Query 037872
Match_columns 146
No_of_seqs 123 out of 1054
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 05:12:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037872.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037872hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK08517 DNA polymerase III su 99.9 1.7E-23 3.6E-28 160.2 12.6 127 1-144 127-256 (257)
2 PRK06195 DNA polymerase III su 99.9 3.6E-22 7.9E-27 156.6 13.1 113 1-130 60-173 (309)
3 PRK06063 DNA polymerase III su 99.9 2.3E-22 5E-27 157.9 10.5 107 1-123 74-180 (313)
4 PRK06309 DNA polymerase III su 99.9 8.5E-22 1.9E-26 148.9 12.5 122 1-136 59-181 (232)
5 TIGR01406 dnaQ_proteo DNA poly 99.9 4.2E-22 9.2E-27 150.0 10.8 108 1-123 62-173 (225)
6 PRK09146 DNA polymerase III su 99.9 6.7E-22 1.4E-26 150.1 11.5 118 1-130 109-238 (239)
7 PRK05711 DNA polymerase III su 99.9 7.8E-22 1.7E-26 149.7 10.7 106 1-121 66-175 (240)
8 COG2176 PolC DNA polymerase II 99.9 5.9E-22 1.3E-26 171.7 9.4 128 1-144 481-612 (1444)
9 PRK06310 DNA polymerase III su 99.9 2.3E-21 5.1E-26 148.0 11.7 120 1-136 67-187 (250)
10 PRK07748 sporulation inhibitor 99.9 1.6E-21 3.4E-26 145.1 10.1 120 1-133 72-198 (207)
11 cd06131 DNA_pol_III_epsilon_Ec 99.9 3.7E-21 8.1E-26 138.1 10.8 103 1-118 61-166 (167)
12 cd06130 DNA_pol_III_epsilon_li 99.9 3.3E-21 7.3E-26 136.5 10.1 99 1-116 57-155 (156)
13 TIGR00573 dnaq exonuclease, DN 99.9 6.9E-21 1.5E-25 142.6 11.6 111 1-123 67-178 (217)
14 PRK07740 hypothetical protein; 99.9 7.7E-21 1.7E-25 144.7 11.5 115 1-131 121-239 (244)
15 PRK07942 DNA polymerase III su 99.8 1.5E-20 3.3E-25 142.1 12.7 119 7-132 72-194 (232)
16 PRK06807 DNA polymerase III su 99.8 5.5E-21 1.2E-25 150.0 10.6 105 1-122 68-172 (313)
17 PRK07883 hypothetical protein; 99.8 1.4E-20 3E-25 157.6 12.4 117 1-131 75-195 (557)
18 TIGR01298 RNaseT ribonuclease 99.8 5.4E-20 1.2E-24 136.3 11.3 113 1-123 76-193 (200)
19 cd06134 RNaseT DEDDh 3'-5' exo 99.8 8.9E-20 1.9E-24 134.0 12.2 109 6-122 76-189 (189)
20 PRK05168 ribonuclease T; Provi 99.8 1.1E-19 2.4E-24 135.7 12.2 110 6-123 88-202 (211)
21 smart00479 EXOIII exonuclease 99.8 9.3E-20 2E-24 130.2 11.2 107 2-122 61-167 (169)
22 PRK08074 bifunctional ATP-depe 99.8 8.3E-20 1.8E-24 160.5 12.5 115 1-131 64-182 (928)
23 PRK07246 bifunctional ATP-depe 99.8 1.7E-19 3.6E-24 156.7 12.4 114 1-131 66-183 (820)
24 PRK06722 exonuclease; Provisio 99.8 1E-19 2.2E-24 140.6 9.8 109 1-121 70-180 (281)
25 TIGR01405 polC_Gram_pos DNA po 99.8 3.1E-19 6.7E-24 159.0 12.4 115 1-131 250-368 (1213)
26 TIGR01407 dinG_rel DnaQ family 99.8 3.5E-19 7.7E-24 155.5 12.5 115 1-131 60-178 (850)
27 PRK09145 DNA polymerase III su 99.8 4.3E-19 9.2E-24 131.5 11.1 107 1-120 91-199 (202)
28 cd06136 TREX1_2 DEDDh 3'-5' ex 99.8 7.1E-19 1.5E-23 128.0 10.8 102 1-117 73-176 (177)
29 PRK07983 exodeoxyribonuclease 99.8 1.7E-18 3.8E-23 129.8 11.4 111 1-139 57-171 (219)
30 cd06133 ERI-1_3'hExo_like DEDD 99.8 3.6E-18 7.7E-23 123.1 10.8 107 1-119 68-176 (176)
31 cd06138 ExoI_N N-terminal DEDD 99.8 2.4E-18 5.3E-23 125.7 9.3 106 1-115 61-182 (183)
32 cd06127 DEDDh DEDDh 3'-5' exon 99.8 7.4E-18 1.6E-22 118.2 10.3 97 6-116 62-159 (159)
33 PRK07247 DNA polymerase III su 99.8 1.1E-17 2.4E-22 123.5 11.2 104 1-123 64-170 (195)
34 PRK05601 DNA polymerase III su 99.8 1E-17 2.2E-22 132.8 11.4 107 1-121 105-248 (377)
35 PRK00448 polC DNA polymerase I 99.7 2E-17 4.3E-22 149.2 13.5 115 1-131 479-597 (1437)
36 cd06145 REX1_like DEDDh 3'-5' 99.7 5.3E-18 1.2E-22 120.4 6.8 93 1-116 54-150 (150)
37 cd06144 REX4_like DEDDh 3'-5' 99.7 3.8E-18 8.1E-23 121.3 5.5 95 1-116 57-152 (152)
38 cd06149 ISG20 DEDDh 3'-5' exon 99.7 7.9E-18 1.7E-22 120.3 5.9 94 1-116 57-157 (157)
39 COG0847 DnaQ DNA polymerase II 99.7 1.3E-16 2.9E-21 120.8 11.1 107 1-121 74-181 (243)
40 cd06137 DEDDh_RNase DEDDh 3'-5 99.7 7.1E-17 1.5E-21 115.8 4.6 89 10-116 70-161 (161)
41 PTZ00315 2'-phosphotransferase 99.7 9.3E-16 2E-20 127.6 11.1 119 1-123 123-256 (582)
42 PRK09182 DNA polymerase III su 99.6 1.7E-15 3.7E-20 118.1 8.6 115 1-138 103-218 (294)
43 PF00929 RNase_T: Exonuclease; 99.6 1.9E-17 4.2E-22 116.3 -4.8 99 6-115 65-164 (164)
44 cd06135 Orn DEDDh 3'-5' exonuc 99.6 7.9E-15 1.7E-19 106.3 8.2 101 1-121 68-171 (173)
45 COG5018 KapD Inhibitor of the 99.5 1.2E-13 2.7E-18 98.2 10.2 111 2-121 73-184 (210)
46 PRK11779 sbcB exonuclease I; P 99.5 8.8E-14 1.9E-18 114.5 10.2 108 8-121 76-197 (476)
47 KOG0542 Predicted exonuclease 99.5 2.4E-13 5.2E-18 102.2 10.1 121 1-129 125-250 (280)
48 PRK05359 oligoribonuclease; Pr 99.5 1.9E-13 4E-18 99.9 9.1 101 1-122 72-175 (181)
49 cd05782 DNA_polB_like1_exo Unc 99.2 4.6E-11 9.9E-16 89.1 9.0 99 8-116 76-207 (208)
50 PF10108 DNA_pol_B_exo2: Predi 99.2 9.6E-11 2.1E-15 87.0 10.6 104 9-122 36-173 (209)
51 cd05160 DEDDy_DNA_polB_exo DED 99.2 3.6E-10 7.7E-15 83.2 9.8 83 6-97 59-162 (199)
52 cd05781 DNA_polB_B3_exo DEDDy 99.1 2.8E-09 6.2E-14 78.3 10.8 81 7-96 45-144 (188)
53 cd05785 DNA_polB_like2_exo Unc 99.1 2.7E-09 5.9E-14 79.5 10.7 86 7-97 55-169 (207)
54 cd05780 DNA_polB_Kod1_like_exo 99.0 7.8E-09 1.7E-13 76.2 10.9 82 8-98 54-157 (195)
55 cd05779 DNA_polB_epsilon_exo D 98.9 2E-08 4.4E-13 74.7 10.9 102 7-115 70-203 (204)
56 cd06125 DnaQ_like_exo DnaQ-lik 98.8 3.7E-08 8E-13 64.8 6.9 48 17-69 35-83 (96)
57 cd05783 DNA_polB_B1_exo DEDDy 98.7 4.4E-07 9.5E-12 67.5 10.9 84 8-97 71-171 (204)
58 KOG4793 Three prime repair exo 98.7 8.1E-08 1.8E-12 73.3 6.8 137 1-137 169-306 (318)
59 cd05784 DNA_polB_II_exo DEDDy 98.6 1E-06 2.2E-11 65.0 11.4 79 8-95 49-152 (193)
60 COG2925 SbcB Exonuclease I [DN 98.6 2.7E-07 5.8E-12 73.6 8.6 107 10-122 81-201 (475)
61 cd06139 DNA_polA_I_Ecoli_like_ 98.6 3.5E-07 7.6E-12 66.4 8.6 109 8-132 50-182 (193)
62 cd05777 DNA_polB_delta_exo DED 98.6 1.3E-06 2.8E-11 66.0 11.6 103 8-119 69-224 (230)
63 PF13482 RNase_H_2: RNase_H su 98.5 2E-07 4.3E-12 66.4 4.8 74 11-98 44-117 (164)
64 cd06143 PAN2_exo DEDDh 3'-5' e 98.5 6.8E-07 1.5E-11 64.8 6.8 88 8-116 86-174 (174)
65 KOG2249 3'-5' exonuclease [Rep 98.4 1.3E-06 2.9E-11 66.5 8.3 98 6-123 167-267 (280)
66 cd05776 DNA_polB_alpha_exo ina 98.4 7.4E-06 1.6E-10 62.1 11.0 82 8-98 80-188 (234)
67 PRK05762 DNA polymerase II; Re 98.3 9.7E-06 2.1E-10 71.1 12.5 103 8-118 201-348 (786)
68 PRK05755 DNA polymerase I; Pro 98.3 1.9E-06 4E-11 76.4 7.2 95 12-123 357-470 (880)
69 KOG4793 Three prime repair exo 98.2 1.3E-05 2.9E-10 61.4 9.5 108 12-123 105-219 (318)
70 PF04857 CAF1: CAF1 family rib 98.0 1.2E-05 2.7E-10 61.8 6.3 78 30-117 149-262 (262)
71 cd05778 DNA_polB_zeta_exo inac 98.0 0.00018 4E-09 54.4 12.0 107 8-123 79-224 (231)
72 COG3359 Predicted exonuclease 98.0 8E-05 1.7E-09 56.5 9.2 65 30-98 156-220 (278)
73 PHA02528 43 DNA polymerase; Pr 97.9 0.0002 4.2E-09 63.6 11.3 103 8-117 176-323 (881)
74 PF01612 DNA_pol_A_exo1: 3'-5' 97.9 3.9E-05 8.5E-10 54.5 5.7 93 13-122 65-175 (176)
75 KOG0304 mRNA deadenylase subun 97.8 7.9E-05 1.7E-09 55.5 7.1 87 29-120 141-237 (239)
76 cd06146 mut-7_like_exo DEDDy 3 97.8 0.00014 2.9E-09 53.6 7.9 100 15-120 72-193 (193)
77 PTZ00166 DNA polymerase delta 97.8 0.00031 6.6E-09 63.6 11.5 103 8-119 328-483 (1054)
78 PHA02524 43A DNA polymerase su 97.8 0.00025 5.4E-09 59.2 9.9 100 8-115 178-321 (498)
79 smart00486 POLBc DNA polymeras 97.7 0.00089 1.9E-08 54.6 11.7 101 9-118 68-220 (471)
80 cd00007 35EXOc 3'-5' exonuclea 97.6 0.00054 1.2E-08 47.3 8.2 94 11-120 40-153 (155)
81 PRK05761 DNA polymerase I; Rev 97.5 0.0011 2.4E-08 58.4 10.3 102 8-115 208-334 (787)
82 PF03104 DNA_pol_B_exo1: DNA p 97.5 0.00077 1.7E-08 52.7 8.2 73 8-89 220-325 (325)
83 cd06129 RNaseD_like DEDDy 3'-5 97.3 0.00071 1.5E-08 48.2 6.2 90 13-119 55-160 (161)
84 PRK10829 ribonuclease D; Provi 97.3 0.0019 4E-08 52.3 8.3 93 14-123 63-171 (373)
85 COG0417 PolB DNA polymerase el 97.2 0.0035 7.6E-08 55.4 10.3 101 9-118 210-350 (792)
86 cd06141 WRN_exo DEDDy 3'-5' ex 97.2 0.0015 3.3E-08 46.6 6.7 91 13-119 61-169 (170)
87 smart00474 35EXOc 3'-5' exonuc 97.1 0.0089 1.9E-07 41.9 9.4 93 13-122 63-171 (172)
88 COG1949 Orn Oligoribonuclease 97.0 0.00059 1.3E-08 48.9 2.9 86 7-111 79-167 (184)
89 KOG1798 DNA polymerase epsilon 97.0 0.011 2.4E-07 54.7 11.1 111 6-120 313-452 (2173)
90 TIGR00592 pol2 DNA polymerase 96.9 0.012 2.7E-07 54.1 11.4 101 9-118 583-722 (1172)
91 PHA02570 dexA exonuclease; Pro 96.9 0.0066 1.4E-07 45.6 7.8 99 6-113 84-190 (220)
92 KOG3242 Oligoribonuclease (3'- 96.8 0.0071 1.5E-07 43.9 6.8 89 6-112 98-189 (208)
93 COG0349 Rnd Ribonuclease D [Tr 96.7 0.015 3.3E-07 46.7 8.8 93 14-123 59-167 (361)
94 TIGR00593 pola DNA polymerase 96.5 0.007 1.5E-07 54.1 6.1 97 10-123 363-478 (887)
95 cd06142 RNaseD_exo DEDDy 3'-5' 96.4 0.052 1.1E-06 38.6 9.5 101 13-130 52-169 (178)
96 TIGR01388 rnd ribonuclease D. 96.2 0.039 8.5E-07 44.6 8.4 93 14-123 59-167 (367)
97 cd06140 DNA_polA_I_Bacillus_li 96.1 0.058 1.3E-06 38.5 8.5 102 13-130 44-165 (178)
98 TIGR03491 RecB family nuclease 95.9 0.045 9.7E-07 45.5 8.0 81 9-98 327-411 (457)
99 COG5228 POP2 mRNA deadenylase 95.9 0.014 2.9E-07 44.0 4.4 87 29-122 157-253 (299)
100 cd06148 Egl_like_exo DEDDy 3'- 95.9 0.072 1.6E-06 39.2 8.3 98 14-123 54-178 (197)
101 KOG2248 3'-5' exonuclease [Rep 95.7 0.016 3.4E-07 47.0 4.3 93 9-121 279-374 (380)
102 PHA03036 DNA polymerase; Provi 95.6 0.056 1.2E-06 48.8 7.6 110 9-128 240-399 (1004)
103 KOG3657 Mitochondrial DNA poly 94.7 0.033 7.1E-07 49.1 3.5 90 28-122 239-383 (1075)
104 KOG1275 PAB-dependent poly(A) 94.5 0.037 8E-07 49.1 3.2 91 11-122 1001-1092(1118)
105 KOG0969 DNA polymerase delta, 94.1 0.11 2.3E-06 45.8 5.2 101 11-123 342-495 (1066)
106 cd09018 DEDDy_polA_RNaseD_like 92.8 0.79 1.7E-05 31.3 7.2 67 14-96 42-109 (150)
107 cd06147 Rrp6p_like_exo DEDDy 3 92.8 0.43 9.2E-06 34.7 6.0 91 15-123 67-173 (192)
108 COG0749 PolA DNA polymerase I 90.2 2.3 4.9E-05 36.7 8.4 97 10-123 63-181 (593)
109 PHA02563 DNA polymerase; Provi 87.3 2.7 5.9E-05 36.5 7.1 44 11-55 47-90 (630)
110 cd06128 DNA_polA_exo DEDDy 3'- 75.4 14 0.0003 25.4 6.0 67 14-96 42-109 (151)
111 PF11074 DUF2779: Domain of un 64.7 15 0.00032 25.4 4.2 60 6-73 53-118 (130)
112 KOG0970 DNA polymerase alpha, 64.1 18 0.00038 33.9 5.4 99 11-118 608-751 (1429)
113 TIGR00592 pol2 DNA polymerase 51.4 8.9 0.00019 35.9 1.6 37 8-48 268-304 (1172)
114 COG1850 RbcL Ribulose 1,5-bisp 49.4 35 0.00077 28.2 4.5 99 8-122 200-307 (429)
115 PF09281 Taq-exonuc: Taq polym 41.9 1.2E+02 0.0026 21.2 5.8 68 42-121 69-137 (138)
116 COG2251 Predicted nuclease (Re 38.6 64 0.0014 27.2 4.5 95 12-117 340-438 (474)
117 PF01388 ARID: ARID/BRIGHT DNA 33.5 1.2E+02 0.0026 18.9 4.8 54 62-120 34-89 (92)
118 COG3545 Predicted esterase of 32.3 98 0.0021 22.7 4.2 32 4-38 37-68 (181)
119 PRK04946 hypothetical protein; 29.4 1.1E+02 0.0025 22.3 4.2 42 9-53 104-145 (181)
120 PRK06193 hypothetical protein; 29.2 89 0.0019 23.3 3.7 29 10-38 137-165 (206)
121 PF06056 Terminase_5: Putative 29.1 79 0.0017 18.5 2.8 27 66-98 2-28 (58)
122 KOG2207 Predicted 3'-5' exonuc 27.5 2.3E+02 0.005 24.8 6.2 107 12-123 458-586 (617)
123 PRK14118 gpmA phosphoglyceromu 24.7 75 0.0016 23.6 2.6 34 5-38 146-183 (227)
124 COG1102 Cmk Cytidylate kinase 24.5 1.2E+02 0.0026 22.2 3.5 46 81-137 11-57 (179)
125 PHA02683 ORF078 thioredoxin-li 24.3 60 0.0013 20.2 1.6 32 6-52 41-72 (75)
126 PF11288 DUF3089: Protein of u 23.6 1.3E+02 0.0029 22.4 3.7 29 9-38 76-104 (207)
127 PF10668 Phage_terminase: Phag 23.4 1.3E+02 0.0029 17.8 3.0 27 68-97 10-36 (60)
128 PF06361 RTBV_P12: Rice tungro 22.9 64 0.0014 20.6 1.6 21 1-23 1-21 (110)
129 PHA02901 virus redox protein; 22.5 67 0.0015 20.0 1.6 32 6-52 41-72 (75)
130 PRK13462 acid phosphatase; Pro 22.2 1.5E+02 0.0032 21.6 3.8 34 5-38 114-149 (203)
131 PRK14117 gpmA phosphoglyceromu 22.1 1.3E+02 0.0028 22.4 3.5 34 5-38 147-184 (230)
132 PF12083 DUF3560: Domain of un 21.9 70 0.0015 22.0 1.8 39 11-54 29-67 (126)
133 PRK14975 bifunctional 3'-5' ex 21.5 2.3E+02 0.005 24.3 5.2 73 46-123 58-145 (553)
134 PF01726 LexA_DNA_bind: LexA D 21.1 39 0.00085 20.2 0.4 30 66-98 11-40 (65)
No 1
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.91 E-value=1.7e-23 Score=160.23 Aligned_cols=127 Identities=27% Similarity=0.386 Sum_probs=111.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||. ++|+|.+|+.+|.+|+++ .++||||+ +||++||.+++.+++.+.... +++||+.+++..++.
T Consensus 127 ~l~--~ap~~~evl~~f~~fl~~-------~v~VaHNa-~FD~~fL~~~l~r~g~~~~~~-~~ldtl~la~~~~~~---- 191 (257)
T PRK08517 127 DLE--NAPSLKEVLEEFRLFLGD-------SVFVAHNV-NFDYNFISRSLEEIGLGPLLN-RKLCTIDLAKRTIES---- 191 (257)
T ss_pred HHc--CCCCHHHHHHHHHHHHCC-------CeEEEECH-HHHHHHHHHHHHHcCCCCCCC-CcEehHHHHHHHccC----
Confidence 466 899999999999999975 69999999 999999999999999876544 789999999988753
Q ss_pred CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh---cCHHHHHHhhcccccccccCC
Q 037872 81 SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN---FTLSDLLKTSFRANFDHSKKN 144 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~---~~~~~l~~~~~~~~~~~~~~~ 144 (146)
.+++|+++++++|++.+ .+|+|++||.+|++||..++.++. .++.+|++-+-++..+.++++
T Consensus 192 -~~~~L~~L~~~lgi~~~-~~HrAl~DA~ata~ll~~ll~~~~~~~~t~~~L~~~~k~~~~~~~~~~ 256 (257)
T PRK08517 192 -PRYGLSFLKELLGIEIE-VHHRAYADALAAYEIFKICLLNLPSYIKTTEDLIDFSKTAKTLKKKKP 256 (257)
T ss_pred -CCCCHHHHHHHcCcCCC-CCCChHHHHHHHHHHHHHHHHHhHHhhcCHHHHHHHhhhcccccCCCC
Confidence 57899999999999988 599999999999999999998875 488999988888888877665
No 2
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.88 E-value=3.6e-22 Score=156.62 Aligned_cols=113 Identities=23% Similarity=0.463 Sum_probs=99.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||+ ++|+|.+++++|.+|+.+ .++||||+ +||++||++++.+++.+++.. .++||+.+++.+++.
T Consensus 60 ~v~--~ap~f~ev~~~~~~fl~~-------~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~-~~idT~~lar~l~~~---- 124 (309)
T PRK06195 60 MVE--DELEFDKIWEKIKHYFNN-------NLVIAHNA-SFDISVLRKTLELYNIPMPSF-EYICTMKLAKNFYSN---- 124 (309)
T ss_pred HHh--CCCCHHHHHHHHHHHhCC-------CEEEEECc-HHHHHHHHHHHHHhCCCCCCC-CEEEHHHHHHHHcCC----
Confidence 677 899999999999999975 69999999 999999999999999887754 899999999999874
Q ss_pred CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh-cCHHHHH
Q 037872 81 SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN-FTLSDLL 130 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~-~~~~~l~ 130 (146)
..+++|.+++++||++. .+|+|++||.+|++||..+..+.+ .++.++.
T Consensus 125 ~~~~~L~~L~~~~gi~~--~~H~Al~DA~ata~l~~~l~~~~~~~~~~~l~ 173 (309)
T PRK06195 125 IDNARLNTVNNFLGYEF--KHHDALADAMACSNILLNISKELNSKDINEIS 173 (309)
T ss_pred CCcCCHHHHHHHcCCCC--cccCCHHHHHHHHHHHHHHHHHhccCCHHHHH
Confidence 47899999999999985 499999999999999999998876 3444443
No 3
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.88 E-value=2.3e-22 Score=157.90 Aligned_cols=107 Identities=30% Similarity=0.448 Sum_probs=96.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||+ ++|+|.+++++|.+|+++ .++||||+ +||++||++++.+++.+.+.. .++||+.+++.+++.
T Consensus 74 ~l~--~ap~f~ev~~~l~~~l~~-------~~lVaHNa-~FD~~fL~~~~~r~g~~~~~~-~~ldTl~lar~~~~~---- 138 (313)
T PRK06063 74 MLE--GQPQFADIAGEVAELLRG-------RTLVAHNV-AFDYSFLAAEAERAGAELPVD-QVMCTVELARRLGLG---- 138 (313)
T ss_pred HHh--CCCCHHHHHHHHHHHcCC-------CEEEEeCH-HHHHHHHHHHHHHcCCCCCCC-CEEehHHHHHHhccC----
Confidence 577 899999999999999975 69999999 999999999999999887754 689999999988653
Q ss_pred CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh
Q 037872 81 SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN 123 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~ 123 (146)
..+++|.+++++||++.. ++|+|++||.+|++||..+++..+
T Consensus 139 ~~~~kL~~l~~~~gi~~~-~~H~Al~DA~ata~l~~~ll~~~~ 180 (313)
T PRK06063 139 LPNLRLETLAAHWGVPQQ-RPHDALDDARVLAGILRPSLERAR 180 (313)
T ss_pred CCCCCHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999987 599999999999999999988764
No 4
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.88 E-value=8.5e-22 Score=148.91 Aligned_cols=122 Identities=32% Similarity=0.497 Sum_probs=102.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||+ ++|+|.+++++|.+|+.+ ..++||||+.+||++||.+++.+++++.+. +.++||+.+++.+++.
T Consensus 59 ~v~--~~p~f~ev~~~~~~fi~~------~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~-~~~iDt~~l~~~~~~~---- 125 (232)
T PRK06309 59 EVA--DAPKFPEAYQKFIEFCGT------DNILVAHNNDAFDFPLLRKECRRHGLEPPT-LRTIDSLKWAQKYRPD---- 125 (232)
T ss_pred HHh--CCCCHHHHHHHHHHHHcC------CCEEEEeCCHHHHHHHHHHHHHHcCCCCCC-CcEEeHHHHHHHHcCC----
Confidence 678 999999999999999974 369999993279999999999999988765 5899999999988763
Q ss_pred CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhhc-CHHHHHHhhccc
Q 037872 81 SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLNF-TLSDLLKTSFRA 136 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~~-~~~~l~~~~~~~ 136 (146)
..+++|..++++||++.. .+|+|++||.+|++||.+++.++.. .+.++...+..|
T Consensus 126 ~~~~~L~~l~~~~~~~~~-~aH~Al~Da~~t~~vl~~l~~~~~~~~l~~l~~~~~~~ 181 (232)
T PRK06309 126 LPKHNLQYLRQVYGFEEN-QAHRALDDVITLHRVFSALVGDLSPQQVYDLLNESCHP 181 (232)
T ss_pred CCCCCHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHHHHHHhhHHHHHHhhccC
Confidence 357899999999999987 5999999999999999999988762 455555444444
No 5
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=99.88 E-value=4.2e-22 Score=149.95 Aligned_cols=108 Identities=29% Similarity=0.445 Sum_probs=93.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCC---CCcceeecHHHHHHHHhhC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIP---DNWRFLDTLPLARELMKQN 77 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~---~~~~~iDt~~l~~~~~~~~ 77 (146)
||+ ++|+|.+++++|.+|+++ .++||||+ +||++||++++.++|...+ ..+.++||+.+++..+|.
T Consensus 62 ~l~--~~p~f~ev~~~f~~fi~~-------~~lVaHNa-~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~- 130 (225)
T TIGR01406 62 FLA--DKPKFKEIADEFLDFIGG-------SELVIHNA-AFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPG- 130 (225)
T ss_pred HHh--CCCCHHHHHHHHHHHhCC-------CEEEEEec-HHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCC-
Confidence 567 889999999999999975 58999999 9999999999999984322 124799999999998873
Q ss_pred CCCCCCCcHHHHHHHhCCCCCC-CCCchHHHHHHHHHHHHHHHhhhh
Q 037872 78 GSVSSKTSLQALREYFGIPLEG-SAHRAMSDVNSLASILERITSDLN 123 (146)
Q Consensus 78 ~~~~~~~~L~~l~~~~gi~~~~-~~H~Al~Da~~ta~l~~~l~~~~~ 123 (146)
.+++|+++|++||++.++ .+|+|+.||.+|++||..|.....
T Consensus 131 ----~~~~L~~L~~~~gi~~~~r~~H~Al~DA~~~a~v~~~l~~~~~ 173 (225)
T TIGR01406 131 ----QRNSLDALCKRFKVDNSHRTLHGALLDAHLLAEVYLALTGGQE 173 (225)
T ss_pred ----CCCCHHHHHHhcCCCCCCCCCcCHHHHHHHHHHHHHHHHcCCc
Confidence 568999999999998764 479999999999999999987654
No 6
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.88 E-value=6.7e-22 Score=150.05 Aligned_cols=118 Identities=19% Similarity=0.329 Sum_probs=98.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhC---
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQN--- 77 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~--- 77 (146)
||. ++|+|.+++.+|.+|+.+ .++||||+ +||++||++++.+++..... .+++||+.+++.+++..
T Consensus 109 ~l~--~ap~~~evl~~l~~~~~~-------~~lVaHna-~FD~~fL~~~l~~~~~~~~~-~~~iDTl~Lar~l~~~~~~~ 177 (239)
T PRK09146 109 ELQ--DAPDLERILDELLEALAG-------KVVVVHYR-RIERDFLDQALRNRIGEGIE-FPVIDTMEIEARIQRKQAGG 177 (239)
T ss_pred HHh--CCCCHHHHHHHHHHHhCC-------CEEEEECH-HHHHHHHHHHHHHhcCCCCC-CceechHHHHHHHccccccc
Confidence 466 899999999999999975 69999999 99999999999886433222 37899999999987532
Q ss_pred ------CCCCCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh---cCHHHHH
Q 037872 78 ------GSVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN---FTLSDLL 130 (146)
Q Consensus 78 ------~~~~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~---~~~~~l~ 130 (146)
+.+..+++|.+++++||++.. .+|+|++||.+|++||..++.... +++++|+
T Consensus 178 ~~~~~~~~~~~~~~L~~l~~~~gl~~~-~~H~Al~DA~ata~l~~~~~~~~~~~~~~~~~l~ 238 (239)
T PRK09146 178 LWNRLKGKKPESIRLADSRLRYGLPAY-SPHHALTDAIATAELLQAQIAHHFSPDTPISKLW 238 (239)
T ss_pred ccchhccCCCCCCCHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHHHHcCCCCCHHHHh
Confidence 111267899999999999987 599999999999999999987764 5788775
No 7
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.87 E-value=7.8e-22 Score=149.67 Aligned_cols=106 Identities=27% Similarity=0.466 Sum_probs=92.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCC---CcceeecHHHHHHHHhhC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPD---NWRFLDTLPLARELMKQN 77 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~---~~~~iDt~~l~~~~~~~~ 77 (146)
||. ++|+|.+++++|.+|+++ .++||||+ .||++||++++.+++...+. ...++||+.+++.++|.
T Consensus 66 ~l~--~~p~f~ev~~~f~~fi~~-------~~lVaHNa-~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~- 134 (240)
T PRK05711 66 FLA--DKPTFAEVADEFLDFIRG-------AELIIHNA-PFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPG- 134 (240)
T ss_pred HHc--CCCCHHHHHHHHHHHhCC-------CEEEEEcc-HHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCC-
Confidence 567 899999999999999975 58999999 99999999999999855542 14689999999999873
Q ss_pred CCCCCCCcHHHHHHHhCCCCCC-CCCchHHHHHHHHHHHHHHHhh
Q 037872 78 GSVSSKTSLQALREYFGIPLEG-SAHRAMSDVNSLASILERITSD 121 (146)
Q Consensus 78 ~~~~~~~~L~~l~~~~gi~~~~-~~H~Al~Da~~ta~l~~~l~~~ 121 (146)
.+++|+++|++||++.++ ..|+|+.||.+|++||.+|...
T Consensus 135 ----~~~~L~aL~~~~gi~~~~r~~H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 135 ----KRNSLDALCKRYGIDNSHRTLHGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred ----CCCCHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCc
Confidence 467999999999998764 4799999999999999999876
No 8
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.86 E-value=5.9e-22 Score=171.72 Aligned_cols=128 Identities=27% Similarity=0.417 Sum_probs=110.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||+ ++++..+|+.+|.+|+.+ .++||||+ +||++||+..++++++.... .++|||+.++|.++|.
T Consensus 481 ml~--~a~~i~~vL~kf~~~~~d-------~IlVAHNa-sFD~gFl~~~~~k~~~~~~~-~pvIDTL~lar~L~P~---- 545 (1444)
T COG2176 481 MLE--NAPEIEEVLEKFREFIGD-------SILVAHNA-SFDMGFLNTNYEKYGLEPLT-NPVIDTLELARALNPE---- 545 (1444)
T ss_pred HHc--CCccHHHHHHHHHHHhcC-------cEEEeccC-ccchhHHHHHHHHhCCcccc-CchhhHHHHHHHhChh----
Confidence 788 999999999999999975 79999999 99999999999999887554 4899999999999986
Q ss_pred CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh----cCHHHHHHhhcccccccccCC
Q 037872 81 SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN----FTLSDLLKTSFRANFDHSKKN 144 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~----~~~~~l~~~~~~~~~~~~~~~ 144 (146)
.++++|..+|+.||+..+ .+|||.+||.+|+.||..+++++. +++.++-....+...+++-++
T Consensus 546 ~ksh~Lg~l~kk~~v~le-~hHRA~yDaeat~~vf~~f~~~~ke~Gi~~l~eln~~l~~~~~ykr~r~ 612 (1444)
T COG2176 546 FKSHRLGTLCKKLGVELE-RHHRADYDAEATAKVFFVFLKDLKEKGITNLSELNDKLSSEDLYKRLRP 612 (1444)
T ss_pred hhhcchHHHHHHhCccHH-HhhhhhhhHHHHHHHHHHHHHHHHHhchhhHHHHhHhhhhhHHHhhccc
Confidence 589999999999999998 699999999999999999998875 467776654444444444443
No 9
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.86 E-value=2.3e-21 Score=148.00 Aligned_cols=120 Identities=28% Similarity=0.478 Sum_probs=101.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCC-CcceeecHHHHHHHHhhCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPD-NWRFLDTLPLARELMKQNGS 79 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~-~~~~iDt~~l~~~~~~~~~~ 79 (146)
||+ ++|+|.+++++|.+|+.+ ..++||||+ +||+++|.+++.+++++++. .+.+|||+.+++.+ +.
T Consensus 67 ~v~--~~p~~~ev~~~~~~fl~~------~~~lvghn~-~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~-~~--- 133 (250)
T PRK06310 67 MLR--DKPKIAEVFPQIKGFFKE------GDYIVGHSV-GFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEY-GD--- 133 (250)
T ss_pred HHh--CCCCHHHHHHHHHHHhCC------CCEEEEECH-HHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhc-cc---
Confidence 567 899999999999999974 269999999 99999999999999988754 25899999999864 31
Q ss_pred CCCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhhcCHHHHHHhhccc
Q 037872 80 VSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLNFTLSDLLKTSFRA 136 (146)
Q Consensus 80 ~~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~~~~~~l~~~~~~~ 136 (146)
..+++|..++++||++..+ +|+|++||.+|++||..++..+. +++++++.+-.|
T Consensus 134 -~~~~~L~~l~~~~g~~~~~-aH~Al~Da~at~~vl~~l~~~~~-~~~~l~~~~~~~ 187 (250)
T PRK06310 134 -SPNNSLEALAVHFNVPYDG-NHRAMKDVEINIKVFKHLCKRFR-TLEQLKQILSKP 187 (250)
T ss_pred -CCCCCHHHHHHHCCCCCCC-CcChHHHHHHHHHHHHHHHHhcc-cHHHHHHHhhcC
Confidence 3579999999999999885 99999999999999999988765 456666655444
No 10
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.86 E-value=1.6e-21 Score=145.11 Aligned_cols=120 Identities=18% Similarity=0.196 Sum_probs=98.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||+ ++|+|.+|+++|.+|+.+. ..++| ||+ +||++||.+++++++++.|....++|+..+++.+++.
T Consensus 72 ~l~--~ap~~~evl~~f~~~~~~~-----~~~iv-~~~-~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~---- 138 (207)
T PRK07748 72 DVD--KGISFEELVEKLAEYDKRC-----KPTIV-TWG-NMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGE---- 138 (207)
T ss_pred HHc--cCCCHHHHHHHHHHHhCcC-----CeEEE-EEC-HHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCc----
Confidence 577 8999999999999999752 23455 557 8999999999999998766534789999888877753
Q ss_pred CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh-------cCHHHHHHhh
Q 037872 81 SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN-------FTLSDLLKTS 133 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~-------~~~~~l~~~~ 133 (146)
...++|.+++++||++..+.+|+|++||.+|++||.++..+.. .+++++++.|
T Consensus 139 ~~~~~L~~~~~~~gi~~~~~~H~Al~DA~~ta~l~~~l~~~~~~~~~~~~~~~~~~~~~~ 198 (207)
T PRK07748 139 RNQTGLWKAIEEYGKEGTGKHHCALDDAMTTYNIFKLVEKDKEYLVKPEPPTIGERVDFS 198 (207)
T ss_pred CCCCCHHHHHHHcCCCCCCCCcChHHHHHHHHHHHHHHHhCcceeecCCCCccccceeHH
Confidence 2568999999999999876789999999999999999998741 5888877643
No 11
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=99.86 E-value=3.7e-21 Score=138.08 Aligned_cols=103 Identities=32% Similarity=0.469 Sum_probs=88.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCC--CCcceeecHHHHHHHHhhCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIP--DNWRFLDTLPLARELMKQNG 78 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~--~~~~~iDt~~l~~~~~~~~~ 78 (146)
||+ ++|+|.+++.+|.+|+++ .++||||+ +||++||.+++.+++...+ ....++||+.+++.+++.
T Consensus 61 ~l~--~~~~~~~v~~~l~~~l~~-------~~lv~hn~-~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~-- 128 (167)
T cd06131 61 FLA--DKPKFAEIADEFLDFIRG-------AELVIHNA-SFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPG-- 128 (167)
T ss_pred HHh--cCCCHHHHHHHHHHHHCC-------CeEEEeCh-HHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCC--
Confidence 456 789999999999999975 58999999 9999999999999876432 235789999999988752
Q ss_pred CCCCCCcHHHHHHHhCCCCCC-CCCchHHHHHHHHHHHHHH
Q 037872 79 SVSSKTSLQALREYFGIPLEG-SAHRAMSDVNSLASILERI 118 (146)
Q Consensus 79 ~~~~~~~L~~l~~~~gi~~~~-~~H~Al~Da~~ta~l~~~l 118 (146)
..++|.+++++||++.++ .+|+|++||++|++||..|
T Consensus 129 ---~~~~L~~l~~~~~i~~~~~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 129 ---KPNSLDALCKRFGIDNSHRTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred ---CCCCHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHh
Confidence 467999999999999764 4899999999999999876
No 12
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=99.86 E-value=3.3e-21 Score=136.51 Aligned_cols=99 Identities=28% Similarity=0.459 Sum_probs=89.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||+ ++|+|.+++.+|.+|+++ .++||||+ +||+++|++++.++|+..+. ..++||+.+++..++.
T Consensus 57 ~l~--~~~~~~~v~~~l~~~l~~-------~~lv~hn~-~fD~~~l~~~~~~~g~~~~~-~~~idt~~~~~~~~~~---- 121 (156)
T cd06130 57 DVA--DAPTFPEVWPEIKPFLGG-------SLVVAHNA-SFDRSVLRAALEAYGLPPPP-YQYLCTVRLARRVWPL---- 121 (156)
T ss_pred HHh--cCCCHHHHHHHHHHHhCC-------CEEEEeCh-HHhHHHHHHHHHHcCCCCCC-CCEEEHHHHHHHHhcc----
Confidence 355 789999999999999975 69999999 99999999999999988765 4899999999998864
Q ss_pred CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHH
Q 037872 81 SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILE 116 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~ 116 (146)
.++++|.+++++||++.. +|+|++||++|++||.
T Consensus 122 ~~~~~L~~l~~~~g~~~~--~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 122 LPNHKLNTVAEHLGIELN--HHDALEDARACAEILL 155 (156)
T ss_pred CCCCCHHHHHHHcCCCcc--CcCchHHHHHHHHHHh
Confidence 478999999999999986 9999999999999985
No 13
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.85 E-value=6.9e-21 Score=142.63 Aligned_cols=111 Identities=26% Similarity=0.329 Sum_probs=94.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||. ++|+|.+++++|.+|+++ .++||||+ +||++||++++.+++...+..+.++||+.+++.+++.. .
T Consensus 67 ~l~--~~p~~~ev~~~~~~~~~~-------~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~--~ 134 (217)
T TIGR00573 67 MLK--DKPDFKEIAEDFADYIRG-------AELVIHNA-SFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEF--P 134 (217)
T ss_pred HHc--CCCCHHHHHHHHHHHhCC-------CEEEEecc-HHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhC--C
Confidence 466 889999999999999975 59999999 99999999999998655444457899999999888743 2
Q ss_pred CCCCcHHHHHHHhCCCCCC-CCCchHHHHHHHHHHHHHHHhhhh
Q 037872 81 SSKTSLQALREYFGIPLEG-SAHRAMSDVNSLASILERITSDLN 123 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~~-~~H~Al~Da~~ta~l~~~l~~~~~ 123 (146)
..+++|.+++++||++..+ .+|+|++||.+|++||..+..+..
T Consensus 135 ~~~~~L~~l~~~~gl~~~~~~~H~Al~DA~~ta~l~~~l~~~~~ 178 (217)
T TIGR00573 135 GKRNTLDALCKRYEITNSHRALHGALADAFILAKLYLVMTGKQT 178 (217)
T ss_pred CCCCCHHHHHHHcCCCCCCcccCCHHHHHHHHHHHHHHHHhcch
Confidence 3578999999999998762 489999999999999999988865
No 14
>PRK07740 hypothetical protein; Provisional
Probab=99.85 E-value=7.7e-21 Score=144.70 Aligned_cols=115 Identities=25% Similarity=0.437 Sum_probs=97.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||+ ++|+|.+++.+|.+|+.+ .++||||+ .||+.||.+++.+.... +....++||+.+++.+++.
T Consensus 121 ~l~--~ap~~~evl~~f~~fi~~-------~~lVahna-~fD~~fL~~~~~~~~~~-~~~~~~iDt~~l~r~l~~~---- 185 (244)
T PRK07740 121 DVA--FAPPLAEVLHRFYAFIGA-------GVLVAHHA-GHDKAFLRHALWRTYRQ-PFTHRLIDTMFLTKLLAHE---- 185 (244)
T ss_pred HHh--CCCCHHHHHHHHHHHhCC-------CEEEEeCH-HHHHHHHHHHHHHhcCC-CcCCCeechHHHHHHHcCC----
Confidence 356 899999999999999975 69999999 99999999998775322 2335899999999988763
Q ss_pred CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh----cCHHHHHH
Q 037872 81 SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN----FTLSDLLK 131 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~----~~~~~l~~ 131 (146)
.++++|++++++||++.++ +|+|++||.+|++||.+++...+ .++.+|+.
T Consensus 186 ~~~~sL~~l~~~~gi~~~~-~H~Al~Da~ata~l~~~ll~~~~~~~~~~~~dl~~ 239 (244)
T PRK07740 186 RDFPTLDDALAYYGIPIPR-RHHALGDALMTAKLWAILLVEAQQRGITTLHDLYA 239 (244)
T ss_pred CCCCCHHHHHHHCCcCCCC-CCCcHHHHHHHHHHHHHHHHHHHHcCCcCHHHHHH
Confidence 3689999999999999985 89999999999999999987764 47777764
No 15
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.85 E-value=1.5e-20 Score=142.12 Aligned_cols=119 Identities=18% Similarity=0.255 Sum_probs=96.1
Q ss_pred CCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcH
Q 037872 7 VPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSL 86 (146)
Q Consensus 7 ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L 86 (146)
++++.+++.+|.+++.+.. .++.++||||+ +||++||++++.+++.+.+...+++||+.+++.+.+.. .++++|
T Consensus 72 g~~~~~vl~e~~~~l~~~~--~~~~~lVahNa-~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~---~~~~~L 145 (232)
T PRK07942 72 GRPAAEVLAEIADALREAW--ARGVPVVVFNA-PYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYR---KGKRTL 145 (232)
T ss_pred CCCHHHHHHHHHHHHHHHh--hcCCEEEEeCc-HhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhccc---CCCCCH
Confidence 5667889999988884210 01368999999 99999999999999876543347899999998877632 257899
Q ss_pred HHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh----cCHHHHHHh
Q 037872 87 QALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN----FTLSDLLKT 132 (146)
Q Consensus 87 ~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~----~~~~~l~~~ 132 (146)
.+++++||++.++ +|+|++||.+|++||.++..++. .++.+|+..
T Consensus 146 ~~l~~~~gi~~~~-aH~Al~Da~ata~l~~~l~~~~~~l~~~~~~~l~~~ 194 (232)
T PRK07942 146 TALCEHYGVRLDN-AHEATADALAAARVAWALARRFPELAALSPAELHEL 194 (232)
T ss_pred HHHHHHcCCCCCC-CCChHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHH
Confidence 9999999999985 99999999999999999987654 577777653
No 16
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.85 E-value=5.5e-21 Score=149.99 Aligned_cols=105 Identities=30% Similarity=0.575 Sum_probs=94.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||+ ++|+|.+|+++|.+|+++ .++||||+ +||++||.+.+.++|++.+.. .++||+.+++.+++.
T Consensus 68 ~l~--~~~~~~evl~~f~~fl~~-------~~lVaHNa-~FD~~fL~~~~~~~gl~~~~~-~~iDtl~la~~~~~~---- 132 (313)
T PRK06807 68 RVS--DAPTIEEVLPLFLAFLHT-------NVIVAHNA-SFDMRFLKSNVNMLGLPEPKN-KVIDTVFLAKKYMKH---- 132 (313)
T ss_pred HHh--CCCCHHHHHHHHHHHHcC-------CeEEEEcH-HHHHHHHHHHHHHcCCCCCCC-CEeeHHHHHHHHhCC----
Confidence 566 889999999999999975 58999999 999999999999999877654 799999999998874
Q ss_pred CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhh
Q 037872 81 SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDL 122 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~ 122 (146)
.++++|.+++++||++. ++|+|++||.+|++||.++....
T Consensus 133 ~~~~kL~~L~~~lgi~~--~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 133 APNHKLETLKRMLGIRL--SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred CCCCCHHHHHHHcCCCC--CCcChHHHHHHHHHHHHHHHHhh
Confidence 36789999999999998 59999999999999999998766
No 17
>PRK07883 hypothetical protein; Validated
Probab=99.84 E-value=1.4e-20 Score=157.58 Aligned_cols=117 Identities=32% Similarity=0.564 Sum_probs=103.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||+ ++|+|.+++.+|.+|+.+ .++||||+ .||++||.+++.++|++++. ..++||+.+++.+++.. .
T Consensus 75 ~l~--~ap~~~evl~~f~~fl~~-------~~lVaHNa-~FD~~fL~~~~~r~g~~~~~-~~~iDTl~lar~l~~~~--~ 141 (557)
T PRK07883 75 MVA--GAPPIEEVLPAFLEFARG-------AVLVAHNA-PFDIGFLRAAAARCGYPWPG-PPVLCTVRLARRVLPRD--E 141 (557)
T ss_pred HHh--CCCCHHHHHHHHHHHhcC-------CEEEEeCc-HHHHHHHHHHHHHcCCCCCC-CCcEecHHHHHHhcccC--C
Confidence 567 899999999999999975 69999999 99999999999999998765 47899999999988732 3
Q ss_pred CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh----cCHHHHHH
Q 037872 81 SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN----FTLSDLLK 131 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~----~~~~~l~~ 131 (146)
..+++|.+++++||++.++ +|+|++||.+|++||.+++++.. .++.+++.
T Consensus 142 ~~~~~L~~L~~~~gi~~~~-~H~Al~DA~ata~l~~~l~~~~~~~~~~~~~~l~~ 195 (557)
T PRK07883 142 APNVRLSTLARLFGATTTP-THRALDDARATVDVLHGLIERLGNLGVHTLEELLT 195 (557)
T ss_pred CCCCCHHHHHHHCCcccCC-CCCHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence 5789999999999999884 99999999999999999998875 47888865
No 18
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=99.83 E-value=5.4e-20 Score=136.28 Aligned_cols=113 Identities=25% Similarity=0.293 Sum_probs=89.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCC--CCCcEEEEeCCCCCCHHHHHHHHHHcCCCC-CC-CcceeecHHHHHHHHhh
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGP--GEIAIFVAHNARRFDVPFLAKEFSRCSMNI-PD-NWRFLDTLPLARELMKQ 76 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~--~~~~~lVahN~~~FD~~~L~~~~~~~~~~~-~~-~~~~iDt~~l~~~~~~~ 76 (146)
||+ ++|++.+++.++.+++.+...+ .++.++||||+ +||++||++++++++... +. ...++||+.+++.+++
T Consensus 76 ~~~--~~~~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~- 151 (200)
T TIGR01298 76 PLR--GAVSEYEALHEIFKVVRKAMKASGCQRAILVGHNA-NFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG- 151 (200)
T ss_pred hhh--cCcchHHHHHHHHHHHHHHHHhcccCCCEEEEECc-hhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC-
Confidence 455 7888888888888887321100 02469999999 999999999999988642 11 2358999999998753
Q ss_pred CCCCCCCCcHHHHHHHhCCCCC-CCCCchHHHHHHHHHHHHHHHhhhh
Q 037872 77 NGSVSSKTSLQALREYFGIPLE-GSAHRAMSDVNSLASILERITSDLN 123 (146)
Q Consensus 77 ~~~~~~~~~L~~l~~~~gi~~~-~~~H~Al~Da~~ta~l~~~l~~~~~ 123 (146)
.++|..++++||++.+ .++|+|++||.+|++||..++.++.
T Consensus 152 ------~~~L~~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~ 193 (200)
T TIGR01298 152 ------QTVLAKACQAAGXDFDSTQAHSALYDTEKTAELFCEIVNRWK 193 (200)
T ss_pred ------cccHHHHHHHcCCCccccchhhhHHhHHHHHHHHHHHHHHHH
Confidence 4689999999999864 2599999999999999999988764
No 19
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=99.83 E-value=8.9e-20 Score=134.00 Aligned_cols=109 Identities=27% Similarity=0.389 Sum_probs=84.3
Q ss_pred CCCCHHHHHHHHHHHHhcccCC--CCCcEEEEeCCCCCCHHHHHHHHHHcCCC-CCC-CcceeecHHHHHHHHhhCCCCC
Q 037872 6 YVPRMEDLIPIVIKYVNSRLGP--GEIAIFVAHNARRFDVPFLAKEFSRCSMN-IPD-NWRFLDTLPLARELMKQNGSVS 81 (146)
Q Consensus 6 ~ap~f~ev~~~~~~~l~~~~~~--~~~~~lVahN~~~FD~~~L~~~~~~~~~~-~~~-~~~~iDt~~l~~~~~~~~~~~~ 81 (146)
+++...+++.+|.+++.+.... .++.++||||+ +||+.||+++++++++. .+. .+.++||+.+++.+++
T Consensus 76 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHna-~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~------ 148 (189)
T cd06134 76 FAVDEKEALKEIFKPIRKALKAQGCTRAILVGHNA-HFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG------ 148 (189)
T ss_pred cccchHHHHHHHHHHHHHHHhhcccCCCeEEEecc-hhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC------
Confidence 5566666777776666422100 12469999999 99999999999999873 221 2468999999998864
Q ss_pred CCCcHHHHHHHhCCCCC-CCCCchHHHHHHHHHHHHHHHhhh
Q 037872 82 SKTSLQALREYFGIPLE-GSAHRAMSDVNSLASILERITSDL 122 (146)
Q Consensus 82 ~~~~L~~l~~~~gi~~~-~~~H~Al~Da~~ta~l~~~l~~~~ 122 (146)
.++|.++|++||++.+ .++|+|++||.+|++||.+|++++
T Consensus 149 -~~~L~~l~~~~gi~~~~~~~H~Al~DA~ata~lf~~l~~~~ 189 (189)
T cd06134 149 -QTVLAKACQAAGIEFDNKEAHSALYDTQKTAELFCKIVNRW 189 (189)
T ss_pred -CCcHHHHHHHCCCCCCCCCCcChHHHHHHHHHHHHHHHHhC
Confidence 4689999999999864 259999999999999999998753
No 20
>PRK05168 ribonuclease T; Provisional
Probab=99.83 E-value=1.1e-19 Score=135.67 Aligned_cols=110 Identities=25% Similarity=0.330 Sum_probs=89.4
Q ss_pred CCCCHHHHHHHHHHHHhcccCC--CCCcEEEEeCCCCCCHHHHHHHHHHcCCCCC--CCcceeecHHHHHHHHhhCCCCC
Q 037872 6 YVPRMEDLIPIVIKYVNSRLGP--GEIAIFVAHNARRFDVPFLAKEFSRCSMNIP--DNWRFLDTLPLARELMKQNGSVS 81 (146)
Q Consensus 6 ~ap~f~ev~~~~~~~l~~~~~~--~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~--~~~~~iDt~~l~~~~~~~~~~~~ 81 (146)
++|++.+++.+|.+|+.+.... .++.++||||+ +||++||+++++++++... ..+.++||+.+++.+++
T Consensus 88 ~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~------ 160 (211)
T PRK05168 88 GAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNA-HFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALG------ 160 (211)
T ss_pred cCCChHHHHHHHHHHHHHHHHhcccCCceEEEecc-HHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC------
Confidence 6789999999999998632110 01369999999 9999999999999986421 12478999999998753
Q ss_pred CCCcHHHHHHHhCCCCCC-CCCchHHHHHHHHHHHHHHHhhhh
Q 037872 82 SKTSLQALREYFGIPLEG-SAHRAMSDVNSLASILERITSDLN 123 (146)
Q Consensus 82 ~~~~L~~l~~~~gi~~~~-~~H~Al~Da~~ta~l~~~l~~~~~ 123 (146)
..+|.++++++|++.++ .+|+|++||.+|++||.+++.+++
T Consensus 161 -~~~L~~l~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~ 202 (211)
T PRK05168 161 -QTVLAKACQAAGIEFDNKEAHSALYDTEKTAELFCEIVNRWK 202 (211)
T ss_pred -CCCHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 35899999999998643 599999999999999999998764
No 21
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.83 E-value=9.3e-20 Score=130.20 Aligned_cols=107 Identities=33% Similarity=0.542 Sum_probs=92.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCC
Q 037872 2 VNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVS 81 (146)
Q Consensus 2 v~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~ 81 (146)
|. ++|+|.+++.+|.+|+.+ .++|+||+.+||+.+|++.+.+++++.|....++||+.+++..++.
T Consensus 61 l~--~~~~~~~~~~~~~~~l~~-------~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~----- 126 (169)
T smart00479 61 LD--DAPTFEEVLEELLEFLKG-------KILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPG----- 126 (169)
T ss_pred Hh--CCCCHHHHHHHHHHHhcC-------CEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCC-----
Confidence 45 689999999999999975 4677787757999999999999998877555789999999887642
Q ss_pred CCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhh
Q 037872 82 SKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDL 122 (146)
Q Consensus 82 ~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~ 122 (146)
.+++|.+++++||++..+.+|+|++||.+|++||..+.+.+
T Consensus 127 ~~~~L~~l~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 127 RKYSLKKLAERLGLEVIGRAHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred CCCCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHHh
Confidence 48999999999999998645999999999999999998764
No 22
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.82 E-value=8.3e-20 Score=160.47 Aligned_cols=115 Identities=34% Similarity=0.523 Sum_probs=101.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||. ++|+|.+++.+|.+|+++ .++||||+ +||++||.+++.+.|.+.+. .++|||+.+++.++|.
T Consensus 64 ~l~--~ap~f~ev~~~l~~~l~~-------~~~VaHN~-~FD~~fL~~~~~~~g~~~~~-~~~iDt~~la~~~~p~---- 128 (928)
T PRK08074 64 MVK--QAPLFEDVAPEIVELLEG-------AYFVAHNV-HFDLNFLNEELERAGYTEIH-CPKLDTVELARILLPT---- 128 (928)
T ss_pred HHh--cCCCHHHHHHHHHHHhCC-------CeEEEECh-HHHHHHHHHHHHHcCCCCCC-CCeeeHHHHHHHhcCC----
Confidence 567 899999999999999975 69999999 99999999999999987654 4899999999999874
Q ss_pred CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh----cCHHHHHH
Q 037872 81 SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN----FTLSDLLK 131 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~----~~~~~l~~ 131 (146)
..+++|.+++++||++.+ ++|+|++||.+|++||.+++.++. .++.+|..
T Consensus 129 ~~~~~L~~l~~~l~i~~~-~~H~Al~DA~ata~l~~~l~~~~~~l~~~~l~~l~~ 182 (928)
T PRK08074 129 AESYKLRDLSEELGLEHD-QPHRADSDAEVTAELFLQLLNKLERLPLVTLQQLRR 182 (928)
T ss_pred CCCCCHHHHHHhCCCCCC-CCCChHHHHHHHHHHHHHHHHHHHhcCCcCHHHHHH
Confidence 378999999999999988 599999999999999999998765 36665554
No 23
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.81 E-value=1.7e-19 Score=156.67 Aligned_cols=114 Identities=25% Similarity=0.384 Sum_probs=99.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||+ +||+|.+|+++|.+|+.+ .++||||+ +||++||.+++.+.|.+.+ .+++||+.+++.++|.
T Consensus 66 ~l~--~ap~~~ev~~~~~~~l~~-------~~lVaHN~-~FD~~fL~~~~~~~g~~~~--~~~iDT~~la~~~~p~---- 129 (820)
T PRK07246 66 QLA--QAPDFSQVARHIYDLIED-------CIFVAHNV-KFDANLLAEALFLEGYELR--TPRVDTVELAQVFFPT---- 129 (820)
T ss_pred HHh--cCCCHHHHHHHHHHHhCC-------CEEEEECc-HHHHHHHHHHHHHcCCCCC--CCceeHHHHHHHHhCC----
Confidence 577 899999999999999975 69999999 9999999999988877654 3689999999999874
Q ss_pred CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh----cCHHHHHH
Q 037872 81 SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN----FTLSDLLK 131 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~----~~~~~l~~ 131 (146)
..+++|.+++++||++.+ .+|+|++||.+|++||..+..++. .++.+|.+
T Consensus 130 ~~~~~L~~L~~~lgl~~~-~~H~Al~DA~ata~L~~~l~~~l~~l~~~~l~~l~~ 183 (820)
T PRK07246 130 LEKYSLSHLSRELNIDLA-DAHTAIADARATAELFLKLLQKIESLPKECLERLLE 183 (820)
T ss_pred CCCCCHHHHHHHcCCCCC-CCCCHHHHHHHHHHHHHHHHHHHhhcCchhHHHHHH
Confidence 368999999999999988 599999999999999999998764 26666554
No 24
>PRK06722 exonuclease; Provisional
Probab=99.81 E-value=1e-19 Score=140.61 Aligned_cols=109 Identities=23% Similarity=0.298 Sum_probs=90.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCC--cceeecHHHHHHHHhhCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDN--WRFLDTLPLARELMKQNG 78 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~--~~~iDt~~l~~~~~~~~~ 78 (146)
||. +||+|.+|+.+|.+|+.+ .++|+||+ .||++||.+++.++|++.|.. ..++|+..++...++..
T Consensus 70 mV~--~AP~f~eVl~ef~~fig~-------~~lvahna-~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l- 138 (281)
T PRK06722 70 DLI--GVEKFPQIIEKFIQFIGE-------DSIFVTWG-KEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEEL- 138 (281)
T ss_pred HHc--CCCCHHHHHHHHHHHHCC-------CcEEEEEe-HHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhh-
Confidence 678 999999999999999964 45677777 899999999999999876642 24689988877666532
Q ss_pred CCCCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhh
Q 037872 79 SVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSD 121 (146)
Q Consensus 79 ~~~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~ 121 (146)
....++|.+++++||++.+|.+|+|++||.+||+||.++..+
T Consensus 139 -~~~~~sL~~l~~~lgL~~~g~~HrAL~DA~~TA~L~l~l~~~ 180 (281)
T PRK06722 139 -FEHTPSLQSAVEQLGLIWEGKQHRALADAENTANILLKAYSE 180 (281)
T ss_pred -ccCCCCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHhcc
Confidence 124578999999999998877999999999999999999843
No 25
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=99.80 E-value=3.1e-19 Score=159.01 Aligned_cols=115 Identities=28% Similarity=0.488 Sum_probs=100.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||+ ++|++.+|+++|.+|+.+ .++||||+ .||++||++++.+++++... .+++||+.+++.++|.
T Consensus 250 ~L~--~ap~~~evl~~f~~fl~~-------~iLVaHNa-~FD~~fL~~~~~r~g~~~~~-~~~IDTl~lar~l~p~---- 314 (1213)
T TIGR01405 250 MLE--NAPEIEEVLEKFKEFFKD-------SILVAHNA-SFDIGFLNTNFEKVGLEPLE-NPVIDTLELARALNPE---- 314 (1213)
T ss_pred HHh--CCCCHHHHHHHHHHHhCC-------CeEEEECh-HHHHHHHHHHHHHcCCCccC-CCEeEHHHHHHHHhcc----
Confidence 567 899999999999999975 69999999 99999999999999886433 4899999999999873
Q ss_pred CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh----cCHHHHHH
Q 037872 81 SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN----FTLSDLLK 131 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~----~~~~~l~~ 131 (146)
.++++|.+++++||++.++ +|+|++||.+|++||..+++++. .++.++..
T Consensus 315 ~k~~kL~~Lak~lgi~~~~-~HrAl~DA~aTa~I~~~ll~~l~~~~i~~~~~l~~ 368 (1213)
T TIGR01405 315 YKSHRLGNICKKLGVDLDD-HHRADYDAEATAKVFKVMVEQLKEKGITNLEELNN 368 (1213)
T ss_pred CCCCCHHHHHHHcCCCCCC-CcCHHHHHHHHHHHHHHHHHHHHHcCCccHHHHHH
Confidence 4789999999999999995 99999999999999999988764 46666653
No 26
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=99.80 E-value=3.5e-19 Score=155.46 Aligned_cols=115 Identities=30% Similarity=0.457 Sum_probs=100.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||. ++|+|.+++.+|.+|+.+ .++||||+ .||++||.+++.++|.+... ..++||+.+++.++|.
T Consensus 60 ~l~--~ap~~~ev~~~l~~~l~~-------~~~VahN~-~fD~~fL~~~~~~~g~~~~~-~~~iDt~~l~~~~~p~---- 124 (850)
T TIGR01407 60 MLQ--QAPYFSQVAQEIYDLLED-------GIFVAHNV-HFDLNFLAKALKDCGYEPLP-KPRIDTVELAQIFFPT---- 124 (850)
T ss_pred HHh--CCCCHHHHHHHHHHHhCC-------CEEEEeCc-HHHHHHHHHHHHHcCCCCCC-CCeEeHHHHHHHhcCC----
Confidence 567 899999999999999975 68999999 99999999999999987443 3789999999998874
Q ss_pred CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh----cCHHHHHH
Q 037872 81 SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN----FTLSDLLK 131 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~----~~~~~l~~ 131 (146)
..+++|.+++++||++.+ .+|+|++||.+|++||.++..+++ .++.+|.+
T Consensus 125 ~~~~~L~~l~~~~gi~~~-~~H~Al~DA~ata~l~~~l~~~~~~l~~~~l~~l~~ 178 (850)
T TIGR01407 125 EESYQLSELSEALGLTHE-NPHRADSDAQATAELLLLLFEKMEKLPLDTLEQLLE 178 (850)
T ss_pred CCCCCHHHHHHHCCCCCC-CCCChHHHHHHHHHHHHHHHHHHHhcCCccHHHHHH
Confidence 368999999999999988 499999999999999999988765 35665543
No 27
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.80 E-value=4.3e-19 Score=131.51 Aligned_cols=107 Identities=16% Similarity=0.237 Sum_probs=86.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHH-cCCCCCCCcceeecHHHHHHHHh-hCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSR-CSMNIPDNWRFLDTLPLARELMK-QNG 78 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~-~~~~~~~~~~~iDt~~l~~~~~~-~~~ 78 (146)
||+ ++|+|.+|+++|.+|+++ .++||||+ +||+.||.+++++ ++.+.+ ..++|++.++..... ...
T Consensus 91 ~l~--~~~~~~~vl~~~~~~i~~-------~~lv~hn~-~fD~~fL~~~~~~~~~~~~~--~~~id~~~l~~~~~~~~~~ 158 (202)
T PRK09145 91 DLE--DGLSEEEALRQLLAFIGN-------RPLVGYYL-EFDVAMLNRYVRPLLGIPLP--NPLIEVSALYYDKKERHLP 158 (202)
T ss_pred HHh--cCCCHHHHHHHHHHHHcC-------CeEEEeCH-HHHHHHHHHHHHHhcCCCCC--CCeeeHHHHHHHHhhccCC
Confidence 456 889999999999999975 58999999 9999999999987 455544 368999887643221 100
Q ss_pred CCCCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHh
Q 037872 79 SVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITS 120 (146)
Q Consensus 79 ~~~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~ 120 (146)
.+..+++|++++++||++..+ +|+|++||.+||+||.++..
T Consensus 159 ~~~~~~~L~~l~~~~gi~~~~-~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 159 DAYIDLRFDAILKHLDLPVLG-RHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred CcccCCCHHHHHHHcCCCCCC-CCCcHHHHHHHHHHHHHHHh
Confidence 123578999999999999885 99999999999999999865
No 28
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=99.80 E-value=7.1e-19 Score=127.96 Aligned_cols=102 Identities=28% Similarity=0.437 Sum_probs=80.8
Q ss_pred CCCCCCCCCHHH-HHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCC
Q 037872 1 MVNRSYVPRMED-LIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGS 79 (146)
Q Consensus 1 mv~~~~ap~f~e-v~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~ 79 (146)
||. ++|+|.+ +++.+.+|+...+ +..++||||+.+||++||++++.++|.+++....++||+.+++.+.
T Consensus 73 ~l~--~~~~~~~~~~~~l~~f~~~~~---~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~----- 142 (177)
T cd06136 73 LLE--HKAPFDSDTANLIKLFLRRQP---KPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELD----- 142 (177)
T ss_pred HHh--cCCCccHHHHHHHHHHHHhcC---CCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhH-----
Confidence 456 7788764 6666667765321 2358999996359999999999999988764446799999999764
Q ss_pred CCCCCcHHHHHHH-hCCCCCCCCCchHHHHHHHHHHHHH
Q 037872 80 VSSKTSLQALREY-FGIPLEGSAHRAMSDVNSLASILER 117 (146)
Q Consensus 80 ~~~~~~L~~l~~~-~gi~~~~~~H~Al~Da~~ta~l~~~ 117 (146)
+ +|++++++ ||++.. .+|+|++||.+|++||.+
T Consensus 143 --~--~L~~l~~~~~~~~~~-~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 143 --Q--SLGSLYKRLFGQEPK-NSHTAEGDVLALLKCALH 176 (177)
T ss_pred --h--hHHHHHHHHhCCCcc-cccchHHHHHHHHHHHhh
Confidence 2 89999985 899988 499999999999999864
No 29
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.78 E-value=1.7e-18 Score=129.80 Aligned_cols=111 Identities=31% Similarity=0.365 Sum_probs=90.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||+ ++|+|.++++.| ++ ..++||||+ .||++||.. .. ..|+||+.++|.++|.
T Consensus 57 ~v~--~ap~~~ev~~~~---~~-------~~~lVaHNa-~FD~~~L~~--------~~--~~~idTl~lar~l~p~---- 109 (219)
T PRK07983 57 MVA--DKPWIEDVIPHY---YG-------SEWYVAHNA-SFDRRVLPE--------MP--GEWICTMKLARRLWPG---- 109 (219)
T ss_pred HHc--CCCCHHHHHHHH---cC-------CCEEEEeCc-HhhHHHHhC--------cC--CCcEeHHHHHHHHccC----
Confidence 677 899999998874 43 369999999 999999852 11 3789999999999874
Q ss_pred CCCCcHHHHHHHhCCCCC----CCCCchHHHHHHHHHHHHHHHhhhhcCHHHHHHhhcccccc
Q 037872 81 SSKTSLQALREYFGIPLE----GSAHRAMSDVNSLASILERITSDLNFTLSDLLKTSFRANFD 139 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~----~~~H~Al~Da~~ta~l~~~l~~~~~~~~~~l~~~~~~~~~~ 139 (146)
..++|..++++||++.. ..+|+|++||++|+.||..+++..+.++.++...+-.|.-.
T Consensus 110 -~~~~l~~L~~~~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~~~~~~~~~~l~~~~~~~~~~ 171 (219)
T PRK07983 110 -IKYSNMALYKSRKLNVQTPPGLHHHRALYDCYITAALLIDIMNTSGWTAEEMADITGRPSLL 171 (219)
T ss_pred -CCCCHHHHHHHcCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHHHcCCCHHHHHHHhcCCccC
Confidence 24899999999998641 25999999999999999999987776788888877666544
No 30
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=99.77 E-value=3.6e-18 Score=123.06 Aligned_cols=107 Identities=19% Similarity=0.321 Sum_probs=87.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCC--CCCCcceeecHHHHHHHHhhCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMN--IPDNWRFLDTLPLARELMKQNG 78 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~--~~~~~~~iDt~~l~~~~~~~~~ 78 (146)
||+ ++|+|.+|+++|.+|+++.. ..+++||+ .||..++.+++.+.+.. .+..+.++|+..+++..++.
T Consensus 68 ~l~--~~~~~~~vl~~~~~~l~~~~-----~~~~v~~~-~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~-- 137 (176)
T cd06133 68 DVD--NAPSFPEVLKEFLEWLGKNG-----KYAFVTWG-DWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGL-- 137 (176)
T ss_pred HHh--cCCCHHHHHHHHHHHHHhCC-----CeEEEeec-HhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCC--
Confidence 456 78999999999999998620 14555556 79999998888887654 23345899999999988753
Q ss_pred CCCCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHH
Q 037872 79 SVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERIT 119 (146)
Q Consensus 79 ~~~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~ 119 (146)
...++|.+++++||++.++++|+|++||++|++||++|.
T Consensus 138 --~~~~~L~~l~~~~gi~~~~~~H~Al~DA~~~a~l~~~~~ 176 (176)
T cd06133 138 --KKRTGLSKALEYLGLEFEGRHHRGLDDARNIARILKRLL 176 (176)
T ss_pred --CCCCCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHhC
Confidence 268999999999999998679999999999999999873
No 31
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=99.77 E-value=2.4e-18 Score=125.69 Aligned_cols=106 Identities=24% Similarity=0.222 Sum_probs=84.2
Q ss_pred CCCCCC-CCCHHHHHHHHHHHHhcccCCCCCcEEEEeC-CCCCCHHHHHHHHHHcCCCCCC-----CcceeecHHHHHHH
Q 037872 1 MVNRSY-VPRMEDLIPIVIKYVNSRLGPGEIAIFVAHN-ARRFDVPFLAKEFSRCSMNIPD-----NWRFLDTLPLAREL 73 (146)
Q Consensus 1 mv~~~~-ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN-~~~FD~~~L~~~~~~~~~~~~~-----~~~~iDt~~l~~~~ 73 (146)
||+ + +|++.+++.+|.+|+.+ ++.++|||| + .||++||++++.+++.+.+. ...++||+.+++..
T Consensus 61 ~l~--~~~~~~~~~l~~~~~~~~~-----~~~~lVahn~~-~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~ 132 (183)
T cd06138 61 QLL--KEGLSEYEFIAKIHRLFNT-----PGTCIVGYNNI-RFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAY 132 (183)
T ss_pred HHH--hcCCCHHHHHHHHHHHHcc-----CCCcEEeeCch-hhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHH
Confidence 455 5 79999999999999964 246899997 6 89999999999999875331 23568999998876
Q ss_pred H---hh------CCCCCCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHH
Q 037872 74 M---KQ------NGSVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASIL 115 (146)
Q Consensus 74 ~---~~------~~~~~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~ 115 (146)
+ |. ...+.++++|++++++||++.. ++|+|++||.+|++|.
T Consensus 133 ~~~~~~~~~~~~~~~~~~~~~L~~l~~~~gi~~~-~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 133 YALRPDGIVWPKNDDGKPSFKLEDLAQANGIEHS-NAHDALSDVEATIALA 182 (183)
T ss_pred HhhChhhccCccccCCCcchhHHHHHHHCCCCcc-ccccHHHHHHHHHHHh
Confidence 4 21 0002367999999999999987 5999999999999985
No 32
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=99.76 E-value=7.4e-18 Score=118.17 Aligned_cols=97 Identities=37% Similarity=0.593 Sum_probs=85.0
Q ss_pred CCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCc
Q 037872 6 YVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTS 85 (146)
Q Consensus 6 ~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~ 85 (146)
+++++.+++.+|.+|+.+ .++||||+ +||+++|.+.+.+++.+.+ ...++||+.+++.+++. ...++
T Consensus 62 ~~~~~~~~~~~~~~~l~~-------~~~v~~n~-~fD~~~l~~~~~~~~~~~~-~~~~iDt~~~~~~~~~~----~~~~~ 128 (159)
T cd06127 62 DAPPFEEVLPEFLEFLGG-------RVLVAHNA-SFDLRFLNRELRRLGGPPL-PNPWIDTLRLARRLLPG----LRSHR 128 (159)
T ss_pred cCCCHHHHHHHHHHHHCC-------CEEEEeCc-HhhHHHHHHHHHHhCCCCC-CCCeeEHHHHHHHHcCC----CCcCc
Confidence 789999999999999975 69999999 9999999999999884433 35899999999998864 36789
Q ss_pred HHHH-HHHhCCCCCCCCCchHHHHHHHHHHHH
Q 037872 86 LQAL-REYFGIPLEGSAHRAMSDVNSLASILE 116 (146)
Q Consensus 86 L~~l-~~~~gi~~~~~~H~Al~Da~~ta~l~~ 116 (146)
|..+ ++++|++.. .+|+|++||.+|++||.
T Consensus 129 l~~~~~~~~~~~~~-~~H~Al~Da~~t~~l~~ 159 (159)
T cd06127 129 LGLLLAERYGIPLE-GAHRALADALATAELLL 159 (159)
T ss_pred hHHHHHHHcCCCCC-CCCCcHHHHHHHHHHhC
Confidence 9998 899999887 59999999999999973
No 33
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.76 E-value=1.1e-17 Score=123.49 Aligned_cols=104 Identities=20% Similarity=0.348 Sum_probs=81.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCC-CCHHHHHHHHHHcCCCCCCCcceeecHHHH--HHHHhhC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARR-FDVPFLAKEFSRCSMNIPDNWRFLDTLPLA--RELMKQN 77 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~-FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~--~~~~~~~ 77 (146)
||+ ++|+|.+++++|.+|+++ .++||||+ . ||++||.+ .+...+.. .++||+..+ ++....
T Consensus 64 ~v~--~ap~~~evl~~f~~f~~~-------~~lVaHNa-~~fD~~fL~~----~g~~~~~~-~~idt~~~~~~~~~~~~- 127 (195)
T PRK07247 64 KIA--DAPKVEEVLAAFKEFVGE-------LPLIGYNA-QKSDLPILAE----NGLDLSDQ-YQVDLYDEAFERRSSDL- 127 (195)
T ss_pred HHh--CCCCHHHHHHHHHHHHCC-------CeEEEEeC-cHhHHHHHHH----cCCCcCCC-ceeehHHHHHHhhcccc-
Confidence 577 899999999999999975 68999999 7 89999864 45544332 568887654 222111
Q ss_pred CCCCCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh
Q 037872 78 GSVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN 123 (146)
Q Consensus 78 ~~~~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~ 123 (146)
.+..+++|.+++++||++. .+|+|++||.+|+.||.+++....
T Consensus 128 -~~~~~~~L~~La~~~gi~~--~~HrAl~DA~~ta~v~~~ll~~~~ 170 (195)
T PRK07247 128 -NGIANLKLQTVADFLGIKG--RGHNSLEDARMTARVYESFLESDQ 170 (195)
T ss_pred -CCCCCCCHHHHHHhcCCCC--CCcCCHHHHHHHHHHHHHHHhhcc
Confidence 1247899999999999985 489999999999999999987754
No 34
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.75 E-value=1e-17 Score=132.77 Aligned_cols=107 Identities=17% Similarity=0.241 Sum_probs=88.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCC-------------------------
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSM------------------------- 55 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~------------------------- 55 (146)
||+ ++|+|.+++++|.+|+.+ .++||||+ .||++||.+++++...
T Consensus 105 ~La--~AP~f~eVl~el~~fL~g-------~vLVaHNA-~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~ 174 (377)
T PRK05601 105 EFA--QGKRFSQILKPLDRLIDG-------RTLILHNA-PRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRV 174 (377)
T ss_pred HHh--cCCCHHHHHHHHHHHhCC-------CEEEEECc-HHHHHHHHHHHHHhhhhhhhccccccccccccccccccccc
Confidence 577 899999999999999986 59999999 9999999999877411
Q ss_pred -CCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHHHHhCCCCC---------CCCCchH--HHHHHHHHHHHHHHhh
Q 037872 56 -NIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREYFGIPLE---------GSAHRAM--SDVNSLASILERITSD 121 (146)
Q Consensus 56 -~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~~gi~~~---------~~~H~Al--~Da~~ta~l~~~l~~~ 121 (146)
..+....++||+.+++.+++. ..+++|.+++++||++.+ ...|+|+ +||..++.||..+.+.
T Consensus 175 g~~p~p~~~iDTL~LARrl~p~----l~~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~~~~ 248 (377)
T PRK05601 175 GHIPKPVVIVDTLATARRQGVA----LDDIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFALRAS 248 (377)
T ss_pred CCCCCCCCEEEhHHHHHHHcCC----CCCCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHhhcc
Confidence 012223689999999999874 478999999999999982 1478888 5999999999987433
No 35
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.74 E-value=2e-17 Score=149.21 Aligned_cols=115 Identities=33% Similarity=0.521 Sum_probs=101.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||. ++|++.++++.|.+|+.+ .++||||+ .||++||++.++++|++.+. ..++||+.+++.+++.
T Consensus 479 ~L~--~aps~~EaL~~f~~figg-------~vLVAHNa-~FD~~fL~~~l~rlgl~~l~-~~~IDTLelar~l~p~---- 543 (1437)
T PRK00448 479 MVK--DAPSIEEVLPKFKEFCGD-------SILVAHNA-SFDVGFINTNYEKLGLEKIK-NPVIDTLELSRFLYPE---- 543 (1437)
T ss_pred HHc--CCCCHHHHHHHHHHHhCC-------CEEEEeCc-cccHHHHHHHHHHcCCcccc-ccceeHHHHHHHHcCc----
Confidence 466 889999999999999975 69999999 99999999999999986544 3789999999998863
Q ss_pred CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh----cCHHHHHH
Q 037872 81 SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN----FTLSDLLK 131 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~----~~~~~l~~ 131 (146)
..+++|.+++++||++.++ +|+|++||.+|++||.++++++. .++.+|..
T Consensus 544 ~k~~kL~~LAk~lGL~~~~-~HrAl~DA~aTa~lf~~ll~~l~~~gi~~~~~L~~ 597 (1437)
T PRK00448 544 LKSHRLNTLAKKFGVELEH-HHRADYDAEATAYLLIKFLKDLKEKGITNLDELNK 597 (1437)
T ss_pred cccccHHHHHHHcCCCCCC-CcChHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHH
Confidence 4789999999999999995 99999999999999999988765 47777763
No 36
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=99.74 E-value=5.3e-18 Score=120.36 Aligned_cols=93 Identities=22% Similarity=0.303 Sum_probs=74.9
Q ss_pred CCCCCCCC-CHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCC
Q 037872 1 MVNRSYVP-RMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGS 79 (146)
Q Consensus 1 mv~~~~ap-~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~ 79 (146)
||+ ++| +|.+++++|.+|+.+ +.++||||+ +||+.||+.. . .+++||+.+++..++.
T Consensus 54 ~l~--~a~~~~~~v~~~~~~fl~~------~~vlVgHn~-~fD~~fL~~~---------~-~~~iDT~~l~r~~~~~--- 111 (150)
T cd06145 54 MLE--NVTTTLEDVQKKLLSLISP------DTILVGHSL-ENDLKALKLI---------H-PRVIDTAILFPHPRGP--- 111 (150)
T ss_pred Hhc--cCCCCHHHHHHHHHHHhCC------CCEEEEcCh-HHHHHHhhcc---------C-CCEEEcHHhccccCCC---
Confidence 677 885 999999999999962 379999999 9999999641 1 2589999999877653
Q ss_pred CCCCCcHHHHHHHh-CCCCC--CCCCchHHHHHHHHHHHH
Q 037872 80 VSSKTSLQALREYF-GIPLE--GSAHRAMSDVNSLASILE 116 (146)
Q Consensus 80 ~~~~~~L~~l~~~~-gi~~~--~~~H~Al~Da~~ta~l~~ 116 (146)
..+++|.++|++| |.... +.+|+|++||++|++||.
T Consensus 112 -~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~~t~~l~~ 150 (150)
T cd06145 112 -PYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELVK 150 (150)
T ss_pred -CCChhHHHHHHHHCCcceeCCCCCCCcHHHHHHHHHHhC
Confidence 2578999999887 53321 258999999999999973
No 37
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=99.73 E-value=3.8e-18 Score=121.29 Aligned_cols=95 Identities=18% Similarity=0.270 Sum_probs=74.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||+ ++|+|.+++++|.+|+++ .++||||+ .||++||+. ..+. ..++||..+.....+. .
T Consensus 57 ~v~--~a~~~~~~~~~l~~~l~~-------~vlVgHn~-~fD~~~L~~-------~~~~-~~~~dt~~l~~~~~~~---~ 115 (152)
T cd06144 57 HLK--DAPDFEEVQKKVAELLKG-------RILVGHAL-KNDLKVLKL-------DHPK-KLIRDTSKYKPLRKTA---K 115 (152)
T ss_pred HHc--CCCCHHHHHHHHHHHhCC-------CEEEEcCc-HHHHHHhcC-------cCCC-ccEEEeEEeecccccc---C
Confidence 577 899999999999999975 69999999 999999962 2232 2578887764333221 1
Q ss_pred CCCCcHHHHHHH-hCCCCCCCCCchHHHHHHHHHHHH
Q 037872 81 SSKTSLQALREY-FGIPLEGSAHRAMSDVNSLASILE 116 (146)
Q Consensus 81 ~~~~~L~~l~~~-~gi~~~~~~H~Al~Da~~ta~l~~ 116 (146)
..+++|++++++ +|++....+|+|++||.+|++||+
T Consensus 116 ~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~at~~l~~ 152 (152)
T cd06144 116 GKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLYR 152 (152)
T ss_pred CCChhHHHHHHHHcCcccCCCCcCcHHHHHHHHHHhC
Confidence 368999999997 599865359999999999999985
No 38
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=99.72 E-value=7.9e-18 Score=120.32 Aligned_cols=94 Identities=15% Similarity=0.192 Sum_probs=75.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHH--HHHH--Hhh
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPL--AREL--MKQ 76 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l--~~~~--~~~ 76 (146)
||+ +||+|.+++++|.+|+.+ .++||||+ .||+++|+.. .+. ..++||..+ +++. +|.
T Consensus 57 ~l~--~a~~~~~v~~~l~~~l~~-------~vlV~Hn~-~~D~~~l~~~-------~~~-~~~~Dt~~l~~~~~~~~~p~ 118 (157)
T cd06149 57 HLV--NATPFAVAQKEILKILKG-------KVVVGHAI-HNDFKALKYF-------HPK-HMTRDTSTIPLLNRKAGFPE 118 (157)
T ss_pred HHh--cCCCHHHHHHHHHHHcCC-------CEEEEeCc-HHHHHHhccc-------CCC-cCEEECcccccchhhcCCcc
Confidence 567 899999999999999975 69999999 9999999743 222 257888654 4443 442
Q ss_pred CCCCCCCCcHHHHHHHh---CCCCCCCCCchHHHHHHHHHHHH
Q 037872 77 NGSVSSKTSLQALREYF---GIPLEGSAHRAMSDVNSLASILE 116 (146)
Q Consensus 77 ~~~~~~~~~L~~l~~~~---gi~~~~~~H~Al~Da~~ta~l~~ 116 (146)
..+++|..++++| +++..++.|+|+.||++|++||+
T Consensus 119 ----~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 119 ----NCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157 (157)
T ss_pred ----cCChhHHHHHHHHcChhhcCCCCCcCcHHHHHHHHHHhC
Confidence 3679999999999 67764468999999999999984
No 39
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.70 E-value=1.3e-16 Score=120.83 Aligned_cols=107 Identities=35% Similarity=0.542 Sum_probs=94.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||. ++|.|.+++++|.+|+.+ ..++||||+ .||++||..++.+++.+.+. ..++||+.+++..++.
T Consensus 74 ~l~--~~p~~~~v~~~~~~~i~~------~~~~Vahna-~fD~~fl~~~~~~~~~~~~~-~~~~~t~~~~r~~~~~---- 139 (243)
T COG0847 74 MLA--DAPKFAEVLPEFLDFIGG------LRLLVAHNA-AFDVGFLRVESERLGIEIPG-DPVLDTLALARRHFPG---- 139 (243)
T ss_pred HHh--cCCCHHHHHHHHHHHHCC------CCeEEEEch-hhcHHHHHHHHHHcCCCccc-CceehHHHHHHHHcCC----
Confidence 566 889999999999999985 269999999 99999999999999988764 4889999999999873
Q ss_pred CCCCcHHHHHHHhCCCCC-CCCCchHHHHHHHHHHHHHHHhh
Q 037872 81 SSKTSLQALREYFGIPLE-GSAHRAMSDVNSLASILERITSD 121 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~-~~~H~Al~Da~~ta~l~~~l~~~ 121 (146)
...++|+.+++++|++.. ...|+|+.||.+|+.+|..+...
T Consensus 140 ~~~~~L~~l~~~~gi~~~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 140 FDRSSLDALAERLGIDRNPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred CccchHHHHHHHcCCCcCCcCCcchHHHHHHHHHHHHHHHhc
Confidence 478999999999999943 15899999999999999999985
No 40
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=99.66 E-value=7.1e-17 Score=115.77 Aligned_cols=89 Identities=24% Similarity=0.318 Sum_probs=71.0
Q ss_pred HHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHH
Q 037872 10 MEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQAL 89 (146)
Q Consensus 10 f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l 89 (146)
|.+++++|.+|+++ ..++||||+ .||++||+.. . ..++||+.+++.+.+... ...+++|.++
T Consensus 70 ~~~~~~~~~~~i~~------~~vlVgHn~-~fD~~fL~~~---------~-~~~iDT~~l~~~~~~~~~-~~~~~~L~~L 131 (161)
T cd06137 70 WEAARAALWKFIDP------DTILVGHSL-QNDLDALRMI---------H-TRVVDTAILTREAVKGPL-AKRQWSLRTL 131 (161)
T ss_pred HHHHHHHHHHhcCC------CcEEEeccH-HHHHHHHhCc---------C-CCeeEehhhhhhccCCCc-CCCCccHHHH
Confidence 56999999999974 269999999 9999999742 1 268999999998876310 0157999999
Q ss_pred HHH-hCCCCC--CCCCchHHHHHHHHHHHH
Q 037872 90 REY-FGIPLE--GSAHRAMSDVNSLASILE 116 (146)
Q Consensus 90 ~~~-~gi~~~--~~~H~Al~Da~~ta~l~~ 116 (146)
+++ ||++.. ...|+|+.||.+|++||+
T Consensus 132 ~~~~~~~~~~~~~~~H~A~~DA~at~~l~~ 161 (161)
T cd06137 132 CRDFLGLKIQGGGEGHDSLEDALAAREVVL 161 (161)
T ss_pred HHHHCCchhcCCCCCCCcHHHHHHHHHHhC
Confidence 986 687753 248999999999999974
No 41
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.65 E-value=9.3e-16 Score=127.59 Aligned_cols=119 Identities=13% Similarity=0.191 Sum_probs=92.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCC---CCCcEEEEeCCCCCCHH-HHHHHHHH---cCCCCCCCcceeec-HHHHHH
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGP---GEIAIFVAHNARRFDVP-FLAKEFSR---CSMNIPDNWRFLDT-LPLARE 72 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~---~~~~~lVahN~~~FD~~-~L~~~~~~---~~~~~~~~~~~iDt-~~l~~~ 72 (146)
||+ +||+|.+|+.+|.+|+.+...+ ....++|+||+ .||+. ||.+++.. .+++..+. .|+|. ..+++.
T Consensus 123 ~V~--~Ap~F~eVl~ef~~fL~~~~~~e~~~~~~~~vah~g-~fDl~~fL~~e~~~~~~~g~p~~f~-~widLk~~lar~ 198 (582)
T PTZ00315 123 MVS--RADPFPVVYCEALQFLAEAGLGDAPPLRSYCVVTCG-DWDLKTMLPSQMRVSGQQGTPLSFQ-RWCNLKKYMSQL 198 (582)
T ss_pred HHh--cCCCHHHHHHHHHHHHhccccccccccCceEEEecc-HHHHHHHHHHHHHHhhhcCCCcccc-eEEEhHHHHHHH
Confidence 678 9999999999999999864211 12347999999 99995 99988873 45554433 56664 356676
Q ss_pred HHhhC---C----CCCCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh
Q 037872 73 LMKQN---G----SVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN 123 (146)
Q Consensus 73 ~~~~~---~----~~~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~ 123 (146)
+++.. | ....+++|.++++.+|++.+|.+|+|++||.+||+||.+|+.+..
T Consensus 199 l~p~~~~~~~~~~~~~~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~~g~ 256 (582)
T PTZ00315 199 GFGNGSGCGGGATPPLGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRGL 256 (582)
T ss_pred hCccccccccccccccCCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHcCC
Confidence 66521 0 123678999999999999998899999999999999999998865
No 42
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.62 E-value=1.7e-15 Score=118.07 Aligned_cols=115 Identities=24% Similarity=0.247 Sum_probs=86.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
||. ++|...+ .+.+|+.. ..++||||+ .||++||.+.+..+. . ..|.||+.......+ +
T Consensus 103 ~v~--~~~~~~~---~l~~fl~~------~~vlVAHNA-~FD~~fL~~~~~~~~----~-~~~~ct~~~i~~~~~----~ 161 (294)
T PRK09182 103 MVA--GQTIDPA---AVDALIAP------ADLIIAHNA-GFDRPFLERFSPVFA----T-KPWACSVSEIDWSAR----G 161 (294)
T ss_pred HHh--cCCCcHH---HHHHHhcC------CCEEEEeCH-HHHHHHHHHHHHhcc----C-CcccccHHHHhhccc----c
Confidence 455 6665544 45666654 259999999 999999998765432 2 257899876543322 2
Q ss_pred CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh-cCHHHHHHhhccccc
Q 037872 81 SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN-FTLSDLLKTSFRANF 138 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~-~~~~~l~~~~~~~~~ 138 (146)
.++++|.+++.+|| ... .+|+|++||.+|++||.+++...+ +.+.+|+..+..|..
T Consensus 162 ~~~~kL~~La~~~g-~~~-~aHrAl~Da~Ata~ll~~~l~~~~~~~l~~Ll~~~~~~~~ 218 (294)
T PRK09182 162 FEGTKLGYLAGQAG-FFH-EGHRAVDDCQALLELLARPLPETGQPPLAELLEASRRSRV 218 (294)
T ss_pred CCCCCHHHHHHHcC-CCC-CCcChHHHHHHHHHHHHHHHhhcCCcCHHHHHHHhccCee
Confidence 47899999999999 444 599999999999999998887665 789999987766554
No 43
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=99.59 E-value=1.9e-17 Score=116.28 Aligned_cols=99 Identities=39% Similarity=0.667 Sum_probs=82.7
Q ss_pred CCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHc-CCCCCCCcceeecHHHHHHHHhhCCCCCCCC
Q 037872 6 YVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRC-SMNIPDNWRFLDTLPLARELMKQNGSVSSKT 84 (146)
Q Consensus 6 ~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~-~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~ 84 (146)
++|++.+++++|.+|+.+. .++||||+ +||.+++.+.+.++ +...|....++|++.+.+..++.. ..+
T Consensus 65 ~~~~~~~~~~~~~~~~~~~------~~~v~~n~-~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~ 133 (164)
T PF00929_consen 65 DAPSFEEALDEFEEFLKKN------DILVGHNA-SFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNR----KKY 133 (164)
T ss_dssp CHCEHHHHHHHHHHHHHHH------TEEEETTC-CHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHH----HHH
T ss_pred cCCcHHHHHHhhhhhhhcc------cccccccc-cchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhcc----ccC
Confidence 7889999999999999852 69999998 99999999998887 333331236899988888877643 448
Q ss_pred cHHHHHHHhCCCCCCCCCchHHHHHHHHHHH
Q 037872 85 SLQALREYFGIPLEGSAHRAMSDVNSLASIL 115 (146)
Q Consensus 85 ~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~ 115 (146)
+|..++++||++..+.+|+|++||.+|++||
T Consensus 134 ~l~~l~~~~~~~~~~~~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 134 SLDDLAEYFGIPFDGTAHDALDDARATAELF 164 (164)
T ss_dssp SHHHHHHHTTSSSTSTTTSHHHHHHHHHHHH
T ss_pred CHHHHHHHcCCCCCCCCcChHHHHHHHhCcC
Confidence 9999999999999865799999999999997
No 44
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=99.58 E-value=7.9e-15 Score=106.30 Aligned_cols=101 Identities=16% Similarity=0.240 Sum_probs=78.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeec---HHHHHHHHhhC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDT---LPLARELMKQN 77 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt---~~l~~~~~~~~ 77 (146)
||. ++|++.+++.+|.+|+.+.. +.+..++||||+ +||+.||++++.+++..+ .++.+|+ +.+++.++|..
T Consensus 68 ~l~--~~~~~~~vl~~~~~f~~~~~-~~~~~~lvgh~~-~FD~~fL~~~~~~~~~~~--~~~~~D~~~l~~l~~~l~p~~ 141 (173)
T cd06135 68 VRA--STVTLAQAEAELLEFIKKYV-PKGKSPLAGNSV-HQDRRFLDKYMPELEEYL--HYRILDVSSIKELARRWYPEI 141 (173)
T ss_pred HHh--CCCCHHHHHHHHHHHHHHhc-CCCCCceeecch-hhCHHHHHHHHHHHhccC--CcchhhHHHHHHHHHHhCcHh
Confidence 456 89999999999999997521 112368999999 999999999999987432 2356887 67888887631
Q ss_pred CCCCCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhh
Q 037872 78 GSVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSD 121 (146)
Q Consensus 78 ~~~~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~ 121 (146)
.+ ++++.. .+|||++||.+|+.+|...++.
T Consensus 142 ----~~---------~~~~~~-~~HrAl~Da~~~~~~~~~~~~~ 171 (173)
T cd06135 142 ----YR---------KAPKKK-GTHRALDDIRESIAELKYYREN 171 (173)
T ss_pred ----hh---------cCCCCC-CCcchHHHHHHHHHHHHHHHHH
Confidence 11 677666 5999999999999999987653
No 45
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.53 E-value=1.2e-13 Score=98.25 Aligned_cols=111 Identities=17% Similarity=0.257 Sum_probs=94.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCC-CCCCcceeecHHHHHHHHhhCCCC
Q 037872 2 VNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMN-IPDNWRFLDTLPLARELMKQNGSV 80 (146)
Q Consensus 2 v~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~-~~~~~~~iDt~~l~~~~~~~~~~~ 80 (146)
|. +||-|..|+++|+.|+..+. +...+.+++|+ .+|+..|.+.+..++++ +++..+++|.-.-++.++.-
T Consensus 73 VD--~apifs~v~E~f~r~L~~h~-Pr~~~~wa~wG--~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~---- 143 (210)
T COG5018 73 VD--EAPIFSMVFEDFIRKLNEHD-PRKNSTWATWG--NMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGD---- 143 (210)
T ss_pred cc--ccchHHHHHHHHHHHHHhcC-cccCCcccccc--chhHHHHHHHHHhcCCCCccccCccchHHHHHHHHhcC----
Confidence 56 89999999999999998763 33445799998 59999999999999987 44445788887777777742
Q ss_pred CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhh
Q 037872 81 SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSD 121 (146)
Q Consensus 81 ~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~ 121 (146)
.+..+|..+++++|..++|+.|+|++||+++++|+..+.+.
T Consensus 144 pr~tgln~ale~~G~sf~G~~HraldDArn~~rl~klv~~~ 184 (210)
T COG5018 144 PRLTGLNKALEEYGDSFTGTHHRALDDARNAYRLFKLVEQD 184 (210)
T ss_pred CccccHHHHHHHhccccCCchhhhHHHHHHHHHHHHHHcch
Confidence 35689999999999999999999999999999999998765
No 46
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.52 E-value=8.8e-14 Score=114.51 Aligned_cols=108 Identities=21% Similarity=0.169 Sum_probs=80.4
Q ss_pred CCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCC-----CCCcceeecHHHHHHHHhhC--C--
Q 037872 8 PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNI-----PDNWRFLDTLPLARELMKQN--G-- 78 (146)
Q Consensus 8 p~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~-----~~~~~~iDt~~l~~~~~~~~--~-- 78 (146)
.+..++++.|.+|+.. ++.++||||..+||..||++.+.+..+.. ......+|++.+++..++.. +
T Consensus 76 ~~e~e~~~~i~~~l~~-----~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~ 150 (476)
T PRK11779 76 LPEAEFAARIHAEFSQ-----PGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGIN 150 (476)
T ss_pred CCHHHHHHHHHHHHhc-----CCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhcccccc
Confidence 3588999999999963 24689999832899999999987654321 11112346666666544310 0
Q ss_pred -----CCCCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhh
Q 037872 79 -----SVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSD 121 (146)
Q Consensus 79 -----~~~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~ 121 (146)
.+..+++|+++++++|++.. .+|+|++||.+|++|+..+.+.
T Consensus 151 ~P~~~~g~~s~rLe~L~~~~gI~~~-~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 151 WPENEDGLPSFKLEHLTKANGIEHE-NAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CcccccCCCCCcHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHHh
Confidence 02478999999999999988 5999999999999999999876
No 47
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=99.49 E-value=2.4e-13 Score=102.21 Aligned_cols=121 Identities=18% Similarity=0.361 Sum_probs=101.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCC-C-CCcEEEEeCCCCCCHH-HHHHHHHHcCCCCCCC-cceeecHHHHHHHHhh
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGP-G-EIAIFVAHNARRFDVP-FLAKEFSRCSMNIPDN-WRFLDTLPLARELMKQ 76 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~-~-~~~~lVahN~~~FD~~-~L~~~~~~~~~~~~~~-~~~iDt~~l~~~~~~~ 76 (146)
+|. .||+|++|+.+|..|+...... . +...+|.++ ..|+. +|..+|++-++..|.. ..|||..+.++..+..
T Consensus 125 tVD--~a~~f~~vl~~f~~Wlr~~~~~~k~~~~Afvtdg--~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~ 200 (280)
T KOG0542|consen 125 TVD--EAPTFPQVLSEFDSWLRKDSLGDKNGKFAFVTDG--DWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNR 200 (280)
T ss_pred hhc--cCCCHHHHHHHHHHHHHHhhcccccCceEEEeCc--hhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcC
Confidence 477 8999999999999999765433 2 567899997 59996 9999999988887731 2899999999999863
Q ss_pred CCCCCCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh-cCHHHH
Q 037872 77 NGSVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN-FTLSDL 129 (146)
Q Consensus 77 ~~~~~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~-~~~~~l 129 (146)
....++..+.+++|++++|.+|++++||.++++|.++|..+.. .+++++
T Consensus 201 ----~~~t~it~mLe~~gL~f~Gr~HsGiDDa~Nia~I~~kM~~dg~~~~In~~ 250 (280)
T KOG0542|consen 201 ----PAPTNITGMLEHYGLQFEGRAHSGIDDARNIARIAQKMIRDGAEFRINEL 250 (280)
T ss_pred ----ccccCHHHHHHHhCCcccCCcccCchhHHHHHHHHHHHHhCCcEEEechh
Confidence 2578999999999999999999999999999999999999876 456544
No 48
>PRK05359 oligoribonuclease; Provisional
Probab=99.49 E-value=1.9e-13 Score=99.89 Aligned_cols=101 Identities=19% Similarity=0.256 Sum_probs=79.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceee--cH-HHHHHHHhhC
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLD--TL-PLARELMKQN 77 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iD--t~-~l~~~~~~~~ 77 (146)
|++ ++|++.+++.+|.+|+++.-. .+..++||||+ .||+.||++.+.+++..+. .+++| |+ .+++.++|.
T Consensus 72 ~l~--~~~~~~e~~~~~l~fl~~~~~-~~~~~l~g~~v-~FD~~FL~~~~~~~~~~l~--~~~~Dv~tl~~l~r~~~P~- 144 (181)
T PRK05359 72 VRA--STVSEAEAEAQTLEFLKQWVP-AGKSPLCGNSI-GQDRRFLARYMPELEAYFH--YRNLDVSTLKELARRWKPE- 144 (181)
T ss_pred HHh--cCCCHHHHHHHHHHHHHHhcC-CCCCceeecch-hhCHHHHHHHHHHhcccCC--CcccchhHHHHHHHHhChh-
Confidence 456 889999999999999975311 22468999999 9999999999988776543 35667 77 799988763
Q ss_pred CCCCCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhh
Q 037872 78 GSVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDL 122 (146)
Q Consensus 78 ~~~~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~ 122 (146)
. +++++..+ .|||++||..+.+.+....+.+
T Consensus 145 ---~----------~~~~~~~~-~HRal~D~~~s~~~~~~~~~~~ 175 (181)
T PRK05359 145 ---I----------LNGFKKQG-THRALADIRESIAELKYYREHF 175 (181)
T ss_pred ---h----------hhCCCCcC-CcccHHHHHHHHHHHHHHHHHh
Confidence 1 36888884 8999999999999998877654
No 49
>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=99.25 E-value=4.6e-11 Score=89.09 Aligned_cols=99 Identities=22% Similarity=0.300 Sum_probs=76.6
Q ss_pred CCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCc---------------ceeecHHHHHH
Q 037872 8 PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNW---------------RFLDTLPLARE 72 (146)
Q Consensus 8 p~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~---------------~~iDt~~l~~~ 72 (146)
..-.+++..|.++++.. ++++||||+++||+++|...+..+|++.|..+ +.+|++.+.+.
T Consensus 76 ~~E~elL~~F~~~i~~~-----~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~ 150 (208)
T cd05782 76 ADEKELLEDFFQLIEKK-----NPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAF 150 (208)
T ss_pred CCHHHHHHHHHHHHHHh-----CCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhc
Confidence 34679999999999874 35899999999999999999999998655321 37899988765
Q ss_pred HHhhCCCCCCCCcHHHHHHHhCCCCCCC------------------CCchHHHHHHHHHHHH
Q 037872 73 LMKQNGSVSSKTSLQALREYFGIPLEGS------------------AHRAMSDVNSLASILE 116 (146)
Q Consensus 73 ~~~~~~~~~~~~~L~~l~~~~gi~~~~~------------------~H~Al~Da~~ta~l~~ 116 (146)
.. ...+++|+++++.+|++.... ...+..||.+|+.||.
T Consensus 151 ~~-----~~~~~~L~~va~~lG~~~K~d~~G~~v~~~y~~g~~~~I~~Yc~~Dv~~t~~l~l 207 (208)
T cd05782 151 YG-----ARARASLDLLAKLLGIPGKMDVDGSQVWELYAEGKLDEIAEYCETDVLNTYLLYL 207 (208)
T ss_pred cC-----ccCCCCHHHHHHHhCCCCCcCCCHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHh
Confidence 32 237899999999999954311 4456778888887775
No 50
>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=99.25 E-value=9.6e-11 Score=87.01 Aligned_cols=104 Identities=25% Similarity=0.350 Sum_probs=83.9
Q ss_pred CHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCC-------Cc---------ceeecHHHHHH
Q 037872 9 RMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPD-------NW---------RFLDTLPLARE 72 (146)
Q Consensus 9 ~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~-------~~---------~~iDt~~l~~~ 72 (146)
...+++..|.+++++. .+.+|+||+++||+++|......+|++.|. +| ..+|+|++...
T Consensus 36 ~E~~lL~~F~~~~~~~-----~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~ 110 (209)
T PF10108_consen 36 DEKELLQDFFDLVEKY-----NPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSF 110 (209)
T ss_pred CHHHHHHHHHHHHHhC-----CCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhc
Confidence 4789999999999874 468999999999999999999999988763 12 35889888543
Q ss_pred HHhhCCCCCCCCcHHHHHHHhCCCCCC------------------CCCchHHHHHHHHHHHHHHHhhh
Q 037872 73 LMKQNGSVSSKTSLQALREYFGIPLEG------------------SAHRAMSDVNSLASILERITSDL 122 (146)
Q Consensus 73 ~~~~~~~~~~~~~L~~l~~~~gi~~~~------------------~~H~Al~Da~~ta~l~~~l~~~~ 122 (146)
+ | .....+|+.+|..+|||... -+.....||++|+.||.++.-..
T Consensus 111 ~----g-~~~~~sLd~la~~lgiPgK~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~~~ 173 (209)
T PF10108_consen 111 Y----G-AKARTSLDELAALLGIPGKDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFELLR 173 (209)
T ss_pred c----C-ccccCCHHHHHHHcCCCCCCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3 1 23689999999999998541 16678999999999999986643
No 51
>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=99.15 E-value=3.6e-10 Score=83.22 Aligned_cols=83 Identities=18% Similarity=0.244 Sum_probs=68.2
Q ss_pred CCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCC-C--------------------Cccee
Q 037872 6 YVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIP-D--------------------NWRFL 64 (146)
Q Consensus 6 ~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~-~--------------------~~~~i 64 (146)
.+++..+++..|.++++.. .+.++||||+.+||+++|.+.+.++|++.. . ...++
T Consensus 59 ~~~~E~~lL~~f~~~i~~~----dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~ 134 (199)
T cd05160 59 YFADEKELLKRFFDIIREY----DPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVF 134 (199)
T ss_pred EeCCHHHHHHHHHHHHHhc----CCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEee
Confidence 4689999999999999875 246999999989999999999999887651 0 12479
Q ss_pred ecHHHHHHHHhhCCCCCCCCcHHHHHHHhCCCC
Q 037872 65 DTLPLARELMKQNGSVSSKTSLQALREYFGIPL 97 (146)
Q Consensus 65 Dt~~l~~~~~~~~~~~~~~~~L~~l~~~~gi~~ 97 (146)
|++.+++..++ ..+++|+++++.++.+.
T Consensus 135 D~~~~~r~~~~-----l~sy~L~~v~~~~l~~~ 162 (199)
T cd05160 135 DLLAAYKRDFK-----LKSYTLDAVAEELLGEG 162 (199)
T ss_pred ehHHHHHHhcC-----cccCCHHHHHHHHhCCC
Confidence 99999998765 47899999999876553
No 52
>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=99.05 E-value=2.8e-09 Score=78.26 Aligned_cols=81 Identities=22% Similarity=0.334 Sum_probs=66.4
Q ss_pred CCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCC-------------------cceeecH
Q 037872 7 VPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDN-------------------WRFLDTL 67 (146)
Q Consensus 7 ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~-------------------~~~iDt~ 67 (146)
.++-.+++..|+++++.. .+.+++|||+.+||+++|...++++|++.+.. -..+|.+
T Consensus 45 ~~~E~~lL~~F~~~i~~~----dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~ 120 (188)
T cd05781 45 GLDDRKIIREFVKYVKEY----DPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLY 120 (188)
T ss_pred CCCHHHHHHHHHHHHHHc----CCCEEEecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhH
Confidence 357889999999999876 35799999999999999999999998754310 0279999
Q ss_pred HHHHHHHhhCCCCCCCCcHHHHHHHhCCC
Q 037872 68 PLARELMKQNGSVSSKTSLQALREYFGIP 96 (146)
Q Consensus 68 ~l~~~~~~~~~~~~~~~~L~~l~~~~gi~ 96 (146)
.+.+...+ ..+++|+++++++|..
T Consensus 121 ~~~~~~~~-----l~~y~L~~Va~~Lg~~ 144 (188)
T cd05781 121 DFAEEIPE-----VKVKTLENVAEYLGVM 144 (188)
T ss_pred HHHHhhCC-----CCCCCHHHHHHHHCCC
Confidence 99887653 5789999999999974
No 53
>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=99.05 E-value=2.7e-09 Score=79.50 Aligned_cols=86 Identities=20% Similarity=0.336 Sum_probs=66.5
Q ss_pred CCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCC---------------------------
Q 037872 7 VPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPD--------------------------- 59 (146)
Q Consensus 7 ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~--------------------------- 59 (146)
.++-.+++.+|++++... .+.++||||+.+||+++|.+.++++|++.+.
T Consensus 55 ~~~E~~lL~~f~~~i~~~----dPdii~g~N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~ 130 (207)
T cd05785 55 DAAEKELLEELVAIIRER----DPDVIEGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYD 130 (207)
T ss_pred CCCHHHHHHHHHHHHHHh----CCCEEeccCCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEE
Confidence 467889999999999876 3579999999999999999999999876520
Q ss_pred --CcceeecHHHHHHHHhhCCCCCCCCcHHHHHHHhCCCC
Q 037872 60 --NWRFLDTLPLARELMKQNGSVSSKTSLQALREYFGIPL 97 (146)
Q Consensus 60 --~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~~gi~~ 97 (146)
....+|++.+.+++.... ....+|+|++++++||+..
T Consensus 131 i~Gr~~iDl~~~~~~~~~~~-~~l~sysL~~Va~~~g~~~ 169 (207)
T cd05785 131 IPGRHVIDTYFLVQLFDVSS-RDLPSYGLKAVAKHFGLAS 169 (207)
T ss_pred ecCEEEEEcHHHHHhhcccc-cCCCCCCHHHHHHHhcccC
Confidence 012389999888643210 1357899999999998744
No 54
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=98.99 E-value=7.8e-09 Score=76.21 Aligned_cols=82 Identities=23% Similarity=0.426 Sum_probs=65.9
Q ss_pred CCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCC---------------------cceeec
Q 037872 8 PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDN---------------------WRFLDT 66 (146)
Q Consensus 8 p~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~---------------------~~~iDt 66 (146)
.+-.+++.+|.+++... .+.++||||+.+||+++|...+.++|++.+.. ...+|+
T Consensus 54 ~~E~~lL~~F~~~i~~~----dpdiivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl 129 (195)
T cd05780 54 KTEKEMIKRFIEIVKEK----DPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDL 129 (195)
T ss_pred CCHHHHHHHHHHHHHHc----CCCEEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeH
Confidence 46679999999999865 24799999998999999999999998875421 137999
Q ss_pred HHHHHHHHhhCCCCCCCCcHHHHHH-HhCCCCC
Q 037872 67 LPLARELMKQNGSVSSKTSLQALRE-YFGIPLE 98 (146)
Q Consensus 67 ~~l~~~~~~~~~~~~~~~~L~~l~~-~~gi~~~ 98 (146)
+.+++...+ ..+++|+++++ .+|.+..
T Consensus 130 ~~~~~~~~~-----l~sy~L~~v~~~~Lg~~k~ 157 (195)
T cd05780 130 YPVARRTLN-----LTRYTLERVYEELFGIEKE 157 (195)
T ss_pred HHHHHhhCC-----CCcCcHHHHHHHHhCCCCC
Confidence 999887543 58999999986 6788754
No 55
>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=98.92 E-value=2e-08 Score=74.65 Aligned_cols=102 Identities=16% Similarity=0.188 Sum_probs=76.7
Q ss_pred CCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCC--C-------------cceeecHHHHH
Q 037872 7 VPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPD--N-------------WRFLDTLPLAR 71 (146)
Q Consensus 7 ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~--~-------------~~~iDt~~l~~ 71 (146)
-++-.+.+.+|.+|+... .+.+++|||+.+||+++|...+.++|++... . ...+|.+.+.+
T Consensus 70 ~~~E~~lL~~f~~~i~~~----~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~ 145 (204)
T cd05779 70 EPDEKALLQRFFEHIREV----KPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVK 145 (204)
T ss_pred CCCHHHHHHHHHHHHHHh----CCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHH
Confidence 357789999999999876 3569999999999999999999998876431 0 12689999887
Q ss_pred HHHhhCCCCCCCCcHHHHHHH-hCCCCCC----------------CCCchHHHHHHHHHHH
Q 037872 72 ELMKQNGSVSSKTSLQALREY-FGIPLEG----------------SAHRAMSDVNSLASIL 115 (146)
Q Consensus 72 ~~~~~~~~~~~~~~L~~l~~~-~gi~~~~----------------~~H~Al~Da~~ta~l~ 115 (146)
..... ..++++|++++++ +|..... -++.++.||.+|..||
T Consensus 146 ~~~~l---~~~sysLd~Va~~~Lg~~K~~~~~~~I~~~~~~~~~~l~~Y~~~D~~~T~~l~ 203 (204)
T cd05779 146 RDSYL---PQGSQGLKAVTKAKLGYDPVELDPEDMVPLAREDPQTLASYSVSDAVATYYLY 203 (204)
T ss_pred HhhcC---CCCCccHHHHHHHHhCCCcCcCCHHHHHHHHhCCcHHHHhccHHHHHHHHHHh
Confidence 64321 1368999999985 8875541 1456677888887776
No 56
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=98.76 E-value=3.7e-08 Score=64.78 Aligned_cols=48 Identities=29% Similarity=0.583 Sum_probs=39.6
Q ss_pred HHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCC-CcceeecHHH
Q 037872 17 VIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPD-NWRFLDTLPL 69 (146)
Q Consensus 17 ~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~-~~~~iDt~~l 69 (146)
|.+|+++. +..++||||+ +||++||.+++.+++++.|. ..+++||+.+
T Consensus 35 f~~~l~~~----~~~v~V~hn~-~fD~~fL~~~~~~~~~~~p~~~~~~lDT~~l 83 (96)
T cd06125 35 LKDILRDK----PLAILVGHNG-SFDLPFLNNRCAELGLKYPLLAGSWIDTIKL 83 (96)
T ss_pred HHHHHhhC----CCCEEEEeCc-HHhHHHHHHHHHHcCCCCCCcCCcEEEehHH
Confidence 88899763 1259999999 89999999999999887663 3479999977
No 57
>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=98.66 E-value=4.4e-07 Score=67.51 Aligned_cols=84 Identities=19% Similarity=0.290 Sum_probs=61.1
Q ss_pred CCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCC---CCC----------CcceeecHHHHHH-H
Q 037872 8 PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMN---IPD----------NWRFLDTLPLARE-L 73 (146)
Q Consensus 8 p~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~---~~~----------~~~~iDt~~l~~~-~ 73 (146)
.+-.+++.+|++++... .++||||+.+||+++|...++++|+. .|. ....+|.+.+.+. .
T Consensus 71 ~~E~~lL~~F~~~i~~~------~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~ 144 (204)
T cd05783 71 DSEKELIREAFKIISEY------PIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRA 144 (204)
T ss_pred CCHHHHHHHHHHHHhcC------CEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccc
Confidence 56789999999999863 69999999999999999999999887 111 1246888876543 1
Q ss_pred Hh--hCCCCCCCCcHHHHHHHh-CCCC
Q 037872 74 MK--QNGSVSSKTSLQALREYF-GIPL 97 (146)
Q Consensus 74 ~~--~~~~~~~~~~L~~l~~~~-gi~~ 97 (146)
.+ ..+....+++|+++++++ |...
T Consensus 145 ~~~~~~~~~~~~~~L~~Va~~~lg~~K 171 (204)
T cd05783 145 IQVYAFGNKYREYTLDAVAKALLGEGK 171 (204)
T ss_pred hhhhhhccccccCcHHHHHHHhcCCCc
Confidence 10 001124799999999876 5443
No 58
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=98.65 E-value=8.1e-08 Score=73.29 Aligned_cols=137 Identities=34% Similarity=0.392 Sum_probs=106.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCC-
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGS- 79 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~- 79 (146)
|++++..+..++....|..+.+.++.+++....+.||+..|+..|..+++-|.+-..+.+|..|+.|..++.-.....+
T Consensus 169 ~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~~ellR~~deqa~pw~~ir~l~~~~~~a~~~~P~ 248 (318)
T KOG4793|consen 169 MVTRPEVRRMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRINELLRWSDEQARPWLLIRPLYLARENAKSVEPT 248 (318)
T ss_pred cccCCCCCcccccchHHHhhhcccCCCcceeeecccchhHHHHHHHHHHHHhhHhhcCCCcccccchhhhhhhccccCCC
Confidence 5666666677778888999999888888888889999989999999999988776555568889988765443221111
Q ss_pred CCCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhhcCHHHHHHhhcccc
Q 037872 80 VSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLNFTLSDLLKTSFRAN 137 (146)
Q Consensus 80 ~~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~~~~~~l~~~~~~~~ 137 (146)
....++|+.++.++....++.+|+|+.|+..+..+++++-.++-.+++++.-..-+..
T Consensus 249 p~~vs~le~Lat~~~~~p~l~ahra~~Dv~~~~k~~q~~~idlla~l~~lai~~~~v~ 306 (318)
T KOG4793|consen 249 PKLVSSLEALATYYSLTPELDAHRALSDVLLLSKVFQKLTIDLLASLSDLAIRCHTVS 306 (318)
T ss_pred CccchhHHHHHHHhhcCcccchhhhccccchhhhHHHHhhhhhhhhhhhhhhhhhccc
Confidence 2367899999999988777779999999999999999998888777777664443333
No 59
>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=98.61 E-value=1e-06 Score=65.04 Aligned_cols=79 Identities=15% Similarity=0.215 Sum_probs=61.9
Q ss_pred CCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCC-----------------------Cccee
Q 037872 8 PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPD-----------------------NWRFL 64 (146)
Q Consensus 8 p~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~-----------------------~~~~i 64 (146)
++-.+.+..|.+++... .+.+++|||+.+||+++|.+.+.+++++... ....+
T Consensus 49 ~~E~~lL~~f~~~i~~~----dPDvi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~ 124 (193)
T cd05784 49 ADEKSLLLALIAWFAQY----DPDIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVL 124 (193)
T ss_pred CCHHHHHHHHHHHHHhh----CCCEEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEE
Confidence 56788999999999876 3579999999999999999999998876420 01268
Q ss_pred ecHHHHHH-HHhhCCCCCCCCcHHHHHHHh-CC
Q 037872 65 DTLPLARE-LMKQNGSVSSKTSLQALREYF-GI 95 (146)
Q Consensus 65 Dt~~l~~~-~~~~~~~~~~~~~L~~l~~~~-gi 95 (146)
|++.+.+. .+ +..+|+|+++++++ |.
T Consensus 125 D~~~~~k~~~~-----kl~sy~L~~Va~~~Lg~ 152 (193)
T cd05784 125 DGIDALKTATY-----HFESFSLENVAQELLGE 152 (193)
T ss_pred EhHHHHHHccC-----CCCcCCHHHHHHHHhCC
Confidence 88888765 23 25899999999865 54
No 60
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=98.60 E-value=2.7e-07 Score=73.63 Aligned_cols=107 Identities=21% Similarity=0.203 Sum_probs=75.2
Q ss_pred HHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCC-CCCCc----ceeecHHHHHHHH---hh-----
Q 037872 10 MEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMN-IPDNW----RFLDTLPLARELM---KQ----- 76 (146)
Q Consensus 10 f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~-~~~~~----~~iDt~~l~~~~~---~~----- 76 (146)
-.+....+..-+.. +..+++|||...||-.+.++-|-|+=+. +...| .-+|.+.+.|.-+ |.
T Consensus 81 E~~F~~~I~~~ls~-----P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp 155 (475)
T COG2925 81 EAAFAARIHAELTQ-----PNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWP 155 (475)
T ss_pred hHHHHHHHHHHhCC-----CCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcccCCCC
Confidence 34555666665654 5689999999999999999888775322 21111 2244455444433 32
Q ss_pred -CCCCCCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhh
Q 037872 77 -NGSVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDL 122 (146)
Q Consensus 77 -~~~~~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~ 122 (146)
.+.|..+++|+.+...-||+.+ ++|+|++||.+|..+-+.+....
T Consensus 156 ~n~dG~pSFkLEhLt~ANgieH~-nAHdAmsDVyATIamAklvk~~Q 201 (475)
T COG2925 156 ENDDGLPSFKLEHLTKANGIEHS-NAHDAMSDVYATIAMAKLVKTAQ 201 (475)
T ss_pred cCCCCCcchhhHHHhhccccccc-hhhHHHHHHHHHHHHHHHHHhhC
Confidence 2235789999999999999998 69999999999998877665543
No 61
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=98.59 E-value=3.5e-07 Score=66.38 Aligned_cols=109 Identities=19% Similarity=0.248 Sum_probs=79.8
Q ss_pred CCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHH
Q 037872 8 PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQ 87 (146)
Q Consensus 8 p~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~ 87 (146)
+.+.+++..|.+++.+. ...+|+||+ .||+.+|. ++|+..+. .++||+.++..+.|. ..+.+|.
T Consensus 50 ~~~~~~~~~l~~~l~~~-----~~~~v~hn~-k~d~~~l~----~~gi~~~~--~~~Dt~l~a~ll~p~----~~~~~l~ 113 (193)
T cd06139 50 LPREEVLAALKPLLEDP-----SIKKVGQNL-KFDLHVLA----NHGIELRG--PAFDTMLASYLLNPG----RRRHGLD 113 (193)
T ss_pred CCHHHHHHHHHHHHhCC-----CCcEEeecc-HHHHHHHH----HCCCCCCC--CcccHHHHHHHhCCC----CCCCCHH
Confidence 56888999999999762 347999999 89999985 45666442 579999999888663 2256999
Q ss_pred HHHHHh-CCCC----------------CC-----CCCchHHHHHHHHHHHHHHHhhhh--cCHHHHHHh
Q 037872 88 ALREYF-GIPL----------------EG-----SAHRAMSDVNSLASILERITSDLN--FTLSDLLKT 132 (146)
Q Consensus 88 ~l~~~~-gi~~----------------~~-----~~H~Al~Da~~ta~l~~~l~~~~~--~~~~~l~~~ 132 (146)
++++.| |... +. ..|+|..||.+|..++..+.+.+. ..+.+++..
T Consensus 114 ~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~~~~~~~~l~~~ 182 (193)
T cd06139 114 DLAERYLGHKTISFEDLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLKEEPGLLELYEE 182 (193)
T ss_pred HHHHHHhCCCCccHHHHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHH
Confidence 998875 4320 00 234689999999999999988774 345566543
No 62
>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=98.58 E-value=1.3e-06 Score=65.98 Aligned_cols=103 Identities=18% Similarity=0.215 Sum_probs=73.4
Q ss_pred CCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCC----------------------------
Q 037872 8 PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPD---------------------------- 59 (146)
Q Consensus 8 p~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~---------------------------- 59 (146)
++-.+.+..|.+++... .+.+++|||+.+||+++|.+.++++|++...
T Consensus 69 ~~E~eLL~~f~~~i~~~----DPDii~GyN~~~FDl~yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~ 144 (230)
T cd05777 69 ETEEELLLAWRDFVQEV----DPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETK 144 (230)
T ss_pred CCHHHHHHHHHHHHHhc----CCCEEEEecCCCCCHHHHHHHHHHhCCccccccccccCCceeEeCCcccccccccccce
Confidence 56789999999999876 3579999999999999999999888765210
Q ss_pred -----CcceeecHHHHHHHHhhCCCCCCCCcHHHHHHH-hCCCCCCC-------------------CCchHHHHHHHHHH
Q 037872 60 -----NWRFLDTLPLARELMKQNGSVSSKTSLQALREY-FGIPLEGS-------------------AHRAMSDVNSLASI 114 (146)
Q Consensus 60 -----~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~~~-------------------~H~Al~Da~~ta~l 114 (146)
.-..+|++.+.+..+ ...+|+|++++++ +|.....- ....+.||..|.+|
T Consensus 145 ~~~i~GR~~iD~~~~~~~~~-----kl~sy~L~~Va~~~Lg~~k~d~~~~~i~~~~~~~~~~~~~l~~Y~~~Da~l~l~L 219 (230)
T cd05777 145 EINIEGRIQFDLLQVIQRDY-----KLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRL 219 (230)
T ss_pred EEEEcCEEeeeHHHHHHHhc-----CcccCcHHHHHHHHhCCCCCCCCHHHHHHHHccCHhHhHHHHHhhHHHHHHHHHH
Confidence 013468888887754 2589999999985 56443310 22445666666666
Q ss_pred HHHHH
Q 037872 115 LERIT 119 (146)
Q Consensus 115 ~~~l~ 119 (146)
+.++.
T Consensus 220 ~~kl~ 224 (230)
T cd05777 220 LDKLM 224 (230)
T ss_pred HHHHh
Confidence 66553
No 63
>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=98.49 E-value=2e-07 Score=66.39 Aligned_cols=74 Identities=23% Similarity=0.486 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHH
Q 037872 11 EDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALR 90 (146)
Q Consensus 11 ~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~ 90 (146)
++.+.++++++.+ ...+|+||+.+||+++|++.+.+++++.+ ..++|++..++... ..+++|.+++
T Consensus 44 e~~~~~~~~~l~~------~~~iv~yng~~FD~p~L~~~~~~~~~~~~--~~~iDl~~~~~~~~------~~~~~Lk~ve 109 (164)
T PF13482_consen 44 EEIILEFFELLDE------ADNIVTYNGKNFDIPFLKRRAKRYGLPPP--FNHIDLLKIIKKHF------LESYSLKNVE 109 (164)
T ss_dssp HHHHHH--HHHHT------T--EEESSTTTTHHHHHHHHH-HHHH--G--GGEEEHHHHHT-TT------SCCTT--SHH
T ss_pred HHHHHHHHHHHhc------CCeEEEEeCcccCHHHHHHHHHHcCCCcc--cchhhHHHHHHhcc------CCCCCHHHHh
Confidence 3444554467775 37899999889999999999988877653 47899999886543 3688999999
Q ss_pred HHhCCCCC
Q 037872 91 EYFGIPLE 98 (146)
Q Consensus 91 ~~~gi~~~ 98 (146)
+.+|++..
T Consensus 110 ~~lg~~~~ 117 (164)
T PF13482_consen 110 KFLGIERR 117 (164)
T ss_dssp H-------
T ss_pred hhcccccc
Confidence 99999775
No 64
>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=98.45 E-value=6.8e-07 Score=64.76 Aligned_cols=88 Identities=19% Similarity=0.289 Sum_probs=66.8
Q ss_pred CCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHH
Q 037872 8 PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQ 87 (146)
Q Consensus 8 p~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~ 87 (146)
.++.++..++.+++.. +.++|||.. +.|+..|+ +..|.. ..+||-.++.. + .....+|.
T Consensus 86 ~t~~~v~~~l~~li~~------~tILVGHsL-~nDL~aL~-------l~hp~~-~viDTa~l~~~--~----~~r~~sLk 144 (174)
T cd06143 86 TTLKSAYLKLRLLVDL------GCIFVGHGL-AKDFRVIN-------IQVPKE-QVIDTVELFHL--P----GQRKLSLR 144 (174)
T ss_pred CCHHHHHHHHHHHcCC------CCEEEeccc-hhHHHHhc-------CcCCCc-ceEEcHHhccC--C----CCCChhHH
Confidence 4789999999999963 479999999 89988874 443432 68999765431 2 13578999
Q ss_pred HHHH-HhCCCCCCCCCchHHHHHHHHHHHH
Q 037872 88 ALRE-YFGIPLEGSAHRAMSDVNSLASILE 116 (146)
Q Consensus 88 ~l~~-~~gi~~~~~~H~Al~Da~~ta~l~~ 116 (146)
.|++ ++|.+.....|++..||.++++||+
T Consensus 145 ~La~~~L~~~IQ~~~HdSvEDArAam~Ly~ 174 (174)
T cd06143 145 FLAWYLLGEKIQSETHDSIEDARTALKLYR 174 (174)
T ss_pred HHHHHHcCCcccCCCcCcHHHHHHHHHHhC
Confidence 9985 5676554348999999999999983
No 65
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=98.44 E-value=1.3e-06 Score=66.54 Aligned_cols=98 Identities=19% Similarity=0.275 Sum_probs=73.1
Q ss_pred CCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHH--HHHHHhhCCCCCCC
Q 037872 6 YVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPL--ARELMKQNGSVSSK 83 (146)
Q Consensus 6 ~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l--~~~~~~~~~~~~~~ 83 (146)
+|.+|..|-.++.++|.+ .|+|||.. .-|+..|.- ..|.. ..-||-.+ .+.++.. ...
T Consensus 167 ~A~pf~~aQ~ev~klL~g-------RIlVGHaL-hnDl~~L~l-------~hp~s-~iRDTs~~~pl~k~~~~----~~t 226 (280)
T KOG2249|consen 167 DAMPFKVAQKEVLKLLKG-------RILVGHAL-HNDLQALKL-------EHPRS-MIRDTSKYPPLMKLLSK----KAT 226 (280)
T ss_pred cCccHHHHHHHHHHHHhC-------CEEecccc-ccHHHHHhh-------hCchh-hhcccccCchHHHHhhc----cCC
Confidence 789999999999999997 49999998 889887753 33332 34555332 2222332 367
Q ss_pred CcHHHHHH-HhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh
Q 037872 84 TSLQALRE-YFGIPLEGSAHRAMSDVNSLASILERITSDLN 123 (146)
Q Consensus 84 ~~L~~l~~-~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~ 123 (146)
.+|..|++ .+|++.....|+...||.+|++||.++..++.
T Consensus 227 pSLK~Lt~~~Lg~~IQ~GeHsSvEDA~AtM~LY~~vk~qwe 267 (280)
T KOG2249|consen 227 PSLKKLTEALLGKDIQVGEHSSVEDARATMELYKRVKVQWE 267 (280)
T ss_pred ccHHHHHHHHhchhhhccccCcHHHHHHHHHHHHHHHHHHH
Confidence 89999985 56876543379999999999999999987764
No 66
>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=98.37 E-value=7.4e-06 Score=62.10 Aligned_cols=82 Identities=20% Similarity=0.328 Sum_probs=63.8
Q ss_pred CCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCC------------CC--------------Cc
Q 037872 8 PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNI------------PD--------------NW 61 (146)
Q Consensus 8 p~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~------------~~--------------~~ 61 (146)
++..+.+..|+.++... .+.++||||..+||+++|.+.++.++++. |. .-
T Consensus 80 ~~E~~LL~~f~~~i~~~----DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GR 155 (234)
T cd05776 80 ENERALLNFFLAKLQKI----DPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGR 155 (234)
T ss_pred CCHHHHHHHHHHHHhhc----CCCEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCc
Confidence 45678899999999876 35799999999999999999998877642 00 01
Q ss_pred ceeecHHHHHHHHhhCCCCCCCCcHHHHHH-HhCCCCC
Q 037872 62 RFLDTLPLARELMKQNGSVSSKTSLQALRE-YFGIPLE 98 (146)
Q Consensus 62 ~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~-~~gi~~~ 98 (146)
..+|++..++.+.+ ..+|+|.++++ .+|.+..
T Consensus 156 l~~D~~~~~k~~~~-----~~sY~L~~va~~~Lg~~k~ 188 (234)
T cd05776 156 LLCDTYLSAKELIR-----CKSYDLTELSQQVLGIERQ 188 (234)
T ss_pred hhhccHHHHHHHhC-----CCCCChHHHHHHHhCcCcc
Confidence 35788888888764 48999999997 6787543
No 67
>PRK05762 DNA polymerase II; Reviewed
Probab=98.34 E-value=9.7e-06 Score=71.13 Aligned_cols=103 Identities=15% Similarity=0.182 Sum_probs=78.1
Q ss_pred CCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCC--------------CC----------cce
Q 037872 8 PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIP--------------DN----------WRF 63 (146)
Q Consensus 8 p~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~--------------~~----------~~~ 63 (146)
++-.+.+..|++++... .+.+++|||+.+||+++|.+.++.+|++.. .. -..
T Consensus 201 ~sE~~LL~~F~~~i~~~----DPDIIvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~ 276 (786)
T PRK05762 201 ADEKALLEKFNAWFAEH----DPDVIIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLV 276 (786)
T ss_pred CCHHHHHHHHHHHHHhc----CCCEEEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEE
Confidence 57789999999999876 357999999999999999999998887531 00 136
Q ss_pred eecHHHHHHHHhhCCCCCCCCcHHHHHHHhCCCCCC--C-------------------CCchHHHHHHHHHHHHHH
Q 037872 64 LDTLPLARELMKQNGSVSSKTSLQALREYFGIPLEG--S-------------------AHRAMSDVNSLASILERI 118 (146)
Q Consensus 64 iDt~~l~~~~~~~~~~~~~~~~L~~l~~~~gi~~~~--~-------------------~H~Al~Da~~ta~l~~~l 118 (146)
+|++.+.+.... ...+++|+++++++..+... . ....+.||..|..|+.++
T Consensus 277 lDl~~~~k~~~~----~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 277 LDGIDALKSATW----VFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred EEHHHHHHHhhc----cCCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHh
Confidence 899999887652 25799999999876543210 1 124688999999999843
No 68
>PRK05755 DNA polymerase I; Provisional
Probab=98.30 E-value=1.9e-06 Score=76.41 Aligned_cols=95 Identities=18% Similarity=0.244 Sum_probs=74.1
Q ss_pred HHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHHH
Q 037872 12 DLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALRE 91 (146)
Q Consensus 12 ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~ 91 (146)
++++.|.+++++ +..+.|+||+ .||+.+|.+ +|++.+. .++||+.++..+.+. . +++|+++++
T Consensus 357 ~~l~~l~~~L~d-----~~v~kV~HNa-kfDl~~L~~----~gi~~~~--~~~DT~iAa~Ll~~~----~-~~~L~~L~~ 419 (880)
T PRK05755 357 EVLAALKPLLED-----PAIKKVGQNL-KYDLHVLAR----YGIELRG--IAFDTMLASYLLDPG----R-RHGLDSLAE 419 (880)
T ss_pred HHHHHHHHHHhC-----CCCcEEEecc-HhHHHHHHh----CCCCcCC--CcccHHHHHHHcCCC----C-CCCHHHHHH
Confidence 688889999986 2456899999 999999974 4766542 689999988777652 2 389999998
Q ss_pred Hh-CCCCC------------------CCCCchHHHHHHHHHHHHHHHhhhh
Q 037872 92 YF-GIPLE------------------GSAHRAMSDVNSLASILERITSDLN 123 (146)
Q Consensus 92 ~~-gi~~~------------------~~~H~Al~Da~~ta~l~~~l~~~~~ 123 (146)
.| |++.. ...|+|..||..|..|+..+.+.+.
T Consensus 420 ~ylg~~~~~~~~~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~L~ 470 (880)
T PRK05755 420 RYLGHKTISFEEVAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKLL 470 (880)
T ss_pred HHhCCCccchHHhcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77 55520 1248999999999999999988764
No 69
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=98.23 E-value=1.3e-05 Score=61.39 Aligned_cols=108 Identities=26% Similarity=0.363 Sum_probs=80.8
Q ss_pred HHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCC-----CCCCCCcH
Q 037872 12 DLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNG-----SVSSKTSL 86 (146)
Q Consensus 12 ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~-----~~~~~~~L 86 (146)
++.+-+..|++.- ....++|+||+..||+++|.+++...|+..|.....+|++...+.+..... ...++++|
T Consensus 105 dla~LL~afls~l---p~p~CLVaHng~~~dfpil~qela~lg~~lpq~lvcvdslpa~~ald~a~s~~tr~~~~~~~~l 181 (318)
T KOG4793|consen 105 DLAKLLTAFLSRL---PTPGCLVAHNGNEYDFPILAQELAGLGYSLPQDLVCVDSLPALNALDRANSMVTRPEVRRMYSL 181 (318)
T ss_pred HHHHHHHHHHhcC---CCCceEEeecCCccccHHHHHHHHhcCccchhhhcCcchhHHHHHHhhhcCcccCCCCCccccc
Confidence 3444555666532 245799999999999999999999999988865566889888777764322 13578999
Q ss_pred HHHHHH-hCC-CCCCCCCchHHHHHHHHHHHHHHHhhhh
Q 037872 87 QALREY-FGI-PLEGSAHRAMSDVNSLASILERITSDLN 123 (146)
Q Consensus 87 ~~l~~~-~gi-~~~~~~H~Al~Da~~ta~l~~~l~~~~~ 123 (146)
..+... ++- +.+ ..|.|+.|+....-+|+-...++.
T Consensus 182 ~~If~ry~~q~epp-a~~~~e~d~~~l~~~fqf~~~ell 219 (318)
T KOG4793|consen 182 GSIFLRYVEQREPP-AGHVAEGDVNGLLFIFQFRINELL 219 (318)
T ss_pred chHHHhhhcccCCC-cceeeecccchhHHHHHHHHHHHH
Confidence 998755 454 444 499999999999999988877653
No 70
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=98.05 E-value=1.2e-05 Score=61.83 Aligned_cols=78 Identities=35% Similarity=0.409 Sum_probs=58.4
Q ss_pred CcEEEEeCCCCCCHHHHHHHHHHcCCCCCCC------------cceeecHHHHHHHHhhCCCCCCCCcHHHHHHHhCCCC
Q 037872 30 IAIFVAHNARRFDVPFLAKEFSRCSMNIPDN------------WRFLDTLPLARELMKQNGSVSSKTSLQALREYFGIPL 97 (146)
Q Consensus 30 ~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~------------~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~~gi~~ 97 (146)
..+|||||+ -+|+.+|.+.+.. +.|.. -.++||.-++.... ....+|+.+.+.++...
T Consensus 149 ~~p~Vghn~-~~Dl~~l~~~f~~---~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~------~~~~~L~~l~~~l~~~~ 218 (262)
T PF04857_consen 149 KKPIVGHNG-LYDLMYLYKKFIG---PLPETLEEFKELLRELFPRIYDTKYLAEECP------GKSTSLQELAEELGIRR 218 (262)
T ss_dssp -SEEEESST-HHHHHHHHHHHTT---S--SSHHHHHHHHHHHSSSEEEHHHHHTSTT------TS-SSHHHHHHHTTSTT
T ss_pred CCcEEEeCh-HhHHHHHHHHhcC---CCCCCHHHHHHHHHHHCcccccHHHHHHhcc------ccccCHHHHHHHhCCCc
Confidence 479999999 8999999887654 33321 25789988876432 25789999999999875
Q ss_pred -----------------------CCC-CCchHHHHHHHHHHHHH
Q 037872 98 -----------------------EGS-AHRAMSDVNSLASILER 117 (146)
Q Consensus 98 -----------------------~~~-~H~Al~Da~~ta~l~~~ 117 (146)
.+. .|.|-.||++|+.||.+
T Consensus 219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~HeAGyDA~mTg~~F~~ 262 (262)
T PF04857_consen 219 NPSSISSPEGFPSYDEEKNNFPMFGEKAHEAGYDAYMTGCVFIK 262 (262)
T ss_dssp ----EEE-TTS-------------SS-TTSHHHHHHHHHHHHHH
T ss_pred cccccccccccccccccccccccCCCCCCCcchHHHHHHHHHcC
Confidence 333 99999999999999864
No 71
>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=98.01 E-value=0.00018 Score=54.43 Aligned_cols=107 Identities=11% Similarity=0.110 Sum_probs=74.5
Q ss_pred CCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCC--------C--------------------
Q 037872 8 PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIP--------D-------------------- 59 (146)
Q Consensus 8 p~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~--------~-------------------- 59 (146)
++-.+.+.+|.+++... .+.+++|||+.+||+++|.+.++.+++... .
T Consensus 79 ~~E~~LL~~f~~~i~~~----DPDii~GyNi~~fd~~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~~g~~~~~~ 154 (231)
T cd05778 79 ESELELFEELIDLVRRF----DPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDEWGYTHTSG 154 (231)
T ss_pred CCHHHHHHHHHHHHHHh----CCCEEEEeccccCcHHHHHHHHHHhCCcchhhhccCCCCCCcccccccccccccccCCc
Confidence 56788999999999877 358999999999999999988877654321 0
Q ss_pred ----CcceeecHHHHHHHHhhCCCCCCCCcHHHHHH-HhCCCCCCCCCchHHHHH------HHHHHHHHHHhhhh
Q 037872 60 ----NWRFLDTLPLARELMKQNGSVSSKTSLQALRE-YFGIPLEGSAHRAMSDVN------SLASILERITSDLN 123 (146)
Q Consensus 60 ----~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~-~~gi~~~~~~H~Al~Da~------~ta~l~~~l~~~~~ 123 (146)
.-..+|++.+.+..+ +..+|+|++++. .+|-..+.-.|..+.+.+ ...++..-++++..
T Consensus 155 ~~i~GRi~lD~~~~~r~~~-----kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~ 224 (231)
T cd05778 155 IKIVGRHILNVWRLMRSEL-----ALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVR 224 (231)
T ss_pred eEEeeEEEeEhHHHHHHHc-----CcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHH
Confidence 012367888777654 368999999997 568766643455566553 34555555555443
No 72
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=97.97 E-value=8e-05 Score=56.53 Aligned_cols=65 Identities=23% Similarity=0.479 Sum_probs=53.9
Q ss_pred CcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHHHHhCCCCC
Q 037872 30 IAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREYFGIPLE 98 (146)
Q Consensus 30 ~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~~gi~~~ 98 (146)
...+|.+|++.||++|+++ +.+..++.......+|.|.-+|+++... ...-+|.++-+.+|+..+
T Consensus 156 ~~~lvsfNGkaFD~PfikR-~v~~~~el~l~~~H~DL~h~~RRlwk~~---l~~c~Lk~VEr~LGi~R~ 220 (278)
T COG3359 156 FNMLVSFNGKAFDIPFIKR-MVRDRLELSLEFGHFDLYHPSRRLWKHL---LPRCGLKTVERILGIRRE 220 (278)
T ss_pred cceEEEecCcccCcHHHHH-HHhcccccCccccchhhhhhhhhhhhcc---CCCCChhhHHHHhCcccc
Confidence 3699999999999999994 7777666554457899999999998653 577899999999999765
No 73
>PHA02528 43 DNA polymerase; Provisional
Probab=97.87 E-value=0.0002 Score=63.63 Aligned_cols=103 Identities=17% Similarity=0.246 Sum_probs=76.6
Q ss_pred CCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHH-cCCCC-------C--------C------------
Q 037872 8 PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSR-CSMNI-------P--------D------------ 59 (146)
Q Consensus 8 p~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~-~~~~~-------~--------~------------ 59 (146)
++-.+.+..|++|+... .+.+++|||+.+||+++|...+++ +|... . .
T Consensus 176 ~sE~eLL~~F~~~i~~~----DPDII~GyNi~~FDlpYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~ 251 (881)
T PHA02528 176 DTEREMLLEYINFWEEN----TPVIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDIS 251 (881)
T ss_pred CCHHHHHHHHHHHHHHh----CCcEEEecCCccCCHHHHHHHHHHHcCcccccccccccccccccccccccccceeEEEc
Confidence 56789999999999776 357999999999999999988875 35321 0 0
Q ss_pred CcceeecHHHHHHHHhhCCCCCCCCcHHHHHHH-hCCCCCC----------------CCCchHHHHHHHHHHHHH
Q 037872 60 NWRFLDTLPLARELMKQNGSVSSKTSLQALREY-FGIPLEG----------------SAHRAMSDVNSLASILER 117 (146)
Q Consensus 60 ~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~~----------------~~H~Al~Da~~ta~l~~~ 117 (146)
.-..+|.+.+.+.+.-. ...+++|++++++ +|..... -.+..+.||..+.+|+.+
T Consensus 252 GRv~lD~~dl~k~~~~~---~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 252 GISILDYLDLYKKFTFT---NQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred ceEEEeHHHHHHHhhhc---ccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 01246778888775211 2579999999985 8875542 145778999999999988
No 74
>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=97.86 E-value=3.9e-05 Score=54.53 Aligned_cols=93 Identities=25% Similarity=0.366 Sum_probs=65.8
Q ss_pred HHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHHHH
Q 037872 13 LIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREY 92 (146)
Q Consensus 13 v~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~ 92 (146)
+++.+.+++++ ++.+.||||+ .||+..|.+. +|+... .++||+-.+..+.+. .+++|.+++..
T Consensus 65 ~~~~l~~ll~~-----~~i~kv~~n~-~~D~~~L~~~---~~i~~~---~~~D~~l~~~~l~~~-----~~~~L~~L~~~ 127 (176)
T PF01612_consen 65 ILDALKELLED-----PNIIKVGHNA-KFDLKWLYRS---FGIDLK---NVFDTMLAAYLLDPT-----RSYSLKDLAEE 127 (176)
T ss_dssp HHHHHHHHHTT-----TTSEEEESSH-HHHHHHHHHH---HTS--S---SEEEHHHHHHHTTTS-----TTSSHHHHHHH
T ss_pred hHHHHHHHHhC-----CCccEEEEEE-echHHHHHHH---hccccC---Cccchhhhhhccccc-----ccccHHHHHHH
Confidence 57788888876 4578999999 8999999875 566532 679995555544331 33999999754
Q ss_pred -hC-CCCC-----C--C---------CCchHHHHHHHHHHHHHHHhhh
Q 037872 93 -FG-IPLE-----G--S---------AHRAMSDVNSLASILERITSDL 122 (146)
Q Consensus 93 -~g-i~~~-----~--~---------~H~Al~Da~~ta~l~~~l~~~~ 122 (146)
+| ++.+ + . ...|..||..|.+|+..+..++
T Consensus 128 ~l~~~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l 175 (176)
T PF01612_consen 128 YLGNIDLDKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQL 175 (176)
T ss_dssp HHSEEE-GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred HhhhccCcHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 57 3321 1 1 3468889999999999998765
No 75
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=97.84 E-value=7.9e-05 Score=55.53 Aligned_cols=87 Identities=23% Similarity=0.244 Sum_probs=66.4
Q ss_pred CCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCC----------cceeecHHHHHHHHhhCCCCCCCCcHHHHHHHhCCCCC
Q 037872 29 EIAIFVAHNARRFDVPFLAKEFSRCSMNIPDN----------WRFLDTLPLARELMKQNGSVSSKTSLQALREYFGIPLE 98 (146)
Q Consensus 29 ~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~----------~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~~gi~~~ 98 (146)
+...||.+.. +||.++|-+-+..-.+|.... ..+.|+..+++.--. .....+|+++|+.+|++.-
T Consensus 141 ~~V~WvTFhs-~YDfgYLlK~Lt~~~LP~~~~eF~~~v~~~fp~vYDiK~l~~~c~~----~~l~~GL~~lA~~L~~~Rv 215 (239)
T KOG0304|consen 141 ENVTWVTFHS-GYDFGYLLKILTGKPLPETEEEFFEIVRQLFPFVYDVKYLMKFCEG----LSLKGGLQRLADLLGLKRV 215 (239)
T ss_pred CceEEEEeec-cchHHHHHHHHcCCCCcchHHHHHHHHHHHcchhhhHHHHHHhhhh----hhhhcCHHHHHHHhCCCee
Confidence 4689999999 999999988776544442210 144666566544321 1257899999999999999
Q ss_pred CCCCchHHHHHHHHHHHHHHHh
Q 037872 99 GSAHRAMSDVNSLASILERITS 120 (146)
Q Consensus 99 ~~~H~Al~Da~~ta~l~~~l~~ 120 (146)
|.+|.|-+|++.|+.+|.++.+
T Consensus 216 G~~HqAGSDSlLT~~~F~kl~~ 237 (239)
T KOG0304|consen 216 GIAHQAGSDSLLTARVFFKLKE 237 (239)
T ss_pred ecccccCcHHHHHHHHHHHHHh
Confidence 9999999999999999999875
No 76
>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=97.80 E-value=0.00014 Score=53.62 Aligned_cols=100 Identities=18% Similarity=0.216 Sum_probs=67.6
Q ss_pred HHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCC------CCCCCCcHHH
Q 037872 15 PIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNG------SVSSKTSLQA 88 (146)
Q Consensus 15 ~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~------~~~~~~~L~~ 88 (146)
+.+.+++.+ +..+-||||+ .+|+..|.+.+............++||..+++.+..... ......+|..
T Consensus 72 ~~L~~ll~d-----~~i~KVg~~~-~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~ 145 (193)
T cd06146 72 RLLKRLFED-----PDVLKLGFGF-KQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLAD 145 (193)
T ss_pred HHHHHHhCC-----CCeeEEEech-HHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHH
Confidence 345566665 3456799999 899999986554321100111378999999887753210 0135789999
Q ss_pred HHHHh-CCCCC---------------CCCCchHHHHHHHHHHHHHHHh
Q 037872 89 LREYF-GIPLE---------------GSAHRAMSDVNSLASILERITS 120 (146)
Q Consensus 89 l~~~~-gi~~~---------------~~~H~Al~Da~~ta~l~~~l~~ 120 (146)
+++.+ |.+.+ .+-+.|..||..+..||.++.+
T Consensus 146 l~~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~~ 193 (193)
T cd06146 146 LVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLLE 193 (193)
T ss_pred HHHHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 99764 65543 1467999999999999998863
No 77
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=97.80 E-value=0.00031 Score=63.59 Aligned_cols=103 Identities=17% Similarity=0.160 Sum_probs=76.6
Q ss_pred CCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCC-C--------C-------------------
Q 037872 8 PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNI-P--------D------------------- 59 (146)
Q Consensus 8 p~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~-~--------~------------------- 59 (146)
++-.+.+..|.+++... .+.+++|||+.+||+++|...++.+++.. . .
T Consensus 328 ~sE~eLL~~f~~~I~~~----DPDII~GYNi~~FDlpYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~ 403 (1054)
T PTZ00166 328 ETEKELLLAWAEFVIAV----DPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESK 403 (1054)
T ss_pred CCHHHHHHHHHHHHHhc----CCCEEEecCCcCCcHHHHHHHHHHhCCCchhhcCcccCCCccccccccccccccccccc
Confidence 46788999999999876 35899999999999999999888766541 0 0
Q ss_pred -----CcceeecHHHHHHHHhhCCCCCCCCcHHHHHHH-hCCCCCCC-------------------CCchHHHHHHHHHH
Q 037872 60 -----NWRFLDTLPLARELMKQNGSVSSKTSLQALREY-FGIPLEGS-------------------AHRAMSDVNSLASI 114 (146)
Q Consensus 60 -----~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~~~-------------------~H~Al~Da~~ta~l 114 (146)
.-..+|++.+.+..+ ...+|+|++++.+ +|...+.- ....+.||..+.+|
T Consensus 404 ~~~i~GR~~iDl~~~~~~~~-----kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L 478 (1054)
T PTZ00166 404 EINIEGRIQFDVMDLIRRDY-----KLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRL 478 (1054)
T ss_pred eeEeeeEEEEEHHHHHHHhc-----CcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHH
Confidence 013578888887764 3689999999985 46544310 22567899999999
Q ss_pred HHHHH
Q 037872 115 LERIT 119 (146)
Q Consensus 115 ~~~l~ 119 (146)
+.++.
T Consensus 479 ~~kl~ 483 (1054)
T PTZ00166 479 LDKLL 483 (1054)
T ss_pred HHHHh
Confidence 88864
No 78
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=97.78 E-value=0.00025 Score=59.18 Aligned_cols=100 Identities=11% Similarity=0.136 Sum_probs=71.4
Q ss_pred CCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHH-cCCC-------CC---C----------------C
Q 037872 8 PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSR-CSMN-------IP---D----------------N 60 (146)
Q Consensus 8 p~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~-~~~~-------~~---~----------------~ 60 (146)
++-.+.+.+|.+|+... .+.+++|||+.+||+++|...+++ +|+. +. . .
T Consensus 178 ~sE~eLL~~F~~~i~~~----DPDIItGYNi~nFDlPYL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~~~G~~~~~~I~G 253 (498)
T PHA02524 178 EDEVDLLLNYIQLWKAN----TPDLVFGWNSEGFDIPYIITRITNILGEKAANQLSPYGKITSKTITNLYGEKIIYKIHG 253 (498)
T ss_pred CCHHHHHHHHHHHHHHh----CCCEEEeCCCcccCHHHHHHHHHHHhCCccccccccccccccccceeecCceeEEEEee
Confidence 56789999999999876 358999999999999999888864 5542 10 0 0
Q ss_pred cceeecHHHHHHH-HhhCCCCCCCCcHHHHHHHh-CCCCCC---------------CCCchHHHHHHHHHHH
Q 037872 61 WRFLDTLPLAREL-MKQNGSVSSKTSLQALREYF-GIPLEG---------------SAHRAMSDVNSLASIL 115 (146)
Q Consensus 61 ~~~iDt~~l~~~~-~~~~~~~~~~~~L~~l~~~~-gi~~~~---------------~~H~Al~Da~~ta~l~ 115 (146)
-..+|.+.+.+.. +. ...+|+|+++++++ |-.... -++.++.||..+..|+
T Consensus 254 Rv~iDl~~l~kk~s~~----~l~sYsL~~Vs~~~Lg~~K~d~~~~I~~l~~~d~~rla~YclkDa~L~~~L~ 321 (498)
T PHA02524 254 IALMDYMDVFKKFSFT----PMPDYKLGNVGYREVKADKLDYEGPINKFRKADHQRYVDYCVRDTDIILLID 321 (498)
T ss_pred EEEeEHHHHHHHhhhc----cCCCCCHHHHHHHhcCCccccchhhHHHHhcCchHHHHHHHHHHHHHHHHHH
Confidence 1347889998875 22 35899999998743 433221 1346788999987776
No 79
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=97.68 E-value=0.00089 Score=54.64 Aligned_cols=101 Identities=14% Similarity=0.300 Sum_probs=74.1
Q ss_pred CHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCC-----------------------------
Q 037872 9 RMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPD----------------------------- 59 (146)
Q Consensus 9 ~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~----------------------------- 59 (146)
...+.+..|.+++... .+.+++|||..+||+++|...+.+++++...
T Consensus 68 ~E~~lL~~f~~~i~~~----dpdii~g~N~~~FD~~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~~~~~ 143 (471)
T smart00486 68 NEKELLKAFLEFIKKY----DPDIIYGHNISNFDLPYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSKSFGKTIKV 143 (471)
T ss_pred CHHHHHHHHHHHHHHh----CCCEEEeecCCCCCHHHHHHHHHHcCCCCHHHcCcCCCCCCcccccCcccccccccccee
Confidence 5678999999999875 3479999999889999999988776553210
Q ss_pred ---CcceeecHHHHHHHHhhCCCCCCCCcHHHHHHHhCC-CCCC-------------------CCCchHHHHHHHHHHHH
Q 037872 60 ---NWRFLDTLPLARELMKQNGSVSSKTSLQALREYFGI-PLEG-------------------SAHRAMSDVNSLASILE 116 (146)
Q Consensus 60 ---~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~~gi-~~~~-------------------~~H~Al~Da~~ta~l~~ 116 (146)
....+|++.+.+..+. ..+++|+++++++.. .... -....+.||..+.+|+.
T Consensus 144 ~~~g~~~~Dl~~~~~~~~k-----l~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~ 218 (471)
T smart00486 144 KIKGRLVIDLYNLYKNKLK-----LPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFN 218 (471)
T ss_pred EeccEEEEEhHHHHHHHhC-----cccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1245899998888763 479999999987543 2221 02234678888888888
Q ss_pred HH
Q 037872 117 RI 118 (146)
Q Consensus 117 ~l 118 (146)
++
T Consensus 219 ~l 220 (471)
T smart00486 219 KL 220 (471)
T ss_pred HH
Confidence 85
No 80
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=97.61 E-value=0.00054 Score=47.31 Aligned_cols=94 Identities=26% Similarity=0.392 Sum_probs=62.5
Q ss_pred HHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHH
Q 037872 11 EDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALR 90 (146)
Q Consensus 11 ~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~ 90 (146)
.++.+.+.+++.+. ....|+||+ .||+.+|.+ .+...+ ..++||+.++..+.|. ..+.+|++++
T Consensus 40 ~~~~~~l~~~l~~~-----~~~~v~~~~-k~d~~~L~~----~~~~~~--~~~~D~~~~ayll~~~----~~~~~l~~l~ 103 (155)
T cd00007 40 EEDLEALKELLEDE-----DITKVGHDA-KFDLVVLAR----DGIELP--GNIFDTMLAAYLLNPG----EGSHSLDDLA 103 (155)
T ss_pred HHHHHHHHHHHcCC-----CCcEEeccH-HHHHHHHHH----CCCCCC--CCcccHHHHHHHhCCC----CCcCCHHHHH
Confidence 46677788999762 356999999 899999864 333333 2579999998888763 1146999999
Q ss_pred HHh-CCCCC------CC------CC-------chHHHHHHHHHHHHHHHh
Q 037872 91 EYF-GIPLE------GS------AH-------RAMSDVNSLASILERITS 120 (146)
Q Consensus 91 ~~~-gi~~~------~~------~H-------~Al~Da~~ta~l~~~l~~ 120 (146)
+.| +.+.. +. .- .|..||.++.+++..+.+
T Consensus 104 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~~l~~ 153 (155)
T cd00007 104 KEYLGIELDKDEQIYGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLE 153 (155)
T ss_pred HHHcCCCCccHHHHhcCCCCccccCCHHHHHHHHHHhHHHHHHHHHHHHh
Confidence 887 43311 00 00 255667777777766654
No 81
>PRK05761 DNA polymerase I; Reviewed
Probab=97.50 E-value=0.0011 Score=58.44 Aligned_cols=102 Identities=15% Similarity=0.185 Sum_probs=71.5
Q ss_pred CCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCC-------cceeecHHHHHHH----Hhh
Q 037872 8 PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDN-------WRFLDTLPLAREL----MKQ 76 (146)
Q Consensus 8 p~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~-------~~~iDt~~l~~~~----~~~ 76 (146)
++-.+++.+|.+|+... .+.|++|+.+||+++|...+.++|++.... ...+|.....+.. +..
T Consensus 208 ~~E~eLL~~f~~~i~~~------dPdi~yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~~~~~y~~ 281 (787)
T PRK05761 208 DSEKELLAELFDIILEY------PPVVTFNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNKAVRSYAF 281 (787)
T ss_pred CCHHHHHHHHHHHHHhc------CCEEEEcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheeecceeeeec
Confidence 56789999999999975 466779999999999999999999864310 0126665543211 100
Q ss_pred CC-CCCCCCcHHHHHH-HhCCCCCC------------CCCchHHHHHHHHHHH
Q 037872 77 NG-SVSSKTSLQALRE-YFGIPLEG------------SAHRAMSDVNSLASIL 115 (146)
Q Consensus 77 ~~-~~~~~~~L~~l~~-~~gi~~~~------------~~H~Al~Da~~ta~l~ 115 (146)
.+ ...++++|+.+++ .+|..... -+..++.||..|.+|+
T Consensus 282 ~~~~~~~~ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 282 YGKYRHREARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred cceeecccCChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 01 1234799999997 67876531 1457899999999985
No 82
>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006133 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold [].; GO: 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 4AHC_A 3A2F_A 2JGU_A 4AIL_C 1NOY_A 1NOZ_B 3IAY_A 1WNS_A 3K5O_A ....
Probab=97.46 E-value=0.00077 Score=52.67 Aligned_cols=73 Identities=21% Similarity=0.313 Sum_probs=55.6
Q ss_pred CCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCC-------C------------------C---
Q 037872 8 PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNI-------P------------------D--- 59 (146)
Q Consensus 8 p~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~-------~------------------~--- 59 (146)
++-.+.+..|++++... .+.+++|||+.+||+++|.+.++.+|+.. . .
T Consensus 220 ~~E~~lL~~f~~~i~~~----dPDii~GyN~~~fD~~yl~~R~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 295 (325)
T PF03104_consen 220 DSEKELLEAFLDIIQEY----DPDIITGYNIDGFDLPYLIERAKKLGIDMFDLNGRRWSRFGRLKRKKWPSSANGSRKFS 295 (325)
T ss_dssp SSHHHHHHHHHHHHHHH----S-SEEEESSTTTTHHHHHHHHHHHTTTCTHHSTTSTTTEEEEEEEEESEECTCCCTTEE
T ss_pred CCHHHHHHHHHHHHHhc----CCcEEEEecccCCCHHHHHHHHHHhCccccccccccccceeEEeecccccccCCCccee
Confidence 56789999999999877 35799999999999999999998884321 0 0
Q ss_pred -----CcceeecHHHHHHHHhhCCCCCCCCcHHHH
Q 037872 60 -----NWRFLDTLPLARELMKQNGSVSSKTSLQAL 89 (146)
Q Consensus 60 -----~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l 89 (146)
.-..+|++.+++..+. ..+|+|+++
T Consensus 296 ~~~~~Gr~~~D~~~~~~~~~~-----l~sY~L~~V 325 (325)
T PF03104_consen 296 RIDIPGRLVLDLYRLARKDYK-----LDSYSLDNV 325 (325)
T ss_dssp EEEETTSEEEEHHHHHHHHS-------SS-SHHHH
T ss_pred EEEECCChHhHHHHHHHhhCC-----CCCCCCCCC
Confidence 0246899999998874 578999874
No 83
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=97.34 E-value=0.00071 Score=48.19 Aligned_cols=90 Identities=21% Similarity=0.153 Sum_probs=65.3
Q ss_pred HHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHHHH
Q 037872 13 LIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREY 92 (146)
Q Consensus 13 v~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~ 92 (146)
..+.+.+++++ ++.+.|||++ ..|+..|.+ .+|+... ..+||+..+..+-+ ..+.+|..+++.
T Consensus 55 ~~~~L~~lL~d-----~~i~Kvg~~~-k~D~~~L~~---~~gi~~~---~~~D~~~aa~ll~~-----~~~~~L~~l~~~ 117 (161)
T cd06129 55 DWQGLKMLLEN-----PSIVKALHGI-EGDLWKLLR---DFGEKLQ---RLFDTTIAANLKGL-----PERWSLASLVEH 117 (161)
T ss_pred CHHHHHHHhCC-----CCEEEEEecc-HHHHHHHHH---HcCCCcc---cHhHHHHHHHHhCC-----CCCchHHHHHHH
Confidence 34566777875 3456799999 899998853 2565532 45999988776532 135699999876
Q ss_pred h-CCCCC---------------CCCCchHHHHHHHHHHHHHHH
Q 037872 93 F-GIPLE---------------GSAHRAMSDVNSLASILERIT 119 (146)
Q Consensus 93 ~-gi~~~---------------~~~H~Al~Da~~ta~l~~~l~ 119 (146)
| |++.+ .+-|.|..||..+..||.+|.
T Consensus 118 ~lg~~l~K~~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 118 FLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred HhCCCCCccceeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 5 87653 147899999999999999875
No 84
>PRK10829 ribonuclease D; Provisional
Probab=97.25 E-value=0.0019 Score=52.34 Aligned_cols=93 Identities=17% Similarity=0.186 Sum_probs=68.5
Q ss_pred HHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHHH-H
Q 037872 14 IPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALRE-Y 92 (146)
Q Consensus 14 ~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~-~ 92 (146)
+..|.+.+.+ +..+-|+|++ .+|+.+|.+ .+|+. | ..++||+..++.+ .. ..+.+|..+++ +
T Consensus 63 ~~~L~~ll~~-----~~ivKV~H~~-~~Dl~~l~~---~~g~~-p--~~~fDTqiaa~~l-g~----~~~~gl~~Lv~~~ 125 (373)
T PRK10829 63 WSPFKALLRD-----PQVTKFLHAG-SEDLEVFLN---AFGEL-P--QPLIDTQILAAFC-GR----PLSCGFASMVEEY 125 (373)
T ss_pred hHHHHHHHcC-----CCeEEEEeCh-HhHHHHHHH---HcCCC-c--CCeeeHHHHHHHc-CC----CccccHHHHHHHH
Confidence 5667778876 3445589999 999999954 44553 2 2689998887654 11 13689999985 5
Q ss_pred hCCCCCC---------------CCCchHHHHHHHHHHHHHHHhhhh
Q 037872 93 FGIPLEG---------------SAHRAMSDVNSLASILERITSDLN 123 (146)
Q Consensus 93 ~gi~~~~---------------~~H~Al~Da~~ta~l~~~l~~~~~ 123 (146)
+|+..+- +-+.|..||..+..||..+...+.
T Consensus 126 lgv~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~ 171 (373)
T PRK10829 126 TGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETE 171 (373)
T ss_pred hCCccCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7886541 367899999999999999988765
No 85
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=97.22 E-value=0.0035 Score=55.35 Aligned_cols=101 Identities=20% Similarity=0.256 Sum_probs=76.0
Q ss_pred CHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCC---------------C---CcceeecHHHH
Q 037872 9 RMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIP---------------D---NWRFLDTLPLA 70 (146)
Q Consensus 9 ~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~---------------~---~~~~iDt~~l~ 70 (146)
+-.+++..|..++... .+.++||||+.+||+++|...+.++|++.. . .+..+|.....
T Consensus 210 ~e~e~l~~~~~~i~~~----dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~ 285 (792)
T COG0417 210 SEAELLERFVELIREY----DPDVIVGYNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPAL 285 (792)
T ss_pred CHHHHHHHHHHHHHhc----CCCEEEeccCCcCChHHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHHH
Confidence 5678999999999876 468999999988999999999999887654 0 13568999888
Q ss_pred HH-HHhhCCCCCCCCcHHHHHHHhCCCCC--C-------------------CCCchHHHHHHHHHHHHHH
Q 037872 71 RE-LMKQNGSVSSKTSLQALREYFGIPLE--G-------------------SAHRAMSDVNSLASILERI 118 (146)
Q Consensus 71 ~~-~~~~~~~~~~~~~L~~l~~~~gi~~~--~-------------------~~H~Al~Da~~ta~l~~~l 118 (146)
+. ... ..+++|..+++.+..... . ...+.+.|+..+.+++.+.
T Consensus 286 ~~~~~~-----~~~ysl~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l~~~~~~~~ 350 (792)
T COG0417 286 RRRPLN-----LKSYSLEAVSEALLGEGKREDIPYDSMEEIWPDWADSKLRLLLYNLSDADLVLRILLKN 350 (792)
T ss_pred hhhhcc-----cccccHHHHHHHhcccccccccCccchhhccccCccchhHHHHHHHHHHHHHHHHHHHH
Confidence 73 432 578999999776544322 0 1334588888888887764
No 86
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=97.22 E-value=0.0015 Score=46.62 Aligned_cols=91 Identities=20% Similarity=0.242 Sum_probs=66.0
Q ss_pred HHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHHHH
Q 037872 13 LIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREY 92 (146)
Q Consensus 13 v~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~ 92 (146)
..+.+.+++.+ +....||||+ .+|+..|.+ .+|+... ..+|++.++..+.+. ....+|.++++.
T Consensus 61 ~~~~l~~ll~~-----~~i~kv~~~~-k~D~~~L~~---~~g~~~~---~~~Dl~~aa~ll~~~----~~~~~l~~l~~~ 124 (170)
T cd06141 61 LPPSLKQLLED-----PSILKVGVGI-KGDARKLAR---DFGIEVR---GVVDLSHLAKRVGPR----RKLVSLARLVEE 124 (170)
T ss_pred ccHHHHHHhcC-----CCeeEEEeee-HHHHHHHHh---HcCCCCC---CeeeHHHHHHHhCCC----cCCccHHHHHHH
Confidence 34567777765 3467799999 899999853 4565532 459999988776542 134699999877
Q ss_pred h-CCCCC-----------------CCCCchHHHHHHHHHHHHHHH
Q 037872 93 F-GIPLE-----------------GSAHRAMSDVNSLASILERIT 119 (146)
Q Consensus 93 ~-gi~~~-----------------~~~H~Al~Da~~ta~l~~~l~ 119 (146)
+ |.+.. .+-|.|..||..+..|+..|.
T Consensus 125 ~l~~~~~k~k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 125 VLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred HcCcccCCCCCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 5 66443 146889999999999998875
No 87
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=97.06 E-value=0.0089 Score=41.88 Aligned_cols=93 Identities=28% Similarity=0.448 Sum_probs=62.9
Q ss_pred HHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHHHH
Q 037872 13 LIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREY 92 (146)
Q Consensus 13 v~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~ 92 (146)
....+.+++.+ .+...|+||+ .+|+..|. ++|+..+ .++||+..+..+.|. ..+.+|..+++.
T Consensus 63 ~~~~l~~~l~~-----~~~~kv~~d~-k~~~~~L~----~~gi~~~---~~~D~~laayll~p~----~~~~~l~~l~~~ 125 (172)
T smart00474 63 DLEILKDLLED-----ETITKVGHNA-KFDLHVLA----RFGIELE---NIFDTMLAAYLLLGG----PSKHGLATLLKE 125 (172)
T ss_pred hHHHHHHHhcC-----CCceEEEech-HHHHHHHH----HCCCccc---chhHHHHHHHHHcCC----CCcCCHHHHHHH
Confidence 34557788875 3467999999 89999986 3676653 249999888777653 233699999876
Q ss_pred h-CCCCCC--------CC---C----chHHHHHHHHHHHHHHHhhh
Q 037872 93 F-GIPLEG--------SA---H----RAMSDVNSLASILERITSDL 122 (146)
Q Consensus 93 ~-gi~~~~--------~~---H----~Al~Da~~ta~l~~~l~~~~ 122 (146)
| |.+.+. .. . .|..||.++.+++..+.+++
T Consensus 126 ~l~~~~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 126 YLGVELDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred HhCCCCCcccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5 655221 00 0 36677888888877776653
No 88
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=97.01 E-value=0.00059 Score=48.85 Aligned_cols=86 Identities=16% Similarity=0.269 Sum_probs=60.7
Q ss_pred CCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeec---HHHHHHHHhhCCCCCCC
Q 037872 7 VPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDT---LPLARELMKQNGSVSSK 83 (146)
Q Consensus 7 ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt---~~l~~~~~~~~~~~~~~ 83 (146)
.-+..++-.+.++|++..-.. +.++++|-.+ .-|++||.+.+-++.--+ ..+.+|+ .++++++.|.-
T Consensus 79 ~~t~~~aE~~~l~flkkwvp~-~~spicGNSI-~qDRrFl~r~MP~Le~yf--HYR~lDVSTlKELa~RW~P~i------ 148 (184)
T COG1949 79 TVTEAEAEAQTLDFLKKWVPK-GVSPICGNSI-AQDRRFLFRYMPKLEAYF--HYRYLDVSTLKELARRWNPEI------ 148 (184)
T ss_pred hccHHHHHHHHHHHHHHhCCC-CCCCCccchh-hHHHHHHHHHhhhHHHHh--hhHhhhHHHHHHHHHhhCcHh------
Confidence 345677777778887765333 6689999998 999999999887753222 2467883 56888887742
Q ss_pred CcHHHHHHHhCCCCCCCCCchHHHHHHH
Q 037872 84 TSLQALREYFGIPLEGSAHRAMSDVNSL 111 (146)
Q Consensus 84 ~~L~~l~~~~gi~~~~~~H~Al~Da~~t 111 (146)
..|.... ..|+||+|..--
T Consensus 149 --------~~~~~K~-~~H~Al~DI~ES 167 (184)
T COG1949 149 --------LAGFKKG-GTHRALDDIRES 167 (184)
T ss_pred --------hhccccc-cchhHHHHHHHH
Confidence 4454445 599999998754
No 89
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=96.98 E-value=0.011 Score=54.68 Aligned_cols=111 Identities=15% Similarity=0.154 Sum_probs=79.7
Q ss_pred CCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCC------------CcceeecHHHHHHH
Q 037872 6 YVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPD------------NWRFLDTLPLAREL 73 (146)
Q Consensus 6 ~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~------------~~~~iDt~~l~~~~ 73 (146)
+.|.-...+..|++-+.+. ++.++|.+|++=||++|+.+....+|+.... ..++++.|...+..
T Consensus 313 Ne~dEv~Ll~RfFeHiq~~----kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrWV 388 (2173)
T KOG1798|consen 313 NEPDEVGLLQRFFEHIQEV----KPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRWV 388 (2173)
T ss_pred cCCcHHHHHHHHHHHHHhc----CCcEEEEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehhhhhhh
Confidence 3455677888888888776 6789999999999999999999999875321 12456667766655
Q ss_pred HhhCCCCCCCCcHHHHHH-HhCCCCCC----------------CCCchHHHHHHHHHHHHHHHh
Q 037872 74 MKQNGSVSSKTSLQALRE-YFGIPLEG----------------SAHRAMSDVNSLASILERITS 120 (146)
Q Consensus 74 ~~~~~~~~~~~~L~~l~~-~~gi~~~~----------------~~H~Al~Da~~ta~l~~~l~~ 120 (146)
-...-...++.+|..+.+ .+|-..-. -+-.+.+||.+|.-+|.+...
T Consensus 389 KRDSYLPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVh 452 (2173)
T KOG1798|consen 389 KRDSYLPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVH 452 (2173)
T ss_pred hhcccCCCcccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhh
Confidence 421112358899999975 57753210 155678999999999988654
No 90
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.95 E-value=0.012 Score=54.06 Aligned_cols=101 Identities=15% Similarity=0.112 Sum_probs=71.8
Q ss_pred CHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCC--------------------CCcceeecHH
Q 037872 9 RMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIP--------------------DNWRFLDTLP 68 (146)
Q Consensus 9 ~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~--------------------~~~~~iDt~~ 68 (146)
+-.+.+..|+.++... .+.+++|||..+||+++|.+.+.+++++.- .....+|++.
T Consensus 583 sEr~lL~~fl~~~~~~----DPDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~~ 658 (1172)
T TIGR00592 583 TERALIKKFMAKVKKI----DPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVEI 658 (1172)
T ss_pred CHHHHHHHHHHHHHhc----CCCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccCCCccccccceECCEEEEEHHH
Confidence 4567788888888744 257999999999999999999988876531 0113588888
Q ss_pred HHHHHHhhCCCCCCCCcHHHHHHH-hCCCCCCC------------------CCchHHHHHHHHHHHHHH
Q 037872 69 LARELMKQNGSVSSKTSLQALREY-FGIPLEGS------------------AHRAMSDVNSLASILERI 118 (146)
Q Consensus 69 l~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~~~------------------~H~Al~Da~~ta~l~~~l 118 (146)
.++..+. ..+|+|.+++.+ +|.+...- ....+.||..+.+|+.++
T Consensus 659 ~~k~~~~-----~~sy~L~~v~~~~L~~~k~~~~~~~i~~~~~~~~~~~~~~~y~~~Da~l~~~L~~~l 722 (1172)
T TIGR00592 659 SAKELIR-----CKSYDLSELVQQILKTERKVIPIDNINNMYSESSSLTYLLEHTWKDAMFILQIMCEL 722 (1172)
T ss_pred HHHHHhC-----cCCCCHHHHHHHHhCCCCcccCHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 8888764 478999999875 56543310 123466777777776653
No 91
>PHA02570 dexA exonuclease; Provisional
Probab=96.91 E-value=0.0066 Score=45.55 Aligned_cols=99 Identities=14% Similarity=0.064 Sum_probs=56.0
Q ss_pred CCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHc----C--CCCCCC-cceeecHHHHHHHHhhCC
Q 037872 6 YVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRC----S--MNIPDN-WRFLDTLPLARELMKQNG 78 (146)
Q Consensus 6 ~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~----~--~~~~~~-~~~iDt~~l~~~~~~~~~ 78 (146)
+..+..+++.+|.+||....-+.....+-|-++ +||..+|...+++. + .+.|.. |.--|+-.+........|
T Consensus 84 ~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~-sFD~~IL~~a~r~~~~~~~~~~~~Pw~fwN~RDVRT~ie~~~l~r~ 162 (220)
T PHA02570 84 EDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGN-SFDFPILVDVIRDIHNTRDTFKLEPVKFWNQRDVRTAIEATLLTRG 162 (220)
T ss_pred ccccHHHHHHHHHHHHHHcCCCccceeEecCCC-ccCHHHHHHHHHHHhcccCcCcCCCeeecCccchHHHHhhhhccCC
Confidence 346799999999999986421112234445555 99999999999987 5 333321 344555444433322222
Q ss_pred CCCCCCcHHHHHHHhCCCCCC-CCCchHHHHHHHHH
Q 037872 79 SVSSKTSLQALREYFGIPLEG-SAHRAMSDVNSLAS 113 (146)
Q Consensus 79 ~~~~~~~L~~l~~~~gi~~~~-~~H~Al~Da~~ta~ 113 (146)
. +.|-...-..+| .+|+|+.||.--+.
T Consensus 163 ~--------~~cp~~~g~l~gfv~H~sihDcakd~l 190 (220)
T PHA02570 163 M--------TTCPLPKGTLDGFVAHDSIHDCAKDIL 190 (220)
T ss_pred c--------ccCCCcCccccchhhcccHHHHHHHHH
Confidence 0 111111111222 58999998865443
No 92
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=96.78 E-value=0.0071 Score=43.88 Aligned_cols=89 Identities=19% Similarity=0.271 Sum_probs=62.8
Q ss_pred CCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeec---HHHHHHHHhhCCCCCC
Q 037872 6 YVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDT---LPLARELMKQNGSVSS 82 (146)
Q Consensus 6 ~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt---~~l~~~~~~~~~~~~~ 82 (146)
..-+..+|-.++++|++..- +++..++.|-.+ .-|+.||..++-...--.+ .+.||+ ..++++++|...
T Consensus 98 S~~tl~~aEnevl~yikk~i-p~~~~~laGNSV-~~DrlFl~k~mPk~~~~lh--yrivDVStIkeL~~Rw~P~~~---- 169 (208)
T KOG3242|consen 98 SKITLADAENEVLEYIKKHI-PKGKCPLAGNSV-YMDRLFLKKYMPKLIKHLH--YRIVDVSTIKELARRWYPDIK---- 169 (208)
T ss_pred hhccHHHHHHHHHHHHHHhC-CCCCCCccCcch-hhHHHHHHHHhHHHHHhcc--eeeeeHHHHHHHHHHhCchhh----
Confidence 45678999999999998763 456667777777 8999999998876532222 477883 678999988521
Q ss_pred CCcHHHHHHHhCCCCCCCCCchHHHHHHHH
Q 037872 83 KTSLQALREYFGIPLEGSAHRAMSDVNSLA 112 (146)
Q Consensus 83 ~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta 112 (146)
++.-... ..|||++|...-.
T Consensus 170 ---------~~aPkK~-~~HrAldDI~ESI 189 (208)
T KOG3242|consen 170 ---------ARAPKKK-ATHRALDDIRESI 189 (208)
T ss_pred ---------ccCcccc-cccchHHHHHHHH
Confidence 1222223 4999999987543
No 93
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=96.68 E-value=0.015 Score=46.68 Aligned_cols=93 Identities=26% Similarity=0.412 Sum_probs=67.9
Q ss_pred HHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHHH-H
Q 037872 14 IPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALRE-Y 92 (146)
Q Consensus 14 ~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~-~ 92 (146)
++-|...+.+ ...+=|-|++ +||+.+|.+.+ |+. | .+.+||...++.. |.+ .+++|+++++ .
T Consensus 59 ~~~l~~Ll~d-----~~v~KIfHaa-~~DL~~l~~~~---g~~-p--~plfdTqiAa~l~----g~~-~~~gl~~Lv~~l 121 (361)
T COG0349 59 LPPLVALLAD-----PNVVKIFHAA-RFDLEVLLNLF---GLL-P--TPLFDTQIAAKLA----GFG-TSHGLADLVEEL 121 (361)
T ss_pred cchHHHHhcC-----Cceeeeeccc-cccHHHHHHhc---CCC-C--CchhHHHHHHHHh----CCc-ccccHHHHHHHH
Confidence 3455666655 3466699999 99999998765 333 2 2689999887654 212 3899999985 5
Q ss_pred hCCCCCC---------------CCCchHHHHHHHHHHHHHHHhhhh
Q 037872 93 FGIPLEG---------------SAHRAMSDVNSLASILERITSDLN 123 (146)
Q Consensus 93 ~gi~~~~---------------~~H~Al~Da~~ta~l~~~l~~~~~ 123 (146)
+|++.+- +--+|..||.....|+.++.+.+.
T Consensus 122 l~v~ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~ 167 (361)
T COG0349 122 LGVELDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELA 167 (361)
T ss_pred hCCcccccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6887661 234899999999999999988764
No 94
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.45 E-value=0.007 Score=54.08 Aligned_cols=97 Identities=18% Similarity=0.205 Sum_probs=69.3
Q ss_pred HHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHH
Q 037872 10 MEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQAL 89 (146)
Q Consensus 10 f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l 89 (146)
..++...+.+|+++ +....|+||+ .||+.+|. ++|+.... .+.|||-.+..+.|. ...+|+++
T Consensus 363 ~~~~~~~l~~~l~~-----~~~~~v~~n~-K~d~~~l~----~~gi~~~~--~~~Dt~la~yll~~~-----~~~~l~~l 425 (887)
T TIGR00593 363 TILTDDKFARWLLN-----EQIKKIGHDA-KFLMHLLK----REGIELGG--VIFDTMLAAYLLDPA-----QVSTLDTL 425 (887)
T ss_pred hHHHHHHHHHHHhC-----CCCcEEEeeH-HHHHHHHH----hCCCCCCC--cchhHHHHHHHcCCC-----CCCCHHHH
Confidence 44566778899976 3456899999 89999985 57776542 579999998877653 23499999
Q ss_pred HHHh-CCCC---C---C------------CCCchHHHHHHHHHHHHHHHhhhh
Q 037872 90 REYF-GIPL---E---G------------SAHRAMSDVNSLASILERITSDLN 123 (146)
Q Consensus 90 ~~~~-gi~~---~---~------------~~H~Al~Da~~ta~l~~~l~~~~~ 123 (146)
+..| +... + | ....|..||.+|.+|+..+.+.+.
T Consensus 426 a~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~ 478 (887)
T TIGR00593 426 ARRYLVEELILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKELD 478 (887)
T ss_pred HHHHcCcccccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 8765 3210 0 0 012578899999999999887764
No 95
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=96.41 E-value=0.052 Score=38.55 Aligned_cols=101 Identities=24% Similarity=0.269 Sum_probs=67.1
Q ss_pred HHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHHHH
Q 037872 13 LIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREY 92 (146)
Q Consensus 13 v~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~ 92 (146)
+...|.+++++ +....|+||+ .+|+..|.+ .+|+. . . ..+||+-.+..+.|. .+.+|+++++.
T Consensus 52 ~~~~l~~ll~~-----~~i~kv~~d~-K~~~~~L~~---~~gi~-~-~-~~~D~~laayLl~p~-----~~~~l~~l~~~ 114 (178)
T cd06142 52 DLSPLKELLAD-----PNIVKVFHAA-REDLELLKR---DFGIL-P-Q-NLFDTQIAARLLGLG-----DSVGLAALVEE 114 (178)
T ss_pred cHHHHHHHHcC-----CCceEEEecc-HHHHHHHHH---HcCCC-C-C-CcccHHHHHHHhCCC-----ccccHHHHHHH
Confidence 44557788875 3467899999 899988753 23665 3 2 569998776665442 23599999875
Q ss_pred -hCCCCC-----C----------CCCchHHHHHHHHHHHHHHHhhhh-cCHHHHH
Q 037872 93 -FGIPLE-----G----------SAHRAMSDVNSLASILERITSDLN-FTLSDLL 130 (146)
Q Consensus 93 -~gi~~~-----~----------~~H~Al~Da~~ta~l~~~l~~~~~-~~~~~l~ 130 (146)
+|.+.. + +.+.|..||.++.+++..+.+++. ..+.+|.
T Consensus 115 ~l~~~~~~~~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~e~~l~~L~ 169 (178)
T cd06142 115 LLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEEEGRLEWA 169 (178)
T ss_pred HhCCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCcHHHH
Confidence 466411 0 012477888999999999888765 3455554
No 96
>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=96.15 E-value=0.039 Score=44.60 Aligned_cols=93 Identities=18% Similarity=0.180 Sum_probs=64.7
Q ss_pred HHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHHHHh
Q 037872 14 IPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREYF 93 (146)
Q Consensus 14 ~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~~ 93 (146)
+..|.+++.+ .+.+.|+|++ .+|+.+|.+. +...+. ..+||+..+..+-+ ....+|..+++.|
T Consensus 59 ~~~L~~lL~d-----~~i~KV~h~~-k~Dl~~L~~~----~~~~~~--~~fDtqlAa~lL~~-----~~~~~l~~Lv~~~ 121 (367)
T TIGR01388 59 WSPLKELLRD-----ESVVKVLHAA-SEDLEVFLNL----FGELPQ--PLFDTQIAAAFCGF-----GMSMGYAKLVQEV 121 (367)
T ss_pred HHHHHHHHCC-----CCceEEEeec-HHHHHHHHHH----hCCCCC--CcccHHHHHHHhCC-----CCCccHHHHHHHH
Confidence 5677788875 3456799999 8999998643 223332 57999987765532 1346999998665
Q ss_pred -CCCCCC---------------CCCchHHHHHHHHHHHHHHHhhhh
Q 037872 94 -GIPLEG---------------SAHRAMSDVNSLASILERITSDLN 123 (146)
Q Consensus 94 -gi~~~~---------------~~H~Al~Da~~ta~l~~~l~~~~~ 123 (146)
|++.+- +.+.|..||..+..++..+.+++.
T Consensus 122 Lg~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~ 167 (367)
T TIGR01388 122 LGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLE 167 (367)
T ss_pred cCCCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 665431 123589999999999999987764
No 97
>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=96.12 E-value=0.058 Score=38.48 Aligned_cols=102 Identities=19% Similarity=0.236 Sum_probs=65.8
Q ss_pred HHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHHHH
Q 037872 13 LIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREY 92 (146)
Q Consensus 13 v~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~ 92 (146)
+...+.+++++ .....|+||+ .+|+.+|. ++|+..+. ...||+-.+..+.|. .+++++.+++..
T Consensus 44 ~~~~l~~~l~~-----~~~~ki~~d~-K~~~~~l~----~~gi~~~~--~~fDt~laaYLL~p~----~~~~~l~~l~~~ 107 (178)
T cd06140 44 DLAALKEWLED-----EKIPKVGHDA-KRAYVALK----RHGIELAG--VAFDTMLAAYLLDPT----RSSYDLADLAKR 107 (178)
T ss_pred HHHHHHHHHhC-----CCCceeccch-hHHHHHHH----HCCCcCCC--cchhHHHHHHHcCCC----CCCCCHHHHHHH
Confidence 44557788875 2456899999 79988874 56776553 469999998877653 234699999876
Q ss_pred h-CCCCC------CC-----C--C-----chHHHHHHHHHHHHHHHhhhh-cCHHHHH
Q 037872 93 F-GIPLE------GS-----A--H-----RAMSDVNSLASILERITSDLN-FTLSDLL 130 (146)
Q Consensus 93 ~-gi~~~------~~-----~--H-----~Al~Da~~ta~l~~~l~~~~~-~~~~~l~ 130 (146)
| +.+.. +. . . .+..||.++..++..+.+++. ..+.+|+
T Consensus 108 yl~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~~L~~~~l~~L~ 165 (178)
T cd06140 108 YLGRELPSDEEVYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEEELEENEQLELY 165 (178)
T ss_pred HcCCCCcchHHhcCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence 5 54421 00 0 1 245567777777777777664 2344444
No 98
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=95.94 E-value=0.045 Score=45.47 Aligned_cols=81 Identities=15% Similarity=0.094 Sum_probs=62.6
Q ss_pred CHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCC----CcceeecHHHHHHHHhhCCCCCCCC
Q 037872 9 RMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPD----NWRFLDTLPLARELMKQNGSVSSKT 84 (146)
Q Consensus 9 ~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~----~~~~iDt~~l~~~~~~~~~~~~~~~ 84 (146)
...+++.+|.+|+... ++..++.|| +|....|++...+++.+... .-+++|.+.+.+..+-. +.+++
T Consensus 327 ~E~~~~~~f~~~l~~~----~~~~i~hY~--~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~---p~~sy 397 (457)
T TIGR03491 327 TEELAWQQFLQLLQSY----PDAPIYHYG--ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWIL---PIESY 397 (457)
T ss_pred HHHHHHHHHHHHHHHC----CCCeEEeeC--HHHHHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEEC---CCCCC
Confidence 3567899999999864 345788888 59999999999999866310 01789999988876532 35899
Q ss_pred cHHHHHHHhCCCCC
Q 037872 85 SLQALREYFGIPLE 98 (146)
Q Consensus 85 ~L~~l~~~~gi~~~ 98 (146)
+|++++..+|.+.+
T Consensus 398 sLK~v~~~lg~~~~ 411 (457)
T TIGR03491 398 SLKSIARWLGFEWR 411 (457)
T ss_pred CHHHHHHHhCcccC
Confidence 99999999999776
No 99
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=95.93 E-value=0.014 Score=44.02 Aligned_cols=87 Identities=16% Similarity=0.227 Sum_probs=62.7
Q ss_pred CCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCC----------cceeecHHHHHHHHhhCCCCCCCCcHHHHHHHhCCCCC
Q 037872 29 EIAIFVAHNARRFDVPFLAKEFSRCSMNIPDN----------WRFLDTLPLARELMKQNGSVSSKTSLQALREYFGIPLE 98 (146)
Q Consensus 29 ~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~----------~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~~gi~~~ 98 (146)
++.+||.+.. .||+++|-+.+...-++.... ....|..-+.+... ..+..|+++..-+++...
T Consensus 157 e~VtWitfHs-aYDfgyLikilt~~plP~~~EdFy~~l~~yfP~fYDik~v~ks~~------~~~KglQei~ndlql~r~ 229 (299)
T COG5228 157 ESVTWITFHS-AYDFGYLIKILTNDPLPNNKEDFYWWLHQYFPNFYDIKLVYKSVL------NNSKGLQEIKNDLQLQRS 229 (299)
T ss_pred cceEEEEeec-chhHHHHHHHHhcCCCCccHHHHHHHHHHHCccccchHHHHHhhh------hhhhHHHHhcCcHhhhcc
Confidence 5689999998 899999988776443322100 12344433444333 245678889899999999
Q ss_pred CCCCchHHHHHHHHHHHHHHHhhh
Q 037872 99 GSAHRAMSDVNSLASILERITSDL 122 (146)
Q Consensus 99 ~~~H~Al~Da~~ta~l~~~l~~~~ 122 (146)
|+.|.|-.||+.|+..|......+
T Consensus 230 g~QhQagsdaLlTa~~ff~~R~~~ 253 (299)
T COG5228 230 GQQHQAGSDALLTADEFFLPRFSI 253 (299)
T ss_pred chhhhccchhhhhhHHhcchhhhe
Confidence 999999999999999998876654
No 100
>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=95.91 E-value=0.072 Score=39.18 Aligned_cols=98 Identities=20% Similarity=0.174 Sum_probs=66.7
Q ss_pred HHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCC---CCCCCCcHHHHH
Q 037872 14 IPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNG---SVSSKTSLQALR 90 (146)
Q Consensus 14 ~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~---~~~~~~~L~~l~ 90 (146)
...+.+++++ +...-|+||+ .+|...|.+ .+|+... ..+||+..+..+.+..+ ......+|..++
T Consensus 54 ~~~L~~iLe~-----~~i~Kv~h~~-k~D~~~L~~---~~gi~~~---~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~ 121 (197)
T cd06148 54 INGLKDILES-----KKILKVIHDC-RRDSDALYH---QYGIKLN---NVFDTQVADALLQEQETGGFNPDRVISLVQLL 121 (197)
T ss_pred HHHHHHHhcC-----CCccEEEEec-hhHHHHHHH---hcCcccc---ceeeHHHHHHHHHHHhcCCccccccccHHHHH
Confidence 4556666765 2456799999 899998743 4565432 45999877766654321 001235899998
Q ss_pred HHh-CCCCC-----------------------CCCCchHHHHHHHHHHHHHHHhhhh
Q 037872 91 EYF-GIPLE-----------------------GSAHRAMSDVNSLASILERITSDLN 123 (146)
Q Consensus 91 ~~~-gi~~~-----------------------~~~H~Al~Da~~ta~l~~~l~~~~~ 123 (146)
+.| |++.+ .+-..|..||..+..|+..+...+.
T Consensus 122 ~~~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~ 178 (197)
T cd06148 122 DKYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALI 178 (197)
T ss_pred HHhhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhh
Confidence 764 76531 1366899999999999999988875
No 101
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=95.71 E-value=0.016 Score=47.05 Aligned_cols=93 Identities=23% Similarity=0.358 Sum_probs=64.0
Q ss_pred CHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHH
Q 037872 9 RMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQA 88 (146)
Q Consensus 9 ~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~ 88 (146)
+..++-.++.+|+.. +.|+|||.. +-|+.-|+- ..+ .+|||-.++.. + .|.-....+|..
T Consensus 279 tl~dvq~~l~~~~~~------~TILVGHSL-enDL~aLKl-------~H~---~ViDTa~lf~~--~-~g~~~~k~sLk~ 338 (380)
T KOG2248|consen 279 TLEDVQKELLELISK------NTILVGHSL-ENDLKALKL-------DHP---SVIDTAVLFKH--P-TGPYPFKSSLKN 338 (380)
T ss_pred CHHHHHHHHHhhcCc------CcEEEeech-hhHHHHHhh-------hCC---ceeeeeEEEec--C-CCCccchHHHHH
Confidence 678899999999975 689999999 999988862 212 57898744221 1 110013456888
Q ss_pred HHH-HhC--CCCCCCCCchHHHHHHHHHHHHHHHhh
Q 037872 89 LRE-YFG--IPLEGSAHRAMSDVNSLASILERITSD 121 (146)
Q Consensus 89 l~~-~~g--i~~~~~~H~Al~Da~~ta~l~~~l~~~ 121 (146)
+++ ++| |+.....|++..||.+|.++.......
T Consensus 339 L~~~~L~~~Iq~~~~~HdS~eDA~acm~Lv~~k~~~ 374 (380)
T KOG2248|consen 339 LAKSYLGKLIQEGVGGHDSVEDALACMKLVKLKIKN 374 (380)
T ss_pred HHHHHHHHHHhccCCCCccHHHHHHHHHHHHHHHhc
Confidence 875 445 441113699999999999998776554
No 102
>PHA03036 DNA polymerase; Provisional
Probab=95.58 E-value=0.056 Score=48.81 Aligned_cols=110 Identities=18% Similarity=0.240 Sum_probs=73.2
Q ss_pred CHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCC-------------------------------
Q 037872 9 RMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNI------------------------------- 57 (146)
Q Consensus 9 ~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~------------------------------- 57 (146)
+-.+++ .|++++... ...+++|+|+.+||+++|...++.+....
T Consensus 240 sE~~ml-~~~~~i~~~----d~D~i~~yNg~nFD~~Yi~~R~~~L~~~~~~~~~~~~~~~~~~~v~~r~~~s~~~~gg~~ 314 (1004)
T PHA03036 240 SEIVLL-RIAKKLLEL----EFDYVVTFNGHNFDLRYISNRLELLTGEKIIFRSPDGKETVHLCIYERNLSSHKGVGGVA 314 (1004)
T ss_pred CHHHHH-HHHHHHHhc----CCCEEEeccCCCcchHHHHHHHHHhccCceeeccCCCcccccceeeccccccccccCccc
Confidence 344444 667777655 35799999999999999998887762200
Q ss_pred ------C--CCcceeecHHHHHHHHhhCCCCCCCCcHHHHHHH-hCCC-----C-CCCCC---chHHHHHHHHHHHHHHH
Q 037872 58 ------P--DNWRFLDTLPLARELMKQNGSVSSKTSLQALREY-FGIP-----L-EGSAH---RAMSDVNSLASILERIT 119 (146)
Q Consensus 58 ------~--~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~-~gi~-----~-~~~~H---~Al~Da~~ta~l~~~l~ 119 (146)
. ..--.+|.+.+.++-+. ..+|+|+++++. ||.. . .+..+ +--.|+...+.||...+
T Consensus 315 ~~t~~i~~~~G~i~fDLy~~i~k~~~-----L~sYkL~~Vsk~~f~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~f~~vl 389 (1004)
T PHA03036 315 NTTYHINNNNGTIFFDLYTFIQKTEK-----LDSYKLDSISKNAFNCNAKVLSENNNEVTFIGDNTTDAKGKASIFSEVL 389 (1004)
T ss_pred cceEEecccCCeEEEEhHHHHhhhcC-----cccccHHHHHHHhhccceeeeecCCceeEEccCcccccccchhhhhhhh
Confidence 0 00134778888777653 689999999976 5431 0 00111 12358888999999999
Q ss_pred hhhh-cCHHH
Q 037872 120 SDLN-FTLSD 128 (146)
Q Consensus 120 ~~~~-~~~~~ 128 (146)
...+ .++++
T Consensus 390 ~t~ny~~i~~ 399 (1004)
T PHA03036 390 STGNYVTIND 399 (1004)
T ss_pred cccceeeecc
Confidence 9887 45555
No 103
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=94.73 E-value=0.033 Score=49.08 Aligned_cols=90 Identities=27% Similarity=0.369 Sum_probs=56.5
Q ss_pred CCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhC------------------C----CC-----
Q 037872 28 GEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQN------------------G----SV----- 80 (146)
Q Consensus 28 ~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~------------------~----~~----- 80 (146)
++..++||||+ +||+.-++.++. +.... .+++|||.|--..+.-. + ..
T Consensus 239 ~ke~liVGHNV-sfDRaRirEeY~---i~~Sk-~rFlDTMSlHia~~Gm~S~Qrplw~ka~k~k~a~~d~~~~ps~~d~~ 313 (1075)
T KOG3657|consen 239 GKEQLIVGHNV-SFDRARIREEYN---INGSK-IRFLDTMSLHIAMSGMCSRQRPLWFKARKAKSAMYDSETNPSISDYD 313 (1075)
T ss_pred CCCceEEeccc-cchHHHHHHHHh---ccccc-eeeeechhhhhhhhccccccchhHhhhhhhhhhhhhcccCCchhhhh
Confidence 35679999999 999999887665 33222 37899987643222000 0 00
Q ss_pred ------CCCCcHHHHHH-HhCCC-CCCC--------------------CCchHHHHHHHHHHHHHHHhhh
Q 037872 81 ------SSKTSLQALRE-YFGIP-LEGS--------------------AHRAMSDVNSLASILERITSDL 122 (146)
Q Consensus 81 ------~~~~~L~~l~~-~~gi~-~~~~--------------------~H~Al~Da~~ta~l~~~l~~~~ 122 (146)
..-.+|.++.+ ++|++ .+-. .-....|+.+|.+||.++....
T Consensus 314 ~pWL~~SS~NSL~dVhk~~c~~~~LdKt~Rd~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~F 383 (1075)
T KOG3657|consen 314 NPWLGRSSLNSLVDVHKFHCGIDALDKTPRDSFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLF 383 (1075)
T ss_pred hhhhhhhhhHHHHHHHHhhCCCCccccchHHhhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHH
Confidence 12234556655 45776 3210 3356789999999999987653
No 104
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=94.45 E-value=0.037 Score=49.15 Aligned_cols=91 Identities=20% Similarity=0.270 Sum_probs=63.7
Q ss_pred HHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHH
Q 037872 11 EDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALR 90 (146)
Q Consensus 11 ~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~ 90 (146)
.-++.++.=.++- ..++|||+. +-|++.|+ +..|.. ..+||..+...- ..+..+|.-|+
T Consensus 1001 K~~Y~Kl~~Li~~------GviFVGHGL-~nDFrvIN-------i~Vp~~-QiiDTv~lf~~~------s~R~LSLrfLa 1059 (1118)
T KOG1275|consen 1001 KVLYLKLRLLIQR------GVIFVGHGL-QNDFRVIN-------IHVPEE-QIIDTVTLFRLG------SQRMLSLRFLA 1059 (1118)
T ss_pred HHHHHHHHHHHHc------CcEEEcccc-cccceEEE-------EecChh-hheeeeEEEecc------cccEEEHHHHH
Confidence 3444554444443 489999998 78877663 555544 689998875431 13568898887
Q ss_pred H-HhCCCCCCCCCchHHHHHHHHHHHHHHHhhh
Q 037872 91 E-YFGIPLEGSAHRAMSDVNSLASILERITSDL 122 (146)
Q Consensus 91 ~-~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~ 122 (146)
- .+|....-++|+...||+.+.++|.+.++..
T Consensus 1060 ~~lLg~~IQ~~~HDSIeDA~taLkLYk~Yl~lk 1092 (1118)
T KOG1275|consen 1060 WELLGETIQMEAHDSIEDARTALKLYKKYLKLK 1092 (1118)
T ss_pred HHHhcchhhccccccHHHHHHHHHHHHHHHHHH
Confidence 4 5676554469999999999999999876543
No 105
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=94.11 E-value=0.11 Score=45.75 Aligned_cols=101 Identities=21% Similarity=0.268 Sum_probs=63.7
Q ss_pred HHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCC-CCC-----C------------------------
Q 037872 11 EDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMN-IPD-----N------------------------ 60 (146)
Q Consensus 11 ~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~-~~~-----~------------------------ 60 (146)
-+.|..|+.-+. +.+|+|||+.+||+++|-...+.+++. +|. +
T Consensus 342 L~~W~~firevD-------PDvI~GYNi~nFDiPYll~RA~~L~Ie~Fp~LGRikn~~s~irDttfSSkq~GtRetK~v~ 414 (1066)
T KOG0969|consen 342 LESWRKFIREVD-------PDVIIGYNICNFDIPYLLNRAKTLGIENFPYLGRIKNSRSVIRDSTFSSKQYGTRETKEVN 414 (1066)
T ss_pred HHHHHHHHHhcC-------CCeEecccccccccceecChHhhcCcccccccceecccceeeeccccchhhcCcccceEEe
Confidence 344555555554 479999999999999887766666653 221 0
Q ss_pred ---cceeecHHHHHHHHhhCCCCCCCCcHHHHHHHh-CCCCCCCCCc-------------------hHHHHHHHHHHHHH
Q 037872 61 ---WRFLDTLPLARELMKQNGSVSSKTSLQALREYF-GIPLEGSAHR-------------------AMSDVNSLASILER 117 (146)
Q Consensus 61 ---~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~~-gi~~~~~~H~-------------------Al~Da~~ta~l~~~ 117 (146)
-..+|.+....+-+ +.++|+|.+++.+| |-+.+..+|+ .|-||..-.+++.+
T Consensus 415 I~GRlqfDllqvi~Rd~-----KLrSytLNaVs~hFL~EQKEDV~~siItdLQng~~~TRRRlA~YCLkDAYLPlRLlek 489 (1066)
T KOG0969|consen 415 IDGRLQFDLLQVILRDY-----KLRSYTLNAVSAHFLGEQKEDVHHSIITDLQNGNEQTRRRLAVYCLKDAYLPLRLLEK 489 (1066)
T ss_pred ecceeeehHHHHHHHhh-----hhhhcchhhhHHHhhhhhcccccccchhhhhcCcHHHHHHHHHHHhhhhcchHHHHHH
Confidence 01245454444433 36899999997664 6666644443 35677777777777
Q ss_pred HHhhhh
Q 037872 118 ITSDLN 123 (146)
Q Consensus 118 l~~~~~ 123 (146)
++--.+
T Consensus 490 LM~ivN 495 (1066)
T KOG0969|consen 490 LMVIVN 495 (1066)
T ss_pred HHHHHh
Confidence 665443
No 106
>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=92.81 E-value=0.79 Score=31.29 Aligned_cols=67 Identities=19% Similarity=0.257 Sum_probs=45.4
Q ss_pred HHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHHHHh
Q 037872 14 IPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREYF 93 (146)
Q Consensus 14 ~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~~ 93 (146)
...+.+++++ .....|+||+ .+|+..|. +.++..+. ...||+-.+..+.|. ..+.+|.++++.|
T Consensus 42 ~~~l~~~l~~-----~~~~kv~~d~-K~~~~~L~----~~~~~~~~--~~~D~~laayLl~p~----~~~~~l~~l~~~~ 105 (150)
T cd09018 42 LELLKPLLED-----EKALKVGQNL-KYDRGILL----NYFIELRG--IAFDTMLEAYILNSV----AGRWDMDSLVERW 105 (150)
T ss_pred HHHHHHHhcC-----CCCceeeecH-HHHHHHHH----HcCCccCC--cchhHHHHHHHhCCC----CCCCCHHHHHHHH
Confidence 4456777865 2466899999 78888874 44555442 569999988777552 1135999998765
Q ss_pred -CCC
Q 037872 94 -GIP 96 (146)
Q Consensus 94 -gi~ 96 (146)
|.+
T Consensus 106 l~~~ 109 (150)
T cd09018 106 LGHK 109 (150)
T ss_pred hCCC
Confidence 654
No 107
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=92.76 E-value=0.43 Score=34.68 Aligned_cols=91 Identities=23% Similarity=0.218 Sum_probs=59.1
Q ss_pred HHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHHHHh-
Q 037872 15 PIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREYF- 93 (146)
Q Consensus 15 ~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~~- 93 (146)
..|.+++++ .....|+||. ..|+..|.+ ++|+... . . +||+-.+..+.| + . .+|..+++.|
T Consensus 67 ~~L~~~L~~-----~~i~kv~~d~-K~~~~~L~~---~~gi~~~-~-~-fD~~laaYLL~p----~-~-~~l~~l~~~yl 128 (192)
T cd06147 67 HILNEVFTD-----PNILKVFHGA-DSDIIWLQR---DFGLYVV-N-L-FDTGQAARVLNL----P-R-HSLAYLLQKYC 128 (192)
T ss_pred HHHHHHhcC-----CCceEEEech-HHHHHHHHH---HhCCCcC-c-h-HHHHHHHHHhCC----C-c-ccHHHHHHHHh
Confidence 447788875 3467899999 788877642 5576543 2 3 999998877654 2 3 4999998765
Q ss_pred CCCC---------CC------CCCchHHHHHHHHHHHHHHHhhhh
Q 037872 94 GIPL---------EG------SAHRAMSDVNSLASILERITSDLN 123 (146)
Q Consensus 94 gi~~---------~~------~~H~Al~Da~~ta~l~~~l~~~~~ 123 (146)
|... +. +.+.+..||.++..++..+.+++.
T Consensus 129 ~~~~~k~~~~~~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~L~ 173 (192)
T cd06147 129 NVDADKKYQLADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELL 173 (192)
T ss_pred CCCcchhhhccccccCCCCHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 5431 10 011255567777888777777654
No 108
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=90.20 E-value=2.3 Score=36.70 Aligned_cols=97 Identities=16% Similarity=0.208 Sum_probs=69.1
Q ss_pred HHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHH
Q 037872 10 MEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQAL 89 (146)
Q Consensus 10 f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l 89 (146)
.-++...+..|++. +....||||. .||..+|. ++|+. + ....|||-.+-.+-|. .+.+.++++
T Consensus 63 ~~~~~~~l~~~l~~-----~~~~kv~~~~-K~d~~~l~----~~Gi~-~--~~~~DtmlasYll~~~----~~~~~~~~l 125 (593)
T COG0749 63 QLNVLAALKPLLED-----EGIKKVGQNL-KYDYKVLA----NLGIE-P--GVAFDTMLASYLLNPG----AGAHNLDDL 125 (593)
T ss_pred hhhhHHHHHHHhhC-----cccchhcccc-chhHHHHH----HcCCc-c--cchHHHHHHHhccCcC----cCcCCHHHH
Confidence 34588999999987 3457999999 89999885 56644 2 2578999886555442 356899999
Q ss_pred HHHh-CCCCCC---------------------CCCchHHHHHHHHHHHHHHHhhhh
Q 037872 90 REYF-GIPLEG---------------------SAHRAMSDVNSLASILERITSDLN 123 (146)
Q Consensus 90 ~~~~-gi~~~~---------------------~~H~Al~Da~~ta~l~~~l~~~~~ 123 (146)
++.| +.+... ..-.+..||..|.+++..+..++.
T Consensus 126 ~~r~l~~~~~~~~~i~~kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~l~ 181 (593)
T COG0749 126 AKRYLGLETITFEDIAGKGKKQLTFADVKLEKATEYAAEDADATLRLESILEPELL 181 (593)
T ss_pred HHHhcCCccchhHHhhccccccCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 8876 333211 023567899999999999887654
No 109
>PHA02563 DNA polymerase; Provisional
Probab=87.34 E-value=2.7 Score=36.54 Aligned_cols=44 Identities=18% Similarity=0.265 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCC
Q 037872 11 EDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSM 55 (146)
Q Consensus 11 ~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~ 55 (146)
.+.+++|++|+..........++..||. .||-.||...+.+++.
T Consensus 47 ~~~~~~f~~~i~~~~~k~~~~~vYfHN~-~FD~~Fil~~L~~~~~ 90 (630)
T PHA02563 47 GNSFDEFLQWIEDTTYKETECIIYFHNL-KFDGSFILKWLLRNGF 90 (630)
T ss_pred cccHHHHHHHHhhccccccceEEEEecC-CccHHHHHHHHHhhcc
Confidence 4557789999983111223579999998 9999999999888663
No 110
>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=75.41 E-value=14 Score=25.36 Aligned_cols=67 Identities=16% Similarity=0.241 Sum_probs=43.8
Q ss_pred HHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHHHHh
Q 037872 14 IPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREYF 93 (146)
Q Consensus 14 ~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~~ 93 (146)
...|.+|+++. ....++||. .+++..| .++|+.... ...||+-.+-.+.|. ..+..|+++++.|
T Consensus 42 ~~~l~~~l~~~-----~~~ki~~d~-K~~~~~l----~~~gi~l~~--~~fD~~LAaYLL~p~----~~~~~l~~la~~y 105 (151)
T cd06128 42 LELLKPLLEDE-----KALKVGQNL-KYDRVIL----ANYGIELRG--IAFDTMLEAYLLDPV----AGRHDMDSLAERW 105 (151)
T ss_pred HHHHHHHHcCC-----CCCEEeeeh-HHHHHHH----HHCCCCCCC--cchhHHHHHHHcCCC----CCCCCHHHHHHHH
Confidence 34577888752 345788887 5666554 577877542 468999777666552 2313999998776
Q ss_pred -CCC
Q 037872 94 -GIP 96 (146)
Q Consensus 94 -gi~ 96 (146)
++.
T Consensus 106 l~~~ 109 (151)
T cd06128 106 LKEK 109 (151)
T ss_pred cCCC
Confidence 554
No 111
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=64.71 E-value=15 Score=25.35 Aligned_cols=60 Identities=23% Similarity=0.145 Sum_probs=41.3
Q ss_pred CCCCHHHHHHHHHHHHhcccCCCCC-cEEEEeCCCCCCHHHHHHHHHHcC-----CCCCCCcceeecHHHHHHH
Q 037872 6 YVPRMEDLIPIVIKYVNSRLGPGEI-AIFVAHNARRFDVPFLAKEFSRCS-----MNIPDNWRFLDTLPLAREL 73 (146)
Q Consensus 6 ~ap~f~ev~~~~~~~l~~~~~~~~~-~~lVahN~~~FD~~~L~~~~~~~~-----~~~~~~~~~iDt~~l~~~~ 73 (146)
+..+-.+.+..|++-|.. . ..+|+||. +|..+.|+...+..- +.... -+.+|.+..++..
T Consensus 53 ~~DPr~~~~~~L~~~i~~------~~g~ivvyN~-sfE~~rL~ela~~~p~~~~~l~~I~-~r~vDL~~~f~~~ 118 (130)
T PF11074_consen 53 GEDPRRELIEALIKAIGS------IYGSIVVYNK-SFEKTRLKELAELFPDYAEKLNSII-ERTVDLLDPFKNH 118 (130)
T ss_pred CCCchHHHHHHHHHHhhh------hcCeEEEech-HHHHHHHHHHHHHhHHHHHHHHHHH-HHHHHHHHHHhhC
Confidence 456677888899999975 4 68999998 999999987555420 00001 2567777777663
No 112
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=64.10 E-value=18 Score=33.86 Aligned_cols=99 Identities=21% Similarity=0.303 Sum_probs=61.0
Q ss_pred HHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCC-----------CCCC--------------cceee
Q 037872 11 EDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMN-----------IPDN--------------WRFLD 65 (146)
Q Consensus 11 ~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~-----------~~~~--------------~~~iD 65 (146)
...+..|+.-+..- +..++||||+.+|++..|-+.+..++++ ++.. -+.+|
T Consensus 608 rALLs~fla~~~~~----dpD~iVgHn~~~~~l~VLl~R~~~~Kip~WS~IgRLrrS~~~kfg~~s~~~e~~~~aGRl~C 683 (1429)
T KOG0970|consen 608 RALLSHFLAMLNKE----DPDVIVGHNIQGFYLDVLLSRLHALKIPNWSSIGRLRRSWPPKFGRSSSFGEFFIIAGRLMC 683 (1429)
T ss_pred HHHHHHHHHHhhcc----CCCEEEEeccccchHHHHHHHHHHhcCcchhhhhhhhhccccccCCcccccccccccceEEe
Confidence 34455555555443 4579999997699999997777655544 2210 13444
Q ss_pred -cHHHHHHHHhhCCCCCCCCcHHHHHHH-hCCCCCC------------C------CCchHHHHHHHHHHHHHH
Q 037872 66 -TLPLARELMKQNGSVSSKTSLQALREY-FGIPLEG------------S------AHRAMSDVNSLASILERI 118 (146)
Q Consensus 66 -t~~l~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~~------------~------~H~Al~Da~~ta~l~~~l 118 (146)
+-..++.+.+ -.+++|.+|+.. ++.+... . --....|+...++|++++
T Consensus 684 D~~~~a~~lik-----~~S~~LseL~q~~l~~eR~~i~~~~i~~~y~~s~~L~~ll~~~~~d~~~~l~i~~~l 751 (1429)
T KOG0970|consen 684 DLNLAARELIK-----AQSYSLSELSQQILKEERKEINANEIPKMYEDSKSLTYLLEHTITDAELILQIMFRL 751 (1429)
T ss_pred ehHHHHHhhhc-----cccccHHHHHHHHHhhhcccCCHhHhhhhccChHHHHHHHHHHhHHHHHHHHHHHHh
Confidence 4334455543 378999999864 4443210 0 123467888888888875
No 113
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=51.36 E-value=8.9 Score=35.88 Aligned_cols=37 Identities=16% Similarity=0.314 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHH
Q 037872 8 PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAK 48 (146)
Q Consensus 8 p~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~ 48 (146)
++..+.+..|.+++.+- .+.+++|+|+.+||++++..
T Consensus 268 ~~E~~~L~~f~~~i~~~----dpdii~gYNi~~FD~pyl~~ 304 (1172)
T TIGR00592 268 SEEISMIKRFWDVIDQE----DTDVEITVNGDNFDLVYLAD 304 (1172)
T ss_pred cchHHHHhhHHHHHhhc----CcchhcccccccCccceecC
Confidence 45567777788888654 34689999999999998866
No 114
>COG1850 RbcL Ribulose 1,5-bisphosphate carboxylase, large subunit [Carbohydrate transport and metabolism]
Probab=49.44 E-value=35 Score=28.17 Aligned_cols=99 Identities=19% Similarity=0.248 Sum_probs=65.8
Q ss_pred CCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHH
Q 037872 8 PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQ 87 (146)
Q Consensus 8 p~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~ 87 (146)
-.|++=...+.+-+...+.+++....-+-|+ +-+..-|.+..++.. ....+..++|.... +..-|+
T Consensus 200 ~~~e~R~~~~m~~i~~aeaeTGekk~y~~NI-Ta~~~EM~rrae~a~-elG~~~~midi~~~------------G~~a~q 265 (429)
T COG1850 200 NRFEERVAKIMEAIDKAEAETGEKKMYAVNI-TAPCEEMMRRAELAA-ELGANYVMIDIVVT------------GFTALQ 265 (429)
T ss_pred ccHHHHHHHHHHHHHHHHHhhCceEEEEeec-cCCHHHHHHHHHHHH-HcCCCEEEEEEEec------------ccHHHH
Confidence 3588888889999988888888889999999 788765544443321 11122466776544 334566
Q ss_pred HHHHH--hCCCCCCCCCchHHHHHH-------HHHHHHHHHhhh
Q 037872 88 ALREY--FGIPLEGSAHRAMSDVNS-------LASILERITSDL 122 (146)
Q Consensus 88 ~l~~~--~gi~~~~~~H~Al~Da~~-------ta~l~~~l~~~~ 122 (146)
.+++. .|+.. -+|||+.+|+. ...++.++....
T Consensus 266 ~lre~~d~gl~i--haHramh~a~tr~p~~Gis~~vlaK~~Rl~ 307 (429)
T COG1850 266 YLREDEDIGLAI--HAHRAMHAAFTRSPNHGISFLVLAKLLRLI 307 (429)
T ss_pred HHHhcccCCceE--EechhhhhhhhcCCCCCccHHHHHHHHHHc
Confidence 66665 77766 48999999875 345555555544
No 115
>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=41.92 E-value=1.2e+02 Score=21.16 Aligned_cols=68 Identities=21% Similarity=0.093 Sum_probs=40.1
Q ss_pred CHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHHHHh-CCCCCCCCCchHHHHHHHHHHHHHHHh
Q 037872 42 DVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREYF-GIPLEGSAHRAMSDVNSLASILERITS 120 (146)
Q Consensus 42 D~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~~-gi~~~~~~H~Al~Da~~ta~l~~~l~~ 120 (146)
.-+-|--...+-|+..+ +-=|-|-++-.+.| .|.....++++| |-+. .-+|-.-|.+|+++++.+..
T Consensus 69 ~AK~LAv~a~~~G~~v~---PGDDPlLlAYLlDP------sNt~p~~varRY~~~~W---~~dA~~RA~~t~~L~~~L~p 136 (138)
T PF09281_consen 69 LAKDLAVHALREGVVVE---PGDDPLLLAYLLDP------SNTNPEGVARRYLGGEW---PEDAATRALATARLLRALPP 136 (138)
T ss_dssp THHHHHHHHHHTT-------B---HHHHHHHH-T------T--SHHHHHHHH-TS------SSHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCcccC---CCCCcchhhhhcCc------cCCChHHHHHHhcCCCC---CccHHHHHHHHHHHHHHhhh
Confidence 33444444556676554 23567888777765 688999999988 5555 45788889999999998865
Q ss_pred h
Q 037872 121 D 121 (146)
Q Consensus 121 ~ 121 (146)
+
T Consensus 137 r 137 (138)
T PF09281_consen 137 R 137 (138)
T ss_dssp H
T ss_pred c
Confidence 4
No 116
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=38.60 E-value=64 Score=27.15 Aligned_cols=95 Identities=14% Similarity=0.099 Sum_probs=57.0
Q ss_pred HHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCC----CcceeecHHHHHHHHhhCCCCCCCCcHH
Q 037872 12 DLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPD----NWRFLDTLPLARELMKQNGSVSSKTSLQ 87 (146)
Q Consensus 12 ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~----~~~~iDt~~l~~~~~~~~~~~~~~~~L~ 87 (146)
.++++|..++... -+.--+-|-+ .++.. ++-.+.+|.+... ...++|...+.+...-- +..+++|+
T Consensus 340 ~~~~efl~~v~~~----yp~~~~YH~~-~ye~~--~rL~klyg~~~~~v~~~l~~~vDi~~lvr~~v~~---p~es~sLK 409 (474)
T COG2251 340 KALQEFLGIVVRQ----YPEATIYHYA-PYEKT--RRLVKLYGVPQNQVSPVLDSLVDIYALVRSSVVV---PVESYSLK 409 (474)
T ss_pred HHHHHHHhhhhee----cCCCCccccC-chhhh--chhheeeccCcchhhHHHHHHhHHHHHHHhcccc---CccchhHH
Confidence 6888999988721 1123344555 67774 2223456655431 12467777777765521 24799999
Q ss_pred HHHHHhCCCCCCCCCchHHHHHHHHHHHHH
Q 037872 88 ALREYFGIPLEGSAHRAMSDVNSLASILER 117 (146)
Q Consensus 88 ~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~ 117 (146)
.++.++|.+.. +.--|.++++.....|..
T Consensus 410 ~la~~lG~~wr-D~~~ag~~~~~~Y~~~~~ 438 (474)
T COG2251 410 ALAPYLGFQWR-DVEAAGDESLEMYERWLT 438 (474)
T ss_pred HhhhhhCCCcc-ccccchHHHHHHHHHHHh
Confidence 99999999765 244455555555544443
No 117
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=33.55 E-value=1.2e+02 Score=18.85 Aligned_cols=54 Identities=19% Similarity=0.284 Sum_probs=33.5
Q ss_pred ceeecHHHHHHHHhhCCCC--CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHh
Q 037872 62 RFLDTLPLARELMKQNGSV--SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITS 120 (146)
Q Consensus 62 ~~iDt~~l~~~~~~~~~~~--~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~ 120 (146)
.-||...+.+......|.. .....+..+++.+|++.. ...+ +..+-.+|.+.+.
T Consensus 34 ~~vDL~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~--~~~~---~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 34 KPVDLYKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPS--STSA---AQQLRQHYEKYLL 89 (92)
T ss_dssp SE-SHHHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TT--SCHH---HHHHHHHHHHHTH
T ss_pred EeCcHHHHHHHHHhCcCcccCcccchHHHHHHHhCCCCC--CCcH---HHHHHHHHHHHhH
Confidence 5688888888777653310 123468999999999864 2222 6667777776543
No 118
>COG3545 Predicted esterase of the alpha/beta hydrolase fold [General function prediction only]
Probab=32.32 E-value=98 Score=22.72 Aligned_cols=32 Identities=28% Similarity=0.320 Sum_probs=24.5
Q ss_pred CCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCC
Q 037872 4 RSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNA 38 (146)
Q Consensus 4 ~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~ 38 (146)
++++|.+.+=+..+.+-+... .++.+||||..
T Consensus 37 ~w~~P~~~dWi~~l~~~v~a~---~~~~vlVAHSL 68 (181)
T COG3545 37 DWEAPVLDDWIARLEKEVNAA---EGPVVLVAHSL 68 (181)
T ss_pred CCCCCCHHHHHHHHHHHHhcc---CCCeEEEEecc
Confidence 467888888888888887654 24689999975
No 119
>PRK04946 hypothetical protein; Provisional
Probab=29.36 E-value=1.1e+02 Score=22.27 Aligned_cols=42 Identities=7% Similarity=-0.094 Sum_probs=32.9
Q ss_pred CHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHc
Q 037872 9 RMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRC 53 (146)
Q Consensus 9 ~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~ 53 (146)
+.+|+.+++.+||..+...+-..++|-|+- +. +.|+......
T Consensus 104 ~~eeA~~~L~~fl~~a~~~g~r~v~IIHGk-G~--gvLk~~V~~w 145 (181)
T PRK04946 104 TQLQAKQELGALIAACRKEHVFCACVMHGH-GK--HILKQQTPLW 145 (181)
T ss_pred CHHHHHHHHHHHHHHHHHcCCCEEEEEcCC-CH--hHHHHHHHHH
Confidence 578999999999987766666789999986 64 7888776553
No 120
>PRK06193 hypothetical protein; Provisional
Probab=29.21 E-value=89 Score=23.27 Aligned_cols=29 Identities=17% Similarity=0.229 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHhcccCCCCCcEEEEeCC
Q 037872 10 MEDLIPIVIKYVNSRLGPGEIAIFVAHNA 38 (146)
Q Consensus 10 f~ev~~~~~~~l~~~~~~~~~~~lVahN~ 38 (146)
...+.+.+.++|..-..+.+..++||||.
T Consensus 137 ~~~y~~~l~~~I~~l~~~~~~vLlVgHnp 165 (206)
T PRK06193 137 NALLKAGLRPLLTTPPDPGTNTVLVGHDD 165 (206)
T ss_pred HHHHHHHHHHHHhhCCCCCCeEEEEeCch
Confidence 44556777777765433345689999996
No 121
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=29.07 E-value=79 Score=18.46 Aligned_cols=27 Identities=26% Similarity=0.338 Sum_probs=20.3
Q ss_pred cHHHHHHHHhhCCCCCCCCcHHHHHHHhCCCCC
Q 037872 66 TLPLARELMKQNGSVSSKTSLQALREYFGIPLE 98 (146)
Q Consensus 66 t~~l~~~~~~~~~~~~~~~~L~~l~~~~gi~~~ 98 (146)
....|+.+|- ..++..++++.+|++..
T Consensus 2 ~k~~A~~LY~------~G~~~~eIA~~Lg~~~~ 28 (58)
T PF06056_consen 2 VKEQARSLYL------QGWSIKEIAEELGVPRS 28 (58)
T ss_pred HHHHHHHHHH------cCCCHHHHHHHHCCChH
Confidence 3456777773 56899999999999843
No 122
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=27.45 E-value=2.3e+02 Score=24.82 Aligned_cols=107 Identities=18% Similarity=0.189 Sum_probs=66.4
Q ss_pred HHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHH--HcCCCCCCCcceeecHHHHHHHHhhCC----CCCCCCc
Q 037872 12 DLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFS--RCSMNIPDNWRFLDTLPLARELMKQNG----SVSSKTS 85 (146)
Q Consensus 12 ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~--~~~~~~~~~~~~iDt~~l~~~~~~~~~----~~~~~~~ 85 (146)
|+|..+...|.+. .....||... .-|+..|....- +...+.......+|..+++..+....+ ......+
T Consensus 458 e~w~~~~s~if~s----~~i~kvGf~~-~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~ 532 (617)
T KOG2207|consen 458 EIWHLLLSQIFES----KSILKVGFSM-REDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKG 532 (617)
T ss_pred HHHHHHHHHHccC----Cceeeeecch-hhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhh
Confidence 7888888888653 5667788887 788888875222 112222222356788888877764322 0123456
Q ss_pred HHHHHHH-hCCCCC--C-------------CCCchHHHHHHHHHHHHHHHhhhh
Q 037872 86 LQALREY-FGIPLE--G-------------SAHRAMSDVNSLASILERITSDLN 123 (146)
Q Consensus 86 L~~l~~~-~gi~~~--~-------------~~H~Al~Da~~ta~l~~~l~~~~~ 123 (146)
|..|..+ +|.... . +--.|--||.....+|.++.+.-+
T Consensus 533 L~~Lt~~llg~~lnKteqcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv~ 586 (617)
T KOG2207|consen 533 LADLTDCLLGKKLNKTEQCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVVE 586 (617)
T ss_pred hhhhhHHHhhhhcccccccchhhcCCchhhHHHHHHhcchhhHHHHHHHHhhcc
Confidence 7777654 455442 1 223566799999999999987654
No 123
>PRK14118 gpmA phosphoglyceromutase; Provisional
Probab=24.75 E-value=75 Score=23.65 Aligned_cols=34 Identities=12% Similarity=0.237 Sum_probs=24.3
Q ss_pred CCCCCHHHHHHHHHHHHhccc----CCCCCcEEEEeCC
Q 037872 5 SYVPRMEDLIPIVIKYVNSRL----GPGEIAIFVAHNA 38 (146)
Q Consensus 5 ~~ap~f~ev~~~~~~~l~~~~----~~~~~~~lVahN~ 38 (146)
|+..++.++.+.+..++..-. .+++..++|+|++
T Consensus 146 p~GEs~~~~~~Rv~~~l~~~~~~~~~~~~~vlvVsHgg 183 (227)
T PRK14118 146 PDAENLKVTLERVLPFWEDQIAPALLSGKRVLVAAHGN 183 (227)
T ss_pred CCCCCHHHHHHHHHHHHHHHHhhhhcCCCeEEEEeCHH
Confidence 567789999999888775421 1235678999986
No 124
>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=24.45 E-value=1.2e+02 Score=22.16 Aligned_cols=46 Identities=22% Similarity=0.358 Sum_probs=32.9
Q ss_pred CCCCcHHH-HHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhhcCHHHHHHhhcccc
Q 037872 81 SSKTSLQA-LREYFGIPLEGSAHRAMSDVNSLASILERITSDLNFTLSDLLKTSFRAN 137 (146)
Q Consensus 81 ~~~~~L~~-l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~~~~~~l~~~~~~~~ 137 (146)
.+...+.. +++++|++.- ....+|..+..+.+.++.++.+..-+-+
T Consensus 11 sG~TTva~~lAe~~gl~~v-----------saG~iFR~~A~e~gmsl~ef~~~AE~~p 57 (179)
T COG1102 11 SGKTTVARELAEHLGLKLV-----------SAGTIFREMARERGMSLEEFSRYAEEDP 57 (179)
T ss_pred CChhHHHHHHHHHhCCcee-----------eccHHHHHHHHHcCCCHHHHHHHHhcCc
Confidence 45566644 5789999765 3467899999999988888876444333
No 125
>PHA02683 ORF078 thioredoxin-like protein; Provisional
Probab=24.33 E-value=60 Score=20.22 Aligned_cols=32 Identities=19% Similarity=0.233 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHH
Q 037872 6 YVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSR 52 (146)
Q Consensus 6 ~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~ 52 (146)
..|.=..++.+|+.+.. |- .||..+|..+++|
T Consensus 41 sqP~k~~iLk~FL~~~R--------------NK-t~~~kiLD~EirR 72 (75)
T PHA02683 41 SQPNKLRILKEFLATCR--------------NK-TFIYKILDDEIRR 72 (75)
T ss_pred cCccHHHHHHHHHHHHh--------------cc-chhhhhcCHHHHH
Confidence 44555566677776665 44 7888888877766
No 126
>PF11288 DUF3089: Protein of unknown function (DUF3089); InterPro: IPR021440 This family of proteins has no known function.
Probab=23.62 E-value=1.3e+02 Score=22.42 Aligned_cols=29 Identities=17% Similarity=0.237 Sum_probs=22.5
Q ss_pred CHHHHHHHHHHHHhcccCCCCCcEEEEeCC
Q 037872 9 RMEDLIPIVIKYVNSRLGPGEIAIFVAHNA 38 (146)
Q Consensus 9 ~f~ev~~~~~~~l~~~~~~~~~~~lVahN~ 38 (146)
.+.+|...|..||... -++.+.||+||.=
T Consensus 76 ay~DV~~AF~~yL~~~-n~GRPfILaGHSQ 104 (207)
T PF11288_consen 76 AYSDVRAAFDYYLANY-NNGRPFILAGHSQ 104 (207)
T ss_pred hHHHHHHHHHHHHHhc-CCCCCEEEEEeCh
Confidence 4789999999999764 2344789999974
No 127
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=23.44 E-value=1.3e+02 Score=17.82 Aligned_cols=27 Identities=26% Similarity=0.379 Sum_probs=19.2
Q ss_pred HHHHHHHhhCCCCCCCCcHHHHHHHhCCCC
Q 037872 68 PLARELMKQNGSVSSKTSLQALREYFGIPL 97 (146)
Q Consensus 68 ~l~~~~~~~~~~~~~~~~L~~l~~~~gi~~ 97 (146)
.-|..+|... .+..+|.++++.+|++.
T Consensus 10 dkA~e~y~~~---~g~i~lkdIA~~Lgvs~ 36 (60)
T PF10668_consen 10 DKAFEIYKES---NGKIKLKDIAEKLGVSE 36 (60)
T ss_pred HHHHHHHHHh---CCCccHHHHHHHHCCCH
Confidence 3445555443 36889999999999975
No 128
>PF06361 RTBV_P12: Rice tungro bacilliform virus P12 protein; InterPro: IPR009417 This family consists of several Rice tungro bacilliform virus P12 proteins. The function of this family is unknown [].
Probab=22.91 E-value=64 Score=20.65 Aligned_cols=21 Identities=10% Similarity=0.139 Sum_probs=17.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhc
Q 037872 1 MVNRSYVPRMEDLIPIVIKYVNS 23 (146)
Q Consensus 1 mv~~~~ap~f~ev~~~~~~~l~~ 23 (146)
|-. +-|+|.|.++.|.+.-++
T Consensus 1 msa--dyptfke~lekf~~les~ 21 (110)
T PF06361_consen 1 MSA--DYPTFKESLEKFQNLESD 21 (110)
T ss_pred CCC--ccchHHHHHHHHhccccc
Confidence 455 889999999999887654
No 129
>PHA02901 virus redox protein; Provisional
Probab=22.47 E-value=67 Score=20.00 Aligned_cols=32 Identities=19% Similarity=0.245 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHH
Q 037872 6 YVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSR 52 (146)
Q Consensus 6 ~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~ 52 (146)
..|.=..++.+|+.+.. |- .||..+|..+++|
T Consensus 41 sqP~k~~iLk~FL~~~R--------------NK-t~~~kiLD~EirR 72 (75)
T PHA02901 41 SQPYKKKILKQFLATSR--------------NK-TFLYKILDPEIRR 72 (75)
T ss_pred cCchHHHHHHHHHHHHh--------------cc-chhhhhcCHHHHH
Confidence 44555566666666664 44 6888888777766
No 130
>PRK13462 acid phosphatase; Provisional
Probab=22.17 E-value=1.5e+02 Score=21.61 Aligned_cols=34 Identities=15% Similarity=0.056 Sum_probs=24.4
Q ss_pred CCCCCHHHHHHHHHHHHhccc--CCCCCcEEEEeCC
Q 037872 5 SYVPRMEDLIPIVIKYVNSRL--GPGEIAIFVAHNA 38 (146)
Q Consensus 5 ~~ap~f~ev~~~~~~~l~~~~--~~~~~~~lVahN~ 38 (146)
|+..++.++...+.++++.-. .+++..++|+|+.
T Consensus 114 p~gES~~~~~~Rv~~~l~~i~~~~~~~~vliVsHg~ 149 (203)
T PRK13462 114 PGGESVAQVNERADRAVALALEHMESRDVVFVSHGH 149 (203)
T ss_pred CCCccHHHHHHHHHHHHHHHHHhCCCCCEEEEeCCH
Confidence 466788899888888876421 2345689999986
No 131
>PRK14117 gpmA phosphoglyceromutase; Provisional
Probab=22.12 E-value=1.3e+02 Score=22.43 Aligned_cols=34 Identities=9% Similarity=0.183 Sum_probs=23.7
Q ss_pred CCCCCHHHHHHHHHHHHhccc----CCCCCcEEEEeCC
Q 037872 5 SYVPRMEDLIPIVIKYVNSRL----GPGEIAIFVAHNA 38 (146)
Q Consensus 5 ~~ap~f~ev~~~~~~~l~~~~----~~~~~~~lVahN~ 38 (146)
|+..++.++.+.+..++..-. ..++..++|+|+.
T Consensus 147 p~GEs~~~~~~Rv~~~l~~~~~~~~~~~~~vlvVsHg~ 184 (230)
T PRK14117 147 PDAENLKVTLERALPFWEDKIAPALKDGKNVFVGAHGN 184 (230)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHhhccCCCEEEEEeChH
Confidence 356689999999888775421 1234578999986
No 132
>PF12083 DUF3560: Domain of unknown function (DUF3560); InterPro: IPR021944 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 120 amino acids in length. This domain has a conserved GHHSE sequence motif.
Probab=21.89 E-value=70 Score=22.00 Aligned_cols=39 Identities=10% Similarity=0.130 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcC
Q 037872 11 EDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCS 54 (146)
Q Consensus 11 ~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~ 54 (146)
.+....+.++|-- |.+|+|||..-.=|.+.+......++
T Consensus 29 ~~~a~~~~~~ip~-----GQPIlVGHHSE~R~Rr~~eR~~~~m~ 67 (126)
T PF12083_consen 29 YEAANRMAEAIPF-----GQPILVGHHSEKRHRRYRERIHNRMG 67 (126)
T ss_pred HHHHHHHHhccCC-----CCCeeccccchHHHHHHHHHHHHHHH
Confidence 3444455555532 56899999975556667766555544
No 133
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=21.50 E-value=2.3e+02 Score=24.30 Aligned_cols=73 Identities=19% Similarity=0.236 Sum_probs=48.0
Q ss_pred HHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCCCCCCcHHHHHHH-hCCCCCC--------------CCCchHHHHHH
Q 037872 46 LAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREY-FGIPLEG--------------SAHRAMSDVNS 110 (146)
Q Consensus 46 L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~~--------------~~H~Al~Da~~ 110 (146)
+...+.++|+... ..+||+-.+..+-+.. +..+.++..+++. +++..+. +...|..|+..
T Consensus 58 l~~~L~~~Gv~~~---~~fDT~LAa~lL~~~~--~~~~~~l~~la~~~l~~~l~k~~~~sdw~rpls~~q~~YAa~Dv~~ 132 (553)
T PRK14975 58 LYPRLLAAGVRVE---RCHDLMLASQLLLGSE--GRAGSSLSAAAARALGEGLDKPPQTSALSDPPDEEQLLYAAADADV 132 (553)
T ss_pred hHHHHHHCCCccC---CCchHHHHHHHcCCCC--CcCCCCHHHHHHHHhCCCCCChhhhccccccchHHHHHHHHHHhHH
Confidence 4444667776532 4799998887764321 0115799999865 4655321 23368889999
Q ss_pred HHHHHHHHHhhhh
Q 037872 111 LASILERITSDLN 123 (146)
Q Consensus 111 ta~l~~~l~~~~~ 123 (146)
+..|+..+..++.
T Consensus 133 l~~L~~~L~~qL~ 145 (553)
T PRK14975 133 LLELYAVLADQLN 145 (553)
T ss_pred HHHHHHHHHHHHH
Confidence 9999988877754
No 134
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=21.14 E-value=39 Score=20.23 Aligned_cols=30 Identities=23% Similarity=0.483 Sum_probs=18.0
Q ss_pred cHHHHHHHHhhCCCCCCCCcHHHHHHHhCCCCC
Q 037872 66 TLPLARELMKQNGSVSSKTSLQALREYFGIPLE 98 (146)
Q Consensus 66 t~~l~~~~~~~~~~~~~~~~L~~l~~~~gi~~~ 98 (146)
++.+.+.+....| .+++..++++++|+...
T Consensus 11 vL~~I~~~~~~~G---~~Pt~rEIa~~~g~~S~ 40 (65)
T PF01726_consen 11 VLEFIREYIEENG---YPPTVREIAEALGLKST 40 (65)
T ss_dssp HHHHHHHHHHHHS---S---HHHHHHHHTSSSH
T ss_pred HHHHHHHHHHHcC---CCCCHHHHHHHhCCCCh
Confidence 3444455544433 56899999999999754
Done!