Query 009284
Match_columns 538
No_of_seqs 210 out of 1209
Neff 5.6
Searched_HMMs 46136
Date Thu Mar 28 22:41:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009284.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009284hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2207 Predicted 3'-5' exonuc 100.0 2E-43 4.3E-48 379.0 16.2 519 1-530 1-615 (617)
2 cd06146 mut-7_like_exo DEDDy 3 99.9 2.4E-25 5.1E-30 215.4 18.9 174 316-490 1-192 (193)
3 cd06129 RNaseD_like DEDDy 3'-5 99.9 1.1E-23 2.4E-28 197.4 18.8 154 325-491 2-161 (161)
4 cd06141 WRN_exo DEDDy 3'-5' ex 99.9 2.1E-22 4.5E-27 189.2 17.4 160 320-490 2-169 (170)
5 PF01612 DNA_pol_A_exo1: 3'-5' 99.9 4E-22 8.8E-27 185.4 18.0 170 316-494 1-176 (176)
6 PRK10829 ribonuclease D; Provi 99.9 2.6E-22 5.7E-27 211.9 18.4 169 315-497 2-174 (373)
7 cd06148 Egl_like_exo DEDDy 3'- 99.9 3.8E-21 8.3E-26 186.4 14.7 157 328-496 3-180 (197)
8 TIGR01388 rnd ribonuclease D. 99.9 1.1E-20 2.3E-25 199.7 18.6 180 318-520 1-184 (367)
9 COG0349 Rnd Ribonuclease D [Tr 99.8 7E-20 1.5E-24 190.5 16.0 165 320-497 2-170 (361)
10 PRK05755 DNA polymerase I; Pro 99.7 2.5E-16 5.5E-21 183.0 19.3 223 251-495 240-471 (880)
11 cd06142 RNaseD_exo DEDDy 3'-5' 99.7 1.3E-15 2.9E-20 142.7 17.8 158 326-497 3-164 (178)
12 smart00474 35EXOc 3'-5' exonuc 99.6 3.5E-14 7.5E-19 130.9 19.7 165 317-494 2-172 (172)
13 cd06147 Rrp6p_like_exo DEDDy 3 99.6 7.3E-14 1.6E-18 134.3 19.1 171 314-498 3-177 (192)
14 TIGR00593 pola DNA polymerase 99.6 2.9E-13 6.3E-18 157.0 23.3 231 251-496 239-480 (887)
15 cd00007 35EXOc 3'-5' exonuclea 99.5 9.3E-13 2E-17 119.1 15.4 145 337-493 2-155 (155)
16 cd09018 DEDDy_polA_RNaseD_like 99.5 1.1E-12 2.4E-17 119.2 14.7 142 337-491 1-150 (150)
17 cd06140 DNA_polA_I_Bacillus_li 99.3 2.5E-11 5.3E-16 114.5 14.2 149 335-496 3-159 (178)
18 COG0749 PolA DNA polymerase I 99.3 9.1E-12 2E-16 137.4 12.8 167 316-496 3-183 (593)
19 KOG2206 Exosome 3'-5' exoribon 99.3 9.8E-12 2.1E-16 134.8 9.0 171 314-497 191-364 (687)
20 cd06139 DNA_polA_I_Ecoli_like_ 99.2 5.3E-10 1.2E-14 106.0 16.5 154 333-495 3-172 (193)
21 PRK14975 bifunctional 3'-5' ex 98.9 4.4E-09 9.5E-14 117.2 11.0 139 315-496 2-147 (553)
22 cd06128 DNA_polA_exo DEDDy 3'- 98.5 1.9E-06 4E-11 79.4 13.1 120 360-490 23-150 (151)
23 KOG4373 Predicted 3'-5' exonuc 98.0 3.9E-05 8.4E-10 79.5 10.1 141 336-486 128-281 (319)
24 cd06137 DEDDh_RNase DEDDh 3'-5 96.2 0.049 1.1E-06 51.3 11.0 78 386-486 75-160 (161)
25 cd06149 ISG20 DEDDh 3'-5' exon 96.2 0.03 6.5E-07 52.7 9.5 82 384-487 67-157 (157)
26 cd06125 DnaQ_like_exo DnaQ-lik 96.1 0.028 6E-07 48.6 7.7 58 338-413 1-61 (96)
27 PRK07740 hypothetical protein; 95.3 0.44 9.5E-06 48.2 14.1 91 384-497 131-230 (244)
28 cd06144 REX4_like DEDDh 3'-5' 95.2 0.097 2.1E-06 48.8 8.6 80 384-487 67-152 (152)
29 KOG2249 3'-5' exonuclease [Rep 95.1 0.29 6.2E-06 50.2 12.0 79 387-489 177-262 (280)
30 PRK06063 DNA polymerase III su 94.6 0.26 5.7E-06 51.7 10.7 93 383-497 83-183 (313)
31 PRK07883 hypothetical protein; 94.6 0.25 5.4E-06 55.8 11.2 93 384-498 85-187 (557)
32 PRK07942 DNA polymerase III su 94.4 0.45 9.8E-06 47.7 11.4 79 397-494 94-181 (232)
33 PRK06310 DNA polymerase III su 94.3 0.8 1.7E-05 46.5 13.2 91 384-493 77-174 (250)
34 cd06131 DNA_pol_III_epsilon_Ec 94.1 1.9 4.1E-05 40.2 14.4 89 384-489 71-166 (167)
35 PRK08517 DNA polymerase III su 93.9 0.77 1.7E-05 46.9 12.1 90 384-495 137-233 (257)
36 PRK05711 DNA polymerase III su 93.9 1.2 2.7E-05 45.0 13.4 94 384-494 76-177 (240)
37 TIGR00573 dnaq exonuclease, DN 93.8 1.5 3.3E-05 43.2 13.7 97 384-497 77-181 (217)
38 TIGR01406 dnaQ_proteo DNA poly 93.7 1.8 3.9E-05 43.3 14.2 95 384-495 72-174 (225)
39 TIGR01405 polC_Gram_pos DNA po 93.4 1 2.3E-05 55.2 14.1 94 383-498 259-360 (1213)
40 smart00479 EXOIII exonuclease 93.3 1.8 3.8E-05 39.8 12.5 90 384-493 70-167 (169)
41 cd06130 DNA_pol_III_epsilon_li 93.3 1.6 3.4E-05 39.9 12.1 81 383-486 66-154 (156)
42 cd05160 DEDDy_DNA_polB_exo DED 93.2 1.4 3E-05 42.5 12.0 100 384-486 66-198 (199)
43 cd06143 PAN2_exo DEDDh 3'-5' e 93.1 0.15 3.2E-06 49.4 5.1 79 386-487 93-174 (174)
44 cd06145 REX1_like DEDDh 3'-5' 93.1 0.29 6.2E-06 45.7 6.9 80 384-486 65-149 (150)
45 PRK07246 bifunctional ATP-depe 92.7 1.8 3.9E-05 51.2 14.4 89 384-495 76-172 (820)
46 PRK09145 DNA polymerase III su 92.5 1.6 3.5E-05 42.5 11.6 84 384-490 101-198 (202)
47 PRK09146 DNA polymerase III su 92.4 1.4 3E-05 44.6 11.2 87 384-493 119-227 (239)
48 PRK06807 DNA polymerase III su 92.2 1.7 3.6E-05 45.8 12.0 87 384-493 78-172 (313)
49 cd06127 DEDDh DEDDh 3'-5' exon 92.1 1.2 2.7E-05 39.7 9.6 83 384-486 69-158 (159)
50 PRK06309 DNA polymerase III su 92.0 3.4 7.4E-05 41.3 13.4 89 384-493 69-166 (232)
51 PRK05168 ribonuclease T; Provi 91.8 3.7 8.1E-05 40.5 13.3 87 396-497 114-205 (211)
52 TIGR01407 dinG_rel DnaQ family 91.7 2.5 5.4E-05 50.2 14.1 90 384-495 70-167 (850)
53 PRK08074 bifunctional ATP-depe 90.0 4.6 0.0001 48.5 14.2 90 384-495 74-171 (928)
54 cd05780 DNA_polB_Kod1_like_exo 89.4 4.3 9.3E-05 39.4 11.1 151 336-488 4-194 (195)
55 cd06136 TREX1_2 DEDDh 3'-5' ex 88.8 3.2 6.9E-05 39.7 9.6 86 384-487 84-175 (177)
56 PRK05601 DNA polymerase III su 87.3 16 0.00035 39.6 14.6 100 383-489 114-245 (377)
57 cd05781 DNA_polB_B3_exo DEDDy 87.2 11 0.00024 36.5 12.4 148 336-488 4-187 (188)
58 PRK07983 exodeoxyribonuclease 86.9 19 0.00041 36.0 14.1 76 397-493 75-154 (219)
59 PRK07247 DNA polymerase III su 85.1 19 0.00041 35.3 12.9 89 384-493 74-169 (195)
60 TIGR01298 RNaseT ribonuclease 85.1 3.3 7.2E-05 40.5 7.6 86 396-496 105-195 (200)
61 cd06134 RNaseT DEDDh 3'-5' exo 83.8 5.1 0.00011 38.7 8.2 80 397-492 103-188 (189)
62 PRK06195 DNA polymerase III su 83.5 3.6 7.8E-05 43.0 7.5 89 384-495 70-166 (309)
63 COG2176 PolC DNA polymerase II 83.3 2.3 4.9E-05 51.6 6.4 141 331-498 417-591 (1444)
64 PRK11779 sbcB exonuclease I; P 82.6 16 0.00035 40.8 12.5 92 384-492 81-197 (476)
65 PRK09182 DNA polymerase III su 81.1 26 0.00057 36.6 12.8 83 386-491 112-199 (294)
66 cd05783 DNA_polB_B1_exo DEDDy 80.7 61 0.0013 31.9 14.7 148 335-487 5-202 (204)
67 cd05779 DNA_polB_epsilon_exo D 79.5 28 0.00061 34.4 11.8 149 336-486 3-203 (204)
68 PRK00448 polC DNA polymerase I 78.7 15 0.00033 46.2 11.7 92 384-497 489-588 (1437)
69 PF13482 RNase_H_2: RNase_H su 78.5 3.5 7.6E-05 38.1 4.9 142 338-489 1-163 (164)
70 cd05785 DNA_polB_like2_exo Unc 78.3 9 0.0002 37.8 7.9 145 335-486 9-206 (207)
71 KOG3657 Mitochondrial DNA poly 77.2 3.6 7.9E-05 48.2 5.3 144 336-494 184-384 (1075)
72 KOG2248 3'-5' exonuclease [Rep 75.1 5.9 0.00013 43.0 6.0 86 384-492 283-374 (380)
73 cd05784 DNA_polB_II_exo DEDDy 74.1 36 0.00079 33.2 10.8 102 384-487 54-193 (193)
74 COG0847 DnaQ DNA polymerase II 66.7 1.3E+02 0.0029 29.6 13.2 96 384-495 84-185 (243)
75 cd06133 ERI-1_3'hExo_like DEDD 62.7 1.2E+02 0.0026 28.0 11.4 90 384-489 78-175 (176)
76 KOG3616 Selective LIM binding 61.8 37 0.00081 39.9 8.9 49 239-287 1299-1353(1636)
77 cd05782 DNA_polB_like1_exo Unc 60.2 1.4E+02 0.003 29.5 11.8 103 383-487 80-207 (208)
78 PF07899 Frigida: Frigida-like 58.6 1.8E+02 0.004 30.4 12.9 157 59-219 39-217 (290)
79 PF01381 HTH_3: Helix-turn-hel 56.1 15 0.00033 27.6 3.4 46 113-158 9-54 (55)
80 PF12844 HTH_19: Helix-turn-he 55.4 17 0.00038 28.3 3.7 54 104-159 5-58 (64)
81 PF10108 DNA_pol_B_exo2: Predi 52.5 1.8E+02 0.0039 29.1 11.1 107 381-490 37-170 (209)
82 PRK14976 5'-3' exonuclease; Pr 51.3 6.7 0.00015 40.7 1.0 38 251-288 244-281 (281)
83 PRK07748 sporulation inhibitor 45.9 1.5E+02 0.0032 28.9 9.4 91 384-493 82-180 (207)
84 PRK05359 oligoribonuclease; Pr 44.7 2.3E+02 0.005 27.3 10.3 91 384-494 82-176 (181)
85 KOG2405 Predicted 3'-5' exonuc 43.2 39 0.00084 36.8 5.1 127 360-497 216-365 (458)
86 PF00392 GntR: Bacterial regul 40.4 42 0.0009 26.4 3.8 47 122-168 2-50 (64)
87 PF09281 Taq-exonuc: Taq polym 38.4 1.3E+02 0.0029 28.1 7.0 69 401-493 67-138 (138)
88 cd06138 ExoI_N N-terminal DEDD 37.0 75 0.0016 30.3 5.7 86 384-486 72-182 (183)
89 PF03997 VPS28: VPS28 protein; 37.0 1.5E+02 0.0033 29.2 7.8 102 178-285 11-128 (188)
90 KOG2405 Predicted 3'-5' exonuc 36.5 1.9 4.1E-05 46.4 -5.8 71 355-433 74-144 (458)
91 cd05777 DNA_polB_delta_exo DED 34.1 40 0.00087 33.5 3.4 64 427-490 153-224 (230)
92 PF04858 TH1: TH1 protein; In 33.4 36 0.00078 39.1 3.2 99 38-154 445-557 (584)
93 PHA01976 helix-turn-helix prot 33.3 60 0.0013 25.4 3.7 54 104-159 8-61 (67)
94 TIGR03070 couple_hipB transcri 33.2 77 0.0017 23.5 4.1 52 103-156 7-58 (58)
95 TIGR02508 type_III_yscG type I 33.1 1.6E+02 0.0034 26.7 6.4 43 185-238 27-70 (115)
96 PRK00118 putative DNA-binding 31.3 2.3E+02 0.0049 25.3 7.3 34 129-162 9-42 (104)
97 KOG4634 Mitochondrial F1F0-ATP 30.8 1.4E+02 0.0029 26.6 5.5 60 98-159 8-83 (105)
98 PLN03218 maturation of RBCL 1; 30.6 1.1E+03 0.025 29.2 18.3 99 187-285 588-710 (1060)
99 KOG0985 Vesicle coat protein c 30.3 1.2E+03 0.026 29.3 14.7 177 96-284 507-749 (1666)
100 PF12960 DUF3849: Protein of u 29.6 74 0.0016 29.7 4.0 62 175-236 27-94 (133)
101 PF04840 Vps16_C: Vps16, C-ter 26.0 4.5E+02 0.0097 27.8 9.7 76 209-284 179-262 (319)
102 cd05778 DNA_polB_zeta_exo inac 25.8 60 0.0013 32.5 3.0 59 428-486 163-230 (231)
103 PF05402 PqqD: Coenzyme PQQ sy 25.7 2.6E+02 0.0057 21.8 6.2 48 126-192 18-65 (68)
104 PRK06424 transcription factor; 25.3 1.1E+02 0.0023 28.9 4.4 55 103-159 89-143 (144)
105 PF07399 DUF1504: Protein of u 24.8 33 0.00071 37.7 1.0 90 63-155 121-215 (438)
106 PRK08359 transcription factor; 24.5 92 0.002 30.4 3.9 57 102-160 89-145 (176)
107 PF08154 NLE: NLE (NUC135) dom 23.1 93 0.002 25.1 3.1 27 59-85 29-55 (65)
108 PF14559 TPR_19: Tetratricopep 23.0 2.3E+02 0.0049 21.5 5.3 34 252-285 18-51 (68)
109 PF08631 SPO22: Meiosis protei 22.9 1.9E+02 0.004 29.6 6.0 58 35-92 51-114 (278)
110 KOG1798 DNA polymerase epsilon 22.7 6.4E+02 0.014 32.7 10.9 151 335-489 246-450 (2173)
111 cd02908 Macro_Appr_pase_like M 22.2 71 0.0015 30.1 2.6 8 77-84 67-74 (165)
112 COG5123 TOA2 Transcription ini 21.8 44 0.00095 29.7 1.0 28 130-157 17-47 (113)
113 cd05776 DNA_polB_alpha_exo ina 21.3 1E+02 0.0022 30.9 3.6 63 427-489 157-226 (234)
114 TIGR02684 dnstrm_HI1420 probab 21.1 1.7E+02 0.0037 25.2 4.5 60 97-157 28-87 (89)
115 TIGR02607 antidote_HigA addict 20.1 1.2E+02 0.0026 24.3 3.2 47 113-159 18-64 (78)
No 1
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=2e-43 Score=378.97 Aligned_cols=519 Identities=27% Similarity=0.360 Sum_probs=411.1
Q ss_pred CChhhhhhhhhcccCCccccceeeeeecccCCCcchHHHHHHHHhhhhcccchhhhhHHHHHHHHHHHhhCCCCCCCcee
Q 009284 1 MGLEERVAESCINGHKADCAWTVSVHTFSDITNISPVVFLYLLKECYIHGTCKATRKFRALQQQVSQALCNSPEPGPATF 80 (538)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (538)
||.+....++++...+.+++.+.|.|.+|+.++++++||.+..|+||-+++-+.+.+|..++.+.|.+..+.|+++|+++
T Consensus 1 M~~~s~~~~l~~a~~e~~e~N~~~~~~~s~~k~~~~i~~~~~~k~~~~~~i~ak~~eff~~~~~s~~~~~g~~~~~~lll 80 (617)
T KOG2207|consen 1 MGNTSALQDLHNAEYERKEANLKALLVKSTDKYLKDIVFGSFSKKFDESTIIAKDAEFFPLDYESHIYANGFPPVNPLLL 80 (617)
T ss_pred CCCchhhhhccchhhhhhhhhHHHHHhhhhhhHHHHhhhhhhhcccchhhHHHhhHHHHHHHHHHHHHhcCCCCCChHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeeeeccccc-ccccchhHHHHHHHHhhhcc---cCCccchhHHHHHHHH-HHHHHhcCCCCChhHHHHHHH-HHhcc
Q 009284 81 IVRCLYVLPIFG-VYSEGFSHLIISALRRHQKT---TVNSADSTQAKEIAAY-LFLDITGGFVDHDEKLMVKIL-EAFDV 154 (538)
Q Consensus 81 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~r~~~~l~-e~f~~ 154 (538)
|+.||+-+|-+| +++|++||.+++++++++|. .+..+|...+..+|++ .++=..+++.-+++.+-+-.+ .|+|+
T Consensus 81 ~l~~l~~lPd~~~v~g~~lS~~vl~~~~~~~kd~~~~~~~~d~~lt~~~~~~~~~v~t~g~~~ll~e~~~i~~~~~~~Di 160 (617)
T KOG2207|consen 81 ILIMLSQLPDRSKVFGESLSHWVLEDVGELLKDGSRMTESEDVALTGKIAFKADFVCTSGTLTLLGEIFKIQKLKQTLDI 160 (617)
T ss_pred HHHHHHhCccccCcchhhhHHHHHHHHHHHhccCcccccccchHhhhhhhhccceeEecchHHHHHHHhcchhhhhhHhH
Confidence 999999999999 99999999999999999998 7889999888888887 777777888888899999888 99999
Q ss_pred ccccHHHHHhhhhhccccchhHHHHHH-----HHHHHHHHhhchhhHHHHHHHhhh-ccccchHHHHHHHhccchHHHHH
Q 009284 155 RLTDIEKAITQLKAQNEHRFDTAKTVI-----EQYIFAMIDSQSYMTAVSLLEHFS-IRQSGESFLLKMIQNKEFKAAEK 228 (538)
Q Consensus 155 ~~~~~~~a~~~~~~~~~~~~~~~~~~~-----~~yi~~~~~~~~~~~~~~li~~f~-~~~~~~~~l~~~~~~~~~~~a~~ 228 (538)
.+.-++.++.....+--...+.-..++ ++|+.-+|-+++...|..+++|+. +|+...+|+++|+.- .+...++
T Consensus 161 ~l~~i~e~lq~~~f~e~a~~~ik~~l~~~~~~e~~~ldlIls~k~q~a~~ll~~~~~~q~p~v~fld~~v~~-~~~v~e~ 239 (617)
T KOG2207|consen 161 TLCKIDEYLQNQRFGEAAPKAIKSLLLSDNAFEQLMLDLILSKKLQIADELLRHLTELQKPYVEFLDQMVLD-NFIVDER 239 (617)
T ss_pred hcchhHHHHHhHHHHHHHHHHHHhhhhhhhhHHHHhccHhhccchhHHHHHHhhhhhhhhhHHHHHHHHHHH-HHHHHHH
Confidence 999999998666655433333444444 899999999999999999999999 888899999999977 8899999
Q ss_pred HHHhcCc-----hHH------------------------------------------HHHHhhhhc-hHHHHHHhhcch-
Q 009284 229 WATFMGK-----PIL------------------------------------------LKRLAEKAC-WDIAEAKTKGDK- 259 (538)
Q Consensus 229 ~~~~~~~-----~~~------------------------------------------~~~l~~k~~-wd~a~~~~~~D~- 259 (538)
|+.+++. +.+ -.+++.|++ |++++.....|.
T Consensus 240 ~~~~~e~~~~~~~tl~~~v~~i~~rn~~~~~f~~~~~~n~v~~~~~kal~~~~~~~e~~~~~~~~f~~~~~~~~t~~~d~ 319 (617)
T KOG2207|consen 240 CAHLLERTINLPKTLTILVQEIINRNQKKYTFSDEYAKNYVQNKNCKALHYIRSEREKGQMADKGFVQHVVETKTKPDDE 319 (617)
T ss_pred HHHHHhhccCCCchhhhhHHHHHhccchhhhhhhhhhhhHhhcccHHHHHHHHHHhhhhhhHHHhhchhheeecccccch
Confidence 9999998 211 456777888 999999998887
Q ss_pred hHHHHHHHHh--hccCCHHHH---------HHHHHHcCCccccccc-----CcccCCcccccccccccCCCCeEEEcCHH
Q 009284 260 RLLEYLVYLA--MEAGYSEKV---------DELCERYSLEGFLKTR-----EPEAGFVHSRFLHLKELVVEDIIWVDEVD 323 (538)
Q Consensus 260 ~l~~~lv~L~--~~~~d~~~L---------~~l~~ryef~s~l~el-----~~~~~~~~~~~~~l~~~~~~~y~~Idt~e 323 (538)
++..||.+.. .++...+.. .+|.+++.-++.-+++ ....+......+.......+.+++|+++.
T Consensus 320 ~~lkyLw~~~~~iEai~~~~~~~i~~~d~~~el~~~~s~~~~~k~~~~~~~~~~~pl~~~~~~~~~~~~~~~i~~V~~e~ 399 (617)
T KOG2207|consen 320 NLLKYLWSFGEHIEAIYLATYDNIDPKDDAKELEKRTSRRGAGKTLFNQRMTTNVPLVCEDLFLFEPPWVESIGMVGNEK 399 (617)
T ss_pred hHHHHHHHHHHhhhhhhhhhhhcCCCchhHHHHhchhhhcccChhhhhcccccccCccchhhhccCCCcccceeeeCCHH
Confidence 8888888887 332222222 1444444333222221 00001111112222224456789999999
Q ss_pred HHHHHH-HHhhcC-CeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchh-HHHHHHHhhcCCCceEE
Q 009284 324 GLHKAI-CHIEGC-KVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDV-LDSCLTRILQSPGILKL 400 (538)
Q Consensus 324 ~L~~ll-e~L~~a-~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~~~a~~IdL~~l~~~~p~~-ll~~Lk~lLed~~i~KV 400 (538)
++..++ +.+... -.||+|.||.+. .+...++++++|++.++.+|++|...+... +.+ +...+..||+++.+.||
T Consensus 400 El~~l~l~~l~~e~~yVGiDsEwkps--~~v~dsk~~IlQif~~~~v~Lidc~~l~~~-~se~w~~~~s~if~s~~i~kv 476 (617)
T KOG2207|consen 400 ELRDLLLESLSEELRYVGIDSEWKPS--KKVSDSKLAILQIFFKDCVYLIDCVKLENL-ASEIWHLLLSQIFESKSILKV 476 (617)
T ss_pred HHHHHHHHHhhhcCEEEEEccccCcc--cCCChhHHHHHHHHhcCeEEEeehHHhhhc-hHHHHHHHHHHHccCCceeee
Confidence 988876 455555 789999999986 223467999999999999999999887543 333 55678889999999999
Q ss_pred EeehHHhHHHHHHHhCCc-ccc--ccchhHh-hHHHh------------hcCCCCCHHHHHHHHhCCCCCcCcccccCCC
Q 009284 401 GYNFQCDIKQLAHSYGEL-ECF--KHYEMLL-DIQNV------------FKEPKGGLSGLAEKILGAGLNKTRRNSNWEQ 464 (538)
Q Consensus 401 GhnlK~Dl~vLa~~~Gil-~~~--~~~~~if-DtmLA------------l~~~s~gLd~LAer~LG~~L~K~e~~S~W~~ 464 (538)
|+++..|++++.++.|-+ .++ .....++ ++.++ +++...+|++|....||..++|++++|+|..
T Consensus 477 Gf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~Lt~~llg~~lnKteqcsnWqc 556 (617)
T KOG2207|consen 477 GFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADLTDCLLGKKLNKTEQCSNWQC 556 (617)
T ss_pred ecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhhhhhhHHHhhhhcccccccchhhc
Confidence 999999999998533310 000 0011111 22222 1245789999999999999999999999999
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCccccchHHHHHhhcCCcccccCCCCcccc
Q 009284 465 RPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTDVSEGHDKIEWKSYIVSHMDNPKKSKKRPTIKKE 530 (538)
Q Consensus 465 rpLt~~Q~~YAAeDA~vlL~L~~~L~~rLee~~~~~~~~~~~w~~~~~~~~~~~~k~~~~~~~~~~ 530 (538)
|||+.+|+-|||.||.++..++..+....+. .+ ..+|..|+ ||+-.++|+|-..++.|.
T Consensus 557 rpLr~nQi~yaalDa~~~~~ifkkv~~vv~~-~~--~~ek~i~e----s~~~~~~~~~~~~s~~~~ 615 (617)
T KOG2207|consen 557 RPLRRNQIYYAALDAVVLVEIFKKVCSVVEH-DA--DIEKFICE----SHLGRPKKKKEHCSVWNR 615 (617)
T ss_pred CCchhhHHHHHHhcchhhHHHHHHHHhhcch-hh--HHHHHHHH----HhcCCccccccccccccc
Confidence 9999999999999999999999999998885 32 45566555 577778888777776664
No 2
>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=99.93 E-value=2.4e-25 Score=215.39 Aligned_cols=174 Identities=40% Similarity=0.734 Sum_probs=146.6
Q ss_pred eEEEcCHHHHHHHHHH--hhcCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchhHHHHHHHhhc
Q 009284 316 IIWVDEVDGLHKAICH--IEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQ 393 (538)
Q Consensus 316 y~~Idt~e~L~~lle~--L~~a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~~~a~~IdL~~l~~~~p~~ll~~Lk~lLe 393 (538)
|++|++++++.++++. +...+++|||+||.+.+..+ ...+++++|+|+++.+|+||+...+....+.+...|+++|+
T Consensus 1 ~~~i~~~~el~~~~~~~~l~~~~vig~D~Ew~~~~~~~-~~~~v~LiQiat~~~~~lid~~~~~~~~~~~~~~~L~~ll~ 79 (193)
T cd06146 1 IHIVDSEEELEALLLALSLEAGRVVGIDSEWKPSFLGD-SDPRVAILQLATEDEVFLLDLLALENLESEDWDRLLKRLFE 79 (193)
T ss_pred CeEecCHHHHHHHHHHHhhccCCEEEEECccCCCccCC-CCCCceEEEEecCCCEEEEEchhccccchHHHHHHHHHHhC
Confidence 4689999999999999 88999999999999874321 24689999999999999999986542222345668999999
Q ss_pred CCCceEEEeehHHhHHHHHHHhCCccc-cccchhHhhHHHhhc---------------CCCCCHHHHHHHHhCCCCCcCc
Q 009284 394 SPGILKLGYNFQCDIKQLAHSYGELEC-FKHYEMLLDIQNVFK---------------EPKGGLSGLAEKILGAGLNKTR 457 (538)
Q Consensus 394 d~~i~KVGhnlK~Dl~vLa~~~Gil~~-~~~~~~ifDtmLAl~---------------~~s~gLd~LAer~LG~~L~K~e 457 (538)
|+++.||||+++.|+..|.+.+|+..+ +....+++||+.+.. ..++||..|++++||.+++|..
T Consensus 80 d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~~l~K~~ 159 (193)
T cd06146 80 DPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLDKSE 159 (193)
T ss_pred CCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCCCcCccc
Confidence 999999999999999999988887321 001367899997621 1468999999999999999999
Q ss_pred ccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009284 458 RNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVR 490 (538)
Q Consensus 458 ~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~ 490 (538)
++|||++|||+++|+.|||.||+++++||+.|.
T Consensus 160 q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 160 QCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred ccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999985
No 3
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=99.92 E-value=1.1e-23 Score=197.45 Aligned_cols=154 Identities=28% Similarity=0.460 Sum_probs=133.1
Q ss_pred HHHHHHHhh-cCCeEEEEeeeecCCccCCcCCceeEEEEEeC-CeEEEEEcCcccCCCchhHHHHHHHhhcCCCceEEEe
Q 009284 325 LHKAICHIE-GCKVVGIDCEWKPNYVKGCKMNKVSIMQIASD-EMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGY 402 (538)
Q Consensus 325 L~~lle~L~-~a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~-~~a~~IdL~~l~~~~p~~ll~~Lk~lLed~~i~KVGh 402 (538)
++++++.+. ..+++|||+||.+.+. ..++++++|++++ +.+|+||+...+. . ...|+++|+|+++.||||
T Consensus 2 l~~~~~~l~~~~~~ig~D~E~~~~~~---~~~~~~liQl~~~~~~~~l~d~~~~~~-~----~~~L~~lL~d~~i~Kvg~ 73 (161)
T cd06129 2 LSSLCEDLSMDGDVIAFDMEWPPGRR---YYGEVALIQLCVSEEKCYLFDPLSLSV-D----WQGLKMLLENPSIVKALH 73 (161)
T ss_pred HHHHHHHHhcCCCEEEEECCccCCCC---CCCceEEEEEEECCCCEEEEecccCcc-C----HHHHHHHhCCCCEEEEEe
Confidence 567788888 9999999999998742 3468999999998 9999999986532 2 346899999999999999
Q ss_pred ehHHhHHHHHHHhCCccccccchhHhhHHHhh---c-CCCCCHHHHHHHHhCCCCCcCcccccCCCCCCCHHHHHHHHHH
Q 009284 403 NFQCDIKQLAHSYGELECFKHYEMLLDIQNVF---K-EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALD 478 (538)
Q Consensus 403 nlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLAl---~-~~s~gLd~LAer~LG~~L~K~e~~S~W~~rpLt~~Q~~YAAeD 478 (538)
|+|.|++.|.+.+|+.. .+++|++++. + ..++||+.+++++||.+++|..+.|+|..|||+++|+.|||.|
T Consensus 74 ~~k~D~~~L~~~~gi~~-----~~~~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~K~~~~s~W~~rpLt~~qi~YAa~D 148 (161)
T cd06129 74 GIEGDLWKLLRDFGEKL-----QRLFDTTIAANLKGLPERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAAD 148 (161)
T ss_pred ccHHHHHHHHHHcCCCc-----ccHhHHHHHHHHhCCCCCchHHHHHHHHhCCCCCccceeccCCCCCCCHHHHHHHHHH
Confidence 99999999987688732 4569999993 3 3367999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHh
Q 009284 479 AVVLLQIFHHVRS 491 (538)
Q Consensus 479 A~vlL~L~~~L~~ 491 (538)
|++++.||+.|++
T Consensus 149 a~~l~~l~~~l~~ 161 (161)
T cd06129 149 VYALLIIYTKLRN 161 (161)
T ss_pred HHHHHHHHHHHhC
Confidence 9999999999863
No 4
>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=99.89 E-value=2.1e-22 Score=189.20 Aligned_cols=160 Identities=34% Similarity=0.599 Sum_probs=136.1
Q ss_pred cCHHHHHHHHHHhh-cCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchhHHHHHHHhhcCCCce
Q 009284 320 DEVDGLHKAICHIE-GCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGIL 398 (538)
Q Consensus 320 dt~e~L~~lle~L~-~a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~~~a~~IdL~~l~~~~p~~ll~~Lk~lLed~~i~ 398 (538)
+++.++..+++.+. ...++|||+||.+.... +...+++++|+|+++.+|+||+.+.. . +...|+++|+++++.
T Consensus 2 ~~~~~~~~~~~~~~~~~~~ig~D~E~~~~~~~-~~~~~~~liQl~~~~~~~l~~~~~~~-~----~~~~l~~ll~~~~i~ 75 (170)
T cd06141 2 DSAQDAEEAVKELLGKEKVVGFDTEWRPSFRK-GKRNKVALLQLATESRCLLFQLAHMD-K----LPPSLKQLLEDPSIL 75 (170)
T ss_pred CCHHHHHHHHHHHhcCCCEEEEeCccCCccCC-CCCCCceEEEEecCCcEEEEEhhhhh-c----ccHHHHHHhcCCCee
Confidence 46678899999998 99999999999987421 13468999999999999999998642 2 234689999999999
Q ss_pred EEEeehHHhHHHHHHHhCCccccccchhHhhHHHhh---c-C-CCCCHHHHHHHHhCCCCC--cCcccccCCCCCCCHHH
Q 009284 399 KLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF---K-E-PKGGLSGLAEKILGAGLN--KTRRNSNWEQRPLSQNQ 471 (538)
Q Consensus 399 KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLAl---~-~-~s~gLd~LAer~LG~~L~--K~e~~S~W~~rpLt~~Q 471 (538)
|+|||+|.|++.|.+.+|+.. .+++|++++. + . .+.||+.|+++++|.++. |..+.|+|..|||+++|
T Consensus 76 kv~~~~k~D~~~L~~~~g~~~-----~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt~~q 150 (170)
T cd06141 76 KVGVGIKGDARKLARDFGIEV-----RGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQ 150 (170)
T ss_pred EEEeeeHHHHHHHHhHcCCCC-----CCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCCCCCCHHH
Confidence 999999999999986689843 4569999993 3 2 347999999999999998 77789999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 009284 472 LEYAALDAVVLLQIFHHVR 490 (538)
Q Consensus 472 ~~YAAeDA~vlL~L~~~L~ 490 (538)
++|||.||++++.||+.|.
T Consensus 151 i~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 151 ILYAATDAYASLELYRKLL 169 (170)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999885
No 5
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=99.89 E-value=4e-22 Score=185.41 Aligned_cols=170 Identities=31% Similarity=0.461 Sum_probs=141.7
Q ss_pred eEEEcCHHHHHHHHHHhhcCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchhHHHHHHHhhcCC
Q 009284 316 IIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSP 395 (538)
Q Consensus 316 y~~Idt~e~L~~lle~L~~a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~~~a~~IdL~~l~~~~p~~ll~~Lk~lLed~ 395 (538)
|++|++.+++.++++.+...+.+|||+||.+..... ....++++|+++.+.+|+++....... .+...|+++|+++
T Consensus 1 y~~v~~~~~l~~~~~~l~~~~~~a~D~E~~~~~~~~-~~~~~~~iq~~~~~~~~i~~~~~~~~~---~~~~~l~~ll~~~ 76 (176)
T PF01612_consen 1 YQIVDTEEELEEAIKKLKNAKVLAFDTETTGLDPYS-YNPKIALIQLATGEGCYIIDPIDLGDN---WILDALKELLEDP 76 (176)
T ss_dssp SEEEHSHHHHHHHHHHHTTTSEEEEEEEEETSTSTT-SSEEEEEEEEEESCEEEEECGTTSTTT---THHHHHHHHHTTT
T ss_pred CEecCCHHHHHHHHHHHcCCCeEEEEEEECCCCccc-cCCeEEEEEEecCCCceeeeecccccc---chHHHHHHHHhCC
Confidence 678999999999999999999999999999874311 256788899999888888776543211 1467899999999
Q ss_pred CceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHhh---c-CCCCCHHHHHHHHhC-CCCCcCcccccCC-CCCCCH
Q 009284 396 GILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF---K-EPKGGLSGLAEKILG-AGLNKTRRNSNWE-QRPLSQ 469 (538)
Q Consensus 396 ~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLAl---~-~~s~gLd~LAer~LG-~~L~K~e~~S~W~-~rpLt~ 469 (538)
++.|||||+++|++.|.+.+|+.. .+++|+|++. + ..++||++|+.+++| ...++.++.++|. .+|+++
T Consensus 77 ~i~kv~~n~~~D~~~L~~~~~i~~-----~~~~D~~l~~~~l~~~~~~~L~~L~~~~l~~~~~~~~~~~~~~~~~~~l~~ 151 (176)
T PF01612_consen 77 NIIKVGHNAKFDLKWLYRSFGIDL-----KNVFDTMLAAYLLDPTRSYSLKDLAEEYLGNIDLDKKEQMSDWRKARPLSE 151 (176)
T ss_dssp TSEEEESSHHHHHHHHHHHHTS-------SSEEEHHHHHHHTTTSTTSSHHHHHHHHHSEEE-GHCCTTSSTTTSSS-HH
T ss_pred CccEEEEEEechHHHHHHHhcccc-----CCccchhhhhhcccccccccHHHHHHHHhhhccCcHHHhhccCCcCCCChH
Confidence 999999999999999998788843 5678999883 3 334999999999999 6667788899999 899999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhccC
Q 009284 470 NQLEYAALDAVVLLQIFHHVRSCSQ 494 (538)
Q Consensus 470 ~Q~~YAAeDA~vlL~L~~~L~~rLe 494 (538)
+|+.|||.||+++++||+.|.++|+
T Consensus 152 ~~~~YAa~D~~~~~~l~~~l~~~l~ 176 (176)
T PF01612_consen 152 EQIEYAAQDAVVTFRLYEKLKPQLE 176 (176)
T ss_dssp HHHHHHHHHHHTHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 9999999999999999999999875
No 6
>PRK10829 ribonuclease D; Provisional
Probab=99.89 E-value=2.6e-22 Score=211.95 Aligned_cols=169 Identities=22% Similarity=0.352 Sum_probs=149.4
Q ss_pred CeEEEcCHHHHHHHHHHhhcCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchhHHHHHHHhhcC
Q 009284 315 DIIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQS 394 (538)
Q Consensus 315 ~y~~Idt~e~L~~lle~L~~a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~~~a~~IdL~~l~~~~p~~ll~~Lk~lLed 394 (538)
.|.+|++.+++..+++.+...+.+|+|||+.+.. .+...++++|+++++.+|+||..... + +..|+++|+|
T Consensus 2 ~~~~I~t~~~L~~~~~~l~~~~~lalDtEf~~~~---ty~~~l~LiQl~~~~~~~LiD~l~~~----d--~~~L~~ll~~ 72 (373)
T PRK10829 2 NYQMITTDDALASVCEAARAFPAIALDTEFVRTR---TYYPQLGLIQLYDGEQLSLIDPLGIT----D--WSPFKALLRD 72 (373)
T ss_pred CcEEeCCHHHHHHHHHHHhcCCeEEEecccccCc---cCCCceeEEEEecCCceEEEecCCcc----c--hHHHHHHHcC
Confidence 4789999999999999999999999999998752 24568999999998899999987542 1 3579999999
Q ss_pred CCceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHhh---c-CCCCCHHHHHHHHhCCCCCcCcccccCCCCCCCHH
Q 009284 395 PGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF---K-EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQN 470 (538)
Q Consensus 395 ~~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLAl---~-~~s~gLd~LAer~LG~~L~K~e~~S~W~~rpLt~~ 470 (538)
+++.||+|+.++|+..|.+.+|+.+ .++||||++. + ..++|+..|+++++|..++|+++.+||.+|||+++
T Consensus 73 ~~ivKV~H~~~~Dl~~l~~~~g~~p-----~~~fDTqiaa~~lg~~~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~ 147 (373)
T PRK10829 73 PQVTKFLHAGSEDLEVFLNAFGELP-----QPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSER 147 (373)
T ss_pred CCeEEEEeChHhHHHHHHHHcCCCc-----CCeeeHHHHHHHcCCCccccHHHHHHHHhCCccCcccccCCCCCCCCCHH
Confidence 9999999999999999977789853 6799999994 3 33689999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccCCCC
Q 009284 471 QLEYAALDAVVLLQIFHHVRSCSQPTD 497 (538)
Q Consensus 471 Q~~YAAeDA~vlL~L~~~L~~rLee~~ 497 (538)
|++|||.|+.+++.||+.|..+|++.+
T Consensus 148 ql~YAa~Dv~~L~~l~~~L~~~L~~~g 174 (373)
T PRK10829 148 QCEYAAADVFYLLPIAAKLMAETEAAG 174 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 999999999999999999999997633
No 7
>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=99.86 E-value=3.8e-21 Score=186.42 Aligned_cols=157 Identities=31% Similarity=0.431 Sum_probs=131.6
Q ss_pred HHHHhhcCCeEEEEeeeecCCccCCcCCceeEEEEEeC-CeEEEEEcCcccCCCchhHHHHHHHhhcCCCceEEEeehHH
Q 009284 328 AICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASD-EMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQC 406 (538)
Q Consensus 328 lle~L~~a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~-~~a~~IdL~~l~~~~p~~ll~~Lk~lLed~~i~KVGhnlK~ 406 (538)
+++.|++++++|||+||.+.. . .+.++++|+++. +.+|+||+...+. ..+...|+++|+++++.|||||+|.
T Consensus 3 ~~~~l~~~~~i~~D~E~~~~~---~-~~~~~LiQia~~~~~v~l~D~~~~~~---~~~~~~L~~iLe~~~i~Kv~h~~k~ 75 (197)
T cd06148 3 AIIHLKKQKVIGLDCEGVNLG---R-KGKLCLVQIATRTGQIYLFDILKLGS---IVFINGLKDILESKKILKVIHDCRR 75 (197)
T ss_pred hhhhhhhCCEEEEEcccccCC---C-CCCEEEEEEeeCCCcEEEEEhhhccc---hhHHHHHHHHhcCCCccEEEEechh
Confidence 456788899999999998653 2 458999999998 9999999987532 2345689999999999999999999
Q ss_pred hHHHHHHHhCCccccccchhHhhHHHhh---c--CC-------CCCHHHHHHHHhCCCCCc--------CcccccCCCCC
Q 009284 407 DIKQLAHSYGELECFKHYEMLLDIQNVF---K--EP-------KGGLSGLAEKILGAGLNK--------TRRNSNWEQRP 466 (538)
Q Consensus 407 Dl~vLa~~~Gil~~~~~~~~ifDtmLAl---~--~~-------s~gLd~LAer~LG~~L~K--------~e~~S~W~~rp 466 (538)
|++.|.+.+|+.. .++|||+++. + .. ..|++.+++++||.++++ .++.++|.+||
T Consensus 76 D~~~L~~~~gi~~-----~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~~~~~~~~s~W~~RP 150 (197)
T cd06148 76 DSDALYHQYGIKL-----NNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVKKLMREDPKFWALRP 150 (197)
T ss_pred HHHHHHHhcCccc-----cceeeHHHHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHHHHHhcCchhhhcCC
Confidence 9999966588843 4569999992 2 11 369999999999998864 35679999999
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhccCCC
Q 009284 467 LSQNQLEYAALDAVVLLQIFHHVRSCSQPT 496 (538)
Q Consensus 467 Lt~~Q~~YAAeDA~vlL~L~~~L~~rLee~ 496 (538)
|+++|+.|||.||++++.||+.|...|.+.
T Consensus 151 Lt~~ql~YAa~Dv~~Ll~l~~~l~~~l~~~ 180 (197)
T cd06148 151 LTEDMIRYAALDVLCLLPLYYAMLDALISK 180 (197)
T ss_pred CCHHHHHHHHHHHHhHHHHHHHHHHHhhhh
Confidence 999999999999999999999999999764
No 8
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=99.86 E-value=1.1e-20 Score=199.72 Aligned_cols=180 Identities=23% Similarity=0.404 Sum_probs=150.5
Q ss_pred EEcCHHHHHHHHHHhhcCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchhHHHHHHHhhcCCCc
Q 009284 318 WVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGI 397 (538)
Q Consensus 318 ~Idt~e~L~~lle~L~~a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~~~a~~IdL~~l~~~~p~~ll~~Lk~lLed~~i 397 (538)
+|++.+++.++++.+..++++||||||.+.. ++...++++|+++++.+|+||+.... . ...|+++|+|+++
T Consensus 1 ~I~t~~~l~~~~~~l~~~~~ia~DtE~~~~~---~y~~~l~LiQia~~~~~~liD~~~~~-~-----~~~L~~lL~d~~i 71 (367)
T TIGR01388 1 WITTDDELATVCEAVRTFPFVALDTEFVRER---TFWPQLGLIQVADGEQLALIDPLVII-D-----WSPLKELLRDESV 71 (367)
T ss_pred CcCCHHHHHHHHHHHhcCCEEEEeccccCCC---CCCCcceEEEEeeCCeEEEEeCCCcc-c-----HHHHHHHHCCCCc
Confidence 4788999999999999999999999998752 23567999999999999999987541 1 4578999999999
Q ss_pred eEEEeehHHhHHHHHHHhCCccccccchhHhhHHHhh---c-CCCCCHHHHHHHHhCCCCCcCcccccCCCCCCCHHHHH
Q 009284 398 LKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF---K-EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLE 473 (538)
Q Consensus 398 ~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLAl---~-~~s~gLd~LAer~LG~~L~K~e~~S~W~~rpLt~~Q~~ 473 (538)
.||+||+|.|++.|.+.+|... +++||||++. + ..++|++.|+++|||..++|+++.++|..|||+.+|+.
T Consensus 72 ~KV~h~~k~Dl~~L~~~~~~~~-----~~~fDtqlAa~lL~~~~~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~ 146 (367)
T TIGR01388 72 VKVLHAASEDLEVFLNLFGELP-----QPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLE 146 (367)
T ss_pred eEEEeecHHHHHHHHHHhCCCC-----CCcccHHHHHHHhCCCCCccHHHHHHHHcCCCCCcccccccCCCCCCCHHHHH
Confidence 9999999999999988555533 6789999993 3 34689999999999999999888999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhccCCCCCCCCccccchHHHHHhhcCCccc
Q 009284 474 YAALDAVVLLQIFHHVRSCSQPTDVSEGHDKIEWKSYIVSHMDNPKK 520 (538)
Q Consensus 474 YAAeDA~vlL~L~~~L~~rLee~~~~~~~~~~~w~~~~~~~~~~~~k 520 (538)
|||.||.+++.||+.|.++|++.+ +..| +..+|...+.
T Consensus 147 YAa~Dv~~L~~L~~~L~~~L~~~g------~~~w---~~ee~~~l~~ 184 (367)
T TIGR01388 147 YAAADVTYLLPLYAKLMERLEESG------RLAW---LEEECTLLTD 184 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcC------cHHH---HHHHHHHHhc
Confidence 999999999999999999997643 2455 4455555443
No 9
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.83 E-value=7e-20 Score=190.50 Aligned_cols=165 Identities=29% Similarity=0.408 Sum_probs=143.5
Q ss_pred cCHHHHHHHHHHhhcCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchhHHHHHHHhhcCCCceE
Q 009284 320 DEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILK 399 (538)
Q Consensus 320 dt~e~L~~lle~L~~a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~~~a~~IdL~~l~~~~p~~ll~~Lk~lLed~~i~K 399 (538)
++.+.+++++..+.+.+.|++|||+.... ++..++++||++.++.+++||......+ ...|..+|.|+++.|
T Consensus 2 ~~~~~l~~~~~~~~~~~~iAiDTEf~r~~---t~~p~LcLIQi~~~e~~~lIdpl~~~~d-----~~~l~~Ll~d~~v~K 73 (361)
T COG0349 2 TTGDLLAAACALLRGSKAIAIDTEFMRLR---TYYPRLCLIQISDGEGASLIDPLAGILD-----LPPLVALLADPNVVK 73 (361)
T ss_pred CchhHHHHHHHHhcCCCceEEeccccccc---ccCCceEEEEEecCCCceEecccccccc-----cchHHHHhcCCceee
Confidence 45566788888888899999999998763 3567999999999877999998763212 246888999999999
Q ss_pred EEeehHHhHHHHHHHhCCccccccchhHhhHHHhhc----CCCCCHHHHHHHHhCCCCCcCcccccCCCCCCCHHHHHHH
Q 009284 400 LGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFK----EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYA 475 (538)
Q Consensus 400 VGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLAl~----~~s~gLd~LAer~LG~~L~K~e~~S~W~~rpLt~~Q~~YA 475 (538)
|.|....|+.+|.+.+|..+ .++|||+++.. ..+||++.|+++++|..++|+++.|||.+|||+++|++||
T Consensus 74 IfHaa~~DL~~l~~~~g~~p-----~plfdTqiAa~l~g~~~~~gl~~Lv~~ll~v~ldK~~q~SDW~~RPLs~~Ql~YA 148 (361)
T COG0349 74 IFHAARFDLEVLLNLFGLLP-----TPLFDTQIAAKLAGFGTSHGLADLVEELLGVELDKSEQRSDWLARPLSEAQLEYA 148 (361)
T ss_pred eeccccccHHHHHHhcCCCC-----CchhHHHHHHHHhCCcccccHHHHHHHHhCCcccccccccccccCCCCHHHHHHH
Confidence 99999999999999778754 78999999942 3489999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhccCCCC
Q 009284 476 ALDAVVLLQIFHHVRSCSQPTD 497 (538)
Q Consensus 476 AeDA~vlL~L~~~L~~rLee~~ 497 (538)
|.|+.+++.||+.|.++|.+.+
T Consensus 149 a~DV~yL~~l~~~L~~~L~~~~ 170 (361)
T COG0349 149 AADVEYLLPLYDKLTEELAREG 170 (361)
T ss_pred HHHHHHHHHHHHHHHHHHHHcC
Confidence 9999999999999999997744
No 10
>PRK05755 DNA polymerase I; Provisional
Probab=99.71 E-value=2.5e-16 Score=183.02 Aligned_cols=223 Identities=22% Similarity=0.226 Sum_probs=174.9
Q ss_pred HHHHhhcchhHHHHHHHHhhccCCHHHHHHHHHHcCCcccccccCcccCCcccccccccccCCCCeEEEcCHHHHHHHHH
Q 009284 251 AEAKTKGDKRLLEYLVYLAMEAGYSEKVDELCERYSLEGFLKTREPEAGFVHSRFLHLKELVVEDIIWVDEVDGLHKAIC 330 (538)
Q Consensus 251 a~~~~~~D~~l~~~lv~L~~~~~d~~~L~~l~~ryef~s~l~el~~~~~~~~~~~~~l~~~~~~~y~~Idt~e~L~~lle 330 (538)
-++++.+|+++...+.++...++|.+++.+++++|||+++++...... . + + ....+|.+|++.+++..+++
T Consensus 240 ~l~~l~~d~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~---~----~-~-~~~~~~~~I~~~~~L~~~l~ 310 (880)
T PRK05755 240 KLATIKTDVPLEVDLEDLELQPPDREKLIALFKELEFKSLLRRAAAAE---A----A-P-LDEEDYETILDEEELEAWLA 310 (880)
T ss_pred hhheeeeCCCCCCCHHHhccCCCCHHHHHHHHHHhCcHHHHHHhhccc---c----c-c-CCCCceEEeCCHHHHHHHHH
Confidence 578899999988778888888999999999999999999987752110 0 0 1 12246888999999999999
Q ss_pred HhhcCCeEEEEeeeecCCccCCcCCceeEEEEEeCC-eEEEEEcCcccCCCchhHHHHHHHhhcCCCceEEEeehHHhHH
Q 009284 331 HIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDE-MVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIK 409 (538)
Q Consensus 331 ~L~~a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~~-~a~~IdL~~l~~~~p~~ll~~Lk~lLed~~i~KVGhnlK~Dl~ 409 (538)
.+..+..+++|+|++++. +....+.++|++.++ .++|+|+.+. +......|.++|+++.+.||+||+|+|++
T Consensus 311 ~l~~~~~~a~DtEt~~l~---~~~~~i~~i~ls~~~g~~~~ip~~~i----~~~~l~~l~~~L~d~~v~kV~HNakfDl~ 383 (880)
T PRK05755 311 KLKAAGLFAFDTETTSLD---PMQAELVGLSFAVEPGEAAYIPLDQL----DREVLAALKPLLEDPAIKKVGQNLKYDLH 383 (880)
T ss_pred HhhccCeEEEEeccCCCC---cccccEEEEEEEeCCCcEEEEecccc----cHHHHHHHHHHHhCCCCcEEEeccHhHHH
Confidence 998889999999998862 234567778888764 4899988643 22456789999999999999999999999
Q ss_pred HHHHHhCCccccccchhHhhHHHhh---c-CCCCCHHHHHHHHhCCCCCcCc----ccccCCCCCCCHHHHHHHHHHHHH
Q 009284 410 QLAHSYGELECFKHYEMLLDIQNVF---K-EPKGGLSGLAEKILGAGLNKTR----RNSNWEQRPLSQNQLEYAALDAVV 481 (538)
Q Consensus 410 vLa~~~Gil~~~~~~~~ifDtmLAl---~-~~s~gLd~LAer~LG~~L~K~e----~~S~W~~rpLt~~Q~~YAAeDA~v 481 (538)
.|.+ +|+.. .+.++|||++. + ..+++|++|+++|+|..+...+ .-.+|+.+|+ +.+.+||+.|+.+
T Consensus 384 ~L~~-~gi~~----~~~~~DT~iAa~Ll~~~~~~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~pl-e~~~~YAa~Dv~~ 457 (880)
T PRK05755 384 VLAR-YGIEL----RGIAFDTMLASYLLDPGRRHGLDSLAERYLGHKTISFEEVAGKQLTFAQVDL-EEAAEYAAEDADV 457 (880)
T ss_pred HHHh-CCCCc----CCCcccHHHHHHHcCCCCCCCHHHHHHHHhCCCccchHHhcCCCCCccccCH-HHHHHHHHHHHHH
Confidence 9987 78732 26789999993 3 2249999999999998753221 1234555677 5789999999999
Q ss_pred HHHHHHHHHhccCC
Q 009284 482 LLQIFHHVRSCSQP 495 (538)
Q Consensus 482 lL~L~~~L~~rLee 495 (538)
+++|++.|.++|.+
T Consensus 458 ~~~L~~~L~~~L~~ 471 (880)
T PRK05755 458 TLRLHEVLKPKLLE 471 (880)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999866
No 11
>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=99.69 E-value=1.3e-15 Score=142.73 Aligned_cols=158 Identities=27% Similarity=0.453 Sum_probs=125.4
Q ss_pred HHHHHHhhcCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchhHHHHHHHhhcCCCceEEEeehH
Q 009284 326 HKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQ 405 (538)
Q Consensus 326 ~~lle~L~~a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~~~a~~IdL~~l~~~~p~~ll~~Lk~lLed~~i~KVGhnlK 405 (538)
..+++.+...+.+++|+|+.+.. +....+.++|+++++.+||+|+... . ....|+++|+++++.|+|||+|
T Consensus 3 ~~~~~~l~~~~~l~~~~e~~~~~---~~~~~~~~i~l~~~~~~~~i~~~~~--~----~~~~l~~ll~~~~i~kv~~d~K 73 (178)
T cd06142 3 EDLCERLASAGVIAVDTEFMRLN---TYYPRLCLIQISTGGEVYLIDPLAI--G----DLSPLKELLADPNIVKVFHAAR 73 (178)
T ss_pred HHHHHHHhcCCeEEEECCccCCC---cCCCceEEEEEeeCCCEEEEeCCCc--c----cHHHHHHHHcCCCceEEEeccH
Confidence 34455555556899999886542 1134678888988765899986521 1 3456899999999999999999
Q ss_pred HhHHHHHHHhCCccccccchhHhhHHHh---hc-CCCCCHHHHHHHHhCCCCCcCcccccCCCCCCCHHHHHHHHHHHHH
Q 009284 406 CDIKQLAHSYGELECFKHYEMLLDIQNV---FK-EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVV 481 (538)
Q Consensus 406 ~Dl~vLa~~~Gil~~~~~~~~ifDtmLA---l~-~~s~gLd~LAer~LG~~L~K~e~~S~W~~rpLt~~Q~~YAAeDA~v 481 (538)
.|++.|.+.+|+. . ++++|++++ ++ ..++++++++++|+|.++.+.+..++|..+|++.+|..|||.||.+
T Consensus 74 ~~~~~L~~~~gi~-~----~~~~D~~laayLl~p~~~~~l~~l~~~~l~~~~~~~~~~~~w~~~~l~~~~~~yaa~~a~~ 148 (178)
T cd06142 74 EDLELLKRDFGIL-P----QNLFDTQIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRY 148 (178)
T ss_pred HHHHHHHHHcCCC-C----CCcccHHHHHHHhCCCccccHHHHHHHHhCCCCCcccccccCCCCCCCHHHHHHHHHhHHH
Confidence 9999998745874 2 667999999 34 3357999999999998866656678999999999999999999999
Q ss_pred HHHHHHHHHhccCCCC
Q 009284 482 LLQIFHHVRSCSQPTD 497 (538)
Q Consensus 482 lL~L~~~L~~rLee~~ 497 (538)
+++|++.|.++|++.+
T Consensus 149 l~~L~~~l~~~L~e~~ 164 (178)
T cd06142 149 LLPLYEKLKEELEEEG 164 (178)
T ss_pred HHHHHHHHHHHHHHcC
Confidence 9999999999997754
No 12
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.63 E-value=3.5e-14 Score=130.90 Aligned_cols=165 Identities=26% Similarity=0.304 Sum_probs=123.6
Q ss_pred EEEcCHHHHHHHHHHhh-cCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchhHHHHHHHhhcCC
Q 009284 317 IWVDEVDGLHKAICHIE-GCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSP 395 (538)
Q Consensus 317 ~~Idt~e~L~~lle~L~-~a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~~~a~~IdL~~l~~~~p~~ll~~Lk~lLed~ 395 (538)
.+|++.+++..|++.+. ....+++|+|+.+... ....+.++|++.++..+|++.... .......|+++|+++
T Consensus 2 ~~i~~~~~~~~~~~~~~~~~~~l~~~~e~~~~~~---~~~~~~~l~l~~~~~~~~i~~~~~----~~~~~~~l~~~l~~~ 74 (172)
T smart00474 2 RVVTDSETLEELLEKLRAAGGEVALDTETTGLNS---YSGKLVLIQISVTGEGAFIIDPLA----LGDDLEILKDLLEDE 74 (172)
T ss_pred EEecCHHHHHHHHHHHHhcCCeEEEeccccCCcc---CCCCEEEEEEeEcCCceEEEEecc----chhhHHHHHHHhcCC
Confidence 46778888888777776 5668999999876521 134677888886543445533211 112245689999999
Q ss_pred CceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHhh---c--CCCCCHHHHHHHHhCCCCCcCcccccCCCCCCCHH
Q 009284 396 GILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF---K--EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQN 470 (538)
Q Consensus 396 ~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLAl---~--~~s~gLd~LAer~LG~~L~K~e~~S~W~~rpLt~~ 470 (538)
.+.|+|||+|.|++.|.+ +|+.. .+++|+|++. + ..+++|++++++|+|....+..+.++|..+|+..+
T Consensus 75 ~~~kv~~d~k~~~~~L~~-~gi~~-----~~~~D~~laayll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~l~~~ 148 (172)
T smart00474 75 TITKVGHNAKFDLHVLAR-FGIEL-----ENIFDTMLAAYLLLGGPSKHGLATLLKEYLGVELDKEEQKSDWGARPLSEE 148 (172)
T ss_pred CceEEEechHHHHHHHHH-CCCcc-----cchhHHHHHHHHHcCCCCcCCHHHHHHHHhCCCCCcccCccccccCCCCHH
Confidence 999999999999999987 88843 3359999992 3 23379999999999987543333457877888999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccC
Q 009284 471 QLEYAALDAVVLLQIFHHVRSCSQ 494 (538)
Q Consensus 471 Q~~YAAeDA~vlL~L~~~L~~rLe 494 (538)
|..|||.||+++++|++.|.++|.
T Consensus 149 ~~~ya~~~a~~~~~L~~~l~~~l~ 172 (172)
T smart00474 149 QLQYAAEDADALLRLYEKLEKELE 172 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhC
Confidence 999999999999999999998763
No 13
>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=99.59 E-value=7.3e-14 Score=134.32 Aligned_cols=171 Identities=23% Similarity=0.374 Sum_probs=129.4
Q ss_pred CCeEEEcCHHHHHHHHHHhhcCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchhHHHHHHHhhc
Q 009284 314 EDIIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQ 393 (538)
Q Consensus 314 ~~y~~Idt~e~L~~lle~L~~a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~~~a~~IdL~~l~~~~p~~ll~~Lk~lLe 393 (538)
+.|.+|++.+++..|++.+...+.+++++|+.+.. +....+..++++.++++|||++... ......|+++|+
T Consensus 3 ~~~~~i~~~~~l~~~~~~l~~~~~l~~~~e~~~~~---~~~~~~~~l~l~~~~~~~~i~~l~~-----~~~~~~L~~~L~ 74 (192)
T cd06147 3 TPLTFVDTEEKLEELVEKLKNCKEIAVDLEHHSYR---SYLGFTCLMQISTREEDYIVDTLKL-----RDDMHILNEVFT 74 (192)
T ss_pred CCcEEECCHHHHHHHHHHHhcCCeEEEEeEecCCc---cCCCceEEEEEecCCCcEEEEeccc-----ccchHHHHHHhc
Confidence 46788866677888777776566899999865431 1123566677887666888874211 112346899999
Q ss_pred CCCceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHh---hc-CCCCCHHHHHHHHhCCCCCcCcccccCCCCCCCH
Q 009284 394 SPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNV---FK-EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQ 469 (538)
Q Consensus 394 d~~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLA---l~-~~s~gLd~LAer~LG~~L~K~e~~S~W~~rpLt~ 469 (538)
++++.|+|||+|.+++.|.+.+|+... +. ||+|++ ++ . +++++.|+++|||..+.|..+.++|+.+|+..
T Consensus 75 ~~~i~kv~~d~K~~~~~L~~~~gi~~~----~~-fD~~laaYLL~p~-~~~l~~l~~~yl~~~~~k~~~~~~~~~~~l~~ 148 (192)
T cd06147 75 DPNILKVFHGADSDIIWLQRDFGLYVV----NL-FDTGQAARVLNLP-RHSLAYLLQKYCNVDADKKYQLADWRIRPLPE 148 (192)
T ss_pred CCCceEEEechHHHHHHHHHHhCCCcC----ch-HHHHHHHHHhCCC-cccHHHHHHHHhCCCcchhhhccccccCCCCH
Confidence 999999999999999999734788432 44 999999 34 4 67999999999987643434566788788888
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCCCC
Q 009284 470 NQLEYAALDAVVLLQIFHHVRSCSQPTDV 498 (538)
Q Consensus 470 ~Q~~YAAeDA~vlL~L~~~L~~rLee~~~ 498 (538)
+|..|++.+|.++++|++.|.++|++...
T Consensus 149 ~~~~y~a~~a~~l~~L~~~L~~~L~e~~~ 177 (192)
T cd06147 149 EMIKYAREDTHYLLYIYDRLRNELLERAN 177 (192)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHHhcc
Confidence 89999999999999999999999976553
No 14
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.56 E-value=2.9e-13 Score=156.99 Aligned_cols=231 Identities=15% Similarity=0.069 Sum_probs=156.8
Q ss_pred HHHHhhcchhHHHHHHHHhhccCCHHHHHHHHHHcCCcccccccCcccCCcccccccccccCCCCeEEEcCHHHHHHHHH
Q 009284 251 AEAKTKGDKRLLEYLVYLAMEAGYSEKVDELCERYSLEGFLKTREPEAGFVHSRFLHLKELVVEDIIWVDEVDGLHKAIC 330 (538)
Q Consensus 251 a~~~~~~D~~l~~~lv~L~~~~~d~~~L~~l~~ryef~s~l~el~~~~~~~~~~~~~l~~~~~~~y~~Idt~e~L~~lle 330 (538)
-++++.+|+++...+.++...++|.+++.++|++|||+++++++..............++.....|..+.+.+++..|++
T Consensus 239 ~L~ti~~d~~l~~~~~~~~~~~~~~~~l~~~~~~lef~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 318 (887)
T TIGR00593 239 ELATIVTDVPLEVDLEDLRLSEPDRERLYALLQELEFKSLLDRLENLESPVIDDHAPVLTEKTSCAKESEEAAPLANPAE 318 (887)
T ss_pred HhheeecCCCCCCCHHHhccCCCCHHHHHHHHHHhCCccHHHHhcccccccccccccccccccccceEeCCHHHHHHHHH
Confidence 57899999999888889999999999999999999999999887310000000000000000113556767777887776
Q ss_pred HhhcCCeEEEEeeeecCCccCCcCCceeEEEEEeC--CeEEEEEcCcccCC-CchhHHHHHHHhhcCCCceEEEeehHHh
Q 009284 331 HIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASD--EMVFIFDLIKLAED-VPDVLDSCLTRILQSPGILKLGYNFQCD 407 (538)
Q Consensus 331 ~L~~a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~--~~a~~IdL~~l~~~-~p~~ll~~Lk~lLed~~i~KVGhnlK~D 407 (538)
. ...+.+++ ++.. +....+..+.++++ +.++|+|+. .+.. ..+.+...|+++|+++.+.|+|||+|+|
T Consensus 319 ~-~~~~~~~~----~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~~l~~~~~~~v~~n~K~d 389 (887)
T TIGR00593 319 K-AEVGGFVL----ERLL---DQLKKALALAFATENQSYVAYASEA-DGIPLLTILTDDKFARWLLNEQIKKIGHDAKFL 389 (887)
T ss_pred h-CcCCeEEE----cCcc---cccCceeEEEEEecCCCceEEEecc-cchhhhhHHHHHHHHHHHhCCCCcEEEeeHHHH
Confidence 5 44456777 2221 01123333446664 348888765 2111 1123556799999999999999999999
Q ss_pred HHHHHHHhCCccccccchhHhhHHHh---hc-CCCCCHHHHHHHHhCCCCCcCccccc----CCCCCCCHHHHHHHHHHH
Q 009284 408 IKQLAHSYGELECFKHYEMLLDIQNV---FK-EPKGGLSGLAEKILGAGLNKTRRNSN----WEQRPLSQNQLEYAALDA 479 (538)
Q Consensus 408 l~vLa~~~Gil~~~~~~~~ifDtmLA---l~-~~s~gLd~LAer~LG~~L~K~e~~S~----W~~rpLt~~Q~~YAAeDA 479 (538)
+++|.+ +|+... +..+|||++ ++ ..+++|++++.+||+..+...++..+ |+..|+ +...+||++||
T Consensus 390 ~~~l~~-~gi~~~----~~~~Dt~la~yll~~~~~~~l~~la~~yl~~~~~~~~~~~~~~~~~~~~~~-~~~~~ya~~d~ 463 (887)
T TIGR00593 390 MHLLKR-EGIELG----GVIFDTMLAAYLLDPAQVSTLDTLARRYLVEELILDEKIGGKLAKFAFPPL-EEATEYLARRA 463 (887)
T ss_pred HHHHHh-CCCCCC----CcchhHHHHHHHcCCCCCCCHHHHHHHHcCcccccHHHhccCCCCcccccH-HHHHHHHHHHH
Confidence 999987 898432 568999999 34 34579999999999977654332222 222232 33468999999
Q ss_pred HHHHHHHHHHHhccCCC
Q 009284 480 VVLLQIFHHVRSCSQPT 496 (538)
Q Consensus 480 ~vlL~L~~~L~~rLee~ 496 (538)
.++++|+..|.++|++.
T Consensus 464 ~~~~~L~~~l~~~l~~~ 480 (887)
T TIGR00593 464 AATKRLAEELLKELDEN 480 (887)
T ss_pred HHHHHHHHHHHHHHhhc
Confidence 99999999999999753
No 15
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=99.48 E-value=9.3e-13 Score=119.11 Aligned_cols=145 Identities=26% Similarity=0.216 Sum_probs=108.2
Q ss_pred eEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchhHHHHHHHhhcCCCceEEEeehHHhHHHHHHHhC
Q 009284 337 VVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYG 416 (538)
Q Consensus 337 ~IgfDtE~~~l~~~~~~~~~VsLiQLAt~~~a~~IdL~~l~~~~p~~ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~G 416 (538)
.+++|+|+.+.. +....+.++|++++++++|++.... ...+...|+++|+++.+.|||||+|+|++.|.+ ++
T Consensus 2 ~l~~d~e~~~~~---~~~~~i~~~~l~~~~~~~~i~~~~~----~~~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~~-~~ 73 (155)
T cd00007 2 EVAFDTETTGLN---YHRGKLVGIQIATAGEAAYIPDELE----LEEDLEALKELLEDEDITKVGHDAKFDLVVLAR-DG 73 (155)
T ss_pred ceEEEEecCCCC---cCCCeEEEEEEEECCcEEEEEcCCC----HHHHHHHHHHHHcCCCCcEEeccHHHHHHHHHH-CC
Confidence 478999887642 1134677888988654677764321 133556689999999999999999999999987 45
Q ss_pred CccccccchhHhhHHHhh---c-CC-CCCHHHHHHHHhCCCCCcCcccccCC----CCCCCHHHHHHHHHHHHHHHHHHH
Q 009284 417 ELECFKHYEMLLDIQNVF---K-EP-KGGLSGLAEKILGAGLNKTRRNSNWE----QRPLSQNQLEYAALDAVVLLQIFH 487 (538)
Q Consensus 417 il~~~~~~~~ifDtmLAl---~-~~-s~gLd~LAer~LG~~L~K~e~~S~W~----~rpLt~~Q~~YAAeDA~vlL~L~~ 487 (538)
+.. .+.++||+++. + .. +++|+.++++|++....+.++..+|. .++++..|..||+.||.++++|++
T Consensus 74 ~~~----~~~~~D~~~~ayll~~~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~ 149 (155)
T cd00007 74 IEL----PGNIFDTMLAAYLLNPGEGSHSLDDLAKEYLGIELDKDEQIYGKGAKTFARPLSEELLEYAAEDADALLRLYE 149 (155)
T ss_pred CCC----CCCcccHHHHHHHhCCCCCcCCHHHHHHHHcCCCCccHHHHhcCCCCccccCCHHHHHHHHHHhHHHHHHHHH
Confidence 422 26689999993 3 33 67999999999998754433344442 467889999999999999999999
Q ss_pred HHHhcc
Q 009284 488 HVRSCS 493 (538)
Q Consensus 488 ~L~~rL 493 (538)
.|.+++
T Consensus 150 ~l~~~~ 155 (155)
T cd00007 150 KLLEEL 155 (155)
T ss_pred HHHhhC
Confidence 998763
No 16
>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=99.47 E-value=1.1e-12 Score=119.21 Aligned_cols=142 Identities=24% Similarity=0.248 Sum_probs=106.4
Q ss_pred eEEEEeeeecCCccCCcCCceeEEEEEeC-CeEEEEEcCcccCCCchhHHHHHHHhhcCCCceEEEeehHHhHHHHHHHh
Q 009284 337 VVGIDCEWKPNYVKGCKMNKVSIMQIASD-EMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSY 415 (538)
Q Consensus 337 ~IgfDtE~~~l~~~~~~~~~VsLiQLAt~-~~a~~IdL~~l~~~~p~~ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~ 415 (538)
++++|+|+.+.. +...++.++|++++ +.++|+++.+. .. ....|+++|+++++.|+|||+|.|++.|.+ +
T Consensus 1 ~~~~~~e~~~~~---~~~~~~~~l~l~~~~~~~~~i~~~~~--~~---~~~~l~~~l~~~~~~kv~~d~K~~~~~L~~-~ 71 (150)
T cd09018 1 VFAFDTETDSLD---NISANLVLIQLAIEPGVAALIPVAHD--YL---ALELLKPLLEDEKALKVGQNLKYDRGILLN-Y 71 (150)
T ss_pred CEEEEeecCCCC---CCCceEEEEEEEcCCCcEEEEEcCCc--cc---CHHHHHHHhcCCCCceeeecHHHHHHHHHH-c
Confidence 378899876542 11346778889886 44889886532 10 134689999999999999999999999987 6
Q ss_pred CCccccccchhHhhHHHh---hc-CC-CCCHHHHHHHHhCCCCCcCcccc--cCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q 009284 416 GELECFKHYEMLLDIQNV---FK-EP-KGGLSGLAEKILGAGLNKTRRNS--NWEQRPLSQNQLEYAALDAVVLLQIFHH 488 (538)
Q Consensus 416 Gil~~~~~~~~ifDtmLA---l~-~~-s~gLd~LAer~LG~~L~K~e~~S--~W~~rpLt~~Q~~YAAeDA~vlL~L~~~ 488 (538)
|+.. .++.||+|++ ++ .. ++++++|+++||+..+.+.++.. +|..++++.+|..||+.||.++++|++.
T Consensus 72 ~~~~----~~~~~D~~laayLl~p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~~a~~l~~L~~~ 147 (150)
T cd09018 72 FIEL----RGIAFDTMLEAYILNSVAGRWDMDSLVERWLGHKLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLK 147 (150)
T ss_pred CCcc----CCcchhHHHHHHHhCCCCCCCCHHHHHHHHhCCCcccHHHhcCCCCcccCCHHHHHHHHHHHHHHHHHHHHH
Confidence 7633 2678999999 34 33 57999999999998755422222 3755777899999999999999999998
Q ss_pred HHh
Q 009284 489 VRS 491 (538)
Q Consensus 489 L~~ 491 (538)
|.+
T Consensus 148 l~~ 150 (150)
T cd09018 148 LWP 150 (150)
T ss_pred hcC
Confidence 864
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=99.32 E-value=2.5e-11 Score=114.51 Aligned_cols=149 Identities=15% Similarity=0.080 Sum_probs=109.0
Q ss_pred CCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchhHHHHHHHhhcCCCceEEEeehHHhHHHHHHH
Q 009284 335 CKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHS 414 (538)
Q Consensus 335 a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~~~a~~IdL~~l~~~~p~~ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~ 414 (538)
.+.+++++|..... +....+..++++.+++++|+|+.+. ......|+++|+++++.|++||+|+|++.|.+
T Consensus 3 ~~~~~~~~~~~~~~---~~~~~l~~i~l~~~~~~~~i~~~~~-----~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l~~- 73 (178)
T cd06140 3 ADEVALYVELLGEN---YHTADIIGLALANGGGAYYIPLELA-----LLDLAALKEWLEDEKIPKVGHDAKRAYVALKR- 73 (178)
T ss_pred CCceEEEEEEcCCC---cceeeEEEEEEEeCCcEEEEeccch-----HHHHHHHHHHHhCCCCceeccchhHHHHHHHH-
Confidence 35677888876541 1123455566777667888886421 01345689999999999999999999999987
Q ss_pred hCCccccccchhHhhHHHh---hc--CCCCCHHHHHHHHhCCCCCcCcccccCC---CCCCCHHHHHHHHHHHHHHHHHH
Q 009284 415 YGELECFKHYEMLLDIQNV---FK--EPKGGLSGLAEKILGAGLNKTRRNSNWE---QRPLSQNQLEYAALDAVVLLQIF 486 (538)
Q Consensus 415 ~Gil~~~~~~~~ifDtmLA---l~--~~s~gLd~LAer~LG~~L~K~e~~S~W~---~rpLt~~Q~~YAAeDA~vlL~L~ 486 (538)
+|+.. .+..||||++ ++ ..++++++++.+||+..+.+.++...|. ..+....+.+|++.||.++++|+
T Consensus 74 ~gi~~----~~~~fDt~laaYLL~p~~~~~~l~~l~~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~ 149 (178)
T cd06140 74 HGIEL----AGVAFDTMLAAYLLDPTRSSYDLADLAKRYLGRELPSDEEVYGKGAKFAVPDEEVLAEHLARKAAAIARLA 149 (178)
T ss_pred CCCcC----CCcchhHHHHHHHcCCCCCCCCHHHHHHHHcCCCCcchHHhcCCCCCcccCCHHHHHHHHHHHHHHHHHHH
Confidence 78733 2567999999 34 2348999999999998765433344442 23445667889999999999999
Q ss_pred HHHHhccCCC
Q 009284 487 HHVRSCSQPT 496 (538)
Q Consensus 487 ~~L~~rLee~ 496 (538)
+.|+++|++.
T Consensus 150 ~~l~~~L~~~ 159 (178)
T cd06140 150 PKLEEELEEN 159 (178)
T ss_pred HHHHHHHHHh
Confidence 9999999764
No 18
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=99.32 E-value=9.1e-12 Score=137.43 Aligned_cols=167 Identities=20% Similarity=0.215 Sum_probs=125.0
Q ss_pred eEEEcCHHHHHHHHHHhhcCCeEEEEeeeecCCccCCcCCceeEEEEE--eCCeEEEEEcCcccCCCchhHHHHHHHhhc
Q 009284 316 IIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIA--SDEMVFIFDLIKLAEDVPDVLDSCLTRILQ 393 (538)
Q Consensus 316 y~~Idt~e~L~~lle~L~~a~~IgfDtE~~~l~~~~~~~~~VsLiQLA--t~~~a~~IdL~~l~~~~p~~ll~~Lk~lLe 393 (538)
|..+.+...+..|+..+.....+++|+|+.++. +....+++++ .+..++|+++.+.+... .....|++||+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~a~~~et~~l~-----~~~~~lvg~s~~~~~~~~yi~~~~~~~~~--~~~~~l~~~l~ 75 (593)
T COG0749 3 YGTITDLAVLNAWLTKLNAAANIAFDTETDGLD-----PHGADLVGLSVASEEEAAYIPLLHGPEQL--NVLAALKPLLE 75 (593)
T ss_pred chhhhHHHHHHHHHHHHhhcccceeeccccccC-----cccCCeeEEEeeccccceeEeeccchhhh--hhHHHHHHHhh
Confidence 344556677788887777666699999999873 2344455554 34578999998732111 25678999999
Q ss_pred CCCceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHh---hc--CCCCCHHHHHHHHhCCCCCcCcccc-------c
Q 009284 394 SPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNV---FK--EPKGGLSGLAEKILGAGLNKTRRNS-------N 461 (538)
Q Consensus 394 d~~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLA---l~--~~s~gLd~LAer~LG~~L~K~e~~S-------~ 461 (538)
++...|+|||+|+|.++|++ +|+. .+..+|||++ ++ .+.|+|++|+++|+++.+..++.+. +
T Consensus 76 ~~~~~kv~~~~K~d~~~l~~-~Gi~-----~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~~~~ 149 (593)
T COG0749 76 DEGIKKVGQNLKYDYKVLAN-LGIE-----PGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQLT 149 (593)
T ss_pred CcccchhccccchhHHHHHH-cCCc-----ccchHHHHHHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhccccccCc
Confidence 99999999999999999999 7853 1678999999 23 4579999999999998876544332 3
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCC
Q 009284 462 WEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPT 496 (538)
Q Consensus 462 W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rLee~ 496 (538)
+...++. ....|+|+||+++++|+..|.+++.+.
T Consensus 150 ~~~~~~~-~~~~y~a~~a~~~~~L~~~l~~~l~~~ 183 (593)
T COG0749 150 FADVKLE-KATEYAAEDADATLRLESILEPELLKT 183 (593)
T ss_pred cccchHH-HHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 3334443 337999999999999999999888663
No 19
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=99.27 E-value=9.8e-12 Score=134.84 Aligned_cols=171 Identities=25% Similarity=0.336 Sum_probs=148.0
Q ss_pred CCeEEEcCHHHHHHHHHHhhcCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchhHHHHHHHhhc
Q 009284 314 EDIIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQ 393 (538)
Q Consensus 314 ~~y~~Idt~e~L~~lle~L~~a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~~~a~~IdL~~l~~~~p~~ll~~Lk~lLe 393 (538)
..+.+|++..++.++.+.+.....+++|+|..+. .++.+..+++||+|..+-|+||...+. + ....|++.|.
T Consensus 191 T~~~~I~t~~el~~l~~~l~~~~Efavdlehhsy---rsf~gltclmqISTr~ed~iIDt~~l~----~-~i~~l~e~fs 262 (687)
T KOG2206|consen 191 TPKVWICTLGELEALPEILDSVIEFAVDLEHHSY---RSFLGLTCLMQISTRTEDFIIDTFKLR----D-HIGILNEVFS 262 (687)
T ss_pred cCceeeechHHHHHHHHHHhhhhhhhhhccccch---hhhcCceeEEEeeccchhheehhHHHH----H-HHHHhhhhcc
Confidence 4588999999999999999888999999998765 134568899999998888999887543 2 2458999999
Q ss_pred CCCceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHhh---cCCCCCHHHHHHHHhCCCCCcCcccccCCCCCCCHH
Q 009284 394 SPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF---KEPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQN 470 (538)
Q Consensus 394 d~~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLAl---~~~s~gLd~LAer~LG~~L~K~e~~S~W~~rpLt~~ 470 (538)
+|++.||.|+.-.|+.+|.+.|||.. -++|||..+. +-.+++|..|.+.+-|.-.+|.-|..+|..|||+++
T Consensus 263 dp~ivkvfhgaD~diiwlqrdfgiyv-----vnLfdt~~a~r~L~~~r~sL~~ll~~~~~v~~nk~yqladwR~rpLp~~ 337 (687)
T KOG2206|consen 263 DPGIVKVFHGADTDIIWLQRDFGIYV-----VNLFDTIQASRLLGLPRPSLAYLLECVCGVLTNKKYQLADWRIRPLPEE 337 (687)
T ss_pred CCCeEEEEecCccchhhhhccceEEE-----EechhhHHHHHHhCCCcccHHHHHHHHHhhhhhhhhhhchhccccCcHH
Confidence 99999999999999999999999943 4689999994 456899999999999988777778899999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccCCCC
Q 009284 471 QLEYAALDAVVLLQIFHHVRSCSQPTD 497 (538)
Q Consensus 471 Q~~YAAeDA~vlL~L~~~L~~rLee~~ 497 (538)
+..||-+|.++++-||+.|+..+...+
T Consensus 338 Mv~yar~dthyllyiyD~lr~el~~~a 364 (687)
T KOG2206|consen 338 MVRYAREDTHYLLYIYDVLRKELKRLA 364 (687)
T ss_pred HHHHHhhcchhHHHHHHHHHHHHHHHh
Confidence 999999999999999999998876655
No 20
>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=99.21 E-value=5.3e-10 Score=105.98 Aligned_cols=154 Identities=24% Similarity=0.288 Sum_probs=109.8
Q ss_pred hcCCeEEEEeeeecCCccCCcCCceeEEEEEeC-CeEEEEEcCcccC---CCchhHHHHHHHhhcCCCceEEEeehHHhH
Q 009284 333 EGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASD-EMVFIFDLIKLAE---DVPDVLDSCLTRILQSPGILKLGYNFQCDI 408 (538)
Q Consensus 333 ~~a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~-~~a~~IdL~~l~~---~~p~~ll~~Lk~lLed~~i~KVGhnlK~Dl 408 (538)
...+.+++|+|+++.. +....+..++++.. +..+|+++.+... .....+...|+++|++..+.+|+||+|+|+
T Consensus 3 ~~~~~~a~d~e~~~~~---~~~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~v~hn~k~d~ 79 (193)
T cd06139 3 EKAKVFAFDTETTSLD---PMQAELVGISFAVEPGEAYYIPLGHDYGGEQLPREEVLAALKPLLEDPSIKKVGQNLKFDL 79 (193)
T ss_pred ccCCeEEEEeecCCCC---cCCCeEEEEEEEcCCCCEEEEecCCCccccCCCHHHHHHHHHHHHhCCCCcEEeeccHHHH
Confidence 3457799999987642 11234555667764 4478888654210 012335667899999988899999999999
Q ss_pred HHHHHHhCCccccccchhHhhHHHh---hc-CC-CCCHHHHHHHHhCCCCC-------cCcccccCCCCCCCHHHHHHHH
Q 009284 409 KQLAHSYGELECFKHYEMLLDIQNV---FK-EP-KGGLSGLAEKILGAGLN-------KTRRNSNWEQRPLSQNQLEYAA 476 (538)
Q Consensus 409 ~vLa~~~Gil~~~~~~~~ifDtmLA---l~-~~-s~gLd~LAer~LG~~L~-------K~e~~S~W~~rpLt~~Q~~YAA 476 (538)
+.|.+ +|+.. .+.++||+++ ++ .. +++++.++++|+|.... ++.+..+|+..|+ ..+.+||+
T Consensus 80 ~~l~~-~gi~~----~~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~-~~~~~ya~ 153 (193)
T cd06139 80 HVLAN-HGIEL----RGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPL-EKAAEYAA 153 (193)
T ss_pred HHHHH-CCCCC----CCCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccCH-HHHHHHHH
Confidence 99987 78743 2567999999 23 33 68999999999986532 2223344555555 55789999
Q ss_pred HHHHHHHHHHHHHHhccCC
Q 009284 477 LDAVVLLQIFHHVRSCSQP 495 (538)
Q Consensus 477 eDA~vlL~L~~~L~~rLee 495 (538)
.|+.++++|++.|.+++++
T Consensus 154 ~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 154 EDADITLRLYELLKPKLKE 172 (193)
T ss_pred HHHHHHHHHHHHHHHHHhh
Confidence 9999999999999999966
No 21
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=98.92 E-value=4.4e-09 Score=117.23 Aligned_cols=139 Identities=24% Similarity=0.249 Sum_probs=113.3
Q ss_pred CeEEEcCHHHHHHHHHHhhcCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchhHHHHHHHhhcC
Q 009284 315 DIIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQS 394 (538)
Q Consensus 315 ~y~~Idt~e~L~~lle~L~~a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~~~a~~IdL~~l~~~~p~~ll~~Lk~lLed 394 (538)
.+.+|++.+++..++..+...+.+++|+|+... ...++++|++.++..+++|... .+.|+
T Consensus 2 ~~~~I~~~~~l~~~~~~l~~~~~~a~DtEf~r~------~t~l~liQ~~~~~~~~liDpl~-----------~l~~~--- 61 (553)
T PRK14975 2 DMKVILAPEELGAALERLSPAGVVAGDTETTGD------DAAAAAAQEGEEEPRWVWASTA-----------ALYPR--- 61 (553)
T ss_pred CceEEeccchhHHHHHHhccCCceeCCccccCC------cchhheeeecCCCceEEECchH-----------HhHHH---
Confidence 356788889999999999999999999998864 1268899999888888886431 12222
Q ss_pred CCceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHh---hc-CC---CCCHHHHHHHHhCCCCCcCcccccCCCCCC
Q 009284 395 PGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNV---FK-EP---KGGLSGLAEKILGAGLNKTRRNSNWEQRPL 467 (538)
Q Consensus 395 ~~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLA---l~-~~---s~gLd~LAer~LG~~L~K~e~~S~W~~rpL 467 (538)
|.+ +|+.. .++||||++ ++ .. ++|++.+++++|+..++|.++.++|. +|+
T Consensus 62 ----------------L~~-~Gv~~-----~~~fDT~LAa~lL~~~~~~~~~~l~~la~~~l~~~l~k~~~~sdw~-rpl 118 (553)
T PRK14975 62 ----------------LLA-AGVRV-----ERCHDLMLASQLLLGSEGRAGSSLSAAAARALGEGLDKPPQTSALS-DPP 118 (553)
T ss_pred ----------------HHH-CCCcc-----CCCchHHHHHHHcCCCCCcCCCCHHHHHHHHhCCCCCChhhhcccc-ccc
Confidence 444 57743 458999999 33 22 78999999999999999988889996 899
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhccCCC
Q 009284 468 SQNQLEYAALDAVVLLQIFHHVRSCSQPT 496 (538)
Q Consensus 468 t~~Q~~YAAeDA~vlL~L~~~L~~rLee~ 496 (538)
++.|..||+.|+.++++||+.|.++|++.
T Consensus 119 s~~q~~YAa~Dv~~l~~L~~~L~~qL~~~ 147 (553)
T PRK14975 119 DEEQLLYAAADADVLLELYAVLADQLNRI 147 (553)
T ss_pred hHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999999764
No 22
>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=98.51 E-value=1.9e-06 Score=79.41 Aligned_cols=120 Identities=22% Similarity=0.196 Sum_probs=80.7
Q ss_pred EEEEeCCeEEEEEcCcccCCCchhHHHHHHHhhcCCCceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHh---hc-
Q 009284 360 MQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNV---FK- 435 (538)
Q Consensus 360 iQLAt~~~a~~IdL~~l~~~~p~~ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLA---l~- 435 (538)
+.++.+++++|+++... . . ...|+++|+++.+.|++||+|.+++.|.+ +|+... +..||+|++ ++
T Consensus 23 lal~~~~~~~yi~~~~~---~--~-~~~l~~~l~~~~~~ki~~d~K~~~~~l~~-~gi~l~----~~~fD~~LAaYLL~p 91 (151)
T cd06128 23 LAFAIEGVAAYIPVAHD---Y--A-LELLKPLLEDEKALKVGQNLKYDRVILAN-YGIELR----GIAFDTMLEAYLLDP 91 (151)
T ss_pred EEEEcCCCeEEEeCCCC---c--C-HHHHHHHHcCCCCCEEeeehHHHHHHHHH-CCCCCC----CcchhHHHHHHHcCC
Confidence 44555556888874321 1 1 34589999999999999999999999977 788432 567999999 34
Q ss_pred CCC-CCHHHHHHHHhCCCCCcCcccccCCC--CCC-CHHHHHHHHHHHHHHHHHHHHHH
Q 009284 436 EPK-GGLSGLAEKILGAGLNKTRRNSNWEQ--RPL-SQNQLEYAALDAVVLLQIFHHVR 490 (538)
Q Consensus 436 ~~s-~gLd~LAer~LG~~L~K~e~~S~W~~--rpL-t~~Q~~YAAeDA~vlL~L~~~L~ 490 (538)
..+ +++++++++||+......++...... .++ ..+...|++..|.++.+|++.|.
T Consensus 92 ~~~~~~l~~la~~yl~~~~~~~~~~~gkg~~~~~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 92 VAGRHDMDSLAERWLKEKTITFEEIAGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred CCCCCCHHHHHHHHcCCCCccHHHHcCCCCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 222 59999999999876322011111110 011 12224588999999999998875
No 23
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=97.96 E-value=3.9e-05 Score=79.49 Aligned_cols=141 Identities=23% Similarity=0.273 Sum_probs=101.4
Q ss_pred CeEEEEeeeecCCccCCcCCceeEEEEEeC-CeEEEEEcCcccCCCchhHHHHHHHhhcCCCceEEEeehHHhHHHHHH-
Q 009284 336 KVVGIDCEWKPNYVKGCKMNKVSIMQIASD-EMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAH- 413 (538)
Q Consensus 336 ~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~-~~a~~IdL~~l~~~~p~~ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~- 413 (538)
..+..+-|+.+....+.....++.+||+++ +.++++.+.+.. ..|. .|+.+|+|++.++||-+...|...|.+
T Consensus 128 ~~~~~~~e~~~~~d~~~~~P~~~~lqlcV~en~C~I~ql~~~~-~IP~----~LR~fl~D~~~~~vgv~~d~D~~KL~r~ 202 (319)
T KOG4373|consen 128 PFVCYRREAQPYLDMGRSDPPPDTLQLCVGENRCLIIQLIHCK-RIPH----ELRSFLEDPDHTFVGVWNDQDAGKLERK 202 (319)
T ss_pred cceeecccccccccccccCCCcchhhhhhcccceeeEEeeccc-cchH----HHHHhhcCCCceEEeccccccHHHHhhh
Confidence 344455566654111122335888999996 888988776642 3444 577789999999999999999999887
Q ss_pred HhCCccccccchhHhhHHHhhc--C----CCCCHHHHHHHHhCCC-----CCcCcccccCCCCCCCHHHHHHHHHHHHHH
Q 009284 414 SYGELECFKHYEMLLDIQNVFK--E----PKGGLSGLAEKILGAG-----LNKTRRNSNWEQRPLSQNQLEYAALDAVVL 482 (538)
Q Consensus 414 ~~Gil~~~~~~~~ifDtmLAl~--~----~s~gLd~LAer~LG~~-----L~K~e~~S~W~~rpLt~~Q~~YAAeDA~vl 482 (538)
.|+.. .+...|+.+..+ . .+.+...++...+|.. +++.-++++|...+|+.+|+.||+.|+++.
T Consensus 203 ~hql~-----I~~~~dlr~~~~d~~g~~~~~~s~e~i~~~~~~~~~~~v~l~~~i~msdw~~~~Ls~~Ql~~asidvy~c 277 (319)
T KOG4373|consen 203 EHQLE-----IGELEDLRLLVNDSLGGSMPNDSFEEIVSETLGYYGKDVRLDKEIRMSDWSVYPLSDDQLLQASIDVYVC 277 (319)
T ss_pred hhccc-----HHhhhhHHhhcchhhccCccCccHHHHHHHHhhccccccccChhcccccceeeeccHHHHHHHHhHHHHH
Confidence 56652 255678777643 1 2356677777766542 234457899999999999999999999999
Q ss_pred HHHH
Q 009284 483 LQIF 486 (538)
Q Consensus 483 L~L~ 486 (538)
..|+
T Consensus 278 ~~lg 281 (319)
T KOG4373|consen 278 HKLG 281 (319)
T ss_pred HHHH
Confidence 9998
No 24
>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=96.23 E-value=0.049 Score=51.27 Aligned_cols=78 Identities=15% Similarity=0.200 Sum_probs=53.9
Q ss_pred HHHHHhhcCCCceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHhhc----C----CCCCHHHHHHHHhCCCCCcCc
Q 009284 386 SCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFK----E----PKGGLSGLAEKILGAGLNKTR 457 (538)
Q Consensus 386 ~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLAl~----~----~s~gLd~LAer~LG~~L~K~e 457 (538)
..|..++.+. ...||||+.+|+..|... . ..++||..... . .+++|..|+++++|.++....
T Consensus 75 ~~~~~~i~~~-~vlVgHn~~fD~~fL~~~-~--------~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~~ 144 (161)
T cd06137 75 AALWKFIDPD-TILVGHSLQNDLDALRMI-H--------TRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGG 144 (161)
T ss_pred HHHHHhcCCC-cEEEeccHHHHHHHHhCc-C--------CCeeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCCC
Confidence 4556666543 457999999999999751 1 23568887732 2 479999999999997653211
Q ss_pred ccccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009284 458 RNSNWEQRPLSQNQLEYAALDAVVLLQIF 486 (538)
Q Consensus 458 ~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~ 486 (538)
. .+-|..||.++.+|+
T Consensus 145 ~-------------~H~A~~DA~at~~l~ 160 (161)
T cd06137 145 E-------------GHDSLEDALAAREVV 160 (161)
T ss_pred C-------------CCCcHHHHHHHHHHh
Confidence 1 123778999988876
No 25
>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=96.23 E-value=0.03 Score=52.70 Aligned_cols=82 Identities=18% Similarity=0.247 Sum_probs=54.5
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHh--h------c-CCCCCHHHHHHHHhCCCCC
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNV--F------K-EPKGGLSGLAEKILGAGLN 454 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLA--l------~-~~s~gLd~LAer~LG~~L~ 454 (538)
+...+..++.+ ...||||+++|+..|...+.. ..+.||... + . ..+++|+.|+++++|..+.
T Consensus 67 v~~~l~~~l~~--~vlV~Hn~~~D~~~l~~~~~~-------~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~ 137 (157)
T cd06149 67 AQKEILKILKG--KVVVGHAIHNDFKALKYFHPK-------HMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQ 137 (157)
T ss_pred HHHHHHHHcCC--CEEEEeCcHHHHHHhcccCCC-------cCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhc
Confidence 56667777764 467999999999988753221 234566432 1 1 2569999999999876554
Q ss_pred cCcccccCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009284 455 KTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFH 487 (538)
Q Consensus 455 K~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~ 487 (538)
.+.+ .+-|.+||.++.+|++
T Consensus 138 ~~~~-------------~H~Al~DA~at~~l~~ 157 (157)
T cd06149 138 VGRQ-------------GHSSVEDARATMELYK 157 (157)
T ss_pred CCCC-------------CcCcHHHHHHHHHHhC
Confidence 3211 1337789999988863
No 26
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=96.05 E-value=0.028 Score=48.64 Aligned_cols=58 Identities=22% Similarity=0.242 Sum_probs=41.8
Q ss_pred EEEEeeeecCCccCCcCCceeEEEEEeC--CeEEEEEcCcccCCCchhHHHHHHHhhcCCC-ceEEEeehHHhHHHHHH
Q 009284 338 VGIDCEWKPNYVKGCKMNKVSIMQIASD--EMVFIFDLIKLAEDVPDVLDSCLTRILQSPG-ILKLGYNFQCDIKQLAH 413 (538)
Q Consensus 338 IgfDtE~~~l~~~~~~~~~VsLiQLAt~--~~a~~IdL~~l~~~~p~~ll~~Lk~lLed~~-i~KVGhnlK~Dl~vLa~ 413 (538)
+++|+|+++.. +....+.++|++.. +..+++| +.+++++.. ...||||..+|+..|.+
T Consensus 1 ~~~DiEt~~~~---~~~~~i~~i~~~~~~~~~~~~~~---------------f~~~l~~~~~~v~V~hn~~fD~~fL~~ 61 (96)
T cd06125 1 IAIDTEATGLD---GAVHEIIEIALADVNPEDTAVID---------------LKDILRDKPLAILVGHNGSFDLPFLNN 61 (96)
T ss_pred CEEEEECCCCC---CCCCcEEEEEEEEccCCCEEEeh---------------HHHHHhhCCCCEEEEeCcHHhHHHHHH
Confidence 47999998862 23456777777654 5666654 456777765 67899999999887765
No 27
>PRK07740 hypothetical protein; Provisional
Probab=95.27 E-value=0.44 Score=48.19 Aligned_cols=91 Identities=15% Similarity=0.111 Sum_probs=62.4
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHH----hCCccccccchhHhhHHHhhc-----CCCCCHHHHHHHHhCCCCC
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS----YGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLN 454 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~----~Gil~~~~~~~~ifDtmLAl~-----~~s~gLd~LAer~LG~~L~ 454 (538)
++..|..++.+ ...||||..+|...|.+. ++. . + ...++||+...+ ..+++|++++.. +|.+..
T Consensus 131 vl~~f~~fi~~--~~lVahna~fD~~fL~~~~~~~~~~-~-~--~~~~iDt~~l~r~l~~~~~~~sL~~l~~~-~gi~~~ 203 (244)
T PRK07740 131 VLHRFYAFIGA--GVLVAHHAGHDKAFLRHALWRTYRQ-P-F--THRLIDTMFLTKLLAHERDFPTLDDALAY-YGIPIP 203 (244)
T ss_pred HHHHHHHHhCC--CEEEEeCHHHHHHHHHHHHHHhcCC-C-c--CCCeechHHHHHHHcCCCCCCCHHHHHHH-CCcCCC
Confidence 44555566654 367899999999888642 121 1 0 145779887732 347899999965 676543
Q ss_pred cCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Q 009284 455 KTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTD 497 (538)
Q Consensus 455 K~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rLee~~ 497 (538)
. .+-|-.||.++.+|+..+..++++.+
T Consensus 204 ~----------------~H~Al~Da~ata~l~~~ll~~~~~~~ 230 (244)
T PRK07740 204 R----------------RHHALGDALMTAKLWAILLVEAQQRG 230 (244)
T ss_pred C----------------CCCcHHHHHHHHHHHHHHHHHHHHcC
Confidence 1 12378999999999999988887644
No 28
>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=95.24 E-value=0.097 Score=48.77 Aligned_cols=80 Identities=18% Similarity=0.332 Sum_probs=55.0
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHh--h-c---CCCCCHHHHHHHHhCCCCCcCc
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNV--F-K---EPKGGLSGLAEKILGAGLNKTR 457 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLA--l-~---~~s~gLd~LAer~LG~~L~K~e 457 (538)
+...|..++.+ . ..||||+.+|+..|.. +... ..++|+... + . ..+++|+.|+++++|.+....
T Consensus 67 ~~~~l~~~l~~-~-vlVgHn~~fD~~~L~~--~~~~-----~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~- 136 (152)
T cd06144 67 VQKKVAELLKG-R-ILVGHALKNDLKVLKL--DHPK-----KLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEG- 136 (152)
T ss_pred HHHHHHHHhCC-C-EEEEcCcHHHHHHhcC--cCCC-----ccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCC-
Confidence 56677788876 3 4599999999999864 2211 234566543 1 1 257999999999999755311
Q ss_pred ccccCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009284 458 RNSNWEQRPLSQNQLEYAALDAVVLLQIFH 487 (538)
Q Consensus 458 ~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~ 487 (538)
.+-|..||.++.+|++
T Consensus 137 --------------~H~Al~DA~at~~l~~ 152 (152)
T cd06144 137 --------------EHSSVEDARAAMRLYR 152 (152)
T ss_pred --------------CcCcHHHHHHHHHHhC
Confidence 1337899999988874
No 29
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=95.12 E-value=0.29 Score=50.17 Aligned_cols=79 Identities=18% Similarity=0.336 Sum_probs=57.6
Q ss_pred HHHHhhcCCCceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHh--h----c-CCCCCHHHHHHHHhCCCCCcCccc
Q 009284 387 CLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNV--F----K-EPKGGLSGLAEKILGAGLNKTRRN 459 (538)
Q Consensus 387 ~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLA--l----~-~~s~gLd~LAer~LG~~L~K~e~~ 459 (538)
.+-.+|.. ...|||.++.|+.+|.-.|.- ..+-||.-. + . ..+-||..|++.+||+.+-.++..
T Consensus 177 ev~klL~g--RIlVGHaLhnDl~~L~l~hp~-------s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~GeHs 247 (280)
T KOG2249|consen 177 EVLKLLKG--RILVGHALHNDLQALKLEHPR-------SMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVGEHS 247 (280)
T ss_pred HHHHHHhC--CEEeccccccHHHHHhhhCch-------hhhcccccCchHHHHhhccCCccHHHHHHHHhchhhhccccC
Confidence 44456654 456999999999998754442 335577655 1 2 467899999999999887555422
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009284 460 SNWEQRPLSQNQLEYAALDAVVLLQIFHHV 489 (538)
Q Consensus 460 S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L 489 (538)
..+||.++.+||...
T Consensus 248 ---------------SvEDA~AtM~LY~~v 262 (280)
T KOG2249|consen 248 ---------------SVEDARATMELYKRV 262 (280)
T ss_pred ---------------cHHHHHHHHHHHHHH
Confidence 458999999999986
No 30
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=94.60 E-value=0.26 Score=51.70 Aligned_cols=93 Identities=19% Similarity=0.134 Sum_probs=63.7
Q ss_pred hHHHHHHHhhcCCCceEEEeehHHhHHHHHHH---hCCccccccchhHhhHHHhhc-----CCCCCHHHHHHHHhCCCCC
Q 009284 383 VLDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLN 454 (538)
Q Consensus 383 ~ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLAl~-----~~s~gLd~LAer~LG~~L~ 454 (538)
++...|..++.+ ...||||+.+|+..|.+. +|+... ....+||+.... ..++.|+.|+++ +|++..
T Consensus 83 ev~~~l~~~l~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~---~~~~ldTl~lar~~~~~~~~~kL~~l~~~-~gi~~~ 156 (313)
T PRK06063 83 DIAGEVAELLRG--RTLVAHNVAFDYSFLAAEAERAGAELP---VDQVMCTVELARRLGLGLPNLRLETLAAH-WGVPQQ 156 (313)
T ss_pred HHHHHHHHHcCC--CEEEEeCHHHHHHHHHHHHHHcCCCCC---CCCEEehHHHHHHhccCCCCCCHHHHHHH-cCCCCC
Confidence 356677777765 367999999999988753 343110 134678887632 457899999986 465431
Q ss_pred cCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Q 009284 455 KTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTD 497 (538)
Q Consensus 455 K~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rLee~~ 497 (538)
+.+-|-.||.++.+|+..+..++.+.+
T Consensus 157 ----------------~~H~Al~DA~ata~l~~~ll~~~~~~~ 183 (313)
T PRK06063 157 ----------------RPHDALDDARVLAGILRPSLERARERD 183 (313)
T ss_pred ----------------CCCCcHHHHHHHHHHHHHHHHHHHhcC
Confidence 123478899999999998888876554
No 31
>PRK07883 hypothetical protein; Validated
Probab=94.59 E-value=0.25 Score=55.85 Aligned_cols=93 Identities=19% Similarity=0.093 Sum_probs=64.9
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHH---hCCccccccchhHhhHHHhh----c---CCCCCHHHHHHHHhCCCC
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVF----K---EPKGGLSGLAEKILGAGL 453 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLAl----~---~~s~gLd~LAer~LG~~L 453 (538)
++..|..++.+ ...||||..+|+..|... +|+... ...++||+... . ..+++|++|+++ +|.+.
T Consensus 85 vl~~f~~fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~---~~~~iDTl~lar~l~~~~~~~~~~L~~L~~~-~gi~~ 158 (557)
T PRK07883 85 VLPAFLEFARG--AVLVAHNAPFDIGFLRAAAARCGYPWP---GPPVLCTVRLARRVLPRDEAPNVRLSTLARL-FGATT 158 (557)
T ss_pred HHHHHHHHhcC--CEEEEeCcHHHHHHHHHHHHHcCCCCC---CCCcEecHHHHHHhcccCCCCCCCHHHHHHH-CCccc
Confidence 45566777765 467899999999988642 344110 13467887652 1 357899999974 57654
Q ss_pred CcCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCC
Q 009284 454 NKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTDV 498 (538)
Q Consensus 454 ~K~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rLee~~~ 498 (538)
. ..+-|..||.++.+|+..+..++.+.+.
T Consensus 159 ~----------------~~H~Al~DA~ata~l~~~l~~~~~~~~~ 187 (557)
T PRK07883 159 T----------------PTHRALDDARATVDVLHGLIERLGNLGV 187 (557)
T ss_pred C----------------CCCCHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 2 0244889999999999999999976554
No 32
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=94.36 E-value=0.45 Score=47.68 Aligned_cols=79 Identities=18% Similarity=0.151 Sum_probs=52.5
Q ss_pred ceEEEeehHHhHHHHHHH---hCCccccccchhHhhHHHhh---c---CCCCCHHHHHHHHhCCCCCcCcccccCCCCCC
Q 009284 397 ILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVF---K---EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPL 467 (538)
Q Consensus 397 i~KVGhnlK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLAl---~---~~s~gLd~LAer~LG~~L~K~e~~S~W~~rpL 467 (538)
...||||..+|+..|.+. +|.... ....++|++... . ..+++|++|++. +|.+...
T Consensus 94 ~~lVahNa~FD~~fL~~~~~r~~~~~~--~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~-~gi~~~~------------ 158 (232)
T PRK07942 94 VPVVVFNAPYDLTVLDRELRRHGLPSL--VPGPVIDPYVIDKAVDRYRKGKRTLTALCEH-YGVRLDN------------ 158 (232)
T ss_pred CEEEEeCcHhhHHHHHHHHHHcCCCCc--cCCcEeeHHHHHhhhhcccCCCCCHHHHHHH-cCCCCCC------------
Confidence 456999999999888643 343100 013467877652 1 246889999987 4764421
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhccC
Q 009284 468 SQNQLEYAALDAVVLLQIFHHVRSCSQ 494 (538)
Q Consensus 468 t~~Q~~YAAeDA~vlL~L~~~L~~rLe 494 (538)
.+-|..||.++.+|+..+..+..
T Consensus 159 ----aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 159 ----AHEATADALAAARVAWALARRFP 181 (232)
T ss_pred ----CCChHHHHHHHHHHHHHHHHHHH
Confidence 23388999999999999876654
No 33
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=94.33 E-value=0.8 Score=46.50 Aligned_cols=91 Identities=16% Similarity=0.201 Sum_probs=59.7
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHH---hCCccccccchhHhhHHHhhc----CCCCCHHHHHHHHhCCCCCcC
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK----EPKGGLSGLAEKILGAGLNKT 456 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLAl~----~~s~gLd~LAer~LG~~L~K~ 456 (538)
+...+..++.+. ...||||+.+|+..|... +|+.... ....++||+-... ..+++|+.|++.+ |.+...
T Consensus 77 v~~~~~~fl~~~-~~lvghn~~FD~~~L~~~~~r~g~~~~~-~~~~~iDtl~lar~~~~~~~~~L~~l~~~~-g~~~~~- 152 (250)
T PRK06310 77 VFPQIKGFFKEG-DYIVGHSVGFDLQVLSQESERIGETFLS-KHYYIIDTLRLAKEYGDSPNNSLEALAVHF-NVPYDG- 152 (250)
T ss_pred HHHHHHHHhCCC-CEEEEECHHHHHHHHHHHHHHcCCCccc-cCCcEEehHHHHHhcccCCCCCHHHHHHHC-CCCCCC-
Confidence 455666677653 467999999999988653 2331100 0134678876532 3468999999875 654321
Q ss_pred cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhcc
Q 009284 457 RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCS 493 (538)
Q Consensus 457 e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rL 493 (538)
.+-|..||.++..|+..+..+.
T Consensus 153 ---------------aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 153 ---------------NHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred ---------------CcChHHHHHHHHHHHHHHHHhc
Confidence 2348899999999999887665
No 34
>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=94.12 E-value=1.9 Score=40.17 Aligned_cols=89 Identities=16% Similarity=0.194 Sum_probs=57.0
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHH---hCCccccccchhHhhHHHhh----cCCCCCHHHHHHHHhCCCCCcC
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVF----KEPKGGLSGLAEKILGAGLNKT 456 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLAl----~~~s~gLd~LAer~LG~~L~K~ 456 (538)
+...|.+++.+. ..||||..+|+..|.+. +|....+.....++||+... ...+++|+.+++++ |.+...
T Consensus 71 v~~~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~~~~L~~l~~~~-~i~~~~- 146 (167)
T cd06131 71 IADEFLDFIRGA--ELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRF-GIDNSH- 146 (167)
T ss_pred HHHHHHHHHCCC--eEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCCCCCHHHHHHHC-CCCCCC-
Confidence 456677777653 35899999999888652 23211000124578998652 23578999999985 654321
Q ss_pred cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009284 457 RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHV 489 (538)
Q Consensus 457 e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L 489 (538)
.+.+-|..||..+.+|+..|
T Consensus 147 -------------~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 147 -------------RTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred -------------CCCCChHHHHHHHHHHHHHh
Confidence 01244889999999988765
No 35
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=93.88 E-value=0.77 Score=46.94 Aligned_cols=90 Identities=21% Similarity=0.173 Sum_probs=61.0
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHH---hCCccccccchhHhhHHHh----hcCCCCCHHHHHHHHhCCCCCcC
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNV----FKEPKGGLSGLAEKILGAGLNKT 456 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLA----l~~~s~gLd~LAer~LG~~L~K~ 456 (538)
++..|..++.+. ..||||+.+|...|.+. +|.... ....+||+-. +...+++|+.|++. +|.+..
T Consensus 137 vl~~f~~fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~~---~~~~ldtl~la~~~~~~~~~~L~~L~~~-lgi~~~-- 208 (257)
T PRK08517 137 VLEEFRLFLGDS--VFVAHNVNFDYNFISRSLEEIGLGPL---LNRKLCTIDLAKRTIESPRYGLSFLKEL-LGIEIE-- 208 (257)
T ss_pred HHHHHHHHHCCC--eEEEECHHHHHHHHHHHHHHcCCCCC---CCCcEehHHHHHHHccCCCCCHHHHHHH-cCcCCC--
Confidence 666777788753 57899999999888642 343111 1335566543 23467999999885 575432
Q ss_pred cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 009284 457 RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQP 495 (538)
Q Consensus 457 e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rLee 495 (538)
+.+-|-.||.++.+|+..+..++..
T Consensus 209 --------------~~HrAl~DA~ata~ll~~ll~~~~~ 233 (257)
T PRK08517 209 --------------VHHRAYADALAAYEIFKICLLNLPS 233 (257)
T ss_pred --------------CCCChHHHHHHHHHHHHHHHHHhHH
Confidence 1234788999999999999887743
No 36
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=93.88 E-value=1.2 Score=45.05 Aligned_cols=94 Identities=16% Similarity=0.207 Sum_probs=59.6
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHH---hCC-ccccccchhHhhHHHhh----cCCCCCHHHHHHHHhCCCCCc
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGE-LECFKHYEMLLDIQNVF----KEPKGGLSGLAEKILGAGLNK 455 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~---~Gi-l~~~~~~~~ifDtmLAl----~~~s~gLd~LAer~LG~~L~K 455 (538)
+...|..++.+. ..|+||..+|+..|.+. +|. ...+.....++||+... ...+++|+.|+++| |++..
T Consensus 76 v~~~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~aL~~~~-gi~~~- 151 (240)
T PRK05711 76 VADEFLDFIRGA--ELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRY-GIDNS- 151 (240)
T ss_pred HHHHHHHHhCCC--EEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCCCCCHHHHHHHC-CCCCC-
Confidence 455566666653 46899999999888642 332 11000013477887663 24578999999876 64321
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccC
Q 009284 456 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQ 494 (538)
Q Consensus 456 ~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rLe 494 (538)
.|. .+-|-.||.++.++|..|.....
T Consensus 152 --------~r~-----~H~AL~DA~~~A~v~~~l~~~~~ 177 (240)
T PRK05711 152 --------HRT-----LHGALLDAEILAEVYLAMTGGQT 177 (240)
T ss_pred --------CCC-----CCCHHHHHHHHHHHHHHHHCccc
Confidence 111 23388999999999999876643
No 37
>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=93.78 E-value=1.5 Score=43.24 Aligned_cols=97 Identities=13% Similarity=0.125 Sum_probs=61.0
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHHhCCccc-cccchhHhhHHHh----hc---CCCCCHHHHHHHHhCCCCCc
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELEC-FKHYEMLLDIQNV----FK---EPKGGLSGLAEKILGAGLNK 455 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~Gil~~-~~~~~~ifDtmLA----l~---~~s~gLd~LAer~LG~~L~K 455 (538)
+...|..++.+ ...||||+.+|+..|.+.+.-... ......++|++.. .. ..+++|..+++++ |.+...
T Consensus 77 v~~~~~~~~~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~-gl~~~~ 153 (217)
T TIGR00573 77 IAEDFADYIRG--AELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRY-EITNSH 153 (217)
T ss_pred HHHHHHHHhCC--CEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHHHc-CCCCCC
Confidence 55666777755 357899999999998764321000 0001345576543 11 3467899999875 643210
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Q 009284 456 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTD 497 (538)
Q Consensus 456 ~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rLee~~ 497 (538)
. ..+-|-.||.++.+|+..+..+....+
T Consensus 154 -~-------------~~H~Al~DA~~ta~l~~~l~~~~~~~~ 181 (217)
T TIGR00573 154 -R-------------ALHGALADAFILAKLYLVMTGKQTKYG 181 (217)
T ss_pred -c-------------ccCCHHHHHHHHHHHHHHHHhcchhhc
Confidence 0 123388999999999999988875544
No 38
>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=93.72 E-value=1.8 Score=43.26 Aligned_cols=95 Identities=15% Similarity=0.205 Sum_probs=61.8
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHH---hCC-ccccccchhHhhHHHhh----cCCCCCHHHHHHHHhCCCCCc
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGE-LECFKHYEMLLDIQNVF----KEPKGGLSGLAEKILGAGLNK 455 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~---~Gi-l~~~~~~~~ifDtmLAl----~~~s~gLd~LAer~LG~~L~K 455 (538)
+...|..++.+. ..|+||..+|+..|... +|. ...+.....++||+.+. ...+++|+.|+++| |++...
T Consensus 72 v~~~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~L~~~~-gi~~~~ 148 (225)
T TIGR01406 72 IADEFLDFIGGS--ELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRF-KVDNSH 148 (225)
T ss_pred HHHHHHHHhCCC--EEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCCCCCHHHHHHhc-CCCCCC
Confidence 455666777653 45899999999888642 341 01010114578988763 24578999999986 543210
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 009284 456 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQP 495 (538)
Q Consensus 456 ~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rLee 495 (538)
+ +.+-|-.||.++.+||..|....+.
T Consensus 149 ---------r-----~~H~Al~DA~~~a~v~~~l~~~~~~ 174 (225)
T TIGR01406 149 ---------R-----TLHGALLDAHLLAEVYLALTGGQES 174 (225)
T ss_pred ---------C-----CCcCHHHHHHHHHHHHHHHHcCCcc
Confidence 0 1233889999999999999766544
No 39
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=93.43 E-value=1 Score=55.25 Aligned_cols=94 Identities=15% Similarity=0.186 Sum_probs=67.3
Q ss_pred hHHHHHHHhhcCCCceEEEeehHHhHHHHHHH---hCCccccccchhHhhHHHhhc-----CCCCCHHHHHHHHhCCCCC
Q 009284 383 VLDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLN 454 (538)
Q Consensus 383 ~ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLAl~-----~~s~gLd~LAer~LG~~L~ 454 (538)
+++..|..++.+ ...||||..+|+..|.+. +|... + ...++||+.... ..+++|+.|++++ |.+..
T Consensus 259 evl~~f~~fl~~--~iLVaHNa~FD~~fL~~~~~r~g~~~-~--~~~~IDTl~lar~l~p~~k~~kL~~Lak~l-gi~~~ 332 (1213)
T TIGR01405 259 EVLEKFKEFFKD--SILVAHNASFDIGFLNTNFEKVGLEP-L--ENPVIDTLELARALNPEYKSHRLGNICKKL-GVDLD 332 (1213)
T ss_pred HHHHHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCc-c--CCCEeEHHHHHHHHhccCCCCCHHHHHHHc-CCCCC
Confidence 366777778865 356899999999988753 34411 1 145678877631 4689999999874 76542
Q ss_pred cCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCC
Q 009284 455 KTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTDV 498 (538)
Q Consensus 455 K~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rLee~~~ 498 (538)
. .+.|-.||.++.+|+..+.+++++.+.
T Consensus 333 ~----------------~HrAl~DA~aTa~I~~~ll~~l~~~~i 360 (1213)
T TIGR01405 333 D----------------HHRADYDAEATAKVFKVMVEQLKEKGI 360 (1213)
T ss_pred C----------------CcCHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 1 255889999999999999988876553
No 40
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=93.29 E-value=1.8 Score=39.84 Aligned_cols=90 Identities=19% Similarity=0.164 Sum_probs=59.8
Q ss_pred HHHHHHHhhcCCCceEEEeeh-HHhHHHHHHHh---CCccccccchhHhhHHHhhc----CCCCCHHHHHHHHhCCCCCc
Q 009284 384 LDSCLTRILQSPGILKLGYNF-QCDIKQLAHSY---GELECFKHYEMLLDIQNVFK----EPKGGLSGLAEKILGAGLNK 455 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnl-K~Dl~vLa~~~---Gil~~~~~~~~ifDtmLAl~----~~s~gLd~LAer~LG~~L~K 455 (538)
+...|..++.+. ..++||. ++|+..|.+.+ |+... ....++|++.... ..+++|+++++.+ |.+..
T Consensus 70 ~~~~~~~~l~~~--~~v~~n~~~fD~~~L~~~~~~~~~~~~--~~~~~iD~~~~~~~~~~~~~~~L~~l~~~~-~~~~~- 143 (169)
T smart00479 70 VLEELLEFLKGK--ILVAGNALNFDLRFLKLEHPRLGIKDP--PKNPVIDTLKLARALNPGRKYSLKKLAERL-GLEVI- 143 (169)
T ss_pred HHHHHHHHhcCC--EEEEeCCHHHhHHHHHHHHHHhCCCCC--cCCCeeEHHHHHHHHCCCCCCCHHHHHHHC-CCCCC-
Confidence 566777888664 3567777 99999887632 32100 0133678876632 3478999999876 43321
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhcc
Q 009284 456 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCS 493 (538)
Q Consensus 456 ~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rL 493 (538)
+. .+.|..||..+.+|+..+.++.
T Consensus 144 --~~------------~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 144 --GR------------AHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred --CC------------CcCcHHHHHHHHHHHHHHHHHh
Confidence 00 2558899999999999987765
No 41
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=93.28 E-value=1.6 Score=39.93 Aligned_cols=81 Identities=25% Similarity=0.171 Sum_probs=54.8
Q ss_pred hHHHHHHHhhcCCCceEEEeehHHhHHHHHHH---hCCccccccchhHhhHHHhhc-----CCCCCHHHHHHHHhCCCCC
Q 009284 383 VLDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLN 454 (538)
Q Consensus 383 ~ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLAl~-----~~s~gLd~LAer~LG~~L~ 454 (538)
++...|..++++ ...||||..+|+..|.+. +|+... ...++|++...+ ..+++|+.+++. +|.+..
T Consensus 66 ~v~~~l~~~l~~--~~lv~hn~~fD~~~l~~~~~~~g~~~~---~~~~idt~~~~~~~~~~~~~~~L~~l~~~-~g~~~~ 139 (156)
T cd06130 66 EVWPEIKPFLGG--SLVVAHNASFDRSVLRAALEAYGLPPP---PYQYLCTVRLARRVWPLLPNHKLNTVAEH-LGIELN 139 (156)
T ss_pred HHHHHHHHHhCC--CEEEEeChHHhHHHHHHHHHHcCCCCC---CCCEEEHHHHHHHHhccCCCCCHHHHHHH-cCCCcc
Confidence 356677788876 467999999999988642 354211 245778887632 357899999986 465432
Q ss_pred cCcccccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009284 455 KTRRNSNWEQRPLSQNQLEYAALDAVVLLQIF 486 (538)
Q Consensus 455 K~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~ 486 (538)
.+-|..||..+.+|+
T Consensus 140 -----------------~H~Al~Da~~ta~l~ 154 (156)
T cd06130 140 -----------------HHDALEDARACAEIL 154 (156)
T ss_pred -----------------CcCchHHHHHHHHHH
Confidence 133778888888775
No 42
>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=93.17 E-value=1.4 Score=42.45 Aligned_cols=100 Identities=27% Similarity=0.459 Sum_probs=61.1
Q ss_pred HHHHHHHhhcC--CCceEEEeeh-HHhHHHHHH---HhCCccc---ccc----------------chhHhhHHHhhc---
Q 009284 384 LDSCLTRILQS--PGILKLGYNF-QCDIKQLAH---SYGELEC---FKH----------------YEMLLDIQNVFK--- 435 (538)
Q Consensus 384 ll~~Lk~lLed--~~i~KVGhnl-K~Dl~vLa~---~~Gil~~---~~~----------------~~~ifDtmLAl~--- 435 (538)
++..+..++++ |. ..+|||. .+|+..|.. .+|+... .+. ....+|+.....
T Consensus 66 lL~~f~~~i~~~dpd-iivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~ 144 (199)
T cd05160 66 LLKRFFDIIREYDPD-ILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDF 144 (199)
T ss_pred HHHHHHHHHHhcCCC-EEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhc
Confidence 55555666654 44 4799999 789877643 2454210 000 012568877642
Q ss_pred -CCCCCHHHHHHHHhCCCCCc--Cccccc--CCCCCCCHHHHHHHHHHHHHHHHHH
Q 009284 436 -EPKGGLSGLAEKILGAGLNK--TRRNSN--WEQRPLSQNQLEYAALDAVVLLQIF 486 (538)
Q Consensus 436 -~~s~gLd~LAer~LG~~L~K--~e~~S~--W~~rpLt~~Q~~YAAeDA~vlL~L~ 486 (538)
..+++|+.+++.+||.+-.. ++.+.. |.. . ...-++|.-.||..+++|+
T Consensus 145 ~l~sy~L~~v~~~~l~~~k~~~~~~~~~~~~~~~-~-~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 145 KLKSYTLDAVAEELLGEGKEKVDGEIIEDAEWEE-D-PERLIEYNLKDAELTLQIL 198 (199)
T ss_pred CcccCCHHHHHHHHhCCCCCcCCHHHHhhccCcc-h-HHHHHHHHHHHHHHHHHhh
Confidence 46899999999999864321 122222 221 2 2345899999999999885
No 43
>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=93.13 E-value=0.15 Score=49.37 Aligned_cols=79 Identities=20% Similarity=0.270 Sum_probs=55.8
Q ss_pred HHHHHhhcCCCceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHhhc---CCCCCHHHHHHHHhCCCCCcCcccccC
Q 009284 386 SCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFK---EPKGGLSGLAEKILGAGLNKTRRNSNW 462 (538)
Q Consensus 386 ~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLAl~---~~s~gLd~LAer~LG~~L~K~e~~S~W 462 (538)
..|..++. +....|||++..|+++|.-.++- ..+.||.+.+. .+..+|..|+.++||..+..+.
T Consensus 93 ~~l~~li~-~~tILVGHsL~nDL~aL~l~hp~-------~~viDTa~l~~~~~~r~~sLk~La~~~L~~~IQ~~~----- 159 (174)
T cd06143 93 LKLRLLVD-LGCIFVGHGLAKDFRVINIQVPK-------EQVIDTVELFHLPGQRKLSLRFLAWYLLGEKIQSET----- 159 (174)
T ss_pred HHHHHHcC-CCCEEEeccchhHHHHhcCcCCC-------cceEEcHHhccCCCCCChhHHHHHHHHcCCcccCCC-----
Confidence 34555553 44577999999999998642221 34569987753 3468999999999998764221
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHH
Q 009284 463 EQRPLSQNQLEYAALDAVVLLQIFH 487 (538)
Q Consensus 463 ~~rpLt~~Q~~YAAeDA~vlL~L~~ 487 (538)
+-..+||.++++||+
T Consensus 160 ----------HdSvEDArAam~Ly~ 174 (174)
T cd06143 160 ----------HDSIEDARTALKLYR 174 (174)
T ss_pred ----------cCcHHHHHHHHHHhC
Confidence 225689999999983
No 44
>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=93.10 E-value=0.29 Score=45.66 Aligned_cols=80 Identities=21% Similarity=0.294 Sum_probs=54.8
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHhhc-----CCCCCHHHHHHHHhCCCCCcCcc
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLNKTRR 458 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLAl~-----~~s~gLd~LAer~LG~~L~K~e~ 458 (538)
+...+.+++.. ....||||+++|+..|.. .. ..++||..... ..+++|+.||++|+|..+....+
T Consensus 65 v~~~~~~fl~~-~~vlVgHn~~fD~~fL~~-~~--------~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~ 134 (150)
T cd06145 65 VQKKLLSLISP-DTILVGHSLENDLKALKL-IH--------PRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEG 134 (150)
T ss_pred HHHHHHHHhCC-CCEEEEcChHHHHHHhhc-cC--------CCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCC
Confidence 55566777752 346799999999999975 11 23568876632 24689999999998854421111
Q ss_pred cccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009284 459 NSNWEQRPLSQNQLEYAALDAVVLLQIF 486 (538)
Q Consensus 459 ~S~W~~rpLt~~Q~~YAAeDA~vlL~L~ 486 (538)
.+-|..||.++.+|+
T Consensus 135 -------------~H~Al~DA~~t~~l~ 149 (150)
T cd06145 135 -------------GHDSVEDARAALELV 149 (150)
T ss_pred -------------CCCcHHHHHHHHHHh
Confidence 133778999998876
No 45
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=92.72 E-value=1.8 Score=51.24 Aligned_cols=89 Identities=18% Similarity=0.157 Sum_probs=63.1
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHHh---CCccccccchhHhhHHHhh----c-CCCCCHHHHHHHHhCCCCCc
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHSY---GELECFKHYEMLLDIQNVF----K-EPKGGLSGLAEKILGAGLNK 455 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~---Gil~~~~~~~~ifDtmLAl----~-~~s~gLd~LAer~LG~~L~K 455 (538)
+...+..++.+ ...||||+.+|+..|.+.+ |... ..+.+||+... . ..+++|++|+++ +|.+..
T Consensus 76 v~~~~~~~l~~--~~lVaHN~~FD~~fL~~~~~~~g~~~----~~~~iDT~~la~~~~p~~~~~~L~~L~~~-lgl~~~- 147 (820)
T PRK07246 76 VARHIYDLIED--CIFVAHNVKFDANLLAEALFLEGYEL----RTPRVDTVELAQVFFPTLEKYSLSHLSRE-LNIDLA- 147 (820)
T ss_pred HHHHHHHHhCC--CEEEEECcHHHHHHHHHHHHHcCCCC----CCCceeHHHHHHHHhCCCCCCCHHHHHHH-cCCCCC-
Confidence 56667777765 4579999999999987532 3311 14567887652 2 357999999986 576532
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 009284 456 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQP 495 (538)
Q Consensus 456 ~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rLee 495 (538)
. .+-|..||.++.+|+..|..++..
T Consensus 148 --~-------------~H~Al~DA~ata~L~~~l~~~l~~ 172 (820)
T PRK07246 148 --D-------------AHTAIADARATAELFLKLLQKIES 172 (820)
T ss_pred --C-------------CCCHHHHHHHHHHHHHHHHHHHhh
Confidence 1 233889999999999999888765
No 46
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=92.53 E-value=1.6 Score=42.46 Aligned_cols=84 Identities=15% Similarity=0.170 Sum_probs=55.0
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHH----hCCccccccchhHhhHHHhh--------c--CCCCCHHHHHHHHh
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS----YGELECFKHYEMLLDIQNVF--------K--EPKGGLSGLAEKIL 449 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~----~Gil~~~~~~~~ifDtmLAl--------~--~~s~gLd~LAer~L 449 (538)
+...|..++.+ ...+|||..+|+..|.+. +|... ....+|++... . ..+++|+++++++
T Consensus 101 vl~~~~~~i~~--~~lv~hn~~fD~~fL~~~~~~~~~~~~----~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~- 173 (202)
T PRK09145 101 ALRQLLAFIGN--RPLVGYYLEFDVAMLNRYVRPLLGIPL----PNPLIEVSALYYDKKERHLPDAYIDLRFDAILKHL- 173 (202)
T ss_pred HHHHHHHHHcC--CeEEEeCHHHHHHHHHHHHHHhcCCCC----CCCeeeHHHHHHHHhhccCCCcccCCCHHHHHHHc-
Confidence 56677777765 357999999999988653 23211 13356775431 1 2358999999775
Q ss_pred CCCCCcCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009284 450 GAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVR 490 (538)
Q Consensus 450 G~~L~K~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~ 490 (538)
|.+.. + .+-|..||.++.+|+..|.
T Consensus 174 gi~~~---~-------------~H~Al~DA~ata~l~~~l~ 198 (202)
T PRK09145 174 DLPVL---G-------------RHDALNDAIMAALIFLRLR 198 (202)
T ss_pred CCCCC---C-------------CCCcHHHHHHHHHHHHHHH
Confidence 65432 1 1337889999999998874
No 47
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=92.38 E-value=1.4 Score=44.61 Aligned_cols=87 Identities=13% Similarity=0.015 Sum_probs=57.1
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHHh----CCccccccchhHhhHHHhhc----C--------------CCCCH
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHSY----GELECFKHYEMLLDIQNVFK----E--------------PKGGL 441 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~----Gil~~~~~~~~ifDtmLAl~----~--------------~s~gL 441 (538)
++..|..++.+ ...||||..+|...|.+.+ +... ...++||+.... . .++.|
T Consensus 119 vl~~l~~~~~~--~~lVaHna~FD~~fL~~~l~~~~~~~~----~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L 192 (239)
T PRK09146 119 ILDELLEALAG--KVVVVHYRRIERDFLDQALRNRIGEGI----EFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRL 192 (239)
T ss_pred HHHHHHHHhCC--CEEEEECHHHHHHHHHHHHHHhcCCCC----CCceechHHHHHHHcccccccccchhccCCCCCCCH
Confidence 44555555544 3578999999999886532 2211 145678887621 1 35678
Q ss_pred HHHHHHHhCCCCCcCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhcc
Q 009284 442 SGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCS 493 (538)
Q Consensus 442 d~LAer~LG~~L~K~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rL 493 (538)
++++.+| |++.. +.+-|..||.++.+|+..+..+.
T Consensus 193 ~~l~~~~-gl~~~----------------~~H~Al~DA~ata~l~~~~~~~~ 227 (239)
T PRK09146 193 ADSRLRY-GLPAY----------------SPHHALTDAIATAELLQAQIAHH 227 (239)
T ss_pred HHHHHHc-CCCCC----------------CCCCcHHHHHHHHHHHHHHHHHH
Confidence 8888874 65432 12348899999999999887776
No 48
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=92.22 E-value=1.7 Score=45.79 Aligned_cols=87 Identities=20% Similarity=0.223 Sum_probs=59.1
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHH---hCCccccccchhHhhHHHhh----c-CCCCCHHHHHHHHhCCCCCc
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVF----K-EPKGGLSGLAEKILGAGLNK 455 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLAl----~-~~s~gLd~LAer~LG~~L~K 455 (538)
++..|..++.+. ..||||..+|+..|.+. +|... .....+||+... . ..+++|+.|++. +|++.
T Consensus 78 vl~~f~~fl~~~--~lVaHNa~FD~~fL~~~~~~~gl~~---~~~~~iDtl~la~~~~~~~~~~kL~~L~~~-lgi~~-- 149 (313)
T PRK06807 78 VLPLFLAFLHTN--VIVAHNASFDMRFLKSNVNMLGLPE---PKNKVIDTVFLAKKYMKHAPNHKLETLKRM-LGIRL-- 149 (313)
T ss_pred HHHHHHHHHcCC--eEEEEcHHHHHHHHHHHHHHcCCCC---CCCCEeeHHHHHHHHhCCCCCCCHHHHHHH-cCCCC--
Confidence 555666666554 35999999999988753 34311 024567887762 2 357899999865 56543
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhcc
Q 009284 456 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCS 493 (538)
Q Consensus 456 ~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rL 493 (538)
+.+-|-.||.++.+|+..+..+.
T Consensus 150 ---------------~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 150 ---------------SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred ---------------CCcChHHHHHHHHHHHHHHHHhh
Confidence 12347789999999999887766
No 49
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=92.10 E-value=1.2 Score=39.71 Aligned_cols=83 Identities=16% Similarity=0.105 Sum_probs=53.6
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHHhCCc--cccccchhHhhHHHhhc-----CCCCCHHHHHHHHhCCCCCcC
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGEL--ECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLNKT 456 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~Gil--~~~~~~~~ifDtmLAl~-----~~s~gLd~LAer~LG~~L~K~ 456 (538)
+...+..+++. ...+|||..+|..+|.+.+... .. ....++|++.... ...+++..+..+++|....
T Consensus 69 ~~~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~--~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~~-- 142 (159)
T cd06127 69 VLPEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPP--LPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLE-- 142 (159)
T ss_pred HHHHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCC--CCCCeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCCC--
Confidence 56677778876 5689999999999887633210 00 0245779987732 3467788774444553221
Q ss_pred cccccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009284 457 RRNSNWEQRPLSQNQLEYAALDAVVLLQIF 486 (538)
Q Consensus 457 e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~ 486 (538)
+.+-|..||..+.+|+
T Consensus 143 --------------~~H~Al~Da~~t~~l~ 158 (159)
T cd06127 143 --------------GAHRALADALATAELL 158 (159)
T ss_pred --------------CCCCcHHHHHHHHHHh
Confidence 1345888999988875
No 50
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=91.99 E-value=3.4 Score=41.30 Aligned_cols=89 Identities=18% Similarity=0.060 Sum_probs=58.2
Q ss_pred HHHHHHHhhcCCCceEEEee-hHHhHHHHHHH---hCCccccccchhHhhHHHhhc-----CCCCCHHHHHHHHhCCCCC
Q 009284 384 LDSCLTRILQSPGILKLGYN-FQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLN 454 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhn-lK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLAl~-----~~s~gLd~LAer~LG~~L~ 454 (538)
+...+..++.+ ....|||| ..+|+..|.+. +|+... ...++||+.... ..+++|+.++..| |.+..
T Consensus 69 v~~~~~~fi~~-~~~lVaHN~~~FD~~~L~~e~~r~g~~~~---~~~~iDt~~l~~~~~~~~~~~~L~~l~~~~-~~~~~ 143 (232)
T PRK06309 69 AYQKFIEFCGT-DNILVAHNNDAFDFPLLRKECRRHGLEPP---TLRTIDSLKWAQKYRPDLPKHNLQYLRQVY-GFEEN 143 (232)
T ss_pred HHHHHHHHHcC-CCEEEEeCCHHHHHHHHHHHHHHcCCCCC---CCcEEeHHHHHHHHcCCCCCCCHHHHHHHc-CCCCC
Confidence 34455556643 34679999 58999988653 343110 134678876632 2468999998776 54322
Q ss_pred cCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhcc
Q 009284 455 KTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCS 493 (538)
Q Consensus 455 K~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rL 493 (538)
..+-|..||.++.+|+..+..++
T Consensus 144 ----------------~aH~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 144 ----------------QAHRALDDVITLHRVFSALVGDL 166 (232)
T ss_pred ----------------CCCCcHHHHHHHHHHHHHHHHHH
Confidence 12348899999999999987766
No 51
>PRK05168 ribonuclease T; Provisional
Probab=91.82 E-value=3.7 Score=40.48 Aligned_cols=87 Identities=13% Similarity=0.054 Sum_probs=55.8
Q ss_pred CceEEEeehHHhHHHHHHH---hCCccccccchhHhhHHHhhc--CCCCCHHHHHHHHhCCCCCcCcccccCCCCCCCHH
Q 009284 396 GILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK--EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQN 470 (538)
Q Consensus 396 ~i~KVGhnlK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLAl~--~~s~gLd~LAer~LG~~L~K~e~~S~W~~rpLt~~ 470 (538)
+...||||+.+|+..|.+. +|+....-....++||..... ...++|+.+++++ |.+....
T Consensus 114 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~~~~L~~l~~~~-gl~~~~~-------------- 178 (211)
T PRK05168 114 RAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALGQTVLAKACQAA-GIEFDNK-------------- 178 (211)
T ss_pred CceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcCCCCHHHHHHHC-CCCCCCC--------------
Confidence 4678999999999888652 333100000013578876642 3346899998874 6543211
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccCCCC
Q 009284 471 QLEYAALDAVVLLQIFHHVRSCSQPTD 497 (538)
Q Consensus 471 Q~~YAAeDA~vlL~L~~~L~~rLee~~ 497 (538)
..+-|..||.++.+|+..+..++.+.+
T Consensus 179 ~~H~Al~DA~ata~l~~~l~~~~~~~~ 205 (211)
T PRK05168 179 EAHSALYDTEKTAELFCEIVNRWKRLG 205 (211)
T ss_pred CCCChHHHHHHHHHHHHHHHHHHHHcc
Confidence 123488999999999999988886544
No 52
>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=91.74 E-value=2.5 Score=50.17 Aligned_cols=90 Identities=19% Similarity=0.138 Sum_probs=62.1
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHH---hCCccccccchhHhhHHHhh----c-CCCCCHHHHHHHHhCCCCCc
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVF----K-EPKGGLSGLAEKILGAGLNK 455 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLAl----~-~~s~gLd~LAer~LG~~L~K 455 (538)
+...|..++.+ ...||||+.+|+..|.+. +|.... ....+||+... . ..+++|++|++. +|.+...
T Consensus 70 v~~~l~~~l~~--~~~VahN~~fD~~fL~~~~~~~g~~~~---~~~~iDt~~l~~~~~p~~~~~~L~~l~~~-~gi~~~~ 143 (850)
T TIGR01407 70 VAQEIYDLLED--GIFVAHNVHFDLNFLAKALKDCGYEPL---PKPRIDTVELAQIFFPTEESYQLSELSEA-LGLTHEN 143 (850)
T ss_pred HHHHHHHHhCC--CEEEEeCcHHHHHHHHHHHHHcCCCCC---CCCeEeHHHHHHHhcCCCCCCCHHHHHHH-CCCCCCC
Confidence 56677778765 357999999999888652 343111 24567887652 2 457999999988 4654321
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 009284 456 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQP 495 (538)
Q Consensus 456 ~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rLee 495 (538)
.+-|..||.++.+|+..+..++.+
T Consensus 144 ----------------~H~Al~DA~ata~l~~~l~~~~~~ 167 (850)
T TIGR01407 144 ----------------PHRADSDAQATAELLLLLFEKMEK 167 (850)
T ss_pred ----------------CCChHHHHHHHHHHHHHHHHHHHh
Confidence 234788999999988888777754
No 53
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=89.98 E-value=4.6 Score=48.52 Aligned_cols=90 Identities=21% Similarity=0.189 Sum_probs=62.6
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHH---hCCccccccchhHhhHHHhh----c-CCCCCHHHHHHHHhCCCCCc
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVF----K-EPKGGLSGLAEKILGAGLNK 455 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLAl----~-~~s~gLd~LAer~LG~~L~K 455 (538)
+...|..++.+ ...||||+.+|+..|.+. +|.... ...++||+... . ..+++|++|++. +|.+..
T Consensus 74 v~~~l~~~l~~--~~~VaHN~~FD~~fL~~~~~~~g~~~~---~~~~iDt~~la~~~~p~~~~~~L~~l~~~-l~i~~~- 146 (928)
T PRK08074 74 VAPEIVELLEG--AYFVAHNVHFDLNFLNEELERAGYTEI---HCPKLDTVELARILLPTAESYKLRDLSEE-LGLEHD- 146 (928)
T ss_pred HHHHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCCC---CCCeeeHHHHHHHhcCCCCCCCHHHHHHh-CCCCCC-
Confidence 55677777765 457999999999988653 343111 14567886652 2 457899999987 465432
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 009284 456 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQP 495 (538)
Q Consensus 456 ~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rLee 495 (538)
+.+-|-.||.++.+|+..|..++.+
T Consensus 147 ---------------~~H~Al~DA~ata~l~~~l~~~~~~ 171 (928)
T PRK08074 147 ---------------QPHRADSDAEVTAELFLQLLNKLER 171 (928)
T ss_pred ---------------CCCChHHHHHHHHHHHHHHHHHHHh
Confidence 1233778999999999999888765
No 54
>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=89.39 E-value=4.3 Score=39.36 Aligned_cols=151 Identities=16% Similarity=0.161 Sum_probs=82.6
Q ss_pred CeEEEEeeeecCCccCCcCCceeEEEEEe--CCeEEEEEcCcc------cCCCchhHHHHHHHhhcC--CCceEEEeehH
Q 009284 336 KVVGIDCEWKPNYVKGCKMNKVSIMQIAS--DEMVFIFDLIKL------AEDVPDVLDSCLTRILQS--PGILKLGYNFQ 405 (538)
Q Consensus 336 ~~IgfDtE~~~l~~~~~~~~~VsLiQLAt--~~~a~~IdL~~l------~~~~p~~ll~~Lk~lLed--~~i~KVGhnlK 405 (538)
.+++||.|+.+..+ .|.+..-.+++|+. .+.-.++..... ......+++..+..++.. |.+ .+|||..
T Consensus 4 ~i~~fDIEt~~~~g-~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~F~~~i~~~dpdi-ivgyN~~ 81 (195)
T cd05780 4 KILSFDIEVLNHEG-EPNPEKDPIIMISFADEGGNKVITWKKFDLPFVEVVKTEKEMIKRFIEIVKEKDPDV-IYTYNGD 81 (195)
T ss_pred eEEEEEEEecCCCC-CCCCCCCcEEEEEEecCCCceEEEecCCCCCeEEEeCCHHHHHHHHHHHHHHcCCCE-EEecCCC
Confidence 57899999975321 11233334555553 221111111100 001122355566666655 654 6899976
Q ss_pred -HhHHHHHH---HhCCcccccc-------------------chhHhhHHHhhc----CCCCCHHHHHHHHhCCCCCc--C
Q 009284 406 -CDIKQLAH---SYGELECFKH-------------------YEMLLDIQNVFK----EPKGGLSGLAEKILGAGLNK--T 456 (538)
Q Consensus 406 -~Dl~vLa~---~~Gil~~~~~-------------------~~~ifDtmLAl~----~~s~gLd~LAer~LG~~L~K--~ 456 (538)
+|+..|.. .+|+...+.. -...+|++.... ..+++|+.+++++||.+... +
T Consensus 82 ~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~~l~sy~L~~v~~~~Lg~~k~d~~~ 161 (195)
T cd05780 82 NFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPG 161 (195)
T ss_pred CCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhCCCCcCcHHHHHHHHhCCCCCcCCH
Confidence 58766542 2454211100 012567776642 46899999999999975321 1
Q ss_pred ccccc-CCCCCCCHHHHHHHHHHHHHHHHHHHH
Q 009284 457 RRNSN-WEQRPLSQNQLEYAALDAVVLLQIFHH 488 (538)
Q Consensus 457 e~~S~-W~~rpLt~~Q~~YAAeDA~vlL~L~~~ 488 (538)
+++.. |...+-...-++|+-.||..+++|...
T Consensus 162 ~~i~~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~ 194 (195)
T cd05780 162 EEIAEAWDSGENLERLFRYSMEDAKYTYEIGKE 194 (195)
T ss_pred HHHHHHHhCCCchHHHHHHhHHHHHHHHHHHhh
Confidence 23332 333322344589999999999999765
No 55
>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=88.83 E-value=3.2 Score=39.71 Aligned_cols=86 Identities=19% Similarity=0.166 Sum_probs=53.4
Q ss_pred HHHHHHHhhcC--CCceEEEeeh-HHhHHHHHHH---hCCccccccchhHhhHHHhhcCCCCCHHHHHHHHhCCCCCcCc
Q 009284 384 LDSCLTRILQS--PGILKLGYNF-QCDIKQLAHS---YGELECFKHYEMLLDIQNVFKEPKGGLSGLAEKILGAGLNKTR 457 (538)
Q Consensus 384 ll~~Lk~lLed--~~i~KVGhnl-K~Dl~vLa~~---~Gil~~~~~~~~ifDtmLAl~~~s~gLd~LAer~LG~~L~K~e 457 (538)
+.+.|..++.. .....||||. .+|+..|.+. +|.... ....++||+........+|+.|+++++|.+..
T Consensus 84 ~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~--~~~~~iDtl~l~r~~~~~L~~l~~~~~~~~~~--- 158 (177)
T cd06136 84 TANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLP--DDILCVDSLPAFRELDQSLGSLYKRLFGQEPK--- 158 (177)
T ss_pred HHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCC--CCCEEEEeHHHHhhhHhhHHHHHHHHhCCCcc---
Confidence 34556666553 2357899998 7999988653 343110 01234688766431112899999988776543
Q ss_pred ccccCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009284 458 RNSNWEQRPLSQNQLEYAALDAVVLLQIFH 487 (538)
Q Consensus 458 ~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~ 487 (538)
..+-|..||.++.+++.
T Consensus 159 -------------~~H~A~~Da~at~~v~~ 175 (177)
T cd06136 159 -------------NSHTAEGDVLALLKCAL 175 (177)
T ss_pred -------------cccchHHHHHHHHHHHh
Confidence 12448899999887753
No 56
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=87.32 E-value=16 Score=39.58 Aligned_cols=100 Identities=10% Similarity=0.120 Sum_probs=57.6
Q ss_pred hHHHHHHHhhcCCCceEEEeehHHhHHHHHHHhCCc---c------------------------ccccchhHhhHHHhhc
Q 009284 383 VLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGEL---E------------------------CFKHYEMLLDIQNVFK 435 (538)
Q Consensus 383 ~ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~Gil---~------------------------~~~~~~~ifDtmLAl~ 435 (538)
+++..|.+++.+. ..|+||..+|+..|.+.+... . .......++||+-...
T Consensus 114 eVl~el~~fL~g~--vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LAR 191 (377)
T PRK05601 114 QILKPLDRLIDGR--TLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATAR 191 (377)
T ss_pred HHHHHHHHHhCCC--EEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHH
Confidence 3677778888754 579999999999876532100 0 0000134679866521
Q ss_pred -----CCCCCHHHHHHHHhCCCCCcCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009284 436 -----EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHV 489 (538)
Q Consensus 436 -----~~s~gLd~LAer~LG~~L~K~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L 489 (538)
..+|.|..||.+ +|++.+... -|. .+..-... ..+-+||.++-+|+..+
T Consensus 192 rl~p~l~~~rL~~La~~-lGi~~p~~~-A~~-~Ra~~p~~--~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 192 RQGVALDDIRIRGVAHT-LGLDAPAAE-ASV-ERAQVPHR--QLCREETLLVARLYFAL 245 (377)
T ss_pred HHcCCCCCCCHHHHHHH-hCCCCCchh-hhh-hhhcCChh--hhhhHHHHHHHHHHHHh
Confidence 357999999997 476653210 000 00001111 11235899998998876
No 57
>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=87.23 E-value=11 Score=36.50 Aligned_cols=148 Identities=17% Similarity=0.124 Sum_probs=77.4
Q ss_pred CeEEEEeeeecCCccCCcCCceeEEEEE--e-CCeEEEEEcCcccCCCchhHHHHHHHhhcCCCc-eEEEeehH-HhHHH
Q 009284 336 KVVGIDCEWKPNYVKGCKMNKVSIMQIA--S-DEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGI-LKLGYNFQ-CDIKQ 410 (538)
Q Consensus 336 ~~IgfDtE~~~l~~~~~~~~~VsLiQLA--t-~~~a~~IdL~~l~~~~p~~ll~~Lk~lLed~~i-~KVGhnlK-~Dl~v 410 (538)
.+++||.|+.+... .+.+..-.+++|+ . .+...++.-. .....+++..+-.++..-+. ..+|||.. +|+-.
T Consensus 4 ~~l~fDIEt~~~~g-fp~~~~d~Ii~Is~~~~~g~~~~~~~~---~~~E~~lL~~F~~~i~~~dPd~i~gyN~~~FDlpy 79 (188)
T cd05781 4 KTLAFDIEVYSKYG-TPNPRRDPIIVISLATSNGDVEFILAE---GLDDRKIIREFVKYVKEYDPDIIVGYNSNAFDWPY 79 (188)
T ss_pred eEEEEEEEecCCCC-CCCCCCCCEEEEEEEeCCCCEEEEEec---CCCHHHHHHHHHHHHHHcCCCEEEecCCCcCcHHH
Confidence 57899999974311 1123333455554 3 3333333211 11123455566666655332 35798854 46544
Q ss_pred HH---HHhCCcccccc-c----------------hhHhhHHHhhc----CCCCCHHHHHHHHhCCC-C-Cc----Ccccc
Q 009284 411 LA---HSYGELECFKH-Y----------------EMLLDIQNVFK----EPKGGLSGLAEKILGAG-L-NK----TRRNS 460 (538)
Q Consensus 411 La---~~~Gil~~~~~-~----------------~~ifDtmLAl~----~~s~gLd~LAer~LG~~-L-~K----~e~~S 460 (538)
|. +.+|+...... . ...+|+...+. ..+++|+.+|+ +||.. - .+ +.++.
T Consensus 80 l~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~l~~y~L~~Va~-~Lg~~k~~~k~~~~~~~i~ 158 (188)
T cd05781 80 LVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPEVKVKTLENVAE-YLGVMKKSERVLIEWYRIY 158 (188)
T ss_pred HHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCCCCCCCHHHHHH-HHCCCccccccCCCHHHHH
Confidence 42 22565211000 0 01556666632 45799999997 58863 1 11 11221
Q ss_pred -cCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q 009284 461 -NWEQRPLSQNQLEYAALDAVVLLQIFHH 488 (538)
Q Consensus 461 -~W~~rpLt~~Q~~YAAeDA~vlL~L~~~ 488 (538)
.|....-...-.+|...|+..++.|+..
T Consensus 159 ~~~~~~~~~~~l~~Y~~~D~~~t~~l~~~ 187 (188)
T cd05781 159 EYWDDEKKRDILLKYNRDDARSTYGLAEK 187 (188)
T ss_pred HHHcCcccHHHHHHHHHHHHHHHHHHHhh
Confidence 3433212355689999999999999875
No 58
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=86.91 E-value=19 Score=35.99 Aligned_cols=76 Identities=11% Similarity=-0.016 Sum_probs=51.7
Q ss_pred ceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHhh----cCCCCCHHHHHHHHhCCCCCcCcccccCCCCCCCHHHH
Q 009284 397 ILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF----KEPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQL 472 (538)
Q Consensus 397 i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLAl----~~~s~gLd~LAer~LG~~L~K~e~~S~W~~rpLt~~Q~ 472 (538)
...||||+.+|...|.. .+ ..++||+... ...++++..|++. +|......+. ...
T Consensus 75 ~~lVaHNa~FD~~~L~~-~~--------~~~idTl~lar~l~p~~~~~l~~L~~~-~~l~~~~~~~-----------~~a 133 (219)
T PRK07983 75 EWYVAHNASFDRRVLPE-MP--------GEWICTMKLARRLWPGIKYSNMALYKS-RKLNVQTPPG-----------LHH 133 (219)
T ss_pred CEEEEeCcHhhHHHHhC-cC--------CCcEeHHHHHHHHccCCCCCHHHHHHH-cCCCCCCCCC-----------CCC
Confidence 46799999999998865 22 3467888763 3345899988875 4543210000 013
Q ss_pred HHHHHHHHHHHHHHHHHHhcc
Q 009284 473 EYAALDAVVLLQIFHHVRSCS 493 (538)
Q Consensus 473 ~YAAeDA~vlL~L~~~L~~rL 493 (538)
+-|..||.++..|+..+..+.
T Consensus 134 HrAl~Da~ata~ll~~l~~~~ 154 (219)
T PRK07983 134 HRALYDCYITAALLIDIMNTS 154 (219)
T ss_pred CcHHHHHHHHHHHHHHHHHHc
Confidence 558899999999999887544
No 59
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=85.14 E-value=19 Score=35.28 Aligned_cols=89 Identities=18% Similarity=0.083 Sum_probs=56.2
Q ss_pred HHHHHHHhhcCCCceEEEeehH-HhHHHHHHHhCCccccccchhHhhHHHhh-----c-CCCCCHHHHHHHHhCCCCCcC
Q 009284 384 LDSCLTRILQSPGILKLGYNFQ-CDIKQLAHSYGELECFKHYEMLLDIQNVF-----K-EPKGGLSGLAEKILGAGLNKT 456 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK-~Dl~vLa~~~Gil~~~~~~~~ifDtmLAl-----~-~~s~gLd~LAer~LG~~L~K~ 456 (538)
++..+..++.+. ..||||.. +|+..|.. +|........-..+|+.... + ..+|+|..|+++ +|.+..
T Consensus 74 vl~~f~~f~~~~--~lVaHNa~~fD~~fL~~-~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~-~gi~~~-- 147 (195)
T PRK07247 74 VLAAFKEFVGEL--PLIGYNAQKSDLPILAE-NGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVADF-LGIKGR-- 147 (195)
T ss_pred HHHHHHHHHCCC--eEEEEeCcHhHHHHHHH-cCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHHHh-cCCCCC--
Confidence 566777788654 46899995 89999987 56521100001123333221 1 257999999986 465321
Q ss_pred cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhcc
Q 009284 457 RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCS 493 (538)
Q Consensus 457 e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rL 493 (538)
.+-|-.||.++..|+..|...-
T Consensus 148 ---------------~HrAl~DA~~ta~v~~~ll~~~ 169 (195)
T PRK07247 148 ---------------GHNSLEDARMTARVYESFLESD 169 (195)
T ss_pred ---------------CcCCHHHHHHHHHHHHHHHhhc
Confidence 1337789999999999886554
No 60
>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=85.14 E-value=3.3 Score=40.50 Aligned_cols=86 Identities=14% Similarity=0.060 Sum_probs=56.2
Q ss_pred CceEEEeehHHhHHHHHHH---hCCccccccchhHhhHHHhhc--CCCCCHHHHHHHHhCCCCCcCcccccCCCCCCCHH
Q 009284 396 GILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK--EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQN 470 (538)
Q Consensus 396 ~i~KVGhnlK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLAl~--~~s~gLd~LAer~LG~~L~K~e~~S~W~~rpLt~~ 470 (538)
+...||||+.+|+..|.+. +|.....-....++||+.... ...++|+.+++++ |.+.. ..
T Consensus 105 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~~~~L~~l~~~~-gi~~~--------------~~ 169 (200)
T TIGR01298 105 RAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYGQTVLAKACQAA-GXDFD--------------ST 169 (200)
T ss_pred CCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcCcccHHHHHHHc-CCCcc--------------cc
Confidence 3468999999999988753 232100000023578887743 3456899999874 65421 11
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccCCC
Q 009284 471 QLEYAALDAVVLLQIFHHVRSCSQPT 496 (538)
Q Consensus 471 Q~~YAAeDA~vlL~L~~~L~~rLee~ 496 (538)
+.+-|..||.++.+|+..+..++.+.
T Consensus 170 ~~H~Al~Da~ata~lf~~l~~~~~~~ 195 (200)
T TIGR01298 170 QAHSALYDTEKTAELFCEIVNRWKRL 195 (200)
T ss_pred chhhhHHhHHHHHHHHHHHHHHHHHc
Confidence 24568899999999999998887553
No 61
>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=83.79 E-value=5.1 Score=38.73 Aligned_cols=80 Identities=15% Similarity=0.137 Sum_probs=51.5
Q ss_pred ceEEEeehHHhHHHHHHH---hCCc-cccccchhHhhHHHhhc--CCCCCHHHHHHHHhCCCCCcCcccccCCCCCCCHH
Q 009284 397 ILKLGYNFQCDIKQLAHS---YGEL-ECFKHYEMLLDIQNVFK--EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQN 470 (538)
Q Consensus 397 i~KVGhnlK~Dl~vLa~~---~Gil-~~~~~~~~ifDtmLAl~--~~s~gLd~LAer~LG~~L~K~e~~S~W~~rpLt~~ 470 (538)
...||||+.+|+..|.+. +|+. ..+ ....++||+.... ...+.|+.+++++ |++....
T Consensus 103 ~~lVaHna~FD~~fL~~~~~~~~~~~~~~-~~~~~lDt~~la~~~~~~~~L~~l~~~~-gi~~~~~-------------- 166 (189)
T cd06134 103 AILVGHNAHFDLGFLNAAVARCKIKRNPF-HPFSTFDTATLAGLAYGQTVLAKACQAA-GIEFDNK-------------- 166 (189)
T ss_pred CeEEEecchhhHHHHHHHHHHhCCCCCCC-CCCcEEEHHHHHHHHhCCCcHHHHHHHC-CCCCCCC--------------
Confidence 568999999999888642 3431 000 0123579877742 3356899999874 6543211
Q ss_pred HHHHHHHHHHHHHHHHHHHHhc
Q 009284 471 QLEYAALDAVVLLQIFHHVRSC 492 (538)
Q Consensus 471 Q~~YAAeDA~vlL~L~~~L~~r 492 (538)
+.+-|..||.++.+|+..+.++
T Consensus 167 ~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 167 EAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred CCcChHHHHHHHHHHHHHHHHh
Confidence 1234889999999999887654
No 62
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=83.50 E-value=3.6 Score=43.01 Aligned_cols=89 Identities=13% Similarity=0.075 Sum_probs=61.3
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHH---hCCccccccchhHhhHHHhh----c-CCCCCHHHHHHHHhCCCCCc
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVF----K-EPKGGLSGLAEKILGAGLNK 455 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLAl----~-~~s~gLd~LAer~LG~~L~K 455 (538)
++..|..++.+ ...||||..+|+..|.+. ++.... ...++||+... . ..+++|+.|++.+ |.+..
T Consensus 70 v~~~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~---~~~~idT~~lar~l~~~~~~~~L~~L~~~~-gi~~~- 142 (309)
T PRK06195 70 IWEKIKHYFNN--NLVIAHNASFDISVLRKTLELYNIPMP---SFEYICTMKLAKNFYSNIDNARLNTVNNFL-GYEFK- 142 (309)
T ss_pred HHHHHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCCCC---CCCEEEHHHHHHHHcCCCCcCCHHHHHHHc-CCCCc-
Confidence 55667777754 467999999999888642 343110 13467887753 2 3578999999885 54311
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 009284 456 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQP 495 (538)
Q Consensus 456 ~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rLee 495 (538)
.+-|..||.++.+|+..+..++..
T Consensus 143 ----------------~H~Al~DA~ata~l~~~l~~~~~~ 166 (309)
T PRK06195 143 ----------------HHDALADAMACSNILLNISKELNS 166 (309)
T ss_pred ----------------ccCCHHHHHHHHHHHHHHHHHhcc
Confidence 244889999999999998887754
No 63
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=83.25 E-value=2.3 Score=51.57 Aligned_cols=141 Identities=17% Similarity=0.196 Sum_probs=92.3
Q ss_pred HhhcCCeEEEEeeeecCCccCCcCCceeEEEEEe----CCe-----EEEEEcCcc-c--------------CCCc--hhH
Q 009284 331 HIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIAS----DEM-----VFIFDLIKL-A--------------EDVP--DVL 384 (538)
Q Consensus 331 ~L~~a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt----~~~-----a~~IdL~~l-~--------------~~~p--~~l 384 (538)
.|.++..+.||.|++++. +.--.+++++. .|+ -++++..+. . ...+ +++
T Consensus 417 ~l~datyVVfDiETTGLs-----~~~d~iIE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~v 491 (1444)
T COG2176 417 KLDDATYVVFDIETTGLS-----PVYDEIIEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEV 491 (1444)
T ss_pred ccccccEEEEEeecCCcC-----cccchhhhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHH
Confidence 466788999999999983 22223455441 111 122222211 0 0112 347
Q ss_pred HHHHHHhhcCCCceEEEeehHHhHHHHHHH---hCCccccccchhHhhHHHh---hc--CCCCCHHHHHHHHhCCCCCcC
Q 009284 385 DSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNV---FK--EPKGGLSGLAEKILGAGLNKT 456 (538)
Q Consensus 385 l~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLA---l~--~~s~gLd~LAer~LG~~L~K~ 456 (538)
+..++.|+.|. .-|.||+.+|+-.|... +|+... -.+++||.-. ++ -.+|+|..||.++ |..+
T Consensus 492 L~kf~~~~~d~--IlVAHNasFD~gFl~~~~~k~~~~~~---~~pvIDTL~lar~L~P~~ksh~Lg~l~kk~-~v~l--- 562 (1444)
T COG2176 492 LEKFREFIGDS--ILVAHNASFDMGFLNTNYEKYGLEPL---TNPVIDTLELARALNPEFKSHRLGTLCKKL-GVEL--- 562 (1444)
T ss_pred HHHHHHHhcCc--EEEeccCccchhHHHHHHHHhCCccc---cCchhhHHHHHHHhChhhhhcchHHHHHHh-CccH---
Confidence 88889999875 56899999999877543 455322 2678898766 22 4689999999986 4322
Q ss_pred cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCC
Q 009284 457 RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTDV 498 (538)
Q Consensus 457 e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rLee~~~ 498 (538)
++.+.|--||.++-+++-.+...+.+.|+
T Consensus 563 -------------e~hHRA~yDaeat~~vf~~f~~~~ke~Gi 591 (1444)
T COG2176 563 -------------ERHHRADYDAEATAKVFFVFLKDLKEKGI 591 (1444)
T ss_pred -------------HHhhhhhhhHHHHHHHHHHHHHHHHHhch
Confidence 34567888999999999999999988654
No 64
>PRK11779 sbcB exonuclease I; Provisional
Probab=82.63 E-value=16 Score=40.78 Aligned_cols=92 Identities=17% Similarity=0.178 Sum_probs=56.3
Q ss_pred HHHHHHHhhcCCCceEEEee-hHHhHHHHHHHhC--Ccccc----c---cchhHhhHHHhhc---------------CCC
Q 009284 384 LDSCLTRILQSPGILKLGYN-FQCDIKQLAHSYG--ELECF----K---HYEMLLDIQNVFK---------------EPK 438 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhn-lK~Dl~vLa~~~G--il~~~----~---~~~~ifDtmLAl~---------------~~s 438 (538)
+...+..++..+....|||| +.+|..++.+.+. ..... . ..-.++|++-+.. ..+
T Consensus 81 ~~~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s 160 (476)
T PRK11779 81 FAARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPS 160 (476)
T ss_pred HHHHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCC
Confidence 45566667765556689997 7899987765321 00000 0 0013456655411 146
Q ss_pred CCHHHHHHHHhCCCCCcCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhc
Q 009284 439 GGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSC 492 (538)
Q Consensus 439 ~gLd~LAer~LG~~L~K~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~r 492 (538)
+.|+.|++++ |++.. +.+-|-.||.++..|+..+..+
T Consensus 161 ~rLe~L~~~~-gI~~~----------------~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 161 FKLEHLTKAN-GIEHE----------------NAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CcHHHHHHHc-CCCCC----------------CCCCcHHHHHHHHHHHHHHHHh
Confidence 8899999875 54432 1234788999999999988765
No 65
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=81.08 E-value=26 Score=36.61 Aligned_cols=83 Identities=14% Similarity=0.020 Sum_probs=51.8
Q ss_pred HHHHHhhcCCCceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHhh--c---CCCCCHHHHHHHHhCCCCCcCcccc
Q 009284 386 SCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF--K---EPKGGLSGLAEKILGAGLNKTRRNS 460 (538)
Q Consensus 386 ~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLAl--~---~~s~gLd~LAer~LG~~L~K~e~~S 460 (538)
..+..+++.. ...|+||..+|+..|.+.+.... ...+.+++... . ..++.|+.|+.++ | ..
T Consensus 112 ~~l~~fl~~~-~vlVAHNA~FD~~fL~~~~~~~~----~~~~~ct~~~i~~~~~~~~~~kL~~La~~~-g-~~------- 177 (294)
T PRK09182 112 AAVDALIAPA-DLIIAHNAGFDRPFLERFSPVFA----TKPWACSVSEIDWSARGFEGTKLGYLAGQA-G-FF------- 177 (294)
T ss_pred HHHHHHhcCC-CEEEEeCHHHHHHHHHHHHHhcc----CCcccccHHHHhhccccCCCCCHHHHHHHc-C-CC-------
Confidence 4566677664 46799999999999976321111 02233444332 1 3578999999875 4 11
Q ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHh
Q 009284 461 NWEQRPLSQNQLEYAALDAVVLLQIFHHVRS 491 (538)
Q Consensus 461 ~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~ 491 (538)
+ ..+-|..||.++..|.....+
T Consensus 178 -~--------~aHrAl~Da~Ata~ll~~~l~ 199 (294)
T PRK09182 178 -H--------EGHRAVDDCQALLELLARPLP 199 (294)
T ss_pred -C--------CCcChHHHHHHHHHHHHHHHh
Confidence 1 124488999999888775443
No 66
>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=80.73 E-value=61 Score=31.93 Aligned_cols=148 Identities=20% Similarity=0.182 Sum_probs=77.7
Q ss_pred CCeEEEEeeeecCC-ccCCcCCc--eeEEEEEeCC-----eEEEEEcCccc--------------CCCchhHHHHHHHhh
Q 009284 335 CKVVGIDCEWKPNY-VKGCKMNK--VSIMQIASDE-----MVFIFDLIKLA--------------EDVPDVLDSCLTRIL 392 (538)
Q Consensus 335 a~~IgfDtE~~~l~-~~~~~~~~--VsLiQLAt~~-----~a~~IdL~~l~--------------~~~p~~ll~~Lk~lL 392 (538)
-.+++||.|+.+.. ...+.+.. -.+++++..+ .++++...... .....+++..+..++
T Consensus 5 lrilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~F~~~i 84 (204)
T cd05783 5 LKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALAGSDGLKRVLVLKREGVEGLEGLLPEGAEVEFFDSEKELIREAFKII 84 (204)
T ss_pred ceEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEcCCCCCcEEEEEecCCcccccccCCCCCeEEecCCHHHHHHHHHHHH
Confidence 36789999987521 11122222 3467777521 34444211100 011233566666677
Q ss_pred cCCCceEEEeehHH-hHHHHHH---HhCCcc-----ccc------cchhHhhHHHhhc------------CCCCCHHHHH
Q 009284 393 QSPGILKLGYNFQC-DIKQLAH---SYGELE-----CFK------HYEMLLDIQNVFK------------EPKGGLSGLA 445 (538)
Q Consensus 393 ed~~i~KVGhnlK~-Dl~vLa~---~~Gil~-----~~~------~~~~ifDtmLAl~------------~~s~gLd~LA 445 (538)
.+. -..+|+|... |+-.|.+ .+|+.. .+. .....+|+...+. ..+++|+.+|
T Consensus 85 ~~~-~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~~~~~~~L~~Va 163 (204)
T cd05783 85 SEY-PIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGNKYREYTLDAVA 163 (204)
T ss_pred hcC-CEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhccccccCcHHHHH
Confidence 766 4678998653 6554422 256530 000 0122456654321 1578999999
Q ss_pred HHHhCCCC-CcCcccccCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009284 446 EKILGAGL-NKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFH 487 (538)
Q Consensus 446 er~LG~~L-~K~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~ 487 (538)
+.+||..- +-..++. .. . .+.-.+|+..||..+++|..
T Consensus 164 ~~~lg~~K~~~~~~i~--~~-~-~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 164 KALLGEGKVELEKNIS--EL-N-LYELAEYNYRDAELTLELTT 202 (204)
T ss_pred HHhcCCCcccCCchhh--hh-c-HHHHHHhhHHHHHHHHHHhc
Confidence 99998532 1111111 11 1 13347999999999999864
No 67
>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=79.47 E-value=28 Score=34.36 Aligned_cols=149 Identities=19% Similarity=0.188 Sum_probs=78.4
Q ss_pred CeEEEEeeeecCCccCCcCCceeEEEEEe--C-CeEEEE--EcCcc--------------------cCCCchhHHHHHHH
Q 009284 336 KVVGIDCEWKPNYVKGCKMNKVSIMQIAS--D-EMVFIF--DLIKL--------------------AEDVPDVLDSCLTR 390 (538)
Q Consensus 336 ~~IgfDtE~~~l~~~~~~~~~VsLiQLAt--~-~~a~~I--dL~~l--------------------~~~~p~~ll~~Lk~ 390 (538)
.+.+||.|..+.....|.+..-.++|||. . +...+. .+... ......+++..+..
T Consensus 3 rilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~f~~ 82 (204)
T cd05779 3 RVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIVNREIVSEDIEDFEYTPKPEYEGPFKVFNEPDEKALLQRFFE 82 (204)
T ss_pred eEEEEEEEecCCCCCCcCCCCCeEEEEEEEEecCCEEEecccccccccccccccCCCCCCCceEEecCCCHHHHHHHHHH
Confidence 57899999976422223455566777774 2 222211 00000 00111235555555
Q ss_pred hhcCCC-ceEEEeehH-HhHHHHH---HHhCCccc----cc--c-------chhHhhHHHhhc------CCCCCHHHHHH
Q 009284 391 ILQSPG-ILKLGYNFQ-CDIKQLA---HSYGELEC----FK--H-------YEMLLDIQNVFK------EPKGGLSGLAE 446 (538)
Q Consensus 391 lLed~~-i~KVGhnlK-~Dl~vLa---~~~Gil~~----~~--~-------~~~ifDtmLAl~------~~s~gLd~LAe 446 (538)
++.+.+ -..+|+|.. +|+-.|. ..+|+... .. . ....+|++-.+. ..+++|+.+|+
T Consensus 83 ~i~~~~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~~sysLd~Va~ 162 (204)
T cd05779 83 HIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQGLKAVTK 162 (204)
T ss_pred HHHHhCCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCCCCccHHHHHH
Confidence 555532 235788864 3554432 12554211 00 0 011456665532 24789999999
Q ss_pred HHhCCCCCc--Cccc-ccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009284 447 KILGAGLNK--TRRN-SNWEQRPLSQNQLEYAALDAVVLLQIF 486 (538)
Q Consensus 447 r~LG~~L~K--~e~~-S~W~~rpLt~~Q~~YAAeDA~vlL~L~ 486 (538)
.+||..-.. ...+ .-|...+ +.-.+|.-.||..++.||
T Consensus 163 ~~Lg~~K~~~~~~~I~~~~~~~~--~~l~~Y~~~D~~~T~~l~ 203 (204)
T cd05779 163 AKLGYDPVELDPEDMVPLAREDP--QTLASYSVSDAVATYYLY 203 (204)
T ss_pred HHhCCCcCcCCHHHHHHHHhCCc--HHHHhccHHHHHHHHHHh
Confidence 999963211 1111 1355433 345899999999999997
No 68
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=78.73 E-value=15 Score=46.19 Aligned_cols=92 Identities=14% Similarity=0.120 Sum_probs=63.2
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHH---hCCccccccchhHhhHHHhhc-----CCCCCHHHHHHHHhCCCCCc
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLNK 455 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLAl~-----~~s~gLd~LAer~LG~~L~K 455 (538)
++..+..++.+ ...|+||..+|...|... +|+.. + ....+|++.... ..+++|+.|+++ +|.....
T Consensus 489 aL~~f~~figg--~vLVAHNa~FD~~fL~~~l~rlgl~~-l--~~~~IDTLelar~l~p~~k~~kL~~LAk~-lGL~~~~ 562 (1437)
T PRK00448 489 VLPKFKEFCGD--SILVAHNASFDVGFINTNYEKLGLEK-I--KNPVIDTLELSRFLYPELKSHRLNTLAKK-FGVELEH 562 (1437)
T ss_pred HHHHHHHHhCC--CEEEEeCccccHHHHHHHHHHcCCcc-c--cccceeHHHHHHHHcCccccccHHHHHHH-cCCCCCC
Confidence 44555555543 578999999999876432 44411 1 145678877631 467999999987 4654421
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Q 009284 456 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTD 497 (538)
Q Consensus 456 ~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rLee~~ 497 (538)
.+.|-.||.++.+|+..+..++.+.+
T Consensus 563 ----------------~HrAl~DA~aTa~lf~~ll~~l~~~g 588 (1437)
T PRK00448 563 ----------------HHRADYDAEATAYLLIKFLKDLKEKG 588 (1437)
T ss_pred ----------------CcChHHHHHHHHHHHHHHHHHHHHcC
Confidence 14588999999999999999987654
No 69
>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=78.46 E-value=3.5 Score=38.14 Aligned_cols=142 Identities=15% Similarity=0.158 Sum_probs=66.5
Q ss_pred EEEEeeeecCCccCCcCCceeEEEEEe--CC-eEEEEEcCcccCCCchhHHHHHHHhhcCCCceEEEeeh-HHhHHHHHH
Q 009284 338 VGIDCEWKPNYVKGCKMNKVSIMQIAS--DE-MVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNF-QCDIKQLAH 413 (538)
Q Consensus 338 IgfDtE~~~l~~~~~~~~~VsLiQLAt--~~-~a~~IdL~~l~~~~p~~ll~~Lk~lLed~~i~KVGhnl-K~Dl~vLa~ 413 (538)
+.||.|++++.. ....+-++|++. .+ ...+.......+.....+.+.+ ..+.+. -..++||. .+|...|.+
T Consensus 1 l~~DIET~Gl~~---~~~~i~liG~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~-~~l~~~-~~iv~yng~~FD~p~L~~ 75 (164)
T PF13482_consen 1 LFFDIETTGLSP---DNDTIYLIGVADFDDDEIITFIQWFAEDPDEEEIILEFF-ELLDEA-DNIVTYNGKNFDIPFLKR 75 (164)
T ss_dssp --EEEEESS-GG----G---EEEEEEE-ETTTTE-EEEE-GGGHHHHHHHHH---HHHHTT---EEESSTTTTHHHHHHH
T ss_pred CcEEecCCCCCC---CCCCEEEEEEEEeCCCceEEeeHhhccCcHHHHHHHHHH-HHHhcC-CeEEEEeCcccCHHHHHH
Confidence 358999998731 234566777764 33 2324333221111112233333 445554 34688996 558877765
Q ss_pred Hh---CCccccccchhHhhHHHhhc---CCCCCHHHHHHHHhCCCCCc----Ccc-cc---cCC---CCCCCHHHHHHHH
Q 009284 414 SY---GELECFKHYEMLLDIQNVFK---EPKGGLSGLAEKILGAGLNK----TRR-NS---NWE---QRPLSQNQLEYAA 476 (538)
Q Consensus 414 ~~---Gil~~~~~~~~ifDtmLAl~---~~s~gLd~LAer~LG~~L~K----~e~-~S---~W~---~rpLt~~Q~~YAA 476 (538)
.+ ++.. ....+|++..+. ..+.+|..++.. +|..-.. +.+ .. .|. ....-+..+.|.-
T Consensus 76 ~~~~~~~~~----~~~~iDl~~~~~~~~~~~~~Lk~ve~~-lg~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~i~~yN~ 150 (164)
T PF13482_consen 76 RAKRYGLPP----PFNHIDLLKIIKKHFLESYSLKNVEKF-LGIERRDDDISGSESVKLYKEYLETGDPEALEEILEYNE 150 (164)
T ss_dssp HH-HHHH------GGGEEEHHHHHT-TTSCCTT--SHHH------------HHHHHHHHHH---TTGGTS--HHHHHHHH
T ss_pred HHHHcCCCc----ccchhhHHHHHHhccCCCCCHHHHhhh-cccccccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence 33 3211 255678887743 356789988877 6654321 110 00 111 0123355689999
Q ss_pred HHHHHHHHHHHHH
Q 009284 477 LDAVVLLQIFHHV 489 (538)
Q Consensus 477 eDA~vlL~L~~~L 489 (538)
.|...+.+|++.|
T Consensus 151 ~Dv~~~~~L~~~l 163 (164)
T PF13482_consen 151 DDVRATRRLYEWL 163 (164)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHh
Confidence 9999999999876
No 70
>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=78.33 E-value=9 Score=37.81 Aligned_cols=145 Identities=18% Similarity=0.173 Sum_probs=76.9
Q ss_pred CCeEEEEeeeecCCcc---CCcCCceeEEEEEe--CCe-EEEEEcCcccCCCchhHHHHHHHhhcC--CCceEEEeeh-H
Q 009284 335 CKVVGIDCEWKPNYVK---GCKMNKVSIMQIAS--DEM-VFIFDLIKLAEDVPDVLDSCLTRILQS--PGILKLGYNF-Q 405 (538)
Q Consensus 335 a~~IgfDtE~~~l~~~---~~~~~~VsLiQLAt--~~~-a~~IdL~~l~~~~p~~ll~~Lk~lLed--~~i~KVGhnl-K 405 (538)
-.+++||.|..+.... ++....-.+++|+. .+. ..++.. ......+++..+..++.. |. ..+|||. .
T Consensus 9 lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~~~~---~~~~E~~lL~~f~~~i~~~dPd-ii~g~N~~~ 84 (207)
T cd05785 9 LRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEVLHA---EDAAEKELLEELVAIIRERDPD-VIEGHNIFR 84 (207)
T ss_pred ceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceeeecc---CCCCHHHHHHHHHHHHHHhCCC-EEeccCCcc
Confidence 3678999998654211 11223345677765 221 112211 111123355555555554 54 4579998 6
Q ss_pred HhHHHHHH---HhCCcccccc--------------------------chh-HhhHHHhhc--------CCCCCHHHHHHH
Q 009284 406 CDIKQLAH---SYGELECFKH--------------------------YEM-LLDIQNVFK--------EPKGGLSGLAEK 447 (538)
Q Consensus 406 ~Dl~vLa~---~~Gil~~~~~--------------------------~~~-ifDtmLAl~--------~~s~gLd~LAer 447 (538)
+|+..|.+ .+|+...+.. .|. .+|++.++. -.+++|+.+|+.
T Consensus 85 FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~~~l~sysL~~Va~~ 164 (207)
T cd05785 85 FDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSSRDLPSYGLKAVAKH 164 (207)
T ss_pred cCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccccCCCCCCHHHHHHH
Confidence 68766532 2454221000 112 268877632 246899999997
Q ss_pred HhCCCCC-----cCcccc-cCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009284 448 ILGAGLN-----KTRRNS-NWEQRPLSQNQLEYAALDAVVLLQIF 486 (538)
Q Consensus 448 ~LG~~L~-----K~e~~S-~W~~rpLt~~Q~~YAAeDA~vlL~L~ 486 (538)
+ |.... ...++. -|...+ ..-.+|...|+..+++|+
T Consensus 165 ~-g~~~~~k~d~~~~~I~~l~~~~~--~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 165 F-GLASPDRTYIDGRQIAEVWRSDP--ARLLAYALDDVRETEGLA 206 (207)
T ss_pred h-cccCCCcCCCCHHHHHHHHhcCH--HHHHHHHHHHHHHHHHhh
Confidence 6 33111 111221 354432 455899999999999885
No 71
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=77.23 E-value=3.6 Score=48.16 Aligned_cols=144 Identities=17% Similarity=0.213 Sum_probs=83.4
Q ss_pred CeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCc----cc-CCCchhHHHHHHHhhcC-CCceEEEeehHHhHH
Q 009284 336 KVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIK----LA-EDVPDVLDSCLTRILQS-PGILKLGYNFQCDIK 409 (538)
Q Consensus 336 ~~IgfDtE~~~l~~~~~~~~~VsLiQLAt~~~a~~IdL~~----l~-~~~p~~ll~~Lk~lLed-~~i~KVGhnlK~Dl~ 409 (538)
..+.||+|.--. .+....++.|....++|-.... ++ .+.|+ ..|-|+=+. ..-+.||||+.+|..
T Consensus 184 ~~lVFDVEvl~~------~g~~ptLAtAlS~dAWY~WcS~P~~li~~sE~p~---~~LIP~~~~~ke~liVGHNVsfDRa 254 (1075)
T KOG3657|consen 184 SILVFDVEVLVR------VGTLPTLATALSRDAWYSWCSDPWDLIYESEIPE---AALIPLGEIGKEQLIVGHNVSFDRA 254 (1075)
T ss_pred ceeEEEEEEEEe------ccCcchhhhhhccchhhhhcCCHHhhcccCCCcH---HhhCcCCcCCCCceEEeccccchHH
Confidence 567899996422 1122233344456677765542 11 12232 345554333 246789999999999
Q ss_pred HHHHHhCCccccccchhHhhHHHhh-------c--C-----------------C----------------CCCHHHHHHH
Q 009284 410 QLAHSYGELECFKHYEMLLDIQNVF-------K--E-----------------P----------------KGGLSGLAEK 447 (538)
Q Consensus 410 vLa~~~Gil~~~~~~~~ifDtmLAl-------~--~-----------------~----------------s~gLd~LAer 447 (538)
.+...|.|.. +-..++|||-+. . . . -.+|.+++..
T Consensus 255 RirEeY~i~~---Sk~rFlDTMSlHia~~Gm~S~Qrplw~ka~k~k~a~~d~~~~ps~~d~~~pWL~~SS~NSL~dVhk~ 331 (1075)
T KOG3657|consen 255 RIREEYNING---SKIRFLDTMSLHIAMSGMCSRQRPLWFKARKAKSAMYDSETNPSISDYDNPWLGRSSLNSLVDVHKF 331 (1075)
T ss_pred HHHHHHhccc---cceeeeechhhhhhhhccccccchhHhhhhhhhhhhhhcccCCchhhhhhhhhhhhhhHHHHHHHHh
Confidence 8887788732 124567998761 0 0 0 1245566666
Q ss_pred HhCCC-CCcCcccccCCCCCCCHHH--------HHHHHHHHHHHHHHHHHHHhccC
Q 009284 448 ILGAG-LNKTRRNSNWEQRPLSQNQ--------LEYAALDAVVLLQIFHHVRSCSQ 494 (538)
Q Consensus 448 ~LG~~-L~K~e~~S~W~~rpLt~~Q--------~~YAAeDA~vlL~L~~~L~~rLe 494 (538)
+.|.. ++|..+. .|- ..+.+| +.|.|.|.+++.+++..+.|..-
T Consensus 332 ~c~~~~LdKt~Rd-~Fv--s~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Fl 384 (1075)
T KOG3657|consen 332 HCGIDALDKTPRD-SFV--SGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFL 384 (1075)
T ss_pred hCCCCccccchHH-hhh--cCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHH
Confidence 66665 5554321 121 112222 58999999999999998877653
No 72
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=75.05 E-value=5.9 Score=42.97 Aligned_cols=86 Identities=19% Similarity=0.243 Sum_probs=59.0
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHhhc---C---CCCCHHHHHHHHhCCCCCcCc
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFK---E---PKGGLSGLAEKILGAGLNKTR 457 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLAl~---~---~s~gLd~LAer~LG~~L~K~e 457 (538)
+-..|..++... -.-|||++-.|+..|.-.|+. ++||.+.++ . ...+|..|++.|||..+..+.
T Consensus 283 vq~~l~~~~~~~-TILVGHSLenDL~aLKl~H~~---------ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~~ 352 (380)
T KOG2248|consen 283 VQKELLELISKN-TILVGHSLENDLKALKLDHPS---------VIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEGV 352 (380)
T ss_pred HHHHHHhhcCcC-cEEEeechhhHHHHHhhhCCc---------eeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhccC
Confidence 445677766555 456899999999999864443 569998764 1 235699999999997653111
Q ss_pred ccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhc
Q 009284 458 RNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSC 492 (538)
Q Consensus 458 ~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~r 492 (538)
. .+-+.+||.++++|.......
T Consensus 353 --~-----------~HdS~eDA~acm~Lv~~k~~~ 374 (380)
T KOG2248|consen 353 --G-----------GHDSVEDALACMKLVKLKIKN 374 (380)
T ss_pred --C-----------CCccHHHHHHHHHHHHHHHhc
Confidence 1 122679999999987765443
No 73
>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=74.13 E-value=36 Score=33.24 Aligned_cols=102 Identities=19% Similarity=0.214 Sum_probs=57.8
Q ss_pred HHHHHHHhhcCCC-ceEEEeehHH-hHHHHHH---HhCCcccccc--------------------ch-hHhhHHHhhc--
Q 009284 384 LDSCLTRILQSPG-ILKLGYNFQC-DIKQLAH---SYGELECFKH--------------------YE-MLLDIQNVFK-- 435 (538)
Q Consensus 384 ll~~Lk~lLed~~-i~KVGhnlK~-Dl~vLa~---~~Gil~~~~~--------------------~~-~ifDtmLAl~-- 435 (538)
++..+..++.+.+ -..+|||... |+..|.+ .+|+...+.. .| ..+|+.....
T Consensus 54 lL~~f~~~i~~~dPDvi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~~ 133 (193)
T cd05784 54 LLLALIAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTA 133 (193)
T ss_pred HHHHHHHHHHhhCCCEEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHHc
Confidence 5555555555433 2468998865 6654422 2454211100 01 1557654432
Q ss_pred ---CCCCCHHHHHHHHhCCCCC-cC-----cccc-cCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009284 436 ---EPKGGLSGLAEKILGAGLN-KT-----RRNS-NWEQRPLSQNQLEYAALDAVVLLQIFH 487 (538)
Q Consensus 436 ---~~s~gLd~LAer~LG~~L~-K~-----e~~S-~W~~rpLt~~Q~~YAAeDA~vlL~L~~ 487 (538)
..+++|+.+|+.+||..-. .. .++. .|...+ ..-.+|+..||..+++|++
T Consensus 134 ~~kl~sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~~~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 134 TYHFESFSLENVAQELLGEGKLIHDVDDRGAEIERLFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred cCCCCcCCHHHHHHHHhCCCccccCcccCHHHHHHHHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 3689999999999985321 11 1222 243322 3458999999999999863
No 74
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=66.71 E-value=1.3e+02 Score=29.64 Aligned_cols=96 Identities=20% Similarity=0.138 Sum_probs=59.3
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHhh----cC-CCCCHHHHHHHHhCCCCCcCcc
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF----KE-PKGGLSGLAEKILGAGLNKTRR 458 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLAl----~~-~s~gLd~LAer~LG~~L~K~e~ 458 (538)
+...+..++.+. -.-|+||..+|...+..........-......|+.-.. .. ..++|+.|+. .+|+... ...
T Consensus 84 v~~~~~~~i~~~-~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~~~L~~l~~-~~gi~~~-~~~ 160 (243)
T COG0847 84 VLPEFLDFIGGL-RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDALAE-RLGIDRN-PFH 160 (243)
T ss_pred HHHHHHHHHCCC-CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCccchHHHHHH-HcCCCcC-CcC
Confidence 445555666654 56799999999998865322210000013455776663 23 5789999999 4565432 110
Q ss_pred cccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhc-cCC
Q 009284 459 NSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSC-SQP 495 (538)
Q Consensus 459 ~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~r-Lee 495 (538)
.+-|..||.++..++..+... +..
T Consensus 161 -------------~H~Al~Da~~~a~~~~~~~~~~~~~ 185 (243)
T COG0847 161 -------------PHRALFDALALAELFLLLQTGLLLK 185 (243)
T ss_pred -------------CcchHHHHHHHHHHHHHHHhccccc
Confidence 133889999999999888775 433
No 75
>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=62.67 E-value=1.2e+02 Score=27.96 Aligned_cols=90 Identities=19% Similarity=0.223 Sum_probs=53.4
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHH---hCCccccccchhHhhHHHhhc-----CCCCCHHHHHHHHhCCCCCc
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLNK 455 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLAl~-----~~s~gLd~LAer~LG~~L~K 455 (538)
++..|..++.+.....+.++.++|...+.+. ++...........+|++..+. ..+++|++++.. +|.+..
T Consensus 78 vl~~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~- 155 (176)
T cd06133 78 VLKEFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEY-LGLEFE- 155 (176)
T ss_pred HHHHHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHHHHH-CCCCCC-
Confidence 5667778887742134455568887765431 222100001245778887632 248899999876 476543
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009284 456 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHV 489 (538)
Q Consensus 456 ~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L 489 (538)
. +.+.|-.||..+.+++..+
T Consensus 156 -~-------------~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 156 -G-------------RHHRGLDDARNIARILKRL 175 (176)
T ss_pred -C-------------CCcCcHHHHHHHHHHHHHh
Confidence 0 1234778999998887765
No 76
>KOG3616 consensus Selective LIM binding factor [Transcription]
Probab=61.82 E-value=37 Score=39.93 Aligned_cols=49 Identities=22% Similarity=0.286 Sum_probs=40.0
Q ss_pred HHHHhhhhchHHHHHHhhcc---hhHHHHHHHHh---hccCCHHHHHHHHHHcCC
Q 009284 239 LKRLAEKACWDIAEAKTKGD---KRLLEYLVYLA---MEAGYSEKVDELCERYSL 287 (538)
Q Consensus 239 ~~~l~~k~~wd~a~~~~~~D---~~l~~~lv~L~---~~~~d~~~L~~l~~ryef 287 (538)
|.-|++.++||.|..+++.. |-|..|+..++ ...+|..++..++.++|-
T Consensus 1299 idl~ien~qwdk~idtak~qnykpil~kyva~yaa~li~~~d~aq~lal~~q~ga 1353 (1636)
T KOG3616|consen 1299 IDLMIENDQWDKAIDTAKKQNYKPILDKYVALYAAHLIHEGDLAQALALLEQHGA 1353 (1636)
T ss_pred HHHHHhcccHHHHHHHHHhcccHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHhCC
Confidence 67789999999999888764 45677776654 468999999999999994
No 77
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=60.21 E-value=1.4e+02 Score=29.49 Aligned_cols=103 Identities=17% Similarity=0.217 Sum_probs=62.4
Q ss_pred hHHHHHHHhhcCCCceEEEeehH-HhHHHHHH---HhCCc-ccc-cc-----------chhHhhHHHhhc----CCCCCH
Q 009284 383 VLDSCLTRILQSPGILKLGYNFQ-CDIKQLAH---SYGEL-ECF-KH-----------YEMLLDIQNVFK----EPKGGL 441 (538)
Q Consensus 383 ~ll~~Lk~lLed~~i~KVGhnlK-~Dl~vLa~---~~Gil-~~~-~~-----------~~~ifDtmLAl~----~~s~gL 441 (538)
+++..+..++++.....||||.+ +|+-.|.. .+|+. +.. .. .+..+|++-.+. ..+.+|
T Consensus 80 elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~~~~~~~L 159 (208)
T cd05782 80 ELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYGARARASL 159 (208)
T ss_pred HHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccCccCCCCH
Confidence 46666666666533467999984 58766543 25651 110 00 012679988863 358899
Q ss_pred HHHHHHHhCCCCC---cCccc-ccCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009284 442 SGLAEKILGAGLN---KTRRN-SNWEQRPLSQNQLEYAALDAVVLLQIFH 487 (538)
Q Consensus 442 d~LAer~LG~~L~---K~e~~-S~W~~rpLt~~Q~~YAAeDA~vlL~L~~ 487 (538)
+.+|+ .||.+-. .+.++ ..|...++ ..-.+|...|+..+..||.
T Consensus 160 ~~va~-~lG~~~K~d~~G~~v~~~y~~g~~-~~I~~Yc~~Dv~~t~~l~l 207 (208)
T cd05782 160 DLLAK-LLGIPGKMDVDGSQVWELYAEGKL-DEIAEYCETDVLNTYLLYL 207 (208)
T ss_pred HHHHH-HhCCCCCcCCCHHHHHHHHHcCCh-HHHHHHHHHHHHHHHHHHh
Confidence 99986 5776321 11111 23544443 4458999999999999874
No 78
>PF07899 Frigida: Frigida-like protein; InterPro: IPR012474 This family is composed of plant proteins that are similar to FRIGIDA protein expressed by Arabidopsis thaliana (Mouse-ear cress) (Q9FDW0 from SWISSPROT). This protein is probably nuclear and is required for the regulation of flowering time in the late-flowering phenotype. It is known to increase RNA levels of flowering locus C. Allelic variation at the FRIGIDA locus is a major determinant of natural variation in flowering time [].
Probab=58.56 E-value=1.8e+02 Score=30.42 Aligned_cols=157 Identities=16% Similarity=0.207 Sum_probs=95.1
Q ss_pred HHHHHHHHHHhhCCCCCCCceeeeeeeee--cccccc------cccc-hhHHHHHHHHhhhcccCCccchhH-HHHHHHH
Q 009284 59 RALQQQVSQALCNSPEPGPATFIVRCLYV--LPIFGV------YSEG-FSHLIISALRRHQKTTVNSADSTQ-AKEIAAY 128 (538)
Q Consensus 59 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~------~~~~-~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~ 128 (538)
..|...|-.+|.-.|-| |-+|.+|+=- .|--+. ..-. =.=+++..|++ .+ +.++.+.-+ |+.+|..
T Consensus 39 ~~lr~Ev~~AL~~A~DP--AkLVLdai~~f~~~~~~~~~~~~~~~~r~~cilLLE~L~~-~~-~~is~~vke~A~~lA~~ 114 (290)
T PF07899_consen 39 ASLREEVPAALRCAPDP--AKLVLDAIEGFYPPGSKNKKDSKLVDVRRACILLLEQLMR-IS-PEISPEVKEEAKKLAEE 114 (290)
T ss_pred HHHHHHHHHHHHcCCCh--HHHHHHHHHcccCCccccccCcchhhHHHHHHHHHHHHhh-cC-CCCCHHHHHHHHHHHHH
Confidence 46889999999887765 7888888621 111100 0000 12356677777 22 344555543 7777766
Q ss_pred HHHHH--hcCCCCChhHHHHHHHHHhccccc-cHHHH--HhhhhhccccchhHHH-----HHHHHHHHHHHhhchhhHHH
Q 009284 129 LFLDI--TGGFVDHDEKLMVKILEAFDVRLT-DIEKA--ITQLKAQNEHRFDTAK-----TVIEQYIFAMIDSQSYMTAV 198 (538)
Q Consensus 129 ~~~~~--~~~~~~~~~r~~~~l~e~f~~~~~-~~~~a--~~~~~~~~~~~~~~~~-----~~~~~yi~~~~~~~~~~~~~ 198 (538)
.=--+ +...-..+..-.+.++=+|||.-+ |.++- +-.+-++.......++ +-+..+|.+||+.|++..||
T Consensus 115 WK~~l~~~~~~~~lea~gFL~lla~fgi~s~Fd~del~~Lv~~va~~~~a~~L~~sLgl~~k~~d~V~~LI~~g~~ieAv 194 (290)
T PF07899_consen 115 WKSKLDGVNNENSLEALGFLQLLAAFGIVSEFDEDELLKLVVSVARRKQAPELCRSLGLSDKMPDIVEKLIKKGKQIEAV 194 (290)
T ss_pred HHHHHHhcccCCCHHHHHHHHHHHHcCCccccCHHHHHHHHHHhcchHhhHHHHHHcCchhhhHHHHHHHHHCCCccchH
Confidence 54444 344455568899999999999432 21111 0111112211222232 33689999999999999999
Q ss_pred HHHHhhhcccc--chHHHHHHHh
Q 009284 199 SLLEHFSIRQS--GESFLLKMIQ 219 (538)
Q Consensus 199 ~li~~f~~~~~--~~~~l~~~~~ 219 (538)
.+|.-|++.-. -.|.|..-++
T Consensus 195 ~fi~~f~L~dkfpPv~lLk~yl~ 217 (290)
T PF07899_consen 195 RFIYAFGLVDKFPPVPLLKSYLE 217 (290)
T ss_pred HHHHHHcCCCCCCCHHHHHHHHH
Confidence 99999999864 4445555553
No 79
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=56.09 E-value=15 Score=27.63 Aligned_cols=46 Identities=15% Similarity=0.113 Sum_probs=39.1
Q ss_pred cCCccchhHHHHHHHHHHHHHhcCCCCChhHHHHHHHHHhcccccc
Q 009284 113 TVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTD 158 (538)
Q Consensus 113 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~l~e~f~~~~~~ 158 (538)
.-+++|+-++=++.-+.+-.+..|........+.++++.||++++.
T Consensus 9 gls~~~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~l~~~~~~ 54 (55)
T PF01381_consen 9 GLSQKELAEKLGISRSTISRIENGKRNPSLDTLKKIAKALGVSPEY 54 (55)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHHHHTSEHHH
T ss_pred CCCHHHHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHHHHCCCHHH
Confidence 4568899999899999999999998888899999999999997654
No 80
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=55.41 E-value=17 Score=28.26 Aligned_cols=54 Identities=22% Similarity=0.278 Sum_probs=40.1
Q ss_pred HHHHhhhcccCCccchhHHHHHHHHHHHHHhcCCCCChhHHHHHHHHHhccccccH
Q 009284 104 SALRRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDI 159 (538)
Q Consensus 104 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~l~e~f~~~~~~~ 159 (538)
-.+|.-.. -+++|+.+.-.+....+-.|..|........+.++++.|||+++.+
T Consensus 5 k~~r~~~~--lt~~~~a~~~~i~~~~i~~~e~g~~~~~~~~l~~i~~~~~v~~~~l 58 (64)
T PF12844_consen 5 KELREEKG--LTQKDLAEKLGISRSTISKIENGKRKPSVSTLKKIAEALGVSLDEL 58 (64)
T ss_dssp HHHHHHCT----HHHHHHHHTS-HHHHHHHHTTSS--BHHHHHHHHHHHTS-HHHH
T ss_pred HHHHHHcC--CCHHHHHHHHCcCHHHHHHHHCCCcCCCHHHHHHHHHHhCCCHHHH
Confidence 34555333 4689999999999999999999988877899999999999987654
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=52.52 E-value=1.8e+02 Score=29.14 Aligned_cols=107 Identities=16% Similarity=0.227 Sum_probs=67.9
Q ss_pred chhHHHHHHHhhcCCCceEEEeehHH-hHHHHHH---HhCCc-ccc-cc----c--------hhHhhHHHhhc----CCC
Q 009284 381 PDVLDSCLTRILQSPGILKLGYNFQC-DIKQLAH---SYGEL-ECF-KH----Y--------EMLLDIQNVFK----EPK 438 (538)
Q Consensus 381 p~~ll~~Lk~lLed~~i~KVGhnlK~-Dl~vLa~---~~Gil-~~~-~~----~--------~~ifDtmLAl~----~~s 438 (538)
..+++..+...++.....-|+||.+. |+-+|.. .+|+. +.+ .. . ..-+|+|-.+. ..+
T Consensus 37 E~~lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~g~~~~ 116 (209)
T PF10108_consen 37 EKELLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFYGAKAR 116 (209)
T ss_pred HHHHHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhccCcccc
Confidence 34577777888887667789999775 7755532 24652 110 00 0 12468987753 457
Q ss_pred CCHHHHHHHHhCCCCCcC----cccc-cCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009284 439 GGLSGLAEKILGAGLNKT----RRNS-NWEQRPLSQNQLEYAALDAVVLLQIFHHVR 490 (538)
Q Consensus 439 ~gLd~LAer~LG~~L~K~----e~~S-~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~ 490 (538)
.+|+.||. .+|+|- |. .++. -|.+..+ ++-..|.-.|+..+..||-.+.
T Consensus 117 ~sLd~la~-~lgiPg-K~~idGs~V~~~y~~g~i-~~I~~YCe~DVl~T~~lylR~~ 170 (209)
T PF10108_consen 117 TSLDELAA-LLGIPG-KDDIDGSQVAELYQEGDI-DEIREYCEKDVLNTYLLYLRFE 170 (209)
T ss_pred CCHHHHHH-HcCCCC-CCCCCHHHHHHHHHcCCH-HHHHHHHHHHHHHHHHHHHHHH
Confidence 88999986 468764 32 1221 2444445 3347999999999999988774
No 82
>PRK14976 5'-3' exonuclease; Provisional
Probab=51.33 E-value=6.7 Score=40.68 Aligned_cols=38 Identities=16% Similarity=0.090 Sum_probs=35.2
Q ss_pred HHHHhhcchhHHHHHHHHhhccCCHHHHHHHHHHcCCc
Q 009284 251 AEAKTKGDKRLLEYLVYLAMEAGYSEKVDELCERYSLE 288 (538)
Q Consensus 251 a~~~~~~D~~l~~~lv~L~~~~~d~~~L~~l~~ryef~ 288 (538)
.++++++|+++...+.+++..++|.+++.++|+++||+
T Consensus 244 ~L~~l~~d~~l~~~l~~~~~~~~~~~~l~~~~~~~e~~ 281 (281)
T PRK14976 244 KLATIKTDVPLDFQIEDIKLKKLDQPELKKIFEELELK 281 (281)
T ss_pred hhhEEeecCCCCCCHHHhccCCCCHHHHHHHHHHcCCC
Confidence 57889999999999999999999999999999999985
No 83
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=45.94 E-value=1.5e+02 Score=28.93 Aligned_cols=91 Identities=22% Similarity=0.104 Sum_probs=58.6
Q ss_pred HHHHHHHhhcCCCceEEEeehHHhHHHHHHH---hCCccccccchhHhhHHHhhc-----CCCCCHHHHHHHHhCCCCCc
Q 009284 384 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLNK 455 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~---~Gil~~~~~~~~ifDtmLAl~-----~~s~gLd~LAer~LG~~L~K 455 (538)
++..|.+++.+.....+ ++..+|+..|.+. +|+...+ ...+.|++.... ...++|+++++++ |++..
T Consensus 82 vl~~f~~~~~~~~~~iv-~~~~fD~~fL~~~~~~~~~~~~~--~~~~~dl~~~~~~~~~~~~~~~L~~~~~~~-gi~~~- 156 (207)
T PRK07748 82 LVEKLAEYDKRCKPTIV-TWGNMDMKVLKHNCEKAGVPFPF--KGQCRDLSLEYKKFFGERNQTGLWKAIEEY-GKEGT- 156 (207)
T ss_pred HHHHHHHHhCcCCeEEE-EECHHHHHHHHHHHHHcCCCCcc--cccceeHHHHHHHHhCcCCCCCHHHHHHHc-CCCCC-
Confidence 66778888876434444 5578999888653 3441111 134667776632 3468999988874 65421
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhcc
Q 009284 456 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCS 493 (538)
Q Consensus 456 ~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rL 493 (538)
. +.+.|..||..+.+|+..|..+.
T Consensus 157 -~-------------~~H~Al~DA~~ta~l~~~l~~~~ 180 (207)
T PRK07748 157 -G-------------KHHCALDDAMTTYNIFKLVEKDK 180 (207)
T ss_pred -C-------------CCcChHHHHHHHHHHHHHHHhCc
Confidence 0 02348899999999999998774
No 84
>PRK05359 oligoribonuclease; Provisional
Probab=44.70 E-value=2.3e+02 Score=27.27 Aligned_cols=91 Identities=19% Similarity=0.089 Sum_probs=46.7
Q ss_pred HHHHHHHhhcC----CCceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHhhcCCCCCHHHHHHHHhCCCCCcCccc
Q 009284 384 LDSCLTRILQS----PGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFKEPKGGLSGLAEKILGAGLNKTRRN 459 (538)
Q Consensus 384 ll~~Lk~lLed----~~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLAl~~~s~gLd~LAer~LG~~L~K~e~~ 459 (538)
+...|.+++.. ....-+|+|+.+|...|.+.+.-.... -....+|+. ++.++++++..... ..
T Consensus 82 ~~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~-l~~~~~Dv~--------tl~~l~r~~~P~~~---~~- 148 (181)
T PRK05359 82 AEAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEAY-FHYRNLDVS--------TLKELARRWKPEIL---NG- 148 (181)
T ss_pred HHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhccc-CCCcccchh--------HHHHHHHHhChhhh---hC-
Confidence 44444555542 223459999999999988743110000 001233421 22245555432110 00
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccC
Q 009284 460 SNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQ 494 (538)
Q Consensus 460 S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rLe 494 (538)
+...+.+.|-.|+...++.+..++..+.
T Consensus 149 -------~~~~~~HRal~D~~~s~~~~~~~~~~~~ 176 (181)
T PRK05359 149 -------FKKQGTHRALADIRESIAELKYYREHFF 176 (181)
T ss_pred -------CCCcCCcccHHHHHHHHHHHHHHHHHhc
Confidence 1111235577888888888888877663
No 85
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=43.17 E-value=39 Score=36.81 Aligned_cols=127 Identities=20% Similarity=0.136 Sum_probs=79.6
Q ss_pred EEEEeCCeEEEEEcCcccCCCchhHHHHHHHhhcCCCceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHhhc----
Q 009284 360 MQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFK---- 435 (538)
Q Consensus 360 iQLAt~~~a~~IdL~~l~~~~p~~ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLAl~---- 435 (538)
+++|++.+.+++|....+... +..-.++.||+..+ +. |.+.+...+...|++. ..+++|+|++..
T Consensus 216 m~ia~~n~i~llD~~~sdi~i---l~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~-----L~nVkDtQia~sLve~ 284 (458)
T KOG2405|consen 216 MNIADGNEIFLLDSLPSDIRI---LFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSA-----LKNVKDTQIASSLVEP 284 (458)
T ss_pred hhhcccchhhhhhhccCCcEE---ecccchhhhhhcce--eh-hhhhhhHHHHhHHHHH-----HHhhHHHHHHHHHhhh
Confidence 456777788888876432111 22335778887654 33 8888888888777763 267899999931
Q ss_pred ---CCCCCHHHHHHH-HhCCC-------CCcC--------cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCC
Q 009284 436 ---EPKGGLSGLAEK-ILGAG-------LNKT--------RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPT 496 (538)
Q Consensus 436 ---~~s~gLd~LAer-~LG~~-------L~K~--------e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L~~rLee~ 496 (538)
.+++..+.+.-. .|+.. ..++ ....+|..||.++...+-++.|+.+++...+.|....-.+
T Consensus 285 ~e~grr~p~~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll~~~~~l~a~~l~H 364 (458)
T KOG2405|consen 285 SEYGRRHPTSILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLLGIFDTLVAVCLSH 364 (458)
T ss_pred HHhcccCCccceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHHHHHHHHHHHHhhHhhhChHh
Confidence 234444433221 12211 0011 1223699999999888999999999999877776555444
Q ss_pred C
Q 009284 497 D 497 (538)
Q Consensus 497 ~ 497 (538)
.
T Consensus 365 L 365 (458)
T KOG2405|consen 365 L 365 (458)
T ss_pred h
Confidence 4
No 86
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=40.37 E-value=42 Score=26.44 Aligned_cols=47 Identities=23% Similarity=0.319 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHhcCCCCChhHH--HHHHHHHhccccccHHHHHhhhhh
Q 009284 122 AKEIAAYLFLDITGGFVDHDEKL--MVKILEAFDVRLTDIEKAITQLKA 168 (538)
Q Consensus 122 ~~~~~~~~~~~~~~~~~~~~~r~--~~~l~e~f~~~~~~~~~a~~~~~~ 168 (538)
...++.++.-+|..|....++++ ...|++.||++-+-+-.|+.....
T Consensus 2 ~~~i~~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~ 50 (64)
T PF00392_consen 2 YEQIYDQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEA 50 (64)
T ss_dssp HHHHHHHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHH
Confidence 35688999999999999999887 678999999977777777644433
No 87
>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=38.35 E-value=1.3e+02 Score=28.11 Aligned_cols=69 Identities=19% Similarity=0.189 Sum_probs=39.8
Q ss_pred EeehHHhHHHHHHHhCCccccccchhHhhHHHh---hcCCCCCHHHHHHHHhCCCCCcCcccccCCCCCCCHHHHHHHHH
Q 009284 401 GYNFQCDIKQLAHSYGELECFKHYEMLLDIQNV---FKEPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAAL 477 (538)
Q Consensus 401 GhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLA---l~~~s~gLd~LAer~LG~~L~K~e~~S~W~~rpLt~~Q~~YAAe 477 (538)
+-+.| |+.++...-|+.. .+--|-|+. ++-.+-++..+++||+|- .|.. -|+.
T Consensus 67 a~~AK-~LAv~a~~~G~~v-----~PGDDPlLlAYLlDPsNt~p~~varRY~~~---------~W~~---------dA~~ 122 (138)
T PF09281_consen 67 AALAK-DLAVHALREGVVV-----EPGDDPLLLAYLLDPSNTNPEGVARRYLGG---------EWPE---------DAAT 122 (138)
T ss_dssp STTHH-HHHHHHHHTT---------B---HHHHHHHH-TT--SHHHHHHHH-TS------------S---------SHHH
T ss_pred HHHHH-HHHHHHHhcCccc-----CCCCCcchhhhhcCccCCChHHHHHHhcCC---------CCCc---------cHHH
Confidence 33444 5555443357632 334588877 455678899999999873 4532 1788
Q ss_pred HHHHHHHHHHHHHhcc
Q 009284 478 DAVVLLQIFHHVRSCS 493 (538)
Q Consensus 478 DA~vlL~L~~~L~~rL 493 (538)
.|.++-+|++.|.++|
T Consensus 123 RA~~t~~L~~~L~prL 138 (138)
T PF09281_consen 123 RALATARLLRALPPRL 138 (138)
T ss_dssp HHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHhhhcC
Confidence 9999999999999876
No 88
>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=36.99 E-value=75 Score=30.32 Aligned_cols=86 Identities=21% Similarity=0.235 Sum_probs=48.7
Q ss_pred HHHHHHHhhcCCCceEEEee-hHHhHHHHHHH---hCCcccc---ccchhHhhHHHh---h----c-----------CCC
Q 009284 384 LDSCLTRILQSPGILKLGYN-FQCDIKQLAHS---YGELECF---KHYEMLLDIQNV---F----K-----------EPK 438 (538)
Q Consensus 384 ll~~Lk~lLed~~i~KVGhn-lK~Dl~vLa~~---~Gil~~~---~~~~~ifDtmLA---l----~-----------~~s 438 (538)
++..+.+++..+....|||| +.+|+..|.+. ++..... ......+|+.-. . . ..+
T Consensus 72 ~l~~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~ 151 (183)
T cd06138 72 FIAKIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPS 151 (183)
T ss_pred HHHHHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcc
Confidence 45566677765444568997 89999988653 2221000 000112354422 1 0 135
Q ss_pred CCHHHHHHHHhCCCCCcCcccccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009284 439 GGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIF 486 (538)
Q Consensus 439 ~gLd~LAer~LG~~L~K~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~ 486 (538)
++|+.|+++ +|.+.. +.+-|..||.++.+|.
T Consensus 152 ~~L~~l~~~-~gi~~~----------------~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 152 FKLEDLAQA-NGIEHS----------------NAHDALSDVEATIALA 182 (183)
T ss_pred hhHHHHHHH-CCCCcc----------------ccccHHHHHHHHHHHh
Confidence 789999986 465431 1355888998887763
No 89
>PF03997 VPS28: VPS28 protein; InterPro: IPR007143 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ].; PDB: 2J9W_B 2J9U_C 2G3K_A 2F66_E 2F6M_D 2J9V_A 2CAZ_E 2P22_B.
Probab=36.99 E-value=1.5e+02 Score=29.19 Aligned_cols=102 Identities=18% Similarity=0.222 Sum_probs=50.0
Q ss_pred HHHH-HHHHHHHHhhchhhH-HHHHHHhhhcccc-----chHHHHHHHhccchH---HHHHHHHhcCchHHHHHHh----
Q 009284 178 KTVI-EQYIFAMIDSQSYMT-AVSLLEHFSIRQS-----GESFLLKMIQNKEFK---AAEKWATFMGKPILLKRLA---- 243 (538)
Q Consensus 178 ~~~~-~~yi~~~~~~~~~~~-~~~li~~f~~~~~-----~~~~l~~~~~~~~~~---~a~~~~~~~~~~~~~~~l~---- 243 (538)
=+.| +.||+..+.+..|.+ |..||.+|..-.. .++-|.+.++.=+.. |.+| ...|.|-.++.-.
T Consensus 11 le~LEkayikD~It~~eYt~~c~kLl~Qyk~~~~~~~~~~~~~le~F~~~y~l~cp~A~~R--l~~G~P~Tie~~~~~~~ 88 (188)
T PF03997_consen 11 LEHLEKAYIKDSITEKEYTTACNKLLNQYKTILKQLKDDEFPDLEEFMKKYNLDCPAALER--LREGVPATIEHRISSSS 88 (188)
T ss_dssp HHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHTSTTHHHHHHHHHHHHHTTS-HHHHHHH--HHCTSS-----------
T ss_pred HHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHcccccCCCHHHHHHHhcccCChHHHH--HHcCCCCchhhhccccc
Confidence 3444 789999998888987 8899998854332 234455544322211 3344 3456776544421
Q ss_pred hhhchHH--HHHHhhcchhHHHHHHHHhhccCCHHHHHHHHHHc
Q 009284 244 EKACWDI--AEAKTKGDKRLLEYLVYLAMEAGYSEKVDELCERY 285 (538)
Q Consensus 244 ~k~~wd~--a~~~~~~D~~l~~~lv~L~~~~~d~~~L~~l~~ry 285 (538)
+++..-+ |+++ ---+..++.+.+.-...+++..++.++
T Consensus 89 ~~~~~ak~Vae~t----~~FIT~mDaLKLn~~a~DqLhPlL~dL 128 (188)
T PF03997_consen 89 DKGNSAKLVAEAT----QNFITLMDALKLNYRAKDQLHPLLSDL 128 (188)
T ss_dssp ---CHHHHHHHHH----HHHHHHHHHHHTT--BHHHHHHHHHHH
T ss_pred CCchHHHHHHHHh----ChhhhhhHHHhccchhHhhHhhHHHHH
Confidence 1222211 2211 124556777777777777776666543
No 90
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=36.48 E-value=1.9 Score=46.42 Aligned_cols=71 Identities=28% Similarity=0.410 Sum_probs=54.3
Q ss_pred CceeEEEEEeCCeEEEEEcCcccCCCchhHHHHHHHhhcCCCceEEEeehHHhHHHHHHHhCCccccccchhHhhHHHh
Q 009284 355 NKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNV 433 (538)
Q Consensus 355 ~~VsLiQLAt~~~a~~IdL~~l~~~~p~~ll~~Lk~lLed~~i~KVGhnlK~Dl~vLa~~~Gil~~~~~~~~ifDtmLA 433 (538)
...+.+|.++.-.+|++|+..++ .......+..++++.+|.|+-|++.--...+...|||+. +++||++.+
T Consensus 74 ~~l~~~q~~~~~~~yl~~i~~~~---~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~~~~~~i~~-----n~v~~~q~~ 144 (458)
T KOG2405|consen 74 GKLCWLQVATNCRVYLFDIFLLG---SRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGILL-----NNVFDTQVA 144 (458)
T ss_pred CcchhHHHHHHHHHHHHHHHHhh---hHHHHHHHHHHhhhhhHhhhHHHHHHHHHHhcccceeee-----cchhhhhhh
Confidence 35666666666667777776443 133566788899999999999998888888888899954 789999998
No 91
>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=34.12 E-value=40 Score=33.51 Aligned_cols=64 Identities=17% Similarity=0.238 Sum_probs=42.3
Q ss_pred HhhHHHhh----cCCCCCHHHHHHHHhCCCCC--cCccccc-CCCCCCC-HHHHHHHHHHHHHHHHHHHHHH
Q 009284 427 LLDIQNVF----KEPKGGLSGLAEKILGAGLN--KTRRNSN-WEQRPLS-QNQLEYAALDAVVLLQIFHHVR 490 (538)
Q Consensus 427 ifDtmLAl----~~~s~gLd~LAer~LG~~L~--K~e~~S~-W~~rpLt-~~Q~~YAAeDA~vlL~L~~~L~ 490 (538)
.+|+.... +-.+++|+.+|+.+||..-. ..+.+.. |...|-. ..-++|...||..+++|...|.
T Consensus 153 ~iD~~~~~~~~~kl~sy~L~~Va~~~Lg~~k~d~~~~~i~~~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl~ 224 (230)
T cd05777 153 QFDLLQVIQRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLM 224 (230)
T ss_pred eeeHHHHHHHhcCcccCcHHHHHHHHhCCCCCCCCHHHHHHHHccCHhHhHHHHHhhHHHHHHHHHHHHHHh
Confidence 34665553 24689999999999996432 1223333 3323321 3348999999999999999874
No 92
>PF04858 TH1: TH1 protein; InterPro: IPR006942 TH1 is a highly conserved but uncharacterised metazoan protein. No homologue has been identified in Caenorhabditis elegans []. TH1 binds specifically to A-Raf kinase [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=33.41 E-value=36 Score=39.06 Aligned_cols=99 Identities=18% Similarity=0.248 Sum_probs=57.8
Q ss_pred HHHHHHHhhhhcccchhhhhHHHHHHHHHHHhhCCCCCCC-------------ceeeeeeeeecccccccccchhHHHHH
Q 009284 38 VFLYLLKECYIHGTCKATRKFRALQQQVSQALCNSPEPGP-------------ATFIVRCLYVLPIFGVYSEGFSHLIIS 104 (538)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~~ 104 (538)
+|+.||+|.--.-.-.-+.=|++|..-.. ++.+..-| ..|.+.|-||+|++..-.+=|..
T Consensus 445 ~~L~LLdeIa~~Hp~lr~~vl~lL~~~le---~~~~~l~~l~~le~kr~ilD~~V~L~s~G~VlPVl~~i~~~~~~---- 517 (584)
T PF04858_consen 445 VHLALLDEIATRHPLLRPSVLDLLVRLLE---SEGDELDILVQLELKRTILDRMVHLLSRGYVLPVLEYIRKCWAR---- 517 (584)
T ss_pred hHHHHhhHHHhcCHhhHHHHHHHHHHHHH---ccCCcccHHHHHHHHHHHHHHHHHHHhCCeeehHHHHHHHHHhc----
Confidence 78888898765555555555666655444 33333333 45789999999988533332222
Q ss_pred HHHhhhcccCCccchhHHHHHHHHHHHHHhcCCCCCh-hHHHHHHHHHhcc
Q 009284 105 ALRRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHD-EKLMVKILEAFDV 154 (538)
Q Consensus 105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~r~~~~l~e~f~~ 154 (538)
.+=|....|+.+.. +|||+++=-..+ -..+++|++.-++
T Consensus 518 ----------~~iD~SLiRyFv~e-VLeii~PPYS~~Fv~~~l~ll~~~~i 557 (584)
T PF04858_consen 518 ----------GDIDPSLIRYFVTE-VLEIIGPPYSPEFVQLFLPLLENAEI 557 (584)
T ss_pred ----------cCCcHHHHHHHHHH-HHHHcCCCCCHHHHHHHHHHHhchhh
Confidence 12344455555444 467777654444 5566677666555
No 93
>PHA01976 helix-turn-helix protein
Probab=33.26 E-value=60 Score=25.40 Aligned_cols=54 Identities=13% Similarity=0.158 Sum_probs=42.2
Q ss_pred HHHHhhhcccCCccchhHHHHHHHHHHHHHhcCCCCChhHHHHHHHHHhccccccH
Q 009284 104 SALRRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDI 159 (538)
Q Consensus 104 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~l~e~f~~~~~~~ 159 (538)
-.+|.-... +++++-+.-.+..+.+-.+-.|........+.++++.||++++.+
T Consensus 8 ~~~R~~~gl--t~~~lA~~~gvs~~~v~~~e~g~~~p~~~~l~~ia~~l~v~~~~l 61 (67)
T PHA01976 8 IKARNARAW--SAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWL 61 (67)
T ss_pred HHHHHHcCC--CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHH
Confidence 344553333 578888888888899999999887667788999999999988776
No 94
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=33.17 E-value=77 Score=23.46 Aligned_cols=52 Identities=17% Similarity=0.287 Sum_probs=41.0
Q ss_pred HHHHHhhhcccCCccchhHHHHHHHHHHHHHhcCCCCChhHHHHHHHHHhcccc
Q 009284 103 ISALRRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRL 156 (538)
Q Consensus 103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~l~e~f~~~~ 156 (538)
|..+|.-. .-+++|+-+.-.+.-..+-.+-.|-.......+.++++.||++|
T Consensus 7 l~~~r~~~--gltq~~lA~~~gvs~~~vs~~e~g~~~~~~~~~~~i~~~lgv~l 58 (58)
T TIGR03070 7 VRARRKAL--GLTQADLADLAGVGLRFIRDVENGKPTVRLDKVLRVLDALGLEL 58 (58)
T ss_pred HHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCC
Confidence 34455433 33588988888889999999999987777888999999999865
No 95
>TIGR02508 type_III_yscG type III secretion protein, YscG family. YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.
Probab=33.13 E-value=1.6e+02 Score=26.70 Aligned_cols=43 Identities=19% Similarity=0.230 Sum_probs=29.7
Q ss_pred HHHHHhhchh-hHHHHHHHhhhccccchHHHHHHHhccchHHHHHHHHhcCchHH
Q 009284 185 IFAMIDSQSY-MTAVSLLEHFSIRQSGESFLLKMIQNKEFKAAEKWATFMGKPIL 238 (538)
Q Consensus 185 i~~~~~~~~~-~~~~~li~~f~~~~~~~~~l~~~~~~~~~~~a~~~~~~~~~~~~ 238 (538)
|-+.+.++.. ..+|.||+--| +|--|+|+.|-+.....-.|++
T Consensus 27 IAdwL~~~~~~~E~v~lIRlsS-----------LmNrG~Yq~Al~l~~~~~~pdl 70 (115)
T TIGR02508 27 IADWLHLKGESEEAVQLIRLSS-----------LMNRGDYQSALQLGNKLCYPDL 70 (115)
T ss_pred HHHHHhcCCchHHHHHHHHHHH-----------HHccchHHHHHHhcCCCCCchH
Confidence 4455566554 56999997544 4566888888887777777776
No 96
>PRK00118 putative DNA-binding protein; Validated
Probab=31.28 E-value=2.3e+02 Score=25.30 Aligned_cols=34 Identities=18% Similarity=0.355 Sum_probs=29.1
Q ss_pred HHHHHhcCCCCChhHHHHHHHHHhccccccHHHH
Q 009284 129 LFLDITGGFVDHDEKLMVKILEAFDVRLTDIEKA 162 (538)
Q Consensus 129 ~~~~~~~~~~~~~~r~~~~l~e~f~~~~~~~~~a 162 (538)
.++|--++..+...|-++++.-.-|.+.+.|+.-
T Consensus 9 ~l~d~~~~~L~ekqRevl~L~y~eg~S~~EIAe~ 42 (104)
T PRK00118 9 LLFDFYGSLLTEKQRNYMELYYLDDYSLGEIAEE 42 (104)
T ss_pred HHHHHHhccCCHHHHHHHHHHHHcCCCHHHHHHH
Confidence 5788889999988999999988889988888666
No 97
>KOG4634 consensus Mitochondrial F1F0-ATP synthase, subunit Cf6 (coupling factor 6) [Energy production and conversion]
Probab=30.77 E-value=1.4e+02 Score=26.61 Aligned_cols=60 Identities=23% Similarity=0.371 Sum_probs=44.5
Q ss_pred hhHHHHHHHHhhhcccCCccchhHHHHHHHHHHHHHhc---------CCCCCh-------hHHHHHHHHHhccccccH
Q 009284 98 FSHLIISALRRHQKTTVNSADSTQAKEIAAYLFLDITG---------GFVDHD-------EKLMVKILEAFDVRLTDI 159 (538)
Q Consensus 98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~-------~r~~~~l~e~f~~~~~~~ 159 (538)
||-.|-|+.++++.+ +---+...+..--|+|+|-|+ ++|+.+ .+-+.||+..||+.-+||
T Consensus 8 ~s~vlrs~vs~~~gv--~a~a~nk~~DpIqqlFldKvREy~~ks~~Gklvds~pe~e~eLk~el~rla~qfg~~~~Dm 83 (105)
T KOG4634|consen 8 FSSVLRSAVSVHLGV--TATAFNKELDPIQQLFLDKVREYKKKSPAGKLVDSDPEYEQELKEELFRLAQQFGLANADM 83 (105)
T ss_pred HHHHHHHHHHHhhch--hhhHHHhhhChHHHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCccCchh
Confidence 567778888877755 233456677788899999874 566666 677899999999766665
No 98
>PLN03218 maturation of RBCL 1; Provisional
Probab=30.60 E-value=1.1e+03 Score=29.19 Aligned_cols=99 Identities=17% Similarity=0.030 Sum_probs=55.9
Q ss_pred HHHhhchhhHHHHHHHhh---hccc--cch-HHHHHHHhccchHHHHHHHHhcC----ch------HHHHHHhhhhchHH
Q 009284 187 AMIDSQSYMTAVSLLEHF---SIRQ--SGE-SFLLKMIQNKEFKAAEKWATFMG----KP------ILLKRLAEKACWDI 250 (538)
Q Consensus 187 ~~~~~~~~~~~~~li~~f---~~~~--~~~-~~l~~~~~~~~~~~a~~~~~~~~----~~------~~~~~l~~k~~wd~ 250 (538)
-+.+.|.+..|..+.+.- ++.- ..+ ..+....++|+++.|.+.=..|. .| .++..+...|.++.
T Consensus 588 ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~ee 667 (1060)
T PLN03218 588 ACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDK 667 (1060)
T ss_pred HHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHH
Confidence 333445555566665322 2211 111 23445556777777765433333 12 23566666777777
Q ss_pred HHHHhhc--------chhHHHHHHHHhhccCCHHHHHHHHHHc
Q 009284 251 AEAKTKG--------DKRLLEYLVYLAMEAGYSEKVDELCERY 285 (538)
Q Consensus 251 a~~~~~~--------D~~l~~~lv~L~~~~~d~~~L~~l~~ry 285 (538)
|....+. |...-..|+......++.+++.++|++.
T Consensus 668 A~~l~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM 710 (1060)
T PLN03218 668 AFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDI 710 (1060)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 7666543 4445556777777778888887777765
No 99
>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.28 E-value=1.2e+03 Score=29.35 Aligned_cols=177 Identities=16% Similarity=0.187 Sum_probs=0.0
Q ss_pred cchhHHHHHHHHhhhcccCCccchhHHHHHHHH--------------------------HHHHHhcCCCCChhHHHHHHH
Q 009284 96 EGFSHLIISALRRHQKTTVNSADSTQAKEIAAY--------------------------LFLDITGGFVDHDEKLMVKIL 149 (538)
Q Consensus 96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------------------~~~~~~~~~~~~~~r~~~~l~ 149 (538)
.|++|=.+.-||. +++ ++.+|-++---..-| ++||+..+.-+.+..+=.||+
T Consensus 507 vGyTPdymflLq~-l~r-~sPD~~~qFa~~l~Q~~~~~~die~I~DlFme~N~iQq~TSFLLdaLK~~~Pd~g~LQTrLL 584 (1666)
T KOG0985|consen 507 VGYTPDYMFLLQQ-LKR-SSPDQALQFAMMLVQDEEPLADIEQIVDLFMELNLIQQCTSFLLDALKLNSPDEGHLQTRLL 584 (1666)
T ss_pred cCCCccHHHHHHH-HHc-cChhHHHHHHHHhhccCCCcccHHHHHHHHHHHHhhhhhHHHHHHHhcCCChhhhhHHHHHH
Q ss_pred HHhccccccHHHHHhhhhhccccchh-----------HHHHH-----------------------HHHHHHHHHhhchhh
Q 009284 150 EAFDVRLTDIEKAITQLKAQNEHRFD-----------TAKTV-----------------------IEQYIFAMIDSQSYM 195 (538)
Q Consensus 150 e~f~~~~~~~~~a~~~~~~~~~~~~~-----------~~~~~-----------------------~~~yi~~~~~~~~~~ 195 (538)
|+=-+...++++||-+|.+-.-++.+ ..|.+ +-.|.-++--.+++.
T Consensus 585 E~NL~~aPqVADAILgN~mFtHyDra~IAqLCEKAGL~qraLehytDl~DIKR~vVhth~L~pEwLv~yFg~lsve~s~e 664 (1666)
T KOG0985|consen 585 EMNLVHAPQVADAILGNDMFTHYDRAEIAQLCEKAGLLQRALEHYTDLYDIKRVVVHTHLLNPEWLVNYFGSLSVEDSLE 664 (1666)
T ss_pred HHHhccchHHHHHHHhccccccccHHHHHHHHHhcchHHHHHHhcccHHHHHHHHHHhccCCHHHHHHHHHhcCHHHHHH
Q ss_pred HHHHHHHhhhccccchHHHHHHHhccchHHHHHHHHhcCchHHHHHHhhhhchHH------HHHHhhcchhHHHHHHHHh
Q 009284 196 TAVSLLEHFSIRQSGESFLLKMIQNKEFKAAEKWATFMGKPILLKRLAEKACWDI------AEAKTKGDKRLLEYLVYLA 269 (538)
Q Consensus 196 ~~~~li~~f~~~~~~~~~l~~~~~~~~~~~a~~~~~~~~~~~~~~~l~~k~~wd~------a~~~~~~D~~l~~~lv~L~ 269 (538)
|+.-+..=||++- |+-++| -|.++..-.|-..+|+-+-.=..+|- -.+-...|+++..-.++-+
T Consensus 665 -clkaml~~NirqN----lQi~VQ-----vatky~eqlg~~~li~lFE~fks~eGL~yfLgSivn~seDpevh~KYIqAA 734 (1666)
T KOG0985|consen 665 -CLKAMLSANIRQN----LQIVVQ-----VATKYHEQLGAQALIELFESFKSYEGLYYFLGSIVNFSEDPEVHFKYIQAA 734 (1666)
T ss_pred -HHHHHHHHHHHhh----hHHHHH-----HHHHHHHHhCHHHHHHHHHhhccchhHHHHHHHHhccccCchHHHHHHHHH
Q ss_pred hccCCHHHHHHHHHH
Q 009284 270 MEAGYSEKVDELCER 284 (538)
Q Consensus 270 ~~~~d~~~L~~l~~r 284 (538)
...+...++...|++
T Consensus 735 ~kt~QikEvERicre 749 (1666)
T KOG0985|consen 735 CKTGQIKEVERICRE 749 (1666)
T ss_pred HhhccHHHHHHHHhc
No 100
>PF12960 DUF3849: Protein of unknown function (DUF3849); InterPro: IPR024383 This domain is found in a family of uncharacterised proteins found by clustering human gut metagenomic sequences [].
Probab=29.61 E-value=74 Score=29.72 Aligned_cols=62 Identities=19% Similarity=0.255 Sum_probs=48.2
Q ss_pred hHHHHHHHHHHHHHHhhchhh-H-HHHHHHhhhccccchH---HHHHHHhccchH-HHHHHHHhcCch
Q 009284 175 DTAKTVIEQYIFAMIDSQSYM-T-AVSLLEHFSIRQSGES---FLLKMIQNKEFK-AAEKWATFMGKP 236 (538)
Q Consensus 175 ~~~~~~~~~yi~~~~~~~~~~-~-~~~li~~f~~~~~~~~---~l~~~~~~~~~~-~a~~~~~~~~~~ 236 (538)
..||+.+++-|.+-...-... . +-.+|++|+.+--.+. ++....|.|+|. ....||..+..|
T Consensus 27 ~~Ck~aIE~aI~~~~~~~~L~~~a~~~vie~fG~eR~~~VLAnTIq~kd~DGRfS~~NK~WAk~~~~~ 94 (133)
T PF12960_consen 27 IACKEAIEQAIREHFDGNRLDPDAVKEVIEKFGYERVAYVLANTIQQKDWDGRFSQDNKDWAKTIPVP 94 (133)
T ss_pred HHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHhccccccCCHHHHHHHHcCCCC
Confidence 478888999999988775555 3 6678899998875554 777888889987 557799998877
No 101
>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm
Probab=25.95 E-value=4.5e+02 Score=27.82 Aligned_cols=76 Identities=26% Similarity=0.274 Sum_probs=47.5
Q ss_pred cchHHHHHHHhccchHHHHHHHHhcCchHH------HHHHhhhhchHHHHHHhhcchhHH--HHHHHHhhccCCHHHHHH
Q 009284 209 SGESFLLKMIQNKEFKAAEKWATFMGKPIL------LKRLAEKACWDIAEAKTKGDKRLL--EYLVYLAMEAGYSEKVDE 280 (538)
Q Consensus 209 ~~~~~l~~~~~~~~~~~a~~~~~~~~~~~~------~~~l~~k~~wd~a~~~~~~D~~l~--~~lv~L~~~~~d~~~L~~ 280 (538)
+=..++.+++..|+.+.|++-......|.- ++.|++.+.||+=+..++.-+--+ ...++.....+...++..
T Consensus 179 Sl~~Ti~~li~~~~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~skKsPIGyepFv~~~~~~~~~~eA~~ 258 (319)
T PF04840_consen 179 SLNDTIRKLIEMGQEKQAEKLKKEFKVPDKRFWWLKIKALAENKDWDELEKFAKSKKSPIGYEPFVEACLKYGNKKEASK 258 (319)
T ss_pred CHHHHHHHHHHCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHhCCCCCCChHHHHHHHHHCCCHHHHHH
Confidence 334588888888888888887777676633 888889999998666655321111 123333334445555555
Q ss_pred HHHH
Q 009284 281 LCER 284 (538)
Q Consensus 281 l~~r 284 (538)
+..+
T Consensus 259 yI~k 262 (319)
T PF04840_consen 259 YIPK 262 (319)
T ss_pred HHHh
Confidence 5555
No 102
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=25.76 E-value=60 Score=32.51 Aligned_cols=59 Identities=15% Similarity=0.207 Sum_probs=39.5
Q ss_pred hhHHHhh----cCCCCCHHHHHHHHhCCCCCc--CcccccCC-CC--CCCHHHHHHHHHHHHHHHHHH
Q 009284 428 LDIQNVF----KEPKGGLSGLAEKILGAGLNK--TRRNSNWE-QR--PLSQNQLEYAALDAVVLLQIF 486 (538)
Q Consensus 428 fDtmLAl----~~~s~gLd~LAer~LG~~L~K--~e~~S~W~-~r--pLt~~Q~~YAAeDA~vlL~L~ 486 (538)
+|+.-.. +..+++|+.++..+||.+.+. ...++.|- .. .-...-++|...||..+++|.
T Consensus 163 lD~~~~~r~~~kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l~l~Ll 230 (231)
T cd05778 163 LNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEIL 230 (231)
T ss_pred eEhHHHHHHHcCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHHHHHhh
Confidence 3555442 346899999999999976542 23455552 21 123344799999999999874
No 103
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=25.67 E-value=2.6e+02 Score=21.83 Aligned_cols=48 Identities=17% Similarity=0.311 Sum_probs=30.5
Q ss_pred HHHHHHHHhcCCCCChhHHHHHHHHHhccccccHHHHHhhhhhccccchhHHHHHHHHHHHHHHhhc
Q 009284 126 AAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDIEKAITQLKAQNEHRFDTAKTVIEQYIFAMIDSQ 192 (538)
Q Consensus 126 ~~~~~~~~~~~~~~~~~r~~~~l~e~f~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~yi~~~~~~~ 192 (538)
.|..+...+.|- ..-+.|+-.+.+.||+ +.+.+++-+.+|+.+|.+.|
T Consensus 18 ~a~~Iw~~~~g~-~t~~ei~~~l~~~y~~------------------~~~~~~~dv~~fl~~L~~~g 65 (68)
T PF05402_consen 18 TAAFIWELLDGP-RTVEEIVDALAEEYDV------------------DPEEAEEDVEEFLEQLREKG 65 (68)
T ss_dssp HHHHHHHH--SS-S-HHHHHHHHHHHTT--------------------HHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHccCC-CCHHHHHHHHHHHcCC------------------CHHHHHHHHHHHHHHHHHCc
Confidence 455666666654 3357788888888888 45566777778888887655
No 104
>PRK06424 transcription factor; Provisional
Probab=25.26 E-value=1.1e+02 Score=28.90 Aligned_cols=55 Identities=16% Similarity=0.124 Sum_probs=46.1
Q ss_pred HHHHHhhhcccCCccchhHHHHHHHHHHHHHhcCCCCChhHHHHHHHHHhccccccH
Q 009284 103 ISALRRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDI 159 (538)
Q Consensus 103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~l~e~f~~~~~~~ 159 (538)
|..+|.-.. -+|+++-+.-.+...++-.|-.|-.......+.+|.+.||+++++.
T Consensus 89 Ir~lRe~~G--LSQ~eLA~~iGvs~stIskiE~G~~~Ps~~~l~kLa~~Lgvsl~e~ 143 (144)
T PRK06424 89 VKNARERLS--MSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGITLIEK 143 (144)
T ss_pred HHHHHHHcC--CCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCCCC
Confidence 456665344 4599998888888999999999999989999999999999998763
No 105
>PF07399 DUF1504: Protein of unknown function (DUF1504); InterPro: IPR009978 This family consists of several hypothetical bacterial proteins of around 440 residues in length. The function of this family is unknown.
Probab=24.80 E-value=33 Score=37.67 Aligned_cols=90 Identities=16% Similarity=0.309 Sum_probs=62.4
Q ss_pred HHHHHHhhCCCCCCCceeeeeeeeecccccccccchhHHHHHHH---HhhhcccCCccchhHHHHHHHHHHHHH-hcCCC
Q 009284 63 QQVSQALCNSPEPGPATFIVRCLYVLPIFGVYSEGFSHLIISAL---RRHQKTTVNSADSTQAKEIAAYLFLDI-TGGFV 138 (538)
Q Consensus 63 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ 138 (538)
+++-+.+..-|.|+|..+..-||.++||+|+.---=.-|.|.|| |||.+.++ ++-+.- ---.=||++| ++|..
T Consensus 121 ~~~v~~iArlp~~s~~a~~~~~L~~~PLlGSfITEpaAMTlaAllL~~~~f~~~~-s~~lkY--aTLGvLFvNISIGGtL 197 (438)
T PF07399_consen 121 ERLVRFIARLPKPSPVAWWWLILTLVPLLGSFITEPAAMTLAALLLRDQFFRLGP-SPRLKY--ATLGVLFVNISIGGTL 197 (438)
T ss_pred HHHHHHHHhCCCCCchhHHHHHHHHHHhhhhhhccHHHHHHHHHHHHHHhccCCC-CHHHHH--HHHHHHheEeeecccc
Confidence 45555666699999999999999999999977666688999997 67777744 332211 1223466666 45555
Q ss_pred CCh-hHHHHHHHHHhccc
Q 009284 139 DHD-EKLMVKILEAFDVR 155 (538)
Q Consensus 139 ~~~-~r~~~~l~e~f~~~ 155 (538)
.|= .+.|+-++.+.|-+
T Consensus 198 T~fAAPPVLMVA~~w~Wd 215 (438)
T PF07399_consen 198 TSFAAPPVLMVASTWGWD 215 (438)
T ss_pred cccccCcceeEecccCCC
Confidence 443 66777777777663
No 106
>PRK08359 transcription factor; Validated
Probab=24.52 E-value=92 Score=30.38 Aligned_cols=57 Identities=12% Similarity=0.109 Sum_probs=48.5
Q ss_pred HHHHHHhhhcccCCccchhHHHHHHHHHHHHHhcCCCCChhHHHHHHHHHhccccccHH
Q 009284 102 IISALRRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDIE 160 (538)
Q Consensus 102 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~l~e~f~~~~~~~~ 160 (538)
.|-.+|. +..-+|+++-+.-++...+|--|=.|..+....++.+|...|||+|....
T Consensus 89 rIkeaRe--~kglSQeeLA~~lgvs~stI~~iE~G~~~Ps~~~l~kLak~l~VsL~e~~ 145 (176)
T PRK08359 89 RVYEAIQ--KSGLSYEELSHEVGLSVNDLRRIAHGEYEPTIKEAKKLERYFKIKLIERV 145 (176)
T ss_pred HHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHCCCcCCCHHHHHHHHHHhCCcccccc
Confidence 4556665 23457999999999999999999999999999999999999999988743
No 107
>PF08154 NLE: NLE (NUC135) domain; InterPro: IPR012972 This domain is located N-terminal to WD40 repeats(IPR001680 from INTERPRO). It is found in the microtubule-associated protein Q12024 from SWISSPROT [].
Probab=23.08 E-value=93 Score=25.06 Aligned_cols=27 Identities=30% Similarity=0.459 Sum_probs=24.0
Q ss_pred HHHHHHHHHHhhCCCCCCCceeeeeee
Q 009284 59 RALQQQVSQALCNSPEPGPATFIVRCL 85 (538)
Q Consensus 59 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (538)
+.|+..|.+.|.|..+|=|+.|.|.=-
T Consensus 29 ~~Ls~LvN~LL~~~~~~vpfdF~i~~~ 55 (65)
T PF08154_consen 29 KELSELVNQLLDDEEEPVPFDFLINGE 55 (65)
T ss_pred HHHHHHHHHHhccCCCCCcEEEEECCE
Confidence 679999999999999999999998743
No 108
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=23.01 E-value=2.3e+02 Score=21.54 Aligned_cols=34 Identities=18% Similarity=0.218 Sum_probs=20.1
Q ss_pred HHHhhcchhHHHHHHHHhhccCCHHHHHHHHHHc
Q 009284 252 EAKTKGDKRLLEYLVYLAMEAGYSEKVDELCERY 285 (538)
Q Consensus 252 ~~~~~~D~~l~~~lv~L~~~~~d~~~L~~l~~ry 285 (538)
...-.++.+....+.....+.++.++....++++
T Consensus 18 l~~~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~ 51 (68)
T PF14559_consen 18 LQRNPDNPEARLLLAQCYLKQGQYDEAEELLERL 51 (68)
T ss_dssp HHHTTTSHHHHHHHHHHHHHTT-HHHHHHHHHCC
T ss_pred HHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 3344455666666666666677777776666543
No 109
>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []. It is also involved in sporulation [].
Probab=22.89 E-value=1.9e+02 Score=29.59 Aligned_cols=58 Identities=17% Similarity=0.107 Sum_probs=33.1
Q ss_pred chHHHHHHHHhhhhc----c-cchhhhhHHHHHHHHHHHhhCCC-CCCCceeeeeeeeeccccc
Q 009284 35 SPVVFLYLLKECYIH----G-TCKATRKFRALQQQVSQALCNSP-EPGPATFIVRCLYVLPIFG 92 (538)
Q Consensus 35 ~~~~~~~~~~~~~~~----~-~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 92 (538)
.+..-..+|++.|-+ | +-+.+..+..|+..|-+.|.|.- +.+...++-.|.-++-+..
T Consensus 51 ~~~~a~~wL~~a~~~l~~~~~~~~~~~~~~elr~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~ 114 (278)
T PF08631_consen 51 KYEEAVKWLQRAYDILEKPGKMDKLSPDGSELRLSILRLLANAYLEWDTYESVEKALNALRLLE 114 (278)
T ss_pred ChHHHHHHHHHHHHHHHhhhhccccCCcHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHH
Confidence 344455677888877 2 34555545445555444444332 3445567777888877773
No 110
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=22.69 E-value=6.4e+02 Score=32.70 Aligned_cols=151 Identities=21% Similarity=0.213 Sum_probs=82.0
Q ss_pred CCeEEEEeeeecCCccCCcCCceeEEEEEe--CCeEEEE--------EcCccc--C-----------CCchhHHHHHHHh
Q 009284 335 CKVVGIDCEWKPNYVKGCKMNKVSIMQIAS--DEMVFIF--------DLIKLA--E-----------DVPDVLDSCLTRI 391 (538)
Q Consensus 335 a~~IgfDtE~~~l~~~~~~~~~VsLiQLAt--~~~a~~I--------dL~~l~--~-----------~~p~~ll~~Lk~l 391 (538)
..+.+||.||+.++.+.|++..-.++=|+. +|+.|+| |+.... + ..|++ ...|.+|
T Consensus 246 p~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREiVs~DIedfEYTPKpE~eG~F~v~Ne~dE-v~Ll~Rf 324 (2173)
T KOG1798|consen 246 PRVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREIVSEDIEDFEYTPKPEYEGPFCVFNEPDE-VGLLQRF 324 (2173)
T ss_pred ceEEEEeeecccCCCCCCCcccceEEEEEEEecCceEEEechhhhccchhhcccCCccccccceEEecCCcH-HHHHHHH
Confidence 467999999987765655554444554554 6777766 221110 0 11222 2345555
Q ss_pred hcC-----CCceEEEeehHH-hHHHH---HHHhCCccccccchhHhhHHHh-----------h---------cCCCCCHH
Q 009284 392 LQS-----PGILKLGYNFQC-DIKQL---AHSYGELECFKHYEMLLDIQNV-----------F---------KEPKGGLS 442 (538)
Q Consensus 392 Led-----~~i~KVGhnlK~-Dl~vL---a~~~Gil~~~~~~~~ifDtmLA-----------l---------~~~s~gLd 442 (538)
|+. |. ..+.||.-+ |+-.+ +..||+.. .+..|..-|.+-. + ...++||.
T Consensus 325 FeHiq~~kP~-iivTyNGDFFDWPFve~Ra~~hGi~m-~eEiGF~~D~~gEyks~~c~HmDcfrWVKRDSYLPqGSqgLK 402 (2173)
T KOG1798|consen 325 FEHIQEVKPT-IIVTYNGDFFDWPFVEARAKIHGISM-NEEIGFRRDSQGEYKSPFCIHMDCFRWVKRDSYLPQGSQGLK 402 (2173)
T ss_pred HHHHHhcCCc-EEEEecCccccchhhHHHHHhcCCCc-chhcCceecccccccccceeehhhhhhhhhcccCCCcccchh
Confidence 554 33 346777543 44332 23367621 1122333342221 1 13589999
Q ss_pred HHHHHHhCCCCC--cCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009284 443 GLAEKILGAGLN--KTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHV 489 (538)
Q Consensus 443 ~LAer~LG~~L~--K~e~~S~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L 489 (538)
.+...-||+... ..|.+..+.. .-++....|.+.||.+++-||=..
T Consensus 403 AVTkaKLGYdPvEvdPEdM~~~A~-EkPQ~lasYSVSDAVATYyLYMkY 450 (2173)
T KOG1798|consen 403 AVTKAKLGYDPVEVDPEDMVRMAM-EKPQTLASYSVSDAVATYYLYMKY 450 (2173)
T ss_pred HHHHHhhCCCcccCCHHHhhhhhh-hCchhhhhcchHHHHHHHHHHHHH
Confidence 999999997543 1233332221 122344789999999999988543
No 111
>cd02908 Macro_Appr_pase_like Macro domain, Appr-1"-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes. This family is composed of uncharacterized proteins that show similarity to Appr-1"-pase, containing conserved putative active site residues. Appr-1"-pase is a phosphatase specific for ADP-ribose-1"-monophosphate.
Probab=22.22 E-value=71 Score=30.11 Aligned_cols=8 Identities=25% Similarity=0.895 Sum_probs=5.6
Q ss_pred Cceeeeee
Q 009284 77 PATFIVRC 84 (538)
Q Consensus 77 ~~~~~~~~ 84 (538)
|+.||+|+
T Consensus 67 ~~~~IiH~ 74 (165)
T cd02908 67 PAKYVIHT 74 (165)
T ss_pred CCCEEEEE
Confidence 46777775
No 112
>COG5123 TOA2 Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=21.77 E-value=44 Score=29.75 Aligned_cols=28 Identities=21% Similarity=0.420 Sum_probs=19.2
Q ss_pred HHHHhcCCCCC---hhHHHHHHHHHhccccc
Q 009284 130 FLDITGGFVDH---DEKLMVKILEAFDVRLT 157 (538)
Q Consensus 130 ~~~~~~~~~~~---~~r~~~~l~e~f~~~~~ 157 (538)
+.|++.-+|.- .+..-+|+|||||.+.+
T Consensus 17 L~dalD~lis~g~isp~lam~vLetFDksv~ 47 (113)
T COG5123 17 LEDALDELISAGVISPNLAMHVLETFDKSVP 47 (113)
T ss_pred HHHHHHHHHhcCCcCHHHHHHHHHHhhhHHH
Confidence 44555444443 48899999999999543
No 113
>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=21.27 E-value=1e+02 Score=30.87 Aligned_cols=63 Identities=19% Similarity=0.204 Sum_probs=41.2
Q ss_pred HhhHHHhh----cCCCCCHHHHHHHHhCCCCC--cCcccc-cCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009284 427 LLDIQNVF----KEPKGGLSGLAEKILGAGLN--KTRRNS-NWEQRPLSQNQLEYAALDAVVLLQIFHHV 489 (538)
Q Consensus 427 ifDtmLAl----~~~s~gLd~LAer~LG~~L~--K~e~~S-~W~~rpLt~~Q~~YAAeDA~vlL~L~~~L 489 (538)
++|+.... ...+++|+++++.+||..-. ..++.. -|....--..-++|...||..+++|...|
T Consensus 157 ~~D~~~~~k~~~~~~sY~L~~va~~~Lg~~k~di~~~~i~~~~~~~~~l~~l~~y~~~Da~l~~~L~~kl 226 (234)
T cd05776 157 LCDTYLSAKELIRCKSYDLTELSQQVLGIERQDIDPEEILNMYNDSESLLKLLEHTEKDAYLILQLMFKL 226 (234)
T ss_pred hhccHHHHHHHhCCCCCChHHHHHHHhCcCcccCCHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55777763 25789999999999996321 111222 23320111223789999999999998877
No 114
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=21.14 E-value=1.7e+02 Score=25.17 Aligned_cols=60 Identities=15% Similarity=0.143 Sum_probs=42.8
Q ss_pred chhHHHHHHHHhhhcccCCccchhHHHHHHHHHHHHHhcCCCCChhHHHHHHHHHhccccc
Q 009284 97 GFSHLIISALRRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLT 157 (538)
Q Consensus 97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~l~e~f~~~~~ 157 (538)
|=++++..+++.+.+.-..+. +-+.-++...++-.|-.|..+..-..+.++++.||++++
T Consensus 28 ~~~~~~~~~l~~~r~~~glSq-LAe~~GIs~stLs~iE~g~~~Ps~~tL~kI~~aLgi~l~ 87 (89)
T TIGR02684 28 GDPAYIAHALGYIARARGMTQ-LARKTGLSRESLYKALSGKGNPTFDTILKVTKALGLKLT 87 (89)
T ss_pred CCHHHHHHHHHHHHHHCChHH-HHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCcee
Confidence 445556666665544423332 555555777889999999988888999999999999774
No 115
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=20.11 E-value=1.2e+02 Score=24.35 Aligned_cols=47 Identities=9% Similarity=0.056 Sum_probs=39.7
Q ss_pred cCCccchhHHHHHHHHHHHHHhcCCCCChhHHHHHHHHHhccccccH
Q 009284 113 TVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDI 159 (538)
Q Consensus 113 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~l~e~f~~~~~~~ 159 (538)
.-+++|+.+.-++....+-++..|...-....+.++++.||++...+
T Consensus 18 ~~t~~~lA~~~gis~~tis~~~~g~~~~~~~~~~~l~~~l~v~~~~l 64 (78)
T TIGR02607 18 GLSIRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGTSPEFW 64 (78)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCCHHHH
Confidence 34588998888888899999999987778889999999999975544
Done!