Query 018586
Match_columns 353
No_of_seqs 255 out of 2491
Neff 8.9
Searched_HMMs 46136
Date Fri Mar 29 10:15:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018586.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018586hhsearch_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 1.4E-39 3E-44 280.0 13.4 268 17-314 3-272 (280)
2 cd06149 ISG20 DEDDh 3'-5' exon 100.0 4.9E-33 1.1E-37 232.7 14.3 150 138-302 1-157 (157)
3 cd06144 REX4_like DEDDh 3'-5' 100.0 9.2E-33 2E-37 230.3 15.2 150 138-302 1-152 (152)
4 cd06145 REX1_like DEDDh 3'-5' 100.0 1.4E-32 3E-37 228.4 14.5 146 138-302 1-150 (150)
5 cd06143 PAN2_exo DEDDh 3'-5' e 100.0 3.4E-31 7.4E-36 220.0 14.4 150 138-302 1-174 (174)
6 cd06137 DEDDh_RNase DEDDh 3'-5 100.0 4.4E-31 9.6E-36 222.2 11.7 147 138-302 1-161 (161)
7 PRK07942 DNA polymerase III su 100.0 2.7E-29 5.8E-34 223.2 11.3 187 132-351 3-203 (232)
8 PRK07740 hypothetical protein; 100.0 1.6E-28 3.5E-33 219.6 14.6 163 129-310 53-228 (244)
9 PRK05711 DNA polymerase III su 100.0 2.6E-28 5.5E-33 216.6 12.7 158 134-308 3-176 (240)
10 TIGR01406 dnaQ_proteo DNA poly 100.0 4.3E-28 9.4E-33 214.2 12.8 161 136-313 1-177 (225)
11 PRK09146 DNA polymerase III su 100.0 7E-28 1.5E-32 214.3 13.9 163 127-308 39-227 (239)
12 PRK07247 DNA polymerase III su 99.9 1.6E-27 3.5E-32 205.3 13.7 157 134-310 4-171 (195)
13 cd06130 DNA_pol_III_epsilon_li 99.9 7.9E-28 1.7E-32 201.7 11.4 146 137-302 1-155 (156)
14 PRK08517 DNA polymerase III su 99.9 1.5E-27 3.2E-32 214.1 13.5 174 130-345 63-247 (257)
15 PRK06195 DNA polymerase III su 99.9 2.3E-27 4.9E-32 219.7 13.2 154 135-308 1-164 (309)
16 PRK06807 DNA polymerase III su 99.9 4E-27 8.6E-32 217.0 12.9 157 133-309 6-173 (313)
17 PRK07983 exodeoxyribonuclease 99.9 5.5E-27 1.2E-31 205.7 12.4 146 137-307 2-153 (219)
18 PRK06310 DNA polymerase III su 99.9 1.1E-26 2.3E-31 208.6 14.2 158 134-309 6-175 (250)
19 PRK06063 DNA polymerase III su 99.9 1.1E-26 2.4E-31 214.6 14.4 159 132-310 12-181 (313)
20 PRK06309 DNA polymerase III su 99.9 2E-26 4.4E-31 205.0 14.0 154 135-308 2-166 (232)
21 TIGR00573 dnaq exonuclease, DN 99.9 1.7E-26 3.7E-31 203.6 12.8 164 133-312 5-181 (217)
22 PRK07748 sporulation inhibitor 99.9 1.3E-26 2.8E-31 203.1 11.8 159 134-310 3-182 (207)
23 cd06131 DNA_pol_III_epsilon_Ec 99.9 1.7E-26 3.6E-31 195.9 12.1 149 137-304 1-166 (167)
24 PRK07883 hypothetical protein; 99.9 3.1E-26 6.8E-31 226.7 13.9 164 128-310 8-184 (557)
25 PRK09145 DNA polymerase III su 99.9 5.8E-26 1.3E-30 198.3 14.0 156 133-307 27-200 (202)
26 PRK06722 exonuclease; Provisio 99.9 4.1E-26 8.8E-31 205.6 11.5 158 134-307 4-180 (281)
27 cd06134 RNaseT DEDDh 3'-5' exo 99.9 7.8E-26 1.7E-30 195.1 12.5 165 134-308 4-189 (189)
28 TIGR01298 RNaseT ribonuclease 99.9 7.6E-26 1.6E-30 196.7 12.0 171 132-312 5-196 (200)
29 COG2176 PolC DNA polymerase II 99.9 1.1E-26 2.3E-31 233.5 7.3 161 131-310 417-588 (1444)
30 PRK07246 bifunctional ATP-depe 99.9 5.8E-26 1.3E-30 234.0 12.8 158 134-310 6-172 (820)
31 cd06136 TREX1_2 DEDDh 3'-5' ex 99.9 1.1E-25 2.3E-30 192.4 10.8 150 137-303 1-176 (177)
32 smart00479 EXOIII exonuclease 99.9 2.2E-25 4.7E-30 189.2 12.7 155 137-308 2-167 (169)
33 PRK05168 ribonuclease T; Provi 99.9 1.8E-25 3.8E-30 196.0 12.4 170 131-310 13-203 (211)
34 PRK08074 bifunctional ATP-depe 99.9 2E-25 4.4E-30 233.7 13.1 157 135-310 3-171 (928)
35 TIGR01407 dinG_rel DnaQ family 99.9 2E-25 4.4E-30 232.6 11.6 156 136-310 1-167 (850)
36 PRK05601 DNA polymerase III su 99.9 6.4E-25 1.4E-29 201.7 13.2 158 131-307 42-248 (377)
37 KOG2248 3'-5' exonuclease [Rep 99.9 2.5E-24 5.4E-29 200.2 12.3 161 131-309 212-376 (380)
38 cd06133 ERI-1_3'hExo_like DEDD 99.9 5.6E-24 1.2E-28 181.9 10.7 153 137-305 1-176 (176)
39 TIGR01405 polC_Gram_pos DNA po 99.9 6.1E-24 1.3E-28 223.7 13.0 159 133-310 188-357 (1213)
40 PRK09182 DNA polymerase III su 99.9 1.2E-22 2.6E-27 185.6 12.1 157 131-307 33-200 (294)
41 COG0847 DnaQ DNA polymerase II 99.9 1.5E-22 3.3E-27 182.1 12.2 157 135-307 13-181 (243)
42 cd06138 ExoI_N N-terminal DEDD 99.9 6E-23 1.3E-27 176.4 9.1 148 138-301 1-182 (183)
43 cd06127 DEDDh DEDDh 3'-5' exon 99.9 2.2E-22 4.7E-27 168.3 11.0 147 138-302 1-159 (159)
44 PTZ00315 2'-phosphotransferase 99.9 8.9E-22 1.9E-26 190.8 14.6 174 131-310 52-257 (582)
45 PF00929 RNase_T: Exonuclease; 99.9 2.8E-24 6.1E-29 180.4 -3.2 149 138-301 1-164 (164)
46 PRK11779 sbcB exonuclease I; P 99.8 5.4E-21 1.2E-25 184.4 11.5 167 133-315 4-205 (476)
47 PRK00448 polC DNA polymerase I 99.8 5E-21 1.1E-25 204.1 12.1 159 133-310 417-586 (1437)
48 cd06135 Orn DEDDh 3'-5' exonuc 99.8 4.2E-21 9E-26 163.4 6.1 151 137-307 1-171 (173)
49 PRK05359 oligoribonuclease; Pr 99.8 1.6E-20 3.6E-25 160.4 9.0 154 134-309 2-176 (181)
50 KOG2462 C2H2-type Zn-finger pr 99.7 1.3E-18 2.7E-23 151.6 5.4 119 11-129 127-266 (279)
51 KOG1275 PAB-dependent poly(A) 99.6 8E-16 1.7E-20 151.9 8.5 165 131-310 906-1094(1118)
52 COG5018 KapD Inhibitor of the 99.5 7E-15 1.5E-19 118.8 2.6 164 135-310 4-187 (210)
53 KOG0542 Predicted exonuclease 99.5 4.8E-14 1.1E-18 121.4 6.1 170 135-312 56-246 (280)
54 KOG2462 C2H2-type Zn-finger pr 99.3 7.2E-13 1.6E-17 115.9 2.9 86 11-100 158-265 (279)
55 KOG3623 Homeobox transcription 99.1 1.1E-11 2.5E-16 120.2 1.6 112 14-129 210-332 (1007)
56 KOG1074 Transcriptional repres 99.1 2.8E-11 6E-16 119.5 4.0 46 81-126 882-927 (958)
57 KOG3576 Ovo and related transc 99.1 3.8E-11 8.2E-16 100.1 2.1 108 7-126 110-232 (267)
58 COG1949 Orn Oligoribonuclease 99.0 4.9E-10 1.1E-14 90.5 7.0 154 133-310 4-180 (184)
59 KOG3608 Zn finger proteins [Ge 99.0 5.9E-11 1.3E-15 106.6 1.2 106 17-124 182-310 (467)
60 COG2925 SbcB Exonuclease I [DN 99.0 8.5E-10 1.8E-14 100.6 8.4 170 134-319 8-212 (475)
61 KOG1074 Transcriptional repres 99.0 2.7E-10 5.9E-15 112.6 4.9 48 14-63 353-401 (958)
62 KOG3242 Oligoribonuclease (3'- 99.0 8.3E-10 1.8E-14 90.0 6.0 156 133-309 24-200 (208)
63 KOG3623 Homeobox transcription 98.8 2E-09 4.4E-14 104.9 2.8 78 10-99 890-971 (1007)
64 cd05160 DEDDy_DNA_polB_exo DED 98.7 4E-08 8.7E-13 85.5 7.8 125 138-282 2-162 (199)
65 cd06139 DNA_polA_I_Ecoli_like_ 98.7 2E-07 4.3E-12 80.5 11.0 145 134-310 4-172 (193)
66 PF01612 DNA_pol_A_exo1: 3'-5' 98.6 3.2E-07 6.8E-12 77.8 11.0 92 204-308 65-175 (176)
67 KOG3576 Ovo and related transc 98.6 2.4E-09 5.2E-14 89.5 -2.3 102 3-106 134-240 (267)
68 KOG3608 Zn finger proteins [Ge 98.6 2.7E-08 5.8E-13 89.8 2.7 139 6-145 199-361 (467)
69 PHA02768 hypothetical protein; 98.3 2.1E-07 4.5E-12 61.9 1.8 42 14-59 5-47 (55)
70 PHA02768 hypothetical protein; 98.3 3.5E-07 7.6E-12 60.8 2.2 36 80-117 7-42 (55)
71 PHA00733 hypothetical protein 98.3 6.7E-07 1.4E-11 71.8 3.7 80 11-103 37-124 (128)
72 PRK05755 DNA polymerase I; Pro 98.3 5E-06 1.1E-10 87.9 10.6 137 134-309 314-470 (880)
73 cd06125 DnaQ_like_exo DnaQ-lik 98.2 5.5E-06 1.2E-10 63.2 8.0 30 229-258 45-83 (96)
74 cd06146 mut-7_like_exo DEDDy 3 98.2 2.1E-05 4.5E-10 68.1 10.8 91 204-306 70-193 (193)
75 cd05780 DNA_polB_Kod1_like_exo 98.0 5.5E-05 1.2E-09 65.6 10.3 121 134-282 2-155 (195)
76 cd06141 WRN_exo DEDDy 3'-5' ex 98.0 0.00012 2.6E-09 61.9 11.5 79 227-305 72-169 (170)
77 PLN03086 PRLI-interacting fact 98.0 1.2E-05 2.6E-10 79.1 5.8 90 11-115 450-550 (567)
78 PHA00616 hypothetical protein 97.9 5.3E-06 1.1E-10 52.5 1.4 32 80-111 3-34 (44)
79 PHA00733 hypothetical protein 97.8 2.4E-05 5.3E-10 62.7 4.2 52 8-63 67-119 (128)
80 cd05781 DNA_polB_B3_exo DEDDy 97.7 0.00021 4.6E-09 61.5 8.9 112 134-282 2-144 (188)
81 cd06129 RNaseD_like DEDDy 3'-5 97.7 0.0003 6.4E-09 59.0 9.6 78 227-305 66-160 (161)
82 PF13482 RNase_H_2: RNase_H su 97.6 7.4E-05 1.6E-09 62.7 5.0 74 227-307 56-136 (164)
83 PF13465 zf-H2C2_2: Zinc-finge 97.6 3E-05 6.5E-10 43.8 1.4 23 93-115 1-23 (26)
84 cd05785 DNA_polB_like2_exo Unc 97.6 0.0019 4.1E-08 56.5 12.9 73 198-282 55-168 (207)
85 PRK10829 ribonuclease D; Provi 97.5 0.00078 1.7E-08 64.0 10.4 83 227-310 73-172 (373)
86 KOG0304 mRNA deadenylase subun 97.5 0.0005 1.1E-08 58.8 7.8 158 135-307 24-238 (239)
87 PHA00616 hypothetical protein 97.5 5.6E-05 1.2E-09 47.9 1.5 33 14-48 1-34 (44)
88 cd05779 DNA_polB_epsilon_exo D 97.5 0.0014 3E-08 57.1 10.6 74 198-282 70-168 (204)
89 cd00007 35EXOc 3'-5' exonuclea 97.4 0.00038 8.3E-09 57.2 6.4 93 202-307 40-154 (155)
90 cd05784 DNA_polB_II_exo DEDDy 97.4 0.0013 2.8E-08 56.9 9.8 120 134-282 2-153 (193)
91 TIGR01388 rnd ribonuclease D. 97.4 0.002 4.3E-08 61.4 11.3 82 227-310 69-168 (367)
92 cd06148 Egl_like_exo DEDDy 3'- 97.3 0.00069 1.5E-08 58.8 7.4 138 134-310 9-179 (197)
93 KOG3993 Transcription factor ( 97.3 0.00017 3.6E-09 67.2 3.2 48 14-63 295-376 (500)
94 PF13465 zf-H2C2_2: Zinc-finge 97.3 0.00014 3E-09 41.0 1.6 24 29-54 1-25 (26)
95 PHA00732 hypothetical protein 97.3 0.00017 3.6E-09 52.6 2.4 44 14-63 1-44 (79)
96 COG0349 Rnd Ribonuclease D [Tr 97.3 0.0019 4E-08 60.3 9.6 137 133-310 15-168 (361)
97 PF00096 zf-C2H2: Zinc finger, 97.1 0.00027 5.8E-09 38.5 1.5 22 80-101 2-23 (23)
98 cd05783 DNA_polB_B1_exo DEDDy 97.1 0.013 2.9E-07 51.0 13.0 75 195-282 67-170 (204)
99 KOG3993 Transcription factor ( 97.1 0.00015 3.2E-09 67.6 0.2 88 14-103 267-381 (500)
100 PF00096 zf-C2H2: Zinc finger, 97.0 0.0005 1.1E-08 37.4 1.9 22 15-36 1-22 (23)
101 PLN03086 PRLI-interacting fact 96.9 0.0007 1.5E-08 67.0 3.3 77 13-102 477-564 (567)
102 smart00474 35EXOc 3'-5' exonuc 96.9 0.0042 9.1E-08 51.9 7.8 89 205-307 64-170 (172)
103 PF10108 DNA_pol_B_exo2: Predi 96.8 0.0057 1.2E-07 53.1 7.7 94 200-307 36-172 (209)
104 PF04857 CAF1: CAF1 family rib 96.8 0.0038 8.2E-08 56.7 6.8 72 227-303 148-262 (262)
105 cd05777 DNA_polB_delta_exo DED 96.7 0.013 2.9E-07 52.1 9.6 129 131-282 3-182 (230)
106 PF13894 zf-C2H2_4: C2H2-type 96.4 0.0023 4.9E-08 34.8 1.7 23 80-102 2-24 (24)
107 cd05778 DNA_polB_zeta_exo inac 96.3 0.028 6.1E-07 50.0 9.5 105 191-307 71-222 (231)
108 cd05782 DNA_polB_like1_exo Unc 96.3 0.013 2.8E-07 51.3 6.9 69 200-282 77-169 (208)
109 PHA02528 43 DNA polymerase; Pr 96.2 0.035 7.7E-07 58.6 10.9 160 133-303 104-323 (881)
110 PF13912 zf-C2H2_6: C2H2-type 96.2 0.0036 7.8E-08 35.4 2.1 23 14-36 1-23 (27)
111 cd06142 RNaseD_exo DEDDy 3'-5' 96.2 0.026 5.6E-07 47.7 8.1 83 227-310 63-162 (178)
112 PRK05762 DNA polymerase II; Re 96.2 0.033 7.1E-07 58.6 10.2 99 195-304 197-348 (786)
113 PHA00732 hypothetical protein 96.1 0.005 1.1E-07 44.9 2.9 44 45-101 3-47 (79)
114 PTZ00166 DNA polymerase delta 96.1 0.033 7.2E-07 60.1 10.0 154 131-305 260-483 (1054)
115 COG0749 PolA DNA polymerase I 95.8 0.039 8.4E-07 55.0 8.3 95 204-310 66-182 (593)
116 cd06140 DNA_polA_I_Bacillus_li 95.8 0.028 6E-07 47.6 6.5 94 204-310 44-158 (178)
117 PF13894 zf-C2H2_4: C2H2-type 95.8 0.0068 1.5E-07 32.8 1.8 22 15-36 1-22 (24)
118 KOG1798 DNA polymerase epsilon 95.7 0.12 2.5E-06 56.0 11.7 185 129-345 240-475 (2173)
119 cd05776 DNA_polB_alpha_exo ina 95.7 0.023 5E-07 50.7 6.0 76 195-282 76-186 (234)
120 PF09237 GAGA: GAGA factor; I 95.6 0.0096 2.1E-07 38.7 2.0 27 80-106 26-52 (54)
121 smart00355 ZnF_C2H2 zinc finge 95.5 0.0099 2.2E-07 32.7 1.9 23 80-102 2-24 (26)
122 PHA02570 dexA exonuclease; Pro 95.3 0.081 1.8E-06 46.0 7.6 169 138-315 4-206 (220)
123 TIGR00593 pola DNA polymerase 95.1 0.045 9.8E-07 58.0 6.7 96 200-309 362-478 (887)
124 PF13912 zf-C2H2_6: C2H2-type 95.1 0.0074 1.6E-07 34.1 0.5 23 80-102 3-25 (27)
125 PF05605 zf-Di19: Drought indu 95.0 0.026 5.6E-07 37.9 2.9 36 14-51 2-39 (54)
126 COG5189 SFP1 Putative transcri 94.8 0.011 2.4E-07 53.4 1.0 24 12-35 347-372 (423)
127 smart00355 ZnF_C2H2 zinc finge 94.5 0.026 5.7E-07 30.9 1.8 22 15-36 1-22 (26)
128 PF12756 zf-C2H2_2: C2H2 type 94.3 0.03 6.5E-07 42.3 2.2 75 16-103 1-75 (100)
129 smart00486 POLBc DNA polymeras 94.3 0.37 7.9E-06 47.3 10.5 93 199-304 67-220 (471)
130 cd09018 DEDDy_polA_RNaseD_like 94.1 0.13 2.9E-06 41.8 6.0 55 227-282 52-109 (150)
131 PF09237 GAGA: GAGA factor; I 94.0 0.059 1.3E-06 35.1 2.7 27 10-36 20-46 (54)
132 PF03104 DNA_pol_B_exo1: DNA p 94.0 0.1 2.2E-06 48.7 5.5 90 133-244 155-255 (325)
133 cd06147 Rrp6p_like_exo DEDDy 3 93.9 0.083 1.8E-06 45.5 4.4 82 227-310 76-174 (192)
134 PHA02524 43A DNA polymerase su 93.8 0.49 1.1E-05 46.7 10.0 93 197-301 176-321 (498)
135 KOG4793 Three prime repair exo 93.3 0.13 2.9E-06 45.7 4.6 130 171-310 70-220 (318)
136 COG0417 PolB DNA polymerase el 93.1 0.93 2E-05 47.8 11.5 77 195-282 205-308 (792)
137 KOG3657 Mitochondrial DNA poly 92.8 0.26 5.7E-06 50.4 6.3 85 226-310 239-385 (1075)
138 COG3359 Predicted exonuclease 92.5 0.4 8.7E-06 42.3 6.3 75 227-304 155-238 (278)
139 PF13913 zf-C2HC_2: zinc-finge 92.3 0.096 2.1E-06 29.1 1.6 21 80-101 4-24 (25)
140 PF12874 zf-met: Zinc-finger o 92.2 0.054 1.2E-06 29.8 0.5 22 80-101 2-23 (25)
141 PF12874 zf-met: Zinc-finger o 92.2 0.13 2.8E-06 28.2 2.1 22 15-36 1-22 (25)
142 PRK04860 hypothetical protein; 92.1 0.1 2.2E-06 43.5 2.2 38 13-56 118-156 (160)
143 PF05605 zf-Di19: Drought indu 92.1 0.23 4.9E-06 33.2 3.5 18 45-63 4-21 (54)
144 PRK04860 hypothetical protein; 90.6 0.17 3.6E-06 42.2 2.1 33 79-115 120-152 (160)
145 TIGR03491 RecB family nuclease 89.8 4.5 9.8E-05 39.9 11.7 90 200-306 327-429 (457)
146 PF13909 zf-H2C2_5: C2H2-type 88.9 0.25 5.5E-06 26.8 1.3 22 80-102 2-23 (24)
147 PF12171 zf-C2H2_jaz: Zinc-fin 88.6 0.068 1.5E-06 30.2 -1.2 20 81-100 4-23 (27)
148 PF10571 UPF0547: Uncharacteri 88.0 0.3 6.6E-06 27.3 1.2 22 68-89 2-25 (26)
149 PF13909 zf-H2C2_5: C2H2-type 87.5 0.43 9.3E-06 25.9 1.6 21 15-36 1-21 (24)
150 PF12756 zf-C2H2_2: C2H2 type 86.7 0.3 6.5E-06 36.7 1.0 20 44-63 51-70 (100)
151 COG1198 PriA Primosomal protei 85.4 0.2 4.4E-06 51.7 -0.8 75 69-147 438-519 (730)
152 PF12171 zf-C2H2_jaz: Zinc-fin 85.4 0.29 6.3E-06 27.5 0.2 22 15-36 2-23 (27)
153 PF09538 FYDLN_acid: Protein o 83.6 0.54 1.2E-05 36.4 1.1 25 67-91 10-39 (108)
154 smart00451 ZnF_U1 U1-like zinc 82.6 1 2.2E-05 26.8 1.8 23 14-36 3-25 (35)
155 COG5189 SFP1 Putative transcri 82.5 0.57 1.2E-05 42.7 0.9 57 42-98 347-418 (423)
156 TIGR00592 pol2 DNA polymerase 82.4 11 0.00024 41.8 10.9 106 187-304 570-722 (1172)
157 PF09986 DUF2225: Uncharacteri 79.0 0.95 2.1E-05 39.7 1.2 12 80-91 50-61 (214)
158 cd06128 DNA_polA_exo DEDDy 3'- 77.1 4 8.7E-05 33.2 4.3 55 227-282 52-109 (151)
159 smart00451 ZnF_U1 U1-like zinc 76.4 1.4 3E-05 26.1 1.0 21 80-100 5-25 (35)
160 KOG2231 Predicted E3 ubiquitin 76.3 2.3 4.9E-05 43.3 3.1 44 16-63 117-169 (669)
161 TIGR02300 FYDLN_acid conserved 75.7 1.5 3.2E-05 34.7 1.2 27 67-93 10-41 (129)
162 COG5048 FOG: Zn-finger [Genera 74.5 1.2 2.6E-05 42.7 0.6 49 13-63 288-343 (467)
163 KOG2186 Cell growth-regulating 72.0 2.4 5.2E-05 37.5 1.8 45 15-63 4-48 (276)
164 PF09845 DUF2072: Zn-ribbon co 71.4 2 4.4E-05 34.1 1.1 21 66-86 1-27 (131)
165 COG4049 Uncharacterized protei 69.6 2.8 6.2E-05 27.8 1.3 28 9-36 12-39 (65)
166 COG1198 PriA Primosomal protei 66.8 2.2 4.8E-05 44.2 0.5 43 45-87 437-484 (730)
167 KOG0969 DNA polymerase delta, 66.3 2.8 6E-05 43.0 1.1 93 131-244 270-371 (1066)
168 PRK05761 DNA polymerase I; Rev 64.8 37 0.0008 36.0 9.1 89 199-301 208-334 (787)
169 KOG4793 Three prime repair exo 62.6 5.4 0.00012 35.8 2.1 43 266-309 250-292 (318)
170 COG5228 POP2 mRNA deadenylase 62.2 3 6.4E-05 36.2 0.4 79 226-307 156-252 (299)
171 KOG3362 Predicted BBOX Zn-fing 61.9 2.7 5.8E-05 33.8 0.1 32 68-100 120-151 (156)
172 PF13240 zinc_ribbon_2: zinc-r 61.9 4.3 9.3E-05 21.9 0.9 18 69-86 2-21 (23)
173 smart00834 CxxC_CXXC_SSSS Puta 61.8 2.9 6.4E-05 25.7 0.2 8 81-88 8-15 (41)
174 PRK14559 putative protein seri 61.4 5.6 0.00012 40.8 2.3 35 45-90 17-53 (645)
175 PRK14873 primosome assembly pr 60.9 2.8 6E-05 43.3 -0.0 42 45-86 385-430 (665)
176 PRK00398 rpoP DNA-directed RNA 60.9 3.4 7.3E-05 26.5 0.4 10 67-76 4-13 (46)
177 PF14353 CpXC: CpXC protein 59.8 4.9 0.00011 32.0 1.3 13 81-93 41-53 (128)
178 PRK04023 DNA polymerase II lar 59.2 6.1 0.00013 42.0 2.1 13 337-349 1028-1040(1121)
179 PF13719 zinc_ribbon_5: zinc-r 59.2 6.6 0.00014 23.9 1.5 32 15-53 3-35 (37)
180 PF09723 Zn-ribbon_8: Zinc rib 58.8 3.2 6.9E-05 26.1 0.0 10 105-114 25-34 (42)
181 TIGR00622 ssl1 transcription f 58.7 14 0.00029 28.8 3.4 22 12-33 13-34 (112)
182 COG4049 Uncharacterized protei 58.5 3.9 8.5E-05 27.2 0.4 22 80-101 19-40 (65)
183 PF09538 FYDLN_acid: Protein o 57.0 7.3 0.00016 30.2 1.7 28 81-119 12-39 (108)
184 smart00614 ZnF_BED BED zinc fi 56.5 8.3 0.00018 25.1 1.7 22 80-101 20-47 (50)
185 TIGR02098 MJ0042_CXXC MJ0042 f 56.2 4.7 0.0001 24.5 0.5 14 15-28 3-16 (38)
186 PRK12496 hypothetical protein; 55.9 4.1 8.9E-05 34.1 0.2 23 66-88 127-153 (164)
187 COG3364 Zn-ribbon containing p 55.6 5.3 0.00012 30.1 0.7 20 66-85 2-27 (112)
188 PF13248 zf-ribbon_3: zinc-rib 55.1 7.6 0.00016 21.5 1.1 20 68-87 4-25 (26)
189 PRK14714 DNA polymerase II lar 54.8 11 0.00024 41.2 3.2 18 288-305 1086-1103(1337)
190 TIGR00595 priA primosomal prot 54.6 6.5 0.00014 39.3 1.4 77 68-147 215-297 (505)
191 TIGR02605 CxxC_CxxC_SSSS putat 54.2 4.4 9.4E-05 26.6 0.1 28 80-114 7-34 (52)
192 PRK04023 DNA polymerase II lar 54.2 5.8 0.00013 42.1 1.0 42 66-115 626-672 (1121)
193 PF09986 DUF2225: Uncharacteri 52.8 2.3 5E-05 37.3 -1.8 20 12-31 3-22 (214)
194 cd00729 rubredoxin_SM Rubredox 52.6 6.1 0.00013 23.6 0.5 9 68-76 4-12 (34)
195 KOG2893 Zn finger protein [Gen 51.7 5.6 0.00012 34.9 0.4 41 17-62 13-53 (341)
196 PF15135 UPF0515: Uncharacteri 50.9 10 0.00023 33.5 1.9 9 81-89 158-166 (278)
197 TIGR00595 priA primosomal prot 50.9 5.5 0.00012 39.8 0.3 43 45-87 215-262 (505)
198 COG1997 RPL43A Ribosomal prote 50.4 9.6 0.00021 28.0 1.3 28 64-91 33-66 (89)
199 cd00350 rubredoxin_like Rubred 49.5 7.5 0.00016 22.9 0.6 7 106-112 17-23 (33)
200 PRK14559 putative protein seri 49.4 15 0.00032 37.9 3.0 21 67-87 16-36 (645)
201 PHA00626 hypothetical protein 48.3 7 0.00015 26.1 0.3 10 80-89 25-34 (59)
202 PF13717 zinc_ribbon_4: zinc-r 48.3 8.8 0.00019 23.2 0.8 14 15-28 3-16 (36)
203 PRK00464 nrdR transcriptional 46.8 6.7 0.00015 32.4 0.1 15 198-212 102-116 (154)
204 KOG2893 Zn finger protein [Gen 46.7 7.7 0.00017 34.1 0.4 41 45-97 12-53 (341)
205 PF04438 zf-HIT: HIT zinc fing 44.2 12 0.00025 21.7 0.8 22 68-90 4-25 (30)
206 KOG1146 Homeobox protein [Gene 42.1 13 0.00029 40.7 1.4 28 9-36 460-487 (1406)
207 PF06524 NOA36: NOA36 protein; 42.1 15 0.00033 32.8 1.5 51 66-118 171-221 (314)
208 COG1592 Rubrerythrin [Energy p 42.1 11 0.00023 31.6 0.6 20 66-85 134-156 (166)
209 smart00531 TFIIE Transcription 41.6 27 0.00059 28.5 3.0 14 45-58 101-114 (147)
210 PF14446 Prok-RING_1: Prokaryo 41.4 13 0.00028 24.8 0.8 19 68-86 7-29 (54)
211 PF00843 Arena_nucleocap: Aren 40.4 23 0.0005 34.2 2.5 141 134-297 371-527 (533)
212 KOG0970 DNA polymerase alpha, 40.3 43 0.00094 36.4 4.7 134 130-281 524-710 (1429)
213 COG4530 Uncharacterized protei 40.1 13 0.00028 28.5 0.7 20 69-88 12-36 (129)
214 PRK14873 primosome assembly pr 40.1 19 0.00042 37.3 2.2 26 39-75 405-431 (665)
215 COG1996 RPC10 DNA-directed RNA 40.1 8.7 0.00019 25.1 -0.2 9 68-76 8-16 (49)
216 PRK05580 primosome assembly pr 39.5 10 0.00023 39.4 0.2 14 133-146 451-464 (679)
217 PF05191 ADK_lid: Adenylate ki 39.3 12 0.00027 22.6 0.4 10 81-90 24-33 (36)
218 COG0068 HypF Hydrogenase matur 38.4 11 0.00024 38.6 0.2 29 81-115 154-182 (750)
219 COG5151 SSL1 RNA polymerase II 36.5 13 0.00028 34.1 0.2 23 80-102 390-412 (421)
220 smart00734 ZnF_Rad18 Rad18-lik 36.1 29 0.00062 19.3 1.6 19 16-35 3-21 (26)
221 PF13878 zf-C2H2_3: zinc-finge 35.4 33 0.00071 21.4 1.9 28 75-102 10-39 (41)
222 TIGR01206 lysW lysine biosynth 34.5 23 0.0005 23.7 1.1 7 81-87 5-11 (54)
223 PF02892 zf-BED: BED zinc fing 34.3 43 0.00093 20.9 2.4 25 11-35 13-41 (45)
224 KOG1146 Homeobox protein [Gene 33.7 12 0.00026 41.0 -0.4 82 15-102 1261-1352(1406)
225 PRK14714 DNA polymerase II lar 33.5 23 0.0005 38.9 1.6 10 106-115 709-718 (1337)
226 PF01780 Ribosomal_L37ae: Ribo 33.3 15 0.00032 27.4 0.1 26 65-90 34-65 (90)
227 TIGR00280 L37a ribosomal prote 32.7 25 0.00053 26.2 1.2 27 65-91 34-66 (91)
228 PF05443 ROS_MUCR: ROS/MUCR tr 32.5 21 0.00047 28.6 0.9 23 81-106 75-97 (132)
229 PTZ00255 60S ribosomal protein 32.3 26 0.00056 26.1 1.2 26 65-90 35-66 (90)
230 COG2888 Predicted Zn-ribbon RN 32.1 40 0.00087 22.9 2.0 10 104-113 48-57 (61)
231 PF01363 FYVE: FYVE zinc finge 31.9 22 0.00047 24.7 0.8 10 45-54 11-20 (69)
232 PRK05580 primosome assembly pr 31.8 13 0.00028 38.6 -0.5 16 69-87 384-399 (679)
233 PRK03824 hypA hydrogenase nick 31.8 18 0.00039 29.2 0.4 11 105-115 106-116 (135)
234 PRK03564 formate dehydrogenase 31.3 8.5 0.00019 35.7 -1.8 37 104-148 250-286 (309)
235 COG4957 Predicted transcriptio 31.0 26 0.00057 28.0 1.1 26 81-109 79-104 (148)
236 COG1439 Predicted nucleic acid 30.6 15 0.00032 31.1 -0.4 23 65-87 138-162 (177)
237 KOG2231 Predicted E3 ubiquitin 30.5 49 0.0011 34.0 3.2 28 45-72 184-212 (669)
238 PF01155 HypA: Hydrogenase exp 30.4 20 0.00043 27.9 0.4 9 69-77 73-81 (113)
239 PF12773 DZR: Double zinc ribb 30.3 42 0.00092 21.5 1.9 6 81-86 15-20 (50)
240 COG1545 Predicted nucleic-acid 30.0 25 0.00054 28.6 0.9 18 69-86 32-51 (140)
241 COG4640 Predicted membrane pro 29.9 30 0.00065 32.9 1.5 29 68-96 3-33 (465)
242 PRK13130 H/ACA RNA-protein com 29.7 33 0.00072 23.1 1.3 20 68-87 7-26 (56)
243 COG5236 Uncharacterized conser 29.6 45 0.00097 31.1 2.5 92 14-113 151-254 (493)
244 PRK03976 rpl37ae 50S ribosomal 29.3 30 0.00066 25.7 1.2 26 65-90 35-66 (90)
245 COG1773 Rubredoxin [Energy pro 28.2 25 0.00055 23.5 0.5 9 45-53 5-13 (55)
246 COG0068 HypF Hydrogenase matur 27.9 12 0.00027 38.3 -1.4 35 45-79 125-164 (750)
247 PRK12380 hydrogenase nickel in 27.4 27 0.00059 27.2 0.7 9 81-89 73-81 (113)
248 TIGR00100 hypA hydrogenase nic 26.8 29 0.00063 27.1 0.8 10 81-90 73-82 (115)
249 TIGR00373 conserved hypothetic 26.1 71 0.0015 26.5 3.0 11 45-55 111-121 (158)
250 cd00065 FYVE FYVE domain; Zinc 26.0 33 0.00071 22.6 0.8 25 45-76 4-28 (57)
251 PF03337 Pox_F12L: Poxvirus F1 25.9 5E+02 0.011 26.8 9.3 98 170-284 226-344 (651)
252 PF07295 DUF1451: Protein of u 25.8 23 0.00051 29.0 0.1 7 81-87 133-139 (146)
253 PF03833 PolC_DP2: DNA polymer 25.5 23 0.0005 37.1 0.0 19 67-85 656-674 (900)
254 KOG0978 E3 ubiquitin ligase in 25.5 26 0.00057 36.1 0.4 12 81-92 681-692 (698)
255 PHA02563 DNA polymerase; Provi 24.9 54 0.0012 33.7 2.4 18 227-244 65-82 (630)
256 KOG2207 Predicted 3'-5' exonuc 24.5 61 0.0013 32.7 2.6 96 203-309 458-586 (617)
257 PRK00564 hypA hydrogenase nick 24.0 32 0.00069 27.0 0.5 10 81-90 74-83 (117)
258 cd00730 rubredoxin Rubredoxin; 23.7 46 0.00099 21.8 1.1 8 46-53 4-11 (50)
259 PRK14975 bifunctional 3'-5' ex 23.5 1.1E+02 0.0024 31.0 4.4 59 252-310 72-146 (553)
260 COG2331 Uncharacterized protei 23.3 19 0.00041 25.7 -0.8 6 81-86 15-20 (82)
261 PF06524 NOA36: NOA36 protein; 23.1 32 0.0007 30.8 0.4 90 10-104 138-235 (314)
262 COG3357 Predicted transcriptio 22.9 39 0.00085 25.1 0.7 10 81-90 61-70 (97)
263 PF09416 UPF1_Zn_bind: RNA hel 22.8 83 0.0018 25.9 2.7 26 68-99 16-41 (152)
264 KOG4167 Predicted DNA-binding 22.6 25 0.00053 36.2 -0.4 21 81-101 795-815 (907)
265 KOG4173 Alpha-SNAP protein [In 22.3 52 0.0011 28.4 1.5 88 12-103 77-172 (253)
266 COG1779 C4-type Zn-finger prot 22.1 42 0.0009 28.9 0.9 11 81-91 46-56 (201)
267 KOG0782 Predicted diacylglycer 21.4 49 0.0011 33.1 1.3 70 16-88 201-286 (1004)
268 TIGR00244 transcriptional regu 21.4 37 0.00081 27.7 0.4 12 67-78 29-40 (147)
269 PRK00420 hypothetical protein; 21.0 53 0.0011 25.6 1.2 9 81-89 43-51 (112)
270 KOG2807 RNA polymerase II tran 20.9 68 0.0015 29.8 2.0 57 14-85 290-360 (378)
271 PF01286 XPA_N: XPA protein N- 20.9 44 0.00095 20.0 0.6 10 69-78 6-15 (34)
272 PF04959 ARS2: Arsenite-resist 20.8 77 0.0017 27.8 2.3 30 11-41 74-103 (214)
273 KOG0696 Serine/threonine prote 20.6 34 0.00073 33.2 0.1 55 11-75 70-130 (683)
274 PRK03681 hypA hydrogenase nick 20.5 44 0.00096 26.0 0.7 8 81-88 73-80 (114)
275 smart00064 FYVE Protein presen 20.5 49 0.0011 22.7 0.9 25 45-76 12-36 (68)
276 PF11288 DUF3089: Protein of u 20.2 1.3E+02 0.0028 26.2 3.5 29 199-235 75-103 (207)
No 1
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=1.4e-39 Score=280.04 Aligned_cols=268 Identities=41% Similarity=0.694 Sum_probs=209.0
Q ss_pred eccccccccChHHHHHHHhhhcCCCCCCccccCcccCCChHHHHhccCCCCCCCCCCccccccccccccccccCchhHHH
Q 018586 17 CVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLIK 96 (353)
Q Consensus 17 C~~C~k~f~~~~~l~~H~~~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~~~~c~~Cgk~f~~~~C~~C~k~F~~~s~L~~ 96 (353)
|..|.+.|.-+..+..|+ +..|....+.|..|.+.-.....+..++..+.+- .|-+.|+...|..|.-.-........
T Consensus 3 ~~~~~~~~~~~~~~~~~~-v~~~~~~~~~~~~~k~~~~~~~~~~e~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (280)
T KOG2249|consen 3 ASSCAQQFNKKEHLPNHK-VSRHKLHERKCGKCKKVARSFESNEEGLIAPLPK-EGKNIFSQRGNRFKATIKASPGKRRI 80 (280)
T ss_pred ccHHHHHhCccccCcccc-chhhccCcchhhhHHHhccCcccccccccCCCCc-ccCccccchhhHHHhhHhhcCCcchh
Confidence 556666676666555555 2113332337777776666666666666444443 66777777777666543333333344
Q ss_pred HHHHhcCCCCCCcccCCcchhhhhhhccccccccccCCCceeeccCccccccCCCCccceeEEeeecCCCCeEEeeeccC
Q 018586 97 HKEACSLSAPVPFEKTLSNAESQKKISGAIDEKRTCRGPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQP 176 (353)
Q Consensus 97 H~~~h~~~k~~~c~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~D~Ettg~~~~~~~~il~~v~ivd~~g~~~~~~lv~P 176 (353)
|+..+... |+.-. ......+..+..++|++||||+|.++++..+++|+|+|||..|.++||.||+|
T Consensus 81 ~~~~~~~~----~~~~~----------~~~k~s~~~~~~r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP 146 (280)
T KOG2249|consen 81 HQGSCQAS----CRMAA----------LGSKDSRMGSLTRVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKP 146 (280)
T ss_pred hhcccCCC----ccccc----------cchhhccccccceEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecCC
Confidence 44333222 21110 11112223344479999999999999999999999999999999999999999
Q ss_pred CCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCcCCCCceeecc
Q 018586 177 QLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTA 256 (353)
Q Consensus 177 ~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~~~~~Dt~ 256 (353)
..+|.+++|+++||++|.+.+|.||+.|..+++++| .|+|||||.+.+||.+|.+.+|...++||+
T Consensus 147 ~~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~klL--------------~gRIlVGHaLhnDl~~L~l~hp~s~iRDTs 212 (280)
T KOG2249|consen 147 TEPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLKLL--------------KGRILVGHALHNDLQALKLEHPRSMIRDTS 212 (280)
T ss_pred CcccccceeeecccCHHHhccCccHHHHHHHHHHHH--------------hCCEEeccccccHHHHHhhhCchhhhcccc
Confidence 999999999999999999999999999999999999 999999999999999999999999999999
Q ss_pred cccCCcc--cCCCCCcHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHhchhhhhhh
Q 018586 257 KYRPLMK--TNLVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQVEEI 314 (353)
Q Consensus 257 ~l~~~~~--~~~~~~~L~~l~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~~~~~~~~ 314 (353)
.+.++.. .....+||+.|++.+||++|+.|.|++.+||+|||+||.++..+|++....
T Consensus 213 ~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~GeHsSvEDA~AtM~LY~~vk~qwe~~~~r 272 (280)
T KOG2249|consen 213 KYPPLMKLLSKKATPSLKKLTEALLGKDIQVGEHSSVEDARATMELYKRVKVQWEKIEAR 272 (280)
T ss_pred cCchHHHHhhccCCccHHHHHHHHhchhhhccccCcHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 9887776 677789999999999999999999999999999999999999999985554
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=4.9e-33 Score=232.72 Aligned_cols=150 Identities=39% Similarity=0.655 Sum_probs=133.0
Q ss_pred eeccCccccccCCC-CccceeEEeeecCCCCeEEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHhcCC
Q 018586 138 VAMDCEMVGGGSNG-TLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNNGE 216 (353)
Q Consensus 138 ~~~D~Ettg~~~~~-~~~il~~v~ivd~~g~~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~~~~~~ 216 (353)
+++||||||+++.+ ..++ +++++++.+|.++|+++|+|..+|+++++.+||||+++|+++|++++|+++|.+|+
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 VAIDCEMVGTGPGGRESEL-ARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKIL---- 75 (157)
T ss_pred CEEEeEeccccCCCCeEEE-EEEEEEeCCCCEEEEEeECCCCccCccceECCCCCHHHHhcCCCHHHHHHHHHHHc----
Confidence 58999999998654 3455 79999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccccCCCCCcEEEecccHHHHHHhcCcCCCCceeecccc--cCCc--ccCCCCCcHHHHHHHHhCCcCCCC--CCCh
Q 018586 217 STGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKY--RPLM--KTNLVSHSLKYLTRTYLGYDIQSG--VHDP 290 (353)
Q Consensus 217 ~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~~~~~Dt~~l--~~~~--~~~~~~~~L~~l~~~~~~~~~~~~--~H~A 290 (353)
++++|||||+.||++||++.++...++||..+ .+.. +|...+++|+.|+++|+|..++.+ +|+|
T Consensus 76 ----------~~~vlV~Hn~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~H~A 145 (157)
T cd06149 76 ----------KGKVVVGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSS 145 (157)
T ss_pred ----------CCCEEEEeCcHHHHHHhcccCCCcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCCCcCc
Confidence 88999999999999999998877778999875 3222 666678999999999987766653 7999
Q ss_pred HHHHHHHHHHHH
Q 018586 291 YEDCVSVMRLYK 302 (353)
Q Consensus 291 l~Da~~t~~l~~ 302 (353)
++||++|++||+
T Consensus 146 l~DA~at~~l~~ 157 (157)
T cd06149 146 VEDARATMELYK 157 (157)
T ss_pred HHHHHHHHHHhC
Confidence 999999999985
No 3
>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=9.2e-33 Score=230.29 Aligned_cols=150 Identities=51% Similarity=0.859 Sum_probs=134.7
Q ss_pred eeccCccccccCCC-CccceeEEeeecCCCCeEEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHhcCC
Q 018586 138 VAMDCEMVGGGSNG-TLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNNGE 216 (353)
Q Consensus 138 ~~~D~Ettg~~~~~-~~~il~~v~ivd~~g~~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~~~~~~ 216 (353)
+++||||||+++.+ .+++ +++.+++.+|.++|++||+|..+++++++.+||||++||+++|++++++++|.+|+
T Consensus 1 v~lD~EttGl~~~~~~~~i-~~v~~v~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~~~v~~a~~~~~~~~~l~~~l---- 75 (152)
T cd06144 1 VALDCEMVGVGPDGSESAL-ARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELL---- 75 (152)
T ss_pred CEEEEEeecccCCCCEEEE-EEEEEEeCCCCEEEEEEECCCCCCCcccccCCCCCHHHHcCCCCHHHHHHHHHHHh----
Confidence 58999999997653 4555 79999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccccCCCCCcEEEecccHHHHHHhcCcCCCCceeecccccCCcccC-CCCCcHHHHHHHHhCCcCCCCCCChHHHHH
Q 018586 217 STGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLMKTN-LVSHSLKYLTRTYLGYDIQSGVHDPYEDCV 295 (353)
Q Consensus 217 ~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~-~~~~~L~~l~~~~~~~~~~~~~H~Al~Da~ 295 (353)
++.+|||||+.||++||+...|...++||..+.....+. ..+++|+.|++.++|+++..++|+|++||+
T Consensus 76 ----------~~~vlVgHn~~fD~~~L~~~~~~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~ 145 (152)
T cd06144 76 ----------KGRILVGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVEDAR 145 (152)
T ss_pred ----------CCCEEEEcCcHHHHHHhcCcCCCccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCCCcCcHHHHH
Confidence 789999999999999999988888899999887655443 478999999999889997767999999999
Q ss_pred HHHHHHH
Q 018586 296 SVMRLYK 302 (353)
Q Consensus 296 ~t~~l~~ 302 (353)
+|++||+
T Consensus 146 at~~l~~ 152 (152)
T cd06144 146 AAMRLYR 152 (152)
T ss_pred HHHHHhC
Confidence 9999984
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=1.4e-32 Score=228.37 Aligned_cols=146 Identities=38% Similarity=0.624 Sum_probs=131.6
Q ss_pred eeccCccccccCCCCccceeEEeeecCCCCeEEeeeccCCCCccccccccCCCCHhhhcCCC-ChHHHHHHHHHHHhcCC
Q 018586 138 VAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAM-PLKEVKDKILEILNNGE 216 (353)
Q Consensus 138 ~~~D~Ettg~~~~~~~~il~~v~ivd~~g~~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~-~~~~v~~~~~~~~~~~~ 216 (353)
+++||||+|.+.. .++ +++++++.+|.++|++||+|..+|+++++++||||++||+++| ++++|+++|.+|+
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--LEL-TRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLI---- 73 (150)
T ss_pred CEEeeeeeeecCC--CEE-EEEEEEeCCCCEEEEEeECCCCccchhccCcCCCCHHHhccCCCCHHHHHHHHHHHh----
Confidence 5799999998543 555 7999999999999999999999999999999999999999995 9999999999999
Q ss_pred CCcccccCCCC-CcEEEecccHHHHHHhcCcCCCCceeecccccCCcccCCCCCcHHHHHHHHhCCcCCC--CCCChHHH
Q 018586 217 STGRLMLDDGK-ARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQS--GVHDPYED 293 (353)
Q Consensus 217 ~~~~~~~~~~~-~~~lvgh~~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~--~~H~Al~D 293 (353)
+ +.+|||||+.||+.||+...+. ++||+.|++...+...+++|+.||+.|++..++. ++|+|++|
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 7899999999999999976654 8999999998877777899999999998877763 68999999
Q ss_pred HHHHHHHHH
Q 018586 294 CVSVMRLYK 302 (353)
Q Consensus 294 a~~t~~l~~ 302 (353)
|++|++||.
T Consensus 142 A~~t~~l~~ 150 (150)
T cd06145 142 ARAALELVK 150 (150)
T ss_pred HHHHHHHhC
Confidence 999999984
No 5
>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=99.97 E-value=3.4e-31 Score=219.97 Aligned_cols=150 Identities=29% Similarity=0.445 Sum_probs=133.1
Q ss_pred eeccCccccccC-------CCCc-------cceeEEeeec----CCCCeEEeeeccCCCCccccccccCCCCHhhhcCCC
Q 018586 138 VAMDCEMVGGGS-------NGTL-------DLCARVCLVD----EDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAM 199 (353)
Q Consensus 138 ~~~D~Ettg~~~-------~~~~-------~il~~v~ivd----~~g~~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~ 199 (353)
+++|||+.|.++ ++.. ..+++|++|| .+|++++|.||+|..+|.++.|+++|||++++.++.
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 467888888764 3444 2359999999 699999999999999999999999999999998764
Q ss_pred ------ChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCcCCCCceeecccccCCcccCCCCCcHHH
Q 018586 200 ------PLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLMKTNLVSHSLKY 273 (353)
Q Consensus 200 ------~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~ 273 (353)
++++|..++.+++ +.++|||||++++||++|++.+|...++||+.+++. +..+.++|+.
T Consensus 81 ~~~~~~t~~~v~~~l~~li-------------~~~tILVGHsL~nDL~aL~l~hp~~~viDTa~l~~~--~~~r~~sLk~ 145 (174)
T cd06143 81 SSKNLTTLKSAYLKLRLLV-------------DLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFHL--PGQRKLSLRF 145 (174)
T ss_pred cccccCCHHHHHHHHHHHc-------------CCCCEEEeccchhHHHHhcCcCCCcceEEcHHhccC--CCCCChhHHH
Confidence 6999999999999 368999999999999999999998889999998875 3445799999
Q ss_pred HHHHHhCCcCCCCCCChHHHHHHHHHHHH
Q 018586 274 LTRTYLGYDIQSGVHDPYEDCVSVMRLYK 302 (353)
Q Consensus 274 l~~~~~~~~~~~~~H~Al~Da~~t~~l~~ 302 (353)
|++.+||..||.+.|++++||+|||+||+
T Consensus 146 La~~~L~~~IQ~~~HdSvEDArAam~Ly~ 174 (174)
T cd06143 146 LAWYLLGEKIQSETHDSIEDARTALKLYR 174 (174)
T ss_pred HHHHHcCCcccCCCcCcHHHHHHHHHHhC
Confidence 99999999999999999999999999984
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=99.97 E-value=4.4e-31 Score=222.17 Aligned_cols=147 Identities=32% Similarity=0.519 Sum_probs=126.4
Q ss_pred eeccCccccccCCCCccceeEEeeecC-CCCeEEeeeccCCCCccccccccCCCCHhhhcCCCC-------hHHHHHHHH
Q 018586 138 VAMDCEMVGGGSNGTLDLCARVCLVDE-DENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMP-------LKEVKDKIL 209 (353)
Q Consensus 138 ~~~D~Ettg~~~~~~~~il~~v~ivd~-~g~~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~-------~~~v~~~~~ 209 (353)
+++||||||+++.. .++ .++.+|+. +|+++|+.||+|..+|+++++++||||++||+++|+ |++++++|.
T Consensus 1 v~lD~EttGl~~~~-d~i-i~Ig~V~v~~g~i~~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~~~~~~~~ 78 (161)
T cd06137 1 VALDCEMVGLADGD-SEV-VRISAVDVLTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAKAGKTIFGWEAARAALW 78 (161)
T ss_pred CEEEeeeeeEcCCC-CEE-EEEEEEEcCCCeEEEeccccCCCCCCccceeccCCCHHHHhhhhhcCCccccHHHHHHHHH
Confidence 58999999997532 233 35555555 888899999999999999999999999999999875 358999999
Q ss_pred HHHhcCCCCcccccCCCCC-cEEEecccHHHHHHhcCcCCCCceeecccccCCcccCC---CCCcHHHHHHHHhCCcCCC
Q 018586 210 EILNNGESTGRLMLDDGKA-RLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLMKTNL---VSHSLKYLTRTYLGYDIQS 285 (353)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~-~~lvgh~~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~---~~~~L~~l~~~~~~~~~~~ 285 (353)
+|+ ++ .+|||||+.||++||+...+ +++||+.+++.+.+.. .+++|+.|++.++|++++.
T Consensus 79 ~~i--------------~~~~vlVgHn~~fD~~fL~~~~~--~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~ 142 (161)
T cd06137 79 KFI--------------DPDTILVGHSLQNDLDALRMIHT--RVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQG 142 (161)
T ss_pred Hhc--------------CCCcEEEeccHHHHHHHHhCcCC--CeeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcC
Confidence 999 66 89999999999999997654 4899999999988765 6899999999988999864
Q ss_pred --CCCChHHHHHHHHHHHH
Q 018586 286 --GVHDPYEDCVSVMRLYK 302 (353)
Q Consensus 286 --~~H~Al~Da~~t~~l~~ 302 (353)
++|+|++||++|++||.
T Consensus 143 ~~~~H~A~~DA~at~~l~~ 161 (161)
T cd06137 143 GGEGHDSLEDALAAREVVL 161 (161)
T ss_pred CCCCCCcHHHHHHHHHHhC
Confidence 48999999999999984
No 7
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.96 E-value=2.7e-29 Score=223.24 Aligned_cols=187 Identities=20% Similarity=0.214 Sum_probs=150.7
Q ss_pred cCCCceeeccCccccccC--CCCccceeEEeeecCCCCe--EEeeeccCCCCccccccccCCCCHhhhcC-CCChHHHHH
Q 018586 132 CRGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKN-AMPLKEVKD 206 (353)
Q Consensus 132 ~~~~~~~~~D~Ettg~~~--~~~~~il~~v~ivd~~g~~--~~~~lv~P~~~i~~~~~~~~GIt~e~l~~-~~~~~~v~~ 206 (353)
+...+++++|+||||+++ ++++++ +.|.+ +.+|.+ .++.+|+|..+|++.++.|||||++++.+ ++++++|+.
T Consensus 3 ~~~~~~vv~D~ETTGl~p~~d~Iiei-g~v~v-~~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~ 80 (232)
T PRK07942 3 WHPGPLAAFDLETTGVDPETARIVTA-ALVVV-DADGEVVESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLA 80 (232)
T ss_pred cccCcEEEEEeccCCCCCCCCeeEEE-EEEEE-eCCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHH
Confidence 456789999999999874 456666 55555 444665 47899999999999999999999999975 788999999
Q ss_pred HHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCc-----C---CCCceeecccccCCcccC-CCCCcHHHHHHH
Q 018586 207 KILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-----Y---PDHMLRDTAKYRPLMKTN-LVSHSLKYLTRT 277 (353)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-----~---~~~~~~Dt~~l~~~~~~~-~~~~~L~~l~~~ 277 (353)
+|.++|.+... ++.+|||||+.||+.||+.. . ....++|+..+.+.+.+. ..+++|.+|+++
T Consensus 81 e~~~~l~~~~~---------~~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~ 151 (232)
T PRK07942 81 EIADALREAWA---------RGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALCEH 151 (232)
T ss_pred HHHHHHHHHhh---------cCCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHHHH
Confidence 99998832211 46799999999999999822 1 124689999888766543 357899999999
Q ss_pred HhCCcCCCCCCChHHHHHHHHHHHHHHHhchhhhhhhcccCCCCCCCCcchhHHhhcChhhhhccCCCCceeee
Q 018586 278 YLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQVEEIGNQNTTGSFDSYKYKELEKMSPNELYQISKSDYRCWC 351 (353)
Q Consensus 278 ~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 351 (353)
| |++. .++|+|++||.+|++||.++.++... +..+++++|+++++.|+.-|.
T Consensus 152 ~-gi~~-~~aH~Al~Da~ata~l~~~l~~~~~~--------------------l~~~~~~~l~~~q~~~~~~~~ 203 (232)
T PRK07942 152 Y-GVRL-DNAHEATADALAAARVAWALARRFPE--------------------LAALSPAELHELQAVWYAEQA 203 (232)
T ss_pred c-CCCC-CCCCChHHHHHHHHHHHHHHHHHHHH--------------------hhcCCHHHHHHHHHHHHHHHH
Confidence 8 9985 45999999999999999999988655 678899999999998887664
No 8
>PRK07740 hypothetical protein; Provisional
Probab=99.96 E-value=1.6e-28 Score=219.59 Aligned_cols=163 Identities=27% Similarity=0.333 Sum_probs=139.3
Q ss_pred ccccCCCceeeccCccccccC---CCCccceeEEeeecCCCCe---EEeeeccCCCCccccccccCCCCHhhhcCCCChH
Q 018586 129 KRTCRGPKAVAMDCEMVGGGS---NGTLDLCARVCLVDEDENV---IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLK 202 (353)
Q Consensus 129 ~~~~~~~~~~~~D~Ettg~~~---~~~~~il~~v~ivd~~g~~---~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~ 202 (353)
..+....+++++|+||||.++ ++++++ ++|.+. .+.+ .|+.+|+|..++++.++++||||+++|+++|++.
T Consensus 53 ~~~~~~~~~vv~D~ETTGl~p~~~deIIeI-gaV~~~--~~~i~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ 129 (244)
T PRK07740 53 DIPLTDLPFVVFDLETTGFSPQQGDEILSI-GAVKTK--GGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLA 129 (244)
T ss_pred CCCccCCCEEEEEEeCCCCCCCCCCeEEEE-EEEEEE--CCEEEEEEEEEEeCcCCCCChhheeccCCCHHHHhCCCCHH
Confidence 345677889999999999875 456666 677663 3333 3889999999999999999999999999999999
Q ss_pred HHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcC------cCC-CCceeecccccCCcccCCCCCcHHHHH
Q 018586 203 EVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM------NYP-DHMLRDTAKYRPLMKTNLVSHSLKYLT 275 (353)
Q Consensus 203 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~------~~~-~~~~~Dt~~l~~~~~~~~~~~~L~~l~ 275 (353)
+|+.+|.+|+ ++.+|||||+.||+.||+. ..| ...++||..+++.+.+....++|++|+
T Consensus 130 evl~~f~~fi--------------~~~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~ 195 (244)
T PRK07740 130 EVLHRFYAFI--------------GAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDAL 195 (244)
T ss_pred HHHHHHHHHh--------------CCCEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHHH
Confidence 9999999999 8889999999999999972 222 256899999998888877789999999
Q ss_pred HHHhCCcCCCCCCChHHHHHHHHHHHHHHHhchhh
Q 018586 276 RTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 276 ~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
.+| |+++. ++|+|++||++|++||.++..+..+
T Consensus 196 ~~~-gi~~~-~~H~Al~Da~ata~l~~~ll~~~~~ 228 (244)
T PRK07740 196 AYY-GIPIP-RRHHALGDALMTAKLWAILLVEAQQ 228 (244)
T ss_pred HHC-CcCCC-CCCCcHHHHHHHHHHHHHHHHHHHH
Confidence 987 99954 5899999999999999999988655
No 9
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.95 E-value=2.6e-28 Score=216.64 Aligned_cols=158 Identities=22% Similarity=0.330 Sum_probs=134.0
Q ss_pred CCceeeccCccccccC---CCCccceeEEeeecCCCC-eEEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHH
Q 018586 134 GPKAVAMDCEMVGGGS---NGTLDLCARVCLVDEDEN-VIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKIL 209 (353)
Q Consensus 134 ~~~~~~~D~Ettg~~~---~~~~~il~~v~ivd~~g~-~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~ 209 (353)
.++++++|+||||+++ ++++|| +.|.+.+.... ..|+.||+|..+|++.+++|||||+++|+++|+|++|+++|.
T Consensus 3 ~~r~vvlDtETTGldp~~~drIIEI-GaV~v~~~~~~~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~p~f~ev~~~f~ 81 (240)
T PRK05711 3 IMRQIVLDTETTGLNQREGHRIIEI-GAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFL 81 (240)
T ss_pred CCeEEEEEeeCCCcCCCCCCeEEEE-EEEEEECCEEeccEEEEEECcCCcCCHHHhhhcCCCHHHHcCCCCHHHHHHHHH
Confidence 4689999999999974 467777 78887543221 258999999999999999999999999999999999999999
Q ss_pred HHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcC-------cCC----CCceeecccccCCcccCCCCCcHHHHHHHH
Q 018586 210 EILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM-------NYP----DHMLRDTAKYRPLMKTNLVSHSLKYLTRTY 278 (353)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~-------~~~----~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~ 278 (353)
+|+ ++.+|||||+.||+.||+. ..| ...++||+.+++.++|. .+++|+.||++|
T Consensus 82 ~fi--------------~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~-~~~~L~aL~~~~ 146 (240)
T PRK05711 82 DFI--------------RGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPG-KRNSLDALCKRY 146 (240)
T ss_pred HHh--------------CCCEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCC-CCCCHHHHHHHC
Confidence 999 8889999999999999982 233 14589999999988876 457999999999
Q ss_pred hCCcCCCC-CCChHHHHHHHHHHHHHHHhch
Q 018586 279 LGYDIQSG-VHDPYEDCVSVMRLYKRFRRQD 308 (353)
Q Consensus 279 ~~~~~~~~-~H~Al~Da~~t~~l~~~~~~~~ 308 (353)
|++.... .|+|+.||.+|++||..+....
T Consensus 147 -gi~~~~r~~H~AL~DA~~~A~v~~~l~~~~ 176 (240)
T PRK05711 147 -GIDNSHRTLHGALLDAEILAEVYLAMTGGQ 176 (240)
T ss_pred -CCCCCCCCCCCHHHHHHHHHHHHHHHHCcc
Confidence 8874432 6999999999999999998663
No 10
>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=99.95 E-value=4.3e-28 Score=214.20 Aligned_cols=161 Identities=21% Similarity=0.280 Sum_probs=136.0
Q ss_pred ceeeccCccccccC---CCCccceeEEeeecCCCC-eEEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHH
Q 018586 136 KAVAMDCEMVGGGS---NGTLDLCARVCLVDEDEN-VIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 211 (353)
Q Consensus 136 ~~~~~D~Ettg~~~---~~~~~il~~v~ivd~~g~-~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~ 211 (353)
+++++|+||||+++ ++++|+ +.|.+++.... ..|+.||+|..+|++.+++|||||+++|+++|+|.+|+.+|.+|
T Consensus 1 r~vvlD~ETTGl~p~~~d~IIEI-gav~~~~~~~~~~~f~~~i~P~~~i~~~a~~vhGIt~e~l~~~p~f~ev~~~f~~f 79 (225)
T TIGR01406 1 RQIILDTETTGLDPKGGHRIVEI-GAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDF 79 (225)
T ss_pred CEEEEEeeCCCcCCCCCCeEEEE-EEEEEECCcEecceEEEEECcCCCCCHHHHhccCCCHHHHhCCCCHHHHHHHHHHH
Confidence 47899999999875 457777 78877643211 25999999999999999999999999999999999999999999
Q ss_pred HhcCCCCcccccCCCCCcEEEecccHHHHHHhc-----Cc--CC----CCceeecccccCCcccCCCCCcHHHHHHHHhC
Q 018586 212 LNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR-----MN--YP----DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLG 280 (353)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~-----~~--~~----~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~ 280 (353)
+ ++.+|||||+.||+.||+ .. .+ ...++||+.+++.++|. .+++|+.||++| |
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 889999999999999998 22 12 15789999999888876 468999999999 8
Q ss_pred CcCCCC-CCChHHHHHHHHHHHHHHHhchhhhhh
Q 018586 281 YDIQSG-VHDPYEDCVSVMRLYKRFRRQDHQVEE 313 (353)
Q Consensus 281 ~~~~~~-~H~Al~Da~~t~~l~~~~~~~~~~~~~ 313 (353)
++.... .|+|+.||.+|++||..+......+..
T Consensus 144 i~~~~r~~H~Al~DA~~~a~v~~~l~~~~~~~~~ 177 (225)
T TIGR01406 144 VDNSHRTLHGALLDAHLLAEVYLALTGGQESLLE 177 (225)
T ss_pred CCCCCCCCcCHHHHHHHHHHHHHHHHcCCcchhh
Confidence 885433 799999999999999999887665443
No 11
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=7e-28 Score=214.30 Aligned_cols=163 Identities=19% Similarity=0.239 Sum_probs=137.0
Q ss_pred ccccccCCCceeeccCccccccC--CCCccceeEEeeecCCCCe----EEeeeccCCCCccccccccCCCCHhhhcCCCC
Q 018586 127 DEKRTCRGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV----IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMP 200 (353)
Q Consensus 127 ~e~~~~~~~~~~~~D~Ettg~~~--~~~~~il~~v~ivd~~g~~----~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~ 200 (353)
....+.....|+++|+||||+++ ++++++ |.|.+. .+.+ .++.+|+|..+|++.++.|||||+++|.++|+
T Consensus 39 ~~~~~~~~~~~vviD~ETTGl~p~~d~IieI-g~v~v~--~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~ 115 (239)
T PRK09146 39 SPDTPLSEVPFVALDFETTGLDAEQDAIVSI-GLVPFT--LQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPD 115 (239)
T ss_pred CCCCCcccCCEEEEEeECCCCCCCCCcEEEE-EEEEEE--CCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCC
Confidence 34456778899999999999874 566777 677663 3333 47899999999999999999999999999999
Q ss_pred hHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCc-------CCCCceeecccccCCcccCC-------
Q 018586 201 LKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-------YPDHMLRDTAKYRPLMKTNL------- 266 (353)
Q Consensus 201 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-------~~~~~~~Dt~~l~~~~~~~~------- 266 (353)
+.+|+.+|.+++ ++.++||||+.||+.||+.. ....+++||+.+++.+.+..
T Consensus 116 ~~evl~~l~~~~--------------~~~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~ 181 (239)
T PRK09146 116 LERILDELLEAL--------------AGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNR 181 (239)
T ss_pred HHHHHHHHHHHh--------------CCCEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccch
Confidence 999999999999 88899999999999999722 12356899999987765432
Q ss_pred ------CCCcHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHhch
Q 018586 267 ------VSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQD 308 (353)
Q Consensus 267 ------~~~~L~~l~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~~ 308 (353)
..++|.+++.+| |++ ..++|+|++||.+|++||..+..+.
T Consensus 182 ~~~~~~~~~~L~~l~~~~-gl~-~~~~H~Al~DA~ata~l~~~~~~~~ 227 (239)
T PRK09146 182 LKGKKPESIRLADSRLRY-GLP-AYSPHHALTDAIATAELLQAQIAHH 227 (239)
T ss_pred hccCCCCCCCHHHHHHHc-CCC-CCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 568999999998 988 5569999999999999999998775
No 12
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=1.6e-27 Score=205.33 Aligned_cols=157 Identities=22% Similarity=0.282 Sum_probs=128.0
Q ss_pred CCceeeccCcccccc-CCCCccceeEEeeecCCCCe--EEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHH
Q 018586 134 GPKAVAMDCEMVGGG-SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILE 210 (353)
Q Consensus 134 ~~~~~~~D~Ettg~~-~~~~~~il~~v~ivd~~g~~--~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~ 210 (353)
...|+++|+||||.+ .+.++++ ++|.+. .|.+ .|++||+|..++++.++++||||++||+++|++.+|+++|.+
T Consensus 4 ~~~~vvlD~EtTGl~~~~eIIeI-gaV~v~--~g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap~~~evl~~f~~ 80 (195)
T PRK07247 4 LETYIAFDLEFNTVNGVSHIIQV-SAVKYD--DHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFKE 80 (195)
T ss_pred CCeEEEEEeeCCCCCCCCeEEEE-EEEEEE--CCEEEEEEEEEECCCCCCCccceecCCCCHHHHhCCCCHHHHHHHHHH
Confidence 457999999999986 3456666 677773 4443 599999999999999999999999999999999999999999
Q ss_pred HHhcCCCCcccccCCCCCcEEEecccH-HHHHHhcCc---CCCCceeeccccc--CCc--ccCCCCCcHHHHHHHHhCCc
Q 018586 211 ILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLRMN---YPDHMLRDTAKYR--PLM--KTNLVSHSLKYLTRTYLGYD 282 (353)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~lvgh~~~-~D~~~l~~~---~~~~~~~Dt~~l~--~~~--~~~~~~~~L~~l~~~~~~~~ 282 (353)
|+ ++.+|||||+. ||+.||... .+....+|+.... +.. .+...+++|..|+++| |++
T Consensus 81 f~--------------~~~~lVaHNa~~fD~~fL~~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~-gi~ 145 (195)
T PRK07247 81 FV--------------GELPLIGYNAQKSDLPILAENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVADFL-GIK 145 (195)
T ss_pred HH--------------CCCeEEEEeCcHhHHHHHHHcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHHHhc-CCC
Confidence 99 88899999997 899999832 2223456775332 221 3455689999999998 888
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHhchhh
Q 018586 283 IQSGVHDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 283 ~~~~~H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
. .+|+|++||++|+.||.++++..+.
T Consensus 146 ~--~~HrAl~DA~~ta~v~~~ll~~~~~ 171 (195)
T PRK07247 146 G--RGHNSLEDARMTARVYESFLESDQN 171 (195)
T ss_pred C--CCcCCHHHHHHHHHHHHHHHhhccc
Confidence 4 4899999999999999999988654
No 13
>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=99.95 E-value=7.9e-28 Score=201.70 Aligned_cols=146 Identities=23% Similarity=0.333 Sum_probs=130.5
Q ss_pred eeeccCccccccCCCCccceeEEeeecCCCCe--EEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHhc
Q 018586 137 AVAMDCEMVGGGSNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNN 214 (353)
Q Consensus 137 ~~~~D~Ettg~~~~~~~~il~~v~ivd~~g~~--~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~~~~ 214 (353)
++++|+||||...+.++++ +.|.+. .|++ .|+.+|+|..++++.++++||||+++|++++++.+|+.+|.+|+
T Consensus 1 ~v~~D~Ettg~~~~~ii~i-g~v~~~--~~~~~~~~~~~i~p~~~~~~~~~~i~GIt~e~l~~~~~~~~v~~~l~~~l-- 75 (156)
T cd06130 1 FVAIDFETANADRASACSI-GLVKVR--DGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFL-- 75 (156)
T ss_pred CEEEEEeCCCCCCCceEEE-EEEEEE--CCEEEEEEEEEeCcCCCCChhhccccCcCHHHHhcCCCHHHHHHHHHHHh--
Confidence 5899999999877888887 677773 4554 48999999999999999999999999999999999999999999
Q ss_pred CCCCcccccCCCCCcEEEecccHHHHHHhc-------CcCCCCceeecccccCCcccCCCCCcHHHHHHHHhCCcCCCCC
Q 018586 215 GESTGRLMLDDGKARLLVGHGLEHDLDSLR-------MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGV 287 (353)
Q Consensus 215 ~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~-------~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~ 287 (353)
++.++||||+.||+.+|+ +..+...++||+.+++.+++...+++|..|++.| |+++. +
T Consensus 76 ------------~~~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~~~~L~~l~~~~-g~~~~--~ 140 (156)
T cd06130 76 ------------GGSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEHL-GIELN--H 140 (156)
T ss_pred ------------CCCEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCCCCCHHHHHHHc-CCCcc--C
Confidence 778999999999999997 3455678999999999988888899999999988 99966 9
Q ss_pred CChHHHHHHHHHHHH
Q 018586 288 HDPYEDCVSVMRLYK 302 (353)
Q Consensus 288 H~Al~Da~~t~~l~~ 302 (353)
|+|++||++|++||.
T Consensus 141 H~Al~Da~~ta~l~~ 155 (156)
T cd06130 141 HDALEDARACAEILL 155 (156)
T ss_pred cCchHHHHHHHHHHh
Confidence 999999999999985
No 14
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.95 E-value=1.5e-27 Score=214.09 Aligned_cols=174 Identities=21% Similarity=0.295 Sum_probs=144.3
Q ss_pred cccCCCceeeccCccccccCC--CCccceeEEeeecCCCCe--EEeeeccCCCCccccccccCCCCHhhhcCCCChHHHH
Q 018586 130 RTCRGPKAVAMDCEMVGGGSN--GTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVK 205 (353)
Q Consensus 130 ~~~~~~~~~~~D~Ettg~~~~--~~~~il~~v~ivd~~g~~--~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~ 205 (353)
++.....|+++|+||||.++. +++|+ |+|.+. +|.+ .|+.+|+|. ++++.++++||||+++|.++|++.+|+
T Consensus 63 ~~~~~~~~vv~DiETTG~~~~~~~IIEI-GAv~v~--~g~i~~~f~~~v~p~-~ip~~~~~itGIt~e~l~~ap~~~evl 138 (257)
T PRK08517 63 TPIKDQVFCFVDIETNGSKPKKHQIIEI-GAVKVK--NGEIIDRFESFVKAK-EVPEYITELTGITYEDLENAPSLKEVL 138 (257)
T ss_pred CCCCCCCEEEEEEeCCCCCCCCCeEEEE-EEEEEE--CCEEEEEEEEEECCC-CCChhhhhhcCcCHHHHcCCCCHHHHH
Confidence 456788999999999998743 57777 777773 4555 489999997 899999999999999999999999999
Q ss_pred HHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhc-----CcC--CCCceeecccccCCcccCCCCCcHHHHHHHH
Q 018586 206 DKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR-----MNY--PDHMLRDTAKYRPLMKTNLVSHSLKYLTRTY 278 (353)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~-----~~~--~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~ 278 (353)
.+|.+|+ ++.++||||+.||+.||+ ... ...+.+||..+++...+. .+++|++|++.+
T Consensus 139 ~~f~~fl--------------~~~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~-~~~~L~~L~~~l 203 (257)
T PRK08517 139 EEFRLFL--------------GDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIES-PRYGLSFLKELL 203 (257)
T ss_pred HHHHHHH--------------CCCeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccC-CCCCHHHHHHHc
Confidence 9999999 788999999999999997 222 225679999998776554 578999999987
Q ss_pred hCCcCCCCCCChHHHHHHHHHHHHHHHhchhhhhhhcccCCCCCCCCcchhHHhhcChhhhhccCCC
Q 018586 279 LGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQVEEIGNQNTTGSFDSYKYKELEKMSPNELYQISKS 345 (353)
Q Consensus 279 ~~~~~~~~~H~Al~Da~~t~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 345 (353)
|++. ..+|+|++||.+|++||..+.++... ...+.++|+++++.
T Consensus 204 -gi~~-~~~HrAl~DA~ata~ll~~ll~~~~~---------------------~~~t~~~L~~~~k~ 247 (257)
T PRK08517 204 -GIEI-EVHHRAYADALAAYEIFKICLLNLPS---------------------YIKTTEDLIDFSKT 247 (257)
T ss_pred -CcCC-CCCCChHHHHHHHHHHHHHHHHHhHH---------------------hhcCHHHHHHHhhh
Confidence 9984 46999999999999999999988654 12356777777765
No 15
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=2.3e-27 Score=219.67 Aligned_cols=154 Identities=18% Similarity=0.307 Sum_probs=135.9
Q ss_pred CceeeccCccccccCCCCccceeEEeeecCCCCe--EEeeeccCCC-CccccccccCCCCHhhhcCCCChHHHHHHHHHH
Q 018586 135 PKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENV--IFHTYVQPQL-PVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 211 (353)
Q Consensus 135 ~~~~~~D~Ettg~~~~~~~~il~~v~ivd~~g~~--~~~~lv~P~~-~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~ 211 (353)
++|+++|+||||...++++++ ++|.+. +|.+ .|++||+|.. .+++.++.|||||+++|+++|+|.+|+++|.+|
T Consensus 1 ~~~vviD~ETTg~~~d~IieI-gav~v~--~g~i~~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~~ap~f~ev~~~~~~f 77 (309)
T PRK06195 1 MNFVAIDFETANEKRNSPCSI-GIVVVK--DGEIVEKVHYLIKPKEMRFMPINIGIHGIRPHMVEDELEFDKIWEKIKHY 77 (309)
T ss_pred CcEEEEEEeCCCCCCCceEEE-EEEEEE--CCEEEEEEEEEECCCCCCCChhheeccCcCHHHHhCCCCHHHHHHHHHHH
Confidence 469999999999877888888 788874 4555 4899999985 578888999999999999999999999999999
Q ss_pred HhcCCCCcccccCCCCCcEEEecccHHHHHHhc-------CcCCCCceeecccccCCcccCCCCCcHHHHHHHHhCCcCC
Q 018586 212 LNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR-------MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQ 284 (353)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~-------~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~ 284 (353)
+ ++.+|||||+.||+.||+ +..|...++||+.+++.+++...+++|..|++.| |++.
T Consensus 78 l--------------~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~~L~~L~~~~-gi~~- 141 (309)
T PRK06195 78 F--------------NNNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFL-GYEF- 141 (309)
T ss_pred h--------------CCCEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcCCHHHHHHHc-CCCC-
Confidence 9 889999999999999997 3345567899999999988888899999999999 8874
Q ss_pred CCCCChHHHHHHHHHHHHHHHhch
Q 018586 285 SGVHDPYEDCVSVMRLYKRFRRQD 308 (353)
Q Consensus 285 ~~~H~Al~Da~~t~~l~~~~~~~~ 308 (353)
.+|+|++||++|++||..+.++.
T Consensus 142 -~~H~Al~DA~ata~l~~~l~~~~ 164 (309)
T PRK06195 142 -KHHDALADAMACSNILLNISKEL 164 (309)
T ss_pred -cccCCHHHHHHHHHHHHHHHHHh
Confidence 49999999999999999998764
No 16
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=4e-27 Score=216.98 Aligned_cols=157 Identities=22% Similarity=0.407 Sum_probs=138.2
Q ss_pred CCCceeeccCccccccC--CCCccceeEEeeecCCCCe--EEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHH
Q 018586 133 RGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKI 208 (353)
Q Consensus 133 ~~~~~~~~D~Ettg~~~--~~~~~il~~v~ivd~~g~~--~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~ 208 (353)
-..+++++|+||||.++ ++++++ ++|.+. .|.+ .|+.+|+|..++++.++++||||+++|+++|++.+|+++|
T Consensus 6 ~~~~~Vv~DlETTGl~p~~~eIIEI-gaV~v~--~g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~evl~~f 82 (313)
T PRK06807 6 LPLDYVVIDFETTGFNPYNDKIIQV-AAVKYR--NHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLF 82 (313)
T ss_pred CCCCEEEEEEECCCCCCCCCeEEEE-EEEEEE--CCEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHHHHHH
Confidence 35679999999999874 567777 677773 5555 4899999999999999999999999999999999999999
Q ss_pred HHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhc-------CcCCCCceeecccccCCcccCCCCCcHHHHHHHHhCC
Q 018586 209 LEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR-------MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGY 281 (353)
Q Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~-------~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~ 281 (353)
.+|+ ++.+|||||+.||+.||. +..+..+++||+.+++.+.+....++|+.|++.| |+
T Consensus 83 ~~fl--------------~~~~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~~~kL~~L~~~l-gi 147 (313)
T PRK06807 83 LAFL--------------HTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRML-GI 147 (313)
T ss_pred HHHH--------------cCCeEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCCCCCHHHHHHHc-CC
Confidence 9999 788999999999999998 2345577999999999888877889999999988 99
Q ss_pred cCCCCCCChHHHHHHHHHHHHHHHhchh
Q 018586 282 DIQSGVHDPYEDCVSVMRLYKRFRRQDH 309 (353)
Q Consensus 282 ~~~~~~H~Al~Da~~t~~l~~~~~~~~~ 309 (353)
+. .+|+|+.||++|++||.++.....
T Consensus 148 ~~--~~H~Al~DA~~ta~l~~~l~~~~~ 173 (313)
T PRK06807 148 RL--SSHNAFDDCITCAAVYQKCASIEE 173 (313)
T ss_pred CC--CCcChHHHHHHHHHHHHHHHHhhh
Confidence 96 699999999999999999998763
No 17
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.94 E-value=5.5e-27 Score=205.67 Aligned_cols=146 Identities=18% Similarity=0.192 Sum_probs=125.5
Q ss_pred eeeccCccccccCCCCccceeEEeeecCCCCe--EEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHhc
Q 018586 137 AVAMDCEMVGGGSNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNN 214 (353)
Q Consensus 137 ~~~~D~Ettg~~~~~~~~il~~v~ivd~~g~~--~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~~~~ 214 (353)
++++|+||||++ ..++|+ +.|.+. +|++ .|+.+|+|..+|++.++.|||||++||+++|++.+|+++ |+
T Consensus 2 ~~vlD~ETTGl~-~~IieI-g~v~v~--~~~i~~~~~~lv~P~~~i~~~~~~ihgIt~e~v~~ap~~~ev~~~---~~-- 72 (219)
T PRK07983 2 LRVIDTETCGLQ-GGIVEI-ASVDVI--DGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPH---YY-- 72 (219)
T ss_pred eEEEEEECCCCC-CCCEEE-EEEEEE--CCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHcCCCCHHHHHHH---Hc--
Confidence 689999999985 357777 777774 4555 489999999999999999999999999999999999886 46
Q ss_pred CCCCcccccCCCCCcEEEecccHHHHHHhcCcCCCCceeecccccCCcccCCCCCcHHHHHHHHhCCcCC----CCCCCh
Q 018586 215 GESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQ----SGVHDP 290 (353)
Q Consensus 215 ~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~----~~~H~A 290 (353)
++.+|||||+.||+.||.. ....++||+.+++.++|... ++|..|+..| |++.. ..+|||
T Consensus 73 ------------~~~~lVaHNa~FD~~~L~~--~~~~~idTl~lar~l~p~~~-~~l~~L~~~~-~l~~~~~~~~~aHrA 136 (219)
T PRK07983 73 ------------GSEWYVAHNASFDRRVLPE--MPGEWICTMKLARRLWPGIK-YSNMALYKSR-KLNVQTPPGLHHHRA 136 (219)
T ss_pred ------------CCCEEEEeCcHhhHHHHhC--cCCCcEeHHHHHHHHccCCC-CCHHHHHHHc-CCCCCCCCCCCCCcH
Confidence 7789999999999999973 22458999999999988755 9999999988 87642 349999
Q ss_pred HHHHHHHHHHHHHHHhc
Q 018586 291 YEDCVSVMRLYKRFRRQ 307 (353)
Q Consensus 291 l~Da~~t~~l~~~~~~~ 307 (353)
++||++|+.||.++.+.
T Consensus 137 l~Da~ata~ll~~l~~~ 153 (219)
T PRK07983 137 LYDCYITAALLIDIMNT 153 (219)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 99999999999999964
No 18
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=1.1e-26 Score=208.59 Aligned_cols=158 Identities=17% Similarity=0.290 Sum_probs=131.4
Q ss_pred CCceeeccCccccccC--CCCccceeEEeeecCCCCeEEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHH
Q 018586 134 GPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 211 (353)
Q Consensus 134 ~~~~~~~D~Ettg~~~--~~~~~il~~v~ivd~~g~~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~ 211 (353)
.++++++|+||||+++ ++++|+ +.|.+........++.+|+|..+|++.++.+||||+|+|+++|++.+|+++|.+|
T Consensus 6 ~~~~v~~D~ETTGl~~~~d~IIEI-a~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~~~f 84 (250)
T PRK06310 6 DTEFVCLDCETTGLDVKKDRIIEF-AAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGF 84 (250)
T ss_pred CCcEEEEEEeCCCCCCCCCeEEEE-EEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHHHHH
Confidence 4679999999999864 567777 6666632221225899999999999999999999999999999999999999999
Q ss_pred HhcCCCCcccccCCCCC-cEEEecccHHHHHHhcCc-------CC--CCceeecccccCCcccCCCCCcHHHHHHHHhCC
Q 018586 212 LNNGESTGRLMLDDGKA-RLLVGHGLEHDLDSLRMN-------YP--DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGY 281 (353)
Q Consensus 212 ~~~~~~~~~~~~~~~~~-~~lvgh~~~~D~~~l~~~-------~~--~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~ 281 (353)
+ ++ .+|||||+.||+.||... .+ ...++||+.+++.+ +...+++|..|+++| |+
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 799999999999999822 21 25689999998864 444678999999998 99
Q ss_pred cCCCCCCChHHHHHHHHHHHHHHHhchh
Q 018586 282 DIQSGVHDPYEDCVSVMRLYKRFRRQDH 309 (353)
Q Consensus 282 ~~~~~~H~Al~Da~~t~~l~~~~~~~~~ 309 (353)
+. .++|+|++||.+|++||..+.++..
T Consensus 149 ~~-~~aH~Al~Da~at~~vl~~l~~~~~ 175 (250)
T PRK06310 149 PY-DGNHRAMKDVEINIKVFKHLCKRFR 175 (250)
T ss_pred CC-CCCcChHHHHHHHHHHHHHHHHhcc
Confidence 84 4599999999999999999987643
No 19
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.94 E-value=1.1e-26 Score=214.58 Aligned_cols=159 Identities=22% Similarity=0.281 Sum_probs=134.4
Q ss_pred cCCCceeeccCccccccCC--CCccceeEEeeecCCCCe--EEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHH
Q 018586 132 CRGPKAVAMDCEMVGGGSN--GTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDK 207 (353)
Q Consensus 132 ~~~~~~~~~D~Ettg~~~~--~~~~il~~v~ivd~~g~~--~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~ 207 (353)
..+.+|+++|+||||+++. +++++ +.|.+ +.+|++ .|..+|+|.. ++..+.|||||+++|.++|+|.+++++
T Consensus 12 ~~~~~fvvlD~ETTGl~p~~d~IIeI-gav~v-~~~g~i~~~~~~lv~P~~--~~~~~~IhGIt~e~l~~ap~f~ev~~~ 87 (313)
T PRK06063 12 HYPRGWAVVDVETSGFRPGQARIISL-AVLGL-DADGNVEQSVVTLLNPGV--DPGPTHVHGLTAEMLEGQPQFADIAGE 87 (313)
T ss_pred CCCCCEEEEEEECCCCCCCCCEEEEE-EEEEE-ECCceeeeEEEEEECcCC--CCCCeecCCCCHHHHhCCCCHHHHHHH
Confidence 3456799999999998754 56666 55555 345666 4899999975 356789999999999999999999999
Q ss_pred HHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhc-------CcCCCCceeecccccCCcccCCCCCcHHHHHHHHhC
Q 018586 208 ILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR-------MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLG 280 (353)
Q Consensus 208 ~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~-------~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~ 280 (353)
|.+|+ ++.+|||||+.||+.||+ ...|...++||+.+++.+.+...+++|.+|+++| |
T Consensus 88 l~~~l--------------~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~~kL~~l~~~~-g 152 (313)
T PRK06063 88 VAELL--------------RGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLAAHW-G 152 (313)
T ss_pred HHHHc--------------CCCEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCCCCHHHHHHHc-C
Confidence 99999 889999999999999998 2234456899999999887777899999999998 9
Q ss_pred CcCCCCCCChHHHHHHHHHHHHHHHhchhh
Q 018586 281 YDIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 281 ~~~~~~~H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
++ ..++|+|++||++|++||..++++..+
T Consensus 153 i~-~~~~H~Al~DA~ata~l~~~ll~~~~~ 181 (313)
T PRK06063 153 VP-QQRPHDALDDARVLAGILRPSLERARE 181 (313)
T ss_pred CC-CCCCCCcHHHHHHHHHHHHHHHHHHHh
Confidence 88 456999999999999999999888654
No 20
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=2e-26 Score=205.02 Aligned_cols=154 Identities=23% Similarity=0.446 Sum_probs=131.2
Q ss_pred CceeeccCccccccC--CCCccceeEEeeecCCCCeEEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHH
Q 018586 135 PKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 212 (353)
Q Consensus 135 ~~~~~~D~Ettg~~~--~~~~~il~~v~ivd~~g~~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~~ 212 (353)
.+++++|+||||++. ++++|+ +. ++......|+.+|+|..+|++.+++|||||+++|+++|+|.+|+++|.+|+
T Consensus 2 ~~~vv~D~ETTGl~~~~d~IIei-g~---v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~~fi 77 (232)
T PRK06309 2 PALIFYDTETTGTQIDKDRIIEI-AA---YNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFC 77 (232)
T ss_pred CcEEEEEeeCCCCCCCCCEEEEE-EE---EcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHH
Confidence 358999999999864 455555 33 454445579999999999999999999999999999999999999999999
Q ss_pred hcCCCCcccccCCCC-CcEEEecc-cHHHHHHhc-------CcCCCCceeecccccCCcccCCCCCcHHHHHHHHhCCcC
Q 018586 213 NNGESTGRLMLDDGK-ARLLVGHG-LEHDLDSLR-------MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDI 283 (353)
Q Consensus 213 ~~~~~~~~~~~~~~~-~~~lvgh~-~~~D~~~l~-------~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~ 283 (353)
+ +.+||||| +.||+.||+ +..+...++||+.+++.+.+...+++|..|+..| |++.
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 46999999 489999998 2234467899999998888877789999999998 8883
Q ss_pred CCCCCChHHHHHHHHHHHHHHHhch
Q 018586 284 QSGVHDPYEDCVSVMRLYKRFRRQD 308 (353)
Q Consensus 284 ~~~~H~Al~Da~~t~~l~~~~~~~~ 308 (353)
.++|+|++||.+|++||.++.++.
T Consensus 143 -~~aH~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 143 -NQAHRALDDVITLHRVFSALVGDL 166 (232)
T ss_pred -CCCCCcHHHHHHHHHHHHHHHHHH
Confidence 459999999999999999998764
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=99.94 E-value=1.7e-26 Score=203.63 Aligned_cols=164 Identities=18% Similarity=0.298 Sum_probs=135.0
Q ss_pred CCCceeeccCccccccCC-CCccceeEEeeecCCCC-eEEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHH
Q 018586 133 RGPKAVAMDCEMVGGGSN-GTLDLCARVCLVDEDEN-VIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILE 210 (353)
Q Consensus 133 ~~~~~~~~D~Ettg~~~~-~~~~il~~v~ivd~~g~-~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~ 210 (353)
....|+++|+||||+++. .++|+ ++|.+.+.... ..|+.+|+|..++++.++.+||||+++|.++|++.+|+++|.+
T Consensus 5 ~~~~fvv~D~ETTGl~~~~~IIeI-gav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~~~~ 83 (217)
T TIGR00573 5 VLDTETTGDNETTGLYAGHDIIEI-GAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFAD 83 (217)
T ss_pred EecCEEEEEecCCCCCCCCCEEEE-EEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHHHHH
Confidence 345799999999998743 26666 77776543222 2689999999999999999999999999999999999999999
Q ss_pred HHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCc--------CCCCceeecccccCCcccCC--CCCcHHHHHHHHhC
Q 018586 211 ILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN--------YPDHMLRDTAKYRPLMKTNL--VSHSLKYLTRTYLG 280 (353)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~--------~~~~~~~Dt~~l~~~~~~~~--~~~~L~~l~~~~~~ 280 (353)
|+ ++.++||||+.||+.||+.. .+...++||..+++.+.+.. .+++|..++++| |
T Consensus 84 ~~--------------~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~-g 148 (217)
T TIGR00573 84 YI--------------RGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRY-E 148 (217)
T ss_pred Hh--------------CCCEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHHHc-C
Confidence 99 78899999999999999822 12256789988877766532 468999999999 8
Q ss_pred CcCCC-CCCChHHHHHHHHHHHHHHHhchhhhh
Q 018586 281 YDIQS-GVHDPYEDCVSVMRLYKRFRRQDHQVE 312 (353)
Q Consensus 281 ~~~~~-~~H~Al~Da~~t~~l~~~~~~~~~~~~ 312 (353)
++... ++|+|++||.+|++||..+..+..+..
T Consensus 149 l~~~~~~~H~Al~DA~~ta~l~~~l~~~~~~~~ 181 (217)
T TIGR00573 149 ITNSHRALHGALADAFILAKLYLVMTGKQTKYG 181 (217)
T ss_pred CCCCCcccCCHHHHHHHHHHHHHHHHhcchhhc
Confidence 88432 589999999999999999999876633
No 22
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.94 E-value=1.3e-26 Score=203.06 Aligned_cols=159 Identities=18% Similarity=0.253 Sum_probs=130.1
Q ss_pred CCceeeccCcccccc--------CCCCccceeEEeeecCCCCe--EEeeeccCCC--CccccccccCCCCHhhhcCCCCh
Q 018586 134 GPKAVAMDCEMVGGG--------SNGTLDLCARVCLVDEDENV--IFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPL 201 (353)
Q Consensus 134 ~~~~~~~D~Ettg~~--------~~~~~~il~~v~ivd~~g~~--~~~~lv~P~~--~i~~~~~~~~GIt~e~l~~~~~~ 201 (353)
.+.|+++|+||||.+ .++++|+ ++|.+. +|++ .|+.||+|.. +++++++++||||+++|+++|+|
T Consensus 3 ~~~~vvlD~EtTg~~~~~~~~~~~~eIIeI-GaV~v~--~~~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~~ 79 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKKPKGFFPEIIEV-GLVSVV--GCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISF 79 (207)
T ss_pred cceEEEEEeecCCcCCCCCCCCCCCceEEE-eEEEEe--cCcChhhhcceECCCccCccChhhhhhcCcCHHHHccCCCH
Confidence 457999999999854 2457777 778774 4444 5999999986 69999999999999999999999
Q ss_pred HHHHHHHHHHHhcCCCCcccccCCCCC-cEEEecccHHHHHHhc-------CcCCC-CceeecccccCCcccCCCCCcHH
Q 018586 202 KEVKDKILEILNNGESTGRLMLDDGKA-RLLVGHGLEHDLDSLR-------MNYPD-HMLRDTAKYRPLMKTNLVSHSLK 272 (353)
Q Consensus 202 ~~v~~~~~~~~~~~~~~~~~~~~~~~~-~~lvgh~~~~D~~~l~-------~~~~~-~~~~Dt~~l~~~~~~~~~~~~L~ 272 (353)
++|+++|.+|+ ++ ..+|+|+..||+.||+ +..|. ..++|++.+++.+++....++|.
T Consensus 80 ~evl~~f~~~~--------------~~~~~~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~~~~L~ 145 (207)
T PRK07748 80 EELVEKLAEYD--------------KRCKPTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLW 145 (207)
T ss_pred HHHHHHHHHHh--------------CcCCeEEEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCCCCCHH
Confidence 99999999999 55 3444455799999997 22343 46788888877777666679999
Q ss_pred HHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHhchhh
Q 018586 273 YLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 273 ~l~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
++++.| |++..+.+|+|++||++|++||.++.++.+.
T Consensus 146 ~~~~~~-gi~~~~~~H~Al~DA~~ta~l~~~l~~~~~~ 182 (207)
T PRK07748 146 KAIEEY-GKEGTGKHHCALDDAMTTYNIFKLVEKDKEY 182 (207)
T ss_pred HHHHHc-CCCCCCCCcChHHHHHHHHHHHHHHHhCcce
Confidence 999998 9995555899999999999999999988653
No 23
>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=99.94 E-value=1.7e-26 Score=195.95 Aligned_cols=149 Identities=21% Similarity=0.355 Sum_probs=125.7
Q ss_pred eeeccCccccccC---CCCccceeEEeeecCCCCe---EEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHH
Q 018586 137 AVAMDCEMVGGGS---NGTLDLCARVCLVDEDENV---IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILE 210 (353)
Q Consensus 137 ~~~~D~Ettg~~~---~~~~~il~~v~ivd~~g~~---~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~ 210 (353)
++++|+||||+++ +.++|+ +.+.+.+ +.+ .|+.+|+|..++++.++++||||++++++++++.+|+.+|.+
T Consensus 1 ~v~~D~ETTGl~~~~~~~iiei-g~v~v~~--~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~~~~v~~~l~~ 77 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEI-GCVELIN--RRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLD 77 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEE-EEEEEEC--CcEeccEEEEEECCCCCCCHHHHHHhCCCHHHHhcCCCHHHHHHHHHH
Confidence 5789999999975 456777 6776633 332 589999999999999999999999999999999999999999
Q ss_pred HHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCc-------C---CCCceeecccccCCcccCCCCCcHHHHHHHHhC
Q 018586 211 ILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-------Y---PDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLG 280 (353)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-------~---~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~ 280 (353)
|+ ++.++||||+.||+.||+.. . ....++||+.+++...+. ..++|++++++| |
T Consensus 78 ~l--------------~~~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~-~~~~L~~l~~~~-~ 141 (167)
T cd06131 78 FI--------------RGAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPG-KPNSLDALCKRF-G 141 (167)
T ss_pred HH--------------CCCeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCC-CCCCHHHHHHHC-C
Confidence 99 77899999999999999721 1 125689999998877654 467999999999 9
Q ss_pred CcCCC-CCCChHHHHHHHHHHHHHH
Q 018586 281 YDIQS-GVHDPYEDCVSVMRLYKRF 304 (353)
Q Consensus 281 ~~~~~-~~H~Al~Da~~t~~l~~~~ 304 (353)
++... ++|+|+.||++|++||.++
T Consensus 142 i~~~~~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 142 IDNSHRTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred CCCCCCCCCChHHHHHHHHHHHHHh
Confidence 88653 4899999999999999876
No 24
>PRK07883 hypothetical protein; Validated
Probab=99.94 E-value=3.1e-26 Score=226.66 Aligned_cols=164 Identities=22% Similarity=0.337 Sum_probs=141.7
Q ss_pred cccccCCCceeeccCccccccC--CCCccceeEEeeecCCCCeE--EeeeccCCCCccccccccCCCCHhhhcCCCChHH
Q 018586 128 EKRTCRGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENVI--FHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKE 203 (353)
Q Consensus 128 e~~~~~~~~~~~~D~Ettg~~~--~~~~~il~~v~ivd~~g~~~--~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~ 203 (353)
-+++.....|+++|+||||+++ +.++++ ++|.+ .+|.++ |+.+|+|..++++.++.+||||+++|+++|++++
T Consensus 8 ~~~~~~~~~~Vv~D~ETTGl~p~~~~IIEI-gaV~v--~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~e 84 (557)
T PRK07883 8 LGTPLRDVTFVVVDLETTGGSPAGDAITEI-GAVKV--RGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEE 84 (557)
T ss_pred hCCCCcCCCEEEEEEecCCCCCCCCeEEEE-EEEEE--ECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHH
Confidence 3456777899999999999875 467777 67777 355554 8999999999999999999999999999999999
Q ss_pred HHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhc-------CcCCCCceeecccccCCccc--CCCCCcHHHH
Q 018586 204 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR-------MNYPDHMLRDTAKYRPLMKT--NLVSHSLKYL 274 (353)
Q Consensus 204 v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~-------~~~~~~~~~Dt~~l~~~~~~--~~~~~~L~~l 274 (353)
|+.+|.+|+ ++.++||||+.||+.||+ +..+...++||+.+++.+.+ ...+++|.+|
T Consensus 85 vl~~f~~fl--------------~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L 150 (557)
T PRK07883 85 VLPAFLEFA--------------RGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTL 150 (557)
T ss_pred HHHHHHHHh--------------cCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHH
Confidence 999999999 788999999999999998 33444668999999988776 6678999999
Q ss_pred HHHHhCCcCCCCCCChHHHHHHHHHHHHHHHhchhh
Q 018586 275 TRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 275 ~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
++++ |++. .++|+|++||.+|++||.++..+...
T Consensus 151 ~~~~-gi~~-~~~H~Al~DA~ata~l~~~l~~~~~~ 184 (557)
T PRK07883 151 ARLF-GATT-TPTHRALDDARATVDVLHGLIERLGN 184 (557)
T ss_pred HHHC-Cccc-CCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 9987 9985 45899999999999999999988754
No 25
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=5.8e-26 Score=198.33 Aligned_cols=156 Identities=19% Similarity=0.329 Sum_probs=127.1
Q ss_pred CCCceeeccCccccccC--CCCccceeEEeeecCCCCe----EEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHH
Q 018586 133 RGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV----IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKD 206 (353)
Q Consensus 133 ~~~~~~~~D~Ettg~~~--~~~~~il~~v~ivd~~g~~----~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~ 206 (353)
.+.+++++|+||||+++ +.++++ ++|.+. .+.+ .|+.+|+|..++++.++++||||+++|++++++.+|++
T Consensus 27 ~~~~~vviD~ETTGl~~~~d~IieI-gaV~~~--~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~ 103 (202)
T PRK09145 27 PPDEWVALDCETTGLDPRRAEIVSI-AAVKIR--GNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALR 103 (202)
T ss_pred CCCCEEEEEeECCCCCCCCCceEEE-EEEEEE--CCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHH
Confidence 44589999999999874 566666 666663 2332 47899999999999999999999999999999999999
Q ss_pred HHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcC------cCC-CCceeecccccCC-----cccCCCCCcHHHH
Q 018586 207 KILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM------NYP-DHMLRDTAKYRPL-----MKTNLVSHSLKYL 274 (353)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~------~~~-~~~~~Dt~~l~~~-----~~~~~~~~~L~~l 274 (353)
+|.+|+ ++.+|||||+.||+.||.. ..+ ...++|+..++.. +.+...+++|+++
T Consensus 104 ~~~~~i--------------~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l 169 (202)
T PRK09145 104 QLLAFI--------------GNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAI 169 (202)
T ss_pred HHHHHH--------------cCCeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHH
Confidence 999999 7889999999999999971 122 2457899766421 2223346899999
Q ss_pred HHHHhCCcCCCCCCChHHHHHHHHHHHHHHHhc
Q 018586 275 TRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQ 307 (353)
Q Consensus 275 ~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~ 307 (353)
++.| |++. .++|+|++||++|++||.++.+.
T Consensus 170 ~~~~-gi~~-~~~H~Al~DA~ata~l~~~l~~~ 200 (202)
T PRK09145 170 LKHL-DLPV-LGRHDALNDAIMAALIFLRLRKG 200 (202)
T ss_pred HHHc-CCCC-CCCCCcHHHHHHHHHHHHHHHhc
Confidence 9998 9985 56899999999999999998754
No 26
>PRK06722 exonuclease; Provisional
Probab=99.93 E-value=4.1e-26 Score=205.60 Aligned_cols=158 Identities=16% Similarity=0.172 Sum_probs=128.2
Q ss_pred CCceeeccCcccccc-----CCCCccceeEEeeecCCCCeE--EeeeccCCCCccccccccCCCCHhhhcCCCChHHHHH
Q 018586 134 GPKAVAMDCEMVGGG-----SNGTLDLCARVCLVDEDENVI--FHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKD 206 (353)
Q Consensus 134 ~~~~~~~D~Ettg~~-----~~~~~~il~~v~ivd~~g~~~--~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~ 206 (353)
...|+++|+|||+.. .++++|+ |+|.+.+..++++ |++||+|..+|+++++.+||||++||.+||++++|+.
T Consensus 4 ~~~~vViD~ETT~~p~~~~~~deIIEI-GAVkV~~g~i~Ivd~F~sLV~P~~~I~~~i~~LTGIT~emV~~AP~f~eVl~ 82 (281)
T PRK06722 4 ATHFIVFDIERNFRPYKSEDPSEIVDI-GAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQIIE 82 (281)
T ss_pred CCEEEEEEeeCCCCCCCCCCCCeEEEE-EEEEEECCceeEEeeEEEEECCCCcCCHhHhhhcCCCHHHHcCCCCHHHHHH
Confidence 456999999999642 2578888 8888855444654 9999999999999999999999999999999999999
Q ss_pred HHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcC-------cCCC---CceeecccccCCcccC--CCCCcHHHH
Q 018586 207 KILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM-------NYPD---HMLRDTAKYRPLMKTN--LVSHSLKYL 274 (353)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~-------~~~~---~~~~Dt~~l~~~~~~~--~~~~~L~~l 274 (353)
+|.+|+ ++.++|+||+.||++||.. ..|. ..++|++.++...++. ...++|..|
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 7667778888999999992 2332 2247777665433332 245789999
Q ss_pred HHHHhCCcCCCCCCChHHHHHHHHHHHHHHHhc
Q 018586 275 TRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQ 307 (353)
Q Consensus 275 ~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~ 307 (353)
++.| |++..+.+|+|++||.+|+.||.++..+
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 9999 9996666999999999999999999854
No 27
>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=99.93 E-value=7.8e-26 Score=195.10 Aligned_cols=165 Identities=22% Similarity=0.258 Sum_probs=126.8
Q ss_pred CCceeeccCccccccC--CCCccceeEEeeecC-CCCe----EEeeeccC--CCCccccccccCCCCHhh-hcCCCChHH
Q 018586 134 GPKAVAMDCEMVGGGS--NGTLDLCARVCLVDE-DENV----IFHTYVQP--QLPVTNYRYEVTGLTEED-IKNAMPLKE 203 (353)
Q Consensus 134 ~~~~~~~D~Ettg~~~--~~~~~il~~v~ivd~-~g~~----~~~~lv~P--~~~i~~~~~~~~GIt~e~-l~~~~~~~~ 203 (353)
+-.++++|+||||+++ ++++|+ ++|.+.+. +|.+ .|+.+|+| ..+|++.+++|||||+++ ++++++..+
T Consensus 4 ~~~~vv~D~ETTGl~~~~d~Iiei-gav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~~ 82 (189)
T cd06134 4 GFLPVVVDVETGGFNPQTDALLEI-AAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEKE 82 (189)
T ss_pred cceeEEEEecCCCCCCCCCeEEEE-EEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchHH
Confidence 3457899999999874 567777 78888643 4543 58999999 578999999999999986 677777777
Q ss_pred HHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcC-----cC---C--CCceeecccccCCcccCCCCCcHHH
Q 018586 204 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM-----NY---P--DHMLRDTAKYRPLMKTNLVSHSLKY 273 (353)
Q Consensus 204 v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~-----~~---~--~~~~~Dt~~l~~~~~~~~~~~~L~~ 273 (353)
++.++.+++.+.- ...+.++.+|||||+.||+.||+. .. + ...++||..+++.+++ +++|..
T Consensus 83 ~~~~~~~~l~~~~-----~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~---~~~L~~ 154 (189)
T cd06134 83 ALKEIFKPIRKAL-----KAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG---QTVLAK 154 (189)
T ss_pred HHHHHHHHHHHHH-----hhcccCCCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC---CCcHHH
Confidence 7777766662100 000013679999999999999981 11 2 2457999999988765 468999
Q ss_pred HHHHHhCCcCC-CCCCChHHHHHHHHHHHHHHHhch
Q 018586 274 LTRTYLGYDIQ-SGVHDPYEDCVSVMRLYKRFRRQD 308 (353)
Q Consensus 274 l~~~~~~~~~~-~~~H~Al~Da~~t~~l~~~~~~~~ 308 (353)
+|++| |+++. ..+|+|++||.+|++||.++.++|
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 99998 99864 358999999999999999999875
No 28
>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=99.93 E-value=7.6e-26 Score=196.72 Aligned_cols=171 Identities=22% Similarity=0.277 Sum_probs=132.5
Q ss_pred cCCCceeeccCccccccC--CCCccceeEEeee-cCCCCe----EEeeeccCC--CCccccccccCCCCHh-hhcCCCCh
Q 018586 132 CRGPKAVAMDCEMVGGGS--NGTLDLCARVCLV-DEDENV----IFHTYVQPQ--LPVTNYRYEVTGLTEE-DIKNAMPL 201 (353)
Q Consensus 132 ~~~~~~~~~D~Ettg~~~--~~~~~il~~v~iv-d~~g~~----~~~~lv~P~--~~i~~~~~~~~GIt~e-~l~~~~~~ 201 (353)
+...-++++|+||||+++ ++++|+ ++|.+. +.+|.+ .|+++|+|. .+|++.+..|||||++ ++.+++++
T Consensus 5 ~~~~~~vv~D~ETTGl~~~~d~IieI-gav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~~ 83 (200)
T TIGR01298 5 FRGYLPVVVDVETGGFNAKTDALLEI-AAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVSE 83 (200)
T ss_pred hcCCeeEEEEeeCCCCCCCCCeEEEE-EEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcch
Confidence 345668999999999974 467777 777775 335555 288999984 7899999999999976 68999999
Q ss_pred HHHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCc-----C-----CCCceeecccccCCcccCCCCCcH
Q 018586 202 KEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-----Y-----PDHMLRDTAKYRPLMKTNLVSHSL 271 (353)
Q Consensus 202 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-----~-----~~~~~~Dt~~l~~~~~~~~~~~~L 271 (353)
++++.++.+++...-. ....++.+|||||+.||++||+.. . +...++||..+++..++ .++|
T Consensus 84 ~~~~~~~~~~l~~~~~-----~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~---~~~L 155 (200)
T TIGR01298 84 YEALHEIFKVVRKAMK-----ASGCQRAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG---QTVL 155 (200)
T ss_pred HHHHHHHHHHHHHHHH-----hcccCCCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC---cccH
Confidence 9988888888721100 000146799999999999999821 1 12458999999987764 3689
Q ss_pred HHHHHHHhCCcCC-CCCCChHHHHHHHHHHHHHHHhchhhhh
Q 018586 272 KYLTRTYLGYDIQ-SGVHDPYEDCVSVMRLYKRFRRQDHQVE 312 (353)
Q Consensus 272 ~~l~~~~~~~~~~-~~~H~Al~Da~~t~~l~~~~~~~~~~~~ 312 (353)
..++++| |+++. ..+|+|++||.+|++||..+.+++.++.
T Consensus 156 ~~l~~~~-gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~~~~ 196 (200)
T TIGR01298 156 AKACQAA-GXDFDSTQAHSALYDTEKTAELFCEIVNRWKRLG 196 (200)
T ss_pred HHHHHHc-CCCccccchhhhHHhHHHHHHHHHHHHHHHHHcc
Confidence 9999998 98864 3599999999999999999999976633
No 29
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.93 E-value=1.1e-26 Score=233.49 Aligned_cols=161 Identities=23% Similarity=0.377 Sum_probs=146.3
Q ss_pred ccCCCceeeccCcccccc--CCCCccceeEEeeecCCCCeE--EeeeccCCCCccccccccCCCCHhhhcCCCChHHHHH
Q 018586 131 TCRGPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENVI--FHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKD 206 (353)
Q Consensus 131 ~~~~~~~~~~D~Ettg~~--~~~~~~il~~v~ivd~~g~~~--~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~ 206 (353)
......||+||.||||++ .+.++++ +++.+ .+|+++ |+.+++|..+++...+.+||||++||++++++.+|+.
T Consensus 417 ~l~datyVVfDiETTGLs~~~d~iIE~-aAvKi--kng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~ 493 (1444)
T COG2176 417 KLDDATYVVFDIETTGLSPVYDEIIEI-AAVKI--KNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLE 493 (1444)
T ss_pred ccccccEEEEEeecCCcCcccchhhhh-eeeee--eCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHH
Confidence 355566999999999987 6778888 89988 778775 8999999999999999999999999999999999999
Q ss_pred HHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCc-----CC--CCceeecccccCCcccCCCCCcHHHHHHHHh
Q 018586 207 KILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-----YP--DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYL 279 (353)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-----~~--~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~ 279 (353)
+|.+|+ +++||||||+.||++||+.. .+ .+++|||+.|++.++|...+++|..||++|
T Consensus 494 kf~~~~--------------~d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh~Lg~l~kk~- 558 (1444)
T COG2176 494 KFREFI--------------GDSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSHRLGTLCKKL- 558 (1444)
T ss_pred HHHHHh--------------cCcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhcchHHHHHHh-
Confidence 999999 99999999999999999922 22 277999999999999999999999999999
Q ss_pred CCcCCCCCCChHHHHHHHHHHHHHHHhchhh
Q 018586 280 GYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 280 ~~~~~~~~H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
|+.+ ..+|||..||.+|+.||..+.+...+
T Consensus 559 ~v~l-e~hHRA~yDaeat~~vf~~f~~~~ke 588 (1444)
T COG2176 559 GVEL-ERHHRADYDAEATAKVFFVFLKDLKE 588 (1444)
T ss_pred CccH-HHhhhhhhhHHHHHHHHHHHHHHHHH
Confidence 9996 55999999999999999999988766
No 30
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=5.8e-26 Score=234.05 Aligned_cols=158 Identities=21% Similarity=0.350 Sum_probs=138.1
Q ss_pred CCceeeccCccccccC-CCCccceeEEeeecCCCCe--EEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHH
Q 018586 134 GPKAVAMDCEMVGGGS-NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILE 210 (353)
Q Consensus 134 ~~~~~~~D~Ettg~~~-~~~~~il~~v~ivd~~g~~--~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~ 210 (353)
..+|+++|+||||.++ ++++++ ++|.+ .+|++ .|.++|+|..+|++.++.+||||++||+++|+|++|+++|.+
T Consensus 6 ~~~~vvvD~ETTGl~~~d~IIeI-gaV~v--~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~~~ 82 (820)
T PRK07246 6 LRKYAVVDLEATGAGPNASIIQV-GIVII--EGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYD 82 (820)
T ss_pred CCCEEEEEEecCCcCCCCeEEEE-EEEEE--ECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHHHH
Confidence 4679999999999863 567777 77777 35555 489999999999999999999999999999999999999999
Q ss_pred HHhcCCCCcccccCCCCCcEEEecccHHHHHHhcC-----cCC-CCceeecccccCCcccCCCCCcHHHHHHHHhCCcCC
Q 018586 211 ILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM-----NYP-DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQ 284 (353)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~-----~~~-~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~ 284 (353)
|+ ++.++||||+.||+.||+. .++ ..+.+||..+++.++|...+++|.+|++.| |++.
T Consensus 83 ~l--------------~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L~~~l-gl~~- 146 (820)
T PRK07246 83 LI--------------EDCIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLSREL-NIDL- 146 (820)
T ss_pred Hh--------------CCCEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHHHHHc-CCCC-
Confidence 99 8899999999999999972 222 256799999999999988899999999988 9985
Q ss_pred CCCCChHHHHHHHHHHHHHHHhchhh
Q 018586 285 SGVHDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 285 ~~~H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
.++|+|++||++|++||..+..+...
T Consensus 147 ~~~H~Al~DA~ata~L~~~l~~~l~~ 172 (820)
T PRK07246 147 ADAHTAIADARATAELFLKLLQKIES 172 (820)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 45999999999999999999987644
No 31
>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=99.93 E-value=1.1e-25 Score=192.35 Aligned_cols=150 Identities=21% Similarity=0.263 Sum_probs=118.6
Q ss_pred eeeccCcccccc---CCCCccceeEEeeecCC---C--------Ce--EEeeeccCCCCccccccccCCCCHhhhcCCCC
Q 018586 137 AVAMDCEMVGGG---SNGTLDLCARVCLVDED---E--------NV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMP 200 (353)
Q Consensus 137 ~~~~D~Ettg~~---~~~~~~il~~v~ivd~~---g--------~~--~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~ 200 (353)
|+++|+||||++ .++++|+ ++|.+.+.. + ++ .|+.+|+|..+|++.++.|||||++++.++|+
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iiei-~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a~~IhGIt~e~l~~~~~ 79 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITEL-CLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHKAP 79 (177)
T ss_pred CeEEeeecCCCCCCCCCceEEE-EEEEEecccccccccccccccceeeeeeEEeCCCCcCChhHHHHhCcCHHHHhcCCC
Confidence 689999999996 3577777 788774221 1 12 47999999999999999999999999999998
Q ss_pred hHH-HHHHHHHHHhcCCCCcccccCCCCCcEEEeccc-HHHHHHhc-------CcCC-CCceeecccccCCcccCCCCCc
Q 018586 201 LKE-VKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-------MNYP-DHMLRDTAKYRPLMKTNLVSHS 270 (353)
Q Consensus 201 ~~~-v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-------~~~~-~~~~~Dt~~l~~~~~~~~~~~~ 270 (353)
+++ +.+.+.+|+... +++.+|||||+ .||+.||+ ...+ ...++||+.+++.+.+ +
T Consensus 80 ~~~~~~~~l~~f~~~~----------~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~~-----~ 144 (177)
T cd06136 80 FDSDTANLIKLFLRRQ----------PKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ-----S 144 (177)
T ss_pred ccHHHHHHHHHHHHhc----------CCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhHh-----h
Confidence 874 667777777221 13469999998 89999997 2222 2456899999988765 8
Q ss_pred HHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHH
Q 018586 271 LKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKR 303 (353)
Q Consensus 271 L~~l~~~~~~~~~~~~~H~Al~Da~~t~~l~~~ 303 (353)
|+.|+++++|++ ..++|+|++||.+|+++|.+
T Consensus 145 L~~l~~~~~~~~-~~~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 145 LGSLYKRLFGQE-PKNSHTAEGDVLALLKCALH 176 (177)
T ss_pred HHHHHHHHhCCC-cccccchHHHHHHHHHHHhh
Confidence 999999765998 45599999999999999975
No 32
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.93 E-value=2.2e-25 Score=189.20 Aligned_cols=155 Identities=29% Similarity=0.487 Sum_probs=128.7
Q ss_pred eeeccCccccccCC--CCccceeEEeeecCCCCeEEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHhc
Q 018586 137 AVAMDCEMVGGGSN--GTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNN 214 (353)
Q Consensus 137 ~~~~D~Ettg~~~~--~~~~il~~v~ivd~~g~~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~~~~ 214 (353)
++++|+||||.++. .++++ +.|.+.+..-...|+.+|+|..++++.++++||||+++|.+++++.+|+.+|.+|+
T Consensus 2 ~v~~D~Ettg~~~~~~~Iiei-g~v~~~~~~~~~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~~~~~~~~~~~~~l-- 78 (169)
T smart00479 2 LVVIDCETTGLDPGKDEIIEI-AAVDVDGGRIIVVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL-- 78 (169)
T ss_pred EEEEEeeCCCCCCCCCeEEEE-EEEEEECCEeEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHHh--
Confidence 78999999998754 56666 55555322212359999999999999999999999999999999999999999999
Q ss_pred CCCCcccccCCCCCcEEEeccc-HHHHHHhcCc-------CCC-CceeecccccCCcccCCCCCcHHHHHHHHhCCcCCC
Q 018586 215 GESTGRLMLDDGKARLLVGHGL-EHDLDSLRMN-------YPD-HMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQS 285 (353)
Q Consensus 215 ~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~~~-------~~~-~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~ 285 (353)
++.++|+||. .||+.+|+.. .|. ..++|++.+++...+.. .++|+.|++.| |++..+
T Consensus 79 ------------~~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~-~~~L~~l~~~~-~~~~~~ 144 (169)
T smart00479 79 ------------KGKILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGR-KYSLKKLAERL-GLEVIG 144 (169)
T ss_pred ------------cCCEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCC-CCCHHHHHHHC-CCCCCC
Confidence 7778888888 9999999921 222 45799999988777653 89999999999 888554
Q ss_pred CCCChHHHHHHHHHHHHHHHhch
Q 018586 286 GVHDPYEDCVSVMRLYKRFRRQD 308 (353)
Q Consensus 286 ~~H~Al~Da~~t~~l~~~~~~~~ 308 (353)
.+|+|++||++|++||.++.+++
T Consensus 145 ~~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 145 RAHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred CCcCcHHHHHHHHHHHHHHHHHh
Confidence 45999999999999999998875
No 33
>PRK05168 ribonuclease T; Provisional
Probab=99.93 E-value=1.8e-25 Score=196.04 Aligned_cols=170 Identities=21% Similarity=0.291 Sum_probs=133.4
Q ss_pred ccCCCceeeccCccccccC--CCCccceeEEeee-cCCCCe----EEeeeccC--CCCccccccccCCCCHhh-hcCCCC
Q 018586 131 TCRGPKAVAMDCEMVGGGS--NGTLDLCARVCLV-DEDENV----IFHTYVQP--QLPVTNYRYEVTGLTEED-IKNAMP 200 (353)
Q Consensus 131 ~~~~~~~~~~D~Ettg~~~--~~~~~il~~v~iv-d~~g~~----~~~~lv~P--~~~i~~~~~~~~GIt~e~-l~~~~~ 200 (353)
......++++|+||||+++ ++++|+ ++|.+. +.+|.+ .|+++|+| ..+|++.++.|||||+++ ++++++
T Consensus 13 ~~~~~~~vv~D~ETTGl~~~~d~IieI-gaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~~~~ 91 (211)
T PRK05168 13 RFRGFLPVVIDVETAGFNAKTDALLEI-AAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAVS 91 (211)
T ss_pred HhcCCceEEEEeeCCCCCCCCCEEEEE-eEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhcCCC
Confidence 3456678999999999874 567777 777775 234543 58999999 468999999999999886 889999
Q ss_pred hHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCc----------CCCCceeecccccCCcccCCCCCc
Q 018586 201 LKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN----------YPDHMLRDTAKYRPLMKTNLVSHS 270 (353)
Q Consensus 201 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~----------~~~~~~~Dt~~l~~~~~~~~~~~~ 270 (353)
+.+++.++.+++...-. ....++.+|||||+.||++||+.. ++..+++||..+++.+++. .+
T Consensus 92 ~~~~l~~~~~~l~~~~~-----~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~~---~~ 163 (211)
T PRK05168 92 EKEALHEIFKMVRKGIK-----ASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALGQ---TV 163 (211)
T ss_pred hHHHHHHHHHHHHHHHH-----hcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcCC---CC
Confidence 99999999998821100 000136899999999999999821 1224589999999877653 58
Q ss_pred HHHHHHHHhCCcCCC-CCCChHHHHHHHHHHHHHHHhchhh
Q 018586 271 LKYLTRTYLGYDIQS-GVHDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 271 L~~l~~~~~~~~~~~-~~H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
|..+++.+ |+++.. .+|+|++||.+|++||.++.++..+
T Consensus 164 L~~l~~~~-gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~~ 203 (211)
T PRK05168 164 LAKACQAA-GIEFDNKEAHSALYDTEKTAELFCEIVNRWKR 203 (211)
T ss_pred HHHHHHHC-CCCCCCCCCCChHHHHHHHHHHHHHHHHHHHH
Confidence 99999998 998653 4899999999999999999998765
No 34
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.92 E-value=2e-25 Score=233.69 Aligned_cols=157 Identities=24% Similarity=0.413 Sum_probs=138.5
Q ss_pred CceeeccCccccccC---CCCccceeEEeeecCCCCe--EEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHH
Q 018586 135 PKAVAMDCEMVGGGS---NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKIL 209 (353)
Q Consensus 135 ~~~~~~D~Ettg~~~---~~~~~il~~v~ivd~~g~~--~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~ 209 (353)
.+|+++|+||||.++ ++++++ +.|.+ .+|++ .|+.+|+|..+|++.++.+||||+++|+++|+|++|+++|.
T Consensus 3 ~~~vvvD~ETTG~~p~~~d~IIei-gav~v--~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~l~ 79 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKGDKIIQI-AAVVV--EDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIV 79 (928)
T ss_pred CCEEEEEEeCCCCCCCCCCcEEEE-EEEEE--ECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHHHH
Confidence 569999999999863 457777 77777 45666 48999999999999999999999999999999999999999
Q ss_pred HHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcC-----cC--CCCceeecccccCCcccCCCCCcHHHHHHHHhCCc
Q 018586 210 EILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM-----NY--PDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 282 (353)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~-----~~--~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 282 (353)
+|+ ++.++||||+.||+.||+. ++ +..+++||..+++.++|...+++|.+|+++| |++
T Consensus 80 ~~l--------------~~~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~~~~L~~l~~~l-~i~ 144 (928)
T PRK08074 80 ELL--------------EGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEEL-GLE 144 (928)
T ss_pred HHh--------------CCCeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCCCCCHHHHHHhC-CCC
Confidence 999 8899999999999999982 22 3367899999999999988899999999998 888
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHhchhh
Q 018586 283 IQSGVHDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 283 ~~~~~H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
..++|+|++||.+|++||.++..+...
T Consensus 145 -~~~~H~Al~DA~ata~l~~~l~~~~~~ 171 (928)
T PRK08074 145 -HDQPHRADSDAEVTAELFLQLLNKLER 171 (928)
T ss_pred -CCCCCChHHHHHHHHHHHHHHHHHHHh
Confidence 446999999999999999999988754
No 35
>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=99.92 E-value=2e-25 Score=232.63 Aligned_cols=156 Identities=22% Similarity=0.338 Sum_probs=137.3
Q ss_pred ceeeccCcccccc--CCCCccceeEEeeecCCCCe--EEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHH
Q 018586 136 KAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 211 (353)
Q Consensus 136 ~~~~~D~Ettg~~--~~~~~~il~~v~ivd~~g~~--~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~ 211 (353)
+|+++|+||||.+ .++++++ +.|.+ .+|++ .|+.+|+|..+|++.++.+||||+++|+++|+|++|+++|.+|
T Consensus 1 ~~vvvD~ETTG~~~~~~~IIei-g~v~v--~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l~~~ 77 (850)
T TIGR01407 1 RYAVVDLETTGTQLSFDKIIQI-GIVVV--EDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDL 77 (850)
T ss_pred CEEEEEEECCCCCCCCCeEEEE-EEEEE--ECCEEEEEEEEEeCCCCCCChhhhhhcCcCHHHHhCCCCHHHHHHHHHHH
Confidence 3899999999986 3567777 67777 45665 4999999999999999999999999999999999999999999
Q ss_pred HhcCCCCcccccCCCCCcEEEecccHHHHHHhcC-----cC--CCCceeecccccCCcccCCCCCcHHHHHHHHhCCcCC
Q 018586 212 LNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM-----NY--PDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQ 284 (353)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~-----~~--~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~ 284 (353)
+ ++.++||||+.||+.||+. +. ...+++||+.+++.+.|...+++|.+|++.| |++.
T Consensus 78 l--------------~~~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~~~~L~~l~~~~-gi~~- 141 (850)
T TIGR01407 78 L--------------EDGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEAL-GLTH- 141 (850)
T ss_pred h--------------CCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCCCCCHHHHHHHC-CCCC-
Confidence 9 8899999999999999982 22 2366899999999998888899999999998 9985
Q ss_pred CCCCChHHHHHHHHHHHHHHHhchhh
Q 018586 285 SGVHDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 285 ~~~H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
.++|+|++||.+|++||.++..++..
T Consensus 142 ~~~H~Al~DA~ata~l~~~l~~~~~~ 167 (850)
T TIGR01407 142 ENPHRADSDAQATAELLLLLFEKMEK 167 (850)
T ss_pred CCCCChHHHHHHHHHHHHHHHHHHHh
Confidence 45999999999999999999888655
No 36
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.92 E-value=6.4e-25 Score=201.66 Aligned_cols=158 Identities=18% Similarity=0.261 Sum_probs=130.9
Q ss_pred ccCCCceeeccCccccccC--CCCccceeEEeeecCCCCe--EEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHH
Q 018586 131 TCRGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKD 206 (353)
Q Consensus 131 ~~~~~~~~~~D~Ettg~~~--~~~~~il~~v~ivd~~g~~--~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~ 206 (353)
.+...+|+++|+||||+++ +.++++ ++|.+. .+|++ .|..||+|..++.+ ..|||||+++|+++|+|.+|++
T Consensus 42 ~~~~~~fVvlDiETTGLdp~~drIIeI-gAV~i~-~~g~ive~f~tLVnP~~~~~p--~~LHGIT~e~La~AP~f~eVl~ 117 (377)
T PRK05601 42 AIEAAPFVAVSIQTSGIHPSTSRLITI-DAVTLT-ADGEEVEHFHAVLNPGEDPGP--FHLHGLSAEEFAQGKRFSQILK 117 (377)
T ss_pred CCCCCCEEEEEEECCCCCCCCCeEEEE-EEEEEE-cCCEEEEEEEEEECcCCCCCC--ccccCCCHHHHhcCCCHHHHHH
Confidence 4566789999999999974 456666 677663 35555 59999999986554 4699999999999999999999
Q ss_pred HHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCc---------------------------------CC-CCce
Q 018586 207 KILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN---------------------------------YP-DHML 252 (353)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~---------------------------------~~-~~~~ 252 (353)
+|.+|| ++.+|||||+.||++||... .| ...+
T Consensus 118 el~~fL--------------~g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~ 183 (377)
T PRK05601 118 PLDRLI--------------DGRTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVI 183 (377)
T ss_pred HHHHHh--------------CCCEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCE
Confidence 999999 89999999999999998731 12 2568
Q ss_pred eecccccCCcccCCCCCcHHHHHHHHhCCcCC---------CCCCChH--HHHHHHHHHHHHHHhc
Q 018586 253 RDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQ---------SGVHDPY--EDCVSVMRLYKRFRRQ 307 (353)
Q Consensus 253 ~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~---------~~~H~Al--~Da~~t~~l~~~~~~~ 307 (353)
+||+.+++.+.+...+|+|..|+++| |++.. ...|+|| +||+.+++||.++.+.
T Consensus 184 iDTL~LARrl~p~l~~~rL~~La~~l-Gi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~~~~ 248 (377)
T PRK05601 184 VDTLATARRQGVALDDIRIRGVAHTL-GLDAPAAEASVERAQVPHRQLCREETLLVARLYFALRAS 248 (377)
T ss_pred EEhHHHHHHHcCCCCCCCHHHHHHHh-CCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHhhcc
Confidence 99999999999998999999999998 98851 1268888 6999999999987433
No 37
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.91 E-value=2.5e-24 Score=200.21 Aligned_cols=161 Identities=40% Similarity=0.670 Sum_probs=144.3
Q ss_pred ccCCCceeeccCccccccCCCCccceeEEeeecCCCCeEEeeeccCCCCccccccccCCCCHhhhcCC-CChHHHHHHHH
Q 018586 131 TCRGPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNA-MPLKEVKDKIL 209 (353)
Q Consensus 131 ~~~~~~~~~~D~Ettg~~~~~~~~il~~v~ivd~~g~~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~-~~~~~v~~~~~ 209 (353)
.....+++++||||+.. ..+ .++ ++|.+||.+++++|+.+|+|..+|.+++|.++|||.++++++ .++.+|..++.
T Consensus 212 v~~~~~i~AlDCEm~~t-e~g-~el-~RVt~VD~~~~vi~D~fVkP~~~VvDy~T~~SGIT~~~~e~~t~tl~dvq~~l~ 288 (380)
T KOG2248|consen 212 VSKSPNIFALDCEMVVT-ENG-LEL-TRVTAVDRDGKVILDTFVKPNKPVVDYNTRYSGITEEDLENSTITLEDVQKELL 288 (380)
T ss_pred CCCCCCeEEEEeeeeee-ccc-eee-EEeeeeeccCcEEeEEeecCCCcccccccccccccHHHHhcCccCHHHHHHHHH
Confidence 35567899999999987 344 666 899999999999999999999999999999999999999866 58999999999
Q ss_pred HHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCcCCCCceeecccccCCcccC-CCCCcHHHHHHHHhCCcCCC--C
Q 018586 210 EILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLMKTN-LVSHSLKYLTRTYLGYDIQS--G 286 (353)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~-~~~~~L~~l~~~~~~~~~~~--~ 286 (353)
+|+ +.++|||||++++||+.|++.||. ++||+.++....+. ....+|+.|++.|||..|+. +
T Consensus 289 ~~~-------------~~~TILVGHSLenDL~aLKl~H~~--ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~~~ 353 (380)
T KOG2248|consen 289 ELI-------------SKNTILVGHSLENDLKALKLDHPS--VIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEGVG 353 (380)
T ss_pred hhc-------------CcCcEEEeechhhHHHHHhhhCCc--eeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhccCC
Confidence 998 488999999999999999999998 89999888777664 66788999999999999994 4
Q ss_pred CCChHHHHHHHHHHHHHHHhchh
Q 018586 287 VHDPYEDCVSVMRLYKRFRRQDH 309 (353)
Q Consensus 287 ~H~Al~Da~~t~~l~~~~~~~~~ 309 (353)
.|++.+||+++++|+....+...
T Consensus 354 ~HdS~eDA~acm~Lv~~k~~~~~ 376 (380)
T KOG2248|consen 354 GHDSVEDALACMKLVKLKIKNSE 376 (380)
T ss_pred CCccHHHHHHHHHHHHHHHhccc
Confidence 89999999999999998877654
No 38
>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=99.90 E-value=5.6e-24 Score=181.86 Aligned_cols=153 Identities=22% Similarity=0.265 Sum_probs=125.8
Q ss_pred eeeccCccccccC-------CCCccceeEEeeecCCCCe--EEeeeccCCC--CccccccccCCCCHhhhcCCCChHHHH
Q 018586 137 AVAMDCEMVGGGS-------NGTLDLCARVCLVDEDENV--IFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPLKEVK 205 (353)
Q Consensus 137 ~~~~D~Ettg~~~-------~~~~~il~~v~ivd~~g~~--~~~~lv~P~~--~i~~~~~~~~GIt~e~l~~~~~~~~v~ 205 (353)
|+++|+||||.+. ++++++ ++|.+.+..+.+ .|+.+|+|.. .+++.++++||||++++.+++++++|+
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieI-gav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~~~~~vl 79 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEI-GAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVL 79 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEE-EEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCCCHHHHH
Confidence 6899999999874 567777 666664333323 5999999998 899999999999999999999999999
Q ss_pred HHHHHHHhcCCCCcccccCCCCCc--EEEecccHHHHHHhc-------C---cCCCCceeecccccCCcccCCCCCcHHH
Q 018586 206 DKILEILNNGESTGRLMLDDGKAR--LLVGHGLEHDLDSLR-------M---NYPDHMLRDTAKYRPLMKTNLVSHSLKY 273 (353)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~--~lvgh~~~~D~~~l~-------~---~~~~~~~~Dt~~l~~~~~~~~~~~~L~~ 273 (353)
++|.+|+ ++. .+++|+..||..+|. . ......++|+..+++...+....++|.+
T Consensus 80 ~~~~~~l--------------~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~ 145 (176)
T cd06133 80 KEFLEWL--------------GKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSK 145 (176)
T ss_pred HHHHHHH--------------HhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHH
Confidence 9999999 554 455555689988766 1 1123678999999998888778999999
Q ss_pred HHHHHhCCcCCCCCCChHHHHHHHHHHHHHHH
Q 018586 274 LTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFR 305 (353)
Q Consensus 274 l~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~ 305 (353)
++++| |++..+..|+|++||++|++||.++.
T Consensus 146 l~~~~-gi~~~~~~H~Al~DA~~~a~l~~~~~ 176 (176)
T cd06133 146 ALEYL-GLEFEGRHHRGLDDARNIARILKRLL 176 (176)
T ss_pred HHHHC-CCCCCCCCcCcHHHHHHHHHHHHHhC
Confidence 99988 99976569999999999999999863
No 39
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=99.90 E-value=6.1e-24 Score=223.69 Aligned_cols=159 Identities=22% Similarity=0.384 Sum_probs=140.3
Q ss_pred CCCceeeccCcccccc--CCCCccceeEEeeecCCCCe--EEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHH
Q 018586 133 RGPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKI 208 (353)
Q Consensus 133 ~~~~~~~~D~Ettg~~--~~~~~~il~~v~ivd~~g~~--~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~ 208 (353)
....++++|+||||++ .++++|+ ++|.+. +|.+ .|+.+|+|..+|++.++++||||+++|++++++++|+++|
T Consensus 188 ~~~~~VVfDiETTGL~~~~d~IIEI-GAVkv~--~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f 264 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQYDEIIEF-GAVKVK--NGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKF 264 (1213)
T ss_pred cCCcEEEEEeEecCCCCCCCeEEEE-EEEEEE--CCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHH
Confidence 4568999999999986 4577777 788874 4555 4999999999999999999999999999999999999999
Q ss_pred HHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcC-----cCC--CCceeecccccCCcccCCCCCcHHHHHHHHhCC
Q 018586 209 LEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM-----NYP--DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGY 281 (353)
Q Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~-----~~~--~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~ 281 (353)
.+|+ ++.+|||||+.||+.||+. ..+ ...++||+.+++.+.|...+++|..|++++ |+
T Consensus 265 ~~fl--------------~~~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k~~kL~~Lak~l-gi 329 (1213)
T TIGR01405 265 KEFF--------------KDSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRLGNICKKL-GV 329 (1213)
T ss_pred HHHh--------------CCCeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCCCCCHHHHHHHc-CC
Confidence 9999 8899999999999999982 222 256899999999998888899999999998 99
Q ss_pred cCCCCCCChHHHHHHHHHHHHHHHhchhh
Q 018586 282 DIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 282 ~~~~~~H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
++.. +|+|++||.+|++||..+.++..+
T Consensus 330 ~~~~-~HrAl~DA~aTa~I~~~ll~~l~~ 357 (1213)
T TIGR01405 330 DLDD-HHRADYDAEATAKVFKVMVEQLKE 357 (1213)
T ss_pred CCCC-CcCHHHHHHHHHHHHHHHHHHHHH
Confidence 9654 999999999999999999987654
No 40
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.88 E-value=1.2e-22 Score=185.55 Aligned_cols=157 Identities=18% Similarity=0.236 Sum_probs=121.1
Q ss_pred ccCCCceeeccCccccccC--CCCccceeEEeeec-CCCCe-----EEeeeccCCCCccccccccCCCCHhhhcCCCChH
Q 018586 131 TCRGPKAVAMDCEMVGGGS--NGTLDLCARVCLVD-EDENV-----IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLK 202 (353)
Q Consensus 131 ~~~~~~~~~~D~Ettg~~~--~~~~~il~~v~ivd-~~g~~-----~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~ 202 (353)
......++++|+||||+++ +.++|+ +.|.+.. .+|.+ .|+.+++|..+|++.++.|||||++||++++...
T Consensus 33 ~~~~~~~vvlD~ETTGLd~~~d~IIEI-g~V~v~~~~~g~i~~v~~~~~~lv~P~~~I~~~~t~IhGIt~e~v~~~~~~~ 111 (294)
T PRK09182 33 GEFVRLGVILDTETTGLDPRKDEIIEI-GMVAFEYDDDGRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDP 111 (294)
T ss_pred CCCCCeEEEEEeeCCCCCCCCCeEEEE-EEEEEEecCCCceeeeeeEEEEEeCCCCCCCHHHHHhcCCCHHHHhcCCCcH
Confidence 3455678999999999974 567777 6777742 24543 4899999999999999999999999999988654
Q ss_pred HHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCc---CCCCceeecccccCCcccCCCCCcHHHHHHHHh
Q 018586 203 EVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN---YPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYL 279 (353)
Q Consensus 203 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~---~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~ 279 (353)
+ .|.+|+. ...+|||||+.||+.||+.. ++...+.+++....+..+...+++|.+|+..|
T Consensus 112 ~---~l~~fl~-------------~~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~~~~~~~~~~kL~~La~~~- 174 (294)
T PRK09182 112 A---AVDALIA-------------PADLIIAHNAGFDRPFLERFSPVFATKPWACSVSEIDWSARGFEGTKLGYLAGQA- 174 (294)
T ss_pred H---HHHHHhc-------------CCCEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHhhccccCCCCCHHHHHHHc-
Confidence 3 4667771 23699999999999999833 22344567765444444455789999999999
Q ss_pred CCcCCCCCCChHHHHHHHHHHHHHHHhc
Q 018586 280 GYDIQSGVHDPYEDCVSVMRLYKRFRRQ 307 (353)
Q Consensus 280 ~~~~~~~~H~Al~Da~~t~~l~~~~~~~ 307 (353)
|. ...+|+|+.||.+|++||..+...
T Consensus 175 g~--~~~aHrAl~Da~Ata~ll~~~l~~ 200 (294)
T PRK09182 175 GF--FHEGHRAVDDCQALLELLARPLPE 200 (294)
T ss_pred CC--CCCCcChHHHHHHHHHHHHHHHhh
Confidence 73 456999999999999999987643
No 41
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.88 E-value=1.5e-22 Score=182.09 Aligned_cols=157 Identities=25% Similarity=0.372 Sum_probs=136.0
Q ss_pred CceeeccCcccccc--CCCCccceeEEeeecCCCC-eEEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHH
Q 018586 135 PKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDEN-VIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 211 (353)
Q Consensus 135 ~~~~~~D~Ettg~~--~~~~~~il~~v~ivd~~g~-~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~ 211 (353)
.+++++|+||||.+ .++++++ ++|.+.+..-. ..|+.+|+|..+|++.+.++||||.++|.++|.|.+|++++.+|
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieI-gav~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~~~~~ 91 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEI-GAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPEFLDF 91 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEE-EeEEEECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHHHHHH
Confidence 67999999999986 6778888 88888544222 23899999988999999999999999999999999999999999
Q ss_pred HhcCCCCcccccCCCCC-cEEEecccHHHHHHhc-------CcCCCCceeecccccCCcccCCCCCcHHHHHHHHhCCcC
Q 018586 212 LNNGESTGRLMLDDGKA-RLLVGHGLEHDLDSLR-------MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDI 283 (353)
Q Consensus 212 ~~~~~~~~~~~~~~~~~-~~lvgh~~~~D~~~l~-------~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~ 283 (353)
+ ++ .++||||+.||+.||+ ...+...++||..+.+..+++...++|+.|+.++ |++.
T Consensus 92 i--------------~~~~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~~~L~~l~~~~-gi~~ 156 (243)
T COG0847 92 I--------------GGLRLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDALAERL-GIDR 156 (243)
T ss_pred H--------------CCCCeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCccchHHHHHHHc-CCCc
Confidence 9 66 9999999999999998 2223456789999999999988899999999988 8884
Q ss_pred CC-CCCChHHHHHHHHHHHHHHHhc
Q 018586 284 QS-GVHDPYEDCVSVMRLYKRFRRQ 307 (353)
Q Consensus 284 ~~-~~H~Al~Da~~t~~l~~~~~~~ 307 (353)
.. ..|+|+.||.+++++|..+...
T Consensus 157 ~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 157 NPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred CCcCCcchHHHHHHHHHHHHHHHhc
Confidence 32 2799999999999999999985
No 42
>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=99.88 E-value=6e-23 Score=176.43 Aligned_cols=148 Identities=22% Similarity=0.249 Sum_probs=114.6
Q ss_pred eeccCcccccc--CCCCccceeEEeeecCCCCe--EEeeeccCCC--CccccccccCCCCHhhhcC-CCChHHHHHHHHH
Q 018586 138 VAMDCEMVGGG--SNGTLDLCARVCLVDEDENV--IFHTYVQPQL--PVTNYRYEVTGLTEEDIKN-AMPLKEVKDKILE 210 (353)
Q Consensus 138 ~~~D~Ettg~~--~~~~~~il~~v~ivd~~g~~--~~~~lv~P~~--~i~~~~~~~~GIt~e~l~~-~~~~~~v~~~~~~ 210 (353)
+++|+||||++ .++++|+ +.|.+ +.++.+ .|+.+|+|.. ++++.+..+||||+++|++ ++++.+++++|.+
T Consensus 1 ~~~D~ETTGl~~~~d~Iiei-g~v~v-~~~~~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~~~ 78 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQF-AAIRT-DENFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKIHR 78 (183)
T ss_pred CEEEeecCCCCCCCCceEEE-EEEEE-CCCCCCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHHHH
Confidence 47999999987 3467777 56655 344344 4899999874 5777899999999999999 8999999999999
Q ss_pred HHhcCCCCcccccCCCCCcEEEecc-cHHHHHHhcCc-----CC--------CCceeecccccCCcc---c---------
Q 018586 211 ILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLRMN-----YP--------DHMLRDTAKYRPLMK---T--------- 264 (353)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~lvgh~-~~~D~~~l~~~-----~~--------~~~~~Dt~~l~~~~~---~--------- 264 (353)
|+ +..+.++|||| +.||+.||+.. .+ ....+||..+++... |
T Consensus 79 ~~------------~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~ 146 (183)
T cd06138 79 LF------------NTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKND 146 (183)
T ss_pred HH------------ccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCcccc
Confidence 99 22457899997 89999999821 11 123478887665432 2
Q ss_pred -CCCCCcHHHHHHHHhCCcCCCCCCChHHHHHHHHHHH
Q 018586 265 -NLVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLY 301 (353)
Q Consensus 265 -~~~~~~L~~l~~~~~~~~~~~~~H~Al~Da~~t~~l~ 301 (353)
...+++|++|+++| |++. .++|+|++||.+|++|.
T Consensus 147 ~~~~~~~L~~l~~~~-gi~~-~~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 147 DGKPSFKLEDLAQAN-GIEH-SNAHDALSDVEATIALA 182 (183)
T ss_pred CCCcchhHHHHHHHC-CCCc-cccccHHHHHHHHHHHh
Confidence 23578999999998 9984 56999999999999986
No 43
>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=99.88 E-value=2.2e-22 Score=168.28 Aligned_cols=147 Identities=28% Similarity=0.409 Sum_probs=124.3
Q ss_pred eeccCcccccc--CCCCccceeEEeeecCCCCe--EEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHh
Q 018586 138 VAMDCEMVGGG--SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILN 213 (353)
Q Consensus 138 ~~~D~Ettg~~--~~~~~~il~~v~ivd~~g~~--~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~~~ 213 (353)
+++|+||||.+ .++++|+ +.+.+ +.++++ .++.+|+|...+++..+.+|||+++++++++++.+++.+|.+++
T Consensus 1 v~~D~Ettg~~~~~~~iiei-~~v~~-~~~~~~~~~~~~~i~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~l- 77 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIEI-GAVKV-DGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFL- 77 (159)
T ss_pred CeEEeeCCCcCCCCCeEEEE-EEEEE-ECCcChhhhhheeeCcCCcCCHhheeccCCCHHHHhcCCCHHHHHHHHHHHH-
Confidence 57999999987 4566676 55555 333333 58999999999999999999999999999999999999999999
Q ss_pred cCCCCcccccCCCCCcEEEecccHHHHHHhcCc-------CCCCceeecccccCCcccCCCCCcHHHH-HHHHhCCcCCC
Q 018586 214 NGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-------YPDHMLRDTAKYRPLMKTNLVSHSLKYL-TRTYLGYDIQS 285 (353)
Q Consensus 214 ~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-------~~~~~~~Dt~~l~~~~~~~~~~~~L~~l-~~~~~~~~~~~ 285 (353)
++.++||||+.||+.+|+.. .+...++||+.+++.+.+....++|..+ ++.+ |++ ..
T Consensus 78 -------------~~~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~-~~~-~~ 142 (159)
T cd06127 78 -------------GGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERY-GIP-LE 142 (159)
T ss_pred -------------CCCEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCCCcCchHHHHHHHc-CCC-CC
Confidence 66899999999999999822 3347789999999999888888999998 6655 887 45
Q ss_pred CCCChHHHHHHHHHHHH
Q 018586 286 GVHDPYEDCVSVMRLYK 302 (353)
Q Consensus 286 ~~H~Al~Da~~t~~l~~ 302 (353)
.+|+|++||++|++||.
T Consensus 143 ~~H~Al~Da~~t~~l~~ 159 (159)
T cd06127 143 GAHRALADALATAELLL 159 (159)
T ss_pred CCCCcHHHHHHHHHHhC
Confidence 69999999999999983
No 44
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.87 E-value=8.9e-22 Score=190.82 Aligned_cols=174 Identities=18% Similarity=0.176 Sum_probs=134.0
Q ss_pred ccCCCceeeccCcccccc-----CCCCccceeEEeeecCCCCe--EEeeeccCCC--CccccccccCCCCHhhhcCCCCh
Q 018586 131 TCRGPKAVAMDCEMVGGG-----SNGTLDLCARVCLVDEDENV--IFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPL 201 (353)
Q Consensus 131 ~~~~~~~~~~D~Ettg~~-----~~~~~~il~~v~ivd~~g~~--~~~~lv~P~~--~i~~~~~~~~GIt~e~l~~~~~~ 201 (353)
...-..|+++|+||||.+ .++++|+ ++|.+-..+|++ .|+.||+|.. +++++++.+||||++||++||+|
T Consensus 52 ~q~~d~~IV~DlETTgl~~~~~~~dEIIEI-GaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap~F 130 (582)
T PTZ00315 52 PQPFDAYVVLDFEATCEADRRIEDAEVIEF-PMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPF 130 (582)
T ss_pred cCCCCeEEEEEEecCCCCCCCCCCCceEEE-EEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCCCH
Confidence 344578999999999975 2567777 677763346766 4899999986 69999999999999999999999
Q ss_pred HHHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHH-Hhc--------CcCC--CCceeecc-cccCCccc-----
Q 018586 202 KEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLD-SLR--------MNYP--DHMLRDTA-KYRPLMKT----- 264 (353)
Q Consensus 202 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~-~l~--------~~~~--~~~~~Dt~-~l~~~~~~----- 264 (353)
.+|+.+|.+|+.+.. +...+..+..+|+||..||+. ||. ...| ...++|+. .+++.+++
T Consensus 131 ~eVl~ef~~fL~~~~----~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p~~~~~ 206 (582)
T PTZ00315 131 PVVYCEALQFLAEAG----LGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFGNGSGC 206 (582)
T ss_pred HHHHHHHHHHHhccc----cccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCcccccc
Confidence 999999999994321 111112345799999999995 774 1333 24456653 45555444
Q ss_pred ------CCCCCcHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHhchhh
Q 018586 265 ------NLVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 265 ------~~~~~~L~~l~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
....++|.++++.+ |+++.+.+|+|++||++|++||.++++++..
T Consensus 207 ~~~~~~~~~~~~L~~al~~l-gL~~eGr~HrAlDDA~ntA~L~~~Ll~~g~~ 257 (582)
T PTZ00315 207 GGGATPPLGPSDMPDMLQML-GLPLQGRHHSGIDDCRNIAAVLCELLRRGLV 257 (582)
T ss_pred ccccccccCCcCHHHHHHHC-CCCCCCCCcCcHHHHHHHHHHHHHHHHcCCE
Confidence 34678999999988 9998777999999999999999999999775
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=99.87 E-value=2.8e-24 Score=180.40 Aligned_cols=149 Identities=27% Similarity=0.457 Sum_probs=125.5
Q ss_pred eeccCccccccC--CCCccceeEEeeecCC--CCeEEeeeccCCCC--ccccccccCCCCHhhhcCCCChHHHHHHHHHH
Q 018586 138 VAMDCEMVGGGS--NGTLDLCARVCLVDED--ENVIFHTYVQPQLP--VTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 211 (353)
Q Consensus 138 ~~~D~Ettg~~~--~~~~~il~~v~ivd~~--g~~~~~~lv~P~~~--i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~ 211 (353)
|++|+||||.+. +.++|+ ++|.+.+.. ....++.+|+|..+ +++.++.+||||+++|.+++++.+++.++.+|
T Consensus 1 v~~D~Ettg~~~~~~~iiei-g~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~~~~~ 79 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEI-GAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDEFEEF 79 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEE-EEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEE-EEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHhhhhh
Confidence 589999999875 677777 788886665 34479999999987 99999999999999999999999999999999
Q ss_pred HhcCCCCcccccCCCCCcEEEecccHHHHHHhc--------CcCC-CCceeecccccCCcccCCCCCcHHHHHHHHhCCc
Q 018586 212 LNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR--------MNYP-DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 282 (353)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~--------~~~~-~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 282 (353)
+. ++.++||||+.||..++. ..+| ...++|+..+.+...+....++|+.|++.| |++
T Consensus 80 ~~-------------~~~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~-~~~ 145 (164)
T PF00929_consen 80 LK-------------KNDILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNRKKYSLDDLAEYF-GIP 145 (164)
T ss_dssp HH-------------HHTEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHHHHHSHHHHHHHT-TSS
T ss_pred hh-------------cccccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhccccCCHHHHHHHc-CCC
Confidence 92 267999999889887776 2233 245789999888877766668999999999 888
Q ss_pred CCCCCCChHHHHHHHHHHH
Q 018586 283 IQSGVHDPYEDCVSVMRLY 301 (353)
Q Consensus 283 ~~~~~H~Al~Da~~t~~l~ 301 (353)
....+|+|++||++|++||
T Consensus 146 ~~~~~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 146 FDGTAHDALDDARATAELF 164 (164)
T ss_dssp STSTTTSHHHHHHHHHHHH
T ss_pred CCCCCcChHHHHHHHhCcC
Confidence 5554799999999999997
No 46
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.84 E-value=5.4e-21 Score=184.41 Aligned_cols=167 Identities=18% Similarity=0.250 Sum_probs=125.7
Q ss_pred CCCceeeccCccccccC--CCCccceeEEeeecCCCCe---EEeeeccCCCC--ccccccccCCCCHhhhcC-CCChHHH
Q 018586 133 RGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV---IFHTYVQPQLP--VTNYRYEVTGLTEEDIKN-AMPLKEV 204 (353)
Q Consensus 133 ~~~~~~~~D~Ettg~~~--~~~~~il~~v~ivd~~g~~---~~~~lv~P~~~--i~~~~~~~~GIt~e~l~~-~~~~~~v 204 (353)
....|+++|+||||+++ ++++++ |+|.+. .++.+ .++.+|+|... +++.++.|||||+++|.+ +.+..++
T Consensus 4 ~~~~fvv~D~ETTGLdP~~DrIIei-AaVrvd-~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~ 81 (476)
T PRK11779 4 MQPTFLWHDYETFGANPALDRPAQF-AGIRTD-ADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEF 81 (476)
T ss_pred CCCcEEEEEEECCCCCCCCCeeEEE-EEEEEe-CCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHH
Confidence 35569999999999974 667777 677663 33333 48999999853 456789999999999965 4579999
Q ss_pred HHHHHHHHhcCCCCcccccCCCCCcEEEecc-cHHHHHHhcCcCC----------------CCceeecccccCCcc----
Q 018586 205 KDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLRMNYP----------------DHMLRDTAKYRPLMK---- 263 (353)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~-~~~D~~~l~~~~~----------------~~~~~Dt~~l~~~~~---- 263 (353)
+.+|.+++. ..++++|||| +.||..||+..+. ...++|++.+...+.
T Consensus 82 ~~~i~~~l~------------~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i 149 (476)
T PRK11779 82 AARIHAEFS------------QPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGI 149 (476)
T ss_pred HHHHHHHHh------------cCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccc
Confidence 999999992 1368999997 7899999883210 122345555443322
Q ss_pred --c----CCCCCcHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHhchhhhhhhc
Q 018586 264 --T----NLVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQVEEIG 315 (353)
Q Consensus 264 --~----~~~~~~L~~l~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~~~~~~~~~ 315 (353)
| +..+++|..|+..+ |++ ..++|+|++||.+|++|++.+.++-.+++++.
T Consensus 150 ~~P~~~~g~~s~rLe~L~~~~-gI~-~~~AHdALsDa~aT~~la~~l~~~qP~l~~~~ 205 (476)
T PRK11779 150 NWPENEDGLPSFKLEHLTKAN-GIE-HENAHDAMSDVYATIAMAKLIKQKQPKLFDYL 205 (476)
T ss_pred cCcccccCCCCCcHHHHHHHc-CCC-CCCCCCcHHHHHHHHHHHHHHHHhChHHHHHH
Confidence 2 23679999999999 988 45699999999999999999998866665554
No 47
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.84 E-value=5e-21 Score=204.09 Aligned_cols=159 Identities=21% Similarity=0.391 Sum_probs=139.3
Q ss_pred CCCceeeccCcccccc--CCCCccceeEEeeecCCCCe--EEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHH
Q 018586 133 RGPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKI 208 (353)
Q Consensus 133 ~~~~~~~~D~Ettg~~--~~~~~~il~~v~ivd~~g~~--~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~ 208 (353)
...+++++|+||||++ .+.++++ +++.+ .+|.+ .|+.+|+|..++++.++.+||||+++|.+++++.+|+++|
T Consensus 417 ~~~~~VVfDLETTGL~~~~deIIEI-gAV~V--~~G~iie~F~~~V~P~~~I~~~~~~LTGIT~e~L~~aps~~EaL~~f 493 (1437)
T PRK00448 417 KDATYVVFDVETTGLSAVYDEIIEI-GAVKI--KNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKF 493 (1437)
T ss_pred ccCcEEEEEhhhcCCCCchhhhhee-eeEEE--eCCeEeeeEEEEECCCCCCCHHHHHHhCCCHHHHcCCCCHHHHHHHH
Confidence 3457999999999986 4567777 67777 45666 4899999999999999999999999999999999999999
Q ss_pred HHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhc-----Cc--CCCCceeecccccCCcccCCCCCcHHHHHHHHhCC
Q 018586 209 LEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR-----MN--YPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGY 281 (353)
Q Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~-----~~--~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~ 281 (353)
.+|+ ++.+|||||+.||+.||+ +. .+...++||+.+++.+.+...+++|..|++.| |+
T Consensus 494 ~~fi--------------gg~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k~~kL~~LAk~l-GL 558 (1437)
T PRK00448 494 KEFC--------------GDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKF-GV 558 (1437)
T ss_pred HHHh--------------CCCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccccccHHHHHHHc-CC
Confidence 9999 889999999999999986 22 23467899999999988888899999999998 99
Q ss_pred cCCCCCCChHHHHHHHHHHHHHHHhchhh
Q 018586 282 DIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 282 ~~~~~~H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
... ++|||++||.+|++||.++.++..+
T Consensus 559 ~~~-~~HrAl~DA~aTa~lf~~ll~~l~~ 586 (1437)
T PRK00448 559 ELE-HHHRADYDAEATAYLLIKFLKDLKE 586 (1437)
T ss_pred CCC-CCcChHHHHHHHHHHHHHHHHHHHH
Confidence 954 5899999999999999999988754
No 48
>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=99.83 E-value=4.2e-21 Score=163.39 Aligned_cols=151 Identities=17% Similarity=0.172 Sum_probs=110.7
Q ss_pred eeeccCccccccC--CCCccceeEEeeecCCCCe--EEeeeccCCCCcc----cccccc---CCCCHhhhcCCCChHHHH
Q 018586 137 AVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVT----NYRYEV---TGLTEEDIKNAMPLKEVK 205 (353)
Q Consensus 137 ~~~~D~Ettg~~~--~~~~~il~~v~ivd~~g~~--~~~~lv~P~~~i~----~~~~~~---~GIt~e~l~~~~~~~~v~ 205 (353)
++++|+||||+++ +.++|+ |+|.+.+..+.+ .|+.+|+|..+++ +++..+ ||||+++++++|++.+|+
T Consensus 1 lv~iD~ETTGl~p~~d~IieI-gaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~~vl 79 (173)
T cd06135 1 LVWIDLEMTGLDPEKDRILEI-ACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQAE 79 (173)
T ss_pred CEEEEEecCCCCCCCCeeEEE-EEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHHHHH
Confidence 4789999999974 567777 777653222333 4899999997655 344555 599999999999999999
Q ss_pred HHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCc-----CCC-Cceeec---ccccCCcccCCCCCcHHHHHH
Q 018586 206 DKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-----YPD-HMLRDT---AKYRPLMKTNLVSHSLKYLTR 276 (353)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-----~~~-~~~~Dt---~~l~~~~~~~~~~~~L~~l~~ 276 (353)
.+|.+|+.+.- .....+|||||+.||+.||+.. .+. .+.+|+ ..+++.+.|...+
T Consensus 80 ~~~~~f~~~~~--------~~~~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~~~l~~l~~~l~p~~~~-------- 143 (173)
T cd06135 80 AELLEFIKKYV--------PKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDVSSIKELARRWYPEIYR-------- 143 (173)
T ss_pred HHHHHHHHHhc--------CCCCCceeecchhhCHHHHHHHHHHHhccCCcchhhHHHHHHHHHHhCcHhhh--------
Confidence 99999993210 0134699999999999999832 221 446787 4466665554322
Q ss_pred HHhCCcCCCCCCChHHHHHHHHHHHHHHHhc
Q 018586 277 TYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQ 307 (353)
Q Consensus 277 ~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~ 307 (353)
+ ++. ....|||++||.+|+.+|+.+++.
T Consensus 144 -~-~~~-~~~~HrAl~Da~~~~~~~~~~~~~ 171 (173)
T cd06135 144 -K-APK-KKGTHRALDDIRESIAELKYYREN 171 (173)
T ss_pred -c-CCC-CCCCcchHHHHHHHHHHHHHHHHH
Confidence 2 555 455899999999999999998864
No 49
>PRK05359 oligoribonuclease; Provisional
Probab=99.83 E-value=1.6e-20 Score=160.39 Aligned_cols=154 Identities=18% Similarity=0.219 Sum_probs=116.1
Q ss_pred CCceeeccCcccccc--CCCCccceeEEeeecCCCCeE---EeeeccCCCC----ccccccccC---CCCHhhhcCCCCh
Q 018586 134 GPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENVI---FHTYVQPQLP----VTNYRYEVT---GLTEEDIKNAMPL 201 (353)
Q Consensus 134 ~~~~~~~D~Ettg~~--~~~~~~il~~v~ivd~~g~~~---~~~lv~P~~~----i~~~~~~~~---GIt~e~l~~~~~~ 201 (353)
..+|+++|+||||++ .++++|+ |+|.+ +.+..++ +..+|+|... +++.++.+| |||++++++++++
T Consensus 2 ~~~~vvlD~ETTGLdp~~d~IieI-gaV~~-~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~~ 79 (181)
T PRK05359 2 EDNLIWIDLEMTGLDPERDRIIEI-ATIVT-DADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVSE 79 (181)
T ss_pred CCcEEEEEeecCCCCCCCCeEEEE-EEEEE-cCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCCH
Confidence 356999999999987 4567777 66644 4444443 8899999865 466777777 8999999999999
Q ss_pred HHHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCcC-----C-CCceee--cc-cccCCcccCCCCCcHH
Q 018586 202 KEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY-----P-DHMLRD--TA-KYRPLMKTNLVSHSLK 272 (353)
Q Consensus 202 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~-----~-~~~~~D--t~-~l~~~~~~~~~~~~L~ 272 (353)
.+|+.+|.+|+...- ..++.+|||||+.||+.||+... + .++++| |. .+++.++|..
T Consensus 80 ~e~~~~~l~fl~~~~--------~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~tl~~l~r~~~P~~------ 145 (181)
T PRK05359 80 AEAEAQTLEFLKQWV--------PAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLDVSTLKELARRWKPEI------ 145 (181)
T ss_pred HHHHHHHHHHHHHhc--------CCCCCceeecchhhCHHHHHHHHHHhcccCCCcccchhHHHHHHHHhChhh------
Confidence 999999999993210 02467899999999999999332 1 255677 44 5677666642
Q ss_pred HHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHhchh
Q 018586 273 YLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDH 309 (353)
Q Consensus 273 ~l~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~~~ 309 (353)
+.+++ ..+.|||++||+++.++|+.+++...
T Consensus 146 -----~~~~~-~~~~HRal~D~~~s~~~~~~~~~~~~ 176 (181)
T PRK05359 146 -----LNGFK-KQGTHRALADIRESIAELKYYREHFF 176 (181)
T ss_pred -----hhCCC-CcCCcccHHHHHHHHHHHHHHHHHhc
Confidence 22666 55689999999999999999988753
No 50
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.74 E-value=1.3e-18 Score=151.62 Aligned_cols=119 Identities=21% Similarity=0.324 Sum_probs=104.7
Q ss_pred CCCceeeccccccccChHHHHHHHhhhcCCCCCC--ccccCcccCCChHHHHhcc---CCCCCCCCCCcccccc------
Q 018586 11 STARHKCVACYKQFKRKDHLIEHMKISYHSVHQP--KCAVCQKLSKSFESLREHL---TGPLSKAHCSGIFSDR------ 79 (353)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~~~h~~~~~--~C~~C~~~f~~~~~l~~H~---~~~~~c~~Cgk~f~~~------ 79 (353)
..-.|.|+.||+.+...++|.+|+.+|.-..++. .|..|++.+.+-..|..|+ +-+..|.+|||.|+++
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGH 206 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGH 206 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcc
Confidence 4567999999999999999999999922223333 9999999999999999999 3377899999999976
Q ss_pred ----------ccccccccccCchhHHHHHHHhcCCCCCCcccCCcchhhhhhhccccccc
Q 018586 80 ----------GCNLCMNIFDSPSSLIKHKEACSLSAPVPFEKTLSNAESQKKISGAIDEK 129 (353)
Q Consensus 80 ----------~C~~C~k~F~~~s~L~~H~~~h~~~k~~~c~~~~~~~~~~~~~~~~~~e~ 129 (353)
+|+.|+|+|.++|+|+.|+++|++.|+|+|+.|+-++...+++.++.+..
T Consensus 207 iRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~ 266 (279)
T KOG2462|consen 207 IRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSESA 266 (279)
T ss_pred cccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhhc
Confidence 39999999999999999999999999999999999999998888777654
No 51
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=99.62 E-value=8e-16 Score=151.92 Aligned_cols=165 Identities=26% Similarity=0.418 Sum_probs=138.8
Q ss_pred ccCCCceeeccCcccccc-------CCCCcc-------ceeEEeeecCCCC----eEEeeeccCCCCccccccccCCCCH
Q 018586 131 TCRGPKAVAMDCEMVGGG-------SNGTLD-------LCARVCLVDEDEN----VIFHTYVQPQLPVTNYRYEVTGLTE 192 (353)
Q Consensus 131 ~~~~~~~~~~D~Ettg~~-------~~~~~~-------il~~v~ivd~~g~----~~~~~lv~P~~~i~~~~~~~~GIt~ 192 (353)
.+.....|++|.|++.++ .|+..+ .+||+++|+.+|. +..|-||.....|.++.|++.||.+
T Consensus 906 mPk~g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msvARiScvRGeGp~eGiPFiDDYv~T~d~VvDYLTqySGI~P 985 (1118)
T KOG1275|consen 906 MPKSGDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSVARISCVRGEGPNEGIPFIDDYVSTDDKVVDYLTQYSGIKP 985 (1118)
T ss_pred cCCCCceeeeehhheecchHHhccccCCceeEeccccceeEEEEEEcccCCCCCCccccceecchhHHHHHHHHhcCCCc
Confidence 566778899999998754 233221 1489999987643 3569999999999999999999999
Q ss_pred hhhcCC------CChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCcCCCCceeecccccCCcccCC
Q 018586 193 EDIKNA------MPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLMKTNL 266 (353)
Q Consensus 193 e~l~~~------~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~ 266 (353)
.||.-. -+++.+..++.=++ +.|.+.|||++.+|+.++++.+|..+++||+.|+..- ..
T Consensus 986 GDLDp~~S~K~Lt~lK~~Y~Kl~~Li-------------~~GviFVGHGL~nDFrvINi~Vp~~QiiDTv~lf~~~--s~ 1050 (1118)
T KOG1275|consen 986 GDLDPTTSEKRLTTLKVLYLKLRLLI-------------QRGVIFVGHGLQNDFRVINIHVPEEQIIDTVTLFRLG--SQ 1050 (1118)
T ss_pred cccCCccCcceehhHHHHHHHHHHHH-------------HcCcEEEcccccccceEEEEecChhhheeeeEEEecc--cc
Confidence 999743 25777888887777 4889999999999999999999999999999998664 46
Q ss_pred CCCcHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHhchhh
Q 018586 267 VSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 267 ~~~~L~~l~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
+..+|+.||..+||..||.++|++++||+.++.||+++++--++
T Consensus 1051 R~LSLrfLa~~lLg~~IQ~~~HDSIeDA~taLkLYk~Yl~lkeq 1094 (1118)
T KOG1275|consen 1051 RMLSLRFLAWELLGETIQMEAHDSIEDARTALKLYKKYLKLKEQ 1094 (1118)
T ss_pred cEEEHHHHHHHHhcchhhccccccHHHHHHHHHHHHHHHHHHHh
Confidence 78999999999999999999999999999999999999876544
No 52
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.50 E-value=7e-15 Score=118.76 Aligned_cols=164 Identities=20% Similarity=0.287 Sum_probs=128.4
Q ss_pred CceeeccCcccccc------CCCCccceeEEeeecC-CCCe--EEeeeccCCC--CccccccccCCCCHhhhcCCCChHH
Q 018586 135 PKAVAMDCEMVGGG------SNGTLDLCARVCLVDE-DENV--IFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPLKE 203 (353)
Q Consensus 135 ~~~~~~D~Ettg~~------~~~~~~il~~v~ivd~-~g~~--~~~~lv~P~~--~i~~~~~~~~GIt~e~l~~~~~~~~ 203 (353)
..++++|.|.|... ...++++ ...+|+. +.++ .|.+||+|.. .++.++..+|||++..|.+||-|+.
T Consensus 4 ~~lLIID~EaT~~eG~~~~~e~eiiei--~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~apifs~ 81 (210)
T COG5018 4 NSLLIIDFEATMPEGKYSPQEFEIIEI--EAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAPIFSM 81 (210)
T ss_pred ceEEEEEeeeeccCCCCCchhceeeee--hhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhccccchHHH
Confidence 34789999999532 1223333 2333333 3333 4899999985 5788999999999999999999999
Q ss_pred HHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCc--------CC-CCceeecccccCCcccCCCCCcHHHH
Q 018586 204 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN--------YP-DHMLRDTAKYRPLMKTNLVSHSLKYL 274 (353)
Q Consensus 204 v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~--------~~-~~~~~Dt~~l~~~~~~~~~~~~L~~l 274 (353)
|+++|..||+.+++ ..+..++.|+ +.|++.|... .+ ..+++|....++.++...+-.+|..+
T Consensus 82 v~E~f~r~L~~h~P--------r~~~~wa~wG-~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~pr~tgln~a 152 (210)
T COG5018 82 VFEDFIRKLNEHDP--------RKNSTWATWG-NMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGDPRLTGLNKA 152 (210)
T ss_pred HHHHHHHHHHhcCc--------ccCCcccccc-chhHHHHHHHHHhcCCCCccccCccchHHHHHHHHhcCCccccHHHH
Confidence 99999999988875 1333577777 7999998811 12 26789999999888888777899999
Q ss_pred HHHHhCCcCCCCCCChHHHHHHHHHHHHHHHhchhh
Q 018586 275 TRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 275 ~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
++.+ |..+++.+|+||+||+.+++|++.+...-..
T Consensus 153 le~~-G~sf~G~~HraldDArn~~rl~klv~~~~~~ 187 (210)
T COG5018 153 LEEY-GDSFTGTHHRALDDARNAYRLFKLVEQDKQY 187 (210)
T ss_pred HHHh-ccccCCchhhhHHHHHHHHHHHHHHcchhhh
Confidence 9999 9999999999999999999999999877444
No 53
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=99.48 E-value=4.8e-14 Score=121.38 Aligned_cols=170 Identities=17% Similarity=0.286 Sum_probs=130.1
Q ss_pred CceeeccCcccccc------CCCCccceeEEeeecC-CCCe--EEeeeccCCC--CccccccccCCCCHhhhcCCCChHH
Q 018586 135 PKAVAMDCEMVGGG------SNGTLDLCARVCLVDE-DENV--IFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPLKE 203 (353)
Q Consensus 135 ~~~~~~D~Ettg~~------~~~~~~il~~v~ivd~-~g~~--~~~~lv~P~~--~i~~~~~~~~GIt~e~l~~~~~~~~ 203 (353)
.-++++|.|+|--. ...+||. .+|.+.+. .+.+ .|++||+|.. .++++++.+|||.++.|..||+|.+
T Consensus 56 dYLliiDFEaTC~e~~~~~~~~EIIEf-P~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~~f~~ 134 (280)
T KOG0542|consen 56 DYLLILDFEATCEEGNKPHYVQEIIEF-PAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAPTFPQ 134 (280)
T ss_pred ceEEEEeeeeeccccCCCCcchheeec-ceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCCCHHH
Confidence 34689999999532 3456666 45544443 4444 4899999984 6899999999999999999999999
Q ss_pred HHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHH-hc-------CcCCC--CceeecccccCCcccCCCCCcHHH
Q 018586 204 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDS-LR-------MNYPD--HMLRDTAKYRPLMKTNLVSHSLKY 273 (353)
Q Consensus 204 v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~-l~-------~~~~~--~~~~Dt~~l~~~~~~~~~~~~L~~ 273 (353)
|+.+|.+|+....-. ...++--+|..+ .-|+.. |. +..|. .++||.-+.++..+..+..-++..
T Consensus 135 vl~~f~~Wlr~~~~~-----~k~~~~Afvtdg-~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it~ 208 (280)
T KOG0542|consen 135 VLSEFDSWLRKDSLG-----DKNGKFAFVTDG-DWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNITG 208 (280)
T ss_pred HHHHHHHHHHHhhcc-----cccCceEEEeCc-hhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCHHH
Confidence 999999999544321 001455677766 445543 22 55664 788999988887766656778999
Q ss_pred HHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHhchhhhh
Q 018586 274 LTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQVE 312 (353)
Q Consensus 274 l~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~~~~~~ 312 (353)
+.+++ |+.+.+.+|+++.||+.+++|..+|.+.+.++.
T Consensus 209 mLe~~-gL~f~Gr~HsGiDDa~Nia~I~~kM~~dg~~~~ 246 (280)
T KOG0542|consen 209 MLEHY-GLQFEGRAHSGIDDARNIARIAQKMIRDGAEFR 246 (280)
T ss_pred HHHHh-CCcccCCcccCchhHHHHHHHHHHHHhCCcEEE
Confidence 99999 999999999999999999999999999987643
No 54
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.31 E-value=7.2e-13 Score=115.87 Aligned_cols=86 Identities=33% Similarity=0.571 Sum_probs=60.0
Q ss_pred CCCceeeccccccccChHHHHHHHhhhcCCCCCC-ccccCcccCCChHHHHhcc-----CCCCCCCCCCcccccc-----
Q 018586 11 STARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL-----TGPLSKAHCSGIFSDR----- 79 (353)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~~~h~~~~~-~C~~C~~~f~~~~~l~~H~-----~~~~~c~~Cgk~f~~~----- 79 (353)
..+.+.|+.|+|.|.+-..|+.|+++ |+ -+ +|..||+.|.+.=-|+.|+ +++|.|..|+|.|.+.
T Consensus 158 s~ka~~C~~C~K~YvSmpALkMHirT--H~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRA 233 (279)
T KOG2462|consen 158 SKKAFSCKYCGKVYVSMPALKMHIRT--HT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRA 233 (279)
T ss_pred ccccccCCCCCceeeehHHHhhHhhc--cC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHH
Confidence 35566677777777766666667766 55 23 6667777666665555665 3455566777776654
Q ss_pred -----------ccccccccccCchhHHHHHHH
Q 018586 80 -----------GCNLCMNIFDSPSSLIKHKEA 100 (353)
Q Consensus 80 -----------~C~~C~k~F~~~s~L~~H~~~ 100 (353)
+|..|+|+|...|-|..|...
T Consensus 234 HmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 234 HMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred HHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 499999999999999999874
No 55
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.14 E-value=1.1e-11 Score=120.24 Aligned_cols=112 Identities=21% Similarity=0.284 Sum_probs=90.1
Q ss_pred ceeeccccccccChHHHHHHHhhhcCCC-CCC-ccccCcccCCChHHHHhccCCCCCC---------CCCCccccccccc
Q 018586 14 RHKCVACYKQFKRKDHLIEHMKISYHSV-HQP-KCAVCQKLSKSFESLREHLTGPLSK---------AHCSGIFSDRGCN 82 (353)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~h~~-~~~-~C~~C~~~f~~~~~l~~H~~~~~~c---------~~Cgk~f~~~~C~ 82 (353)
...|+.|.+.+.+-..|+.|++.- |.. +.. .|..|..+|.....|.+|+.-..+| ..|.+.| +|.
T Consensus 210 lltcpycdrgykrltslkeHikyr-hekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKF---KCt 285 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYR-HEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKF---KCT 285 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHH-HhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccc---ccc
Confidence 457999999999999999999741 432 222 9999999999999999999222222 3344444 699
Q ss_pred cccccccCchhHHHHHHHhcCCCCCCcccCCcchhhhhhhccccccc
Q 018586 83 LCMNIFDSPSSLIKHKEACSLSAPVPFEKTLSNAESQKKISGAIDEK 129 (353)
Q Consensus 83 ~C~k~F~~~s~L~~H~~~h~~~k~~~c~~~~~~~~~~~~~~~~~~e~ 129 (353)
+|||+|..+-+|+.|.|+|+|||||.|++|+-.++.+.-|+.++..+
T Consensus 286 ECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSSK 332 (1007)
T KOG3623|consen 286 ECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSSK 332 (1007)
T ss_pred ccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccccc
Confidence 99999999999999999999999999999998888877787776544
No 56
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.13 E-value=2.8e-11 Score=119.51 Aligned_cols=46 Identities=17% Similarity=0.257 Sum_probs=41.0
Q ss_pred cccccccccCchhHHHHHHHhcCCCCCCcccCCcchhhhhhhcccc
Q 018586 81 CNLCMNIFDSPSSLIKHKEACSLSAPVPFEKTLSNAESQKKISGAI 126 (353)
Q Consensus 81 C~~C~k~F~~~s~L~~H~~~h~~~k~~~c~~~~~~~~~~~~~~~~~ 126 (353)
|+.||+.|...+.|..|+|+|+++|||.|.-|.+-+--...+|.+.
T Consensus 882 C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHM 927 (958)
T KOG1074|consen 882 CNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHM 927 (958)
T ss_pred hccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhh
Confidence 9999999999999999999999999999999987777666666544
No 57
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.08 E-value=3.8e-11 Score=100.09 Aligned_cols=108 Identities=23% Similarity=0.288 Sum_probs=86.0
Q ss_pred CCCCCCCceeeccccccccChHHHHHHHhhhcCCCCCC-ccccCcccCCChHHHHhcc---CCCCCCCCCCccccccccc
Q 018586 7 LPKRSTARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL---TGPLSKAHCSGIFSDRGCN 82 (353)
Q Consensus 7 ~~h~~~k~~~C~~C~k~f~~~~~l~~H~~~~~h~~~~~-~C~~C~~~f~~~~~l~~H~---~~~~~c~~Cgk~f~~~~C~ 82 (353)
-+.++...|.|..|+|.|....-|++|++. |+..+. .|..||+.|...-.|.+|+ +|..|+ .|+
T Consensus 110 gsssd~d~ftCrvCgK~F~lQRmlnrh~kc--h~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpy----------kc~ 177 (267)
T KOG3576|consen 110 GSSSDQDSFTCRVCGKKFGLQRMLNRHLKC--HSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPY----------KCS 177 (267)
T ss_pred cCCCCCCeeeeehhhhhhhHHHHHHHHhhh--ccHHHHHHHhhccCcccchhhhhhhhccccCcccc----------chh
Confidence 344567789999999999999999999999 888777 9999999999999999998 565565 588
Q ss_pred cccccccCchhHHHHHHH-hc----------CCCCCCcccCCcchhhhhhhcccc
Q 018586 83 LCMNIFDSPSSLIKHKEA-CS----------LSAPVPFEKTLSNAESQKKISGAI 126 (353)
Q Consensus 83 ~C~k~F~~~s~L~~H~~~-h~----------~~k~~~c~~~~~~~~~~~~~~~~~ 126 (353)
.|+|+|+++.+|..|.+. |. ++|.|.|+.|+.+.+....+..+.
T Consensus 178 ~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~ 232 (267)
T KOG3576|consen 178 LCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHL 232 (267)
T ss_pred hhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHH
Confidence 999999999999999664 42 466777777776655444444433
No 58
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=99.05 E-value=4.9e-10 Score=90.52 Aligned_cols=154 Identities=18% Similarity=0.292 Sum_probs=108.2
Q ss_pred CCCceeeccCccccccC--CCCccceeEEeeecCCCCeEE---eeeccCC----CCcccccccc---CCCCHhhhcCCCC
Q 018586 133 RGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENVIF---HTYVQPQ----LPVTNYRYEV---TGLTEEDIKNAMP 200 (353)
Q Consensus 133 ~~~~~~~~D~Ettg~~~--~~~~~il~~v~ivd~~g~~~~---~~lv~P~----~~i~~~~~~~---~GIt~e~l~~~~~ 200 (353)
...+.+.+||||||+++ ++++|+ +..|-|.+.+++- +..|... ..+.+++++- +|++..-.+...+
T Consensus 4 ~~~nLiWIDlEMTGLd~~~drIIEi--A~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~t 81 (184)
T COG1949 4 NKNNLIWIDLEMTGLDPERDRIIEI--ATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTVT 81 (184)
T ss_pred cCCceEEEeeeeccCCcCcceEEEE--EEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhcc
Confidence 45679999999999984 556666 4444466766653 3333333 2455666655 4777776677789
Q ss_pred hHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCcCCC------CceeecccccCCcccCCCCCcHHHH
Q 018586 201 LKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPD------HMLRDTAKYRPLMKTNLVSHSLKYL 274 (353)
Q Consensus 201 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~------~~~~Dt~~l~~~~~~~~~~~~L~~l 274 (353)
..++..++++||+.-- ..+.++|.|.++.-|..||....|. ++.+|+.. |++|
T Consensus 82 ~~~aE~~~l~flkkwv--------p~~~spicGNSI~qDRrFl~r~MP~Le~yfHYR~lDVST-------------lKEL 140 (184)
T COG1949 82 EAEAEAQTLDFLKKWV--------PKGVSPICGNSIAQDRRFLFRYMPKLEAYFHYRYLDVST-------------LKEL 140 (184)
T ss_pred HHHHHHHHHHHHHHhC--------CCCCCCCccchhhHHHHHHHHHhhhHHHHhhhHhhhHHH-------------HHHH
Confidence 9999999999994332 2377899999999999999966664 55677653 3444
Q ss_pred HHHH-----hCCcCCCCCCChHHHHHHHHHHHHHHHhchhh
Q 018586 275 TRTY-----LGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 275 ~~~~-----~~~~~~~~~H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
|.+. .|.. .++.|+||+|.+-...-++.+++.+-.
T Consensus 141 a~RW~P~i~~~~~-K~~~H~Al~DI~ESI~EL~~YR~~f~~ 180 (184)
T COG1949 141 ARRWNPEILAGFK-KGGTHRALDDIRESIAELRYYREHFLK 180 (184)
T ss_pred HHhhCcHhhhccc-cccchhHHHHHHHHHHHHHHHHHHhcc
Confidence 4333 2323 566999999999999998888887543
No 59
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.03 E-value=5.9e-11 Score=106.64 Aligned_cols=106 Identities=26% Similarity=0.428 Sum_probs=92.1
Q ss_pred eccccccccChHHHHHHHhhhcCCCCCC-ccccCcccCCChHHHHhcc-------CCCCCCCCCCcccccc---------
Q 018586 17 CVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL-------TGPLSKAHCSGIFSDR--------- 79 (353)
Q Consensus 17 C~~C~k~f~~~~~l~~H~~~~~h~~~~~-~C~~C~~~f~~~~~l~~H~-------~~~~~c~~Cgk~f~~~--------- 79 (353)
+..|-+.+..++.|.+|.+. |++++. .|..||..|+.+..|-.|. ..++.|..|-|+|...
T Consensus 182 W~~Ct~~~~~k~~LreH~r~--Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~r 259 (467)
T KOG3608|consen 182 WAMCTKHMGNKYRLREHIRT--HSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVR 259 (467)
T ss_pred chhhhhhhccHHHHHHHHHh--cCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHH
Confidence 34699999999999999999 999999 9999999999999999998 4578899999999875
Q ss_pred -----ccccccccccCchhHHHHHH-HhcCCCCCCcccCCcchhhhhhhcc
Q 018586 80 -----GCNLCMNIFDSPSSLIKHKE-ACSLSAPVPFEKTLSNAESQKKISG 124 (353)
Q Consensus 80 -----~C~~C~k~F~~~s~L~~H~~-~h~~~k~~~c~~~~~~~~~~~~~~~ 124 (353)
+|+.|+-+...+++|..|++ .|+.+|||+|..|..+.-..+.+.+
T Consensus 260 Hvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~k 310 (467)
T KOG3608|consen 260 HVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAK 310 (467)
T ss_pred hhhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHH
Confidence 49999999999999999998 5889999999998766444444443
No 60
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=99.02 E-value=8.5e-10 Score=100.64 Aligned_cols=170 Identities=19% Similarity=0.224 Sum_probs=123.1
Q ss_pred CCceeeccCccccccC--CCCccceeEEeeecCCCCe---EEeeeccCCCC-cc-ccccccCCCCHhhhc-CCCChHHHH
Q 018586 134 GPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV---IFHTYVQPQLP-VT-NYRYEVTGLTEEDIK-NAMPLKEVK 205 (353)
Q Consensus 134 ~~~~~~~D~Ettg~~~--~~~~~il~~v~ivd~~g~~---~~~~lv~P~~~-i~-~~~~~~~GIt~e~l~-~~~~~~~v~ 205 (353)
...|.+.|-||.|..+ ++..+. +.|.- |.+-++ ...-|++|... +| +.+.-|||||++... ++.+-.+..
T Consensus 8 ~~tF~~yDYETfG~~Pa~DRPaQF-AgiRT-D~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~F~ 85 (475)
T COG2925 8 QPTFLFYDYETFGVHPALDRPAQF-AGIRT-DIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAAFA 85 (475)
T ss_pred CCcEEEEehhhcCCCcccccchhh-heeec-cccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHHHH
Confidence 4569999999999873 455555 44443 344444 36889999853 33 567789999988865 778888888
Q ss_pred HHHHHHHhcCCCCcccccCCCCCcEEEecc-cHHHHHHhcCc------CC----------CCceeecccccCCccc----
Q 018586 206 DKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLRMN------YP----------DHMLRDTAKYRPLMKT---- 264 (353)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~-~~~D~~~l~~~------~~----------~~~~~Dt~~l~~~~~~---- 264 (353)
..|...+ .--++.++|+| +.||-.+-+.. -| +..++|++...--+.|
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 9998888 33678999987 88898887711 11 1223444443323333
Q ss_pred ------CCCCCcHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHhchhhhhhhcccCC
Q 018586 265 ------NLVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQVEEIGNQNT 319 (353)
Q Consensus 265 ------~~~~~~L~~l~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~~~~~~~~~~~~~ 319 (353)
+..+++|+.|...- |+. .+++|+|++|++||..+.+.+..+-..+++|-++..
T Consensus 154 Wp~n~dG~pSFkLEhLt~AN-gie-H~nAHdAmsDVyATIamAklvk~~QPrLfdy~f~~R 212 (475)
T COG2925 154 WPENDDGLPSFKLEHLTKAN-GIE-HSNAHDAMSDVYATIAMAKLVKTAQPRLFDYLFQLR 212 (475)
T ss_pred CCcCCCCCcchhhHHHhhcc-ccc-cchhhHHHHHHHHHHHHHHHHHhhCcHHHHHHHHhc
Confidence 34479999999988 888 677999999999999999999988888888876543
No 61
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.01 E-value=2.7e-10 Score=112.61 Aligned_cols=48 Identities=31% Similarity=0.642 Sum_probs=46.0
Q ss_pred ceeeccccccccChHHHHHHHhhhcCCCCCC-ccccCcccCCChHHHHhcc
Q 018586 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL 63 (353)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~h~~~~~-~C~~C~~~f~~~~~l~~H~ 63 (353)
+++|-.|.+.|.+.+.|+.|.|. |++++| +|+.||..|..+.+|+.|.
T Consensus 353 khkCr~CakvfgS~SaLqiHlRS--HTGERPfqCnvCG~~FSTkGNLKvH~ 401 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRS--HTGERPFQCNVCGNRFSTKGNLKVHF 401 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhc--cCCCCCeeecccccccccccceeeee
Confidence 57899999999999999999999 999999 9999999999999999997
No 62
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=98.98 E-value=8.3e-10 Score=90.00 Aligned_cols=156 Identities=17% Similarity=0.254 Sum_probs=109.4
Q ss_pred CCCceeeccCcccccc--CCCCccceeEEeeecCCCCeE---EeeeccCCC----Ccccccccc---CCCCHhhhcCCCC
Q 018586 133 RGPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENVI---FHTYVQPQL----PVTNYRYEV---TGLTEEDIKNAMP 200 (353)
Q Consensus 133 ~~~~~~~~D~Ettg~~--~~~~~~il~~v~ivd~~g~~~---~~~lv~P~~----~i~~~~~~~---~GIt~e~l~~~~~ 200 (353)
-..++|.+||||||++ .+.++|+ +..|-|.+..++ ++..|+... .+.++...- +|+|..-++...+
T Consensus 24 l~q~lVWiD~EMTGLdvekd~i~Ei--acIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~t 101 (208)
T KOG3242|consen 24 LKQPLVWIDCEMTGLDVEKDRIIEI--ACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKIT 101 (208)
T ss_pred ccCceEEEeeeccccccccceeEEE--EEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhcc
Confidence 4567999999999987 5667666 444545655553 567776553 344444433 5888888889999
Q ss_pred hHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCcCC------CCceeeccc---ccCCcccCCCCCcH
Q 018586 201 LKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP------DHMLRDTAK---YRPLMKTNLVSHSL 271 (353)
Q Consensus 201 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~------~~~~~Dt~~---l~~~~~~~~~~~~L 271 (353)
+++|-.++++||.-. . ..+..+|.|.++-.|..||.-.+| .+++||+.. |++.++|....
T Consensus 102 l~~aEnevl~yikk~------i--p~~~~~laGNSV~~DrlFl~k~mPk~~~~lhyrivDVStIkeL~~Rw~P~~~~--- 170 (208)
T KOG3242|consen 102 LADAENEVLEYIKKH------I--PKGKCPLAGNSVYMDRLFLKKYMPKLIKHLHYRIVDVSTIKELARRWYPDIKA--- 170 (208)
T ss_pred HHHHHHHHHHHHHHh------C--CCCCCCccCcchhhHHHHHHHHhHHHHHhcceeeeeHHHHHHHHHHhCchhhc---
Confidence 999999999999322 2 247779999999999999994444 377889764 44444443111
Q ss_pred HHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHhchh
Q 018586 272 KYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDH 309 (353)
Q Consensus 272 ~~l~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~~~ 309 (353)
+ -+-....|||+.|.+....-+..+++.+-
T Consensus 171 ------~--aPkK~~~HrAldDI~ESI~ELq~Yr~nif 200 (208)
T KOG3242|consen 171 ------R--APKKKATHRALDDIRESIKELQYYRENIF 200 (208)
T ss_pred ------c--CcccccccchHHHHHHHHHHHHHHHHHhc
Confidence 1 02133389999999999988888887753
No 63
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.80 E-value=2e-09 Score=104.88 Aligned_cols=78 Identities=28% Similarity=0.548 Sum_probs=61.9
Q ss_pred CCCCceeeccccccccChHHHHHHHhhhcCCCCCC-ccccCcccCCChHHHHhcc---CCCCCCCCCCcccccccccccc
Q 018586 10 RSTARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL---TGPLSKAHCSGIFSDRGCNLCM 85 (353)
Q Consensus 10 ~~~k~~~C~~C~k~f~~~~~l~~H~~~~~h~~~~~-~C~~C~~~f~~~~~l~~H~---~~~~~c~~Cgk~f~~~~C~~C~ 85 (353)
+.+..|.|+.|+|.|...+.|.+|.-- |+|++| +|..|.+.|..+..|..|+ .|++++ .|..|+
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYE--HsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPf----------QCdKCl 957 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYE--HSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPF----------QCDKCL 957 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhh--hcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcc----------hhhhhh
Confidence 445678899999999888889999887 888888 8888888888888888887 566665 467777
Q ss_pred ccccCchhHHHHHH
Q 018586 86 NIFDSPSSLIKHKE 99 (353)
Q Consensus 86 k~F~~~s~L~~H~~ 99 (353)
|.|....+..+||.
T Consensus 958 KRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 958 KRFSHSGSYSQHMN 971 (1007)
T ss_pred hhcccccchHhhhc
Confidence 77777777777774
No 64
>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=98.71 E-value=4e-08 Score=85.54 Aligned_cols=125 Identities=15% Similarity=0.147 Sum_probs=85.0
Q ss_pred eeccCccccc----cCCCCccceeEEeeecC-CCCeE-EeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHH
Q 018586 138 VAMDCEMVGG----GSNGTLDLCARVCLVDE-DENVI-FHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 211 (353)
Q Consensus 138 ~~~D~Ettg~----~~~~~~~il~~v~ivd~-~g~~~-~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~ 211 (353)
+++|+||+|. ++. ..++ ..++++.. +|... +.....+.....+ ||+..+|...++..+++..|.++
T Consensus 2 ~~~DIEt~~~~~~p~~~-~d~I-i~I~~~~~~~g~~~~~~~~~~~~~~~~~------~i~~~~v~~~~~E~~lL~~f~~~ 73 (199)
T cd05160 2 LSFDIETTPPVGGPEPD-RDPI-ICITYADSFDGVKVVFLLKTSTVGDDIE------FIDGIEVEYFADEKELLKRFFDI 73 (199)
T ss_pred ccEEEeecCCCCCcCCC-CCCE-EEEEEEEeeCCceeeEEEeecccCCcCC------CCCCceEEEeCCHHHHHHHHHHH
Confidence 6799999997 221 2223 24444433 55543 2222222221111 88888999999999999999999
Q ss_pred HhcCCCCcccccCCCCCcEEEeccc-HHHHHHhc-----CcCC------------------------CCceeecccccCC
Q 018586 212 LNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-----MNYP------------------------DHMLRDTAKYRPL 261 (353)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-----~~~~------------------------~~~~~Dt~~l~~~ 261 (353)
+.+. ...+|||||+ .||+.+|. +..+ ...++|+..+.+.
T Consensus 74 i~~~-----------dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~ 142 (199)
T cd05160 74 IREY-----------DPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKR 142 (199)
T ss_pred HHhc-----------CCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHH
Confidence 9432 1259999999 89999988 1111 1246899888877
Q ss_pred cccCCCCCcHHHHHHHHhCCc
Q 018586 262 MKTNLVSHSLKYLTRTYLGYD 282 (353)
Q Consensus 262 ~~~~~~~~~L~~l~~~~~~~~ 282 (353)
..+ ..+|+|+++++.++|..
T Consensus 143 ~~~-l~sy~L~~v~~~~l~~~ 162 (199)
T cd05160 143 DFK-LKSYTLDAVAEELLGEG 162 (199)
T ss_pred hcC-cccCCHHHHHHHHhCCC
Confidence 665 78899999999997765
No 65
>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=98.67 E-value=2e-07 Score=80.45 Aligned_cols=145 Identities=21% Similarity=0.250 Sum_probs=96.8
Q ss_pred CCceeeccCccccccCCCCccceeEEeeecCCCCeEEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHh
Q 018586 134 GPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILN 213 (353)
Q Consensus 134 ~~~~~~~D~Ettg~~~~~~~~il~~v~ivd~~g~~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~~~ 213 (353)
..+++++|+|++|..+-. ..+ ..+.+....+...+ + |. .. +. ..+++++.+++..+.+++.
T Consensus 4 ~~~~~a~d~e~~~~~~~~-~~i-~~l~~~~~~~~~~~---~-~~---~~--~~--------~~~~~~~~~~~~~l~~~l~ 64 (193)
T cd06139 4 KAKVFAFDTETTSLDPMQ-AEL-VGISFAVEPGEAYY---I-PL---GH--DY--------GGEQLPREEVLAALKPLLE 64 (193)
T ss_pred cCCeEEEEeecCCCCcCC-CeE-EEEEEEcCCCCEEE---E-ec---CC--Cc--------cccCCCHHHHHHHHHHHHh
Confidence 456789999999875311 122 34555434443322 1 10 00 00 1145678889999999992
Q ss_pred cCCCCcccccCCCCCcEEEecccHHHHHHhcC---cCCCCceeecccccCCcccCCCCCcHHHHHHHHhCCcC-C-----
Q 018586 214 NGESTGRLMLDDGKARLLVGHGLEHDLDSLRM---NYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDI-Q----- 284 (353)
Q Consensus 214 ~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~---~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~-~----- 284 (353)
+.+.++|+||+.||+.+|.. ..+ ..++||+.++..+.|....++|+++++.|++..+ .
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 23358999999999999972 222 4578999999988886535799999999976541 0
Q ss_pred ----------C-----CCCChHHHHHHHHHHHHHHHhchhh
Q 018586 285 ----------S-----GVHDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 285 ----------~-----~~H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
. ..|.|..||.++.+|+..+..+.++
T Consensus 132 ~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 132 GKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred CCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 0 1235888999999999999887643
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=98.64 E-value=3.2e-07 Score=77.83 Aligned_cols=92 Identities=28% Similarity=0.356 Sum_probs=65.9
Q ss_pred HHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcC--cCCCCceeecccccCCcccCCCCCcHHHHHHHHhC-
Q 018586 204 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM--NYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLG- 280 (353)
Q Consensus 204 v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~--~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~- 280 (353)
+.+.+.+++ .+.+.+.||||+.||+.+|.. +.+...++|| .++..+.....+++|++|+..++|
T Consensus 65 ~~~~l~~ll------------~~~~i~kv~~n~~~D~~~L~~~~~i~~~~~~D~-~l~~~~l~~~~~~~L~~L~~~~l~~ 131 (176)
T PF01612_consen 65 ILDALKELL------------EDPNIIKVGHNAKFDLKWLYRSFGIDLKNVFDT-MLAAYLLDPTRSYSLKDLAEEYLGN 131 (176)
T ss_dssp HHHHHHHHH------------TTTTSEEEESSHHHHHHHHHHHHTS--SSEEEH-HHHHHHTTTSTTSSHHHHHHHHHSE
T ss_pred hHHHHHHHH------------hCCCccEEEEEEechHHHHHHHhccccCCccch-hhhhhcccccccccHHHHHHHHhhh
Confidence 777888888 345679999999999999993 3344568999 444444433344999999999999
Q ss_pred CcCCCC----CC---C---------hHHHHHHHHHHHHHHHhch
Q 018586 281 YDIQSG----VH---D---------PYEDCVSVMRLYKRFRRQD 308 (353)
Q Consensus 281 ~~~~~~----~H---~---------Al~Da~~t~~l~~~~~~~~ 308 (353)
...... .- + |..||..+.+||..+..+.
T Consensus 132 ~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l 175 (176)
T PF01612_consen 132 IDLDKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQL 175 (176)
T ss_dssp EE-GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred ccCcHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 433211 12 2 5669999999999998764
No 67
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.63 E-value=2.4e-09 Score=89.46 Aligned_cols=102 Identities=25% Similarity=0.312 Sum_probs=80.8
Q ss_pred CCCCCCCCCCCceeeccccccccChHHHHHHHhhhcCCCCCC-ccccCcccCCChHHHHhcc---CC-CCCCCCCCcccc
Q 018586 3 TEAELPKRSTARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL---TG-PLSKAHCSGIFS 77 (353)
Q Consensus 3 ~~~~~~h~~~k~~~C~~C~k~f~~~~~l~~H~~~~~h~~~~~-~C~~C~~~f~~~~~l~~H~---~~-~~~c~~Cgk~f~ 77 (353)
|+....|+.-|.|-|.-||+.|..--+|++|+++ |++.+| +|..|++.|.+.-+|..|. .+ +.++..=.++-.
T Consensus 134 nrh~kch~~vkr~lct~cgkgfndtfdlkrh~rt--htgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~k 211 (267)
T KOG3576|consen 134 NRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRT--HTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAK 211 (267)
T ss_pred HHHhhhccHHHHHHHhhccCcccchhhhhhhhcc--ccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhh
Confidence 4556788889999999999999999999999999 999999 9999999999999999998 22 111111112222
Q ss_pred ccccccccccccCchhHHHHHHHhcCCCC
Q 018586 78 DRGCNLCMNIFDSPSSLIKHKEACSLSAP 106 (353)
Q Consensus 78 ~~~C~~C~k~F~~~s~L~~H~~~h~~~k~ 106 (353)
...|..||.+-.....+..|...|+...|
T Consensus 212 l~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 212 LYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred eeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 23589999988888888899998876555
No 68
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.57 E-value=2.7e-08 Score=89.77 Aligned_cols=139 Identities=17% Similarity=0.223 Sum_probs=105.0
Q ss_pred CCCCCCCCceeeccccccccChHHHHHHHhhhcCCCCCC-ccccCcccCCChHHHHhcc---CCCCCCCCCCcccccc--
Q 018586 6 ELPKRSTARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL---TGPLSKAHCSGIFSDR-- 79 (353)
Q Consensus 6 ~~~h~~~k~~~C~~C~k~f~~~~~l~~H~~~~~h~~~~~-~C~~C~~~f~~~~~l~~H~---~~~~~c~~Cgk~f~~~-- 79 (353)
.|+|+++|.-.|+.||.-|..+..|-.|.+.-.--...+ .|..|.+.|....-|..|+ ...+.|+.|.-+.+..
T Consensus 199 ~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ss 278 (467)
T KOG3608|consen 199 IRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASS 278 (467)
T ss_pred HHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHH
Confidence 578999999999999999999999999986400223445 9999999999999999998 3467888888777754
Q ss_pred ---------------ccccccccccCchhHHHHHHHhcCCCCCCccc--CCcchhhhhhhcccccccc-ccCCCceeecc
Q 018586 80 ---------------GCNLCMNIFDSPSSLIKHKEACSLSAPVPFEK--TLSNAESQKKISGAIDEKR-TCRGPKAVAMD 141 (353)
Q Consensus 80 ---------------~C~~C~k~F~~~s~L~~H~~~h~~~k~~~c~~--~~~~~~~~~~~~~~~~e~~-~~~~~~~~~~D 141 (353)
+|..|++.|...+.|.+|..+|+ +..|.|.- |..+.........+..+-. ...+..|.+-=
T Consensus 279 L~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~ 357 (467)
T KOG3608|consen 279 LTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHC 357 (467)
T ss_pred HHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeec
Confidence 39999999999999999999998 78888855 7766555555544333322 34445555555
Q ss_pred Cccc
Q 018586 142 CEMV 145 (353)
Q Consensus 142 ~Ett 145 (353)
|+-+
T Consensus 358 Cdr~ 361 (467)
T KOG3608|consen 358 CDRF 361 (467)
T ss_pred chhh
Confidence 5544
No 69
>PHA02768 hypothetical protein; Provisional
Probab=98.35 E-value=2.1e-07 Score=61.90 Aligned_cols=42 Identities=19% Similarity=0.483 Sum_probs=37.0
Q ss_pred ceeeccccccccChHHHHHHHhhhcCCCCCC-ccccCcccCCChHHH
Q 018586 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESL 59 (353)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~h~~~~~-~C~~C~~~f~~~~~l 59 (353)
.|+|+.||+.|...++|..|+++ |+ ++ +|..|++.|.+.+.+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~--H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK--HN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh--cC--CcccCCcccceeccccee
Confidence 48999999999999999999999 87 45 899999998877665
No 70
>PHA02768 hypothetical protein; Provisional
Probab=98.31 E-value=3.5e-07 Score=60.84 Aligned_cols=36 Identities=17% Similarity=0.328 Sum_probs=31.3
Q ss_pred ccccccccccCchhHHHHHHHhcCCCCCCcccCCcchh
Q 018586 80 GCNLCMNIFDSPSSLIKHKEACSLSAPVPFEKTLSNAE 117 (353)
Q Consensus 80 ~C~~C~k~F~~~s~L~~H~~~h~~~k~~~c~~~~~~~~ 117 (353)
.|+.||+.|.+.++|..|+++|+ +|++|..|+..+.
T Consensus 7 ~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~ 42 (55)
T PHA02768 7 ECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISL 42 (55)
T ss_pred CcchhCCeeccHHHHHHHHHhcC--CcccCCcccceec
Confidence 69999999999999999999998 7888888865433
No 71
>PHA00733 hypothetical protein
Probab=98.28 E-value=6.7e-07 Score=71.75 Aligned_cols=80 Identities=21% Similarity=0.257 Sum_probs=62.5
Q ss_pred CCCceeeccccccccChHHHHHH------HhhhcCCCCCC-ccccCcccCCChHHHHhccC-CCCCCCCCCccccccccc
Q 018586 11 STARHKCVACYKQFKRKDHLIEH------MKISYHSVHQP-KCAVCQKLSKSFESLREHLT-GPLSKAHCSGIFSDRGCN 82 (353)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H------~~~~~h~~~~~-~C~~C~~~f~~~~~l~~H~~-~~~~c~~Cgk~f~~~~C~ 82 (353)
.++++.|..|.+.|.....|..+ +.. ++ .++ .|..|++.|.+...|..|+. ...+. .|+
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~--~~-~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~----------~C~ 103 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTS--KA-VSPYVCPLCLMPFSSSVSLKQHIRYTEHSK----------VCP 103 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhccc--CC-CCCccCCCCCCcCCCHHHHHHHHhcCCcCc----------cCC
Confidence 46889999999988877666654 222 33 556 99999999999999999983 12222 689
Q ss_pred cccccccCchhHHHHHHHhcC
Q 018586 83 LCMNIFDSPSSLIKHKEACSL 103 (353)
Q Consensus 83 ~C~k~F~~~s~L~~H~~~h~~ 103 (353)
.|+++|...++|..|+...++
T Consensus 104 ~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 104 VCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCccCCHHHHHHHHHHhcC
Confidence 999999999999999987664
No 72
>PRK05755 DNA polymerase I; Provisional
Probab=98.25 E-value=5e-06 Score=87.90 Aligned_cols=137 Identities=23% Similarity=0.241 Sum_probs=94.7
Q ss_pred CCceeeccCccccccCCCCccceeEEeeecCCCCeEEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHh
Q 018586 134 GPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILN 213 (353)
Q Consensus 134 ~~~~~~~D~Ettg~~~~~~~~il~~v~ivd~~g~~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~~~ 213 (353)
...++++|+|++|.++.... + ..+.+...+|...+ + |- +++. .++++.|.+++
T Consensus 314 ~~~~~a~DtEt~~l~~~~~~-i-~~i~ls~~~g~~~~---i-p~----------~~i~----------~~~l~~l~~~L- 366 (880)
T PRK05755 314 AAGLFAFDTETTSLDPMQAE-L-VGLSFAVEPGEAAY---I-PL----------DQLD----------REVLAALKPLL- 366 (880)
T ss_pred ccCeEEEEeccCCCCccccc-E-EEEEEEeCCCcEEE---E-ec----------cccc----------HHHHHHHHHHH-
Confidence 45789999999998643222 2 23444334443221 1 11 1121 16788899999
Q ss_pred cCCCCcccccCCCCCcEEEecccHHHHHHhcC-cCC-CCceeecccccCCcccCCCCCcHHHHHHHHhCCcCCC------
Q 018586 214 NGESTGRLMLDDGKARLLVGHGLEHDLDSLRM-NYP-DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQS------ 285 (353)
Q Consensus 214 ~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~-~~~-~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~------ 285 (353)
++...++|+||+.||+.+|.. +.+ ...++||+..+..+.+... ++|++|++.|+|..+..
T Consensus 367 -----------~d~~v~kV~HNakfDl~~L~~~gi~~~~~~~DT~iAa~Ll~~~~~-~~L~~L~~~ylg~~~~~~~~~~g 434 (880)
T PRK05755 367 -----------EDPAIKKVGQNLKYDLHVLARYGIELRGIAFDTMLASYLLDPGRR-HGLDSLAERYLGHKTISFEEVAG 434 (880)
T ss_pred -----------hCCCCcEEEeccHhHHHHHHhCCCCcCCCcccHHHHHHHcCCCCC-CCHHHHHHHHhCCCccchHHhcC
Confidence 234456899999999999982 222 2458999998888887653 99999999998776310
Q ss_pred ------------CCCChHHHHHHHHHHHHHHHhchh
Q 018586 286 ------------GVHDPYEDCVSVMRLYKRFRRQDH 309 (353)
Q Consensus 286 ------------~~H~Al~Da~~t~~l~~~~~~~~~ 309 (353)
..|.|..||.+++.||..+..+..
T Consensus 435 k~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~L~ 470 (880)
T PRK05755 435 KQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKLL 470 (880)
T ss_pred CCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 137899999999999999998754
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=98.25 E-value=5.5e-06 Score=63.22 Aligned_cols=30 Identities=40% Similarity=0.558 Sum_probs=23.2
Q ss_pred cEEEecccHHHHHHhc-------CcCC--CCceeecccc
Q 018586 229 RLLVGHGLEHDLDSLR-------MNYP--DHMLRDTAKY 258 (353)
Q Consensus 229 ~~lvgh~~~~D~~~l~-------~~~~--~~~~~Dt~~l 258 (353)
.++||||+.||+.||+ ...| ..+++||+.+
T Consensus 45 ~v~V~hn~~fD~~fL~~~~~~~~~~~p~~~~~~lDT~~l 83 (96)
T cd06125 45 AILVGHNGSFDLPFLNNRCAELGLKYPLLAGSWIDTIKL 83 (96)
T ss_pred CEEEEeCcHHhHHHHHHHHHHcCCCCCCcCCcEEEehHH
Confidence 6899999999999998 2222 2568888876
No 74
>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=98.16 E-value=2.1e-05 Score=68.08 Aligned_cols=91 Identities=15% Similarity=0.284 Sum_probs=67.5
Q ss_pred HHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCcCC--------CCceeecccccCCcccC----------
Q 018586 204 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP--------DHMLRDTAKYRPLMKTN---------- 265 (353)
Q Consensus 204 v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~--------~~~~~Dt~~l~~~~~~~---------- 265 (353)
+.+.+.+++ .+.+.+-|||++.+|+..|.-.++ ...++|++.++..+...
T Consensus 70 ~~~~L~~ll------------~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~ 137 (193)
T cd06146 70 WDRLLKRLF------------EDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLP 137 (193)
T ss_pred HHHHHHHHh------------CCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccC
Confidence 344566777 234467799999999999994332 24689999877655431
Q ss_pred CCCCcHHHHHHHHhCCcCCCC------C---------CChHHHHHHHHHHHHHHHh
Q 018586 266 LVSHSLKYLTRTYLGYDIQSG------V---------HDPYEDCVSVMRLYKRFRR 306 (353)
Q Consensus 266 ~~~~~L~~l~~~~~~~~~~~~------~---------H~Al~Da~~t~~l~~~~~~ 306 (353)
...++|+.|++.+||.++... . +-|..||..+..||.++.+
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 357899999999999887654 1 4478899999999998864
No 75
>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=98.00 E-value=5.5e-05 Score=65.58 Aligned_cols=121 Identities=15% Similarity=0.187 Sum_probs=75.3
Q ss_pred CCceeeccCcccccc--CC-CCccceeEEeeecCCCCeEEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHH
Q 018586 134 GPKAVAMDCEMVGGG--SN-GTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILE 210 (353)
Q Consensus 134 ~~~~~~~D~Ettg~~--~~-~~~~il~~v~ivd~~g~~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~ 210 (353)
.-+++++|+||++.+ ++ ....| ..++++...++.++.. .+. ....+....+-.+++.+|.+
T Consensus 2 ~l~i~~fDIEt~~~~g~p~~~~d~I-i~Is~~~~~~~~~~~~--~~~-------------~~~~v~~~~~E~~lL~~F~~ 65 (195)
T cd05780 2 DLKILSFDIEVLNHEGEPNPEKDPI-IMISFADEGGNKVITW--KKF-------------DLPFVEVVKTEKEMIKRFIE 65 (195)
T ss_pred CceEEEEEEEecCCCCCCCCCCCcE-EEEEEecCCCceEEEe--cCC-------------CCCeEEEeCCHHHHHHHHHH
Confidence 346889999998421 12 12233 3555554444433211 110 11133445667899999999
Q ss_pred HHhcCCCCcccccCCCCCcEEEeccc-HHHHHHhc-------CcCC----------------------CCceeecccccC
Q 018586 211 ILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-------MNYP----------------------DHMLRDTAKYRP 260 (353)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-------~~~~----------------------~~~~~Dt~~l~~ 260 (353)
++.+.+ ..+|||||. .||+.+|. +..+ ....+|+..+.+
T Consensus 66 ~i~~~d-----------pdiivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~ 134 (195)
T cd05780 66 IVKEKD-----------PDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVAR 134 (195)
T ss_pred HHHHcC-----------CCEEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHH
Confidence 995432 359999996 58999987 2211 123677777665
Q ss_pred CcccCCCCCcHHHHHHHHhCCc
Q 018586 261 LMKTNLVSHSLKYLTRTYLGYD 282 (353)
Q Consensus 261 ~~~~~~~~~~L~~l~~~~~~~~ 282 (353)
.. ....+|+|+.+++.+||.+
T Consensus 135 ~~-~~l~sy~L~~v~~~~Lg~~ 155 (195)
T cd05780 135 RT-LNLTRYTLERVYEELFGIE 155 (195)
T ss_pred hh-CCCCcCcHHHHHHHHhCCC
Confidence 53 3567999999999998987
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=0.00012 Score=61.91 Aligned_cols=79 Identities=19% Similarity=0.205 Sum_probs=61.7
Q ss_pred CCcEEEecccHHHHHHhc--CcCCCCceeecccccCCcccCCCCCcHHHHHHHHhCCcCC--CC------C---------
Q 018586 227 KARLLVGHGLEHDLDSLR--MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQ--SG------V--------- 287 (353)
Q Consensus 227 ~~~~lvgh~~~~D~~~l~--~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~--~~------~--------- 287 (353)
.+.+.|||++.+|+..|. .+.....++|++.++..+.+.....+|+.|++.++|..+. .. .
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 556789999999999996 2332344699999988887764556999999999999876 21 1
Q ss_pred CChHHHHHHHHHHHHHHH
Q 018586 288 HDPYEDCVSVMRLYKRFR 305 (353)
Q Consensus 288 H~Al~Da~~t~~l~~~~~ 305 (353)
+-|..||..+..||..+.
T Consensus 152 ~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 152 LYAATDAYASLELYRKLL 169 (170)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 447889999999998875
No 77
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.95 E-value=1.2e-05 Score=79.10 Aligned_cols=90 Identities=19% Similarity=0.445 Sum_probs=63.8
Q ss_pred CCCceeeccccccccChHHHHHHHhhhcCCCCCC-ccccCcccCCChHHHHhccCCCCCCCCCCcccccccccccccccc
Q 018586 11 STARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFD 89 (353)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~~~h~~~~~-~C~~C~~~f~~~~~l~~H~~~~~~c~~Cgk~f~~~~C~~C~k~F~ 89 (353)
-++.+.|+.|++.|. ...|..|+.. |. .+ .|. |++.+ .+..|..|+... | ++ ....|+.|++.|.
T Consensus 450 l~~H~~C~~Cgk~f~-~s~LekH~~~--~H--kpv~Cp-Cg~~~-~R~~L~~H~~th--C---p~--Kpi~C~fC~~~v~ 515 (567)
T PLN03086 450 AKNHVHCEKCGQAFQ-QGEMEKHMKV--FH--EPLQCP-CGVVL-EKEQMVQHQAST--C---PL--RLITCRFCGDMVQ 515 (567)
T ss_pred cccCccCCCCCCccc-hHHHHHHHHh--cC--CCccCC-CCCCc-chhHHHhhhhcc--C---CC--CceeCCCCCCccc
Confidence 356678999999996 6779999998 52 55 998 99755 668899997211 1 10 0113666776663
Q ss_pred ----------CchhHHHHHHHhcCCCCCCcccCCcc
Q 018586 90 ----------SPSSLIKHKEACSLSAPVPFEKTLSN 115 (353)
Q Consensus 90 ----------~~s~L~~H~~~h~~~k~~~c~~~~~~ 115 (353)
..+.|+.|..++ +.+++.|..|+..
T Consensus 516 ~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~ 550 (567)
T PLN03086 516 AGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRS 550 (567)
T ss_pred cCccccchhhhhhhHHHHHHhc-CCcceEccccCCe
Confidence 245899999886 8999999999644
No 78
>PHA00616 hypothetical protein
Probab=97.89 E-value=5.3e-06 Score=52.52 Aligned_cols=32 Identities=22% Similarity=0.374 Sum_probs=29.8
Q ss_pred ccccccccccCchhHHHHHHHhcCCCCCCccc
Q 018586 80 GCNLCMNIFDSPSSLIKHKEACSLSAPVPFEK 111 (353)
Q Consensus 80 ~C~~C~k~F~~~s~L~~H~~~h~~~k~~~c~~ 111 (353)
+|+.||+.|.+.+.|..|++.|++++++.|+.
T Consensus 3 qC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 3 QCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred ccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 59999999999999999999999999988864
No 79
>PHA00733 hypothetical protein
Probab=97.80 E-value=2.4e-05 Score=62.74 Aligned_cols=52 Identities=21% Similarity=0.469 Sum_probs=46.2
Q ss_pred CCCCCCceeeccccccccChHHHHHHHhhhcCCCCCC-ccccCcccCCChHHHHhcc
Q 018586 8 PKRSTARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL 63 (353)
Q Consensus 8 ~h~~~k~~~C~~C~k~f~~~~~l~~H~~~~~h~~~~~-~C~~C~~~f~~~~~l~~H~ 63 (353)
.+.+.+||.|+.|++.|.....|..|++. |. .+ .|..|++.|.....|..|+
T Consensus 67 ~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~--h~--~~~~C~~CgK~F~~~~sL~~H~ 119 (128)
T PHA00733 67 TSKAVSPYVCPLCLMPFSSSVSLKQHIRY--TE--HSKVCPVCGKEFRNTDSTLDHV 119 (128)
T ss_pred ccCCCCCccCCCCCCcCCCHHHHHHHHhc--CC--cCccCCCCCCccCCHHHHHHHH
Confidence 33458899999999999999999999997 63 34 9999999999999999998
No 80
>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=97.71 E-value=0.00021 Score=61.49 Aligned_cols=112 Identities=14% Similarity=0.199 Sum_probs=70.6
Q ss_pred CCceeeccCcccccc--CC-CCccceeEEeeecCCCCeEEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHH
Q 018586 134 GPKAVAMDCEMVGGG--SN-GTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILE 210 (353)
Q Consensus 134 ~~~~~~~D~Ettg~~--~~-~~~~il~~v~ivd~~g~~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~ 210 (353)
.-+.+++|+||++.. ++ ....| ..+++...+|.+.+-. ....+-.+++..|.+
T Consensus 2 ~l~~l~fDIEt~~~~gfp~~~~d~I-i~Is~~~~~g~~~~~~-----------------------~~~~~E~~lL~~F~~ 57 (188)
T cd05781 2 DLKTLAFDIEVYSKYGTPNPRRDPI-IVISLATSNGDVEFIL-----------------------AEGLDDRKIIREFVK 57 (188)
T ss_pred CceEEEEEEEecCCCCCCCCCCCCE-EEEEEEeCCCCEEEEE-----------------------ecCCCHHHHHHHHHH
Confidence 346889999999421 11 12233 3555555555532110 124678899999999
Q ss_pred HHhcCCCCcccccCCCCCcEEEecc-cHHHHHHhc-------CcCC--C------------------CceeecccccCCc
Q 018586 211 ILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLR-------MNYP--D------------------HMLRDTAKYRPLM 262 (353)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~lvgh~-~~~D~~~l~-------~~~~--~------------------~~~~Dt~~l~~~~ 262 (353)
++.+.+ ..+|+||| ..||+.+|. +..+ + ...+|...+.+..
T Consensus 58 ~i~~~d-----------Pd~i~gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~ 126 (188)
T cd05781 58 YVKEYD-----------PDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEI 126 (188)
T ss_pred HHHHcC-----------CCEEEecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhh
Confidence 996543 35999999 558999987 1111 0 1256776665544
Q ss_pred ccCCCCCcHHHHHHHHhCCc
Q 018586 263 KTNLVSHSLKYLTRTYLGYD 282 (353)
Q Consensus 263 ~~~~~~~~L~~l~~~~~~~~ 282 (353)
. ...+|+|+.+|+. ||..
T Consensus 127 ~-~l~~y~L~~Va~~-Lg~~ 144 (188)
T cd05781 127 P-EVKVKTLENVAEY-LGVM 144 (188)
T ss_pred C-CCCCCCHHHHHHH-HCCC
Confidence 3 3678999999986 4863
No 81
>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=97.70 E-value=0.0003 Score=59.03 Aligned_cols=78 Identities=23% Similarity=0.220 Sum_probs=59.2
Q ss_pred CCcEEEecccHHHHHHhcC--cCCCCceeecccccCCcccCCCCCcHHHHHHHHhCCcCCCC---------------CCC
Q 018586 227 KARLLVGHGLEHDLDSLRM--NYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSG---------------VHD 289 (353)
Q Consensus 227 ~~~~lvgh~~~~D~~~l~~--~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~---------------~H~ 289 (353)
.+.+.|||++..|+..|.. +.....++|++..+..+.+. .+.+|+.+++.|+|..+... -+-
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 4457799999999999863 33334468999877766543 35699999999999876443 245
Q ss_pred hHHHHHHHHHHHHHHH
Q 018586 290 PYEDCVSVMRLYKRFR 305 (353)
Q Consensus 290 Al~Da~~t~~l~~~~~ 305 (353)
|..||..+..||.++.
T Consensus 145 Aa~Da~~l~~l~~~l~ 160 (161)
T cd06129 145 AAADVYALLIIYTKLR 160 (161)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 7789999999999875
No 82
>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=97.63 E-value=7.4e-05 Score=62.73 Aligned_cols=74 Identities=22% Similarity=0.188 Sum_probs=38.4
Q ss_pred CCcEEEecc-cHHHHHHhc-----CcCC-CCceeecccccCCcccCCCCCcHHHHHHHHhCCcCCCCCCChHHHHHHHHH
Q 018586 227 KARLLVGHG-LEHDLDSLR-----MNYP-DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMR 299 (353)
Q Consensus 227 ~~~~lvgh~-~~~D~~~l~-----~~~~-~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~H~Al~Da~~t~~ 299 (353)
+...+|+|| ..||+.+|+ ...| ....+|+....+.... .+++|+.++..+ |+... .--.+-.....
T Consensus 56 ~~~~iv~yng~~FD~p~L~~~~~~~~~~~~~~~iDl~~~~~~~~~--~~~~Lk~ve~~l-g~~~~----~~~~~G~~~~~ 128 (164)
T PF13482_consen 56 EADNIVTYNGKNFDIPFLKRRAKRYGLPPPFNHIDLLKIIKKHFL--ESYSLKNVEKFL-GIERR----DDDISGSESVK 128 (164)
T ss_dssp TT--EEESSTTTTHHHHHHHHH-HHHH--GGGEEEHHHHHT-TTS--CCTT--SHHH----------------HHHHHHH
T ss_pred cCCeEEEEeCcccCHHHHHHHHHHcCCCcccchhhHHHHHHhccC--CCCCHHHHhhhc-ccccc----cCCCCHHHHHH
Confidence 556889988 688999999 2223 4668999887754433 678999999987 77732 12244445566
Q ss_pred HHHHHHhc
Q 018586 300 LYKRFRRQ 307 (353)
Q Consensus 300 l~~~~~~~ 307 (353)
+|..+...
T Consensus 129 ~~~~~~~~ 136 (164)
T PF13482_consen 129 LYKEYLET 136 (164)
T ss_dssp HHH---TT
T ss_pred HHHHHHhc
Confidence 66665433
No 83
>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=97.60 E-value=3e-05 Score=43.83 Aligned_cols=23 Identities=13% Similarity=0.075 Sum_probs=20.4
Q ss_pred hHHHHHHHhcCCCCCCcccCCcc
Q 018586 93 SLIKHKEACSLSAPVPFEKTLSN 115 (353)
Q Consensus 93 ~L~~H~~~h~~~k~~~c~~~~~~ 115 (353)
+|.+|+++|++++||+|+.|...
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~ 23 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKS 23 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEE
T ss_pred CHHHHhhhcCCCCCCCCCCCcCe
Confidence 58899999999999999999543
No 84
>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=97.56 E-value=0.0019 Score=56.49 Aligned_cols=73 Identities=23% Similarity=0.392 Sum_probs=52.0
Q ss_pred CCChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEeccc-HHHHHHhc-------CcCC---------------------
Q 018586 198 AMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-------MNYP--------------------- 248 (353)
Q Consensus 198 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-------~~~~--------------------- 248 (353)
..+..+++..|.+++.+.++ .+|||||+ .||+.+|. +..+
T Consensus 55 ~~~E~~lL~~f~~~i~~~dP-----------dii~g~N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~ 123 (207)
T cd05785 55 DAAEKELLEELVAIIRERDP-----------DVIEGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERL 123 (207)
T ss_pred CCCHHHHHHHHHHHHHHhCC-----------CEEeccCCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccc
Confidence 57889999999999965432 59999998 89999987 1111
Q ss_pred ---------CCceeecccccCCc---ccCCCCCcHHHHHHHHhCCc
Q 018586 249 ---------DHMLRDTAKYRPLM---KTNLVSHSLKYLTRTYLGYD 282 (353)
Q Consensus 249 ---------~~~~~Dt~~l~~~~---~~~~~~~~L~~l~~~~~~~~ 282 (353)
...++|+..+.+.. .....+|+|+.+|+.+ |+.
T Consensus 124 ~~~~~~~i~Gr~~iDl~~~~~~~~~~~~~l~sysL~~Va~~~-g~~ 168 (207)
T cd05785 124 IDYPRYDIPGRHVIDTYFLVQLFDVSSRDLPSYGLKAVAKHF-GLA 168 (207)
T ss_pred cccceEEecCEEEEEcHHHHHhhcccccCCCCCCHHHHHHHh-ccc
Confidence 01226777655532 2245689999999988 654
No 85
>PRK10829 ribonuclease D; Provisional
Probab=97.50 E-value=0.00078 Score=64.04 Aligned_cols=83 Identities=12% Similarity=0.117 Sum_probs=63.7
Q ss_pred CCcEEEecccHHHHHHhc--CcCCCCceeecccccCCcccCCCCCcHHHHHHHHhCCcCCCCC---------------CC
Q 018586 227 KARLLVGHGLEHDLDSLR--MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGV---------------HD 289 (353)
Q Consensus 227 ~~~~lvgh~~~~D~~~l~--~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~---------------H~ 289 (353)
.+.+-|+|++.+|+.+|. ++.....++||+..+..+ +...+.+|+.|++.++|+.+..+. +-
T Consensus 73 ~~ivKV~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~l-g~~~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~ql~Y 151 (373)
T PRK10829 73 PQVTKFLHAGSEDLEVFLNAFGELPQPLIDTQILAAFC-GRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEY 151 (373)
T ss_pred CCeEEEEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHc-CCCccccHHHHHHHHhCCccCcccccCCCCCCCCCHHHHHH
Confidence 445668999999999985 334445689998777554 333468999999999999877651 33
Q ss_pred hHHHHHHHHHHHHHHHhchhh
Q 018586 290 PYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 290 Al~Da~~t~~l~~~~~~~~~~ 310 (353)
|..|+.....||..+..+..+
T Consensus 152 Aa~Dv~~L~~l~~~L~~~L~~ 172 (373)
T PRK10829 152 AAADVFYLLPIAAKLMAETEA 172 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 678999999999999887654
No 86
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=97.48 E-value=0.0005 Score=58.83 Aligned_cols=158 Identities=15% Similarity=0.135 Sum_probs=100.7
Q ss_pred CceeeccCcccccc-----------------------CCCCccceeEEeeecCCCCe------EEeeecc---CC-CCcc
Q 018586 135 PKAVAMDCEMVGGG-----------------------SNGTLDLCARVCLVDEDENV------IFHTYVQ---PQ-LPVT 181 (353)
Q Consensus 135 ~~~~~~D~Ettg~~-----------------------~~~~~~il~~v~ivd~~g~~------~~~~lv~---P~-~~i~ 181 (353)
-++|++|+|.-|.= .-..|++ ...+.|.+|+. +|+--.+ +. ....
T Consensus 24 y~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQl--GlTlsd~~Gn~p~~g~~tWqfNF~dF~~~~D~~a 101 (239)
T KOG0304|consen 24 YPYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQL--GLTLSDEKGNLPDCGTDTWQFNFSDFNLEKDMYA 101 (239)
T ss_pred CCeeEecCcCCceeeecCccccCChHHHHHHHHhchhhhhhhhe--eeeeeccCCCCCCCCCceeEEecccCCchhhccc
Confidence 45899999988731 1122333 56677777765 2333222 22 2222
Q ss_pred cccc---ccCCCCHhhhc-CCCChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhc-----Cc------
Q 018586 182 NYRY---EVTGLTEEDIK-NAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR-----MN------ 246 (353)
Q Consensus 182 ~~~~---~~~GIt~e~l~-~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~-----~~------ 246 (353)
+... +=+||.-+... .+....+..+.+..-..- -+++..+|..+..+|+..|- -.
T Consensus 102 ~~SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v----------~~~~V~WvTFhs~YDfgYLlK~Lt~~~LP~~~~ 171 (239)
T KOG0304|consen 102 QDSIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLV----------LDENVTWVTFHSGYDFGYLLKILTGKPLPETEE 171 (239)
T ss_pred hhhHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhh----------ccCceEEEEeeccchHHHHHHHHcCCCCcchHH
Confidence 2222 33788866654 455555444444433210 13678999999899999876 11
Q ss_pred ---------CCCCceeecccccCCcccCCCCCcHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHhc
Q 018586 247 ---------YPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQ 307 (353)
Q Consensus 247 ---------~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~ 307 (353)
+|. +.|+..+++.......+.+|+.+|+.+ ++.-.+-+|.|-.|+..|+..|.++.+.
T Consensus 172 eF~~~v~~~fp~--vYDiK~l~~~c~~~~l~~GL~~lA~~L-~~~RvG~~HqAGSDSlLT~~~F~kl~~~ 238 (239)
T KOG0304|consen 172 EFFEIVRQLFPF--VYDVKYLMKFCEGLSLKGGLQRLADLL-GLKRVGIAHQAGSDSLLTARVFFKLKEL 238 (239)
T ss_pred HHHHHHHHHcch--hhhHHHHHHhhhhhhhhcCHHHHHHHh-CCCeeecccccCcHHHHHHHHHHHHHhc
Confidence 233 557777776665555678999999998 9995444999999999999999998764
No 87
>PHA00616 hypothetical protein
Probab=97.47 E-value=5.6e-05 Score=47.88 Aligned_cols=33 Identities=21% Similarity=0.410 Sum_probs=28.9
Q ss_pred ceeeccccccccChHHHHHHHhhhcCCCCCC-cccc
Q 018586 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAV 48 (353)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~h~~~~~-~C~~ 48 (353)
||+|..||+.|..++++.+|++. |.++.+ .|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~--~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLS--VHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHH--hcCCCccceeE
Confidence 68999999999999999999998 777777 6643
No 88
>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=97.46 E-value=0.0014 Score=57.15 Aligned_cols=74 Identities=18% Similarity=0.134 Sum_probs=50.8
Q ss_pred CCChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecc-cHHHHHHhc-----CcCC------C------------Ccee
Q 018586 198 AMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLR-----MNYP------D------------HMLR 253 (353)
Q Consensus 198 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~-~~~D~~~l~-----~~~~------~------------~~~~ 253 (353)
..+-.+++.+|.+++.+.+ ..+|+||| ..||+.+|. .+.+ + ...+
T Consensus 70 ~~~E~~lL~~f~~~i~~~~-----------Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~i 138 (204)
T cd05779 70 EPDEKALLQRFFEHIREVK-----------PHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHM 138 (204)
T ss_pred CCCHHHHHHHHHHHHHHhC-----------CCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEE
Confidence 4678899999999995442 25999999 568999987 1111 0 1145
Q ss_pred ecccccCCc-ccCCCCCcHHHHHHHHhCCc
Q 018586 254 DTAKYRPLM-KTNLVSHSLKYLTRTYLGYD 282 (353)
Q Consensus 254 Dt~~l~~~~-~~~~~~~~L~~l~~~~~~~~ 282 (353)
|...+.+.. ......++|+.+|+.+||..
T Consensus 139 Dl~~~~~~~~~l~~~sysLd~Va~~~Lg~~ 168 (204)
T cd05779 139 DCFRWVKRDSYLPQGSQGLKAVTKAKLGYD 168 (204)
T ss_pred EhHHHHHHhhcCCCCCccHHHHHHHHhCCC
Confidence 666555432 22335899999999988875
No 89
>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=97.42 E-value=0.00038 Score=57.20 Aligned_cols=93 Identities=28% Similarity=0.391 Sum_probs=65.2
Q ss_pred HHHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCc---CCCCceeecccccCCcccCCCCCcHHHHHHHH
Q 018586 202 KEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN---YPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTY 278 (353)
Q Consensus 202 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~---~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~ 278 (353)
.++.+.+.+++ .+.+..+||||+.+|+.+|... .+ ..++||+..+..+.|....++|+.+++.|
T Consensus 40 ~~~~~~l~~~l------------~~~~~~~v~~~~k~d~~~L~~~~~~~~-~~~~D~~~~ayll~~~~~~~~l~~l~~~~ 106 (155)
T cd00007 40 EEDLEALKELL------------EDEDITKVGHDAKFDLVVLARDGIELP-GNIFDTMLAAYLLNPGEGSHSLDDLAKEY 106 (155)
T ss_pred HHHHHHHHHHH------------cCCCCcEEeccHHHHHHHHHHCCCCCC-CCcccHHHHHHHhCCCCCcCCHHHHHHHH
Confidence 56777788998 2244579999999999999722 22 34789999998888865357999999999
Q ss_pred hCCcCCC-C-----------CC-------ChHHHHHHHHHHHHHHHhc
Q 018586 279 LGYDIQS-G-----------VH-------DPYEDCVSVMRLYKRFRRQ 307 (353)
Q Consensus 279 ~~~~~~~-~-----------~H-------~Al~Da~~t~~l~~~~~~~ 307 (353)
++..+.. . .. -|..||.++.+|+..+..+
T Consensus 107 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 107 LGIELDKDEQIYGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred cCCCCccHHHHhcCCCCccccCCHHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 8776321 0 00 1455666777777666543
No 90
>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=97.41 E-value=0.0013 Score=56.85 Aligned_cols=120 Identities=18% Similarity=0.265 Sum_probs=71.9
Q ss_pred CCceeeccCccccccCCCCccceeEEeeecCCCCeEEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHh
Q 018586 134 GPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILN 213 (353)
Q Consensus 134 ~~~~~~~D~Ettg~~~~~~~~il~~v~ivd~~g~~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~~~ 213 (353)
.-++++||+|+.+.+ ++ -.+...+...+.++-. -.+. +. .| ..+.--++-.+++..|.+++.
T Consensus 2 ~l~~~~fDIE~~~~~-----~i-~~i~~~~~~~~~i~~~-~~~~-~~-------~~---~~v~~~~~E~~lL~~f~~~i~ 63 (193)
T cd05784 2 KLKVVSLDIETSMDG-----EL-YSIGLYGEGQERVLMV-GDPE-DD-------AP---DNIEWFADEKSLLLALIAWFA 63 (193)
T ss_pred CccEEEEEeecCCCC-----CE-EEEEeecCCCCEEEEE-CCCC-CC-------CC---CEEEEECCHHHHHHHHHHHHH
Confidence 346899999998753 33 2444433333322211 0111 10 01 123334678889999999995
Q ss_pred cCCCCcccccCCCCCcEEEeccc-HHHHHHhc-------CcC------------------------CCCceeecccccCC
Q 018586 214 NGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-------MNY------------------------PDHMLRDTAKYRPL 261 (353)
Q Consensus 214 ~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-------~~~------------------------~~~~~~Dt~~l~~~ 261 (353)
+.++ .+|+|||+ .||+.+|. +.. +...++|+..+.+.
T Consensus 64 ~~dP-----------Dvi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~ 132 (193)
T cd05784 64 QYDP-----------DIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKT 132 (193)
T ss_pred hhCC-----------CEEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHH
Confidence 5432 59999995 56999987 111 01225676665543
Q ss_pred cccCCCCCcHHHHHHHHhCCc
Q 018586 262 MKTNLVSHSLKYLTRTYLGYD 282 (353)
Q Consensus 262 ~~~~~~~~~L~~l~~~~~~~~ 282 (353)
......+|+|+++|+.+||..
T Consensus 133 ~~~kl~sy~L~~Va~~~Lg~~ 153 (193)
T cd05784 133 ATYHFESFSLENVAQELLGEG 153 (193)
T ss_pred ccCCCCcCCHHHHHHHHhCCC
Confidence 223577999999999998875
No 91
>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=97.36 E-value=0.002 Score=61.44 Aligned_cols=82 Identities=18% Similarity=0.250 Sum_probs=61.8
Q ss_pred CCcEEEecccHHHHHHhc---CcCCCCceeecccccCCcccCCCCCcHHHHHHHHhCCcCCCC------CCC--------
Q 018586 227 KARLLVGHGLEHDLDSLR---MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSG------VHD-------- 289 (353)
Q Consensus 227 ~~~~lvgh~~~~D~~~l~---~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~------~H~-------- 289 (353)
.+.+.|+|++.+|+.+|. ...| ..++||+..+..+.+. .+.+|+.|++.|+|+.+..+ ..+
T Consensus 69 ~~i~KV~h~~k~Dl~~L~~~~~~~~-~~~fDtqlAa~lL~~~-~~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~ 146 (367)
T TIGR01388 69 ESVVKVLHAASEDLEVFLNLFGELP-QPLFDTQIAAAFCGFG-MSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLE 146 (367)
T ss_pred CCceEEEeecHHHHHHHHHHhCCCC-CCcccHHHHHHHhCCC-CCccHHHHHHHHcCCCCCcccccccCCCCCCCHHHHH
Confidence 456789999999999987 2233 4578998877666443 34699999999999887543 122
Q ss_pred -hHHHHHHHHHHHHHHHhchhh
Q 018586 290 -PYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 290 -Al~Da~~t~~l~~~~~~~~~~ 310 (353)
|..||.....||..+..+..+
T Consensus 147 YAa~Dv~~L~~L~~~L~~~L~~ 168 (367)
T TIGR01388 147 YAAADVTYLLPLYAKLMERLEE 168 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 778999999999999877654
No 92
>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=97.35 E-value=0.00069 Score=58.80 Aligned_cols=138 Identities=22% Similarity=0.216 Sum_probs=86.3
Q ss_pred CCceeeccCccccccCCCCccceeEEeeecCCCCe-EEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHH
Q 018586 134 GPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENV-IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 212 (353)
Q Consensus 134 ~~~~~~~D~Ettg~~~~~~~~il~~v~ivd~~g~~-~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~~ 212 (353)
..+++++|+|..+.+..+.+. -+.+....+.+ +||.+-.+. ......+.+++
T Consensus 9 ~~~~i~~D~E~~~~~~~~~~~---LiQia~~~~~v~l~D~~~~~~------------------------~~~~~~L~~iL 61 (197)
T cd06148 9 KQKVIGLDCEGVNLGRKGKLC---LVQIATRTGQIYLFDILKLGS------------------------IVFINGLKDIL 61 (197)
T ss_pred hCCEEEEEcccccCCCCCCEE---EEEEeeCCCcEEEEEhhhccc------------------------hhHHHHHHHHh
Confidence 457999999998776544333 33332231332 344332111 01224455667
Q ss_pred hcCCCCcccccCCCCCcEEEecccHHHHHHhc--CcCCCCceeecccccCCcccCC-------CCCcHHHHHHHHhCCcC
Q 018586 213 NNGESTGRLMLDDGKARLLVGHGLEHDLDSLR--MNYPDHMLRDTAKYRPLMKTNL-------VSHSLKYLTRTYLGYDI 283 (353)
Q Consensus 213 ~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~--~~~~~~~~~Dt~~l~~~~~~~~-------~~~~L~~l~~~~~~~~~ 283 (353)
.+.+.+.|+|++.+|+.+|. .+.....++||+..+..+.+.. ...+|+.+++.|+|+++
T Consensus 62 ------------e~~~i~Kv~h~~k~D~~~L~~~~gi~~~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~ 129 (197)
T cd06148 62 ------------ESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISI 129 (197)
T ss_pred ------------cCCCccEEEEechhHHHHHHHhcCccccceeeHHHHHHHHHHHhcCCccccccccHHHHHHHhhCCCh
Confidence 22445679999999999983 3332234689987665554422 13589999999999876
Q ss_pred CC--------------CC---------CChHHHHHHHHHHHHHHHhchhh
Q 018586 284 QS--------------GV---------HDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 284 ~~--------------~~---------H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
.. .. .-|..||..+..||..+......
T Consensus 130 ~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~~ 179 (197)
T cd06148 130 SLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALIS 179 (197)
T ss_pred HHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhhh
Confidence 31 11 33677999999999999888655
No 93
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.31 E-value=0.00017 Score=67.24 Aligned_cols=48 Identities=27% Similarity=0.454 Sum_probs=40.6
Q ss_pred ceeeccccccccChHHHHHHHhhhcCC--------CCC--------------------------CccccCcccCCChHHH
Q 018586 14 RHKCVACYKQFKRKDHLIEHMKISYHS--------VHQ--------------------------PKCAVCQKLSKSFESL 59 (353)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~h~--------~~~--------------------------~~C~~C~~~f~~~~~l 59 (353)
-|+|++|+|.|+...+|..|.|+ |- +.+ +.|+.|++.|.+..-|
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 49999999999999999999999 61 111 1699999999999999
Q ss_pred Hhcc
Q 018586 60 REHL 63 (353)
Q Consensus 60 ~~H~ 63 (353)
+.|+
T Consensus 373 rKHq 376 (500)
T KOG3993|consen 373 RKHQ 376 (500)
T ss_pred HHhH
Confidence 9995
No 94
>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=97.29 E-value=0.00014 Score=41.04 Aligned_cols=24 Identities=38% Similarity=0.724 Sum_probs=16.5
Q ss_pred HHHHHHhhhcCCCCCC-ccccCcccCC
Q 018586 29 HLIEHMKISYHSVHQP-KCAVCQKLSK 54 (353)
Q Consensus 29 ~l~~H~~~~~h~~~~~-~C~~C~~~f~ 54 (353)
+|.+|+++ |+++++ .|+.|++.|.
T Consensus 1 ~l~~H~~~--H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRT--HTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHH--HSSSSSEEESSSSEEES
T ss_pred CHHHHhhh--cCCCCCCCCCCCcCeeC
Confidence 36677777 777777 7777776664
No 95
>PHA00732 hypothetical protein
Probab=97.28 E-value=0.00017 Score=52.59 Aligned_cols=44 Identities=30% Similarity=0.519 Sum_probs=32.5
Q ss_pred ceeeccccccccChHHHHHHHhhhcCCCCCCccccCcccCCChHHHHhcc
Q 018586 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHL 63 (353)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~h~~~~~~C~~C~~~f~~~~~l~~H~ 63 (353)
||.|+.|++.|.+.+.|..|++.+ |.+. .|..|++.|. ++..|.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~-H~~~--~C~~CgKsF~---~l~~H~ 44 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRN-HTLT--KCPVCNKSYR---RLNQHF 44 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcc-cCCC--ccCCCCCEeC---Chhhhh
Confidence 688999999999999999998731 4432 6777877776 355665
No 96
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=97.27 E-value=0.0019 Score=60.29 Aligned_cols=137 Identities=22% Similarity=0.273 Sum_probs=91.3
Q ss_pred CCCceeeccCccccccCCCCccceeEEeeecCCCCeEEeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHH
Q 018586 133 RGPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 212 (353)
Q Consensus 133 ~~~~~~~~D~Ettg~~~~~~~~il~~v~ivd~~g~~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~~ 212 (353)
.+..++++|+|+.+...- .-. ++-|-|.+.++. .+|.|-.+ ..+.++|.. ++
T Consensus 15 ~~~~~iAiDTEf~r~~t~-~p~-LcLIQi~~~e~~----~lIdpl~~---------------~~d~~~l~~-------Ll 66 (361)
T COG0349 15 RGSKAIAIDTEFMRLRTY-YPR-LCLIQISDGEGA----SLIDPLAG---------------ILDLPPLVA-------LL 66 (361)
T ss_pred cCCCceEEeccccccccc-CCc-eEEEEEecCCCc----eEeccccc---------------ccccchHHH-------Hh
Confidence 345689999999997422 212 255666445552 33333321 112333333 33
Q ss_pred hcCCCCcccccCCCCCcEEEecccHHHHHHhc--CcCCCCceeecccccCCcccCCCCCcHHHHHHHHhCCcCCCCC---
Q 018586 213 NNGESTGRLMLDDGKARLLVGHGLEHDLDSLR--MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGV--- 287 (353)
Q Consensus 213 ~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~--~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~--- 287 (353)
.+.+.+=|=|++.||+.+|. ++.-..+++||...++..-... +++|++|++.++|+.|..++
T Consensus 67 ------------~d~~v~KIfHaa~~DL~~l~~~~g~~p~plfdTqiAa~l~g~~~-~~gl~~Lv~~ll~v~ldK~~q~S 133 (361)
T COG0349 67 ------------ADPNVVKIFHAARFDLEVLLNLFGLLPTPLFDTQIAAKLAGFGT-SHGLADLVEELLGVELDKSEQRS 133 (361)
T ss_pred ------------cCCceeeeeccccccHHHHHHhcCCCCCchhHHHHHHHHhCCcc-cccHHHHHHHHhCCccccccccc
Confidence 12445668899999999998 3433456899988776553333 89999999999999998872
Q ss_pred ---CC---------hHHHHHHHHHHHHHHHhchhh
Q 018586 288 ---HD---------PYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 288 ---H~---------Al~Da~~t~~l~~~~~~~~~~ 310 (353)
++ |..|+.....||.++.+...+
T Consensus 134 DW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~ 168 (361)
T COG0349 134 DWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAR 168 (361)
T ss_pred ccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33 577999999999999887655
No 97
>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=97.11 E-value=0.00027 Score=38.51 Aligned_cols=22 Identities=32% Similarity=0.594 Sum_probs=20.1
Q ss_pred ccccccccccCchhHHHHHHHh
Q 018586 80 GCNLCMNIFDSPSSLIKHKEAC 101 (353)
Q Consensus 80 ~C~~C~k~F~~~s~L~~H~~~h 101 (353)
.|+.|+++|...+.|..|++.|
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 4899999999999999999875
No 98
>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=97.11 E-value=0.013 Score=51.01 Aligned_cols=75 Identities=16% Similarity=0.186 Sum_probs=51.4
Q ss_pred hcCCCChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecc-cHHHHHHhc-----CcCC----------------CCce
Q 018586 195 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLR-----MNYP----------------DHML 252 (353)
Q Consensus 195 l~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~-~~~D~~~l~-----~~~~----------------~~~~ 252 (353)
+..-.+-.+++.+|.+++.+ . .+||||| ..||+.+|. .+.+ ....
T Consensus 67 v~~~~~E~~lL~~F~~~i~~------------~-~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~ 133 (204)
T cd05783 67 VEFFDSEKELIREAFKIISE------------Y-PIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIH 133 (204)
T ss_pred EEecCCHHHHHHHHHHHHhc------------C-CEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEE
Confidence 33446789999999999932 2 4899999 568999987 2222 1334
Q ss_pred eecccccCC-c-----c-cCCCCCcHHHHHHHHhCCc
Q 018586 253 RDTAKYRPL-M-----K-TNLVSHSLKYLTRTYLGYD 282 (353)
Q Consensus 253 ~Dt~~l~~~-~-----~-~~~~~~~L~~l~~~~~~~~ 282 (353)
+|....... . + ....+++|+.+|+.+||..
T Consensus 134 iDl~~~~~~~~~~~~~~~~~~~~~~L~~Va~~~lg~~ 170 (204)
T cd05783 134 IDLYKFFSNRAIQVYAFGNKYREYTLDAVAKALLGEG 170 (204)
T ss_pred eECHHHhhccchhhhhhccccccCcHHHHHHHhcCCC
Confidence 666554332 1 1 1346899999999998876
No 99
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.06 E-value=0.00015 Score=67.61 Aligned_cols=88 Identities=20% Similarity=0.277 Sum_probs=64.9
Q ss_pred ceeeccccccccChHHHHHHHhhhcCCCCC-CccccCcccCCChHHHHhccCCCCCCCCCCcccc---------------
Q 018586 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQ-PKCAVCQKLSKSFESLREHLTGPLSKAHCSGIFS--------------- 77 (353)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~h~~~~-~~C~~C~~~f~~~~~l~~H~~~~~~c~~Cgk~f~--------------- 77 (353)
-|.|..|...|...-.|.+|.=. ..-.. .+|..|++.|+-..+|..|.++.++-.+=++.-.
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~--RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~e 344 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCP--RIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQE 344 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCC--eeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhh
Confidence 38899999999999999998732 22222 3999999999999999999844433211111000
Q ss_pred -----------ccccccccccccCchhHHHHHHHhcC
Q 018586 78 -----------DRGCNLCMNIFDSPSSLIKHKEACSL 103 (353)
Q Consensus 78 -----------~~~C~~C~k~F~~~s~L~~H~~~h~~ 103 (353)
-..|..|+|+|.....|+.|+-+|+.
T Consensus 345 a~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 345 AERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred ccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 01399999999999999999999873
No 100
>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=97.00 E-value=0.0005 Score=37.42 Aligned_cols=22 Identities=41% Similarity=0.689 Sum_probs=20.6
Q ss_pred eeeccccccccChHHHHHHHhh
Q 018586 15 HKCVACYKQFKRKDHLIEHMKI 36 (353)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (353)
|.|+.|++.|..++.|..|++.
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 7899999999999999999986
No 101
>PLN03086 PRLI-interacting factor K; Provisional
Probab=96.90 E-value=0.0007 Score=66.95 Aligned_cols=77 Identities=17% Similarity=0.372 Sum_probs=55.2
Q ss_pred CceeeccccccccChHHHHHHHhhhcCCCCCC-ccccCcccCCC----------hHHHHhccCCCCCCCCCCcccccccc
Q 018586 13 ARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKS----------FESLREHLTGPLSKAHCSGIFSDRGC 81 (353)
Q Consensus 13 k~~~C~~C~k~f~~~~~l~~H~~~~~h~~~~~-~C~~C~~~f~~----------~~~l~~H~~~~~~c~~Cgk~f~~~~C 81 (353)
+|+.|+ ||+.+ .+..|..|+.+ |..+++ .|..|+..+.. .+.|..|... ||..- ..|
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~t--hCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~------CG~rt--~~C 544 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQAS--TCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESI------CGSRT--APC 544 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhc--cCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHh------cCCcc--eEc
Confidence 789999 99765 56889999998 999999 99999998852 3578888611 11111 147
Q ss_pred ccccccccCchhHHHHHHHhc
Q 018586 82 NLCMNIFDSPSSLIKHKEACS 102 (353)
Q Consensus 82 ~~C~k~F~~~s~L~~H~~~h~ 102 (353)
..||+.+..+ .+..|+...+
T Consensus 545 ~~Cgk~Vrlr-dm~~H~~~~h 564 (567)
T PLN03086 545 DSCGRSVMLK-EMDIHQIAVH 564 (567)
T ss_pred cccCCeeeeh-hHHHHHHHhh
Confidence 7788777666 4667776543
No 102
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=96.90 E-value=0.0042 Score=51.94 Aligned_cols=89 Identities=24% Similarity=0.394 Sum_probs=63.8
Q ss_pred HHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhc---CcCCCCceeecccccCCcccCCCCCcHHHHHHHHhCC
Q 018586 205 KDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR---MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGY 281 (353)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~---~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~ 281 (353)
...+.+++. +.+...||||+.+|+.+|. +..+. ++||+..+..+.|....++|+.++..|+|.
T Consensus 64 ~~~l~~~l~------------~~~~~kv~~d~k~~~~~L~~~gi~~~~--~~D~~laayll~p~~~~~~l~~l~~~~l~~ 129 (172)
T smart00474 64 LEILKDLLE------------DETITKVGHNAKFDLHVLARFGIELEN--IFDTMLAAYLLLGGPSKHGLATLLKEYLGV 129 (172)
T ss_pred HHHHHHHhc------------CCCceEEEechHHHHHHHHHCCCcccc--hhHHHHHHHHHcCCCCcCCHHHHHHHHhCC
Confidence 455777772 2456799999999999996 22322 489998888787766546999999999888
Q ss_pred cCCCC--------CC-------ChHHHHHHHHHHHHHHHhc
Q 018586 282 DIQSG--------VH-------DPYEDCVSVMRLYKRFRRQ 307 (353)
Q Consensus 282 ~~~~~--------~H-------~Al~Da~~t~~l~~~~~~~ 307 (353)
.+... .. -|..||.++.+|+..+.++
T Consensus 130 ~~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~ 170 (172)
T smart00474 130 ELDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKE 170 (172)
T ss_pred CCCcccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 74310 00 1566788888888777665
No 103
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=96.79 E-value=0.0057 Score=53.07 Aligned_cols=94 Identities=19% Similarity=0.224 Sum_probs=65.9
Q ss_pred ChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecc-cHHHHHHhc-------CcCCC-----------------Cceee
Q 018586 200 PLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLR-------MNYPD-----------------HMLRD 254 (353)
Q Consensus 200 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~-~~~D~~~l~-------~~~~~-----------------~~~~D 254 (353)
..++++.+|.+++.. ....||+|| -.||+.+|. +..|. ...+|
T Consensus 36 ~E~~lL~~F~~~~~~------------~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~D 103 (209)
T PF10108_consen 36 DEKELLQDFFDLVEK------------YNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLD 103 (209)
T ss_pred CHHHHHHHHHHHHHh------------CCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCccccc
Confidence 378899999999942 345799999 789999988 22221 23467
Q ss_pred cccccCCcccCCCCCcHHHHHHHHhCCcCCCCCCCh------------------HHHHHHHHHHHHHHHhc
Q 018586 255 TAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGVHDP------------------YEDCVSVMRLYKRFRRQ 307 (353)
Q Consensus 255 t~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~H~A------------------l~Da~~t~~l~~~~~~~ 307 (353)
++.+.... +.....+|+.||..+ |++-..+-.-+ ..|+++|+.||.++.--
T Consensus 104 Lmd~l~~~-g~~~~~sLd~la~~l-giPgK~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~~ 172 (209)
T PF10108_consen 104 LMDLLSFY-GAKARTSLDELAALL-GIPGKDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFELL 172 (209)
T ss_pred HHHHHhcc-CccccCCHHHHHHHc-CCCCCCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 77654332 244578999999988 99844332211 34999999999998754
No 104
>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=96.77 E-value=0.0038 Score=56.73 Aligned_cols=72 Identities=22% Similarity=0.170 Sum_probs=55.5
Q ss_pred CCcEEEecccHHHHHHhc-------------------CcCCCCceeecccccCCcccCCCCCcHHHHHHHHhCCcC----
Q 018586 227 KARLLVGHGLEHDLDSLR-------------------MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDI---- 283 (353)
Q Consensus 227 ~~~~lvgh~~~~D~~~l~-------------------~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~---- 283 (353)
...+|||||.-+|+.+|- .-+|. ++||..++.... ....+|+.|++.+ +...
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 458999999999999976 11565 889998887664 3467899999988 6653
Q ss_pred -------------------CCC-CCChHHHHHHHHHHHHH
Q 018586 284 -------------------QSG-VHDPYEDCVSVMRLYKR 303 (353)
Q Consensus 284 -------------------~~~-~H~Al~Da~~t~~l~~~ 303 (353)
.+. .|.|-.||.+|+.+|.+
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 233 89999999999999864
No 105
>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=96.68 E-value=0.013 Score=52.08 Aligned_cols=129 Identities=13% Similarity=0.174 Sum_probs=73.2
Q ss_pred ccCCCceeeccCcccccc---CCC-CccceeEEeee-cCCCC--eEEee-ec-cCCCCccccccccCCCCHhhhcCCCCh
Q 018586 131 TCRGPKAVAMDCEMVGGG---SNG-TLDLCARVCLV-DEDEN--VIFHT-YV-QPQLPVTNYRYEVTGLTEEDIKNAMPL 201 (353)
Q Consensus 131 ~~~~~~~~~~D~Ettg~~---~~~-~~~il~~v~iv-d~~g~--~~~~~-lv-~P~~~i~~~~~~~~GIt~e~l~~~~~~ 201 (353)
+.+..+.+++|+|+.... ++. ..+| ..++++ ...|. ..... ++ .+..++ ....|....+.
T Consensus 3 ~~p~l~~ls~DIE~~s~~g~fP~p~~D~I-i~Is~~~~~~~~~~~~~~~~~~l~~~~~~----------~~~~v~~~~~E 71 (230)
T cd05777 3 KIAPLRILSFDIECAGRKGVFPEPEKDPV-IQIANVVTRQGEGEPFIRNIFTLKTCAPI----------VGAQVFSFETE 71 (230)
T ss_pred CCCCceEEEEEEEECCCCCCCCCCCCCeE-EEEEEEEEeCCCCCCceeEEEEeCCCCCC----------CCCEEEEECCH
Confidence 346677899999998421 222 2233 344444 22332 11111 11 111111 11223345688
Q ss_pred HHHHHHHHHHHhcCCCCcccccCCCCCcEEEeccc-HHHHHHhc-----CcCCC--------------------------
Q 018586 202 KEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-----MNYPD-------------------------- 249 (353)
Q Consensus 202 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-----~~~~~-------------------------- 249 (353)
.+++..|.+++...++ .+|+|||+ .||+.+|. +..+.
T Consensus 72 ~eLL~~f~~~i~~~DP-----------Dii~GyN~~~FDl~yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~ 140 (230)
T cd05777 72 EELLLAWRDFVQEVDP-----------DIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGT 140 (230)
T ss_pred HHHHHHHHHHHHhcCC-----------CEEEEecCCCCCHHHHHHHHHHhCCccccccccccCCceeEeCCccccccccc
Confidence 8999999999955433 59999995 46999976 11110
Q ss_pred ----------CceeecccccCCcccCCCCCcHHHHHHHHhCCc
Q 018586 250 ----------HMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 282 (353)
Q Consensus 250 ----------~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 282 (353)
..++|+..+.+.. ....+|+|+++|+.+||..
T Consensus 141 ~~~~~~~i~GR~~iD~~~~~~~~-~kl~sy~L~~Va~~~Lg~~ 182 (230)
T cd05777 141 RETKEINIEGRIQFDLLQVIQRD-YKLRSYSLNSVSAHFLGEQ 182 (230)
T ss_pred ccceEEEEcCEEeeeHHHHHHHh-cCcccCcHHHHHHHHhCCC
Confidence 1123444433332 2467899999999998876
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=96.37 E-value=0.0023 Score=34.82 Aligned_cols=23 Identities=30% Similarity=0.541 Sum_probs=18.9
Q ss_pred ccccccccccCchhHHHHHHHhc
Q 018586 80 GCNLCMNIFDSPSSLIKHKEACS 102 (353)
Q Consensus 80 ~C~~C~k~F~~~s~L~~H~~~h~ 102 (353)
.|+.|++.|.+...|..|+++|+
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 48999999999999999999874
No 107
>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=96.34 E-value=0.028 Score=50.00 Aligned_cols=105 Identities=9% Similarity=0.107 Sum_probs=66.9
Q ss_pred CHhhhcCCCChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEeccc-HHHHHHhc-----CcCC-------C--------
Q 018586 191 TEEDIKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-----MNYP-------D-------- 249 (353)
Q Consensus 191 t~e~l~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-----~~~~-------~-------- 249 (353)
....|.-.++..+++.+|.+++..-++ .+|+|||+ .||+.+|- +..+ +
T Consensus 71 ~~~~v~~~~~E~~LL~~f~~~i~~~DP-----------Dii~GyNi~~fd~~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~ 139 (231)
T cd05778 71 SGIPVEVVESELELFEELIDLVRRFDP-----------DILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGK 139 (231)
T ss_pred CCCeEEEeCCHHHHHHHHHHHHHHhCC-----------CEEEEeccccCcHHHHHHHHHHhCCcchhhhccCCCCCCccc
Confidence 334455667889999999999966644 69999997 57888865 1100 0
Q ss_pred --------------------CceeecccccCCcccCCCCCcHHHHHHHHhCCcCCCCCCChHHHHH------HHHHHHHH
Q 018586 250 --------------------HMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGVHDPYEDCV------SVMRLYKR 303 (353)
Q Consensus 250 --------------------~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~H~Al~Da~------~t~~l~~~ 303 (353)
..++|+..+.+.- ....+|+|..++..+||.....-.+..+.+.+ ...++...
T Consensus 140 ~~~~~~~~g~~~~~~~~i~GRi~lD~~~~~r~~-~kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y 218 (231)
T cd05778 140 FGDRDDEWGYTHTSGIKIVGRHILNVWRLMRSE-LALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEY 218 (231)
T ss_pred ccccccccccccCCceEEeeEEEeEhHHHHHHH-cCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHH
Confidence 1122333333221 25678999999999999975544566666653 34455555
Q ss_pred HHhc
Q 018586 304 FRRQ 307 (353)
Q Consensus 304 ~~~~ 307 (353)
+.++
T Consensus 219 ~l~d 222 (231)
T cd05778 219 YLKR 222 (231)
T ss_pred HHHH
Confidence 5554
No 108
>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=96.29 E-value=0.013 Score=51.29 Aligned_cols=69 Identities=20% Similarity=0.249 Sum_probs=48.7
Q ss_pred ChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEeccc-HHHHHHhc-------CcCCC----------------Cceeec
Q 018586 200 PLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-------MNYPD----------------HMLRDT 255 (353)
Q Consensus 200 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-------~~~~~----------------~~~~Dt 255 (353)
+-.+++.+|.++|.+ .+.+|||||. .||+.+|. +..|. ...+|+
T Consensus 77 ~E~elL~~F~~~i~~------------~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL 144 (208)
T cd05782 77 DEKELLEDFFQLIEK------------KNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDL 144 (208)
T ss_pred CHHHHHHHHHHHHHH------------hCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccH
Confidence 347899999999943 2348999995 88999998 22221 126777
Q ss_pred ccccCCcccCCCCCcHHHHHHHHhCCc
Q 018586 256 AKYRPLMKTNLVSHSLKYLTRTYLGYD 282 (353)
Q Consensus 256 ~~l~~~~~~~~~~~~L~~l~~~~~~~~ 282 (353)
..+.+.. ....+++|+.+|+.+ |++
T Consensus 145 ~~~~~~~-~~~~~~~L~~va~~l-G~~ 169 (208)
T cd05782 145 MDLLAFY-GARARASLDLLAKLL-GIP 169 (208)
T ss_pred HHHHhcc-CccCCCCHHHHHHHh-CCC
Confidence 7765443 224689999999876 875
No 109
>PHA02528 43 DNA polymerase; Provisional
Probab=96.24 E-value=0.035 Score=58.56 Aligned_cols=160 Identities=13% Similarity=0.028 Sum_probs=87.4
Q ss_pred CCCceeeccCcccccc----CCCCccceeEEeeecCCCCeEEeeeccCCCCccccccccC--CCCHhhhcCCCChHHHHH
Q 018586 133 RGPKAVAMDCEMVGGG----SNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVT--GLTEEDIKNAMPLKEVKD 206 (353)
Q Consensus 133 ~~~~~~~~D~Ettg~~----~~~~~~il~~v~ivd~~g~~~~~~lv~P~~~i~~~~~~~~--GIt~e~l~~~~~~~~v~~ 206 (353)
+.-+++++|+|++..+ +......+..+++.+..+..++-..+....+......... ....-.+.--.+-.+++.
T Consensus 104 p~lrv~s~DIE~~~~~gfP~p~~~~d~IisIsl~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~sE~eLL~ 183 (881)
T PHA02528 104 SKIRIANLDIEVTAEDGFPDPEEAKYEIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPQEILDKVVYMPFDTEREMLL 183 (881)
T ss_pred CCccEEEEEEEECCCCCCCCcccCCCcEEEEEEecCCCCEEEEEEecCcccccccCCcccccccCCeeEEEcCCHHHHHH
Confidence 5778999999997521 1111212246666666655432222211000000000000 001111222467889999
Q ss_pred HHHHHHhcCCCCcccccCCCCCcEEEecc-cHHHHHHhc------CcC------C-C-----------------------
Q 018586 207 KILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLR------MNY------P-D----------------------- 249 (353)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~lvgh~-~~~D~~~l~------~~~------~-~----------------------- 249 (353)
.|.+++...++ .+|+||| ..||+.+|. ++. . .
T Consensus 184 ~F~~~i~~~DP-----------DII~GyNi~~FDlpYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~G 252 (881)
T PHA02528 184 EYINFWEENTP-----------VIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISG 252 (881)
T ss_pred HHHHHHHHhCC-----------cEEEecCCccCCHHHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcc
Confidence 99999965543 5999999 557999876 110 0 0
Q ss_pred CceeecccccCCc-ccCCCCCcHHHHHHHHhCCcCCCC----------------CCChHHHHHHHHHHHHH
Q 018586 250 HMLRDTAKYRPLM-KTNLVSHSLKYLTRTYLGYDIQSG----------------VHDPYEDCVSVMRLYKR 303 (353)
Q Consensus 250 ~~~~Dt~~l~~~~-~~~~~~~~L~~l~~~~~~~~~~~~----------------~H~Al~Da~~t~~l~~~ 303 (353)
.-++|...+.+.+ .....+|+|+.+++.+||..-..- .+-.+.||..+.+|+.+
T Consensus 253 Rv~lD~~dl~k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 253 ISILDYLDLYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred eEEEeHHHHHHHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 0022333333322 224678999999999988763220 11225699999999888
No 110
>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=96.23 E-value=0.0036 Score=35.43 Aligned_cols=23 Identities=30% Similarity=0.504 Sum_probs=21.8
Q ss_pred ceeeccccccccChHHHHHHHhh
Q 018586 14 RHKCVACYKQFKRKDHLIEHMKI 36 (353)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~ 36 (353)
||+|..|++.|.....|..|++.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~ 23 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRS 23 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCT
T ss_pred CCCCCccCCccCChhHHHHHhHH
Confidence 68999999999999999999987
No 111
>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=96.18 E-value=0.026 Score=47.66 Aligned_cols=83 Identities=20% Similarity=0.227 Sum_probs=60.2
Q ss_pred CCcEEEecccHHHHHHhcC--cCCCCceeecccccCCcccCCCCCcHHHHHHHHhCCcCCCC------C---------CC
Q 018586 227 KARLLVGHGLEHDLDSLRM--NYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSG------V---------HD 289 (353)
Q Consensus 227 ~~~~lvgh~~~~D~~~l~~--~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~------~---------H~ 289 (353)
.+...||||+.+|+..|.. +.....+.|++..+..+.|... .+|+.+++.|+|..+... . +-
T Consensus 63 ~~i~kv~~d~K~~~~~L~~~~gi~~~~~~D~~laayLl~p~~~-~~l~~l~~~~l~~~~~~~~~~~~w~~~~l~~~~~~y 141 (178)
T cd06142 63 PNIVKVFHAAREDLELLKRDFGILPQNLFDTQIAARLLGLGDS-VGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEY 141 (178)
T ss_pred CCceEEEeccHHHHHHHHHHcCCCCCCcccHHHHHHHhCCCcc-ccHHHHHHHHhCCCCCcccccccCCCCCCCHHHHHH
Confidence 4568999999999999952 2223346899887777777544 599999999988763211 0 12
Q ss_pred hHHHHHHHHHHHHHHHhchhh
Q 018586 290 PYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 290 Al~Da~~t~~l~~~~~~~~~~ 310 (353)
|..||.++.+|+..+..+..+
T Consensus 142 aa~~a~~l~~L~~~l~~~L~e 162 (178)
T cd06142 142 AALDVRYLLPLYEKLKEELEE 162 (178)
T ss_pred HHHhHHHHHHHHHHHHHHHHH
Confidence 667788899999888877654
No 112
>PRK05762 DNA polymerase II; Reviewed
Probab=96.16 E-value=0.033 Score=58.58 Aligned_cols=99 Identities=18% Similarity=0.278 Sum_probs=67.0
Q ss_pred hcCCCChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEeccc-HHHHHHhc-------CcC--------------CC---
Q 018586 195 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-------MNY--------------PD--- 249 (353)
Q Consensus 195 l~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-------~~~--------------~~--- 249 (353)
+..-++-.+++..|.+++.+.++ .+|||||+ .||+.+|. +.. +.
T Consensus 197 v~~~~sE~~LL~~F~~~i~~~DP-----------DIIvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~ 265 (786)
T PRK05762 197 LEYVADEKALLEKFNAWFAEHDP-----------DVIIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSG 265 (786)
T ss_pred EEEcCCHHHHHHHHHHHHHhcCC-----------CEEEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCC
Confidence 45567889999999999965533 59999995 47999987 111 10
Q ss_pred --------CceeecccccCCcccCCCCCcHHHHHHHHhCCcCCC-CCC-------------------ChHHHHHHHHHHH
Q 018586 250 --------HMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQS-GVH-------------------DPYEDCVSVMRLY 301 (353)
Q Consensus 250 --------~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~-~~H-------------------~Al~Da~~t~~l~ 301 (353)
..++|+..+.+.......+|+|+.+++.+||..-.. ..+ -.+.||..|.+|+
T Consensus 266 ~~~~~i~GRv~lDl~~~~k~~~~~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~ 345 (786)
T PRK05762 266 YGFASVPGRLVLDGIDALKSATWVFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIF 345 (786)
T ss_pred cceEEEeeEEEEEHHHHHHHhhccCCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHH
Confidence 114555555444333567899999999998865321 111 1367999999998
Q ss_pred HHH
Q 018586 302 KRF 304 (353)
Q Consensus 302 ~~~ 304 (353)
.++
T Consensus 346 ~kl 348 (786)
T PRK05762 346 EKT 348 (786)
T ss_pred HHh
Confidence 844
No 113
>PHA00732 hypothetical protein
Probab=96.13 E-value=0.005 Score=44.88 Aligned_cols=44 Identities=20% Similarity=0.436 Sum_probs=25.8
Q ss_pred ccccCcccCCChHHHHhccCC-CCCCCCCCccccccccccccccccCchhHHHHHHHh
Q 018586 45 KCAVCQKLSKSFESLREHLTG-PLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEAC 101 (353)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~-~~~c~~Cgk~f~~~~C~~C~k~F~~~s~L~~H~~~h 101 (353)
.|..|++.|.+.+.|..|+.. ..+ ..|+.|+++|. .|..|.+++
T Consensus 3 ~C~~Cgk~F~s~s~Lk~H~r~~H~~----------~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 3 KCPICGFTTVTLFALKQHARRNHTL----------TKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred cCCCCCCccCCHHHHHHHhhcccCC----------CccCCCCCEeC---Chhhhhccc
Confidence 577777777777777777631 111 13666666665 355666443
No 114
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=96.09 E-value=0.033 Score=60.14 Aligned_cols=154 Identities=16% Similarity=0.137 Sum_probs=88.0
Q ss_pred ccCCCceeeccCcccccc----CC-CCccceeEEee-ecCCCCe--EE-eeeccCCCCccccccccCCCCHhhhcCCCCh
Q 018586 131 TCRGPKAVAMDCEMVGGG----SN-GTLDLCARVCL-VDEDENV--IF-HTYVQPQLPVTNYRYEVTGLTEEDIKNAMPL 201 (353)
Q Consensus 131 ~~~~~~~~~~D~Ettg~~----~~-~~~~il~~v~i-vd~~g~~--~~-~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~ 201 (353)
..++.++++||+|+.+.. ++ ....+ ..++. +...|.. .+ ..++-+.. ...+.| ..|.-..+-
T Consensus 260 ~~pplrilSfDIE~~~~~g~~FP~~~~D~I-IqIs~~~~~~g~~~~~~~r~vftl~~-----c~~i~g---~~V~~f~sE 330 (1054)
T PTZ00166 260 TIAPLRILSFDIECIKLKGLGFPEAENDPV-IQISSVVTNQGDEEEPLTKFIFTLKE-----CASIAG---ANVLSFETE 330 (1054)
T ss_pred CCCCcEEEEEEEEECCCCCCCCCCCCCCcE-EEEEEEEeeCCCccCCcceEEEecCc-----cccCCC---ceEEEeCCH
Confidence 457778999999998631 11 12233 23333 2334432 11 11121211 111222 223445688
Q ss_pred HHHHHHHHHHHhcCCCCcccccCCCCCcEEEeccc-HHHHHHhc-----CcCCC--------------------------
Q 018586 202 KEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-----MNYPD-------------------------- 249 (353)
Q Consensus 202 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-----~~~~~-------------------------- 249 (353)
.+++..|.+++..-++ .||+|||+ .||+.+|- +..+.
T Consensus 331 ~eLL~~f~~~I~~~DP-----------DII~GYNi~~FDlpYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~ 399 (1054)
T PTZ00166 331 KELLLAWAEFVIAVDP-----------DFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGT 399 (1054)
T ss_pred HHHHHHHHHHHHhcCC-----------CEEEecCCcCCcHHHHHHHHHHhCCCchhhcCcccCCCccccccccccccccc
Confidence 8999999999965543 69999996 47999876 11110
Q ss_pred ----------CceeecccccCCcccCCCCCcHHHHHHHHhCCcCCCCCC-------------------ChHHHHHHHHHH
Q 018586 250 ----------HMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGVH-------------------DPYEDCVSVMRL 300 (353)
Q Consensus 250 ----------~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~H-------------------~Al~Da~~t~~l 300 (353)
..++|+..+.+.. ....+|+|+.++.++||.....-.| -.+.||..+.+|
T Consensus 400 ~~~~~~~i~GR~~iDl~~~~~~~-~kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L 478 (1054)
T PTZ00166 400 RESKEINIEGRIQFDVMDLIRRD-YKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRL 478 (1054)
T ss_pred cccceeEeeeEEEEEHHHHHHHh-cCcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHH
Confidence 1223444444332 2567899999999999976321111 124688888888
Q ss_pred HHHHH
Q 018586 301 YKRFR 305 (353)
Q Consensus 301 ~~~~~ 305 (353)
+.++.
T Consensus 479 ~~kl~ 483 (1054)
T PTZ00166 479 LDKLL 483 (1054)
T ss_pred HHHHh
Confidence 87764
No 115
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=95.80 E-value=0.039 Score=55.04 Aligned_cols=95 Identities=21% Similarity=0.189 Sum_probs=72.8
Q ss_pred HHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCcCC-CCceeecccccCCcccCCCCCcHHHHHHHHhCCc
Q 018586 204 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP-DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 282 (353)
Q Consensus 204 v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~-~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 282 (353)
+...+..|+ .+.+...||||+.+|+.+|..... .....||+...-.+.|..+.+.+++|++.+++..
T Consensus 66 ~~~~l~~~l------------~~~~~~kv~~~~K~d~~~l~~~Gi~~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~ 133 (593)
T COG0749 66 VLAALKPLL------------EDEGIKKVGQNLKYDYKVLANLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLE 133 (593)
T ss_pred hHHHHHHHh------------hCcccchhccccchhHHHHHHcCCcccchHHHHHHHhccCcCcCcCCHHHHHHHhcCCc
Confidence 788888999 446668999999999999983332 1346799999888888888899999999997765
Q ss_pred CCCC---------------------CCChHHHHHHHHHHHHHHHhchhh
Q 018586 283 IQSG---------------------VHDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 283 ~~~~---------------------~H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
.... .-.+..||.+|.+|+..+..+..+
T Consensus 134 ~~~~~~i~~kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~l~~ 182 (593)
T COG0749 134 TITFEDIAGKGKKQLTFADVKLEKATEYAAEDADATLRLESILEPELLK 182 (593)
T ss_pred cchhHHhhccccccCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 3221 123467999999999988866544
No 116
>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=95.78 E-value=0.028 Score=47.62 Aligned_cols=94 Identities=19% Similarity=0.216 Sum_probs=65.8
Q ss_pred HHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhc---CcCCCCceeecccccCCcccCCCCCcHHHHHHHHhC
Q 018586 204 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR---MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLG 280 (353)
Q Consensus 204 v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~---~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~ 280 (353)
+...+.+++. +.+...|+||+.+|+.+|. +..+ ..+.||+..+..+.|....++|++++..|++
T Consensus 44 ~~~~l~~~l~------------~~~~~ki~~d~K~~~~~l~~~gi~~~-~~~fDt~laaYLL~p~~~~~~l~~l~~~yl~ 110 (178)
T cd06140 44 DLAALKEWLE------------DEKIPKVGHDAKRAYVALKRHGIELA-GVAFDTMLAAYLLDPTRSSYDLADLAKRYLG 110 (178)
T ss_pred HHHHHHHHHh------------CCCCceeccchhHHHHHHHHCCCcCC-CcchhHHHHHHHcCCCCCCCCHHHHHHHHcC
Confidence 4455777782 2456799999999999996 3333 3468999999888887655799999999988
Q ss_pred CcCCC------CC-------C-----ChHHHHHHHHHHHHHHHhchhh
Q 018586 281 YDIQS------GV-------H-----DPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 281 ~~~~~------~~-------H-----~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
..+.. .. . -+..||.++..|+..+.++..+
T Consensus 111 ~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~~L~~ 158 (178)
T cd06140 111 RELPSDEEVYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEEELEE 158 (178)
T ss_pred CCCcchHHhcCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 76321 00 0 1445567777777777776543
No 117
>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=95.77 E-value=0.0068 Score=32.84 Aligned_cols=22 Identities=36% Similarity=0.765 Sum_probs=18.6
Q ss_pred eeeccccccccChHHHHHHHhh
Q 018586 15 HKCVACYKQFKRKDHLIEHMKI 36 (353)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (353)
|.|+.|++.|.....|..|+..
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 6899999999999999999986
No 118
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=95.73 E-value=0.12 Score=55.99 Aligned_cols=185 Identities=15% Similarity=0.159 Sum_probs=108.6
Q ss_pred ccccCCCceeeccCcccccc---CC-CCccceeEEeeecCCCCeEEeeeccCCCCccccccccCCCCHhh------hcCC
Q 018586 129 KRTCRGPKAVAMDCEMVGGG---SN-GTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEED------IKNA 198 (353)
Q Consensus 129 ~~~~~~~~~~~~D~Ettg~~---~~-~~~~il~~v~ivd~~g~~~~~~lv~P~~~i~~~~~~~~GIt~e~------l~~~ 198 (353)
....+..++.+||+|||-+. +| ...+|.-.--++|..|-.+.+.-| |+..+..+.=-..++ +-+.
T Consensus 240 ~i~radp~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREi-----Vs~DIedfEYTPKpE~eG~F~v~Ne 314 (2173)
T KOG1798|consen 240 LIERADPRVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREI-----VSEDIEDFEYTPKPEYEGPFCVFNE 314 (2173)
T ss_pred ccccCCceEEEEeeecccCCCCCCCcccceEEEEEEEecCceEEEechhh-----hccchhhcccCCccccccceEEecC
Confidence 34467778999999999864 33 233443344456777776644322 111111111111111 2245
Q ss_pred CChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHH-HHHHhcC-------cCCC--Cceeeccc-----------
Q 018586 199 MPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEH-DLDSLRM-------NYPD--HMLRDTAK----------- 257 (353)
Q Consensus 199 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~-D~~~l~~-------~~~~--~~~~Dt~~----------- 257 (353)
+.-..++..+.+-+.+. +..|+|.+|-+| |+.|+.. .... ....|..-
T Consensus 315 ~dEv~Ll~RfFeHiq~~-----------kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmD 383 (2173)
T KOG1798|consen 315 PDEVGLLQRFFEHIQEV-----------KPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMD 383 (2173)
T ss_pred CcHHHHHHHHHHHHHhc-----------CCcEEEEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehh
Confidence 66778888888888554 667999999655 9999881 1100 11123222
Q ss_pred ccCCc----ccCCCCCcHHHHHHHHhCCcCCCC----------------CCChHHHHHHHHHHHHHHHhchhhhhhhccc
Q 018586 258 YRPLM----KTNLVSHSLKYLTRTYLGYDIQSG----------------VHDPYEDCVSVMRLYKRFRRQDHQVEEIGNQ 317 (353)
Q Consensus 258 l~~~~----~~~~~~~~L~~l~~~~~~~~~~~~----------------~H~Al~Da~~t~~l~~~~~~~~~~~~~~~~~ 317 (353)
-+++. +-..++.+|+.+.+.-||...-.- +--+..||+||.-||.++..-+- +..-
T Consensus 384 cfrWVKRDSYLPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVhPFI--FsLc-- 459 (2173)
T KOG1798|consen 384 CFRWVKRDSYLPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVHPFI--FSLC-- 459 (2173)
T ss_pred hhhhhhhcccCCCcccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhhhHH--hhhh--
Confidence 11222 224557889998888778762211 34458899999999999876531 1111
Q ss_pred CCCCCCCCcchhHHhhcChhhhhccCCC
Q 018586 318 NTTGSFDSYKYKELEKMSPNELYQISKS 345 (353)
Q Consensus 318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 345 (353)
-+.++.|+|.+.-+.+
T Consensus 460 ------------tIIPl~PDevLRKGSG 475 (2173)
T KOG1798|consen 460 ------------TIIPLNPDEVLRKGSG 475 (2173)
T ss_pred ------------hccccChHHHHhcCcc
Confidence 1577889988876654
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=95.72 E-value=0.023 Score=50.69 Aligned_cols=76 Identities=26% Similarity=0.321 Sum_probs=54.9
Q ss_pred hcCCCChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEeccc-HHHHHHhc-----CcCC--------------------
Q 018586 195 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-----MNYP-------------------- 248 (353)
Q Consensus 195 l~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-----~~~~-------------------- 248 (353)
|.-..+..+.+..|.+++.+.++ .+|||||+ .||+.+|- +..+
T Consensus 76 v~~~~~E~~LL~~f~~~i~~~DP-----------DiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~ 144 (234)
T cd05776 76 VRIFENERALLNFFLAKLQKIDP-----------DVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGG 144 (234)
T ss_pred EEEeCCHHHHHHHHHHHHhhcCC-----------CEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccc
Confidence 44457788999999999976644 69999998 88999976 1111
Q ss_pred ---------CCceeecccccCCcccCCCCCcHHHHHHHHhCCc
Q 018586 249 ---------DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 282 (353)
Q Consensus 249 ---------~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 282 (353)
...++|+..+++.+. ...+|+|.++++.+||..
T Consensus 145 ~~~~~~~~~GRl~~D~~~~~k~~~-~~~sY~L~~va~~~Lg~~ 186 (234)
T cd05776 145 KFGERELTAGRLLCDTYLSAKELI-RCKSYDLTELSQQVLGIE 186 (234)
T ss_pred cccccccccCchhhccHHHHHHHh-CCCCCChHHHHHHHhCcC
Confidence 012345655555443 367999999999998974
No 120
>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=95.55 E-value=0.0096 Score=38.71 Aligned_cols=27 Identities=22% Similarity=0.531 Sum_probs=21.2
Q ss_pred ccccccccccCchhHHHHHHHhcCCCC
Q 018586 80 GCNLCMNIFDSPSSLIKHKEACSLSAP 106 (353)
Q Consensus 80 ~C~~C~k~F~~~s~L~~H~~~h~~~k~ 106 (353)
.|++|+..+.+.-+|++|++.+++.||
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 599999999999999999999888876
No 121
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.51 E-value=0.0099 Score=32.68 Aligned_cols=23 Identities=30% Similarity=0.567 Sum_probs=20.4
Q ss_pred ccccccccccCchhHHHHHHHhc
Q 018586 80 GCNLCMNIFDSPSSLIKHKEACS 102 (353)
Q Consensus 80 ~C~~C~k~F~~~s~L~~H~~~h~ 102 (353)
.|+.|+++|...+.|..|++.|.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHHhc
Confidence 48899999999999999999775
No 122
>PHA02570 dexA exonuclease; Provisional
Probab=95.31 E-value=0.081 Score=45.99 Aligned_cols=169 Identities=20% Similarity=0.202 Sum_probs=84.5
Q ss_pred eeccCccccccCCCCccceeEEeeecCCCCe-EEeeeccCCCCcccccc------ccCCC--------CHhh---hc---
Q 018586 138 VAMDCEMVGGGSNGTLDLCARVCLVDEDENV-IFHTYVQPQLPVTNYRY------EVTGL--------TEED---IK--- 196 (353)
Q Consensus 138 ~~~D~Ettg~~~~~~~~il~~v~ivd~~g~~-~~~~lv~P~~~i~~~~~------~~~GI--------t~e~---l~--- 196 (353)
+.+|.||-|..++..+-.+++|.+....|.. .|+.+|.....+.-... .+.+= ++|. |.
T Consensus 4 lMIDlETmG~~p~AaIisIgAV~Fdp~~~~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~L~~s~ 83 (220)
T PHA02570 4 FIIDFETFGNTPDGAVIDLAVIAFEHDPHNPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEARKNLKPSD 83 (220)
T ss_pred EEEEeeccCCCCCceEEEEEEEEecCCCCccccHHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHHHHhccCCC
Confidence 5799999999877665444666664333322 36666653211111000 01111 1111 11
Q ss_pred CCCChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCcCCC-CceeecccccCCcccCCCCCcHHHHH
Q 018586 197 NAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPD-HMLRDTAKYRPLMKTNLVSHSLKYLT 275 (353)
Q Consensus 197 ~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~-~~~~Dt~~l~~~~~~~~~~~~L~~l~ 275 (353)
+..++.+++.+|.+||..... ......+=|-+..||+.+|+--+-. +...+|-...+..+.+.+. -..+.
T Consensus 84 ~~~~l~~al~~F~~fi~~~~~-------~~~~~~vWgnG~sFD~~IL~~a~r~~~~~~~~~~~~Pw~fwN~RD--VRT~i 154 (220)
T PHA02570 84 EDVSTYEGHKKFFEYLEANGV-------DPWKSQGWCRGNSFDFPILVDVIRDIHNTRDTFKLEPVKFWNQRD--VRTAI 154 (220)
T ss_pred ccccHHHHHHHHHHHHHHcCC-------CccceeEecCCCccCHHHHHHHHHHHhcccCcCcCCCeeecCccc--hHHHH
Confidence 235699999999999943210 0123566778899999999611100 0011222222222222221 11222
Q ss_pred HH-HhCCc-----CC----CC--CCChHHHHHHHHHHHHHHHhchhhhhhhc
Q 018586 276 RT-YLGYD-----IQ----SG--VHDPYEDCVSVMRLYKRFRRQDHQVEEIG 315 (353)
Q Consensus 276 ~~-~~~~~-----~~----~~--~H~Al~Da~~t~~l~~~~~~~~~~~~~~~ 315 (353)
+. +|+.. +. .| +|+|+-||.--+..+..-.+-...+++.+
T Consensus 155 e~~~l~r~~~~cp~~~g~l~gfv~H~sihDcakd~lml~y~~rya~~le~~p 206 (220)
T PHA02570 155 EATLLTRGMTTCPLPKGTLDGFVAHDSIHDCAKDILMLIYAKRYALGLEDLP 206 (220)
T ss_pred hhhhccCCcccCCCcCccccchhhcccHHHHHHHHHHHHHHHHHhcCCCcCC
Confidence 21 12222 11 11 79999999877777666666555555554
No 123
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.14 E-value=0.045 Score=57.96 Aligned_cols=96 Identities=18% Similarity=0.144 Sum_probs=70.2
Q ss_pred ChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhc---CcCCCCceeecccccCCcccCCCCCcHHHHHH
Q 018586 200 PLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR---MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTR 276 (353)
Q Consensus 200 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~---~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~ 276 (353)
+...+...+..++. +.+...||||+.||+.+|. +..+ ..+.||+..+..+.|... .+|++++.
T Consensus 362 ~~~~~~~~l~~~l~------------~~~~~~v~~n~K~d~~~l~~~gi~~~-~~~~Dt~la~yll~~~~~-~~l~~la~ 427 (887)
T TIGR00593 362 LTILTDDKFARWLL------------NEQIKKIGHDAKFLMHLLKREGIELG-GVIFDTMLAAYLLDPAQV-STLDTLAR 427 (887)
T ss_pred hhHHHHHHHHHHHh------------CCCCcEEEeeHHHHHHHHHhCCCCCC-CcchhHHHHHHHcCCCCC-CCHHHHHH
Confidence 35567777888883 3445689999999999997 2222 346899998888887554 59999999
Q ss_pred HHhCCcCCC-------C----C-------CChHHHHHHHHHHHHHHHhchh
Q 018586 277 TYLGYDIQS-------G----V-------HDPYEDCVSVMRLYKRFRRQDH 309 (353)
Q Consensus 277 ~~~~~~~~~-------~----~-------H~Al~Da~~t~~l~~~~~~~~~ 309 (353)
.|++...-. + . .-|..||.+|..||..+..+..
T Consensus 428 ~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~ 478 (887)
T TIGR00593 428 RYLVEELILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKELD 478 (887)
T ss_pred HHcCcccccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 997754110 0 0 1367789999999999887754
No 124
>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=95.13 E-value=0.0074 Score=34.10 Aligned_cols=23 Identities=35% Similarity=0.599 Sum_probs=20.4
Q ss_pred ccccccccccCchhHHHHHHHhc
Q 018586 80 GCNLCMNIFDSPSSLIKHKEACS 102 (353)
Q Consensus 80 ~C~~C~k~F~~~s~L~~H~~~h~ 102 (353)
.|..|++.|.....|..|++.|.
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 48999999999999999998775
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=94.96 E-value=0.026 Score=37.89 Aligned_cols=36 Identities=25% Similarity=0.537 Sum_probs=22.1
Q ss_pred ceeeccccccccChHHHHHHHhhhcCCCCC-C-ccccCcc
Q 018586 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQ-P-KCAVCQK 51 (353)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~h~~~~-~-~C~~C~~ 51 (353)
.|.|+.|++. .+...|..|.... |..+. . .|+.|..
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~-H~~~~~~v~CPiC~~ 39 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDE-HRSESKNVVCPICSS 39 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhH-CcCCCCCccCCCchh
Confidence 4788889884 4456788887653 54432 2 4444443
No 126
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=94.84 E-value=0.011 Score=53.37 Aligned_cols=24 Identities=33% Similarity=0.577 Sum_probs=21.8
Q ss_pred CCceeecc--ccccccChHHHHHHHh
Q 018586 12 TARHKCVA--CYKQFKRKDHLIEHMK 35 (353)
Q Consensus 12 ~k~~~C~~--C~k~f~~~~~l~~H~~ 35 (353)
+|||+|++ |.|+++....|+-|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~l 372 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHML 372 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhh
Confidence 59999997 9999999999999987
No 127
>smart00355 ZnF_C2H2 zinc finger.
Probab=94.53 E-value=0.026 Score=30.88 Aligned_cols=22 Identities=45% Similarity=0.760 Sum_probs=19.9
Q ss_pred eeeccccccccChHHHHHHHhh
Q 018586 15 HKCVACYKQFKRKDHLIEHMKI 36 (353)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (353)
|.|+.|++.|.....+..|++.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~ 22 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRT 22 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHH
Confidence 5799999999999999999986
No 128
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=94.31 E-value=0.03 Score=42.30 Aligned_cols=75 Identities=25% Similarity=0.415 Sum_probs=21.0
Q ss_pred eeccccccccChHHHHHHHhhhcCCCCCCccccCcccCCChHHHHhccCCCCCCCCCCccccccccccccccccCchhHH
Q 018586 16 KCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLI 95 (353)
Q Consensus 16 ~C~~C~k~f~~~~~l~~H~~~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~~~~c~~Cgk~f~~~~C~~C~k~F~~~s~L~ 95 (353)
+|..|+..|.....+..|+... |.-..+.. ..+.....+..+.... ......|..|++.|.+...|.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~-H~~~~~~~----~~l~~~~~~~~~~~~~--------~~~~~~C~~C~~~f~s~~~l~ 67 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKK-HGFDIPDQ----KYLVDPNRLLNYLRKK--------VKESFRCPYCNKTFRSREALQ 67 (100)
T ss_dssp -------------------------------------------------------------SSEEBSSSS-EESSHHHHH
T ss_pred Cccccccccccccccccccccc-cccccccc----cccccccccccccccc--------cCCCCCCCccCCCCcCHHHHH
Confidence 4889999999999999998642 43222211 1111122222222100 000236999999999999999
Q ss_pred HHHHHhcC
Q 018586 96 KHKEACSL 103 (353)
Q Consensus 96 ~H~~~h~~ 103 (353)
.|++.+..
T Consensus 68 ~Hm~~~~H 75 (100)
T PF12756_consen 68 EHMRSKHH 75 (100)
T ss_dssp HHHHHTTT
T ss_pred HHHcCccC
Confidence 99998643
No 129
>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=94.31 E-value=0.37 Score=47.26 Aligned_cols=93 Identities=18% Similarity=0.298 Sum_probs=61.9
Q ss_pred CChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecccH-HHHHHhc-----CcCC------------------------
Q 018586 199 MPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLR-----MNYP------------------------ 248 (353)
Q Consensus 199 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~-~D~~~l~-----~~~~------------------------ 248 (353)
....+.+..|.+++...+ ..+++|||.. ||+.+|. +..+
T Consensus 67 ~~E~~lL~~f~~~i~~~d-----------pdii~g~N~~~FD~~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~ 135 (471)
T smart00486 67 NNEKELLKAFLEFIKKYD-----------PDIIYGHNISNFDLPYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSK 135 (471)
T ss_pred CCHHHHHHHHHHHHHHhC-----------CCEEEeecCCCCCHHHHHHHHHHcCCCCHHHcCcCCCCCCcccccCccccc
Confidence 377888999999985442 3699999975 8999976 1110
Q ss_pred -----------CCceeecccccCCcccCCCCCcHHHHHHHHhCCcCCCCC--C------------------ChHHHHHHH
Q 018586 249 -----------DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGV--H------------------DPYEDCVSV 297 (353)
Q Consensus 249 -----------~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~--H------------------~Al~Da~~t 297 (353)
....+|+..+.+... ....++|+.+++.+||.. ...- . -.+.||..+
T Consensus 136 ~~~~~~~~~~~g~~~~Dl~~~~~~~~-kl~~~~L~~va~~~l~~~-k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~ 213 (471)
T smart00486 136 SFGKTIKVKIKGRLVIDLYNLYKNKL-KLPSYKLDTVAEYLLGKE-KDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLT 213 (471)
T ss_pred cccccceeEeccEEEEEhHHHHHHHh-CcccCCHHHHHHHHhCCC-CCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHH
Confidence 023456666555444 367899999999998844 2211 1 114588888
Q ss_pred HHHHHHH
Q 018586 298 MRLYKRF 304 (353)
Q Consensus 298 ~~l~~~~ 304 (353)
.+|+.++
T Consensus 214 ~~l~~~l 220 (471)
T smart00486 214 LKLFNKL 220 (471)
T ss_pred HHHHHHH
Confidence 8888885
No 130
>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=94.13 E-value=0.13 Score=41.82 Aligned_cols=55 Identities=20% Similarity=0.190 Sum_probs=42.6
Q ss_pred CCcEEEecccHHHHHHhcC---cCCCCceeecccccCCcccCCCCCcHHHHHHHHhCCc
Q 018586 227 KARLLVGHGLEHDLDSLRM---NYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 282 (353)
Q Consensus 227 ~~~~lvgh~~~~D~~~l~~---~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 282 (353)
.+...|+|++..|+.+|.. ..+ ..+.||+..+..+.|...+.+|+.|++.|++..
T Consensus 52 ~~~~kv~~d~K~~~~~L~~~~~~~~-~~~~D~~laayLl~p~~~~~~l~~l~~~~l~~~ 109 (150)
T cd09018 52 EKALKVGQNLKYDRGILLNYFIELR-GIAFDTMLEAYILNSVAGRWDMDSLVERWLGHK 109 (150)
T ss_pred CCCceeeecHHHHHHHHHHcCCccC-CcchhHHHHHHHhCCCCCCCCHHHHHHHHhCCC
Confidence 4567899999999999962 222 346899998888877542359999999998877
No 131
>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=94.00 E-value=0.059 Score=35.10 Aligned_cols=27 Identities=22% Similarity=0.476 Sum_probs=18.5
Q ss_pred CCCCceeeccccccccChHHHHHHHhh
Q 018586 10 RSTARHKCVACYKQFKRKDHLIEHMKI 36 (353)
Q Consensus 10 ~~~k~~~C~~C~k~f~~~~~l~~H~~~ 36 (353)
..+.|..|+.|+..+.+..+|.+|+..
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~ 46 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEI 46 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHH
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHH
Confidence 346788999999999999999999975
No 132
>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=93.97 E-value=0.1 Score=48.70 Aligned_cols=90 Identities=13% Similarity=0.161 Sum_probs=53.9
Q ss_pred CCCceeeccCccccccC----CCCccceeEEee-ecCCC-----CeEEeeeccCCCCccccccccCCCCHhhhcCCCChH
Q 018586 133 RGPKAVAMDCEMVGGGS----NGTLDLCARVCL-VDEDE-----NVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLK 202 (353)
Q Consensus 133 ~~~~~~~~D~Ettg~~~----~~~~~il~~v~i-vd~~g-----~~~~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~ 202 (353)
+...++++|+|+...+. ....+| ..+++ +...| ....-.+..+... .. ...+.-..+..
T Consensus 155 p~l~i~s~DIe~~~~~~~~P~~~~d~I-~~Is~~~~~~~~~~~~~~~~~~~~~~~~~-~~---------~~~v~~~~~E~ 223 (325)
T PF03104_consen 155 PPLRILSFDIETYSNDGKFPDPEKDEI-IMISYVVYRNGSSEPYRRKVFTLGSCDSI-ED---------NVEVIYFDSEK 223 (325)
T ss_dssp GGSEEEEEEEEECSSSSSS-TTTTSEE-EEEEEEEEETTEEETTEEEEEECSCSCCT-TC---------TTEEEEESSHH
T ss_pred cccceeEEEEEEccccCCCCCCCCCeE-EEEEEEEEeccccCCCceEEEEecCCCCC-CC---------CcEEEEECCHH
Confidence 67789999999997641 223333 34443 22222 1112222222211 11 33444557788
Q ss_pred HHHHHHHHHHhcCCCCcccccCCCCCcEEEecccH-HHHHHhc
Q 018586 203 EVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLR 244 (353)
Q Consensus 203 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~-~D~~~l~ 244 (353)
+++..|.++|.+.++ .+|+|||+. ||+.+|-
T Consensus 224 ~lL~~f~~~i~~~dP-----------Dii~GyN~~~fD~~yl~ 255 (325)
T PF03104_consen 224 ELLEAFLDIIQEYDP-----------DIITGYNIDGFDLPYLI 255 (325)
T ss_dssp HHHHHHHHHHHHHS------------SEEEESSTTTTHHHHHH
T ss_pred HHHHHHHHHHHhcCC-----------cEEEEecccCCCHHHHH
Confidence 999999999966543 599999966 7999987
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=93.88 E-value=0.083 Score=45.45 Aligned_cols=82 Identities=26% Similarity=0.309 Sum_probs=57.6
Q ss_pred CCcEEEecccHHHHHHhc--CcCCCCceeecccccCCcccCCCCCcHHHHHHHHhCCcCCC-------CCC--------C
Q 018586 227 KARLLVGHGLEHDLDSLR--MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQS-------GVH--------D 289 (353)
Q Consensus 227 ~~~~lvgh~~~~D~~~l~--~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~-------~~H--------~ 289 (353)
.+...|+|++..|+..|. .+.....++|++..+..+.|. . .+|+.|++.|++..+.. +.. -
T Consensus 76 ~~i~kv~~d~K~~~~~L~~~~gi~~~~~fD~~laaYLL~p~-~-~~l~~l~~~yl~~~~~k~~~~~~~~~~~l~~~~~~y 153 (192)
T cd06147 76 PNILKVFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLP-R-HSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKY 153 (192)
T ss_pred CCceEEEechHHHHHHHHHHhCCCcCchHHHHHHHHHhCCC-c-ccHHHHHHHHhCCCcchhhhccccccCCCCHHHHHH
Confidence 557899999999999984 222111238999988888887 5 49999999998776210 112 1
Q ss_pred hHHHHHHHHHHHHHHHhchhh
Q 018586 290 PYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 290 Al~Da~~t~~l~~~~~~~~~~ 310 (353)
+..||.+...|+..+..+.++
T Consensus 154 ~a~~a~~l~~L~~~L~~~L~e 174 (192)
T cd06147 154 AREDTHYLLYIYDRLRNELLE 174 (192)
T ss_pred HHhhHHHHHHHHHHHHHHHHH
Confidence 455677778888888777654
No 134
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=93.82 E-value=0.49 Score=46.65 Aligned_cols=93 Identities=10% Similarity=0.010 Sum_probs=61.1
Q ss_pred CCCChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecc-cHHHHHHhc------CcC---------CC-----------
Q 018586 197 NAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLR------MNY---------PD----------- 249 (353)
Q Consensus 197 ~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~-~~~D~~~l~------~~~---------~~----------- 249 (353)
.-++-.+++.++.+|+.+.++ .+|+||| ..||+.+|- ++. .+
T Consensus 176 ~f~sE~eLL~~F~~~i~~~DP-----------DIItGYNi~nFDlPYL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~~~G 244 (498)
T PHA02524 176 PFEDEVDLLLNYIQLWKANTP-----------DLVFGWNSEGFDIPYIITRITNILGEKAANQLSPYGKITSKTITNLYG 244 (498)
T ss_pred EeCCHHHHHHHHHHHHHHhCC-----------CEEEeCCCcccCHHHHHHHHHHHhCCccccccccccccccccceeecC
Confidence 457889999999999965533 6999999 457888765 111 00
Q ss_pred ---------CceeecccccCCc-ccCCCCCcHHHHHHHHhCCcCCCCCCC----------------hHHHHHHHHHHH
Q 018586 250 ---------HMLRDTAKYRPLM-KTNLVSHSLKYLTRTYLGYDIQSGVHD----------------PYEDCVSVMRLY 301 (353)
Q Consensus 250 ---------~~~~Dt~~l~~~~-~~~~~~~~L~~l~~~~~~~~~~~~~H~----------------Al~Da~~t~~l~ 301 (353)
.-++|...+.+.. .....+|+|+.++..++|.. ....|. .+.||..+..|+
T Consensus 245 ~~~~~~I~GRv~iDl~~l~kk~s~~~l~sYsL~~Vs~~~Lg~~-K~d~~~~I~~l~~~d~~rla~YclkDa~L~~~L~ 321 (498)
T PHA02524 245 EKIIYKIHGIALMDYMDVFKKFSFTPMPDYKLGNVGYREVKAD-KLDYEGPINKFRKADHQRYVDYCVRDTDIILLID 321 (498)
T ss_pred ceeEEEEeeEEEeEHHHHHHHhhhccCCCCCHHHHHHHhcCCc-cccchhhHHHHhcCchHHHHHHHHHHHHHHHHHH
Confidence 1123445555443 34678999999999887765 333332 245888876665
No 135
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=93.26 E-value=0.13 Score=45.73 Aligned_cols=130 Identities=15% Similarity=0.124 Sum_probs=81.9
Q ss_pred eeeccCCCCccccccccCCCCHhhhc--CCCCh-HHHHHHHHHHHhcCCCCcccccCCCCCcEEEecc-cHHHHHHhc--
Q 018586 171 HTYVQPQLPVTNYRYEVTGLTEEDIK--NAMPL-KEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLR-- 244 (353)
Q Consensus 171 ~~lv~P~~~i~~~~~~~~GIt~e~l~--~~~~~-~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~-~~~D~~~l~-- 244 (353)
..++.|.....+.+.+|+|++++-+. ...-| .++..-+..|+..- +.---||+|| -++|+.+|.
T Consensus 70 svl~~p~~v~~p~aeeitgls~~~~~l~rr~~~D~dla~LL~afls~l----------p~p~CLVaHng~~~dfpil~qe 139 (318)
T KOG4793|consen 70 SVLGGPVPVTRPIAEEITGLSQPFLALQRRLAFDKDLAKLLTAFLSRL----------PTPGCLVAHNGNEYDFPILAQE 139 (318)
T ss_pred hhccCCcCCcChhhhhhcccccHHHHHHHHhhhhHHHHHHHHHHHhcC----------CCCceEEeecCCccccHHHHHH
Confidence 56677777788888999999986554 32333 34555555666221 2444689999 445666665
Q ss_pred -----CcCCC-CceeecccccCCc--------cc-CCCCCcHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHhchh
Q 018586 245 -----MNYPD-HMLRDTAKYRPLM--------KT-NLVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDH 309 (353)
Q Consensus 245 -----~~~~~-~~~~Dt~~l~~~~--------~~-~~~~~~L~~l~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~~~ 309 (353)
+..|. ...+|+......+ .+ ..++|+|..+-..|.+-.-..+.|.|..|.-...-+|....+++-
T Consensus 140 la~lg~~lpq~lvcvdslpa~~ald~a~s~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~~ell 219 (318)
T KOG4793|consen 140 LAGLGYSLPQDLVCVDSLPALNALDRANSMVTRPEVRRMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRINELL 219 (318)
T ss_pred HHhcCccchhhhcCcchhHHHHHHhhhcCcccCCCCCcccccchHHHhhhcccCCCcceeeecccchhHHHHHHHHHHHH
Confidence 44444 2234554432211 11 345799999988886663245589999998888777777666643
Q ss_pred h
Q 018586 310 Q 310 (353)
Q Consensus 310 ~ 310 (353)
.
T Consensus 220 R 220 (318)
T KOG4793|consen 220 R 220 (318)
T ss_pred h
Confidence 3
No 136
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=93.14 E-value=0.93 Score=47.85 Aligned_cols=77 Identities=19% Similarity=0.247 Sum_probs=55.8
Q ss_pred hcCCCChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecccH-HHHHHhc-----CcCCC-------------------
Q 018586 195 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLR-----MNYPD------------------- 249 (353)
Q Consensus 195 l~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~-~D~~~l~-----~~~~~------------------- 249 (353)
+....+-.+++..|.+++.+.+ ..++||||.. ||+.+|. +..+.
T Consensus 205 v~~~~~e~e~l~~~~~~i~~~d-----------PdVIvgyn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~ 273 (792)
T COG0417 205 VEVVISEAELLERFVELIREYD-----------PDVIVGYNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQ 273 (792)
T ss_pred eEEecCHHHHHHHHHHHHHhcC-----------CCEEEeccCCcCChHHHHHHHHHhCCCccccccccccceeecccccc
Confidence 4555678899999999997664 4799999987 8999987 11111
Q ss_pred --CceeecccccCCcccCCCCCcHHHHHHHHhCCc
Q 018586 250 --HMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 282 (353)
Q Consensus 250 --~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 282 (353)
...+|+..+..........|+|...++.+++..
T Consensus 274 ~Gr~~iDl~~~~~~~~~~~~~ysl~~v~~~~l~~~ 308 (792)
T COG0417 274 VGRLHIDLYPALRRRPLNLKSYSLEAVSEALLGEG 308 (792)
T ss_pred cceEEEecHHHHhhhhcccccccHHHHHHHhcccc
Confidence 235666666653233567899999999997766
No 137
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=92.77 E-value=0.26 Score=50.43 Aligned_cols=85 Identities=22% Similarity=0.276 Sum_probs=57.4
Q ss_pred CCCcEEEecccHHHHHHhc----CcCCCCceeecccccCCcccC------------------------------------
Q 018586 226 GKARLLVGHGLEHDLDSLR----MNYPDHMLRDTAKYRPLMKTN------------------------------------ 265 (353)
Q Consensus 226 ~~~~~lvgh~~~~D~~~l~----~~~~~~~~~Dt~~l~~~~~~~------------------------------------ 265 (353)
.++.++||||+.||..-++ +.-....++||+.|.--..+.
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 3778999999999999998 333347789998765322210
Q ss_pred -CCCCcHHHHHHHHhCCc-CCCCCCCh--------------------HHHHHHHHHHHHHHHhchhh
Q 018586 266 -LVSHSLKYLTRTYLGYD-IQSGVHDP--------------------YEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 266 -~~~~~L~~l~~~~~~~~-~~~~~H~A--------------------l~Da~~t~~l~~~~~~~~~~ 310 (353)
..-.||.++++.+.|++ +...-.+. .-|+++|.+||..++=.+.+
T Consensus 319 ~SS~NSL~dVhk~~c~~~~LdKt~Rd~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Fle 385 (1075)
T KOG3657|consen 319 RSSLNSLVDVHKFHCGIDALDKTPRDSFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLE 385 (1075)
T ss_pred hhhhHHHHHHHHhhCCCCccccchHHhhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHH
Confidence 00256788888887777 33321111 12899999999998876654
No 138
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=92.46 E-value=0.4 Score=42.31 Aligned_cols=75 Identities=20% Similarity=0.220 Sum_probs=43.2
Q ss_pred CCcEEEecc-cHHHHHHhc------CcC-CCCceeecccccCCcc-cCCCCCcHHHHHHHHhCCcCCCCCCChHHHHHHH
Q 018586 227 KARLLVGHG-LEHDLDSLR------MNY-PDHMLRDTAKYRPLMK-TNLVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSV 297 (353)
Q Consensus 227 ~~~~lvgh~-~~~D~~~l~------~~~-~~~~~~Dt~~l~~~~~-~~~~~~~L~~l~~~~~~~~~~~~~H~Al~Da~~t 297 (353)
.-..||.+| ..||..|++ +.. +...-+|.+--.+.+. ....+-+|+.+-+ +||+.-... ---.|+...
T Consensus 155 ~~~~lvsfNGkaFD~PfikR~v~~~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr-~LGi~R~ed--tdG~~~p~l 231 (278)
T COG3359 155 DFNMLVSFNGKAFDIPFIKRMVRDRLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTVER-ILGIRREED--TDGYDGPEL 231 (278)
T ss_pred CcceEEEecCcccCcHHHHHHHhcccccCccccchhhhhhhhhhhhccCCCCChhhHHH-HhCcccccc--CCCcchHHH
Confidence 445889988 778999998 111 1234567766555443 2445678999666 557763321 112344455
Q ss_pred HHHHHHH
Q 018586 298 MRLYKRF 304 (353)
Q Consensus 298 ~~l~~~~ 304 (353)
.++|+..
T Consensus 232 yr~~~~~ 238 (278)
T COG3359 232 YRLYRRY 238 (278)
T ss_pred HHHHHHc
Confidence 5555444
No 139
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=92.30 E-value=0.096 Score=29.06 Aligned_cols=21 Identities=38% Similarity=0.910 Sum_probs=15.7
Q ss_pred ccccccccccCchhHHHHHHHh
Q 018586 80 GCNLCMNIFDSPSSLIKHKEAC 101 (353)
Q Consensus 80 ~C~~C~k~F~~~s~L~~H~~~h 101 (353)
.|+.||+.| ..+.|..|+.+.
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 488899999 556778887653
No 140
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=92.23 E-value=0.054 Score=29.81 Aligned_cols=22 Identities=32% Similarity=0.588 Sum_probs=18.6
Q ss_pred ccccccccccCchhHHHHHHHh
Q 018586 80 GCNLCMNIFDSPSSLIKHKEAC 101 (353)
Q Consensus 80 ~C~~C~k~F~~~s~L~~H~~~h 101 (353)
.|..|++.|.+...|..|.+.+
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCcCCHHHHHHHHCcC
Confidence 3889999999999999998754
No 141
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=92.23 E-value=0.13 Score=28.22 Aligned_cols=22 Identities=27% Similarity=0.640 Sum_probs=19.6
Q ss_pred eeeccccccccChHHHHHHHhh
Q 018586 15 HKCVACYKQFKRKDHLIEHMKI 36 (353)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (353)
|.|..|++.|.+...+..|++.
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 6799999999999999999875
No 142
>PRK04860 hypothetical protein; Provisional
Probab=92.09 E-value=0.1 Score=43.49 Aligned_cols=38 Identities=13% Similarity=0.267 Sum_probs=31.0
Q ss_pred CceeeccccccccChHHHHHHHhhhcCCCCCC-ccccCcccCCCh
Q 018586 13 ARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSF 56 (353)
Q Consensus 13 k~~~C~~C~k~f~~~~~l~~H~~~~~h~~~~~-~C~~C~~~f~~~ 56 (353)
=+|.|. |++ ....+.+|.++ |+++++ .|..|++.|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri--~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRV--VRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHH--hcCCccEECCCCCceeEEe
Confidence 368998 987 66778899999 999887 999999887543
No 143
>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=92.08 E-value=0.23 Score=33.24 Aligned_cols=18 Identities=44% Similarity=0.600 Sum_probs=10.8
Q ss_pred ccccCcccCCChHHHHhcc
Q 018586 45 KCAVCQKLSKSFESLREHL 63 (353)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~ 63 (353)
.|+.|++ ......|..|.
T Consensus 4 ~CP~C~~-~~~~~~L~~H~ 21 (54)
T PF05605_consen 4 TCPYCGK-GFSESSLVEHC 21 (54)
T ss_pred CCCCCCC-ccCHHHHHHHH
Confidence 5666666 34455666665
No 144
>PRK04860 hypothetical protein; Provisional
Probab=90.64 E-value=0.17 Score=42.22 Aligned_cols=33 Identities=12% Similarity=0.220 Sum_probs=28.6
Q ss_pred cccccccccccCchhHHHHHHHhcCCCCCCcccCCcc
Q 018586 79 RGCNLCMNIFDSPSSLIKHKEACSLSAPVPFEKTLSN 115 (353)
Q Consensus 79 ~~C~~C~k~F~~~s~L~~H~~~h~~~k~~~c~~~~~~ 115 (353)
..|. |++ ...++++|.++|+++++|.|..|...
T Consensus 120 Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~ 152 (160)
T PRK04860 120 YRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGET 152 (160)
T ss_pred EEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCce
Confidence 3687 987 77889999999999999999999554
No 145
>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=89.81 E-value=4.5 Score=39.86 Aligned_cols=90 Identities=19% Similarity=0.259 Sum_probs=56.7
Q ss_pred ChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhc-----CcCCC-------CceeecccccC-CcccCC
Q 018586 200 PLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR-----MNYPD-------HMLRDTAKYRP-LMKTNL 266 (353)
Q Consensus 200 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~-----~~~~~-------~~~~Dt~~l~~-~~~~~~ 266 (353)
...+++.+|.+|+.+. .+..|+.|| .+....|+ ...+. ..++|.....+ .+....
T Consensus 327 ~E~~~~~~f~~~l~~~-----------~~~~i~hY~-~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~ 394 (457)
T TIGR03491 327 TEELAWQQFLQLLQSY-----------PDAPIYHYG-ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPI 394 (457)
T ss_pred HHHHHHHHHHHHHHHC-----------CCCeEEeeC-HHHHHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCC
Confidence 3566888889988443 445888888 78888877 12221 15678776543 233344
Q ss_pred CCCcHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHh
Q 018586 267 VSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRR 306 (353)
Q Consensus 267 ~~~~L~~l~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~ 306 (353)
++|+|+.++..+ |.... ....|.-.++..|..+..
T Consensus 395 ~sysLK~v~~~l-g~~~~----~~~~~G~~ai~~y~~~~~ 429 (457)
T TIGR03491 395 ESYSLKSIARWL-GFEWR----QKEASGAKSLLWYRQWKK 429 (457)
T ss_pred CCCCHHHHHHHh-CcccC----CCCCCHHHHHHHHHHHHH
Confidence 789999999888 77644 223444455555655543
No 146
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=88.86 E-value=0.25 Score=26.80 Aligned_cols=22 Identities=23% Similarity=0.348 Sum_probs=16.9
Q ss_pred ccccccccccCchhHHHHHHHhc
Q 018586 80 GCNLCMNIFDSPSSLIKHKEACS 102 (353)
Q Consensus 80 ~C~~C~k~F~~~s~L~~H~~~h~ 102 (353)
.|+.|+.+.. .+.|..|++.|+
T Consensus 2 ~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 2 KCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp E-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCcCC-HHHHHHHHHhhC
Confidence 4888998887 889999998865
No 147
>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=88.58 E-value=0.068 Score=30.15 Aligned_cols=20 Identities=30% Similarity=0.695 Sum_probs=15.0
Q ss_pred cccccccccCchhHHHHHHH
Q 018586 81 CNLCMNIFDSPSSLIKHKEA 100 (353)
Q Consensus 81 C~~C~k~F~~~s~L~~H~~~ 100 (353)
|..|++.|.+...+..|+++
T Consensus 4 C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 4 CDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp BTTTTBBBSSHHHHHCCTTS
T ss_pred cccCCCCcCCHHHHHHHHcc
Confidence 77788888888777777653
No 148
>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=88.04 E-value=0.3 Score=27.34 Aligned_cols=22 Identities=18% Similarity=0.427 Sum_probs=15.3
Q ss_pred CCCCCCcccccc--cccccccccc
Q 018586 68 SKAHCSGIFSDR--GCNLCMNIFD 89 (353)
Q Consensus 68 ~c~~Cgk~f~~~--~C~~C~k~F~ 89 (353)
.|+.|++.-+.. .|+.||..|.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCCc
Confidence 467777666543 4888888875
No 149
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=87.50 E-value=0.43 Score=25.86 Aligned_cols=21 Identities=33% Similarity=0.513 Sum_probs=16.6
Q ss_pred eeeccccccccChHHHHHHHhh
Q 018586 15 HKCVACYKQFKRKDHLIEHMKI 36 (353)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (353)
|+|+.|+.... +..|.+|++.
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 78999998887 8899999986
No 150
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=86.73 E-value=0.3 Score=36.68 Aligned_cols=20 Identities=40% Similarity=0.753 Sum_probs=17.6
Q ss_pred CccccCcccCCChHHHHhcc
Q 018586 44 PKCAVCQKLSKSFESLREHL 63 (353)
Q Consensus 44 ~~C~~C~~~f~~~~~l~~H~ 63 (353)
..|..|++.|.+...+..|+
T Consensus 51 ~~C~~C~~~f~s~~~l~~Hm 70 (100)
T PF12756_consen 51 FRCPYCNKTFRSREALQEHM 70 (100)
T ss_dssp EEBSSSS-EESSHHHHHHHH
T ss_pred CCCCccCCCCcCHHHHHHHH
Confidence 38999999999999999999
No 151
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=85.38 E-value=0.2 Score=51.66 Aligned_cols=75 Identities=17% Similarity=0.193 Sum_probs=45.8
Q ss_pred CCCCCccccccccccccccccC---chhHHHHHHHhcCCCCCCcccCCcchhhhhhhcc----ccccccccCCCceeecc
Q 018586 69 KAHCSGIFSDRGCNLCMNIFDS---PSSLIKHKEACSLSAPVPFEKTLSNAESQKKISG----AIDEKRTCRGPKAVAMD 141 (353)
Q Consensus 69 c~~Cgk~f~~~~C~~C~k~F~~---~s~L~~H~~~h~~~k~~~c~~~~~~~~~~~~~~~----~~~e~~~~~~~~~~~~D 141 (353)
|..||..+ .|+.|+..++- ...|.=|..-|....|..||+|++. .-...=.+ ..+-.+-++..+++.+|
T Consensus 438 C~~Cg~v~---~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~-~L~~~G~GterieeeL~~~FP~~rv~r~d 513 (730)
T COG1198 438 CRDCGYIA---ECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE-HLRAVGPGTERIEEELKRLFPGARIIRID 513 (730)
T ss_pred cccCCCcc---cCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC-eeEEecccHHHHHHHHHHHCCCCcEEEEc
Confidence 88888777 68888765432 2222333333456788899999866 11111111 11223457888999999
Q ss_pred Cccccc
Q 018586 142 CEMVGG 147 (353)
Q Consensus 142 ~Ettg~ 147 (353)
.++|..
T Consensus 514 ~Dtt~~ 519 (730)
T COG1198 514 SDTTRR 519 (730)
T ss_pred cccccc
Confidence 999974
No 152
>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=85.35 E-value=0.29 Score=27.48 Aligned_cols=22 Identities=41% Similarity=0.694 Sum_probs=16.3
Q ss_pred eeeccccccccChHHHHHHHhh
Q 018586 15 HKCVACYKQFKRKDHLIEHMKI 36 (353)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (353)
|-|..|++.|.....+..|++.
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 5688888888887777777653
No 153
>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=83.63 E-value=0.54 Score=36.39 Aligned_cols=25 Identities=24% Similarity=0.424 Sum_probs=16.3
Q ss_pred CCCCCCCcccccc-----ccccccccccCc
Q 018586 67 LSKAHCSGIFSDR-----GCNLCMNIFDSP 91 (353)
Q Consensus 67 ~~c~~Cgk~f~~~-----~C~~C~k~F~~~ 91 (353)
+.|+.||++|..- .||.||..|.-.
T Consensus 10 R~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 3477777777643 377777777665
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=82.64 E-value=1 Score=26.75 Aligned_cols=23 Identities=22% Similarity=0.355 Sum_probs=20.0
Q ss_pred ceeeccccccccChHHHHHHHhh
Q 018586 14 RHKCVACYKQFKRKDHLIEHMKI 36 (353)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~ 36 (353)
+|.|+.|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 68899999999998888888864
No 155
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=82.51 E-value=0.57 Score=42.67 Aligned_cols=57 Identities=28% Similarity=0.562 Sum_probs=36.7
Q ss_pred CCC-cccc--CcccCCChHHHHhcc-CC-------CCCCCCCCccc----cccccccccccccCchhHHHHH
Q 018586 42 HQP-KCAV--CQKLSKSFESLREHL-TG-------PLSKAHCSGIF----SDRGCNLCMNIFDSPSSLIKHK 98 (353)
Q Consensus 42 ~~~-~C~~--C~~~f~~~~~l~~H~-~~-------~~~c~~Cgk~f----~~~~C~~C~k~F~~~s~L~~H~ 98 (353)
++| +|.. |.+.+.....|+.|+ .| +.|-++--..| ....|+.|+|.|..-..|+-|+
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 356 7754 888888888888887 22 22233333445 2335888888888888887775
No 156
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=82.43 E-value=11 Score=41.76 Aligned_cols=106 Identities=14% Similarity=0.226 Sum_probs=69.2
Q ss_pred cCCCCHhhhcCCCChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecc-cHHHHHHhc-----CcCC------------
Q 018586 187 VTGLTEEDIKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLR-----MNYP------------ 248 (353)
Q Consensus 187 ~~GIt~e~l~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~-~~~D~~~l~-----~~~~------------ 248 (353)
.-|+.+..|..-.+-.+.+..++.++.+.+ ..+++||| .+||+.+|- +..+
T Consensus 570 ~~~~~~~~L~~~~sEr~lL~~fl~~~~~~D-----------PDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~ 638 (1172)
T TIGR00592 570 FPGKKPSLVEDLATERALIKKFMAKVKKID-----------PDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSP 638 (1172)
T ss_pred hhccCCcEEEEecCHHHHHHHHHHHHHhcC-----------CCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccCC
Confidence 345556666777788888888888885443 35999999 456888765 2222
Q ss_pred -----------CCceeecccccCCcccCCCCCcHHHHHHHHhCCcCCCC------------------CCChHHHHHHHHH
Q 018586 249 -----------DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSG------------------VHDPYEDCVSVMR 299 (353)
Q Consensus 249 -----------~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~------------------~H~Al~Da~~t~~ 299 (353)
...++|+..+++... ...+|+|.+++..+||..-..- ....+.||..+++
T Consensus 639 ~~~~~~~~~~~Grl~~D~~~~~k~~~-~~~sy~L~~v~~~~L~~~k~~~~~~~i~~~~~~~~~~~~~~~y~~~Da~l~~~ 717 (1172)
T TIGR00592 639 KFGRRFGERTCGRMICDVEISAKELI-RCKSYDLSELVQQILKTERKVIPIDNINNMYSESSSLTYLLEHTWKDAMFILQ 717 (1172)
T ss_pred CccccccceECCEEEEEHHHHHHHHh-CcCCCCHHHHHHHHhCCCCcccCHHHHHHHHhCcHHHHHHHHHHHHHHHHHHH
Confidence 123466666665544 3678999999999998642110 1123567777777
Q ss_pred HHHHH
Q 018586 300 LYKRF 304 (353)
Q Consensus 300 l~~~~ 304 (353)
|+.++
T Consensus 718 L~~~l 722 (1172)
T TIGR00592 718 IMCEL 722 (1172)
T ss_pred HHHHH
Confidence 76654
No 157
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=79.02 E-value=0.95 Score=39.72 Aligned_cols=12 Identities=17% Similarity=0.116 Sum_probs=8.1
Q ss_pred ccccccccccCc
Q 018586 80 GCNLCMNIFDSP 91 (353)
Q Consensus 80 ~C~~C~k~F~~~ 91 (353)
.||.||.+|...
T Consensus 50 vCP~CgyA~~~~ 61 (214)
T PF09986_consen 50 VCPHCGYAAFEE 61 (214)
T ss_pred ECCCCCCccccc
Confidence 378888776544
No 158
>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=77.06 E-value=4 Score=33.23 Aligned_cols=55 Identities=22% Similarity=0.202 Sum_probs=41.9
Q ss_pred CCcEEEecccHHHHHHhc---CcCCCCceeecccccCCcccCCCCCcHHHHHHHHhCCc
Q 018586 227 KARLLVGHGLEHDLDSLR---MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 282 (353)
Q Consensus 227 ~~~~lvgh~~~~D~~~l~---~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 282 (353)
.+...|+||+..++.+|. +..+ ....|++..+-.+.|......|+++++.||+..
T Consensus 52 ~~~~ki~~d~K~~~~~l~~~gi~l~-~~~fD~~LAaYLL~p~~~~~~l~~la~~yl~~~ 109 (151)
T cd06128 52 EKALKVGQNLKYDRVILANYGIELR-GIAFDTMLEAYLLDPVAGRHDMDSLAERWLKEK 109 (151)
T ss_pred CCCCEEeeehHHHHHHHHHCCCCCC-CcchhHHHHHHHcCCCCCCCCHHHHHHHHcCCC
Confidence 445689999999999985 3333 235799988888888655139999999998776
No 159
>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=76.40 E-value=1.4 Score=26.12 Aligned_cols=21 Identities=29% Similarity=0.485 Sum_probs=17.6
Q ss_pred ccccccccccCchhHHHHHHH
Q 018586 80 GCNLCMNIFDSPSSLIKHKEA 100 (353)
Q Consensus 80 ~C~~C~k~F~~~s~L~~H~~~ 100 (353)
.|..|++.|.+...+..|.+.
T Consensus 5 ~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 5 YCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred EccccCCccCCHHHHHHHHCh
Confidence 489999999988888888764
No 160
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.31 E-value=2.3 Score=43.28 Aligned_cols=44 Identities=30% Similarity=0.643 Sum_probs=23.8
Q ss_pred eeccccccccChHHHHHHHhhhcCCCCCCccccCc---------ccCCChHHHHhcc
Q 018586 16 KCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQ---------KLSKSFESLREHL 63 (353)
Q Consensus 16 ~C~~C~k~f~~~~~l~~H~~~~~h~~~~~~C~~C~---------~~f~~~~~l~~H~ 63 (353)
+|..| ..|.....|+.|+.- .|.. ..|..|- ........|+.|+
T Consensus 117 ~~~~c-~~~~s~~~Lk~H~~~-~H~~--~~c~lC~~~~kif~~e~k~Yt~~el~~h~ 169 (669)
T KOG2231|consen 117 ECLHC-TEFKSVENLKNHMRD-QHKL--HLCSLCLQNLKIFINERKLYTRAELNLHL 169 (669)
T ss_pred CCccc-cchhHHHHHHHHHHH-hhhh--hccccccccceeeeeeeehehHHHHHHHH
Confidence 45555 445577888888852 1322 1333332 2234556777777
No 161
>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=75.67 E-value=1.5 Score=34.67 Aligned_cols=27 Identities=11% Similarity=-0.011 Sum_probs=17.8
Q ss_pred CCCCCCCcccccc-----ccccccccccCchh
Q 018586 67 LSKAHCSGIFSDR-----GCNLCMNIFDSPSS 93 (353)
Q Consensus 67 ~~c~~Cgk~f~~~-----~C~~C~k~F~~~s~ 93 (353)
+.|+.||++|... .|+.||..|.....
T Consensus 10 r~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~~~ 41 (129)
T TIGR02300 10 RICPNTGSKFYDLNRRPAVSPYTGEQFPPEEA 41 (129)
T ss_pred ccCCCcCccccccCCCCccCCCcCCccCcchh
Confidence 4577777777653 38888887755533
No 162
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=74.52 E-value=1.2 Score=42.73 Aligned_cols=49 Identities=31% Similarity=0.603 Sum_probs=35.7
Q ss_pred CceeeccccccccChHHHHHHHh--hhcCCCC--CC-ccc--cCcccCCChHHHHhcc
Q 018586 13 ARHKCVACYKQFKRKDHLIEHMK--ISYHSVH--QP-KCA--VCQKLSKSFESLREHL 63 (353)
Q Consensus 13 k~~~C~~C~k~f~~~~~l~~H~~--~~~h~~~--~~-~C~--~C~~~f~~~~~l~~H~ 63 (353)
.++.|..|...|.....+.+|.+ . |+++ ++ .|. .|++.|.+...+..|.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~--h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~ 343 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVN--HSGESLKPFSCPYSLCGKLFSRNDALKRHI 343 (467)
T ss_pred cCCCCccccCCccccccccccccccc--cccccCCceeeeccCCCccccccccccCCc
Confidence 46777777777777777777777 6 7777 66 776 6777777777776666
No 163
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=72.01 E-value=2.4 Score=37.52 Aligned_cols=45 Identities=22% Similarity=0.373 Sum_probs=35.5
Q ss_pred eeeccccccccChHHHHHHHhhhcCCCCCCccccCcccCCChHHHHhcc
Q 018586 15 HKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHL 63 (353)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~~~h~~~~~~C~~C~~~f~~~~~l~~H~ 63 (353)
|.|..||.+..- ..+-+|+.. -.+..+.|..|+..|.. .+...|.
T Consensus 4 FtCnvCgEsvKK-p~vekH~sr--Crn~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSR--CRNAYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHh--ccCCeeEEeeccccccc-chhhhhh
Confidence 789999998774 557889976 56655599999999988 5566776
No 164
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=71.39 E-value=2 Score=34.13 Aligned_cols=21 Identities=33% Similarity=0.825 Sum_probs=14.7
Q ss_pred CCCCCCCCcccccc------ccccccc
Q 018586 66 PLSKAHCSGIFSDR------GCNLCMN 86 (353)
Q Consensus 66 ~~~c~~Cgk~f~~~------~C~~C~k 86 (353)
+|.|-.||+.|..- .||.||-
T Consensus 1 PH~Ct~Cg~~f~dgs~eil~GCP~CGg 27 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKEILSGCPECGG 27 (131)
T ss_pred CcccCcCCCCcCCCcHHHHccCcccCC
Confidence 46677777777754 3888883
No 165
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=69.56 E-value=2.8 Score=27.84 Aligned_cols=28 Identities=21% Similarity=0.509 Sum_probs=22.9
Q ss_pred CCCCCceeeccccccccChHHHHHHHhh
Q 018586 9 KRSTARHKCVACYKQFKRKDHLIEHMKI 36 (353)
Q Consensus 9 h~~~k~~~C~~C~k~f~~~~~l~~H~~~ 36 (353)
--|+.-+.|+.|+..|....+..+|...
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 3467778999999999998888888864
No 166
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=66.75 E-value=2.2 Score=44.22 Aligned_cols=43 Identities=23% Similarity=0.332 Sum_probs=31.5
Q ss_pred ccccCcccCCCh---HHHHhcc-CCCCCCCCCCccccc-ccccccccc
Q 018586 45 KCAVCQKLSKSF---ESLREHL-TGPLSKAHCSGIFSD-RGCNLCMNI 87 (353)
Q Consensus 45 ~C~~C~~~f~~~---~~l~~H~-~~~~~c~~Cgk~f~~-~~C~~C~k~ 87 (353)
.|..||..+... ..|..|+ ++...|+.||..-.. ..|+.||..
T Consensus 437 ~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 437 LCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 777777776432 5678888 677789999988333 369999965
No 167
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=66.26 E-value=2.8 Score=43.04 Aligned_cols=93 Identities=10% Similarity=0.230 Sum_probs=51.0
Q ss_pred ccCCCceeeccCcccccc-------CCCCccceeEEeeecCCCCeEE-eeeccCCCCccccccccCCCCHhhhcCCCChH
Q 018586 131 TCRGPKAVAMDCEMVGGG-------SNGTLDLCARVCLVDEDENVIF-HTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLK 202 (353)
Q Consensus 131 ~~~~~~~~~~D~Ettg~~-------~~~~~~il~~v~ivd~~g~~~~-~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~ 202 (353)
..++-++..+|+|..|.. .+-++++ +.+.....+++..+ +.+.-+. ..||.--+|..-..-+
T Consensus 270 ~~APlrvlSfDIECagrkg~FPe~~~DPvIQI-an~v~~~Ge~~pf~rnvf~l~~---------capI~G~~V~~~~~e~ 339 (1066)
T KOG0969|consen 270 KIAPLRVLSFDIECAGRKGVFPEAKIDPVIQI-ANLVTLQGENEPFVRNVFTLKT---------CAPIVGSNVHSYETEK 339 (1066)
T ss_pred ccccccccceeEEeccCCCCCCccccChHHHH-HHHHHHhcCCchHHHhhhcccC---------cCCCCCceeEEeccHH
Confidence 455667889999999853 3344444 33333223333321 3333222 2233334444444556
Q ss_pred HHHHHHHHHHhcCCCCcccccCCCCCcEEEeccc-HHHHHHhc
Q 018586 203 EVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (353)
Q Consensus 203 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~ 244 (353)
++++.-..|+..- ...+|+|||+ .||+..|-
T Consensus 340 elL~~W~~firev-----------DPDvI~GYNi~nFDiPYll 371 (1066)
T KOG0969|consen 340 ELLESWRKFIREV-----------DPDVIIGYNICNFDIPYLL 371 (1066)
T ss_pred HHHHHHHHHHHhc-----------CCCeEecccccccccceec
Confidence 6666666666433 4469999996 56776543
No 168
>PRK05761 DNA polymerase I; Reviewed
Probab=64.83 E-value=37 Score=36.00 Aligned_cols=89 Identities=18% Similarity=0.181 Sum_probs=56.0
Q ss_pred CChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecc-cHHHHHHhc-----CcCCC----------CceeecccccCCc
Q 018586 199 MPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLR-----MNYPD----------HMLRDTAKYRPLM 262 (353)
Q Consensus 199 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~-~~~D~~~l~-----~~~~~----------~~~~Dt~~l~~~~ 262 (353)
.+-.+++.+|.+++.+. .+.|++| ..||+.+|. ++.+. ...+|....+...
T Consensus 208 ~~E~eLL~~f~~~i~~~-------------dPdi~yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~ 274 (787)
T PRK05761 208 DSEKELLAELFDIILEY-------------PPVVTFNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNK 274 (787)
T ss_pred CCHHHHHHHHHHHHHhc-------------CCEEEEcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheeec
Confidence 67889999999999543 3445577 558999987 22211 0014443332211
Q ss_pred -------cc--CCCCCcHHHHHHHHhCCcCCCC-------------CCChHHHHHHHHHHH
Q 018586 263 -------KT--NLVSHSLKYLTRTYLGYDIQSG-------------VHDPYEDCVSVMRLY 301 (353)
Q Consensus 263 -------~~--~~~~~~L~~l~~~~~~~~~~~~-------------~H~Al~Da~~t~~l~ 301 (353)
.+ ..+.++|..+++.+||.. ... +.-.+.||..|.+|+
T Consensus 275 ~~~~y~~~~~~~~~~ysL~~Va~~~Lg~~-K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 275 AVRSYAFYGKYRHREARLDAVGRALLGIS-KVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred ceeeeeccceeecccCChHHHHHHHhCCC-cccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 01 223789999999998876 321 233578999999985
No 169
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=62.61 E-value=5.4 Score=35.84 Aligned_cols=43 Identities=14% Similarity=0.240 Sum_probs=36.6
Q ss_pred CCCCcHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHHHhchh
Q 018586 266 LVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDH 309 (353)
Q Consensus 266 ~~~~~L~~l~~~~~~~~~~~~~H~Al~Da~~t~~l~~~~~~~~~ 309 (353)
..-++|..|+.++ +.....++|+|+.|+..+-+++.++...+.
T Consensus 250 ~~vs~le~Lat~~-~~~p~l~ahra~~Dv~~~~k~~q~~~idll 292 (318)
T KOG4793|consen 250 KLVSSLEALATYY-SLTPELDAHRALSDVLLLSKVFQKLTIDLL 292 (318)
T ss_pred ccchhHHHHHHHh-hcCcccchhhhccccchhhhHHHHhhhhhh
Confidence 3468899999999 666578899999999999999999887753
No 170
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=62.24 E-value=3 Score=36.23 Aligned_cols=79 Identities=11% Similarity=0.007 Sum_probs=50.0
Q ss_pred CCCcEEEecccHHHHHHhc-----CcCCC-----Cc--------eeecccccCCcccCCCCCcHHHHHHHHhCCcCCCCC
Q 018586 226 GKARLLVGHGLEHDLDSLR-----MNYPD-----HM--------LRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGV 287 (353)
Q Consensus 226 ~~~~~lvgh~~~~D~~~l~-----~~~~~-----~~--------~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~ 287 (353)
++..++|.++..+|+.+|- ...|. +. ..|...+++-.. .....|++++.-+ ++--.+..
T Consensus 156 ~e~VtWitfHsaYDfgyLikilt~~plP~~~EdFy~~l~~yfP~fYDik~v~ks~~--~~~KglQei~ndl-ql~r~g~Q 232 (299)
T COG5228 156 DESVTWITFHSAYDFGYLIKILTNDPLPNNKEDFYWWLHQYFPNFYDIKLVYKSVL--NNSKGLQEIKNDL-QLQRSGQQ 232 (299)
T ss_pred ccceEEEEeecchhHHHHHHHHhcCCCCccHHHHHHHHHHHCccccchHHHHHhhh--hhhhHHHHhcCcH-hhhccchh
Confidence 4778999999999999986 12222 00 123322222221 1235677777766 66633448
Q ss_pred CChHHHHHHHHHHHHHHHhc
Q 018586 288 HDPYEDCVSVMRLYKRFRRQ 307 (353)
Q Consensus 288 H~Al~Da~~t~~l~~~~~~~ 307 (353)
|.|-.||..|++.|-..+..
T Consensus 233 hQagsdaLlTa~~ff~~R~~ 252 (299)
T COG5228 233 HQAGSDALLTADEFFLPRFS 252 (299)
T ss_pred hhccchhhhhhHHhcchhhh
Confidence 99999999999988766554
No 171
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=61.91 E-value=2.7 Score=33.82 Aligned_cols=32 Identities=28% Similarity=0.321 Sum_probs=27.0
Q ss_pred CCCCCCccccccccccccccccCchhHHHHHHH
Q 018586 68 SKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEA 100 (353)
Q Consensus 68 ~c~~Cgk~f~~~~C~~C~k~F~~~s~L~~H~~~ 100 (353)
.|.+|| -++.++|-.||-.+.+.+-+..|+.+
T Consensus 120 fCaVCG-~~S~ysC~~CG~kyCsv~C~~~HneT 151 (156)
T KOG3362|consen 120 FCAVCG-YDSKYSCVNCGTKYCSVRCLKTHNET 151 (156)
T ss_pred hhhhcC-CCchhHHHhcCCceeechhhhhcccc
Confidence 399999 67777899999999999888877654
No 172
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=61.87 E-value=4.3 Score=21.91 Aligned_cols=18 Identities=22% Similarity=0.462 Sum_probs=8.1
Q ss_pred CCCCCcccccc--ccccccc
Q 018586 69 KAHCSGIFSDR--GCNLCMN 86 (353)
Q Consensus 69 c~~Cgk~f~~~--~C~~C~k 86 (353)
|+.||+..... -|+.||.
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CcccCCCCCCcCcchhhhCC
Confidence 34444444332 1666664
No 173
>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=61.78 E-value=2.9 Score=25.74 Aligned_cols=8 Identities=38% Similarity=0.999 Sum_probs=3.5
Q ss_pred cccccccc
Q 018586 81 CNLCMNIF 88 (353)
Q Consensus 81 C~~C~k~F 88 (353)
|+.||+.|
T Consensus 8 C~~Cg~~f 15 (41)
T smart00834 8 CEDCGHTF 15 (41)
T ss_pred cCCCCCEE
Confidence 44444444
No 174
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=61.38 E-value=5.6 Score=40.83 Aligned_cols=35 Identities=14% Similarity=0.237 Sum_probs=24.3
Q ss_pred ccccCcccCCChHHHHhccCCCCCCCCCCcccccc--ccccccccccC
Q 018586 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDR--GCNLCMNIFDS 90 (353)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~c~~Cgk~f~~~--~C~~C~k~F~~ 90 (353)
-|..||..+. ...|..||...... -|+.||.....
T Consensus 17 FC~~CG~~l~-----------~~~Cp~CG~~~~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 17 FCQKCGTSLT-----------HKPCPQCGTEVPVDEAHCPNCGAETGT 53 (645)
T ss_pred cccccCCCCC-----------CCcCCCCCCCCCcccccccccCCcccc
Confidence 5888887653 23589998876543 39999976544
No 175
>PRK14873 primosome assembly protein PriA; Provisional
Probab=60.92 E-value=2.8 Score=43.31 Aligned_cols=42 Identities=21% Similarity=0.375 Sum_probs=18.8
Q ss_pred ccccCcccCCC---hHHHHhcc-CCCCCCCCCCccccccccccccc
Q 018586 45 KCAVCQKLSKS---FESLREHL-TGPLSKAHCSGIFSDRGCNLCMN 86 (353)
Q Consensus 45 ~C~~C~~~f~~---~~~l~~H~-~~~~~c~~Cgk~f~~~~C~~C~k 86 (353)
.|..||..+.- ...|..|. .+.-.|..||.......|+.||.
T Consensus 385 ~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs 430 (665)
T PRK14873 385 ACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGS 430 (665)
T ss_pred EhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcC
Confidence 55555544321 12344444 22334555555443344555554
No 176
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=60.91 E-value=3.4 Score=26.47 Aligned_cols=10 Identities=20% Similarity=0.288 Sum_probs=4.8
Q ss_pred CCCCCCCccc
Q 018586 67 LSKAHCSGIF 76 (353)
Q Consensus 67 ~~c~~Cgk~f 76 (353)
+.|..||..|
T Consensus 4 y~C~~CG~~~ 13 (46)
T PRK00398 4 YKCARCGREV 13 (46)
T ss_pred EECCCCCCEE
Confidence 3455555444
No 177
>PF14353 CpXC: CpXC protein
Probab=59.81 E-value=4.9 Score=31.98 Aligned_cols=13 Identities=23% Similarity=0.467 Sum_probs=6.4
Q ss_pred cccccccccCchh
Q 018586 81 CNLCMNIFDSPSS 93 (353)
Q Consensus 81 C~~C~k~F~~~s~ 93 (353)
||.||..|.-...
T Consensus 41 CP~Cg~~~~~~~p 53 (128)
T PF14353_consen 41 CPSCGHKFRLEYP 53 (128)
T ss_pred CCCCCCceecCCC
Confidence 5555555544333
No 178
>PRK04023 DNA polymerase II large subunit; Validated
Probab=59.24 E-value=6.1 Score=42.00 Aligned_cols=13 Identities=31% Similarity=0.856 Sum_probs=9.0
Q ss_pred hhhhccCCCCcee
Q 018586 337 NELYQISKSDYRC 349 (353)
Q Consensus 337 ~~~~~~~~~~~~~ 349 (353)
..|-+||++.+||
T Consensus 1028 GNLRaFsrQ~fRC 1040 (1121)
T PRK04023 1028 GNLRAFSRQEFRC 1040 (1121)
T ss_pred hhhhhhcccceee
Confidence 3455777887777
No 179
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=59.20 E-value=6.6 Score=23.88 Aligned_cols=32 Identities=19% Similarity=0.529 Sum_probs=17.2
Q ss_pred eeeccccccccChHHHHHHHhhhcCCCCCC-ccccCcccC
Q 018586 15 HKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLS 53 (353)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~~~h~~~~~-~C~~C~~~f 53 (353)
-.|+.|+..|.-..+- + ..+... +|..|+..|
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 3577777777665521 1 112223 677776554
No 180
>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=58.76 E-value=3.2 Score=26.09 Aligned_cols=10 Identities=40% Similarity=0.517 Sum_probs=4.8
Q ss_pred CCCCcccCCc
Q 018586 105 APVPFEKTLS 114 (353)
Q Consensus 105 k~~~c~~~~~ 114 (353)
.+-.||.|+.
T Consensus 25 ~~~~CP~Cg~ 34 (42)
T PF09723_consen 25 DPVPCPECGS 34 (42)
T ss_pred CCCcCCCCCC
Confidence 4444555543
No 181
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=58.68 E-value=14 Score=28.78 Aligned_cols=22 Identities=18% Similarity=0.282 Sum_probs=15.6
Q ss_pred CCceeeccccccccChHHHHHH
Q 018586 12 TARHKCVACYKQFKRKDHLIEH 33 (353)
Q Consensus 12 ~k~~~C~~C~k~f~~~~~l~~H 33 (353)
+-|-+|+.||-..-...+|.+.
T Consensus 13 ~LP~~CpiCgLtLVss~HLARS 34 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARS 34 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHh
Confidence 4567788888877777766654
No 182
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=58.53 E-value=3.9 Score=27.20 Aligned_cols=22 Identities=23% Similarity=0.523 Sum_probs=18.4
Q ss_pred ccccccccccCchhHHHHHHHh
Q 018586 80 GCNLCMNIFDSPSSLIKHKEAC 101 (353)
Q Consensus 80 ~C~~C~k~F~~~s~L~~H~~~h 101 (353)
.||.||..|....+..+|....
T Consensus 19 rCPRC~~~FR~~K~Y~RHVNKa 40 (65)
T COG4049 19 RCPRCGMVFRRRKDYIRHVNKA 40 (65)
T ss_pred eCCchhHHHHHhHHHHHHhhHH
Confidence 3999999999988999997653
No 183
>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=57.04 E-value=7.3 Score=30.15 Aligned_cols=28 Identities=18% Similarity=0.297 Sum_probs=14.6
Q ss_pred cccccccccCchhHHHHHHHhcCCCCCCcccCCcchhhh
Q 018586 81 CNLCMNIFDSPSSLIKHKEACSLSAPVPFEKTLSNAESQ 119 (353)
Q Consensus 81 C~~C~k~F~~~s~L~~H~~~h~~~k~~~c~~~~~~~~~~ 119 (353)
|+.||+.|-.-.. .|-.||+|+......
T Consensus 12 Cp~CG~kFYDLnk-----------~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 12 CPSCGAKFYDLNK-----------DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCCCcchhccCCC-----------CCccCCCCCCccCcc
Confidence 6666666654331 345566666554444
No 184
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=56.50 E-value=8.3 Score=25.09 Aligned_cols=22 Identities=23% Similarity=0.460 Sum_probs=15.2
Q ss_pred ccccccccccC-----chhHHHHHH-Hh
Q 018586 80 GCNLCMNIFDS-----PSSLIKHKE-AC 101 (353)
Q Consensus 80 ~C~~C~k~F~~-----~s~L~~H~~-~h 101 (353)
.|..|++.+.. .|+|.+|++ .|
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~~~h 47 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLRRKH 47 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHHhHC
Confidence 46777766644 478999988 45
No 185
>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=56.17 E-value=4.7 Score=24.49 Aligned_cols=14 Identities=29% Similarity=0.693 Sum_probs=8.4
Q ss_pred eeeccccccccChH
Q 018586 15 HKCVACYKQFKRKD 28 (353)
Q Consensus 15 ~~C~~C~k~f~~~~ 28 (353)
.+|+.|+..|.-..
T Consensus 3 ~~CP~C~~~~~v~~ 16 (38)
T TIGR02098 3 IQCPNCKTSFRVVD 16 (38)
T ss_pred EECCCCCCEEEeCH
Confidence 45666766665544
No 186
>PRK12496 hypothetical protein; Provisional
Probab=55.85 E-value=4.1 Score=34.12 Aligned_cols=23 Identities=13% Similarity=0.378 Sum_probs=17.3
Q ss_pred CCCCCCCCccccc----cccccccccc
Q 018586 66 PLSKAHCSGIFSD----RGCNLCMNIF 88 (353)
Q Consensus 66 ~~~c~~Cgk~f~~----~~C~~C~k~F 88 (353)
.+.|..|++.|.. ..|+.||..-
T Consensus 127 ~~~C~gC~~~~~~~~~~~~C~~CG~~~ 153 (164)
T PRK12496 127 RKVCKGCKKKYPEDYPDDVCEICGSPV 153 (164)
T ss_pred eEECCCCCccccCCCCCCcCCCCCChh
Confidence 4669999999953 2499999643
No 187
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=55.62 E-value=5.3 Score=30.15 Aligned_cols=20 Identities=35% Similarity=0.879 Sum_probs=12.5
Q ss_pred CCCCCCCCcccccc------cccccc
Q 018586 66 PLSKAHCSGIFSDR------GCNLCM 85 (353)
Q Consensus 66 ~~~c~~Cgk~f~~~------~C~~C~ 85 (353)
+++|-.||..|..- .|+.||
T Consensus 2 pH~CtrCG~vf~~g~~~il~GCp~CG 27 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEILSGCPKCG 27 (112)
T ss_pred CceecccccccccccHHHHccCcccc
Confidence 45566666666652 377777
No 188
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=55.12 E-value=7.6 Score=21.53 Aligned_cols=20 Identities=15% Similarity=0.237 Sum_probs=10.4
Q ss_pred CCCCCCcccccc--cccccccc
Q 018586 68 SKAHCSGIFSDR--GCNLCMNI 87 (353)
Q Consensus 68 ~c~~Cgk~f~~~--~C~~C~k~ 87 (353)
.|+.||+.-... -|+.||..
T Consensus 4 ~Cp~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 4 FCPNCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred CCcccCCcCCcccccChhhCCC
Confidence 466666532221 27777753
No 189
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=54.83 E-value=11 Score=41.16 Aligned_cols=18 Identities=22% Similarity=0.012 Sum_probs=8.3
Q ss_pred CChHHHHHHHHHHHHHHH
Q 018586 288 HDPYEDCVSVMRLYKRFR 305 (353)
Q Consensus 288 H~Al~Da~~t~~l~~~~~ 305 (353)
|+--.||-+.|-|+..++
T Consensus 1086 HsCDGDED~VMLLlD~ll 1103 (1337)
T PRK14714 1086 GQCDGDEDCVMLLLDGLL 1103 (1337)
T ss_pred eccCchHHHHHHHHHHHH
Confidence 334444445555544444
No 190
>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=54.60 E-value=6.5 Score=39.30 Aligned_cols=77 Identities=13% Similarity=0.091 Sum_probs=37.6
Q ss_pred CCCCCCccccccccccccccccC---chhHHHHHHHhcCCCCCCcccCCcchhhh---hhhccccccccccCCCceeecc
Q 018586 68 SKAHCSGIFSDRGCNLCMNIFDS---PSSLIKHKEACSLSAPVPFEKTLSNAESQ---KKISGAIDEKRTCRGPKAVAMD 141 (353)
Q Consensus 68 ~c~~Cgk~f~~~~C~~C~k~F~~---~s~L~~H~~~h~~~k~~~c~~~~~~~~~~---~~~~~~~~e~~~~~~~~~~~~D 141 (353)
.|..||... .|+.|+-..+. ...|.=|.--+...-|..||.|++..=.. ...+-..+-...++..++..+|
T Consensus 215 ~C~~Cg~~~---~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~~l~~~g~Gte~~~e~l~~~fp~~~v~~~d 291 (505)
T TIGR00595 215 LCRSCGYIL---CCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARID 291 (505)
T ss_pred EhhhCcCcc---CCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCCeeEeecccHHHHHHHHHhhCCCCcEEEEe
Confidence 377777665 57777743322 12222222223445567788886531000 0000000111234566788899
Q ss_pred Cccccc
Q 018586 142 CEMVGG 147 (353)
Q Consensus 142 ~Ettg~ 147 (353)
.+++..
T Consensus 292 ~d~~~~ 297 (505)
T TIGR00595 292 SDTTSR 297 (505)
T ss_pred cccccC
Confidence 998854
No 191
>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=54.21 E-value=4.4 Score=26.58 Aligned_cols=28 Identities=11% Similarity=0.227 Sum_probs=14.0
Q ss_pred ccccccccccCchhHHHHHHHhcCCCCCCcccCCc
Q 018586 80 GCNLCMNIFDSPSSLIKHKEACSLSAPVPFEKTLS 114 (353)
Q Consensus 80 ~C~~C~k~F~~~s~L~~H~~~h~~~k~~~c~~~~~ 114 (353)
.|+.||..|....... . +.+-.||.|+.
T Consensus 7 ~C~~Cg~~fe~~~~~~------~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQKMS------D-DPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEEecC------C-CCCCCCCCCCC
Confidence 3666666665432211 1 34455777754
No 192
>PRK04023 DNA polymerase II large subunit; Validated
Probab=54.18 E-value=5.8 Score=42.14 Aligned_cols=42 Identities=14% Similarity=0.008 Sum_probs=22.8
Q ss_pred CCCCCCCCcccccccccccccc-----ccCchhHHHHHHHhcCCCCCCcccCCcc
Q 018586 66 PLSKAHCSGIFSDRGCNLCMNI-----FDSPSSLIKHKEACSLSAPVPFEKTLSN 115 (353)
Q Consensus 66 ~~~c~~Cgk~f~~~~C~~C~k~-----F~~~s~L~~H~~~h~~~k~~~c~~~~~~ 115 (353)
.+.|+.||.......|+.||.. |+... -....++.|++|+..
T Consensus 626 ~RfCpsCG~~t~~frCP~CG~~Te~i~fCP~C--------G~~~~~y~CPKCG~E 672 (1121)
T PRK04023 626 RRKCPSCGKETFYRRCPFCGTHTEPVYRCPRC--------GIEVEEDECEKCGRE 672 (1121)
T ss_pred CccCCCCCCcCCcccCCCCCCCCCcceeCccc--------cCcCCCCcCCCCCCC
Confidence 4456666666555556666653 11111 112335779999744
No 193
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=52.78 E-value=2.3 Score=37.29 Aligned_cols=20 Identities=30% Similarity=0.502 Sum_probs=15.1
Q ss_pred CCceeeccccccccChHHHH
Q 018586 12 TARHKCVACYKQFKRKDHLI 31 (353)
Q Consensus 12 ~k~~~C~~C~k~f~~~~~l~ 31 (353)
+|...|+.|++.|..+.-..
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs 22 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRS 22 (214)
T ss_pred CCceECCCCCCeeeeeEEEc
Confidence 46688999999999876333
No 194
>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=52.64 E-value=6.1 Score=23.58 Aligned_cols=9 Identities=22% Similarity=0.235 Sum_probs=4.1
Q ss_pred CCCCCCccc
Q 018586 68 SKAHCSGIF 76 (353)
Q Consensus 68 ~c~~Cgk~f 76 (353)
.|..||..+
T Consensus 4 ~C~~CG~i~ 12 (34)
T cd00729 4 VCPVCGYIH 12 (34)
T ss_pred ECCCCCCEe
Confidence 444444443
No 195
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=51.66 E-value=5.6 Score=34.87 Aligned_cols=41 Identities=34% Similarity=0.589 Sum_probs=27.1
Q ss_pred eccccccccChHHHHHHHhhhcCCCCCCccccCcccCCChHHHHhc
Q 018586 17 CVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREH 62 (353)
Q Consensus 17 C~~C~k~f~~~~~l~~H~~~~~h~~~~~~C~~C~~~f~~~~~l~~H 62 (353)
|=.|.+.|.....|..|++. +.++|+.|.+.+.+--.|..|
T Consensus 13 cwycnrefddekiliqhqka-----khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA-----KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhhh-----ccceeeeehhhhccCCCceee
Confidence 77788888877777777765 223777777665554444444
No 196
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=50.93 E-value=10 Score=33.54 Aligned_cols=9 Identities=33% Similarity=0.866 Sum_probs=4.7
Q ss_pred ccccccccc
Q 018586 81 CNLCMNIFD 89 (353)
Q Consensus 81 C~~C~k~F~ 89 (353)
|+.|+..|.
T Consensus 158 C~~C~h~F~ 166 (278)
T PF15135_consen 158 CPKCRHNFR 166 (278)
T ss_pred cccccccch
Confidence 555555554
No 197
>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=50.93 E-value=5.5 Score=39.77 Aligned_cols=43 Identities=23% Similarity=0.268 Sum_probs=29.9
Q ss_pred ccccCcccCCC---hHHHHhcc-CCCCCCCCCCccccc-ccccccccc
Q 018586 45 KCAVCQKLSKS---FESLREHL-TGPLSKAHCSGIFSD-RGCNLCMNI 87 (353)
Q Consensus 45 ~C~~C~~~f~~---~~~l~~H~-~~~~~c~~Cgk~f~~-~~C~~C~k~ 87 (353)
.|..||....- ...|..|. .+...|..||..... ..|+.||..
T Consensus 215 ~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 215 LCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred EhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 66666665432 24677777 455679999988773 469999974
No 198
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=50.40 E-value=9.6 Score=28.01 Aligned_cols=28 Identities=18% Similarity=0.313 Sum_probs=16.0
Q ss_pred CCCCCCCCCCcccccc------ccccccccccCc
Q 018586 64 TGPLSKAHCSGIFSDR------GCNLCMNIFDSP 91 (353)
Q Consensus 64 ~~~~~c~~Cgk~f~~~------~C~~C~k~F~~~ 91 (353)
...|.|+.|++.-... .|..||..|.-.
T Consensus 33 ~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 33 RAKHVCPFCGRTTVKRIATGIWKCRKCGAKFAGG 66 (89)
T ss_pred hcCCcCCCCCCcceeeeccCeEEcCCCCCeeccc
Confidence 3456666666652221 377777777543
No 199
>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=49.53 E-value=7.5 Score=22.93 Aligned_cols=7 Identities=14% Similarity=-0.012 Sum_probs=2.9
Q ss_pred CCCcccC
Q 018586 106 PVPFEKT 112 (353)
Q Consensus 106 ~~~c~~~ 112 (353)
+..||.|
T Consensus 17 ~~~CP~C 23 (33)
T cd00350 17 PWVCPVC 23 (33)
T ss_pred CCcCcCC
Confidence 3344444
No 200
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=49.41 E-value=15 Score=37.87 Aligned_cols=21 Identities=14% Similarity=0.341 Sum_probs=12.3
Q ss_pred CCCCCCCcccccccccccccc
Q 018586 67 LSKAHCSGIFSDRGCNLCMNI 87 (353)
Q Consensus 67 ~~c~~Cgk~f~~~~C~~C~k~ 87 (353)
+.|+.||..+....|+.||..
T Consensus 16 kFC~~CG~~l~~~~Cp~CG~~ 36 (645)
T PRK14559 16 RFCQKCGTSLTHKPCPQCGTE 36 (645)
T ss_pred ccccccCCCCCCCcCCCCCCC
Confidence 346666666655556666654
No 201
>PHA00626 hypothetical protein
Probab=48.31 E-value=7 Score=26.09 Aligned_cols=10 Identities=20% Similarity=0.075 Sum_probs=4.7
Q ss_pred cccccccccc
Q 018586 80 GCNLCMNIFD 89 (353)
Q Consensus 80 ~C~~C~k~F~ 89 (353)
.|+.||..|+
T Consensus 25 kCkdCGY~ft 34 (59)
T PHA00626 25 VCCDCGYNDS 34 (59)
T ss_pred EcCCCCCeec
Confidence 3455554443
No 202
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=48.26 E-value=8.8 Score=23.21 Aligned_cols=14 Identities=21% Similarity=0.650 Sum_probs=7.9
Q ss_pred eeeccccccccChH
Q 018586 15 HKCVACYKQFKRKD 28 (353)
Q Consensus 15 ~~C~~C~k~f~~~~ 28 (353)
..|+.|+..|.-..
T Consensus 3 i~Cp~C~~~y~i~d 16 (36)
T PF13717_consen 3 ITCPNCQAKYEIDD 16 (36)
T ss_pred EECCCCCCEEeCCH
Confidence 35666666665544
No 203
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=46.78 E-value=6.7 Score=32.43 Aligned_cols=15 Identities=33% Similarity=0.607 Sum_probs=10.5
Q ss_pred CCChHHHHHHHHHHH
Q 018586 198 AMPLKEVKDKILEIL 212 (353)
Q Consensus 198 ~~~~~~v~~~~~~~~ 212 (353)
.++.+++.+.+.+-|
T Consensus 102 ~IsveEIqDiVE~~L 116 (154)
T PRK00464 102 EVPSKEIGELVMEEL 116 (154)
T ss_pred CCCHHHHHHHHHHHH
Confidence 466777777777777
No 204
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=46.68 E-value=7.7 Score=34.06 Aligned_cols=41 Identities=20% Similarity=0.265 Sum_probs=28.0
Q ss_pred ccccCcccCCChHHHHhcc-CCCCCCCCCCccccccccccccccccCchhHHHH
Q 018586 45 KCAVCQKLSKSFESLREHL-TGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKH 97 (353)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~-~~~~~c~~Cgk~f~~~~C~~C~k~F~~~s~L~~H 97 (353)
=|=.|++.|-....|.+|+ .+.+.| .+|.|...+.-.|..|
T Consensus 12 wcwycnrefddekiliqhqkakhfkc------------hichkkl~sgpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKAKHFKC------------HICHKKLFSGPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhhhhhcccee------------eeehhhhccCCCceee
Confidence 5778888888888888888 555554 5555555454555555
No 205
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=44.20 E-value=12 Score=21.71 Aligned_cols=22 Identities=18% Similarity=0.294 Sum_probs=13.9
Q ss_pred CCCCCCccccccccccccccccC
Q 018586 68 SKAHCSGIFSDRGCNLCMNIFDS 90 (353)
Q Consensus 68 ~c~~Cgk~f~~~~C~~C~k~F~~ 90 (353)
.|.+|+. +....|+.|+..+.+
T Consensus 4 ~C~vC~~-~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 4 LCSVCGN-PAKYRCPRCGARYCS 25 (30)
T ss_dssp EETSSSS-EESEE-TTT--EESS
T ss_pred CCccCcC-CCEEECCCcCCceeC
Confidence 3677888 777788888877654
No 206
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=42.14 E-value=13 Score=40.66 Aligned_cols=28 Identities=25% Similarity=0.338 Sum_probs=22.1
Q ss_pred CCCCCceeeccccccccChHHHHHHHhh
Q 018586 9 KRSTARHKCVACYKQFKRKDHLIEHMKI 36 (353)
Q Consensus 9 h~~~k~~~C~~C~k~f~~~~~l~~H~~~ 36 (353)
|+-.|.+.|+.|+..|+....|..|++.
T Consensus 460 ~S~~kt~~cpkc~~~yk~a~~L~vhmRs 487 (1406)
T KOG1146|consen 460 HSFFKTLKCPKCNWHYKLAQTLGVHMRS 487 (1406)
T ss_pred ecccccccCCccchhhhhHHHhhhcccc
Confidence 4455778888888888888888888875
No 207
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=42.09 E-value=15 Score=32.79 Aligned_cols=51 Identities=16% Similarity=0.231 Sum_probs=28.8
Q ss_pred CCCCCCCCccccccccccccccccCchhHHHHHHHhcCCCCCCcccCCcchhh
Q 018586 66 PLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEACSLSAPVPFEKTLSNAES 118 (353)
Q Consensus 66 ~~~c~~Cgk~f~~~~C~~C~k~F~~~s~L~~H~~~h~~~k~~~c~~~~~~~~~ 118 (353)
.+.|.-|.+ +.+.+|-.|.-.|...-..+.-. .-...++++||+|+.--..
T Consensus 171 ~~KC~SCNr-lGq~sCLRCK~cfCddHvrrKg~-ky~k~k~~PCPKCg~et~e 221 (314)
T PF06524_consen 171 TFKCQSCNR-LGQYSCLRCKICFCDDHVRRKGF-KYEKGKPIPCPKCGYETQE 221 (314)
T ss_pred ccccccccc-ccchhhhheeeeehhhhhhhccc-ccccCCCCCCCCCCCcccc
Confidence 455655543 44556777777776653222111 2345689999999754333
No 208
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=42.06 E-value=11 Score=31.63 Aligned_cols=20 Identities=15% Similarity=0.302 Sum_probs=10.9
Q ss_pred CCCCCCCCcccccc---cccccc
Q 018586 66 PLSKAHCSGIFSDR---GCNLCM 85 (353)
Q Consensus 66 ~~~c~~Cgk~f~~~---~C~~C~ 85 (353)
.|.|++||..+-.. .||.||
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCC
Confidence 35566666555442 266665
No 209
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=41.63 E-value=27 Score=28.53 Aligned_cols=14 Identities=36% Similarity=0.645 Sum_probs=8.1
Q ss_pred ccccCcccCCChHH
Q 018586 45 KCAVCQKLSKSFES 58 (353)
Q Consensus 45 ~C~~C~~~f~~~~~ 58 (353)
.|+.|+..|.....
T Consensus 101 ~Cp~C~~~y~~~ea 114 (147)
T smart00531 101 KCPNCQSKYTFLEA 114 (147)
T ss_pred ECcCCCCEeeHHHH
Confidence 66666666654433
No 210
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=41.40 E-value=13 Score=24.80 Aligned_cols=19 Identities=26% Similarity=0.480 Sum_probs=11.2
Q ss_pred CCCCCCcccccc----ccccccc
Q 018586 68 SKAHCSGIFSDR----GCNLCMN 86 (353)
Q Consensus 68 ~c~~Cgk~f~~~----~C~~C~k 86 (353)
.|..||+.|... .|+.|+.
T Consensus 7 ~C~~Cg~~~~~~dDiVvCp~Cga 29 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIVVCPECGA 29 (54)
T ss_pred cChhhCCcccCCCCEEECCCCCC
Confidence 466666666432 3777765
No 211
>PF00843 Arena_nucleocap: Arenavirus nucleocapsid protein; InterPro: IPR000229 Arenaviruses are single stranded RNA viruses. The arenavirus S RNAs that have been characterised include conserved terminal sequences, an ambisense arrangement of the coding regions for the precursor glycoprotein (GPC) and nucleocapsid (N) proteins and an intergenic region capable of forming a base-paired "hairpin" structure. The mature glycoproteins that result are G1 and G2 and the N protein []. This family represents the nucleocapsid protein that encapsulates the viral ssRNA [].; GO: 0019013 viral nucleocapsid; PDB: 3MX5_A 3MX2_C 3MWT_C 3Q7C_A 3MWP_B 3Q7B_A 3T5Q_E 3T5N_A 3R3L_B.
Probab=40.37 E-value=23 Score=34.16 Aligned_cols=141 Identities=19% Similarity=0.233 Sum_probs=70.3
Q ss_pred CCceeeccCccccccCCCCccceeEEeeecCCCCeEEeeeccCCC--CccccccccCCCCHhhhcCCCChHHHHHHHHHH
Q 018586 134 GPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 211 (353)
Q Consensus 134 ~~~~~~~D~Ettg~~~~~~~~il~~v~ivd~~g~~~~~~lv~P~~--~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~ 211 (353)
+..-..+|+|-.. +.-. .+++.-.+..-.++-|=.|.. .+.+....-|||--.||.++.| -+...++..
T Consensus 371 p~~ttWiDIEG~p---~DPV----ElAiyQP~sg~YiHcyR~P~D~K~FK~~SKysHGillkDl~~aqP--GL~S~vi~~ 441 (533)
T PF00843_consen 371 PNATTWIDIEGPP---NDPV----ELAIYQPSSGNYIHCYREPHDEKQFKNQSKYSHGILLKDLENAQP--GLTSAVIEL 441 (533)
T ss_dssp TTS-EEEEEESET---TSES----EEEEEETTTTEEEEEE---S-HHHHHHHHHHTT-B-GGGCTTB-T--THHHHHHHH
T ss_pred CCCCeeEecCCCC---CCCe----EEEEeccCCCcEEEEecCCcchhhhcccccccccccHHHHhhhcc--chHHHHHHh
Confidence 3344567777653 3333 444443444444577777875 5667777789999999999876 456667777
Q ss_pred HhcCCCCcccccCCCCCcEEEecccHHHHHHhcCcCCC-Cceeeccc---ccCCcccCCCCCcHHHHHHHHhCCcCCC--
Q 018586 212 LNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPD-HMLRDTAK---YRPLMKTNLVSHSLKYLTRTYLGYDIQS-- 285 (353)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~-~~~~Dt~~---l~~~~~~~~~~~~L~~l~~~~~~~~~~~-- 285 (353)
| +.+.+|-+.+.+-=.+.|.+.--+ ..+||+.. -++.+ ...-.-+...||...-|+-+..
T Consensus 442 L-------------P~~MVlT~QGsDDIrkLld~hGRrDiKlvDV~lt~eqaR~F-Ed~VWd~f~~LC~~H~GvVv~KKK 507 (533)
T PF00843_consen 442 L-------------PKNMVLTCQGSDDIRKLLDMHGRRDIKLVDVKLTSEQARKF-EDQVWDRFGHLCKKHTGVVVKKKK 507 (533)
T ss_dssp S--------------TT-EEEESSHHHHHHHHHCTT-TTSEEEE----HHHHTTT-HHHHHHHHGGG---B-S-EEE--S
T ss_pred C-------------CcCcEEEeeChHHHHHHHHhcCCCcceEEEeecCHHHHHHH-HHHHHHHHHHHHHhcCceEEeccc
Confidence 7 488899999965444445544332 66788753 22222 1111123446677665654322
Q ss_pred --------CCCChHHHHHHH
Q 018586 286 --------GVHDPYEDCVSV 297 (353)
Q Consensus 286 --------~~H~Al~Da~~t 297 (353)
+.|-||-|+++-
T Consensus 508 kg~~~~~t~PHCALlDCiMf 527 (533)
T PF00843_consen 508 KGKKPESTNPHCALLDCIMF 527 (533)
T ss_dssp SSS-EEE-----HHHHHHHH
T ss_pred CCCCCCCCCchHHHHHHHHH
Confidence 279999999864
No 212
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=40.26 E-value=43 Score=36.36 Aligned_cols=134 Identities=15% Similarity=0.169 Sum_probs=73.1
Q ss_pred cccCCCceeeccCccccccCCCCccceeEEeee-cC-------CCCe----EEeeeccCCCCccccccccCCCC---Hhh
Q 018586 130 RTCRGPKAVAMDCEMVGGGSNGTLDLCARVCLV-DE-------DENV----IFHTYVQPQLPVTNYRYEVTGLT---EED 194 (353)
Q Consensus 130 ~~~~~~~~~~~D~Ettg~~~~~~~~il~~v~iv-d~-------~g~~----~~~~lv~P~~~i~~~~~~~~GIt---~e~ 194 (353)
.+.++....++..+|+-.......+| ..+++. .. .+.. .+.++++|...+-+. |+. .+.
T Consensus 524 a~~Ppl~llsL~i~T~~N~k~~~~Ei-v~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~~~fP~-----g~~ela~~k 597 (1429)
T KOG0970|consen 524 APPPPLTLLSLNIRTSMNPKQNKNEI-VMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPGTSFPL-----GLKELAKQK 597 (1429)
T ss_pred CCCCCeeEEEeeeeehhccccchhhh-hhhhhhhcccccccCCCCCCcccCcceeEecCCCCcCCc-----hHHHHHHhc
Confidence 34666677888888887654443344 222221 01 1111 367788887532221 222 000
Q ss_pred ---hcCCCChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecc-cHHHHHHhc-----CcCC-------------C---
Q 018586 195 ---IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLR-----MNYP-------------D--- 249 (353)
Q Consensus 195 ---l~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~-~~~D~~~l~-----~~~~-------------~--- 249 (353)
|.-..+...++..|+..++.- ...+||||| ..+++++|- +..| .
T Consensus 598 ~~~v~~~~sErALLs~fla~~~~~-----------dpD~iVgHn~~~~~l~VLl~R~~~~Kip~WS~IgRLrrS~~~kfg 666 (1429)
T KOG0970|consen 598 LSKVVLHNSERALLSHFLAMLNKE-----------DPDVIVGHNIQGFYLDVLLSRLHALKIPNWSSIGRLRRSWPPKFG 666 (1429)
T ss_pred cCceEEecCHHHHHHHHHHHhhcc-----------CCCEEEEeccccchHHHHHHHHHHhcCcchhhhhhhhhccccccC
Confidence 222334556666676666433 446999999 888998882 1111 0
Q ss_pred -------------CceeecccccCCcccCCCCCcHHHHHHHHhCC
Q 018586 250 -------------HMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGY 281 (353)
Q Consensus 250 -------------~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~ 281 (353)
..+-|+...++.+. ...+|+|.+|+...|+.
T Consensus 667 ~~s~~~e~~~~aGRl~CD~~~~a~~li-k~~S~~LseL~q~~l~~ 710 (1429)
T KOG0970|consen 667 RSSSFGEFFIIAGRLMCDLNLAARELI-KAQSYSLSELSQQILKE 710 (1429)
T ss_pred CcccccccccccceEEeehHHHHHhhh-ccccccHHHHHHHHHhh
Confidence 12234422223332 24689999999999887
No 213
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.15 E-value=13 Score=28.53 Aligned_cols=20 Identities=10% Similarity=0.027 Sum_probs=13.4
Q ss_pred CCCCCcccccc-----ccccccccc
Q 018586 69 KAHCSGIFSDR-----GCNLCMNIF 88 (353)
Q Consensus 69 c~~Cgk~f~~~-----~C~~C~k~F 88 (353)
|+.||+.|... .||+||++|
T Consensus 12 dPetg~KFYDLNrdPiVsPytG~s~ 36 (129)
T COG4530 12 DPETGKKFYDLNRDPIVSPYTGKSY 36 (129)
T ss_pred CccccchhhccCCCccccCcccccc
Confidence 66666666543 378888877
No 214
>PRK14873 primosome assembly protein PriA; Provisional
Probab=40.13 E-value=19 Score=37.26 Aligned_cols=26 Identities=15% Similarity=0.334 Sum_probs=17.8
Q ss_pred CCCCCC-ccccCcccCCChHHHHhccCCCCCCCCCCcc
Q 018586 39 HSVHQP-KCAVCQKLSKSFESLREHLTGPLSKAHCSGI 75 (353)
Q Consensus 39 h~~~~~-~C~~C~~~f~~~~~l~~H~~~~~~c~~Cgk~ 75 (353)
|..... .|+.||.. ..++.|+.||..
T Consensus 405 h~~~~~l~Ch~CG~~-----------~~p~~Cp~Cgs~ 431 (665)
T PRK14873 405 PSAGGTPRCRWCGRA-----------APDWRCPRCGSD 431 (665)
T ss_pred ecCCCeeECCCCcCC-----------CcCccCCCCcCC
Confidence 443344 99999953 126789999865
No 215
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=40.13 E-value=8.7 Score=25.07 Aligned_cols=9 Identities=22% Similarity=0.320 Sum_probs=4.1
Q ss_pred CCCCCCccc
Q 018586 68 SKAHCSGIF 76 (353)
Q Consensus 68 ~c~~Cgk~f 76 (353)
.|-.||+.|
T Consensus 8 ~C~~Cg~~~ 16 (49)
T COG1996 8 KCARCGREV 16 (49)
T ss_pred EhhhcCCee
Confidence 344444444
No 216
>PRK05580 primosome assembly protein PriA; Validated
Probab=39.45 E-value=10 Score=39.37 Aligned_cols=14 Identities=7% Similarity=0.188 Sum_probs=9.7
Q ss_pred CCCceeeccCcccc
Q 018586 133 RGPKAVAMDCEMVG 146 (353)
Q Consensus 133 ~~~~~~~~D~Ettg 146 (353)
+..++..+|.+|+.
T Consensus 451 p~~~v~~~~~d~~~ 464 (679)
T PRK05580 451 PEARILRIDRDTTR 464 (679)
T ss_pred CCCcEEEEeccccc
Confidence 44567778888875
No 217
>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=39.30 E-value=12 Score=22.61 Aligned_cols=10 Identities=20% Similarity=0.524 Sum_probs=4.9
Q ss_pred cccccccccC
Q 018586 81 CNLCMNIFDS 90 (353)
Q Consensus 81 C~~C~k~F~~ 90 (353)
|..||..+.+
T Consensus 24 Cd~cg~~L~q 33 (36)
T PF05191_consen 24 CDNCGGELVQ 33 (36)
T ss_dssp CTTTTEBEBE
T ss_pred cCCCCCeeEe
Confidence 5555544433
No 218
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=38.39 E-value=11 Score=38.58 Aligned_cols=29 Identities=21% Similarity=0.447 Sum_probs=23.0
Q ss_pred cccccccccCchhHHHHHHHhcCCCCCCcccCCcc
Q 018586 81 CNLCMNIFDSPSSLIKHKEACSLSAPVPFEKTLSN 115 (353)
Q Consensus 81 C~~C~k~F~~~s~L~~H~~~h~~~k~~~c~~~~~~ 115 (353)
|+.|.+.|.++-+.+-|. .|..||.|+..
T Consensus 154 C~~C~~EY~dP~nRRfHA------Qp~aCp~CGP~ 182 (750)
T COG0068 154 CPFCDKEYKDPLNRRFHA------QPIACPKCGPH 182 (750)
T ss_pred CHHHHHHhcCcccccccc------ccccCcccCCC
Confidence 999999999998776554 46789999853
No 219
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=36.51 E-value=13 Score=34.08 Aligned_cols=23 Identities=26% Similarity=0.496 Sum_probs=14.8
Q ss_pred ccccccccccCchhHHHHHHHhc
Q 018586 80 GCNLCMNIFDSPSSLIKHKEACS 102 (353)
Q Consensus 80 ~C~~C~k~F~~~s~L~~H~~~h~ 102 (353)
.|+.|...|......-.|...|.
T Consensus 390 ~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 390 QCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred echhhhhhhhhhhHHHHHHHHhh
Confidence 36666666666666666776664
No 220
>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=36.10 E-value=29 Score=19.27 Aligned_cols=19 Identities=16% Similarity=0.746 Sum_probs=13.7
Q ss_pred eeccccccccChHHHHHHHh
Q 018586 16 KCVACYKQFKRKDHLIEHMK 35 (353)
Q Consensus 16 ~C~~C~k~f~~~~~l~~H~~ 35 (353)
.|+.|++.+ ....++.|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 588888887 4456777765
No 221
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=35.36 E-value=33 Score=21.36 Aligned_cols=28 Identities=21% Similarity=0.437 Sum_probs=16.7
Q ss_pred cccccccccccccccC--chhHHHHHHHhc
Q 018586 75 IFSDRGCNLCMNIFDS--PSSLIKHKEACS 102 (353)
Q Consensus 75 ~f~~~~C~~C~k~F~~--~s~L~~H~~~h~ 102 (353)
.|....|+.||-.|.. ...-..|.+-|.
T Consensus 10 ~~~~~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 10 SFGATTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred ccCCcCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 3444468888877754 444556666553
No 222
>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=34.46 E-value=23 Score=23.66 Aligned_cols=7 Identities=29% Similarity=0.553 Sum_probs=2.9
Q ss_pred ccccccc
Q 018586 81 CNLCMNI 87 (353)
Q Consensus 81 C~~C~k~ 87 (353)
|+.||..
T Consensus 5 CP~CG~~ 11 (54)
T TIGR01206 5 CPDCGAE 11 (54)
T ss_pred CCCCCCE
Confidence 4444443
No 223
>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=34.26 E-value=43 Score=20.87 Aligned_cols=25 Identities=32% Similarity=0.542 Sum_probs=15.4
Q ss_pred CCCceeeccccccccCh----HHHHHHHh
Q 018586 11 STARHKCVACYKQFKRK----DHLIEHMK 35 (353)
Q Consensus 11 ~~k~~~C~~C~k~f~~~----~~l~~H~~ 35 (353)
+.....|..|++.+... ++|.+|++
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 35567899999887764 67888884
No 224
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=33.72 E-value=12 Score=40.97 Aligned_cols=82 Identities=13% Similarity=0.237 Sum_probs=51.4
Q ss_pred eeeccccccccChHHHHHHHhhhcCCCCCC-ccccCcccCCChHHHHhccCC-CCCCCCCCcccc--------ccccccc
Q 018586 15 HKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHLTG-PLSKAHCSGIFS--------DRGCNLC 84 (353)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~~~h~~~~~-~C~~C~~~f~~~~~l~~H~~~-~~~c~~Cgk~f~--------~~~C~~C 84 (353)
+.|..|.+.|.-.-.+. |+-+ ..+ .|..|...|...+.+..|.++ -+.-+.-++... ..-|+.|
T Consensus 1261 ~~c~~~~~~~~~~~~~~-~l~~-----~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~c~~c 1334 (1406)
T KOG1146|consen 1261 GECGAVDELLTPSFGIS-TLDV-----THRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYHCLAC 1334 (1406)
T ss_pred chhhhccccccCcccee-eccc-----chhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCccccccchHH
Confidence 56778877776655444 4432 233 888888888888888888610 000000000000 0129999
Q ss_pred cccccCchhHHHHHHHhc
Q 018586 85 MNIFDSPSSLIKHKEACS 102 (353)
Q Consensus 85 ~k~F~~~s~L~~H~~~h~ 102 (353)
...|.+...|+.|++.-.
T Consensus 1335 ~~~~~~~~alqihm~~~~ 1352 (1406)
T KOG1146|consen 1335 EVLLSGREALQIHMRSSA 1352 (1406)
T ss_pred HhhcchhHHHHHHHHHhh
Confidence 999999999999999644
No 225
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=33.48 E-value=23 Score=38.88 Aligned_cols=10 Identities=10% Similarity=-0.037 Sum_probs=6.3
Q ss_pred CCCcccCCcc
Q 018586 106 PVPFEKTLSN 115 (353)
Q Consensus 106 ~~~c~~~~~~ 115 (353)
...|+.|+..
T Consensus 709 a~~CP~CGtp 718 (1337)
T PRK14714 709 RVECPRCDVE 718 (1337)
T ss_pred cccCCCCCCc
Confidence 3468888733
No 226
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=33.30 E-value=15 Score=27.37 Aligned_cols=26 Identities=19% Similarity=0.428 Sum_probs=14.1
Q ss_pred CCCCCCCCCcccccc------ccccccccccC
Q 018586 65 GPLSKAHCSGIFSDR------GCNLCMNIFDS 90 (353)
Q Consensus 65 ~~~~c~~Cgk~f~~~------~C~~C~k~F~~ 90 (353)
..|.|+.||+.-... .|..|++.|.-
T Consensus 34 ~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKRVATGIWKCKKCGKKFAG 65 (90)
T ss_dssp S-BEESSSSSSEEEEEETTEEEETTTTEEEE-
T ss_pred CCCcCCCCCCceeEEeeeEEeecCCCCCEEeC
Confidence 455666666554322 37777776643
No 227
>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=32.66 E-value=25 Score=26.24 Aligned_cols=27 Identities=15% Similarity=0.254 Sum_probs=14.5
Q ss_pred CCCCCCCCCccccc------cccccccccccCc
Q 018586 65 GPLSKAHCSGIFSD------RGCNLCMNIFDSP 91 (353)
Q Consensus 65 ~~~~c~~Cgk~f~~------~~C~~C~k~F~~~ 91 (353)
..|.|+.||+.-.. +.|..|++.|.-.
T Consensus 34 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 34 AKYVCPFCGKKTVKRGSTGIWTCRKCGAKFAGG 66 (91)
T ss_pred cCccCCCCCCCceEEEeeEEEEcCCCCCEEeCC
Confidence 45566666543221 1377777766543
No 228
>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=32.50 E-value=21 Score=28.63 Aligned_cols=23 Identities=26% Similarity=0.452 Sum_probs=14.6
Q ss_pred cccccccccCchhHHHHHHHhcCCCC
Q 018586 81 CNLCMNIFDSPSSLIKHKEACSLSAP 106 (353)
Q Consensus 81 C~~C~k~F~~~s~L~~H~~~h~~~k~ 106 (353)
|-+|||.|.. |++|.+.|+|-.|
T Consensus 75 clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 75 CLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp -TBT--EESB---HHHHHHHTT-S-H
T ss_pred EccCCcccch---HHHHHHHccCCCH
Confidence 8889997765 5899999987665
No 229
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=32.32 E-value=26 Score=26.08 Aligned_cols=26 Identities=12% Similarity=0.208 Sum_probs=13.7
Q ss_pred CCCCCCCCCccccc------cccccccccccC
Q 018586 65 GPLSKAHCSGIFSD------RGCNLCMNIFDS 90 (353)
Q Consensus 65 ~~~~c~~Cgk~f~~------~~C~~C~k~F~~ 90 (353)
..|.|+.||+.-.. +.|..|++.|.-
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGKHAVKRQAVGIWRCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCCCceeeeeeEEEEcCCCCCEEeC
Confidence 35556666543221 137777776654
No 230
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=32.07 E-value=40 Score=22.90 Aligned_cols=10 Identities=20% Similarity=0.092 Sum_probs=6.0
Q ss_pred CCCCCcccCC
Q 018586 104 SAPVPFEKTL 113 (353)
Q Consensus 104 ~k~~~c~~~~ 113 (353)
..+|.|++|+
T Consensus 48 g~~Y~Cp~CG 57 (61)
T COG2888 48 GNPYRCPKCG 57 (61)
T ss_pred CCceECCCcC
Confidence 3556666665
No 231
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=31.90 E-value=22 Score=24.69 Aligned_cols=10 Identities=30% Similarity=0.786 Sum_probs=3.4
Q ss_pred ccccCcccCC
Q 018586 45 KCAVCQKLSK 54 (353)
Q Consensus 45 ~C~~C~~~f~ 54 (353)
.|..|++.|.
T Consensus 11 ~C~~C~~~F~ 20 (69)
T PF01363_consen 11 NCMICGKKFS 20 (69)
T ss_dssp B-TTT--B-B
T ss_pred cCcCcCCcCC
Confidence 5666666653
No 232
>PRK05580 primosome assembly protein PriA; Validated
Probab=31.84 E-value=13 Score=38.63 Aligned_cols=16 Identities=19% Similarity=0.418 Sum_probs=9.1
Q ss_pred CCCCCcccccccccccccc
Q 018586 69 KAHCSGIFSDRGCNLCMNI 87 (353)
Q Consensus 69 c~~Cgk~f~~~~C~~C~k~ 87 (353)
|..||... .|+.|+-.
T Consensus 384 C~~Cg~~~---~C~~C~~~ 399 (679)
T PRK05580 384 CRDCGWVA---ECPHCDAS 399 (679)
T ss_pred hhhCcCcc---CCCCCCCc
Confidence 66666554 46666643
No 233
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.80 E-value=18 Score=29.21 Aligned_cols=11 Identities=27% Similarity=-0.019 Sum_probs=7.0
Q ss_pred CCCCcccCCcc
Q 018586 105 APVPFEKTLSN 115 (353)
Q Consensus 105 k~~~c~~~~~~ 115 (353)
.-+.||.|++.
T Consensus 106 ~~~~CP~Cgs~ 116 (135)
T PRK03824 106 AFLKCPKCGSR 116 (135)
T ss_pred cCcCCcCCCCC
Confidence 44668888643
No 234
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=31.27 E-value=8.5 Score=35.66 Aligned_cols=37 Identities=16% Similarity=-0.084 Sum_probs=17.8
Q ss_pred CCCCCcccCCcchhhhhhhccccccccccCCCceeeccCcccccc
Q 018586 104 SAPVPFEKTLSNAESQKKISGAIDEKRTCRGPKAVAMDCEMVGGG 148 (353)
Q Consensus 104 ~k~~~c~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~D~Ettg~~ 148 (353)
.+...|..|+. ++|-...+. ......++-|+.|..++
T Consensus 250 ~r~e~C~~C~~------YlK~~~~~~--d~~~~p~adDlatL~LD 286 (309)
T PRK03564 250 VKAESCGDCGT------YLKILYQEK--DPKVEAVADDLASLVLD 286 (309)
T ss_pred eEeeecccccc------cceeccccc--CCCCCcchhHHhhhHhH
Confidence 35566887732 223322222 12233456677766653
No 235
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=30.99 E-value=26 Score=28.02 Aligned_cols=26 Identities=23% Similarity=0.214 Sum_probs=20.6
Q ss_pred cccccccccCchhHHHHHHHhcCCCCCCc
Q 018586 81 CNLCMNIFDSPSSLIKHKEACSLSAPVPF 109 (353)
Q Consensus 81 C~~C~k~F~~~s~L~~H~~~h~~~k~~~c 109 (353)
|-++||.|. +|++|..+|.+-.|=..
T Consensus 79 cLEDGkkfK---SLKRHL~t~~gmTPd~Y 104 (148)
T COG4957 79 CLEDGKKFK---SLKRHLTTHYGLTPDEY 104 (148)
T ss_pred EeccCcchH---HHHHHHhcccCCCHHHH
Confidence 888998875 58999999988776433
No 236
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=30.57 E-value=15 Score=31.06 Aligned_cols=23 Identities=26% Similarity=0.476 Sum_probs=17.6
Q ss_pred CCCCCCCCCccccc--ccccccccc
Q 018586 65 GPLSKAHCSGIFSD--RGCNLCMNI 87 (353)
Q Consensus 65 ~~~~c~~Cgk~f~~--~~C~~C~k~ 87 (353)
+.+.|..|++.|.. .-|+.||..
T Consensus 138 w~~rC~GC~~~f~~~~~~Cp~CG~~ 162 (177)
T COG1439 138 WRLRCHGCKRIFPEPKDFCPICGSP 162 (177)
T ss_pred eeEEEecCceecCCCCCcCCCCCCc
Confidence 34569999999993 359999964
No 237
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.52 E-value=49 Score=34.03 Aligned_cols=28 Identities=21% Similarity=0.316 Sum_probs=16.1
Q ss_pred ccccCcccCCChHHHHhcc-CCCCCCCCC
Q 018586 45 KCAVCQKLSKSFESLREHL-TGPLSKAHC 72 (353)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~-~~~~~c~~C 72 (353)
.|..|...|-....+..|+ ...+.|..|
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h~~chfC 212 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDHEFCHFC 212 (669)
T ss_pred cchhhhhhhccHHHHHHhhccceeheeec
Confidence 5666666666666666666 233445544
No 238
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=30.39 E-value=20 Score=27.95 Aligned_cols=9 Identities=22% Similarity=0.445 Sum_probs=3.6
Q ss_pred CCCCCcccc
Q 018586 69 KAHCSGIFS 77 (353)
Q Consensus 69 c~~Cgk~f~ 77 (353)
|..||+.|.
T Consensus 73 C~~Cg~~~~ 81 (113)
T PF01155_consen 73 CRDCGHEFE 81 (113)
T ss_dssp ETTTS-EEE
T ss_pred CCCCCCEEe
Confidence 444444443
No 239
>PF12773 DZR: Double zinc ribbon
Probab=30.34 E-value=42 Score=21.49 Aligned_cols=6 Identities=33% Similarity=0.955 Sum_probs=2.8
Q ss_pred cccccc
Q 018586 81 CNLCMN 86 (353)
Q Consensus 81 C~~C~k 86 (353)
|+.||.
T Consensus 15 C~~CG~ 20 (50)
T PF12773_consen 15 CPHCGT 20 (50)
T ss_pred ChhhcC
Confidence 444444
No 240
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=30.00 E-value=25 Score=28.58 Aligned_cols=18 Identities=17% Similarity=0.528 Sum_probs=9.4
Q ss_pred CCCCCccccccc--cccccc
Q 018586 69 KAHCSGIFSDRG--CNLCMN 86 (353)
Q Consensus 69 c~~Cgk~f~~~~--C~~C~k 86 (353)
|..||..|-.+. |+.|+.
T Consensus 32 C~~CG~v~~PPr~~Cp~C~~ 51 (140)
T COG1545 32 CKKCGRVYFPPRAYCPKCGS 51 (140)
T ss_pred cCCCCeEEcCCcccCCCCCC
Confidence 555555554432 555554
No 241
>COG4640 Predicted membrane protein [Function unknown]
Probab=29.89 E-value=30 Score=32.93 Aligned_cols=29 Identities=24% Similarity=0.366 Sum_probs=18.3
Q ss_pred CCCCCCc--cccccccccccccccCchhHHH
Q 018586 68 SKAHCSG--IFSDRGCNLCMNIFDSPSSLIK 96 (353)
Q Consensus 68 ~c~~Cgk--~f~~~~C~~C~k~F~~~s~L~~ 96 (353)
.|+.||+ .=-...|+.||..|...+++..
T Consensus 3 fC~kcG~qk~Ed~~qC~qCG~~~t~~~sqan 33 (465)
T COG4640 3 FCPKCGSQKAEDDVQCTQCGHKFTSRQSQAN 33 (465)
T ss_pred cccccccccccccccccccCCcCCchhhhhh
Confidence 3666661 1112248889988888877665
No 242
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=29.70 E-value=33 Score=23.09 Aligned_cols=20 Identities=15% Similarity=0.283 Sum_probs=14.4
Q ss_pred CCCCCCcccccccccccccc
Q 018586 68 SKAHCSGIFSDRGCNLCMNI 87 (353)
Q Consensus 68 ~c~~Cgk~f~~~~C~~C~k~ 87 (353)
.|..||.-.....|+.||..
T Consensus 7 ~C~~CgvYTLk~~CP~CG~~ 26 (56)
T PRK13130 7 KCPKCGVYTLKEICPVCGGK 26 (56)
T ss_pred ECCCCCCEEccccCcCCCCC
Confidence 47777776666678888854
No 243
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=29.60 E-value=45 Score=31.15 Aligned_cols=92 Identities=24% Similarity=0.305 Sum_probs=52.7
Q ss_pred ceeecc--ccccccChHHHHHHHhhhcCCCCCCccccCc---c------cCCChHHHHhccCCCCCCCCCCccccc-ccc
Q 018586 14 RHKCVA--CYKQFKRKDHLIEHMKISYHSVHQPKCAVCQ---K------LSKSFESLREHLTGPLSKAHCSGIFSD-RGC 81 (353)
Q Consensus 14 ~~~C~~--C~k~f~~~~~l~~H~~~~~h~~~~~~C~~C~---~------~f~~~~~l~~H~~~~~~c~~Cgk~f~~-~~C 81 (353)
.|.|+. |......-..|+.|.+.. | + +.-|..|- + ..-+++.|+.|..+-.. +..|.. +.|
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~-H-~-~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~----e~GFKGHP~C 223 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQ-H-G-FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLE----EEGFKGHPLC 223 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhh-c-C-cEEhHhhhcCcccCccceeeeecccccccccCCcc----ccCcCCCchh
Confidence 366775 666656667788888762 2 1 11444442 2 22344566677621111 113332 258
Q ss_pred ccccccccCchhHHHHHHHhcCCCCCCcccCC
Q 018586 82 NLCMNIFDSPSSLIKHKEACSLSAPVPFEKTL 113 (353)
Q Consensus 82 ~~C~k~F~~~s~L~~H~~~h~~~k~~~c~~~~ 113 (353)
..|...|-+...|..|.|-.+ ++=+-|....
T Consensus 224 ~FC~~~FYdDDEL~~HcR~~H-E~ChICD~v~ 254 (493)
T COG5236 224 IFCKIYFYDDDELRRHCRLRH-EACHICDMVG 254 (493)
T ss_pred hhccceecChHHHHHHHHhhh-hhhhhhhccC
Confidence 899999999999999988543 4555555443
No 244
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=29.30 E-value=30 Score=25.72 Aligned_cols=26 Identities=15% Similarity=0.220 Sum_probs=14.8
Q ss_pred CCCCCCCCCccccc------cccccccccccC
Q 018586 65 GPLSKAHCSGIFSD------RGCNLCMNIFDS 90 (353)
Q Consensus 65 ~~~~c~~Cgk~f~~------~~C~~C~k~F~~ 90 (353)
..|.|+.||+.-.. +.|..|++.|.-
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRPKVKRVGTGIWECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCCceEEEEEEEEEcCCCCCEEeC
Confidence 45666666544222 137777777654
No 245
>COG1773 Rubredoxin [Energy production and conversion]
Probab=28.18 E-value=25 Score=23.51 Aligned_cols=9 Identities=33% Similarity=0.999 Sum_probs=4.9
Q ss_pred ccccCcccC
Q 018586 45 KCAVCQKLS 53 (353)
Q Consensus 45 ~C~~C~~~f 53 (353)
+|..||..|
T Consensus 5 ~C~~CG~vY 13 (55)
T COG1773 5 RCSVCGYVY 13 (55)
T ss_pred EecCCceEe
Confidence 555565544
No 246
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=27.93 E-value=12 Score=38.28 Aligned_cols=35 Identities=17% Similarity=0.329 Sum_probs=16.4
Q ss_pred ccccCcccCCChHHHHhcc----CCCCC-CCCCCcccccc
Q 018586 45 KCAVCQKLSKSFESLREHL----TGPLS-KAHCSGIFSDR 79 (353)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~----~~~~~-c~~Cgk~f~~~ 79 (353)
.|..||-.|+--..|..-. ..+++ |+.|.+.+.++
T Consensus 125 ~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP 164 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDP 164 (750)
T ss_pred ccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCc
Confidence 5666666555433332222 22333 55555555543
No 247
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=27.39 E-value=27 Score=27.17 Aligned_cols=9 Identities=22% Similarity=0.763 Sum_probs=4.2
Q ss_pred ccccccccc
Q 018586 81 CNLCMNIFD 89 (353)
Q Consensus 81 C~~C~k~F~ 89 (353)
|+.||..|.
T Consensus 73 C~~Cg~~~~ 81 (113)
T PRK12380 73 CWDCSQVVE 81 (113)
T ss_pred cccCCCEEe
Confidence 455554443
No 248
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=26.82 E-value=29 Score=27.10 Aligned_cols=10 Identities=20% Similarity=0.591 Sum_probs=5.7
Q ss_pred cccccccccC
Q 018586 81 CNLCMNIFDS 90 (353)
Q Consensus 81 C~~C~k~F~~ 90 (353)
|+.|+..|..
T Consensus 73 C~~Cg~~~~~ 82 (115)
T TIGR00100 73 CEDCSEEVSP 82 (115)
T ss_pred cccCCCEEec
Confidence 6666655544
No 249
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=26.07 E-value=71 Score=26.49 Aligned_cols=11 Identities=9% Similarity=-0.155 Sum_probs=4.5
Q ss_pred ccccCcccCCC
Q 018586 45 KCAVCQKLSKS 55 (353)
Q Consensus 45 ~C~~C~~~f~~ 55 (353)
-|+.|+..|+.
T Consensus 111 ~Cp~c~~r~tf 121 (158)
T TIGR00373 111 ICPNMCVRFTF 121 (158)
T ss_pred ECCCCCcEeeH
Confidence 44444443333
No 250
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=26.03 E-value=33 Score=22.63 Aligned_cols=25 Identities=24% Similarity=0.368 Sum_probs=12.3
Q ss_pred ccccCcccCCChHHHHhccCCCCCCCCCCccc
Q 018586 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIF 76 (353)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~c~~Cgk~f 76 (353)
.|..|++.|... .+.+.|..||+.|
T Consensus 4 ~C~~C~~~F~~~-------~rk~~Cr~Cg~~~ 28 (57)
T cd00065 4 SCMGCGKPFTLT-------RRRHHCRNCGRIF 28 (57)
T ss_pred cCcccCccccCC-------ccccccCcCcCCc
Confidence 455566555541 2234455555554
No 251
>PF03337 Pox_F12L: Poxvirus F12L protein; InterPro: IPR005005 The vaccinia virus F12L gene encodes a 65 kDa protein that is expressed late during infection and is important for plaque formation, EEV production and virulence. The F12L protein is located on intracellular enveloped virus (IEV) particles, but is absent from immature virions, intracellular mature virus and cell-associated enveloped virus. F12L shows co-localization with endosomal compartments and microtubules and appears to play a role in the the transport of IEV particles to the cell surface on microtubules [].; GO: 0016032 viral reproduction
Probab=25.92 E-value=5e+02 Score=26.85 Aligned_cols=98 Identities=20% Similarity=0.260 Sum_probs=57.7
Q ss_pred EeeeccCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHhc-CCCCcccccCCCCCcEEEec-ccHHHHHHhcCcC
Q 018586 170 FHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNN-GESTGRLMLDDGKARLLVGH-GLEHDLDSLRMNY 247 (353)
Q Consensus 170 ~~~lv~P~~~i~~~~~~~~GIt~e~l~~~~~~~~v~~~~~~~~~~-~~~~~~~~~~~~~~~~lvgh-~~~~D~~~l~~~~ 247 (353)
+++.+.|.++.+-.++-..|.+ .-++.+-+.+..+|++||.+ -+ ...+.-+|||+ +--||+..|+...
T Consensus 226 v~a~it~~gp~iymIstyPG~~---F~nf~s~~~li~~FL~Wl~e~~~-------~n~~ti~LvGy~ss~FD~pLLra~w 295 (651)
T PF03337_consen 226 VNAIITPNGPSIYMISTYPGKC---FINFDSNKALISDFLKWLRECIM-------KNIRTIILVGYFSSFFDFPLLRAYW 295 (651)
T ss_pred EEEEecCCCceeEEEEecCCce---EEeCCCchHHHHHHHHHHHHHHh-------ccCceEEEeehhhhhhccHHHHhhc
Confidence 4666666666555555433433 23555667788899999844 11 12345688995 5567999999555
Q ss_pred CCC-------------------ceeecccccCCcccCCCCCcHHHHHHHHhCCcCC
Q 018586 248 PDH-------------------MLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQ 284 (353)
Q Consensus 248 ~~~-------------------~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~ 284 (353)
|.. -++|.+.++ ...++++-|++..|..+.
T Consensus 296 p~~sGW~~~~n~~ivs~~G~kvil~D~a~Fs-------~~~~~~eYc~~W~~~~~~ 344 (651)
T PF03337_consen 296 PKNSGWNFIGNNTIVSKDGLKVILVDAANFS-------PGMSLSEYCEHWTGKNVS 344 (651)
T ss_pred ccCCCceEecCceEEeCCCcEEEEEehhhhc-------cCCCHHHHHHhhccCCCC
Confidence 431 122333222 234788888888555543
No 252
>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=25.81 E-value=23 Score=28.98 Aligned_cols=7 Identities=29% Similarity=0.814 Sum_probs=4.4
Q ss_pred ccccccc
Q 018586 81 CNLCMNI 87 (353)
Q Consensus 81 C~~C~k~ 87 (353)
|+.||..
T Consensus 133 Cp~C~~~ 139 (146)
T PF07295_consen 133 CPKCGHT 139 (146)
T ss_pred CCCCCCC
Confidence 6666654
No 253
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=25.54 E-value=23 Score=37.15 Aligned_cols=19 Identities=16% Similarity=0.197 Sum_probs=0.0
Q ss_pred CCCCCCCcccccccccccc
Q 018586 67 LSKAHCSGIFSDRGCNLCM 85 (353)
Q Consensus 67 ~~c~~Cgk~f~~~~C~~C~ 85 (353)
+.|+.||+.-....|+.||
T Consensus 656 r~Cp~Cg~~t~~~~Cp~CG 674 (900)
T PF03833_consen 656 RRCPKCGKETFYNRCPECG 674 (900)
T ss_dssp -------------------
T ss_pred ccCcccCCcchhhcCcccC
Confidence 3444454444444444444
No 254
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=25.50 E-value=26 Score=36.10 Aligned_cols=12 Identities=25% Similarity=0.681 Sum_probs=6.2
Q ss_pred cccccccccCch
Q 018586 81 CNLCMNIFDSPS 92 (353)
Q Consensus 81 C~~C~k~F~~~s 92 (353)
||.|+.+|....
T Consensus 681 CP~Cn~aFganD 692 (698)
T KOG0978|consen 681 CPKCNAAFGAND 692 (698)
T ss_pred CCCCCCCCCccc
Confidence 555555554443
No 255
>PHA02563 DNA polymerase; Provisional
Probab=24.92 E-value=54 Score=33.71 Aligned_cols=18 Identities=17% Similarity=0.137 Sum_probs=15.7
Q ss_pred CCcEEEecccHHHHHHhc
Q 018586 227 KARLLVGHGLEHDLDSLR 244 (353)
Q Consensus 227 ~~~~lvgh~~~~D~~~l~ 244 (353)
.+.++..||+.||..||-
T Consensus 65 ~~~~vYfHN~~FD~~Fil 82 (630)
T PHA02563 65 TECIIYFHNLKFDGSFIL 82 (630)
T ss_pred cceEEEEecCCccHHHHH
Confidence 367999999999999987
No 256
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=24.54 E-value=61 Score=32.71 Aligned_cols=96 Identities=21% Similarity=0.265 Sum_probs=64.3
Q ss_pred HHHHHHHHHHhcCCCCcccccCCCCCcEEEecccHHHHHHhcCcCCC----------CceeecccccCCccc--------
Q 018586 203 EVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPD----------HMLRDTAKYRPLMKT-------- 264 (353)
Q Consensus 203 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~----------~~~~Dt~~l~~~~~~-------- 264 (353)
+++..+...|-+ ......||..+..|+..|.+..|. ..+++..+++..+..
T Consensus 458 e~w~~~~s~if~-----------s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~ 526 (617)
T KOG2207|consen 458 EIWHLLLSQIFE-----------SKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENL 526 (617)
T ss_pred HHHHHHHHHHcc-----------CCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhh
Confidence 777777777743 356788999999999999954441 112333334332211
Q ss_pred CCCCCcHHHHHHHHhCCcCCCC------CC---------ChHHHHHHHHHHHHHHHhchh
Q 018586 265 NLVSHSLKYLTRTYLGYDIQSG------VH---------DPYEDCVSVMRLYKRFRRQDH 309 (353)
Q Consensus 265 ~~~~~~L~~l~~~~~~~~~~~~------~H---------~Al~Da~~t~~l~~~~~~~~~ 309 (353)
+...-+|..|...++|..+... +- .|.-||...+.+|+++.+..+
T Consensus 527 ~~~~~~L~~Lt~~llg~~lnKteqcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv~ 586 (617)
T KOG2207|consen 527 NEATKGLADLTDCLLGKKLNKTEQCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVVE 586 (617)
T ss_pred cchhhhhhhhhHHHhhhhcccccccchhhcCCchhhHHHHHHhcchhhHHHHHHHHhhcc
Confidence 2225789999999999987522 22 244599999999999987754
No 257
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=24.03 E-value=32 Score=27.00 Aligned_cols=10 Identities=30% Similarity=1.019 Sum_probs=5.3
Q ss_pred cccccccccC
Q 018586 81 CNLCMNIFDS 90 (353)
Q Consensus 81 C~~C~k~F~~ 90 (353)
|+.||..|..
T Consensus 74 C~~Cg~~~~~ 83 (117)
T PRK00564 74 CKDCSHVFKP 83 (117)
T ss_pred hhhCCCcccc
Confidence 5666654443
No 258
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=23.72 E-value=46 Score=21.81 Aligned_cols=8 Identities=25% Similarity=0.970 Sum_probs=3.5
Q ss_pred cccCcccC
Q 018586 46 CAVCQKLS 53 (353)
Q Consensus 46 C~~C~~~f 53 (353)
|..||..+
T Consensus 4 C~~CgyiY 11 (50)
T cd00730 4 CRICGYIY 11 (50)
T ss_pred CCCCCeEE
Confidence 44444443
No 259
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=23.47 E-value=1.1e+02 Score=31.03 Aligned_cols=59 Identities=17% Similarity=0.094 Sum_probs=42.7
Q ss_pred eeecccccCCcccCCC--CCcHHHHHHHHhCCcCCCCC--------------CChHHHHHHHHHHHHHHHhchhh
Q 018586 252 LRDTAKYRPLMKTNLV--SHSLKYLTRTYLGYDIQSGV--------------HDPYEDCVSVMRLYKRFRRQDHQ 310 (353)
Q Consensus 252 ~~Dt~~l~~~~~~~~~--~~~L~~l~~~~~~~~~~~~~--------------H~Al~Da~~t~~l~~~~~~~~~~ 310 (353)
++||+..+.++.+... +.+|+.++..++++.+.... .-|..|+..+..||..+..+...
T Consensus 72 ~fDT~LAa~lL~~~~~~~~~~l~~la~~~l~~~l~k~~~~sdw~rpls~~q~~YAa~Dv~~l~~L~~~L~~qL~~ 146 (553)
T PRK14975 72 CHDLMLASQLLLGSEGRAGSSLSAAAARALGEGLDKPPQTSALSDPPDEEQLLYAAADADVLLELYAVLADQLNR 146 (553)
T ss_pred CchHHHHHHHcCCCCCcCCCCHHHHHHHHhCCCCCChhhhccccccchHHHHHHHHHHhHHHHHHHHHHHHHHHh
Confidence 5688777766655432 57999999999888865421 12677888999999998887654
No 260
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.26 E-value=19 Score=25.70 Aligned_cols=6 Identities=50% Similarity=1.165 Sum_probs=2.6
Q ss_pred cccccc
Q 018586 81 CNLCMN 86 (353)
Q Consensus 81 C~~C~k 86 (353)
|..||.
T Consensus 15 c~~cg~ 20 (82)
T COG2331 15 CTECGN 20 (82)
T ss_pred ecccch
Confidence 444443
No 261
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=23.13 E-value=32 Score=30.76 Aligned_cols=90 Identities=18% Similarity=0.225 Sum_probs=46.9
Q ss_pred CCCCceeeccccccccChHHHHHHHhh-hcCCCCCCccccCcccCCChHHHHhccCCCCCC--CCCCccccc-----ccc
Q 018586 10 RSTARHKCVACYKQFKRKDHLIEHMKI-SYHSVHQPKCAVCQKLSKSFESLREHLTGPLSK--AHCSGIFSD-----RGC 81 (353)
Q Consensus 10 ~~~k~~~C~~C~k~f~~~~~l~~H~~~-~~h~~~~~~C~~C~~~f~~~~~l~~H~~~~~~c--~~Cgk~f~~-----~~C 81 (353)
-|.+.|+|..|..-... ...-.|+.. -.-..+.++|..|++. .+.+-|+--+ --| .+=.|.|.. ..|
T Consensus 138 hGGrif~CsfC~~flCE-DDQFEHQAsCQvLe~E~~KC~SCNrl-Gq~sCLRCK~---cfCddHvrrKg~ky~k~k~~PC 212 (314)
T PF06524_consen 138 HGGRIFKCSFCDNFLCE-DDQFEHQASCQVLESETFKCQSCNRL-GQYSCLRCKI---CFCDDHVRRKGFKYEKGKPIPC 212 (314)
T ss_pred CCCeEEEeecCCCeeec-cchhhhhhhhhhhhcccccccccccc-cchhhhheee---eehhhhhhhcccccccCCCCCC
Confidence 36788999999864443 334445531 0023344488888752 3323322111 000 000122221 138
Q ss_pred ccccccccCchhHHHHHHHhcCC
Q 018586 82 NLCMNIFDSPSSLIKHKEACSLS 104 (353)
Q Consensus 82 ~~C~k~F~~~s~L~~H~~~h~~~ 104 (353)
|.||........|..-.|+|.-.
T Consensus 213 PKCg~et~eTkdLSmStR~hkyG 235 (314)
T PF06524_consen 213 PKCGYETQETKDLSMSTRSHKYG 235 (314)
T ss_pred CCCCCcccccccceeeeecchhc
Confidence 99998888888887777777543
No 262
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=22.93 E-value=39 Score=25.07 Aligned_cols=10 Identities=30% Similarity=0.654 Sum_probs=5.2
Q ss_pred cccccccccC
Q 018586 81 CNLCMNIFDS 90 (353)
Q Consensus 81 C~~C~k~F~~ 90 (353)
|..||..|.+
T Consensus 61 CkkCGfef~~ 70 (97)
T COG3357 61 CKKCGFEFRD 70 (97)
T ss_pred hcccCccccc
Confidence 5555555544
No 263
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=22.84 E-value=83 Score=25.93 Aligned_cols=26 Identities=31% Similarity=0.431 Sum_probs=12.7
Q ss_pred CCCCCCccccccccccccccccCchhHHHHHH
Q 018586 68 SKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKE 99 (353)
Q Consensus 68 ~c~~Cgk~f~~~~C~~C~k~F~~~s~L~~H~~ 99 (353)
.|..|+|.| |+.-+. +..|++..|..
T Consensus 16 ~C~~c~kWF----CNg~~~--~s~SHIv~HLv 41 (152)
T PF09416_consen 16 KCNTCNKWF----CNGRGN--TSGSHIVNHLV 41 (152)
T ss_dssp EETTTTEEE----ES--TT--SSS-HHHHHHH
T ss_pred EcCCCCcEe----ecCCCC--CcccHHHHHHH
Confidence 355555555 322222 36677777754
No 264
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=22.61 E-value=25 Score=36.18 Aligned_cols=21 Identities=24% Similarity=0.365 Sum_probs=0.0
Q ss_pred cccccccccCchhHHHHHHHh
Q 018586 81 CNLCMNIFDSPSSLIKHKEAC 101 (353)
Q Consensus 81 C~~C~k~F~~~s~L~~H~~~h 101 (353)
|.+|+|.|---.++..||++|
T Consensus 795 CreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 795 CRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred hHHHHHHHHHHhhhhHHHHHH
No 265
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.25 E-value=52 Score=28.42 Aligned_cols=88 Identities=18% Similarity=0.307 Sum_probs=52.3
Q ss_pred CCceeecc--ccccccChHHHHHHHhhhcCCCCCCccccCcccCCChHHHHhccCCCCCC---CCCCcccccccc--ccc
Q 018586 12 TARHKCVA--CYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHLTGPLSK---AHCSGIFSDRGC--NLC 84 (353)
Q Consensus 12 ~k~~~C~~--C~k~f~~~~~l~~H~~~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~~~~c---~~Cgk~f~~~~C--~~C 84 (353)
.+.|.|+. |-..|....+...|. |+-....|..|.+.|.+..-|..|+...+-| -.-.+.....+| ..|
T Consensus 77 ~~~~~cqvagc~~~~d~lD~~E~hY----~~~h~~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgC 152 (253)
T KOG4173|consen 77 VPAFACQVAGCCQVFDALDDYEHHY----HTLHGNSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGC 152 (253)
T ss_pred cccccccccchHHHHhhhhhHHHhh----hhcccchhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhh
Confidence 45678886 666676666555555 3333338999999999988888887211111 000000111234 568
Q ss_pred cccccCchhHHHHHH-HhcC
Q 018586 85 MNIFDSPSSLIKHKE-ACSL 103 (353)
Q Consensus 85 ~k~F~~~s~L~~H~~-~h~~ 103 (353)
+..|...-....|+- +|.-
T Consensus 153 t~KFkT~r~RkdH~I~~Hk~ 172 (253)
T KOG4173|consen 153 TEKFKTSRDRKDHMIRMHKY 172 (253)
T ss_pred hhhhhhhhhhhhHHHHhccC
Confidence 888888777777865 4543
No 266
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=22.08 E-value=42 Score=28.87 Aligned_cols=11 Identities=18% Similarity=0.313 Sum_probs=7.0
Q ss_pred cccccccccCc
Q 018586 81 CNLCMNIFDSP 91 (353)
Q Consensus 81 C~~C~k~F~~~ 91 (353)
|..||..++.-
T Consensus 46 C~~CgYR~~DV 56 (201)
T COG1779 46 CERCGYRSTDV 56 (201)
T ss_pred ccccCCcccce
Confidence 77777655543
No 267
>KOG0782 consensus Predicted diacylglycerol kinase [Signal transduction mechanisms]
Probab=21.43 E-value=49 Score=33.10 Aligned_cols=70 Identities=17% Similarity=0.286 Sum_probs=0.0
Q ss_pred eeccccccccChHHHHHHHhhhcCCCCCCccccCcccCCChHHHHhcc-----CCCCCCCCCCcccccc-----------
Q 018586 16 KCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHL-----TGPLSKAHCSGIFSDR----------- 79 (353)
Q Consensus 16 ~C~~C~k~f~~~~~l~~H~~~~~h~~~~~~C~~C~~~f~~~~~l~~H~-----~~~~~c~~Cgk~f~~~----------- 79 (353)
+|..|.-.-.... +..-.++ ...=++.-...+..-...+.+.+|- +.+-.|..|||.|.++
T Consensus 201 kCAaCkIVvHT~C-ieqLeKi--NfrCKptFRe~gsr~~rE~~fvrHHWVHrrRqeGkC~~CgKgFQQKf~FhsKEivAi 277 (1004)
T KOG0782|consen 201 KCAACKIVVHTNC-IEQLEKI--NFRCKPTFREYGSRKTRESGFVRHHWVHRRRQEGKCNTCGKGFQQKFFFHSKEIVAI 277 (1004)
T ss_pred cceeeeEEEechH-HHHHHHh--ccccccchhhccccCcccccchHHhHhhHhhhccccchhhhhhhhheeeccccEEEE
Q ss_pred ccccccccc
Q 018586 80 GCNLCMNIF 88 (353)
Q Consensus 80 ~C~~C~k~F 88 (353)
+|.-|..+|
T Consensus 278 sCSWCKqay 286 (1004)
T KOG0782|consen 278 SCSWCKQAY 286 (1004)
T ss_pred EehHHHHHh
No 268
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=21.41 E-value=37 Score=27.71 Aligned_cols=12 Identities=17% Similarity=0.307 Sum_probs=5.4
Q ss_pred CCCCCCCccccc
Q 018586 67 LSKAHCSGIFSD 78 (353)
Q Consensus 67 ~~c~~Cgk~f~~ 78 (353)
..|..||++|+.
T Consensus 29 ReC~~C~~RFTT 40 (147)
T TIGR00244 29 RECLECHERFTT 40 (147)
T ss_pred ccCCccCCccce
Confidence 334444444443
No 269
>PRK00420 hypothetical protein; Validated
Probab=20.99 E-value=53 Score=25.60 Aligned_cols=9 Identities=11% Similarity=0.475 Sum_probs=5.7
Q ss_pred ccccccccc
Q 018586 81 CNLCMNIFD 89 (353)
Q Consensus 81 C~~C~k~F~ 89 (353)
|+.||....
T Consensus 43 Cp~Cg~~~~ 51 (112)
T PRK00420 43 CPVHGKVYI 51 (112)
T ss_pred CCCCCCeee
Confidence 777776444
No 270
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=20.92 E-value=68 Score=29.80 Aligned_cols=57 Identities=28% Similarity=0.553 Sum_probs=0.0
Q ss_pred ceeeccccccccChHHHHHHHhhhcC------CCCCC--c------cccCcccCCChHHHHhccCCCCCCCCCCcccccc
Q 018586 14 RHKCVACYKQFKRKDHLIEHMKISYH------SVHQP--K------CAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDR 79 (353)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~h------~~~~~--~------C~~C~~~f~~~~~l~~H~~~~~~c~~Cgk~f~~~ 79 (353)
|-+|+.|+-+.....+|.+... | -.+.| . |-.|+..... .+.|.|..|-..|
T Consensus 290 P~eCpiC~ltLVss~hLARSyh---hL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~--------~~~y~C~~Ck~~F--- 355 (378)
T KOG2807|consen 290 PIECPICSLTLVSSPHLARSYH---HLFPLKPFVEIPETEYNGSRFCFACQGELLS--------SGRYRCESCKNVF--- 355 (378)
T ss_pred CccCCccceeEecchHHHHHHH---hhcCCcchhhccccccCCCcceeeeccccCC--------CCcEEchhcccee---
Q ss_pred cccccc
Q 018586 80 GCNLCM 85 (353)
Q Consensus 80 ~C~~C~ 85 (353)
|-.|+
T Consensus 356 -CldCD 360 (378)
T KOG2807|consen 356 -CLDCD 360 (378)
T ss_pred -eccch
No 271
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=20.92 E-value=44 Score=20.00 Aligned_cols=10 Identities=30% Similarity=0.528 Sum_probs=2.6
Q ss_pred CCCCCccccc
Q 018586 69 KAHCSGIFSD 78 (353)
Q Consensus 69 c~~Cgk~f~~ 78 (353)
|.+|++.|..
T Consensus 6 C~eC~~~f~d 15 (34)
T PF01286_consen 6 CDECGKPFMD 15 (34)
T ss_dssp -TTT--EES-
T ss_pred HhHhCCHHHH
Confidence 3444444443
No 272
>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=20.84 E-value=77 Score=27.79 Aligned_cols=30 Identities=23% Similarity=0.458 Sum_probs=21.8
Q ss_pred CCCceeeccccccccChHHHHHHHhhhcCCC
Q 018586 11 STARHKCVACYKQFKRKDHLIEHMKISYHSV 41 (353)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~~~h~~ 41 (353)
.+..|.|..|+|.|....-+..|+..- |.+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nK-H~e 103 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNK-HPE 103 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH--HH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhc-CHH
Confidence 456799999999999999888999752 543
No 273
>KOG0696 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=20.61 E-value=34 Score=33.15 Aligned_cols=55 Identities=18% Similarity=0.411 Sum_probs=30.8
Q ss_pred CCCceeeccccccccChHHHHHHHhhhcCCCCCCccccCcccCCChHHHHhcc------CCCCCCCCCCcc
Q 018586 11 STARHKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHL------TGPLSKAHCSGI 75 (353)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~~~h~~~~~~C~~C~~~f~~~~~l~~H~------~~~~~c~~Cgk~ 75 (353)
|+.-|+|+.|. +..|++. |.=..+.|+.-++.+..-..-.+|. ..+--|+.||-.
T Consensus 70 gKQGfQCqvC~--------fvvHkrC--hefVtF~CPGadkg~dtDdpr~kHkf~~~tYssPTFCDhCGsL 130 (683)
T KOG0696|consen 70 GKQGFQCQVCC--------FVVHKRC--HEFVTFSCPGADKGPDTDDPRSKHKFKIHTYSSPTFCDHCGSL 130 (683)
T ss_pred ccCceeeeEEe--------ehhhhhh--cceEEEECCCCCCCCCCCCcccccceeeeecCCCchhhhHHHH
Confidence 34456666663 5678887 6544447766666655554445554 344446555543
No 274
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=20.52 E-value=44 Score=26.04 Aligned_cols=8 Identities=25% Similarity=0.903 Sum_probs=3.7
Q ss_pred cccccccc
Q 018586 81 CNLCMNIF 88 (353)
Q Consensus 81 C~~C~k~F 88 (353)
|+.||..|
T Consensus 73 C~~Cg~~~ 80 (114)
T PRK03681 73 CETCQQYV 80 (114)
T ss_pred cccCCCee
Confidence 45555433
No 275
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF11288 DUF3089: Protein of unknown function (DUF3089); InterPro: IPR021440 This family of proteins has no known function.
Probab=20.20 E-value=1.3e+02 Score=26.25 Aligned_cols=29 Identities=24% Similarity=0.436 Sum_probs=24.1
Q ss_pred CChHHHHHHHHHHHhcCCCCcccccCCCCCcEEEecc
Q 018586 199 MPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG 235 (353)
Q Consensus 199 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~ 235 (353)
..+.||...|..||++.. .++.-||+||.
T Consensus 75 ~ay~DV~~AF~~yL~~~n--------~GRPfILaGHS 103 (207)
T PF11288_consen 75 LAYSDVRAAFDYYLANYN--------NGRPFILAGHS 103 (207)
T ss_pred hhHHHHHHHHHHHHHhcC--------CCCCEEEEEeC
Confidence 578999999999997664 34678999999
Done!