Query 019380
Match_columns 342
No_of_seqs 244 out of 3129
Neff 8.8
Searched_HMMs 46136
Date Fri Mar 29 08:59:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019380.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019380hhsearch_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 4.1E-40 9E-45 283.5 13.5 269 16-303 2-272 (280)
2 cd06149 ISG20 DEDDh 3'-5' exon 100.0 1.8E-32 3.8E-37 229.1 13.8 150 127-291 1-157 (157)
3 cd06145 REX1_like DEDDh 3'-5' 100.0 3.1E-32 6.6E-37 226.1 14.0 146 127-291 1-150 (150)
4 cd06144 REX4_like DEDDh 3'-5' 100.0 4.1E-32 8.8E-37 226.1 14.4 150 127-291 1-152 (152)
5 cd06143 PAN2_exo DEDDh 3'-5' e 100.0 4.3E-31 9.3E-36 219.4 13.6 149 127-291 1-174 (174)
6 cd06137 DEDDh_RNase DEDDh 3'-5 100.0 1.9E-30 4E-35 218.1 12.0 147 127-291 1-161 (161)
7 PRK07942 DNA polymerase III su 100.0 1.3E-28 2.9E-33 218.5 10.2 185 122-339 4-202 (232)
8 PRK07740 hypothetical protein; 99.9 1.3E-27 2.8E-32 213.5 13.3 159 122-299 57-228 (244)
9 PRK05711 DNA polymerase III su 99.9 3.1E-27 6.8E-32 209.5 11.6 158 123-297 3-176 (240)
10 TIGR01406 dnaQ_proteo DNA poly 99.9 3.6E-27 7.8E-32 208.1 11.6 161 125-302 1-177 (225)
11 cd06130 DNA_pol_III_epsilon_li 99.9 4.4E-27 9.5E-32 196.8 11.2 146 126-291 1-155 (156)
12 PRK07247 DNA polymerase III su 99.9 1E-26 2.2E-31 200.2 13.4 158 122-299 3-171 (195)
13 PRK09146 DNA polymerase III su 99.9 1.1E-26 2.3E-31 206.5 13.1 159 120-297 43-227 (239)
14 PRK08517 DNA polymerase III su 99.9 2E-26 4.4E-31 206.5 13.2 173 121-335 65-248 (257)
15 PRK06195 DNA polymerase III su 99.9 1.5E-26 3.1E-31 214.0 12.5 154 124-297 1-164 (309)
16 PRK07983 exodeoxyribonuclease 99.9 2.3E-26 5E-31 201.6 11.9 146 126-296 2-153 (219)
17 PRK06807 DNA polymerase III su 99.9 2.2E-26 4.8E-31 211.8 11.9 157 122-298 6-173 (313)
18 PRK07748 sporulation inhibitor 99.9 1.4E-26 3.1E-31 202.4 9.9 159 123-299 3-182 (207)
19 PRK06063 DNA polymerase III su 99.9 6.1E-26 1.3E-30 209.4 13.8 159 121-299 12-181 (313)
20 PRK06310 DNA polymerase III su 99.9 6.3E-26 1.4E-30 203.3 13.2 159 123-299 6-176 (250)
21 PRK06309 DNA polymerase III su 99.9 1.2E-25 2.7E-30 199.7 13.2 155 124-297 2-166 (232)
22 TIGR00573 dnaq exonuclease, DN 99.9 7.3E-26 1.6E-30 199.4 11.4 161 123-299 6-179 (217)
23 cd06131 DNA_pol_III_epsilon_Ec 99.9 1.2E-25 2.6E-30 190.3 11.2 151 126-293 1-166 (167)
24 PRK07246 bifunctional ATP-depe 99.9 1.8E-25 3.9E-30 230.0 12.6 160 121-299 4-172 (820)
25 PRK09145 DNA polymerase III su 99.9 4.3E-25 9.3E-30 192.5 12.7 156 122-296 27-200 (202)
26 COG2176 PolC DNA polymerase II 99.9 4.4E-26 9.6E-31 228.9 6.8 158 123-299 420-588 (1444)
27 cd06134 RNaseT DEDDh 3'-5' exo 99.9 3.2E-25 7E-30 191.0 11.0 163 125-297 6-189 (189)
28 PRK06722 exonuclease; Provisio 99.9 2.5E-25 5.3E-30 200.4 10.6 158 123-296 4-180 (281)
29 PRK07883 hypothetical protein; 99.9 5.1E-25 1.1E-29 217.7 13.1 159 122-299 13-184 (557)
30 smart00479 EXOIII exonuclease 99.9 5.9E-25 1.3E-29 186.1 11.7 155 126-297 2-167 (169)
31 PRK08074 bifunctional ATP-depe 99.9 7.5E-25 1.6E-29 228.9 12.8 158 123-299 2-171 (928)
32 TIGR01407 dinG_rel DnaQ family 99.9 5.4E-25 1.2E-29 228.9 11.4 156 125-299 1-167 (850)
33 cd06136 TREX1_2 DEDDh 3'-5' ex 99.9 1E-24 2.2E-29 186.1 10.4 150 126-292 1-176 (177)
34 TIGR01298 RNaseT ribonuclease 99.9 1E-24 2.2E-29 189.4 10.6 167 123-299 7-194 (200)
35 KOG2248 3'-5' exonuclease [Rep 99.9 1.8E-24 3.8E-29 201.1 12.0 160 121-298 213-376 (380)
36 PRK05168 ribonuclease T; Provi 99.9 3.2E-24 7E-29 187.8 11.7 168 122-299 15-203 (211)
37 PRK05601 DNA polymerase III su 99.9 5.1E-24 1.1E-28 195.7 12.8 156 122-296 44-248 (377)
38 cd06133 ERI-1_3'hExo_like DEDD 99.9 3E-23 6.5E-28 176.9 9.9 153 126-294 1-176 (176)
39 TIGR01405 polC_Gram_pos DNA po 99.9 3.2E-23 6.9E-28 217.9 11.8 158 123-299 189-357 (1213)
40 PRK09182 DNA polymerase III su 99.9 5.7E-22 1.2E-26 180.9 11.6 157 120-296 33-200 (294)
41 COG0847 DnaQ DNA polymerase II 99.9 8.4E-22 1.8E-26 176.9 11.5 157 124-296 13-181 (243)
42 PF00929 RNase_T: Exonuclease; 99.9 7.1E-24 1.5E-28 177.4 -2.1 149 127-290 1-164 (164)
43 cd06127 DEDDh DEDDh 3'-5' exon 99.9 7.7E-22 1.7E-26 164.4 10.0 147 127-291 1-159 (159)
44 cd06138 ExoI_N N-terminal DEDD 99.9 5E-22 1.1E-26 170.5 8.6 148 127-290 1-182 (183)
45 PTZ00315 2'-phosphotransferase 99.9 2.1E-21 4.5E-26 188.1 13.6 179 115-299 47-257 (582)
46 PRK00448 polC DNA polymerase I 99.8 1.7E-20 3.7E-25 199.7 11.8 157 124-299 419-586 (1437)
47 cd06135 Orn DEDDh 3'-5' exonuc 99.8 1.1E-20 2.3E-25 160.7 6.2 151 126-296 1-171 (173)
48 PRK11779 sbcB exonuclease I; P 99.8 6.4E-20 1.4E-24 176.8 11.5 166 122-303 4-204 (476)
49 PRK05359 oligoribonuclease; Pr 99.8 2.3E-20 5E-25 159.3 6.5 154 123-298 2-176 (181)
50 KOG2462 C2H2-type Zn-finger pr 99.7 1.3E-17 2.8E-22 145.3 4.4 107 11-117 127-254 (279)
51 KOG1275 PAB-dependent poly(A) 99.6 8.3E-16 1.8E-20 151.7 7.9 160 124-299 910-1094(1118)
52 COG5018 KapD Inhibitor of the 99.5 1.8E-14 3.9E-19 116.5 1.9 164 124-299 4-187 (210)
53 KOG2462 C2H2-type Zn-finger pr 99.4 7.7E-14 1.7E-18 121.9 3.8 87 12-102 159-267 (279)
54 KOG0542 Predicted exonuclease 99.4 3.1E-13 6.7E-18 116.5 5.5 167 125-299 57-244 (280)
55 KOG1074 Transcriptional repres 99.1 4.1E-11 8.9E-16 118.2 5.3 37 81-117 882-918 (958)
56 KOG3576 Ovo and related transc 99.0 6.7E-11 1.4E-15 98.7 1.8 98 8-119 111-225 (267)
57 KOG3623 Homeobox transcription 99.0 1.3E-10 2.7E-15 113.1 2.5 104 14-121 210-324 (1007)
58 KOG1074 Transcriptional repres 99.0 2E-10 4.3E-15 113.5 3.9 48 14-63 353-401 (958)
59 KOG3623 Homeobox transcription 99.0 1.9E-10 4.1E-15 111.9 2.6 81 7-99 887-971 (1007)
60 KOG3608 Zn finger proteins [Ge 99.0 1.7E-10 3.6E-15 103.8 1.9 103 11-115 173-301 (467)
61 COG1949 Orn Oligoribonuclease 99.0 7.6E-10 1.6E-14 89.5 4.9 153 122-298 4-179 (184)
62 KOG3242 Oligoribonuclease (3'- 98.9 1.3E-09 2.7E-14 89.0 5.7 155 122-297 24-199 (208)
63 COG2925 SbcB Exonuclease I [DN 98.8 1.2E-08 2.5E-13 93.4 8.7 171 121-307 6-211 (475)
64 PHA02768 hypothetical protein; 98.7 1.3E-08 2.9E-13 67.7 2.6 44 14-60 5-48 (55)
65 cd05160 DEDDy_DNA_polB_exo DED 98.7 6.9E-08 1.5E-12 83.9 7.7 124 126-271 1-162 (199)
66 KOG3608 Zn finger proteins [Ge 98.6 1.2E-08 2.6E-13 92.0 1.9 102 12-116 235-362 (467)
67 PHA00733 hypothetical protein 98.6 4.2E-08 9E-13 78.7 3.8 83 11-104 37-125 (128)
68 cd06139 DNA_polA_I_Ecoli_like_ 98.6 4.8E-07 1E-11 77.9 10.6 146 123-299 4-172 (193)
69 PF01612 DNA_pol_A_exo1: 3'-5' 98.5 7.3E-07 1.6E-11 75.4 10.1 92 193-297 65-175 (176)
70 KOG3576 Ovo and related transc 98.4 4.2E-08 9.1E-13 82.2 -0.4 95 11-107 142-241 (267)
71 PHA02768 hypothetical protein; 98.2 1.1E-06 2.5E-11 58.5 3.0 36 80-117 7-42 (55)
72 cd06125 DnaQ_like_exo DnaQ-lik 98.1 8.6E-06 1.9E-10 62.1 7.1 30 218-247 45-83 (96)
73 cd06146 mut-7_like_exo DEDDy 3 98.1 1.7E-05 3.8E-10 68.5 9.9 81 215-295 80-193 (193)
74 PRK05755 DNA polymerase I; Pro 98.1 9.7E-06 2.1E-10 85.6 9.7 137 123-298 314-470 (880)
75 PHA00733 hypothetical protein 98.1 2.9E-06 6.4E-11 68.0 4.2 53 8-63 67-119 (128)
76 PLN03086 PRLI-interacting fact 98.0 6.2E-06 1.3E-10 81.1 5.7 97 11-117 450-552 (567)
77 cd05780 DNA_polB_Kod1_like_exo 97.9 7E-05 1.5E-09 64.8 8.9 122 123-271 2-155 (195)
78 cd06141 WRN_exo DEDDy 3'-5' ex 97.8 9E-05 1.9E-09 62.5 8.6 79 216-294 72-169 (170)
79 PHA00732 hypothetical protein 97.8 1.5E-05 3.3E-10 58.1 2.9 44 14-63 1-44 (79)
80 PHA00616 hypothetical protein 97.8 1E-05 2.2E-10 51.4 1.2 32 80-111 3-34 (44)
81 PHA00616 hypothetical protein 97.8 1.5E-05 3.2E-10 50.6 1.8 33 14-48 1-34 (44)
82 cd06129 RNaseD_like DEDDy 3'-5 97.7 0.00019 4.2E-09 60.0 8.4 78 216-294 66-160 (161)
83 PF13465 zf-H2C2_2: Zinc-finge 97.7 2.6E-05 5.6E-10 44.1 1.8 25 29-55 1-26 (26)
84 cd05781 DNA_polB_B3_exo DEDDy 97.6 0.00024 5.3E-09 61.0 8.2 113 123-271 2-144 (188)
85 COG0349 Rnd Ribonuclease D [Tr 97.6 0.00029 6.3E-09 65.5 9.1 137 122-299 15-168 (361)
86 PF13482 RNase_H_2: RNase_H su 97.6 6.3E-05 1.4E-09 63.0 4.2 74 216-296 56-136 (164)
87 PRK10829 ribonuclease D; Provi 97.5 0.00056 1.2E-08 64.9 10.1 83 216-299 73-172 (373)
88 KOG3993 Transcription factor ( 97.5 2.1E-05 4.5E-10 73.1 0.4 89 13-104 266-382 (500)
89 KOG3993 Transcription factor ( 97.5 5E-05 1.1E-09 70.6 2.8 48 14-63 295-376 (500)
90 TIGR01388 rnd ribonuclease D. 97.4 0.0014 3E-08 62.3 10.9 82 216-299 69-168 (367)
91 PF00096 zf-C2H2: Zinc finger, 97.4 8.7E-05 1.9E-09 40.6 1.6 22 15-36 1-22 (23)
92 PF13465 zf-H2C2_2: Zinc-finge 97.3 0.0001 2.2E-09 41.7 1.1 24 93-116 1-24 (26)
93 cd00007 35EXOc 3'-5' exonuclea 97.3 0.00047 1E-08 56.5 5.5 69 191-271 40-110 (155)
94 cd05779 DNA_polB_epsilon_exo D 97.3 0.002 4.4E-08 56.0 9.3 74 187-271 70-168 (204)
95 cd05784 DNA_polB_II_exo DEDDy 97.3 0.0033 7.1E-08 54.3 10.6 120 123-271 2-153 (193)
96 PLN03086 PRLI-interacting fact 97.2 0.00022 4.7E-09 70.4 3.5 73 13-102 477-564 (567)
97 cd06148 Egl_like_exo DEDDy 3'- 97.2 0.00095 2.1E-08 57.8 6.4 138 123-299 9-179 (197)
98 cd05785 DNA_polB_like2_exo Unc 97.1 0.009 2E-07 52.1 12.0 73 187-271 55-168 (207)
99 PF00096 zf-C2H2: Zinc finger, 97.1 0.00027 5.9E-09 38.5 1.3 21 81-101 3-23 (23)
100 KOG0304 mRNA deadenylase subun 97.0 0.0015 3.3E-08 55.9 5.8 109 175-296 109-238 (239)
101 PF13894 zf-C2H2_4: C2H2-type 96.9 0.00067 1.4E-08 37.0 2.1 23 15-37 1-23 (24)
102 cd05783 DNA_polB_B1_exo DEDDy 96.8 0.028 6.1E-07 48.9 12.5 75 184-271 67-170 (204)
103 PF13912 zf-C2H2_6: C2H2-type 96.8 0.00077 1.7E-08 38.3 1.7 23 14-36 1-23 (27)
104 smart00474 35EXOc 3'-5' exonuc 96.7 0.0065 1.4E-07 50.6 7.1 89 194-296 64-170 (172)
105 PF13894 zf-C2H2_4: C2H2-type 96.6 0.0012 2.7E-08 35.9 1.6 22 81-102 3-24 (24)
106 PF04857 CAF1: CAF1 family rib 96.4 0.0067 1.4E-07 55.0 5.8 72 216-292 148-262 (262)
107 PF05605 zf-Di19: Drought indu 96.4 0.0038 8.1E-08 42.0 3.1 36 14-51 2-39 (54)
108 cd05777 DNA_polB_delta_exo DED 96.3 0.044 9.6E-07 48.6 10.3 39 184-233 65-104 (230)
109 COG5189 SFP1 Putative transcri 96.2 0.0019 4E-08 58.2 1.1 69 11-99 346-419 (423)
110 PF09237 GAGA: GAGA factor; I 96.1 0.0035 7.6E-08 40.8 1.8 27 80-106 26-52 (54)
111 PF10108 DNA_pol_B_exo2: Predi 96.1 0.021 4.6E-07 49.5 7.2 94 189-296 36-172 (209)
112 PHA00732 hypothetical protein 96.1 0.0047 1E-07 45.0 2.5 19 45-63 3-21 (79)
113 smart00355 ZnF_C2H2 zinc finge 96.0 0.0061 1.3E-07 33.6 2.4 22 15-36 1-22 (26)
114 PF12756 zf-C2H2_2: C2H2 type 95.9 0.0053 1.2E-07 46.4 2.4 75 16-104 1-76 (100)
115 PF13912 zf-C2H2_6: C2H2-type 95.9 0.0047 1E-07 35.0 1.5 24 80-103 3-26 (27)
116 cd06142 RNaseD_exo DEDDy 3'-5' 95.9 0.037 8E-07 46.6 7.6 83 216-299 63-162 (178)
117 PRK05762 DNA polymerase II; Re 95.8 0.058 1.2E-06 56.6 10.0 99 184-293 197-348 (786)
118 cd05782 DNA_polB_like1_exo Unc 95.8 0.016 3.5E-07 50.6 5.0 69 189-271 77-169 (208)
119 PHA02528 43 DNA polymerase; Pr 95.6 0.091 2E-06 55.4 10.5 160 122-292 104-323 (881)
120 PF12874 zf-met: Zinc-finger o 95.5 0.0075 1.6E-07 33.4 1.2 22 15-36 1-22 (25)
121 COG0749 PolA DNA polymerase I 95.4 0.047 1E-06 54.4 7.5 95 193-299 66-182 (593)
122 cd05778 DNA_polB_zeta_exo inac 95.4 0.1 2.3E-06 46.3 8.8 105 180-296 71-222 (231)
123 smart00355 ZnF_C2H2 zinc finge 95.3 0.013 2.7E-07 32.3 1.9 23 80-102 2-24 (26)
124 cd06140 DNA_polA_I_Bacillus_li 95.2 0.04 8.7E-07 46.5 5.5 93 193-298 44-157 (178)
125 PF09237 GAGA: GAGA factor; I 95.2 0.021 4.5E-07 37.2 2.6 27 10-36 20-46 (54)
126 KOG1798 DNA polymerase epsilon 95.0 0.26 5.7E-06 53.4 11.6 179 121-332 243-473 (2173)
127 PTZ00166 DNA polymerase delta 95.0 0.12 2.6E-06 55.8 9.5 99 184-294 324-483 (1054)
128 cd05776 DNA_polB_alpha_exo ina 94.6 0.06 1.3E-06 47.9 5.1 76 184-271 76-186 (234)
129 KOG4793 Three prime repair exo 94.3 0.067 1.5E-06 47.6 4.7 129 160-298 70-219 (318)
130 PF05605 zf-Di19: Drought indu 94.2 0.051 1.1E-06 36.4 2.9 52 44-103 3-54 (54)
131 cd06147 Rrp6p_like_exo DEDDy 3 94.2 0.056 1.2E-06 46.4 3.9 82 216-299 76-174 (192)
132 TIGR00593 pola DNA polymerase 94.2 0.087 1.9E-06 55.8 6.0 96 189-298 362-478 (887)
133 smart00486 POLBc DNA polymeras 93.6 0.53 1.2E-05 45.9 10.1 94 188-293 67-220 (471)
134 cd09018 DEDDy_polA_RNaseD_like 93.5 0.14 3.1E-06 41.5 5.0 55 216-271 52-109 (150)
135 PRK04860 hypothetical protein; 93.5 0.031 6.7E-07 46.5 1.0 39 13-57 118-157 (160)
136 PF12171 zf-C2H2_jaz: Zinc-fin 93.5 0.02 4.3E-07 32.4 -0.1 22 15-36 2-23 (27)
137 PHA02570 dexA exonuclease; Pro 93.5 0.4 8.7E-06 41.7 7.8 100 127-233 4-124 (220)
138 KOG3657 Mitochondrial DNA poly 93.2 0.18 3.8E-06 51.6 5.8 85 215-299 239-385 (1075)
139 PF13909 zf-H2C2_5: C2H2-type 93.1 0.073 1.6E-06 29.1 1.8 22 15-37 1-22 (24)
140 PF12874 zf-met: Zinc-finger o 93.0 0.053 1.2E-06 29.8 1.2 21 81-101 3-23 (25)
141 PHA02524 43A DNA polymerase su 93.0 0.57 1.2E-05 46.2 9.0 93 186-290 176-321 (498)
142 PF13913 zf-C2HC_2: zinc-finge 93.0 0.073 1.6E-06 29.6 1.7 20 80-100 4-23 (25)
143 COG3359 Predicted exonuclease 92.4 0.41 9E-06 42.2 6.3 75 216-293 155-238 (278)
144 COG0417 PolB DNA polymerase el 91.8 1.5 3.3E-05 46.2 11.0 77 184-271 205-308 (792)
145 PF12171 zf-C2H2_jaz: Zinc-fin 91.7 0.068 1.5E-06 30.2 0.6 20 81-100 4-23 (27)
146 PF13909 zf-H2C2_5: C2H2-type 91.4 0.1 2.3E-06 28.4 1.1 23 80-103 2-24 (24)
147 PF10571 UPF0547: Uncharacteri 91.1 0.14 3E-06 28.8 1.4 22 68-89 2-25 (26)
148 PF13913 zf-C2HC_2: zinc-finge 91.1 0.19 4.2E-06 27.9 1.9 21 15-36 3-23 (25)
149 smart00451 ZnF_U1 U1-like zinc 89.3 0.31 6.8E-06 29.1 2.0 23 14-36 3-25 (35)
150 TIGR03491 RecB family nuclease 89.2 3.6 7.7E-05 40.5 10.4 89 190-295 328-429 (457)
151 COG1198 PriA Primosomal protei 87.5 0.4 8.8E-06 49.4 2.7 36 101-136 470-519 (730)
152 PRK04860 hypothetical protein; 87.3 0.38 8.2E-06 40.1 1.9 35 80-118 121-155 (160)
153 PF12756 zf-C2H2_2: C2H2 type 86.8 0.57 1.2E-05 35.1 2.5 28 14-41 50-77 (100)
154 PF03104 DNA_pol_B_exo1: DNA p 86.6 1.1 2.3E-05 41.6 4.8 91 122-233 155-255 (325)
155 COG5048 FOG: Zn-finger [Genera 86.3 0.37 8E-06 46.1 1.6 49 13-63 288-343 (467)
156 KOG2231 Predicted E3 ubiquitin 84.7 0.87 1.9E-05 46.2 3.3 72 25-102 125-206 (669)
157 TIGR00622 ssl1 transcription f 83.6 1.9 4.2E-05 33.4 4.1 22 81-102 84-105 (112)
158 PF09538 FYDLN_acid: Protein o 83.3 0.65 1.4E-05 35.9 1.4 25 67-91 10-39 (108)
159 PRK14873 primosome assembly pr 82.5 0.82 1.8E-05 47.0 2.2 43 45-87 385-431 (665)
160 PF09986 DUF2225: Uncharacteri 81.9 0.69 1.5E-05 40.6 1.2 14 45-58 7-20 (214)
161 KOG1146 Homeobox protein [Gene 81.2 1.1 2.3E-05 48.5 2.5 80 10-100 461-540 (1406)
162 smart00451 ZnF_U1 U1-like zinc 80.5 1.1 2.4E-05 26.6 1.4 21 80-100 5-25 (35)
163 PRK04023 DNA polymerase II lar 78.8 1.9 4.2E-05 45.5 3.4 20 67-86 652-671 (1121)
164 COG5189 SFP1 Putative transcri 78.6 1.3 2.9E-05 40.4 1.9 19 82-100 355-373 (423)
165 KOG4793 Three prime repair exo 77.5 3.4 7.4E-05 37.1 4.1 83 214-297 195-291 (318)
166 PRK14714 DNA polymerase II lar 77.0 2.1 4.5E-05 46.4 3.1 33 45-87 681-718 (1337)
167 TIGR02300 FYDLN_acid conserved 76.4 1.5 3.4E-05 34.6 1.5 27 67-93 10-41 (129)
168 TIGR00592 pol2 DNA polymerase 75.6 18 0.0004 40.0 10.0 107 176-294 570-723 (1172)
169 PF03833 PolC_DP2: DNA polymer 74.5 0.98 2.1E-05 46.7 0.0 29 64-92 678-706 (900)
170 cd06128 DNA_polA_exo DEDDy 3'- 73.5 4.3 9.2E-05 33.0 3.6 55 216-271 52-109 (151)
171 PF09538 FYDLN_acid: Protein o 72.4 2.7 5.9E-05 32.5 2.0 10 81-90 12-21 (108)
172 KOG4173 Alpha-SNAP protein [In 71.3 2.8 6.1E-05 35.9 2.0 97 1-111 66-180 (253)
173 PF15135 UPF0515: Uncharacteri 70.9 2.2 4.8E-05 37.6 1.3 59 10-79 108-168 (278)
174 PF09986 DUF2225: Uncharacteri 70.4 0.56 1.2E-05 41.1 -2.5 18 12-29 3-20 (214)
175 COG4049 Uncharacterized protei 70.1 1.6 3.5E-05 29.0 0.2 23 81-103 20-42 (65)
176 PF05443 ROS_MUCR: ROS/MUCR tr 68.6 2.2 4.9E-05 34.2 0.8 25 81-108 75-99 (132)
177 PF13240 zinc_ribbon_2: zinc-r 68.0 3.2 6.9E-05 22.5 1.1 18 69-86 2-21 (23)
178 PRK14559 putative protein seri 67.8 5 0.00011 41.1 3.3 36 45-91 17-54 (645)
179 PRK05761 DNA polymerase I; Rev 67.7 22 0.00047 37.6 8.1 89 188-290 208-334 (787)
180 TIGR02098 MJ0042_CXXC MJ0042 f 67.0 2.8 6.1E-05 25.5 0.9 10 16-25 4-13 (38)
181 PF14353 CpXC: CpXC protein 66.4 1.4 3E-05 35.2 -0.8 17 81-97 41-57 (128)
182 PF09845 DUF2072: Zn-ribbon co 65.9 3.6 7.7E-05 32.8 1.4 24 66-89 1-31 (131)
183 PRK00398 rpoP DNA-directed RNA 65.8 3.2 6.9E-05 26.6 1.0 8 81-88 24-31 (46)
184 COG4049 Uncharacterized protei 65.6 3.2 6.9E-05 27.7 0.9 28 9-36 12-39 (65)
185 PF13717 zinc_ribbon_4: zinc-r 65.5 3.7 8.1E-05 24.9 1.2 9 46-54 5-13 (36)
186 COG1198 PriA Primosomal protei 65.3 3.8 8.2E-05 42.5 1.9 43 45-87 437-484 (730)
187 PRK00464 nrdR transcriptional 64.9 2.7 5.8E-05 34.8 0.6 15 187-201 102-116 (154)
188 KOG2893 Zn finger protein [Gen 64.8 3.2 7E-05 36.3 1.1 29 45-73 12-41 (341)
189 KOG0969 DNA polymerase delta, 64.0 4.9 0.00011 41.3 2.3 91 122-233 272-371 (1066)
190 PRK07217 replication factor A; 63.7 17 0.00038 33.5 5.6 50 147-201 218-271 (311)
191 KOG2893 Zn finger protein [Gen 63.3 2.9 6.3E-05 36.6 0.5 41 17-62 13-53 (341)
192 PF13719 zinc_ribbon_5: zinc-r 63.1 4.3 9.4E-05 24.7 1.1 11 46-56 5-15 (37)
193 PRK14559 putative protein seri 63.0 6.8 0.00015 40.2 3.2 51 45-118 3-53 (645)
194 smart00614 ZnF_BED BED zinc fi 62.3 5.5 0.00012 26.0 1.6 20 81-100 21-45 (50)
195 COG5228 POP2 mRNA deadenylase 62.3 3 6.5E-05 36.2 0.5 80 215-297 156-253 (299)
196 PHA00626 hypothetical protein 60.7 4.8 0.0001 26.9 1.1 9 81-89 26-34 (59)
197 PF13248 zf-ribbon_3: zinc-rib 59.4 6.2 0.00013 21.9 1.3 20 68-87 4-25 (26)
198 PRK03564 formate dehydrogenase 58.2 3.4 7.5E-05 38.2 0.1 20 67-86 213-234 (309)
199 COG5236 Uncharacterized conser 58.1 8.8 0.00019 35.6 2.7 78 16-106 222-309 (493)
200 cd00729 rubredoxin_SM Rubredox 57.3 6.4 0.00014 23.5 1.2 9 67-75 3-11 (34)
201 smart00531 TFIIE Transcription 57.2 8 0.00017 31.6 2.1 31 45-75 101-132 (147)
202 PRK14890 putative Zn-ribbon RN 56.7 13 0.00028 25.2 2.7 10 66-75 25-34 (59)
203 PF09723 Zn-ribbon_8: Zinc rib 56.6 4.2 9.2E-05 25.5 0.3 6 108-113 28-33 (42)
204 COG0068 HypF Hydrogenase matur 56.6 3.5 7.7E-05 42.0 -0.1 31 81-117 154-184 (750)
205 KOG2186 Cell growth-regulating 56.5 5.9 0.00013 35.1 1.3 45 15-63 4-48 (276)
206 TIGR02300 FYDLN_acid conserved 54.8 9.1 0.0002 30.3 1.9 11 66-76 26-36 (129)
207 PF05290 Baculo_IE-1: Baculovi 53.9 9.9 0.00021 30.4 2.0 15 12-26 78-92 (140)
208 PRK05580 primosome assembly pr 53.5 12 0.00025 38.9 3.1 19 277-295 591-609 (679)
209 PRK00464 nrdR transcriptional 53.3 6.3 0.00014 32.6 0.9 10 81-90 31-40 (154)
210 COG3364 Zn-ribbon containing p 53.2 7 0.00015 29.6 1.0 20 66-85 2-27 (112)
211 smart00734 ZnF_Rad18 Rad18-lik 53.1 12 0.00027 20.8 1.8 19 16-35 3-21 (26)
212 KOG1146 Homeobox protein [Gene 52.8 7.7 0.00017 42.3 1.6 84 12-106 1258-1356(1406)
213 PF02892 zf-BED: BED zinc fing 52.7 8.6 0.00019 24.2 1.3 20 81-100 19-42 (45)
214 COG1997 RPL43A Ribosomal prote 52.6 7.9 0.00017 28.5 1.2 10 81-90 56-65 (89)
215 PRK12496 hypothetical protein; 52.2 7.7 0.00017 32.4 1.3 25 66-90 127-155 (164)
216 TIGR01562 FdhE formate dehydro 51.8 5 0.00011 37.1 0.1 21 67-87 211-233 (305)
217 PF07754 DUF1610: Domain of un 51.5 11 0.00024 20.7 1.4 9 65-73 15-23 (24)
218 TIGR00595 priA primosomal prot 51.2 14 0.00031 36.8 3.2 13 123-135 284-296 (505)
219 KOG2231 Predicted E3 ubiquitin 51.2 13 0.00028 38.0 2.9 53 20-73 156-213 (669)
220 KOG2482 Predicted C2H2-type Zn 51.1 9.5 0.0002 35.4 1.7 26 81-106 198-223 (423)
221 KOG2785 C2H2-type Zn-finger pr 50.7 18 0.00039 34.1 3.5 26 11-36 65-90 (390)
222 COG4957 Predicted transcriptio 50.6 8.6 0.00019 30.7 1.2 25 81-108 79-103 (148)
223 smart00531 TFIIE Transcription 50.4 16 0.00035 29.8 2.9 12 14-25 99-110 (147)
224 TIGR02605 CxxC_CxxC_SSSS putat 50.4 6.2 0.00013 25.8 0.4 9 81-89 8-16 (52)
225 KOG3408 U1-like Zn-finger-cont 49.6 11 0.00025 29.4 1.7 30 5-36 50-79 (129)
226 COG2888 Predicted Zn-ribbon RN 48.6 14 0.00031 25.0 1.9 26 45-75 11-36 (61)
227 KOG2807 RNA polymerase II tran 48.6 18 0.00039 33.4 3.1 58 45-102 292-369 (378)
228 KOG0978 E3 ubiquitin ligase in 47.9 2.9 6.2E-05 42.8 -2.3 18 80-97 680-697 (698)
229 TIGR00595 priA primosomal prot 47.7 11 0.00023 37.6 1.7 41 45-85 215-260 (505)
230 PRK14714 DNA polymerase II lar 47.2 18 0.00039 39.6 3.3 19 277-295 1086-1104(1337)
231 KOG0320 Predicted E3 ubiquitin 46.3 9.4 0.0002 32.1 0.9 23 5-27 122-144 (187)
232 TIGR01206 lysW lysine biosynth 46.3 13 0.00028 24.9 1.3 10 108-117 24-33 (54)
233 KOG1280 Uncharacterized conser 46.2 19 0.00041 33.6 2.8 51 64-117 68-120 (381)
234 COG4530 Uncharacterized protei 45.6 9.6 0.00021 29.2 0.8 22 68-89 11-37 (129)
235 KOG3362 Predicted BBOX Zn-fing 44.7 7.8 0.00017 31.3 0.2 32 68-100 120-151 (156)
236 COG1592 Rubrerythrin [Energy p 44.5 13 0.00028 31.1 1.4 12 66-77 134-145 (166)
237 PF15269 zf-C2H2_7: Zinc-finge 42.5 28 0.0006 22.2 2.3 26 11-36 15-42 (54)
238 PF06524 NOA36: NOA36 protein; 41.0 10 0.00022 33.9 0.3 16 7-22 135-150 (314)
239 PRK04023 DNA polymerase II lar 40.9 18 0.00038 38.7 2.0 12 106-117 663-674 (1121)
240 PF01780 Ribosomal_L37ae: Ribo 39.6 10 0.00023 28.2 0.2 13 64-76 51-63 (90)
241 TIGR00280 L37a ribosomal prote 38.9 15 0.00033 27.3 0.9 9 81-89 56-64 (91)
242 PF14446 Prok-RING_1: Prokaryo 38.8 19 0.0004 24.1 1.2 23 68-90 7-33 (54)
243 PRK14873 primosome assembly pr 38.1 19 0.00041 37.2 1.8 26 39-75 405-431 (665)
244 COG1773 Rubredoxin [Energy pro 37.6 19 0.00041 24.2 1.1 10 45-54 5-14 (55)
245 PTZ00255 60S ribosomal protein 37.5 18 0.00039 26.9 1.1 13 64-76 52-64 (90)
246 PRK06266 transcription initiat 37.1 12 0.00025 31.8 0.1 10 106-115 136-145 (178)
247 PRK06266 transcription initiat 36.0 18 0.00038 30.7 1.0 28 45-76 119-146 (178)
248 PF01363 FYVE: FYVE zinc finge 35.7 20 0.00043 24.9 1.1 30 45-85 11-40 (69)
249 cd00065 FYVE FYVE domain; Zinc 35.5 22 0.00048 23.4 1.3 11 45-55 4-14 (57)
250 PF07191 zinc-ribbons_6: zinc- 34.8 9.7 0.00021 26.9 -0.6 22 65-86 16-38 (70)
251 PRK03976 rpl37ae 50S ribosomal 34.7 19 0.00042 26.7 0.9 10 81-90 57-66 (90)
252 KOG0978 E3 ubiquitin ligase in 34.6 14 0.00031 37.8 0.3 15 64-78 676-690 (698)
253 KOG4167 Predicted DNA-binding 34.5 9.2 0.0002 39.1 -1.1 24 81-104 795-818 (907)
254 PRK05580 primosome assembly pr 34.4 22 0.00049 36.8 1.7 43 45-87 383-430 (679)
255 COG5236 Uncharacterized conser 33.0 57 0.0012 30.5 3.8 89 14-110 151-251 (493)
256 COG5151 SSL1 RNA polymerase II 32.7 24 0.00053 32.3 1.4 22 81-102 391-412 (421)
257 COG4640 Predicted membrane pro 32.4 28 0.0006 33.1 1.7 28 69-96 4-33 (465)
258 PF06524 NOA36: NOA36 protein; 31.6 33 0.00071 30.7 2.0 78 39-119 138-222 (314)
259 PF07295 DUF1451: Protein of u 31.3 18 0.00039 29.6 0.3 6 81-86 133-138 (146)
260 KOG2593 Transcription initiati 31.1 28 0.00061 33.5 1.6 35 44-78 129-165 (436)
261 PF12013 DUF3505: Protein of u 30.8 31 0.00068 26.4 1.6 22 82-103 88-109 (109)
262 COG3357 Predicted transcriptio 30.8 31 0.00067 25.6 1.4 13 43-55 57-70 (97)
263 PF13878 zf-C2H2_3: zinc-finge 30.6 47 0.001 20.6 2.1 28 75-102 10-39 (41)
264 smart00064 FYVE Protein presen 30.6 29 0.00062 23.9 1.2 25 45-76 12-36 (68)
265 COG0068 HypF Hydrogenase matur 30.5 12 0.00027 38.2 -0.9 14 45-58 125-138 (750)
266 TIGR00373 conserved hypothetic 30.3 48 0.001 27.5 2.7 14 45-58 111-124 (158)
267 COG1327 Predicted transcriptio 29.6 30 0.00065 28.3 1.3 10 81-90 31-40 (156)
268 KOG3990 Uncharacterized conser 29.5 23 0.00051 31.4 0.7 72 12-85 4-91 (305)
269 TIGR00244 transcriptional regu 28.2 31 0.00067 28.2 1.2 11 81-91 31-41 (147)
270 COG2331 Uncharacterized protei 28.2 12 0.00026 26.7 -1.0 35 11-54 9-44 (82)
271 PRK03824 hypA hydrogenase nick 26.9 32 0.00069 27.7 1.0 10 81-90 73-82 (135)
272 COG1571 Predicted DNA-binding 26.8 39 0.00084 32.7 1.7 10 81-90 370-379 (421)
273 KOG0970 DNA polymerase alpha, 26.0 2.2E+02 0.0048 31.3 7.0 132 121-271 526-711 (1429)
274 COG3809 Uncharacterized protei 25.6 77 0.0017 22.9 2.6 35 68-102 3-45 (88)
275 PTZ00303 phosphatidylinositol 25.6 42 0.00091 34.9 1.8 39 45-89 462-500 (1374)
276 PRK06393 rpoE DNA-directed RNA 24.5 45 0.00097 23.1 1.2 18 69-86 8-25 (64)
277 cd00730 rubredoxin Rubredoxin; 24.4 52 0.0011 21.6 1.5 11 45-55 3-13 (50)
278 PRK12380 hydrogenase nickel in 24.3 37 0.00081 26.4 1.0 9 81-89 73-81 (113)
279 PRK00420 hypothetical protein; 24.2 46 0.001 25.9 1.4 8 81-88 43-50 (112)
280 COG5151 SSL1 RNA polymerase II 24.2 46 0.00099 30.6 1.6 8 13-20 307-314 (421)
281 PF09332 Mcm10: Mcm10 replicat 24.1 30 0.00065 32.6 0.5 9 45-53 254-262 (344)
282 KOG4167 Predicted DNA-binding 24.0 24 0.00052 36.2 -0.2 27 12-40 790-816 (907)
283 KOG4317 Predicted Zn-finger pr 23.9 27 0.00059 32.1 0.1 13 159-171 122-134 (383)
284 PF04438 zf-HIT: HIT zinc fing 23.8 32 0.0007 19.9 0.4 20 68-88 4-23 (30)
285 TIGR00100 hypA hydrogenase nic 23.8 40 0.00088 26.3 1.1 10 81-90 73-82 (115)
286 PF01155 HypA: Hydrogenase exp 23.3 28 0.00061 27.0 0.1 9 81-89 73-81 (113)
287 KOG3276 Uncharacterized conser 23.1 1.3E+02 0.0028 23.5 3.6 47 151-201 29-79 (125)
288 PRK14892 putative transcriptio 23.0 37 0.0008 25.8 0.7 7 81-87 45-51 (99)
289 PF00301 Rubredoxin: Rubredoxi 22.7 43 0.00092 21.7 0.8 12 45-56 3-14 (47)
290 COG5112 UFD2 U1-like Zn-finger 22.4 51 0.0011 25.2 1.3 30 5-36 48-77 (126)
291 COG4357 Zinc finger domain con 22.2 19 0.0004 27.0 -1.0 13 81-93 83-95 (105)
292 COG1439 Predicted nucleic acid 22.1 40 0.00087 28.5 0.8 23 65-87 138-162 (177)
293 PF12096 DUF3572: Protein of u 21.4 72 0.0016 23.7 1.9 31 174-204 28-58 (88)
294 PF10013 DUF2256: Uncharacteri 21.4 36 0.00078 21.4 0.3 15 80-94 10-24 (42)
295 smart00504 Ubox Modified RING 21.4 1.1E+02 0.0024 20.3 2.8 33 67-100 2-34 (63)
296 PF04423 Rad50_zn_hook: Rad50 21.3 34 0.00074 22.6 0.2 10 81-90 23-32 (54)
297 PF04959 ARS2: Arsenite-resist 21.1 61 0.0013 28.4 1.7 29 11-40 74-102 (214)
298 COG5048 FOG: Zn-finger [Genera 21.0 65 0.0014 30.4 2.1 28 83-110 328-355 (467)
299 PRK09678 DNA-binding transcrip 20.4 41 0.00089 23.9 0.4 9 83-91 34-42 (72)
300 PF13453 zf-TFIIB: Transcripti 20.4 74 0.0016 19.6 1.6 15 81-95 22-36 (41)
No 1
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=4.1e-40 Score=283.46 Aligned_cols=269 Identities=42% Similarity=0.694 Sum_probs=215.9
Q ss_pred cccccccccCCHHHHHHHHhhhccCCCCCccccCccccCChhhhhhhcCCCcccCCCCCcccCCcccccccccCChhhHH
Q 019380 16 KCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLI 95 (342)
Q Consensus 16 ~C~~C~k~f~~~~~L~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~~C~~C~k~F~~~~~L~ 95 (342)
+|..|.+.|.-+..+-.|+ +-.|....++|..|.+.......+..++..+.+= .|...|+...|..|.-.-......+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~-v~~~~~~~~~~~~~k~~~~~~~~~~e~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (280)
T KOG2249|consen 2 KASSCAQQFNKKEHLPNHK-VSRHKLHERKCGKCKKVARSFESNEEGLIAPLPK-EGKNIFSQRGNRFKATIKASPGKRR 79 (280)
T ss_pred CccHHHHHhCccccCcccc-chhhccCcchhhhHHHhccCcccccccccCCCCc-ccCccccchhhHHHhhHhhcCCcch
Confidence 3566777787777666676 2225544558888888888888888887554443 6666677666666544333344444
Q ss_pred HHHhhcCCCCCCCCcccccccccccCCCCcceecccccccccCCCcccccceEEeecCCCCeEEeeecCCCCCccccccc
Q 019380 96 KHKEACSLSAPVPFKISGAIDEKRTCRGPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYE 175 (342)
Q Consensus 96 ~H~~~h~~~~~~~~~~c~~~~~~~~~~~~~~v~~D~Ettg~~~~~~~~il~~v~vv~~~~~~~~~~lv~p~~~i~~~~~~ 175 (342)
.|+..+.+..+..+.. ..+....+..++||+||||.|.|+++..+++++++|||..|.++|+.||+|..+|.+|.|+
T Consensus 80 ~~~~~~~~~~~~~~~~---~k~s~~~~~~r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP~~~VtDyRT~ 156 (280)
T KOG2249|consen 80 IHQGSCQASCRMAALG---SKDSRMGSLTRVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKPTEPVTDYRTR 156 (280)
T ss_pred hhhcccCCCccccccc---hhhccccccceEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecCCCcccccceee
Confidence 4444444332222221 2222223334699999999999999999999999999999999999999999999999999
Q ss_pred cCCCCHhhhcCCCChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhccccCCCcceeeccccccccc--c
Q 019380 176 VTGLTEEDIKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLMK--T 253 (342)
Q Consensus 176 i~GIt~e~l~~~~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~~~~~Dt~~l~~~~~--~ 253 (342)
++||++|.+.+|++|+.|+.+++++| .|+|||||.+.+||..|.+.||...+.||+.+.++.. .
T Consensus 157 vSGIrpehm~~A~pf~~aQ~ev~klL--------------~gRIlVGHaLhnDl~~L~l~hp~s~iRDTs~~~pl~k~~~ 222 (280)
T KOG2249|consen 157 VSGIRPEHMRDAMPFKVAQKEVLKLL--------------KGRILVGHALHNDLQALKLEHPRSMIRDTSKYPPLMKLLS 222 (280)
T ss_pred ecccCHHHhccCccHHHHHHHHHHHH--------------hCCEEeccccccHHHHHhhhCchhhhcccccCchHHHHhh
Confidence 99999999999999999999999999 9999999999999999999999999999999888776 5
Q ss_pred CCCCccHHHHHHHHhCCcCCCCCCCcHHHHHHHHHHHHHHHhhhhhhhhh
Q 019380 254 NLVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQVEEI 303 (342)
Q Consensus 254 ~~~~~~L~~l~~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~~~~~~~ 303 (342)
.....||+.|++.+||+.||.+.|++++||++||+||.++..+|++....
T Consensus 223 ~~~tpSLK~Lt~~~Lg~~IQ~GeHsSvEDA~AtM~LY~~vk~qwe~~~~r 272 (280)
T KOG2249|consen 223 KKATPSLKKLTEALLGKDIQVGEHSSVEDARATMELYKRVKVQWEKIEAR 272 (280)
T ss_pred ccCCccHHHHHHHHhchhhhccccCcHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 67789999999999999999999999999999999999999999885443
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=1.8e-32 Score=229.14 Aligned_cols=150 Identities=39% Similarity=0.655 Sum_probs=133.4
Q ss_pred eecccccccccCCC-cccccceEEeecCCCCeEEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHhcCC
Q 019380 127 VAMDCEMVGGGSNG-TLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNNGE 205 (342)
Q Consensus 127 v~~D~Ettg~~~~~-~~~il~~v~vv~~~~~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~l~~~~ 205 (342)
|++||||||+++.+ ..++ +++++|+.+|.++|+++|+|..+++++++.+||||++|++++|++++++++|.+|+
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 4555 89999998999999999999999999999999999999999999999999999999
Q ss_pred CccccccCCCCCeEEEeeCchhhhhhccccCCCcceeecccc--cccc--ccCCCCccHHHHHHHHhCCcCCCC--CCCc
Q 019380 206 STGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKY--RPLM--KTNLVSHSLKYLTRTYLGYDIQSG--VHDP 279 (342)
Q Consensus 206 ~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~~~~~Dt~~l--~~~~--~~~~~~~~L~~l~~~~~~~~~~~~--~H~A 279 (342)
+++||||||+.||++||++.++...++||..+ .+.. +|...+++|+.|+++|+|..++.+ +|+|
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 88999999999999999988877778999875 3322 566678999999999987777653 7999
Q ss_pred HHHHHHHHHHHH
Q 019380 280 YEDCVSVMRLYK 291 (342)
Q Consensus 280 ~~Da~~t~~l~~ 291 (342)
++||++|++||+
T Consensus 146 l~DA~at~~l~~ 157 (157)
T cd06149 146 VEDARATMELYK 157 (157)
T ss_pred HHHHHHHHHHhC
Confidence 999999999984
No 3
>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=3.1e-32 Score=226.08 Aligned_cols=146 Identities=38% Similarity=0.624 Sum_probs=132.0
Q ss_pred eecccccccccCCCcccccceEEeecCCCCeEEeeecCCCCCccccccccCCCCHhhhcCCC-ChHHHHHHHHHHHhcCC
Q 019380 127 VAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAM-PLKEVKDKILEILNNGE 205 (342)
Q Consensus 127 v~~D~Ettg~~~~~~~~il~~v~vv~~~~~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~-~~~~v~~~~~~~l~~~~ 205 (342)
+++||||+|.+.. .++ +++.+|+.+|+++|++||+|..+++++++++||||++||+++| ++.+|+++|.+|+
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 5799999998643 566 9999999999999999999999999999999999999999995 9999999999999
Q ss_pred CccccccCCCC-CeEEEeeCchhhhhhccccCCCcceeeccccccccccCCCCccHHHHHHHHhCCcCCC--CCCCcHHH
Q 019380 206 STGRLMLDDGK-ARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQS--GVHDPYED 282 (342)
Q Consensus 206 ~~~~~~~~~~~-~~~lvgh~~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~--~~H~A~~D 282 (342)
+ +.+|||||+.||+.||+...+. ++||+.+++...+...+++|+.||++|+|..++. ++|||++|
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 8999999998877667899999999998887763 68999999
Q ss_pred HHHHHHHHH
Q 019380 283 CVSVMRLYK 291 (342)
Q Consensus 283 a~~t~~l~~ 291 (342)
|++|++||.
T Consensus 142 A~~t~~l~~ 150 (150)
T cd06145 142 ARAALELVK 150 (150)
T ss_pred HHHHHHHhC
Confidence 999999983
No 4
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=99.98 E-value=4.1e-32 Score=226.11 Aligned_cols=150 Identities=51% Similarity=0.859 Sum_probs=134.7
Q ss_pred eecccccccccCCC-cccccceEEeecCCCCeEEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHhcCC
Q 019380 127 VAMDCEMVGGGSNG-TLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNNGE 205 (342)
Q Consensus 127 v~~D~Ettg~~~~~-~~~il~~v~vv~~~~~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~l~~~~ 205 (342)
|++||||||+++.. .+++ +.+.+++..|.++|+++|+|..+++.+++.+||||++||+++|++.+++++|.+|+
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 88999988999999999999999999999999999999999999999999999999
Q ss_pred CccccccCCCCCeEEEeeCchhhhhhccccCCCcceeeccccccccccC-CCCccHHHHHHHHhCCcCCCCCCCcHHHHH
Q 019380 206 STGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLMKTN-LVSHSLKYLTRTYLGYDIQSGVHDPYEDCV 284 (342)
Q Consensus 206 ~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~-~~~~~L~~l~~~~~~~~~~~~~H~A~~Da~ 284 (342)
++.+|||||+.||+.||+...+...++||..+.....+. ..+++|+.||++|+|++++.++|||++||+
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 779999999999999999888878899999887665442 468999999999889998767999999999
Q ss_pred HHHHHHH
Q 019380 285 SVMRLYK 291 (342)
Q Consensus 285 ~t~~l~~ 291 (342)
+|++||+
T Consensus 146 at~~l~~ 152 (152)
T cd06144 146 AAMRLYR 152 (152)
T ss_pred HHHHHhC
Confidence 9999984
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=4.3e-31 Score=219.40 Aligned_cols=149 Identities=30% Similarity=0.467 Sum_probs=132.8
Q ss_pred eecccccccccC-------CCcc--------cccceEEeec----CCCCeEEeeecCCCCCccccccccCCCCHhhhcCC
Q 019380 127 VAMDCEMVGGGS-------NGTL--------DLCARVCLVD----EDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNA 187 (342)
Q Consensus 127 v~~D~Ettg~~~-------~~~~--------~il~~v~vv~----~~~~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~ 187 (342)
+++|||+.|.++ ++.. ++ +++++|| .+|+++++.||+|..+|.+|.|+++|||++++.++
T Consensus 1 ~a~d~e~v~~~~~~~~~~~~g~~~~~~~~~~~L-aRVsiVd~~~~~~g~vllD~~VkP~~~V~DYrT~~SGIt~~~L~~a 79 (174)
T cd06143 1 VAIDAEFVKLKPEETEIRSDGTKSTIRPSQMSL-ARVSVVRGEGELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPK 79 (174)
T ss_pred CceeeeEEEecchhceecCCCcEeeeccCCcee-EEEEEEcCCCCcCCCEEEeeeECCCCCccCcCccccccCHHHcCcc
Confidence 467888877664 4444 44 9999999 68999999999999999999999999999999987
Q ss_pred C------ChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhccccCCCcceeeccccccccccCCCCccHH
Q 019380 188 M------PLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLMKTNLVSHSLK 261 (342)
Q Consensus 188 ~------~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~~~~~L~ 261 (342)
. ++.++..++.++| +.++|||||.+++||++|++.+|...++||+.+++.. ...+++|+
T Consensus 80 ~~~~~~~t~~~v~~~l~~li-------------~~~tILVGHsL~nDL~aL~l~hp~~~viDTa~l~~~~--~~r~~sLk 144 (174)
T cd06143 80 TSSKNLTTLKSAYLKLRLLV-------------DLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFHLP--GQRKLSLR 144 (174)
T ss_pred ccccccCCHHHHHHHHHHHc-------------CCCCEEEeccchhHHHHhcCcCCCcceEEcHHhccCC--CCCChhHH
Confidence 4 6999999999998 3689999999999999999999988899999998764 33579999
Q ss_pred HHHHHHhCCcCCCCCCCcHHHHHHHHHHHH
Q 019380 262 YLTRTYLGYDIQSGVHDPYEDCVSVMRLYK 291 (342)
Q Consensus 262 ~l~~~~~~~~~~~~~H~A~~Da~~t~~l~~ 291 (342)
.|++.|||..||.+.|++++||+++|+||+
T Consensus 145 ~La~~~L~~~IQ~~~HdSvEDArAam~Ly~ 174 (174)
T cd06143 145 FLAWYLLGEKIQSETHDSIEDARTALKLYR 174 (174)
T ss_pred HHHHHHcCCcccCCCcCcHHHHHHHHHHhC
Confidence 999999999999999999999999999984
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=1.9e-30 Score=218.10 Aligned_cols=147 Identities=32% Similarity=0.519 Sum_probs=127.2
Q ss_pred eecccccccccCCCcccccceEEeecC-CCCeEEeeecCCCCCccccccccCCCCHhhhcCCCC-------hHHHHHHHH
Q 019380 127 VAMDCEMVGGGSNGTLDLCARVCLVDE-DENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMP-------LKEVKDKIL 198 (342)
Q Consensus 127 v~~D~Ettg~~~~~~~~il~~v~vv~~-~~~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~-------~~~v~~~~~ 198 (342)
|++||||||+++.. .++ .++.+|+. +|+++|+++|+|..+|+++++++||||++||+++|+ +++++++|.
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 56666665 888899999999999999999999999999999875 358999999
Q ss_pred HHHhcCCCccccccCCCCC-eEEEeeCchhhhhhccccCCCcceeeccccccccccCC---CCccHHHHHHHHhCCcCCC
Q 019380 199 EILNNGESTGRLMLDDGKA-RLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLMKTNL---VSHSLKYLTRTYLGYDIQS 274 (342)
Q Consensus 199 ~~l~~~~~~~~~~~~~~~~-~~lvgh~~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~---~~~~L~~l~~~~~~~~~~~ 274 (342)
+|+ ++ .+|||||+.||++||+...+ +++||+.+++.+.+.. .+++|+.||+.|+|++++.
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 6899999999988999865
Q ss_pred --CCCCcHHHHHHHHHHHH
Q 019380 275 --GVHDPYEDCVSVMRLYK 291 (342)
Q Consensus 275 --~~H~A~~Da~~t~~l~~ 291 (342)
++|+|++||++|++||.
T Consensus 143 ~~~~H~A~~DA~at~~l~~ 161 (161)
T cd06137 143 GGEGHDSLEDALAAREVVL 161 (161)
T ss_pred CCCCCCcHHHHHHHHHHhC
Confidence 48999999999999983
No 7
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.95 E-value=1.3e-28 Score=218.48 Aligned_cols=185 Identities=21% Similarity=0.217 Sum_probs=149.2
Q ss_pred CCCcceecccccccccC--CCcccccceEEeecCCCCe--EEeeecCCCCCccccccccCCCCHhhhcC-CCChHHHHHH
Q 019380 122 RGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKN-AMPLKEVKDK 196 (342)
Q Consensus 122 ~~~~~v~~D~Ettg~~~--~~~~~il~~v~vv~~~~~~--~~~~lv~p~~~i~~~~~~i~GIt~e~l~~-~~~~~~v~~~ 196 (342)
...++++||+||||+++ ++++++ +.+.+ +.+|.+ .++++|+|..+|++.++.+||||++++.+ ++++.+++++
T Consensus 4 ~~~~~vv~D~ETTGl~p~~d~Iiei-g~v~v-~~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~e 81 (232)
T PRK07942 4 HPGPLAAFDLETTGVDPETARIVTA-ALVVV-DADGEVVESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLAE 81 (232)
T ss_pred ccCcEEEEEeccCCCCCCCCeeEEE-EEEEE-eCCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHHH
Confidence 45679999999999874 456666 55544 444555 48999999999999999999999999975 7889999999
Q ss_pred HHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhcccc-----C---CCcceeeccccccccccC-CCCccHHHHHHHH
Q 019380 197 ILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-----Y---PDHMLRDTAKYRPLMKTN-LVSHSLKYLTRTY 267 (342)
Q Consensus 197 ~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-----~---~~~~~~Dt~~l~~~~~~~-~~~~~L~~l~~~~ 267 (342)
|..+|.+... ++.+|||||+.||+.||+.. . ....++|+..+.+.+.+. ..+++|.+|++.|
T Consensus 82 ~~~~l~~~~~---------~~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~ 152 (232)
T PRK07942 82 IADALREAWA---------RGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALCEHY 152 (232)
T ss_pred HHHHHHHHhh---------cCCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHHHHc
Confidence 9998832211 56799999999999999822 1 125689999888766553 3578999999998
Q ss_pred hCCcCCCCCCCcHHHHHHHHHHHHHHHhhhhhhhhhccCCCCCCCCchhhHHhhhCChhhhhhccCCceeee
Q 019380 268 LGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQVEEIGNQNTTGSFDSYKYKELEKMSPNELYQISKSDYRCW 339 (342)
Q Consensus 268 ~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 339 (342)
|++. .++|+|++||++|++||.++.++..+ +..+++++|.+++..|++.|
T Consensus 153 -gi~~-~~aH~Al~Da~ata~l~~~l~~~~~~--------------------l~~~~~~~l~~~q~~~~~~~ 202 (232)
T PRK07942 153 -GVRL-DNAHEATADALAAARVAWALARRFPE--------------------LAALSPAELHELQAVWYAEQ 202 (232)
T ss_pred -CCCC-CCCCChHHHHHHHHHHHHHHHHHHHH--------------------hhcCCHHHHHHHHHHHHHHH
Confidence 9985 45999999999999999999988755 67889999999999888765
No 8
>PRK07740 hypothetical protein; Provisional
Probab=99.95 E-value=1.3e-27 Score=213.49 Aligned_cols=159 Identities=28% Similarity=0.339 Sum_probs=136.8
Q ss_pred CCCcceecccccccccC---CCcccccceEEeecCCCCe---EEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHH
Q 019380 122 RGPKAVAMDCEMVGGGS---NGTLDLCARVCLVDEDENV---IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKD 195 (342)
Q Consensus 122 ~~~~~v~~D~Ettg~~~---~~~~~il~~v~vv~~~~~~---~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~ 195 (342)
...++|+||+||||.++ ++++++ +++.+. ++.+ .|+.+|+|..++++.+.++||||+++|+++|++.+|+.
T Consensus 57 ~~~~~vv~D~ETTGl~p~~~deIIeI-gaV~~~--~~~i~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~evl~ 133 (244)
T PRK07740 57 TDLPFVVFDLETTGFSPQQGDEILSI-GAVKTK--GGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLH 133 (244)
T ss_pred cCCCEEEEEEeCCCCCCCCCCeEEEE-EEEEEE--CCEEEEEEEEEEeCcCCCCChhheeccCCCHHHHhCCCCHHHHHH
Confidence 45679999999999875 457777 777663 3333 48899999999999999999999999999999999999
Q ss_pred HHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhccc------cCCC-cceeeccccccccccCCCCccHHHHHHHHh
Q 019380 196 KILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM------NYPD-HMLRDTAKYRPLMKTNLVSHSLKYLTRTYL 268 (342)
Q Consensus 196 ~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~------~~~~-~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~ 268 (342)
+|.+|+ ++.+|||||+.||+.||+. ..+. ..++||..+++.+.+....++|++|+.+|
T Consensus 134 ~f~~fi--------------~~~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~~- 198 (244)
T PRK07740 134 RFYAFI--------------GAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAYY- 198 (244)
T ss_pred HHHHHh--------------CCCEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHHHHHC-
Confidence 999999 7889999999999999972 1222 57899999999888877789999999987
Q ss_pred CCcCCCCCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 269 GYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 269 ~~~~~~~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
|+++. ++|+|++||++|++||.+++.+..+
T Consensus 199 gi~~~-~~H~Al~Da~ata~l~~~ll~~~~~ 228 (244)
T PRK07740 199 GIPIP-RRHHALGDALMTAKLWAILLVEAQQ 228 (244)
T ss_pred CcCCC-CCCCcHHHHHHHHHHHHHHHHHHHH
Confidence 99964 5899999999999999999988655
No 9
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.94 E-value=3.1e-27 Score=209.49 Aligned_cols=158 Identities=22% Similarity=0.327 Sum_probs=134.3
Q ss_pred CCcceecccccccccC---CCcccccceEEeecCCC-CeEEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHH
Q 019380 123 GPKAVAMDCEMVGGGS---NGTLDLCARVCLVDEDE-NVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKIL 198 (342)
Q Consensus 123 ~~~~v~~D~Ettg~~~---~~~~~il~~v~vv~~~~-~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~ 198 (342)
.+++|++|+||||+++ +++++| +.+.+.+... ...|+.+|+|..++++.++++||||+++|.++|+|.+|+++|.
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 4679999999999874 467888 8888764422 1258999999999999999999999999999999999999999
Q ss_pred HHHhcCCCccccccCCCCCeEEEeeCchhhhhhcccc-------CC----CcceeeccccccccccCCCCccHHHHHHHH
Q 019380 199 EILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-------YP----DHMLRDTAKYRPLMKTNLVSHSLKYLTRTY 267 (342)
Q Consensus 199 ~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-------~~----~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~ 267 (342)
+|+ ++.+|||||+.||+.||+.. .| ...++||..+++.++|. .+++|+.||++|
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 88899999999999999822 33 14589999999988886 467999999999
Q ss_pred hCCcCCC-CCCCcHHHHHHHHHHHHHHHhhh
Q 019380 268 LGYDIQS-GVHDPYEDCVSVMRLYKRFRRQD 297 (342)
Q Consensus 268 ~~~~~~~-~~H~A~~Da~~t~~l~~~~~~~~ 297 (342)
|++... ..|+|+.||.++++||..+....
T Consensus 147 -gi~~~~r~~H~AL~DA~~~A~v~~~l~~~~ 176 (240)
T PRK05711 147 -GIDNSHRTLHGALLDAEILAEVYLAMTGGQ 176 (240)
T ss_pred -CCCCCCCCCCCHHHHHHHHHHHHHHHHCcc
Confidence 887432 26999999999999999998763
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=99.94 E-value=3.6e-27 Score=208.08 Aligned_cols=161 Identities=21% Similarity=0.275 Sum_probs=136.3
Q ss_pred cceecccccccccC---CCcccccceEEeecCCC-CeEEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHH
Q 019380 125 KAVAMDCEMVGGGS---NGTLDLCARVCLVDEDE-NVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 200 (342)
Q Consensus 125 ~~v~~D~Ettg~~~---~~~~~il~~v~vv~~~~-~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~ 200 (342)
++|++|+||||+++ ++++++ +.+.+++... ...|+.+|+|..++++.++++||||+++++++|+|.+|+.+|.+|
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 467888 8887765321 125999999999999999999999999999999999999999999
Q ss_pred HhcCCCccccccCCCCCeEEEeeCchhhhhhcccc-------CC----CcceeeccccccccccCCCCccHHHHHHHHhC
Q 019380 201 LNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-------YP----DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLG 269 (342)
Q Consensus 201 l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-------~~----~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~ 269 (342)
| ++.+|||||+.||+.||+.. .+ ...++||+.+++..+|. .+++|+.||++| |
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 88899999999999999821 12 15799999999988876 478999999999 8
Q ss_pred CcCCCC-CCCcHHHHHHHHHHHHHHHhhhhhhhh
Q 019380 270 YDIQSG-VHDPYEDCVSVMRLYKRFRRQDHQVEE 302 (342)
Q Consensus 270 ~~~~~~-~H~A~~Da~~t~~l~~~~~~~~~~~~~ 302 (342)
++.... .|+|+.||+++++||..+......+..
T Consensus 144 i~~~~r~~H~Al~DA~~~a~v~~~l~~~~~~~~~ 177 (225)
T TIGR01406 144 VDNSHRTLHGALLDAHLLAEVYLALTGGQESLLE 177 (225)
T ss_pred CCCCCCCCcCHHHHHHHHHHHHHHHHcCCcchhh
Confidence 885432 799999999999999999887765443
No 11
>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=99.94 E-value=4.4e-27 Score=196.75 Aligned_cols=146 Identities=23% Similarity=0.333 Sum_probs=130.2
Q ss_pred ceecccccccccCCCcccccceEEeecCCCCe--EEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHhc
Q 019380 126 AVAMDCEMVGGGSNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNN 203 (342)
Q Consensus 126 ~v~~D~Ettg~~~~~~~~il~~v~vv~~~~~~--~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~l~~ 203 (342)
+|++|+||||...++++++ +.+.+. .|++ .|+.+|+|..++++.++++||||++++.+++++.+++++|.+|+
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 5899999999878888887 777663 4444 48999999999999999999999999999999999999999999
Q ss_pred CCCccccccCCCCCeEEEeeCchhhhhhcc-------ccCCCcceeeccccccccccCCCCccHHHHHHHHhCCcCCCCC
Q 019380 204 GESTGRLMLDDGKARLLVGHGLEHDLDSLR-------MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGV 276 (342)
Q Consensus 204 ~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~-------~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~ 276 (342)
++.++||||+.||+.+|+ +..+..+++|++.+++.+++....++|..|++.| |++++ +
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 3345577999999999988887889999999988 99976 9
Q ss_pred CCcHHHHHHHHHHHH
Q 019380 277 HDPYEDCVSVMRLYK 291 (342)
Q Consensus 277 H~A~~Da~~t~~l~~ 291 (342)
|+|++||++|++||.
T Consensus 141 H~Al~Da~~ta~l~~ 155 (156)
T cd06130 141 HDALEDARACAEILL 155 (156)
T ss_pred cCchHHHHHHHHHHh
Confidence 999999999999985
No 12
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=1e-26 Score=200.24 Aligned_cols=158 Identities=22% Similarity=0.290 Sum_probs=127.9
Q ss_pred CCCcceeccccccccc-CCCcccccceEEeecCCCCe--EEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHH
Q 019380 122 RGPKAVAMDCEMVGGG-SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKIL 198 (342)
Q Consensus 122 ~~~~~v~~D~Ettg~~-~~~~~~il~~v~vv~~~~~~--~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~ 198 (342)
....++++|+||||.+ .++++++ +++.+. +|.+ .|++||+|..+++.+++++||||++||+++|++.+|+.+|.
T Consensus 3 ~~~~~vvlD~EtTGl~~~~eIIeI-gaV~v~--~g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap~~~evl~~f~ 79 (195)
T PRK07247 3 RLETYIAFDLEFNTVNGVSHIIQV-SAVKYD--DHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFK 79 (195)
T ss_pred cCCeEEEEEeeCCCCCCCCeEEEE-EEEEEE--CCEEEEEEEEEECCCCCCCccceecCCCCHHHHhCCCCHHHHHHHHH
Confidence 3457999999999986 3556666 766663 3443 59999999999999999999999999999999999999999
Q ss_pred HHHhcCCCccccccCCCCCeEEEeeCch-hhhhhcccc---CCCcceeeccccc--ccc--ccCCCCccHHHHHHHHhCC
Q 019380 199 EILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLRMN---YPDHMLRDTAKYR--PLM--KTNLVSHSLKYLTRTYLGY 270 (342)
Q Consensus 199 ~~l~~~~~~~~~~~~~~~~~~lvgh~~~-~D~~~l~~~---~~~~~~~Dt~~l~--~~~--~~~~~~~~L~~l~~~~~~~ 270 (342)
+|+ ++.+|||||+. ||+.||+.. .+....+|+.... +.. .+...+++|..||++| |+
T Consensus 80 ~f~--------------~~~~lVaHNa~~fD~~fL~~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~-gi 144 (195)
T PRK07247 80 EFV--------------GELPLIGYNAQKSDLPILAENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVADFL-GI 144 (195)
T ss_pred HHH--------------CCCeEEEEeCcHhHHHHHHHcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHHHhc-CC
Confidence 999 88899999997 899999832 2223356664322 222 3455689999999998 88
Q ss_pred cCCCCCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 271 DIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 271 ~~~~~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
+. .+|+|++||++|+.||.++++..+.
T Consensus 145 ~~--~~HrAl~DA~~ta~v~~~ll~~~~~ 171 (195)
T PRK07247 145 KG--RGHNSLEDARMTARVYESFLESDQN 171 (195)
T ss_pred CC--CCcCCHHHHHHHHHHHHHHHhhccc
Confidence 84 4899999999999999999988654
No 13
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=1.1e-26 Score=206.49 Aligned_cols=159 Identities=19% Similarity=0.244 Sum_probs=134.0
Q ss_pred cCCCCcceecccccccccC--CCcccccceEEeecCCCCe----EEeeecCCCCCccccccccCCCCHhhhcCCCChHHH
Q 019380 120 TCRGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV----IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEV 193 (342)
Q Consensus 120 ~~~~~~~v~~D~Ettg~~~--~~~~~il~~v~vv~~~~~~----~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v 193 (342)
......++++|+||||+++ ++++++ +.+.+. ++.+ .|+++|+|..+|+..++.+||||+++|.++|++.+|
T Consensus 43 ~~~~~~~vviD~ETTGl~p~~d~IieI-g~v~v~--~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~ev 119 (239)
T PRK09146 43 PLSEVPFVALDFETTGLDAEQDAIVSI-GLVPFT--LQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERI 119 (239)
T ss_pred CcccCCEEEEEeECCCCCCCCCcEEEE-EEEEEE--CCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHH
Confidence 3456789999999999874 567777 776663 3332 578999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhcccc-------CCCcceeeccccccccccCC-----------
Q 019380 194 KDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-------YPDHMLRDTAKYRPLMKTNL----------- 255 (342)
Q Consensus 194 ~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-------~~~~~~~Dt~~l~~~~~~~~----------- 255 (342)
+++|.+++ ++.++||||+.||+.||+.. ....+++||+.+++.+.+..
T Consensus 120 l~~l~~~~--------------~~~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~ 185 (239)
T PRK09146 120 LDELLEAL--------------AGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGK 185 (239)
T ss_pred HHHHHHHh--------------CCCEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccC
Confidence 99999999 88899999999999999832 12367899999987765432
Q ss_pred --CCccHHHHHHHHhCCcCCCCCCCcHHHHHHHHHHHHHHHhhh
Q 019380 256 --VSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQD 297 (342)
Q Consensus 256 --~~~~L~~l~~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~ 297 (342)
.+++|.+++..| |++ ..++|+|++||.+|++||..+..+.
T Consensus 186 ~~~~~~L~~l~~~~-gl~-~~~~H~Al~DA~ata~l~~~~~~~~ 227 (239)
T PRK09146 186 KPESIRLADSRLRY-GLP-AYSPHHALTDAIATAELLQAQIAHH 227 (239)
T ss_pred CCCCCCHHHHHHHc-CCC-CCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 568999999998 888 4569999999999999999998875
No 14
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.94 E-value=2e-26 Score=206.52 Aligned_cols=173 Identities=21% Similarity=0.289 Sum_probs=142.9
Q ss_pred CCCCcceecccccccccC--CCcccccceEEeecCCCCe--EEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHH
Q 019380 121 CRGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDK 196 (342)
Q Consensus 121 ~~~~~~v~~D~Ettg~~~--~~~~~il~~v~vv~~~~~~--~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~ 196 (342)
.....++++|+||||..+ +.++++ +++.+. +|++ .|+++|+|. +++..++++||||++++.++|++.+|+.+
T Consensus 65 ~~~~~~vv~DiETTG~~~~~~~IIEI-GAv~v~--~g~i~~~f~~~v~p~-~ip~~~~~itGIt~e~l~~ap~~~evl~~ 140 (257)
T PRK08517 65 IKDQVFCFVDIETNGSKPKKHQIIEI-GAVKVK--NGEIIDRFESFVKAK-EVPEYITELTGITYEDLENAPSLKEVLEE 140 (257)
T ss_pred CCCCCEEEEEEeCCCCCCCCCeEEEE-EEEEEE--CCEEEEEEEEEECCC-CCChhhhhhcCcCHHHHcCCCCHHHHHHH
Confidence 355679999999999874 357777 777774 4555 489999996 79999999999999999999999999999
Q ss_pred HHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhccc-----cC--CCcceeeccccccccccCCCCccHHHHHHHHhC
Q 019380 197 ILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM-----NY--PDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLG 269 (342)
Q Consensus 197 ~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~-----~~--~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~ 269 (342)
|.+|+ ++.++||||+.||++||+. .. ...+.+||..+++...+. .+++|++|++.+ |
T Consensus 141 f~~fl--------------~~~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~-~~~~L~~L~~~l-g 204 (257)
T PRK08517 141 FRLFL--------------GDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIES-PRYGLSFLKELL-G 204 (257)
T ss_pred HHHHH--------------CCCeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccC-CCCCHHHHHHHc-C
Confidence 99999 7789999999999999972 12 225689999998876654 579999999987 9
Q ss_pred CcCCCCCCCcHHHHHHHHHHHHHHHhhhhhhhhhccCCCCCCCCchhhHHhhhCChhhhhhccCCc
Q 019380 270 YDIQSGVHDPYEDCVSVMRLYKRFRRQDHQVEEIGNQNTTGSFDSYKYKELEKMSPNELYQISKSD 335 (342)
Q Consensus 270 ~~~~~~~H~A~~Da~~t~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 335 (342)
++. ..+|+|++||.+|++||.+++.+.+. ...+.++++++++.+
T Consensus 205 i~~-~~~HrAl~DA~ata~ll~~ll~~~~~---------------------~~~t~~~L~~~~k~~ 248 (257)
T PRK08517 205 IEI-EVHHRAYADALAAYEIFKICLLNLPS---------------------YIKTTEDLIDFSKTA 248 (257)
T ss_pred cCC-CCCCChHHHHHHHHHHHHHHHHHhHH---------------------hhcCHHHHHHHhhhc
Confidence 984 36999999999999999999988644 123567777777754
No 15
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=1.5e-26 Score=213.95 Aligned_cols=154 Identities=18% Similarity=0.307 Sum_probs=135.5
Q ss_pred CcceecccccccccCCCcccccceEEeecCCCCe--EEeeecCCCC-CccccccccCCCCHhhhcCCCChHHHHHHHHHH
Q 019380 124 PKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENV--IFHTYVQPQL-PVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 200 (342)
Q Consensus 124 ~~~v~~D~Ettg~~~~~~~~il~~v~vv~~~~~~--~~~~lv~p~~-~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~ 200 (342)
+.|++||+||||...+.++++ +.+.+. +|++ .|++||+|.. .+++.++.+||||++||+++|+|.+|+++|.+|
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 368999999999878888888 888874 4444 4899999985 578888999999999999999999999999999
Q ss_pred HhcCCCccccccCCCCCeEEEeeCchhhhhhcc-------ccCCCcceeeccccccccccCCCCccHHHHHHHHhCCcCC
Q 019380 201 LNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR-------MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQ 273 (342)
Q Consensus 201 l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~-------~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~ 273 (342)
+ ++.+|||||+.||+.||+ +..|...++||+.+++.+++...+++|..|+..| |+++
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 2344567899999999988887899999999999 8875
Q ss_pred CCCCCcHHHHHHHHHHHHHHHhhh
Q 019380 274 SGVHDPYEDCVSVMRLYKRFRRQD 297 (342)
Q Consensus 274 ~~~H~A~~Da~~t~~l~~~~~~~~ 297 (342)
.+|+|++||++|++||..+.++.
T Consensus 142 -~~H~Al~DA~ata~l~~~l~~~~ 164 (309)
T PRK06195 142 -KHHDALADAMACSNILLNISKEL 164 (309)
T ss_pred -cccCCHHHHHHHHHHHHHHHHHh
Confidence 48999999999999999998764
No 16
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.94 E-value=2.3e-26 Score=201.58 Aligned_cols=146 Identities=18% Similarity=0.193 Sum_probs=125.4
Q ss_pred ceecccccccccCCCcccccceEEeecCCCCe--EEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHhc
Q 019380 126 AVAMDCEMVGGGSNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNN 203 (342)
Q Consensus 126 ~v~~D~Ettg~~~~~~~~il~~v~vv~~~~~~--~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~l~~ 203 (342)
+++||+||||++ ..++++ +.+.++ +|++ .|+++++|..+|+..++.+||||++||+++|++.+++++ |+
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 678999999985 457787 777775 4455 589999999999999999999999999999999999887 45
Q ss_pred CCCccccccCCCCCeEEEeeCchhhhhhccccCCCcceeeccccccccccCCCCccHHHHHHHHhCCcCC----CCCCCc
Q 019380 204 GESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQ----SGVHDP 279 (342)
Q Consensus 204 ~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~----~~~H~A 279 (342)
++.+|||||+.||+.||... ...++||+.+++.++|... ++|..|+..| |+++. ..+|||
T Consensus 73 ------------~~~~lVaHNa~FD~~~L~~~--~~~~idTl~lar~l~p~~~-~~l~~L~~~~-~l~~~~~~~~~aHrA 136 (219)
T PRK07983 73 ------------GSEWYVAHNASFDRRVLPEM--PGEWICTMKLARRLWPGIK-YSNMALYKSR-KLNVQTPPGLHHHRA 136 (219)
T ss_pred ------------CCCEEEEeCcHhhHHHHhCc--CCCcEeHHHHHHHHccCCC-CCHHHHHHHc-CCCCCCCCCCCCCcH
Confidence 67899999999999999732 2468999999999988754 9999999988 87642 349999
Q ss_pred HHHHHHHHHHHHHHHhh
Q 019380 280 YEDCVSVMRLYKRFRRQ 296 (342)
Q Consensus 280 ~~Da~~t~~l~~~~~~~ 296 (342)
++||++|+.||.++++.
T Consensus 137 l~Da~ata~ll~~l~~~ 153 (219)
T PRK07983 137 LYDCYITAALLIDIMNT 153 (219)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 99999999999999965
No 17
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=2.2e-26 Score=211.79 Aligned_cols=157 Identities=22% Similarity=0.407 Sum_probs=138.1
Q ss_pred CCCcceecccccccccC--CCcccccceEEeecCCCCe--EEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHH
Q 019380 122 RGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKI 197 (342)
Q Consensus 122 ~~~~~v~~D~Ettg~~~--~~~~~il~~v~vv~~~~~~--~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~ 197 (342)
-...+|+||+||||+++ ++++++ +++.+. +|++ .|+++|+|..++++.++++||||++||.++|++.+|+++|
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 45689999999999874 567777 777663 4555 4899999999999999999999999999999999999999
Q ss_pred HHHHhcCCCccccccCCCCCeEEEeeCchhhhhhcc-------ccCCCcceeeccccccccccCCCCccHHHHHHHHhCC
Q 019380 198 LEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR-------MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGY 270 (342)
Q Consensus 198 ~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~-------~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~ 270 (342)
.+|+ ++.+|||||+.||+.||. +..+..+++||+.+++.+++....++|+.|++.| |+
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 778999999999999998 2244577999999999888877889999999988 99
Q ss_pred cCCCCCCCcHHHHHHHHHHHHHHHhhhh
Q 019380 271 DIQSGVHDPYEDCVSVMRLYKRFRRQDH 298 (342)
Q Consensus 271 ~~~~~~H~A~~Da~~t~~l~~~~~~~~~ 298 (342)
+. .+|+|++||++|++||.++.....
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 699999999999999999998764
No 18
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.94 E-value=1.4e-26 Score=202.45 Aligned_cols=159 Identities=18% Similarity=0.253 Sum_probs=129.9
Q ss_pred CCcceeccccccccc--------CCCcccccceEEeecCCCCe--EEeeecCCCC--CccccccccCCCCHhhhcCCCCh
Q 019380 123 GPKAVAMDCEMVGGG--------SNGTLDLCARVCLVDEDENV--IFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPL 190 (342)
Q Consensus 123 ~~~~v~~D~Ettg~~--------~~~~~~il~~v~vv~~~~~~--~~~~lv~p~~--~i~~~~~~i~GIt~e~l~~~~~~ 190 (342)
...|+++|+||||.. .++++|+ +++.+. +|++ .|++||+|.. +++++++++||||++||+++|+|
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 356999999999853 2467888 888774 3444 5999999986 68999999999999999999999
Q ss_pred HHHHHHHHHHHhcCCCccccccCCCCC-eEEEeeCchhhhhhcc-------ccCCC-cceeeccccccccccCCCCccHH
Q 019380 191 KEVKDKILEILNNGESTGRLMLDDGKA-RLLVGHGLEHDLDSLR-------MNYPD-HMLRDTAKYRPLMKTNLVSHSLK 261 (342)
Q Consensus 191 ~~v~~~~~~~l~~~~~~~~~~~~~~~~-~~lvgh~~~~D~~~l~-------~~~~~-~~~~Dt~~l~~~~~~~~~~~~L~ 261 (342)
.+|+++|.+|+ ++ .++|+||..||+.||+ +..|. ..++|++.+++..++....++|.
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 3444456799999998 22333 56788888777776666679999
Q ss_pred HHHHHHhCCcCCCCCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 262 YLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 262 ~l~~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
++++.| |++..+.+|+|++||++|++||.++.++.+.
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 9985555899999999999999999988643
No 19
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.93 E-value=6.1e-26 Score=209.41 Aligned_cols=159 Identities=22% Similarity=0.281 Sum_probs=134.1
Q ss_pred CCCCcceecccccccccCC--CcccccceEEeecCCCCe--EEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHH
Q 019380 121 CRGPKAVAMDCEMVGGGSN--GTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDK 196 (342)
Q Consensus 121 ~~~~~~v~~D~Ettg~~~~--~~~~il~~v~vv~~~~~~--~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~ 196 (342)
.....|++||+||||+++. +++++ +.+.+ +.+|++ .|+++|+|.. ++..+.+||||++||.++|+|.+++++
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 3456899999999998754 67777 55555 345665 4899999975 356789999999999999999999999
Q ss_pred HHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhccc-------cCCCcceeeccccccccccCCCCccHHHHHHHHhC
Q 019380 197 ILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM-------NYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLG 269 (342)
Q Consensus 197 ~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~-------~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~ 269 (342)
|.+|+ ++.+|||||+.||+.||+. ..|...++||+.+++.+.+...+++|+.|+++| |
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 8899999999999999982 234456899999999887777899999999988 9
Q ss_pred CcCCCCCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 270 YDIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 270 ~~~~~~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
++ ..++|+|++||++|++||..++++..+
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
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=6.3e-26 Score=203.31 Aligned_cols=159 Identities=17% Similarity=0.288 Sum_probs=132.2
Q ss_pred CCcceecccccccccC--CCcccccceEEeecCCCCeEEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHH
Q 019380 123 GPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 200 (342)
Q Consensus 123 ~~~~v~~D~Ettg~~~--~~~~~il~~v~vv~~~~~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~ 200 (342)
..++|+||+||||+++ ++++|+ +.+.+........|+.+|+|..+|+..++.+||||+|+|+++|++.+|+++|.+|
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 3679999999999864 567777 6666632211225899999999999999999999999999999999999999999
Q ss_pred HhcCCCccccccCCCCC-eEEEeeCchhhhhhcccc-------CC--CcceeeccccccccccCCCCccHHHHHHHHhCC
Q 019380 201 LNNGESTGRLMLDDGKA-RLLVGHGLEHDLDSLRMN-------YP--DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGY 270 (342)
Q Consensus 201 l~~~~~~~~~~~~~~~~-~~lvgh~~~~D~~~l~~~-------~~--~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~ 270 (342)
+ ++ .+|||||+.||+.||... .+ ...++||+.+++.+ +...+++|..|+.+| |+
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 44 799999999999999822 11 15689999998864 444578999999998 99
Q ss_pred cCCCCCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 271 DIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 271 ~~~~~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
+. .++|+|++||.+|++||..+.++...
T Consensus 149 ~~-~~aH~Al~Da~at~~vl~~l~~~~~~ 176 (250)
T PRK06310 149 PY-DGNHRAMKDVEINIKVFKHLCKRFRT 176 (250)
T ss_pred CC-CCCcChHHHHHHHHHHHHHHHHhccc
Confidence 84 45999999999999999999877544
No 21
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=1.2e-25 Score=199.69 Aligned_cols=155 Identities=23% Similarity=0.452 Sum_probs=131.3
Q ss_pred CcceecccccccccC--CCcccccceEEeecCCCCeEEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHH
Q 019380 124 PKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 201 (342)
Q Consensus 124 ~~~v~~D~Ettg~~~--~~~~~il~~v~vv~~~~~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~l 201 (342)
..+++||+||||++. ++++++ + +++......|+.+++|..+|++.++++||||++||+++|+|.+++++|.+|+
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-A---AYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFC 77 (232)
T ss_pred CcEEEEEeeCCCCCCCCCEEEEE-E---EEcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHH
Confidence 358999999999864 445555 3 3555455679999999999999999999999999999999999999999999
Q ss_pred hcCCCccccccCCCCCeEEEeeCc-hhhhhhccc-------cCCCcceeeccccccccccCCCCccHHHHHHHHhCCcCC
Q 019380 202 NNGESTGRLMLDDGKARLLVGHGL-EHDLDSLRM-------NYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQ 273 (342)
Q Consensus 202 ~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~~-------~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~ 273 (342)
+++.+|||||+ .||+.||+. ..+...++||+.+++.+.+...+++|..|+..| |++.
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 13569999995 899999982 223467899999999888877789999999999 8873
Q ss_pred CCCCCcHHHHHHHHHHHHHHHhhh
Q 019380 274 SGVHDPYEDCVSVMRLYKRFRRQD 297 (342)
Q Consensus 274 ~~~H~A~~Da~~t~~l~~~~~~~~ 297 (342)
.++|+|++||.+|++||.+++++.
T Consensus 143 ~~aH~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 143 NQAHRALDDVITLHRVFSALVGDL 166 (232)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHHH
Confidence 459999999999999999998764
No 22
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.93 E-value=7.3e-26 Score=199.35 Aligned_cols=161 Identities=18% Similarity=0.328 Sum_probs=133.8
Q ss_pred CCcceecccccccccCC-CcccccceEEeecCCCC-eEEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHH
Q 019380 123 GPKAVAMDCEMVGGGSN-GTLDLCARVCLVDEDEN-VIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 200 (342)
Q Consensus 123 ~~~~v~~D~Ettg~~~~-~~~~il~~v~vv~~~~~-~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~ 200 (342)
...||++|+||||+++. .++++ +++.+++.... ..|+++|+|..++++.+..+||||++++.++|++.+|+.+|.+|
T Consensus 6 ~~~fvv~D~ETTGl~~~~~IIeI-gav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~~~~~ 84 (217)
T TIGR00573 6 LDTETTGDNETTGLYAGHDIIEI-GAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADY 84 (217)
T ss_pred ecCEEEEEecCCCCCCCCCEEEE-EEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHHHHHH
Confidence 45799999999998743 26777 77776544222 26899999999999999999999999999999999999999999
Q ss_pred HhcCCCccccccCCCCCeEEEeeCchhhhhhccccC--------CCcceeeccccccccccCC--CCccHHHHHHHHhCC
Q 019380 201 LNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY--------PDHMLRDTAKYRPLMKTNL--VSHSLKYLTRTYLGY 270 (342)
Q Consensus 201 l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~--------~~~~~~Dt~~l~~~~~~~~--~~~~L~~l~~~~~~~ 270 (342)
+ ++.++||||+.||+.||+..+ +...++|+..+++.+.+.. .+++|..|+..| |+
T Consensus 85 ~--------------~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~-gl 149 (217)
T TIGR00573 85 I--------------RGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRY-EI 149 (217)
T ss_pred h--------------CCCEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHHHc-CC
Confidence 9 778999999999999998221 2256889988877766532 468999999998 88
Q ss_pred cCCC-CCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 271 DIQS-GVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 271 ~~~~-~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
+... ++|+|++||++|++||.++..+..+
T Consensus 150 ~~~~~~~H~Al~DA~~ta~l~~~l~~~~~~ 179 (217)
T TIGR00573 150 TNSHRALHGALADAFILAKLYLVMTGKQTK 179 (217)
T ss_pred CCCCcccCCHHHHHHHHHHHHHHHHhcchh
Confidence 8432 5899999999999999999998765
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=99.93 E-value=1.2e-25 Score=190.34 Aligned_cols=151 Identities=21% Similarity=0.336 Sum_probs=125.9
Q ss_pred ceecccccccccC---CCcccccceEEeecCCCC-eEEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHH
Q 019380 126 AVAMDCEMVGGGS---NGTLDLCARVCLVDEDEN-VIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 201 (342)
Q Consensus 126 ~v~~D~Ettg~~~---~~~~~il~~v~vv~~~~~-~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~l 201 (342)
+|++|+||||+++ +.++++ +.+.+.+.... ..|+.+++|..++++.++++||||+++++++|++.+++++|.+|+
T Consensus 1 ~v~~D~ETTGl~~~~~~~iiei-g~v~v~~~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~~~~v~~~l~~~l 79 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEI-GCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFI 79 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEE-EEEEEECCcEeccEEEEEECCCCCCCHHHHHHhCCCHHHHhcCCCHHHHHHHHHHHH
Confidence 5789999999875 467777 77766432111 258999999999999999999999999999999999999999999
Q ss_pred hcCCCccccccCCCCCeEEEeeCchhhhhhcccc-------C---CCcceeeccccccccccCCCCccHHHHHHHHhCCc
Q 019380 202 NNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-------Y---PDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 202 ~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-------~---~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 271 (342)
++.++||||+.||+.||+.. . ....++||+.+++..++. ..++|++|+++| |++
T Consensus 80 --------------~~~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~-~~~~L~~l~~~~-~i~ 143 (167)
T cd06131 80 --------------RGAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPG-KPNSLDALCKRF-GID 143 (167)
T ss_pred --------------CCCeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCC-CCCCHHHHHHHC-CCC
Confidence 77899999999999999721 1 125689999998877654 467999999999 988
Q ss_pred CCC-CCCCcHHHHHHHHHHHHHH
Q 019380 272 IQS-GVHDPYEDCVSVMRLYKRF 293 (342)
Q Consensus 272 ~~~-~~H~A~~Da~~t~~l~~~~ 293 (342)
... ++|+|++||++|++||.++
T Consensus 144 ~~~~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 144 NSHRTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred CCCCCCCChHHHHHHHHHHHHHh
Confidence 643 4899999999999999875
No 24
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.92 E-value=1.8e-25 Score=229.99 Aligned_cols=160 Identities=20% Similarity=0.335 Sum_probs=138.9
Q ss_pred CCCCcceeccccccccc-CCCcccccceEEeecCCCCe--EEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHH
Q 019380 121 CRGPKAVAMDCEMVGGG-SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKI 197 (342)
Q Consensus 121 ~~~~~~v~~D~Ettg~~-~~~~~~il~~v~vv~~~~~~--~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~ 197 (342)
.....++++|+||||.+ .++++++ +++.+. +|++ .|+++|+|..+|++.++.+||||++||.++|+|++|+++|
T Consensus 4 ~~~~~~vvvD~ETTGl~~~d~IIeI-gaV~v~--~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~ 80 (820)
T PRK07246 4 KKLRKYAVVDLEATGAGPNASIIQV-GIVIIE--GGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHI 80 (820)
T ss_pred ccCCCEEEEEEecCCcCCCCeEEEE-EEEEEE--CCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHH
Confidence 34567999999999986 4567777 777663 4555 5899999999999999999999999999999999999999
Q ss_pred HHHHhcCCCccccccCCCCCeEEEeeCchhhhhhccc-----cCC-CcceeeccccccccccCCCCccHHHHHHHHhCCc
Q 019380 198 LEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM-----NYP-DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 198 ~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~-----~~~-~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 271 (342)
.+|+ ++.++||||+.||+.||+. .++ ..+.+||..+++.++|...+++|.+||..| |++
T Consensus 81 ~~~l--------------~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L~~~l-gl~ 145 (820)
T PRK07246 81 YDLI--------------EDCIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLSREL-NID 145 (820)
T ss_pred HHHh--------------CCCEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHHHHHc-CCC
Confidence 9999 8899999999999999973 122 256899999999999988899999999988 998
Q ss_pred CCCCCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 272 IQSGVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 272 ~~~~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
. ..+|+|++||++|++||.+++++...
T Consensus 146 ~-~~~H~Al~DA~ata~L~~~l~~~l~~ 172 (820)
T PRK07246 146 L-ADAHTAIADARATAELFLKLLQKIES 172 (820)
T ss_pred C-CCCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 5 46899999999999999999988644
No 25
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.92 E-value=4.3e-25 Score=192.53 Aligned_cols=156 Identities=19% Similarity=0.313 Sum_probs=126.9
Q ss_pred CCCcceecccccccccC--CCcccccceEEeecCCCCe----EEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHH
Q 019380 122 RGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV----IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKD 195 (342)
Q Consensus 122 ~~~~~v~~D~Ettg~~~--~~~~~il~~v~vv~~~~~~----~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~ 195 (342)
....+|++|+||||+++ +.++++ +.+.+.+ +.+ .|+.+|+|..++++.++++||||+++++++|++.+|++
T Consensus 27 ~~~~~vviD~ETTGl~~~~d~IieI-gaV~~~~--~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~ 103 (202)
T PRK09145 27 PPDEWVALDCETTGLDPRRAEIVSI-AAVKIRG--NRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALR 103 (202)
T ss_pred CCCCEEEEEeECCCCCCCCCceEEE-EEEEEEC--CEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHH
Confidence 34589999999999874 567777 6666632 332 48899999999999999999999999999999999999
Q ss_pred HHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhcccc------CC-Ccceeeccccccc----ccc-CCCCccHHHH
Q 019380 196 KILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN------YP-DHMLRDTAKYRPL----MKT-NLVSHSLKYL 263 (342)
Q Consensus 196 ~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~------~~-~~~~~Dt~~l~~~----~~~-~~~~~~L~~l 263 (342)
+|.+|+ ++.+|||||+.||+.||... .+ ...++|+..++.. ..+ ...+++|++|
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 78899999999999999822 22 2557898765421 122 2346899999
Q ss_pred HHHHhCCcCCCCCCCcHHHHHHHHHHHHHHHhh
Q 019380 264 TRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQ 296 (342)
Q Consensus 264 ~~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~ 296 (342)
++.| |++. .++|+|++||++|++||.++++.
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 46899999999999999998764
No 26
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.92 E-value=4.4e-26 Score=228.93 Aligned_cols=158 Identities=23% Similarity=0.388 Sum_probs=143.7
Q ss_pred CCcceeccccccccc--CCCcccccceEEeecCCCCeE--EeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHH
Q 019380 123 GPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENVI--FHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKIL 198 (342)
Q Consensus 123 ~~~~v~~D~Ettg~~--~~~~~~il~~v~vv~~~~~~~--~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~ 198 (342)
...||+||.||||++ .+.++++ +++.+ .+|+++ |+.|++|..+++...+.+||||++||++++++.+|+.+|.
T Consensus 420 datyVVfDiETTGLs~~~d~iIE~-aAvKi--kng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~kf~ 496 (1444)
T COG2176 420 DATYVVFDIETTGLSPVYDEIIEI-AAVKI--KNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEKFR 496 (1444)
T ss_pred cccEEEEEeecCCcCcccchhhhh-eeeee--eCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHHHHH
Confidence 345999999999987 6778888 88888 677774 9999999999999999999999999999999999999999
Q ss_pred HHHhcCCCccccccCCCCCeEEEeeCchhhhhhcccc-----CC--CcceeeccccccccccCCCCccHHHHHHHHhCCc
Q 019380 199 EILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-----YP--DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 199 ~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-----~~--~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 271 (342)
+|+ +++|||+||+.||++||+.. .+ .+++|||+.|++.++|...+++|..||+.| |+.
T Consensus 497 ~~~--------------~d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh~Lg~l~kk~-~v~ 561 (1444)
T COG2176 497 EFI--------------GDSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSHRLGTLCKKL-GVE 561 (1444)
T ss_pred HHh--------------cCcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhcchHHHHHHh-Ccc
Confidence 999 99999999999999999922 22 288999999999999999999999999999 999
Q ss_pred CCCCCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 272 IQSGVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 272 ~~~~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
+ ..+|||.+||.+|+.||..+++...+
T Consensus 562 l-e~hHRA~yDaeat~~vf~~f~~~~ke 588 (1444)
T COG2176 562 L-ERHHRADYDAEATAKVFFVFLKDLKE 588 (1444)
T ss_pred H-HHhhhhhhhHHHHHHHHHHHHHHHHH
Confidence 7 55999999999999999999988765
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=99.92 E-value=3.2e-25 Score=191.02 Aligned_cols=163 Identities=21% Similarity=0.255 Sum_probs=126.8
Q ss_pred cceeccccccccc--CCCcccccceEEeecC-CCCe----EEeeecCC--CCCccccccccCCCCHhh-hcCCCChHHHH
Q 019380 125 KAVAMDCEMVGGG--SNGTLDLCARVCLVDE-DENV----IFHTYVQP--QLPVTNYRYEVTGLTEED-IKNAMPLKEVK 194 (342)
Q Consensus 125 ~~v~~D~Ettg~~--~~~~~~il~~v~vv~~-~~~~----~~~~lv~p--~~~i~~~~~~i~GIt~e~-l~~~~~~~~v~ 194 (342)
..|++|+||||++ .+.++++ +++.+.+. +|.+ .|+++|+| ..+|++.+.++||||+++ +.++++..+++
T Consensus 6 ~~vv~D~ETTGl~~~~d~Iiei-gav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~~~~ 84 (189)
T cd06134 6 LPVVVDVETGGFNPQTDALLEI-AAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEKEAL 84 (189)
T ss_pred eeEEEEecCCCCCCCCCeEEEE-EEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchHHHH
Confidence 4689999999987 4567888 88888643 4543 69999999 578999999999999987 67777777777
Q ss_pred HHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhcccc-----C---C--CcceeeccccccccccCCCCccHHHHH
Q 019380 195 DKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-----Y---P--DHMLRDTAKYRPLMKTNLVSHSLKYLT 264 (342)
Q Consensus 195 ~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-----~---~--~~~~~Dt~~l~~~~~~~~~~~~L~~l~ 264 (342)
.+|.+++.+.- ...+.++.+|||||+.||+.||+.. . + ...++||..+++.+++ +++|..+|
T Consensus 85 ~~~~~~l~~~~-----~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~---~~~L~~l~ 156 (189)
T cd06134 85 KEIFKPIRKAL-----KAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG---QTVLAKAC 156 (189)
T ss_pred HHHHHHHHHHH-----hhcccCCCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC---CCcHHHHH
Confidence 77777662110 0001136799999999999999821 1 2 2457999999998765 36899999
Q ss_pred HHHhCCcCC-CCCCCcHHHHHHHHHHHHHHHhhh
Q 019380 265 RTYLGYDIQ-SGVHDPYEDCVSVMRLYKRFRRQD 297 (342)
Q Consensus 265 ~~~~~~~~~-~~~H~A~~Da~~t~~l~~~~~~~~ 297 (342)
++| |+++. ..+|+|++||++|++||.+++++|
T Consensus 157 ~~~-gi~~~~~~~H~Al~DA~ata~lf~~l~~~~ 189 (189)
T cd06134 157 QAA-GIEFDNKEAHSALYDTQKTAELFCKIVNRW 189 (189)
T ss_pred HHC-CCCCCCCCCcChHHHHHHHHHHHHHHHHhC
Confidence 998 99864 358999999999999999999876
No 28
>PRK06722 exonuclease; Provisional
Probab=99.92 E-value=2.5e-25 Score=200.40 Aligned_cols=158 Identities=15% Similarity=0.160 Sum_probs=127.9
Q ss_pred CCcceeccccccccc-----CCCcccccceEEeecCCCCe--EEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHH
Q 019380 123 GPKAVAMDCEMVGGG-----SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKD 195 (342)
Q Consensus 123 ~~~~v~~D~Ettg~~-----~~~~~~il~~v~vv~~~~~~--~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~ 195 (342)
...++++|+||||.. .++++++ +++.+.+..+++ .|++||+|..+++++++.+||||++||++||++.+|++
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 467999999999632 2678888 888885544455 49999999999999999999999999999999999999
Q ss_pred HHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhcccc-------CCC---cceeeccccccccccC--CCCccHHHH
Q 019380 196 KILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-------YPD---HMLRDTAKYRPLMKTN--LVSHSLKYL 263 (342)
Q Consensus 196 ~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-------~~~---~~~~Dt~~l~~~~~~~--~~~~~L~~l 263 (342)
+|.+|+ ++.++|+||..||++||... .|. ...+|++.++...++. ...++|..|
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 66677888889999999932 222 2246777655433332 235789999
Q ss_pred HHHHhCCcCCCCCCCcHHHHHHHHHHHHHHHhh
Q 019380 264 TRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQ 296 (342)
Q Consensus 264 ~~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~ 296 (342)
++.| |++..+.+|+|++||.+|+.||.+++++
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 9998 9996666999999999999999999854
No 29
>PRK07883 hypothetical protein; Validated
Probab=99.92 E-value=5.1e-25 Score=217.69 Aligned_cols=159 Identities=23% Similarity=0.343 Sum_probs=138.0
Q ss_pred CCCcceecccccccccC--CCcccccceEEeecCCCCe--EEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHH
Q 019380 122 RGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKI 197 (342)
Q Consensus 122 ~~~~~v~~D~Ettg~~~--~~~~~il~~v~vv~~~~~~--~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~ 197 (342)
....+|+||+||||+++ +.++++ +++.+. +|.+ .|+.+|+|..+++++++.+||||++++.++|++.+++++|
T Consensus 13 ~~~~~Vv~D~ETTGl~p~~~~IIEI-gaV~v~--~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~f 89 (557)
T PRK07883 13 RDVTFVVVDLETTGGSPAGDAITEI-GAVKVR--GGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAF 89 (557)
T ss_pred cCCCEEEEEEecCCCCCCCCeEEEE-EEEEEE--CCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHH
Confidence 44689999999999875 567777 777773 4555 4899999999999999999999999999999999999999
Q ss_pred HHHHhcCCCccccccCCCCCeEEEeeCchhhhhhcc-------ccCCCcceeecccccccccc--CCCCccHHHHHHHHh
Q 019380 198 LEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR-------MNYPDHMLRDTAKYRPLMKT--NLVSHSLKYLTRTYL 268 (342)
Q Consensus 198 ~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~-------~~~~~~~~~Dt~~l~~~~~~--~~~~~~L~~l~~~~~ 268 (342)
.+|+ ++.++||||+.||+.||+ +..+...++||+.+++.+.+ ...+++|.+|+.+|
T Consensus 90 ~~fl--------------~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L~~~~- 154 (557)
T PRK07883 90 LEFA--------------RGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLARLF- 154 (557)
T ss_pred HHHh--------------cCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHHHHHC-
Confidence 9999 778999999999999998 23444678999999988776 56789999999987
Q ss_pred CCcCCCCCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 269 GYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 269 ~~~~~~~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
|++. .++|+|++||++|++||.++..+...
T Consensus 155 gi~~-~~~H~Al~DA~ata~l~~~l~~~~~~ 184 (557)
T PRK07883 155 GATT-TPTHRALDDARATVDVLHGLIERLGN 184 (557)
T ss_pred Cccc-CCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 9985 45899999999999999999988754
No 30
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.92 E-value=5.9e-25 Score=186.06 Aligned_cols=155 Identities=29% Similarity=0.487 Sum_probs=129.0
Q ss_pred ceecccccccccCC--CcccccceEEeecCCCCeEEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHhc
Q 019380 126 AVAMDCEMVGGGSN--GTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNN 203 (342)
Q Consensus 126 ~v~~D~Ettg~~~~--~~~~il~~v~vv~~~~~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~l~~ 203 (342)
++++|+||||.++. +++++ +.+.+.+..-...|+.+|+|..+++++++++||||++++.+++++.+|+.+|.+|+
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 78999999998743 56666 65555322213369999999999999999999999999999999999999999999
Q ss_pred CCCccccccCCCCCeEEEeeCc-hhhhhhcccc-------CCC-cceeeccccccccccCCCCccHHHHHHHHhCCcCCC
Q 019380 204 GESTGRLMLDDGKARLLVGHGL-EHDLDSLRMN-------YPD-HMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQS 274 (342)
Q Consensus 204 ~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~~~-------~~~-~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~ 274 (342)
++.++|+||. .||+.+|+.. .|. ..++|+..+++...+.. .++|++|++.| |++..+
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 6778888888 9999999922 222 45899999998877654 89999999999 888554
Q ss_pred CCCCcHHHHHHHHHHHHHHHhhh
Q 019380 275 GVHDPYEDCVSVMRLYKRFRRQD 297 (342)
Q Consensus 275 ~~H~A~~Da~~t~~l~~~~~~~~ 297 (342)
.+|+|++||++|++||.++++++
T Consensus 145 ~~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 145 RAHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred CCcCcHHHHHHHHHHHHHHHHHh
Confidence 45999999999999999998876
No 31
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.92 E-value=7.5e-25 Score=228.94 Aligned_cols=158 Identities=24% Similarity=0.411 Sum_probs=138.7
Q ss_pred CCcceecccccccccC---CCcccccceEEeecCCCCe--EEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHH
Q 019380 123 GPKAVAMDCEMVGGGS---NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKI 197 (342)
Q Consensus 123 ~~~~v~~D~Ettg~~~---~~~~~il~~v~vv~~~~~~--~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~ 197 (342)
...+|++|+||||.++ ++++++ +.+.+ .+|++ .|+.+|+|..+|+++++.+||||++||+++|+|.+|+++|
T Consensus 2 ~~~~vvvD~ETTG~~p~~~d~IIei-gav~v--~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~l 78 (928)
T PRK08074 2 SKRFVVVDLETTGNSPKKGDKIIQI-AAVVV--EDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEI 78 (928)
T ss_pred CCCEEEEEEeCCCCCCCCCCcEEEE-EEEEE--ECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHHH
Confidence 3569999999999763 467777 77777 35555 5999999999999999999999999999999999999999
Q ss_pred HHHHhcCCCccccccCCCCCeEEEeeCchhhhhhccc-----cC--CCcceeeccccccccccCCCCccHHHHHHHHhCC
Q 019380 198 LEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM-----NY--PDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGY 270 (342)
Q Consensus 198 ~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~-----~~--~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~ 270 (342)
.+|+ ++.++||||+.||+.||+. .+ +..+++||+.+++..+|...+++|.+|+++| |+
T Consensus 79 ~~~l--------------~~~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~~~~L~~l~~~l-~i 143 (928)
T PRK08074 79 VELL--------------EGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEEL-GL 143 (928)
T ss_pred HHHh--------------CCCeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCCCCCHHHHHHhC-CC
Confidence 9999 8899999999999999982 12 2367899999999999988899999999998 88
Q ss_pred cCCCCCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 271 DIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 271 ~~~~~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
+ ..++|+|++||++|++||.+++++...
T Consensus 144 ~-~~~~H~Al~DA~ata~l~~~l~~~~~~ 171 (928)
T PRK08074 144 E-HDQPHRADSDAEVTAELFLQLLNKLER 171 (928)
T ss_pred C-CCCCCChHHHHHHHHHHHHHHHHHHHh
Confidence 8 446999999999999999999998754
No 32
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=99.92 E-value=5.4e-25 Score=228.91 Aligned_cols=156 Identities=22% Similarity=0.336 Sum_probs=137.3
Q ss_pred cceeccccccccc--CCCcccccceEEeecCCCCe--EEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHH
Q 019380 125 KAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 200 (342)
Q Consensus 125 ~~v~~D~Ettg~~--~~~~~~il~~v~vv~~~~~~--~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~ 200 (342)
.||++|+||||.+ .++++++ +.+.+ .+|++ .|+++|+|..+|++.++++||||++|+.++|+|.+++.+|.+|
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 4677777 77766 34555 4999999999999999999999999999999999999999999
Q ss_pred HhcCCCccccccCCCCCeEEEeeCchhhhhhcccc-----C--CCcceeeccccccccccCCCCccHHHHHHHHhCCcCC
Q 019380 201 LNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-----Y--PDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQ 273 (342)
Q Consensus 201 l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-----~--~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~ 273 (342)
+ ++.++||||+.||+.||+.. . ....++||+.+++.++|...+++|.+|++.| |++.
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 78899999999999999821 2 2367899999999998888899999999998 9985
Q ss_pred CCCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 274 SGVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 274 ~~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
.++|+|++||.+|++||.++.++...
T Consensus 142 ~~~H~Al~DA~ata~l~~~l~~~~~~ 167 (850)
T TIGR01407 142 ENPHRADSDAQATAELLLLLFEKMEK 167 (850)
T ss_pred CCCCChHHHHHHHHHHHHHHHHHHHh
Confidence 46999999999999999999988755
No 33
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=99.91 E-value=1e-24 Score=186.07 Aligned_cols=150 Identities=21% Similarity=0.262 Sum_probs=118.4
Q ss_pred ceeccccccccc---CCCcccccceEEeecCC---CC--------e--EEeeecCCCCCccccccccCCCCHhhhcCCCC
Q 019380 126 AVAMDCEMVGGG---SNGTLDLCARVCLVDED---EN--------V--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMP 189 (342)
Q Consensus 126 ~v~~D~Ettg~~---~~~~~~il~~v~vv~~~---~~--------~--~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~ 189 (342)
|++||+||||++ .++++++ +++.+.+.. +. + .|+++|+|..+|++.++.+||||++++.++|+
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 3577788 888774321 11 2 48999999999999999999999999999998
Q ss_pred hHH-HHHHHHHHHhcCCCccccccCCCCCeEEEeeCc-hhhhhhccc-------cCC-CcceeeccccccccccCCCCcc
Q 019380 190 LKE-VKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLRM-------NYP-DHMLRDTAKYRPLMKTNLVSHS 259 (342)
Q Consensus 190 ~~~-v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~~-------~~~-~~~~~Dt~~l~~~~~~~~~~~~ 259 (342)
+.+ +.+.+.+|+... +++.+|||||+ .||+.||+. ..+ ...++||+.+++.+.+ +
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 666677776211 13469999998 899999972 222 2456899999988764 8
Q ss_pred HHHHHHHHhCCcCCCCCCCcHHHHHHHHHHHHH
Q 019380 260 LKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKR 292 (342)
Q Consensus 260 L~~l~~~~~~~~~~~~~H~A~~Da~~t~~l~~~ 292 (342)
|+.|+.+++|++ ..++|+|++||.+|+++|.+
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 999999755888 45699999999999999875
No 34
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=99.91 E-value=1e-24 Score=189.36 Aligned_cols=167 Identities=21% Similarity=0.277 Sum_probs=130.6
Q ss_pred CCcceecccccccccC--CCcccccceEEeecC-CCCe----EEeeecCC--CCCccccccccCCCCHh-hhcCCCChHH
Q 019380 123 GPKAVAMDCEMVGGGS--NGTLDLCARVCLVDE-DENV----IFHTYVQP--QLPVTNYRYEVTGLTEE-DIKNAMPLKE 192 (342)
Q Consensus 123 ~~~~v~~D~Ettg~~~--~~~~~il~~v~vv~~-~~~~----~~~~lv~p--~~~i~~~~~~i~GIt~e-~l~~~~~~~~ 192 (342)
..-++++|+||||+++ ++++|+ +++.+... +|.+ .|+++++| ..+|+..+.++||||++ ++.+++++++
T Consensus 7 ~~~~vv~D~ETTGl~~~~d~IieI-gav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~~~~ 85 (200)
T TIGR01298 7 GYLPVVVDVETGGFNAKTDALLEI-AAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVSEYE 85 (200)
T ss_pred CCeeEEEEeeCCCCCCCCCeEEEE-EEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcchHH
Confidence 4457899999999874 567777 88877533 4554 38899997 47899999999999976 6899999999
Q ss_pred HHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhcccc-----C---C--CcceeeccccccccccCCCCccHHH
Q 019380 193 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-----Y---P--DHMLRDTAKYRPLMKTNLVSHSLKY 262 (342)
Q Consensus 193 v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-----~---~--~~~~~Dt~~l~~~~~~~~~~~~L~~ 262 (342)
++.++.+++...-. ....++.+|||||+.||+.||+.. . + ...++||..+++..++ .++|..
T Consensus 86 ~~~~~~~~l~~~~~-----~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~---~~~L~~ 157 (200)
T TIGR01298 86 ALHEIFKVVRKAMK-----ASGCQRAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG---QTVLAK 157 (200)
T ss_pred HHHHHHHHHHHHHH-----hcccCCCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC---cccHHH
Confidence 98888888721100 000146799999999999999822 1 1 2458999999988765 368999
Q ss_pred HHHHHhCCcCC-CCCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 263 LTRTYLGYDIQ-SGVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 263 l~~~~~~~~~~-~~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
||++| |+++. ..+|+|++||.+|++||..+.++..+
T Consensus 158 l~~~~-gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~~ 194 (200)
T TIGR01298 158 ACQAA-GXDFDSTQAHSALYDTEKTAELFCEIVNRWKR 194 (200)
T ss_pred HHHHc-CCCccccchhhhHHhHHHHHHHHHHHHHHHHH
Confidence 99998 98864 35899999999999999999999765
No 35
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.91 E-value=1.8e-24 Score=201.08 Aligned_cols=160 Identities=41% Similarity=0.675 Sum_probs=144.1
Q ss_pred CCCCcceecccccccccCCCcccccceEEeecCCCCeEEeeecCCCCCccccccccCCCCHhhhcCC-CChHHHHHHHHH
Q 019380 121 CRGPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNA-MPLKEVKDKILE 199 (342)
Q Consensus 121 ~~~~~~v~~D~Ettg~~~~~~~~il~~v~vv~~~~~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~-~~~~~v~~~~~~ 199 (342)
....+++++||||+.+ ..+ .++ +++.+||.+++++|+.+|+|..+|.+|+++++|||.+++.++ .+++++..+++.
T Consensus 213 ~~~~~i~AlDCEm~~t-e~g-~el-~RVt~VD~~~~vi~D~fVkP~~~VvDy~T~~SGIT~~~~e~~t~tl~dvq~~l~~ 289 (380)
T KOG2248|consen 213 SKSPNIFALDCEMVVT-ENG-LEL-TRVTAVDRDGKVILDTFVKPNKPVVDYNTRYSGITEEDLENSTITLEDVQKELLE 289 (380)
T ss_pred CCCCCeEEEEeeeeee-ccc-eee-EEeeeeeccCcEEeEEeecCCCcccccccccccccHHHHhcCccCHHHHHHHHHh
Confidence 4457799999999987 444 677 999999999999999999999999999999999999999865 589999999999
Q ss_pred HHhcCCCccccccCCCCCeEEEeeCchhhhhhccccCCCcceeeccccccccccC-CCCccHHHHHHHHhCCcCCC--CC
Q 019380 200 ILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLMKTN-LVSHSLKYLTRTYLGYDIQS--GV 276 (342)
Q Consensus 200 ~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~-~~~~~L~~l~~~~~~~~~~~--~~ 276 (342)
|+ ..++|||||.++.||+.|++.||. +|||+.++....+. ..+.+|+.||+.|||..||. +.
T Consensus 290 ~~-------------~~~TILVGHSLenDL~aLKl~H~~--ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~~~~ 354 (380)
T KOG2248|consen 290 LI-------------SKNTILVGHSLENDLKALKLDHPS--VIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEGVGG 354 (380)
T ss_pred hc-------------CcCcEEEeechhhHHHHHhhhCCc--eeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhccCCC
Confidence 99 388999999999999999999998 99999999888773 67888999999999999993 48
Q ss_pred CCcHHHHHHHHHHHHHHHhhhh
Q 019380 277 HDPYEDCVSVMRLYKRFRRQDH 298 (342)
Q Consensus 277 H~A~~Da~~t~~l~~~~~~~~~ 298 (342)
|++.+||.++++|+........
T Consensus 355 HdS~eDA~acm~Lv~~k~~~~~ 376 (380)
T KOG2248|consen 355 HDSVEDALACMKLVKLKIKNSE 376 (380)
T ss_pred CccHHHHHHHHHHHHHHHhccc
Confidence 9999999999999988776643
No 36
>PRK05168 ribonuclease T; Provisional
Probab=99.91 E-value=3.2e-24 Score=187.81 Aligned_cols=168 Identities=20% Similarity=0.280 Sum_probs=132.1
Q ss_pred CCCcceeccccccccc--CCCcccccceEEeecC-CCCe----EEeeecCC--CCCccccccccCCCCHhh-hcCCCChH
Q 019380 122 RGPKAVAMDCEMVGGG--SNGTLDLCARVCLVDE-DENV----IFHTYVQP--QLPVTNYRYEVTGLTEED-IKNAMPLK 191 (342)
Q Consensus 122 ~~~~~v~~D~Ettg~~--~~~~~~il~~v~vv~~-~~~~----~~~~lv~p--~~~i~~~~~~i~GIt~e~-l~~~~~~~ 191 (342)
....++++|+||||++ .++++++ +++.+... +|.+ .|+++|+| ..++++.++.+||||+++ +.+++++.
T Consensus 15 ~~~~~vv~D~ETTGl~~~~d~IieI-gaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~~~~~~ 93 (211)
T PRK05168 15 RGFLPVVIDVETAGFNAKTDALLEI-AAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAVSEK 93 (211)
T ss_pred cCCceEEEEeeCCCCCCCCCEEEEE-eEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhcCCChH
Confidence 3455799999999987 4567777 87877532 4543 58999999 568999999999999986 78999999
Q ss_pred HHHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhcccc----------CCCcceeeccccccccccCCCCccHH
Q 019380 192 EVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN----------YPDHMLRDTAKYRPLMKTNLVSHSLK 261 (342)
Q Consensus 192 ~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~----------~~~~~~~Dt~~l~~~~~~~~~~~~L~ 261 (342)
+++.++.+|+..... .....+.++||||+.||+.||+.. ++..+++||..+++.+++. .+|.
T Consensus 94 ~~l~~~~~~l~~~~~-----~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~~---~~L~ 165 (211)
T PRK05168 94 EALHEIFKMVRKGIK-----ASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALGQ---TVLA 165 (211)
T ss_pred HHHHHHHHHHHHHHH-----hcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcCC---CCHH
Confidence 999999998832100 000136899999999999999822 1123589999999887653 5899
Q ss_pred HHHHHHhCCcCCC-CCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 262 YLTRTYLGYDIQS-GVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 262 ~l~~~~~~~~~~~-~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
.++..+ |+++.. .+|+|++||.+|++||.++.++..+
T Consensus 166 ~l~~~~-gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~~ 203 (211)
T PRK05168 166 KACQAA-GIEFDNKEAHSALYDTEKTAELFCEIVNRWKR 203 (211)
T ss_pred HHHHHC-CCCCCCCCCCChHHHHHHHHHHHHHHHHHHHH
Confidence 999998 998653 4899999999999999999998755
No 37
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.91 E-value=5.1e-24 Score=195.65 Aligned_cols=156 Identities=19% Similarity=0.268 Sum_probs=129.2
Q ss_pred CCCcceecccccccccC--CCcccccceEEeecCCCCe--EEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHH
Q 019380 122 RGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKI 197 (342)
Q Consensus 122 ~~~~~v~~D~Ettg~~~--~~~~~il~~v~vv~~~~~~--~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~ 197 (342)
....|++||+||||+++ +.++++ +++.+. .+|++ .|++||+|...+.+ ..|||||++||+++|+|.+++++|
T Consensus 44 ~~~~fVvlDiETTGLdp~~drIIeI-gAV~i~-~~g~ive~f~tLVnP~~~~~p--~~LHGIT~e~La~AP~f~eVl~el 119 (377)
T PRK05601 44 EAAPFVAVSIQTSGIHPSTSRLITI-DAVTLT-ADGEEVEHFHAVLNPGEDPGP--FHLHGLSAEEFAQGKRFSQILKPL 119 (377)
T ss_pred CCCCEEEEEEECCCCCCCCCeEEEE-EEEEEE-cCCEEEEEEEEEECcCCCCCC--ccccCCCHHHHhcCCCHHHHHHHH
Confidence 44679999999999974 456677 777664 34555 69999999976544 479999999999999999999999
Q ss_pred HHHHhcCCCccccccCCCCCeEEEeeCchhhhhhcccc---------------------------------CCC-cceee
Q 019380 198 LEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN---------------------------------YPD-HMLRD 243 (342)
Q Consensus 198 ~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~---------------------------------~~~-~~~~D 243 (342)
.+|| ++.+|||||+.||++||... .|. ..++|
T Consensus 120 ~~fL--------------~g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iD 185 (377)
T PRK05601 120 DRLI--------------DGRTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVD 185 (377)
T ss_pred HHHh--------------CCCEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEE
Confidence 9999 89999999999999998732 122 56899
Q ss_pred ccccccccccCCCCccHHHHHHHHhCCcCC---------CCCCCcH--HHHHHHHHHHHHHHhh
Q 019380 244 TAKYRPLMKTNLVSHSLKYLTRTYLGYDIQ---------SGVHDPY--EDCVSVMRLYKRFRRQ 296 (342)
Q Consensus 244 t~~l~~~~~~~~~~~~L~~l~~~~~~~~~~---------~~~H~A~--~Da~~t~~l~~~~~~~ 296 (342)
|+.+++.+++...+++|..||.+| |++.. ...|+++ +||+.+++||.+..+.
T Consensus 186 TL~LARrl~p~l~~~rL~~La~~l-Gi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~~~~ 248 (377)
T PRK05601 186 TLATARRQGVALDDIRIRGVAHTL-GLDAPAAEASVERAQVPHRQLCREETLLVARLYFALRAS 248 (377)
T ss_pred hHHHHHHHcCCCCCCCHHHHHHHh-CCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHhhcc
Confidence 999999999988999999999999 98851 2258888 6999999999987433
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=99.89 E-value=3e-23 Score=176.93 Aligned_cols=153 Identities=22% Similarity=0.261 Sum_probs=125.7
Q ss_pred ceecccccccccC-------CCcccccceEEeecCCCCe--EEeeecCCCC--CccccccccCCCCHhhhcCCCChHHHH
Q 019380 126 AVAMDCEMVGGGS-------NGTLDLCARVCLVDEDENV--IFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPLKEVK 194 (342)
Q Consensus 126 ~v~~D~Ettg~~~-------~~~~~il~~v~vv~~~~~~--~~~~lv~p~~--~i~~~~~~i~GIt~e~l~~~~~~~~v~ 194 (342)
+|++|+||||... ++++++ +++.+....+++ .|+.+|+|.. .++++++.+||||++++.++|++.+|+
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 5899999999874 567777 666653333323 5999999997 899999999999999999999999999
Q ss_pred HHHHHHHhcCCCccccccCCCCCe--EEEeeCchhhhhhcc-------cc--C-CCcceeeccccccccccCCCCccHHH
Q 019380 195 DKILEILNNGESTGRLMLDDGKAR--LLVGHGLEHDLDSLR-------MN--Y-PDHMLRDTAKYRPLMKTNLVSHSLKY 262 (342)
Q Consensus 195 ~~~~~~l~~~~~~~~~~~~~~~~~--~lvgh~~~~D~~~l~-------~~--~-~~~~~~Dt~~l~~~~~~~~~~~~L~~ 262 (342)
++|.+|+ ++. .+++|+..+|+.++. .. . ....++|+..+++...+....++|.+
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 11 1 12678999999998888778999999
Q ss_pred HHHHHhCCcCCCCCCCcHHHHHHHHHHHHHHH
Q 019380 263 LTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFR 294 (342)
Q Consensus 263 l~~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~ 294 (342)
|+.+| |++..+..|+|++||++|++||.++.
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 99976569999999999999998863
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=99.89 E-value=3.2e-23 Score=217.90 Aligned_cols=158 Identities=23% Similarity=0.394 Sum_probs=139.3
Q ss_pred CCcceeccccccccc--CCCcccccceEEeecCCCCe--EEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHH
Q 019380 123 GPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKIL 198 (342)
Q Consensus 123 ~~~~v~~D~Ettg~~--~~~~~~il~~v~vv~~~~~~--~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~ 198 (342)
...+|+||+||||++ .+.++++ +++.+. +|.+ .|+.+|+|..+|++.++++||||+++|+++|++.+|+++|.
T Consensus 189 ~~~~VVfDiETTGL~~~~d~IIEI-GAVkv~--~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f~ 265 (1213)
T TIGR01405 189 DATYVVFDIETTGLSPQYDEIIEF-GAVKVK--NGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKFK 265 (1213)
T ss_pred CCcEEEEEeEecCCCCCCCeEEEE-EEEEEE--CCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHH
Confidence 457999999999986 4677888 888774 4555 49999999999999999999999999999999999999999
Q ss_pred HHHhcCCCccccccCCCCCeEEEeeCchhhhhhcccc-----CC--CcceeeccccccccccCCCCccHHHHHHHHhCCc
Q 019380 199 EILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-----YP--DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 199 ~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-----~~--~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 271 (342)
+|+ ++.+|||||+.||+.||+.. .+ ...++||+.+++.+.|...+++|..||+.| |++
T Consensus 266 ~fl--------------~~~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k~~kL~~Lak~l-gi~ 330 (1213)
T TIGR01405 266 EFF--------------KDSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRLGNICKKL-GVD 330 (1213)
T ss_pred HHh--------------CCCeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCCCCCHHHHHHHc-CCC
Confidence 999 78999999999999999822 21 267899999999998888899999999998 999
Q ss_pred CCCCCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 272 IQSGVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 272 ~~~~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
+.. +|+|++||.+|++||.+++++..+
T Consensus 331 ~~~-~HrAl~DA~aTa~I~~~ll~~l~~ 357 (1213)
T TIGR01405 331 LDD-HHRADYDAEATAKVFKVMVEQLKE 357 (1213)
T ss_pred CCC-CcCHHHHHHHHHHHHHHHHHHHHH
Confidence 654 999999999999999999988654
No 40
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.87 E-value=5.7e-22 Score=180.88 Aligned_cols=157 Identities=18% Similarity=0.236 Sum_probs=121.0
Q ss_pred cCCCCcceecccccccccC--CCcccccceEEeec-CCCCe-----EEeeecCCCCCccccccccCCCCHhhhcCCCChH
Q 019380 120 TCRGPKAVAMDCEMVGGGS--NGTLDLCARVCLVD-EDENV-----IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLK 191 (342)
Q Consensus 120 ~~~~~~~v~~D~Ettg~~~--~~~~~il~~v~vv~-~~~~~-----~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~ 191 (342)
......++++|+||||+++ +.++++ +.+.+.. .+|.+ .|+.+++|..+|++.++.+||||++|+.+++...
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 678888 7777752 24533 4899999999999999999999999999998754
Q ss_pred HHHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhcccc---CCCcceeeccccccccccCCCCccHHHHHHHHh
Q 019380 192 EVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN---YPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYL 268 (342)
Q Consensus 192 ~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~---~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~ 268 (342)
+ .|.+|+. ...+|||||+.||+.||+.. ++...+.+++....+..+...+++|.+|+..|
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 4 4666771 33699999999999999833 22244567665444444455789999999999
Q ss_pred CCcCCCCCCCcHHHHHHHHHHHHHHHhh
Q 019380 269 GYDIQSGVHDPYEDCVSVMRLYKRFRRQ 296 (342)
Q Consensus 269 ~~~~~~~~H~A~~Da~~t~~l~~~~~~~ 296 (342)
|. ..++|+|++||.+|++||..++..
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 346999999999999999987654
No 41
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.87 E-value=8.4e-22 Score=176.85 Aligned_cols=157 Identities=25% Similarity=0.370 Sum_probs=136.2
Q ss_pred Ccceeccccccccc--CCCcccccceEEeecCCCC-eEEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHH
Q 019380 124 PKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDEN-VIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 200 (342)
Q Consensus 124 ~~~v~~D~Ettg~~--~~~~~~il~~v~vv~~~~~-~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~ 200 (342)
..++++|+||||.+ .+.++++ +++.+++..-. ..|+.+++|..++++.+.++||||.+++.++|.|.++++++.+|
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 67899999999986 6778888 88888544222 23899999988999999999999999999999999999999999
Q ss_pred HhcCCCccccccCCCCC-eEEEeeCchhhhhhccc-------cCCCcceeeccccccccccCCCCccHHHHHHHHhCCcC
Q 019380 201 LNNGESTGRLMLDDGKA-RLLVGHGLEHDLDSLRM-------NYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDI 272 (342)
Q Consensus 201 l~~~~~~~~~~~~~~~~-~~lvgh~~~~D~~~l~~-------~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~ 272 (342)
+ ++ .++||||+.||+.||+. ..+...++||..+.+..+++...++|+.||.++ |+..
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 99999999999999982 222356889999999999988899999999988 8884
Q ss_pred CC-CCCCcHHHHHHHHHHHHHHHhh
Q 019380 273 QS-GVHDPYEDCVSVMRLYKRFRRQ 296 (342)
Q Consensus 273 ~~-~~H~A~~Da~~t~~l~~~~~~~ 296 (342)
.. ..|+|+.||.+++++|..+...
T Consensus 157 ~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 157 NPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred CCcCCcchHHHHHHHHHHHHHHHhc
Confidence 32 2799999999999999999985
No 42
>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=7.1e-24 Score=177.41 Aligned_cols=149 Identities=27% Similarity=0.457 Sum_probs=126.8
Q ss_pred eecccccccccC--CCcccccceEEeecCC--CCeEEeeecCCCCC--ccccccccCCCCHhhhcCCCChHHHHHHHHHH
Q 019380 127 VAMDCEMVGGGS--NGTLDLCARVCLVDED--ENVIFHTYVQPQLP--VTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 200 (342)
Q Consensus 127 v~~D~Ettg~~~--~~~~~il~~v~vv~~~--~~~~~~~lv~p~~~--i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~ 200 (342)
|+||+||||.+. +.++++ +++.+.+.. ....|+++|+|..+ ++++++.+||||.+++.+++++.+++++|.+|
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 689999999875 678888 888887665 34479999999987 99999999999999999999999999999999
Q ss_pred HhcCCCccccccCCCCCeEEEeeCchhhhhhcc--------ccCC-CcceeeccccccccccCCCCccHHHHHHHHhCCc
Q 019380 201 LNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR--------MNYP-DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 201 l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~--------~~~~-~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 271 (342)
+. ++.++||||+.||..++. ..+| ...++|+..+.+...+....++|+.|++.| |++
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 368999999999998887 1133 245889999888877765568999999999 888
Q ss_pred CCCCCCCcHHHHHHHHHHH
Q 019380 272 IQSGVHDPYEDCVSVMRLY 290 (342)
Q Consensus 272 ~~~~~H~A~~Da~~t~~l~ 290 (342)
....+|+|++||++|++||
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 5555799999999999997
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=99.86 E-value=7.7e-22 Score=164.44 Aligned_cols=147 Identities=28% Similarity=0.409 Sum_probs=124.4
Q ss_pred eeccccccccc--CCCcccccceEEeecCCCCe--EEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHh
Q 019380 127 VAMDCEMVGGG--SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILN 202 (342)
Q Consensus 127 v~~D~Ettg~~--~~~~~~il~~v~vv~~~~~~--~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~l~ 202 (342)
|++|+||||.. .++++++ +.+.+ +.++++ .|+.+++|...+.+..+.++||+++++.+++++.+++++|.+|+
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 57899999987 4667777 55555 333333 58999999999999999999999999999999999999999999
Q ss_pred cCCCccccccCCCCCeEEEeeCchhhhhhcccc-------CCCcceeeccccccccccCCCCccHHHH-HHHHhCCcCCC
Q 019380 203 NGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-------YPDHMLRDTAKYRPLMKTNLVSHSLKYL-TRTYLGYDIQS 274 (342)
Q Consensus 203 ~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~-------~~~~~~~Dt~~l~~~~~~~~~~~~L~~l-~~~~~~~~~~~ 274 (342)
++.++||||+.||+.+|+.. .....++|++.+++..++....++|..+ +..+ |+. ..
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 66899999999999999832 2347799999999999888888999998 6655 876 45
Q ss_pred CCCCcHHHHHHHHHHHH
Q 019380 275 GVHDPYEDCVSVMRLYK 291 (342)
Q Consensus 275 ~~H~A~~Da~~t~~l~~ 291 (342)
.+|+|++||++|++||.
T Consensus 143 ~~H~Al~Da~~t~~l~~ 159 (159)
T cd06127 143 GAHRALADALATAELLL 159 (159)
T ss_pred CCCCcHHHHHHHHHHhC
Confidence 69999999999999983
No 44
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=99.86 E-value=5e-22 Score=170.48 Aligned_cols=148 Identities=22% Similarity=0.262 Sum_probs=114.6
Q ss_pred eeccccccccc--CCCcccccceEEeecCCCCe--EEeeecCCCC--CccccccccCCCCHhhhcC-CCChHHHHHHHHH
Q 019380 127 VAMDCEMVGGG--SNGTLDLCARVCLVDEDENV--IFHTYVQPQL--PVTNYRYEVTGLTEEDIKN-AMPLKEVKDKILE 199 (342)
Q Consensus 127 v~~D~Ettg~~--~~~~~~il~~v~vv~~~~~~--~~~~lv~p~~--~i~~~~~~i~GIt~e~l~~-~~~~~~v~~~~~~ 199 (342)
++||+||||++ .+.++++ +.+.+ +.++.+ .|+.+++|.. .+++.+..+||||+++|.+ +|++.+++++|.+
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 46999999987 4567777 66555 344344 4899999874 5677888999999999999 8999999999999
Q ss_pred HHhcCCCccccccCCCCCeEEEeeC-chhhhhhccccC------C-------Ccceeeccccccccc---c---------
Q 019380 200 ILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLRMNY------P-------DHMLRDTAKYRPLMK---T--------- 253 (342)
Q Consensus 200 ~l~~~~~~~~~~~~~~~~~~lvgh~-~~~D~~~l~~~~------~-------~~~~~Dt~~l~~~~~---~--------- 253 (342)
|+ +..+.++|||| +.||+.||+... + .+..+|+..+++... +
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 22467999997 899999998221 1 133578887665432 2
Q ss_pred -CCCCccHHHHHHHHhCCcCCCCCCCcHHHHHHHHHHH
Q 019380 254 -NLVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLY 290 (342)
Q Consensus 254 -~~~~~~L~~l~~~~~~~~~~~~~H~A~~Da~~t~~l~ 290 (342)
...+++|++|+++| |++. .++|||++||++|++|.
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 9985 56999999999999986
No 45
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.86 E-value=2.1e-21 Score=188.14 Aligned_cols=179 Identities=18% Similarity=0.174 Sum_probs=136.7
Q ss_pred ccccccCCCCcceeccccccccc-----CCCcccccceEEeecCCCCe--EEeeecCCCC--CccccccccCCCCHhhhc
Q 019380 115 IDEKRTCRGPKAVAMDCEMVGGG-----SNGTLDLCARVCLVDEDENV--IFHTYVQPQL--PVTNYRYEVTGLTEEDIK 185 (342)
Q Consensus 115 ~~~~~~~~~~~~v~~D~Ettg~~-----~~~~~~il~~v~vv~~~~~~--~~~~lv~p~~--~i~~~~~~i~GIt~e~l~ 185 (342)
++.....+...|++||+||||.. .++++|+ +++.+-..++++ .|++||+|.. +++.+++.+||||++||+
T Consensus 47 ~~~~~~q~~d~~IV~DlETTgl~~~~~~~dEIIEI-GaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~ 125 (582)
T PTZ00315 47 FPEIAPQPFDAYVVLDFEATCEADRRIEDAEVIEF-PMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVS 125 (582)
T ss_pred CcccccCCCCeEEEEEEecCCCCCCCCCCCceEEE-EEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHh
Confidence 33444455678999999999975 3677888 666663246666 4899999986 699999999999999999
Q ss_pred CCCChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhh-hcc--------ccCC--Ccceeecc-cccccccc
Q 019380 186 NAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLD-SLR--------MNYP--DHMLRDTA-KYRPLMKT 253 (342)
Q Consensus 186 ~~~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~-~l~--------~~~~--~~~~~Dt~-~l~~~~~~ 253 (342)
+||+|.+|+.+|.+||.+.. ++.++..+..+|+||.+||+. ||. ...| ...++|.. .+.+..++
T Consensus 126 ~Ap~F~eVl~ef~~fL~~~~----~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p 201 (582)
T PTZ00315 126 RADPFPVVYCEALQFLAEAG----LGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFG 201 (582)
T ss_pred cCCCHHHHHHHHHHHHhccc----cccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCc
Confidence 99999999999999994321 111222345899999999995 774 1233 24466653 34455444
Q ss_pred -----------CCCCccHHHHHHHHhCCcCCCCCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 254 -----------NLVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 254 -----------~~~~~~L~~l~~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
....++|.++++.+ |+++.+.+|+|++||++|++||.++++++..
T Consensus 202 ~~~~~~~~~~~~~~~~~L~~al~~l-gL~~eGr~HrAlDDA~ntA~L~~~Ll~~g~~ 257 (582)
T PTZ00315 202 NGSGCGGGATPPLGPSDMPDMLQML-GLPLQGRHHSGIDDCRNIAAVLCELLRRGLV 257 (582)
T ss_pred cccccccccccccCCcCHHHHHHHC-CCCCCCCCcCcHHHHHHHHHHHHHHHHcCCE
Confidence 34578999999988 9998777999999999999999999998765
No 46
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.83 E-value=1.7e-20 Score=199.73 Aligned_cols=157 Identities=22% Similarity=0.391 Sum_probs=137.7
Q ss_pred Ccceeccccccccc--CCCcccccceEEeecCCCCe--EEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHH
Q 019380 124 PKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILE 199 (342)
Q Consensus 124 ~~~v~~D~Ettg~~--~~~~~~il~~v~vv~~~~~~--~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~ 199 (342)
..+|++|+||||++ .+.++++ +++.+ .+|.+ .|+.+|+|..++++.++.+||||++++.++|++.+|+++|.+
T Consensus 419 ~~~VVfDLETTGL~~~~deIIEI-gAV~V--~~G~iie~F~~~V~P~~~I~~~~~~LTGIT~e~L~~aps~~EaL~~f~~ 495 (1437)
T PRK00448 419 ATYVVFDVETTGLSAVYDEIIEI-GAVKI--KNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKE 495 (1437)
T ss_pred CcEEEEEhhhcCCCCchhhhhee-eeEEE--eCCeEeeeEEEEECCCCCCCHHHHHHhCCCHHHHcCCCCHHHHHHHHHH
Confidence 56999999999986 4567777 77766 35555 499999999999999999999999999999999999999999
Q ss_pred HHhcCCCccccccCCCCCeEEEeeCchhhhhhcc-------ccCCCcceeeccccccccccCCCCccHHHHHHHHhCCcC
Q 019380 200 ILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR-------MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDI 272 (342)
Q Consensus 200 ~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~-------~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~ 272 (342)
|+ ++.+|||||+.||+.||+ +..+...++||+.+++.+.+....++|..||+.| |+.+
T Consensus 496 fi--------------gg~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k~~kL~~LAk~l-GL~~ 560 (1437)
T PRK00448 496 FC--------------GDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKF-GVEL 560 (1437)
T ss_pred Hh--------------CCCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccccccHHHHHHHc-CCCC
Confidence 99 889999999999999986 2223467899999999998888899999999998 9985
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 273 QSGVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 273 ~~~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
. ++|+|++||.+|++||.+++++..+
T Consensus 561 ~-~~HrAl~DA~aTa~lf~~ll~~l~~ 586 (1437)
T PRK00448 561 E-HHHRADYDAEATAYLLIKFLKDLKE 586 (1437)
T ss_pred C-CCcChHHHHHHHHHHHHHHHHHHHH
Confidence 4 5899999999999999999988754
No 47
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=99.82 E-value=1.1e-20 Score=160.66 Aligned_cols=151 Identities=17% Similarity=0.180 Sum_probs=110.8
Q ss_pred ceecccccccccC--CCcccccceEEeecCCCCe--EEeeecCCCCCccc----ccccc---CCCCHhhhcCCCChHHHH
Q 019380 126 AVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTN----YRYEV---TGLTEEDIKNAMPLKEVK 194 (342)
Q Consensus 126 ~v~~D~Ettg~~~--~~~~~il~~v~vv~~~~~~--~~~~lv~p~~~i~~----~~~~i---~GIt~e~l~~~~~~~~v~ 194 (342)
++++|+||||+++ +.++++ +++.+.+..+++ .|+.+|+|..+++. +...+ |||++++++++|++.+++
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 5789999999884 667788 777653323333 49999999976553 34455 599999999999999999
Q ss_pred HHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhccccC-----CC-cceeec---cccccccccCCCCccHHHHHH
Q 019380 195 DKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY-----PD-HMLRDT---AKYRPLMKTNLVSHSLKYLTR 265 (342)
Q Consensus 195 ~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~-----~~-~~~~Dt---~~l~~~~~~~~~~~~L~~l~~ 265 (342)
.+|.+|+.+.. .....+|||||+.||+.||+... +. ++.+|+ ..+++.++|...+
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 01346999999999999998322 21 456787 4466666554322
Q ss_pred HHhCCcCCCCCCCcHHHHHHHHHHHHHHHhh
Q 019380 266 TYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQ 296 (342)
Q Consensus 266 ~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~ 296 (342)
+ ++. ....|||++||++|+.+|+.+++-
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 48
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.82 E-value=6.4e-20 Score=176.77 Aligned_cols=166 Identities=18% Similarity=0.248 Sum_probs=124.0
Q ss_pred CCCcceecccccccccC--CCcccccceEEeecCCCCe---EEeeecCCCCC--ccccccccCCCCHhhhcC-CCChHHH
Q 019380 122 RGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV---IFHTYVQPQLP--VTNYRYEVTGLTEEDIKN-AMPLKEV 193 (342)
Q Consensus 122 ~~~~~v~~D~Ettg~~~--~~~~~il~~v~vv~~~~~~---~~~~lv~p~~~--i~~~~~~i~GIt~e~l~~-~~~~~~v 193 (342)
....|+++|+||||+++ +.++++ ++|.+. .++.+ .+..+++|... +++.+..+||||++++.+ +.+..++
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 45569999999999984 667777 777663 33322 48999999853 456788999999999965 4578999
Q ss_pred HHHHHHHHhcCCCccccccCCCCCeEEEeeC-chhhhhhccccCC----------------Ccceeecccccccc-----
Q 019380 194 KDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLRMNYP----------------DHMLRDTAKYRPLM----- 251 (342)
Q Consensus 194 ~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~-~~~D~~~l~~~~~----------------~~~~~Dt~~l~~~~----- 251 (342)
+.+|.+++. ..++++|||| +.||..||+..+. ...++|++.+....
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 1468999997 7999999873211 01234544433332
Q ss_pred -cc----CCCCccHHHHHHHHhCCcCCCCCCCcHHHHHHHHHHHHHHHhhhhhhhhh
Q 019380 252 -KT----NLVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQVEEI 303 (342)
Q Consensus 252 -~~----~~~~~~L~~l~~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~~~~~~~ 303 (342)
+| +..+++|+.|+..+ |++ ..++|+|++||++|++|+..+.++..+++++
T Consensus 150 ~~P~~~~g~~s~rLe~L~~~~-gI~-~~~AHdALsDa~aT~~la~~l~~~qP~l~~~ 204 (476)
T PRK11779 150 NWPENEDGLPSFKLEHLTKAN-GIE-HENAHDAMSDVYATIAMAKLIKQKQPKLFDY 204 (476)
T ss_pred cCcccccCCCCCcHHHHHHHc-CCC-CCCCCCcHHHHHHHHHHHHHHHHhChHHHHH
Confidence 22 24679999999999 988 4569999999999999999999886565544
No 49
>PRK05359 oligoribonuclease; Provisional
Probab=99.81 E-value=2.3e-20 Score=159.31 Aligned_cols=154 Identities=18% Similarity=0.231 Sum_probs=116.0
Q ss_pred CCcceeccccccccc--CCCcccccceEEeecCCCCeE---EeeecCCCCC----ccccccccC---CCCHhhhcCCCCh
Q 019380 123 GPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENVI---FHTYVQPQLP----VTNYRYEVT---GLTEEDIKNAMPL 190 (342)
Q Consensus 123 ~~~~v~~D~Ettg~~--~~~~~~il~~v~vv~~~~~~~---~~~lv~p~~~----i~~~~~~i~---GIt~e~l~~~~~~ 190 (342)
...++++|+||||++ .+.++|+ +++.+ +.+..++ |..+++|... +++++..+| |||+++++++|++
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 457999999999987 4667777 66644 4444333 8889999864 456677776 8999999999999
Q ss_pred HHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhccccCC-----C-cceee--cc-ccccccccCCCCccHH
Q 019380 191 KEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP-----D-HMLRD--TA-KYRPLMKTNLVSHSLK 261 (342)
Q Consensus 191 ~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~-----~-~~~~D--t~-~l~~~~~~~~~~~~L~ 261 (342)
.+|+.+|++|+...- ..++.+|||||+.||+.||+...+ . ++++| +. .+++.++|..
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 014578999999999999994321 1 55677 44 5677766642
Q ss_pred HHHHHHhCCcCCCCCCCcHHHHHHHHHHHHHHHhhhh
Q 019380 262 YLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDH 298 (342)
Q Consensus 262 ~l~~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~~ 298 (342)
+.+++ ..+.|||++||+++.+.|..+++...
T Consensus 146 -----~~~~~-~~~~HRal~D~~~s~~~~~~~~~~~~ 176 (181)
T PRK05359 146 -----LNGFK-KQGTHRALADIRESIAELKYYREHFF 176 (181)
T ss_pred -----hhCCC-CcCCcccHHHHHHHHHHHHHHHHHhc
Confidence 22666 55689999999999999999998753
No 50
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.69 E-value=1.3e-17 Score=145.34 Aligned_cols=107 Identities=24% Similarity=0.349 Sum_probs=94.0
Q ss_pred CCCcccccccccccCCHHHHHHHHhhhccCCCCC--ccccCccccCChhhhhhhc---CCCcccCCCCCcccCCc-----
Q 019380 11 STARHKCVACYKQFKRKDHLIEHMKISYHSVHQP--KCAVCQKLSKSFESLREHL---TGPLSKAHCSGIFSDRG----- 80 (342)
Q Consensus 11 ~~~~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~--~C~~C~~~f~~~~~l~~H~---~~~~~C~~C~k~f~~~~----- 80 (342)
..-.|+|+.|||++++.++|.+|+.+|--...+. .|++|+|.+.+...|+.|. +-+..|.+|||.|++..
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 4557999999999999999999999932223343 8999999999999999998 34788999999999753
Q ss_pred -----------ccccccccCChhhHHHHHhhcCCCCCCCCcccccccc
Q 019380 81 -----------CNLCMNIFDSPSSLIKHKEACSLSAPVPFKISGAIDE 117 (342)
Q Consensus 81 -----------C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~c~~~~~ 117 (342)
|++|+|.|.++++||-||++|.+.++++|..|+++..
T Consensus 207 iRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFs 254 (279)
T KOG2462|consen 207 IRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFA 254 (279)
T ss_pred cccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHH
Confidence 9999999999999999999999999999999998754
No 51
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=99.61 E-value=8.3e-16 Score=151.71 Aligned_cols=160 Identities=27% Similarity=0.447 Sum_probs=134.3
Q ss_pred Ccceeccccccccc-------CCCc--------ccccceEEeecCCCC----eEEeeecCCCCCccccccccCCCCHhhh
Q 019380 124 PKAVAMDCEMVGGG-------SNGT--------LDLCARVCLVDEDEN----VIFHTYVQPQLPVTNYRYEVTGLTEEDI 184 (342)
Q Consensus 124 ~~~v~~D~Ettg~~-------~~~~--------~~il~~v~vv~~~~~----~~~~~lv~p~~~i~~~~~~i~GIt~e~l 184 (342)
...|++|.|+..+. .++. ..+ +++.+|+++|. +..+.+|...+.|.+|.|+++||.+.||
T Consensus 910 g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msv-ARiScvRGeGp~eGiPFiDDYv~T~d~VvDYLTqySGI~PGDL 988 (1118)
T KOG1275|consen 910 GDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSV-ARISCVRGEGPNEGIPFIDDYVSTDDKVVDYLTQYSGIKPGDL 988 (1118)
T ss_pred CceeeeehhheecchHHhccccCCceeEecccccee-EEEEEEcccCCCCCCccccceecchhHHHHHHHHhcCCCcccc
Confidence 45788888887543 2222 234 89999988632 2459999999999999999999999999
Q ss_pred cCC------CChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhccccCCCcceeeccccccccccCCCCc
Q 019380 185 KNA------MPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLMKTNLVSH 258 (342)
Q Consensus 185 ~~~------~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~~~~ 258 (342)
+.. .++.-++.++.-.+ +.|.+.|||++.+|+..+++.+|..+++||+.|+.... ....
T Consensus 989 Dp~~S~K~Lt~lK~~Y~Kl~~Li-------------~~GviFVGHGL~nDFrvINi~Vp~~QiiDTv~lf~~~s--~R~L 1053 (1118)
T KOG1275|consen 989 DPTTSEKRLTTLKVLYLKLRLLI-------------QRGVIFVGHGLQNDFRVINIHVPEEQIIDTVTLFRLGS--QRML 1053 (1118)
T ss_pred CCccCcceehhHHHHHHHHHHHH-------------HcCcEEEcccccccceEEEEecChhhheeeeEEEeccc--ccEE
Confidence 854 25677777777776 48899999999999999999999999999999987764 4679
Q ss_pred cHHHHHHHHhCCcCCCCCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 259 SLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 259 ~L~~l~~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
||+.||..+||-+||.++|++++||+.++.||+++++-.++
T Consensus 1054 SLrfLa~~lLg~~IQ~~~HDSIeDA~taLkLYk~Yl~lkeq 1094 (1118)
T KOG1275|consen 1054 SLRFLAWELLGETIQMEAHDSIEDARTALKLYKKYLKLKEQ 1094 (1118)
T ss_pred EHHHHHHHHhcchhhccccccHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999887655
No 52
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.46 E-value=1.8e-14 Score=116.52 Aligned_cols=164 Identities=20% Similarity=0.253 Sum_probs=125.5
Q ss_pred Ccceecccccccc---c---CCCcccccceEEeecC-CCCe--EEeeecCCCC--CccccccccCCCCHhhhcCCCChHH
Q 019380 124 PKAVAMDCEMVGG---G---SNGTLDLCARVCLVDE-DENV--IFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPLKE 192 (342)
Q Consensus 124 ~~~v~~D~Ettg~---~---~~~~~~il~~v~vv~~-~~~~--~~~~lv~p~~--~i~~~~~~i~GIt~e~l~~~~~~~~ 192 (342)
..++++|.|.|-. . ...+++| . ..+|+. +..+ .|++||+|.. .+..++..++||++..|+.||-|..
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-E-AGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAPIFSM 81 (210)
T ss_pred ceEEEEEeeeeccCCCCCchhceeeee-h-hhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhccccchHHH
Confidence 4578899999842 2 2234444 2 233333 3333 4999999984 5778999999999999999999999
Q ss_pred HHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhcccc------CCC---cceeeccccccccccCCCCccHHHH
Q 019380 193 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN------YPD---HMLRDTAKYRPLMKTNLVSHSLKYL 263 (342)
Q Consensus 193 v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~------~~~---~~~~Dt~~l~~~~~~~~~~~~L~~l 263 (342)
|+++|.-||+.|.. ..+..++.++ +.|+..|... .|. .+++|....+...+..+.-.+|..+
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 99999999988864 2333344444 6788888711 111 7789999888888887777899999
Q ss_pred HHHHhCCcCCCCCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 264 TRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 264 ~~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
++.+ |..+++.+|+|++||+.+++|+..+......
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 9999999999999999999999999877655
No 53
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.43 E-value=7.7e-14 Score=121.92 Aligned_cols=87 Identities=31% Similarity=0.563 Sum_probs=72.0
Q ss_pred CCcccccccccccCCHHHHHHHHhhhccCCCCC-ccccCccccCChhhhhhhc-----CCCcccCCCCCcccCCc-----
Q 019380 12 TARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL-----TGPLSKAHCSGIFSDRG----- 80 (342)
Q Consensus 12 ~~~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~-----~~~~~C~~C~k~f~~~~----- 80 (342)
.+.+.|+.|+|.|..-.+|..|.++ |+ .+ +|.+|||.|.+.+-|..|+ ++||.|+.|+|+|.+++
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirT--H~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAH 234 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRT--HT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAH 234 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhc--cC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHH
Confidence 5678888888888888888888888 66 33 7888888888888887777 56888888888888764
Q ss_pred -----------ccccccccCChhhHHHHHhhcC
Q 019380 81 -----------CNLCMNIFDSPSSLIKHKEACS 102 (342)
Q Consensus 81 -----------C~~C~k~F~~~~~L~~H~~~h~ 102 (342)
|+.|+|+|...+-|.+|.....
T Consensus 235 mQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~C 267 (279)
T KOG2462|consen 235 MQTHSDVKKHQCPRCGKSFALKSYLNKHSESAC 267 (279)
T ss_pred HHhhcCCccccCcchhhHHHHHHHHHHhhhhcc
Confidence 9999999999999999986544
No 54
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=99.40 E-value=3.1e-13 Score=116.50 Aligned_cols=167 Identities=17% Similarity=0.275 Sum_probs=125.9
Q ss_pred cceeccccccccc------CCCcccccceEEeecC-CCCe--EEeeecCCCC--CccccccccCCCCHhhhcCCCChHHH
Q 019380 125 KAVAMDCEMVGGG------SNGTLDLCARVCLVDE-DENV--IFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPLKEV 193 (342)
Q Consensus 125 ~~v~~D~Ettg~~------~~~~~~il~~v~vv~~-~~~~--~~~~lv~p~~--~i~~~~~~i~GIt~e~l~~~~~~~~v 193 (342)
=++++|.|+|--. ..+++|. ..|.+.+. .+.+ .|++||+|.. .+.++.+.+|||.++.|+.||+|.+|
T Consensus 57 YLliiDFEaTC~e~~~~~~~~EIIEf-P~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~~f~~v 135 (280)
T KOG0542|consen 57 YLLILDFEATCEEGNKPHYVQEIIEF-PAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAPTFPQV 135 (280)
T ss_pred eEEEEeeeeeccccCCCCcchheeec-ceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCCCHHHH
Confidence 3678999998532 3456666 45534333 4444 4999999974 57899999999999999999999999
Q ss_pred HHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhh-hcc-------ccCCC--cceeeccccccccccCCCCccHHHH
Q 019380 194 KDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLD-SLR-------MNYPD--HMLRDTAKYRPLMKTNLVSHSLKYL 263 (342)
Q Consensus 194 ~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~-~l~-------~~~~~--~~~~Dt~~l~~~~~~~~~~~~L~~l 263 (342)
+.+|..||...... ...++--+|..+- -|+. ||. +..|. +++||.-..++..+..+..-++..+
T Consensus 136 l~~f~~Wlr~~~~~-----~k~~~~Afvtdg~-wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it~m 209 (280)
T KOG0542|consen 136 LSEFDSWLRKDSLG-----DKNGKFAFVTDGD-WDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNITGM 209 (280)
T ss_pred HHHHHHHHHHhhcc-----cccCceEEEeCch-hhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCHHHH
Confidence 99999999655331 0013445555542 3333 333 55554 7889998888877666567889999
Q ss_pred HHHHhCCcCCCCCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 264 TRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 264 ~~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
.+++ |+.+.+.+|++++||+.+++|..++.+.+.+
T Consensus 210 Le~~-gL~f~Gr~HsGiDDa~Nia~I~~kM~~dg~~ 244 (280)
T KOG0542|consen 210 LEHY-GLQFEGRAHSGIDDARNIARIAQKMIRDGAE 244 (280)
T ss_pred HHHh-CCcccCCcccCchhHHHHHHHHHHHHhCCcE
Confidence 9999 9999988999999999999999999998765
No 55
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.14 E-value=4.1e-11 Score=118.23 Aligned_cols=37 Identities=22% Similarity=0.321 Sum_probs=34.5
Q ss_pred ccccccccCChhhHHHHHhhcCCCCCCCCcccccccc
Q 019380 81 CNLCMNIFDSPSSLIKHKEACSLSAPVPFKISGAIDE 117 (342)
Q Consensus 81 C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~c~~~~~ 117 (342)
|..||+.|...+.|..|+++|.+++|+.|..|+....
T Consensus 882 C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFt 918 (958)
T KOG1074|consen 882 CNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFT 918 (958)
T ss_pred hccchhcccchHHHHHhhhcCCCCCCccchhhhhhhh
Confidence 9999999999999999999999999999999876643
No 56
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.04 E-value=6.7e-11 Score=98.72 Aligned_cols=98 Identities=23% Similarity=0.330 Sum_probs=77.5
Q ss_pred CCCCCCcccccccccccCCHHHHHHHHhhhccCCCCC-ccccCccccCChhhhhhhc-----CCCcccCCCCCcccCCcc
Q 019380 8 PKRSTARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL-----TGPLSKAHCSGIFSDRGC 81 (342)
Q Consensus 8 ~~~~~~~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~-----~~~~~C~~C~k~f~~~~C 81 (342)
++++.-.|.|..|+|.|.-...|++|++- |+..+. -|.-||+.|...-.|++|+ .+||.|
T Consensus 111 sssd~d~ftCrvCgK~F~lQRmlnrh~kc--h~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc------------ 176 (267)
T KOG3576|consen 111 SSSDQDSFTCRVCGKKFGLQRMLNRHLKC--HSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKC------------ 176 (267)
T ss_pred CCCCCCeeeeehhhhhhhHHHHHHHHhhh--ccHHHHHHHhhccCcccchhhhhhhhccccCccccch------------
Confidence 45567789999999999999999999999 887766 8999999999999999998 346655
Q ss_pred cccccccCChhhHHHHHhhcCC-----------CCCCCCcccccccccc
Q 019380 82 NLCMNIFDSPSSLIKHKEACSL-----------SAPVPFKISGAIDEKR 119 (342)
Q Consensus 82 ~~C~k~F~~~~~L~~H~~~h~~-----------~~~~~~~~c~~~~~~~ 119 (342)
..|+|+|+++.+|..|.+.-|| .+.+.|+.||.+...+
T Consensus 177 ~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~ 225 (267)
T KOG3576|consen 177 SLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERP 225 (267)
T ss_pred hhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCCh
Confidence 6677777777777777765443 3455677777776644
No 57
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.01 E-value=1.3e-10 Score=113.08 Aligned_cols=104 Identities=21% Similarity=0.295 Sum_probs=84.7
Q ss_pred cccccccccccCCHHHHHHHHhhhccCCCCC--ccccCccccCChhhhhhhcCCCccc---------CCCCCcccCCccc
Q 019380 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQP--KCAVCQKLSKSFESLREHLTGPLSK---------AHCSGIFSDRGCN 82 (342)
Q Consensus 14 ~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~--~C~~C~~~f~~~~~l~~H~~~~~~C---------~~C~k~f~~~~C~ 82 (342)
...|+.|.+++.+-..|+.|.+.. |....+ .|..|.+.|.....|.+|+.-..+| ..|.+.| +|+
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 356999999999999999999864 443333 8999999999999999999333333 2233333 699
Q ss_pred ccccccCChhhHHHHHhhcCCCCCCCCcccccccccccC
Q 019380 83 LCMNIFDSPSSLIKHKEACSLSAPVPFKISGAIDEKRTC 121 (342)
Q Consensus 83 ~C~k~F~~~~~L~~H~~~h~~~~~~~~~~c~~~~~~~~~ 121 (342)
+|||.|+.+.+|+.|.|+|.|++||.|+.|++.....+.
T Consensus 286 ECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGS 324 (1007)
T KOG3623|consen 286 ECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGS 324 (1007)
T ss_pred ccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCc
Confidence 999999999999999999999999999999988765554
No 58
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.01 E-value=2e-10 Score=113.52 Aligned_cols=48 Identities=31% Similarity=0.642 Sum_probs=46.2
Q ss_pred cccccccccccCCHHHHHHHHhhhccCCCCC-ccccCccccCChhhhhhhc
Q 019380 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL 63 (342)
Q Consensus 14 ~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~ 63 (342)
+++|..|.|.|...+.|+.|.+. ||+++| +|.+||..|.++.+|+.|.
T Consensus 353 khkCr~CakvfgS~SaLqiHlRS--HTGERPfqCnvCG~~FSTkGNLKvH~ 401 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRS--HTGERPFQCNVCGNRFSTKGNLKVHF 401 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhc--cCCCCCeeecccccccccccceeeee
Confidence 47899999999999999999999 999999 9999999999999999997
No 59
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.98 E-value=1.9e-10 Score=111.91 Aligned_cols=81 Identities=28% Similarity=0.534 Sum_probs=70.1
Q ss_pred CCCCCCCcccccccccccCCHHHHHHHHhhhccCCCCC-ccccCccccCChhhhhhhc---CCCcccCCCCCcccCCccc
Q 019380 7 LPKRSTARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL---TGPLSKAHCSGIFSDRGCN 82 (342)
Q Consensus 7 ~~~~~~~~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~---~~~~~C~~C~k~f~~~~C~ 82 (342)
+-.+++.+|.|+.|+|.|...+.|.+|.-. |+|++| +|.+|.|.|+.+..|..|+ .|.+++ .|.
T Consensus 887 ~~kte~gmyaCDqCDK~FqKqSSLaRHKYE--HsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPf----------QCd 954 (1007)
T KOG3623|consen 887 HAKTEDGMYACDQCDKAFQKQSSLARHKYE--HSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPF----------QCD 954 (1007)
T ss_pred cccCccccchHHHHHHHHHhhHHHHHhhhh--hcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcc----------hhh
Confidence 445788999999999999999999999999 999999 9999999999999999998 343333 357
Q ss_pred ccccccCChhhHHHHHh
Q 019380 83 LCMNIFDSPSSLIKHKE 99 (342)
Q Consensus 83 ~C~k~F~~~~~L~~H~~ 99 (342)
.|+|.|+.+.++..||.
T Consensus 955 KClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 955 KCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred hhhhhcccccchHhhhc
Confidence 78888888888888883
No 60
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.98 E-value=1.7e-10 Score=103.82 Aligned_cols=103 Identities=28% Similarity=0.444 Sum_probs=90.3
Q ss_pred CCCc-ccc--cccccccCCHHHHHHHHhhhccCCCCC-ccccCccccCChhhhhhhc-------CCCcccCCCCCcccCC
Q 019380 11 STAR-HKC--VACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL-------TGPLSKAHCSGIFSDR 79 (342)
Q Consensus 11 ~~~~-~~C--~~C~k~f~~~~~L~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~-------~~~~~C~~C~k~f~~~ 79 (342)
.+|| +.| ..|-+.|..++.|.+|.+. |++++- .|+.||..|+++..|-.|. ..+|.|..|.|+|...
T Consensus 173 D~~pv~~C~W~~Ct~~~~~k~~LreH~r~--Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTe 250 (467)
T KOG3608|consen 173 DERPVTMCNWAMCTKHMGNKYRLREHIRT--HSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATE 250 (467)
T ss_pred CCCceeeccchhhhhhhccHHHHHHHHHh--cCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHH
Confidence 4444 677 6799999999999999999 999998 9999999999999999997 5689999999999875
Q ss_pred c--------------ccccccccCChhhHHHHHh-hcCCCCCCCCcccccc
Q 019380 80 G--------------CNLCMNIFDSPSSLIKHKE-ACSLSAPVPFKISGAI 115 (342)
Q Consensus 80 ~--------------C~~C~k~F~~~~~L~~H~~-~h~~~~~~~~~~c~~~ 115 (342)
. |+.|+-+...+++|++|++ .|...+|++|+.|...
T Consensus 251 klL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~ 301 (467)
T KOG3608|consen 251 KLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTR 301 (467)
T ss_pred HHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhh
Confidence 3 9999999999999999998 5777889888876543
No 61
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=98.96 E-value=7.6e-10 Score=89.53 Aligned_cols=153 Identities=18% Similarity=0.287 Sum_probs=107.3
Q ss_pred CCCcceeccccccccc--CCCcccccceEEeecCCCCeEE---eeecCCCC----Ccccccccc---CCCCHhhhcCCCC
Q 019380 122 RGPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENVIF---HTYVQPQL----PVTNYRYEV---TGLTEEDIKNAMP 189 (342)
Q Consensus 122 ~~~~~v~~D~Ettg~~--~~~~~~il~~v~vv~~~~~~~~---~~lv~p~~----~i~~~~~~i---~GIt~e~l~~~~~ 189 (342)
...+.|-+||||||++ .+.++|+ +..|.|.+-.++- ...|.... .+.+++++- +|+++.-.+...+
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 4567899999999998 4455655 5555566666642 33333332 344555544 5777777777889
Q ss_pred hHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhccccCCC------cceeeccccccccccCCCCccHHHH
Q 019380 190 LKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPD------HMLRDTAKYRPLMKTNLVSHSLKYL 263 (342)
Q Consensus 190 ~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~------~~~~Dt~~l~~~~~~~~~~~~L~~l 263 (342)
..+|..++++||.... +.+-.+++|..+.-|..||...+|. .+.+|++ +|++|
T Consensus 82 ~~~aE~~~l~flkkwv--------p~~~spicGNSI~qDRrFl~r~MP~Le~yfHYR~lDVS-------------TlKEL 140 (184)
T COG1949 82 EAEAEAQTLDFLKKWV--------PKGVSPICGNSIAQDRRFLFRYMPKLEAYFHYRYLDVS-------------TLKEL 140 (184)
T ss_pred HHHHHHHHHHHHHHhC--------CCCCCCCccchhhHHHHHHHHHhhhHHHHhhhHhhhHH-------------HHHHH
Confidence 9999999999995432 2366899999999999999977775 3445554 35555
Q ss_pred HHHH-----hCCcCCCCCCCcHHHHHHHHHHHHHHHhhhh
Q 019380 264 TRTY-----LGYDIQSGVHDPYEDCVSVMRLYKRFRRQDH 298 (342)
Q Consensus 264 ~~~~-----~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~~ 298 (342)
|++. .|.. .++.|+|++|.+-...=+..+++.+-
T Consensus 141 a~RW~P~i~~~~~-K~~~H~Al~DI~ESI~EL~~YR~~f~ 179 (184)
T COG1949 141 ARRWNPEILAGFK-KGGTHRALDDIRESIAELRYYREHFL 179 (184)
T ss_pred HHhhCcHhhhccc-cccchhHHHHHHHHHHHHHHHHHHhc
Confidence 5443 2433 56699999999999998888888763
No 62
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=98.94 E-value=1.3e-09 Score=89.03 Aligned_cols=155 Identities=17% Similarity=0.253 Sum_probs=109.0
Q ss_pred CCCcceeccccccccc--CCCcccccceEEeecCCCCeE---EeeecCCCCCcc----cccccc---CCCCHhhhcCCCC
Q 019380 122 RGPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENVI---FHTYVQPQLPVT----NYRYEV---TGLTEEDIKNAMP 189 (342)
Q Consensus 122 ~~~~~v~~D~Ettg~~--~~~~~~il~~v~vv~~~~~~~---~~~lv~p~~~i~----~~~~~i---~GIt~e~l~~~~~ 189 (342)
-..++|.+||||||++ .+.++|+ +..|.|++-.++ ++..|+.+.++. ++...- +|+|..-++...+
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 6667766 555556655553 677777664433 344433 5788888889999
Q ss_pred hHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhccccCCC------cceeeccc---cccccccCCCCccH
Q 019380 190 LKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPD------HMLRDTAK---YRPLMKTNLVSHSL 260 (342)
Q Consensus 190 ~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~~------~~~~Dt~~---l~~~~~~~~~~~~L 260 (342)
+++|..++++||.-+ .+ .+..+|.|..+..|..||...+|. .+++|+.. |+++++|....
T Consensus 102 l~~aEnevl~yikk~------ip--~~~~~laGNSV~~DrlFl~k~mPk~~~~lhyrivDVStIkeL~~Rw~P~~~~--- 170 (208)
T KOG3242|consen 102 LADAENEVLEYIKKH------IP--KGKCPLAGNSVYMDRLFLKKYMPKLIKHLHYRIVDVSTIKELARRWYPDIKA--- 170 (208)
T ss_pred HHHHHHHHHHHHHHh------CC--CCCCCccCcchhhHHHHHHHHhHHHHHhcceeeeeHHHHHHHHHHhCchhhc---
Confidence 999999999999433 22 366789999999999999966553 66777764 44444443110
Q ss_pred HHHHHHHhCCcCCCCCCCcHHHHHHHHHHHHHHHhhh
Q 019380 261 KYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQD 297 (342)
Q Consensus 261 ~~l~~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~ 297 (342)
+ -+-....|||++|.+-...-++.+++.+
T Consensus 171 ------~--aPkK~~~HrAldDI~ESI~ELq~Yr~ni 199 (208)
T KOG3242|consen 171 ------R--APKKKATHRALDDIRESIKELQYYRENI 199 (208)
T ss_pred ------c--CcccccccchHHHHHHHHHHHHHHHHHh
Confidence 1 1112348999999999999888888776
No 63
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=98.84 E-value=1.2e-08 Score=93.37 Aligned_cols=171 Identities=18% Similarity=0.220 Sum_probs=119.9
Q ss_pred CCCCcceecccccccccCC--CcccccceEEeecCCCCe---EEeeecCCCCCc--cccccccCCCCHhhhc-CCCChHH
Q 019380 121 CRGPKAVAMDCEMVGGGSN--GTLDLCARVCLVDEDENV---IFHTYVQPQLPV--TNYRYEVTGLTEEDIK-NAMPLKE 192 (342)
Q Consensus 121 ~~~~~~v~~D~Ettg~~~~--~~~~il~~v~vv~~~~~~---~~~~lv~p~~~i--~~~~~~i~GIt~e~l~-~~~~~~~ 192 (342)
.....|..+|-||.|..+. +..+. +.+.- |.+-.+ ...-|++|.... .+.+.-|||||++... ++.+..+
T Consensus 6 ~~~~tF~~yDYETfG~~Pa~DRPaQF-AgiRT-D~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~ 83 (475)
T COG2925 6 TKQPTFLFYDYETFGVHPALDRPAQF-AGIRT-DIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAA 83 (475)
T ss_pred CCCCcEEEEehhhcCCCcccccchhh-heeec-cccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHH
Confidence 3455688999999998743 33333 33332 223333 367788887543 2567899999998875 6788888
Q ss_pred HHHHHHHHHhcCCCccccccCCCCCeEEEeeC-chhhhhhcccc------------CCC----cceeecccccccccc--
Q 019380 193 VKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLRMN------------YPD----HMLRDTAKYRPLMKT-- 253 (342)
Q Consensus 193 v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~-~~~D~~~l~~~------------~~~----~~~~Dt~~l~~~~~~-- 253 (342)
...+|..-+ .-.++.++|+| ++||=.+-+.. +.. ..++|.+...-.+.|
T Consensus 84 F~~~I~~~l------------s~P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeG 151 (475)
T COG2925 84 FAARIHAEL------------TQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEG 151 (475)
T ss_pred HHHHHHHHh------------CCCCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCccc
Confidence 888888887 23789999986 88887776611 111 223444432222222
Q ss_pred --------CCCCccHHHHHHHHhCCcCCCCCCCcHHHHHHHHHHHHHHHhhhhhhhhhccCC
Q 019380 254 --------NLVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDHQVEEIGNQN 307 (342)
Q Consensus 254 --------~~~~~~L~~l~~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~~~~~~~~~~~ 307 (342)
+..+.+|+.|...- |+. .+++|+|++|++||..+.+.++.+-..++++-++.
T Consensus 152 I~Wp~n~dG~pSFkLEhLt~AN-gie-H~nAHdAmsDVyATIamAklvk~~QPrLfdy~f~~ 211 (475)
T COG2925 152 INWPENDDGLPSFKLEHLTKAN-GIE-HSNAHDAMSDVYATIAMAKLVKTAQPRLFDYLFQL 211 (475)
T ss_pred CCCCcCCCCCcchhhHHHhhcc-ccc-cchhhHHHHHHHHHHHHHHHHHhhCcHHHHHHHHh
Confidence 44578899999988 888 77799999999999999999998888888886644
No 64
>PHA02768 hypothetical protein; Provisional
Probab=98.67 E-value=1.3e-08 Score=67.67 Aligned_cols=44 Identities=18% Similarity=0.435 Sum_probs=38.4
Q ss_pred cccccccccccCCHHHHHHHHhhhccCCCCCccccCccccCChhhhh
Q 019380 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLR 60 (342)
Q Consensus 14 ~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~ 60 (342)
-|+|+.||+.|++..+|..|+++ |+ ..++|..|++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~--H~-k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK--HN-TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh--cC-CcccCCcccceecccceeE
Confidence 58999999999999999999999 87 3338999999999887764
No 65
>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=98.66 E-value=6.9e-08 Score=83.89 Aligned_cols=124 Identities=15% Similarity=0.151 Sum_probs=84.6
Q ss_pred ceecccccccc----c--CCCcccccceEEeecC-CCCeE-EeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHH
Q 019380 126 AVAMDCEMVGG----G--SNGTLDLCARVCLVDE-DENVI-FHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKI 197 (342)
Q Consensus 126 ~v~~D~Ettg~----~--~~~~~~il~~v~vv~~-~~~~~-~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~ 197 (342)
.++||.||+|. + .+.+ ..++++.. +|... +.....+...... ||+..++...++..+++.+|
T Consensus 1 v~~~DIEt~~~~~~p~~~~d~I----i~I~~~~~~~g~~~~~~~~~~~~~~~~~------~i~~~~v~~~~~E~~lL~~f 70 (199)
T cd05160 1 VLSFDIETTPPVGGPEPDRDPI----ICITYADSFDGVKVVFLLKTSTVGDDIE------FIDGIEVEYFADEKELLKRF 70 (199)
T ss_pred CccEEEeecCCCCCcCCCCCCE----EEEEEEEeeCCceeeEEEeecccCCcCC------CCCCceEEEeCCHHHHHHHH
Confidence 36799999986 2 2333 34444433 55543 3222222211111 88888999999999999999
Q ss_pred HHHHhcCCCccccccCCCCCeEEEeeCc-hhhhhhcc-------ccCC----------------------Ccceeecccc
Q 019380 198 LEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-------MNYP----------------------DHMLRDTAKY 247 (342)
Q Consensus 198 ~~~l~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-------~~~~----------------------~~~~~Dt~~l 247 (342)
.+++.+. ...+|||||+ .||+.+|. +... -..++|+..+
T Consensus 71 ~~~i~~~-----------dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~ 139 (199)
T cd05160 71 FDIIREY-----------DPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAA 139 (199)
T ss_pred HHHHHhc-----------CCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHH
Confidence 9999321 1249999999 89999988 1120 1246888888
Q ss_pred ccccccCCCCccHHHHHHHHhCCc
Q 019380 248 RPLMKTNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 248 ~~~~~~~~~~~~L~~l~~~~~~~~ 271 (342)
.+...+ ..+|+|+.+|+.++|..
T Consensus 140 ~r~~~~-l~sy~L~~v~~~~l~~~ 162 (199)
T cd05160 140 YKRDFK-LKSYTLDAVAEELLGEG 162 (199)
T ss_pred HHHhcC-cccCCHHHHHHHHhCCC
Confidence 877665 67899999999997765
No 66
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.63 E-value=1.2e-08 Score=92.05 Aligned_cols=102 Identities=21% Similarity=0.397 Sum_probs=75.1
Q ss_pred CCcccccccccccCCHHHHHHHHhhhccCCCCCccccCccccCChhhhhhhc------CCCcccCCCCCcccCCc-----
Q 019380 12 TARHKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHL------TGPLSKAHCSGIFSDRG----- 80 (342)
Q Consensus 12 ~~~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~------~~~~~C~~C~k~f~~~~----- 80 (342)
.-+|.|..|.|.|.++..|..|+.. |- .-++|+.|.......++|.+|+ .++|+|+.|+++|.+.+
T Consensus 235 ~n~fqC~~C~KrFaTeklL~~Hv~r--Hv-n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH 311 (467)
T KOG3608|consen 235 TNSFQCAQCFKRFATEKLLKSHVVR--HV-NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKH 311 (467)
T ss_pred CCchHHHHHHHHHhHHHHHHHHHHH--hh-hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHH
Confidence 3478888888888888888888877 43 2347888888888888888887 56888888888887643
Q ss_pred ----------ccc--cccccCChhhHHHHHhhcC-CCCC--CCCccccccc
Q 019380 81 ----------CNL--CMNIFDSPSSLIKHKEACS-LSAP--VPFKISGAID 116 (342)
Q Consensus 81 ----------C~~--C~k~F~~~~~L~~H~~~h~-~~~~--~~~~~c~~~~ 116 (342)
|+. |..+|++...+++|++.++ |.+| |.|-.|.+..
T Consensus 312 ~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~f 362 (467)
T KOG3608|consen 312 VQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFF 362 (467)
T ss_pred HHhccccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhh
Confidence 766 8888888888888887655 4444 4566655443
No 67
>PHA00733 hypothetical protein
Probab=98.59 E-value=4.2e-08 Score=78.68 Aligned_cols=83 Identities=19% Similarity=0.215 Sum_probs=64.9
Q ss_pred CCCcccccccccccCCHHHHHHH--Hhh--hccCCCCC-ccccCccccCChhhhhhhcCC-CcccCCCCCcccCCccccc
Q 019380 11 STARHKCVACYKQFKRKDHLIEH--MKI--SYHSVHQP-KCAVCQKLSKSFESLREHLTG-PLSKAHCSGIFSDRGCNLC 84 (342)
Q Consensus 11 ~~~~~~C~~C~k~f~~~~~L~~H--~~~--~~H~~~~~-~C~~C~~~f~~~~~l~~H~~~-~~~C~~C~k~f~~~~C~~C 84 (342)
+.+++.|.+|.+.|..+..|..| ++. ..|+ .++ .|..|++.|.+..+|..|+.. ..+ ..|+.|
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~-~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~----------~~C~~C 105 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKA-VSPYVCPLCLMPFSSSVSLKQHIRYTEHS----------KVCPVC 105 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCC-CCCccCCCCCCcCCCHHHHHHHHhcCCcC----------ccCCCC
Confidence 68899999999999998887766 211 1134 444 999999999999999999831 111 157999
Q ss_pred ccccCChhhHHHHHhhcCCC
Q 019380 85 MNIFDSPSSLIKHKEACSLS 104 (342)
Q Consensus 85 ~k~F~~~~~L~~H~~~h~~~ 104 (342)
++.|....+|..|+...|+-
T Consensus 106 gK~F~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 106 GKEFRNTDSTLDHVCKKHNI 125 (128)
T ss_pred CCccCCHHHHHHHHHHhcCc
Confidence 99999999999999887753
No 68
>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=98.58 E-value=4.8e-07 Score=77.86 Aligned_cols=146 Identities=21% Similarity=0.210 Sum_probs=96.5
Q ss_pred CCcceecccccccccCCCcccccceEEeecCCCCeEEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHh
Q 019380 123 GPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILN 202 (342)
Q Consensus 123 ~~~~v~~D~Ettg~~~~~~~~il~~v~vv~~~~~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~l~ 202 (342)
..+++++|+|++|...... .+ ..+.+....+...+ .-+.+ +. ..+++.+.+++..|.+++.
T Consensus 4 ~~~~~a~d~e~~~~~~~~~-~i-~~l~~~~~~~~~~~-~~~~~--------~~--------~~~~~~~~~~~~~l~~~l~ 64 (193)
T cd06139 4 KAKVFAFDTETTSLDPMQA-EL-VGISFAVEPGEAYY-IPLGH--------DY--------GGEQLPREEVLAALKPLLE 64 (193)
T ss_pred cCCeEEEEeecCCCCcCCC-eE-EEEEEEcCCCCEEE-EecCC--------Cc--------cccCCCHHHHHHHHHHHHh
Confidence 3567899999998753111 22 34445433332322 10111 00 1145678889999999992
Q ss_pred cCCCccccccCCCCCeEEEeeCchhhhhhccccC--CCcceeeccccccccccCCCCccHHHHHHHHhCCcCCC------
Q 019380 203 NGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY--PDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQS------ 274 (342)
Q Consensus 203 ~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~--~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~------ 274 (342)
+.+.++|+||+.||+.+|.... ....+.||+.++..+.|....++|++++..|+|..+..
T Consensus 65 ------------~~~~~~v~hn~k~d~~~l~~~gi~~~~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~ 132 (193)
T cd06139 65 ------------DPSIKKVGQNLKFDLHVLANHGIELRGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLVG 132 (193)
T ss_pred ------------CCCCcEEeeccHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHHHcC
Confidence 2345899999999999997221 12457999999998888654579999999997754110
Q ss_pred ---------------CCCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 275 ---------------GVHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 275 ---------------~~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
..|.|..||.++..|+..+..+.++
T Consensus 133 k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 133 KGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred CCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 1235788899999999999887643
No 69
>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=98.52 E-value=7.3e-07 Score=75.37 Aligned_cols=92 Identities=29% Similarity=0.364 Sum_probs=65.6
Q ss_pred HHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhccc--cCCCcceeeccccccccccCCCCccHHHHHHHHhC-
Q 019380 193 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM--NYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLG- 269 (342)
Q Consensus 193 v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~--~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~- 269 (342)
+.+.|.+++ ++.+.+.||||+.||+.+|.. ......++|++.....+.+. .+++|++|+..|+|
T Consensus 65 ~~~~l~~ll------------~~~~i~kv~~n~~~D~~~L~~~~~i~~~~~~D~~l~~~~l~~~-~~~~L~~L~~~~l~~ 131 (176)
T PF01612_consen 65 ILDALKELL------------EDPNIIKVGHNAKFDLKWLYRSFGIDLKNVFDTMLAAYLLDPT-RSYSLKDLAEEYLGN 131 (176)
T ss_dssp HHHHHHHHH------------TTTTSEEEESSHHHHHHHHHHHHTS--SSEEEHHHHHHHTTTS-TTSSHHHHHHHHHSE
T ss_pred hHHHHHHHH------------hCCCccEEEEEEechHHHHHHHhccccCCccchhhhhhccccc-ccccHHHHHHHHhhh
Confidence 777788888 346789999999999999994 23335589995444444443 33999999999999
Q ss_pred CcCCCC----CC---C---------cHHHHHHHHHHHHHHHhhh
Q 019380 270 YDIQSG----VH---D---------PYEDCVSVMRLYKRFRRQD 297 (342)
Q Consensus 270 ~~~~~~----~H---~---------A~~Da~~t~~l~~~~~~~~ 297 (342)
...... .- + |..||..+.+||..+..+.
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 333111 11 2 5569999999999998764
No 70
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.41 E-value=4.2e-08 Score=82.18 Aligned_cols=95 Identities=25% Similarity=0.335 Sum_probs=73.3
Q ss_pred CCCcccccccccccCCHHHHHHHHhhhccCCCCC-ccccCccccCChhhhhhhcCC----CcccCCCCCcccCCcccccc
Q 019380 11 STARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHLTG----PLSKAHCSGIFSDRGCNLCM 85 (342)
Q Consensus 11 ~~~~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~~~----~~~C~~C~k~f~~~~C~~C~ 85 (342)
.-|.|.|..|||.|...-.|++|+++ |++.+| +|..|+++|...-+|..|..+ +..+-+=.++-.-.-|+.||
T Consensus 142 ~vkr~lct~cgkgfndtfdlkrh~rt--htgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg 219 (267)
T KOG3576|consen 142 DVKRHLCTFCGKGFNDTFDLKRHTRT--HTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCG 219 (267)
T ss_pred HHHHHHHhhccCcccchhhhhhhhcc--ccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccC
Confidence 44689999999999999999999999 999999 999999999999999999721 11110000111111388999
Q ss_pred cccCChhhHHHHHhhcCCCCCC
Q 019380 86 NIFDSPSSLIKHKEACSLSAPV 107 (342)
Q Consensus 86 k~F~~~~~L~~H~~~h~~~~~~ 107 (342)
.+-.....+..|.+.|+...|.
T Consensus 220 ~t~~~~e~~~~h~~~~hp~Spa 241 (267)
T KOG3576|consen 220 YTSERPEVYYLHLKLHHPFSPA 241 (267)
T ss_pred CCCCChhHHHHHHHhcCCCCHH
Confidence 8888888999999999866554
No 71
>PHA02768 hypothetical protein; Provisional
Probab=98.21 E-value=1.1e-06 Score=58.51 Aligned_cols=36 Identities=19% Similarity=0.362 Sum_probs=31.9
Q ss_pred cccccccccCChhhHHHHHhhcCCCCCCCCcccccccc
Q 019380 80 GCNLCMNIFDSPSSLIKHKEACSLSAPVPFKISGAIDE 117 (342)
Q Consensus 80 ~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~c~~~~~ 117 (342)
.|+.||+.|+..++|..|+++|+ ++++|..|++...
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 58999999999999999999999 7889998887644
No 72
>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=98.14 E-value=8.6e-06 Score=62.08 Aligned_cols=30 Identities=40% Similarity=0.498 Sum_probs=22.8
Q ss_pred eEEEeeCchhhhhhcccc-------CC--Ccceeecccc
Q 019380 218 RLLVGHGLEHDLDSLRMN-------YP--DHMLRDTAKY 247 (342)
Q Consensus 218 ~~lvgh~~~~D~~~l~~~-------~~--~~~~~Dt~~l 247 (342)
.++||||+.||+.||+.. .| ..+++||+.+
T Consensus 45 ~v~V~hn~~fD~~fL~~~~~~~~~~~p~~~~~~lDT~~l 83 (96)
T cd06125 45 AILVGHNGSFDLPFLNNRCAELGLKYPLLAGSWIDTIKL 83 (96)
T ss_pred CEEEEeCcHHhHHHHHHHHHHcCCCCCCcCCcEEEehHH
Confidence 699999999999998822 22 2567888866
No 73
>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=98.14 E-value=1.7e-05 Score=68.48 Aligned_cols=81 Identities=17% Similarity=0.323 Sum_probs=61.9
Q ss_pred CCCeEEEeeCchhhhhhccccCC--------CcceeeccccccccccC----------CCCccHHHHHHHHhCCcCCCC-
Q 019380 215 GKARLLVGHGLEHDLDSLRMNYP--------DHMLRDTAKYRPLMKTN----------LVSHSLKYLTRTYLGYDIQSG- 275 (342)
Q Consensus 215 ~~~~~lvgh~~~~D~~~l~~~~~--------~~~~~Dt~~l~~~~~~~----------~~~~~L~~l~~~~~~~~~~~~- 275 (342)
+.+.+-|||++.+|+.+|...++ ...++|+..++..+... ...+||+.|++.++|..+++.
T Consensus 80 d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~~l~K~~ 159 (193)
T cd06146 80 DPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLDKSE 159 (193)
T ss_pred CCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCCCcCccc
Confidence 35567799999999999984332 24689998877654321 357899999999999888755
Q ss_pred --------------CCCcHHHHHHHHHHHHHHHh
Q 019380 276 --------------VHDPYEDCVSVMRLYKRFRR 295 (342)
Q Consensus 276 --------------~H~A~~Da~~t~~l~~~~~~ 295 (342)
-+-|..||..+..||.++.+
T Consensus 160 q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~~ 193 (193)
T cd06146 160 QCSNWERRPLREEQILYAALDAYCLLEVFDKLLE 193 (193)
T ss_pred ccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 14477899999999998863
No 74
>PRK05755 DNA polymerase I; Provisional
Probab=98.13 E-value=9.7e-06 Score=85.58 Aligned_cols=137 Identities=23% Similarity=0.241 Sum_probs=93.6
Q ss_pred CCcceecccccccccCCCcccccceEEeecCCCCeEEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHh
Q 019380 123 GPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILN 202 (342)
Q Consensus 123 ~~~~v~~D~Ettg~~~~~~~~il~~v~vv~~~~~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~l~ 202 (342)
...++++|+||+|..+.... + ..+.+...+|...+ + |. +++. .++++.|.+++
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 35688999999997532221 2 33333324443221 1 11 1111 16788899999
Q ss_pred cCCCccccccCCCCCeEEEeeCchhhhhhccc-cCC-CcceeeccccccccccCCCCccHHHHHHHHhCCcCCC------
Q 019380 203 NGESTGRLMLDDGKARLLVGHGLEHDLDSLRM-NYP-DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQS------ 274 (342)
Q Consensus 203 ~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~-~~~-~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~------ 274 (342)
++...++|+||+.||+.+|.. ..+ ...++||+..+..+.+... ++|++|+..|+|.....
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 335567899999999999982 121 2568999998888887653 99999999998776310
Q ss_pred ------------CCCCcHHHHHHHHHHHHHHHhhhh
Q 019380 275 ------------GVHDPYEDCVSVMRLYKRFRRQDH 298 (342)
Q Consensus 275 ------------~~H~A~~Da~~t~~l~~~~~~~~~ 298 (342)
..|.|..||..++.||.++.++..
T Consensus 435 k~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~L~ 470 (880)
T PRK05755 435 KQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKLL 470 (880)
T ss_pred CCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 136799999999999999998753
No 75
>PHA00733 hypothetical protein
Probab=98.11 E-value=2.9e-06 Score=68.01 Aligned_cols=53 Identities=23% Similarity=0.486 Sum_probs=47.1
Q ss_pred CCCCCCcccccccccccCCHHHHHHHHhhhccCCCCCccccCccccCChhhhhhhc
Q 019380 8 PKRSTARHKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHL 63 (342)
Q Consensus 8 ~~~~~~~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~ 63 (342)
++..++||.|+.|++.|.+...|..|++. |+ ..+.|..|++.|.....|..|+
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 45678999999999999999999999997 63 2349999999999999999997
No 76
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.04 E-value=6.2e-06 Score=81.06 Aligned_cols=97 Identities=19% Similarity=0.392 Sum_probs=65.2
Q ss_pred CCCcccccccccccCCHHHHHHHHhhhccCCCCCccccCccccCChhhhhhhc-----CCCcccCCCCCcccCCcccccc
Q 019380 11 STARHKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHL-----TGPLSKAHCSGIFSDRGCNLCM 85 (342)
Q Consensus 11 ~~~~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~-----~~~~~C~~C~k~f~~~~C~~C~ 85 (342)
.++.+.|+.|++.|. ...|..|+++ |. ....|+ |++.+ ....|..|+ .+++.|+.|++.|..-....
T Consensus 450 l~~H~~C~~Cgk~f~-~s~LekH~~~--~H-kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~-- 521 (567)
T PLN03086 450 AKNHVHCEKCGQAFQ-QGEMEKHMKV--FH-EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAM-- 521 (567)
T ss_pred cccCccCCCCCCccc-hHHHHHHHHh--cC-CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCcccc--
Confidence 356689999999996 6789999999 53 333899 99765 567899997 34555544444432100000
Q ss_pred ccc-CChhhHHHHHhhcCCCCCCCCcccccccc
Q 019380 86 NIF-DSPSSLIKHKEACSLSAPVPFKISGAIDE 117 (342)
Q Consensus 86 k~F-~~~~~L~~H~~~h~~~~~~~~~~c~~~~~ 117 (342)
.| ...+.|..|...+ |.+++.|..|++...
T Consensus 522 -d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vr 552 (567)
T PLN03086 522 -DVRDRLRGMSEHESIC-GSRTAPCDSCGRSVM 552 (567)
T ss_pred -chhhhhhhHHHHHHhc-CCcceEccccCCeee
Confidence 00 0245789998885 899999999987644
No 77
>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=97.89 E-value=7e-05 Score=64.84 Aligned_cols=122 Identities=16% Similarity=0.172 Sum_probs=73.8
Q ss_pred CCcceeccccccccc--CCCcccccceEEeecCCCCeEEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHH
Q 019380 123 GPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 200 (342)
Q Consensus 123 ~~~~v~~D~Ettg~~--~~~~~~il~~v~vv~~~~~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~ 200 (342)
.-++++||+||++.+ ++.....+..++++...+..++.. .+. ....+.......+++.+|.++
T Consensus 2 ~l~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~~--~~~-------------~~~~v~~~~~E~~lL~~F~~~ 66 (195)
T cd05780 2 DLKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVITW--KKF-------------DLPFVEVVKTEKEMIKRFIEI 66 (195)
T ss_pred CceEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEEe--cCC-------------CCCeEEEeCCHHHHHHHHHHH
Confidence 346789999998421 122222224555554444332211 110 111334456678999999999
Q ss_pred HhcCCCccccccCCCCCeEEEeeCch-hhhhhcc-------ccCCC----------------------cceeeccccccc
Q 019380 201 LNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLR-------MNYPD----------------------HMLRDTAKYRPL 250 (342)
Q Consensus 201 l~~~~~~~~~~~~~~~~~~lvgh~~~-~D~~~l~-------~~~~~----------------------~~~~Dt~~l~~~ 250 (342)
+.+. .-.+|||||.. ||+.+|. +..+. ...+|+..+.+.
T Consensus 67 i~~~-----------dpdiivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~ 135 (195)
T cd05780 67 VKEK-----------DPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARR 135 (195)
T ss_pred HHHc-----------CCCEEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHh
Confidence 9432 13599999965 8999987 22111 235676666655
Q ss_pred cccCCCCccHHHHHHHHhCCc
Q 019380 251 MKTNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 251 ~~~~~~~~~L~~l~~~~~~~~ 271 (342)
.. ...+++|+.+|+.+||.+
T Consensus 136 ~~-~l~sy~L~~v~~~~Lg~~ 155 (195)
T cd05780 136 TL-NLTRYTLERVYEELFGIE 155 (195)
T ss_pred hC-CCCcCcHHHHHHHHhCCC
Confidence 33 456899999999999987
No 78
>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=97.84 E-value=9e-05 Score=62.54 Aligned_cols=79 Identities=19% Similarity=0.220 Sum_probs=61.5
Q ss_pred CCeEEEeeCchhhhhhcccc--CCCcceeeccccccccccCCCCccHHHHHHHHhCCcCC--CC---------------C
Q 019380 216 KARLLVGHGLEHDLDSLRMN--YPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQ--SG---------------V 276 (342)
Q Consensus 216 ~~~~lvgh~~~~D~~~l~~~--~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~--~~---------------~ 276 (342)
.+.+.|||++.+|+.+|... .....++|++.++..+.+.....+|++|+..++|..+. .. -
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 56678999999999998622 22244689999888887754456999999999999886 22 1
Q ss_pred CCcHHHHHHHHHHHHHHH
Q 019380 277 HDPYEDCVSVMRLYKRFR 294 (342)
Q Consensus 277 H~A~~Da~~t~~l~~~~~ 294 (342)
+-|..||..+..||.++.
T Consensus 152 ~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 152 LYAATDAYASLELYRKLL 169 (170)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 457889999999998875
No 79
>PHA00732 hypothetical protein
Probab=97.81 E-value=1.5e-05 Score=58.07 Aligned_cols=44 Identities=30% Similarity=0.519 Sum_probs=36.2
Q ss_pred cccccccccccCCHHHHHHHHhhhccCCCCCccccCccccCChhhhhhhc
Q 019380 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHL 63 (342)
Q Consensus 14 ~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~ 63 (342)
||+|+.|++.|.+...|..|++.+ |++. .|+.|++.|. ++..|.
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 689999999999999999999842 5532 7999999887 466776
No 80
>PHA00616 hypothetical protein
Probab=97.77 E-value=1e-05 Score=51.36 Aligned_cols=32 Identities=19% Similarity=0.364 Sum_probs=29.5
Q ss_pred cccccccccCChhhHHHHHhhcCCCCCCCCcc
Q 019380 80 GCNLCMNIFDSPSSLIKHKEACSLSAPVPFKI 111 (342)
Q Consensus 80 ~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~ 111 (342)
.|+.||+.|.+++.|..|++.|||++++.++-
T Consensus 3 qC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 3 QCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred ccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 48999999999999999999999999988764
No 81
>PHA00616 hypothetical protein
Probab=97.75 E-value=1.5e-05 Score=50.57 Aligned_cols=33 Identities=21% Similarity=0.410 Sum_probs=29.0
Q ss_pred cccccccccccCCHHHHHHHHhhhccCCCCC-cccc
Q 019380 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAV 48 (342)
Q Consensus 14 ~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~-~C~~ 48 (342)
||+|+.||+.|.+++.|..|++. |+++++ .|..
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 79999999999999999999999 777766 6654
No 82
>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=0.00019 Score=60.04 Aligned_cols=78 Identities=23% Similarity=0.220 Sum_probs=59.4
Q ss_pred CCeEEEeeCchhhhhhccc--cCCCcceeeccccccccccCCCCccHHHHHHHHhCCcCCCC---------------CCC
Q 019380 216 KARLLVGHGLEHDLDSLRM--NYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSG---------------VHD 278 (342)
Q Consensus 216 ~~~~lvgh~~~~D~~~l~~--~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~---------------~H~ 278 (342)
.+.+.|||++..|+..|.. ......++|++..+..+.+. .+.+|+.|+..|+|..+++. -+-
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 5567799999999999863 23223468998877766553 45799999999999987544 145
Q ss_pred cHHHHHHHHHHHHHHH
Q 019380 279 PYEDCVSVMRLYKRFR 294 (342)
Q Consensus 279 A~~Da~~t~~l~~~~~ 294 (342)
|..||..+..||.++.
T Consensus 145 Aa~Da~~l~~l~~~l~ 160 (161)
T cd06129 145 AAADVYALLIIYTKLR 160 (161)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 7779999999998875
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=97.67 E-value=2.6e-05 Score=44.15 Aligned_cols=25 Identities=36% Similarity=0.707 Sum_probs=21.7
Q ss_pred HHHHHHhhhccCCCCC-ccccCccccCC
Q 019380 29 HLIEHMKISYHSVHQP-KCAVCQKLSKS 55 (342)
Q Consensus 29 ~L~~H~~~~~H~~~~~-~C~~C~~~f~~ 55 (342)
+|.+|+++ |++++| .|+.|++.|.+
T Consensus 1 ~l~~H~~~--H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRT--HTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHH--HSSSSSEEESSSSEEESS
T ss_pred CHHHHhhh--cCCCCCCCCCCCcCeeCc
Confidence 58899999 999998 99999998863
No 84
>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=97.63 E-value=0.00024 Score=61.04 Aligned_cols=113 Identities=15% Similarity=0.187 Sum_probs=68.8
Q ss_pred CCcceeccccccccc--CCCcccccceEEeecCCCCeEEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHH
Q 019380 123 GPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 200 (342)
Q Consensus 123 ~~~~v~~D~Ettg~~--~~~~~~il~~v~vv~~~~~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~ 200 (342)
.-+.++||.||++.. ++.....+..++....+|.+.+-. ....+..+++.+|.++
T Consensus 2 ~l~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~~-----------------------~~~~~E~~lL~~F~~~ 58 (188)
T cd05781 2 DLKTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFIL-----------------------AEGLDDRKIIREFVKY 58 (188)
T ss_pred CceEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEEEE-----------------------ecCCCHHHHHHHHHHH
Confidence 346789999998421 222222224555554445432110 1246788999999999
Q ss_pred HhcCCCccccccCCCCCeEEEeeCc-hhhhhhcc-------ccCCC--------------------cceeeccccccccc
Q 019380 201 LNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-------MNYPD--------------------HMLRDTAKYRPLMK 252 (342)
Q Consensus 201 l~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-------~~~~~--------------------~~~~Dt~~l~~~~~ 252 (342)
+.+. ...+|+|||. .||+.+|. +..+. ...+|...+.+...
T Consensus 59 i~~~-----------dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~ 127 (188)
T cd05781 59 VKEY-----------DPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIP 127 (188)
T ss_pred HHHc-----------CCCEEEecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhC
Confidence 9543 2359999995 48999987 11110 11566655554443
Q ss_pred cCCCCccHHHHHHHHhCCc
Q 019380 253 TNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 253 ~~~~~~~L~~l~~~~~~~~ 271 (342)
...+++|+.+|.. ||..
T Consensus 128 -~l~~y~L~~Va~~-Lg~~ 144 (188)
T cd05781 128 -EVKVKTLENVAEY-LGVM 144 (188)
T ss_pred -CCCCCCHHHHHHH-HCCC
Confidence 3578999999986 5864
No 85
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=97.63 E-value=0.00029 Score=65.52 Aligned_cols=137 Identities=23% Similarity=0.277 Sum_probs=92.4
Q ss_pred CCCcceecccccccccCCCcccccceEEeecCCCCeEEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHH
Q 019380 122 RGPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 201 (342)
Q Consensus 122 ~~~~~v~~D~Ettg~~~~~~~~il~~v~vv~~~~~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~l 201 (342)
....++++|+|+.+...-.. .+ +-|.|.+.++ ..+|.|..+ ..+.++|. ..+
T Consensus 15 ~~~~~iAiDTEf~r~~t~~p-~L-cLIQi~~~e~----~~lIdpl~~---------------~~d~~~l~-------~Ll 66 (361)
T COG0349 15 RGSKAIAIDTEFMRLRTYYP-RL-CLIQISDGEG----ASLIDPLAG---------------ILDLPPLV-------ALL 66 (361)
T ss_pred cCCCceEEecccccccccCC-ce-EEEEEecCCC----ceEeccccc---------------ccccchHH-------HHh
Confidence 34568999999998743222 22 5666655555 233333331 11233333 334
Q ss_pred hcCCCccccccCCCCCeEEEeeCchhhhhhccc--cCCCcceeeccccccccccCCCCccHHHHHHHHhCCcCCCCC---
Q 019380 202 NNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM--NYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGV--- 276 (342)
Q Consensus 202 ~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~--~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~--- 276 (342)
.+.+.+=|-|+++||+.+|.- ..-..+++||...++...... +++|++|++.++|++|.++.
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 235566688999999999982 222356899998777664443 89999999999999998872
Q ss_pred ---CC---------cHHHHHHHHHHHHHHHhhhhh
Q 019380 277 ---HD---------PYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 277 ---H~---------A~~Da~~t~~l~~~~~~~~~~ 299 (342)
++ |..|+.....||.++.++..+
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 567888999999999877554
No 86
>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=97.61 E-value=6.3e-05 Score=63.02 Aligned_cols=74 Identities=22% Similarity=0.182 Sum_probs=38.3
Q ss_pred CCeEEEeeC-chhhhhhccc-----cCC-CcceeeccccccccccCCCCccHHHHHHHHhCCcCCCCCCCcHHHHHHHHH
Q 019380 216 KARLLVGHG-LEHDLDSLRM-----NYP-DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMR 288 (342)
Q Consensus 216 ~~~~lvgh~-~~~D~~~l~~-----~~~-~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~H~A~~Da~~t~~ 288 (342)
+...+|+|| ..||+.+|+- ..+ ....+|+....+.... .+++|+.++..+ |+..+ .--.+-..+..
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 557899998 6889999992 223 4668898877654433 678999999987 87732 12234455666
Q ss_pred HHHHHHhh
Q 019380 289 LYKRFRRQ 296 (342)
Q Consensus 289 l~~~~~~~ 296 (342)
+|..++..
T Consensus 129 ~~~~~~~~ 136 (164)
T PF13482_consen 129 LYKEYLET 136 (164)
T ss_dssp HHH---TT
T ss_pred HHHHHHhc
Confidence 66665544
No 87
>PRK10829 ribonuclease D; Provisional
Probab=97.55 E-value=0.00056 Score=64.93 Aligned_cols=83 Identities=12% Similarity=0.117 Sum_probs=63.7
Q ss_pred CCeEEEeeCchhhhhhcc--ccCCCcceeeccccccccccCCCCccHHHHHHHHhCCcCCCCC---------------CC
Q 019380 216 KARLLVGHGLEHDLDSLR--MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGV---------------HD 278 (342)
Q Consensus 216 ~~~~lvgh~~~~D~~~l~--~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~---------------H~ 278 (342)
.+-+-|+|++.+|+.+|. .......++||+..+..+. ...+.+|..|++.++|+.++++. +-
T Consensus 73 ~~ivKV~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg-~~~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~ql~Y 151 (373)
T PRK10829 73 PQVTKFLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCG-RPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEY 151 (373)
T ss_pred CCeEEEEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHcC-CCccccHHHHHHHHhCCccCcccccCCCCCCCCCHHHHHH
Confidence 555668999999999985 3333356999988776653 23468999999999999887661 33
Q ss_pred cHHHHHHHHHHHHHHHhhhhh
Q 019380 279 PYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 279 A~~Da~~t~~l~~~~~~~~~~ 299 (342)
|..|+..+..||.++.++..+
T Consensus 152 Aa~Dv~~L~~l~~~L~~~L~~ 172 (373)
T PRK10829 152 AAADVFYLLPIAAKLMAETEA 172 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 677999999999999877654
No 88
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.55 E-value=2.1e-05 Score=73.09 Aligned_cols=89 Identities=20% Similarity=0.351 Sum_probs=65.4
Q ss_pred CcccccccccccCCHHHHHHHH--hhhccCCCCCccccCccccCChhhhhhhcCCCcccCCCC-----------------
Q 019380 13 ARHKCVACYKQFKRKDHLIEHM--KISYHSVHQPKCAVCQKLSKSFESLREHLTGPLSKAHCS----------------- 73 (342)
Q Consensus 13 ~~~~C~~C~k~f~~~~~L~~H~--~~~~H~~~~~~C~~C~~~f~~~~~l~~H~~~~~~C~~C~----------------- 73 (342)
..|.|..|...|-..-.|-+|+ ++. | .+|+|.+|+|.|+...+|..|..+.++-..-.
T Consensus 266 GdyiCqLCK~kYeD~F~LAQHrC~RIV-~--vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~ 342 (500)
T KOG3993|consen 266 GDYICQLCKEKYEDAFALAQHRCPRIV-H--VEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEV 342 (500)
T ss_pred HHHHHHHHHHhhhhHHHHhhccCCeeE-E--eeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhh
Confidence 3588999999999999999997 331 2 35699999999999999999983332221111
Q ss_pred ----CcccCC-----cccccccccCChhhHHHHHhhcCCC
Q 019380 74 ----GIFSDR-----GCNLCMNIFDSPSSLIKHKEACSLS 104 (342)
Q Consensus 74 ----k~f~~~-----~C~~C~k~F~~~~~L~~H~~~h~~~ 104 (342)
+.=.++ .|..|+|.|.+...|+.|+.+|+..
T Consensus 343 ~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~ 382 (500)
T KOG3993|consen 343 QEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRA 382 (500)
T ss_pred hhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhcc
Confidence 000001 2999999999999999999988833
No 89
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.54 E-value=5e-05 Score=70.61 Aligned_cols=48 Identities=27% Similarity=0.454 Sum_probs=40.2
Q ss_pred cccccccccccCCHHHHHHHHhhhccC--------CCC--------------------------CccccCccccCChhhh
Q 019380 14 RHKCVACYKQFKRKDHLIEHMKISYHS--------VHQ--------------------------PKCAVCQKLSKSFESL 59 (342)
Q Consensus 14 ~~~C~~C~k~f~~~~~L~~H~~~~~H~--------~~~--------------------------~~C~~C~~~f~~~~~l 59 (342)
.|+|+.|+|.|+...+|-.|++= |. +.. +.|..|+|.|++...|
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 49999999999999999999986 42 111 2599999999999999
Q ss_pred hhhc
Q 019380 60 REHL 63 (342)
Q Consensus 60 ~~H~ 63 (342)
+.|+
T Consensus 373 rKHq 376 (500)
T KOG3993|consen 373 RKHQ 376 (500)
T ss_pred HHhH
Confidence 9996
No 90
>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=97.41 E-value=0.0014 Score=62.34 Aligned_cols=82 Identities=18% Similarity=0.240 Sum_probs=61.9
Q ss_pred CCeEEEeeCchhhhhhccc---cCCCcceeeccccccccccCCCCccHHHHHHHHhCCcCCCCC------CC--------
Q 019380 216 KARLLVGHGLEHDLDSLRM---NYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGV------HD-------- 278 (342)
Q Consensus 216 ~~~~lvgh~~~~D~~~l~~---~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~------H~-------- 278 (342)
.+.+.|+|++..|+.+|.. ..| ..+.||+..+..+.+. .+.+|+.|++.|+|+.+.++. .+
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 5567899999999999872 233 4578998877666554 346999999999999876531 22
Q ss_pred -cHHHHHHHHHHHHHHHhhhhh
Q 019380 279 -PYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 279 -A~~Da~~t~~l~~~~~~~~~~ 299 (342)
|..||..+..||..+.++..+
T Consensus 147 YAa~Dv~~L~~L~~~L~~~L~~ 168 (367)
T TIGR01388 147 YAAADVTYLLPLYAKLMERLEE 168 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 677899999999999877654
No 91
>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=97.41 E-value=8.7e-05 Score=40.57 Aligned_cols=22 Identities=41% Similarity=0.689 Sum_probs=20.8
Q ss_pred ccccccccccCCHHHHHHHHhh
Q 019380 15 HKCVACYKQFKRKDHLIEHMKI 36 (342)
Q Consensus 15 ~~C~~C~k~f~~~~~L~~H~~~ 36 (342)
|+|+.|++.|.++..|..|++.
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 7899999999999999999987
No 92
>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=97.30 E-value=0.0001 Score=41.71 Aligned_cols=24 Identities=17% Similarity=0.144 Sum_probs=21.6
Q ss_pred hHHHHHhhcCCCCCCCCccccccc
Q 019380 93 SLIKHKEACSLSAPVPFKISGAID 116 (342)
Q Consensus 93 ~L~~H~~~h~~~~~~~~~~c~~~~ 116 (342)
+|.+|+++|.+++|+.|+.|+++.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSF 24 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEE
T ss_pred CHHHHhhhcCCCCCCCCCCCcCee
Confidence 589999999999999999998763
No 93
>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=97.29 E-value=0.00047 Score=56.51 Aligned_cols=69 Identities=29% Similarity=0.315 Sum_probs=53.0
Q ss_pred HHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhccccC--CCcceeeccccccccccCCCCccHHHHHHHHh
Q 019380 191 KEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY--PDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYL 268 (342)
Q Consensus 191 ~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~--~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~ 268 (342)
..+.+.+.+++ .+.+..+||||+.+|+.+|.-.. ....++||+.++..+.|....++|++|++.|+
T Consensus 40 ~~~~~~l~~~l------------~~~~~~~v~~~~k~d~~~L~~~~~~~~~~~~D~~~~ayll~~~~~~~~l~~l~~~~l 107 (155)
T cd00007 40 EEDLEALKELL------------EDEDITKVGHDAKFDLVVLARDGIELPGNIFDTMLAAYLLNPGEGSHSLDDLAKEYL 107 (155)
T ss_pred HHHHHHHHHHH------------cCCCCcEEeccHHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCCcCCHHHHHHHHc
Confidence 56777788888 22456799999999999997221 11447899999988888653579999999998
Q ss_pred CCc
Q 019380 269 GYD 271 (342)
Q Consensus 269 ~~~ 271 (342)
+..
T Consensus 108 ~~~ 110 (155)
T cd00007 108 GIE 110 (155)
T ss_pred CCC
Confidence 776
No 94
>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=97.26 E-value=0.002 Score=56.04 Aligned_cols=74 Identities=19% Similarity=0.157 Sum_probs=49.2
Q ss_pred CCChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCc-hhhhhhcc-------ccCC----C------------ccee
Q 019380 187 AMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-------MNYP----D------------HMLR 242 (342)
Q Consensus 187 ~~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-------~~~~----~------------~~~~ 242 (342)
.....+++.+|.+++.+. .-.+++|||. .||+.+|. +... . ...+
T Consensus 70 ~~~E~~lL~~f~~~i~~~-----------~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~i 138 (204)
T cd05779 70 EPDEKALLQRFFEHIREV-----------KPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHM 138 (204)
T ss_pred CCCHHHHHHHHHHHHHHh-----------CCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEE
Confidence 467889999999999432 2249999994 58999987 1111 0 1135
Q ss_pred ecccccccc-ccCCCCccHHHHHHHHhCCc
Q 019380 243 DTAKYRPLM-KTNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 243 Dt~~l~~~~-~~~~~~~~L~~l~~~~~~~~ 271 (342)
|...+.+.. .....+++|+.+|+.+||..
T Consensus 139 Dl~~~~~~~~~l~~~sysLd~Va~~~Lg~~ 168 (204)
T cd05779 139 DCFRWVKRDSYLPQGSQGLKAVTKAKLGYD 168 (204)
T ss_pred EhHHHHHHhhcCCCCCccHHHHHHHHhCCC
Confidence 555544432 21235899999999988975
No 95
>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=97.26 E-value=0.0033 Score=54.28 Aligned_cols=120 Identities=18% Similarity=0.225 Sum_probs=70.5
Q ss_pred CCcceecccccccccCCCcccccceEEeecCCCCeEEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHHh
Q 019380 123 GPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILN 202 (342)
Q Consensus 123 ~~~~v~~D~Ettg~~~~~~~~il~~v~vv~~~~~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~l~ 202 (342)
.-++++||+|+++.+ ++ -.+...+.....++-. -.+. +. .| ..+.-.++..+++..|.+++.
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 346889999998653 33 3344433332322211 1111 10 01 123334678889999999995
Q ss_pred cCCCccccccCCCCCeEEEeeCch-hhhhhcc-------ccCC------------------------Ccceeeccccccc
Q 019380 203 NGESTGRLMLDDGKARLLVGHGLE-HDLDSLR-------MNYP------------------------DHMLRDTAKYRPL 250 (342)
Q Consensus 203 ~~~~~~~~~~~~~~~~~lvgh~~~-~D~~~l~-------~~~~------------------------~~~~~Dt~~l~~~ 250 (342)
+. .-.+|+|||+. ||+.+|. +..+ -..++|+..+.+.
T Consensus 64 ~~-----------dPDvi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~ 132 (193)
T cd05784 64 QY-----------DPDIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKT 132 (193)
T ss_pred hh-----------CCCEEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHH
Confidence 43 22499999965 5998877 1111 0125566555443
Q ss_pred cccCCCCccHHHHHHHHhCCc
Q 019380 251 MKTNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 251 ~~~~~~~~~L~~l~~~~~~~~ 271 (342)
......+|+|+++|+.+||..
T Consensus 133 ~~~kl~sy~L~~Va~~~Lg~~ 153 (193)
T cd05784 133 ATYHFESFSLENVAQELLGEG 153 (193)
T ss_pred ccCCCCcCCHHHHHHHHhCCC
Confidence 222467999999999998875
No 96
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.24 E-value=0.00022 Score=70.35 Aligned_cols=73 Identities=16% Similarity=0.380 Sum_probs=55.3
Q ss_pred CcccccccccccCCHHHHHHHHhhhccCCCCC-ccccCccccCC----------hhhhhhhc----CCCcccCCCCCccc
Q 019380 13 ARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKS----------FESLREHL----TGPLSKAHCSGIFS 77 (342)
Q Consensus 13 ~~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~-~C~~C~~~f~~----------~~~l~~H~----~~~~~C~~C~k~f~ 77 (342)
+|+.|+ |++.+ .+..|..|+.+ |...++ .|..|++.+.. .+.|..|. .+++.
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~t--hCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~--------- 543 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQAS--TCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAP--------- 543 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhc--cCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhcCCcceE---------
Confidence 789999 99755 67899999998 998888 99999999852 34688886 23333
Q ss_pred CCcccccccccCChhhHHHHHhhcC
Q 019380 78 DRGCNLCMNIFDSPSSLIKHKEACS 102 (342)
Q Consensus 78 ~~~C~~C~k~F~~~~~L~~H~~~h~ 102 (342)
|..||+.+..+. +..|+...|
T Consensus 544 ---C~~Cgk~Vrlrd-m~~H~~~~h 564 (567)
T PLN03086 544 ---CDSCGRSVMLKE-MDIHQIAVH 564 (567)
T ss_pred ---ccccCCeeeehh-HHHHHHHhh
Confidence 677887777664 667776544
No 97
>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=97.18 E-value=0.00095 Score=57.84 Aligned_cols=138 Identities=22% Similarity=0.222 Sum_probs=85.3
Q ss_pred CCcceecccccccccCCCcccccceEEeecCCCCe-EEeeecCCCCCccccccccCCCCHhhhcCCCChHHHHHHHHHHH
Q 019380 123 GPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENV-IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 201 (342)
Q Consensus 123 ~~~~v~~D~Ettg~~~~~~~~il~~v~vv~~~~~~-~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~l 201 (342)
..+++++|+|+.+.+..+.+ .-+.+-...+.+ +|+.+-.+. ......+.+++
T Consensus 9 ~~~~i~~D~E~~~~~~~~~~---~LiQia~~~~~v~l~D~~~~~~------------------------~~~~~~L~~iL 61 (197)
T cd06148 9 KQKVIGLDCEGVNLGRKGKL---CLVQIATRTGQIYLFDILKLGS------------------------IVFINGLKDIL 61 (197)
T ss_pred hCCEEEEEcccccCCCCCCE---EEEEEeeCCCcEEEEEhhhccc------------------------hhHHHHHHHHh
Confidence 36789999999877654333 233332231233 455442111 01224455666
Q ss_pred hcCCCccccccCCCCCeEEEeeCchhhhhhcc--ccCCCcceeeccccccccccCC-------CCccHHHHHHHHhCCcC
Q 019380 202 NNGESTGRLMLDDGKARLLVGHGLEHDLDSLR--MNYPDHMLRDTAKYRPLMKTNL-------VSHSLKYLTRTYLGYDI 272 (342)
Q Consensus 202 ~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~--~~~~~~~~~Dt~~l~~~~~~~~-------~~~~L~~l~~~~~~~~~ 272 (342)
++.+.+-|+|++.+|+.+|. .......+.||+..+..+.+.. ...+|+.++..|+|+++
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 23555679999999999983 2222234689987655554322 13689999999999886
Q ss_pred CC-------------C-C---------CCcHHHHHHHHHHHHHHHhhhhh
Q 019380 273 QS-------------G-V---------HDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 273 ~~-------------~-~---------H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
.. + . .=|..||..+..||..++.....
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 1 1 33667999999999999888644
No 98
>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=97.12 E-value=0.009 Score=52.15 Aligned_cols=73 Identities=23% Similarity=0.364 Sum_probs=50.4
Q ss_pred CCChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCc-hhhhhhcc-------ccCCC--------------------
Q 019380 187 AMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-------MNYPD-------------------- 238 (342)
Q Consensus 187 ~~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-------~~~~~-------------------- 238 (342)
..+..+++.+|++++.+. .-.+|||||+ .||+.+|. +..+.
T Consensus 55 ~~~E~~lL~~f~~~i~~~-----------dPdii~g~N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~ 123 (207)
T cd05785 55 DAAEKELLEELVAIIRER-----------DPDVIEGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERL 123 (207)
T ss_pred CCCHHHHHHHHHHHHHHh-----------CCCEEeccCCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccc
Confidence 578899999999999442 1259999998 89999987 11110
Q ss_pred ----------cceeecccccccc---ccCCCCccHHHHHHHHhCCc
Q 019380 239 ----------HMLRDTAKYRPLM---KTNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 239 ----------~~~~Dt~~l~~~~---~~~~~~~~L~~l~~~~~~~~ 271 (342)
..++|+..+.+.. .....+|+|+.+|..| |+.
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 1226776654431 2244689999999988 653
No 99
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.07 E-value=0.00027 Score=38.55 Aligned_cols=21 Identities=33% Similarity=0.640 Sum_probs=18.9
Q ss_pred ccccccccCChhhHHHHHhhc
Q 019380 81 CNLCMNIFDSPSSLIKHKEAC 101 (342)
Q Consensus 81 C~~C~k~F~~~~~L~~H~~~h 101 (342)
|+.|+++|..++.|..|++.|
T Consensus 3 C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 3 CPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp ETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCccCCHHHHHHHHhHC
Confidence 789999999999999999874
No 100
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=97.00 E-value=0.0015 Score=55.95 Aligned_cols=109 Identities=13% Similarity=0.127 Sum_probs=76.5
Q ss_pred ccCCCCHhhhc-CCCChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhcc-----cc-------------
Q 019380 175 EVTGLTEEDIK-NAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR-----MN------------- 235 (342)
Q Consensus 175 ~i~GIt~e~l~-~~~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~-----~~------------- 235 (342)
+-+||.-+... .+....+..+.+..-..- -+++..+|.....+|+..|- -.
T Consensus 109 r~~Gidf~K~~e~GI~~~~F~ellm~sg~v----------~~~~V~WvTFhs~YDfgYLlK~Lt~~~LP~~~~eF~~~v~ 178 (239)
T KOG0304|consen 109 RRSGIDFEKHREEGIDIEEFAELLMTSGLV----------LDENVTWVTFHSGYDFGYLLKILTGKPLPETEEEFFEIVR 178 (239)
T ss_pred HHcCcCHHHHHHcCCCHHHHHHHHHHhhhh----------ccCceEEEEeeccchHHHHHHHHcCCCCcchHHHHHHHHH
Confidence 34777766665 345544444444433211 13678999999999999876 11
Q ss_pred --CCCcceeeccccccccccCCCCccHHHHHHHHhCCcCCCCCCCcHHHHHHHHHHHHHHHhh
Q 019380 236 --YPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQ 296 (342)
Q Consensus 236 --~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~ 296 (342)
+|. +.|+..+++.......+.+|+.+|..+ |++-.+-+|.|=.|+..|+..|.++.+.
T Consensus 179 ~~fp~--vYDiK~l~~~c~~~~l~~GL~~lA~~L-~~~RvG~~HqAGSDSlLT~~~F~kl~~~ 238 (239)
T KOG0304|consen 179 QLFPF--VYDVKYLMKFCEGLSLKGGLQRLADLL-GLKRVGIAHQAGSDSLLTARVFFKLKEL 238 (239)
T ss_pred HHcch--hhhHHHHHHhhhhhhhhcCHHHHHHHh-CCCeeecccccCcHHHHHHHHHHHHHhc
Confidence 233 567777777765555689999999998 9995444999999999999999998764
No 101
>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=96.94 E-value=0.00067 Score=37.04 Aligned_cols=23 Identities=35% Similarity=0.729 Sum_probs=19.3
Q ss_pred ccccccccccCCHHHHHHHHhhh
Q 019380 15 HKCVACYKQFKRKDHLIEHMKIS 37 (342)
Q Consensus 15 ~~C~~C~k~f~~~~~L~~H~~~~ 37 (342)
|.|+.|++.|.+...|..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 78999999999999999999873
No 102
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=96.82 E-value=0.028 Score=48.93 Aligned_cols=75 Identities=16% Similarity=0.184 Sum_probs=50.1
Q ss_pred hcCCCChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCc-hhhhhhcc-----ccCC----------------Ccce
Q 019380 184 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-----MNYP----------------DHML 241 (342)
Q Consensus 184 l~~~~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-----~~~~----------------~~~~ 241 (342)
+..-....+++.+|.+++.+ . .+|||||. .||+.+|. ...+ ....
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 3 48999995 57999987 1122 1234
Q ss_pred eeccccccc-c-----c-cCCCCccHHHHHHHHhCCc
Q 019380 242 RDTAKYRPL-M-----K-TNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 242 ~Dt~~l~~~-~-----~-~~~~~~~L~~l~~~~~~~~ 271 (342)
+|...+... . + ....+++|+.+|+.+||..
T Consensus 134 iDl~~~~~~~~~~~~~~~~~~~~~~L~~Va~~~lg~~ 170 (204)
T cd05783 134 IDLYKFFSNRAIQVYAFGNKYREYTLDAVAKALLGEG 170 (204)
T ss_pred eECHHHhhccchhhhhhccccccCcHHHHHHHhcCCC
Confidence 565443322 1 1 1346899999999998876
No 103
>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=96.80 E-value=0.00077 Score=38.30 Aligned_cols=23 Identities=30% Similarity=0.504 Sum_probs=22.0
Q ss_pred cccccccccccCCHHHHHHHHhh
Q 019380 14 RHKCVACYKQFKRKDHLIEHMKI 36 (342)
Q Consensus 14 ~~~C~~C~k~f~~~~~L~~H~~~ 36 (342)
||+|..|++.|.+...|..|++.
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 68999999999999999999988
No 104
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=96.65 E-value=0.0065 Score=50.61 Aligned_cols=89 Identities=24% Similarity=0.385 Sum_probs=63.0
Q ss_pred HHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhcc---ccCCCcceeeccccccccccCCCCccHHHHHHHHhCC
Q 019380 194 KDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR---MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGY 270 (342)
Q Consensus 194 ~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~---~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~ 270 (342)
.+.+.+++. +.+...||||+.+|+.+|. +..+ .+.|++..+..+.|....++|+.++..|+|.
T Consensus 64 ~~~l~~~l~------------~~~~~kv~~d~k~~~~~L~~~gi~~~--~~~D~~laayll~p~~~~~~l~~l~~~~l~~ 129 (172)
T smart00474 64 LEILKDLLE------------DETITKVGHNAKFDLHVLARFGIELE--NIFDTMLAAYLLLGGPSKHGLATLLKEYLGV 129 (172)
T ss_pred HHHHHHHhc------------CCCceEEEechHHHHHHHHHCCCccc--chhHHHHHHHHHcCCCCcCCHHHHHHHHhCC
Confidence 455677772 2556899999999999996 2222 2489998888777766546999999999888
Q ss_pred cCCCC-C----------C----CcHHHHHHHHHHHHHHHhh
Q 019380 271 DIQSG-V----------H----DPYEDCVSVMRLYKRFRRQ 296 (342)
Q Consensus 271 ~~~~~-~----------H----~A~~Da~~t~~l~~~~~~~ 296 (342)
.+... . . -|..||.++.+|+..+.++
T Consensus 130 ~~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~ 170 (172)
T smart00474 130 ELDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKE 170 (172)
T ss_pred CCCcccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 74310 0 0 1556677788887777655
No 105
>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=96.60 E-value=0.0012 Score=35.93 Aligned_cols=22 Identities=32% Similarity=0.581 Sum_probs=18.3
Q ss_pred ccccccccCChhhHHHHHhhcC
Q 019380 81 CNLCMNIFDSPSSLIKHKEACS 102 (342)
Q Consensus 81 C~~C~k~F~~~~~L~~H~~~h~ 102 (342)
|+.|++.|.....|+.|++.||
T Consensus 3 C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 3 CPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp -SSTS-EESSHHHHHHHHHHHS
T ss_pred CcCCCCcCCcHHHHHHHHHhhC
Confidence 7899999999999999998875
No 106
>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=96.39 E-value=0.0067 Score=55.01 Aligned_cols=72 Identities=22% Similarity=0.170 Sum_probs=55.2
Q ss_pred CCeEEEeeCchhhhhhcc-------------------ccCCCcceeeccccccccccCCCCccHHHHHHHHhCCcC----
Q 019380 216 KARLLVGHGLEHDLDSLR-------------------MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDI---- 272 (342)
Q Consensus 216 ~~~~lvgh~~~~D~~~l~-------------------~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~---- 272 (342)
...+|||||.-.|+.+|- .-+|. ++||..++.... ....+|+.|+..+ +...
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 458999999999999866 11455 889988887664 3467899999988 6653
Q ss_pred -------------------CCC-CCCcHHHHHHHHHHHHH
Q 019380 273 -------------------QSG-VHDPYEDCVSVMRLYKR 292 (342)
Q Consensus 273 -------------------~~~-~H~A~~Da~~t~~l~~~ 292 (342)
.+. .|.|=.||.+|+.+|.+
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 107
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=96.37 E-value=0.0038 Score=42.02 Aligned_cols=36 Identities=25% Similarity=0.537 Sum_probs=23.4
Q ss_pred cccccccccccCCHHHHHHHHhhhccCCCC-C-ccccCcc
Q 019380 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQ-P-KCAVCQK 51 (342)
Q Consensus 14 ~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~-~-~C~~C~~ 51 (342)
.|.||.|++. .....|..|.... |..+. . .|++|..
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 4889999995 4567799998663 55432 2 4555543
No 108
>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=96.26 E-value=0.044 Score=48.61 Aligned_cols=39 Identities=13% Similarity=0.106 Sum_probs=29.3
Q ss_pred hcCCCChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCch-hhhhhcc
Q 019380 184 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLR 233 (342)
Q Consensus 184 l~~~~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~-~D~~~l~ 233 (342)
+....+..+++.+|.++|... .-.+|+|||+. ||+.+|.
T Consensus 65 v~~~~~E~eLL~~f~~~i~~~-----------DPDii~GyN~~~FDl~yL~ 104 (230)
T cd05777 65 VFSFETEEELLLAWRDFVQEV-----------DPDIITGYNICNFDLPYLL 104 (230)
T ss_pred EEEECCHHHHHHHHHHHHHhc-----------CCCEEEEecCCCCCHHHHH
Confidence 334568899999999999432 22599999965 5999876
No 109
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.20 E-value=0.0019 Score=58.23 Aligned_cols=69 Identities=20% Similarity=0.372 Sum_probs=44.1
Q ss_pred CCCcccccc--cccccCCHHHHHHHHhhhccCCCCC---ccccCccccCChhhhhhhcCCCcccCCCCCcccCCcccccc
Q 019380 11 STARHKCVA--CYKQFKRKDHLIEHMKISYHSVHQP---KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCM 85 (342)
Q Consensus 11 ~~~~~~C~~--C~k~f~~~~~L~~H~~~~~H~~~~~---~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~~C~~C~ 85 (342)
++|||+|++ |.|.|+...-|+=|+.- .|..++. .-++--..|.- ..+||. |++|+
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lh-GH~~~~~~~~p~p~~~~~F~~-------~~KPYr------------CevC~ 405 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLH-GHQNQKLHENPSPEKMNIFSA-------KDKPYR------------CEVCD 405 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhc-cccCcccCCCCCccccccccc-------cCCcee------------ccccc
Confidence 569999964 99999999999999973 3543322 11111111210 034554 57788
Q ss_pred cccCChhhHHHHHh
Q 019380 86 NIFDSPSSLIKHKE 99 (342)
Q Consensus 86 k~F~~~~~L~~H~~ 99 (342)
|.|+....|+.|++
T Consensus 406 KRYKNlNGLKYHr~ 419 (423)
T COG5189 406 KRYKNLNGLKYHRK 419 (423)
T ss_pred hhhccCccceeccc
Confidence 88888888888864
No 110
>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=96.13 E-value=0.0035 Score=40.77 Aligned_cols=27 Identities=22% Similarity=0.531 Sum_probs=21.1
Q ss_pred cccccccccCChhhHHHHHhhcCCCCC
Q 019380 80 GCNLCMNIFDSPSSLIKHKEACSLSAP 106 (342)
Q Consensus 80 ~C~~C~k~F~~~~~L~~H~~~h~~~~~ 106 (342)
.|++|+..+.+..+|++|++.+|+.+|
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 489999999999999999999998876
No 111
>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=96.12 E-value=0.021 Score=49.51 Aligned_cols=94 Identities=19% Similarity=0.224 Sum_probs=63.9
Q ss_pred ChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeC-chhhhhhcc-------ccCCC-----------------cceee
Q 019380 189 PLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLR-------MNYPD-----------------HMLRD 243 (342)
Q Consensus 189 ~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~-~~~D~~~l~-------~~~~~-----------------~~~~D 243 (342)
...+++.+|.+++.. .+-.||+|| -.||+.+|. +..|. ..-+|
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 344799999 678999988 22222 12356
Q ss_pred ccccccccccCCCCccHHHHHHHHhCCcCCCCCCCc------------------HHHHHHHHHHHHHHHhh
Q 019380 244 TAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGVHDP------------------YEDCVSVMRLYKRFRRQ 296 (342)
Q Consensus 244 t~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~H~A------------------~~Da~~t~~l~~~~~~~ 296 (342)
++.+.... +.....+|+.||..+ |++-+.+.+-+ ..|+.+|+.||.++.--
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 65442222 134578999999988 98854332211 34999999999998764
No 112
>PHA00732 hypothetical protein
Probab=96.07 E-value=0.0047 Score=45.03 Aligned_cols=19 Identities=26% Similarity=0.662 Sum_probs=9.7
Q ss_pred ccccCccccCChhhhhhhc
Q 019380 45 KCAVCQKLSKSFESLREHL 63 (342)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~ 63 (342)
.|..|++.|.+.++|..|+
T Consensus 3 ~C~~Cgk~F~s~s~Lk~H~ 21 (79)
T PHA00732 3 KCPICGFTTVTLFALKQHA 21 (79)
T ss_pred cCCCCCCccCCHHHHHHHh
Confidence 3555555555555555554
No 113
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.04 E-value=0.0061 Score=33.59 Aligned_cols=22 Identities=45% Similarity=0.760 Sum_probs=20.6
Q ss_pred ccccccccccCCHHHHHHHHhh
Q 019380 15 HKCVACYKQFKRKDHLIEHMKI 36 (342)
Q Consensus 15 ~~C~~C~k~f~~~~~L~~H~~~ 36 (342)
|+|+.|++.|.....|..|++.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~ 22 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRT 22 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHH
Confidence 6899999999999999999987
No 114
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.93 E-value=0.0053 Score=46.45 Aligned_cols=75 Identities=25% Similarity=0.410 Sum_probs=20.7
Q ss_pred cccccccccCCHHHHHHHHhhhccCCCCCccccCccccCChhhhhhhcCCCcccCCCCCccc-CCcccccccccCChhhH
Q 019380 16 KCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHLTGPLSKAHCSGIFS-DRGCNLCMNIFDSPSSL 94 (342)
Q Consensus 16 ~C~~C~k~f~~~~~L~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~-~~~C~~C~k~F~~~~~L 94 (342)
+|..|+..|.....|..|+... |.-..+.. ..+.....+..+... ... ...|..|++.|.....|
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~-H~~~~~~~----~~l~~~~~~~~~~~~---------~~~~~~~C~~C~~~f~s~~~l 66 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKK-HGFDIPDQ----KYLVDPNRLLNYLRK---------KVKESFRCPYCNKTFRSREAL 66 (100)
T ss_dssp --------------------------------------------------------------SSEEBSSSS-EESSHHHH
T ss_pred Cccccccccccccccccccccc-cccccccc----ccccccccccccccc---------ccCCCCCCCccCCCCcCHHHH
Confidence 5899999999999999999653 44332211 111122222222110 001 12589999999999999
Q ss_pred HHHHhhcCCC
Q 019380 95 IKHKEACSLS 104 (342)
Q Consensus 95 ~~H~~~h~~~ 104 (342)
..|++.+...
T Consensus 67 ~~Hm~~~~H~ 76 (100)
T PF12756_consen 67 QEHMRSKHHK 76 (100)
T ss_dssp HHHHHHTTTT
T ss_pred HHHHcCccCC
Confidence 9999975433
No 115
>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=95.88 E-value=0.0047 Score=34.96 Aligned_cols=24 Identities=33% Similarity=0.545 Sum_probs=20.9
Q ss_pred cccccccccCChhhHHHHHhhcCC
Q 019380 80 GCNLCMNIFDSPSSLIKHKEACSL 103 (342)
Q Consensus 80 ~C~~C~k~F~~~~~L~~H~~~h~~ 103 (342)
.|..|++.|.....|..|++.|+.
T Consensus 3 ~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 3 ECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp EETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCccCCccCChhHHHHHhHHhcC
Confidence 378999999999999999988864
No 116
>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=95.86 E-value=0.037 Score=46.61 Aligned_cols=83 Identities=20% Similarity=0.227 Sum_probs=59.7
Q ss_pred CCeEEEeeCchhhhhhccc--cCCCcceeeccccccccccCCCCccHHHHHHHHhCCcCCCC------C---------CC
Q 019380 216 KARLLVGHGLEHDLDSLRM--NYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSG------V---------HD 278 (342)
Q Consensus 216 ~~~~lvgh~~~~D~~~l~~--~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~------~---------H~ 278 (342)
.+...||||+.+|+.+|.. ......+.|++..+..+.|... .+|++|++.|+|..+... . +-
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 5678999999999999852 2223456899887777777544 599999999988863211 0 12
Q ss_pred cHHHHHHHHHHHHHHHhhhhh
Q 019380 279 PYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 279 A~~Da~~t~~l~~~~~~~~~~ 299 (342)
|..||.++.+|+..+.++.++
T Consensus 142 aa~~a~~l~~L~~~l~~~L~e 162 (178)
T cd06142 142 AALDVRYLLPLYEKLKEELEE 162 (178)
T ss_pred HHHhHHHHHHHHHHHHHHHHH
Confidence 566788888888888877644
No 117
>PRK05762 DNA polymerase II; Reviewed
Probab=95.76 E-value=0.058 Score=56.61 Aligned_cols=99 Identities=18% Similarity=0.258 Sum_probs=64.8
Q ss_pred hcCCCChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCch-hhhhhcc-------ccC--------------CC---
Q 019380 184 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLR-------MNY--------------PD--- 238 (342)
Q Consensus 184 l~~~~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~-~D~~~l~-------~~~--------------~~--- 238 (342)
+...++..+++.+|.+++.+. .-.||+|||+. ||+.+|. +.. +.
T Consensus 197 v~~~~sE~~LL~~F~~~i~~~-----------DPDIIvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~ 265 (786)
T PRK05762 197 LEYVADEKALLEKFNAWFAEH-----------DPDVIIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSG 265 (786)
T ss_pred EEEcCCHHHHHHHHHHHHHhc-----------CCCEEEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCC
Confidence 455678899999999999543 22599999955 7999987 111 00
Q ss_pred --------cceeeccccccccccCCCCccHHHHHHHHhCCcCCC-CCC-------------------CcHHHHHHHHHHH
Q 019380 239 --------HMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQS-GVH-------------------DPYEDCVSVMRLY 290 (342)
Q Consensus 239 --------~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~-~~H-------------------~A~~Da~~t~~l~ 290 (342)
..++|+..+.+.......+++|+.+|..+||..... ..+ -.+.||..|.+|+
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 113444444333332456899999999998865321 111 1367999999998
Q ss_pred HHH
Q 019380 291 KRF 293 (342)
Q Consensus 291 ~~~ 293 (342)
.++
T Consensus 346 ~kl 348 (786)
T PRK05762 346 EKT 348 (786)
T ss_pred HHh
Confidence 854
No 118
>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=95.75 E-value=0.016 Score=50.57 Aligned_cols=69 Identities=20% Similarity=0.249 Sum_probs=47.6
Q ss_pred ChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCc-hhhhhhcc-------ccCCC----------------cceeec
Q 019380 189 PLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-------MNYPD----------------HMLRDT 244 (342)
Q Consensus 189 ~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-------~~~~~----------------~~~~Dt 244 (342)
+..+++.+|.++|.+ .+-+|||||. .||+.+|. +..|. ...+|+
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 457899999999943 2348999996 78999998 22221 125676
Q ss_pred cccccccccCCCCccHHHHHHHHhCCc
Q 019380 245 AKYRPLMKTNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 245 ~~l~~~~~~~~~~~~L~~l~~~~~~~~ 271 (342)
..+.+... ...+++|+.+|..+ |++
T Consensus 145 ~~~~~~~~-~~~~~~L~~va~~l-G~~ 169 (208)
T cd05782 145 MDLLAFYG-ARARASLDLLAKLL-GIP 169 (208)
T ss_pred HHHHhccC-ccCCCCHHHHHHHh-CCC
Confidence 66544322 24689999999866 885
No 119
>PHA02528 43 DNA polymerase; Provisional
Probab=95.57 E-value=0.091 Score=55.45 Aligned_cols=160 Identities=14% Similarity=0.053 Sum_probs=85.6
Q ss_pred CCCcceecccccccc-c-CCCc--ccccceEEeecCCCCeEEeeecCCCCCccccccccC--CCCHhhhcCCCChHHHHH
Q 019380 122 RGPKAVAMDCEMVGG-G-SNGT--LDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVT--GLTEEDIKNAMPLKEVKD 195 (342)
Q Consensus 122 ~~~~~v~~D~Ettg~-~-~~~~--~~il~~v~vv~~~~~~~~~~lv~p~~~i~~~~~~i~--GIt~e~l~~~~~~~~v~~ 195 (342)
+..++++||+|++.. + ++.. ...+..+++.+..+...+-..+....+......... ......+.-.++..+++.
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 567789999999752 1 2222 222366666655555422222211111000000000 001111122467889999
Q ss_pred HHHHHHhcCCCccccccCCCCCeEEEeeCc-hhhhhhcc------ccC------C-Cc----------------------
Q 019380 196 KILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR------MNY------P-DH---------------------- 239 (342)
Q Consensus 196 ~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~------~~~------~-~~---------------------- 239 (342)
+|.+|+.+. .-.||+|||+ .||+.+|. +.. . ..
T Consensus 184 ~F~~~i~~~-----------DPDII~GyNi~~FDlpYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~G 252 (881)
T PHA02528 184 EYINFWEEN-----------TPVIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISG 252 (881)
T ss_pred HHHHHHHHh-----------CCcEEEecCCccCCHHHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcc
Confidence 999999543 2259999995 47998876 110 0 00
Q ss_pred -ceeecccccccc-ccCCCCccHHHHHHHHhCCcCCCC----------------CCCcHHHHHHHHHHHHH
Q 019380 240 -MLRDTAKYRPLM-KTNLVSHSLKYLTRTYLGYDIQSG----------------VHDPYEDCVSVMRLYKR 292 (342)
Q Consensus 240 -~~~Dt~~l~~~~-~~~~~~~~L~~l~~~~~~~~~~~~----------------~H~A~~Da~~t~~l~~~ 292 (342)
.++|...+.+.+ +....+|+|+.+|+.+||..-..- .+-.+.||..+.+|+.+
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 012222222221 224568999999999989763321 12235589999999888
No 120
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.46 E-value=0.0075 Score=33.39 Aligned_cols=22 Identities=27% Similarity=0.640 Sum_probs=20.1
Q ss_pred ccccccccccCCHHHHHHHHhh
Q 019380 15 HKCVACYKQFKRKDHLIEHMKI 36 (342)
Q Consensus 15 ~~C~~C~k~f~~~~~L~~H~~~ 36 (342)
|.|..|+++|.+...++.|++.
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 6799999999999999999976
No 121
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=95.44 E-value=0.047 Score=54.38 Aligned_cols=95 Identities=21% Similarity=0.189 Sum_probs=72.4
Q ss_pred HHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhccccCC-CcceeeccccccccccCCCCccHHHHHHHHhCCc
Q 019380 193 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP-DHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 193 v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~~~~~-~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 271 (342)
+...+..|+ .+.+...||||+.+|+.+|...-. .....||+...-.+.|+...+.|++|+..|++..
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 888889999 346778999999999999983332 2446799988888888878899999999997765
Q ss_pred CCCC---------------------CCCcHHHHHHHHHHHHHHHhhhhh
Q 019380 272 IQSG---------------------VHDPYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 272 ~~~~---------------------~H~A~~Da~~t~~l~~~~~~~~~~ 299 (342)
.-.. .-.+..||.++.+|+..+..+..+
T Consensus 134 ~~~~~~i~~kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~l~~ 182 (593)
T COG0749 134 TITFEDIAGKGKKQLTFADVKLEKATEYAAEDADATLRLESILEPELLK 182 (593)
T ss_pred cchhHHhhccccccCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 3211 123567899999999988865443
No 122
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=95.35 E-value=0.1 Score=46.29 Aligned_cols=105 Identities=9% Similarity=0.099 Sum_probs=63.4
Q ss_pred CHhhhcCCCChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCc-hhhhhhcc-----ccCC-------C--------
Q 019380 180 TEEDIKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-----MNYP-------D-------- 238 (342)
Q Consensus 180 t~e~l~~~~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-----~~~~-------~-------- 238 (342)
....+.-.+...+++.+|.+++..- .-.||+|||+ .||+.+|- +..+ +
T Consensus 71 ~~~~v~~~~~E~~LL~~f~~~i~~~-----------DPDii~GyNi~~fd~~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~ 139 (231)
T cd05778 71 SGIPVEVVESELELFEELIDLVRRF-----------DPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGK 139 (231)
T ss_pred CCCeEEEeCCHHHHHHHHHHHHHHh-----------CCCEEEEeccccCcHHHHHHHHHHhCCcchhhhccCCCCCCccc
Confidence 3344555678889999999998443 2349999997 56888765 1000 0
Q ss_pred --------------------cceeeccccccccccCCCCccHHHHHHHHhCCcCCCCCCCcHHHHH------HHHHHHHH
Q 019380 239 --------------------HMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGVHDPYEDCV------SVMRLYKR 292 (342)
Q Consensus 239 --------------------~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~H~A~~Da~------~t~~l~~~ 292 (342)
..++|...+.+.- -...+|+|+.++..+||.....-.+..+.+.. ...++...
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 1112222222221 14568999999999999975544555555542 33445555
Q ss_pred HHhh
Q 019380 293 FRRQ 296 (342)
Q Consensus 293 ~~~~ 296 (342)
++++
T Consensus 219 ~l~d 222 (231)
T cd05778 219 YLKR 222 (231)
T ss_pred HHHH
Confidence 5544
No 123
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.33 E-value=0.013 Score=32.25 Aligned_cols=23 Identities=30% Similarity=0.567 Sum_probs=19.9
Q ss_pred cccccccccCChhhHHHHHhhcC
Q 019380 80 GCNLCMNIFDSPSSLIKHKEACS 102 (342)
Q Consensus 80 ~C~~C~k~F~~~~~L~~H~~~h~ 102 (342)
.|+.|+++|.....|..|++.|.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHHhc
Confidence 37889999999999999998664
No 124
>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=95.22 E-value=0.04 Score=46.51 Aligned_cols=93 Identities=19% Similarity=0.213 Sum_probs=64.4
Q ss_pred HHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhcc---ccCCCcceeeccccccccccCCCCccHHHHHHHHhC
Q 019380 193 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR---MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLG 269 (342)
Q Consensus 193 v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~---~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~ 269 (342)
+...+.+++. +.+...|+||+.+|+.+|. +..+ ..+.||+..+-.+.|...+++|++|+..|++
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 4555777772 2556799999999999996 2332 3468999988888887655799999999988
Q ss_pred CcCCC-C-----C-------C-----CcHHHHHHHHHHHHHHHhhhh
Q 019380 270 YDIQS-G-----V-------H-----DPYEDCVSVMRLYKRFRRQDH 298 (342)
Q Consensus 270 ~~~~~-~-----~-------H-----~A~~Da~~t~~l~~~~~~~~~ 298 (342)
..+.. . . . -+..||.++..|+..+.++.+
T Consensus 111 ~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~~L~ 157 (178)
T cd06140 111 RELPSDEEVYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEEELE 157 (178)
T ss_pred CCCcchHHhcCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77321 0 0 0 134456667777777766654
No 125
>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=95.15 E-value=0.021 Score=37.24 Aligned_cols=27 Identities=22% Similarity=0.476 Sum_probs=17.3
Q ss_pred CCCCcccccccccccCCHHHHHHHHhh
Q 019380 10 RSTARHKCVACYKQFKRKDHLIEHMKI 36 (342)
Q Consensus 10 ~~~~~~~C~~C~k~f~~~~~L~~H~~~ 36 (342)
..+.|..|+.|+..+.+..+|.+|+..
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 356678888888888888888888866
No 126
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=95.03 E-value=0.26 Score=53.38 Aligned_cols=179 Identities=15% Similarity=0.134 Sum_probs=103.9
Q ss_pred CCCCcceeccccccccc---CCCc-ccccceEEeecCCCCeEEe-eecCCCCCccccccccCCCCHhh------hcCCCC
Q 019380 121 CRGPKAVAMDCEMVGGG---SNGT-LDLCARVCLVDEDENVIFH-TYVQPQLPVTNYRYEVTGLTEED------IKNAMP 189 (342)
Q Consensus 121 ~~~~~~v~~D~Ettg~~---~~~~-~~il~~v~vv~~~~~~~~~-~lv~p~~~i~~~~~~i~GIt~e~------l~~~~~ 189 (342)
.+...+.|||+|||-+. +|.. .+|...--+||+.|..+.+ ..|..+ +..+.=-+.++ +-+.+.
T Consensus 243 radp~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREiVs~D------IedfEYTPKpE~eG~F~v~Ne~d 316 (2173)
T KOG1798|consen 243 RADPRVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREIVSED------IEDFEYTPKPEYEGPFCVFNEPD 316 (2173)
T ss_pred cCCceEEEEeeecccCCCCCCCcccceEEEEEEEecCceEEEechhhhccc------hhhcccCCccccccceEEecCCc
Confidence 35567899999999753 3332 2232233345666655432 222211 11111111111 235677
Q ss_pred hHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCchh-hhhhcc-------ccC----CC---------cceeeccccc
Q 019380 190 LKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEH-DLDSLR-------MNY----PD---------HMLRDTAKYR 248 (342)
Q Consensus 190 ~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~-D~~~l~-------~~~----~~---------~~~~Dt~~l~ 248 (342)
...++.++.+-+.+. +.+|+|.+|-+| |+.|+. +.+ .+ .+....+.-+
T Consensus 317 Ev~Ll~RfFeHiq~~-----------kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcf 385 (2173)
T KOG1798|consen 317 EVGLLQRFFEHIQEV-----------KPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCF 385 (2173)
T ss_pred HHHHHHHHHHHHHhc-----------CCcEEEEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehhhh
Confidence 788899999888554 568999999775 999988 111 01 1111122222
Q ss_pred ccc----ccCCCCccHHHHHHHHhCCcCCCC----------------CCCcHHHHHHHHHHHHHHHhhhhhhhhhccCCC
Q 019380 249 PLM----KTNLVSHSLKYLTRTYLGYDIQSG----------------VHDPYEDCVSVMRLYKRFRRQDHQVEEIGNQNT 308 (342)
Q Consensus 249 ~~~----~~~~~~~~L~~l~~~~~~~~~~~~----------------~H~A~~Da~~t~~l~~~~~~~~~~~~~~~~~~~ 308 (342)
++. +-..++.+|+.+...=||...-.- +--++.||.||..||.++..-+- +.+
T Consensus 386 rWVKRDSYLPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVhPFI--FsL----- 458 (2173)
T KOG1798|consen 386 RWVKRDSYLPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVHPFI--FSL----- 458 (2173)
T ss_pred hhhhhcccCCCcccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhhhHH--hhh-----
Confidence 322 334557889998887777763211 45678999999999999987642 111
Q ss_pred CCCCCchhhHHhhhCChhhhhhcc
Q 019380 309 TGSFDSYKYKELEKMSPNELYQIS 332 (342)
Q Consensus 309 ~~~~~~~~~~~~~~~~~~~~~~~~ 332 (342)
--|.++.|+|.+.-.
T Consensus 459 ---------ctIIPl~PDevLRKG 473 (2173)
T KOG1798|consen 459 ---------CTIIPLNPDEVLRKG 473 (2173)
T ss_pred ---------hhccccChHHHHhcC
Confidence 115778888887643
No 127
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=95.01 E-value=0.12 Score=55.81 Aligned_cols=99 Identities=18% Similarity=0.133 Sum_probs=62.6
Q ss_pred hcCCCChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCch-hhhhhcc-----ccCC------C-------------
Q 019380 184 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLR-----MNYP------D------------- 238 (342)
Q Consensus 184 l~~~~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~-~D~~~l~-----~~~~------~------------- 238 (342)
+.-..+..+++.+|.+++..- .-.||+|||+. ||+.+|- +..+ +
T Consensus 324 V~~f~sE~eLL~~f~~~I~~~-----------DPDII~GYNi~~FDlpYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~ 392 (1054)
T PTZ00166 324 VLSFETEKELLLAWAEFVIAV-----------DPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKF 392 (1054)
T ss_pred EEEeCCHHHHHHHHHHHHHhc-----------CCCEEEecCCcCCcHHHHHHHHHHhCCCchhhcCcccCCCcccccccc
Confidence 334567889999999998433 23599999975 7998876 1111 0
Q ss_pred -----------------cceeeccccccccccCCCCccHHHHHHHHhCCcCCCCCC-------------------CcHHH
Q 019380 239 -----------------HMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGVH-------------------DPYED 282 (342)
Q Consensus 239 -----------------~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~H-------------------~A~~D 282 (342)
..++|+..+.+.- ....+|+|+.++..+||.....-.| -.+.|
T Consensus 393 ~~~~~g~~~~~~~~i~GR~~iDl~~~~~~~-~kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~D 471 (1054)
T PTZ00166 393 SSKQMGTRESKEINIEGRIQFDVMDLIRRD-YKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKD 471 (1054)
T ss_pred ccccccccccceeEeeeEEEEEHHHHHHHh-cCcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHH
Confidence 1123333333322 1456899999999999976321121 12458
Q ss_pred HHHHHHHHHHHH
Q 019380 283 CVSVMRLYKRFR 294 (342)
Q Consensus 283 a~~t~~l~~~~~ 294 (342)
|..+.+|+.++.
T Consensus 472 a~L~~~L~~kl~ 483 (1054)
T PTZ00166 472 AILPLRLLDKLL 483 (1054)
T ss_pred HHHHHHHHHHHh
Confidence 888888887764
No 128
>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=94.58 E-value=0.06 Score=47.92 Aligned_cols=76 Identities=26% Similarity=0.312 Sum_probs=52.1
Q ss_pred hcCCCChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCc-hhhhhhcc-----ccCCC-------------------
Q 019380 184 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-----MNYPD------------------- 238 (342)
Q Consensus 184 l~~~~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-----~~~~~------------------- 238 (342)
+.-.....+++..|.++|... .-.||||||+ .||+.+|- +..+.
T Consensus 76 v~~~~~E~~LL~~f~~~i~~~-----------DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~ 144 (234)
T cd05776 76 VRIFENERALLNFFLAKLQKI-----------DPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGG 144 (234)
T ss_pred EEEeCCHHHHHHHHHHHHhhc-----------CCCEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccc
Confidence 334567889999999999543 2249999998 78999876 11110
Q ss_pred ----------cceeeccccccccccCCCCccHHHHHHHHhCCc
Q 019380 239 ----------HMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 239 ----------~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 271 (342)
..++|+..+.+... ...+|+|.++|..+||..
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 12345555444443 367899999999998985
No 129
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=94.35 E-value=0.067 Score=47.57 Aligned_cols=129 Identities=15% Similarity=0.107 Sum_probs=80.2
Q ss_pred eeecCCCCCccccccccCCCCHhhhc--CCCChHH-HHHHHHHHHhcCCCccccccCCCCCeEEEeeCc-hhhhhhcc--
Q 019380 160 HTYVQPQLPVTNYRYEVTGLTEEDIK--NAMPLKE-VKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-- 233 (342)
Q Consensus 160 ~~lv~p~~~i~~~~~~i~GIt~e~l~--~~~~~~~-v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-- 233 (342)
..++.|.....+...+++|++++-+. ...-|+. +..-+..|+ ++. ..---||+||- .+|+..|.
T Consensus 70 svl~~p~~v~~p~aeeitgls~~~~~l~rr~~~D~dla~LL~afl-s~l---------p~p~CLVaHng~~~dfpil~qe 139 (318)
T KOG4793|consen 70 SVLGGPVPVTRPIAEEITGLSQPFLALQRRLAFDKDLAKLLTAFL-SRL---------PTPGCLVAHNGNEYDFPILAQE 139 (318)
T ss_pred hhccCCcCCcChhhhhhcccccHHHHHHHHhhhhHHHHHHHHHHH-hcC---------CCCceEEeecCCccccHHHHHH
Confidence 45667777788889999999986654 3333444 444555555 222 14446899994 35666555
Q ss_pred -----ccCCC-cceeecccccccc--------cc-CCCCccHHHHHHHHhCCcCCCCCCCcHHHHHHHHHHHHHHHhhhh
Q 019380 234 -----MNYPD-HMLRDTAKYRPLM--------KT-NLVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRRQDH 298 (342)
Q Consensus 234 -----~~~~~-~~~~Dt~~l~~~~--------~~-~~~~~~L~~l~~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~~~ 298 (342)
+..|. .-.+|+....... .+ ....|+|..+-..|.+..-..+.|.+..|.-...-+|....++.-
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 44443 2224554432211 11 345789999888886764355689999998888877777766643
No 130
>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=94.21 E-value=0.051 Score=36.45 Aligned_cols=52 Identities=27% Similarity=0.382 Sum_probs=31.0
Q ss_pred CccccCccccCChhhhhhhcCCCcccCCCCCcccCCcccccccccCChhhHHHHHhhcCC
Q 019380 44 PKCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEACSL 103 (342)
Q Consensus 44 ~~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~~C~~C~k~F~~~~~L~~H~~~h~~ 103 (342)
+.|+.|++ ..+...|..|....+.-. ++ ...||.|...++ .+|..|+..+|+
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~--~~---~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSE--SK---NVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCC--CC---CccCCCchhhhh--hHHHHHHHHhcC
Confidence 47999999 455677888861111100 00 013677766544 488999987763
No 131
>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=94.18 E-value=0.056 Score=46.43 Aligned_cols=82 Identities=26% Similarity=0.309 Sum_probs=57.1
Q ss_pred CCeEEEeeCchhhhhhcc--ccCCCcceeeccccccccccCCCCccHHHHHHHHhCCcCCC-------CCC--------C
Q 019380 216 KARLLVGHGLEHDLDSLR--MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQS-------GVH--------D 278 (342)
Q Consensus 216 ~~~~lvgh~~~~D~~~l~--~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~-------~~H--------~ 278 (342)
.+...|+|++..|+..|. .......+.|++..+..+.|. . .+|+.|+..|++..+.. +.. -
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 567899999999999985 222111238999988888887 4 49999999998776311 011 1
Q ss_pred cHHHHHHHHHHHHHHHhhhhh
Q 019380 279 PYEDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 279 A~~Da~~t~~l~~~~~~~~~~ 299 (342)
+..||.++..|+..+..+.++
T Consensus 154 ~a~~a~~l~~L~~~L~~~L~e 174 (192)
T cd06147 154 AREDTHYLLYIYDRLRNELLE 174 (192)
T ss_pred HHhhHHHHHHHHHHHHHHHHH
Confidence 445577778888888777644
No 132
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.16 E-value=0.087 Score=55.76 Aligned_cols=96 Identities=18% Similarity=0.144 Sum_probs=69.6
Q ss_pred ChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhcc---ccCCCcceeeccccccccccCCCCccHHHHHH
Q 019380 189 PLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR---MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTR 265 (342)
Q Consensus 189 ~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~---~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~ 265 (342)
+...+.+.|..++. +.+...||||+.||+.+|. +..+ ..+.||+..+-.+.|... .+|++|+.
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 35567778888883 3556789999999999997 2222 346899988888877544 59999999
Q ss_pred HHhCCcCCC-------C----C-------CCcHHHHHHHHHHHHHHHhhhh
Q 019380 266 TYLGYDIQS-------G----V-------HDPYEDCVSVMRLYKRFRRQDH 298 (342)
Q Consensus 266 ~~~~~~~~~-------~----~-------H~A~~Da~~t~~l~~~~~~~~~ 298 (342)
.|++..... + . .-|..||.+|.+||..+..+..
T Consensus 428 ~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~ 478 (887)
T TIGR00593 428 RYLVEELILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKELD 478 (887)
T ss_pred HHcCcccccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 998754211 0 0 1366789999999998887754
No 133
>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=93.57 E-value=0.53 Score=45.94 Aligned_cols=94 Identities=18% Similarity=0.235 Sum_probs=60.7
Q ss_pred CChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCch-hhhhhcc-----ccCC------C-----------------
Q 019380 188 MPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLR-----MNYP------D----------------- 238 (342)
Q Consensus 188 ~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~-~D~~~l~-----~~~~------~----------------- 238 (342)
....+++.+|.+++... ...+++|||.. ||+.+|. +..+ +
T Consensus 67 ~~E~~lL~~f~~~i~~~-----------dpdii~g~N~~~FD~~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~ 135 (471)
T smart00486 67 NNEKELLKAFLEFIKKY-----------DPDIIYGHNISNFDLPYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSK 135 (471)
T ss_pred CCHHHHHHHHHHHHHHh-----------CCCEEEeecCCCCCHHHHHHHHHHcCCCCHHHcCcCCCCCCcccccCccccc
Confidence 36788899999988432 23599999986 8999876 1110 0
Q ss_pred ------------cceeeccccccccccCCCCccHHHHHHHHhCCcCCCCCC-------------------CcHHHHHHHH
Q 019380 239 ------------HMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGVH-------------------DPYEDCVSVM 287 (342)
Q Consensus 239 ------------~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~H-------------------~A~~Da~~t~ 287 (342)
...+|+..+.+.... ...++|+.++..+||.....-.. -.+.||..+.
T Consensus 136 ~~~~~~~~~~~g~~~~Dl~~~~~~~~k-l~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~ 214 (471)
T smart00486 136 SFGKTIKVKIKGRLVIDLYNLYKNKLK-LPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTL 214 (471)
T ss_pred cccccceeEeccEEEEEhHHHHHHHhC-cccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHH
Confidence 133455555544433 57899999999998844221111 1145888888
Q ss_pred HHHHHH
Q 019380 288 RLYKRF 293 (342)
Q Consensus 288 ~l~~~~ 293 (342)
+|+.++
T Consensus 215 ~l~~~l 220 (471)
T smart00486 215 KLFNKL 220 (471)
T ss_pred HHHHHH
Confidence 888876
No 134
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=93.52 E-value=0.14 Score=41.54 Aligned_cols=55 Identities=20% Similarity=0.190 Sum_probs=42.6
Q ss_pred CCeEEEeeCchhhhhhccc---cCCCcceeeccccccccccCCCCccHHHHHHHHhCCc
Q 019380 216 KARLLVGHGLEHDLDSLRM---NYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 216 ~~~~lvgh~~~~D~~~l~~---~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 271 (342)
.+...|+||+..|+.+|.. ..+ ..+.|++..+-.+.|...+.+|++|+..|++..
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 5567899999999999862 222 346899988888877542359999999998877
No 135
>PRK04860 hypothetical protein; Provisional
Probab=93.52 E-value=0.031 Score=46.52 Aligned_cols=39 Identities=13% Similarity=0.254 Sum_probs=31.6
Q ss_pred CcccccccccccCCHHHHHHHHhhhccCCCCC-ccccCccccCChh
Q 019380 13 ARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFE 57 (342)
Q Consensus 13 ~~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~-~C~~C~~~f~~~~ 57 (342)
-+|.|. |++ ....+.+|.++ |+++++ .|..|++.|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri--~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRV--VRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHH--hcCCccEECCCCCceeEEec
Confidence 469998 987 66778999999 988876 9999998886543
No 136
>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=93.51 E-value=0.02 Score=32.42 Aligned_cols=22 Identities=41% Similarity=0.694 Sum_probs=18.4
Q ss_pred ccccccccccCCHHHHHHHHhh
Q 019380 15 HKCVACYKQFKRKDHLIEHMKI 36 (342)
Q Consensus 15 ~~C~~C~k~f~~~~~L~~H~~~ 36 (342)
|.|..|++.|.+...+..|++.
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 6788888888888888888765
No 137
>PHA02570 dexA exonuclease; Provisional
Probab=93.48 E-value=0.4 Score=41.74 Aligned_cols=100 Identities=18% Similarity=0.130 Sum_probs=54.7
Q ss_pred eecccccccccCCCcccccceEEeecCCCC-eEEeeecCCCCCcccccc--------------ccCCCCHhh---hc---
Q 019380 127 VAMDCEMVGGGSNGTLDLCARVCLVDEDEN-VIFHTYVQPQLPVTNYRY--------------EVTGLTEED---IK--- 185 (342)
Q Consensus 127 v~~D~Ettg~~~~~~~~il~~v~vv~~~~~-~~~~~lv~p~~~i~~~~~--------------~i~GIt~e~---l~--- 185 (342)
+.+|.||-|..++..+-.++++......+. ..|+.+|.....+.-... .+-.=++|- +.
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 569999999987775544355554332332 246666653211111101 111112211 11
Q ss_pred CCCChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhcc
Q 019380 186 NAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR 233 (342)
Q Consensus 186 ~~~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~ 233 (342)
+..++.+++.+|.+||..... ......+=|-+..||+..|+
T Consensus 84 ~~~~l~~al~~F~~fi~~~~~-------~~~~~~vWgnG~sFD~~IL~ 124 (220)
T PHA02570 84 EDVSTYEGHKKFFEYLEANGV-------DPWKSQGWCRGNSFDFPILV 124 (220)
T ss_pred ccccHHHHHHHHHHHHHHcCC-------CccceeEecCCCccCHHHHH
Confidence 235799999999999953210 01224555667899999996
No 138
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=93.17 E-value=0.18 Score=51.58 Aligned_cols=85 Identities=22% Similarity=0.314 Sum_probs=56.0
Q ss_pred CCCeEEEeeCchhhhhhcc----ccCCCcceeecccccccccc-------------------------------------
Q 019380 215 GKARLLVGHGLEHDLDSLR----MNYPDHMLRDTAKYRPLMKT------------------------------------- 253 (342)
Q Consensus 215 ~~~~~lvgh~~~~D~~~l~----~~~~~~~~~Dt~~l~~~~~~------------------------------------- 253 (342)
.++.++||||+.||..-++ +.-....++||+.|--.+++
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 3778999999999999988 22334778999865422211
Q ss_pred CCCCccHHHHHHHHhCCc-CCCCCCCcH--------------------HHHHHHHHHHHHHHhhhhh
Q 019380 254 NLVSHSLKYLTRTYLGYD-IQSGVHDPY--------------------EDCVSVMRLYKRFRRQDHQ 299 (342)
Q Consensus 254 ~~~~~~L~~l~~~~~~~~-~~~~~H~A~--------------------~Da~~t~~l~~~~~~~~~~ 299 (342)
....-||.++++.+.|++ ++....+.. .|+.+|.++|.+++=.+.+
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 011246778888887777 443322221 2889999999888766543
No 139
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=93.08 E-value=0.073 Score=29.05 Aligned_cols=22 Identities=32% Similarity=0.487 Sum_probs=17.4
Q ss_pred ccccccccccCCHHHHHHHHhhh
Q 019380 15 HKCVACYKQFKRKDHLIEHMKIS 37 (342)
Q Consensus 15 ~~C~~C~k~f~~~~~L~~H~~~~ 37 (342)
|+|+.|+.... +..|.+|++.+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 78999998887 88999999873
No 140
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=93.02 E-value=0.053 Score=29.85 Aligned_cols=21 Identities=33% Similarity=0.680 Sum_probs=17.9
Q ss_pred ccccccccCChhhHHHHHhhc
Q 019380 81 CNLCMNIFDSPSSLIKHKEAC 101 (342)
Q Consensus 81 C~~C~k~F~~~~~L~~H~~~h 101 (342)
|..|++.|.....|+.|++.+
T Consensus 3 C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 3 CDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp ETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCcCCHHHHHHHHCcC
Confidence 788999999999999998754
No 141
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=93.01 E-value=0.57 Score=46.16 Aligned_cols=93 Identities=12% Similarity=0.050 Sum_probs=58.2
Q ss_pred CCCChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCch-hhhhhcc--------cc-------CCC-----------
Q 019380 186 NAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLR--------MN-------YPD----------- 238 (342)
Q Consensus 186 ~~~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~-~D~~~l~--------~~-------~~~----------- 238 (342)
.-++..+++.+|.+|+.+- .-.||+|||+. ||+.+|. +. +..
T Consensus 176 ~f~sE~eLL~~F~~~i~~~-----------DPDIItGYNi~nFDlPYL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~~~G 244 (498)
T PHA02524 176 PFEDEVDLLLNYIQLWKAN-----------TPDLVFGWNSEGFDIPYIITRITNILGEKAANQLSPYGKITSKTITNLYG 244 (498)
T ss_pred EeCCHHHHHHHHHHHHHHh-----------CCCEEEeCCCcccCHHHHHHHHHHHhCCccccccccccccccccceeecC
Confidence 4578899999999999442 22599999954 7887765 10 100
Q ss_pred ---------cceeecccccccc-ccCCCCccHHHHHHHHhCCcCCCCCCC----------------cHHHHHHHHHHH
Q 019380 239 ---------HMLRDTAKYRPLM-KTNLVSHSLKYLTRTYLGYDIQSGVHD----------------PYEDCVSVMRLY 290 (342)
Q Consensus 239 ---------~~~~Dt~~l~~~~-~~~~~~~~L~~l~~~~~~~~~~~~~H~----------------A~~Da~~t~~l~ 290 (342)
..++|...+.+.. +....+|+|+.++..+||.. ....|. .+.||..+.+|+
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 1123334444433 33567899999999887765 222221 245777776665
No 142
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=92.95 E-value=0.073 Score=29.58 Aligned_cols=20 Identities=35% Similarity=0.765 Sum_probs=15.5
Q ss_pred cccccccccCChhhHHHHHhh
Q 019380 80 GCNLCMNIFDSPSSLIKHKEA 100 (342)
Q Consensus 80 ~C~~C~k~F~~~~~L~~H~~~ 100 (342)
.|+.||+.| ..+.|.+|++.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHHh
Confidence 378888888 57778888765
No 143
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=92.40 E-value=0.41 Score=42.21 Aligned_cols=75 Identities=20% Similarity=0.221 Sum_probs=43.2
Q ss_pred CCeEEEeeC-chhhhhhcc------ccC-CCcceeeccccccccc-cCCCCccHHHHHHHHhCCcCCCCCCCcHHHHHHH
Q 019380 216 KARLLVGHG-LEHDLDSLR------MNY-PDHMLRDTAKYRPLMK-TNLVSHSLKYLTRTYLGYDIQSGVHDPYEDCVSV 286 (342)
Q Consensus 216 ~~~~lvgh~-~~~D~~~l~------~~~-~~~~~~Dt~~l~~~~~-~~~~~~~L~~l~~~~~~~~~~~~~H~A~~Da~~t 286 (342)
....||.+| ..||+.|++ +.. +...-+|..--.|.+. .....-+|+.+-+ .||+.-.. ---=.|+...
T Consensus 155 ~~~~lvsfNGkaFD~PfikR~v~~~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr-~LGi~R~e--dtdG~~~p~l 231 (278)
T COG3359 155 DFNMLVSFNGKAFDIPFIKRMVRDRLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTVER-ILGIRREE--DTDGYDGPEL 231 (278)
T ss_pred CcceEEEecCcccCcHHHHHHHhcccccCccccchhhhhhhhhhhhccCCCCChhhHHH-HhCccccc--cCCCcchHHH
Confidence 456888887 779999998 111 1133456655444443 2445788999766 55777321 1112355555
Q ss_pred HHHHHHH
Q 019380 287 MRLYKRF 293 (342)
Q Consensus 287 ~~l~~~~ 293 (342)
.++|.+.
T Consensus 232 yr~~~~~ 238 (278)
T COG3359 232 YRLYRRY 238 (278)
T ss_pred HHHHHHc
Confidence 5555555
No 144
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=91.81 E-value=1.5 Score=46.18 Aligned_cols=77 Identities=19% Similarity=0.237 Sum_probs=53.9
Q ss_pred hcCCCChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCch-hhhhhcc-----ccCCC-------------------
Q 019380 184 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLR-----MNYPD------------------- 238 (342)
Q Consensus 184 l~~~~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~-~D~~~l~-----~~~~~------------------- 238 (342)
+....+-.+++.+|.+++.+. ...|+||||.. ||+.+|. +..+.
T Consensus 205 v~~~~~e~e~l~~~~~~i~~~-----------dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~ 273 (792)
T COG0417 205 VEVVISEAELLERFVELIREY-----------DPDVIVGYNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQ 273 (792)
T ss_pred eEEecCHHHHHHHHHHHHHhc-----------CCCEEEeccCCcCChHHHHHHHHHhCCCccccccccccceeecccccc
Confidence 455567889999999999654 34699999988 8999987 11111
Q ss_pred --cceeeccccccccccCCCCccHHHHHHHHhCCc
Q 019380 239 --HMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 239 --~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 271 (342)
...+|...+.+.-......++|+..+..+++..
T Consensus 274 ~Gr~~iDl~~~~~~~~~~~~~ysl~~v~~~~l~~~ 308 (792)
T COG0417 274 VGRLHIDLYPALRRRPLNLKSYSLEAVSEALLGEG 308 (792)
T ss_pred cceEEEecHHHHhhhhcccccccHHHHHHHhcccc
Confidence 134566555553223456899999999997766
No 145
>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=91.75 E-value=0.068 Score=30.19 Aligned_cols=20 Identities=30% Similarity=0.695 Sum_probs=15.3
Q ss_pred ccccccccCChhhHHHHHhh
Q 019380 81 CNLCMNIFDSPSSLIKHKEA 100 (342)
Q Consensus 81 C~~C~k~F~~~~~L~~H~~~ 100 (342)
|..|++.|.....+..|++.
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 67788888888888877754
No 146
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=91.37 E-value=0.1 Score=28.41 Aligned_cols=23 Identities=22% Similarity=0.300 Sum_probs=17.2
Q ss_pred cccccccccCChhhHHHHHhhcCC
Q 019380 80 GCNLCMNIFDSPSSLIKHKEACSL 103 (342)
Q Consensus 80 ~C~~C~k~F~~~~~L~~H~~~h~~ 103 (342)
.|+.|+.+.+ +..|.+|++.+++
T Consensus 2 ~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 2 KCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp E-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCcCC-HHHHHHHHHhhCc
Confidence 3788888887 8899999998763
No 147
>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=91.13 E-value=0.14 Score=28.79 Aligned_cols=22 Identities=18% Similarity=0.427 Sum_probs=15.3
Q ss_pred ccCCCCCcccCC--cccccccccC
Q 019380 68 SKAHCSGIFSDR--GCNLCMNIFD 89 (342)
Q Consensus 68 ~C~~C~k~f~~~--~C~~C~k~F~ 89 (342)
.|+.|++..... .|+.||..|.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCCc
Confidence 467777666543 3888988875
No 148
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=91.08 E-value=0.19 Score=27.88 Aligned_cols=21 Identities=38% Similarity=0.694 Sum_probs=16.8
Q ss_pred ccccccccccCCHHHHHHHHhh
Q 019380 15 HKCVACYKQFKRKDHLIEHMKI 36 (342)
Q Consensus 15 ~~C~~C~k~f~~~~~L~~H~~~ 36 (342)
.+|+.||++| ....|..|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4799999999 56778888764
No 149
>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=89.29 E-value=0.31 Score=29.06 Aligned_cols=23 Identities=22% Similarity=0.355 Sum_probs=20.6
Q ss_pred cccccccccccCCHHHHHHHHhh
Q 019380 14 RHKCVACYKQFKRKDHLIEHMKI 36 (342)
Q Consensus 14 ~~~C~~C~k~f~~~~~L~~H~~~ 36 (342)
+|.|+.|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 68899999999999999999865
No 150
>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=89.19 E-value=3.6 Score=40.49 Aligned_cols=89 Identities=19% Similarity=0.248 Sum_probs=56.8
Q ss_pred hHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCchhhhhhcc---ccCCC---------cceeecccccc-ccccCCC
Q 019380 190 LKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR---MNYPD---------HMLRDTAKYRP-LMKTNLV 256 (342)
Q Consensus 190 ~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~~D~~~l~---~~~~~---------~~~~Dt~~l~~-~~~~~~~ 256 (342)
..+++.+|.+|+... .+..|+.+| .+...+|+ -.++. .+++|...+.+ .......
T Consensus 328 E~~~~~~f~~~l~~~-----------~~~~i~hY~-~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~ 395 (457)
T TIGR03491 328 EELAWQQFLQLLQSY-----------PDAPIYHYG-ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIE 395 (457)
T ss_pred HHHHHHHHHHHHHHC-----------CCCeEEeeC-HHHHHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCC
Confidence 456788888888432 456888888 78887777 11211 25677765444 2323446
Q ss_pred CccHHHHHHHHhCCcCCCCCCCcHHHHHHHHHHHHHHHh
Q 019380 257 SHSLKYLTRTYLGYDIQSGVHDPYEDCVSVMRLYKRFRR 295 (342)
Q Consensus 257 ~~~L~~l~~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~ 295 (342)
+|||+.++..+ |.... +...|.-.++..|..++.
T Consensus 396 sysLK~v~~~l-g~~~~----~~~~~G~~ai~~y~~~~~ 429 (457)
T TIGR03491 396 SYSLKSIARWL-GFEWR----QKEASGAKSLLWYRQWKK 429 (457)
T ss_pred CCCHHHHHHHh-CcccC----CCCCCHHHHHHHHHHHHH
Confidence 89999999988 88744 234455556666666644
No 151
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=87.49 E-value=0.4 Score=49.41 Aligned_cols=36 Identities=11% Similarity=0.182 Sum_probs=22.8
Q ss_pred cCCCCCCCCcccccccccc--------------cCCCCcceecccccccc
Q 019380 101 CSLSAPVPFKISGAIDEKR--------------TCRGPKAVAMDCEMVGG 136 (342)
Q Consensus 101 h~~~~~~~~~~c~~~~~~~--------------~~~~~~~v~~D~Ettg~ 136 (342)
|+...|..|+.|+...-.. -=+..+++.+|.++|..
T Consensus 470 ~~~~~p~~Cp~Cgs~~L~~~G~GterieeeL~~~FP~~rv~r~d~Dtt~~ 519 (730)
T COG1198 470 YQEPIPQSCPECGSEHLRAVGPGTERIEEELKRLFPGARIIRIDSDTTRR 519 (730)
T ss_pred CCCCCCCCCCCCCCCeeEEecccHHHHHHHHHHHCCCCcEEEEccccccc
Confidence 3445566777777662211 11566788999999964
No 152
>PRK04860 hypothetical protein; Provisional
Probab=87.28 E-value=0.38 Score=40.07 Aligned_cols=35 Identities=14% Similarity=0.208 Sum_probs=29.7
Q ss_pred cccccccccCChhhHHHHHhhcCCCCCCCCccccccccc
Q 019380 80 GCNLCMNIFDSPSSLIKHKEACSLSAPVPFKISGAIDEK 118 (342)
Q Consensus 80 ~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~c~~~~~~ 118 (342)
.|. |++ ...++++|.++|.+++++.|..|+.....
T Consensus 121 ~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 121 RCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 477 876 77789999999999999999999876543
No 153
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=86.76 E-value=0.57 Score=35.06 Aligned_cols=28 Identities=32% Similarity=0.673 Sum_probs=23.3
Q ss_pred cccccccccccCCHHHHHHHHhhhccCC
Q 019380 14 RHKCVACYKQFKRKDHLIEHMKISYHSV 41 (342)
Q Consensus 14 ~~~C~~C~k~f~~~~~L~~H~~~~~H~~ 41 (342)
.+.|..|++.|.+...|..|++.+.|..
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~ 77 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKK 77 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCC
Confidence 6999999999999999999999854543
No 154
>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=86.59 E-value=1.1 Score=41.64 Aligned_cols=91 Identities=14% Similarity=0.142 Sum_probs=52.4
Q ss_pred CCCcceecccccccccC---CCcccccceEEe-ecCC-----CCeEEeeecCCCCCccccccccCCCCHhhhcCCCChHH
Q 019380 122 RGPKAVAMDCEMVGGGS---NGTLDLCARVCL-VDED-----ENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKE 192 (342)
Q Consensus 122 ~~~~~v~~D~Ettg~~~---~~~~~il~~v~v-v~~~-----~~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~ 192 (342)
+...+++||+|+...+. +.....+..+++ +... ....+-.+..+... .. ...+.-.....+
T Consensus 155 p~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~~~~~~~-~~---------~~~v~~~~~E~~ 224 (325)
T PF03104_consen 155 PPLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTLGSCDSI-ED---------NVEVIYFDSEKE 224 (325)
T ss_dssp GGSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEECSCSCCT-TC---------TTEEEEESSHHH
T ss_pred cccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEecCCCCC-CC---------CcEEEEECCHHH
Confidence 56778999999986541 222222244443 2212 11122222222211 11 334444578899
Q ss_pred HHHHHHHHHhcCCCccccccCCCCCeEEEeeCch-hhhhhcc
Q 019380 193 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLR 233 (342)
Q Consensus 193 v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~-~D~~~l~ 233 (342)
++..|.++|.+. .-.+|+|||+. ||+.+|.
T Consensus 225 lL~~f~~~i~~~-----------dPDii~GyN~~~fD~~yl~ 255 (325)
T PF03104_consen 225 LLEAFLDIIQEY-----------DPDIITGYNIDGFDLPYLI 255 (325)
T ss_dssp HHHHHHHHHHHH-----------S-SEEEESSTTTTHHHHHH
T ss_pred HHHHHHHHHHhc-----------CCcEEEEecccCCCHHHHH
Confidence 999999999543 22499999976 7999887
No 155
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=86.34 E-value=0.37 Score=46.09 Aligned_cols=49 Identities=31% Similarity=0.603 Sum_probs=43.6
Q ss_pred CcccccccccccCCHHHHHHHHh--hhccCCC--CC-ccc--cCccccCChhhhhhhc
Q 019380 13 ARHKCVACYKQFKRKDHLIEHMK--ISYHSVH--QP-KCA--VCQKLSKSFESLREHL 63 (342)
Q Consensus 13 ~~~~C~~C~k~f~~~~~L~~H~~--~~~H~~~--~~-~C~--~C~~~f~~~~~l~~H~ 63 (342)
.++.|..|...|+....+..|.+ . |+.+ ++ .|. .|++.|.....+..|.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~--h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~ 343 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVN--HSGESLKPFSCPYSLCGKLFSRNDALKRHI 343 (467)
T ss_pred cCCCCccccCCccccccccccccccc--cccccCCceeeeccCCCccccccccccCCc
Confidence 47999999999999999999999 7 8888 77 888 7999999999888887
No 156
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.67 E-value=0.87 Score=46.15 Aligned_cols=72 Identities=25% Similarity=0.306 Sum_probs=35.5
Q ss_pred CCHHHHHHHHhhhccCCCCC-cc-------ccCccccCChhhhhhhc-CCCcccCCCCCcccC-CcccccccccCChhhH
Q 019380 25 KRKDHLIEHMKISYHSVHQP-KC-------AVCQKLSKSFESLREHL-TGPLSKAHCSGIFSD-RGCNLCMNIFDSPSSL 94 (342)
Q Consensus 25 ~~~~~L~~H~~~~~H~~~~~-~C-------~~C~~~f~~~~~l~~H~-~~~~~C~~C~k~f~~-~~C~~C~k~F~~~~~L 94 (342)
.....|+.|+.. .|....- -| ..+.+. -+...|..|. .+.. +++.|.. ..|..|...|.....|
T Consensus 125 ~s~~~Lk~H~~~-~H~~~~c~lC~~~~kif~~e~k~-Yt~~el~~h~~~gd~----d~~s~rGhp~C~~C~~~fld~~el 198 (669)
T KOG2231|consen 125 KSVENLKNHMRD-QHKLHLCSLCLQNLKIFINERKL-YTRAELNLHLMFGDP----DDESCRGHPLCKFCHERFLDDDEL 198 (669)
T ss_pred hHHHHHHHHHHH-hhhhhccccccccceeeeeeeeh-ehHHHHHHHHhcCCC----ccccccCCccchhhhhhhccHHHH
Confidence 366778888842 1432211 12 222222 2344566665 2211 3333333 3466666666666666
Q ss_pred HHHHhhcC
Q 019380 95 IKHKEACS 102 (342)
Q Consensus 95 ~~H~~~h~ 102 (342)
.+|++.+|
T Consensus 199 ~rH~~~~h 206 (669)
T KOG2231|consen 199 YRHLRFDH 206 (669)
T ss_pred HHhhccce
Confidence 66666544
No 157
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.62 E-value=1.9 Score=33.42 Aligned_cols=22 Identities=23% Similarity=0.588 Sum_probs=13.8
Q ss_pred ccccccccCChhhHHHHHhhcC
Q 019380 81 CNLCMNIFDSPSSLIKHKEACS 102 (342)
Q Consensus 81 C~~C~k~F~~~~~L~~H~~~h~ 102 (342)
|+.|.+.|-.....-.|...|+
T Consensus 84 C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 84 CAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred CCCCCCccccccchhhhhhccC
Confidence 6666666666556666765555
No 158
>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=83.28 E-value=0.65 Score=35.95 Aligned_cols=25 Identities=24% Similarity=0.473 Sum_probs=15.5
Q ss_pred cccCCCCCcccCCc-----ccccccccCCh
Q 019380 67 LSKAHCSGIFSDRG-----CNLCMNIFDSP 91 (342)
Q Consensus 67 ~~C~~C~k~f~~~~-----C~~C~k~F~~~ 91 (342)
..|+.||+.|..-. |+.||..|...
T Consensus 10 R~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 34666666665432 77777777655
No 159
>PRK14873 primosome assembly protein PriA; Provisional
Probab=82.52 E-value=0.82 Score=46.99 Aligned_cols=43 Identities=21% Similarity=0.329 Sum_probs=25.5
Q ss_pred ccccCccccCCh---hhhhhhc-CCCcccCCCCCcccCCcccccccc
Q 019380 45 KCAVCQKLSKSF---ESLREHL-TGPLSKAHCSGIFSDRGCNLCMNI 87 (342)
Q Consensus 45 ~C~~C~~~f~~~---~~l~~H~-~~~~~C~~C~k~f~~~~C~~C~k~ 87 (342)
.|..||..+... ..|.-|. .+...|..||.......|+.||..
T Consensus 385 ~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 385 ACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred EhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 466665554332 3355565 345668888776555568888754
No 160
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=81.92 E-value=0.69 Score=40.55 Aligned_cols=14 Identities=36% Similarity=0.596 Sum_probs=10.2
Q ss_pred ccccCccccCChhh
Q 019380 45 KCAVCQKLSKSFES 58 (342)
Q Consensus 45 ~C~~C~~~f~~~~~ 58 (342)
.|++|++.|.++.-
T Consensus 7 ~CPvC~~~F~~~~v 20 (214)
T PF09986_consen 7 TCPVCGKEFKTKKV 20 (214)
T ss_pred ECCCCCCeeeeeEE
Confidence 78888888876643
No 161
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=81.25 E-value=1.1 Score=48.52 Aligned_cols=80 Identities=20% Similarity=0.275 Sum_probs=40.8
Q ss_pred CCCCcccccccccccCCHHHHHHHHhhhccCCCCCccccCccccCChhhhhhhcCCCcccCCCCCcccCCcccccccccC
Q 019380 10 RSTARHKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFD 89 (342)
Q Consensus 10 ~~~~~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~~C~~C~k~F~ 89 (342)
+-.+-|+|+.|+..|.....|..||+++ |.+... ..|. .+...-.+.+ .-.|.|.+ .-..|..|..+++
T Consensus 461 S~~kt~~cpkc~~~yk~a~~L~vhmRsk-hp~~~~--~~c~-~gq~~~~~ar--g~~~~~~~-----~p~~C~~C~~stt 529 (1406)
T KOG1146|consen 461 SFFKTLKCPKCNWHYKLAQTLGVHMRSK-HPESQS--AYCK-AGQNHPRLAR--GEVYRCPG-----KPYPCRACNYSTT 529 (1406)
T ss_pred cccccccCCccchhhhhHHHhhhccccc-ccccch--hHhH-hccccccccc--cccccCCC-----Ccccceeeeeeee
Confidence 3446667777777777777777777653 222211 1111 0110000000 00122211 0113788889999
Q ss_pred ChhhHHHHHhh
Q 019380 90 SPSSLIKHKEA 100 (342)
Q Consensus 90 ~~~~L~~H~~~ 100 (342)
.+.+|.+|++.
T Consensus 530 tng~LsihlqS 540 (1406)
T KOG1146|consen 530 TNGNLSIHLQS 540 (1406)
T ss_pred cchHHHHHHHH
Confidence 99999999875
No 162
>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=80.48 E-value=1.1 Score=26.62 Aligned_cols=21 Identities=29% Similarity=0.485 Sum_probs=17.5
Q ss_pred cccccccccCChhhHHHHHhh
Q 019380 80 GCNLCMNIFDSPSSLIKHKEA 100 (342)
Q Consensus 80 ~C~~C~k~F~~~~~L~~H~~~ 100 (342)
.|..|++.|.....+..|++.
T Consensus 5 ~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 5 YCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred EccccCCccCCHHHHHHHHCh
Confidence 478899999988889998854
No 163
>PRK04023 DNA polymerase II large subunit; Validated
Probab=78.77 E-value=1.9 Score=45.47 Aligned_cols=20 Identities=15% Similarity=0.386 Sum_probs=10.5
Q ss_pred cccCCCCCcccCCccccccc
Q 019380 67 LSKAHCSGIFSDRGCNLCMN 86 (342)
Q Consensus 67 ~~C~~C~k~f~~~~C~~C~k 86 (342)
+.|+.|+.......|+.||.
T Consensus 652 ~fCP~CG~~~~~y~CPKCG~ 671 (1121)
T PRK04023 652 YRCPRCGIEVEEDECEKCGR 671 (1121)
T ss_pred eeCccccCcCCCCcCCCCCC
Confidence 44555555554445555553
No 164
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=78.55 E-value=1.3 Score=40.36 Aligned_cols=19 Identities=16% Similarity=0.228 Sum_probs=16.1
Q ss_pred cccccccCChhhHHHHHhh
Q 019380 82 NLCMNIFDSPSSLIKHKEA 100 (342)
Q Consensus 82 ~~C~k~F~~~~~L~~H~~~ 100 (342)
+-|.|.|+....|+.|+.-
T Consensus 355 ~gC~K~YknqnGLKYH~lh 373 (423)
T COG5189 355 EGCNKKYKNQNGLKYHMLH 373 (423)
T ss_pred CCchhhhccccchhhhhhc
Confidence 4589999999999999864
No 165
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=77.48 E-value=3.4 Score=37.06 Aligned_cols=83 Identities=10% Similarity=0.032 Sum_probs=52.8
Q ss_pred CCCCeEEEeeC-chhhhhhccc-------cCCC-cceeeccccccc----ccc-CCCCccHHHHHHHHhCCcCCCCCCCc
Q 019380 214 DGKARLLVGHG-LEHDLDSLRM-------NYPD-HMLRDTAKYRPL----MKT-NLVSHSLKYLTRTYLGYDIQSGVHDP 279 (342)
Q Consensus 214 ~~~~~~lvgh~-~~~D~~~l~~-------~~~~-~~~~Dt~~l~~~----~~~-~~~~~~L~~l~~~~~~~~~~~~~H~A 279 (342)
++...+.+.|| +.+++.|... +.+. ...|+.+.+.+. ..| ....++|..|+.++ ......++|+|
T Consensus 195 pa~~~~e~d~~~l~~~fqf~~~ellR~~deqa~pw~~ir~l~~~~~~a~~~~P~p~~vs~le~Lat~~-~~~p~l~ahra 273 (318)
T KOG4793|consen 195 PAGHVAEGDVNGLLFIFQFRINELLRWSDEQARPWLLIRPLYLARENAKSVEPTPKLVSSLEALATYY-SLTPELDAHRA 273 (318)
T ss_pred CcceeeecccchhHHHHHHHHHHHHhhHhhcCCCcccccchhhhhhhccccCCCCccchhHHHHHHHh-hcCcccchhhh
Confidence 33444444444 4556666541 1111 234555544322 234 33468899999999 66657779999
Q ss_pred HHHHHHHHHHHHHHHhhh
Q 019380 280 YEDCVSVMRLYKRFRRQD 297 (342)
Q Consensus 280 ~~Da~~t~~l~~~~~~~~ 297 (342)
+.|+..+-+++.++....
T Consensus 274 ~~Dv~~~~k~~q~~~idl 291 (318)
T KOG4793|consen 274 LSDVLLLSKVFQKLTIDL 291 (318)
T ss_pred ccccchhhhHHHHhhhhh
Confidence 999999999999987664
No 166
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=76.96 E-value=2.1 Score=46.39 Aligned_cols=33 Identities=15% Similarity=0.361 Sum_probs=20.1
Q ss_pred ccccCccccCChhhhhhhcCCCcccCCCCCcccCC-----cccccccc
Q 019380 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDR-----GCNLCMNI 87 (342)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~-----~C~~C~k~ 87 (342)
.|+.||... ...+.|+.|+...... .|+.||..
T Consensus 681 fCP~CGs~t----------e~vy~CPsCGaev~~des~a~~CP~CGtp 718 (1337)
T PRK14714 681 RCPDCGTHT----------EPVYVCPDCGAEVPPDESGRVECPRCDVE 718 (1337)
T ss_pred cCcccCCcC----------CCceeCccCCCccCCCccccccCCCCCCc
Confidence 566676442 2245788887765544 58888743
No 167
>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=76.42 E-value=1.5 Score=34.56 Aligned_cols=27 Identities=11% Similarity=0.035 Sum_probs=17.8
Q ss_pred cccCCCCCcccCCc-----ccccccccCChhh
Q 019380 67 LSKAHCSGIFSDRG-----CNLCMNIFDSPSS 93 (342)
Q Consensus 67 ~~C~~C~k~f~~~~-----C~~C~k~F~~~~~ 93 (342)
..|+.||+.|..-. |+.||..|.....
T Consensus 10 r~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~~~ 41 (129)
T TIGR02300 10 RICPNTGSKFYDLNRRPAVSPYTGEQFPPEEA 41 (129)
T ss_pred ccCCCcCccccccCCCCccCCCcCCccCcchh
Confidence 45777777776542 8888888765533
No 168
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=75.59 E-value=18 Score=39.98 Aligned_cols=107 Identities=14% Similarity=0.223 Sum_probs=67.4
Q ss_pred cCCCCHhhhcCCCChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCc-hhhhhhcc-----ccCCC-----------
Q 019380 176 VTGLTEEDIKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR-----MNYPD----------- 238 (342)
Q Consensus 176 i~GIt~e~l~~~~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~-----~~~~~----------- 238 (342)
.-|+.+..|..-..-.+.+..++.++... ...+++|||+ .||+.+|- +..+.
T Consensus 570 ~~~~~~~~L~~~~sEr~lL~~fl~~~~~~-----------DPDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~ 638 (1172)
T TIGR00592 570 FPGKKPSLVEDLATERALIKKFMAKVKKI-----------DPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSP 638 (1172)
T ss_pred hhccCCcEEEEecCHHHHHHHHHHHHHhc-----------CCCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccCC
Confidence 34555566666777888888888888322 2349999995 46777765 11111
Q ss_pred ------------cceeeccccccccccCCCCccHHHHHHHHhCCcCCCC------------------CCCcHHHHHHHHH
Q 019380 239 ------------HMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSG------------------VHDPYEDCVSVMR 288 (342)
Q Consensus 239 ------------~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~------------------~H~A~~Da~~t~~ 288 (342)
..++|+..+.+... ...+|+|..++..+||..-..- ....+.||..+++
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 23456655554443 3578999999999998642110 1223567777777
Q ss_pred HHHHHH
Q 019380 289 LYKRFR 294 (342)
Q Consensus 289 l~~~~~ 294 (342)
|+.++.
T Consensus 718 L~~~l~ 723 (1172)
T TIGR00592 718 IMCELN 723 (1172)
T ss_pred HHHHHh
Confidence 766543
No 169
>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=74.55 E-value=0.98 Score=46.70 Aligned_cols=29 Identities=17% Similarity=0.154 Sum_probs=0.0
Q ss_pred CCCcccCCCCCcccCCcccccccccCChh
Q 019380 64 TGPLSKAHCSGIFSDRGCNLCMNIFDSPS 92 (342)
Q Consensus 64 ~~~~~C~~C~k~f~~~~C~~C~k~F~~~~ 92 (342)
...|.|+.|+.......|+.|+......+
T Consensus 678 ~~~~~Cp~C~~~~~~~~C~~C~~~~~~~~ 706 (900)
T PF03833_consen 678 EPVYVCPDCGIEVEEDECPKCGRETTSYS 706 (900)
T ss_dssp -----------------------------
T ss_pred ccceeccccccccCccccccccccCcccc
Confidence 34578888888888888999987655443
No 170
>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=73.48 E-value=4.3 Score=33.00 Aligned_cols=55 Identities=22% Similarity=0.202 Sum_probs=41.5
Q ss_pred CCeEEEeeCchhhhhhcc---ccCCCcceeeccccccccccCCCCccHHHHHHHHhCCc
Q 019380 216 KARLLVGHGLEHDLDSLR---MNYPDHMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 216 ~~~~lvgh~~~~D~~~l~---~~~~~~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 271 (342)
.+...|+||+..++.+|+ +..+ ....|++..+-.+.|.....+|++|++.|++..
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 455689999999999985 3332 335799988878888655239999999998776
No 171
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=72.39 E-value=2.7 Score=32.52 Aligned_cols=10 Identities=30% Similarity=0.627 Sum_probs=4.5
Q ss_pred ccccccccCC
Q 019380 81 CNLCMNIFDS 90 (342)
Q Consensus 81 C~~C~k~F~~ 90 (342)
|+.||+.|..
T Consensus 12 Cp~CG~kFYD 21 (108)
T PF09538_consen 12 CPSCGAKFYD 21 (108)
T ss_pred CCCCcchhcc
Confidence 4444444443
No 172
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=71.26 E-value=2.8 Score=35.88 Aligned_cols=97 Identities=20% Similarity=0.337 Sum_probs=60.9
Q ss_pred CCCCCCCCCCCCCcccccc--cccccCCHHHHHHHHhhhccCCCCCccccCccccCChhhhhhhcC------------C-
Q 019380 1 MDTEAELPKRSTARHKCVA--CYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHLT------------G- 65 (342)
Q Consensus 1 ~~~~~~~~~~~~~~~~C~~--C~k~f~~~~~L~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~~------------~- 65 (342)
||..+.+-.-+.+.+.|+. |-..|..-.....|- |+.....|..|.+.|.+..-|..|.. +
T Consensus 66 ~d~~d~~~~~~~~~~~cqvagc~~~~d~lD~~E~hY----~~~h~~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG 141 (253)
T KOG4173|consen 66 MDVADVPEKPRVPAFACQVAGCCQVFDALDDYEHHY----HTLHGNSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERG 141 (253)
T ss_pred eeccccccccccccccccccchHHHHhhhhhHHHhh----hhcccchhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcC
Confidence 3444444434566799976 555566555444444 55444589999999999998888871 1
Q ss_pred --CcccCCCCCcccCCcccccccccCChhhHHHHH-hhcCCCCCCCCcc
Q 019380 66 --PLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHK-EACSLSAPVPFKI 111 (342)
Q Consensus 66 --~~~C~~C~k~f~~~~C~~C~k~F~~~~~L~~H~-~~h~~~~~~~~~~ 111 (342)
-|+|- =..|+..|.+.-.-..|+ +.|.....+....
T Consensus 142 ~dMy~Cl----------vEgCt~KFkT~r~RkdH~I~~Hk~Pa~frFdk 180 (253)
T KOG4173|consen 142 QDMYQCL----------VEGCTEKFKTSRDRKDHMIRMHKYPADFRFDK 180 (253)
T ss_pred ccHHHHH----------HHhhhhhhhhhhhhhhHHHHhccCCcceeecC
Confidence 13441 145777777776667776 4566665655554
No 173
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=70.89 E-value=2.2 Score=37.63 Aligned_cols=59 Identities=14% Similarity=0.291 Sum_probs=29.8
Q ss_pred CCCCcccccccccccCCHHHHHHHHhhhccCCCCC--ccccCccccCChhhhhhhcCCCcccCCCCCcccCC
Q 019380 10 RSTARHKCVACYKQFKRKDHLIEHMKISYHSVHQP--KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDR 79 (342)
Q Consensus 10 ~~~~~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~--~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~ 79 (342)
+..+.|.|..|...|=. + ....+. +|.-|.+.|.---.=+..-...|.|+.|+..|...
T Consensus 108 ~~drqFaC~~Cd~~WwR--------r---vp~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 108 SVDRQFACSSCDHMWWR--------R---VPQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred ccceeeeccccchHHHh--------c---cCcccccccccccccccCCCccccccceeeeecccccccchhh
Confidence 56677778777644321 1 122222 67777766543321111114466666666666543
No 174
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=70.42 E-value=0.56 Score=41.14 Aligned_cols=18 Identities=33% Similarity=0.632 Sum_probs=14.9
Q ss_pred CCcccccccccccCCHHH
Q 019380 12 TARHKCVACYKQFKRKDH 29 (342)
Q Consensus 12 ~~~~~C~~C~k~f~~~~~ 29 (342)
++...||.|++.|.++..
T Consensus 3 ~k~~~CPvC~~~F~~~~v 20 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKV 20 (214)
T ss_pred CCceECCCCCCeeeeeEE
Confidence 467899999999998663
No 175
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=70.15 E-value=1.6 Score=29.03 Aligned_cols=23 Identities=22% Similarity=0.449 Sum_probs=18.5
Q ss_pred ccccccccCChhhHHHHHhhcCC
Q 019380 81 CNLCMNIFDSPSSLIKHKEACSL 103 (342)
Q Consensus 81 C~~C~k~F~~~~~L~~H~~~h~~ 103 (342)
||.||..|....++.+|....|+
T Consensus 20 CPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 20 CPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCchhHHHHHhHHHHHHhhHHhh
Confidence 88888888888888888866554
No 176
>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=68.57 E-value=2.2 Score=34.21 Aligned_cols=25 Identities=24% Similarity=0.384 Sum_probs=16.6
Q ss_pred ccccccccCChhhHHHHHhhcCCCCCCC
Q 019380 81 CNLCMNIFDSPSSLIKHKEACSLSAPVP 108 (342)
Q Consensus 81 C~~C~k~F~~~~~L~~H~~~h~~~~~~~ 108 (342)
|-+||+.|+ .|++|.+.|||-.|-.
T Consensus 75 clecGk~~k---~LkrHL~~~~gltp~e 99 (132)
T PF05443_consen 75 CLECGKKFK---TLKRHLRTHHGLTPEE 99 (132)
T ss_dssp -TBT--EES---BHHHHHHHTT-S-HHH
T ss_pred EccCCcccc---hHHHHHHHccCCCHHH
Confidence 899999998 4689999999887743
No 177
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=67.98 E-value=3.2 Score=22.45 Aligned_cols=18 Identities=22% Similarity=0.567 Sum_probs=9.0
Q ss_pred cCCCCCcccCCc--cccccc
Q 019380 69 KAHCSGIFSDRG--CNLCMN 86 (342)
Q Consensus 69 C~~C~k~f~~~~--C~~C~k 86 (342)
|+.|++...... |+.||.
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CcccCCCCCCcCcchhhhCC
Confidence 445555444332 666664
No 178
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=67.76 E-value=5 Score=41.11 Aligned_cols=36 Identities=14% Similarity=0.215 Sum_probs=25.8
Q ss_pred ccccCccccCChhhhhhhcCCCcccCCCCCcccCC--cccccccccCCh
Q 019380 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDR--GCNLCMNIFDSP 91 (342)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~--~C~~C~k~F~~~ 91 (342)
.|..||..+.. ..|+.||...... -|+.||....+.
T Consensus 17 FC~~CG~~l~~-----------~~Cp~CG~~~~~~~~fC~~CG~~~~~~ 54 (645)
T PRK14559 17 FCQKCGTSLTH-----------KPCPQCGTEVPVDEAHCPNCGAETGTI 54 (645)
T ss_pred cccccCCCCCC-----------CcCCCCCCCCCcccccccccCCcccch
Confidence 69999877631 3699999875543 399999776654
No 179
>PRK05761 DNA polymerase I; Reviewed
Probab=67.72 E-value=22 Score=37.60 Aligned_cols=89 Identities=18% Similarity=0.173 Sum_probs=55.3
Q ss_pred CChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeCch-hhhhhcc-----ccCCC---------cc-eeecccccccc
Q 019380 188 MPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLR-----MNYPD---------HM-LRDTAKYRPLM 251 (342)
Q Consensus 188 ~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~~-~D~~~l~-----~~~~~---------~~-~~Dt~~l~~~~ 251 (342)
.+..+++.+|.+++.+ . .+.|++|.. ||+..|. +..+. .. .+|....+...
T Consensus 208 ~~E~eLL~~f~~~i~~------------~-dPdi~yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~ 274 (787)
T PRK05761 208 DSEKELLAELFDIILE------------Y-PPVVTFNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNK 274 (787)
T ss_pred CCHHHHHHHHHHHHHh------------c-CCEEEEcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheeec
Confidence 6789999999999943 2 355668854 7998877 11111 00 13433322211
Q ss_pred -------cc--CCCCccHHHHHHHHhCCcCCCC-------------CCCcHHHHHHHHHHH
Q 019380 252 -------KT--NLVSHSLKYLTRTYLGYDIQSG-------------VHDPYEDCVSVMRLY 290 (342)
Q Consensus 252 -------~~--~~~~~~L~~l~~~~~~~~~~~~-------------~H~A~~Da~~t~~l~ 290 (342)
.+ ....++|..+++.+||.. +.. +.=.+.||..|.+|.
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 122689999999998986 321 233577999999985
No 180
>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=66.99 E-value=2.8 Score=25.50 Aligned_cols=10 Identities=30% Similarity=1.009 Sum_probs=4.9
Q ss_pred cccccccccC
Q 019380 16 KCVACYKQFK 25 (342)
Q Consensus 16 ~C~~C~k~f~ 25 (342)
+|+.|+..|.
T Consensus 4 ~CP~C~~~~~ 13 (38)
T TIGR02098 4 QCPNCKTSFR 13 (38)
T ss_pred ECCCCCCEEE
Confidence 4555555443
No 181
>PF14353 CpXC: CpXC protein
Probab=66.37 E-value=1.4 Score=35.15 Aligned_cols=17 Identities=29% Similarity=0.567 Sum_probs=10.5
Q ss_pred ccccccccCChhhHHHH
Q 019380 81 CNLCMNIFDSPSSLIKH 97 (342)
Q Consensus 81 C~~C~k~F~~~~~L~~H 97 (342)
|+.||..|.-...+..|
T Consensus 41 CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 41 CPSCGHKFRLEYPLLYH 57 (128)
T ss_pred CCCCCCceecCCCEEEE
Confidence 77777777655444433
No 182
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=65.94 E-value=3.6 Score=32.79 Aligned_cols=24 Identities=38% Similarity=0.850 Sum_probs=13.5
Q ss_pred CcccCCCCCcccCC------cccccc-cccC
Q 019380 66 PLSKAHCSGIFSDR------GCNLCM-NIFD 89 (342)
Q Consensus 66 ~~~C~~C~k~f~~~------~C~~C~-k~F~ 89 (342)
|+.|-.|++.|..- .|+.|| +-|.
T Consensus 1 PH~Ct~Cg~~f~dgs~eil~GCP~CGg~kF~ 31 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKEILSGCPECGGNKFQ 31 (131)
T ss_pred CcccCcCCCCcCCCcHHHHccCcccCCcceE
Confidence 34555566666543 388885 3343
No 183
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=65.77 E-value=3.2 Score=26.60 Aligned_cols=8 Identities=25% Similarity=0.658 Sum_probs=4.3
Q ss_pred cccccccc
Q 019380 81 CNLCMNIF 88 (342)
Q Consensus 81 C~~C~k~F 88 (342)
|+.||..+
T Consensus 24 Cp~CG~~~ 31 (46)
T PRK00398 24 CPYCGYRI 31 (46)
T ss_pred CCCCCCeE
Confidence 66665433
No 184
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=65.56 E-value=3.2 Score=27.66 Aligned_cols=28 Identities=21% Similarity=0.509 Sum_probs=23.7
Q ss_pred CCCCCcccccccccccCCHHHHHHHHhh
Q 019380 9 KRSTARHKCVACYKQFKRKDHLIEHMKI 36 (342)
Q Consensus 9 ~~~~~~~~C~~C~k~f~~~~~L~~H~~~ 36 (342)
.-+|--+.||.|+..|.....+.+|+..
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 3466778999999999999999999854
No 185
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=65.51 E-value=3.7 Score=24.89 Aligned_cols=9 Identities=33% Similarity=0.763 Sum_probs=3.6
Q ss_pred cccCccccC
Q 019380 46 CAVCQKLSK 54 (342)
Q Consensus 46 C~~C~~~f~ 54 (342)
|+.|+..|.
T Consensus 5 Cp~C~~~y~ 13 (36)
T PF13717_consen 5 CPNCQAKYE 13 (36)
T ss_pred CCCCCCEEe
Confidence 334443333
No 186
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=65.30 E-value=3.8 Score=42.51 Aligned_cols=43 Identities=23% Similarity=0.356 Sum_probs=30.5
Q ss_pred ccccCccccCCh---hhhhhhc-CCCcccCCCCCccc-CCcccccccc
Q 019380 45 KCAVCQKLSKSF---ESLREHL-TGPLSKAHCSGIFS-DRGCNLCMNI 87 (342)
Q Consensus 45 ~C~~C~~~f~~~---~~l~~H~-~~~~~C~~C~k~f~-~~~C~~C~k~ 87 (342)
.|..||+.+..+ ..|.-|+ ++...|..||..-. -.+|+.||..
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 688888777544 4477777 67778999988722 2359999865
No 187
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=64.95 E-value=2.7 Score=34.77 Aligned_cols=15 Identities=33% Similarity=0.607 Sum_probs=9.7
Q ss_pred CCChHHHHHHHHHHH
Q 019380 187 AMPLKEVKDKILEIL 201 (342)
Q Consensus 187 ~~~~~~v~~~~~~~l 201 (342)
.++..++.+-+.+-|
T Consensus 102 ~IsveEIqDiVE~~L 116 (154)
T PRK00464 102 EVPSKEIGELVMEEL 116 (154)
T ss_pred CCCHHHHHHHHHHHH
Confidence 456666666666666
No 188
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=64.77 E-value=3.2 Score=36.35 Aligned_cols=29 Identities=17% Similarity=0.264 Sum_probs=16.8
Q ss_pred ccccCccccCChhhhhhhc-CCCcccCCCC
Q 019380 45 KCAVCQKLSKSFESLREHL-TGPLSKAHCS 73 (342)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~-~~~~~C~~C~ 73 (342)
=|=+|++.|....-|.+|+ ++.|+|..|.
T Consensus 12 wcwycnrefddekiliqhqkakhfkchich 41 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKAKHFKCHICH 41 (341)
T ss_pred eeeecccccchhhhhhhhhhhccceeeeeh
Confidence 4566666666666666665 5555554444
No 189
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=63.99 E-value=4.9 Score=41.30 Aligned_cols=91 Identities=10% Similarity=0.238 Sum_probs=48.6
Q ss_pred CCCcceeccccccccc-------CCCcccccceEEeecCCCCeEE-eeecCCCCCccccccccCCCCHhhhcCCCChHHH
Q 019380 122 RGPKAVAMDCEMVGGG-------SNGTLDLCARVCLVDEDENVIF-HTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEV 193 (342)
Q Consensus 122 ~~~~~v~~D~Ettg~~-------~~~~~~il~~v~vv~~~~~~~~-~~lv~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v 193 (342)
++-.+..||+|..|-. .+..+++ +.+......+.+.+ +.+.-+. ..||.-.+|..-..-+++
T Consensus 272 APlrvlSfDIECagrkg~FPe~~~DPvIQI-an~v~~~Ge~~pf~rnvf~l~~---------capI~G~~V~~~~~e~el 341 (1066)
T KOG0969|consen 272 APLRVLSFDIECAGRKGVFPEAKIDPVIQI-ANLVTLQGENEPFVRNVFTLKT---------CAPIVGSNVHSYETEKEL 341 (1066)
T ss_pred ccccccceeEEeccCCCCCCccccChHHHH-HHHHHHhcCCchHHHhhhcccC---------cCCCCCceeEEeccHHHH
Confidence 4455778999998743 3344444 33333223333321 2222222 224444445444555667
Q ss_pred HHHHHHHHhcCCCccccccCCCCCeEEEeeCc-hhhhhhcc
Q 019380 194 KDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 233 (342)
Q Consensus 194 ~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~~-~~D~~~l~ 233 (342)
++....|+.+- .-.+|+|+|+ .||+-.|-
T Consensus 342 L~~W~~firev-----------DPDvI~GYNi~nFDiPYll 371 (1066)
T KOG0969|consen 342 LESWRKFIREV-----------DPDVIIGYNICNFDIPYLL 371 (1066)
T ss_pred HHHHHHHHHhc-----------CCCeEecccccccccceec
Confidence 77777776322 3359999996 46776544
No 190
>PRK07217 replication factor A; Reviewed
Probab=63.67 E-value=17 Score=33.53 Aligned_cols=50 Identities=28% Similarity=0.290 Sum_probs=30.2
Q ss_pred eEEeecCCCCeEEeeecCCCCCccccccccCCCCHhhhcC----CCChHHHHHHHHHHH
Q 019380 147 RVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKN----AMPLKEVKDKILEIL 201 (342)
Q Consensus 147 ~v~vv~~~~~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~~----~~~~~~v~~~~~~~l 201 (342)
++..|=.+|.-.+..++.-.. ...++||+.++.+. +..-..|+.++.+.|
T Consensus 218 rik~vlDDGt~~~~~~~~~e~-----te~l~G~~l~eak~~a~dald~~vv~~~i~~~l 271 (311)
T PRK07217 218 RIKGVLDDGEEVQEVIFNREA-----TEELTGITLEEAKQMAMDALDTGVVLDELKEKL 271 (311)
T ss_pred EEEEEEECCCCeEEEEEChHH-----hHHHhCCCHHHHHHHHHHhhchhhHHHHHHHhh
Confidence 333333555555555544332 45789999988873 344556777777777
No 191
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=63.28 E-value=2.9 Score=36.62 Aligned_cols=41 Identities=34% Similarity=0.589 Sum_probs=32.7
Q ss_pred ccccccccCCHHHHHHHHhhhccCCCCCccccCccccCChhhhhhh
Q 019380 17 CVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREH 62 (342)
Q Consensus 17 C~~C~k~f~~~~~L~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H 62 (342)
|=.|++.|....-|.+|++. +.++|.+|.|.+-+---|.-|
T Consensus 13 cwycnrefddekiliqhqka-----khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA-----KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhhh-----ccceeeeehhhhccCCCceee
Confidence 77899999999999999986 334999998877666556555
No 192
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=63.07 E-value=4.3 Score=24.73 Aligned_cols=11 Identities=27% Similarity=0.510 Sum_probs=4.6
Q ss_pred cccCccccCCh
Q 019380 46 CAVCQKLSKSF 56 (342)
Q Consensus 46 C~~C~~~f~~~ 56 (342)
|+.|+..|.-.
T Consensus 5 CP~C~~~f~v~ 15 (37)
T PF13719_consen 5 CPNCQTRFRVP 15 (37)
T ss_pred CCCCCceEEcC
Confidence 44444444333
No 193
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=63.02 E-value=6.8 Score=40.17 Aligned_cols=51 Identities=16% Similarity=0.238 Sum_probs=34.0
Q ss_pred ccccCccccCChhhhhhhcCCCcccCCCCCcccCCcccccccccCChhhHHHHHhhcCCCCCCCCccccccccc
Q 019380 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEACSLSAPVPFKISGAIDEK 118 (342)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~c~~~~~~ 118 (342)
.|+.||..-. .+..-|+.||..+....|+.||.... ....-|+.||.....
T Consensus 3 ~Cp~Cg~~n~---------~~akFC~~CG~~l~~~~Cp~CG~~~~--------------~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 3 ICPQCQFENP---------NNNRFCQKCGTSLTHKPCPQCGTEVP--------------VDEAHCPNCGAETGT 53 (645)
T ss_pred cCCCCCCcCC---------CCCccccccCCCCCCCcCCCCCCCCC--------------cccccccccCCcccc
Confidence 5888874422 33456999999988778999987532 233457777766543
No 194
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=62.31 E-value=5.5 Score=25.99 Aligned_cols=20 Identities=25% Similarity=0.542 Sum_probs=13.2
Q ss_pred ccccccccCC-----hhhHHHHHhh
Q 019380 81 CNLCMNIFDS-----PSSLIKHKEA 100 (342)
Q Consensus 81 C~~C~k~F~~-----~~~L~~H~~~ 100 (342)
|..|++.++. .++|.+|++.
T Consensus 21 C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 21 CKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred ecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 5555555544 4789999883
No 195
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=62.29 E-value=3 Score=36.18 Aligned_cols=80 Identities=11% Similarity=-0.013 Sum_probs=52.8
Q ss_pred CCCeEEEeeCchhhhhhcc-----ccCCC-------------cceeeccccccccccCCCCccHHHHHHHHhCCcCCCCC
Q 019380 215 GKARLLVGHGLEHDLDSLR-----MNYPD-------------HMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYDIQSGV 276 (342)
Q Consensus 215 ~~~~~lvgh~~~~D~~~l~-----~~~~~-------------~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~~~~~~ 276 (342)
++..++|.++..+|+.+|- ...|. -.+.|...+++.. ...+..|++++..+ ++.-.+..
T Consensus 156 ~e~VtWitfHsaYDfgyLikilt~~plP~~~EdFy~~l~~yfP~fYDik~v~ks~--~~~~KglQei~ndl-ql~r~g~Q 232 (299)
T COG5228 156 DESVTWITFHSAYDFGYLIKILTNDPLPNNKEDFYWWLHQYFPNFYDIKLVYKSV--LNNSKGLQEIKNDL-QLQRSGQQ 232 (299)
T ss_pred ccceEEEEeecchhHHHHHHHHhcCCCCccHHHHHHHHHHHCccccchHHHHHhh--hhhhhHHHHhcCcH-hhhccchh
Confidence 4778999999999999986 11221 0023333333322 22356788888877 77633448
Q ss_pred CCcHHHHHHHHHHHHHHHhhh
Q 019380 277 HDPYEDCVSVMRLYKRFRRQD 297 (342)
Q Consensus 277 H~A~~Da~~t~~l~~~~~~~~ 297 (342)
|.|-.||..|++.|-.-+...
T Consensus 233 hQagsdaLlTa~~ff~~R~~~ 253 (299)
T COG5228 233 HQAGSDALLTADEFFLPRFSI 253 (299)
T ss_pred hhccchhhhhhHHhcchhhhe
Confidence 999999999999887665543
No 196
>PHA00626 hypothetical protein
Probab=60.67 E-value=4.8 Score=26.88 Aligned_cols=9 Identities=22% Similarity=0.205 Sum_probs=4.4
Q ss_pred ccccccccC
Q 019380 81 CNLCMNIFD 89 (342)
Q Consensus 81 C~~C~k~F~ 89 (342)
|+.||..|+
T Consensus 26 CkdCGY~ft 34 (59)
T PHA00626 26 CCDCGYNDS 34 (59)
T ss_pred cCCCCCeec
Confidence 455554444
No 197
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=59.39 E-value=6.2 Score=21.92 Aligned_cols=20 Identities=15% Similarity=0.237 Sum_probs=10.1
Q ss_pred ccCCCCCcccCC--cccccccc
Q 019380 68 SKAHCSGIFSDR--GCNLCMNI 87 (342)
Q Consensus 68 ~C~~C~k~f~~~--~C~~C~k~ 87 (342)
.|+.|++..... -|+.||..
T Consensus 4 ~Cp~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 4 FCPNCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred CCcccCCcCCcccccChhhCCC
Confidence 455666532221 27777653
No 198
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=58.15 E-value=3.4 Score=38.18 Aligned_cols=20 Identities=20% Similarity=0.464 Sum_probs=12.0
Q ss_pred cccCCCCCccc--CCccccccc
Q 019380 67 LSKAHCSGIFS--DRGCNLCMN 86 (342)
Q Consensus 67 ~~C~~C~k~f~--~~~C~~C~k 86 (342)
..|..|+..+. +..|+.||.
T Consensus 213 L~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 213 LHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred EEcCCCCCcccccCccCCCCCC
Confidence 35666665443 335888885
No 199
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=58.14 E-value=8.8 Score=35.61 Aligned_cols=78 Identities=24% Similarity=0.525 Sum_probs=46.0
Q ss_pred cccccccccCCHHHHHHHHhhhccCCCCCccccCccc-------cCChhhhhhhcC-CCccc--CCCCCcccCCcccccc
Q 019380 16 KCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKL-------SKSFESLREHLT-GPLSK--AHCSGIFSDRGCNLCM 85 (342)
Q Consensus 16 ~C~~C~k~f~~~~~L~~H~~~~~H~~~~~~C~~C~~~-------f~~~~~l~~H~~-~~~~C--~~C~k~f~~~~C~~C~ 85 (342)
.|..|.+.|-.-..|..|++.- |. +|.+|.+. |.+..+|..|.. ..|.| +.|.. ..|
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~-HE----~ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy~ct~qtc~~-------~k~- 288 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLR-HE----ACHICDMVGPIRYQYFKSYEDLEAHFRNAHYCCTFQTCRV-------GKC- 288 (493)
T ss_pred hhhhccceecChHHHHHHHHhh-hh----hhhhhhccCccchhhhhCHHHHHHHhhcCceEEEEEEEec-------CcE-
Confidence 4777887777777788777651 22 56666543 455555666653 34444 22211 112
Q ss_pred cccCChhhHHHHHhhcCCCCC
Q 019380 86 NIFDSPSSLIKHKEACSLSAP 106 (342)
Q Consensus 86 k~F~~~~~L~~H~~~h~~~~~ 106 (342)
..|.....|..|.-..|+...
T Consensus 289 ~vf~~~~el~~h~~~~h~~~~ 309 (493)
T COG5236 289 YVFPYHTELLEHLTRFHKVNA 309 (493)
T ss_pred EEeccHHHHHHHHHHHhhccc
Confidence 458888888888866555433
No 200
>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=57.27 E-value=6.4 Score=23.51 Aligned_cols=9 Identities=22% Similarity=0.213 Sum_probs=3.9
Q ss_pred cccCCCCCc
Q 019380 67 LSKAHCSGI 75 (342)
Q Consensus 67 ~~C~~C~k~ 75 (342)
|.|..||..
T Consensus 3 ~~C~~CG~i 11 (34)
T cd00729 3 WVCPVCGYI 11 (34)
T ss_pred EECCCCCCE
Confidence 344444443
No 201
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=57.16 E-value=8 Score=31.64 Aligned_cols=31 Identities=23% Similarity=0.460 Sum_probs=13.3
Q ss_pred ccccCccccCChhhhhh-hcCCCcccCCCCCc
Q 019380 45 KCAVCQKLSKSFESLRE-HLTGPLSKAHCSGI 75 (342)
Q Consensus 45 ~C~~C~~~f~~~~~l~~-H~~~~~~C~~C~k~ 75 (342)
.|+.|+..|.....+.. +..+.|.|+.||..
T Consensus 101 ~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~ 132 (147)
T smart00531 101 KCPNCQSKYTFLEANQLLDMDGTFTCPRCGEE 132 (147)
T ss_pred ECcCCCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence 45555555544333221 12333555544443
No 202
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=56.74 E-value=13 Score=25.23 Aligned_cols=10 Identities=10% Similarity=0.408 Sum_probs=4.7
Q ss_pred CcccCCCCCc
Q 019380 66 PLSKAHCSGI 75 (342)
Q Consensus 66 ~~~C~~C~k~ 75 (342)
.|.|+.||+.
T Consensus 25 ~F~CPnCG~~ 34 (59)
T PRK14890 25 KFLCPNCGEV 34 (59)
T ss_pred EeeCCCCCCe
Confidence 3455555443
No 203
>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=56.63 E-value=4.2 Score=25.53 Aligned_cols=6 Identities=33% Similarity=0.567 Sum_probs=2.3
Q ss_pred CCcccc
Q 019380 108 PFKISG 113 (342)
Q Consensus 108 ~~~~c~ 113 (342)
.|+.|+
T Consensus 28 ~CP~Cg 33 (42)
T PF09723_consen 28 PCPECG 33 (42)
T ss_pred cCCCCC
Confidence 333333
No 204
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=56.57 E-value=3.5 Score=41.97 Aligned_cols=31 Identities=19% Similarity=0.379 Sum_probs=23.0
Q ss_pred ccccccccCChhhHHHHHhhcCCCCCCCCcccccccc
Q 019380 81 CNLCMNIFDSPSSLIKHKEACSLSAPVPFKISGAIDE 117 (342)
Q Consensus 81 C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~c~~~~~ 117 (342)
|+.|.+.|.++-+-|-| ..|..|+.||....
T Consensus 154 C~~C~~EY~dP~nRRfH------AQp~aCp~CGP~~~ 184 (750)
T COG0068 154 CPFCDKEYKDPLNRRFH------AQPIACPKCGPHLF 184 (750)
T ss_pred CHHHHHHhcCccccccc------cccccCcccCCCeE
Confidence 89999988888775544 35777888887444
No 205
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=56.47 E-value=5.9 Score=35.13 Aligned_cols=45 Identities=24% Similarity=0.377 Sum_probs=31.2
Q ss_pred ccccccccccCCHHHHHHHHhhhccCCCCCccccCccccCChhhhhhhc
Q 019380 15 HKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHL 63 (342)
Q Consensus 15 ~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~ 63 (342)
|.|..||.+.. +..+.+|+-. =.+..+.|-.|++.|-. .++..|.
T Consensus 4 FtCnvCgEsvK-Kp~vekH~sr--Crn~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVK-KPQVEKHMSR--CRNAYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhcc-ccchHHHHHh--ccCCeeEEeeccccccc-chhhhhh
Confidence 77888988765 3557778865 44444488888888877 4466664
No 206
>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=54.83 E-value=9.1 Score=30.32 Aligned_cols=11 Identities=18% Similarity=0.238 Sum_probs=5.5
Q ss_pred CcccCCCCCcc
Q 019380 66 PLSKAHCSGIF 76 (342)
Q Consensus 66 ~~~C~~C~k~f 76 (342)
|..|+.||..|
T Consensus 26 p~vcP~cg~~~ 36 (129)
T TIGR02300 26 PAVSPYTGEQF 36 (129)
T ss_pred CccCCCcCCcc
Confidence 44455555544
No 207
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=53.91 E-value=9.9 Score=30.36 Aligned_cols=15 Identities=13% Similarity=0.286 Sum_probs=11.1
Q ss_pred CCcccccccccccCC
Q 019380 12 TARHKCVACYKQFKR 26 (342)
Q Consensus 12 ~~~~~C~~C~k~f~~ 26 (342)
.+.|+|..|..+...
T Consensus 78 ~~lYeCnIC~etS~e 92 (140)
T PF05290_consen 78 PKLYECNICKETSAE 92 (140)
T ss_pred CCceeccCcccccch
Confidence 468999999876543
No 208
>PRK05580 primosome assembly protein PriA; Validated
Probab=53.47 E-value=12 Score=38.89 Aligned_cols=19 Identities=5% Similarity=-0.062 Sum_probs=9.6
Q ss_pred CCcHHHHHHHHHHHHHHHh
Q 019380 277 HDPYEDCVSVMRLYKRFRR 295 (342)
Q Consensus 277 H~A~~Da~~t~~l~~~~~~ 295 (342)
|.-.+.|...+.-+...++
T Consensus 591 ~~~~~~~~~~~~~~~~~l~ 609 (679)
T PRK05580 591 AKDEEKAEKFAQQLAALLP 609 (679)
T ss_pred cCCHHHHHHHHHHHHHHHH
Confidence 4455555555554444443
No 209
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=53.28 E-value=6.3 Score=32.58 Aligned_cols=10 Identities=30% Similarity=0.740 Sum_probs=5.5
Q ss_pred ccccccccCC
Q 019380 81 CNLCMNIFDS 90 (342)
Q Consensus 81 C~~C~k~F~~ 90 (342)
|+.||++|..
T Consensus 31 c~~c~~~f~~ 40 (154)
T PRK00464 31 CLACGKRFTT 40 (154)
T ss_pred ccccCCcceE
Confidence 4555555553
No 210
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=53.15 E-value=7 Score=29.55 Aligned_cols=20 Identities=35% Similarity=0.879 Sum_probs=11.9
Q ss_pred CcccCCCCCcccCC------cccccc
Q 019380 66 PLSKAHCSGIFSDR------GCNLCM 85 (342)
Q Consensus 66 ~~~C~~C~k~f~~~------~C~~C~ 85 (342)
++.|-.||..|..- .|+.||
T Consensus 2 pH~CtrCG~vf~~g~~~il~GCp~CG 27 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEILSGCPKCG 27 (112)
T ss_pred CceecccccccccccHHHHccCcccc
Confidence 34555566666542 388886
No 211
>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=53.12 E-value=12 Score=20.79 Aligned_cols=19 Identities=16% Similarity=0.746 Sum_probs=14.4
Q ss_pred cccccccccCCHHHHHHHHh
Q 019380 16 KCVACYKQFKRKDHLIEHMK 35 (342)
Q Consensus 16 ~C~~C~k~f~~~~~L~~H~~ 35 (342)
.||.|++.+ ....+++|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 689999888 5566777765
No 212
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=52.80 E-value=7.7 Score=42.29 Aligned_cols=84 Identities=13% Similarity=0.168 Sum_probs=58.5
Q ss_pred CCcccccccccccCCHHHHHHHHhhhccCCCCCccccCccccCChhhhhhhcCCCcccCCCCCcccC-------------
Q 019380 12 TARHKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSD------------- 78 (342)
Q Consensus 12 ~~~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~------------- 78 (342)
...+.|..|.+.|...-.+. |+-+ ...+.|..|...|...+.|..|+ .+| .+.|..
T Consensus 1258 sGe~~c~~~~~~~~~~~~~~-~l~~----~~~~~~~~~~~~~~~~~~l~~~~---~k~---~~~~~~~~~~~~~~l~~~d 1326 (1406)
T KOG1146|consen 1258 SGEGECGAVDELLTPSFGIS-TLDV----THRYLCRQCKMAFDGEAPLTAHQ---RKF---CFAGRGSGGSMPPPLRVPD 1326 (1406)
T ss_pred CCcchhhhccccccCcccee-eccc----chhHHHHHHHhhhcchhHHHHHH---HHH---HhccCccccCCCCcccCcc
Confidence 34578889998888776666 5543 23348999999999888888886 000 111111
Q ss_pred --CcccccccccCChhhHHHHHhhcCCCCC
Q 019380 79 --RGCNLCMNIFDSPSSLIKHKEACSLSAP 106 (342)
Q Consensus 79 --~~C~~C~k~F~~~~~L~~H~~~h~~~~~ 106 (342)
..|..|...|.....|..||+..+++..
T Consensus 1327 ~~~~c~~c~~~~~~~~alqihm~~~~~~~k 1356 (1406)
T KOG1146|consen 1327 CTYHCLACEVLLSGREALQIHMRSSAHRRK 1356 (1406)
T ss_pred ccccchHHHhhcchhHHHHHHHHHhhhccc
Confidence 1289999999999999999997665544
No 213
>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=52.70 E-value=8.6 Score=24.18 Aligned_cols=20 Identities=25% Similarity=0.605 Sum_probs=11.7
Q ss_pred ccccccccCC----hhhHHHHHhh
Q 019380 81 CNLCMNIFDS----PSSLIKHKEA 100 (342)
Q Consensus 81 C~~C~k~F~~----~~~L~~H~~~ 100 (342)
|..|++.+.. .++|.+|++.
T Consensus 19 C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 19 CKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp ETTTTEE-----SSTHHHHHHHHH
T ss_pred eCCCCeEEeeCCCcHHHHHHhhhh
Confidence 6666666655 4788888844
No 214
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=52.59 E-value=7.9 Score=28.46 Aligned_cols=10 Identities=30% Similarity=0.747 Sum_probs=5.5
Q ss_pred ccccccccCC
Q 019380 81 CNLCMNIFDS 90 (342)
Q Consensus 81 C~~C~k~F~~ 90 (342)
|..||..|.-
T Consensus 56 C~kCg~~fAG 65 (89)
T COG1997 56 CRKCGAKFAG 65 (89)
T ss_pred cCCCCCeecc
Confidence 5556655543
No 215
>PRK12496 hypothetical protein; Provisional
Probab=52.17 E-value=7.7 Score=32.43 Aligned_cols=25 Identities=12% Similarity=0.352 Sum_probs=18.7
Q ss_pred CcccCCCCCcccCC----cccccccccCC
Q 019380 66 PLSKAHCSGIFSDR----GCNLCMNIFDS 90 (342)
Q Consensus 66 ~~~C~~C~k~f~~~----~C~~C~k~F~~ 90 (342)
.|.|..|++.|... -|+.||..-..
T Consensus 127 ~~~C~gC~~~~~~~~~~~~C~~CG~~~~r 155 (164)
T PRK12496 127 RKVCKGCKKKYPEDYPDDVCEICGSPVKR 155 (164)
T ss_pred eEECCCCCccccCCCCCCcCCCCCChhhh
Confidence 47899999999542 39999965443
No 216
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=51.80 E-value=5 Score=37.10 Aligned_cols=21 Identities=24% Similarity=0.485 Sum_probs=12.6
Q ss_pred cccCCCCCccc--CCcccccccc
Q 019380 67 LSKAHCSGIFS--DRGCNLCMNI 87 (342)
Q Consensus 67 ~~C~~C~k~f~--~~~C~~C~k~ 87 (342)
..|..|+..+. +..|+.||.+
T Consensus 211 L~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 211 LSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred EEcCCCCCcccccCccCCCCCCC
Confidence 35666665443 3358888864
No 217
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=51.53 E-value=11 Score=20.67 Aligned_cols=9 Identities=22% Similarity=0.641 Sum_probs=4.7
Q ss_pred CCcccCCCC
Q 019380 65 GPLSKAHCS 73 (342)
Q Consensus 65 ~~~~C~~C~ 73 (342)
-+|+|+.||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 345555554
No 218
>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=51.23 E-value=14 Score=36.82 Aligned_cols=13 Identities=15% Similarity=0.465 Sum_probs=8.0
Q ss_pred CCcceeccccccc
Q 019380 123 GPKAVAMDCEMVG 135 (342)
Q Consensus 123 ~~~~v~~D~Ettg 135 (342)
..++..+|.+++.
T Consensus 284 ~~~v~~~d~d~~~ 296 (505)
T TIGR00595 284 GARIARIDSDTTS 296 (505)
T ss_pred CCcEEEEeccccc
Confidence 3456667777764
No 219
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=51.19 E-value=13 Score=37.97 Aligned_cols=53 Identities=19% Similarity=0.264 Sum_probs=30.3
Q ss_pred cccccCCHHHHHHHHhhhccCCC----CCccccCccccCChhhhhhhc-CCCcccCCCC
Q 019380 20 CYKQFKRKDHLIEHMKISYHSVH----QPKCAVCQKLSKSFESLREHL-TGPLSKAHCS 73 (342)
Q Consensus 20 C~k~f~~~~~L~~H~~~~~H~~~----~~~C~~C~~~f~~~~~l~~H~-~~~~~C~~C~ 73 (342)
+.|.|+ ...|+.|++...+.++ .+.|..|...|-....|.+|+ ...|.|..|.
T Consensus 156 e~k~Yt-~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~h~~chfC~ 213 (669)
T KOG2231|consen 156 ERKLYT-RAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRFDHEFCHFCD 213 (669)
T ss_pred eeeheh-HHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhccceeheeecC
Confidence 444443 4556666655333111 236777777777777777777 3445566664
No 220
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=51.06 E-value=9.5 Score=35.39 Aligned_cols=26 Identities=23% Similarity=0.401 Sum_probs=21.8
Q ss_pred ccccccccCChhhHHHHHhhcCCCCC
Q 019380 81 CNLCMNIFDSPSSLIKHKEACSLSAP 106 (342)
Q Consensus 81 C~~C~k~F~~~~~L~~H~~~h~~~~~ 106 (342)
|-.|.+.|..+..|+.||+.....+.
T Consensus 198 CLyCekifrdkntLkeHMrkK~Hrri 223 (423)
T KOG2482|consen 198 CLYCEKIFRDKNTLKEHMRKKRHRRI 223 (423)
T ss_pred eeeeccccCCcHHHHHHHHhccCccc
Confidence 99999999999999999986544433
No 221
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=50.67 E-value=18 Score=34.14 Aligned_cols=26 Identities=27% Similarity=0.431 Sum_probs=22.2
Q ss_pred CCCcccccccccccCCHHHHHHHHhh
Q 019380 11 STARHKCVACYKQFKRKDHLIEHMKI 36 (342)
Q Consensus 11 ~~~~~~C~~C~k~f~~~~~L~~H~~~ 36 (342)
.+-++.|..|.++|....+...|+..
T Consensus 65 ~~~~~~c~~c~k~~~s~~a~~~hl~S 90 (390)
T KOG2785|consen 65 AESVVYCEACNKSFASPKAHENHLKS 90 (390)
T ss_pred cccceehHHhhccccChhhHHHHHHH
Confidence 34479999999999999999999865
No 222
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=50.56 E-value=8.6 Score=30.69 Aligned_cols=25 Identities=24% Similarity=0.155 Sum_probs=22.0
Q ss_pred ccccccccCChhhHHHHHhhcCCCCCCC
Q 019380 81 CNLCMNIFDSPSSLIKHKEACSLSAPVP 108 (342)
Q Consensus 81 C~~C~k~F~~~~~L~~H~~~h~~~~~~~ 108 (342)
|-++|+.|+ +|++|..+|++-.|-.
T Consensus 79 cLEDGkkfK---SLKRHL~t~~gmTPd~ 103 (148)
T COG4957 79 CLEDGKKFK---SLKRHLTTHYGLTPDE 103 (148)
T ss_pred EeccCcchH---HHHHHHhcccCCCHHH
Confidence 899999987 7999999999988754
No 223
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=50.38 E-value=16 Score=29.84 Aligned_cols=12 Identities=25% Similarity=0.700 Sum_probs=6.1
Q ss_pred cccccccccccC
Q 019380 14 RHKCVACYKQFK 25 (342)
Q Consensus 14 ~~~C~~C~k~f~ 25 (342)
-|.|+.|+..|+
T Consensus 99 ~Y~Cp~C~~~y~ 110 (147)
T smart00531 99 YYKCPNCQSKYT 110 (147)
T ss_pred EEECcCCCCEee
Confidence 455555555554
No 224
>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=50.37 E-value=6.2 Score=25.82 Aligned_cols=9 Identities=33% Similarity=1.010 Sum_probs=4.2
Q ss_pred ccccccccC
Q 019380 81 CNLCMNIFD 89 (342)
Q Consensus 81 C~~C~k~F~ 89 (342)
|..||..|.
T Consensus 8 C~~Cg~~fe 16 (52)
T TIGR02605 8 CTACGHRFE 16 (52)
T ss_pred eCCCCCEeE
Confidence 444444444
No 225
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=49.64 E-value=11 Score=29.44 Aligned_cols=30 Identities=27% Similarity=0.606 Sum_probs=25.0
Q ss_pred CCCCCCCCCcccccccccccCCHHHHHHHHhh
Q 019380 5 AELPKRSTARHKCVACYKQFKRKDHLIEHMKI 36 (342)
Q Consensus 5 ~~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~~ 36 (342)
+++| |-..|-|-.|.+-|.+...|+.|.++
T Consensus 50 ~dlP--G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 50 PDLP--GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCC--CCceeehhhhhhhhcchHHHHHHHhc
Confidence 3455 77789999999999999999999876
No 226
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=48.64 E-value=14 Score=25.02 Aligned_cols=26 Identities=15% Similarity=0.385 Sum_probs=13.1
Q ss_pred ccccCccccCChhhhhhhcCCCcccCCCCCc
Q 019380 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGI 75 (342)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~ 75 (342)
.|..||....-... .-.|+|+.||+.
T Consensus 11 ~CtSCg~~i~p~e~-----~v~F~CPnCGe~ 36 (61)
T COG2888 11 VCTSCGREIAPGET-----AVKFPCPNCGEV 36 (61)
T ss_pred eeccCCCEeccCCc-----eeEeeCCCCCce
Confidence 67777655422221 234566666543
No 227
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=48.56 E-value=18 Score=33.40 Aligned_cols=58 Identities=21% Similarity=0.404 Sum_probs=37.4
Q ss_pred ccccCccccCChhhhhhhc---------------C--CCcccCCC-CCcccC--CcccccccccCChhhHHHHHhhcC
Q 019380 45 KCAVCQKLSKSFESLREHL---------------T--GPLSKAHC-SGIFSD--RGCNLCMNIFDSPSSLIKHKEACS 102 (342)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~---------------~--~~~~C~~C-~k~f~~--~~C~~C~k~F~~~~~L~~H~~~h~ 102 (342)
.|+.|+-......+|.+-. + +.-.|-.| +...+. ..|..|...|-.-...-.|...|.
T Consensus 292 eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~ 369 (378)
T KOG2807|consen 292 ECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHN 369 (378)
T ss_pred cCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhccceeeccchHHHHhhhhc
Confidence 7888888887777666543 1 11126666 222222 238889888888888778876665
No 228
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=47.86 E-value=2.9 Score=42.76 Aligned_cols=18 Identities=22% Similarity=0.409 Sum_probs=12.5
Q ss_pred cccccccccCChhhHHHH
Q 019380 80 GCNLCMNIFDSPSSLIKH 97 (342)
Q Consensus 80 ~C~~C~k~F~~~~~L~~H 97 (342)
.||.|+.+|....-++.|
T Consensus 680 KCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 680 KCPKCNAAFGANDVHRIH 697 (698)
T ss_pred CCCCCCCCCCcccccccC
Confidence 478888888776665554
No 229
>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=47.67 E-value=11 Score=37.65 Aligned_cols=41 Identities=24% Similarity=0.327 Sum_probs=16.8
Q ss_pred ccccCccccCCh---hhhhhhc-CCCcccCCCCCccc-CCcccccc
Q 019380 45 KCAVCQKLSKSF---ESLREHL-TGPLSKAHCSGIFS-DRGCNLCM 85 (342)
Q Consensus 45 ~C~~C~~~f~~~---~~l~~H~-~~~~~C~~C~k~f~-~~~C~~C~ 85 (342)
.|..||.....+ ..|.-|. .+...|..||.... ...|+.||
T Consensus 215 ~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~ 260 (505)
T TIGR00595 215 LCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCG 260 (505)
T ss_pred EhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCC
Confidence 455555443222 2233333 33344555544433 22355554
No 230
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=47.20 E-value=18 Score=39.59 Aligned_cols=19 Identities=21% Similarity=0.016 Sum_probs=13.1
Q ss_pred CCcHHHHHHHHHHHHHHHh
Q 019380 277 HDPYEDCVSVMRLYKRFRR 295 (342)
Q Consensus 277 H~A~~Da~~t~~l~~~~~~ 295 (342)
|+=-.||-+.|.|+-.+++
T Consensus 1086 HsCDGDED~VMLLlD~llN 1104 (1337)
T PRK14714 1086 GQCDGDEDCVMLLLDGLLN 1104 (1337)
T ss_pred eccCchHHHHHHHHHHHHh
Confidence 5555677777777777764
No 231
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.32 E-value=9.4 Score=32.11 Aligned_cols=23 Identities=26% Similarity=0.439 Sum_probs=15.6
Q ss_pred CCCCCCCCCcccccccccccCCH
Q 019380 5 AELPKRSTARHKCVACYKQFKRK 27 (342)
Q Consensus 5 ~~~~~~~~~~~~C~~C~k~f~~~ 27 (342)
...|...+..|+|+.|-..|+.+
T Consensus 122 ~v~~~~~~~~~~CPiCl~~~sek 144 (187)
T KOG0320|consen 122 DVDPLRKEGTYKCPICLDSVSEK 144 (187)
T ss_pred cccccccccccCCCceecchhhc
Confidence 34455666779999997766543
No 232
>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=46.27 E-value=13 Score=24.89 Aligned_cols=10 Identities=30% Similarity=0.016 Sum_probs=4.7
Q ss_pred CCcccccccc
Q 019380 108 PFKISGAIDE 117 (342)
Q Consensus 108 ~~~~c~~~~~ 117 (342)
.|+.|+...+
T Consensus 24 ~Cp~CGaele 33 (54)
T TIGR01206 24 ICDECGAELE 33 (54)
T ss_pred eCCCCCCEEE
Confidence 4555554443
No 233
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=46.18 E-value=19 Score=33.56 Aligned_cols=51 Identities=16% Similarity=0.075 Sum_probs=36.0
Q ss_pred CCCcccCCCCCcccCCcccccccccCChhhHHHHHhhcCCCCCCC--Ccccccccc
Q 019380 64 TGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEACSLSAPVP--FKISGAIDE 117 (342)
Q Consensus 64 ~~~~~C~~C~k~f~~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~--~~~c~~~~~ 117 (342)
.+.+.|..|...| .|+.|++.=.....|..|....|.+.+.. |+.|+....
T Consensus 68 ~Ge~i~~y~~qSf---tCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~~~~ 120 (381)
T KOG1280|consen 68 GGEPISHYDPQSF---TCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAANPE 120 (381)
T ss_pred cCccccccccccc---cCCcccccccchhHHHHHhhhcCcccCcceeeeccccCcc
Confidence 4555565666644 69999988888888999998777776653 666654433
No 234
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.55 E-value=9.6 Score=29.22 Aligned_cols=22 Identities=9% Similarity=0.043 Sum_probs=14.1
Q ss_pred ccCCCCCcccCCc-----ccccccccC
Q 019380 68 SKAHCSGIFSDRG-----CNLCMNIFD 89 (342)
Q Consensus 68 ~C~~C~k~f~~~~-----C~~C~k~F~ 89 (342)
.|+.|++.|..-. |+.||++|.
T Consensus 11 idPetg~KFYDLNrdPiVsPytG~s~P 37 (129)
T COG4530 11 IDPETGKKFYDLNRDPIVSPYTGKSYP 37 (129)
T ss_pred cCccccchhhccCCCccccCcccccch
Confidence 4566666665432 788888883
No 235
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=44.71 E-value=7.8 Score=31.27 Aligned_cols=32 Identities=28% Similarity=0.321 Sum_probs=26.2
Q ss_pred ccCCCCCcccCCcccccccccCChhhHHHHHhh
Q 019380 68 SKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEA 100 (342)
Q Consensus 68 ~C~~C~k~f~~~~C~~C~k~F~~~~~L~~H~~~ 100 (342)
-|.+|| -++-.+|.-||-.+-....+..|..+
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 488899 67777899999999999888888644
No 236
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=44.54 E-value=13 Score=31.14 Aligned_cols=12 Identities=8% Similarity=-0.014 Sum_probs=5.6
Q ss_pred CcccCCCCCccc
Q 019380 66 PLSKAHCSGIFS 77 (342)
Q Consensus 66 ~~~C~~C~k~f~ 77 (342)
.|.|++||..+.
T Consensus 134 ~~vC~vCGy~~~ 145 (166)
T COG1592 134 VWVCPVCGYTHE 145 (166)
T ss_pred EEEcCCCCCccc
Confidence 355555444433
No 237
>PF15269 zf-C2H2_7: Zinc-finger
Probab=42.55 E-value=28 Score=22.17 Aligned_cols=26 Identities=35% Similarity=0.568 Sum_probs=19.2
Q ss_pred CCCc--ccccccccccCCHHHHHHHHhh
Q 019380 11 STAR--HKCVACYKQFKRKDHLIEHMKI 36 (342)
Q Consensus 11 ~~~~--~~C~~C~k~f~~~~~L~~H~~~ 36 (342)
..+| |+|=+|.-+...+++|-.||+-
T Consensus 15 ~gkp~~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 15 PGKPFKYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred CCCCccceeecCCcccchHHHHHHHHHH
Confidence 3445 6687887777778888888875
No 238
>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=41.03 E-value=10 Score=33.87 Aligned_cols=16 Identities=19% Similarity=0.314 Sum_probs=10.0
Q ss_pred CCCCCCCccccccccc
Q 019380 7 LPKRSTARHKCVACYK 22 (342)
Q Consensus 7 ~~~~~~~~~~C~~C~k 22 (342)
+-.++.|.|+|..|+.
T Consensus 135 vw~hGGrif~CsfC~~ 150 (314)
T PF06524_consen 135 VWDHGGRIFKCSFCDN 150 (314)
T ss_pred cccCCCeEEEeecCCC
Confidence 3345667777777764
No 239
>PRK04023 DNA polymerase II large subunit; Validated
Probab=40.89 E-value=18 Score=38.69 Aligned_cols=12 Identities=8% Similarity=-0.081 Sum_probs=7.5
Q ss_pred CCCCcccccccc
Q 019380 106 PVPFKISGAIDE 117 (342)
Q Consensus 106 ~~~~~~c~~~~~ 117 (342)
++.|+.|+....
T Consensus 663 ~y~CPKCG~El~ 674 (1121)
T PRK04023 663 EDECEKCGREPT 674 (1121)
T ss_pred CCcCCCCCCCCC
Confidence 356777775544
No 240
>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=39.59 E-value=10 Score=28.16 Aligned_cols=13 Identities=31% Similarity=0.488 Sum_probs=6.0
Q ss_pred CCCcccCCCCCcc
Q 019380 64 TGPLSKAHCSGIF 76 (342)
Q Consensus 64 ~~~~~C~~C~k~f 76 (342)
.+-|.|..|++.|
T Consensus 51 ~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 51 TGIWKCKKCGKKF 63 (90)
T ss_dssp TTEEEETTTTEEE
T ss_pred eEEeecCCCCCEE
Confidence 4445554444443
No 241
>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=38.85 E-value=15 Score=27.35 Aligned_cols=9 Identities=33% Similarity=0.814 Sum_probs=4.6
Q ss_pred ccccccccC
Q 019380 81 CNLCMNIFD 89 (342)
Q Consensus 81 C~~C~k~F~ 89 (342)
|..|++.|.
T Consensus 56 C~~C~~~~A 64 (91)
T TIGR00280 56 CRKCGAKFA 64 (91)
T ss_pred cCCCCCEEe
Confidence 455555544
No 242
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=38.82 E-value=19 Score=24.08 Aligned_cols=23 Identities=22% Similarity=0.436 Sum_probs=11.2
Q ss_pred ccCCCCCcccCC----cccccccccCC
Q 019380 68 SKAHCSGIFSDR----GCNLCMNIFDS 90 (342)
Q Consensus 68 ~C~~C~k~f~~~----~C~~C~k~F~~ 90 (342)
.|+.|++.|... .|+.|+..+-+
T Consensus 7 ~C~~Cg~~~~~~dDiVvCp~CgapyHR 33 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIVVCPECGAPYHR 33 (54)
T ss_pred cChhhCCcccCCCCEEECCCCCCcccH
Confidence 345555555322 26666654443
No 243
>PRK14873 primosome assembly protein PriA; Provisional
Probab=38.08 E-value=19 Score=37.20 Aligned_cols=26 Identities=19% Similarity=0.429 Sum_probs=17.2
Q ss_pred cCCCC-CccccCccccCChhhhhhhcCCCcccCCCCCc
Q 019380 39 HSVHQ-PKCAVCQKLSKSFESLREHLTGPLSKAHCSGI 75 (342)
Q Consensus 39 H~~~~-~~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~ 75 (342)
|.... ..|..||.. ..++.|+.|+..
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 54333 389999843 126689999874
No 244
>COG1773 Rubredoxin [Energy production and conversion]
Probab=37.64 E-value=19 Score=24.16 Aligned_cols=10 Identities=30% Similarity=0.916 Sum_probs=6.2
Q ss_pred ccccCccccC
Q 019380 45 KCAVCQKLSK 54 (342)
Q Consensus 45 ~C~~C~~~f~ 54 (342)
+|..||..|.
T Consensus 5 ~C~~CG~vYd 14 (55)
T COG1773 5 RCSVCGYVYD 14 (55)
T ss_pred EecCCceEec
Confidence 5666666554
No 245
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=37.51 E-value=18 Score=26.94 Aligned_cols=13 Identities=15% Similarity=0.220 Sum_probs=6.0
Q ss_pred CCCcccCCCCCcc
Q 019380 64 TGPLSKAHCSGIF 76 (342)
Q Consensus 64 ~~~~~C~~C~k~f 76 (342)
.+-|.|..|++.|
T Consensus 52 ~GIW~C~~C~~~~ 64 (90)
T PTZ00255 52 VGIWRCKGCKKTV 64 (90)
T ss_pred eEEEEcCCCCCEE
Confidence 4445554444443
No 246
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=37.08 E-value=12 Score=31.82 Aligned_cols=10 Identities=10% Similarity=0.119 Sum_probs=4.6
Q ss_pred CCCCcccccc
Q 019380 106 PVPFKISGAI 115 (342)
Q Consensus 106 ~~~~~~c~~~ 115 (342)
-|.|+.||..
T Consensus 136 ~F~Cp~Cg~~ 145 (178)
T PRK06266 136 GFRCPQCGEM 145 (178)
T ss_pred CCcCCCCCCC
Confidence 3445554443
No 247
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=35.97 E-value=18 Score=30.73 Aligned_cols=28 Identities=14% Similarity=0.271 Sum_probs=15.6
Q ss_pred ccccCccccCChhhhhhhcCCCcccCCCCCcc
Q 019380 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIF 76 (342)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f 76 (342)
.|+.|+..|.....+ ...|.|+.||...
T Consensus 119 ~Cp~C~~rytf~eA~----~~~F~Cp~Cg~~L 146 (178)
T PRK06266 119 FCPNCHIRFTFDEAM----EYGFRCPQCGEML 146 (178)
T ss_pred ECCCCCcEEeHHHHh----hcCCcCCCCCCCC
Confidence 677776666655543 2346565555443
No 248
>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=35.71 E-value=20 Score=24.86 Aligned_cols=30 Identities=23% Similarity=0.629 Sum_probs=12.9
Q ss_pred ccccCccccCChhhhhhhcCCCcccCCCCCcccCCcccccc
Q 019380 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCM 85 (342)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~~C~~C~ 85 (342)
.|..|++.|... .+.+.|..||..| |..|.
T Consensus 11 ~C~~C~~~F~~~-------~rrhhCr~CG~~v----C~~Cs 40 (69)
T PF01363_consen 11 NCMICGKKFSLF-------RRRHHCRNCGRVV----CSSCS 40 (69)
T ss_dssp B-TTT--B-BSS-------S-EEE-TTT--EE----ECCCS
T ss_pred cCcCcCCcCCCc-------eeeEccCCCCCEE----CCchh
Confidence 688888888432 3455677777655 55553
No 249
>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=35.49 E-value=22 Score=23.45 Aligned_cols=11 Identities=27% Similarity=0.431 Sum_probs=6.2
Q ss_pred ccccCccccCC
Q 019380 45 KCAVCQKLSKS 55 (342)
Q Consensus 45 ~C~~C~~~f~~ 55 (342)
.|..|++.|..
T Consensus 4 ~C~~C~~~F~~ 14 (57)
T cd00065 4 SCMGCGKPFTL 14 (57)
T ss_pred cCcccCccccC
Confidence 35566666554
No 250
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=34.82 E-value=9.7 Score=26.88 Aligned_cols=22 Identities=18% Similarity=0.462 Sum_probs=12.2
Q ss_pred CCcccCCCCCcccCCc-cccccc
Q 019380 65 GPLSKAHCSGIFSDRG-CNLCMN 86 (342)
Q Consensus 65 ~~~~C~~C~k~f~~~~-C~~C~k 86 (342)
+.|.|..|.+.|.... ||.|+.
T Consensus 16 ~~~~C~~C~~~~~~~a~CPdC~~ 38 (70)
T PF07191_consen 16 GHYHCEACQKDYKKEAFCPDCGQ 38 (70)
T ss_dssp TEEEETTT--EEEEEEE-TTT-S
T ss_pred CEEECccccccceecccCCCccc
Confidence 5677777777776544 777765
No 251
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=34.68 E-value=19 Score=26.74 Aligned_cols=10 Identities=30% Similarity=0.747 Sum_probs=5.4
Q ss_pred ccccccccCC
Q 019380 81 CNLCMNIFDS 90 (342)
Q Consensus 81 C~~C~k~F~~ 90 (342)
|..|++.|.-
T Consensus 57 C~~C~~~~AG 66 (90)
T PRK03976 57 CRKCGAKFAG 66 (90)
T ss_pred cCCCCCEEeC
Confidence 5555555543
No 252
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=34.56 E-value=14 Score=37.85 Aligned_cols=15 Identities=20% Similarity=0.368 Sum_probs=11.0
Q ss_pred CCCcccCCCCCcccC
Q 019380 64 TGPLSKAHCSGIFSD 78 (342)
Q Consensus 64 ~~~~~C~~C~k~f~~ 78 (342)
++...||.|+.+|+.
T Consensus 676 tRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 676 TRQRKCPKCNAAFGA 690 (698)
T ss_pred HhcCCCCCCCCCCCc
Confidence 566678888888864
No 253
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=34.52 E-value=9.2 Score=39.07 Aligned_cols=24 Identities=21% Similarity=0.297 Sum_probs=21.8
Q ss_pred ccccccccCChhhHHHHHhhcCCC
Q 019380 81 CNLCMNIFDSPSSLIKHKEACSLS 104 (342)
Q Consensus 81 C~~C~k~F~~~~~L~~H~~~h~~~ 104 (342)
|.+|+|.|-.-.++..|||+|.-.
T Consensus 795 CreC~kvF~KiKSrNAHMK~Hr~q 818 (907)
T KOG4167|consen 795 CRECGKVFFKIKSRNAHMKTHRQQ 818 (907)
T ss_pred hHHHHHHHHHHhhhhHHHHHHHHH
Confidence 899999999999999999999843
No 254
>PRK05580 primosome assembly protein PriA; Validated
Probab=34.45 E-value=22 Score=36.83 Aligned_cols=43 Identities=23% Similarity=0.356 Sum_probs=22.0
Q ss_pred ccccCccccCCh---hhhhhhc-CCCcccCCCCCccc-CCcccccccc
Q 019380 45 KCAVCQKLSKSF---ESLREHL-TGPLSKAHCSGIFS-DRGCNLCMNI 87 (342)
Q Consensus 45 ~C~~C~~~f~~~---~~l~~H~-~~~~~C~~C~k~f~-~~~C~~C~k~ 87 (342)
.|..||.....+ ..|.-|. .+...|..||.... ...|+.||..
T Consensus 383 ~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 383 LCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred EhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 566666554322 2344444 34445666666544 2346666543
No 255
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=33.02 E-value=57 Score=30.48 Aligned_cols=89 Identities=25% Similarity=0.333 Sum_probs=47.7
Q ss_pred cccccc--cccccCCHHHHHHHHhhhccCCCCCccccC---ccccC------ChhhhhhhcCCCcccCCCCCcccC-Ccc
Q 019380 14 RHKCVA--CYKQFKRKDHLIEHMKISYHSVHQPKCAVC---QKLSK------SFESLREHLTGPLSKAHCSGIFSD-RGC 81 (342)
Q Consensus 14 ~~~C~~--C~k~f~~~~~L~~H~~~~~H~~~~~~C~~C---~~~f~------~~~~l~~H~~~~~~C~~C~k~f~~-~~C 81 (342)
.|.||. |...-.....|+.|.+.. |. +.-|..| .+.|. ++..|+.|.++-- -+..|.. ..|
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-HG--FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGL----EEEGFKGHPLC 223 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhh-cC--cEEhHhhhcCcccCccceeeeecccccccccCCc----cccCcCCCchh
Confidence 366753 555545567788888762 21 1234433 33332 3344666662110 0112221 237
Q ss_pred cccccccCChhhHHHHHhhcCCCCCCCCc
Q 019380 82 NLCMNIFDSPSSLIKHKEACSLSAPVPFK 110 (342)
Q Consensus 82 ~~C~k~F~~~~~L~~H~~~h~~~~~~~~~ 110 (342)
..|...|..-..|.+|+|.-| ++.+-|+
T Consensus 224 ~FC~~~FYdDDEL~~HcR~~H-E~ChICD 251 (493)
T COG5236 224 IFCKIYFYDDDELRRHCRLRH-EACHICD 251 (493)
T ss_pred hhccceecChHHHHHHHHhhh-hhhhhhh
Confidence 888888888888888887655 4444443
No 256
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=32.72 E-value=24 Score=32.31 Aligned_cols=22 Identities=27% Similarity=0.534 Sum_probs=13.7
Q ss_pred ccccccccCChhhHHHHHhhcC
Q 019380 81 CNLCMNIFDSPSSLIKHKEACS 102 (342)
Q Consensus 81 C~~C~k~F~~~~~L~~H~~~h~ 102 (342)
|+.|...|-.-...-.|...|.
T Consensus 391 Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 391 CELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred chhhhhhhhhhhHHHHHHHHhh
Confidence 5666666666556666766554
No 257
>COG4640 Predicted membrane protein [Function unknown]
Probab=32.37 E-value=28 Score=33.10 Aligned_cols=28 Identities=25% Similarity=0.412 Sum_probs=16.8
Q ss_pred cCCCCC--cccCCcccccccccCChhhHHH
Q 019380 69 KAHCSG--IFSDRGCNLCMNIFDSPSSLIK 96 (342)
Q Consensus 69 C~~C~k--~f~~~~C~~C~k~F~~~~~L~~ 96 (342)
|+.||+ .-....|++||..|+..++..+
T Consensus 4 C~kcG~qk~Ed~~qC~qCG~~~t~~~sqan 33 (465)
T COG4640 4 CPKCGSQKAEDDVQCTQCGHKFTSRQSQAN 33 (465)
T ss_pred ccccccccccccccccccCCcCCchhhhhh
Confidence 556652 1122238888888887776654
No 258
>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=31.58 E-value=33 Score=30.72 Aligned_cols=78 Identities=18% Similarity=0.298 Sum_probs=41.4
Q ss_pred cCCCCCccccCccccCChhhhhhhc-------CCCcccCCCCCcccCCcccccccccCChhhHHHHHhhcCCCCCCCCcc
Q 019380 39 HSVHQPKCAVCQKLSKSFESLREHL-------TGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEACSLSAPVPFKI 111 (342)
Q Consensus 39 H~~~~~~C~~C~~~f~~~~~l~~H~-------~~~~~C~~C~k~f~~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~ 111 (342)
|.+..++|..|... .-....-.|+ .-.|+|.-|++ +...+|-.|.-.|-.-...+.-.+ ....++++|+.
T Consensus 138 hGGrif~CsfC~~f-lCEDDQFEHQAsCQvLe~E~~KC~SCNr-lGq~sCLRCK~cfCddHvrrKg~k-y~k~k~~PCPK 214 (314)
T PF06524_consen 138 HGGRIFKCSFCDNF-LCEDDQFEHQASCQVLESETFKCQSCNR-LGQYSCLRCKICFCDDHVRRKGFK-YEKGKPIPCPK 214 (314)
T ss_pred CCCeEEEeecCCCe-eeccchhhhhhhhhhhhccccccccccc-ccchhhhheeeeehhhhhhhcccc-cccCCCCCCCC
Confidence 44444466666533 2233333454 34677777765 344566666655655433333333 23347888888
Q ss_pred cccccccc
Q 019380 112 SGAIDEKR 119 (342)
Q Consensus 112 c~~~~~~~ 119 (342)
|+.--..+
T Consensus 215 Cg~et~eT 222 (314)
T PF06524_consen 215 CGYETQET 222 (314)
T ss_pred CCCccccc
Confidence 87554433
No 259
>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=31.34 E-value=18 Score=29.59 Aligned_cols=6 Identities=33% Similarity=0.982 Sum_probs=3.8
Q ss_pred cccccc
Q 019380 81 CNLCMN 86 (342)
Q Consensus 81 C~~C~k 86 (342)
|+.||.
T Consensus 133 Cp~C~~ 138 (146)
T PF07295_consen 133 CPKCGH 138 (146)
T ss_pred CCCCCC
Confidence 677754
No 260
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=31.09 E-value=28 Score=33.49 Aligned_cols=35 Identities=31% Similarity=0.499 Sum_probs=23.5
Q ss_pred CccccCccccCChhhhhhhc--CCCcccCCCCCcccC
Q 019380 44 PKCAVCQKLSKSFESLREHL--TGPLSKAHCSGIFSD 78 (342)
Q Consensus 44 ~~C~~C~~~f~~~~~l~~H~--~~~~~C~~C~k~f~~ 78 (342)
+.|+.|++.|..-..++--. ++.|.|..|+-...-
T Consensus 129 Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelve 165 (436)
T KOG2593|consen 129 YVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVE 165 (436)
T ss_pred ccCCccccchhhhHHHHhhcccCceEEEecCCCchhc
Confidence 37888888877665543222 678888888766553
No 261
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=30.84 E-value=31 Score=26.42 Aligned_cols=22 Identities=23% Similarity=0.108 Sum_probs=20.4
Q ss_pred cccccccCChhhHHHHHhhcCC
Q 019380 82 NLCMNIFDSPSSLIKHKEACSL 103 (342)
Q Consensus 82 ~~C~k~F~~~~~L~~H~~~h~~ 103 (342)
..|+........+++|.+.+||
T Consensus 88 ~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 88 PHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCCcEeccHHHHHHHHHHhcC
Confidence 8999999999999999998875
No 262
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=30.83 E-value=31 Score=25.61 Aligned_cols=13 Identities=23% Similarity=0.667 Sum_probs=10.9
Q ss_pred CC-ccccCccccCC
Q 019380 43 QP-KCAVCQKLSKS 55 (342)
Q Consensus 43 ~~-~C~~C~~~f~~ 55 (342)
+| .|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 44 89999999987
No 263
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=30.65 E-value=47 Score=20.65 Aligned_cols=28 Identities=21% Similarity=0.437 Sum_probs=16.2
Q ss_pred cccCCcccccccccCC--hhhHHHHHhhcC
Q 019380 75 IFSDRGCNLCMNIFDS--PSSLIKHKEACS 102 (342)
Q Consensus 75 ~f~~~~C~~C~k~F~~--~~~L~~H~~~h~ 102 (342)
.|....|+.||-.|.. +.--..|.+-|.
T Consensus 10 ~~~~~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 10 SFGATTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred ccCCcCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 3444567888876665 344455665543
No 264
>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 COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=30.50 E-value=12 Score=38.21 Aligned_cols=14 Identities=21% Similarity=0.468 Sum_probs=7.2
Q ss_pred ccccCccccCChhh
Q 019380 45 KCAVCQKLSKSFES 58 (342)
Q Consensus 45 ~C~~C~~~f~~~~~ 58 (342)
.|..||-+|+--..
T Consensus 125 ~CT~CGPRfTIi~a 138 (750)
T COG0068 125 NCTNCGPRFTIIEA 138 (750)
T ss_pred ccCCCCcceeeecc
Confidence 45555555544433
No 266
>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=30.31 E-value=48 Score=27.47 Aligned_cols=14 Identities=14% Similarity=-0.083 Sum_probs=6.6
Q ss_pred ccccCccccCChhh
Q 019380 45 KCAVCQKLSKSFES 58 (342)
Q Consensus 45 ~C~~C~~~f~~~~~ 58 (342)
.|+.|+..|+....
T Consensus 111 ~Cp~c~~r~tf~eA 124 (158)
T TIGR00373 111 ICPNMCVRFTFNEA 124 (158)
T ss_pred ECCCCCcEeeHHHH
Confidence 45555544444443
No 267
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=29.60 E-value=30 Score=28.33 Aligned_cols=10 Identities=30% Similarity=0.690 Sum_probs=7.7
Q ss_pred ccccccccCC
Q 019380 81 CNLCMNIFDS 90 (342)
Q Consensus 81 C~~C~k~F~~ 90 (342)
|+.||+.|++
T Consensus 31 C~~C~~RFTT 40 (156)
T COG1327 31 CLECGERFTT 40 (156)
T ss_pred ccccccccch
Confidence 7888887774
No 268
>KOG3990 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.51 E-value=23 Score=31.41 Aligned_cols=72 Identities=19% Similarity=0.390 Sum_probs=40.8
Q ss_pred CCcccccccccccCCHHHHHHHH--hhhccCCCCC--ccccCccccCChhhhh------hhc----CCCcccCCCC--Cc
Q 019380 12 TARHKCVACYKQFKRKDHLIEHM--KISYHSVHQP--KCAVCQKLSKSFESLR------EHL----TGPLSKAHCS--GI 75 (342)
Q Consensus 12 ~~~~~C~~C~k~f~~~~~L~~H~--~~~~H~~~~~--~C~~C~~~f~~~~~l~------~H~----~~~~~C~~C~--k~ 75 (342)
.-.|.|..|-..|....--+..+ +. =....+ +|.+|...|...+.-. .|. ..|++|..|. -+
T Consensus 4 ~iL~aCtkC~~r~p~eals~gQqlCk~--Cr~a~~vgKctyCrse~q~askt~t~CkkCah~~~kfG~P~pC~~CkiiaA 81 (305)
T KOG3990|consen 4 PILYACTKCRQRLPFEALSQGQQLCKE--CRIAHPVGKCTYCRSEFQQASKTNTICKKCAHNVRKFGTPKPCQYCKIIAA 81 (305)
T ss_pred hHHHHHHhHhhhCcHHHHHHHHHHHHH--hcccCCccccchhHHHhhhhhhhhhHHHHHHHHHHhcCCCCcchhhhhhhh
Confidence 34688888877765433222221 11 111222 8888887776554311 111 6789999887 45
Q ss_pred ccCCcccccc
Q 019380 76 FSDRGCNLCM 85 (342)
Q Consensus 76 f~~~~C~~C~ 85 (342)
|....|..|.
T Consensus 82 F~g~kc~rct 91 (305)
T KOG3990|consen 82 FIGRKCQRCT 91 (305)
T ss_pred hccchhhhcc
Confidence 6666676663
No 269
>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=28.18 E-value=31 Score=28.16 Aligned_cols=11 Identities=27% Similarity=0.579 Sum_probs=8.2
Q ss_pred ccccccccCCh
Q 019380 81 CNLCMNIFDSP 91 (342)
Q Consensus 81 C~~C~k~F~~~ 91 (342)
|..||+.|++-
T Consensus 31 C~~C~~RFTTy 41 (147)
T TIGR00244 31 CLECHERFTTF 41 (147)
T ss_pred CCccCCcccee
Confidence 78888888754
No 270
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.17 E-value=12 Score=26.71 Aligned_cols=35 Identities=23% Similarity=0.488 Sum_probs=21.0
Q ss_pred CCCcccccccccccCCHHHHHHHHhhhccCCCCC-ccccCccccC
Q 019380 11 STARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSK 54 (342)
Q Consensus 11 ~~~~~~C~~C~k~f~~~~~L~~H~~~~~H~~~~~-~C~~C~~~f~ 54 (342)
..=.|+|..|+..| .+.+||.- ... .|+.|+..++
T Consensus 9 PtY~Y~c~~cg~~~----dvvq~~~d-----dplt~ce~c~a~~k 44 (82)
T COG2331 9 PTYSYECTECGNRF----DVVQAMTD-----DPLTTCEECGARLK 44 (82)
T ss_pred cceEEeecccchHH----HHHHhccc-----CccccChhhChHHH
Confidence 34468999998654 34444432 233 7888886543
No 271
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.94 E-value=32 Score=27.74 Aligned_cols=10 Identities=30% Similarity=0.663 Sum_probs=6.2
Q ss_pred ccccccccCC
Q 019380 81 CNLCMNIFDS 90 (342)
Q Consensus 81 C~~C~k~F~~ 90 (342)
|..||..|..
T Consensus 73 C~~CG~~~~~ 82 (135)
T PRK03824 73 CRNCGNEWSL 82 (135)
T ss_pred CCCCCCEEec
Confidence 6666666654
No 272
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=26.81 E-value=39 Score=32.66 Aligned_cols=10 Identities=20% Similarity=0.464 Sum_probs=5.4
Q ss_pred ccccccccCC
Q 019380 81 CNLCMNIFDS 90 (342)
Q Consensus 81 C~~C~k~F~~ 90 (342)
|+.||..+..
T Consensus 370 C~kCg~~~~~ 379 (421)
T COG1571 370 CKKCGTRARE 379 (421)
T ss_pred cccccccCCc
Confidence 5556555543
No 273
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=26.05 E-value=2.2e+02 Score=31.29 Aligned_cols=132 Identities=16% Similarity=0.180 Sum_probs=69.8
Q ss_pred CCCCcceecccccccccCCCcccccceEEee--------cCCCCe----EEeeecCCCCCccccccccCCCCHhh-----
Q 019380 121 CRGPKAVAMDCEMVGGGSNGTLDLCARVCLV--------DEDENV----IFHTYVQPQLPVTNYRYEVTGLTEED----- 183 (342)
Q Consensus 121 ~~~~~~v~~D~Ettg~~~~~~~~il~~v~vv--------~~~~~~----~~~~lv~p~~~i~~~~~~i~GIt~e~----- 183 (342)
.++....++..+|+-.......++ ..+++. ...+.. .+..+++|...+-++ |+. +.
T Consensus 526 ~Ppl~llsL~i~T~~N~k~~~~Ei-v~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~~~fP~-----g~~-ela~~k~ 598 (1429)
T KOG0970|consen 526 PPPLTLLSLNIRTSMNPKQNKNEI-VMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPGTSFPL-----GLK-ELAKQKL 598 (1429)
T ss_pred CCCeeEEEeeeeehhccccchhhh-hhhhhhhcccccccCCCCCCcccCcceeEecCCCCcCCc-----hHH-HHHHhcc
Confidence 344556677777775544443333 222221 111111 367788887543332 221 11
Q ss_pred --hcCCCChHHHHHHHHHHHhcCCCccccccCCCCCeEEEeeC-chhhhhhcc-----ccCC-------------C----
Q 019380 184 --IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLR-----MNYP-------------D---- 238 (342)
Q Consensus 184 --l~~~~~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~lvgh~-~~~D~~~l~-----~~~~-------------~---- 238 (342)
+.-..+...++..|+..++. ..-.++|||| ..+++++|- +..| .
T Consensus 599 ~~v~~~~sErALLs~fla~~~~-----------~dpD~iVgHn~~~~~l~VLl~R~~~~Kip~WS~IgRLrrS~~~kfg~ 667 (1429)
T KOG0970|consen 599 SKVVLHNSERALLSHFLAMLNK-----------EDPDVIVGHNIQGFYLDVLLSRLHALKIPNWSSIGRLRRSWPPKFGR 667 (1429)
T ss_pred CceEEecCHHHHHHHHHHHhhc-----------cCCCEEEEeccccchHHHHHHHHHHhcCcchhhhhhhhhccccccCC
Confidence 22234556677777777732 1345999999 778888872 1111 1
Q ss_pred ------------cceeeccccccccccCCCCccHHHHHHHHhCCc
Q 019380 239 ------------HMLRDTAKYRPLMKTNLVSHSLKYLTRTYLGYD 271 (342)
Q Consensus 239 ------------~~~~Dt~~l~~~~~~~~~~~~L~~l~~~~~~~~ 271 (342)
..+-|+...++-+. ...+|+|++|+...|+.+
T Consensus 668 ~s~~~e~~~~aGRl~CD~~~~a~~li-k~~S~~LseL~q~~l~~e 711 (1429)
T KOG0970|consen 668 SSSFGEFFIIAGRLMCDLNLAARELI-KAQSYSLSELSQQILKEE 711 (1429)
T ss_pred cccccccccccceEEeehHHHHHhhh-ccccccHHHHHHHHHhhh
Confidence 11224422223332 246899999999998873
No 274
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.57 E-value=77 Score=22.85 Aligned_cols=35 Identities=17% Similarity=0.168 Sum_probs=25.4
Q ss_pred ccCCCCCcccCCc--------ccccccccCChhhHHHHHhhcC
Q 019380 68 SKAHCSGIFSDRG--------CNLCMNIFDSPSSLIKHKEACS 102 (342)
Q Consensus 68 ~C~~C~k~f~~~~--------C~~C~k~F~~~~~L~~H~~~h~ 102 (342)
.|+.|+.....+. |+.|+-.......|..-+....
T Consensus 3 lCP~C~v~l~~~~rs~vEiD~CPrCrGVWLDrGELdKli~r~r 45 (88)
T COG3809 3 LCPICGVELVMSVRSGVEIDYCPRCRGVWLDRGELDKLIERSR 45 (88)
T ss_pred ccCcCCceeeeeeecCceeeeCCccccEeecchhHHHHHHHhc
Confidence 4777776665432 9999998999998887765544
No 275
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=25.56 E-value=42 Score=34.90 Aligned_cols=39 Identities=18% Similarity=0.314 Sum_probs=23.6
Q ss_pred ccccCccccCChhhhhhhcCCCcccCCCCCcccCCcccccccccC
Q 019380 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFD 89 (342)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~~C~~C~k~F~ 89 (342)
.|..|++.|.....+. ..+.+.|+.||..| |..|.....
T Consensus 462 tC~~C~kkFfSlsK~L--~~RKHHCRkCGrVF----C~~CSSnRs 500 (1374)
T PTZ00303 462 SCPSCGRAFISLSRPL--GTRAHHCRSCGIRL----CVFCITKRA 500 (1374)
T ss_pred cccCcCCccccccccc--ccccccccCCcccc----CccccCCcc
Confidence 5888888886542100 13455788888776 777754333
No 276
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=24.50 E-value=45 Score=23.14 Aligned_cols=18 Identities=11% Similarity=0.429 Sum_probs=7.9
Q ss_pred cCCCCCcccCCccccccc
Q 019380 69 KAHCSGIFSDRGCNLCMN 86 (342)
Q Consensus 69 C~~C~k~f~~~~C~~C~k 86 (342)
|..|........|+.||.
T Consensus 8 C~~C~~i~~~~~Cp~Cgs 25 (64)
T PRK06393 8 CKKCKRLTPEKTCPVHGD 25 (64)
T ss_pred HhhCCcccCCCcCCCCCC
Confidence 444444433334555543
No 277
>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=24.39 E-value=52 Score=21.57 Aligned_cols=11 Identities=18% Similarity=0.770 Sum_probs=6.7
Q ss_pred ccccCccccCC
Q 019380 45 KCAVCQKLSKS 55 (342)
Q Consensus 45 ~C~~C~~~f~~ 55 (342)
.|..||+.+.-
T Consensus 3 ~C~~CgyiYd~ 13 (50)
T cd00730 3 ECRICGYIYDP 13 (50)
T ss_pred CCCCCCeEECC
Confidence 56667666543
No 278
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=24.33 E-value=37 Score=26.40 Aligned_cols=9 Identities=22% Similarity=0.763 Sum_probs=4.3
Q ss_pred ccccccccC
Q 019380 81 CNLCMNIFD 89 (342)
Q Consensus 81 C~~C~k~F~ 89 (342)
|..||..|.
T Consensus 73 C~~Cg~~~~ 81 (113)
T PRK12380 73 CWDCSQVVE 81 (113)
T ss_pred cccCCCEEe
Confidence 455554443
No 279
>PRK00420 hypothetical protein; Validated
Probab=24.25 E-value=46 Score=25.91 Aligned_cols=8 Identities=13% Similarity=0.692 Sum_probs=4.1
Q ss_pred cccccccc
Q 019380 81 CNLCMNIF 88 (342)
Q Consensus 81 C~~C~k~F 88 (342)
|+.||...
T Consensus 43 Cp~Cg~~~ 50 (112)
T PRK00420 43 CPVHGKVY 50 (112)
T ss_pred CCCCCCee
Confidence 55555533
No 280
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=24.16 E-value=46 Score=30.62 Aligned_cols=8 Identities=25% Similarity=0.825 Sum_probs=4.6
Q ss_pred Cccccccc
Q 019380 13 ARHKCVAC 20 (342)
Q Consensus 13 ~~~~C~~C 20 (342)
.-|.|+.|
T Consensus 307 gGy~CP~C 314 (421)
T COG5151 307 GGYECPVC 314 (421)
T ss_pred CceeCCcc
Confidence 34666666
No 281
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=24.12 E-value=30 Score=32.57 Aligned_cols=9 Identities=22% Similarity=0.755 Sum_probs=3.2
Q ss_pred ccccCcccc
Q 019380 45 KCAVCQKLS 53 (342)
Q Consensus 45 ~C~~C~~~f 53 (342)
.|..|.+..
T Consensus 254 ~C~~C~yt~ 262 (344)
T PF09332_consen 254 TCKQCKYTA 262 (344)
T ss_dssp EETTT--EE
T ss_pred EcCCCCCcc
Confidence 345554443
No 282
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=24.00 E-value=24 Score=36.24 Aligned_cols=27 Identities=33% Similarity=0.456 Sum_probs=22.3
Q ss_pred CCcccccccccccCCHHHHHHHHhhhccC
Q 019380 12 TARHKCVACYKQFKRKDHLIEHMKISYHS 40 (342)
Q Consensus 12 ~~~~~C~~C~k~f~~~~~L~~H~~~~~H~ 40 (342)
..-|.|..|+|.|..-..++.||++ |.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~--Hr 816 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKT--HR 816 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHH--HH
Confidence 4568899999998888888899988 55
No 283
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=23.91 E-value=27 Score=32.06 Aligned_cols=13 Identities=23% Similarity=0.205 Sum_probs=6.9
Q ss_pred EeeecCCCCCccc
Q 019380 159 FHTYVQPQLPVTN 171 (342)
Q Consensus 159 ~~~lv~p~~~i~~ 171 (342)
.+.++.|-.++--
T Consensus 122 ~~~~~~pw~pww~ 134 (383)
T KOG4317|consen 122 IDEYELPWGPWWR 134 (383)
T ss_pred hhhccCCCcHHHH
Confidence 3556666655443
No 284
>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=23.83 E-value=32 Score=19.87 Aligned_cols=20 Identities=15% Similarity=0.340 Sum_probs=10.2
Q ss_pred ccCCCCCcccCCccccccccc
Q 019380 68 SKAHCSGIFSDRGCNLCMNIF 88 (342)
Q Consensus 68 ~C~~C~k~f~~~~C~~C~k~F 88 (342)
.|.+|+. +....|+.|+..+
T Consensus 4 ~C~vC~~-~~kY~Cp~C~~~~ 23 (30)
T PF04438_consen 4 LCSVCGN-PAKYRCPRCGARY 23 (30)
T ss_dssp EETSSSS-EESEE-TTT--EE
T ss_pred CCccCcC-CCEEECCCcCCce
Confidence 4566666 5555677776544
No 285
>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=23.82 E-value=40 Score=26.27 Aligned_cols=10 Identities=20% Similarity=0.591 Sum_probs=5.7
Q ss_pred ccccccccCC
Q 019380 81 CNLCMNIFDS 90 (342)
Q Consensus 81 C~~C~k~F~~ 90 (342)
|..||+.|..
T Consensus 73 C~~Cg~~~~~ 82 (115)
T TIGR00100 73 CEDCSEEVSP 82 (115)
T ss_pred cccCCCEEec
Confidence 6666655553
No 286
>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=23.32 E-value=28 Score=27.04 Aligned_cols=9 Identities=33% Similarity=0.888 Sum_probs=3.3
Q ss_pred ccccccccC
Q 019380 81 CNLCMNIFD 89 (342)
Q Consensus 81 C~~C~k~F~ 89 (342)
|..||+.|.
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 287
>KOG3276 consensus Uncharacterized conserved protein, contains YggU domain [Function unknown]
Probab=23.06 E-value=1.3e+02 Score=23.51 Aligned_cols=47 Identities=23% Similarity=0.268 Sum_probs=35.7
Q ss_pred ecCCCCeEEeeecCCCCCccccccccCCCCHhhhc---CC-CChHHHHHHHHHHH
Q 019380 151 VDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIK---NA-MPLKEVKDKILEIL 201 (342)
Q Consensus 151 v~~~~~~~~~~lv~p~~~i~~~~~~i~GIt~e~l~---~~-~~~~~v~~~~~~~l 201 (342)
++..|.+......+|... ...||+|+.|+|. +| |.-.++=.++++|+
T Consensus 29 ~d~~g~V~i~IhakpgaK----~s~It~v~~e~V~V~IaApp~eGeANaeLl~yl 79 (125)
T KOG3276|consen 29 VDTGGLVQIAIHAKPGAK----QSAITDVGDEAVGVAIAAPPREGEANAELLEYL 79 (125)
T ss_pred ecCCCeEEEEEEecCCcc----ccceeeccccccceEEecCCccchhhHHHHHHH
Confidence 345677777778888764 5788999998876 44 46778888999998
No 288
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=23.01 E-value=37 Score=25.81 Aligned_cols=7 Identities=29% Similarity=0.629 Sum_probs=3.6
Q ss_pred ccccccc
Q 019380 81 CNLCMNI 87 (342)
Q Consensus 81 C~~C~k~ 87 (342)
|+.||..
T Consensus 45 C~~CG~y 51 (99)
T PRK14892 45 CGNCGLY 51 (99)
T ss_pred CCCCCCc
Confidence 5555543
No 289
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=22.68 E-value=43 Score=21.66 Aligned_cols=12 Identities=25% Similarity=0.611 Sum_probs=6.6
Q ss_pred ccccCccccCCh
Q 019380 45 KCAVCQKLSKSF 56 (342)
Q Consensus 45 ~C~~C~~~f~~~ 56 (342)
.|..|+..+.-.
T Consensus 3 ~C~~CgyvYd~~ 14 (47)
T PF00301_consen 3 QCPVCGYVYDPE 14 (47)
T ss_dssp EETTTSBEEETT
T ss_pred CCCCCCEEEcCC
Confidence 466666555433
No 290
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=22.43 E-value=51 Score=25.19 Aligned_cols=30 Identities=37% Similarity=0.716 Sum_probs=23.8
Q ss_pred CCCCCCCCCcccccccccccCCHHHHHHHHhh
Q 019380 5 AELPKRSTARHKCVACYKQFKRKDHLIEHMKI 36 (342)
Q Consensus 5 ~~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~~ 36 (342)
+++| |-..|-|-.|.+-|.+...|..|.+.
T Consensus 48 p~lP--GlGqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 48 PELP--GLGQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred CCCC--CCceeeeehhHHHHHHHHHHHHHhcc
Confidence 3455 67778899999999998888888764
No 291
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=22.22 E-value=19 Score=27.02 Aligned_cols=13 Identities=23% Similarity=0.708 Sum_probs=8.7
Q ss_pred ccccccccCChhh
Q 019380 81 CNLCMNIFDSPSS 93 (342)
Q Consensus 81 C~~C~k~F~~~~~ 93 (342)
|+.|...|.....
T Consensus 83 Cp~C~spFNp~Ck 95 (105)
T COG4357 83 CPYCQSPFNPGCK 95 (105)
T ss_pred CCCcCCCCCcccc
Confidence 7777777776543
No 292
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=22.08 E-value=40 Score=28.45 Aligned_cols=23 Identities=26% Similarity=0.444 Sum_probs=17.7
Q ss_pred CCcccCCCCCccc--CCcccccccc
Q 019380 65 GPLSKAHCSGIFS--DRGCNLCMNI 87 (342)
Q Consensus 65 ~~~~C~~C~k~f~--~~~C~~C~k~ 87 (342)
..+.|..|.+.|. ..-|+.||..
T Consensus 138 w~~rC~GC~~~f~~~~~~Cp~CG~~ 162 (177)
T COG1439 138 WRLRCHGCKRIFPEPKDFCPICGSP 162 (177)
T ss_pred eeEEEecCceecCCCCCcCCCCCCc
Confidence 3577999999998 3349999864
No 293
>PF12096 DUF3572: Protein of unknown function (DUF3572); InterPro: IPR021955 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 100 amino acids in length.
Probab=21.42 E-value=72 Score=23.68 Aligned_cols=31 Identities=23% Similarity=0.335 Sum_probs=26.5
Q ss_pred cccCCCCHhhhcCCCChHHHHHHHHHHHhcC
Q 019380 174 YEVTGLTEEDIKNAMPLKEVKDKILEILNNG 204 (342)
Q Consensus 174 ~~i~GIt~e~l~~~~~~~~v~~~~~~~l~~~ 204 (342)
-..||++++++..+-.-.+.+..+++||.++
T Consensus 28 La~TG~~p~~LR~~a~dp~FL~~VLdFl~~d 58 (88)
T PF12096_consen 28 LALTGLSPDDLRAAAGDPAFLAAVLDFLLMD 58 (88)
T ss_pred HHHhCCCHHHHHHHccChHHHHHHHHHHHcc
Confidence 3569999999999888888999999999554
No 294
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=21.39 E-value=36 Score=21.41 Aligned_cols=15 Identities=20% Similarity=0.355 Sum_probs=10.1
Q ss_pred cccccccccCChhhH
Q 019380 80 GCNLCMNIFDSPSSL 94 (342)
Q Consensus 80 ~C~~C~k~F~~~~~L 94 (342)
.|..||+.|+.+...
T Consensus 10 ~C~~C~rpf~WRKKW 24 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKW 24 (42)
T ss_pred cCcccCCcchHHHHH
Confidence 378888888765443
No 295
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=21.38 E-value=1.1e+02 Score=20.30 Aligned_cols=33 Identities=6% Similarity=-0.053 Sum_probs=22.0
Q ss_pred cccCCCCCcccCCcccccccccCChhhHHHHHhh
Q 019380 67 LSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEA 100 (342)
Q Consensus 67 ~~C~~C~k~f~~~~C~~C~k~F~~~~~L~~H~~~ 100 (342)
+.|+.|+..+.+.-...||.+|.... +..+.+.
T Consensus 2 ~~Cpi~~~~~~~Pv~~~~G~v~~~~~-i~~~~~~ 34 (63)
T smart00504 2 FLCPISLEVMKDPVILPSGQTYERRA-IEKWLLS 34 (63)
T ss_pred cCCcCCCCcCCCCEECCCCCEEeHHH-HHHHHHH
Confidence 45777887777766667888776544 4555544
No 296
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=21.33 E-value=34 Score=22.56 Aligned_cols=10 Identities=40% Similarity=0.906 Sum_probs=4.8
Q ss_pred ccccccccCC
Q 019380 81 CNLCMNIFDS 90 (342)
Q Consensus 81 C~~C~k~F~~ 90 (342)
||.|++.|..
T Consensus 23 CPlC~r~l~~ 32 (54)
T PF04423_consen 23 CPLCGRPLDE 32 (54)
T ss_dssp -TTT--EE-H
T ss_pred CCCCCCCCCH
Confidence 7888888875
No 297
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=21.05 E-value=61 Score=28.36 Aligned_cols=29 Identities=24% Similarity=0.495 Sum_probs=21.3
Q ss_pred CCCcccccccccccCCHHHHHHHHhhhccC
Q 019380 11 STARHKCVACYKQFKRKDHLIEHMKISYHS 40 (342)
Q Consensus 11 ~~~~~~C~~C~k~f~~~~~L~~H~~~~~H~ 40 (342)
.+..|.|+.|+|.|.-......|+..- |.
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nK-H~ 102 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNK-HP 102 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH--H
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhc-CH
Confidence 455799999999999999999998652 54
No 298
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=21.02 E-value=65 Score=30.40 Aligned_cols=28 Identities=25% Similarity=0.381 Sum_probs=15.2
Q ss_pred ccccccCChhhHHHHHhhcCCCCCCCCc
Q 019380 83 LCMNIFDSPSSLIKHKEACSLSAPVPFK 110 (342)
Q Consensus 83 ~C~k~F~~~~~L~~H~~~h~~~~~~~~~ 110 (342)
.|++.|.+...+..|...|.+..+..+.
T Consensus 328 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 328 LCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred CCCccccccccccCCcccccCCCccccc
Confidence 4555555555555555555555544433
No 299
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=20.44 E-value=41 Score=23.92 Aligned_cols=9 Identities=22% Similarity=0.290 Sum_probs=5.0
Q ss_pred ccccccCCh
Q 019380 83 LCMNIFDSP 91 (342)
Q Consensus 83 ~C~k~F~~~ 91 (342)
.||.+|...
T Consensus 34 eCg~tF~t~ 42 (72)
T PRK09678 34 NCSATFITY 42 (72)
T ss_pred CCCCEEEEE
Confidence 566666543
No 300
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=20.40 E-value=74 Score=19.58 Aligned_cols=15 Identities=27% Similarity=0.505 Sum_probs=10.2
Q ss_pred ccccccccCChhhHH
Q 019380 81 CNLCMNIFDSPSSLI 95 (342)
Q Consensus 81 C~~C~k~F~~~~~L~ 95 (342)
|+.|+-.+-....|.
T Consensus 22 C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 22 CPSCGGIWFDAGELE 36 (41)
T ss_pred CCCCCeEEccHHHHH
Confidence 777777666666654
Done!