLDREVLAALKPLLEDPA 370 (880)
T ss_pred EeCCHHHHHHHHHHhhc-----cCeEEEEeccCCC--CcccccEEEEEEEeCCCcEEEEecccccHHHHHHHHHHHhCCC
Confidence 45588999999988876 3899999999886 45788999999999988 7777885532 23467999999999
Q ss_pred eEEEEEeecchHHHHhhhcCCccCc-eeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCce--eccCCCCCCCCH
Q 037014 96 VVFVGIEVEEIMSKLKNEYGLCIKK-KIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKV--CMNNLESGFLDT 172 (198)
Q Consensus 96 i~kvG~~~~~D~~~L~~~~gi~~~~-~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~--~~s~W~~~~L~~ 172 (198)
+.||+||+++|+..|. .+|+.+.+ ++|+ +++.+.++ |.. .+||++|+++++|..+.....+ ...+|...|+ +
T Consensus 371 v~kV~HNakfDl~~L~-~~gi~~~~~~~DT-~iAa~Ll~-~~~-~~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~pl-e 445 (880)
T PRK05755 371 IKKVGQNLKYDLHVLA-RYGIELRGIAFDT-MLASYLLD-PGR-RHGLDSLAERYLGHKTISFEEVAGKQLTFAQVDL-E 445 (880)
T ss_pred CcEEEeccHhHHHHHH-hCCCCcCCCcccH-HHHHHHcC-CCC-CCCHHHHHHHHhCCCccchHHhcCCCCCccccCH-H
Confidence 9999999999999995 57887644 5666 55667776 443 3899999999999874221100 1223444567 5
Q ss_pred HHHHHHHHhHHHHHHHHHHHhcc
Q 037014 173 ELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 173 ~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
.|.+||+.|+.++++||.+|.++
T Consensus 446 ~~~~YAa~Dv~~~~~L~~~L~~~ 468 (880)
T PRK05755 446 EAAEYAAEDADVTLRLHEVLKPK 468 (880)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 78999999999999999998864
No 18
>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases. Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Probab=99.61 E-value=1.7e-14 Score=111.88 Aligned_cols=148 Identities=16% Similarity=0.038 Sum_probs=112.7
Q ss_pred eEEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEccccCcccHHHHHhhcCCCeEEEEEeecchHHHHhhhcCCccCc
Q 037014 41 LIVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYMDCIPLSIKNFLSDPNVVFVGIEVEEIMSKLKNEYGLCIKK 120 (198)
Q Consensus 41 ~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~~~~~~~L~~lL~d~~i~kvG~~~~~D~~~L~~~~gi~~~~ 120 (198)
..+.+|+|.... .+..+++.++++|++++++.+++.+.-.....|+++|+|+++.|+||++|.|...| ..+|+.+.+
T Consensus 4 ~~~~~~~~~~~~--~~~~~~l~~i~l~~~~~~~~i~~~~~~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~~~~ 80 (178)
T cd06140 4 DEVALYVELLGE--NYHTADIIGLALANGGGAYYIPLELALLDLAALKEWLEDEKIPKVGHDAKRAYVAL-KRHGIELAG 80 (178)
T ss_pred CceEEEEEEcCC--CcceeeEEEEEEEeCCcEEEEeccchHHHHHHHHHHHhCCCCceeccchhHHHHHH-HHCCCcCCC
Confidence 567888888776 34578899999998877666675431012345899999999999999999999999 568998887
Q ss_pred eeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCC---CCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 037014 121 KIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLE---SGFLDTELIKFACIDAYVSCAIGTKLLL 194 (198)
Q Consensus 121 ~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~---~~~L~~~Qi~YAA~Da~~~~~l~~~L~~ 194 (198)
.+.+.++++|+++ |..+++++++++.++++..+.+... .+.|+ .++....|..||+.||.++.+++..|.+
T Consensus 81 ~~fDt~laaYLL~-p~~~~~~l~~l~~~yl~~~~~~~~~--~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~ 154 (178)
T cd06140 81 VAFDTMLAAYLLD-PTRSSYDLADLAKRYLGRELPSDEE--VYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEE 154 (178)
T ss_pred cchhHHHHHHHcC-CCCCCCCHHHHHHHHcCCCCcchHH--hcCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7566688999998 5444469999999999988655221 23332 2345666889999999999999998864
No 19
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=99.56 E-value=1.4e-13 Score=107.72 Aligned_cols=150 Identities=15% Similarity=0.154 Sum_probs=109.0
Q ss_pred CeEEEEeeeecCCCCCCCCCceeEEEeeeCCe-EEEEEcccc--------CcccHHHHHhhcCCCeEEEEEeecchHHHH
Q 037014 40 ILIVGLNCKWKPHPIPSLSGKIATLQLCVDTK-CLILQLLYM--------DCIPLSIKNFLSDPNVVFVGIEVEEIMSKL 110 (198)
Q Consensus 40 ~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~-~~i~~l~~~--------~~~~~~L~~lL~d~~i~kvG~~~~~D~~~L 110 (198)
...+++|+|..+. .....+++.+++|.+++ .+.+++.+. +.+...|+++|++..+.+|||+++.|...|
T Consensus 5 ~~~~a~d~e~~~~--~~~~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~v~hn~k~d~~~l 82 (193)
T cd06139 5 AKVFAFDTETTSL--DPMQAELVGISFAVEPGEAYYIPLGHDYGGEQLPREEVLAALKPLLEDPSIKKVGQNLKFDLHVL 82 (193)
T ss_pred CCeEEEEeecCCC--CcCCCeEEEEEEEcCCCCEEEEecCCCccccCCCHHHHHHHHHHHHhCCCCcEEeeccHHHHHHH
Confidence 4789999998654 34467899999998765 555565431 112244899999999999999999999999
Q ss_pred hhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCC-C----CceeccCCCCCCCCHHHHHHHHHhHHHH
Q 037014 111 KNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWK-P----KKVCMNNLESGFLDTELIKFACIDAYVS 185 (198)
Q Consensus 111 ~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K-~----~~~~~s~W~~~~L~~~Qi~YAA~Da~~~ 185 (198)
+.+|+.+.+.+.+..++.+.++ |...+.+|+++++++++..+.+ + +.....+|...|+ ..+.+||+.|+.++
T Consensus 83 -~~~gi~~~~~~~Dt~l~a~ll~-p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~-~~~~~ya~~d~~~~ 159 (193)
T cd06139 83 -ANHGIELRGPAFDTMLASYLLN-PGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPL-EKAAEYAAEDADIT 159 (193)
T ss_pred -HHCCCCCCCCcccHHHHHHHhC-CCCCCCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccCH-HHHHHHHHHHHHHH
Confidence 5678887766455567777776 5443569999999999865211 0 1112345654445 66889999999999
Q ss_pred HHHHHHHhc
Q 037014 186 CAIGTKLLL 194 (198)
Q Consensus 186 ~~l~~~L~~ 194 (198)
++|+..|.+
T Consensus 160 ~~l~~~l~~ 168 (193)
T cd06139 160 LRLYELLKP 168 (193)
T ss_pred HHHHHHHHH
Confidence 999999875
No 20
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.41 E-value=9.3e-13 Score=119.04 Aligned_cols=137 Identities=18% Similarity=0.047 Sum_probs=111.5
Q ss_pred EcCCHHHHHHHHHHHHhhccCCCeEEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEccccCcccHHHHHhhcCCCeE
Q 037014 18 VTSTTSVAENWLLKIRSLHSAQILIVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYMDCIPLSIKNFLSDPNVV 97 (198)
Q Consensus 18 v~~~~~~~~~~i~~~~~~~~~~~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~~~~~~~L~~lL~d~~i~ 97 (198)
++.+++++..++..+... +.+++|+|+.... . .++++|++.++.++|+|... . +.++
T Consensus 5 ~I~~~~~l~~~~~~l~~~-----~~~a~DtEf~r~~--t---~l~liQ~~~~~~~~liDpl~--~----l~~~------- 61 (553)
T PRK14975 5 VILAPEELGAALERLSPA-----GVVAGDTETTGDD--A---AAAAAQEGEEEPRWVWASTA--A----LYPR------- 61 (553)
T ss_pred EEeccchhHHHHHHhccC-----CceeCCccccCCc--c---hhheeeecCCCceEEECchH--H----hHHH-------
Confidence 455888999999998874 9999999999862 2 89999999999999988643 1 2222
Q ss_pred EEEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCC--CchHHHHHHHHcCCcCCCCCceeccCCCCCCCCHHHH
Q 037014 98 FVGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLG--KPGLKVLAYQLLRLRPWKPKKVCMNNLESGFLDTELI 175 (198)
Q Consensus 98 kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~--~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~~Qi 175 (198)
| ..+|+.+.+++|+ ++++++++. +.. +.|++.+++.+++..++|.. +.+||. +||+++|+
T Consensus 62 ------------L-~~~Gv~~~~~fDT-~LAa~lL~~-~~~~~~~~l~~la~~~l~~~l~k~~--~~sdw~-rpls~~q~ 123 (553)
T PRK14975 62 ------------L-LAAGVRVERCHDL-MLASQLLLG-SEGRAGSSLSAAAARALGEGLDKPP--QTSALS-DPPDEEQL 123 (553)
T ss_pred ------------H-HHCCCccCCCchH-HHHHHHcCC-CCCcCCCCHHHHHHHHhCCCCCChh--hhcccc-ccchHHHH
Confidence 4 4569988898987 566778874 221 67999999999999999854 579997 89999999
Q ss_pred HHHHHhHHHHHHHHHHHhcc
Q 037014 176 KFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 176 ~YAA~Da~~~~~l~~~L~~~ 195 (198)
.|||.|+.++..+|..|.++
T Consensus 124 ~YAa~Dv~~l~~L~~~L~~q 143 (553)
T PRK14975 124 LYAAADADVLLELYAVLADQ 143 (553)
T ss_pred HHHHHHhHHHHHHHHHHHHH
Confidence 99999999999999998754
No 21
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=99.38 E-value=3.8e-12 Score=113.88 Aligned_cols=162 Identities=17% Similarity=0.176 Sum_probs=126.1
Q ss_pred CHHHHHHHHHHHHhhccCCCeEEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEcccc-C--cccHHHHHhhcCCCeE
Q 037014 21 TTSVAENWLLKIRSLHSAQILIVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYM-D--CIPLSIKNFLSDPNVV 97 (198)
Q Consensus 21 ~~~~~~~~i~~~~~~~~~~~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~-~--~~~~~L~~lL~d~~i~ 97 (198)
+......|+...... ..+++|+|+... ......+..+.+|.++..+.+++.+. . ..-..|+++|+|+.+.
T Consensus 8 ~~~~~~~~~~~~~~~-----~~~a~~~et~~l--~~~~~~lvg~s~~~~~~~~yi~~~~~~~~~~~~~~l~~~l~~~~~~ 80 (593)
T COG0749 8 DLAVLNAWLTKLNAA-----ANIAFDTETDGL--DPHGADLVGLSVASEEEAAYIPLLHGPEQLNVLAALKPLLEDEGIK 80 (593)
T ss_pred HHHHHHHHHHHHhhc-----ccceeecccccc--CcccCCeeEEEeeccccceeEeeccchhhhhhHHHHHHHhhCcccc
Confidence 677788888888775 449999999987 45788888899998886444477651 1 2337899999999999
Q ss_pred EEEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCCCCCCCH-----
Q 037014 98 FVGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLESGFLDT----- 172 (198)
Q Consensus 98 kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~----- 172 (198)
|+||+.|.|.+.| +.+|+. .+...+.++++|.++ |+.+.++++.|++++++......+.+... +...++.
T Consensus 81 kv~~~~K~d~~~l-~~~Gi~-~~~~~DtmlasYll~-~~~~~~~~~~l~~r~l~~~~~~~~~i~~k--g~~~~~~~~~~~ 155 (593)
T COG0749 81 KVGQNLKYDYKVL-ANLGIE-PGVAFDTMLASYLLN-PGAGAHNLDDLAKRYLGLETITFEDIAGK--GKKQLTFADVKL 155 (593)
T ss_pred hhccccchhHHHH-HHcCCc-ccchHHHHHHHhccC-cCcCcCCHHHHHHHhcCCccchhHHhhcc--ccccCccccchH
Confidence 9999999999999 577866 577777799999887 55568999999999999876655444333 2222444
Q ss_pred HH-HHHHHHhHHHHHHHHHHHhc
Q 037014 173 EL-IKFACIDAYVSCAIGTKLLL 194 (198)
Q Consensus 173 ~Q-i~YAA~Da~~~~~l~~~L~~ 194 (198)
++ ..|||.||.+.++++..|..
T Consensus 156 ~~~~~y~a~~a~~~~~L~~~l~~ 178 (593)
T COG0749 156 EKATEYAAEDADATLRLESILEP 178 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33 49999999999999999875
No 22
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.10 E-value=2.4e-09 Score=101.34 Aligned_cols=159 Identities=14% Similarity=0.037 Sum_probs=109.3
Q ss_pred CHHHHHHHHHHHHhhccCCCeEEEEeeeecCCCCCCCCCceeEEEeeeCC-e-EEEEEccc-----cCcccHHHHHhhcC
Q 037014 21 TTSVAENWLLKIRSLHSAQILIVGLNCKWKPHPIPSLSGKIATLQLCVDT-K-CLILQLLY-----MDCIPLSIKNFLSD 93 (198)
Q Consensus 21 ~~~~~~~~i~~~~~~~~~~~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~-~-~~i~~l~~-----~~~~~~~L~~lL~d 93 (198)
+.++++.|++. .. ...+++ ..+ .+....+..+.+|+++ + .+-+++.. .+.....|+++|+|
T Consensus 309 ~~~~~~~~~~~-~~-----~~~~~~-~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~ 376 (887)
T TIGR00593 309 EAAPLANPAEK-AE-----VGGFVL-ERL-----LDQLKKALALAFATENQSYVAYASEADGIPLLTILTDDKFARWLLN 376 (887)
T ss_pred CHHHHHHHHHh-Cc-----CCeEEE-cCc-----ccccCceeEEEEEecCCCceEEEecccchhhhhHHHHHHHHHHHhC
Confidence 55677777754 21 245666 111 2345678899999976 3 33334431 11222459999999
Q ss_pred CCeEEEEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCCCCCCCHH
Q 037014 94 PNVVFVGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLESGFLDTE 173 (198)
Q Consensus 94 ~~i~kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~~ 173 (198)
+.+.|||||+|.|+..| ..+|+.+.+.+.+.+++.++++ |.. +++|++++.++++..+.+...+..+...-..++.+
T Consensus 377 ~~~~~v~~n~K~d~~~l-~~~gi~~~~~~~Dt~la~yll~-~~~-~~~l~~la~~yl~~~~~~~~~~~~~~~~~~~~~~~ 453 (887)
T TIGR00593 377 EQIKKIGHDAKFLMHLL-KREGIELGGVIFDTMLAAYLLD-PAQ-VSTLDTLARRYLVEELILDEKIGGKLAKFAFPPLE 453 (887)
T ss_pred CCCcEEEeeHHHHHHHH-HhCCCCCCCcchhHHHHHHHcC-CCC-CCCHHHHHHHHcCcccccHHHhccCCCCcccccHH
Confidence 99999999999999999 5789998887667799999987 543 46999999999997754422222211111134333
Q ss_pred -HHHHHHHhHHHHHHHHHHHhc
Q 037014 174 -LIKFACIDAYVSCAIGTKLLL 194 (198)
Q Consensus 174 -Qi~YAA~Da~~~~~l~~~L~~ 194 (198)
...||+.||.+.++||..|..
T Consensus 454 ~~~~ya~~d~~~~~~L~~~l~~ 475 (887)
T TIGR00593 454 EATEYLARRAAATKRLAEELLK 475 (887)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 458999999999999998865
No 23
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
Probab=98.91 E-value=7e-08 Score=72.77 Aligned_cols=130 Identities=17% Similarity=0.173 Sum_probs=91.2
Q ss_pred CCceeEEEeeeCCeEEEEEccccCcccHHHHHhhcCCCeEEEEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCC
Q 037014 58 SGKIATLQLCVDTKCLILQLLYMDCIPLSIKNFLSDPNVVFVGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCL 137 (198)
Q Consensus 58 ~~~~~liQla~~~~~~i~~l~~~~~~~~~L~~lL~d~~i~kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~ 137 (198)
..++..+.+|++++++.+++.. +.....|+++|+|+++.|+||+.|.++..| +.+|+.+.+...+.++++|+++ |..
T Consensus 17 ~~~~~glal~~~~~~~yi~~~~-~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~l~~~~fD~~LAaYLL~-p~~ 93 (151)
T cd06128 17 SANLVGLAFAIEGVAAYIPVAH-DYALELLKPLLEDEKALKVGQNLKYDRVIL-ANYGIELRGIAFDTMLEAYLLD-PVA 93 (151)
T ss_pred cCcEEEEEEEcCCCeEEEeCCC-CcCHHHHHHHHcCCCCCEEeeehHHHHHHH-HHCCCCCCCcchhHHHHHHHcC-CCC
Confidence 4568889999876655555432 101345899999999999999999999998 6789998888666689999998 644
Q ss_pred CCchHHHHHHHHcCCc-CCCCCceeccCCCCC--CCCHH-HHHHHHHhHHHHHHHHHHHh
Q 037014 138 GKPGLKVLAYQLLRLR-PWKPKKVCMNNLESG--FLDTE-LIKFACIDAYVSCAIGTKLL 193 (198)
Q Consensus 138 ~~~~L~~l~~~~l~~~-l~K~~~~~~s~W~~~--~L~~~-Qi~YAA~Da~~~~~l~~~L~ 193 (198)
+..+++++++++|+.. +.-. .+... ++. .+... .-.|++..|.++++|+++|.
T Consensus 94 ~~~~l~~la~~yl~~~~~~~~-~~~gk--g~~~~~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 94 GRHDMDSLAERWLKEKTITFE-EIAGK--GLTFNQIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred CCCCHHHHHHHHcCCCCccHH-HHcCC--CCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4249999999999877 3301 11111 110 11111 12488888999999998875
No 24
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=98.14 E-value=1.9e-05 Score=55.31 Aligned_cols=60 Identities=15% Similarity=0.209 Sum_probs=47.9
Q ss_pred EEEeeeecCCCCCCCCCceeEEEeeeC--CeEEEEEccccCcccHHHHHhhcCCC-eEEEEEeecchHHHHhhhc
Q 037014 43 VGLNCKWKPHPIPSLSGKIATLQLCVD--TKCLILQLLYMDCIPLSIKNFLSDPN-VVFVGIEVEEIMSKLKNEY 114 (198)
Q Consensus 43 vg~D~Ew~~~~~~~~~~~~~liQla~~--~~~~i~~l~~~~~~~~~L~~lL~d~~-i~kvG~~~~~D~~~L~~~~ 114 (198)
+.+|+|+... ++..++++++|++.+ ++.++++ +.+++.++. .++||||...|+..|.+.+
T Consensus 1 ~~~DiEt~~~--~~~~~~i~~i~~~~~~~~~~~~~~----------f~~~l~~~~~~v~V~hn~~fD~~fL~~~~ 63 (96)
T cd06125 1 IAIDTEATGL--DGAVHEIIEIALADVNPEDTAVID----------LKDILRDKPLAILVGHNGSFDLPFLNNRC 63 (96)
T ss_pred CEEEEECCCC--CCCCCcEEEEEEEEccCCCEEEeh----------HHHHHhhCCCCEEEEeCcHHhHHHHHHHH
Confidence 4799999886 568899999999887 4455545 778888776 7899999999998886543
No 25
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=97.94 E-value=0.00011 Score=60.01 Aligned_cols=130 Identities=18% Similarity=0.200 Sum_probs=83.7
Q ss_pred eEEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEcccc---------------------Cccc-----HHHHHhhcCC
Q 037014 41 LIVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYM---------------------DCIP-----LSIKNFLSDP 94 (198)
Q Consensus 41 ~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~---------------------~~~~-----~~L~~lL~d~ 94 (198)
++|++|||..+...++...-+|=+.|-...+-+|||=.-- +..| ..+.+||..
T Consensus 106 r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP~~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~klL~g- 184 (280)
T KOG2249|consen 106 RVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKPTEPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLKLLKG- 184 (280)
T ss_pred eEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecCCCcccccceeeecccCHHHhccCccHHHHHHHHHHHHhC-
Confidence 5999999999874444444455555555555444443210 1222 457778875
Q ss_pred CeEEEEEeecchHHHHhhhcCCccCceeehHH---HHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCCCCCCC
Q 037014 95 NVVFVGIEVEEIMSKLKNEYGLCIKKKIDVRT---LAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLESGFLD 171 (198)
Q Consensus 95 ~i~kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~---l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~~L~ 171 (198)
-+-|||++++|++.|.-.+.-.. +=|++. +.+. + +.....||+.|++.+||..+.-.+ ..|
T Consensus 185 -RIlVGHaLhnDl~~L~l~hp~s~--iRDTs~~~pl~k~-~--~~~~tpSLK~Lt~~~Lg~~IQ~Ge--HsS-------- 248 (280)
T KOG2249|consen 185 -RILVGHALHNDLQALKLEHPRSM--IRDTSKYPPLMKL-L--SKKATPSLKKLTEALLGKDIQVGE--HSS-------- 248 (280)
T ss_pred -CEEeccccccHHHHHhhhCchhh--hcccccCchHHHH-h--hccCCccHHHHHHHHhchhhhccc--cCc--------
Confidence 45799999999999975554322 223333 2221 1 122478999999999998886532 333
Q ss_pred HHHHHHHHHhHHHHHHHHHHHhc
Q 037014 172 TELIKFACIDAYVSCAIGTKLLL 194 (198)
Q Consensus 172 ~~Qi~YAA~Da~~~~~l~~~L~~ 194 (198)
..||-+..+||.+...
T Consensus 249 -------vEDA~AtM~LY~~vk~ 264 (280)
T KOG2249|consen 249 -------VEDARATMELYKRVKV 264 (280)
T ss_pred -------HHHHHHHHHHHHHHHH
Confidence 6899999999987653
No 26
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=97.93 E-value=0.00027 Score=55.77 Aligned_cols=149 Identities=14% Similarity=0.166 Sum_probs=89.7
Q ss_pred CeEEEEeeeecCC--CCCCCCCceeEEEeeeCCeEEEEEcc----------cc-CcccHHHHHhhc--CCCeEEEEEeec
Q 037014 40 ILIVGLNCKWKPH--PIPSLSGKIATLQLCVDTKCLILQLL----------YM-DCIPLSIKNFLS--DPNVVFVGIEVE 104 (198)
Q Consensus 40 ~~~vg~D~Ew~~~--~~~~~~~~~~liQla~~~~~~i~~l~----------~~-~~~~~~L~~lL~--d~~i~kvG~~~~ 104 (198)
..++.||+|.... +......++..|.++....-.++... .. ..+...+.+++. ||++ .+|||+.
T Consensus 3 l~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~F~~~i~~~dpdi-ivgyN~~ 81 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVITWKKFDLPFVEVVKTEKEMIKRFIEIVKEKDPDV-IYTYNGD 81 (195)
T ss_pred ceEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEEecCCCCCeEEEeCCHHHHHHHHHHHHHHcCCCE-EEecCCC
Confidence 3789999999843 21334556666665553331111211 11 123244444444 4775 7999986
Q ss_pred -chHHHHhhh---cCCccC------------------------ceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCC
Q 037014 105 -EIMSKLKNE---YGLCIK------------------------KKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWK 156 (198)
Q Consensus 105 -~D~~~L~~~---~gi~~~------------------------~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K 156 (198)
.|+..|.++ +|+... -.+|+-.+++..++ +.+.+|+.+++++||.+-..
T Consensus 82 ~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~~---l~sy~L~~v~~~~Lg~~k~d 158 (195)
T cd05780 82 NFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLN---LTRYTLERVYEELFGIEKED 158 (195)
T ss_pred CCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhCC---CCcCcHHHHHHHHhCCCCCc
Confidence 599888743 454311 25788777765443 44889999999999975221
Q ss_pred CCceecc-CCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 037014 157 PKKVCMN-NLESGFLDTELIKFACIDAYVSCAIGTKL 192 (198)
Q Consensus 157 ~~~~~~s-~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L 192 (198)
-..-..+ -|...+--..-++|+-.||...++|.++|
T Consensus 159 ~~~~~i~~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 159 VPGEEIAEAWDSGENLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred CCHHHHHHHHhCCCchHHHHHHhHHHHHHHHHHHhhC
Confidence 1111122 24544434445699999999999998764
No 27
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=97.84 E-value=0.00022 Score=54.41 Aligned_cols=87 Identities=21% Similarity=0.092 Sum_probs=57.0
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhhcCCccCceeehHHH--HHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceec
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNEYGLCIKKKIDVRTL--AKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCM 162 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~l--~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~ 162 (198)
+.+.+++.+ -+.|||+++.|+..|...+ ....+.|+..+ ++...+.|...+++|+.|++++++..+....+.
T Consensus 69 ~~l~~~l~~--~vlV~Hn~~~D~~~l~~~~--~~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~-- 142 (157)
T cd06149 69 KEILKILKG--KVVVGHAIHNDFKALKYFH--PKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQG-- 142 (157)
T ss_pred HHHHHHcCC--CEEEEeCcHHHHHHhcccC--CCcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCCC--
Confidence 567777764 4689999999999995432 22346776543 332323344457999999999998777652111
Q ss_pred cCCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 037014 163 NNLESGFLDTELIKFACIDAYVSCAIGT 190 (198)
Q Consensus 163 s~W~~~~L~~~Qi~YAA~Da~~~~~l~~ 190 (198)
+=|..||.++.+||+
T Consensus 143 -------------H~Al~DA~at~~l~~ 157 (157)
T cd06149 143 -------------HSSVEDARATMELYK 157 (157)
T ss_pred -------------cCcHHHHHHHHHHhC
Confidence 124678888888773
No 28
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=97.78 E-value=0.00074 Score=53.11 Aligned_cols=144 Identities=16% Similarity=0.162 Sum_probs=84.8
Q ss_pred EEEEeeeecCCCC--CCCCCceeEEEeeeC-Ce-EEEEEccc-----------------c---CcccHHHHHhhc--CCC
Q 037014 42 IVGLNCKWKPHPI--PSLSGKIATLQLCVD-TK-CLILQLLY-----------------M---DCIPLSIKNFLS--DPN 95 (198)
Q Consensus 42 ~vg~D~Ew~~~~~--~~~~~~~~liQla~~-~~-~~i~~l~~-----------------~---~~~~~~L~~lL~--d~~ 95 (198)
++.||+|.++... .....++..|.++.. ++ -.++.... . ..+-..+.+++. ||+
T Consensus 1 v~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~~~g~~~~~~~~~~~~~~~~~~i~~~~v~~~~~E~~lL~~f~~~i~~~dpd 80 (199)
T cd05160 1 VLSFDIETTPPVGGPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDDIEFIDGIEVEYFADEKELLKRFFDIIREYDPD 80 (199)
T ss_pred CccEEEeecCCCCCcCCCCCCEEEEEEEEeeCCceeeEEEeecccCCcCCCCCCceEEEeCCHHHHHHHHHHHHHhcCCC
Confidence 4689999987522 234566666665553 22 11211110 0 112234445554 455
Q ss_pred eEEEEEee-cchHHHHhh---hcCCcc------------------------CceeehHHHHHHhCCCCCCCCchHHHHHH
Q 037014 96 VVFVGIEV-EEIMSKLKN---EYGLCI------------------------KKKIDVRTLAKLHFPISCLGKPGLKVLAY 147 (198)
Q Consensus 96 i~kvG~~~-~~D~~~L~~---~~gi~~------------------------~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~ 147 (198)
| .|||++ ..|+..|.+ .+|+.. .-.+|+-.+++.... +.+.+|+.+++
T Consensus 81 i-ivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~~---l~sy~L~~v~~ 156 (199)
T cd05160 81 I-LTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFK---LKSYTLDAVAE 156 (199)
T ss_pred E-EEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhcC---cccCCHHHHHH
Confidence 5 799999 789998875 355544 125788888765443 45889999999
Q ss_pred HHcCCcCCCCCceeccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 037014 148 QLLRLRPWKPKKVCMNNLESGFLDTELIKFACIDAYVSCAIG 189 (198)
Q Consensus 148 ~~l~~~l~K~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~ 189 (198)
.++|.+-..-..-...+|....--..-++|.-.||...++|+
T Consensus 157 ~~l~~~k~~~~~~~~~~~~~~~~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 157 ELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred HHhCCCCCcCCHHHHhhccCcchHHHHHHHHHHHHHHHHHhh
Confidence 999864222111122332111223345699999999999886
No 29
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=97.73 E-value=0.00025 Score=53.70 Aligned_cols=84 Identities=21% Similarity=0.116 Sum_probs=55.3
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccC
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNN 164 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~ 164 (198)
+.|.+++.+ .+ -|||++..|+..|.. +......+|+..+.. ........+++|++||+.++|.++... .
T Consensus 69 ~~l~~~l~~-~v-lVgHn~~fD~~~L~~--~~~~~~~~dt~~l~~-~~~~~~~~~~sL~~l~~~~lgi~~~~~---~--- 137 (152)
T cd06144 69 KKVAELLKG-RI-LVGHALKNDLKVLKL--DHPKKLIRDTSKYKP-LRKTAKGKSPSLKKLAKQLLGLDIQEG---E--- 137 (152)
T ss_pred HHHHHHhCC-CE-EEEcCcHHHHHHhcC--cCCCccEEEeEEeec-cccccCCCChhHHHHHHHHcCcccCCC---C---
Confidence 467778876 44 599999999999953 322234667655432 221100247899999999999766431 1
Q ss_pred CCCCCCCHHHHHHHHHhHHHHHHHHH
Q 037014 165 LESGFLDTELIKFACIDAYVSCAIGT 190 (198)
Q Consensus 165 W~~~~L~~~Qi~YAA~Da~~~~~l~~ 190 (198)
+=|..||.++.+||+
T Consensus 138 -----------H~Al~DA~at~~l~~ 152 (152)
T cd06144 138 -----------HSSVEDARAAMRLYR 152 (152)
T ss_pred -----------cCcHHHHHHHHHHhC
Confidence 225789999988874
No 30
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=97.55 E-value=0.0037 Score=51.02 Aligned_cols=90 Identities=14% Similarity=0.130 Sum_probs=61.6
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhh---cCCc------cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCC
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNE---YGLC------IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPW 155 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~---~gi~------~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~ 155 (198)
..+.+|+.+.. .|||++..|+..|.+. +|.. ...++|+-.+++..++. .+.+|.+||+. +|.+..
T Consensus 78 ~~f~~fi~~~~--lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~---~~~~L~aL~~~-~gi~~~ 151 (240)
T PRK05711 78 DEFLDFIRGAE--LIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPG---KRNSLDALCKR-YGIDNS 151 (240)
T ss_pred HHHHHHhCCCE--EEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCC---CCCCHHHHHHH-CCCCCC
Confidence 34666666543 5899999999988753 3322 23578988888776642 25699999986 464322
Q ss_pred CCCceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 037014 156 KPKKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLEE 196 (198)
Q Consensus 156 K~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~~ 196 (198)
. . +.+=|-.||.++.++|.+|...+
T Consensus 152 ~--r--------------~~H~AL~DA~~~A~v~~~l~~~~ 176 (240)
T PRK05711 152 H--R--------------TLHGALLDAEILAEVYLAMTGGQ 176 (240)
T ss_pred C--C--------------CCCCHHHHHHHHHHHHHHHHCcc
Confidence 1 1 11337899999999999988653
No 31
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=97.48 E-value=0.00037 Score=53.99 Aligned_cols=80 Identities=19% Similarity=0.182 Sum_probs=57.1
Q ss_pred HHHhhcCCCeEEEEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCC
Q 037014 87 IKNFLSDPNVVFVGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLE 166 (198)
Q Consensus 87 L~~lL~d~~i~kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~ 166 (198)
|.+++ +++-+-|||++.+|++.|.-.+ .-..++|+..+.. . |..++.||+.|++++||..+... --.
T Consensus 95 l~~li-~~~tILVGHsL~nDL~aL~l~h--p~~~viDTa~l~~--~--~~~r~~sLk~La~~~L~~~IQ~~--~Hd---- 161 (174)
T cd06143 95 LRLLV-DLGCIFVGHGLAKDFRVINIQV--PKEQVIDTVELFH--L--PGQRKLSLRFLAWYLLGEKIQSE--THD---- 161 (174)
T ss_pred HHHHc-CCCCEEEeccchhHHHHhcCcC--CCcceEEcHHhcc--C--CCCCChhHHHHHHHHcCCcccCC--CcC----
Confidence 44444 5667899999999999994322 1247899987643 2 33347899999999999988652 111
Q ss_pred CCCCCHHHHHHHHHhHHHHHHHHH
Q 037014 167 SGFLDTELIKFACIDAYVSCAIGT 190 (198)
Q Consensus 167 ~~~L~~~Qi~YAA~Da~~~~~l~~ 190 (198)
...||.++++||+
T Consensus 162 -----------SvEDArAam~Ly~ 174 (174)
T cd06143 162 -----------SIEDARTALKLYR 174 (174)
T ss_pred -----------cHHHHHHHHHHhC
Confidence 2689999999883
No 32
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=97.43 E-value=0.0047 Score=50.70 Aligned_cols=87 Identities=23% Similarity=0.137 Sum_probs=60.9
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhh---cCCcc----CceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCC
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNE---YGLCI----KKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKP 157 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~---~gi~~----~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~ 157 (198)
+.+.+++.+. -+.|||++..|...|.+. .|+.. ..++|+..+++. ++. ..+++|..+++.+ |.+...
T Consensus 79 ~~~~~fl~~~-~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~-~~~--~~~~~L~~l~~~~-g~~~~~- 152 (250)
T PRK06310 79 PQIKGFFKEG-DYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKE-YGD--SPNNSLEALAVHF-NVPYDG- 152 (250)
T ss_pred HHHHHHhCCC-CEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHh-ccc--CCCCCHHHHHHHC-CCCCCC-
Confidence 3566677653 368999999999999754 34432 467999888764 542 2367999999764 654322
Q ss_pred CceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 037014 158 KKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLL 194 (198)
Q Consensus 158 ~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~ 194 (198)
-+=|..||+++..++..+.+
T Consensus 153 -----------------aH~Al~Da~at~~vl~~l~~ 172 (250)
T PRK06310 153 -----------------NHRAMKDVEINIKVFKHLCK 172 (250)
T ss_pred -----------------CcChHHHHHHHHHHHHHHHH
Confidence 13368999999999998874
No 33
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=97.41 E-value=0.0035 Score=47.89 Aligned_cols=84 Identities=14% Similarity=0.147 Sum_probs=58.2
Q ss_pred HHHHhhcCCCeEEEEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCC-CCCchHHHHHHHHcCCcCCCCCceeccC
Q 037014 86 SIKNFLSDPNVVFVGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISC-LGKPGLKVLAYQLLRLRPWKPKKVCMNN 164 (198)
Q Consensus 86 ~L~~lL~d~~i~kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~-~~~~~L~~l~~~~l~~~l~K~~~~~~s~ 164 (198)
.+.+|+.+. -+.|||++..|+..|... ...++|+..+++...+... ..+++|+.||+.++|.++..... .
T Consensus 76 ~~~~~i~~~-~vlVgHn~~fD~~fL~~~----~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~~~-~--- 146 (161)
T cd06137 76 ALWKFIDPD-TILVGHSLQNDLDALRMI----HTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGGE-G--- 146 (161)
T ss_pred HHHHhcCCC-cEEEeccHHHHHHHHhCc----CCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCCCC-C---
Confidence 456666643 458999999999999532 2457999999876544221 03789999999999987754111 1
Q ss_pred CCCCCCCHHHHHHHHHhHHHHHHHH
Q 037014 165 LESGFLDTELIKFACIDAYVSCAIG 189 (198)
Q Consensus 165 W~~~~L~~~Qi~YAA~Da~~~~~l~ 189 (198)
+=|..||.++.+||
T Consensus 147 -----------H~A~~DA~at~~l~ 160 (161)
T cd06137 147 -----------HDSLEDALAAREVV 160 (161)
T ss_pred -----------CCcHHHHHHHHHHh
Confidence 22568888888776
No 34
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=97.31 E-value=0.0034 Score=47.45 Aligned_cols=82 Identities=23% Similarity=0.159 Sum_probs=57.2
Q ss_pred HHHHhhcCCCeEEEEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCC
Q 037014 86 SIKNFLSDPNVVFVGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNL 165 (198)
Q Consensus 86 ~L~~lL~d~~i~kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W 165 (198)
.+.+|+. ++-+-|||++..|+..|.. . ...++|+..+++..++. ..+++|+.||+++++..+...+
T Consensus 68 ~~~~fl~-~~~vlVgHn~~fD~~fL~~-~---~~~~iDT~~l~r~~~~~--~~~~~L~~L~~~~~~~~i~~~~------- 133 (150)
T cd06145 68 KLLSLIS-PDTILVGHSLENDLKALKL-I---HPRVIDTAILFPHPRGP--PYKPSLKNLAKKYLGRDIQQGE------- 133 (150)
T ss_pred HHHHHhC-CCCEEEEcChHHHHHHhhc-c---CCCEEEcHHhccccCCC--CCChhHHHHHHHHCCcceeCCC-------
Confidence 5666665 3456899999999999953 2 24579998887655542 2368999999999886554310
Q ss_pred CCCCCCHHHHHHHHHhHHHHHHHH
Q 037014 166 ESGFLDTELIKFACIDAYVSCAIG 189 (198)
Q Consensus 166 ~~~~L~~~Qi~YAA~Da~~~~~l~ 189 (198)
+-+=|..||.++.+||
T Consensus 134 --------~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 134 --------GGHDSVEDARAALELV 149 (150)
T ss_pred --------CCCCcHHHHHHHHHHh
Confidence 0122578999988886
No 35
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=97.28 E-value=0.0076 Score=51.14 Aligned_cols=87 Identities=25% Similarity=0.121 Sum_probs=60.6
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhh---cCCc--cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCc
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNE---YGLC--IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKK 159 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~---~gi~--~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~ 159 (198)
+.+.+|+.+.. -|||+...|...|.+. +|+. ....+|+..+++..++ ....++|.+|++. +|.+. +
T Consensus 80 ~~f~~fl~~~~--lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~--~~~~~kL~~L~~~-lgi~~-~--- 150 (313)
T PRK06807 80 PLFLAFLHTNV--IVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMK--HAPNHKLETLKRM-LGIRL-S--- 150 (313)
T ss_pred HHHHHHHcCCe--EEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhC--CCCCCCHHHHHHH-cCCCC-C---
Confidence 34555666543 4999999999999764 4542 3457999998876664 2347799999865 67554 2
Q ss_pred eeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 160 VCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 160 ~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
-+=|-.||+++..||.++...
T Consensus 151 ---------------~H~Al~DA~~ta~l~~~l~~~ 171 (313)
T PRK06807 151 ---------------SHNAFDDCITCAAVYQKCASI 171 (313)
T ss_pred ---------------CcChHHHHHHHHHHHHHHHHh
Confidence 122568899999998887754
No 36
>PRK07883 hypothetical protein; Validated
Probab=97.26 E-value=0.008 Score=54.89 Aligned_cols=90 Identities=18% Similarity=0.081 Sum_probs=64.4
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhh---cCCcc--CceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCc
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNE---YGLCI--KKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKK 159 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~---~gi~~--~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~ 159 (198)
..+.+|+.+ -+.|||++..|...|.+. +|+.. ...+|+..++...++.....+++|.++++ .+|.+...
T Consensus 87 ~~f~~fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L~~-~~gi~~~~--- 160 (557)
T PRK07883 87 PAFLEFARG--AVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLAR-LFGATTTP--- 160 (557)
T ss_pred HHHHHHhcC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHHHH-HCCcccCC---
Confidence 345666664 457999999999999753 46543 35689988887666432345889999987 46765422
Q ss_pred eeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 160 VCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 160 ~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
-+-|..||.+...|+.+++++
T Consensus 161 ---------------~H~Al~DA~ata~l~~~l~~~ 181 (557)
T PRK07883 161 ---------------THRALDDARATVDVLHGLIER 181 (557)
T ss_pred ---------------CCCHHHHHHHHHHHHHHHHHH
Confidence 134789999999999988754
No 37
>PRK07740 hypothetical protein; Provisional
Probab=97.21 E-value=0.033 Score=45.57 Aligned_cols=147 Identities=16% Similarity=0.100 Sum_probs=90.3
Q ss_pred HHHHHHHHHHHhhccC---------CCeEEEEeeeecCCCCCCCCCceeEEEeee----CCeE------EEEEcccc---
Q 037014 23 SVAENWLLKIRSLHSA---------QILIVGLNCKWKPHPIPSLSGKIATLQLCV----DTKC------LILQLLYM--- 80 (198)
Q Consensus 23 ~~~~~~i~~~~~~~~~---------~~~~vg~D~Ew~~~~~~~~~~~~~liQla~----~~~~------~i~~l~~~--- 80 (198)
..-..|++.+.+.... +..+|.||+|+++.. +.. .-.+||++. ++.. .+++....
T Consensus 33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vv~D~ETTGl~--p~~-~deIIeIgaV~~~~~~i~~~~f~~lv~P~~~i~~ 109 (244)
T PRK07740 33 LQQEAWIRSIQKEAKRDDVLDIPLTDLPFVVFDLETTGFS--PQQ-GDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPE 109 (244)
T ss_pred HHHHHHHHHHHHHhccCCccCCCccCCCEEEEEEeCCCCC--CCC-CCeEEEEEEEEEECCEEEEEEEEEEeCcCCCCCh
Confidence 5677899998765331 237999999998752 111 123455552 1111 11222210
Q ss_pred ----------------CcccH---HHHHhhcCCCeEEEEEeecchHHHHhhh----cCCcc-CceeehHHHHHHhCCCCC
Q 037014 81 ----------------DCIPL---SIKNFLSDPNVVFVGIEVEEIMSKLKNE----YGLCI-KKKIDVRTLAKLHFPISC 136 (198)
Q Consensus 81 ----------------~~~~~---~L~~lL~d~~i~kvG~~~~~D~~~L~~~----~gi~~-~~~~Dl~~l~~~~l~~~~ 136 (198)
..+++ .+.+++.+ -+.|||++..|...|.+. ++... ...+|+..+++...+ .
T Consensus 110 ~~~~ltGIt~e~l~~ap~~~evl~~f~~fi~~--~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~--~ 185 (244)
T PRK07740 110 HILELTGITAEDVAFAPPLAEVLHRFYAFIGA--GVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAH--E 185 (244)
T ss_pred hheeccCCCHHHHhCCCCHHHHHHHHHHHhCC--CEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcC--C
Confidence 01223 34444454 368999999999988642 33333 468999988875543 3
Q ss_pred CCCchHHHHHHHHcCCcCCCCCceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 137 LGKPGLKVLAYQLLRLRPWKPKKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 137 ~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
...++|+++++. +|.+.... +-|..||.+..+||.+++.+
T Consensus 186 ~~~~sL~~l~~~-~gi~~~~~------------------H~Al~Da~ata~l~~~ll~~ 225 (244)
T PRK07740 186 RDFPTLDDALAY-YGIPIPRR------------------HHALGDALMTAKLWAILLVE 225 (244)
T ss_pred CCCCCHHHHHHH-CCcCCCCC------------------CCcHHHHHHHHHHHHHHHHH
Confidence 357899999975 67654321 23578999999999998754
No 38
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=97.20 E-value=0.023 Score=44.52 Aligned_cols=79 Identities=15% Similarity=0.063 Sum_probs=56.7
Q ss_pred CeEEEEEeecchHHHHhh---hcCCc-----cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCC
Q 037014 95 NVVFVGIEVEEIMSKLKN---EYGLC-----IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLE 166 (198)
Q Consensus 95 ~i~kvG~~~~~D~~~L~~---~~gi~-----~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~ 166 (198)
+-+.|||++..|+..|.+ .+|+. ....+|+..+++...+ ..+|.++|+. +|.++...
T Consensus 102 ~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~-----~~~L~~l~~~-~gi~~~~~--------- 166 (189)
T cd06134 102 RAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG-----QTVLAKACQA-AGIEFDNK--------- 166 (189)
T ss_pred CCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC-----CCcHHHHHHH-CCCCCCCC---------
Confidence 357999999999998874 35551 2357999999876654 3579999886 56654211
Q ss_pred CCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 167 SGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 167 ~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
+-+=|..||.+..+|+.+|+++
T Consensus 167 -------~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 167 -------EAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred -------CCcChHHHHHHHHHHHHHHHHh
Confidence 1133689999999999998753
No 39
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=97.19 E-value=0.013 Score=47.27 Aligned_cols=90 Identities=18% Similarity=0.182 Sum_probs=62.1
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhh---cC--Cc----cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCC
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNE---YG--LC----IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPW 155 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~---~g--i~----~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~ 155 (198)
+.+.+|+.+. ..|+|++..|+..|.+. +| +. ...++|+..+++..++ + .+.+|++||+. +|.+..
T Consensus 74 ~~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p--~-~~~~L~~L~~~-~gi~~~ 147 (225)
T TIGR01406 74 DEFLDFIGGS--ELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFP--G-QRNSLDALCKR-FKVDNS 147 (225)
T ss_pred HHHHHHhCCC--EEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcC--C-CCCCHHHHHHh-cCCCCC
Confidence 3556666653 35999999999999743 45 22 1468999888877664 2 26799999987 464432
Q ss_pred CCCceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 037014 156 KPKKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLEE 196 (198)
Q Consensus 156 K~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~~ 196 (198)
.. +.+=|..||.++.+||..|....
T Consensus 148 ~r----------------~~H~Al~DA~~~a~v~~~l~~~~ 172 (225)
T TIGR01406 148 HR----------------TLHGALLDAHLLAEVYLALTGGQ 172 (225)
T ss_pred CC----------------CCcCHHHHHHHHHHHHHHHHcCC
Confidence 11 11237899999999999987654
No 40
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=97.12 E-value=0.0064 Score=51.57 Aligned_cols=88 Identities=23% Similarity=0.089 Sum_probs=62.0
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhh---cCCc--cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCc
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNE---YGLC--IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKK 159 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~---~gi~--~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~ 159 (198)
+.|.+|+.+. +.|||++..|+..|.+. +|.. ....+|+..+++... +...+++|.++++. +|.+....
T Consensus 86 ~~l~~~l~~~--~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~--~~~~~~kL~~l~~~-~gi~~~~~-- 158 (313)
T PRK06063 86 GEVAELLRGR--TLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLG--LGLPNLRLETLAAH-WGVPQQRP-- 158 (313)
T ss_pred HHHHHHcCCC--EEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhc--cCCCCCCHHHHHHH-cCCCCCCC--
Confidence 4567777653 57999999999999754 3443 346799988877543 22347889999985 56553221
Q ss_pred eeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 160 VCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 160 ~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
+-|..||.++.+|+..+++.
T Consensus 159 ----------------H~Al~DA~ata~l~~~ll~~ 178 (313)
T PRK06063 159 ----------------HDALDDARVLAGILRPSLER 178 (313)
T ss_pred ----------------CCcHHHHHHHHHHHHHHHHH
Confidence 23678999999999887643
No 41
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=97.11 E-value=0.016 Score=47.88 Aligned_cols=86 Identities=28% Similarity=0.242 Sum_probs=60.4
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhh---hcCCc--cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCc
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKN---EYGLC--IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKK 159 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~---~~gi~--~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~ 159 (198)
..+.+++.+. +.|||++..|...|.+ .+|.. ....+|+..+++..+.. .+.+|+.|++. +|.+..+
T Consensus 139 ~~f~~fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~---~~~~L~~L~~~-lgi~~~~--- 209 (257)
T PRK08517 139 EEFRLFLGDS--VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIES---PRYGLSFLKEL-LGIEIEV--- 209 (257)
T ss_pred HHHHHHHCCC--eEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccC---CCCCHHHHHHH-cCcCCCC---
Confidence 4566666653 5899999999998864 34443 24568888888765542 37899999874 6755432
Q ss_pred eeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 037014 160 VCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLL 194 (198)
Q Consensus 160 ~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~ 194 (198)
-+=|..||.++.+|+.++..
T Consensus 210 ---------------~HrAl~DA~ata~ll~~ll~ 229 (257)
T PRK08517 210 ---------------HHRAYADALAAYEIFKICLL 229 (257)
T ss_pred ---------------CCChHHHHHHHHHHHHHHHH
Confidence 12367899999999998874
No 42
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=97.10 E-value=0.014 Score=47.29 Aligned_cols=80 Identities=23% Similarity=0.115 Sum_probs=53.8
Q ss_pred CeEEEEEeecchHHHHhhh---cCCc---cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCCCC
Q 037014 95 NVVFVGIEVEEIMSKLKNE---YGLC---IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLESG 168 (198)
Q Consensus 95 ~i~kvG~~~~~D~~~L~~~---~gi~---~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~ 168 (198)
..+.|||+...|...|.+. +|.. ...++|...++....... .++++|.++++. +|.+....
T Consensus 93 ~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~-~~~~~L~~l~~~-~gi~~~~a----------- 159 (232)
T PRK07942 93 GVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYR-KGKRTLTALCEH-YGVRLDNA----------- 159 (232)
T ss_pred CCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhccc-CCCCCHHHHHHH-cCCCCCCC-----------
Confidence 3456999999999988653 4542 245788776665432211 236789999976 57654331
Q ss_pred CCCHHHHHHHHHhHHHHHHHHHHHhc
Q 037014 169 FLDTELIKFACIDAYVSCAIGTKLLL 194 (198)
Q Consensus 169 ~L~~~Qi~YAA~Da~~~~~l~~~L~~ 194 (198)
+=|..||.++.+|+.+|.+
T Consensus 160 -------H~Al~Da~ata~l~~~l~~ 178 (232)
T PRK07942 160 -------HEATADALAAARVAWALAR 178 (232)
T ss_pred -------CChHHHHHHHHHHHHHHHH
Confidence 2267899999999988865
No 43
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.07 E-value=0.012 Score=47.08 Aligned_cols=93 Identities=13% Similarity=0.096 Sum_probs=60.8
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhhcC---C---ccCceeehHHHHHHhCCC-CCCCCchHHHHHHHHcCCcCCCC
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNEYG---L---CIKKKIDVRTLAKLHFPI-SCLGKPGLKVLAYQLLRLRPWKP 157 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~~g---i---~~~~~~Dl~~l~~~~l~~-~~~~~~~L~~l~~~~l~~~l~K~ 157 (198)
+.+.+++.+ -..|||++..|...|.+.+. . ....++|+..++....+. ++ .+.+|..+++. +|.+....
T Consensus 79 ~~~~~~~~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~-~~~~L~~l~~~-~gl~~~~~ 154 (217)
T TIGR00573 79 EDFADYIRG--AELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPG-KRNTLDALCKR-YEITNSHR 154 (217)
T ss_pred HHHHHHhCC--CEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCC-CCCCHHHHHHH-cCCCCCCc
Confidence 345666655 35789999999999986542 1 123568877766544321 21 36789999976 46442210
Q ss_pred CceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcccC
Q 037014 158 KKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLEET 197 (198)
Q Consensus 158 ~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~~~ 197 (198)
.-+=|..||.++.+|+.++..+..
T Consensus 155 ----------------~~H~Al~DA~~ta~l~~~l~~~~~ 178 (217)
T TIGR00573 155 ----------------ALHGALADAFILAKLYLVMTGKQT 178 (217)
T ss_pred ----------------ccCCHHHHHHHHHHHHHHHHhcch
Confidence 112368899999999999987653
No 44
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=97.06 E-value=0.019 Score=46.57 Aligned_cols=130 Identities=14% Similarity=0.050 Sum_probs=81.5
Q ss_pred CeEEEEeeeecCCCCCCCCCceeEEEeeeCC----e--EEEEEcccc----------------C---ccc---HHHHHhh
Q 037014 40 ILIVGLNCKWKPHPIPSLSGKIATLQLCVDT----K--CLILQLLYM----------------D---CIP---LSIKNFL 91 (198)
Q Consensus 40 ~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~----~--~~i~~l~~~----------------~---~~~---~~L~~lL 91 (198)
+.++.||+|+++. .+.. -.+||+|.-+ . ..++++... . .+. +.+.+|+
T Consensus 2 ~~~vv~D~ETTGl--~~~~--d~IIeig~v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~~fi 77 (232)
T PRK06309 2 PALIFYDTETTGT--QIDK--DRIIEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFC 77 (232)
T ss_pred CcEEEEEeeCCCC--CCCC--CEEEEEEEEcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHH
Confidence 3689999999986 2222 3567776422 1 223343221 0 111 2455555
Q ss_pred cCCCeEEEEEee-cchHHHHhhh---cCCc--cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCC
Q 037014 92 SDPNVVFVGIEV-EEIMSKLKNE---YGLC--IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNL 165 (198)
Q Consensus 92 ~d~~i~kvG~~~-~~D~~~L~~~---~gi~--~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W 165 (198)
.+ .-..||||. ..|...|.+. +|+. ....+|+..++....+ ...+++|..+++.+ |.+...
T Consensus 78 ~~-~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~--~~~~~~L~~l~~~~-~~~~~~--------- 144 (232)
T PRK06309 78 GT-DNILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRP--DLPKHNLQYLRQVY-GFEENQ--------- 144 (232)
T ss_pred cC-CCEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcC--CCCCCCHHHHHHHc-CCCCCC---------
Confidence 43 456899995 8999999754 3443 2467999998876543 33467899998764 544322
Q ss_pred CCCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 166 ESGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 166 ~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
-+=|..||+++..|+.+++++
T Consensus 145 ---------aH~Al~Da~~t~~vl~~l~~~ 165 (232)
T PRK06309 145 ---------AHRALDDVITLHRVFSALVGD 165 (232)
T ss_pred ---------CCCcHHHHHHHHHHHHHHHHH
Confidence 123689999999999998753
No 45
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=97.01 E-value=0.019 Score=46.36 Aligned_cols=69 Identities=14% Similarity=0.167 Sum_probs=43.9
Q ss_pred eehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccC-CCCCCCC-HHHHHHHHHhHHHHHHHHHHHh
Q 037014 122 IDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNN-LESGFLD-TELIKFACIDAYVSCAIGTKLL 193 (198)
Q Consensus 122 ~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~-W~~~~L~-~~Qi~YAA~Da~~~~~l~~~L~ 193 (198)
+|+-..++... .+.+.+|+++|+++||..-..-.....++ |...|-. ..-++|...||...++|+.+|.
T Consensus 154 iD~~~~~~~~~---kl~sy~L~~Va~~~Lg~~k~d~~~~~i~~~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl~ 224 (230)
T cd05777 154 FDLLQVIQRDY---KLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLM 224 (230)
T ss_pred eeHHHHHHHhc---CcccCcHHHHHHHHhCCCCCCCCHHHHHHHHccCHhHhHHHHHhhHHHHHHHHHHHHHHh
Confidence 45555554332 34588999999999996532111112233 3333322 3446999999999999999986
No 46
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=96.97 E-value=0.008 Score=45.75 Aligned_cols=86 Identities=21% Similarity=0.218 Sum_probs=58.4
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhh---cCC-----ccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCC
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNE---YGL-----CIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWK 156 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~---~gi-----~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K 156 (198)
..|.+++.+.. .|||++..|...|.+. +|. .....+|+..++....+ . ...+|.++++. +|.+...
T Consensus 73 ~~l~~~l~~~~--lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~--~-~~~~L~~l~~~-~~i~~~~ 146 (167)
T cd06131 73 DEFLDFIRGAE--LVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFP--G-KPNSLDALCKR-FGIDNSH 146 (167)
T ss_pred HHHHHHHCCCe--EEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcC--C-CCCCHHHHHHH-CCCCCCC
Confidence 35666776533 5999999999988653 233 22467998877765543 2 26799999987 4644321
Q ss_pred CCceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 037014 157 PKKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKL 192 (198)
Q Consensus 157 ~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L 192 (198)
.+-+-|..||.+..+|+.+|
T Consensus 147 ----------------~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 147 ----------------RTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred ----------------CCCCChHHHHHHHHHHHHHh
Confidence 11234789999999999876
No 47
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=96.89 E-value=0.03 Score=42.21 Aligned_cols=88 Identities=27% Similarity=0.187 Sum_probs=60.5
Q ss_pred HHHHHhhcCCCeEEEEEee-cchHHHHhhh---cCCc---cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCC
Q 037014 85 LSIKNFLSDPNVVFVGIEV-EEIMSKLKNE---YGLC---IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKP 157 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~-~~D~~~L~~~---~gi~---~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~ 157 (198)
..+..++.+. + .|+|+. ..|...|.+. +|+. ....+|+..++....+.+ ..+|+++++.+ |.+....
T Consensus 72 ~~~~~~l~~~-~-~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~---~~~L~~l~~~~-~~~~~~~ 145 (169)
T smart00479 72 EELLEFLKGK-I-LVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGR---KYSLKKLAERL-GLEVIGR 145 (169)
T ss_pred HHHHHHhcCC-E-EEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCC---CCCHHHHHHHC-CCCCCCC
Confidence 4566677653 3 456666 9999999753 3432 234799988887655422 78999999874 4332210
Q ss_pred CceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 158 KKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 158 ~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
.+.|..||.+..+|+.++..+
T Consensus 146 -----------------~H~A~~Da~~t~~l~~~~~~~ 166 (169)
T smart00479 146 -----------------AHRALDDARATAKLFKKLVER 166 (169)
T ss_pred -----------------CcCcHHHHHHHHHHHHHHHHH
Confidence 366899999999999998764
No 48
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.86 E-value=0.02 Score=54.66 Aligned_cols=88 Identities=26% Similarity=0.323 Sum_probs=63.1
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhh---cCCcc-CceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCce
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNE---YGLCI-KKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKV 160 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~---~gi~~-~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~ 160 (198)
+.+.+++.+ -+.|||++..|+..|.+. .|..+ ...+|+..++...++ ...+++|.+|++. +|.+....
T Consensus 78 ~~~~~~l~~--~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p--~~~~~~L~~L~~~-lgl~~~~~--- 149 (820)
T PRK07246 78 RHIYDLIED--CIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFP--TLEKYSLSHLSRE-LNIDLADA--- 149 (820)
T ss_pred HHHHHHhCC--CEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhC--CCCCCCHHHHHHH-cCCCCCCC---
Confidence 456677775 457999999999999754 24443 346898888876654 3457899999986 67654321
Q ss_pred eccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 161 CMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 161 ~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
+=|..||.+...|+.+|..+
T Consensus 150 ---------------H~Al~DA~ata~L~~~l~~~ 169 (820)
T PRK07246 150 ---------------HTAIADARATAELFLKLLQK 169 (820)
T ss_pred ---------------CCHHHHHHHHHHHHHHHHHH
Confidence 23678999999999888754
No 49
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=96.85 E-value=0.02 Score=42.20 Aligned_cols=83 Identities=19% Similarity=0.064 Sum_probs=57.1
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhhcC-----CccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCc
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNEYG-----LCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKK 159 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~~g-----i~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~ 159 (198)
..+.++++. -..|||+...|...|.+.+. ......+|+..+++..++.. ...++..+..+.+|....
T Consensus 71 ~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~--~~~~l~~~~~~~~~~~~~---- 142 (159)
T cd06127 71 PEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGL--RSHRLGLLLAERYGIPLE---- 142 (159)
T ss_pred HHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCC--CcCchHHHHHHHcCCCCC----
Confidence 456677776 56899999999999976543 34567899999887766532 467788774444453221
Q ss_pred eeccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 037014 160 VCMNNLESGFLDTELIKFACIDAYVSCAIG 189 (198)
Q Consensus 160 ~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~ 189 (198)
+-+-|..||.++.+||
T Consensus 143 --------------~~H~Al~Da~~t~~l~ 158 (159)
T cd06127 143 --------------GAHRALADALATAELL 158 (159)
T ss_pred --------------CCCCcHHHHHHHHHHh
Confidence 2234678898888876
No 50
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=96.84 E-value=0.024 Score=54.28 Aligned_cols=87 Identities=28% Similarity=0.263 Sum_probs=61.4
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhh---cCCc--cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCc
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNE---YGLC--IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKK 159 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~---~gi~--~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~ 159 (198)
+.|.+++.+ -+.|||++..|...|.+. .|+. ....+|+..++...++ ...+++|.+|++. +|.+....
T Consensus 72 ~~l~~~l~~--~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p--~~~~~~L~~l~~~-~gi~~~~~-- 144 (850)
T TIGR01407 72 QEIYDLLED--GIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFP--TEESYQLSELSEA-LGLTHENP-- 144 (850)
T ss_pred HHHHHHhCC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcC--CCCCCCHHHHHHH-CCCCCCCC--
Confidence 456677764 348999999999999753 4544 3567999888876654 3457899999987 67654331
Q ss_pred eeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 037014 160 VCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLL 194 (198)
Q Consensus 160 ~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~ 194 (198)
+=|..||.+..+|+.+|.+
T Consensus 145 ----------------H~Al~DA~ata~l~~~l~~ 163 (850)
T TIGR01407 145 ----------------HRADSDAQATAELLLLLFE 163 (850)
T ss_pred ----------------CChHHHHHHHHHHHHHHHH
Confidence 2357788888888777754
No 51
>PRK05168 ribonuclease T; Provisional
Probab=96.83 E-value=0.086 Score=42.07 Aligned_cols=79 Identities=15% Similarity=0.052 Sum_probs=56.4
Q ss_pred CeEEEEEeecchHHHHhh---hcCCc-----cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCC
Q 037014 95 NVVFVGIEVEEIMSKLKN---EYGLC-----IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLE 166 (198)
Q Consensus 95 ~i~kvG~~~~~D~~~L~~---~~gi~-----~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~ 166 (198)
+-+.|||++..|+..|.+ .+|+. .-.++|+..+++..++ ..+|..+++. +|.++....
T Consensus 114 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~-----~~~L~~l~~~-~gl~~~~~~-------- 179 (211)
T PRK05168 114 RAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALG-----QTVLAKACQA-AGIEFDNKE-------- 179 (211)
T ss_pred CceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC-----CCCHHHHHHH-CCCCCCCCC--------
Confidence 567999999999998875 34542 1247999999876554 3579999986 566543211
Q ss_pred CCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 167 SGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 167 ~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
-+=|..||.+..+|+.+|..+
T Consensus 180 --------~H~Al~DA~ata~l~~~l~~~ 200 (211)
T PRK05168 180 --------AHSALYDTEKTAELFCEIVNR 200 (211)
T ss_pred --------CCChHHHHHHHHHHHHHHHHH
Confidence 123689999999999988754
No 52
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=96.77 E-value=0.0072 Score=56.47 Aligned_cols=107 Identities=15% Similarity=0.082 Sum_probs=71.3
Q ss_pred ccc-HHHHHhhcC-CCeEEEEEeecchHHHHhhhcCCccC--ceeehHHHHHHhCC------------------------
Q 037014 82 CIP-LSIKNFLSD-PNVVFVGIEVEEIMSKLKNEYGLCIK--KKIDVRTLAKLHFP------------------------ 133 (198)
Q Consensus 82 ~~~-~~L~~lL~d-~~i~kvG~~~~~D~~~L~~~~gi~~~--~~~Dl~~l~~~~l~------------------------ 133 (198)
..| ..|.++=+. ..-+.||||+..|-.++++.|+++-. .++|+.-+..-..|
T Consensus 226 E~p~~~LIP~~~~~ke~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTMSlHia~~Gm~S~Qrplw~ka~k~k~a~~d~~~ 305 (1075)
T KOG3657|consen 226 EIPEAALIPLGEIGKEQLIVGHNVSFDRARIREEYNINGSKIRFLDTMSLHIAMSGMCSRQRPLWFKARKAKSAMYDSET 305 (1075)
T ss_pred CCcHHhhCcCCcCCCCceEEeccccchHHHHHHHHhccccceeeeechhhhhhhhccccccchhHhhhhhhhhhhhhccc
Confidence 455 556665533 34578999999999999999988643 23555332211111
Q ss_pred --------CCCC---CCchHHHHHHHHcCCc-CCCCCceeccCCCCCCCCHHHH--------HHHHHhHHHHHHHHHHHh
Q 037014 134 --------ISCL---GKPGLKVLAYQLLRLR-PWKPKKVCMNNLESGFLDTELI--------KFACIDAYVSCAIGTKLL 193 (198)
Q Consensus 134 --------~~~~---~~~~L~~l~~~~l~~~-l~K~~~~~~s~W~~~~L~~~Qi--------~YAA~Da~~~~~l~~~L~ 193 (198)
.|.+ +-.||.++++-+.|.. ++|..+-. .. .++.+|| .|+|.|+++..+||.++.
T Consensus 306 ~ps~~d~~~pWL~~SS~NSL~dVhk~~c~~~~LdKt~Rd~---Fv--s~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lf 380 (1075)
T KOG3657|consen 306 NPSISDYDNPWLGRSSLNSLVDVHKFHCGIDALDKTPRDS---FV--SGTKEQIRENFQPLMNYCARDVIATHQVFFRLF 380 (1075)
T ss_pred CCchhhhhhhhhhhhhhHHHHHHHHhhCCCCccccchHHh---hh--cCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHh
Confidence 0111 2346888888888877 88865321 12 3777887 899999999999999875
No 53
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.73 E-value=0.036 Score=53.62 Aligned_cols=88 Identities=27% Similarity=0.261 Sum_probs=62.6
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhh---cCCc--cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCc
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNE---YGLC--IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKK 159 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~---~gi~--~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~ 159 (198)
+.|.+|+.+ -+.|||++..|...|.+. .|.. ....+|+..++...++ ...+++|.+|++. +|.+....
T Consensus 76 ~~l~~~l~~--~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p--~~~~~~L~~l~~~-l~i~~~~~-- 148 (928)
T PRK08074 76 PEIVELLEG--AYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLP--TAESYKLRDLSEE-LGLEHDQP-- 148 (928)
T ss_pred HHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcC--CCCCCCHHHHHHh-CCCCCCCC--
Confidence 456777764 467999999999999753 3443 2467999998876654 3457899999986 56544322
Q ss_pred eeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 160 VCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 160 ~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
+=|-.||.+...|+.+|+++
T Consensus 149 ----------------H~Al~DA~ata~l~~~l~~~ 168 (928)
T PRK08074 149 ----------------HRADSDAEVTAELFLQLLNK 168 (928)
T ss_pred ----------------CChHHHHHHHHHHHHHHHHH
Confidence 22568888888888888653
No 54
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=96.72 E-value=0.022 Score=45.00 Aligned_cols=99 Identities=17% Similarity=0.207 Sum_probs=60.6
Q ss_pred HHHHHhh--cCCCeEEEEEeecc-hHHHHhh---hcCCcc------------------------Cc--eeehHHHHHH-h
Q 037014 85 LSIKNFL--SDPNVVFVGIEVEE-IMSKLKN---EYGLCI------------------------KK--KIDVRTLAKL-H 131 (198)
Q Consensus 85 ~~L~~lL--~d~~i~kvG~~~~~-D~~~L~~---~~gi~~------------------------~~--~~Dl~~l~~~-~ 131 (198)
..+.+++ .||+| -+|||+.+ |+..|.+ .+|+.+ .| .+|+-.+++. .
T Consensus 56 ~~f~~~i~~~dPDv-i~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~~~ 134 (193)
T cd05784 56 LALIAWFAQYDPDI-IIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTAT 134 (193)
T ss_pred HHHHHHHHhhCCCE-EEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHHcc
Confidence 4444444 34554 68998865 9988764 244432 11 4676655543 2
Q ss_pred CCCCCCCCchHHHHHHHHcCCcCC-CC-----CceeccCCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 037014 132 FPISCLGKPGLKVLAYQLLRLRPW-KP-----KKVCMNNLESGFLDTELIKFACIDAYVSCAIGT 190 (198)
Q Consensus 132 l~~~~~~~~~L~~l~~~~l~~~l~-K~-----~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~ 190 (198)
+ .+.+.+|+++|+++||..-. .. +++. .-|...+ ..-++|+..||+.+++|++
T Consensus 135 ~---kl~sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~-~~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 135 Y---HFESFSLENVAQELLGEGKLIHDVDDRGAEIE-RLFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred C---CCCcCCHHHHHHHHhCCCccccCcccCHHHHH-HHHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 2 24588999999999996321 11 1121 1244333 3457999999999999873
No 55
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=96.68 E-value=0.049 Score=42.74 Aligned_cols=146 Identities=14% Similarity=0.135 Sum_probs=87.8
Q ss_pred eEEEEeeeecCC--CCCCCCCceeEEEeeeCCe-EEEEEc--cccCcccHHHHHhh--cCCCeEEEEEeec-chHHHHhh
Q 037014 41 LIVGLNCKWKPH--PIPSLSGKIATLQLCVDTK-CLILQL--LYMDCIPLSIKNFL--SDPNVVFVGIEVE-EIMSKLKN 112 (198)
Q Consensus 41 ~~vg~D~Ew~~~--~~~~~~~~~~liQla~~~~-~~i~~l--~~~~~~~~~L~~lL--~d~~i~kvG~~~~-~D~~~L~~ 112 (198)
+++.||+|.... +......++..|.++..++ ..++-- .....+...+..++ .||++ -+|||+. .|+-.|..
T Consensus 4 ~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~~~~~~~E~~lL~~F~~~i~~~dPd~-i~gyN~~~FDlpyl~~ 82 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFILAEGLDDRKIIREFVKYVKEYDPDI-IVGYNSNAFDWPYLVE 82 (188)
T ss_pred eEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEEEEecCCCHHHHHHHHHHHHHHcCCCE-EEecCCCcCcHHHHHH
Confidence 689999999842 2234456777777777444 333221 11112334444444 45665 5699874 69987764
Q ss_pred ---hcCCccC--------------------c--eeehHHHHHHhCCCCCCCCchHHHHHHHHcCCc--CCCCC----cee
Q 037014 113 ---EYGLCIK--------------------K--KIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLR--PWKPK----KVC 161 (198)
Q Consensus 113 ---~~gi~~~--------------------~--~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~--l~K~~----~~~ 161 (198)
.+|+.+. | .+|+-.+++.... +.+.+|+.+|+ .||.. ..|.. ++
T Consensus 83 Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~---l~~y~L~~Va~-~Lg~~k~~~k~~~~~~~i- 157 (188)
T cd05781 83 RARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPE---VKVKTLENVAE-YLGVMKKSERVLIEWYRI- 157 (188)
T ss_pred HHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCC---CCCCCHHHHHH-HHCCCccccccCCCHHHH-
Confidence 4564321 1 6787777665432 45889999997 58853 22221 11
Q ss_pred ccCCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 037014 162 MNNLESGFLDTELIKFACIDAYVSCAIGTKL 192 (198)
Q Consensus 162 ~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L 192 (198)
..-|....-...-.+|+..|+...+.|++++
T Consensus 158 ~~~~~~~~~~~~l~~Y~~~D~~~t~~l~~~~ 188 (188)
T cd05781 158 YEYWDDEKKRDILLKYNRDDARSTYGLAEKL 188 (188)
T ss_pred HHHHcCcccHHHHHHHHHHHHHHHHHHHhhC
Confidence 1235432133566799999999999999864
No 56
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=96.66 E-value=0.077 Score=41.90 Aligned_cols=91 Identities=18% Similarity=0.125 Sum_probs=59.6
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhh----cCCcc-CceeehHHHHHHhCC--CC-CCCCchHHHHHHHHcCCcCCC
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNE----YGLCI-KKKIDVRTLAKLHFP--IS-CLGKPGLKVLAYQLLRLRPWK 156 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~----~gi~~-~~~~Dl~~l~~~~l~--~~-~~~~~~L~~l~~~~l~~~l~K 156 (198)
+.+.+++.+ -..|||++..|...|.+. +|..+ ...+|+..++..... .+ ...+.+|+++++. +|.+...
T Consensus 103 ~~~~~~i~~--~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~~ 179 (202)
T PRK09145 103 RQLLAFIGN--RPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILKH-LDLPVLG 179 (202)
T ss_pred HHHHHHHcC--CeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHHHH-cCCCCCC
Confidence 355566664 347999999999988753 24433 457888766532111 11 1236799999976 5655432
Q ss_pred CCceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhccc
Q 037014 157 PKKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLEE 196 (198)
Q Consensus 157 ~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~~ 196 (198)
. +=|..||++...||.+|.++.
T Consensus 180 ~------------------H~Al~DA~ata~l~~~l~~~~ 201 (202)
T PRK09145 180 R------------------HDALNDAIMAALIFLRLRKGD 201 (202)
T ss_pred C------------------CCcHHHHHHHHHHHHHHHhcC
Confidence 1 225789999999999998764
No 57
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=96.48 E-value=0.013 Score=50.95 Aligned_cols=90 Identities=20% Similarity=0.093 Sum_probs=63.5
Q ss_pred ccHHHHHhhcCCCeEEEEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceec
Q 037014 83 IPLSIKNFLSDPNVVFVGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCM 162 (198)
Q Consensus 83 ~~~~L~~lL~d~~i~kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~ 162 (198)
+-..|++| -+++-+-|||++.+|++.|+-.| ..++|++.+.....|. ...+.+|+.|++.+||..+. ....+.
T Consensus 283 vq~~l~~~-~~~~TILVGHSLenDL~aLKl~H----~~ViDTa~lf~~~~g~-~~~k~sLk~L~~~~L~~~Iq-~~~~~H 355 (380)
T KOG2248|consen 283 VQKELLEL-ISKNTILVGHSLENDLKALKLDH----PSVIDTAVLFKHPTGP-YPFKSSLKNLAKSYLGKLIQ-EGVGGH 355 (380)
T ss_pred HHHHHHhh-cCcCcEEEeechhhHHHHHhhhC----CceeeeeEEEecCCCC-ccchHHHHHHHHHHHHHHHh-ccCCCC
Confidence 33567774 45666789999999999997655 3488998777655552 12477899999999998887 111111
Q ss_pred cCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 037014 163 NNLESGFLDTELIKFACIDAYVSCAIGTKLL 193 (198)
Q Consensus 163 s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~ 193 (198)
. .+.||.++.++.....
T Consensus 356 d--------------S~eDA~acm~Lv~~k~ 372 (380)
T KOG2248|consen 356 D--------------SVEDALACMKLVKLKI 372 (380)
T ss_pred c--------------cHHHHHHHHHHHHHHH
Confidence 1 2789999998876544
No 58
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=96.40 E-value=0.17 Score=40.66 Aligned_cols=87 Identities=18% Similarity=0.110 Sum_probs=59.9
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccC
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNN 164 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~ 164 (198)
..+.+|.. .-+-||||+..|...|. .++ ...+|+-.+++..++. . ++++..|++. +|.....+..
T Consensus 66 ev~~~~~~--~~~lVaHNa~FD~~~L~-~~~---~~~idTl~lar~l~p~--~-~~~l~~L~~~-~~l~~~~~~~----- 130 (219)
T PRK07983 66 DVIPHYYG--SEWYVAHNASFDRRVLP-EMP---GEWICTMKLARRLWPG--I-KYSNMALYKS-RKLNVQTPPG----- 130 (219)
T ss_pred HHHHHHcC--CCEEEEeCcHhhHHHHh-CcC---CCcEeHHHHHHHHccC--C-CCCHHHHHHH-cCCCCCCCCC-----
Confidence 34455544 34689999999999994 332 4689999998877653 3 4789999875 5544321100
Q ss_pred CCCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 037014 165 LESGFLDTELIKFACIDAYVSCAIGTKLLL 194 (198)
Q Consensus 165 W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~ 194 (198)
.+-+=|..||+++..|+.++++
T Consensus 131 --------~~aHrAl~Da~ata~ll~~l~~ 152 (219)
T PRK07983 131 --------LHHHRALYDCYITAALLIDIMN 152 (219)
T ss_pred --------CCCCcHHHHHHHHHHHHHHHHH
Confidence 1234588999999999999885
No 59
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=96.38 E-value=0.072 Score=41.25 Aligned_cols=82 Identities=18% Similarity=0.069 Sum_probs=55.5
Q ss_pred HHHHHhhcC--CCeEEEEEee-cchHHHHhhh---cCCcc---CceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCC
Q 037014 85 LSIKNFLSD--PNVVFVGIEV-EEIMSKLKNE---YGLCI---KKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPW 155 (198)
Q Consensus 85 ~~L~~lL~d--~~i~kvG~~~-~~D~~~L~~~---~gi~~---~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~ 155 (198)
+.|.+|+.. ...+.||||+ ..|+..|.+. +|... ..++|.-.++.... + +|.+|+++++|.+..
T Consensus 86 ~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~------~-~L~~l~~~~~~~~~~ 158 (177)
T cd06136 86 NLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELD------Q-SLGSLYKRLFGQEPK 158 (177)
T ss_pred HHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhH------h-hHHHHHHHHhCCCcc
Confidence 456677653 3468999998 8999999753 45442 23478766655321 2 899999988776654
Q ss_pred CCCceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHH
Q 037014 156 KPKKVCMNNLESGFLDTELIKFACIDAYVSCAIGTK 191 (198)
Q Consensus 156 K~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~ 191 (198)
.. +=|..||.++.+++.+
T Consensus 159 ~~------------------H~A~~Da~at~~v~~~ 176 (177)
T cd06136 159 NS------------------HTAEGDVLALLKCALH 176 (177)
T ss_pred cc------------------cchHHHHHHHHHHHhh
Confidence 32 3367899999888753
No 60
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=96.36 E-value=0.1 Score=44.17 Aligned_cols=87 Identities=20% Similarity=0.181 Sum_probs=61.9
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhh---cCCcc--CceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCc
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNE---YGLCI--KKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKK 159 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~---~gi~~--~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~ 159 (198)
+.|.+++.+ -+.|||++..|+..|.+. +|... ...+|+..+++..++ ....++|..|++. +|.+. .
T Consensus 72 ~~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~--~~~~~~L~~L~~~-~gi~~-~--- 142 (309)
T PRK06195 72 EKIKHYFNN--NLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYS--NIDNARLNTVNNF-LGYEF-K--- 142 (309)
T ss_pred HHHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcC--CCCcCCHHHHHHH-cCCCC-c---
Confidence 356666654 468999999999998653 45432 357898888876654 3347899999987 45432 1
Q ss_pred eeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 160 VCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 160 ~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
-+-|..||+++.+|+..|.++
T Consensus 143 ---------------~H~Al~DA~ata~l~~~l~~~ 163 (309)
T PRK06195 143 ---------------HHDALADAMACSNILLNISKE 163 (309)
T ss_pred ---------------ccCCHHHHHHHHHHHHHHHHH
Confidence 144789999999999988754
No 61
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=96.34 E-value=0.14 Score=40.39 Aligned_cols=88 Identities=17% Similarity=0.235 Sum_probs=56.2
Q ss_pred HHHHHhhcCCCeEEEEEeec-chHHHHhhhcCCccCc--eeehHHHH--HHhCCCCCCCCchHHHHHHHHcCCcCCCCCc
Q 037014 85 LSIKNFLSDPNVVFVGIEVE-EIMSKLKNEYGLCIKK--KIDVRTLA--KLHFPISCLGKPGLKVLAYQLLRLRPWKPKK 159 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~-~D~~~L~~~~gi~~~~--~~Dl~~l~--~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~ 159 (198)
+.+.+|+.+. ..|||++. .|+..|. ..|..+.+ .+|+-..+ ......+...+++|.+|++. +|.+..
T Consensus 76 ~~f~~f~~~~--~lVaHNa~~fD~~fL~-~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~-~gi~~~---- 147 (195)
T PRK07247 76 AAFKEFVGEL--PLIGYNAQKSDLPILA-ENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVADF-LGIKGR---- 147 (195)
T ss_pred HHHHHHHCCC--eEEEEeCcHhHHHHHH-HcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHHHh-cCCCCC----
Confidence 4566666654 37999996 7999994 56665443 25554332 11111133457899999986 565421
Q ss_pred eeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 160 VCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 160 ~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
. +=|..||.++..||.+|+..
T Consensus 148 -~--------------HrAl~DA~~ta~v~~~ll~~ 168 (195)
T PRK07247 148 -G--------------HNSLEDARMTARVYESFLES 168 (195)
T ss_pred -C--------------cCCHHHHHHHHHHHHHHHhh
Confidence 1 22578999999999998754
No 62
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=96.29 E-value=0.07 Score=52.89 Aligned_cols=87 Identities=18% Similarity=0.102 Sum_probs=64.4
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhh---cCCc--cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCc
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNE---YGLC--IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKK 159 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~---~gi~--~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~ 159 (198)
+.+.+|+.+ -+.|||++..|...|.+. +|.. ....+|+..+++..+ |....++|.+|++. +|.++..
T Consensus 262 ~~f~~fl~~--~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~--p~~k~~kL~~Lak~-lgi~~~~--- 333 (1213)
T TIGR01405 262 EKFKEFFKD--SILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALN--PEYKSHRLGNICKK-LGVDLDD--- 333 (1213)
T ss_pred HHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHh--ccCCCCCHHHHHHH-cCCCCCC---
Confidence 456666665 357999999999999753 4553 246799988887654 34568999999987 5665432
Q ss_pred eeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 037014 160 VCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLL 194 (198)
Q Consensus 160 ~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~ 194 (198)
-+-|..||.++.+|+.+|++
T Consensus 334 ---------------~HrAl~DA~aTa~I~~~ll~ 353 (1213)
T TIGR01405 334 ---------------HHRADYDAEATAKVFKVMVE 353 (1213)
T ss_pred ---------------CcCHHHHHHHHHHHHHHHHH
Confidence 15688999999999998874
No 63
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=96.28 E-value=0.27 Score=39.11 Aligned_cols=141 Identities=13% Similarity=0.089 Sum_probs=80.6
Q ss_pred eEEEEeeeecCC----CCCCCCCceeEEEeeeCC-----eEEEEEc------------------ccc-CcccHHHHHhhc
Q 037014 41 LIVGLNCKWKPH----PIPSLSGKIATLQLCVDT-----KCLILQL------------------LYM-DCIPLSIKNFLS 92 (198)
Q Consensus 41 ~~vg~D~Ew~~~----~~~~~~~~~~liQla~~~-----~~~i~~l------------------~~~-~~~~~~L~~lL~ 92 (198)
++++||+|.... |.......-.++|++..+ +.+++.. +.. ..+...+.+++.
T Consensus 6 rilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~F~~~i~ 85 (204)
T cd05783 6 KRIAIDIEVYTPIKGRIPDPKTAEYPVISVALAGSDGLKRVLVLKREGVEGLEGLLPEGAEVEFFDSEKELIREAFKIIS 85 (204)
T ss_pred eEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEcCCCCCcEEEEEecCCcccccccCCCCCeEEecCCHHHHHHHHHHHHh
Confidence 789999999753 222223223457776532 2444331 000 123345555566
Q ss_pred CCCeEEEEEeec-chHHHHhh---hcCCcc----------------CceeehHHHHHH------hCCCCCCCCchHHHHH
Q 037014 93 DPNVVFVGIEVE-EIMSKLKN---EYGLCI----------------KKKIDVRTLAKL------HFPISCLGKPGLKVLA 146 (198)
Q Consensus 93 d~~i~kvG~~~~-~D~~~L~~---~~gi~~----------------~~~~Dl~~l~~~------~l~~~~~~~~~L~~l~ 146 (198)
+.. +-+|||.. .|+-.|.+ .+|+.. .-.+|+-...+. .++. .+.+.+|+++|
T Consensus 86 ~~~-~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~-~~~~~~L~~Va 163 (204)
T cd05783 86 EYP-IVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGN-KYREYTLDAVA 163 (204)
T ss_pred cCC-EEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhcc-ccccCcHHHHH
Confidence 554 56799875 59988864 456651 124677554432 1221 23478999999
Q ss_pred HHHcCCc-CCCCCceeccCCCCCCCCHHH-HHHHHHhHHHHHHHHH
Q 037014 147 YQLLRLR-PWKPKKVCMNNLESGFLDTEL-IKFACIDAYVSCAIGT 190 (198)
Q Consensus 147 ~~~l~~~-l~K~~~~~~s~W~~~~L~~~Q-i~YAA~Da~~~~~l~~ 190 (198)
+.+||.. ++-..++ |. +..+. ++|+..||...++|.+
T Consensus 164 ~~~lg~~K~~~~~~i----~~---~~~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 164 KALLGEGKVELEKNI----SE---LNLYELAEYNYRDAELTLELTT 202 (204)
T ss_pred HHhcCCCcccCCchh----hh---hcHHHHHHhhHHHHHHHHHHhc
Confidence 9999963 2221111 11 24444 4999999999998864
No 64
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=96.21 E-value=0.21 Score=40.73 Aligned_cols=89 Identities=15% Similarity=-0.012 Sum_probs=58.5
Q ss_pred HHHHhhcCCCeEEEEEeecchHHHHhhh----cCCcc-CceeehHHHHHHhCCCC-----------CCCCchHHHHHHHH
Q 037014 86 SIKNFLSDPNVVFVGIEVEEIMSKLKNE----YGLCI-KKKIDVRTLAKLHFPIS-----------CLGKPGLKVLAYQL 149 (198)
Q Consensus 86 ~L~~lL~d~~i~kvG~~~~~D~~~L~~~----~gi~~-~~~~Dl~~l~~~~l~~~-----------~~~~~~L~~l~~~~ 149 (198)
.+.+++.+ -+.|||+...|...|.+. ++..+ ..++|+..++...++.. .....+|.++++.
T Consensus 122 ~l~~~~~~--~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~- 198 (239)
T PRK09146 122 ELLEALAG--KVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLR- 198 (239)
T ss_pred HHHHHhCC--CEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHH-
Confidence 34444443 458999999999998753 33333 45799999887654311 0135678888875
Q ss_pred cCCcCCCCCceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 150 LRLRPWKPKKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 150 l~~~l~K~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
+|.+... -+=|..||.++..|+..+..+
T Consensus 199 ~gl~~~~------------------~H~Al~DA~ata~l~~~~~~~ 226 (239)
T PRK09146 199 YGLPAYS------------------PHHALTDAIATAELLQAQIAH 226 (239)
T ss_pred cCCCCCC------------------CCCcHHHHHHHHHHHHHHHHH
Confidence 4544322 133689999999999988754
No 65
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=96.19 E-value=0.13 Score=44.59 Aligned_cols=94 Identities=9% Similarity=0.029 Sum_probs=61.5
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhhc-------------------------------CCc-cCceeehHHHHHHhC
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNEY-------------------------------GLC-IKKKIDVRTLAKLHF 132 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~~-------------------------------gi~-~~~~~Dl~~l~~~~l 132 (198)
+.|.+|+.+. +-|+|+...|+..|.+.+ ++. ...++|+-.+++..+
T Consensus 117 ~el~~fL~g~--vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~ 194 (377)
T PRK05601 117 KPLDRLIDGR--TLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQG 194 (377)
T ss_pred HHHHHHhCCC--EEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHc
Confidence 5677888754 479999999999887543 112 235799988888655
Q ss_pred CCCCCCCchHHHHHHHHcCCcCCCCCceeccCCCCCCCCHHHHHHHH---HhHHHHHHHHHHH
Q 037014 133 PISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLESGFLDTELIKFAC---IDAYVSCAIGTKL 192 (198)
Q Consensus 133 ~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~~Qi~YAA---~Da~~~~~l~~~L 192 (198)
+.+.+++|..||+. +|...+... . .....|....+ .||-++..||.++
T Consensus 195 --p~l~~~rL~~La~~-lGi~~p~~~-A--------~~~Ra~~p~~~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 195 --VALDDIRIRGVAHT-LGLDAPAAE-A--------SVERAQVPHRQLCREETLLVARLYFAL 245 (377)
T ss_pred --CCCCCCCHHHHHHH-hCCCCCchh-h--------hhhhhcCChhhhhhHHHHHHHHHHHHh
Confidence 34568999999997 676654311 0 11122221122 3888888998876
No 66
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=96.02 E-value=0.24 Score=39.34 Aligned_cols=90 Identities=16% Similarity=-0.008 Sum_probs=60.0
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhh---cCCcc---CceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCC
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNE---YGLCI---KKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPK 158 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~---~gi~~---~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~ 158 (198)
+.|.+++.+...+.+++ ...|+..|.+. +|+.. ...+|+..+.+...+. ...++|.++++. +|.+....
T Consensus 84 ~~f~~~~~~~~~~iv~~-~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~--~~~~~L~~~~~~-~gi~~~~~- 158 (207)
T PRK07748 84 EKLAEYDKRCKPTIVTW-GNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGE--RNQTGLWKAIEE-YGKEGTGK- 158 (207)
T ss_pred HHHHHHhCcCCeEEEEE-CHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCc--CCCCCHHHHHHH-cCCCCCCC-
Confidence 45777777644555655 68999999753 45542 4567887766555442 236799998876 56543210
Q ss_pred ceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 159 KVCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 159 ~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
-+-|..||.++.+|+.+|..+
T Consensus 159 ----------------~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 159 ----------------HHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred ----------------CcChHHHHHHHHHHHHHHHhC
Confidence 123689999999999998866
No 67
>PHA02528 43 DNA polymerase; Provisional
Probab=95.96 E-value=0.42 Score=46.09 Aligned_cols=181 Identities=18% Similarity=0.183 Sum_probs=105.1
Q ss_pred EEcCeEEEEEEcCCHHHHHHHHHHHHhhcc-------------------------CCCeEEEEeeeecCC--CCCCC--C
Q 037014 8 SFCGKIIETTVTSTTSVAENWLLKIRSLHS-------------------------AQILIVGLNCKWKPH--PIPSL--S 58 (198)
Q Consensus 8 ~f~~~~i~~~v~~~~~~~~~~i~~~~~~~~-------------------------~~~~~vg~D~Ew~~~--~~~~~--~ 58 (198)
+|.|+.+......+..++.+|.+.+...-. ..-++++||+|..+. +..+. .
T Consensus 49 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~merfi~~~~~~~~~~~~~~~~p~lrv~s~DIE~~~~~gfP~p~~~~ 128 (881)
T PHA02528 49 DIYGKNCRPKKFDSMRDARKWMKRMKDVGFEALGMDDFKLQYISDTYPGEIKYDRSKIRIANLDIEVTAEDGFPDPEEAK 128 (881)
T ss_pred ccCCCEEeEEECCCHHHHHHHHHHHHhcCCceeehhHHhhhhhhhhcCCCCCCCCCCccEEEEEEEECCCCCCCCcccCC
Confidence 467888888888899999999988876411 124899999999753 22222 2
Q ss_pred CceeEEEeeeC--CeEEEEEcc--------------c-c--------C---cccHHHHHhh--cCCCeEEEEEeec-chH
Q 037014 59 GKIATLQLCVD--TKCLILQLL--------------Y-M--------D---CIPLSIKNFL--SDPNVVFVGIEVE-EIM 107 (198)
Q Consensus 59 ~~~~liQla~~--~~~~i~~l~--------------~-~--------~---~~~~~L~~lL--~d~~i~kvG~~~~-~D~ 107 (198)
+++..|.+... ++.+++.+. . . + .+...+..++ .||+| -+|||+. .|+
T Consensus 129 d~IisIsl~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~sE~eLL~~F~~~i~~~DPDI-I~GyNi~~FDl 207 (881)
T PHA02528 129 YEIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPQEILDKVVYMPFDTEREMLLEYINFWEENTPVI-FTGWNVELFDV 207 (881)
T ss_pred CcEEEEEEecCCCCEEEEEEecCcccccccCCcccccccCCeeEEEcCCHHHHHHHHHHHHHHhCCcE-EEecCCccCCH
Confidence 34444444322 223444330 0 0 0 1223333443 57887 6899875 588
Q ss_pred HHHhhh----cCCc----------------------------cCc--eeehHHHHHHhCCCCCCCCchHHHHHHHHcCCc
Q 037014 108 SKLKNE----YGLC----------------------------IKK--KIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLR 153 (198)
Q Consensus 108 ~~L~~~----~gi~----------------------------~~~--~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~ 153 (198)
..|.++ +|.. +.| .+|.-.+++.. ....+.+.+|+++++.+||..
T Consensus 208 pYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~GRv~lD~~dl~k~~-~~~~l~SYsLe~VA~~~LG~~ 286 (881)
T PHA02528 208 PYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISGISILDYLDLYKKF-TFTNQPSYRLDYIAEVELGKK 286 (881)
T ss_pred HHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcceEEEeHHHHHHHh-hhcccccCCHHHHHHHHhCCC
Confidence 776532 2321 111 24554554431 112345889999999999964
Q ss_pred CCCCCceeccC-CCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 037014 154 PWKPKKVCMNN-LESGFLDTELIKFACIDAYVSCAIGTKL 192 (198)
Q Consensus 154 l~K~~~~~~s~-W~~~~L~~~Qi~YAA~Da~~~~~l~~~L 192 (198)
-.....-..+. |...+ ..=++|...||...++|+.++
T Consensus 287 K~d~~~~eI~~l~~~d~--~~l~~Ynl~Da~Lv~~L~~kl 324 (881)
T PHA02528 287 KLDYSDGPFKKFRETDH--QKYIEYNIIDVELVDRLDDKR 324 (881)
T ss_pred CccCCHHHHHHHHhcCH--HHHHHHHHHHHHHHHHHHHHH
Confidence 32211111223 33322 445799999999999999984
No 68
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=95.67 E-value=0.33 Score=38.65 Aligned_cols=145 Identities=17% Similarity=0.170 Sum_probs=79.1
Q ss_pred CeEEEEeeeecCCCCC----CCCCceeEEEeeeC--Ce-EEEEEcccc--CcccHHHHHhh--cCCCeEEEEEee-cchH
Q 037014 40 ILIVGLNCKWKPHPIP----SLSGKIATLQLCVD--TK-CLILQLLYM--DCIPLSIKNFL--SDPNVVFVGIEV-EEIM 107 (198)
Q Consensus 40 ~~~vg~D~Ew~~~~~~----~~~~~~~liQla~~--~~-~~i~~l~~~--~~~~~~L~~lL--~d~~i~kvG~~~-~~D~ 107 (198)
-+++.||+|....... +....-.++|||.. ++ -.++..... ..+...+.+++ .||+| -+|||+ ..|+
T Consensus 9 lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~E~~lL~~f~~~i~~~dPdi-i~g~N~~~FD~ 87 (207)
T cd05785 9 LRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEVLHAEDAAEKELLEELVAIIRERDPDV-IEGHNIFRFDL 87 (207)
T ss_pred ceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceeeeccCCCCHHHHHHHHHHHHHHhCCCE-EeccCCcccCH
Confidence 4799999999764211 22333456777653 22 222221111 12323444444 35774 679998 6799
Q ss_pred HHHhh---hcCCcc--------------------------------CceeehHHHHHHh-CCCCCCCCchHHHHHHHHcC
Q 037014 108 SKLKN---EYGLCI--------------------------------KKKIDVRTLAKLH-FPISCLGKPGLKVLAYQLLR 151 (198)
Q Consensus 108 ~~L~~---~~gi~~--------------------------------~~~~Dl~~l~~~~-l~~~~~~~~~L~~l~~~~l~ 151 (198)
..|.+ .+|+.. .-.+|+-.+++.. .....+.+.+|+.+|+.+ |
T Consensus 88 pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~~~l~sysL~~Va~~~-g 166 (207)
T cd05785 88 PYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSSRDLPSYGLKAVAKHF-G 166 (207)
T ss_pred HHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccccCCCCCCHHHHHHHh-c
Confidence 88764 345433 1126776655421 101123478999999975 4
Q ss_pred CcCC-CC----CceeccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 037014 152 LRPW-KP----KKVCMNNLESGFLDTELIKFACIDAYVSCAIG 189 (198)
Q Consensus 152 ~~l~-K~----~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~ 189 (198)
..-. |. +++ ..-|...+ ..-++|+..||...++|+
T Consensus 167 ~~~~~k~d~~~~~I-~~l~~~~~--~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 167 LASPDRTYIDGRQI-AEVWRSDP--ARLLAYALDDVRETEGLA 206 (207)
T ss_pred ccCCCcCCCCHHHH-HHHHhcCH--HHHHHHHHHHHHHHHHhh
Confidence 3111 11 111 12355442 455699999999999875
No 69
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=95.67 E-value=0.26 Score=39.18 Aligned_cols=92 Identities=16% Similarity=0.107 Sum_probs=57.6
Q ss_pred CCCeEEEEEee-cchHHHHhh---hcCCccC--------c----------eeehHHHHHHhCCCCCCCCchHHHHHHHHc
Q 037014 93 DPNVVFVGIEV-EEIMSKLKN---EYGLCIK--------K----------KIDVRTLAKLHFPISCLGKPGLKVLAYQLL 150 (198)
Q Consensus 93 d~~i~kvG~~~-~~D~~~L~~---~~gi~~~--------~----------~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l 150 (198)
||++ .+|||. ..|+..|.+ .+|+.+. + .+|+-.+++.... ......+|+.+|+.+|
T Consensus 88 ~Pd~-i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~-l~~~sysLd~Va~~~L 165 (204)
T cd05779 88 KPHI-IVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSY-LPQGSQGLKAVTKAKL 165 (204)
T ss_pred CCCE-EEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhc-CCCCCccHHHHHHHHh
Confidence 5665 688877 469988764 3554422 1 4677776653111 1113678999999999
Q ss_pred CCc-CCC-CCceeccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 037014 151 RLR-PWK-PKKVCMNNLESGFLDTELIKFACIDAYVSCAIG 189 (198)
Q Consensus 151 ~~~-l~K-~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~ 189 (198)
|.. .+= ...+. .-|...+ ..-++|+-.||...+.||
T Consensus 166 g~~K~~~~~~~I~-~~~~~~~--~~l~~Y~~~D~~~T~~l~ 203 (204)
T cd05779 166 GYDPVELDPEDMV-PLAREDP--QTLASYSVSDAVATYYLY 203 (204)
T ss_pred CCCcCcCCHHHHH-HHHhCCc--HHHHhccHHHHHHHHHHh
Confidence 963 111 11121 1455544 456799999999999987
No 70
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=95.51 E-value=0.63 Score=35.25 Aligned_cols=88 Identities=18% Similarity=0.146 Sum_probs=59.0
Q ss_pred HHHHHhhcCC-CeEEEEEeecchHHHHhh---hcCC-----ccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCC
Q 037014 85 LSIKNFLSDP-NVVFVGIEVEEIMSKLKN---EYGL-----CIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPW 155 (198)
Q Consensus 85 ~~L~~lL~d~-~i~kvG~~~~~D~~~L~~---~~gi-----~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~ 155 (198)
+.+.+++.+. ....++++ ..|...+.+ .++. ...+.+|+..++....+.+ ...+|.++++. +|.+..
T Consensus 80 ~~~~~~l~~~~~~~~v~~~-~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~--~~~~L~~l~~~-~gi~~~ 155 (176)
T cd06133 80 KEFLEWLGKNGKYAFVTWG-DWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLK--KRTGLSKALEY-LGLEFE 155 (176)
T ss_pred HHHHHHHHhCCCeEEEeec-HhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCC--CCCCHHHHHHH-CCCCCC
Confidence 4667777764 25566665 788766543 2332 3457899999988777643 47899999865 576554
Q ss_pred CCCceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 037014 156 KPKKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKLL 193 (198)
Q Consensus 156 K~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~ 193 (198)
. +-+-|-.||.+..+++.+|.
T Consensus 156 ~-----------------~~H~Al~DA~~~a~l~~~~~ 176 (176)
T cd06133 156 G-----------------RHHRGLDDARNIARILKRLL 176 (176)
T ss_pred C-----------------CCcCcHHHHHHHHHHHHHhC
Confidence 1 11235789999999988763
No 71
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=95.01 E-value=0.12 Score=39.02 Aligned_cols=141 Identities=16% Similarity=0.076 Sum_probs=71.4
Q ss_pred EEEeeeecCCCCCCCCCceeEEEeee--CCe-EEEEEccccC-cccHHHH---HhhcCCCeEEEEEee-cchHHHHhhhc
Q 037014 43 VGLNCKWKPHPIPSLSGKIATLQLCV--DTK-CLILQLLYMD-CIPLSIK---NFLSDPNVVFVGIEV-EEIMSKLKNEY 114 (198)
Q Consensus 43 vg~D~Ew~~~~~~~~~~~~~liQla~--~~~-~~i~~l~~~~-~~~~~L~---~lL~d~~i~kvG~~~-~~D~~~L~~~~ 114 (198)
+-||+|+++. .+..+.+-++.++. ++. ....+....+ .-...+. .++..... .|+|+. ..|...|.+.+
T Consensus 1 l~~DIET~Gl--~~~~~~i~liG~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~~~l~~~~~-iv~yng~~FD~p~L~~~~ 77 (164)
T PF13482_consen 1 LFFDIETTGL--SPDNDTIYLIGVADFDDDEIITFIQWFAEDPDEEEIILEFFELLDEADN-IVTYNGKNFDIPFLKRRA 77 (164)
T ss_dssp --EEEEESS---GG-G---EEEEEEE-ETTTTE-EEEE-GGGHHHHHHHHH--HHHHTT---EEESSTTTTHHHHHHHHH
T ss_pred CcEEecCCCC--CCCCCCEEEEEEEEeCCCceEEeeHhhccCcHHHHHHHHHHHHHhcCCe-EEEEeCcccCHHHHHHHH
Confidence 3589999976 34456688888885 333 3233433221 1122333 34544443 566765 66998887644
Q ss_pred ---CCc-cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceec-------cCCC---CCCCCHHHHHHHHH
Q 037014 115 ---GLC-IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCM-------NNLE---SGFLDTELIKFACI 180 (198)
Q Consensus 115 ---gi~-~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~-------s~W~---~~~L~~~Qi~YAA~ 180 (198)
++. ..+.+|+...+..... .+.||+.++.. +|..-.+. .+.+ ..|. .+...+.-+.|.-.
T Consensus 78 ~~~~~~~~~~~iDl~~~~~~~~~----~~~~Lk~ve~~-lg~~~~~~-~~~G~~~~~~~~~~~~~~~~~~~~~i~~yN~~ 151 (164)
T PF13482_consen 78 KRYGLPPPFNHIDLLKIIKKHFL----ESYSLKNVEKF-LGIERRDD-DISGSESVKLYKEYLETGDPEALEEILEYNED 151 (164)
T ss_dssp -HHHH--GGGEEEHHHHHT-TTS----CCTT--SHHH-------------HHHHHHHHHH---TTGGTS--HHHHHHHHH
T ss_pred HHcCCCcccchhhHHHHHHhccC----CCCCHHHHhhh-cccccccC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence 444 6788999888753322 36799999887 67654421 1111 1221 12355666799999
Q ss_pred hHHHHHHHHHHH
Q 037014 181 DAYVSCAIGTKL 192 (198)
Q Consensus 181 Da~~~~~l~~~L 192 (198)
|+.++.+|++.|
T Consensus 152 Dv~~~~~L~~~l 163 (164)
T PF13482_consen 152 DVRATRRLYEWL 163 (164)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHh
Confidence 999999999886
No 72
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=94.94 E-value=0.0096 Score=56.15 Aligned_cols=82 Identities=23% Similarity=0.219 Sum_probs=59.2
Q ss_pred HhhcCCCeEEEEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCCCC
Q 037014 89 NFLSDPNVVFVGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLESG 168 (198)
Q Consensus 89 ~lL~d~~i~kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~ 168 (198)
.+|-+..++|||||+.+|.+.+ ...+..+.++|...+. .+|. -+..||+-||..+||..+.-. +=..
T Consensus 1008 ~~Li~~GviFVGHGL~nDFrvI--Ni~Vp~~QiiDTv~lf--~~~s--~R~LSLrfLa~~lLg~~IQ~~------~HDS- 1074 (1118)
T KOG1275|consen 1008 RLLIQRGVIFVGHGLQNDFRVI--NIHVPEEQIIDTVTLF--RLGS--QRMLSLRFLAWELLGETIQME------AHDS- 1074 (1118)
T ss_pred HHHHHcCcEEEcccccccceEE--EEecChhhheeeeEEE--eccc--ccEEEHHHHHHHHhcchhhcc------cccc-
Confidence 4578889999999999999887 3334445688887764 3442 247899999999999776532 1121
Q ss_pred CCCHHHHHHHHHhHHHHHHHHHHHh
Q 037014 169 FLDTELIKFACIDAYVSCAIGTKLL 193 (198)
Q Consensus 169 ~L~~~Qi~YAA~Da~~~~~l~~~L~ 193 (198)
..||..+++||++-+
T Consensus 1075 ----------IeDA~taLkLYk~Yl 1089 (1118)
T KOG1275|consen 1075 ----------IEDARTALKLYKKYL 1089 (1118)
T ss_pred ----------HHHHHHHHHHHHHHH
Confidence 578888888887654
No 73
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=94.21 E-value=0.4 Score=37.88 Aligned_cols=79 Identities=15% Similarity=0.045 Sum_probs=55.7
Q ss_pred CeEEEEEeecchHHHHhhh---cCCc-----cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCC
Q 037014 95 NVVFVGIEVEEIMSKLKNE---YGLC-----IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLE 166 (198)
Q Consensus 95 ~i~kvG~~~~~D~~~L~~~---~gi~-----~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~ 166 (198)
+-+.|||++..|+..|.+. +|.. ....+|+..+++...+ ..+|..+++. +|.+...
T Consensus 105 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~-----~~~L~~l~~~-~gi~~~~---------- 168 (200)
T TIGR01298 105 RAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG-----QTVLAKACQA-AGXDFDS---------- 168 (200)
T ss_pred CCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC-----cccHHHHHHH-cCCCccc----------
Confidence 4468999999999999753 3432 2347999998876543 4579999986 4654321
Q ss_pred CCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 167 SGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 167 ~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
.+-+=|..||.+..+|+.+|+.+
T Consensus 169 ------~~~H~Al~Da~ata~lf~~l~~~ 191 (200)
T TIGR01298 169 ------TQAHSALYDTEKTAELFCEIVNR 191 (200)
T ss_pred ------cchhhhHHhHHHHHHHHHHHHHH
Confidence 12345788999999999988753
No 74
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=93.76 E-value=0.74 Score=34.17 Aligned_cols=81 Identities=26% Similarity=0.194 Sum_probs=57.4
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhh---cCCc--cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCc
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNE---YGLC--IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKK 159 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~---~gi~--~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~ 159 (198)
+.|.+++.+ .+.|||++..|...|.+. +|+. ....+|+..+++..++ ...+.+|..+++. +|.+.. .
T Consensus 69 ~~l~~~l~~--~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~--~~~~~~L~~l~~~-~g~~~~-~-- 140 (156)
T cd06130 69 PEIKPFLGG--SLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWP--LLPNHKLNTVAEH-LGIELN-H-- 140 (156)
T ss_pred HHHHHHhCC--CEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhc--cCCCCCHHHHHHH-cCCCcc-C--
Confidence 456777775 468999999999999653 3543 3467999888876654 2457899999986 566543 1
Q ss_pred eeccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 037014 160 VCMNNLESGFLDTELIKFACIDAYVSCAIG 189 (198)
Q Consensus 160 ~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~ 189 (198)
+=|..||.+..+|+
T Consensus 141 ----------------H~Al~Da~~ta~l~ 154 (156)
T cd06130 141 ----------------HDALEDARACAEIL 154 (156)
T ss_pred ----------------cCchHHHHHHHHHH
Confidence 22467888888776
No 75
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=93.36 E-value=2.5 Score=34.04 Aligned_cols=91 Identities=21% Similarity=0.184 Sum_probs=63.8
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhh---cCCc--cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCc
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNE---YGLC--IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKK 159 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~---~gi~--~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~ 159 (198)
+.+.+++.+. -..|+|+...|...|... ++.. ....+|.-.+++..++ +....+|+.|+. .+|........
T Consensus 86 ~~~~~~i~~~-~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~--~~~~~~L~~l~~-~~gi~~~~~~~ 161 (243)
T COG0847 86 PEFLDFIGGL-RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFP--GFDRSSLDALAE-RLGIDRNPFHP 161 (243)
T ss_pred HHHHHHHCCC-CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcC--CCccchHHHHHH-HcCCCcCCcCC
Confidence 4455666654 558999999999999754 3444 3456788888876664 334889999999 56765432110
Q ss_pred eeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 160 VCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 160 ~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
+=|..||.++..+|..+..+
T Consensus 162 ----------------H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 162 ----------------HRALFDALALAELFLLLQTG 181 (243)
T ss_pred ----------------cchHHHHHHHHHHHHHHHhc
Confidence 33789999999999988763
No 76
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=93.19 E-value=2.7 Score=35.40 Aligned_cols=86 Identities=12% Similarity=-0.006 Sum_probs=52.0
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhhcC-CccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceecc
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNEYG-LCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMN 163 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~~g-i~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s 163 (198)
+.+..|+.+. -+.||||+..|...|.+.+. +......+...... +..+...+++|..|+.. +|. ..
T Consensus 112 ~~l~~fl~~~-~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~--~~~~~~~~~kL~~La~~-~g~--~~------- 178 (294)
T PRK09182 112 AAVDALIAPA-DLIIAHNAGFDRPFLERFSPVFATKPWACSVSEID--WSARGFEGTKLGYLAGQ-AGF--FH------- 178 (294)
T ss_pred HHHHHHhcCC-CEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHh--hccccCCCCCHHHHHHH-cCC--CC-------
Confidence 5677788764 46799999999999965331 11112222211111 11223357899999986 451 11
Q ss_pred CCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 037014 164 NLESGFLDTELIKFACIDAYVSCAIGTKLL 193 (198)
Q Consensus 164 ~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~ 193 (198)
. -+=|..||.++..|+..++
T Consensus 179 --~--------aHrAl~Da~Ata~ll~~~l 198 (294)
T PRK09182 179 --E--------GHRAVDDCQALLELLARPL 198 (294)
T ss_pred --C--------CcChHHHHHHHHHHHHHHH
Confidence 1 1337899999999998765
No 77
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=93.18 E-value=0.71 Score=36.75 Aligned_cols=129 Identities=17% Similarity=0.146 Sum_probs=76.3
Q ss_pred CCCCCceeEEEeee---CCeEEEEE-ccccC--cccHHHHHhhcCCCeEEEEEee-cchHHHHhh---hcCCccC-----
Q 037014 55 PSLSGKIATLQLCV---DTKCLILQ-LLYMD--CIPLSIKNFLSDPNVVFVGIEV-EEIMSKLKN---EYGLCIK----- 119 (198)
Q Consensus 55 ~~~~~~~~liQla~---~~~~~i~~-l~~~~--~~~~~L~~lL~d~~i~kvG~~~-~~D~~~L~~---~~gi~~~----- 119 (198)
....+++.+|.++. .++.+.+. ....+ .+-..+.++++..+-+.||||. ..|+-.|.. .+|+.+.
T Consensus 47 ~~~~~~Iv~Is~~~~~~~~~~~~~~~~~~~~E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~ 126 (208)
T cd05782 47 PLPFHKVVSISALYRDDDGGFLKVRTLDGADEKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDL 126 (208)
T ss_pred ccccCceEEEEEEEEecCCCeEEEeecCCCCHHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCc
Confidence 34567888888887 34433322 11111 2334444555542235699988 569988875 3566321
Q ss_pred -------------ceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCcee----ccCCCCCCCCHHHHHHHHHhH
Q 037014 120 -------------KKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVC----MNNLESGFLDTELIKFACIDA 182 (198)
Q Consensus 120 -------------~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~----~s~W~~~~L~~~Qi~YAA~Da 182 (198)
..+|+-.+.+. .+ ...+.+|+.+|+ .||.+ .|.. +. ..-|.... -.+=.+|+..||
T Consensus 127 ~~~~~~y~~r~~~~h~DL~~~~~~-~~--~~~~~~L~~va~-~lG~~-~K~d-~~G~~v~~~y~~g~-~~~I~~Yc~~Dv 199 (208)
T cd05782 127 GNKDWNYRNRYSERHLDLMDLLAF-YG--ARARASLDLLAK-LLGIP-GKMD-VDGSQVWELYAEGK-LDEIAEYCETDV 199 (208)
T ss_pred ccchhhccCcCCCCcccHHHHHhc-cC--ccCCCCHHHHHH-HhCCC-CCcC-CCHHHHHHHHHcCC-hHHHHHHHHHHH
Confidence 15777776653 22 134889999987 57763 2321 22 22355544 344459999999
Q ss_pred HHHHHHHH
Q 037014 183 YVSCAIGT 190 (198)
Q Consensus 183 ~~~~~l~~ 190 (198)
...+.||.
T Consensus 200 ~~t~~l~l 207 (208)
T cd05782 200 LNTYLLYL 207 (208)
T ss_pred HHHHHHHh
Confidence 99999985
No 78
>PRK05762 DNA polymerase II; Reviewed
Probab=93.03 E-value=1.9 Score=41.27 Aligned_cols=145 Identities=14% Similarity=0.141 Sum_probs=80.1
Q ss_pred CeEEEEeeeecCCCC-------CCCCCceeEEEeee--CC-eEEEEEccccCcccHHHHHhh--cCCCeEEEEEeec-ch
Q 037014 40 ILIVGLNCKWKPHPI-------PSLSGKIATLQLCV--DT-KCLILQLLYMDCIPLSIKNFL--SDPNVVFVGIEVE-EI 106 (198)
Q Consensus 40 ~~~vg~D~Ew~~~~~-------~~~~~~~~liQla~--~~-~~~i~~l~~~~~~~~~L~~lL--~d~~i~kvG~~~~-~D 106 (198)
..++.||+|...... ....+ .++.++. ++ ..++........+...+..++ .||+| -+|||+. .|
T Consensus 155 lrvlsfDIE~~~~~~i~sI~~~~~~~~--~vi~ig~~~~~~~~~v~~~~sE~~LL~~F~~~i~~~DPDI-IvGyNi~~FD 231 (786)
T PRK05762 155 LKVVSLDIETSNKGELYSIGLEGCGQR--PVIMLGPPNGEALDFLEYVADEKALLEKFNAWFAEHDPDV-IIGWNVVQFD 231 (786)
T ss_pred CeEEEEEEEEcCCCceEEeeecCCCCC--eEEEEECCCCCCcceEEEcCCHHHHHHHHHHHHHhcCCCE-EEEeCCCCCc
Confidence 489999999876410 00111 2333332 21 122222111112334444444 46776 6899975 59
Q ss_pred HHHHhh---hcCCccC---------------------------ceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCC
Q 037014 107 MSKLKN---EYGLCIK---------------------------KKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWK 156 (198)
Q Consensus 107 ~~~L~~---~~gi~~~---------------------------~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K 156 (198)
+..|.+ .+|+.+. -.+|+-.+++.... ...+.+|+.+++.+||..-..
T Consensus 232 lpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~~~~--~l~sysL~~Va~~~Lg~~K~~ 309 (786)
T PRK05762 232 LRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATW--VFDSFSLEYVSQRLLGEGKAI 309 (786)
T ss_pred HHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHHhhc--cCCCCCHHHHHHHHhCCCeec
Confidence 988874 3444320 14677666654321 235889999999999854211
Q ss_pred --C----CceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHH
Q 037014 157 --P----KKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKL 192 (198)
Q Consensus 157 --~----~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L 192 (198)
. +++ ..-|... ...-.+|...||...+.|+.++
T Consensus 310 ~d~~~~~~eI-~~~~~~~--~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 310 DDPYDRMDEI-DRRFAED--KPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred cCccccHHHH-HHHHhhh--HHHHHHHHHHHHHHHHHHHHHh
Confidence 1 111 1123321 1344699999999999999865
No 79
>PRK06722 exonuclease; Provisional
Probab=92.58 E-value=2.3 Score=35.56 Aligned_cols=91 Identities=18% Similarity=0.073 Sum_probs=56.1
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhh---cCCcc-----CceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCC
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNE---YGLCI-----KKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWK 156 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~---~gi~~-----~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K 156 (198)
..+.+|+.+.. + |+|+...|...|.+. +|+.. ...+|++.++...+..-....++|.++++. +|.+...
T Consensus 82 ~ef~~fig~~~-l-vahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~~~-lgL~~~g 158 (281)
T PRK06722 82 EKFIQFIGEDS-I-FVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAVEQ-LGLIWEG 158 (281)
T ss_pred HHHHHHHCCCc-E-EEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHHHH-CCCCCCC
Confidence 45666666533 3 455568999999763 45543 224788776643332100124689999986 5655321
Q ss_pred CCceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 157 PKKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 157 ~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
. -+=|-.||.++.+|+.+|..+
T Consensus 159 ~-----------------~HrAL~DA~~TA~L~l~l~~~ 180 (281)
T PRK06722 159 K-----------------QHRALADAENTANILLKAYSE 180 (281)
T ss_pred C-----------------CcCcHHHHHHHHHHHHHHhcc
Confidence 1 122578999999999998854
No 80
>PRK11779 sbcB exonuclease I; Provisional
Probab=92.55 E-value=1.2 Score=40.14 Aligned_cols=91 Identities=14% Similarity=0.116 Sum_probs=53.8
Q ss_pred HHHHhhcCCCeEEEEEe-ecchHHHHhhhcCCc-----------cCceeehHHHHHHhC---C----CC----CCCCchH
Q 037014 86 SIKNFLSDPNVVFVGIE-VEEIMSKLKNEYGLC-----------IKKKIDVRTLAKLHF---P----IS----CLGKPGL 142 (198)
Q Consensus 86 ~L~~lL~d~~i~kvG~~-~~~D~~~L~~~~gi~-----------~~~~~Dl~~l~~~~l---~----~~----~~~~~~L 142 (198)
.+.+++..++-+.|||+ +..|...|...+... ....+|+-++++... . .| +..+++|
T Consensus 84 ~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rL 163 (476)
T PRK11779 84 RIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKL 163 (476)
T ss_pred HHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCcH
Confidence 56666765556689996 789999886544211 111234444443111 0 01 1236788
Q ss_pred HHHHHHHcCCcCCCCCceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 143 KVLAYQLLRLRPWKPKKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 143 ~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
..|++. +|.+... -+=|..||++...|+.+|.+.
T Consensus 164 e~L~~~-~gI~~~~------------------AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 164 EHLTKA-NGIEHEN------------------AHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred HHHHHH-cCCCCCC------------------CCCcHHHHHHHHHHHHHHHHh
Confidence 888886 3543321 133678999999999888755
No 81
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=92.54 E-value=0.54 Score=46.21 Aligned_cols=87 Identities=23% Similarity=0.191 Sum_probs=63.8
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhhh---cCCcc--CceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCc
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKNE---YGLCI--KKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKK 159 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~~---~gi~~--~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~ 159 (198)
+.+++|+.| -+-|.||+..|+..|..+ +|+.. ..++|+-.+++.+. |...+++|..||+++ |..+
T Consensus 493 ~kf~~~~~d--~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~--P~~ksh~Lg~l~kk~-~v~l----- 562 (1444)
T COG2176 493 EKFREFIGD--SILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALN--PEFKSHRLGTLCKKL-GVEL----- 562 (1444)
T ss_pred HHHHHHhcC--cEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhC--hhhhhcchHHHHHHh-CccH-----
Confidence 566777775 567999999999999754 45543 46799999887543 556799999999873 4333
Q ss_pred eeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhc
Q 037014 160 VCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLL 194 (198)
Q Consensus 160 ~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~ 194 (198)
++-+-|-.||.+..+++-.+++
T Consensus 563 -------------e~hHRA~yDaeat~~vf~~f~~ 584 (1444)
T COG2176 563 -------------ERHHRADYDAEATAKVFFVFLK 584 (1444)
T ss_pred -------------HHhhhhhhhHHHHHHHHHHHHH
Confidence 4555677888888888877764
No 82
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=92.01 E-value=2.8 Score=41.44 Aligned_cols=69 Identities=17% Similarity=0.236 Sum_probs=43.3
Q ss_pred eehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCC-CCCCCC-HHHHHHHHHhHHHHHHHHHHHh
Q 037014 122 IDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNL-ESGFLD-TELIKFACIDAYVSCAIGTKLL 193 (198)
Q Consensus 122 ~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W-~~~~L~-~~Qi~YAA~Da~~~~~l~~~L~ 193 (198)
+|+-.++.... .+.+.+|.+++.++||..-..-..-..+.| ...+=+ ..-+.|...||...++|..+|.
T Consensus 413 iDl~~~~~~~~---kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L~~kl~ 483 (1054)
T PTZ00166 413 FDVMDLIRRDY---KLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLL 483 (1054)
T ss_pred EEHHHHHHHhc---CcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 56655554332 345889999999999964321111112333 222222 2346999999999999999874
No 83
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=91.56 E-value=1.6 Score=44.26 Aligned_cols=89 Identities=19% Similarity=0.194 Sum_probs=61.9
Q ss_pred HHHHhhc-CCCeEEEEEeecchHHHHhh---hcCCc--cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCc
Q 037014 86 SIKNFLS-DPNVVFVGIEVEEIMSKLKN---EYGLC--IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKK 159 (198)
Q Consensus 86 ~L~~lL~-d~~i~kvG~~~~~D~~~L~~---~~gi~--~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~ 159 (198)
.+..|++ -.....|+|+...|...|.+ .+|+. ....+|...+++...+ ....++|.+|++. +|......
T Consensus 489 aL~~f~~figg~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p--~~k~~kL~~LAk~-lGL~~~~~-- 563 (1437)
T PRK00448 489 VLPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYP--ELKSHRLNTLAKK-FGVELEHH-- 563 (1437)
T ss_pred HHHHHHHHhCCCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcC--ccccccHHHHHHH-cCCCCCCC--
Confidence 3444433 23567899999999987753 45553 2456898888765543 3458999999986 56554321
Q ss_pred eeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcc
Q 037014 160 VCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLE 195 (198)
Q Consensus 160 ~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~ 195 (198)
+-|-.||.++.+|+.+|+++
T Consensus 564 ----------------HrAl~DA~aTa~lf~~ll~~ 583 (1437)
T PRK00448 564 ----------------HRADYDAEATAYLLIKFLKD 583 (1437)
T ss_pred ----------------cChHHHHHHHHHHHHHHHHH
Confidence 55789999999999998753
No 84
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=90.63 E-value=0.0039 Score=53.53 Aligned_cols=71 Identities=15% Similarity=0.335 Sum_probs=60.7
Q ss_pred CCCceeEEEeeeCCeEEEEEccccC--cccHHHHHhhcCCCeEEEEEeecchHHHHhhhcCCccCceeehHHH
Q 037014 57 LSGKIATLQLCVDTKCLILQLLYMD--CIPLSIKNFLSDPNVVFVGIEVEEIMSKLKNEYGLCIKKKIDVRTL 127 (198)
Q Consensus 57 ~~~~~~liQla~~~~~~i~~l~~~~--~~~~~L~~lL~d~~i~kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~l 127 (198)
..+++|.+|.++.-+.|++++...+ .....+..|++|++|.|+-|++..-.+.+...|||..+|++|++..
T Consensus 72 ~~~~l~~~q~~~~~~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~~~~~~i~~n~v~~~q~~ 144 (458)
T KOG2405|consen 72 RHGKLCWLQVATNCRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQVA 144 (458)
T ss_pred ccCcchhHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhhHhhhHHHHHHHHHHhcccceeeecchhhhhhh
Confidence 4569999999999889998887653 2446788999999999999999888888888999999999998874
No 85
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=89.65 E-value=0.18 Score=43.53 Aligned_cols=145 Identities=13% Similarity=0.047 Sum_probs=93.3
Q ss_pred CeEEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEccccC-cccH-HHHHhhcCCCeEEEEEeecchHHHHhhhcCCc
Q 037014 40 ILIVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYMD-CIPL-SIKNFLSDPNVVFVGIEVEEIMSKLKNEYGLC 117 (198)
Q Consensus 40 ~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~~-~~~~-~L~~lL~d~~i~kvG~~~~~D~~~L~~~~gi~ 117 (198)
..+||.|.-..- .+-...+-.+++|+++..+++|....+ .++. ..++.|++-.+ +- +.+.+...|...|++.
T Consensus 195 ~~~i~~~~~s~~---~~~~~e~~~m~ia~~n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~ 268 (458)
T KOG2405|consen 195 VWFIRPVSPSLL---KILALEATYMNIADGNEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSA 268 (458)
T ss_pred eeEeecCchhHH---HhhhhhhhhhhhcccchhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHHH
Confidence 367777765443 234455566899999999999987643 2333 36777876665 33 8888999998899999
Q ss_pred cCceeehHHHHHH----hCCCCCCCCchHHHHH-HHHcCC-------cCCCC----Cceec--cCCCCCCCCHHHHHHHH
Q 037014 118 IKKKIDVRTLAKL----HFPISCLGKPGLKVLA-YQLLRL-------RPWKP----KKVCM--NNLESGFLDTELIKFAC 179 (198)
Q Consensus 118 ~~~~~Dl~~l~~~----~l~~~~~~~~~L~~l~-~~~l~~-------~l~K~----~~~~~--s~W~~~~L~~~Qi~YAA 179 (198)
+.|++|.+...+. .+|+. +....+. ...|+. ..-+. +-+.. .+|.-||-++...+-++
T Consensus 269 L~nVkDtQia~sLve~~e~grr----~p~~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h 344 (458)
T KOG2405|consen 269 LKNVKDTQIASSLVEPSEYGRR----HPTSILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLH 344 (458)
T ss_pred HHhhHHHHHHHHHhhhHHhccc----CCccceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHH
Confidence 9999999876543 22321 1111110 011111 00000 01122 36999999999999999
Q ss_pred HhHHHHHHHHHHHhc
Q 037014 180 IDAYVSCAIGTKLLL 194 (198)
Q Consensus 180 ~Da~~~~~l~~~L~~ 194 (198)
.|+..++.++..|.+
T Consensus 345 ~dv~~Ll~~~~~l~a 359 (458)
T KOG2405|consen 345 RDVISLLGIFDTLVA 359 (458)
T ss_pred HHHHHHHHHHhhHhh
Confidence 999999998876653
No 86
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=88.66 E-value=7.7 Score=31.04 Aligned_cols=101 Identities=16% Similarity=0.182 Sum_probs=63.6
Q ss_pred HHHHHhhcCCCeEEEEEeec-chHHHHhh---hcCCccCc-------------------eeehHHHHHHhCCCCCCCCch
Q 037014 85 LSIKNFLSDPNVVFVGIEVE-EIMSKLKN---EYGLCIKK-------------------KIDVRTLAKLHFPISCLGKPG 141 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~-~D~~~L~~---~~gi~~~~-------------------~~Dl~~l~~~~l~~~~~~~~~ 141 (198)
..+.++++......|+||.+ .|+-.|.. .+|+.+.. -+|+-++.+ ..| .....+
T Consensus 42 ~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~-~~g--~~~~~s 118 (209)
T PF10108_consen 42 QDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLS-FYG--AKARTS 118 (209)
T ss_pred HHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHh-ccC--ccccCC
Confidence 44555566555668999986 49988864 36776432 355555443 222 234889
Q ss_pred HHHHHHHHcCCcCCCCCceecc----CCCCCCCCHHHH-HHHHHhHHHHHHHHHHHh
Q 037014 142 LKVLAYQLLRLRPWKPKKVCMN----NLESGFLDTELI-KFACIDAYVSCAIGTKLL 193 (198)
Q Consensus 142 L~~l~~~~l~~~l~K~~~~~~s----~W~~~~L~~~Qi-~YAA~Da~~~~~l~~~L~ 193 (198)
|+.||. .||++- |. .+.+| -|... .-+.| .|.-.||...+.||.++.
T Consensus 119 Ld~la~-~lgiPg-K~-~idGs~V~~~y~~g--~i~~I~~YCe~DVl~T~~lylR~~ 170 (209)
T PF10108_consen 119 LDELAA-LLGIPG-KD-DIDGSQVAELYQEG--DIDEIREYCEKDVLNTYLLYLRFE 170 (209)
T ss_pred HHHHHH-HcCCCC-CC-CCCHHHHHHHHHcC--CHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999997 478764 43 23222 13221 22334 999999999999998875
No 87
>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=86.18 E-value=16 Score=31.87 Aligned_cols=69 Identities=25% Similarity=0.151 Sum_probs=45.1
Q ss_pred eeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCC-CceeccCCCCC-CCCHHHHHHHHHhHHHHHHHHHHH
Q 037014 121 KIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKP-KKVCMNNLESG-FLDTELIKFACIDAYVSCAIGTKL 192 (198)
Q Consensus 121 ~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~-~~~~~s~W~~~-~L~~~Qi~YAA~Da~~~~~l~~~L 192 (198)
.+|+-.+++..++ +...+|+.+++.+||..-..- ...-...|... ..-..-++|...|+..+++|+.++
T Consensus 150 ~~Dl~~~~~~~~k---l~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 150 VIDLYNLYKNKLK---LPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred EEEhHHHHHHHhC---cccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3677666665443 348899999999999432211 11122334433 233456799999999999999987
No 88
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=84.63 E-value=1.6 Score=35.28 Aligned_cols=65 Identities=14% Similarity=0.108 Sum_probs=44.6
Q ss_pred eehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceeccCCC-C--CCCCHHHHHHHHHhHHHHHHHH
Q 037014 122 IDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLE-S--GFLDTELIKFACIDAYVSCAIG 189 (198)
Q Consensus 122 ~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~-~--~~L~~~Qi~YAA~Da~~~~~l~ 189 (198)
+|+-.+++..+ .+.+.+|..++.++||.+.+.-..-..++|- . ..-...-++|...||...++|.
T Consensus 163 lD~~~~~r~~~---kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l~l~Ll 230 (231)
T cd05778 163 LNVWRLMRSEL---ALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEIL 230 (231)
T ss_pred eEhHHHHHHHc---CcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHHHHHhh
Confidence 56666665433 3458999999999999875544333456763 2 2234445699999999999874
No 89
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=80.15 E-value=4.7 Score=31.15 Aligned_cols=84 Identities=14% Similarity=0.076 Sum_probs=49.6
Q ss_pred HHHHhhcCCCeEEEEEe-ecchHHHHhhhc---CCc--------cCceeehHHHHHHhC-------CCC----CCCCchH
Q 037014 86 SIKNFLSDPNVVFVGIE-VEEIMSKLKNEY---GLC--------IKKKIDVRTLAKLHF-------PIS----CLGKPGL 142 (198)
Q Consensus 86 ~L~~lL~d~~i~kvG~~-~~~D~~~L~~~~---gi~--------~~~~~Dl~~l~~~~l-------~~~----~~~~~~L 142 (198)
.+.+|+..+.-+.|||+ +..|...|.+.+ +.. ....+|.-.+++... ..| ...+++|
T Consensus 75 ~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L 154 (183)
T cd06138 75 KIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKL 154 (183)
T ss_pred HHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhH
Confidence 45566654555568996 799999997543 321 112356666655321 111 1236789
Q ss_pred HHHHHHHcCCcCCCCCceeccCCCCCCCCHHHHHHHHHhHHHHHHH
Q 037014 143 KVLAYQLLRLRPWKPKKVCMNNLESGFLDTELIKFACIDAYVSCAI 188 (198)
Q Consensus 143 ~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l 188 (198)
.++++. +|.+... -+-|..||.+..+|
T Consensus 155 ~~l~~~-~gi~~~~------------------~H~Al~Da~~ta~l 181 (183)
T cd06138 155 EDLAQA-NGIEHSN------------------AHDALSDVEATIAL 181 (183)
T ss_pred HHHHHH-CCCCccc------------------cccHHHHHHHHHHH
Confidence 999986 5654321 24467888887665
No 90
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=77.85 E-value=38 Score=27.98 Aligned_cols=149 Identities=14% Similarity=0.119 Sum_probs=87.9
Q ss_pred eEEEEeeeecCCCCCCCCCceeEEEeeeCCe-EEEEEccccCccc----HHHHHhhcCCCe-EEEEEee-cchHHHHh--
Q 037014 41 LIVGLNCKWKPHPIPSLSGKIATLQLCVDTK-CLILQLLYMDCIP----LSIKNFLSDPNV-VFVGIEV-EEIMSKLK-- 111 (198)
Q Consensus 41 ~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~-~~i~~l~~~~~~~----~~L~~lL~d~~i-~kvG~~~-~~D~~~L~-- 111 (198)
.++-||+|+++. ++..+.+-++-.+-+.. ...++-.-.+ -| ..|..|+.++++ .-|.+|- ..|.=.++
T Consensus 99 ~~~FFDiETTGL--~~ag~~I~~~g~a~~~~~~~~Vrq~~lp-~p~~E~avle~fl~~~~~~~lvsfNGkaFD~PfikR~ 175 (278)
T COG3359 99 DVAFFDIETTGL--DRAGNTITLVGGARGVDDTMHVRQHFLP-APEEEVAVLENFLHDPDFNMLVSFNGKAFDIPFIKRM 175 (278)
T ss_pred ceEEEeeecccc--CCCCCeEEEEEEEEccCceEEEEeecCC-CcchhhHHHHHHhcCCCcceEEEecCcccCcHHHHHH
Confidence 589999999987 44667777777776544 3333432221 12 368889988843 3566655 46876665
Q ss_pred -h-hcCCccC-ceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCC--CCc---eeccCCCC---CCCCHHHHHHHHH
Q 037014 112 -N-EYGLCIK-KKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWK--PKK---VCMNNLES---GFLDTELIKFACI 180 (198)
Q Consensus 112 -~-~~gi~~~-~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K--~~~---~~~s~W~~---~~L~~~Qi~YAA~ 180 (198)
+ .+...+. +-+|+-...+.+++ ..+.+.+|+.+=+ .||.+=.. +-. ..--.|.+ .-|-.--++|--.
T Consensus 176 v~~~~el~l~~~H~DL~h~~RRlwk-~~l~~c~Lk~VEr-~LGi~R~edtdG~~~p~lyr~~~~~~dp~ll~~l~~hN~e 253 (278)
T COG3359 176 VRDRLELSLEFGHFDLYHPSRRLWK-HLLPRCGLKTVER-ILGIRREEDTDGYDGPELYRLYRRYGDPGLLDGLVLHNRE 253 (278)
T ss_pred HhcccccCccccchhhhhhhhhhhh-ccCCCCChhhHHH-HhCccccccCCCcchHHHHHHHHHcCCHHHHHHHHHccHH
Confidence 2 2344444 45898777776665 3356889988766 89965221 100 01112322 1233333467777
Q ss_pred hHHHHHHHHHHHhc
Q 037014 181 DAYVSCAIGTKLLL 194 (198)
Q Consensus 181 Da~~~~~l~~~L~~ 194 (198)
|+.-+..|+..+.+
T Consensus 254 DvlnL~~i~~h~~~ 267 (278)
T COG3359 254 DVLNLPTIIKHVSK 267 (278)
T ss_pred HHHhHHHHHHHHHH
Confidence 88877777776653
No 91
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=72.19 E-value=16 Score=36.64 Aligned_cols=96 Identities=23% Similarity=0.180 Sum_probs=60.1
Q ss_pred CCCeEEEEEeecc-hHHHHhhh---cCCc---------------------cCc--eeehHHHHHHhCCCCCCCCchHHHH
Q 037014 93 DPNVVFVGIEVEE-IMSKLKNE---YGLC---------------------IKK--KIDVRTLAKLHFPISCLGKPGLKVL 145 (198)
Q Consensus 93 d~~i~kvG~~~~~-D~~~L~~~---~gi~---------------------~~~--~~Dl~~l~~~~l~~~~~~~~~L~~l 145 (198)
||.+ .+||++.+ |+..|.++ +++. +.| ++|+-..++..+. ..+.+|..+
T Consensus 599 DPDi-i~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~~~~k~~~~---~~sy~L~~v 674 (1172)
T TIGR00592 599 DPDE-IVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVEISAKELIR---CKSYDLSEL 674 (1172)
T ss_pred CCCE-EEEEcccCccHHHHHHHHHHcCCCcccccCccccCCCccccccceECCEEEEEHHHHHHHHhC---cCCCCHHHH
Confidence 8886 67998865 88777652 2222 112 3677777665543 348899999
Q ss_pred HHHHcCCcC-CCC-CceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 037014 146 AYQLLRLRP-WKP-KKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKLL 193 (198)
Q Consensus 146 ~~~~l~~~l-~K~-~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~ 193 (198)
+..+||.+- +-+ ..+ ..-|....--..-+.|...||..+++|..+|.
T Consensus 675 ~~~~L~~~k~~~~~~~i-~~~~~~~~~~~~~~~y~~~Da~l~~~L~~~l~ 723 (1172)
T TIGR00592 675 VQQILKTERKVIPIDNI-NNMYSESSSLTYLLEHTWKDAMFILQIMCELN 723 (1172)
T ss_pred HHHHhCCCCcccCHHHH-HHHHhCcHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 999998531 100 111 11244322223446999999999999988764
No 92
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=69.64 E-value=5.4 Score=32.23 Aligned_cols=97 Identities=22% Similarity=0.165 Sum_probs=60.5
Q ss_pred cCCCeEEEEEee-cchHHHHhhh---cCCc---------------------------cCc--eeehHHHHHHhCCCCCCC
Q 037014 92 SDPNVVFVGIEV-EEIMSKLKNE---YGLC---------------------------IKK--KIDVRTLAKLHFPISCLG 138 (198)
Q Consensus 92 ~d~~i~kvG~~~-~~D~~~L~~~---~gi~---------------------------~~~--~~Dl~~l~~~~l~~~~~~ 138 (198)
.||+| .+||++ ..|+..|.++ .|+. +.| ++|+-..++.... ..
T Consensus 96 ~DPDi-ivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~~~~k~~~~---~~ 171 (234)
T cd05776 96 IDPDV-LVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYLSAKELIR---CK 171 (234)
T ss_pred cCCCE-EEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCchhhccHHHHHHHhC---CC
Confidence 68887 699999 5698877642 2321 001 3466556554432 35
Q ss_pred CchHHHHHHHHcCCcC-C-CCCceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 037014 139 KPGLKVLAYQLLRLRP-W-KPKKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKLL 193 (198)
Q Consensus 139 ~~~L~~l~~~~l~~~l-~-K~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~ 193 (198)
+.+|.++++.+||.+- + ..+.+. .-|....--..=++|...||+..++|..+|.
T Consensus 172 sY~L~~va~~~Lg~~k~di~~~~i~-~~~~~~~~l~~l~~y~~~Da~l~~~L~~kl~ 227 (234)
T cd05776 172 SYDLTELSQQVLGIERQDIDPEEIL-NMYNDSESLLKLLEHTEKDAYLILQLMFKLN 227 (234)
T ss_pred CCChHHHHHHHhCcCcccCCHHHHH-HHHhCHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence 8899999999999631 1 111221 1244311122335999999999999999875
No 93
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=66.31 E-value=12 Score=30.66 Aligned_cols=92 Identities=18% Similarity=0.100 Sum_probs=53.3
Q ss_pred CCCeEEEEEeecchHHHHhhhcCCc---------------cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCC
Q 037014 93 DPNVVFVGIEVEEIMSKLKNEYGLC---------------IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKP 157 (198)
Q Consensus 93 d~~i~kvG~~~~~D~~~L~~~~gi~---------------~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~ 157 (198)
+.++..|||+.-.|+-.|.+.|--. ...++|+..++...- ....+|+.+++.+ +..- ++
T Consensus 147 ~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~----~~~~~L~~l~~~l-~~~~-~~ 220 (262)
T PF04857_consen 147 SSKKPIVGHNGLYDLMYLYKKFIGPLPETLEEFKELLRELFPRIYDTKYLAEECP----GKSTSLQELAEEL-GIRR-NP 220 (262)
T ss_dssp CC-SEEEESSTHHHHHHHHHHHTTS--SSHHHHHHHHHHHSSSEEEHHHHHTSTT----TS-SSHHHHHHHT-TSTT---
T ss_pred ccCCcEEEeChHhHHHHHHHHhcCCCCCCHHHHHHHHHHHCcccccHHHHHHhcc----ccccCHHHHHHHh-CCCc-cc
Confidence 4458899999999999887754211 245899988876322 1367999999874 4322 11
Q ss_pred CceeccCCCCCC--------CCHHHHHHHHHhHHHHHHHHH
Q 037014 158 KKVCMNNLESGF--------LDTELIKFACIDAYVSCAIGT 190 (198)
Q Consensus 158 ~~~~~s~W~~~~--------L~~~Qi~YAA~Da~~~~~l~~ 190 (198)
............ -..++.+=|+.|||....+|-
T Consensus 221 ~~~~~~~~~~~~~~~~~~~~~~~~~~HeAGyDA~mTg~~F~ 261 (262)
T PF04857_consen 221 SSISSPEGFPSYDEEKNNFPMFGEKAHEAGYDAYMTGCVFI 261 (262)
T ss_dssp --EEE-TTS-------------SS-TTSHHHHHHHHHHHHH
T ss_pred cccccccccccccccccccccCCCCCCCcchHHHHHHHHHc
Confidence 112222111111 123336789999999887764
No 94
>PTZ00315 2'-phosphotransferase; Provisional
Probab=65.16 E-value=1.2e+02 Score=28.24 Aligned_cols=95 Identities=16% Similarity=0.090 Sum_probs=59.0
Q ss_pred HHHHHhhcCCC--------eEEEEEeecchHH-HHhhh------cCCc--cCceeehHHH-HHHhCCC---------CCC
Q 037014 85 LSIKNFLSDPN--------VVFVGIEVEEIMS-KLKNE------YGLC--IKKKIDVRTL-AKLHFPI---------SCL 137 (198)
Q Consensus 85 ~~L~~lL~d~~--------i~kvG~~~~~D~~-~L~~~------~gi~--~~~~~Dl~~l-~~~~l~~---------~~~ 137 (198)
+.+.+||.+.. -..++++...|++ .|.+. .|+. ....+|++.. +...++. +..
T Consensus 135 ~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p~~~~~~~~~~~~~ 214 (582)
T PTZ00315 135 CEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFGNGSGCGGGATPPL 214 (582)
T ss_pred HHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCcccccccccccccc
Confidence 45667776543 1467899999986 55332 2443 3456787633 3333321 123
Q ss_pred CCchHHHHHHHHcCCcCCCCCceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHHHhcccC
Q 037014 138 GKPGLKVLAYQLLRLRPWKPKKVCMNNLESGFLDTELIKFACIDAYVSCAIGTKLLLEET 197 (198)
Q Consensus 138 ~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~L~~~~~ 197 (198)
..++|.+|++. +|.+..-. ..+ |--||....+|+.+|+.+.+
T Consensus 215 ~~~~L~~al~~-lgL~~eGr---~Hr--------------AlDDA~ntA~L~~~Ll~~g~ 256 (582)
T PTZ00315 215 GPSDMPDMLQM-LGLPLQGR---HHS--------------GIDDCRNIAAVLCELLRRGL 256 (582)
T ss_pred CCcCHHHHHHH-CCCCCCCC---CcC--------------cHHHHHHHHHHHHHHHHcCC
Confidence 46899999985 67664321 111 45799999999999987653
No 95
>COG4328 Predicted nuclease (RNAse H fold) [General function prediction only]
Probab=64.77 E-value=10 Score=30.71 Aligned_cols=34 Identities=26% Similarity=0.363 Sum_probs=26.8
Q ss_pred eEEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEcccc
Q 037014 41 LIVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYM 80 (198)
Q Consensus 41 ~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~ 80 (198)
.+||||.-|... .+..+-+|+..+ +|.|.++.+.
T Consensus 2 ~fvGiDlaW~~~-----ppg~~cl~~~dg-~~~i~~~~rr 35 (266)
T COG4328 2 KFVGIDLAWASR-----PPGLCCLQLADG-GLLIGDLARR 35 (266)
T ss_pred ceEEeeeecccC-----CCceEEEEEcCC-CceEeechhh
Confidence 689999999875 356777888877 7888787664
No 96
>PF00843 Arena_nucleocap: Arenavirus nucleocapsid protein; InterPro: IPR000229 Arenaviruses are single stranded RNA viruses. The arenavirus S RNAs that have been characterised include conserved terminal sequences, an ambisense arrangement of the coding regions for the precursor glycoprotein (GPC) and nucleocapsid (N) proteins and an intergenic region capable of forming a base-paired "hairpin" structure. The mature glycoproteins that result are G1 and G2 and the N protein []. This family represents the nucleocapsid protein that encapsulates the viral ssRNA [].; GO: 0019013 viral nucleocapsid; PDB: 3MX5_A 3MX2_C 3MWT_C 3Q7C_A 3MWP_B 3Q7B_A 3T5Q_E 3T5N_A 3R3L_B.
Probab=50.09 E-value=9.3 Score=33.93 Aligned_cols=112 Identities=13% Similarity=0.001 Sum_probs=56.6
Q ss_pred CeEEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEcccc-----------------------CcccHHHHHhhc-CCC
Q 037014 40 ILIVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYM-----------------------DCIPLSIKNFLS-DPN 95 (198)
Q Consensus 40 ~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~-----------------------~~~~~~L~~lL~-d~~ 95 (198)
..-..+|+|-.|. .+-.+|+.|=.++ +|| |+.+. +.-|.-+..+++ -|.
T Consensus 372 ~~ttWiDIEG~p~----DPVElAiyQP~sg--~Yi-HcyR~P~D~K~FK~~SKysHGillkDl~~aqPGL~S~vi~~LP~ 444 (533)
T PF00843_consen 372 NATTWIDIEGPPN----DPVELAIYQPSSG--NYI-HCYREPHDEKQFKNQSKYSHGILLKDLENAQPGLTSAVIELLPK 444 (533)
T ss_dssp TS-EEEEEESETT----SESEEEEEETTTT--EEE-EEE---S-HHHHHHHHHHTT-B-GGGCTTB-TTHHHHHHHHS-T
T ss_pred CCCeeEecCCCCC----CCeEEEEeccCCC--cEE-EEecCCcchhhhcccccccccccHHHHhhhccchHHHHHHhCCc
Confidence 3678999998875 4456778876655 666 55432 123434444442 255
Q ss_pred eEEEEEeecchHHHHhhhcCCccCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCC
Q 037014 96 VVFVGIEVEEIMSKLKNEYGLCIKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPK 158 (198)
Q Consensus 96 i~kvG~~~~~D~~~L~~~~gi~~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~ 158 (198)
-..+...-..|.++|...+|-.=-.++|+..-.....-....-=..+..||...-|.-+.|.|
T Consensus 445 ~MVlT~QGsDDIrkLld~hGRrDiKlvDV~lt~eqaR~FEd~VWd~f~~LC~~H~GvVv~KKK 507 (533)
T PF00843_consen 445 NMVLTCQGSDDIRKLLDMHGRRDIKLVDVKLTSEQARKFEDQVWDRFGHLCKKHTGVVVKKKK 507 (533)
T ss_dssp T-EEEESSHHHHHHHHHCTT-TTSEEEE----HHHHTTTHHHHHHHHGGG---B-S-EEE--S
T ss_pred CcEEEeeChHHHHHHHHhcCCCcceEEEeecCHHHHHHHHHHHHHHHHHHHHhcCceEEeccc
Confidence 556667778999999988886655678886654332111100011355667766676666543
No 97
>PF00169 PH: PH domain; InterPro: IPR001849 The pleckstrin homology (PH) domain is a domain of about 100 residues that occurs in a wide range of proteins involved in intracellular signalling or as constituents of the cytoskeleton [, , , , , , ]. The pleckstrin homology domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids. The 3D structure of several PH domains has been determined []. All known cases have a common structure consisting of two perpendicular anti-parallel beta sheets, followed by a C-terminal amphipathic helix. The loops connecting the beta-strands differ greatly in length, making the PH domain relatively difficult to detect. There are no totally invariant residues within the PH domain. Proteins reported to contain one more PH domains belong to the following families: Pleckstrin, the protein where this domain was first detected, is the major substrate of protein kinase C in platelets. Pleckstrin is one of the rare proteins to contains two PH domains. Ser/Thr protein kinases such as the Akt/Rac family, the beta-adrenergic receptor kinases, the mu isoform of PKC and the trypanosomal NrkA family. Tyrosine protein kinases belonging to the Btk/Itk/Tec subfamily. Insulin Receptor Substrate 1 (IRS-1). Regulators of small G-proteins like guanine nucleotide releasing factor GNRP (Ras-GRF) (which contains 2 PH domains), guanine nucleotide exchange proteins like vav, dbl, SoS and Saccharomyces cerevisiae CDC24, GTPase activating proteins like rasGAP and BEM2/IPL2, and the human break point cluster protein bcr. Cytoskeletal proteins such as dynamin (see IPR001401 from INTERPRO), Caenorhabditis elegans kinesin-like protein unc-104 (see IPR001752 from INTERPRO), spectrin beta-chain, syntrophin (2 PH domains) and S. cerevisiae nuclear migration protein NUM1. Mammalian phosphatidylinositol-specific phospholipase C (PI-PLC) (see IPR000909 from INTERPRO) isoforms gamma and delta. Isoform gamma contains two PH domains, the second one is split into two parts separated by about 400 residues. Oxysterol binding proteins OSBP, S. cerevisiae OSH1 and YHR073w. Mouse protein citron, a putative rho/rac effector that binds to the GTP-bound forms of rho and rac. Several S. cerevisiae proteins involved in cell cycle regulation and bud formation like BEM2, BEM3, BUD4 and the BEM1-binding proteins BOI2 (BEB1) and BOI1 (BOB1). C. elegans protein MIG-10. C. elegans hypothetical proteins C04D8.1, K06H7.4 and ZK632.12. S. cerevisiae hypothetical proteins YBR129c and YHR155w. ; GO: 0005515 protein binding; PDB: 1DYN_B 2DYN_B 3SNH_A 3ZYS_C 1X05_A 2I5F_A 1ZM0_B 1XX0_A 2I5C_C 3A8P_D ....
Probab=49.36 E-value=56 Score=21.28 Aligned_cols=33 Identities=9% Similarity=0.062 Sum_probs=26.4
Q ss_pred eeEEEEEcCeEEEEEEcCCHHHHHHHHHHHHhh
Q 037014 3 YAQSISFCGKIIETTVTSTTSVAENWLLKIRSL 35 (198)
Q Consensus 3 ~~~~v~f~~~~i~~~v~~~~~~~~~~i~~~~~~ 35 (198)
+.+.+.+.+.......++++++..+|++.+...
T Consensus 70 ~~f~i~~~~~~~~~~~~~s~~~~~~W~~~i~~~ 102 (104)
T PF00169_consen 70 NCFEITTPNGKSYLFSAESEEERKRWIQAIQKA 102 (104)
T ss_dssp SEEEEEETTSEEEEEEESSHHHHHHHHHHHHHH
T ss_pred cEEEEEeCCCcEEEEEcCCHHHHHHHHHHHHHH
Confidence 567888888755555678999999999998763
No 98
>PRK05761 DNA polymerase I; Reviewed
Probab=48.56 E-value=1.4e+02 Score=28.83 Aligned_cols=99 Identities=16% Similarity=0.142 Sum_probs=55.4
Q ss_pred ccHHHHHhhcCCCeEEEEEeec-chHHHHhh---hcCCccC---------c-eeehHHHHHHh------C-CCCCCCCch
Q 037014 83 IPLSIKNFLSDPNVVFVGIEVE-EIMSKLKN---EYGLCIK---------K-KIDVRTLAKLH------F-PISCLGKPG 141 (198)
Q Consensus 83 ~~~~L~~lL~d~~i~kvG~~~~-~D~~~L~~---~~gi~~~---------~-~~Dl~~l~~~~------l-~~~~~~~~~ 141 (198)
+...+..++.+-++. |++|.. .|+-.|.+ .+|+... . .+|+-..+... . +.-.....+
T Consensus 213 LL~~f~~~i~~~dPd-i~yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~~~~~y~~~~~~~~~~ys 291 (787)
T PRK05761 213 LLAELFDIILEYPPV-VTFNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNKAVRSYAFYGKYRHREAR 291 (787)
T ss_pred HHHHHHHHHHhcCCE-EEEcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheeecceeeeeccceeecccCC
Confidence 334555555443332 336664 58877764 4666432 0 15554443210 0 100112578
Q ss_pred HHHHHHHHcCCc-CCCCCceeccCCCCCCCCHHH-HHHHHHhHHHHHHHH
Q 037014 142 LKVLAYQLLRLR-PWKPKKVCMNNLESGFLDTEL-IKFACIDAYVSCAIG 189 (198)
Q Consensus 142 L~~l~~~~l~~~-l~K~~~~~~s~W~~~~L~~~Q-i~YAA~Da~~~~~l~ 189 (198)
|..+++.+||.. ++-+..+ ..++.+. ++|+-.||...++|.
T Consensus 292 L~~Va~~~Lg~~K~~~~~~i-------~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 292 LDAVGRALLGISKVELETNI-------SELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred hHHHHHHHhCCCcccccccc-------cccCHHHHHHHHHHHHHHHHHHH
Confidence 999999999963 2222222 1256666 499999999999984
No 99
>cd01246 PH_oxysterol_bp Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=47.84 E-value=45 Score=21.73 Aligned_cols=32 Identities=9% Similarity=0.116 Sum_probs=23.2
Q ss_pred eeEEEEEcCeEEEEEEcCCHHHHHHHHHHHHh
Q 037014 3 YAQSISFCGKIIETTVTSTTSVAENWLLKIRS 34 (198)
Q Consensus 3 ~~~~v~f~~~~i~~~v~~~~~~~~~~i~~~~~ 34 (198)
+.+.|...+.......+++.++..+|+..+..
T Consensus 59 ~~F~i~~~~~~~~~~~a~s~~e~~~Wi~al~~ 90 (91)
T cd01246 59 KCFTIDTGGDKTLHLRANSEEERQRWVDALEL 90 (91)
T ss_pred cEEEEEcCCCCEEEEECCCHHHHHHHHHHHHh
Confidence 45667665544455567899999999998864
No 100
>COG5233 GRH1 Peripheral Golgi membrane protein [Intracellular trafficking and secretion]
Probab=47.65 E-value=12 Score=31.86 Aligned_cols=44 Identities=16% Similarity=0.274 Sum_probs=32.6
Q ss_pred CceeEEEEEcCeEEEEEEcCCHHHHHHHHHHHHhhccCCCeEEEEeeeecCC
Q 037014 1 MAYAQSISFCGKIIETTVTSTTSVAENWLLKIRSLHSAQILIVGLNCKWKPH 52 (198)
Q Consensus 1 ~~~~~~v~f~~~~i~~~v~~~~~~~~~~i~~~~~~~~~~~~~vg~D~Ew~~~ 52 (198)
|+|.|.|.|.-+...+.+. .++.+.-++.++. ..+|+|+.|.+.
T Consensus 137 ~~~~~~I~~~~~~~~V~~N--sde~r~~~~~~~~------k~~G~~iqws~l 180 (417)
T COG5233 137 MGELYKIPFSQRRCKVEFN--SDEIRNDVRRLRR------KLRGKDIQWSRL 180 (417)
T ss_pred cceeEeccccccccceeec--hhhhhchHHHHHH------hhhcceeeeeec
Confidence 8899999998777666554 3344455666665 789999999986
No 101
>PHA03334 putative DNA polymerase catalytic subunit; Provisional
Probab=41.52 E-value=93 Score=31.98 Aligned_cols=72 Identities=14% Similarity=0.090 Sum_probs=43.5
Q ss_pred eeehHHHHHHh-CCCCCCCCchHHHHHHHHcCCcCC-CC-------Cceecc----CCCCCCCCHHHH-HHHHHhHHHHH
Q 037014 121 KIDVRTLAKLH-FPISCLGKPGLKVLAYQLLRLRPW-KP-------KKVCMN----NLESGFLDTELI-KFACIDAYVSC 186 (198)
Q Consensus 121 ~~Dl~~l~~~~-l~~~~~~~~~L~~l~~~~l~~~l~-K~-------~~~~~s----~W~~~~L~~~Qi-~YAA~Da~~~~ 186 (198)
.+|+-.+.+.. .. -.+++.+|..+++.+||..-+ |. +.+..+ -|...+=+...+ .|...||+..+
T Consensus 471 iiDMy~Vc~~K~~~-~kL~sYkLNTVA~~~LgeqKp~k~~~k~~K~eDV~YkeI~~lf~~g~e~RaRla~YCLkDA~Lvl 549 (1545)
T PHA03334 471 IIDLMRVCNTKSIK-AKCSSRKLDTVARLIISKSKPHKNPPKIGKMDDVKYTEMDGMFTAGGAALARYLIYNLVDSELLI 549 (1545)
T ss_pred EEehHHHHhhcccc-cCccCCcHHHHHHHHHhcccccccccccCcccCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHH
Confidence 37887776542 11 124578999999999996542 11 111111 122222222222 89999999999
Q ss_pred HHHHHHh
Q 037014 187 AIGTKLL 193 (198)
Q Consensus 187 ~l~~~L~ 193 (198)
+|.++|.
T Consensus 550 rLlkkl~ 556 (1545)
T PHA03334 550 RIAKNLD 556 (1545)
T ss_pred HHHHHHH
Confidence 9999875
No 102
>cd00821 PH Pleckstrin homology (PH) domain. Pleckstrin homology (PH) domain. PH domains are only found in eukaryotes. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=36.96 E-value=81 Score=19.74 Aligned_cols=32 Identities=13% Similarity=0.085 Sum_probs=22.5
Q ss_pred eeEEEEEcCeEEEEEEcCCHHHHHHHHHHHHh
Q 037014 3 YAQSISFCGKIIETTVTSTTSVAENWLLKIRS 34 (198)
Q Consensus 3 ~~~~v~f~~~~i~~~v~~~~~~~~~~i~~~~~ 34 (198)
+.+.+...+..-....+.++++...|++.+..
T Consensus 64 ~~f~i~~~~~~~~~~~~~s~~~~~~W~~~l~~ 95 (96)
T cd00821 64 NCFEIRTPDGRSYLLQAESEEEREEWIEALQS 95 (96)
T ss_pred cEEEEecCCCcEEEEEeCCHHHHHHHHHHHhc
Confidence 45667766633334456699999999998864
No 103
>cd01260 PH_CNK Connector enhancer of KSR (Kinase suppressor of ras) (CNK) pleckstrin homology (PH) domain. Connector enhancer of KSR (Kinase suppressor of ras) (CNK) pleckstrin homology (PH) domain. CNK is believed to regulate the activity and the subcellular localization of RAS activated RAF. CNK is composed of N-terminal SAM and PDZ domains along with a central or C-terminal PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, a well as cytoskelet
Probab=36.44 E-value=75 Score=21.31 Aligned_cols=32 Identities=13% Similarity=0.058 Sum_probs=22.1
Q ss_pred eeEEEEEcCeEEEEEEcCCHHHHHHHHHHHHh
Q 037014 3 YAQSISFCGKIIETTVTSTTSVAENWLLKIRS 34 (198)
Q Consensus 3 ~~~~v~f~~~~i~~~v~~~~~~~~~~i~~~~~ 34 (198)
+.+.+...+.....-.+++++++.+|+..+.+
T Consensus 64 ~~F~I~~~~~~~~~f~a~s~~e~~~Wi~ai~~ 95 (96)
T cd01260 64 YAFKVCHPVYKSFYFAAETLDDLSQWVNHLIT 95 (96)
T ss_pred eEEEECCCCCcEEEEEeCCHHHHHHHHHHHHh
Confidence 45556555534444457899999999998864
No 104
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=36.12 E-value=4.1e+02 Score=25.70 Aligned_cols=148 Identities=14% Similarity=0.121 Sum_probs=83.5
Q ss_pred CeEEEEeeeecCCCC---CCCCCceeEEEeeeCCeEE-------------EEEcccc-CcccHHHHHhh--cCCCeEEEE
Q 037014 40 ILIVGLNCKWKPHPI---PSLSGKIATLQLCVDTKCL-------------ILQLLYM-DCIPLSIKNFL--SDPNVVFVG 100 (198)
Q Consensus 40 ~~~vg~D~Ew~~~~~---~~~~~~~~liQla~~~~~~-------------i~~l~~~-~~~~~~L~~lL--~d~~i~kvG 100 (198)
.++++||+|...... .+..+++..+..+...... .+...+. ..+...+..++ .||+| -+|
T Consensus 154 l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~~~~~~~~~~~~~v~~~~~e~e~l~~~~~~i~~~dPdV-Ivg 232 (792)
T COG0417 154 LRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLIEVFIYTSGEGFSVEVVISEAELLERFVELIREYDPDV-IVG 232 (792)
T ss_pred ceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCccccccccCCCCceeEEecCHHHHHHHHHHHHHhcCCCE-EEe
Confidence 378999999886532 2235566666666553321 0111111 12334444444 67776 578
Q ss_pred Eeec-chHHHHhh---hcCCccC---------------------ceeehHHHHH-HhCCCCCCCCchHHHHHHHHcCCcC
Q 037014 101 IEVE-EIMSKLKN---EYGLCIK---------------------KKIDVRTLAK-LHFPISCLGKPGLKVLAYQLLRLRP 154 (198)
Q Consensus 101 ~~~~-~D~~~L~~---~~gi~~~---------------------~~~Dl~~l~~-~~l~~~~~~~~~L~~l~~~~l~~~l 154 (198)
|+.. .|+..|.+ .+|++.. ..+|+-.++. ..+ .....+|.+.++.+++..-
T Consensus 233 yn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~~~~~~---~~~~ysl~~v~~~~l~~~k 309 (792)
T COG0417 233 YNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPALRRRPL---NLKSYSLEAVSEALLGEGK 309 (792)
T ss_pred ccCCcCChHHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHHHhhhhc---ccccccHHHHHHHhccccc
Confidence 8886 79888764 3565543 3477777765 222 3458899999999998543
Q ss_pred --CCCCceeccCCCCCCCC-HHHHHHHHHhHHHHHHHHHH
Q 037014 155 --WKPKKVCMNNLESGFLD-TELIKFACIDAYVSCAIGTK 191 (198)
Q Consensus 155 --~K~~~~~~s~W~~~~L~-~~Qi~YAA~Da~~~~~l~~~ 191 (198)
..+...-..-|...+-+ ...+.|.-.|+....++..+
T Consensus 310 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l~~~~~~~ 349 (792)
T COG0417 310 REDIPYDSMEEIWPDWADSKLRLLLYNLSDADLVLRILLK 349 (792)
T ss_pred ccccCccchhhccccCccchhHHHHHHHHHHHHHHHHHHH
Confidence 22111111223333322 34467777777777666554
No 105
>PHA02563 DNA polymerase; Provisional
Probab=34.83 E-value=4e+02 Score=25.17 Aligned_cols=147 Identities=9% Similarity=-0.079 Sum_probs=72.2
Q ss_pred CeEEEEeeeecCCCCCCCCCceeEEEeeeCCeEEEEEccccCcccHHHHHhhc-----CCCeEEEEEeecchHHHHhhh-
Q 037014 40 ILIVGLNCKWKPHPIPSLSGKIATLQLCVDTKCLILQLLYMDCIPLSIKNFLS-----DPNVVFVGIEVEEIMSKLKNE- 113 (198)
Q Consensus 40 ~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~~i~~l~~~~~~~~~L~~lL~-----d~~i~kvG~~~~~D~~~L~~~- 113 (198)
..++..|+|++.......+-..+.+..-..+..++ ....+.+..++. ..+.+...|+.+.|...|.+.
T Consensus 12 ~~~~~~DfET~t~~~~~~~~~~~~~d~~~~~s~~~------~~~~~~f~~~i~~~~~k~~~~~vYfHN~~FD~~Fil~~L 85 (630)
T PHA02563 12 RKILACDFETTTINKDCRRWFWGEIDVEDFPSYYG------GNSFDEFLQWIEDTTYKETECIIYFHNLKFDGSFILKWL 85 (630)
T ss_pred ceEEEEEEEecccCCcceeeeeeEeccceeceeec------cccHHHHHHHHhhccccccceEEEEecCCccHHHHHHHH
Confidence 48999999988763211222222222211111222 223344444444 456788999999999888762
Q ss_pred ----cCCccC----ce--ee-----hHHHH------HHhCCCCCCCCchHHHHHHHHcCCcCCC-------CCceeccCC
Q 037014 114 ----YGLCIK----KK--ID-----VRTLA------KLHFPISCLGKPGLKVLAYQLLRLRPWK-------PKKVCMNNL 165 (198)
Q Consensus 114 ----~gi~~~----~~--~D-----l~~l~------~~~l~~~~~~~~~L~~l~~~~l~~~l~K-------~~~~~~s~W 165 (198)
|+.... +. ++ -+... ......=.+-+.+|+.|+..+ +..+.| .+.+...-+
T Consensus 86 ~~~~~~~~~e~~~~~~~~~~~~i~~~g~~~~i~~~~~~f~DS~~llp~~L~~l~~~F-~~~~~k~~~d~~~~~~~~y~~~ 164 (630)
T PHA02563 86 LRNGFNWILELRVRSSKNFDTTIFINGRWYTITDSFMKFRDSLKLLPFSLEKLKKDF-GLTILKKDIDLNKERPVGYEFT 164 (630)
T ss_pred HhhcccccccccccCcccccceEeeCCEEEEEEEEEEEEEehHhhhhHHHHHHHHHh-CcccccCCcCccccccccceec
Confidence 211100 00 00 00000 000000001156788988865 333222 211100001
Q ss_pred CCCCCCHHHHHHHHHhHHHHHHHHHHHh
Q 037014 166 ESGFLDTELIKFACIDAYVSCAIGTKLL 193 (198)
Q Consensus 166 ~~~~L~~~Qi~YAA~Da~~~~~l~~~L~ 193 (198)
.-..|.+++++|--.|...++.+.....
T Consensus 165 ~~~~~~~e~~~Yl~~D~~il~~~~~i~~ 192 (630)
T PHA02563 165 TFEKLDPEELEYIHNDCVIIAGMLDIHF 192 (630)
T ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHH
Confidence 2235789999999999877777665544
No 106
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=34.51 E-value=1.4e+02 Score=27.24 Aligned_cols=166 Identities=11% Similarity=0.107 Sum_probs=96.5
Q ss_pred CCHHHHHHHHHHHHhhcc-------------------------CCCeEEEEeeeecCC-CCCC--CCCceeEEEee--e-
Q 037014 20 STTSVAENWLLKIRSLHS-------------------------AQILIVGLNCKWKPH-PIPS--LSGKIATLQLC--V- 68 (198)
Q Consensus 20 ~~~~~~~~~i~~~~~~~~-------------------------~~~~~vg~D~Ew~~~-~~~~--~~~~~~liQla--~- 68 (198)
.+..+.++|+++...... +...+..+|+|.... |... ...++-.|+.. .
T Consensus 61 ~~~~~a~~~~~~~~~~~~~~~g~~~~~~~yi~~~y~~~~~~d~~~i~~~~~DIEv~~~~fp~~~~a~~~i~~i~~~d~~~ 140 (498)
T PHA02524 61 ENIWEAKQWIKRMEEVGMDAMGMDDYGISYISDTYRGVIDFDRDDVVIDVVDIEVTAPEFPEPKYAKYEIDMISHVRLHN 140 (498)
T ss_pred CCHHHHHHHHHHHhhcChhhccchHHHHHHHHHhcCCccccchhhceEEEEEEEecCCCCCChhhcCCceEEEEeeeccc
Confidence 467788999988876521 113788899998543 2222 23456666662 2
Q ss_pred -CCeEEEEEcccc---------------------------CcccHHHHHhh--cCCCeEEEEEeec-chHHHHhhh----
Q 037014 69 -DTKCLILQLLYM---------------------------DCIPLSIKNFL--SDPNVVFVGIEVE-EIMSKLKNE---- 113 (198)
Q Consensus 69 -~~~~~i~~l~~~---------------------------~~~~~~L~~lL--~d~~i~kvG~~~~-~D~~~L~~~---- 113 (198)
.++.+++.+... ..+...+.+++ .||+| .+|||+. .|+..|.++
T Consensus 141 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~f~sE~eLL~~F~~~i~~~DPDI-ItGYNi~nFDlPYL~~Ra~~~ 219 (498)
T PHA02524 141 GKKTYYIFDLVKDVGHWDPKKSVLEKYILDNVVYMPFEDEVDLLLNYIQLWKANTPDL-VFGWNSEGFDIPYIITRITNI 219 (498)
T ss_pred CCccEEEEeccccccCCCcccccccccccCCeEEEEeCCHHHHHHHHHHHHHHhCCCE-EEeCCCcccCHHHHHHHHHHH
Confidence 334666664210 01223444444 45887 5899885 588766532
Q ss_pred cCCc---------------------------cCc--eeehHHHHHHhCCCCCCCCchHHHHHHHHcCCc-CCCCCceecc
Q 037014 114 YGLC---------------------------IKK--KIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLR-PWKPKKVCMN 163 (198)
Q Consensus 114 ~gi~---------------------------~~~--~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~-l~K~~~~~~s 163 (198)
+|+. +.| .+|+-.+++.. ....+.+.+|..+++..||.. ++-...+ ..
T Consensus 220 lGi~~~~~~~~~Gr~~~~~s~~~~G~~~~~~I~GRv~iDl~~l~kk~-s~~~l~sYsL~~Vs~~~Lg~~K~d~~~~I-~~ 297 (498)
T PHA02524 220 LGEKAANQLSPYGKITSKTITNLYGEKIIYKIHGIALMDYMDVFKKF-SFTPMPDYKLGNVGYREVKADKLDYEGPI-NK 297 (498)
T ss_pred hCCccccccccccccccccceeecCceeEEEEeeEEEeEHHHHHHHh-hhccCCCCCHHHHHHHhcCCccccchhhH-HH
Confidence 3432 111 25666666532 112345889999999888854 3322122 22
Q ss_pred CCCCCCCCHHHHHHHHHhHHHHHHHHH
Q 037014 164 NLESGFLDTELIKFACIDAYVSCAIGT 190 (198)
Q Consensus 164 ~W~~~~L~~~Qi~YAA~Da~~~~~l~~ 190 (198)
-|...+ ..-+.|+..||...+.|..
T Consensus 298 l~~~d~--~rla~YclkDa~L~~~L~~ 322 (498)
T PHA02524 298 FRKADH--QRYVDYCVRDTDIILLIDG 322 (498)
T ss_pred HhcCch--HHHHHHHHHHHHHHHHHHH
Confidence 365433 3447999999999988874
No 107
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=33.70 E-value=1.2e+02 Score=24.81 Aligned_cols=27 Identities=11% Similarity=0.073 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHhhccCCCeEEEEeeeecCCC
Q 037014 22 TSVAENWLLKIRSLHSAQILIVGLNCKWKPHP 53 (198)
Q Consensus 22 ~~~~~~~i~~~~~~~~~~~~~vg~D~Ew~~~~ 53 (198)
++++....+.+.+ ...|++|+|+.+..
T Consensus 9 ~~~l~~i~~~i~~-----~~fvaiD~EftGl~ 35 (262)
T PF04857_consen 9 EEELPEILQAISK-----ADFVAIDTEFTGLV 35 (262)
T ss_dssp HHHHHHHHHHHHH-----SSEEEEEEEES-S-
T ss_pred HHHHHHHHHHHhh-----CCEEEEEeeccccc
Confidence 4556666666666 48999999998764
No 108
>smart00233 PH Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
Probab=33.32 E-value=1.2e+02 Score=19.05 Aligned_cols=33 Identities=12% Similarity=0.128 Sum_probs=23.6
Q ss_pred eeEEEEEcCeEEEEEEcCCHHHHHHHHHHHHhh
Q 037014 3 YAQSISFCGKIIETTVTSTTSVAENWLLKIRSL 35 (198)
Q Consensus 3 ~~~~v~f~~~~i~~~v~~~~~~~~~~i~~~~~~ 35 (198)
+.+.+...+.....-.+.++++...|++.+...
T Consensus 68 ~~f~l~~~~~~~~~f~~~s~~~~~~W~~~i~~~ 100 (102)
T smart00233 68 HCFEIKTADRRSYLLQAESEEEREEWVDALRKA 100 (102)
T ss_pred eEEEEEecCCceEEEEcCCHHHHHHHHHHHHHh
Confidence 456666666634444567999999999998763
No 109
>cd01253 PH_beta_spectrin Beta-spectrin pleckstrin homology (PH) domain. Beta-spectrin pleckstrin homology (PH) domain. Beta spectrin binds actin and functions as a major component of the cytoskeleton underlying cellular membranes. Beta spectrin consists of multiple spectrin repeats followed by a PH domain, which binds to Inositol-1,4,5-Trisphosphate. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. PH domains are often involved in targeting proteins to the plasma membrane via lipid binding. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=31.09 E-value=1.2e+02 Score=20.53 Aligned_cols=32 Identities=6% Similarity=0.043 Sum_probs=21.8
Q ss_pred eeEEEEEcCeEEEEEEcCCHHHHHHHHHHHHh
Q 037014 3 YAQSISFCGKIIETTVTSTTSVAENWLLKIRS 34 (198)
Q Consensus 3 ~~~~v~f~~~~i~~~v~~~~~~~~~~i~~~~~ 34 (198)
+.+.+...+...+.--+++++++.+|+..+..
T Consensus 72 ~~F~l~~~~~~~~~f~a~s~e~~~~Wi~aL~~ 103 (104)
T cd01253 72 HVFRLRLPDGAEFLFQAPDEEEMSSWVRALKS 103 (104)
T ss_pred eEEEEEecCCCEEEEECCCHHHHHHHHHHHhc
Confidence 34555554444444457899999999998864
No 110
>cd01251 PH_centaurin_alpha Centaurin alpha Pleckstrin homology (PH) domain. Centaurin alpha Pleckstrin homology (PH) domain. Centaurin alpha is a phophatidlyinositide binding protein consisting of an N-terminal ArfGAP domain and two PH domains. In response to growth factor activation, PI3K phosphorylates phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 1 is recruited to the plasma membrane following growth factor stimulation by specific binding of its PH domain to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 2 is constitutively bound to the plasma membrane since it binds phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate with equal affinity. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specifici
Probab=30.81 E-value=1.4e+02 Score=20.54 Aligned_cols=31 Identities=6% Similarity=0.079 Sum_probs=21.5
Q ss_pred eEEEEEcCeEEEEEEcCCHHHHHHHHHHHHhh
Q 037014 4 AQSISFCGKIIETTVTSTTSVAENWLLKIRSL 35 (198)
Q Consensus 4 ~~~v~f~~~~i~~~v~~~~~~~~~~i~~~~~~ 35 (198)
.+.|... +..+...++++++.++|++.+...
T Consensus 69 ~F~i~t~-~Rty~l~a~s~~e~~~Wi~ai~~v 99 (103)
T cd01251 69 GVTLVTP-ERKFLFACETEQDRREWIAAFQNV 99 (103)
T ss_pred eEEEEeC-CeEEEEECCCHHHHHHHHHHHHHH
Confidence 3444443 344445778999999999999864
No 111
>PF03633 Glyco_hydro_65C: Glycosyl hydrolase family 65, C-terminal domain ; InterPro: IPR005194 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This family of glycosyl hydrolases (GH65 from CAZY) contains this domain and includes vacuolar acid trehalase and maltose phosphorylases. Maltose phosphorylase (MP) is a dimeric enzyme that catalyzes the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The C-terminal domain forms a two layered jelly roll motif. This domain is situated at the base of the catalytic domain, however its function remains unknown [].; PDB: 1H54_A.
Probab=30.38 E-value=97 Score=18.57 Aligned_cols=18 Identities=17% Similarity=0.412 Sum_probs=15.3
Q ss_pred ceeEEEEEcCeEEEEEEc
Q 037014 2 AYAQSISFCGKIIETTVT 19 (198)
Q Consensus 2 ~~~~~v~f~~~~i~~~v~ 19 (198)
.|.|++.+.|..+.++++
T Consensus 9 ~l~F~~~~rg~~l~v~i~ 26 (54)
T PF03633_consen 9 SLSFRLRYRGHWLEVEIT 26 (54)
T ss_dssp EEEEEEEETTEEEEEEEE
T ss_pred EeEEEEEECCEEEEEEEE
Confidence 478899999999888877
No 112
>PF13289 SIR2_2: SIR2-like domain
Probab=30.17 E-value=44 Score=23.89 Aligned_cols=30 Identities=17% Similarity=0.443 Sum_probs=22.5
Q ss_pred cccHHHHHhhcCCCeEEEEEeecc-hHHHHh
Q 037014 82 CIPLSIKNFLSDPNVVFVGIEVEE-IMSKLK 111 (198)
Q Consensus 82 ~~~~~L~~lL~d~~i~kvG~~~~~-D~~~L~ 111 (198)
.++..|+.+|....++++|+++.. |++.+.
T Consensus 75 ~~~~~l~~~l~~~~~lfiGys~~D~~i~~~l 105 (143)
T PF13289_consen 75 WFPNFLRSLLRSKTLLFIGYSFNDPDIRQLL 105 (143)
T ss_pred HHHHHHHHHHcCCCEEEEEECCCCHHHHHHH
Confidence 355778899999999999999864 344443
No 113
>KOG0685 consensus Flavin-containing amine oxidase [Coenzyme transport and metabolism]
Probab=29.98 E-value=43 Score=30.24 Aligned_cols=34 Identities=26% Similarity=0.206 Sum_probs=28.1
Q ss_pred chHHHHHHHHcC-CcCCCCCceeccCCCCCCCCHH
Q 037014 140 PGLKVLAYQLLR-LRPWKPKKVCMNNLESGFLDTE 173 (198)
Q Consensus 140 ~~L~~l~~~~l~-~~l~K~~~~~~s~W~~~~L~~~ 173 (198)
-++..+..++|+ .+++|++++.+|+|...|+..-
T Consensus 392 e~~~~~lr~fl~n~~iP~p~kilRs~W~snp~frG 426 (498)
T KOG0685|consen 392 EGLTKLLRKFLKNPEIPKPKKILRSQWISNPFFRG 426 (498)
T ss_pred HHHHHHHHHhcCCCCCCCchhhhhhcccCCCccCc
Confidence 356777778888 8899999999999999887653
No 114
>cd01247 PH_GPBP Goodpasture antigen binding protein (GPBP) Pleckstrin homology (PH) domain. Goodpasture antigen binding protein (GPBP) Pleckstrin homology (PH) domain. The GPBP protein is a kinase that phosphorylates an N-terminal region of the alpha 3 chain of type IV collagen , which is commonly known as the goodpasture antigen. It has has an N-terminal PH domain and a C-terminal START domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cyt
Probab=29.40 E-value=1.7e+02 Score=19.70 Aligned_cols=31 Identities=10% Similarity=0.089 Sum_probs=22.0
Q ss_pred eEEEEEcCeEEEEEEcCCHHHHHHHHHHHHh
Q 037014 4 AQSISFCGKIIETTVTSTTSVAENWLLKIRS 34 (198)
Q Consensus 4 ~~~v~f~~~~i~~~v~~~~~~~~~~i~~~~~ 34 (198)
.+.+...+....-..++++++-++|++.+.+
T Consensus 60 ~F~i~~~~~r~~~L~A~s~~e~~~Wi~al~~ 90 (91)
T cd01247 60 RFDISVNENVVWYLRAENSQSRLLWMDSVVR 90 (91)
T ss_pred EEEEEeCCCeEEEEEeCCHHHHHHHHHHHhh
Confidence 3455555545555567899999999998875
No 115
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=29.15 E-value=4.7e+02 Score=27.78 Aligned_cols=145 Identities=14% Similarity=0.092 Sum_probs=83.5
Q ss_pred CCeEEEEeeeecCC---CCCCCCCceeEEEeeeCCeEEEEEcccc--------Cc--------------cc---HHHHHh
Q 037014 39 QILIVGLNCKWKPH---PIPSLSGKIATLQLCVDTKCLILQLLYM--------DC--------------IP---LSIKNF 90 (198)
Q Consensus 39 ~~~~vg~D~Ew~~~---~~~~~~~~~~liQla~~~~~~i~~l~~~--------~~--------------~~---~~L~~l 90 (198)
++.+.+||+|++.. |.+....++-.|.--+...-|||--..+ +. -| .-|+.|
T Consensus 245 dp~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREiVs~DIedfEYTPKpE~eG~F~v~Ne~dEv~Ll~Rf 324 (2173)
T KOG1798|consen 245 DPRVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREIVSEDIEDFEYTPKPEYEGPFCVFNEPDEVGLLQRF 324 (2173)
T ss_pred CceEEEEeeecccCCCCCCCcccceEEEEEEEecCceEEEechhhhccchhhcccCCccccccceEEecCCcHHHHHHHH
Confidence 47999999999955 3345678888888888777666543221 00 11 456777
Q ss_pred hcC-----CCeEEEEEee-cchHHHHhh---hcCCccC---ceeehH---------------HHHHH--hCCCCCCCCch
Q 037014 91 LSD-----PNVVFVGIEV-EEIMSKLKN---EYGLCIK---KKIDVR---------------TLAKL--HFPISCLGKPG 141 (198)
Q Consensus 91 L~d-----~~i~kvG~~~-~~D~~~L~~---~~gi~~~---~~~Dl~---------------~l~~~--~l~~~~~~~~~ 141 (198)
+++ |+| -|.||- -.|.-.+.+ .+|+.+. |+.-+. ..+++ .| | .+++|
T Consensus 325 FeHiq~~kP~i-ivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrWVKRDSYL--P-qGSqg 400 (2173)
T KOG1798|consen 325 FEHIQEVKPTI-IVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRWVKRDSYL--P-QGSQG 400 (2173)
T ss_pred HHHHHhcCCcE-EEEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehhhhhhhhhcccC--C-Ccccc
Confidence 754 555 455544 356655543 4676543 222210 01110 11 2 25889
Q ss_pred HHHHHHHHcCCc---CCCCCceeccCCCCCCCCHHHHHHHHHhHHHHHHHHHH
Q 037014 142 LKVLAYQLLRLR---PWKPKKVCMNNLESGFLDTELIKFACIDAYVSCAIGTK 191 (198)
Q Consensus 142 L~~l~~~~l~~~---l~K~~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~~~ 191 (198)
|+++++.=||.. ++..-...+. ..-.+..-.|.+.||.+.+.||-+
T Consensus 401 LKAVTkaKLGYdPvEvdPEdM~~~A----~EkPQ~lasYSVSDAVATYyLYMk 449 (2173)
T KOG1798|consen 401 LKAVTKAKLGYDPVEVDPEDMVRMA----MEKPQTLASYSVSDAVATYYLYMK 449 (2173)
T ss_pred hhHHHHHhhCCCcccCCHHHhhhhh----hhCchhhhhcchHHHHHHHHHHHH
Confidence 999999999964 3321111111 111122238999999999999876
No 116
>KOG1097 consensus Adenine deaminase/adenosine deaminase [Nucleotide transport and metabolism]
Probab=27.99 E-value=2e+02 Score=25.45 Aligned_cols=146 Identities=13% Similarity=0.023 Sum_probs=68.8
Q ss_pred CHHHHHHHHHHHHhhccC-CCeEEEEeeeecCCCCCCCCCceeEEEeeeCCe-EEEEEccccCcccHHHHHhhcCCCeEE
Q 037014 21 TTSVAENWLLKIRSLHSA-QILIVGLNCKWKPHPIPSLSGKIATLQLCVDTK-CLILQLLYMDCIPLSIKNFLSDPNVVF 98 (198)
Q Consensus 21 ~~~~~~~~i~~~~~~~~~-~~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~-~~i~~l~~~~~~~~~L~~lL~d~~i~k 98 (198)
.++.+.+.+....+.+.. ...++|||.-..+....+....+-+++.+-.++ -+-+|....+.-++..+++|..=+..-
T Consensus 189 ~~e~~~e~v~~~~~~~~~~~~~VvGidL~G~e~~~~p~~~f~~vl~~~~~~gi~~t~HaGE~~~~~~~v~~~LD~l~~~R 268 (399)
T KOG1097|consen 189 PPEVAEETVSEAKELNKLFPNFVVGIDLVGQEDLGGPLSLFLEVLAKAPAKGIHLTFHAGETNGGASVVKNALDLLGTER 268 (399)
T ss_pred ChHHHHHHHHHHHHHHHhCCCeEEEEecCCCCCCCCChhhhHHHHHhhhhcCCcEEEEccccCCChHHHHHHHHhhCCcc
Confidence 344455666665553222 358999999877742223333333344443233 233365543323455666665334556
Q ss_pred EEEeec--chH--HHHhhhcCCccCceeehHHHHHHhCCC-CCCCCchHHHHHHHHcCCcCCCCCceeccCCCCCCCCHH
Q 037014 99 VGIEVE--EIM--SKLKNEYGLCIKKKIDVRTLAKLHFPI-SCLGKPGLKVLAYQLLRLRPWKPKKVCMNNLESGFLDTE 173 (198)
Q Consensus 99 vG~~~~--~D~--~~L~~~~gi~~~~~~Dl~~l~~~~l~~-~~~~~~~L~~l~~~~l~~~l~K~~~~~~s~W~~~~L~~~ 173 (198)
+|||+. .|= ..+.+.+++.+ ++..+.+..++. +..+.+-++.+.+.-.-..+..+. .+-|...|||.+
T Consensus 269 IGHG~~l~~dp~L~~~~k~~nI~l----EiCP~SN~vl~~v~d~rnhp~~~~~~~~vP~vI~sDD---P~~f~~~~Lt~d 341 (399)
T KOG1097|consen 269 IGHGYFLTKDPELINLLKSRNIAL----EICPISNQVLGLVSDLRNHPVARLLAAGVPVVINSDD---PGFFGAAPLTLD 341 (399)
T ss_pred ccCceeccCCHHHHHHHHhcCceE----EEccchhhheeccccccccHHHHHHhCCCCEEEeCCC---cccccCccccHH
Confidence 788763 343 22335566532 222333333321 123355566665532222233221 134666655553
No 117
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/
Probab=27.25 E-value=1.6e+02 Score=19.71 Aligned_cols=35 Identities=14% Similarity=0.240 Sum_probs=22.6
Q ss_pred CeEEEEEccccCc-ccHHH-HHhhcCCCeEEEEEeec
Q 037014 70 TKCLILQLLYMDC-IPLSI-KNFLSDPNVVFVGIEVE 104 (198)
Q Consensus 70 ~~~~i~~l~~~~~-~~~~L-~~lL~d~~i~kvG~~~~ 104 (198)
+.+..|.+...+. +...| ..++.||+|.+.||.+.
T Consensus 8 ~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~fAgY~vp 44 (83)
T cd07027 8 KNSVTVEMENEDHTLGNLLREELLKDDQVDFARYYIK 44 (83)
T ss_pred CCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEEecC
Confidence 3455556654432 33445 45579999999999863
No 118
>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=27.06 E-value=4.5e+02 Score=23.40 Aligned_cols=146 Identities=14% Similarity=0.128 Sum_probs=77.3
Q ss_pred CeEEEEeeeecCCCCCCCCCceeEEEeeeCCeE--EEEEccccC-c----ccHHHHHhhc-CCCeEEEEEeecch---HH
Q 037014 40 ILIVGLNCKWKPHPIPSLSGKIATLQLCVDTKC--LILQLLYMD-C----IPLSIKNFLS-DPNVVFVGIEVEEI---MS 108 (198)
Q Consensus 40 ~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~~--~i~~l~~~~-~----~~~~L~~lL~-d~~i~kvG~~~~~D---~~ 108 (198)
.+.+-||+|..|. .+..-..+++....+... |. ++...+ . ....+.++|. .|+-.-+-|+ ... ++
T Consensus 284 ~~~~ffDiEt~P~--~~~~yL~G~~~~~~~~~~~~~~-~fla~~~~~E~~~~~~f~~~l~~~~~~~i~hY~-~~e~~~l~ 359 (457)
T TIGR03491 284 PGELIFDIESDPD--ENLDYLHGFLVVDKGQENEKYR-PFLAEDPNTEELAWQQFLQLLQSYPDAPIYHYG-ETEKDSLR 359 (457)
T ss_pred CccEEEEecCCCC--CCCceEEEEEEecCCCCCccee-eeecCCchHHHHHHHHHHHHHHHCCCCeEEeeC-HHHHHHHH
Confidence 4667899999874 233334444443222111 33 332221 1 1134444664 3543344555 333 35
Q ss_pred HHhhhcCCc-------cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCCCceec-------cCC---CCCCCC
Q 037014 109 KLKNEYGLC-------IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKPKKVCM-------NNL---ESGFLD 171 (198)
Q Consensus 109 ~L~~~~gi~-------~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~~~~~~-------s~W---~~~~L~ 171 (198)
+|...||.. ++.++|+-..++..+-.| .++.||+.++.- +|.+.... ...+ ..| +.+.+-
T Consensus 360 rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p-~~sysLK~v~~~-lg~~~~~~-~~~G~~ai~~y~~~~~~~~~~~l 436 (457)
T TIGR03491 360 RLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILP-IESYSLKSIARW-LGFEWRQK-EASGAKSLLWYRQWKKTGDRRLL 436 (457)
T ss_pred HHHHHcCCCHHHHHHHHHHheehHHHHHhhEECC-CCCCCHHHHHHH-hCcccCCC-CCCHHHHHHHHHHHHHhCCHHHH
Confidence 555677765 236799987776432223 247899999875 58754421 1111 112 122233
Q ss_pred HHHHHHHHHhHHHHHHHHHHH
Q 037014 172 TELIKFACIDAYVSCAIGTKL 192 (198)
Q Consensus 172 ~~Qi~YAA~Da~~~~~l~~~L 192 (198)
+.-+.|-..|+.+...|.+.|
T Consensus 437 ~~l~~YN~dD~~At~~l~~wL 457 (457)
T TIGR03491 437 ERILRYNEDDCRATWIVADWL 457 (457)
T ss_pred HHHHHHhHHHHHHHHHHHHhC
Confidence 333489999999999887654
No 119
>cd01257 PH_IRS Insulin receptor substrate (IRS) pleckstrin homology (PH) domain. Insulin receptor substrate (IRS) pleckstrin homology (PH) domain. PH domains are only found in eukaryotes, and are often involved in targeting proteins to the plasma membrane via lipid binding. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes. The IRS PH domain targets IRS molecules to the plasma membrane, usually in response to insulin stimulation.
Probab=26.97 E-value=1.9e+02 Score=20.13 Aligned_cols=31 Identities=3% Similarity=0.030 Sum_probs=22.7
Q ss_pred eeEEEEEcCeEEEEEEcCCHHHHHHHHHHHHh
Q 037014 3 YAQSISFCGKIIETTVTSTTSVAENWLLKIRS 34 (198)
Q Consensus 3 ~~~~v~f~~~~i~~~v~~~~~~~~~~i~~~~~ 34 (198)
|.+.+.+.. .....+++++++.++|++.+..
T Consensus 70 ~~f~i~t~d-r~f~l~aese~E~~~Wi~~i~~ 100 (101)
T cd01257 70 HLIALYTRD-EYFAVAAENEAEQDSWYQALLE 100 (101)
T ss_pred eEEEEEeCC-ceEEEEeCCHHHHHHHHHHHhh
Confidence 445555544 4566688899999999998864
No 120
>cd01244 PH_RasGAP_CG9209 RAS_GTPase activating protein (GAP)_CG9209 pleckstrin homology (PH) domain. RAS_GTPase activating protein (GAP)_CG9209 pleckstrin homology (PH) domain. This protein consists of two C2 domains, followed by a RasGAP domain, a PH domain and a BTK domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=26.18 E-value=1.7e+02 Score=20.20 Aligned_cols=31 Identities=13% Similarity=0.145 Sum_probs=21.4
Q ss_pred eeEEEEEcCeEEEEEEcCCHHHHHHHHHHHHh
Q 037014 3 YAQSISFCGKIIETTVTSTTSVAENWLLKIRS 34 (198)
Q Consensus 3 ~~~~v~f~~~~i~~~v~~~~~~~~~~i~~~~~ 34 (198)
|.++|......+ ....+++++.++||+.+..
T Consensus 67 ~~fqivt~~r~~-yi~a~s~~E~~~Wi~al~k 97 (98)
T cd01244 67 DIITIVCEDDTM-QLQFEAPVEATDWLNALEK 97 (98)
T ss_pred ceEEEEeCCCeE-EEECCCHHHHHHHHHHHhc
Confidence 455665554433 3467799999999998864
No 121
>PF07808 RED_N: RED-like protein N-terminal region; InterPro: IPR012916 This domain contains sequences that are similar to the N-terminal region of Red protein (Q13123 from SWISSPROT). This and related proteins contain a RED repeat which consists of a number of RE and RD sequence elements []. The region in question has several conserved NLS sequences and a putative trimeric coiled-coil region [], suggesting that these proteins are expressed in the nucleus []. The function of Red protein is unknown, but efficient sequestration to nuclear bodies suggests that its expression may be tightly regulated, or that the protein self-aggregates extremely efficiently []. ; GO: 0005634 nucleus
Probab=26.01 E-value=21 Score=29.09 Aligned_cols=27 Identities=22% Similarity=0.137 Sum_probs=20.8
Q ss_pred CceeEEEEEc--CeEEEEEEcCCHHHHHH
Q 037014 1 MAYAQSISFC--GKIIETTVTSTTSVAEN 27 (198)
Q Consensus 1 ~~~~~~v~f~--~~~i~~~v~~~~~~~~~ 27 (198)
|+|.|.++-. .+.|.||++.+-++|..
T Consensus 172 MaYvfdL~~e~~~~DIPTTliRSK~Dcp~ 200 (238)
T PF07808_consen 172 MAYVFDLDDEYAESDIPTTLIRSKADCPV 200 (238)
T ss_pred eEEEEecCCCcccccCCCeeecchhhCcc
Confidence 8899988876 46789998877777543
No 122
>PF10364 NKWYS: Putative capsular polysaccharide synthesis protein; InterPro: IPR018831 This entry contains proteins of no known function. They are found predominantly in Vibrio and cyanobacterial species and are characterised by having a NKWYS sequence motif.
Probab=25.60 E-value=1.6e+02 Score=22.04 Aligned_cols=61 Identities=18% Similarity=0.318 Sum_probs=39.1
Q ss_pred HHHHHHHHhhccCCCeEEEEeeeecCCCCCCCCCceeEEEeeeCCe--EEEEEccccCcccHHHHHhhcCCCeEE
Q 037014 26 ENWLLKIRSLHSAQILIVGLNCKWKPHPIPSLSGKIATLQLCVDTK--CLILQLLYMDCIPLSIKNFLSDPNVVF 98 (198)
Q Consensus 26 ~~~i~~~~~~~~~~~~~vg~D~Ew~~~~~~~~~~~~~liQla~~~~--~~i~~l~~~~~~~~~L~~lL~d~~i~k 98 (198)
..|.+.-.+ .++|+|+--.|.. .--+-|+--.++ .+|+++-.++.+++.+++||.-+++.-
T Consensus 34 ~~WFD~Eik------~~fGiDV~~~~Fd------~~qGyqi~~~~n~~lLlir~E~L~~~~~~i~efL~i~~f~l 96 (141)
T PF10364_consen 34 LNWFDNEIK------KVFGIDVYSHPFD------HEQGYQIFNNDNFELLLIRCEKLDSLQEAIREFLGIDNFTL 96 (141)
T ss_pred hhHHHHHHH------HhcCceeecCcCC------CCCCeEEeecCCEEEEEEehhhhhhHHHHHHHHhCCCCccc
Confidence 456654443 7899998765541 222334444443 788888887778899999998545433
No 123
>PF10584 Proteasome_A_N: Proteasome subunit A N-terminal signature; InterPro: IPR000426 The proteasome (or macropain) (3.4.25.1 from EC) [, , , , ] is a eukaryotic and archaeal multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of about 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700 kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). This family contains the alpha subunit sequences which range from 210 to 290 amino acids. These sequences are classified as non-peptidase homologues in MEROPS peptidase family T1 (clan PB(T)). ; GO: 0004175 endopeptidase activity, 0006511 ubiquitin-dependent protein catabolic process, 0019773 proteasome core complex, alpha-subunit complex; PDB: 3H4P_M 1IRU_O 3UN4_U 1FNT_A 3OEV_G 3OEU_U 3SDK_U 3DY3_G 3MG7_G 3L5Q_C ....
Probab=24.63 E-value=42 Score=17.00 Aligned_cols=7 Identities=14% Similarity=0.259 Sum_probs=5.1
Q ss_pred HHHHHHH
Q 037014 173 ELIKFAC 179 (198)
Q Consensus 173 ~Qi~YAA 179 (198)
-||+||.
T Consensus 15 ~QVEYA~ 21 (23)
T PF10584_consen 15 FQVEYAM 21 (23)
T ss_dssp HHHHHHH
T ss_pred EeeEeee
Confidence 5888874
No 124
>cd01265 PH_PARIS-1 PARIS-1 pleckstrin homology (PH) domain. PARIS-1 pleckstrin homology (PH) domain. PARIS-1 contains a PH domain and a TBC-type GTPase catalytic domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=23.72 E-value=2e+02 Score=19.39 Aligned_cols=31 Identities=16% Similarity=0.159 Sum_probs=22.7
Q ss_pred eEEEEEcCeEEEEEEcCCHHHHHHHHHHHHhh
Q 037014 4 AQSISFCGKIIETTVTSTTSVAENWLLKIRSL 35 (198)
Q Consensus 4 ~~~v~f~~~~i~~~v~~~~~~~~~~i~~~~~~ 35 (198)
.|.|... +..+...++|+++.++||+.+...
T Consensus 63 ~F~i~t~-~r~y~l~A~s~~e~~~Wi~al~~~ 93 (95)
T cd01265 63 RFEIHSN-NEVIALKASSDKQMNYWLQALQSK 93 (95)
T ss_pred EEEEEcC-CcEEEEECCCHHHHHHHHHHHHhh
Confidence 4566544 445566788999999999998863
No 125
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=22.25 E-value=1.1e+02 Score=21.82 Aligned_cols=84 Identities=24% Similarity=0.131 Sum_probs=44.4
Q ss_pred HHHHHhhcCCCeEEEEEeecchHHHHhh---hc-CCc---cCceeehHHHHHHhCCCCCCCCchHHHHHHHHcCCcCCCC
Q 037014 85 LSIKNFLSDPNVVFVGIEVEEIMSKLKN---EY-GLC---IKKKIDVRTLAKLHFPISCLGKPGLKVLAYQLLRLRPWKP 157 (198)
Q Consensus 85 ~~L~~lL~d~~i~kvG~~~~~D~~~L~~---~~-gi~---~~~~~Dl~~l~~~~l~~~~~~~~~L~~l~~~~l~~~l~K~ 157 (198)
..+.+++. +..+.|||+...|...+.+ .+ +.. ...++|...+....++ .....+|+.+++.+.. +..+.
T Consensus 74 ~~~~~~~~-~~~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~l~~l~~~~~~-~~~~~ 149 (164)
T PF00929_consen 74 DEFEEFLK-KNDILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFP--NRKKYSLDDLAEYFGI-PFDGT 149 (164)
T ss_dssp HHHHHHHH-HHTEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHH--HHHHHSHHHHHHHTTS-SSTST
T ss_pred Hhhhhhhh-cccccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHhh--ccccCCHHHHHHHcCC-CCCCC
Confidence 34556665 2356788887777654432 12 221 1234444443332221 1124689999987543 33221
Q ss_pred CceeccCCCCCCCCHHHHHHHHHhHHHHHHHH
Q 037014 158 KKVCMNNLESGFLDTELIKFACIDAYVSCAIG 189 (198)
Q Consensus 158 ~~~~~s~W~~~~L~~~Qi~YAA~Da~~~~~l~ 189 (198)
-+=|..||++..+||
T Consensus 150 -----------------~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 150 -----------------AHDALDDARATAELF 164 (164)
T ss_dssp -----------------TTSHHHHHHHHHHHH
T ss_pred -----------------CcChHHHHHHHhCcC
Confidence 112678888888875
No 126
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Probab=22.03 E-value=2.4e+02 Score=18.87 Aligned_cols=34 Identities=24% Similarity=0.315 Sum_probs=21.3
Q ss_pred eEEEEEccccCc-ccHHH-HHhhcCCCeEEEEEeec
Q 037014 71 KCLILQLLYMDC-IPLSI-KNFLSDPNVVFVGIEVE 104 (198)
Q Consensus 71 ~~~i~~l~~~~~-~~~~L-~~lL~d~~i~kvG~~~~ 104 (198)
.+..|.+...+. +...| ..++.||+|.+.||.+.
T Consensus 9 n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vp 44 (83)
T cd06927 9 NELELEIEGEDHTLLNLLKEELLRDPGVKVASYDIE 44 (83)
T ss_pred CEEEEEEeCCCchHHHHHHHHHhcCCCeEEEEeecC
Confidence 344555544332 33445 44579999999999854
No 127
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=21.94 E-value=67 Score=21.73 Aligned_cols=32 Identities=22% Similarity=0.476 Sum_probs=19.8
Q ss_pred EEEEEccccCc-ccHHHH-HhhcCCCeEEEEEee
Q 037014 72 CLILQLLYMDC-IPLSIK-NFLSDPNVVFVGIEV 103 (198)
Q Consensus 72 ~~i~~l~~~~~-~~~~L~-~lL~d~~i~kvG~~~ 103 (198)
+..|.+...+. +-..|+ .++.||+|.++||.+
T Consensus 10 ~~~~~i~~EdHTLgNlLr~~L~~~p~V~fagY~v 43 (85)
T cd07029 10 CATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSI 43 (85)
T ss_pred eEEEEEeCCCcchHHHHHHHHhhCCCceEEeecc
Confidence 44444443332 324454 456999999999986
No 128
>KOG0095 consensus GTPase Rab30, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.55 E-value=1.3e+02 Score=23.07 Aligned_cols=37 Identities=14% Similarity=0.330 Sum_probs=29.1
Q ss_pred EEEEEcccc---CcccHHHHHh--hcCCCeEEEEEeecchHH
Q 037014 72 CLILQLLYM---DCIPLSIKNF--LSDPNVVFVGIEVEEIMS 108 (198)
Q Consensus 72 ~~i~~l~~~---~~~~~~L~~l--L~d~~i~kvG~~~~~D~~ 108 (198)
.+++|+.+. +.+|+-|+++ ..+.++.||-+|.|-|..
T Consensus 84 ilvydiscqpsfdclpewlreie~yan~kvlkilvgnk~d~~ 125 (213)
T KOG0095|consen 84 ILVYDISCQPSFDCLPEWLREIEQYANNKVLKILVGNKIDLA 125 (213)
T ss_pred EEEEecccCcchhhhHHHHHHHHHHhhcceEEEeeccccchh
Confidence 556777553 5788888887 578899999999998874
No 129
>cd01266 PH_Gab Gab (Grb2-associated binder) pleckstrin homology (PH) domain. Gab (Grb2-associated binder) pleckstrin homology (PH) domain. The Gab subfamily includes several Gab proteins, Drosophila DOS and C. elegans SOC-1. They are scaffolding adaptor proteins, which possess N-terminal PH domains and a C-terminus with proline-rich regions and multiple phosphorylation sites. Following activation of growth factor receptors, Gab proteins are tyrosine phosphorylated and activate PI3K, which generates 3-phosphoinositide lipids. By binding to these lipids via the PH domain, Gab proteins remain in proximity to the receptor, leading to further signaling. While not all Gab proteins depend on the PH domain for recruitment, it is required for Gab activity. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display str
Probab=21.46 E-value=2.2e+02 Score=19.66 Aligned_cols=24 Identities=13% Similarity=-0.098 Sum_probs=19.2
Q ss_pred CeEEEEEEcCCHHHHHHHHHHHHh
Q 037014 11 GKIIETTVTSTTSVAENWLLKIRS 34 (198)
Q Consensus 11 ~~~i~~~v~~~~~~~~~~i~~~~~ 34 (198)
++..+...+.++++.++|++.+.+
T Consensus 83 ~~r~y~l~A~s~ee~~~Wi~~I~~ 106 (108)
T cd01266 83 IVRDLYLVAKNEEEMTLWVNCICK 106 (108)
T ss_pred CCccEEEEECCHHHHHHHHHHHHh
Confidence 344555678899999999999875
No 130
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=21.45 E-value=85 Score=20.72 Aligned_cols=20 Identities=35% Similarity=0.624 Sum_probs=15.1
Q ss_pred HHHHH-hhcCCCeEEEEEeec
Q 037014 85 LSIKN-FLSDPNVVFVGIEVE 104 (198)
Q Consensus 85 ~~L~~-lL~d~~i~kvG~~~~ 104 (198)
..|+. ++.||+|.++||.+.
T Consensus 16 NlLr~~L~~~p~V~fagY~vp 36 (77)
T PF13656_consen 16 NLLRYELLKDPDVEFAGYRVP 36 (77)
T ss_dssp HHHHHCCTTSTTEEEEEEEES
T ss_pred HHHHHHHhhCCCeEEEEeccC
Confidence 34544 469999999999864
No 131
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=21.30 E-value=2.5e+02 Score=18.90 Aligned_cols=33 Identities=21% Similarity=0.284 Sum_probs=21.3
Q ss_pred EEEEEccccCc-ccHHH-HHhhcCCCeEEEEEeec
Q 037014 72 CLILQLLYMDC-IPLSI-KNFLSDPNVVFVGIEVE 104 (198)
Q Consensus 72 ~~i~~l~~~~~-~~~~L-~~lL~d~~i~kvG~~~~ 104 (198)
+..|.+...+. +...| ..++.||+|.+.||.+.
T Consensus 12 ~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vp 46 (85)
T PRK01146 12 ELELEIEGEDHTLMNLLKEELLEDPGVEAASYDID 46 (85)
T ss_pred EEEEEEeCCCchHHHHHHHHHhcCCCeeEEEeecC
Confidence 55555554332 33445 44579999999999864
No 132
>PF00982 Glyco_transf_20: Glycosyltransferase family 20; InterPro: IPR001830 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 20 GT20 from CAZY comprises enzymes with only one known activity; alpha, alpha-trehalose-phosphate synthase [UDP-forming] (2.4.1.15 from EC). Synthesis of trehalose in the yeast Saccharomyces cerevisiae is catalysed by the trehalose-6-phosphate (Tre6P) synthase/phosphatase complex, which is composed of at least three different subunits encoded by the genes TPS1, TPS2, and TSL1. Tps1 and Tps2 carry the catalytic activities of trehalose synthesis, namely Tre6P synthase (Tps1) and Tre6P phosphatase (Tps2), while TsI1 has regulatory functions. There is some evidence that TsI1 and Tps3 may share a common function with respect to regulation and/or structural stabilisation of the Tre6P synthase/phosphatase complex in exponentially growing, heat-shocked cells []. OtsA (trehalose-6-phosphate synthase) from Escherichia coli has homology to the full-length TPS1, the N-terminal part of TPS2 and an internal region of TPS3 (TSL1) of yeast [].; GO: 0003824 catalytic activity, 0005992 trehalose biosynthetic process; PDB: 1UQU_A 2WTX_A 1UQT_B 1GZ5_B.
Probab=20.57 E-value=1e+02 Score=27.82 Aligned_cols=66 Identities=17% Similarity=0.364 Sum_probs=33.5
Q ss_pred EEEEcCeEEEEEEc---CCHHHH---------HHHHHHHHhhccCC-CeEEEEee-eecCCC-------------CCCCC
Q 037014 6 SISFCGKIIETTVT---STTSVA---------ENWLLKIRSLHSAQ-ILIVGLNC-KWKPHP-------------IPSLS 58 (198)
Q Consensus 6 ~v~f~~~~i~~~v~---~~~~~~---------~~~i~~~~~~~~~~-~~~vg~D~-Ew~~~~-------------~~~~~ 58 (198)
+|.++|..+.+.+. =+++.+ .++++.+++...++ ..++|+|- ++...- .+...
T Consensus 230 ~v~~~Gr~v~v~~~pigId~~~~~~~~~~~~v~~~~~~l~~~~~~~~~ii~gvDrld~~kGi~~kl~Afe~fL~~~P~~~ 309 (474)
T PF00982_consen 230 TVEYNGRRVRVGVFPIGIDPDAFAQLARSPEVQERAEELREKFKGKRKIIVGVDRLDYTKGIPEKLRAFERFLERYPEYR 309 (474)
T ss_dssp -EEETTEEEEEEE------HHHHHHHHH-S---HHHHHHHHHTTT-SEEEEEE--B-GGG-HHHHHHHHHHHHHH-GGGT
T ss_pred eEEECCEEEEEEEeeccCChHHHHhhccChHHHHHHHHHHHhcCCCcEEEEEeccchhhcCHHHHHHHHHHHHHhCcCcc
Confidence 68888998777631 133333 34555565544443 57999994 332210 01257
Q ss_pred CceeEEEeeeCCe
Q 037014 59 GKIATLQLCVDTK 71 (198)
Q Consensus 59 ~~~~liQla~~~~ 71 (198)
+++.++|+|.+++
T Consensus 310 ~kv~liQi~~psr 322 (474)
T PF00982_consen 310 GKVVLIQIAVPSR 322 (474)
T ss_dssp TTEEEEEE--B-S
T ss_pred CcEEEEEEeeccC
Confidence 8999999998765
Done!