Query 002293
Match_columns 940
No_of_seqs 262 out of 1926
Neff 5.0
Searched_HMMs 46136
Date Thu Mar 28 20:50:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002293.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002293hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0749 PolA DNA polymerase I 100.0 1.7E-78 3.7E-83 698.1 33.3 413 345-920 3-417 (593)
2 TIGR00593 pola DNA polymerase 100.0 1.2E-70 2.6E-75 667.5 39.8 417 344-937 303-723 (887)
3 PRK05755 DNA polymerase I; Pro 100.0 2.1E-69 4.6E-74 661.4 40.2 421 344-937 295-716 (880)
4 PRK14975 bifunctional 3'-5' ex 100.0 7.8E-58 1.7E-62 535.1 28.3 375 344-936 2-387 (553)
5 cd08637 DNA_pol_A_pol_I_C Poly 100.0 2.3E-44 5E-49 404.2 17.7 215 620-937 1-216 (377)
6 PF00476 DNA_pol_A: DNA polyme 100.0 5.8E-43 1.2E-47 393.6 18.6 204 619-919 1-207 (383)
7 cd08643 DNA_pol_A_pol_I_B Poly 100.0 2.6E-41 5.6E-46 383.7 15.5 198 619-912 1-233 (429)
8 cd08642 DNA_pol_A_pol_I_A Poly 100.0 6.5E-41 1.4E-45 373.8 15.1 200 629-937 7-237 (378)
9 cd08640 DNA_pol_A_plastid_like 100.0 4E-41 8.7E-46 376.4 11.9 191 728-939 1-191 (371)
10 cd08638 DNA_pol_A_theta DNA po 100.0 6.9E-39 1.5E-43 359.6 13.9 139 792-936 46-204 (373)
11 cd08639 DNA_pol_A_Aquificae_li 100.0 1.8E-34 3.9E-39 318.3 8.1 138 789-936 29-167 (324)
12 cd06444 DNA_pol_A Family A pol 100.0 3.9E-34 8.5E-39 318.5 7.0 138 789-936 26-164 (347)
13 cd08641 DNA_pol_gammaA Pol gam 99.8 7.2E-21 1.6E-25 212.0 5.7 89 819-915 94-203 (425)
14 PF01612 DNA_pol_A_exo1: 3'-5' 99.8 4.3E-19 9.2E-24 175.7 17.7 173 345-578 1-176 (176)
15 PRK10829 ribonuclease D; Provi 99.8 1.8E-18 4E-23 194.7 23.1 172 344-581 2-174 (373)
16 cd06139 DNA_polA_I_Ecoli_like_ 99.8 1.9E-18 4.1E-23 174.4 18.9 182 368-611 6-193 (193)
17 cd06140 DNA_polA_I_Bacillus_li 99.8 2.9E-18 6.3E-23 172.2 16.8 174 368-610 4-177 (178)
18 COG0349 Rnd Ribonuclease D [Tr 99.8 5.2E-18 1.1E-22 187.9 18.2 216 348-636 1-222 (361)
19 TIGR01388 rnd ribonuclease D. 99.8 1.6E-17 3.6E-22 187.0 20.4 169 347-580 1-169 (367)
20 smart00482 POLAc DNA polymeras 99.7 6E-18 1.3E-22 176.5 3.9 77 855-936 2-78 (206)
21 cd06129 RNaseD_like DEDDy 3'-5 99.7 4.3E-16 9.4E-21 155.9 14.1 157 354-574 2-160 (161)
22 cd06141 WRN_exo DEDDy 3'-5' ex 99.6 2.2E-15 4.7E-20 150.9 15.1 164 349-574 2-169 (170)
23 cd06146 mut-7_like_exo DEDDy 3 99.6 2.8E-15 6E-20 154.9 15.4 174 345-574 1-192 (193)
24 cd06148 Egl_like_exo DEDDy 3'- 99.6 2.6E-15 5.7E-20 155.3 12.9 172 358-580 4-180 (197)
25 smart00474 35EXOc 3'-5' exonuc 99.6 1.1E-13 2.3E-18 135.9 16.7 170 345-577 1-171 (172)
26 cd06142 RNaseD_exo DEDDy 3'-5' 99.5 1.3E-12 2.8E-17 130.6 17.8 167 355-599 3-170 (178)
27 cd06147 Rrp6p_like_exo DEDDy 3 99.4 7.2E-12 1.6E-16 128.6 17.2 171 344-580 4-175 (192)
28 cd00007 35EXOc 3'-5' exonuclea 99.4 7.8E-12 1.7E-16 120.5 15.6 153 369-576 2-154 (155)
29 KOG2206 Exosome 3'-5' exoribon 99.4 7.2E-13 1.6E-17 152.2 9.2 224 269-580 132-363 (687)
30 cd09018 DEDDy_polA_RNaseD_like 99.4 1.3E-11 2.7E-16 119.7 14.4 149 369-574 1-149 (150)
31 cd06128 DNA_polA_exo DEDDy 3'- 98.9 1.9E-08 4.2E-13 98.9 14.8 75 411-491 31-105 (151)
32 COG2176 PolC DNA polymerase II 98.6 1.5E-07 3.3E-12 115.7 11.7 117 367-491 421-558 (1444)
33 PRK05711 DNA polymerase III su 98.6 1E-06 2.2E-11 94.9 14.8 112 368-491 5-146 (240)
34 PRK09146 DNA polymerase III su 98.5 1.7E-06 3.7E-11 93.0 15.3 117 367-490 47-198 (239)
35 TIGR01406 dnaQ_proteo DNA poly 98.5 2.6E-06 5.7E-11 90.7 15.1 111 369-491 2-142 (225)
36 PRK07942 DNA polymerase III su 98.5 2.8E-06 6.1E-11 90.8 15.1 116 368-491 7-152 (232)
37 PRK06063 DNA polymerase III su 98.5 2.6E-06 5.6E-11 95.0 15.4 112 368-490 16-150 (313)
38 PRK05601 DNA polymerase III su 98.4 2.3E-06 5E-11 96.7 11.8 113 368-491 47-209 (377)
39 cd06131 DNA_pol_III_epsilon_Ec 98.3 1.2E-05 2.5E-10 80.6 14.3 111 369-491 1-140 (167)
40 PRK07740 hypothetical protein; 98.3 1.5E-05 3.1E-10 86.1 15.9 112 368-490 60-197 (244)
41 PRK06310 DNA polymerase III su 98.3 2.2E-05 4.8E-10 84.9 16.2 111 368-490 8-145 (250)
42 TIGR01298 RNaseT ribonuclease 98.3 1.8E-05 4E-10 82.7 14.9 113 368-490 9-161 (200)
43 PRK06309 DNA polymerase III su 98.2 2.6E-05 5.7E-10 83.3 16.0 110 368-491 3-138 (232)
44 PRK07246 bifunctional ATP-depe 98.2 1.6E-05 3.4E-10 99.0 15.3 110 368-490 8-141 (820)
45 PRK06807 DNA polymerase III su 98.2 2.4E-05 5.2E-10 87.4 14.9 111 368-490 9-144 (313)
46 PRK09145 DNA polymerase III su 98.2 3.7E-05 8.1E-10 80.2 14.9 114 368-490 30-172 (202)
47 cd06134 RNaseT DEDDh 3'-5' exo 98.2 3.6E-05 7.9E-10 79.7 14.7 113 369-491 7-159 (189)
48 TIGR01405 polC_Gram_pos DNA po 98.2 2.1E-05 4.6E-10 100.7 15.5 111 368-490 191-326 (1213)
49 TIGR00573 dnaq exonuclease, DN 98.2 3.2E-05 6.9E-10 81.7 14.2 113 368-490 8-146 (217)
50 PRK08517 DNA polymerase III su 98.1 5.1E-05 1.1E-09 82.6 15.2 110 368-490 69-202 (257)
51 PRK05168 ribonuclease T; Provi 98.1 8.1E-05 1.8E-09 78.5 15.5 124 354-490 7-170 (211)
52 cd06137 DEDDh_RNase DEDDh 3'-5 98.1 8.3E-06 1.8E-10 82.2 7.6 63 423-490 72-134 (161)
53 TIGR01407 dinG_rel DnaQ family 98.0 5.3E-05 1.1E-09 94.8 15.5 111 369-491 2-137 (850)
54 PRK09182 DNA polymerase III su 98.0 6E-05 1.3E-09 83.6 14.3 116 368-491 38-174 (294)
55 PRK07883 hypothetical protein; 98.0 6.8E-05 1.5E-09 89.8 15.2 111 368-490 16-153 (557)
56 smart00479 EXOIII exonuclease 98.0 0.00014 3E-09 72.0 14.7 109 369-490 2-137 (169)
57 PRK06195 DNA polymerase III su 98.0 0.00015 3.2E-09 80.8 15.8 65 421-490 67-136 (309)
58 cd06149 ISG20 DEDDh 3'-5' exon 97.9 4.5E-05 9.8E-10 76.9 9.1 63 421-490 64-130 (157)
59 PRK08074 bifunctional ATP-depe 97.9 0.00016 3.5E-09 91.3 15.7 111 368-490 4-140 (928)
60 PRK07247 DNA polymerase III su 97.9 0.00019 4E-09 75.3 13.4 65 421-490 71-141 (195)
61 cd06144 REX4_like DEDDh 3'-5' 97.8 6E-05 1.3E-09 75.3 8.5 63 421-490 64-127 (152)
62 cd06136 TREX1_2 DEDDh 3'-5' ex 97.7 0.00014 3.1E-09 74.5 10.0 110 369-490 1-151 (177)
63 cd06130 DNA_pol_III_epsilon_li 97.7 0.00025 5.4E-09 69.8 11.1 64 422-490 65-133 (156)
64 PRK07983 exodeoxyribonuclease 97.6 0.00093 2E-08 71.3 14.6 46 437-490 75-120 (219)
65 cd06145 REX1_like DEDDh 3'-5' 97.6 0.00021 4.6E-09 71.4 8.5 62 421-490 62-123 (150)
66 cd06125 DnaQ_like_exo DnaQ-lik 97.6 0.0001 2.2E-09 68.5 5.5 75 370-468 1-83 (96)
67 PRK05359 oligoribonuclease; Pr 97.6 0.00034 7.4E-09 72.4 9.7 103 368-475 4-144 (181)
68 cd06127 DEDDh DEDDh 3'-5' exon 97.5 0.00043 9.2E-09 66.8 9.1 107 370-487 1-132 (159)
69 cd06138 ExoI_N N-terminal DEDD 97.5 0.00073 1.6E-08 69.6 10.6 116 370-491 1-161 (183)
70 PRK00448 polC DNA polymerase I 97.5 0.00089 1.9E-08 87.4 13.8 112 368-491 420-556 (1437)
71 PRK11779 sbcB exonuclease I; P 97.4 0.0013 2.9E-08 77.4 13.6 119 368-491 7-170 (476)
72 cd05160 DEDDy_DNA_polB_exo DED 97.4 0.0014 3.1E-08 67.7 12.4 65 421-490 63-157 (199)
73 cd06135 Orn DEDDh 3'-5' exonuc 97.4 0.00042 9.2E-09 70.8 8.2 103 369-476 1-141 (173)
74 PRK07748 sporulation inhibitor 97.3 0.0035 7.5E-08 65.9 13.7 67 421-491 79-151 (207)
75 COG0847 DnaQ DNA polymerase II 97.3 0.0021 4.4E-08 68.5 11.4 113 368-490 14-151 (243)
76 PF13482 RNase_H_2: RNase_H su 96.9 0.0033 7.2E-08 62.7 7.9 155 370-573 1-163 (164)
77 cd06133 ERI-1_3'hExo_like DEDD 96.8 0.0092 2E-07 59.8 10.7 67 421-490 75-149 (176)
78 PRK06722 exonuclease; Provisio 96.8 0.042 9E-07 61.0 16.1 67 421-490 77-151 (281)
79 cd05785 DNA_polB_like2_exo Unc 96.6 0.027 5.9E-07 59.6 13.0 112 368-491 10-165 (207)
80 cd05780 DNA_polB_Kod1_like_exo 96.1 0.058 1.3E-06 56.3 11.6 110 421-573 56-195 (195)
81 PF10108 DNA_pol_B_exo2: Predi 96.0 0.071 1.5E-06 56.9 12.2 112 421-575 37-171 (209)
82 KOG2207 Predicted 3'-5' exonuc 96.0 0.036 7.8E-07 66.1 10.8 178 344-578 391-586 (617)
83 cd05781 DNA_polB_B3_exo DEDDy 95.8 0.2 4.3E-06 52.3 14.2 109 368-489 4-139 (188)
84 PTZ00315 2'-phosphotransferase 95.5 0.18 4E-06 60.8 13.9 118 368-490 57-225 (582)
85 cd05782 DNA_polB_like1_exo Unc 95.3 0.22 4.8E-06 52.8 12.5 67 420-490 77-165 (208)
86 PF00929 RNase_T: Exonuclease; 95.0 0.0022 4.7E-08 61.9 -3.4 112 370-490 1-141 (164)
87 COG3359 Predicted exonuclease 94.0 0.79 1.7E-05 50.1 12.9 164 368-579 99-271 (278)
88 cd05784 DNA_polB_II_exo DEDDy 93.6 0.8 1.7E-05 48.2 11.9 67 421-490 51-148 (193)
89 cd05783 DNA_polB_B1_exo DEDDy 92.2 2.9 6.3E-05 44.4 13.7 66 421-490 73-165 (204)
90 cd05779 DNA_polB_epsilon_exo D 91.6 2.4 5.1E-05 45.2 12.3 67 421-490 73-163 (204)
91 KOG3657 Mitochondrial DNA poly 91.6 1.7 3.6E-05 54.1 12.3 92 822-916 687-794 (1075)
92 cd05777 DNA_polB_delta_exo DED 89.4 10 0.00022 40.7 15.0 23 553-575 203-225 (230)
93 PHA02528 43 DNA polymerase; Pr 87.8 11 0.00023 48.6 15.8 22 552-573 303-324 (881)
94 KOG2249 3'-5' exonuclease [Rep 85.5 3.8 8.2E-05 45.3 8.9 62 421-490 171-235 (280)
95 PRK05762 DNA polymerase II; Re 82.0 14 0.0003 46.9 13.1 66 421-490 203-301 (786)
96 cd05776 DNA_polB_alpha_exo ina 75.6 14 0.00029 40.0 9.0 110 421-573 82-226 (234)
97 KOG4373 Predicted 3'-5' exonuc 72.3 14 0.00031 41.9 8.3 107 424-570 172-281 (319)
98 cd06143 PAN2_exo DEDDh 3'-5' e 70.8 8.3 0.00018 40.4 5.7 59 424-490 91-149 (174)
99 KOG1798 DNA polymerase epsilon 59.8 69 0.0015 43.2 11.5 110 423-575 316-452 (2173)
100 KOG3657 Mitochondrial DNA poly 59.1 4.5 9.7E-05 50.6 1.3 72 553-646 359-436 (1075)
101 PF09281 Taq-exonuc: Taq polym 57.6 23 0.0005 35.6 5.7 41 445-491 70-111 (138)
102 PTZ00166 DNA polymerase delta 56.5 2E+02 0.0044 38.1 15.5 23 552-574 461-483 (1054)
103 smart00486 POLBc DNA polymeras 50.1 2.9E+02 0.0063 31.9 14.1 22 552-573 199-220 (471)
104 TIGR03491 RecB family nuclease 46.5 1.5E+02 0.0033 35.3 11.3 116 422-573 329-457 (457)
105 COG2925 SbcB Exonuclease I [DN 42.1 2.4E+02 0.0051 33.5 11.2 104 368-475 10-150 (475)
106 KOG0304 mRNA deadenylase subun 38.3 2.7E+02 0.0058 30.7 10.3 55 433-490 139-209 (239)
107 PF04857 CAF1: CAF1 family rib 31.8 57 0.0012 35.9 4.4 51 434-490 147-213 (262)
108 PHA02563 DNA polymerase; Provi 29.1 89 0.0019 39.0 5.8 67 367-453 12-83 (630)
109 KOG2405 Predicted 3'-5' exonuc 27.2 28 0.0006 40.6 1.0 140 404-576 217-360 (458)
110 PHA02524 43A DNA polymerase su 21.9 3E+02 0.0065 33.7 8.2 30 421-451 180-212 (498)
111 PF04857 CAF1: CAF1 family rib 21.3 96 0.0021 34.1 3.7 30 351-383 9-38 (262)
No 1
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.7e-78 Score=698.15 Aligned_cols=413 Identities=31% Similarity=0.424 Sum_probs=355.9
Q ss_pred eEEecCHHHHHHHHHHHhccCCCceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCC-Chhh
Q 002293 345 VMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDG-GGRD 423 (940)
Q Consensus 345 y~lV~t~e~L~eli~~L~~a~~~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~-~~e~ 423 (940)
|..+.+.+.+..|...+..+. .+++|+||++++++...++| +++..++ .++|++..+. ..-.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~---~~a~~~et~~l~~~~~~lvg------~s~~~~~--------~~~yi~~~~~~~~~~ 65 (593)
T COG0749 3 YGTITDLAVLNAWLTKLNAAA---NIAFDTETDGLDPHGADLVG------LSVASEE--------EAAYIPLLHGPEQLN 65 (593)
T ss_pred chhhhHHHHHHHHHHHHhhcc---cceeeccccccCcccCCeeE------EEeeccc--------cceeEeeccchhhhh
Confidence 456667777888888877762 49999999999998877765 5555432 3567766541 1124
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhhc
Q 002293 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQK 503 (940)
Q Consensus 424 ~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg~~~ 503 (940)
+...|++||+++...+|+||+|+|+++|.++|+. .+..+|||||+||++|+.. .+++++|+++ |++++
T Consensus 66 ~~~~l~~~l~~~~~~kv~~~~K~d~~~l~~~Gi~-~~~~~DtmlasYll~~~~~---~~~~~~l~~r-------~l~~~- 133 (593)
T COG0749 66 VLAALKPLLEDEGIKKVGQNLKYDYKVLANLGIE-PGVAFDTMLASYLLNPGAG---AHNLDDLAKR-------YLGLE- 133 (593)
T ss_pred hHHHHHHHhhCcccchhccccchhHHHHHHcCCc-ccchHHHHHHHhccCcCcC---cCCHHHHHHH-------hcCCc-
Confidence 7889999999999999999999999999999976 6789999999999999875 6999999998 44443
Q ss_pred cccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Q 002293 504 DMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWK 583 (940)
Q Consensus 504 ~l~k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~~~Lee~~~~ 583 (940)
...++.++|++.. +.++ ...+ .+....|++.|++++++|+..|.+++.+.
T Consensus 134 -------------~~~~~~i~~kg~~--~~~~----~~~~--------~~~~~~y~a~~a~~~~~L~~~l~~~l~~~--- 183 (593)
T COG0749 134 -------------TITFEDIAGKGKK--QLTF----ADVK--------LEKATEYAAEDADATLRLESILEPELLKT--- 183 (593)
T ss_pred -------------cchhHHhhccccc--cCcc----ccch--------HHHHHHHHHHHHHHHHHHHHHHHHHhhhh---
Confidence 1234455665531 1221 1122 35678999999999999999999988874
Q ss_pred cCCCCCCCchHHHHHHHHhcchHHHHHHHhHcCcccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccccCCCHHH
Q 002293 584 LDGKPVPGKSMFDFYQEYWQPFGEILVKMETEGMLVDREYLSEIEKVARAEQEAAVNRFRKWASKHCPDAKYMNVGSDTQ 663 (940)
Q Consensus 584 ~~~~~~~~~~l~~Ly~~IEmPL~~VLa~ME~~GI~VD~E~L~el~~~l~~e~e~le~ei~~~a~k~~~~g~~fNl~SpkQ 663 (940)
..+..+|.++|||++.||+.||.+||.||.++|.++...+..++..+++++++++ |++||++||||
T Consensus 184 --------~~L~~l~~~iE~Pl~~VLa~ME~~Gi~vD~~~L~~l~~el~~~l~~le~eiy~la------G~~FNi~SPKQ 249 (593)
T COG0749 184 --------PVLLELYEEIEMPLVRVLARMERNGIKVDVQYLKELSKELGCELAELEEEIYELA------GEEFNINSPKQ 249 (593)
T ss_pred --------hhHHHHHHHHhccHHHHHHHhHhcCceecHHHHHHHHHHHHHHHHHHHHHHHHHh------cCcCCCCCHHH
Confidence 4679999999999999999999999999999999999999999999999997765 89999999999
Q ss_pred HHHHhcCCCCCCCCCCCCCCcccccccCCCccccccCCCCCcccccchhcccccCCCCccccccCCCcCcHHHHHHHHhc
Q 002293 664 LRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVIAEGKKTPSKFRNITLRSIGVDLPTEMYTATGWPSVGGDALKTLARN 743 (940)
Q Consensus 664 L~~lLF~~~~~~~~~~l~LP~er~~k~~~~~~~~~~~Kktp~~~~~i~l~~lG~~lp~~~kTktG~~STd~evLe~L~~~ 743 (940)
|+.+||+ +||||. ..++||+|+|||++++|++|+..
T Consensus 250 L~~ILfe--------Kl~Lp~------------------------------------~~kKtktG~yST~~~vLe~L~~~ 285 (593)
T COG0749 250 LGEILFE--------KLGLPP------------------------------------GLKKTKTGNYSTDAEVLEKLADD 285 (593)
T ss_pred HHHHHHH--------hcCCCc------------------------------------cccccCCCCCccHHHHHHHHhhc
Confidence 9999999 799983 12468999999999999999988
Q ss_pred cCccccccCCCCCCCCCCCcccccchhcccccchhhhhHHHHHHHhHHHHHHHHHHHHhhhHhhhhhccccCCccCCCCc
Q 002293 744 ISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNKIFATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGR 823 (940)
Q Consensus 744 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~i~~LLeyR~l~KLlstyi~~L~~~~~~~~dGR 823 (940)
||++ +.||+||+++||.|||+++|++ ++++.+||
T Consensus 286 h~i~---------------------------------------------~~iL~~Rql~KLksTY~d~L~~-~i~~~t~R 319 (593)
T COG0749 286 HPLP---------------------------------------------KLILEYRQLAKLKSTYTDGLPK-LINPDTGR 319 (593)
T ss_pred CccH---------------------------------------------HHHHHHHHHHHHHHHhhhccHH-hhCCCCCc
Confidence 8853 5699999999999999999997 67667799
Q ss_pred eeeeecC-CCccceeeecCCCccccCCCccchhhccceeecCCCCeEEEeeccchhHHHHHHhcCCHHHHHHHhcCCCch
Q 002293 824 VHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFH 902 (940)
Q Consensus 824 IH~s~nq-gTaTGRLSSs~PNLQNIP~~~~~~~~iR~~Fia~~G~~LvsaDYSQIELRILAhlS~D~~Li~af~~g~DiH 902 (940)
||++|+| +|+||||||++|||||||.|++.|+.||++|+|.+|+++++|||||||||||||+|+|+.|++||.+|.|||
T Consensus 320 IHTsf~Q~~t~TGRLSSsdPNLQNIPiRse~Gr~IR~aFva~~g~~~i~aDYSQIELRilAHls~D~~Ll~AF~~g~DiH 399 (593)
T COG0749 320 IHTSFNQTGTATGRLSSSDPNLQNIPIRSEEGRKIRKAFVAEKGYTLISADYSQIELRILAHLSQDEGLLRAFTEGEDIH 399 (593)
T ss_pred cCcchHHHHHHhhcccCCCCCcccCCcCCHhHHhhhhceeCCCCCeEEEechHHHHHHHHHHhcCCHHHHHHHhcCccHH
Confidence 9999999 999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHcCCCccccccc
Q 002293 903 SRTAMNMYPHIRNAVETG 920 (940)
Q Consensus 903 ~~tAs~~fg~~~eeVtk~ 920 (940)
+.||+.+||+++++||++
T Consensus 400 ~~TA~~vFgv~~~~Vt~e 417 (593)
T COG0749 400 TATAAEVFGVPIEEVTSE 417 (593)
T ss_pred HHHHHHHhCCChhhCCHH
Confidence 999999999999998875
No 2
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=1.2e-70 Score=667.52 Aligned_cols=417 Identities=27% Similarity=0.341 Sum_probs=346.0
Q ss_pred ceEEecCHHHHHHHHHHHhccCCCceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCC---CC
Q 002293 344 NVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD---GG 420 (940)
Q Consensus 344 ~y~lV~t~e~L~eli~~L~~a~~~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~---~~ 420 (940)
.|..|.+.+++..|++. ... +.+++ ++++++...++| ++++... + +..+|++... ..
T Consensus 303 ~~~~~~~~~~~~~~~~~-~~~---~~~~~----~~~~~~~~~~~~------~~~~~~~-----~-~~~~~~~~~~~~~~~ 362 (887)
T TIGR00593 303 CAKESEEAAPLANPAEK-AEV---GGFVL----ERLLDQLKKALA------LAFATEN-----Q-SYVAYASEADGIPLL 362 (887)
T ss_pred cceEeCCHHHHHHHHHh-CcC---CeEEE----cCcccccCceeE------EEEEecC-----C-CceEEEecccchhhh
Confidence 36678777888887755 222 36777 667766666554 4444322 0 1256765321 12
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchh
Q 002293 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKA 500 (940)
Q Consensus 421 ~e~~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg 500 (940)
...+.+.|+++|+++.+.+|+||+|||+++|.++|+.+.+.+||||||+|||+|+.. ++|++|+.+ |++
T Consensus 363 ~~~~~~~l~~~l~~~~~~~v~~n~K~d~~~l~~~gi~~~~~~~Dt~la~yll~~~~~----~~l~~la~~-------yl~ 431 (887)
T TIGR00593 363 TILTDDKFARWLLNEQIKKIGHDAKFLMHLLKREGIELGGVIFDTMLAAYLLDPAQV----STLDTLARR-------YLV 431 (887)
T ss_pred hHHHHHHHHHHHhCCCCcEEEeeHHHHHHHHHhCCCCCCCcchhHHHHHHHcCCCCC----CCHHHHHHH-------HcC
Confidence 234567799999999999999999999999999999998889999999999999764 699999998 444
Q ss_pred hhccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 002293 501 YQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEM 580 (940)
Q Consensus 501 ~~~~l~k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~~~Lee~ 580 (940)
++ ...+.+++|++. .+...| .+.+..||+.|+.+|++||..|.++|.+
T Consensus 432 ~~--------------~~~~~~~~~~~~---------~~~~~~--------~~~~~~ya~~d~~~~~~L~~~l~~~l~~- 479 (887)
T TIGR00593 432 EE--------------LILDEKIGGKLA---------KFAFPP--------LEEATEYLARRAAATKRLAEELLKELDE- 479 (887)
T ss_pred cc--------------cccHHHhccCCC---------Cccccc--------HHHHHHHHHHHHHHHHHHHHHHHHHHhh-
Confidence 32 011122333221 111223 3567899999999999999999999987
Q ss_pred ccccCCCCCCCchHHHHHHHHhcchHHHHHHHhHcCcccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccccCCC
Q 002293 581 SWKLDGKPVPGKSMFDFYQEYWQPFGEILVKMETEGMLVDREYLSEIEKVARAEQEAAVNRFRKWASKHCPDAKYMNVGS 660 (940)
Q Consensus 581 ~~~~~~~~~~~~~l~~Ly~~IEmPL~~VLa~ME~~GI~VD~E~L~el~~~l~~e~e~le~ei~~~a~k~~~~g~~fNl~S 660 (940)
.++..+|.+||||++++|++||.+||+||+++|.++...+..+++.+++++++++ |..||++|
T Consensus 480 -----------~~l~~l~~~iE~pl~~vLa~ME~~Gi~vD~~~l~~~~~~~~~~l~~le~~i~~~~------g~~fN~~S 542 (887)
T TIGR00593 480 -----------NKLLSLYREIELPLSKVLAEMEKTGIKVDADYLQELSQEFGEEIADLEEEIYELA------GEEFNINS 542 (887)
T ss_pred -----------ccHHHHHHHHHHHHHHHHHHHHhCCEEeCHHHHHHHHHHHHHHHHHHHHHHHHHh------CCCCCCCC
Confidence 3789999999999999999999999999999999999999999999999998766 67899999
Q ss_pred HHHHHHHhcCCCCCCCCCCCCCCcccccccCCCccccccCCCCCcccccchhcccccCCCCccccccCCCcCcHHHHHHH
Q 002293 661 DTQLRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVIAEGKKTPSKFRNITLRSIGVDLPTEMYTATGWPSVGGDALKTL 740 (940)
Q Consensus 661 pkQL~~lLF~~~~~~~~~~l~LP~er~~k~~~~~~~~~~~Kktp~~~~~i~l~~lG~~lp~~~kTktG~~STd~evLe~L 740 (940)
|+||+++||+ +||||. .++||+| |||++++|+.|
T Consensus 543 pkQl~~~Lf~--------~lgl~~-------------------------------------~kktktg-~ST~~~vL~~L 576 (887)
T TIGR00593 543 PKQLGEVLFE--------KLGLPV-------------------------------------GKKTKTG-YSTDADVLEKL 576 (887)
T ss_pred HHHHHHHHHH--------hCCCCC-------------------------------------CCCCCCC-CCChHHHHHHh
Confidence 9999999998 688873 2468899 99999999999
Q ss_pred HhccCccccccCCCCCCCCCCCcccccchhcccccchhhhhHHHHHHHhHHHHHHHHHHHHhhhHhhhhhccccCCccCC
Q 002293 741 ARNISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNKIFATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGK 820 (940)
Q Consensus 741 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~i~~LLeyR~l~KLlstyi~~L~~~~~~~~ 820 (940)
+..||+ +..||+||+++|+++||+++|++ .+...
T Consensus 577 ~~~hp~---------------------------------------------~~~ileyR~l~Kl~sty~~~l~~-~i~~~ 610 (887)
T TIGR00593 577 REKHPI---------------------------------------------IALILEYRQLTKLKSTYVDGLPE-LVNPD 610 (887)
T ss_pred hhcCcH---------------------------------------------HHHHHHHHHHHHHHHHHHHHHHH-HhcCC
Confidence 988875 34588999999999999999997 55555
Q ss_pred CCceeeeecC-CCccceeeecCCCccccCCCccchhhccceeecCCCCeEEEeeccchhHHHHHHhcCCHHHHHHHhcCC
Q 002293 821 NGRVHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGG 899 (940)
Q Consensus 821 dGRIH~s~nq-gTaTGRLSSs~PNLQNIP~~~~~~~~iR~~Fia~~G~~LvsaDYSQIELRILAhlS~D~~Li~af~~g~ 899 (940)
+||||++|+| +|+||||||++|||||||++++.|..||+||+|++|++||+|||||||||||||||+|+.|+++|++|.
T Consensus 611 tgRIh~~~~q~~t~TGRlSs~~PNLQNIP~r~~~g~~iR~~Fia~~G~~lv~aDySQIELRilAhls~D~~Li~af~~g~ 690 (887)
T TIGR00593 611 TGRIHTTFNQTGTATGRLSSSNPNLQNIPIRSEEGRKIRKAFVAEKGWLLISADYSQIELRVLAHLSQDENLIEAFQNGE 690 (887)
T ss_pred CCceeeeeEecccceeeecccCCCccccCCCCcccchhhheEecCCCCeEEEechhHhHHHHHHHHcCCHHHHHHHhcCC
Confidence 6999999998 999999999999999999999989999999999999999999999999999999999999999999999
Q ss_pred CchHHHHHHHcCCCccccccccccccccCCCCCCCCCC
Q 002293 900 DFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLL 937 (940)
Q Consensus 900 DiH~~tAs~~fg~~~eeVtk~~~~~~~~~~~k~~~~~~ 937 (940)
|||+.||+.|||+|+++|++ +.|+.+|+-+|.+
T Consensus 691 DiH~~tA~~~fg~~~e~vt~-----~~R~~AK~infGi 723 (887)
T TIGR00593 691 DIHTETASRLFGVEIEDVTP-----NMRRIAKTINFGV 723 (887)
T ss_pred ChHHHHHHHHhCCChhhCCH-----HHHhhhhHhhcCc
Confidence 99999999999999998874 6788888877754
No 3
>PRK05755 DNA polymerase I; Provisional
Probab=100.00 E-value=2.1e-69 Score=661.39 Aligned_cols=421 Identities=32% Similarity=0.442 Sum_probs=359.4
Q ss_pred ceEEecCHHHHHHHHHHHhccCCCceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhh
Q 002293 344 NVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRD 423 (940)
Q Consensus 344 ~y~lV~t~e~L~eli~~L~~a~~~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~ 423 (940)
+|.+|+++++|.++++++..+ .+++|||||+|++++.+++++ ++++..+ +..+|++..+.+ ..
T Consensus 295 ~~~~I~~~~~L~~~l~~l~~~---~~~a~DtEt~~l~~~~~~i~~------i~ls~~~-------g~~~~ip~~~i~-~~ 357 (880)
T PRK05755 295 DYETILDEEELEAWLAKLKAA---GLFAFDTETTSLDPMQAELVG------LSFAVEP-------GEAAYIPLDQLD-RE 357 (880)
T ss_pred ceEEeCCHHHHHHHHHHhhcc---CeEEEEeccCCCCcccccEEE------EEEEeCC-------CcEEEEeccccc-HH
Confidence 588999999999999998765 589999999999998877654 5554433 236778775432 25
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhhc
Q 002293 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQK 503 (940)
Q Consensus 424 ~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg~~~ 503 (940)
+++.|+++|+++.+.||+||++||+++|.++|+.+++.+||||+|+||++|+. .++|++|+++| ++.+
T Consensus 358 ~l~~l~~~L~d~~v~kV~HNakfDl~~L~~~gi~~~~~~~DT~iAa~Ll~~~~----~~~L~~L~~~y-------lg~~- 425 (880)
T PRK05755 358 VLAALKPLLEDPAIKKVGQNLKYDLHVLARYGIELRGIAFDTMLASYLLDPGR----RHGLDSLAERY-------LGHK- 425 (880)
T ss_pred HHHHHHHHHhCCCCcEEEeccHhHHHHHHhCCCCcCCCcccHHHHHHHcCCCC----CCCHHHHHHHH-------hCCC-
Confidence 78889999999999999999999999999999998888999999999999976 28999999984 4332
Q ss_pred cccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Q 002293 504 DMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWK 583 (940)
Q Consensus 504 ~l~k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~~~Lee~~~~ 583 (940)
...+.+++|++. .|+.+|+ +.+..||+.|+.++++||..|.++|.+.
T Consensus 426 -------------~~~~~~~~gk~~---------~~~~~pl--------e~~~~YAa~Dv~~~~~L~~~L~~~L~~~--- 472 (880)
T PRK05755 426 -------------TISFEEVAGKQL---------TFAQVDL--------EEAAEYAAEDADVTLRLHEVLKPKLLEE--- 472 (880)
T ss_pred -------------ccchHHhcCCCC---------CccccCH--------HHHHHHHHHHHHHHHHHHHHHHHHHHhc---
Confidence 011233444321 2333343 4678999999999999999999999874
Q ss_pred cCCCCCCCchHHHHHHHHhcchHHHHHHHhHcCcccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccccCCCHHH
Q 002293 584 LDGKPVPGKSMFDFYQEYWQPFGEILVKMETEGMLVDREYLSEIEKVARAEQEAAVNRFRKWASKHCPDAKYMNVGSDTQ 663 (940)
Q Consensus 584 ~~~~~~~~~~l~~Ly~~IEmPL~~VLa~ME~~GI~VD~E~L~el~~~l~~e~e~le~ei~~~a~k~~~~g~~fNl~SpkQ 663 (940)
.++..+|.++|||++++|++||.+||+||+++++++...++.++++++++++.++ |..||++||+|
T Consensus 473 --------~~l~~l~~eiE~p~~~~l~~me~~Gi~vD~~~~~~~~~~~~~~~~~l~~~~~~~~------g~~fn~~S~~q 538 (880)
T PRK05755 473 --------PGLLELYEEIELPLVPVLARMERNGIKVDREYLKELSAELAQRLAELEQEIYELA------GEEFNINSPKQ 538 (880)
T ss_pred --------ccHHHHHHHhhchHHHHHHHHHhcCeEeCHHHHHHHHHHHHHHHHHHHHHHHHHh------CCCCCCCCHHH
Confidence 4789999999999999999999999999999999999999999999999998775 67899999999
Q ss_pred HHHHhcCCCCCCCCCCCCCCcccccccCCCccccccCCCCCcccccchhcccccCCCCccccccCCCcCcHHHHHHHHhc
Q 002293 664 LRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVIAEGKKTPSKFRNITLRSIGVDLPTEMYTATGWPSVGGDALKTLARN 743 (940)
Q Consensus 664 L~~lLF~~~~~~~~~~l~LP~er~~k~~~~~~~~~~~Kktp~~~~~i~l~~lG~~lp~~~kTktG~~STd~evLe~L~~~ 743 (940)
|+++||+ ++|+|. .++|++| +||++++|+.|+..
T Consensus 539 l~~~L~~--------~lgl~~-------------------------------------~~kt~~g-~st~~~~L~~l~~~ 572 (880)
T PRK05755 539 LGEILFE--------KLGLPV-------------------------------------GKKTKTG-YSTDAEVLEKLADD 572 (880)
T ss_pred HHHHHHH--------hcCCCC-------------------------------------CCCCCCC-CCCcHHHHHHHHhc
Confidence 9999998 678863 2357788 89999999999887
Q ss_pred cCccccccCCCCCCCCCCCcccccchhcccccchhhhhHHHHHHHhHHHHHHHHHHHHhhhHhhhhhccccCCccCCCCc
Q 002293 744 ISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNKIFATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGR 823 (940)
Q Consensus 744 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~i~~LLeyR~l~KLlstyi~~L~~~~~~~~dGR 823 (940)
||+ ++.|++||+++|+++||+++|.+ .+...+||
T Consensus 573 ~p~---------------------------------------------~~~lle~r~~~kl~sty~~~l~~-~~~~~~~r 606 (880)
T PRK05755 573 HPI---------------------------------------------PDKILEYRQLSKLKSTYTDALPK-LINPDTGR 606 (880)
T ss_pred ChH---------------------------------------------HHHHHHHHHHHHHHHHHHHHHHH-HhccCCCe
Confidence 764 45789999999999999999987 45444569
Q ss_pred eeeeecC-CCccceeeecCCCccccCCCccchhhccceeecCCCCeEEEeeccchhHHHHHHhcCCHHHHHHHhcCCCch
Q 002293 824 VHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFH 902 (940)
Q Consensus 824 IH~s~nq-gTaTGRLSSs~PNLQNIP~~~~~~~~iR~~Fia~~G~~LvsaDYSQIELRILAhlS~D~~Li~af~~g~DiH 902 (940)
||++|+| +|+||||||++|||||||+++..+..||+||+|++|++||++||||||||||||+|+|+.|+++|++|.|+|
T Consensus 607 ih~~~~~~~t~TGRlss~~PnlQniP~~~~~~~~iR~~f~~~~G~~lv~~DysqiElRilA~ls~D~~l~~~~~~g~Dih 686 (880)
T PRK05755 607 IHTSFNQTVTATGRLSSSDPNLQNIPIRTEEGRRIRKAFVAPEGYKLLSADYSQIELRILAHLSGDEGLIEAFAEGEDIH 686 (880)
T ss_pred ecceEeecccceeeeeccCCCcccCCCCCccchhhhheEecCCCCEEEEechhhhHHHHHHHHcCCHHHHHHHhcCCCHH
Confidence 9999998 999999999999999999988888899999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHcCCCccccccccccccccCCCCCCCCCC
Q 002293 903 SRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLL 937 (940)
Q Consensus 903 ~~tAs~~fg~~~eeVtk~~~~~~~~~~~k~~~~~~ 937 (940)
+.||+.|||+++++|++ +.|+.+|..+|.+
T Consensus 687 ~~~A~~~~~~~~~~v~~-----~~R~~aK~~~fg~ 716 (880)
T PRK05755 687 TATASEVFGVPLEEVTS-----EQRRRAKAINFGI 716 (880)
T ss_pred HHHHHHHhCCChhhCCH-----HHHHHHHHHhcch
Confidence 99999999999998875 5688888777654
No 4
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=100.00 E-value=7.8e-58 Score=535.08 Aligned_cols=375 Identities=23% Similarity=0.213 Sum_probs=299.8
Q ss_pred ceEEecCHHHHHHHHHHHhccCCCceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhh
Q 002293 344 NVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRD 423 (940)
Q Consensus 344 ~y~lV~t~e~L~eli~~L~~a~~~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~ 423 (940)
.+.+|++++++..++.++..+ +.+++|||++..++ .++ .+++. .+...+.||+..
T Consensus 2 ~~~~I~~~~~l~~~~~~l~~~---~~~a~DtEf~r~~t---~l~------liQ~~--------~~~~~~liDpl~----- 56 (553)
T PRK14975 2 DMKVILAPEELGAALERLSPA---GVVAGDTETTGDDA---AAA------AAQEG--------EEEPRWVWASTA----- 56 (553)
T ss_pred CceEEeccchhHHHHHHhccC---CceeCCccccCCcc---hhh------eeeec--------CCCceEEECchH-----
Confidence 367999999999999999887 58999999998887 221 22332 223456667641
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhhc
Q 002293 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQK 503 (940)
Q Consensus 424 ~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg~~~ 503 (940)
++. .+|.++|+.+.+ +||||||++||+++.. ..+++|+.++.. |++++
T Consensus 57 ~l~----------------------~~L~~~Gv~~~~-~fDT~LAa~lL~~~~~-~~~~~l~~la~~-------~l~~~- 104 (553)
T PRK14975 57 ALY----------------------PRLLAAGVRVER-CHDLMLASQLLLGSEG-RAGSSLSAAAAR-------ALGEG- 104 (553)
T ss_pred HhH----------------------HHHHHCCCccCC-CchHHHHHHHcCCCCC-cCCCCHHHHHHH-------HhCCC-
Confidence 111 226677988765 8999999999999651 013799999987 45442
Q ss_pred cccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Q 002293 504 DMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWK 583 (940)
Q Consensus 504 ~l~k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~~~Lee~~~~ 583 (940)
+.+ .. +. ++|. +|+ ++.+..||+.|+.++++||..|.++|++..
T Consensus 105 -----------l~k---------~~---~~---sdw~-rpl-------s~~q~~YAa~Dv~~l~~L~~~L~~qL~~~~-- 148 (553)
T PRK14975 105 -----------LDK---------PP---QT---SALS-DPP-------DEEQLLYAAADADVLLELYAVLADQLNRIA-- 148 (553)
T ss_pred -----------CCC---------hh---hh---cccc-ccc-------hHHHHHHHHHHhHHHHHHHHHHHHHHHhhh--
Confidence 011 00 11 2675 554 577899999999999999999999998730
Q ss_pred cCCCCCCCchHHHHHHHHhcchHHHHHHHhHcCcccCHHHHHHHHHHHH----------HHHHHHHHHHHHHhhhcCCCC
Q 002293 584 LDGKPVPGKSMFDFYQEYWQPFGEILVKMETEGMLVDREYLSEIEKVAR----------AEQEAAVNRFRKWASKHCPDA 653 (940)
Q Consensus 584 ~~~~~~~~~~l~~Ly~~IEmPL~~VLa~ME~~GI~VD~E~L~el~~~l~----------~e~e~le~ei~~~a~k~~~~g 653 (940)
.. ...++..+|.++|||++++|++||.+||+||.+.++++...+. .+++.++++++..++ .
T Consensus 149 --~~--~~~g~l~ll~~~E~~~~~~l~~me~~Gi~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~g-----~ 219 (553)
T PRK14975 149 --AA--AHPGRLRLLAAAESAGALAAAEMELAGLPWDTDVHEALLAELLGPRPAAGGRPARLAELAAEIREALG-----R 219 (553)
T ss_pred --cc--cchhHHHHHHHHHhhHHHHHHHHHHhCeEeCHHHHHHHHHHHhcccccccchHHHHHHHHHHHHHHhC-----C
Confidence 00 0126889999999999999999999999999999999999888 778899999987762 2
Q ss_pred ccccCCCHHHHHHHhcCCCCCCCCCCCCCCcccccccCCCccccccCCCCCcccccchhcccccCCCCccccccCCCcCc
Q 002293 654 KYMNVGSDTQLRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVIAEGKKTPSKFRNITLRSIGVDLPTEMYTATGWPSVG 733 (940)
Q Consensus 654 ~~fNl~SpkQL~~lLF~~~~~~~~~~l~LP~er~~k~~~~~~~~~~~Kktp~~~~~i~l~~lG~~lp~~~kTktG~~STd 733 (940)
..||++||+||.++| + ++|+|. ++|+
T Consensus 220 ~~~n~~S~~ql~~~L-~--------~~g~~~---------------------------------------------~~t~ 245 (553)
T PRK14975 220 PRLNPDSPQQVLRAL-R--------RAGIEL---------------------------------------------PSTR 245 (553)
T ss_pred CCCCCCCHHHHHHHH-H--------HCCCCC---------------------------------------------CCCc
Confidence 359999999999999 3 466642 2566
Q ss_pred HHHHHHHHhccCccccccCCCCCCCCCCCcccccchhcccccchhhhhHHHHHHHhHHHHHHHHHHHHhhhHhhhhhccc
Q 002293 734 GDALKTLARNISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNKIFATEQEAREACDAISALCEVCSIDSLISNFILPLQ 813 (940)
Q Consensus 734 ~evLe~L~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~i~~LLeyR~l~KLlstyi~~L~ 813 (940)
+++| +...||+ +..|++||+++|++++|+++++
T Consensus 246 ~~~L--~~~~hp~---------------------------------------------~~~ile~r~~~kl~st~~~~~~ 278 (553)
T PRK14975 246 KWEL--REIDHPA---------------------------------------------VEPLLEYRKLSKLLSANGWAWL 278 (553)
T ss_pred HHHh--ccCCCch---------------------------------------------HHHHHHHHHHHHHHHHHHHHHH
Confidence 7888 3344553 4679999999999999999998
Q ss_pred cCCccCCCCceeeeecC-CCccceeeecCCCccccCCCccchhhccceeecCCCCeEEEeeccchhHHHHHHhcCCHHHH
Q 002293 814 GSNVSGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSML 892 (940)
Q Consensus 814 ~~~~~~~dGRIH~s~nq-gTaTGRLSSs~PNLQNIP~~~~~~~~iR~~Fia~~G~~LvsaDYSQIELRILAhlS~D~~Li 892 (940)
+ .+. .|||||++|+| +|+||||||++|||||||+ .||+||+|++|++||++||||||||||||||+|+.|+
T Consensus 279 ~-~~~-~~grih~~~~~~gt~TGRlss~~pnlQniP~------~iR~~f~a~~G~~lv~aDysqiElRvlA~ls~D~~l~ 350 (553)
T PRK14975 279 D-YWV-RDGRFHPEYVPGGVVTGRWASRGPNAQQIPR------DIRSAFVADPGWKLVVADASQIELRVLAAYSGDERMI 350 (553)
T ss_pred H-Hhc-cCCcccceeeecceeecccccCCCccccCCH------HHhceEEcCCCCEEEEechhhhHHHHHHHHcCCHHHH
Confidence 7 343 79999999998 8999999999999999997 5999999999999999999999999999999999999
Q ss_pred HHHhcCCCchHHHHHHHcCCCccccccccccccccCCCCCCCCC
Q 002293 893 DAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPL 936 (940)
Q Consensus 893 ~af~~g~DiH~~tAs~~fg~~~eeVtk~~~~~~~~~~~k~~~~~ 936 (940)
++|++|+|||+.||+.+||+++++ ++.|+.+|..+|.
T Consensus 351 ~~~~~g~Dih~~~A~~~~~~~~~~-------~~~R~~aK~~~~g 387 (553)
T PRK14975 351 EAFRTGGDLHRLTASVGFGKPEEE-------KEERALAKAANFG 387 (553)
T ss_pred HHHhcCCCHHHHHHHHHhCCCccc-------hhHHHHHHHHHHH
Confidence 999999999999999999999987 5667777765543
No 5
>cd08637 DNA_pol_A_pol_I_C Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuc
Probab=100.00 E-value=2.3e-44 Score=404.22 Aligned_cols=215 Identities=35% Similarity=0.499 Sum_probs=192.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccccCCCHHHHHHHhcCCCCCCCCCCCCCCcccccccCCCcccccc
Q 002293 620 DREYLSEIEKVARAEQEAAVNRFRKWASKHCPDAKYMNVGSDTQLRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVIAE 699 (940)
Q Consensus 620 D~E~L~el~~~l~~e~e~le~ei~~~a~k~~~~g~~fNl~SpkQL~~lLF~~~~~~~~~~l~LP~er~~k~~~~~~~~~~ 699 (940)
|.++|+++.+.+..+++.++++++.++ |..||++||+|++++||+ .+|+|+
T Consensus 1 d~~~l~~~~~~~~~~~~~l~~~~~~l~------g~~fn~~S~~qv~~~L~~--------~lgl~~--------------- 51 (377)
T cd08637 1 DTEYLEELSEELEKELAELEEEIYELA------GEEFNINSPKQLGEVLFE--------KLGLPV--------------- 51 (377)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHh------CCCCCCCCHHHHHHHHHH--------hCCCCC---------------
Confidence 789999999999999999999998765 678999999999999998 678764
Q ss_pred CCCCCcccccchhcccccCCCCccccccCCCcCcHHHHHHHHhccCccccccCCCCCCCCCCCcccccchhcccccchhh
Q 002293 700 GKKTPSKFRNITLRSIGVDLPTEMYTATGWPSVGGDALKTLARNISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNKIF 779 (940)
Q Consensus 700 ~Kktp~~~~~i~l~~lG~~lp~~~kTktG~~STd~evLe~L~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f 779 (940)
.++|++|. +|++++|+.|+..||+
T Consensus 52 ----------------------~~~t~~~~-~t~~~~L~~l~~~~p~--------------------------------- 75 (377)
T cd08637 52 ----------------------GKKTKTGY-STDAEVLEKLADEHPI--------------------------------- 75 (377)
T ss_pred ----------------------CCcCCCCC-CchHHHHHhhhhcChH---------------------------------
Confidence 13577775 7888899999877763
Q ss_pred hhHHHHHHHhHHHHHHHHHHHHhhhHhhhhhccccCCccCCCCceeeeecC-CCccceeeecCCCccccCCCccchhhcc
Q 002293 780 ATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIR 858 (940)
Q Consensus 780 ~~~~~~~~~~~~i~~LLeyR~l~KLlstyi~~L~~~~~~~~dGRIH~s~nq-gTaTGRLSSs~PNLQNIP~~~~~~~~iR 858 (940)
+..|++||+++|++++|++++++ .+...|||||++|+| +|+||||||++|||||||+++..+..+|
T Consensus 76 ------------~~~lle~r~l~k~~~t~~~~l~~-~~~~~dgrih~~~~~~gt~TGRlS~~~PNlQniP~~~~~~~~~R 142 (377)
T cd08637 76 ------------VELILEYRELTKLKSTYVDALPK-LINPKTGRIHTSFNQTVTATGRLSSSDPNLQNIPIRTEEGREIR 142 (377)
T ss_pred ------------HHHHHHHHHHHHHHHHHHHHHHH-HcCCCCCceeeeeeeccccccchhcccCccccCCCCccchHhHH
Confidence 45789999999999999999997 454349999999998 9999999999999999999877788999
Q ss_pred ceeecCCCCeEEEeeccchhHHHHHHhcCCHHHHHHHhcCCCchHHHHHHHcCCCccccccccccccccCCCCCCCCCC
Q 002293 859 QAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLL 937 (940)
Q Consensus 859 ~~Fia~~G~~LvsaDYSQIELRILAhlS~D~~Li~af~~g~DiH~~tAs~~fg~~~eeVtk~~~~~~~~~~~k~~~~~~ 937 (940)
+||+|++|++||++||||||||||||||+|+.|+++|++|.|+|+.+|+.|||+++++|++ +.|+.+|+.++.+
T Consensus 143 ~~f~~~~G~~lv~aDysqiElRilA~ls~D~~l~~~~~~g~Dih~~~A~~~~g~~~~~v~~-----~~R~~aK~~~~g~ 216 (377)
T cd08637 143 KAFVAEEGWVLLSADYSQIELRILAHLSGDEALIEAFKNGEDIHTRTAAEVFGVPPEEVTP-----EMRRIAKAVNFGI 216 (377)
T ss_pred HheeCCCCCEEEEechhHhHHHHHHHHhCCHHHHHHHhcCCCHHHHHHHHHhCCChhhCCH-----HHHhhhhHhhcch
Confidence 9999999999999999999999999999999999999999999999999999999998874 6688888877754
No 6
>PF00476 DNA_pol_A: DNA polymerase family A; InterPro: IPR001098 Synonym(s): DNA nucleotidyltransferase (DNA-directed) DNA-directed DNA polymerases(2.7.7.7 from EC) are the key enzymes catalysing the accurate replication of DNA. They require either a small RNA molecule or a protein as a primer for the de novo synthesis of a DNA chain. A number of polymerases belong to this family [, , ].; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=100.00 E-value=5.8e-43 Score=393.63 Aligned_cols=204 Identities=37% Similarity=0.525 Sum_probs=180.9
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccccCCCHHHHHHHhcCCCCCCCCCCCCCCcccccccCCCccccc
Q 002293 619 VDREYLSEIEKVARAEQEAAVNRFRKWASKHCPDAKYMNVGSDTQLRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVIA 698 (940)
Q Consensus 619 VD~E~L~el~~~l~~e~e~le~ei~~~a~k~~~~g~~fNl~SpkQL~~lLF~~~~~~~~~~l~LP~er~~k~~~~~~~~~ 698 (940)
||.++|+.+...+..+++.+++++...+ |..||++||+|++++||+ .+|+|+
T Consensus 1 ~d~~~~~~~~~~~~~~~~~~~~~~~~~~------g~~fN~~S~~q~~~~L~~--------~lgl~~-------------- 52 (383)
T PF00476_consen 1 VDREYLEQQSEELDAKLRELEAKAYKLA------GEEFNPNSPKQLAEVLFE--------ELGLPP-------------- 52 (383)
T ss_dssp ETHHHHHHHHHHHHHHHHHHHHHHHHHH------TSCSSTTTHHHHHHHHHT--------TSSSTT--------------
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHhHHhc------CCccCCCCHHHHHHHHHH--------cCCCCC--------------
Confidence 7999999999999999999999987665 789999999999999998 688873
Q ss_pred cCCCCCcccccchhcccccCCCCcccccc-CCCcCcHHHHHHHHh-ccCccccccCCCCCCCCCCCcccccchhcccccc
Q 002293 699 EGKKTPSKFRNITLRSIGVDLPTEMYTAT-GWPSVGGDALKTLAR-NISAEYDCVDGAHDLDDSGCTEETEYKGAVASNN 776 (940)
Q Consensus 699 ~~Kktp~~~~~i~l~~lG~~lp~~~kTkt-G~~STd~evLe~L~~-~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 776 (940)
.++|++ |.+||++++|+.|.. .||
T Consensus 53 -----------------------~~~t~~~g~~st~~~~L~~l~~~~~~------------------------------- 78 (383)
T PF00476_consen 53 -----------------------TKKTKKKGKPSTDKEVLKKLAEDAHP------------------------------- 78 (383)
T ss_dssp -----------------------SSBETTCSEBHCTHHHHHHHCCCCHT-------------------------------
T ss_pred -----------------------CCCCcccchhhhHHHHHHHhhhhhhh-------------------------------
Confidence 123444 999999999999986 444
Q ss_pred hhhhhHHHHHHHhHHHHHHHHHHHHhhhHhhhhhccccCCccCCCCceeeeecC-CCccceeeecCCCccccCCCccchh
Q 002293 777 KIFATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEKDRY 855 (940)
Q Consensus 777 ~~f~~~~~~~~~~~~i~~LLeyR~l~KLlstyi~~L~~~~~~~~dGRIH~s~nq-gTaTGRLSSs~PNLQNIP~~~~~~~ 855 (940)
++..+++||+++|+.++|++++.. .+...||||||+|++ +|+|||+||++|||||||++...+.
T Consensus 79 --------------~~~~~l~~r~~~kl~~~~~~~~~~-~~~~~dgrih~~~~~~gt~TGRls~~~PNlQniP~~~~~~~ 143 (383)
T PF00476_consen 79 --------------IAKLLLEYRKLSKLRSTYIDNLLD-KVDPEDGRIHPSFNQTGTATGRLSSSNPNLQNIPKRDPYGK 143 (383)
T ss_dssp --------------HHHHHHHHHHHHHHHHHTTHHHHH-HSBTTTTEE--EEESSSSSSS--EEESSCTSSSSSSSHHHH
T ss_pred --------------hHHHHHHHHHHHHHHhhhhhHHHH-hccccCCeecceeeecccccCCceeechhhhccccccccCc
Confidence 357799999999999999999886 454589999999998 9999999999999999999987788
Q ss_pred hccceeecCCCCeEEEeeccchhHHHHHHhcCCHHHHHHHhcCCCchHHHHHHHcCCCcccccc
Q 002293 856 KIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVET 919 (940)
Q Consensus 856 ~iR~~Fia~~G~~LvsaDYSQIELRILAhlS~D~~Li~af~~g~DiH~~tAs~~fg~~~eeVtk 919 (940)
.||+||+|++|++||++||||||||||||||+|+.|+++|++|.|+|+.+|+.+||+++++|++
T Consensus 144 ~~R~~f~a~~G~~lv~aD~sqiElRvlA~ls~D~~l~~~~~~g~D~h~~~a~~~~~~~~~~v~~ 207 (383)
T PF00476_consen 144 EIRSAFVAPPGYVLVSADYSQIELRVLAHLSGDENLIEAFRNGEDIHTETASDIFGKPYEEVTK 207 (383)
T ss_dssp GGGGGEEGSSTEEEEEEEESSHHHHHHHHHHTHHHHHHHHHTTCCHHHHHHHHHTTCHGGGTTH
T ss_pred ccceeEecCccceeeeeehhhhhHHHHHHhcccHHHHHhhcccccHHHHHHHHhcCCCccccch
Confidence 9999999999999999999999999999999999999999999999999999999999998665
No 7
>cd08643 DNA_pol_A_pol_I_B Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5
Probab=100.00 E-value=2.6e-41 Score=383.66 Aligned_cols=198 Identities=23% Similarity=0.246 Sum_probs=171.0
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHhh-h-------------------cC-------CCCccccCCCHHHHHHHhcCC
Q 002293 619 VDREYLSEIEKVARAEQEAAVNRFRKWAS-K-------------------HC-------PDAKYMNVGSDTQLRQLLFGG 671 (940)
Q Consensus 619 VD~E~L~el~~~l~~e~e~le~ei~~~a~-k-------------------~~-------~~g~~fNl~SpkQL~~lLF~~ 671 (940)
+|.+....+...+..+++.++.++++.++ + |. .....||++||+||+++||+
T Consensus 1 ~d~~~a~~l~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fN~~S~~ql~~~L~~- 79 (429)
T cd08643 1 FNQEKAAKLYAQLAGRREDLENELQEVFPPWYVSDGFVPKKRTTNNSVRGYVKGAPYTKIKLVTFNPSSRKHIAKRLKA- 79 (429)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccccccccCccccCCcccceecCCCccccCCccCCCCCHHHHHHHHHH-
Confidence 68899999999999999999999987652 0 10 12348999999999999997
Q ss_pred CCCCCCCCCCCCcccccccCCCccccccCCCCCcccccchhcccccCCCCccccccCCCcCcHHHHHHHHhccCcccccc
Q 002293 672 KPNSKDDSESLPIERIFKVPNTEGVIAEGKKTPSKFRNITLRSIGVDLPTEMYTATGWPSVGGDALKTLARNISAEYDCV 751 (940)
Q Consensus 672 ~~~~~~~~l~LP~er~~k~~~~~~~~~~~Kktp~~~~~i~l~~lG~~lp~~~kTktG~~STd~evLe~L~~~~p~~~~~~ 751 (940)
++|+|+ .++|++|+||||+++|+.|. ||+
T Consensus 80 -------~lg~~~-------------------------------------~~~t~~G~~std~~vL~~l~--~p~----- 108 (429)
T cd08643 80 -------KYGWEP-------------------------------------QEFTESGEPKVDEDVLSKLD--YPE----- 108 (429)
T ss_pred -------hcCCCC-------------------------------------CCcCCCCCCCcCHHHHHhcc--chH-----
Confidence 577753 25689999999999999996 664
Q ss_pred CCCCCCCCCCCcccccchhcccccchhhhhHHHHHHHhHHHHHHHHHHHHhhhHhhhhhc---cccCCccCCCCceeeee
Q 002293 752 DGAHDLDDSGCTEETEYKGAVASNNKIFATEQEAREACDAISALCEVCSIDSLISNFILP---LQGSNVSGKNGRVHCSL 828 (940)
Q Consensus 752 ~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~i~~LLeyR~l~KLlstyi~~---L~~~~~~~~dGRIH~s~ 828 (940)
+++|++||.++|++++|+++ |++ ....|||||++|
T Consensus 109 ----------------------------------------~~~ileyr~l~K~~st~~~~~~~~l~--~v~~dgRIH~~~ 146 (429)
T cd08643 109 ----------------------------------------AKLLAEYLLVQKRLGQLADGNNAWLK--LVHEDGRIHGAV 146 (429)
T ss_pred ----------------------------------------HHHHHHHHHHHHHHHHHHhhHHHHHH--HcCCCCceeeeE
Confidence 35689999999999999987 444 245789999999
Q ss_pred cC-CCccceeeecCCCccccCC-CccchhhccceeecCCCCeEEEeeccchhHHHHHHhcCC---HHHHHHHhcCCCchH
Q 002293 829 NI-NTETGRLSARRPNLQNQPA-LEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANC---KSMLDAFKAGGDFHS 903 (940)
Q Consensus 829 nq-gTaTGRLSSs~PNLQNIP~-~~~~~~~iR~~Fia~~G~~LvsaDYSQIELRILAhlS~D---~~Li~af~~g~DiH~ 903 (940)
+| +|+||||||++|||||||+ +++.|..||++|+|++|++||++||||||||||||||+| +.|++ |..|+|||+
T Consensus 147 nq~gt~TGRlSss~PNLQnIP~~~~~~G~~iR~~Fva~~G~~lv~aDySQiELRiLAhls~d~~~~~l~~-~~~~~DiH~ 225 (429)
T cd08643 147 NTNGAVTGRATHFSPNMAQVPAVGSPYGKECRELFGVPPGWSLVGADASGLELRCLAHYLARYDGGAYTR-KVLGGDIHW 225 (429)
T ss_pred EeCCccccccccCCCcccCCCCCCcccchhhhheEecCCCCEEEEecHHHHHHHHHHHHhcccchHHHHh-hhcccchhH
Confidence 98 8999999999999999995 567788999999999999999999999999999999998 78888 788999999
Q ss_pred HHHHHHcCC
Q 002293 904 RTAMNMYPH 912 (940)
Q Consensus 904 ~tAs~~fg~ 912 (940)
.||+. +|+
T Consensus 226 ~ta~~-~g~ 233 (429)
T cd08643 226 ANAQA-MGL 233 (429)
T ss_pred HHHHH-hCh
Confidence 99987 665
No 8
>cd08642 DNA_pol_A_pol_I_A Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. P
Probab=100.00 E-value=6.5e-41 Score=373.75 Aligned_cols=200 Identities=23% Similarity=0.208 Sum_probs=168.9
Q ss_pred HHHHHHHHHHHHHHHHHhhhcCCCCccccCCCHHHHHHHhcCCCCCCCCCCCCCCcccccccCCCccccccCCCCCcccc
Q 002293 629 KVARAEQEAAVNRFRKWASKHCPDAKYMNVGSDTQLRQLLFGGKPNSKDDSESLPIERIFKVPNTEGVIAEGKKTPSKFR 708 (940)
Q Consensus 629 ~~l~~e~e~le~ei~~~a~k~~~~g~~fNl~SpkQL~~lLF~~~~~~~~~~l~LP~er~~k~~~~~~~~~~~Kktp~~~~ 708 (940)
....+..++++++|++++ |.. |++||+||.++||+ ++++|.+ .+
T Consensus 7 ~~~~~~k~~l~~~i~~~~------g~~-n~~SpkQL~~~Lf~--------~~~l~~~-------------~~-------- 50 (378)
T cd08642 7 ACDDQYKEELLEEAKELT------GLD-NPNSPAQLKDWLNE--------QGGEVDS-------------LL-------- 50 (378)
T ss_pred HHHHHHHHHHHHHHHHHh------CCC-CCCCHHHHHHHHHH--------cCCCCCC-------------Cc--------
Confidence 445566778888887776 555 99999999999998 6777631 00
Q ss_pred cchhcccccCCCCccccccCCCcCcHHHHHHHHhccCccccccCCCCCCCCCCCcccccchhcccccchhhhhHHHHHHH
Q 002293 709 NITLRSIGVDLPTEMYTATGWPSVGGDALKTLARNISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNKIFATEQEAREA 788 (940)
Q Consensus 709 ~i~l~~lG~~lp~~~kTktG~~STd~evLe~L~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~ 788 (940)
++| | +|+.|++.||+
T Consensus 51 --------------k~t------t---vl~~l~~~~~~------------------------------------------ 65 (378)
T cd08642 51 --------------KKD------V---VALLLKTAPGD------------------------------------------ 65 (378)
T ss_pred --------------hhH------H---HHHHhcccCcH------------------------------------------
Confidence 111 2 88888766653
Q ss_pred hHHHHHHHHHHHHhhhHh-hhhhccccCCccCCCCceeeeecC-C-CccceeeecCCCccccCC----------------
Q 002293 789 CDAISALCEVCSIDSLIS-NFILPLQGSNVSGKNGRVHCSLNI-N-TETGRLSARRPNLQNQPA---------------- 849 (940)
Q Consensus 789 ~~~i~~LLeyR~l~KLls-tyi~~L~~~~~~~~dGRIH~s~nq-g-TaTGRLSSs~PNLQNIP~---------------- 849 (940)
++.||+||++.|+.+ +|+++|++ .+ ++|||||++|+| + |+||||||++|||||||+
T Consensus 66 ---~~~iL~~R~~~k~~s~t~~~~l~~-~~-~~~gRih~~~~~~gat~TGRlss~~pnlQNiP~~~~~~~~~~~~~~~~~ 140 (378)
T cd08642 66 ---VKRVLELRQELSKTSVKKYEAMER-AV-CSDGRVRGLLQFYGANRTGRWAGRLVQVQNLPRNYLKDLDLARELVKSG 140 (378)
T ss_pred ---HHHHHHHHHHHhhccHHHHHHHHH-Hc-CCCCceeeeeeeecchhccccccCCCCcccCCCCcccchHHHHHHhhcc
Confidence 356999999999998 99999997 34 578999999998 8 999999999999999999
Q ss_pred ------------CccchhhccceeecCCCCeEEEeeccchhHHHHHHhcCCHHHHHHHhcCCCchHHHHHHHcCCCcccc
Q 002293 850 ------------LEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAV 917 (940)
Q Consensus 850 ------------~~~~~~~iR~~Fia~~G~~LvsaDYSQIELRILAhlS~D~~Li~af~~g~DiH~~tAs~~fg~~~eeV 917 (940)
++..+..||+||+|++|++|+++||||||||||||||+|+.|+++|++|.|||+.||+.|||+|++++
T Consensus 141 d~~~~~~~~~~~~~~~~~~iR~aFva~~G~~lvsaDySQIElRVLAhlS~D~~li~af~~g~Dih~~tAs~if~vp~e~~ 220 (378)
T cd08642 141 DFDALELLYGSVPDVLSQLIRTAFIPSEGHRFIVSDFSAIEARVIAWLAGEQWRLDVFATHGKIYEASASQMFGVPVEKI 220 (378)
T ss_pred chhhhhhhccccccHHHHHhHHheecCCCCEEEEecHHHHHHHHHHHHhCCHHHHHHHhcCCChHHHHHHHHhCCChhhc
Confidence 44556789999999999999999999999999999999999999999999999999999999999864
Q ss_pred ccccccccccCCCCCCCCCC
Q 002293 918 ETGQVLLEWHGEDKPPVPLL 937 (940)
Q Consensus 918 tk~~~~~~~~~~~k~~~~~~ 937 (940)
+|.++.|+.+|..+|.+
T Consensus 221 ---~v~~~~R~~AK~vnfGi 237 (378)
T cd08642 221 ---GKNSHLRQKGKVAELAL 237 (378)
T ss_pred ---ccCHHHHHHhhhhhccc
Confidence 46678888999888753
No 9
>cd08640 DNA_pol_A_plastid_like DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication. DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including
Probab=100.00 E-value=4e-41 Score=376.43 Aligned_cols=191 Identities=63% Similarity=1.004 Sum_probs=165.4
Q ss_pred CCCcCcHHHHHHHHhccCccccccCCCCCCCCCCCcccccchhcccccchhhhhHHHHHHHhHHHHHHHHHHHHhhhHhh
Q 002293 728 GWPSVGGDALKTLARNISAEYDCVDGAHDLDDSGCTEETEYKGAVASNNKIFATEQEAREACDAISALCEVCSIDSLISN 807 (940)
Q Consensus 728 G~~STd~evLe~L~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~i~~LLeyR~l~KLlst 807 (940)
|+||++.++|..++.+.+..- + ..-|.-++ -..+++..++.++++..||+||+++||+||
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~--------~-~~~~~~~~-----------~~~~~~~~~~~~~~~~~il~~r~~~Kl~st 60 (371)
T cd08640 1 GLPSVDSEALRELAGDPEADI--------L-LYEWCYEN-----------GVSGGEEGKEACEAIEALKEIKSISTLLST 60 (371)
T ss_pred CCCccchHHHHHhcCCccccc--------h-hhHHHHHh-----------ccCCccccchhhHHHHHHHHHHHHHHHHHH
Confidence 457999999999987643211 1 00111000 011455667889999999999999999999
Q ss_pred hhhccccCCccCCCCceeeeecCCCccceeeecCCCccccCCCccchhhccceeecCCCCeEEEeeccchhHHHHHHhcC
Q 002293 808 FILPLQGSNVSGKNGRVHCSLNINTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLAN 887 (940)
Q Consensus 808 yi~~L~~~~~~~~dGRIH~s~nqgTaTGRLSSs~PNLQNIP~~~~~~~~iR~~Fia~~G~~LvsaDYSQIELRILAhlS~ 887 (940)
|+++|++ .+++.|||||++|+|.|+||||||++|||||||++++.++.||+||+|++|++||++||||||||||||||+
T Consensus 61 y~~~l~~-~~~~~dgRih~~~~~~t~TGRlSs~~PNLQNiP~~~~~~~~iR~~Fva~~G~~lv~aDySQiElRvlA~lS~ 139 (371)
T cd08640 61 FIIPLQE-LLNDSTGRIHCSLNINTETGRLSSRNPNLQNQPALEKDRYKIRKAFIASPGNTLIVADYSQLELRLLAHMTR 139 (371)
T ss_pred HHHHHHH-HccCCCCCeeeeEeeccceeehhcCCCCCCCCCCCCccccchhheEecCCCCEEEEechhhhhHHHHHHHcC
Confidence 9999997 455788999999998899999999999999999998888899999999999999999999999999999999
Q ss_pred CHHHHHHHhcCCCchHHHHHHHcCCCccccccccccccccCCCCCCCCCCCC
Q 002293 888 CKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPLLKN 939 (940)
Q Consensus 888 D~~Li~af~~g~DiH~~tAs~~fg~~~eeVtk~~~~~~~~~~~k~~~~~~~~ 939 (940)
|+.|+++|++|.|||+.||+.+||+++|+|++++++.+|..++|+|+|.+++
T Consensus 140 D~~Li~af~~g~DiH~~tA~~if~~~~e~v~~~~~~~~~~~~~~~~~~~~~~ 191 (371)
T cd08640 140 CKSMIEAFNAGGDFHSRTASGMYPHVAEAVANGEVLLEWKSEGKPPAPLLKD 191 (371)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHhCCCHHHhcccccccccccccccccccccc
Confidence 9999999999999999999999999999999999999999999999987764
No 10
>cd08638 DNA_pol_A_theta DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis and in somatic hypermutation. DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis (TLS) and in somatic hypermutation (SHM). DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Pol theta is an exception among family A polymerases and generates processive single base substitutions. Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondri
Probab=100.00 E-value=6.9e-39 Score=359.56 Aligned_cols=139 Identities=34% Similarity=0.443 Sum_probs=125.7
Q ss_pred HHHHHHHHHHhhhHhhhhhccccCCcc----CCCCceeeeecC-CCccceeeecCCCccccCCCcc--------------
Q 002293 792 ISALCEVCSIDSLISNFILPLQGSNVS----GKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEK-------------- 852 (940)
Q Consensus 792 i~~LLeyR~l~KLlstyi~~L~~~~~~----~~dGRIH~s~nq-gTaTGRLSSs~PNLQNIP~~~~-------------- 852 (940)
++.|++||+++|+++||+++++.+ +. +.||||||+|+| +|+||||||++|||||||+++.
T Consensus 46 ~~~ile~r~l~Kl~sty~~~~~~~-~~~~~~~~~grih~~~~~~gt~TGRlSs~~PNlQniP~~~~~~~~~~~~~~~~~~ 124 (373)
T cd08638 46 PKLILEYRKLSKLLTTYVEPLLLL-CKLSSSLQMYRIHPTWNQTGTATGRLSSSEPNLQNVPKDFEIKDAPSPPAGSEGD 124 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-hhcccCCCCCeEeeEEEEccceeeeeeeccCCcCCCCCCCccccccccccccccc
Confidence 467999999999999999999973 32 678999999998 8999999999999999999753
Q ss_pred -chhhccceeecCCCCeEEEeeccchhHHHHHHhcCCHHHHHHHhcCCCchHHHHHHHcCCCccccccccccccccCCCC
Q 002293 853 -DRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDK 931 (940)
Q Consensus 853 -~~~~iR~~Fia~~G~~LvsaDYSQIELRILAhlS~D~~Li~af~~g~DiH~~tAs~~fg~~~eeVtk~~~~~~~~~~~k 931 (940)
.+..+|+||+|++|++||++||||||||||||+|+|+.|+++|++|+|+|+.+|+.|||+|+++|++ +.|+.+|
T Consensus 125 ~~~~~iR~~f~a~~G~~lv~~DysqiElRvlA~ls~D~~l~~~~~~g~Dih~~~A~~~~g~~~~~v~~-----~~R~~aK 199 (373)
T cd08638 125 IPTISLRHAFIPPPGRVLLSADYSQLELRILAHLSGDPALIELLNSGGDVFKMIAAQWLGKPVEEVTD-----EERQQAK 199 (373)
T ss_pred hhhhhhhheeeCCCCCEEEEechhhhHHHHHHHHhCCHHHHHHHhcCCCHHHHHHHHHhCCChhhCCH-----HHHHHHh
Confidence 3578999999999999999999999999999999999999999999999999999999999997764 6677777
Q ss_pred CCCCC
Q 002293 932 PPVPL 936 (940)
Q Consensus 932 ~~~~~ 936 (940)
+.+|.
T Consensus 200 ~~~fg 204 (373)
T cd08638 200 QLVYG 204 (373)
T ss_pred HHHHh
Confidence 76654
No 11
>cd08639 DNA_pol_A_Aquificae_like Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nucleas
Probab=100.00 E-value=1.8e-34 Score=318.31 Aligned_cols=138 Identities=33% Similarity=0.450 Sum_probs=126.0
Q ss_pred hHHHHHHHHHHHHhhhHhhhhhccccCCccCCCCceeeeecC-CCccceeeecCCCccccCCCccchhhccceeecCCCC
Q 002293 789 CDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGN 867 (940)
Q Consensus 789 ~~~i~~LLeyR~l~KLlstyi~~L~~~~~~~~dGRIH~s~nq-gTaTGRLSSs~PNLQNIP~~~~~~~~iR~~Fia~~G~ 867 (940)
++++..|++||+++|+++||++++++ .+.+.||||||+|+| +|+|||+||++|||||||+. ..+|++|+|+||+
T Consensus 29 ~p~~~~lle~r~~~kl~~t~~~~l~~-~~~~~~grih~~~~~~gt~TGRlS~~~PnlQniP~~----~~iR~~f~a~~G~ 103 (324)
T cd08639 29 HPAVRLLLEYRKLNKLISTFGEKLPK-HIHPVTGRIHPSFNQIGAASGRMSCSNPNLQQIPRE----REFRRCFVAPEGN 103 (324)
T ss_pred ChHHHHHHHHHHHhHHHHHHHHHHHH-HccCCCCceeeeEEecccceeehhhccCccccCCCC----cccceeEEcCCCC
Confidence 45788999999999999999999997 454578999999998 89999999999999999974 3799999999999
Q ss_pred eEEEeeccchhHHHHHHhcCCHHHHHHHhcCCCchHHHHHHHcCCCccccccccccccccCCCCCCCCC
Q 002293 868 SLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPL 936 (940)
Q Consensus 868 ~LvsaDYSQIELRILAhlS~D~~Li~af~~g~DiH~~tAs~~fg~~~eeVtk~~~~~~~~~~~k~~~~~ 936 (940)
+||++||||||||||||||+|+.|+++|++|.|+|+.+|+.+||+++++|++ +.|+.+|+.+|.
T Consensus 104 ~lv~aDysqiElRilA~ls~D~~l~~~~~~g~Dih~~~A~~~~g~~~~~v~~-----~~R~~aK~~~fg 167 (324)
T cd08639 104 KLIIADYSQIELRIAAEISGDERMISAYQKGEDLHRLTASLITGKPIEEITK-----EERQLAKAVNFG 167 (324)
T ss_pred EEEEechhhhHHHHHHHHhCCHHHHHHHhcCCCHhHHHHHHHhCCChhhCCH-----HHHHHhhhHHHH
Confidence 9999999999999999999999999999999999999999999999998875 567778876654
No 12
>cd06444 DNA_pol_A Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication. DNA polymerase family A, 5'-3' polymerase domain. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gamma, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic polymerase I (pol I) has two functional domains located on the same polypeptide; a 5'-
Probab=100.00 E-value=3.9e-34 Score=318.49 Aligned_cols=138 Identities=34% Similarity=0.347 Sum_probs=126.6
Q ss_pred hHHHHHHHHHHHHhhhHhhhhhccccCCccCCCCceeeeecC-CCccceeeecCCCccccCCCccchhhccceeecCCCC
Q 002293 789 CDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLNI-NTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGN 867 (940)
Q Consensus 789 ~~~i~~LLeyR~l~KLlstyi~~L~~~~~~~~dGRIH~s~nq-gTaTGRLSSs~PNLQNIP~~~~~~~~iR~~Fia~~G~ 867 (940)
++++..|++||+++|++++|++++++ .+ ..||||||+|+| +|+|||+||++|||||||+++..+..||++|+|++|+
T Consensus 26 hp~~~~ile~r~~~Kl~st~~~~~~~-~~-~~~gRih~~~~~~gT~TGRlSs~~PNlQniP~~~~~g~~iR~~f~a~~G~ 103 (347)
T cd06444 26 HPAVPLLLEYKKLAKLWSANGWPWLD-QW-VRDGRFHPEYVPGGTVTGRWASRGGNAQQIPRRDPLGRDIRQAFVADPGW 103 (347)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHH-Hh-cccCccccEEEEcccceeeeccCCCccccCCCCCchhhhhhheEecCCCC
Confidence 35678899999999999999999997 34 369999999998 8999999999999999999988888999999999999
Q ss_pred eEEEeeccchhHHHHHHhcCCHHHHHHHhcCCCchHHHHHHHcCCCccccccccccccccCCCCCCCCC
Q 002293 868 SLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPVPL 936 (940)
Q Consensus 868 ~LvsaDYSQIELRILAhlS~D~~Li~af~~g~DiH~~tAs~~fg~~~eeVtk~~~~~~~~~~~k~~~~~ 936 (940)
+||++||||||||||||||+|+.|+++|++|.|+|+.||+.+||+| +.++.|+.+|+.+|.
T Consensus 104 ~lv~aDysqiElRilA~ls~D~~l~~~f~~g~Dih~~~A~~~~~~~--------v~~~~R~~AK~~~fg 164 (347)
T cd06444 104 TLVVADASQLELRVLAALSGDEALAEAFGRGGDLYTATASAMFGVP--------VGGGERQHAKIANLG 164 (347)
T ss_pred EEEEechhHHHHHHHHHHhCCHHHHHHHhcCCCHHHHHHHHHhCCC--------CCHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999998 456777777776653
No 13
>cd08641 DNA_pol_gammaA Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. DNA polymerase gamma (Pol gamma), 5'-3' polymerase domain (Pol gammaA). Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gammaA, and several bacteriophage polymerases including those from odd-nu
Probab=99.82 E-value=7.2e-21 Score=211.96 Aligned_cols=89 Identities=27% Similarity=0.287 Sum_probs=83.7
Q ss_pred CCCCceeeeecC-CCccce------eeecCCCccccCCCccchhhccceeecCCCCeEEEeeccchhHHHHHHhcCCHHH
Q 002293 819 GKNGRVHCSLNI-NTETGR------LSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSM 891 (940)
Q Consensus 819 ~~dGRIH~s~nq-gTaTGR------LSSs~PNLQNIP~~~~~~~~iR~~Fia~~G~~LvsaDYSQIELRILAhlS~D~~L 891 (940)
..+|||||.|++ ||+||| +|+++||+||+|+ +||++|+|+|||+||+|||||||||| ||||+|+.|
T Consensus 94 ~~~Gri~p~~~~~GtvTgRa~~~tW~tas~~~~~~iG~------eiR~aF~ap~G~~lVgADySQiELRi-A~lsgD~~l 166 (425)
T cd08641 94 PGYGAILPQVVPMGTITRRAVEPTWLTASNAKKNRVGS------ELKAMVQAPPGYSFVGADVDSQELWI-ASVLGDAHF 166 (425)
T ss_pred CCCCeEeeeeecCcccccccccccccccCCCCcchhhH------HHHhheecCCCCEEEEEchhHHHHHH-HHHcCCHhh
Confidence 468999999998 999999 8889999999987 79999999999999999999999998 999999999
Q ss_pred H-----HHH---------hcCCCchHHHHHHHcCCCcc
Q 002293 892 L-----DAF---------KAGGDFHSRTAMNMYPHIRN 915 (940)
Q Consensus 892 i-----~af---------~~g~DiH~~tAs~~fg~~~e 915 (940)
+ .|| .+|.|||+.||+ +||+++.
T Consensus 167 ~~~~~~~AF~~~~l~g~k~~g~DIH~~TA~-i~gisR~ 203 (425)
T cd08641 167 GGIHGATAIGWMTLQGKKSEGTDLHSKTAS-ILGISRD 203 (425)
T ss_pred hhccccchhhhhhhcccccCCCCHHHHHHH-HhCCCHH
Confidence 9 899 889999999999 8999853
No 14
>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=99.82 E-value=4.3e-19 Score=175.67 Aligned_cols=173 Identities=30% Similarity=0.440 Sum_probs=132.0
Q ss_pred eEEecCHHHHHHHHHHHhccCCCceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhhh
Q 002293 345 VMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDL 424 (940)
Q Consensus 345 y~lV~t~e~L~eli~~L~~a~~~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~~ 424 (940)
|++|+|.+++.+++..+.+. +.+|||+|+++++...... ++.+++++.+. .+++++.........
T Consensus 1 y~~v~~~~~l~~~~~~l~~~---~~~a~D~E~~~~~~~~~~~----~~~~iq~~~~~--------~~~i~~~~~~~~~~~ 65 (176)
T PF01612_consen 1 YQIVDTEEELEEAIKKLKNA---KVLAFDTETTGLDPYSYNP----KIALIQLATGE--------GCYIIDPIDLGDNWI 65 (176)
T ss_dssp SEEEHSHHHHHHHHHHHTTT---SEEEEEEEEETSTSTTSSE----EEEEEEEEESC--------EEEEECGTTSTTTTH
T ss_pred CEecCCHHHHHHHHHHHcCC---CeEEEEEEECCCCccccCC----eEEEEEEecCC--------Cceeeeeccccccch
Confidence 78999999999999999886 4899999999999854332 34567766543 345556554321125
Q ss_pred HhhhhhhhcCCCceEEEeccHHHHHHHHH-cCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchh-hh
Q 002293 425 LNEFAPFFEDPSIKKVWHNYSFDNHVLEN-YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKA-YQ 502 (940)
Q Consensus 425 l~~Lk~~Led~~i~KVgHNaKfDL~~L~r-~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg-~~ 502 (940)
...|+++|+++.+.||+||++||+++|.+ +|+.+.+ ++||++|++++++... ++|++|+.. |++ +.
T Consensus 66 ~~~l~~ll~~~~i~kv~~n~~~D~~~L~~~~~i~~~~-~~D~~l~~~~l~~~~~----~~L~~L~~~-------~l~~~~ 133 (176)
T PF01612_consen 66 LDALKELLEDPNIIKVGHNAKFDLKWLYRSFGIDLKN-VFDTMLAAYLLDPTRS----YSLKDLAEE-------YLGNID 133 (176)
T ss_dssp HHHHHHHHTTTTSEEEESSHHHHHHHHHHHHTS--SS-EEEHHHHHHHTTTSTT----SSHHHHHHH-------HHSEEE
T ss_pred HHHHHHHHhCCCccEEEEEEechHHHHHHHhccccCC-ccchhhhhhccccccc----ccHHHHHHH-------Hhhhcc
Confidence 78999999999999999999999999988 8998866 7999999999999873 899999988 443 21
Q ss_pred ccccCCCCccccccccchhhhhcccccccCCCCCcccc-ccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 002293 503 KDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKIST-IAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLL 578 (940)
Q Consensus 503 ~~l~k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~-~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~~~Le 578 (940)
. .+.. .. .+|. .+|+ ++.++.|||.||.++++||+.|.++|+
T Consensus 134 ---------------~------~~~~---~~---~~~~~~~~l-------~~~~~~YAa~D~~~~~~l~~~l~~~l~ 176 (176)
T PF01612_consen 134 ---------------L------DKKE---QM---SDWRKARPL-------SEEQIEYAAQDAVVTFRLYEKLKPQLE 176 (176)
T ss_dssp ----------------------GHCC---TT---SSTTTSSS--------HHHHHHHHHHHHHTHHHHHHHHHHHHC
T ss_pred ---------------C------cHHH---hh---ccCCcCCCC-------hHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 0 0000 01 2566 5665 578999999999999999999999874
No 15
>PRK10829 ribonuclease D; Provisional
Probab=99.81 E-value=1.8e-18 Score=194.66 Aligned_cols=172 Identities=17% Similarity=0.146 Sum_probs=139.6
Q ss_pred ceEEecCHHHHHHHHHHHhccCCCceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhh
Q 002293 344 NVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRD 423 (940)
Q Consensus 344 ~y~lV~t~e~L~eli~~L~~a~~~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~ 423 (940)
.|.+|+|+++|.++++.+... +.+|||||+.+.+++.+.++ .+++.. ++..+.||+..+.
T Consensus 2 ~~~~I~t~~~L~~~~~~l~~~---~~lalDtEf~~~~ty~~~l~------LiQl~~--------~~~~~LiD~l~~~--- 61 (373)
T PRK10829 2 NYQMITTDDALASVCEAARAF---PAIALDTEFVRTRTYYPQLG------LIQLYD--------GEQLSLIDPLGIT--- 61 (373)
T ss_pred CcEEeCCHHHHHHHHHHHhcC---CeEEEecccccCccCCCcee------EEEEec--------CCceEEEecCCcc---
Confidence 488999999999999998876 58999999999999877653 344433 3447889987542
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHH-HcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhh
Q 002293 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLE-NYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQ 502 (940)
Q Consensus 424 ~l~~Lk~~Led~~i~KVgHNaKfDL~~L~-r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg~~ 502 (940)
.+..|.++|+++.+.||+|++.+|+.+|. .+|+.+ ..+|||++|+.+++-+. ++||..|++. ++|++
T Consensus 62 d~~~L~~ll~~~~ivKV~H~~~~Dl~~l~~~~g~~p-~~~fDTqiaa~~lg~~~----~~gl~~Lv~~-------~lgv~ 129 (373)
T PRK10829 62 DWSPFKALLRDPQVTKFLHAGSEDLEVFLNAFGELP-QPLIDTQILAAFCGRPL----SCGFASMVEE-------YTGVT 129 (373)
T ss_pred chHHHHHHHcCCCeEEEEeChHhHHHHHHHHcCCCc-CCeeeHHHHHHHcCCCc----cccHHHHHHH-------HhCCc
Confidence 47889999999999999999999999985 489876 45899999999998654 3799999997 55543
Q ss_pred ccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 002293 503 KDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMS 581 (940)
Q Consensus 503 ~~l~k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~~~Lee~~ 581 (940)
+ .|+. +. +||..+|| ++.|+.|||.||.+++.||+.|..+|.+.+
T Consensus 130 --l-------------------dK~~---~~---sDW~~RPL-------s~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g 174 (373)
T PRK10829 130 --L-------------------DKSE---SR---TDWLARPL-------SERQCEYAAADVFYLLPIAAKLMAETEAAG 174 (373)
T ss_pred --c-------------------Cccc---cc---CCCCCCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 1 1111 11 48999998 578999999999999999999999999753
No 16
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=99.80 E-value=1.9e-18 Score=174.38 Aligned_cols=182 Identities=34% Similarity=0.442 Sum_probs=134.4
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCC------CChhhhHhhhhhhhcCCCceEEE
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD------GGGRDLLNEFAPFFEDPSIKKVW 441 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~------~~~e~~l~~Lk~~Led~~i~KVg 441 (940)
..+++|+|++|++++.+.++ +++++.++ +..+|++..+ .....++..|+++|++..+.+|+
T Consensus 6 ~~~a~d~e~~~~~~~~~~i~------~l~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~v~ 72 (193)
T cd06139 6 KVFAFDTETTSLDPMQAELV------GISFAVEP-------GEAYYIPLGHDYGGEQLPREEVLAALKPLLEDPSIKKVG 72 (193)
T ss_pred CeEEEEeecCCCCcCCCeEE------EEEEEcCC-------CCEEEEecCCCccccCCCHHHHHHHHHHHHhCCCCcEEe
Confidence 57999999999998766654 46665443 2256665432 12345667799999988778999
Q ss_pred eccHHHHHHHHHcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhhccccCCCCccccccccchh
Q 002293 442 HNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMK 521 (940)
Q Consensus 442 HNaKfDL~~L~r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg~~~~l~k~~s~eELvGk~s~k 521 (940)
||++||+++|.++|+.+.+.++||++++|+++|+.. +++|++++++ |++.+ ...+.
T Consensus 73 hn~k~d~~~l~~~gi~~~~~~~Dt~l~a~ll~p~~~---~~~l~~l~~~-------~l~~~--------------~~~~~ 128 (193)
T cd06139 73 QNLKFDLHVLANHGIELRGPAFDTMLASYLLNPGRR---RHGLDDLAER-------YLGHK--------------TISFE 128 (193)
T ss_pred eccHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCC---CCCHHHHHHH-------HhCCC--------------CccHH
Confidence 999999999999999988889999999999999863 3799999998 44321 01122
Q ss_pred hhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCchHHHHHHHH
Q 002293 522 DIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWKLDGKPVPGKSMFDFYQEY 601 (940)
Q Consensus 522 elfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~~~Lee~~~~~~~~~~~~~~l~~Ly~~I 601 (940)
.+++++. +. .+|...| ...+..||+.|+.++++|++.|.++|++. .++.++|++|
T Consensus 129 ~~~~k~~--~~----~~~~~~~--------~~~~~~ya~~d~~~~~~l~~~l~~~l~~~-----------~~~~~l~~~i 183 (193)
T cd06139 129 DLVGKGK--KQ----ITFDQVP--------LEKAAEYAAEDADITLRLYELLKPKLKEE-----------PGLLELYEEI 183 (193)
T ss_pred HHcCCCc--Cc----CCccccC--------HHHHHHHHHHHHHHHHHHHHHHHHHHhhh-----------hhHHHHHHHH
Confidence 3444321 11 1233223 24578899999999999999999999861 3689999999
Q ss_pred hcchHHHHHH
Q 002293 602 WQPFGEILVK 611 (940)
Q Consensus 602 EmPL~~VLa~ 611 (940)
|||+++||++
T Consensus 184 E~Pl~~vL~~ 193 (193)
T cd06139 184 EMPLIPVLAE 193 (193)
T ss_pred hccHHHHhcC
Confidence 9999999963
No 17
>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases. Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Probab=99.78 E-value=2.9e-18 Score=172.15 Aligned_cols=174 Identities=22% Similarity=0.265 Sum_probs=131.5
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcCCCceEEEeccHHH
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFEDPSIKKVWHNYSFD 447 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~~l~~Lk~~Led~~i~KVgHNaKfD 447 (940)
..+++|+|+++.+++..+++ +++++.+. ..+|++..+. ......|+++|+++.+.|++||+|+|
T Consensus 4 ~~~~~~~~~~~~~~~~~~l~------~i~l~~~~--------~~~~i~~~~~--~~~~~~l~~~l~~~~~~ki~~d~K~~ 67 (178)
T cd06140 4 DEVALYVELLGENYHTADII------GLALANGG--------GAYYIPLELA--LLDLAALKEWLEDEKIPKVGHDAKRA 67 (178)
T ss_pred CceEEEEEEcCCCcceeeEE------EEEEEeCC--------cEEEEeccch--HHHHHHHHHHHhCCCCceeccchhHH
Confidence 46899999999998766654 45555321 3577875321 02456688999999999999999999
Q ss_pred HHHHHHcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhhccccCCCCccccccccchhhhhccc
Q 002293 448 NHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRR 527 (940)
Q Consensus 448 L~~L~r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg~~~~l~k~~s~eELvGk~s~kelfGK~ 527 (940)
+++|.++|+.+++.+|||+||+||++|+.. +++|++|+.+ |++++ .....+++|++
T Consensus 68 ~~~l~~~gi~~~~~~fDt~laaYLL~p~~~---~~~l~~l~~~-------yl~~~--------------~~~~~~~~~~~ 123 (178)
T cd06140 68 YVALKRHGIELAGVAFDTMLAAYLLDPTRS---SYDLADLAKR-------YLGRE--------------LPSDEEVYGKG 123 (178)
T ss_pred HHHHHHCCCcCCCcchhHHHHHHHcCCCCC---CCCHHHHHHH-------HcCCC--------------CcchHHhcCCC
Confidence 999999999998889999999999999864 5799999998 44332 00112233332
Q ss_pred ccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCchHHHHHHHHhcchHH
Q 002293 528 KLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWKLDGKPVPGKSMFDFYQEYWQPFGE 607 (940)
Q Consensus 528 k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~~~Lee~~~~~~~~~~~~~~l~~Ly~~IEmPL~~ 607 (940)
+ + +...+ .+.+..|++.|+.++++|++.|.++|++ .++..+|++|||||++
T Consensus 124 ~--~-------~~~~~--------~~~~~~y~~~~a~~l~~l~~~l~~~L~~------------~~l~~L~~~iE~PL~~ 174 (178)
T cd06140 124 A--K-------FAVPD--------EEVLAEHLARKAAAIARLAPKLEEELEE------------NEQLELYYEVELPLAE 174 (178)
T ss_pred C--C-------cccCC--------HHHHHHHHHHHHHHHHHHHHHHHHHHHH------------hHHHHHHHHHHhhHHH
Confidence 1 0 11111 3557889999999999999999999997 3799999999999999
Q ss_pred HHH
Q 002293 608 ILV 610 (940)
Q Consensus 608 VLa 610 (940)
||+
T Consensus 175 VL~ 177 (178)
T cd06140 175 VLA 177 (178)
T ss_pred Hhc
Confidence 996
No 18
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.77 E-value=5.2e-18 Score=187.90 Aligned_cols=216 Identities=20% Similarity=0.168 Sum_probs=156.6
Q ss_pred ecCHHHHHHHHHHHhccCCCceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhhhHhh
Q 002293 348 VDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNE 427 (940)
Q Consensus 348 V~t~e~L~eli~~L~~a~~~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~~l~~ 427 (940)
|++.+.+++++..+.+. +.||+||||.++.++.+++| .++++.++ ....||+... ...++.
T Consensus 1 i~~~~~l~~~~~~~~~~---~~iAiDTEf~r~~t~~p~Lc------LIQi~~~e--------~~~lIdpl~~--~~d~~~ 61 (361)
T COG0349 1 ITTGDLLAAACALLRGS---KAIAIDTEFMRLRTYYPRLC------LIQISDGE--------GASLIDPLAG--ILDLPP 61 (361)
T ss_pred CCchhHHHHHHHHhcCC---CceEEecccccccccCCceE------EEEEecCC--------CceEeccccc--ccccch
Confidence 46778888999888875 58999999999999998864 35666554 2567888642 246788
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHHc-CCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhhcccc
Q 002293 428 FAPFFEDPSIKKVWHNYSFDNHVLENY-GLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMS 506 (940)
Q Consensus 428 Lk~~Led~~i~KVgHNaKfDL~~L~r~-GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg~~~~l~ 506 (940)
|..+|.|+.+.||+|.+.||+.+|.+. |+. +.++|||+||+.+++... ++||++|+++ +++++
T Consensus 62 l~~Ll~d~~v~KIfHaa~~DL~~l~~~~g~~-p~plfdTqiAa~l~g~~~----~~gl~~Lv~~-------ll~v~---- 125 (361)
T COG0349 62 LVALLADPNVVKIFHAARFDLEVLLNLFGLL-PTPLFDTQIAAKLAGFGT----SHGLADLVEE-------LLGVE---- 125 (361)
T ss_pred HHHHhcCCceeeeeccccccHHHHHHhcCCC-CCchhHHHHHHHHhCCcc----cccHHHHHHH-------HhCCc----
Confidence 999999999999999999999999886 654 467999999999999875 4999999998 55553
Q ss_pred CCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCC
Q 002293 507 KGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWKLDG 586 (940)
Q Consensus 507 k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~~~Lee~~~~~~~ 586 (940)
+.| +. + .+||..+|| ++.|+.||+.||.+++.||..|..+|.+.+|.-
T Consensus 126 --------ldK---------~~---q---~SDW~~RPL-------s~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r~~-- 173 (361)
T COG0349 126 --------LDK---------SE---Q---RSDWLARPL-------SEAQLEYAAADVEYLLPLYDKLTEELAREGRLE-- 173 (361)
T ss_pred --------ccc---------cc---c---ccccccCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchH--
Confidence 111 11 2 249999998 588999999999999999999999999975521
Q ss_pred CCCCCchHHHHHHHHhc----chHHHHHHHhHc-CcccCHHHHHHHHHHHHHHHH
Q 002293 587 KPVPGKSMFDFYQEYWQ----PFGEILVKMETE-GMLVDREYLSEIEKVARAEQE 636 (940)
Q Consensus 587 ~~~~~~~l~~Ly~~IEm----PL~~VLa~ME~~-GI~VD~E~L~el~~~l~~e~e 636 (940)
...+.+.-++. +..+-.+.-+.. ....+...+..++..+.-+.+
T Consensus 174 ------~a~~ef~~l~~r~~~~~~~~~~w~~i~~a~~~~p~~la~l~~La~wRe~ 222 (361)
T COG0349 174 ------WAEDEFRLLPTRRTYKVLPEDAWREIKIAHSLDPRELAVLRELAAWRER 222 (361)
T ss_pred ------HHHHHHHHhhhccccccChHhHHHHhhhhhcCChHHHHHHHHHHHHHHH
Confidence 11111221111 122333334333 455666667766665554433
No 19
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=99.76 E-value=1.6e-17 Score=186.96 Aligned_cols=169 Identities=18% Similarity=0.105 Sum_probs=135.8
Q ss_pred EecCHHHHHHHHHHHhccCCCceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhhhHh
Q 002293 347 VVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLN 426 (940)
Q Consensus 347 lV~t~e~L~eli~~L~~a~~~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~~l~ 426 (940)
+|+|+++|.++++.+.++ ++||||||+.+.+++.+.++ .+++. +++.+++||+... ..+.
T Consensus 1 ~I~t~~~l~~~~~~l~~~---~~ia~DtE~~~~~~y~~~l~------LiQia--------~~~~~~liD~~~~---~~~~ 60 (367)
T TIGR01388 1 WITTDDELATVCEAVRTF---PFVALDTEFVRERTFWPQLG------LIQVA--------DGEQLALIDPLVI---IDWS 60 (367)
T ss_pred CcCCHHHHHHHHHHHhcC---CEEEEeccccCCCCCCCcce------EEEEe--------eCCeEEEEeCCCc---ccHH
Confidence 588999999999999886 59999999999998877653 23333 3345788898753 2578
Q ss_pred hhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhhcccc
Q 002293 427 EFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMS 506 (940)
Q Consensus 427 ~Lk~~Led~~i~KVgHNaKfDL~~L~r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg~~~~l~ 506 (940)
.|+++|+|+.+.||+|++++|+++|.+.|..+++.+|||++|+||++++.. ++|++|++. |+++.
T Consensus 61 ~L~~lL~d~~i~KV~h~~k~Dl~~L~~~~~~~~~~~fDtqlAa~lL~~~~~----~~l~~Lv~~-------~Lg~~---- 125 (367)
T TIGR01388 61 PLKELLRDESVVKVLHAASEDLEVFLNLFGELPQPLFDTQIAAAFCGFGMS----MGYAKLVQE-------VLGVE---- 125 (367)
T ss_pred HHHHHHCCCCceEEEeecHHHHHHHHHHhCCCCCCcccHHHHHHHhCCCCC----ccHHHHHHH-------HcCCC----
Confidence 899999999999999999999999988766666779999999999999753 799999987 55442
Q ss_pred CCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 002293 507 KGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEM 580 (940)
Q Consensus 507 k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~~~Lee~ 580 (940)
+ .|+. + .++|..+|+ ++.++.||+.||.+++.||+.|..+|++.
T Consensus 126 --------l---------~K~~---~---~sdW~~rPL-------~~~q~~YAa~Dv~~L~~L~~~L~~~L~~~ 169 (367)
T TIGR01388 126 --------L---------DKSE---S---RTDWLARPL-------TDAQLEYAAADVTYLLPLYAKLMERLEES 169 (367)
T ss_pred --------C---------Cccc---c---cccCCCCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 0 1111 1 137877887 46799999999999999999999999875
No 20
>smart00482 POLAc DNA polymerase A domain.
Probab=99.70 E-value=6e-18 Score=176.53 Aligned_cols=77 Identities=43% Similarity=0.635 Sum_probs=69.9
Q ss_pred hhccceeecCCCCeEEEeeccchhHHHHHHhcCCHHHHHHHhcCCCchHHHHHHHcCCCccccccccccccccCCCCCCC
Q 002293 855 YKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMYPHIRNAVETGQVLLEWHGEDKPPV 934 (940)
Q Consensus 855 ~~iR~~Fia~~G~~LvsaDYSQIELRILAhlS~D~~Li~af~~g~DiH~~tAs~~fg~~~eeVtk~~~~~~~~~~~k~~~ 934 (940)
..||++|+|+||++||++||||||||||||||+|+.|+++|++|.|+|+.+|+.+||+++|+|++ +.|+.+|+-+
T Consensus 2 ~~iR~~f~a~~G~~lv~~DysqiElRilA~ls~D~~l~~~~~~g~D~h~~~A~~~~g~~~~~v~~-----~~R~~aK~~~ 76 (206)
T smart00482 2 REIRRAFVAPPGYVLVSADYSQIELRILAHLSGDENLLEAFNNGGDIHSKTAAQVFGVPEEEVTK-----ELRRAAKAIN 76 (206)
T ss_pred chhhheeeCCCCCEEEEeeHHHHHHHHHHHHcCCHHHHHHHhcCCCHHHHHHHHHhCCChhhCCH-----HHHHHHhHHH
Confidence 47999999999999999999999999999999999999999999999999999999999998764 5577777655
Q ss_pred CC
Q 002293 935 PL 936 (940)
Q Consensus 935 ~~ 936 (940)
+.
T Consensus 77 ~g 78 (206)
T smart00482 77 FG 78 (206)
T ss_pred HH
Confidence 43
No 21
>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=99.68 E-value=4.3e-16 Score=155.86 Aligned_cols=157 Identities=21% Similarity=0.151 Sum_probs=119.7
Q ss_pred HHHHHHHHh-ccCCCceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhhhHhhhhhhh
Q 002293 354 AKKVVWMLT-NKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFF 432 (940)
Q Consensus 354 L~eli~~L~-~a~~~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~~l~~Lk~~L 432 (940)
|+++++.|. .. +.|+||||+.+...+...+ ..++++.+. ..++.+|+.... .....|+++|
T Consensus 2 l~~~~~~l~~~~---~~ig~D~E~~~~~~~~~~~------~liQl~~~~-------~~~~l~d~~~~~--~~~~~L~~lL 63 (161)
T cd06129 2 LSSLCEDLSMDG---DVIAFDMEWPPGRRYYGEV------ALIQLCVSE-------EKCYLFDPLSLS--VDWQGLKMLL 63 (161)
T ss_pred HHHHHHHHhcCC---CEEEEECCccCCCCCCCce------EEEEEEECC-------CCEEEEecccCc--cCHHHHHHHh
Confidence 567888888 64 5999999999887754432 234444321 447778886542 2467789999
Q ss_pred cCCCceEEEeccHHHHHHHHH-cCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhhccccCCCCc
Q 002293 433 EDPSIKKVWHNYSFDNHVLEN-YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTD 511 (940)
Q Consensus 433 ed~~i~KVgHNaKfDL~~L~r-~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg~~~~l~k~~s~ 511 (940)
+++.+.||+|+++.|++.|.+ +|+.+.+ +|||++|++++++.. .++|++|+++ |++.. +
T Consensus 64 ~d~~i~Kvg~~~k~D~~~L~~~~gi~~~~-~~D~~~aa~ll~~~~----~~~L~~l~~~-------~lg~~--l------ 123 (161)
T cd06129 64 ENPSIVKALHGIEGDLWKLLRDFGEKLQR-LFDTTIAANLKGLPE----RWSLASLVEH-------FLGKT--L------ 123 (161)
T ss_pred CCCCEEEEEeccHHHHHHHHHHcCCCccc-HhHHHHHHHHhCCCC----CchHHHHHHH-------HhCCC--C------
Confidence 999999999999999999976 8998866 599999999999864 3699999987 45432 0
Q ss_pred cccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 002293 512 EGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLK 574 (940)
Q Consensus 512 eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~ 574 (940)
.|.. +. ++|..+|| ++.|+.|||.||.+++.||+.|.
T Consensus 124 -------------~K~~---~~---s~W~~rpL-------t~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 124 -------------DKSI---SC---ADWSYRPL-------TEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred -------------Cccc---ee---ccCCCCCC-------CHHHHHHHHHHHHHHHHHHHHHh
Confidence 1110 11 38999998 57899999999999999999885
No 22
>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=99.65 E-value=2.2e-15 Score=150.94 Aligned_cols=164 Identities=25% Similarity=0.304 Sum_probs=123.7
Q ss_pred cCHHHHHHHHHHHh-ccCCCceEEEEeccCCCCc--ccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhhhH
Q 002293 349 DNVSAAKKVVWMLT-NKYKHLVHACDTEVAKIDV--KQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLL 425 (940)
Q Consensus 349 ~t~e~L~eli~~L~-~a~~~~~VAfDTETTGLd~--~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~~l 425 (940)
+++++++++++.+. .. ..++||+|+++... ....+ ..++++. +..++.+++... ....
T Consensus 2 ~~~~~~~~~~~~~~~~~---~~ig~D~E~~~~~~~~~~~~~------~liQl~~--------~~~~~l~~~~~~--~~~~ 62 (170)
T cd06141 2 DSAQDAEEAVKELLGKE---KVVGFDTEWRPSFRKGKRNKV------ALLQLAT--------ESRCLLFQLAHM--DKLP 62 (170)
T ss_pred CCHHHHHHHHHHHhcCC---CEEEEeCccCCccCCCCCCCc------eEEEEec--------CCcEEEEEhhhh--hccc
Confidence 57788999999987 54 58999999998765 33322 2344443 345777887653 2345
Q ss_pred hhhhhhhcCCCceEEEeccHHHHHHHH-HcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhhcc
Q 002293 426 NEFAPFFEDPSIKKVWHNYSFDNHVLE-NYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKD 504 (940)
Q Consensus 426 ~~Lk~~Led~~i~KVgHNaKfDL~~L~-r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg~~~~ 504 (940)
..|+++|+++.+.||+|++++|+..|. .+|+.+.+ +|||++|++++++... ..+|++|+.. +++..
T Consensus 63 ~~l~~ll~~~~i~kv~~~~k~D~~~L~~~~g~~~~~-~~Dl~~aa~ll~~~~~---~~~l~~l~~~-------~l~~~-- 129 (170)
T cd06141 63 PSLKQLLEDPSILKVGVGIKGDARKLARDFGIEVRG-VVDLSHLAKRVGPRRK---LVSLARLVEE-------VLGLP-- 129 (170)
T ss_pred HHHHHHhcCCCeeEEEeeeHHHHHHHHhHcCCCCCC-eeeHHHHHHHhCCCcC---CccHHHHHHH-------HcCcc--
Confidence 678999999999999999999999997 68999877 4999999999999742 3699999987 44432
Q ss_pred ccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 002293 505 MSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLK 574 (940)
Q Consensus 505 l~k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~ 574 (940)
+ .+ .|. .+. ++|..+|| ++.|+.|||.||.+++.||+.|.
T Consensus 130 ~----------~k-------~k~---~~~---s~W~~rpL-------t~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 130 L----------SK-------PKK---VRC---SNWEARPL-------SKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred c----------CC-------CCC---ccc---CCCCCCCC-------CHHHHHHHHHHHHHHHHHHHHHh
Confidence 1 11 000 011 38999998 57899999999999999999875
No 23
>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=99.64 E-value=2.8e-15 Score=154.90 Aligned_cols=174 Identities=19% Similarity=0.209 Sum_probs=124.5
Q ss_pred eEEecCHHHHHHHHHH--HhccCCCceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCC--
Q 002293 345 VMVVDNVSAAKKVVWM--LTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGG-- 420 (940)
Q Consensus 345 y~lV~t~e~L~eli~~--L~~a~~~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~-- 420 (940)
+++|++++++.+++.. +... .+|+||+|+++...... .+++..++++ +++.++.+|....+
T Consensus 1 ~~~i~~~~el~~~~~~~~l~~~---~vig~D~Ew~~~~~~~~----~~~v~LiQia--------t~~~~~lid~~~~~~~ 65 (193)
T cd06146 1 IHIVDSEEELEALLLALSLEAG---RVVGIDSEWKPSFLGDS----DPRVAILQLA--------TEDEVFLLDLLALENL 65 (193)
T ss_pred CeEecCHHHHHHHHHHHhhccC---CEEEEECccCCCccCCC----CCCceEEEEe--------cCCCEEEEEchhcccc
Confidence 4799999999999999 6664 58999999987765420 0122233333 33457888886542
Q ss_pred -hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHH-cCCCC-----CCccccHHHHHHhcCCCCC-------CCCCCCHHH
Q 002293 421 -GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLEN-YGLKV-----SGFHADTMHMARLWDSSRR-------TEGGYSLEA 486 (940)
Q Consensus 421 -~e~~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r-~GI~l-----~n~vfDTmIAA~LLdp~~~-------~~~s~sLe~ 486 (940)
.+...+.|+++|+|+.+.||+|++++|+..|.+ +|+.. ...++||+.+++.+..... ....+||.+
T Consensus 66 ~~~~~~~~L~~ll~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~ 145 (193)
T cd06146 66 ESEDWDRLLKRLFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLAD 145 (193)
T ss_pred chHHHHHHHHHHhCCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHH
Confidence 123446789999999999999999999999975 66632 2458999998887653210 012589999
Q ss_pred HHhccccccccchhhhccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHH
Q 002293 487 LTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINT 566 (940)
Q Consensus 487 La~~y~~~~e~yLg~~~~l~k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~t 566 (940)
|+++ +|+.. + .|.. +. ++|..+|| ++.|+.|||.||.++
T Consensus 146 l~~~-------~lg~~--l-------------------~K~~---q~---SdW~~rpL-------s~~Qi~YAA~Da~~l 184 (193)
T cd06146 146 LVQE-------VLGKP--L-------------------DKSE---QC---SNWERRPL-------REEQILYAALDAYCL 184 (193)
T ss_pred HHHH-------HhCCC--c-------------------Cccc---cc---CCCCCCCC-------CHHHHHHHHHHHHHH
Confidence 9987 45432 1 1110 11 38999998 578999999999999
Q ss_pred HHHHHHHH
Q 002293 567 LKLYKSLK 574 (940)
Q Consensus 567 lrLye~L~ 574 (940)
+.||+.|.
T Consensus 185 ~~l~~~L~ 192 (193)
T cd06146 185 LEVFDKLL 192 (193)
T ss_pred HHHHHHHh
Confidence 99999885
No 24
>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins. The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.
Probab=99.62 E-value=2.6e-15 Score=155.35 Aligned_cols=172 Identities=23% Similarity=0.272 Sum_probs=120.1
Q ss_pred HHHHhccCCCceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcCCCc
Q 002293 358 VWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFEDPSI 437 (940)
Q Consensus 358 i~~L~~a~~~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~~l~~Lk~~Led~~i 437 (940)
++.|.++ +.+|||+|+.++... +. +..+++.... +.++.+|+...+.......|+++|+++.+
T Consensus 4 ~~~l~~~---~~i~~D~E~~~~~~~-~~------~~LiQia~~~-------~~v~l~D~~~~~~~~~~~~L~~iLe~~~i 66 (197)
T cd06148 4 IIHLKKQ---KVIGLDCEGVNLGRK-GK------LCLVQIATRT-------GQIYLFDILKLGSIVFINGLKDILESKKI 66 (197)
T ss_pred hhhhhhC---CEEEEEcccccCCCC-CC------EEEEEEeeCC-------CcEEEEEhhhccchhHHHHHHHHhcCCCc
Confidence 3445554 589999999877652 22 2334443220 45778898764322356789999999999
Q ss_pred eEEEeccHHHHHHH-HHcCCCCCCccccHHHHHHhcCCCCC----CCCCCCHHHHHhccccccccchhhhccccCCCCcc
Q 002293 438 KKVWHNYSFDNHVL-ENYGLKVSGFHADTMHMARLWDSSRR----TEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDE 512 (940)
Q Consensus 438 ~KVgHNaKfDL~~L-~r~GI~l~n~vfDTmIAA~LLdp~~~----~~~s~sLe~La~~y~~~~e~yLg~~~~l~k~~s~e 512 (940)
.||+||+++|+++| .++|+.+.+ +|||++|++|+++... .....+|++++++ |++.. ++
T Consensus 67 ~Kv~h~~k~D~~~L~~~~gi~~~~-~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~-------~l~~~--------~~ 130 (197)
T cd06148 67 LKVIHDCRRDSDALYHQYGIKLNN-VFDTQVADALLQEQETGGFNPDRVISLVQLLDK-------YLYIS--------IS 130 (197)
T ss_pred cEEEEechhHHHHHHHhcCccccc-eeeHHHHHHHHHHHhcCCccccccccHHHHHHH-------hhCCC--------hH
Confidence 99999999999999 468998876 5999999999987532 0113699999988 44432 00
Q ss_pred ccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 002293 513 GFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEM 580 (940)
Q Consensus 513 ELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~~~Lee~ 580 (940)
+. .. ..+.+ ..+ ..+|..+|+ ++.|+.|||.||.+++.||..|...|.+.
T Consensus 131 ----k~--~~-~~~~~-~~~---~s~W~~RPL-------t~~ql~YAa~Dv~~Ll~l~~~l~~~l~~~ 180 (197)
T cd06148 131 ----LK--ED-VKKLM-RED---PKFWALRPL-------TEDMIRYAALDVLCLLPLYYAMLDALISK 180 (197)
T ss_pred ----HH--HH-HHHHH-hcC---chhhhcCCC-------CHHHHHHHHHHHHhHHHHHHHHHHHhhhh
Confidence 00 00 00000 011 148999998 57899999999999999999999999873
No 25
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.55 E-value=1.1e-13 Score=135.89 Aligned_cols=170 Identities=25% Similarity=0.233 Sum_probs=120.4
Q ss_pred eEEecCHHHHHHHHHHHh-ccCCCceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhh
Q 002293 345 VMVVDNVSAAKKVVWMLT-NKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRD 423 (940)
Q Consensus 345 y~lV~t~e~L~eli~~L~-~a~~~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~ 423 (940)
+.+|++++++.++++.+. .. ..+++|+|+.+...+...+ .+++++.+. . .+|+.... ....
T Consensus 1 ~~~i~~~~~~~~~~~~~~~~~---~~l~~~~e~~~~~~~~~~~------~~l~l~~~~-------~-~~~i~~~~-~~~~ 62 (172)
T smart00474 1 VRVVTDSETLEELLEKLRAAG---GEVALDTETTGLNSYSGKL------VLIQISVTG-------E-GAFIIDPL-ALGD 62 (172)
T ss_pred CEEecCHHHHHHHHHHHHhcC---CeEEEeccccCCccCCCCE------EEEEEeEcC-------C-ceEEEEec-cchh
Confidence 468889988888777775 32 4799999988777654444 345554321 1 34553221 1123
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhhc
Q 002293 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQK 503 (940)
Q Consensus 424 ~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg~~~ 503 (940)
....|+++|+++.+.||+||+|+|+++|+++|+.+.+. |||++|+||++|... .++|+.++.+ |++..
T Consensus 63 ~~~~l~~~l~~~~~~kv~~d~k~~~~~L~~~gi~~~~~-~D~~laayll~p~~~---~~~l~~l~~~-------~l~~~- 130 (172)
T smart00474 63 DLEILKDLLEDETITKVGHNAKFDLHVLARFGIELENI-FDTMLAAYLLLGGPS---KHGLATLLKE-------YLGVE- 130 (172)
T ss_pred hHHHHHHHhcCCCceEEEechHHHHHHHHHCCCcccch-hHHHHHHHHHcCCCC---cCCHHHHHHH-------HhCCC-
Confidence 35668999999999999999999999998899999875 999999999999753 4799999987 44331
Q ss_pred cccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002293 504 DMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKL 577 (940)
Q Consensus 504 ~l~k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~~~L 577 (940)
.++ .++++ +|..+|+ ...+..||+.|+.++++|++.|.++|
T Consensus 131 -------~~~---------~~~~~----------~~~~~~l-------~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 131 -------LDK---------EEQKS----------DWGARPL-------SEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred -------CCc---------ccCcc----------ccccCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 011 11211 3422332 35688999999999999999998876
No 26
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=99.48 E-value=1.3e-12 Score=130.58 Aligned_cols=167 Identities=24% Similarity=0.258 Sum_probs=118.0
Q ss_pred HHHHHHHhccCCCceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcC
Q 002293 355 KKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFED 434 (940)
Q Consensus 355 ~eli~~L~~a~~~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~~l~~Lk~~Led 434 (940)
.++++.+... +.+++|+|+.+..++...+ .+++++.+ +.++|++.... ...+.|+++|++
T Consensus 3 ~~~~~~l~~~---~~l~~~~e~~~~~~~~~~~------~~i~l~~~--------~~~~~i~~~~~---~~~~~l~~ll~~ 62 (178)
T cd06142 3 EDLCERLASA---GVIAVDTEFMRLNTYYPRL------CLIQISTG--------GEVYLIDPLAI---GDLSPLKELLAD 62 (178)
T ss_pred HHHHHHHhcC---CeEEEECCccCCCcCCCce------EEEEEeeC--------CCEEEEeCCCc---ccHHHHHHHHcC
Confidence 3445444332 4799999987776544444 34555432 22677775421 245668899999
Q ss_pred CCceEEEeccHHHHHHHHHc-CCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhhccccCCCCccc
Q 002293 435 PSIKKVWHNYSFDNHVLENY-GLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEG 513 (940)
Q Consensus 435 ~~i~KVgHNaKfDL~~L~r~-GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg~~~~l~k~~s~eE 513 (940)
+.+.||+||+|+|+++|.++ |+. .+.+|||++|+||++|... ++|++|+++ |++..
T Consensus 63 ~~i~kv~~d~K~~~~~L~~~~gi~-~~~~~D~~laayLl~p~~~----~~l~~l~~~-------~l~~~----------- 119 (178)
T cd06142 63 PNIVKVFHAAREDLELLKRDFGIL-PQNLFDTQIAARLLGLGDS----VGLAALVEE-------LLGVE----------- 119 (178)
T ss_pred CCceEEEeccHHHHHHHHHHcCCC-CCCcccHHHHHHHhCCCcc----ccHHHHHHH-------HhCCC-----------
Confidence 99999999999999999876 998 6778999999999999753 699999998 44331
Q ss_pred cccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCch
Q 002293 514 FMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEMSWKLDGKPVPGKS 593 (940)
Q Consensus 514 LvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~~~Lee~~~~~~~~~~~~~~ 593 (940)
+. + ...++ .|..+|+. ..+..|++.|+.++++|++.|.++|++. +
T Consensus 120 ~~-~---~~~~~------------~w~~~~l~-------~~~~~yaa~~a~~l~~L~~~l~~~L~e~------------~ 164 (178)
T cd06142 120 LD-K---GEQRS------------DWSKRPLT-------DEQLEYAALDVRYLLPLYEKLKEELEEE------------G 164 (178)
T ss_pred CC-c---ccccc------------cCCCCCCC-------HHHHHHHHHhHHHHHHHHHHHHHHHHHc------------C
Confidence 00 0 00111 24434442 4578899999999999999999999983 6
Q ss_pred HHHHHH
Q 002293 594 MFDFYQ 599 (940)
Q Consensus 594 l~~Ly~ 599 (940)
+.++|.
T Consensus 165 l~~L~~ 170 (178)
T cd06142 165 RLEWAE 170 (178)
T ss_pred cHHHHH
Confidence 777764
No 27
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=99.40 E-value=7.2e-12 Score=128.59 Aligned_cols=171 Identities=27% Similarity=0.261 Sum_probs=123.6
Q ss_pred ceEEecCHHHHHHHHHHHhccCCCceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhh
Q 002293 344 NVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRD 423 (940)
Q Consensus 344 ~y~lV~t~e~L~eli~~L~~a~~~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~ 423 (940)
.|.+|++++++..+++.+... +.+++|+|+....++...+ .++++..+. + .+|++.... ..
T Consensus 4 ~~~~i~~~~~l~~~~~~l~~~---~~l~~~~e~~~~~~~~~~~------~~l~l~~~~-------~-~~~i~~l~~--~~ 64 (192)
T cd06147 4 PLTFVDTEEKLEELVEKLKNC---KEIAVDLEHHSYRSYLGFT------CLMQISTRE-------E-DYIVDTLKL--RD 64 (192)
T ss_pred CcEEECCHHHHHHHHHHHhcC---CeEEEEeEecCCccCCCce------EEEEEecCC-------C-cEEEEeccc--cc
Confidence 578997778888877766432 4799999887776655444 445555432 2 567763211 23
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHH-HcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhh
Q 002293 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLE-NYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQ 502 (940)
Q Consensus 424 ~l~~Lk~~Led~~i~KVgHNaKfDL~~L~-r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg~~ 502 (940)
....|+++|+++.+.||+||+|.|+++|. ++|+.+.+. ||||||+|||+|. . ++|+.|+++ |++..
T Consensus 65 ~~~~L~~~L~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~-fD~~laaYLL~p~-~----~~l~~l~~~-------yl~~~ 131 (192)
T cd06147 65 DMHILNEVFTDPNILKVFHGADSDIIWLQRDFGLYVVNL-FDTGQAARVLNLP-R----HSLAYLLQK-------YCNVD 131 (192)
T ss_pred chHHHHHHhcCCCceEEEechHHHHHHHHHHhCCCcCch-HHHHHHHHHhCCC-c----ccHHHHHHH-------HhCCC
Confidence 45568899999999999999999999998 899999887 9999999999998 5 499999998 44331
Q ss_pred ccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 002293 503 KDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEM 580 (940)
Q Consensus 503 ~~l~k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~~~Lee~ 580 (940)
+ + + + .+. .+|+..|+ ...+..|++.++.++++|++.|.++|+++
T Consensus 132 ------------~---~------k-~--~~~---~~~~~~~l-------~~~~~~y~a~~a~~l~~L~~~L~~~L~e~ 175 (192)
T cd06147 132 ------------A---D------K-K--YQL---ADWRIRPL-------PEEMIKYAREDTHYLLYIYDRLRNELLER 175 (192)
T ss_pred ------------c---c------h-h--hhc---cccccCCC-------CHHHHHHHHhhHHHHHHHHHHHHHHHHHh
Confidence 0 0 1 0 011 12443332 24577899999999999999999999874
No 28
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=99.39 E-value=7.8e-12 Score=120.47 Aligned_cols=153 Identities=25% Similarity=0.327 Sum_probs=105.6
Q ss_pred eEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcCCCceEEEeccHHHH
Q 002293 369 VHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFEDPSIKKVWHNYSFDN 448 (940)
Q Consensus 369 ~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~~l~~Lk~~Led~~i~KVgHNaKfDL 448 (940)
.+++|+|+.+..++...+ .+++++.+ +..+|++.... ...+.+.|+++|+++.+.+|+||+++|+
T Consensus 2 ~l~~d~e~~~~~~~~~~i------~~~~l~~~--------~~~~~i~~~~~-~~~~~~~l~~~l~~~~~~~v~~~~k~d~ 66 (155)
T cd00007 2 EVAFDTETTGLNYHRGKL------VGIQIATA--------GEAAYIPDELE-LEEDLEALKELLEDEDITKVGHDAKFDL 66 (155)
T ss_pred ceEEEEecCCCCcCCCeE------EEEEEEEC--------CcEEEEEcCCC-HHHHHHHHHHHHcCCCCcEEeccHHHHH
Confidence 588999988777544443 45555532 12456653321 1346667899999998899999999999
Q ss_pred HHHHHcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhhccccCCCCccccccccchhhhhcccc
Q 002293 449 HVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRK 528 (940)
Q Consensus 449 ~~L~r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg~~~~l~k~~s~eELvGk~s~kelfGK~k 528 (940)
++|.++|+...+.++||++|+|+++|... +++|++|+++| ++.. +. + .....++++
T Consensus 67 ~~L~~~~~~~~~~~~D~~~~ayll~~~~~---~~~l~~l~~~~-------l~~~-----------~~-~--~~~~~~~~~ 122 (155)
T cd00007 67 VVLARDGIELPGNIFDTMLAAYLLNPGEG---SHSLDDLAKEY-------LGIE-----------LD-K--DEQIYGKGA 122 (155)
T ss_pred HHHHHCCCCCCCCcccHHHHHHHhCCCCC---cCCHHHHHHHH-------cCCC-----------Cc-c--HHHHhcCCC
Confidence 99998888777789999999999999763 37999999984 3221 00 0 011222110
Q ss_pred cccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002293 529 LKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKK 576 (940)
Q Consensus 529 ~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~~~ 576 (940)
. |..+|+ ...+..||+.|+.++++|++.|.++
T Consensus 123 --------~-~~~~~~-------~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 123 --------K-TFARPL-------SEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred --------C-ccccCC-------HHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 0 111232 4568899999999999999998765
No 29
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=99.38 E-value=7.2e-13 Score=152.21 Aligned_cols=224 Identities=22% Similarity=0.243 Sum_probs=170.7
Q ss_pred EEecCCC-cCcccce---eeccCCCc-CCCCCc-cc-ccccccCCCCCCccccccCCCcccccccccchhHHHHhhhhcc
Q 002293 269 LTVPNLS-DFRNSEI---ECFEDGSS-YTPPPK-LV-SFKRSNQKNPKNDAAEGTGQNKKASENENSEKLEILRSKLASF 341 (940)
Q Consensus 269 ~~~~~~~-~~~~~~~---~~~~~~~~-~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 341 (940)
.-|+|++ ||.+.+. |+.+||-+ +.||.+ .. -|. ....+....++..+.-++ -.
T Consensus 132 ~~idn~~~pf~~~~~~~vEr~e~~~~~~~hpye~e~~~f~-------------~~~~~le~~~~~~~~~le-------~T 191 (687)
T KOG2206|consen 132 EGIDNLHHPFCSMLASEVERLEDRPREVQHPYEDEERHFR-------------QIDKQLEEGEPRKSSPLE-------IT 191 (687)
T ss_pred hccccccCCchhhhhhhhhchhhcchhccCcchhhhhhhc-------------ccchhhhcccccCCCccc-------cc
Confidence 3578888 9999888 99999999 999987 32 233 233334444444444444 56
Q ss_pred CCceEEecCHHHHHHHHHHHhccCCCceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCCh
Q 002293 342 YSNVMVVDNVSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGG 421 (940)
Q Consensus 342 p~~y~lV~t~e~L~eli~~L~~a~~~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~ 421 (940)
| +.||++..+|.++.+.|... ..+|+|+|+-....|. | +.|+ +||.++.+-+.||...+
T Consensus 192 ~--~~~I~t~~el~~l~~~l~~~---~Efavdlehhsyrsf~----g---ltcl-------mqISTr~ed~iIDt~~l-- 250 (687)
T KOG2206|consen 192 P--KVWICTLGELEALPEILDSV---IEFAVDLEHHSYRSFL----G---LTCL-------MQISTRTEDFIIDTFKL-- 250 (687)
T ss_pred C--ceeeechHHHHHHHHHHhhh---hhhhhhccccchhhhc----C---ceeE-------EEeeccchhheehhHHH--
Confidence 5 88999999999999998875 4699999999887764 3 2232 34555566788898754
Q ss_pred hhhHhhhhhhhcCCCceEEEeccHHHHHHHHH-cCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchh
Q 002293 422 RDLLNEFAPFFEDPSIKKVWHNYSFDNHVLEN-YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKA 500 (940)
Q Consensus 422 e~~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r-~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg 500 (940)
.+.+..|.++|.+|.++||+|.+.-|+.||++ +||.+-+ .|||..|+++|+-.. ++|..|.+.|+.
T Consensus 251 ~~~i~~l~e~fsdp~ivkvfhgaD~diiwlqrdfgiyvvn-Lfdt~~a~r~L~~~r-----~sL~~ll~~~~~------- 317 (687)
T KOG2206|consen 251 RDHIGILNEVFSDPGIVKVFHGADTDIIWLQRDFGIYVVN-LFDTIQASRLLGLPR-----PSLAYLLECVCG------- 317 (687)
T ss_pred HHHHHHhhhhccCCCeEEEEecCccchhhhhccceEEEEe-chhhHHHHHHhCCCc-----ccHHHHHHHHHh-------
Confidence 45677999999999999999999999999987 8998766 799999999998765 699988876332
Q ss_pred hhccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 002293 501 YQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLEM 580 (940)
Q Consensus 501 ~~~~l~k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~~~Lee~ 580 (940)
+. . .+. -|. .+|.++|| ++.+..||-.|+.+++-+|+.|...|.+.
T Consensus 318 v~----------------~-----nk~---yql---adwR~rpL-------p~~Mv~yar~dthyllyiyD~lr~el~~~ 363 (687)
T KOG2206|consen 318 VL----------------T-----NKK---YQL---ADWRIRPL-------PEEMVRYAREDTHYLLYIYDVLRKELKRL 363 (687)
T ss_pred hh----------------h-----hhh---hhh---chhccccC-------cHHHHHHHhhcchhHHHHHHHHHHHHHHH
Confidence 21 0 000 011 38999998 68899999999999999999999877763
No 30
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=99.35 E-value=1.3e-11 Score=119.74 Aligned_cols=149 Identities=23% Similarity=0.283 Sum_probs=103.6
Q ss_pred eEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcCCCceEEEeccHHHH
Q 002293 369 VHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFEDPSIKKVWHNYSFDN 448 (940)
Q Consensus 369 ~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~~l~~Lk~~Led~~i~KVgHNaKfDL 448 (940)
++++|+|+.+..++..++ .+++++.+. +..+|++..+. ......|+++|+++.+.||+||+|+|+
T Consensus 1 ~~~~~~e~~~~~~~~~~~------~~l~l~~~~-------~~~~~i~~~~~--~~~~~~l~~~l~~~~~~kv~~d~K~~~ 65 (150)
T cd09018 1 VFAFDTETDSLDNISANL------VLIQLAIEP-------GVAALIPVAHD--YLALELLKPLLEDEKALKVGQNLKYDR 65 (150)
T ss_pred CEEEEeecCCCCCCCceE------EEEEEEcCC-------CcEEEEEcCCc--ccCHHHHHHHhcCCCCceeeecHHHHH
Confidence 378899887777654444 446665432 22567765421 112456889999999999999999999
Q ss_pred HHHHHcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhhccccCCCCccccccccchhhhhcccc
Q 002293 449 HVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRK 528 (940)
Q Consensus 449 ~~L~r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg~~~~l~k~~s~eELvGk~s~kelfGK~k 528 (940)
++|.+.|+.+.+.+|||++|+||++|... +++|++|+++ |++.. ++ ...+.+|+
T Consensus 66 ~~L~~~~~~~~~~~~D~~laayLl~p~~~---~~~l~~l~~~-------~l~~~-----------~~---~~~~~~~~-- 119 (150)
T cd09018 66 GILLNYFIELRGIAFDTMLEAYILNSVAG---RWDMDSLVER-------WLGHK-----------LI---KFESIAGK-- 119 (150)
T ss_pred HHHHHcCCccCCcchhHHHHHHHhCCCCC---CCCHHHHHHH-------HhCCC-----------cc---cHHHhcCC--
Confidence 99999999888889999999999999762 2599999988 44321 00 01112222
Q ss_pred cccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 002293 529 LKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLK 574 (940)
Q Consensus 529 ~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~ 574 (940)
.|..+++ ...+..||+.|+.++.+|++.|.
T Consensus 120 ---------~~~~~~~-------~~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 120 ---------LWFNQPL-------TEEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred ---------CCcccCC-------HHHHHHHHHHHHHHHHHHHHHhc
Confidence 1311222 35688999999999999999874
No 31
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
Probab=98.93 E-value=1.9e-08 Score=98.94 Aligned_cols=75 Identities=27% Similarity=0.416 Sum_probs=61.5
Q ss_pred EEEEeCCCCChhhhHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 411 CIWVDLLDGGGRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 411 ~~yID~~~~~~e~~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
.+|++.... . ..+.|+++|++..+.|++||+|+++++|.++|+.+.+.+||||||+|||+|... +++|++|+.+
T Consensus 31 ~~yi~~~~~-~--~~~~l~~~l~~~~~~ki~~d~K~~~~~l~~~gi~l~~~~fD~~LAaYLL~p~~~---~~~l~~la~~ 104 (151)
T cd06128 31 AAYIPVAHD-Y--ALELLKPLLEDEKALKVGQNLKYDRVILANYGIELRGIAFDTMLEAYLLDPVAG---RHDMDSLAER 104 (151)
T ss_pred eEEEeCCCC-c--CHHHHHHHHcCCCCCEEeeehHHHHHHHHHCCCCCCCcchhHHHHHHHcCCCCC---CCCHHHHHHH
Confidence 567763210 0 244588999998889999999999999999999999889999999999999763 2599999998
Q ss_pred c
Q 002293 491 R 491 (940)
Q Consensus 491 y 491 (940)
|
T Consensus 105 y 105 (151)
T cd06128 105 W 105 (151)
T ss_pred H
Confidence 4
No 32
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=98.62 E-value=1.5e-07 Score=115.74 Aligned_cols=117 Identities=23% Similarity=0.268 Sum_probs=84.8
Q ss_pred CceEEEEeccCCCCcccCccccCcceeEEEeecCCCc----ccCCCc---eEEEEeCCCC---------ChhhhHhhhhh
Q 002293 367 HLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEA----DFGNGK---SCIWVDLLDG---------GGRDLLNEFAP 430 (940)
Q Consensus 367 ~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gI----q~g~~~---~~~yID~~~~---------~~e~~l~~Lk~ 430 (940)
..+|+||.|||||++..+.|+. +.+..+..|..| .|-.++ ....+...++ +.++++..+++
T Consensus 421 atyVVfDiETTGLs~~~d~iIE---~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~kf~~ 497 (1444)
T COG2176 421 ATYVVFDIETTGLSPVYDEIIE---IAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEKFRE 497 (1444)
T ss_pred ccEEEEEeecCCcCcccchhhh---heeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHHHHHH
Confidence 4699999999999999999886 335555544321 010100 0111111111 25678899999
Q ss_pred hhcCCCceEEEeccHHHHHHHHH----cCCC-CCCccccHHHHHHhcCCCCCCCCCCCHHHHHhcc
Q 002293 431 FFEDPSIKKVWHNYSFDNHVLEN----YGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGDR 491 (940)
Q Consensus 431 ~Led~~i~KVgHNaKfDL~~L~r----~GI~-l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y 491 (940)
|+.|. ..|.||+.||+.+|.. +|+. +.++++||+-+||.|+|... +|+|..|++++
T Consensus 498 ~~~d~--IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~k---sh~Lg~l~kk~ 558 (1444)
T COG2176 498 FIGDS--ILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFK---SHRLGTLCKKL 558 (1444)
T ss_pred HhcCc--EEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhh---hcchHHHHHHh
Confidence 99986 6899999999999963 5655 56899999999999999886 79999999873
No 33
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=98.56 E-value=1e-06 Score=94.90 Aligned_cols=112 Identities=19% Similarity=0.223 Sum_probs=75.9
Q ss_pred ceEEEEeccCCCCcc-cCccccCcceeEEEeecCCCcccCCCceEEEEeCCC-----------C---------ChhhhHh
Q 002293 368 LVHACDTEVAKIDVK-QETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD-----------G---------GGRDLLN 426 (940)
Q Consensus 368 ~~VAfDTETTGLd~~-~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~-----------~---------~~e~~l~ 426 (940)
.+|+|||||||+++. .++|+. |-++.+.++. + .+ .....||.+.. + ...+++.
T Consensus 5 r~vvlDtETTGldp~~~drIIE---IGaV~v~~~~-~-~~-~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~p~f~ev~~ 78 (240)
T PRK05711 5 RQIVLDTETTGLNQREGHRIIE---IGAVELINRR-L-TG-RNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVAD 78 (240)
T ss_pred eEEEEEeeCCCcCCCCCCeEEE---EEEEEEECCE-E-ec-cEEEEEECcCCcCCHHHhhhcCCCHHHHcCCCCHHHHHH
Confidence 479999999999986 677765 2244443221 1 11 11234555521 1 1345667
Q ss_pred hhhhhhcCCCceEEEeccHHHHHHHHH----cCCCCC-----CccccHHHHHHhcCCCCCCCCCCCHHHHHhcc
Q 002293 427 EFAPFFEDPSIKKVWHNYSFDNHVLEN----YGLKVS-----GFHADTMHMARLWDSSRRTEGGYSLEALTGDR 491 (940)
Q Consensus 427 ~Lk~~Led~~i~KVgHNaKfDL~~L~r----~GI~l~-----n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y 491 (940)
.|.+|+.+. .+|+||+.||+.+|.+ +|..++ ..++||+.+++.+.|+. .++|++|+++|
T Consensus 79 ~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~----~~~L~aL~~~~ 146 (240)
T PRK05711 79 EFLDFIRGA--ELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGK----RNSLDALCKRY 146 (240)
T ss_pred HHHHHhCCC--EEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCC----CCCHHHHHHHC
Confidence 788888764 4799999999999853 554332 34899999999888875 47999999874
No 34
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=98.52 E-value=1.7e-06 Score=93.04 Aligned_cols=117 Identities=15% Similarity=0.034 Sum_probs=73.1
Q ss_pred CceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCC-----------CC---------ChhhhHh
Q 002293 367 HLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-----------DG---------GGRDLLN 426 (940)
Q Consensus 367 ~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~-----------~~---------~~e~~l~ 426 (940)
..+++||+||||+++..++|+.. -++.+..+ .+.... ....+|.+. ++ +..+++.
T Consensus 47 ~~~vviD~ETTGl~p~~d~IieI---g~v~v~~~-~i~~~~-~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~evl~ 121 (239)
T PRK09146 47 VPFVALDFETTGLDAEQDAIVSI---GLVPFTLQ-RIRCRQ-ARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILD 121 (239)
T ss_pred CCEEEEEeECCCCCCCCCcEEEE---EEEEEECC-eEeecc-eEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHHHH
Confidence 36899999999999988888762 12222221 121111 112233321 11 1345667
Q ss_pred hhhhhhcCCCceEEEeccHHHHHHHHH-----cCCCCCCccccHHHHHHhcCCCC---------CC-CCCCCHHHHHhc
Q 002293 427 EFAPFFEDPSIKKVWHNYSFDNHVLEN-----YGLKVSGFHADTMHMARLWDSSR---------RT-EGGYSLEALTGD 490 (940)
Q Consensus 427 ~Lk~~Led~~i~KVgHNaKfDL~~L~r-----~GI~l~n~vfDTmIAA~LLdp~~---------~~-~~s~sLe~La~~ 490 (940)
.|.+++.+. ..|+||+.||+.+|.+ .|..+..+++||+..++-+.+.. .. ..+++|++++++
T Consensus 122 ~l~~~~~~~--~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~ 198 (239)
T PRK09146 122 ELLEALAGK--VVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLR 198 (239)
T ss_pred HHHHHhCCC--EEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHH
Confidence 777777653 5899999999999954 35556677999999998665432 00 135788888876
No 35
>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=98.47 E-value=2.6e-06 Score=90.68 Aligned_cols=111 Identities=25% Similarity=0.256 Sum_probs=74.7
Q ss_pred eEEEEeccCCCCccc-CccccCcceeEEEeecCCCcccCCCceEEEEeCCC-----------C---------ChhhhHhh
Q 002293 369 VHACDTEVAKIDVKQ-ETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD-----------G---------GGRDLLNE 427 (940)
Q Consensus 369 ~VAfDTETTGLd~~~-d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~-----------~---------~~e~~l~~ 427 (940)
.|++||||||+++.. ++|+. |-++.+.++. + .+. ....||.+.. + ...+++..
T Consensus 2 ~vvlD~ETTGl~p~~~d~IIE---Igav~~~~~~-~-~~~-~f~~~i~P~~~i~~~a~~vhGIt~e~l~~~p~f~ev~~~ 75 (225)
T TIGR01406 2 QIILDTETTGLDPKGGHRIVE---IGAVELVNRM-L-TGD-NFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADE 75 (225)
T ss_pred EEEEEeeCCCcCCCCCCeEEE---EEEEEEECCc-E-ecc-eEEEEECcCCCCCHHHHhccCCCHHHHhCCCCHHHHHHH
Confidence 689999999999875 67765 2244343221 1 111 2234554421 1 13457778
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHH----cCC--C-CC--CccccHHHHHHhcCCCCCCCCCCCHHHHHhcc
Q 002293 428 FAPFFEDPSIKKVWHNYSFDNHVLEN----YGL--K-VS--GFHADTMHMARLWDSSRRTEGGYSLEALTGDR 491 (940)
Q Consensus 428 Lk~~Led~~i~KVgHNaKfDL~~L~r----~GI--~-l~--n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y 491 (940)
|.+|+.+. ..|+||+.||+.+|.+ +|. . +. ..++||+.+++.+.|+. +++|++|+++|
T Consensus 76 f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~----~~~L~~L~~~~ 142 (225)
T TIGR01406 76 FLDFIGGS--ELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQ----RNSLDALCKRF 142 (225)
T ss_pred HHHHhCCC--EEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCC----CCCHHHHHHhc
Confidence 88888764 5799999999999953 563 2 22 46899999999888875 48999999874
No 36
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=98.47 E-value=2.8e-06 Score=90.77 Aligned_cols=116 Identities=21% Similarity=0.188 Sum_probs=71.0
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCC-----------CCh----------hhhHh
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD-----------GGG----------RDLLN 426 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~-----------~~~----------e~~l~ 426 (940)
.+++||+||||+++..++|+. +|+......+..+. ....++++.. ++. .+++.
T Consensus 7 ~~vv~D~ETTGl~p~~d~Iie----ig~v~v~~~g~~~~--~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~ 80 (232)
T PRK07942 7 PLAAFDLETTGVDPETARIVT----AALVVVDADGEVVE--SREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLA 80 (232)
T ss_pred cEEEEEeccCCCCCCCCeeEE----EEEEEEeCCCcccc--ceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHH
Confidence 589999999999998888765 33322221121110 1123454421 111 22344
Q ss_pred hhhhhhcC---CCceEEEeccHHHHHHHH----HcCCCC--CCccccHHHHHHhcCCCCCCCCCCCHHHHHhcc
Q 002293 427 EFAPFFED---PSIKKVWHNYSFDNHVLE----NYGLKV--SGFHADTMHMARLWDSSRRTEGGYSLEALTGDR 491 (940)
Q Consensus 427 ~Lk~~Led---~~i~KVgHNaKfDL~~L~----r~GI~l--~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y 491 (940)
.+.+++.+ ....+|+||+.||+.+|. ++|+.. ..+++||+.+++.+.+.. .++++|++|++.|
T Consensus 81 e~~~~l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~--~~~~~L~~l~~~~ 152 (232)
T PRK07942 81 EIADALREAWARGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYR--KGKRTLTALCEHY 152 (232)
T ss_pred HHHHHHHHHhhcCCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhccc--CCCCCHHHHHHHc
Confidence 44444421 234689999999999985 356542 356899999998777643 1368999999863
No 37
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=98.47 E-value=2.6e-06 Score=94.99 Aligned_cols=112 Identities=17% Similarity=0.118 Sum_probs=75.3
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCC---------CC---------ChhhhHhhhh
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL---------DG---------GGRDLLNEFA 429 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~---------~~---------~~e~~l~~Lk 429 (940)
.+++||+||||+++..++|+. |-++.+.. .+... . ....+|.+. ++ ...+++..|.
T Consensus 16 ~fvvlD~ETTGl~p~~d~IIe---Igav~v~~-~g~i~-~-~~~~lv~P~~~~~~~~IhGIt~e~l~~ap~f~ev~~~l~ 89 (313)
T PRK06063 16 GWAVVDVETSGFRPGQARIIS---LAVLGLDA-DGNVE-Q-SVVTLLNPGVDPGPTHVHGLTAEMLEGQPQFADIAGEVA 89 (313)
T ss_pred CEEEEEEECCCCCCCCCEEEE---EEEEEEEC-Cceee-e-EEEEEECcCCCCCCeecCCCCHHHHhCCCCHHHHHHHHH
Confidence 589999999999998888876 22233321 11100 0 111233221 11 1345777888
Q ss_pred hhhcCCCceEEEeccHHHHHHHHH----cCCCCC-CccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 430 PFFEDPSIKKVWHNYSFDNHVLEN----YGLKVS-GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 430 ~~Led~~i~KVgHNaKfDL~~L~r----~GI~l~-n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
.++++. ..|+||+.||+.+|.+ +|+.++ +.++||+..++.+.+... +|+|++|++.
T Consensus 90 ~~l~~~--~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~---~~kL~~l~~~ 150 (313)
T PRK06063 90 ELLRGR--TLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLP---NLRLETLAAH 150 (313)
T ss_pred HHcCCC--EEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCC---CCCHHHHHHH
Confidence 888764 6899999999999963 576644 458999999988877654 6999999985
No 38
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=98.36 E-value=2.3e-06 Score=96.71 Aligned_cols=113 Identities=9% Similarity=0.010 Sum_probs=77.9
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCC---------CC---------ChhhhHhhhh
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL---------DG---------GGRDLLNEFA 429 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~---------~~---------~~e~~l~~Lk 429 (940)
.+++||+||||+++..+.|+. |-++.+..+..+ . .....+|.+. ++ ...+++..|.
T Consensus 47 ~fVvlDiETTGLdp~~drIIe---IgAV~i~~~g~i--v-e~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~eVl~el~ 120 (377)
T PRK05601 47 PFVAVSIQTSGIHPSTSRLIT---IDAVTLTADGEE--V-EHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFSQILKPLD 120 (377)
T ss_pred CEEEEEEECCCCCCCCCeEEE---EEEEEEEcCCEE--E-EEEEEEECcCCCCCCccccCCCHHHHhcCCCHHHHHHHHH
Confidence 599999999999998888765 223333311111 0 0112233221 11 2567888899
Q ss_pred hhhcCCCceEEEeccHHHHHHHHH----c----------------------------CCCCCCccccHHHHHHhcCCCCC
Q 002293 430 PFFEDPSIKKVWHNYSFDNHVLEN----Y----------------------------GLKVSGFHADTMHMARLWDSSRR 477 (940)
Q Consensus 430 ~~Led~~i~KVgHNaKfDL~~L~r----~----------------------------GI~l~n~vfDTmIAA~LLdp~~~ 477 (940)
+++.+. .+|+||+.||+.||.+ . ++..++.++||+-.++.+.|...
T Consensus 121 ~fL~g~--vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l~ 198 (377)
T PRK05601 121 RLIDGR--TLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGVALD 198 (377)
T ss_pred HHhCCC--EEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHcCCCC
Confidence 999875 6899999999999853 1 23444678999999999998765
Q ss_pred CCCCCCHHHHHhcc
Q 002293 478 TEGGYSLEALTGDR 491 (940)
Q Consensus 478 ~~~s~sLe~La~~y 491 (940)
+|+|..|++.|
T Consensus 199 ---~~rL~~La~~l 209 (377)
T PRK05601 199 ---DIRIRGVAHTL 209 (377)
T ss_pred ---CCCHHHHHHHh
Confidence 69999999864
No 39
>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=98.31 E-value=1.2e-05 Score=80.58 Aligned_cols=111 Identities=23% Similarity=0.254 Sum_probs=71.4
Q ss_pred eEEEEeccCCCCc-ccCccccCcceeEEEeecCCCcccCCCceEEEEeCCC-----------C---------ChhhhHhh
Q 002293 369 VHACDTEVAKIDV-KQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD-----------G---------GGRDLLNE 427 (940)
Q Consensus 369 ~VAfDTETTGLd~-~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~-----------~---------~~e~~l~~ 427 (940)
+|+||+||||+++ ..+.|+. |-++.+..+. + .+ .....++.+.. + ...+++..
T Consensus 1 ~v~~D~ETTGl~~~~~~~iie---ig~v~v~~~~-~-~~-~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~~~~v~~~ 74 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIE---IGCVELINRR-L-TG-NTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADE 74 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEE---EEEEEEECCc-E-ec-cEEEEEECCCCCCCHHHHHHhCCCHHHHhcCCCHHHHHHH
Confidence 3889999999998 5566665 1223333221 1 11 11123444421 1 13456778
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHH----cCCC----CCCccccHHHHHHhcCCCCCCCCCCCHHHHHhcc
Q 002293 428 FAPFFEDPSIKKVWHNYSFDNHVLEN----YGLK----VSGFHADTMHMARLWDSSRRTEGGYSLEALTGDR 491 (940)
Q Consensus 428 Lk~~Led~~i~KVgHNaKfDL~~L~r----~GI~----l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y 491 (940)
|.+++++. ..|+||+.||+.+|.+ +|+. .+..++||+.+++.+.+.. .++|+++++.|
T Consensus 75 l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~----~~~L~~l~~~~ 140 (167)
T cd06131 75 FLDFIRGA--ELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGK----PNSLDALCKRF 140 (167)
T ss_pred HHHHHCCC--eEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCC----CCCHHHHHHHC
Confidence 88888764 4799999999999853 4443 2356899998888777764 47999999863
No 40
>PRK07740 hypothetical protein; Provisional
Probab=98.31 E-value=1.5e-05 Score=86.05 Aligned_cols=112 Identities=17% Similarity=0.127 Sum_probs=73.3
Q ss_pred ceEEEEeccCCCCccc-CccccCcceeEEEeecCCCcccCCCceEEEEeCC-----------CC---------ChhhhHh
Q 002293 368 LVHACDTEVAKIDVKQ-ETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-----------DG---------GGRDLLN 426 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~-d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~-----------~~---------~~e~~l~ 426 (940)
.+|+||+||||+++.. +.|+. |-++.+..+. + ... ....+|.+. ++ +..+++.
T Consensus 60 ~~vv~D~ETTGl~p~~~deIIe---IgaV~~~~~~-i-~~~-~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~evl~ 133 (244)
T PRK07740 60 PFVVFDLETTGFSPQQGDEILS---IGAVKTKGGE-V-ETD-TFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLH 133 (244)
T ss_pred CEEEEEEeCCCCCCCCCCeEEE---EEEEEEECCE-E-EEE-EEEEEeCcCCCCChhheeccCCCHHHHhCCCCHHHHHH
Confidence 5899999999999865 56655 2233333221 1 000 001122221 11 2455677
Q ss_pred hhhhhhcCCCceEEEeccHHHHHHHHH-----cCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 427 EFAPFFEDPSIKKVWHNYSFDNHVLEN-----YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 427 ~Lk~~Led~~i~KVgHNaKfDL~~L~r-----~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
.|..++++. ..|+||+.||+.+|.+ .+..+...++||+.+++.+.+... +++|++++..
T Consensus 134 ~f~~fi~~~--~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~---~~sL~~l~~~ 197 (244)
T PRK07740 134 RFYAFIGAG--VLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERD---FPTLDDALAY 197 (244)
T ss_pred HHHHHhCCC--EEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCC---CCCHHHHHHH
Confidence 777777764 6899999999999854 355566779999999998887654 6899999975
No 41
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=98.26 E-value=2.2e-05 Score=84.92 Aligned_cols=111 Identities=21% Similarity=0.242 Sum_probs=72.4
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCC-----------CC---------ChhhhHhh
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-----------DG---------GGRDLLNE 427 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~-----------~~---------~~e~~l~~ 427 (940)
.+|+||+||||+++..++|+. |.++.+..+. + .. ....+|.+. ++ ...+++..
T Consensus 8 ~~v~~D~ETTGl~~~~d~IIE---Ia~v~v~~~~-~--~~-~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~ 80 (250)
T PRK06310 8 EFVCLDCETTGLDVKKDRIIE---FAAIRFTFDE-V--ID-SVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQ 80 (250)
T ss_pred cEEEEEEeCCCCCCCCCeEEE---EEEEEEECCe-E--EE-EEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHH
Confidence 589999999999998888876 2233332211 0 00 011233321 11 13456667
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHH----cCCCCC---CccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 428 FAPFFEDPSIKKVWHNYSFDNHVLEN----YGLKVS---GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 428 Lk~~Led~~i~KVgHNaKfDL~~L~r----~GI~l~---n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
+.+++.+.. .+|+||+.||+.+|.+ +|+... ..++||+-.++.+.+.. +++|++|++.
T Consensus 81 ~~~fl~~~~-~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~~----~~~L~~l~~~ 145 (250)
T PRK06310 81 IKGFFKEGD-YIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDSP----NNSLEALAVH 145 (250)
T ss_pred HHHHhCCCC-EEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcccCC----CCCHHHHHHH
Confidence 888886633 6899999999999953 566542 46899999998764433 4899999976
No 42
>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=98.26 E-value=1.8e-05 Score=82.73 Aligned_cols=113 Identities=18% Similarity=0.099 Sum_probs=65.7
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecC-CC-cccCCCceEEEEeCC-------------CCCh----------h
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSG-PE-ADFGNGKSCIWVDLL-------------DGGG----------R 422 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~-~g-Iq~g~~~~~~yID~~-------------~~~~----------e 422 (940)
..++||+||||+++..++|+. |-++.+..+ .+ +.... ....++.+. +++. .
T Consensus 9 ~~vv~D~ETTGl~~~~d~Iie---Igav~v~~~~~g~i~~~~-~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~~~ 84 (200)
T TIGR01298 9 LPVVVDVETGGFNAKTDALLE---IAAITLKMDEQGWLFPDT-TLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVSEY 84 (200)
T ss_pred eeEEEEeeCCCCCCCCCeEEE---EEEEEEEEcCCCcEeecc-eeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcchH
Confidence 479999999999998787765 223444321 11 11110 112233221 1111 1
Q ss_pred hhHhhhhhhh----cC---CCceEEEeccHHHHHHHHH----cCCC---C-CCccccHHHHHHhcCCCCCCCCCCCHHHH
Q 002293 423 DLLNEFAPFF----ED---PSIKKVWHNYSFDNHVLEN----YGLK---V-SGFHADTMHMARLWDSSRRTEGGYSLEAL 487 (940)
Q Consensus 423 ~~l~~Lk~~L----ed---~~i~KVgHNaKfDL~~L~r----~GI~---l-~n~vfDTmIAA~LLdp~~~~~~s~sLe~L 487 (940)
+++..+.+++ .. .....|+||+.||+.+|.+ +|+. . ...++||+..++.+.+. ++|+.+
T Consensus 85 ~~~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~~------~~L~~l 158 (200)
T TIGR01298 85 EALHEIFKVVRKAMKASGCQRAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYGQ------TVLAKA 158 (200)
T ss_pred HHHHHHHHHHHHHHHhcccCCCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcCc------ccHHHH
Confidence 2233333333 11 2346899999999999964 4543 1 23479999999877653 579999
Q ss_pred Hhc
Q 002293 488 TGD 490 (940)
Q Consensus 488 a~~ 490 (940)
+++
T Consensus 159 ~~~ 161 (200)
T TIGR01298 159 CQA 161 (200)
T ss_pred HHH
Confidence 986
No 43
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=98.24 E-value=2.6e-05 Score=83.29 Aligned_cols=110 Identities=18% Similarity=0.165 Sum_probs=72.2
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCC-----------CC---------ChhhhHhh
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-----------DG---------GGRDLLNE 427 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~-----------~~---------~~e~~l~~ 427 (940)
.+++||+||||+++..++|+. +++.+... ......++.+. ++ ...+++..
T Consensus 3 ~~vv~D~ETTGl~~~~d~IIe------ig~v~~~~----~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~ 72 (232)
T PRK06309 3 ALIFYDTETTGTQIDKDRIIE------IAAYNGVT----SESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQK 72 (232)
T ss_pred cEEEEEeeCCCCCCCCCEEEE------EEEEcCcc----ccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHH
Confidence 479999999999988887765 22222110 00111233321 11 13456667
Q ss_pred hhhhhcCCCceEEEec-cHHHHHHHH----HcCCCCC-CccccHHHHHHhcCCCCCCCCCCCHHHHHhcc
Q 002293 428 FAPFFEDPSIKKVWHN-YSFDNHVLE----NYGLKVS-GFHADTMHMARLWDSSRRTEGGYSLEALTGDR 491 (940)
Q Consensus 428 Lk~~Led~~i~KVgHN-aKfDL~~L~----r~GI~l~-n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y 491 (940)
|.+++.+. ...|+|| +.||+.+|. ++|+... ..++||+-.++.+.|+.. .++|..|+..|
T Consensus 73 ~~~fi~~~-~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~---~~~L~~l~~~~ 138 (232)
T PRK06309 73 FIEFCGTD-NILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLP---KHNLQYLRQVY 138 (232)
T ss_pred HHHHHcCC-CEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCC---CCCHHHHHHHc
Confidence 77788653 3689999 589999995 3677643 468999999988777654 58999999763
No 44
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=98.21 E-value=1.6e-05 Score=98.99 Aligned_cols=110 Identities=19% Similarity=0.178 Sum_probs=75.9
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCC-----------CC---------ChhhhHhh
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-----------DG---------GGRDLLNE 427 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~-----------~~---------~~e~~l~~ 427 (940)
.+++||+||||+++ .++|+.+ -++.+..+. + + . ....+|.+. ++ ..++++..
T Consensus 8 ~~vvvD~ETTGl~~-~d~IIeI---gaV~v~~g~-i-~-~-~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~ 79 (820)
T PRK07246 8 KYAVVDLEATGAGP-NASIIQV---GIVIIEGGE-I-I-D-SYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARH 79 (820)
T ss_pred CEEEEEEecCCcCC-CCeEEEE---EEEEEECCE-E-E-E-EEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHH
Confidence 58999999999987 4677652 233333221 1 0 0 011223321 11 13467778
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHH----cCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 428 FAPFFEDPSIKKVWHNYSFDNHVLEN----YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 428 Lk~~Led~~i~KVgHNaKfDL~~L~r----~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
|.+++.+. ..|+||+.||+.+|.+ .|+.+.++++||+..++.+.|... +|+|++|+..
T Consensus 80 ~~~~l~~~--~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~---~~~L~~L~~~ 141 (820)
T PRK07246 80 IYDLIEDC--IFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLE---KYSLSHLSRE 141 (820)
T ss_pred HHHHhCCC--EEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCC---CCCHHHHHHH
Confidence 88888764 6899999999999964 577777789999999998888765 6999999985
No 45
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=98.19 E-value=2.4e-05 Score=87.42 Aligned_cols=111 Identities=20% Similarity=0.180 Sum_probs=74.7
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCC-----------CC---------ChhhhHhh
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-----------DG---------GGRDLLNE 427 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~-----------~~---------~~e~~l~~ 427 (940)
.+|+||+||||+++..+.|+. |-++.+..+. + + . ....+|.+. ++ +..+++..
T Consensus 9 ~~Vv~DlETTGl~p~~~eIIE---IgaV~v~~g~-i-~-~-~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~evl~~ 81 (313)
T PRK06807 9 DYVVIDFETTGFNPYNDKIIQ---VAAVKYRNHE-L-V-D-QFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPL 81 (313)
T ss_pred CEEEEEEECCCCCCCCCeEEE---EEEEEEECCE-E-E-E-EEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHHHHH
Confidence 589999999999998777765 2233333221 1 0 0 001222221 11 23557778
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHH----cCCC-CCCccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 428 FAPFFEDPSIKKVWHNYSFDNHVLEN----YGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 428 Lk~~Led~~i~KVgHNaKfDL~~L~r----~GI~-l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
|..++.+. ..|+||+.||+.+|.+ +|+. +.+.++||+..++.+.+... +++|++|++.
T Consensus 82 f~~fl~~~--~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~---~~kL~~L~~~ 144 (313)
T PRK06807 82 FLAFLHTN--VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAP---NHKLETLKRM 144 (313)
T ss_pred HHHHHcCC--eEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCC---CCCHHHHHHH
Confidence 88888765 4799999999999964 5764 45678999998887777654 6899999975
No 46
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=98.17 E-value=3.7e-05 Score=80.15 Aligned_cols=114 Identities=13% Similarity=0.084 Sum_probs=71.2
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCC-----------C---------ChhhhHhh
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD-----------G---------GGRDLLNE 427 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~-----------~---------~~e~~l~~ 427 (940)
.+|++|+||||+++..+.|+. |-++.+..+ .+..+. ....+|.+.. + ...+++..
T Consensus 30 ~~vviD~ETTGl~~~~d~Iie---IgaV~~~~~-~~~~~~-~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~~ 104 (202)
T PRK09145 30 EWVALDCETTGLDPRRAEIVS---IAAVKIRGN-RILTSE-RLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQ 104 (202)
T ss_pred CEEEEEeECCCCCCCCCceEE---EEEEEEECC-EEeecC-ceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHHH
Confidence 589999999999998777765 223333322 121111 1223444321 1 24567778
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHH-----cCCCCCCccccHHHHHH--hc--CCCCCCCCCCCHHHHHhc
Q 002293 428 FAPFFEDPSIKKVWHNYSFDNHVLEN-----YGLKVSGFHADTMHMAR--LW--DSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 428 Lk~~Led~~i~KVgHNaKfDL~~L~r-----~GI~l~n~vfDTmIAA~--LL--dp~~~~~~s~sLe~La~~ 490 (940)
|..++++. .+|+||+.||+.+|.+ +|..++..++|++-... +. .+.. ..+++|+++++.
T Consensus 105 ~~~~i~~~--~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~--~~~~~L~~l~~~ 172 (202)
T PRK09145 105 LLAFIGNR--PLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDA--YIDLRFDAILKH 172 (202)
T ss_pred HHHHHcCC--eEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCc--ccCCCHHHHHHH
Confidence 88888764 5899999999999953 46667777889864432 11 1211 125899999986
No 47
>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=98.17 E-value=3.6e-05 Score=79.71 Aligned_cols=113 Identities=14% Similarity=0.057 Sum_probs=67.2
Q ss_pred eEEEEeccCCCCcccCccccCcceeEEEeecC-CC-cccCCCceEEEEeCC-------------CCCh----------hh
Q 002293 369 VHACDTEVAKIDVKQETPVDHGEVICFSIYSG-PE-ADFGNGKSCIWVDLL-------------DGGG----------RD 423 (940)
Q Consensus 369 ~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~-~g-Iq~g~~~~~~yID~~-------------~~~~----------e~ 423 (940)
.|+||+||||+++..+.|+. |-++.+..+ .+ +.+.. ....++.+. +++. .+
T Consensus 7 ~vv~D~ETTGl~~~~d~Iie---igav~v~~~~~~~i~~~~-~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~~ 82 (189)
T cd06134 7 PVVVDVETGGFNPQTDALLE---IAAVTLEMDEQGNLYPDE-TFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEKE 82 (189)
T ss_pred eEEEEecCCCCCCCCCeEEE---EEEEEEEECCCCceeccc-eEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchHH
Confidence 69999999999998888765 234444422 11 11111 112334331 0111 11
Q ss_pred hHhhhhhhhc----C---CCceEEEeccHHHHHHHHH----cCCC---C-CCccccHHHHHHhcCCCCCCCCCCCHHHHH
Q 002293 424 LLNEFAPFFE----D---PSIKKVWHNYSFDNHVLEN----YGLK---V-SGFHADTMHMARLWDSSRRTEGGYSLEALT 488 (940)
Q Consensus 424 ~l~~Lk~~Le----d---~~i~KVgHNaKfDL~~L~r----~GI~---l-~n~vfDTmIAA~LLdp~~~~~~s~sLe~La 488 (940)
.+..+.+++. . .....|+||+.||+.+|.+ +|+. . +..++||+.+++.+.+. ++|++++
T Consensus 83 ~~~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~~------~~L~~l~ 156 (189)
T cd06134 83 ALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYGQ------TVLAKAC 156 (189)
T ss_pred HHHHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhCC------CcHHHHH
Confidence 3333333332 1 1346899999999999953 5662 2 23479999999888663 5799999
Q ss_pred hcc
Q 002293 489 GDR 491 (940)
Q Consensus 489 ~~y 491 (940)
.+|
T Consensus 157 ~~~ 159 (189)
T cd06134 157 QAA 159 (189)
T ss_pred HHC
Confidence 863
No 48
>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=98.16 E-value=2.1e-05 Score=100.69 Aligned_cols=111 Identities=21% Similarity=0.292 Sum_probs=79.0
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCC--------------------CChhhhHhh
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD--------------------GGGRDLLNE 427 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~--------------------~~~e~~l~~ 427 (940)
.+|+||+||||+++..+.|+. |-++.+..+..+ . ....+|.+.. .+..+++..
T Consensus 191 ~~VVfDiETTGL~~~~d~IIE---IGAVkv~~g~ii---d-~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~ 263 (1213)
T TIGR01405 191 TYVVFDIETTGLSPQYDEIIE---FGAVKVKNGRII---D-KFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEK 263 (1213)
T ss_pred cEEEEEeEecCCCCCCCeEEE---EEEEEEECCeEE---E-EEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHH
Confidence 589999999999998888876 224444332111 0 0122333221 124568888
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHH----cCCC-CCCccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 428 FAPFFEDPSIKKVWHNYSFDNHVLEN----YGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 428 Lk~~Led~~i~KVgHNaKfDL~~L~r----~GI~-l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
|..|+.+. .+|+||+.||+.+|++ +|+. +...++||+.+++.+.|... .++|++|+++
T Consensus 264 f~~fl~~~--iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k---~~kL~~Lak~ 326 (1213)
T TIGR01405 264 FKEFFKDS--ILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYK---SHRLGNICKK 326 (1213)
T ss_pred HHHHhCCC--eEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCC---CCCHHHHHHH
Confidence 88999864 6899999999999963 5765 45678999999999988765 6999999986
No 49
>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=98.15 E-value=3.2e-05 Score=81.73 Aligned_cols=113 Identities=18% Similarity=0.159 Sum_probs=71.6
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCC-----------C---------ChhhhHhh
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD-----------G---------GGRDLLNE 427 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~-----------~---------~~e~~l~~ 427 (940)
.+|+||+||||+++..+ |+. |-++.+..+. .. .. ....++.+.. + ...+++..
T Consensus 8 ~fvv~D~ETTGl~~~~~-IIe---Igav~v~~~~-~~-~~-~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~ 80 (217)
T TIGR00573 8 TETTGDNETTGLYAGHD-IIE---IGAVEIINRR-IT-GN-KFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAED 80 (217)
T ss_pred CEEEEEecCCCCCCCCC-EEE---EEEEEEECCC-Ee-ee-EEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHH
Confidence 58999999999998766 765 2233333321 10 00 1123343321 1 13456777
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHH----cCC--CCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 428 FAPFFEDPSIKKVWHNYSFDNHVLEN----YGL--KVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 428 Lk~~Led~~i~KVgHNaKfDL~~L~r----~GI--~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
|..|+.+. ..|+||+.||+.+|.+ .+. .....++||+-.++++.+... ..+++|.+|+++
T Consensus 81 ~~~~~~~~--~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~-~~~~~L~~l~~~ 146 (217)
T TIGR00573 81 FADYIRGA--ELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFP-GKRNTLDALCKR 146 (217)
T ss_pred HHHHhCCC--EEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCC-CCCCCHHHHHHH
Confidence 88888663 6899999999999964 232 233568899988877765432 225799999986
No 50
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=98.12 E-value=5.1e-05 Score=82.65 Aligned_cols=110 Identities=21% Similarity=0.251 Sum_probs=72.8
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCC-------------------CChhhhHhhh
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD-------------------GGGRDLLNEF 428 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~-------------------~~~e~~l~~L 428 (940)
.+++||+||||+++..++|+. |-++.+..+. + +. ....+|.+.. ....+++..|
T Consensus 69 ~~vv~DiETTG~~~~~~~IIE---IGAv~v~~g~-i-~~--~f~~~v~p~~ip~~~~~itGIt~e~l~~ap~~~evl~~f 141 (257)
T PRK08517 69 VFCFVDIETNGSKPKKHQIIE---IGAVKVKNGE-I-ID--RFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEF 141 (257)
T ss_pred CEEEEEEeCCCCCCCCCeEEE---EEEEEEECCE-E-EE--EEEEEECCCCCChhhhhhcCcCHHHHcCCCCHHHHHHHH
Confidence 589999999999998777765 2234443221 1 00 1112333211 1245677888
Q ss_pred hhhhcCCCceEEEeccHHHHHHHH----HcCCC-CCCccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 429 APFFEDPSIKKVWHNYSFDNHVLE----NYGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 429 k~~Led~~i~KVgHNaKfDL~~L~----r~GI~-l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
..++++. ..|+||+.||+.+|. ++|+. +.+..+||+-.++.+-+.. .++|++|++.
T Consensus 142 ~~fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~~----~~~L~~L~~~ 202 (257)
T PRK08517 142 RLFLGDS--VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESP----RYGLSFLKEL 202 (257)
T ss_pred HHHHCCC--eEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccCC----CCCHHHHHHH
Confidence 8888764 589999999999985 45654 4467899997776554443 4899999974
No 51
>PRK05168 ribonuclease T; Provisional
Probab=98.09 E-value=8.1e-05 Score=78.54 Aligned_cols=124 Identities=17% Similarity=0.099 Sum_probs=72.5
Q ss_pred HHHHHHHHhccCCCceEEEEeccCCCCcccCccccCcceeEEEeecC-CC-cccCCCceEEEEeCC-------------C
Q 002293 354 AKKVVWMLTNKYKHLVHACDTEVAKIDVKQETPVDHGEVICFSIYSG-PE-ADFGNGKSCIWVDLL-------------D 418 (940)
Q Consensus 354 L~eli~~L~~a~~~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~-~g-Iq~g~~~~~~yID~~-------------~ 418 (940)
+.-+-.++... .+++||+||||+++..++|+. |-++.+... .+ +.... ....+|.+. +
T Consensus 7 ~~~~~~~~~~~---~~vv~D~ETTGl~~~~d~Iie---IgaV~v~~d~~g~i~~~~-~f~~lv~P~~~~~i~~~~~~ihG 79 (211)
T PRK05168 7 LNPLKDRFRGF---LPVVIDVETAGFNAKTDALLE---IAAVTLKMDEQGWLYPDE-TLHFHVEPFEGANLEPEALAFNG 79 (211)
T ss_pred cchHHHHhcCC---ceEEEEeeCCCCCCCCCEEEE---EeEEEEEecCCCcEeccc-eEEEEECCCCCCCCCHHHHhhcC
Confidence 34445666665 489999999999998888765 223433321 11 11111 112344331 0
Q ss_pred CC----------hhhhHhhhhhhhcC-------CCceEEEeccHHHHHHHHH----cCCC---C-CCccccHHHHHHhcC
Q 002293 419 GG----------GRDLLNEFAPFFED-------PSIKKVWHNYSFDNHVLEN----YGLK---V-SGFHADTMHMARLWD 473 (940)
Q Consensus 419 ~~----------~e~~l~~Lk~~Led-------~~i~KVgHNaKfDL~~L~r----~GI~---l-~n~vfDTmIAA~LLd 473 (940)
++ ..+++..+.+++.+ .....|+||+.||+.+|.+ +|+. . +..++||+..++.+.
T Consensus 80 It~e~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~ 159 (211)
T PRK05168 80 IDPDNPLRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLAL 159 (211)
T ss_pred CCchhhhhcCCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHc
Confidence 11 11223333444321 2357899999999999854 5653 1 124799999998776
Q ss_pred CCCCCCCCCCHHHHHhc
Q 002293 474 SSRRTEGGYSLEALTGD 490 (940)
Q Consensus 474 p~~~~~~s~sLe~La~~ 490 (940)
+. ++|.++++.
T Consensus 160 ~~------~~L~~l~~~ 170 (211)
T PRK05168 160 GQ------TVLAKACQA 170 (211)
T ss_pred CC------CCHHHHHHH
Confidence 53 579998876
No 52
>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=98.07 E-value=8.3e-06 Score=82.24 Aligned_cols=63 Identities=19% Similarity=0.096 Sum_probs=47.6
Q ss_pred hhHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 423 DLLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 423 ~~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
+++..|.+++++. ...|+||+.||+.+|... .+.++||+..++.+.+......+++|++|+++
T Consensus 72 ~~~~~~~~~i~~~-~vlVgHn~~fD~~fL~~~----~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~ 134 (161)
T cd06137 72 AARAALWKFIDPD-TILVGHSLQNDLDALRMI----HTRVVDTAILTREAVKGPLAKRQWSLRTLCRD 134 (161)
T ss_pred HHHHHHHHhcCCC-cEEEeccHHHHHHHHhCc----CCCeeEehhhhhhccCCCcCCCCccHHHHHHH
Confidence 4556778888763 368999999999999753 34589999999988876410026999999986
No 53
>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=98.05 E-value=5.3e-05 Score=94.81 Aligned_cols=111 Identities=18% Similarity=0.167 Sum_probs=76.0
Q ss_pred eEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCC-----------CC---------ChhhhHhhh
Q 002293 369 VHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-----------DG---------GGRDLLNEF 428 (940)
Q Consensus 369 ~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~-----------~~---------~~e~~l~~L 428 (940)
+|+||+||||+++..++|+.+ -++.+..+. + + .....+|.+. ++ ...+++..|
T Consensus 2 ~vvvD~ETTG~~~~~~~IIei---g~v~v~~~~-i-~--~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l 74 (850)
T TIGR01407 2 YAVVDLETTGTQLSFDKIIQI---GIVVVEDGE-I-V--DTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEI 74 (850)
T ss_pred EEEEEEECCCCCCCCCeEEEE---EEEEEECCE-E-E--EEEEEEeCCCCCCChhhhhhcCcCHHHHhCCCCHHHHHHHH
Confidence 799999999999877887652 233332221 1 0 0112233322 11 134567778
Q ss_pred hhhhcCCCceEEEeccHHHHHHHHH----cCCC-CCCccccHHHHHHhcCCCCCCCCCCCHHHHHhcc
Q 002293 429 APFFEDPSIKKVWHNYSFDNHVLEN----YGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGDR 491 (940)
Q Consensus 429 k~~Led~~i~KVgHNaKfDL~~L~r----~GI~-l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y 491 (940)
.+++++. ..|+||+.||+.+|.+ +|+. +++.++||+..++.+.|... +++|.+|++.|
T Consensus 75 ~~~l~~~--~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~---~~~L~~l~~~~ 137 (850)
T TIGR01407 75 YDLLEDG--IFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEE---SYQLSELSEAL 137 (850)
T ss_pred HHHhCCC--EEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCC---CCCHHHHHHHC
Confidence 8888764 5899999999999953 6776 46778999999998888665 69999999863
No 54
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=98.05 E-value=6e-05 Score=83.57 Aligned_cols=116 Identities=15% Similarity=0.028 Sum_probs=68.8
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecC-CC-c-ccCCCceEEEEeCCC-----------CCh------hhhHhh
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSG-PE-A-DFGNGKSCIWVDLLD-----------GGG------RDLLNE 427 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~-~g-I-q~g~~~~~~yID~~~-----------~~~------e~~l~~ 427 (940)
.++++||||||+++..+.|+.+ -++.+..+ .+ + ++.. ....++++.. ++. ....+.
T Consensus 38 ~~vvlD~ETTGLd~~~d~IIEI---g~V~v~~~~~g~i~~v~~-~~~~lv~P~~~I~~~~t~IhGIt~e~v~~~~~~~~~ 113 (294)
T PRK09182 38 LGVILDTETTGLDPRKDEIIEI---GMVAFEYDDDGRIGDVLD-TFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDPAA 113 (294)
T ss_pred eEEEEEeeCCCCCCCCCeEEEE---EEEEEEecCCCceeeeee-EEEEEeCCCCCCCHHHHHhcCCCHHHHhcCCCcHHH
Confidence 4799999999999988888762 23333211 11 1 1111 1123444321 111 112346
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHHcCCCCC-CccccHHHHHHhcCCCCCCCCCCCHHHHHhcc
Q 002293 428 FAPFFEDPSIKKVWHNYSFDNHVLENYGLKVS-GFHADTMHMARLWDSSRRTEGGYSLEALTGDR 491 (940)
Q Consensus 428 Lk~~Led~~i~KVgHNaKfDL~~L~r~GI~l~-n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y 491 (940)
+..+++.. ..+|+||+.||+.+|.+.+..+. ..+.||+.......+... +++|++|+..|
T Consensus 114 l~~fl~~~-~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~~~~~~~~---~~kL~~La~~~ 174 (294)
T PRK09182 114 VDALIAPA-DLIIAHNAGFDRPFLERFSPVFATKPWACSVSEIDWSARGFE---GTKLGYLAGQA 174 (294)
T ss_pred HHHHhcCC-CEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHhhccccCC---CCCHHHHHHHc
Confidence 77777764 36899999999999987654433 346777754433333333 68999999763
No 55
>PRK07883 hypothetical protein; Validated
Probab=98.02 E-value=6.8e-05 Score=89.75 Aligned_cols=111 Identities=17% Similarity=0.072 Sum_probs=73.3
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCC-----------CC---------ChhhhHhh
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-----------DG---------GGRDLLNE 427 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~-----------~~---------~~e~~l~~ 427 (940)
.+|+||+||||+++..+.|+. |-++.+..+. +. + ....+|.+. ++ ...+++..
T Consensus 16 ~~Vv~D~ETTGl~p~~~~IIE---IgaV~v~~g~-iv--~-~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~ 88 (557)
T PRK07883 16 TFVVVDLETTGGSPAGDAITE---IGAVKVRGGE-VL--G-EFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPA 88 (557)
T ss_pred CEEEEEEecCCCCCCCCeEEE---EEEEEEECCE-EE--E-EEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHH
Confidence 589999999999998777765 2233332221 10 0 112233331 11 13456677
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHH----HcCCCCC-CccccHHHHHHhcCC--CCCCCCCCCHHHHHhc
Q 002293 428 FAPFFEDPSIKKVWHNYSFDNHVLE----NYGLKVS-GFHADTMHMARLWDS--SRRTEGGYSLEALTGD 490 (940)
Q Consensus 428 Lk~~Led~~i~KVgHNaKfDL~~L~----r~GI~l~-n~vfDTmIAA~LLdp--~~~~~~s~sLe~La~~ 490 (940)
|..|+++ ...|+||+.||+.+|. ++|+... ..++||+..++-+.+ ... +++|++|++.
T Consensus 89 f~~fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~---~~~L~~L~~~ 153 (557)
T PRK07883 89 FLEFARG--AVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAP---NVRLSTLARL 153 (557)
T ss_pred HHHHhcC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCC---CCCHHHHHHH
Confidence 8888876 3679999999999985 3687754 568999988876555 333 6899999975
No 56
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=98.01 E-value=0.00014 Score=72.04 Aligned_cols=109 Identities=22% Similarity=0.257 Sum_probs=71.9
Q ss_pred eEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCC--------------------CChhhhHhhh
Q 002293 369 VHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD--------------------GGGRDLLNEF 428 (940)
Q Consensus 369 ~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~--------------------~~~e~~l~~L 428 (940)
+|+||+||||+++..+.|+. |-++.+..+. + . .....||.+.. .+..+++..|
T Consensus 2 ~v~~D~Ettg~~~~~~~Iie---ig~v~~~~~~-~--~-~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~~~~~~~~~~ 74 (169)
T smart00479 2 LVVIDCETTGLDPGKDEIIE---IAAVDVDGGR-I--I-VVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEEL 74 (169)
T ss_pred EEEEEeeCCCCCCCCCeEEE---EEEEEEECCE-e--E-EEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHH
Confidence 68999999999987666665 2233333221 0 0 01123443311 1244677888
Q ss_pred hhhhcCCCceEEEecc-HHHHHHHHH----cCCCCC--CccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 429 APFFEDPSIKKVWHNY-SFDNHVLEN----YGLKVS--GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 429 k~~Led~~i~KVgHNa-KfDL~~L~r----~GI~l~--n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
..++.+. ..|+||+ .||+.+|.+ +|+..+ ..++||+-.++.+.+.. +++|++|++.
T Consensus 75 ~~~l~~~--~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~----~~~L~~l~~~ 137 (169)
T smart00479 75 LEFLKGK--ILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGR----KYSLKKLAER 137 (169)
T ss_pred HHHhcCC--EEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCC----CCCHHHHHHH
Confidence 8888764 4688888 999999964 565533 34799999998877654 4899999986
No 57
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=97.98 E-value=0.00015 Score=80.83 Aligned_cols=65 Identities=22% Similarity=0.229 Sum_probs=50.7
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHH----HcCCCCC-CccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLE----NYGLKVS-GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 421 ~e~~l~~Lk~~Led~~i~KVgHNaKfDL~~L~----r~GI~l~-n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
..+++..|.+++.+. ..|+||+.||+.+|. ++|+..+ ..++||+..++-+.|... +++|.+|+..
T Consensus 67 f~ev~~~~~~fl~~~--~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~---~~~L~~L~~~ 136 (309)
T PRK06195 67 FDKIWEKIKHYFNNN--LVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNID---NARLNTVNNF 136 (309)
T ss_pred HHHHHHHHHHHhCCC--EEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCC---cCCHHHHHHH
Confidence 345777888888763 689999999999985 3676643 568999998887777654 6899999986
No 58
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=97.90 E-value=4.5e-05 Score=76.86 Aligned_cols=63 Identities=17% Similarity=0.071 Sum_probs=45.1
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccccHHHH---HH-hcCCCCCCCCCCCHHHHHhc
Q 002293 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHM---AR-LWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 421 ~e~~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r~GI~l~n~vfDTmIA---A~-LLdp~~~~~~s~sLe~La~~ 490 (940)
.++++..|.+++.+. ..|+||++||+.+|... .....+.||... .+ .+.|... +|+|+.|+++
T Consensus 64 ~~~v~~~l~~~l~~~--vlV~Hn~~~D~~~l~~~--~~~~~~~Dt~~l~~~~~~~~~p~~~---~~~L~~L~~~ 130 (157)
T cd06149 64 FAVAQKEILKILKGK--VVVGHAIHNDFKALKYF--HPKHMTRDTSTIPLLNRKAGFPENC---RVSLKVLAKR 130 (157)
T ss_pred HHHHHHHHHHHcCCC--EEEEeCcHHHHHHhccc--CCCcCEEECcccccchhhcCCcccC---ChhHHHHHHH
Confidence 466788888888764 68999999999999643 223457788643 22 2355443 6999999987
No 59
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=97.88 E-value=0.00016 Score=91.30 Aligned_cols=111 Identities=20% Similarity=0.248 Sum_probs=75.0
Q ss_pred ceEEEEeccCCCCccc-CccccCcceeEEEeecCCCcccCCCceEEEEeCC-----------CC---------ChhhhHh
Q 002293 368 LVHACDTEVAKIDVKQ-ETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-----------DG---------GGRDLLN 426 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~-d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~-----------~~---------~~e~~l~ 426 (940)
.+|+||+||||+++.. ++|+. |-++.+..+. + + + ....+|.+. ++ ...+++.
T Consensus 4 ~~vvvD~ETTG~~p~~~d~IIe---igav~v~~~~-i-~-~-~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~ 76 (928)
T PRK08074 4 RFVVVDLETTGNSPKKGDKIIQ---IAAVVVEDGE-I-L-E-RFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAP 76 (928)
T ss_pred CEEEEEEeCCCCCCCCCCcEEE---EEEEEEECCE-E-E-E-EEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHH
Confidence 5899999999998764 56665 2233333221 1 0 0 111233332 11 1345777
Q ss_pred hhhhhhcCCCceEEEeccHHHHHHHHH----cCCC-CCCccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 427 EFAPFFEDPSIKKVWHNYSFDNHVLEN----YGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 427 ~Lk~~Led~~i~KVgHNaKfDL~~L~r----~GI~-l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
.|..++++. ..|+||+.||+.+|.+ .|+. +.+.++||+-.++.+.|... +|+|.+|++.
T Consensus 77 ~l~~~l~~~--~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~---~~~L~~l~~~ 140 (928)
T PRK08074 77 EIVELLEGA--YFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAE---SYKLRDLSEE 140 (928)
T ss_pred HHHHHhCCC--eEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCC---CCCHHHHHHh
Confidence 788888764 6899999999999964 5765 34678999999999888765 7999999985
No 60
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=97.87 E-value=0.00019 Score=75.26 Aligned_cols=65 Identities=18% Similarity=0.202 Sum_probs=45.9
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccH-HHHHHHHHcCCCCCC-ccccHH---HHHHhc-CCCCCCCCCCCHHHHHhc
Q 002293 421 GRDLLNEFAPFFEDPSIKKVWHNYS-FDNHVLENYGLKVSG-FHADTM---HMARLW-DSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 421 ~e~~l~~Lk~~Led~~i~KVgHNaK-fDL~~L~r~GI~l~n-~vfDTm---IAA~LL-dp~~~~~~s~sLe~La~~ 490 (940)
..+++..|..|+++. .+|+||+. ||+.+|.++|+.+.+ ..+||. .+.++. .++.. +|+|.+|+++
T Consensus 71 ~~evl~~f~~f~~~~--~lVaHNa~~fD~~fL~~~g~~~~~~~~idt~~~~~~~~~~~~~~~~---~~~L~~La~~ 141 (195)
T PRK07247 71 VEEVLAAFKEFVGEL--PLIGYNAQKSDLPILAENGLDLSDQYQVDLYDEAFERRSSDLNGIA---NLKLQTVADF 141 (195)
T ss_pred HHHHHHHHHHHHCCC--eEEEEeCcHhHHHHHHHcCCCcCCCceeehHHHHHHhhccccCCCC---CCCHHHHHHh
Confidence 456778888888765 48999995 899999998887654 345664 222322 23333 6999999985
No 61
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=97.82 E-value=6e-05 Score=75.28 Aligned_cols=63 Identities=19% Similarity=0.149 Sum_probs=45.6
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccccHHHHHHhcCCC-CCCCCCCCHHHHHhc
Q 002293 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSS-RRTEGGYSLEALTGD 490 (940)
Q Consensus 421 ~e~~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r~GI~l~n~vfDTmIAA~LLdp~-~~~~~s~sLe~La~~ 490 (940)
..+++..|..++++. ..|+||+.||+.+|.. +. ....++||.....+..+. .. +++|++|++.
T Consensus 64 ~~~~~~~l~~~l~~~--vlVgHn~~fD~~~L~~-~~-~~~~~~dt~~l~~~~~~~~~~---~~sL~~l~~~ 127 (152)
T cd06144 64 FEEVQKKVAELLKGR--ILVGHALKNDLKVLKL-DH-PKKLIRDTSKYKPLRKTAKGK---SPSLKKLAKQ 127 (152)
T ss_pred HHHHHHHHHHHhCCC--EEEEcCcHHHHHHhcC-cC-CCccEEEeEEeeccccccCCC---ChhHHHHHHH
Confidence 456778888999763 5799999999999963 22 224578988765555442 22 6999999986
No 62
>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=97.75 E-value=0.00014 Score=74.53 Aligned_cols=110 Identities=19% Similarity=0.135 Sum_probs=66.5
Q ss_pred eEEEEeccCCCC-cccCccccCcceeEEEeecCCCcccCC----------CceEEEEeCCC-----------CC------
Q 002293 369 VHACDTEVAKID-VKQETPVDHGEVICFSIYSGPEADFGN----------GKSCIWVDLLD-----------GG------ 420 (940)
Q Consensus 369 ~VAfDTETTGLd-~~~d~IvG~g~Ii~LSi~~~~gIq~g~----------~~~~~yID~~~-----------~~------ 420 (940)
+++||+||||++ +..++|+. |-++.+..+. +..+. .....++.+.. ++
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iie---i~av~v~~~~-~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a~~IhGIt~e~l~~ 76 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITE---LCLVAVHRDH-LLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEH 76 (177)
T ss_pred CeEEeeecCCCCCCCCCceEE---EEEEEEeccc-ccccccccccccceeeeeeEEeCCCCcCChhHHHHhCcCHHHHhc
Confidence 478999999999 57788876 2344443221 10000 00123343321 11
Q ss_pred ----hhhhHhhhhhhhcC--CCceEEEecc-HHHHHHHH----HcCCCCC--CccccHHHHHHhcCCCCCCCCCCCHHHH
Q 002293 421 ----GRDLLNEFAPFFED--PSIKKVWHNY-SFDNHVLE----NYGLKVS--GFHADTMHMARLWDSSRRTEGGYSLEAL 487 (940)
Q Consensus 421 ----~e~~l~~Lk~~Led--~~i~KVgHNa-KfDL~~L~----r~GI~l~--n~vfDTmIAA~LLdp~~~~~~s~sLe~L 487 (940)
...+.+.|.+|+.. .....|+||+ .||+.+|. ++|+.+. ..++||+.+++.+.+ +|++|
T Consensus 77 ~~~~~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~~--------~L~~l 148 (177)
T cd06136 77 KAPFDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ--------SLGSL 148 (177)
T ss_pred CCCccHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhHh--------hHHHH
Confidence 01244566666653 2347899998 89999995 4676643 456899999886653 68888
Q ss_pred Hhc
Q 002293 488 TGD 490 (940)
Q Consensus 488 a~~ 490 (940)
+++
T Consensus 149 ~~~ 151 (177)
T cd06136 149 YKR 151 (177)
T ss_pred HHH
Confidence 875
No 63
>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=97.73 E-value=0.00025 Score=69.78 Aligned_cols=64 Identities=28% Similarity=0.295 Sum_probs=50.6
Q ss_pred hhhHhhhhhhhcCCCceEEEeccHHHHHHHHH----cCCC-CCCccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 422 RDLLNEFAPFFEDPSIKKVWHNYSFDNHVLEN----YGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 422 e~~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r----~GI~-l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
.+++..|..++++. ..|+||+.||+.+|.+ +|+. ++..++||+..+..+.+... +++|+.|++.
T Consensus 65 ~~v~~~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~---~~~L~~l~~~ 133 (156)
T cd06130 65 PEVWPEIKPFLGGS--LVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLP---NHKLNTVAEH 133 (156)
T ss_pred HHHHHHHHHHhCCC--EEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCC---CCCHHHHHHH
Confidence 45777888888873 6899999999999853 5766 34568999988887777654 6899999985
No 64
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=97.65 E-value=0.00093 Score=71.26 Aligned_cols=46 Identities=37% Similarity=0.257 Sum_probs=38.0
Q ss_pred ceEEEeccHHHHHHHHHcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 437 IKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 437 i~KVgHNaKfDL~~L~r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
..+|+||+.||+.+|... .+.++||+-+++.+.|+. .+++..|+..
T Consensus 75 ~~lVaHNa~FD~~~L~~~----~~~~idTl~lar~l~p~~----~~~l~~L~~~ 120 (219)
T PRK07983 75 EWYVAHNASFDRRVLPEM----PGEWICTMKLARRLWPGI----KYSNMALYKS 120 (219)
T ss_pred CEEEEeCcHhhHHHHhCc----CCCcEeHHHHHHHHccCC----CCCHHHHHHH
Confidence 368999999999999753 356899999999888876 3899988875
No 65
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=97.60 E-value=0.00021 Score=71.41 Aligned_cols=62 Identities=16% Similarity=0.015 Sum_probs=47.8
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 421 ~e~~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
.++++..|.+|+... ..+|+||+.||+.+|... .+.++||+..++.+.+... +|+|++|+++
T Consensus 62 ~~~v~~~~~~fl~~~-~vlVgHn~~fD~~fL~~~----~~~~iDT~~l~r~~~~~~~---~~~L~~L~~~ 123 (150)
T cd06145 62 LEDVQKKLLSLISPD-TILVGHSLENDLKALKLI----HPRVIDTAILFPHPRGPPY---KPSLKNLAKK 123 (150)
T ss_pred HHHHHHHHHHHhCCC-CEEEEcChHHHHHHhhcc----CCCEEEcHHhccccCCCCC---ChhHHHHHHH
Confidence 456777888888632 368999999999999753 2458999998887665443 5899999987
No 66
>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=97.58 E-value=0.0001 Score=68.48 Aligned_cols=75 Identities=28% Similarity=0.335 Sum_probs=52.4
Q ss_pred EEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcCCC-ceEEEeccHHHH
Q 002293 370 HACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFEDPS-IKKVWHNYSFDN 448 (940)
Q Consensus 370 VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~~l~~Lk~~Led~~-i~KVgHNaKfDL 448 (940)
+++|+||+|++++.+.|+. +++..+. ++..++++ |.+++++.. ..+|+||+.||+
T Consensus 1 ~~~DiEt~~~~~~~~~i~~------i~~~~~~------~~~~~~~~------------f~~~l~~~~~~v~V~hn~~fD~ 56 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIE------IALADVN------PEDTAVID------------LKDILRDKPLAILVGHNGSFDL 56 (96)
T ss_pred CEEEEECCCCCCCCCcEEE------EEEEEcc------CCCEEEeh------------HHHHHhhCCCCEEEEeCcHHhH
Confidence 4799999999998877654 4443321 12245544 667777765 678999999999
Q ss_pred HHHHH----cCCCC---CCccccHHHH
Q 002293 449 HVLEN----YGLKV---SGFHADTMHM 468 (940)
Q Consensus 449 ~~L~r----~GI~l---~n~vfDTmIA 468 (940)
.+|.+ +|+.. ...++||+.+
T Consensus 57 ~fL~~~~~~~~~~~p~~~~~~lDT~~l 83 (96)
T cd06125 57 PFLNNRCAELGLKYPLLAGSWIDTIKL 83 (96)
T ss_pred HHHHHHHHHcCCCCCCcCCcEEEehHH
Confidence 98853 55543 3568999987
No 67
>PRK05359 oligoribonuclease; Provisional
Probab=97.57 E-value=0.00034 Score=72.35 Aligned_cols=103 Identities=12% Similarity=0.108 Sum_probs=63.4
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCC------------------C---------CC
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL------------------D---------GG 420 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~------------------~---------~~ 420 (940)
.+|++|+|||||++..++|+. |-++.+. +..+.+.. ....++.+. + .+
T Consensus 4 ~~vvlD~ETTGLdp~~d~Iie---IgaV~~~-~~~~~~~~-~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~ 78 (181)
T PRK05359 4 NLIWIDLEMTGLDPERDRIIE---IATIVTD-ADLNILAE-GPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVS 78 (181)
T ss_pred cEEEEEeecCCCCCCCCeEEE---EEEEEEc-CCceEccc-ceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCC
Confidence 589999999999999888876 2233322 21111111 011111100 1 12
Q ss_pred hhhhHhhhhhhhcC----CCceEEEeccHHHHHHHHH----cCCCCCCcccc--HH-HHHHhcCCC
Q 002293 421 GRDLLNEFAPFFED----PSIKKVWHNYSFDNHVLEN----YGLKVSGFHAD--TM-HMARLWDSS 475 (940)
Q Consensus 421 ~e~~l~~Lk~~Led----~~i~KVgHNaKfDL~~L~r----~GI~l~n~vfD--Tm-IAA~LLdp~ 475 (940)
..+++..|.+|+++ .....++||+.||+.+|.+ .|..+.++++| |+ -+++.+.|+
T Consensus 79 ~~e~~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~tl~~l~r~~~P~ 144 (181)
T PRK05359 79 EAEAEAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLDVSTLKELARRWKPE 144 (181)
T ss_pred HHHHHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhcccCCCcccchhHHHHHHHHhChh
Confidence 45677777888863 2345799999999999975 36667777777 66 577777764
No 68
>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=97.52 E-value=0.00043 Score=66.75 Aligned_cols=107 Identities=25% Similarity=0.226 Sum_probs=67.4
Q ss_pred EEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCC--------------------CChhhhHhhhh
Q 002293 370 HACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD--------------------GGGRDLLNEFA 429 (940)
Q Consensus 370 VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~--------------------~~~e~~l~~Lk 429 (940)
|.+|+||||+++..+.|+. +|........ .... ....|+.+.. ....+++..+.
T Consensus 1 v~~D~Ettg~~~~~~~iie----i~~v~~~~~~-~~~~-~~~~~i~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~ 74 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIE----IGAVKVDGGI-EIVE-RFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFL 74 (159)
T ss_pred CeEEeeCCCcCCCCCeEEE----EEEEEEECCc-Chhh-hhheeeCcCCcCCHhheeccCCCHHHHhcCCCHHHHHHHHH
Confidence 4789999999987777765 3332222110 0000 1122332221 11345777888
Q ss_pred hhhcCCCceEEEeccHHHHHHHHH----cCC-CCCCccccHHHHHHhcCCCCCCCCCCCHHHH
Q 002293 430 PFFEDPSIKKVWHNYSFDNHVLEN----YGL-KVSGFHADTMHMARLWDSSRRTEGGYSLEAL 487 (940)
Q Consensus 430 ~~Led~~i~KVgHNaKfDL~~L~r----~GI-~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~L 487 (940)
.++++ ..+|+||+.||+.+|.+ +|. .....++||+..+..+.+... .+++..+
T Consensus 75 ~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~~---~~~l~~~ 132 (159)
T cd06127 75 EFLGG--RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLR---SHRLGLL 132 (159)
T ss_pred HHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCCC---cCchHHH
Confidence 88877 46899999999999964 342 234568999988887776554 5778777
No 69
>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=97.47 E-value=0.00073 Score=69.58 Aligned_cols=116 Identities=14% Similarity=0.139 Sum_probs=65.9
Q ss_pred EEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCC-------------CC----------ChhhhHh
Q 002293 370 HACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-------------DG----------GGRDLLN 426 (940)
Q Consensus 370 VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~-------------~~----------~~e~~l~ 426 (940)
+.||+||||+++..++|+. |-++.+. +.+..+ . ....++.+. ++ +..+++.
T Consensus 1 ~~~D~ETTGl~~~~d~Iie---ig~v~v~-~~~~~~-~-~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~ 74 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQ---FAAIRTD-ENFNEI-E-PFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIA 74 (183)
T ss_pred CEEEeecCCCCCCCCceEE---EEEEEEC-CCCCCc-c-ceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHH
Confidence 3699999999998888765 2223232 211111 1 112233111 11 1234566
Q ss_pred hhhhhhcCCCceEEEec-cHHHHHHHHH----cCCCC-------CCccccHHHHHHhcC---CC------CC-CCCCCCH
Q 002293 427 EFAPFFEDPSIKKVWHN-YSFDNHVLEN----YGLKV-------SGFHADTMHMARLWD---SS------RR-TEGGYSL 484 (940)
Q Consensus 427 ~Lk~~Led~~i~KVgHN-aKfDL~~L~r----~GI~l-------~n~vfDTmIAA~LLd---p~------~~-~~~s~sL 484 (940)
.|..++.......|+|| +.||+.+|.+ +|+.. .+..+||+-.++++. |. .. ...+|+|
T Consensus 75 ~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L 154 (183)
T cd06138 75 KIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKL 154 (183)
T ss_pred HHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhH
Confidence 77778865444678997 7999999964 45431 123578887666532 31 00 0125889
Q ss_pred HHHHhcc
Q 002293 485 EALTGDR 491 (940)
Q Consensus 485 e~La~~y 491 (940)
++|+++|
T Consensus 155 ~~l~~~~ 161 (183)
T cd06138 155 EDLAQAN 161 (183)
T ss_pred HHHHHHC
Confidence 9999863
No 70
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=97.47 E-value=0.00089 Score=87.43 Aligned_cols=112 Identities=21% Similarity=0.269 Sum_probs=76.8
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCC--------------------CChhhhHhh
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD--------------------GGGRDLLNE 427 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~--------------------~~~e~~l~~ 427 (940)
.+|++|+||||+++..+.|+.+| ++.+..+. + + .....|+.+.. .+..+++..
T Consensus 420 ~~VVfDLETTGL~~~~deIIEIg---AV~V~~G~-i-i--e~F~~~V~P~~~I~~~~~~LTGIT~e~L~~aps~~EaL~~ 492 (1437)
T PRK00448 420 TYVVFDVETTGLSAVYDEIIEIG---AVKIKNGE-I-I--DKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPK 492 (1437)
T ss_pred cEEEEEhhhcCCCCchhhhheee---eEEEeCCe-E-e--eeEEEEECCCCCCCHHHHHHhCCCHHHHcCCCCHHHHHHH
Confidence 58999999999999888887622 23332221 1 0 01123333321 124567777
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHH----HcCCC-CCCccccHHHHHHhcCCCCCCCCCCCHHHHHhcc
Q 002293 428 FAPFFEDPSIKKVWHNYSFDNHVLE----NYGLK-VSGFHADTMHMARLWDSSRRTEGGYSLEALTGDR 491 (940)
Q Consensus 428 Lk~~Led~~i~KVgHNaKfDL~~L~----r~GI~-l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y 491 (940)
+..|+.+ ..+|+||+.||+.+|. ++|+. +...++||+-+++.+.|... .++|++|+++|
T Consensus 493 f~~figg--~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k---~~kL~~LAk~l 556 (1437)
T PRK00448 493 FKEFCGD--SILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELK---SHRLNTLAKKF 556 (1437)
T ss_pred HHHHhCC--CEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccc---cccHHHHHHHc
Confidence 7777766 4789999999999874 46774 55678999999998888654 69999999863
No 71
>PRK11779 sbcB exonuclease I; Provisional
Probab=97.44 E-value=0.0013 Score=77.45 Aligned_cols=119 Identities=13% Similarity=0.081 Sum_probs=66.2
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCC-------------CC----------Chhhh
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL-------------DG----------GGRDL 424 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~-------------~~----------~~e~~ 424 (940)
.++++|+||||+++..++|+. +.++.+..+ .+.++. ...+|+.+. ++ +..++
T Consensus 7 ~fvv~D~ETTGLdP~~DrIIe---iAaVrvd~~-~~~i~e-~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~ 81 (476)
T PRK11779 7 TFLWHDYETFGANPALDRPAQ---FAGIRTDAD-LNIIGE-PLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEF 81 (476)
T ss_pred cEEEEEEECCCCCCCCCeeEE---EEEEEEeCC-Cceecc-eeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHH
Confidence 589999999999999888875 224433322 111111 112333221 11 12345
Q ss_pred HhhhhhhhcCCCceEEEec-cHHHHHHHHHc----CCC-C------CCccccHHHHHH---hcCCCC---C----CCCCC
Q 002293 425 LNEFAPFFEDPSIKKVWHN-YSFDNHVLENY----GLK-V------SGFHADTMHMAR---LWDSSR---R----TEGGY 482 (940)
Q Consensus 425 l~~Lk~~Led~~i~KVgHN-aKfDL~~L~r~----GI~-l------~n~vfDTmIAA~---LLdp~~---~----~~~s~ 482 (940)
+..+..++..+....|+|| +.||..++++. .+. . .+..+|++-.++ -+.|+. . ...++
T Consensus 82 ~~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~ 161 (476)
T PRK11779 82 AARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSF 161 (476)
T ss_pred HHHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCC
Confidence 6677777864455689997 68999998652 221 1 122345555444 332211 0 01268
Q ss_pred CHHHHHhcc
Q 002293 483 SLEALTGDR 491 (940)
Q Consensus 483 sLe~La~~y 491 (940)
+|++|+..|
T Consensus 162 rLe~L~~~~ 170 (476)
T PRK11779 162 KLEHLTKAN 170 (476)
T ss_pred cHHHHHHHc
Confidence 999999863
No 72
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=97.44 E-value=0.0014 Score=67.68 Aligned_cols=65 Identities=22% Similarity=0.306 Sum_probs=48.5
Q ss_pred hhhhHhhhhhhhcC--CCceEEEecc-HHHHHHHH----HcCCCCC-----------------------CccccHHHHHH
Q 002293 421 GRDLLNEFAPFFED--PSIKKVWHNY-SFDNHVLE----NYGLKVS-----------------------GFHADTMHMAR 470 (940)
Q Consensus 421 ~e~~l~~Lk~~Led--~~i~KVgHNa-KfDL~~L~----r~GI~l~-----------------------n~vfDTmIAA~ 470 (940)
+.+.+..|..++.+ +. ..|+||. .||+.+|. ++|+... ..++|++..++
T Consensus 63 E~~lL~~f~~~i~~~dpd-iivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r 141 (199)
T cd05160 63 EKELLKRFFDIIREYDPD-ILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYK 141 (199)
T ss_pred HHHHHHHHHHHHHhcCCC-EEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHH
Confidence 45677777777765 44 5899999 89999984 2676651 23789998888
Q ss_pred hcCCCCCCCCCCCHHHHHhc
Q 002293 471 LWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 471 LLdp~~~~~~s~sLe~La~~ 490 (940)
-..+ .. +|+|+++++.
T Consensus 142 ~~~~-l~---sy~L~~v~~~ 157 (199)
T cd05160 142 RDFK-LK---SYTLDAVAEE 157 (199)
T ss_pred HhcC-cc---cCCHHHHHHH
Confidence 6665 43 6999999987
No 73
>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=97.43 E-value=0.00042 Score=70.81 Aligned_cols=103 Identities=13% Similarity=0.112 Sum_probs=62.5
Q ss_pred eEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCC------------------CC---------Ch
Q 002293 369 VHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLL------------------DG---------GG 421 (940)
Q Consensus 369 ~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~------------------~~---------~~ 421 (940)
.+.+|+||||+++..+.|+. |-++.+ .+..++++. ....++.+. ++ +.
T Consensus 1 lv~iD~ETTGl~p~~d~Iie---IgaV~~-~~~~~~i~~-~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~ 75 (173)
T cd06135 1 LVWIDLEMTGLDPEKDRILE---IACIIT-DGDLNIIAE-GPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTL 75 (173)
T ss_pred CEEEEEecCCCCCCCCeeEE---EEEEEE-eCCCceecC-ceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCH
Confidence 37899999999998888766 223333 222122211 111222221 11 13
Q ss_pred hhhHhhhhhhhcC----CCceEEEeccHHHHHHHHH----cCCCCCCccccH---HHHHHhcCCCC
Q 002293 422 RDLLNEFAPFFED----PSIKKVWHNYSFDNHVLEN----YGLKVSGFHADT---MHMARLWDSSR 476 (940)
Q Consensus 422 e~~l~~Lk~~Led----~~i~KVgHNaKfDL~~L~r----~GI~l~n~vfDT---mIAA~LLdp~~ 476 (940)
.+++..|..|+.+ .....++||+.||+.+|.+ +|..+.++..|| ..+++.+.|+.
T Consensus 76 ~~vl~~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~~~l~~l~~~l~p~~ 141 (173)
T cd06135 76 AQAEAELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDVSSIKELARRWYPEI 141 (173)
T ss_pred HHHHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHHhccCCcchhhHHHHHHHHHHhCcHh
Confidence 4567778888864 2457889999999999964 465566667887 44666666654
No 74
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=97.32 E-value=0.0035 Score=65.90 Aligned_cols=67 Identities=15% Similarity=0.101 Sum_probs=47.5
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHH----HcCCCCC--CccccHHHHHHhcCCCCCCCCCCCHHHHHhcc
Q 002293 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLE----NYGLKVS--GFHADTMHMARLWDSSRRTEGGYSLEALTGDR 491 (940)
Q Consensus 421 ~e~~l~~Lk~~Led~~i~KVgHNaKfDL~~L~----r~GI~l~--n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y 491 (940)
..+++..|.+++.+.. ..++|++.||+.+|. ++|+..+ +.+.|++...+.+.+... .++|++++++|
T Consensus 79 ~~evl~~f~~~~~~~~-~~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~---~~~L~~~~~~~ 151 (207)
T PRK07748 79 FEELVEKLAEYDKRCK-PTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERN---QTGLWKAIEEY 151 (207)
T ss_pred HHHHHHHHHHHhCcCC-eEEEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCC---CCCHHHHHHHc
Confidence 4567888889998733 345677899999995 3676543 457888877765555433 58999999863
No 75
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=97.27 E-value=0.0021 Score=68.53 Aligned_cols=113 Identities=21% Similarity=0.192 Sum_probs=76.8
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCC-----------CC---------hhhhHhh
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD-----------GG---------GRDLLNE 427 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~-----------~~---------~e~~l~~ 427 (940)
..++||+||||+++..+.++. |-++.+..+.-+ ......|+.+.. ++ ..++++.
T Consensus 14 ~~vv~D~ETtg~~~~~~~iie---Igav~~~~~~i~---~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~ 87 (243)
T COG0847 14 RFVVIDLETTGLNPKKDRIIE---IGAVTLEDGRIV---ERSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPE 87 (243)
T ss_pred cEEEEecccCCCCCCCCceEE---EEeEEEECCeee---cceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHH
Confidence 479999999999998888775 234444433210 001123333311 11 2456677
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHH----cCCCC-CCccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 428 FAPFFEDPSIKKVWHNYSFDNHVLEN----YGLKV-SGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 428 Lk~~Led~~i~KVgHNaKfDL~~L~r----~GI~l-~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
+..++.+. ...|+||+.||+.+|.. +++.+ ...+.||+-.++-..|+.. .++|+.|+.+
T Consensus 88 ~~~~i~~~-~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~---~~~L~~l~~~ 151 (243)
T COG0847 88 FLDFIGGL-RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFD---RSSLDALAER 151 (243)
T ss_pred HHHHHCCC-CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCc---cchHHHHHHH
Confidence 77788774 46899999999999953 56654 3568899999999999843 5899999986
No 76
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=96.86 E-value=0.0033 Score=62.72 Aligned_cols=155 Identities=21% Similarity=0.280 Sum_probs=70.1
Q ss_pred EEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCC--Chhh-hHhhhhhhhcCCCceEEEec-cH
Q 002293 370 HACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDG--GGRD-LLNEFAPFFEDPSIKKVWHN-YS 445 (940)
Q Consensus 370 VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~--~~e~-~l~~Lk~~Led~~i~KVgHN-aK 445 (940)
+.||+||+|+++....+. ++|+...++.. ...+...... ..+. .+..+ .++.+.. .+|+|| ..
T Consensus 1 l~~DIET~Gl~~~~~~i~----liG~~~~~~~~-------~~~~~~~~~~~~~ee~~~~~~~-~~l~~~~-~iv~yng~~ 67 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIY----LIGVADFDDDE-------IITFIQWFAEDPDEEEIILEFF-ELLDEAD-NIVTYNGKN 67 (164)
T ss_dssp --EEEEESS-GG-G---E----EEEEEE-ETTT-------TE-EEEE-GGGHHHHHHHHH---HHHHTT---EEESSTTT
T ss_pred CcEEecCCCCCCCCCCEE----EEEEEEeCCCc-------eEEeeHhhccCcHHHHHHHHHH-HHHhcCC-eEEEEeCcc
Confidence 469999999998655442 23444333221 1212221111 1111 22222 4555554 467788 57
Q ss_pred HHHHHHHH----cCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhhccccCCCCccccccccchh
Q 002293 446 FDNHVLEN----YGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMK 521 (940)
Q Consensus 446 fDL~~L~r----~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg~~~~l~k~~s~eELvGk~s~k 521 (940)
||+.+|++ +++......+|++-.++=... . +++|+++++. +++.+ ..+++-|... -
T Consensus 68 FD~p~L~~~~~~~~~~~~~~~iDl~~~~~~~~~--~---~~~Lk~ve~~--------lg~~~------~~~~~~G~~~-~ 127 (164)
T PF13482_consen 68 FDIPFLKRRAKRYGLPPPFNHIDLLKIIKKHFL--E---SYSLKNVEKF--------LGIER------RDDDISGSES-V 127 (164)
T ss_dssp THHHHHHHHH-HHHH--GGGEEEHHHHHT-TTS--C---CTT--SHHH-------------------------HHHHH-H
T ss_pred cCHHHHHHHHHHcCCCcccchhhHHHHHHhccC--C---CCCHHHHhhh--------ccccc------ccCCCCHHHH-H
Confidence 99999964 455445668899887753222 2 5899999974 33321 1111112211 1
Q ss_pred hhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHH
Q 002293 522 DIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSL 573 (940)
Q Consensus 522 elfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L 573 (940)
..|..-. ..+ ++ ...+..+.|+..|+..|.+|+++|
T Consensus 128 ~~~~~~~--~~~----~~----------~~~~~i~~yN~~Dv~~~~~L~~~l 163 (164)
T PF13482_consen 128 KLYKEYL--ETG----DP----------EALEEILEYNEDDVRATRRLYEWL 163 (164)
T ss_dssp HHHH-----TTG----GT----------S--HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHH--hcC----CH----------HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 1221100 000 00 114678999999999999999986
No 77
>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=96.81 E-value=0.0092 Score=59.82 Aligned_cols=67 Identities=12% Similarity=0.013 Sum_probs=46.7
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHH----cCCC----CCCccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLEN----YGLK----VSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 421 ~e~~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r----~GI~----l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
..+++..|..|+.+.....+.|++.||+.++.+ .+.. ....++|++-.+..+.+... .++|.++++.
T Consensus 75 ~~~vl~~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~---~~~L~~l~~~ 149 (176)
T cd06133 75 FPEVLKEFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKK---RTGLSKALEY 149 (176)
T ss_pred HHHHHHHHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCC---CCCHHHHHHH
Confidence 346778888898874113567778999887643 3332 33568999988887766543 5899999975
No 78
>PRK06722 exonuclease; Provisional
Probab=96.76 E-value=0.042 Score=61.05 Aligned_cols=67 Identities=12% Similarity=0.010 Sum_probs=43.3
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHH----cCCCCCC----ccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLEN----YGLKVSG----FHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 421 ~e~~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r----~GI~l~n----~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
.++++..|..|+.+. ..|+||+.||+.+|.+ +|+..+. .++|++-.++-+.+... ...++|+++++.
T Consensus 77 f~eVl~ef~~fig~~--~lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~-~~~~sL~~l~~~ 151 (281)
T PRK06722 77 FPQIIEKFIQFIGED--SIFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELF-EHTPSLQSAVEQ 151 (281)
T ss_pred HHHHHHHHHHHHCCC--cEEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhc-cCCCCHHHHHHH
Confidence 456778888888764 3578889999999964 6765432 24677654432222210 013689999975
No 79
>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=96.62 E-value=0.027 Score=59.60 Aligned_cols=112 Identities=20% Similarity=0.230 Sum_probs=65.1
Q ss_pred ceEEEEeccCCCCccc---CccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcC--CCceEEEe
Q 002293 368 LVHACDTEVAKIDVKQ---ETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFED--PSIKKVWH 442 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~---d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~~l~~Lk~~Led--~~i~KVgH 442 (940)
..++||.|+.+..... +.. ....|++++.....+ . ...+.....++.+.+..|..++.. |. .+++|
T Consensus 10 kilsfDIE~~~~~~~~~p~p~~-~~d~Ii~Is~~~~~~------~-~~~~~~~~~~E~~lL~~f~~~i~~~dPd-ii~g~ 80 (207)
T cd05785 10 RRLQLDIETYSLPGFFFSNPDR-GDDRIIIVALRDNRG------W-EEVLHAEDAAEKELLEELVAIIRERDPD-VIEGH 80 (207)
T ss_pred eEEEEEEEecCCCCccCCCCCC-CCCeEEEEecccCCC------c-eeeeccCCCCHHHHHHHHHHHHHHhCCC-EEecc
Confidence 4799999997654321 111 112355666543221 1 111211122355677777777765 44 56799
Q ss_pred cc-HHHHHHHH----HcCCCCC------------------------------Cc-cccHHHHHHhcCC---CCCCCCCCC
Q 002293 443 NY-SFDNHVLE----NYGLKVS------------------------------GF-HADTMHMARLWDS---SRRTEGGYS 483 (940)
Q Consensus 443 Na-KfDL~~L~----r~GI~l~------------------------------n~-vfDTmIAA~LLdp---~~~~~~s~s 483 (940)
|. .||+..|. ++|+... ++ ++|++.+..-.+. ... +|+
T Consensus 81 N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~~~l~---sys 157 (207)
T cd05785 81 NIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSSRDLP---SYG 157 (207)
T ss_pred CCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccccCCC---CCC
Confidence 98 89999984 3566541 12 3798876664322 223 699
Q ss_pred HHHHHhcc
Q 002293 484 LEALTGDR 491 (940)
Q Consensus 484 Le~La~~y 491 (940)
|+++|+.+
T Consensus 158 L~~Va~~~ 165 (207)
T cd05785 158 LKAVAKHF 165 (207)
T ss_pred HHHHHHHh
Confidence 99999864
No 80
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=96.07 E-value=0.058 Score=56.25 Aligned_cols=110 Identities=22% Similarity=0.324 Sum_probs=67.7
Q ss_pred hhhhHhhhhhhhcC--CCceEEEecc-HHHHHHHH----HcCCCCC----------------------C-ccccHHHHHH
Q 002293 421 GRDLLNEFAPFFED--PSIKKVWHNY-SFDNHVLE----NYGLKVS----------------------G-FHADTMHMAR 470 (940)
Q Consensus 421 ~e~~l~~Lk~~Led--~~i~KVgHNa-KfDL~~L~----r~GI~l~----------------------n-~vfDTmIAA~ 470 (940)
+.+.+..|..++.. +. .+|+||. .||+..|. ++|+..+ + .++|++..++
T Consensus 56 E~~lL~~F~~~i~~~dpd-iivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~ 134 (195)
T cd05780 56 EKEMIKRFIEIVKEKDPD-VIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVAR 134 (195)
T ss_pred HHHHHHHHHHHHHHcCCC-EEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHH
Confidence 45677777777765 65 5899996 59999984 2576532 1 2778887776
Q ss_pred hcCCCCCCCCCCCHHHHHhccccccccchhhhccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHh
Q 002293 471 LWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQRE 550 (940)
Q Consensus 471 LLdp~~~~~~s~sLe~La~~y~~~~e~yLg~~~~l~k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~ 550 (940)
-.. ... +|+|+++++. +||..+ .++-++ .+..+|..+ +
T Consensus 135 ~~~-~l~---sy~L~~v~~~-------~Lg~~k--------~d~~~~-~i~~~~~~~---------------~------- 172 (195)
T cd05780 135 RTL-NLT---RYTLERVYEE-------LFGIEK--------EDVPGE-EIAEAWDSG---------------E------- 172 (195)
T ss_pred hhC-CCC---cCcHHHHHHH-------HhCCCC--------CcCCHH-HHHHHHhCC---------------C-------
Confidence 422 223 6999999987 454320 111110 111122110 0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHH
Q 002293 551 ERELWISYSAFDSINTLKLYKSL 573 (940)
Q Consensus 551 ~~e~~l~YAA~DA~~tlrLye~L 573 (940)
.......|+..||..|++|...+
T Consensus 173 ~~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 173 NLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred chHHHHHHhHHHHHHHHHHHhhC
Confidence 13567899999999999998753
No 81
>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=96.05 E-value=0.071 Score=56.86 Aligned_cols=112 Identities=22% Similarity=0.317 Sum_probs=71.1
Q ss_pred hhhhHhhhhhhhcCCCceEEEecc-HHHHHHHHH----cCCCCCC------------------ccccHHHHHHhcCCCCC
Q 002293 421 GRDLLNEFAPFFEDPSIKKVWHNY-SFDNHVLEN----YGLKVSG------------------FHADTMHMARLWDSSRR 477 (940)
Q Consensus 421 ~e~~l~~Lk~~Led~~i~KVgHNa-KfDL~~L~r----~GI~l~n------------------~vfDTmIAA~LLdp~~~ 477 (940)
+.+.+..|..+++......|+||. .||+.+|.+ +|+.++. ..+|+|-....-+...
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 EKELLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFYGAKA- 115 (209)
T ss_pred HHHHHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhccCccc-
Confidence 567788888888876668899996 599999842 7887642 2468776644444322
Q ss_pred CCCCCCHHHHHhccccccccchhhhccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHH
Q 002293 478 TEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWIS 557 (940)
Q Consensus 478 ~~~s~sLe~La~~y~~~~e~yLg~~~~l~k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~ 557 (940)
..+|+.||.- +|+. ...++.|. ...++| ++...+....
T Consensus 116 ---~~sLd~la~~--------lgiP-------gK~~idGs-~V~~~y-----------------------~~g~i~~I~~ 153 (209)
T PF10108_consen 116 ---RTSLDELAAL--------LGIP-------GKDDIDGS-QVAELY-----------------------QEGDIDEIRE 153 (209)
T ss_pred ---cCCHHHHHHH--------cCCC-------CCCCCCHH-HHHHHH-----------------------HcCCHHHHHH
Confidence 4789999974 3331 00111110 001111 1122466789
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 002293 558 YSAFDSINTLKLYKSLKK 575 (940)
Q Consensus 558 YAA~DA~~tlrLye~L~~ 575 (940)
|+..||..|..||-++.-
T Consensus 154 YCe~DVl~T~~lylR~~~ 171 (209)
T PF10108_consen 154 YCEKDVLNTYLLYLRFEL 171 (209)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 999999999999998754
No 82
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=96.02 E-value=0.036 Score=66.12 Aligned_cols=178 Identities=18% Similarity=0.177 Sum_probs=106.1
Q ss_pred ceEEecCHHHHHHHH-HHHhccCCCceEEEEeccCCC-CcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCC--
Q 002293 344 NVMVVDNVSAAKKVV-WMLTNKYKHLVHACDTEVAKI-DVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDG-- 419 (940)
Q Consensus 344 ~y~lV~t~e~L~eli-~~L~~a~~~~~VAfDTETTGL-d~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~-- 419 (940)
.+++|+++..++.++ ..|... .-+|++|.|-..- .....++ .- +|+..+..+++||....
T Consensus 391 ~i~~V~~e~El~~l~l~~l~~e--~~yVGiDsEwkps~~v~dsk~------~I--------lQif~~~~v~Lidc~~l~~ 454 (617)
T KOG2207|consen 391 SIGMVGNEKELRDLLLESLSEE--LRYVGIDSEWKPSKKVSDSKL------AI--------LQIFFKDCVYLIDCVKLEN 454 (617)
T ss_pred ceeeeCCHHHHHHHHHHHhhhc--CEEEEEccccCcccCCChhHH------HH--------HHHHhcCeEEEeehHHhhh
Confidence 578999999999888 234332 2489999997654 1111111 11 45555455677888653
Q ss_pred ChhhhHhh-hhhhhcCCCceEEEeccHHHHHHHHH------cCCCCC---CccccHHHHHHhcCCCCC----CCCCCCHH
Q 002293 420 GGRDLLNE-FAPFFEDPSIKKVWHNYSFDNHVLEN------YGLKVS---GFHADTMHMARLWDSSRR----TEGGYSLE 485 (940)
Q Consensus 420 ~~e~~l~~-Lk~~Led~~i~KVgHNaKfDL~~L~r------~GI~l~---n~vfDTmIAA~LLdp~~~----~~~s~sLe 485 (940)
...+.+.. +..+|+++.+.|||++...|++++++ ....+. +.+-++.++..+.+-... ..-..+|.
T Consensus 455 ~~se~w~~~~s~if~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~ 534 (617)
T KOG2207|consen 455 LASEIWHLLLSQIFESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLA 534 (617)
T ss_pred chHHHHHHHHHHHccCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhhh
Confidence 12344443 45689999999999999999999983 222222 223445555554443211 00012233
Q ss_pred HHHhccccccccchhhhccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHH
Q 002293 486 ALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSIN 565 (940)
Q Consensus 486 ~La~~y~~~~e~yLg~~~~l~k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~ 565 (940)
+|.. .++|+.--|. ..-.+|..+|+ +..|+.|||-|+..
T Consensus 535 ~Lt~--------------------------------~llg~~lnKt--eqcsnWqcrpL-------r~nQi~yaalDa~~ 573 (617)
T KOG2207|consen 535 DLTD--------------------------------CLLGKKLNKT--EQCSNWQCRPL-------RRNQIYYAALDAVV 573 (617)
T ss_pred hhhH--------------------------------HHhhhhcccc--cccchhhcCCc-------hhhHHHHHHhcchh
Confidence 2222 2233321110 11237999998 46899999999999
Q ss_pred HHHHHHHHHHHHh
Q 002293 566 TLKLYKSLKKKLL 578 (940)
Q Consensus 566 tlrLye~L~~~Le 578 (940)
+..++.++.+..+
T Consensus 574 ~~~ifkkv~~vv~ 586 (617)
T KOG2207|consen 574 LVEIFKKVCSVVE 586 (617)
T ss_pred hHHHHHHHHhhcc
Confidence 9999998876544
No 83
>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=95.82 E-value=0.2 Score=52.29 Aligned_cols=109 Identities=19% Similarity=0.185 Sum_probs=63.3
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhcCCCc-eEEEecc-H
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFEDPSI-KKVWHNY-S 445 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~~l~~Lk~~Led~~i-~KVgHNa-K 445 (940)
..++||+||++..-+... +...|+++++....+ ...++.. ...++.+.+..|..++...+. ..+++|. .
T Consensus 4 ~~l~fDIEt~~~~gfp~~--~~d~Ii~Is~~~~~g------~~~~~~~-~~~~E~~lL~~F~~~i~~~dPd~i~gyN~~~ 74 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNP--RRDPIIVISLATSNG------DVEFILA-EGLDDRKIIREFVKYVKEYDPDIIVGYNSNA 74 (188)
T ss_pred eEEEEEEEecCCCCCCCC--CCCCEEEEEEEeCCC------CEEEEEe-cCCCHHHHHHHHHHHHHHcCCCEEEecCCCc
Confidence 478999999854332111 113456666654321 1122222 122345677777777764332 4789995 6
Q ss_pred HHHHHHH----HcCCCCC-----C----------------ccccHHHHHHhcCCCCCCCCCCCHHHHHh
Q 002293 446 FDNHVLE----NYGLKVS-----G----------------FHADTMHMARLWDSSRRTEGGYSLEALTG 489 (940)
Q Consensus 446 fDL~~L~----r~GI~l~-----n----------------~vfDTmIAA~LLdp~~~~~~s~sLe~La~ 489 (940)
||+..|. .+|+.+. + .++|.+-..+-... .. +++|+++|+
T Consensus 75 FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~-l~---~y~L~~Va~ 139 (188)
T cd05781 75 FDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPE-VK---VKTLENVAE 139 (188)
T ss_pred CcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCC-CC---CCCHHHHHH
Confidence 9999984 3676542 0 16777766653332 22 699999996
No 84
>PTZ00315 2'-phosphotransferase; Provisional
Probab=95.45 E-value=0.18 Score=60.84 Aligned_cols=118 Identities=11% Similarity=-0.018 Sum_probs=66.4
Q ss_pred ceEEEEeccCCCCccc---CccccCcceeEEEeecCCCcccCCCceEEEEeCCC-------------C---------Chh
Q 002293 368 LVHACDTEVAKIDVKQ---ETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD-------------G---------GGR 422 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~---d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~-------------~---------~~e 422 (940)
.+++||+||||+++.. +.|+.+ -++.+....+..+ .....||-+.. + +..
T Consensus 57 ~~IV~DlETTgl~~~~~~~dEIIEI---GaV~Vd~~ng~Ii--~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap~F~ 131 (582)
T PTZ00315 57 AYVVLDFEATCEADRRIEDAEVIEF---PMVLVDARTATPV--AEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFP 131 (582)
T ss_pred eEEEEEEecCCCCCCCCCCCceEEE---EEEEEEccCCEEE--EEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCCCHH
Confidence 4899999999988643 555541 1222221111000 01223554421 1 245
Q ss_pred hhHhhhhhhhcCCC--------ceEEEeccHHHHH-HHHH-------cCCCCCCc-cccHH-HHHHhcCCCC--------
Q 002293 423 DLLNEFAPFFEDPS--------IKKVWHNYSFDNH-VLEN-------YGLKVSGF-HADTM-HMARLWDSSR-------- 476 (940)
Q Consensus 423 ~~l~~Lk~~Led~~--------i~KVgHNaKfDL~-~L~r-------~GI~l~n~-vfDTm-IAA~LLdp~~-------- 476 (940)
+++..|..||.+.. -..++||+.||+. +|.. .|+.+... ++|.. ..+.++.|+.
T Consensus 132 eVl~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p~~~~~~~~~~ 211 (582)
T PTZ00315 132 VVYCEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFGNGSGCGGGAT 211 (582)
T ss_pred HHHHHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCccccccccccc
Confidence 68888889987653 1478999999996 6632 36655433 44532 5555555521
Q ss_pred CCCCCCCHHHHHhc
Q 002293 477 RTEGGYSLEALTGD 490 (940)
Q Consensus 477 ~~~~s~sLe~La~~ 490 (940)
....+++|+++++.
T Consensus 212 ~~~~~~~L~~al~~ 225 (582)
T PTZ00315 212 PPLGPSDMPDMLQM 225 (582)
T ss_pred cccCCcCHHHHHHH
Confidence 01125899999975
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=95.30 E-value=0.22 Score=52.82 Aligned_cols=67 Identities=27% Similarity=0.354 Sum_probs=46.0
Q ss_pred ChhhhHhhhhhhhcCCCceEEEecc-HHHHHHHHH----cCCCCC-----------------CccccHHHHHHhcCCCCC
Q 002293 420 GGRDLLNEFAPFFEDPSIKKVWHNY-SFDNHVLEN----YGLKVS-----------------GFHADTMHMARLWDSSRR 477 (940)
Q Consensus 420 ~~e~~l~~Lk~~Led~~i~KVgHNa-KfDL~~L~r----~GI~l~-----------------n~vfDTmIAA~LLdp~~~ 477 (940)
++.+.+..|..++++....+|+||. .||+.+|.. +|+.++ +..+|++-+..-.+. ..
T Consensus 77 ~E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~~-~~ 155 (208)
T cd05782 77 DEKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYGA-RA 155 (208)
T ss_pred CHHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccCc-cC
Confidence 3456777888888764446899997 699999853 677533 126788876553332 12
Q ss_pred CCCCCCHHHHHhc
Q 002293 478 TEGGYSLEALTGD 490 (940)
Q Consensus 478 ~~~s~sLe~La~~ 490 (940)
+++|+.+++.
T Consensus 156 ---~~~L~~va~~ 165 (208)
T cd05782 156 ---RASLDLLAKL 165 (208)
T ss_pred ---CCCHHHHHHH
Confidence 5899999974
No 86
>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=94.97 E-value=0.0022 Score=61.90 Aligned_cols=112 Identities=23% Similarity=0.292 Sum_probs=65.7
Q ss_pred EEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCC---C-------------------ChhhhHhh
Q 002293 370 HACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLD---G-------------------GGRDLLNE 427 (940)
Q Consensus 370 VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~---~-------------------~~e~~l~~ 427 (940)
|+||+||||+++..+.++. |.++.+..+.... ......||.+.. . ...+++..
T Consensus 1 v~~D~Ettg~~~~~~~iie---ig~v~~~~~~~~~--~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~ 75 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIE---IGAVKVDDDENEE--VESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDE 75 (164)
T ss_dssp EEEEEEESSSTTTTCTEEE---EEEEEEETTTTEE--EEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEE---EEEEEeeCCcccc--ceeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHh
Confidence 6899999999997777765 2334444332100 001122332221 0 12335666
Q ss_pred hhhhhcCCCceEEEeccHHHHHHHHH----c-CCCCC--CccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 428 FAPFFEDPSIKKVWHNYSFDNHVLEN----Y-GLKVS--GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 428 Lk~~Led~~i~KVgHNaKfDL~~L~r----~-GI~l~--n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
+..++... ...|+||+.||+.++.+ + +...+ ..++||+...+...+... .++|+.|++.
T Consensus 76 ~~~~~~~~-~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~l~~l~~~ 141 (164)
T PF00929_consen 76 FEEFLKKN-DILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNRK---KYSLDDLAEY 141 (164)
T ss_dssp HHHHHHHH-TEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHHH---HHSHHHHHHH
T ss_pred hhhhhhcc-cccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhccc---cCCHHHHHHH
Confidence 77788632 47899999999876632 3 22222 347888877776665443 3688888875
No 87
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=94.04 E-value=0.79 Score=50.05 Aligned_cols=164 Identities=19% Similarity=0.103 Sum_probs=90.7
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCC-hhhhHhhhhhhhcCCC-ceEEEecc-
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGG-GRDLLNEFAPFFEDPS-IKKVWHNY- 444 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~-~e~~l~~Lk~~Led~~-i~KVgHNa- 444 (940)
.++-||+||||++.....| +.+....+. +..++|-..-++ .+.-...+..|+.++. ..+|.+|.
T Consensus 99 ~~~FFDiETTGL~~ag~~I------~~~g~a~~~-------~~~~~Vrq~~lp~p~~E~avle~fl~~~~~~~lvsfNGk 165 (278)
T COG3359 99 DVAFFDIETTGLDRAGNTI------TLVGGARGV-------DDTMHVRQHFLPAPEEEVAVLENFLHDPDFNMLVSFNGK 165 (278)
T ss_pred ceEEEeeeccccCCCCCeE------EEEEEEEcc-------CceEEEEeecCCCcchhhHHHHHHhcCCCcceEEEecCc
Confidence 3777999999999843332 223333322 123444332111 1223345566666653 24688886
Q ss_pred HHHHHHHHH---c--CCCCCCccccHHHHHHhcCCC-CCCCCCCCHHHHHhccccccccchhhhccccCCCCcccccccc
Q 002293 445 SFDNHVLEN---Y--GLKVSGFHADTMHMARLWDSS-RRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKI 518 (940)
Q Consensus 445 KfDL~~L~r---~--GI~l~n~vfDTmIAA~LLdp~-~~~~~s~sLe~La~~y~~~~e~yLg~~~~l~k~~s~eELvGk~ 518 (940)
.||+.++++ . -..+....||.+-.++-|.-. .. .-+|+.+=+ +||+.. .++.-|..
T Consensus 166 aFD~PfikR~v~~~~el~l~~~H~DL~h~~RRlwk~~l~---~c~Lk~VEr--------~LGi~R-------~edtdG~~ 227 (278)
T COG3359 166 AFDIPFIKRMVRDRLELSLEFGHFDLYHPSRRLWKHLLP---RCGLKTVER--------ILGIRR-------EEDTDGYD 227 (278)
T ss_pred ccCcHHHHHHHhcccccCccccchhhhhhhhhhhhccCC---CCChhhHHH--------HhCccc-------cccCCCcc
Confidence 599999983 3 334556789999999866622 22 356765543 455431 11112222
Q ss_pred chhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 002293 519 SMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLYKSLKKKLLE 579 (940)
Q Consensus 519 s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLye~L~~~Lee 579 (940)
+....+. ..++++ | ........|.-.|+..+..|+..+.+++-+
T Consensus 228 ~p~lyr~---~~~~~d--------p------~ll~~l~~hN~eDvlnL~~i~~h~~~~i~~ 271 (278)
T COG3359 228 GPELYRL---YRRYGD--------P------GLLDGLVLHNREDVLNLPTIIKHVSKKILE 271 (278)
T ss_pred hHHHHHH---HHHcCC--------H------HHHHHHHHccHHHHHhHHHHHHHHHHHHHH
Confidence 1111110 001111 1 113556789999999999999999988765
No 88
>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=93.62 E-value=0.8 Score=48.20 Aligned_cols=67 Identities=21% Similarity=0.278 Sum_probs=42.0
Q ss_pred hhhhHhhhhhhhcCCCc-eEEEecc-HHHHHHHH----HcCCCCC------------------------Cc-cccHHHHH
Q 002293 421 GRDLLNEFAPFFEDPSI-KKVWHNY-SFDNHVLE----NYGLKVS------------------------GF-HADTMHMA 469 (940)
Q Consensus 421 ~e~~l~~Lk~~Led~~i-~KVgHNa-KfDL~~L~----r~GI~l~------------------------n~-vfDTmIAA 469 (940)
+.+.+..|..++...+. .+++||. .||+..|. .+|+... +. ++|++-..
T Consensus 51 E~~lL~~f~~~i~~~dPDvi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~ 130 (193)
T cd05784 51 EKSLLLALIAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDAL 130 (193)
T ss_pred HHHHHHHHHHHHHhhCCCEEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHH
Confidence 45667777777664322 5899995 69999984 2555431 21 67876554
Q ss_pred HhcCCCCCCCCCCCHHHHHhc
Q 002293 470 RLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 470 ~LLdp~~~~~~s~sLe~La~~ 490 (940)
+--..... +|+|+++++.
T Consensus 131 k~~~~kl~---sy~L~~Va~~ 148 (193)
T cd05784 131 KTATYHFE---SFSLENVAQE 148 (193)
T ss_pred HHccCCCC---cCCHHHHHHH
Confidence 42111233 7999999987
No 89
>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=92.17 E-value=2.9 Score=44.40 Aligned_cols=66 Identities=21% Similarity=0.324 Sum_probs=42.8
Q ss_pred hhhhHhhhhhhhcCCCceEEEecc-HHHHHHHH----HcCCCC--------------C-CccccHHHHHH-------hcC
Q 002293 421 GRDLLNEFAPFFEDPSIKKVWHNY-SFDNHVLE----NYGLKV--------------S-GFHADTMHMAR-------LWD 473 (940)
Q Consensus 421 ~e~~l~~Lk~~Led~~i~KVgHNa-KfDL~~L~----r~GI~l--------------~-n~vfDTmIAA~-------LLd 473 (940)
+.+.+..|..++.+.. .+|++|. .||+..|. ++|+.. . ...+|.+-... ...
T Consensus 73 E~~lL~~F~~~i~~~~-~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~ 151 (204)
T cd05783 73 EKELIREAFKIISEYP-IVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFG 151 (204)
T ss_pred HHHHHHHHHHHHhcCC-EEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhc
Confidence 4667888888888764 6789995 69999984 367761 1 23567654321 111
Q ss_pred CCCCCCCCCCHHHHHhc
Q 002293 474 SSRRTEGGYSLEALTGD 490 (940)
Q Consensus 474 p~~~~~~s~sLe~La~~ 490 (940)
.... +++|+++|+.
T Consensus 152 ~~~~---~~~L~~Va~~ 165 (204)
T cd05783 152 NKYR---EYTLDAVAKA 165 (204)
T ss_pred cccc---cCcHHHHHHH
Confidence 1222 6899999986
No 90
>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=91.59 E-value=2.4 Score=45.16 Aligned_cols=67 Identities=25% Similarity=0.288 Sum_probs=40.5
Q ss_pred hhhhHhhhhhhhcC--CCceEEEecc-HHHHHHHH----HcCCCCC-------C----------ccccHHHHHHhcCCCC
Q 002293 421 GRDLLNEFAPFFED--PSIKKVWHNY-SFDNHVLE----NYGLKVS-------G----------FHADTMHMARLWDSSR 476 (940)
Q Consensus 421 ~e~~l~~Lk~~Led--~~i~KVgHNa-KfDL~~L~----r~GI~l~-------n----------~vfDTmIAA~LLdp~~ 476 (940)
+.+.+..|..++.+ |. .++++|. .||+..|. ++|+.+. + ..+|.+-...--.-..
T Consensus 73 E~~lL~~f~~~i~~~~Pd-~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~ 151 (204)
T cd05779 73 EKALLQRFFEHIREVKPH-IIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLP 151 (204)
T ss_pred HHHHHHHHHHHHHHhCCC-EEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCC
Confidence 44566777777664 44 4699995 69999984 3676533 0 1467665443211100
Q ss_pred CCCCCCCHHHHHhc
Q 002293 477 RTEGGYSLEALTGD 490 (940)
Q Consensus 477 ~~~~s~sLe~La~~ 490 (940)
.++++|+.+|+.
T Consensus 152 --~~sysLd~Va~~ 163 (204)
T cd05779 152 --QGSQGLKAVTKA 163 (204)
T ss_pred --CCCccHHHHHHH
Confidence 125899999986
No 91
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=91.55 E-value=1.7 Score=54.14 Aligned_cols=92 Identities=26% Similarity=0.247 Sum_probs=59.0
Q ss_pred CceeeeecC-CCccceeeecCCCcc--ccCCCccchhhccceeecCCCCeEEEeeccchhHHHHHHhcC---C-----HH
Q 002293 822 GRVHCSLNI-NTETGRLSARRPNLQ--NQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLAN---C-----KS 890 (940)
Q Consensus 822 GRIH~s~nq-gTaTGRLSSs~PNLQ--NIP~~~~~~~~iR~~Fia~~G~~LvsaDYSQIELRILAhlS~---D-----~~ 890 (940)
|-|-+.... ||.|-|---.-=|.- ..| +.-|..||.+..|+||+.||+||--.-|+-|.|.|+. | ..
T Consensus 687 gaI~p~vvp~gtitrrave~tw~tasNs~~--~Rigselkamvqappgy~LVgaDvdsqElwiaa~lgda~~~~~hg~ta 764 (1075)
T KOG3657|consen 687 GAIAPQVVPAGTITRRAVEPTWLTASNARP--DRIGSELKAMVQAPPGYRLVGADVDSQELWIAALLGDASAEGVHGKTA 764 (1075)
T ss_pred hccCccccccchhhhhhhhhhhhhhcccCh--hhhhHHHHHhhcCCCcceEeeccccHHHHHHHHHhhhhhhhcccCcch
Confidence 455555544 677766221111111 112 2235689999999999999999999999999998873 1 11
Q ss_pred HH-----HHHhcCCCchHHHHHHHcCCCccc
Q 002293 891 ML-----DAFKAGGDFHSRTAMNMYPHIRNA 916 (940)
Q Consensus 891 Li-----~af~~g~DiH~~tAs~~fg~~~ee 916 (940)
+- ..-.+|-|+|+.||.. .|++++.
T Consensus 765 ~gwM~Lag~ks~gtdlhs~ta~~-lgiSr~h 794 (1075)
T KOG3657|consen 765 FGWMTLAGSKSDGTDLHSKTASQ-LGISRNH 794 (1075)
T ss_pred hhhhhhcCccccCchHhHhhhhh-ccccHhh
Confidence 11 1112478999999955 7777754
No 92
>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=89.39 E-value=10 Score=40.68 Aligned_cols=23 Identities=22% Similarity=0.182 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 002293 553 ELWISYSAFDSINTLKLYKSLKK 575 (940)
Q Consensus 553 e~~l~YAA~DA~~tlrLye~L~~ 575 (940)
...++|+..||..+++|+.+|.-
T Consensus 203 ~~l~~Y~~~Da~l~l~L~~kl~~ 225 (230)
T cd05777 203 RRLAVYCLKDAYLPLRLLDKLMC 225 (230)
T ss_pred HHHHHhhHHHHHHHHHHHHHHhh
Confidence 46789999999999999998753
No 93
>PHA02528 43 DNA polymerase; Provisional
Probab=87.75 E-value=11 Score=48.55 Aligned_cols=22 Identities=18% Similarity=0.209 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 002293 552 RELWISYSAFDSINTLKLYKSL 573 (940)
Q Consensus 552 ~e~~l~YAA~DA~~tlrLye~L 573 (940)
....+.|+..||..+++|..++
T Consensus 303 ~~~l~~Ynl~Da~Lv~~L~~kl 324 (881)
T PHA02528 303 HQKYIEYNIIDVELVDRLDDKR 324 (881)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999984
No 94
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=85.52 E-value=3.8 Score=45.35 Aligned_cols=62 Identities=19% Similarity=0.091 Sum_probs=40.3
Q ss_pred hhhhHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccccHHHH---HHhcCCCCCCCCCCCHHHHHhc
Q 002293 421 GRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHM---ARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 421 ~e~~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r~GI~l~n~vfDTmIA---A~LLdp~~~~~~s~sLe~La~~ 490 (940)
...+...+.++|.+. .+|||.+..|+.+|.-. .+...+.||--- ..++.... ..||+.|++.
T Consensus 171 f~~aQ~ev~klL~gR--IlVGHaLhnDl~~L~l~--hp~s~iRDTs~~~pl~k~~~~~~----tpSLK~Lt~~ 235 (280)
T KOG2249|consen 171 FKVAQKEVLKLLKGR--ILVGHALHNDLQALKLE--HPRSMIRDTSKYPPLMKLLSKKA----TPSLKKLTEA 235 (280)
T ss_pred HHHHHHHHHHHHhCC--EEeccccccHHHHHhhh--CchhhhcccccCchHHHHhhccC----CccHHHHHHH
Confidence 344566778888874 68999999999999531 112235676532 22333333 4799999987
No 95
>PRK05762 DNA polymerase II; Reviewed
Probab=82.00 E-value=14 Score=46.89 Aligned_cols=66 Identities=24% Similarity=0.441 Sum_probs=42.4
Q ss_pred hhhhHhhhhhhhcC--CCceEEEecc-HHHHHHHH----HcCCCCC-------------------------C-ccccHHH
Q 002293 421 GRDLLNEFAPFFED--PSIKKVWHNY-SFDNHVLE----NYGLKVS-------------------------G-FHADTMH 467 (940)
Q Consensus 421 ~e~~l~~Lk~~Led--~~i~KVgHNa-KfDL~~L~----r~GI~l~-------------------------n-~vfDTmI 467 (940)
+.+.+..|..++.. |+ .+++||. .||+..|. .+|+.+. + .++|++.
T Consensus 203 E~~LL~~F~~~i~~~DPD-IIvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~ 281 (786)
T PRK05762 203 EKALLEKFNAWFAEHDPD-VIIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGID 281 (786)
T ss_pred HHHHHHHHHHHHHhcCCC-EEEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHH
Confidence 35566676666654 55 4799995 69999984 2566431 1 1567776
Q ss_pred HHHhcCCCCCCCCCCCHHHHHhc
Q 002293 468 MARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 468 AA~LLdp~~~~~~s~sLe~La~~ 490 (940)
...-..-... +|+|+++++.
T Consensus 282 ~~k~~~~~l~---sysL~~Va~~ 301 (786)
T PRK05762 282 ALKSATWVFD---SFSLEYVSQR 301 (786)
T ss_pred HHHHhhccCC---CCCHHHHHHH
Confidence 6553321222 6999999986
No 96
>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=75.60 E-value=14 Score=40.02 Aligned_cols=110 Identities=24% Similarity=0.279 Sum_probs=65.7
Q ss_pred hhhhHhhhhhhhc--CCCceEEEecc-HHHHHHHH----HcCCCC---------------------------CC-ccccH
Q 002293 421 GRDLLNEFAPFFE--DPSIKKVWHNY-SFDNHVLE----NYGLKV---------------------------SG-FHADT 465 (940)
Q Consensus 421 ~e~~l~~Lk~~Le--d~~i~KVgHNa-KfDL~~L~----r~GI~l---------------------------~n-~vfDT 465 (940)
+.+.+..|..++. ||+ ..+|||. .||+..|. .+|+.. .| .+.|+
T Consensus 82 E~~LL~~f~~~i~~~DPD-iivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~ 160 (234)
T cd05776 82 ERALLNFFLAKLQKIDPD-VLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDT 160 (234)
T ss_pred HHHHHHHHHHHHhhcCCC-EEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCchhhcc
Confidence 3456666666654 677 5799997 89999873 234321 11 15688
Q ss_pred HHHHHhcCCCCCCCCCCCHHHHHhccccccccchhhhccccCCCCccccccccchhhhhcccccccCCCCCccccccchh
Q 002293 466 MHMARLWDSSRRTEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVE 545 (940)
Q Consensus 466 mIAA~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg~~~~l~k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~ 545 (940)
...++=+.. .. +|+|+++++. +|+.++ .++ ..+++.. .|.. +
T Consensus 161 ~~~~k~~~~-~~---sY~L~~va~~-------~Lg~~k--------~di----~~~~i~~------------~~~~-~-- 202 (234)
T cd05776 161 YLSAKELIR-CK---SYDLTELSQQ-------VLGIER--------QDI----DPEEILN------------MYND-S-- 202 (234)
T ss_pred HHHHHHHhC-CC---CCChHHHHHH-------HhCcCc--------ccC----CHHHHHH------------HHhC-H--
Confidence 877764433 33 6999999986 444320 111 0111110 1111 1
Q ss_pred HhhHhhHHHHHHHHHHHHHHHHHHHHHH
Q 002293 546 ELQREERELWISYSAFDSINTLKLYKSL 573 (940)
Q Consensus 546 ~l~~~~~e~~l~YAA~DA~~tlrLye~L 573 (940)
......+.|+..||..+++|..+|
T Consensus 203 ----~~l~~l~~y~~~Da~l~~~L~~kl 226 (234)
T cd05776 203 ----ESLLKLLEHTEKDAYLILQLMFKL 226 (234)
T ss_pred ----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 114567899999999999998876
No 97
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=72.31 E-value=14 Score=41.94 Aligned_cols=107 Identities=19% Similarity=0.139 Sum_probs=65.2
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHHH--cCCCCCCccccHHHHH-HhcCCCCCCCCCCCHHHHHhccccccccchh
Q 002293 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLEN--YGLKVSGFHADTMHMA-RLWDSSRRTEGGYSLEALTGDRKVMSEDKKA 500 (940)
Q Consensus 424 ~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r--~GI~l~n~vfDTmIAA-~LLdp~~~~~~s~sLe~La~~y~~~~e~yLg 500 (940)
+-..|+.||+|++...|+-+.+.|..-|.+ +++.+.. +.|..... -.++++.. .-+.+.|+.. .++
T Consensus 172 IP~~LR~fl~D~~~~~vgv~~d~D~~KL~r~~hql~I~~-~~dlr~~~~d~~g~~~~---~~s~e~i~~~-------~~~ 240 (319)
T KOG4373|consen 172 IPHELRSFLEDPDHTFVGVWNDQDAGKLERKEHQLEIGE-LEDLRLLVNDSLGGSMP---NDSFEEIVSE-------TLG 240 (319)
T ss_pred chHHHHHhhcCCCceEEeccccccHHHHhhhhhcccHHh-hhhHHhhcchhhccCcc---CccHHHHHHH-------Hhh
Confidence 445677889999999999999999988865 6766532 33432111 12333222 2456666654 222
Q ss_pred hhccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHHHH
Q 002293 501 YQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLKLY 570 (940)
Q Consensus 501 ~~~~l~k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlrLy 570 (940)
+. .+....+. . ... .+|...|+ +..|+.||+-||.+.+.|+
T Consensus 241 ~~---~~~v~l~~-----------------~-i~m-sdw~~~~L-------s~~Ql~~asidvy~c~~lg 281 (319)
T KOG4373|consen 241 YY---GKDVRLDK-----------------E-IRM-SDWSVYPL-------SDDQLLQASIDVYVCHKLG 281 (319)
T ss_pred cc---ccccccCh-----------------h-ccc-ccceeeec-------cHHHHHHHHhHHHHHHHHH
Confidence 21 00000000 0 111 37999887 5789999999999999999
No 98
>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=70.76 E-value=8.3 Score=40.40 Aligned_cols=59 Identities=19% Similarity=0.079 Sum_probs=39.0
Q ss_pred hHhhhhhhhcCCCceEEEeccHHHHHHHHHcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 424 LLNEFAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 424 ~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
+...|..++. +...+|||.+..|+++|+-. .+...++||-+.-.+ |... ..+|+.|++.
T Consensus 91 v~~~l~~li~-~~tILVGHsL~nDL~aL~l~--hp~~~viDTa~l~~~--~~~r---~~sLk~La~~ 149 (174)
T cd06143 91 AYLKLRLLVD-LGCIFVGHGLAKDFRVINIQ--VPKEQVIDTVELFHL--PGQR---KLSLRFLAWY 149 (174)
T ss_pred HHHHHHHHcC-CCCEEEeccchhHHHHhcCc--CCCcceEEcHHhccC--CCCC---ChhHHHHHHH
Confidence 3445666664 34578999999999999531 122458899754332 3222 5799999987
No 99
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=59.77 E-value=69 Score=43.22 Aligned_cols=110 Identities=26% Similarity=0.300 Sum_probs=62.2
Q ss_pred hhHhhhhhhhcC----CCceEEEeccH-HHHHHHH----HcCCCCC---CccccH---HHHHHhcC----------CCCC
Q 002293 423 DLLNEFAPFFED----PSIKKVWHNYS-FDNHVLE----NYGLKVS---GFHADT---MHMARLWD----------SSRR 477 (940)
Q Consensus 423 ~~l~~Lk~~Led----~~i~KVgHNaK-fDL~~L~----r~GI~l~---n~vfDT---mIAA~LLd----------p~~~ 477 (940)
+-...|+.||+. .....|.+|.. ||+.++. .+|+.+. +..-|. ..+.+..+ +-+
T Consensus 316 dEv~Ll~RfFeHiq~~kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrWVKRDSYL- 394 (2173)
T KOG1798|consen 316 DEVGLLQRFFEHIQEVKPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRWVKRDSYL- 394 (2173)
T ss_pred cHHHHHHHHHHHHHhcCCcEEEEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehhhhhhhhhcccC-
Confidence 345566666652 22357888876 7999984 3788864 222231 11111111 111
Q ss_pred CCCCCCHHHHHhccccccccchhhhccccCCCCc--cccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHH
Q 002293 478 TEGGYSLEALTGDRKVMSEDKKAYQKDMSKGNTD--EGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELW 555 (940)
Q Consensus 478 ~~~s~sLe~La~~y~~~~e~yLg~~~~l~k~~s~--eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~ 555 (940)
..|+++|+++.+. .|||. .+.+ |+|++. +-+.+..+
T Consensus 395 PqGSqgLKAVTka-------KLGYd-----PvEvdPEdM~~~------------------------------A~EkPQ~l 432 (2173)
T KOG1798|consen 395 PQGSQGLKAVTKA-------KLGYD-----PVEVDPEDMVRM------------------------------AMEKPQTL 432 (2173)
T ss_pred CCcccchhHHHHH-------hhCCC-----cccCCHHHhhhh------------------------------hhhCchhh
Confidence 2578999999986 56664 1111 111110 00113456
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 002293 556 ISYSAFDSINTLKLYKSLKK 575 (940)
Q Consensus 556 l~YAA~DA~~tlrLye~L~~ 575 (940)
..|.+.||.+|+-||-+.-.
T Consensus 433 asYSVSDAVATYyLYMkYVh 452 (2173)
T KOG1798|consen 433 ASYSVSDAVATYYLYMKYVH 452 (2173)
T ss_pred hhcchHHHHHHHHHHHHHhh
Confidence 79999999999999976543
No 100
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=59.13 E-value=4.5 Score=50.61 Aligned_cols=72 Identities=25% Similarity=0.311 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCchHHHHHHHHhcchHHHHHHHhHcC---cccCHH---HHHH
Q 002293 553 ELWISYSAFDSINTLKLYKSLKKKLLEMSWKLDGKPVPGKSMFDFYQEYWQPFGEILVKMETEG---MLVDRE---YLSE 626 (940)
Q Consensus 553 e~~l~YAA~DA~~tlrLye~L~~~Lee~~~~~~~~~~~~~~l~~Ly~~IEmPL~~VLa~ME~~G---I~VD~E---~L~e 626 (940)
.....|+|.|+.+|.+++..+.+..-+. .|-...|+.|-.-| .+||-. |+.+
T Consensus 359 q~L~~YCA~Dv~aThqVf~~lfP~Fler----------------------cPHPaTlagMLsmGsvyLPvN~nW~rYin~ 416 (1075)
T KOG3657|consen 359 QPLMNYCARDVIATHQVFFRLFPLFLER----------------------CPHPATLAGMLSMGSVYLPVNSNWERYINE 416 (1075)
T ss_pred HHHHHHHhhhhHHHHHHHHHHhHHHHHh----------------------CCChHhHHHHHhcCcEEeeccccHHHHHHH
Confidence 4568999999999999999998876552 24444566666666 566654 2334
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q 002293 627 IEKVARAEQEAAVNRFRKWA 646 (940)
Q Consensus 627 l~~~l~~e~e~le~ei~~~a 646 (940)
....+++-...++..|-+.|
T Consensus 417 ~e~tYeq~~~~~~~kl~~~A 436 (1075)
T KOG3657|consen 417 AEQTYEQLKTEAKRKIIESA 436 (1075)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 44445444444555554444
No 101
>PF09281 Taq-exonuc: Taq polymerase, exonuclease; InterPro: IPR015361 This domain is found in prokaryotic Taq DNA polymerase (thermostable), where it assumes a ribonuclease H-like motif. The domain confers 5'-3' exonuclease activity to the polymerase []. ; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 4DF4_A 3T3F_A 1QSY_A 3OJS_A 3PO5_A 3OJU_A 1QTM_A 1QSS_A 3PY8_A 4DFJ_A ....
Probab=57.63 E-value=23 Score=35.60 Aligned_cols=41 Identities=24% Similarity=0.169 Sum_probs=23.8
Q ss_pred HHHHHH-HHHcCCCCCCccccHHHHHHhcCCCCCCCCCCCHHHHHhcc
Q 002293 445 SFDNHV-LENYGLKVSGFHADTMHMARLWDSSRRTEGGYSLEALTGDR 491 (940)
Q Consensus 445 KfDL~~-L~r~GI~l~n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~y 491 (940)
..|+.+ +.+.|+.+. +--|.|+.+|||+|.. .+...++++|
T Consensus 70 AK~LAv~a~~~G~~v~-PGDDPlLlAYLlDPsN-----t~p~~varRY 111 (138)
T PF09281_consen 70 AKDLAVHALREGVVVE-PGDDPLLLAYLLDPSN-----TNPEGVARRY 111 (138)
T ss_dssp HHHHHHHHHHTT-----B---HHHHHHHH-TT-------SHHHHHHHH
T ss_pred HHHHHHHHHhcCcccC-CCCCcchhhhhcCccC-----CChHHHHHHh
Confidence 345554 567898874 3469999999999975 3788888874
No 102
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=56.52 E-value=2e+02 Score=38.12 Aligned_cols=23 Identities=30% Similarity=0.332 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 002293 552 RELWISYSAFDSINTLKLYKSLK 574 (940)
Q Consensus 552 ~e~~l~YAA~DA~~tlrLye~L~ 574 (940)
....+.|+..|+..+++|..+|.
T Consensus 461 ~~~l~~Y~l~Da~L~~~L~~kl~ 483 (1054)
T PTZ00166 461 RRRIAVYCLKDAILPLRLLDKLL 483 (1054)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 34578999999999999998774
No 103
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=50.10 E-value=2.9e+02 Score=31.89 Aligned_cols=22 Identities=36% Similarity=0.622 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 002293 552 RELWISYSAFDSINTLKLYKSL 573 (940)
Q Consensus 552 ~e~~l~YAA~DA~~tlrLye~L 573 (940)
....+.|+..|+..+++|+..+
T Consensus 199 ~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 199 RDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4668999999999999999886
No 104
>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=46.53 E-value=1.5e+02 Score=35.32 Aligned_cols=116 Identities=15% Similarity=0.119 Sum_probs=62.0
Q ss_pred hhhHhhhhhhhcC-CCceEEEeccHHHHHHHHH----cCCCCC------CccccHHHHHH--hcCCCCCCCCCCCHHHHH
Q 002293 422 RDLLNEFAPFFED-PSIKKVWHNYSFDNHVLEN----YGLKVS------GFHADTMHMAR--LWDSSRRTEGGYSLEALT 488 (940)
Q Consensus 422 e~~l~~Lk~~Led-~~i~KVgHNaKfDL~~L~r----~GI~l~------n~vfDTmIAA~--LLdp~~~~~~s~sLe~La 488 (940)
..++..|..++.. +...++.+| .+....|++ +|.... ..++|.....+ ++.|.. +|||+.++
T Consensus 329 ~~~~~~f~~~l~~~~~~~i~hY~-~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~----sysLK~v~ 403 (457)
T TIGR03491 329 ELAWQQFLQLLQSYPDAPIYHYG-ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIE----SYSLKSIA 403 (457)
T ss_pred HHHHHHHHHHHHHCCCCeEEeeC-HHHHHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCC----CCCHHHHH
Confidence 4466777777765 333445555 777777764 454411 14566654333 445543 69999999
Q ss_pred hccccccccchhhhccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHHHHHHHHHHH
Q 002293 489 GDRKVMSEDKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYSAFDSINTLK 568 (940)
Q Consensus 489 ~~y~~~~e~yLg~~~~l~k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YAA~DA~~tlr 568 (940)
.- +|.++. .+..-|..++. .|. .|...+-.. ..+..+.|...|+.+|++
T Consensus 404 ~~--------lg~~~~------~~~~~G~~ai~-~y~------------~~~~~~~~~----~l~~l~~YN~dD~~At~~ 452 (457)
T TIGR03491 404 RW--------LGFEWR------QKEASGAKSLL-WYR------------QWKKTGDRR----LLERILRYNEDDCRATWI 452 (457)
T ss_pred HH--------hCcccC------CCCCCHHHHHH-HHH------------HHHHhCCHH----HHHHHHHHhHHHHHHHHH
Confidence 74 343311 11111211111 110 111000000 146678999999999999
Q ss_pred HHHHH
Q 002293 569 LYKSL 573 (940)
Q Consensus 569 Lye~L 573 (940)
|.++|
T Consensus 453 l~~wL 457 (457)
T TIGR03491 453 VADWL 457 (457)
T ss_pred HHHhC
Confidence 98875
No 105
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=42.15 E-value=2.4e+02 Score=33.48 Aligned_cols=104 Identities=10% Similarity=0.038 Sum_probs=59.3
Q ss_pred ceEEEEeccCCCCcccCccccCcceeEEEeec-------------CCC-cccCCCceEEEEe-CC-------CCChhhhH
Q 002293 368 LVHACDTEVAKIDVKQETPVDHGEVICFSIYS-------------GPE-ADFGNGKSCIWVD-LL-------DGGGRDLL 425 (940)
Q Consensus 368 ~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~-------------~~g-Iq~g~~~~~~yID-~~-------~~~~e~~l 425 (940)
.++-.|-||.|.++..+++..+ .|+-... .+. =-++.++ +++|- .. ++++.+..
T Consensus 10 tF~~yDYETfG~~Pa~DRPaQF---AgiRTD~~~NiIgeP~~fyCkpsdDyLP~P~-a~LITGITPQ~~~~~G~~E~~F~ 85 (475)
T COG2925 10 TFLFYDYETFGVHPALDRPAQF---AGIRTDIEFNIIGEPIVFYCKPADDYLPQPG-AVLITGITPQEAREKGINEAAFA 85 (475)
T ss_pred cEEEEehhhcCCCcccccchhh---heeeccccccccCCCeEEEecCccccCCCCC-ceeeecCCHHHHHhcCCChHHHH
Confidence 4788999999999998877542 2322211 110 0011212 11111 10 12344566
Q ss_pred hhhhhhhcCCCceEEEec-cHHHHHHHH----HcCCC-----CCC-----ccccHHHHHHhcCCC
Q 002293 426 NEFAPFFEDPSIKKVWHN-YSFDNHVLE----NYGLK-----VSG-----FHADTMHMARLWDSS 475 (940)
Q Consensus 426 ~~Lk~~Led~~i~KVgHN-aKfDL~~L~----r~GI~-----l~n-----~vfDTmIAA~LLdp~ 475 (940)
..+...|..|....+|+| +.||=++-+ +.=++ .++ -++|.+-|+|-|.|+
T Consensus 86 ~~I~~~ls~P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPe 150 (475)
T COG2925 86 ARIHAELTQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPE 150 (475)
T ss_pred HHHHHHhCCCCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcc
Confidence 677778889998999998 789887753 22222 111 156777777777774
No 106
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=38.26 E-value=2.7e+02 Score=30.71 Aligned_cols=55 Identities=16% Similarity=0.122 Sum_probs=34.9
Q ss_pred cCCCceEEEeccHHHHHHHHH--cCCCCC--------------CccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 433 EDPSIKKVWHNYSFDNHVLEN--YGLKVS--------------GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 433 ed~~i~KVgHNaKfDL~~L~r--~GI~l~--------------n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
-++.+.+|.+...||...|-+ -+-.++ ..++|+..++...+.-.. ..||+.||..
T Consensus 139 ~~~~V~WvTFhs~YDfgYLlK~Lt~~~LP~~~~eF~~~v~~~fp~vYDiK~l~~~c~~~~l---~~GL~~lA~~ 209 (239)
T KOG0304|consen 139 LDENVTWVTFHSGYDFGYLLKILTGKPLPETEEEFFEIVRQLFPFVYDVKYLMKFCEGLSL---KGGLQRLADL 209 (239)
T ss_pred ccCceEEEEeeccchHHHHHHHHcCCCCcchHHHHHHHHHHHcchhhhHHHHHHhhhhhhh---hcCHHHHHHH
Confidence 357889999999999987743 233333 136677777776654111 3577777763
No 107
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=31.78 E-value=57 Score=35.86 Aligned_cols=51 Identities=24% Similarity=0.147 Sum_probs=36.8
Q ss_pred CCCceEEEeccHHHHHHHHH--cCCCCC--------------CccccHHHHHHhcCCCCCCCCCCCHHHHHhc
Q 002293 434 DPSIKKVWHNYSFDNHVLEN--YGLKVS--------------GFHADTMHMARLWDSSRRTEGGYSLEALTGD 490 (940)
Q Consensus 434 d~~i~KVgHNaKfDL~~L~r--~GI~l~--------------n~vfDTmIAA~LLdp~~~~~~s~sLe~La~~ 490 (940)
+..+++|+||+-+|+-.|.+ .| +++ ..++||..++...... ..+|+.|+..
T Consensus 147 ~~~~p~Vghn~~~Dl~~l~~~f~~-~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~~~-----~~~L~~l~~~ 213 (262)
T PF04857_consen 147 SSKKPIVGHNGLYDLMYLYKKFIG-PLPETLEEFKELLRELFPRIYDTKYLAEECPGK-----STSLQELAEE 213 (262)
T ss_dssp CC-SEEEESSTHHHHHHHHHHHTT-S--SSHHHHHHHHHHHSSSEEEHHHHHTSTTTS------SSHHHHHHH
T ss_pred ccCCcEEEeChHhHHHHHHHHhcC-CCCCCHHHHHHHHHHHCcccccHHHHHHhcccc-----ccCHHHHHHH
Confidence 34478999999999988765 35 443 2389999999977632 3699999975
No 108
>PHA02563 DNA polymerase; Provisional
Probab=29.11 E-value=89 Score=39.03 Aligned_cols=67 Identities=18% Similarity=0.262 Sum_probs=39.0
Q ss_pred CceEEEEeccCCCCcccCccccCcceeEEEeecCCCcccCCCceEEEEeCCCCChhhhHhhhhhhhc-----CCCceEEE
Q 002293 367 HLVHACDTEVAKIDVKQETPVDHGEVICFSIYSGPEADFGNGKSCIWVDLLDGGGRDLLNEFAPFFE-----DPSIKKVW 441 (940)
Q Consensus 367 ~~~VAfDTETTGLd~~~d~IvG~g~Ii~LSi~~~~gIq~g~~~~~~yID~~~~~~e~~l~~Lk~~Le-----d~~i~KVg 441 (940)
...+++|+||+..+.-. + -.++.+.++. ....+|+.. ..+.+-.++. .....+.+
T Consensus 12 ~~~~~~DfET~t~~~~~----~---~~~~~~~d~~------~~~s~~~~~-------~~~~f~~~i~~~~~k~~~~~vYf 71 (630)
T PHA02563 12 RKILACDFETTTINKDC----R---RWFWGEIDVE------DFPSYYGGN-------SFDEFLQWIEDTTYKETECIIYF 71 (630)
T ss_pred ceEEEEEEEecccCCcc----e---eeeeeEeccc------eeceeeccc-------cHHHHHHHHhhccccccceEEEE
Confidence 35899999999876421 1 1233333322 012344432 2344455555 33567899
Q ss_pred eccHHHHHHHHH
Q 002293 442 HNYSFDNHVLEN 453 (940)
Q Consensus 442 HNaKfDL~~L~r 453 (940)
||.+||..+|..
T Consensus 72 HN~~FD~~Fil~ 83 (630)
T PHA02563 72 HNLKFDGSFILK 83 (630)
T ss_pred ecCCccHHHHHH
Confidence 999999999754
No 109
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=27.21 E-value=28 Score=40.63 Aligned_cols=140 Identities=17% Similarity=0.081 Sum_probs=0.0
Q ss_pred ccCCCceEEEEeCCCCChhhhHhhhhhhhcCCCceEEEeccHHHHHHHHH-cCCCCCCccccHHHHHHhcCCCC--CCCC
Q 002293 404 DFGNGKSCIWVDLLDGGGRDLLNEFAPFFEDPSIKKVWHNYSFDNHVLEN-YGLKVSGFHADTMHMARLWDSSR--RTEG 480 (940)
Q Consensus 404 q~g~~~~~~yID~~~~~~e~~l~~Lk~~Led~~i~KVgHNaKfDL~~L~r-~GI~l~n~vfDTmIAA~LLdp~~--~~~~ 480 (940)
+++.+.+.+.+|....+.--...-.++.|+...+ +. |++.+...+.. +++.+.+ ++||++|..|+.+.. .
T Consensus 217 ~ia~~n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~L~n-VkDtQia~sLve~~e~gr--- 289 (458)
T KOG2405|consen 217 NIADGNEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSALKN-VKDTQIASSLVEPSEYGR--- 289 (458)
T ss_pred hhcccchhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHHHHHh-hHHHHHHHHHhhhHHhcc---
Q ss_pred CCCHHHHHhccccccc-cchhhhccccCCCCccccccccchhhhhcccccccCCCCCccccccchhHhhHhhHHHHHHHH
Q 002293 481 GYSLEALTGDRKVMSE-DKKAYQKDMSKGNTDEGFMGKISMKDIFGRRKLKKDGSAGKISTIAPVEELQREERELWISYS 559 (940)
Q Consensus 481 s~sLe~La~~y~~~~e-~yLg~~~~l~k~~s~eELvGk~s~kelfGK~k~kkd~s~~~dw~~~PL~~l~~~~~e~~l~YA 559 (940)
.+....+...-..... +|.+.. ....+++.+. +++..+ .|.++|. ++.+..-+
T Consensus 290 r~p~~~lIsft~Lq~~~~y~~~s-----~~~~eev~~~-----l~~dp~---------~w~irp~-------te~~~~~~ 343 (458)
T KOG2405|consen 290 RHPTSILISFTCLQTYIFYIKAS-----GLIFEEVAKI-----LEADPP---------RWVIRPS-------TEIADHLL 343 (458)
T ss_pred cCCccceeeeEeccccceeehhh-----hhhHHHHHHH-----HhcCCC---------cceeccc-------HHHHHHHH
Q ss_pred HHHHHHHHHHHHHHHHH
Q 002293 560 AFDSINTLKLYKSLKKK 576 (940)
Q Consensus 560 A~DA~~tlrLye~L~~~ 576 (940)
++|+..++-.+..+...
T Consensus 344 h~dv~~Ll~~~~~l~a~ 360 (458)
T KOG2405|consen 344 HRDVISLLGIFDTLVAV 360 (458)
T ss_pred HHHHHHHHHHHhhHhhh
No 110
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=21.93 E-value=3e+02 Score=33.66 Aligned_cols=30 Identities=23% Similarity=0.332 Sum_probs=21.8
Q ss_pred hhhhHhhhhhhhcC--CCceEEEecc-HHHHHHH
Q 002293 421 GRDLLNEFAPFFED--PSIKKVWHNY-SFDNHVL 451 (940)
Q Consensus 421 ~e~~l~~Lk~~Led--~~i~KVgHNa-KfDL~~L 451 (940)
+.+.+..+..++.+ |+ .++|||. .||+..|
T Consensus 180 E~eLL~~F~~~i~~~DPD-IItGYNi~nFDlPYL 212 (498)
T PHA02524 180 EVDLLLNYIQLWKANTPD-LVFGWNSEGFDIPYI 212 (498)
T ss_pred HHHHHHHHHHHHHHhCCC-EEEeCCCcccCHHHH
Confidence 34566677777654 66 5799995 6999987
No 111
>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=21.25 E-value=96 Score=34.08 Aligned_cols=30 Identities=17% Similarity=0.131 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHhccCCCceEEEEeccCCCCccc
Q 002293 351 VSAAKKVVWMLTNKYKHLVHACDTEVAKIDVKQ 383 (940)
Q Consensus 351 ~e~L~eli~~L~~a~~~~~VAfDTETTGLd~~~ 383 (940)
.+.+..+.+.|..+ .+||+|+|++|+....
T Consensus 9 ~~~l~~i~~~i~~~---~fvaiD~EftGl~~~~ 38 (262)
T PF04857_consen 9 EEELPEILQAISKA---DFVAIDTEFTGLVSKP 38 (262)
T ss_dssp HHHHHHHHHHHHHS---SEEEEEEEES-S-SSS
T ss_pred HHHHHHHHHHHhhC---CEEEEEeeccccccCC
Confidence 34566777777776 5999999999997643
Done!