Query 009000
Match_columns 547
No_of_seqs 212 out of 1216
Neff 5.6
Searched_HMMs 46136
Date Thu Mar 28 19:11:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009000.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009000hhsearch_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 1.3E-43 2.7E-48 381.3 17.3 520 10-539 1-615 (617)
2 cd06146 mut-7_like_exo DEDDy 3 99.9 1.4E-25 3E-30 217.4 19.2 174 325-499 1-192 (193)
3 cd06129 RNaseD_like DEDDy 3'-5 99.9 8.9E-24 1.9E-28 198.5 18.7 154 334-500 2-161 (161)
4 cd06141 WRN_exo DEDDy 3'-5' ex 99.9 1.5E-22 3.2E-27 190.6 17.4 160 329-499 2-169 (170)
5 PRK10829 ribonuclease D; Provi 99.9 1.7E-22 3.7E-27 213.8 19.0 169 324-506 2-174 (373)
6 PF01612 DNA_pol_A_exo1: 3'-5' 99.9 3.2E-22 6.9E-27 186.4 18.6 170 325-503 1-176 (176)
7 cd06148 Egl_like_exo DEDDy 3'- 99.9 7.4E-22 1.6E-26 191.8 13.7 170 337-519 3-193 (197)
8 TIGR01388 rnd ribonuclease D. 99.9 1.9E-20 4.1E-25 198.3 19.2 166 327-506 1-170 (367)
9 COG0349 Rnd Ribonuclease D [Tr 99.8 4.4E-20 9.5E-25 192.4 15.9 165 329-506 2-170 (361)
10 PRK05755 DNA polymerase I; Pro 99.7 3.5E-16 7.5E-21 182.3 19.6 223 260-504 240-471 (880)
11 cd06142 RNaseD_exo DEDDy 3'-5' 99.7 1.8E-15 3.8E-20 142.2 18.0 158 335-506 3-164 (178)
12 smart00474 35EXOc 3'-5' exonuc 99.6 4E-14 8.6E-19 130.7 19.8 165 326-503 2-172 (172)
13 cd06147 Rrp6p_like_exo DEDDy 3 99.6 7.5E-14 1.6E-18 134.5 19.2 171 323-507 3-177 (192)
14 TIGR00593 pola DNA polymerase 99.5 4.3E-13 9.3E-18 155.9 23.4 230 260-504 239-479 (887)
15 cd00007 35EXOc 3'-5' exonuclea 99.5 1.3E-12 2.9E-17 118.3 15.9 145 346-502 2-155 (155)
16 cd09018 DEDDy_polA_RNaseD_like 99.5 1.3E-12 2.7E-17 119.1 14.6 142 346-500 1-150 (150)
17 KOG2206 Exosome 3'-5' exoribon 99.3 2E-12 4.3E-17 140.4 9.2 198 322-538 190-390 (687)
18 cd06140 DNA_polA_I_Bacillus_li 99.3 4.9E-11 1.1E-15 112.7 14.4 149 344-505 3-159 (178)
19 COG0749 PolA DNA polymerase I 99.3 1.9E-11 4.1E-16 135.2 12.8 166 325-504 3-182 (593)
20 cd06139 DNA_polA_I_Ecoli_like_ 99.2 7.8E-10 1.7E-14 105.0 16.9 154 342-504 3-172 (193)
21 PRK14975 bifunctional 3'-5' ex 98.9 3.7E-09 8E-14 118.0 11.3 139 324-505 2-147 (553)
22 cd06128 DNA_polA_exo DEDDy 3'- 98.5 2.9E-06 6.3E-11 78.3 13.0 120 369-499 23-150 (151)
23 KOG4373 Predicted 3'-5' exonuc 97.9 4.4E-05 9.5E-10 79.3 9.9 142 345-496 128-282 (319)
24 cd06149 ISG20 DEDDh 3'-5' exon 96.1 0.049 1.1E-06 51.4 10.4 82 393-496 67-157 (157)
25 cd06125 DnaQ_like_exo DnaQ-lik 95.9 0.039 8.5E-07 47.8 8.2 59 347-423 1-62 (96)
26 cd06137 DEDDh_RNase DEDDh 3'-5 95.9 0.09 1.9E-06 49.6 11.3 78 395-495 75-160 (161)
27 PRK08517 DNA polymerase III su 95.4 0.61 1.3E-05 47.8 15.6 90 393-504 137-233 (257)
28 KOG2249 3'-5' exonuclease [Rep 95.3 0.23 5E-06 51.0 12.0 79 396-498 177-262 (280)
29 cd06144 REX4_like DEDDh 3'-5' 95.0 0.17 3.7E-06 47.2 9.5 80 393-496 67-152 (152)
30 PRK06310 DNA polymerase III su 94.8 0.51 1.1E-05 48.0 13.2 90 394-502 78-174 (250)
31 PRK07740 hypothetical protein; 94.8 0.82 1.8E-05 46.4 14.6 90 394-506 132-230 (244)
32 PRK06063 DNA polymerase III su 94.7 0.55 1.2E-05 49.4 13.5 92 393-506 84-183 (313)
33 PRK07883 hypothetical protein; 94.7 0.32 7E-06 55.1 12.5 92 394-507 86-187 (557)
34 PRK07942 DNA polymerase III su 94.6 0.58 1.3E-05 47.0 12.8 79 406-503 94-181 (232)
35 cd06143 PAN2_exo DEDDh 3'-5' e 94.2 0.088 1.9E-06 51.0 5.6 78 396-496 94-174 (174)
36 PRK05711 DNA polymerase III su 94.1 1.2 2.5E-05 45.3 13.8 93 394-503 77-177 (240)
37 cd06131 DNA_pol_III_epsilon_Ec 93.6 3 6.4E-05 38.9 14.7 88 394-498 72-166 (167)
38 TIGR01406 dnaQ_proteo DNA poly 93.6 1.8 4E-05 43.3 14.1 94 394-504 73-174 (225)
39 TIGR00573 dnaq exonuclease, DN 93.1 2.7 5.9E-05 41.6 14.4 96 394-506 78-181 (217)
40 cd06130 DNA_pol_III_epsilon_li 92.9 2.2 4.7E-05 39.1 12.5 80 393-495 67-154 (156)
41 PRK07246 bifunctional ATP-depe 92.9 1.8 4E-05 51.3 14.7 89 393-504 76-172 (820)
42 PRK09145 DNA polymerase III su 92.9 3.5 7.6E-05 40.2 14.5 85 393-500 101-199 (202)
43 cd05160 DEDDy_DNA_polB_exo DED 92.7 1.7 3.6E-05 42.0 11.8 102 392-495 65-198 (199)
44 cd06145 REX1_like DEDDh 3'-5' 92.7 0.43 9.2E-06 44.6 7.4 79 394-495 66-149 (150)
45 TIGR01405 polC_Gram_pos DNA po 92.5 1.3 2.8E-05 54.6 13.1 92 393-506 260-359 (1213)
46 PRK06807 DNA polymerase III su 92.5 1.7 3.8E-05 45.8 12.5 86 394-502 79-172 (313)
47 smart00479 EXOIII exonuclease 92.0 3.6 7.9E-05 37.8 12.8 90 393-502 70-167 (169)
48 PRK09146 DNA polymerase III su 91.9 1.8 3.8E-05 43.9 11.3 87 394-503 120-228 (239)
49 TIGR01407 dinG_rel DnaQ family 91.4 2.2 4.8E-05 50.7 13.2 90 393-504 70-167 (850)
50 PRK06309 DNA polymerase III su 90.3 5.8 0.00013 39.7 13.2 88 395-503 71-167 (232)
51 cd05780 DNA_polB_Kod1_like_exo 90.2 4.1 9E-05 39.6 11.7 151 345-497 4-194 (195)
52 PRK08074 bifunctional ATP-depe 89.6 6.1 0.00013 47.7 14.8 89 394-504 75-171 (928)
53 cd06136 TREX1_2 DEDDh 3'-5' ex 89.3 4.2 9.1E-05 39.0 10.9 84 395-496 86-175 (177)
54 cd05781 DNA_polB_B3_exo DEDDy 88.9 8.8 0.00019 37.3 12.9 148 345-497 4-187 (188)
55 PRK05601 DNA polymerase III su 86.8 17 0.00037 39.5 14.5 100 392-498 114-245 (377)
56 TIGR01298 RNaseT ribonuclease 85.6 3.3 7.1E-05 40.6 7.9 86 405-505 105-195 (200)
57 cd06134 RNaseT DEDDh 3'-5' exo 85.2 4.6 9.9E-05 39.2 8.6 80 406-501 103-188 (189)
58 PRK07983 exodeoxyribonuclease 84.7 31 0.00066 34.6 14.4 76 406-502 75-154 (219)
59 PRK07247 DNA polymerase III su 84.2 18 0.00038 35.6 12.2 88 393-504 74-171 (195)
60 PRK06195 DNA polymerase III su 82.3 4.9 0.00011 42.1 8.0 88 394-504 71-166 (309)
61 PRK09182 DNA polymerase III su 82.0 19 0.00042 37.7 12.2 83 395-500 112-199 (294)
62 PF13482 RNase_H_2: RNase_H su 81.7 3 6.4E-05 38.7 5.5 142 347-498 1-163 (164)
63 COG2176 PolC DNA polymerase II 81.3 3.7 8E-05 50.0 7.2 140 340-506 417-590 (1444)
64 PRK11779 sbcB exonuclease I; P 81.3 39 0.00085 37.9 14.9 91 394-501 82-197 (476)
65 PRK05168 ribonuclease T; Provi 81.1 7.5 0.00016 38.4 8.4 87 405-506 114-205 (211)
66 cd05785 DNA_polB_like2_exo Unc 80.6 11 0.00023 37.4 9.3 145 344-495 9-206 (207)
67 cd05779 DNA_polB_epsilon_exo D 79.3 33 0.00072 34.0 12.2 148 345-495 3-203 (204)
68 KOG3657 Mitochondrial DNA poly 78.8 3.3 7.2E-05 48.6 5.6 143 345-502 184-383 (1075)
69 cd05784 DNA_polB_II_exo DEDDy 78.6 33 0.00072 33.6 11.9 59 436-496 123-193 (193)
70 cd06127 DEDDh DEDDh 3'-5' exon 78.2 13 0.00027 33.2 8.3 85 393-495 69-158 (159)
71 cd05783 DNA_polB_B1_exo DEDDy 77.4 78 0.0017 31.3 15.1 100 392-496 75-202 (204)
72 PRK00448 polC DNA polymerase I 75.9 34 0.00073 43.4 13.5 91 394-506 490-588 (1437)
73 KOG2248 3'-5' exonuclease [Rep 69.8 11 0.00024 40.9 6.7 85 394-501 284-374 (380)
74 cd05782 DNA_polB_like1_exo Unc 68.0 85 0.0019 31.0 12.0 104 391-496 79-207 (208)
75 PF10108 DNA_pol_B_exo2: Predi 67.4 1.2E+02 0.0025 30.5 12.8 108 390-500 37-171 (209)
76 KOG2405 Predicted 3'-5' exonuc 65.9 0.35 7.5E-06 52.0 -5.6 72 363-442 73-144 (458)
77 COG0847 DnaQ DNA polymerase II 64.5 1.5E+02 0.0033 29.3 13.6 92 394-504 85-185 (243)
78 KOG3616 Selective LIM binding 61.6 37 0.00081 40.0 8.9 49 248-296 1299-1353(1636)
79 cd06133 ERI-1_3'hExo_like DEDD 57.0 1.6E+02 0.0035 27.1 11.6 89 394-498 79-175 (176)
80 PF07899 Frigida: Frigida-like 56.4 2E+02 0.0043 30.3 12.7 158 67-228 38-217 (290)
81 PF01381 HTH_3: Helix-turn-hel 54.9 16 0.00035 27.6 3.4 46 122-167 9-54 (55)
82 PRK14976 5'-3' exonuclease; Pr 52.4 6.4 0.00014 41.0 1.0 38 260-297 244-281 (281)
83 PF12844 HTH_19: Helix-turn-he 52.3 21 0.00045 27.9 3.7 54 113-168 5-58 (64)
84 KOG2405 Predicted 3'-5' exonuc 48.0 27 0.00058 38.1 4.8 127 369-506 216-365 (458)
85 PRK07748 sporulation inhibitor 42.4 2E+02 0.0043 28.1 9.7 91 393-502 82-180 (207)
86 PF00392 GntR: Bacterial regul 39.7 44 0.00095 26.4 3.8 47 131-177 2-50 (64)
87 PF03997 VPS28: VPS28 protein; 37.8 1.4E+02 0.0031 29.4 7.8 101 188-294 12-128 (188)
88 PF09281 Taq-exonuc: Taq polym 37.2 1.5E+02 0.0032 27.9 7.2 65 415-502 71-138 (138)
89 cd05777 DNA_polB_delta_exo DED 35.9 39 0.00085 33.7 3.7 64 436-499 153-224 (230)
90 PRK00118 putative DNA-binding 34.7 1.9E+02 0.0041 25.9 7.3 35 138-172 9-43 (104)
91 cd06138 ExoI_N N-terminal DEDD 31.2 1.2E+02 0.0025 29.1 6.0 85 394-495 73-182 (183)
92 PLN03218 maturation of RBCL 1; 30.9 1.1E+03 0.025 29.3 18.2 98 197-294 589-710 (1060)
93 PHA01976 helix-turn-helix prot 30.4 71 0.0015 25.1 3.6 53 114-168 9-61 (67)
94 TIGR02508 type_III_yscG type I 30.0 1.8E+02 0.0039 26.4 6.3 74 194-278 27-110 (115)
95 PF04858 TH1: TH1 protein; In 29.6 44 0.00096 38.5 3.1 99 47-163 445-557 (584)
96 TIGR03070 couple_hipB transcri 29.1 96 0.0021 23.0 4.1 52 112-165 7-58 (58)
97 PF12960 DUF3849: Protein of u 28.0 83 0.0018 29.5 4.1 62 184-245 27-94 (133)
98 KOG4634 Mitochondrial F1F0-ATP 27.8 1.6E+02 0.0035 26.2 5.5 60 107-168 8-83 (105)
99 cd05778 DNA_polB_zeta_exo inac 26.0 64 0.0014 32.4 3.3 59 437-495 163-230 (231)
100 PF05402 PqqD: Coenzyme PQQ sy 25.4 2.7E+02 0.0057 21.9 6.2 48 135-201 18-65 (68)
101 KOG1798 DNA polymerase epsilon 25.1 3.6E+02 0.0077 34.9 9.5 151 344-497 246-449 (2173)
102 PF07399 DUF1504: Protein of u 24.0 34 0.00073 37.7 0.9 90 72-164 121-215 (438)
103 PF08154 NLE: NLE (NUC135) dom 23.8 88 0.0019 25.3 3.1 27 68-94 29-55 (65)
104 PF04840 Vps16_C: Vps16, C-ter 23.3 7.2E+02 0.016 26.3 10.6 76 218-293 179-262 (319)
105 PF14833 NAD_binding_11: NAD-b 22.8 2.2E+02 0.0047 25.2 5.8 89 154-267 24-112 (122)
106 PRK06424 transcription factor; 22.3 1.2E+02 0.0025 28.7 4.0 55 112-168 89-143 (144)
107 PRK08359 transcription factor; 22.1 1.1E+02 0.0024 30.0 3.9 57 111-169 89-145 (176)
108 PF14559 TPR_19: Tetratricopep 21.6 2.3E+02 0.0051 21.5 5.1 34 261-294 18-51 (68)
109 cd02908 Macro_Appr_pase_like M 20.6 80 0.0017 29.8 2.6 8 86-93 67-74 (165)
110 cd05776 DNA_polB_alpha_exo ina 20.3 1.1E+02 0.0024 30.7 3.6 63 436-498 157-226 (234)
No 1
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=1.3e-43 Score=381.30 Aligned_cols=520 Identities=27% Similarity=0.368 Sum_probs=411.3
Q ss_pred ccchhhhhhhhcccCCccccceEeeeecccCCCcchHHHHHHHHhhhhcccchhchhHHHHHHHHHHHhhCCCCCCCcee
Q 009000 10 MGLEERVAESCINGHKADCAWTVSVHTFSDITNISPVVFLYLLKECYIHGTCKATRKFRALQQQVSQALCNSPEPGPATF 89 (547)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (547)
||.+....++++...+.+++.+.|.|.+|+.++++++||.+..|+||-+++-+.+.+|..++.+.|.+.++.|+++|+++
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 009000 90 IVRCLYVLPIFG-VYSEGFSHLIISALRRHQKT---TVNSADSTQAKEIAAY-LFLDITGGFVDHDEKLMVKIL-EAFDV 163 (547)
Q Consensus 90 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~r~~~~l~-e~f~~ 163 (547)
|+.||+-+|-+| +++|++||.+++++++++|. .+..+|...+..+|+. .++=..+++.-+++.+-+-.+ .|+|+
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 677777888888899999888 99999
Q ss_pred cccchHHHHhhhhhccccchhHHHHHH-----HHHHHHHHhhchhhHHHHHHHhhh-ccccchHHHHHHHhccchHHHHH
Q 009000 164 RLTDIEKAITQLKAQNEHRFDTAKTVI-----EQYIFAMIDSQSYMTAVSLLEHFS-IRQSGESFLLKMIQNKEFKAAEK 237 (547)
Q Consensus 164 ~~~~~~~a~~~~~~~~~~~~~~~~~~~-----~~~i~~~~~~~~~~~~~~li~~f~-~~~~~~~~l~~~~~~~~~~~a~~ 237 (547)
.+.-++.++.....+--...+.-..++ ++|+.-+|-+++...|..+++|+. +|+...+|++.|+.- ++...++
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 999999998766665543344444444 999999999999999999999999 888899999999986 8899999
Q ss_pred HHHhcCc-----hHH------------------------------------------HHHHhhhcc-hHHHHHHhhcch-
Q 009000 238 WATFMGK-----PIL------------------------------------------LKRLAEKAC-WDIAEAKTKGDK- 268 (547)
Q Consensus 238 ~~~~~~~-----~~~------------------------------------------~~~l~~k~~-wd~a~~~~~~D~- 268 (547)
|+.+++. +.+ -.+++.|+. |++++.....|.
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--hccCCHHHHH---------HHHHHcCCccccccc-----CcccCCcccccccccccCCcCeEEEcCHH
Q 009000 269 RLLEYLVYLA--MEAGYSEKVD---------ELCERYSLEGFLKTR-----EPEAGFVHSRFLHLKELVVEDIIWVDEVD 332 (547)
Q Consensus 269 ~l~~~lv~L~--~~~~d~~~L~---------~l~~ryef~sll~el-----~~~~~~~~~~~~~l~~~~~~~y~~Idt~e 332 (547)
++..||.+.. .++...+... +|.+++.-++.-+++ ....+......+.......+.+.+|+++.
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 8888988887 3322222221 444444333222221 00000111112222224456789999999
Q ss_pred HHHHHH-HHhhCC-CeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchHHHHHHHHhhcCCCceEEE
Q 009000 333 GLHKAI-CHIEGC-KVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLG 410 (547)
Q Consensus 333 eL~~ll-e~L~~a-~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~I~KVG 410 (547)
++..++ +.+... -.||+|.||.|. .+...++++++|++.++.+|++|..++.....+-+...+..+|+++++.|||
T Consensus 400 El~~l~l~~l~~e~~yVGiDsEwkps--~~v~dsk~~IlQif~~~~v~Lidc~~l~~~~se~w~~~~s~if~s~~i~kvG 477 (617)
T KOG2207|consen 400 ELRDLLLESLSEELRYVGIDSEWKPS--KKVSDSKLAILQIFFKDCVYLIDCVKLENLASEIWHLLLSQIFESKSILKVG 477 (617)
T ss_pred HHHHHHHHHhhhcCEEEEEccccCcc--cCCChhHHHHHHHHhcCeEEEeehHHhhhchHHHHHHHHHHHccCCceeeee
Confidence 998876 455555 789999999987 1223679999999999999999998875433333556788899999999999
Q ss_pred echHHHHHHHHHHhCCc-cccc--ccchhh-hHHHh------------hcCCCCCHHHHHHHHhCCCCCCCcccccCCCC
Q 009000 411 YNFQCDIKQLAHSYGEL-ECFK--HYEMLL-DIQNV------------FKEPKGGLSGLAEKILGAGLNKTRRNSNWEQR 474 (547)
Q Consensus 411 hnlK~Dl~vLa~~~GIl-~~~~--~~~~vf-DtmLA------------l~~~~~gLd~LAer~Lg~~L~K~e~~SdW~~r 474 (547)
+++..|++++.++-|-+ .+++ ....++ ++.++ +++...+|.+|+...+|..++|++++|+|..|
T Consensus 478 f~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~Lt~~llg~~lnKteqcsnWqcr 557 (617)
T KOG2207|consen 478 FSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADLTDCLLGKKLNKTEQCSNWQCR 557 (617)
T ss_pred cchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhhhhhhHHHhhhhcccccccchhhcC
Confidence 99999999998533310 0000 011111 12222 12457899999999999999999999999999
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCcccchhHHHHHhhccCcccccCCCCcccc
Q 009000 475 PLSQNQLEYAALDAVVLLQIFHHVRSCSQPTDVSEGHDKIEWKSYIVSHMDNPKKSKKRPTIKKE 539 (547)
Q Consensus 475 pLt~~Qi~YAAeDA~vlLrL~~~L~~rLee~~~~~~~~~~~w~s~~~~~~~~~~k~~~~~~~~~~ 539 (547)
||+.+|+-|||.||.++..++..+....+. .+ ..+|..|+| |+..++|.|-..++.|.
T Consensus 558 pLr~nQi~yaalDa~~~~~ifkkv~~vv~~-~~--~~ek~i~es----~~~~~~~~~~~~s~~~~ 615 (617)
T KOG2207|consen 558 PLRRNQIYYAALDAVVLVEIFKKVCSVVEH-DA--DIEKFICES----HLGRPKKKKEHCSVWNR 615 (617)
T ss_pred CchhhHHHHHHhcchhhHHHHHHHHhhcch-hh--HHHHHHHHH----hcCCccccccccccccc
Confidence 999999999999999999999999998885 33 455666665 67777777777776654
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=99.94 E-value=1.4e-25 Score=217.40 Aligned_cols=174 Identities=40% Similarity=0.734 Sum_probs=147.1
Q ss_pred eEEEcCHHHHHHHHHH--hhCCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchHHHHHHHHhhc
Q 009000 325 IIWVDEVDGLHKAICH--IEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQ 402 (547)
Q Consensus 325 y~~Idt~eeL~~lle~--L~~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLe 402 (547)
|++|++++++.++++. +...+++|||+||.+.+..+ ..++++++|+++++.+|+||+...+....+.+...|+++|+
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 5789999999999999 89999999999999874321 24689999999999999999987542223445678999999
Q ss_pred CCCceEEEechHHHHHHHHHHhCCccc-ccccchhhhHHHhhc---------------CCCCCHHHHHHHHhCCCCCCCc
Q 009000 403 SPGILKLGYNFQCDIKQLAHSYGELEC-FKHYEMLLDIQNVFK---------------EPKGGLSGLAEKILGAGLNKTR 466 (547)
Q Consensus 403 d~~I~KVGhnlK~Dl~vLa~~~GIl~~-~~~~~~vfDtmLAl~---------------~~~~gLd~LAer~Lg~~L~K~e 466 (547)
|+++.||||+++.|+..|.+.+|+..+ +....+++||+.+.. ..++||..|++++||.+++|..
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 001367899997631 1468999999999999999999
Q ss_pred ccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009000 467 RNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVR 499 (547)
Q Consensus 467 ~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~ 499 (547)
++|||+.|||+++|+.|||.||+++++||+.|.
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=8.9e-24 Score=198.52 Aligned_cols=154 Identities=28% Similarity=0.460 Sum_probs=133.4
Q ss_pred HHHHHHHhh-CCCeEEEEeeeecCCccCCcCCceeEEEEEeC-CeEEEEEcCcccCCCchHHHHHHHHhhcCCCceEEEe
Q 009000 334 LHKAICHIE-GCKVVGIDCEWKPNYVKGCKMNKVSIMQIASD-EMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGY 411 (547)
Q Consensus 334 L~~lle~L~-~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~-~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~I~KVGh 411 (547)
++++++.+. ..+++|||+||.+.+. ..++++++|++++ +.+|+||+...+. . ...|+++|+|+++.||||
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 9999999999998743 3568999999998 9999999986532 2 246899999999999999
Q ss_pred chHHHHHHHHHHhCCcccccccchhhhHHHhh---c-CCCCCHHHHHHHHhCCCCCCCcccccCCCCCCCHHHHHHHHHH
Q 009000 412 NFQCDIKQLAHSYGELECFKHYEMLLDIQNVF---K-EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALD 487 (547)
Q Consensus 412 nlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl---~-~~~~gLd~LAer~Lg~~L~K~e~~SdW~~rpLt~~Qi~YAAeD 487 (547)
|+|.|++.|.+.+|+.. .++||++++. + ..++||+.+++++||.+++|..+.|+|..|||+++|++|||.|
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 99999999987688742 4569999994 3 3367999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHh
Q 009000 488 AVVLLQIFHHVRS 500 (547)
Q Consensus 488 A~vlLrL~~~L~~ 500 (547)
|++++.||+.|++
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=99.90 E-value=1.5e-22 Score=190.59 Aligned_cols=160 Identities=34% Similarity=0.599 Sum_probs=136.5
Q ss_pred cCHHHHHHHHHHhh-CCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchHHHHHHHHhhcCCCce
Q 009000 329 DEVDGLHKAICHIE-GCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGIL 407 (547)
Q Consensus 329 dt~eeL~~lle~L~-~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~I~ 407 (547)
++++++..+++.+. ...++|||+||.+.... ....+++++|+|+++.+|+||+.+.. . +...|+++|+++++.
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 13568999999999999999998642 2 234689999999999
Q ss_pred EEEechHHHHHHHHHHhCCcccccccchhhhHHHhh---c-C-CCCCHHHHHHHHhCCCCC--CCcccccCCCCCCCHHH
Q 009000 408 KLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF---K-E-PKGGLSGLAEKILGAGLN--KTRRNSNWEQRPLSQNQ 480 (547)
Q Consensus 408 KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl---~-~-~~~gLd~LAer~Lg~~L~--K~e~~SdW~~rpLt~~Q 480 (547)
|||||+|.|++.|.+.+|+.. .+++|++++. + . .+.||++++++++|.+++ |..+.|+|..|||+++|
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 2 2 347999999999999998 77789999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 009000 481 LEYAALDAVVLLQIFHHVR 499 (547)
Q Consensus 481 i~YAAeDA~vlLrL~~~L~ 499 (547)
++|||.||++++.||+.|.
T Consensus 151 i~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 151 ILYAATDAYASLELYRKLL 169 (170)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999885
No 5
>PRK10829 ribonuclease D; Provisional
Probab=99.89 E-value=1.7e-22 Score=213.82 Aligned_cols=169 Identities=22% Similarity=0.352 Sum_probs=149.7
Q ss_pred CeEEEcCHHHHHHHHHHhhCCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchHHHHHHHHhhcC
Q 009000 324 DIIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQS 403 (547)
Q Consensus 324 ~y~~Idt~eeL~~lle~L~~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed 403 (547)
.|.+|++.+++..+++.+...+.+|+|||+.+.. .+..+++++|+++++.+|+||+.... + .+.|+++|+|
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 4789999999999999999999999999998763 24568999999998899999987542 1 2578999999
Q ss_pred CCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHhh---c-CCCCCHHHHHHHHhCCCCCCCcccccCCCCCCCHH
Q 009000 404 PGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF---K-EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQN 479 (547)
Q Consensus 404 ~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl---~-~~~~gLd~LAer~Lg~~L~K~e~~SdW~~rpLt~~ 479 (547)
+++.||+|+.++|+..|.+.+|+.+ .++|||+++. + ..+.|+..|+++++|..++|+++.+||.+|||+++
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 7799999994 3 33689999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccCCCC
Q 009000 480 QLEYAALDAVVLLQIFHHVRSCSQPTD 506 (547)
Q Consensus 480 Qi~YAAeDA~vlLrL~~~L~~rLee~~ 506 (547)
|++|||.|+.+++.||+.|..+|++.+
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 6
>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=3.2e-22 Score=186.43 Aligned_cols=170 Identities=31% Similarity=0.461 Sum_probs=142.4
Q ss_pred eEEEcCHHHHHHHHHHhhCCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchHHHHHHHHhhcCC
Q 009000 325 IIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSP 404 (547)
Q Consensus 325 y~~Idt~eeL~~lle~L~~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~ 404 (547)
|++|++.+++.++++.+...+.+|||+||.+..... ....++++|+++.+.+|+++....... .+...|+++|+++
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 678999999999999999999999999999874321 256788999999988888877643221 1456899999999
Q ss_pred CceEEEechHHHHHHHHHHhCCcccccccchhhhHHHhh---c-CCCCCHHHHHHHHhC-CCCCCCcccccCC-CCCCCH
Q 009000 405 GILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF---K-EPKGGLSGLAEKILG-AGLNKTRRNSNWE-QRPLSQ 478 (547)
Q Consensus 405 ~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl---~-~~~~gLd~LAer~Lg-~~L~K~e~~SdW~-~rpLt~ 478 (547)
++.|||||+++|++.|.+.+|+.. .+++|+|++. + ..++||++|+.+++| ...++.++.++|. .+|+++
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 6788999883 3 334999999999999 6667788899999 899999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhccC
Q 009000 479 NQLEYAALDAVVLLQIFHHVRSCSQ 503 (547)
Q Consensus 479 ~Qi~YAAeDA~vlLrL~~~L~~rLe 503 (547)
+|+.|||.||+++++||+.|.++|+
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 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=99.87 E-value=7.4e-22 Score=191.82 Aligned_cols=170 Identities=29% Similarity=0.366 Sum_probs=136.9
Q ss_pred HHHHhhCCCeEEEEeeeecCCccCCcCCceeEEEEEeC-CeEEEEEcCcccCCCchHHHHHHHHhhcCCCceEEEechHH
Q 009000 337 AICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASD-EMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQC 415 (547)
Q Consensus 337 lle~L~~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~-~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~I~KVGhnlK~ 415 (547)
+++.+++++++|||+||.+... .++++++|+++. +.+|+||+...+. ..+...|+++|+++++.|||||+|.
T Consensus 3 ~~~~l~~~~~i~~D~E~~~~~~----~~~~~LiQia~~~~~v~l~D~~~~~~---~~~~~~L~~iLe~~~i~Kv~h~~k~ 75 (197)
T cd06148 3 AIIHLKKQKVIGLDCEGVNLGR----KGKLCLVQIATRTGQIYLFDILKLGS---IVFINGLKDILESKKILKVIHDCRR 75 (197)
T ss_pred hhhhhhhCCEEEEEcccccCCC----CCCEEEEEEeeCCCcEEEEEhhhccc---hhHHHHHHHHhcCCCccEEEEechh
Confidence 4567888999999999986532 458999999998 9999999987532 2345688999999999999999999
Q ss_pred HHHHHHHHhCCcccccccchhhhHHHhh---c--CC-------CCCHHHHHHHHhCCCCCC--------CcccccCCCCC
Q 009000 416 DIKQLAHSYGELECFKHYEMLLDIQNVF---K--EP-------KGGLSGLAEKILGAGLNK--------TRRNSNWEQRP 475 (547)
Q Consensus 416 Dl~vLa~~~GIl~~~~~~~~vfDtmLAl---~--~~-------~~gLd~LAer~Lg~~L~K--------~e~~SdW~~rp 475 (547)
|++.|.+.+|+.. .++|||+++. + .. ..|+++++++|||.++++ .++.++|.+||
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 9999976689843 5569999992 2 11 369999999999998864 35679999999
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCcccchhHHH
Q 009000 476 LSQNQLEYAALDAVVLLQIFHHVRSCSQPTDVSEGHDKIEWKSY 519 (547)
Q Consensus 476 Lt~~Qi~YAAeDA~vlLrL~~~L~~rLee~~~~~~~~~~~w~s~ 519 (547)
|+++|+.|||.||++++.||+.|...|.+.. +--.++..|+++
T Consensus 151 Lt~~ql~YAa~Dv~~Ll~l~~~l~~~l~~~~-~~~~~~~~~~~~ 193 (197)
T cd06148 151 LTEDMIRYAALDVLCLLPLYYAMLDALISKF-LKAVFKYLNTER 193 (197)
T ss_pred CCHHHHHHHHHHHHhHHHHHHHHHHHhhhhH-HHHHHHHhhhhh
Confidence 9999999999999999999999999997742 223334444443
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=99.85 E-value=1.9e-20 Score=198.27 Aligned_cols=166 Identities=25% Similarity=0.407 Sum_probs=144.0
Q ss_pred EEcCHHHHHHHHHHhhCCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchHHHHHHHHhhcCCCc
Q 009000 327 WVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGI 406 (547)
Q Consensus 327 ~Idt~eeL~~lle~L~~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~I 406 (547)
+|++.+++..+++.+..++++|||||+.+.. .+..+++++|+++++.+|+||+.... + .+.|+++|+|+++
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 4788999999999999999999999998763 23568999999999999999987541 1 2578999999999
Q ss_pred eEEEechHHHHHHHHHHhCCcccccccchhhhHHHhh---c-CCCCCHHHHHHHHhCCCCCCCcccccCCCCCCCHHHHH
Q 009000 407 LKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF---K-EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLE 482 (547)
Q Consensus 407 ~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl---~-~~~~gLd~LAer~Lg~~L~K~e~~SdW~~rpLt~~Qi~ 482 (547)
.||+||+|.|++.|.+.+|... +++||||++. + ..++|++.|+++|||..++|+++.++|.+|||+.+|+.
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 9999999999999988555532 6789999993 3 34579999999999999999888999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhccCCCC
Q 009000 483 YAALDAVVLLQIFHHVRSCSQPTD 506 (547)
Q Consensus 483 YAAeDA~vlLrL~~~L~~rLee~~ 506 (547)
|||.||.+++.||+.|.++|++.+
T Consensus 147 YAa~Dv~~L~~L~~~L~~~L~~~g 170 (367)
T TIGR01388 147 YAAADVTYLLPLYAKLMERLEESG 170 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcC
Confidence 999999999999999999997743
No 9
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.83 E-value=4.4e-20 Score=192.42 Aligned_cols=165 Identities=29% Similarity=0.419 Sum_probs=143.8
Q ss_pred cCHHHHHHHHHHhhCCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchHHHHHHHHhhcCCCceE
Q 009000 329 DEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILK 408 (547)
Q Consensus 329 dt~eeL~~lle~L~~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~I~K 408 (547)
++.+.++.++..+.+.+.|++|||+.... ++..++++||++.++++++||+.....+. ..|..+|.|+++.|
T Consensus 2 ~~~~~l~~~~~~~~~~~~iAiDTEf~r~~---t~~p~LcLIQi~~~e~~~lIdpl~~~~d~-----~~l~~Ll~d~~v~K 73 (361)
T COG0349 2 TTGDLLAAACALLRGSKAIAIDTEFMRLR---TYYPRLCLIQISDGEGASLIDPLAGILDL-----PPLVALLADPNVVK 73 (361)
T ss_pred CchhHHHHHHHHhcCCCceEEeccccccc---ccCCceEEEEEecCCCceEeccccccccc-----chHHHHhcCCceee
Confidence 34566788888888899999999998763 34679999999998779999987632222 36888999999999
Q ss_pred EEechHHHHHHHHHHhCCcccccccchhhhHHHhhc----CCCCCHHHHHHHHhCCCCCCCcccccCCCCCCCHHHHHHH
Q 009000 409 LGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFK----EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYA 484 (547)
Q Consensus 409 VGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl~----~~~~gLd~LAer~Lg~~L~K~e~~SdW~~rpLt~~Qi~YA 484 (547)
|.|...+|+.+|.+.+|..+ .++|||+++.. ..++|+++|+++++|..++|+++.|||.+|||+++|++||
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 99999999999999788854 78999999942 3489999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhccCCCC
Q 009000 485 ALDAVVLLQIFHHVRSCSQPTD 506 (547)
Q Consensus 485 AeDA~vlLrL~~~L~~rLee~~ 506 (547)
|.|+.+++.||+.|..+|.+.+
T Consensus 149 a~DV~yL~~l~~~L~~~L~~~~ 170 (361)
T COG0349 149 AADVEYLLPLYDKLTEELAREG 170 (361)
T ss_pred HHHHHHHHHHHHHHHHHHHHcC
Confidence 9999999999999999998754
No 10
>PRK05755 DNA polymerase I; Provisional
Probab=99.70 E-value=3.5e-16 Score=182.25 Aligned_cols=223 Identities=22% Similarity=0.221 Sum_probs=174.5
Q ss_pred HHHHhhcchhHHHHHHHHhhccCCHHHHHHHHHHcCCcccccccCcccCCcccccccccccCCcCeEEEcCHHHHHHHHH
Q 009000 260 AEAKTKGDKRLLEYLVYLAMEAGYSEKVDELCERYSLEGFLKTREPEAGFVHSRFLHLKELVVEDIIWVDEVDGLHKAIC 339 (547)
Q Consensus 260 a~~~~~~D~~l~~~lv~L~~~~~d~~~L~~l~~ryef~sll~el~~~~~~~~~~~~~l~~~~~~~y~~Idt~eeL~~lle 339 (547)
-++++.+|+++...+.++...++|.+++.+++++|||+++++..... .. + + ....+|.+|++.+++..+++
T Consensus 240 ~l~~l~~d~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~---~~----~-~-~~~~~~~~I~~~~~L~~~l~ 310 (880)
T PRK05755 240 KLATIKTDVPLEVDLEDLELQPPDREKLIALFKELEFKSLLRRAAAA---EA----A-P-LDEEDYETILDEEELEAWLA 310 (880)
T ss_pred hhheeeeCCCCCCCHHHhccCCCCHHHHHHHHHHhCcHHHHHHhhcc---cc----c-c-CCCCceEEeCCHHHHHHHHH
Confidence 57889999998877888888899999999999999999998775211 00 0 1 12246888999999999999
Q ss_pred HhhCCCeEEEEeeeecCCccCCcCCceeEEEEEeCCe-EEEEEcCcccCCCchHHHHHHHHhhcCCCceEEEechHHHHH
Q 009000 340 HIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEM-VFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIK 418 (547)
Q Consensus 340 ~L~~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~-a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~I~KVGhnlK~Dl~ 418 (547)
.+..+..+++|+|+++.. +....+.++|++.+++ ++++|+.+. +......|.++|+++.+.||+||+|+|++
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 998889999999998763 2345677788887544 899988542 22345678999999999999999999999
Q ss_pred HHHHHhCCcccccccchhhhHHHhh---c-CCCCCHHHHHHHHhCCCCCCCc----ccccCCCCCCCHHHHHHHHHHHHH
Q 009000 419 QLAHSYGELECFKHYEMLLDIQNVF---K-EPKGGLSGLAEKILGAGLNKTR----RNSNWEQRPLSQNQLEYAALDAVV 490 (547)
Q Consensus 419 vLa~~~GIl~~~~~~~~vfDtmLAl---~-~~~~gLd~LAer~Lg~~L~K~e----~~SdW~~rpLt~~Qi~YAAeDA~v 490 (547)
.|.+ +|+.. .++++|||++. + ...++|++++++|+|..+...+ ...+|+.+|+ +.|.+||+.|+.+
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 2 2248999999999998743221 1234555577 5789999999999
Q ss_pred HHHHHHHHHhccCC
Q 009000 491 LLQIFHHVRSCSQP 504 (547)
Q Consensus 491 lLrL~~~L~~rLee 504 (547)
+++||+.|.++|.+
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=99.68 E-value=1.8e-15 Score=142.21 Aligned_cols=158 Identities=27% Similarity=0.444 Sum_probs=125.5
Q ss_pred HHHHHHhhCCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchHHHHHHHHhhcCCCceEEEechH
Q 009000 335 HKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQ 414 (547)
Q Consensus 335 ~~lle~L~~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~I~KVGhnlK 414 (547)
..+++.+...+.+++|+|+.+.. +....+.++|+++++.+||+|+... . ..+.|+++|+++++.|+|||+|
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 34455555566899999886542 1134678888988765899986521 1 2356899999999999999999
Q ss_pred HHHHHHHHHhCCcccccccchhhhHHHhh---c-CCCCCHHHHHHHHhCCCCCCCcccccCCCCCCCHHHHHHHHHHHHH
Q 009000 415 CDIKQLAHSYGELECFKHYEMLLDIQNVF---K-EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVV 490 (547)
Q Consensus 415 ~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl---~-~~~~gLd~LAer~Lg~~L~K~e~~SdW~~rpLt~~Qi~YAAeDA~v 490 (547)
.|.+.|.+.+|+. . ++++|++++. + ..++++++++++|+|.++.+.+..++|..+|++.+|..|||.||.+
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 9999998755874 2 6689999993 3 3357999999999998866666778999999999999999999999
Q ss_pred HHHHHHHHHhccCCCC
Q 009000 491 LLQIFHHVRSCSQPTD 506 (547)
Q Consensus 491 lLrL~~~L~~rLee~~ 506 (547)
+++|++.|.++|++.+
T Consensus 149 l~~L~~~l~~~L~e~~ 164 (178)
T cd06142 149 LLPLYEKLKEELEEEG 164 (178)
T ss_pred HHHHHHHHHHHHHHcC
Confidence 9999999999997744
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=99.62 E-value=4e-14 Score=130.72 Aligned_cols=165 Identities=26% Similarity=0.304 Sum_probs=123.5
Q ss_pred EEEcCHHHHHHHHHHhh-CCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchHHHHHHHHhhcCC
Q 009000 326 IWVDEVDGLHKAICHIE-GCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSP 404 (547)
Q Consensus 326 ~~Idt~eeL~~lle~L~-~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~ 404 (547)
.+|++.+++..|++.+. ....+++|+|+.+... ....+.++|++.++..+|++.... .......|+++|+++
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 56788888888777776 5669999999876521 134677888886443444432211 111235689999999
Q ss_pred CceEEEechHHHHHHHHHHhCCcccccccchhhhHHHhh---c--CCCCCHHHHHHHHhCCCCCCCcccccCCCCCCCHH
Q 009000 405 GILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF---K--EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQN 479 (547)
Q Consensus 405 ~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl---~--~~~~gLd~LAer~Lg~~L~K~e~~SdW~~rpLt~~ 479 (547)
++.|+|||+|.|.+.|.+ +|+.. .+++|||++. + ...++|++++++|+|....+..+.++|..+|+..+
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 89843 3459999993 3 23379999999999987544334457877888999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccC
Q 009000 480 QLEYAALDAVVLLQIFHHVRSCSQ 503 (547)
Q Consensus 480 Qi~YAAeDA~vlLrL~~~L~~rLe 503 (547)
|..|||.||+++++|++.|.++|.
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=7.5e-14 Score=134.50 Aligned_cols=171 Identities=23% Similarity=0.374 Sum_probs=129.5
Q ss_pred cCeEEEcCHHHHHHHHHHhhCCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchHHHHHHHHhhc
Q 009000 323 EDIIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQ 402 (547)
Q Consensus 323 ~~y~~Idt~eeL~~lle~L~~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLe 402 (547)
+.|.+|++.+++..|++.+...+.+++++|+.+.. +....+..++++.++++||+++... ......|+++|+
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 46888966677888777776566899999865431 1123566677887666888874211 111245889999
Q ss_pred CCCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHh---hc-CCCCCHHHHHHHHhCCCCCCCcccccCCCCCCCH
Q 009000 403 SPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNV---FK-EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQ 478 (547)
Q Consensus 403 d~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLA---l~-~~~~gLd~LAer~Lg~~L~K~e~~SdW~~rpLt~ 478 (547)
++++.|+|||+|.+++.|.+.+|+... +. ||+|++ ++ . +++++.++++||+..+.|..+.++|+.+|+..
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 57999999999987643444566788788889
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCCCC
Q 009000 479 NQLEYAALDAVVLLQIFHHVRSCSQPTDV 507 (547)
Q Consensus 479 ~Qi~YAAeDA~vlLrL~~~L~~rLee~~~ 507 (547)
+|..|++.+|.++++|++.|.++|+++.+
T Consensus 149 ~~~~y~a~~a~~l~~L~~~L~~~L~e~~~ 177 (192)
T cd06147 149 EMIKYAREDTHYLLYIYDRLRNELLERAN 177 (192)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHHhcc
Confidence 99999999999999999999999977654
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=99.55 E-value=4.3e-13 Score=155.91 Aligned_cols=230 Identities=15% Similarity=0.059 Sum_probs=155.6
Q ss_pred HHHHhhcchhHHHHHHHHhhccCCHHHHHHHHHHcCCcccccccCcccCCcccccccccccCCcCeEEEcCHHHHHHHHH
Q 009000 260 AEAKTKGDKRLLEYLVYLAMEAGYSEKVDELCERYSLEGFLKTREPEAGFVHSRFLHLKELVVEDIIWVDEVDGLHKAIC 339 (547)
Q Consensus 260 a~~~~~~D~~l~~~lv~L~~~~~d~~~L~~l~~ryef~sll~el~~~~~~~~~~~~~l~~~~~~~y~~Idt~eeL~~lle 339 (547)
-++++++|+++...+.+++..++|.+++.++|++|||+++++++..............++.....|..+.+.+++..+++
T Consensus 239 ~L~ti~~d~~l~~~~~~~~~~~~~~~~l~~~~~~lef~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 318 (887)
T TIGR00593 239 ELATIVTDVPLEVDLEDLRLSEPDRERLYALLQELEFKSLLDRLENLESPVIDDHAPVLTEKTSCAKESEEAAPLANPAE 318 (887)
T ss_pred HhheeecCCCCCCCHHHhccCCCCHHHHHHHHHHhCCccHHHHhcccccccccccccccccccccceEeCCHHHHHHHHH
Confidence 57899999999888899999999999999999999999999887310000000000000000113556767777887775
Q ss_pred HhhCCCeEEEEeeeecCCccCCcCCceeEEEEEeC--CeEEEEEcCcccCC-CchHHHHHHHHhhcCCCceEEEechHHH
Q 009000 340 HIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASD--EMVFIFDLIKLAED-VPDVLDSCLTRILQSPGILKLGYNFQCD 416 (547)
Q Consensus 340 ~L~~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~--~~a~~Idl~~l~~~-~p~~Ll~~Lk~LLed~~I~KVGhnlK~D 416 (547)
. ...+.+++ ++.. +....+..+.++++ +.++|+++. .+.. ..+.....|+++|+++.+.|+|||+|+|
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 2211 01123333446664 348888764 1111 1123346799999999999999999999
Q ss_pred HHHHHHHhCCcccccccchhhhHHHh---hc-CCCCCHHHHHHHHhCCCCCCCccccc----CCCCCCCHHHHHHHHHHH
Q 009000 417 IKQLAHSYGELECFKHYEMLLDIQNV---FK-EPKGGLSGLAEKILGAGLNKTRRNSN----WEQRPLSQNQLEYAALDA 488 (547)
Q Consensus 417 l~vLa~~~GIl~~~~~~~~vfDtmLA---l~-~~~~gLd~LAer~Lg~~L~K~e~~Sd----W~~rpLt~~Qi~YAAeDA 488 (547)
+++|.+ +|+... +.++|||++ ++ ..+++|++++.+||+..+...++... +...| .+....||+.||
T Consensus 390 ~~~l~~-~gi~~~----~~~~Dt~la~yll~~~~~~~l~~la~~yl~~~~~~~~~~~~~~~~~~~~~-~~~~~~ya~~d~ 463 (887)
T TIGR00593 390 MHLLKR-EGIELG----GVIFDTMLAAYLLDPAQVSTLDTLARRYLVEELILDEKIGGKLAKFAFPP-LEEATEYLARRA 463 (887)
T ss_pred HHHHHh-CCCCCC----CcchhHHHHHHHcCCCCCCCHHHHHHHHcCcccccHHHhccCCCCccccc-HHHHHHHHHHHH
Confidence 999987 798432 568999999 34 44679999999999976554332222 22222 234578999999
Q ss_pred HHHHHHHHHHHhccCC
Q 009000 489 VVLLQIFHHVRSCSQP 504 (547)
Q Consensus 489 ~vlLrL~~~L~~rLee 504 (547)
.++++||..|.++|++
T Consensus 464 ~~~~~L~~~l~~~l~~ 479 (887)
T TIGR00593 464 AATKRLAEELLKELDE 479 (887)
T ss_pred HHHHHHHHHHHHHHhh
Confidence 9999999999999976
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=1.3e-12 Score=118.33 Aligned_cols=145 Identities=26% Similarity=0.216 Sum_probs=107.9
Q ss_pred eEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchHHHHHHHHhhcCCCceEEEechHHHHHHHHHHhC
Q 009000 346 VVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYG 425 (547)
Q Consensus 346 vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~~G 425 (547)
.+++|+|+.+.. .....+.++|++++++++|++.... ...+.+.|+++|+++.+.|||||+|+|++.|.+ ++
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 578999887642 1134678888988654667654321 133445689999999999999999999999987 45
Q ss_pred CcccccccchhhhHHHhh---c-CC-CCCHHHHHHHHhCCCCCCCcccccCC----CCCCCHHHHHHHHHHHHHHHHHHH
Q 009000 426 ELECFKHYEMLLDIQNVF---K-EP-KGGLSGLAEKILGAGLNKTRRNSNWE----QRPLSQNQLEYAALDAVVLLQIFH 496 (547)
Q Consensus 426 Il~~~~~~~~vfDtmLAl---~-~~-~~gLd~LAer~Lg~~L~K~e~~SdW~----~rpLt~~Qi~YAAeDA~vlLrL~~ 496 (547)
+.. .+.++||+++. + .. +++|++++++|++.+..+.++..+|. .++++..|..||+.||.++++|++
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 432 26789999993 3 33 57999999999998754433344442 467889999999999999999999
Q ss_pred HHHhcc
Q 009000 497 HVRSCS 502 (547)
Q Consensus 497 ~L~~rL 502 (547)
.|.+++
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=99.46 E-value=1.3e-12 Score=119.13 Aligned_cols=142 Identities=24% Similarity=0.248 Sum_probs=106.4
Q ss_pred eEEEEeeeecCCccCCcCCceeEEEEEeC-CeEEEEEcCcccCCCchHHHHHHHHhhcCCCceEEEechHHHHHHHHHHh
Q 009000 346 VVGIDCEWKPNYVKGCKMNKVSIMQIASD-EMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSY 424 (547)
Q Consensus 346 vIgfDtE~~~l~~~~~~~~~VsLlQLAt~-~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~~ 424 (547)
++++|+|+.+.. +...++..+|++++ +.++|+++.+. .. ....|+++|+++++.|+|||+|.|++.|.+ +
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 478899876542 11346788889876 44888886531 10 124689999999999999999999999987 6
Q ss_pred CCcccccccchhhhHHHh---hc-CC-CCCHHHHHHHHhCCCCCCCcccc--cCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q 009000 425 GELECFKHYEMLLDIQNV---FK-EP-KGGLSGLAEKILGAGLNKTRRNS--NWEQRPLSQNQLEYAALDAVVLLQIFHH 497 (547)
Q Consensus 425 GIl~~~~~~~~vfDtmLA---l~-~~-~~gLd~LAer~Lg~~L~K~e~~S--dW~~rpLt~~Qi~YAAeDA~vlLrL~~~ 497 (547)
|+.. .++.||++++ ++ .+ ++++++|+++||+..+.+.++.. +|..+++..+|..||+.||.++++|++.
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 7643 2678999999 23 33 57999999999998755422222 3755778899999999999999999998
Q ss_pred HHh
Q 009000 498 VRS 500 (547)
Q Consensus 498 L~~ 500 (547)
|.+
T Consensus 148 l~~ 150 (150)
T cd09018 148 LWP 150 (150)
T ss_pred hcC
Confidence 864
No 17
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=99.35 E-value=2e-12 Score=140.41 Aligned_cols=198 Identities=24% Similarity=0.302 Sum_probs=160.1
Q ss_pred CcCeEEEcCHHHHHHHHHHhhCCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchHHHHHHHHhh
Q 009000 322 VEDIIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRIL 401 (547)
Q Consensus 322 ~~~y~~Idt~eeL~~lle~L~~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LL 401 (547)
...+.+|++..++.++.+.+.....+++|+|..+. +++.+..+++||+|..+-|+||...+. +.+ ..|++.|
T Consensus 190 ~T~~~~I~t~~el~~l~~~l~~~~Efavdlehhsy---rsf~gltclmqISTr~ed~iIDt~~l~----~~i-~~l~e~f 261 (687)
T KOG2206|consen 190 ITPKVWICTLGELEALPEILDSVIEFAVDLEHHSY---RSFLGLTCLMQISTRTEDFIIDTFKLR----DHI-GILNEVF 261 (687)
T ss_pred ccCceeeechHHHHHHHHHHhhhhhhhhhccccch---hhhcCceeEEEeeccchhheehhHHHH----HHH-HHhhhhc
Confidence 34588999999999999999888999999998764 134568899999998888999887653 223 4899999
Q ss_pred cCCCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHhh---cCCCCCHHHHHHHHhCCCCCCCcccccCCCCCCCH
Q 009000 402 QSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF---KEPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQ 478 (547)
Q Consensus 402 ed~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl---~~~~~gLd~LAer~Lg~~L~K~e~~SdW~~rpLt~ 478 (547)
.+|++.||.|+.-.|+.+|++.|||.. .++|||..+. +-.+++|..|.+.+.|.-.+|.-|..+|..|||++
T Consensus 262 sdp~ivkvfhgaD~diiwlqrdfgiyv-----vnLfdt~~a~r~L~~~r~sL~~ll~~~~~v~~nk~yqladwR~rpLp~ 336 (687)
T KOG2206|consen 262 SDPGIVKVFHGADTDIIWLQRDFGIYV-----VNLFDTIQASRLLGLPRPSLAYLLECVCGVLTNKKYQLADWRIRPLPE 336 (687)
T ss_pred cCCCeEEEEecCccchhhhhccceEEE-----EechhhHHHHHHhCCCcccHHHHHHHHHhhhhhhhhhhchhccccCcH
Confidence 999999999999999999999999943 6789999994 45689999999999998888777899999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCcccchhHHHHHhhccCcccccCCCCccc
Q 009000 479 NQLEYAALDAVVLLQIFHHVRSCSQPTDVSEGHDKIEWKSYIVSHMDNPKKSKKRPTIKK 538 (547)
Q Consensus 479 ~Qi~YAAeDA~vlLrL~~~L~~rLee~~~~~~~~~~~w~s~~~~~~~~~~k~~~~~~~~~ 538 (547)
+++.||-+|.++++-+|+.|+..+.+.+- |..-..- .|....++.-++++-+.+
T Consensus 337 ~Mv~yar~dthyllyiyD~lr~el~~~a~--~~~~~~~----~~~d~c~~~~~k~~~~~~ 390 (687)
T KOG2206|consen 337 EMVRYAREDTHYLLYIYDVLRKELKRLAK--GRAVTYS----ESRDMCTNGYKKKTFCTK 390 (687)
T ss_pred HHHHHHhhcchhHHHHHHHHHHHHHHHhc--ccccccc----hhhhhhhcceecccCCCc
Confidence 99999999999999999999988866552 3311111 344445555555555443
No 18
>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases. Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Probab=99.29 E-value=4.9e-11 Score=112.72 Aligned_cols=149 Identities=15% Similarity=0.079 Sum_probs=108.5
Q ss_pred CCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchHHHHHHHHhhcCCCceEEEechHHHHHHHHHH
Q 009000 344 CKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHS 423 (547)
Q Consensus 344 a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~ 423 (547)
...+++++|..... +....+..++++.+++++|+|+.+. ......|+++|+++++.|++||+|+|++.|.+
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 35577888876542 1133555566777667888885421 01235688999999999999999999999987
Q ss_pred hCCcccccccchhhhHHHh---hc-C-CCCCHHHHHHHHhCCCCCCCcccccCC---CCCCCHHHHHHHHHHHHHHHHHH
Q 009000 424 YGELECFKHYEMLLDIQNV---FK-E-PKGGLSGLAEKILGAGLNKTRRNSNWE---QRPLSQNQLEYAALDAVVLLQIF 495 (547)
Q Consensus 424 ~GIl~~~~~~~~vfDtmLA---l~-~-~~~gLd~LAer~Lg~~L~K~e~~SdW~---~rpLt~~Qi~YAAeDA~vlLrL~ 495 (547)
+|+.. .++.||||++ ++ . +++++++++.+|++..+.+.++...|. .++....+.+|+|.||.++++|+
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 78743 2667999999 34 2 347999999999998765433333441 23445667889999999999999
Q ss_pred HHHHhccCCC
Q 009000 496 HHVRSCSQPT 505 (547)
Q Consensus 496 ~~L~~rLee~ 505 (547)
+.|+++|++.
T Consensus 150 ~~l~~~L~~~ 159 (178)
T cd06140 150 PKLEEELEEN 159 (178)
T ss_pred HHHHHHHHHh
Confidence 9999999763
No 19
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=99.29 E-value=1.9e-11 Score=135.22 Aligned_cols=166 Identities=20% Similarity=0.211 Sum_probs=124.0
Q ss_pred eEEEcCHHHHHHHHHHhhCCCeEEEEeeeecCCccCCcCCceeEEEEE--eCCeEEEEEcCcccCCCchHHHHHHHHhhc
Q 009000 325 IIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIA--SDEMVFIFDLIKLAEDVPDVLDSCLTRILQ 402 (547)
Q Consensus 325 y~~Idt~eeL~~lle~L~~a~vIgfDtE~~~l~~~~~~~~~VsLlQLA--t~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLe 402 (547)
|..+.+.+.+..|+..+.....+++|+|+.++. +....+++++ .+..++|+++.+.+... .....|++||+
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 344556677788888777666699999998873 2344555555 34578888887631111 14578999999
Q ss_pred CCCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHh---hc--CCCCCHHHHHHHHhCCCCCCCcccc-------c
Q 009000 403 SPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNV---FK--EPKGGLSGLAEKILGAGLNKTRRNS-------N 470 (547)
Q Consensus 403 d~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLA---l~--~~~~gLd~LAer~Lg~~L~K~e~~S-------d 470 (547)
++.+.|+|||+|+|.++|++ +|+. .+..+|||++ ++ .+.++|++|+++|+++.+..++... +
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 2678999999 23 4579999999999998876444322 2
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 009000 471 WEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQP 504 (547)
Q Consensus 471 W~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLee 504 (547)
+...++. .-..|+|+||+++++|+..|.+++.+
T Consensus 150 ~~~~~~~-~~~~y~a~~a~~~~~L~~~l~~~l~~ 182 (593)
T COG0749 150 FADVKLE-KATEYAAEDADATLRLESILEPELLK 182 (593)
T ss_pred cccchHH-HHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 3333343 33799999999999999999988866
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=99.19 E-value=7.8e-10 Score=105.04 Aligned_cols=154 Identities=24% Similarity=0.277 Sum_probs=109.4
Q ss_pred hCCCeEEEEeeeecCCccCCcCCceeEEEEEeC-CeEEEEEcCcccC---CCchHHHHHHHHhhcCCCceEEEechHHHH
Q 009000 342 EGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASD-EMVFIFDLIKLAE---DVPDVLDSCLTRILQSPGILKLGYNFQCDI 417 (547)
Q Consensus 342 ~~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~-~~a~~Idl~~l~~---~~p~~Ll~~Lk~LLed~~I~KVGhnlK~Dl 417 (547)
...+.+++|+|+++.. +....+..++++.. +..+|+++.+... .....+...|+++|++..+.+|+||+|+|+
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 3467899999887642 11234555667764 4478887653210 012334556889999988899999999999
Q ss_pred HHHHHHhCCcccccccchhhhHHHhh---c-CC-CCCHHHHHHHHhCCCCC-------CCcccccCCCCCCCHHHHHHHH
Q 009000 418 KQLAHSYGELECFKHYEMLLDIQNVF---K-EP-KGGLSGLAEKILGAGLN-------KTRRNSNWEQRPLSQNQLEYAA 485 (547)
Q Consensus 418 ~vLa~~~GIl~~~~~~~~vfDtmLAl---~-~~-~~gLd~LAer~Lg~~L~-------K~e~~SdW~~rpLt~~Qi~YAA 485 (547)
+.|.+ +|+.. .+.++||+++. + .. +++++.++++|++.... ++.+..+|+..|+ ..+.+||+
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 25679999992 3 33 68999999999986532 2223344555455 56789999
Q ss_pred HHHHHHHHHHHHHHhccCC
Q 009000 486 LDAVVLLQIFHHVRSCSQP 504 (547)
Q Consensus 486 eDA~vlLrL~~~L~~rLee 504 (547)
.|+.++++|++.|.+++++
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=98.94 E-value=3.7e-09 Score=118.04 Aligned_cols=139 Identities=24% Similarity=0.237 Sum_probs=113.7
Q ss_pred CeEEEcCHHHHHHHHHHhhCCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchHHHHHHHHhhcC
Q 009000 324 DIIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQS 403 (547)
Q Consensus 324 ~y~~Idt~eeL~~lle~L~~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed 403 (547)
.+.+|++.+++..++..+...+.+++|+|+.... . .++++|++.++..|++|... .+.|+
T Consensus 2 ~~~~I~~~~~l~~~~~~l~~~~~~a~DtEf~r~~-----t-~l~liQ~~~~~~~~liDpl~-----------~l~~~--- 61 (553)
T PRK14975 2 DMKVILAPEELGAALERLSPAGVVAGDTETTGDD-----A-AAAAAQEGEEEPRWVWASTA-----------ALYPR--- 61 (553)
T ss_pred CceEEeccchhHHHHHHhccCCceeCCccccCCc-----c-hhheeeecCCCceEEECchH-----------HhHHH---
Confidence 3578889999999999999999999999988641 2 68899999888899887531 12222
Q ss_pred CCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHhh---c-CC---CCCHHHHHHHHhCCCCCCCcccccCCCCCC
Q 009000 404 PGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF---K-EP---KGGLSGLAEKILGAGLNKTRRNSNWEQRPL 476 (547)
Q Consensus 404 ~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl---~-~~---~~gLd~LAer~Lg~~L~K~e~~SdW~~rpL 476 (547)
|.+ +|+.. .++||||++. + .. ++|++.+++++++..++|.++.++|. +|+
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 4589999992 3 23 68999999999999999988889996 899
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhccCCC
Q 009000 477 SQNQLEYAALDAVVLLQIFHHVRSCSQPT 505 (547)
Q Consensus 477 t~~Qi~YAAeDA~vlLrL~~~L~~rLee~ 505 (547)
++.|..|||.|+.++++||+.|.+++++.
T Consensus 119 s~~q~~YAa~Dv~~l~~L~~~L~~qL~~~ 147 (553)
T PRK14975 119 DEEQLLYAAADADVLLELYAVLADQLNRI 147 (553)
T ss_pred hHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999999763
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=98.45 E-value=2.9e-06 Score=78.25 Aligned_cols=120 Identities=22% Similarity=0.207 Sum_probs=80.4
Q ss_pred EEEEeCCeEEEEEcCcccCCCchHHHHHHHHhhcCCCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHh---hc-
Q 009000 369 MQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNV---FK- 444 (547)
Q Consensus 369 lQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLA---l~- 444 (547)
+.++.+++++|+++.. . . . ...|+++|+++++.|++||+|.+++.|.+ +|+.. .+..||+|++ ++
T Consensus 23 lal~~~~~~~yi~~~~-~--~--~-~~~l~~~l~~~~~~ki~~d~K~~~~~l~~-~gi~l----~~~~fD~~LAaYLL~p 91 (151)
T cd06128 23 LAFAIEGVAAYIPVAH-D--Y--A-LELLKPLLEDEKALKVGQNLKYDRVILAN-YGIEL----RGIAFDTMLEAYLLDP 91 (151)
T ss_pred EEEEcCCCeEEEeCCC-C--c--C-HHHHHHHHcCCCCCEEeeehHHHHHHHHH-CCCCC----CCcchhHHHHHHHcCC
Confidence 4455555688887432 1 1 1 24588999999999999999999999976 78843 2667999999 34
Q ss_pred CCC-CCHHHHHHHHhCCCCCCCcccccCCC--CCC-CHHHHHHHHHHHHHHHHHHHHHH
Q 009000 445 EPK-GGLSGLAEKILGAGLNKTRRNSNWEQ--RPL-SQNQLEYAALDAVVLLQIFHHVR 499 (547)
Q Consensus 445 ~~~-~gLd~LAer~Lg~~L~K~e~~SdW~~--rpL-t~~Qi~YAAeDA~vlLrL~~~L~ 499 (547)
..+ +++++++++||+......++...+.. .++ ..+..+|++..|.++.+|++.|.
T Consensus 92 ~~~~~~l~~la~~yl~~~~~~~~~~~gkg~~~~~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 92 VAGRHDMDSLAERWLKEKTITFEEIAGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred CCCCCCHHHHHHHHcCCCCccHHHHcCCCCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 232 59999999999876322011111110 011 12224588999999999999875
No 23
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=97.94 E-value=4.4e-05 Score=79.28 Aligned_cols=142 Identities=23% Similarity=0.276 Sum_probs=101.3
Q ss_pred CeEEEEeeeecCCccCCcCCceeEEEEEeC-CeEEEEEcCcccCCCchHHHHHHHHhhcCCCceEEEechHHHHHHHHH-
Q 009000 345 KVVGIDCEWKPNYVKGCKMNKVSIMQIASD-EMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAH- 422 (547)
Q Consensus 345 ~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~-~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~- 422 (547)
+.+..+-|+.+....+.....++.+||+++ +.++++.+.+.. ..|. .|+.+|+|++.++||-+...|...|.+
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 344455566654111112335888999996 788888776542 3454 567789999999999999999999877
Q ss_pred HhCCcccccccchhhhHHHhhc------CCCCCHHHHHHHHhCC-----CCCCCcccccCCCCCCCHHHHHHHHHHHHHH
Q 009000 423 SYGELECFKHYEMLLDIQNVFK------EPKGGLSGLAEKILGA-----GLNKTRRNSNWEQRPLSQNQLEYAALDAVVL 491 (547)
Q Consensus 423 ~~GIl~~~~~~~~vfDtmLAl~------~~~~gLd~LAer~Lg~-----~L~K~e~~SdW~~rpLt~~Qi~YAAeDA~vl 491 (547)
.|+.. .+...|+.+..+ -.+.+...++...+|. .+++.-++++|...+|+.+|+.||+.|++++
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 1235666777766653 2334447899999999999999999999999
Q ss_pred HHHHH
Q 009000 492 LQIFH 496 (547)
Q Consensus 492 LrL~~ 496 (547)
..|+.
T Consensus 278 ~~lg~ 282 (319)
T KOG4373|consen 278 HKLGV 282 (319)
T ss_pred HHHHH
Confidence 99983
No 24
>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=96.12 E-value=0.049 Score=51.36 Aligned_cols=82 Identities=20% Similarity=0.267 Sum_probs=53.8
Q ss_pred HHHHHHHhhcCCCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHh--------hc-CCCCCHHHHHHHHhCCCCC
Q 009000 393 LDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNV--------FK-EPKGGLSGLAEKILGAGLN 463 (547)
Q Consensus 393 Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLA--------l~-~~~~gLd~LAer~Lg~~L~ 463 (547)
....+..++.+ ...||||+++|+..|...+.. .++.||... +. ..+++|+.|++++++..+.
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 34566667754 467999999999988753221 234576532 11 2469999999999876554
Q ss_pred CCcccccCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009000 464 KTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFH 496 (547)
Q Consensus 464 K~e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~ 496 (547)
.+.+ .+-|..||.++.+||+
T Consensus 138 ~~~~-------------~H~Al~DA~at~~l~~ 157 (157)
T cd06149 138 VGRQ-------------GHSSVEDARATMELYK 157 (157)
T ss_pred CCCC-------------CcCcHHHHHHHHHHhC
Confidence 2211 1337789999988874
No 25
>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=95.95 E-value=0.039 Score=47.80 Aligned_cols=59 Identities=22% Similarity=0.237 Sum_probs=41.9
Q ss_pred EEEEeeeecCCccCCcCCceeEEEEEeC--CeEEEEEcCcccCCCchHHHHHHHHhhcCCC-ceEEEechHHHHHHHHHH
Q 009000 347 VGIDCEWKPNYVKGCKMNKVSIMQIASD--EMVFIFDLIKLAEDVPDVLDSCLTRILQSPG-ILKLGYNFQCDIKQLAHS 423 (547)
Q Consensus 347 IgfDtE~~~l~~~~~~~~~VsLlQLAt~--~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~-I~KVGhnlK~Dl~vLa~~ 423 (547)
+++|+|+++.. +....+.++|++.. +..+++| +.+++++.. ...||||..+|+..|.+.
T Consensus 1 ~~~DiEt~~~~---~~~~~i~~i~~~~~~~~~~~~~~---------------f~~~l~~~~~~v~V~hn~~fD~~fL~~~ 62 (96)
T cd06125 1 IAIDTEATGLD---GAVHEIIEIALADVNPEDTAVID---------------LKDILRDKPLAILVGHNGSFDLPFLNNR 62 (96)
T ss_pred CEEEEECCCCC---CCCCcEEEEEEEEccCCCEEEeh---------------HHHHHhhCCCCEEEEeCcHHhHHHHHHH
Confidence 47999998763 23456777877654 6666654 455776665 678999999998877653
No 26
>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=95.94 E-value=0.09 Score=49.63 Aligned_cols=78 Identities=15% Similarity=0.200 Sum_probs=53.7
Q ss_pred HHHHHhhcCCCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHhhc----C----CCCCHHHHHHHHhCCCCCCCc
Q 009000 395 SCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFK----E----PKGGLSGLAEKILGAGLNKTR 466 (547)
Q Consensus 395 ~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl~----~----~~~gLd~LAer~Lg~~L~K~e 466 (547)
..|..++.+. ...||||+.+|+..|... . ..++||..... . .+++|..|+++++|.++....
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 3455566543 457999999999999751 1 34679887742 2 479999999999997653211
Q ss_pred ccccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009000 467 RNSNWEQRPLSQNQLEYAALDAVVLLQIF 495 (547)
Q Consensus 467 ~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~ 495 (547)
. .+-|..||.++.+|+
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 27
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=95.36 E-value=0.61 Score=47.79 Aligned_cols=90 Identities=20% Similarity=0.165 Sum_probs=60.5
Q ss_pred HHHHHHHhhcCCCceEEEechHHHHHHHHH---HhCCcccccccchhhhHHHh----hcCCCCCHHHHHHHHhCCCCCCC
Q 009000 393 LDSCLTRILQSPGILKLGYNFQCDIKQLAH---SYGELECFKHYEMLLDIQNV----FKEPKGGLSGLAEKILGAGLNKT 465 (547)
Q Consensus 393 Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~---~~GIl~~~~~~~~vfDtmLA----l~~~~~gLd~LAer~Lg~~L~K~ 465 (547)
+...+..++.+. ..||||+.+|...|.+ .+|.... ....+||+-. +...+++|+.|++. +|.+..
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 345667777653 5799999999988864 2443111 1345666544 23467899999875 575432
Q ss_pred cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 009000 466 RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQP 504 (547)
Q Consensus 466 e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLee 504 (547)
+.+-|-.||.++.+|+..+..++..
T Consensus 209 --------------~~HrAl~DA~ata~ll~~ll~~~~~ 233 (257)
T PRK08517 209 --------------VHHRAYADALAAYEIFKICLLNLPS 233 (257)
T ss_pred --------------CCCChHHHHHHHHHHHHHHHHHhHH
Confidence 1234788999999999999887743
No 28
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=95.31 E-value=0.23 Score=50.97 Aligned_cols=79 Identities=18% Similarity=0.336 Sum_probs=57.9
Q ss_pred HHHHhhcCCCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHh--h----c-CCCCCHHHHHHHHhCCCCCCCccc
Q 009000 396 CLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNV--F----K-EPKGGLSGLAEKILGAGLNKTRRN 468 (547)
Q Consensus 396 ~Lk~LLed~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLA--l----~-~~~~gLd~LAer~Lg~~L~K~e~~ 468 (547)
....+|.. ...|||.++.|+.+|.-.|.- ..+-||.-. + . ..+-+|..|++.+||+.+-.++..
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 44556665 456999999999998754442 334577655 1 2 467899999999999887555532
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009000 469 SNWEQRPLSQNQLEYAALDAVVLLQIFHHV 498 (547)
Q Consensus 469 SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L 498 (547)
..+||.++.+||...
T Consensus 248 ---------------SvEDA~AtM~LY~~v 262 (280)
T KOG2249|consen 248 ---------------SVEDARATMELYKRV 262 (280)
T ss_pred ---------------cHHHHHHHHHHHHHH
Confidence 358999999999976
No 29
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=94.98 E-value=0.17 Score=47.25 Aligned_cols=80 Identities=18% Similarity=0.332 Sum_probs=54.5
Q ss_pred HHHHHHHhhcCCCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHh--h-c---CCCCCHHHHHHHHhCCCCCCCc
Q 009000 393 LDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNV--F-K---EPKGGLSGLAEKILGAGLNKTR 466 (547)
Q Consensus 393 Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLA--l-~---~~~~gLd~LAer~Lg~~L~K~e 466 (547)
....|..++.+ . ..||||+.+|+..|.. +... ..++|+... + . ..+++|+.|+++++|++....
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 35567778875 3 4599999999999864 2211 235576543 1 1 257999999999999764311
Q ss_pred ccccCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009000 467 RNSNWEQRPLSQNQLEYAALDAVVLLQIFH 496 (547)
Q Consensus 467 ~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~ 496 (547)
.+-|..||.++.+|++
T Consensus 137 --------------~H~Al~DA~at~~l~~ 152 (152)
T cd06144 137 --------------EHSSVEDARAAMRLYR 152 (152)
T ss_pred --------------CcCcHHHHHHHHHHhC
Confidence 1337889999988874
No 30
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=94.83 E-value=0.51 Score=48.04 Aligned_cols=90 Identities=17% Similarity=0.197 Sum_probs=58.7
Q ss_pred HHHHHHhhcCCCceEEEechHHHHHHHHHH---hCCcccccccchhhhHHHhhc----CCCCCHHHHHHHHhCCCCCCCc
Q 009000 394 DSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK----EPKGGLSGLAEKILGAGLNKTR 466 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl~----~~~~gLd~LAer~Lg~~L~K~e 466 (547)
...+..++.+. ...||||+.+|+..|... +|+.... ....++||+-... ..+++|+.|++.+ |.+...
T Consensus 78 ~~~~~~fl~~~-~~lvghn~~FD~~~L~~~~~r~g~~~~~-~~~~~iDtl~lar~~~~~~~~~L~~l~~~~-g~~~~~-- 152 (250)
T PRK06310 78 FPQIKGFFKEG-DYIVGHSVGFDLQVLSQESERIGETFLS-KHYYIIDTLRLAKEYGDSPNNSLEALAVHF-NVPYDG-- 152 (250)
T ss_pred HHHHHHHhCCC-CEEEEECHHHHHHHHHHHHHHcCCCccc-cCCcEEehHHHHHhcccCCCCCHHHHHHHC-CCCCCC--
Confidence 34566666553 467999999999988653 2331100 0134678876632 3468999999775 654321
Q ss_pred ccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhcc
Q 009000 467 RNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCS 502 (547)
Q Consensus 467 ~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rL 502 (547)
.+-|..||.++..|+..+..+.
T Consensus 153 --------------aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 153 --------------NHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred --------------CcChHHHHHHHHHHHHHHHHhc
Confidence 2348899999999999887654
No 31
>PRK07740 hypothetical protein; Provisional
Probab=94.82 E-value=0.82 Score=46.35 Aligned_cols=90 Identities=14% Similarity=0.058 Sum_probs=61.3
Q ss_pred HHHHHHhhcCCCceEEEechHHHHHHHHHH----hCCcccccccchhhhHHHhhc-----CCCCCHHHHHHHHhCCCCCC
Q 009000 394 DSCLTRILQSPGILKLGYNFQCDIKQLAHS----YGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLNK 464 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~----~GIl~~~~~~~~vfDtmLAl~-----~~~~gLd~LAer~Lg~~L~K 464 (547)
...|..++.+ -..||||..+|...|.+. ++... ...++||+.... ..+++|++++.. +|++...
T Consensus 132 l~~f~~fi~~--~~lVahna~fD~~fL~~~~~~~~~~~~----~~~~iDt~~l~r~l~~~~~~~sL~~l~~~-~gi~~~~ 204 (244)
T PRK07740 132 LHRFYAFIGA--GVLVAHHAGHDKAFLRHALWRTYRQPF----THRLIDTMFLTKLLAHERDFPTLDDALAY-YGIPIPR 204 (244)
T ss_pred HHHHHHHhCC--CEEEEeCHHHHHHHHHHHHHHhcCCCc----CCCeechHHHHHHHcCCCCCCCHHHHHHH-CCcCCCC
Confidence 3445555554 367899999999887642 12111 245789887732 347899999965 6765431
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Q 009000 465 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTD 506 (547)
Q Consensus 465 ~e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLee~~ 506 (547)
.+-|-.||..+.+|+..+..++++.+
T Consensus 205 ----------------~H~Al~Da~ata~l~~~ll~~~~~~~ 230 (244)
T PRK07740 205 ----------------RHHALGDALMTAKLWAILLVEAQQRG 230 (244)
T ss_pred ----------------CCCcHHHHHHHHHHHHHHHHHHHHcC
Confidence 12377899999999999988887644
No 32
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=94.74 E-value=0.55 Score=49.44 Aligned_cols=92 Identities=21% Similarity=0.157 Sum_probs=63.1
Q ss_pred HHHHHHHhhcCCCceEEEechHHHHHHHHHH---hCCcccccccchhhhHHHhhc-----CCCCCHHHHHHHHhCCCCCC
Q 009000 393 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLNK 464 (547)
Q Consensus 393 Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl~-----~~~~gLd~LAer~Lg~~L~K 464 (547)
+...|..++.+ ...||||+.+|+.+|.+. +|+... ....+||+.... ..++.|++|+++ +|++..
T Consensus 84 v~~~l~~~l~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~---~~~~ldTl~lar~~~~~~~~~kL~~l~~~-~gi~~~- 156 (313)
T PRK06063 84 IAGEVAELLRG--RTLVAHNVAFDYSFLAAEAERAGAELP---VDQVMCTVELARRLGLGLPNLRLETLAAH-WGVPQQ- 156 (313)
T ss_pred HHHHHHHHcCC--CEEEEeCHHHHHHHHHHHHHHcCCCCC---CCCEEehHHHHHHhccCCCCCCHHHHHHH-cCCCCC-
Confidence 45567777765 367999999999988653 343111 134678887632 357899999986 465432
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Q 009000 465 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTD 506 (547)
Q Consensus 465 ~e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLee~~ 506 (547)
+ .+-|-.||.++.+|+..+..++.+.+
T Consensus 157 --~-------------~H~Al~DA~ata~l~~~ll~~~~~~~ 183 (313)
T PRK06063 157 --R-------------PHDALDDARVLAGILRPSLERARERD 183 (313)
T ss_pred --C-------------CCCcHHHHHHHHHHHHHHHHHHHhcC
Confidence 1 23478899999999999888876654
No 33
>PRK07883 hypothetical protein; Validated
Probab=94.72 E-value=0.32 Score=55.10 Aligned_cols=92 Identities=20% Similarity=0.104 Sum_probs=64.0
Q ss_pred HHHHHHhhcCCCceEEEechHHHHHHHHHH---hCCcccccccchhhhHHHhh----c---CCCCCHHHHHHHHhCCCCC
Q 009000 394 DSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVF----K---EPKGGLSGLAEKILGAGLN 463 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl----~---~~~~gLd~LAer~Lg~~L~ 463 (547)
...+..++.+ ...||||..+|+..|... +|+... ...++||+... . ..+++|++|++ ++|++..
T Consensus 86 l~~f~~fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~---~~~~iDTl~lar~l~~~~~~~~~~L~~L~~-~~gi~~~ 159 (557)
T PRK07883 86 LPAFLEFARG--AVLVAHNAPFDIGFLRAAAARCGYPWP---GPPVLCTVRLARRVLPRDEAPNVRLSTLAR-LFGATTT 159 (557)
T ss_pred HHHHHHHhcC--CEEEEeCcHHHHHHHHHHHHHcCCCCC---CCCcEecHHHHHHhcccCCCCCCCHHHHHH-HCCcccC
Confidence 4456667764 456899999999988642 454210 13567987763 1 35789999987 4676542
Q ss_pred CCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCC
Q 009000 464 KTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTDV 507 (547)
Q Consensus 464 K~e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLee~~~ 507 (547)
. .+-|..||.++.+|+..+..++.+.+.
T Consensus 160 ~----------------~H~Al~DA~ata~l~~~l~~~~~~~~~ 187 (557)
T PRK07883 160 P----------------THRALDDARATVDVLHGLIERLGNLGV 187 (557)
T ss_pred C----------------CCCHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 1 244889999999999999999876554
No 34
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=94.61 E-value=0.58 Score=47.02 Aligned_cols=79 Identities=18% Similarity=0.151 Sum_probs=52.8
Q ss_pred ceEEEechHHHHHHHHHH---hCCcccccccchhhhHHHhh---c---CCCCCHHHHHHHHhCCCCCCCcccccCCCCCC
Q 009000 406 ILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVF---K---EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPL 476 (547)
Q Consensus 406 I~KVGhnlK~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl---~---~~~~gLd~LAer~Lg~~L~K~e~~SdW~~rpL 476 (547)
...||||..+|+..|.+. +|...- ...+++|++... . ..+++|++|+++ +|++...
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 456999999999887542 343110 013567887662 1 236789999987 4765431
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhccC
Q 009000 477 SQNQLEYAALDAVVLLQIFHHVRSCSQ 503 (547)
Q Consensus 477 t~~Qi~YAAeDA~vlLrL~~~L~~rLe 503 (547)
.+-|..||.++.+|+..+..+..
T Consensus 159 ----aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 159 ----AHEATADALAAARVAWALARRFP 181 (232)
T ss_pred ----CCChHHHHHHHHHHHHHHHHHHH
Confidence 13388999999999999876654
No 35
>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=94.15 E-value=0.088 Score=51.04 Aligned_cols=78 Identities=21% Similarity=0.281 Sum_probs=55.7
Q ss_pred HHHHhhcCCCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHhhc---CCCCCHHHHHHHHhCCCCCCCcccccCC
Q 009000 396 CLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFK---EPKGGLSGLAEKILGAGLNKTRRNSNWE 472 (547)
Q Consensus 396 ~Lk~LLed~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl~---~~~~gLd~LAer~Lg~~L~K~e~~SdW~ 472 (547)
.|..++ +++...|||++..|+++|.-.|+- ..+.||.+.+. .+..+|..|+.++||..+..+.
T Consensus 94 ~l~~li-~~~tILVGHsL~nDL~aL~l~hp~-------~~viDTa~l~~~~~~r~~sLk~La~~~L~~~IQ~~~------ 159 (174)
T cd06143 94 KLRLLV-DLGCIFVGHGLAKDFRVINIQVPK-------EQVIDTVELFHLPGQRKLSLRFLAWYLLGEKIQSET------ 159 (174)
T ss_pred HHHHHc-CCCCEEEeccchhHHHHhcCcCCC-------cceEEcHHhccCCCCCChhHHHHHHHHcCCcccCCC------
Confidence 455555 344677999999999998642221 34679987753 3468999999999998764321
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHH
Q 009000 473 QRPLSQNQLEYAALDAVVLLQIFH 496 (547)
Q Consensus 473 ~rpLt~~Qi~YAAeDA~vlLrL~~ 496 (547)
+-..+||.++++||+
T Consensus 160 ---------HdSvEDArAam~Ly~ 174 (174)
T cd06143 160 ---------HDSIEDARTALKLYR 174 (174)
T ss_pred ---------cCcHHHHHHHHHHhC
Confidence 125689999999983
No 36
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=94.12 E-value=1.2 Score=45.33 Aligned_cols=93 Identities=16% Similarity=0.203 Sum_probs=58.9
Q ss_pred HHHHHHhhcCCCceEEEechHHHHHHHHHH---hCC-cccccccchhhhHHHhh----cCCCCCHHHHHHHHhCCCCCCC
Q 009000 394 DSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGE-LECFKHYEMLLDIQNVF----KEPKGGLSGLAEKILGAGLNKT 465 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~---~GI-l~~~~~~~~vfDtmLAl----~~~~~gLd~LAer~Lg~~L~K~ 465 (547)
...+..++.+. ..|+||..+|+..|.+. +|. ...+.....++||.... ...+++|+.|+++| |++..
T Consensus 77 ~~~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~aL~~~~-gi~~~-- 151 (240)
T PRK05711 77 ADEFLDFIRGA--ELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRY-GIDNS-- 151 (240)
T ss_pred HHHHHHHhCCC--EEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCCCCCHHHHHHHC-CCCCC--
Confidence 34555666553 46899999999887642 332 11000113478987663 34578999999875 64321
Q ss_pred cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccC
Q 009000 466 RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQ 503 (547)
Q Consensus 466 e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLe 503 (547)
.|. .+-|-.||.++.++|..|.....
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 011 23378999999999999877633
No 37
>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=93.60 E-value=3 Score=38.91 Aligned_cols=88 Identities=16% Similarity=0.184 Sum_probs=56.0
Q ss_pred HHHHHHhhcCCCceEEEechHHHHHHHHHH---hCCcccccccchhhhHHHhh----cCCCCCHHHHHHHHhCCCCCCCc
Q 009000 394 DSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVF----KEPKGGLSGLAEKILGAGLNKTR 466 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl----~~~~~gLd~LAer~Lg~~L~K~e 466 (547)
...|..++.+. ..||||..+|+.+|.+. +|....+.....++||+... ...+++|+++++++ |.+....
T Consensus 72 ~~~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~~~~L~~l~~~~-~i~~~~~- 147 (167)
T cd06131 72 ADEFLDFIRGA--ELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRF-GIDNSHR- 147 (167)
T ss_pred HHHHHHHHCCC--eEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCCCCCHHHHHHHC-CCCCCCC-
Confidence 45666677653 35999999999888642 23211000124578998653 23578999999885 6543210
Q ss_pred ccccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009000 467 RNSNWEQRPLSQNQLEYAALDAVVLLQIFHHV 498 (547)
Q Consensus 467 ~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L 498 (547)
+.+.|..||..+.+|+..|
T Consensus 148 -------------~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 148 -------------TLHGALLDAELLAEVYLEL 166 (167)
T ss_pred -------------CCCChHHHHHHHHHHHHHh
Confidence 1244889999999988765
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=93.60 E-value=1.8 Score=43.28 Aligned_cols=94 Identities=15% Similarity=0.198 Sum_probs=61.0
Q ss_pred HHHHHHhhcCCCceEEEechHHHHHHHHHH---hCC-cccccccchhhhHHHhh----cCCCCCHHHHHHHHhCCCCCCC
Q 009000 394 DSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGE-LECFKHYEMLLDIQNVF----KEPKGGLSGLAEKILGAGLNKT 465 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~---~GI-l~~~~~~~~vfDtmLAl----~~~~~gLd~LAer~Lg~~L~K~ 465 (547)
...|..++.+. ..|+||..+|+..|... +|. ...+.....++||+... ...+++|+.|+++| |++...
T Consensus 73 ~~~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~L~~~~-gi~~~~- 148 (225)
T TIGR01406 73 ADEFLDFIGGS--ELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRF-KVDNSH- 148 (225)
T ss_pred HHHHHHHhCCC--EEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCCCCCHHHHHHhc-CCCCCC-
Confidence 44556666653 45899999999888642 341 01011124578988763 34578999999986 543210
Q ss_pred cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 009000 466 RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQP 504 (547)
Q Consensus 466 e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLee 504 (547)
+. .+-|..||..+.+||..|....+.
T Consensus 149 --------r~-----~H~Al~DA~~~a~v~~~l~~~~~~ 174 (225)
T TIGR01406 149 --------RT-----LHGALLDAHLLAEVYLALTGGQES 174 (225)
T ss_pred --------CC-----CcCHHHHHHHHHHHHHHHHcCCcc
Confidence 01 233889999999999999776544
No 39
>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=93.15 E-value=2.7 Score=41.58 Aligned_cols=96 Identities=14% Similarity=0.126 Sum_probs=59.8
Q ss_pred HHHHHHhhcCCCceEEEechHHHHHHHHHHhCCcc-cccccchhhhHHHh----hc---CCCCCHHHHHHHHhCCCCCCC
Q 009000 394 DSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELE-CFKHYEMLLDIQNV----FK---EPKGGLSGLAEKILGAGLNKT 465 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~~GIl~-~~~~~~~vfDtmLA----l~---~~~~gLd~LAer~Lg~~L~K~ 465 (547)
...|..++.+ ...||||+.+|+..|.+.+.-.. .......++|++.. .. ..+++|..+++++ |.+...
T Consensus 78 ~~~~~~~~~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~-gl~~~~- 153 (217)
T TIGR00573 78 AEDFADYIRG--AELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRY-EITNSH- 153 (217)
T ss_pred HHHHHHHhCC--CEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHHHc-CCCCCC-
Confidence 4556666655 35789999999999876432100 00001345676543 11 3467899999875 643210
Q ss_pred cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Q 009000 466 RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTD 506 (547)
Q Consensus 466 e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLee~~ 506 (547)
. ..+-|..||.++.+|+..+..+....+
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 123388999999999999988875533
No 40
>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=92.95 E-value=2.2 Score=39.06 Aligned_cols=80 Identities=25% Similarity=0.181 Sum_probs=53.9
Q ss_pred HHHHHHHhhcCCCceEEEechHHHHHHHHHH---hCCcccccccchhhhHHHhhc-----CCCCCHHHHHHHHhCCCCCC
Q 009000 393 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLNK 464 (547)
Q Consensus 393 Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl~-----~~~~gLd~LAer~Lg~~L~K 464 (547)
....|..++++ ...||||..+|...|.+. +|+... ...++|++...+ ..+++|+.+++. +|.+..
T Consensus 67 v~~~l~~~l~~--~~lv~hn~~fD~~~l~~~~~~~g~~~~---~~~~idt~~~~~~~~~~~~~~~L~~l~~~-~g~~~~- 139 (156)
T cd06130 67 VWPEIKPFLGG--SLVVAHNASFDRSVLRAALEAYGLPPP---PYQYLCTVRLARRVWPLLPNHKLNTVAEH-LGIELN- 139 (156)
T ss_pred HHHHHHHHhCC--CEEEEeChHHhHHHHHHHHHHcCCCCC---CCCEEEHHHHHHHHhccCCCCCHHHHHHH-cCCCcc-
Confidence 34567777776 467999999999988542 454211 245789987732 356899999986 565432
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009000 465 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIF 495 (547)
Q Consensus 465 ~e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~ 495 (547)
.+-|..||..+.+|+
T Consensus 140 ----------------~H~Al~Da~~ta~l~ 154 (156)
T cd06130 140 ----------------HHDALEDARACAEIL 154 (156)
T ss_pred ----------------CcCchHHHHHHHHHH
Confidence 133678888888776
No 41
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=92.87 E-value=1.8 Score=51.30 Aligned_cols=89 Identities=18% Similarity=0.160 Sum_probs=62.7
Q ss_pred HHHHHHHhhcCCCceEEEechHHHHHHHHHHh---CCcccccccchhhhHHHhh----c-CCCCCHHHHHHHHhCCCCCC
Q 009000 393 LDSCLTRILQSPGILKLGYNFQCDIKQLAHSY---GELECFKHYEMLLDIQNVF----K-EPKGGLSGLAEKILGAGLNK 464 (547)
Q Consensus 393 Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~~---GIl~~~~~~~~vfDtmLAl----~-~~~~gLd~LAer~Lg~~L~K 464 (547)
+...+..++.+ ...||||+.+|+..|.+.+ |... ..+.+||+... . ..+++|++|+++ +|.+...
T Consensus 76 v~~~~~~~l~~--~~lVaHN~~FD~~fL~~~~~~~g~~~----~~~~iDT~~la~~~~p~~~~~~L~~L~~~-lgl~~~~ 148 (820)
T PRK07246 76 VARHIYDLIED--CIFVAHNVKFDANLLAEALFLEGYEL----RTPRVDTVELAQVFFPTLEKYSLSHLSRE-LNIDLAD 148 (820)
T ss_pred HHHHHHHHhCC--CEEEEECcHHHHHHHHHHHHHcCCCC----CCCceeHHHHHHHHhCCCCCCCHHHHHHH-cCCCCCC
Confidence 34566667765 4579999999999987532 3311 24567887652 2 357999999986 5765321
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 009000 465 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQP 504 (547)
Q Consensus 465 ~e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLee 504 (547)
.+-|..||.++.+|+..|..++.+
T Consensus 149 ----------------~H~Al~DA~ata~L~~~l~~~l~~ 172 (820)
T PRK07246 149 ----------------AHTAIADARATAELFLKLLQKIES 172 (820)
T ss_pred ----------------CCCHHHHHHHHHHHHHHHHHHHhh
Confidence 133889999999999999888865
No 42
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=92.85 E-value=3.5 Score=40.21 Aligned_cols=85 Identities=15% Similarity=0.169 Sum_probs=54.7
Q ss_pred HHHHHHHhhcCCCceEEEechHHHHHHHHHH----hCCcccccccchhhhHHHhh--------c--CCCCCHHHHHHHHh
Q 009000 393 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS----YGELECFKHYEMLLDIQNVF--------K--EPKGGLSGLAEKIL 458 (547)
Q Consensus 393 Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~----~GIl~~~~~~~~vfDtmLAl--------~--~~~~gLd~LAer~L 458 (547)
+...+..++.+ ...||||..+|...|.+. +|... ....+|++... . ..+++|+++++++
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 34566667765 357999999999988653 23211 13456775431 1 2358999999764
Q ss_pred CCCCCCCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHh
Q 009000 459 GAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRS 500 (547)
Q Consensus 459 g~~L~K~e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~ 500 (547)
|.+.. + .+-|..||.++.+|+..|..
T Consensus 174 gi~~~---~-------------~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 174 DLPVL---G-------------RHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred CCCCC---C-------------CCCcHHHHHHHHHHHHHHHh
Confidence 65432 1 12377899999999988743
No 43
>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=92.68 E-value=1.7 Score=41.96 Aligned_cols=102 Identities=24% Similarity=0.353 Sum_probs=60.9
Q ss_pred HHHHHHHHhhcC--CCceEEEech-HHHHHHHHH---HhCCccc---ccc----------------cchhhhHHHhhc--
Q 009000 392 VLDSCLTRILQS--PGILKLGYNF-QCDIKQLAH---SYGELEC---FKH----------------YEMLLDIQNVFK-- 444 (547)
Q Consensus 392 ~Ll~~Lk~LLed--~~I~KVGhnl-K~Dl~vLa~---~~GIl~~---~~~----------------~~~vfDtmLAl~-- 444 (547)
+++..+..++++ |. ..+|||. .+|+..|.. .+|+... .+. ....+|+.....
T Consensus 65 ~lL~~f~~~i~~~dpd-iivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~ 143 (199)
T cd05160 65 ELLKRFFDIIREYDPD-ILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRD 143 (199)
T ss_pred HHHHHHHHHHHhcCCC-EEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHh
Confidence 344555555554 44 4699999 689877643 2454220 000 013568877742
Q ss_pred --CCCCCHHHHHHHHhCCCCC--CCcccccC-CCCCCCHHHHHHHHHHHHHHHHHH
Q 009000 445 --EPKGGLSGLAEKILGAGLN--KTRRNSNW-EQRPLSQNQLEYAALDAVVLLQIF 495 (547)
Q Consensus 445 --~~~~gLd~LAer~Lg~~L~--K~e~~SdW-~~rpLt~~Qi~YAAeDA~vlLrL~ 495 (547)
..+++|+.+++.+|+.+-. .+..+..| .... ...-++|.-.||..+++|+
T Consensus 144 ~~l~sy~L~~v~~~~l~~~k~~~~~~~~~~~~~~~~-~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 144 FKLKSYTLDAVAEELLGEGKEKVDGEIIEDAEWEED-PERLIEYNLKDAELTLQIL 198 (199)
T ss_pred cCcccCCHHHHHHHHhCCCCCcCCHHHHhhccCcch-HHHHHHHHHHHHHHHHHhh
Confidence 4579999999999986432 11223332 1112 2345899999999999886
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=92.65 E-value=0.43 Score=44.61 Aligned_cols=79 Identities=22% Similarity=0.286 Sum_probs=53.7
Q ss_pred HHHHHHhhcCCCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHhhc-----CCCCCHHHHHHHHhCCCCCCCccc
Q 009000 394 DSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLNKTRRN 468 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl~-----~~~~gLd~LAer~Lg~~L~K~e~~ 468 (547)
...+..++.. +...||||+++|+..|... . ..++||..... ..+++|+.|+++|++..+....+
T Consensus 66 ~~~~~~fl~~-~~vlVgHn~~fD~~fL~~~-~--------~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~- 134 (150)
T cd06145 66 QKKLLSLISP-DTILVGHSLENDLKALKLI-H--------PRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEG- 134 (150)
T ss_pred HHHHHHHhCC-CCEEEEcChHHHHHHhhcc-C--------CCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCC-
Confidence 4456666752 3467999999999999751 1 33578886632 23689999999998854321111
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009000 469 SNWEQRPLSQNQLEYAALDAVVLLQIF 495 (547)
Q Consensus 469 SdW~~rpLt~~Qi~YAAeDA~vlLrL~ 495 (547)
.+-|..||.++.+|+
T Consensus 135 ------------~H~Al~DA~~t~~l~ 149 (150)
T cd06145 135 ------------GHDSVEDARAALELV 149 (150)
T ss_pred ------------CCCcHHHHHHHHHHh
Confidence 133778999998886
No 45
>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=92.53 E-value=1.3 Score=54.63 Aligned_cols=92 Identities=15% Similarity=0.186 Sum_probs=65.9
Q ss_pred HHHHHHHhhcCCCceEEEechHHHHHHHHHH---hCCcccccccchhhhHHHhhc-----CCCCCHHHHHHHHhCCCCCC
Q 009000 393 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLNK 464 (547)
Q Consensus 393 Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl~-----~~~~gLd~LAer~Lg~~L~K 464 (547)
+...+..++.+ ...||||..+|...|.+. +|... + ...++||+.... ..+++|+.|++++ |.+...
T Consensus 260 vl~~f~~fl~~--~iLVaHNa~FD~~fL~~~~~r~g~~~-~--~~~~IDTl~lar~l~p~~k~~kL~~Lak~l-gi~~~~ 333 (1213)
T TIGR01405 260 VLEKFKEFFKD--SILVAHNASFDIGFLNTNFEKVGLEP-L--ENPVIDTLELARALNPEYKSHRLGNICKKL-GVDLDD 333 (1213)
T ss_pred HHHHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCc-c--CCCEeEHHHHHHHHhccCCCCCHHHHHHHc-CCCCCC
Confidence 45666777765 356999999999988653 34421 1 245789887631 4679999999874 765431
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Q 009000 465 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTD 506 (547)
Q Consensus 465 ~e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLee~~ 506 (547)
.+.|..||.++.+++..+.+++++.+
T Consensus 334 ----------------~HrAl~DA~aTa~I~~~ll~~l~~~~ 359 (1213)
T TIGR01405 334 ----------------HHRADYDAEATAKVFKVMVEQLKEKG 359 (1213)
T ss_pred ----------------CcCHHHHHHHHHHHHHHHHHHHHHcC
Confidence 25588999999999999999887654
No 46
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=92.50 E-value=1.7 Score=45.79 Aligned_cols=86 Identities=20% Similarity=0.218 Sum_probs=58.0
Q ss_pred HHHHHHhhcCCCceEEEechHHHHHHHHHH---hCCcccccccchhhhHHHhh----c-CCCCCHHHHHHHHhCCCCCCC
Q 009000 394 DSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVF----K-EPKGGLSGLAEKILGAGLNKT 465 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl----~-~~~~gLd~LAer~Lg~~L~K~ 465 (547)
...|..++.+. ..||||..+|+..|.+. +|... ....++||+... . ..+++|+.|++. +|++. +
T Consensus 79 l~~f~~fl~~~--~lVaHNa~FD~~fL~~~~~~~gl~~---~~~~~iDtl~la~~~~~~~~~~kL~~L~~~-lgi~~-~- 150 (313)
T PRK06807 79 LPLFLAFLHTN--VIVAHNASFDMRFLKSNVNMLGLPE---PKNKVIDTVFLAKKYMKHAPNHKLETLKRM-LGIRL-S- 150 (313)
T ss_pred HHHHHHHHcCC--eEEEEcHHHHHHHHHHHHHHcCCCC---CCCCEeeHHHHHHHHhCCCCCCCHHHHHHH-cCCCC-C-
Confidence 44555566543 35999999999988753 34311 124577987763 2 356899999865 56543 1
Q ss_pred cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhcc
Q 009000 466 RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCS 502 (547)
Q Consensus 466 e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rL 502 (547)
.+-|-.||.++.+|+..+....
T Consensus 151 ---------------~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 151 ---------------SHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred ---------------CcChHHHHHHHHHHHHHHHHhh
Confidence 2347789999999999887766
No 47
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=92.02 E-value=3.6 Score=37.81 Aligned_cols=90 Identities=19% Similarity=0.172 Sum_probs=59.1
Q ss_pred HHHHHHHhhcCCCceEEEech-HHHHHHHHHH---hCCcccccccchhhhHHHhhc----CCCCCHHHHHHHHhCCCCCC
Q 009000 393 LDSCLTRILQSPGILKLGYNF-QCDIKQLAHS---YGELECFKHYEMLLDIQNVFK----EPKGGLSGLAEKILGAGLNK 464 (547)
Q Consensus 393 Ll~~Lk~LLed~~I~KVGhnl-K~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl~----~~~~gLd~LAer~Lg~~L~K 464 (547)
....+..++.+. ..++||. ++|+..|.+. +|+... ....++|++.... ..+++|+++++.+ |.+..
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 345677778654 3577777 9999988763 232110 0133678876632 3478999999876 43322
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhcc
Q 009000 465 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCS 502 (547)
Q Consensus 465 ~e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rL 502 (547)
+. .+.|..||..+.+|+..+.++.
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 48
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=91.86 E-value=1.8 Score=43.92 Aligned_cols=87 Identities=13% Similarity=-0.009 Sum_probs=56.6
Q ss_pred HHHHHHhhcCCCceEEEechHHHHHHHHHH----hCCcccccccchhhhHHHhhc----C--------------CCCCHH
Q 009000 394 DSCLTRILQSPGILKLGYNFQCDIKQLAHS----YGELECFKHYEMLLDIQNVFK----E--------------PKGGLS 451 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~----~GIl~~~~~~~~vfDtmLAl~----~--------------~~~gLd 451 (547)
...|..++.+ ...||||..+|...|.+. ++... ..+++||+.... . .++.|+
T Consensus 120 l~~l~~~~~~--~~lVaHna~FD~~fL~~~l~~~~~~~~----~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~ 193 (239)
T PRK09146 120 LDELLEALAG--KVVVVHYRRIERDFLDQALRNRIGEGI----EFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLA 193 (239)
T ss_pred HHHHHHHhCC--CEEEEECHHHHHHHHHHHHHHhcCCCC----CCceechHHHHHHHcccccccccchhccCCCCCCCHH
Confidence 3444455544 357899999999988653 22211 145779888621 1 356788
Q ss_pred HHHHHHhCCCCCCCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccC
Q 009000 452 GLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQ 503 (547)
Q Consensus 452 ~LAer~Lg~~L~K~e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLe 503 (547)
+++.+| |++... .+-|..||.++.+|+..+..+.-
T Consensus 194 ~l~~~~-gl~~~~----------------~H~Al~DA~ata~l~~~~~~~~~ 228 (239)
T PRK09146 194 DSRLRY-GLPAYS----------------PHHALTDAIATAELLQAQIAHHF 228 (239)
T ss_pred HHHHHc-CCCCCC----------------CCCcHHHHHHHHHHHHHHHHHHc
Confidence 888874 654320 23488999999999998877763
No 49
>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=91.39 E-value=2.2 Score=50.74 Aligned_cols=90 Identities=19% Similarity=0.138 Sum_probs=61.6
Q ss_pred HHHHHHHhhcCCCceEEEechHHHHHHHHHH---hCCcccccccchhhhHHHhh----c-CCCCCHHHHHHHHhCCCCCC
Q 009000 393 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVF----K-EPKGGLSGLAEKILGAGLNK 464 (547)
Q Consensus 393 Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl----~-~~~~gLd~LAer~Lg~~L~K 464 (547)
+...+..++.+ ...||||+.+|+..|.+. +|.... ..+.+||+... . ..+++|++|+++ +|.+...
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 34566677765 357999999999888642 344211 24577887652 2 457899999987 5765321
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 009000 465 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQP 504 (547)
Q Consensus 465 ~e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLee 504 (547)
.+-|..||.++.+|+..+..++.+
T Consensus 144 ----------------~H~Al~DA~ata~l~~~l~~~~~~ 167 (850)
T TIGR01407 144 ----------------PHRADSDAQATAELLLLLFEKMEK 167 (850)
T ss_pred ----------------CCChHHHHHHHHHHHHHHHHHHHh
Confidence 234788999999988888777754
No 50
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=90.28 E-value=5.8 Score=39.75 Aligned_cols=88 Identities=17% Similarity=0.072 Sum_probs=57.5
Q ss_pred HHHHHhhcCCCceEEEec-hHHHHHHHHHH---hCCcccccccchhhhHHHhhc-----CCCCCHHHHHHHHhCCCCCCC
Q 009000 395 SCLTRILQSPGILKLGYN-FQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLNKT 465 (547)
Q Consensus 395 ~~Lk~LLed~~I~KVGhn-lK~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl~-----~~~~gLd~LAer~Lg~~L~K~ 465 (547)
..+..++.+ ....|||| ..+|+..|.+. +|+... ...++||+.... ..+++|+.+++.| |.+...
T Consensus 71 ~~~~~fi~~-~~~lVaHN~~~FD~~~L~~e~~r~g~~~~---~~~~iDt~~l~~~~~~~~~~~~L~~l~~~~-~~~~~~- 144 (232)
T PRK06309 71 QKFIEFCGT-DNILVAHNNDAFDFPLLRKECRRHGLEPP---TLRTIDSLKWAQKYRPDLPKHNLQYLRQVY-GFEENQ- 144 (232)
T ss_pred HHHHHHHcC-CCEEEEeCCHHHHHHHHHHHHHHcCCCCC---CCcEEeHHHHHHHHcCCCCCCCHHHHHHHc-CCCCCC-
Confidence 344555543 34679999 48999988652 343211 135678876632 2468999998776 544221
Q ss_pred cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccC
Q 009000 466 RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQ 503 (547)
Q Consensus 466 e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLe 503 (547)
.+-|..||.++.+|+..+.+++.
T Consensus 145 ---------------aH~Al~Da~~t~~vl~~l~~~~~ 167 (232)
T PRK06309 145 ---------------AHRALDDVITLHRVFSALVGDLS 167 (232)
T ss_pred ---------------CCCcHHHHHHHHHHHHHHHHHHH
Confidence 23388999999999999877663
No 51
>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=90.17 E-value=4.1 Score=39.58 Aligned_cols=151 Identities=16% Similarity=0.161 Sum_probs=82.3
Q ss_pred CeEEEEeeeecCCccCCcCCceeEEEEEe--CCeEEEEEcCcc------cCCCchHHHHHHHHhhcC--CCceEEEechH
Q 009000 345 KVVGIDCEWKPNYVKGCKMNKVSIMQIAS--DEMVFIFDLIKL------AEDVPDVLDSCLTRILQS--PGILKLGYNFQ 414 (547)
Q Consensus 345 ~vIgfDtE~~~l~~~~~~~~~VsLlQLAt--~~~a~~Idl~~l------~~~~p~~Ll~~Lk~LLed--~~I~KVGhnlK 414 (547)
.+++||.|+.+..+ .|.+..-.+++|+. .+.-.++..... ......+++..+..++.. |.+ .+|||..
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 57899999974321 11223334555553 221111111100 001123445555555554 654 6899986
Q ss_pred -HHHHHHHH---HhCCcccccc-------------------cchhhhHHHhhc----CCCCCHHHHHHHHhCCCCCC--C
Q 009000 415 -CDIKQLAH---SYGELECFKH-------------------YEMLLDIQNVFK----EPKGGLSGLAEKILGAGLNK--T 465 (547)
Q Consensus 415 -~Dl~vLa~---~~GIl~~~~~-------------------~~~vfDtmLAl~----~~~~gLd~LAer~Lg~~L~K--~ 465 (547)
+|+..|.. .+|+...+.. -...+|++.... ..+++|+.+++++||.+-.. +
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 2455211100 012567777642 45899999999999975321 1
Q ss_pred ccccc-CCCCCCCHHHHHHHHHHHHHHHHHHHH
Q 009000 466 RRNSN-WEQRPLSQNQLEYAALDAVVLLQIFHH 497 (547)
Q Consensus 466 e~~Sd-W~~rpLt~~Qi~YAAeDA~vlLrL~~~ 497 (547)
+++.. |...+-...-++|+-.||..+++|...
T Consensus 162 ~~i~~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~ 194 (195)
T cd05780 162 EEIAEAWDSGENLERLFRYSMEDAKYTYEIGKE 194 (195)
T ss_pred HHHHHHHhCCCchHHHHHHhHHHHHHHHHHHhh
Confidence 23332 333322344589999999999999764
No 52
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=89.63 E-value=6.1 Score=47.65 Aligned_cols=89 Identities=20% Similarity=0.179 Sum_probs=61.9
Q ss_pred HHHHHHhhcCCCceEEEechHHHHHHHHHH---hCCcccccccchhhhHHHhh----c-CCCCCHHHHHHHHhCCCCCCC
Q 009000 394 DSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVF----K-EPKGGLSGLAEKILGAGLNKT 465 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl----~-~~~~gLd~LAer~Lg~~L~K~ 465 (547)
...|..++.+ ...||||+.+|+..|.+. +|.... ...++||+... . ..+++|++|++. +|.+...
T Consensus 75 ~~~l~~~l~~--~~~VaHN~~FD~~fL~~~~~~~g~~~~---~~~~iDt~~la~~~~p~~~~~~L~~l~~~-l~i~~~~- 147 (928)
T PRK08074 75 APEIVELLEG--AYFVAHNVHFDLNFLNEELERAGYTEI---HCPKLDTVELARILLPTAESYKLRDLSEE-LGLEHDQ- 147 (928)
T ss_pred HHHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCCC---CCCeeeHHHHHHHhcCCCCCCCHHHHHHh-CCCCCCC-
Confidence 4566777765 457999999999988652 344211 24578987652 2 457899999987 4654321
Q ss_pred cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 009000 466 RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQP 504 (547)
Q Consensus 466 e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLee 504 (547)
.+-|-.||.++.+|+..|.+++.+
T Consensus 148 ---------------~H~Al~DA~ata~l~~~l~~~~~~ 171 (928)
T PRK08074 148 ---------------PHRADSDAEVTAELFLQLLNKLER 171 (928)
T ss_pred ---------------CCChHHHHHHHHHHHHHHHHHHHh
Confidence 233778999999999999888765
No 53
>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=89.31 E-value=4.2 Score=38.95 Aligned_cols=84 Identities=19% Similarity=0.176 Sum_probs=52.7
Q ss_pred HHHHHhhcC--CCceEEEech-HHHHHHHHHH---hCCcccccccchhhhHHHhhcCCCCCHHHHHHHHhCCCCCCCccc
Q 009000 395 SCLTRILQS--PGILKLGYNF-QCDIKQLAHS---YGELECFKHYEMLLDIQNVFKEPKGGLSGLAEKILGAGLNKTRRN 468 (547)
Q Consensus 395 ~~Lk~LLed--~~I~KVGhnl-K~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl~~~~~gLd~LAer~Lg~~L~K~e~~ 468 (547)
+.|..++.. .....||||. .+|+..|.+. +|.... ....++||+........+|++|+++++|.+...
T Consensus 86 ~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~--~~~~~iDtl~l~r~~~~~L~~l~~~~~~~~~~~---- 159 (177)
T cd06136 86 NLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLP--DDILCVDSLPAFRELDQSLGSLYKRLFGQEPKN---- 159 (177)
T ss_pred HHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCC--CCCEEEEeHHHHhhhHhhHHHHHHHHhCCCccc----
Confidence 455555543 2357899998 7999988542 343110 012346887664421128999999888865431
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009000 469 SNWEQRPLSQNQLEYAALDAVVLLQIFH 496 (547)
Q Consensus 469 SdW~~rpLt~~Qi~YAAeDA~vlLrL~~ 496 (547)
.+-|..||.++.+++.
T Consensus 160 ------------~H~A~~Da~at~~v~~ 175 (177)
T cd06136 160 ------------SHTAEGDVLALLKCAL 175 (177)
T ss_pred ------------ccchHHHHHHHHHHHh
Confidence 2448889999887753
No 54
>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=88.87 E-value=8.8 Score=37.32 Aligned_cols=148 Identities=17% Similarity=0.126 Sum_probs=77.7
Q ss_pred CeEEEEeeeecCCccCCcCCceeEEEEE--e-CCeEEEEEcCcccCCCchHHHHHHHHhhcCCCc-eEEEechH-HHHHH
Q 009000 345 KVVGIDCEWKPNYVKGCKMNKVSIMQIA--S-DEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGI-LKLGYNFQ-CDIKQ 419 (547)
Q Consensus 345 ~vIgfDtE~~~l~~~~~~~~~VsLlQLA--t-~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~I-~KVGhnlK-~Dl~v 419 (547)
.+++||.|+.+... .+.+..-.+++|+ . .+...++.-. .....+++..+-.++..-+. ..+|||.. +|+-.
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 3433333211 11123454555555554322 35799854 56654
Q ss_pred HH---HHhCCcccccccc-----------------hhhhHHHhhc----CCCCCHHHHHHHHhCCC-C-CC----Ccccc
Q 009000 420 LA---HSYGELECFKHYE-----------------MLLDIQNVFK----EPKGGLSGLAEKILGAG-L-NK----TRRNS 469 (547)
Q Consensus 420 La---~~~GIl~~~~~~~-----------------~vfDtmLAl~----~~~~gLd~LAer~Lg~~-L-~K----~e~~S 469 (547)
|. ..+|+.....+.. ..+|+..... ..+++|+.+|+ +||.. - .+ +.++.
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 2356521110000 1567766642 45799999997 58853 1 11 11222
Q ss_pred -cCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q 009000 470 -NWEQRPLSQNQLEYAALDAVVLLQIFHH 497 (547)
Q Consensus 470 -dW~~rpLt~~Qi~YAAeDA~vlLrL~~~ 497 (547)
.|....-...-.+|...|+..++.|+..
T Consensus 159 ~~~~~~~~~~~l~~Y~~~D~~~t~~l~~~ 187 (188)
T cd05781 159 EYWDDEKKRDILLKYNRDDARSTYGLAEK 187 (188)
T ss_pred HHHcCcccHHHHHHHHHHHHHHHHHHHhh
Confidence 2433213355689999999999999875
No 55
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=86.76 E-value=17 Score=39.46 Aligned_cols=100 Identities=10% Similarity=0.120 Sum_probs=56.9
Q ss_pred HHHHHHHHhhcCCCceEEEechHHHHHHHHHHhCCc---c------------------------cccccchhhhHHHhhc
Q 009000 392 VLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGEL---E------------------------CFKHYEMLLDIQNVFK 444 (547)
Q Consensus 392 ~Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~~GIl---~------------------------~~~~~~~vfDtmLAl~ 444 (547)
++...|.+++.+. ..|+||..+|+..|.+.+... . .......++||+-...
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 3456777788753 579999999999876532100 0 0000134689876521
Q ss_pred -----CCCCCHHHHHHHHhCCCCCCCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009000 445 -----EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHV 498 (547)
Q Consensus 445 -----~~~~gLd~LAer~Lg~~L~K~e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L 498 (547)
..+|.|+.|+.+ +|++.+... -|. .+..-... +.+-+||.++-+|+..+
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 11235889998898876
No 56
>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=85.59 E-value=3.3 Score=40.61 Aligned_cols=86 Identities=14% Similarity=0.060 Sum_probs=56.5
Q ss_pred CceEEEechHHHHHHHHHH---hCCcccccccchhhhHHHhhc--CCCCCHHHHHHHHhCCCCCCCcccccCCCCCCCHH
Q 009000 405 GILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK--EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQN 479 (547)
Q Consensus 405 ~I~KVGhnlK~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl~--~~~~gLd~LAer~Lg~~L~K~e~~SdW~~rpLt~~ 479 (547)
+...||||+.+|+..|.+. +|.....-....++||+.... ...++|+.+++++ |.+.. ..
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 3468999999999988653 232100000123679987743 3356899999864 65421 11
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccCCC
Q 009000 480 QLEYAALDAVVLLQIFHHVRSCSQPT 505 (547)
Q Consensus 480 Qi~YAAeDA~vlLrL~~~L~~rLee~ 505 (547)
+.+-|..||.++.+|+..+..++.+.
T Consensus 170 ~~H~Al~Da~ata~lf~~l~~~~~~~ 195 (200)
T TIGR01298 170 QAHSALYDTEKTAELFCEIVNRWKRL 195 (200)
T ss_pred chhhhHHhHHHHHHHHHHHHHHHHHc
Confidence 24568899999999999998888653
No 57
>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=85.24 E-value=4.6 Score=39.16 Aligned_cols=80 Identities=15% Similarity=0.132 Sum_probs=51.6
Q ss_pred ceEEEechHHHHHHHHHH---hCCc-ccccccchhhhHHHhhc--CCCCCHHHHHHHHhCCCCCCCcccccCCCCCCCHH
Q 009000 406 ILKLGYNFQCDIKQLAHS---YGEL-ECFKHYEMLLDIQNVFK--EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQN 479 (547)
Q Consensus 406 I~KVGhnlK~Dl~vLa~~---~GIl-~~~~~~~~vfDtmLAl~--~~~~gLd~LAer~Lg~~L~K~e~~SdW~~rpLt~~ 479 (547)
...||||+.+|+..|.+. +|+. ..+ ....++||+.... ...+.|+.++++| |++.....
T Consensus 103 ~~lVaHna~FD~~fL~~~~~~~~~~~~~~-~~~~~lDt~~la~~~~~~~~L~~l~~~~-gi~~~~~~------------- 167 (189)
T cd06134 103 AILVGHNAHFDLGFLNAAVARCKIKRNPF-HPFSTFDTATLAGLAYGQTVLAKACQAA-GIEFDNKE------------- 167 (189)
T ss_pred CeEEEecchhhHHHHHHHHHHhCCCCCCC-CCCcEEEHHHHHHHHhCCCcHHHHHHHC-CCCCCCCC-------------
Confidence 468999999999888642 3431 000 0123689987742 2356899998874 66532111
Q ss_pred HHHHHHHHHHHHHHHHHHHHhc
Q 009000 480 QLEYAALDAVVLLQIFHHVRSC 501 (547)
Q Consensus 480 Qi~YAAeDA~vlLrL~~~L~~r 501 (547)
.+-|..||.++.+|+..+.++
T Consensus 168 -~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 168 -AHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred -CcChHHHHHHHHHHHHHHHHh
Confidence 233888999999999888654
No 58
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=84.74 E-value=31 Score=34.56 Aligned_cols=76 Identities=11% Similarity=-0.016 Sum_probs=51.6
Q ss_pred ceEEEechHHHHHHHHHHhCCcccccccchhhhHHHhh----cCCCCCHHHHHHHHhCCCCCCCcccccCCCCCCCHHHH
Q 009000 406 ILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF----KEPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQL 481 (547)
Q Consensus 406 I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl----~~~~~gLd~LAer~Lg~~L~K~e~~SdW~~rpLt~~Qi 481 (547)
...||||+.+|...|.. .+ ..++||+... ....+++..|++. +|......+. ...
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 46799999999998864 22 4567988763 3445899988865 4543211000 013
Q ss_pred HHHHHHHHHHHHHHHHHHhcc
Q 009000 482 EYAALDAVVLLQIFHHVRSCS 502 (547)
Q Consensus 482 ~YAAeDA~vlLrL~~~L~~rL 502 (547)
+-|..||.++..|+..+.++.
T Consensus 134 HrAl~Da~ata~ll~~l~~~~ 154 (219)
T PRK07983 134 HRALYDCYITAALLIDIMNTS 154 (219)
T ss_pred CcHHHHHHHHHHHHHHHHHHc
Confidence 558899999999999887543
No 59
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=84.18 E-value=18 Score=35.63 Aligned_cols=88 Identities=18% Similarity=0.137 Sum_probs=56.2
Q ss_pred HHHHHHHhhcCCCceEEEechH-HHHHHHHHHhCCcccccccchhhhH---HHhh-----c-CCCCCHHHHHHHHhCCCC
Q 009000 393 LDSCLTRILQSPGILKLGYNFQ-CDIKQLAHSYGELECFKHYEMLLDI---QNVF-----K-EPKGGLSGLAEKILGAGL 462 (547)
Q Consensus 393 Ll~~Lk~LLed~~I~KVGhnlK-~Dl~vLa~~~GIl~~~~~~~~vfDt---mLAl-----~-~~~~gLd~LAer~Lg~~L 462 (547)
+...+..++.+. ..||||.. +|+..|.. +|.... ....+|+ .... + ..+++|..|+++ +|.+.
T Consensus 74 vl~~f~~f~~~~--~lVaHNa~~fD~~fL~~-~g~~~~---~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~-~gi~~ 146 (195)
T PRK07247 74 VLAAFKEFVGEL--PLIGYNAQKSDLPILAE-NGLDLS---DQYQVDLYDEAFERRSSDLNGIANLKLQTVADF-LGIKG 146 (195)
T ss_pred HHHHHHHHHCCC--eEEEEeCcHhHHHHHHH-cCCCcC---CCceeehHHHHHHhhccccCCCCCCCHHHHHHh-cCCCC
Confidence 345666777654 46999995 89999987 565211 1122343 3221 1 247899999986 46542
Q ss_pred CCCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 009000 463 NKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQP 504 (547)
Q Consensus 463 ~K~e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLee 504 (547)
. .+-|-.||.++..|+..|...-+.
T Consensus 147 ~-----------------~HrAl~DA~~ta~v~~~ll~~~~~ 171 (195)
T PRK07247 147 R-----------------GHNSLEDARMTARVYESFLESDQN 171 (195)
T ss_pred C-----------------CcCCHHHHHHHHHHHHHHHhhccc
Confidence 1 133778999999999988665443
No 60
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=82.31 E-value=4.9 Score=42.13 Aligned_cols=88 Identities=14% Similarity=0.065 Sum_probs=60.4
Q ss_pred HHHHHHhhcCCCceEEEechHHHHHHHHHH---hCCcccccccchhhhHHHhh----c-CCCCCHHHHHHHHhCCCCCCC
Q 009000 394 DSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVF----K-EPKGGLSGLAEKILGAGLNKT 465 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl----~-~~~~gLd~LAer~Lg~~L~K~ 465 (547)
...|..++.+ -..|+||..+|+..|.+. +|.... ...++||+... . ..+++|+.|++.+ |.+..
T Consensus 71 ~~~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~---~~~~idT~~lar~l~~~~~~~~L~~L~~~~-gi~~~-- 142 (309)
T PRK06195 71 WEKIKHYFNN--NLVIAHNASFDISVLRKTLELYNIPMP---SFEYICTMKLAKNFYSNIDNARLNTVNNFL-GYEFK-- 142 (309)
T ss_pred HHHHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCCCC---CCCEEEHHHHHHHHcCCCCcCCHHHHHHHc-CCCCc--
Confidence 4566666654 467999999999888542 343110 13577997763 2 3578999999875 54321
Q ss_pred cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 009000 466 RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQP 504 (547)
Q Consensus 466 e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLee 504 (547)
.+-|..||.++.+|+..+..++..
T Consensus 143 ---------------~H~Al~DA~ata~l~~~l~~~~~~ 166 (309)
T PRK06195 143 ---------------HHDALADAMACSNILLNISKELNS 166 (309)
T ss_pred ---------------ccCCHHHHHHHHHHHHHHHHHhcc
Confidence 244889999999999998887754
No 61
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=82.03 E-value=19 Score=37.68 Aligned_cols=83 Identities=16% Similarity=0.028 Sum_probs=51.9
Q ss_pred HHHHHhhcCCCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHhh--c---CCCCCHHHHHHHHhCCCCCCCcccc
Q 009000 395 SCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF--K---EPKGGLSGLAEKILGAGLNKTRRNS 469 (547)
Q Consensus 395 ~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl--~---~~~~gLd~LAer~Lg~~L~K~e~~S 469 (547)
..+..+++.. ...|+||..+|...|.+.+.-.. ...+.+++... . ..++.|+.|+.++ | ..
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 12234444332 1 3578999999875 4 11
Q ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHh
Q 009000 470 NWEQRPLSQNQLEYAALDAVVLLQIFHHVRS 500 (547)
Q Consensus 470 dW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~ 500 (547)
++ .+-|..||.++.+|.....+
T Consensus 178 -~~--------aHrAl~Da~Ata~ll~~~l~ 199 (294)
T PRK09182 178 -HE--------GHRAVDDCQALLELLARPLP 199 (294)
T ss_pred -CC--------CcChHHHHHHHHHHHHHHHh
Confidence 10 24488999999888775544
No 62
>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=81.71 E-value=3 Score=38.72 Aligned_cols=142 Identities=15% Similarity=0.182 Sum_probs=67.0
Q ss_pred EEEEeeeecCCccCCcCCceeEEEEEe--CC-eEEEEEcCcccCCCchHHHHHHHHhhcCCCceEEEech-HHHHHHHHH
Q 009000 347 VGIDCEWKPNYVKGCKMNKVSIMQIAS--DE-MVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNF-QCDIKQLAH 422 (547)
Q Consensus 347 IgfDtE~~~l~~~~~~~~~VsLlQLAt--~~-~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~I~KVGhnl-K~Dl~vLa~ 422 (547)
+.||+|++++.. ..+.+-++|+.. .+ ...+.......+.....+.+.+ ..+.+. -..++||. .+|...|.+
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 358999997732 234566777764 33 2324333221111122233333 344444 34688996 469877765
Q ss_pred H---hCCcccccccchhhhHHHhhc---CCCCCHHHHHHHHhCCCCCC----Ccc-cc---cCC---CCCCCHHHHHHHH
Q 009000 423 S---YGELECFKHYEMLLDIQNVFK---EPKGGLSGLAEKILGAGLNK----TRR-NS---NWE---QRPLSQNQLEYAA 485 (547)
Q Consensus 423 ~---~GIl~~~~~~~~vfDtmLAl~---~~~~gLd~LAer~Lg~~L~K----~e~-~S---dW~---~rpLt~~Qi~YAA 485 (547)
. |++.. ....+|++..+. ..+.+|+.++.. +|..-.. +.+ .. .|. ....-+..+.|.-
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 3 33311 255679988753 356789988876 6654321 110 00 110 1123456689999
Q ss_pred HHHHHHHHHHHHH
Q 009000 486 LDAVVLLQIFHHV 498 (547)
Q Consensus 486 eDA~vlLrL~~~L 498 (547)
.|+..+.+|++.|
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 63
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=81.34 E-value=3.7 Score=49.99 Aligned_cols=140 Identities=16% Similarity=0.167 Sum_probs=90.8
Q ss_pred HhhCCCeEEEEeeeecCCccCCcCCceeEEEEEe----CCe-----EEEEEcCcccC---------------CCc--hHH
Q 009000 340 HIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIAS----DEM-----VFIFDLIKLAE---------------DVP--DVL 393 (547)
Q Consensus 340 ~L~~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt----~~~-----a~~Idl~~l~~---------------~~p--~~L 393 (547)
.|.++..+.||.|++++. +.--.+++++- .++ -+++.+.+.-+ ..+ +++
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 466788999999999883 22223455441 111 12222221100 011 234
Q ss_pred HHHHHHhhcCCCceEEEechHHHHHHHHHH---hCCcccccccchhhhHHHhh---c--CCCCCHHHHHHHHhCCCCCCC
Q 009000 394 DSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVF---K--EPKGGLSGLAEKILGAGLNKT 465 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl---~--~~~~gLd~LAer~Lg~~L~K~ 465 (547)
+..++.|+.|. .-|.||+.+|+..|... +|+... ..+++||.-.. + -++|+|..|+.++ |..+
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 67788888874 56999999999877543 455321 36788987662 2 4689999999986 4322
Q ss_pred cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Q 009000 466 RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTD 506 (547)
Q Consensus 466 e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLee~~ 506 (547)
++.+.|--||.++-+++-.+.+.+.+.|
T Consensus 563 -------------e~hHRA~yDaeat~~vf~~f~~~~ke~G 590 (1444)
T COG2176 563 -------------ERHHRADYDAEATAKVFFVFLKDLKEKG 590 (1444)
T ss_pred -------------HHhhhhhhhHHHHHHHHHHHHHHHHHhc
Confidence 3456677899999999999999998855
No 64
>PRK11779 sbcB exonuclease I; Provisional
Probab=81.32 E-value=39 Score=37.89 Aligned_cols=91 Identities=18% Similarity=0.173 Sum_probs=54.8
Q ss_pred HHHHHHhhcCCCceEEEec-hHHHHHHHHHHhC--Ccccc----c---ccchhhhHHHhhc---------------CCCC
Q 009000 394 DSCLTRILQSPGILKLGYN-FQCDIKQLAHSYG--ELECF----K---HYEMLLDIQNVFK---------------EPKG 448 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhn-lK~Dl~vLa~~~G--Il~~~----~---~~~~vfDtmLAl~---------------~~~~ 448 (547)
...+..++..+....|||| +.+|..++.+.+. ..... . ..-.++|++-+.. ..++
T Consensus 82 ~~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~ 161 (476)
T PRK11779 82 AARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSF 161 (476)
T ss_pred HHHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCC
Confidence 4456666754555689997 7899987765321 00000 0 0013456555310 1458
Q ss_pred CHHHHHHHHhCCCCCCCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhc
Q 009000 449 GLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSC 501 (547)
Q Consensus 449 gLd~LAer~Lg~~L~K~e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~r 501 (547)
.|+.|++++ |++.. +.+-|-.||.++.+|+..+..+
T Consensus 162 rLe~L~~~~-gI~~~----------------~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 162 KLEHLTKAN-GIEHE----------------NAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred cHHHHHHHc-CCCCC----------------CCCCcHHHHHHHHHHHHHHHHh
Confidence 899999875 55432 1234788999999999988765
No 65
>PRK05168 ribonuclease T; Provisional
Probab=81.12 E-value=7.5 Score=38.44 Aligned_cols=87 Identities=13% Similarity=0.049 Sum_probs=55.9
Q ss_pred CceEEEechHHHHHHHHHH---hCCcccccccchhhhHHHhhc--CCCCCHHHHHHHHhCCCCCCCcccccCCCCCCCHH
Q 009000 405 GILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK--EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQN 479 (547)
Q Consensus 405 ~I~KVGhnlK~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl~--~~~~gLd~LAer~Lg~~L~K~e~~SdW~~rpLt~~ 479 (547)
+...||||+.+|+..|.+. +|+....-....++||..... ...++|+.+++++ |.+.....
T Consensus 114 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~~~~L~~l~~~~-gl~~~~~~------------- 179 (211)
T PRK05168 114 RAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALGQTVLAKACQAA-GIEFDNKE------------- 179 (211)
T ss_pred CceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcCCCCHHHHHHHC-CCCCCCCC-------------
Confidence 4578999999999888652 343100000013678876643 2346899988874 65532111
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccCCCC
Q 009000 480 QLEYAALDAVVLLQIFHHVRSCSQPTD 506 (547)
Q Consensus 480 Qi~YAAeDA~vlLrL~~~L~~rLee~~ 506 (547)
.+-|..||.++.+|+..+..++.+.+
T Consensus 180 -~H~Al~DA~ata~l~~~l~~~~~~~~ 205 (211)
T PRK05168 180 -AHSALYDTEKTAELFCEIVNRWKRLG 205 (211)
T ss_pred -CCChHHHHHHHHHHHHHHHHHHHHcc
Confidence 23488999999999999988886544
No 66
>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=80.63 E-value=11 Score=37.38 Aligned_cols=145 Identities=18% Similarity=0.174 Sum_probs=76.3
Q ss_pred CCeEEEEeeeecCCcc---CCcCCceeEEEEEe--CCe-EEEEEcCcccCCCchHHHHHHHHhhcC--CCceEEEech-H
Q 009000 344 CKVVGIDCEWKPNYVK---GCKMNKVSIMQIAS--DEM-VFIFDLIKLAEDVPDVLDSCLTRILQS--PGILKLGYNF-Q 414 (547)
Q Consensus 344 a~vIgfDtE~~~l~~~---~~~~~~VsLlQLAt--~~~-a~~Idl~~l~~~~p~~Ll~~Lk~LLed--~~I~KVGhnl-K 414 (547)
-.+++||.|..+.... ++....-.+++|+. .+. ..++.. ......+++..+..++.. |. ..+|||. .
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 3679999998654211 11222335677764 221 112211 111123444444444444 55 4579998 5
Q ss_pred HHHHHHHH---HhCCcccccc--------------------------cc-hhhhHHHhhc--------CCCCCHHHHHHH
Q 009000 415 CDIKQLAH---SYGELECFKH--------------------------YE-MLLDIQNVFK--------EPKGGLSGLAEK 456 (547)
Q Consensus 415 ~Dl~vLa~---~~GIl~~~~~--------------------------~~-~vfDtmLAl~--------~~~~gLd~LAer 456 (547)
+|+..|.+ .+|+...+.+ .| .++|++.++. -.+++|+.+|+.
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 78766532 2554221100 01 2368877632 246899999997
Q ss_pred HhCCCCC-----CCcccc-cCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009000 457 ILGAGLN-----KTRRNS-NWEQRPLSQNQLEYAALDAVVLLQIF 495 (547)
Q Consensus 457 ~Lg~~L~-----K~e~~S-dW~~rpLt~~Qi~YAAeDA~vlLrL~ 495 (547)
+ |..-. ...++. -|...+ +.-.+|+..|+..+++|+
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 111222 354432 455899999999999885
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=79.27 E-value=33 Score=33.97 Aligned_cols=148 Identities=20% Similarity=0.202 Sum_probs=78.6
Q ss_pred CeEEEEeeeecCCccCCcCCceeEEEEEe--C-CeEEEE--EcCcc--------------------cCCCchHHHHHHHH
Q 009000 345 KVVGIDCEWKPNYVKGCKMNKVSIMQIAS--D-EMVFIF--DLIKL--------------------AEDVPDVLDSCLTR 399 (547)
Q Consensus 345 ~vIgfDtE~~~l~~~~~~~~~VsLlQLAt--~-~~a~~I--dl~~l--------------------~~~~p~~Ll~~Lk~ 399 (547)
.+++||.|..+.....|.+..-.++|||. . .+..+. .+... ......+++..+..
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 57899999976422223455556777764 2 222211 00000 00112234455555
Q ss_pred hhcC--CCceEEEechH-HHHHHHH---HHhCCccc--c--cc---------cchhhhHHHhhc------CCCCCHHHHH
Q 009000 400 ILQS--PGILKLGYNFQ-CDIKQLA---HSYGELEC--F--KH---------YEMLLDIQNVFK------EPKGGLSGLA 454 (547)
Q Consensus 400 LLed--~~I~KVGhnlK-~Dl~vLa---~~~GIl~~--~--~~---------~~~vfDtmLAl~------~~~~gLd~LA 454 (547)
++.+ |.+ .+|||.. +|+..|. ..+|+... + .. ....+|++-.+. ..+++|+.+|
T Consensus 83 ~i~~~~Pd~-i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~~sysLd~Va 161 (204)
T cd05779 83 HIREVKPHI-IVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQGLKAVT 161 (204)
T ss_pred HHHHhCCCE-EEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCCCCccHHHHH
Confidence 5544 433 5788865 5665442 22565211 0 00 011457666532 2478999999
Q ss_pred HHHhCCCCCC--Ccccc-cCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009000 455 EKILGAGLNK--TRRNS-NWEQRPLSQNQLEYAALDAVVLLQIF 495 (547)
Q Consensus 455 er~Lg~~L~K--~e~~S-dW~~rpLt~~Qi~YAAeDA~vlLrL~ 495 (547)
+.+||..-.. ...+. -|...+ +.-++|.-.||..++.||
T Consensus 162 ~~~Lg~~K~~~~~~~I~~~~~~~~--~~l~~Y~~~D~~~T~~l~ 203 (204)
T cd05779 162 KAKLGYDPVELDPEDMVPLAREDP--QTLASYSVSDAVATYYLY 203 (204)
T ss_pred HHHhCCCcCcCCHHHHHHHHhCCc--HHHHhccHHHHHHHHHHh
Confidence 9999963211 11111 354433 455899999999999997
No 68
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=78.79 E-value=3.3 Score=48.60 Aligned_cols=143 Identities=17% Similarity=0.212 Sum_probs=83.6
Q ss_pred CeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCc----cc-CCCchHHHHHHHHhhcC-CCceEEEechHHHHH
Q 009000 345 KVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIK----LA-EDVPDVLDSCLTRILQS-PGILKLGYNFQCDIK 418 (547)
Q Consensus 345 ~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~a~~Idl~~----l~-~~~p~~Ll~~Lk~LLed-~~I~KVGhnlK~Dl~ 418 (547)
..+.||+|.--.. +....++.|....++|-.+.. ++ .+.|+ ..|-|+=+. ..-+.||||+.+|..
T Consensus 184 ~~lVFDVEvl~~~------g~~ptLAtAlS~dAWY~WcS~P~~li~~sE~p~---~~LIP~~~~~ke~liVGHNVsfDRa 254 (1075)
T KOG3657|consen 184 SILVFDVEVLVRV------GTLPTLATALSRDAWYSWCSDPWDLIYESEIPE---AALIPLGEIGKEQLIVGHNVSFDRA 254 (1075)
T ss_pred ceeEEEEEEEEec------cCcchhhhhhccchhhhhcCCHHhhcccCCCcH---HhhCcCCcCCCCceEEeccccchHH
Confidence 5678999864221 122233344456667754431 11 12332 234444322 346789999999999
Q ss_pred HHHHHhCCcccccccchhhhHHHhh----c-----C-----------------C----------------CCCHHHHHHH
Q 009000 419 QLAHSYGELECFKHYEMLLDIQNVF----K-----E-----------------P----------------KGGLSGLAEK 456 (547)
Q Consensus 419 vLa~~~GIl~~~~~~~~vfDtmLAl----~-----~-----------------~----------------~~gLd~LAer 456 (547)
.++..|.|.. +....+|||-+. . . . --+|.+++..
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 124467998761 0 0 0 1246666777
Q ss_pred HhCCC-CCCCcccccCCCCCCCHHH--------HHHHHHHHHHHHHHHHHHHhcc
Q 009000 457 ILGAG-LNKTRRNSNWEQRPLSQNQ--------LEYAALDAVVLLQIFHHVRSCS 502 (547)
Q Consensus 457 ~Lg~~-L~K~e~~SdW~~rpLt~~Q--------i~YAAeDA~vlLrL~~~L~~rL 502 (547)
+.|.. ++|..+.+ |- ..+.+| +.|.|.|.+++.+++..+.+..
T Consensus 332 ~c~~~~LdKt~Rd~-Fv--s~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~F 383 (1075)
T KOG3657|consen 332 HCGIDALDKTPRDS-FV--SGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLF 383 (1075)
T ss_pred hCCCCccccchHHh-hh--cCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHH
Confidence 77776 66554321 11 122222 5899999999999999887754
No 69
>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=78.57 E-value=33 Score=33.61 Aligned_cols=59 Identities=20% Similarity=0.274 Sum_probs=38.4
Q ss_pred hhhHHHhhc-----CCCCCHHHHHHHHhCCCCC-CC-----cccc-cCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009000 436 LLDIQNVFK-----EPKGGLSGLAEKILGAGLN-KT-----RRNS-NWEQRPLSQNQLEYAALDAVVLLQIFH 496 (547)
Q Consensus 436 vfDtmLAl~-----~~~~gLd~LAer~Lg~~L~-K~-----e~~S-dW~~rpLt~~Qi~YAAeDA~vlLrL~~ 496 (547)
.+|+..... ..+++|+.+|+.+||..-. .. .++. .|...+ ..-++|+..||..+++|++
T Consensus 123 ~~D~~~~~k~~~~kl~sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~~~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 123 VLDGIDALKTATYHFESFSLENVAQELLGEGKLIHDVDDRGAEIERLFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred EEEhHHHHHHccCCCCcCCHHHHHHHHhCCCccccCcccCHHHHHHHHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 567655432 3689999999999985321 11 1222 243322 3458999999999999863
No 70
>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=78.22 E-value=13 Score=33.16 Aligned_cols=85 Identities=15% Similarity=0.088 Sum_probs=53.0
Q ss_pred HHHHHHHhhcCCCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHhhc-----CCCCCHHHHHHHHhCCCCCCCcc
Q 009000 393 LDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLNKTRR 467 (547)
Q Consensus 393 Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl~-----~~~~gLd~LAer~Lg~~L~K~e~ 467 (547)
....+..++++ ...||||..+|..+|.+.+...........++|++.... ...+++..+..+++|....
T Consensus 69 ~~~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~~---- 142 (159)
T cd06127 69 VLPEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLE---- 142 (159)
T ss_pred HHHHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCCC----
Confidence 34567777776 568999999999988763321000000255789987732 3457788774445554221
Q ss_pred cccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009000 468 NSNWEQRPLSQNQLEYAALDAVVLLQIF 495 (547)
Q Consensus 468 ~SdW~~rpLt~~Qi~YAAeDA~vlLrL~ 495 (547)
+.+-|..||..+.+++
T Consensus 143 ------------~~H~Al~Da~~t~~l~ 158 (159)
T cd06127 143 ------------GAHRALADALATAELL 158 (159)
T ss_pred ------------CCCCcHHHHHHHHHHh
Confidence 1344888999988875
No 71
>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=77.40 E-value=78 Score=31.26 Aligned_cols=100 Identities=21% Similarity=0.228 Sum_probs=57.4
Q ss_pred HHHHHHHHhhcCCCceEEEechH-HHHHHHHH---HhCCc-----cccc------ccchhhhHHHhhc------------
Q 009000 392 VLDSCLTRILQSPGILKLGYNFQ-CDIKQLAH---SYGEL-----ECFK------HYEMLLDIQNVFK------------ 444 (547)
Q Consensus 392 ~Ll~~Lk~LLed~~I~KVGhnlK-~Dl~vLa~---~~GIl-----~~~~------~~~~vfDtmLAl~------------ 444 (547)
+++..+..++.+. -..+|+|.. +|+..|.. .+|+. ..+. .....+|+...+.
T Consensus 75 ~lL~~F~~~i~~~-~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~~ 153 (204)
T cd05783 75 ELIREAFKIISEY-PIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGNK 153 (204)
T ss_pred HHHHHHHHHHhcC-CEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhccc
Confidence 4555566666665 356899976 57665432 25653 0000 0123456655421
Q ss_pred CCCCCHHHHHHHHhCCC-CCCCcccccCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009000 445 EPKGGLSGLAEKILGAG-LNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFH 496 (547)
Q Consensus 445 ~~~~gLd~LAer~Lg~~-L~K~e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~ 496 (547)
..+++|+.+|+.+||.. .+-..++... . .+.-.+|+..||..+++|..
T Consensus 154 ~~~~~L~~Va~~~lg~~K~~~~~~i~~~---~-~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 154 YREYTLDAVAKALLGEGKVELEKNISEL---N-LYELAEYNYRDAELTLELTT 202 (204)
T ss_pred cccCcHHHHHHHhcCCCcccCCchhhhh---c-HHHHHHhhHHHHHHHHHHhc
Confidence 15789999999999853 2111111111 1 13347999999999999864
No 72
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=75.88 E-value=34 Score=43.41 Aligned_cols=91 Identities=14% Similarity=0.113 Sum_probs=62.1
Q ss_pred HHHHHHhhcCCCceEEEechHHHHHHHHHH---hCCcccccccchhhhHHHhhc-----CCCCCHHHHHHHHhCCCCCCC
Q 009000 394 DSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLNKT 465 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl~-----~~~~gLd~LAer~Lg~~L~K~ 465 (547)
...+..++. ....|+||..+|...|... +|+.. + ....+|++.... ..+++|+.|+++ +|.+...
T Consensus 490 L~~f~~fig--g~vLVAHNa~FD~~fL~~~l~rlgl~~-l--~~~~IDTLelar~l~p~~k~~kL~~LAk~-lGL~~~~- 562 (1437)
T PRK00448 490 LPKFKEFCG--DSILVAHNASFDVGFINTNYEKLGLEK-I--KNPVIDTLELSRFLYPELKSHRLNTLAKK-FGVELEH- 562 (1437)
T ss_pred HHHHHHHhC--CCEEEEeCccccHHHHHHHHHHcCCcc-c--cccceeHHHHHHHHcCccccccHHHHHHH-cCCCCCC-
Confidence 344444444 3678999999999876432 44411 1 245679877631 467999999987 4654431
Q ss_pred cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Q 009000 466 RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTD 506 (547)
Q Consensus 466 e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLee~~ 506 (547)
.+.|-.||.++.+|+..+..++.+.+
T Consensus 563 ---------------~HrAl~DA~aTa~lf~~ll~~l~~~g 588 (1437)
T PRK00448 563 ---------------HHRADYDAEATAYLLIKFLKDLKEKG 588 (1437)
T ss_pred ---------------CcChHHHHHHHHHHHHHHHHHHHHcC
Confidence 14588999999999999999987644
No 73
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=69.81 E-value=11 Score=40.92 Aligned_cols=85 Identities=19% Similarity=0.238 Sum_probs=58.4
Q ss_pred HHHHHHhhcCCCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHhhc---C---CCCCHHHHHHHHhCCCCCCCcc
Q 009000 394 DSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFK---E---PKGGLSGLAEKILGAGLNKTRR 467 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl~---~---~~~gLd~LAer~Lg~~L~K~e~ 467 (547)
-..|..++.. +-.-|||++-.|+..|.-.|+ .++||.+.++ . ...+|..|++.|||..+..+.
T Consensus 284 q~~l~~~~~~-~TILVGHSLenDL~aLKl~H~---------~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~~- 352 (380)
T KOG2248|consen 284 QKELLELISK-NTILVGHSLENDLKALKLDHP---------SVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEGV- 352 (380)
T ss_pred HHHHHhhcCc-CcEEEeechhhHHHHHhhhCC---------ceeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhccC-
Confidence 4567775554 455699999999999986444 3569998864 1 234699999999997653111
Q ss_pred cccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhc
Q 009000 468 NSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSC 501 (547)
Q Consensus 468 ~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~r 501 (547)
. -+-+.+||.++++|.......
T Consensus 353 -~-----------~HdS~eDA~acm~Lv~~k~~~ 374 (380)
T KOG2248|consen 353 -G-----------GHDSVEDALACMKLVKLKIKN 374 (380)
T ss_pred -C-----------CCccHHHHHHHHHHHHHHHhc
Confidence 0 012678999999988765443
No 74
>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=67.98 E-value=85 Score=31.00 Aligned_cols=104 Identities=15% Similarity=0.193 Sum_probs=62.6
Q ss_pred hHHHHHHHHhhcCCCceEEEechH-HHHHHHHH---HhCCc-ccccc------------cchhhhHHHhhc----CCCCC
Q 009000 391 DVLDSCLTRILQSPGILKLGYNFQ-CDIKQLAH---SYGEL-ECFKH------------YEMLLDIQNVFK----EPKGG 449 (547)
Q Consensus 391 ~~Ll~~Lk~LLed~~I~KVGhnlK-~Dl~vLa~---~~GIl-~~~~~------------~~~vfDtmLAl~----~~~~g 449 (547)
.+++..+..++++.....||||.+ +|+-.|.. .+|+. +.... .+..+|++..+. ..+.+
T Consensus 79 ~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~~~~~~~ 158 (208)
T cd05782 79 KELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYGARARAS 158 (208)
T ss_pred HHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccCccCCCC
Confidence 345556666666533457999996 68876643 25651 11000 012679988853 25789
Q ss_pred HHHHHHHHhCCCCC---CCccc-ccCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009000 450 LSGLAEKILGAGLN---KTRRN-SNWEQRPLSQNQLEYAALDAVVLLQIFH 496 (547)
Q Consensus 450 Ld~LAer~Lg~~L~---K~e~~-SdW~~rpLt~~Qi~YAAeDA~vlLrL~~ 496 (547)
|+.+|+ +||.+-. .+.++ ..|...+ ...-.+|...|+..+..||.
T Consensus 159 L~~va~-~lG~~~K~d~~G~~v~~~y~~g~-~~~I~~Yc~~Dv~~t~~l~l 207 (208)
T cd05782 159 LDLLAK-LLGIPGKMDVDGSQVWELYAEGK-LDEIAEYCETDVLNTYLLYL 207 (208)
T ss_pred HHHHHH-HhCCCCCcCCCHHHHHHHHHcCC-hHHHHHHHHHHHHHHHHHHh
Confidence 999986 5776321 11111 2354444 34558999999999999874
No 75
>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=67.37 E-value=1.2e+02 Score=30.53 Aligned_cols=108 Identities=16% Similarity=0.209 Sum_probs=68.3
Q ss_pred chHHHHHHHHhhcCCCceEEEechH-HHHHHHHH---HhCCcc-ccccc-------------chhhhHHHhhc----CCC
Q 009000 390 PDVLDSCLTRILQSPGILKLGYNFQ-CDIKQLAH---SYGELE-CFKHY-------------EMLLDIQNVFK----EPK 447 (547)
Q Consensus 390 p~~Ll~~Lk~LLed~~I~KVGhnlK-~Dl~vLa~---~~GIl~-~~~~~-------------~~vfDtmLAl~----~~~ 447 (547)
..+++..+...++.....-|+||.+ +|+-+|.. .+|+.. .+-.. ..-+|+|-.+. ..+
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 4566777777887766778999988 58766532 256521 10000 12478987753 357
Q ss_pred CCHHHHHHHHhCCCCCCC----cccc-cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHh
Q 009000 448 GGLSGLAEKILGAGLNKT----RRNS-NWEQRPLSQNQLEYAALDAVVLLQIFHHVRS 500 (547)
Q Consensus 448 ~gLd~LAer~Lg~~L~K~----e~~S-dW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~ 500 (547)
.+|+.||. .+|+|- |. .++. -|.+..+ ++-..|.-.|+..+..||-.+..
T Consensus 117 ~sLd~la~-~lgiPg-K~~idGs~V~~~y~~g~i-~~I~~YCe~DVl~T~~lylR~~~ 171 (209)
T PF10108_consen 117 TSLDELAA-LLGIPG-KDDIDGSQVAELYQEGDI-DEIREYCEKDVLNTYLLYLRFEL 171 (209)
T ss_pred CCHHHHHH-HcCCCC-CCCCCHHHHHHHHHcCCH-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 88999886 568764 32 1221 2444444 33478999999999999887643
No 76
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=65.89 E-value=0.35 Score=51.96 Aligned_cols=72 Identities=28% Similarity=0.399 Sum_probs=58.0
Q ss_pred CCceeEEEEEeCCeEEEEEcCcccCCCchHHHHHHHHhhcCCCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHh
Q 009000 363 MNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNV 442 (547)
Q Consensus 363 ~~~VsLlQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLA 442 (547)
..+.+++|.++.-.+|++|+...+ ...+...+..+++|.+|.|+.|++...+..++..|||.. +++|||+++
T Consensus 73 ~~~l~~~q~~~~~~~yl~~i~~~~---~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~~~~~~i~~-----n~v~~~q~~ 144 (458)
T KOG2405|consen 73 HGKLCWLQVATNCRVYLFDIFLLG---SRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGILL-----NNVFDTQVA 144 (458)
T ss_pred cCcchhHHHHHHHHHHHHHHHHhh---hHHHHHHHHHHhhhhhHhhhHHHHHHHHHHhcccceeee-----cchhhhhhh
Confidence 346777777777777888876543 234567889999999999999999998888888899954 789999998
No 77
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=64.51 E-value=1.5e+02 Score=29.26 Aligned_cols=92 Identities=21% Similarity=0.140 Sum_probs=58.6
Q ss_pred HHHHHHhhcCCCceEEEechHHHHHHHHHHh---CCcccccccchhhhHHHhh----cC-CCCCHHHHHHHHhCCCCCCC
Q 009000 394 DSCLTRILQSPGILKLGYNFQCDIKQLAHSY---GELECFKHYEMLLDIQNVF----KE-PKGGLSGLAEKILGAGLNKT 465 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~~---GIl~~~~~~~~vfDtmLAl----~~-~~~gLd~LAer~Lg~~L~K~ 465 (547)
...+..++.+. -.-|+||..+|...+.... +.... ...+.|+.... .. ..++|+.|+. .+|++.. .
T Consensus 85 ~~~~~~~i~~~-~~~Vahna~fD~~fl~~~~~~~~~~~~---~~~~~~t~~~~r~~~~~~~~~~L~~l~~-~~gi~~~-~ 158 (243)
T COG0847 85 LPEFLDFIGGL-RLLVAHNAAFDVGFLRVESERLGIEIP---GDPVLDTLALARRHFPGFDRSSLDALAE-RLGIDRN-P 158 (243)
T ss_pred HHHHHHHHCCC-CeEEEEchhhcHHHHHHHHHHcCCCcc---cCceehHHHHHHHHcCCCccchHHHHHH-HcCCCcC-C
Confidence 34555566554 5679999999999886532 22110 13455776663 23 5789999999 4575432 1
Q ss_pred cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhc-cCC
Q 009000 466 RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSC-SQP 504 (547)
Q Consensus 466 e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~r-Lee 504 (547)
.. .+-|..||.++..++..+... +..
T Consensus 159 ~~-------------~H~Al~Da~~~a~~~~~~~~~~~~~ 185 (243)
T COG0847 159 FH-------------PHRALFDALALAELFLLLQTGLLLK 185 (243)
T ss_pred cC-------------CcchHHHHHHHHHHHHHHHhccccc
Confidence 10 133889999999999888775 443
No 78
>KOG3616 consensus Selective LIM binding factor [Transcription]
Probab=61.63 E-value=37 Score=40.03 Aligned_cols=49 Identities=20% Similarity=0.262 Sum_probs=39.4
Q ss_pred HHHHhhhcchHHHHHHhhcc---hhHHHHHHHH---hhccCCHHHHHHHHHHcCC
Q 009000 248 LKRLAEKACWDIAEAKTKGD---KRLLEYLVYL---AMEAGYSEKVDELCERYSL 296 (547)
Q Consensus 248 ~~~l~~k~~wd~a~~~~~~D---~~l~~~lv~L---~~~~~d~~~L~~l~~ryef 296 (547)
|.-|++.++||.|..+++.. |-|..|+.-+ +...+|..++..++.++|-
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 77789999999999888754 3566676554 4568999999999999994
No 79
>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=56.98 E-value=1.6e+02 Score=27.11 Aligned_cols=89 Identities=19% Similarity=0.219 Sum_probs=52.1
Q ss_pred HHHHHHhhcCCCceEEEechHHHHHHHHHH---hCCcccccccchhhhHHHhhc-----CCCCCHHHHHHHHhCCCCCCC
Q 009000 394 DSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLNKT 465 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl~-----~~~~gLd~LAer~Lg~~L~K~ 465 (547)
...+..++.+.....++++.++|...+.+. ++...........+|++..+. ..+++|++++++ +|.+..
T Consensus 79 l~~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~-- 155 (176)
T cd06133 79 LKEFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEY-LGLEFE-- 155 (176)
T ss_pred HHHHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHHHHH-CCCCCC--
Confidence 456777777641134455568887655431 222100001245779887732 247899999876 476543
Q ss_pred cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009000 466 RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHV 498 (547)
Q Consensus 466 e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L 498 (547)
. +.+.|-.||..+.+++..+
T Consensus 156 ~-------------~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 156 G-------------RHHRGLDDARNIARILKRL 175 (176)
T ss_pred C-------------CCcCcHHHHHHHHHHHHHh
Confidence 0 1233778899998888765
No 80
>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=56.41 E-value=2e+02 Score=30.27 Aligned_cols=158 Identities=16% Similarity=0.215 Sum_probs=95.5
Q ss_pred HHHHHHHHHHHhhCCCCCCCceeeeeeee--ecccccc------cccc-hhHHHHHHHHhhhcccCCccchhH-HHHHHH
Q 009000 67 FRALQQQVSQALCNSPEPGPATFIVRCLY--VLPIFGV------YSEG-FSHLIISALRRHQKTTVNSADSTQ-AKEIAA 136 (547)
Q Consensus 67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~------~~~~-~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~ 136 (547)
-..|...|-.+|.-.|-| |-+|.+|+= ..|--+. ..-. =.=+++..|++ .+ +.++.+.-+ |+.+|.
T Consensus 38 ~~~lr~Ev~~AL~~A~DP--AkLVLdai~~f~~~~~~~~~~~~~~~~r~~cilLLE~L~~-~~-~~is~~vke~A~~lA~ 113 (290)
T PF07899_consen 38 LASLREEVPAALRCAPDP--AKLVLDAIEGFYPPGSKNKKDSKLVDVRRACILLLEQLMR-IS-PEISPEVKEEAKKLAE 113 (290)
T ss_pred HHHHHHHHHHHHHcCCCh--HHHHHHHHHcccCCccccccCcchhhHHHHHHHHHHHHhh-cC-CCCCHHHHHHHHHHHH
Confidence 346889999999887765 788888862 1111110 0000 12356677777 22 345555544 777776
Q ss_pred HHHHHH--hcCCCCChhHHHHHHHHHhccccc-chHHHH--hhhhhccccchhHHH-----HHHHHHHHHHHhhchhhHH
Q 009000 137 YLFLDI--TGGFVDHDEKLMVKILEAFDVRLT-DIEKAI--TQLKAQNEHRFDTAK-----TVIEQYIFAMIDSQSYMTA 206 (547)
Q Consensus 137 ~~~~~~--~~~~~~~~~r~~~~l~e~f~~~~~-~~~~a~--~~~~~~~~~~~~~~~-----~~~~~~i~~~~~~~~~~~~ 206 (547)
..=--+ +..--..+..-.+.++=+|||.-+ |.++-+ -.+-++.......++ +-+..+|.+||+.|++..|
T Consensus 114 ~WK~~l~~~~~~~~lea~gFL~lla~fgi~s~Fd~del~~Lv~~va~~~~a~~L~~sLgl~~k~~d~V~~LI~~g~~ieA 193 (290)
T PF07899_consen 114 EWKSKLDGVNNENSLEALGFLQLLAAFGIVSEFDEDELLKLVVSVARRKQAPELCRSLGLSDKMPDIVEKLIKKGKQIEA 193 (290)
T ss_pred HHHHHHHhcccCCCHHHHHHHHHHHHcCCccccCHHHHHHHHHHhcchHhhHHHHHHcCchhhhHHHHHHHHHCCCccch
Confidence 554444 344455568899999999999532 211110 011111211222222 3368999999999999999
Q ss_pred HHHHHhhhcccc--chHHHHHHHh
Q 009000 207 VSLLEHFSIRQS--GESFLLKMIQ 228 (547)
Q Consensus 207 ~~li~~f~~~~~--~~~~l~~~~~ 228 (547)
|.+|.-|++.-. -.|.|..-++
T Consensus 194 v~fi~~f~L~dkfpPv~lLk~yl~ 217 (290)
T PF07899_consen 194 VRFIYAFGLVDKFPPVPLLKSYLE 217 (290)
T ss_pred HHHHHHHcCCCCCCCHHHHHHHHH
Confidence 999999999864 4445555554
No 81
>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=54.87 E-value=16 Score=27.56 Aligned_cols=46 Identities=15% Similarity=0.113 Sum_probs=39.0
Q ss_pred cCCccchhHHHHHHHHHHHHHhcCCCCChhHHHHHHHHHhcccccc
Q 009000 122 TVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTD 167 (547)
Q Consensus 122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~l~e~f~~~~~~ 167 (547)
.-+++|+-++=++.-+.+-.+..|........+.++++.||++++.
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 4568899998899999999999998888899999999999997654
No 82
>PRK14976 5'-3' exonuclease; Provisional
Probab=52.37 E-value=6.4 Score=40.96 Aligned_cols=38 Identities=16% Similarity=0.090 Sum_probs=35.2
Q ss_pred HHHHhhcchhHHHHHHHHhhccCCHHHHHHHHHHcCCc
Q 009000 260 AEAKTKGDKRLLEYLVYLAMEAGYSEKVDELCERYSLE 297 (547)
Q Consensus 260 a~~~~~~D~~l~~~lv~L~~~~~d~~~L~~l~~ryef~ 297 (547)
.++++++|+++...+.+++..++|.+++.++|+++||+
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
>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=52.32 E-value=21 Score=27.91 Aligned_cols=54 Identities=22% Similarity=0.278 Sum_probs=39.9
Q ss_pred HHHHhhhcccCCccchhHHHHHHHHHHHHHhcCCCCChhHHHHHHHHHhcccccch
Q 009000 113 SALRRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDI 168 (547)
Q Consensus 113 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~l~e~f~~~~~~~ 168 (547)
-.+|.-. .-+++|+.+.-.+....+-.+..|........+.++++.|||+++.+
T Consensus 5 k~~r~~~--~lt~~~~a~~~~i~~~~i~~~e~g~~~~~~~~l~~i~~~~~v~~~~l 58 (64)
T PF12844_consen 5 KELREEK--GLTQKDLAEKLGISRSTISKIENGKRKPSVSTLKKIAEALGVSLDEL 58 (64)
T ss_dssp HHHHHHC--T--HHHHHHHHTS-HHHHHHHHTTSS--BHHHHHHHHHHHTS-HHHH
T ss_pred HHHHHHc--CCCHHHHHHHHCcCHHHHHHHHCCCcCCCHHHHHHHHHHhCCCHHHH
Confidence 3455533 34689999999999999999999988877899999999999987654
No 84
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=48.04 E-value=27 Score=38.08 Aligned_cols=127 Identities=20% Similarity=0.148 Sum_probs=79.7
Q ss_pred EEEEeCCeEEEEEcCcccCCCchHHHHHHHHhhcCCCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHhhc----
Q 009000 369 MQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFK---- 444 (547)
Q Consensus 369 lQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl~---- 444 (547)
+++|.+...+++|....+.. .+.+-.++.|++..+ +. |.+.+...+...|++. ..+++|+|++..
T Consensus 216 m~ia~~n~i~llD~~~sdi~---il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~-----L~nVkDtQia~sLve~ 284 (458)
T KOG2405|consen 216 MNIADGNEIFLLDSLPSDIR---ILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSA-----LKNVKDTQIASSLVEP 284 (458)
T ss_pred hhhcccchhhhhhhccCCcE---Eecccchhhhhhcce--eh-hhhhhhHHHHhHHHHH-----HHhhHHHHHHHHHhhh
Confidence 45677778888887643211 122345777877654 44 8888888888778873 367899999931
Q ss_pred ---CCCCCHHHHHHH-HhCC-------CCCCC--------cccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCC
Q 009000 445 ---EPKGGLSGLAEK-ILGA-------GLNKT--------RRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPT 505 (547)
Q Consensus 445 ---~~~~gLd~LAer-~Lg~-------~L~K~--------e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rLee~ 505 (547)
.+++..+.+.-. .|+. ...++ ....+|..||.++...+-++.|+.+++...+.|....-.+
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 234443333211 1111 00011 1223699999999989999999999999877776554443
Q ss_pred C
Q 009000 506 D 506 (547)
Q Consensus 506 ~ 506 (547)
.
T Consensus 365 L 365 (458)
T KOG2405|consen 365 L 365 (458)
T ss_pred h
Confidence 3
No 85
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=42.41 E-value=2e+02 Score=28.14 Aligned_cols=91 Identities=22% Similarity=0.109 Sum_probs=57.7
Q ss_pred HHHHHHHhhcCCCceEEEechHHHHHHHHHH---hCCcccccccchhhhHHHhhc-----CCCCCHHHHHHHHhCCCCCC
Q 009000 393 LDSCLTRILQSPGILKLGYNFQCDIKQLAHS---YGELECFKHYEMLLDIQNVFK-----EPKGGLSGLAEKILGAGLNK 464 (547)
Q Consensus 393 Ll~~Lk~LLed~~I~KVGhnlK~Dl~vLa~~---~GIl~~~~~~~~vfDtmLAl~-----~~~~gLd~LAer~Lg~~L~K 464 (547)
+...|..++.+.....+ ++..+|+..|.+. +|+...+ ...+.|++.... ...++|+++++++ |++..
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 35667778876334444 5578999888643 3542111 144667776632 3468999988874 65421
Q ss_pred CcccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhcc
Q 009000 465 TRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCS 502 (547)
Q Consensus 465 ~e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~L~~rL 502 (547)
.+ .+.|..||..+.+|+..+..+.
T Consensus 157 -~~-------------~H~Al~DA~~ta~l~~~l~~~~ 180 (207)
T PRK07748 157 -GK-------------HHCALDDAMTTYNIFKLVEKDK 180 (207)
T ss_pred -CC-------------CcChHHHHHHHHHHHHHHHhCc
Confidence 00 2348899999999999998774
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=39.73 E-value=44 Score=26.39 Aligned_cols=47 Identities=23% Similarity=0.319 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHhcCCCCChhHH--HHHHHHHhcccccchHHHHhhhhh
Q 009000 131 AKEIAAYLFLDITGGFVDHDEKL--MVKILEAFDVRLTDIEKAITQLKA 177 (547)
Q Consensus 131 ~~~~~~~~~~~~~~~~~~~~~r~--~~~l~e~f~~~~~~~~~a~~~~~~ 177 (547)
...++.++.-+|..|....++++ ...|++.||++-+-+-.|+.....
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 678999999987777777644433
No 87
>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=37.76 E-value=1.4e+02 Score=29.43 Aligned_cols=101 Identities=18% Similarity=0.231 Sum_probs=50.0
Q ss_pred HHH-HHHHHHHHhhchhhH-HHHHHHhhhcccc-----chHHHHHHHhccchH---HHHHHHHhcCchHHHHHHh----h
Q 009000 188 TVI-EQYIFAMIDSQSYMT-AVSLLEHFSIRQS-----GESFLLKMIQNKEFK---AAEKWATFMGKPILLKRLA----E 253 (547)
Q Consensus 188 ~~~-~~~i~~~~~~~~~~~-~~~li~~f~~~~~-----~~~~l~~~~~~~~~~---~a~~~~~~~~~~~~~~~l~----~ 253 (547)
+.| +.||+..+.+..|.+ |..||.+|..-.. .++-|.+.++.=+.. |.+| ...|.|-.++.-. +
T Consensus 12 e~LEkayikD~It~~eYt~~c~kLl~Qyk~~~~~~~~~~~~~le~F~~~y~l~cp~A~~R--l~~G~P~Tie~~~~~~~~ 89 (188)
T PF03997_consen 12 EHLEKAYIKDSITEKEYTTACNKLLNQYKTILKQLKDDEFPDLEEFMKKYNLDCPAALER--LREGVPATIEHRISSSSD 89 (188)
T ss_dssp HHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHTSTTHHHHHHHHHHHHHTTS-HHHHHHH--HHCTSS------------
T ss_pred HHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHcccccCCCHHHHHHHhcccCChHHHH--HHcCCCCchhhhcccccC
Confidence 344 789999998888987 8899998854332 234444544322221 3344 3356776544422 1
Q ss_pred hcchHH--HHHHhhcchhHHHHHHHHhhccCCHHHHHHHHHHc
Q 009000 254 KACWDI--AEAKTKGDKRLLEYLVYLAMEAGYSEKVDELCERY 294 (547)
Q Consensus 254 k~~wd~--a~~~~~~D~~l~~~lv~L~~~~~d~~~L~~l~~ry 294 (547)
++..-+ |+++ ---+..++.+++.-...+++..++.++
T Consensus 90 ~~~~ak~Vae~t----~~FIT~mDaLKLn~~a~DqLhPlL~dL 128 (188)
T PF03997_consen 90 KGNSAKLVAEAT----QNFITLMDALKLNYRAKDQLHPLLSDL 128 (188)
T ss_dssp --CHHHHHHHHH----HHHHHHHHHHHTT--BHHHHHHHHHHH
T ss_pred CchHHHHHHHHh----ChhhhhhHHHhccchhHhhHhhHHHHH
Confidence 222211 2221 124556777777777777776666543
No 88
>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=37.19 E-value=1.5e+02 Score=27.90 Aligned_cols=65 Identities=20% Similarity=0.215 Sum_probs=38.2
Q ss_pred HHHHHHHHHhCCcccccccchhhhHHHh---hcCCCCCHHHHHHHHhCCCCCCCcccccCCCCCCCHHHHHHHHHHHHHH
Q 009000 415 CDIKQLAHSYGELECFKHYEMLLDIQNV---FKEPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVL 491 (547)
Q Consensus 415 ~Dl~vLa~~~GIl~~~~~~~~vfDtmLA---l~~~~~gLd~LAer~Lg~~L~K~e~~SdW~~rpLt~~Qi~YAAeDA~vl 491 (547)
.|+.++...-|+.. .+--|-|+. ++-.+.++..+++||+|- +|.. -|+..|.++
T Consensus 71 K~LAv~a~~~G~~v-----~PGDDPlLlAYLlDPsNt~p~~varRY~~~---------~W~~---------dA~~RA~~t 127 (138)
T PF09281_consen 71 KDLAVHALREGVVV-----EPGDDPLLLAYLLDPSNTNPEGVARRYLGG---------EWPE---------DAATRALAT 127 (138)
T ss_dssp HHHHHHHHHTT---------B---HHHHHHHH-TT--SHHHHHHHH-TS------------S---------SHHHHHHHH
T ss_pred HHHHHHHHhcCccc-----CCCCCcchhhhhcCccCCChHHHHHHhcCC---------CCCc---------cHHHHHHHH
Confidence 45555443357632 444588887 455678899999999874 3422 178889999
Q ss_pred HHHHHHHHhcc
Q 009000 492 LQIFHHVRSCS 502 (547)
Q Consensus 492 LrL~~~L~~rL 502 (547)
-+|++.|.++|
T Consensus 128 ~~L~~~L~prL 138 (138)
T PF09281_consen 128 ARLLRALPPRL 138 (138)
T ss_dssp HHHHHHHHHHT
T ss_pred HHHHHHhhhcC
Confidence 99999998875
No 89
>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=35.90 E-value=39 Score=33.67 Aligned_cols=64 Identities=17% Similarity=0.229 Sum_probs=42.5
Q ss_pred hhhHHHhh----cCCCCCHHHHHHHHhCCCCC--CCccccc-CCCCCC-CHHHHHHHHHHHHHHHHHHHHHH
Q 009000 436 LLDIQNVF----KEPKGGLSGLAEKILGAGLN--KTRRNSN-WEQRPL-SQNQLEYAALDAVVLLQIFHHVR 499 (547)
Q Consensus 436 vfDtmLAl----~~~~~gLd~LAer~Lg~~L~--K~e~~Sd-W~~rpL-t~~Qi~YAAeDA~vlLrL~~~L~ 499 (547)
.+|+.... +-.+++|+.+|+++||..-. ..+.+.. |...|- ...-++|...||..+++|...|.
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 24589999999999996432 1223333 332222 13448999999999999999874
No 90
>PRK00118 putative DNA-binding protein; Validated
Probab=34.67 E-value=1.9e+02 Score=25.92 Aligned_cols=35 Identities=17% Similarity=0.355 Sum_probs=29.6
Q ss_pred HHHHHhcCCCCChhHHHHHHHHHhcccccchHHHH
Q 009000 138 LFLDITGGFVDHDEKLMVKILEAFDVRLTDIEKAI 172 (547)
Q Consensus 138 ~~~~~~~~~~~~~~r~~~~l~e~f~~~~~~~~~a~ 172 (547)
.++|--++..+...|-++++.-.-|.+.++|+.-+
T Consensus 9 ~l~d~~~~~L~ekqRevl~L~y~eg~S~~EIAe~l 43 (104)
T PRK00118 9 LLFDFYGSLLTEKQRNYMELYYLDDYSLGEIAEEF 43 (104)
T ss_pred HHHHHHhccCCHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 57888899999889999999888899888887663
No 91
>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=31.18 E-value=1.2e+02 Score=29.08 Aligned_cols=85 Identities=21% Similarity=0.230 Sum_probs=47.6
Q ss_pred HHHHHHhhcCCCceEEEec-hHHHHHHHHHH---hCCcccc---cccchhhhHHHh---h----c-----------CCCC
Q 009000 394 DSCLTRILQSPGILKLGYN-FQCDIKQLAHS---YGELECF---KHYEMLLDIQNV---F----K-----------EPKG 448 (547)
Q Consensus 394 l~~Lk~LLed~~I~KVGhn-lK~Dl~vLa~~---~GIl~~~---~~~~~vfDtmLA---l----~-----------~~~~ 448 (547)
...+.+++..+....|||| +.+|...|.+. +|...-. ......+|+.-. . . ..++
T Consensus 73 l~~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~ 152 (183)
T cd06138 73 IAKIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSF 152 (183)
T ss_pred HHHHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcch
Confidence 3455666654444568997 89999988653 2321000 000122455422 1 0 1357
Q ss_pred CHHHHHHHHhCCCCCCCcccccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009000 449 GLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIF 495 (547)
Q Consensus 449 gLd~LAer~Lg~~L~K~e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~ 495 (547)
+|+.|+++ +|.+.. +.+.|..||..+.+|.
T Consensus 153 ~L~~l~~~-~gi~~~----------------~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 153 KLEDLAQA-NGIEHS----------------NAHDALSDVEATIALA 182 (183)
T ss_pred hHHHHHHH-CCCCcc----------------ccccHHHHHHHHHHHh
Confidence 89999986 465431 1355888998887763
No 92
>PLN03218 maturation of RBCL 1; Provisional
Probab=30.88 E-value=1.1e+03 Score=29.27 Aligned_cols=98 Identities=16% Similarity=0.022 Sum_probs=56.2
Q ss_pred HHhhchhhHHHHHHHhh---hccc--cch-HHHHHHHhccchHHHHHHHHhcCc----h------HHHHHHhhhcchHHH
Q 009000 197 MIDSQSYMTAVSLLEHF---SIRQ--SGE-SFLLKMIQNKEFKAAEKWATFMGK----P------ILLKRLAEKACWDIA 260 (547)
Q Consensus 197 ~~~~~~~~~~~~li~~f---~~~~--~~~-~~l~~~~~~~~~~~a~~~~~~~~~----~------~~~~~l~~k~~wd~a 260 (547)
+.+.|.+..|..+.+.- ++.- ..+ ..+....++|+++.|.+.-..|.. | .++..+...|.++.|
T Consensus 589 y~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA 668 (1060)
T PLN03218 589 CANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKA 668 (1060)
T ss_pred HHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHH
Confidence 33445555566665322 2211 111 134455567777766654444332 2 236666667777877
Q ss_pred HHHhhc--------chhHHHHHHHHhhccCCHHHHHHHHHHc
Q 009000 261 EAKTKG--------DKRLLEYLVYLAMEAGYSEKVDELCERY 294 (547)
Q Consensus 261 ~~~~~~--------D~~l~~~lv~L~~~~~d~~~L~~l~~ry 294 (547)
....+. |...-..|++.....++.+++.++|++.
T Consensus 669 ~~l~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM 710 (1060)
T PLN03218 669 FEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDI 710 (1060)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 766543 4445556777777788888888887765
No 93
>PHA01976 helix-turn-helix protein
Probab=30.45 E-value=71 Score=25.06 Aligned_cols=53 Identities=13% Similarity=0.178 Sum_probs=41.6
Q ss_pred HHHhhhcccCCccchhHHHHHHHHHHHHHhcCCCCChhHHHHHHHHHhcccccch
Q 009000 114 ALRRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDI 168 (547)
Q Consensus 114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~l~e~f~~~~~~~ 168 (547)
.+|.-.. -+++++-+.-.+....+-.+-.|........+.++++.||++++.+
T Consensus 9 ~~R~~~g--lt~~~lA~~~gvs~~~v~~~e~g~~~p~~~~l~~ia~~l~v~~~~l 61 (67)
T PHA01976 9 KARNARA--WSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWL 61 (67)
T ss_pred HHHHHcC--CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHH
Confidence 4454333 3578888887888889999998887667788999999999988776
No 94
>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=29.96 E-value=1.8e+02 Score=26.44 Aligned_cols=74 Identities=20% Similarity=0.239 Sum_probs=40.6
Q ss_pred HHHHHhhchh-hHHHHHHHhhhccccchHHHHHHHhccchHHHHHHHHhcCchHHH--HHHhh--hcchHHHHHHh----
Q 009000 194 IFAMIDSQSY-MTAVSLLEHFSIRQSGESFLLKMIQNKEFKAAEKWATFMGKPILL--KRLAE--KACWDIAEAKT---- 264 (547)
Q Consensus 194 i~~~~~~~~~-~~~~~li~~f~~~~~~~~~l~~~~~~~~~~~a~~~~~~~~~~~~~--~~l~~--k~~wd~a~~~~---- 264 (547)
|-+.+.++.. ..+|.||+--|| |--|+|+.|-+.....-.|+++ ..|++ -|.-++++.+.
T Consensus 27 IAdwL~~~~~~~E~v~lIRlsSL-----------mNrG~Yq~Al~l~~~~~~pdlepw~ALce~rlGl~s~l~~rl~rla 95 (115)
T TIGR02508 27 IADWLHLKGESEEAVQLIRLSSL-----------MNRGDYQSALQLGNKLCYPDLEPWLALCEWRLGLGSALESRLNRLA 95 (115)
T ss_pred HHHHHhcCCchHHHHHHHHHHHH-----------HccchHHHHHHhcCCCCCchHHHHHHHHHHhhccHHHHHHHHHHHH
Confidence 4455566443 569999986554 4567777777766666666652 12221 22333333332
Q ss_pred -hcchhHHHHHHHHh
Q 009000 265 -KGDKRLLEYLVYLA 278 (547)
Q Consensus 265 -~~D~~l~~~lv~L~ 278 (547)
++|++++.|...++
T Consensus 96 ~sg~p~lq~Faag~r 110 (115)
T TIGR02508 96 ASGDPRLQTFVAGMR 110 (115)
T ss_pred hCCCHHHHHHHHHHH
Confidence 45666666655543
No 95
>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=29.63 E-value=44 Score=38.47 Aligned_cols=99 Identities=18% Similarity=0.248 Sum_probs=57.7
Q ss_pred HHHHHHHhhhhcccchhchhHHHHHHHHHHHhhCCCCCCC-------------ceeeeeeeeecccccccccchhHHHHH
Q 009000 47 VFLYLLKECYIHGTCKATRKFRALQQQVSQALCNSPEPGP-------------ATFIVRCLYVLPIFGVYSEGFSHLIIS 113 (547)
Q Consensus 47 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~~ 113 (547)
+|+.||+|.-..-.-+-+.=|++|..-.. ++.+..-| ..|.+.|-||+|++..-.+=|..
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 78888998765555555555666555444 23333333 45789999999988533322222
Q ss_pred HHHhhhcccCCccchhHHHHHHHHHHHHHhcCCCCCh-hHHHHHHHHHhcc
Q 009000 114 ALRRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHD-EKLMVKILEAFDV 163 (547)
Q Consensus 114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~r~~~~l~e~f~~ 163 (547)
.+-|....|+.+.. +|||+++=-..+ ...+++|++.-++
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 12344555555444 467777654444 5566677665555
No 96
>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=29.10 E-value=96 Score=22.96 Aligned_cols=52 Identities=17% Similarity=0.287 Sum_probs=40.7
Q ss_pred HHHHHhhhcccCCccchhHHHHHHHHHHHHHhcCCCCChhHHHHHHHHHhcccc
Q 009000 112 ISALRRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRL 165 (547)
Q Consensus 112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~l~e~f~~~~ 165 (547)
|..+|.-. .-+++|+-+.-.+.-..+-.+-.|-.......+.++++.||+++
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 34455422 34588888888888999999999987777888999999999865
No 97
>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=27.96 E-value=83 Score=29.48 Aligned_cols=62 Identities=19% Similarity=0.255 Sum_probs=48.3
Q ss_pred hHHHHHHHHHHHHHHhhchhh-H-HHHHHHhhhccccchH---HHHHHHhccchH-HHHHHHHhcCch
Q 009000 184 DTAKTVIEQYIFAMIDSQSYM-T-AVSLLEHFSIRQSGES---FLLKMIQNKEFK-AAEKWATFMGKP 245 (547)
Q Consensus 184 ~~~~~~~~~~i~~~~~~~~~~-~-~~~li~~f~~~~~~~~---~l~~~~~~~~~~-~a~~~~~~~~~~ 245 (547)
..||+.+++-|.+-...-... . +-.+|++|+.+--.+. ++....|.|+|. ....||..+..|
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 478888999999987775555 3 6677899998875554 777788888887 688899997777
No 98
>KOG4634 consensus Mitochondrial F1F0-ATP synthase, subunit Cf6 (coupling factor 6) [Energy production and conversion]
Probab=27.81 E-value=1.6e+02 Score=26.24 Aligned_cols=60 Identities=23% Similarity=0.371 Sum_probs=44.5
Q ss_pred hhHHHHHHHHhhhcccCCccchhHHHHHHHHHHHHHhc---------CCCCCh-------hHHHHHHHHHhcccccch
Q 009000 107 FSHLIISALRRHQKTTVNSADSTQAKEIAAYLFLDITG---------GFVDHD-------EKLMVKILEAFDVRLTDI 168 (547)
Q Consensus 107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~-------~r~~~~l~e~f~~~~~~~ 168 (547)
||-.|-|+.++++.+ +---+...+..--|+|+|-|+ ++|+.+ .+-+.||+..||+.-+||
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 567778888877765 223456677778899999874 566666 677899999999766665
No 99
>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=25.98 E-value=64 Score=32.36 Aligned_cols=59 Identities=15% Similarity=0.207 Sum_probs=39.8
Q ss_pred hhHHHhh----cCCCCCHHHHHHHHhCCCCCC--CcccccCC-CC--CCCHHHHHHHHHHHHHHHHHH
Q 009000 437 LDIQNVF----KEPKGGLSGLAEKILGAGLNK--TRRNSNWE-QR--PLSQNQLEYAALDAVVLLQIF 495 (547)
Q Consensus 437 fDtmLAl----~~~~~gLd~LAer~Lg~~L~K--~e~~SdW~-~r--pLt~~Qi~YAAeDA~vlLrL~ 495 (547)
+|+.... +-.+++|++++.++||.+.+. ...++.|. .. .-...-++|...||..+++|.
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 4555442 246899999999999976542 23455552 11 223445799999999999874
No 100
>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=25.37 E-value=2.7e+02 Score=21.88 Aligned_cols=48 Identities=17% Similarity=0.311 Sum_probs=30.5
Q ss_pred HHHHHHHHhcCCCCChhHHHHHHHHHhcccccchHHHHhhhhhccccchhHHHHHHHHHHHHHHhhc
Q 009000 135 AAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDIEKAITQLKAQNEHRFDTAKTVIEQYIFAMIDSQ 201 (547)
Q Consensus 135 ~~~~~~~~~~~~~~~~~r~~~~l~e~f~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~ 201 (547)
.|..+...+.|- ..-+.|+-.+++.||+ +.+.+++-+.+|+.+|.+.|
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 455666666664 3357788888888888 45566777778888887655
No 101
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=25.07 E-value=3.6e+02 Score=34.86 Aligned_cols=151 Identities=21% Similarity=0.205 Sum_probs=80.4
Q ss_pred CCeEEEEeeeecCCccCCcCCceeEEEEE--eCCeEEEE--------EcCccc--C-----------CCchHHHHHHHHh
Q 009000 344 CKVVGIDCEWKPNYVKGCKMNKVSIMQIA--SDEMVFIF--------DLIKLA--E-----------DVPDVLDSCLTRI 400 (547)
Q Consensus 344 a~vIgfDtE~~~l~~~~~~~~~VsLlQLA--t~~~a~~I--------dl~~l~--~-----------~~p~~Ll~~Lk~L 400 (547)
..+.|||.|++.++.+.|++..--++=|| ++|+.|+| |+.... + ..|++. ..|+++
T Consensus 246 p~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREiVs~DIedfEYTPKpE~eG~F~v~Ne~dEv-~Ll~Rf 324 (2173)
T KOG1798|consen 246 PRVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREIVSEDIEDFEYTPKPEYEGPFCVFNEPDEV-GLLQRF 324 (2173)
T ss_pred ceEEEEeeecccCCCCCCCcccceEEEEEEEecCceEEEechhhhccchhhcccCCccccccceEEecCCcHH-HHHHHH
Confidence 46899999998776555544444455456 36766765 221110 0 012222 345555
Q ss_pred hcC----CCceEEEechH-HHHHHH---HHHhCCcccccccchhhhHHHh-----------h---------cCCCCCHHH
Q 009000 401 LQS----PGILKLGYNFQ-CDIKQL---AHSYGELECFKHYEMLLDIQNV-----------F---------KEPKGGLSG 452 (547)
Q Consensus 401 Led----~~I~KVGhnlK-~Dl~vL---a~~~GIl~~~~~~~~vfDtmLA-----------l---------~~~~~gLd~ 452 (547)
|+. .--..|.||.- +|+-.+ +..||+-. ....|..-|.+-. + +..++||..
T Consensus 325 FeHiq~~kP~iivTyNGDFFDWPFve~Ra~~hGi~m-~eEiGF~~D~~gEyks~~c~HmDcfrWVKRDSYLPqGSqgLKA 403 (2173)
T KOG1798|consen 325 FEHIQEVKPTIIVTYNGDFFDWPFVEARAKIHGISM-NEEIGFRRDSQGEYKSPFCIHMDCFRWVKRDSYLPQGSQGLKA 403 (2173)
T ss_pred HHHHHhcCCcEEEEecCccccchhhHHHHHhcCCCc-chhcCceecccccccccceeehhhhhhhhhcccCCCcccchhH
Confidence 554 22345777765 354333 22367621 1112333342211 1 135799999
Q ss_pred HHHHHhCCCCC--CCcccccCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q 009000 453 LAEKILGAGLN--KTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHH 497 (547)
Q Consensus 453 LAer~Lg~~L~--K~e~~SdW~~rpLt~~Qi~YAAeDA~vlLrL~~~ 497 (547)
+++.-||+... ..|.+..+.. .-++....|.+.||.+++-||=.
T Consensus 404 VTkaKLGYdPvEvdPEdM~~~A~-EkPQ~lasYSVSDAVATYyLYMk 449 (2173)
T KOG1798|consen 404 VTKAKLGYDPVEVDPEDMVRMAM-EKPQTLASYSVSDAVATYYLYMK 449 (2173)
T ss_pred HHHHhhCCCcccCCHHHhhhhhh-hCchhhhhcchHHHHHHHHHHHH
Confidence 99999997432 1122332221 11234478999999999988754
No 102
>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=24.01 E-value=34 Score=37.68 Aligned_cols=90 Identities=16% Similarity=0.307 Sum_probs=62.3
Q ss_pred HHHHHHhhCCCCCCCceeeeeeeeecccccccccchhHHHHHHH---HhhhcccCCccchhHHHHHHHHHHHHH-hcCCC
Q 009000 72 QQVSQALCNSPEPGPATFIVRCLYVLPIFGVYSEGFSHLIISAL---RRHQKTTVNSADSTQAKEIAAYLFLDI-TGGFV 147 (547)
Q Consensus 72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ 147 (547)
+++-+.+..-|.|+|..+..-||.+.||+|+.---=.-|.|.|| |||.+.++ ++-+. ----.=||++| ++|..
T Consensus 121 ~~~v~~iArlp~~s~~a~~~~~L~~~PLlGSfITEpaAMTlaAllL~~~~f~~~~-s~~lk--YaTLGvLFvNISIGGtL 197 (438)
T PF07399_consen 121 ERLVRFIARLPKPSPVAWWWLILTLVPLLGSFITEPAAMTLAALLLRDQFFRLGP-SPRLK--YATLGVLFVNISIGGTL 197 (438)
T ss_pred HHHHHHHHhCCCCCchhHHHHHHHHHHhhhhhhccHHHHHHHHHHHHHHhccCCC-CHHHH--HHHHHHHheEeeecccc
Confidence 45555666699999999999999999999977666688999997 67777744 32221 11223466666 45554
Q ss_pred CCh-hHHHHHHHHHhccc
Q 009000 148 DHD-EKLMVKILEAFDVR 164 (547)
Q Consensus 148 ~~~-~r~~~~l~e~f~~~ 164 (547)
.|= .+.|+-++.+.|-+
T Consensus 198 T~fAAPPVLMVA~~w~Wd 215 (438)
T PF07399_consen 198 TSFAAPPVLMVASTWGWD 215 (438)
T ss_pred cccccCcceeEecccCCC
Confidence 443 66777777776663
No 103
>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=23.75 E-value=88 Score=25.26 Aligned_cols=27 Identities=30% Similarity=0.459 Sum_probs=24.0
Q ss_pred HHHHHHHHHHhhCCCCCCCceeeeeee
Q 009000 68 RALQQQVSQALCNSPEPGPATFIVRCL 94 (547)
Q Consensus 68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (547)
+.|+..|...|.|..+|=|+.|.|.=-
T Consensus 29 ~~Ls~LvN~LL~~~~~~vpfdF~i~~~ 55 (65)
T PF08154_consen 29 KELSELVNQLLDDEEEPVPFDFLINGE 55 (65)
T ss_pred HHHHHHHHHHhccCCCCCcEEEEECCE
Confidence 679999999999999999999998643
No 104
>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=23.26 E-value=7.2e+02 Score=26.34 Aligned_cols=76 Identities=26% Similarity=0.274 Sum_probs=48.0
Q ss_pred cchHHHHHHHhccchHHHHHHHHhcCchHH------HHHHhhhcchHHHHHHhhcchhHH--HHHHHHhhccCCHHHHHH
Q 009000 218 SGESFLLKMIQNKEFKAAEKWATFMGKPIL------LKRLAEKACWDIAEAKTKGDKRLL--EYLVYLAMEAGYSEKVDE 289 (547)
Q Consensus 218 ~~~~~l~~~~~~~~~~~a~~~~~~~~~~~~------~~~l~~k~~wd~a~~~~~~D~~l~--~~lv~L~~~~~d~~~L~~ 289 (547)
+=..++.+++..|+.+.|++-......|.- ++.|++.+.||+=+..++.-+--+ ...++.....+...++..
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 334588888888888888888777777743 888899999998666655321111 123333334445555555
Q ss_pred HHHH
Q 009000 290 LCER 293 (547)
Q Consensus 290 l~~r 293 (547)
+..+
T Consensus 259 yI~k 262 (319)
T PF04840_consen 259 YIPK 262 (319)
T ss_pred HHHh
Confidence 5555
No 105
>PF14833 NAD_binding_11: NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase; PDB: 3OBB_A 3Q3C_A 2UYY_D 3G0O_A 1WP4_A 2CVZ_B 1YB4_A 3PDU_G 2I9P_D 2GF2_D ....
Probab=22.77 E-value=2.2e+02 Score=25.20 Aligned_cols=89 Identities=18% Similarity=0.239 Sum_probs=54.1
Q ss_pred HHHHHHHhcccccchHHHHhhhhhccccchhHHHHHHHHHHHHHHhhchhhHHHHHHHhhhccccchHHHHHHHhccchH
Q 009000 154 MVKILEAFDVRLTDIEKAITQLKAQNEHRFDTAKTVIEQYIFAMIDSQSYMTAVSLLEHFSIRQSGESFLLKMIQNKEFK 233 (547)
Q Consensus 154 ~~~l~e~f~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~li~~f~~~~~~~~~l~~~~~~~~~~ 233 (547)
.+.++|-+||+.+.+-++|+.+...+. .++.+....+.++.+.+ . |-++++. ++..
T Consensus 24 a~~la~~~Gld~~~~~~vl~~~~~~s~--------~~~~~~~~~~~~~~~~~----------~-----f~l~~~~-KDl~ 79 (122)
T PF14833_consen 24 ALALAEKAGLDPEQLLDVLSAGSGGSW--------MLKNRAPRMILNGDFDP----------G-----FSLDLAR-KDLR 79 (122)
T ss_dssp HHHHHHHTTS-HHHHHHHHHTSTTHBH--------HHHHHHHHHHHTTTTCS----------S-----SBHHHHH-HHHH
T ss_pred HHHHHHHhCCCHHHHHHHHccCCcCch--------HHHhhhhhhhhcccCCc----------c-----chhHhhc-cHHH
Confidence 578999999999999999976666552 23455544344443321 1 3345553 7788
Q ss_pred HHHHHHHhcCchHHHHHHhhhcchHHHHHHhhcc
Q 009000 234 AAEKWATFMGKPILLKRLAEKACWDIAEAKTKGD 267 (547)
Q Consensus 234 ~a~~~~~~~~~~~~~~~l~~k~~wd~a~~~~~~D 267 (547)
.+.+.|...|.|+-+-.++ ...|+.|...=..|
T Consensus 80 l~~~~a~~~g~~~p~~~~~-~~~~~~a~~~g~g~ 112 (122)
T PF14833_consen 80 LALDLAKEAGVPLPLGSAA-RQLYQAAKAQGGGD 112 (122)
T ss_dssp HHHHHHHHTT---HHHHHH-HHHHHHHHHTTTTT
T ss_pred HHHHHHHHcCCCCHHHHHH-HHHHHHHHhcCCCC
Confidence 8999999999886544544 35566666554444
No 106
>PRK06424 transcription factor; Provisional
Probab=22.28 E-value=1.2e+02 Score=28.72 Aligned_cols=55 Identities=16% Similarity=0.132 Sum_probs=45.7
Q ss_pred HHHHHhhhcccCCccchhHHHHHHHHHHHHHhcCCCCChhHHHHHHHHHhcccccch
Q 009000 112 ISALRRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDI 168 (547)
Q Consensus 112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~l~e~f~~~~~~~ 168 (547)
|..+|.-. .-+|+++-+.-.+...++-.|-.|........+.+|.+.||+++++.
T Consensus 89 Ir~lRe~~--GLSQ~eLA~~iGvs~stIskiE~G~~~Ps~~~l~kLa~~Lgvsl~e~ 143 (144)
T PRK06424 89 VKNARERL--SMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGITLIEK 143 (144)
T ss_pred HHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCCCC
Confidence 45566533 34589998888888899999999999989999999999999998763
No 107
>PRK08359 transcription factor; Validated
Probab=22.11 E-value=1.1e+02 Score=29.98 Aligned_cols=57 Identities=12% Similarity=0.109 Sum_probs=48.4
Q ss_pred HHHHHHhhhcccCCccchhHHHHHHHHHHHHHhcCCCCChhHHHHHHHHHhcccccchH
Q 009000 111 IISALRRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDIE 169 (547)
Q Consensus 111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~l~e~f~~~~~~~~ 169 (547)
.|-.+|. +..-+|+++-+.-++...++--|=.|..+....++.||...|||+|....
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 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=21.55 E-value=2.3e+02 Score=21.50 Aligned_cols=34 Identities=18% Similarity=0.218 Sum_probs=19.6
Q ss_pred HHHhhcchhHHHHHHHHhhccCCHHHHHHHHHHc
Q 009000 261 EAKTKGDKRLLEYLVYLAMEAGYSEKVDELCERY 294 (547)
Q Consensus 261 ~~~~~~D~~l~~~lv~L~~~~~d~~~L~~l~~ry 294 (547)
...-.++.+....+.....+.++.++..+.++++
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 3334455566666666666666666666666543
No 109
>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=20.57 E-value=80 Score=29.83 Aligned_cols=8 Identities=25% Similarity=0.895 Sum_probs=5.4
Q ss_pred Cceeeeee
Q 009000 86 PATFIVRC 93 (547)
Q Consensus 86 ~~~~~~~~ 93 (547)
|+.||+|+
T Consensus 67 ~~~~IiH~ 74 (165)
T cd02908 67 PAKYVIHT 74 (165)
T ss_pred CCCEEEEE
Confidence 46677775
No 110
>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=20.31 E-value=1.1e+02 Score=30.72 Aligned_cols=63 Identities=19% Similarity=0.204 Sum_probs=41.0
Q ss_pred hhhHHHhh----cCCCCCHHHHHHHHhCCCCC--CCcccc-cCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009000 436 LLDIQNVF----KEPKGGLSGLAEKILGAGLN--KTRRNS-NWEQRPLSQNQLEYAALDAVVLLQIFHHV 498 (547)
Q Consensus 436 vfDtmLAl----~~~~~gLd~LAer~Lg~~L~--K~e~~S-dW~~rpLt~~Qi~YAAeDA~vlLrL~~~L 498 (547)
++|+.... ...+++|+++++.+||..-. ..+... -|....--..-++|...||..+++|...|
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 25689999999999996321 111222 23321111223789999999999998876
Done!