Query psy3897
Match_columns 240
No_of_seqs 221 out of 1488
Neff 7.0
Searched_HMMs 46136
Date Fri Aug 16 20:10:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3897.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3897hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06143 PAN2_exo DEDDh 3'-5' e 100.0 6.6E-40 1.4E-44 271.0 15.2 146 81-228 1-173 (174)
2 KOG2248|consensus 100.0 1.8E-39 3.8E-44 297.2 17.3 188 51-239 186-379 (380)
3 cd06145 REX1_like DEDDh 3'-5' 100.0 4.7E-38 1E-42 255.9 16.5 147 81-228 1-149 (150)
4 KOG2249|consensus 100.0 5.5E-37 1.2E-41 264.5 14.5 149 79-230 106-261 (280)
5 cd06137 DEDDh_RNase DEDDh 3'-5 100.0 6.8E-36 1.5E-40 245.7 13.5 149 81-229 1-161 (161)
6 cd06149 ISG20 DEDDh 3'-5' exon 100.0 3.1E-35 6.7E-40 241.1 16.5 146 81-229 1-157 (157)
7 cd06144 REX4_like DEDDh 3'-5' 100.0 4.7E-33 1E-37 226.7 16.5 146 81-229 1-152 (152)
8 PRK07247 DNA polymerase III su 100.0 1.3E-27 2.9E-32 202.4 17.4 151 78-235 5-169 (195)
9 PRK07740 hypothetical protein; 100.0 1.4E-27 2.9E-32 208.9 17.9 156 75-235 56-226 (244)
10 PRK09146 DNA polymerase III su 100.0 1.9E-27 4.1E-32 207.3 17.1 171 60-235 28-227 (239)
11 cd06130 DNA_pol_III_epsilon_li 100.0 1.3E-27 2.9E-32 193.4 15.0 144 80-230 1-156 (156)
12 PRK06309 DNA polymerase III su 100.0 3.9E-27 8.4E-32 204.5 16.5 152 79-234 3-165 (232)
13 PRK06310 DNA polymerase III su 99.9 5.9E-27 1.3E-31 205.5 17.6 153 77-234 6-173 (250)
14 PRK05711 DNA polymerase III su 99.9 8E-27 1.7E-31 203.4 15.6 152 78-234 4-175 (240)
15 TIGR01406 dnaQ_proteo DNA poly 99.9 8.2E-27 1.8E-31 201.7 15.5 151 79-234 1-171 (225)
16 smart00479 EXOIII exonuclease 99.9 9.9E-27 2.1E-31 189.8 14.7 152 79-235 1-167 (169)
17 PRK09145 DNA polymerase III su 99.9 2.3E-26 5.1E-31 195.4 17.2 153 77-234 28-200 (202)
18 PRK06807 DNA polymerase III su 99.9 2.6E-26 5.6E-31 207.2 17.3 153 77-235 7-172 (313)
19 PRK07942 DNA polymerase III su 99.9 2.3E-26 4.9E-31 199.7 16.0 157 75-234 3-179 (232)
20 PRK07983 exodeoxyribonuclease 99.9 2.3E-26 5E-31 198.1 15.6 145 80-234 2-153 (219)
21 TIGR00573 dnaq exonuclease, DN 99.9 2.7E-26 5.8E-31 197.2 15.9 159 77-239 6-181 (217)
22 PRK06063 DNA polymerase III su 99.9 1.1E-25 2.3E-30 203.4 18.6 152 77-235 14-179 (313)
23 PRK08517 DNA polymerase III su 99.9 8.7E-26 1.9E-30 198.8 17.4 153 75-234 65-230 (257)
24 cd06131 DNA_pol_III_epsilon_Ec 99.9 5.4E-26 1.2E-30 186.6 14.8 147 80-231 1-166 (167)
25 PRK06195 DNA polymerase III su 99.9 9.5E-26 2.1E-30 203.4 17.2 149 79-234 2-163 (309)
26 cd06136 TREX1_2 DEDDh 3'-5' ex 99.9 1.6E-26 3.4E-31 192.9 10.8 144 80-231 1-177 (177)
27 PRK07748 sporulation inhibitor 99.9 5.4E-26 1.2E-30 194.0 14.1 155 78-235 4-180 (207)
28 PRK07246 bifunctional ATP-depe 99.9 3E-25 6.4E-30 222.3 17.4 154 77-235 6-170 (820)
29 TIGR01298 RNaseT ribonuclease 99.9 9.4E-25 2E-29 185.6 15.2 156 76-237 6-194 (200)
30 PRK07883 hypothetical protein; 99.9 1.6E-24 3.4E-29 209.1 17.7 156 75-235 12-182 (557)
31 cd06134 RNaseT DEDDh 3'-5' exo 99.9 1.8E-24 3.9E-29 182.3 14.8 150 79-234 6-188 (189)
32 PRK05168 ribonuclease T; Provi 99.9 2.9E-24 6.3E-29 184.0 15.4 155 77-237 16-203 (211)
33 PRK06722 exonuclease; Provisio 99.9 2.3E-24 4.9E-29 191.5 14.4 152 77-234 4-180 (281)
34 PRK08074 bifunctional ATP-depe 99.9 5.1E-24 1.1E-28 216.1 17.3 153 78-235 3-169 (928)
35 TIGR01407 dinG_rel DnaQ family 99.9 6.3E-24 1.4E-28 213.9 17.3 151 79-234 1-164 (850)
36 cd06133 ERI-1_3'hExo_like DEDD 99.9 3.1E-24 6.7E-29 176.7 12.1 148 80-231 1-175 (176)
37 cd06127 DEDDh DEDDh 3'-5' exon 99.9 1.4E-23 3E-28 167.7 13.4 144 81-229 1-159 (159)
38 COG2176 PolC DNA polymerase II 99.9 1.3E-24 2.8E-29 216.2 7.0 155 76-235 419-586 (1444)
39 TIGR01405 polC_Gram_pos DNA po 99.9 2.9E-23 6.4E-28 213.2 17.1 155 76-235 188-355 (1213)
40 PRK09182 DNA polymerase III su 99.9 8.1E-23 1.8E-27 183.0 16.8 150 77-234 36-200 (294)
41 PRK05601 DNA polymerase III su 99.9 1.6E-22 3.5E-27 184.2 17.1 151 75-231 43-245 (377)
42 COG0847 DnaQ DNA polymerase II 99.9 2.9E-22 6.2E-27 174.1 15.1 154 78-234 13-181 (243)
43 cd06138 ExoI_N N-terminal DEDD 99.9 1.2E-22 2.6E-27 170.2 11.9 144 81-228 1-182 (183)
44 PF00929 RNase_T: Exonuclease; 99.9 8.6E-25 1.9E-29 175.0 -1.8 145 81-228 1-164 (164)
45 PTZ00315 2'-phosphotransferase 99.8 2.3E-20 5E-25 178.4 16.4 158 78-238 56-258 (582)
46 PRK00448 polC DNA polymerase I 99.8 5.1E-20 1.1E-24 191.6 14.1 154 77-235 418-584 (1437)
47 PRK11779 sbcB exonuclease I; P 99.8 1.7E-19 3.6E-24 170.7 15.7 155 77-234 5-197 (476)
48 PRK05359 oligoribonuclease; Pr 99.8 2.2E-19 4.7E-24 150.5 13.2 146 78-237 3-177 (181)
49 cd06135 Orn DEDDh 3'-5' exonuc 99.8 7.5E-20 1.6E-24 152.1 9.2 141 80-233 1-170 (173)
50 KOG1275|consensus 99.8 3.5E-19 7.6E-24 173.8 7.1 158 74-233 906-1090(1118)
51 COG5018 KapD Inhibitor of the 99.2 6E-12 1.3E-16 103.0 3.9 154 78-234 4-184 (210)
52 KOG0542|consensus 99.2 4.8E-11 1E-15 103.3 7.1 155 79-237 57-244 (280)
53 COG1949 Orn Oligoribonuclease 99.0 1.8E-09 3.9E-14 88.0 8.6 146 77-237 5-180 (184)
54 KOG3242|consensus 99.0 1.8E-09 3.8E-14 88.9 8.3 143 77-234 25-198 (208)
55 cd05160 DEDDy_DNA_polB_exo DED 99.0 7.5E-09 1.6E-13 87.2 11.1 121 80-209 1-162 (199)
56 cd06139 DNA_polA_I_Ecoli_like_ 98.7 2.4E-07 5.3E-12 76.8 13.0 139 77-234 4-169 (193)
57 COG2925 SbcB Exonuclease I [DN 98.7 1.8E-07 3.9E-12 85.5 10.8 148 77-229 8-195 (475)
58 PF01612 DNA_pol_A_exo1: 3'-5' 98.5 1.4E-06 3.1E-11 70.8 11.4 129 78-233 20-173 (176)
59 cd06125 DnaQ_like_exo DnaQ-lik 98.5 1.3E-06 2.9E-11 65.7 9.2 57 81-174 1-61 (96)
60 cd06146 mut-7_like_exo DEDDy 3 98.4 4.3E-06 9.4E-11 70.6 11.6 87 146-232 70-192 (193)
61 PRK05755 DNA polymerase I; Pro 98.2 1.3E-05 2.8E-10 82.0 12.4 131 77-234 314-468 (880)
62 cd05780 DNA_polB_Kod1_like_exo 98.1 4.2E-05 9E-10 64.6 12.0 115 78-210 3-156 (195)
63 PF04857 CAF1: CAF1 family rib 97.9 0.00013 2.8E-09 64.5 11.6 73 155-230 147-262 (262)
64 cd06129 RNaseD_like DEDDy 3'-5 97.9 0.00013 2.9E-09 59.5 9.9 79 152-231 61-159 (161)
65 cd06141 WRN_exo DEDDy 3'-5' ex 97.9 0.00018 4E-09 58.8 10.5 82 150-231 65-168 (170)
66 cd00007 35EXOc 3'-5' exonuclea 97.7 0.0013 2.7E-08 51.8 13.2 66 145-210 41-111 (155)
67 PRK10829 ribonuclease D; Provi 97.7 0.00047 1E-08 64.1 12.1 129 76-234 20-169 (373)
68 cd05779 DNA_polB_epsilon_exo D 97.6 0.0014 3.1E-08 56.0 12.4 126 78-209 2-168 (204)
69 cd05781 DNA_polB_B3_exo DEDDy 97.5 0.0013 2.8E-08 55.4 10.3 104 78-208 3-143 (188)
70 cd05784 DNA_polB_II_exo DEDDy 97.4 0.0028 6.2E-08 53.6 11.9 115 78-209 3-153 (193)
71 COG0349 Rnd Ribonuclease D [Tr 97.4 0.0014 3E-08 60.4 10.5 129 77-233 16-164 (361)
72 PF13482 RNase_H_2: RNase_H su 97.4 0.00063 1.4E-08 55.2 7.2 105 81-211 1-117 (164)
73 TIGR01388 rnd ribonuclease D. 97.3 0.0048 1E-07 57.3 13.1 75 157-232 70-163 (367)
74 cd06148 Egl_like_exo DEDDy 3'- 97.2 0.0024 5.3E-08 53.9 9.4 85 150-234 57-176 (197)
75 cd05783 DNA_polB_B1_exo DEDDy 97.2 0.013 2.8E-07 50.1 13.6 127 77-209 4-170 (204)
76 cd05777 DNA_polB_delta_exo DED 96.8 0.045 9.7E-07 47.3 13.3 85 77-173 6-104 (230)
77 cd05785 DNA_polB_like2_exo Unc 96.4 0.013 2.8E-07 50.2 7.4 73 77-174 8-92 (207)
78 cd06142 RNaseD_exo DEDDy 3'-5' 96.3 0.1 2.3E-06 42.3 12.1 59 150-209 56-119 (178)
79 cd05778 DNA_polB_zeta_exo inac 96.3 0.076 1.7E-06 46.1 11.8 155 78-235 4-223 (231)
80 PHA02570 dexA exonuclease; Pro 96.2 0.023 4.9E-07 49.0 7.6 150 81-232 4-196 (220)
81 smart00474 35EXOc 3'-5' exonuc 96.1 0.033 7.2E-07 44.5 7.9 85 148-232 65-168 (172)
82 PF10108 DNA_pol_B_exo2: Predi 96.0 0.035 7.6E-07 47.7 7.7 88 143-232 37-170 (209)
83 PRK05762 DNA polymerase II; Re 95.8 0.13 2.9E-06 52.3 12.3 137 76-229 153-346 (786)
84 KOG4793|consensus 95.6 0.014 3.1E-07 51.7 4.2 161 76-237 11-220 (318)
85 cd05782 DNA_polB_like1_exo Unc 95.6 0.02 4.4E-07 48.9 5.0 65 143-209 78-169 (208)
86 PTZ00166 DNA polymerase delta 95.5 0.21 4.5E-06 52.6 12.7 86 76-173 262-363 (1054)
87 cd06140 DNA_polA_I_Bacillus_li 94.9 0.65 1.4E-05 37.8 11.6 105 78-210 3-113 (178)
88 PF03104 DNA_pol_B_exo1: DNA p 94.7 0.17 3.8E-06 45.1 8.5 87 76-174 155-256 (325)
89 cd05776 DNA_polB_alpha_exo ina 94.5 0.11 2.4E-06 45.1 6.5 128 79-209 4-186 (234)
90 COG3359 Predicted exonuclease 94.3 0.44 9.6E-06 41.9 9.5 106 77-209 97-218 (278)
91 COG0749 PolA DNA polymerase I 94.1 0.28 6E-06 48.2 8.9 128 81-234 25-179 (593)
92 TIGR00593 pola DNA polymerase 93.8 0.25 5.4E-06 51.0 8.3 91 143-234 363-476 (887)
93 PHA02528 43 DNA polymerase; Pr 93.5 0.49 1.1E-05 48.9 9.7 92 76-173 104-211 (881)
94 KOG3657|consensus 92.9 0.17 3.6E-06 51.2 5.2 31 155-185 239-275 (1075)
95 smart00486 POLBc DNA polymeras 92.9 0.3 6.6E-06 45.5 6.9 84 78-173 3-102 (471)
96 KOG0304|consensus 92.9 0.33 7.1E-06 41.9 6.3 105 126-232 109-236 (239)
97 cd06147 Rrp6p_like_exo DEDDy 3 92.4 1.6 3.4E-05 36.3 9.9 58 150-209 69-131 (192)
98 KOG1798|consensus 91.9 2 4.3E-05 46.4 11.6 150 76-233 244-452 (2173)
99 cd09018 DEDDy_polA_RNaseD_like 88.6 0.89 1.9E-05 35.5 4.8 60 150-209 45-109 (150)
100 COG0417 PolB DNA polymerase el 88.1 7.4 0.00016 39.9 12.1 119 76-209 152-308 (792)
101 TIGR00592 pol2 DNA polymerase 87.0 7.3 0.00016 41.7 11.7 127 79-208 507-681 (1172)
102 PRK05761 DNA polymerase I; Rev 86.0 7.1 0.00015 40.0 10.6 86 143-228 210-334 (787)
103 TIGR03491 RecB family nuclease 85.3 15 0.00032 35.1 11.9 66 144-211 329-411 (457)
104 PHA02524 43A DNA polymerase su 83.2 4.4 9.5E-05 39.3 7.3 91 77-173 105-213 (498)
105 PF00843 Arena_nucleocap: Aren 81.5 1.9 4.1E-05 40.9 4.0 134 77-223 371-526 (533)
106 cd06128 DNA_polA_exo DEDDy 3'- 74.9 6.3 0.00014 31.0 4.8 59 150-209 45-109 (151)
107 PF13017 Maelstrom: piRNA path 59.3 12 0.00025 32.2 3.6 60 95-155 9-79 (213)
108 KOG0969|consensus 54.6 8.4 0.00018 39.3 2.1 86 77-172 273-370 (1066)
109 PHA02563 DNA polymerase; Provi 37.4 90 0.0019 31.4 6.3 19 156-174 65-83 (630)
110 COG5228 POP2 mRNA deadenylase 32.4 51 0.0011 28.9 3.2 150 76-229 40-247 (299)
111 PF06821 Ser_hydrolase: Serine 27.9 66 0.0014 26.4 3.1 33 138-172 36-73 (171)
112 KOG0970|consensus 27.7 1.4E+02 0.0031 32.1 6.0 88 78-172 529-639 (1429)
113 PF07819 PGAP1: PGAP1-like pro 27.5 43 0.00092 28.7 2.0 25 143-167 66-96 (225)
114 PF03337 Pox_F12L: Poxvirus F1 24.5 2.9E+02 0.0063 27.9 7.3 19 157-175 275-294 (651)
115 PF10109 FluMu_gp41: Mu-like p 24.4 48 0.001 23.2 1.5 33 122-154 49-81 (82)
116 PF11906 DUF3426: Protein of u 23.3 2.5E+02 0.0054 21.9 5.7 55 77-131 66-123 (149)
117 KOG2613|consensus 20.2 1.1E+02 0.0023 29.3 3.2 60 77-136 312-385 (502)
No 1
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=100.00 E-value=6.6e-40 Score=270.96 Aligned_cols=146 Identities=36% Similarity=0.490 Sum_probs=132.0
Q ss_pred EEEEEeecCCCC--------Cc---------cEEEEEEEE----cCCcEEEEEEEcCCCcccccceecCCCCHHhhccCC
Q psy3897 81 YALDTEMVYTVH--------GL---------EVARVTVVN----VDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNP 139 (240)
Q Consensus 81 valD~E~tg~~~--------g~---------ei~~v~vv~----~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~ 139 (240)
||+||||+++++ |. +++||++|| .+|+++||.||+|..+|.||+|+|||||+++|.++.
T Consensus 1 ~a~d~e~v~~~~~~~~~~~~g~~~~~~~~~~~LaRVsiVd~~~~~~g~vllD~~VkP~~~V~DYrT~~SGIt~~~L~~a~ 80 (174)
T cd06143 1 VAIDAEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKT 80 (174)
T ss_pred CceeeeEEEecchhceecCCCcEeeeccCCceeEEEEEEcCCCCcCCCEEEeeeECCCCCccCcCccccccCHHHcCccc
Confidence 578888888776 32 699999999 689999999999999999999999999999999875
Q ss_pred C----CCHHHHHHHHHhhhcCCcEEEEEchHHHHHHHhccCC--CeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCC
Q psy3897 140 Y----KTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHS--NIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSG 213 (240)
Q Consensus 140 ~----~~~~ev~~~l~~~i~~~~iLVGH~~~~Dl~~L~~~~~--~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~ 213 (240)
. .+++++++++.++++.++|||||+++|||++|++.|+ .+|||+.+|+...+ .++||+.|++.+||++||.+
T Consensus 81 ~~~~~~t~~~v~~~l~~li~~~tILVGHsL~nDL~aL~l~hp~~~viDTa~l~~~~~~--r~~sLk~La~~~L~~~IQ~~ 158 (174)
T cd06143 81 SSKNLTTLKSAYLKLRLLVDLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFHLPGQ--RKLSLRFLAWYLLGEKIQSE 158 (174)
T ss_pred cccccCCHHHHHHHHHHHcCCCCEEEeccchhHHHHhcCcCCCcceEEcHHhccCCCC--CChhHHHHHHHHcCCcccCC
Confidence 2 2399999999999988999999999999999999966 79999999987543 36899999999999999998
Q ss_pred CCChHHHHHHHHHHH
Q psy3897 214 THDSFEDARACIDLI 228 (240)
Q Consensus 214 ~H~A~eDA~at~~L~ 228 (240)
+|||+|||+|||+||
T Consensus 159 ~HdSvEDArAam~Ly 173 (174)
T cd06143 159 THDSIEDARTALKLY 173 (174)
T ss_pred CcCcHHHHHHHHHHh
Confidence 999999999999997
No 2
>KOG2248|consensus
Probab=100.00 E-value=1.8e-39 Score=297.17 Aligned_cols=188 Identities=44% Similarity=0.698 Sum_probs=169.4
Q ss_pred cCcccC--CCCCcccccccCCCCC-CCCCCCcEEEEEEeecCCCCCccEEEEEEEEcCCcEEEEEEEcCCCcccccceec
Q psy3897 51 LDHVGG--INGPLEGYVKTKPRKS-PPPNGYGVYALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKY 127 (240)
Q Consensus 51 ~~hv~~--~~~~~~~fv~t~~~~~-~~~~~~~~valD~E~tg~~~g~ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~ 127 (240)
+.||.. .......|+++....+ ......+++|+||||+.+..|.|++||++||.+++++||.||+|..||.||+|++
T Consensus 186 ~~~~~~~~~~~~~~~~v~~~~~~~~~v~~~~~i~AlDCEm~~te~g~el~RVt~VD~~~~vi~D~fVkP~~~VvDy~T~~ 265 (380)
T KOG2248|consen 186 DYHVEILFPSESLDEFVQTLGAKGKAVSKSPNIFALDCEMVVTENGLELTRVTAVDRDGKVILDTFVKPNKPVVDYNTRY 265 (380)
T ss_pred cccccccCccccccceecccccCCCCCCCCCCeEEEEeeeeeeccceeeEEeeeeeccCcEEeEEeecCCCccccccccc
Confidence 455553 2345667888876543 3466789999999999999999999999999999999999999999999999999
Q ss_pred CCCCHHhhccCCCCCHHHHHHHHHhhhcCCcEEEEEchHHHHHHHhccCCCeeeccccCcccCCC-CCCccHHHHHHHHc
Q psy3897 128 SGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHSNIIDTSVLFPHSFGL-PYRRSLKSIVSQLL 206 (240)
Q Consensus 128 ~GIt~edl~~a~~~~~~ev~~~l~~~i~~~~iLVGH~~~~Dl~~L~~~~~~~iDT~~l~~~~~~~-~~~~sL~~L~~~~L 206 (240)
||||++++++++.. +++|+.+|++|++.++|||||++++||++|++.|+.+|||+.+|++..++ +.+.+|++||+.||
T Consensus 266 SGIT~~~~e~~t~t-l~dvq~~l~~~~~~~TILVGHSLenDL~aLKl~H~~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L 344 (380)
T KOG2248|consen 266 SGITEEDLENSTIT-LEDVQKELLELISKNTILVGHSLENDLKALKLDHPSVIDTAVLFKHPTGPYPFKSSLKNLAKSYL 344 (380)
T ss_pred ccccHHHHhcCccC-HHHHHHHHHhhcCcCcEEEeechhhHHHHHhhhCCceeeeeEEEecCCCCccchHHHHHHHHHHH
Confidence 99999999999887 99999999999999999999999999999999999999999999998874 77889999999999
Q ss_pred CCCCCC--CCCChHHHHHHHHHHHHHHHhhhhccC
Q psy3897 207 HQSIQS--GTHDSFEDARACIDLILWKLLSDFRYN 239 (240)
Q Consensus 207 ~~~iq~--~~H~A~eDA~at~~L~~~~l~~~~~~~ 239 (240)
|+.||. ++|+|.+||.|||+|+.++++.+..+|
T Consensus 345 ~~~Iq~~~~~HdS~eDA~acm~Lv~~k~~~~~~~g 379 (380)
T KOG2248|consen 345 GKLIQEGVGGHDSVEDALACMKLVKLKIKNSESQG 379 (380)
T ss_pred HHHHhccCCCCccHHHHHHHHHHHHHHHhcccccC
Confidence 999994 389999999999999999999887765
No 3
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=100.00 E-value=4.7e-38 Score=255.90 Aligned_cols=147 Identities=53% Similarity=0.904 Sum_probs=135.1
Q ss_pred EEEEEeecCCCCCccEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhhcCCcEE
Q psy3897 81 YALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSII 160 (240)
Q Consensus 81 valD~E~tg~~~g~ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~~~~iL 160 (240)
|++||||+|++.|.||++|++|+.+|.++|++||+|..+|+++++++||||++||+++|++ +++++++|.+|++++++|
T Consensus 1 ~~iD~E~~g~~~g~ei~~i~~v~~~~~~~f~~lv~P~~~i~~~~t~itGIt~~~l~~a~~~-~~~v~~~~~~fl~~~~vl 79 (150)
T cd06145 1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTT-LEDVQKKLLSLISPDTIL 79 (150)
T ss_pred CEEeeeeeeecCCCEEEEEEEEeCCCCEEEEEeECCCCccchhccCcCCCCHHHhccCCCC-HHHHHHHHHHHhCCCCEE
Confidence 6899999999988999999999999999999999999999999999999999999999633 999999999999658999
Q ss_pred EEEchHHHHHHHhccCCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCC--CCCChHHHHHHHHHHH
Q psy3897 161 VGHGLENDLRALKLIHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQS--GTHDSFEDARACIDLI 228 (240)
Q Consensus 161 VGH~~~~Dl~~L~~~~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~--~~H~A~eDA~at~~L~ 228 (240)
||||+.||+.+|+..+++++||+.+++...+...+++|+.||+.|++..++. ++|+|++||++|++||
T Consensus 80 VgHn~~fD~~fL~~~~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 80 VGHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELV 149 (150)
T ss_pred EEcChHHHHHHhhccCCCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCCCCCcHHHHHHHHHHh
Confidence 9999999999999999999999999987654444679999999888988874 5899999999999987
No 4
>KOG2249|consensus
Probab=100.00 E-value=5.5e-37 Score=264.47 Aligned_cols=149 Identities=39% Similarity=0.520 Sum_probs=136.4
Q ss_pred cEEEEEEeecCCCCC-c--cEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhhc
Q psy3897 79 GVYALDTEMVYTVHG-L--EVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVS 155 (240)
Q Consensus 79 ~~valD~E~tg~~~g-~--ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~ 155 (240)
++||+||||+|+.++ . .++||+|||..|.++||.||+|..+|.||.|++|||+++.+.++.+ |+.|+.++.++|.
T Consensus 106 r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP~~~VtDyRT~vSGIrpehm~~A~p--f~~aQ~ev~klL~ 183 (280)
T KOG2249|consen 106 RVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKPTEPVTDYRTRVSGIRPEHMRDAMP--FKVAQKEVLKLLK 183 (280)
T ss_pred eEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecCCCcccccceeeecccCHHHhccCcc--HHHHHHHHHHHHh
Confidence 599999999999874 3 5999999999999999999999999999999999999999999999 9999999999995
Q ss_pred CCcEEEEEchHHHHHHHhccCCC--eeeccccCcccC--CCCCCccHHHHHHHHcCCCCCCCCCChHHHHHHHHHHHHH
Q psy3897 156 KDSIIVGHGLENDLRALKLIHSN--IIDTSVLFPHSF--GLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARACIDLILW 230 (240)
Q Consensus 156 ~~~iLVGH~~~~Dl~~L~~~~~~--~iDT~~l~~~~~--~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~at~~L~~~ 230 (240)
|+|||||.+.|||.+|+..|++ +.||+..-|... .....+||+.|++.+||++||.+.|+|.+||+|||+||..
T Consensus 184 -gRIlVGHaLhnDl~~L~l~hp~s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~GeHsSvEDA~AtM~LY~~ 261 (280)
T KOG2249|consen 184 -GRILVGHALHNDLQALKLEHPRSMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVGEHSSVEDARATMELYKR 261 (280)
T ss_pred -CCEEeccccccHHHHHhhhCchhhhcccccCchHHHHhhccCCccHHHHHHHHhchhhhccccCcHHHHHHHHHHHHH
Confidence 9999999999999999999984 799998655443 2334689999999999999999899999999999999874
No 5
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=100.00 E-value=6.8e-36 Score=245.68 Aligned_cols=149 Identities=35% Similarity=0.606 Sum_probs=132.0
Q ss_pred EEEEEeecCCCC-CccEEEEEEEEc-CCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCC-----CHHHHHHHHHhh
Q psy3897 81 YALDTEMVYTVH-GLEVARVTVVNV-DGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYK-----TLKDVQNDLMGF 153 (240)
Q Consensus 81 valD~E~tg~~~-g~ei~~v~vv~~-~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~-----~~~ev~~~l~~~ 153 (240)
|+|||||||+++ +.+|++|++|+. +|+++|++||+|..+|+++++++||||++|++++|.. ++++++++|.+|
T Consensus 1 v~lD~EttGl~~~~d~ii~Ig~V~v~~g~i~~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~~~~~~~~~~ 80 (161)
T cd06137 1 VALDCEMVGLADGDSEVVRISAVDVLTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAKAGKTIFGWEAARAALWKF 80 (161)
T ss_pred CEEEeeeeeEcCCCCEEEEEEEEEcCCCeEEEeccccCCCCCCccceeccCCCHHHHhhhhhcCCccccHHHHHHHHHHh
Confidence 689999999997 568999999997 8898999999999999999999999999999998741 146999999999
Q ss_pred hcCCcEEEEEchHHHHHHHhccCCCeeeccccCcccCCCC---CCccHHHHHHHHcCCCCCC--CCCChHHHHHHHHHHH
Q psy3897 154 VSKDSIIVGHGLENDLRALKLIHSNIIDTSVLFPHSFGLP---YRRSLKSIVSQLLHQSIQS--GTHDSFEDARACIDLI 228 (240)
Q Consensus 154 i~~~~iLVGH~~~~Dl~~L~~~~~~~iDT~~l~~~~~~~~---~~~sL~~L~~~~L~~~iq~--~~H~A~eDA~at~~L~ 228 (240)
++++++|||||+.||++||+..+++++||+.+++...... .+++|+.||+.++|++++. .+|+|++||+||++||
T Consensus 81 i~~~~vlVgHn~~fD~~fL~~~~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~~~~H~A~~DA~at~~l~ 160 (161)
T cd06137 81 IDPDTILVGHSLQNDLDALRMIHTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGGEGHDSLEDALAAREVV 160 (161)
T ss_pred cCCCcEEEeccHHHHHHHHhCcCCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCCCCCCCcHHHHHHHHHHh
Confidence 9644999999999999999999999999999998764332 3689999999889999875 4799999999999997
Q ss_pred H
Q psy3897 229 L 229 (240)
Q Consensus 229 ~ 229 (240)
+
T Consensus 161 ~ 161 (161)
T cd06137 161 L 161 (161)
T ss_pred C
Confidence 4
No 6
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=100.00 E-value=3.1e-35 Score=241.08 Aligned_cols=146 Identities=37% Similarity=0.637 Sum_probs=128.6
Q ss_pred EEEEEeecCCCCC---ccEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhhcCC
Q psy3897 81 YALDTEMVYTVHG---LEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKD 157 (240)
Q Consensus 81 valD~E~tg~~~g---~ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~~~ 157 (240)
|||||||||++++ .+|++|++|+.+|.++|++||+|..+|+++++++||||++|++++|+ +++++++|.+|++ +
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~~~~~~lv~P~~~i~~~~~~i~GIt~~~l~~a~~--~~~v~~~l~~~l~-~ 77 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATP--FAVAQKEILKILK-G 77 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCCEEEEEeECCCCccCccceECCCCCHHHHhcCCC--HHHHHHHHHHHcC-C
Confidence 6899999999976 58999999999999999999999999999999999999999999999 9999999999995 9
Q ss_pred cEEEEEchHHHHHHHhccCCC--eeeccccCc--ccCCCC--CCccHHHHHHHHcCCCCCCC--CCChHHHHHHHHHHHH
Q psy3897 158 SIIVGHGLENDLRALKLIHSN--IIDTSVLFP--HSFGLP--YRRSLKSIVSQLLHQSIQSG--THDSFEDARACIDLIL 229 (240)
Q Consensus 158 ~iLVGH~~~~Dl~~L~~~~~~--~iDT~~l~~--~~~~~~--~~~sL~~L~~~~L~~~iq~~--~H~A~eDA~at~~L~~ 229 (240)
+||||||+.||+++|+..++. ++||+.+.. ...+.| .+++|+.||+.+++..+|.+ +|+|++||+||++||.
T Consensus 78 ~vlV~Hn~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 78 KVVVGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157 (157)
T ss_pred CEEEEeCcHHHHHHhcccCCCcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCCCcCcHHHHHHHHHHhC
Confidence 999999999999999998654 899987633 221122 35799999998887778763 7999999999999973
No 7
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=100.00 E-value=4.7e-33 Score=226.70 Aligned_cols=146 Identities=42% Similarity=0.562 Sum_probs=128.3
Q ss_pred EEEEEeecCCCCC---ccEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhhcCC
Q psy3897 81 YALDTEMVYTVHG---LEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKD 157 (240)
Q Consensus 81 valD~E~tg~~~g---~ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~~~ 157 (240)
|+|||||||++++ .++++|++++.+|.++|++||+|..+|+++++++||||++|++++|+ +.+++++|.+|++ +
T Consensus 1 v~lD~EttGl~~~~~~~~i~~v~~v~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~~~v~~a~~--~~~~~~~l~~~l~-~ 77 (152)
T cd06144 1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPD--FEEVQKKVAELLK-G 77 (152)
T ss_pred CEEEEEeecccCCCCEEEEEEEEEEeCCCCEEEEEEECCCCCCCcccccCCCCCHHHHcCCCC--HHHHHHHHHHHhC-C
Confidence 6899999999876 47899999999999999999999999999999999999999999998 9999999999996 7
Q ss_pred cEEEEEchHHHHHHHhccCC--CeeeccccCcccCCC-CCCccHHHHHHHHcCCCCCCCCCChHHHHHHHHHHHH
Q psy3897 158 SIIVGHGLENDLRALKLIHS--NIIDTSVLFPHSFGL-PYRRSLKSIVSQLLHQSIQSGTHDSFEDARACIDLIL 229 (240)
Q Consensus 158 ~iLVGH~~~~Dl~~L~~~~~--~~iDT~~l~~~~~~~-~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~at~~L~~ 229 (240)
++|||||+.||+++|+..++ .++||..+....... ..+++|+.||+.+||++++.++|+|++||++|++||+
T Consensus 78 ~vlVgHn~~fD~~~L~~~~~~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~at~~l~~ 152 (152)
T cd06144 78 RILVGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLYR 152 (152)
T ss_pred CEEEEcCcHHHHHHhcCcCCCccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCCCcCcHHHHHHHHHHhC
Confidence 99999999999999998654 589998865443221 2368999999877898876558999999999999973
No 8
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=1.3e-27 Score=202.43 Aligned_cols=151 Identities=22% Similarity=0.262 Sum_probs=125.5
Q ss_pred CcEEEEEEeecCCCCCccEEEEEEEEc-CCcE--EEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhh
Q psy3897 78 YGVYALDTEMVYTVHGLEVARVTVVNV-DGRL--IYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFV 154 (240)
Q Consensus 78 ~~~valD~E~tg~~~g~ei~~v~vv~~-~g~~--~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i 154 (240)
.++|+|||||||.+...+|++|++|.. +|.+ .|++||+|..+|+++++++||||++||+++|. +.+++++|.+|+
T Consensus 5 ~~~vvlD~EtTGl~~~~eIIeIgaV~v~~g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap~--~~evl~~f~~f~ 82 (195)
T PRK07247 5 ETYIAFDLEFNTVNGVSHIIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPK--VEEVLAAFKEFV 82 (195)
T ss_pred CeEEEEEeeCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCCCccceecCCCCHHHHhCCCC--HHHHHHHHHHHH
Confidence 479999999999987779999999996 5543 49999999999999999999999999999998 999999999999
Q ss_pred cCCcEEEEEchH-HHHHHHhcc-----CCCeeecccc-Cccc----CCCCCCccHHHHHHHHcCCCCCCCCCChHHHHHH
Q psy3897 155 SKDSIIVGHGLE-NDLRALKLI-----HSNIIDTSVL-FPHS----FGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARA 223 (240)
Q Consensus 155 ~~~~iLVGH~~~-~Dl~~L~~~-----~~~~iDT~~l-~~~~----~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~a 223 (240)
+ +.++||||+. ||+.+|+.. ....+||... +... .+. .+++|..||+ +||++. .+|+|++||++
T Consensus 83 ~-~~~lVaHNa~~fD~~fL~~~g~~~~~~~~idt~~~~~~~~~~~~~~~-~~~~L~~La~-~~gi~~--~~HrAl~DA~~ 157 (195)
T PRK07247 83 G-ELPLIGYNAQKSDLPILAENGLDLSDQYQVDLYDEAFERRSSDLNGI-ANLKLQTVAD-FLGIKG--RGHNSLEDARM 157 (195)
T ss_pred C-CCeEEEEeCcHhHHHHHHHcCCCcCCCceeehHHHHHHhhccccCCC-CCCCHHHHHH-hcCCCC--CCcCCHHHHHH
Confidence 5 8999999996 899999863 2245777532 2111 111 2578999996 699664 47999999999
Q ss_pred HHHHHHHHHhhh
Q psy3897 224 CIDLILWKLLSD 235 (240)
Q Consensus 224 t~~L~~~~l~~~ 235 (240)
|+.||+++++.+
T Consensus 158 ta~v~~~ll~~~ 169 (195)
T PRK07247 158 TARVYESFLESD 169 (195)
T ss_pred HHHHHHHHHhhc
Confidence 999999888764
No 9
>PRK07740 hypothetical protein; Provisional
Probab=99.96 E-value=1.4e-27 Score=208.85 Aligned_cols=156 Identities=21% Similarity=0.237 Sum_probs=132.7
Q ss_pred CCCCcEEEEEEeecCCCCC--ccEEEEEEEEcCCcEE----EEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHH
Q psy3897 75 PNGYGVYALDTEMVYTVHG--LEVARVTVVNVDGRLI----YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQN 148 (240)
Q Consensus 75 ~~~~~~valD~E~tg~~~g--~ei~~v~vv~~~g~~~----~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~ 148 (240)
..+.++|+|||||||.++. .+|++|++|..++..+ |+++|+|..+|++.++++||||+++++++|+ +.+++.
T Consensus 56 ~~~~~~vv~D~ETTGl~p~~~deIIeIgaV~~~~~~i~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~--~~evl~ 133 (244)
T PRK07740 56 LTDLPFVVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPP--LAEVLH 133 (244)
T ss_pred ccCCCEEEEEEeCCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEEeCcCCCCChhheeccCCCHHHHhCCCC--HHHHHH
Confidence 3566899999999999865 5899999999754333 8899999999999999999999999999988 999999
Q ss_pred HHHhhhcCCcEEEEEchHHHHHHHhcc---------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHH
Q psy3897 149 DLMGFVSKDSIIVGHGLENDLRALKLI---------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFE 219 (240)
Q Consensus 149 ~l~~~i~~~~iLVGH~~~~Dl~~L~~~---------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~e 219 (240)
+|.+|++ +.++||||+.||+.+|+.. ..+++||..+++........++|..|+. ++|+++.+ .|+|++
T Consensus 134 ~f~~fi~-~~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~~-~~gi~~~~-~H~Al~ 210 (244)
T PRK07740 134 RFYAFIG-AGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALA-YYGIPIPR-RHHALG 210 (244)
T ss_pred HHHHHhC-CCEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHHHH-HCCcCCCC-CCCcHH
Confidence 9999995 8999999999999999752 2479999988765432223578999996 69977764 799999
Q ss_pred HHHHHHHHHHHHHhhh
Q psy3897 220 DARACIDLILWKLLSD 235 (240)
Q Consensus 220 DA~at~~L~~~~l~~~ 235 (240)
||++|++||.+.+.+.
T Consensus 211 Da~ata~l~~~ll~~~ 226 (244)
T PRK07740 211 DALMTAKLWAILLVEA 226 (244)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999999887764
No 10
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=1.9e-27 Score=207.31 Aligned_cols=171 Identities=17% Similarity=0.153 Sum_probs=136.0
Q ss_pred CcccccccCCCC-CCCCCCCcEEEEEEeecCCCCC-ccEEEEEEEEcCC-cE----EEEEEEcCCCcccccceecCCCCH
Q psy3897 60 PLEGYVKTKPRK-SPPPNGYGVYALDTEMVYTVHG-LEVARVTVVNVDG-RL----IYNTLVKPDCEIIDYNTKYSGISA 132 (240)
Q Consensus 60 ~~~~fv~t~~~~-~~~~~~~~~valD~E~tg~~~g-~ei~~v~vv~~~g-~~----~~d~lVkP~~~I~~~~t~~~GIt~ 132 (240)
.+..|..++.+. .......++++||+||||+++. .+|++|++|..++ .+ .|+++|+|+.+|+..++++||||+
T Consensus 28 ~l~~~~~~~~~~~~~~~~~~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~ 107 (239)
T PRK09146 28 RLKRFYAAGLVSPDTPLSEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITH 107 (239)
T ss_pred HHHHHhhCCCCCCCCCcccCCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCH
Confidence 344454444332 2235567899999999999965 6899999998643 32 488999999999999999999999
Q ss_pred HhhccCCCCCHHHHHHHHHhhhcCCcEEEEEchHHHHHHHhcc---------CCCeeeccccCcccC------------C
Q psy3897 133 KDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLI---------HSNIIDTSVLFPHSF------------G 191 (240)
Q Consensus 133 edl~~a~~~~~~ev~~~l~~~i~~~~iLVGH~~~~Dl~~L~~~---------~~~~iDT~~l~~~~~------------~ 191 (240)
+++.++|. +.+|+.+|.++++ +.++||||+.||+.||+.. ...+|||+.+++... +
T Consensus 108 e~l~~ap~--~~evl~~l~~~~~-~~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~ 184 (239)
T PRK09146 108 SELQDAPD--LERILDELLEALA-GKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKG 184 (239)
T ss_pred HHHhCCCC--HHHHHHHHHHHhC-CCEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhcc
Confidence 99999988 9999999999995 8999999999999999762 246899998754321 1
Q ss_pred CC-CCccHHHHHHHHcCCCCCCCCCChHHHHHHHHHHHHHHHhhh
Q psy3897 192 LP-YRRSLKSIVSQLLHQSIQSGTHDSFEDARACIDLILWKLLSD 235 (240)
Q Consensus 192 ~~-~~~sL~~L~~~~L~~~iq~~~H~A~eDA~at~~L~~~~l~~~ 235 (240)
.. ..++|.+++. .+|++.. .+|+|++||++|++||..++.+.
T Consensus 185 ~~~~~~~L~~l~~-~~gl~~~-~~H~Al~DA~ata~l~~~~~~~~ 227 (239)
T PRK09146 185 KKPESIRLADSRL-RYGLPAY-SPHHALTDAIATAELLQAQIAHH 227 (239)
T ss_pred CCCCCCCHHHHHH-HcCCCCC-CCCCcHHHHHHHHHHHHHHHHHH
Confidence 10 2458999997 5996543 37999999999999999988764
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=1.3e-27 Score=193.38 Aligned_cols=144 Identities=25% Similarity=0.413 Sum_probs=123.0
Q ss_pred EEEEEEeecCCCCCccEEEEEEEEc-CCcE--EEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhhcC
Q psy3897 80 VYALDTEMVYTVHGLEVARVTVVNV-DGRL--IYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSK 156 (240)
Q Consensus 80 ~valD~E~tg~~~g~ei~~v~vv~~-~g~~--~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~~ 156 (240)
+|+|||||||.. ..+|++|++|.. .|++ .|+.+|+|..++++.++++||||++++++++. +++++++|.++++
T Consensus 1 ~v~~D~Ettg~~-~~~ii~ig~v~~~~~~~~~~~~~~i~p~~~~~~~~~~i~GIt~e~l~~~~~--~~~v~~~l~~~l~- 76 (156)
T cd06130 1 FVAIDFETANAD-RASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPT--FPEVWPEIKPFLG- 76 (156)
T ss_pred CEEEEEeCCCCC-CCceEEEEEEEEECCEEEEEEEEEeCcCCCCChhhccccCcCHHHHhcCCC--HHHHHHHHHHHhC-
Confidence 589999999866 357999999886 4444 38899999999999999999999999999988 9999999999996
Q ss_pred CcEEEEEchHHHHHHHhcc---------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHHHHHHHHHH
Q psy3897 157 DSIIVGHGLENDLRALKLI---------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARACIDL 227 (240)
Q Consensus 157 ~~iLVGH~~~~Dl~~L~~~---------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~at~~L 227 (240)
+.++||||+.||+.+|+.. ..+++||..+++...+....++|..|++ ++|.+.+ +|+|++||++|++|
T Consensus 77 ~~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~~~~L~~l~~-~~g~~~~--~H~Al~Da~~ta~l 153 (156)
T cd06130 77 GSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAE-HLGIELN--HHDALEDARACAEI 153 (156)
T ss_pred CCEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCCCCCHHHHHH-HcCCCcc--CcCchHHHHHHHHH
Confidence 7999999999999999742 3468999988766533223579999997 6998877 79999999999999
Q ss_pred HHH
Q psy3897 228 ILW 230 (240)
Q Consensus 228 ~~~ 230 (240)
|++
T Consensus 154 ~~~ 156 (156)
T cd06130 154 LLA 156 (156)
T ss_pred HhC
Confidence 863
No 12
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=3.9e-27 Score=204.48 Aligned_cols=152 Identities=17% Similarity=0.169 Sum_probs=129.7
Q ss_pred cEEEEEEeecCCCCC-ccEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhhcCC
Q psy3897 79 GVYALDTEMVYTVHG-LEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKD 157 (240)
Q Consensus 79 ~~valD~E~tg~~~g-~ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~~~ 157 (240)
++++||+||||+++. .+|++|++++......|+.+|+|+.+|++.++++||||++|++++|+ +.++.++|.+|++++
T Consensus 3 ~~vv~D~ETTGl~~~~d~IIeig~v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~--f~ev~~~~~~fi~~~ 80 (232)
T PRK06309 3 ALIFYDTETTGTQIDKDRIIEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPK--FPEAYQKFIEFCGTD 80 (232)
T ss_pred cEEEEEeeCCCCCCCCCEEEEEEEEcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCC--HHHHHHHHHHHHcCC
Confidence 699999999999865 58999999986556679999999999999999999999999999999 999999999999766
Q ss_pred cEEEEEc-hHHHHHHHhcc---------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHHHHHHHHHH
Q psy3897 158 SIIVGHG-LENDLRALKLI---------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARACIDL 227 (240)
Q Consensus 158 ~iLVGH~-~~~Dl~~L~~~---------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~at~~L 227 (240)
.+||||| ..||+.+|+.. ..++|||..+++...+...+++|..|++ ++|.+... +|+|++||.+|++|
T Consensus 81 ~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~~~~L~~l~~-~~~~~~~~-aH~Al~Da~~t~~v 158 (232)
T PRK06309 81 NILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLRQ-VYGFEENQ-AHRALDDVITLHRV 158 (232)
T ss_pred CEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCCCCCHHHHHH-HcCCCCCC-CCCcHHHHHHHHHH
Confidence 8999999 58999999852 2378999988765432222568999996 58866543 89999999999999
Q ss_pred HHHHHhh
Q psy3897 228 ILWKLLS 234 (240)
Q Consensus 228 ~~~~l~~ 234 (240)
|..++.+
T Consensus 159 l~~l~~~ 165 (232)
T PRK06309 159 FSALVGD 165 (232)
T ss_pred HHHHHHH
Confidence 9988764
No 13
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=5.9e-27 Score=205.52 Aligned_cols=153 Identities=20% Similarity=0.210 Sum_probs=129.8
Q ss_pred CCcEEEEEEeecCCCCC-ccEEEEEEEEcCCc---EEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHh
Q psy3897 77 GYGVYALDTEMVYTVHG-LEVARVTVVNVDGR---LIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMG 152 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g-~ei~~v~vv~~~g~---~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~ 152 (240)
..++|+|||||||+++. .+|++|++|..++. ..|+.+|+|+.+|++.++.+||||+++++++|. +.++.++|.+
T Consensus 6 ~~~~v~~D~ETTGl~~~~d~IIEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~--~~ev~~~~~~ 83 (250)
T PRK06310 6 DTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPK--IAEVFPQIKG 83 (250)
T ss_pred CCcEEEEEEeCCCCCCCCCeEEEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCC--HHHHHHHHHH
Confidence 35799999999999865 58999999986443 248999999999999999999999999999998 9999999999
Q ss_pred hhcCCcEEEEEchHHHHHHHhcc-----------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHHHH
Q psy3897 153 FVSKDSIIVGHGLENDLRALKLI-----------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDA 221 (240)
Q Consensus 153 ~i~~~~iLVGH~~~~Dl~~L~~~-----------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA 221 (240)
|++++.+|||||+.||+.+|+.. +.++|||..+++.....+ +++|..|+. ++|.+... +|+|++||
T Consensus 84 fl~~~~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~~-~~~L~~l~~-~~g~~~~~-aH~Al~Da 160 (250)
T PRK06310 84 FFKEGDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDSP-NNSLEALAV-HFNVPYDG-NHRAMKDV 160 (250)
T ss_pred HhCCCCEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcccCC-CCCHHHHHH-HCCCCCCC-CcChHHHH
Confidence 99755999999999999999752 257899998876542222 478999996 68977654 89999999
Q ss_pred HHHHHHHHHHHhh
Q psy3897 222 RACIDLILWKLLS 234 (240)
Q Consensus 222 ~at~~L~~~~l~~ 234 (240)
++|++|+.+++++
T Consensus 161 ~at~~vl~~l~~~ 173 (250)
T PRK06310 161 EINIKVFKHLCKR 173 (250)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999988753
No 14
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.95 E-value=8e-27 Score=203.40 Aligned_cols=152 Identities=18% Similarity=0.248 Sum_probs=127.0
Q ss_pred CcEEEEEEeecCCCC--CccEEEEEEEEc-CCcE---EEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHH
Q psy3897 78 YGVYALDTEMVYTVH--GLEVARVTVVNV-DGRL---IYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLM 151 (240)
Q Consensus 78 ~~~valD~E~tg~~~--g~ei~~v~vv~~-~g~~---~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~ 151 (240)
-++|+||+||||+++ +.+|++|++|.. ++.+ .|+.||+|..+|++.++++||||+++|.++|. |++|+++|.
T Consensus 4 ~r~vvlDtETTGldp~~~drIIEIGaV~v~~~~~~~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~p~--f~ev~~~f~ 81 (240)
T PRK05711 4 MRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPT--FAEVADEFL 81 (240)
T ss_pred CeEEEEEeeCCCcCCCCCCeEEEEEEEEEECCEEeccEEEEEECcCCcCCHHHhhhcCCCHHHHcCCCC--HHHHHHHHH
Confidence 479999999999986 468999999885 3332 48999999999999999999999999999998 999999999
Q ss_pred hhhcCCcEEEEEchHHHHHHHhcc-------------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCC-CCCCh
Q psy3897 152 GFVSKDSIIVGHGLENDLRALKLI-------------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQS-GTHDS 217 (240)
Q Consensus 152 ~~i~~~~iLVGH~~~~Dl~~L~~~-------------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~-~~H~A 217 (240)
+|++ +.+|||||+.||+.||+.. ...++||..+.+.... ..+++|..||+ ++|++... ..|+|
T Consensus 82 ~fi~-~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p-~~~~~L~aL~~-~~gi~~~~r~~H~A 158 (240)
T PRK05711 82 DFIR-GAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFP-GKRNSLDALCK-RYGIDNSHRTLHGA 158 (240)
T ss_pred HHhC-CCEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcC-CCCCCHHHHHH-HCCCCCCCCCCCCH
Confidence 9995 8999999999999999752 1358999887665422 23568999997 58965543 25999
Q ss_pred HHHHHHHHHHHHHHHhh
Q psy3897 218 FEDARACIDLILWKLLS 234 (240)
Q Consensus 218 ~eDA~at~~L~~~~l~~ 234 (240)
+.||.++++||+.+...
T Consensus 159 L~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 159 LLDAEILAEVYLAMTGG 175 (240)
T ss_pred HHHHHHHHHHHHHHHCc
Confidence 99999999999987754
No 15
>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=8.2e-27 Score=201.67 Aligned_cols=151 Identities=19% Similarity=0.243 Sum_probs=126.1
Q ss_pred cEEEEEEeecCCCCC--ccEEEEEEEEc-CCc---EEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHh
Q psy3897 79 GVYALDTEMVYTVHG--LEVARVTVVNV-DGR---LIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMG 152 (240)
Q Consensus 79 ~~valD~E~tg~~~g--~ei~~v~vv~~-~g~---~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~ 152 (240)
++|+||+||||+++. .+|++|++|.. ++. ..|+.||+|..+|++.++++||||+++++++|+ +++|+++|.+
T Consensus 1 r~vvlD~ETTGl~p~~~d~IIEIgav~~~~~~~~~~~f~~~i~P~~~i~~~a~~vhGIt~e~l~~~p~--f~ev~~~f~~ 78 (225)
T TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPK--FKEIADEFLD 78 (225)
T ss_pred CEEEEEeeCCCcCCCCCCeEEEEEEEEEECCcEecceEEEEECcCCCCCHHHHhccCCCHHHHhCCCC--HHHHHHHHHH
Confidence 589999999999864 68999998864 332 249999999999999999999999999999998 9999999999
Q ss_pred hhcCCcEEEEEchHHHHHHHhcc-----------C--CCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCC-CCChH
Q psy3897 153 FVSKDSIIVGHGLENDLRALKLI-----------H--SNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSG-THDSF 218 (240)
Q Consensus 153 ~i~~~~iLVGH~~~~Dl~~L~~~-----------~--~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~-~H~A~ 218 (240)
|++ +.+|||||+.||+.||+.. . .+++||..+++.... ..+++|..||+ ++|++.+.. .|+|+
T Consensus 79 fi~-~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p-~~~~~L~~L~~-~~gi~~~~r~~H~Al 155 (225)
T TIGR01406 79 FIG-GSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFP-GQRNSLDALCK-RFKVDNSHRTLHGAL 155 (225)
T ss_pred HhC-CCEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcC-CCCCCHHHHHH-hcCCCCCCCCCcCHH
Confidence 995 8999999999999999741 1 368999987665432 23579999997 589665432 69999
Q ss_pred HHHHHHHHHHHHHHhh
Q psy3897 219 EDARACIDLILWKLLS 234 (240)
Q Consensus 219 eDA~at~~L~~~~l~~ 234 (240)
.||.+|++||+.+...
T Consensus 156 ~DA~~~a~v~~~l~~~ 171 (225)
T TIGR01406 156 LDAHLLAEVYLALTGG 171 (225)
T ss_pred HHHHHHHHHHHHHHcC
Confidence 9999999999987653
No 16
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.95 E-value=9.9e-27 Score=189.80 Aligned_cols=152 Identities=30% Similarity=0.399 Sum_probs=128.7
Q ss_pred cEEEEEEeecCCCCC-ccEEEEEEEEcCC---cEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhh
Q psy3897 79 GVYALDTEMVYTVHG-LEVARVTVVNVDG---RLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFV 154 (240)
Q Consensus 79 ~~valD~E~tg~~~g-~ei~~v~vv~~~g---~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i 154 (240)
.+|+|||||||+.++ .+|++|++|..++ ...|+.||+|..+|+++++++||||++++.++++ +.+++++|.+|+
T Consensus 1 ~~v~~D~Ettg~~~~~~~Iieig~v~~~~~~~~~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~~--~~~~~~~~~~~l 78 (169)
T smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGRIIVVFDTYVKPDRPITDYATEIHGITPEMLDDAPT--FEEVLEELLEFL 78 (169)
T ss_pred CEEEEEeeCCCCCCCCCeEEEEEEEEEECCEeEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCC--HHHHHHHHHHHh
Confidence 479999999999987 6899999999644 3459999999999999999999999999999888 999999999999
Q ss_pred cCCcEEEEEch-HHHHHHHhccC----------CCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHHHHHH
Q psy3897 155 SKDSIIVGHGL-ENDLRALKLIH----------SNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARA 223 (240)
Q Consensus 155 ~~~~iLVGH~~-~~Dl~~L~~~~----------~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~a 223 (240)
+ +.++||||. .||+.+|+... ..++||..+++...+.. .++|+.|++ ++|.+..+..|+|++||++
T Consensus 79 ~-~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~-~~~L~~l~~-~~~~~~~~~~H~A~~Da~~ 155 (169)
T smart00479 79 K-GKILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGR-KYSLKKLAE-RLGLEVIGRAHRALDDARA 155 (169)
T ss_pred c-CCEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCC-CCCHHHHHH-HCCCCCCCCCcCcHHHHHH
Confidence 6 778888887 99999998731 24799988876654332 679999997 5886665435999999999
Q ss_pred HHHHHHHHHhhh
Q psy3897 224 CIDLILWKLLSD 235 (240)
Q Consensus 224 t~~L~~~~l~~~ 235 (240)
|++||.+++++.
T Consensus 156 t~~l~~~~~~~~ 167 (169)
T smart00479 156 TAKLFKKLVERL 167 (169)
T ss_pred HHHHHHHHHHHh
Confidence 999999887764
No 17
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=2.3e-26 Score=195.37 Aligned_cols=153 Identities=20% Similarity=0.242 Sum_probs=126.9
Q ss_pred CCcEEEEEEeecCCCCC-ccEEEEEEEEcCCc-E----EEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHH
Q psy3897 77 GYGVYALDTEMVYTVHG-LEVARVTVVNVDGR-L----IYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDL 150 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g-~ei~~v~vv~~~g~-~----~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l 150 (240)
..++|+||+||||+++. .+|++|++|..++. + .|+.+|+|..+|++.++++||||++++++++. +.+|+++|
T Consensus 28 ~~~~vviD~ETTGl~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~--~~~vl~~~ 105 (202)
T PRK09145 28 PDEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLS--EEEALRQL 105 (202)
T ss_pred CCCEEEEEeECCCCCCCCCceEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCC--HHHHHHHH
Confidence 35899999999999875 68999999987543 2 38899999999999999999999999999988 99999999
Q ss_pred HhhhcCCcEEEEEchHHHHHHHhcc---------CCCeeeccccCccc-----CCCCCCccHHHHHHHHcCCCCCCCCCC
Q psy3897 151 MGFVSKDSIIVGHGLENDLRALKLI---------HSNIIDTSVLFPHS-----FGLPYRRSLKSIVSQLLHQSIQSGTHD 216 (240)
Q Consensus 151 ~~~i~~~~iLVGH~~~~Dl~~L~~~---------~~~~iDT~~l~~~~-----~~~~~~~sL~~L~~~~L~~~iq~~~H~ 216 (240)
.+|++ +.++||||+.||+.+|+.. ...++|++.++... .....+++|..|++ ++|++.. +.|+
T Consensus 106 ~~~i~-~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~-~~gi~~~-~~H~ 182 (202)
T PRK09145 106 LAFIG-NRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILK-HLDLPVL-GRHD 182 (202)
T ss_pred HHHHc-CCeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHHH-HcCCCCC-CCCC
Confidence 99995 8999999999999999752 24689998765321 11112478999996 6997764 3799
Q ss_pred hHHHHHHHHHHHHHHHhh
Q psy3897 217 SFEDARACIDLILWKLLS 234 (240)
Q Consensus 217 A~eDA~at~~L~~~~l~~ 234 (240)
|++||++|++||.+..+.
T Consensus 183 Al~DA~ata~l~~~l~~~ 200 (202)
T PRK09145 183 ALNDAIMAALIFLRLRKG 200 (202)
T ss_pred cHHHHHHHHHHHHHHHhc
Confidence 999999999999977653
No 18
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=2.6e-26 Score=207.24 Aligned_cols=153 Identities=21% Similarity=0.301 Sum_probs=129.6
Q ss_pred CCcEEEEEEeecCCCCC-ccEEEEEEEEc-CCcEE--EEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHh
Q psy3897 77 GYGVYALDTEMVYTVHG-LEVARVTVVNV-DGRLI--YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMG 152 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g-~ei~~v~vv~~-~g~~~--~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~ 152 (240)
..++|+||+||||+++. .+|++|++|.. +|.++ |+++|+|..+|++.++++||||+++++++|+ +.+|+.+|.+
T Consensus 7 ~~~~Vv~DlETTGl~p~~~eIIEIgaV~v~~g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~--~~evl~~f~~ 84 (313)
T PRK06807 7 PLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPT--IEEVLPLFLA 84 (313)
T ss_pred CCCEEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCCCC--HHHHHHHHHH
Confidence 34899999999999875 58999999986 55544 8999999999999999999999999999988 9999999999
Q ss_pred hhcCCcEEEEEchHHHHHHHhcc---------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHHHHHH
Q psy3897 153 FVSKDSIIVGHGLENDLRALKLI---------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARA 223 (240)
Q Consensus 153 ~i~~~~iLVGH~~~~Dl~~L~~~---------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~a 223 (240)
|++ +.+|||||+.||+.+|+.. ...+|||..+++...+....++|..||+ +||++. .+|+|+.||++
T Consensus 85 fl~-~~~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~~~kL~~L~~-~lgi~~--~~H~Al~DA~~ 160 (313)
T PRK06807 85 FLH-TNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKR-MLGIRL--SSHNAFDDCIT 160 (313)
T ss_pred HHc-CCeEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCCCCCHHHHHH-HcCCCC--CCcChHHHHHH
Confidence 995 8899999999999999852 2468999887654322222468999996 699777 47999999999
Q ss_pred HHHHHHHHHhhh
Q psy3897 224 CIDLILWKLLSD 235 (240)
Q Consensus 224 t~~L~~~~l~~~ 235 (240)
|++||+.+..+.
T Consensus 161 ta~l~~~l~~~~ 172 (313)
T PRK06807 161 CAAVYQKCASIE 172 (313)
T ss_pred HHHHHHHHHHhh
Confidence 999999877654
No 19
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.94 E-value=2.3e-26 Score=199.71 Aligned_cols=157 Identities=17% Similarity=0.142 Sum_probs=125.7
Q ss_pred CCCCcEEEEEEeecCCCCC-ccEEEEEEEEcC--CcEE--EEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHH
Q psy3897 75 PNGYGVYALDTEMVYTVHG-LEVARVTVVNVD--GRLI--YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQND 149 (240)
Q Consensus 75 ~~~~~~valD~E~tg~~~g-~ei~~v~vv~~~--g~~~--~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~ 149 (240)
+...++++||+||||+++. .+|++|++|..+ |.++ |++||+|+.+|++.++++||||++++.+.+.+ +.+++++
T Consensus 3 ~~~~~~vv~D~ETTGl~p~~d~Iieig~v~v~~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~-~~~vl~e 81 (232)
T PRK07942 3 WHPGPLAAFDLETTGVDPETARIVTAALVVVDADGEVVESREWLADPGVEIPEEASAVHGITTEYARAHGRP-AAEVLAE 81 (232)
T ss_pred cccCcEEEEEeccCCCCCCCCeeEEEEEEEEeCCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCC-HHHHHHH
Confidence 4567899999999999875 479999998753 7654 89999999999999999999999999875443 7788887
Q ss_pred HHhhh----cCCcEEEEEchHHHHHHHhcc----------CCCeeeccccCcccCC-CCCCccHHHHHHHHcCCCCCCCC
Q psy3897 150 LMGFV----SKDSIIVGHGLENDLRALKLI----------HSNIIDTSVLFPHSFG-LPYRRSLKSIVSQLLHQSIQSGT 214 (240)
Q Consensus 150 l~~~i----~~~~iLVGH~~~~Dl~~L~~~----------~~~~iDT~~l~~~~~~-~~~~~sL~~L~~~~L~~~iq~~~ 214 (240)
|..++ .++.+|||||+.||+.+|+.. ...++||..+...... ...+++|..||+ ++|++... +
T Consensus 82 ~~~~l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~-~~gi~~~~-a 159 (232)
T PRK07942 82 IADALREAWARGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALCE-HYGVRLDN-A 159 (232)
T ss_pred HHHHHHHHhhcCCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHHH-HcCCCCCC-C
Confidence 77765 258899999999999999752 1358999877543211 112568999996 69977654 8
Q ss_pred CChHHHHHHHHHHHHHHHhh
Q psy3897 215 HDSFEDARACIDLILWKLLS 234 (240)
Q Consensus 215 H~A~eDA~at~~L~~~~l~~ 234 (240)
|+|++||+||++||..++++
T Consensus 160 H~Al~Da~ata~l~~~l~~~ 179 (232)
T PRK07942 160 HEATADALAAARVAWALARR 179 (232)
T ss_pred CChHHHHHHHHHHHHHHHHH
Confidence 99999999999999987754
No 20
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.94 E-value=2.3e-26 Score=198.11 Aligned_cols=145 Identities=21% Similarity=0.252 Sum_probs=122.1
Q ss_pred EEEEEEeecCCCCCccEEEEEEEEc-CCcEE--EEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhhcC
Q psy3897 80 VYALDTEMVYTVHGLEVARVTVVNV-DGRLI--YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSK 156 (240)
Q Consensus 80 ~valD~E~tg~~~g~ei~~v~vv~~-~g~~~--~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~~ 156 (240)
+++||+||||++++ |++|++|+. +|+++ |++||+|+.+|+..++.+||||++|++++|. +.++++. |+ +
T Consensus 2 ~~vlD~ETTGl~~~--IieIg~v~v~~~~i~~~~~~lv~P~~~i~~~~~~ihgIt~e~v~~ap~--~~ev~~~---~~-~ 73 (219)
T PRK07983 2 LRVIDTETCGLQGG--IVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPW--IEDVIPH---YY-G 73 (219)
T ss_pred eEEEEEECCCCCCC--CEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHcCCCC--HHHHHHH---Hc-C
Confidence 68999999998754 888888774 55554 9999999999999999999999999999998 9998776 45 5
Q ss_pred CcEEEEEchHHHHHHHhccCCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCC----CCCCChHHHHHHHHHHHHHHH
Q psy3897 157 DSIIVGHGLENDLRALKLIHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQ----SGTHDSFEDARACIDLILWKL 232 (240)
Q Consensus 157 ~~iLVGH~~~~Dl~~L~~~~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq----~~~H~A~eDA~at~~L~~~~l 232 (240)
+.+|||||+.||+.+|.....++|||..+++...+. .+++|..||. ++|.... ..+|+|++||++|++||++.+
T Consensus 74 ~~~lVaHNa~FD~~~L~~~~~~~idTl~lar~l~p~-~~~~l~~L~~-~~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~ 151 (219)
T PRK07983 74 SEWYVAHNASFDRRVLPEMPGEWICTMKLARRLWPG-IKYSNMALYK-SRKLNVQTPPGLHHHRALYDCYITAALLIDIM 151 (219)
T ss_pred CCEEEEeCcHhhHHHHhCcCCCcEeHHHHHHHHccC-CCCCHHHHHH-HcCCCCCCCCCCCCCcHHHHHHHHHHHHHHHH
Confidence 899999999999999998888999999877654321 2478999996 6886642 238999999999999999988
Q ss_pred hh
Q psy3897 233 LS 234 (240)
Q Consensus 233 ~~ 234 (240)
++
T Consensus 152 ~~ 153 (219)
T PRK07983 152 NT 153 (219)
T ss_pred HH
Confidence 53
No 21
>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=99.94 E-value=2.7e-26 Score=197.25 Aligned_cols=159 Identities=19% Similarity=0.220 Sum_probs=130.2
Q ss_pred CCcEEEEEEeecCCCCCccEEEEEEEE-cCCc---EEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHh
Q psy3897 77 GYGVYALDTEMVYTVHGLEVARVTVVN-VDGR---LIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMG 152 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g~ei~~v~vv~-~~g~---~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~ 152 (240)
...||+||+||||.+++.+|++|++|. .++. ..|+++|+|..+|++.++.+||||++++.++|. +++++++|.+
T Consensus 6 ~~~fvv~D~ETTGl~~~~~IIeIgav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~--~~ev~~~~~~ 83 (217)
T TIGR00573 6 LDTETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPD--FKEIAEDFAD 83 (217)
T ss_pred ecCEEEEEecCCCCCCCCCEEEEEEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCC--HHHHHHHHHH
Confidence 457999999999999876699999988 4443 259999999999999999999999999999988 9999999999
Q ss_pred hhcCCcEEEEEchHHHHHHHhcc----------CCCeeeccccCcccC--CCCCCccHHHHHHHHcCCCCCC-CCCChHH
Q psy3897 153 FVSKDSIIVGHGLENDLRALKLI----------HSNIIDTSVLFPHSF--GLPYRRSLKSIVSQLLHQSIQS-GTHDSFE 219 (240)
Q Consensus 153 ~i~~~~iLVGH~~~~Dl~~L~~~----------~~~~iDT~~l~~~~~--~~~~~~sL~~L~~~~L~~~iq~-~~H~A~e 219 (240)
|++ +.++||||+.||+.+|+.. ..+++||..+++... .+..+++|..|++ ++|.+... ..|+|++
T Consensus 84 ~~~-~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~-~~gl~~~~~~~H~Al~ 161 (217)
T TIGR00573 84 YIR-GAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCK-RYEITNSHRALHGALA 161 (217)
T ss_pred HhC-CCEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHH-HcCCCCCCcccCCHHH
Confidence 995 8999999999999999852 135788876543221 1123578999996 58966542 3799999
Q ss_pred HHHHHHHHHHHHHhhhhccC
Q psy3897 220 DARACIDLILWKLLSDFRYN 239 (240)
Q Consensus 220 DA~at~~L~~~~l~~~~~~~ 239 (240)
||++|++||...+.+.-+++
T Consensus 162 DA~~ta~l~~~l~~~~~~~~ 181 (217)
T TIGR00573 162 DAFILAKLYLVMTGKQTKYG 181 (217)
T ss_pred HHHHHHHHHHHHHhcchhhc
Confidence 99999999999988765443
No 22
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.94 E-value=1.1e-25 Score=203.42 Aligned_cols=152 Identities=19% Similarity=0.194 Sum_probs=126.9
Q ss_pred CCcEEEEEEeecCCCCC-ccEEEEEEEEc--CCcEE--EEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHH
Q psy3897 77 GYGVYALDTEMVYTVHG-LEVARVTVVNV--DGRLI--YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLM 151 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g-~ei~~v~vv~~--~g~~~--~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~ 151 (240)
..+||+||+||||++++ .+|++|++|.. +|.++ |.+||+|.. ++.++.+||||++|+.++|. |.+++++|.
T Consensus 14 ~~~fvvlD~ETTGl~p~~d~IIeIgav~v~~~g~i~~~~~~lv~P~~--~~~~~~IhGIt~e~l~~ap~--f~ev~~~l~ 89 (313)
T PRK06063 14 PRGWAVVDVETSGFRPGQARIISLAVLGLDADGNVEQSVVTLLNPGV--DPGPTHVHGLTAEMLEGQPQ--FADIAGEVA 89 (313)
T ss_pred CCCEEEEEEECCCCCCCCCEEEEEEEEEEECCceeeeEEEEEECcCC--CCCCeecCCCCHHHHhCCCC--HHHHHHHHH
Confidence 46799999999999977 58999999874 56654 999999975 45679999999999999998 999999999
Q ss_pred hhhcCCcEEEEEchHHHHHHHhcc---------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHHHHH
Q psy3897 152 GFVSKDSIIVGHGLENDLRALKLI---------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDAR 222 (240)
Q Consensus 152 ~~i~~~~iLVGH~~~~Dl~~L~~~---------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~ 222 (240)
+|++ +.+|||||+.||+.||+.. ...++||+.+.+.......+++|..||+ ++|++.. .+|+|++||+
T Consensus 90 ~~l~-~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~~kL~~l~~-~~gi~~~-~~H~Al~DA~ 166 (313)
T PRK06063 90 ELLR-GRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLAA-HWGVPQQ-RPHDALDDAR 166 (313)
T ss_pred HHcC-CCEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCCCCHHHHHH-HcCCCCC-CCCCcHHHHH
Confidence 9995 8999999999999999862 2368999988765422223578999996 6996643 3799999999
Q ss_pred HHHHHHHHHHhhh
Q psy3897 223 ACIDLILWKLLSD 235 (240)
Q Consensus 223 at~~L~~~~l~~~ 235 (240)
+|++||...+++.
T Consensus 167 ata~l~~~ll~~~ 179 (313)
T PRK06063 167 VLAGILRPSLERA 179 (313)
T ss_pred HHHHHHHHHHHHH
Confidence 9999998877664
No 23
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.94 E-value=8.7e-26 Score=198.77 Aligned_cols=153 Identities=24% Similarity=0.343 Sum_probs=130.3
Q ss_pred CCCCcEEEEEEeecCCCCCc-cEEEEEEEEc-CCcEE--EEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHH
Q psy3897 75 PNGYGVYALDTEMVYTVHGL-EVARVTVVNV-DGRLI--YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDL 150 (240)
Q Consensus 75 ~~~~~~valD~E~tg~~~g~-ei~~v~vv~~-~g~~~--~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l 150 (240)
.....+|+||+||||..++. +|++|++|.. +|.++ |+++|+|. +|++.++++||||++++.++|. +.+|+.+|
T Consensus 65 ~~~~~~vv~DiETTG~~~~~~~IIEIGAv~v~~g~i~~~f~~~v~p~-~ip~~~~~itGIt~e~l~~ap~--~~evl~~f 141 (257)
T PRK08517 65 IKDQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAK-EVPEYITELTGITYEDLENAPS--LKEVLEEF 141 (257)
T ss_pred CCCCCEEEEEEeCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCC-CCChhhhhhcCcCHHHHcCCCC--HHHHHHHH
Confidence 44668999999999998764 8999999986 55554 89999996 8999999999999999999998 99999999
Q ss_pred HhhhcCCcEEEEEchHHHHHHHhc---------cCCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHHHH
Q psy3897 151 MGFVSKDSIIVGHGLENDLRALKL---------IHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDA 221 (240)
Q Consensus 151 ~~~i~~~~iLVGH~~~~Dl~~L~~---------~~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA 221 (240)
.+|++ +.++||||+.||+.+|+. ..++.+||..+++.... ..+++|..|++ ++|.+.. .+|+|+.||
T Consensus 142 ~~fl~-~~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~-~~~~~L~~L~~-~lgi~~~-~~HrAl~DA 217 (257)
T PRK08517 142 RLFLG-DSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIE-SPRYGLSFLKE-LLGIEIE-VHHRAYADA 217 (257)
T ss_pred HHHHC-CCeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHcc-CCCCCHHHHHH-HcCcCCC-CCCChHHHH
Confidence 99995 899999999999999975 23578999887765422 23678999996 6997664 489999999
Q ss_pred HHHHHHHHHHHhh
Q psy3897 222 RACIDLILWKLLS 234 (240)
Q Consensus 222 ~at~~L~~~~l~~ 234 (240)
.+|++||..++.+
T Consensus 218 ~ata~ll~~ll~~ 230 (257)
T PRK08517 218 LAAYEIFKICLLN 230 (257)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999988865
No 24
>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=99.94 E-value=5.4e-26 Score=186.64 Aligned_cols=147 Identities=20% Similarity=0.276 Sum_probs=122.2
Q ss_pred EEEEEEeecCCCC-C-ccEEEEEEEEc-CCcE---EEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhh
Q psy3897 80 VYALDTEMVYTVH-G-LEVARVTVVNV-DGRL---IYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGF 153 (240)
Q Consensus 80 ~valD~E~tg~~~-g-~ei~~v~vv~~-~g~~---~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~ 153 (240)
+|+||+||||.++ + .+|++|++|.. ++.+ .|+.+|+|..+|++.++++||||++++++++. +.+++++|.+|
T Consensus 1 ~v~~D~ETTGl~~~~~~~iieig~v~v~~~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~--~~~v~~~l~~~ 78 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPK--FAEIADEFLDF 78 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEEEEEEEECCcEeccEEEEEECCCCCCCHHHHHHhCCCHHHHhcCCC--HHHHHHHHHHH
Confidence 5899999999987 3 58999998864 3332 58999999999999999999999999999998 99999999999
Q ss_pred hcCCcEEEEEchHHHHHHHhcc------------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCC-CCCChHHH
Q psy3897 154 VSKDSIIVGHGLENDLRALKLI------------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQS-GTHDSFED 220 (240)
Q Consensus 154 i~~~~iLVGH~~~~Dl~~L~~~------------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~-~~H~A~eD 220 (240)
++ +.++||||+.||+.+|+.. ...++||..+++.... ...++|..+++ ++|.+.+. ..|+|+.|
T Consensus 79 l~-~~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~-~~~~~L~~l~~-~~~i~~~~~~~H~Al~D 155 (167)
T cd06131 79 IR-GAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFP-GKPNSLDALCK-RFGIDNSHRTLHGALLD 155 (167)
T ss_pred HC-CCeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcC-CCCCCHHHHHH-HCCCCCCCCCCCChHHH
Confidence 95 8899999999999999752 1357999887655321 13468999997 58977653 36999999
Q ss_pred HHHHHHHHHHH
Q psy3897 221 ARACIDLILWK 231 (240)
Q Consensus 221 A~at~~L~~~~ 231 (240)
|++|++||.++
T Consensus 156 a~~~a~l~~~l 166 (167)
T cd06131 156 AELLAEVYLEL 166 (167)
T ss_pred HHHHHHHHHHh
Confidence 99999999764
No 25
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=9.5e-26 Score=203.42 Aligned_cols=149 Identities=19% Similarity=0.276 Sum_probs=124.6
Q ss_pred cEEEEEEeecCCCCCccEEEEEEEEc-CCcEE--EEEEEcCCC-cccccceecCCCCHHhhccCCCCCHHHHHHHHHhhh
Q psy3897 79 GVYALDTEMVYTVHGLEVARVTVVNV-DGRLI--YNTLVKPDC-EIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFV 154 (240)
Q Consensus 79 ~~valD~E~tg~~~g~ei~~v~vv~~-~g~~~--~d~lVkP~~-~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i 154 (240)
+||+||+||||.. ..+|++|++|.. +|.++ |++||+|.. .+++.++++||||++||+++|. |.+++++|.+|+
T Consensus 2 ~~vviD~ETTg~~-~d~IieIgav~v~~g~i~~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~~ap~--f~ev~~~~~~fl 78 (309)
T PRK06195 2 NFVAIDFETANEK-RNSPCSIGIVVVKDGEIVEKVHYLIKPKEMRFMPINIGIHGIRPHMVEDELE--FDKIWEKIKHYF 78 (309)
T ss_pred cEEEEEEeCCCCC-CCceEEEEEEEEECCEEEEEEEEEECCCCCCCChhheeccCcCHHHHhCCCC--HHHHHHHHHHHh
Confidence 5899999999753 468999999886 55544 899999985 6788899999999999999998 999999999999
Q ss_pred cCCcEEEEEchHHHHHHHhcc---------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHHHHHHHH
Q psy3897 155 SKDSIIVGHGLENDLRALKLI---------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARACI 225 (240)
Q Consensus 155 ~~~~iLVGH~~~~Dl~~L~~~---------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~at~ 225 (240)
+ +.+|||||+.||+.+|+.. ...++||..+++........++|..||. ++|.+. .+|+|++||++|+
T Consensus 79 ~-~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~~L~~L~~-~~gi~~--~~H~Al~DA~ata 154 (309)
T PRK06195 79 N-NNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNN-FLGYEF--KHHDALADAMACS 154 (309)
T ss_pred C-CCEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcCCHHHHHH-HcCCCC--cccCCHHHHHHHH
Confidence 5 8999999999999999752 2468999887765432222578999997 599664 4799999999999
Q ss_pred HHHHHHHhh
Q psy3897 226 DLILWKLLS 234 (240)
Q Consensus 226 ~L~~~~l~~ 234 (240)
+||..++++
T Consensus 155 ~l~~~l~~~ 163 (309)
T PRK06195 155 NILLNISKE 163 (309)
T ss_pred HHHHHHHHH
Confidence 999988765
No 26
>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=99.94 E-value=1.6e-26 Score=192.85 Aligned_cols=144 Identities=22% Similarity=0.208 Sum_probs=115.5
Q ss_pred EEEEEEeecCCC-C-CccEEEEEEEEcCC-c-------------E--EEEEEEcCCCcccccceecCCCCHHhhccCCCC
Q psy3897 80 VYALDTEMVYTV-H-GLEVARVTVVNVDG-R-------------L--IYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYK 141 (240)
Q Consensus 80 ~valD~E~tg~~-~-g~ei~~v~vv~~~g-~-------------~--~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~ 141 (240)
|++||+||||++ + ..+|++|++|...+ . + .|+++|+|+.+|++.++++||||++++.++|.
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a~~IhGIt~e~l~~~~~- 79 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHKAP- 79 (177)
T ss_pred CeEEeeecCCCCCCCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCCcCChhHHHHhCcCHHHHhcCCC-
Confidence 689999999998 3 46899999988532 1 1 38999999999999999999999999999987
Q ss_pred CHH-HHHHHHHhhh---cCCcEEEEEch-HHHHHHHhcc----------CCCeeeccccCcccCCCCCCccHHHHHHHHc
Q psy3897 142 TLK-DVQNDLMGFV---SKDSIIVGHGL-ENDLRALKLI----------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLL 206 (240)
Q Consensus 142 ~~~-ev~~~l~~~i---~~~~iLVGH~~-~~Dl~~L~~~----------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L 206 (240)
++ ++.+.+.+|+ +++.+|||||+ .||+.+|+.. ...++||+.+++... ++|..|++.++
T Consensus 80 -~~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~-----~~L~~l~~~~~ 153 (177)
T cd06136 80 -FDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELD-----QSLGSLYKRLF 153 (177)
T ss_pred -ccHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhH-----hhHHHHHHHHh
Confidence 54 3555555555 44569999998 8999999752 134689999887653 18999998778
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHHH
Q psy3897 207 HQSIQSGTHDSFEDARACIDLILWK 231 (240)
Q Consensus 207 ~~~iq~~~H~A~eDA~at~~L~~~~ 231 (240)
|.+... +|+|++||.||+++|+++
T Consensus 154 ~~~~~~-~H~A~~Da~at~~v~~~~ 177 (177)
T cd06136 154 GQEPKN-SHTAEGDVLALLKCALHK 177 (177)
T ss_pred CCCccc-ccchHHHHHHHHHHHhhC
Confidence 866544 799999999999998763
No 27
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.94 E-value=5.4e-26 Score=193.96 Aligned_cols=155 Identities=17% Similarity=0.212 Sum_probs=124.4
Q ss_pred CcEEEEEEeecCCCCC-------ccEEEEEEEEc-CCcE--EEEEEEcCCC--cccccceecCCCCHHhhccCCCCCHHH
Q psy3897 78 YGVYALDTEMVYTVHG-------LEVARVTVVNV-DGRL--IYNTLVKPDC--EIIDYNTKYSGISAKDFIRNPYKTLKD 145 (240)
Q Consensus 78 ~~~valD~E~tg~~~g-------~ei~~v~vv~~-~g~~--~~d~lVkP~~--~I~~~~t~~~GIt~edl~~a~~~~~~e 145 (240)
-+||+||+||||.+.+ .||++|++|.. +|.+ .|++||+|.. +|+++++++||||++|+.++|+ +++
T Consensus 4 ~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~--~~e 81 (207)
T PRK07748 4 QQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGIS--FEE 81 (207)
T ss_pred ceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecCcChhhhcceECCCccCccChhhhhhcCcCHHHHccCCC--HHH
Confidence 4699999999997542 48999999985 4443 3999999987 7999999999999999999988 999
Q ss_pred HHHHHHhhhcCCcEEEEEchHHHHHHHhcc----------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCC
Q psy3897 146 VQNDLMGFVSKDSIIVGHGLENDLRALKLI----------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTH 215 (240)
Q Consensus 146 v~~~l~~~i~~~~iLVGH~~~~Dl~~L~~~----------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H 215 (240)
|+++|.+|+++..++|+||..||+.+|+.. ...++|+..+++...+....++|..+++ ++|++.....|
T Consensus 82 vl~~f~~~~~~~~~~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~~~~L~~~~~-~~gi~~~~~~H 160 (207)
T PRK07748 82 LVEKLAEYDKRCKPTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKAIE-EYGKEGTGKHH 160 (207)
T ss_pred HHHHHHHHhCcCCeEEEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCCCCCHHHHHH-HcCCCCCCCCc
Confidence 999999999632455556679999999752 1357888876654433333578999996 69977544479
Q ss_pred ChHHHHHHHHHHHHHHHhhh
Q psy3897 216 DSFEDARACIDLILWKLLSD 235 (240)
Q Consensus 216 ~A~eDA~at~~L~~~~l~~~ 235 (240)
+|++||++|++||.+++++.
T Consensus 161 ~Al~DA~~ta~l~~~l~~~~ 180 (207)
T PRK07748 161 CALDDAMTTYNIFKLVEKDK 180 (207)
T ss_pred ChHHHHHHHHHHHHHHHhCc
Confidence 99999999999999988774
No 28
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=3e-25 Score=222.27 Aligned_cols=154 Identities=23% Similarity=0.284 Sum_probs=131.3
Q ss_pred CCcEEEEEEeecCCCCCccEEEEEEEEc-CCcEE--EEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhh
Q psy3897 77 GYGVYALDTEMVYTVHGLEVARVTVVNV-DGRLI--YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGF 153 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g~ei~~v~vv~~-~g~~~--~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~ 153 (240)
..++|+||+||||+++..+|++|++|.. +|+++ |+++|+|..+|+++++++||||++|+.++|. +++|+++|.+|
T Consensus 6 ~~~~vvvD~ETTGl~~~d~IIeIgaV~v~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~--~~ev~~~~~~~ 83 (820)
T PRK07246 6 LRKYAVVDLEATGAGPNASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPD--FSQVARHIYDL 83 (820)
T ss_pred CCCEEEEEEecCCcCCCCeEEEEEEEEEECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCC--HHHHHHHHHHH
Confidence 4679999999999987779999999986 55544 8999999999999999999999999999998 99999999999
Q ss_pred hcCCcEEEEEchHHHHHHHhcc--------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHHHHHHHH
Q psy3897 154 VSKDSIIVGHGLENDLRALKLI--------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARACI 225 (240)
Q Consensus 154 i~~~~iLVGH~~~~Dl~~L~~~--------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~at~ 225 (240)
++ +.++||||+.||+.+|+.. ...++||..+.+...+...+++|.+||. ++|.+... +|+|++||++|+
T Consensus 84 l~-~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L~~-~lgl~~~~-~H~Al~DA~ata 160 (820)
T PRK07246 84 IE-DCIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLSR-ELNIDLAD-AHTAIADARATA 160 (820)
T ss_pred hC-CCEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHHHH-HcCCCCCC-CCCHHHHHHHHH
Confidence 95 8999999999999999752 2467999876554322223579999996 69976653 799999999999
Q ss_pred HHHHHHHhhh
Q psy3897 226 DLILWKLLSD 235 (240)
Q Consensus 226 ~L~~~~l~~~ 235 (240)
+||..++++.
T Consensus 161 ~L~~~l~~~l 170 (820)
T PRK07246 161 ELFLKLLQKI 170 (820)
T ss_pred HHHHHHHHHH
Confidence 9999887654
No 29
>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=99.93 E-value=9.4e-25 Score=185.60 Aligned_cols=156 Identities=19% Similarity=0.220 Sum_probs=123.6
Q ss_pred CCCcEEEEEEeecCCCCC-ccEEEEEEEEc----CCcE----EEEEEEcC--CCcccccceecCCCCHH-hhccCCCCCH
Q psy3897 76 NGYGVYALDTEMVYTVHG-LEVARVTVVNV----DGRL----IYNTLVKP--DCEIIDYNTKYSGISAK-DFIRNPYKTL 143 (240)
Q Consensus 76 ~~~~~valD~E~tg~~~g-~ei~~v~vv~~----~g~~----~~d~lVkP--~~~I~~~~t~~~GIt~e-dl~~a~~~~~ 143 (240)
....+++||+||||+++. .+|++|++|.. +|.+ .|+++|+| +.+|+..++++||||++ ++.+++. .
T Consensus 6 ~~~~~vv~D~ETTGl~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~--~ 83 (200)
T TIGR01298 6 RGYLPVVVDVETGGFNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVS--E 83 (200)
T ss_pred cCCeeEEEEeeCCCCCCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcc--h
Confidence 455789999999999975 57888888863 3444 38999998 46999999999999976 6888877 7
Q ss_pred HHHHHHHHhhhc--------CCcEEEEEchHHHHHHHhcc------------CCCeeeccccCcccCCCCCCccHHHHHH
Q psy3897 144 KDVQNDLMGFVS--------KDSIIVGHGLENDLRALKLI------------HSNIIDTSVLFPHSFGLPYRRSLKSIVS 203 (240)
Q Consensus 144 ~ev~~~l~~~i~--------~~~iLVGH~~~~Dl~~L~~~------------~~~~iDT~~l~~~~~~~~~~~sL~~L~~ 203 (240)
.+++.++.+++. ++.+|||||+.||++||+.. +..++||..+.+...+ ..+|..+|+
T Consensus 84 ~~~~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~---~~~L~~l~~ 160 (200)
T TIGR01298 84 YEALHEIFKVVRKAMKASGCQRAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG---QTVLAKACQ 160 (200)
T ss_pred HHHHHHHHHHHHHHHHhcccCCCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC---cccHHHHHH
Confidence 777777776651 47899999999999999852 1248999998765432 347999997
Q ss_pred HHcCCCCCC-CCCChHHHHHHHHHHHHHHHhhhhc
Q psy3897 204 QLLHQSIQS-GTHDSFEDARACIDLILWKLLSDFR 237 (240)
Q Consensus 204 ~~L~~~iq~-~~H~A~eDA~at~~L~~~~l~~~~~ 237 (240)
++|+++.. ..|+|++||.+|++||..++.+-..
T Consensus 161 -~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~~ 194 (200)
T TIGR01298 161 -AAGXDFDSTQAHSALYDTEKTAELFCEIVNRWKR 194 (200)
T ss_pred -HcCCCccccchhhhHHhHHHHHHHHHHHHHHHHH
Confidence 68977642 4799999999999999998876543
No 30
>PRK07883 hypothetical protein; Validated
Probab=99.92 E-value=1.6e-24 Score=209.05 Aligned_cols=156 Identities=20% Similarity=0.281 Sum_probs=132.6
Q ss_pred CCCCcEEEEEEeecCCCCC-ccEEEEEEEEc-CCcEE--EEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHH
Q psy3897 75 PNGYGVYALDTEMVYTVHG-LEVARVTVVNV-DGRLI--YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDL 150 (240)
Q Consensus 75 ~~~~~~valD~E~tg~~~g-~ei~~v~vv~~-~g~~~--~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l 150 (240)
.....+|+||+||||+++. .+|++|++|.. +|.++ |+++|+|..+|+++++++||||+++++++|. +++++..|
T Consensus 12 ~~~~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~--~~evl~~f 89 (557)
T PRK07883 12 LRDVTFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPP--IEEVLPAF 89 (557)
T ss_pred CcCCCEEEEEEecCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCC--HHHHHHHH
Confidence 4567899999999999876 68999999996 55555 9999999999999999999999999999988 99999999
Q ss_pred HhhhcCCcEEEEEchHHHHHHHhcc---------CCCeeeccccCcccCC--CCCCccHHHHHHHHcCCCCCCCCCChHH
Q psy3897 151 MGFVSKDSIIVGHGLENDLRALKLI---------HSNIIDTSVLFPHSFG--LPYRRSLKSIVSQLLHQSIQSGTHDSFE 219 (240)
Q Consensus 151 ~~~i~~~~iLVGH~~~~Dl~~L~~~---------~~~~iDT~~l~~~~~~--~~~~~sL~~L~~~~L~~~iq~~~H~A~e 219 (240)
.+|++ +.++||||+.||+.+|+.. ...++||..++..... ...+++|.+|+. ++|++... .|+|++
T Consensus 90 ~~fl~-~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L~~-~~gi~~~~-~H~Al~ 166 (557)
T PRK07883 90 LEFAR-GAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLAR-LFGATTTP-THRALD 166 (557)
T ss_pred HHHhc-CCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHHHH-HCCcccCC-CCCHHH
Confidence 99995 8999999999999999852 2468999887654321 123578999996 79977654 799999
Q ss_pred HHHHHHHHHHHHHhhh
Q psy3897 220 DARACIDLILWKLLSD 235 (240)
Q Consensus 220 DA~at~~L~~~~l~~~ 235 (240)
||.+|++||...+.+.
T Consensus 167 DA~ata~l~~~l~~~~ 182 (557)
T PRK07883 167 DARATVDVLHGLIERL 182 (557)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999999887764
No 31
>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=1.8e-24 Score=182.29 Aligned_cols=150 Identities=17% Similarity=0.203 Sum_probs=115.7
Q ss_pred cEEEEEEeecCCCCC-ccEEEEEEEEc----CCcE----EEEEEEcC--CCcccccceecCCCCHHh-hccCCCCCHHHH
Q psy3897 79 GVYALDTEMVYTVHG-LEVARVTVVNV----DGRL----IYNTLVKP--DCEIIDYNTKYSGISAKD-FIRNPYKTLKDV 146 (240)
Q Consensus 79 ~~valD~E~tg~~~g-~ei~~v~vv~~----~g~~----~~d~lVkP--~~~I~~~~t~~~GIt~ed-l~~a~~~~~~ev 146 (240)
..|+||+||||+++. .+|++|++|.. +|.+ .|+++|+| +.+|++.++++||||+++ +++++. ..++
T Consensus 6 ~~vv~D~ETTGl~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~--~~~~ 83 (189)
T cd06134 6 LPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVD--EKEA 83 (189)
T ss_pred eeEEEEecCCCCCCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccc--hHHH
Confidence 469999999999965 57888888874 3432 59999999 569999999999999987 455544 4444
Q ss_pred HH----HHHhhhc----CCcEEEEEchHHHHHHHhcc-----------C-CCeeeccccCcccCCCCCCccHHHHHHHHc
Q psy3897 147 QN----DLMGFVS----KDSIIVGHGLENDLRALKLI-----------H-SNIIDTSVLFPHSFGLPYRRSLKSIVSQLL 206 (240)
Q Consensus 147 ~~----~l~~~i~----~~~iLVGH~~~~Dl~~L~~~-----------~-~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L 206 (240)
+. .|.+++. ++.+|||||+.||+.||+.. + .+++||..|.+...+ +.+|..+|+ ++
T Consensus 84 ~~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~---~~~L~~l~~-~~ 159 (189)
T cd06134 84 LKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG---QTVLAKACQ-AA 159 (189)
T ss_pred HHHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC---CCcHHHHHH-HC
Confidence 44 4444442 26899999999999999852 1 147999998766532 347999997 59
Q ss_pred CCCCCC-CCCChHHHHHHHHHHHHHHHhh
Q psy3897 207 HQSIQS-GTHDSFEDARACIDLILWKLLS 234 (240)
Q Consensus 207 ~~~iq~-~~H~A~eDA~at~~L~~~~l~~ 234 (240)
|++++. ..|+|++||++|++||.+++++
T Consensus 160 gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 160 GIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred CCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 977653 4799999999999999988764
No 32
>PRK05168 ribonuclease T; Provisional
Probab=99.92 E-value=2.9e-24 Score=184.02 Aligned_cols=155 Identities=18% Similarity=0.222 Sum_probs=124.5
Q ss_pred CCcEEEEEEeecCCCCC-ccEEEEEEEEc----CCcE----EEEEEEcC--CCcccccceecCCCCHHh-hccCCCCCHH
Q psy3897 77 GYGVYALDTEMVYTVHG-LEVARVTVVNV----DGRL----IYNTLVKP--DCEIIDYNTKYSGISAKD-FIRNPYKTLK 144 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g-~ei~~v~vv~~----~g~~----~~d~lVkP--~~~I~~~~t~~~GIt~ed-l~~a~~~~~~ 144 (240)
...+|+||+||||+++. .+|++|++|.. +|.+ .|+++|+| +.+|++.++++||||+++ +++++. ..
T Consensus 16 ~~~~vv~D~ETTGl~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~~~~--~~ 93 (211)
T PRK05168 16 GFLPVVIDVETAGFNAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAVS--EK 93 (211)
T ss_pred CCceEEEEeeCCCCCCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhcCCC--hH
Confidence 45789999999999975 58999998874 3542 49999999 568999999999999986 777776 78
Q ss_pred HHHHHHHhhhc--------CCcEEEEEchHHHHHHHhcc-----------C-CCeeeccccCcccCCCCCCccHHHHHHH
Q psy3897 145 DVQNDLMGFVS--------KDSIIVGHGLENDLRALKLI-----------H-SNIIDTSVLFPHSFGLPYRRSLKSIVSQ 204 (240)
Q Consensus 145 ev~~~l~~~i~--------~~~iLVGH~~~~Dl~~L~~~-----------~-~~~iDT~~l~~~~~~~~~~~sL~~L~~~ 204 (240)
+++.++.+++. ++.++||||+.||+.||+.. + .+++||..+++...+ ..+|..+|.
T Consensus 94 ~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~---~~~L~~l~~- 169 (211)
T PRK05168 94 EALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALG---QTVLAKACQ- 169 (211)
T ss_pred HHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC---CCCHHHHHH-
Confidence 88888777663 26899999999999999752 1 158999988765432 247999997
Q ss_pred HcCCCCCC-CCCChHHHHHHHHHHHHHHHhhhhc
Q psy3897 205 LLHQSIQS-GTHDSFEDARACIDLILWKLLSDFR 237 (240)
Q Consensus 205 ~L~~~iq~-~~H~A~eDA~at~~L~~~~l~~~~~ 237 (240)
++|++++. .+|+|++||.+|++||.+++++...
T Consensus 170 ~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~~ 203 (211)
T PRK05168 170 AAGIEFDNKEAHSALYDTEKTAELFCEIVNRWKR 203 (211)
T ss_pred HCCCCCCCCCCCChHHHHHHHHHHHHHHHHHHHH
Confidence 58977653 4899999999999999998876543
No 33
>PRK06722 exonuclease; Provisional
Probab=99.92 E-value=2.3e-24 Score=191.45 Aligned_cols=152 Identities=22% Similarity=0.293 Sum_probs=122.3
Q ss_pred CCcEEEEEEeecCCCC----CccEEEEEEEEc-CC--cEE--EEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHH
Q psy3897 77 GYGVYALDTEMVYTVH----GLEVARVTVVNV-DG--RLI--YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQ 147 (240)
Q Consensus 77 ~~~~valD~E~tg~~~----g~ei~~v~vv~~-~g--~~~--~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~ 147 (240)
...|++||+|||+... +.+|++|++|.. +| +++ |++||+|..+|+++++++||||++||.++|. +++|+
T Consensus 4 ~~~~vViD~ETT~~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~~I~~~i~~LTGIT~emV~~AP~--f~eVl 81 (281)
T PRK06722 4 ATHFIVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEK--FPQII 81 (281)
T ss_pred CCEEEEEEeeCCCCCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCCcCCHhHhhhcCCCHHHHcCCCC--HHHHH
Confidence 3579999999995432 258999999885 34 444 9999999999999999999999999999998 99999
Q ss_pred HHHHhhhcCCcEEEEEchHHHHHHHhcc-------CC-----CeeeccccC----cccCCCCCCccHHHHHHHHcCCCCC
Q psy3897 148 NDLMGFVSKDSIIVGHGLENDLRALKLI-------HS-----NIIDTSVLF----PHSFGLPYRRSLKSIVSQLLHQSIQ 211 (240)
Q Consensus 148 ~~l~~~i~~~~iLVGH~~~~Dl~~L~~~-------~~-----~~iDT~~l~----~~~~~~~~~~sL~~L~~~~L~~~iq 211 (240)
++|.+|++ +.++|+||..||++||+.. .+ +++|+..++ +... +..++|..|++ ++|++..
T Consensus 82 ~ef~~fig-~~~lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~--~~~~sL~~l~~-~lgL~~~ 157 (281)
T PRK06722 82 EKFIQFIG-EDSIFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELF--EHTPSLQSAVE-QLGLIWE 157 (281)
T ss_pred HHHHHHHC-CCcEEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhc--cCCCCHHHHHH-HCCCCCC
Confidence 99999995 6677777789999999872 11 247887643 2221 22468999996 6997765
Q ss_pred CCCCChHHHHHHHHHHHHHHHhh
Q psy3897 212 SGTHDSFEDARACIDLILWKLLS 234 (240)
Q Consensus 212 ~~~H~A~eDA~at~~L~~~~l~~ 234 (240)
+..|+|++||.+|++|++.++.+
T Consensus 158 g~~HrAL~DA~~TA~L~l~l~~~ 180 (281)
T PRK06722 158 GKQHRALADAENTANILLKAYSE 180 (281)
T ss_pred CCCcCcHHHHHHHHHHHHHHhcc
Confidence 44799999999999999988854
No 34
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.91 E-value=5.1e-24 Score=216.08 Aligned_cols=153 Identities=22% Similarity=0.298 Sum_probs=129.5
Q ss_pred CcEEEEEEeecCCCC--CccEEEEEEEEc-CCcEE--EEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHh
Q psy3897 78 YGVYALDTEMVYTVH--GLEVARVTVVNV-DGRLI--YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMG 152 (240)
Q Consensus 78 ~~~valD~E~tg~~~--g~ei~~v~vv~~-~g~~~--~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~ 152 (240)
.+||+||+||||+.+ +.+|++|++|.. +|+++ |+++|+|..+|+++++++||||++|+.++|. +.+|+..|.+
T Consensus 3 ~~~vvvD~ETTG~~p~~~d~IIeigav~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~--f~ev~~~l~~ 80 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKGDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPL--FEDVAPEIVE 80 (928)
T ss_pred CCEEEEEEeCCCCCCCCCCcEEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCC--HHHHHHHHHH
Confidence 479999999999875 468999999986 56654 9999999999999999999999999999998 9999999999
Q ss_pred hhcCCcEEEEEchHHHHHHHhcc---------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHHHHHH
Q psy3897 153 FVSKDSIIVGHGLENDLRALKLI---------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARA 223 (240)
Q Consensus 153 ~i~~~~iLVGH~~~~Dl~~L~~~---------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~a 223 (240)
|++ +.++||||+.||+.+|+.. ..++|||..+.+...+....++|..|++ +||++.. .+|+|++||++
T Consensus 81 ~l~-~~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~~~~L~~l~~-~l~i~~~-~~H~Al~DA~a 157 (928)
T PRK08074 81 LLE-GAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSE-ELGLEHD-QPHRADSDAEV 157 (928)
T ss_pred HhC-CCeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCCCCCHHHHHH-hCCCCCC-CCCChHHHHHH
Confidence 995 9999999999999999852 3478999876543322123578999996 6996544 38999999999
Q ss_pred HHHHHHHHHhhh
Q psy3897 224 CIDLILWKLLSD 235 (240)
Q Consensus 224 t~~L~~~~l~~~ 235 (240)
|++||..++++.
T Consensus 158 ta~l~~~l~~~~ 169 (928)
T PRK08074 158 TAELFLQLLNKL 169 (928)
T ss_pred HHHHHHHHHHHH
Confidence 999999887754
No 35
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=99.91 E-value=6.3e-24 Score=213.93 Aligned_cols=151 Identities=25% Similarity=0.330 Sum_probs=129.5
Q ss_pred cEEEEEEeecCCCCC-ccEEEEEEEEc-CCcEE--EEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhh
Q psy3897 79 GVYALDTEMVYTVHG-LEVARVTVVNV-DGRLI--YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFV 154 (240)
Q Consensus 79 ~~valD~E~tg~~~g-~ei~~v~vv~~-~g~~~--~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i 154 (240)
+||+||+||||++++ .+|++|++|.. +|+++ |+++|+|..+|+++++++||||++|+.++|. ++++.++|.+++
T Consensus 1 ~~vvvD~ETTG~~~~~~~IIeig~v~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~ap~--~~ev~~~l~~~l 78 (850)
T TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPY--FSQVAQEIYDLL 78 (850)
T ss_pred CEEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEeCCCCCCChhhhhhcCcCHHHHhCCCC--HHHHHHHHHHHh
Confidence 489999999999865 68999999986 56654 9999999999999999999999999999998 999999999999
Q ss_pred cCCcEEEEEchHHHHHHHhcc---------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHHHHHHHH
Q psy3897 155 SKDSIIVGHGLENDLRALKLI---------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARACI 225 (240)
Q Consensus 155 ~~~~iLVGH~~~~Dl~~L~~~---------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~at~ 225 (240)
+ +.++||||+.||+.+|+.. ...++||..+.+...+...+++|.+||+ ++|.+... +|+|++||.+|+
T Consensus 79 ~-~~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~~~~L~~l~~-~~gi~~~~-~H~Al~DA~ata 155 (850)
T TIGR01407 79 E-DGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSE-ALGLTHEN-PHRADSDAQATA 155 (850)
T ss_pred C-CCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCCCCCHHHHHH-HCCCCCCC-CCChHHHHHHHH
Confidence 5 8999999999999999852 3468999887654432223578999997 59976653 899999999999
Q ss_pred HHHHHHHhh
Q psy3897 226 DLILWKLLS 234 (240)
Q Consensus 226 ~L~~~~l~~ 234 (240)
+||...+.+
T Consensus 156 ~l~~~l~~~ 164 (850)
T TIGR01407 156 ELLLLLFEK 164 (850)
T ss_pred HHHHHHHHH
Confidence 999988765
No 36
>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=99.91 E-value=3.1e-24 Score=176.72 Aligned_cols=148 Identities=20% Similarity=0.304 Sum_probs=122.4
Q ss_pred EEEEEEeecCCCCC------ccEEEEEEEEc--CCc-E--EEEEEEcCCC--cccccceecCCCCHHhhccCCCCCHHHH
Q psy3897 80 VYALDTEMVYTVHG------LEVARVTVVNV--DGR-L--IYNTLVKPDC--EIIDYNTKYSGISAKDFIRNPYKTLKDV 146 (240)
Q Consensus 80 ~valD~E~tg~~~g------~ei~~v~vv~~--~g~-~--~~d~lVkP~~--~I~~~~t~~~GIt~edl~~a~~~~~~ev 146 (240)
+|+||+||||..++ .+|++|++|.. ++. + .|++||+|.. +|+++++++||||++++.+++. +++|
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~~--~~~v 78 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPS--FPEV 78 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCCC--HHHH
Confidence 58999999999874 58999999864 333 2 4999999998 9999999999999999999988 9999
Q ss_pred HHHHHhhhcCCc--EEEEEchHHHHHHHhcc------------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCC
Q psy3897 147 QNDLMGFVSKDS--IIVGHGLENDLRALKLI------------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQS 212 (240)
Q Consensus 147 ~~~l~~~i~~~~--iLVGH~~~~Dl~~L~~~------------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~ 212 (240)
+++|.+|++ +. .+++|+..+|+.+|... ..+++|+..+++...+....++|..|+. ++|.+...
T Consensus 79 l~~~~~~l~-~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l~~-~~gi~~~~ 156 (176)
T cd06133 79 LKEFLEWLG-KNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALE-YLGLEFEG 156 (176)
T ss_pred HHHHHHHHH-hCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHHHH-HCCCCCCC
Confidence 999999996 54 55555669998876541 2368999998886655444679999996 69987764
Q ss_pred CCCChHHHHHHHHHHHHHH
Q psy3897 213 GTHDSFEDARACIDLILWK 231 (240)
Q Consensus 213 ~~H~A~eDA~at~~L~~~~ 231 (240)
..|+|+.||++|++|+.++
T Consensus 157 ~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 157 RHHRGLDDARNIARILKRL 175 (176)
T ss_pred CCcCcHHHHHHHHHHHHHh
Confidence 5899999999999999875
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=99.91 E-value=1.4e-23 Score=167.72 Aligned_cols=144 Identities=25% Similarity=0.301 Sum_probs=122.0
Q ss_pred EEEEEeecCCCC-CccEEEEEEEEcCC----cEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhhc
Q psy3897 81 YALDTEMVYTVH-GLEVARVTVVNVDG----RLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVS 155 (240)
Q Consensus 81 valD~E~tg~~~-g~ei~~v~vv~~~g----~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~ 155 (240)
|++||||||..+ ..+|++|+++..++ ...|+.||+|..++.++.+.+|||+++++.+++. +.++...|.+++.
T Consensus 1 v~~D~Ettg~~~~~~~iiei~~v~~~~~~~~~~~~~~~i~p~~~~~~~~~~~~gi~~~~~~~~~~--~~~~~~~~~~~l~ 78 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPP--FEEVLPEFLEFLG 78 (159)
T ss_pred CeEEeeCCCcCCCCCeEEEEEEEEEECCcChhhhhheeeCcCCcCCHhheeccCCCHHHHhcCCC--HHHHHHHHHHHHC
Confidence 589999999987 46899999998643 2459999999999999999999999999999888 9999999999996
Q ss_pred CCcEEEEEchHHHHHHHhcc---------CCCeeeccccCcccCCCCCCccHHHH-HHHHcCCCCCCCCCChHHHHHHHH
Q psy3897 156 KDSIIVGHGLENDLRALKLI---------HSNIIDTSVLFPHSFGLPYRRSLKSI-VSQLLHQSIQSGTHDSFEDARACI 225 (240)
Q Consensus 156 ~~~iLVGH~~~~Dl~~L~~~---------~~~~iDT~~l~~~~~~~~~~~sL~~L-~~~~L~~~iq~~~H~A~eDA~at~ 225 (240)
+.++||||..||+.+|+.. +..++||+.+++...+....++|+.+ ++ +++.+.. ..|+|++||++|+
T Consensus 79 -~~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~-~~H~Al~Da~~t~ 155 (159)
T cd06127 79 -GRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAE-RYGIPLE-GAHRALADALATA 155 (159)
T ss_pred -CCEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCCCcCchHHHHHH-HcCCCCC-CCCCcHHHHHHHH
Confidence 6999999999999999763 44789999988766544445689888 54 6886543 3899999999999
Q ss_pred HHHH
Q psy3897 226 DLIL 229 (240)
Q Consensus 226 ~L~~ 229 (240)
+||.
T Consensus 156 ~l~~ 159 (159)
T cd06127 156 ELLL 159 (159)
T ss_pred HHhC
Confidence 9873
No 38
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.90 E-value=1.3e-24 Score=216.15 Aligned_cols=155 Identities=21% Similarity=0.273 Sum_probs=135.8
Q ss_pred CCCcEEEEEEeecCCCCC-ccEEEEEEEEc-CCcEE--EEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHH
Q psy3897 76 NGYGVYALDTEMVYTVHG-LEVARVTVVNV-DGRLI--YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLM 151 (240)
Q Consensus 76 ~~~~~valD~E~tg~~~g-~ei~~v~vv~~-~g~~~--~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~ 151 (240)
....||+||+||||+++- .+|++++++.. +|+++ |+.|++|..|++...|.+||||+++|++++. +.+|+.+|.
T Consensus 419 ~datyVVfDiETTGLs~~~d~iIE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~--i~~vL~kf~ 496 (1444)
T COG2176 419 DDATYVVFDIETTGLSPVYDEIIEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPE--IEEVLEKFR 496 (1444)
T ss_pred ccccEEEEEeecCCcCcccchhhhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCcc--HHHHHHHHH
Confidence 356799999999999987 58999999995 78777 9999999999999999999999999999999 999999999
Q ss_pred hhhcCCcEEEEEchHHHHHHHhc---------cCCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHHHHH
Q psy3897 152 GFVSKDSIIVGHGLENDLRALKL---------IHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDAR 222 (240)
Q Consensus 152 ~~i~~~~iLVGH~~~~Dl~~L~~---------~~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~ 222 (240)
+|++ ++|||+||+.||+.||+. ..+.+|||+.|.+...+.-.+++|..||+. ||..... +|+|..||.
T Consensus 497 ~~~~-d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh~Lg~l~kk-~~v~le~-hHRA~yDae 573 (1444)
T COG2176 497 EFIG-DSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSHRLGTLCKK-LGVELER-HHRADYDAE 573 (1444)
T ss_pred HHhc-CcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhcchHHHHHH-hCccHHH-hhhhhhhHH
Confidence 9994 999999999999999986 245799999876655433336899999985 9977743 899999999
Q ss_pred HHHHHHHHHHhhh
Q psy3897 223 ACIDLILWKLLSD 235 (240)
Q Consensus 223 at~~L~~~~l~~~ 235 (240)
||+.||..++++.
T Consensus 574 at~~vf~~f~~~~ 586 (1444)
T COG2176 574 ATAKVFFVFLKDL 586 (1444)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999888754
No 39
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=99.90 E-value=2.9e-23 Score=213.20 Aligned_cols=155 Identities=22% Similarity=0.250 Sum_probs=133.2
Q ss_pred CCCcEEEEEEeecCCCCC-ccEEEEEEEEc-CCcEE--EEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHH
Q psy3897 76 NGYGVYALDTEMVYTVHG-LEVARVTVVNV-DGRLI--YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLM 151 (240)
Q Consensus 76 ~~~~~valD~E~tg~~~g-~ei~~v~vv~~-~g~~~--~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~ 151 (240)
...++|+||+||||+++. .+|++|++|.. +|.++ |++||+|..+|++.++++||||+++|+++++ +++|+++|.
T Consensus 188 ~~~~~VVfDiETTGL~~~~d~IIEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~--~~evl~~f~ 265 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPE--IEEVLEKFK 265 (1213)
T ss_pred cCCcEEEEEeEecCCCCCCCeEEEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCC--HHHHHHHHH
Confidence 355899999999999876 58999999985 56554 9999999999999999999999999999988 999999999
Q ss_pred hhhcCCcEEEEEchHHHHHHHhcc---------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHHHHH
Q psy3897 152 GFVSKDSIIVGHGLENDLRALKLI---------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDAR 222 (240)
Q Consensus 152 ~~i~~~~iLVGH~~~~Dl~~L~~~---------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~ 222 (240)
+|++ +++|||||+.||+.+|+.. ...+|||+.+++.......+++|..||+ .+|.+... +|+|++||.
T Consensus 266 ~fl~-~~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k~~kL~~Lak-~lgi~~~~-~HrAl~DA~ 342 (1213)
T TIGR01405 266 EFFK-DSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRLGNICK-KLGVDLDD-HHRADYDAE 342 (1213)
T ss_pred HHhC-CCeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCCCCCHHHHHH-HcCCCCCC-CcCHHHHHH
Confidence 9995 8999999999999999852 3478999987765432223579999997 58977765 899999999
Q ss_pred HHHHHHHHHHhhh
Q psy3897 223 ACIDLILWKLLSD 235 (240)
Q Consensus 223 at~~L~~~~l~~~ 235 (240)
+|++||..++++.
T Consensus 343 aTa~I~~~ll~~l 355 (1213)
T TIGR01405 343 ATAKVFKVMVEQL 355 (1213)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999887654
No 40
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.90 E-value=8.1e-23 Score=183.04 Aligned_cols=150 Identities=17% Similarity=0.133 Sum_probs=117.3
Q ss_pred CCcEEEEEEeecCCCCC-ccEEEEEEEEc----CCcE-----EEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHH
Q psy3897 77 GYGVYALDTEMVYTVHG-LEVARVTVVNV----DGRL-----IYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDV 146 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g-~ei~~v~vv~~----~g~~-----~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev 146 (240)
...+|+||+||||+++. .+|++|++|.. +|.+ .|+.|++|..+|++.++++||||++|+.+++.. .
T Consensus 36 ~~~~vvlD~ETTGLd~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~~I~~~~t~IhGIt~e~v~~~~~~-~--- 111 (294)
T PRK09182 36 VRLGVILDTETTGLDPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTID-P--- 111 (294)
T ss_pred CCeEEEEEeeCCCCCCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCCCCCHHHHHhcCCCHHHHhcCCCc-H---
Confidence 45799999999999975 58999999875 3532 389999999999999999999999999999873 3
Q ss_pred HHHHHhhhcCCcEEEEEchHHHHHHHhcc-----CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHHHH
Q psy3897 147 QNDLMGFVSKDSIIVGHGLENDLRALKLI-----HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDA 221 (240)
Q Consensus 147 ~~~l~~~i~~~~iLVGH~~~~Dl~~L~~~-----~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA 221 (240)
+.|.+|+....+|||||+.||+.||+.. ...+.||............+++|.+||. .+| +...+|+|+.||
T Consensus 112 -~~l~~fl~~~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~~~~~~~~~~kL~~La~-~~g--~~~~aHrAl~Da 187 (294)
T PRK09182 112 -AAVDALIAPADLIIAHNAGFDRPFLERFSPVFATKPWACSVSEIDWSARGFEGTKLGYLAG-QAG--FFHEGHRAVDDC 187 (294)
T ss_pred -HHHHHHhcCCCEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHhhccccCCCCCHHHHHH-HcC--CCCCCcChHHHH
Confidence 3456677656799999999999999863 2356777654332111113578999997 588 334589999999
Q ss_pred HHHHHHHHHHHhh
Q psy3897 222 RACIDLILWKLLS 234 (240)
Q Consensus 222 ~at~~L~~~~l~~ 234 (240)
+||++||..++.+
T Consensus 188 ~Ata~ll~~~l~~ 200 (294)
T PRK09182 188 QALLELLARPLPE 200 (294)
T ss_pred HHHHHHHHHHHhh
Confidence 9999999977654
No 41
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.90 E-value=1.6e-22 Score=184.17 Aligned_cols=151 Identities=12% Similarity=0.116 Sum_probs=122.3
Q ss_pred CCCCcEEEEEEeecCCCCC-ccEEEEEEEEc--CCcE--EEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHH
Q psy3897 75 PNGYGVYALDTEMVYTVHG-LEVARVTVVNV--DGRL--IYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQND 149 (240)
Q Consensus 75 ~~~~~~valD~E~tg~~~g-~ei~~v~vv~~--~g~~--~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~ 149 (240)
.....||+||+||||+++. .+|++|++|.. +|.+ .|++||+|..++.+ ..+||||+++|+++|. |.+++++
T Consensus 43 ~~~~~fVvlDiETTGLdp~~drIIeIgAV~i~~~g~ive~f~tLVnP~~~~~p--~~LHGIT~e~La~AP~--f~eVl~e 118 (377)
T PRK05601 43 IEAAPFVAVSIQTSGIHPSTSRLITIDAVTLTADGEEVEHFHAVLNPGEDPGP--FHLHGLSAEEFAQGKR--FSQILKP 118 (377)
T ss_pred CCCCCEEEEEEECCCCCCCCCeEEEEEEEEEEcCCEEEEEEEEEECcCCCCCC--ccccCCCHHHHhcCCC--HHHHHHH
Confidence 4456899999999999976 58999998874 5655 49999999886544 4799999999999999 9999999
Q ss_pred HHhhhcCCcEEEEEchHHHHHHHhcc------------------------------------CCCeeeccccCcccCCCC
Q psy3897 150 LMGFVSKDSIIVGHGLENDLRALKLI------------------------------------HSNIIDTSVLFPHSFGLP 193 (240)
Q Consensus 150 l~~~i~~~~iLVGH~~~~Dl~~L~~~------------------------------------~~~~iDT~~l~~~~~~~~ 193 (240)
|.+|++ +.+|||||+.||+.||... ...+|||+.+.+......
T Consensus 119 l~~fL~-g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l 197 (377)
T PRK05601 119 LDRLID-GRTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGVAL 197 (377)
T ss_pred HHHHhC-CCEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHcCCC
Confidence 999995 9999999999999998652 125899998765543222
Q ss_pred CCccHHHHHHHHcCCCCCC--------C-CCChH--HHHHHHHHHHHHH
Q psy3897 194 YRRSLKSIVSQLLHQSIQS--------G-THDSF--EDARACIDLILWK 231 (240)
Q Consensus 194 ~~~sL~~L~~~~L~~~iq~--------~-~H~A~--eDA~at~~L~~~~ 231 (240)
.+++|..||+ +||++... . .|+++ +||+.+++||.+.
T Consensus 198 ~~~rL~~La~-~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 198 DDIRIRGVAH-TLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFAL 245 (377)
T ss_pred CCCCHHHHHH-HhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHh
Confidence 2578999997 69977611 1 68888 6999999999875
No 42
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.89 E-value=2.9e-22 Score=174.08 Aligned_cols=154 Identities=23% Similarity=0.287 Sum_probs=129.0
Q ss_pred CcEEEEEEeecCCCC-CccEEEEEEEEc-CCcEE---EEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHh
Q psy3897 78 YGVYALDTEMVYTVH-GLEVARVTVVNV-DGRLI---YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMG 152 (240)
Q Consensus 78 ~~~valD~E~tg~~~-g~ei~~v~vv~~-~g~~~---~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~ 152 (240)
.++++||+||||... +.+|++|++|.. ++.++ |+++|+|..+|++.+.++||||.+++.++|. +.++.+++.+
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~--~~~v~~~~~~ 90 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAPK--FAEVLPEFLD 90 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcCCC--HHHHHHHHHH
Confidence 479999999999996 678999999986 44443 8899999889999999999999999999988 9999999999
Q ss_pred hhcCCcEEEEEchHHHHHHHhcc---------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCC-CCCChHHHHH
Q psy3897 153 FVSKDSIIVGHGLENDLRALKLI---------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQS-GTHDSFEDAR 222 (240)
Q Consensus 153 ~i~~~~iLVGH~~~~Dl~~L~~~---------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~-~~H~A~eDA~ 222 (240)
++++..++||||+.||+.+|+.. ...++||..+.+.......+++|+.||. ++|+.... ..|+|+.||+
T Consensus 91 ~i~~~~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~~~L~~l~~-~~gi~~~~~~~H~Al~Da~ 169 (243)
T COG0847 91 FIGGLRLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDALAE-RLGIDRNPFHPHRALFDAL 169 (243)
T ss_pred HHCCCCeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCccchHHHHHH-HcCCCcCCcCCcchHHHHH
Confidence 99743999999999999999852 2357899877655432223679999997 69966322 2699999999
Q ss_pred HHHHHHHHHHhh
Q psy3897 223 ACIDLILWKLLS 234 (240)
Q Consensus 223 at~~L~~~~l~~ 234 (240)
+++++++.....
T Consensus 170 ~~a~~~~~~~~~ 181 (243)
T COG0847 170 ALAELFLLLQTG 181 (243)
T ss_pred HHHHHHHHHHhc
Confidence 999999988874
No 43
>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=99.89 E-value=1.2e-22 Score=170.22 Aligned_cols=144 Identities=14% Similarity=0.105 Sum_probs=112.6
Q ss_pred EEEEEeecCCCCC-ccEEEEEEEEcC--CcEE--EEEEEcCCC--cccccceecCCCCHHhhcc-CCCCCHHHHHHHHHh
Q psy3897 81 YALDTEMVYTVHG-LEVARVTVVNVD--GRLI--YNTLVKPDC--EIIDYNTKYSGISAKDFIR-NPYKTLKDVQNDLMG 152 (240)
Q Consensus 81 valD~E~tg~~~g-~ei~~v~vv~~~--g~~~--~d~lVkP~~--~I~~~~t~~~GIt~edl~~-a~~~~~~ev~~~l~~ 152 (240)
++||+||||+++. .+|++|++|..+ +.++ |+++|+|.. ++++.++.+||||++++.+ ++. +.+++++|.+
T Consensus 1 ~~~D~ETTGl~~~~d~Iieig~v~v~~~~~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~--~~~~l~~~~~ 78 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQFAAIRTDENFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLS--EYEFIAKIHR 78 (183)
T ss_pred CEEEeecCCCCCCCCceEEEEEEEECCCCCCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCC--HHHHHHHHHH
Confidence 4799999999975 589999998753 3443 899999975 5777899999999999999 677 9999999999
Q ss_pred hhc-CCcEEEEEc-hHHHHHHHhccC---------------CCeeeccccCccc-------CCC------CCCccHHHHH
Q psy3897 153 FVS-KDSIIVGHG-LENDLRALKLIH---------------SNIIDTSVLFPHS-------FGL------PYRRSLKSIV 202 (240)
Q Consensus 153 ~i~-~~~iLVGH~-~~~Dl~~L~~~~---------------~~~iDT~~l~~~~-------~~~------~~~~sL~~L~ 202 (240)
|+. ++.++|||| +.||+.||+... ..++||..+.+.. ... ..+++|..||
T Consensus 79 ~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L~~l~ 158 (183)
T cd06138 79 LFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKLEDLA 158 (183)
T ss_pred HHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhHHHHH
Confidence 995 367999997 899999998521 1347887533211 011 1246899999
Q ss_pred HHHcCCCCCCCCCChHHHHHHHHHHH
Q psy3897 203 SQLLHQSIQSGTHDSFEDARACIDLI 228 (240)
Q Consensus 203 ~~~L~~~iq~~~H~A~eDA~at~~L~ 228 (240)
+ ++|++.. .+|+|++||++|++|+
T Consensus 159 ~-~~gi~~~-~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 159 Q-ANGIEHS-NAHDALSDVEATIALA 182 (183)
T ss_pred H-HCCCCcc-ccccHHHHHHHHHHHh
Confidence 7 5996664 3799999999999985
No 44
>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=8.6e-25 Score=174.96 Aligned_cols=145 Identities=27% Similarity=0.392 Sum_probs=116.9
Q ss_pred EEEEEeecCCCC-CccEEEEEEEEcC-----CcEEEEEEEcCCCc--ccccceecCCCCHHhhccCCCCCHHHHHHHHHh
Q psy3897 81 YALDTEMVYTVH-GLEVARVTVVNVD-----GRLIYNTLVKPDCE--IIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMG 152 (240)
Q Consensus 81 valD~E~tg~~~-g~ei~~v~vv~~~-----g~~~~d~lVkP~~~--I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~ 152 (240)
|+|||||||+.+ ..+|++|++|..+ +...|++||+|..+ |+++++++||||.+++.+++. +.++.+++.+
T Consensus 1 v~~D~Ettg~~~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~--~~~~~~~~~~ 78 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPS--FEEALDEFEE 78 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCE--HHHHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCCc--HHHHHHhhhh
Confidence 789999999998 4688888888742 23469999999998 999999999999999999998 9999999999
Q ss_pred hhcCCcEEEEEchHHHHHHHhc--------cC---CCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHHHH
Q psy3897 153 FVSKDSIIVGHGLENDLRALKL--------IH---SNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDA 221 (240)
Q Consensus 153 ~i~~~~iLVGH~~~~Dl~~L~~--------~~---~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA 221 (240)
++.++.++||||..||..++.. .. ..++||..+.+...+....++|+.|++ +++.+....+|+|++||
T Consensus 79 ~~~~~~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~-~~~~~~~~~~H~Al~Da 157 (164)
T PF00929_consen 79 FLKKNDILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNRKKYSLDDLAE-YFGIPFDGTAHDALDDA 157 (164)
T ss_dssp HHHHHTEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHHHHHSHHHHHH-HTTSSSTSTTTSHHHHH
T ss_pred hhhcccccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhccccCCHHHHHH-HcCCCCCCCCcChHHHH
Confidence 9976899999998887766543 12 357899877654321111368999997 57766554469999999
Q ss_pred HHHHHHH
Q psy3897 222 RACIDLI 228 (240)
Q Consensus 222 ~at~~L~ 228 (240)
++|++||
T Consensus 158 ~~t~~l~ 164 (164)
T PF00929_consen 158 RATAELF 164 (164)
T ss_dssp HHHHHHH
T ss_pred HHHhCcC
Confidence 9999986
No 45
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.85 E-value=2.3e-20 Score=178.44 Aligned_cols=158 Identities=17% Similarity=0.169 Sum_probs=124.6
Q ss_pred CcEEEEEEeecCCCC----CccEEEEEEEEc---CCcEE--EEEEEcCCC--cccccceecCCCCHHhhccCCCCCHHHH
Q psy3897 78 YGVYALDTEMVYTVH----GLEVARVTVVNV---DGRLI--YNTLVKPDC--EIIDYNTKYSGISAKDFIRNPYKTLKDV 146 (240)
Q Consensus 78 ~~~valD~E~tg~~~----g~ei~~v~vv~~---~g~~~--~d~lVkP~~--~I~~~~t~~~GIt~edl~~a~~~~~~ev 146 (240)
..|++||+||||..+ ..||++|++|.. +|+++ |++||+|.. +|+++++++||||++||+++|. |++|
T Consensus 56 d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap~--F~eV 133 (582)
T PTZ00315 56 DAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADP--FPVV 133 (582)
T ss_pred CeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCCC--HHHH
Confidence 579999999999874 358999999885 56554 999999986 7999999999999999999999 9999
Q ss_pred HHHHHhhhcCC---------cEEEEEchHHHHH-HHhc------------cCCCeeeccc-----cCcccC-------CC
Q psy3897 147 QNDLMGFVSKD---------SIIVGHGLENDLR-ALKL------------IHSNIIDTSV-----LFPHSF-------GL 192 (240)
Q Consensus 147 ~~~l~~~i~~~---------~iLVGH~~~~Dl~-~L~~------------~~~~~iDT~~-----l~~~~~-------~~ 192 (240)
+.+|.+|+.+. .++|+||..||+. +|.. ....++|... +||... ..
T Consensus 134 l~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p~~~~~~~~~~~~ 213 (582)
T PTZ00315 134 YCEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFGNGSGCGGGATPP 213 (582)
T ss_pred HHHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCccccccccccccc
Confidence 99999999532 3699999999995 7642 0224566421 243210 01
Q ss_pred CCCccHHHHHHHHcCCCCCCCCCChHHHHHHHHHHHHHHHhhhhcc
Q psy3897 193 PYRRSLKSIVSQLLHQSIQSGTHDSFEDARACIDLILWKLLSDFRY 238 (240)
Q Consensus 193 ~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~at~~L~~~~l~~~~~~ 238 (240)
...++|.++++ ++|+++.+..|+|+.||+++++||..+++++..+
T Consensus 214 ~~~~~L~~al~-~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~~g~~~ 258 (582)
T PTZ00315 214 LGPSDMPDMLQ-MLGLPLQGRHHSGIDDCRNIAAVLCELLRRGLVI 258 (582)
T ss_pred cCCcCHHHHHH-HCCCCCCCCCcCcHHHHHHHHHHHHHHHHcCCEE
Confidence 12468999997 6998877668999999999999999999887543
No 46
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.83 E-value=5.1e-20 Score=191.59 Aligned_cols=154 Identities=21% Similarity=0.285 Sum_probs=130.1
Q ss_pred CCcEEEEEEeecCCCCC-ccEEEEEEEEc-CCcEE--EEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHh
Q psy3897 77 GYGVYALDTEMVYTVHG-LEVARVTVVNV-DGRLI--YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMG 152 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g-~ei~~v~vv~~-~g~~~--~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~ 152 (240)
..++|++|+||||.++. .+|++++++.. +|.++ |+.||+|..+|++.++++||||++++.++++ +.++++.|.+
T Consensus 418 ~~~~VVfDLETTGL~~~~deIIEIgAV~V~~G~iie~F~~~V~P~~~I~~~~~~LTGIT~e~L~~aps--~~EaL~~f~~ 495 (1437)
T PRK00448 418 DATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPS--IEEVLPKFKE 495 (1437)
T ss_pred cCcEEEEEhhhcCCCCchhhhheeeeEEEeCCeEeeeEEEEECCCCCCCHHHHHHhCCCHHHHcCCCC--HHHHHHHHHH
Confidence 45799999999999876 47888888774 56554 9999999999999999999999999999888 9999999999
Q ss_pred hhcCCcEEEEEchHHHHHHHhc---------cCCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHHHHHH
Q psy3897 153 FVSKDSIIVGHGLENDLRALKL---------IHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARA 223 (240)
Q Consensus 153 ~i~~~~iLVGH~~~~Dl~~L~~---------~~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~a 223 (240)
|++ +.+|||||..||+.+|+. ....++||..+++.......+++|..||+ .+|+.... +|+|++||.+
T Consensus 496 fig-g~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k~~kL~~LAk-~lGL~~~~-~HrAl~DA~a 572 (1437)
T PRK00448 496 FCG-DSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAK-KFGVELEH-HHRADYDAEA 572 (1437)
T ss_pred HhC-CCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccccccHHHHHH-HcCCCCCC-CcChHHHHHH
Confidence 995 899999999999999863 23468999987665433233679999997 59977764 7999999999
Q ss_pred HHHHHHHHHhhh
Q psy3897 224 CIDLILWKLLSD 235 (240)
Q Consensus 224 t~~L~~~~l~~~ 235 (240)
|++||..++++.
T Consensus 573 Ta~lf~~ll~~l 584 (1437)
T PRK00448 573 TAYLLIKFLKDL 584 (1437)
T ss_pred HHHHHHHHHHHH
Confidence 999999887764
No 47
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.82 E-value=1.7e-19 Score=170.68 Aligned_cols=155 Identities=14% Similarity=0.094 Sum_probs=118.5
Q ss_pred CCcEEEEEEeecCCCCC-ccEEEEEEEEcCC--cE---EEEEEEcCCCc--ccccceecCCCCHHhhccCCCCCHHHHHH
Q psy3897 77 GYGVYALDTEMVYTVHG-LEVARVTVVNVDG--RL---IYNTLVKPDCE--IIDYNTKYSGISAKDFIRNPYKTLKDVQN 148 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g-~ei~~v~vv~~~g--~~---~~d~lVkP~~~--I~~~~t~~~GIt~edl~~a~~~~~~ev~~ 148 (240)
..+||++|+||||+++. .+|++|++|..++ .+ .+..||+|..+ +++.++.+||||++++.+.+.+ ..++.+
T Consensus 5 ~~~fvv~D~ETTGLdP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~-e~e~~~ 83 (476)
T PRK11779 5 QPTFLWHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLP-EAEFAA 83 (476)
T ss_pred CCcEEEEEEECCCCCCCCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCC-HHHHHH
Confidence 45799999999999975 5899999998532 23 38999999863 4567899999999999887765 899999
Q ss_pred HHHhhhc-CCcEEEEEc-hHHHHHHHhccC-C-----------------CeeeccccCccc----CCCC------CCccH
Q psy3897 149 DLMGFVS-KDSIIVGHG-LENDLRALKLIH-S-----------------NIIDTSVLFPHS----FGLP------YRRSL 198 (240)
Q Consensus 149 ~l~~~i~-~~~iLVGH~-~~~Dl~~L~~~~-~-----------------~~iDT~~l~~~~----~~~~------~~~sL 198 (240)
.|.+++. +++++|||| +.||..||+... . .++|++.++... ...| ..++|
T Consensus 84 ~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rL 163 (476)
T PRK11779 84 RIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKL 163 (476)
T ss_pred HHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCcH
Confidence 9999994 579999997 799999987631 1 234555532211 0111 24789
Q ss_pred HHHHHHHcCCCCCCCCCChHHHHHHHHHHHHHHHhh
Q psy3897 199 KSIVSQLLHQSIQSGTHDSFEDARACIDLILWKLLS 234 (240)
Q Consensus 199 ~~L~~~~L~~~iq~~~H~A~eDA~at~~L~~~~l~~ 234 (240)
..|+. .+|+... .+|+|++||++|++|+....++
T Consensus 164 e~L~~-~~gI~~~-~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 164 EHLTK-ANGIEHE-NAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred HHHHH-HcCCCCC-CCCCcHHHHHHHHHHHHHHHHh
Confidence 99997 5895544 3899999999999998877655
No 48
>PRK05359 oligoribonuclease; Provisional
Probab=99.82 E-value=2.2e-19 Score=150.55 Aligned_cols=146 Identities=18% Similarity=0.213 Sum_probs=110.8
Q ss_pred CcEEEEEEeecCCCCC-ccEEEEEEEEcCC--cEE---EEEEEcCCCc----ccccceecC---CCCHHhhccCCCCCHH
Q psy3897 78 YGVYALDTEMVYTVHG-LEVARVTVVNVDG--RLI---YNTLVKPDCE----IIDYNTKYS---GISAKDFIRNPYKTLK 144 (240)
Q Consensus 78 ~~~valD~E~tg~~~g-~ei~~v~vv~~~g--~~~---~d~lVkP~~~----I~~~~t~~~---GIt~edl~~a~~~~~~ 144 (240)
.++|+|||||||+++. .+|++|++|..++ .++ |..+|+|... +++.++.+| |||++++++++. +.
T Consensus 3 ~~~vvlD~ETTGLdp~~d~IieIgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~--~~ 80 (181)
T PRK05359 3 DNLIWIDLEMTGLDPERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVS--EA 80 (181)
T ss_pred CcEEEEEeecCCCCCCCCeEEEEEEEEEcCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCC--HH
Confidence 5799999999999976 5799999988644 233 8999999875 466788887 899999999888 99
Q ss_pred HHHHHHHhhhc-----CCcEEEEEchHHHHHHHhcc--------CCCeeecccc---CcccCCCCCCccHHHHHHHHcCC
Q psy3897 145 DVQNDLMGFVS-----KDSIIVGHGLENDLRALKLI--------HSNIIDTSVL---FPHSFGLPYRRSLKSIVSQLLHQ 208 (240)
Q Consensus 145 ev~~~l~~~i~-----~~~iLVGH~~~~Dl~~L~~~--------~~~~iDT~~l---~~~~~~~~~~~sL~~L~~~~L~~ 208 (240)
++..+|++|++ ++.+|||||+.||+.||+.. +.+++|++.+ .+.. .+.+ +++.
T Consensus 81 e~~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~tl~~l~r~~-----~P~~------~~~~ 149 (181)
T PRK05359 81 EAEAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLDVSTLKELARRW-----KPEI------LNGF 149 (181)
T ss_pred HHHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhcccCCCcccchhHHHHHHHHh-----Chhh------hhCC
Confidence 99999999995 36899999999999999873 3466775433 2221 1111 1232
Q ss_pred CCCCCCCChHHHHHHHHHHHHHHHhhhhc
Q psy3897 209 SIQSGTHDSFEDARACIDLILWKLLSDFR 237 (240)
Q Consensus 209 ~iq~~~H~A~eDA~at~~L~~~~l~~~~~ 237 (240)
.- .+.|+|++||+++.+.+.+..+...+
T Consensus 150 ~~-~~~HRal~D~~~s~~~~~~~~~~~~~ 177 (181)
T PRK05359 150 KK-QGTHRALADIRESIAELKYYREHFFK 177 (181)
T ss_pred CC-cCCcccHHHHHHHHHHHHHHHHHhcc
Confidence 22 23799999999999999887765443
No 49
>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=99.81 E-value=7.5e-20 Score=152.08 Aligned_cols=141 Identities=21% Similarity=0.305 Sum_probs=104.6
Q ss_pred EEEEEEeecCCCC-CccEEEEEEEEcCCc--E---EEEEEEcCCCccc----ccceec---CCCCHHhhccCCCCCHHHH
Q psy3897 80 VYALDTEMVYTVH-GLEVARVTVVNVDGR--L---IYNTLVKPDCEII----DYNTKY---SGISAKDFIRNPYKTLKDV 146 (240)
Q Consensus 80 ~valD~E~tg~~~-g~ei~~v~vv~~~g~--~---~~d~lVkP~~~I~----~~~t~~---~GIt~edl~~a~~~~~~ev 146 (240)
+++||+||||+++ ..+|++|++|..++. . .|+.+|+|..+++ +...++ |||+++++.++|. +.++
T Consensus 1 lv~iD~ETTGl~p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~--~~~v 78 (173)
T cd06135 1 LVWIDLEMTGLDPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVT--LAQA 78 (173)
T ss_pred CEEEEEecCCCCCCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCC--HHHH
Confidence 5899999999996 468999999986542 2 3999999988665 344555 5999999999998 9999
Q ss_pred HHHHHhhhcC-----CcEEEEEchHHHHHHHhcc--------CCCeeeccc---cCcccCCCCCCccHHHHHHHHcCCCC
Q psy3897 147 QNDLMGFVSK-----DSIIVGHGLENDLRALKLI--------HSNIIDTSV---LFPHSFGLPYRRSLKSIVSQLLHQSI 210 (240)
Q Consensus 147 ~~~l~~~i~~-----~~iLVGH~~~~Dl~~L~~~--------~~~~iDT~~---l~~~~~~~~~~~sL~~L~~~~L~~~i 210 (240)
+.+|.+|+.+ ..+|||||+.||+.||+.. +++.+||.. +.+... + .++. ++..
T Consensus 79 l~~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~~~l~~l~~~l~-p----~~~~-----~~~~- 147 (173)
T cd06135 79 EAELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDVSSIKELARRWY-P----EIYR-----KAPK- 147 (173)
T ss_pred HHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHHhccCCcchhhHHHHHHHHHHhC-c----Hhhh-----cCCC-
Confidence 9999999962 3699999999999999863 245577633 222111 0 1111 2321
Q ss_pred CCCCCChHHHHHHHHHHHHHHHh
Q psy3897 211 QSGTHDSFEDARACIDLILWKLL 233 (240)
Q Consensus 211 q~~~H~A~eDA~at~~L~~~~l~ 233 (240)
....|+|+.||++|+.++.+.++
T Consensus 148 ~~~~HrAl~Da~~~~~~~~~~~~ 170 (173)
T cd06135 148 KKGTHRALDDIRESIAELKYYRE 170 (173)
T ss_pred CCCCcchHHHHHHHHHHHHHHHH
Confidence 22379999999999999987765
No 50
>KOG1275|consensus
Probab=99.77 E-value=3.5e-19 Score=173.75 Aligned_cols=158 Identities=34% Similarity=0.471 Sum_probs=133.1
Q ss_pred CCCCCcEEEEEEeecCCCC--------C---------ccEEEEEEEEcCC----cEEEEEEEcCCCcccccceecCCCCH
Q psy3897 74 PPNGYGVYALDTEMVYTVH--------G---------LEVARVTVVNVDG----RLIYNTLVKPDCEIIDYNTKYSGISA 132 (240)
Q Consensus 74 ~~~~~~~valD~E~tg~~~--------g---------~ei~~v~vv~~~g----~~~~d~lVkP~~~I~~~~t~~~GIt~ 132 (240)
.+.+..+|+||-|++.+.. | ..++||++|+++| ....|-||--...|.||.|++|||.+
T Consensus 906 mPk~g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msvARiScvRGeGp~eGiPFiDDYv~T~d~VvDYLTqySGI~P 985 (1118)
T KOG1275|consen 906 MPKSGDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSVARISCVRGEGPNEGIPFIDDYVSTDDKVVDYLTQYSGIKP 985 (1118)
T ss_pred cCCCCceeeeehhheecchHHhccccCCceeEeccccceeEEEEEEcccCCCCCCccccceecchhHHHHHHHHhcCCCc
Confidence 3557889999999986542 2 1689999999764 34589999999999999999999999
Q ss_pred HhhccCCC----CCHHHHHHHHHhhhcCCcEEEEEchHHHHHHHhccC--CCeeeccccCcccCCCCCCccHHHHHHHHc
Q psy3897 133 KDFIRNPY----KTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIH--SNIIDTSVLFPHSFGLPYRRSLKSIVSQLL 206 (240)
Q Consensus 133 edl~~a~~----~~~~ev~~~l~~~i~~~~iLVGH~~~~Dl~~L~~~~--~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L 206 (240)
.||..... .+++-++.++.=+++.|.++|||++.+|++++++.- .++|||+.+|.... .+..||+.||+++|
T Consensus 986 GDLDp~~S~K~Lt~lK~~Y~Kl~~Li~~GviFVGHGL~nDFrvINi~Vp~~QiiDTv~lf~~~s--~R~LSLrfLa~~lL 1063 (1118)
T KOG1275|consen 986 GDLDPTTSEKRLTTLKVLYLKLRLLIQRGVIFVGHGLQNDFRVINIHVPEEQIIDTVTLFRLGS--QRMLSLRFLAWELL 1063 (1118)
T ss_pred cccCCccCcceehhHHHHHHHHHHHHHcCcEEEcccccccceEEEEecChhhheeeeEEEeccc--ccEEEHHHHHHHHh
Confidence 99985432 137888999999999999999999999999999853 46999999986543 34579999999999
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHHHHh
Q psy3897 207 HQSIQSGTHDSFEDARACIDLILWKLL 233 (240)
Q Consensus 207 ~~~iq~~~H~A~eDA~at~~L~~~~l~ 233 (240)
|..||.+.|||.+||++|+.||.+.++
T Consensus 1064 g~~IQ~~~HDSIeDA~taLkLYk~Yl~ 1090 (1118)
T KOG1275|consen 1064 GETIQMEAHDSIEDARTALKLYKKYLK 1090 (1118)
T ss_pred cchhhccccccHHHHHHHHHHHHHHHH
Confidence 999999999999999999999986544
No 51
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.23 E-value=6e-12 Score=103.01 Aligned_cols=154 Identities=18% Similarity=0.257 Sum_probs=118.4
Q ss_pred CcEEEEEEeecCCCCC-----ccEEEEEE--EEc-CCcE--EEEEEEcCCC--cccccceecCCCCHHhhccCCCCCHHH
Q psy3897 78 YGVYALDTEMVYTVHG-----LEVARVTV--VNV-DGRL--IYNTLVKPDC--EIIDYNTKYSGISAKDFIRNPYKTLKD 145 (240)
Q Consensus 78 ~~~valD~E~tg~~~g-----~ei~~v~v--v~~-~g~~--~~d~lVkP~~--~I~~~~t~~~GIt~edl~~a~~~~~~e 145 (240)
....+||+|.|-...+ .||++|.+ |+. +-.+ .|++||+|.. ...+++..++||++..+..+|. |..
T Consensus 4 ~~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~api--fs~ 81 (210)
T COG5018 4 NSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAPI--FSM 81 (210)
T ss_pred ceEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhccccch--HHH
Confidence 3578999999876654 26766654 443 3333 3999999976 5789999999999999999999 999
Q ss_pred HHHHHHhhhcCCcE----EEEEchHHHHHHHhcc-----------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCC
Q psy3897 146 VQNDLMGFVSKDSI----IVGHGLENDLRALKLI-----------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSI 210 (240)
Q Consensus 146 v~~~l~~~i~~~~i----LVGH~~~~Dl~~L~~~-----------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~i 210 (240)
|+++|..+++...+ -++-....|+++|..- ....+|....|....+.|.--+|..+.+ ..|..+
T Consensus 82 v~E~f~r~L~~h~Pr~~~~wa~wG~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~pr~tgln~ale-~~G~sf 160 (210)
T COG5018 82 VFEDFIRKLNEHDPRKNSTWATWGNMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGDPRLTGLNKALE-EYGDSF 160 (210)
T ss_pred HHHHHHHHHHhcCcccCCccccccchhHHHHHHHHHhcCCCCccccCccchHHHHHHHHhcCCccccHHHHHH-Hhcccc
Confidence 99999999863221 2334458899999851 1256888888888777765467888886 589888
Q ss_pred CCCCCChHHHHHHHHHHHHHHHhh
Q psy3897 211 QSGTHDSFEDARACIDLILWKLLS 234 (240)
Q Consensus 211 q~~~H~A~eDA~at~~L~~~~l~~ 234 (240)
++..|+|++||+.+++||......
T Consensus 161 ~G~~HraldDArn~~rl~klv~~~ 184 (210)
T COG5018 161 TGTHHRALDDARNAYRLFKLVEQD 184 (210)
T ss_pred CCchhhhHHHHHHHHHHHHHHcch
Confidence 887999999999999998766544
No 52
>KOG0542|consensus
Probab=99.18 E-value=4.8e-11 Score=103.27 Aligned_cols=155 Identities=15% Similarity=0.239 Sum_probs=116.0
Q ss_pred cEEEEEEeecCCCCC-----ccEEEEEEEEc----CCcE--EEEEEEcCCC--cccccceecCCCCHHhhccCCCCCHHH
Q psy3897 79 GVYALDTEMVYTVHG-----LEVARVTVVNV----DGRL--IYNTLVKPDC--EIIDYNTKYSGISAKDFIRNPYKTLKD 145 (240)
Q Consensus 79 ~~valD~E~tg~~~g-----~ei~~v~vv~~----~g~~--~~d~lVkP~~--~I~~~~t~~~GIt~edl~~a~~~~~~e 145 (240)
-+++||+|+|--... .||++.-+|-. .+.+ -|+.||+|.. ...++++.+|||.++.+..+++ |++
T Consensus 57 YLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~~--f~~ 134 (280)
T KOG0542|consen 57 YLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAPT--FPQ 134 (280)
T ss_pred eEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCCC--HHH
Confidence 468999999866533 38999888832 2322 4999999965 6889999999999999999999 999
Q ss_pred HHHHHHhhhcC--------CcEEEEEchHHHHHHH-hc-----------cCCCeeeccccCcccCCCCCCccHHHHHHHH
Q psy3897 146 VQNDLMGFVSK--------DSIIVGHGLENDLRAL-KL-----------IHSNIIDTSVLFPHSFGLPYRRSLKSIVSQL 205 (240)
Q Consensus 146 v~~~l~~~i~~--------~~iLVGH~~~~Dl~~L-~~-----------~~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~ 205 (240)
|+.+|..++.. +--+|.. ...|+... .. ..+.+||.-..|......+..-++..+-+ +
T Consensus 135 vl~~f~~Wlr~~~~~~k~~~~Afvtd-g~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it~mLe-~ 212 (280)
T KOG0542|consen 135 VLSEFDSWLRKDSLGDKNGKFAFVTD-GDWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNITGMLE-H 212 (280)
T ss_pred HHHHHHHHHHHhhcccccCceEEEeC-chhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCHHHHHH-H
Confidence 99999998841 2223333 35555542 21 12478999888876533333446888885 6
Q ss_pred cCCCCCCCCCChHHHHHHHHHHHHHHHhhhhc
Q psy3897 206 LHQSIQSGTHDSFEDARACIDLILWKLLSDFR 237 (240)
Q Consensus 206 L~~~iq~~~H~A~eDA~at~~L~~~~l~~~~~ 237 (240)
+|+.+++..|+.+.||+..++|+..+++.+..
T Consensus 213 ~gL~f~Gr~HsGiDDa~Nia~I~~kM~~dg~~ 244 (280)
T KOG0542|consen 213 YGLQFEGRAHSGIDDARNIARIAQKMIRDGAE 244 (280)
T ss_pred hCCcccCCcccCchhHHHHHHHHHHHHhCCcE
Confidence 99888888999999999999999999887654
No 53
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=99.00 E-value=1.8e-09 Score=88.02 Aligned_cols=146 Identities=17% Similarity=0.209 Sum_probs=101.4
Q ss_pred CCcEEEEEEeecCCCCCc-cEEEEEEEE--cCCcEE---EEEEEcCCC----cccccceec---CCCCHHhhccCCCCCH
Q psy3897 77 GYGVYALDTEMVYTVHGL-EVARVTVVN--VDGRLI---YNTLVKPDC----EIIDYNTKY---SGISAKDFIRNPYKTL 143 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g~-ei~~v~vv~--~~g~~~---~d~lVkP~~----~I~~~~t~~---~GIt~edl~~a~~~~~ 143 (240)
..++|-|||||||++++. .|++|+.+- .+-+++ .+.-|..+. ...+.+++- ||+++.-.+..-+ .
T Consensus 5 ~~nLiWIDlEMTGLd~~~drIIEiA~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~t--~ 82 (184)
T COG1949 5 KNNLIWIDLEMTGLDPERDRIIEIATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTVT--E 82 (184)
T ss_pred CCceEEEeeeeccCCcCcceEEEEEEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhcc--H
Confidence 468999999999999986 689988765 344444 344444332 566777765 5677766555555 8
Q ss_pred HHHHHHHHhhhc-----CCcEEEEEchHHHHHHHhcc--------CCCeeeccccCcccCCCCCCccHHHHHHHHc----
Q psy3897 144 KDVQNDLMGFVS-----KDSIIVGHGLENDLRALKLI--------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLL---- 206 (240)
Q Consensus 144 ~ev~~~l~~~i~-----~~~iLVGH~~~~Dl~~L~~~--------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L---- 206 (240)
.++..+++.||+ +.+++.|.++.-|.+||... |.+++|++. |+.||++..
T Consensus 83 ~~aE~~~l~flkkwvp~~~spicGNSI~qDRrFl~r~MP~Le~yfHYR~lDVST-------------lKELa~RW~P~i~ 149 (184)
T COG1949 83 AEAEAQTLDFLKKWVPKGVSPICGNSIAQDRRFLFRYMPKLEAYFHYRYLDVST-------------LKELARRWNPEIL 149 (184)
T ss_pred HHHHHHHHHHHHHhCCCCCCCCccchhhHHHHHHHHHhhhHHHHhhhHhhhHHH-------------HHHHHHhhCcHhh
Confidence 999999888884 57899999999999999874 445666653 555554321
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHHHHhhhhc
Q psy3897 207 HQSIQSGTHDSFEDARACIDLILWKLLSDFR 237 (240)
Q Consensus 207 ~~~iq~~~H~A~eDA~at~~L~~~~l~~~~~ 237 (240)
......+.|.|++|.+-+..=+.+..+.-++
T Consensus 150 ~~~~K~~~H~Al~DI~ESI~EL~~YR~~f~~ 180 (184)
T COG1949 150 AGFKKGGTHRALDDIRESIAELRYYREHFLK 180 (184)
T ss_pred hccccccchhHHHHHHHHHHHHHHHHHHhcc
Confidence 1122334799999999988777766555443
No 54
>KOG3242|consensus
Probab=98.99 E-value=1.8e-09 Score=88.90 Aligned_cols=143 Identities=18% Similarity=0.284 Sum_probs=102.0
Q ss_pred CCcEEEEEEeecCCCCCc-cEEEEEEEEcCC--cEE---EEEEEcCCCccc----ccce---ecCCCCHHhhccCCCCCH
Q psy3897 77 GYGVYALDTEMVYTVHGL-EVARVTVVNVDG--RLI---YNTLVKPDCEII----DYNT---KYSGISAKDFIRNPYKTL 143 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g~-ei~~v~vv~~~g--~~~---~d~lVkP~~~I~----~~~t---~~~GIt~edl~~a~~~~~ 143 (240)
..++|.+||||||++-+. .|++|+.+--+| ..+ ++..|+.+.++. +.+. .-+|+|..-++..-+ +
T Consensus 25 ~q~lVWiD~EMTGLdvekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~t--l 102 (208)
T KOG3242|consen 25 KQPLVWIDCEMTGLDVEKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKIT--L 102 (208)
T ss_pred cCceEEEeeeccccccccceeEEEEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhcc--H
Confidence 357999999999999774 688888765433 333 778887655433 3332 347899988888877 9
Q ss_pred HHHHHHHHhhhc-----CCcEEEEEchHHHHHHHhcc--------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCC-
Q psy3897 144 KDVQNDLMGFVS-----KDSIIVGHGLENDLRALKLI--------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQS- 209 (240)
Q Consensus 144 ~ev~~~l~~~i~-----~~~iLVGH~~~~Dl~~L~~~--------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~- 209 (240)
.|+-.++++|+. +..+|.|.++.-|..||... |.++||++. .+.||+++....
T Consensus 103 ~~aEnevl~yikk~ip~~~~~laGNSV~~DrlFl~k~mPk~~~~lhyrivDVSt-------------IkeL~~Rw~P~~~ 169 (208)
T KOG3242|consen 103 ADAENEVLEYIKKHIPKGKCPLAGNSVYMDRLFLKKYMPKLIKHLHYRIVDVST-------------IKELARRWYPDIK 169 (208)
T ss_pred HHHHHHHHHHHHHhCCCCCCCccCcchhhHHHHHHHHhHHHHHhcceeeeeHHH-------------HHHHHHHhCchhh
Confidence 999999999884 57889999999999999874 556777764 344444433211
Q ss_pred ----CCCCCCChHHHHHHHHHHHHHHHhh
Q psy3897 210 ----IQSGTHDSFEDARACIDLILWKLLS 234 (240)
Q Consensus 210 ----iq~~~H~A~eDA~at~~L~~~~l~~ 234 (240)
-....|+|+.|.+-+..-+++..+.
T Consensus 170 ~~aPkK~~~HrAldDI~ESI~ELq~Yr~n 198 (208)
T KOG3242|consen 170 ARAPKKKATHRALDDIRESIKELQYYREN 198 (208)
T ss_pred ccCcccccccchHHHHHHHHHHHHHHHHH
Confidence 1122699999999887766665443
No 55
>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=98.95 E-value=7.5e-09 Score=87.19 Aligned_cols=121 Identities=16% Similarity=0.177 Sum_probs=87.4
Q ss_pred EEEEEEeecCC----CC-CccEEEEEEEEc-CCcEE-EEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHh
Q psy3897 80 VYALDTEMVYT----VH-GLEVARVTVVNV-DGRLI-YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMG 152 (240)
Q Consensus 80 ~valD~E~tg~----~~-g~ei~~v~vv~~-~g~~~-~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~ 152 (240)
+++||+||++. ++ +.+|+.|+++.. +|... +.....|...... ||+..++...+. ..+++..|.+
T Consensus 1 v~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~~~g~~~~~~~~~~~~~~~~~------~i~~~~v~~~~~--E~~lL~~f~~ 72 (199)
T cd05160 1 VLSFDIETTPPVGGPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDDIE------FIDGIEVEYFAD--EKELLKRFFD 72 (199)
T ss_pred CccEEEeecCCCCCcCCCCCCEEEEEEEEeeCCceeeEEEeecccCCcCC------CCCCceEEEeCC--HHHHHHHHHH
Confidence 47999999997 33 368999999996 77543 3333333322221 888889998888 8999999999
Q ss_pred hhcC--CcEEEEEch-HHHHHHHhcc-------C------------------------CCeeeccccCcccCCCCCCccH
Q psy3897 153 FVSK--DSIIVGHGL-ENDLRALKLI-------H------------------------SNIIDTSVLFPHSFGLPYRRSL 198 (240)
Q Consensus 153 ~i~~--~~iLVGH~~-~~Dl~~L~~~-------~------------------------~~~iDT~~l~~~~~~~~~~~sL 198 (240)
+++. -.++||||. .||+.+|..- . .-++|+..+++.... -.+++|
T Consensus 73 ~i~~~dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~~-l~sy~L 151 (199)
T cd05160 73 IIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFK-LKSYTL 151 (199)
T ss_pred HHHhcCCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhcC-cccCCH
Confidence 9962 259999999 8999998641 1 125788777655433 235799
Q ss_pred HHHHHHHcCCC
Q psy3897 199 KSIVSQLLHQS 209 (240)
Q Consensus 199 ~~L~~~~L~~~ 209 (240)
+.+|+.+|+..
T Consensus 152 ~~v~~~~l~~~ 162 (199)
T cd05160 152 DAVAEELLGEG 162 (199)
T ss_pred HHHHHHHhCCC
Confidence 99999888754
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=98.74 E-value=2.4e-07 Score=76.80 Aligned_cols=139 Identities=18% Similarity=0.089 Sum_probs=90.2
Q ss_pred CCcEEEEEEeecCCCC-CccEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhhc
Q psy3897 77 GYGVYALDTEMVYTVH-GLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVS 155 (240)
Q Consensus 77 ~~~~valD~E~tg~~~-g~ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~ 155 (240)
...++++|+|+++..+ ...++.+++....+...| .-+.+ +.+ .+.+. +.++...|.+++.
T Consensus 4 ~~~~~a~d~e~~~~~~~~~~i~~l~~~~~~~~~~~-~~~~~--------~~~--------~~~~~--~~~~~~~l~~~l~ 64 (193)
T cd06139 4 KAKVFAFDTETTSLDPMQAELVGISFAVEPGEAYY-IPLGH--------DYG--------GEQLP--REEVLAALKPLLE 64 (193)
T ss_pred cCCeEEEEeecCCCCcCCCeEEEEEEEcCCCCEEE-EecCC--------Ccc--------ccCCC--HHHHHHHHHHHHh
Confidence 3568999999998875 346777887655443322 10111 101 12334 7888999999886
Q ss_pred CC-cEEEEEchHHHHHHHhcc----CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCC----------------C--
Q psy3897 156 KD-SIIVGHGLENDLRALKLI----HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQ----------------S-- 212 (240)
Q Consensus 156 ~~-~iLVGH~~~~Dl~~L~~~----~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq----------------~-- 212 (240)
+. ..+||||+.+|+.+|+.. ...++||..+.....+...+.+|+.+++.|++..+. .
T Consensus 65 ~~~~~~v~hn~k~d~~~l~~~gi~~~~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~ 144 (193)
T cd06139 65 DPSIKKVGQNLKFDLHVLANHGIELRGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVP 144 (193)
T ss_pred CCCCcEEeeccHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccC
Confidence 33 379999999999999863 346799987654332211145899999998875421 0
Q ss_pred ---CCCChHHHHHHHHHHHHHHHhh
Q psy3897 213 ---GTHDSFEDARACIDLILWKLLS 234 (240)
Q Consensus 213 ---~~H~A~eDA~at~~L~~~~l~~ 234 (240)
..|.|..||.++.+|+.....+
T Consensus 145 ~~~~~~ya~~d~~~~~~l~~~l~~~ 169 (193)
T cd06139 145 LEKAAEYAAEDADITLRLYELLKPK 169 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 0134788888888887765543
No 57
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=98.67 E-value=1.8e-07 Score=85.53 Aligned_cols=148 Identities=17% Similarity=0.213 Sum_probs=105.8
Q ss_pred CCcEEEEEEeecCCCCCc-cEEEEEEEEc--CCcEE---EEEEEcCCCccc--ccceecCCCCHHhhccCCCCCHHHHHH
Q psy3897 77 GYGVYALDTEMVYTVHGL-EVARVTVVNV--DGRLI---YNTLVKPDCEII--DYNTKYSGISAKDFIRNPYKTLKDVQN 148 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g~-ei~~v~vv~~--~g~~~---~d~lVkP~~~I~--~~~t~~~GIt~edl~~a~~~~~~ev~~ 148 (240)
..+|++.|-||.|..+.. .+++.+.|+- +-+++ ...|++|...+. +.++-+||||++.....+.. -.+..+
T Consensus 8 ~~tF~~yDYETfG~~Pa~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~-E~~F~~ 86 (475)
T COG2925 8 QPTFLFYDYETFGVHPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGIN-EAAFAA 86 (475)
T ss_pred CCcEEEEehhhcCCCcccccchhhheeeccccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCC-hHHHHH
Confidence 458999999999999875 6888888874 32333 788999987433 34789999999999888775 566666
Q ss_pred HHH-hhhcCCcEEEEEc-hHHHHHHHhccC-C-----------------Ceeeccc----cCccc-------CCCCCCcc
Q psy3897 149 DLM-GFVSKDSIIVGHG-LENDLRALKLIH-S-----------------NIIDTSV----LFPHS-------FGLPYRRS 197 (240)
Q Consensus 149 ~l~-~~i~~~~iLVGH~-~~~Dl~~L~~~~-~-----------------~~iDT~~----l~~~~-------~~~~~~~s 197 (240)
.|. ++..++++++|+| +.||=.+-+... . .++|.+. |-|.. -|.+ ..+
T Consensus 87 ~I~~~ls~P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n~dG~p-SFk 165 (475)
T COG2925 87 RIHAELTQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDDGLP-SFK 165 (475)
T ss_pred HHHHHhCCCCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcCCCCCc-chh
Confidence 664 5666899999987 788888876521 1 1345443 22222 2222 467
Q ss_pred HHHHHHHHcCCCCCCC-CCChHHHHHHHHHHHH
Q psy3897 198 LKSIVSQLLHQSIQSG-THDSFEDARACIDLIL 229 (240)
Q Consensus 198 L~~L~~~~L~~~iq~~-~H~A~eDA~at~~L~~ 229 (240)
|+.|++. =| |+++ +|||++|++||..+..
T Consensus 166 LEhLt~A-Ng--ieH~nAHdAmsDVyATIamAk 195 (475)
T COG2925 166 LEHLTKA-NG--IEHSNAHDAMSDVYATIAMAK 195 (475)
T ss_pred hHHHhhc-cc--cccchhhHHHHHHHHHHHHHH
Confidence 9999964 55 6654 8999999999987644
No 58
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=98.52 E-value=1.4e-06 Score=70.77 Aligned_cols=129 Identities=21% Similarity=0.158 Sum_probs=78.0
Q ss_pred CcEEEEEEeecCCCCCc---cEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhh
Q psy3897 78 YGVYALDTEMVYTVHGL---EVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFV 154 (240)
Q Consensus 78 ~~~valD~E~tg~~~g~---ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i 154 (240)
.++++||+|+++...-. .++-|++-..++.. ++.|-.. +.. + +.+.|.+++
T Consensus 20 ~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~----i~~~~~~-------------------~~~-~--~~~~l~~ll 73 (176)
T PF01612_consen 20 AKVLAFDTETTGLDPYSYNPKIALIQLATGEGCY----IIDPIDL-------------------GDN-W--ILDALKELL 73 (176)
T ss_dssp TSEEEEEEEEETSTSTTSSEEEEEEEEEESCEEE----EECGTTS-------------------TTT-T--HHHHHHHHH
T ss_pred CCeEEEEEEECCCCccccCCeEEEEEEecCCCce----eeeeccc-------------------ccc-c--hHHHHHHHH
Confidence 35999999999988722 34444444432211 1122110 000 0 345555555
Q ss_pred c-CCcEEEEEchHHHHHHHhcc----CCCeeeccccCcccCCCCCCccHHHHHHHHcC-CCCC----CC-CC--C-----
Q psy3897 155 S-KDSIIVGHGLENDLRALKLI----HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLH-QSIQ----SG-TH--D----- 216 (240)
Q Consensus 155 ~-~~~iLVGH~~~~Dl~~L~~~----~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~-~~iq----~~-~H--~----- 216 (240)
. ++.+.||||+.||+.+|... ...++||. +.....+...+.+|+.|+..++| .... .+ .. +
T Consensus 74 ~~~~i~kv~~n~~~D~~~L~~~~~i~~~~~~D~~-l~~~~l~~~~~~~L~~L~~~~l~~~~~~~~~~~~~~~~~~~l~~~ 152 (176)
T PF01612_consen 74 EDPNIIKVGHNAKFDLKWLYRSFGIDLKNVFDTM-LAAYLLDPTRSYSLKDLAEEYLGNIDLDKKEQMSDWRKARPLSEE 152 (176)
T ss_dssp TTTTSEEEESSHHHHHHHHHHHHTS--SSEEEHH-HHHHHTTTSTTSSHHHHHHHHHSEEE-GHCCTTSSTTTSSS-HHH
T ss_pred hCCCccEEEEEEechHHHHHHHhccccCCccchh-hhhhcccccccccHHHHHHHHhhhccCcHHHhhccCCcCCCChHH
Confidence 3 45689999999999999873 35789994 44333333333799999999999 3321 11 22 2
Q ss_pred ----hHHHHHHHHHHHHHHHh
Q psy3897 217 ----SFEDARACIDLILWKLL 233 (240)
Q Consensus 217 ----A~eDA~at~~L~~~~l~ 233 (240)
|..||.++.+|+..+..
T Consensus 153 ~~~YAa~D~~~~~~l~~~l~~ 173 (176)
T PF01612_consen 153 QIEYAAQDAVVTFRLYEKLKP 173 (176)
T ss_dssp HHHHHHHHHHTHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 45699999988765543
No 59
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=98.47 E-value=1.3e-06 Score=65.66 Aligned_cols=57 Identities=25% Similarity=0.297 Sum_probs=42.1
Q ss_pred EEEEEeecCCCCCc-cEEEEEEEEcC-CcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhhcCC-
Q psy3897 81 YALDTEMVYTVHGL-EVARVTVVNVD-GRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKD- 157 (240)
Q Consensus 81 valD~E~tg~~~g~-ei~~v~vv~~~-g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~~~- 157 (240)
+++|+||+|+.+.. +|+.|++.+.+ +...+ .. |.+++.+.
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~~~~----~~---------------------------------f~~~l~~~~ 43 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPEDTAV----ID---------------------------------LKDILRDKP 43 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCCCEEE----eh---------------------------------HHHHHhhCC
Confidence 58999999988664 79999998873 33221 11 55566433
Q ss_pred -cEEEEEchHHHHHHHhc
Q psy3897 158 -SIIVGHGLENDLRALKL 174 (240)
Q Consensus 158 -~iLVGH~~~~Dl~~L~~ 174 (240)
.++||||..||+.+|+.
T Consensus 44 ~~v~V~hn~~fD~~fL~~ 61 (96)
T cd06125 44 LAILVGHNGSFDLPFLNN 61 (96)
T ss_pred CCEEEEeCcHHhHHHHHH
Confidence 59999999999999886
No 60
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=98.40 E-value=4.3e-06 Score=70.64 Aligned_cols=87 Identities=18% Similarity=0.216 Sum_probs=61.9
Q ss_pred HHHHHHhhhcCC-cEEEEEchHHHHHHHhccC----------CCeeeccccCcccCC----------CCCCccHHHHHHH
Q psy3897 146 VQNDLMGFVSKD-SIIVGHGLENDLRALKLIH----------SNIIDTSVLFPHSFG----------LPYRRSLKSIVSQ 204 (240)
Q Consensus 146 v~~~l~~~i~~~-~iLVGH~~~~Dl~~L~~~~----------~~~iDT~~l~~~~~~----------~~~~~sL~~L~~~ 204 (240)
..+.|.+++... -+-|||++.+|+..|.... ..++||..++....+ ...+.||..||+.
T Consensus 70 ~~~~L~~ll~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~ 149 (193)
T cd06146 70 WDRLLKRLFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQE 149 (193)
T ss_pred HHHHHHHHhCCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHH
Confidence 444566776533 4559999999999998632 468999876543211 1235799999999
Q ss_pred HcCCCCCCC---------------CCChHHHHHHHHHHHHHHH
Q psy3897 205 LLHQSIQSG---------------THDSFEDARACIDLILWKL 232 (240)
Q Consensus 205 ~L~~~iq~~---------------~H~A~eDA~at~~L~~~~l 232 (240)
+||..++.. -+=|..||+++.+|+.++.
T Consensus 150 ~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 150 VLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred HhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 999887542 1446789999999987654
No 61
>PRK05755 DNA polymerase I; Provisional
Probab=98.22 E-value=1.3e-05 Score=82.03 Aligned_cols=131 Identities=21% Similarity=0.161 Sum_probs=88.4
Q ss_pred CCcEEEEEEeecCCCCC-ccEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhhc
Q psy3897 77 GYGVYALDTEMVYTVHG-LEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVS 155 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g-~ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~ 155 (240)
...++++|+||+++++. .+++.|++-..+|... +| |. +++. . ++...|.+++.
T Consensus 314 ~~~~~a~DtEt~~l~~~~~~i~~i~ls~~~g~~~---~i-p~----------~~i~-----------~-~~l~~l~~~L~ 367 (880)
T PRK05755 314 AAGLFAFDTETTSLDPMQAELVGLSFAVEPGEAA---YI-PL----------DQLD-----------R-EVLAALKPLLE 367 (880)
T ss_pred ccCeEEEEeccCCCCcccccEEEEEEEeCCCcEE---EE-ec----------cccc-----------H-HHHHHHHHHHh
Confidence 45789999999998865 4677777644455332 12 21 1111 1 45666777775
Q ss_pred CC-cEEEEEchHHHHHHHhcc----CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCC------------------
Q psy3897 156 KD-SIIVGHGLENDLRALKLI----HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQS------------------ 212 (240)
Q Consensus 156 ~~-~iLVGH~~~~Dl~~L~~~----~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~------------------ 212 (240)
.. .++|+||+.||+.+|... ...++||..+........ .++|+.|++.|+|...-.
T Consensus 368 d~~v~kV~HNakfDl~~L~~~gi~~~~~~~DT~iAa~Ll~~~~-~~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~ple~ 446 (880)
T PRK05755 368 DPAIKKVGQNLKYDLHVLARYGIELRGIAFDTMLASYLLDPGR-RHGLDSLAERYLGHKTISFEEVAGKQLTFAQVDLEE 446 (880)
T ss_pred CCCCcEEEeccHhHHHHHHhCCCCcCCCcccHHHHHHHcCCCC-CCCHHHHHHHHhCCCccchHHhcCCCCCccccCHHH
Confidence 33 348999999999999862 346899987544332211 379999999988865200
Q ss_pred CCCChHHHHHHHHHHHHHHHhh
Q psy3897 213 GTHDSFEDARACIDLILWKLLS 234 (240)
Q Consensus 213 ~~H~A~eDA~at~~L~~~~l~~ 234 (240)
..|-|..|+.++++|+.++..+
T Consensus 447 ~~~YAa~Dv~~~~~L~~~L~~~ 468 (880)
T PRK05755 447 AAEYAAEDADVTLRLHEVLKPK 468 (880)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 0367899999999998877665
No 62
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=98.14 E-value=4.2e-05 Score=64.63 Aligned_cols=115 Identities=13% Similarity=0.086 Sum_probs=74.6
Q ss_pred CcEEEEEEeecCCC----C-CccEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHh
Q psy3897 78 YGVYALDTEMVYTV----H-GLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMG 152 (240)
Q Consensus 78 ~~~valD~E~tg~~----~-g~ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~ 152 (240)
.++++||+||++.. + ..+|+.|+++...++.++.. ++... ..+..... -.+++..|.+
T Consensus 3 l~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~~--~~~~~-------------~~v~~~~~--E~~lL~~F~~ 65 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVITW--KKFDL-------------PFVEVVKT--EKEMIKRFIE 65 (195)
T ss_pred ceEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEEe--cCCCC-------------CeEEEeCC--HHHHHHHHHH
Confidence 47899999998432 2 24799999988655544321 11110 12333334 6788999999
Q ss_pred hhcC--CcEEEEEch-HHHHHHHhcc------C-C------------------------CeeeccccCcccCCCCCCccH
Q psy3897 153 FVSK--DSIIVGHGL-ENDLRALKLI------H-S------------------------NIIDTSVLFPHSFGLPYRRSL 198 (240)
Q Consensus 153 ~i~~--~~iLVGH~~-~~Dl~~L~~~------~-~------------------------~~iDT~~l~~~~~~~~~~~sL 198 (240)
++.. -.+|||||. .||+.+|..- . + ..+|+..+++.....+ .++|
T Consensus 66 ~i~~~dpdiivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~~l~-sy~L 144 (195)
T cd05780 66 IVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLNLT-RYTL 144 (195)
T ss_pred HHHHcCCCEEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhCCCC-cCcH
Confidence 8864 479999997 5899998631 0 0 1466666554433322 6799
Q ss_pred HHHHHHHcCCCC
Q psy3897 199 KSIVSQLLHQSI 210 (240)
Q Consensus 199 ~~L~~~~L~~~i 210 (240)
+++|+.+||..-
T Consensus 145 ~~v~~~~Lg~~k 156 (195)
T cd05780 145 ERVYEELFGIEK 156 (195)
T ss_pred HHHHHHHhCCCC
Confidence 999999999653
No 63
>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=97.94 E-value=0.00013 Score=64.52 Aligned_cols=73 Identities=25% Similarity=0.129 Sum_probs=54.2
Q ss_pred cCCcEEEEEchHHHHHHHhc-------------------cCCCeeeccccCcccCCCCCCccHHHHHHHHcCCCC-----
Q psy3897 155 SKDSIIVGHGLENDLRALKL-------------------IHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSI----- 210 (240)
Q Consensus 155 ~~~~iLVGH~~~~Dl~~L~~-------------------~~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~i----- 210 (240)
+...++||||.-.|+.+|-. ..|.++||-.|..... ....+|..|+. .|+..-
T Consensus 147 ~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~--~~~~~L~~l~~-~l~~~~~~~~~ 223 (262)
T PF04857_consen 147 SSKKPIVGHNGLYDLMYLYKKFIGPLPETLEEFKELLRELFPRIYDTKYLAEECP--GKSTSLQELAE-ELGIRRNPSSI 223 (262)
T ss_dssp CC-SEEEESSTHHHHHHHHHHHTTS--SSHHHHHHHHHHHSSSEEEHHHHHTSTT--TS-SSHHHHHH-HTTSTT----E
T ss_pred ccCCcEEEeChHhHHHHHHHHhcCCCCCCHHHHHHHHHHHCcccccHHHHHHhcc--ccccCHHHHHH-HhCCCcccccc
Confidence 45699999999999998642 2467999988876543 22458999996 577543
Q ss_pred ------------------CCC-CCChHHHHHHHHHHHHH
Q psy3897 211 ------------------QSG-THDSFEDARACIDLILW 230 (240)
Q Consensus 211 ------------------q~~-~H~A~eDA~at~~L~~~ 230 (240)
.+. .|.|-.||+.|+.+|.+
T Consensus 224 ~~~~~~~~~~~~~~~~~~~~~~~HeAGyDA~mTg~~F~~ 262 (262)
T PF04857_consen 224 SSPEGFPSYDEEKNNFPMFGEKAHEAGYDAYMTGCVFIK 262 (262)
T ss_dssp EE-TTS-------------SS-TTSHHHHHHHHHHHHHH
T ss_pred ccccccccccccccccccCCCCCCCcchHHHHHHHHHcC
Confidence 222 79999999999999874
No 64
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=97.87 E-value=0.00013 Score=59.52 Aligned_cols=79 Identities=24% Similarity=0.270 Sum_probs=55.6
Q ss_pred hhhc-CCcEEEEEchHHHHHHHhcc----CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCC-------------
Q psy3897 152 GFVS-KDSIIVGHGLENDLRALKLI----HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSG------------- 213 (240)
Q Consensus 152 ~~i~-~~~iLVGH~~~~Dl~~L~~~----~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~------------- 213 (240)
+++. ++.+.|||++..|+..|... ...++||+..+... +.+.+.+|+.+++.+||..+...
T Consensus 61 ~lL~d~~i~Kvg~~~k~D~~~L~~~~gi~~~~~~D~~~aa~ll-~~~~~~~L~~l~~~~lg~~l~K~~~~s~W~~rpLt~ 139 (161)
T cd06129 61 MLLENPSIVKALHGIEGDLWKLLRDFGEKLQRLFDTTIAANLK-GLPERWSLASLVEHFLGKTLDKSISCADWSYRPLTE 139 (161)
T ss_pred HHhCCCCEEEEEeccHHHHHHHHHHcCCCcccHhHHHHHHHHh-CCCCCchHHHHHHHHhCCCCCccceeccCCCCCCCH
Confidence 4443 34466999999999999752 23579998765543 33335699999999999876432
Q ss_pred --CCChHHHHHHHHHHHHHH
Q psy3897 214 --THDSFEDARACIDLILWK 231 (240)
Q Consensus 214 --~H~A~eDA~at~~L~~~~ 231 (240)
-+=|..||+++.+|+..+
T Consensus 140 ~qi~YAa~Da~~l~~l~~~l 159 (161)
T cd06129 140 DQKLYAAADVYALLIIYTKL 159 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 144678999998887654
No 65
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=97.85 E-value=0.00018 Score=58.81 Aligned_cols=82 Identities=22% Similarity=0.174 Sum_probs=57.8
Q ss_pred HHhhhc-CCcEEEEEchHHHHHHHhcc----CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCC--CC---------
Q psy3897 150 LMGFVS-KDSIIVGHGLENDLRALKLI----HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQ--SG--------- 213 (240)
Q Consensus 150 l~~~i~-~~~iLVGH~~~~Dl~~L~~~----~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq--~~--------- 213 (240)
|.+++. ++.+.|||++.+|+..|... ...++||..++....+...+.+|+.|+..+||..+. ..
T Consensus 65 l~~ll~~~~i~kv~~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~r 144 (170)
T cd06141 65 LKQLLEDPSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEAR 144 (170)
T ss_pred HHHHhcCCCeeEEEeeeHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCCC
Confidence 444553 34567999999999999742 346799998766553322235999999999998776 21
Q ss_pred ------CCChHHHHHHHHHHHHHH
Q psy3897 214 ------THDSFEDARACIDLILWK 231 (240)
Q Consensus 214 ------~H~A~eDA~at~~L~~~~ 231 (240)
-|=|..||+.+.+|+..+
T Consensus 145 pLt~~qi~YAa~Da~~~~~l~~~l 168 (170)
T cd06141 145 PLSKEQILYAATDAYASLELYRKL 168 (170)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
Confidence 144678999988887654
No 66
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=97.73 E-value=0.0013 Score=51.80 Aligned_cols=66 Identities=23% Similarity=0.155 Sum_probs=45.4
Q ss_pred HHHHHHHhhhcC-CcEEEEEchHHHHHHHhcc----CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCC
Q psy3897 145 DVQNDLMGFVSK-DSIIVGHGLENDLRALKLI----HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSI 210 (240)
Q Consensus 145 ev~~~l~~~i~~-~~iLVGH~~~~Dl~~L~~~----~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~i 210 (240)
++.+.|.+++.. +..+||||+.+|+.+|+.. ...++||..+.........+.+|+.|+++|++..+
T Consensus 41 ~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~~~~~~~~~~~~D~~~~ayll~~~~~~~~l~~l~~~~l~~~~ 111 (155)
T cd00007 41 EDLEALKELLEDEDITKVGHDAKFDLVVLARDGIELPGNIFDTMLAAYLLNPGEGSHSLDDLAKEYLGIEL 111 (155)
T ss_pred HHHHHHHHHHcCCCCcEEeccHHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCCcCCHHHHHHHHcCCCC
Confidence 455566677742 3469999999999999753 34679998754433221113589999999988663
No 67
>PRK10829 ribonuclease D; Provisional
Probab=97.73 E-value=0.00047 Score=64.10 Aligned_cols=129 Identities=18% Similarity=0.230 Sum_probs=81.0
Q ss_pred CCCcEEEEEEeecCCCCCc-cEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhh
Q psy3897 76 NGYGVYALDTEMVYTVHGL-EVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFV 154 (240)
Q Consensus 76 ~~~~~valD~E~tg~~~g~-ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i 154 (240)
...+++|||+|+.....-. .++-|.+-+.++. .+|.|-. +.+ ...|.+++
T Consensus 20 ~~~~~lalDtEf~~~~ty~~~l~LiQl~~~~~~----~LiD~l~-~~d------------------------~~~L~~ll 70 (373)
T PRK10829 20 RAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQL----SLIDPLG-ITD------------------------WSPFKALL 70 (373)
T ss_pred hcCCeEEEecccccCccCCCceeEEEEecCCce----EEEecCC-ccc------------------------hHHHHHHH
Confidence 3567899999988765422 3333333333222 3444421 111 12345555
Q ss_pred cCCcEE-EEEchHHHHHHHhc----cCCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCC------C---------
Q psy3897 155 SKDSII-VGHGLENDLRALKL----IHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSG------T--------- 214 (240)
Q Consensus 155 ~~~~iL-VGH~~~~Dl~~L~~----~~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~------~--------- 214 (240)
....|+ |+|+..+|+.+|.. ....++||....... |.+.+.+|..|++.+||..+..+ +
T Consensus 71 ~~~~ivKV~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~l-g~~~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~ql 149 (373)
T PRK10829 71 RDPQVTKFLHAGSEDLEVFLNAFGELPQPLIDTQILAAFC-GRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQC 149 (373)
T ss_pred cCCCeEEEEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHc-CCCccccHHHHHHHHhCCccCcccccCCCCCCCCCHHHH
Confidence 445554 89999999999844 245799998765443 44445799999999999877543 1
Q ss_pred CChHHHHHHHHHHHHHHHhh
Q psy3897 215 HDSFEDARACIDLILWKLLS 234 (240)
Q Consensus 215 H~A~eDA~at~~L~~~~l~~ 234 (240)
+=|..|+....+|+..+..+
T Consensus 150 ~YAa~Dv~~L~~l~~~L~~~ 169 (373)
T PRK10829 150 EYAAADVFYLLPIAAKLMAE 169 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 22568888888887765543
No 68
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=97.60 E-value=0.0014 Score=56.00 Aligned_cols=126 Identities=20% Similarity=0.180 Sum_probs=70.3
Q ss_pred CcEEEEEEeecCCCCC------ccEEEEEEEEc-CCcEE-EEEEEcCCCcccccc----eecCCCCHHhhccCCCCCHHH
Q psy3897 78 YGVYALDTEMVYTVHG------LEVARVTVVNV-DGRLI-YNTLVKPDCEIIDYN----TKYSGISAKDFIRNPYKTLKD 145 (240)
Q Consensus 78 ~~~valD~E~tg~~~g------~ei~~v~vv~~-~g~~~-~d~lVkP~~~I~~~~----t~~~GIt~edl~~a~~~~~~e 145 (240)
.+++++|+|+.....| ..|+.|+++.. .|..+ ...++.+. +..+. -.+.|.. .+..... -.+
T Consensus 2 lrilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~~~g~~~~~~~~~~~~--~~~~~~~~~~~~~~~~--~v~~~~~--E~~ 75 (204)
T cd05779 2 PRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIVNREIVSED--IEDFEYTPKPEYEGPF--KVFNEPD--EKA 75 (204)
T ss_pred ceEEEEEEEecCCCCCCcCCCCCeEEEEEEEEecCCEEEecccccccc--cccccccCCCCCCCce--EEecCCC--HHH
Confidence 3689999999753322 36999999864 45322 11111110 00000 0111210 1111233 688
Q ss_pred HHHHHHhhhcCC--cEEEEEch-HHHHHHHhcc---C----C--------C----------eeeccccCcccCCC-CCCc
Q psy3897 146 VQNDLMGFVSKD--SIIVGHGL-ENDLRALKLI---H----S--------N----------IIDTSVLFPHSFGL-PYRR 196 (240)
Q Consensus 146 v~~~l~~~i~~~--~iLVGH~~-~~Dl~~L~~~---~----~--------~----------~iDT~~l~~~~~~~-~~~~ 196 (240)
++.+|.+++..- .+++|||. .||+.+|..- + . . .+|...+++..... ...+
T Consensus 76 lL~~f~~~i~~~~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~~sy 155 (204)
T cd05779 76 LLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQ 155 (204)
T ss_pred HHHHHHHHHHHhCCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCCCCc
Confidence 999999998633 49999996 6899998631 0 0 0 35555544421111 1257
Q ss_pred cHHHHHHHHcCCC
Q psy3897 197 SLKSIVSQLLHQS 209 (240)
Q Consensus 197 sL~~L~~~~L~~~ 209 (240)
+|...|+.+||..
T Consensus 156 sLd~Va~~~Lg~~ 168 (204)
T cd05779 156 GLKAVTKAKLGYD 168 (204)
T ss_pred cHHHHHHHHhCCC
Confidence 8999999889953
No 69
>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=97.48 E-value=0.0013 Score=55.45 Aligned_cols=104 Identities=13% Similarity=0.109 Sum_probs=68.3
Q ss_pred CcEEEEEEeecCC----CCC-ccEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHh
Q psy3897 78 YGVYALDTEMVYT----VHG-LEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMG 152 (240)
Q Consensus 78 ~~~valD~E~tg~----~~g-~ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~ 152 (240)
-++++||+||++- +++ ..|+.|++...+|...+-+ ..... -.+++..|.+
T Consensus 3 l~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~~-----------------------~~~~~--E~~lL~~F~~ 57 (188)
T cd05781 3 LKTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFIL-----------------------AEGLD--DRKIIREFVK 57 (188)
T ss_pred ceEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEEEE-----------------------ecCCC--HHHHHHHHHH
Confidence 4789999999832 222 3799999988766532111 01233 6788999998
Q ss_pred hhcCC--cEEEEEch-HHHHHHHhcc---C---------C-----------------CeeeccccCcccCCCCCCccHHH
Q psy3897 153 FVSKD--SIIVGHGL-ENDLRALKLI---H---------S-----------------NIIDTSVLFPHSFGLPYRRSLKS 200 (240)
Q Consensus 153 ~i~~~--~iLVGH~~-~~Dl~~L~~~---~---------~-----------------~~iDT~~l~~~~~~~~~~~sL~~ 200 (240)
+++.- .+|+|||. .||+.+|..- + . -.||...+.+..... .+++|++
T Consensus 58 ~i~~~dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~l-~~y~L~~ 136 (188)
T cd05781 58 YVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPEV-KVKTLEN 136 (188)
T ss_pred HHHHcCCCEEEecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCCC-CCCCHHH
Confidence 88633 68999996 6899998630 0 0 046665554443222 2589999
Q ss_pred HHHHHcCC
Q psy3897 201 IVSQLLHQ 208 (240)
Q Consensus 201 L~~~~L~~ 208 (240)
+|. +||.
T Consensus 137 Va~-~Lg~ 143 (188)
T cd05781 137 VAE-YLGV 143 (188)
T ss_pred HHH-HHCC
Confidence 996 6985
No 70
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=97.43 E-value=0.0028 Score=53.63 Aligned_cols=115 Identities=17% Similarity=0.142 Sum_probs=68.1
Q ss_pred CcEEEEEEeecCCCCCccEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhhcCC
Q psy3897 78 YGVYALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKD 157 (240)
Q Consensus 78 ~~~valD~E~tg~~~g~ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~~~ 157 (240)
-++++||+|+++.. +|..++..+...+.++- +=.+ .++. |. .+.-.+. -.+++..|.+++..-
T Consensus 3 l~~~~fDIE~~~~~---~i~~i~~~~~~~~~i~~-~~~~-~~~~-------~~---~v~~~~~--E~~lL~~f~~~i~~~ 65 (193)
T cd05784 3 LKVVSLDIETSMDG---ELYSIGLYGEGQERVLM-VGDP-EDDA-------PD---NIEWFAD--EKSLLLALIAWFAQY 65 (193)
T ss_pred ccEEEEEeecCCCC---CEEEEEeecCCCCEEEE-ECCC-CCCC-------CC---EEEEECC--HHHHHHHHHHHHHhh
Confidence 47999999997533 77778776643333221 1111 1111 11 1222234 677888888888633
Q ss_pred --cEEEEEch-HHHHHHHhc-------cC-------------------------CC-eeeccccCcccCCCCCCccHHHH
Q psy3897 158 --SIIVGHGL-ENDLRALKL-------IH-------------------------SN-IIDTSVLFPHSFGLPYRRSLKSI 201 (240)
Q Consensus 158 --~iLVGH~~-~~Dl~~L~~-------~~-------------------------~~-~iDT~~l~~~~~~~~~~~sL~~L 201 (240)
.||+|||. .||+.+|.. .+ .+ ++|+..+.+.....-.+++|.++
T Consensus 66 dPDvi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~~~~kl~sy~L~~V 145 (193)
T cd05784 66 DPDIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTATYHFESFSLENV 145 (193)
T ss_pred CCCEEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHHccCCCCcCCHHHH
Confidence 58999997 569999753 01 01 45655444321111236899999
Q ss_pred HHHHcCCC
Q psy3897 202 VSQLLHQS 209 (240)
Q Consensus 202 ~~~~L~~~ 209 (240)
|+.+||..
T Consensus 146 a~~~Lg~~ 153 (193)
T cd05784 146 AQELLGEG 153 (193)
T ss_pred HHHHhCCC
Confidence 99999853
No 71
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=97.42 E-value=0.0014 Score=60.40 Aligned_cols=129 Identities=19% Similarity=0.247 Sum_probs=83.1
Q ss_pred CCcEEEEEEeecCCCCC-ccEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhhc
Q psy3897 77 GYGVYALDTEMVYTVHG-LEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVS 155 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g-~ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~ 155 (240)
..++|+||+|+.+..+- ..++=|-+-+.++ ..+|.|..++.+ .+. |..++ .+
T Consensus 16 ~~~~iAiDTEf~r~~t~~p~LcLIQi~~~e~----~~lIdpl~~~~d---------------~~~--l~~Ll------~d 68 (361)
T COG0349 16 GSKAIAIDTEFMRLRTYYPRLCLIQISDGEG----ASLIDPLAGILD---------------LPP--LVALL------AD 68 (361)
T ss_pred CCCceEEecccccccccCCceEEEEEecCCC----ceEecccccccc---------------cch--HHHHh------cC
Confidence 35799999999988764 3566666666655 355666443221 222 32221 12
Q ss_pred CCcEEEEEchHHHHHHHhcc----CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCC------CCChH-------
Q psy3897 156 KDSIIVGHGLENDLRALKLI----HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSG------THDSF------- 218 (240)
Q Consensus 156 ~~~iLVGH~~~~Dl~~L~~~----~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~------~H~A~------- 218 (240)
.+-+=|=|+..+|+.+|... ...++||....+.. |.+.+.+|++|+++++|.+|..+ +++.+
T Consensus 69 ~~v~KIfHaa~~DL~~l~~~~g~~p~plfdTqiAa~l~-g~~~~~gl~~Lv~~ll~v~ldK~~q~SDW~~RPLs~~Ql~Y 147 (361)
T COG0349 69 PNVVKIFHAARFDLEVLLNLFGLLPTPLFDTQIAAKLA-GFGTSHGLADLVEELLGVELDKSEQRSDWLARPLSEAQLEY 147 (361)
T ss_pred CceeeeeccccccHHHHHHhcCCCCCchhHHHHHHHHh-CCcccccHHHHHHHHhCCcccccccccccccCCCCHHHHHH
Confidence 34444889999999998864 45789998765543 33337899999999999998754 44443
Q ss_pred --HHHHHHHHHHHHHHh
Q psy3897 219 --EDARACIDLILWKLL 233 (240)
Q Consensus 219 --eDA~at~~L~~~~l~ 233 (240)
.|+.....|+....+
T Consensus 148 Aa~DV~yL~~l~~~L~~ 164 (361)
T COG0349 148 AAADVEYLLPLYDKLTE 164 (361)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 555555555544433
No 72
>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=97.39 E-value=0.00063 Score=55.15 Aligned_cols=105 Identities=18% Similarity=0.116 Sum_probs=52.2
Q ss_pred EEEEEeecCCCCCc-cEEEEEEEEc-CCcEE-EEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhhcCC
Q psy3897 81 YALDTEMVYTVHGL-EVARVTVVNV-DGRLI-YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKD 157 (240)
Q Consensus 81 valD~E~tg~~~g~-ei~~v~vv~~-~g~~~-~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~~~ 157 (240)
++||+||+|+.++. .+.-|++... +++.. |..+..+.. .. .+.+.+.+ +.+.+.
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~~~~~~~~~~---------------------~e-e~~~~~~~-~~l~~~ 57 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIITFIQWFAEDP---------------------DE-EEIILEFF-ELLDEA 57 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE-EEEE-GGGH---------------------HH-HHHHHH---HHHHTT
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEEeeHhhccCc---------------------HH-HHHHHHHH-HHHhcC
Confidence 57999999998754 5777777764 22222 333332211 10 12223333 556567
Q ss_pred cEEEEEc-hHHHHHHHhcc--------CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCC
Q psy3897 158 SIIVGHG-LENDLRALKLI--------HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQ 211 (240)
Q Consensus 158 ~iLVGH~-~~~Dl~~L~~~--------~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq 211 (240)
..+|+|| ..||+.+|+.. ....+|+......... .+++|+.+++ +||...+
T Consensus 58 ~~iv~yng~~FD~p~L~~~~~~~~~~~~~~~iDl~~~~~~~~~--~~~~Lk~ve~-~lg~~~~ 117 (164)
T PF13482_consen 58 DNIVTYNGKNFDIPFLKRRAKRYGLPPPFNHIDLLKIIKKHFL--ESYSLKNVEK-FLGIERR 117 (164)
T ss_dssp --EEESSTTTTHHHHHHHHH-HHHH--GGGEEEHHHHHT-TTS--CCTT--SHHH--------
T ss_pred CeEEEEeCcccCHHHHHHHHHHcCCCcccchhhHHHHHHhccC--CCCCHHHHhh-hcccccc
Confidence 8999999 58899999863 2357898876654322 3568999997 5885543
No 73
>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=97.32 E-value=0.0048 Score=57.29 Aligned_cols=75 Identities=15% Similarity=0.194 Sum_probs=51.0
Q ss_pred CcEEEEEchHHHHHHHhcc----CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCC------CCC---------h
Q psy3897 157 DSIIVGHGLENDLRALKLI----HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSG------THD---------S 217 (240)
Q Consensus 157 ~~iLVGH~~~~Dl~~L~~~----~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~------~H~---------A 217 (240)
+.+.|+|++.+|+.+|+.. ...++||....... +...+.+|..|++.|||..+..+ ..+ |
T Consensus 70 ~i~KV~h~~k~Dl~~L~~~~~~~~~~~fDtqlAa~lL-~~~~~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~YA 148 (367)
T TIGR01388 70 SVVKVLHAASEDLEVFLNLFGELPQPLFDTQIAAAFC-GFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYA 148 (367)
T ss_pred CceEEEeecHHHHHHHHHHhCCCCCCcccHHHHHHHh-CCCCCccHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHH
Confidence 4557999999999999753 34689998644322 33334699999999999876532 122 5
Q ss_pred HHHHHHHHHHHHHHH
Q psy3897 218 FEDARACIDLILWKL 232 (240)
Q Consensus 218 ~eDA~at~~L~~~~l 232 (240)
..||.+...|+..+.
T Consensus 149 a~Dv~~L~~L~~~L~ 163 (367)
T TIGR01388 149 AADVTYLLPLYAKLM 163 (367)
T ss_pred HHHHHHHHHHHHHHH
Confidence 667777776655443
No 74
>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=97.23 E-value=0.0024 Score=53.94 Aligned_cols=85 Identities=24% Similarity=0.124 Sum_probs=54.2
Q ss_pred HHhhhc-CCcEEEEEchHHHHHHHhc----cCCCeeeccccC----cccCC---CCCCccHHHHHHHHcCCCCCC-----
Q psy3897 150 LMGFVS-KDSIIVGHGLENDLRALKL----IHSNIIDTSVLF----PHSFG---LPYRRSLKSIVSQLLHQSIQS----- 212 (240)
Q Consensus 150 l~~~i~-~~~iLVGH~~~~Dl~~L~~----~~~~~iDT~~l~----~~~~~---~~~~~sL~~L~~~~L~~~iq~----- 212 (240)
|.+++. ++.+-|||++.+|+..|.. ....++||...+ +...+ .....+|..+++.|||.++..
T Consensus 57 L~~iLe~~~i~Kv~h~~k~D~~~L~~~~gi~~~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~ 136 (197)
T cd06148 57 LKDILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVK 136 (197)
T ss_pred HHHHhcCCCccEEEEechhHHHHHHHhcCccccceeeHHHHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHH
Confidence 334443 3445699999999999942 234679998642 22111 112358999999999976621
Q ss_pred --------C-C---------CChHHHHHHHHHHHHHHHhh
Q psy3897 213 --------G-T---------HDSFEDARACIDLILWKLLS 234 (240)
Q Consensus 213 --------~-~---------H~A~eDA~at~~L~~~~l~~ 234 (240)
. . .=|..||..+..|+..+..+
T Consensus 137 ~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~ 176 (197)
T cd06148 137 KLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDA 176 (197)
T ss_pred HHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 1 1 22568999988887766554
No 75
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=97.21 E-value=0.013 Score=50.06 Aligned_cols=127 Identities=19% Similarity=0.160 Sum_probs=71.5
Q ss_pred CCcEEEEEEeecCCC----C-----CccEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHH
Q psy3897 77 GYGVYALDTEMVYTV----H-----GLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQ 147 (240)
Q Consensus 77 ~~~~valD~E~tg~~----~-----g~ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~ 147 (240)
+-++++||+|+.... + +.+|+.|++.+.+|...+-.+=++.....+.... -| ..+..... -.+++
T Consensus 4 ~lrilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~~~~~~~~v~~~~~~~~~~~~~~~~-~~---~~v~~~~~--E~~lL 77 (204)
T cd05783 4 KLKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALAGSDGLKRVLVLKREGVEGLEGLLP-EG---AEVEFFDS--EKELI 77 (204)
T ss_pred CceEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEcCCCCCcEEEEEecCCcccccccCC-CC---CeEEecCC--HHHHH
Confidence 357999999997522 1 1369999987644532111111111110000000 01 11222234 78899
Q ss_pred HHHHhhhcCCcEEEEEch-HHHHHHHhcc------C-----------------CCeeeccccCccc------CC-CCCCc
Q psy3897 148 NDLMGFVSKDSIIVGHGL-ENDLRALKLI------H-----------------SNIIDTSVLFPHS------FG-LPYRR 196 (240)
Q Consensus 148 ~~l~~~i~~~~iLVGH~~-~~Dl~~L~~~------~-----------------~~~iDT~~l~~~~------~~-~~~~~ 196 (240)
..|.++++.-.++||||. .||+.+|..- . ...+|....+... .+ .-..+
T Consensus 78 ~~F~~~i~~~~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~~~~~~ 157 (204)
T cd05783 78 REAFKIISEYPIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGNKYREY 157 (204)
T ss_pred HHHHHHHhcCCEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhccccccC
Confidence 999999987789999996 6899998641 1 1135554433221 00 11257
Q ss_pred cHHHHHHHHcCCC
Q psy3897 197 SLKSIVSQLLHQS 209 (240)
Q Consensus 197 sL~~L~~~~L~~~ 209 (240)
+|+.+|+.+||..
T Consensus 158 ~L~~Va~~~lg~~ 170 (204)
T cd05783 158 TLDAVAKALLGEG 170 (204)
T ss_pred cHHHHHHHhcCCC
Confidence 9999999888853
No 76
>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=96.76 E-value=0.045 Score=47.33 Aligned_cols=85 Identities=20% Similarity=0.221 Sum_probs=51.7
Q ss_pred CCcEEEEEEeecCCC-----CC-ccEEEEEEEEc-CCc--EEE-EEE-EcCCCcccccceecCCCCHHhhccCCCCCHHH
Q psy3897 77 GYGVYALDTEMVYTV-----HG-LEVARVTVVNV-DGR--LIY-NTL-VKPDCEIIDYNTKYSGISAKDFIRNPYKTLKD 145 (240)
Q Consensus 77 ~~~~valD~E~tg~~-----~g-~ei~~v~vv~~-~g~--~~~-d~l-VkP~~~I~~~~t~~~GIt~edl~~a~~~~~~e 145 (240)
+-+++++|+|+.... +. .+|+.|+++.. +|. ... ..+ +.+..+++ | ..+...+. -.+
T Consensus 6 ~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~~~~~~~-------~---~~v~~~~~--E~e 73 (230)
T cd05777 6 PLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIV-------G---AQVFSFET--EEE 73 (230)
T ss_pred CceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeCCCCCCC-------C---CEEEEECC--HHH
Confidence 457999999997432 22 37999998853 442 111 111 23322222 1 11222334 678
Q ss_pred HHHHHHhhhcC--CcEEEEEch-HHHHHHHh
Q psy3897 146 VQNDLMGFVSK--DSIIVGHGL-ENDLRALK 173 (240)
Q Consensus 146 v~~~l~~~i~~--~~iLVGH~~-~~Dl~~L~ 173 (240)
++..|.+++.. -.|++|||+ .||+.+|.
T Consensus 74 LL~~f~~~i~~~DPDii~GyN~~~FDl~yL~ 104 (230)
T cd05777 74 LLLAWRDFVQEVDPDIITGYNICNFDLPYLL 104 (230)
T ss_pred HHHHHHHHHHhcCCCEEEEecCCCCCHHHHH
Confidence 88888888852 369999996 56999975
No 77
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=96.42 E-value=0.013 Score=50.17 Aligned_cols=73 Identities=18% Similarity=0.223 Sum_probs=50.3
Q ss_pred CCcEEEEEEeecCCCC---------CccEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHH
Q psy3897 77 GYGVYALDTEMVYTVH---------GLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQ 147 (240)
Q Consensus 77 ~~~~valD~E~tg~~~---------g~ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~ 147 (240)
+-++++||+|+..... +..|+.|++.+..|.... +.. .... -.+++
T Consensus 8 ~lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~---~~~--------------------~~~~--E~~lL 62 (207)
T cd05785 8 DLRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEV---LHA--------------------EDAA--EKELL 62 (207)
T ss_pred CceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceee---ecc--------------------CCCC--HHHHH
Confidence 4579999999965321 136888888766542111 000 1233 78899
Q ss_pred HHHHhhhcC--CcEEEEEch-HHHHHHHhc
Q psy3897 148 NDLMGFVSK--DSIIVGHGL-ENDLRALKL 174 (240)
Q Consensus 148 ~~l~~~i~~--~~iLVGH~~-~~Dl~~L~~ 174 (240)
..|.+++.. -.||||||. .||+.+|..
T Consensus 63 ~~f~~~i~~~dPdii~g~N~~~FD~pyl~~ 92 (207)
T cd05785 63 EELVAIIRERDPDVIEGHNIFRFDLPYLRR 92 (207)
T ss_pred HHHHHHHHHhCCCEEeccCCcccCHHHHHH
Confidence 999999863 279999998 899999763
No 78
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=96.31 E-value=0.1 Score=42.27 Aligned_cols=59 Identities=27% Similarity=0.299 Sum_probs=40.4
Q ss_pred HHhhhc-CCcEEEEEchHHHHHHHhcc----CCCeeeccccCcccCCCCCCccHHHHHHHHcCCC
Q psy3897 150 LMGFVS-KDSIIVGHGLENDLRALKLI----HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQS 209 (240)
Q Consensus 150 l~~~i~-~~~iLVGH~~~~Dl~~L~~~----~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~ 209 (240)
|..++. ++...||||+.+|+..|+.. .+.+.||+...--. ++..+.+|+.+++.||+..
T Consensus 56 l~~ll~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~~D~~laayLl-~p~~~~~l~~l~~~~l~~~ 119 (178)
T cd06142 56 LKELLADPNIVKVFHAAREDLELLKRDFGILPQNLFDTQIAARLL-GLGDSVGLAALVEELLGVE 119 (178)
T ss_pred HHHHHcCCCceEEEeccHHHHHHHHHHcCCCCCCcccHHHHHHHh-CCCccccHHHHHHHHhCCC
Confidence 444453 35678999999999999643 34578998543222 2222358999999999876
No 79
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=96.30 E-value=0.076 Score=46.09 Aligned_cols=155 Identities=14% Similarity=0.106 Sum_probs=83.8
Q ss_pred CcEEEEEEeecCCCCC------ccEEEEEEEEc-CCcEE-E------EEEEcCCCcccccceecCCCCHHhhccCCCCCH
Q psy3897 78 YGVYALDTEMVYTVHG------LEVARVTVVNV-DGRLI-Y------NTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTL 143 (240)
Q Consensus 78 ~~~valD~E~tg~~~g------~ei~~v~vv~~-~g~~~-~------d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~ 143 (240)
-++.++|+|+.....+ ++|+.|+.+-. +.... . --++.+...-.+.-....++....+.-.+. -
T Consensus 4 l~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~v~~~~~--E 81 (231)
T cd05778 4 LTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKSNASNGRIRSGLSGIPVEVVES--E 81 (231)
T ss_pred eEEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccchhhhhccccCCCCCeEEEeCC--H
Confidence 3678999998643322 25777776643 22111 1 122333221000001112333333333444 6
Q ss_pred HHHHHHHHhhhc--CCcEEEEEch-HHHHHHHhc----------------cC----CC----------------------
Q psy3897 144 KDVQNDLMGFVS--KDSIIVGHGL-ENDLRALKL----------------IH----SN---------------------- 178 (240)
Q Consensus 144 ~ev~~~l~~~i~--~~~iLVGH~~-~~Dl~~L~~----------------~~----~~---------------------- 178 (240)
.+.+.+|.+++. .-.|++|||+ .||+..|-. .. .+
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 777777777664 3579999998 578888642 00 00
Q ss_pred eeeccccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHHHHH------HHHHHHHHHHhhh
Q psy3897 179 IIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDAR------ACIDLILWKLLSD 235 (240)
Q Consensus 179 ~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~------at~~L~~~~l~~~ 235 (240)
++|+..+.+..... ..++|.++|..+||.....-.+..+.+.+ ...+++.|+++..
T Consensus 162 ~lD~~~~~r~~~kl-~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~ 223 (231)
T cd05778 162 ILNVWRLMRSELAL-TNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRV 223 (231)
T ss_pred EeEhHHHHHHHcCc-ccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHH
Confidence 12333333222111 25899999999999776654566666653 4566777777653
No 80
>PHA02570 dexA exonuclease; Provisional
Probab=96.18 E-value=0.023 Score=49.02 Aligned_cols=150 Identities=19% Similarity=0.247 Sum_probs=81.2
Q ss_pred EEEEEeecCCCCCccEEEEEEEEcC--CcE--EEEEEEcCCCcc------------cccce--ecCCCCHHh---hccCC
Q psy3897 81 YALDTEMVYTVHGLEVARVTVVNVD--GRL--IYNTLVKPDCEI------------IDYNT--KYSGISAKD---FIRNP 139 (240)
Q Consensus 81 valD~E~tg~~~g~ei~~v~vv~~~--g~~--~~d~lVkP~~~I------------~~~~t--~~~GIt~ed---l~~a~ 139 (240)
+.||+||.|+.+.--|+.|++|-++ ... .|+.+|..+..| ++..| -+-.-++|- |....
T Consensus 4 lMIDlETmG~~p~AaIisIgAV~Fdp~~~~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~L~~s~ 83 (220)
T PHA02570 4 FIIDFETFGNTPDGAVIDLAVIAFEHDPHNPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEARKNLKPSD 83 (220)
T ss_pred EEEEeeccCCCCCceEEEEEEEEecCCCCccccHHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHHHHhccCCC
Confidence 6899999999998899999999542 212 255555432211 11111 111111111 11000
Q ss_pred -CCCHHHHHHHHHhhhcCCc------EEEEEchHHHHHHHhccCCCe---eeccccCcccCCCCCCccHHHHHHH-HcCC
Q psy3897 140 -YKTLKDVQNDLMGFVSKDS------IIVGHGLENDLRALKLIHSNI---IDTSVLFPHSFGLPYRRSLKSIVSQ-LLHQ 208 (240)
Q Consensus 140 -~~~~~ev~~~l~~~i~~~~------iLVGH~~~~Dl~~L~~~~~~~---iDT~~l~~~~~~~~~~~sL~~L~~~-~L~~ 208 (240)
..++.+++.+|.+||..+. -+.|-+.+||...|+....+. .+|-...|..... .+-.+.+.+. .|++
T Consensus 84 ~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD~~IL~~a~r~~~~~~~~~~~~Pw~fwN--~RDVRT~ie~~~l~r 161 (220)
T PHA02570 84 EDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDFPILVDVIRDIHNTRDTFKLEPVKFWN--QRDVRTAIEATLLTR 161 (220)
T ss_pred ccccHHHHHHHHHHHHHHcCCCccceeEecCCCccCHHHHHHHHHHHhcccCcCcCCCeeecC--ccchHHHHhhhhccC
Confidence 1128899999999996333 478888999999997543222 2443333333211 1223333322 2444
Q ss_pred CCC-----C----C--CCChHHHHHHHHHHHHHHH
Q psy3897 209 SIQ-----S----G--THDSFEDARACIDLILWKL 232 (240)
Q Consensus 209 ~iq-----~----~--~H~A~eDA~at~~L~~~~l 232 (240)
.+. . + .|+|+-|+.--+..++|..
T Consensus 162 ~~~~cp~~~g~l~gfv~H~sihDcakd~lml~y~~ 196 (220)
T PHA02570 162 GMTTCPLPKGTLDGFVAHDSIHDCAKDILMLIYAK 196 (220)
T ss_pred CcccCCCcCccccchhhcccHHHHHHHHHHHHHHH
Confidence 421 1 1 6999988876655555443
No 81
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=96.10 E-value=0.033 Score=44.46 Aligned_cols=85 Identities=24% Similarity=0.243 Sum_probs=52.7
Q ss_pred HHHHhhhc-CCcEEEEEchHHHHHHHhcc---CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCC-CC-------
Q psy3897 148 NDLMGFVS-KDSIIVGHGLENDLRALKLI---HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSG-TH------- 215 (240)
Q Consensus 148 ~~l~~~i~-~~~iLVGH~~~~Dl~~L~~~---~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~-~H------- 215 (240)
..|.+++. .+...||||+.+|+.+|+.. -..++||+..+....+.....+|+.++..|++..++.. +.
T Consensus 65 ~~l~~~l~~~~~~kv~~d~k~~~~~L~~~gi~~~~~~D~~laayll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~ 144 (172)
T smart00474 65 EILKDLLEDETITKVGHNAKFDLHVLARFGIELENIFDTMLAAYLLLGGPSKHGLATLLKEYLGVELDKEEQKSDWGARP 144 (172)
T ss_pred HHHHHHhcCCCceEEEechHHHHHHHHHCCCcccchhHHHHHHHHHcCCCCcCCHHHHHHHHhCCCCCcccCccccccCC
Confidence 33445554 34669999999999999752 12358998754432221222589999999988764310 11
Q ss_pred -------ChHHHHHHHHHHHHHHH
Q psy3897 216 -------DSFEDARACIDLILWKL 232 (240)
Q Consensus 216 -------~A~eDA~at~~L~~~~l 232 (240)
-+..||.++.+|+....
T Consensus 145 l~~~~~~ya~~~a~~~~~L~~~l~ 168 (172)
T smart00474 145 LSEEQLQYAAEDADALLRLYEKLE 168 (172)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHH
Confidence 15566777777655443
No 82
>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=95.96 E-value=0.035 Score=47.69 Aligned_cols=88 Identities=24% Similarity=0.225 Sum_probs=60.2
Q ss_pred HHHHHHHHHhhhcC-CcEEEEEc-hHHHHHHHhc---cC-----------------------CCeeeccccCcccCCCCC
Q psy3897 143 LKDVQNDLMGFVSK-DSIIVGHG-LENDLRALKL---IH-----------------------SNIIDTSVLFPHSFGLPY 194 (240)
Q Consensus 143 ~~ev~~~l~~~i~~-~~iLVGH~-~~~Dl~~L~~---~~-----------------------~~~iDT~~l~~~~~~~~~ 194 (240)
-+++++.|.+++++ ...||+|| -+||+.+|.. .| .+-+|++.++... +...
T Consensus 37 E~~lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~-g~~~ 115 (209)
T PF10108_consen 37 EKELLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFY-GAKA 115 (209)
T ss_pred HHHHHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhcc-Cccc
Confidence 57889999999964 44799999 5899999874 11 1236777665433 2233
Q ss_pred CccHHHHHHHHcCCCCCCCCCC------------------hHHHHHHHHHHHHHHH
Q psy3897 195 RRSLKSIVSQLLHQSIQSGTHD------------------SFEDARACIDLILWKL 232 (240)
Q Consensus 195 ~~sL~~L~~~~L~~~iq~~~H~------------------A~eDA~at~~L~~~~l 232 (240)
+.+|..||. .||++-..+-+. ...|+++|+.||++..
T Consensus 116 ~~sLd~la~-~lgiPgK~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~ 170 (209)
T PF10108_consen 116 RTSLDELAA-LLGIPGKDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFE 170 (209)
T ss_pred cCCHHHHHH-HcCCCCCCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 579999996 699664322121 2589999999988654
No 83
>PRK05762 DNA polymerase II; Reviewed
Probab=95.77 E-value=0.13 Score=52.30 Aligned_cols=137 Identities=15% Similarity=0.122 Sum_probs=79.0
Q ss_pred CCCcEEEEEEeecCCCCCccEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhhc
Q psy3897 76 NGYGVYALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVS 155 (240)
Q Consensus 76 ~~~~~valD~E~tg~~~g~ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~ 155 (240)
.+.++++||+|+... .+|..|+........++- +.+..+.. .+.+...+. -.+++..|.+++.
T Consensus 153 p~lrvlsfDIE~~~~---~~i~sI~~~~~~~~~vi~--ig~~~~~~----------~~~v~~~~s--E~~LL~~F~~~i~ 215 (786)
T PRK05762 153 PPLKVVSLDIETSNK---GELYSIGLEGCGQRPVIM--LGPPNGEA----------LDFLEYVAD--EKALLEKFNAWFA 215 (786)
T ss_pred CCCeEEEEEEEEcCC---CceEEeeecCCCCCeEEE--EECCCCCC----------cceEEEcCC--HHHHHHHHHHHHH
Confidence 456899999998753 267777765432222211 12211110 111333444 6888899888885
Q ss_pred C--CcEEEEEch-HHHHHHHhcc---C------------------C-------------CeeeccccCcccCCCCCCccH
Q psy3897 156 K--DSIIVGHGL-ENDLRALKLI---H------------------S-------------NIIDTSVLFPHSFGLPYRRSL 198 (240)
Q Consensus 156 ~--~~iLVGH~~-~~Dl~~L~~~---~------------------~-------------~~iDT~~l~~~~~~~~~~~sL 198 (240)
. -.|++|||+ .||+.+|..- + + -++|+..+.+.....-..++|
T Consensus 216 ~~DPDIIvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~~~~~l~sysL 295 (786)
T PRK05762 216 EHDPDVIIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATWVFDSFSL 295 (786)
T ss_pred hcCCCEEEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHHhhccCCCCCH
Confidence 3 359999996 5799998530 0 0 034444433322111225789
Q ss_pred HHHHHHHcCCCCCC-CCCC-------------------hHHHHHHHHHHHH
Q psy3897 199 KSIVSQLLHQSIQS-GTHD-------------------SFEDARACIDLIL 229 (240)
Q Consensus 199 ~~L~~~~L~~~iq~-~~H~-------------------A~eDA~at~~L~~ 229 (240)
+++|+.+||..... ..|+ .+.||..+.+|+.
T Consensus 296 ~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~ 346 (786)
T PRK05762 296 EYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFE 346 (786)
T ss_pred HHHHHHHhCCCeeccCccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHH
Confidence 99999989854321 1111 3578888888776
No 84
>KOG4793|consensus
Probab=95.65 E-value=0.014 Score=51.70 Aligned_cols=161 Identities=17% Similarity=0.096 Sum_probs=99.5
Q ss_pred CCCcEEEEEEeecCCCCC-ccEEEEEEEEc-----CCc---------------EE---EEEEEcCCCcccccceecCCCC
Q psy3897 76 NGYGVYALDTEMVYTVHG-LEVARVTVVNV-----DGR---------------LI---YNTLVKPDCEIIDYNTKYSGIS 131 (240)
Q Consensus 76 ~~~~~valD~E~tg~~~g-~ei~~v~vv~~-----~g~---------------~~---~d~lVkP~~~I~~~~t~~~GIt 131 (240)
+-..++++|.|+||+..- .+|.++++.+. +|+ .+ ...++.|.....+...+++|.+
T Consensus 11 r~~tf~fldleat~lp~~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~v~~p~aeeitgls 90 (318)
T KOG4793|consen 11 RLRTFSFLDLEATGLPGWIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVPVTRPIAEEITGLS 90 (318)
T ss_pred ceeEEEeeeeccccCCcccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcCCcChhhhhhcccc
Confidence 345799999999998643 35666555432 222 11 4566778777777788999999
Q ss_pred HHhhccC--CCCCHHHHHHHHHhhh---cCCcEEEEEch-HHHHHHHhcc--------CC--CeeeccccCccc------
Q psy3897 132 AKDFIRN--PYKTLKDVQNDLMGFV---SKDSIIVGHGL-ENDLRALKLI--------HS--NIIDTSVLFPHS------ 189 (240)
Q Consensus 132 ~edl~~a--~~~~~~ev~~~l~~~i---~~~~iLVGH~~-~~Dl~~L~~~--------~~--~~iDT~~l~~~~------ 189 (240)
..-+.-. ... -.++.+.|..|+ ..--.||+||- ++|+..|+.. .. -.+|+...+...
T Consensus 91 ~~~~~l~rr~~~-D~dla~LL~afls~lp~p~CLVaHng~~~dfpil~qela~lg~~lpq~lvcvdslpa~~ald~a~s~ 169 (318)
T KOG4793|consen 91 QPFLALQRRLAF-DKDLAKLLTAFLSRLPTPGCLVAHNGNEYDFPILAQELAGLGYSLPQDLVCVDSLPALNALDRANSM 169 (318)
T ss_pred cHHHHHHHHhhh-hHHHHHHHHHHHhcCCCCceEEeecCCccccHHHHHHHHhcCccchhhhcCcchhHHHHHHhhhcCc
Confidence 8555422 111 233444444444 34456999994 6788887752 11 235655433211
Q ss_pred --CCC-CCCccHHHHHHHHcCCCCCCCCCChHHHHHHHHHHHHHHHhhhhc
Q psy3897 190 --FGL-PYRRSLKSIVSQLLHQSIQSGTHDSFEDARACIDLILWKLLSDFR 237 (240)
Q Consensus 190 --~~~-~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~at~~L~~~~l~~~~~ 237 (240)
.+. +..++|..+-..|.+-.-..++|.+..|.-+-.-+|++.+.+-++
T Consensus 170 ~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~~ellR 220 (318)
T KOG4793|consen 170 VTRPEVRRMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRINELLR 220 (318)
T ss_pred ccCCCCCcccccchHHHhhhcccCCCcceeeecccchhHHHHHHHHHHHHh
Confidence 111 234688888777666432234899999999988888888876543
No 85
>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=95.63 E-value=0.02 Score=48.93 Aligned_cols=65 Identities=25% Similarity=0.263 Sum_probs=46.0
Q ss_pred HHHHHHHHHhhhcC-CcEEEEEch-HHHHHHHhcc---C----C------------------CeeeccccCcccCCCCCC
Q psy3897 143 LKDVQNDLMGFVSK-DSIIVGHGL-ENDLRALKLI---H----S------------------NIIDTSVLFPHSFGLPYR 195 (240)
Q Consensus 143 ~~ev~~~l~~~i~~-~~iLVGH~~-~~Dl~~L~~~---~----~------------------~~iDT~~l~~~~~~~~~~ 195 (240)
-.+++..|.++++. +.+|||||. .||+.+|..- + + +.+|+..+..... ...+
T Consensus 78 E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~-~~~~ 156 (208)
T cd05782 78 EKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYG-ARAR 156 (208)
T ss_pred HHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccC-ccCC
Confidence 46788888888875 568999997 7899998751 0 1 2567776654432 2236
Q ss_pred ccHHHHHHHHcCCC
Q psy3897 196 RSLKSIVSQLLHQS 209 (240)
Q Consensus 196 ~sL~~L~~~~L~~~ 209 (240)
.+|+.+|+ +||.+
T Consensus 157 ~~L~~va~-~lG~~ 169 (208)
T cd05782 157 ASLDLLAK-LLGIP 169 (208)
T ss_pred CCHHHHHH-HhCCC
Confidence 79999996 68863
No 86
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=95.48 E-value=0.21 Score=52.56 Aligned_cols=86 Identities=17% Similarity=0.208 Sum_probs=51.3
Q ss_pred CCCcEEEEEEeecCCCC-C------ccEEEEEEEE-cCCcE---EEEEEEcCC--CcccccceecCCCCHHhhccCCCCC
Q psy3897 76 NGYGVYALDTEMVYTVH-G------LEVARVTVVN-VDGRL---IYNTLVKPD--CEIIDYNTKYSGISAKDFIRNPYKT 142 (240)
Q Consensus 76 ~~~~~valD~E~tg~~~-g------~ei~~v~vv~-~~g~~---~~d~lVkP~--~~I~~~~t~~~GIt~edl~~a~~~~ 142 (240)
.+-++.+||+|+.+... | .+|+.|+.+- ..|.. ....++-+. .++. |. .+..-..
T Consensus 262 pplrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~~~~~r~vftl~~c~~i~-------g~---~V~~f~s-- 329 (1054)
T PTZ00166 262 APLRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLTKFIFTLKECASIA-------GA---NVLSFET-- 329 (1054)
T ss_pred CCcEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCccCCcceEEEecCccccCC-------Cc---eEEEeCC--
Confidence 35679999999986432 2 4799999864 34431 111111121 1222 21 1222233
Q ss_pred HHHHHHHHHhhhc--CCcEEEEEch-HHHHHHHh
Q psy3897 143 LKDVQNDLMGFVS--KDSIIVGHGL-ENDLRALK 173 (240)
Q Consensus 143 ~~ev~~~l~~~i~--~~~iLVGH~~-~~Dl~~L~ 173 (240)
-.+++..|.+++. .-.|++|||+ .||+..|-
T Consensus 330 E~eLL~~f~~~I~~~DPDII~GYNi~~FDlpYL~ 363 (1054)
T PTZ00166 330 EKELLLAWAEFVIAVDPDFLTGYNIINFDLPYLL 363 (1054)
T ss_pred HHHHHHHHHHHHHhcCCCEEEecCCcCCcHHHHH
Confidence 5777777777664 2579999997 57999864
No 87
>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases. Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Probab=94.86 E-value=0.65 Score=37.78 Aligned_cols=105 Identities=14% Similarity=0.057 Sum_probs=63.3
Q ss_pred CcEEEEEEeecCCCCC-ccEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhhc-
Q psy3897 78 YGVYALDTEMVYTVHG-LEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVS- 155 (240)
Q Consensus 78 ~~~valD~E~tg~~~g-~ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~- 155 (240)
.+.+++|+|+.+.++. .++..+++-..+ ... ||.+... + .+...+.+++.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~l~~i~l~~~~-~~~---~i~~~~~----------~--------------~~~~~l~~~l~~ 54 (178)
T cd06140 3 ADEVALYVELLGENYHTADIIGLALANGG-GAY---YIPLELA----------L--------------LDLAALKEWLED 54 (178)
T ss_pred CCceEEEEEEcCCCcceeeEEEEEEEeCC-cEE---EEeccch----------H--------------HHHHHHHHHHhC
Confidence 3578999999998863 356666665432 222 2322111 0 02233444443
Q ss_pred CCcEEEEEchHHHHHHHhcc----CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCC
Q psy3897 156 KDSIIVGHGLENDLRALKLI----HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSI 210 (240)
Q Consensus 156 ~~~iLVGH~~~~Dl~~L~~~----~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~i 210 (240)
.+...|+||+.+|+.+|... ...+.||....--........+|+.++.+||+..+
T Consensus 55 ~~~~ki~~d~K~~~~~l~~~gi~~~~~~fDt~laaYLL~p~~~~~~l~~l~~~yl~~~~ 113 (178)
T cd06140 55 EKIPKVGHDAKRAYVALKRHGIELAGVAFDTMLAAYLLDPTRSSYDLADLAKRYLGREL 113 (178)
T ss_pred CCCceeccchhHHHHHHHHCCCcCCCcchhHHHHHHHcCCCCCCCCHHHHHHHHcCCCC
Confidence 34579999999999999752 23568998643222111112589999999998764
No 88
>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=94.73 E-value=0.17 Score=45.07 Aligned_cols=87 Identities=21% Similarity=0.158 Sum_probs=52.6
Q ss_pred CCCcEEEEEEeecCCCC------CccEEEEEEEE-cC-----CcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCH
Q psy3897 76 NGYGVYALDTEMVYTVH------GLEVARVTVVN-VD-----GRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTL 143 (240)
Q Consensus 76 ~~~~~valD~E~tg~~~------g~ei~~v~vv~-~~-----g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~ 143 (240)
.+-++++||+||..... +.+|+.|+++- .. .....-++..+.. +.+ ...+...+. -
T Consensus 155 p~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~~~~~~-~~~---------~~~v~~~~~--E 222 (325)
T PF03104_consen 155 PPLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTLGSCDS-IED---------NVEVIYFDS--E 222 (325)
T ss_dssp GGSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEECSCSCC-TTC---------TTEEEEESS--H
T ss_pred cccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEecCCCC-CCC---------CcEEEEECC--H
Confidence 35689999999987652 35899999642 22 2222333333332 221 222222334 5
Q ss_pred HHHHHHHHhhhc--CCcEEEEEchH-HHHHHHhc
Q psy3897 144 KDVQNDLMGFVS--KDSIIVGHGLE-NDLRALKL 174 (240)
Q Consensus 144 ~ev~~~l~~~i~--~~~iLVGH~~~-~Dl~~L~~ 174 (240)
.+++..|.+++. .-.|++|||+. ||+..|..
T Consensus 223 ~~lL~~f~~~i~~~dPDii~GyN~~~fD~~yl~~ 256 (325)
T PF03104_consen 223 KELLEAFLDIIQEYDPDIITGYNIDGFDLPYLIE 256 (325)
T ss_dssp HHHHHHHHHHHHHHS-SEEEESSTTTTHHHHHHH
T ss_pred HHHHHHHHHHHHhcCCcEEEEecccCCCHHHHHH
Confidence 677777777664 35699999974 89999863
No 89
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=94.52 E-value=0.11 Score=45.08 Aligned_cols=128 Identities=19% Similarity=0.141 Sum_probs=74.0
Q ss_pred cEEEEEEeecCCCCC--ccEEEEEEEEc-----CCc-------EEEEEEEcCCCc--ccccceecCCCCHHhhccCCCCC
Q psy3897 79 GVYALDTEMVYTVHG--LEVARVTVVNV-----DGR-------LIYNTLVKPDCE--IIDYNTKYSGISAKDFIRNPYKT 142 (240)
Q Consensus 79 ~~valD~E~tg~~~g--~ei~~v~vv~~-----~g~-------~~~d~lVkP~~~--I~~~~t~~~GIt~edl~~a~~~~ 142 (240)
.+++|-+-|+.-..+ .||+.|+++-. ++. .-+-++++|... .++.....-......+.-.+.
T Consensus 4 ~v~sls~~T~~n~k~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~v~~~~~-- 81 (234)
T cd05776 4 TVMSLSIKTVLNSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKVRIFEN-- 81 (234)
T ss_pred EEEEEEeEEEecCcCCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCCCCCchHHHHHHhcCCcEEEeCC--
Confidence 466777777654443 68999888643 221 124566677543 222222221111122333344
Q ss_pred HHHHHHHHHhhhc--CCcEEEEEch-HHHHHHHhc-------cC----------------------------CC-eeecc
Q psy3897 143 LKDVQNDLMGFVS--KDSIIVGHGL-ENDLRALKL-------IH----------------------------SN-IIDTS 183 (240)
Q Consensus 143 ~~ev~~~l~~~i~--~~~iLVGH~~-~~Dl~~L~~-------~~----------------------------~~-~iDT~ 183 (240)
-.+.+..|.+++. .--|+||||+ .||+.+|-. .+ .+ ++|+.
T Consensus 82 E~~LL~~f~~~i~~~DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~ 161 (234)
T cd05776 82 ERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTY 161 (234)
T ss_pred HHHHHHHHHHHHhhcCCCEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCchhhccH
Confidence 5777888877774 3579999998 789999742 00 01 34555
Q ss_pred ccCcccCCCCCCccHHHHHHHHcCCC
Q psy3897 184 VLFPHSFGLPYRRSLKSIVSQLLHQS 209 (240)
Q Consensus 184 ~l~~~~~~~~~~~sL~~L~~~~L~~~ 209 (240)
...+.... ...++|.++|..+||..
T Consensus 162 ~~~k~~~~-~~sY~L~~va~~~Lg~~ 186 (234)
T cd05776 162 LSAKELIR-CKSYDLTELSQQVLGIE 186 (234)
T ss_pred HHHHHHhC-CCCCChHHHHHHHhCcC
Confidence 44443322 23689999999999964
No 90
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=94.25 E-value=0.44 Score=41.94 Aligned_cols=106 Identities=16% Similarity=0.084 Sum_probs=61.4
Q ss_pred CCcEEEEEEeecCCCCCcc-EEEEEEEEcCCcE-EEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhh
Q psy3897 77 GYGVYALDTEMVYTVHGLE-VARVTVVNVDGRL-IYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFV 154 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g~e-i~~v~vv~~~g~~-~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i 154 (240)
..++++||+||||++.... |.-+++....+.+ ..-.+.-| +|.. -..|++.|+...
T Consensus 97 ~e~~~FFDiETTGL~~ag~~I~~~g~a~~~~~~~~Vrq~~lp---------------------~p~~-E~avle~fl~~~ 154 (278)
T COG3359 97 AEDVAFFDIETTGLDRAGNTITLVGGARGVDDTMHVRQHFLP---------------------APEE-EVAVLENFLHDP 154 (278)
T ss_pred ccceEEEeeeccccCCCCCeEEEEEEEEccCceEEEEeecCC---------------------Ccch-hhHHHHHHhcCC
Confidence 4679999999999997443 4444444433322 22222222 2221 234677777777
Q ss_pred cCCcEEEEEc-hHHHHHHHhccCC---------Ceeeccc----cCcccCCCCCCccHHHHHHHHcCCC
Q psy3897 155 SKDSIIVGHG-LENDLRALKLIHS---------NIIDTSV----LFPHSFGLPYRRSLKSIVSQLLHQS 209 (240)
Q Consensus 155 ~~~~iLVGH~-~~~Dl~~L~~~~~---------~~iDT~~----l~~~~~~~~~~~sL~~L~~~~L~~~ 209 (240)
..+.||-.| ..||..++++.-. .=+|-.. |.++.. .+.+|+..-+ +||..
T Consensus 155 -~~~~lvsfNGkaFD~PfikR~v~~~~el~l~~~H~DL~h~~RRlwk~~l---~~c~Lk~VEr-~LGi~ 218 (278)
T COG3359 155 -DFNMLVSFNGKAFDIPFIKRMVRDRLELSLEFGHFDLYHPSRRLWKHLL---PRCGLKTVER-ILGIR 218 (278)
T ss_pred -CcceEEEecCcccCcHHHHHHHhcccccCccccchhhhhhhhhhhhccC---CCCChhhHHH-HhCcc
Confidence 477999988 5799999993111 1134332 222221 2457999886 79954
No 91
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=94.14 E-value=0.28 Score=48.24 Aligned_cols=128 Identities=20% Similarity=0.154 Sum_probs=80.3
Q ss_pred EEEEEeecCCCC-CccEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhhc-CCc
Q psy3897 81 YALDTEMVYTVH-GLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVS-KDS 158 (240)
Q Consensus 81 valD~E~tg~~~-g~ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~-~~~ 158 (240)
+++|+||++.++ +..++.+++...+ ... | -|.. |+ +. .-++...+..++. .+.
T Consensus 25 ~a~~~et~~l~~~~~~lvg~s~~~~~-~~~---y-i~~~---------~~---------~~--~~~~~~~l~~~l~~~~~ 79 (593)
T COG0749 25 IAFDTETDGLDPHGADLVGLSVASEE-EAA---Y-IPLL---------HG---------PE--QLNVLAALKPLLEDEGI 79 (593)
T ss_pred ceeeccccccCcccCCeeEEEeeccc-cce---e-Eeec---------cc---------hh--hhhhHHHHHHHhhCccc
Confidence 999999999986 3456666654433 111 1 1110 00 11 2226777777774 244
Q ss_pred EEEEEchHHHHHHHhccC---CCeeeccccCcccCC-CCCCccHHHHHHHHcCCCCCCC---------------------
Q psy3897 159 IIVGHGLENDLRALKLIH---SNIIDTSVLFPHSFG-LPYRRSLKSIVSQLLHQSIQSG--------------------- 213 (240)
Q Consensus 159 iLVGH~~~~Dl~~L~~~~---~~~iDT~~l~~~~~~-~~~~~sL~~L~~~~L~~~iq~~--------------------- 213 (240)
..||||+.+|+.+|...- ....||+.. ..... ......+..|++.|++......
T Consensus 80 ~kv~~~~K~d~~~l~~~Gi~~~~~~Dtmla-sYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~~~~~~~~~~~~~ 158 (593)
T COG0749 80 KKVGQNLKYDYKVLANLGIEPGVAFDTMLA-SYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQLTFADVKLEKA 158 (593)
T ss_pred chhccccchhHHHHHHcCCcccchHHHHHH-HhccCcCcCcCCHHHHHHHhcCCccchhHHhhccccccCccccchHHHH
Confidence 699999999999999855 456888853 22222 1224689999999887653211
Q ss_pred CCChHHHHHHHHHHHHHHHhh
Q psy3897 214 THDSFEDARACIDLILWKLLS 234 (240)
Q Consensus 214 ~H~A~eDA~at~~L~~~~l~~ 234 (240)
.-.+.+||.++.+|......+
T Consensus 159 ~~y~a~~a~~~~~L~~~l~~~ 179 (593)
T COG0749 159 TEYAAEDADATLRLESILEPE 179 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 123468888888887766543
No 92
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.80 E-value=0.25 Score=51.03 Aligned_cols=91 Identities=14% Similarity=0.002 Sum_probs=59.3
Q ss_pred HHHHHHHHHhhhcC-CcEEEEEchHHHHHHHhcc----CCCeeeccccCcccCCCCCCccHHHHHHHHcCCCCCC-----
Q psy3897 143 LKDVQNDLMGFVSK-DSIIVGHGLENDLRALKLI----HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQS----- 212 (240)
Q Consensus 143 ~~ev~~~l~~~i~~-~~iLVGH~~~~Dl~~L~~~----~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~----- 212 (240)
...+...|..++.. +...||||+.+|+.+|... ...+.||+...--.. +..+.+|+.++..||+.....
T Consensus 363 ~~~~~~~l~~~l~~~~~~~v~~n~K~d~~~l~~~gi~~~~~~~Dt~la~yll~-~~~~~~l~~la~~yl~~~~~~~~~~~ 441 (887)
T TIGR00593 363 TILTDDKFARWLLNEQIKKIGHDAKFLMHLLKREGIELGGVIFDTMLAAYLLD-PAQVSTLDTLARRYLVEELILDEKIG 441 (887)
T ss_pred hHHHHHHHHHHHhCCCCcEEEeeHHHHHHHHHhCCCCCCCcchhHHHHHHHcC-CCCCCCHHHHHHHHcCcccccHHHhc
Confidence 45666777777753 3458999999999999853 235689986432221 112348999999998854211
Q ss_pred -CC------------CChHHHHHHHHHHHHHHHhh
Q psy3897 213 -GT------------HDSFEDARACIDLILWKLLS 234 (240)
Q Consensus 213 -~~------------H~A~eDA~at~~L~~~~l~~ 234 (240)
.+ .-+..||.++.+|+..+..+
T Consensus 442 ~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~ 476 (887)
T TIGR00593 442 GKLAKFAFPPLEEATEYLARRAAATKRLAEELLKE 476 (887)
T ss_pred cCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 01 12567888888887755443
No 93
>PHA02528 43 DNA polymerase; Provisional
Probab=93.47 E-value=0.49 Score=48.89 Aligned_cols=92 Identities=11% Similarity=0.086 Sum_probs=53.6
Q ss_pred CCCcEEEEEEeecCCC----C---CccEEEEEEEEcCCcEEEEEEEcCC------CcccccceecCCCCHHhhccCCCCC
Q psy3897 76 NGYGVYALDTEMVYTV----H---GLEVARVTVVNVDGRLIYNTLVKPD------CEIIDYNTKYSGISAKDFIRNPYKT 142 (240)
Q Consensus 76 ~~~~~valD~E~tg~~----~---g~ei~~v~vv~~~g~~~~d~lVkP~------~~I~~~~t~~~GIt~edl~~a~~~~ 142 (240)
.+-++++||+|+.... + ..+|+.|++.+..+..++-..+... .+..+. ....++ ++.....
T Consensus 104 p~lrv~s~DIE~~~~~gfP~p~~~~d~IisIsl~~~~~~~~~v~~~~~~~~~~~~~~~~~~-~~~~~v---~~~~~~s-- 177 (881)
T PHA02528 104 SKIRIANLDIEVTAEDGFPDPEEAKYEIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPQ-EILDKV---VYMPFDT-- 177 (881)
T ss_pred CCccEEEEEEEECCCCCCCCcccCCCcEEEEEEecCCCCEEEEEEecCcccccccCCcccc-cccCCe---eEEEcCC--
Confidence 4568999999997522 1 2369999998776654333333110 110000 000011 1111233
Q ss_pred HHHHHHHHHhhhc--CCcEEEEEch-HHHHHHHh
Q psy3897 143 LKDVQNDLMGFVS--KDSIIVGHGL-ENDLRALK 173 (240)
Q Consensus 143 ~~ev~~~l~~~i~--~~~iLVGH~~-~~Dl~~L~ 173 (240)
-.+++..|.+++. .-.||+|||+ .||+..|.
T Consensus 178 E~eLL~~F~~~i~~~DPDII~GyNi~~FDlpYL~ 211 (881)
T PHA02528 178 EREMLLEYINFWEENTPVIFTGWNVELFDVPYII 211 (881)
T ss_pred HHHHHHHHHHHHHHhCCcEEEecCCccCCHHHHH
Confidence 6788888888884 2469999996 67999975
No 94
>KOG3657|consensus
Probab=92.94 E-value=0.17 Score=51.24 Aligned_cols=31 Identities=29% Similarity=0.418 Sum_probs=25.5
Q ss_pred cCCcEEEEEchHHHHHHHhccC------CCeeecccc
Q psy3897 155 SKDSIIVGHGLENDLRALKLIH------SNIIDTSVL 185 (240)
Q Consensus 155 ~~~~iLVGH~~~~Dl~~L~~~~------~~~iDT~~l 185 (240)
.++.++||||+.||..-++... .+++||+-|
T Consensus 239 ~ke~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTMSl 275 (1075)
T KOG3657|consen 239 GKEQLIVGHNVSFDRARIREEYNINGSKIRFLDTMSL 275 (1075)
T ss_pred CCCceEEeccccchHHHHHHHHhccccceeeeechhh
Confidence 3689999999999999998632 368999865
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=92.94 E-value=0.3 Score=45.52 Aligned_cols=84 Identities=21% Similarity=0.249 Sum_probs=50.9
Q ss_pred CcEEEEEEeecCCCC--------CccEEEEEEEEcCCcE-----EEEEEEcCCCcccccceecCCCCHHhhccCCCCCHH
Q psy3897 78 YGVYALDTEMVYTVH--------GLEVARVTVVNVDGRL-----IYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLK 144 (240)
Q Consensus 78 ~~~valD~E~tg~~~--------g~ei~~v~vv~~~g~~-----~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ 144 (240)
..++++|+||+.... ..+++.++.+..++.. .......|..++. |+. +..... -.
T Consensus 3 ~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~---~~~~~~--E~ 70 (471)
T smart00486 3 LKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCKEID-------GVE---VYEFNN--EK 70 (471)
T ss_pred ceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcCCCC-------CCe---EEecCC--HH
Confidence 478999999975432 3578888888753321 1222223333332 221 111123 56
Q ss_pred HHHHHHHhhhcC--CcEEEEEchH-HHHHHHh
Q psy3897 145 DVQNDLMGFVSK--DSIIVGHGLE-NDLRALK 173 (240)
Q Consensus 145 ev~~~l~~~i~~--~~iLVGH~~~-~Dl~~L~ 173 (240)
+.+..|.+++.. ..+++|||.. ||+.+|.
T Consensus 71 ~lL~~f~~~i~~~dpdii~g~N~~~FD~~~i~ 102 (471)
T smart00486 71 ELLKAFLEFIKKYDPDIIYGHNISNFDLPYII 102 (471)
T ss_pred HHHHHHHHHHHHhCCCEEEeecCCCCCHHHHH
Confidence 777777777742 3599999985 8999975
No 96
>KOG0304|consensus
Probab=92.92 E-value=0.33 Score=41.94 Aligned_cols=105 Identities=16% Similarity=0.154 Sum_probs=74.1
Q ss_pred ecCCCCHHhhccCCCCCHHHHHHHHH---hhhcCCcEEEEEchHHHHHHHhc--------------------cCCCeeec
Q psy3897 126 KYSGISAKDFIRNPYKTLKDVQNDLM---GFVSKDSIIVGHGLENDLRALKL--------------------IHSNIIDT 182 (240)
Q Consensus 126 ~~~GIt~edl~~a~~~~~~ev~~~l~---~~i~~~~iLVGH~~~~Dl~~L~~--------------------~~~~~iDT 182 (240)
+-+||.-+..+..+.. ..+..+.+. -.++++-.+|-.+..+|+..|=. ..+.+-|+
T Consensus 109 r~~Gidf~K~~e~GI~-~~~F~ellm~sg~v~~~~V~WvTFhs~YDfgYLlK~Lt~~~LP~~~~eF~~~v~~~fp~vYDi 187 (239)
T KOG0304|consen 109 RRSGIDFEKHREEGID-IEEFAELLMTSGLVLDENVTWVTFHSGYDFGYLLKILTGKPLPETEEEFFEIVRQLFPFVYDV 187 (239)
T ss_pred HHcCcCHHHHHHcCCC-HHHHHHHHHHhhhhccCceEEEEeeccchHHHHHHHHcCCCCcchHHHHHHHHHHHcchhhhH
Confidence 5688888887777664 443333332 34455777888777899988643 12456677
Q ss_pred cccCcccCCCCCCccHHHHHHHHcCCCCCCCCCChHHHHHHHHHHHHHHH
Q psy3897 183 SVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARACIDLILWKL 232 (240)
Q Consensus 183 ~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~~H~A~eDA~at~~L~~~~l 232 (240)
-.+...+.+...+.+|+.+|. .|+.+-.+..|.|-+|+..|+..|.+..
T Consensus 188 K~l~~~c~~~~l~~GL~~lA~-~L~~~RvG~~HqAGSDSlLT~~~F~kl~ 236 (239)
T KOG0304|consen 188 KYLMKFCEGLSLKGGLQRLAD-LLGLKRVGIAHQAGSDSLLTARVFFKLK 236 (239)
T ss_pred HHHHHhhhhhhhhcCHHHHHH-HhCCCeeecccccCcHHHHHHHHHHHHH
Confidence 777666655445679999997 5996665558999999999999988654
No 97
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=92.41 E-value=1.6 Score=36.33 Aligned_cols=58 Identities=24% Similarity=0.282 Sum_probs=39.1
Q ss_pred HHhhhc-CCcEEEEEchHHHHHHHh-cc---CCCeeeccccCcccCCCCCCccHHHHHHHHcCCC
Q psy3897 150 LMGFVS-KDSIIVGHGLENDLRALK-LI---HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQS 209 (240)
Q Consensus 150 l~~~i~-~~~iLVGH~~~~Dl~~L~-~~---~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~ 209 (240)
|.+++. .+...|||++..|+..|+ .. ...++||+...--. ++. +.+|+.|++.||+..
T Consensus 69 L~~~L~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~fD~~laaYLL-~p~-~~~l~~l~~~yl~~~ 131 (192)
T cd06147 69 LNEVFTDPNILKVFHGADSDIIWLQRDFGLYVVNLFDTGQAARVL-NLP-RHSLAYLLQKYCNVD 131 (192)
T ss_pred HHHHhcCCCceEEEechHHHHHHHHHHhCCCcCchHHHHHHHHHh-CCC-cccHHHHHHHHhCCC
Confidence 445553 346789999999999997 31 12238998644332 222 248999999998765
No 98
>KOG1798|consensus
Probab=91.95 E-value=2 Score=46.42 Aligned_cols=150 Identities=19% Similarity=0.157 Sum_probs=84.9
Q ss_pred CCCcEEEEEEeecCCCCC------ccEEEEEE-EEcCCcEEEEEEE-cCCC------cccccceecCCCCHHhhccCCCC
Q psy3897 76 NGYGVYALDTEMVYTVHG------LEVARVTV-VNVDGRLIYNTLV-KPDC------EIIDYNTKYSGISAKDFIRNPYK 141 (240)
Q Consensus 76 ~~~~~valD~E~tg~~~g------~ei~~v~v-v~~~g~~~~d~lV-kP~~------~I~~~~t~~~GIt~edl~~a~~~ 141 (240)
....+.|||+|||-+.-. ++|.=|+. ||+.|-.+.+.=| --+. |=++|.-.|. +-+.+.
T Consensus 244 adp~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREiVs~DIedfEYTPKpE~eG~F~------v~Ne~d- 316 (2173)
T KOG1798|consen 244 ADPRVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREIVSEDIEDFEYTPKPEYEGPFC------VFNEPD- 316 (2173)
T ss_pred CCceEEEEeeecccCCCCCCCcccceEEEEEEEecCceEEEechhhhccchhhcccCCccccccceE------EecCCc-
Confidence 456899999999986532 25666664 5677765533211 1100 0011111110 112233
Q ss_pred CHHHHHHHHHhhhc--CCcEEEEEchH-HHHHHHhc---cCC-------------------CeeeccccCcccC---CCC
Q psy3897 142 TLKDVQNDLMGFVS--KDSIIVGHGLE-NDLRALKL---IHS-------------------NIIDTSVLFPHSF---GLP 193 (240)
Q Consensus 142 ~~~ev~~~l~~~i~--~~~iLVGH~~~-~Dl~~L~~---~~~-------------------~~iDT~~l~~~~~---~~~ 193 (240)
-..+++.+.+.+. +-+|+|-+|.. ||+.|+.. +|. ++..-+.-|+... .+|
T Consensus 317 -Ev~Ll~RfFeHiq~~kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrWVKRDSYLP 395 (2173)
T KOG1798|consen 317 -EVGLLQRFFEHIQEVKPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRWVKRDSYLP 395 (2173)
T ss_pred -HHHHHHHHHHHHHhcCCcEEEEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehhhhhhhhhcccCC
Confidence 3456666666654 46899999875 59999864 121 1222233343321 222
Q ss_pred -CCccHHHHHHHHcCCCCCC-C---------------CCChHHHHHHHHHHHHHHHh
Q psy3897 194 -YRRSLKSIVSQLLHQSIQS-G---------------THDSFEDARACIDLILWKLL 233 (240)
Q Consensus 194 -~~~sL~~L~~~~L~~~iq~-~---------------~H~A~eDA~at~~L~~~~l~ 233 (240)
...+|+..++..||.+--. + +-=|.+||.||.-||++.+.
T Consensus 396 qGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVh 452 (2173)
T KOG1798|consen 396 QGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVH 452 (2173)
T ss_pred CcccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhh
Confidence 2468999999889966211 0 45678999999999887654
No 99
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=88.64 E-value=0.89 Score=35.50 Aligned_cols=60 Identities=20% Similarity=0.179 Sum_probs=40.2
Q ss_pred HHhhhc-CCcEEEEEchHHHHHHHhcc----CCCeeeccccCcccCCCCCCccHHHHHHHHcCCC
Q psy3897 150 LMGFVS-KDSIIVGHGLENDLRALKLI----HSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQS 209 (240)
Q Consensus 150 l~~~i~-~~~iLVGH~~~~Dl~~L~~~----~~~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~ 209 (240)
|.+++. .+...|||++..|+..|+.. ...+.||+...--......+.+|+.|+++||+..
T Consensus 45 l~~~l~~~~~~kv~~d~K~~~~~L~~~~~~~~~~~~D~~laayLl~p~~~~~~l~~l~~~~l~~~ 109 (150)
T cd09018 45 LKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAFDTMLEAYILNSVAGRWDMDSLVERWLGHK 109 (150)
T ss_pred HHHHhcCCCCceeeecHHHHHHHHHHcCCccCCcchhHHHHHHHhCCCCCCCCHHHHHHHHhCCC
Confidence 334443 35668999999999999752 3457899865332221110248999999998876
No 100
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=88.09 E-value=7.4 Score=39.90 Aligned_cols=119 Identities=18% Similarity=0.076 Sum_probs=67.0
Q ss_pred CCCcEEEEEEeecCCCCC------ccEEEEEEEEc-CCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHH
Q psy3897 76 NGYGVYALDTEMVYTVHG------LEVARVTVVNV-DGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQN 148 (240)
Q Consensus 76 ~~~~~valD~E~tg~~~g------~ei~~v~vv~~-~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~ 148 (240)
...++++||+|+...... ..+..|+.... .+... .+ ...+...|.. +..... -.+++.
T Consensus 152 p~l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~-----~~-----~~~~~~~~~~---v~~~~~--e~e~l~ 216 (792)
T COG0417 152 PPLRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLI-----EV-----FIYTSGEGFS---VEVVIS--EAELLE 216 (792)
T ss_pred CCceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCcc-----cc-----ccccCCCCce---eEEecC--HHHHHH
Confidence 356789999999875533 24566665553 22211 10 0011111111 333334 567777
Q ss_pred HHHhhhc--CCcEEEEEchH-HHHHHHhcc------C---------------------C-CeeeccccCcccCCCCCCcc
Q psy3897 149 DLMGFVS--KDSIIVGHGLE-NDLRALKLI------H---------------------S-NIIDTSVLFPHSFGLPYRRS 197 (240)
Q Consensus 149 ~l~~~i~--~~~iLVGH~~~-~Dl~~L~~~------~---------------------~-~~iDT~~l~~~~~~~~~~~s 197 (240)
.|..++. ...|+||||.. ||+..|..- + . -.+|...++.........++
T Consensus 217 ~~~~~i~~~dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~~~~~~~~~~ys 296 (792)
T COG0417 217 RFVELIREYDPDVIVGYNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPALRRRPLNLKSYS 296 (792)
T ss_pred HHHHHHHhcCCCEEEeccCCcCChHHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHHHhhhhccccccc
Confidence 7777663 36799999987 899998641 0 0 13555554442111223579
Q ss_pred HHHHHHHHcCCC
Q psy3897 198 LKSIVSQLLHQS 209 (240)
Q Consensus 198 L~~L~~~~L~~~ 209 (240)
|+..+..+|+..
T Consensus 297 l~~v~~~~l~~~ 308 (792)
T COG0417 297 LEAVSEALLGEG 308 (792)
T ss_pred HHHHHHHhcccc
Confidence 999998877744
No 101
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=86.99 E-value=7.3 Score=41.72 Aligned_cols=127 Identities=15% Similarity=0.127 Sum_probs=70.8
Q ss_pred cEEEEEEeecCCCCC-ccEEEEEEEEc-C-------Cc----EEEEEEEcCCC-ccc-ccceecCCCCHHhhccCCCCCH
Q psy3897 79 GVYALDTEMVYTVHG-LEVARVTVVNV-D-------GR----LIYNTLVKPDC-EII-DYNTKYSGISAKDFIRNPYKTL 143 (240)
Q Consensus 79 ~~valD~E~tg~~~g-~ei~~v~vv~~-~-------g~----~~~d~lVkP~~-~I~-~~~t~~~GIt~edl~~a~~~~~ 143 (240)
.++.|++|+.+.+.- .+++.++.+-. + +. ..+...++|.. ..| ++....-|+.+..|..-.. -
T Consensus 507 ~vLdFsi~SlyPsi~~~~nl~iS~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~L~~~~s--E 584 (1172)
T TIGR00592 507 VVLDFSMKSLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKDCSFPLDLKGEFPGKKPSLVEDLAT--E 584 (1172)
T ss_pred EEEEeeeEEecCccccCceEEEEEEEeecccccCCCCCCccceEEEEEEccCCCCCCchhhhhhhccCCcEEEEecC--H
Confidence 445556556655432 46777665432 2 11 12334445522 111 1222344555555555555 5
Q ss_pred HHHHHHHHhhhc--CCcEEEEEch-HHHHHHHhc-----------------------------cCCC-eeeccccCcccC
Q psy3897 144 KDVQNDLMGFVS--KDSIIVGHGL-ENDLRALKL-----------------------------IHSN-IIDTSVLFPHSF 190 (240)
Q Consensus 144 ~ev~~~l~~~i~--~~~iLVGH~~-~~Dl~~L~~-----------------------------~~~~-~iDT~~l~~~~~ 190 (240)
.+.+..+++++. ...+++|||+ .||+++|-. +..+ ++|+...++...
T Consensus 585 r~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~~~~k~~~ 664 (1172)
T TIGR00592 585 RALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVEISAKELI 664 (1172)
T ss_pred HHHHHHHHHHHHhcCCCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccCCCccccccceECCEEEEEHHHHHHHHh
Confidence 667777777775 5789999996 679988643 0111 356655544332
Q ss_pred CCCCCccHHHHHHHHcCC
Q psy3897 191 GLPYRRSLKSIVSQLLHQ 208 (240)
Q Consensus 191 ~~~~~~sL~~L~~~~L~~ 208 (240)
. ...++|..++..+||.
T Consensus 665 ~-~~sy~L~~v~~~~L~~ 681 (1172)
T TIGR00592 665 R-CKSYDLSELVQQILKT 681 (1172)
T ss_pred C-cCCCCHHHHHHHHhCC
Confidence 2 2368999999999984
No 102
>PRK05761 DNA polymerase I; Reviewed
Probab=86.02 E-value=7.1 Score=40.04 Aligned_cols=86 Identities=21% Similarity=0.203 Sum_probs=55.7
Q ss_pred HHHHHHHHHhhhcCCcEEEEEch-HHHHHHHhcc------CC----------C-eeeccccCccc-------CCC-C-CC
Q psy3897 143 LKDVQNDLMGFVSKDSIIVGHGL-ENDLRALKLI------HS----------N-IIDTSVLFPHS-------FGL-P-YR 195 (240)
Q Consensus 143 ~~ev~~~l~~~i~~~~iLVGH~~-~~Dl~~L~~~------~~----------~-~iDT~~l~~~~-------~~~-~-~~ 195 (240)
-.+++..|.+++....+.|++|. .||+..|..- .. . .+|....|... .+. . ..
T Consensus 210 E~eLL~~f~~~i~~~dPdi~yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~~~~~y~~~~~~~~~~ 289 (787)
T PRK05761 210 EKELLAELFDIILEYPPVVTFNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNKAVRSYAFYGKYRHRE 289 (787)
T ss_pred HHHHHHHHHHHHHhcCCEEEEcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheeecceeeeeccceeeccc
Confidence 78899999999987788888886 5799998641 00 1 15554443221 010 0 14
Q ss_pred ccHHHHHHHHcCCCCCC-------C-----CCChHHHHHHHHHHH
Q psy3897 196 RSLKSIVSQLLHQSIQS-------G-----THDSFEDARACIDLI 228 (240)
Q Consensus 196 ~sL~~L~~~~L~~~iq~-------~-----~H~A~eDA~at~~L~ 228 (240)
++|...++.+||..-.. . +.=++.||..+++|+
T Consensus 290 ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 290 ARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred CChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 68999999899954210 0 122578999999985
No 103
>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=85.30 E-value=15 Score=35.10 Aligned_cols=66 Identities=20% Similarity=0.201 Sum_probs=39.9
Q ss_pred HHHHHHHHhhhc--CCcEEEEEchHHHHHHHhccC--------------CCeeeccccCccc-CCCCCCccHHHHHHHHc
Q psy3897 144 KDVQNDLMGFVS--KDSIIVGHGLENDLRALKLIH--------------SNIIDTSVLFPHS-FGLPYRRSLKSIVSQLL 206 (240)
Q Consensus 144 ~ev~~~l~~~i~--~~~iLVGH~~~~Dl~~L~~~~--------------~~~iDT~~l~~~~-~~~~~~~sL~~L~~~~L 206 (240)
.+++.+|.+++. ++..++.+| .+...+|+... .+++|...+.+.. ..+..++|||.++. ++
T Consensus 329 ~~~~~~f~~~l~~~~~~~i~hY~-~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~sysLK~v~~-~l 406 (457)
T TIGR03491 329 ELAWQQFLQLLQSYPDAPIYHYG-ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIESYSLKSIAR-WL 406 (457)
T ss_pred HHHHHHHHHHHHHCCCCeEEeeC-HHHHHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCCCCCHHHHHH-Hh
Confidence 345555555553 466788888 88888887631 1456765433221 11223589999996 68
Q ss_pred CCCCC
Q psy3897 207 HQSIQ 211 (240)
Q Consensus 207 ~~~iq 211 (240)
|....
T Consensus 407 g~~~~ 411 (457)
T TIGR03491 407 GFEWR 411 (457)
T ss_pred CcccC
Confidence 86544
No 104
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=83.21 E-value=4.4 Score=39.32 Aligned_cols=91 Identities=11% Similarity=0.184 Sum_probs=52.5
Q ss_pred CCcEEEEEEeecCCC-CC-----ccEEEEEEEEcC-CcE---EEEEE--EcC---CCcccccceecCCCCHHhhccCCCC
Q psy3897 77 GYGVYALDTEMVYTV-HG-----LEVARVTVVNVD-GRL---IYNTL--VKP---DCEIIDYNTKYSGISAKDFIRNPYK 141 (240)
Q Consensus 77 ~~~~valD~E~tg~~-~g-----~ei~~v~vv~~~-g~~---~~d~l--VkP---~~~I~~~~t~~~GIt~edl~~a~~~ 141 (240)
.-+++.||+|.+... +. .+|..|+..|.. +.. +|+.+ +.+ ...+....+ +-|+ .+..-+.
T Consensus 105 ~i~~~~~DIEv~~~~fp~~~~a~~~i~~i~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~v---~v~~f~s- 179 (498)
T PHA02524 105 DVVIDVVDIEVTAPEFPEPKYAKYEIDMISHVRLHNGKKTYYIFDLVKDVGHWDPKKSVLEKYI-LDNV---VYMPFED- 179 (498)
T ss_pred hceEEEEEEEecCCCCCChhhcCCceEEEEeeecccCCccEEEEeccccccCCCcccccccccc-cCCe---EEEEeCC-
Confidence 457899999997532 11 278889988853 322 34333 211 111111111 1111 1112233
Q ss_pred CHHHHHHHHHhhhcC--CcEEEEEch-HHHHHHHh
Q psy3897 142 TLKDVQNDLMGFVSK--DSIIVGHGL-ENDLRALK 173 (240)
Q Consensus 142 ~~~ev~~~l~~~i~~--~~iLVGH~~-~~Dl~~L~ 173 (240)
-.+++.++.+++.. -.|++|||+ .||+..|.
T Consensus 180 -E~eLL~~F~~~i~~~DPDIItGYNi~nFDlPYL~ 213 (498)
T PHA02524 180 -EVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYII 213 (498)
T ss_pred -HHHHHHHHHHHHHHhCCCEEEeCCCcccCHHHHH
Confidence 67889999998862 489999996 67998864
No 105
>PF00843 Arena_nucleocap: Arenavirus nucleocapsid protein; InterPro: IPR000229 Arenaviruses are single stranded RNA viruses. The arenavirus S RNAs that have been characterised include conserved terminal sequences, an ambisense arrangement of the coding regions for the precursor glycoprotein (GPC) and nucleocapsid (N) proteins and an intergenic region capable of forming a base-paired "hairpin" structure. The mature glycoproteins that result are G1 and G2 and the N protein []. This family represents the nucleocapsid protein that encapsulates the viral ssRNA [].; GO: 0019013 viral nucleocapsid; PDB: 3MX5_A 3MX2_C 3MWT_C 3Q7C_A 3MWP_B 3Q7B_A 3T5Q_E 3T5N_A 3R3L_B.
Probab=81.51 E-value=1.9 Score=40.91 Aligned_cols=134 Identities=13% Similarity=0.190 Sum_probs=78.2
Q ss_pred CCcEEEEEEeecCCCCCccEEEEEEEEcCCcEEEEEEEcCCC--cccccceecCCCCHHhhccCCCCCHHHHHHHHHhhh
Q psy3897 77 GYGVYALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDC--EIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFV 154 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g~ei~~v~vv~~~g~~~~d~lVkP~~--~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i 154 (240)
+..-..||+| .+-.+.+++++.-.+..-..+.|-+|.. ...+....-|||--.||.++.+- +...+...+
T Consensus 371 p~~ttWiDIE----G~p~DPVElAiyQP~sg~YiHcyR~P~D~K~FK~~SKysHGillkDl~~aqPG----L~S~vi~~L 442 (533)
T PF00843_consen 371 PNATTWIDIE----GPPNDPVELAIYQPSSGNYIHCYREPHDEKQFKNQSKYSHGILLKDLENAQPG----LTSAVIELL 442 (533)
T ss_dssp TTS-EEEEEE----SETTSESEEEEEETTTTEEEEEE---S-HHHHHHHHHHTT-B-GGGCTTB-TT----HHHHHHHHS
T ss_pred CCCCeeEecC----CCCCCCeEEEEeccCCCcEEEEecCCcchhhhcccccccccccHHHHhhhccc----hHHHHHHhC
Confidence 3456899999 4445789999999766666788888965 56666778899999999988663 577788888
Q ss_pred cCCcEEEEEchHHHHHHHhccCC----Ceeeccc------cCcccCCCCCCccHHHHHHHHcCCCCCC----------CC
Q psy3897 155 SKDSIIVGHGLENDLRALKLIHS----NIIDTSV------LFPHSFGLPYRRSLKSIVSQLLHQSIQS----------GT 214 (240)
Q Consensus 155 ~~~~iLVGH~~~~Dl~~L~~~~~----~~iDT~~------l~~~~~~~~~~~sL~~L~~~~L~~~iq~----------~~ 214 (240)
..+-||-+.+ .-|++-|=..|. ++||... .|..... -....||..+-|+.+.. ++
T Consensus 443 P~~MVlT~QG-sDDIrkLld~hGRrDiKlvDV~lt~eqaR~FEd~VW----d~f~~LC~~H~GvVv~KKKkg~~~~~t~P 517 (533)
T PF00843_consen 443 PKNMVLTCQG-SDDIRKLLDMHGRRDIKLVDVKLTSEQARKFEDQVW----DRFGHLCKKHTGVVVKKKKKGKKPESTNP 517 (533)
T ss_dssp -TT-EEEESS-HHHHHHHHHCTT-TTSEEEE----HHHHTTTHHHHH----HHHGGG---B-S-EEE--SSSS-EEE---
T ss_pred CcCcEEEeeC-hHHHHHHHHhcCCCcceEEEeecCHHHHHHHHHHHH----HHHHHHHHhcCceEEecccCCCCCCCCCc
Confidence 6566666666 678877766664 5899852 3433211 24667887777765532 27
Q ss_pred CChHHHHHH
Q psy3897 215 HDSFEDARA 223 (240)
Q Consensus 215 H~A~eDA~a 223 (240)
|.|+=|+..
T Consensus 518 HCALlDCiM 526 (533)
T PF00843_consen 518 HCALLDCIM 526 (533)
T ss_dssp --HHHHHHH
T ss_pred hHHHHHHHH
Confidence 999999873
No 106
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
Probab=74.89 E-value=6.3 Score=31.03 Aligned_cols=59 Identities=17% Similarity=0.155 Sum_probs=38.1
Q ss_pred HHhhhc-CCcEEEEEchHHHHHHHhcc----CCCeeeccccCcccCCCCCC-ccHHHHHHHHcCCC
Q psy3897 150 LMGFVS-KDSIIVGHGLENDLRALKLI----HSNIIDTSVLFPHSFGLPYR-RSLKSIVSQLLHQS 209 (240)
Q Consensus 150 l~~~i~-~~~iLVGH~~~~Dl~~L~~~----~~~~iDT~~l~~~~~~~~~~-~sL~~L~~~~L~~~ 209 (240)
|.+++. .+...|+|++.+++.+|+.. ...+.||+...=-. .+..+ .+|+.|+++||+..
T Consensus 45 l~~~l~~~~~~ki~~d~K~~~~~l~~~gi~l~~~~fD~~LAaYLL-~p~~~~~~l~~la~~yl~~~ 109 (151)
T cd06128 45 LKPLLEDEKALKVGQNLKYDRVILANYGIELRGIAFDTMLEAYLL-DPVAGRHDMDSLAERWLKEK 109 (151)
T ss_pred HHHHHcCCCCCEEeeehHHHHHHHHHCCCCCCCcchhHHHHHHHc-CCCCCCCCHHHHHHHHcCCC
Confidence 344453 23558999999999999652 33468998532111 12111 38999999998866
No 107
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=59.29 E-value=12 Score=32.15 Aligned_cols=60 Identities=15% Similarity=0.290 Sum_probs=42.6
Q ss_pred cEEEEEEEEc---CCc-EEEEEEEcCCCcccccc-------eecCCCCHHhhccCCCCCHHHHHHHHHhhhc
Q psy3897 95 EVARVTVVNV---DGR-LIYNTLVKPDCEIIDYN-------TKYSGISAKDFIRNPYKTLKDVQNDLMGFVS 155 (240)
Q Consensus 95 ei~~v~vv~~---~g~-~~~d~lVkP~~~I~~~~-------t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~ 155 (240)
-+++++++.+ +|. ..|+++|+|+.....+. ..-|+|...-....... +..+..+|.+||.
T Consensus 9 ~PaEiai~~fSL~~GI~~~~H~~I~Pg~~p~G~~~~a~~hs~~tH~ip~~~~~~~~~d-~~~l~~~l~~fl~ 79 (213)
T PF13017_consen 9 VPAEIAICKFSLKEGIIDSFHTFINPGQIPLGYRYDAQHHSDETHQIPIPPNALGESD-YSELYNELLNFLK 79 (213)
T ss_pred EeEEEEEEEEecCCccchhhhcccCCCCCCcHHHHHHHHhhhhhcCCCCCCcccccCC-HHHHHHHHHHHhh
Confidence 4788898885 553 34999999986444433 24577776645545544 8999999999996
No 108
>KOG0969|consensus
Probab=54.64 E-value=8.4 Score=39.29 Aligned_cols=86 Identities=21% Similarity=0.244 Sum_probs=47.7
Q ss_pred CCcEEEEEEeecCCCCCc------cEEEEEE-EEcCC--cEE-EEEEE-cCCCcccccceecCCCCHHhhccCCCCCHHH
Q psy3897 77 GYGVYALDTEMVYTVHGL------EVARVTV-VNVDG--RLI-YNTLV-KPDCEIIDYNTKYSGISAKDFIRNPYKTLKD 145 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g~------ei~~v~v-v~~~g--~~~-~d~lV-kP~~~I~~~~t~~~GIt~edl~~a~~~~~~e 145 (240)
+-++..||+|++|-.+.. .+++|+= |...| ... -+.|. +|-.||+.-+. ++-+++++ +-+
T Consensus 273 PlrvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~Ge~~pf~rnvf~l~~capI~G~~V-~~~~~e~e--------lL~ 343 (1066)
T KOG0969|consen 273 PLRVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQGENEPFVRNVFTLKTCAPIVGSNV-HSYETEKE--------LLE 343 (1066)
T ss_pred cccccceeEEeccCCCCCCccccChHHHHHHHHHHhcCCchHHHhhhcccCcCCCCCcee-EEeccHHH--------HHH
Confidence 457899999999977653 2455442 22233 221 23332 34445554222 22233332 334
Q ss_pred HHHHHHhhhcCCcEEEEEch-HHHHHHH
Q psy3897 146 VQNDLMGFVSKDSIIVGHGL-ENDLRAL 172 (240)
Q Consensus 146 v~~~l~~~i~~~~iLVGH~~-~~Dl~~L 172 (240)
.+..|..-++ -.|++|+|+ .||+..|
T Consensus 344 ~W~~firevD-PDvI~GYNi~nFDiPYl 370 (1066)
T KOG0969|consen 344 SWRKFIREVD-PDVIIGYNICNFDIPYL 370 (1066)
T ss_pred HHHHHHHhcC-CCeEeccccccccccee
Confidence 4556666665 679999997 5687654
No 109
>PHA02563 DNA polymerase; Provisional
Probab=37.42 E-value=90 Score=31.37 Aligned_cols=19 Identities=26% Similarity=0.169 Sum_probs=16.2
Q ss_pred CCcEEEEEchHHHHHHHhc
Q psy3897 156 KDSIIVGHGLENDLRALKL 174 (240)
Q Consensus 156 ~~~iLVGH~~~~Dl~~L~~ 174 (240)
.+.++.-||+.||..||-.
T Consensus 65 ~~~~vYfHN~~FD~~Fil~ 83 (630)
T PHA02563 65 TECIIYFHNLKFDGSFILK 83 (630)
T ss_pred cceEEEEecCCccHHHHHH
Confidence 3779999999999999764
No 110
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=32.44 E-value=51 Score=28.86 Aligned_cols=150 Identities=21% Similarity=0.251 Sum_probs=83.2
Q ss_pred CCCcEEEEEEeecCCCC---C-------------------ccEEEEEE--EEcCCcE-------EEEEEEcCCCccccc-
Q psy3897 76 NGYGVYALDTEMVYTVH---G-------------------LEVARVTV--VNVDGRL-------IYNTLVKPDCEIIDY- 123 (240)
Q Consensus 76 ~~~~~valD~E~tg~~~---g-------------------~ei~~v~v--v~~~g~~-------~~d~lVkP~~~I~~~- 123 (240)
+.+++|.+|+|..|+-. | ..|+++++ -|.+|+. .|+.-..|...+-..
T Consensus 40 ~rYn~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQlGlsLSDe~GN~P~~~sTWQFNF~F~l~~dmya~E 119 (299)
T COG5228 40 SRYNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDENGNKPNGPSTWQFNFEFDLKKDMYATE 119 (299)
T ss_pred HhCCceeeccccCceeecccccccccchHHHHHHhcccchhhhhheeeeeccccCCCCCCCceeEEEEEecchhhhcchH
Confidence 46788999999988642 1 03555554 3455542 155555665433211
Q ss_pred ---ceecCCCCHHhhccCCCCCHHHHHHHHHh---hhcCCcEEEEEchHHHHHHHhcc------CCCeee----ccccCc
Q psy3897 124 ---NTKYSGISAKDFIRNPYKTLKDVQNDLMG---FVSKDSIIVGHGLENDLRALKLI------HSNIID----TSVLFP 187 (240)
Q Consensus 124 ---~t~~~GIt~edl~~a~~~~~~ev~~~l~~---~i~~~~iLVGH~~~~Dl~~L~~~------~~~~iD----T~~l~~ 187 (240)
..+-+||.-+.=++.+.. ..|..+.|.. .++++.+.|-.+..+|+..|=.+ +.+.=| ...+||
T Consensus 120 SieLL~ksgIdFkkHe~~GI~-v~eF~elLm~SGLvm~e~VtWitfHsaYDfgyLikilt~~plP~~~EdFy~~l~~yfP 198 (299)
T COG5228 120 SIELLRKSGIDFKKHENLGID-VFEFSELLMDSGLVMDESVTWITFHSAYDFGYLIKILTNDPLPNNKEDFYWWLHQYFP 198 (299)
T ss_pred HHHHHHHcCCChhhHhhcCCC-HHHHHHHHhccCceeccceEEEEeecchhHHHHHHHHhcCCCCccHHHHHHHHHHHCc
Confidence 234577776666655554 3443333332 34567888888889999987542 111111 112344
Q ss_pred ccCC--------CCCCccHHHHHHHHcCCCCCCC--CCChHHHHHHHHHHHH
Q psy3897 188 HSFG--------LPYRRSLKSIVSQLLHQSIQSG--THDSFEDARACIDLIL 229 (240)
Q Consensus 188 ~~~~--------~~~~~sL~~L~~~~L~~~iq~~--~H~A~eDA~at~~L~~ 229 (240)
.... ...+..|+..+.. |+ ++.. .|.|-.||..|++.|.
T Consensus 199 ~fYDik~v~ks~~~~~KglQei~nd-lq--l~r~g~QhQagsdaLlTa~~ff 247 (299)
T COG5228 199 NFYDIKLVYKSVLNNSKGLQEIKND-LQ--LQRSGQQHQAGSDALLTADEFF 247 (299)
T ss_pred cccchHHHHHhhhhhhhHHHHhcCc-Hh--hhccchhhhccchhhhhhHHhc
Confidence 3311 1112356666543 44 3332 6999999999998765
No 111
>PF06821 Ser_hydrolase: Serine hydrolase; InterPro: IPR010662 This family contains a number of hypothetical bacterial proteins of unknown function, which may be cytosolic. The Crystal Structure Of The Yden Gene Product Swiss:P96671 from B. Subtilis has been solved. The structure shows an alpha-beta hydrolase fold suggesting an enzymatic function for these proteins [].; GO: 0016787 hydrolase activity; PDB: 3BDV_B 2QS9_A 1UXO_A.
Probab=27.95 E-value=66 Score=26.37 Aligned_cols=33 Identities=33% Similarity=0.432 Sum_probs=21.2
Q ss_pred CCCCCHHHHHHHHHhhh---cCCcEEEEEchHH--HHHHH
Q psy3897 138 NPYKTLKDVQNDLMGFV---SKDSIIVGHGLEN--DLRAL 172 (240)
Q Consensus 138 a~~~~~~ev~~~l~~~i---~~~~iLVGH~~~~--Dl~~L 172 (240)
.|. +++-...|.+.+ +++++||||++.- =++.|
T Consensus 36 ~P~--~~~W~~~l~~~i~~~~~~~ilVaHSLGc~~~l~~l 73 (171)
T PF06821_consen 36 NPD--LDEWVQALDQAIDAIDEPTILVAHSLGCLTALRWL 73 (171)
T ss_dssp S----HHHHHHHHHHCCHC-TTTEEEEEETHHHHHHHHHH
T ss_pred CCC--HHHHHHHHHHHHhhcCCCeEEEEeCHHHHHHHHHH
Confidence 454 666666666654 4678999999754 45555
No 112
>KOG0970|consensus
Probab=27.75 E-value=1.4e+02 Score=32.13 Aligned_cols=88 Identities=14% Similarity=0.217 Sum_probs=48.8
Q ss_pred CcEEEEEEeecCCCC--CccEEEEEEEEcC--------Cc----EEEEEEEcCCCcccccc------eecCCCCHHhhcc
Q psy3897 78 YGVYALDTEMVYTVH--GLEVARVTVVNVD--------GR----LIYNTLVKPDCEIIDYN------TKYSGISAKDFIR 137 (240)
Q Consensus 78 ~~~valD~E~tg~~~--g~ei~~v~vv~~~--------g~----~~~d~lVkP~~~I~~~~------t~~~GIt~edl~~ 137 (240)
-.+.+|-++|.--.. ..||+.|++.-+. +. .-+..+++|...+-++- .+.+++. -
T Consensus 529 l~llsL~i~T~~N~k~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~~~fP~g~~ela~~k~~~v~-----~ 603 (1429)
T KOG0970|consen 529 LTLLSLNIRTSMNPKQNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPGTSFPLGLKELAKQKLSKVV-----L 603 (1429)
T ss_pred eeEEEeeeeehhccccchhhhhhhhhhhcccccccCCCCCCcccCcceeEecCCCCcCCchHHHHHHhccCceE-----E
Confidence 345667777654332 2478777765321 11 12778889877555541 1222211 1
Q ss_pred CCCCCHHHHHHHHHhhhc--CCcEEEEEc-hHHHHHHH
Q psy3897 138 NPYKTLKDVQNDLMGFVS--KDSIIVGHG-LENDLRAL 172 (240)
Q Consensus 138 a~~~~~~ev~~~l~~~i~--~~~iLVGH~-~~~Dl~~L 172 (240)
... -...+..|+..++ +-.++|||| ..++|.+|
T Consensus 604 ~~s--ErALLs~fla~~~~~dpD~iVgHn~~~~~l~VL 639 (1429)
T KOG0970|consen 604 HNS--ERALLSHFLAMLNKEDPDVIVGHNIQGFYLDVL 639 (1429)
T ss_pred ecC--HHHHHHHHHHHhhccCCCEEEEeccccchHHHH
Confidence 111 2344555554443 367999999 68888887
No 113
>PF07819 PGAP1: PGAP1-like protein; InterPro: IPR012908 The sequences found in this family are similar to PGAP1 (Q765A7 from SWISSPROT). This is an endoplasmic reticulum membrane protein with a catalytic serine-containing motif that is conserved in a number of lipases. PGAP1 functions as a GPI inositol-deacylase; this deacylation is important for the efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi body [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006505 GPI anchor metabolic process, 0006886 intracellular protein transport, 0031227 intrinsic to endoplasmic reticulum membrane
Probab=27.54 E-value=43 Score=28.73 Aligned_cols=25 Identities=20% Similarity=0.486 Sum_probs=19.1
Q ss_pred HHHHHHHHHhhh------cCCcEEEEEchHH
Q psy3897 143 LKDVQNDLMGFV------SKDSIIVGHGLEN 167 (240)
Q Consensus 143 ~~ev~~~l~~~i------~~~~iLVGH~~~~ 167 (240)
+.++.+.|++.. ...-+||||+...
T Consensus 66 ~~~~i~~i~~~~~~~~~~~~~vilVgHSmGG 96 (225)
T PF07819_consen 66 LAEAIKYILELYKSNRPPPRSVILVGHSMGG 96 (225)
T ss_pred HHHHHHHHHHhhhhccCCCCceEEEEEchhh
Confidence 677777777766 3578999999765
No 114
>PF03337 Pox_F12L: Poxvirus F12L protein; InterPro: IPR005005 The vaccinia virus F12L gene encodes a 65 kDa protein that is expressed late during infection and is important for plaque formation, EEV production and virulence. The F12L protein is located on intracellular enveloped virus (IEV) particles, but is absent from immature virions, intracellular mature virus and cell-associated enveloped virus. F12L shows co-localization with endosomal compartments and microtubules and appears to play a role in the the transport of IEV particles to the cell surface on microtubules [].; GO: 0016032 viral reproduction
Probab=24.53 E-value=2.9e+02 Score=27.92 Aligned_cols=19 Identities=26% Similarity=0.275 Sum_probs=15.1
Q ss_pred CcEEEE-EchHHHHHHHhcc
Q psy3897 157 DSIIVG-HGLENDLRALKLI 175 (240)
Q Consensus 157 ~~iLVG-H~~~~Dl~~L~~~ 175 (240)
.-+||| |+--||+..|+..
T Consensus 275 ti~LvGy~ss~FD~pLLra~ 294 (651)
T PF03337_consen 275 TIILVGYFSSFFDFPLLRAY 294 (651)
T ss_pred eEEEeehhhhhhccHHHHhh
Confidence 567888 6677899999974
No 115
>PF10109 FluMu_gp41: Mu-like prophage FluMu protein gp41; InterPro: IPR019289 Members of this family of prokaryotic proteins include various Gp41 proteins and related sequences [].
Probab=24.43 E-value=48 Score=23.17 Aligned_cols=33 Identities=15% Similarity=0.353 Sum_probs=26.2
Q ss_pred ccceecCCCCHHhhccCCCCCHHHHHHHHHhhh
Q psy3897 122 DYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFV 154 (240)
Q Consensus 122 ~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i 154 (240)
....+++|++++++.+-+...+..+.+.+..|+
T Consensus 49 ~l~a~l~gl~~~~l~~L~~~D~~~l~~~~~~Fl 81 (82)
T PF10109_consen 49 ALIARLTGLPPEDLDQLDARDYNRLQEAVNGFL 81 (82)
T ss_pred HHHHHhcCCCHHHHHcCCHHHHHHHHHHHHHhc
Confidence 346789999999999877544778888888776
No 116
>PF11906 DUF3426: Protein of unknown function (DUF3426); InterPro: IPR021834 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 262 to 463 amino acids in length.
Probab=23.35 E-value=2.5e+02 Score=21.94 Aligned_cols=55 Identities=11% Similarity=0.167 Sum_probs=40.7
Q ss_pred CCcEEEEEEeecCCCCCc---cEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCC
Q psy3897 77 GYGVYALDTEMVYTVHGL---EVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGIS 131 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g~---ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt 131 (240)
..+.+.++.+..+..... -.+++++.|.+|+.++...+.|...+.+....-.||-
T Consensus 66 ~~~~l~v~g~i~N~~~~~~~~P~l~l~L~D~~g~~l~~r~~~P~~yl~~~~~~~~~l~ 123 (149)
T PF11906_consen 66 GPGVLVVSGTIRNRADFPQALPALELSLLDAQGQPLARRVFTPADYLPPGLAAQAGLP 123 (149)
T ss_pred CCCEEEEEEEEEeCCCCcccCceEEEEEECCCCCEEEEEEEChHHhcccccccccccC
Confidence 457889999888876553 4799999999999999999999665554433334443
No 117
>KOG2613|consensus
Probab=20.23 E-value=1.1e+02 Score=29.28 Aligned_cols=60 Identities=20% Similarity=0.267 Sum_probs=39.0
Q ss_pred CCcEEEEEEeecCCCCCc----cEEEEEEEEc-CC----cEE-----EEEEEcCCCcccccceecCCCCHHhhc
Q psy3897 77 GYGVYALDTEMVYTVHGL----EVARVTVVNV-DG----RLI-----YNTLVKPDCEIIDYNTKYSGISAKDFI 136 (240)
Q Consensus 77 ~~~~valD~E~tg~~~g~----ei~~v~vv~~-~g----~~~-----~d~lVkP~~~I~~~~t~~~GIt~edl~ 136 (240)
-..|+++|+|-+|-..|. .++-|.++.. ++ +.. +--+.+|+..|..|..+-..+.++.++
T Consensus 312 L~ef~V~dv~~v~~~~~~g~kh~l~dv~v~r~sd~g~nd~~~~~RtHLGhil~~gD~vlgydl~~~N~N~~~~d 385 (502)
T KOG2613|consen 312 LTEFIVLDVDPVGEAGGKGQKHALADVWVARSSDLGMNDKFHYARTHLGHILKPGDLVLGYDLANANLNDEEFD 385 (502)
T ss_pred heEEEEEEEecccccCCccceeeeeeEEEEEcCccCcccceeeehhhccccCCCCCeeeeeeeccCccchhhhh
Confidence 357999999988876652 7888888874 32 221 224556766776666666666655444
Done!