Query 048020
Match_columns 304
No_of_seqs 325 out of 1524
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 05:31:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048020.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048020hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2176 PolC DNA polymerase II 100.0 6.7E-44 1.5E-48 373.4 6.6 207 6-219 419-662 (1444)
2 TIGR01405 polC_Gram_pos DNA po 100.0 4.7E-36 1E-40 324.7 18.5 203 7-216 189-428 (1213)
3 PRK00448 polC DNA polymerase I 100.0 1.3E-32 2.9E-37 301.2 15.4 203 7-216 418-657 (1437)
4 TIGR00573 dnaq exonuclease, DN 100.0 8.8E-31 1.9E-35 237.0 18.7 172 7-195 6-216 (217)
5 PRK07748 sporulation inhibitor 100.0 9.8E-29 2.1E-33 222.0 16.6 155 6-163 2-195 (207)
6 PRK09146 DNA polymerase III su 100.0 4.3E-28 9.4E-33 223.2 19.1 143 6-151 45-229 (239)
7 PRK07247 DNA polymerase III su 100.0 7.9E-28 1.7E-32 215.4 18.1 139 8-150 5-170 (195)
8 PRK06807 DNA polymerase III su 100.0 1.4E-27 3.1E-32 227.6 19.8 145 1-150 1-173 (313)
9 PRK07740 hypothetical protein; 100.0 1.5E-27 3.3E-32 220.1 18.3 141 6-150 57-227 (244)
10 PRK06195 DNA polymerase III su 100.0 1.4E-27 3.1E-32 226.9 18.7 140 8-151 1-166 (309)
11 cd06130 DNA_pol_III_epsilon_li 100.0 3.8E-27 8.2E-32 199.7 16.5 129 10-143 1-155 (156)
12 PRK05711 DNA polymerase III su 99.9 6.3E-27 1.4E-31 215.7 18.6 137 7-148 3-175 (240)
13 TIGR01406 dnaQ_proteo DNA poly 99.9 8.9E-27 1.9E-31 212.6 18.2 135 9-148 1-171 (225)
14 smart00479 EXOIII exonuclease 99.9 2.8E-26 6.2E-31 195.5 19.3 136 9-150 1-168 (169)
15 cd06133 ERI-1_3'hExo_like DEDD 99.9 1E-26 2.3E-31 200.3 16.5 136 10-146 1-176 (176)
16 cd06131 DNA_pol_III_epsilon_Ec 99.9 1.7E-26 3.8E-31 198.7 17.8 131 10-145 1-166 (167)
17 PRK09145 DNA polymerase III su 99.9 2.2E-26 4.8E-31 205.7 19.0 141 5-147 26-199 (202)
18 PRK08517 DNA polymerase III su 99.9 2E-26 4.3E-31 214.3 19.0 138 6-150 66-232 (257)
19 PRK07983 exodeoxyribonuclease 99.9 1.2E-26 2.6E-31 211.1 17.1 135 10-150 2-155 (219)
20 PRK06722 exonuclease; Provisio 99.9 1.1E-26 2.4E-31 218.3 17.2 140 6-148 3-180 (281)
21 PRK06310 DNA polymerase III su 99.9 2.1E-26 4.6E-31 213.1 18.8 137 7-149 6-174 (250)
22 PRK06063 DNA polymerase III su 99.9 1.9E-26 4.2E-31 219.8 17.9 140 5-150 12-180 (313)
23 PRK06309 DNA polymerase III su 99.9 3.2E-26 6.9E-31 209.4 17.8 135 8-150 2-167 (232)
24 PRK07942 DNA polymerase III su 99.9 4.5E-26 9.8E-31 208.6 18.4 141 6-150 4-181 (232)
25 PRK07246 bifunctional ATP-depe 99.9 4.5E-26 9.7E-31 240.9 19.6 143 3-150 2-171 (820)
26 PRK07883 hypothetical protein; 99.9 3.8E-25 8.3E-30 225.2 20.1 143 3-150 10-183 (557)
27 PRK08074 bifunctional ATP-depe 99.9 2.7E-25 5.9E-30 237.7 19.8 140 6-150 1-170 (928)
28 cd06136 TREX1_2 DEDDh 3'-5' ex 99.9 1.9E-25 4.1E-30 196.3 14.3 127 10-144 1-176 (177)
29 PRK05168 ribonuclease T; Provi 99.9 1E-24 2.2E-29 197.0 18.6 140 7-150 16-202 (211)
30 TIGR01298 RNaseT ribonuclease 99.9 2.5E-24 5.5E-29 192.9 18.1 141 6-150 6-193 (200)
31 TIGR01407 dinG_rel DnaQ family 99.9 2.2E-24 4.8E-29 228.9 19.2 137 9-150 1-166 (850)
32 cd06134 RNaseT DEDDh 3'-5' exo 99.9 3.2E-24 6.9E-29 190.5 16.9 138 8-149 5-189 (189)
33 cd06137 DEDDh_RNase DEDDh 3'-5 99.9 1.1E-24 2.3E-29 188.7 9.7 126 11-143 1-161 (161)
34 cd06138 ExoI_N N-terminal DEDD 99.9 6E-24 1.3E-28 187.4 14.4 131 11-142 1-182 (183)
35 PTZ00315 2'-phosphotransferase 99.9 1.7E-23 3.7E-28 211.7 18.7 143 7-150 55-256 (582)
36 PRK05601 DNA polymerase III su 99.9 2.1E-23 4.6E-28 201.5 17.1 137 6-148 44-248 (377)
37 cd06127 DEDDh DEDDh 3'-5' exon 99.9 3.7E-23 8E-28 172.1 14.1 129 11-143 1-159 (159)
38 cd06144 REX4_like DEDDh 3'-5' 99.9 1.6E-23 3.4E-28 179.6 11.2 128 11-143 1-152 (152)
39 PRK09182 DNA polymerase III su 99.9 1E-22 2.2E-27 192.9 17.2 141 6-149 35-201 (294)
40 cd06145 REX1_like DEDDh 3'-5' 99.9 3.5E-23 7.6E-28 177.5 11.9 125 11-143 1-150 (150)
41 cd06149 ISG20 DEDDh 3'-5' exon 99.9 4.2E-23 9.2E-28 178.4 11.4 126 11-143 1-157 (157)
42 COG0847 DnaQ DNA polymerase II 99.9 2.8E-22 6.2E-27 182.7 17.1 136 8-148 13-181 (243)
43 PF00929 RNase_T: Exonuclease; 99.9 6E-24 1.3E-28 177.0 2.4 131 11-142 1-164 (164)
44 PRK11779 sbcB exonuclease I; P 99.9 3E-21 6.4E-26 193.2 18.6 144 5-148 3-197 (476)
45 cd06135 Orn DEDDh 3'-5' exonuc 99.9 1.1E-21 2.3E-26 172.0 13.1 129 10-148 1-171 (173)
46 PRK05359 oligoribonuclease; Pr 99.9 1.4E-20 2.9E-25 166.6 15.3 133 7-150 2-176 (181)
47 KOG0542 Predicted exonuclease 99.8 1.9E-19 4.1E-24 165.0 8.4 143 6-149 54-242 (280)
48 COG5018 KapD Inhibitor of the 99.7 1.4E-17 3E-22 145.0 5.9 148 8-156 4-193 (210)
49 KOG2249 3'-5' exonuclease [Rep 99.2 6.5E-11 1.4E-15 109.8 11.6 136 9-149 106-266 (280)
50 COG2925 SbcB Exonuclease I [DN 99.1 2.3E-10 4.9E-15 110.8 10.5 141 6-146 7-198 (475)
51 cd06143 PAN2_exo DEDDh 3'-5' e 99.1 6.2E-10 1.3E-14 98.4 11.4 131 6-143 3-174 (174)
52 KOG3242 Oligoribonuclease (3'- 98.8 1.8E-08 3.9E-13 88.7 8.4 143 6-150 24-200 (208)
53 COG1949 Orn Oligoribonuclease 98.8 8.3E-08 1.8E-12 83.8 10.8 146 4-149 2-178 (184)
54 cd05160 DEDDy_DNA_polB_exo DED 98.6 4.7E-07 1E-11 80.1 12.5 103 10-125 1-161 (199)
55 KOG2248 3'-5' exonuclease [Rep 98.4 6.1E-07 1.3E-11 88.1 8.6 136 5-147 213-373 (380)
56 cd06139 DNA_polA_I_Ecoli_like_ 97.7 0.00074 1.6E-08 58.5 12.4 120 6-150 3-171 (193)
57 PRK05755 DNA polymerase I; Pro 97.3 0.0019 4.2E-08 69.9 12.0 61 88-150 389-470 (880)
58 COG3359 Predicted exonuclease 97.0 0.005 1.1E-07 57.5 9.8 114 7-125 97-218 (278)
59 PF13482 RNase_H_2: RNase_H su 96.9 0.00095 2E-08 57.0 3.8 104 11-126 1-116 (164)
60 PHA02570 dexA exonuclease; Pro 96.8 0.0054 1.2E-07 56.3 8.4 74 11-87 4-99 (220)
61 KOG4793 Three prime repair exo 96.7 0.0015 3.3E-08 61.5 3.8 83 3-87 8-114 (318)
62 cd06125 DnaQ_like_exo DnaQ-lik 96.5 0.014 3.1E-07 46.3 7.5 22 11-32 1-25 (96)
63 cd05780 DNA_polB_Kod1_like_exo 96.3 0.085 1.8E-06 46.9 12.5 31 94-126 125-156 (195)
64 PF04857 CAF1: CAF1 family rib 96.2 0.1 2.2E-06 48.8 12.7 48 94-144 189-262 (262)
65 KOG0304 mRNA deadenylase subun 96.2 0.031 6.7E-07 51.4 8.7 139 8-148 24-238 (239)
66 cd05779 DNA_polB_epsilon_exo D 96.1 0.11 2.4E-06 47.1 12.4 31 95-125 137-168 (204)
67 cd05781 DNA_polB_B3_exo DEDDy 96.1 0.12 2.5E-06 46.1 12.3 29 95-125 116-144 (188)
68 PF01612 DNA_pol_A_exo1: 3'-5' 95.7 0.44 9.5E-06 40.2 13.6 132 7-149 19-175 (176)
69 cd05785 DNA_polB_like2_exo Unc 94.6 1.1 2.3E-05 40.6 13.4 30 96-125 137-168 (207)
70 COG0349 Rnd Ribonuclease D [Tr 94.5 0.62 1.3E-05 45.9 12.1 133 7-152 16-169 (361)
71 TIGR03491 RecB family nuclease 94.1 0.28 6.1E-06 49.4 9.3 117 7-125 283-409 (457)
72 KOG1275 PAB-dependent poly(A) 93.0 0.14 3.1E-06 55.3 5.2 138 5-147 907-1090(1118)
73 PF10108 DNA_pol_B_exo2: Predi 92.9 2.3 5.1E-05 38.9 12.4 52 94-147 100-171 (209)
74 cd05777 DNA_polB_delta_exo DED 92.7 2.4 5.2E-05 38.7 12.3 70 6-87 5-82 (230)
75 cd05778 DNA_polB_zeta_exo inac 91.7 3.4 7.3E-05 37.9 12.0 139 8-150 4-224 (231)
76 cd06141 WRN_exo DEDDy 3'-5' ex 88.5 3.9 8.5E-05 34.9 9.1 125 7-146 17-169 (170)
77 cd05784 DNA_polB_II_exo DEDDy 88.4 9 0.0002 34.3 11.7 30 95-125 123-153 (193)
78 cd06129 RNaseD_like DEDDy 3'-5 87.7 4.2 9E-05 34.8 8.8 125 7-146 12-160 (161)
79 cd06146 mut-7_like_exo DEDDy 3 87.4 2.5 5.5E-05 37.6 7.5 55 92-146 111-192 (193)
80 PTZ00166 DNA polymerase delta 87.1 7.4 0.00016 43.6 12.4 29 94-124 411-440 (1054)
81 PF13017 Maelstrom: piRNA path 86.9 0.72 1.6E-05 42.0 3.7 63 23-87 9-78 (213)
82 PF03104 DNA_pol_B_exo1: DNA p 86.5 3.3 7.2E-05 38.7 8.1 70 7-87 156-233 (325)
83 PRK06826 dnaE DNA polymerase I 86.1 0.17 3.7E-06 56.7 -0.9 42 174-215 86-133 (1151)
84 TIGR01388 rnd ribonuclease D. 85.1 18 0.00038 35.7 12.7 127 7-150 17-167 (367)
85 PRK05673 dnaE DNA polymerase I 84.7 0.56 1.2E-05 52.6 2.2 42 173-214 80-128 (1135)
86 cd00007 35EXOc 3'-5' exonuclea 83.2 8.8 0.00019 31.1 8.3 32 91-123 76-107 (155)
87 cd05783 DNA_polB_B1_exo DEDDy 81.3 22 0.00049 32.0 10.9 18 70-87 67-84 (204)
88 PRK10829 ribonuclease D; Provi 81.0 27 0.00058 34.7 12.1 122 7-150 21-171 (373)
89 cd05782 DNA_polB_like1_exo Unc 80.6 28 0.00061 31.3 11.3 30 94-125 140-169 (208)
90 PRK05762 DNA polymerase II; Re 80.0 14 0.00031 39.9 10.7 50 95-145 276-348 (786)
91 PRK09532 DNA polymerase III su 79.1 0.43 9.3E-06 52.1 -1.2 43 172-214 79-132 (874)
92 PHA02528 43 DNA polymerase; Pr 77.5 29 0.00063 38.3 12.1 50 95-144 255-323 (881)
93 PRK07374 dnaE DNA polymerase I 76.9 0.63 1.4E-05 52.4 -0.8 42 173-214 82-134 (1170)
94 TIGR00594 polc DNA-directed DN 76.7 0.56 1.2E-05 52.1 -1.2 42 173-214 82-129 (1022)
95 smart00486 POLBc DNA polymeras 76.0 28 0.0006 34.0 10.6 50 94-145 149-220 (471)
96 COG0749 PolA DNA polymerase I 57.3 1E+02 0.0022 32.7 10.6 57 92-149 100-180 (593)
97 COG5228 POP2 mRNA deadenylase 55.4 8.5 0.00018 35.9 2.2 141 8-150 42-254 (299)
98 PHA02524 43A DNA polymerase su 54.0 58 0.0013 33.7 8.1 27 95-121 256-282 (498)
99 cd05776 DNA_polB_alpha_exo ina 51.9 1.2E+02 0.0026 27.7 9.2 115 9-125 4-186 (234)
100 PRK06920 dnaE DNA polymerase I 42.3 5.6 0.00012 44.8 -1.3 87 115-214 24-119 (1107)
101 cd06140 DNA_polA_I_Bacillus_li 39.5 1.6E+02 0.0034 24.9 7.6 62 88-150 75-157 (178)
102 smart00474 35EXOc 3'-5' exonuc 39.0 1.5E+02 0.0032 24.3 7.1 60 88-149 94-171 (172)
103 PRK05672 dnaE2 error-prone DNA 37.0 6.9 0.00015 43.8 -1.7 43 174-216 78-126 (1046)
104 KOG1798 DNA polymerase epsilon 34.0 4E+02 0.0087 31.8 11.1 41 110-150 396-455 (2173)
105 TIGR00592 pol2 DNA polymerase 33.2 8E+02 0.017 28.2 14.2 113 9-124 505-681 (1172)
106 cd06142 RNaseD_exo DEDDy 3'-5' 30.2 2E+02 0.0043 24.0 6.7 57 92-150 87-161 (178)
107 cd06148 Egl_like_exo DEDDy 3'- 24.5 70 0.0015 28.3 2.9 57 93-150 89-178 (197)
108 PF09281 Taq-exonuc: Taq polym 23.3 3.1E+02 0.0067 23.6 6.3 53 94-149 86-138 (138)
No 1
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=100.00 E-value=6.7e-44 Score=373.36 Aligned_cols=207 Identities=19% Similarity=0.218 Sum_probs=190.2
Q ss_pred CCCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHH
Q 048020 6 DRSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADT 82 (304)
Q Consensus 6 ~~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~ 82 (304)
.+.+|||||+||||+++ +|||||||++.+| +++++|+.|++|.. ++|..++++||||++||.++++..+|+.+
T Consensus 419 ~datyVVfDiETTGLs~~~d~iIE~aAvKikng--~iId~f~~Fi~P~~--pl~~~~telTgITdeml~~a~~i~~vL~k 494 (1444)
T COG2176 419 DDATYVVFDIETTGLSPVYDEIIEIAAVKIKNG--RIIDKFQFFIKPGR--PLSATITELTGITDEMLENAPEIEEVLEK 494 (1444)
T ss_pred ccccEEEEEeecCCcCcccchhhhheeeeeeCC--cchHHHHHhcCCCC--cCchhhhhccccCHHHHcCCccHHHHHHH
Confidence 35679999999999987 9999999999988 89999999999999 99999999999999999999999999999
Q ss_pred HHHHh-------------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChHHHHH
Q 048020 83 VFDIL-------------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG-QQTHRSLDDVL 136 (304)
Q Consensus 83 f~~fl-------------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~-~~~HrAL~DA~ 136 (304)
|.+|+ ..++.+++||||.|+| .++|..++|+|+.||+.||+. +.||||.+||.
T Consensus 495 f~~~~~d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar-~L~P~~ksh~Lg~l~kk~~v~le~hHRA~yDae 573 (1444)
T COG2176 495 FREFIGDSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELAR-ALNPEFKSHRLGTLCKKLGVELERHHRADYDAE 573 (1444)
T ss_pred HHHHhcCcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHH-HhChhhhhcchHHHHHHhCccHHHhhhhhhhHH
Confidence 99999 4567899999999999 789999999999999999997 99999999999
Q ss_pred HHHHHHHHHHHHhhhccCCc--cccccCCCCCCCccccCCCceeeec---cCcccc---cccccccccccCcccCCCCcc
Q 048020 137 MNLEVLKYCATVLLLESSLP--DIFTGNGCVSQNATARSRINVRSSP---EGTSQN---LSAPSSKFKFENASNVSPPDQ 208 (304)
Q Consensus 137 aTa~L~~~ll~~l~le~~lp--~~l~~~~~~~~~~~~~~r~~h~~il---~~glkn---lvs~s~~~yf~~~prip~s~~ 208 (304)
||++||..+++.+. +.++. ..+|.. +.....|+|.|++|++|+ |.|||| |||.||++|||++||||||+|
T Consensus 574 at~~vf~~f~~~~k-e~Gi~~l~eln~~-l~~~~~ykr~r~~h~~i~vknq~GlKnLykLvS~s~~kyf~~~PrI~~S~L 651 (1444)
T COG2176 574 ATAKVFFVFLKDLK-EKGITNLSELNDK-LSSEDLYKRLRPKHATIYVKNQVGLKNLYKLVSISHTKYFYGRPRIPRSVL 651 (1444)
T ss_pred HHHHHHHHHHHHHH-HhchhhHHHHhHh-hhhhHHHhhccccceEEEEechHhHHHHHHHHHHHHHHhhccCCCCcHHHH
Confidence 99999999999986 44654 567765 356788999999999999 899999 999999999999999999999
Q ss_pred ccCCCccceee
Q 048020 209 GKEGIHPIFTL 219 (304)
Q Consensus 209 ~~~~~~~~~~~ 219 (304)
.+|.-.-++.+
T Consensus 652 ~~~regLligs 662 (1444)
T COG2176 652 KKNREGLLIGS 662 (1444)
T ss_pred HHhhcCeeecc
Confidence 99887766653
No 2
>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=100.00 E-value=4.7e-36 Score=324.71 Aligned_cols=203 Identities=21% Similarity=0.247 Sum_probs=180.4
Q ss_pred CCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHH
Q 048020 7 RSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTV 83 (304)
Q Consensus 7 ~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f 83 (304)
+.+|||||+||||+++ +|||||||+++++ +++++|++||+|.. +|++.++++||||++||+++|++.+++++|
T Consensus 189 ~~~~VVfDiETTGL~~~~d~IIEIGAVkv~~g--~iid~f~~~V~P~~--~I~~~~~~ltGIT~e~L~~ap~~~evl~~f 264 (1213)
T TIGR01405 189 DATYVVFDIETTGLSPQYDEIIEFGAVKVKNG--RIIDKFQFFIKPHE--PLSAFVTELTGITQDMLENAPEIEEVLEKF 264 (1213)
T ss_pred CCcEEEEEeEecCCCCCCCeEEEEEEEEEECC--eEEEEEEEEECCCC--CCCHHHHHHhCCCHHHHhCCCCHHHHHHHH
Confidence 4589999999999865 9999999999987 78899999999998 999999999999999999999999999999
Q ss_pred HHHh-------------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChHHHHHH
Q 048020 84 FDIL-------------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG-QQTHRSLDDVLM 137 (304)
Q Consensus 84 ~~fl-------------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~-~~~HrAL~DA~a 137 (304)
.+|+ ..++.++++||+.++| .++|..++++|++||++||++ .++|||++||.+
T Consensus 265 ~~fl~~~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar-~l~p~~k~~kL~~Lak~lgi~~~~~HrAl~DA~a 343 (1213)
T TIGR01405 265 KEFFKDSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELAR-ALNPEYKSHRLGNICKKLGVDLDDHHRADYDAEA 343 (1213)
T ss_pred HHHhCCCeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHH-HHhccCCCCCHHHHHHHcCCCCCCCcCHHHHHHH
Confidence 9999 2346789999999999 567888999999999999997 789999999999
Q ss_pred HHHHHHHHHHHhhhccCCc--cccccCCCCCCCccccCCCceeeec---cCcccc---cccccccccccCcccCCCCccc
Q 048020 138 NLEVLKYCATVLLLESSLP--DIFTGNGCVSQNATARSRINVRSSP---EGTSQN---LSAPSSKFKFENASNVSPPDQG 209 (304)
Q Consensus 138 Ta~L~~~ll~~l~le~~lp--~~l~~~~~~~~~~~~~~r~~h~~il---~~glkn---lvs~s~~~yf~~~prip~s~~~ 209 (304)
|++||.++++++. +.++. ..+|.. +..+..++|.|++|.++| +.|+|| |||.||++|||++||||++.|.
T Consensus 344 Ta~I~~~ll~~l~-~~~i~~~~~l~~~-~~~~~~~~k~~~~hl~lLAkn~~G~~nL~kLvS~a~~~~f~~~Pri~~~~L~ 421 (1213)
T TIGR01405 344 TAKVFKVMVEQLK-EKGITNLEELNNK-LSSEELYKRLRPNHIIIYAKNQAGLKNLYKLVSISLTKYFYTRPRILRSLLK 421 (1213)
T ss_pred HHHHHHHHHHHHH-HcCCccHHHHHHh-hccchhhhhcCCcceEEEEechhhHHHHHHHHHHHHHcCCCCCcccCHHHHH
Confidence 9999999998885 33432 455543 334567999999999999 789999 9999999999999999999999
Q ss_pred cCCCccc
Q 048020 210 KEGIHPI 216 (304)
Q Consensus 210 ~~~~~~~ 216 (304)
+|.-+-+
T Consensus 422 ~~~egLi 428 (1213)
T TIGR01405 422 KYREGLL 428 (1213)
T ss_pred hhCCCeE
Confidence 9986633
No 3
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=100.00 E-value=1.3e-32 Score=301.22 Aligned_cols=203 Identities=22% Similarity=0.220 Sum_probs=178.8
Q ss_pred CCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHH
Q 048020 7 RSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTV 83 (304)
Q Consensus 7 ~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f 83 (304)
..+|||||+||||++. +|||||||++++| .++++|+.||+|.. +++++++++||||++||.+++++.+++.+|
T Consensus 418 ~~~~VVfDLETTGL~~~~deIIEIgAV~V~~G--~iie~F~~~V~P~~--~I~~~~~~LTGIT~e~L~~aps~~EaL~~f 493 (1437)
T PRK00448 418 DATYVVFDVETTGLSAVYDEIIEIGAVKIKNG--EIIDKFEFFIKPGH--PLSAFTTELTGITDDMVKDAPSIEEVLPKF 493 (1437)
T ss_pred cCcEEEEEhhhcCCCCchhhhheeeeEEEeCC--eEeeeEEEEECCCC--CCCHHHHHHhCCCHHHHcCCCCHHHHHHHH
Confidence 3479999999999865 9999999999977 77899999999998 999999999999999999999999999999
Q ss_pred HHHh-------------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChHHHHHH
Q 048020 84 FDIL-------------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG-QQTHRSLDDVLM 137 (304)
Q Consensus 84 ~~fl-------------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~-~~~HrAL~DA~a 137 (304)
.+|+ ..++..+++||+.+++ .+.|..++++|++||++||++ ..+|||++||.+
T Consensus 494 ~~figg~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar-~l~p~~k~~kL~~LAk~lGL~~~~~HrAl~DA~a 572 (1437)
T PRK00448 494 KEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSR-FLYPELKSHRLNTLAKKFGVELEHHHRADYDAEA 572 (1437)
T ss_pred HHHhCCCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHH-HHcCccccccHHHHHHHcCCCCCCCcChHHHHHH
Confidence 9987 1245678999999999 567888999999999999997 789999999999
Q ss_pred HHHHHHHHHHHhhhccCCc--cccccCCCCCCCccccCCCceeeec---cCcccc---cccccccccccCcccCCCCccc
Q 048020 138 NLEVLKYCATVLLLESSLP--DIFTGNGCVSQNATARSRINVRSSP---EGTSQN---LSAPSSKFKFENASNVSPPDQG 209 (304)
Q Consensus 138 Ta~L~~~ll~~l~le~~lp--~~l~~~~~~~~~~~~~~r~~h~~il---~~glkn---lvs~s~~~yf~~~prip~s~~~ 209 (304)
|++||.++++++. +.++. ..|+.. ......+++.|++|.++| +.|+|| |||.||++||+++||||++.|.
T Consensus 573 Ta~lf~~ll~~l~-~~gi~~~~~L~~~-~~~~~~~~~~~~~h~~llAkn~~G~knL~kLvS~s~~~~f~~~Pri~~~~L~ 650 (1437)
T PRK00448 573 TAYLLIKFLKDLK-EKGITNLDELNKK-LGSEDAYKKARPKHATILVKNQVGLKNLFKLVSLSNTKYFYRVPRIPRSLLD 650 (1437)
T ss_pred HHHHHHHHHHHHH-HcCCCCHHHHHHH-hccccchhccCcccceEEeCCHHHHHHHHHHHHHHHHhcCCCCCcCCHHHHH
Confidence 9999999999986 44432 456643 233567899999999999 779999 9999999999999999999999
Q ss_pred cCCCccc
Q 048020 210 KEGIHPI 216 (304)
Q Consensus 210 ~~~~~~~ 216 (304)
+|.-+-+
T Consensus 651 ~~~egLi 657 (1437)
T PRK00448 651 KYREGLL 657 (1437)
T ss_pred hhCCCcE
Confidence 9986533
No 4
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.97 E-value=8.8e-31 Score=236.97 Aligned_cols=172 Identities=17% Similarity=0.179 Sum_probs=144.7
Q ss_pred CCcEEEEEEeecCCCC--ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHHH
Q 048020 7 RSEIVFFDVETTFPIR--HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTVF 84 (304)
Q Consensus 7 ~~~~VvfDlETTGl~~--~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f~ 84 (304)
..+|||||+||||+++ .|||||||++.++. .+.++|+++|+|.. +++++++++||||++||+++|+|.+++.+|.
T Consensus 6 ~~~fvv~D~ETTGl~~~~~IIeIgav~v~~~~-~~~~~f~~li~P~~--~i~~~a~~ihGIt~e~l~~~p~~~ev~~~~~ 82 (217)
T TIGR00573 6 LDTETTGDNETTGLYAGHDIIEIGAVEIINRR-ITGNKFHTYIKPDR--PIDPDAIKIHGITDDMLKDKPDFKEIAEDFA 82 (217)
T ss_pred ecCEEEEEecCCCCCCCCCEEEEEEEEEECCC-EeeeEEEEEECcCC--CCCHHHHhhcCCCHHHHcCCCCHHHHHHHHH
Confidence 4689999999999875 79999999987653 46789999999998 9999999999999999999999999999999
Q ss_pred HHh--------------------------cCCCCCCceehHHHHHHHhcCCC--CCCCHHHHHHHhCCC-C--CCCChHH
Q 048020 85 DIL--------------------------QAPKPKGTIDSLNLLTERFGRRA--GDMKMASLATYFGLG-Q--QTHRSLD 133 (304)
Q Consensus 85 ~fl--------------------------~~~~~~~~IDTl~Lark~l~p~~--~~~kL~~Lak~lGI~-~--~~HrAL~ 133 (304)
+|+ ..+...+++||+.+++ .++|.. .+++|..++++||++ . .+|+|++
T Consensus 83 ~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~-~~~~~~~~~~~~L~~l~~~~gl~~~~~~~H~Al~ 161 (217)
T TIGR00573 83 DYIRGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQ-YARPEFPGKRNTLDALCKRYEITNSHRALHGALA 161 (217)
T ss_pred HHhCCCEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHH-HHHHhCCCCCCCHHHHHHHcCCCCCCcccCCHHH
Confidence 999 1234568999999988 444443 467899999999996 4 7899999
Q ss_pred HHHHHHHHHHHHHHHhhhccCCccccccCCCCCCCccccCCCceeeec---cCcccc---cccccccc
Q 048020 134 DVLMNLEVLKYCATVLLLESSLPDIFTGNGCVSQNATARSRINVRSSP---EGTSQN---LSAPSSKF 195 (304)
Q Consensus 134 DA~aTa~L~~~ll~~l~le~~lp~~l~~~~~~~~~~~~~~r~~h~~il---~~glkn---lvs~s~~~ 195 (304)
||.+|++||.+++++.. +.. .+ .+ ++.|+||++++ +.|||| |||.||+-
T Consensus 162 DA~~ta~l~~~l~~~~~-~~~----~~------~~--~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 216 (217)
T TIGR00573 162 DAFILAKLYLVMTGKQT-KYG----EN------EG--QQSRPYHAIKSIVKKDMLLKLIKAVSTELQA 216 (217)
T ss_pred HHHHHHHHHHHHHhcch-hhc----cc------cc--cccCCccceEeeeccccccceeecCHHhHhc
Confidence 99999999999988752 111 11 11 68899999998 889999 99999864
No 5
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.96 E-value=9.8e-29 Score=221.98 Aligned_cols=155 Identities=21% Similarity=0.253 Sum_probs=128.5
Q ss_pred CCCcEEEEEEeecCCC--------C-ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCH
Q 048020 6 DRSEIVFFDVETTFPI--------R-HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTF 76 (304)
Q Consensus 6 ~~~~~VvfDlETTGl~--------~-~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f 76 (304)
++++|||||+||||++ . +|||||||+++++ ++.++|++||||...++++++++++||||++||+++|+|
T Consensus 2 ~~~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~--~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~~ 79 (207)
T PRK07748 2 DEQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGC--EVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISF 79 (207)
T ss_pred CcceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecC--cChhhhcceECCCccCccChhhhhhcCcCHHHHccCCCH
Confidence 5678999999999953 1 8999999999976 788999999999876579999999999999999999999
Q ss_pred HHHHHHHHHHh---------------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC--CC
Q 048020 77 ADIADTVFDIL---------------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG--QQ 127 (304)
Q Consensus 77 ~eVl~~f~~fl---------------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~--~~ 127 (304)
.+++.+|.+|+ ..++...|+|+..+.++ +++....++|++++++||++ .+
T Consensus 80 ~evl~~f~~~~~~~~~~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~-~~~~~~~~~L~~~~~~~gi~~~~~ 158 (207)
T PRK07748 80 EELVEKLAEYDKRCKPTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKK-FFGERNQTGLWKAIEEYGKEGTGK 158 (207)
T ss_pred HHHHHHHHHHhCcCCeEEEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHH-HhCcCCCCCHHHHHHHcCCCCCCC
Confidence 99999999998 12344678999887774 45555678999999999997 46
Q ss_pred CCChHHHHHHHHHHHHHHHHHhh-hccCCccccccCC
Q 048020 128 THRSLDDVLMNLEVLKYCATVLL-LESSLPDIFTGNG 163 (304)
Q Consensus 128 ~HrAL~DA~aTa~L~~~ll~~l~-le~~lp~~l~~~~ 163 (304)
+|||++||++|++||.++.++.. +...-+..++..+
T Consensus 159 ~H~Al~DA~~ta~l~~~l~~~~~~~~~~~~~~~~~~~ 195 (207)
T PRK07748 159 HHCALDDAMTTYNIFKLVEKDKEYLVKPEPPTIGERV 195 (207)
T ss_pred CcChHHHHHHHHHHHHHHHhCcceeecCCCCccccce
Confidence 89999999999999999998753 2233344454443
No 6
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=4.3e-28 Score=223.21 Aligned_cols=143 Identities=19% Similarity=0.234 Sum_probs=126.3
Q ss_pred CCCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHH
Q 048020 6 DRSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADT 82 (304)
Q Consensus 6 ~~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~ 82 (304)
.+..|||||+||||+++ +|||||+|+++++.....++|+++|+|+. +|++.++++||||+++|+++|+|.+|+.+
T Consensus 45 ~~~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~--~i~~~~~~IhGIt~e~l~~ap~~~evl~~ 122 (239)
T PRK09146 45 SEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRR--PLEEESVVIHGITHSELQDAPDLERILDE 122 (239)
T ss_pred ccCCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCC--CCChhhhhhcCCCHHHHhCCCCHHHHHHH
Confidence 46789999999999875 99999999999874444689999999999 99999999999999999999999999999
Q ss_pred HHHHh-------------------------cCCCCCCceehHHHHHHHhcCCC-------------CCCCHHHHHHHhCC
Q 048020 83 VFDIL-------------------------QAPKPKGTIDSLNLLTERFGRRA-------------GDMKMASLATYFGL 124 (304)
Q Consensus 83 f~~fl-------------------------~~~~~~~~IDTl~Lark~l~p~~-------------~~~kL~~Lak~lGI 124 (304)
|.+|+ ..++.++++||+.++|+. .|.. .+++|++++++||+
T Consensus 123 l~~~~~~~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l-~~~~~~~~~~~~~~~~~~~~~L~~l~~~~gl 201 (239)
T PRK09146 123 LLEALAGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARI-QRKQAGGLWNRLKGKKPESIRLADSRLRYGL 201 (239)
T ss_pred HHHHhCCCEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHH-cccccccccchhccCCCCCCCHHHHHHHcCC
Confidence 99998 234567999999999954 3321 67899999999999
Q ss_pred C-CCCCChHHHHHHHHHHHHHHHHHhhh
Q 048020 125 G-QQTHRSLDDVLMNLEVLKYCATVLLL 151 (304)
Q Consensus 125 ~-~~~HrAL~DA~aTa~L~~~ll~~l~l 151 (304)
+ .++|||++||.+|++||.+++++.+.
T Consensus 202 ~~~~~H~Al~DA~ata~l~~~~~~~~~~ 229 (239)
T PRK09146 202 PAYSPHHALTDAIATAELLQAQIAHHFS 229 (239)
T ss_pred CCCCCCCcHHHHHHHHHHHHHHHHHHcC
Confidence 7 78999999999999999999988853
No 7
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=7.9e-28 Score=215.38 Aligned_cols=139 Identities=18% Similarity=0.247 Sum_probs=119.6
Q ss_pred CcEEEEEEeecCCCC--ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHHHH
Q 048020 8 SEIVFFDVETTFPIR--HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTVFD 85 (304)
Q Consensus 8 ~~~VvfDlETTGl~~--~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f~~ 85 (304)
.+|||||+||||++. +|||||||++++| .++++|++||+|.. +++++++++||||++||+++|++.+++++|.+
T Consensus 5 ~~~vvlD~EtTGl~~~~eIIeIgaV~v~~g--~~~~~f~~lv~P~~--~i~~~~~~lhGIt~~~v~~ap~~~evl~~f~~ 80 (195)
T PRK07247 5 ETYIAFDLEFNTVNGVSHIIQVSAVKYDDH--KEVDSFDSYVYTDV--PLQSFINGLTGITADKIADAPKVEEVLAAFKE 80 (195)
T ss_pred CeEEEEEeeCCCCCCCCeEEEEEEEEEECC--EEEEEEEEEECCCC--CCCccceecCCCCHHHHhCCCCHHHHHHHHHH
Confidence 489999999999865 9999999999977 67899999999998 99999999999999999999999999999999
Q ss_pred Hh---------------------cC-CCCCCceehHHHHHH-Hh--cCCCCCCCHHHHHHHhCCCCCCCChHHHHHHHHH
Q 048020 86 IL---------------------QA-PKPKGTIDSLNLLTE-RF--GRRAGDMKMASLATYFGLGQQTHRSLDDVLMNLE 140 (304)
Q Consensus 86 fl---------------------~~-~~~~~~IDTl~Lark-~l--~p~~~~~kL~~Lak~lGI~~~~HrAL~DA~aTa~ 140 (304)
|+ +. .....++||+..+.. .. .++.++++|.+||++||++..+|||++||++|++
T Consensus 81 f~~~~~lVaHNa~~fD~~fL~~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~gi~~~~HrAl~DA~~ta~ 160 (195)
T PRK07247 81 FVGELPLIGYNAQKSDLPILAENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVADFLGIKGRGHNSLEDARMTAR 160 (195)
T ss_pred HHCCCeEEEEeCcHhHHHHHHHcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHHHhcCCCCCCcCCHHHHHHHHH
Confidence 99 11 112356788755421 11 4667889999999999998778999999999999
Q ss_pred HHHHHHHHhh
Q 048020 141 VLKYCATVLL 150 (304)
Q Consensus 141 L~~~ll~~l~ 150 (304)
||.++++...
T Consensus 161 v~~~ll~~~~ 170 (195)
T PRK07247 161 VYESFLESDQ 170 (195)
T ss_pred HHHHHHhhcc
Confidence 9999987653
No 8
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=1.4e-27 Score=227.59 Aligned_cols=145 Identities=23% Similarity=0.318 Sum_probs=132.3
Q ss_pred CCCCCCCCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHH
Q 048020 1 MGPTQDRSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFA 77 (304)
Q Consensus 1 ~~~~~~~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~ 77 (304)
||.-.+.++||+||+||||+++ +|||||||+++++ +++++|+.+|+|.. ++++.++++||||++||+++|+|.
T Consensus 1 ~~~~~~~~~~Vv~DlETTGl~p~~~eIIEIgaV~v~~g--~i~~~f~~lVkP~~--~I~~~a~~ihGIT~e~l~~~~~~~ 76 (313)
T PRK06807 1 MGNISLPLDYVVIDFETTGFNPYNDKIIQVAAVKYRNH--ELVDQFVSYVNPER--PIPDRITSLTGITNYRVSDAPTIE 76 (313)
T ss_pred CCCcCCCCCEEEEEEECCCCCCCCCeEEEEEEEEEECC--EEEEEEEEEECcCC--CCCHhhhccCCCCHHHHhCCCCHH
Confidence 6778889999999999999865 9999999999976 78999999999999 999999999999999999999999
Q ss_pred HHHHHHHHHh-------------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCCCCCCChH
Q 048020 78 DIADTVFDIL-------------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLGQQTHRSL 132 (304)
Q Consensus 78 eVl~~f~~fl-------------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~~~~HrAL 132 (304)
+|+.+|.+|+ ......+++||+.++++ ++|..++++|++|+++||++.++|||+
T Consensus 77 evl~~f~~fl~~~~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~-~~~~~~~~kL~~L~~~lgi~~~~H~Al 155 (313)
T PRK06807 77 EVLPLFLAFLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKK-YMKHAPNHKLETLKRMLGIRLSSHNAF 155 (313)
T ss_pred HHHHHHHHHHcCCeEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHH-HhCCCCCCCHHHHHHHcCCCCCCcChH
Confidence 9999999998 12345789999999994 567788999999999999977899999
Q ss_pred HHHHHHHHHHHHHHHHhh
Q 048020 133 DDVLMNLEVLKYCATVLL 150 (304)
Q Consensus 133 ~DA~aTa~L~~~ll~~l~ 150 (304)
+||++|++||.++.....
T Consensus 156 ~DA~~ta~l~~~l~~~~~ 173 (313)
T PRK06807 156 DDCITCAAVYQKCASIEE 173 (313)
T ss_pred HHHHHHHHHHHHHHHhhh
Confidence 999999999999988763
No 9
>PRK07740 hypothetical protein; Provisional
Probab=99.95 E-value=1.5e-27 Score=220.06 Aligned_cols=141 Identities=23% Similarity=0.340 Sum_probs=126.6
Q ss_pred CCCcEEEEEEeecCCCC----ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHH
Q 048020 6 DRSEIVFFDVETTFPIR----HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIAD 81 (304)
Q Consensus 6 ~~~~~VvfDlETTGl~~----~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~ 81 (304)
.+.+|||||+||||+++ +|||||||+++++.. +.++|+++|+|.. ++++.+.++||||+++|+++|++.+++.
T Consensus 57 ~~~~~vv~D~ETTGl~p~~~deIIeIgaV~~~~~~i-~~~~f~~lv~P~~--~i~~~~~~ltGIt~e~l~~ap~~~evl~ 133 (244)
T PRK07740 57 TDLPFVVFDLETTGFSPQQGDEILSIGAVKTKGGEV-ETDTFYSLVKPKR--PIPEHILELTGITAEDVAFAPPLAEVLH 133 (244)
T ss_pred cCCCEEEEEEeCCCCCCCCCCeEEEEEEEEEECCEE-EEEEEEEEeCcCC--CCChhheeccCCCHHHHhCCCCHHHHHH
Confidence 45589999999999753 899999999997632 3899999999998 9999999999999999999999999999
Q ss_pred HHHHHh-------------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChHHHH
Q 048020 82 TVFDIL-------------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG-QQTHRSLDDV 135 (304)
Q Consensus 82 ~f~~fl-------------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~-~~~HrAL~DA 135 (304)
+|.+|+ ..++..+++||+.+++ .+.|..++++|++++++||++ ..+|+|++||
T Consensus 134 ~f~~fi~~~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r-~l~~~~~~~sL~~l~~~~gi~~~~~H~Al~Da 212 (244)
T PRK07740 134 RFYAFIGAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTK-LLAHERDFPTLDDALAYYGIPIPRRHHALGDA 212 (244)
T ss_pred HHHHHhCCCEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHH-HHcCCCCCCCHHHHHHHCCcCCCCCCCcHHHH
Confidence 999998 3456789999999998 567777889999999999997 7789999999
Q ss_pred HHHHHHHHHHHHHhh
Q 048020 136 LMNLEVLKYCATVLL 150 (304)
Q Consensus 136 ~aTa~L~~~ll~~l~ 150 (304)
++|++||.+++.++.
T Consensus 213 ~ata~l~~~ll~~~~ 227 (244)
T PRK07740 213 LMTAKLWAILLVEAQ 227 (244)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999998874
No 10
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=1.4e-27 Score=226.91 Aligned_cols=140 Identities=18% Similarity=0.223 Sum_probs=125.6
Q ss_pred CcEEEEEEeecCCCC-ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHHHHH
Q 048020 8 SEIVFFDVETTFPIR-HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTVFDI 86 (304)
Q Consensus 8 ~~~VvfDlETTGl~~-~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f~~f 86 (304)
++|||||+||||+.. +|||||||+++++ +++++|++||||... .+++.++++||||++||+++|+|.+++++|.+|
T Consensus 1 ~~~vviD~ETTg~~~d~IieIgav~v~~g--~i~~~f~~lv~P~~~-~~~~~~~~IhGIT~e~v~~ap~f~ev~~~~~~f 77 (309)
T PRK06195 1 MNFVAIDFETANEKRNSPCSIGIVVVKDG--EIVEKVHYLIKPKEM-RFMPINIGIHGIRPHMVEDELEFDKIWEKIKHY 77 (309)
T ss_pred CcEEEEEEeCCCCCCCceEEEEEEEEECC--EEEEEEEEEECCCCC-CCChhheeccCcCHHHHhCCCCHHHHHHHHHHH
Confidence 579999999999877 9999999999976 788999999999852 578889999999999999999999999999999
Q ss_pred h-------------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCCCCCCChHHHHHHHHHH
Q 048020 87 L-------------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLGQQTHRSLDDVLMNLEV 141 (304)
Q Consensus 87 l-------------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~~~~HrAL~DA~aTa~L 141 (304)
+ ......+|+||+.+++ .++|..++++|.+|+++||++..+|||++||++|++|
T Consensus 78 l~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar-~l~~~~~~~~L~~L~~~~gi~~~~H~Al~DA~ata~l 156 (309)
T PRK06195 78 FNNNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAK-NFYSNIDNARLNTVNNFLGYEFKHHDALADAMACSNI 156 (309)
T ss_pred hCCCEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHH-HHcCCCCcCCHHHHHHHcCCCCcccCCHHHHHHHHHH
Confidence 9 1223468999999999 5678888999999999999987799999999999999
Q ss_pred HHHHHHHhhh
Q 048020 142 LKYCATVLLL 151 (304)
Q Consensus 142 ~~~ll~~l~l 151 (304)
|.++++++..
T Consensus 157 ~~~l~~~~~~ 166 (309)
T PRK06195 157 LLNISKELNS 166 (309)
T ss_pred HHHHHHHhcc
Confidence 9999988753
No 11
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=99.95 E-value=3.8e-27 Score=199.68 Aligned_cols=129 Identities=26% Similarity=0.359 Sum_probs=117.1
Q ss_pred EEEEEEeecCCCC-ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHHHHHh-
Q 048020 10 IVFFDVETTFPIR-HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTVFDIL- 87 (304)
Q Consensus 10 ~VvfDlETTGl~~-~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f~~fl- 87 (304)
||+||+||||+.. +|||||+|+++++ ++.++|+.+|+|+. +++++++++||||+++|++++++.+++.+|.+|+
T Consensus 1 ~v~~D~Ettg~~~~~ii~ig~v~~~~~--~~~~~~~~~i~p~~--~~~~~~~~i~GIt~e~l~~~~~~~~v~~~l~~~l~ 76 (156)
T cd06130 1 FVAIDFETANADRASACSIGLVKVRDG--QIVDTFYTLIRPPT--RFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLG 76 (156)
T ss_pred CEEEEEeCCCCCCCceEEEEEEEEECC--EEEEEEEEEeCcCC--CCChhhccccCcCHHHHhcCCCHHHHHHHHHHHhC
Confidence 6999999999876 9999999999976 78899999999999 9999999999999999999999999999999999
Q ss_pred ------------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCCCCCCChHHHHHHHHHHHH
Q 048020 88 ------------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLGQQTHRSLDDVLMNLEVLK 143 (304)
Q Consensus 88 ------------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~~~~HrAL~DA~aTa~L~~ 143 (304)
..+.+.+++||+.++++ .++..++++|..++++||++..+|||++||++|++||.
T Consensus 77 ~~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~-~~~~~~~~~L~~l~~~~g~~~~~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 77 GSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARR-VWPLLPNHKLNTVAEHLGIELNHHDALEDARACAEILL 155 (156)
T ss_pred CCEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHH-HhccCCCCCHHHHHHHcCCCccCcCchHHHHHHHHHHh
Confidence 12346789999999995 56778899999999999997339999999999999985
No 12
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.95 E-value=6.3e-27 Score=215.72 Aligned_cols=137 Identities=23% Similarity=0.255 Sum_probs=118.4
Q ss_pred CCcEEEEEEeecCCCC----ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHH
Q 048020 7 RSEIVFFDVETTFPIR----HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADT 82 (304)
Q Consensus 7 ~~~~VvfDlETTGl~~----~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~ 82 (304)
.++|||||+||||+++ +|||||+|.+.++. ...++|+.||+|.. +|+++++++||||++||+++|+|.+++.+
T Consensus 3 ~~r~vvlDtETTGldp~~~drIIEIGaV~v~~~~-~~~~~f~~~i~P~~--~i~~~a~~VHGIT~e~l~~~p~f~ev~~~ 79 (240)
T PRK05711 3 IMRQIVLDTETTGLNQREGHRIIEIGAVELINRR-LTGRNFHVYIKPDR--LVDPEALAVHGITDEFLADKPTFAEVADE 79 (240)
T ss_pred CCeEEEEEeeCCCcCCCCCCeEEEEEEEEEECCE-EeccEEEEEECcCC--cCCHHHhhhcCCCHHHHcCCCCHHHHHHH
Confidence 4689999999999763 89999999999763 23468999999998 99999999999999999999999999999
Q ss_pred HHHHh------------------------cCCC-----CCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC---CCCCC
Q 048020 83 VFDIL------------------------QAPK-----PKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG---QQTHR 130 (304)
Q Consensus 83 f~~fl------------------------~~~~-----~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~---~~~Hr 130 (304)
|.+|+ +..+ ...++||+.++|+ ++|+ .+++|+.||++||++ ..+|+
T Consensus 80 f~~fi~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~-~~p~-~~~~L~aL~~~~gi~~~~r~~H~ 157 (240)
T PRK05711 80 FLDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARR-MFPG-KRNSLDALCKRYGIDNSHRTLHG 157 (240)
T ss_pred HHHHhCCCEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHH-HcCC-CCCCHHHHHHHCCCCCCCCCCCC
Confidence 99999 1112 2569999999995 5665 467999999999996 24699
Q ss_pred hHHHHHHHHHHHHHHHHH
Q 048020 131 SLDDVLMNLEVLKYCATV 148 (304)
Q Consensus 131 AL~DA~aTa~L~~~ll~~ 148 (304)
|+.||++|++||.+|...
T Consensus 158 AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 158 ALLDAEILAEVYLAMTGG 175 (240)
T ss_pred HHHHHHHHHHHHHHHHCc
Confidence 999999999999998754
No 13
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=99.95 E-value=8.9e-27 Score=212.56 Aligned_cols=135 Identities=24% Similarity=0.243 Sum_probs=117.4
Q ss_pred cEEEEEEeecCCCC----ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHHH
Q 048020 9 EIVFFDVETTFPIR----HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTVF 84 (304)
Q Consensus 9 ~~VvfDlETTGl~~----~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f~ 84 (304)
++||||+||||+++ +|||||||++.++. ...++|+.||+|.. +|+++++++||||++||+++|+|.+++.+|.
T Consensus 1 r~vvlD~ETTGl~p~~~d~IIEIgav~~~~~~-~~~~~f~~~i~P~~--~i~~~a~~vhGIt~e~l~~~p~f~ev~~~f~ 77 (225)
T TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRM-LTGDNFHVYVNPER--DMPAEAAKVHGITDEFLADKPKFKEIADEFL 77 (225)
T ss_pred CEEEEEeeCCCcCCCCCCeEEEEEEEEEECCc-EecceEEEEECcCC--CCCHHHHhccCCCHHHHhCCCCHHHHHHHHH
Confidence 58999999999764 89999999998752 34579999999998 9999999999999999999999999999999
Q ss_pred HHh------------------------c---CCCC--CCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC---CCCCChH
Q 048020 85 DIL------------------------Q---APKP--KGTIDSLNLLTERFGRRAGDMKMASLATYFGLG---QQTHRSL 132 (304)
Q Consensus 85 ~fl------------------------~---~~~~--~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~---~~~HrAL 132 (304)
+|+ + .++. .+|+||+.++|+ ++|. .+++|+.||++||++ ..+|+|+
T Consensus 78 ~fi~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~-~~p~-~~~~L~~L~~~~gi~~~~r~~H~Al 155 (225)
T TIGR01406 78 DFIGGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARE-RFPG-QRNSLDALCKRFKVDNSHRTLHGAL 155 (225)
T ss_pred HHhCCCEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHH-HcCC-CCCCHHHHHHhcCCCCCCCCCcCHH
Confidence 999 2 1122 689999999995 4565 568999999999996 3579999
Q ss_pred HHHHHHHHHHHHHHHH
Q 048020 133 DDVLMNLEVLKYCATV 148 (304)
Q Consensus 133 ~DA~aTa~L~~~ll~~ 148 (304)
+||++|++||.+|...
T Consensus 156 ~DA~~~a~v~~~l~~~ 171 (225)
T TIGR01406 156 LDAHLLAEVYLALTGG 171 (225)
T ss_pred HHHHHHHHHHHHHHcC
Confidence 9999999999998764
No 14
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.95 E-value=2.8e-26 Score=195.51 Aligned_cols=136 Identities=28% Similarity=0.394 Sum_probs=119.5
Q ss_pred cEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHHHH
Q 048020 9 EIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTVFD 85 (304)
Q Consensus 9 ~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f~~ 85 (304)
.||+||+||||+++ +|||||+|+++++ .+.+.|+.+|+|.. +++++++++||||++++++++++.+++.+|.+
T Consensus 1 ~~v~~D~Ettg~~~~~~~Iieig~v~~~~~--~~~~~f~~~v~p~~--~i~~~~~~~~Git~~~l~~~~~~~~~~~~~~~ 76 (169)
T smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGG--RIIVVFDTYVKPDR--PITDYATEIHGITPEMLDDAPTFEEVLEELLE 76 (169)
T ss_pred CEEEEEeeCCCCCCCCCeEEEEEEEEEECC--EeEEEEEEEECCCC--CCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHH
Confidence 48999999999765 8999999999987 47899999999977 99999999999999999999999999999999
Q ss_pred Hh---------------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC-CC-CCChHHHHH
Q 048020 86 IL---------------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG-QQ-THRSLDDVL 136 (304)
Q Consensus 86 fl---------------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~-~~-~HrAL~DA~ 136 (304)
|+ ..+...+++||+.++++ +.+. .+++|++++++||++ .+ +|+|++||+
T Consensus 77 ~l~~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~-~~~~-~~~~L~~l~~~~~~~~~~~~H~A~~Da~ 154 (169)
T smart00479 77 FLKGKILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARA-LNPG-RKYSLKKLAERLGLEVIGRAHRALDDAR 154 (169)
T ss_pred HhcCCEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHH-HCCC-CCCCHHHHHHHCCCCCCCCCcCcHHHHH
Confidence 99 12334569999999994 4444 389999999999996 44 599999999
Q ss_pred HHHHHHHHHHHHhh
Q 048020 137 MNLEVLKYCATVLL 150 (304)
Q Consensus 137 aTa~L~~~ll~~l~ 150 (304)
+|++||.++++++.
T Consensus 155 ~t~~l~~~~~~~~~ 168 (169)
T smart00479 155 ATAKLFKKLVERLL 168 (169)
T ss_pred HHHHHHHHHHHHhh
Confidence 99999999988753
No 15
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=99.95 E-value=1e-26 Score=200.35 Aligned_cols=136 Identities=28% Similarity=0.392 Sum_probs=120.8
Q ss_pred EEEEEEeecCCC--------CceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHH
Q 048020 10 IVFFDVETTFPI--------RHIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIAD 81 (304)
Q Consensus 10 ~VvfDlETTGl~--------~~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~ 81 (304)
|||||+||||++ .+|||||||+++++..+++++|+++|+|.....++++++++||||+++++++|++.+++.
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~~~~~vl~ 80 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCCCHHHHHH
Confidence 799999999975 289999999999865558899999999998668999999999999999999999999999
Q ss_pred HHHHHh---------------------------c---CCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC--CCCC
Q 048020 82 TVFDIL---------------------------Q---APKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG--QQTH 129 (304)
Q Consensus 82 ~f~~fl---------------------------~---~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~--~~~H 129 (304)
+|.+|+ . .++...++|+..++++ ..+..+.++|++++++||++ .++|
T Consensus 81 ~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~-~~~~~~~~~L~~l~~~~gi~~~~~~H 159 (176)
T cd06133 81 EFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAK-FYGLKKRTGLSKALEYLGLEFEGRHH 159 (176)
T ss_pred HHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHH-HhCCCCCCCHHHHHHHCCCCCCCCCc
Confidence 999997 1 3466789999999995 45666789999999999996 4899
Q ss_pred ChHHHHHHHHHHHHHHH
Q 048020 130 RSLDDVLMNLEVLKYCA 146 (304)
Q Consensus 130 rAL~DA~aTa~L~~~ll 146 (304)
+|++||++|++||++|+
T Consensus 160 ~Al~DA~~~a~l~~~~~ 176 (176)
T cd06133 160 RGLDDARNIARILKRLL 176 (176)
T ss_pred CcHHHHHHHHHHHHHhC
Confidence 99999999999999873
No 16
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=99.95 E-value=1.7e-26 Score=198.74 Aligned_cols=131 Identities=24% Similarity=0.262 Sum_probs=113.9
Q ss_pred EEEEEEeecCCCC----ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHHHH
Q 048020 10 IVFFDVETTFPIR----HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTVFD 85 (304)
Q Consensus 10 ~VvfDlETTGl~~----~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f~~ 85 (304)
||+||+||||+++ +|||||||+++++. ...+.|+.+|+|.. +++++++++||||+++++++|++.+++.+|.+
T Consensus 1 ~v~~D~ETTGl~~~~~~~iieig~v~v~~~~-~~~~~~~~~v~P~~--~i~~~~~~ihGIt~e~l~~~~~~~~v~~~l~~ 77 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELINRR-LTGNTFHVYINPER--DIPEEAFKVHGITDEFLADKPKFAEIADEFLD 77 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEEEEEEEECCc-EeccEEEEEECCCC--CCCHHHHHHhCCCHHHHhcCCCHHHHHHHHHH
Confidence 6999999999853 89999999998763 23468999999999 89999999999999999999999999999999
Q ss_pred Hh----------------------c------CCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC---CCCCChHHH
Q 048020 86 IL----------------------Q------APKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG---QQTHRSLDD 134 (304)
Q Consensus 86 fl----------------------~------~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~---~~~HrAL~D 134 (304)
|+ . .+.+..|+||+.++++ ++|. ..++|++++++||++ .++|+|++|
T Consensus 78 ~l~~~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~-~~~~-~~~~L~~l~~~~~i~~~~~~~H~Al~D 155 (167)
T cd06131 78 FIRGAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARK-KFPG-KPNSLDALCKRFGIDNSHRTLHGALLD 155 (167)
T ss_pred HHCCCeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHH-HcCC-CCCCHHHHHHHCCCCCCCCCCCChHHH
Confidence 99 0 1134689999999995 4554 568999999999996 357999999
Q ss_pred HHHHHHHHHHH
Q 048020 135 VLMNLEVLKYC 145 (304)
Q Consensus 135 A~aTa~L~~~l 145 (304)
|++|++||.+|
T Consensus 156 a~~~a~l~~~l 166 (167)
T cd06131 156 AELLAEVYLEL 166 (167)
T ss_pred HHHHHHHHHHh
Confidence 99999999876
No 17
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=2.2e-26 Score=205.70 Aligned_cols=141 Identities=17% Similarity=0.199 Sum_probs=120.3
Q ss_pred CCCCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHH
Q 048020 5 QDRSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIAD 81 (304)
Q Consensus 5 ~~~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~ 81 (304)
+.+.+||+||+||||+++ +|||||+|+++++.....+.|+.+|+|.. +++++++++||||++||+++|++.+++.
T Consensus 26 ~~~~~~vviD~ETTGl~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~--~i~~~~~~ihGIt~~~l~~~~~~~~vl~ 103 (202)
T PRK09145 26 PPPDEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQ--SLSAESIKIHRLRHQDLEDGLSEEEALR 103 (202)
T ss_pred CCCCCEEEEEeECCCCCCCCCceEEEEEEEEECCEEeecCceEEEECCCC--CCCHhHhhhcCcCHHHHhcCCCHHHHHH
Confidence 355789999999999864 99999999999864333478999999998 8999999999999999999999999999
Q ss_pred HHHHHh-------------------------cCCCCCCceehHHHHHHHh---cC-CCCCCCHHHHHHHhCCC-CCCCCh
Q 048020 82 TVFDIL-------------------------QAPKPKGTIDSLNLLTERF---GR-RAGDMKMASLATYFGLG-QQTHRS 131 (304)
Q Consensus 82 ~f~~fl-------------------------~~~~~~~~IDTl~Lark~l---~p-~~~~~kL~~Lak~lGI~-~~~HrA 131 (304)
+|.+|+ ..+++.+++|+..++.... .| ..++++|++++++||++ ..+|+|
T Consensus 104 ~~~~~i~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~gi~~~~~H~A 183 (202)
T PRK09145 104 QLLAFIGNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILKHLDLPVLGRHDA 183 (202)
T ss_pred HHHHHHcCCeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHHHHcCCCCCCCCCc
Confidence 999998 2345678999988764321 22 24568999999999997 788999
Q ss_pred HHHHHHHHHHHHHHHH
Q 048020 132 LDDVLMNLEVLKYCAT 147 (304)
Q Consensus 132 L~DA~aTa~L~~~ll~ 147 (304)
++||++||+||.++.+
T Consensus 184 l~DA~ata~l~~~l~~ 199 (202)
T PRK09145 184 LNDAIMAALIFLRLRK 199 (202)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 9999999999998864
No 18
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.95 E-value=2e-26 Score=214.35 Aligned_cols=138 Identities=23% Similarity=0.343 Sum_probs=123.6
Q ss_pred CCCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHH
Q 048020 6 DRSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADT 82 (304)
Q Consensus 6 ~~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~ 82 (304)
.+..|||||+||||+++ +|||||||+++++ +++++|+++|+|. ++++.++++||||++|++++|++.+|+.+
T Consensus 66 ~~~~~vv~DiETTG~~~~~~~IIEIGAv~v~~g--~i~~~f~~~v~p~---~ip~~~~~itGIt~e~l~~ap~~~evl~~ 140 (257)
T PRK08517 66 KDQVFCFVDIETNGSKPKKHQIIEIGAVKVKNG--EIIDRFESFVKAK---EVPEYITELTGITYEDLENAPSLKEVLEE 140 (257)
T ss_pred CCCCEEEEEEeCCCCCCCCCeEEEEEEEEEECC--EEEEEEEEEECCC---CCChhhhhhcCcCHHHHcCCCCHHHHHHH
Confidence 46689999999999764 9999999999976 7889999999995 68999999999999999999999999999
Q ss_pred HHHHh-------------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChHHHHH
Q 048020 83 VFDIL-------------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG-QQTHRSLDDVL 136 (304)
Q Consensus 83 f~~fl-------------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~-~~~HrAL~DA~ 136 (304)
|.+|+ ..++.++++||+.++++ +.+ ..+++|++|+++||++ .++|||++||.
T Consensus 141 f~~fl~~~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~-~~~-~~~~~L~~L~~~lgi~~~~~HrAl~DA~ 218 (257)
T PRK08517 141 FRLFLGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKR-TIE-SPRYGLSFLKELLGIEIEVHHRAYADAL 218 (257)
T ss_pred HHHHHCCCeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHH-Hcc-CCCCCHHHHHHHcCcCCCCCCChHHHHH
Confidence 99999 23456789999999995 444 3679999999999997 79999999999
Q ss_pred HHHHHHHHHHHHhh
Q 048020 137 MNLEVLKYCATVLL 150 (304)
Q Consensus 137 aTa~L~~~ll~~l~ 150 (304)
+|++||.+++.++.
T Consensus 219 ata~ll~~ll~~~~ 232 (257)
T PRK08517 219 AAYEIFKICLLNLP 232 (257)
T ss_pred HHHHHHHHHHHHhH
Confidence 99999999998774
No 19
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.95 E-value=1.2e-26 Score=211.11 Aligned_cols=135 Identities=19% Similarity=0.145 Sum_probs=118.7
Q ss_pred EEEEEEeecCCCCceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHHHHH--h
Q 048020 10 IVFFDVETTFPIRHIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTVFDI--L 87 (304)
Q Consensus 10 ~VvfDlETTGl~~~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f~~f--l 87 (304)
++|||+||||++.+|||||+|++.++ ++.++|+++|+|+. +|+++++++||||++||+++|++.+++++|..- +
T Consensus 2 ~~vlD~ETTGl~~~IieIg~v~v~~~--~i~~~~~~lv~P~~--~i~~~~~~ihgIt~e~v~~ap~~~ev~~~~~~~~~l 77 (219)
T PRK07983 2 LRVIDTETCGLQGGIVEIASVDVIDG--KIVNPMSHLVRPDR--PISPQAMAIHRITEAMVADKPWIEDVIPHYYGSEWY 77 (219)
T ss_pred eEEEEEECCCCCCCCEEEEEEEEECC--EEEEEEEEEECcCC--CCCHHHhhcCCCCHHHHcCCCCHHHHHHHHcCCCEE
Confidence 89999999999878999999999976 78899999999999 999999999999999999999999999986431 1
Q ss_pred -----------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC------CCCCChHHHHHHHHHHHHHHHHHhh
Q 048020 88 -----------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG------QQTHRSLDDVLMNLEVLKYCATVLL 150 (304)
Q Consensus 88 -----------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~------~~~HrAL~DA~aTa~L~~~ll~~l~ 150 (304)
...+..+|+||++++|+ ++|+.+ ++|..|+++||+. .++|||++||++|++||.++++..+
T Consensus 78 VaHNa~FD~~~L~~~~~~~idTl~lar~-l~p~~~-~~l~~L~~~~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~~~~~ 155 (219)
T PRK07983 78 VAHNASFDRRVLPEMPGEWICTMKLARR-LWPGIK-YSNMALYKSRKLNVQTPPGLHHHRALYDCYITAALLIDIMNTSG 155 (219)
T ss_pred EEeCcHhhHHHHhCcCCCcEeHHHHHHH-HccCCC-CCHHHHHHHcCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHHHcC
Confidence 22345799999999994 678765 9999999999984 4699999999999999999987653
No 20
>PRK06722 exonuclease; Provisional
Probab=99.95 E-value=1.1e-26 Score=218.31 Aligned_cols=140 Identities=19% Similarity=0.351 Sum_probs=119.0
Q ss_pred CCCcEEEEEEeecCCC-----C-ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHH
Q 048020 6 DRSEIVFFDVETTFPI-----R-HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADI 79 (304)
Q Consensus 6 ~~~~~VvfDlETTGl~-----~-~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eV 79 (304)
|...|||||+||||.. . +|||||||++++|.++++++|++||+|.. +|+++++++||||++||++||+|.+|
T Consensus 3 ~~~~~vViD~ETT~~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~--~I~~~i~~LTGIT~emV~~AP~f~eV 80 (281)
T PRK06722 3 NATHFIVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGA--RLTRHTTKLTGITKKDLIGVEKFPQI 80 (281)
T ss_pred CCCEEEEEEeeCCCCCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCC--cCCHhHhhhcCCCHHHHcCCCCHHHH
Confidence 6689999999999731 2 99999999999877788999999999998 99999999999999999999999999
Q ss_pred HHHHHHHh------------------------c--CC--CCCCceehHHHHHHHhcCCC--CCCCHHHHHHHhCCC--CC
Q 048020 80 ADTVFDIL------------------------Q--AP--KPKGTIDSLNLLTERFGRRA--GDMKMASLATYFGLG--QQ 127 (304)
Q Consensus 80 l~~f~~fl------------------------~--~~--~~~~~IDTl~Lark~l~p~~--~~~kL~~Lak~lGI~--~~ 127 (304)
+.+|.+|+ + .+ ....++|+.++++.. ++.. ..++|++++++||++ ++
T Consensus 81 l~ef~~fig~~~lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~-~~~l~~~~~sL~~l~~~lgL~~~g~ 159 (281)
T PRK06722 81 IEKFIQFIGEDSIFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQA-YEELFEHTPSLQSAVEQLGLIWEGK 159 (281)
T ss_pred HHHHHHHHCCCcEEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHH-hhhhccCCCCHHHHHHHCCCCCCCC
Confidence 99999999 1 11 113468888877642 3332 347899999999997 57
Q ss_pred CCChHHHHHHHHHHHHHHHHH
Q 048020 128 THRSLDDVLMNLEVLKYCATV 148 (304)
Q Consensus 128 ~HrAL~DA~aTa~L~~~ll~~ 148 (304)
+|||++||++||+||.+|++.
T Consensus 160 ~HrAL~DA~~TA~L~l~l~~~ 180 (281)
T PRK06722 160 QHRALADAENTANILLKAYSE 180 (281)
T ss_pred CcCcHHHHHHHHHHHHHHhcc
Confidence 999999999999999999854
No 21
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=2.1e-26 Score=213.08 Aligned_cols=137 Identities=27% Similarity=0.345 Sum_probs=122.3
Q ss_pred CCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHH
Q 048020 7 RSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTV 83 (304)
Q Consensus 7 ~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f 83 (304)
+++||+||+||||++. +|||||+|++..+ .+.++|+.+|+|+. +|+++++++||||++||+++|+|.+++.+|
T Consensus 6 ~~~~v~~D~ETTGl~~~~d~IIEIa~v~v~~~--~~~~~~~~li~P~~--~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~ 81 (250)
T PRK06310 6 DTEFVCLDCETTGLDVKKDRIIEFAAIRFTFD--EVIDSVEFLINPER--VVSAESQRIHHISDAMLRDKPKIAEVFPQI 81 (250)
T ss_pred CCcEEEEEEeCCCCCCCCCeEEEEEEEEEECC--eEEEEEEEEECcCC--CCCHhhhhccCcCHHHHhCCCCHHHHHHHH
Confidence 4689999999999865 9999999999876 67889999999999 999999999999999999999999999999
Q ss_pred HHHh-------------------------cCC---CCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChHHH
Q 048020 84 FDIL-------------------------QAP---KPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG-QQTHRSLDD 134 (304)
Q Consensus 84 ~~fl-------------------------~~~---~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~-~~~HrAL~D 134 (304)
.+|+ +.+ ...++|||+.++++ + +...+++|..|+++||++ .++|||++|
T Consensus 82 ~~fl~~~~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~-~-~~~~~~~L~~l~~~~g~~~~~aH~Al~D 159 (250)
T PRK06310 82 KGFFKEGDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKE-Y-GDSPNNSLEALAVHFNVPYDGNHRAMKD 159 (250)
T ss_pred HHHhCCCCEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHh-c-ccCCCCCHHHHHHHCCCCCCCCcChHHH
Confidence 9998 111 23689999999994 4 455789999999999997 789999999
Q ss_pred HHHHHHHHHHHHHHh
Q 048020 135 VLMNLEVLKYCATVL 149 (304)
Q Consensus 135 A~aTa~L~~~ll~~l 149 (304)
|.+|++||.++++++
T Consensus 160 a~at~~vl~~l~~~~ 174 (250)
T PRK06310 160 VEINIKVFKHLCKRF 174 (250)
T ss_pred HHHHHHHHHHHHHhc
Confidence 999999999998765
No 22
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.94 E-value=1.9e-26 Score=219.79 Aligned_cols=140 Identities=22% Similarity=0.235 Sum_probs=122.5
Q ss_pred CCCCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHH
Q 048020 5 QDRSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIAD 81 (304)
Q Consensus 5 ~~~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~ 81 (304)
.+..+|||||+||||+++ +|||||+|+++.+ +++.++|+++|+|.. ++.++.+||||++||+++|+|.+++.
T Consensus 12 ~~~~~fvvlD~ETTGl~p~~d~IIeIgav~v~~~-g~i~~~~~~lv~P~~----~~~~~~IhGIt~e~l~~ap~f~ev~~ 86 (313)
T PRK06063 12 HYPRGWAVVDVETSGFRPGQARIISLAVLGLDAD-GNVEQSVVTLLNPGV----DPGPTHVHGLTAEMLEGQPQFADIAG 86 (313)
T ss_pred CCCCCEEEEEEECCCCCCCCCEEEEEEEEEEECC-ceeeeEEEEEECcCC----CCCCeecCCCCHHHHhCCCCHHHHHH
Confidence 466789999999999875 9999999999742 378899999999976 34568999999999999999999999
Q ss_pred HHHHHh------------------------cC-CCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChHHHH
Q 048020 82 TVFDIL------------------------QA-PKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG-QQTHRSLDDV 135 (304)
Q Consensus 82 ~f~~fl------------------------~~-~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~-~~~HrAL~DA 135 (304)
+|.+|+ .. ...+.++||+.++| .+++..++++|++||++||++ .++|||++||
T Consensus 87 ~l~~~l~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar-~~~~~~~~~kL~~l~~~~gi~~~~~H~Al~DA 165 (313)
T PRK06063 87 EVAELLRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELAR-RLGLGLPNLRLETLAAHWGVPQQRPHDALDDA 165 (313)
T ss_pred HHHHHcCCCEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHH-HhccCCCCCCHHHHHHHcCCCCCCCCCcHHHH
Confidence 999999 11 12357999999999 466778899999999999997 8899999999
Q ss_pred HHHHHHHHHHHHHhh
Q 048020 136 LMNLEVLKYCATVLL 150 (304)
Q Consensus 136 ~aTa~L~~~ll~~l~ 150 (304)
++|++||.++++++.
T Consensus 166 ~ata~l~~~ll~~~~ 180 (313)
T PRK06063 166 RVLAGILRPSLERAR 180 (313)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999998875
No 23
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=3.2e-26 Score=209.43 Aligned_cols=135 Identities=26% Similarity=0.369 Sum_probs=119.5
Q ss_pred CcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHHH
Q 048020 8 SEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTVF 84 (304)
Q Consensus 8 ~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f~ 84 (304)
.++||||+||||++. +|||||++. . ...+.|+.+|+|+. +|+++++++||||++||+++|+|.+++++|.
T Consensus 2 ~~~vv~D~ETTGl~~~~d~IIeig~v~--~---~~~~~f~~lv~P~~--~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~ 74 (232)
T PRK06309 2 PALIFYDTETTGTQIDKDRIIEIAAYN--G---VTSESFQTLVNPEI--PIPAEASKIHGITTDEVADAPKFPEAYQKFI 74 (232)
T ss_pred CcEEEEEeeCCCCCCCCCEEEEEEEEc--C---ccccEEEEEeCCCC--CCChhHHhhcCCCHHHHhCCCCHHHHHHHHH
Confidence 469999999999864 999999963 2 34578999999999 9999999999999999999999999999999
Q ss_pred HHh---------------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChHHHHH
Q 048020 85 DIL---------------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG-QQTHRSLDDVL 136 (304)
Q Consensus 85 ~fl---------------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~-~~~HrAL~DA~ 136 (304)
+|+ ......+++||+.+++ .+.|...+++|..++++||++ .++|||++||.
T Consensus 75 ~fi~~~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~-~~~~~~~~~~L~~l~~~~~~~~~~aH~Al~Da~ 153 (232)
T PRK06309 75 EFCGTDNILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQ-KYRPDLPKHNLQYLRQVYGFEENQAHRALDDVI 153 (232)
T ss_pred HHHcCCCEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHH-HHcCCCCCCCHHHHHHHcCCCCCCCCCcHHHHH
Confidence 998 1112368999999999 467888889999999999997 88999999999
Q ss_pred HHHHHHHHHHHHhh
Q 048020 137 MNLEVLKYCATVLL 150 (304)
Q Consensus 137 aTa~L~~~ll~~l~ 150 (304)
+|++||.++++++.
T Consensus 154 ~t~~vl~~l~~~~~ 167 (232)
T PRK06309 154 TLHRVFSALVGDLS 167 (232)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999998764
No 24
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.94 E-value=4.5e-26 Score=208.61 Aligned_cols=141 Identities=20% Similarity=0.194 Sum_probs=119.4
Q ss_pred CCCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhC-CCCHHHHHH
Q 048020 6 DRSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFS-APTFADIAD 81 (304)
Q Consensus 6 ~~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~-ap~f~eVl~ 81 (304)
.+.+||+||+||||+++ +|||||+|++++. +.++++|+++|+|.. +|+++++++||||++|+++ ++++.+++.
T Consensus 4 ~~~~~vv~D~ETTGl~p~~d~Iieig~v~v~~~-g~~~~~~~~lv~P~~--~i~~~a~~IhGIt~e~l~~~g~~~~~vl~ 80 (232)
T PRK07942 4 HPGPLAAFDLETTGVDPETARIVTAALVVVDAD-GEVVESREWLADPGV--EIPEEASAVHGITTEYARAHGRPAAEVLA 80 (232)
T ss_pred ccCcEEEEEeccCCCCCCCCeeEEEEEEEEeCC-CccccceEEEECCCC--CCCHHHHHHhCCCHHHHHhhCCCHHHHHH
Confidence 46789999999999875 9999999999851 267889999999998 9999999999999999986 778888888
Q ss_pred HHHHHh-----------------------------c--CCCCCCceehHHHHHHHhcCC-CCCCCHHHHHHHhCCC-CCC
Q 048020 82 TVFDIL-----------------------------Q--APKPKGTIDSLNLLTERFGRR-AGDMKMASLATYFGLG-QQT 128 (304)
Q Consensus 82 ~f~~fl-----------------------------~--~~~~~~~IDTl~Lark~l~p~-~~~~kL~~Lak~lGI~-~~~ 128 (304)
+|.+++ + .+...+++||+.++++ +.+. ..+++|++||++||++ .++
T Consensus 81 e~~~~l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~-~~~~~~~~~~L~~l~~~~gi~~~~a 159 (232)
T PRK07942 81 EIADALREAWARGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKA-VDRYRKGKRTLTALCEHYGVRLDNA 159 (232)
T ss_pred HHHHHHHHHhhcCCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhh-hhcccCCCCCHHHHHHHcCCCCCCC
Confidence 887764 1 1124679999999984 3342 3578999999999997 789
Q ss_pred CChHHHHHHHHHHHHHHHHHhh
Q 048020 129 HRSLDDVLMNLEVLKYCATVLL 150 (304)
Q Consensus 129 HrAL~DA~aTa~L~~~ll~~l~ 150 (304)
|||++||.+|++||.++.+++.
T Consensus 160 H~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 160 HEATADALAAARVAWALARRFP 181 (232)
T ss_pred CChHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999988764
No 25
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=4.5e-26 Score=240.91 Aligned_cols=143 Identities=18% Similarity=0.280 Sum_probs=130.7
Q ss_pred CCCCCCcEEEEEEeecCCCC--ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHH
Q 048020 3 PTQDRSEIVFFDVETTFPIR--HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIA 80 (304)
Q Consensus 3 ~~~~~~~~VvfDlETTGl~~--~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl 80 (304)
++.+..+|||||+||||+++ +|||||||++++| +++++|+++|||.. +|+++++++||||++||+++|+|++|+
T Consensus 2 ~~~~~~~~vvvD~ETTGl~~~d~IIeIgaV~v~~g--~i~~~f~~lv~P~~--~i~~~~~~ltGIt~e~l~~ap~~~ev~ 77 (820)
T PRK07246 2 TQKKLRKYAVVDLEATGAGPNASIIQVGIVIIEGG--EIIDSYTTDVNPHE--PLDEHIKHLTGITDQQLAQAPDFSQVA 77 (820)
T ss_pred ccccCCCEEEEEEecCCcCCCCeEEEEEEEEEECC--EEEEEEEEEeCcCC--CCCHhHhhcCCCCHHHHhcCCCHHHHH
Confidence 45567899999999999865 9999999999987 78999999999998 999999999999999999999999999
Q ss_pred HHHHHHh------------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChHHHH
Q 048020 81 DTVFDIL------------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG-QQTHRSLDDV 135 (304)
Q Consensus 81 ~~f~~fl------------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~-~~~HrAL~DA 135 (304)
++|.+|+ +.++.++++||+.+++ .++|...+++|++||++||++ .++|||++||
T Consensus 78 ~~~~~~l~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~-~~~p~~~~~~L~~L~~~lgl~~~~~H~Al~DA 156 (820)
T PRK07246 78 RHIYDLIEDCIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQ-VFFPTLEKYSLSHLSRELNIDLADAHTAIADA 156 (820)
T ss_pred HHHHHHhCCCEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHH-HHhCCCCCCCHHHHHHHcCCCCCCCCCHHHHH
Confidence 9999999 2334578999999999 577888899999999999997 7899999999
Q ss_pred HHHHHHHHHHHHHhh
Q 048020 136 LMNLEVLKYCATVLL 150 (304)
Q Consensus 136 ~aTa~L~~~ll~~l~ 150 (304)
++|++||.++++++.
T Consensus 157 ~ata~L~~~l~~~l~ 171 (820)
T PRK07246 157 RATAELFLKLLQKIE 171 (820)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999999998874
No 26
>PRK07883 hypothetical protein; Validated
Probab=99.93 E-value=3.8e-25 Score=225.20 Aligned_cols=143 Identities=25% Similarity=0.292 Sum_probs=127.8
Q ss_pred CCCCCCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHH
Q 048020 3 PTQDRSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADI 79 (304)
Q Consensus 3 ~~~~~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eV 79 (304)
....+..|||||+||||+++ +|||||||+++++ .++++|+.+|+|.. +|+++++++||||++||+++|+|.++
T Consensus 10 ~~~~~~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~g--~iv~~f~~lV~P~~--~i~~~~~~itGIt~e~l~~ap~~~ev 85 (557)
T PRK07883 10 TPLRDVTFVVVDLETTGGSPAGDAITEIGAVKVRGG--EVLGEFATLVNPGR--PIPPFITVLTGITTAMVAGAPPIEEV 85 (557)
T ss_pred CCCcCCCEEEEEEecCCCCCCCCeEEEEEEEEEECC--EEEEEEEEEECCCC--CCChhHHhhcCCCHHHHhCCCCHHHH
Confidence 33456799999999999765 9999999999976 78899999999998 99999999999999999999999999
Q ss_pred HHHHHHHh------------------------c-CCCCCCceehHHHHHHHhcC--CCCCCCHHHHHHHhCCC-CCCCCh
Q 048020 80 ADTVFDIL------------------------Q-APKPKGTIDSLNLLTERFGR--RAGDMKMASLATYFGLG-QQTHRS 131 (304)
Q Consensus 80 l~~f~~fl------------------------~-~~~~~~~IDTl~Lark~l~p--~~~~~kL~~Lak~lGI~-~~~HrA 131 (304)
+.+|.+|+ + .+....++||+.++++ +++ ...+++|++|+++||++ .++|||
T Consensus 86 l~~f~~fl~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~-l~~~~~~~~~~L~~L~~~~gi~~~~~H~A 164 (557)
T PRK07883 86 LPAFLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARR-VLPRDEAPNVRLSTLARLFGATTTPTHRA 164 (557)
T ss_pred HHHHHHHhcCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHH-hcccCCCCCCCHHHHHHHCCcccCCCCCH
Confidence 99999999 1 2224689999999995 445 66789999999999997 889999
Q ss_pred HHHHHHHHHHHHHHHHHhh
Q 048020 132 LDDVLMNLEVLKYCATVLL 150 (304)
Q Consensus 132 L~DA~aTa~L~~~ll~~l~ 150 (304)
++||.+|++||.++++++.
T Consensus 165 l~DA~ata~l~~~l~~~~~ 183 (557)
T PRK07883 165 LDDARATVDVLHGLIERLG 183 (557)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999885
No 27
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=2.7e-25 Score=237.73 Aligned_cols=140 Identities=24% Similarity=0.318 Sum_probs=128.7
Q ss_pred CCCcEEEEEEeecCCCC----ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHH
Q 048020 6 DRSEIVFFDVETTFPIR----HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIAD 81 (304)
Q Consensus 6 ~~~~~VvfDlETTGl~~----~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~ 81 (304)
|.++|||||+||||.++ +|||||||+++++ +++++|+++|||.. +||++++++||||++||+++|+|.++++
T Consensus 1 ~~~~~vvvD~ETTG~~p~~~d~IIeigav~v~~~--~i~~~f~~~v~P~~--~i~~~~~~ltGIt~~~l~~ap~f~ev~~ 76 (928)
T PRK08074 1 MSKRFVVVDLETTGNSPKKGDKIIQIAAVVVEDG--EILERFSSFVNPER--PIPPFITELTGISEEMVKQAPLFEDVAP 76 (928)
T ss_pred CCCCEEEEEEeCCCCCCCCCCcEEEEEEEEEECC--EEEEEEEEEECcCC--CCCHHHhhcCCCCHHHHhcCCCHHHHHH
Confidence 46789999999999642 8999999999977 78999999999998 9999999999999999999999999999
Q ss_pred HHHHHh-------------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChHHHH
Q 048020 82 TVFDIL-------------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG-QQTHRSLDDV 135 (304)
Q Consensus 82 ~f~~fl-------------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~-~~~HrAL~DA 135 (304)
+|.+|+ ..++.+++|||+.+++ .++|...+++|.+|+++||++ .++|||++||
T Consensus 77 ~l~~~l~~~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~-~~~p~~~~~~L~~l~~~l~i~~~~~H~Al~DA 155 (928)
T PRK08074 77 EIVELLEGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELAR-ILLPTAESYKLRDLSEELGLEHDQPHRADSDA 155 (928)
T ss_pred HHHHHhCCCeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHH-HhcCCCCCCCHHHHHHhCCCCCCCCCChHHHH
Confidence 999999 2345679999999999 678888999999999999997 8999999999
Q ss_pred HHHHHHHHHHHHHhh
Q 048020 136 LMNLEVLKYCATVLL 150 (304)
Q Consensus 136 ~aTa~L~~~ll~~l~ 150 (304)
++|++||.+|++++.
T Consensus 156 ~ata~l~~~l~~~~~ 170 (928)
T PRK08074 156 EVTAELFLQLLNKLE 170 (928)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999998874
No 28
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=99.93 E-value=1.9e-25 Score=196.29 Aligned_cols=127 Identities=25% Similarity=0.286 Sum_probs=104.0
Q ss_pred EEEEEEeecCCC-C---ceEEEEEEEEeCCce-----------eeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCC
Q 048020 10 IVFFDVETTFPI-R---HIWEFGAILVCPRKL-----------EELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAP 74 (304)
Q Consensus 10 ~VvfDlETTGl~-~---~IIEIGAV~v~~g~~-----------~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap 74 (304)
|||||+||||++ . +|||||||++.++.. +++++|+++|||+. +|++.++++||||++|+.++|
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~--~I~~~a~~IhGIt~e~l~~~~ 78 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGR--AISPGASEITGLSNDLLEHKA 78 (177)
T ss_pred CeEEeeecCCCCCCCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCC--cCChhHHHHhCcCHHHHhcCC
Confidence 799999999987 2 999999999987531 25679999999998 999999999999999999999
Q ss_pred CHHH-HHHHHHHHh-----------------------------c--CCCCCCceehHHHHHHHhcCCCCCCCHHHHHHH-
Q 048020 75 TFAD-IADTVFDIL-----------------------------Q--APKPKGTIDSLNLLTERFGRRAGDMKMASLATY- 121 (304)
Q Consensus 75 ~f~e-Vl~~f~~fl-----------------------------~--~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~- 121 (304)
+|.+ +++.|.+|+ + .+....++||+.++|+ +.+ +|+.|+++
T Consensus 79 ~~~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~-~~~-----~L~~l~~~~ 152 (177)
T cd06136 79 PFDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRE-LDQ-----SLGSLYKRL 152 (177)
T ss_pred CccHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhh-hHh-----hHHHHHHHH
Confidence 8763 444444443 1 1123567999999995 443 89999985
Q ss_pred hCCC-CCCCChHHHHHHHHHHHHH
Q 048020 122 FGLG-QQTHRSLDDVLMNLEVLKY 144 (304)
Q Consensus 122 lGI~-~~~HrAL~DA~aTa~L~~~ 144 (304)
||++ .++|||++||.+|++||.+
T Consensus 153 ~~~~~~~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 153 FGQEPKNSHTAEGDVLALLKCALH 176 (177)
T ss_pred hCCCcccccchHHHHHHHHHHHhh
Confidence 8997 8899999999999999975
No 29
>PRK05168 ribonuclease T; Provisional
Probab=99.93 E-value=1e-24 Score=197.02 Aligned_cols=140 Identities=19% Similarity=0.129 Sum_probs=115.1
Q ss_pred CCcEEEEEEeecCCCC---ceEEEEEEEEeC---CceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHH-HhCCCCHHHH
Q 048020 7 RSEIVFFDVETTFPIR---HIWEFGAILVCP---RKLEELDKYTTLVRPADPSLVSNLCARRNDITPED-VFSAPTFADI 79 (304)
Q Consensus 7 ~~~~VvfDlETTGl~~---~IIEIGAV~v~~---g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~-L~~ap~f~eV 79 (304)
+..+||||+||||+++ +|||||||+++. |...+.++|+++|+|....+|+++++++||||+++ +++++++.++
T Consensus 16 ~~~~vv~D~ETTGl~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~~~~~~~~ 95 (211)
T PRK05168 16 GFLPVVIDVETAGFNAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAVSEKEA 95 (211)
T ss_pred CCceEEEEeeCCCCCCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhcCCChHHH
Confidence 4578999999999865 999999999973 32335689999999953338999999999999986 8899999888
Q ss_pred HHHHHHHh---------------------------------c---CCC-CCCceehHHHHHHHhcCCCCCCCHHHHHHHh
Q 048020 80 ADTVFDIL---------------------------------Q---APK-PKGTIDSLNLLTERFGRRAGDMKMASLATYF 122 (304)
Q Consensus 80 l~~f~~fl---------------------------------~---~~~-~~~~IDTl~Lark~l~p~~~~~kL~~Lak~l 122 (304)
+.+|.+|+ + .++ +.+++||+.++|+ +++ .++|+++|++|
T Consensus 96 l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~-~~~---~~~L~~l~~~~ 171 (211)
T PRK05168 96 LHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGL-ALG---QTVLAKACQAA 171 (211)
T ss_pred HHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHH-HcC---CCCHHHHHHHC
Confidence 88877753 1 111 2368999999994 444 36899999999
Q ss_pred CCC---CCCCChHHHHHHHHHHHHHHHHHhh
Q 048020 123 GLG---QQTHRSLDDVLMNLEVLKYCATVLL 150 (304)
Q Consensus 123 GI~---~~~HrAL~DA~aTa~L~~~ll~~l~ 150 (304)
|++ ..+|||++||++|++||.++++++.
T Consensus 172 gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~ 202 (211)
T PRK05168 172 GIEFDNKEAHSALYDTEKTAELFCEIVNRWK 202 (211)
T ss_pred CCCCCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 996 4689999999999999999999885
No 30
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=99.92 E-value=2.5e-24 Score=192.91 Aligned_cols=141 Identities=18% Similarity=0.078 Sum_probs=114.1
Q ss_pred CCCcEEEEEEeecCCCC---ceEEEEEEEEeC---CceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHH-HHhCCCCHHH
Q 048020 6 DRSEIVFFDVETTFPIR---HIWEFGAILVCP---RKLEELDKYTTLVRPADPSLVSNLCARRNDITPE-DVFSAPTFAD 78 (304)
Q Consensus 6 ~~~~~VvfDlETTGl~~---~IIEIGAV~v~~---g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e-~L~~ap~f~e 78 (304)
....+||||+||||++. +|||||||++.. |.....++|+++|+|....+|+++++++||||++ |+++++++.+
T Consensus 6 ~~~~~vv~D~ETTGl~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~~~~ 85 (200)
T TIGR01298 6 RGYLPVVVDVETGGFNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVSEYE 85 (200)
T ss_pred cCCeeEEEEeeCCCCCCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcchHH
Confidence 45689999999999875 999999999973 3222246899999985333899999999999976 7999999888
Q ss_pred HHHHHHHHh---------------------------------cC---CC-CCCceehHHHHHHHhcCCCCCCCHHHHHHH
Q 048020 79 IADTVFDIL---------------------------------QA---PK-PKGTIDSLNLLTERFGRRAGDMKMASLATY 121 (304)
Q Consensus 79 Vl~~f~~fl---------------------------------~~---~~-~~~~IDTl~Lark~l~p~~~~~kL~~Lak~ 121 (304)
++.+|.+|+ +. ++ +..++||+.++++ ++| .++|+.+|++
T Consensus 86 ~~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~-~~~---~~~L~~l~~~ 161 (200)
T TIGR01298 86 ALHEIFKVVRKAMKASGCQRAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGL-AYG---QTVLAKACQA 161 (200)
T ss_pred HHHHHHHHHHHHHHhcccCCCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHH-HcC---cccHHHHHHH
Confidence 888776653 11 11 2458999999994 444 4689999999
Q ss_pred hCCC---CCCCChHHHHHHHHHHHHHHHHHhh
Q 048020 122 FGLG---QQTHRSLDDVLMNLEVLKYCATVLL 150 (304)
Q Consensus 122 lGI~---~~~HrAL~DA~aTa~L~~~ll~~l~ 150 (304)
||++ .++|||++||.+|++||.++++++.
T Consensus 162 ~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~ 193 (200)
T TIGR01298 162 AGXDFDSTQAHSALYDTEKTAELFCEIVNRWK 193 (200)
T ss_pred cCCCccccchhhhHHhHHHHHHHHHHHHHHHH
Confidence 9996 4799999999999999999998874
No 31
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=99.92 E-value=2.2e-24 Score=228.92 Aligned_cols=137 Identities=25% Similarity=0.368 Sum_probs=126.1
Q ss_pred cEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHHHH
Q 048020 9 EIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTVFD 85 (304)
Q Consensus 9 ~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f~~ 85 (304)
+|||||+||||+++ +|||||+|++++| +++++|+++|+|.. +|+++++++||||++||+++|+|.+++.+|.+
T Consensus 1 ~~vvvD~ETTG~~~~~~~IIeig~v~v~~~--~i~~~f~~~v~P~~--~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l~~ 76 (850)
T TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVEDG--EIVDTFHTDVNPNE--PIPPFIQELTGISDNMLQQAPYFSQVAQEIYD 76 (850)
T ss_pred CEEEEEEECCCCCCCCCeEEEEEEEEEECC--EEEEEEEEEeCCCC--CCChhhhhhcCcCHHHHhCCCCHHHHHHHHHH
Confidence 59999999999864 9999999999876 78899999999998 99999999999999999999999999999999
Q ss_pred Hh-------------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChHHHHHHHH
Q 048020 86 IL-------------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG-QQTHRSLDDVLMNL 139 (304)
Q Consensus 86 fl-------------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~-~~~HrAL~DA~aTa 139 (304)
|+ ..+++++++||+.+++ .++|...+++|.+|+++||++ .++|||++||.+|+
T Consensus 77 ~l~~~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~-~~~p~~~~~~L~~l~~~~gi~~~~~H~Al~DA~ata 155 (850)
T TIGR01407 77 LLEDGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQ-IFFPTEESYQLSELSEALGLTHENPHRADSDAQATA 155 (850)
T ss_pred HhCCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHH-HhcCCCCCCCHHHHHHHCCCCCCCCCChHHHHHHHH
Confidence 99 2335789999999999 677888899999999999997 88999999999999
Q ss_pred HHHHHHHHHhh
Q 048020 140 EVLKYCATVLL 150 (304)
Q Consensus 140 ~L~~~ll~~l~ 150 (304)
+||.++++++.
T Consensus 156 ~l~~~l~~~~~ 166 (850)
T TIGR01407 156 ELLLLLFEKME 166 (850)
T ss_pred HHHHHHHHHHH
Confidence 99999988764
No 32
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=99.92 E-value=3.2e-24 Score=190.50 Aligned_cols=138 Identities=18% Similarity=0.121 Sum_probs=108.8
Q ss_pred CcEEEEEEeecCCCC---ceEEEEEEEEeC---CceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHH-HhCCCCHHHHH
Q 048020 8 SEIVFFDVETTFPIR---HIWEFGAILVCP---RKLEELDKYTTLVRPADPSLVSNLCARRNDITPED-VFSAPTFADIA 80 (304)
Q Consensus 8 ~~~VvfDlETTGl~~---~IIEIGAV~v~~---g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~-L~~ap~f~eVl 80 (304)
-.+||||+||||+++ +|||||||++++ |...+.++|+++|+|....+|++.++++||||+++ +++++...+++
T Consensus 5 ~~~vv~D~ETTGl~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~~~~ 84 (189)
T cd06134 5 FLPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEKEAL 84 (189)
T ss_pred ceeEEEEecCCCCCCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchHHHH
Confidence 468999999999865 999999999974 22235789999999943228999999999999986 66777666666
Q ss_pred HHHHHHh---------------------------------cC---CC-CCCceehHHHHHHHhcCCCCCCCHHHHHHHhC
Q 048020 81 DTVFDIL---------------------------------QA---PK-PKGTIDSLNLLTERFGRRAGDMKMASLATYFG 123 (304)
Q Consensus 81 ~~f~~fl---------------------------------~~---~~-~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lG 123 (304)
.+|.+|+ +. ++ +.+++||+.+++. +++ .++|+++|++||
T Consensus 85 ~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~-~~~---~~~L~~l~~~~g 160 (189)
T cd06134 85 KEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGL-AYG---QTVLAKACQAAG 160 (189)
T ss_pred HHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHH-HhC---CCcHHHHHHHCC
Confidence 5555432 11 22 3468999999994 444 468999999999
Q ss_pred CC---CCCCChHHHHHHHHHHHHHHHHHh
Q 048020 124 LG---QQTHRSLDDVLMNLEVLKYCATVL 149 (304)
Q Consensus 124 I~---~~~HrAL~DA~aTa~L~~~ll~~l 149 (304)
++ .++|+|++||++|++||.+|++++
T Consensus 161 i~~~~~~~H~Al~DA~ata~lf~~l~~~~ 189 (189)
T cd06134 161 IEFDNKEAHSALYDTQKTAELFCKIVNRW 189 (189)
T ss_pred CCCCCCCCcChHHHHHHHHHHHHHHHHhC
Confidence 96 478999999999999999998763
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=99.91 E-value=1.1e-24 Score=188.68 Aligned_cols=126 Identities=24% Similarity=0.290 Sum_probs=107.0
Q ss_pred EEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCC-------HHHHH
Q 048020 11 VFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPT-------FADIA 80 (304)
Q Consensus 11 VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~-------f~eVl 80 (304)
|+||+||||+++ +|||||||++.+| +++ |++||+|.. +|+++++++||||++||+++|+ |++++
T Consensus 1 v~lD~EttGl~~~~d~ii~Ig~V~v~~g--~i~--~~~~v~P~~--~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~~~~ 74 (161)
T cd06137 1 VALDCEMVGLADGDSEVVRISAVDVLTG--EVL--IDSLVRPSV--RVTDWRTRFSGVTPADLEEAAKAGKTIFGWEAAR 74 (161)
T ss_pred CEEEeeeeeEcCCCCEEEEEEEEEcCCC--eEE--EeccccCCC--CCCccceeccCCCHHHHhhhhhcCCccccHHHHH
Confidence 689999999865 9999999999766 454 999999998 9999999999999999999875 45899
Q ss_pred HHHHHHh-----------------cCCCCCCceehHHHHHHHhcCCC---CCCCHHHHHHH-hCCC----CCCCChHHHH
Q 048020 81 DTVFDIL-----------------QAPKPKGTIDSLNLLTERFGRRA---GDMKMASLATY-FGLG----QQTHRSLDDV 135 (304)
Q Consensus 81 ~~f~~fl-----------------~~~~~~~~IDTl~Lark~l~p~~---~~~kL~~Lak~-lGI~----~~~HrAL~DA 135 (304)
++|.+|+ ......+++||+.++++ +.|.. ++++|++||++ ||++ ..+|+|++||
T Consensus 75 ~~~~~~i~~~~vlVgHn~~fD~~fL~~~~~~~iDT~~l~~~-~~~~~~~~~~~~L~~L~~~~~~~~~~~~~~~H~A~~DA 153 (161)
T cd06137 75 AALWKFIDPDTILVGHSLQNDLDALRMIHTRVVDTAILTRE-AVKGPLAKRQWSLRTLCRDFLGLKIQGGGEGHDSLEDA 153 (161)
T ss_pred HHHHHhcCCCcEEEeccHHHHHHHHhCcCCCeeEehhhhhh-ccCCCcCCCCccHHHHHHHHCCchhcCCCCCCCcHHHH
Confidence 9999999 11124689999999994 55665 68999999987 6875 3589999999
Q ss_pred HHHHHHHH
Q 048020 136 LMNLEVLK 143 (304)
Q Consensus 136 ~aTa~L~~ 143 (304)
++|++||.
T Consensus 154 ~at~~l~~ 161 (161)
T cd06137 154 LAAREVVL 161 (161)
T ss_pred HHHHHHhC
Confidence 99999973
No 34
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=99.91 E-value=6e-24 Score=187.44 Aligned_cols=131 Identities=20% Similarity=0.281 Sum_probs=108.4
Q ss_pred EEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhC-CCCHHHHHHHHHHH
Q 048020 11 VFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFS-APTFADIADTVFDI 86 (304)
Q Consensus 11 VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~-ap~f~eVl~~f~~f 86 (304)
++||+||||++. +|||||+|+++++. .++++|+.+|+|.....+++.+.++||||++||.+ ++++.+++.+|.+|
T Consensus 1 ~~~D~ETTGl~~~~d~Iieig~v~v~~~~-~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~~~~ 79 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQFAAIRTDENF-NEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKIHRL 79 (183)
T ss_pred CEEEeecCCCCCCCCceEEEEEEEECCCC-CCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHHHHH
Confidence 589999999875 99999999998642 45589999999986436788999999999999999 89999999999998
Q ss_pred h----------------------------cCCC------CCCceehHHHHHHHh--cC----------CCCCCCHHHHHH
Q 048020 87 L----------------------------QAPK------PKGTIDSLNLLTERF--GR----------RAGDMKMASLAT 120 (304)
Q Consensus 87 l----------------------------~~~~------~~~~IDTl~Lark~l--~p----------~~~~~kL~~Lak 120 (304)
+ ..++ .+.++||+.+++... .| +.++++|++|++
T Consensus 80 ~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L~~l~~ 159 (183)
T cd06138 80 FNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKLEDLAQ 159 (183)
T ss_pred HccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhHHHHHH
Confidence 7 0111 234589999888422 23 346799999999
Q ss_pred HhCCC-CCCCChHHHHHHHHHHH
Q 048020 121 YFGLG-QQTHRSLDDVLMNLEVL 142 (304)
Q Consensus 121 ~lGI~-~~~HrAL~DA~aTa~L~ 142 (304)
+||++ .++|||++||++|++|+
T Consensus 160 ~~gi~~~~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 160 ANGIEHSNAHDALSDVEATIALA 182 (183)
T ss_pred HCCCCccccccHHHHHHHHHHHh
Confidence 99997 78999999999999886
No 35
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.91 E-value=1.7e-23 Score=211.75 Aligned_cols=143 Identities=22% Similarity=0.232 Sum_probs=118.0
Q ss_pred CCcEEEEEEeecCCCC------ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHH
Q 048020 7 RSEIVFFDVETTFPIR------HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIA 80 (304)
Q Consensus 7 ~~~~VvfDlETTGl~~------~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl 80 (304)
-..|||||+||||++. +|||||||+++..+++++++|++||+|...++|+++++++||||++||++||+|.+|+
T Consensus 55 ~d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap~F~eVl 134 (582)
T PTZ00315 55 FDAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFPVVY 134 (582)
T ss_pred CCeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCCCHHHHH
Confidence 3689999999999642 9999999999743448899999999999866799999999999999999999999999
Q ss_pred HHHHHHhc--------------------------------------CCC-CCCceehH-HHHHHHhcC-----------C
Q 048020 81 DTVFDILQ--------------------------------------APK-PKGTIDSL-NLLTERFGR-----------R 109 (304)
Q Consensus 81 ~~f~~fl~--------------------------------------~~~-~~~~IDTl-~Lark~l~p-----------~ 109 (304)
.+|.+|+. .++ ...|+|.. .+++ +++| .
T Consensus 135 ~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar-~l~p~~~~~~~~~~~~ 213 (582)
T PTZ00315 135 CEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQ-LGFGNGSGCGGGATPP 213 (582)
T ss_pred HHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHH-HhCccccccccccccc
Confidence 99999960 011 12455532 3555 5555 3
Q ss_pred CCCCCHHHHHHHhCCC--CCCCChHHHHHHHHHHHHHHHHHhh
Q 048020 110 AGDMKMASLATYFGLG--QQTHRSLDDVLMNLEVLKYCATVLL 150 (304)
Q Consensus 110 ~~~~kL~~Lak~lGI~--~~~HrAL~DA~aTa~L~~~ll~~l~ 150 (304)
.+.++|.++++.+|++ +.+|||++||++||+||.+|+++..
T Consensus 214 ~~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~~g~ 256 (582)
T PTZ00315 214 LGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRGL 256 (582)
T ss_pred cCCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHcCC
Confidence 4668999999999996 6799999999999999999998764
No 36
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.91 E-value=2.1e-23 Score=201.50 Aligned_cols=137 Identities=18% Similarity=0.315 Sum_probs=116.2
Q ss_pred CCCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHH
Q 048020 6 DRSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADT 82 (304)
Q Consensus 6 ~~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~ 82 (304)
.+..|||||+||||+++ +|||||||++..+ ++++++|+++|||.. .+.+ ..+||||++||+++|.|.+++++
T Consensus 44 ~~~~fVvlDiETTGLdp~~drIIeIgAV~i~~~-g~ive~f~tLVnP~~--~~~p--~~LHGIT~e~La~AP~f~eVl~e 118 (377)
T PRK05601 44 EAAPFVAVSIQTSGIHPSTSRLITIDAVTLTAD-GEEVEHFHAVLNPGE--DPGP--FHLHGLSAEEFAQGKRFSQILKP 118 (377)
T ss_pred CCCCEEEEEEECCCCCCCCCeEEEEEEEEEEcC-CEEEEEEEEEECcCC--CCCC--ccccCCCHHHHhcCCCHHHHHHH
Confidence 34689999999999875 9999999999842 278899999999998 4443 37999999999999999999999
Q ss_pred HHHHh----------------------c------------------------------CCCCCCceehHHHHHHHhcCCC
Q 048020 83 VFDIL----------------------Q------------------------------APKPKGTIDSLNLLTERFGRRA 110 (304)
Q Consensus 83 f~~fl----------------------~------------------------------~~~~~~~IDTl~Lark~l~p~~ 110 (304)
|.+|+ . .+.+++++||+.++| .++|.+
T Consensus 119 l~~fL~g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LAR-rl~p~l 197 (377)
T PRK05601 119 LDRLIDGRTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATAR-RQGVAL 197 (377)
T ss_pred HHHHhCCCEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHH-HHcCCC
Confidence 99999 0 134567999999999 567889
Q ss_pred CCCCHHHHHHHhCCC-----------CCCCChH--HHHHHHHHHHHHHHHH
Q 048020 111 GDMKMASLATYFGLG-----------QQTHRSL--DDVLMNLEVLKYCATV 148 (304)
Q Consensus 111 ~~~kL~~Lak~lGI~-----------~~~HrAL--~DA~aTa~L~~~ll~~ 148 (304)
++|+|.+||++||++ ...|+|+ +||+.+++||.++.++
T Consensus 198 ~~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~~~~ 248 (377)
T PRK05601 198 DDIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFALRAS 248 (377)
T ss_pred CCCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHhhcc
Confidence 999999999999994 2458888 6999999999887443
No 37
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=99.90 E-value=3.7e-23 Score=172.10 Aligned_cols=129 Identities=31% Similarity=0.440 Sum_probs=116.2
Q ss_pred EEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHHHHHh
Q 048020 11 VFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTVFDIL 87 (304)
Q Consensus 11 VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f~~fl 87 (304)
|+||+||||+++ +|||||+|+++++ +++++.|+.+|+|+. .+++.++++|||+++++.+++++.+++.+|.+|+
T Consensus 1 v~~D~Ettg~~~~~~~iiei~~v~~~~~-~~~~~~~~~~i~p~~--~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~l 77 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGG-IEIVERFETLVNPGR--PIPPEATAIHGITDEMLADAPPFEEVLPEFLEFL 77 (159)
T ss_pred CeEEeeCCCcCCCCCeEEEEEEEEEECC-cChhhhhheeeCcCC--cCCHhheeccCCCHHHHhcCCCHHHHHHHHHHHH
Confidence 689999999863 9999999999975 578899999999999 8999999999999999999999999999999999
Q ss_pred -------------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHH-HHHhCCC-CCCCChHHHHHHHHH
Q 048020 88 -------------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASL-ATYFGLG-QQTHRSLDDVLMNLE 140 (304)
Q Consensus 88 -------------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~L-ak~lGI~-~~~HrAL~DA~aTa~ 140 (304)
..++...++||+.+++ .+.+....+++..+ ++++|++ .++|+|++||.+|++
T Consensus 78 ~~~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~-~~~~~~~~~~l~~~~~~~~~~~~~~~H~Al~Da~~t~~ 156 (159)
T cd06127 78 GGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLAR-RLLPGLRSHRLGLLLAERYGIPLEGAHRALADALATAE 156 (159)
T ss_pred CCCEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHH-HHcCCCCcCchHHHHHHHcCCCCCCCCCcHHHHHHHHH
Confidence 1256789999999999 45667788999999 8899996 789999999999999
Q ss_pred HHH
Q 048020 141 VLK 143 (304)
Q Consensus 141 L~~ 143 (304)
||.
T Consensus 157 l~~ 159 (159)
T cd06127 157 LLL 159 (159)
T ss_pred HhC
Confidence 973
No 38
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=99.90 E-value=1.6e-23 Score=179.65 Aligned_cols=128 Identities=20% Similarity=0.248 Sum_probs=103.3
Q ss_pred EEEEEeecCCCC--ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHHHHHh-
Q 048020 11 VFFDVETTFPIR--HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTVFDIL- 87 (304)
Q Consensus 11 VvfDlETTGl~~--~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f~~fl- 87 (304)
|+||+||||+++ +++||+.|.+.+..+.+ .|++||+|.. +++.+++++||||++||+++|++.+++.+|.+|+
T Consensus 1 v~lD~EttGl~~~~~~~~i~~v~~v~~~~~~--~~~~~v~P~~--~i~~~~~~ihGIt~~~v~~a~~~~~~~~~l~~~l~ 76 (152)
T cd06144 1 VALDCEMVGVGPDGSESALARVSIVNEDGNV--VYDTYVKPQE--PVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLK 76 (152)
T ss_pred CEEEEEeecccCCCCEEEEEEEEEEeCCCCE--EEEEEECCCC--CCCcccccCCCCCHHHHcCCCCHHHHHHHHHHHhC
Confidence 689999999876 57888766655433234 3999999998 8999999999999999999999999999999999
Q ss_pred -----------------cCCCCCCceehHHHHHHHhcCC-CCCCCHHHHHHH-hCCC--CCCCChHHHHHHHHHHHH
Q 048020 88 -----------------QAPKPKGTIDSLNLLTERFGRR-AGDMKMASLATY-FGLG--QQTHRSLDDVLMNLEVLK 143 (304)
Q Consensus 88 -----------------~~~~~~~~IDTl~Lark~l~p~-~~~~kL~~Lak~-lGI~--~~~HrAL~DA~aTa~L~~ 143 (304)
.......++||+.+.+ ...+. .++++|+.||++ ||++ ..+|||++||++|++||+
T Consensus 77 ~~vlVgHn~~fD~~~L~~~~~~~~~~dt~~l~~-~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~at~~l~~ 152 (152)
T cd06144 77 GRILVGHALKNDLKVLKLDHPKKLIRDTSKYKP-LRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLYR 152 (152)
T ss_pred CCEEEEcCcHHHHHHhcCcCCCccEEEeEEeec-cccccCCCChhHHHHHHHHcCcccCCCCcCcHHHHHHHHHHhC
Confidence 1122357889877654 22222 478999999997 5995 479999999999999984
No 39
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.90 E-value=1e-22 Score=192.89 Aligned_cols=141 Identities=23% Similarity=0.153 Sum_probs=115.0
Q ss_pred CCCcEEEEEEeecCCCC---ceEEEEEEEEe---CCce-eeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHH
Q 048020 6 DRSEIVFFDVETTFPIR---HIWEFGAILVC---PRKL-EELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFAD 78 (304)
Q Consensus 6 ~~~~~VvfDlETTGl~~---~IIEIGAV~v~---~g~~-~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~e 78 (304)
...++||||+||||++. +|||||+|+++ +|.+ .+.++|+.+++|.. +|+++++++||||++||++++...+
T Consensus 35 ~~~~~vvlD~ETTGLd~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~--~I~~~~t~IhGIt~e~v~~~~~~~~ 112 (294)
T PRK09182 35 FVRLGVILDTETTGLDPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSR--PIPPEITRLTGITDEMVAGQTIDPA 112 (294)
T ss_pred CCCeEEEEEeeCCCCCCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCC--CCCHHHHHhcCCCHHHHhcCCCcHH
Confidence 34579999999999875 99999999998 3322 46789999999998 9999999999999999999987666
Q ss_pred HHHHHHHHh-------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCCCCCCChHHHHHHHH
Q 048020 79 IADTVFDIL-------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLGQQTHRSLDDVLMNL 139 (304)
Q Consensus 79 Vl~~f~~fl-------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~~~~HrAL~DA~aTa 139 (304)
.+.+|+++. ......+|.|++..++ +..+...+++|++|+.+||...++|||++||.+|+
T Consensus 113 ~l~~fl~~~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~-~~~~~~~~~kL~~La~~~g~~~~aHrAl~Da~Ata 191 (294)
T PRK09182 113 AVDALIAPADLIIAHNAGFDRPFLERFSPVFATKPWACSVSEID-WSARGFEGTKLGYLAGQAGFFHEGHRAVDDCQALL 191 (294)
T ss_pred HHHHHhcCCCEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHh-hccccCCCCCHHHHHHHcCCCCCCcChHHHHHHHH
Confidence 666665542 1223457899987766 33456688999999999996578999999999999
Q ss_pred HHHHHHHHHh
Q 048020 140 EVLKYCATVL 149 (304)
Q Consensus 140 ~L~~~ll~~l 149 (304)
+||.+++...
T Consensus 192 ~ll~~~l~~~ 201 (294)
T PRK09182 192 ELLARPLPET 201 (294)
T ss_pred HHHHHHHhhc
Confidence 9999877544
No 40
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=99.90 E-value=3.5e-23 Score=177.53 Aligned_cols=125 Identities=18% Similarity=0.235 Sum_probs=106.5
Q ss_pred EEEEEeecCCCC--ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCC-CHHHHHHHHHHHh
Q 048020 11 VFFDVETTFPIR--HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAP-TFADIADTVFDIL 87 (304)
Q Consensus 11 VvfDlETTGl~~--~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap-~f~eVl~~f~~fl 87 (304)
|++|+||||... +|++||+|+++++ + .|++||+|.. +++++++++||||++||+++| ++++++++|.+|+
T Consensus 1 ~~iD~E~~g~~~g~ei~~i~~v~~~~~---~--~f~~lv~P~~--~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~~~fl 73 (150)
T cd06145 1 FALDCEMCYTTDGLELTRVTVVDENGK---V--VLDELVKPDG--EIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLI 73 (150)
T ss_pred CEEeeeeeeecCCCEEEEEEEEeCCCC---E--EEEEeECCCC--ccchhccCcCCCCHHHhccCCCCHHHHHHHHHHHh
Confidence 589999999865 9999999988543 3 4999999998 999999999999999999995 9999999999999
Q ss_pred -----------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHh-CC--C--CCCCChHHHHHHHHHHHH
Q 048020 88 -----------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYF-GL--G--QQTHRSLDDVLMNLEVLK 143 (304)
Q Consensus 88 -----------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~l-GI--~--~~~HrAL~DA~aTa~L~~ 143 (304)
.....++++||+.++|+ ..+..++++|++||++| |. + ..+|||++||++|++||.
T Consensus 74 ~~~~vlVgHn~~fD~~fL~~~~~~~iDT~~l~r~-~~~~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~~t~~l~~ 150 (150)
T cd06145 74 SPDTILVGHSLENDLKALKLIHPRVIDTAILFPH-PRGPPYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELVK 150 (150)
T ss_pred CCCCEEEEcChHHHHHHhhccCCCEEEcHHhccc-cCCCCCChhHHHHHHHHCCcceeCCCCCCCcHHHHHHHHHHhC
Confidence 11234679999999984 45555689999999987 53 2 478999999999999983
No 41
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=99.89 E-value=4.2e-23 Score=178.38 Aligned_cols=126 Identities=21% Similarity=0.248 Sum_probs=105.0
Q ss_pred EEEEEeecCCCC-----ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHHHH
Q 048020 11 VFFDVETTFPIR-----HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTVFD 85 (304)
Q Consensus 11 VvfDlETTGl~~-----~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f~~ 85 (304)
|+||+||||+++ +|++|++|.+++ .++ |+++|+|.. +|+++++++||||++||++||++++++++|.+
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g---~~~--~~~lv~P~~--~i~~~~~~i~GIt~~~l~~a~~~~~v~~~l~~ 73 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHG---DVL--YDKYIRPEG--PVTDYRTRWSGIRRQHLVNATPFAVAQKEILK 73 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCC---CEE--EEEeECCCC--ccCccceECCCCCHHHHhcCCCHHHHHHHHHH
Confidence 689999999863 788888887744 343 999999998 99999999999999999999999999999999
Q ss_pred Hh------------------cCCCCCCceehHHH--HHHH-hcCCCCCCCHHHHHHHh---CCC--CCCCChHHHHHHHH
Q 048020 86 IL------------------QAPKPKGTIDSLNL--LTER-FGRRAGDMKMASLATYF---GLG--QQTHRSLDDVLMNL 139 (304)
Q Consensus 86 fl------------------~~~~~~~~IDTl~L--ark~-l~p~~~~~kL~~Lak~l---GI~--~~~HrAL~DA~aTa 139 (304)
|+ .......++||..+ +++. .+|..++++|+.||++| +++ .++|||++||++|+
T Consensus 74 ~l~~~vlV~Hn~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~at~ 153 (157)
T cd06149 74 ILKGKVVVGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATM 153 (157)
T ss_pred HcCCCEEEEeCcHHHHHHhcccCCCcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCCCcCcHHHHHHHH
Confidence 99 12234568898764 5533 36777889999999999 564 46899999999999
Q ss_pred HHHH
Q 048020 140 EVLK 143 (304)
Q Consensus 140 ~L~~ 143 (304)
+||+
T Consensus 154 ~l~~ 157 (157)
T cd06149 154 ELYK 157 (157)
T ss_pred HHhC
Confidence 9984
No 42
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.89 E-value=2.8e-22 Score=182.69 Aligned_cols=136 Identities=26% Similarity=0.313 Sum_probs=121.7
Q ss_pred CcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeee-EEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHH
Q 048020 8 SEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDK-YTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTV 83 (304)
Q Consensus 8 ~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~-f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f 83 (304)
.++++||+||||.+. +|||||+|.+.++ .+++. |+.+|+|.. +|++++.++||||.+||.++|.|.+++++|
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~--~i~~~~~~~~v~P~~--~i~~~~~~i~git~e~l~~~p~~~~v~~~~ 88 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDG--RIVERSFHTLVNPER--PIPPEIFKIHGITDEMLADAPKFAEVLPEF 88 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEECC--eeecceeEEEECCCC--CCChhhhhhcCCCHHHHhcCCCHHHHHHHH
Confidence 478999999999863 9999999999987 66644 999999977 899999999999999999999999999999
Q ss_pred HHHh--------------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC---CCCCChHHH
Q 048020 84 FDIL--------------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG---QQTHRSLDD 134 (304)
Q Consensus 84 ~~fl--------------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~---~~~HrAL~D 134 (304)
.+|+ .......++||+.++| ..+|+...++|+.||.++|++ ..+|+|+.|
T Consensus 89 ~~~i~~~~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r-~~~~~~~~~~L~~l~~~~gi~~~~~~~H~Al~D 167 (243)
T COG0847 89 LDFIGGLRLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALAR-RHFPGFDRSSLDALAERLGIDRNPFHPHRALFD 167 (243)
T ss_pred HHHHCCCCeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHH-HHcCCCccchHHHHHHHcCCCcCCcCCcchHHH
Confidence 9998 1223578999999999 567888899999999999996 577999999
Q ss_pred HHHHHHHHHHHHHH
Q 048020 135 VLMNLEVLKYCATV 148 (304)
Q Consensus 135 A~aTa~L~~~ll~~ 148 (304)
|.+++.+|.++...
T Consensus 168 a~~~a~~~~~~~~~ 181 (243)
T COG0847 168 ALALAELFLLLQTG 181 (243)
T ss_pred HHHHHHHHHHHHhc
Confidence 99999999999875
No 43
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=99.88 E-value=6e-24 Score=176.97 Aligned_cols=131 Identities=33% Similarity=0.498 Sum_probs=106.6
Q ss_pred EEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHHHHHh
Q 048020 11 VFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTVFDIL 87 (304)
Q Consensus 11 VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f~~fl 87 (304)
||||+||||++. +|||||+|+++++...+...|+++|+|.....++++++++||||+++|++++++.+++.+|.+|+
T Consensus 1 v~~D~Ettg~~~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~~~~~~ 80 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDEFEEFL 80 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHhhhhhh
Confidence 799999999864 99999999999874447889999999999444999999999999999999999999999999999
Q ss_pred ---------cCCC-------------------CCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC-C-CCCChHHHHHH
Q 048020 88 ---------QAPK-------------------PKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG-Q-QTHRSLDDVLM 137 (304)
Q Consensus 88 ---------~~~~-------------------~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~-~-~~HrAL~DA~a 137 (304)
...+ ...++|++.+.+. ..+....++|+.++++||++ . .+|+|++||++
T Consensus 81 ~~~~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~l~~~~~~~~~~~~H~Al~Da~~ 159 (164)
T PF00929_consen 81 KKNDILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARA-LFPNRKKYSLDDLAEYFGIPFDGTAHDALDDARA 159 (164)
T ss_dssp HHHTEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHH-HHHHHHHHSHHHHHHHTTSSSTSTTTSHHHHHHH
T ss_pred hcccccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHH-HhhccccCCHHHHHHHcCCCCCCCCcChHHHHHH
Confidence 0011 1235565555552 22333448999999999996 3 37999999999
Q ss_pred HHHHH
Q 048020 138 NLEVL 142 (304)
Q Consensus 138 Ta~L~ 142 (304)
|++||
T Consensus 160 t~~l~ 164 (164)
T PF00929_consen 160 TAELF 164 (164)
T ss_dssp HHHHH
T ss_pred HhCcC
Confidence 99987
No 44
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.87 E-value=3e-21 Score=193.16 Aligned_cols=144 Identities=17% Similarity=0.159 Sum_probs=115.5
Q ss_pred CCCCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCC-CCHHHHH
Q 048020 5 QDRSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSA-PTFADIA 80 (304)
Q Consensus 5 ~~~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~a-p~f~eVl 80 (304)
.+..+|||||+||||+++ +|||||||+++++...+.+.|+.+|+|.....+++.++.+||||++|+.++ .+..+++
T Consensus 3 ~~~~~fvv~D~ETTGLdP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~ 82 (476)
T PRK11779 3 KMQPTFLWHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEFA 82 (476)
T ss_pred CCCCcEEEEEEECCCCCCCCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHHH
Confidence 467789999999999876 999999999997644556789999999974346789999999999999764 4789999
Q ss_pred HHHHHHh---------c--CC-----------------------CCCCceehHHHHHHH--h------cC----CCCCCC
Q 048020 81 DTVFDIL---------Q--AP-----------------------KPKGTIDSLNLLTER--F------GR----RAGDMK 114 (304)
Q Consensus 81 ~~f~~fl---------~--~~-----------------------~~~~~IDTl~Lark~--l------~p----~~~~~k 114 (304)
.+|.+|+ . .. ..+..+|++.++|.. + +| +..+++
T Consensus 83 ~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~r 162 (476)
T PRK11779 83 ARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFK 162 (476)
T ss_pred HHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCc
Confidence 9999888 0 00 012235777777622 1 12 347799
Q ss_pred HHHHHHHhCCC-CCCCChHHHHHHHHHHHHHHHHH
Q 048020 115 MASLATYFGLG-QQTHRSLDDVLMNLEVLKYCATV 148 (304)
Q Consensus 115 L~~Lak~lGI~-~~~HrAL~DA~aTa~L~~~ll~~ 148 (304)
|+.|+++||++ .++|||++||++|++|++++.++
T Consensus 163 Le~L~~~~gI~~~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 163 LEHLTKANGIEHENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred HHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHh
Confidence 99999999997 89999999999999999998876
No 45
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=99.87 E-value=1.1e-21 Score=171.95 Aligned_cols=129 Identities=19% Similarity=0.194 Sum_probs=99.8
Q ss_pred EEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCC--CCChHHHHhc---CCCHHHHhCCCCHHHHHH
Q 048020 10 IVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPS--LVSNLCARRN---DITPEDVFSAPTFADIAD 81 (304)
Q Consensus 10 ~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~--~I~~~~~~lt---GIT~e~L~~ap~f~eVl~ 81 (304)
+|+||+||||+++ +|||||||+++++.+++.++|+.+|+|.... .+++++.++| |||+++++++|++.+++.
T Consensus 1 lv~iD~ETTGl~p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~~vl~ 80 (173)
T cd06135 1 LVWIDLEMTGLDPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQAEA 80 (173)
T ss_pred CEEEEEecCCCCCCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHHHHHH
Confidence 5899999999875 9999999999986667889999999998721 2345677775 999999999999999999
Q ss_pred HHHHHh------------------------------cCCCCCCceeh---HHHHHHHhcCCCCCCCHHHHHHHhCCC-CC
Q 048020 82 TVFDIL------------------------------QAPKPKGTIDS---LNLLTERFGRRAGDMKMASLATYFGLG-QQ 127 (304)
Q Consensus 82 ~f~~fl------------------------------~~~~~~~~IDT---l~Lark~l~p~~~~~kL~~Lak~lGI~-~~ 127 (304)
+|.+|+ ..++.++.+|+ +.++| .++|+..+ ++++ ..
T Consensus 81 ~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~~~l~~l~~-~l~p~~~~---------~~~~~~~ 150 (173)
T cd06135 81 ELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDVSSIKELAR-RWYPEIYR---------KAPKKKG 150 (173)
T ss_pred HHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHHhccCCcchhhHHHHHHHHH-HhCcHhhh---------cCCCCCC
Confidence 999888 12233445555 34555 34443221 4554 77
Q ss_pred CCChHHHHHHHHHHHHHHHHH
Q 048020 128 THRSLDDVLMNLEVLKYCATV 148 (304)
Q Consensus 128 ~HrAL~DA~aTa~L~~~ll~~ 148 (304)
+|||++||.+|+.+|++.++-
T Consensus 151 ~HrAl~Da~~~~~~~~~~~~~ 171 (173)
T cd06135 151 THRALDDIRESIAELKYYREN 171 (173)
T ss_pred CcchHHHHHHHHHHHHHHHHH
Confidence 899999999999999988764
No 46
>PRK05359 oligoribonuclease; Provisional
Probab=99.85 E-value=1.4e-20 Score=166.65 Aligned_cols=133 Identities=20% Similarity=0.233 Sum_probs=105.7
Q ss_pred CCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCC--CCCChHHHHhc---CCCHHHHhCCCCHHH
Q 048020 7 RSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADP--SLVSNLCARRN---DITPEDVFSAPTFAD 78 (304)
Q Consensus 7 ~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~--~~I~~~~~~lt---GIT~e~L~~ap~f~e 78 (304)
..+||+||+||||+++ +|||||||+++++...+.+.|+.+|+|... ..+++++..+| |||++++++++++.+
T Consensus 2 ~~~~vvlD~ETTGLdp~~d~IieIgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~~~e 81 (181)
T PRK05359 2 EDNLIWIDLEMTGLDPERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVSEAE 81 (181)
T ss_pred CCcEEEEEeecCCCCCCCCeEEEEEEEEEcCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCCHHH
Confidence 4689999999999875 999999999987543445779999999872 13578899998 899999999999999
Q ss_pred HHHHHHHHh------------------------------cCCCCCCcee--hH-HHHHHHhcCCCCCCCHHHHHHHhCCC
Q 048020 79 IADTVFDIL------------------------------QAPKPKGTID--SL-NLLTERFGRRAGDMKMASLATYFGLG 125 (304)
Q Consensus 79 Vl~~f~~fl------------------------------~~~~~~~~ID--Tl-~Lark~l~p~~~~~kL~~Lak~lGI~ 125 (304)
++.+|.+|+ ...+.++++| |+ .++| .++|+. +++++
T Consensus 82 ~~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~tl~~l~r-~~~P~~----------~~~~~ 150 (181)
T PRK05359 82 AEAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLDVSTLKELAR-RWKPEI----------LNGFK 150 (181)
T ss_pred HHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhcccCCCcccchhHHHHHHH-HhChhh----------hhCCC
Confidence 999999987 1234456666 55 5666 455542 34675
Q ss_pred -CCCCChHHHHHHHHHHHHHHHHHhh
Q 048020 126 -QQTHRSLDDVLMNLEVLKYCATVLL 150 (304)
Q Consensus 126 -~~~HrAL~DA~aTa~L~~~ll~~l~ 150 (304)
...|||++||+++.+.++.+.+.+.
T Consensus 151 ~~~~HRal~D~~~s~~~~~~~~~~~~ 176 (181)
T PRK05359 151 KQGTHRALADIRESIAELKYYREHFF 176 (181)
T ss_pred CcCCcccHHHHHHHHHHHHHHHHHhc
Confidence 6789999999999999999887664
No 47
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=99.79 E-value=1.9e-19 Score=165.00 Aligned_cols=143 Identities=20% Similarity=0.282 Sum_probs=122.1
Q ss_pred CCCcEEEEEEeecCCC-----C--ceEEEEEEEEeCCceeeee-eEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHH
Q 048020 6 DRSEIVFFDVETTFPI-----R--HIWEFGAILVCPRKLEELD-KYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFA 77 (304)
Q Consensus 6 ~~~~~VvfDlETTGl~-----~--~IIEIGAV~v~~g~~~iid-~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~ 77 (304)
.-.-++++|+|+|+-. . +|||+.||.+++-...+++ +|+.||+|..++.++.+|+.+|||.+++|..||+|.
T Consensus 54 ~fdYLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~~f~ 133 (280)
T KOG0542|consen 54 PFDYLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAPTFP 133 (280)
T ss_pred ccceEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCCCHH
Confidence 3456899999999942 2 9999999977754334455 999999999999999999999999999999999999
Q ss_pred HHHHHHHHHh------------------------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHH
Q 048020 78 DIADTVFDIL------------------------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATY 121 (304)
Q Consensus 78 eVl~~f~~fl------------------------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~ 121 (304)
+|+.+|..|+ .+.+-++|||..+..+ -++......++..+.++
T Consensus 134 ~vl~~f~~Wlr~~~~~~k~~~~Afvtdg~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk-~~y~~~~~t~it~mLe~ 212 (280)
T KOG0542|consen 134 QVLSEFDSWLRKDSLGDKNGKFAFVTDGDWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYK-NFYNRPAPTNITGMLEH 212 (280)
T ss_pred HHHHHHHHHHHHhhcccccCceEEEeCchhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHH-HHhcCccccCHHHHHHH
Confidence 9999999999 3344568999888888 44554466789999999
Q ss_pred hCCC--CCCCChHHHHHHHHHHHHHHHHHh
Q 048020 122 FGLG--QQTHRSLDDVLMNLEVLKYCATVL 149 (304)
Q Consensus 122 lGI~--~~~HrAL~DA~aTa~L~~~ll~~l 149 (304)
+|++ +.+|++++||..++.|.++|+...
T Consensus 213 ~gL~f~Gr~HsGiDDa~Nia~I~~kM~~dg 242 (280)
T KOG0542|consen 213 YGLQFEGRAHSGIDDARNIARIAQKMIRDG 242 (280)
T ss_pred hCCcccCCcccCchhHHHHHHHHHHHHhCC
Confidence 9996 899999999999999999998765
No 48
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.70 E-value=1.4e-17 Score=145.05 Aligned_cols=148 Identities=23% Similarity=0.267 Sum_probs=117.5
Q ss_pred CcEEEEEEeecCCCC-------ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHH
Q 048020 8 SEIVFFDVETTFPIR-------HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIA 80 (304)
Q Consensus 8 ~~~VvfDlETTGl~~-------~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl 80 (304)
..++++|+|+|.+.. +||||+|..++.-+-++++.|++||||.+.+.++.+|..+|||++..|.+||-|..|+
T Consensus 4 ~~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~apifs~v~ 83 (210)
T COG5018 4 NSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAPIFSMVF 83 (210)
T ss_pred ceEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhccccchHHHHH
Confidence 357899999998632 9999999888733337899999999999999999999999999999999999999999
Q ss_pred HHHHHHh--------------------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC--C
Q 048020 81 DTVFDIL--------------------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG--Q 126 (304)
Q Consensus 81 ~~f~~fl--------------------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~--~ 126 (304)
++|..|+ ..++..+.+|.....+.. +....-.+|+..++.+|.. +
T Consensus 84 E~f~r~L~~h~Pr~~~~wa~wG~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v-~~~pr~tgln~ale~~G~sf~G 162 (210)
T COG5018 84 EDFIRKLNEHDPRKNSTWATWGNMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNV-FGDPRLTGLNKALEEYGDSFTG 162 (210)
T ss_pred HHHHHHHHhcCcccCCccccccchhHHHHHHHHHhcCCCCccccCccchHHHHHHHH-hcCCccccHHHHHHHhccccCC
Confidence 9999999 123445666655444432 2222336799999999995 8
Q ss_pred CCCChHHHHHHHHHHHHHHHHH-hhhccCCc
Q 048020 127 QTHRSLDDVLMNLEVLKYCATV-LLLESSLP 156 (304)
Q Consensus 127 ~~HrAL~DA~aTa~L~~~ll~~-l~le~~lp 156 (304)
.+|||++||+.++++|..+... ..+|..-|
T Consensus 163 ~~HraldDArn~~rl~klv~~~~~~~e~~~~ 193 (210)
T COG5018 163 THHRALDDARNAYRLFKLVEQDKQYLEKPKP 193 (210)
T ss_pred chhhhHHHHHHHHHHHHHHcchhhhccCCCC
Confidence 9999999999999999987643 33444333
No 49
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.24 E-value=6.5e-11 Score=109.80 Aligned_cols=136 Identities=18% Similarity=0.188 Sum_probs=101.6
Q ss_pred cEEEEEEeecCCCC--ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHHHHHH
Q 048020 9 EIVFFDVETTFPIR--HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADTVFDI 86 (304)
Q Consensus 9 ~~VvfDlETTGl~~--~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~f~~f 86 (304)
++|++|+|..|..+ +.=.+|=|.|.+..+.++ |+.||+|.. +|+.+.++++||+++.+.+|.+|+.|-.+++++
T Consensus 106 r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~Vv--yDkyVkP~~--~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~kl 181 (280)
T KOG2249|consen 106 RVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVV--YDKYVKPTE--PVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLKL 181 (280)
T ss_pred eEEEEeeeEeccCCCccceeeeEEEEeeccCcEe--eeeecCCCc--ccccceeeecccCHHHhccCccHHHHHHHHHHH
Confidence 69999999999654 444555555554433454 999999999 999999999999999999999999999999999
Q ss_pred h------------------cCCCCCCceehHH--HHHHHhcCCCCCCCHHHHHHH-hCCC--CCCCChHHHHHHHHHHHH
Q 048020 87 L------------------QAPKPKGTIDSLN--LLTERFGRRAGDMKMASLATY-FGLG--QQTHRSLDDVLMNLEVLK 143 (304)
Q Consensus 87 l------------------~~~~~~~~IDTl~--Lark~l~p~~~~~kL~~Lak~-lGI~--~~~HrAL~DA~aTa~L~~ 143 (304)
| ......-+-||-. -+++. .......+|..|++. ||+. ...|+...||.||++||.
T Consensus 182 L~gRIlVGHaLhnDl~~L~l~hp~s~iRDTs~~~pl~k~-~~~~~tpSLK~Lt~~~Lg~~IQ~GeHsSvEDA~AtM~LY~ 260 (280)
T KOG2249|consen 182 LKGRILVGHALHNDLQALKLEHPRSMIRDTSKYPPLMKL-LSKKATPSLKKLTEALLGKDIQVGEHSSVEDARATMELYK 260 (280)
T ss_pred HhCCEEeccccccHHHHHhhhCchhhhcccccCchHHHH-hhccCCccHHHHHHHHhchhhhccccCcHHHHHHHHHHHH
Confidence 9 0111122345532 11212 234456789999985 5763 455999999999999999
Q ss_pred HHHHHh
Q 048020 144 YCATVL 149 (304)
Q Consensus 144 ~ll~~l 149 (304)
++...+
T Consensus 261 ~vk~qw 266 (280)
T KOG2249|consen 261 RVKVQW 266 (280)
T ss_pred HHHHHH
Confidence 886655
No 50
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=99.14 E-value=2.3e-10 Score=110.85 Aligned_cols=141 Identities=18% Similarity=0.185 Sum_probs=111.9
Q ss_pred CCCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHh-CCCCHHHHHH
Q 048020 6 DRSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVF-SAPTFADIAD 81 (304)
Q Consensus 6 ~~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~-~ap~f~eVl~ 81 (304)
+..+|.+.|.||.|..+ ++.|||+|+.+..-..|.+....||+|....--.|.+.-+||||+.... .+.+..+...
T Consensus 7 ~~~tF~~yDYETfG~~Pa~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~F~~ 86 (475)
T COG2925 7 KQPTFLFYDYETFGVHPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAAFAA 86 (475)
T ss_pred CCCcEEEEehhhcCCCcccccchhhheeeccccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHHHHH
Confidence 45689999999999765 9999999999875556778889999999864334788999999998866 5778888888
Q ss_pred HHHHHh----------------------------cCC------CCCCceehHHHHHHH--hcC----------CCCCCCH
Q 048020 82 TVFDIL----------------------------QAP------KPKGTIDSLNLLTER--FGR----------RAGDMKM 115 (304)
Q Consensus 82 ~f~~fl----------------------------~~~------~~~~~IDTl~Lark~--l~p----------~~~~~kL 115 (304)
++..-+ ..| -.+.-+|.+.+.|.. +.| ++.++||
T Consensus 87 ~I~~~ls~P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n~dG~pSFkL 166 (475)
T COG2925 87 RIHAELTQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDDGLPSFKL 166 (475)
T ss_pred HHHHHhCCCCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcCCCCCcchhh
Confidence 888766 011 135678888888842 222 3578999
Q ss_pred HHHHHHhCCC-CCCCChHHHHHHHHHHHHHHH
Q 048020 116 ASLATYFGLG-QQTHRSLDDVLMNLEVLKYCA 146 (304)
Q Consensus 116 ~~Lak~lGI~-~~~HrAL~DA~aTa~L~~~ll 146 (304)
+.|.+.-|+. .++|+|++|++||..+.+.+.
T Consensus 167 EhLt~ANgieH~nAHdAmsDVyATIamAklvk 198 (475)
T COG2925 167 EHLTKANGIEHSNAHDAMSDVYATIAMAKLVK 198 (475)
T ss_pred HHHhhccccccchhhHHHHHHHHHHHHHHHHH
Confidence 9999999995 999999999999988776554
No 51
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=99.12 E-value=6.2e-10 Score=98.37 Aligned_cols=131 Identities=18% Similarity=0.170 Sum_probs=95.2
Q ss_pred CCCcEEEEEEeecCCCC---c-e-----EEEEEEEEeC----CceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhC
Q 048020 6 DRSEIVFFDVETTFPIR---H-I-----WEFGAILVCP----RKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFS 72 (304)
Q Consensus 6 ~~~~~VvfDlETTGl~~---~-I-----IEIGAV~v~~----g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ 72 (304)
++-+||-+|.|+++... + + .|+|=|.+.+ ..+++ -|+.||+|.. +|..+.++++|||++++.+
T Consensus 3 ~d~e~v~~~~~~~~~~~~g~~~~~~~~~~~LaRVsiVd~~~~~~g~v--llD~~VkP~~--~V~DYrT~~SGIt~~~L~~ 78 (174)
T cd06143 3 IDAEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVP--FIDDYISTTE--PVVDYLTRFSGIKPGDLDP 78 (174)
T ss_pred eeeeEEEecchhceecCCCcEeeeccCCceeEEEEEEcCCCCcCCCE--EEeeeECCCC--CccCcCccccccCHHHcCc
Confidence 45567777777776422 2 1 2455554444 12234 3899999998 9999999999999999998
Q ss_pred CC------CHHHHHHHHHHHh-------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHH-hCC--
Q 048020 73 AP------TFADIADTVFDIL-------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATY-FGL-- 124 (304)
Q Consensus 73 ap------~f~eVl~~f~~fl-------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~-lGI-- 124 (304)
+. +++++..++.+++ .......++||..+.+ .|....++|..|++. +|.
T Consensus 79 a~~~~~~~t~~~v~~~l~~li~~~tILVGHsL~nDL~aL~l~hp~~~viDTa~l~~---~~~~r~~sLk~La~~~L~~~I 155 (174)
T cd06143 79 KTSSKNLTTLKSAYLKLRLLVDLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFH---LPGQRKLSLRFLAWYLLGEKI 155 (174)
T ss_pred cccccccCCHHHHHHHHHHHcCCCCEEEeccchhHHHHhcCcCCCcceEEcHHhcc---CCCCCChhHHHHHHHHcCCcc
Confidence 75 5889999998888 1111346899986654 233456899999996 465
Q ss_pred CCCCCChHHHHHHHHHHHH
Q 048020 125 GQQTHRSLDDVLMNLEVLK 143 (304)
Q Consensus 125 ~~~~HrAL~DA~aTa~L~~ 143 (304)
+...|+.+.||+|+++||+
T Consensus 156 Q~~~HdSvEDArAam~Ly~ 174 (174)
T cd06143 156 QSETHDSIEDARTALKLYR 174 (174)
T ss_pred cCCCcCcHHHHHHHHHHhC
Confidence 4668999999999999984
No 52
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=98.80 E-value=1.8e-08 Score=88.71 Aligned_cols=143 Identities=20% Similarity=0.253 Sum_probs=96.8
Q ss_pred CCCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCC--CCCChHHHHhc---CCCHHHHhCCCCHH
Q 048020 6 DRSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADP--SLVSNLCARRN---DITPEDVFSAPTFA 77 (304)
Q Consensus 6 ~~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~--~~I~~~~~~lt---GIT~e~L~~ap~f~ 77 (304)
+..++|.+|+|.||++- +|||||++..++....+.+-++..|+.+.. ..++++|.+-| |+|..-++...++.
T Consensus 24 l~q~lVWiD~EMTGLdvekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~tl~ 103 (208)
T KOG3242|consen 24 LKQPLVWIDCEMTGLDVEKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKITLA 103 (208)
T ss_pred ccCceEEEeeeccccccccceeEEEEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhccHH
Confidence 67889999999999975 999999998887544556677777776542 25778898887 58888889999999
Q ss_pred HHHHHHHHHh--c-----CCCC--CCceehHHHHHHHhcCCC---------CCCCHHHHHHHhCC------C--CCCCCh
Q 048020 78 DIADTVFDIL--Q-----APKP--KGTIDSLNLLTERFGRRA---------GDMKMASLATYFGL------G--QQTHRS 131 (304)
Q Consensus 78 eVl~~f~~fl--~-----~~~~--~~~IDTl~Lark~l~p~~---------~~~kL~~Lak~lGI------~--~~~HrA 131 (304)
++-.++++|+ . .++. --+.|-+-+.+ +.|.. .--....||+++.- | ...|||
T Consensus 104 ~aEnevl~yikk~ip~~~~~laGNSV~~DrlFl~k--~mPk~~~~lhyrivDVStIkeL~~Rw~P~~~~~aPkK~~~HrA 181 (208)
T KOG3242|consen 104 DAENEVLEYIKKHIPKGKCPLAGNSVYMDRLFLKK--YMPKLIKHLHYRIVDVSTIKELARRWYPDIKARAPKKKATHRA 181 (208)
T ss_pred HHHHHHHHHHHHhCCCCCCCccCcchhhHHHHHHH--HhHHHHHhcceeeeeHHHHHHHHHHhCchhhccCcccccccch
Confidence 9999999999 1 1111 12233332222 11211 11124455555422 2 457999
Q ss_pred HHHHHHHHHHHHHHHHHhh
Q 048020 132 LDDVLMNLEVLKYCATVLL 150 (304)
Q Consensus 132 L~DA~aTa~L~~~ll~~l~ 150 (304)
++|.+-...=++...+.++
T Consensus 182 ldDI~ESI~ELq~Yr~nif 200 (208)
T KOG3242|consen 182 LDDIRESIKELQYYRENIF 200 (208)
T ss_pred HHHHHHHHHHHHHHHHHhc
Confidence 9999887777766655543
No 53
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=98.75 E-value=8.3e-08 Score=83.78 Aligned_cols=146 Identities=18% Similarity=0.190 Sum_probs=95.6
Q ss_pred CCCCCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCC--CCCCChHHHHhc---CCCHHHHhCCCC
Q 048020 4 TQDRSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPAD--PSLVSNLCARRN---DITPEDVFSAPT 75 (304)
Q Consensus 4 ~~~~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~--~~~I~~~~~~lt---GIT~e~L~~ap~ 75 (304)
..+..++|.+|+|.||++. +|||||++..+.+...+.+-+...|.... ...+.+++++.| |++..-.+...+
T Consensus 2 ~~~~~nLiWIDlEMTGLd~~~drIIEiA~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~t 81 (184)
T COG1949 2 SANKNNLIWIDLEMTGLDPERDRIIEIATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTVT 81 (184)
T ss_pred CCcCCceEEEeeeeccCCcCcceEEEEEEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhcc
Confidence 4577899999999999876 99999999888653333444455554333 125667888887 577777778889
Q ss_pred HHHHHHHHHHHh--c-----CCCCCCceeh--HHHHHH-------HhcCCCCCCCHHHHHHHhC------CC-CCCCChH
Q 048020 76 FADIADTVFDIL--Q-----APKPKGTIDS--LNLLTE-------RFGRRAGDMKMASLATYFG------LG-QQTHRSL 132 (304)
Q Consensus 76 f~eVl~~f~~fl--~-----~~~~~~~IDT--l~Lark-------~l~p~~~~~kL~~Lak~lG------I~-~~~HrAL 132 (304)
..++-.+.++|+ . .|.-...|+. .-|+|. +.++...--.|..||+++. .. ...|+||
T Consensus 82 ~~~aE~~~l~flkkwvp~~~spicGNSI~qDRrFl~r~MP~Le~yfHYR~lDVSTlKELa~RW~P~i~~~~~K~~~H~Al 161 (184)
T COG1949 82 EAEAEAQTLDFLKKWVPKGVSPICGNSIAQDRRFLFRYMPKLEAYFHYRYLDVSTLKELARRWNPEILAGFKKGGTHRAL 161 (184)
T ss_pred HHHHHHHHHHHHHHhCCCCCCCCccchhhHHHHHHHHHhhhHHHHhhhHhhhHHHHHHHHHhhCcHhhhccccccchhHH
Confidence 999999999998 1 1222222322 222221 1122222345778888764 22 6889999
Q ss_pred HHHHHHHHHHHHHHHHh
Q 048020 133 DDVLMNLEVLKYCATVL 149 (304)
Q Consensus 133 ~DA~aTa~L~~~ll~~l 149 (304)
+|.+-...=++...+.+
T Consensus 162 ~DI~ESI~EL~~YR~~f 178 (184)
T COG1949 162 DDIRESIAELRYYREHF 178 (184)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 99987776666655544
No 54
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=98.64 E-value=4.7e-07 Score=80.14 Aligned_cols=103 Identities=15% Similarity=0.023 Sum_probs=74.5
Q ss_pred EEEEEEeecCC----CC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHH
Q 048020 10 IVFFDVETTFP----IR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADT 82 (304)
Q Consensus 10 ~VvfDlETTGl----~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~ 82 (304)
.++||+||||+ +. +|++||++...+|. .. .+.....+.. ...+ ||+..++...++..+++.+
T Consensus 1 v~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~~~g~--~~-~~~~~~~~~~--~~~~------~i~~~~v~~~~~E~~lL~~ 69 (199)
T cd05160 1 VLSFDIETTPPVGGPEPDRDPIICITYADSFDGV--KV-VFLLKTSTVG--DDIE------FIDGIEVEYFADEKELLKR 69 (199)
T ss_pred CccEEEeecCCCCCcCCCCCCEEEEEEEEeeCCc--ee-eEEEeecccC--CcCC------CCCCceEEEeCCHHHHHHH
Confidence 37899999997 43 99999999885552 21 2333333322 1111 8899999999999999999
Q ss_pred HHHHh----------------------------cCCC-----------------------CCCceehHHHHHHHhcCCCC
Q 048020 83 VFDIL----------------------------QAPK-----------------------PKGTIDSLNLLTERFGRRAG 111 (304)
Q Consensus 83 f~~fl----------------------------~~~~-----------------------~~~~IDTl~Lark~l~p~~~ 111 (304)
|.+++ +.+. ...++|++.++|+ ..+ +.
T Consensus 70 f~~~i~~~dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~-~~~-l~ 147 (199)
T cd05160 70 FFDIIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKR-DFK-LK 147 (199)
T ss_pred HHHHHHhcCCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHH-hcC-cc
Confidence 99999 1111 2347899999995 444 88
Q ss_pred CCCHHHHHHHhCCC
Q 048020 112 DMKMASLATYFGLG 125 (304)
Q Consensus 112 ~~kL~~Lak~lGI~ 125 (304)
+|+|+++|+.++..
T Consensus 148 sy~L~~v~~~~l~~ 161 (199)
T cd05160 148 SYTLDAVAEELLGE 161 (199)
T ss_pred cCCHHHHHHHHhCC
Confidence 99999999988663
No 55
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=98.44 E-value=6.1e-07 Score=88.11 Aligned_cols=136 Identities=20% Similarity=0.252 Sum_probs=102.8
Q ss_pred CCCCcEEEEEEeecCCCC--ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCC-CCHHHHHH
Q 048020 5 QDRSEIVFFDVETTFPIR--HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSA-PTFADIAD 81 (304)
Q Consensus 5 ~~~~~~VvfDlETTGl~~--~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~a-p~f~eVl~ 81 (304)
.-..+++++|+|...... ++..|++|-+++. + -|..||+|.. +|-.+.++.+|||.++++++ .+.+++-.
T Consensus 213 ~~~~~i~AlDCEm~~te~g~el~RVt~VD~~~~---v--i~D~fVkP~~--~VvDy~T~~SGIT~~~~e~~t~tl~dvq~ 285 (380)
T KOG2248|consen 213 SKSPNIFALDCEMVVTENGLELTRVTAVDRDGK---V--ILDTFVKPNK--PVVDYNTRYSGITEEDLENSTITLEDVQK 285 (380)
T ss_pred CCCCCeEEEEeeeeeeccceeeEEeeeeeccCc---E--EeEEeecCCC--cccccccccccccHHHHhcCccCHHHHHH
Confidence 345689999999998654 8999999988764 3 4899999999 99999999999999999865 57899999
Q ss_pred HHHHHh-----------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHH-hCC--C--CCCCChHHHHHHHH
Q 048020 82 TVFDIL-----------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATY-FGL--G--QQTHRSLDDVLMNL 139 (304)
Q Consensus 82 ~f~~fl-----------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~-lGI--~--~~~HrAL~DA~aTa 139 (304)
++..|+ .......+|||..++.....|.....+|..||+. +|. . ...|+...||.+|.
T Consensus 286 ~l~~~~~~~TILVGHSLenDL~aLKl~H~~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~~~~HdS~eDA~acm 365 (380)
T KOG2248|consen 286 ELLELISKNTILVGHSLENDLKALKLDHPSVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEGVGGHDSVEDALACM 365 (380)
T ss_pred HHHhhcCcCcEEEeechhhHHHHHhhhCCceeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhccCCCCccHHHHHHHH
Confidence 999998 2224568899874433111110122348888885 454 3 45699999999999
Q ss_pred HHHHHHHH
Q 048020 140 EVLKYCAT 147 (304)
Q Consensus 140 ~L~~~ll~ 147 (304)
+++.....
T Consensus 366 ~Lv~~k~~ 373 (380)
T KOG2248|consen 366 KLVKLKIK 373 (380)
T ss_pred HHHHHHHh
Confidence 99876554
No 56
>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=97.70 E-value=0.00074 Score=58.52 Aligned_cols=120 Identities=13% Similarity=0.122 Sum_probs=75.6
Q ss_pred CCCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHHHHHH
Q 048020 6 DRSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFADIADT 82 (304)
Q Consensus 6 ~~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~eVl~~ 82 (304)
.+..+++||+||||+.. +|+.++... .++ ..|..-+++.. .. +++.+.+++..
T Consensus 3 ~~~~~~a~d~e~~~~~~~~~~i~~l~~~~-~~~-----~~~~~~~~~~~---~~---------------~~~~~~~~~~~ 58 (193)
T cd06139 3 EKAKVFAFDTETTSLDPMQAELVGISFAV-EPG-----EAYYIPLGHDY---GG---------------EQLPREEVLAA 58 (193)
T ss_pred ccCCeEEEEeecCCCCcCCCeEEEEEEEc-CCC-----CEEEEecCCCc---cc---------------cCCCHHHHHHH
Confidence 45678999999999763 888877542 221 12322122211 10 22233344444
Q ss_pred HHHHh----------------------cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHh-CCC--------------
Q 048020 83 VFDIL----------------------QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYF-GLG-------------- 125 (304)
Q Consensus 83 f~~fl----------------------~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~l-GI~-------------- 125 (304)
|.+|+ +..+...++||+.+++ .+.|...+++|+.+++.| |..
T Consensus 59 l~~~l~~~~~~~v~hn~k~d~~~l~~~gi~~~~~~~Dt~l~a~-ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~ 137 (193)
T cd06139 59 LKPLLEDPSIKKVGQNLKFDLHVLANHGIELRGPAFDTMLASY-LLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQ 137 (193)
T ss_pred HHHHHhCCCCcEEeeccHHHHHHHHHCCCCCCCCcccHHHHHH-HhCCCCCCCCHHHHHHHHhCCCCccHHHHcCCCcCc
Confidence 44433 3345668899998888 678876457999999976 321
Q ss_pred ---------CCCCChHHHHHHHHHHHHHHHHHhh
Q 048020 126 ---------QQTHRSLDDVLMNLEVLKYCATVLL 150 (304)
Q Consensus 126 ---------~~~HrAL~DA~aTa~L~~~ll~~l~ 150 (304)
...|.|..||.++.+++..+.+++.
T Consensus 138 ~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~ 171 (193)
T cd06139 138 ITFDQVPLEKAAEYAAEDADITLRLYELLKPKLK 171 (193)
T ss_pred CCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 0223588899999999999988874
No 57
>PRK05755 DNA polymerase I; Provisional
Probab=97.32 E-value=0.0019 Score=69.92 Aligned_cols=61 Identities=15% Similarity=0.098 Sum_probs=47.6
Q ss_pred cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHh-CCCC--------------------CCCChHHHHHHHHHHHHHHH
Q 048020 88 QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYF-GLGQ--------------------QTHRSLDDVLMNLEVLKYCA 146 (304)
Q Consensus 88 ~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~l-GI~~--------------------~~HrAL~DA~aTa~L~~~ll 146 (304)
+..+..+++||+.+++ ++.|+. +++|+.+++.| |+.. ..|.|..||.++++|+.++.
T Consensus 389 gi~~~~~~~DT~iAa~-Ll~~~~-~~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~ 466 (880)
T PRK05755 389 GIELRGIAFDTMLASY-LLDPGR-RHGLDSLAERYLGHKTISFEEVAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLK 466 (880)
T ss_pred CCCcCCCcccHHHHHH-HcCCCC-CCCHHHHHHHHhCCCccchHHhcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444578999998777 777765 38999999987 4430 24789999999999999998
Q ss_pred HHhh
Q 048020 147 TVLL 150 (304)
Q Consensus 147 ~~l~ 150 (304)
+++.
T Consensus 467 ~~L~ 470 (880)
T PRK05755 467 PKLL 470 (880)
T ss_pred HHHH
Confidence 8763
No 58
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=97.02 E-value=0.005 Score=57.45 Aligned_cols=114 Identities=18% Similarity=0.146 Sum_probs=67.9
Q ss_pred CCcEEEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCC-HHHHh--CCCCHH--H
Q 048020 7 RSEIVFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDIT-PEDVF--SAPTFA--D 78 (304)
Q Consensus 7 ~~~~VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT-~e~L~--~ap~f~--e 78 (304)
..+++|||+||||+++ .|+=+|...+.++...+ +-+.+=.|.. .. .-...+++.- ..|+. ++..|. .
T Consensus 97 ~e~~~FFDiETTGL~~ag~~I~~~g~a~~~~~~~~V--rq~~lp~p~~--E~-avle~fl~~~~~~~lvsfNGkaFD~Pf 171 (278)
T COG3359 97 AEDVAFFDIETTGLDRAGNTITLVGGARGVDDTMHV--RQHFLPAPEE--EV-AVLENFLHDPDFNMLVSFNGKAFDIPF 171 (278)
T ss_pred ccceEEEeeeccccCCCCCeEEEEEEEEccCceEEE--EeecCCCcch--hh-HHHHHHhcCCCcceEEEecCcccCcHH
Confidence 5689999999999985 77777777776652222 2122222222 10 0123344433 23333 333333 2
Q ss_pred HHHHHHHHhcCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC
Q 048020 79 IADTVFDILQAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG 125 (304)
Q Consensus 79 Vl~~f~~fl~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~ 125 (304)
+-..+...+...+.+.-+|.+.-+|+++...+.+-+|.++-+.+|+.
T Consensus 172 ikR~v~~~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr~LGi~ 218 (278)
T COG3359 172 IKRMVRDRLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTVERILGIR 218 (278)
T ss_pred HHHHHhcccccCccccchhhhhhhhhhhhccCCCCChhhHHHHhCcc
Confidence 32222233455567788999999997665556788999999999984
No 59
>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=96.90 E-value=0.00095 Score=56.95 Aligned_cols=104 Identities=16% Similarity=0.221 Sum_probs=48.2
Q ss_pred EEEEEeecCCCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHh--------CCCCHH-H
Q 048020 11 VFFDVETTFPIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVF--------SAPTFA-D 78 (304)
Q Consensus 11 VvfDlETTGl~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~--------~ap~f~-e 78 (304)
++||+||||+++ .|.-||++.++++.. ..|..+..... .-.....+.. +.+. ++..|+ -
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~---~~~~~~~~~~~--~ee~~~~~~~----~~l~~~~~iv~yng~~FD~p 71 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEI---ITFIQWFAEDP--DEEEIILEFF----ELLDEADNIVTYNGKNFDIP 71 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTT---E-EEEE-GGGH--HHHHHHHH------HHHHTT--EEESSTTTTHHH
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCce---EEeeHhhccCc--HHHHHHHHHH----HHHhcCCeEEEEeCcccCHH
Confidence 689999999865 899999998887532 22555554432 1111111111 2222 233333 2
Q ss_pred HHHHHHHHhcCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCCC
Q 048020 79 IADTVFDILQAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLGQ 126 (304)
Q Consensus 79 Vl~~f~~fl~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~~ 126 (304)
++.+.......+.....+|++..+++... .+++|..+++.+|+..
T Consensus 72 ~L~~~~~~~~~~~~~~~iDl~~~~~~~~~---~~~~Lk~ve~~lg~~~ 116 (164)
T PF13482_consen 72 FLKRRAKRYGLPPPFNHIDLLKIIKKHFL---ESYSLKNVEKFLGIER 116 (164)
T ss_dssp HHHHHH-HHHH--GGGEEEHHHHHT-TTS---CCTT--SHHH------
T ss_pred HHHHHHHHcCCCcccchhhHHHHHHhccC---CCCCHHHHhhhccccc
Confidence 33333333222227899999998885433 7889999999999953
No 60
>PHA02570 dexA exonuclease; Provisional
Probab=96.85 E-value=0.0054 Score=56.31 Aligned_cols=74 Identities=14% Similarity=0.102 Sum_probs=48.4
Q ss_pred EEEEEeecCCCC--ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcC--CC------------HHH---Hh
Q 048020 11 VFFDVETTFPIR--HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRND--IT------------PED---VF 71 (304)
Q Consensus 11 VvfDlETTGl~~--~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltG--IT------------~e~---L~ 71 (304)
+++|+||.|..+ .||+||||.++...+ ...+|+.+|.......+....+ .| .. +|. +.
T Consensus 4 lMIDlETmG~~p~AaIisIgAV~Fdp~~~-~g~tF~elV~~~~~~k~d~~sq--~g~~~~d~~TI~WW~kQS~EAR~~L~ 80 (220)
T PHA02570 4 FIIDFETFGNTPDGAVIDLAVIAFEHDPH-NPPTFEELVSRGRRIKFDLKSQ--KGKRLFDKSTIEWWKNQSPEARKNLK 80 (220)
T ss_pred EEEEeeccCCCCCceEEEEEEEEecCCCC-ccccHHHHhhcccccccchhhc--cCCCccCchHHHHHHhCCHHHHHhcc
Confidence 689999999655 999999999996433 6788988886433111111111 12 11 111 21
Q ss_pred ---CCCCHHHHHHHHHHHh
Q 048020 72 ---SAPTFADIADTVFDIL 87 (304)
Q Consensus 72 ---~ap~f~eVl~~f~~fl 87 (304)
+..++.+++.+|.+|+
T Consensus 81 ~s~~~~~l~~al~~F~~fi 99 (220)
T PHA02570 81 PSDEDVSTYEGHKKFFEYL 99 (220)
T ss_pred CCCccccHHHHHHHHHHHH
Confidence 2467899999999999
No 61
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=96.70 E-value=0.0015 Score=61.54 Aligned_cols=83 Identities=18% Similarity=0.191 Sum_probs=53.5
Q ss_pred CCCCCCcEEEEEEeecCCCC---ceEEEEEEEEe-----CCc-------------eeeeeeEEEEEcCCCCCCCChHHHH
Q 048020 3 PTQDRSEIVFFDVETTFPIR---HIWEFGAILVC-----PRK-------------LEELDKYTTLVRPADPSLVSNLCAR 61 (304)
Q Consensus 3 ~~~~~~~~VvfDlETTGl~~---~IIEIGAV~v~-----~g~-------------~~iid~f~~lV~P~~~~~I~~~~~~ 61 (304)
..+.-..|+|+|+|+||+.. .|-|+....|. +.. -++.++.+-+..|.. ...+.+.+
T Consensus 8 e~pr~~tf~fldleat~lp~~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~--v~~p~aee 85 (318)
T KOG4793|consen 8 EVPRLRTFSFLDLEATGLPGWIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVP--VTRPIAEE 85 (318)
T ss_pred cCCceeEEEeeeeccccCCcccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcC--CcChhhhh
Confidence 44556789999999999643 66665443322 110 034567777888888 88899999
Q ss_pred hcCCCHHHHh--CCCCHHH-HHHHHHHHh
Q 048020 62 RNDITPEDVF--SAPTFAD-IADTVFDIL 87 (304)
Q Consensus 62 ltGIT~e~L~--~ap~f~e-Vl~~f~~fl 87 (304)
+||++++-+. ..--|+. +.+-+..|+
T Consensus 86 itgls~~~~~l~rr~~~D~dla~LL~afl 114 (318)
T KOG4793|consen 86 ITGLSQPFLALQRRLAFDKDLAKLLTAFL 114 (318)
T ss_pred hcccccHHHHHHHHhhhhHHHHHHHHHHH
Confidence 9999996554 2333433 334444555
No 62
>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=96.47 E-value=0.014 Score=46.31 Aligned_cols=22 Identities=27% Similarity=0.093 Sum_probs=18.7
Q ss_pred EEEEEeecCCCC---ceEEEEEEEE
Q 048020 11 VFFDVETTFPIR---HIWEFGAILV 32 (304)
Q Consensus 11 VvfDlETTGl~~---~IIEIGAV~v 32 (304)
++||+||||++. +|++|++...
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~ 25 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADV 25 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEc
Confidence 479999999765 8999998765
No 63
>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=96.32 E-value=0.085 Score=46.94 Aligned_cols=31 Identities=10% Similarity=0.165 Sum_probs=24.3
Q ss_pred CceehHHHHHHHhcCCCCCCCHHHHHH-HhCCCC
Q 048020 94 GTIDSLNLLTERFGRRAGDMKMASLAT-YFGLGQ 126 (304)
Q Consensus 94 ~~IDTl~Lark~l~p~~~~~kL~~Lak-~lGI~~ 126 (304)
..+|++.++++. ..+.+++|+++++ .+|.+.
T Consensus 125 ~~lDl~~~~~~~--~~l~sy~L~~v~~~~Lg~~k 156 (195)
T cd05780 125 IHVDLYPVARRT--LNLTRYTLERVYEELFGIEK 156 (195)
T ss_pred EEEeHHHHHHhh--CCCCcCcHHHHHHHHhCCCC
Confidence 478999999853 3578999999988 568753
No 64
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=96.19 E-value=0.1 Score=48.78 Aligned_cols=48 Identities=19% Similarity=0.179 Sum_probs=35.2
Q ss_pred CceehHHHHHHHhcCCCCCCCHHHHHHHhCCC--------------------------CCCCChHHHHHHHHHHHHH
Q 048020 94 GTIDSLNLLTERFGRRAGDMKMASLATYFGLG--------------------------QQTHRSLDDVLMNLEVLKY 144 (304)
Q Consensus 94 ~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~--------------------------~~~HrAL~DA~aTa~L~~~ 144 (304)
.++||.-+++ .. ......|+.|++.++.. ...|.|-.||++|+.+|.+
T Consensus 189 ~i~DtK~la~-~~--~~~~~~L~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~HeAGyDA~mTg~~F~~ 262 (262)
T PF04857_consen 189 RIYDTKYLAE-EC--PGKSTSLQELAEELGIRRNPSSISSPEGFPSYDEEKNNFPMFGEKAHEAGYDAYMTGCVFIK 262 (262)
T ss_dssp SEEEHHHHHT-ST--TTS-SSHHHHHHHTTSTT----EEE-TTS-------------SS-TTSHHHHHHHHHHHHHH
T ss_pred ccccHHHHHH-hc--cccccCHHHHHHHhCCCccccccccccccccccccccccccCCCCCCCcchHHHHHHHHHcC
Confidence 4778776666 22 13567899999998752 2389999999999999864
No 65
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=96.15 E-value=0.031 Score=51.38 Aligned_cols=139 Identities=17% Similarity=0.082 Sum_probs=87.1
Q ss_pred CcEEEEEEeecCC---------CC---------------ceEEEEEEEEeCCceeeee----eEEE--E-EcCCCCC--C
Q 048020 8 SEIVFFDVETTFP---------IR---------------HIWEFGAILVCPRKLEELD----KYTT--L-VRPADPS--L 54 (304)
Q Consensus 8 ~~~VvfDlETTGl---------~~---------------~IIEIGAV~v~~g~~~iid----~f~~--l-V~P~~~~--~ 54 (304)
-.||++|+|.-|. +. .+||+|.-..+.+ ++..+ +|+. - .++.... +
T Consensus 24 y~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQlGlTlsd~~-Gn~p~~g~~tWqfNF~dF~~~~D~~a~ 102 (239)
T KOG0304|consen 24 YPYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQLGLTLSDEK-GNLPDCGTDTWQFNFSDFNLEKDMYAQ 102 (239)
T ss_pred CCeeEecCcCCceeeecCccccCChHHHHHHHHhchhhhhhhheeeeeeccC-CCCCCCCCceeEEecccCCchhhccch
Confidence 4689999999882 10 8999999988842 12322 3332 2 2333211 2
Q ss_pred CChHHHHhcCCCHHHHhC-CCCHHHHHHHHHHHh--------------------------cCCCC--------------C
Q 048020 55 VSNLCARRNDITPEDVFS-APTFADIADTVFDIL--------------------------QAPKP--------------K 93 (304)
Q Consensus 55 I~~~~~~ltGIT~e~L~~-ap~f~eVl~~f~~fl--------------------------~~~~~--------------~ 93 (304)
-|-+..+-+||.-+..+. +....+..+.+..-. ..+++ .
T Consensus 103 ~SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs~YDfgYLlK~Lt~~~LP~~~~eF~~~v~~~fp 182 (239)
T KOG0304|consen 103 DSIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHSGYDFGYLLKILTGKPLPETEEEFFEIVRQLFP 182 (239)
T ss_pred hhHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeeccchHHHHHHHHcCCCCcchHHHHHHHHHHHcc
Confidence 234445668888877664 445544444433321 11111 3
Q ss_pred CceehHHHHHHHhcCCCCCCCHHHHHHHhCCC--CCCCChHHHHHHHHHHHHHHHHH
Q 048020 94 GTIDSLNLLTERFGRRAGDMKMASLATYFGLG--QQTHRSLDDVLMNLEVLKYCATV 148 (304)
Q Consensus 94 ~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~--~~~HrAL~DA~aTa~L~~~ll~~ 148 (304)
.+.|+-.+++ .........+|+.+|..+|++ +.+|.|-.|+..|+.+|.++.+.
T Consensus 183 ~vYDiK~l~~-~c~~~~l~~GL~~lA~~L~~~RvG~~HqAGSDSlLT~~~F~kl~~~ 238 (239)
T KOG0304|consen 183 FVYDVKYLMK-FCEGLSLKGGLQRLADLLGLKRVGIAHQAGSDSLLTARVFFKLKEL 238 (239)
T ss_pred hhhhHHHHHH-hhhhhhhhcCHHHHHHHhCCCeeecccccCcHHHHHHHHHHHHHhc
Confidence 5666666666 321112457899999999997 88999999999999999998653
No 66
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=96.15 E-value=0.11 Score=47.05 Aligned_cols=31 Identities=10% Similarity=0.195 Sum_probs=23.2
Q ss_pred ceehHHHHHHHhcCCCCCCCHHHHHHH-hCCC
Q 048020 95 TIDSLNLLTERFGRRAGDMKMASLATY-FGLG 125 (304)
Q Consensus 95 ~IDTl~Lark~l~p~~~~~kL~~Lak~-lGI~ 125 (304)
.+|.+.++++..+...++++|+.+|++ +|..
T Consensus 137 ~iDl~~~~~~~~~l~~~sysLd~Va~~~Lg~~ 168 (204)
T cd05779 137 HMDCFRWVKRDSYLPQGSQGLKAVTKAKLGYD 168 (204)
T ss_pred EEEhHHHHHHhhcCCCCCccHHHHHHHHhCCC
Confidence 588888888543333468999999995 8885
No 67
>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=96.12 E-value=0.12 Score=46.11 Aligned_cols=29 Identities=17% Similarity=0.305 Sum_probs=24.1
Q ss_pred ceehHHHHHHHhcCCCCCCCHHHHHHHhCCC
Q 048020 95 TIDSLNLLTERFGRRAGDMKMASLATYFGLG 125 (304)
Q Consensus 95 ~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~ 125 (304)
.+|.+.+.++. . .+++++|+++|+++|+.
T Consensus 116 ~iDl~~~~~~~-~-~l~~y~L~~Va~~Lg~~ 144 (188)
T cd05781 116 NVDLYDFAEEI-P-EVKVKTLENVAEYLGVM 144 (188)
T ss_pred EEEhHHHHHhh-C-CCCCCCHHHHHHHHCCC
Confidence 78999999853 3 47899999999999874
No 68
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=95.70 E-value=0.44 Score=40.18 Aligned_cols=132 Identities=13% Similarity=0.114 Sum_probs=67.2
Q ss_pred CCcEEEEEEeecCCCC--ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCC--CChHHHHhcCCCHHHH-hCCCCHHHHHH
Q 048020 7 RSEIVFFDVETTFPIR--HIWEFGAILVCPRKLEELDKYTTLVRPADPSL--VSNLCARRNDITPEDV-FSAPTFADIAD 81 (304)
Q Consensus 7 ~~~~VvfDlETTGl~~--~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~--I~~~~~~ltGIT~e~L-~~ap~f~eVl~ 81 (304)
..++++||+||+|... .-..+..+.+..+ ....++.|..... +.....++-. ++.+ .=+-....-+.
T Consensus 19 ~~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~------~~~~i~~~~~~~~~~~~~~l~~ll~--~~~i~kv~~n~~~D~~ 90 (176)
T PF01612_consen 19 NAKVLAFDTETTGLDPYSYNPKIALIQLATG------EGCYIIDPIDLGDNWILDALKELLE--DPNIIKVGHNAKFDLK 90 (176)
T ss_dssp TTSEEEEEEEEETSTSTTSSEEEEEEEEEES------CEEEEECGTTSTTTTHHHHHHHHHT--TTTSEEEESSHHHHHH
T ss_pred CCCeEEEEEEECCCCccccCCeEEEEEEecC------CCceeeeeccccccchHHHHHHHHh--CCCccEEEEEEechHH
Confidence 3469999999999754 3333444444432 1233444443111 0111111110 0000 00112222233
Q ss_pred HHHHHhcCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHh-C-CC-------CCCC--C---------hHHHHHHHHHH
Q 048020 82 TVFDILQAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYF-G-LG-------QQTH--R---------SLDDVLMNLEV 141 (304)
Q Consensus 82 ~f~~fl~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~l-G-I~-------~~~H--r---------AL~DA~aTa~L 141 (304)
.+....+.. ..+++|| .++...+.+... ++|++|+..+ | +. .... + |..||..+.+|
T Consensus 91 ~L~~~~~i~-~~~~~D~-~l~~~~l~~~~~-~~L~~L~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l 167 (176)
T PF01612_consen 91 WLYRSFGID-LKNVFDT-MLAAYLLDPTRS-YSLKDLAEEYLGNIDLDKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRL 167 (176)
T ss_dssp HHHHHHTS---SSEEEH-HHHHHHTTTSTT-SSHHHHHHHHHSEEE-GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHH
T ss_pred HHHHHhccc-cCCccch-hhhhhccccccc-ccHHHHHHHHhhhccCcHHHhhccCCcCCCChHHHHHHHHHHHHHHHHH
Confidence 333322333 4578999 455546655433 9999998854 7 31 1112 3 56699999999
Q ss_pred HHHHHHHh
Q 048020 142 LKYCATVL 149 (304)
Q Consensus 142 ~~~ll~~l 149 (304)
+.+|.+++
T Consensus 168 ~~~l~~~l 175 (176)
T PF01612_consen 168 YEKLKPQL 175 (176)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHhh
Confidence 99998775
No 69
>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=94.63 E-value=1.1 Score=40.64 Aligned_cols=30 Identities=27% Similarity=0.305 Sum_probs=23.2
Q ss_pred eehHHHHHHHh--cCCCCCCCHHHHHHHhCCC
Q 048020 96 IDSLNLLTERF--GRRAGDMKMASLATYFGLG 125 (304)
Q Consensus 96 IDTl~Lark~l--~p~~~~~kL~~Lak~lGI~ 125 (304)
+|++.++++.- ...+.+|+|+++|++||+.
T Consensus 137 iDl~~~~~~~~~~~~~l~sysL~~Va~~~g~~ 168 (207)
T cd05785 137 IDTYFLVQLFDVSSRDLPSYGLKAVAKHFGLA 168 (207)
T ss_pred EEcHHHHHhhcccccCCCCCCHHHHHHHhccc
Confidence 89999888421 2356789999999999873
No 70
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=94.46 E-value=0.62 Score=45.92 Aligned_cols=133 Identities=17% Similarity=0.170 Sum_probs=74.9
Q ss_pred CCcEEEEEEeecCCCCceEEEEEEEEeCCceeeeeeEEEEEcCCCC-CCCChHHHHhc--CCCHHHHhCCCCHHHHHHHH
Q 048020 7 RSEIVFFDVETTFPIRHIWEFGAILVCPRKLEELDKYTTLVRPADP-SLVSNLCARRN--DITPEDVFSAPTFADIADTV 83 (304)
Q Consensus 7 ~~~~VvfDlETTGl~~~IIEIGAV~v~~g~~~iid~f~~lV~P~~~-~~I~~~~~~lt--GIT~e~L~~ap~f~eVl~~f 83 (304)
...++.+|+||.|....==+.+.|-+..+. . ..+|+|-.. ...++...-+. +|+. +-.+..|. +.-|
T Consensus 16 ~~~~iAiDTEf~r~~t~~p~LcLIQi~~~e-----~-~~lIdpl~~~~d~~~l~~Ll~d~~v~K--IfHaa~~D--L~~l 85 (361)
T COG0349 16 GSKAIAIDTEFMRLRTYYPRLCLIQISDGE-----G-ASLIDPLAGILDLPPLVALLADPNVVK--IFHAARFD--LEVL 85 (361)
T ss_pred CCCceEEecccccccccCCceEEEEEecCC-----C-ceEecccccccccchHHHHhcCCceee--eecccccc--HHHH
Confidence 356999999999965411113333344331 1 466777651 12333222111 1111 22222221 1112
Q ss_pred HHHhcCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHH-hCCC-CCC-------CC---------hHHHHHHHHHHHHHH
Q 048020 84 FDILQAPKPKGTIDSLNLLTERFGRRAGDMKMASLATY-FGLG-QQT-------HR---------SLDDVLMNLEVLKYC 145 (304)
Q Consensus 84 ~~fl~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~-lGI~-~~~-------Hr---------AL~DA~aTa~L~~~l 145 (304)
... ....+.+++||.-.++ +.+-.. +++|.+|++. +|+. ... +| |..||..+..++.++
T Consensus 86 ~~~-~g~~p~plfdTqiAa~-l~g~~~-~~gl~~Lv~~ll~v~ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L 162 (361)
T COG0349 86 LNL-FGLLPTPLFDTQIAAK-LAGFGT-SHGLADLVEELLGVELDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKL 162 (361)
T ss_pred HHh-cCCCCCchhHHHHHHH-HhCCcc-cccHHHHHHHHhCCcccccccccccccCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 222 2445789999987777 554333 8999999986 4763 111 22 688999999999999
Q ss_pred HHHhhhc
Q 048020 146 ATVLLLE 152 (304)
Q Consensus 146 l~~l~le 152 (304)
.+++..+
T Consensus 163 ~~~L~~~ 169 (361)
T COG0349 163 TEELARE 169 (361)
T ss_pred HHHHHHc
Confidence 8887543
No 71
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=94.10 E-value=0.28 Score=49.45 Aligned_cols=117 Identities=14% Similarity=0.168 Sum_probs=62.9
Q ss_pred CCcEEEEEEeecCCCCceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCC---ChHHHHhcCCCHHHHh-CCCCHHHHHHH
Q 048020 7 RSEIVFFDVETTFPIRHIWEFGAILVCPRKLEELDKYTTLVRPADPSLV---SNLCARRNDITPEDVF-SAPTFADIADT 82 (304)
Q Consensus 7 ~~~~VvfDlETTGl~~~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I---~~~~~~ltGIT~e~L~-~ap~f~eVl~~ 82 (304)
....++||+||+.-..-.-.+|++..+++ ...+.|..|.......+- ..+..-+......-+- -+......+.+
T Consensus 283 ~~~~~ffDiEt~P~~~~~yL~G~~~~~~~--~~~~~~~~fla~~~~~E~~~~~~f~~~l~~~~~~~i~hY~~~e~~~l~r 360 (457)
T TIGR03491 283 APGELIFDIESDPDENLDYLHGFLVVDKG--QENEKYRPFLAEDPNTEELAWQQFLQLLQSYPDAPIYHYGETEKDSLRR 360 (457)
T ss_pred CCccEEEEecCCCCCCCceEEEEEEecCC--CCCcceeeeecCCchHHHHHHHHHHHHHHHCCCCeEEeeCHHHHHHHHH
Confidence 35678999999942236788998776654 233458878766541100 1111111111100010 01111222222
Q ss_pred HHHHhcCC------CCCCceehHHHHHHHhcCCCCCCCHHHHHHHhCCC
Q 048020 83 VFDILQAP------KPKGTIDSLNLLTERFGRRAGDMKMASLATYFGLG 125 (304)
Q Consensus 83 f~~fl~~~------~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~ 125 (304)
+..-.+.+ +..+++|.....++.+.-...+|+|..++..+|..
T Consensus 361 la~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~sysLK~v~~~lg~~ 409 (457)
T TIGR03491 361 LAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIESYSLKSIARWLGFE 409 (457)
T ss_pred HHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCCCCCHHHHHHHhCcc
Confidence 22222111 12288999988886554445889999999999995
No 72
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=93.00 E-value=0.14 Score=55.32 Aligned_cols=138 Identities=17% Similarity=0.150 Sum_probs=88.1
Q ss_pred CCCCcEEEEEEeecCCCCceEEE----------------EEEEEeCCc--eeeeeeEEEEEcCCCCCCCChHHHHhcCCC
Q 048020 5 QDRSEIVFFDVETTFPIRHIWEF----------------GAILVCPRK--LEELDKYTTLVRPADPSLVSNLCARRNDIT 66 (304)
Q Consensus 5 ~~~~~~VvfDlETTGl~~~IIEI----------------GAV~v~~g~--~~iid~f~~lV~P~~~~~I~~~~~~ltGIT 66 (304)
|-...+|.+|-|..-++.+..|| |-+.+-.|. ++-+---.-||--.. .+-.+.++..||-
T Consensus 907 Pk~g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msvARiScvRGeGp~eGiPFiDDYv~T~d--~VvDYLTqySGI~ 984 (1118)
T KOG1275|consen 907 PKSGDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSVARISCVRGEGPNEGIPFIDDYVSTDD--KVVDYLTQYSGIK 984 (1118)
T ss_pred CCCCceeeeehhheecchHHhccccCCceeEeccccceeEEEEEEcccCCCCCCccccceecchh--HHHHHHHHhcCCC
Confidence 34567899999988865422222 222222221 111222244666666 7889999999999
Q ss_pred HHHHhCCC------CHHHHHHHHHHHh---------c----------CCCCCCceehHHHHHHHhcCCCCCCCHHHHHHH
Q 048020 67 PEDVFSAP------TFADIADTVFDIL---------Q----------APKPKGTIDSLNLLTERFGRRAGDMKMASLATY 121 (304)
Q Consensus 67 ~e~L~~ap------~f~eVl~~f~~fl---------~----------~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~ 121 (304)
+.||.-.. +...++.++.-.+ + .-....++||+.+.+ .+...-.+|..||.+
T Consensus 985 PGDLDp~~S~K~Lt~lK~~Y~Kl~~Li~~GviFVGHGL~nDFrvINi~Vp~~QiiDTv~lf~---~~s~R~LSLrfLa~~ 1061 (1118)
T KOG1275|consen 985 PGDLDPTTSEKRLTTLKVLYLKLRLLIQRGVIFVGHGLQNDFRVINIHVPEEQIIDTVTLFR---LGSQRMLSLRFLAWE 1061 (1118)
T ss_pred ccccCCccCcceehhHHHHHHHHHHHHHcCcEEEcccccccceEEEEecChhhheeeeEEEe---cccccEEEHHHHHHH
Confidence 99997432 3455555554444 0 111346788876655 233455679999987
Q ss_pred h-CC--CCCCCChHHHHHHHHHHHHHHHH
Q 048020 122 F-GL--GQQTHRSLDDVLMNLEVLKYCAT 147 (304)
Q Consensus 122 l-GI--~~~~HrAL~DA~aTa~L~~~ll~ 147 (304)
+ |- ...+|+...||+.+.++|++.++
T Consensus 1062 lLg~~IQ~~~HDSIeDA~taLkLYk~Yl~ 1090 (1118)
T KOG1275|consen 1062 LLGETIQMEAHDSIEDARTALKLYKKYLK 1090 (1118)
T ss_pred HhcchhhccccccHHHHHHHHHHHHHHHH
Confidence 5 54 47899999999999999988764
No 73
>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=92.93 E-value=2.3 Score=38.89 Aligned_cols=52 Identities=19% Similarity=0.294 Sum_probs=38.0
Q ss_pred CceehHHHHHHHhcCCCCCCCHHHHHHHhCCCCC---------------C-----CChHHHHHHHHHHHHHHHH
Q 048020 94 GTIDSLNLLTERFGRRAGDMKMASLATYFGLGQQ---------------T-----HRSLDDVLMNLEVLKYCAT 147 (304)
Q Consensus 94 ~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~~~---------------~-----HrAL~DA~aTa~L~~~ll~ 147 (304)
+-+|++++.. .++ .....+|+.||+.+|||+. . .=-..||.+|+.||.++.-
T Consensus 100 ~H~DLmd~l~-~~g-~~~~~sLd~la~~lgiPgK~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~ 171 (209)
T PF10108_consen 100 RHLDLMDLLS-FYG-AKARTSLDELAALLGIPGKDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFEL 171 (209)
T ss_pred ccccHHHHHh-ccC-ccccCCHHHHHHHcCCCCCCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4688888776 332 3467899999999999621 1 1126799999999998854
No 74
>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=92.73 E-value=2.4 Score=38.66 Aligned_cols=70 Identities=16% Similarity=0.155 Sum_probs=40.6
Q ss_pred CCCcEEEEEEeecC-----CCC---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHH
Q 048020 6 DRSEIVFFDVETTF-----PIR---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFA 77 (304)
Q Consensus 6 ~~~~~VvfDlETTG-----l~~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~ 77 (304)
-..+.+.||+||+. |++ +|+.|+++.-.++......+.-..+++.. +++ ...+..-++..
T Consensus 5 p~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~~~~--~~~----------~~~v~~~~~E~ 72 (230)
T cd05777 5 APLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCA--PIV----------GAQVFSFETEE 72 (230)
T ss_pred CCceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeCCCC--CCC----------CCEEEEECCHH
Confidence 34578999999985 233 99999988655442122122111233322 222 12233356778
Q ss_pred HHHHHHHHHh
Q 048020 78 DIADTVFDIL 87 (304)
Q Consensus 78 eVl~~f~~fl 87 (304)
+.+.+|.+++
T Consensus 73 eLL~~f~~~i 82 (230)
T cd05777 73 ELLLAWRDFV 82 (230)
T ss_pred HHHHHHHHHH
Confidence 8888888877
No 75
>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=91.68 E-value=3.4 Score=37.92 Aligned_cols=139 Identities=12% Similarity=0.059 Sum_probs=83.1
Q ss_pred CcEEEEEEeecC-----CCC---ceEEEEEEEEeCCceeee---eeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCH
Q 048020 8 SEIVFFDVETTF-----PIR---HIWEFGAILVCPRKLEEL---DKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTF 76 (304)
Q Consensus 8 ~~~VvfDlETTG-----l~~---~IIEIGAV~v~~g~~~ii---d~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f 76 (304)
.+++.||+|+.+ |++ .|+.|+.+.-.+...... ....-++.+... ..... .....+....|.--++.
T Consensus 4 l~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~-~~~~~~~~~~v~~~~~E 81 (231)
T cd05778 4 LTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKS-NASNG-RIRSGLSGIPVEVVESE 81 (231)
T ss_pred eEEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccc-hhhhh-ccccCCCCCeEEEeCCH
Confidence 468899999986 233 999999885443311111 112344444431 11100 01123333445567888
Q ss_pred HHHHHHHHHHh------------------------------cC-------------C--------C-----------CCC
Q 048020 77 ADIADTVFDIL------------------------------QA-------------P--------K-----------PKG 94 (304)
Q Consensus 77 ~eVl~~f~~fl------------------------------~~-------------~--------~-----------~~~ 94 (304)
.+.+.+|.+++ .. . + ..-
T Consensus 82 ~~LL~~f~~~i~~~DPDii~GyNi~~fd~~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~~g~~~~~~~~i~GRi 161 (231)
T cd05778 82 LELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDEWGYTHTSGIKIVGRH 161 (231)
T ss_pred HHHHHHHHHHHHHhCCCEEEEeccccCcHHHHHHHHHHhCCcchhhhccCCCCCCcccccccccccccccCCceEEeeEE
Confidence 89999999888 00 0 0 012
Q ss_pred ceehHHHHHHHhcCCCCCCCHHHHHHH-hCC--CCCCCChHHHHH------HHHHHHHHHHHHhh
Q 048020 95 TIDSLNLLTERFGRRAGDMKMASLATY-FGL--GQQTHRSLDDVL------MNLEVLKYCATVLL 150 (304)
Q Consensus 95 ~IDTl~Lark~l~p~~~~~kL~~Lak~-lGI--~~~~HrAL~DA~------aTa~L~~~ll~~l~ 150 (304)
.+|.+.++|+. -.+.+|+|++++.+ ||- +.-+|..+.+.+ ...+++.+++++..
T Consensus 162 ~lD~~~~~r~~--~kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~ 224 (231)
T cd05778 162 ILNVWRLMRSE--LALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVR 224 (231)
T ss_pred EeEhHHHHHHH--cCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHH
Confidence 46788888853 36789999999995 565 355667677764 45677777777654
No 76
>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=88.51 E-value=3.9 Score=34.85 Aligned_cols=125 Identities=17% Similarity=0.171 Sum_probs=70.1
Q ss_pred CCcEEEEEEeecCCC------C-ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHh-CCCCHHH
Q 048020 7 RSEIVFFDVETTFPI------R-HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVF-SAPTFAD 78 (304)
Q Consensus 7 ~~~~VvfDlETTGl~------~-~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~-~ap~f~e 78 (304)
....+.||+|+++.. + .+|||+. .+ ...++++.....+++...++-. +..+. -+-....
T Consensus 17 ~~~~ig~D~E~~~~~~~~~~~~~~liQl~~---~~--------~~~l~~~~~~~~~~~~l~~ll~--~~~i~kv~~~~k~ 83 (170)
T cd06141 17 KEKVVGFDTEWRPSFRKGKRNKVALLQLAT---ES--------RCLLFQLAHMDKLPPSLKQLLE--DPSILKVGVGIKG 83 (170)
T ss_pred CCCEEEEeCccCCccCCCCCCCceEEEEec---CC--------cEEEEEhhhhhcccHHHHHHhc--CCCeeEEEeeeHH
Confidence 568999999999852 2 7888872 21 1233443331134443433321 11110 0111233
Q ss_pred HHHHHHHHhcCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHh-CCC-C------------------CCCChHHHHHHH
Q 048020 79 IADTVFDILQAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYF-GLG-Q------------------QTHRSLDDVLMN 138 (304)
Q Consensus 79 Vl~~f~~fl~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~l-GI~-~------------------~~HrAL~DA~aT 138 (304)
-+..+....+... ..++|+..++. .+.+.....+|..+++.| |+. . +-|=|..||+.+
T Consensus 84 D~~~L~~~~g~~~-~~~~Dl~~aa~-ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt~~qi~YAa~Da~~~ 161 (170)
T cd06141 84 DARKLARDFGIEV-RGVVDLSHLAK-RVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYAS 161 (170)
T ss_pred HHHHHHhHcCCCC-CCeeeHHHHHH-HhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCCCCCCHHHHHHHHHHHHHH
Confidence 3333433333333 34599998887 666654446999999986 552 1 124578899999
Q ss_pred HHHHHHHH
Q 048020 139 LEVLKYCA 146 (304)
Q Consensus 139 a~L~~~ll 146 (304)
.+|+.+|.
T Consensus 162 ~~l~~~l~ 169 (170)
T cd06141 162 LELYRKLL 169 (170)
T ss_pred HHHHHHHh
Confidence 99988764
No 77
>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=88.43 E-value=9 Score=34.27 Aligned_cols=30 Identities=17% Similarity=0.317 Sum_probs=22.5
Q ss_pred ceehHHHHHHHhcCCCCCCCHHHHHHHh-CCC
Q 048020 95 TIDSLNLLTERFGRRAGDMKMASLATYF-GLG 125 (304)
Q Consensus 95 ~IDTl~Lark~l~p~~~~~kL~~Lak~l-GI~ 125 (304)
.+|++.+.++.. ..+.+|+|+++|+++ |..
T Consensus 123 ~~D~~~~~k~~~-~kl~sy~L~~Va~~~Lg~~ 153 (193)
T cd05784 123 VLDGIDALKTAT-YHFESFSLENVAQELLGEG 153 (193)
T ss_pred EEEhHHHHHHcc-CCCCcCCHHHHHHHHhCCC
Confidence 788888887422 358999999999965 443
No 78
>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=87.67 E-value=4.2 Score=34.79 Aligned_cols=125 Identities=15% Similarity=0.071 Sum_probs=68.8
Q ss_pred CCcEEEEEEeecCCCC-----ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHh-CCCCHHHHH
Q 048020 7 RSEIVFFDVETTFPIR-----HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVF-SAPTFADIA 80 (304)
Q Consensus 7 ~~~~VvfDlETTGl~~-----~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~-~ap~f~eVl 80 (304)
...++.||+|+..... .+|||+. .++. ..++++......++...++-. +..+. -+-....-+
T Consensus 12 ~~~~ig~D~E~~~~~~~~~~~~liQl~~---~~~~-------~~l~d~~~~~~~~~~L~~lL~--d~~i~Kvg~~~k~D~ 79 (161)
T cd06129 12 DGDVIAFDMEWPPGRRYYGEVALIQLCV---SEEK-------CYLFDPLSLSVDWQGLKMLLE--NPSIVKALHGIEGDL 79 (161)
T ss_pred CCCEEEEECCccCCCCCCCceEEEEEEE---CCCC-------EEEEecccCccCHHHHHHHhC--CCCEEEEEeccHHHH
Confidence 6789999999998532 7888874 2121 233333321112332323211 11110 011122223
Q ss_pred HHHHHHhcCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHh-CCC-----------------CCCCChHHHHHHHHHHH
Q 048020 81 DTVFDILQAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYF-GLG-----------------QQTHRSLDDVLMNLEVL 142 (304)
Q Consensus 81 ~~f~~fl~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~l-GI~-----------------~~~HrAL~DA~aTa~L~ 142 (304)
..+....+... ...+||...++ .+.+. .+.+|..+++.| |+. .+-|=|..||+++.+||
T Consensus 80 ~~L~~~~gi~~-~~~~D~~~aa~-ll~~~-~~~~L~~l~~~~lg~~l~K~~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~ 156 (161)
T cd06129 80 WKLLRDFGEKL-QRLFDTTIAAN-LKGLP-ERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIY 156 (161)
T ss_pred HHHHHHcCCCc-ccHhHHHHHHH-HhCCC-CCchHHHHHHHHhCCCCCccceeccCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 33333223332 35699987777 66654 456999999975 652 12356889999999999
Q ss_pred HHHH
Q 048020 143 KYCA 146 (304)
Q Consensus 143 ~~ll 146 (304)
.+|.
T Consensus 157 ~~l~ 160 (161)
T cd06129 157 TKLR 160 (161)
T ss_pred HHHh
Confidence 8764
No 79
>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=87.44 E-value=2.5 Score=37.55 Aligned_cols=55 Identities=22% Similarity=0.126 Sum_probs=39.3
Q ss_pred CCCceehHHHHHHHhcC---------CCCCCCHHHHHHHh-CCC-----------------CCCCChHHHHHHHHHHHHH
Q 048020 92 PKGTIDSLNLLTERFGR---------RAGDMKMASLATYF-GLG-----------------QQTHRSLDDVLMNLEVLKY 144 (304)
Q Consensus 92 ~~~~IDTl~Lark~l~p---------~~~~~kL~~Lak~l-GI~-----------------~~~HrAL~DA~aTa~L~~~ 144 (304)
...++||..+++..... ....++|..|++.+ |.+ .+-+=|..||+++..||.+
T Consensus 111 ~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~ 190 (193)
T cd06146 111 VQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDK 190 (193)
T ss_pred CCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 47899999888843221 12468999999975 542 1235588999999999998
Q ss_pred HH
Q 048020 145 CA 146 (304)
Q Consensus 145 ll 146 (304)
|.
T Consensus 191 L~ 192 (193)
T cd06146 191 LL 192 (193)
T ss_pred Hh
Confidence 75
No 80
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=87.12 E-value=7.4 Score=43.60 Aligned_cols=29 Identities=10% Similarity=0.147 Sum_probs=22.3
Q ss_pred CceehHHHHHHHhcCCCCCCCHHHHHHHh-CC
Q 048020 94 GTIDSLNLLTERFGRRAGDMKMASLATYF-GL 124 (304)
Q Consensus 94 ~~IDTl~Lark~l~p~~~~~kL~~Lak~l-GI 124 (304)
-.+|++.++++. ..+.+|+|++++.+| |.
T Consensus 411 ~~iDl~~~~~~~--~kl~sYsL~~Vs~~~Lg~ 440 (1054)
T PTZ00166 411 IQFDVMDLIRRD--YKLKSYSLNYVSFEFLKE 440 (1054)
T ss_pred EEEEHHHHHHHh--cCcCcCCHHHHHHHHhCC
Confidence 457888888853 367899999999965 54
No 81
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=86.93 E-value=0.72 Score=42.02 Aligned_cols=63 Identities=10% Similarity=0.171 Sum_probs=46.2
Q ss_pred ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCC------hHHHHhcCCCHHHHhCCC-CHHHHHHHHHHHh
Q 048020 23 HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVS------NLCARRNDITPEDVFSAP-TFADIADTVFDIL 87 (304)
Q Consensus 23 ~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~------~~~~~ltGIT~e~L~~ap-~f~eVl~~f~~fl 87 (304)
-++|||++++.-..| +++.|+++|+|+.. ++. ..+...|+|..+-.+.+. .+..++.++.+|+
T Consensus 9 ~PaEiai~~fSL~~G-I~~~~H~~I~Pg~~-p~G~~~~a~~hs~~tH~ip~~~~~~~~~d~~~l~~~l~~fl 78 (213)
T PF13017_consen 9 VPAEIAICKFSLKEG-IIDSFHTFINPGQI-PLGYRYDAQHHSDETHQIPIPPNALGESDYSELYNELLNFL 78 (213)
T ss_pred EeEEEEEEEEecCCc-cchhhhcccCCCCC-CcHHHHHHHHhhhhhcCCCCCCcccccCCHHHHHHHHHHHh
Confidence 679999999985443 88999999999973 222 122345666655455555 6999999999999
No 82
>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006133 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold [].; GO: 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 4AHC_A 3A2F_A 2JGU_A 4AIL_C 1NOY_A 1NOZ_B 3IAY_A 1WNS_A 3K5O_A ....
Probab=86.48 E-value=3.3 Score=38.70 Aligned_cols=70 Identities=16% Similarity=0.173 Sum_probs=42.9
Q ss_pred CCcEEEEEEeecCCC-----C---ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHHH
Q 048020 7 RSEIVFFDVETTFPI-----R---HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFAD 78 (304)
Q Consensus 7 ~~~~VvfDlETTGl~-----~---~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~e 78 (304)
..+++.||+||.... + +|+.|+++.-..+...........+++.. .... ...+.-.++..+
T Consensus 156 ~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~~~~~--~~~~---------~~~v~~~~~E~~ 224 (325)
T PF03104_consen 156 PLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTLGSCD--SIED---------NVEVIYFDSEKE 224 (325)
T ss_dssp GSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEECSCSC--CTTC---------TTEEEEESSHHH
T ss_pred ccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEecCCC--CCCC---------CcEEEEECCHHH
Confidence 457899999999853 2 99999988765431112222222233333 1111 334445678888
Q ss_pred HHHHHHHHh
Q 048020 79 IADTVFDIL 87 (304)
Q Consensus 79 Vl~~f~~fl 87 (304)
.+..|.+++
T Consensus 225 lL~~f~~~i 233 (325)
T PF03104_consen 225 LLEAFLDII 233 (325)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 888888888
No 83
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=86.11 E-value=0.17 Score=56.67 Aligned_cols=42 Identities=10% Similarity=-0.126 Sum_probs=37.2
Q ss_pred CCceeeec---cCcccc---cccccccccccCcccCCCCccccCCCcc
Q 048020 174 RINVRSSP---EGTSQN---LSAPSSKFKFENASNVSPPDQGKEGIHP 215 (304)
Q Consensus 174 r~~h~~il---~~glkn---lvs~s~~~yf~~~prip~s~~~~~~~~~ 215 (304)
..+|.++| +.|.+| |+|.+|++.||.+|||+++.|.+|.-+-
T Consensus 86 ~~~~l~lLAkn~~Gy~nL~kL~S~a~~~~~~~~pri~~~~L~~~~~gL 133 (1151)
T PRK06826 86 ETYHLVLLAKNETGYKNLMKIVSKAFTEGFYYKPRVDHELLKEHSEGL 133 (1151)
T ss_pred CCceEEEEEcCcHHHHHHHHHHHHHhccCCcCCccCCHHHHHhhCCCC
Confidence 45799999 779999 9999999999888999999999988653
No 84
>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=85.07 E-value=18 Score=35.65 Aligned_cols=127 Identities=16% Similarity=0.068 Sum_probs=69.8
Q ss_pred CCcEEEEEEeecCCCC-----ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHh-CCCCHHHHH
Q 048020 7 RSEIVFFDVETTFPIR-----HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVF-SAPTFADIA 80 (304)
Q Consensus 7 ~~~~VvfDlETTGl~~-----~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~-~ap~f~eVl 80 (304)
...++.||+|+.+... -+|||+. ++ -..+|.|-....+++ ..++-. +..+. -.-...+-+
T Consensus 17 ~~~~ia~DtE~~~~~~y~~~l~LiQia~----~~-------~~~liD~~~~~~~~~-L~~lL~--d~~i~KV~h~~k~Dl 82 (367)
T TIGR01388 17 TFPFVALDTEFVRERTFWPQLGLIQVAD----GE-------QLALIDPLVIIDWSP-LKELLR--DESVVKVLHAASEDL 82 (367)
T ss_pred cCCEEEEeccccCCCCCCCcceEEEEee----CC-------eEEEEeCCCcccHHH-HHHHHC--CCCceEEEeecHHHH
Confidence 3579999999988532 6677763 22 124566654101111 111111 11110 001112222
Q ss_pred HHHHHHhcCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHh-CCC--CC------CCC---------hHHHHHHHHHHH
Q 048020 81 DTVFDILQAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYF-GLG--QQ------THR---------SLDDVLMNLEVL 142 (304)
Q Consensus 81 ~~f~~fl~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~l-GI~--~~------~Hr---------AL~DA~aTa~L~ 142 (304)
..|... ....+..++||.-.+. .+++.. +++|..|++.| |+. .. ..| |..||.++..++
T Consensus 83 ~~L~~~-~~~~~~~~fDtqlAa~-lL~~~~-~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~ 159 (367)
T TIGR01388 83 EVFLNL-FGELPQPLFDTQIAAA-FCGFGM-SMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLY 159 (367)
T ss_pred HHHHHH-hCCCCCCcccHHHHHH-HhCCCC-CccHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 333322 2234567899986665 676643 46999998865 663 11 133 788899999999
Q ss_pred HHHHHHhh
Q 048020 143 KYCATVLL 150 (304)
Q Consensus 143 ~~ll~~l~ 150 (304)
..+.+++.
T Consensus 160 ~~L~~~L~ 167 (367)
T TIGR01388 160 AKLMERLE 167 (367)
T ss_pred HHHHHHHH
Confidence 99988775
No 85
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=84.68 E-value=0.56 Score=52.60 Aligned_cols=42 Identities=10% Similarity=-0.130 Sum_probs=36.9
Q ss_pred CCCceeeec---cCcccc---ccccccccccc-CcccCCCCccccCCCc
Q 048020 173 SRINVRSSP---EGTSQN---LSAPSSKFKFE-NASNVSPPDQGKEGIH 214 (304)
Q Consensus 173 ~r~~h~~il---~~glkn---lvs~s~~~yf~-~~prip~s~~~~~~~~ 214 (304)
.+.+|.++| +.|.+| |+|.+|++.|| .+|||++..|.+|.-+
T Consensus 80 ~~~~~l~llAkn~~Gy~nL~kL~S~~~~~~~~~~~p~i~~~~L~~~~~g 128 (1135)
T PRK05673 80 GAYTHLTLLAKNETGYRNLFKLSSRAYLEGQYGYKPRIDREWLAEHSEG 128 (1135)
T ss_pred cCCCceEEEecCHHHHHHHHHHHHHHHhcCCCCCCcccCHHHHHccCCC
Confidence 456799999 779999 99999999988 8899999999999754
No 86
>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=83.15 E-value=8.8 Score=31.07 Aligned_cols=32 Identities=16% Similarity=0.196 Sum_probs=25.1
Q ss_pred CCCCceehHHHHHHHhcCCCCCCCHHHHHHHhC
Q 048020 91 KPKGTIDSLNLLTERFGRRAGDMKMASLATYFG 123 (304)
Q Consensus 91 ~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~lG 123 (304)
....++||+.+++ .+.|...+++|+.+++.|.
T Consensus 76 ~~~~~~D~~~~ay-ll~~~~~~~~l~~l~~~~l 107 (155)
T cd00007 76 LPGNIFDTMLAAY-LLNPGEGSHSLDDLAKEYL 107 (155)
T ss_pred CCCCcccHHHHHH-HhCCCCCcCCHHHHHHHHc
Confidence 4567899987777 7788653579999999873
No 87
>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=81.29 E-value=22 Score=31.98 Aligned_cols=18 Identities=17% Similarity=0.180 Sum_probs=14.2
Q ss_pred HhCCCCHHHHHHHHHHHh
Q 048020 70 VFSAPTFADIADTVFDIL 87 (304)
Q Consensus 70 L~~ap~f~eVl~~f~~fl 87 (304)
+..-.+..+++.+|.+|+
T Consensus 67 v~~~~~E~~lL~~F~~~i 84 (204)
T cd05783 67 VEFFDSEKELIREAFKII 84 (204)
T ss_pred EEecCCHHHHHHHHHHHH
Confidence 334568889999999988
No 88
>PRK10829 ribonuclease D; Provisional
Probab=81.02 E-value=27 Score=34.67 Aligned_cols=122 Identities=15% Similarity=0.074 Sum_probs=70.1
Q ss_pred CCcEEEEEEeecCCCC-----ceEEEEEEEEeCCceeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCC------C
Q 048020 7 RSEIVFFDVETTFPIR-----HIWEFGAILVCPRKLEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAP------T 75 (304)
Q Consensus 7 ~~~~VvfDlETTGl~~-----~IIEIGAV~v~~g~~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap------~ 75 (304)
...+++||+|+.+... .+|||+ .++ -..+|.|-....+++. .+-+.+.. .
T Consensus 21 ~~~~lalDtEf~~~~ty~~~l~LiQl~----~~~-------~~~LiD~l~~~d~~~L--------~~ll~~~~ivKV~H~ 81 (373)
T PRK10829 21 AFPAIALDTEFVRTRTYYPQLGLIQLY----DGE-------QLSLIDPLGITDWSPF--------KALLRDPQVTKFLHA 81 (373)
T ss_pred cCCeEEEecccccCccCCCceeEEEEe----cCC-------ceEEEecCCccchHHH--------HHHHcCCCeEEEEeC
Confidence 4578999999998543 666666 122 1356666541111111 11111111 0
Q ss_pred HHHHHHHHHHHhcCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHH-hCCC----C-------------CCCChHHHHHH
Q 048020 76 FADIADTVFDILQAPKPKGTIDSLNLLTERFGRRAGDMKMASLATY-FGLG----Q-------------QTHRSLDDVLM 137 (304)
Q Consensus 76 f~eVl~~f~~fl~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~-lGI~----~-------------~~HrAL~DA~a 137 (304)
..+=+.-|...++. .+.+++||.-.++ .++.+ .+++|..|++. +|+. . +-+=|..||..
T Consensus 82 ~~~Dl~~l~~~~g~-~p~~~fDTqiaa~-~lg~~-~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~ 158 (373)
T PRK10829 82 GSEDLEVFLNAFGE-LPQPLIDTQILAA-FCGRP-LSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFY 158 (373)
T ss_pred hHhHHHHHHHHcCC-CcCCeeeHHHHHH-HcCCC-ccccHHHHHHHHhCCccCcccccCCCCCCCCCHHHHHHHHHHHHH
Confidence 11112223333333 3578999986666 55422 36799999885 5773 1 12347899999
Q ss_pred HHHHHHHHHHHhh
Q 048020 138 NLEVLKYCATVLL 150 (304)
Q Consensus 138 Ta~L~~~ll~~l~ 150 (304)
+..|+.+|.+++.
T Consensus 159 L~~l~~~L~~~L~ 171 (373)
T PRK10829 159 LLPIAAKLMAETE 171 (373)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999988775
No 89
>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=80.57 E-value=28 Score=31.35 Aligned_cols=30 Identities=23% Similarity=0.452 Sum_probs=24.0
Q ss_pred CceehHHHHHHHhcCCCCCCCHHHHHHHhCCC
Q 048020 94 GTIDSLNLLTERFGRRAGDMKMASLATYFGLG 125 (304)
Q Consensus 94 ~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~ 125 (304)
+.+|++.+.+. +. ...+++|+.+|+.+|++
T Consensus 140 ~h~DL~~~~~~-~~-~~~~~~L~~va~~lG~~ 169 (208)
T cd05782 140 RHLDLMDLLAF-YG-ARARASLDLLAKLLGIP 169 (208)
T ss_pred CcccHHHHHhc-cC-ccCCCCHHHHHHHhCCC
Confidence 47899988873 32 35789999999999995
No 90
>PRK05762 DNA polymerase II; Reviewed
Probab=80.02 E-value=14 Score=39.94 Aligned_cols=50 Identities=10% Similarity=0.155 Sum_probs=35.7
Q ss_pred ceehHHHHHHHhcCCCCCCCHHHHHHHhCC-CCCCCC----------------------hHHHHHHHHHHHHHH
Q 048020 95 TIDSLNLLTERFGRRAGDMKMASLATYFGL-GQQTHR----------------------SLDDVLMNLEVLKYC 145 (304)
Q Consensus 95 ~IDTl~Lark~l~p~~~~~kL~~Lak~lGI-~~~~Hr----------------------AL~DA~aTa~L~~~l 145 (304)
.+|++.++++.+ ..+.+++|+++|+++.. ...-|+ .+.||..|.+|+.++
T Consensus 276 ~lDl~~~~k~~~-~~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 276 VLDGIDALKSAT-WVFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred EEEHHHHHHHhh-ccCCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHh
Confidence 689999988543 36789999999998644 211111 367888999888744
No 91
>PRK09532 DNA polymerase III subunit alpha; Reviewed
Probab=79.07 E-value=0.43 Score=52.14 Aligned_cols=43 Identities=12% Similarity=-0.109 Sum_probs=36.7
Q ss_pred cCCCceeeec---cCcccc---cccccccccc-----cCcccCCCCccccCCCc
Q 048020 172 RSRINVRSSP---EGTSQN---LSAPSSKFKF-----ENASNVSPPDQGKEGIH 214 (304)
Q Consensus 172 ~~r~~h~~il---~~glkn---lvs~s~~~yf-----~~~prip~s~~~~~~~~ 214 (304)
+.+.+|.++| +.|.+| |+|.+|++.| +.+|||++..|.+|.-+
T Consensus 79 ~~~~~~lvLLAkN~~GY~NL~kL~S~a~~~~~~~~~~~~~P~i~~e~L~~~~~g 132 (874)
T PRK09532 79 RRRKYHQVVLAKNTQGYKNLVKLTTISHLQGVQGKGIFARPCINKELLEQYHEG 132 (874)
T ss_pred ccccceeEEEecCHHHHHHHHHHHhHHHHhcccccCccCCCcCCHHHHHhcCCC
Confidence 4567899999 669999 8999999987 57899999999998754
No 92
>PHA02528 43 DNA polymerase; Provisional
Probab=77.50 E-value=29 Score=38.31 Aligned_cols=50 Identities=14% Similarity=0.079 Sum_probs=35.6
Q ss_pred ceehHHHHHHHhcCCCCCCCHHHHHHH-hCCCCCCC------------------ChHHHHHHHHHHHHH
Q 048020 95 TIDSLNLLTERFGRRAGDMKMASLATY-FGLGQQTH------------------RSLDDVLMNLEVLKY 144 (304)
Q Consensus 95 ~IDTl~Lark~l~p~~~~~kL~~Lak~-lGI~~~~H------------------rAL~DA~aTa~L~~~ 144 (304)
.+|.+.++++..+..+.+|+|+++|++ ||.....| =.+.||..+.+|+.+
T Consensus 255 ~lD~~dl~k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 255 ILDYLDLYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred EEeHHHHHHHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 467788888533456789999999995 78742111 126789999999887
No 93
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=76.85 E-value=0.63 Score=52.36 Aligned_cols=42 Identities=7% Similarity=-0.172 Sum_probs=35.3
Q ss_pred CCCceeeec---cCcccc---ccccccccc-----ccCcccCCCCccccCCCc
Q 048020 173 SRINVRSSP---EGTSQN---LSAPSSKFK-----FENASNVSPPDQGKEGIH 214 (304)
Q Consensus 173 ~r~~h~~il---~~glkn---lvs~s~~~y-----f~~~prip~s~~~~~~~~ 214 (304)
.+.+|.++| +.|.+| |+|.+|++. ||.+|||++..|.+|.-+
T Consensus 82 ~~~~~l~LLAkN~~Gy~nL~kL~S~a~~~~~~~~~~~~~Pri~~~~L~~~~~g 134 (1170)
T PRK07374 82 EKRYHLVVLAKNATGYKNLVKLTTISHLNGMRGRGIFSRPCIDKELLKQYSEG 134 (1170)
T ss_pred cccceEEEEEeCcHHHHHHHHHHHHHHHhcccccCcCCCCcCcHHHHHhcCCC
Confidence 356899999 779999 999999875 455799999999999865
No 94
>TIGR00594 polc DNA-directed DNA polymerase III (polc). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.71 E-value=0.56 Score=52.10 Aligned_cols=42 Identities=10% Similarity=-0.122 Sum_probs=37.1
Q ss_pred CCCceeeec---cCcccc---cccccccccccCcccCCCCccccCCCc
Q 048020 173 SRINVRSSP---EGTSQN---LSAPSSKFKFENASNVSPPDQGKEGIH 214 (304)
Q Consensus 173 ~r~~h~~il---~~glkn---lvs~s~~~yf~~~prip~s~~~~~~~~ 214 (304)
.+.+|.++| +.|.+| |+|.+|++.|+.+|||++..|.+|.-+
T Consensus 82 ~~~~~l~llAkn~~Gy~nL~kL~S~a~~~~~~~~p~i~~~~l~~~~~g 129 (1022)
T TIGR00594 82 KEAYHLILLAKNNTGYRNLMKLSSLAYLEGFYYKPRIDKELLEEHSEG 129 (1022)
T ss_pred CCCccEEEEeCCHHHHHHHHHHHHHHHhhCCCCCcccCHHHHHhcCCC
Confidence 456799999 779999 999999999998999999999998755
No 95
>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=76.02 E-value=28 Score=33.99 Aligned_cols=50 Identities=18% Similarity=0.312 Sum_probs=33.6
Q ss_pred CceehHHHHHHHhcCCCCCCCHHHHHHHhCC-CCC---CC------------------ChHHHHHHHHHHHHHH
Q 048020 94 GTIDSLNLLTERFGRRAGDMKMASLATYFGL-GQQ---TH------------------RSLDDVLMNLEVLKYC 145 (304)
Q Consensus 94 ~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI-~~~---~H------------------rAL~DA~aTa~L~~~l 145 (304)
-.+|++.+.++.+ .+.+++|+.+++++.- ... .+ --+.||..+.+++.++
T Consensus 149 ~~~Dl~~~~~~~~--kl~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 149 LVIDLYNLYKNKL--KLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred EEEEhHHHHHHHh--CcccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4678888888543 3789999999987533 211 00 0155888888888775
No 96
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=57.26 E-value=1e+02 Score=32.70 Aligned_cols=57 Identities=21% Similarity=0.239 Sum_probs=40.6
Q ss_pred CCCceehHHHHHHHhcCCCCCCCHHHHHHHh-CCCCC-----------------------CCChHHHHHHHHHHHHHHHH
Q 048020 92 PKGTIDSLNLLTERFGRRAGDMKMASLATYF-GLGQQ-----------------------THRSLDDVLMNLEVLKYCAT 147 (304)
Q Consensus 92 ~~~~IDTl~Lark~l~p~~~~~kL~~Lak~l-GI~~~-----------------------~HrAL~DA~aTa~L~~~ll~ 147 (304)
.....||+-.+. .+.|+...+.+++|+++| +.... .-.+..||.++.+++..+..
T Consensus 100 ~~~~~DtmlasY-ll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~ 178 (593)
T COG0749 100 PGVAFDTMLASY-LLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQLTFADVKLEKATEYAAEDADATLRLESILEP 178 (593)
T ss_pred ccchHHHHHHHh-ccCcCcCcCCHHHHHHHhcCCccchhHHhhccccccCccccchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 367889985544 778888889999999987 32100 12346788899999988876
Q ss_pred Hh
Q 048020 148 VL 149 (304)
Q Consensus 148 ~l 149 (304)
++
T Consensus 179 ~l 180 (593)
T COG0749 179 EL 180 (593)
T ss_pred Hh
Confidence 54
No 97
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=55.37 E-value=8.5 Score=35.90 Aligned_cols=141 Identities=13% Similarity=0.093 Sum_probs=79.1
Q ss_pred CcEEEEEEeecCC---------C----------C-----ceEEEEEEEEeCCceee----eeeEEEEEcCCCCCCCChHH
Q 048020 8 SEIVFFDVETTFP---------I----------R-----HIWEFGAILVCPRKLEE----LDKYTTLVRPADPSLVSNLC 59 (304)
Q Consensus 8 ~~~VvfDlETTGl---------~----------~-----~IIEIGAV~v~~g~~~i----id~f~~lV~P~~~~~I~~~~ 59 (304)
-++|.+|+|.-|. + . .||++|...-+..+... .=.|+.-.+|...- ..++.
T Consensus 42 Yn~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQlGlsLSDe~GN~P~~~sTWQFNF~F~l~~dm-ya~ES 120 (299)
T COG5228 42 YNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDENGNKPNGPSTWQFNFEFDLKKDM-YATES 120 (299)
T ss_pred CCceeeccccCceeecccccccccchHHHHHHhcccchhhhhheeeeeccccCCCCCCCceeEEEEEecchhhh-cchHH
Confidence 4689999999992 0 0 89999988776432222 22566667776631 22333
Q ss_pred H---HhcCCCHHHHhC-CCCHHHHHHHHHH----------Hh----------------cCCCCCCceehHHHHHHHhcCC
Q 048020 60 A---RRNDITPEDVFS-APTFADIADTVFD----------IL----------------QAPKPKGTIDSLNLLTERFGRR 109 (304)
Q Consensus 60 ~---~ltGIT~e~L~~-ap~f~eVl~~f~~----------fl----------------~~~~~~~~IDTl~Lark~l~p~ 109 (304)
. .-.||.-+.-+. +....|..+-+.. |+ ..|+++..=|-..+.. .++|+
T Consensus 121 ieLL~ksgIdFkkHe~~GI~v~eF~elLm~SGLvm~e~VtWitfHsaYDfgyLikilt~~plP~~~EdFy~~l~-~yfP~ 199 (299)
T COG5228 121 IELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITFHSAYDFGYLIKILTNDPLPNNKEDFYWWLH-QYFPN 199 (299)
T ss_pred HHHHHHcCCChhhHhhcCCCHHHHHHHHhccCceeccceEEEEeecchhHHHHHHHHhcCCCCccHHHHHHHHH-HHCcc
Confidence 2 234665544332 2222211111111 11 3455555555555554 34553
Q ss_pred CCC------------CCHHHHHHHhCCC--CCCCChHHHHHHHHHHHHHHHHHhh
Q 048020 110 AGD------------MKMASLATYFGLG--QQTHRSLDDVLMNLEVLKYCATVLL 150 (304)
Q Consensus 110 ~~~------------~kL~~Lak~lGI~--~~~HrAL~DA~aTa~L~~~ll~~l~ 150 (304)
.-+ ..|.+++.-+++. ++.|.|-.||..|+..|......++
T Consensus 200 fYDik~v~ks~~~~~KglQei~ndlql~r~g~QhQagsdaLlTa~~ff~~R~~~F 254 (299)
T COG5228 200 FYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRFSIF 254 (299)
T ss_pred ccchHHHHHhhhhhhhHHHHhcCcHhhhccchhhhccchhhhhhHHhcchhhhee
Confidence 222 2355556666774 7889999999999999977665554
No 98
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=53.96 E-value=58 Score=33.70 Aligned_cols=27 Identities=11% Similarity=0.125 Sum_probs=20.5
Q ss_pred ceehHHHHHHHhcCCCCCCCHHHHHHH
Q 048020 95 TIDSLNLLTERFGRRAGDMKMASLATY 121 (304)
Q Consensus 95 ~IDTl~Lark~l~p~~~~~kL~~Lak~ 121 (304)
.+|.+.++++.-...+.+|+|++++..
T Consensus 256 ~iDl~~l~kk~s~~~l~sYsL~~Vs~~ 282 (498)
T PHA02524 256 LMDYMDVFKKFSFTPMPDYKLGNVGYR 282 (498)
T ss_pred EeEHHHHHHHhhhccCCCCCHHHHHHH
Confidence 467888888431357899999999874
No 99
>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=51.91 E-value=1.2e+02 Score=27.68 Aligned_cols=115 Identities=14% Similarity=0.112 Sum_probs=69.2
Q ss_pred cEEEEEEeecCC--C-C-ceEEEEEEEEeCCc-------eeeeeeEEEEEcCCCCCCCChHHHHhcCCCHHHHhCCCCHH
Q 048020 9 EIVFFDVETTFP--I-R-HIWEFGAILVCPRK-------LEELDKYTTLVRPADPSLVSNLCARRNDITPEDVFSAPTFA 77 (304)
Q Consensus 9 ~~VvfDlETTGl--~-~-~IIEIGAV~v~~g~-------~~iid~f~~lV~P~~~~~I~~~~~~ltGIT~e~L~~ap~f~ 77 (304)
+++.|-+-|.-- . . +|+.|+++...+-. ......+..+++|......+......-.-....+.-.++..
T Consensus 4 ~v~sls~~T~~n~k~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~v~~~~~E~ 83 (234)
T cd05776 4 TVMSLSIKTVLNSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKVRIFENER 83 (234)
T ss_pred EEEEEEeEEEecCcCCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCCCCCchHHHHHHhcCCcEEEeCCHH
Confidence 345566666432 1 2 99999987755210 01234567777887642223322222222233456678889
Q ss_pred HHHHHHHHHh------------------------------------c------CC--------------CCCCceehHHH
Q 048020 78 DIADTVFDIL------------------------------------Q------AP--------------KPKGTIDSLNL 101 (304)
Q Consensus 78 eVl~~f~~fl------------------------------------~------~~--------------~~~~~IDTl~L 101 (304)
+.+..|.+++ + .+ ...-.+|++..
T Consensus 84 ~LL~~f~~~i~~~DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~~~ 163 (234)
T cd05776 84 ALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYLS 163 (234)
T ss_pred HHHHHHHHHHhhcCCCEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCchhhccHHH
Confidence 9999999988 0 00 01236788888
Q ss_pred HHHHhcCCCCCCCHHHHHH-HhCCC
Q 048020 102 LTERFGRRAGDMKMASLAT-YFGLG 125 (304)
Q Consensus 102 ark~l~p~~~~~kL~~Lak-~lGI~ 125 (304)
++.. .. ..+|+|+++|+ .+|..
T Consensus 164 ~k~~-~~-~~sY~L~~va~~~Lg~~ 186 (234)
T cd05776 164 AKEL-IR-CKSYDLTELSQQVLGIE 186 (234)
T ss_pred HHHH-hC-CCCCChHHHHHHHhCcC
Confidence 8854 33 79999999999 56763
No 100
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=42.34 E-value=5.6 Score=44.76 Aligned_cols=87 Identities=10% Similarity=0.004 Sum_probs=51.7
Q ss_pred HHHHHHHhCCC---CCCCChHHHHHHHHHHHHHHHHHhhhccCCccccccCCCCCCCccccCCCceeeec---cCcccc-
Q 048020 115 MASLATYFGLG---QQTHRSLDDVLMNLEVLKYCATVLLLESSLPDIFTGNGCVSQNATARSRINVRSSP---EGTSQN- 187 (304)
Q Consensus 115 L~~Lak~lGI~---~~~HrAL~DA~aTa~L~~~ll~~l~le~~lp~~l~~~~~~~~~~~~~~r~~h~~il---~~glkn- 187 (304)
|-..|+.+|.+ -.-|..+.-|. +.++.+.+ .++.--+--.+. +. +.. ....+|.++| +.|.+|
T Consensus 24 lv~~A~~~g~~alAlTDh~~m~Ga~---~F~~~a~~-~gIkPIiG~e~~---v~-~~~--~~~~~~l~LLAkn~~Gy~nL 93 (1107)
T PRK06920 24 LVVRAKELGYSSLAITDENVMYGVI---PFYKACKK-HGIHPIIGLTAS---IF-SEE--EEKSYPLVLLAENEIGYQNL 93 (1107)
T ss_pred HHHHHHHCCCCEEEEEeCChHhHHH---HHHHHHHH-cCCCEeeeeEEE---Ee-cCC--CCCcccEEEEeCCHHHHHHH
Confidence 34456668886 45677776554 33444433 222211110111 00 100 1146799999 779999
Q ss_pred --cccccccccccCcccCCCCccccCCCc
Q 048020 188 --LSAPSSKFKFENASNVSPPDQGKEGIH 214 (304)
Q Consensus 188 --lvs~s~~~yf~~~prip~s~~~~~~~~ 214 (304)
|+|.+|++. .|||+++.|.+|.-+
T Consensus 94 ~kL~S~~~~~~---~p~i~~~~L~~~~~g 119 (1107)
T PRK06920 94 LKISSSIMTKS---KEGIPKKWLAHYAKG 119 (1107)
T ss_pred HHHHHHHHhcC---CCCCCHHHHHhhCCC
Confidence 888888765 699999999998755
No 101
>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=39.54 E-value=1.6e+02 Score=24.86 Aligned_cols=62 Identities=10% Similarity=0.005 Sum_probs=40.4
Q ss_pred cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHh-CCC-C-------CCC------------ChHHHHHHHHHHHHHHH
Q 048020 88 QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYF-GLG-Q-------QTH------------RSLDDVLMNLEVLKYCA 146 (304)
Q Consensus 88 ~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~l-GI~-~-------~~H------------rAL~DA~aTa~L~~~ll 146 (304)
+..++..++||+-.+. ++.|...++++.++++.| |.. . ... -+..||.++..++..+.
T Consensus 75 gi~~~~~~fDt~laaY-LL~p~~~~~~l~~l~~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~ 153 (178)
T cd06140 75 GIELAGVAFDTMLAAY-LLDPTRSSYDLADLAKRYLGRELPSDEEVYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLE 153 (178)
T ss_pred CCcCCCcchhHHHHHH-HcCCCCCCCCHHHHHHHHcCCCCcchHHhcCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445567899986666 888876667999998875 442 1 000 14445666777777777
Q ss_pred HHhh
Q 048020 147 TVLL 150 (304)
Q Consensus 147 ~~l~ 150 (304)
+++.
T Consensus 154 ~~L~ 157 (178)
T cd06140 154 EELE 157 (178)
T ss_pred HHHH
Confidence 7664
No 102
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=38.98 E-value=1.5e+02 Score=24.27 Aligned_cols=60 Identities=12% Similarity=0.102 Sum_probs=37.3
Q ss_pred cCCCCCCceehHHHHHHHhcCCCCCCCHHHHHHHh-CCC-CC------------CC----ChHHHHHHHHHHHHHHHHHh
Q 048020 88 QAPKPKGTIDSLNLLTERFGRRAGDMKMASLATYF-GLG-QQ------------TH----RSLDDVLMNLEVLKYCATVL 149 (304)
Q Consensus 88 ~~~~~~~~IDTl~Lark~l~p~~~~~kL~~Lak~l-GI~-~~------------~H----rAL~DA~aTa~L~~~ll~~l 149 (304)
+....+ ++||+-.+. .+.|....++|..+++.| |.. .. .. -|..||.++.+++..+.+++
T Consensus 94 gi~~~~-~~D~~laay-ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 94 GIELEN-IFDTMLAAY-LLLGGPSKHGLATLLKEYLGVELDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred CCcccc-hhHHHHHHH-HHcCCCCcCCHHHHHHHHhCCCCCcccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 333343 499986666 677765547999999876 543 11 00 15566777777777666554
No 103
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=37.02 E-value=6.9 Score=43.84 Aligned_cols=43 Identities=5% Similarity=-0.252 Sum_probs=36.4
Q ss_pred CCceeeec---cCcccc---cccccccccccCcccCCCCccccCCCccc
Q 048020 174 RINVRSSP---EGTSQN---LSAPSSKFKFENASNVSPPDQGKEGIHPI 216 (304)
Q Consensus 174 r~~h~~il---~~glkn---lvs~s~~~yf~~~prip~s~~~~~~~~~~ 216 (304)
..+|.+.| +.|++| |+|.++++.|+..|||+...+.+|.-.-+
T Consensus 78 ~~~hllllAkn~~Gy~nL~kL~S~a~~~~~~~~p~i~~e~L~~~~~gli 126 (1046)
T PRK05672 78 GGPHLLVLARDREGYGRLSRLITRARLRAGKGEYRLDLDDLAEPAGGHW 126 (1046)
T ss_pred CCceEEEEEcChHHHHHHHHHHHHHHHhCCCCCccccHHHHHhhcCCCE
Confidence 46799988 669999 99999999888889999999999865443
No 104
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=33.97 E-value=4e+02 Score=31.82 Aligned_cols=41 Identities=7% Similarity=0.182 Sum_probs=29.4
Q ss_pred CCCCCHHHHHH-HhCC-C--------------CCCCCh---HHHHHHHHHHHHHHHHHhh
Q 048020 110 AGDMKMASLAT-YFGL-G--------------QQTHRS---LDDVLMNLEVLKYCATVLL 150 (304)
Q Consensus 110 ~~~~kL~~Lak-~lGI-~--------------~~~HrA---L~DA~aTa~L~~~ll~~l~ 150 (304)
.++.+|..+.+ ++|. | ...|-| ..||.||..+|.+...-+-
T Consensus 396 qGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVhPFI 455 (2173)
T KOG1798|consen 396 QGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVHPFI 455 (2173)
T ss_pred CcccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhhhHH
Confidence 46788888877 5776 2 123433 8899999999998877653
No 105
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=33.16 E-value=8e+02 Score=28.19 Aligned_cols=113 Identities=14% Similarity=-0.002 Sum_probs=68.6
Q ss_pred cEEEEEEe--ecCCCC---ceEEEEEEEEeCCce-------eeeeeEEEEEcCCCCCCCChH-HHHhcCCCHHHHhCCCC
Q 048020 9 EIVFFDVE--TTFPIR---HIWEFGAILVCPRKL-------EELDKYTTLVRPADPSLVSNL-CARRNDITPEDVFSAPT 75 (304)
Q Consensus 9 ~~VvfDlE--TTGl~~---~IIEIGAV~v~~g~~-------~iid~f~~lV~P~~~~~I~~~-~~~ltGIT~e~L~~ap~ 75 (304)
.++++|+- +..++. ++|.|+++...+... .....|...++|... .+|.. .....|+.+..|..-.+
T Consensus 505 Pl~vLdFsi~SlyPsi~~~~nl~iS~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~~-~~p~~~~~~~~~~~~~~L~~~~s 583 (1172)
T TIGR00592 505 PLVVLDFSMKSLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKDC-SFPLDLKGEFPGKKPSLVEDLAT 583 (1172)
T ss_pred CeEEEEeeeEEecCccccCceEEEEEEEeecccccCCCCCCccceEEEEEEccCCC-CCCchhhhhhhccCCcEEEEecC
Confidence 46666555 655553 999998887664210 112345556677321 23332 22455666667777778
Q ss_pred HHHHHHHHHHHhc----------------------------C----------------------CCCCCceehHHHHHHH
Q 048020 76 FADIADTVFDILQ----------------------------A----------------------PKPKGTIDSLNLLTER 105 (304)
Q Consensus 76 f~eVl~~f~~fl~----------------------------~----------------------~~~~~~IDTl~Lark~ 105 (304)
..+.+..|++++. . ....-.+|++..++..
T Consensus 584 Er~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~~~~k~~ 663 (1172)
T TIGR00592 584 ERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVEISAKEL 663 (1172)
T ss_pred HHHHHHHHHHHHHhcCCCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccCCCccccccceECCEEEEEHHHHHHHH
Confidence 8888888888770 0 0112357888888754
Q ss_pred hcCCCCCCCHHHHHHHh-CC
Q 048020 106 FGRRAGDMKMASLATYF-GL 124 (304)
Q Consensus 106 l~p~~~~~kL~~Lak~l-GI 124 (304)
+ ...+|+|+++++++ |.
T Consensus 664 ~--~~~sy~L~~v~~~~L~~ 681 (1172)
T TIGR00592 664 I--RCKSYDLSELVQQILKT 681 (1172)
T ss_pred h--CcCCCCHHHHHHHHhCC
Confidence 3 47899999999964 54
No 106
>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=30.24 E-value=2e+02 Score=24.00 Aligned_cols=57 Identities=18% Similarity=0.175 Sum_probs=39.2
Q ss_pred CCCceehHHHHHHHhcCCCCCCCHHHHHHHh-CCC-CCC----------------CChHHHHHHHHHHHHHHHHHhh
Q 048020 92 PKGTIDSLNLLTERFGRRAGDMKMASLATYF-GLG-QQT----------------HRSLDDVLMNLEVLKYCATVLL 150 (304)
Q Consensus 92 ~~~~IDTl~Lark~l~p~~~~~kL~~Lak~l-GI~-~~~----------------HrAL~DA~aTa~L~~~ll~~l~ 150 (304)
.+.++||+-.+. .+.|... ++|.++++.| |+. ... +-|..||.++.+++..+.+++.
T Consensus 87 ~~~~~D~~laay-Ll~p~~~-~~l~~l~~~~l~~~~~~~~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~ 161 (178)
T cd06142 87 PQNLFDTQIAAR-LLGLGDS-VGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELE 161 (178)
T ss_pred CCCcccHHHHHH-HhCCCcc-ccHHHHHHHHhCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 456799985555 7787644 5999998865 553 100 1266778888888888887774
No 107
>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=24.53 E-value=70 Score=28.27 Aligned_cols=57 Identities=12% Similarity=0.092 Sum_probs=37.1
Q ss_pred CCceehHHHHHHHhcCCCC-------CCCHHHHHHHh-CCC-------------------------CCCCChHHHHHHHH
Q 048020 93 KGTIDSLNLLTERFGRRAG-------DMKMASLATYF-GLG-------------------------QQTHRSLDDVLMNL 139 (304)
Q Consensus 93 ~~~IDTl~Lark~l~p~~~-------~~kL~~Lak~l-GI~-------------------------~~~HrAL~DA~aTa 139 (304)
..++||.-.+. .+.+... ..+|..+++.| |++ .+-+=|..||..+.
T Consensus 89 ~~~fDt~iA~~-lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll 167 (197)
T cd06148 89 NNVFDTQVADA-LLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLL 167 (197)
T ss_pred cceeeHHHHHH-HHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHH
Confidence 35589875444 4444221 25788887764 442 11233688999999
Q ss_pred HHHHHHHHHhh
Q 048020 140 EVLKYCATVLL 150 (304)
Q Consensus 140 ~L~~~ll~~l~ 150 (304)
.++..|.+.+.
T Consensus 168 ~l~~~l~~~l~ 178 (197)
T cd06148 168 PLYYAMLDALI 178 (197)
T ss_pred HHHHHHHHHhh
Confidence 99999988874
No 108
>PF09281 Taq-exonuc: Taq polymerase, exonuclease; InterPro: IPR015361 This domain is found in prokaryotic Taq DNA polymerase (thermostable), where it assumes a ribonuclease H-like motif. The domain confers 5'-3' exonuclease activity to the polymerase []. ; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 4DF4_A 3T3F_A 1QSY_A 3OJS_A 3PO5_A 3OJU_A 1QTM_A 1QSS_A 3PY8_A 4DFJ_A ....
Probab=23.26 E-value=3.1e+02 Score=23.60 Aligned_cols=53 Identities=15% Similarity=0.093 Sum_probs=34.3
Q ss_pred CceehHHHHHHHhcCCCCCCCHHHHHHHhCCCCCCCChHHHHHHHHHHHHHHHHHh
Q 048020 94 GTIDSLNLLTERFGRRAGDMKMASLATYFGLGQQTHRSLDDVLMNLEVLKYCATVL 149 (304)
Q Consensus 94 ~~IDTl~Lark~l~p~~~~~kL~~Lak~lGI~~~~HrAL~DA~aTa~L~~~ll~~l 149 (304)
+-=|-|-++. ++.| .+.....++++||-..=.-+|-.-|.+++++++.|..++
T Consensus 86 PGDDPlLlAY-LlDP--sNt~p~~varRY~~~~W~~dA~~RA~~t~~L~~~L~prL 138 (138)
T PF09281_consen 86 PGDDPLLLAY-LLDP--SNTNPEGVARRYLGGEWPEDAATRALATARLLRALPPRL 138 (138)
T ss_dssp B---HHHHHH-HH-T--T--SHHHHHHHH-TS---SSHHHHHHHHHHHHHHHHHHT
T ss_pred CCCCcchhhh-hcCc--cCCChHHHHHHhcCCCCCccHHHHHHHHHHHHHHhhhcC
Confidence 4557776676 7776 577899999999776555677888889999999887653
Done!