Query 018558
Match_columns 354
No_of_seqs 371 out of 2856
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 10:01:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018558.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018558hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2249 3'-5' exonuclease [Rep 100.0 7.2E-46 1.6E-50 324.4 15.1 272 14-315 2-276 (280)
2 cd06149 ISG20 DEDDh 3'-5' exon 100.0 8.2E-36 1.8E-40 253.1 14.8 151 135-299 1-157 (157)
3 cd06143 PAN2_exo DEDDh 3'-5' e 100.0 6.3E-36 1.4E-40 252.4 14.0 150 135-299 1-174 (174)
4 cd06145 REX1_like DEDDh 3'-5' 100.0 4.2E-35 9.1E-40 247.0 14.7 145 135-298 1-149 (150)
5 cd06144 REX4_like DEDDh 3'-5' 100.0 1.5E-34 3.4E-39 244.3 15.3 151 135-299 1-152 (152)
6 cd06137 DEDDh_RNase DEDDh 3'-5 100.0 2.7E-33 5.9E-38 238.9 12.2 147 135-299 1-161 (161)
7 PRK07247 DNA polymerase III su 100.0 1.5E-27 3.3E-32 208.6 15.0 157 130-306 3-170 (195)
8 KOG2248 3'-5' exonuclease [Rep 99.9 2.2E-27 4.7E-32 224.0 13.0 158 129-304 213-374 (380)
9 PRK07740 hypothetical protein; 99.9 1E-26 2.2E-31 210.9 16.8 161 130-307 57-228 (244)
10 PRK09146 DNA polymerase III su 99.9 1E-26 2.2E-31 209.8 14.7 158 130-306 45-228 (239)
11 PRK06309 DNA polymerase III su 99.9 2.4E-26 5.2E-31 207.4 14.5 155 132-305 2-166 (232)
12 PRK07942 DNA polymerase III su 99.9 1.5E-26 3.3E-31 208.5 13.0 164 131-307 5-182 (232)
13 PRK05711 DNA polymerase III su 99.9 1.3E-26 2.8E-31 208.8 11.6 157 132-305 4-176 (240)
14 PRK06807 DNA polymerase III su 99.9 4.5E-26 9.8E-31 213.0 14.7 158 130-306 6-173 (313)
15 PRK06063 DNA polymerase III su 99.9 8.9E-26 1.9E-30 211.5 16.5 157 130-307 13-181 (313)
16 TIGR01406 dnaQ_proteo DNA poly 99.9 4.1E-26 8.8E-31 204.5 13.3 158 133-307 1-174 (225)
17 cd06130 DNA_pol_III_epsilon_li 99.9 6.4E-26 1.4E-30 192.3 13.0 145 134-299 1-155 (156)
18 PRK09145 DNA polymerase III su 99.9 1.1E-25 2.4E-30 199.1 14.9 156 131-304 28-200 (202)
19 PRK06310 DNA polymerase III su 99.9 9E-26 2E-30 205.4 14.0 155 132-305 7-174 (250)
20 PRK06195 DNA polymerase III su 99.9 1E-25 2.3E-30 211.4 14.6 152 133-305 2-164 (309)
21 TIGR00573 dnaq exonuclease, DN 99.9 1.3E-25 2.8E-30 200.8 12.7 159 131-307 6-179 (217)
22 PRK07983 exodeoxyribonuclease 99.9 2.9E-25 6.2E-30 197.7 14.7 145 134-304 2-153 (219)
23 PRK07246 bifunctional ATP-depe 99.9 1.7E-25 3.6E-30 233.7 14.6 158 131-307 6-172 (820)
24 PRK08517 DNA polymerase III su 99.9 5.9E-25 1.3E-29 200.1 15.5 158 130-307 66-233 (257)
25 PRK07748 sporulation inhibitor 99.9 4.1E-25 8.9E-30 196.1 12.6 159 132-305 4-180 (207)
26 cd06131 DNA_pol_III_epsilon_Ec 99.9 2.4E-25 5.1E-30 191.2 10.7 151 134-301 1-166 (167)
27 smart00479 EXOIII exonuclease 99.9 4.2E-25 9.1E-30 189.5 11.6 155 134-306 2-168 (169)
28 COG2176 PolC DNA polymerase II 99.9 6.5E-26 1.4E-30 231.2 7.5 182 108-307 397-588 (1444)
29 PRK07883 hypothetical protein; 99.9 1.9E-24 4.1E-29 216.9 16.0 160 130-307 13-184 (557)
30 PRK08074 bifunctional ATP-depe 99.9 1.2E-24 2.7E-29 230.7 15.4 158 132-307 3-171 (928)
31 PRK06722 exonuclease; Provisio 99.9 1.5E-24 3.3E-29 198.4 13.6 158 131-304 4-180 (281)
32 TIGR01407 dinG_rel DnaQ family 99.9 1.7E-24 3.7E-29 228.5 13.9 157 133-307 1-167 (850)
33 cd06136 TREX1_2 DEDDh 3'-5' ex 99.9 8.8E-25 1.9E-29 189.2 9.6 150 134-300 1-176 (177)
34 PRK05168 ribonuclease T; Provi 99.9 4.5E-24 9.7E-29 189.8 12.1 166 131-307 16-203 (211)
35 cd06134 RNaseT DEDDh 3'-5' exo 99.9 4.2E-24 9.2E-29 186.9 11.6 161 133-305 6-189 (189)
36 TIGR01298 RNaseT ribonuclease 99.9 5.9E-24 1.3E-28 187.4 12.3 165 132-307 8-194 (200)
37 PRK05601 DNA polymerase III su 99.9 5.2E-23 1.1E-27 192.1 15.2 154 130-302 44-246 (377)
38 TIGR01405 polC_Gram_pos DNA po 99.9 2.8E-23 6.1E-28 221.6 13.4 160 130-307 188-357 (1213)
39 cd06133 ERI-1_3'hExo_like DEDD 99.9 1.4E-22 3.1E-27 175.1 10.5 153 134-301 1-175 (176)
40 PRK09182 DNA polymerase III su 99.9 6.9E-22 1.5E-26 183.1 13.8 153 129-302 34-198 (294)
41 cd06127 DEDDh DEDDh 3'-5' exon 99.9 7.6E-22 1.6E-26 166.5 10.7 146 135-298 1-158 (159)
42 PTZ00315 2'-phosphotransferase 99.9 2.4E-21 5.2E-26 190.6 15.3 174 130-308 54-258 (582)
43 COG0847 DnaQ DNA polymerase II 99.9 1.7E-21 3.8E-26 177.3 12.4 156 132-304 13-181 (243)
44 cd06138 ExoI_N N-terminal DEDD 99.9 5.5E-22 1.2E-26 172.7 8.0 147 135-298 1-182 (183)
45 PF00929 RNase_T: Exonuclease; 99.8 4.5E-23 9.8E-28 174.7 -1.8 148 135-298 1-164 (164)
46 PRK00448 polC DNA polymerase I 99.8 1.5E-20 3.3E-25 203.1 12.1 159 131-307 418-586 (1437)
47 cd06135 Orn DEDDh 3'-5' exonuc 99.8 9.6E-20 2.1E-24 157.1 8.0 148 134-304 1-171 (173)
48 PRK11779 sbcB exonuclease I; P 99.8 1.9E-19 4.2E-24 176.2 10.9 157 131-304 5-197 (476)
49 PRK05359 oligoribonuclease; Pr 99.8 4.5E-19 9.8E-24 153.7 9.1 153 132-307 3-177 (181)
50 KOG1275 PAB-dependent poly(A) 99.7 3.1E-18 6.6E-23 171.2 5.5 164 126-304 904-1091(1118)
51 KOG2462 C2H2-type Zn-finger pr 99.5 3.4E-15 7.3E-20 132.5 1.3 89 10-102 159-269 (279)
52 KOG2462 C2H2-type Zn-finger pr 99.4 7.3E-14 1.6E-18 124.1 4.5 93 10-104 128-243 (279)
53 KOG3623 Homeobox transcription 99.2 2E-12 4.4E-17 127.2 1.4 82 11-105 893-978 (1007)
54 COG5018 KapD Inhibitor of the 99.2 9E-12 2E-16 102.8 1.6 165 133-307 5-187 (210)
55 KOG0542 Predicted exonuclease 99.1 5.8E-11 1.3E-15 104.3 5.2 166 133-307 57-244 (280)
56 KOG3576 Ovo and related transc 99.1 1.3E-11 2.7E-16 104.7 0.4 82 7-100 112-197 (267)
57 cd05160 DEDDy_DNA_polB_exo DED 99.0 3.6E-09 7.9E-14 93.2 11.0 126 134-280 1-163 (199)
58 cd06139 DNA_polA_I_Ecoli_like_ 98.7 1.7E-07 3.6E-12 81.8 11.8 144 131-306 4-171 (193)
59 COG2925 SbcB Exonuclease I [DN 98.7 6.9E-08 1.5E-12 89.8 9.6 156 131-303 8-199 (475)
60 KOG3623 Homeobox transcription 98.7 6.6E-09 1.4E-13 102.9 1.7 74 11-96 239-329 (1007)
61 KOG3576 Ovo and related transc 98.7 5.4E-09 1.2E-13 88.9 0.7 92 8-101 141-237 (267)
62 KOG1074 Transcriptional repres 98.7 1.1E-08 2.5E-13 102.9 3.0 90 5-102 598-694 (958)
63 KOG1074 Transcriptional repres 98.6 1.6E-08 3.4E-13 101.9 3.4 48 12-61 353-401 (958)
64 PHA02768 hypothetical protein; 98.6 1.8E-08 4E-13 68.3 2.4 44 12-59 5-49 (55)
65 PHA00733 hypothetical protein 98.6 1.8E-08 3.9E-13 82.1 2.3 84 5-101 33-124 (128)
66 PF01612 DNA_pol_A_exo1: 3'-5' 98.6 7.1E-07 1.5E-11 76.5 12.0 136 133-305 21-175 (176)
67 KOG3242 Oligoribonuclease (3'- 98.6 1.1E-07 2.4E-12 79.2 6.4 155 130-307 24-201 (208)
68 COG1949 Orn Oligoribonuclease 98.4 1.4E-06 3E-11 72.0 7.2 154 131-307 5-180 (184)
69 cd06146 mut-7_like_exo DEDDy 3 98.2 1.1E-05 2.3E-10 70.8 10.9 91 201-303 70-193 (193)
70 PRK05755 DNA polymerase I; Pro 98.2 8.8E-06 1.9E-10 87.1 11.0 137 131-307 314-471 (880)
71 KOG3608 Zn finger proteins [Ge 98.2 6.8E-07 1.5E-11 82.2 1.7 93 11-104 262-381 (467)
72 cd05780 DNA_polB_Kod1_like_exo 98.1 3.4E-05 7.3E-10 67.8 11.6 123 131-280 2-156 (195)
73 cd06125 DnaQ_like_exo DnaQ-lik 98.1 9E-06 2E-10 63.0 6.7 60 135-242 1-61 (96)
74 KOG3608 Zn finger proteins [Ge 98.1 1.1E-06 2.4E-11 80.8 0.8 77 9-99 234-315 (467)
75 PHA00733 hypothetical protein 98.0 2.3E-06 4.9E-11 69.8 2.3 52 6-61 67-119 (128)
76 cd06141 WRN_exo DEDDy 3'-5' ex 98.0 7.1E-05 1.5E-09 64.1 10.2 79 224-302 72-169 (170)
77 cd06129 RNaseD_like DEDDy 3'-5 97.9 0.00014 3E-09 61.9 10.0 78 224-302 66-160 (161)
78 PLN03086 PRLI-interacting fact 97.8 1.1E-05 2.3E-10 80.6 3.5 76 10-102 451-540 (567)
79 PHA02768 hypothetical protein; 97.8 4.8E-06 1E-10 56.6 0.0 41 43-93 7-48 (55)
80 KOG3993 Transcription factor ( 97.8 8.6E-06 1.9E-10 76.7 1.3 48 12-61 295-376 (500)
81 PF13465 zf-H2C2_2: Zinc-finge 97.8 1.4E-05 3E-10 46.1 1.6 25 27-53 1-26 (26)
82 PHA00616 hypothetical protein 97.7 1E-05 2.3E-10 52.2 1.1 38 12-51 1-39 (44)
83 PLN03086 PRLI-interacting fact 97.7 1.8E-05 3.8E-10 79.1 3.2 76 11-101 477-565 (567)
84 PHA00732 hypothetical protein 97.7 1.9E-05 4.1E-10 58.6 2.4 44 12-61 1-44 (79)
85 cd00007 35EXOc 3'-5' exonuclea 97.6 0.00069 1.5E-08 56.2 11.0 93 199-304 40-154 (155)
86 cd05781 DNA_polB_B3_exo DEDDy 97.6 0.00036 7.8E-09 60.9 9.0 76 131-240 2-80 (188)
87 cd05779 DNA_polB_epsilon_exo D 97.6 0.00082 1.8E-08 59.4 11.2 154 132-298 2-203 (204)
88 KOG3993 Transcription factor ( 97.6 1.7E-05 3.6E-10 74.9 -0.0 91 13-105 268-385 (500)
89 cd05777 DNA_polB_delta_exo DED 97.5 0.002 4.3E-08 58.1 12.4 90 130-240 5-103 (230)
90 cd05785 DNA_polB_like2_exo Unc 97.4 0.001 2.2E-08 59.0 9.0 77 130-240 7-90 (207)
91 cd05784 DNA_polB_II_exo DEDDy 97.4 0.0025 5.3E-08 55.9 11.0 120 131-279 2-153 (193)
92 COG0349 Rnd Ribonuclease D [Tr 97.3 0.0015 3.2E-08 61.8 10.0 134 132-307 17-168 (361)
93 TIGR01388 rnd ribonuclease D. 97.3 0.0027 5.8E-08 61.3 11.9 82 224-307 69-168 (367)
94 PRK10829 ribonuclease D; Provi 97.3 0.0027 5.9E-08 61.2 11.0 83 224-307 73-172 (373)
95 PHA00732 hypothetical protein 97.1 0.00019 4.2E-09 53.2 1.0 41 43-96 3-44 (79)
96 PF00096 zf-C2H2: Zinc finger, 97.1 0.00026 5.7E-09 39.3 1.2 22 13-34 1-22 (23)
97 cd05783 DNA_polB_B1_exo DEDDy 97.0 0.018 3.9E-07 50.9 12.8 131 131-279 4-170 (204)
98 cd06148 Egl_like_exo DEDDy 3'- 96.9 0.004 8.8E-08 54.7 8.3 82 224-307 64-179 (197)
99 smart00474 35EXOc 3'-5' exonuc 96.8 0.0053 1.2E-07 51.8 7.4 90 202-305 64-171 (172)
100 PF13912 zf-C2H2_6: C2H2-type 96.6 0.0014 2.9E-08 37.9 1.9 25 12-38 1-25 (27)
101 PF13482 RNase_H_2: RNase_H su 96.6 0.0046 9.9E-08 52.4 5.7 72 224-302 56-134 (164)
102 PF13465 zf-H2C2_2: Zinc-finge 96.6 0.0004 8.7E-09 39.9 -0.7 23 56-88 1-26 (26)
103 PHA02528 43 DNA polymerase; Pr 96.5 0.055 1.2E-06 57.8 13.9 204 85-300 59-323 (881)
104 PF00096 zf-C2H2: Zinc finger, 96.4 0.0012 2.5E-08 36.6 0.5 22 78-99 2-23 (23)
105 PTZ00166 DNA polymerase delta 96.2 0.04 8.7E-07 60.2 11.8 154 129-302 261-483 (1054)
106 PF13894 zf-C2H2_4: C2H2-type 96.1 0.0031 6.7E-08 34.9 1.4 22 13-34 1-22 (24)
107 PF05605 zf-Di19: Drought indu 96.1 0.0029 6.2E-08 43.3 1.5 46 12-61 2-49 (54)
108 COG5189 SFP1 Putative transcri 96.1 0.0025 5.4E-08 58.3 1.5 67 10-96 347-418 (423)
109 cd06142 RNaseD_exo DEDDy 3'-5' 96.1 0.024 5.3E-07 48.4 7.6 92 201-307 52-162 (178)
110 PRK05762 DNA polymerase II; Re 95.8 0.048 1E-06 58.0 9.6 143 130-301 153-348 (786)
111 PF09237 GAGA: GAGA factor; I 95.7 0.0093 2E-07 39.6 2.5 34 7-42 19-52 (54)
112 PHA00616 hypothetical protein 95.7 0.0043 9.4E-08 40.2 0.9 27 78-104 3-29 (44)
113 COG0749 PolA DNA polymerase I 95.6 0.043 9.3E-07 55.5 8.0 95 201-307 66-182 (593)
114 PF13894 zf-C2H2_4: C2H2-type 95.6 0.0046 1E-07 34.1 0.8 23 78-100 2-24 (24)
115 cd06140 DNA_polA_I_Bacillus_li 95.6 0.031 6.7E-07 47.9 6.3 94 201-307 44-158 (178)
116 PF04857 CAF1: CAF1 family rib 95.5 0.033 7.2E-07 51.2 6.3 72 224-300 148-262 (262)
117 PF12756 zf-C2H2_2: C2H2 type 95.5 0.0068 1.5E-07 46.5 1.4 72 14-100 1-74 (100)
118 smart00355 ZnF_C2H2 zinc finge 95.4 0.011 2.4E-07 33.1 1.8 24 13-38 1-24 (26)
119 cd05776 DNA_polB_alpha_exo ina 95.4 0.048 1E-06 49.3 6.8 135 133-280 4-187 (234)
120 PF10108 DNA_pol_B_exo2: Predi 95.2 0.087 1.9E-06 46.5 7.7 94 198-305 37-173 (209)
121 cd05778 DNA_polB_zeta_exo inac 95.1 0.23 5E-06 44.7 10.4 147 133-291 5-203 (231)
122 TIGR00593 pola DNA polymerase 94.7 0.073 1.6E-06 57.1 6.8 96 197-306 362-478 (887)
123 PF13912 zf-C2H2_6: C2H2-type 94.3 0.013 2.8E-07 33.7 0.2 23 78-100 3-25 (27)
124 cd05782 DNA_polB_like1_exo Unc 94.1 0.15 3.2E-06 45.3 6.5 88 198-299 78-207 (208)
125 PF05605 zf-Di19: Drought indu 93.6 0.037 8E-07 37.8 1.3 45 43-100 4-53 (54)
126 PF12874 zf-met: Zinc-finger o 93.4 0.046 9.9E-07 30.7 1.3 22 13-34 1-22 (25)
127 cd09018 DEDDy_polA_RNaseD_like 93.3 0.2 4.4E-06 41.2 5.7 56 224-280 52-110 (150)
128 PF13913 zf-C2HC_2: zinc-finge 93.3 0.047 1E-06 31.0 1.2 21 78-99 4-24 (25)
129 smart00355 ZnF_C2H2 zinc finge 93.1 0.051 1.1E-06 30.2 1.2 22 78-99 2-23 (26)
130 PF03104 DNA_pol_B_exo1: DNA p 92.7 0.31 6.7E-06 45.8 6.7 90 130-240 155-254 (325)
131 PF12171 zf-C2H2_jaz: Zinc-fin 92.3 0.074 1.6E-06 30.6 1.2 22 13-34 2-23 (27)
132 KOG4793 Three prime repair exo 92.3 0.2 4.3E-06 45.4 4.4 127 169-305 71-218 (318)
133 cd06147 Rrp6p_like_exo DEDDy 3 92.1 0.21 4.6E-06 43.5 4.4 80 224-307 76-174 (192)
134 PHA02570 dexA exonuclease; Pro 92.1 0.96 2.1E-05 40.1 8.3 97 135-241 4-124 (220)
135 PF09237 GAGA: GAGA factor; I 91.8 0.11 2.4E-06 34.6 1.6 27 78-104 26-52 (54)
136 KOG1798 DNA polymerase epsilon 90.7 3.2 7E-05 46.2 12.0 156 130-305 244-454 (2173)
137 PF13909 zf-H2C2_5: C2H2-type 89.8 0.17 3.7E-06 28.1 1.0 21 13-34 1-21 (24)
138 COG0417 PolB DNA polymerase el 89.5 4.1 9E-05 43.5 11.9 128 130-280 152-309 (792)
139 PF13913 zf-C2HC_2: zinc-finge 89.5 0.25 5.4E-06 28.0 1.5 21 13-34 3-23 (25)
140 KOG0304 mRNA deadenylase subun 88.7 0.59 1.3E-05 41.1 4.0 76 224-304 141-238 (239)
141 PF12874 zf-met: Zinc-finger o 88.5 0.16 3.4E-06 28.4 0.3 21 78-98 2-22 (25)
142 smart00486 POLBc DNA polymeras 88.0 0.99 2.1E-05 44.6 5.8 148 132-301 3-220 (471)
143 COG5048 FOG: Zn-finger [Genera 87.1 0.4 8.7E-06 46.4 2.3 49 11-61 288-343 (467)
144 PF12171 zf-C2H2_jaz: Zinc-fin 87.0 0.15 3.2E-06 29.3 -0.4 21 78-98 3-23 (27)
145 smart00451 ZnF_U1 U1-like zinc 85.2 0.62 1.4E-05 28.2 1.7 23 12-34 3-25 (35)
146 COG3359 Predicted exonuclease 84.4 7.3 0.00016 35.2 8.5 16 131-146 97-112 (278)
147 KOG2231 Predicted E3 ubiquitin 83.2 0.61 1.3E-05 47.9 1.6 77 13-97 100-203 (669)
148 TIGR00592 pol2 DNA polymerase 81.1 13 0.00028 41.7 11.0 107 183-301 569-722 (1172)
149 KOG0969 DNA polymerase delta, 80.1 1.2 2.6E-05 46.2 2.4 141 127-288 269-458 (1066)
150 KOG1146 Homeobox protein [Gene 78.9 1.7 3.7E-05 47.7 3.2 23 78-100 520-542 (1406)
151 cd06128 DNA_polA_exo DEDDy 3'- 77.5 3.7 8E-05 33.9 4.3 54 225-279 53-109 (151)
152 PF09538 FYDLN_acid: Protein o 75.4 2 4.4E-05 33.8 2.0 29 43-89 11-39 (108)
153 KOG3657 Mitochondrial DNA poly 75.3 2.6 5.6E-05 44.1 3.2 89 223-311 239-389 (1075)
154 smart00451 ZnF_U1 U1-like zinc 73.0 2 4.3E-05 25.9 1.1 21 78-98 5-25 (35)
155 PF09538 FYDLN_acid: Protein o 72.7 2 4.3E-05 33.8 1.3 30 13-55 10-40 (108)
156 PRK05761 DNA polymerase I; Rev 71.2 7.7 0.00017 41.5 5.7 90 196-298 208-334 (787)
157 PF12756 zf-C2H2_2: C2H2 type 70.9 2.9 6.4E-05 31.5 1.9 23 12-34 50-72 (100)
158 PHA02524 43A DNA polymerase su 70.1 23 0.0005 35.6 8.4 200 84-298 58-321 (498)
159 TIGR02098 MJ0042_CXXC MJ0042 f 69.5 2.4 5.1E-05 26.3 0.9 33 13-52 3-36 (38)
160 PRK04860 hypothetical protein; 69.2 2.4 5.3E-05 35.8 1.2 33 43-89 121-156 (160)
161 COG4049 Uncharacterized protei 67.6 2.4 5.3E-05 28.7 0.7 28 7-34 12-39 (65)
162 PF09986 DUF2225: Uncharacteri 67.3 1.6 3.4E-05 38.9 -0.4 13 78-90 50-62 (214)
163 KOG2186 Cell growth-regulating 67.0 2.5 5.4E-05 38.0 0.8 45 12-61 3-48 (276)
164 PRK04860 hypothetical protein; 66.7 1.5 3.2E-05 37.1 -0.6 33 18-55 124-157 (160)
165 PF09986 DUF2225: Uncharacteri 65.2 4 8.7E-05 36.3 1.8 17 10-26 3-19 (214)
166 PF13719 zinc_ribbon_5: zinc-r 64.3 3.8 8.3E-05 25.4 1.1 32 13-51 3-35 (37)
167 PF10571 UPF0547: Uncharacteri 62.5 4.4 9.6E-05 23.1 1.0 10 78-87 16-25 (26)
168 TIGR02300 FYDLN_acid conserved 61.9 5.1 0.00011 32.2 1.7 37 39-93 7-43 (129)
169 PF13717 zinc_ribbon_4: zinc-r 61.6 4.5 9.7E-05 25.0 1.0 32 13-51 3-35 (36)
170 TIGR02300 FYDLN_acid conserved 60.9 6.5 0.00014 31.7 2.1 30 13-55 10-40 (129)
171 PF09723 Zn-ribbon_8: Zinc rib 60.5 3.1 6.7E-05 26.7 0.2 29 12-49 5-34 (42)
172 KOG2893 Zn finger protein [Gen 56.9 6.2 0.00013 35.2 1.5 41 14-60 12-53 (341)
173 PF05191 ADK_lid: Adenylate ki 54.7 6.1 0.00013 24.4 0.8 31 13-53 2-33 (36)
174 cd00729 rubredoxin_SM Rubredox 54.3 6.7 0.00014 23.9 0.9 10 12-21 2-11 (34)
175 PRK00464 nrdR transcriptional 52.9 3.7 8E-05 34.5 -0.5 15 78-92 30-44 (154)
176 PF15269 zf-C2H2_7: Zinc-finge 52.8 8.3 0.00018 24.9 1.2 22 78-99 22-43 (54)
177 smart00614 ZnF_BED BED zinc fi 51.6 8.8 0.00019 25.4 1.3 23 78-100 20-48 (50)
178 TIGR03491 RecB family nuclease 51.3 95 0.0021 30.9 9.1 89 198-303 328-429 (457)
179 TIGR00622 ssl1 transcription f 48.7 36 0.00077 26.9 4.4 25 78-102 83-107 (112)
180 TIGR02605 CxxC_CxxC_SSSS putat 45.7 7.9 0.00017 25.7 0.3 28 13-49 6-34 (52)
181 PF14353 CpXC: CpXC protein 45.1 13 0.00029 29.9 1.6 19 78-96 40-58 (128)
182 PF09845 DUF2072: Zn-ribbon co 44.9 12 0.00026 30.4 1.2 9 78-86 21-30 (131)
183 PF13017 Maelstrom: piRNA path 43.9 33 0.00071 30.4 4.0 59 151-209 8-78 (213)
184 PF03604 DNA_RNApol_7kD: DNA d 43.8 17 0.00036 21.9 1.5 11 13-23 1-11 (32)
185 COG3364 Zn-ribbon containing p 43.1 13 0.00027 28.7 1.1 12 12-23 2-13 (112)
186 COG1997 RPL43A Ribosomal prote 42.4 11 0.00023 28.3 0.5 7 43-49 37-43 (89)
187 smart00659 RPOLCX RNA polymera 42.2 13 0.00028 24.1 0.9 25 13-50 3-28 (44)
188 PHA02563 DNA polymerase; Provi 40.1 27 0.00059 36.2 3.3 16 225-240 66-81 (630)
189 COG0068 HypF Hydrogenase matur 39.9 9.8 0.00021 39.5 0.1 42 43-84 125-181 (750)
190 PRK00398 rpoP DNA-directed RNA 39.8 12 0.00026 24.3 0.5 28 12-51 3-31 (46)
191 COG1996 RPC10 DNA-directed RNA 39.8 13 0.00028 24.7 0.6 12 11-22 5-16 (49)
192 PF02892 zf-BED: BED zinc fing 39.6 20 0.00043 22.8 1.5 25 9-33 13-41 (45)
193 cd00350 rubredoxin_like Rubred 39.5 17 0.00036 21.9 1.0 9 13-21 2-10 (33)
194 KOG0970 DNA polymerase alpha, 38.9 55 0.0012 36.0 5.3 95 129-240 526-639 (1429)
195 KOG2785 C2H2-type Zn-finger pr 38.6 15 0.00033 35.2 1.1 74 12-97 3-89 (390)
196 KOG4173 Alpha-SNAP protein [In 37.5 9 0.00019 33.5 -0.5 83 11-97 78-167 (253)
197 COG1198 PriA Primosomal protei 37.1 13 0.00029 39.1 0.6 15 130-144 505-519 (730)
198 PF07295 DUF1451: Protein of u 34.3 20 0.00042 29.9 1.0 15 36-50 102-121 (146)
199 COG1571 Predicted DNA-binding 34.2 26 0.00056 34.3 1.9 13 78-90 369-381 (421)
200 smart00734 ZnF_Rad18 Rad18-lik 32.9 31 0.00066 19.6 1.4 21 78-99 3-23 (26)
201 smart00531 TFIIE Transcription 32.6 27 0.00059 28.9 1.6 13 12-24 99-111 (147)
202 PF15135 UPF0515: Uncharacteri 32.6 32 0.00069 31.1 2.1 36 8-53 108-144 (278)
203 TIGR01206 lysW lysine biosynth 31.3 13 0.00028 25.3 -0.5 32 12-52 2-33 (54)
204 PF05290 Baculo_IE-1: Baculovi 31.3 22 0.00049 28.9 0.8 14 78-91 123-136 (140)
205 COG2331 Uncharacterized protei 30.9 12 0.00027 27.1 -0.6 31 12-52 12-44 (82)
206 PF07754 DUF1610: Domain of un 30.5 21 0.00044 20.0 0.4 10 11-20 15-24 (24)
207 KOG3846 L-kynurenine hydrolase 30.2 23 0.0005 33.2 0.8 9 344-352 266-274 (465)
208 KOG2893 Zn finger protein [Gen 28.7 15 0.00032 32.9 -0.7 42 43-95 12-53 (341)
209 PRK09678 DNA-binding transcrip 28.0 22 0.00047 25.8 0.2 10 81-90 34-43 (72)
210 COG2888 Predicted Zn-ribbon RN 27.8 30 0.00065 24.0 0.8 8 43-50 29-36 (61)
211 KOG0782 Predicted diacylglycer 27.3 13 0.00028 37.5 -1.4 33 14-54 255-289 (1004)
212 KOG4167 Predicted DNA-binding 27.0 12 0.00025 38.9 -1.8 27 78-104 794-820 (907)
213 PF11906 DUF3426: Protein of u 26.7 1.4E+02 0.0031 24.3 5.1 59 131-189 66-124 (149)
214 KOG1146 Homeobox protein [Gene 26.6 67 0.0014 36.0 3.6 80 12-102 1260-1354(1406)
215 COG4888 Uncharacterized Zn rib 26.3 14 0.00029 28.5 -1.1 11 11-21 21-31 (104)
216 COG5151 SSL1 RNA polymerase II 26.2 36 0.00077 31.8 1.3 25 78-102 390-414 (421)
217 PF06821 Ser_hydrolase: Serine 25.3 65 0.0014 27.4 2.7 37 194-240 35-73 (171)
218 COG4530 Uncharacterized protei 25.2 29 0.00062 27.2 0.4 10 78-87 28-37 (129)
219 KOG0978 E3 ubiquitin ligase in 25.2 20 0.00043 37.4 -0.5 19 77-95 679-697 (698)
220 COG3357 Predicted transcriptio 25.1 39 0.00084 25.6 1.1 13 41-53 57-70 (97)
221 KOG4167 Predicted DNA-binding 25.1 22 0.00048 37.0 -0.2 27 11-39 791-817 (907)
222 PLN03238 probable histone acet 25.0 47 0.001 30.8 1.8 28 78-105 50-77 (290)
223 COG1592 Rubrerythrin [Energy p 24.7 41 0.00089 28.6 1.3 21 43-83 136-156 (166)
224 PRK14873 primosome assembly pr 24.4 23 0.0005 37.1 -0.2 18 68-85 414-431 (665)
225 PF12096 DUF3572: Protein of u 23.6 48 0.001 25.0 1.3 28 183-210 29-56 (88)
226 TIGR00595 priA primosomal prot 23.6 29 0.00062 35.1 0.2 12 132-143 285-296 (505)
227 smart00834 CxxC_CXXC_SSSS Puta 23.5 31 0.00067 21.3 0.3 30 12-50 5-35 (41)
228 PF14446 Prok-RING_1: Prokaryo 22.7 45 0.00098 22.7 1.0 6 43-48 23-28 (54)
229 KOG3408 U1-like Zn-finger-cont 22.4 50 0.0011 26.4 1.3 26 9-34 54-79 (129)
230 smart00211 TY Thyroglobulin ty 22.3 40 0.00087 22.0 0.7 8 347-354 20-27 (46)
231 PF13878 zf-C2H2_3: zinc-finge 22.3 79 0.0017 20.0 2.0 27 73-99 10-38 (41)
232 KOG2747 Histone acetyltransfer 22.1 42 0.00092 32.5 1.0 28 78-105 160-187 (396)
233 PF05443 ROS_MUCR: ROS/MUCR tr 21.8 55 0.0012 26.7 1.5 24 12-40 72-95 (132)
234 KOG2186 Cell growth-regulating 21.3 41 0.00088 30.5 0.7 41 43-96 5-48 (276)
235 PF04959 ARS2: Arsenite-resist 21.2 57 0.0012 29.0 1.6 29 9-38 74-102 (214)
236 PHA00626 hypothetical protein 21.1 44 0.00095 22.9 0.6 16 10-25 21-36 (59)
237 PTZ00255 60S ribosomal protein 21.0 37 0.0008 25.7 0.3 7 43-49 38-44 (90)
238 PF04606 Ogr_Delta: Ogr/Delta- 20.9 25 0.00054 23.0 -0.6 6 15-20 2-7 (47)
239 TIGR00280 L37a ribosomal prote 20.8 35 0.00076 25.9 0.1 7 43-49 37-43 (91)
240 COG3545 Predicted esterase of 20.1 1.5E+02 0.0034 25.5 3.9 32 195-236 40-71 (181)
241 PRK04023 DNA polymerase II lar 20.0 84 0.0018 34.3 2.8 20 68-87 655-674 (1121)
No 1
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=7.2e-46 Score=324.43 Aligned_cols=272 Identities=49% Similarity=0.791 Sum_probs=218.9
Q ss_pred cccccccccCChHHHHHhhhhccccCccccccccccccCCccccccccCCCCCcccccccccccccccccccCCCChhHH
Q 018558 14 KCAACFRQFNRLEHLVEHMRTSYHSVHEPVCGICKKHCRSFESLREHLIGPLPKQECKNVFNNRGCRFCLAILDGPNARR 93 (354)
Q Consensus 14 ~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~~C~~C~k~f~~~~~L~~H~~~e~p~~~C~k~F~~~~C~~C~k~f~~~~~l~ 93 (354)
+|..|-+.|.....+..|+ +.+|....+.|..|.+.-.....+..++.+..+- .|...|....|..|.-.-.......
T Consensus 2 ~~~~~~~~~~~~~~~~~~~-v~~~~~~~~~~~~~k~~~~~~~~~~e~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (280)
T KOG2249|consen 2 KASSCAQQFNKKEHLPNHK-VSRHKLHERKCGKCKKVARSFESNEEGLIAPLPK-EGKNIFSQRGNRFKATIKASPGKRR 79 (280)
T ss_pred CccHHHHHhCccccCcccc-chhhccCcchhhhHHHhccCcccccccccCCCCc-ccCccccchhhHHHhhHhhcCCcch
Confidence 3556777777777777777 3224432227888877766666666666332222 6778888888888766555566666
Q ss_pred HHHhhccccCCCCccchhhhhccCCCCCcccCCCCC-CCCceEEeeccccccCCCCCccceeeEEEEecCCceEEeeeec
Q 018558 94 LHQERCQMVSSATTGLNARLANLGVRDSLTIDNTHT-RDPQVVAIACKMVGGGSDGSLDLCGRVCIIDEYENIIFHAYVK 172 (354)
Q Consensus 94 ~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~i~~~~v~ 172 (354)
.|+..|+...+... . ..+.... ...++||+||||+|+|+++..+.+++++|||..|.++||+||+
T Consensus 80 ~~~~~~~~~~~~~~--------~------~~k~s~~~~~~r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVk 145 (280)
T KOG2249|consen 80 IHQGSCQASCRMAA--------L------GSKDSRMGSLTRVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVK 145 (280)
T ss_pred hhhcccCCCccccc--------c------chhhccccccceEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecC
Confidence 66655554422111 0 1111112 2226999999999999999999999999999999999999999
Q ss_pred CCccccCceeeecCCChhhhcCCCCHHHHHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcccCCCceeeec
Q 018558 173 PPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVEYPAIMTRDT 252 (354)
Q Consensus 173 P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~~~~~~~~Dt 252 (354)
|..+|++|+|+++||+|+++.+|.+|+.|+.++++|| .|+|||||.+.+||.+|++.||..+++||
T Consensus 146 P~~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~klL--------------~gRIlVGHaLhnDl~~L~l~hp~s~iRDT 211 (280)
T KOG2249|consen 146 PTEPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLKLL--------------KGRILVGHALHNDLQALKLEHPRSMIRDT 211 (280)
T ss_pred CCcccccceeeecccCHHHhccCccHHHHHHHHHHHH--------------hCCEEeccccccHHHHHhhhCchhhhccc
Confidence 9999999999999999999999999999999999999 89999999999999999999999999999
Q ss_pred cccCCCcc--CCCCCchHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHHhhhhccCCCCCC
Q 018558 253 AKYPPLMK--TSKLSNSLKYLTQAYLGYDIQIGIQDPYDDCVATMRLYMRMKSQAHKREDYPLAS 315 (354)
Q Consensus 253 ~~~~~~~~--~~~~~~~L~~l~~~~l~~~i~~~~H~Al~DA~at~~l~~~~~~~~~~~~~~~~~~ 315 (354)
+.+.+++. .....++|+.|++.+||++||.|.|++++||+|||+||.+++.+|++....++..
T Consensus 212 s~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~GeHsSvEDA~AtM~LY~~vk~qwe~~~~r~l~~ 276 (280)
T KOG2249|consen 212 SKYPPLMKLLSKKATPSLKKLTEALLGKDIQVGEHSSVEDARATMELYKRVKVQWEKIEARPLAT 276 (280)
T ss_pred ccCchHHHHhhccCCccHHHHHHHHhchhhhccccCcHHHHHHHHHHHHHHHHHHHHHhhccccc
Confidence 99999887 4667899999999999999999999999999999999999999998866655433
No 2
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=100.00 E-value=8.2e-36 Score=253.07 Aligned_cols=151 Identities=37% Similarity=0.605 Sum_probs=135.5
Q ss_pred EEeeccccccCCCCCccceeeEEEEecCCceEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHHHhcCCC
Q 018558 135 VAIACKMVGGGSDGSLDLCGRVCIIDEYENIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDFLCNGEP 214 (354)
Q Consensus 135 vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~i~~~~~ 214 (354)
|++||||||+++.++.++|+++++|+.+|.++|++||+|..+|+++++++||||++||++||+|++++++|++|+
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~~~~~~lv~P~~~i~~~~~~i~GIt~~~l~~a~~~~~v~~~l~~~l----- 75 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKIL----- 75 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCCEEEEEeECCCCccCccceECCCCCHHHHhcCCCHHHHHHHHHHHc-----
Confidence 689999999988766788999999999999999999999999999999999999999999999999999999999
Q ss_pred CccccCCCCCCcEEEEechhhhhhhhcccCCCceeeeccccCCCc----cCCCCCchHHHHHHHHhCCcCCCC--CCChH
Q 018558 215 MWKIRPRGSRARILVGHGLDHDLDRLQVEYPAIMTRDTAKYPPLM----KTSKLSNSLKYLTQAYLGYDIQIG--IQDPY 288 (354)
Q Consensus 215 ~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~~~~~~~~Dt~~~~~~~----~~~~~~~~L~~l~~~~l~~~i~~~--~H~Al 288 (354)
+++||||||+.||+++|++.++...++||+.+.... .+...+++|+.||++|++.+|+.+ +|||+
T Consensus 76 ---------~~~vlV~Hn~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~H~Al 146 (157)
T cd06149 76 ---------KGKVVVGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSV 146 (157)
T ss_pred ---------CCCEEEEeCcHHHHHHhcccCCCcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCCCcCcH
Confidence 899999999999999999987776688998764322 233356899999999999888753 79999
Q ss_pred HHHHHHHHHHH
Q 018558 289 DDCVATMRLYM 299 (354)
Q Consensus 289 ~DA~at~~l~~ 299 (354)
+||+|||+||+
T Consensus 147 ~DA~at~~l~~ 157 (157)
T cd06149 147 EDARATMELYK 157 (157)
T ss_pred HHHHHHHHHhC
Confidence 99999999984
No 3
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=100.00 E-value=6.3e-36 Score=252.43 Aligned_cols=150 Identities=27% Similarity=0.386 Sum_probs=133.8
Q ss_pred EEeeccccccCC-------CCCc-------cceeeEEEEe----cCCceEEeeeecCCccccCceeeecCCChhhhcCCC
Q 018558 135 VAIACKMVGGGS-------DGSL-------DLCGRVCIID----EYENIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAI 196 (354)
Q Consensus 135 vaiD~Ettg~~~-------~~~~-------~~i~~i~vv~----~~g~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap 196 (354)
+|+|||++|+++ ++.. .+++++++|| .+|+++||+||+|..+|.+|+|+++|||++++++++
T Consensus 1 ~a~d~e~v~~~~~~~~~~~~g~~~~~~~~~~~LaRVsiVd~~~~~~g~vllD~~VkP~~~V~DYrT~~SGIt~~~L~~a~ 80 (174)
T cd06143 1 VAIDAEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKT 80 (174)
T ss_pred CceeeeEEEecchhceecCCCcEeeeccCCceeEEEEEEcCCCCcCCCEEEeeeECCCCCccCcCccccccCHHHcCccc
Confidence 467777777776 3444 3799999999 689999999999999999999999999999999875
Q ss_pred ------CHHHHHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcccCCCceeeeccccCCCccCCCCCchHHH
Q 018558 197 ------PLKQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVEYPAIMTRDTAKYPPLMKTSKLSNSLKY 270 (354)
Q Consensus 197 ------~~~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~~~~~~~~Dt~~~~~~~~~~~~~~~L~~ 270 (354)
++++++.++.+++ ..++|||||++++||++|++.||...++||+.+++... ..+++|+.
T Consensus 81 ~~~~~~t~~~v~~~l~~li-------------~~~tILVGHsL~nDL~aL~l~hp~~~viDTa~l~~~~~--~r~~sLk~ 145 (174)
T cd06143 81 SSKNLTTLKSAYLKLRLLV-------------DLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFHLPG--QRKLSLRF 145 (174)
T ss_pred cccccCCHHHHHHHHHHHc-------------CCCCEEEeccchhHHHHhcCcCCCcceEEcHHhccCCC--CCChhHHH
Confidence 6999999999999 26899999999999999999999877999999987643 34789999
Q ss_pred HHHHHhCCcCCCCCCChHHHHHHHHHHHH
Q 018558 271 LTQAYLGYDIQIGIQDPYDDCVATMRLYM 299 (354)
Q Consensus 271 l~~~~l~~~i~~~~H~Al~DA~at~~l~~ 299 (354)
|++.+||++||.+.|++++||+|||+||+
T Consensus 146 La~~~L~~~IQ~~~HdSvEDArAam~Ly~ 174 (174)
T cd06143 146 LAWYLLGEKIQSETHDSIEDARTALKLYR 174 (174)
T ss_pred HHHHHcCCcccCCCcCcHHHHHHHHHHhC
Confidence 99999999999889999999999999993
No 4
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=100.00 E-value=4.2e-35 Score=246.98 Aligned_cols=145 Identities=33% Similarity=0.493 Sum_probs=131.9
Q ss_pred EEeeccccccCCCCCccceeeEEEEecCCceEEeeeecCCccccCceeeecCCChhhhcCCC-CHHHHHHHHHHHHhcCC
Q 018558 135 VAIACKMVGGGSDGSLDLCGRVCIIDEYENIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAI-PLKQVQRKIQDFLCNGE 213 (354)
Q Consensus 135 vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap-~~~~v~~~~~~~i~~~~ 213 (354)
+++||||+|++.. ++|+++++|+.+|+++|++||+|..+|+++++++||||++||+++| +|++++++|++|+
T Consensus 1 ~~iD~E~~g~~~g---~ei~~i~~v~~~~~~~f~~lv~P~~~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~~~fl---- 73 (150)
T cd06145 1 FALDCEMCYTTDG---LELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLI---- 73 (150)
T ss_pred CEEeeeeeeecCC---CEEEEEEEEeCCCCEEEEEeECCCCccchhccCcCCCCHHHhccCCCCHHHHHHHHHHHh----
Confidence 5899999998642 7899999999999999999999999999999999999999999995 9999999999999
Q ss_pred CCccccCCCCC-CcEEEEechhhhhhhhcccCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCcCCC--CCCChHHH
Q 018558 214 PMWKIRPRGSR-ARILVGHGLDHDLDRLQVEYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQI--GIQDPYDD 290 (354)
Q Consensus 214 ~~~~~~~~~~~-~~ilVgHn~~~Dl~~L~~~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~~--~~H~Al~D 290 (354)
+ +.+|||||+.||+++|+..++. ++||+.+++...+...+++|+.||+.|++..++. ++|+|++|
T Consensus 74 ----------~~~~vlVgHn~~fD~~fL~~~~~~--~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~D 141 (150)
T cd06145 74 ----------SPDTILVGHSLENDLKALKLIHPR--VIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGGHDSVED 141 (150)
T ss_pred ----------CCCCEEEEcChHHHHHHhhccCCC--EEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCCCCCcHHH
Confidence 5 7899999999999999987655 7899999887665556789999999999988873 58999999
Q ss_pred HHHHHHHH
Q 018558 291 CVATMRLY 298 (354)
Q Consensus 291 A~at~~l~ 298 (354)
|++|++||
T Consensus 142 A~~t~~l~ 149 (150)
T cd06145 142 ARAALELV 149 (150)
T ss_pred HHHHHHHh
Confidence 99999998
No 5
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=100.00 E-value=1.5e-34 Score=244.30 Aligned_cols=151 Identities=49% Similarity=0.800 Sum_probs=136.0
Q ss_pred EEeeccccccCCCCCccceeeEEEEecCCceEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHHHhcCCC
Q 018558 135 VAIACKMVGGGSDGSLDLCGRVCIIDEYENIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDFLCNGEP 214 (354)
Q Consensus 135 vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~i~~~~~ 214 (354)
|++||||||+++..+..+|+++++++.+|.++|++||+|..+++++++++||||++||++||+|.+++++|.+|+
T Consensus 1 v~lD~EttGl~~~~~~~~i~~v~~v~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~~~v~~a~~~~~~~~~l~~~l----- 75 (152)
T cd06144 1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELL----- 75 (152)
T ss_pred CEEEEEeecccCCCCEEEEEEEEEEeCCCCEEEEEEECCCCCCCcccccCCCCCHHHHcCCCCHHHHHHHHHHHh-----
Confidence 589999999976555678889999999999999999999999999999999999999999999999999999999
Q ss_pred CccccCCCCCCcEEEEechhhhhhhhcccCCCceeeeccccCCCccCC-CCCchHHHHHHHHhCCcCCCCCCChHHHHHH
Q 018558 215 MWKIRPRGSRARILVGHGLDHDLDRLQVEYPAIMTRDTAKYPPLMKTS-KLSNSLKYLTQAYLGYDIQIGIQDPYDDCVA 293 (354)
Q Consensus 215 ~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~~~~~~~~Dt~~~~~~~~~~-~~~~~L~~l~~~~l~~~i~~~~H~Al~DA~a 293 (354)
++.++||||+.||+++|++..+...++||+.+..+.... ..+++|+.||+++||++++.++|+|++||++
T Consensus 76 ---------~~~vlVgHn~~fD~~~L~~~~~~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~a 146 (152)
T cd06144 76 ---------KGRILVGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARA 146 (152)
T ss_pred ---------CCCEEEEcCcHHHHHHhcCcCCCccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCCCcCcHHHHHH
Confidence 789999999999999999888777788999876655433 4679999999998998887668999999999
Q ss_pred HHHHHH
Q 018558 294 TMRLYM 299 (354)
Q Consensus 294 t~~l~~ 299 (354)
|++||+
T Consensus 147 t~~l~~ 152 (152)
T cd06144 147 AMRLYR 152 (152)
T ss_pred HHHHhC
Confidence 999984
No 6
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=100.00 E-value=2.7e-33 Score=238.90 Aligned_cols=147 Identities=28% Similarity=0.438 Sum_probs=130.2
Q ss_pred EEeeccccccCCCCCccceeeEEEEec-CCceEEeeeecCCccccCceeeecCCChhhhcCCCC-------HHHHHHHHH
Q 018558 135 VAIACKMVGGGSDGSLDLCGRVCIIDE-YENIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIP-------LKQVQRKIQ 206 (354)
Q Consensus 135 vaiD~Ettg~~~~~~~~~i~~i~vv~~-~g~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~-------~~~v~~~~~ 206 (354)
|++||||||+++. .++|++|++|+. +|+++|++||+|..+|+++++++||||++||+++|+ |++++++|+
T Consensus 1 v~lD~EttGl~~~--~d~ii~Ig~V~v~~g~i~~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~~~~~~~~ 78 (161)
T cd06137 1 VALDCEMVGLADG--DSEVVRISAVDVLTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAKAGKTIFGWEAARAALW 78 (161)
T ss_pred CEEEeeeeeEcCC--CCEEEEEEEEEcCCCeEEEeccccCCCCCCccceeccCCCHHHHhhhhhcCCccccHHHHHHHHH
Confidence 6899999999764 457899999998 788889999999999999999999999999999885 469999999
Q ss_pred HHHhcCCCCccccCCCCCC-cEEEEechhhhhhhhcccCCCceeeeccccCCCccCCC---CCchHHHHHHHHhCCcCCC
Q 018558 207 DFLCNGEPMWKIRPRGSRA-RILVGHGLDHDLDRLQVEYPAIMTRDTAKYPPLMKTSK---LSNSLKYLTQAYLGYDIQI 282 (354)
Q Consensus 207 ~~i~~~~~~~~~~~~~~~~-~ilVgHn~~~Dl~~L~~~~~~~~~~Dt~~~~~~~~~~~---~~~~L~~l~~~~l~~~i~~ 282 (354)
+|+ ++ .||||||+.||++||+..++. ++||+.+++...+.. .+++|+.||+.|+|.+++.
T Consensus 79 ~~i--------------~~~~vlVgHn~~fD~~fL~~~~~~--~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~ 142 (161)
T cd06137 79 KFI--------------DPDTILVGHSLQNDLDALRMIHTR--VVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQG 142 (161)
T ss_pred Hhc--------------CCCcEEEeccHHHHHHHHhCcCCC--eeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcC
Confidence 999 66 899999999999999987655 789999998766654 5799999999999998874
Q ss_pred --CCCChHHHHHHHHHHHH
Q 018558 283 --GIQDPYDDCVATMRLYM 299 (354)
Q Consensus 283 --~~H~Al~DA~at~~l~~ 299 (354)
++|+|++||+|||+||+
T Consensus 143 ~~~~H~A~~DA~at~~l~~ 161 (161)
T cd06137 143 GGEGHDSLEDALAAREVVL 161 (161)
T ss_pred CCCCCCcHHHHHHHHHHhC
Confidence 48999999999999983
No 7
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=1.5e-27 Score=208.61 Aligned_cols=157 Identities=17% Similarity=0.193 Sum_probs=123.3
Q ss_pred CCCceEEeeccccccCCCCCccceeeEEEEecC-Cce--EEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHH
Q 018558 130 RDPQVVAIACKMVGGGSDGSLDLCGRVCIIDEY-ENI--IFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQ 206 (354)
Q Consensus 130 ~~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~-g~~--i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~ 206 (354)
....+|++|+||||+.+ .++|++|++|..+ |.+ .|++||+|..++++++++|||||++||++||+|.+|+++|.
T Consensus 3 ~~~~~vvlD~EtTGl~~---~~eIIeIgaV~v~~g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap~~~evl~~f~ 79 (195)
T PRK07247 3 RLETYIAFDLEFNTVNG---VSHIIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFK 79 (195)
T ss_pred cCCeEEEEEeeCCCCCC---CCeEEEEEEEEEECCEEEEEEEEEECCCCCCCccceecCCCCHHHHhCCCCHHHHHHHHH
Confidence 34589999999999853 3457888888754 433 39999999999999999999999999999999999999999
Q ss_pred HHHhcCCCCccccCCCCCCcEEEEechh-hhhhhhccc---CCCceeeeccccC--CCc--cCCCCCchHHHHHHHHhCC
Q 018558 207 DFLCNGEPMWKIRPRGSRARILVGHGLD-HDLDRLQVE---YPAIMTRDTAKYP--PLM--KTSKLSNSLKYLTQAYLGY 278 (354)
Q Consensus 207 ~~i~~~~~~~~~~~~~~~~~ilVgHn~~-~Dl~~L~~~---~~~~~~~Dt~~~~--~~~--~~~~~~~~L~~l~~~~l~~ 278 (354)
+|+ ++.++||||+. ||+.+|... .+....+|+.... ... .+...+++|.+||++|
T Consensus 80 ~f~--------------~~~~lVaHNa~~fD~~fL~~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~--- 142 (195)
T PRK07247 80 EFV--------------GELPLIGYNAQKSDLPILAENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVADFL--- 142 (195)
T ss_pred HHH--------------CCCeEEEEeCcHhHHHHHHHcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHHHhc---
Confidence 999 88999999997 899998642 2222245664221 111 1233578999999965
Q ss_pred cCCCCCCChHHHHHHHHHHHHHHHHhhh
Q 018558 279 DIQIGIQDPYDDCVATMRLYMRMKSQAH 306 (354)
Q Consensus 279 ~i~~~~H~Al~DA~at~~l~~~~~~~~~ 306 (354)
+|...+|+|++||++|+.||.++.+...
T Consensus 143 gi~~~~HrAl~DA~~ta~v~~~ll~~~~ 170 (195)
T PRK07247 143 GIKGRGHNSLEDARMTARVYESFLESDQ 170 (195)
T ss_pred CCCCCCcCCHHHHHHHHHHHHHHHhhcc
Confidence 4444589999999999999999887663
No 8
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.95 E-value=2.2e-27 Score=223.97 Aligned_cols=158 Identities=32% Similarity=0.541 Sum_probs=140.8
Q ss_pred CCCCceEEeeccccccCCCCCccceeeEEEEecCCceEEeeeecCCccccCceeeecCCChhhhcCCC-CHHHHHHHHHH
Q 018558 129 TRDPQVVAIACKMVGGGSDGSLDLCGRVCIIDEYENIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAI-PLKQVQRKIQD 207 (354)
Q Consensus 129 ~~~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap-~~~~v~~~~~~ 207 (354)
..+.+++|+||||+.+. .+ .++++|.+||.+++++||+||+|..+|.+|+|+++|||++|+++++ +.++|+.+|++
T Consensus 213 ~~~~~i~AlDCEm~~te-~g--~el~RVt~VD~~~~vi~D~fVkP~~~VvDy~T~~SGIT~~~~e~~t~tl~dvq~~l~~ 289 (380)
T KOG2248|consen 213 SKSPNIFALDCEMVVTE-NG--LELTRVTAVDRDGKVILDTFVKPNKPVVDYNTRYSGITEEDLENSTITLEDVQKELLE 289 (380)
T ss_pred CCCCCeEEEEeeeeeec-cc--eeeEEeeeeeccCcEEeEEeecCCCcccccccccccccHHHHhcCccCHHHHHHHHHh
Confidence 45678999999999863 33 6789999999999999999999999999999999999999999765 89999999999
Q ss_pred HHhcCCCCccccCCCCCCcEEEEechhhhhhhhcccCCCceeeeccccCCCccCC-CCCchHHHHHHHHhCCcCC--CCC
Q 018558 208 FLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVEYPAIMTRDTAKYPPLMKTS-KLSNSLKYLTQAYLGYDIQ--IGI 284 (354)
Q Consensus 208 ~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~~~~~~~~Dt~~~~~~~~~~-~~~~~L~~l~~~~l~~~i~--~~~ 284 (354)
|++ .++|||||++++||++|++.|+. ++||+.++...... ..+.+|+.||+.|||+.|| .+.
T Consensus 290 ~~~-------------~~TILVGHSLenDL~aLKl~H~~--ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~~~~ 354 (380)
T KOG2248|consen 290 LIS-------------KNTILVGHSLENDLKALKLDHPS--VIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEGVGG 354 (380)
T ss_pred hcC-------------cCcEEEeechhhHHHHHhhhCCc--eeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhccCCC
Confidence 993 89999999999999999999998 78999888877663 6678899999999999999 348
Q ss_pred CChHHHHHHHHHHHHHHHHh
Q 018558 285 QDPYDDCVATMRLYMRMKSQ 304 (354)
Q Consensus 285 H~Al~DA~at~~l~~~~~~~ 304 (354)
|++.+||.|||+|+......
T Consensus 355 HdS~eDA~acm~Lv~~k~~~ 374 (380)
T KOG2248|consen 355 HDSVEDALACMKLVKLKIKN 374 (380)
T ss_pred CccHHHHHHHHHHHHHHHhc
Confidence 99999999999998654443
No 9
>PRK07740 hypothetical protein; Provisional
Probab=99.95 E-value=1e-26 Score=210.89 Aligned_cols=161 Identities=22% Similarity=0.240 Sum_probs=131.0
Q ss_pred CCCceEEeeccccccCCCCCccceeeEEEEecCCceE----EeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHH
Q 018558 130 RDPQVVAIACKMVGGGSDGSLDLCGRVCIIDEYENII----FHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKI 205 (354)
Q Consensus 130 ~~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~i----~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~ 205 (354)
...++|++|+||||.++... ++|+++++|..++..+ |.++|+|..+|+++++++||||+++|+++|+|.+++.+|
T Consensus 57 ~~~~~vv~D~ETTGl~p~~~-deIIeIgaV~~~~~~i~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~evl~~f 135 (244)
T PRK07740 57 TDLPFVVFDLETTGFSPQQG-DEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRF 135 (244)
T ss_pred cCCCEEEEEEeCCCCCCCCC-CeEEEEEEEEEECCEEEEEEEEEEeCcCCCCChhheeccCCCHHHHhCCCCHHHHHHHH
Confidence 45689999999999865432 4667787777655444 778999999999999999999999999999999999999
Q ss_pred HHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhccc------C-CCceeeeccccCCCccCCCCCchHHHHHHHHhCC
Q 018558 206 QDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVE------Y-PAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGY 278 (354)
Q Consensus 206 ~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~------~-~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~ 278 (354)
.+|+ ++.++||||+.||+.+|+.. . ....++||..+++...+....++|..++.+ +|.
T Consensus 136 ~~fi--------------~~~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~-~gi 200 (244)
T PRK07740 136 YAFI--------------GAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAY-YGI 200 (244)
T ss_pred HHHh--------------CCCEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHHHHH-CCc
Confidence 9999 88999999999999988521 1 123478999877655555567899999985 455
Q ss_pred cCCCCCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 279 DIQIGIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 279 ~i~~~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
.+. +.|+|++||++|++||.++..+..+
T Consensus 201 ~~~-~~H~Al~Da~ata~l~~~ll~~~~~ 228 (244)
T PRK07740 201 PIP-RRHHALGDALMTAKLWAILLVEAQQ 228 (244)
T ss_pred CCC-CCCCcHHHHHHHHHHHHHHHHHHHH
Confidence 444 4799999999999999999887754
No 10
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=1e-26 Score=209.83 Aligned_cols=158 Identities=18% Similarity=0.158 Sum_probs=128.1
Q ss_pred CCCceEEeeccccccCCCCCccceeeEEEEecCCce-----EEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHH
Q 018558 130 RDPQVVAIACKMVGGGSDGSLDLCGRVCIIDEYENI-----IFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRK 204 (354)
Q Consensus 130 ~~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~-----i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~ 204 (354)
....++++|+||||+.+ ..++|++|++|..++.. .|.++|+|+.+|++.+++|||||++||+++|+|.+|+++
T Consensus 45 ~~~~~vviD~ETTGl~p--~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~evl~~ 122 (239)
T PRK09146 45 SEVPFVALDFETTGLDA--EQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDE 122 (239)
T ss_pred ccCCEEEEEeECCCCCC--CCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHHHHH
Confidence 45689999999999865 34567788887765432 378899999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhccc-------CCCceeeeccccCCCccCC-------------CC
Q 018558 205 IQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVE-------YPAIMTRDTAKYPPLMKTS-------------KL 264 (354)
Q Consensus 205 ~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~-------~~~~~~~Dt~~~~~~~~~~-------------~~ 264 (354)
|.+++ ++.++||||+.||+.||+.. .....++||..+++...+. ..
T Consensus 123 l~~~~--------------~~~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~ 188 (239)
T PRK09146 123 LLEAL--------------AGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPE 188 (239)
T ss_pred HHHHh--------------CCCEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCC
Confidence 99999 88999999999999998532 1233478999865432111 14
Q ss_pred CchHHHHHHHHhCCcCC-CCCCChHHHHHHHHHHHHHHHHhhh
Q 018558 265 SNSLKYLTQAYLGYDIQ-IGIQDPYDDCVATMRLYMRMKSQAH 306 (354)
Q Consensus 265 ~~~L~~l~~~~l~~~i~-~~~H~Al~DA~at~~l~~~~~~~~~ 306 (354)
+++|..++.+| ++. .++|+|++||++|++||..+.++..
T Consensus 189 ~~~L~~l~~~~---gl~~~~~H~Al~DA~ata~l~~~~~~~~~ 228 (239)
T PRK09146 189 SIRLADSRLRY---GLPAYSPHHALTDAIATAELLQAQIAHHF 228 (239)
T ss_pred CCCHHHHHHHc---CCCCCCCCCcHHHHHHHHHHHHHHHHHHc
Confidence 67899999977 665 4589999999999999999887773
No 11
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=2.4e-26 Score=207.36 Aligned_cols=155 Identities=21% Similarity=0.339 Sum_probs=129.1
Q ss_pred CceEEeeccccccCCCCCccceeeEEEEecCCceEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHHHhc
Q 018558 132 PQVVAIACKMVGGGSDGSLDLCGRVCIIDEYENIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDFLCN 211 (354)
Q Consensus 132 ~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~i~~ 211 (354)
.+++++|+||||+. ...++|+++++++......|+.+|+|+.+|++..++|||||++||+++|+|.+++++|.+|+
T Consensus 2 ~~~vv~D~ETTGl~--~~~d~IIeig~v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~~fi-- 77 (232)
T PRK06309 2 PALIFYDTETTGTQ--IDKDRIIEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFC-- 77 (232)
T ss_pred CcEEEEEeeCCCCC--CCCCEEEEEEEEcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHH--
Confidence 35899999999984 34467889988876666779999999999999999999999999999999999999999999
Q ss_pred CCCCccccCCCCC-CcEEEEec-hhhhhhhhcc-------cCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCcCC-
Q 018558 212 GEPMWKIRPRGSR-ARILVGHG-LDHDLDRLQV-------EYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQ- 281 (354)
Q Consensus 212 ~~~~~~~~~~~~~-~~ilVgHn-~~~Dl~~L~~-------~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~- 281 (354)
+ +.++|||| ..||+.+|+. ..+...++||..+++...+...+++|..|+..| ++.
T Consensus 78 ------------~~~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~~~~L~~l~~~~---~~~~ 142 (232)
T PRK06309 78 ------------GTDNILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLRQVY---GFEE 142 (232)
T ss_pred ------------cCCCEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCCCCCHHHHHHHc---CCCC
Confidence 4 57999999 5899998852 223345789998876555544568999999876 454
Q ss_pred CCCCChHHHHHHHHHHHHHHHHhh
Q 018558 282 IGIQDPYDDCVATMRLYMRMKSQA 305 (354)
Q Consensus 282 ~~~H~Al~DA~at~~l~~~~~~~~ 305 (354)
.++|+|++||.+|++||.++.++.
T Consensus 143 ~~aH~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 143 NQAHRALDDVITLHRVFSALVGDL 166 (232)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHHH
Confidence 449999999999999999987654
No 12
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.94 E-value=1.5e-26 Score=208.46 Aligned_cols=164 Identities=16% Similarity=0.142 Sum_probs=124.4
Q ss_pred CCceEEeeccccccCCCCCccceeeEEEEecC--CceE--EeeeecCCccccCceeeecCCChhhhcC-CCCHHHHHHHH
Q 018558 131 DPQVVAIACKMVGGGSDGSLDLCGRVCIIDEY--ENII--FHAYVKPPIPVTSYRYETTGIRPEHLRD-AIPLKQVQRKI 205 (354)
Q Consensus 131 ~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~--g~~i--~~~~v~P~~~i~~~~~~itGIt~~~l~~-ap~~~~v~~~~ 205 (354)
..++++||+||||+.+. .++|+++++|..+ |.++ +.+||+|+.+|++.+++|||||++|+.+ ++++++++.+|
T Consensus 5 ~~~~vv~D~ETTGl~p~--~d~Iieig~v~v~~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~e~ 82 (232)
T PRK07942 5 PGPLAAFDLETTGVDPE--TARIVTAALVVVDADGEVVESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLAEI 82 (232)
T ss_pred cCcEEEEEeccCCCCCC--CCeeEEEEEEEEeCCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHHHH
Confidence 35789999999998654 3456777766543 6654 8889999999999999999999999976 78888999998
Q ss_pred HHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcccC--------CCceeeeccccCCCccC-CCCCchHHHHHHHHh
Q 018558 206 QDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVEY--------PAIMTRDTAKYPPLMKT-SKLSNSLKYLTQAYL 276 (354)
Q Consensus 206 ~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~~--------~~~~~~Dt~~~~~~~~~-~~~~~~L~~l~~~~l 276 (354)
.++|.+ ...++.+|||||+.||+.+|+... ....++||..+...... ...+++|..|+++|
T Consensus 83 ~~~l~~---------~~~~~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~- 152 (232)
T PRK07942 83 ADALRE---------AWARGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALCEHY- 152 (232)
T ss_pred HHHHHH---------HhhcCCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHHHHc-
Confidence 887710 001467999999999999985311 12336898876543322 23467999999875
Q ss_pred CCcCCCCCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 277 GYDIQIGIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 277 ~~~i~~~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
|+.. .++|+|++||+||++||.++.+++.+
T Consensus 153 gi~~-~~aH~Al~Da~ata~l~~~l~~~~~~ 182 (232)
T PRK07942 153 GVRL-DNAHEATADALAAARVAWALARRFPE 182 (232)
T ss_pred CCCC-CCCCChHHHHHHHHHHHHHHHHHHHH
Confidence 4433 34899999999999999999887754
No 13
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.94 E-value=1.3e-26 Score=208.76 Aligned_cols=157 Identities=21% Similarity=0.269 Sum_probs=124.4
Q ss_pred CceEEeeccccccCCCCCccceeeEEEEecCC-c---eEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHH
Q 018558 132 PQVVAIACKMVGGGSDGSLDLCGRVCIIDEYE-N---IIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQD 207 (354)
Q Consensus 132 ~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g-~---~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~ 207 (354)
.++|++|+||||+.+.. .+.|++|++|...+ . ..|..||+|..+|++.+++|||||++||+++|+|++|+++|.+
T Consensus 4 ~r~vvlDtETTGldp~~-~drIIEIGaV~v~~~~~~~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~p~f~ev~~~f~~ 82 (240)
T PRK05711 4 MRQIVLDTETTGLNQRE-GHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLD 82 (240)
T ss_pred CeEEEEEeeCCCcCCCC-CCeEEEEEEEEEECCEEeccEEEEEECcCCcCCHHHhhhcCCCHHHHcCCCCHHHHHHHHHH
Confidence 47899999999987642 23556666665432 2 2488999999999999999999999999999999999999999
Q ss_pred HHhcCCCCccccCCCCCCcEEEEechhhhhhhhcc-------cCC----CceeeeccccCCCccCCCCCchHHHHHHHHh
Q 018558 208 FLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQV-------EYP----AIMTRDTAKYPPLMKTSKLSNSLKYLTQAYL 276 (354)
Q Consensus 208 ~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~-------~~~----~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l 276 (354)
|+ ++.+|||||+.||+.||+. ..+ ...++||..+.+...+. .+++|..||++|
T Consensus 83 fi--------------~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~-~~~~L~aL~~~~- 146 (240)
T PRK05711 83 FI--------------RGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPG-KRNSLDALCKRY- 146 (240)
T ss_pred Hh--------------CCCEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCC-CCCCHHHHHHHC-
Confidence 99 8899999999999998852 122 13378998877655443 457999999976
Q ss_pred CCcCCC-CCCChHHHHHHHHHHHHHHHHhh
Q 018558 277 GYDIQI-GIQDPYDDCVATMRLYMRMKSQA 305 (354)
Q Consensus 277 ~~~i~~-~~H~Al~DA~at~~l~~~~~~~~ 305 (354)
|++... ..|+|+.||+++++||..|....
T Consensus 147 gi~~~~r~~H~AL~DA~~~A~v~~~l~~~~ 176 (240)
T PRK05711 147 GIDNSHRTLHGALLDAEILAEVYLAMTGGQ 176 (240)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHCcc
Confidence 443322 36999999999999999987653
No 14
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=4.5e-26 Score=212.98 Aligned_cols=158 Identities=22% Similarity=0.318 Sum_probs=130.2
Q ss_pred CCCceEEeeccccccCCCCCccceeeEEEEecC-CceE--EeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHH
Q 018558 130 RDPQVVAIACKMVGGGSDGSLDLCGRVCIIDEY-ENII--FHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQ 206 (354)
Q Consensus 130 ~~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~-g~~i--~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~ 206 (354)
-+..+|++|+||||+.+. .++|+++++|..+ |+++ |+++|+|..++++.++++||||++||+++|+|.+|+++|.
T Consensus 6 ~~~~~Vv~DlETTGl~p~--~~eIIEIgaV~v~~g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~evl~~f~ 83 (313)
T PRK06807 6 LPLDYVVIDFETTGFNPY--NDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFL 83 (313)
T ss_pred CCCCEEEEEEECCCCCCC--CCeEEEEEEEEEECCEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHHHHHHH
Confidence 356899999999998653 4567788877654 4433 7889999999999999999999999999999999999999
Q ss_pred HHHhcCCCCccccCCCCCCcEEEEechhhhhhhhc-------ccCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCc
Q 018558 207 DFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQ-------VEYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYD 279 (354)
Q Consensus 207 ~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~-------~~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~ 279 (354)
+|+ ++.++||||+.||+.+|. +..+...++||..++....+....++|..|+++ +|+.
T Consensus 84 ~fl--------------~~~~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~~~kL~~L~~~-lgi~ 148 (313)
T PRK06807 84 AFL--------------HTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRM-LGIR 148 (313)
T ss_pred HHH--------------cCCeEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCCCCCHHHHHHH-cCCC
Confidence 999 888999999999999885 233445588998876655444456899999875 5655
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHHhhh
Q 018558 280 IQIGIQDPYDDCVATMRLYMRMKSQAH 306 (354)
Q Consensus 280 i~~~~H~Al~DA~at~~l~~~~~~~~~ 306 (354)
. .+|+|++||++|++||.++.....
T Consensus 149 ~--~~H~Al~DA~~ta~l~~~l~~~~~ 173 (313)
T PRK06807 149 L--SSHNAFDDCITCAAVYQKCASIEE 173 (313)
T ss_pred C--CCcChHHHHHHHHHHHHHHHHhhh
Confidence 5 599999999999999998887773
No 15
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.94 E-value=8.9e-26 Score=211.51 Aligned_cols=157 Identities=15% Similarity=0.166 Sum_probs=126.9
Q ss_pred CCCceEEeeccccccCCCCCccceeeEEEEec--CCceE--EeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHH
Q 018558 130 RDPQVVAIACKMVGGGSDGSLDLCGRVCIIDE--YENII--FHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKI 205 (354)
Q Consensus 130 ~~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~--~g~~i--~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~ 205 (354)
.+.+||++|+||||+.+. .+.|++|++|.. +|+++ |.+||+|.. ++..+.|||||++||+++|+|.+++++|
T Consensus 13 ~~~~fvvlD~ETTGl~p~--~d~IIeIgav~v~~~g~i~~~~~~lv~P~~--~~~~~~IhGIt~e~l~~ap~f~ev~~~l 88 (313)
T PRK06063 13 YPRGWAVVDVETSGFRPG--QARIISLAVLGLDADGNVEQSVVTLLNPGV--DPGPTHVHGLTAEMLEGQPQFADIAGEV 88 (313)
T ss_pred CCCCEEEEEEECCCCCCC--CCEEEEEEEEEEECCceeeeEEEEEECcCC--CCCCeecCCCCHHHHhCCCCHHHHHHHH
Confidence 456899999999998653 356778877753 46554 889999985 3567899999999999999999999999
Q ss_pred HHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcc-------cCCCceeeeccccCCCccCCCCCchHHHHHHHHhCC
Q 018558 206 QDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQV-------EYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGY 278 (354)
Q Consensus 206 ~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~-------~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~ 278 (354)
.+|+ ++.+|||||+.||+.||+. ..+...++||..+++...+...+++|..|+++|
T Consensus 89 ~~~l--------------~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~~kL~~l~~~~--- 151 (313)
T PRK06063 89 AELL--------------RGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLAAHW--- 151 (313)
T ss_pred HHHc--------------CCCEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCCCCHHHHHHHc---
Confidence 9999 8899999999999999863 233334789998876554455678999999965
Q ss_pred cCC-CCCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 279 DIQ-IGIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 279 ~i~-~~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
+|. .++|+|++||++|++||..+.++..+
T Consensus 152 gi~~~~~H~Al~DA~ata~l~~~ll~~~~~ 181 (313)
T PRK06063 152 GVPQQRPHDALDDARVLAGILRPSLERARE 181 (313)
T ss_pred CCCCCCCCCcHHHHHHHHHHHHHHHHHHHh
Confidence 554 45999999999999999888776643
No 16
>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=99.94 E-value=4.1e-26 Score=204.50 Aligned_cols=158 Identities=19% Similarity=0.221 Sum_probs=124.8
Q ss_pred ceEEeeccccccCCCCCccceeeEEEEec-CCc---eEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHH
Q 018558 133 QVVAIACKMVGGGSDGSLDLCGRVCIIDE-YEN---IIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDF 208 (354)
Q Consensus 133 ~~vaiD~Ettg~~~~~~~~~i~~i~vv~~-~g~---~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~ 208 (354)
++|++|+||||+.+... +.|++|++|.. ++. ..|..||+|..+|++.+++|||||++||+++|+|++|+++|.+|
T Consensus 1 r~vvlD~ETTGl~p~~~-d~IIEIgav~~~~~~~~~~~f~~~i~P~~~i~~~a~~vhGIt~e~l~~~p~f~ev~~~f~~f 79 (225)
T TIGR01406 1 RQIILDTETTGLDPKGG-HRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDF 79 (225)
T ss_pred CEEEEEeeCCCcCCCCC-CeEEEEEEEEEECCcEecceEEEEECcCCCCCHHHHhccCCCHHHHhCCCCHHHHHHHHHHH
Confidence 47999999999876432 34566665532 222 24899999999999999999999999999999999999999999
Q ss_pred HhcCCCCccccCCCCCCcEEEEechhhhhhhhccc-------CC----CceeeeccccCCCccCCCCCchHHHHHHHHhC
Q 018558 209 LCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVE-------YP----AIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLG 277 (354)
Q Consensus 209 i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~-------~~----~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~ 277 (354)
+ ++.+|||||+.||+.||+.. .+ ...++||..+++...+. .+++|..||++| |
T Consensus 80 i--------------~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~-~~~~L~~L~~~~-g 143 (225)
T TIGR01406 80 I--------------GGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPG-QRNSLDALCKRF-K 143 (225)
T ss_pred h--------------CCCEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCC-CCCCHHHHHHhc-C
Confidence 9 88999999999999988521 11 13588998876654433 468999999976 4
Q ss_pred CcCCC-CCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 278 YDIQI-GIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 278 ~~i~~-~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
++... ..|+|+.||+++++||..|......
T Consensus 144 i~~~~r~~H~Al~DA~~~a~v~~~l~~~~~~ 174 (225)
T TIGR01406 144 VDNSHRTLHGALLDAHLLAEVYLALTGGQES 174 (225)
T ss_pred CCCCCCCCcCHHHHHHHHHHHHHHHHcCCcc
Confidence 33322 2699999999999999999876654
No 17
>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=99.93 E-value=6.4e-26 Score=192.31 Aligned_cols=145 Identities=20% Similarity=0.330 Sum_probs=119.7
Q ss_pred eEEeeccccccCCCCCccceeeEEEEecCCceE---EeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHHHh
Q 018558 134 VVAIACKMVGGGSDGSLDLCGRVCIIDEYENII---FHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDFLC 210 (354)
Q Consensus 134 ~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~i---~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~i~ 210 (354)
+|++|+||||.. ..+|++|++|..++..+ |+.||+|..++++.++++||||+++|+++|+|.+++.+|.+|+
T Consensus 1 ~v~~D~Ettg~~----~~~ii~ig~v~~~~~~~~~~~~~~i~p~~~~~~~~~~i~GIt~e~l~~~~~~~~v~~~l~~~l- 75 (156)
T cd06130 1 FVAIDFETANAD----RASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFL- 75 (156)
T ss_pred CEEEEEeCCCCC----CCceEEEEEEEEECCEEEEEEEEEeCcCCCCChhhccccCcCHHHHhcCCCHHHHHHHHHHHh-
Confidence 589999999753 23456777776544433 7789999999999999999999999999999999999999999
Q ss_pred cCCCCccccCCCCCCcEEEEechhhhhhhhc-------ccCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCcCCCC
Q 018558 211 NGEPMWKIRPRGSRARILVGHGLDHDLDRLQ-------VEYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQIG 283 (354)
Q Consensus 211 ~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~-------~~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~~~ 283 (354)
++.++||||+.||+.+|+ +..+...++||..+++...+...+++|..|+++ +|...+
T Consensus 76 -------------~~~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~~~~L~~l~~~-~g~~~~-- 139 (156)
T cd06130 76 -------------GGSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEH-LGIELN-- 139 (156)
T ss_pred -------------CCCEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCCCCCHHHHHHH-cCCCcc--
Confidence 779999999999999984 344555689998776655544567899999986 566555
Q ss_pred CCChHHHHHHHHHHHH
Q 018558 284 IQDPYDDCVATMRLYM 299 (354)
Q Consensus 284 ~H~Al~DA~at~~l~~ 299 (354)
+|+|++||++|++||.
T Consensus 140 ~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 140 HHDALEDARACAEILL 155 (156)
T ss_pred CcCchHHHHHHHHHHh
Confidence 9999999999999985
No 18
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=1.1e-25 Score=199.12 Aligned_cols=156 Identities=15% Similarity=0.251 Sum_probs=122.7
Q ss_pred CCceEEeeccccccCCCCCccceeeEEEEecCCce-----EEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHH
Q 018558 131 DPQVVAIACKMVGGGSDGSLDLCGRVCIIDEYENI-----IFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKI 205 (354)
Q Consensus 131 ~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~-----i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~ 205 (354)
...+|++|+||||+.+. .++|++|++|..++.. .|+.+|+|..+++++++++||||++||+++|++.+|+++|
T Consensus 28 ~~~~vviD~ETTGl~~~--~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~~~ 105 (202)
T PRK09145 28 PDEWVALDCETTGLDPR--RAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQL 105 (202)
T ss_pred CCCEEEEEeECCCCCCC--CCceEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHHHH
Confidence 35899999999998653 3567888887765442 2788999999999999999999999999999999999999
Q ss_pred HHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhccc------C-CCceeeeccccCCC-----ccCCCCCchHHHHHH
Q 018558 206 QDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVE------Y-PAIMTRDTAKYPPL-----MKTSKLSNSLKYLTQ 273 (354)
Q Consensus 206 ~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~------~-~~~~~~Dt~~~~~~-----~~~~~~~~~L~~l~~ 273 (354)
.+|+ ++.++||||+.||+.+|... . ....++|+..++.. ......+++|..+++
T Consensus 106 ~~~i--------------~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~ 171 (202)
T PRK09145 106 LAFI--------------GNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILK 171 (202)
T ss_pred HHHH--------------cCCeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHHH
Confidence 9999 88999999999999988521 1 12236788755321 111223689999998
Q ss_pred HHhCCcCCCCCCChHHHHHHHHHHHHHHHHh
Q 018558 274 AYLGYDIQIGIQDPYDDCVATMRLYMRMKSQ 304 (354)
Q Consensus 274 ~~l~~~i~~~~H~Al~DA~at~~l~~~~~~~ 304 (354)
+| |... .++|+|++||++|++||.++++.
T Consensus 172 ~~-gi~~-~~~H~Al~DA~ata~l~~~l~~~ 200 (202)
T PRK09145 172 HL-DLPV-LGRHDALNDAIMAALIFLRLRKG 200 (202)
T ss_pred Hc-CCCC-CCCCCcHHHHHHHHHHHHHHHhc
Confidence 65 4443 45899999999999999988653
No 19
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=9e-26 Score=205.41 Aligned_cols=155 Identities=19% Similarity=0.246 Sum_probs=124.9
Q ss_pred CceEEeeccccccCCCCCccceeeEEEEecCCce---EEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHH
Q 018558 132 PQVVAIACKMVGGGSDGSLDLCGRVCIIDEYENI---IFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDF 208 (354)
Q Consensus 132 ~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~---i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~ 208 (354)
.++|++|+||||+.+ ..+.|++|++|...+.. .|+.+|+|..+|++..+.+||||++||+++|+|.+|+++|.+|
T Consensus 7 ~~~v~~D~ETTGl~~--~~d~IIEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~~~f 84 (250)
T PRK06310 7 TEFVCLDCETTGLDV--KKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGF 84 (250)
T ss_pred CcEEEEEEeCCCCCC--CCCeEEEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHHHHH
Confidence 579999999999854 44567788777654433 3888999999999999999999999999999999999999999
Q ss_pred HhcCCCCccccCCCCCC-cEEEEechhhhhhhhccc-------C--CCceeeeccccCCCccCCCCCchHHHHHHHHhCC
Q 018558 209 LCNGEPMWKIRPRGSRA-RILVGHGLDHDLDRLQVE-------Y--PAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGY 278 (354)
Q Consensus 209 i~~~~~~~~~~~~~~~~-~ilVgHn~~~Dl~~L~~~-------~--~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~ 278 (354)
+ ++ .+|||||+.||+.+|... . ....++||..+++.. +...+++|..|+.+| |.
T Consensus 85 l--------------~~~~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~-~~~~~~~L~~l~~~~-g~ 148 (250)
T PRK06310 85 F--------------KEGDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEY-GDSPNNSLEALAVHF-NV 148 (250)
T ss_pred h--------------CCCCEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhc-ccCCCCCHHHHHHHC-CC
Confidence 9 54 899999999999988531 1 124479998877643 223468999999865 44
Q ss_pred cCCCCCCChHHHHHHHHHHHHHHHHhh
Q 018558 279 DIQIGIQDPYDDCVATMRLYMRMKSQA 305 (354)
Q Consensus 279 ~i~~~~H~Al~DA~at~~l~~~~~~~~ 305 (354)
.. .++|+|++||.+|++||..+.+.+
T Consensus 149 ~~-~~aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 149 PY-DGNHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred CC-CCCcChHHHHHHHHHHHHHHHHhc
Confidence 43 349999999999999999887654
No 20
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=1e-25 Score=211.39 Aligned_cols=152 Identities=17% Similarity=0.279 Sum_probs=123.5
Q ss_pred ceEEeeccccccCCCCCccceeeEEEEec-CCceE--EeeeecCCc-cccCceeeecCCChhhhcCCCCHHHHHHHHHHH
Q 018558 133 QVVAIACKMVGGGSDGSLDLCGRVCIIDE-YENII--FHAYVKPPI-PVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDF 208 (354)
Q Consensus 133 ~~vaiD~Ettg~~~~~~~~~i~~i~vv~~-~g~~i--~~~~v~P~~-~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~ 208 (354)
+||+||+||||. . .+.|++|++|.. +|+++ |++||+|.. .+++.+++|||||++||+++|+|.+|+++|.+|
T Consensus 2 ~~vviD~ETTg~--~--~d~IieIgav~v~~g~i~~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~~ap~f~ev~~~~~~f 77 (309)
T PRK06195 2 NFVAIDFETANE--K--RNSPCSIGIVVVKDGEIVEKVHYLIKPKEMRFMPINIGIHGIRPHMVEDELEFDKIWEKIKHY 77 (309)
T ss_pred cEEEEEEeCCCC--C--CCceEEEEEEEEECCEEEEEEEEEECCCCCCCChhheeccCcCHHHHhCCCCHHHHHHHHHHH
Confidence 589999999964 2 235667776664 44444 889999985 578889999999999999999999999999999
Q ss_pred HhcCCCCccccCCCCCCcEEEEechhhhhhhhcc-------cCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCcCC
Q 018558 209 LCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQV-------EYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQ 281 (354)
Q Consensus 209 i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~-------~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~ 281 (354)
+ ++.+|||||+.||+.+|+. ..+...++||..+++...+...+++|..|+.+| | +.
T Consensus 78 l--------------~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~~L~~L~~~~-g--i~ 140 (309)
T PRK06195 78 F--------------NNNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFL-G--YE 140 (309)
T ss_pred h--------------CCCEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcCCHHHHHHHc-C--CC
Confidence 9 8899999999999999852 334455889988776554444678999999975 4 44
Q ss_pred CCCCChHHHHHHHHHHHHHHHHhh
Q 018558 282 IGIQDPYDDCVATMRLYMRMKSQA 305 (354)
Q Consensus 282 ~~~H~Al~DA~at~~l~~~~~~~~ 305 (354)
..+|+|++||++|++||.++.++.
T Consensus 141 ~~~H~Al~DA~ata~l~~~l~~~~ 164 (309)
T PRK06195 141 FKHHDALADAMACSNILLNISKEL 164 (309)
T ss_pred CcccCCHHHHHHHHHHHHHHHHHh
Confidence 359999999999999999888765
No 21
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.93 E-value=1.3e-25 Score=200.76 Aligned_cols=159 Identities=20% Similarity=0.260 Sum_probs=124.4
Q ss_pred CCceEEeeccccccCCCCCccceeeEEEEe-cCCc---eEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHH
Q 018558 131 DPQVVAIACKMVGGGSDGSLDLCGRVCIID-EYEN---IIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQ 206 (354)
Q Consensus 131 ~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~-~~g~---~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~ 206 (354)
...||++|+||||+.+.. + |++|++|. .++. ..|.+||+|..++++..+.+||||++||+++|+|.+|+++|.
T Consensus 6 ~~~fvv~D~ETTGl~~~~--~-IIeIgav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~~~ 82 (217)
T TIGR00573 6 LDTETTGDNETTGLYAGH--D-IIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFA 82 (217)
T ss_pred ecCEEEEEecCCCCCCCC--C-EEEEEEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHHHH
Confidence 357999999999986543 3 56666665 3332 248899999999999999999999999999999999999999
Q ss_pred HHHhcCCCCccccCCCCCCcEEEEechhhhhhhhccc--------CCCceeeeccccCCCccC--CCCCchHHHHHHHHh
Q 018558 207 DFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVE--------YPAIMTRDTAKYPPLMKT--SKLSNSLKYLTQAYL 276 (354)
Q Consensus 207 ~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~--------~~~~~~~Dt~~~~~~~~~--~~~~~~L~~l~~~~l 276 (354)
+|+ ++.++||||+.||+.+|+.. .+...++||..+.+...+ ...+++|..|+.++
T Consensus 83 ~~~--------------~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~- 147 (217)
T TIGR00573 83 DYI--------------RGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRY- 147 (217)
T ss_pred HHh--------------CCCEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHHHc-
Confidence 999 88999999999999998632 122336787655443222 22467999999876
Q ss_pred CCcCCC-CCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 277 GYDIQI-GIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 277 ~~~i~~-~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
|..... ++|+|++||++|++||.++.+++.+
T Consensus 148 gl~~~~~~~H~Al~DA~~ta~l~~~l~~~~~~ 179 (217)
T TIGR00573 148 EITNSHRALHGALADAFILAKLYLVMTGKQTK 179 (217)
T ss_pred CCCCCCcccCCHHHHHHHHHHHHHHHHhcchh
Confidence 443321 5899999999999999999888754
No 22
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.93 E-value=2.9e-25 Score=197.69 Aligned_cols=145 Identities=17% Similarity=0.152 Sum_probs=116.3
Q ss_pred eEEeeccccccCCCCCccceeeEEEEec-CCceE--EeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHHHh
Q 018558 134 VVAIACKMVGGGSDGSLDLCGRVCIIDE-YENII--FHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDFLC 210 (354)
Q Consensus 134 ~vaiD~Ettg~~~~~~~~~i~~i~vv~~-~g~~i--~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~i~ 210 (354)
++++|+||||+. +. |++|++|.. +|+++ |.+||+|+.+|+..+++|||||++||+++|+|.+++++ |+
T Consensus 2 ~~vlD~ETTGl~--~~---IieIg~v~v~~~~i~~~~~~lv~P~~~i~~~~~~ihgIt~e~v~~ap~~~ev~~~---~~- 72 (219)
T PRK07983 2 LRVIDTETCGLQ--GG---IVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPH---YY- 72 (219)
T ss_pred eEEEEEECCCCC--CC---CEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHcCCCCHHHHHHH---Hc-
Confidence 689999999974 33 455555543 34443 89999999999999999999999999999999999886 56
Q ss_pred cCCCCccccCCCCCCcEEEEechhhhhhhhcccCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCcCC----CCCCC
Q 018558 211 NGEPMWKIRPRGSRARILVGHGLDHDLDRLQVEYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQ----IGIQD 286 (354)
Q Consensus 211 ~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~----~~~H~ 286 (354)
++.+|||||+.||+++|.... ..++||..+++...+.. +++|..|+..+ +.... ..+||
T Consensus 73 -------------~~~~lVaHNa~FD~~~L~~~~--~~~idTl~lar~l~p~~-~~~l~~L~~~~-~l~~~~~~~~~aHr 135 (219)
T PRK07983 73 -------------GSEWYVAHNASFDRRVLPEMP--GEWICTMKLARRLWPGI-KYSNMALYKSR-KLNVQTPPGLHHHR 135 (219)
T ss_pred -------------CCCEEEEeCcHhhHHHHhCcC--CCcEeHHHHHHHHccCC-CCCHHHHHHHc-CCCCCCCCCCCCCc
Confidence 788999999999999997533 33789998877555543 48999999854 54431 24999
Q ss_pred hHHHHHHHHHHHHHHHHh
Q 018558 287 PYDDCVATMRLYMRMKSQ 304 (354)
Q Consensus 287 Al~DA~at~~l~~~~~~~ 304 (354)
|++||.+|+.||.++.+.
T Consensus 136 Al~Da~ata~ll~~l~~~ 153 (219)
T PRK07983 136 ALYDCYITAALLIDIMNT 153 (219)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 999999999999998853
No 23
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=1.7e-25 Score=233.70 Aligned_cols=158 Identities=22% Similarity=0.294 Sum_probs=130.3
Q ss_pred CCceEEeeccccccCCCCCccceeeEEEEecCCc-eE--EeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHH
Q 018558 131 DPQVVAIACKMVGGGSDGSLDLCGRVCIIDEYEN-II--FHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQD 207 (354)
Q Consensus 131 ~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~-~i--~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~ 207 (354)
..++|++|+||||.++. ++|++|++|...+. ++ |.+||+|..+|+++++++||||++||++||+|++|+++|.+
T Consensus 6 ~~~~vvvD~ETTGl~~~---d~IIeIgaV~v~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~~~ 82 (820)
T PRK07246 6 LRKYAVVDLEATGAGPN---ASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYD 82 (820)
T ss_pred CCCEEEEEEecCCcCCC---CeEEEEEEEEEECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHHHH
Confidence 45799999999998642 46778887775444 33 88889999999999999999999999999999999999999
Q ss_pred HHhcCCCCccccCCCCCCcEEEEechhhhhhhhccc-----C-CCceeeeccccCCCccCCCCCchHHHHHHHHhCCcCC
Q 018558 208 FLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVE-----Y-PAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQ 281 (354)
Q Consensus 208 ~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~-----~-~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~ 281 (354)
|+ ++.++||||+.||+.+|+.. . .....+||..+++...+...+++|..||.++ |....
T Consensus 83 ~l--------------~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L~~~l-gl~~~ 147 (820)
T PRK07246 83 LI--------------EDCIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLSREL-NIDLA 147 (820)
T ss_pred Hh--------------CCCEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHHHHHc-CCCCC
Confidence 99 89999999999999998531 1 1223689998776655555689999999865 54433
Q ss_pred CCCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 282 IGIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 282 ~~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
++|+|++||++|++||.++.++...
T Consensus 148 -~~H~Al~DA~ata~L~~~l~~~l~~ 172 (820)
T PRK07246 148 -DAHTAIADARATAELFLKLLQKIES 172 (820)
T ss_pred -CCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 4899999999999999999888754
No 24
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.93 E-value=5.9e-25 Score=200.12 Aligned_cols=158 Identities=21% Similarity=0.263 Sum_probs=124.5
Q ss_pred CCCceEEeeccccccCCCCCccceeeEEEEec-CCceE--EeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHH
Q 018558 130 RDPQVVAIACKMVGGGSDGSLDLCGRVCIIDE-YENII--FHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQ 206 (354)
Q Consensus 130 ~~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~-~g~~i--~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~ 206 (354)
....++++|+||||..+. ..+|++|++|.. +|+++ |..||+|. +++++++++||||++||++||+|.+|+.+|.
T Consensus 66 ~~~~~vv~DiETTG~~~~--~~~IIEIGAv~v~~g~i~~~f~~~v~p~-~ip~~~~~itGIt~e~l~~ap~~~evl~~f~ 142 (257)
T PRK08517 66 KDQVFCFVDIETNGSKPK--KHQIIEIGAVKVKNGEIIDRFESFVKAK-EVPEYITELTGITYEDLENAPSLKEVLEEFR 142 (257)
T ss_pred CCCCEEEEEEeCCCCCCC--CCeEEEEEEEEEECCEEEEEEEEEECCC-CCChhhhhhcCcCHHHHcCCCCHHHHHHHHH
Confidence 355799999999998654 335677776665 44444 78899996 8999999999999999999999999999999
Q ss_pred HHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcc-------cCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCc
Q 018558 207 DFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQV-------EYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYD 279 (354)
Q Consensus 207 ~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~-------~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~ 279 (354)
+|+ ++.++||||+.||+.+|+. .......+||..+++... ...+++|..|++. +|..
T Consensus 143 ~fl--------------~~~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~-~~~~~~L~~L~~~-lgi~ 206 (257)
T PRK08517 143 LFL--------------GDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTI-ESPRYGLSFLKEL-LGIE 206 (257)
T ss_pred HHH--------------CCCeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHc-cCCCCCHHHHHHH-cCcC
Confidence 999 8899999999999999852 111223578876654322 2356899999985 4554
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 280 IQIGIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 280 i~~~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
.. .+|+|++||++|++||.++.+++..
T Consensus 207 ~~-~~HrAl~DA~ata~ll~~ll~~~~~ 233 (257)
T PRK08517 207 IE-VHHRAYADALAAYEIFKICLLNLPS 233 (257)
T ss_pred CC-CCCChHHHHHHHHHHHHHHHHHhHH
Confidence 43 5999999999999999999887743
No 25
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.92 E-value=4.1e-25 Score=196.13 Aligned_cols=159 Identities=15% Similarity=0.167 Sum_probs=120.0
Q ss_pred CceEEeeccccccCCCC----CccceeeEEEEecC-CceE--EeeeecCCc--cccCceeeecCCChhhhcCCCCHHHHH
Q 018558 132 PQVVAIACKMVGGGSDG----SLDLCGRVCIIDEY-ENII--FHAYVKPPI--PVTSYRYETTGIRPEHLRDAIPLKQVQ 202 (354)
Q Consensus 132 ~~~vaiD~Ettg~~~~~----~~~~i~~i~vv~~~-g~~i--~~~~v~P~~--~i~~~~~~itGIt~~~l~~ap~~~~v~ 202 (354)
..+|++|+||||..... ...+|++|++|..+ |+++ |.+||+|.. +++++++++||||++||++||+|++|+
T Consensus 4 ~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~~~evl 83 (207)
T PRK07748 4 QQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFEELV 83 (207)
T ss_pred ceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecCcChhhhcceECCCccCccChhhhhhcCcCHHHHccCCCHHHHH
Confidence 46999999999864321 13567888877653 4333 999999997 689999999999999999999999999
Q ss_pred HHHHHHHhcCCCCccccCCCCCC-cEEEEechhhhhhhhcc-------cCCC-ceeeeccccCCCccCCCCCchHHHHHH
Q 018558 203 RKIQDFLCNGEPMWKIRPRGSRA-RILVGHGLDHDLDRLQV-------EYPA-IMTRDTAKYPPLMKTSKLSNSLKYLTQ 273 (354)
Q Consensus 203 ~~~~~~i~~~~~~~~~~~~~~~~-~ilVgHn~~~Dl~~L~~-------~~~~-~~~~Dt~~~~~~~~~~~~~~~L~~l~~ 273 (354)
++|.+|+ ++ .++|.||..||+.+|.. ..+. ..++|+..++.........++|..+++
T Consensus 84 ~~f~~~~--------------~~~~~~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~~~~L~~~~~ 149 (207)
T PRK07748 84 EKLAEYD--------------KRCKPTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKAIE 149 (207)
T ss_pred HHHHHHh--------------CcCCeEEEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCCCCCHHHHHH
Confidence 9999999 66 45555668999999852 2222 235677665443333334679999988
Q ss_pred HHhCCcCCCCCCChHHHHHHHHHHHHHHHHhh
Q 018558 274 AYLGYDIQIGIQDPYDDCVATMRLYMRMKSQA 305 (354)
Q Consensus 274 ~~l~~~i~~~~H~Al~DA~at~~l~~~~~~~~ 305 (354)
+| |+.....+|+|++||++|++||.++.+..
T Consensus 150 ~~-gi~~~~~~H~Al~DA~~ta~l~~~l~~~~ 180 (207)
T PRK07748 150 EY-GKEGTGKHHCALDDAMTTYNIFKLVEKDK 180 (207)
T ss_pred Hc-CCCCCCCCcChHHHHHHHHHHHHHHHhCc
Confidence 65 44433348999999999999999988775
No 26
>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=99.92 E-value=2.4e-25 Score=191.16 Aligned_cols=151 Identities=19% Similarity=0.258 Sum_probs=118.5
Q ss_pred eEEeeccccccCCCCCccceeeEEEEec-CCc---eEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHHH
Q 018558 134 VVAIACKMVGGGSDGSLDLCGRVCIIDE-YEN---IIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDFL 209 (354)
Q Consensus 134 ~vaiD~Ettg~~~~~~~~~i~~i~vv~~-~g~---~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~i 209 (354)
+|++|+||||+.+. ..++|+++++|.. ++. ..|+.+|+|..++++..+++||||+++|+++|+|++++++|.+|+
T Consensus 1 ~v~~D~ETTGl~~~-~~~~iieig~v~v~~~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~~~~v~~~l~~~l 79 (167)
T cd06131 1 QIVLDTETTGLDPR-EGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFI 79 (167)
T ss_pred CEEEEeeCCCCCCC-CCCeEEEEEEEEEECCcEeccEEEEEECCCCCCCHHHHHHhCCCHHHHhcCCCHHHHHHHHHHHH
Confidence 58999999998652 2245666665543 232 247899999999999999999999999999999999999999999
Q ss_pred hcCCCCccccCCCCCCcEEEEechhhhhhhhccc-------C---CCceeeeccccCCCccCCCCCchHHHHHHHHhCCc
Q 018558 210 CNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVE-------Y---PAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYD 279 (354)
Q Consensus 210 ~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~-------~---~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~ 279 (354)
++.++||||+.||+.+|+.. . ....++||..+++...+. ..++|..+++++ |..
T Consensus 80 --------------~~~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~-~~~~L~~l~~~~-~i~ 143 (167)
T cd06131 80 --------------RGAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPG-KPNSLDALCKRF-GID 143 (167)
T ss_pred --------------CCCeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCC-CCCCHHHHHHHC-CCC
Confidence 78899999999999988521 1 123478998776543322 457999999965 544
Q ss_pred CCC-CCCChHHHHHHHHHHHHHH
Q 018558 280 IQI-GIQDPYDDCVATMRLYMRM 301 (354)
Q Consensus 280 i~~-~~H~Al~DA~at~~l~~~~ 301 (354)
... ++|+|++||++|++||.+|
T Consensus 144 ~~~~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 144 NSHRTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred CCCCCCCChHHHHHHHHHHHHHh
Confidence 432 4799999999999999876
No 27
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.92 E-value=4.2e-25 Score=189.48 Aligned_cols=155 Identities=30% Similarity=0.451 Sum_probs=125.3
Q ss_pred eEEeeccccccCCCCCccceeeEEEEecCC---ceEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHHHh
Q 018558 134 VVAIACKMVGGGSDGSLDLCGRVCIIDEYE---NIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDFLC 210 (354)
Q Consensus 134 ~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g---~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~i~ 210 (354)
+|++|+||||..+. ..+|+++++|..++ ...|+.||+|..+++++.+++||||+++|+++|+|.+++.+|.+|+
T Consensus 2 ~v~~D~Ettg~~~~--~~~Iieig~v~~~~~~~~~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~~~~~~~~~~~~~l- 78 (169)
T smart00479 2 LVVIDCETTGLDPG--KDEIIEIAAVDVDGGRIIVVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL- 78 (169)
T ss_pred EEEEEeeCCCCCCC--CCeEEEEEEEEEECCEeEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHHh-
Confidence 79999999998543 45678888887654 3449999999999999999999999999999999999999999999
Q ss_pred cCCCCccccCCCCCCcEEEEech-hhhhhhhccc-------CC-CceeeeccccCCCccCCCCCchHHHHHHHHhCCcCC
Q 018558 211 NGEPMWKIRPRGSRARILVGHGL-DHDLDRLQVE-------YP-AIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQ 281 (354)
Q Consensus 211 ~~~~~~~~~~~~~~~~ilVgHn~-~~Dl~~L~~~-------~~-~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~ 281 (354)
++.++||||. .||+.+|+.. .| ...++||..+++...+. ..++|..|++.+ |....
T Consensus 79 -------------~~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~-~~~~L~~l~~~~-~~~~~ 143 (169)
T smart00479 79 -------------KGKILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPG-RKYSLKKLAERL-GLEVI 143 (169)
T ss_pred -------------cCCEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCC-CCCCHHHHHHHC-CCCCC
Confidence 7778888888 9999988632 12 12268998776654433 278999999865 44433
Q ss_pred CCCCChHHHHHHHHHHHHHHHHhhh
Q 018558 282 IGIQDPYDDCVATMRLYMRMKSQAH 306 (354)
Q Consensus 282 ~~~H~Al~DA~at~~l~~~~~~~~~ 306 (354)
..+|+|++||++|++||.++.++|.
T Consensus 144 ~~~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 144 GRAHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred CCCcCcHHHHHHHHHHHHHHHHHhh
Confidence 3359999999999999999988873
No 28
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.92 E-value=6.5e-26 Score=231.20 Aligned_cols=182 Identities=23% Similarity=0.293 Sum_probs=149.5
Q ss_pred cchhhhhccCCCCCcccCCCCCCCCceEEeeccccccCCCCCccceeeEEEEec-CCceE--EeeeecCCccccCceeee
Q 018558 108 GLNARLANLGVRDSLTIDNTHTRDPQVVAIACKMVGGGSDGSLDLCGRVCIIDE-YENII--FHAYVKPPIPVTSYRYET 184 (354)
Q Consensus 108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~-~g~~i--~~~~v~P~~~i~~~~~~i 184 (354)
+++..+...+++-...+.+.......||++|+||||+++. .+.|+++++|.. +|++| |+.|++|..|++..+|++
T Consensus 397 G~EanlvdD~vpiv~N~~d~~l~datyVVfDiETTGLs~~--~d~iIE~aAvKikng~iId~f~~Fi~P~~pl~~~~tel 474 (1444)
T COG2176 397 GLEANLVDDGVPIVYNPDDQKLDDATYVVFDIETTGLSPV--YDEIIEIAAVKIKNGRIIDKFQFFIKPGRPLSATITEL 474 (1444)
T ss_pred eeeeeeccCCCceecCccccccccccEEEEEeecCCcCcc--cchhhhheeeeeeCCcchHHHHHhcCCCCcCchhhhhc
Confidence 3455555566666666666666677899999999998653 455677777765 56666 888999999999999999
Q ss_pred cCCChhhhcCCCCHHHHHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhccc-------CCCceeeeccccCC
Q 018558 185 TGIRPEHLRDAIPLKQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVE-------YPAIMTRDTAKYPP 257 (354)
Q Consensus 185 tGIt~~~l~~ap~~~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~-------~~~~~~~Dt~~~~~ 257 (354)
||||++||++|++..+|+.+|.+|+ +++|||+||+.||+.||+.. .-...+|||..+++
T Consensus 475 TgITdeml~~a~~i~~vL~kf~~~~--------------~d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar 540 (1444)
T COG2176 475 TGITDEMLENAPEIEEVLEKFREFI--------------GDSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELAR 540 (1444)
T ss_pred cccCHHHHcCCccHHHHHHHHHHHh--------------cCcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHH
Confidence 9999999999999999999999999 99999999999999999731 11223789999998
Q ss_pred CccCCCCCchHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 258 LMKTSKLSNSLKYLTQAYLGYDIQIGIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 258 ~~~~~~~~~~L~~l~~~~l~~~i~~~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
...|.-.+|+|..||+.| +..+ ..+|||..||.||+.||..+.+...+
T Consensus 541 ~L~P~~ksh~Lg~l~kk~-~v~l-e~hHRA~yDaeat~~vf~~f~~~~ke 588 (1444)
T COG2176 541 ALNPEFKSHRLGTLCKKL-GVEL-ERHHRADYDAEATAKVFFVFLKDLKE 588 (1444)
T ss_pred HhChhhhhcchHHHHHHh-CccH-HHhhhhhhhHHHHHHHHHHHHHHHHH
Confidence 888877899999999976 4444 44999999999999999888887755
No 29
>PRK07883 hypothetical protein; Validated
Probab=99.92 E-value=1.9e-24 Score=216.90 Aligned_cols=160 Identities=20% Similarity=0.300 Sum_probs=131.1
Q ss_pred CCCceEEeeccccccCCCCCccceeeEEEEecC-CceE--EeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHH
Q 018558 130 RDPQVVAIACKMVGGGSDGSLDLCGRVCIIDEY-ENII--FHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQ 206 (354)
Q Consensus 130 ~~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~-g~~i--~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~ 206 (354)
....+|+||+||||+.+. .++|++|++|..+ |.++ |++||+|..+|+++++++||||++||+++|+|.+++.+|.
T Consensus 13 ~~~~~Vv~D~ETTGl~p~--~~~IIEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~f~ 90 (557)
T PRK07883 13 RDVTFVVVDLETTGGSPA--GDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFL 90 (557)
T ss_pred cCCCEEEEEEecCCCCCC--CCeEEEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHH
Confidence 346899999999998553 3567788877764 4444 8899999999999999999999999999999999999999
Q ss_pred HHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcc-------cCCCceeeeccccCCCccC--CCCCchHHHHHHHHhC
Q 018558 207 DFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQV-------EYPAIMTRDTAKYPPLMKT--SKLSNSLKYLTQAYLG 277 (354)
Q Consensus 207 ~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~-------~~~~~~~~Dt~~~~~~~~~--~~~~~~L~~l~~~~l~ 277 (354)
+|+ ++.++||||+.||+.+|+. ..+...++||..+++...+ ...+++|..|+.+ +|
T Consensus 91 ~fl--------------~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L~~~-~g 155 (557)
T PRK07883 91 EFA--------------RGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLARL-FG 155 (557)
T ss_pred HHh--------------cCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHHHHH-CC
Confidence 999 8899999999999999852 3344457899877654333 4467899999985 45
Q ss_pred CcCCCCCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 278 YDIQIGIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 278 ~~i~~~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
..+ .++|+|++||++|++||.++.+++..
T Consensus 156 i~~-~~~H~Al~DA~ata~l~~~l~~~~~~ 184 (557)
T PRK07883 156 ATT-TPTHRALDDARATVDVLHGLIERLGN 184 (557)
T ss_pred ccc-CCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 554 34899999999999999999888854
No 30
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.92 E-value=1.2e-24 Score=230.66 Aligned_cols=158 Identities=19% Similarity=0.307 Sum_probs=131.9
Q ss_pred CceEEeeccccccCCCCCccceeeEEEEec-CCceE--EeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHH
Q 018558 132 PQVVAIACKMVGGGSDGSLDLCGRVCIIDE-YENII--FHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDF 208 (354)
Q Consensus 132 ~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~-~g~~i--~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~ 208 (354)
.+||++|+||||..+... ++|++|++|.. +|+++ |++||+|..+|+++++++||||++||++||+|++|+++|.+|
T Consensus 3 ~~~vvvD~ETTG~~p~~~-d~IIeigav~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~l~~~ 81 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKG-DKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVEL 81 (928)
T ss_pred CCEEEEEEeCCCCCCCCC-CcEEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHHHHHH
Confidence 469999999999865433 45677777665 44444 888999999999999999999999999999999999999999
Q ss_pred HhcCCCCccccCCCCCCcEEEEechhhhhhhhcc-------cCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCcCC
Q 018558 209 LCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQV-------EYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQ 281 (354)
Q Consensus 209 i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~-------~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~ 281 (354)
+ ++.++||||+.||+.+|+. ..+...++||..+++...+...+++|..|++++ +|.
T Consensus 82 l--------------~~~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~~~~L~~l~~~l---~i~ 144 (928)
T PRK08074 82 L--------------EGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEEL---GLE 144 (928)
T ss_pred h--------------CCCeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCCCCCHHHHHHhC---CCC
Confidence 9 8999999999999999863 223344789988776655666788999999975 454
Q ss_pred -CCCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 282 -IGIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 282 -~~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
.++|+|++||++|++||.++.+++..
T Consensus 145 ~~~~H~Al~DA~ata~l~~~l~~~~~~ 171 (928)
T PRK08074 145 HDQPHRADSDAEVTAELFLQLLNKLER 171 (928)
T ss_pred CCCCCChHHHHHHHHHHHHHHHHHHHh
Confidence 35899999999999999999998865
No 31
>PRK06722 exonuclease; Provisional
Probab=99.92 E-value=1.5e-24 Score=198.40 Aligned_cols=158 Identities=16% Similarity=0.115 Sum_probs=119.1
Q ss_pred CCceEEeeccccccCCC--CCccceeeEEEEecC-C--ceE--EeeeecCCccccCceeeecCCChhhhcCCCCHHHHHH
Q 018558 131 DPQVVAIACKMVGGGSD--GSLDLCGRVCIIDEY-E--NII--FHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQR 203 (354)
Q Consensus 131 ~~~~vaiD~Ettg~~~~--~~~~~i~~i~vv~~~-g--~~i--~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~ 203 (354)
...+|++|+|||+ .+. ...++|++|++|..+ | +++ |++||+|..+|++++++|||||++||++||+|++|++
T Consensus 4 ~~~~vViD~ETT~-~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~~I~~~i~~LTGIT~emV~~AP~f~eVl~ 82 (281)
T PRK06722 4 ATHFIVFDIERNF-RPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQIIE 82 (281)
T ss_pred CCEEEEEEeeCCC-CCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCCcCCHhHhhhcCCCHHHHcCCCCHHHHHH
Confidence 3579999999995 332 233567777777654 3 444 9999999999999999999999999999999999999
Q ss_pred HHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcc-------cCCCc---eeeeccccCCCcc--CCCCCchHHHH
Q 018558 204 KIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQV-------EYPAI---MTRDTAKYPPLMK--TSKLSNSLKYL 271 (354)
Q Consensus 204 ~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~-------~~~~~---~~~Dt~~~~~~~~--~~~~~~~L~~l 271 (354)
+|.+|+ ++.++|+||..||+++|.. ..|.. .++|+..++.... .....++|..|
T Consensus 83 ef~~fi--------------g~~~lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l 148 (281)
T PRK06722 83 KFIQFI--------------GEDSIFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSA 148 (281)
T ss_pred HHHHHH--------------CCCcEEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHH
Confidence 999999 7778888888999999863 12211 1356654331111 12235689999
Q ss_pred HHHHhCCcCCCCCCChHHHHHHHHHHHHHHHHh
Q 018558 272 TQAYLGYDIQIGIQDPYDDCVATMRLYMRMKSQ 304 (354)
Q Consensus 272 ~~~~l~~~i~~~~H~Al~DA~at~~l~~~~~~~ 304 (354)
++++ |+.....+|+|++||++|+.||.++.++
T Consensus 149 ~~~l-gL~~~g~~HrAL~DA~~TA~L~l~l~~~ 180 (281)
T PRK06722 149 VEQL-GLIWEGKQHRALADAENTANILLKAYSE 180 (281)
T ss_pred HHHC-CCCCCCCCcCcHHHHHHHHHHHHHHhcc
Confidence 9865 5444344899999999999999998753
No 32
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=99.91 E-value=1.7e-24 Score=228.50 Aligned_cols=157 Identities=25% Similarity=0.302 Sum_probs=130.9
Q ss_pred ceEEeeccccccCCCCCccceeeEEEEec-CCceE--EeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHHH
Q 018558 133 QVVAIACKMVGGGSDGSLDLCGRVCIIDE-YENII--FHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDFL 209 (354)
Q Consensus 133 ~~vaiD~Ettg~~~~~~~~~i~~i~vv~~-~g~~i--~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~i 209 (354)
+||++|+||||..+. .++|+++++|.. +|+++ |+++|+|..+|+++++++||||++||+++|+|++++++|.+|+
T Consensus 1 ~~vvvD~ETTG~~~~--~~~IIeig~v~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l~~~l 78 (850)
T TIGR01407 1 RYAVVDLETTGTQLS--FDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLL 78 (850)
T ss_pred CEEEEEEECCCCCCC--CCeEEEEEEEEEECCEEEEEEEEEeCCCCCCChhhhhhcCcCHHHHhCCCCHHHHHHHHHHHh
Confidence 489999999998643 466778877765 45544 8999999999999999999999999999999999999999999
Q ss_pred hcCCCCccccCCCCCCcEEEEechhhhhhhhcc-------cCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCcCCC
Q 018558 210 CNGEPMWKIRPRGSRARILVGHGLDHDLDRLQV-------EYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQI 282 (354)
Q Consensus 210 ~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~-------~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~~ 282 (354)
++.++||||+.||+.+|+. ......++||..+.+...+...+++|.+|++++ |... .
T Consensus 79 --------------~~~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~~~~L~~l~~~~-gi~~-~ 142 (850)
T TIGR01407 79 --------------EDGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEAL-GLTH-E 142 (850)
T ss_pred --------------CCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCCCCCHHHHHHHC-CCCC-C
Confidence 8899999999999999863 212334789988776665555689999999975 5443 3
Q ss_pred CCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 283 GIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 283 ~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
++|+|++||++|++||.++.+++..
T Consensus 143 ~~H~Al~DA~ata~l~~~l~~~~~~ 167 (850)
T TIGR01407 143 NPHRADSDAQATAELLLLLFEKMEK 167 (850)
T ss_pred CCCChHHHHHHHHHHHHHHHHHHHh
Confidence 5899999999999999999988855
No 33
>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=99.91 E-value=8.8e-25 Score=189.24 Aligned_cols=150 Identities=17% Similarity=0.240 Sum_probs=111.5
Q ss_pred eEEeeccccccCCCCCccceeeEEEEecCCc--------------e--EEeeeecCCccccCceeeecCCChhhhcCCCC
Q 018558 134 VVAIACKMVGGGSDGSLDLCGRVCIIDEYEN--------------I--IFHAYVKPPIPVTSYRYETTGIRPEHLRDAIP 197 (354)
Q Consensus 134 ~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~--------------~--i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~ 197 (354)
|+++|+||||+.+ ...+.|+++++|...+. + -|++||+|+.+|++.+++|||||++||.++|+
T Consensus 1 ~vv~D~ETTGl~~-~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a~~IhGIt~e~l~~~~~ 79 (177)
T cd06136 1 FVFLDLETTGLPK-HNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHKAP 79 (177)
T ss_pred CeEEeeecCCCCC-CCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCCcCChhHHHHhCcCHHHHhcCCC
Confidence 5899999999852 23345667766654321 1 27889999999999999999999999999999
Q ss_pred HHH-HHHHHHHHHhcCCCCccccCCCCCCcEEEEech-hhhhhhhcc-------cCC-CceeeeccccCCCccCCCCCch
Q 018558 198 LKQ-VQRKIQDFLCNGEPMWKIRPRGSRARILVGHGL-DHDLDRLQV-------EYP-AIMTRDTAKYPPLMKTSKLSNS 267 (354)
Q Consensus 198 ~~~-v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~-~~Dl~~L~~-------~~~-~~~~~Dt~~~~~~~~~~~~~~~ 267 (354)
|.+ +++.+.+|+... .++.+|||||+ .||+++|+. ..+ ...++||..+++... ++
T Consensus 80 ~~~~~~~~l~~f~~~~----------~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~-----~~ 144 (177)
T cd06136 80 FDSDTANLIKLFLRRQ----------PKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELD-----QS 144 (177)
T ss_pred ccHHHHHHHHHHHHhc----------CCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhH-----hh
Confidence 874 666677776100 13469999998 899999852 222 234579988776542 29
Q ss_pred HHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHH
Q 018558 268 LKYLTQAYLGYDIQIGIQDPYDDCVATMRLYMR 300 (354)
Q Consensus 268 L~~l~~~~l~~~i~~~~H~Al~DA~at~~l~~~ 300 (354)
|..|+.+++|.... ++|+|++||.||+++|.+
T Consensus 145 L~~l~~~~~~~~~~-~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 145 LGSLYKRLFGQEPK-NSHTAEGDVLALLKCALH 176 (177)
T ss_pred HHHHHHHHhCCCcc-cccchHHHHHHHHHHHhh
Confidence 99999876555543 489999999999999864
No 34
>PRK05168 ribonuclease T; Provisional
Probab=99.91 E-value=4.5e-24 Score=189.77 Aligned_cols=166 Identities=22% Similarity=0.259 Sum_probs=123.0
Q ss_pred CCceEEeeccccccCCCCCccceeeEEEEec----CCc----eEEeeeecC--CccccCceeeecCCChhh-hcCCCCHH
Q 018558 131 DPQVVAIACKMVGGGSDGSLDLCGRVCIIDE----YEN----IIFHAYVKP--PIPVTSYRYETTGIRPEH-LRDAIPLK 199 (354)
Q Consensus 131 ~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~----~g~----~i~~~~v~P--~~~i~~~~~~itGIt~~~-l~~ap~~~ 199 (354)
...+|++|+||||+.+. .+.|++|++|.. +|. ..|++||+| +.+|++.+++|||||+++ ++++|++.
T Consensus 16 ~~~~vv~D~ETTGl~~~--~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~~~~~~ 93 (211)
T PRK05168 16 GFLPVVIDVETAGFNAK--TDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAVSEK 93 (211)
T ss_pred CCceEEEEeeCCCCCCC--CCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhcCCChH
Confidence 34679999999998654 345667766643 243 248899999 578999999999999986 89999999
Q ss_pred HHHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhccc----------CCCceeeeccccCCCccCCCCCchHH
Q 018558 200 QVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVE----------YPAIMTRDTAKYPPLMKTSKLSNSLK 269 (354)
Q Consensus 200 ~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~----------~~~~~~~Dt~~~~~~~~~~~~~~~L~ 269 (354)
+++.++++++.+. +..-..++.++||||+.||+.||... .+...++||..+++...+ ..+|.
T Consensus 94 ~~l~~~~~~l~~~-----~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~---~~~L~ 165 (211)
T PRK05168 94 EALHEIFKMVRKG-----IKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALG---QTVLA 165 (211)
T ss_pred HHHHHHHHHHHHH-----HHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC---CCCHH
Confidence 9999998887100 00000136899999999999988531 112247899988764422 35899
Q ss_pred HHHHHHhCCcCC-CCCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 270 YLTQAYLGYDIQ-IGIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 270 ~l~~~~l~~~i~-~~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
.++.++ |..++ ..+|+|++||++|++||.++.+++.+
T Consensus 166 ~l~~~~-gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~~ 203 (211)
T PRK05168 166 KACQAA-GIEFDNKEAHSALYDTEKTAELFCEIVNRWKR 203 (211)
T ss_pred HHHHHC-CCCCCCCCCCChHHHHHHHHHHHHHHHHHHHH
Confidence 999864 55554 34899999999999999999998865
No 35
>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=99.91 E-value=4.2e-24 Score=186.86 Aligned_cols=161 Identities=23% Similarity=0.249 Sum_probs=116.0
Q ss_pred ceEEeeccccccCCCCCccceeeEEEEec----CCc----eEEeeeecC--CccccCceeeecCCChhh-hcCCCCHHHH
Q 018558 133 QVVAIACKMVGGGSDGSLDLCGRVCIIDE----YEN----IIFHAYVKP--PIPVTSYRYETTGIRPEH-LRDAIPLKQV 201 (354)
Q Consensus 133 ~~vaiD~Ettg~~~~~~~~~i~~i~vv~~----~g~----~i~~~~v~P--~~~i~~~~~~itGIt~~~-l~~ap~~~~v 201 (354)
..|++|+||||+.+.. +.|++|++|.. +|. ..|++||+| +.+|++.+++|||||+++ +++++...++
T Consensus 6 ~~vv~D~ETTGl~~~~--d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~~~ 83 (189)
T cd06134 6 LPVVVDVETGGFNPQT--DALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEKEA 83 (189)
T ss_pred eeEEEEecCCCCCCCC--CeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchHHH
Confidence 4699999999987643 44566665543 233 248999999 578999999999999986 6777776666
Q ss_pred HHHHHHHHhcCCCCccccC-CCCCCcEEEEechhhhhhhhccc----------CCCceeeeccccCCCccCCCCCchHHH
Q 018558 202 QRKIQDFLCNGEPMWKIRP-RGSRARILVGHGLDHDLDRLQVE----------YPAIMTRDTAKYPPLMKTSKLSNSLKY 270 (354)
Q Consensus 202 ~~~~~~~i~~~~~~~~~~~-~~~~~~ilVgHn~~~Dl~~L~~~----------~~~~~~~Dt~~~~~~~~~~~~~~~L~~ 270 (354)
+.+|++++.+ +.. .+.++.+|||||+.||+.||+.. .+...++||..+.+...+ .++|..
T Consensus 84 ~~~~~~~l~~------~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~---~~~L~~ 154 (189)
T cd06134 84 LKEIFKPIRK------ALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG---QTVLAK 154 (189)
T ss_pred HHHHHHHHHH------HHhhcccCCCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC---CCcHHH
Confidence 6666665510 000 00136799999999999998631 112236899988765432 358999
Q ss_pred HHHHHhCCcCC-CCCCChHHHHHHHHHHHHHHHHhh
Q 018558 271 LTQAYLGYDIQ-IGIQDPYDDCVATMRLYMRMKSQA 305 (354)
Q Consensus 271 l~~~~l~~~i~-~~~H~Al~DA~at~~l~~~~~~~~ 305 (354)
+|+.| |+.+. ..+|+|++||++|++||.++.++|
T Consensus 155 l~~~~-gi~~~~~~~H~Al~DA~ata~lf~~l~~~~ 189 (189)
T cd06134 155 ACQAA-GIEFDNKEAHSALYDTQKTAELFCKIVNRW 189 (189)
T ss_pred HHHHC-CCCCCCCCCcChHHHHHHHHHHHHHHHHhC
Confidence 99965 55543 358999999999999999999887
No 36
>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=99.91 E-value=5.9e-24 Score=187.44 Aligned_cols=165 Identities=22% Similarity=0.249 Sum_probs=121.3
Q ss_pred CceEEeeccccccCCCCCccceeeEEEEec----CCce----EEeeeecC--CccccCceeeecCCChh-hhcCCCCHHH
Q 018558 132 PQVVAIACKMVGGGSDGSLDLCGRVCIIDE----YENI----IFHAYVKP--PIPVTSYRYETTGIRPE-HLRDAIPLKQ 200 (354)
Q Consensus 132 ~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~----~g~~----i~~~~v~P--~~~i~~~~~~itGIt~~-~l~~ap~~~~ 200 (354)
..+|++|+||||+++. .+.|++|++|.. .|.+ .|.++|+| +.+|++.+++|||||++ |++++|++.+
T Consensus 8 ~~~vv~D~ETTGl~~~--~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~~~~ 85 (200)
T TIGR01298 8 YLPVVVDVETGGFNAK--TDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVSEYE 85 (200)
T ss_pred CeeEEEEeeCCCCCCC--CCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcchHH
Confidence 4579999999998764 344566665542 3433 28899997 47899999999999976 6999999999
Q ss_pred HHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhccc----------CCCceeeeccccCCCccCCCCCchHHH
Q 018558 201 VQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVE----------YPAIMTRDTAKYPPLMKTSKLSNSLKY 270 (354)
Q Consensus 201 v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~----------~~~~~~~Dt~~~~~~~~~~~~~~~L~~ 270 (354)
+++++++++.+. +.....++.++||||+.||++||+.. .+...++||..+++... ..++|..
T Consensus 86 ~~~~~~~~l~~~-----~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~---~~~~L~~ 157 (200)
T TIGR01298 86 ALHEIFKVVRKA-----MKASGCQRAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAY---GQTVLAK 157 (200)
T ss_pred HHHHHHHHHHHH-----HHhcccCCCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHc---CcccHHH
Confidence 888888876100 00000146799999999999998631 11233789998876543 2358999
Q ss_pred HHHHHhCCcCC-CCCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 271 LTQAYLGYDIQ-IGIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 271 l~~~~l~~~i~-~~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
+|+++ |..+. ..+|+|++||++|++||.++.+++.+
T Consensus 158 l~~~~-gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~~ 194 (200)
T TIGR01298 158 ACQAA-GXDFDSTQAHSALYDTEKTAELFCEIVNRWKR 194 (200)
T ss_pred HHHHc-CCCccccchhhhHHhHHHHHHHHHHHHHHHHH
Confidence 99965 55543 35899999999999999999998865
No 37
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.90 E-value=5.2e-23 Score=192.12 Aligned_cols=154 Identities=14% Similarity=0.193 Sum_probs=121.4
Q ss_pred CCCceEEeeccccccCCCCCccceeeEEEEec--CCceE--EeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHH
Q 018558 130 RDPQVVAIACKMVGGGSDGSLDLCGRVCIIDE--YENII--FHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKI 205 (354)
Q Consensus 130 ~~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~--~g~~i--~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~ 205 (354)
....||+||+||||+.+.. +.|++|++|.. +|+++ |.+||+|..++.+ ..|||||++||++||+|.+|+++|
T Consensus 44 ~~~~fVvlDiETTGLdp~~--drIIeIgAV~i~~~g~ive~f~tLVnP~~~~~p--~~LHGIT~e~La~AP~f~eVl~el 119 (377)
T PRK05601 44 EAAPFVAVSIQTSGIHPST--SRLITIDAVTLTADGEEVEHFHAVLNPGEDPGP--FHLHGLSAEEFAQGKRFSQILKPL 119 (377)
T ss_pred CCCCEEEEEEECCCCCCCC--CeEEEEEEEEEEcCCEEEEEEEEEECcCCCCCC--ccccCCCHHHHhcCCCHHHHHHHH
Confidence 3457999999999986643 45667766643 45543 8999999986554 379999999999999999999999
Q ss_pred HHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhccc----------------------------------CCCceeee
Q 018558 206 QDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVE----------------------------------YPAIMTRD 251 (354)
Q Consensus 206 ~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~----------------------------------~~~~~~~D 251 (354)
.+|| ++.+|||||+.||+.||... .....++|
T Consensus 120 ~~fL--------------~g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iD 185 (377)
T PRK05601 120 DRLI--------------DGRTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVD 185 (377)
T ss_pred HHHh--------------CCCEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEE
Confidence 9999 89999999999999987431 11234799
Q ss_pred ccccCCCccCCCCCchHHHHHHHHhCCcCC---------CCCCChH--HHHHHHHHHHHHHH
Q 018558 252 TAKYPPLMKTSKLSNSLKYLTQAYLGYDIQ---------IGIQDPY--DDCVATMRLYMRMK 302 (354)
Q Consensus 252 t~~~~~~~~~~~~~~~L~~l~~~~l~~~i~---------~~~H~Al--~DA~at~~l~~~~~ 302 (354)
|+.+.+...+...+++|..||.+| |+... .-.|++| +||+.+++||.+.+
T Consensus 186 TL~LARrl~p~l~~~rL~~La~~l-Gi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~~ 246 (377)
T PRK05601 186 TLATARRQGVALDDIRIRGVAHTL-GLDAPAAEASVERAQVPHRQLCREETLLVARLYFALR 246 (377)
T ss_pred hHHHHHHHcCCCCCCCHHHHHHHh-CCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHhh
Confidence 998887776666789999999965 55441 1158888 69999999998763
No 38
>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=99.89 E-value=2.8e-23 Score=221.63 Aligned_cols=160 Identities=23% Similarity=0.316 Sum_probs=132.3
Q ss_pred CCCceEEeeccccccCCCCCccceeeEEEEec-CCceE--EeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHH
Q 018558 130 RDPQVVAIACKMVGGGSDGSLDLCGRVCIIDE-YENII--FHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQ 206 (354)
Q Consensus 130 ~~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~-~g~~i--~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~ 206 (354)
....+|++|+||||+++. .+.|+++++|.. +|+++ |++||+|..+|++.++++||||++||+++|++++|+++|.
T Consensus 188 ~~~~~VVfDiETTGL~~~--~d~IIEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f~ 265 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQ--YDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKFK 265 (1213)
T ss_pred cCCcEEEEEeEecCCCCC--CCeEEEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHH
Confidence 455899999999998653 456677777664 44544 8999999999999999999999999999999999999999
Q ss_pred HHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcc-------cCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCc
Q 018558 207 DFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQV-------EYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYD 279 (354)
Q Consensus 207 ~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~-------~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~ 279 (354)
+|+ ++.+|||||+.||+.+|+. ......++||..+++...+...+++|..||+++ |..
T Consensus 266 ~fl--------------~~~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k~~kL~~Lak~l-gi~ 330 (1213)
T TIGR01405 266 EFF--------------KDSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRLGNICKKL-GVD 330 (1213)
T ss_pred HHh--------------CCCeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCCCCCHHHHHHHc-CCC
Confidence 999 8899999999999999863 112234789998877665555689999999975 555
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 280 IQIGIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 280 i~~~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
+.. +|+|++||++|++||.++.+++.+
T Consensus 331 ~~~-~HrAl~DA~aTa~I~~~ll~~l~~ 357 (1213)
T TIGR01405 331 LDD-HHRADYDAEATAKVFKVMVEQLKE 357 (1213)
T ss_pred CCC-CcCHHHHHHHHHHHHHHHHHHHHH
Confidence 543 999999999999999999887754
No 39
>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=99.88 E-value=1.4e-22 Score=175.08 Aligned_cols=153 Identities=19% Similarity=0.146 Sum_probs=118.9
Q ss_pred eEEeeccccccCCCC---CccceeeEEEEe--cCCc-e--EEeeeecCCc--cccCceeeecCCChhhhcCCCCHHHHHH
Q 018558 134 VVAIACKMVGGGSDG---SLDLCGRVCIID--EYEN-I--IFHAYVKPPI--PVTSYRYETTGIRPEHLRDAIPLKQVQR 203 (354)
Q Consensus 134 ~vaiD~Ettg~~~~~---~~~~i~~i~vv~--~~g~-~--i~~~~v~P~~--~i~~~~~~itGIt~~~l~~ap~~~~v~~ 203 (354)
||++|+||||..+.. ...+|++|++|. .++. + .|++||+|.. +++++++++||||+++|+++|+|++|++
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~~~~~vl~ 80 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCCCHHHHHH
Confidence 589999999986531 235677887774 3333 2 3999999998 8999999999999999999999999999
Q ss_pred HHHHHHhcCCCCccccCCCCCCc--EEEEechhhhhhhhcc----------cCCCceeeeccccCCCccCCCCCchHHHH
Q 018558 204 KIQDFLCNGEPMWKIRPRGSRAR--ILVGHGLDHDLDRLQV----------EYPAIMTRDTAKYPPLMKTSKLSNSLKYL 271 (354)
Q Consensus 204 ~~~~~i~~~~~~~~~~~~~~~~~--ilVgHn~~~Dl~~L~~----------~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l 271 (354)
+|.+|+ ++. .+++||..||+.++.. ......++|+..++....+....++|..+
T Consensus 81 ~~~~~l--------------~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l 146 (176)
T cd06133 81 EFLEWL--------------GKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKA 146 (176)
T ss_pred HHHHHH--------------HhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHH
Confidence 999999 665 5666667999876531 11223478998877765555568899999
Q ss_pred HHHHhCCcCCCCCCChHHHHHHHHHHHHHH
Q 018558 272 TQAYLGYDIQIGIQDPYDDCVATMRLYMRM 301 (354)
Q Consensus 272 ~~~~l~~~i~~~~H~Al~DA~at~~l~~~~ 301 (354)
+.+| |.+....+|+|++||++|++||.+|
T Consensus 147 ~~~~-gi~~~~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 147 LEYL-GLEFEGRHHRGLDDARNIARILKRL 175 (176)
T ss_pred HHHC-CCCCCCCCcCcHHHHHHHHHHHHHh
Confidence 8854 6555545999999999999999876
No 40
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.87 E-value=6.9e-22 Score=183.15 Aligned_cols=153 Identities=16% Similarity=0.112 Sum_probs=112.0
Q ss_pred CCCCceEEeeccccccCCCCCccceeeEEEEec----CCce-----EEeeeecCCccccCceeeecCCChhhhcCCCCHH
Q 018558 129 TRDPQVVAIACKMVGGGSDGSLDLCGRVCIIDE----YENI-----IFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLK 199 (354)
Q Consensus 129 ~~~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~----~g~~-----i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~ 199 (354)
.....+|++|+||||+.+. .++|++|++|.. +|.+ .|+.||+|..+|++.+++|||||++||+++|...
T Consensus 34 ~~~~~~vvlD~ETTGLd~~--~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~~I~~~~t~IhGIt~e~v~~~~~~~ 111 (294)
T PRK09182 34 EFVRLGVILDTETTGLDPR--KDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDP 111 (294)
T ss_pred CCCCeEEEEEeeCCCCCCC--CCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCCCCCHHHHHhcCCCHHHHhcCCCcH
Confidence 3456799999999998653 455677776653 3432 2888999999999999999999999999998754
Q ss_pred HHHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcccC---CCceeeeccccCCCccCCCCCchHHHHHHHHh
Q 018558 200 QVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVEY---PAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYL 276 (354)
Q Consensus 200 ~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~~---~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l 276 (354)
..|.+|+ +...+|||||+.||+.||+... +...+.++............+++|..|+..|
T Consensus 112 ---~~l~~fl-------------~~~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~~~~~~~~~~kL~~La~~~- 174 (294)
T PRK09182 112 ---AAVDALI-------------APADLIIAHNAGFDRPFLERFSPVFATKPWACSVSEIDWSARGFEGTKLGYLAGQA- 174 (294)
T ss_pred ---HHHHHHh-------------cCCCEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHhhccccCCCCCHHHHHHHc-
Confidence 3567778 1346999999999999997422 1222344443222222233578999999965
Q ss_pred CCcCCCCCCChHHHHHHHHHHHHHHH
Q 018558 277 GYDIQIGIQDPYDDCVATMRLYMRMK 302 (354)
Q Consensus 277 ~~~i~~~~H~Al~DA~at~~l~~~~~ 302 (354)
| +...+|+|++||+||++|+.+..
T Consensus 175 g--~~~~aHrAl~Da~Ata~ll~~~l 198 (294)
T PRK09182 175 G--FFHEGHRAVDDCQALLELLARPL 198 (294)
T ss_pred C--CCCCCcChHHHHHHHHHHHHHHH
Confidence 4 44458999999999999998654
No 41
>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=99.87 E-value=7.6e-22 Score=166.55 Aligned_cols=146 Identities=25% Similarity=0.280 Sum_probs=117.9
Q ss_pred EEeeccccccCCCCCccceeeEEEEecCC--c--eEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHHHh
Q 018558 135 VAIACKMVGGGSDGSLDLCGRVCIIDEYE--N--IIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDFLC 210 (354)
Q Consensus 135 vaiD~Ettg~~~~~~~~~i~~i~vv~~~g--~--~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~i~ 210 (354)
|++|+||||..+ ...+|++++++..++ + ..|+.||+|..+++++.+.+||||++++++++++.+++.+|.+|+
T Consensus 1 v~~D~Ettg~~~--~~~~iiei~~v~~~~~~~~~~~~~~~i~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~l- 77 (159)
T cd06127 1 VVFDTETTGLDP--KKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFL- 77 (159)
T ss_pred CeEEeeCCCcCC--CCCeEEEEEEEEEECCcChhhhhheeeCcCCcCCHhheeccCCCHHHHhcCCCHHHHHHHHHHHH-
Confidence 579999998754 345667887776543 2 348999999999999999999999999999999999999999999
Q ss_pred cCCCCccccCCCCCCcEEEEechhhhhhhhccc-------CCCceeeeccccCCCccCCCCCchHHHH-HHHHhCCcCCC
Q 018558 211 NGEPMWKIRPRGSRARILVGHGLDHDLDRLQVE-------YPAIMTRDTAKYPPLMKTSKLSNSLKYL-TQAYLGYDIQI 282 (354)
Q Consensus 211 ~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~-------~~~~~~~Dt~~~~~~~~~~~~~~~L~~l-~~~~l~~~i~~ 282 (354)
.+.++||||+.||+.+|+.. .....++||..++....+....++|+.+ +. +++... .
T Consensus 78 -------------~~~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~-~~~~~~-~ 142 (159)
T cd06127 78 -------------GGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAE-RYGIPL-E 142 (159)
T ss_pred -------------CCCEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCCCcCchHHHHHH-HcCCCC-C
Confidence 67899999999999988632 2344589999877655555566788888 55 445433 3
Q ss_pred CCCChHHHHHHHHHHH
Q 018558 283 GIQDPYDDCVATMRLY 298 (354)
Q Consensus 283 ~~H~Al~DA~at~~l~ 298 (354)
.+|+|++||++|++||
T Consensus 143 ~~H~Al~Da~~t~~l~ 158 (159)
T cd06127 143 GAHRALADALATAELL 158 (159)
T ss_pred CCCCcHHHHHHHHHHh
Confidence 5899999999999998
No 42
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.86 E-value=2.4e-21 Score=190.62 Aligned_cols=174 Identities=16% Similarity=0.092 Sum_probs=124.1
Q ss_pred CCCceEEeeccccccCCCC-CccceeeEEEEec---CCceE--EeeeecCCc--cccCceeeecCCChhhhcCCCCHHHH
Q 018558 130 RDPQVVAIACKMVGGGSDG-SLDLCGRVCIIDE---YENII--FHAYVKPPI--PVTSYRYETTGIRPEHLRDAIPLKQV 201 (354)
Q Consensus 130 ~~~~~vaiD~Ettg~~~~~-~~~~i~~i~vv~~---~g~~i--~~~~v~P~~--~i~~~~~~itGIt~~~l~~ap~~~~v 201 (354)
.-..|++||+||||..+.. ..++|+++++|.. +|+++ |.+||+|.. +|++++++|||||++||++||+|.+|
T Consensus 54 ~~d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap~F~eV 133 (582)
T PTZ00315 54 PFDAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFPVV 133 (582)
T ss_pred CCCeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCCCHHHH
Confidence 3468999999999975432 2457788877764 55554 899999986 69999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhh-hhc--------ccCC--Cceeeecc-ccCCCcc---------
Q 018558 202 QRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLD-RLQ--------VEYP--AIMTRDTA-KYPPLMK--------- 260 (354)
Q Consensus 202 ~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~-~L~--------~~~~--~~~~~Dt~-~~~~~~~--------- 260 (354)
+++|.+|+.+.. + ......+..+|+||..||+. +|. ...+ ...++|.. .+.....
T Consensus 134 l~ef~~fL~~~~--~--~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p~~~~~~~~ 209 (582)
T PTZ00315 134 YCEALQFLAEAG--L--GDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFGNGSGCGGG 209 (582)
T ss_pred HHHHHHHHhccc--c--ccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCccccccccc
Confidence 999999992100 0 00001234799999999995 662 1112 22245542 2222221
Q ss_pred --CCCCCchHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHHhhhhc
Q 018558 261 --TSKLSNSLKYLTQAYLGYDIQIGIQDPYDDCVATMRLYMRMKSQAHKR 308 (354)
Q Consensus 261 --~~~~~~~L~~l~~~~l~~~i~~~~H~Al~DA~at~~l~~~~~~~~~~~ 308 (354)
....+++|..+++. +|+.+.+.+|+|++||++||+||.+|.++..-+
T Consensus 210 ~~~~~~~~~L~~al~~-lgL~~eGr~HrAlDDA~ntA~L~~~Ll~~g~~~ 258 (582)
T PTZ00315 210 ATPPLGPSDMPDMLQM-LGLPLQGRHHSGIDDCRNIAAVLCELLRRGLVI 258 (582)
T ss_pred cccccCCcCHHHHHHH-CCCCCCCCCcCcHHHHHHHHHHHHHHHHcCCEE
Confidence 12346899999885 566655558999999999999999999877553
No 43
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.86 E-value=1.7e-21 Score=177.28 Aligned_cols=156 Identities=25% Similarity=0.318 Sum_probs=125.5
Q ss_pred CceEEeeccccccCCCCCccceeeEEEEecC-CceE---EeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHH
Q 018558 132 PQVVAIACKMVGGGSDGSLDLCGRVCIIDEY-ENII---FHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQD 207 (354)
Q Consensus 132 ~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~-g~~i---~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~ 207 (354)
.+++++|+||||..+ ....|++|++|... +.++ |+.||+|..+|++.++++||||++||+++|.|.++.+++.+
T Consensus 13 ~~~vv~D~ETtg~~~--~~~~iieIgav~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~~~~ 90 (243)
T COG0847 13 TRFVVIDLETTGLNP--KKDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPEFLD 90 (243)
T ss_pred CcEEEEecccCCCCC--CCCceEEEEeEEEECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHHHHH
Confidence 578999999999855 33455666666543 3332 88999999999999999999999999999999999999999
Q ss_pred HHhcCCCCccccCCCCCC-cEEEEechhhhhhhhcc-------cCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCc
Q 018558 208 FLCNGEPMWKIRPRGSRA-RILVGHGLDHDLDRLQV-------EYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYD 279 (354)
Q Consensus 208 ~i~~~~~~~~~~~~~~~~-~ilVgHn~~~Dl~~L~~-------~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~ 279 (354)
|+ ++ .++||||+.||+.+|+. ..+...++||..+.+...+...+++|+.||. ++|+.
T Consensus 91 ~i--------------~~~~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~~~L~~l~~-~~gi~ 155 (243)
T COG0847 91 FI--------------GGLRLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDALAE-RLGID 155 (243)
T ss_pred HH--------------CCCCeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCccchHHHHHH-HcCCC
Confidence 99 66 99999999999999863 2223336788877766555556789999999 45555
Q ss_pred CC-CCCCChHHHHHHHHHHHHHHHHh
Q 018558 280 IQ-IGIQDPYDDCVATMRLYMRMKSQ 304 (354)
Q Consensus 280 i~-~~~H~Al~DA~at~~l~~~~~~~ 304 (354)
.. ...|+|+.||.+++++|.++...
T Consensus 156 ~~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 156 RNPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred cCCcCCcchHHHHHHHHHHHHHHHhc
Confidence 32 23799999999999999988885
No 44
>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=99.86 E-value=5.5e-22 Score=172.74 Aligned_cols=147 Identities=22% Similarity=0.226 Sum_probs=108.6
Q ss_pred EEeeccccccCCCCCccceeeEEEEecCC--ceE--EeeeecCCc--cccCceeeecCCChhhhcC-CCCHHHHHHHHHH
Q 018558 135 VAIACKMVGGGSDGSLDLCGRVCIIDEYE--NII--FHAYVKPPI--PVTSYRYETTGIRPEHLRD-AIPLKQVQRKIQD 207 (354)
Q Consensus 135 vaiD~Ettg~~~~~~~~~i~~i~vv~~~g--~~i--~~~~v~P~~--~i~~~~~~itGIt~~~l~~-ap~~~~v~~~~~~ 207 (354)
+.+|+||||+.+. .++|++|++|..++ .++ |+++|+|.. ++++..+.+||||++||++ +|++.+++++|.+
T Consensus 1 ~~~D~ETTGl~~~--~d~Iieig~v~v~~~~~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~~~ 78 (183)
T cd06138 1 LFYDYETFGLNPS--FDQILQFAAIRTDENFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKIHR 78 (183)
T ss_pred CEEEeecCCCCCC--CCceEEEEEEEECCCCCCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHHHH
Confidence 4799999998653 34677887775433 344 888999874 5677889999999999999 8999999999999
Q ss_pred HHhcCCCCccccCCCCCCcEEEEec-hhhhhhhhcccC-------C------CceeeeccccCCCc---------cC---
Q 018558 208 FLCNGEPMWKIRPRGSRARILVGHG-LDHDLDRLQVEY-------P------AIMTRDTAKYPPLM---------KT--- 261 (354)
Q Consensus 208 ~i~~~~~~~~~~~~~~~~~ilVgHn-~~~Dl~~L~~~~-------~------~~~~~Dt~~~~~~~---------~~--- 261 (354)
|+. .++.++|||| +.||+.||+... + ....+||..+.+.. .+
T Consensus 79 ~~~------------~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~ 146 (183)
T cd06138 79 LFN------------TPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKND 146 (183)
T ss_pred HHc------------cCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCcccc
Confidence 991 1357999997 899999986311 0 11235766433211 11
Q ss_pred -CCCCchHHHHHHHHhCCcCC-CCCCChHHHHHHHHHHH
Q 018558 262 -SKLSNSLKYLTQAYLGYDIQ-IGIQDPYDDCVATMRLY 298 (354)
Q Consensus 262 -~~~~~~L~~l~~~~l~~~i~-~~~H~Al~DA~at~~l~ 298 (354)
...+++|..|+++| ++. .++|+|++||++|++|.
T Consensus 147 ~~~~~~~L~~l~~~~---gi~~~~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 147 DGKPSFKLEDLAQAN---GIEHSNAHDALSDVEATIALA 182 (183)
T ss_pred CCCcchhHHHHHHHC---CCCccccccHHHHHHHHHHHh
Confidence 12468999999976 554 45899999999999985
No 45
>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=99.85 E-value=4.5e-23 Score=174.65 Aligned_cols=148 Identities=24% Similarity=0.363 Sum_probs=110.6
Q ss_pred EEeeccccccCCCCCccceeeEEEE---ecC--CceEEeeeecCCcc--ccCceeeecCCChhhhcCCCCHHHHHHHHHH
Q 018558 135 VAIACKMVGGGSDGSLDLCGRVCII---DEY--ENIIFHAYVKPPIP--VTSYRYETTGIRPEHLRDAIPLKQVQRKIQD 207 (354)
Q Consensus 135 vaiD~Ettg~~~~~~~~~i~~i~vv---~~~--g~~i~~~~v~P~~~--i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~ 207 (354)
|++|+||||..+ ....|++|++| +.. ....|++||+|..+ ++++.+++||||+++|+++|++.+++++|.+
T Consensus 1 v~~D~Ettg~~~--~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~~~~ 78 (164)
T PF00929_consen 1 VVFDTETTGLDP--RQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDEFEE 78 (164)
T ss_dssp EEEEEEESSSTT--TTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHHHHH
T ss_pred cEEEeEcCCCCC--CCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHhhhh
Confidence 689999999865 23334455544 333 23459999999988 9999999999999999999999999999999
Q ss_pred HHhcCCCCccccCCCCCCcEEEEechhhhhhhhc--------ccCC-CceeeeccccCCCccCCCCCchHHHHHHHHhCC
Q 018558 208 FLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQ--------VEYP-AIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGY 278 (354)
Q Consensus 208 ~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~--------~~~~-~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~ 278 (354)
|+. ++.++||||..||..++. ...+ ...++|+..+..........++|+.|++.| +.
T Consensus 79 ~~~-------------~~~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~-~~ 144 (164)
T PF00929_consen 79 FLK-------------KNDILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNRKKYSLDDLAEYF-GI 144 (164)
T ss_dssp HHH-------------HHTEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHHHHHSHHHHHHHT-TS
T ss_pred hhh-------------cccccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhccccCCHHHHHHHc-CC
Confidence 991 378999999999987653 2222 223567776554333222337999999976 33
Q ss_pred cCCCCCCChHHHHHHHHHHH
Q 018558 279 DIQIGIQDPYDDCVATMRLY 298 (354)
Q Consensus 279 ~i~~~~H~Al~DA~at~~l~ 298 (354)
.....+|+|++||++|++||
T Consensus 145 ~~~~~~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 145 PFDGTAHDALDDARATAELF 164 (164)
T ss_dssp SSTSTTTSHHHHHHHHHHHH
T ss_pred CCCCCCcChHHHHHHHhCcC
Confidence 33333799999999999997
No 46
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.83 E-value=1.5e-20 Score=203.07 Aligned_cols=159 Identities=22% Similarity=0.324 Sum_probs=129.9
Q ss_pred CCceEEeeccccccCCCCCccceeeEEEEec-CCceE--EeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHH
Q 018558 131 DPQVVAIACKMVGGGSDGSLDLCGRVCIIDE-YENII--FHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQD 207 (354)
Q Consensus 131 ~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~-~g~~i--~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~ 207 (354)
...+|++|+||||+.+. .+.|++++++.. +|.++ |+.||+|..+++++++++||||++||.++|++.+++++|.+
T Consensus 418 ~~~~VVfDLETTGL~~~--~deIIEIgAV~V~~G~iie~F~~~V~P~~~I~~~~~~LTGIT~e~L~~aps~~EaL~~f~~ 495 (1437)
T PRK00448 418 DATYVVFDVETTGLSAV--YDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKE 495 (1437)
T ss_pred cCcEEEEEhhhcCCCCc--hhhhheeeeEEEeCCeEeeeEEEEECCCCCCCHHHHHHhCCCHHHHcCCCCHHHHHHHHHH
Confidence 45799999999998543 344556655543 45544 89999999999999999999999999999999999999999
Q ss_pred HHhcCCCCccccCCCCCCcEEEEechhhhhhhhc-------ccCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCcC
Q 018558 208 FLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQ-------VEYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDI 280 (354)
Q Consensus 208 ~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~-------~~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i 280 (354)
|+ ++.++||||+.||+.+|+ +..+...++||..+++...+...+++|..||+.+ |..+
T Consensus 496 fi--------------gg~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k~~kL~~LAk~l-GL~~ 560 (1437)
T PRK00448 496 FC--------------GDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKF-GVEL 560 (1437)
T ss_pred Hh--------------CCCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccccccHHHHHHHc-CCCC
Confidence 99 889999999999998873 3233344789988876666566789999999965 4444
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 281 QIGIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 281 ~~~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
. ++|||++||++|++||.++.++..+
T Consensus 561 ~-~~HrAl~DA~aTa~lf~~ll~~l~~ 586 (1437)
T PRK00448 561 E-HHHRADYDAEATAYLLIKFLKDLKE 586 (1437)
T ss_pred C-CCcChHHHHHHHHHHHHHHHHHHHH
Confidence 3 4899999999999999999887754
No 47
>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=99.80 E-value=9.6e-20 Score=157.15 Aligned_cols=148 Identities=17% Similarity=0.182 Sum_probs=101.4
Q ss_pred eEEeeccccccCCCCCccceeeEEEEecCCc--eE---EeeeecCCccccC----ceeee---cCCChhhhcCCCCHHHH
Q 018558 134 VVAIACKMVGGGSDGSLDLCGRVCIIDEYEN--II---FHAYVKPPIPVTS----YRYET---TGIRPEHLRDAIPLKQV 201 (354)
Q Consensus 134 ~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~--~i---~~~~v~P~~~i~~----~~~~i---tGIt~~~l~~ap~~~~v 201 (354)
++++|+||||+.+. .+.|++|++|..++. .+ |+.+|+|..+++. +..++ ||||+++++++|++.++
T Consensus 1 lv~iD~ETTGl~p~--~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~~v 78 (173)
T cd06135 1 LVWIDLEMTGLDPE--KDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQA 78 (173)
T ss_pred CEEEEEecCCCCCC--CCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHHHH
Confidence 47999999998653 345677777765542 22 8999999986653 44445 69999999999999999
Q ss_pred HHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcccCC------CceeeeccccCCCccCCCCCchHHHHHHHH
Q 018558 202 QRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVEYP------AIMTRDTAKYPPLMKTSKLSNSLKYLTQAY 275 (354)
Q Consensus 202 ~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~~~------~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~ 275 (354)
+.+|.+|+.+. ......++||||+.||+.||+.... ....+|+..+. .|++.+
T Consensus 79 l~~~~~f~~~~--------~~~~~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~~~l~-------------~l~~~l 137 (173)
T cd06135 79 EAELLEFIKKY--------VPKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDVSSIK-------------ELARRW 137 (173)
T ss_pred HHHHHHHHHHh--------cCCCCCceeecchhhCHHHHHHHHHHHhccCCcchhhHHHHH-------------HHHHHh
Confidence 99999999210 0002369999999999999964221 11235653221 122211
Q ss_pred hC----CcCC-CCCCChHHHHHHHHHHHHHHHHh
Q 018558 276 LG----YDIQ-IGIQDPYDDCVATMRLYMRMKSQ 304 (354)
Q Consensus 276 l~----~~i~-~~~H~Al~DA~at~~l~~~~~~~ 304 (354)
+- ..+. .+.|+|++||++|+.+|..+++.
T Consensus 138 ~p~~~~~~~~~~~~HrAl~Da~~~~~~~~~~~~~ 171 (173)
T cd06135 138 YPEIYRKAPKKKGTHRALDDIRESIAELKYYREN 171 (173)
T ss_pred CcHhhhcCCCCCCCcchHHHHHHHHHHHHHHHHH
Confidence 00 1232 34899999999999999888764
No 48
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.80 E-value=1.9e-19 Score=176.16 Aligned_cols=157 Identities=19% Similarity=0.188 Sum_probs=115.7
Q ss_pred CCceEEeeccccccCCCCCccceeeEEEEecCC--ce---EEeeeecCCcc--ccCceeeecCCChhhhcCC-CCHHHHH
Q 018558 131 DPQVVAIACKMVGGGSDGSLDLCGRVCIIDEYE--NI---IFHAYVKPPIP--VTSYRYETTGIRPEHLRDA-IPLKQVQ 202 (354)
Q Consensus 131 ~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g--~~---i~~~~v~P~~~--i~~~~~~itGIt~~~l~~a-p~~~~v~ 202 (354)
...+|++|+||||+.+. .+.|+++++|..++ .+ .+..||+|... +++..+.|||||++||+++ .+..+++
T Consensus 5 ~~~fvv~D~ETTGLdP~--~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~ 82 (476)
T PRK11779 5 QPTFLWHDYETFGANPA--LDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEFA 82 (476)
T ss_pred CCcEEEEEEECCCCCCC--CCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHHH
Confidence 45699999999998653 45677777776432 23 38899999963 4567899999999999764 4789999
Q ss_pred HHHHHHHhcCCCCccccCCCCCCcEEEEec-hhhhhhhhcccC----------------CCceeeeccccCCC------c
Q 018558 203 RKIQDFLCNGEPMWKIRPRGSRARILVGHG-LDHDLDRLQVEY----------------PAIMTRDTAKYPPL------M 259 (354)
Q Consensus 203 ~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn-~~~Dl~~L~~~~----------------~~~~~~Dt~~~~~~------~ 259 (354)
++|.+|+. .+++++|||| +.||+.||+... ....++|++.+... .
T Consensus 83 ~~i~~~l~------------~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~ 150 (476)
T PRK11779 83 ARIHAEFS------------QPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGIN 150 (476)
T ss_pred HHHHHHHh------------cCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhcccccc
Confidence 99999991 1478999997 799998875321 11224565553221 1
Q ss_pred cC----CCCCchHHHHHHHHhCCcCC-CCCCChHHHHHHHHHHHHHHHHh
Q 018558 260 KT----SKLSNSLKYLTQAYLGYDIQ-IGIQDPYDDCVATMRLYMRMKSQ 304 (354)
Q Consensus 260 ~~----~~~~~~L~~l~~~~l~~~i~-~~~H~Al~DA~at~~l~~~~~~~ 304 (354)
.+ ...+++|..|+.++ +|. .++|+|++||.||++|+.+++++
T Consensus 151 ~P~~~~g~~s~rLe~L~~~~---gI~~~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 151 WPENEDGLPSFKLEHLTKAN---GIEHENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CcccccCCCCCcHHHHHHHc---CCCCCCCCCcHHHHHHHHHHHHHHHHh
Confidence 11 23568999999987 665 45899999999999999888865
No 49
>PRK05359 oligoribonuclease; Provisional
Probab=99.78 E-value=4.5e-19 Score=153.72 Aligned_cols=153 Identities=13% Similarity=0.129 Sum_probs=108.3
Q ss_pred CceEEeeccccccCCCCCccceeeEEEEecCCc--eE---EeeeecCCcc----ccCceeeec---CCChhhhcCCCCHH
Q 018558 132 PQVVAIACKMVGGGSDGSLDLCGRVCIIDEYEN--II---FHAYVKPPIP----VTSYRYETT---GIRPEHLRDAIPLK 199 (354)
Q Consensus 132 ~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~--~i---~~~~v~P~~~----i~~~~~~it---GIt~~~l~~ap~~~ 199 (354)
.++|++|+||||+++. .+.|.+|++|..++. ++ |..+|+|... ++++++.+| |||+++++++|++.
T Consensus 3 ~~~vvlD~ETTGLdp~--~d~IieIgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~~~ 80 (181)
T PRK05359 3 DNLIWIDLEMTGLDPE--RDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVSEA 80 (181)
T ss_pred CcEEEEEeecCCCCCC--CCeEEEEEEEEEcCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCCHH
Confidence 4699999999998664 455677777765442 33 7889999865 467788877 99999999999999
Q ss_pred HHHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcccCC------CceeeeccccCCCccCCCCCchHHHHHH
Q 018558 200 QVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVEYP------AIMTRDTAKYPPLMKTSKLSNSLKYLTQ 273 (354)
Q Consensus 200 ~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~~~------~~~~~Dt~~~~~~~~~~~~~~~L~~l~~ 273 (354)
+++++|++|+.. ....++.+|||||+.||+.||+...+ ...++|++.+. .|++
T Consensus 81 e~~~~~l~fl~~--------~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~tl~-------------~l~r 139 (181)
T PRK05359 81 EAEAQTLEFLKQ--------WVPAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLDVSTLK-------------ELAR 139 (181)
T ss_pred HHHHHHHHHHHH--------hcCCCCCceeecchhhCHHHHHHHHHHhcccCCCcccchhHHH-------------HHHH
Confidence 999999999910 00013578999999999999974321 12245643221 1222
Q ss_pred HHhC---CcCC-CCCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 274 AYLG---YDIQ-IGIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 274 ~~l~---~~i~-~~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
.++. .++. .+.|||++||+++.+.|..+++....
T Consensus 140 ~~~P~~~~~~~~~~~HRal~D~~~s~~~~~~~~~~~~~ 177 (181)
T PRK05359 140 RWKPEILNGFKKQGTHRALADIRESIAELKYYREHFFK 177 (181)
T ss_pred HhChhhhhCCCCcCCcccHHHHHHHHHHHHHHHHHhcc
Confidence 1110 1443 45899999999999999999887743
No 50
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=99.72 E-value=3.1e-18 Score=171.25 Aligned_cols=164 Identities=26% Similarity=0.386 Sum_probs=135.1
Q ss_pred CCCCCCCceEEeeccccccCC-------CC-------CccceeeEEEEecCCc---e-EEeeeecCCccccCceeeecCC
Q 018558 126 NTHTRDPQVVAIACKMVGGGS-------DG-------SLDLCGRVCIIDEYEN---I-IFHAYVKPPIPVTSYRYETTGI 187 (354)
Q Consensus 126 ~~~~~~~~~vaiD~Ettg~~~-------~~-------~~~~i~~i~vv~~~g~---~-i~~~~v~P~~~i~~~~~~itGI 187 (354)
+.++.++..|++|-|.+-+.. ++ ....+++|++|+.+|. + ..|.||.-..+|.||.|+++||
T Consensus 904 dEmPk~g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msvARiScvRGeGp~eGiPFiDDYv~T~d~VvDYLTqySGI 983 (1118)
T KOG1275|consen 904 DEMPKSGDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSVARISCVRGEGPNEGIPFIDDYVSTDDKVVDYLTQYSGI 983 (1118)
T ss_pred cccCCCCceeeeehhheecchHHhccccCCceeEeccccceeEEEEEEcccCCCCCCccccceecchhHHHHHHHHhcCC
Confidence 345667889999999885532 22 1226789999987742 2 3788999999999999999999
Q ss_pred ChhhhcCC------CCHHHHHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcccCCCceeeeccccCCCccC
Q 018558 188 RPEHLRDA------IPLKQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVEYPAIMTRDTAKYPPLMKT 261 (354)
Q Consensus 188 t~~~l~~a------p~~~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~~~~~~~~Dt~~~~~~~~~ 261 (354)
.|.||... .+.+.+..++.=++ + .|.++|||++.+|++++++..|..+++||+.++....
T Consensus 984 ~PGDLDp~~S~K~Lt~lK~~Y~Kl~~Li-~------------~GviFVGHGL~nDFrvINi~Vp~~QiiDTv~lf~~~s- 1049 (1118)
T KOG1275|consen 984 KPGDLDPTTSEKRLTTLKVLYLKLRLLI-Q------------RGVIFVGHGLQNDFRVINIHVPEEQIIDTVTLFRLGS- 1049 (1118)
T ss_pred CccccCCccCcceehhHHHHHHHHHHHH-H------------cCcEEEcccccccceEEEEecChhhheeeeEEEeccc-
Confidence 99999763 35778888887666 2 8899999999999999999999989999999886543
Q ss_pred CCCCchHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHHh
Q 018558 262 SKLSNSLKYLTQAYLGYDIQIGIQDPYDDCVATMRLYMRMKSQ 304 (354)
Q Consensus 262 ~~~~~~L~~l~~~~l~~~i~~~~H~Al~DA~at~~l~~~~~~~ 304 (354)
.+.-+|+.||.++||..||.++||+++||+.|+.||.++.+-
T Consensus 1050 -~R~LSLrfLa~~lLg~~IQ~~~HDSIeDA~taLkLYk~Yl~l 1091 (1118)
T KOG1275|consen 1050 -QRMLSLRFLAWELLGETIQMEAHDSIEDARTALKLYKKYLKL 1091 (1118)
T ss_pred -ccEEEHHHHHHHHhcchhhccccccHHHHHHHHHHHHHHHHH
Confidence 355699999999999999999999999999999999776553
No 51
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.51 E-value=3.4e-15 Score=132.53 Aligned_cols=89 Identities=27% Similarity=0.460 Sum_probs=54.4
Q ss_pred CccccccccccccCChHHHHHhhhhccccCccc-cccccccccCCcccccccc---CCCCCc--cccccccccc------
Q 018558 10 TLRNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRSFESLREHL---IGPLPK--QECKNVFNNR------ 77 (354)
Q Consensus 10 ~k~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~~~~L~~H~---~~e~p~--~~C~k~F~~~------ 77 (354)
.+-+.|+.|||.|.....|..|+++ |+ -+ +|.+|||.|.+.--|+.|+ |||||| +.|+|+|.++
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirT--H~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAH 234 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRT--HT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAH 234 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhc--cC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHH
Confidence 3446666666666666666666666 55 24 5666666666666666665 566666 3344444432
Q ss_pred ----------ccccccccCCCChhHHHHHhhcccc
Q 018558 78 ----------GCRFCLAILDGPNARRLHQERCQMV 102 (354)
Q Consensus 78 ----------~C~~C~k~f~~~~~l~~H~~~~~~~ 102 (354)
.|..|+|+|+..+.|.+|.......
T Consensus 235 mQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~C~~ 269 (279)
T KOG2462|consen 235 MQTHSDVKKHQCPRCGKSFALKSYLNKHSESACLK 269 (279)
T ss_pred HHhhcCCccccCcchhhHHHHHHHHHHhhhhcccc
Confidence 6888888888888887777655444
No 52
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.44 E-value=7.3e-14 Score=124.07 Aligned_cols=93 Identities=25% Similarity=0.474 Sum_probs=82.2
Q ss_pred CccccccccccccCChHHHHHhhhhccccC---ccc-cccccccccCCcccccccc-CCCCCc--cccccccccc-----
Q 018558 10 TLRNKCAACFRQFNRLEHLVEHMRTSYHSV---HEP-VCGICKKHCRSFESLREHL-IGPLPK--QECKNVFNNR----- 77 (354)
Q Consensus 10 ~k~~~C~~Cgk~f~~~~~L~~H~~~~~H~~---~k~-~C~~C~k~f~~~~~L~~H~-~~e~p~--~~C~k~F~~~----- 77 (354)
...|+|.+|||.+...++|.+|+++ |.. .+. .|..|+|.|.+...|+.|+ |...|+ ..|||.|...
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~--H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQG 205 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQT--HRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQG 205 (279)
T ss_pred CCceeccccccccccccccchhhcc--cccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhc
Confidence 3459999999999999999999999 864 333 8999999999999999999 888888 8899999965
Q ss_pred -----------ccccccccCCCChhHHHHHhhccccCC
Q 018558 78 -----------GCRFCLAILDGPNARRLHQERCQMVSS 104 (354)
Q Consensus 78 -----------~C~~C~k~f~~~~~l~~H~~~~~~~~~ 104 (354)
.|..|+|+|...+||..||+||.-...
T Consensus 206 HiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~ 243 (279)
T KOG2462|consen 206 HIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKK 243 (279)
T ss_pred ccccccCCCCccCCcccchhcchHHHHHHHHhhcCCcc
Confidence 599999999999999999999965543
No 53
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.23 E-value=2e-12 Score=127.23 Aligned_cols=82 Identities=27% Similarity=0.435 Sum_probs=76.7
Q ss_pred ccccccccccccCChHHHHHhhhhccccCccc-cccccccccCCcccccccc---CCCCCcccccccccccccccccccC
Q 018558 11 LRNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRSFESLREHL---IGPLPKQECKNVFNNRGCRFCLAIL 86 (354)
Q Consensus 11 k~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~~~~L~~H~---~~e~p~~~C~k~F~~~~C~~C~k~f 86 (354)
-+|.|..|+|.|...++|.+|.-- |+|.+| +|.+|.|.|.++.+|..|+ .||||| .|..|+|.|
T Consensus 893 gmyaCDqCDK~FqKqSSLaRHKYE--HsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPf----------QCdKClKRF 960 (1007)
T KOG3623|consen 893 GMYACDQCDKAFQKQSSLARHKYE--HSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPF----------QCDKCLKRF 960 (1007)
T ss_pred ccchHHHHHHHHHhhHHHHHhhhh--hcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcc----------hhhhhhhhc
Confidence 469999999999999999999999 999999 9999999999999999999 899999 999999999
Q ss_pred CCChhHHHHHhhccccCCC
Q 018558 87 DGPNARRLHQERCQMVSSA 105 (354)
Q Consensus 87 ~~~~~l~~H~~~~~~~~~~ 105 (354)
++++++.+|| -|.++...
T Consensus 961 SHSGSYSQHM-NHRYSYCK 978 (1007)
T KOG3623|consen 961 SHSGSYSQHM-NHRYSYCK 978 (1007)
T ss_pred ccccchHhhh-ccchhccc
Confidence 9999999999 46666443
No 54
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.16 E-value=9e-12 Score=102.76 Aligned_cols=165 Identities=14% Similarity=0.097 Sum_probs=106.2
Q ss_pred ceEEeeccccccCCC--CCccceeeEE--EEec-CCceE--EeeeecCCc-c-ccCceeeecCCChhhhcCCCCHHHHHH
Q 018558 133 QVVAIACKMVGGGSD--GSLDLCGRVC--IIDE-YENII--FHAYVKPPI-P-VTSYRYETTGIRPEHLRDAIPLKQVQR 203 (354)
Q Consensus 133 ~~vaiD~Ettg~~~~--~~~~~i~~i~--vv~~-~g~~i--~~~~v~P~~-~-i~~~~~~itGIt~~~l~~ap~~~~v~~ 203 (354)
...+||+|.|.-... ....+|+++. +|+. +.+++ |.+||+|.. | ++++...+|||+...|.+||-|+.|++
T Consensus 5 ~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~apifs~v~E 84 (210)
T COG5018 5 SLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAPIFSMVFE 84 (210)
T ss_pred eEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhccccchHHHHHH
Confidence 468999999832111 1122333332 3332 33333 889999984 3 789999999999999999999999999
Q ss_pred HHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcc-------c-C-CCceeeeccccCCCccCCCCCchHHHHHHH
Q 018558 204 KIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQV-------E-Y-PAIMTRDTAKYPPLMKTSKLSNSLKYLTQA 274 (354)
Q Consensus 204 ~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~-------~-~-~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~ 274 (354)
+|..+++.-++ +-..-.+-+-..|++.|.. . . .+...+|....|.-....+..-+|....+
T Consensus 85 ~f~r~L~~h~P---------r~~~~wa~wG~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~pr~tgln~ale- 154 (210)
T COG5018 85 DFIRKLNEHDP---------RKNSTWATWGNMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGDPRLTGLNKALE- 154 (210)
T ss_pred HHHHHHHhcCc---------ccCCccccccchhHHHHHHHHHhcCCCCccccCccchHHHHHHHHhcCCccccHHHHHH-
Confidence 99999932121 1112334455678877742 1 0 12224566554432222223346666444
Q ss_pred HhCCcCCCCCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 275 YLGYDIQIGIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 275 ~l~~~i~~~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
..|..+++.+|+|++||+.+++|+.++...-..
T Consensus 155 ~~G~sf~G~~HraldDArn~~rl~klv~~~~~~ 187 (210)
T COG5018 155 EYGDSFTGTHHRALDDARNAYRLFKLVEQDKQY 187 (210)
T ss_pred HhccccCCchhhhHHHHHHHHHHHHHHcchhhh
Confidence 557777777999999999999999887765533
No 55
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=99.13 E-value=5.8e-11 Score=104.32 Aligned_cols=166 Identities=17% Similarity=0.169 Sum_probs=107.4
Q ss_pred ceEEeeccccccCCC--CCccceeeEEEEe---cC-Cce--EEeeeecCCc--cccCceeeecCCChhhhcCCCCHHHHH
Q 018558 133 QVVAIACKMVGGGSD--GSLDLCGRVCIID---EY-ENI--IFHAYVKPPI--PVTSYRYETTGIRPEHLRDAIPLKQVQ 202 (354)
Q Consensus 133 ~~vaiD~Ettg~~~~--~~~~~i~~i~vv~---~~-g~~--i~~~~v~P~~--~i~~~~~~itGIt~~~l~~ap~~~~v~ 202 (354)
-++++|+|+|-.... .-..+|++.-+|- .+ +.+ .|++||+|.. .+++|.+.+|||..++|..||+|.+|+
T Consensus 57 YLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~~f~~vl 136 (280)
T KOG0542|consen 57 YLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAPTFPQVL 136 (280)
T ss_pred eEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCCCHHHHH
Confidence 468999999943221 1224666666662 22 222 3899999984 378999999999999999999999999
Q ss_pred HHHHHHHhcCCCCccccCCCC--CCcEEEEechhhhhh-hh-------cccCCC--ceeeeccccCCCccCCCCCchHHH
Q 018558 203 RKIQDFLCNGEPMWKIRPRGS--RARILVGHGLDHDLD-RL-------QVEYPA--IMTRDTAKYPPLMKTSKLSNSLKY 270 (354)
Q Consensus 203 ~~~~~~i~~~~~~~~~~~~~~--~~~ilVgHn~~~Dl~-~L-------~~~~~~--~~~~Dt~~~~~~~~~~~~~~~L~~ 270 (354)
.+|..|+.+ ..... ++--+|- .-+-||. +| ++..|. ..+||....|.........-++..
T Consensus 137 ~~f~~Wlr~-------~~~~~k~~~~Afvt-dg~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it~ 208 (280)
T KOG0542|consen 137 SEFDSWLRK-------DSLGDKNGKFAFVT-DGDWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNITG 208 (280)
T ss_pred HHHHHHHHH-------hhcccccCceEEEe-CchhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCHHH
Confidence 999999932 11111 2233332 2334442 22 333332 236666554432211213345666
Q ss_pred HHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 271 LTQAYLGYDIQIGIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 271 l~~~~l~~~i~~~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
+-+ ++|..+++.+|++++||+..+.|..+|.+.+.+
T Consensus 209 mLe-~~gL~f~Gr~HsGiDDa~Nia~I~~kM~~dg~~ 244 (280)
T KOG0542|consen 209 MLE-HYGLQFEGRAHSGIDDARNIARIAQKMIRDGAE 244 (280)
T ss_pred HHH-HhCCcccCCcccCchhHHHHHHHHHHHHhCCcE
Confidence 544 556666677999999999999999999987755
No 56
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.11 E-value=1.3e-11 Score=104.75 Aligned_cols=82 Identities=23% Similarity=0.427 Sum_probs=75.7
Q ss_pred CCCCccccccccccccCChHHHHHhhhhccccCccc-cccccccccCCcccccccc---CCCCCcccccccccccccccc
Q 018558 7 SSETLRNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRSFESLREHL---IGPLPKQECKNVFNNRGCRFC 82 (354)
Q Consensus 7 ~~~~k~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~~~~L~~H~---~~e~p~~~C~k~F~~~~C~~C 82 (354)
+++...|.|..|||.|....-|.+|+++ |+..+. .|..|||.|...-.|++|+ +|.+|| +|..|
T Consensus 112 ssd~d~ftCrvCgK~F~lQRmlnrh~kc--h~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpy----------kc~~c 179 (267)
T KOG3576|consen 112 SSDQDSFTCRVCGKKFGLQRMLNRHLKC--HSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPY----------KCSLC 179 (267)
T ss_pred CCCCCeeeeehhhhhhhHHHHHHHHhhh--ccHHHHHHHhhccCcccchhhhhhhhccccCcccc----------chhhh
Confidence 3445679999999999999999999999 999888 9999999999999999999 899999 99999
Q ss_pred cccCCCChhHHHHHhhcc
Q 018558 83 LAILDGPNARRLHQERCQ 100 (354)
Q Consensus 83 ~k~f~~~~~l~~H~~~~~ 100 (354)
+|+|.+..+|..|.++.+
T Consensus 180 ~kaftqrcsleshl~kvh 197 (267)
T KOG3576|consen 180 EKAFTQRCSLESHLKKVH 197 (267)
T ss_pred hHHHHhhccHHHHHHHHc
Confidence 999999999999987654
No 57
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=98.99 E-value=3.6e-09 Score=93.24 Aligned_cols=126 Identities=16% Similarity=0.066 Sum_probs=86.9
Q ss_pred eEEeeccccccCC--CCCccceeeEEEEec-CCceE-EeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHHH
Q 018558 134 VVAIACKMVGGGS--DGSLDLCGRVCIIDE-YENII-FHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDFL 209 (354)
Q Consensus 134 ~vaiD~Ettg~~~--~~~~~~i~~i~vv~~-~g~~i-~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~i 209 (354)
++++|+||+|... +...++|..|+++.. +|... +.....+.....+ ||+..++...++..+++..|++++
T Consensus 1 v~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~~~g~~~~~~~~~~~~~~~~~------~i~~~~v~~~~~E~~lL~~f~~~i 74 (199)
T cd05160 1 VLSFDIETTPPVGGPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDDIE------FIDGIEVEYFADEKELLKRFFDII 74 (199)
T ss_pred CccEEEeecCCCCCcCCCCCCEEEEEEEEeeCCceeeEEEeecccCCcCC------CCCCceEEEeCCHHHHHHHHHHHH
Confidence 3689999998622 334567888888876 66543 2222223221111 899999999999999999999999
Q ss_pred hcCCCCccccCCCCCC---cEEEEech-hhhhhhhc-------ccCC----------------------CceeeeccccC
Q 018558 210 CNGEPMWKIRPRGSRA---RILVGHGL-DHDLDRLQ-------VEYP----------------------AIMTRDTAKYP 256 (354)
Q Consensus 210 ~~~~~~~~~~~~~~~~---~ilVgHn~-~~Dl~~L~-------~~~~----------------------~~~~~Dt~~~~ 256 (354)
++ .++||||+ .||+.+|. +... ...++|+..+.
T Consensus 75 --------------~~~dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~ 140 (199)
T cd05160 75 --------------REYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAY 140 (199)
T ss_pred --------------HhcCCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHH
Confidence 44 59999999 89998763 2220 12357777665
Q ss_pred CCccCCCCCchHHHHHHHHhCCcC
Q 018558 257 PLMKTSKLSNSLKYLTQAYLGYDI 280 (354)
Q Consensus 257 ~~~~~~~~~~~L~~l~~~~l~~~i 280 (354)
+.... ..+++|+.+|+.+|+.+-
T Consensus 141 r~~~~-l~sy~L~~v~~~~l~~~k 163 (199)
T cd05160 141 KRDFK-LKSYTLDAVAEELLGEGK 163 (199)
T ss_pred HHhcC-cccCCHHHHHHHHhCCCC
Confidence 43322 467999999999987643
No 58
>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=98.71 E-value=1.7e-07 Score=81.82 Aligned_cols=144 Identities=19% Similarity=0.205 Sum_probs=94.2
Q ss_pred CCceEEeeccccccCCCCCccceeeEEEEecCCceEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHHHh
Q 018558 131 DPQVVAIACKMVGGGSDGSLDLCGRVCIIDEYENIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDFLC 210 (354)
Q Consensus 131 ~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~i~ 210 (354)
...++++|+|++|..+.. ..|..+++....+..+| + | +.+ +. ..+++++++++..|.+++.
T Consensus 4 ~~~~~a~d~e~~~~~~~~--~~i~~l~~~~~~~~~~~---~-~---~~~--~~--------~~~~~~~~~~~~~l~~~l~ 64 (193)
T cd06139 4 KAKVFAFDTETTSLDPMQ--AELVGISFAVEPGEAYY---I-P---LGH--DY--------GGEQLPREEVLAALKPLLE 64 (193)
T ss_pred cCCeEEEEeecCCCCcCC--CeEEEEEEEcCCCCEEE---E-e---cCC--Cc--------cccCCCHHHHHHHHHHHHh
Confidence 346799999999764322 23455555544443222 1 1 110 00 1145678889999999992
Q ss_pred cCCCCccccCCCCCCcEEEEechhhhhhhhcc---cCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCcC-C-----
Q 018558 211 NGEPMWKIRPRGSRARILVGHGLDHDLDRLQV---EYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDI-Q----- 281 (354)
Q Consensus 211 ~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~---~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i-~----- 281 (354)
+.+..+||||++||+.+|.. ..+ ..+.||..+..+..+...+++|+.++..|++..+ .
T Consensus 65 ------------~~~~~~v~hn~k~d~~~l~~~gi~~~-~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~ 131 (193)
T cd06139 65 ------------DPSIKKVGQNLKFDLHVLANHGIELR-GPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLV 131 (193)
T ss_pred ------------CCCCcEEeeccHHHHHHHHHCCCCCC-CCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHHHc
Confidence 12348999999999999853 222 2367998877666554424699999999987542 1
Q ss_pred ----------C-----CCCChHHHHHHHHHHHHHHHHhhh
Q 018558 282 ----------I-----GIQDPYDDCVATMRLYMRMKSQAH 306 (354)
Q Consensus 282 ----------~-----~~H~Al~DA~at~~l~~~~~~~~~ 306 (354)
. ..|.|..||.++.+|+..+.++..
T Consensus 132 ~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~ 171 (193)
T cd06139 132 GKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLK 171 (193)
T ss_pred CCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 0 124588899999999999888773
No 59
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=98.71 E-value=6.9e-08 Score=89.80 Aligned_cols=156 Identities=21% Similarity=0.202 Sum_probs=104.7
Q ss_pred CCceEEeeccccccCCCCCccceeeEEEEec--CCceE---EeeeecCCcc-cc-CceeeecCCChhhhcC-CCCHHHHH
Q 018558 131 DPQVVAIACKMVGGGSDGSLDLCGRVCIIDE--YENII---FHAYVKPPIP-VT-SYRYETTGIRPEHLRD-AIPLKQVQ 202 (354)
Q Consensus 131 ~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~--~g~~i---~~~~v~P~~~-i~-~~~~~itGIt~~~l~~-ap~~~~v~ 202 (354)
...+...|.||.|..|. .+..++.+-|.. +-.+| ..-|++|... +| +...=||||||..... +.+-.+..
T Consensus 8 ~~tF~~yDYETfG~~Pa--~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~F~ 85 (475)
T COG2925 8 QPTFLFYDYETFGVHPA--LDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAAFA 85 (475)
T ss_pred CCcEEEEehhhcCCCcc--cccchhhheeeccccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHHHH
Confidence 44689999999998654 444566666643 22333 6678999865 44 5688899999998854 66666677
Q ss_pred HHHHHHHhcCCCCccccCCCCCCcEEEEec-hhhhhhhhcc--------------cC--CCceeeeccccCCCccC----
Q 018558 203 RKIQDFLCNGEPMWKIRPRGSRARILVGHG-LDHDLDRLQV--------------EY--PAIMTRDTAKYPPLMKT---- 261 (354)
Q Consensus 203 ~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn-~~~Dl~~L~~--------------~~--~~~~~~Dt~~~~~~~~~---- 261 (354)
..|..-+ .-.++.+||+| +.||=.+-+. .+ ....++|.+...-..++
T Consensus 86 ~~I~~~l------------s~P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~ 153 (475)
T COG2925 86 ARIHAEL------------TQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGIN 153 (475)
T ss_pred HHHHHHh------------CCCCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcccCC
Confidence 7776666 23789999986 7998655431 11 11223454432111111
Q ss_pred ------CCCCchHHHHHHHHhCCcCCCC-CCChHHHHHHHHHHHHHHHH
Q 018558 262 ------SKLSNSLKYLTQAYLGYDIQIG-IQDPYDDCVATMRLYMRMKS 303 (354)
Q Consensus 262 ------~~~~~~L~~l~~~~l~~~i~~~-~H~Al~DA~at~~l~~~~~~ 303 (354)
...+.+|..|++.- +|+.+ +|+|++|+.||..+-++.+.
T Consensus 154 Wp~n~dG~pSFkLEhLt~AN---gieH~nAHdAmsDVyATIamAklvk~ 199 (475)
T COG2925 154 WPENDDGLPSFKLEHLTKAN---GIEHSNAHDAMSDVYATIAMAKLVKT 199 (475)
T ss_pred CCcCCCCCcchhhHHHhhcc---ccccchhhHHHHHHHHHHHHHHHHHh
Confidence 23477899998876 77744 99999999999998776664
No 60
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.67 E-value=6.6e-09 Score=102.90 Aligned_cols=74 Identities=26% Similarity=0.403 Sum_probs=67.1
Q ss_pred ccccccccccccCChHHHHHhhhhccccC-------------ccc-cccccccccCCcccccccc---CCCCCccccccc
Q 018558 11 LRNKCAACFRQFNRLEHLVEHMRTSYHSV-------------HEP-VCGICKKHCRSFESLREHL---IGPLPKQECKNV 73 (354)
Q Consensus 11 k~~~C~~Cgk~f~~~~~L~~H~~~~~H~~-------------~k~-~C~~C~k~f~~~~~L~~H~---~~e~p~~~C~k~ 73 (354)
-.|.|..|..+|..+..|.+|+.. |.. -+. +|.+|||.|..+.+|+.|+ .|||||
T Consensus 239 ~nfsC~lCsytFAyRtQLErhm~~--hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPf------ 310 (1007)
T KOG3623|consen 239 PNFSCMLCSYTFAYRTQLERHMQL--HKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPF------ 310 (1007)
T ss_pred CCCcchhhhhhhhhHHHHHHHHHh--hcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCc------
Confidence 348899999999999999999988 753 133 8999999999999999998 899999
Q ss_pred ccccccccccccCCCChhHHHHH
Q 018558 74 FNNRGCRFCLAILDGPNARRLHQ 96 (354)
Q Consensus 74 F~~~~C~~C~k~f~~~~~l~~H~ 96 (354)
.|+-|+|.|++++++..||
T Consensus 311 ----eCpnCkKRFSHSGSySSHm 329 (1007)
T KOG3623|consen 311 ----ECPNCKKRFSHSGSYSSHM 329 (1007)
T ss_pred ----CCcccccccccCCcccccc
Confidence 9999999999999999997
No 61
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.66 E-value=5.4e-09 Score=88.92 Aligned_cols=92 Identities=27% Similarity=0.355 Sum_probs=71.5
Q ss_pred CCCccccccccccccCChHHHHHhhhhccccCccc-cccccccccCCcccccccc---CCCC-Ccccccccccccccccc
Q 018558 8 SETLRNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRSFESLREHL---IGPL-PKQECKNVFNNRGCRFC 82 (354)
Q Consensus 8 ~~~k~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~~~~L~~H~---~~e~-p~~~C~k~F~~~~C~~C 82 (354)
+..+.|-|..|||.|+....|++|+++ |+|.+| +|..|+|.|.+.-+|..|. .|.. .|..=.+.-+-..|+.|
T Consensus 141 ~~vkr~lct~cgkgfndtfdlkrh~rt--htgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedc 218 (267)
T KOG3576|consen 141 SDVKRHLCTFCGKGFNDTFDLKRHTRT--HTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDC 218 (267)
T ss_pred cHHHHHHHhhccCcccchhhhhhhhcc--ccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeeccc
Confidence 345779999999999999999999999 999999 9999999999999999997 2211 11000000001179999
Q ss_pred cccCCCChhHHHHHhhccc
Q 018558 83 LAILDGPNARRLHQERCQM 101 (354)
Q Consensus 83 ~k~f~~~~~l~~H~~~~~~ 101 (354)
|..-.....+..|.+.++-
T Consensus 219 g~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 219 GYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred CCCCCChhHHHHHHHhcCC
Confidence 9999999999999977653
No 62
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.66 E-value=1.1e-08 Score=102.86 Aligned_cols=90 Identities=23% Similarity=0.378 Sum_probs=76.1
Q ss_pred CCCCCCccccccccccccCChHHHHHhhhhccccCccc-cccccccccCCcccccccc--CCCCCc-ccccccccccccc
Q 018558 5 TESSETLRNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRSFESLREHL--IGPLPK-QECKNVFNNRGCR 80 (354)
Q Consensus 5 ~~~~~~k~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~~~~L~~H~--~~e~p~-~~C~k~F~~~~C~ 80 (354)
.++...-|.+|-.|-++...++.|+.|.++ |+||+| +|.+||+.|..+.||+.|+ ...+|- ..| ..|+
T Consensus 598 ~~~~~TdPNqCiiC~rVlSC~saLqmHyrt--HtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q------~ScP 669 (958)
T KOG1074|consen 598 SENKRTDPNQCIICLRVLSCPSALQMHYRT--HTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQ------FSCP 669 (958)
T ss_pred cccccCCccceeeeeecccchhhhhhhhhc--ccCcCccccccccchhccccchhhcccccccCcccccc------ccCC
Confidence 345556689999999999999999999999 999999 9999999999999999999 333322 111 1899
Q ss_pred ---cccccCCCChhHHHHHhhcccc
Q 018558 81 ---FCLAILDGPNARRLHQERCQMV 102 (354)
Q Consensus 81 ---~C~k~f~~~~~l~~H~~~~~~~ 102 (354)
+|-+.|...-.|.+|.+.|...
T Consensus 670 ~~~ic~~kftn~V~lpQhIriH~~~ 694 (958)
T KOG1074|consen 670 STFICQKKFTNAVTLPQHIRIHLGG 694 (958)
T ss_pred chhhhcccccccccccceEEeecCC
Confidence 9999999999999999887644
No 63
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.64 E-value=1.6e-08 Score=101.90 Aligned_cols=48 Identities=27% Similarity=0.636 Sum_probs=46.6
Q ss_pred cccccccccccCChHHHHHhhhhccccCccc-cccccccccCCcccccccc
Q 018558 12 RNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRSFESLREHL 61 (354)
Q Consensus 12 ~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~~~~L~~H~ 61 (354)
+++|..|.|.|...+.|+.|.+. |+|++| +|.+||.+|+.+.+|+.|.
T Consensus 353 khkCr~CakvfgS~SaLqiHlRS--HTGERPfqCnvCG~~FSTkGNLKvH~ 401 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRS--HTGERPFQCNVCGNRFSTKGNLKVHF 401 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhc--cCCCCCeeecccccccccccceeeee
Confidence 48999999999999999999999 999999 9999999999999999997
No 64
>PHA02768 hypothetical protein; Provisional
Probab=98.63 E-value=1.8e-08 Score=68.26 Aligned_cols=44 Identities=18% Similarity=0.375 Sum_probs=40.1
Q ss_pred cccccccccccCChHHHHHhhhhccccCccc-cccccccccCCcccccc
Q 018558 12 RNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRSFESLRE 59 (354)
Q Consensus 12 ~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~~~~L~~ 59 (354)
-|+|+.||+.|.+.++|..|+++ |+ ++ +|..|++.|...+.|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~--H~--k~~kc~~C~k~f~~~s~l~~ 49 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK--HN--TNLKLSNCKRISLRTGEYIE 49 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh--cC--CcccCCcccceecccceeEE
Confidence 48999999999999999999999 99 68 99999999998887763
No 65
>PHA00733 hypothetical protein
Probab=98.61 E-value=1.8e-08 Score=82.12 Aligned_cols=84 Identities=20% Similarity=0.226 Sum_probs=68.0
Q ss_pred CCCCCCccccccccccccCChHHHHHh------hhhccccCccc-cccccccccCCcccccccc-CCCCCcccccccccc
Q 018558 5 TESSETLRNKCAACFRQFNRLEHLVEH------MRTSYHSVHEP-VCGICKKHCRSFESLREHL-IGPLPKQECKNVFNN 76 (354)
Q Consensus 5 ~~~~~~k~~~C~~Cgk~f~~~~~L~~H------~~~~~H~~~k~-~C~~C~k~f~~~~~L~~H~-~~e~p~~~C~k~F~~ 76 (354)
......+++.|..|++.|.....|..| +. +.+.+| .|+.|++.|.+..+|..|+ ..+.+|
T Consensus 33 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~---~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~--------- 100 (128)
T PHA00733 33 SLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLT---SKAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSK--------- 100 (128)
T ss_pred cCChhhhhHHHHHHhhhccChhhhcchHHHHhhcc---cCCCCCccCCCCCCcCCCHHHHHHHHhcCCcCc---------
Confidence 334556789999999988877665554 33 334778 9999999999999999998 446778
Q ss_pred cccccccccCCCChhHHHHHhhccc
Q 018558 77 RGCRFCLAILDGPNARRLHQERCQM 101 (354)
Q Consensus 77 ~~C~~C~k~f~~~~~l~~H~~~~~~ 101 (354)
.|..|++.|....+|..|+...+.
T Consensus 101 -~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 101 -VCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred -cCCCCCCccCCHHHHHHHHHHhcC
Confidence 999999999999999999876553
No 66
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=98.59 E-value=7.1e-07 Score=76.46 Aligned_cols=136 Identities=24% Similarity=0.273 Sum_probs=82.3
Q ss_pred ceEEeeccccccCCCCCccceeeEEEEecCCceEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHHHhcC
Q 018558 133 QVVAIACKMVGGGSDGSLDLCGRVCIIDEYENIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDFLCNG 212 (354)
Q Consensus 133 ~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~i~~~ 212 (354)
+++++|+|+++.........++.+.+-...+..++ .|-. ..... +.+.|.+++.+
T Consensus 21 ~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~----~~~~-----------~~~~~---------~~~~l~~ll~~- 75 (176)
T PF01612_consen 21 KVLAFDTETTGLDPYSYNPKIALIQLATGEGCYII----DPID-----------LGDNW---------ILDALKELLED- 75 (176)
T ss_dssp SEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEE----CGTT-----------STTTT---------HHHHHHHHHTT-
T ss_pred CeEEEEEEECCCCccccCCeEEEEEEecCCCceee----eecc-----------ccccc---------hHHHHHHHHhC-
Confidence 48999999998765333333333333333221111 1111 00000 77888888832
Q ss_pred CCCccccCCCCCCcEEEEechhhhhhhhccc--CCCceeeeccccCCCccCCCCCchHHHHHHHHhC-CcCC----CC--
Q 018558 213 EPMWKIRPRGSRARILVGHGLDHDLDRLQVE--YPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLG-YDIQ----IG-- 283 (354)
Q Consensus 213 ~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~--~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~-~~i~----~~-- 283 (354)
.+.+.||||+.||+.+|... .....+.||........+. .+++|+.|+..++| .... .+
T Consensus 76 -----------~~i~kv~~n~~~D~~~L~~~~~i~~~~~~D~~l~~~~l~~~-~~~~L~~L~~~~l~~~~~~~~~~~~~~ 143 (176)
T PF01612_consen 76 -----------PNIIKVGHNAKFDLKWLYRSFGIDLKNVFDTMLAAYLLDPT-RSYSLKDLAEEYLGNIDLDKKEQMSDW 143 (176)
T ss_dssp -----------TTSEEEESSHHHHHHHHHHHHTS--SSEEEHHHHHHHTTTS-TTSSHHHHHHHHHSEEE-GHCCTTSST
T ss_pred -----------CCccEEEEEEechHHHHHHHhccccCCccchhhhhhccccc-ccccHHHHHHHHhhhccCcHHHhhccC
Confidence 56799999999999888541 1222267995443333222 23899999999999 3332 11
Q ss_pred C----------CChHHHHHHHHHHHHHHHHhh
Q 018558 284 I----------QDPYDDCVATMRLYMRMKSQA 305 (354)
Q Consensus 284 ~----------H~Al~DA~at~~l~~~~~~~~ 305 (354)
. .-|..||..+.+||..+..+.
T Consensus 144 ~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l 175 (176)
T PF01612_consen 144 RKARPLSEEQIEYAAQDAVVTFRLYEKLKPQL 175 (176)
T ss_dssp TTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred CcCCCChHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 1 125669999999999988765
No 67
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=98.59 E-value=1.1e-07 Score=79.20 Aligned_cols=155 Identities=15% Similarity=0.180 Sum_probs=105.4
Q ss_pred CCCceEEeeccccccCCCCCccceeeEEEEecCCc--eE---EeeeecCCcc----ccCceeee---cCCChhhhcCCCC
Q 018558 130 RDPQVVAIACKMVGGGSDGSLDLCGRVCIIDEYEN--II---FHAYVKPPIP----VTSYRYET---TGIRPEHLRDAIP 197 (354)
Q Consensus 130 ~~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~--~i---~~~~v~P~~~----i~~~~~~i---tGIt~~~l~~ap~ 197 (354)
-..++|-|||||||+. -..+.|.+++.+-.+|. .+ ++..|+-..+ +.+|...- +|+|..-++..-+
T Consensus 24 l~q~lVWiD~EMTGLd--vekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~t 101 (208)
T KOG3242|consen 24 LKQPLVWIDCEMTGLD--VEKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKIT 101 (208)
T ss_pred ccCceEEEeeeccccc--cccceeEEEEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhcc
Confidence 3457899999999984 44455666665544443 22 5666664433 44555543 5888888899999
Q ss_pred HHHHHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcccCC------CceeeeccccCCCccCCCCCchHHHH
Q 018558 198 LKQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVEYP------AIMTRDTAKYPPLMKTSKLSNSLKYL 271 (354)
Q Consensus 198 ~~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~~~------~~~~~Dt~~~~~~~~~~~~~~~L~~l 271 (354)
++++-.++++|+ .+..+.+..+|.|.++.-|..||....| ...++|++.+ +.|
T Consensus 102 l~~aEnevl~yi--------kk~ip~~~~~laGNSV~~DrlFl~k~mPk~~~~lhyrivDVStI-------------keL 160 (208)
T KOG3242|consen 102 LADAENEVLEYI--------KKHIPKGKCPLAGNSVYMDRLFLKKYMPKLIKHLHYRIVDVSTI-------------KEL 160 (208)
T ss_pred HHHHHHHHHHHH--------HHhCCCCCCCccCcchhhHHHHHHHHhHHHHHhcceeeeeHHHH-------------HHH
Confidence 999999999999 3444557779999999999999975433 3346776643 334
Q ss_pred HHHHhC----CcC-CCCCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 272 TQAYLG----YDI-QIGIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 272 ~~~~l~----~~i-~~~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
|+...- ..- ....|||++|.+-+..=++.+++.+..
T Consensus 161 ~~Rw~P~~~~~aPkK~~~HrAldDI~ESI~ELq~Yr~nifk 201 (208)
T KOG3242|consen 161 ARRWYPDIKARAPKKKATHRALDDIRESIKELQYYRENIFK 201 (208)
T ss_pred HHHhCchhhccCcccccccchHHHHHHHHHHHHHHHHHhcc
Confidence 443211 011 133799999999999888888877743
No 68
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=98.35 E-value=1.4e-06 Score=72.05 Aligned_cols=154 Identities=18% Similarity=0.172 Sum_probs=99.8
Q ss_pred CCceEEeeccccccCCCCCccceeeEEEEe--cCCceE---Eeeeec-CC---ccccCceeeec---CCChhhhcCCCCH
Q 018558 131 DPQVVAIACKMVGGGSDGSLDLCGRVCIID--EYENII---FHAYVK-PP---IPVTSYRYETT---GIRPEHLRDAIPL 198 (354)
Q Consensus 131 ~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~--~~g~~i---~~~~v~-P~---~~i~~~~~~it---GIt~~~l~~ap~~ 198 (354)
..+.|-|||||||+.+. .+.|++|+.+- .+-.++ .+.-|. |. ..+.+|+++.| |++..-.+..-+.
T Consensus 5 ~~nLiWIDlEMTGLd~~--~drIIEiA~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~t~ 82 (184)
T COG1949 5 KNNLIWIDLEMTGLDPE--RDRIIEIATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTVTE 82 (184)
T ss_pred CCceEEEeeeeccCCcC--cceEEEEEEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhccH
Confidence 35689999999998654 44556666543 333333 222232 22 23567777765 6777666677888
Q ss_pred HHHHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcccCCCc------eeeeccccCCCccCCCCCchHHHHH
Q 018558 199 KQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVEYPAI------MTRDTAKYPPLMKTSKLSNSLKYLT 272 (354)
Q Consensus 199 ~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~~~~~------~~~Dt~~~~~~~~~~~~~~~L~~l~ 272 (354)
.++-.++++||. +.. ..+-.++.|.++.-|-+||-...|.. ..+|++ +|+.||
T Consensus 83 ~~aE~~~l~flk------kwv--p~~~spicGNSI~qDRrFl~r~MP~Le~yfHYR~lDVS-------------TlKELa 141 (184)
T COG1949 83 AEAEAQTLDFLK------KWV--PKGVSPICGNSIAQDRRFLFRYMPKLEAYFHYRYLDVS-------------TLKELA 141 (184)
T ss_pred HHHHHHHHHHHH------HhC--CCCCCCCccchhhHHHHHHHHHhhhHHHHhhhHhhhHH-------------HHHHHH
Confidence 998888888882 222 23557999999999999997555532 133443 455555
Q ss_pred HHH----hCCcCCCCCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 273 QAY----LGYDIQIGIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 273 ~~~----l~~~i~~~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
... +..-...+.|+||+|.+-+..=++.+++.+..
T Consensus 142 ~RW~P~i~~~~~K~~~H~Al~DI~ESI~EL~~YR~~f~~ 180 (184)
T COG1949 142 RRWNPEILAGFKKGGTHRALDDIRESIAELRYYREHFLK 180 (184)
T ss_pred HhhCcHhhhccccccchhHHHHHHHHHHHHHHHHHHhcc
Confidence 542 11112245899999999999888888887744
No 69
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=98.24 E-value=1.1e-05 Score=70.85 Aligned_cols=91 Identities=18% Similarity=0.283 Sum_probs=63.7
Q ss_pred HHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcccCC--------CceeeeccccCCCccC----------C
Q 018558 201 VQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVEYP--------AIMTRDTAKYPPLMKT----------S 262 (354)
Q Consensus 201 v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~~~--------~~~~~Dt~~~~~~~~~----------~ 262 (354)
+.+.+.+++.| ++-+.|||++.+|+..|.-..+ ...++|+..++..... .
T Consensus 70 ~~~~L~~ll~d------------~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~ 137 (193)
T cd06146 70 WDRLLKRLFED------------PDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLP 137 (193)
T ss_pred HHHHHHHHhCC------------CCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccC
Confidence 34456777722 4557799999999998863221 1247899765442211 1
Q ss_pred CCCchHHHHHHHHhCCcCCCC---------------CCChHHHHHHHHHHHHHHHH
Q 018558 263 KLSNSLKYLTQAYLGYDIQIG---------------IQDPYDDCVATMRLYMRMKS 303 (354)
Q Consensus 263 ~~~~~L~~l~~~~l~~~i~~~---------------~H~Al~DA~at~~l~~~~~~ 303 (354)
...++|..|++.+||..+... -+-|..||.++..||.++.+
T Consensus 138 ~~~~sL~~l~~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~~ 193 (193)
T cd06146 138 SKTKGLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLLE 193 (193)
T ss_pred cccCCHHHHHHHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 346799999999999887632 16688999999999988753
No 70
>PRK05755 DNA polymerase I; Provisional
Probab=98.19 E-value=8.8e-06 Score=87.09 Aligned_cols=137 Identities=20% Similarity=0.200 Sum_probs=91.7
Q ss_pred CCceEEeeccccccCCCCCccceeeEEEEecCCceEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHHHh
Q 018558 131 DPQVVAIACKMVGGGSDGSLDLCGRVCIIDEYENIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDFLC 210 (354)
Q Consensus 131 ~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~i~ 210 (354)
...++++|+||+|+.+. ...|..+++-..+|... +| | +++|. .++++.|.+++.
T Consensus 314 ~~~~~a~DtEt~~l~~~--~~~i~~i~ls~~~g~~~---~i-p----------~~~i~----------~~~l~~l~~~L~ 367 (880)
T PRK05755 314 AAGLFAFDTETTSLDPM--QAELVGLSFAVEPGEAA---YI-P----------LDQLD----------REVLAALKPLLE 367 (880)
T ss_pred ccCeEEEEeccCCCCcc--cccEEEEEEEeCCCcEE---EE-e----------ccccc----------HHHHHHHHHHHh
Confidence 35689999999987543 33344555433344322 12 1 12221 167888999992
Q ss_pred cCCCCccccCCCCCCcEEEEechhhhhhhhcc---cCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCcCCC-----
Q 018558 211 NGEPMWKIRPRGSRARILVGHGLDHDLDRLQV---EYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQI----- 282 (354)
Q Consensus 211 ~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~---~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~~----- 282 (354)
+ ...++|+||+.||+.+|.. ..+ ..++||.....+..+.. .++|+.|+..|+|..+..
T Consensus 368 d------------~~v~kV~HNakfDl~~L~~~gi~~~-~~~~DT~iAa~Ll~~~~-~~~L~~L~~~ylg~~~~~~~~~~ 433 (880)
T PRK05755 368 D------------PAIKKVGQNLKYDLHVLARYGIELR-GIAFDTMLASYLLDPGR-RHGLDSLAERYLGHKTISFEEVA 433 (880)
T ss_pred C------------CCCcEEEeccHhHHHHHHhCCCCcC-CCcccHHHHHHHcCCCC-CCCHHHHHHHHhCCCccchHHhc
Confidence 1 3456899999999999853 222 23789988766655543 389999999998776310
Q ss_pred -------------CCCChHHHHHHHHHHHHHHHHhhhh
Q 018558 283 -------------GIQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 283 -------------~~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
..|.|..||.+++.||..+.++..+
T Consensus 434 gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~L~~ 471 (880)
T PRK05755 434 GKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKLLE 471 (880)
T ss_pred CCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 1378999999999999999887643
No 71
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.17 E-value=6.8e-07 Score=82.21 Aligned_cols=93 Identities=19% Similarity=0.378 Sum_probs=65.5
Q ss_pred ccccccccccccCChHHHHHhhhhccccCccc-cccccccccCCcccccccc--CCCCCc----cccccccccc------
Q 018558 11 LRNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRSFESLREHL--IGPLPK----QECKNVFNNR------ 77 (354)
Q Consensus 11 k~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~~~~L~~H~--~~e~p~----~~C~k~F~~~------ 77 (354)
..|+|+.|+-.....++|..|++. .|+..+| +|+.|.+.|...+.|.+|. ..+--| +.|..+|++.
T Consensus 262 n~ykCplCdmtc~~~ssL~~H~r~-rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~H 340 (467)
T KOG3608|consen 262 NCYKCPLCDMTCSSASSLTTHIRY-RHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRRH 340 (467)
T ss_pred hcccccccccCCCChHHHHHHHHh-hhccCCCccccchhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHHH
Confidence 347777777777777777777765 3777777 7777777777777777776 223233 4466665543
Q ss_pred -------------ccccccccCCCChhHHHHH-hhccccCC
Q 018558 78 -------------GCRFCLAILDGPNARRLHQ-ERCQMVSS 104 (354)
Q Consensus 78 -------------~C~~C~k~f~~~~~l~~H~-~~~~~~~~ 104 (354)
.|..|.+.|.+-.+|..|. +.|++.-|
T Consensus 341 ~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~P 381 (467)
T KOG3608|consen 341 FLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRLP 381 (467)
T ss_pred HHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccCC
Confidence 5999999999999999995 55666644
No 72
>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=98.13 E-value=3.4e-05 Score=67.82 Aligned_cols=123 Identities=11% Similarity=0.086 Sum_probs=75.1
Q ss_pred CCceEEeecccccc--CCCCCccceeeEEEEecCCceEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHH
Q 018558 131 DPQVVAIACKMVGG--GSDGSLDLCGRVCIIDEYENIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDF 208 (354)
Q Consensus 131 ~~~~vaiD~Ettg~--~~~~~~~~i~~i~vv~~~g~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~ 208 (354)
..+++++|+||++- -|+...+.|..|+++...+..++.. ++.. ...+..-.+-.+++.+|.++
T Consensus 2 ~l~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~~--~~~~-------------~~~v~~~~~E~~lL~~F~~~ 66 (195)
T cd05780 2 DLKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVITW--KKFD-------------LPFVEVVKTEKEMIKRFIEI 66 (195)
T ss_pred CceEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEEe--cCCC-------------CCeEEEeCCHHHHHHHHHHH
Confidence 34689999999832 1355667888888877555433211 1111 11233345558899999999
Q ss_pred HhcCCCCccccCCCCCCcEEEEech-hhhhhhh-------cccCC----------------------CceeeeccccCCC
Q 018558 209 LCNGEPMWKIRPRGSRARILVGHGL-DHDLDRL-------QVEYP----------------------AIMTRDTAKYPPL 258 (354)
Q Consensus 209 i~~~~~~~~~~~~~~~~~ilVgHn~-~~Dl~~L-------~~~~~----------------------~~~~~Dt~~~~~~ 258 (354)
+.+- .-.+|||||. .||+.+| ++..+ ....+|+..+...
T Consensus 67 i~~~-----------dpdiivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~ 135 (195)
T cd05780 67 VKEK-----------DPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARR 135 (195)
T ss_pred HHHc-----------CCCEEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHh
Confidence 9210 1259999997 5899765 22211 1124565544332
Q ss_pred ccCCCCCchHHHHHHHHhCCcC
Q 018558 259 MKTSKLSNSLKYLTQAYLGYDI 280 (354)
Q Consensus 259 ~~~~~~~~~L~~l~~~~l~~~i 280 (354)
.....+++|+.+++++||.+-
T Consensus 136 -~~~l~sy~L~~v~~~~Lg~~k 156 (195)
T cd05780 136 -TLNLTRYTLERVYEELFGIEK 156 (195)
T ss_pred -hCCCCcCcHHHHHHHHhCCCC
Confidence 123458999999999998754
No 73
>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=98.11 E-value=9e-06 Score=62.95 Aligned_cols=60 Identities=27% Similarity=0.335 Sum_probs=40.1
Q ss_pred EEeeccccccCCCCCccceeeEEEEecCCceEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHHHhcCCC
Q 018558 135 VAIACKMVGGGSDGSLDLCGRVCIIDEYENIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDFLCNGEP 214 (354)
Q Consensus 135 vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~i~~~~~ 214 (354)
+++|+||+|.. +...+|..+++.+.+++. .++.. |.+|+.+
T Consensus 1 ~~~DiEt~~~~--~~~~~i~~i~~~~~~~~~---~~~~~-------------------------------f~~~l~~--- 41 (96)
T cd06125 1 IAIDTEATGLD--GAVHEIIEIALADVNPED---TAVID-------------------------------LKDILRD--- 41 (96)
T ss_pred CEEEEECCCCC--CCCCcEEEEEEEEccCCC---EEEeh-------------------------------HHHHHhh---
Confidence 47999999864 445667788877763221 11111 7788811
Q ss_pred CccccCCCCCC-cEEEEechhhhhhhhcc
Q 018558 215 MWKIRPRGSRA-RILVGHGLDHDLDRLQV 242 (354)
Q Consensus 215 ~~~~~~~~~~~-~ilVgHn~~~Dl~~L~~ 242 (354)
.. .++||||..||+.+|+.
T Consensus 42 ---------~~~~v~V~hn~~fD~~fL~~ 61 (96)
T cd06125 42 ---------KPLAILVGHNGSFDLPFLNN 61 (96)
T ss_pred ---------CCCCEEEEeCcHHhHHHHHH
Confidence 22 68999999999988753
No 74
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.06 E-value=1.1e-06 Score=80.84 Aligned_cols=77 Identities=26% Similarity=0.418 Sum_probs=57.4
Q ss_pred CCccccccccccccCChHHHHHhhhhccccCccc-cccccccccCCcccccccc----CCCCCccccccccccccccccc
Q 018558 9 ETLRNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRSFESLREHL----IGPLPKQECKNVFNNRGCRFCL 83 (354)
Q Consensus 9 ~~k~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~~~~L~~H~----~~e~p~~~C~k~F~~~~C~~C~ 83 (354)
..++|.|..|.|.|..+..|..|++. |-. - +|+.|..+....++|.+|+ ...+|| +|..|.
T Consensus 234 ~~n~fqC~~C~KrFaTeklL~~Hv~r--Hvn--~ykCplCdmtc~~~ssL~~H~r~rHs~dkpf----------KCd~Cd 299 (467)
T KOG3608|consen 234 NTNSFQCAQCFKRFATEKLLKSHVVR--HVN--CYKCPLCDMTCSSASSLTTHIRYRHSKDKPF----------KCDECD 299 (467)
T ss_pred cCCchHHHHHHHHHhHHHHHHHHHHH--hhh--cccccccccCCCChHHHHHHHHhhhccCCCc----------cccchh
Confidence 35688888888888888888888877 653 4 8888888888899999998 568888 555555
Q ss_pred ccCCCChhHHHHHhhc
Q 018558 84 AILDGPNARRLHQERC 99 (354)
Q Consensus 84 k~f~~~~~l~~H~~~~ 99 (354)
+.|...+.|++|..+|
T Consensus 300 ~~c~~esdL~kH~~~H 315 (467)
T KOG3608|consen 300 TRCVRESDLAKHVQVH 315 (467)
T ss_pred hhhccHHHHHHHHHhc
Confidence 5555555555555444
No 75
>PHA00733 hypothetical protein
Probab=98.04 E-value=2.3e-06 Score=69.78 Aligned_cols=52 Identities=27% Similarity=0.532 Sum_probs=47.0
Q ss_pred CCCCCccccccccccccCChHHHHHhhhhccccCccc-cccccccccCCcccccccc
Q 018558 6 ESSETLRNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRSFESLREHL 61 (354)
Q Consensus 6 ~~~~~k~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~~~~L~~H~ 61 (354)
.+++++||.|+.||+.|...+.|..|++. | +.+ .|..|++.|....+|..|+
T Consensus 67 ~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~--h--~~~~~C~~CgK~F~~~~sL~~H~ 119 (128)
T PHA00733 67 TSKAVSPYVCPLCLMPFSSSVSLKQHIRY--T--EHSKVCPVCGKEFRNTDSTLDHV 119 (128)
T ss_pred ccCCCCCccCCCCCCcCCCHHHHHHHHhc--C--CcCccCCCCCCccCCHHHHHHHH
Confidence 35568899999999999999999999998 7 357 9999999999999999997
No 76
>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=97.96 E-value=7.1e-05 Score=64.05 Aligned_cols=79 Identities=20% Similarity=0.264 Sum_probs=57.9
Q ss_pred CCcEEEEechhhhhhhhcccC--CCceeeeccccCCCccCCCCCchHHHHHHHHhCCcCC--CC---------------C
Q 018558 224 RARILVGHGLDHDLDRLQVEY--PAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQ--IG---------------I 284 (354)
Q Consensus 224 ~~~ilVgHn~~~Dl~~L~~~~--~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~--~~---------------~ 284 (354)
.+.+.|||++.+|+..|...+ ....++|+..++....+.....+|+.|+..+||..+. .. -
T Consensus 72 ~~i~kv~~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt~~qi 151 (170)
T cd06141 72 PSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQI 151 (170)
T ss_pred CCeeEEEeeeHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCCCCCCHHHH
Confidence 456789999999999885211 1112579988776655443346999999999998776 21 2
Q ss_pred CChHHHHHHHHHHHHHHH
Q 018558 285 QDPYDDCVATMRLYMRMK 302 (354)
Q Consensus 285 H~Al~DA~at~~l~~~~~ 302 (354)
+-|..||..+.+||.++.
T Consensus 152 ~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 152 LYAATDAYASLELYRKLL 169 (170)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 668899999999998875
No 77
>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=97.85 E-value=0.00014 Score=61.86 Aligned_cols=78 Identities=21% Similarity=0.174 Sum_probs=56.3
Q ss_pred CCcEEEEechhhhhhhhcc--cCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCcCCCC---------------CCC
Q 018558 224 RARILVGHGLDHDLDRLQV--EYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQIG---------------IQD 286 (354)
Q Consensus 224 ~~~ilVgHn~~~Dl~~L~~--~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~~~---------------~H~ 286 (354)
.+.+.|||++..|+..|.. ......++||...+....+. .+.+|+.|+..+||..+... -+-
T Consensus 66 ~~i~Kvg~~~k~D~~~L~~~~gi~~~~~~D~~~aa~ll~~~-~~~~L~~l~~~~lg~~l~K~~~~s~W~~rpLt~~qi~Y 144 (161)
T cd06129 66 PSIVKALHGIEGDLWKLLRDFGEKLQRLFDTTIAANLKGLP-ERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLY 144 (161)
T ss_pred CCEEEEEeccHHHHHHHHHHcCCCcccHhHHHHHHHHhCCC-CCchHHHHHHHHhCCCCCccceeccCCCCCCCHHHHHH
Confidence 4457799999999998753 11111257988766544332 34699999999999877421 266
Q ss_pred hHHHHHHHHHHHHHHH
Q 018558 287 PYDDCVATMRLYMRMK 302 (354)
Q Consensus 287 Al~DA~at~~l~~~~~ 302 (354)
|..||.+...||.+++
T Consensus 145 Aa~Da~~l~~l~~~l~ 160 (161)
T cd06129 145 AAADVYALLIIYTKLR 160 (161)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 7899999999998876
No 78
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.85 E-value=1.1e-05 Score=80.62 Aligned_cols=76 Identities=22% Similarity=0.427 Sum_probs=60.7
Q ss_pred CccccccccccccCChHHHHHhhhhccccCccc-cccccccccCCcccccccc---CCCCCccccccccccccccccccc
Q 018558 10 TLRNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRSFESLREHL---IGPLPKQECKNVFNNRGCRFCLAI 85 (354)
Q Consensus 10 ~k~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~~~~L~~H~---~~e~p~~~C~k~F~~~~C~~C~k~ 85 (354)
++++.|+.|++.|. .+.|..|+.. |+ ++ .|+ ||+.+ .+..|..|+ .+++|+ .|.+|++.
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~--~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi----------~C~fC~~~ 513 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKV--FH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLI----------TCRFCGDM 513 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHh--cC--CCccCC-CCCCc-chhHHHhhhhccCCCCce----------eCCCCCCc
Confidence 56789999999996 6789999999 74 78 999 99765 668999998 667888 89999988
Q ss_pred CCC----------ChhHHHHHhhcccc
Q 018558 86 LDG----------PNARRLHQERCQMV 102 (354)
Q Consensus 86 f~~----------~~~l~~H~~~~~~~ 102 (354)
|.. ...|+.|+.+|...
T Consensus 514 v~~g~~~~d~~d~~s~Lt~HE~~CG~r 540 (567)
T PLN03086 514 VQAGGSAMDVRDRLRGMSEHESICGSR 540 (567)
T ss_pred cccCccccchhhhhhhHHHHHHhcCCc
Confidence 842 34788888776433
No 79
>PHA02768 hypothetical protein; Provisional
Probab=97.79 E-value=4.8e-06 Score=56.55 Aligned_cols=41 Identities=20% Similarity=0.136 Sum_probs=33.6
Q ss_pred cccccccccCCcccccccc-CCCCCcccccccccccccccccccCCCChhHH
Q 018558 43 VCGICKKHCRSFESLREHL-IGPLPKQECKNVFNNRGCRFCLAILDGPNARR 93 (354)
Q Consensus 43 ~C~~C~k~f~~~~~L~~H~-~~e~p~~~C~k~F~~~~C~~C~k~f~~~~~l~ 93 (354)
.|+.||+.|++.++|..|+ +..+|| +|..|++.|++.+.|.
T Consensus 7 ~C~~CGK~Fs~~~~L~~H~r~H~k~~----------kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 7 ECPICGEIYIKRKSMITHLRKHNTNL----------KLSNCKRISLRTGEYI 48 (55)
T ss_pred CcchhCCeeccHHHHHHHHHhcCCcc----------cCCcccceecccceeE
Confidence 6899999999999999998 444788 8888888888777664
No 80
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.77 E-value=8.6e-06 Score=76.74 Aligned_cols=48 Identities=29% Similarity=0.510 Sum_probs=40.4
Q ss_pred cccccccccccCChHHHHHhhhhccccC--------cc-------------------------c-cccccccccCCcccc
Q 018558 12 RNKCAACFRQFNRLEHLVEHMRTSYHSV--------HE-------------------------P-VCGICKKHCRSFESL 57 (354)
Q Consensus 12 ~~~C~~Cgk~f~~~~~L~~H~~~~~H~~--------~k-------------------------~-~C~~C~k~f~~~~~L 57 (354)
.|+|++|+|.|+...+|..|.+. |.. .. . .|..|+|.|.+...|
T Consensus 295 EYrCPEC~KVFsCPANLASHRRW--HKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYL 372 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRW--HKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYL 372 (500)
T ss_pred eecCCcccccccCchhhhhhhcc--cCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHH
Confidence 49999999999999999999988 842 11 1 488999999999999
Q ss_pred cccc
Q 018558 58 REHL 61 (354)
Q Consensus 58 ~~H~ 61 (354)
+.|+
T Consensus 373 rKHq 376 (500)
T KOG3993|consen 373 RKHQ 376 (500)
T ss_pred HHhH
Confidence 9986
No 81
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=97.75 E-value=1.4e-05 Score=46.11 Aligned_cols=25 Identities=40% Similarity=0.737 Sum_probs=22.3
Q ss_pred HHHHhhhhccccCccc-cccccccccCC
Q 018558 27 HLVEHMRTSYHSVHEP-VCGICKKHCRS 53 (354)
Q Consensus 27 ~L~~H~~~~~H~~~k~-~C~~C~k~f~~ 53 (354)
+|..|+++ |++++| .|+.|++.|.+
T Consensus 1 ~l~~H~~~--H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRT--HTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHH--HSSSSSEEESSSSEEESS
T ss_pred CHHHHhhh--cCCCCCCCCCCCcCeeCc
Confidence 47899999 999999 99999999863
No 82
>PHA00616 hypothetical protein
Probab=97.75 E-value=1e-05 Score=52.24 Aligned_cols=38 Identities=13% Similarity=0.214 Sum_probs=33.0
Q ss_pred cccccccccccCChHHHHHhhhhccccCccc-ccccccccc
Q 018558 12 RNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHC 51 (354)
Q Consensus 12 ~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f 51 (354)
||+|..||+.|.+.+.|..|++. |+++++ .|+.--..|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~--~hg~~~~~~~~~y~~f 39 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLS--VHKQNKLTLEYFYIYF 39 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHH--hcCCCccceeEEEEEE
Confidence 69999999999999999999999 999999 887643333
No 83
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.75 E-value=1.8e-05 Score=79.10 Aligned_cols=76 Identities=18% Similarity=0.330 Sum_probs=63.3
Q ss_pred ccccccccccccCChHHHHHhhhhccccCccc-cccccccccCC----------cccccccc--CCCCCccccccccccc
Q 018558 11 LRNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRS----------FESLREHL--IGPLPKQECKNVFNNR 77 (354)
Q Consensus 11 k~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~----------~~~L~~H~--~~e~p~~~C~k~F~~~ 77 (354)
+|+.|+ ||+.+ .+..|..|+.+ |.++++ .|..|++.|.. .+.|..|. .|.+++
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~t--hCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~---------- 542 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQAS--TCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTA---------- 542 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhc--cCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhcCCcce----------
Confidence 789999 99765 67899999999 999999 99999999852 34788898 788888
Q ss_pred ccccccccCCCChhHHHHHhhccc
Q 018558 78 GCRFCLAILDGPNARRLHQERCQM 101 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~~~~ 101 (354)
.|..|++.+.. ..+..|+..+|.
T Consensus 543 ~C~~Cgk~Vrl-rdm~~H~~~~h~ 565 (567)
T PLN03086 543 PCDSCGRSVML-KEMDIHQIAVHQ 565 (567)
T ss_pred EccccCCeeee-hhHHHHHHHhhc
Confidence 99999998855 457888876654
No 84
>PHA00732 hypothetical protein
Probab=97.73 E-value=1.9e-05 Score=58.59 Aligned_cols=44 Identities=32% Similarity=0.555 Sum_probs=36.5
Q ss_pred cccccccccccCChHHHHHhhhhccccCccccccccccccCCcccccccc
Q 018558 12 RNKCAACFRQFNRLEHLVEHMRTSYHSVHEPVCGICKKHCRSFESLREHL 61 (354)
Q Consensus 12 ~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~~C~~C~k~f~~~~~L~~H~ 61 (354)
||+|..||+.|.+.+.|..|++. .|.+. .|+.|++.|. .+..|.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~-~H~~~--~C~~CgKsF~---~l~~H~ 44 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARR-NHTLT--KCPVCNKSYR---RLNQHF 44 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhc-ccCCC--ccCCCCCEeC---Chhhhh
Confidence 68999999999999999999984 05422 8999999997 477887
No 85
>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=97.64 E-value=0.00069 Score=56.22 Aligned_cols=93 Identities=26% Similarity=0.318 Sum_probs=62.2
Q ss_pred HHHHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcc---cCCCceeeeccccCCCccCCCCCchHHHHHHHH
Q 018558 199 KQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQV---EYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAY 275 (354)
Q Consensus 199 ~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~---~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~ 275 (354)
.++.+.+.+++. +.+..+||||+++|+.+|.. ..+. .+.||..+.....+...+++|+.|++.|
T Consensus 40 ~~~~~~l~~~l~------------~~~~~~v~~~~k~d~~~L~~~~~~~~~-~~~D~~~~ayll~~~~~~~~l~~l~~~~ 106 (155)
T cd00007 40 EEDLEALKELLE------------DEDITKVGHDAKFDLVVLARDGIELPG-NIFDTMLAAYLLNPGEGSHSLDDLAKEY 106 (155)
T ss_pred HHHHHHHHHHHc------------CCCCcEEeccHHHHHHHHHHCCCCCCC-CcccHHHHHHHhCCCCCcCCHHHHHHHH
Confidence 567788889992 13456999999999999852 2222 2679987776665544246999999999
Q ss_pred hCCcCCC------CC----C---------ChHHHHHHHHHHHHHHHHh
Q 018558 276 LGYDIQI------GI----Q---------DPYDDCVATMRLYMRMKSQ 304 (354)
Q Consensus 276 l~~~i~~------~~----H---------~Al~DA~at~~l~~~~~~~ 304 (354)
++..+.. .. - -|..||.++.+|+..+.++
T Consensus 107 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 107 LGIELDKDEQIYGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred cCCCCccHHHHhcCCCCccccCCHHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 8776321 00 0 1455677777777666543
No 86
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=97.60 E-value=0.00036 Score=60.93 Aligned_cols=76 Identities=13% Similarity=0.182 Sum_probs=51.9
Q ss_pred CCceEEeecccccc--CCCCCccceeeEEEEecCCceEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHH
Q 018558 131 DPQVVAIACKMVGG--GSDGSLDLCGRVCIIDEYENIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDF 208 (354)
Q Consensus 131 ~~~~vaiD~Ettg~--~~~~~~~~i~~i~vv~~~g~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~ 208 (354)
..+++++|+||++- -|+...+.|..|++...+|.+.+-. ....+-.+++..|.++
T Consensus 2 ~l~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~~-----------------------~~~~~E~~lL~~F~~~ 58 (188)
T cd05781 2 DLKTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFIL-----------------------AEGLDDRKIIREFVKY 58 (188)
T ss_pred CceEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEEEE-----------------------ecCCCHHHHHHHHHHH
Confidence 34789999999932 1455567888888887666532100 1245678899999999
Q ss_pred HhcCCCCccccCCCCCCcEEEEech-hhhhhhh
Q 018558 209 LCNGEPMWKIRPRGSRARILVGHGL-DHDLDRL 240 (354)
Q Consensus 209 i~~~~~~~~~~~~~~~~~ilVgHn~-~~Dl~~L 240 (354)
+..- .-.+|||+|. .||+.+|
T Consensus 59 i~~~-----------dPd~i~gyN~~~FDlpyl 80 (188)
T cd05781 59 VKEY-----------DPDIIVGYNSNAFDWPYL 80 (188)
T ss_pred HHHc-----------CCCEEEecCCCcCcHHHH
Confidence 9311 1258999995 6899765
No 87
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=97.60 E-value=0.00082 Score=59.39 Aligned_cols=154 Identities=20% Similarity=0.172 Sum_probs=83.4
Q ss_pred CceEEeecccccc---CCCCCccceeeEEEEecC-CceEE-eeeecCCcc-cc-CceeeecCCChhhhcCCCCHHHHHHH
Q 018558 132 PQVVAIACKMVGG---GSDGSLDLCGRVCIIDEY-ENIIF-HAYVKPPIP-VT-SYRYETTGIRPEHLRDAIPLKQVQRK 204 (354)
Q Consensus 132 ~~~vaiD~Ettg~---~~~~~~~~i~~i~vv~~~-g~~i~-~~~v~P~~~-i~-~~~~~itGIt~~~l~~ap~~~~v~~~ 204 (354)
.+++++|+|+.+. -|+...+.|..|+++... |..+. ..++.+... +. .....+.|. -.+..-++-.+++.+
T Consensus 2 lrilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~v~~~~~E~~lL~~ 79 (204)
T cd05779 2 PRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIVNREIVSEDIEDFEYTPKPEYEGP--FKVFNEPDEKALLQR 79 (204)
T ss_pred ceEEEEEEEecCCCCCCcCCCCCeEEEEEEEEecCCEEEecccccccccccccccCCCCCCCc--eEEecCCCHHHHHHH
Confidence 3679999999752 256677888888887543 42221 111111000 00 000001110 111223577889999
Q ss_pred HHHHHhcCCCCccccCCCCCCcEEEEech-hhhhhhhc-------ccCC----------------CceeeeccccCCCc-
Q 018558 205 IQDFLCNGEPMWKIRPRGSRARILVGHGL-DHDLDRLQ-------VEYP----------------AIMTRDTAKYPPLM- 259 (354)
Q Consensus 205 ~~~~i~~~~~~~~~~~~~~~~~ilVgHn~-~~Dl~~L~-------~~~~----------------~~~~~Dt~~~~~~~- 259 (354)
|.+++.+- .-.+|+|+|. .||+.+|. +... ....+|...+....
T Consensus 80 f~~~i~~~-----------~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~ 148 (204)
T cd05779 80 FFEHIREV-----------KPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDS 148 (204)
T ss_pred HHHHHHHh-----------CCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhh
Confidence 99999210 1149999996 78997652 2111 00134444332211
Q ss_pred cCCCCCchHHHHHHHHhCCcCC-C----------C-----CCChHHHHHHHHHHH
Q 018558 260 KTSKLSNSLKYLTQAYLGYDIQ-I----------G-----IQDPYDDCVATMRLY 298 (354)
Q Consensus 260 ~~~~~~~~L~~l~~~~l~~~i~-~----------~-----~H~Al~DA~at~~l~ 298 (354)
.....+++|+.+|+++||.+=. . + ++-.+.||.+|..||
T Consensus 149 ~l~~~sysLd~Va~~~Lg~~K~~~~~~~I~~~~~~~~~~l~~Y~~~D~~~T~~l~ 203 (204)
T cd05779 149 YLPQGSQGLKAVTKAKLGYDPVELDPEDMVPLAREDPQTLASYSVSDAVATYYLY 203 (204)
T ss_pred cCCCCCccHHHHHHHHhCCCcCcCCHHHHHHHHhCCcHHHHhccHHHHHHHHHHh
Confidence 1122478999999999985321 1 0 244577888888877
No 88
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.56 E-value=1.7e-05 Score=74.88 Aligned_cols=91 Identities=23% Similarity=0.292 Sum_probs=66.9
Q ss_pred ccccccccccCChHHHHHhhhhccccCccc-cccccccccCCccccccccC-----------CCCCcc----------cc
Q 018558 13 NKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRSFESLREHLI-----------GPLPKQ----------EC 70 (354)
Q Consensus 13 ~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~~~~L~~H~~-----------~e~p~~----------~C 70 (354)
|-|..|...|.....|.+|.-. -....- +|.+|+|.|+-..||..|.. +..|-. +-
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~--RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea 345 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCP--RIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEA 345 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCC--eeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhc
Confidence 8999999999999999999643 223333 89999999999999988871 222210 00
Q ss_pred ccc---cc--ccccccccccCCCChhHHHHHhhccccCCC
Q 018558 71 KNV---FN--NRGCRFCLAILDGPNARRLHQERCQMVSSA 105 (354)
Q Consensus 71 ~k~---F~--~~~C~~C~k~f~~~~~l~~H~~~~~~~~~~ 105 (354)
.++ -. -..|..|+|.|.....|++|+.+||...-.
T Consensus 346 ~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~ 385 (500)
T KOG3993|consen 346 ERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLA 385 (500)
T ss_pred cccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccc
Confidence 000 00 015999999999999999999999987554
No 89
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=97.48 E-value=0.002 Score=58.12 Aligned_cols=90 Identities=12% Similarity=0.171 Sum_probs=54.7
Q ss_pred CCCceEEeecccccc---CCCCCccceeeEEEEec-CCc--eEEee-e-ecCCccccCceeeecCCChhhhcCCCCHHHH
Q 018558 130 RDPQVVAIACKMVGG---GSDGSLDLCGRVCIIDE-YEN--IIFHA-Y-VKPPIPVTSYRYETTGIRPEHLRDAIPLKQV 201 (354)
Q Consensus 130 ~~~~~vaiD~Ettg~---~~~~~~~~i~~i~vv~~-~g~--~i~~~-~-v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v 201 (354)
++.+++++|+|+... -|+...+.|..|+.+.. .|. ..... + +++..+++ ...+..-++-.++
T Consensus 5 p~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~~~~~~~----------~~~v~~~~~E~eL 74 (230)
T cd05777 5 APLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIV----------GAQVFSFETEEEL 74 (230)
T ss_pred CCceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeCCCCCCC----------CCEEEEECCHHHH
Confidence 345789999999842 35667778888887743 342 11111 1 22222222 1222334677889
Q ss_pred HHHHHHHHhcCCCCccccCCCCCCcEEEEech-hhhhhhh
Q 018558 202 QRKIQDFLCNGEPMWKIRPRGSRARILVGHGL-DHDLDRL 240 (354)
Q Consensus 202 ~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~-~~Dl~~L 240 (354)
+..|.++|..- .=.||+|||+ .||+..|
T Consensus 75 L~~f~~~i~~~-----------DPDii~GyN~~~FDl~yL 103 (230)
T cd05777 75 LLAWRDFVQEV-----------DPDIITGYNICNFDLPYL 103 (230)
T ss_pred HHHHHHHHHhc-----------CCCEEEEecCCCCCHHHH
Confidence 99999999211 1159999996 6798654
No 90
>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=97.38 E-value=0.001 Score=58.96 Aligned_cols=77 Identities=14% Similarity=0.138 Sum_probs=50.4
Q ss_pred CCCceEEeeccccccC------CCCCccceeeEEEEecCCceEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHH
Q 018558 130 RDPQVVAIACKMVGGG------SDGSLDLCGRVCIIDEYENIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQR 203 (354)
Q Consensus 130 ~~~~~vaiD~Ettg~~------~~~~~~~i~~i~vv~~~g~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~ 203 (354)
+..+++++|+|+.... ++...+.|..|++.+..+.... +. ...++-.+++.
T Consensus 7 ~~lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~---~~--------------------~~~~~E~~lL~ 63 (207)
T cd05785 7 DDLRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEV---LH--------------------AEDAAEKELLE 63 (207)
T ss_pred CCceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceee---ec--------------------cCCCCHHHHHH
Confidence 3557899999997542 2334456777777655442110 00 12577788999
Q ss_pred HHHHHHhcCCCCccccCCCCCCcEEEEech-hhhhhhh
Q 018558 204 KIQDFLCNGEPMWKIRPRGSRARILVGHGL-DHDLDRL 240 (354)
Q Consensus 204 ~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~-~~Dl~~L 240 (354)
.|++++.+- .-.||||||+ .||+.+|
T Consensus 64 ~f~~~i~~~-----------dPdii~g~N~~~FD~pyl 90 (207)
T cd05785 64 ELVAIIRER-----------DPDVIEGHNIFRFDLPYL 90 (207)
T ss_pred HHHHHHHHh-----------CCCEEeccCCcccCHHHH
Confidence 999999321 1169999998 8999765
No 91
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=97.35 E-value=0.0025 Score=55.88 Aligned_cols=120 Identities=15% Similarity=0.119 Sum_probs=67.3
Q ss_pred CCceEEeeccccccCCCCCccceeeEEEEecCCceEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHHHh
Q 018558 131 DPQVVAIACKMVGGGSDGSLDLCGRVCIIDEYENIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDFLC 210 (354)
Q Consensus 131 ~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~i~ 210 (354)
+-+++++|+|+++.+ .|-.++..+...+.++ .+-.+. +.. | ..+.--++-.+++..|.+++.
T Consensus 2 ~l~~~~fDIE~~~~~------~i~~i~~~~~~~~~i~-~~~~~~-~~~-------~---~~v~~~~~E~~lL~~f~~~i~ 63 (193)
T cd05784 2 KLKVVSLDIETSMDG------ELYSIGLYGEGQERVL-MVGDPE-DDA-------P---DNIEWFADEKSLLLALIAWFA 63 (193)
T ss_pred CccEEEEEeecCCCC------CEEEEEeecCCCCEEE-EECCCC-CCC-------C---CEEEEECCHHHHHHHHHHHHH
Confidence 357899999998642 4455555554333222 110011 110 1 112223566788999999993
Q ss_pred cCCCCccccCCCCCCcEEEEech-hhhhhhh-------cccCC------------------------CceeeeccccCCC
Q 018558 211 NGEPMWKIRPRGSRARILVGHGL-DHDLDRL-------QVEYP------------------------AIMTRDTAKYPPL 258 (354)
Q Consensus 211 ~~~~~~~~~~~~~~~~ilVgHn~-~~Dl~~L-------~~~~~------------------------~~~~~Dt~~~~~~ 258 (354)
+- .-.||||||+ .||+.+| ++... -..++|+..+.+.
T Consensus 64 ~~-----------dPDvi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~ 132 (193)
T cd05784 64 QY-----------DPDIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKT 132 (193)
T ss_pred hh-----------CCCEEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHH
Confidence 21 1148999997 6798765 22210 1114565443322
Q ss_pred ccCCCCCchHHHHHHHHhCCc
Q 018558 259 MKTSKLSNSLKYLTQAYLGYD 279 (354)
Q Consensus 259 ~~~~~~~~~L~~l~~~~l~~~ 279 (354)
......+|+|.++|.++||..
T Consensus 133 ~~~kl~sy~L~~Va~~~Lg~~ 153 (193)
T cd05784 133 ATYHFESFSLENVAQELLGEG 153 (193)
T ss_pred ccCCCCcCCHHHHHHHHhCCC
Confidence 112456899999999999863
No 92
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=97.35 E-value=0.0015 Score=61.83 Aligned_cols=134 Identities=19% Similarity=0.214 Sum_probs=85.6
Q ss_pred CceEEeeccccccCCCCCccceeeEEEEecCCceEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHHHhc
Q 018558 132 PQVVAIACKMVGGGSDGSLDLCGRVCIIDEYENIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDFLCN 211 (354)
Q Consensus 132 ~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~i~~ 211 (354)
.++|+||.|+.+..+ ....++-|-+-+.++ ..+|.|..+ + .+.|+| ..++.|
T Consensus 17 ~~~iAiDTEf~r~~t--~~p~LcLIQi~~~e~----~~lIdpl~~----------~-----~d~~~l-------~~Ll~d 68 (361)
T COG0349 17 SKAIAIDTEFMRLRT--YYPRLCLIQISDGEG----ASLIDPLAG----------I-----LDLPPL-------VALLAD 68 (361)
T ss_pred CCceEEecccccccc--cCCceEEEEEecCCC----ceEeccccc----------c-----cccchH-------HHHhcC
Confidence 468999999998743 333444454444444 345555432 1 123433 344411
Q ss_pred CCCCccccCCCCCCcEEEEechhhhhhhhccc---CCCceeeeccccCCCccCCCCCchHHHHHHHHhCCcCCCC-----
Q 018558 212 GEPMWKIRPRGSRARILVGHGLDHDLDRLQVE---YPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQIG----- 283 (354)
Q Consensus 212 ~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~---~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~~~----- 283 (354)
.+.+=|-|+..||+.+|... .|.. ++||.....+..... +++|++|++.++|++|..+
T Consensus 69 ------------~~v~KIfHaa~~DL~~l~~~~g~~p~p-lfdTqiAa~l~g~~~-~~gl~~Lv~~ll~v~ldK~~q~SD 134 (361)
T COG0349 69 ------------PNVVKIFHAARFDLEVLLNLFGLLPTP-LFDTQIAAKLAGFGT-SHGLADLVEELLGVELDKSEQRSD 134 (361)
T ss_pred ------------CceeeeeccccccHHHHHHhcCCCCCc-hhHHHHHHHHhCCcc-cccHHHHHHHHhCCcccccccccc
Confidence 44456889999999887532 2222 789987665543333 8999999999999999754
Q ss_pred -CCC---------hHHHHHHHHHHHHHHHHhhhh
Q 018558 284 -IQD---------PYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 284 -~H~---------Al~DA~at~~l~~~~~~~~~~ 307 (354)
.++ |..|+.--..||.++.++..+
T Consensus 135 W~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~ 168 (361)
T COG0349 135 WLARPLSEAQLEYAAADVEYLLPLYDKLTEELAR 168 (361)
T ss_pred cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333 366777778888888877644
No 93
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=97.32 E-value=0.0027 Score=61.31 Aligned_cols=82 Identities=20% Similarity=0.235 Sum_probs=58.2
Q ss_pred CCcEEEEechhhhhhhhcc---cCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCcCCCC------CC---------
Q 018558 224 RARILVGHGLDHDLDRLQV---EYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQIG------IQ--------- 285 (354)
Q Consensus 224 ~~~ilVgHn~~~Dl~~L~~---~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~~~------~H--------- 285 (354)
.+.+.|+|++++|+.+|.. ..+. .+.||.....+..+. ...+|..|++.|||..+..+ ..
T Consensus 69 ~~i~KV~h~~k~Dl~~L~~~~~~~~~-~~fDtqlAa~lL~~~-~~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~ 146 (367)
T TIGR01388 69 ESVVKVLHAASEDLEVFLNLFGELPQ-PLFDTQIAAAFCGFG-MSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLE 146 (367)
T ss_pred CCceEEEeecHHHHHHHHHHhCCCCC-CcccHHHHHHHhCCC-CCccHHHHHHHHcCCCCCcccccccCCCCCCCHHHHH
Confidence 4456799999999998852 2332 267998755444332 24699999999999887532 12
Q ss_pred ChHHHHHHHHHHHHHHHHhhhh
Q 018558 286 DPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 286 ~Al~DA~at~~l~~~~~~~~~~ 307 (354)
-|..||.....||..+.++..+
T Consensus 147 YAa~Dv~~L~~L~~~L~~~L~~ 168 (367)
T TIGR01388 147 YAAADVTYLLPLYAKLMERLEE 168 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 2677898899999988877644
No 94
>PRK10829 ribonuclease D; Provisional
Probab=97.26 E-value=0.0027 Score=61.19 Aligned_cols=83 Identities=12% Similarity=0.080 Sum_probs=60.4
Q ss_pred CCcEEEEechhhhhhhhcc--cCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCcCCCCC---------------CC
Q 018558 224 RARILVGHGLDHDLDRLQV--EYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQIGI---------------QD 286 (354)
Q Consensus 224 ~~~ilVgHn~~~Dl~~L~~--~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~~~~---------------H~ 286 (354)
.+-+-|+|+..+|+.+|.. ......++||...+.+.. .+.+.+|..|++.+||..+..+. +-
T Consensus 73 ~~ivKV~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg-~~~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~ql~Y 151 (373)
T PRK10829 73 PQVTKFLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCG-RPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEY 151 (373)
T ss_pred CCeEEEEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHcC-CCccccHHHHHHHHhCCccCcccccCCCCCCCCCHHHHHH
Confidence 4445689999999998732 112223789987665442 22357999999999999886431 55
Q ss_pred hHHHHHHHHHHHHHHHHhhhh
Q 018558 287 PYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 287 Al~DA~at~~l~~~~~~~~~~ 307 (354)
|..|+.....||.++.++..+
T Consensus 152 Aa~Dv~~L~~l~~~L~~~L~~ 172 (373)
T PRK10829 152 AAADVFYLLPIAAKLMAETEA 172 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 788999999999998887654
No 95
>PHA00732 hypothetical protein
Probab=97.09 E-value=0.00019 Score=53.19 Aligned_cols=41 Identities=20% Similarity=0.316 Sum_probs=35.0
Q ss_pred cccccccccCCcccccccc-CCCCCcccccccccccccccccccCCCChhHHHHH
Q 018558 43 VCGICKKHCRSFESLREHL-IGPLPKQECKNVFNNRGCRFCLAILDGPNARRLHQ 96 (354)
Q Consensus 43 ~C~~C~k~f~~~~~L~~H~-~~e~p~~~C~k~F~~~~C~~C~k~f~~~~~l~~H~ 96 (354)
.|+.|++.|.+..+|..|+ ....++ .|+.|+++|. .+..|.
T Consensus 3 ~C~~Cgk~F~s~s~Lk~H~r~~H~~~----------~C~~CgKsF~---~l~~H~ 44 (79)
T PHA00732 3 KCPICGFTTVTLFALKQHARRNHTLT----------KCPVCNKSYR---RLNQHF 44 (79)
T ss_pred cCCCCCCccCCHHHHHHHhhcccCCC----------ccCCCCCEeC---Chhhhh
Confidence 7999999999999999998 345566 8999999997 577777
No 96
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.07 E-value=0.00026 Score=39.29 Aligned_cols=22 Identities=36% Similarity=0.705 Sum_probs=20.5
Q ss_pred ccccccccccCChHHHHHhhhh
Q 018558 13 NKCAACFRQFNRLEHLVEHMRT 34 (354)
Q Consensus 13 ~~C~~Cgk~f~~~~~L~~H~~~ 34 (354)
|+|+.|++.|...+.|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 6899999999999999999986
No 97
>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=96.99 E-value=0.018 Score=50.90 Aligned_cols=131 Identities=13% Similarity=-0.012 Sum_probs=70.7
Q ss_pred CCceEEeecccccc----CCCCCc--cceeeEEEEecCCceEEeeeec-CCccccCceeeecCCChhhhcCCCCHHHHHH
Q 018558 131 DPQVVAIACKMVGG----GSDGSL--DLCGRVCIIDEYENIIFHAYVK-PPIPVTSYRYETTGIRPEHLRDAIPLKQVQR 203 (354)
Q Consensus 131 ~~~~vaiD~Ettg~----~~~~~~--~~i~~i~vv~~~g~~i~~~~v~-P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~ 203 (354)
..+++++|+|+..- -|+.+. +.|..|++...+|...+- ++. +.....+.- . .....+..-.+-.+++.
T Consensus 4 ~lrilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~~~~~~~~v~-~~~~~~~~~~~~~--~--~~~~~v~~~~~E~~lL~ 78 (204)
T cd05783 4 KLKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALAGSDGLKRVL-VLKREGVEGLEGL--L--PEGAEVEFFDSEKELIR 78 (204)
T ss_pred CceEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEcCCCCCcEEE-EEecCCccccccc--C--CCCCeEEecCCHHHHHH
Confidence 45789999999842 233333 567778776544432111 111 111100000 0 00011222356788999
Q ss_pred HHHHHHhcCCCCccccCCCCCCcEEEEech-hhhhhhh-------ccc---C-----------CCceeeeccccCCCc--
Q 018558 204 KIQDFLCNGEPMWKIRPRGSRARILVGHGL-DHDLDRL-------QVE---Y-----------PAIMTRDTAKYPPLM-- 259 (354)
Q Consensus 204 ~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~-~~Dl~~L-------~~~---~-----------~~~~~~Dt~~~~~~~-- 259 (354)
+|.+++. .-.+|||+|. .||+.+| ++. . +....+|...+....
T Consensus 79 ~F~~~i~-------------~~~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~ 145 (204)
T cd05783 79 EAFKIIS-------------EYPIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAI 145 (204)
T ss_pred HHHHHHh-------------cCCEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccch
Confidence 9999992 2259999996 7899765 222 0 111245554432210
Q ss_pred ----c-CCCCCchHHHHHHHHhCCc
Q 018558 260 ----K-TSKLSNSLKYLTQAYLGYD 279 (354)
Q Consensus 260 ----~-~~~~~~~L~~l~~~~l~~~ 279 (354)
. ....+++|+.+|+++||.+
T Consensus 146 ~~~~~~~~~~~~~L~~Va~~~lg~~ 170 (204)
T cd05783 146 QVYAFGNKYREYTLDAVAKALLGEG 170 (204)
T ss_pred hhhhhccccccCcHHHHHHHhcCCC
Confidence 0 0225789999999998853
No 98
>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=96.94 E-value=0.004 Score=54.70 Aligned_cols=82 Identities=23% Similarity=0.201 Sum_probs=56.4
Q ss_pred CCcEEEEechhhhhhhhc----ccCCCceeeeccccCCCccCC-------CCCchHHHHHHHHhCCcCCC----------
Q 018558 224 RARILVGHGLDHDLDRLQ----VEYPAIMTRDTAKYPPLMKTS-------KLSNSLKYLTQAYLGYDIQI---------- 282 (354)
Q Consensus 224 ~~~ilVgHn~~~Dl~~L~----~~~~~~~~~Dt~~~~~~~~~~-------~~~~~L~~l~~~~l~~~i~~---------- 282 (354)
.+.+.|||++++|+.+|. +.... +.||.....+..+. ....+|..++..|||..+..
T Consensus 64 ~~i~Kv~h~~k~D~~~L~~~~gi~~~~--~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~~~~~~ 141 (197)
T cd06148 64 KKILKVIHDCRRDSDALYHQYGIKLNN--VFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVKKLMRE 141 (197)
T ss_pred CCccEEEEechhHHHHHHHhcCccccc--eeeHHHHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHHHHHhc
Confidence 445679999999999883 22222 57987653332211 12358999999999887621
Q ss_pred ---C----------CCChHHHHHHHHHHHHHHHHhhhh
Q 018558 283 ---G----------IQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 283 ---~----------~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
+ -.-|..||.....||..+++....
T Consensus 142 ~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~~ 179 (197)
T cd06148 142 DPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALIS 179 (197)
T ss_pred CchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhhh
Confidence 0 155688999999999999888744
No 99
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=96.76 E-value=0.0053 Score=51.82 Aligned_cols=90 Identities=24% Similarity=0.333 Sum_probs=61.0
Q ss_pred HHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhc---ccCCCceeeeccccCCCccCCCCCchHHHHHHHHhCC
Q 018558 202 QRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQ---VEYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGY 278 (354)
Q Consensus 202 ~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~---~~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~ 278 (354)
.+.+.+++.+ .+...||||+++|+.+|. +..+. +.||...+....+....++|+.++..|++.
T Consensus 64 ~~~l~~~l~~------------~~~~kv~~d~k~~~~~L~~~gi~~~~--~~D~~laayll~p~~~~~~l~~l~~~~l~~ 129 (172)
T smart00474 64 LEILKDLLED------------ETITKVGHNAKFDLHVLARFGIELEN--IFDTMLAAYLLLGGPSKHGLATLLKEYLGV 129 (172)
T ss_pred HHHHHHHhcC------------CCceEEEechHHHHHHHHHCCCcccc--hhHHHHHHHHHcCCCCcCCHHHHHHHHhCC
Confidence 4557778821 456799999999999984 33333 379987766555544436999999999987
Q ss_pred cCCC--C------C---C----ChHHHHHHHHHHHHHHHHhh
Q 018558 279 DIQI--G------I---Q----DPYDDCVATMRLYMRMKSQA 305 (354)
Q Consensus 279 ~i~~--~------~---H----~Al~DA~at~~l~~~~~~~~ 305 (354)
.+.. + . . -|..||.++.+|+..+.++.
T Consensus 130 ~~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 130 ELDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred CCCcccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 6531 0 0 0 15667878888887776653
No 100
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=96.62 E-value=0.0014 Score=37.92 Aligned_cols=25 Identities=36% Similarity=0.680 Sum_probs=23.1
Q ss_pred cccccccccccCChHHHHHhhhhcccc
Q 018558 12 RNKCAACFRQFNRLEHLVEHMRTSYHS 38 (354)
Q Consensus 12 ~~~C~~Cgk~f~~~~~L~~H~~~~~H~ 38 (354)
||+|..|++.|.....|..|++. |.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~--h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRS--HC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCT--TT
T ss_pred CCCCCccCCccCChhHHHHHhHH--hc
Confidence 68999999999999999999988 65
No 101
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=96.58 E-value=0.0046 Score=52.38 Aligned_cols=72 Identities=22% Similarity=0.166 Sum_probs=33.7
Q ss_pred CCcEEEEec-hhhhhhhhccc-----CC-CceeeeccccCCCccCCCCCchHHHHHHHHhCCcCCCCCCChHHHHHHHHH
Q 018558 224 RARILVGHG-LDHDLDRLQVE-----YP-AIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQIGIQDPYDDCVATMR 296 (354)
Q Consensus 224 ~~~ilVgHn-~~~Dl~~L~~~-----~~-~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~~~~H~Al~DA~at~~ 296 (354)
+...+|+|| ..||+.+|+-. .+ ....+|+....... ...+++|+.++.. ||...+ ..-.+...+..
T Consensus 56 ~~~~iv~yng~~FD~p~L~~~~~~~~~~~~~~~iDl~~~~~~~--~~~~~~Lk~ve~~-lg~~~~----~~~~~G~~~~~ 128 (164)
T PF13482_consen 56 EADNIVTYNGKNFDIPFLKRRAKRYGLPPPFNHIDLLKIIKKH--FLESYSLKNVEKF-LGIERR----DDDISGSESVK 128 (164)
T ss_dssp TT--EEESSTTTTHHHHHHHHH-HHHH--GGGEEEHHHHHT-T--TSCCTT--SHHH----------------HHHHHHH
T ss_pred cCCeEEEEeCcccCHHHHHHHHHHcCCCcccchhhHHHHHHhc--cCCCCCHHHHhhh-cccccc----cCCCCHHHHHH
Confidence 557899988 58999988631 12 34467877654322 1266799999886 444332 12244455566
Q ss_pred HHHHHH
Q 018558 297 LYMRMK 302 (354)
Q Consensus 297 l~~~~~ 302 (354)
+|..+.
T Consensus 129 ~~~~~~ 134 (164)
T PF13482_consen 129 LYKEYL 134 (164)
T ss_dssp HHH---
T ss_pred HHHHHH
Confidence 665443
No 102
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=96.56 E-value=0.0004 Score=39.94 Aligned_cols=23 Identities=30% Similarity=0.726 Sum_probs=18.7
Q ss_pred cccccc---CCCCCcccccccccccccccccccCCC
Q 018558 56 SLREHL---IGPLPKQECKNVFNNRGCRFCLAILDG 88 (354)
Q Consensus 56 ~L~~H~---~~e~p~~~C~k~F~~~~C~~C~k~f~~ 88 (354)
+|.+|+ +|++|| .|+.|+++|.+
T Consensus 1 ~l~~H~~~H~~~k~~----------~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPY----------KCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSE----------EESSSSEEESS
T ss_pred CHHHHhhhcCCCCCC----------CCCCCcCeeCc
Confidence 366787 999999 88899888863
No 103
>PHA02528 43 DNA polymerase; Provisional
Probab=96.45 E-value=0.055 Score=57.85 Aligned_cols=204 Identities=12% Similarity=0.017 Sum_probs=105.5
Q ss_pred cCCCChhHHHHHhhccccCCCCccchhhhhccCCCCCcccCCCCC-CCCceEEeecccccc--CCCCC--ccceeeEEEE
Q 018558 85 ILDGPNARRLHQERCQMVSSATTGLNARLANLGVRDSLTIDNTHT-RDPQVVAIACKMVGG--GSDGS--LDLCGRVCII 159 (354)
Q Consensus 85 ~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~vaiD~Ettg~--~~~~~--~~~i~~i~vv 159 (354)
-|.+...+.+-++.-.-.+...-++++|....-. ....-+-... +..+++++|+|+... -|+.. ...|..|++.
T Consensus 59 ~~~~~~~~~~~~~~~~~~~~~~~~merfi~~~~~-~~~~~~~~~~~p~lrv~s~DIE~~~~~gfP~p~~~~d~IisIsl~ 137 (881)
T PHA02528 59 KFDSMRDARKWMKRMKDVGFEALGMDDFKLQYIS-DTYPGEIKYDRSKIRIANLDIEVTAEDGFPDPEEAKYEIDAITHY 137 (881)
T ss_pred ECCCHHHHHHHHHHHHhcCCceeehhHHhhhhhh-hhcCCCCCCCCCCccEEEEEEEECCCCCCCCcccCCCcEEEEEEe
Confidence 4555555555554433333334466777664332 1111111222 577899999999741 13333 4578888887
Q ss_pred ecCCceEEeeeecCCccccCceeeec--CCChhhhcCCCCHHHHHHHHHHHHhcCCCCccccCCCCCCcEEEEech-hhh
Q 018558 160 DEYENIIFHAYVKPPIPVTSYRYETT--GIRPEHLRDAIPLKQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGL-DHD 236 (354)
Q Consensus 160 ~~~g~~i~~~~v~P~~~i~~~~~~it--GIt~~~l~~ap~~~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~-~~D 236 (354)
+..+..++-..+....+......... -...-.+..-++-.+++..|.+++..- .-.||+|||+ .||
T Consensus 138 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~sE~eLL~~F~~~i~~~-----------DPDII~GyNi~~FD 206 (881)
T PHA02528 138 DSIDDRFYVFDLGSVEEWDAKGDEVPQEILDKVVYMPFDTEREMLLEYINFWEEN-----------TPVIFTGWNVELFD 206 (881)
T ss_pred cCCCCEEEEEEecCcccccccCCcccccccCCeeEEEcCCHHHHHHHHHHHHHHh-----------CCcEEEecCCccCC
Confidence 76665432222211000000000000 000111112356788999999999321 1259999996 789
Q ss_pred hhhh--------cccC----C-C-----------------------ceeeeccccCCCc-cCCCCCchHHHHHHHHhCCc
Q 018558 237 LDRL--------QVEY----P-A-----------------------IMTRDTAKYPPLM-KTSKLSNSLKYLTQAYLGYD 279 (354)
Q Consensus 237 l~~L--------~~~~----~-~-----------------------~~~~Dt~~~~~~~-~~~~~~~~L~~l~~~~l~~~ 279 (354)
+..| +... . . ..++|...++... .....+++|..+|.++||.+
T Consensus 207 lpYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~GRv~lD~~dl~k~~~~~~l~SYsLe~VA~~~LG~~ 286 (881)
T PHA02528 207 VPYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISGISILDYLDLYKKFTFTNQPSYRLDYIAEVELGKK 286 (881)
T ss_pred HHHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcceEEEeHHHHHHHhhhcccccCCHHHHHHHHhCCC
Confidence 8654 2110 0 0 0012222222211 11345889999999999865
Q ss_pred CCCC----------------CCChHHHHHHHHHHHHH
Q 018558 280 IQIG----------------IQDPYDDCVATMRLYMR 300 (354)
Q Consensus 280 i~~~----------------~H~Al~DA~at~~l~~~ 300 (354)
-..- .+-.+.||+.+.+|+.+
T Consensus 287 K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 287 KLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred CccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 4320 13347899999999877
No 104
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=96.36 E-value=0.0012 Score=36.60 Aligned_cols=22 Identities=18% Similarity=0.386 Sum_probs=19.4
Q ss_pred ccccccccCCCChhHHHHHhhc
Q 018558 78 GCRFCLAILDGPNARRLHQERC 99 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~~ 99 (354)
.|+.|+++|..+..|..|++.|
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCccCCHHHHHHHHhHC
Confidence 5899999999999999999763
No 105
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=96.25 E-value=0.04 Score=60.20 Aligned_cols=154 Identities=12% Similarity=0.071 Sum_probs=88.7
Q ss_pred CCCCceEEeecccccc----CCCCCccceeeEEEE-ecCCce---EEeeeecCCccccCceeeecCCChhhhcCCCCHHH
Q 018558 129 TRDPQVVAIACKMVGG----GSDGSLDLCGRVCII-DEYENI---IFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQ 200 (354)
Q Consensus 129 ~~~~~~vaiD~Ettg~----~~~~~~~~i~~i~vv-~~~g~~---i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~ 200 (354)
.++.++.++|+|+.+. -|+...+.|+.|+.+ ...|.. ....++-+.. ...+.| ..+..-++-.+
T Consensus 261 ~pplrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~~~~~r~vftl~~-----c~~i~g---~~V~~f~sE~e 332 (1054)
T PTZ00166 261 IAPLRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLTKFIFTLKE-----CASIAG---ANVLSFETEKE 332 (1054)
T ss_pred CCCcEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCccCCcceEEEecCc-----cccCCC---ceEEEeCCHHH
Confidence 4677899999999863 244456777788765 444431 1111111111 111112 22333467788
Q ss_pred HHHHHHHHHhcCCCCccccCCCCCCcEEEEech-hhhhhhh-------cccC----------C-----------------
Q 018558 201 VQRKIQDFLCNGEPMWKIRPRGSRARILVGHGL-DHDLDRL-------QVEY----------P----------------- 245 (354)
Q Consensus 201 v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~-~~Dl~~L-------~~~~----------~----------------- 245 (354)
++..|.+++..- .=.||+|||+ .||+..| ++.. +
T Consensus 333 LL~~f~~~I~~~-----------DPDII~GYNi~~FDlpYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~ 401 (1054)
T PTZ00166 333 LLLAWAEFVIAV-----------DPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRE 401 (1054)
T ss_pred HHHHHHHHHHhc-----------CCCEEEecCCcCCcHHHHHHHHHHhCCCchhhcCcccCCCccccccccccccccccc
Confidence 999999998321 2269999997 5898644 2210 0
Q ss_pred -------CceeeeccccCCCccCCCCCchHHHHHHHHhCCcCCCCC-------------------CChHHHHHHHHHHHH
Q 018558 246 -------AIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQIGI-------------------QDPYDDCVATMRLYM 299 (354)
Q Consensus 246 -------~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~~~~-------------------H~Al~DA~at~~l~~ 299 (354)
-..++|+..+.... ....+|+|.+++.++||.....-. .-.+.||..+.+|+.
T Consensus 402 ~~~~~i~GR~~iDl~~~~~~~-~kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L~~ 480 (1054)
T PTZ00166 402 SKEINIEGRIQFDVMDLIRRD-YKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLD 480 (1054)
T ss_pred cceeEeeeEEEEEHHHHHHHh-cCcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHH
Confidence 01133443333211 234589999999999996543111 123679999999987
Q ss_pred HHH
Q 018558 300 RMK 302 (354)
Q Consensus 300 ~~~ 302 (354)
++.
T Consensus 481 kl~ 483 (1054)
T PTZ00166 481 KLL 483 (1054)
T ss_pred HHh
Confidence 764
No 106
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=96.12 E-value=0.0031 Score=34.88 Aligned_cols=22 Identities=36% Similarity=0.688 Sum_probs=18.6
Q ss_pred ccccccccccCChHHHHHhhhh
Q 018558 13 NKCAACFRQFNRLEHLVEHMRT 34 (354)
Q Consensus 13 ~~C~~Cgk~f~~~~~L~~H~~~ 34 (354)
|.|+.|++.|.....|..|+..
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHh
Confidence 6899999999999999999987
No 107
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=96.11 E-value=0.0029 Score=43.33 Aligned_cols=46 Identities=30% Similarity=0.520 Sum_probs=29.9
Q ss_pred cccccccccccCChHHHHHhhhhccccCcc-c-cccccccccCCcccccccc
Q 018558 12 RNKCAACFRQFNRLEHLVEHMRTSYHSVHE-P-VCGICKKHCRSFESLREHL 61 (354)
Q Consensus 12 ~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k-~-~C~~C~k~f~~~~~L~~H~ 61 (354)
.|.|+.||+. .....|..|... .|..+. . .|++|...+. .+|..|+
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~-~H~~~~~~v~CPiC~~~~~--~~l~~Hl 49 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCED-EHRSESKNVVCPICSSRVT--DNLIRHL 49 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHh-HCcCCCCCccCCCchhhhh--hHHHHHH
Confidence 4899999994 556789999766 266543 3 6777765433 2455443
No 108
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.11 E-value=0.0025 Score=58.34 Aligned_cols=67 Identities=19% Similarity=0.278 Sum_probs=45.3
Q ss_pred Cccccccc--cccccCChHHHHHhhhhccccCccccccccccccCCcccccccc---CCCCCcccccccccccccccccc
Q 018558 10 TLRNKCAA--CFRQFNRLEHLVEHMRTSYHSVHEPVCGICKKHCRSFESLREHL---IGPLPKQECKNVFNNRGCRFCLA 84 (354)
Q Consensus 10 ~k~~~C~~--Cgk~f~~~~~L~~H~~~~~H~~~k~~C~~C~k~f~~~~~L~~H~---~~e~p~~~C~k~F~~~~C~~C~k 84 (354)
+|||+|++ |.|.++..-.|+.|+.- -|...+. .....-..|. ...||| .|++|+|
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lh-GH~~~~~---------~~~p~p~~~~~F~~~~KPY----------rCevC~K 406 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLH-GHQNQKL---------HENPSPEKMNIFSAKDKPY----------RCEVCDK 406 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhc-cccCccc---------CCCCCccccccccccCCce----------eccccch
Confidence 58888865 88888888888888654 1322221 1111111222 456888 9999999
Q ss_pred cCCCChhHHHHH
Q 018558 85 ILDGPNARRLHQ 96 (354)
Q Consensus 85 ~f~~~~~l~~H~ 96 (354)
.|.....|+.|.
T Consensus 407 RYKNlNGLKYHr 418 (423)
T COG5189 407 RYKNLNGLKYHR 418 (423)
T ss_pred hhccCccceecc
Confidence 999999999887
No 109
>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=96.10 E-value=0.024 Score=48.37 Aligned_cols=92 Identities=20% Similarity=0.215 Sum_probs=63.2
Q ss_pred HHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhc----ccCCCceeeeccccCCCccCCCCCchHHHHHHHHh
Q 018558 201 VQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQ----VEYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYL 276 (354)
Q Consensus 201 v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~----~~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l 276 (354)
+.+.|.+++.| .+...||||+++|+.+|. +. . ..+.||.....+..+... .+|+.++..||
T Consensus 52 ~~~~l~~ll~~------------~~i~kv~~d~K~~~~~L~~~~gi~-~-~~~~D~~laayLl~p~~~-~~l~~l~~~~l 116 (178)
T cd06142 52 DLSPLKELLAD------------PNIVKVFHAAREDLELLKRDFGIL-P-QNLFDTQIAARLLGLGDS-VGLAALVEELL 116 (178)
T ss_pred cHHHHHHHHcC------------CCceEEEeccHHHHHHHHHHcCCC-C-CCcccHHHHHHHhCCCcc-ccHHHHHHHHh
Confidence 34556677821 456899999999999883 33 2 235799876655554433 59999999998
Q ss_pred CCcCC-C---CC-----------CChHHHHHHHHHHHHHHHHhhhh
Q 018558 277 GYDIQ-I---GI-----------QDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 277 ~~~i~-~---~~-----------H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
+..+. . +. +.+..||.++..|+..+.++..+
T Consensus 117 ~~~~~~~~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~e 162 (178)
T cd06142 117 GVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEE 162 (178)
T ss_pred CCCCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence 87632 1 00 12667788889999888887754
No 110
>PRK05762 DNA polymerase II; Reviewed
Probab=95.77 E-value=0.048 Score=57.98 Aligned_cols=143 Identities=17% Similarity=0.216 Sum_probs=80.9
Q ss_pred CCCceEEeeccccccCCCCCccceeeEEEEecCCceEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHHHHH
Q 018558 130 RDPQVVAIACKMVGGGSDGSLDLCGRVCIIDEYENIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQDFL 209 (354)
Q Consensus 130 ~~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~~~i 209 (354)
+..+++++|+|+...+ +|..|+........++ .+.+..+. ..+.+..-++-.+++..|++++
T Consensus 153 p~lrvlsfDIE~~~~~------~i~sI~~~~~~~~~vi--~ig~~~~~----------~~~~v~~~~sE~~LL~~F~~~i 214 (786)
T PRK05762 153 PPLKVVSLDIETSNKG------ELYSIGLEGCGQRPVI--MLGPPNGE----------ALDFLEYVADEKALLEKFNAWF 214 (786)
T ss_pred CCCeEEEEEEEEcCCC------ceEEeeecCCCCCeEE--EEECCCCC----------CcceEEEcCCHHHHHHHHHHHH
Confidence 5678999999998531 3444444322222111 11221111 0111444567788999999999
Q ss_pred hcCCCCccccCCCCCCcEEEEech-hhhhhhh-------cccC--------------C-----------CceeeeccccC
Q 018558 210 CNGEPMWKIRPRGSRARILVGHGL-DHDLDRL-------QVEY--------------P-----------AIMTRDTAKYP 256 (354)
Q Consensus 210 ~~~~~~~~~~~~~~~~~ilVgHn~-~~Dl~~L-------~~~~--------------~-----------~~~~~Dt~~~~ 256 (354)
.+- .-.||||||+ .||+.+| ++.. + ...++|+..+.
T Consensus 215 ~~~-----------DPDIIvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~ 283 (786)
T PRK05762 215 AEH-----------DPDVIIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDAL 283 (786)
T ss_pred Hhc-----------CCCEEEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHH
Confidence 321 1159999996 6898765 2211 0 00133444332
Q ss_pred CCccCCCCCchHHHHHHHHhCCcCCC-CC-------------------CChHHHHHHHHHHHHHH
Q 018558 257 PLMKTSKLSNSLKYLTQAYLGYDIQI-GI-------------------QDPYDDCVATMRLYMRM 301 (354)
Q Consensus 257 ~~~~~~~~~~~L~~l~~~~l~~~i~~-~~-------------------H~Al~DA~at~~l~~~~ 301 (354)
........+++|+++|.++||..-.. .. .-.+.||..|..|+.++
T Consensus 284 k~~~~~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 284 KSATWVFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred HHhhccCCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHh
Confidence 21111335789999999999865431 11 12478999999998744
No 111
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.72 E-value=0.0093 Score=39.59 Aligned_cols=34 Identities=18% Similarity=0.376 Sum_probs=20.2
Q ss_pred CCCCccccccccccccCChHHHHHhhhhccccCccc
Q 018558 7 SSETLRNKCAACFRQFNRLEHLVEHMRTSYHSVHEP 42 (354)
Q Consensus 7 ~~~~k~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~ 42 (354)
+..++|..|++|+..+.+..+|++|+.. +.+.+|
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~--~H~~k~ 52 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEI--RHFKKP 52 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHH--HTTTS-
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHH--HhcccC
Confidence 4456778888888888888888888876 555444
No 112
>PHA00616 hypothetical protein
Probab=95.70 E-value=0.0043 Score=40.17 Aligned_cols=27 Identities=15% Similarity=0.138 Sum_probs=21.8
Q ss_pred ccccccccCCCChhHHHHHhhccccCC
Q 018558 78 GCRFCLAILDGPNARRLHQERCQMVSS 104 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~~~~~~~ 104 (354)
.|..||+.|..+..|..|+++++-..+
T Consensus 3 qC~~CG~~F~~~s~l~~H~r~~hg~~~ 29 (44)
T PHA00616 3 QCLRCGGIFRKKKEVIEHLLSVHKQNK 29 (44)
T ss_pred ccchhhHHHhhHHHHHHHHHHhcCCCc
Confidence 788888888888888888888776543
No 113
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=95.63 E-value=0.043 Score=55.49 Aligned_cols=95 Identities=22% Similarity=0.183 Sum_probs=69.1
Q ss_pred HHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcccCC-CceeeeccccCCCccCCCCCchHHHHHHHHhCCc
Q 018558 201 VQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQVEYP-AIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYD 279 (354)
Q Consensus 201 v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~~~~-~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~ 279 (354)
+...+..|+.+ .+...||||+++|+.+|...-. .....||+.......+....+.+..|+..||+..
T Consensus 66 ~~~~l~~~l~~------------~~~~kv~~~~K~d~~~l~~~Gi~~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~ 133 (593)
T COG0749 66 VLAALKPLLED------------EGIKKVGQNLKYDYKVLANLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLE 133 (593)
T ss_pred hHHHHHHHhhC------------cccchhccccchhHHHHHHcCCcccchHHHHHHHhccCcCcCcCCHHHHHHHhcCCc
Confidence 78889999933 5567999999999988753221 1235699887777766666789999999998765
Q ss_pred CCCC---------------------CCChHHHHHHHHHHHHHHHHhhhh
Q 018558 280 IQIG---------------------IQDPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 280 i~~~---------------------~H~Al~DA~at~~l~~~~~~~~~~ 307 (354)
.... .-.+..||.++.+|+..+..+..+
T Consensus 134 ~~~~~~i~~kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~l~~ 182 (593)
T COG0749 134 TITFEDIAGKGKKQLTFADVKLEKATEYAAEDADATLRLESILEPELLK 182 (593)
T ss_pred cchhHHhhccccccCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 4310 123567899999999888865543
No 114
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=95.63 E-value=0.0046 Score=34.13 Aligned_cols=23 Identities=17% Similarity=0.348 Sum_probs=18.6
Q ss_pred ccccccccCCCChhHHHHHhhcc
Q 018558 78 GCRFCLAILDGPNARRLHQERCQ 100 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~~~ 100 (354)
.|+.|++.|.+...|..|+++++
T Consensus 2 ~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp E-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCcCCCCcCCcHHHHHHHHHhhC
Confidence 58999999999999999998764
No 115
>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=95.63 E-value=0.031 Score=47.90 Aligned_cols=94 Identities=19% Similarity=0.240 Sum_probs=62.0
Q ss_pred HHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhc---ccCCCceeeeccccCCCccCCCCCchHHHHHHHHhC
Q 018558 201 VQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQ---VEYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLG 277 (354)
Q Consensus 201 v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~---~~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~ 277 (354)
+...+.+++.+ .+...|+||+++|+.+|. +..+. .+.||.....+..+...+++|+.++..||+
T Consensus 44 ~~~~l~~~l~~------------~~~~ki~~d~K~~~~~l~~~gi~~~~-~~fDt~laaYLL~p~~~~~~l~~l~~~yl~ 110 (178)
T cd06140 44 DLAALKEWLED------------EKIPKVGHDAKRAYVALKRHGIELAG-VAFDTMLAAYLLDPTRSSYDLADLAKRYLG 110 (178)
T ss_pred HHHHHHHHHhC------------CCCceeccchhHHHHHHHHCCCcCCC-cchhHHHHHHHcCCCCCCCCHHHHHHHHcC
Confidence 45567778821 456799999999999884 33332 247998877666655444699999999988
Q ss_pred CcCCC------CCC------------ChHHHHHHHHHHHHHHHHhhhh
Q 018558 278 YDIQI------GIQ------------DPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 278 ~~i~~------~~H------------~Al~DA~at~~l~~~~~~~~~~ 307 (354)
..+.. ... -+..||.++..|+..++++..+
T Consensus 111 ~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~~L~~ 158 (178)
T cd06140 111 RELPSDEEVYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEEELEE 158 (178)
T ss_pred CCCcchHHhcCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77421 000 1344566677777777776643
No 116
>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=95.49 E-value=0.033 Score=51.22 Aligned_cols=72 Identities=22% Similarity=0.176 Sum_probs=49.8
Q ss_pred CCcEEEEechhhhhhhhc-------------------ccCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCcC----
Q 018558 224 RARILVGHGLDHDLDRLQ-------------------VEYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDI---- 280 (354)
Q Consensus 224 ~~~ilVgHn~~~Dl~~L~-------------------~~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i---- 280 (354)
...++||||.-.|+.+|- ...|. ++||-.+..... ....+|..|+..+ +..-
T Consensus 148 ~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF~~~~~~~FP~--i~DtK~la~~~~--~~~~~L~~l~~~l-~~~~~~~~ 222 (262)
T PF04857_consen 148 SKKPIVGHNGLYDLMYLYKKFIGPLPETLEEFKELLRELFPR--IYDTKYLAEECP--GKSTSLQELAEEL-GIRRNPSS 222 (262)
T ss_dssp C-SEEEESSTHHHHHHHHHHHTTS--SSHHHHHHHHHHHSSS--EEEHHHHHTSTT--TS-SSHHHHHHHT-TSTT----
T ss_pred cCCcEEEeChHhHHHHHHHHhcCCCCCCHHHHHHHHHHHCcc--cccHHHHHHhcc--ccccCHHHHHHHh-CCCccccc
Confidence 558999999999986541 12344 789887766442 3456899998854 4322
Q ss_pred --------------------CCCCCChHHHHHHHHHHHHH
Q 018558 281 --------------------QIGIQDPYDDCVATMRLYMR 300 (354)
Q Consensus 281 --------------------~~~~H~Al~DA~at~~l~~~ 300 (354)
....|.|--||.+|+.+|.+
T Consensus 223 ~~~~~~~~~~~~~~~~~~~~~~~~HeAGyDA~mTg~~F~~ 262 (262)
T PF04857_consen 223 ISSPEGFPSYDEEKNNFPMFGEKAHEAGYDAYMTGCVFIK 262 (262)
T ss_dssp EEE-TTS-------------SS-TTSHHHHHHHHHHHHHH
T ss_pred cccccccccccccccccccCCCCCCCcchHHHHHHHHHcC
Confidence 22389999999999999853
No 117
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.46 E-value=0.0068 Score=46.49 Aligned_cols=72 Identities=21% Similarity=0.322 Sum_probs=21.2
Q ss_pred cccccccccCChHHHHHhhhhccccCccccccccccccCCcccccccc--CCCCCcccccccccccccccccccCCCChh
Q 018558 14 KCAACFRQFNRLEHLVEHMRTSYHSVHEPVCGICKKHCRSFESLREHL--IGPLPKQECKNVFNNRGCRFCLAILDGPNA 91 (354)
Q Consensus 14 ~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~~C~~C~k~f~~~~~L~~H~--~~e~p~~~C~k~F~~~~C~~C~k~f~~~~~ 91 (354)
+|..|+..|.....|..|+.. .|.-..+.. ..+.....+..+. .-...+ .|..|++.|.+...
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~-~H~~~~~~~----~~l~~~~~~~~~~~~~~~~~~----------~C~~C~~~f~s~~~ 65 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKK-KHGFDIPDQ----KYLVDPNRLLNYLRKKVKESF----------RCPYCNKTFRSREA 65 (100)
T ss_dssp -----------------------------------------------------SSE----------EBSSSS-EESSHHH
T ss_pred Ccccccccccccccccccccc-ccccccccc----cccccccccccccccccCCCC----------CCCccCCCCcCHHH
Confidence 588999999999999999866 244322211 1111222222222 111234 89999999999999
Q ss_pred HHHHHhhcc
Q 018558 92 RRLHQERCQ 100 (354)
Q Consensus 92 l~~H~~~~~ 100 (354)
|..|++.+.
T Consensus 66 l~~Hm~~~~ 74 (100)
T PF12756_consen 66 LQEHMRSKH 74 (100)
T ss_dssp HHHHHHHTT
T ss_pred HHHHHcCcc
Confidence 999998654
No 118
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.39 E-value=0.011 Score=33.08 Aligned_cols=24 Identities=42% Similarity=0.771 Sum_probs=21.7
Q ss_pred ccccccccccCChHHHHHhhhhcccc
Q 018558 13 NKCAACFRQFNRLEHLVEHMRTSYHS 38 (354)
Q Consensus 13 ~~C~~Cgk~f~~~~~L~~H~~~~~H~ 38 (354)
|+|..|++.|...+.|..|++. |.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~--H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRT--HX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHH--hc
Confidence 6799999999999999999987 65
No 119
>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=95.36 E-value=0.048 Score=49.26 Aligned_cols=135 Identities=19% Similarity=0.125 Sum_probs=71.5
Q ss_pred ceEEeeccccccCCCCCccceeeEEEEecCC-----c---eE----EeeeecCCcc--ccCceeeecCCChhhhcCCCCH
Q 018558 133 QVVAIACKMVGGGSDGSLDLCGRVCIIDEYE-----N---II----FHAYVKPPIP--VTSYRYETTGIRPEHLRDAIPL 198 (354)
Q Consensus 133 ~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g-----~---~i----~~~~v~P~~~--i~~~~~~itGIt~~~l~~ap~~ 198 (354)
.++++.+-|+-- +.....+|..|+++-.+. . .. +-++++|... .+......-......+.--++-
T Consensus 4 ~v~sls~~T~~n-~k~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~v~~~~~E 82 (234)
T cd05776 4 TVMSLSIKTVLN-SKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKVRIFENE 82 (234)
T ss_pred EEEEEEeEEEec-CcCCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCCCCCchHHHHHHhcCCcEEEeCCH
Confidence 456666666532 233345667777653221 1 11 2334555432 1222112211122223344677
Q ss_pred HHHHHHHHHHHhcCCCCccccCCCCCCcEEEEech-hhhhhhh-------cccC------------C-------------
Q 018558 199 KQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGL-DHDLDRL-------QVEY------------P------------- 245 (354)
Q Consensus 199 ~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~-~~Dl~~L-------~~~~------------~------------- 245 (354)
.+.+..|..++..- .=.||||||+ .||+.+| ++.. |
T Consensus 83 ~~LL~~f~~~i~~~-----------DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~ 151 (234)
T cd05776 83 RALLNFFLAKLQKI-----------DPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGEREL 151 (234)
T ss_pred HHHHHHHHHHHhhc-----------CCCEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCcccccccccccccc
Confidence 88999999998321 2259999998 8898765 2210 0
Q ss_pred --CceeeeccccCCCccCCCCCchHHHHHHHHhCCcC
Q 018558 246 --AIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDI 280 (354)
Q Consensus 246 --~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i 280 (354)
...++|+....+.. ....+|+|..+|..+||.+-
T Consensus 152 ~~GRl~~D~~~~~k~~-~~~~sY~L~~va~~~Lg~~k 187 (234)
T cd05776 152 TAGRLLCDTYLSAKEL-IRCKSYDLTELSQQVLGIER 187 (234)
T ss_pred ccCchhhccHHHHHHH-hCCCCCChHHHHHHHhCcCc
Confidence 01133444333211 13468999999999999743
No 120
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=95.22 E-value=0.087 Score=46.50 Aligned_cols=94 Identities=21% Similarity=0.192 Sum_probs=58.7
Q ss_pred HHHHHHHHHHHHhcCCCCccccCCCCCCcEEEEec-hhhhhhhhc-------ccCCCc-----------------eeeec
Q 018558 198 LKQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHG-LDHDLDRLQ-------VEYPAI-----------------MTRDT 252 (354)
Q Consensus 198 ~~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn-~~~Dl~~L~-------~~~~~~-----------------~~~Dt 252 (354)
-++++.+|.+++.. ..-.||+|| -.||+.+|. +..|.. .-+|+
T Consensus 37 E~~lL~~F~~~~~~------------~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DL 104 (209)
T PF10108_consen 37 EKELLQDFFDLVEK------------YNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDL 104 (209)
T ss_pred HHHHHHHHHHHHHh------------CCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccH
Confidence 57899999999921 344799999 589998763 332221 12455
Q ss_pred cccCCCccCCCCCchHHHHHHHHhCCcCCCCC------------------CChHHHHHHHHHHHHHHHHhh
Q 018558 253 AKYPPLMKTSKLSNSLKYLTQAYLGYDIQIGI------------------QDPYDDCVATMRLYMRMKSQA 305 (354)
Q Consensus 253 ~~~~~~~~~~~~~~~L~~l~~~~l~~~i~~~~------------------H~Al~DA~at~~l~~~~~~~~ 305 (354)
+.+..... ...+.+|+.||..+ |+.-..+. .--..|+++|+.||.++.-.-
T Consensus 105 md~l~~~g-~~~~~sLd~la~~l-giPgK~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~~~ 173 (209)
T PF10108_consen 105 MDLLSFYG-AKARTSLDELAALL-GIPGKDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFELLR 173 (209)
T ss_pred HHHHhccC-ccccCCHHHHHHHc-CCCCCCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 54322111 23467999999854 43211111 122679999999999887644
No 121
>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=95.11 E-value=0.23 Score=44.74 Aligned_cols=147 Identities=10% Similarity=0.031 Sum_probs=79.0
Q ss_pred ceEEeecccccc---CCCCCccceeeEEEEecCCceEEe-------ee-ecCCccccCceeeecCCChhhhcCCCCHHHH
Q 018558 133 QVVAIACKMVGG---GSDGSLDLCGRVCIIDEYENIIFH-------AY-VKPPIPVTSYRYETTGIRPEHLRDAIPLKQV 201 (354)
Q Consensus 133 ~~vaiD~Ettg~---~~~~~~~~i~~i~vv~~~g~~i~~-------~~-v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v 201 (354)
.+.++|+|+.+. -|++..+.|..|+.+-......+. .+ +.+...-........++....|.--++-.++
T Consensus 5 ~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~v~~~~~E~~L 84 (231)
T cd05778 5 TILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKSNASNGRIRSGLSGIPVEVVESELEL 84 (231)
T ss_pred EEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccchhhhhccccCCCCCeEEEeCCHHHH
Confidence 568899998742 356666777777655332221111 12 2222211110011223334445556778889
Q ss_pred HHHHHHHHhcCCCCccccCCCCCCcEEEEech-hhhhhhh-------cccC-----------CC----------------
Q 018558 202 QRKIQDFLCNGEPMWKIRPRGSRARILVGHGL-DHDLDRL-------QVEY-----------PA---------------- 246 (354)
Q Consensus 202 ~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~-~~Dl~~L-------~~~~-----------~~---------------- 246 (354)
+.+|.+++..- .=.||+|||+ .||+..| ++.. +.
T Consensus 85 L~~f~~~i~~~-----------DPDii~GyNi~~fd~~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~~g~~~~~ 153 (231)
T cd05778 85 FEELIDLVRRF-----------DPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDEWGYTHTS 153 (231)
T ss_pred HHHHHHHHHHh-----------CCCEEEEeccccCcHHHHHHHHHHhCCcchhhhccCCCCCCcccccccccccccccCC
Confidence 99999998322 2259999998 6787544 1110 00
Q ss_pred ------ceeeeccccCCCccCCCCCchHHHHHHHHhCCcCCCCCCChHHHH
Q 018558 247 ------IMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQIGIQDPYDDC 291 (354)
Q Consensus 247 ------~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~~~~H~Al~DA 291 (354)
..++|...+.+. .....+|+|..+|.++||...+.-.+..+.+.
T Consensus 154 ~~~i~GRi~lD~~~~~r~-~~kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~ 203 (231)
T cd05778 154 GIKIVGRHILNVWRLMRS-ELALTNYTLENVVYHVLHQRIPLYSNKTLTEW 203 (231)
T ss_pred ceEEeeEEEeEhHHHHHH-HcCcccCCHHHHHHHHhCCCCCCCCHHHHHHH
Confidence 002233222211 11345899999999999997764345545443
No 122
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.65 E-value=0.073 Score=57.13 Aligned_cols=96 Identities=19% Similarity=0.182 Sum_probs=66.8
Q ss_pred CHHHHHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhc---ccCCCceeeeccccCCCccCCCCCchHHHHHH
Q 018558 197 PLKQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQ---VEYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQ 273 (354)
Q Consensus 197 ~~~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~---~~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~ 273 (354)
....+...|.+++.+ .+..+||||++||+.+|. +.... .+.||.....+..+.. +++|+.|+.
T Consensus 362 ~~~~~~~~l~~~l~~------------~~~~~v~~n~K~d~~~l~~~gi~~~~-~~~Dt~la~yll~~~~-~~~l~~la~ 427 (887)
T TIGR00593 362 LTILTDDKFARWLLN------------EQIKKIGHDAKFLMHLLKREGIELGG-VIFDTMLAAYLLDPAQ-VSTLDTLAR 427 (887)
T ss_pred hhHHHHHHHHHHHhC------------CCCcEEEeeHHHHHHHHHhCCCCCCC-cchhHHHHHHHcCCCC-CCCHHHHHH
Confidence 355677788889822 345689999999999984 32222 2579987666555433 359999999
Q ss_pred HHhCCcCCC-------C-----------CCChHHHHHHHHHHHHHHHHhhh
Q 018558 274 AYLGYDIQI-------G-----------IQDPYDDCVATMRLYMRMKSQAH 306 (354)
Q Consensus 274 ~~l~~~i~~-------~-----------~H~Al~DA~at~~l~~~~~~~~~ 306 (354)
.||+..+.. + ...|..||.+|..||..+..+..
T Consensus 428 ~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~ 478 (887)
T TIGR00593 428 RYLVEELILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKELD 478 (887)
T ss_pred HHcCcccccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 998864210 0 01367789999999988887764
No 123
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=94.32 E-value=0.013 Score=33.68 Aligned_cols=23 Identities=22% Similarity=0.294 Sum_probs=19.7
Q ss_pred ccccccccCCCChhHHHHHhhcc
Q 018558 78 GCRFCLAILDGPNARRLHQERCQ 100 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~~~ 100 (354)
.|..|++.|.....|..|++.|.
T Consensus 3 ~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 3 ECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCccCCccCChhHHHHHhHHhc
Confidence 68999999999999999997653
No 124
>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=94.08 E-value=0.15 Score=45.25 Aligned_cols=88 Identities=22% Similarity=0.246 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHHhcCCCCccccCCCCCCcEEEEech-hhhhhhhc-------ccCCCc----------------eeeecc
Q 018558 198 LKQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGL-DHDLDRLQ-------VEYPAI----------------MTRDTA 253 (354)
Q Consensus 198 ~~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~-~~Dl~~L~-------~~~~~~----------------~~~Dt~ 253 (354)
-.+++.+|.+++.+ .+.+|||||. .||+.+|. +..|.. ..+|+.
T Consensus 78 E~elL~~F~~~i~~------------~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~ 145 (208)
T cd05782 78 EKELLEDFFQLIEK------------KNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLM 145 (208)
T ss_pred HHHHHHHHHHHHHH------------hCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHH
Confidence 37899999999921 2458999996 89997763 322210 134655
Q ss_pred ccCCCccCCCCCchHHHHHHHHhCCcCCCC------------------CCChHHHHHHHHHHHH
Q 018558 254 KYPPLMKTSKLSNSLKYLTQAYLGYDIQIG------------------IQDPYDDCVATMRLYM 299 (354)
Q Consensus 254 ~~~~~~~~~~~~~~L~~l~~~~l~~~i~~~------------------~H~Al~DA~at~~l~~ 299 (354)
.+.... ....+++|+.+|+ +||..-..+ ..-...|+++|..||.
T Consensus 146 ~~~~~~-~~~~~~~L~~va~-~lG~~~K~d~~G~~v~~~y~~g~~~~I~~Yc~~Dv~~t~~l~l 207 (208)
T cd05782 146 DLLAFY-GARARASLDLLAK-LLGIPGKMDVDGSQVWELYAEGKLDEIAEYCETDVLNTYLLYL 207 (208)
T ss_pred HHHhcc-CccCCCCHHHHHH-HhCCCCCcCCCHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHh
Confidence 443221 1235789999987 455521111 1223668888888775
No 125
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=93.56 E-value=0.037 Score=37.78 Aligned_cols=45 Identities=24% Similarity=0.293 Sum_probs=33.3
Q ss_pred cccccccccCCcccccccc-----CCCCCcccccccccccccccccccCCCChhHHHHHhhcc
Q 018558 43 VCGICKKHCRSFESLREHL-----IGPLPKQECKNVFNNRGCRFCLAILDGPNARRLHQERCQ 100 (354)
Q Consensus 43 ~C~~C~k~f~~~~~L~~H~-----~~e~p~~~C~k~F~~~~C~~C~k~f~~~~~l~~H~~~~~ 100 (354)
.|+.|++. .+...|..|. ...+.+ .|++|...+. .+|..|++..+
T Consensus 4 ~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v----------~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 4 TCPYCGKG-FSESSLVEHCEDEHRSESKNV----------VCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CCCCCCCc-cCHHHHHHHHHhHCcCCCCCc----------cCCCchhhhh--hHHHHHHHHhc
Confidence 69999995 4567899997 223456 8999998654 49999986543
No 126
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=93.41 E-value=0.046 Score=30.68 Aligned_cols=22 Identities=27% Similarity=0.619 Sum_probs=19.9
Q ss_pred ccccccccccCChHHHHHhhhh
Q 018558 13 NKCAACFRQFNRLEHLVEHMRT 34 (354)
Q Consensus 13 ~~C~~Cgk~f~~~~~L~~H~~~ 34 (354)
|.|..|++.|.....+..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 6799999999999999999876
No 127
>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=93.32 E-value=0.2 Score=41.20 Aligned_cols=56 Identities=20% Similarity=0.256 Sum_probs=39.8
Q ss_pred CCcEEEEechhhhhhhhc---ccCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCcC
Q 018558 224 RARILVGHGLDHDLDRLQ---VEYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDI 280 (354)
Q Consensus 224 ~~~ilVgHn~~~Dl~~L~---~~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i 280 (354)
.+...||||++.|+.+|. +..+. .+.||...+.+..+...+.+|+.|+..||+..+
T Consensus 52 ~~~~kv~~d~K~~~~~L~~~~~~~~~-~~~D~~laayLl~p~~~~~~l~~l~~~~l~~~~ 110 (150)
T cd09018 52 EKALKVGQNLKYDRGILLNYFIELRG-IAFDTMLEAYILNSVAGRWDMDSLVERWLGHKL 110 (150)
T ss_pred CCCceeeecHHHHHHHHHHcCCccCC-cchhHHHHHHHhCCCCCCCCHHHHHHHHhCCCc
Confidence 456789999999999884 22222 257988776655554313599999999988773
No 128
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=93.28 E-value=0.047 Score=30.97 Aligned_cols=21 Identities=24% Similarity=0.637 Sum_probs=18.1
Q ss_pred ccccccccCCCChhHHHHHhhc
Q 018558 78 GCRFCLAILDGPNARRLHQERC 99 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~~ 99 (354)
.|+.||+.| ..+.|..|++.|
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~~C 24 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEKIC 24 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHHhc
Confidence 588999999 788899998776
No 129
>smart00355 ZnF_C2H2 zinc finger.
Probab=93.11 E-value=0.051 Score=30.18 Aligned_cols=22 Identities=18% Similarity=0.345 Sum_probs=19.7
Q ss_pred ccccccccCCCChhHHHHHhhc
Q 018558 78 GCRFCLAILDGPNARRLHQERC 99 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~~ 99 (354)
.|..|++.|.....|..|++.|
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHHh
Confidence 5899999999999999999755
No 130
>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=92.70 E-value=0.31 Score=45.82 Aligned_cols=90 Identities=10% Similarity=0.037 Sum_probs=54.0
Q ss_pred CCCceEEeeccccccC---CCCCccceeeEEEE-ecCC-----ceEEeeeecCCccccCceeeecCCChhhhcCCCCHHH
Q 018558 130 RDPQVVAIACKMVGGG---SDGSLDLCGRVCII-DEYE-----NIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQ 200 (354)
Q Consensus 130 ~~~~~vaiD~Ettg~~---~~~~~~~i~~i~vv-~~~g-----~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~ 200 (354)
++..++++|+||...+ |+...++|..|+.+ ...| ...+-++..+.. +.. ...+.-.++-.+
T Consensus 155 p~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~~~~~~-~~~---------~~~v~~~~~E~~ 224 (325)
T PF03104_consen 155 PPLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTLGSCDS-IED---------NVEVIYFDSEKE 224 (325)
T ss_dssp GGSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEECSCSCC-TTC---------TTEEEEESSHHH
T ss_pred cccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEecCCCC-CCC---------CcEEEEECCHHH
Confidence 5678999999999654 24456677888753 2222 112222322221 111 333334467788
Q ss_pred HHHHHHHHHhcCCCCccccCCCCCCcEEEEech-hhhhhhh
Q 018558 201 VQRKIQDFLCNGEPMWKIRPRGSRARILVGHGL-DHDLDRL 240 (354)
Q Consensus 201 v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~-~~Dl~~L 240 (354)
++..|+++|..- .=.||+|||+ .||+..|
T Consensus 225 lL~~f~~~i~~~-----------dPDii~GyN~~~fD~~yl 254 (325)
T PF03104_consen 225 LLEAFLDIIQEY-----------DPDIITGYNIDGFDLPYL 254 (325)
T ss_dssp HHHHHHHHHHHH-----------S-SEEEESSTTTTHHHHH
T ss_pred HHHHHHHHHHhc-----------CCcEEEEecccCCCHHHH
Confidence 899999988321 2259999997 5898765
No 131
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=92.35 E-value=0.074 Score=30.59 Aligned_cols=22 Identities=32% Similarity=0.635 Sum_probs=19.1
Q ss_pred ccccccccccCChHHHHHhhhh
Q 018558 13 NKCAACFRQFNRLEHLVEHMRT 34 (354)
Q Consensus 13 ~~C~~Cgk~f~~~~~L~~H~~~ 34 (354)
|.|..|++.|.....+..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 6799999999999999888765
No 132
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=92.29 E-value=0.2 Score=45.38 Aligned_cols=127 Identities=16% Similarity=0.134 Sum_probs=73.5
Q ss_pred eeecCCccccCceeeecCCChhhhcC--CCCHHH-HHHHHHHHHhcCCCCccccCCCCCCcEEEEec-hhhhhh------
Q 018558 169 AYVKPPIPVTSYRYETTGIRPEHLRD--AIPLKQ-VQRKIQDFLCNGEPMWKIRPRGSRARILVGHG-LDHDLD------ 238 (354)
Q Consensus 169 ~~v~P~~~i~~~~~~itGIt~~~l~~--ap~~~~-v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn-~~~Dl~------ 238 (354)
.++.|.....+...+|||++..-++- .--|+. +.+-+..|+.. .+ .---||+|| -++|+.
T Consensus 71 vl~~p~~v~~p~aeeitgls~~~~~l~rr~~~D~dla~LL~afls~-------lp---~p~CLVaHng~~~dfpil~qel 140 (318)
T KOG4793|consen 71 VLGGPVPVTRPIAEEITGLSQPFLALQRRLAFDKDLAKLLTAFLSR-------LP---TPGCLVAHNGNEYDFPILAQEL 140 (318)
T ss_pred hccCCcCCcChhhhhhcccccHHHHHHHHhhhhHHHHHHHHHHHhc-------CC---CCceEEeecCCccccHHHHHHH
Confidence 35778777778888999999855533 334544 33444555521 11 122589999 355554
Q ss_pred -hhcccCCCce-eeeccccCC------Cc---cCCCCCchHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHHhh
Q 018558 239 -RLQVEYPAIM-TRDTAKYPP------LM---KTSKLSNSLKYLTQAYLGYDIQIGIQDPYDDCVATMRLYMRMKSQA 305 (354)
Q Consensus 239 -~L~~~~~~~~-~~Dt~~~~~------~~---~~~~~~~~L~~l~~~~l~~~i~~~~H~Al~DA~at~~l~~~~~~~~ 305 (354)
.|++..|... -+|+..... .+ ......++|..+-..|.+-.=..+.|.+..|.-+-.-+|+-..+++
T Consensus 141 a~lg~~lpq~lvcvdslpa~~ald~a~s~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~~el 218 (318)
T KOG4793|consen 141 AGLGYSLPQDLVCVDSLPALNALDRANSMVTRPEVRRMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRINEL 218 (318)
T ss_pred HhcCccchhhhcCcchhHHHHHHhhhcCcccCCCCCcccccchHHHhhhcccCCCcceeeecccchhHHHHHHHHHHH
Confidence 4555544321 234432111 11 1123477888887766444323458999998888777776666555
No 133
>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=92.13 E-value=0.21 Score=43.45 Aligned_cols=80 Identities=25% Similarity=0.290 Sum_probs=55.3
Q ss_pred CCcEEEEechhhhhhhhc----ccCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCcCCC-------CCC-------
Q 018558 224 RARILVGHGLDHDLDRLQ----VEYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQI-------GIQ------- 285 (354)
Q Consensus 224 ~~~ilVgHn~~~Dl~~L~----~~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~~-------~~H------- 285 (354)
.+...|||+++.|+.+|. +.... +.|+.....+..+. . .+|+.|+..||+..+.. ...
T Consensus 76 ~~i~kv~~d~K~~~~~L~~~~gi~~~~--~fD~~laaYLL~p~-~-~~l~~l~~~yl~~~~~k~~~~~~~~~~~l~~~~~ 151 (192)
T cd06147 76 PNILKVFHGADSDIIWLQRDFGLYVVN--LFDTGQAARVLNLP-R-HSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMI 151 (192)
T ss_pred CCceEEEechHHHHHHHHHHhCCCcCc--hHHHHHHHHHhCCC-c-ccHHHHHHHHhCCCcchhhhccccccCCCCHHHH
Confidence 456899999999999884 22222 27998877666665 4 49999999998775310 112
Q ss_pred -ChHHHHHHHHHHHHHHHHhhhh
Q 018558 286 -DPYDDCVATMRLYMRMKSQAHK 307 (354)
Q Consensus 286 -~Al~DA~at~~l~~~~~~~~~~ 307 (354)
-+..||.+...|+..+..+.++
T Consensus 152 ~y~a~~a~~l~~L~~~L~~~L~e 174 (192)
T cd06147 152 KYAREDTHYLLYIYDRLRNELLE 174 (192)
T ss_pred HHHHhhHHHHHHHHHHHHHHHHH
Confidence 1455577778888888887755
No 134
>PHA02570 dexA exonuclease; Provisional
Probab=92.07 E-value=0.96 Score=40.07 Aligned_cols=97 Identities=15% Similarity=0.130 Sum_probs=52.3
Q ss_pred EEeeccccccCCCCCccceeeEEEE--ecCCce--EEeeeecCCccccCc--------------eeeecCCChhh---hc
Q 018558 135 VAIACKMVGGGSDGSLDLCGRVCII--DEYENI--IFHAYVKPPIPVTSY--------------RYETTGIRPEH---LR 193 (354)
Q Consensus 135 vaiD~Ettg~~~~~~~~~i~~i~vv--~~~g~~--i~~~~v~P~~~i~~~--------------~~~itGIt~~~---l~ 193 (354)
+.||+||.|..++. .|+.|++| +.+... .|..+|..+..+.-. +..+-.-++|- |.
T Consensus 4 lMIDlETmG~~p~A---aIisIgAV~Fdp~~~~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~L~ 80 (220)
T PHA02570 4 FIIDFETFGNTPDG---AVIDLAVIAFEHDPHNPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEARKNLK 80 (220)
T ss_pred EEEEeeccCCCCCc---eEEEEEEEEecCCCCccccHHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHHHHhcc
Confidence 68999999987654 34666666 333222 255566532221110 11111111111 11
Q ss_pred ---CCCCHHHHHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhc
Q 018558 194 ---DAIPLKQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQ 241 (354)
Q Consensus 194 ---~ap~~~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~ 241 (354)
+..++.+++.+|.+||.. . ........+=|-+.+||+..|.
T Consensus 81 ~s~~~~~l~~al~~F~~fi~~-~------~~~~~~~~vWgnG~sFD~~IL~ 124 (220)
T PHA02570 81 PSDEDVSTYEGHKKFFEYLEA-N------GVDPWKSQGWCRGNSFDFPILV 124 (220)
T ss_pred CCCccccHHHHHHHHHHHHHH-c------CCCccceeEecCCCccCHHHHH
Confidence 235789999999999931 0 0000113455788999998884
No 135
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=91.77 E-value=0.11 Score=34.57 Aligned_cols=27 Identities=22% Similarity=0.375 Sum_probs=16.7
Q ss_pred ccccccccCCCChhHHHHHhhccccCC
Q 018558 78 GCRFCLAILDGPNARRLHQERCQMVSS 104 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~~~~~~~ 104 (354)
.|++|+..+.++.+|..|++..|+..+
T Consensus 26 tCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 26 TCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp E-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCcchhhccchhhHHHHHHHHhcccC
Confidence 677777777778888888766665543
No 136
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=90.71 E-value=3.2 Score=46.18 Aligned_cols=156 Identities=21% Similarity=0.174 Sum_probs=90.5
Q ss_pred CCCceEEeeccccccC---CCCCccceeeEEEE-ecCCceEEeee-e---------cCCccccCceeeecCCChhhhcCC
Q 018558 130 RDPQVVAIACKMVGGG---SDGSLDLCGRVCII-DEYENIIFHAY-V---------KPPIPVTSYRYETTGIRPEHLRDA 195 (354)
Q Consensus 130 ~~~~~vaiD~Ettg~~---~~~~~~~i~~i~vv-~~~g~~i~~~~-v---------~P~~~i~~~~~~itGIt~~~l~~a 195 (354)
+...+.|||+|||-+- |+.+.+.|..|+.. |..|.-|.+.= | -|..+..-+- .+-|.
T Consensus 244 adp~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREiVs~DIedfEYTPKpE~eG~F---------~v~Ne 314 (2173)
T KOG1798|consen 244 ADPRVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREIVSEDIEDFEYTPKPEYEGPF---------CVFNE 314 (2173)
T ss_pred CCceEEEEeeecccCCCCCCCcccceEEEEEEEecCceEEEechhhhccchhhcccCCccccccce---------EEecC
Confidence 4567899999999663 34455677777644 55665443321 1 1211111110 12245
Q ss_pred CCHHHHHHHHHHHHhcCCCCccccCCCCCCcEEEEechhh-hhhhhc-------ccC----------------CCceeee
Q 018558 196 IPLKQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDH-DLDRLQ-------VEY----------------PAIMTRD 251 (354)
Q Consensus 196 p~~~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~-Dl~~L~-------~~~----------------~~~~~~D 251 (354)
|.-.+++.++.+.+- ..+-+|+|-+|-+| |+.|+. +.. +...-.|
T Consensus 315 ~dEv~Ll~RfFeHiq-----------~~kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmD 383 (2173)
T KOG1798|consen 315 PDEVGLLQRFFEHIQ-----------EVKPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMD 383 (2173)
T ss_pred CcHHHHHHHHHHHHH-----------hcCCcEEEEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehh
Confidence 566778888888882 12457999998654 887763 110 0111123
Q ss_pred ccccCCCc-cCCCCCchHHHHHHHHhCCcCCC----------------CCCChHHHHHHHHHHHHHHHHhh
Q 018558 252 TAKYPPLM-KTSKLSNSLKYLTQAYLGYDIQI----------------GIQDPYDDCVATMRLYMRMKSQA 305 (354)
Q Consensus 252 t~~~~~~~-~~~~~~~~L~~l~~~~l~~~i~~----------------~~H~Al~DA~at~~l~~~~~~~~ 305 (354)
.-.|-..- .....+.+|+.+++.-||++--. -+--++.||.||-.||.++-.-+
T Consensus 384 cfrWVKRDSYLPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVhPF 454 (2173)
T KOG1798|consen 384 CFRWVKRDSYLPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVHPF 454 (2173)
T ss_pred hhhhhhhcccCCCcccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhhhH
Confidence 22332211 11334789999999999976421 14667999999999998876544
No 137
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=89.82 E-value=0.17 Score=28.05 Aligned_cols=21 Identities=24% Similarity=0.507 Sum_probs=17.0
Q ss_pred ccccccccccCChHHHHHhhhh
Q 018558 13 NKCAACFRQFNRLEHLVEHMRT 34 (354)
Q Consensus 13 ~~C~~Cgk~f~~~~~L~~H~~~ 34 (354)
|+|+.|+.+.. ...|..|++.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 68999999888 8899999887
No 138
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=89.50 E-value=4.1 Score=43.55 Aligned_cols=128 Identities=16% Similarity=0.088 Sum_probs=70.0
Q ss_pred CCCceEEeeccccccCCC---CCccceeeEEEEecCCceEEeeeecCCccccCceeeecCCChhhhcCCCCHHHHHHHHH
Q 018558 130 RDPQVVAIACKMVGGGSD---GSLDLCGRVCIIDEYENIIFHAYVKPPIPVTSYRYETTGIRPEHLRDAIPLKQVQRKIQ 206 (354)
Q Consensus 130 ~~~~~vaiD~Ettg~~~~---~~~~~i~~i~vv~~~g~~i~~~~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v~~~~~ 206 (354)
+..+++++|+|+...... +..+.+..++.....+.... ..+. .+...|.. +....+-.+++..|.
T Consensus 152 p~l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~---~~~~------~~~~~~~~---v~~~~~e~e~l~~~~ 219 (792)
T COG0417 152 PPLRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLI---EVFI------YTSGEGFS---VEVVISEAELLERFV 219 (792)
T ss_pred CCceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCcc---cccc------ccCCCCce---eEEecCHHHHHHHHH
Confidence 567899999999965322 22334444444433221111 0000 00111111 444456678899999
Q ss_pred HHHhcCCCCccccCCCCCCcEEEEechh-hhhhhhc-------ccCC-------------------CceeeeccccCCCc
Q 018558 207 DFLCNGEPMWKIRPRGSRARILVGHGLD-HDLDRLQ-------VEYP-------------------AIMTRDTAKYPPLM 259 (354)
Q Consensus 207 ~~i~~~~~~~~~~~~~~~~~ilVgHn~~-~Dl~~L~-------~~~~-------------------~~~~~Dt~~~~~~~ 259 (354)
+++.+. .-.|+||||.+ ||+..|. +... ....+|........
T Consensus 220 ~~i~~~-----------dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~~~~ 288 (792)
T COG0417 220 ELIREY-----------DPDVIVGYNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPALRRR 288 (792)
T ss_pred HHHHhc-----------CCCEEEeccCCcCChHHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHHHhhh
Confidence 988332 34699999986 8987652 2111 11234544433322
Q ss_pred cCCCCCchHHHHHHHHhCCcC
Q 018558 260 KTSKLSNSLKYLTQAYLGYDI 280 (354)
Q Consensus 260 ~~~~~~~~L~~l~~~~l~~~i 280 (354)
......++|...+..+|+..-
T Consensus 289 ~~~~~~ysl~~v~~~~l~~~k 309 (792)
T COG0417 289 PLNLKSYSLEAVSEALLGEGK 309 (792)
T ss_pred hcccccccHHHHHHHhccccc
Confidence 234457899999998887544
No 139
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=89.49 E-value=0.25 Score=27.96 Aligned_cols=21 Identities=29% Similarity=0.610 Sum_probs=16.7
Q ss_pred ccccccccccCChHHHHHhhhh
Q 018558 13 NKCAACFRQFNRLEHLVEHMRT 34 (354)
Q Consensus 13 ~~C~~Cgk~f~~~~~L~~H~~~ 34 (354)
..|+.||+.| ....|..|+..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4799999999 56778888754
No 140
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=88.67 E-value=0.59 Score=41.11 Aligned_cols=76 Identities=17% Similarity=0.282 Sum_probs=52.1
Q ss_pred CCcEEEEechhhhhhhh-cc-------------------cCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCcCC-C
Q 018558 224 RARILVGHGLDHDLDRL-QV-------------------EYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQ-I 282 (354)
Q Consensus 224 ~~~ilVgHn~~~Dl~~L-~~-------------------~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~-~ 282 (354)
++-..|-....+|+..| ++ ..|. +.|+-.+..+......+.+|+.||..+ ++. .
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 ENVTWVTFHSGYDFGYLLKILTGKPLPETEEEFFEIVRQLFPF--VYDVKYLMKFCEGLSLKGGLQRLADLL---GLKRV 215 (239)
T ss_pred CceEEEEeeccchHHHHHHHHcCCCCcchHHHHHHHHHHHcch--hhhHHHHHHhhhhhhhhcCHHHHHHHh---CCCee
Confidence 45678877778887644 11 1233 345555555443344577999999866 554 3
Q ss_pred C-CCChHHHHHHHHHHHHHHHHh
Q 018558 283 G-IQDPYDDCVATMRLYMRMKSQ 304 (354)
Q Consensus 283 ~-~H~Al~DA~at~~l~~~~~~~ 304 (354)
| .|.|-.|++.|+..|.++++.
T Consensus 216 G~~HqAGSDSlLT~~~F~kl~~~ 238 (239)
T KOG0304|consen 216 GIAHQAGSDSLLTARVFFKLKEL 238 (239)
T ss_pred ecccccCcHHHHHHHHHHHHHhc
Confidence 3 899999999999999998864
No 141
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=88.51 E-value=0.16 Score=28.40 Aligned_cols=21 Identities=24% Similarity=0.434 Sum_probs=17.8
Q ss_pred ccccccccCCCChhHHHHHhh
Q 018558 78 GCRFCLAILDGPNARRLHQER 98 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~ 98 (354)
.|..|++.|.+...+..|++.
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCcCCHHHHHHHHCc
Confidence 488899999999999999854
No 142
>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=88.01 E-value=0.99 Score=44.60 Aligned_cols=148 Identities=14% Similarity=0.141 Sum_probs=81.2
Q ss_pred CceEEeeccccccC---CCCC--ccceeeEEEEecCCce--E--Eee-eecCCccccCceeeecCCChhhhcCCCCHHHH
Q 018558 132 PQVVAIACKMVGGG---SDGS--LDLCGRVCIIDEYENI--I--FHA-YVKPPIPVTSYRYETTGIRPEHLRDAIPLKQV 201 (354)
Q Consensus 132 ~~~vaiD~Ettg~~---~~~~--~~~i~~i~vv~~~g~~--i--~~~-~v~P~~~i~~~~~~itGIt~~~l~~ap~~~~v 201 (354)
.+++++|+||+... |... .+.+..++.+...+.. . ... .+.+..++. |+. +..-..-.++
T Consensus 3 ~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~---~~~~~~E~~l 72 (471)
T smart00486 3 LKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCKEID-------GVE---VYEFNNEKEL 72 (471)
T ss_pred ceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcCCCC-------CCe---EEecCCHHHH
Confidence 46899999998532 2222 3456666665543321 1 111 122322222 221 2222366788
Q ss_pred HHHHHHHHhcCCCCccccCCCCCCcEEEEechh-hhhhhhc-------ccCC----------------------------
Q 018558 202 QRKIQDFLCNGEPMWKIRPRGSRARILVGHGLD-HDLDRLQ-------VEYP---------------------------- 245 (354)
Q Consensus 202 ~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~-~Dl~~L~-------~~~~---------------------------- 245 (354)
+..|.+++..- ...+++|||.. ||+.+|- +...
T Consensus 73 L~~f~~~i~~~-----------dpdii~g~N~~~FD~~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~~~ 141 (471)
T smart00486 73 LKAFLEFIKKY-----------DPDIIYGHNISNFDLPYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSKSFGKTI 141 (471)
T ss_pred HHHHHHHHHHh-----------CCCEEEeecCCCCCHHHHHHHHHHcCCCCHHHcCcCCCCCCcccccCccccccccccc
Confidence 88888888210 22599999984 8986542 1000
Q ss_pred -----CceeeeccccCCCccCCCCCchHHHHHHHHhCCcCCC-CC------------------CChHHHHHHHHHHHHHH
Q 018558 246 -----AIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQI-GI------------------QDPYDDCVATMRLYMRM 301 (354)
Q Consensus 246 -----~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~~-~~------------------H~Al~DA~at~~l~~~~ 301 (354)
....+|+..+..... ...+++|+.++.++||..-.. .. .-.+.||..+.+|+.++
T Consensus 142 ~~~~~g~~~~Dl~~~~~~~~-kl~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 142 KVKIKGRLVIDLYNLYKNKL-KLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred eeEeccEEEEEhHHHHHHHh-CcccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 012345544333221 245789999999998843321 00 11266999999998775
No 143
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=87.10 E-value=0.4 Score=46.36 Aligned_cols=49 Identities=33% Similarity=0.613 Sum_probs=45.3
Q ss_pred ccccccccccccCChHHHHHhhh--hccccCc--cc-ccc--ccccccCCcccccccc
Q 018558 11 LRNKCAACFRQFNRLEHLVEHMR--TSYHSVH--EP-VCG--ICKKHCRSFESLREHL 61 (354)
Q Consensus 11 k~~~C~~Cgk~f~~~~~L~~H~~--~~~H~~~--k~-~C~--~C~k~f~~~~~L~~H~ 61 (354)
.++.|..|...|.....+..|.+ . |.++ ++ .|. .|++.|.+...+..|.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~--h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~ 343 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVN--HSGESLKPFSCPYSLCGKLFSRNDALKRHI 343 (467)
T ss_pred cCCCCccccCCccccccccccccccc--cccccCCceeeeccCCCccccccccccCCc
Confidence 47999999999999999999999 8 9999 89 999 7999999999999887
No 144
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=87.04 E-value=0.15 Score=29.29 Aligned_cols=21 Identities=19% Similarity=0.354 Sum_probs=16.7
Q ss_pred ccccccccCCCChhHHHHHhh
Q 018558 78 GCRFCLAILDGPNARRLHQER 98 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~ 98 (354)
.|..|++.|.....+..|++.
T Consensus 3 ~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 3 YCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp BBTTTTBBBSSHHHHHCCTTS
T ss_pred CcccCCCCcCCHHHHHHHHcc
Confidence 588888888888888888754
No 145
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=85.18 E-value=0.62 Score=28.20 Aligned_cols=23 Identities=17% Similarity=0.319 Sum_probs=20.3
Q ss_pred cccccccccccCChHHHHHhhhh
Q 018558 12 RNKCAACFRQFNRLEHLVEHMRT 34 (354)
Q Consensus 12 ~~~C~~Cgk~f~~~~~L~~H~~~ 34 (354)
+|.|..|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999999999765
No 146
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=84.37 E-value=7.3 Score=35.17 Aligned_cols=16 Identities=13% Similarity=0.077 Sum_probs=13.7
Q ss_pred CCceEEeeccccccCC
Q 018558 131 DPQVVAIACKMVGGGS 146 (354)
Q Consensus 131 ~~~~vaiD~Ettg~~~ 146 (354)
..+++.+|+||||++.
T Consensus 97 ~e~~~FFDiETTGL~~ 112 (278)
T COG3359 97 AEDVAFFDIETTGLDR 112 (278)
T ss_pred ccceEEEeeeccccCC
Confidence 4578999999999976
No 147
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.20 E-value=0.61 Score=47.88 Aligned_cols=77 Identities=29% Similarity=0.571 Sum_probs=39.6
Q ss_pred ccccccccccC---------------ChHHHHHhhhhccccCcccccccc----------ccccCCcccccccc-CCCCC
Q 018558 13 NKCAACFRQFN---------------RLEHLVEHMRTSYHSVHEPVCGIC----------KKHCRSFESLREHL-IGPLP 66 (354)
Q Consensus 13 ~~C~~Cgk~f~---------------~~~~L~~H~~~~~H~~~k~~C~~C----------~k~f~~~~~L~~H~-~~e~p 66 (354)
+.|..|++.|. ....|+.|+.- +|... .|..| .|. .....|..|+ .|+-
T Consensus 100 ~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~-~H~~~--~c~lC~~~~kif~~e~k~-Yt~~el~~h~~~gd~- 174 (669)
T KOG2231|consen 100 HSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRD-QHKLH--LCSLCLQNLKIFINERKL-YTRAELNLHLMFGDP- 174 (669)
T ss_pred hhcCccccchhhhcccCCCccccchhHHHHHHHHHHH-hhhhh--ccccccccceeeeeeeeh-ehHHHHHHHHhcCCC-
Confidence 56677776663 66788999854 25433 33333 333 3445667776 3321
Q ss_pred cccccccccc-cccccccccCCCChhHHHHHh
Q 018558 67 KQECKNVFNN-RGCRFCLAILDGPNARRLHQE 97 (354)
Q Consensus 67 ~~~C~k~F~~-~~C~~C~k~f~~~~~l~~H~~ 97 (354)
|.++|.. ..|..|...|.....|..|++
T Consensus 175 ---d~~s~rGhp~C~~C~~~fld~~el~rH~~ 203 (669)
T KOG2231|consen 175 ---DDESCRGHPLCKFCHERFLDDDELYRHLR 203 (669)
T ss_pred ---ccccccCCccchhhhhhhccHHHHHHhhc
Confidence 3333332 234555555555555555544
No 148
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=81.14 E-value=13 Score=41.73 Aligned_cols=107 Identities=17% Similarity=0.209 Sum_probs=65.2
Q ss_pred eecCCChhhhcCCCCHHHHHHHHHHHHhcCCCCccccCCCCCCcEEEEech-hhhhhhh-------cccC----------
Q 018558 183 ETTGIRPEHLRDAIPLKQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGL-DHDLDRL-------QVEY---------- 244 (354)
Q Consensus 183 ~itGIt~~~l~~ap~~~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~-~~Dl~~L-------~~~~---------- 244 (354)
..-|+.+..|..-.+-.+.+..+++++.+- .-.+++|||+ .|||.+| ++..
T Consensus 569 ~~~~~~~~~L~~~~sEr~lL~~fl~~~~~~-----------DPDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~ 637 (1172)
T TIGR00592 569 EFPGKKPSLVEDLATERALIKKFMAKVKKI-----------DPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRS 637 (1172)
T ss_pred hhhccCCcEEEEecCHHHHHHHHHHHHHhc-----------CCCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccC
Confidence 455666677777778888888888888211 2259999996 7788654 2211
Q ss_pred -----------CCceeeeccccCCCccCCCCCchHHHHHHHHhCCcCCCC------------------CCChHHHHHHHH
Q 018558 245 -----------PAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYDIQIG------------------IQDPYDDCVATM 295 (354)
Q Consensus 245 -----------~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~i~~~------------------~H~Al~DA~at~ 295 (354)
....++|+....... ....+|+|..++.++||.+-..- ....+.||..++
T Consensus 638 ~~~~~~~~~~~~Grl~~D~~~~~k~~-~~~~sy~L~~v~~~~L~~~k~~~~~~~i~~~~~~~~~~~~~~~y~~~Da~l~~ 716 (1172)
T TIGR00592 638 PKFGRRFGERTCGRMICDVEISAKEL-IRCKSYDLSELVQQILKTERKVIPIDNINNMYSESSSLTYLLEHTWKDAMFIL 716 (1172)
T ss_pred CCccccccceECCEEEEEHHHHHHHH-hCcCCCCHHHHHHHHhCCCCcccCHHHHHHHHhCcHHHHHHHHHHHHHHHHHH
Confidence 111234554433221 12457999999999998532210 123467888887
Q ss_pred HHHHHH
Q 018558 296 RLYMRM 301 (354)
Q Consensus 296 ~l~~~~ 301 (354)
.|+.++
T Consensus 717 ~L~~~l 722 (1172)
T TIGR00592 717 QIMCEL 722 (1172)
T ss_pred HHHHHH
Confidence 776543
No 149
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=80.09 E-value=1.2 Score=46.17 Aligned_cols=141 Identities=14% Similarity=0.196 Sum_probs=72.7
Q ss_pred CCCCCCceEEeeccccccCC---CCCccceeeEE-EEecCCce-EE--eee-ecCCccccCceeeecCCChhhhcCCCCH
Q 018558 127 THTRDPQVVAIACKMVGGGS---DGSLDLCGRVC-IIDEYENI-IF--HAY-VKPPIPVTSYRYETTGIRPEHLRDAIPL 198 (354)
Q Consensus 127 ~~~~~~~~vaiD~Ettg~~~---~~~~~~i~~i~-vv~~~g~~-i~--~~~-v~P~~~i~~~~~~itGIt~~~l~~ap~~ 198 (354)
...++..+..+|+|++|... ....+.+++|+ +|...|+. .| +.| ++|-.+|+.-. -+.-++.++ .
T Consensus 269 ~~~APlrvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~Ge~~pf~rnvf~l~~capI~G~~-V~~~~~e~e------l 341 (1066)
T KOG0969|consen 269 SKIAPLRVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQGENEPFVRNVFTLKTCAPIVGSN-VHSYETEKE------L 341 (1066)
T ss_pred cccccccccceeEEeccCCCCCCccccChHHHHHHHHHHhcCCchHHHhhhcccCcCCCCCce-eEEeccHHH------H
Confidence 34477889999999997642 33444444443 33333331 12 122 23334444211 112223222 2
Q ss_pred HHHHHHHHHHHhcCCCCccccCCCCCCcEEEEech-hhhhh-------hhccc--------C-CCceeeeccccCC----
Q 018558 199 KQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGL-DHDLD-------RLQVE--------Y-PAIMTRDTAKYPP---- 257 (354)
Q Consensus 199 ~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~-~~Dl~-------~L~~~--------~-~~~~~~Dt~~~~~---- 257 (354)
-+.|..|+.-+ .-.||+|+|+ .||+- .|++. . ....+.||..-..
T Consensus 342 L~~W~~firev--------------DPDvI~GYNi~nFDiPYll~RA~~L~Ie~Fp~LGRikn~~s~irDttfSSkq~Gt 407 (1066)
T KOG0969|consen 342 LESWRKFIREV--------------DPDVIIGYNICNFDIPYLLNRAKTLGIENFPYLGRIKNSRSVIRDSTFSSKQYGT 407 (1066)
T ss_pred HHHHHHHHHhc--------------CCCeEecccccccccceecChHhhcCcccccccceecccceeeeccccchhhcCc
Confidence 33455555555 4579999997 67873 23321 1 1222445431110
Q ss_pred --------------------CccCCCCCchHHHHHHHHhCCcCCCCCCChH
Q 018558 258 --------------------LMKTSKLSNSLKYLTQAYLGYDIQIGIQDPY 288 (354)
Q Consensus 258 --------------------~~~~~~~~~~L~~l~~~~l~~~i~~~~H~Al 288 (354)
.+.....+|+|..++.+||+..-+.-+|+.+
T Consensus 408 RetK~v~I~GRlqfDllqvi~Rd~KLrSytLNaVs~hFL~EQKEDV~~siI 458 (1066)
T KOG0969|consen 408 RETKEVNIDGRLQFDLLQVILRDYKLRSYTLNAVSAHFLGEQKEDVHHSII 458 (1066)
T ss_pred ccceEEeecceeeehHHHHHHHhhhhhhcchhhhHHHhhhhhcccccccch
Confidence 0111335889999999999876554466653
No 150
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=78.94 E-value=1.7 Score=47.69 Aligned_cols=23 Identities=17% Similarity=0.221 Sum_probs=20.6
Q ss_pred ccccccccCCCChhHHHHHhhcc
Q 018558 78 GCRFCLAILDGPNARRLHQERCQ 100 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~~~ 100 (354)
.|..|..+++...+|.+|++.+-
T Consensus 520 ~C~~C~~stttng~LsihlqS~~ 542 (1406)
T KOG1146|consen 520 PCRACNYSTTTNGNLSIHLQSDL 542 (1406)
T ss_pred cceeeeeeeecchHHHHHHHHHh
Confidence 79999999999999999987543
No 151
>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=77.55 E-value=3.7 Score=33.87 Aligned_cols=54 Identities=20% Similarity=0.216 Sum_probs=38.8
Q ss_pred CcEEEEechhhhhhhhc---ccCCCceeeeccccCCCccCCCCCchHHHHHHHHhCCc
Q 018558 225 ARILVGHGLDHDLDRLQ---VEYPAIMTRDTAKYPPLMKTSKLSNSLKYLTQAYLGYD 279 (354)
Q Consensus 225 ~~ilVgHn~~~Dl~~L~---~~~~~~~~~Dt~~~~~~~~~~~~~~~L~~l~~~~l~~~ 279 (354)
+...|+||+++++.+|+ +.... ...|+.....+..+......|+.|+..||+..
T Consensus 53 ~~~ki~~d~K~~~~~l~~~gi~l~~-~~fD~~LAaYLL~p~~~~~~l~~la~~yl~~~ 109 (151)
T cd06128 53 KALKVGQNLKYDRVILANYGIELRG-IAFDTMLEAYLLDPVAGRHDMDSLAERWLKEK 109 (151)
T ss_pred CCCEEeeehHHHHHHHHHCCCCCCC-cchhHHHHHHHcCCCCCCCCHHHHHHHHcCCC
Confidence 45689999999999883 33332 24688877666666544139999999998776
No 152
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=75.35 E-value=2 Score=33.76 Aligned_cols=29 Identities=17% Similarity=0.330 Sum_probs=19.2
Q ss_pred cccccccccCCccccccccCCCCCcccccccccccccccccccCCCC
Q 018558 43 VCGICKKHCRSFESLREHLIGPLPKQECKNVFNNRGCRFCLAILDGP 89 (354)
Q Consensus 43 ~C~~C~k~f~~~~~L~~H~~~e~p~~~C~k~F~~~~C~~C~k~f~~~ 89 (354)
.|..||+.|+-.. ..|- .|+.||..|.-.
T Consensus 11 ~Cp~CG~kFYDLn--------k~Pi----------vCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAKFYDLN--------KDPI----------VCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcchhccCC--------CCCc----------cCCCCCCccCcc
Confidence 6777777665422 2344 699999988666
No 153
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=75.34 E-value=2.6 Score=44.14 Aligned_cols=89 Identities=20% Similarity=0.239 Sum_probs=53.6
Q ss_pred CCCcEEEEechhhhhhhhc----ccCCCceeeeccccC-------CCccC------------------------------
Q 018558 223 SRARILVGHGLDHDLDRLQ----VEYPAIMTRDTAKYP-------PLMKT------------------------------ 261 (354)
Q Consensus 223 ~~~~ilVgHn~~~Dl~~L~----~~~~~~~~~Dt~~~~-------~~~~~------------------------------ 261 (354)
.++.++||||+.||-..++ +.-.+...+||+.|. .+.++
T Consensus 239 ~ke~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTMSlHia~~Gm~S~Qrplw~ka~k~k~a~~d~~~~ps~~d~~~pWL~ 318 (1075)
T KOG3657|consen 239 GKEQLIVGHNVSFDRARIREEYNINGSKIRFLDTMSLHIAMSGMCSRQRPLWFKARKAKSAMYDSETNPSISDYDNPWLG 318 (1075)
T ss_pred CCCceEEeccccchHHHHHHHHhccccceeeeechhhhhhhhccccccchhHhhhhhhhhhhhhcccCCchhhhhhhhhh
Confidence 4778999999999987765 222344467876321 11110
Q ss_pred CCCCchHHHHHHHHhCCc-CCCCCC--------------------ChHHHHHHHHHHHHHHHHhhhhccCC
Q 018558 262 SKLSNSLKYLTQAYLGYD-IQIGIQ--------------------DPYDDCVATMRLYMRMKSQAHKREDY 311 (354)
Q Consensus 262 ~~~~~~L~~l~~~~l~~~-i~~~~H--------------------~Al~DA~at~~l~~~~~~~~~~~~~~ 311 (354)
...-.+|..+++.+.|.+ +..... --..|..+|.+||.++.-.+.+.=++
T Consensus 319 ~SS~NSL~dVhk~~c~~~~LdKt~Rd~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~FlercPH 389 (1075)
T KOG3657|consen 319 RSSLNSLVDVHKFHCGIDALDKTPRDSFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLERCPH 389 (1075)
T ss_pred hhhhHHHHHHHHhhCCCCccccchHHhhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHHhCCC
Confidence 011346777777776666 332111 11458899999998888777553344
No 154
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=73.00 E-value=2 Score=25.88 Aligned_cols=21 Identities=14% Similarity=0.349 Sum_probs=18.4
Q ss_pred ccccccccCCCChhHHHHHhh
Q 018558 78 GCRFCLAILDGPNARRLHQER 98 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~ 98 (354)
.|..|++.|....++..|++.
T Consensus 5 ~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 5 YCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred EccccCCccCCHHHHHHHHCh
Confidence 699999999999999999853
No 155
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=72.72 E-value=2 Score=33.82 Aligned_cols=30 Identities=23% Similarity=0.551 Sum_probs=23.3
Q ss_pred ccccccccccCChHHHHHhhhhccccCccc-cccccccccCCcc
Q 018558 13 NKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRSFE 55 (354)
Q Consensus 13 ~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~~~ 55 (354)
..|+.||+.|- -....| .|+.||..|....
T Consensus 10 R~Cp~CG~kFY-------------DLnk~PivCP~CG~~~~~~~ 40 (108)
T PF09538_consen 10 RTCPSCGAKFY-------------DLNKDPIVCPKCGTEFPPEP 40 (108)
T ss_pred ccCCCCcchhc-------------cCCCCCccCCCCCCccCccc
Confidence 67999999883 334567 9999999987653
No 156
>PRK05761 DNA polymerase I; Reviewed
Probab=71.20 E-value=7.7 Score=41.47 Aligned_cols=90 Identities=18% Similarity=0.117 Sum_probs=54.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCccccCCCCCCcEEEEech-hhhhhhh-------cccCC---C----ce-eeeccccCCCc
Q 018558 196 IPLKQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGL-DHDLDRL-------QVEYP---A----IM-TRDTAKYPPLM 259 (354)
Q Consensus 196 p~~~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~-~~Dl~~L-------~~~~~---~----~~-~~Dt~~~~~~~ 259 (354)
++-.+++.+|.+++. .-.+.|++|. .||+..| ++... . .. .+|....+...
T Consensus 208 ~~E~eLL~~f~~~i~-------------~~dPdi~yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~ 274 (787)
T PRK05761 208 DSEKELLAELFDIIL-------------EYPPVVTFNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNK 274 (787)
T ss_pred CCHHHHHHHHHHHHH-------------hcCCEEEEcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheeec
Confidence 677889999999993 3346677885 6898654 33211 0 00 13332222110
Q ss_pred ---------cCCCCCchHHHHHHHHhCCcCC-------C-C----CCChHHHHHHHHHHH
Q 018558 260 ---------KTSKLSNSLKYLTQAYLGYDIQ-------I-G----IQDPYDDCVATMRLY 298 (354)
Q Consensus 260 ---------~~~~~~~~L~~l~~~~l~~~i~-------~-~----~H~Al~DA~at~~l~ 298 (354)
......++|..++..+||.+=. . + +.-.+.||..|.+|.
T Consensus 275 ~~~~y~~~~~~~~~~ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 275 AVRSYAFYGKYRHREARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred ceeeeeccceeecccCChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 0111268999999999986421 0 0 244588999999984
No 157
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=70.86 E-value=2.9 Score=31.48 Aligned_cols=23 Identities=39% Similarity=0.730 Sum_probs=20.4
Q ss_pred cccccccccccCChHHHHHhhhh
Q 018558 12 RNKCAACFRQFNRLEHLVEHMRT 34 (354)
Q Consensus 12 ~~~C~~Cgk~f~~~~~L~~H~~~ 34 (354)
.+.|..|++.|.....|..|++.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCCccCCCCcCHHHHHHHHcC
Confidence 58999999999999999999987
No 158
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=70.06 E-value=23 Score=35.62 Aligned_cols=200 Identities=9% Similarity=-0.032 Sum_probs=98.1
Q ss_pred ccCCCChhHHHHHhhccccCCCCccchhhhhccCCCCCcccCCCCCCCCceEEeeccccccCC-CC--CccceeeEEEEe
Q 018558 84 AILDGPNARRLHQERCQMVSSATTGLNARLANLGVRDSLTIDNTHTRDPQVVAIACKMVGGGS-DG--SLDLCGRVCIID 160 (354)
Q Consensus 84 k~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vaiD~Ettg~~~-~~--~~~~i~~i~vv~ 160 (354)
+.|.+...-.+-++...-.+-..-++++|...+=...-+..-.-....-++..+|+|.++-+. +. ...+|..|+..+
T Consensus 58 ~~f~~~~~a~~~~~~~~~~~~~~~g~~~~~~~yi~~~y~~~~~~d~~~i~~~~~DIEv~~~~fp~~~~a~~~i~~i~~~d 137 (498)
T PHA02524 58 KKHENIWEAKQWIKRMEEVGMDAMGMDDYGISYISDTYRGVIDFDRDDVVIDVVDIEVTAPEFPEPKYAKYEIDMISHVR 137 (498)
T ss_pred cCCCCHHHHHHHHHHHhhcChhhccchHHHHHHHHHhcCCccccchhhceEEEEEEEecCCCCCChhhcCCceEEEEeee
Confidence 566666665555554433333334455554432211111111112235578999999975321 11 123555566555
Q ss_pred cC-Cc---eEEeeeecCCccccCceeeecCCChhhhc-----CCCCHHHHHHHHHHHHhcCCCCccccCCCCCCcEEEEe
Q 018558 161 EY-EN---IIFHAYVKPPIPVTSYRYETTGIRPEHLR-----DAIPLKQVQRKIQDFLCNGEPMWKIRPRGSRARILVGH 231 (354)
Q Consensus 161 ~~-g~---~i~~~~v~P~~~i~~~~~~itGIt~~~l~-----~ap~~~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgH 231 (354)
.. +. .+|+.+ +. ...|.....=..++.+. .-++-.+++.+|.+|+.+- .=.||+||
T Consensus 138 ~~~~~~~~~~~~~~--~~--~~~~~~~~~~~~~~~~~~v~v~~f~sE~eLL~~F~~~i~~~-----------DPDIItGY 202 (498)
T PHA02524 138 LHNGKKTYYIFDLV--KD--VGHWDPKKSVLEKYILDNVVYMPFEDEVDLLLNYIQLWKAN-----------TPDLVFGW 202 (498)
T ss_pred cccCCccEEEEecc--cc--ccCCCcccccccccccCCeEEEEeCCHHHHHHHHHHHHHHh-----------CCCEEEeC
Confidence 32 11 224333 11 11111111101111122 2367789999999999321 12699999
Q ss_pred ch-hhhhhh--------hccc-------CCC--------------------ceeeeccccCCCc-cCCCCCchHHHHHHH
Q 018558 232 GL-DHDLDR--------LQVE-------YPA--------------------IMTRDTAKYPPLM-KTSKLSNSLKYLTQA 274 (354)
Q Consensus 232 n~-~~Dl~~--------L~~~-------~~~--------------------~~~~Dt~~~~~~~-~~~~~~~~L~~l~~~ 274 (354)
|+ .||+.. |++. ... ..++|...+.... .....+++|.+++..
T Consensus 203 Ni~nFDlPYL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~~~G~~~~~~I~GRv~iDl~~l~kk~s~~~l~sYsL~~Vs~~ 282 (498)
T PHA02524 203 NSEGFDIPYIITRITNILGEKAANQLSPYGKITSKTITNLYGEKIIYKIHGIALMDYMDVFKKFSFTPMPDYKLGNVGYR 282 (498)
T ss_pred CCcccCHHHHHHHHHHHhCCccccccccccccccccceeecCceeEEEEeeEEEeEHHHHHHHhhhccCCCCCHHHHHHH
Confidence 96 789853 3321 000 0023333333221 124468999999998
Q ss_pred HhCCcCCCC---------------CCChHHHHHHHHHHH
Q 018558 275 YLGYDIQIG---------------IQDPYDDCVATMRLY 298 (354)
Q Consensus 275 ~l~~~i~~~---------------~H~Al~DA~at~~l~ 298 (354)
+||..-... +.-.+.||..+..|+
T Consensus 283 ~Lg~~K~d~~~~I~~l~~~d~~rla~YclkDa~L~~~L~ 321 (498)
T PHA02524 283 EVKADKLDYEGPINKFRKADHQRYVDYCVRDTDIILLID 321 (498)
T ss_pred hcCCccccchhhHHHHhcCchHHHHHHHHHHHHHHHHHH
Confidence 887543211 122377999887665
No 159
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=69.55 E-value=2.4 Score=26.33 Aligned_cols=33 Identities=18% Similarity=0.436 Sum_probs=20.1
Q ss_pred ccccccccccCChHHHHHhhhhccccCccc-cccccccccC
Q 018558 13 NKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCR 52 (354)
Q Consensus 13 ~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~ 52 (354)
++|+.|+..|.-..... ...... .|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~-------~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL-------GANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHc-------CCCCCEEECCCCCCEEE
Confidence 57888988876554321 111123 7888887663
No 160
>PRK04860 hypothetical protein; Provisional
Probab=69.22 E-value=2.4 Score=35.82 Aligned_cols=33 Identities=27% Similarity=0.413 Sum_probs=23.5
Q ss_pred cccccccccCCcccccccc---CCCCCcccccccccccccccccccCCCC
Q 018558 43 VCGICKKHCRSFESLREHL---IGPLPKQECKNVFNNRGCRFCLAILDGP 89 (354)
Q Consensus 43 ~C~~C~k~f~~~~~L~~H~---~~e~p~~~C~k~F~~~~C~~C~k~f~~~ 89 (354)
.|. |++ ...++.+|. +|+++| .|..|++.|...
T Consensus 121 ~C~-C~~---~~~~~rrH~ri~~g~~~Y----------rC~~C~~~l~~~ 156 (160)
T PRK04860 121 RCK-CQE---HQLTVRRHNRVVRGEAVY----------RCRRCGETLVFK 156 (160)
T ss_pred EcC-CCC---eeCHHHHHHHHhcCCccE----------ECCCCCceeEEe
Confidence 786 776 556667776 778888 777777776544
No 161
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=67.62 E-value=2.4 Score=28.74 Aligned_cols=28 Identities=18% Similarity=0.362 Sum_probs=23.4
Q ss_pred CCCCccccccccccccCChHHHHHhhhh
Q 018558 7 SSETLRNKCAACFRQFNRLEHLVEHMRT 34 (354)
Q Consensus 7 ~~~~k~~~C~~Cgk~f~~~~~L~~H~~~ 34 (354)
..|+.-++|+.||..|........|...
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 3567789999999999998888888765
No 162
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=67.27 E-value=1.6 Score=38.90 Aligned_cols=13 Identities=15% Similarity=0.168 Sum_probs=10.1
Q ss_pred ccccccccCCCCh
Q 018558 78 GCRFCLAILDGPN 90 (354)
Q Consensus 78 ~C~~C~k~f~~~~ 90 (354)
.|+.||.+|....
T Consensus 50 vCP~CgyA~~~~~ 62 (214)
T PF09986_consen 50 VCPHCGYAAFEED 62 (214)
T ss_pred ECCCCCCcccccc
Confidence 5999998877663
No 163
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=66.98 E-value=2.5 Score=38.04 Aligned_cols=45 Identities=20% Similarity=0.292 Sum_probs=35.4
Q ss_pred cccccccccccCChHHHHHhhhhccccCccc-cccccccccCCcccccccc
Q 018558 12 RNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRSFESLREHL 61 (354)
Q Consensus 12 ~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~~~~L~~H~ 61 (354)
-|.|..||.+.. +..+..|+.. -++ .- .|-.|++.|.. .+...|.
T Consensus 3 ~FtCnvCgEsvK-Kp~vekH~sr--Crn-~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 3 FFTCNVCGESVK-KPQVEKHMSR--CRN-AYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred EEehhhhhhhcc-ccchHHHHHh--ccC-CeeEEeeccccccc-chhhhhh
Confidence 388999998876 4467779866 555 34 99999999988 7788887
No 164
>PRK04860 hypothetical protein; Provisional
Probab=66.72 E-value=1.5 Score=37.13 Aligned_cols=33 Identities=15% Similarity=0.143 Sum_probs=28.1
Q ss_pred cccccCChHHHHHhhhhccccCccc-cccccccccCCcc
Q 018558 18 CFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRSFE 55 (354)
Q Consensus 18 Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~~~ 55 (354)
|++ ....+..|.++ |+++++ .|..|++.|....
T Consensus 124 C~~---~~~~~rrH~ri--~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 124 CQE---HQLTVRRHNRV--VRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred CCC---eeCHHHHHHHH--hcCCccEECCCCCceeEEec
Confidence 987 67788999999 999999 9999999886543
No 165
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=65.18 E-value=4 Score=36.29 Aligned_cols=17 Identities=18% Similarity=0.534 Sum_probs=12.1
Q ss_pred CccccccccccccCChH
Q 018558 10 TLRNKCAACFRQFNRLE 26 (354)
Q Consensus 10 ~k~~~C~~Cgk~f~~~~ 26 (354)
++...|+.|++.|..+.
T Consensus 3 ~k~~~CPvC~~~F~~~~ 19 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKK 19 (214)
T ss_pred CCceECCCCCCeeeeeE
Confidence 35677888888887654
No 166
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=64.30 E-value=3.8 Score=25.43 Aligned_cols=32 Identities=16% Similarity=0.322 Sum_probs=19.4
Q ss_pred ccccccccccCChHHHHHhhhhccccCccc-ccccccccc
Q 018558 13 NKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHC 51 (354)
Q Consensus 13 ~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f 51 (354)
..|+.|+..|.-...- . ..+... +|..|+..|
T Consensus 3 i~CP~C~~~f~v~~~~-----l--~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK-----L--PAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHH-----c--ccCCcEEECCCCCcEe
Confidence 4688888887655432 1 122234 788887766
No 167
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=62.54 E-value=4.4 Score=23.11 Aligned_cols=10 Identities=20% Similarity=0.371 Sum_probs=7.7
Q ss_pred ccccccccCC
Q 018558 78 GCRFCLAILD 87 (354)
Q Consensus 78 ~C~~C~k~f~ 87 (354)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 6888888774
No 168
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=61.91 E-value=5.1 Score=32.23 Aligned_cols=37 Identities=8% Similarity=0.075 Sum_probs=24.0
Q ss_pred CccccccccccccCCccccccccCCCCCcccccccccccccccccccCCCChhHH
Q 018558 39 VHEPVCGICKKHCRSFESLREHLIGPLPKQECKNVFNNRGCRFCLAILDGPNARR 93 (354)
Q Consensus 39 ~~k~~C~~C~k~f~~~~~L~~H~~~e~p~~~C~k~F~~~~C~~C~k~f~~~~~l~ 93 (354)
|.|..|+.||+.|+-.. ..|- .|+.||..|.....++
T Consensus 7 GtKr~Cp~cg~kFYDLn--------k~p~----------vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 7 GTKRICPNTGSKFYDLN--------RRPA----------VSPYTGEQFPPEEALK 43 (129)
T ss_pred CccccCCCcCccccccC--------CCCc----------cCCCcCCccCcchhhc
Confidence 33337888888886522 3455 7888888876664444
No 169
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=61.55 E-value=4.5 Score=24.99 Aligned_cols=32 Identities=13% Similarity=0.320 Sum_probs=19.6
Q ss_pred ccccccccccCChHHHHHhhhhccccCccc-ccccccccc
Q 018558 13 NKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHC 51 (354)
Q Consensus 13 ~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f 51 (354)
..|+.|+..|.-.... + -..... +|+.|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~-----i--p~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK-----I--PPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHH-----C--CCCCcEEECCCCCCEe
Confidence 4688888887765542 1 222223 788887765
No 170
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=60.90 E-value=6.5 Score=31.66 Aligned_cols=30 Identities=17% Similarity=0.180 Sum_probs=21.1
Q ss_pred ccccccccccCChHHHHHhhhhccccCccc-cccccccccCCcc
Q 018558 13 NKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRSFE 55 (354)
Q Consensus 13 ~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~~~ 55 (354)
..|+.||+.|- -..+.| .|+.||..|....
T Consensus 10 r~Cp~cg~kFY-------------DLnk~p~vcP~cg~~~~~~~ 40 (129)
T TIGR02300 10 RICPNTGSKFY-------------DLNRRPAVSPYTGEQFPPEE 40 (129)
T ss_pred ccCCCcCcccc-------------ccCCCCccCCCcCCccCcch
Confidence 57888988773 334567 8999988775543
No 171
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=60.46 E-value=3.1 Score=26.65 Aligned_cols=29 Identities=24% Similarity=0.681 Sum_probs=18.6
Q ss_pred cccccccccccCChHHHHHhhhhccccCccc-ccccccc
Q 018558 12 RNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKK 49 (354)
Q Consensus 12 ~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k 49 (354)
.|+|..||..|.... .. .. ..+ .|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~------~~--~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQ------SI--SE-DDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEE------Ec--CC-CCCCcCCCCCC
Confidence 388999998875332 22 22 344 8888886
No 172
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=56.93 E-value=6.2 Score=35.21 Aligned_cols=41 Identities=32% Similarity=0.545 Sum_probs=30.1
Q ss_pred cccccccccCChHHHHHhhhhccccCccc-cccccccccCCccccccc
Q 018558 14 KCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRSFESLREH 60 (354)
Q Consensus 14 ~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~~~~L~~H 60 (354)
.|=.|++.|....-|.+|++. +. +|.+|.|.+.+-..|..|
T Consensus 12 wcwycnrefddekiliqhqka------khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA------KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhhhhh------ccceeeeehhhhccCCCceee
Confidence 377788888888888888766 33 788888777666666655
No 173
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=54.70 E-value=6.1 Score=24.45 Aligned_cols=31 Identities=19% Similarity=0.369 Sum_probs=18.4
Q ss_pred ccccccccccCChHHHHHhhhhccccCccc-cccccccccCC
Q 018558 13 NKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRS 53 (354)
Q Consensus 13 ~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~ 53 (354)
..|+.||+.|... . ...... .|+.||-.+.+
T Consensus 2 r~C~~Cg~~Yh~~--------~--~pP~~~~~Cd~cg~~L~q 33 (36)
T PF05191_consen 2 RICPKCGRIYHIE--------F--NPPKVEGVCDNCGGELVQ 33 (36)
T ss_dssp EEETTTTEEEETT--------T--B--SSTTBCTTTTEBEBE
T ss_pred cCcCCCCCccccc--------c--CCCCCCCccCCCCCeeEe
Confidence 3588888877422 2 334445 88888876544
No 174
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=54.28 E-value=6.7 Score=23.88 Aligned_cols=10 Identities=20% Similarity=0.242 Sum_probs=6.6
Q ss_pred cccccccccc
Q 018558 12 RNKCAACFRQ 21 (354)
Q Consensus 12 ~~~C~~Cgk~ 21 (354)
.|.|..||..
T Consensus 2 ~~~C~~CG~i 11 (34)
T cd00729 2 VWVCPVCGYI 11 (34)
T ss_pred eEECCCCCCE
Confidence 3677778754
No 175
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=52.86 E-value=3.7 Score=34.49 Aligned_cols=15 Identities=13% Similarity=0.133 Sum_probs=11.2
Q ss_pred ccccccccCCCChhH
Q 018558 78 GCRFCLAILDGPNAR 92 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l 92 (354)
.|+.||++|......
T Consensus 30 ~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 30 ECLACGKRFTTFERV 44 (154)
T ss_pred eccccCCcceEeEec
Confidence 788888888777644
No 176
>PF15269 zf-C2H2_7: Zinc-finger
Probab=52.76 E-value=8.3 Score=24.95 Aligned_cols=22 Identities=14% Similarity=0.099 Sum_probs=19.5
Q ss_pred ccccccccCCCChhHHHHHhhc
Q 018558 78 GCRFCLAILDGPNARRLHQERC 99 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~~ 99 (354)
+|-.|...+..+++|-+||+..
T Consensus 22 kcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 22 KCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred eeecCCcccchHHHHHHHHHHH
Confidence 7999999999999999999743
No 177
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=51.61 E-value=8.8 Score=25.42 Aligned_cols=23 Identities=22% Similarity=0.488 Sum_probs=15.7
Q ss_pred ccccccccCCCC-----hhHHHHHh-hcc
Q 018558 78 GCRFCLAILDGP-----NARRLHQE-RCQ 100 (354)
Q Consensus 78 ~C~~C~k~f~~~-----~~l~~H~~-~~~ 100 (354)
.|..|++.++.. ++|..|++ +|+
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 477777766554 58888887 453
No 178
>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=51.31 E-value=95 Score=30.94 Aligned_cols=89 Identities=16% Similarity=0.150 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhhhhhhcc-----cCCC-------ceeeeccccCC-CccCCCC
Q 018558 198 LKQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHDLDRLQV-----EYPA-------IMTRDTAKYPP-LMKTSKL 264 (354)
Q Consensus 198 ~~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~Dl~~L~~-----~~~~-------~~~~Dt~~~~~-~~~~~~~ 264 (354)
-.+++.+|++|+.. -.+.+|+.+| .+...+|+- ..+. ..++|.-.+.+ .......
T Consensus 328 E~~~~~~f~~~l~~-----------~~~~~i~hY~-~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~ 395 (457)
T TIGR03491 328 EELAWQQFLQLLQS-----------YPDAPIYHYG-ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIE 395 (457)
T ss_pred HHHHHHHHHHHHHH-----------CCCCeEEeeC-HHHHHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCC
Confidence 35577888888821 1445788888 777665531 1110 02456543222 2222335
Q ss_pred CchHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHH
Q 018558 265 SNSLKYLTQAYLGYDIQIGIQDPYDDCVATMRLYMRMKS 303 (354)
Q Consensus 265 ~~~L~~l~~~~l~~~i~~~~H~Al~DA~at~~l~~~~~~ 303 (354)
+++||.++. +||.+.. +...|...++..|..+..
T Consensus 396 sysLK~v~~-~lg~~~~----~~~~~G~~ai~~y~~~~~ 429 (457)
T TIGR03491 396 SYSLKSIAR-WLGFEWR----QKEASGAKSLLWYRQWKK 429 (457)
T ss_pred CCCHHHHHH-HhCcccC----CCCCCHHHHHHHHHHHHH
Confidence 799999887 5565543 234555666777766544
No 179
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=48.70 E-value=36 Score=26.93 Aligned_cols=25 Identities=12% Similarity=0.115 Sum_probs=19.6
Q ss_pred ccccccccCCCChhHHHHHhhcccc
Q 018558 78 GCRFCLAILDGPNARRLHQERCQMV 102 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~~~~~ 102 (354)
.|..|.+.|-..-..-.|...|.-.
T Consensus 83 ~C~~C~~~FC~dCD~fiHe~Lh~CP 107 (112)
T TIGR00622 83 VCAVCKNVFCVDCDVFVHESLHCCP 107 (112)
T ss_pred eCCCCCCccccccchhhhhhccCCc
Confidence 6999999888888888888666544
No 180
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=45.67 E-value=7.9 Score=25.74 Aligned_cols=28 Identities=25% Similarity=0.623 Sum_probs=17.2
Q ss_pred ccccccccccCChHHHHHhhhhccccCccc-ccccccc
Q 018558 13 NKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKK 49 (354)
Q Consensus 13 ~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k 49 (354)
|+|..||..|.... .. +. ... .|+.||.
T Consensus 6 y~C~~Cg~~fe~~~------~~--~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQ------KM--SD-DPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEE------ec--CC-CCCCCCCCCCC
Confidence 78888888775321 11 22 234 7888875
No 181
>PF14353 CpXC: CpXC protein
Probab=45.13 E-value=13 Score=29.88 Aligned_cols=19 Identities=16% Similarity=0.162 Sum_probs=12.7
Q ss_pred ccccccccCCCChhHHHHH
Q 018558 78 GCRFCLAILDGPNARRLHQ 96 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~ 96 (354)
.|+.||+.|.-...+..|-
T Consensus 40 ~CP~Cg~~~~~~~p~lY~D 58 (128)
T PF14353_consen 40 TCPSCGHKFRLEYPLLYHD 58 (128)
T ss_pred ECCCCCCceecCCCEEEEc
Confidence 5777777666666666665
No 182
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=44.87 E-value=12 Score=30.38 Aligned_cols=9 Identities=33% Similarity=0.741 Sum_probs=6.9
Q ss_pred cccccc-ccC
Q 018558 78 GCRFCL-AIL 86 (354)
Q Consensus 78 ~C~~C~-k~f 86 (354)
+|+.|| +.|
T Consensus 21 GCP~CGg~kF 30 (131)
T PF09845_consen 21 GCPECGGNKF 30 (131)
T ss_pred cCcccCCcce
Confidence 799998 555
No 183
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=43.94 E-value=33 Score=30.44 Aligned_cols=59 Identities=20% Similarity=0.211 Sum_probs=41.4
Q ss_pred cceeeEEEEec--CCceE--EeeeecCCccccC-------ceeeecCCChhhhcCCC-CHHHHHHHHHHHH
Q 018558 151 DLCGRVCIIDE--YENII--FHAYVKPPIPVTS-------YRYETTGIRPEHLRDAI-PLKQVQRKIQDFL 209 (354)
Q Consensus 151 ~~i~~i~vv~~--~g~~i--~~~~v~P~~~i~~-------~~~~itGIt~~~l~~ap-~~~~v~~~~~~~i 209 (354)
-..++++++.. +.+++ |.++|+|+..... ....-|+|...-.+.+. .+..++.+|.+||
T Consensus 8 y~PaEiai~~fSL~~GI~~~~H~~I~Pg~~p~G~~~~a~~hs~~tH~ip~~~~~~~~~d~~~l~~~l~~fl 78 (213)
T PF13017_consen 8 YVPAEIAICKFSLKEGIIDSFHTFINPGQIPLGYRYDAQHHSDETHQIPIPPNALGESDYSELYNELLNFL 78 (213)
T ss_pred EEeEEEEEEEEecCCccchhhhcccCCCCCCcHHHHHHHHhhhhhcCCCCCCcccccCCHHHHHHHHHHHh
Confidence 34567777754 22343 9999999954432 23456888877666665 6999999999999
No 184
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=43.77 E-value=17 Score=21.88 Aligned_cols=11 Identities=18% Similarity=0.513 Sum_probs=6.8
Q ss_pred ccccccccccC
Q 018558 13 NKCAACFRQFN 23 (354)
Q Consensus 13 ~~C~~Cgk~f~ 23 (354)
|.|..||..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 56777776653
No 185
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=43.14 E-value=13 Score=28.73 Aligned_cols=12 Identities=25% Similarity=0.769 Sum_probs=5.6
Q ss_pred cccccccccccC
Q 018558 12 RNKCAACFRQFN 23 (354)
Q Consensus 12 ~~~C~~Cgk~f~ 23 (354)
||.|..||..|.
T Consensus 2 pH~CtrCG~vf~ 13 (112)
T COG3364 2 PHQCTRCGEVFD 13 (112)
T ss_pred Cceecccccccc
Confidence 344545554443
No 186
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=42.39 E-value=11 Score=28.31 Aligned_cols=7 Identities=43% Similarity=1.303 Sum_probs=3.6
Q ss_pred ccccccc
Q 018558 43 VCGICKK 49 (354)
Q Consensus 43 ~C~~C~k 49 (354)
.|+.|++
T Consensus 37 ~Cp~C~~ 43 (89)
T COG1997 37 VCPFCGR 43 (89)
T ss_pred cCCCCCC
Confidence 4555554
No 187
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=42.21 E-value=13 Score=24.09 Aligned_cols=25 Identities=20% Similarity=0.397 Sum_probs=16.2
Q ss_pred ccccccccccCChHHHHHhhhhccccCccc-cccccccc
Q 018558 13 NKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKH 50 (354)
Q Consensus 13 ~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~ 50 (354)
|.|..||..|... ...+ +|+.||..
T Consensus 3 Y~C~~Cg~~~~~~-------------~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-------------SKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-------------CCCceECCCCCce
Confidence 7888888776422 1234 78888754
No 188
>PHA02563 DNA polymerase; Provisional
Probab=40.09 E-value=27 Score=36.25 Aligned_cols=16 Identities=25% Similarity=0.200 Sum_probs=13.4
Q ss_pred CcEEEEechhhhhhhh
Q 018558 225 ARILVGHGLDHDLDRL 240 (354)
Q Consensus 225 ~~ilVgHn~~~Dl~~L 240 (354)
+.++--||+.||..||
T Consensus 66 ~~~vYfHN~~FD~~Fi 81 (630)
T PHA02563 66 ECIIYFHNLKFDGSFI 81 (630)
T ss_pred ceEEEEecCCccHHHH
Confidence 5688899999998765
No 189
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=39.93 E-value=9.8 Score=39.48 Aligned_cols=42 Identities=17% Similarity=0.309 Sum_probs=23.3
Q ss_pred cccccccccCCcccccccc--CCCCCc---cccccccccc----------ccccccc
Q 018558 43 VCGICKKHCRSFESLREHL--IGPLPK---QECKNVFNNR----------GCRFCLA 84 (354)
Q Consensus 43 ~C~~C~k~f~~~~~L~~H~--~~e~p~---~~C~k~F~~~----------~C~~C~k 84 (354)
.|..||.+|+--..|---. |.=..| +.|.+.|... .|+.||-
T Consensus 125 ~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRfHAQp~aCp~CGP 181 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRFHAQPIACPKCGP 181 (750)
T ss_pred ccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccccccccccccCcccCC
Confidence 6777887776655443222 222223 4555555533 5888883
No 190
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=39.79 E-value=12 Score=24.25 Aligned_cols=28 Identities=29% Similarity=0.446 Sum_probs=17.2
Q ss_pred cccccccccccCChHHHHHhhhhccccCccc-ccccccccc
Q 018558 12 RNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHC 51 (354)
Q Consensus 12 ~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f 51 (354)
.|.|+.||..|.... .... .|+.||..+
T Consensus 3 ~y~C~~CG~~~~~~~------------~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDE------------YGTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECC------------CCCceECCCCCCeE
Confidence 578888887654321 1114 788887654
No 191
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=39.77 E-value=13 Score=24.72 Aligned_cols=12 Identities=42% Similarity=0.863 Sum_probs=9.8
Q ss_pred cccccccccccc
Q 018558 11 LRNKCAACFRQF 22 (354)
Q Consensus 11 k~~~C~~Cgk~f 22 (354)
..|.|..||+.|
T Consensus 5 ~~Y~C~~Cg~~~ 16 (49)
T COG1996 5 MEYKCARCGREV 16 (49)
T ss_pred EEEEhhhcCCee
Confidence 458899999887
No 192
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=39.58 E-value=20 Score=22.85 Aligned_cols=25 Identities=20% Similarity=0.484 Sum_probs=15.3
Q ss_pred CCccccccccccccCCh----HHHHHhhh
Q 018558 9 ETLRNKCAACFRQFNRL----EHLVEHMR 33 (354)
Q Consensus 9 ~~k~~~C~~Cgk~f~~~----~~L~~H~~ 33 (354)
+.+..+|..|++.+... +.|..|++
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 34567899999887664 68888873
No 193
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=39.52 E-value=17 Score=21.85 Aligned_cols=9 Identities=22% Similarity=0.423 Sum_probs=5.6
Q ss_pred ccccccccc
Q 018558 13 NKCAACFRQ 21 (354)
Q Consensus 13 ~~C~~Cgk~ 21 (354)
|.|..||..
T Consensus 2 ~~C~~CGy~ 10 (33)
T cd00350 2 YVCPVCGYI 10 (33)
T ss_pred EECCCCCCE
Confidence 567777644
No 194
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=38.92 E-value=55 Score=36.03 Aligned_cols=95 Identities=12% Similarity=0.114 Sum_probs=51.7
Q ss_pred CCCCceEEeeccccccCCCCCccceeeEEEEecCC--------c----eEEeeeecCCccccCc------eeeecCCChh
Q 018558 129 TRDPQVVAIACKMVGGGSDGSLDLCGRVCIIDEYE--------N----IIFHAYVKPPIPVTSY------RYETTGIRPE 190 (354)
Q Consensus 129 ~~~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g--------~----~i~~~~v~P~~~i~~~------~~~itGIt~~ 190 (354)
.++..+.++.++|..- +.....+|+.+++.-... . .-+-.+++|..-+-++ ....++
T Consensus 526 ~Ppl~llsL~i~T~~N-~k~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~~~fP~g~~ela~~k~~~---- 600 (1429)
T KOG0970|consen 526 PPPLTLLSLNIRTSMN-PKQNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPGTSFPLGLKELAKQKLSK---- 600 (1429)
T ss_pred CCCeeEEEeeeeehhc-cccchhhhhhhhhhhcccccccCCCCCCcccCcceeEecCCCCcCCchHHHHHHhccCc----
Confidence 3455677888888753 344455666666542211 1 1255677777543332 011111
Q ss_pred hhcCCCCHHHHHHHHHHHHhcCCCCccccCCCCCCcEEEEec-hhhhhhhh
Q 018558 191 HLRDAIPLKQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHG-LDHDLDRL 240 (354)
Q Consensus 191 ~l~~ap~~~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn-~~~Dl~~L 240 (354)
|.-.-+-...+..|+..++ .+ .-.+||||| ..|+|.+|
T Consensus 601 -v~~~~sErALLs~fla~~~-~~----------dpD~iVgHn~~~~~l~VL 639 (1429)
T KOG0970|consen 601 -VVLHNSERALLSHFLAMLN-KE----------DPDVIVGHNIQGFYLDVL 639 (1429)
T ss_pred -eEEecCHHHHHHHHHHHhh-cc----------CCCEEEEeccccchHHHH
Confidence 1112344556666666662 11 346999999 68888776
No 195
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=38.62 E-value=15 Score=35.17 Aligned_cols=74 Identities=14% Similarity=0.168 Sum_probs=43.6
Q ss_pred cccccccccccCChHHHHHhhhhccccCccc-------cccccccccCCcccccccc------CCCCCcccccccccccc
Q 018558 12 RNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-------VCGICKKHCRSFESLREHL------IGPLPKQECKNVFNNRG 78 (354)
Q Consensus 12 ~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-------~C~~C~k~f~~~~~L~~H~------~~e~p~~~C~k~F~~~~ 78 (354)
-|+|..|...|......+.|+.+ -+..-. .-++--..|..+-.-..-. .++.++ .
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKS--dWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~----------~ 70 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKS--DWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVV----------Y 70 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhh--hHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccce----------e
Confidence 48999999999988888888876 322111 1111111111110000000 122334 7
Q ss_pred cccccccCCCChhHHHHHh
Q 018558 79 CRFCLAILDGPNARRLHQE 97 (354)
Q Consensus 79 C~~C~k~f~~~~~l~~H~~ 97 (354)
|..|.++|.+.....+|++
T Consensus 71 c~~c~k~~~s~~a~~~hl~ 89 (390)
T KOG2785|consen 71 CEACNKSFASPKAHENHLK 89 (390)
T ss_pred hHHhhccccChhhHHHHHH
Confidence 9999999999999999975
No 196
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=37.53 E-value=9 Score=33.46 Aligned_cols=83 Identities=19% Similarity=0.331 Sum_probs=51.3
Q ss_pred ccccccc--cccccCChHHHHHhhhhccccCccccccccccccCCccccccccC--CCCCc-cccccccccccc--cccc
Q 018558 11 LRNKCAA--CFRQFNRLEHLVEHMRTSYHSVHEPVCGICKKHCRSFESLREHLI--GPLPK-QECKNVFNNRGC--RFCL 83 (354)
Q Consensus 11 k~~~C~~--Cgk~f~~~~~L~~H~~~~~H~~~k~~C~~C~k~f~~~~~L~~H~~--~e~p~-~~C~k~F~~~~C--~~C~ 83 (354)
..|.|.. |-+.|........|..+ -|.. .|..|.+.|.....|..|.+ ...-| ..-.+......| ..|+
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~-~h~~---sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt 153 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHT-LHGN---SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCT 153 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhh-cccc---hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhh
Confidence 4477865 65777766666677544 1322 79999999999999998871 00000 000000111156 3488
Q ss_pred ccCCCChhHHHHHh
Q 018558 84 AILDGPNARRLHQE 97 (354)
Q Consensus 84 k~f~~~~~l~~H~~ 97 (354)
..|.....-+.|+-
T Consensus 154 ~KFkT~r~RkdH~I 167 (253)
T KOG4173|consen 154 EKFKTSRDRKDHMI 167 (253)
T ss_pred hhhhhhhhhhhHHH
Confidence 88988888888863
No 197
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=37.09 E-value=13 Score=39.11 Aligned_cols=15 Identities=7% Similarity=0.186 Sum_probs=11.7
Q ss_pred CCCceEEeecccccc
Q 018558 130 RDPQVVAIACKMVGG 144 (354)
Q Consensus 130 ~~~~~vaiD~Ettg~ 144 (354)
+..+++.+|-+||..
T Consensus 505 P~~rv~r~d~Dtt~~ 519 (730)
T COG1198 505 PGARIIRIDSDTTRR 519 (730)
T ss_pred CCCcEEEEccccccc
Confidence 345789999999953
No 198
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=34.28 E-value=20 Score=29.88 Aligned_cols=15 Identities=40% Similarity=0.713 Sum_probs=10.9
Q ss_pred cccCccc-----cccccccc
Q 018558 36 YHSVHEP-----VCGICKKH 50 (354)
Q Consensus 36 ~H~~~k~-----~C~~C~k~ 50 (354)
||+|+++ .|..||..
T Consensus 102 Y~sGE~~g~G~l~C~~Cg~~ 121 (146)
T PF07295_consen 102 YHSGEVVGPGTLVCENCGHE 121 (146)
T ss_pred eecCcEecCceEecccCCCE
Confidence 6788765 68888754
No 199
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=34.20 E-value=26 Score=34.31 Aligned_cols=13 Identities=15% Similarity=0.258 Sum_probs=10.3
Q ss_pred ccccccccCCCCh
Q 018558 78 GCRFCLAILDGPN 90 (354)
Q Consensus 78 ~C~~C~k~f~~~~ 90 (354)
.|..||..+....
T Consensus 369 rC~kCg~~~~~~~ 381 (421)
T COG1571 369 RCKKCGTRARETL 381 (421)
T ss_pred ccccccccCCccc
Confidence 7999998886654
No 200
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=32.86 E-value=31 Score=19.55 Aligned_cols=21 Identities=24% Similarity=0.578 Sum_probs=14.8
Q ss_pred ccccccccCCCChhHHHHHhhc
Q 018558 78 GCRFCLAILDGPNARRLHQERC 99 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~~ 99 (354)
.|+.|.+.+ ....+..|...|
T Consensus 3 ~CPiC~~~v-~~~~in~HLD~C 23 (26)
T smart00734 3 QCPVCFREV-PENLINSHLDSC 23 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHHHh
Confidence 488888877 556777777544
No 201
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=32.63 E-value=27 Score=28.94 Aligned_cols=13 Identities=23% Similarity=0.618 Sum_probs=7.4
Q ss_pred cccccccccccCC
Q 018558 12 RNKCAACFRQFNR 24 (354)
Q Consensus 12 ~~~C~~Cgk~f~~ 24 (354)
.|.|+.|+..|..
T Consensus 99 ~Y~Cp~C~~~y~~ 111 (147)
T smart00531 99 YYKCPNCQSKYTF 111 (147)
T ss_pred EEECcCCCCEeeH
Confidence 4566666655553
No 202
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=32.59 E-value=32 Score=31.05 Aligned_cols=36 Identities=22% Similarity=0.398 Sum_probs=21.4
Q ss_pred CCCccccccccccccCChHHHHHhhhhccccCccc-cccccccccCC
Q 018558 8 SETLRNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRS 53 (354)
Q Consensus 8 ~~~k~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~ 53 (354)
+.++.|.|..|...+= .++ -..++. .|..|.+.|--
T Consensus 108 ~~drqFaC~~Cd~~Ww--------Rrv--p~rKeVSRCr~C~~rYDP 144 (278)
T PF15135_consen 108 SVDRQFACSSCDHMWW--------RRV--PQRKEVSRCRKCRKRYDP 144 (278)
T ss_pred ccceeeeccccchHHH--------hcc--CcccccccccccccccCC
Confidence 3456799999964321 123 222333 89999887754
No 203
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=31.33 E-value=13 Score=25.34 Aligned_cols=32 Identities=13% Similarity=0.286 Sum_probs=19.2
Q ss_pred cccccccccccCChHHHHHhhhhccccCccccccccccccC
Q 018558 12 RNKCAACFRQFNRLEHLVEHMRTSYHSVHEPVCGICKKHCR 52 (354)
Q Consensus 12 ~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~~C~~C~k~f~ 52 (354)
.++|+.||..+.-... ..++...|+.||..|-
T Consensus 2 ~~~CP~CG~~iev~~~---------~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 2 QFECPDCGAEIELENP---------ELGELVICDECGAELE 33 (54)
T ss_pred ccCCCCCCCEEecCCC---------ccCCEEeCCCCCCEEE
Confidence 3689999987643211 1232118999987663
No 204
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=31.27 E-value=22 Score=28.86 Aligned_cols=14 Identities=14% Similarity=0.498 Sum_probs=11.4
Q ss_pred ccccccccCCCChh
Q 018558 78 GCRFCLAILDGPNA 91 (354)
Q Consensus 78 ~C~~C~k~f~~~~~ 91 (354)
.|+.|..+|.++..
T Consensus 123 vCPvCkTSFKss~~ 136 (140)
T PF05290_consen 123 VCPVCKTSFKSSSS 136 (140)
T ss_pred CCCccccccccccc
Confidence 69999999987653
No 205
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.86 E-value=12 Score=27.15 Aligned_cols=31 Identities=26% Similarity=0.730 Sum_probs=20.5
Q ss_pred cccccccccccCChHHHHHhhhhccccCccc--cccccccccC
Q 018558 12 RNKCAACFRQFNRLEHLVEHMRTSYHSVHEP--VCGICKKHCR 52 (354)
Q Consensus 12 ~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~--~C~~C~k~f~ 52 (354)
.|+|..||..| .+.+|++ +.| .|+.|+..|.
T Consensus 12 ~Y~c~~cg~~~----dvvq~~~------ddplt~ce~c~a~~k 44 (82)
T COG2331 12 SYECTECGNRF----DVVQAMT------DDPLTTCEECGARLK 44 (82)
T ss_pred EEeecccchHH----HHHHhcc------cCccccChhhChHHH
Confidence 48999999765 3444433 234 8999987653
No 206
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=30.55 E-value=21 Score=20.01 Aligned_cols=10 Identities=20% Similarity=0.394 Sum_probs=8.3
Q ss_pred cccccccccc
Q 018558 11 LRNKCAACFR 20 (354)
Q Consensus 11 k~~~C~~Cgk 20 (354)
.+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4699999985
No 207
>KOG3846 consensus L-kynurenine hydrolase [Amino acid transport and metabolism]
Probab=30.17 E-value=23 Score=33.24 Aligned_cols=9 Identities=44% Similarity=1.505 Sum_probs=7.9
Q ss_pred CCCceeeec
Q 018558 344 RSDYYCWCL 352 (354)
Q Consensus 344 ~~~~~~~~~ 352 (354)
..||+|||.
T Consensus 266 gVDFACWCS 274 (465)
T KOG3846|consen 266 GVDFACWCS 274 (465)
T ss_pred CCceEEEee
Confidence 789999995
No 208
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=28.72 E-value=15 Score=32.91 Aligned_cols=42 Identities=19% Similarity=0.305 Sum_probs=30.3
Q ss_pred cccccccccCCccccccccCCCCCcccccccccccccccccccCCCChhHHHH
Q 018558 43 VCGICKKHCRSFESLREHLIGPLPKQECKNVFNNRGCRFCLAILDGPNARRLH 95 (354)
Q Consensus 43 ~C~~C~k~f~~~~~L~~H~~~e~p~~~C~k~F~~~~C~~C~k~f~~~~~l~~H 95 (354)
-|=.|.+.|.....|.+|+ ..+.| +|.+|.|..-+--.|..|
T Consensus 12 wcwycnrefddekiliqhq-kakhf----------kchichkkl~sgpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQ-KAKHF----------KCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhhh-hhccc----------eeeeehhhhccCCCceee
Confidence 5788999999999999996 23457 899998655444444444
No 209
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=27.95 E-value=22 Score=25.78 Aligned_cols=10 Identities=20% Similarity=0.102 Sum_probs=4.8
Q ss_pred cccccCCCCh
Q 018558 81 FCLAILDGPN 90 (354)
Q Consensus 81 ~C~k~f~~~~ 90 (354)
.||.+|....
T Consensus 34 eCg~tF~t~e 43 (72)
T PRK09678 34 NCSATFITYE 43 (72)
T ss_pred CCCCEEEEEE
Confidence 4555554433
No 210
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=27.76 E-value=30 Score=23.96 Aligned_cols=8 Identities=25% Similarity=0.621 Sum_probs=4.9
Q ss_pred cccccccc
Q 018558 43 VCGICKKH 50 (354)
Q Consensus 43 ~C~~C~k~ 50 (354)
.|+.||..
T Consensus 29 ~CPnCGe~ 36 (61)
T COG2888 29 PCPNCGEV 36 (61)
T ss_pred eCCCCCce
Confidence 56666643
No 211
>KOG0782 consensus Predicted diacylglycerol kinase [Signal transduction mechanisms]
Probab=27.31 E-value=13 Score=37.46 Aligned_cols=33 Identities=27% Similarity=0.503 Sum_probs=0.0
Q ss_pred cccccccccCChHHHHHhhhhccccCccc--cccccccccCCc
Q 018558 14 KCAACFRQFNRLEHLVEHMRTSYHSVHEP--VCGICKKHCRSF 54 (354)
Q Consensus 14 ~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~--~C~~C~k~f~~~ 54 (354)
+|..|||.|.++..+ |+.+.. .|+.|...|-.+
T Consensus 255 kC~~CgKgFQQKf~F--------hsKEivAisCSWCKqayH~K 289 (1004)
T KOG0782|consen 255 KCNTCGKGFQQKFFF--------HSKEIVAISCSWCKQAYHLK 289 (1004)
T ss_pred ccchhhhhhhhheee--------ccccEEEEEehHHHHHhhcc
No 212
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=27.02 E-value=12 Score=38.89 Aligned_cols=27 Identities=19% Similarity=0.299 Sum_probs=24.5
Q ss_pred ccccccccCCCChhHHHHHhhccccCC
Q 018558 78 GCRFCLAILDGPNARRLHQERCQMVSS 104 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~~~~~~~ 104 (354)
.|.+|+|+|---.++..|||+|.+...
T Consensus 794 pCreC~kvF~KiKSrNAHMK~Hr~q~~ 820 (907)
T KOG4167|consen 794 PCRECGKVFFKIKSRNAHMKTHRQQEE 820 (907)
T ss_pred ehHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence 599999999999999999999987754
No 213
>PF11906 DUF3426: Protein of unknown function (DUF3426); InterPro: IPR021834 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 262 to 463 amino acids in length.
Probab=26.71 E-value=1.4e+02 Score=24.31 Aligned_cols=59 Identities=10% Similarity=0.100 Sum_probs=41.5
Q ss_pred CCceEEeeccccccCCCCCccceeeEEEEecCCceEEeeeecCCccccCceeeecCCCh
Q 018558 131 DPQVVAIACKMVGGGSDGSLDLCGRVCIIDEYENIIFHAYVKPPIPVTSYRYETTGIRP 189 (354)
Q Consensus 131 ~~~~vaiD~Ettg~~~~~~~~~i~~i~vv~~~g~~i~~~~v~P~~~i~~~~~~itGIt~ 189 (354)
......++.+..+.+.....-...++.+.|.+|+.++...+.|...+.+....-.||.+
T Consensus 66 ~~~~l~v~g~i~N~~~~~~~~P~l~l~L~D~~g~~l~~r~~~P~~yl~~~~~~~~~l~p 124 (149)
T PF11906_consen 66 GPGVLVVSGTIRNRADFPQALPALELSLLDAQGQPLARRVFTPADYLPPGLAAQAGLPP 124 (149)
T ss_pred CCCEEEEEEEEEeCCCCcccCceEEEEEECCCCCEEEEEEEChHHhcccccccccccCC
Confidence 45677888888877655544555788888999999999999897666654333444443
No 214
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=26.62 E-value=67 Score=36.01 Aligned_cols=80 Identities=19% Similarity=0.335 Sum_probs=56.5
Q ss_pred cccccccccccCChHHHHHhhhhccccCccc-cccccccccCCcccccccc-----------CCCCCc---ccccccccc
Q 018558 12 RNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKHCRSFESLREHL-----------IGPLPK---QECKNVFNN 76 (354)
Q Consensus 12 ~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~f~~~~~L~~H~-----------~~e~p~---~~C~k~F~~ 76 (354)
.+.|..|.+.|.....+. |.-+ ..+ .|..|...|.....|..|. .+.-|+ ..|.
T Consensus 1260 e~~c~~~~~~~~~~~~~~-~l~~-----~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~----- 1328 (1406)
T KOG1146|consen 1260 EGECGAVDELLTPSFGIS-TLDV-----THRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCT----- 1328 (1406)
T ss_pred cchhhhccccccCcccee-eccc-----chhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccc-----
Confidence 378999999888776665 5433 345 8999999999988888886 011111 1111
Q ss_pred cccccccccCCCChhHHHHHhhcccc
Q 018558 77 RGCRFCLAILDGPNARRLHQERCQMV 102 (354)
Q Consensus 77 ~~C~~C~k~f~~~~~l~~H~~~~~~~ 102 (354)
..|..|..-|+....|+.|++.-+..
T Consensus 1329 ~~c~~c~~~~~~~~alqihm~~~~~~ 1354 (1406)
T KOG1146|consen 1329 YHCLACEVLLSGREALQIHMRSSAHR 1354 (1406)
T ss_pred ccchHHHhhcchhHHHHHHHHHhhhc
Confidence 13999999999999999999864433
No 215
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=26.30 E-value=14 Score=28.50 Aligned_cols=11 Identities=18% Similarity=0.440 Sum_probs=7.2
Q ss_pred ccccccccccc
Q 018558 11 LRNKCAACFRQ 21 (354)
Q Consensus 11 k~~~C~~Cgk~ 21 (354)
+.|.|+.||..
T Consensus 21 k~FtCp~Cghe 31 (104)
T COG4888 21 KTFTCPRCGHE 31 (104)
T ss_pred ceEecCccCCe
Confidence 45777777743
No 216
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=26.21 E-value=36 Score=31.77 Aligned_cols=25 Identities=12% Similarity=0.275 Sum_probs=19.6
Q ss_pred ccccccccCCCChhHHHHHhhcccc
Q 018558 78 GCRFCLAILDGPNARRLHQERCQMV 102 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~~~~~ 102 (354)
.|+.|...|..-...-.|...|-..
T Consensus 390 ~Ce~CK~~FC~dCdvfiHe~Lh~C~ 414 (421)
T COG5151 390 QCELCKSTFCSDCDVFIHETLHFCI 414 (421)
T ss_pred echhhhhhhhhhhHHHHHHHHhhCC
Confidence 7999999998888888887555433
No 217
>PF06821 Ser_hydrolase: Serine hydrolase; InterPro: IPR010662 This family contains a number of hypothetical bacterial proteins of unknown function, which may be cytosolic. The Crystal Structure Of The Yden Gene Product Swiss:P96671 from B. Subtilis has been solved. The structure shows an alpha-beta hydrolase fold suggesting an enzymatic function for these proteins [].; GO: 0016787 hydrolase activity; PDB: 3BDV_B 2QS9_A 1UXO_A.
Probab=25.29 E-value=65 Score=27.38 Aligned_cols=37 Identities=24% Similarity=0.266 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCccccCCCCCCcEEEEechhh--hhhhh
Q 018558 194 DAIPLKQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDH--DLDRL 240 (354)
Q Consensus 194 ~ap~~~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~--Dl~~L 240 (354)
+.|..++-...|.+-|.. ..++++||||++.- =++.|
T Consensus 35 ~~P~~~~W~~~l~~~i~~----------~~~~~ilVaHSLGc~~~l~~l 73 (171)
T PF06821_consen 35 DNPDLDEWVQALDQAIDA----------IDEPTILVAHSLGCLTALRWL 73 (171)
T ss_dssp TS--HHHHHHHHHHCCHC-----------TTTEEEEEETHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHhh----------cCCCeEEEEeCHHHHHHHHHH
Confidence 778888888888888721 23678999999643 34444
No 218
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.24 E-value=29 Score=27.19 Aligned_cols=10 Identities=0% Similarity=-0.223 Sum_probs=8.5
Q ss_pred ccccccccCC
Q 018558 78 GCRFCLAILD 87 (354)
Q Consensus 78 ~C~~C~k~f~ 87 (354)
.|+.||++|.
T Consensus 28 VsPytG~s~P 37 (129)
T COG4530 28 VSPYTGKSYP 37 (129)
T ss_pred ccCcccccch
Confidence 7999999993
No 219
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=25.22 E-value=20 Score=37.40 Aligned_cols=19 Identities=32% Similarity=0.686 Sum_probs=14.6
Q ss_pred cccccccccCCCChhHHHH
Q 018558 77 RGCRFCLAILDGPNARRLH 95 (354)
Q Consensus 77 ~~C~~C~k~f~~~~~l~~H 95 (354)
++|+.|+.+|...+-+..|
T Consensus 679 RKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 679 RKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred CCCCCCCCCCCcccccccC
Confidence 3899999999877765544
No 220
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=25.14 E-value=39 Score=25.56 Aligned_cols=13 Identities=31% Similarity=0.672 Sum_probs=9.5
Q ss_pred cc-cccccccccCC
Q 018558 41 EP-VCGICKKHCRS 53 (354)
Q Consensus 41 k~-~C~~C~k~f~~ 53 (354)
+| .|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 56 78888877754
No 221
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=25.11 E-value=22 Score=36.95 Aligned_cols=27 Identities=26% Similarity=0.417 Sum_probs=19.6
Q ss_pred ccccccccccccCChHHHHHhhhhccccC
Q 018558 11 LRNKCAACFRQFNRLEHLVEHMRTSYHSV 39 (354)
Q Consensus 11 k~~~C~~Cgk~f~~~~~L~~H~~~~~H~~ 39 (354)
-.|.|.+|+|.|....++..||++ |.-
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~--Hr~ 817 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKT--HRQ 817 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHH--HHH
Confidence 347788888877777777777777 653
No 222
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=25.03 E-value=47 Score=30.83 Aligned_cols=28 Identities=18% Similarity=0.523 Sum_probs=25.0
Q ss_pred ccccccccCCCChhHHHHHhhccccCCC
Q 018558 78 GCRFCLAILDGPNARRLHQERCQMVSSA 105 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~~~~~~~~ 105 (354)
.|+.|-+-|.+...+..|+..|....+|
T Consensus 50 iCe~Clky~~~~~~l~~H~~~C~~r~PP 77 (290)
T PLN03238 50 ICEYCLKYMRKKKSLLRHLAKCDIRQPP 77 (290)
T ss_pred EcCCCcchhCCHHHHHHHHHhCCCCCCC
Confidence 6999999999999999999999887543
No 223
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=24.72 E-value=41 Score=28.61 Aligned_cols=21 Identities=33% Similarity=0.786 Sum_probs=14.7
Q ss_pred cccccccccCCccccccccCCCCCccccccccccccccccc
Q 018558 43 VCGICKKHCRSFESLREHLIGPLPKQECKNVFNNRGCRFCL 83 (354)
Q Consensus 43 ~C~~C~k~f~~~~~L~~H~~~e~p~~~C~k~F~~~~C~~C~ 83 (354)
.|.+||..+ .|+-|- .|++||
T Consensus 136 vC~vCGy~~----------~ge~P~----------~CPiCg 156 (166)
T COG1592 136 VCPVCGYTH----------EGEAPE----------VCPICG 156 (166)
T ss_pred EcCCCCCcc----------cCCCCC----------cCCCCC
Confidence 788887654 345566 788887
No 224
>PRK14873 primosome assembly protein PriA; Provisional
Probab=24.42 E-value=23 Score=37.09 Aligned_cols=18 Identities=17% Similarity=0.302 Sum_probs=10.6
Q ss_pred cccccccccccccccccc
Q 018558 68 QECKNVFNNRGCRFCLAI 85 (354)
Q Consensus 68 ~~C~k~F~~~~C~~C~k~ 85 (354)
..||..-....|+.|+..
T Consensus 414 h~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 414 RWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred CCCcCCCcCccCCCCcCC
Confidence 345554333379999854
No 225
>PF12096 DUF3572: Protein of unknown function (DUF3572); InterPro: IPR021955 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 100 amino acids in length.
Probab=23.61 E-value=48 Score=25.04 Aligned_cols=28 Identities=32% Similarity=0.452 Sum_probs=24.1
Q ss_pred eecCCChhhhcCCCCHHHHHHHHHHHHh
Q 018558 183 ETTGIRPEHLRDAIPLKQVQRKIQDFLC 210 (354)
Q Consensus 183 ~itGIt~~~l~~ap~~~~v~~~~~~~i~ 210 (354)
..||+++++|..+-.=.+.+.-+++|+.
T Consensus 29 a~TG~~p~~LR~~a~dp~FL~~VLdFl~ 56 (88)
T PF12096_consen 29 ALTGLSPDDLRAAAGDPAFLAAVLDFLL 56 (88)
T ss_pred HHhCCCHHHHHHHccChHHHHHHHHHHH
Confidence 5799999999998777788888999983
No 226
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.57 E-value=29 Score=35.15 Aligned_cols=12 Identities=8% Similarity=0.238 Sum_probs=8.8
Q ss_pred CceEEeeccccc
Q 018558 132 PQVVAIACKMVG 143 (354)
Q Consensus 132 ~~~vaiD~Ettg 143 (354)
.+++.+|-+++.
T Consensus 285 ~~v~~~d~d~~~ 296 (505)
T TIGR00595 285 ARIARIDSDTTS 296 (505)
T ss_pred CcEEEEeccccc
Confidence 367888888874
No 227
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=23.50 E-value=31 Score=21.32 Aligned_cols=30 Identities=20% Similarity=0.514 Sum_probs=18.8
Q ss_pred cccccccccccCChHHHHHhhhhccccCccc-cccccccc
Q 018558 12 RNKCAACFRQFNRLEHLVEHMRTSYHSVHEP-VCGICKKH 50 (354)
Q Consensus 12 ~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~k~-~C~~C~k~ 50 (354)
.|+|..||..|..... . .. ... .|+.||..
T Consensus 5 ~y~C~~Cg~~fe~~~~------~--~~-~~~~~CP~Cg~~ 35 (41)
T smart00834 5 EYRCEDCGHTFEVLQK------I--SD-DPLATCPECGGD 35 (41)
T ss_pred EEEcCCCCCEEEEEEe------c--CC-CCCCCCCCCCCc
Confidence 3889999988753321 1 12 234 89998863
No 228
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=22.73 E-value=45 Score=22.68 Aligned_cols=6 Identities=50% Similarity=1.165 Sum_probs=2.4
Q ss_pred cccccc
Q 018558 43 VCGICK 48 (354)
Q Consensus 43 ~C~~C~ 48 (354)
.|+.|+
T Consensus 23 vCp~Cg 28 (54)
T PF14446_consen 23 VCPECG 28 (54)
T ss_pred ECCCCC
Confidence 344443
No 229
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=22.36 E-value=50 Score=26.38 Aligned_cols=26 Identities=27% Similarity=0.399 Sum_probs=20.1
Q ss_pred CCccccccccccccCChHHHHHhhhh
Q 018558 9 ETLRNKCAACFRQFNRLEHLVEHMRT 34 (354)
Q Consensus 9 ~~k~~~C~~Cgk~f~~~~~L~~H~~~ 34 (354)
|.-.|-|-+|.+-|.....|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 33458888888888888888888776
No 230
>smart00211 TY Thyroglobulin type I repeats. The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases and binding partners of heparin.
Probab=22.31 E-value=40 Score=22.02 Aligned_cols=8 Identities=50% Similarity=1.555 Sum_probs=5.9
Q ss_pred ceeeecCC
Q 018558 347 YYCWCLDR 354 (354)
Q Consensus 347 ~~~~~~~~ 354 (354)
-+|||-|.
T Consensus 20 g~CwCVd~ 27 (46)
T smart00211 20 GQCWCVDA 27 (46)
T ss_pred CcEEEECC
Confidence 47999773
No 231
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=22.27 E-value=79 Score=20.01 Aligned_cols=27 Identities=19% Similarity=0.408 Sum_probs=16.2
Q ss_pred cccccccccccccCCCC--hhHHHHHhhc
Q 018558 73 VFNNRGCRFCLAILDGP--NARRLHQERC 99 (354)
Q Consensus 73 ~F~~~~C~~C~k~f~~~--~~l~~H~~~~ 99 (354)
.|....|..||-.|... ..-..|.+-|
T Consensus 10 ~~~~~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 10 SFGATTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred ccCCcCCCCCCCEECCCCHHHHHHHHHHH
Confidence 34444788888666543 4456666554
No 232
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=22.12 E-value=42 Score=32.54 Aligned_cols=28 Identities=21% Similarity=0.630 Sum_probs=25.8
Q ss_pred ccccccccCCCChhHHHHHhhccccCCC
Q 018558 78 GCRFCLAILDGPNARRLHQERCQMVSSA 105 (354)
Q Consensus 78 ~C~~C~k~f~~~~~l~~H~~~~~~~~~~ 105 (354)
.|.+|-+-+.+...|+.|++.|....||
T Consensus 160 iCEfCLkY~~s~~~l~rH~~kC~~rhPP 187 (396)
T KOG2747|consen 160 ICEFCLKYMKSRTSLQRHLKKCKLRHPP 187 (396)
T ss_pred EehHHHhHhchHHHHHHHHHhcCCCCCC
Confidence 5999999999999999999999988665
No 233
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=21.82 E-value=55 Score=26.73 Aligned_cols=24 Identities=33% Similarity=0.569 Sum_probs=11.8
Q ss_pred cccccccccccCChHHHHHhhhhccccCc
Q 018558 12 RNKCAACFRQFNRLEHLVEHMRTSYHSVH 40 (354)
Q Consensus 12 ~~~C~~Cgk~f~~~~~L~~H~~~~~H~~~ 40 (354)
...|-+|||.|. .|.+|.+. |.|-
T Consensus 72 ~i~clecGk~~k---~LkrHL~~--~~gl 95 (132)
T PF05443_consen 72 YIICLECGKKFK---TLKRHLRT--HHGL 95 (132)
T ss_dssp -EE-TBT--EES---BHHHHHHH--TT-S
T ss_pred eeEEccCCcccc---hHHHHHHH--ccCC
Confidence 356777777765 34667766 6443
No 234
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=21.27 E-value=41 Score=30.50 Aligned_cols=41 Identities=15% Similarity=0.352 Sum_probs=30.2
Q ss_pred cccccccccCCcccccccc---CCCCCcccccccccccccccccccCCCChhHHHHH
Q 018558 43 VCGICKKHCRSFESLREHL---IGPLPKQECKNVFNNRGCRFCLAILDGPNARRLHQ 96 (354)
Q Consensus 43 ~C~~C~k~f~~~~~L~~H~---~~e~p~~~C~k~F~~~~C~~C~k~f~~~~~l~~H~ 96 (354)
.|..||... -+..+.+|+ ++ ..| .|--|++.|-. .++..|.
T Consensus 5 tCnvCgEsv-KKp~vekH~srCrn-~~f----------SCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 5 TCNVCGESV-KKPQVEKHMSRCRN-AYF----------SCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred ehhhhhhhc-cccchHHHHHhccC-Cee----------EEeeccccccc-chhhhhh
Confidence 588898775 345677787 33 445 78889999977 7788886
No 235
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=21.16 E-value=57 Score=28.99 Aligned_cols=29 Identities=21% Similarity=0.457 Sum_probs=21.3
Q ss_pred CCccccccccccccCChHHHHHhhhhcccc
Q 018558 9 ETLRNKCAACFRQFNRLEHLVEHMRTSYHS 38 (354)
Q Consensus 9 ~~k~~~C~~Cgk~f~~~~~L~~H~~~~~H~ 38 (354)
.+..|.|..|+|.|....-...|+..+ |.
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nK-H~ 102 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNK-HP 102 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH--H
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhc-CH
Confidence 345699999999999999999998762 54
No 236
>PHA00626 hypothetical protein
Probab=21.08 E-value=44 Score=22.86 Aligned_cols=16 Identities=13% Similarity=0.129 Sum_probs=12.6
Q ss_pred CccccccccccccCCh
Q 018558 10 TLRNKCAACFRQFNRL 25 (354)
Q Consensus 10 ~k~~~C~~Cgk~f~~~ 25 (354)
...|+|+.||..|+..
T Consensus 21 snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD 36 (59)
T ss_pred CcceEcCCCCCeechh
Confidence 4679999999888644
No 237
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=20.99 E-value=37 Score=25.72 Aligned_cols=7 Identities=43% Similarity=1.170 Sum_probs=4.4
Q ss_pred ccccccc
Q 018558 43 VCGICKK 49 (354)
Q Consensus 43 ~C~~C~k 49 (354)
.|+.|++
T Consensus 38 ~CpfCgk 44 (90)
T PTZ00255 38 FCPFCGK 44 (90)
T ss_pred cCCCCCC
Confidence 5666654
No 238
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=20.90 E-value=25 Score=22.98 Aligned_cols=6 Identities=33% Similarity=0.949 Sum_probs=3.2
Q ss_pred cccccc
Q 018558 15 CAACFR 20 (354)
Q Consensus 15 C~~Cgk 20 (354)
|+.||.
T Consensus 2 CP~Cg~ 7 (47)
T PF04606_consen 2 CPHCGS 7 (47)
T ss_pred cCCCCC
Confidence 555554
No 239
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=20.78 E-value=35 Score=25.89 Aligned_cols=7 Identities=57% Similarity=1.326 Sum_probs=4.4
Q ss_pred ccccccc
Q 018558 43 VCGICKK 49 (354)
Q Consensus 43 ~C~~C~k 49 (354)
.|+.|++
T Consensus 37 ~CpfCgk 43 (91)
T TIGR00280 37 VCPFCGK 43 (91)
T ss_pred cCCCCCC
Confidence 5666654
No 240
>COG3545 Predicted esterase of the alpha/beta hydrolase fold [General function prediction only]
Probab=20.14 E-value=1.5e+02 Score=25.47 Aligned_cols=32 Identities=19% Similarity=0.202 Sum_probs=23.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCccccCCCCCCcEEEEechhhh
Q 018558 195 AIPLKQVQRKIQDFLCNGEPMWKIRPRGSRARILVGHGLDHD 236 (354)
Q Consensus 195 ap~~~~v~~~~~~~i~~~~~~~~~~~~~~~~~ilVgHn~~~D 236 (354)
+|.+++-..++.+-++. . .+..|||+|++.--
T Consensus 40 ~P~~~dWi~~l~~~v~a-~---------~~~~vlVAHSLGc~ 71 (181)
T COG3545 40 APVLDDWIARLEKEVNA-A---------EGPVVLVAHSLGCA 71 (181)
T ss_pred CCCHHHHHHHHHHHHhc-c---------CCCeEEEEecccHH
Confidence 68888888888887732 1 15589999996543
No 241
>PRK04023 DNA polymerase II large subunit; Validated
Probab=20.01 E-value=84 Score=34.33 Aligned_cols=20 Identities=15% Similarity=0.282 Sum_probs=13.2
Q ss_pred ccccccccccccccccccCC
Q 018558 68 QECKNVFNNRGCRFCLAILD 87 (354)
Q Consensus 68 ~~C~k~F~~~~C~~C~k~f~ 87 (354)
+.|++......|+.|+..-.
T Consensus 655 P~CG~~~~~y~CPKCG~El~ 674 (1121)
T PRK04023 655 PRCGIEVEEDECEKCGREPT 674 (1121)
T ss_pred ccccCcCCCCcCCCCCCCCC
Confidence 66766666567888885443
Done!