Query 009783
Match_columns 526
No_of_seqs 397 out of 1451
Neff 6.8
Searched_HMMs 46136
Date Thu Mar 28 17:16:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009783.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009783hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01927 Mut7-C: Mut7-C RNAse 100.0 3.4E-45 7.4E-50 336.8 14.0 146 361-517 1-146 (147)
2 COG1656 Uncharacterized conser 100.0 1.6E-43 3.5E-48 321.8 11.5 148 358-516 4-151 (165)
3 PRK10829 ribonuclease D; Provi 100.0 4.5E-32 9.7E-37 283.5 22.4 217 10-270 2-220 (373)
4 cd06146 mut-7_like_exo DEDDy 3 100.0 1.3E-29 2.9E-34 243.6 20.3 184 11-213 1-192 (193)
5 COG0349 Rnd Ribonuclease D [Tr 100.0 5.6E-30 1.2E-34 261.6 18.1 211 19-270 4-216 (361)
6 cd06129 RNaseD_like DEDDy 3'-5 100.0 1.1E-28 2.3E-33 230.5 18.5 158 22-213 2-160 (161)
7 TIGR01388 rnd ribonuclease D. 100.0 2.4E-28 5.3E-33 256.3 22.2 213 14-270 2-216 (367)
8 cd06141 WRN_exo DEDDy 3'-5' ex 99.9 1.7E-26 3.8E-31 216.9 19.0 163 19-213 4-169 (170)
9 cd06148 Egl_like_exo DEDDy 3'- 99.9 4.6E-26 9.9E-31 219.8 16.8 170 25-220 3-181 (197)
10 PF01612 DNA_pol_A_exo1: 3'-5' 99.9 5.6E-25 1.2E-29 205.8 19.0 174 11-217 1-176 (176)
11 cd06142 RNaseD_exo DEDDy 3'-5' 99.8 3.3E-19 7.1E-24 167.8 19.6 174 22-232 2-175 (178)
12 smart00474 35EXOc 3'-5' exonuc 99.8 5.7E-17 1.2E-21 150.5 19.9 169 12-216 2-171 (172)
13 KOG2207 Predicted 3'-5' exonuc 99.7 3.7E-18 8.1E-23 181.9 9.0 195 5-217 386-586 (617)
14 cd06147 Rrp6p_like_exo DEDDy 3 99.7 1.2E-15 2.5E-20 146.5 20.6 174 8-219 2-175 (192)
15 KOG2206 Exosome 3'-5' exoribon 99.7 9.2E-17 2E-21 170.2 9.2 173 11-221 193-365 (687)
16 cd00007 35EXOc 3'-5' exonuclea 99.6 1.3E-14 2.9E-19 132.1 16.7 149 34-215 2-154 (155)
17 cd09018 DEDDy_polA_RNaseD_like 99.6 1.8E-14 3.9E-19 131.4 15.7 147 34-213 1-149 (150)
18 PRK05755 DNA polymerase I; Pro 99.6 3.2E-14 6.8E-19 165.3 21.3 187 8-231 293-483 (880)
19 KOG2207 Predicted 3'-5' exonuc 99.6 3.9E-17 8.5E-22 174.2 -6.7 369 135-511 154-571 (617)
20 cd06140 DNA_polA_I_Bacillus_li 99.5 1.5E-13 3.3E-18 129.6 16.3 164 32-231 3-169 (178)
21 cd06139 DNA_polA_I_Ecoli_like_ 99.5 3.1E-12 6.8E-17 121.7 18.1 168 30-231 3-184 (193)
22 PRK14975 bifunctional 3'-5' ex 99.3 5.5E-12 1.2E-16 139.6 12.7 146 10-219 2-147 (553)
23 COG0749 PolA DNA polymerase I 99.2 2.1E-10 4.6E-15 125.1 13.1 179 19-231 9-194 (593)
24 TIGR00593 pola DNA polymerase 99.1 1.9E-09 4.2E-14 124.6 19.8 180 11-231 304-490 (887)
25 KOG4373 Predicted 3'-5' exonuc 98.8 1.7E-08 3.6E-13 102.1 9.5 149 32-209 127-281 (319)
26 COG4634 Uncharacterized protei 98.6 2.1E-07 4.5E-12 79.7 8.1 73 361-433 1-79 (113)
27 cd06128 DNA_polA_exo DEDDy 3'- 98.6 1.5E-06 3.1E-11 79.9 13.7 118 78-213 30-150 (151)
28 PRK06063 DNA polymerase III su 97.2 0.012 2.7E-07 61.0 15.6 102 91-221 83-184 (313)
29 cd06137 DEDDh_RNase DEDDh 3'-5 97.1 0.0057 1.2E-07 57.1 11.5 86 94-209 75-160 (161)
30 cd06149 ISG20 DEDDh 3'-5' exon 97.0 0.0052 1.1E-07 57.2 10.0 89 91-210 66-157 (157)
31 PRK07942 DNA polymerase III su 96.9 0.065 1.4E-06 53.2 17.8 90 105-219 94-183 (232)
32 PRK06310 DNA polymerase III su 96.8 0.045 9.7E-07 55.0 15.8 150 29-216 4-174 (250)
33 cd06131 DNA_pol_III_epsilon_Ec 96.7 0.055 1.2E-06 50.3 14.8 95 92-212 71-166 (167)
34 PRK06309 DNA polymerase III su 96.7 0.085 1.8E-06 52.3 16.8 145 33-218 3-168 (232)
35 KOG2249 3'-5' exonuclease [Rep 96.7 0.013 2.8E-07 58.4 10.6 95 93-219 175-269 (280)
36 PRK08517 DNA polymerase III su 96.7 0.08 1.7E-06 53.4 16.7 98 91-218 136-233 (257)
37 PRK06807 DNA polymerase III su 96.7 0.05 1.1E-06 56.5 15.2 96 92-217 78-173 (313)
38 TIGR01405 polC_Gram_pos DNA po 96.7 0.035 7.5E-07 67.0 15.8 103 91-222 259-361 (1213)
39 PRK07883 hypothetical protein; 96.6 0.057 1.2E-06 60.4 16.1 161 25-222 8-188 (557)
40 PRK07740 hypothetical protein; 96.6 0.11 2.4E-06 51.9 16.7 101 92-222 131-232 (244)
41 cd06144 REX4_like DEDDh 3'-5' 96.6 0.0085 1.8E-07 55.4 8.0 86 91-210 66-152 (152)
42 PRK05168 ribonuclease T; Provi 96.5 0.2 4.3E-06 49.0 17.4 93 104-222 114-207 (211)
43 cd05780 DNA_polB_Kod1_like_exo 96.5 0.067 1.4E-06 51.5 13.9 113 91-212 58-195 (195)
44 cd06143 PAN2_exo DEDDh 3'-5' e 96.5 0.0084 1.8E-07 56.8 7.3 80 95-209 94-173 (174)
45 PRK05711 DNA polymerase III su 96.5 0.098 2.1E-06 52.3 15.2 98 92-214 76-174 (240)
46 TIGR01298 RNaseT ribonuclease 96.5 0.15 3.4E-06 49.3 16.2 92 105-222 106-198 (200)
47 smart00479 EXOIII exonuclease 96.4 0.14 2.9E-06 47.2 15.2 98 91-216 69-167 (169)
48 TIGR00573 dnaq exonuclease, DN 96.3 0.078 1.7E-06 52.0 13.4 104 92-219 77-180 (217)
49 cd06125 DnaQ_like_exo DnaQ-lik 96.2 0.029 6.4E-07 47.7 8.7 82 35-145 1-83 (96)
50 PRK09145 DNA polymerase III su 96.2 0.23 5E-06 48.0 15.9 99 91-214 100-199 (202)
51 PRK09146 DNA polymerase III su 96.2 0.23 4.9E-06 49.6 15.9 103 92-217 119-228 (239)
52 cd06130 DNA_pol_III_epsilon_li 96.1 0.19 4.1E-06 45.9 14.3 89 91-209 66-154 (156)
53 cd06145 REX1_like DEDDh 3'-5' 96.1 0.021 4.5E-07 52.7 7.9 86 91-209 64-149 (150)
54 TIGR01407 dinG_rel DnaQ family 96.1 0.12 2.6E-06 60.9 15.9 99 91-218 69-167 (850)
55 cd05160 DEDDy_DNA_polB_exo DED 96.1 0.11 2.5E-06 49.7 13.1 110 91-209 65-198 (199)
56 cd06127 DEDDh DEDDh 3'-5' exon 95.7 0.35 7.6E-06 43.3 13.7 91 91-209 68-158 (159)
57 PRK08074 bifunctional ATP-depe 95.6 0.43 9.2E-06 56.8 17.5 99 91-218 73-171 (928)
58 cd05781 DNA_polB_B3_exo DEDDy 94.8 0.78 1.7E-05 44.0 13.8 156 33-212 4-188 (188)
59 COG2176 PolC DNA polymerase II 94.8 0.11 2.5E-06 61.0 9.1 103 91-222 490-592 (1444)
60 TIGR01406 dnaQ_proteo DNA poly 94.7 0.29 6.2E-06 48.4 10.7 99 91-214 71-170 (225)
61 PRK07246 bifunctional ATP-depe 94.1 0.32 6.9E-06 57.0 11.2 100 91-220 75-174 (820)
62 PRK05601 DNA polymerase III su 93.5 1.5 3.2E-05 46.4 13.7 108 91-212 114-245 (377)
63 PRK06195 DNA polymerase III su 93.3 0.64 1.4E-05 48.1 10.5 99 91-219 69-167 (309)
64 PRK00448 polC DNA polymerase I 93.2 1.2 2.5E-05 55.2 14.1 102 92-222 489-590 (1437)
65 cd05784 DNA_polB_II_exo DEDDy 93.0 2.7 5.9E-05 40.5 13.7 110 91-210 53-193 (193)
66 cd06134 RNaseT DEDDh 3'-5' exo 92.9 0.99 2.1E-05 43.2 10.5 84 105-214 103-187 (189)
67 cd05785 DNA_polB_like2_exo Unc 92.9 1.8 3.9E-05 42.2 12.4 158 33-209 10-206 (207)
68 cd05777 DNA_polB_delta_exo DED 92.3 2.6 5.7E-05 41.6 12.9 55 160-214 167-225 (230)
69 cd00814 MetRS_core catalytic c 90.6 0.59 1.3E-05 48.5 6.6 102 372-505 29-131 (319)
70 cd05783 DNA_polB_B1_exo DEDDy 90.1 13 0.00028 36.1 15.2 161 33-210 6-202 (204)
71 PF14803 Nudix_N_2: Nudix N-te 89.4 0.27 5.9E-06 33.9 2.0 31 457-506 3-33 (34)
72 cd06136 TREX1_2 DEDDh 3'-5' ex 89.3 1.6 3.5E-05 41.3 7.9 89 92-210 84-175 (177)
73 KOG2405 Predicted 3'-5' exonuc 89.2 0.04 8.6E-07 57.5 -3.3 130 51-204 73-215 (458)
74 KOG2405 Predicted 3'-5' exonuc 88.8 0.11 2.4E-06 54.3 -0.4 126 77-214 222-359 (458)
75 PF13482 RNase_H_2: RNase_H su 88.8 0.52 1.1E-05 43.5 4.2 148 35-212 1-163 (164)
76 PF13719 zinc_ribbon_5: zinc-r 87.0 0.53 1.1E-05 33.0 2.3 33 455-505 3-35 (37)
77 PRK11779 sbcB exonuclease I; P 87.0 10 0.00022 41.7 13.4 106 92-215 81-197 (476)
78 PF08792 A2L_zn_ribbon: A2L zi 86.9 0.58 1.3E-05 32.0 2.3 29 454-505 3-31 (33)
79 PLN02224 methionine-tRNA ligas 85.7 2.4 5.2E-05 48.1 7.9 34 372-405 98-131 (616)
80 cd05779 DNA_polB_epsilon_exo D 85.6 13 0.00028 36.2 11.9 111 91-210 75-204 (204)
81 PF13717 zinc_ribbon_4: zinc-r 85.6 0.67 1.5E-05 32.3 2.2 32 456-505 4-35 (36)
82 KOG2248 3'-5' exonuclease [Rep 85.6 0.7 1.5E-05 49.2 3.4 91 91-214 282-373 (380)
83 PRK09182 DNA polymerase III su 85.2 25 0.00055 36.2 14.5 88 93-213 111-198 (294)
84 PRK07748 sporulation inhibitor 84.9 8.6 0.00019 37.2 10.4 99 91-215 81-179 (207)
85 PRK12268 methionyl-tRNA synthe 84.5 1.3 2.9E-05 49.4 5.2 55 347-405 9-66 (556)
86 PRK07983 exodeoxyribonuclease 83.8 9.3 0.0002 37.6 10.2 87 94-214 66-152 (219)
87 PRK00133 metG methionyl-tRNA s 83.2 2.3 4.9E-05 48.9 6.4 33 372-404 31-63 (673)
88 PF09334 tRNA-synt_1g: tRNA sy 83.2 1 2.3E-05 48.2 3.5 34 372-405 28-61 (391)
89 COG4049 Uncharacterized protei 83.0 0.37 8.1E-06 36.7 -0.0 18 491-508 13-30 (65)
90 TIGR00398 metG methionyl-tRNA 82.7 2.4 5.2E-05 47.1 6.3 34 372-405 28-61 (530)
91 TIGR02098 MJ0042_CXXC MJ0042 f 82.7 1.1 2.3E-05 31.3 2.2 34 455-506 3-36 (38)
92 cd05776 DNA_polB_alpha_exo ina 82.5 2.7 5.8E-05 41.7 5.9 113 91-213 84-227 (234)
93 PRK11893 methionyl-tRNA synthe 81.9 2.8 6.1E-05 46.2 6.3 34 372-405 30-63 (511)
94 PRK07247 DNA polymerase III su 81.1 10 0.00022 36.7 9.1 92 91-215 73-168 (195)
95 PRK00464 nrdR transcriptional 80.3 0.54 1.2E-05 43.7 0.0 44 456-515 2-45 (154)
96 COG0143 MetG Methionyl-tRNA sy 79.9 3.1 6.7E-05 46.6 5.8 33 372-405 34-67 (558)
97 cd05782 DNA_polB_like1_exo Unc 79.4 19 0.00042 35.0 10.6 110 90-210 79-207 (208)
98 KOG3657 Mitochondrial DNA poly 79.4 6.2 0.00014 45.5 7.8 108 104-219 241-386 (1075)
99 PRK12267 methionyl-tRNA synthe 79.3 3.6 7.9E-05 47.0 6.3 33 372-404 33-65 (648)
100 PF09281 Taq-exonuc: Taq polym 78.8 10 0.00023 34.1 7.6 55 135-216 84-138 (138)
101 cd06138 ExoI_N N-terminal DEDD 77.0 15 0.00032 34.8 8.8 99 92-209 72-182 (183)
102 smart00661 RPOL9 RNA polymeras 76.1 3.3 7.1E-05 30.7 3.2 17 494-510 19-35 (52)
103 COG0847 DnaQ DNA polymerase II 75.9 20 0.00043 35.3 9.7 98 92-215 84-181 (243)
104 PF13453 zf-TFIIB: Transcripti 75.8 1.9 4.2E-05 30.7 1.8 24 493-516 17-40 (41)
105 cd06133 ERI-1_3'hExo_like DEDD 75.7 25 0.00055 32.3 9.9 97 91-212 77-175 (176)
106 PRK00420 hypothetical protein; 75.6 2 4.3E-05 37.9 2.2 48 431-507 5-52 (112)
107 PRK05762 DNA polymerase II; Re 75.4 58 0.0013 38.3 14.8 112 91-212 205-348 (786)
108 PRK12496 hypothetical protein; 75.1 4.1 8.8E-05 38.3 4.3 46 369-418 60-105 (164)
109 PF07754 DUF1610: Domain of un 74.9 2.7 5.9E-05 26.7 2.0 9 457-465 1-9 (24)
110 PF05191 ADK_lid: Adenylate ki 74.1 1.9 4.1E-05 30.1 1.3 11 496-506 2-12 (36)
111 PLN02610 probable methionyl-tR 73.8 6.4 0.00014 46.1 6.4 33 372-404 47-79 (801)
112 TIGR00435 cysS cysteinyl-tRNA 73.6 7.3 0.00016 42.8 6.5 35 371-405 48-82 (465)
113 PF00301 Rubredoxin: Rubredoxi 73.5 1.7 3.6E-05 32.3 1.0 39 456-503 3-42 (47)
114 PHA02119 hypothetical protein 72.4 1.4 2.9E-05 35.2 0.3 15 371-385 58-72 (87)
115 COG1579 Zn-ribbon protein, pos 72.3 0.92 2E-05 45.2 -0.8 55 439-511 182-238 (239)
116 KOG1275 PAB-dependent poly(A) 71.2 1.1 2.3E-05 51.8 -0.7 89 99-222 1009-1097(1118)
117 PF00096 zf-C2H2: Zinc finger, 71.2 2.6 5.5E-05 25.6 1.3 14 496-509 1-14 (23)
118 COG3809 Uncharacterized protei 71.1 3.7 8.1E-05 33.6 2.5 39 456-515 3-41 (88)
119 PF09986 DUF2225: Uncharacteri 70.6 1.3 2.8E-05 43.5 -0.3 54 455-508 6-61 (214)
120 PF13005 zf-IS66: zinc-finger 70.5 1 2.2E-05 32.9 -0.8 43 455-502 3-47 (47)
121 TIGR03830 CxxCG_CxxCG_HTH puta 69.4 2.2 4.7E-05 37.7 1.0 27 492-518 28-54 (127)
122 PRK06722 exonuclease; Provisio 69.2 34 0.00073 35.1 9.7 100 91-214 79-179 (281)
123 KOG2907 RNA polymerase I trans 68.0 3.5 7.7E-05 36.0 1.9 45 452-509 72-116 (116)
124 cd00672 CysRS_core catalytic c 67.9 4 8.6E-05 40.0 2.6 34 371-404 47-80 (213)
125 PF02591 DUF164: Putative zinc 67.7 4.7 0.0001 30.7 2.4 33 455-504 23-55 (56)
126 PF14353 CpXC: CpXC protein 66.3 5.1 0.00011 35.7 2.8 19 487-505 30-48 (128)
127 TIGR03447 mycothiol_MshC cyste 66.1 5.1 0.00011 43.2 3.1 34 372-405 64-97 (411)
128 COG2956 Predicted N-acetylgluc 65.8 3 6.6E-05 43.3 1.3 11 493-503 366-376 (389)
129 PRK12418 cysteinyl-tRNA synthe 64.5 5.3 0.00011 42.7 2.9 36 371-406 36-71 (384)
130 PRK12366 replication factor A; 64.4 2.4 5.2E-05 48.4 0.3 36 451-513 529-564 (637)
131 PF10122 Mu-like_Com: Mu-like 64.1 1 2.2E-05 33.8 -1.8 10 455-464 5-14 (51)
132 TIGR00396 leuS_bact leucyl-tRN 63.3 15 0.00032 43.5 6.5 18 372-389 58-75 (842)
133 PF11672 DUF3268: Protein of u 63.0 5.9 0.00013 34.3 2.4 43 455-511 3-45 (102)
134 TIGR00515 accD acetyl-CoA carb 61.4 4.3 9.4E-05 41.6 1.5 32 450-503 22-53 (285)
135 PF08271 TF_Zn_Ribbon: TFIIB z 61.1 6.2 0.00014 28.3 1.9 14 491-504 15-28 (43)
136 PRK00432 30S ribosomal protein 60.7 8 0.00017 29.0 2.5 14 494-507 36-49 (50)
137 PHA02325 hypothetical protein 60.4 4.8 0.0001 31.6 1.2 16 496-511 4-25 (72)
138 PF15135 UPF0515: Uncharacteri 59.8 6.5 0.00014 39.1 2.3 36 452-505 130-165 (278)
139 cd00730 rubredoxin Rubredoxin; 59.7 5.5 0.00012 29.9 1.4 39 456-503 3-42 (50)
140 PF06397 Desulfoferrod_N: Desu 59.0 6.5 0.00014 27.5 1.6 14 492-505 3-16 (36)
141 PF09538 FYDLN_acid: Protein o 58.7 3.6 7.7E-05 36.1 0.3 12 497-508 28-39 (108)
142 PF13894 zf-C2H2_4: C2H2-type 57.4 6.7 0.00015 23.4 1.3 12 496-507 1-12 (24)
143 COG2835 Uncharacterized conser 57.3 8.5 0.00018 30.0 2.1 11 495-505 26-36 (60)
144 cd00812 LeuRS_core catalytic c 56.8 19 0.00041 37.3 5.4 35 371-405 28-62 (314)
145 COG1655 Uncharacterized protei 56.8 3 6.6E-05 41.0 -0.5 13 490-502 57-69 (267)
146 PRK05654 acetyl-CoA carboxylas 56.7 6.1 0.00013 40.7 1.7 17 449-465 22-38 (292)
147 PRK00390 leuS leucyl-tRNA synt 56.6 18 0.00039 42.6 5.7 18 372-389 61-78 (805)
148 PLN02946 cysteine-tRNA ligase 56.3 8.3 0.00018 43.3 2.7 35 371-405 107-141 (557)
149 COG1773 Rubredoxin [Energy pro 56.2 6.3 0.00014 30.2 1.2 40 455-503 4-44 (55)
150 PRK08579 anaerobic ribonucleos 56.0 16 0.00035 41.6 5.0 58 434-524 544-605 (625)
151 PRK03824 hypA hydrogenase nick 56.0 3.8 8.3E-05 37.2 0.0 50 449-503 65-115 (135)
152 PF01396 zf-C4_Topoisom: Topoi 55.9 9.1 0.0002 27.1 2.0 31 456-507 3-36 (39)
153 KOG2041 WD40 repeat protein [G 55.7 17 0.00036 41.5 4.8 97 395-503 1061-1164(1189)
154 CHL00174 accD acetyl-CoA carbo 55.5 6.3 0.00014 40.6 1.5 38 443-503 28-65 (296)
155 PF04032 Rpr2: RNAse P Rpr2/Rp 55.1 17 0.00038 29.6 3.9 60 434-503 26-85 (85)
156 cd00729 rubredoxin_SM Rubredox 54.9 8.1 0.00018 26.5 1.5 15 495-510 2-16 (34)
157 PRK07218 replication factor A; 54.8 5.7 0.00012 43.0 1.1 14 451-464 294-307 (423)
158 PLN02563 aminoacyl-tRNA ligase 54.8 19 0.00042 43.1 5.6 18 372-389 140-157 (963)
159 COG1096 Predicted RNA-binding 54.2 7 0.00015 37.4 1.5 13 453-465 148-160 (188)
160 smart00531 TFIIE Transcription 53.8 8.2 0.00018 35.5 1.9 17 490-506 94-110 (147)
161 PF10571 UPF0547: Uncharacteri 53.6 5.4 0.00012 25.8 0.4 9 497-505 16-24 (26)
162 PRK11827 hypothetical protein; 53.2 12 0.00026 29.3 2.3 10 456-465 10-19 (60)
163 PHA00616 hypothetical protein 52.3 3.4 7.3E-05 30.2 -0.8 18 496-513 2-19 (44)
164 COG0215 CysS Cysteinyl-tRNA sy 52.2 11 0.00025 41.1 2.9 35 371-405 49-83 (464)
165 PRK00260 cysS cysteinyl-tRNA s 52.0 13 0.00028 40.8 3.3 35 371-405 50-84 (463)
166 PRK12380 hydrogenase nickel in 50.4 6.2 0.00013 34.7 0.5 31 434-464 41-80 (113)
167 TIGR00305 probable toxin-antit 50.2 20 0.00044 30.9 3.7 28 389-416 85-113 (114)
168 COG1412 Uncharacterized protei 50.2 44 0.00095 30.5 5.9 52 377-430 73-125 (136)
169 PRK08402 replication factor A; 50.1 6.4 0.00014 41.7 0.6 29 453-504 211-239 (355)
170 PRK14535 cysS cysteinyl-tRNA s 49.8 13 0.00028 42.6 3.0 55 346-405 254-309 (699)
171 PRK05359 oligoribonuclease; Pr 49.8 2.3E+02 0.005 26.8 12.5 20 198-217 157-176 (181)
172 PF14446 Prok-RING_1: Prokaryo 49.3 15 0.00032 28.1 2.3 27 454-505 5-31 (54)
173 cd00668 Ile_Leu_Val_MetRS_core 49.2 33 0.00072 35.3 5.7 40 372-411 29-68 (312)
174 PF01783 Ribosomal_L32p: Ribos 48.4 9.7 0.00021 29.2 1.2 11 453-463 25-35 (56)
175 TIGR00319 desulf_FeS4 desulfof 48.4 12 0.00026 25.4 1.6 13 493-505 5-17 (34)
176 PF14787 zf-CCHC_5: GAG-polypr 48.2 8.7 0.00019 26.8 0.8 13 497-513 4-16 (36)
177 PF07282 OrfB_Zn_ribbon: Putat 47.5 34 0.00073 26.8 4.3 48 434-504 5-55 (69)
178 PRK06386 replication factor A; 47.4 7.6 0.00016 41.1 0.6 15 450-464 232-246 (358)
179 TIGR01206 lysW lysine biosynth 47.4 17 0.00037 27.8 2.4 30 455-505 3-32 (54)
180 PF09297 zf-NADH-PPase: NADH p 47.3 16 0.00034 24.5 2.0 27 456-505 5-31 (32)
181 PTZ00399 cysteinyl-tRNA-synthe 47.1 15 0.00033 42.1 3.0 34 372-405 88-122 (651)
182 PRK06266 transcription initiat 47.0 12 0.00026 35.7 1.9 16 490-505 112-127 (178)
183 cd00974 DSRD Desulforedoxin (D 46.3 14 0.00029 25.2 1.6 13 493-505 2-14 (34)
184 PRK07111 anaerobic ribonucleos 46.2 15 0.00033 42.7 2.8 28 435-462 657-688 (735)
185 PF12813 XPG_I_2: XPG domain c 46.0 21 0.00047 35.7 3.6 45 370-416 7-54 (246)
186 cd00350 rubredoxin_like Rubred 45.8 13 0.00027 25.3 1.3 12 495-506 1-12 (33)
187 PRK00564 hypA hydrogenase nick 45.6 8.8 0.00019 34.0 0.7 18 447-464 64-81 (117)
188 PF13465 zf-H2C2_2: Zinc-finge 45.4 16 0.00035 23.2 1.7 15 492-506 11-25 (26)
189 PRK00398 rpoP DNA-directed RNA 45.2 14 0.00031 26.8 1.6 11 455-465 4-14 (46)
190 PHA00626 hypothetical protein 45.1 16 0.00036 28.0 1.9 16 492-507 20-35 (59)
191 PRK14534 cysS cysteinyl-tRNA s 44.7 16 0.00034 40.4 2.6 36 371-406 48-93 (481)
192 PF02150 RNA_POL_M_15KD: RNA p 44.6 14 0.0003 25.6 1.4 11 456-466 3-13 (35)
193 PF01406 tRNA-synt_1e: tRNA sy 43.8 12 0.00027 38.6 1.5 34 372-406 36-70 (300)
194 PHA02998 RNA polymerase subuni 43.7 19 0.00041 34.2 2.5 48 443-505 134-181 (195)
195 PRK12495 hypothetical protein; 43.3 27 0.00058 34.3 3.6 45 434-508 27-71 (226)
196 PF13248 zf-ribbon_3: zinc-rib 43.0 13 0.00028 23.8 1.0 10 455-464 3-12 (26)
197 COG1997 RPL43A Ribosomal prote 42.6 20 0.00044 30.0 2.3 18 493-510 51-68 (89)
198 TIGR00373 conserved hypothetic 42.4 19 0.00041 33.6 2.4 34 449-504 104-137 (158)
199 PRK00762 hypA hydrogenase nick 42.1 11 0.00024 33.8 0.7 30 434-464 41-79 (124)
200 PF11781 RRN7: RNA polymerase 42.1 18 0.00039 25.2 1.6 13 492-504 22-34 (36)
201 PRK09521 exosome complex RNA-b 42.0 6.5 0.00014 37.7 -0.8 30 452-505 147-176 (189)
202 TIGR00686 phnA alkylphosphonat 41.7 17 0.00037 31.7 1.8 26 455-504 3-28 (109)
203 cd05778 DNA_polB_zeta_exo inac 41.7 36 0.00079 33.6 4.4 51 159-209 175-230 (231)
204 PRK03681 hypA hydrogenase nick 41.4 11 0.00023 33.3 0.6 31 434-464 41-80 (114)
205 PF09845 DUF2072: Zn-ribbon co 41.3 16 0.00034 33.0 1.6 9 456-464 3-11 (131)
206 PF01780 Ribosomal_L37ae: Ribo 41.1 19 0.00041 30.5 1.9 17 493-509 51-67 (90)
207 PF04981 NMD3: NMD3 family ; 40.9 22 0.00048 35.3 2.8 21 493-514 33-53 (236)
208 COG1645 Uncharacterized Zn-fin 40.9 20 0.00044 32.4 2.2 26 435-465 14-39 (131)
209 TIGR00373 conserved hypothetic 40.9 17 0.00037 33.9 1.8 16 490-505 104-119 (158)
210 COG4416 Com Mu-like prophage p 40.0 7.1 0.00015 29.6 -0.7 10 455-464 5-14 (60)
211 PF12172 DUF35_N: Rubredoxin-l 39.9 19 0.00042 24.8 1.6 16 493-508 9-24 (37)
212 TIGR02300 FYDLN_acid conserved 39.6 16 0.00035 32.8 1.4 10 456-465 11-20 (129)
213 PRK05978 hypothetical protein; 39.5 16 0.00035 33.8 1.4 9 497-505 54-62 (148)
214 TIGR00100 hypA hydrogenase nic 39.1 13 0.00028 32.9 0.7 31 434-464 41-80 (115)
215 PRK06266 transcription initiat 39.1 25 0.00054 33.5 2.7 34 449-504 112-145 (178)
216 TIGR01031 rpmF_bact ribosomal 38.8 21 0.00046 27.3 1.8 10 454-463 26-35 (55)
217 PF04810 zf-Sec23_Sec24: Sec23 38.1 28 0.00061 24.7 2.2 31 455-504 3-33 (40)
218 PF07975 C1_4: TFIIH C1-like d 37.9 18 0.00039 27.3 1.2 13 493-505 19-31 (51)
219 PHA02768 hypothetical protein; 37.2 13 0.00028 28.6 0.3 18 496-513 6-23 (55)
220 PRK14704 anaerobic ribonucleos 37.2 41 0.0009 38.3 4.5 59 434-523 535-597 (618)
221 PRK11032 hypothetical protein; 36.8 19 0.0004 33.9 1.4 11 455-465 125-135 (160)
222 PF07295 DUF1451: Protein of u 36.6 19 0.00042 33.2 1.5 12 454-465 112-123 (146)
223 TIGR00354 polC DNA polymerase, 36.5 24 0.00052 41.7 2.4 10 455-464 1013-1022(1095)
224 PRK14536 cysS cysteinyl-tRNA s 36.5 31 0.00068 38.2 3.3 36 371-406 50-95 (490)
225 PRK03954 ribonuclease P protei 36.4 36 0.00077 30.5 3.0 33 434-466 44-76 (121)
226 smart00834 CxxC_CXXC_SSSS Puta 36.4 20 0.00044 24.9 1.3 12 496-507 6-17 (41)
227 COG0675 Transposase and inacti 36.3 42 0.0009 34.1 4.1 30 433-462 285-317 (364)
228 PF03119 DNA_ligase_ZBD: NAD-d 36.2 19 0.00041 23.6 1.0 10 456-465 1-10 (28)
229 TIGR00280 L37a ribosomal prote 36.2 24 0.00052 29.9 1.8 17 493-509 51-67 (91)
230 PTZ00255 60S ribosomal protein 36.1 25 0.00055 29.7 1.9 17 493-509 52-68 (90)
231 COG2023 RPR2 RNase P subunit R 35.5 42 0.00092 29.2 3.2 56 435-505 37-92 (105)
232 smart00531 TFIIE Transcription 35.4 47 0.001 30.4 3.9 39 449-504 94-132 (147)
233 cd00758 MoCF_BD MoCF_BD: molyb 35.4 78 0.0017 28.2 5.2 49 363-411 15-66 (133)
234 COG1571 Predicted DNA-binding 35.1 18 0.0004 38.9 1.2 30 454-507 350-379 (421)
235 PRK02261 methylaspartate mutas 35.0 53 0.0011 29.8 4.0 36 368-404 17-54 (137)
236 COG1058 CinA Predicted nucleot 34.9 48 0.001 33.5 4.0 49 363-411 17-68 (255)
237 TIGR00592 pol2 DNA polymerase 34.9 1.5E+02 0.0033 36.5 9.1 102 102-213 599-723 (1172)
238 PRK05452 anaerobic nitric oxid 34.6 19 0.0004 39.8 1.2 41 454-503 425-466 (479)
239 PF04900 Fcf1: Fcf1; InterPro 34.6 71 0.0015 27.1 4.6 39 392-430 53-93 (101)
240 KOG3277 Uncharacterized conser 34.1 25 0.00053 32.7 1.7 33 455-503 80-112 (165)
241 PRK04023 DNA polymerase II lar 33.9 29 0.00063 41.2 2.6 10 455-464 1038-1047(1121)
242 PF13240 zinc_ribbon_2: zinc-r 33.8 21 0.00046 22.3 0.9 9 456-464 1-9 (23)
243 COG3364 Zn-ribbon containing p 33.8 22 0.00049 30.6 1.3 10 454-463 20-29 (112)
244 cd00671 ArgRS_core catalytic c 33.7 26 0.00057 34.0 2.0 38 368-405 24-62 (212)
245 TIGR03599 YloV DAK2 domain fus 33.4 2.2E+02 0.0047 32.0 9.3 84 361-445 315-407 (530)
246 PF13912 zf-C2H2_6: C2H2-type 33.3 27 0.00058 21.9 1.3 15 496-510 2-16 (27)
247 cd00802 class_I_aaRS_core cata 33.0 38 0.00083 30.4 2.8 33 371-403 25-57 (143)
248 PRK03976 rpl37ae 50S ribosomal 33.0 28 0.00061 29.5 1.7 17 493-509 52-68 (90)
249 PF13913 zf-C2HC_2: zinc-finge 32.8 23 0.00049 22.5 0.9 10 496-505 3-12 (25)
250 cd00817 ValRS_core catalytic c 32.8 65 0.0014 34.4 4.9 18 372-389 30-47 (382)
251 TIGR03831 YgiT_finger YgiT-typ 32.7 24 0.00052 25.0 1.1 17 492-508 29-45 (46)
252 KOG2691 RNA polymerase II subu 32.5 49 0.0011 28.9 3.1 59 402-463 20-82 (113)
253 PF08274 PhnA_Zn_Ribbon: PhnA 32.4 26 0.00056 23.5 1.1 27 454-504 2-28 (30)
254 COG0266 Nei Formamidopyrimidin 32.3 24 0.00052 36.0 1.5 12 492-503 262-273 (273)
255 PRK10220 hypothetical protein; 31.9 33 0.00072 30.0 2.0 12 493-504 18-29 (111)
256 cd00885 cinA Competence-damage 31.5 73 0.0016 30.0 4.5 49 363-411 15-66 (170)
257 PRK00241 nudC NADH pyrophospha 31.4 36 0.00079 34.3 2.6 32 454-508 99-130 (256)
258 PF09332 Mcm10: Mcm10 replicat 30.9 26 0.00056 37.0 1.4 58 434-503 235-293 (344)
259 PRK03673 hypothetical protein; 30.9 88 0.0019 33.7 5.5 49 363-411 17-68 (396)
260 PF01807 zf-CHC2: CHC2 zinc fi 30.7 26 0.00057 29.8 1.3 47 437-503 15-62 (97)
261 PRK03670 competence damage-ind 30.7 76 0.0017 32.0 4.8 24 363-386 16-39 (252)
262 PRK13264 3-hydroxyanthranilate 30.7 9.5 0.0002 36.3 -1.6 43 456-504 122-166 (177)
263 PRK09678 DNA-binding transcrip 30.5 40 0.00087 27.3 2.2 43 455-512 2-46 (72)
264 PF01873 eIF-5_eIF-2B: Domain 29.8 38 0.00083 30.4 2.2 45 434-504 79-123 (125)
265 PRK14714 DNA polymerase II lar 29.6 37 0.0008 41.4 2.5 17 202-218 844-860 (1337)
266 TIGR01501 MthylAspMutase methy 29.6 73 0.0016 29.0 4.0 33 372-405 21-53 (134)
267 cd02072 Glm_B12_BD B12 binding 29.3 75 0.0016 28.7 4.0 33 372-405 19-51 (128)
268 PRK12286 rpmF 50S ribosomal pr 29.3 35 0.00075 26.4 1.6 10 454-463 27-36 (57)
269 PF04959 ARS2: Arsenite-resist 29.2 32 0.0007 33.8 1.7 30 483-513 65-94 (214)
270 COG1998 RPS31 Ribosomal protei 29.1 37 0.00081 25.4 1.6 17 492-508 34-50 (51)
271 PTZ00396 Casein kinase II subu 28.6 49 0.0011 33.3 2.9 54 435-509 106-162 (251)
272 PF14205 Cys_rich_KTR: Cystein 28.3 21 0.00046 27.3 0.2 10 455-464 5-14 (55)
273 TIGR02487 NrdD anaerobic ribon 28.2 69 0.0015 36.3 4.4 41 422-462 485-532 (579)
274 PRK03988 translation initiatio 28.2 70 0.0015 29.3 3.6 46 433-504 87-132 (138)
275 PF03966 Trm112p: Trm112p-like 28.1 31 0.00067 27.3 1.1 15 491-505 49-63 (68)
276 PRK14810 formamidopyrimidine-D 28.0 32 0.0007 35.0 1.5 12 492-503 261-272 (272)
277 COG1499 NMD3 NMD protein affec 27.8 55 0.0012 34.7 3.3 20 493-513 41-60 (355)
278 PRK12496 hypothetical protein; 27.8 26 0.00057 32.9 0.8 10 496-505 128-137 (164)
279 cd02067 B12-binding B12 bindin 27.6 86 0.0019 27.1 4.0 32 371-403 18-49 (119)
280 PF01096 TFIIS_C: Transcriptio 27.3 41 0.00089 23.7 1.5 13 493-505 26-38 (39)
281 PF15446 zf-PHD-like: PHD/FYVE 27.2 73 0.0016 30.2 3.5 52 454-505 71-134 (175)
282 TIGR00244 transcriptional regu 27.2 19 0.00041 33.3 -0.3 12 494-505 27-38 (147)
283 COG5134 Uncharacterized conser 26.9 49 0.0011 32.4 2.4 21 445-465 32-53 (272)
284 cd00924 Cyt_c_Oxidase_Vb Cytoc 26.8 37 0.00081 29.2 1.5 13 493-505 77-89 (97)
285 PRK08271 anaerobic ribonucleos 26.8 76 0.0017 36.3 4.4 69 422-523 528-602 (623)
286 PF05180 zf-DNL: DNL zinc fing 26.6 21 0.00044 28.5 -0.1 34 456-505 6-39 (66)
287 PRK13945 formamidopyrimidine-D 26.6 28 0.00062 35.5 0.9 11 493-503 272-282 (282)
288 PRK14890 putative Zn-ribbon RN 26.1 68 0.0015 25.0 2.6 11 455-465 8-18 (59)
289 PF10083 DUF2321: Uncharacteri 26.0 32 0.00069 32.0 1.0 36 455-505 40-78 (158)
290 smart00653 eIF2B_5 domain pres 25.6 69 0.0015 28.1 3.0 44 434-503 66-109 (110)
291 TIGR03037 anthran_nbaC 3-hydro 25.6 14 0.00031 34.6 -1.4 40 457-502 117-158 (159)
292 PRK14811 formamidopyrimidine-D 25.5 36 0.00077 34.6 1.3 13 493-505 253-265 (269)
293 PF09723 Zn-ribbon_8: Zinc rib 25.5 40 0.00087 24.1 1.2 10 496-505 6-15 (42)
294 PF01155 HypA: Hydrogenase exp 25.1 13 0.00028 32.7 -1.7 31 434-464 41-80 (113)
295 TIGR01384 TFS_arch transcripti 25.0 48 0.001 28.3 1.8 11 495-505 16-26 (104)
296 PRK10445 endonuclease VIII; Pr 24.7 32 0.00069 34.8 0.8 28 455-503 236-263 (263)
297 COG0777 AccD Acetyl-CoA carbox 24.7 39 0.00084 34.4 1.4 31 451-503 25-55 (294)
298 KOG2186 Cell growth-regulating 24.4 29 0.00063 34.8 0.4 43 454-511 3-45 (276)
299 COG1592 Rubrerythrin [Energy p 24.2 44 0.00096 31.5 1.6 11 454-464 134-144 (166)
300 TIGR02605 CxxC_CxxC_SSSS putat 24.1 42 0.00092 24.7 1.2 10 496-505 6-15 (52)
301 cd04476 RPA1_DBD_C RPA1_DBD_C: 24.0 43 0.00094 31.1 1.5 30 452-505 32-61 (166)
302 smart00440 ZnF_C2C2 C2C2 Zinc 23.8 48 0.001 23.5 1.4 13 493-505 26-38 (40)
303 TIGR01391 dnaG DNA primase, ca 23.8 68 0.0015 34.7 3.2 47 437-503 16-63 (415)
304 PHA02540 61 DNA primase; Provi 23.5 72 0.0016 33.6 3.1 52 436-503 9-63 (337)
305 PRK11788 tetratricopeptide rep 23.4 69 0.0015 33.2 3.1 10 494-503 367-376 (389)
306 PRK01215 competence damage-ind 23.3 1.2E+02 0.0025 30.8 4.6 49 363-411 19-70 (264)
307 PF09862 DUF2089: Protein of u 23.2 30 0.00065 30.6 0.2 9 457-465 1-9 (113)
308 COG1326 Uncharacterized archae 23.1 72 0.0016 30.8 2.8 15 493-507 28-42 (201)
309 PRK01103 formamidopyrimidine/5 23.1 46 0.001 33.8 1.6 12 492-503 262-273 (274)
310 PF12171 zf-C2H2_jaz: Zinc-fin 23.0 40 0.00086 21.4 0.7 10 496-505 2-11 (27)
311 PF04606 Ogr_Delta: Ogr/Delta- 23.0 43 0.00093 24.6 1.0 35 456-505 1-37 (47)
312 PRK05667 dnaG DNA primase; Val 22.9 76 0.0017 35.9 3.5 47 437-503 18-65 (580)
313 PF05991 NYN_YacP: YacP-like N 22.9 1.4E+02 0.0031 27.8 4.8 65 375-441 62-131 (166)
314 PF14311 DUF4379: Domain of un 22.8 51 0.0011 24.8 1.4 21 492-513 25-45 (55)
315 COG1327 Predicted transcriptio 22.7 26 0.00057 32.4 -0.2 38 455-505 1-38 (156)
316 COG1545 Predicted nucleic-acid 22.6 44 0.00095 30.6 1.2 19 492-510 26-44 (140)
317 PRK08270 anaerobic ribonucleos 22.5 38 0.00083 38.9 1.0 41 422-462 586-634 (656)
318 PRK03094 hypothetical protein; 22.5 1.9E+02 0.004 24.1 4.7 72 362-442 3-76 (80)
319 COG3677 Transposase and inacti 22.4 75 0.0016 28.7 2.7 14 493-506 51-64 (129)
320 PF03698 UPF0180: Uncharacteri 22.1 1.2E+02 0.0026 25.2 3.5 42 362-411 3-44 (80)
321 PLN02294 cytochrome c oxidase 22.1 45 0.00097 31.6 1.2 13 493-505 139-151 (174)
322 PF03833 PolC_DP2: DNA polymer 22.0 30 0.00065 40.4 0.0 12 374-385 557-568 (900)
323 PRK09263 anaerobic ribonucleos 22.0 79 0.0017 36.8 3.4 41 422-462 603-649 (711)
324 cd06167 LabA_like LabA_like pr 21.9 2.4E+02 0.0053 25.0 6.0 71 369-439 54-141 (149)
325 PF09706 Cas_CXXC_CXXC: CRISPR 21.7 31 0.00068 27.6 0.1 24 482-505 38-61 (69)
326 cd00886 MogA_MoaB MogA_MoaB fa 21.7 1.2E+02 0.0026 27.8 4.0 48 364-411 17-69 (152)
327 COG4133 CcmA ABC-type transpor 21.7 55 0.0012 31.8 1.7 18 499-516 54-71 (209)
328 KOG1701 Focal adhesion adaptor 21.6 36 0.00077 36.7 0.4 44 454-505 394-437 (468)
329 TIGR00177 molyb_syn molybdenum 21.5 1.4E+02 0.003 27.0 4.3 48 363-411 23-74 (144)
330 COG2051 RPS27A Ribosomal prote 21.4 61 0.0013 25.8 1.6 20 488-507 31-50 (67)
331 PF01215 COX5B: Cytochrome c o 21.4 41 0.00089 30.7 0.8 13 493-505 110-122 (136)
332 COG2824 PhnA Uncharacterized Z 21.3 57 0.0012 28.5 1.5 11 495-505 20-30 (112)
333 COG5041 SKB2 Casein kinase II, 21.2 91 0.002 30.4 3.0 56 435-510 107-164 (242)
334 PF08790 zf-LYAR: LYAR-type C2 21.0 61 0.0013 21.4 1.3 14 497-510 2-15 (28)
335 PHA02942 putative transposase; 20.8 1.2E+02 0.0026 32.4 4.3 11 494-504 341-351 (383)
336 KOG3092 Casein kinase II, beta 20.7 1.1E+02 0.0024 29.6 3.5 54 436-510 93-149 (216)
337 PF09855 DUF2082: Nucleic-acid 20.5 27 0.00059 27.6 -0.5 13 492-504 33-45 (64)
338 TIGR00640 acid_CoA_mut_C methy 20.3 1.3E+02 0.0029 27.0 3.9 32 372-404 22-53 (132)
339 PF02639 DUF188: Uncharacteriz 20.2 2.4E+02 0.0052 25.5 5.4 29 392-421 41-69 (130)
340 PRK14873 primosome assembly pr 20.2 37 0.00079 39.1 0.2 14 494-507 421-434 (665)
341 PF01214 CK_II_beta: Casein ki 20.1 92 0.002 29.9 2.9 52 435-507 85-139 (184)
342 PF12874 zf-met: Zinc-finger o 20.0 67 0.0014 19.6 1.3 15 496-510 1-15 (25)
No 1
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=100.00 E-value=3.4e-45 Score=336.75 Aligned_cols=146 Identities=35% Similarity=0.637 Sum_probs=134.0
Q ss_pred CEEEEecccHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecChhHHHhhcccCCcEEEEcCCCHHHHHHHH
Q 009783 361 PKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQLLEV 440 (526)
Q Consensus 361 ~kfl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~RiiLTrd~~l~~~~~~~~~~~~~v~~~~~~~QL~~v 440 (526)
||||||.|||+||||||++||||++.. +.+|.+++++|++|+|||||+|++|+++....++ ++++.++++.+||.+|
T Consensus 1 ~rfl~D~~L~~Lar~LR~lG~Dt~~~~--~~~D~~il~~A~~e~RillTrd~~l~~~~~~~~~-~~li~~~~~~~QL~ev 77 (147)
T PF01927_consen 1 MRFLVDAMLGRLARWLRLLGYDTLYSR--DIDDDEILELAREEGRILLTRDRDLLKRRRVSGG-VILIRSDDPEEQLREV 77 (147)
T ss_pred CEEEEeCCHHHHHHHHHHCCCcEEEeC--CCChHHHHHHhhhCCeEEEECCHHHHHHhhccCC-EEEEcCCCHHHHHHHH
Confidence 799999999999999999999999886 4588999999999999999999999998765544 7888999999999999
Q ss_pred HHHcCccccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecccchhhHHhh
Q 009783 441 IEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVMSAYLFIFL 517 (526)
Q Consensus 441 l~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~GsH~~r~~~~ 517 (526)
+++|++.+.++++||||++||++|. +++++++. +.||++|++.+++||+|++||||||+||||+|+...
T Consensus 78 ~~~~~l~~~~~~~~sRC~~CN~~L~--~v~~~~v~------~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~~~~~~ 146 (147)
T PF01927_consen 78 LERFGLKLRLDPIFSRCPKCNGPLR--PVSKEEVK------DRVPPYVYETYDEFWRCPGCGKIYWEGSHWRRMEER 146 (147)
T ss_pred HHHcCCccccCCCCCccCCCCcEee--echhhccc------cccCccccccCCeEEECCCCCCEecccccHHHHHhh
Confidence 9999999999999999999999985 68888875 489999999999999999999999999999998753
No 2
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.6e-43 Score=321.75 Aligned_cols=148 Identities=30% Similarity=0.494 Sum_probs=135.5
Q ss_pred CCCCEEEEecccHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecChhHHHhhcccCCcEEEEcCCCHHHHH
Q 009783 358 DGYPKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQL 437 (526)
Q Consensus 358 ~~~~kfl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~RiiLTrd~~l~~~~~~~~~~~~~v~~~~~~~QL 437 (526)
.+.|||+||+|||+||||||++||||++.+ ..+|.+++.+|..|||||||||+.|+++. +.+.++++|+++++++|+
T Consensus 4 ~~~~kF~vD~mLG~LARwLRllGydt~~~~--~~~d~~i~~i~~~e~rIllTRDr~L~~r~-k~g~~~i~i~~~s~~~Ql 80 (165)
T COG1656 4 MGEMKFVVDAMLGKLARWLRLLGYDTVYSS--NESDDEIILIAKKEGRILLTRDRELYKRA-KLGIKAILIRSDSIEEQL 80 (165)
T ss_pred ccceeeeHHHhHHHHHHHHHHcCCceeeec--cCCcHHHHHHHhcCCeEEEeccHHHHHHh-hccCceEEEeCCCHHHHH
Confidence 467899999999999999999999999875 35778999999999999999999999987 567789999999999999
Q ss_pred HHHHHHcCccccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecccchhhHHh
Q 009783 438 LEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVMSAYLFIF 516 (526)
Q Consensus 438 ~~vl~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~GsH~~r~~~ 516 (526)
.++++++++.......|+||+.||++|. ++++|+|++ .||+.|+..+++||+|++|||+||.||||+||-.
T Consensus 81 ~e~~~~~~l~~~~~~e~~RCp~CN~~L~--~vs~eev~~------~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw~~m~~ 151 (165)
T COG1656 81 AEFLARLGLKPRLFPEFSRCPECNGELE--KVSREEVKE------KVPEKVYRNYEEFYRCPKCGKIYWKGSHWRRMVE 151 (165)
T ss_pred HHHHHHhccchhcccccccCcccCCEec--cCcHHHHhh------ccchhhhhcccceeECCCCcccccCchHHHHHHH
Confidence 9999999998855555999999999996 699999875 8999999999999999999999999999999765
No 3
>PRK10829 ribonuclease D; Provisional
Probab=100.00 E-value=4.5e-32 Score=283.46 Aligned_cols=217 Identities=21% Similarity=0.331 Sum_probs=188.1
Q ss_pred cEEEEeCCChHHHHHHHHHhcCCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCc
Q 009783 10 KIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPL 89 (526)
Q Consensus 10 ~i~~V~t~~~~el~~~~~~L~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~ 89 (526)
.|++|++ ++++..+++.+...++||||+|+..... |.++++||||++. +++|+||+..+.
T Consensus 2 ~~~~I~t--~~~L~~~~~~l~~~~~lalDtEf~~~~t---y~~~l~LiQl~~~--------------~~~~LiD~l~~~- 61 (373)
T PRK10829 2 NYQMITT--DDALASVCEAARAFPAIALDTEFVRTRT---YYPQLGLIQLYDG--------------EQLSLIDPLGIT- 61 (373)
T ss_pred CcEEeCC--HHHHHHHHHHHhcCCeEEEecccccCcc---CCCceeEEEEecC--------------CceEEEecCCcc-
Confidence 4788998 8999999999999999999999988764 8899999999974 679999998764
Q ss_pred hhhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHH
Q 009783 90 PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (526)
Q Consensus 90 ~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~ 169 (526)
.+.+|.++|+|++|+||+|++++|+..|.+.+|+ . +.++|| |++|+.+++.+ .+.||+.|++
T Consensus 62 --d~~~L~~ll~~~~ivKV~H~~~~Dl~~l~~~~g~---~-----p~~~fD-Tqiaa~~lg~~-------~~~gl~~Lv~ 123 (373)
T PRK10829 62 --DWSPFKALLRDPQVTKFLHAGSEDLEVFLNAFGE---L-----PQPLID-TQILAAFCGRP-------LSCGFASMVE 123 (373)
T ss_pred --chHHHHHHHcCCCeEEEEeChHhHHHHHHHHcCC---C-----cCCeee-HHHHHHHcCCC-------ccccHHHHHH
Confidence 2678999999999999999999999999777665 2 478999 99999999853 3689999999
Q ss_pred HHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchhhhhhhhccCcc-cCCC-CCCcc
Q 009783 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGFAAGNSCSSISELDSSNL-DLGL-KGILE 247 (526)
Q Consensus 170 ~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~~~~~~~e~~~~~~~~~-~~~~-~~~~~ 247 (526)
++||+.++|+++.+||++|||+++|+.|||.||++|+.||+.|.++|.+.|.. +|+.+|++.+..... .... ..|++
T Consensus 124 ~~lgv~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g~~-~w~~ee~~~l~~~~~~~~~~~~~~~~ 202 (373)
T PRK10829 124 EYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGWL-PAALDECRLLCQRRQEVLAPEEAYRD 202 (373)
T ss_pred HHhCCccCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcH-HHHHHHHHHHHhccccCCChHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999 999999998854321 1111 34777
Q ss_pred cCCCCCcccccchhhHHHHHHHh
Q 009783 248 KPDIGNKTVRFKLCEALDIIRAT 270 (526)
Q Consensus 248 ~~~~~~~~~~~~~~~~~~~~~~~ 270 (526)
..+ ..+++ +++|+++|++
T Consensus 203 ik~----~~~L~-~~~lavl~~L 220 (373)
T PRK10829 203 ITN----AWQLR-TRQLACLQLL 220 (373)
T ss_pred hcc----ccCCC-HHHHHHHHHH
Confidence 663 34455 9999999999
No 4
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=99.97 E-value=1.3e-29 Score=243.59 Aligned_cols=184 Identities=46% Similarity=0.765 Sum_probs=150.4
Q ss_pred EEEEeCCChHHHHHHHHH--hcCCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCC
Q 009783 11 IHLVTSTESPEFTHLARA--LSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIP 88 (526)
Q Consensus 11 i~~V~t~~~~el~~~~~~--L~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~ 88 (526)
||+|++ ++++++++.. +....+||||+||.+.+.. +..++++|||||+. +.+|+||+..++
T Consensus 1 ~~~i~~--~~el~~~~~~~~l~~~~vig~D~Ew~~~~~~-~~~~~v~LiQiat~--------------~~~~lid~~~~~ 63 (193)
T cd06146 1 IHIVDS--EEELEALLLALSLEAGRVVGIDSEWKPSFLG-DSDPRVAILQLATE--------------DEVFLLDLLALE 63 (193)
T ss_pred CeEecC--HHHHHHHHHHHhhccCCEEEEECccCCCccC-CCCCCceEEEEecC--------------CCEEEEEchhcc
Confidence 689999 8999999999 8899999999999988742 13689999999985 689999998765
Q ss_pred ---chhhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCC---CCCcCCc
Q 009783 89 ---LPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGR---KLPKETK 162 (526)
Q Consensus 89 ---~~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~---~~~~~~~ 162 (526)
...+...|+++|+|++|+||||++++|+..|++.||+.... +..+.+++|+..++..+.....++ ..+....
T Consensus 64 ~~~~~~~~~~L~~ll~d~~i~KVg~~~~~D~~~L~~~~~~~~~~--~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~ 141 (193)
T cd06146 64 NLESEDWDRLLKRLFEDPDVLKLGFGFKQDLKALSASYPALKCM--FERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTK 141 (193)
T ss_pred ccchHHHHHHHHHHhCCCCeeEEEechHHHHHHHHHhcCccccc--cccCCceEEHHHHHHHHhhccccccccccCcccC
Confidence 23466789999999999999999999999999988763210 113579999544555554321111 1113578
Q ss_pred cHHHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009783 163 SLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (526)
Q Consensus 163 gL~~Lv~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~ 213 (526)
||+.|++++||.+++|..|+|||+.|||+++|+.|||.||+++++||+.|.
T Consensus 142 sL~~l~~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 142 GLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred CHHHHHHHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999999999999999999999985
No 5
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=5.6e-30 Score=261.57 Aligned_cols=211 Identities=25% Similarity=0.290 Sum_probs=187.2
Q ss_pred hHHHHHHHHHhcCCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHH
Q 009783 19 SPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKE 98 (526)
Q Consensus 19 ~~el~~~~~~L~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~ 98 (526)
...++.++..+.+++.|++|+|+...++ +.+++|||||+.. +++++||+.... .-+..|..
T Consensus 4 ~~~l~~~~~~~~~~~~iAiDTEf~r~~t---~~p~LcLIQi~~~--------------e~~~lIdpl~~~--~d~~~l~~ 64 (361)
T COG0349 4 GDLLAAACALLRGSKAIAIDTEFMRLRT---YYPRLCLIQISDG--------------EGASLIDPLAGI--LDLPPLVA 64 (361)
T ss_pred hhHHHHHHHHhcCCCceEEecccccccc---cCCceEEEEEecC--------------CCceEecccccc--cccchHHH
Confidence 4678888899999999999999998885 8999999999985 349999988732 13678999
Q ss_pred hhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcc
Q 009783 99 LFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSK 178 (526)
Q Consensus 99 lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~K 178 (526)
+|.|++|+||.|.+++|+.+|.+.||. . +.++|| |++|+.+.+.+ .++||++||++++|+.++|
T Consensus 65 Ll~d~~v~KIfHaa~~DL~~l~~~~g~---~-----p~plfd-TqiAa~l~g~~-------~~~gl~~Lv~~ll~v~ldK 128 (361)
T COG0349 65 LLADPNVVKIFHAARFDLEVLLNLFGL---L-----PTPLFD-TQIAAKLAGFG-------TSHGLADLVEELLGVELDK 128 (361)
T ss_pred HhcCCceeeeeccccccHHHHHHhcCC---C-----CCchhH-HHHHHHHhCCc-------ccccHHHHHHHHhCCcccc
Confidence 999999999999999999999988665 2 489999 99999999875 4899999999999999999
Q ss_pred cccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchhhhhhhhccC--cccCCCCCCcccCCCCCccc
Q 009783 179 ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGFAAGNSCSSISELDSS--NLDLGLKGILEKPDIGNKTV 256 (526)
Q Consensus 179 ~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~~~~~~~e~~~~~~~--~~~~~~~~~~~~~~~~~~~~ 256 (526)
++|.|||.+||||++|++|||.||.+|+.||+.|.++|.++|.. .|+.+||+.+.+. ........|++.. + .
T Consensus 129 ~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r~-~~a~~ef~~l~~r~~~~~~~~~~w~~i~----~-a 202 (361)
T COG0349 129 SEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAREGRL-EWAEDEFRLLPTRRTYKVLPEDAWREIK----I-A 202 (361)
T ss_pred cccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCch-HHHHHHHHHhhhccccccChHhHHHHhh----h-h
Confidence 99999999999999999999999999999999999999999999 8999999999776 4446667898766 2 5
Q ss_pred ccchhhHHHHHHHh
Q 009783 257 RFKLCEALDIIRAT 270 (526)
Q Consensus 257 ~~~~~~~~~~~~~~ 270 (526)
+.+.+++++++|.+
T Consensus 203 ~~~~p~~la~l~~L 216 (361)
T COG0349 203 HSLDPRELAVLREL 216 (361)
T ss_pred hcCChHHHHHHHHH
Confidence 67889999999999
No 6
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=99.96 E-value=1.1e-28 Score=230.50 Aligned_cols=158 Identities=34% Similarity=0.581 Sum_probs=140.4
Q ss_pred HHHHHHHhc-CCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhh
Q 009783 22 FTHLARALS-QSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELF 100 (526)
Q Consensus 22 l~~~~~~L~-~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL 100 (526)
++++++.|. .+++||||+||.+.+. +.++++|||||+. ++.+||||+..++. .+..|+++|
T Consensus 2 l~~~~~~l~~~~~~ig~D~E~~~~~~---~~~~~~liQl~~~-------------~~~~~l~d~~~~~~--~~~~L~~lL 63 (161)
T cd06129 2 LSSLCEDLSMDGDVIAFDMEWPPGRR---YYGEVALIQLCVS-------------EEKCYLFDPLSLSV--DWQGLKMLL 63 (161)
T ss_pred HHHHHHHHhcCCCEEEEECCccCCCC---CCCceEEEEEEEC-------------CCCEEEEecccCcc--CHHHHHHHh
Confidence 567888888 9999999999999874 5689999999995 37899999987652 467899999
Q ss_pred CCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcccc
Q 009783 101 VSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKEL 180 (526)
Q Consensus 101 ~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~K~~ 180 (526)
++++|+||||++++|+..|.+.+|+ ...++|| +++++|++++. .+.||+.+++++||..++|..
T Consensus 64 ~d~~i~Kvg~~~k~D~~~L~~~~gi--------~~~~~~D-~~~aa~ll~~~-------~~~~L~~l~~~~lg~~l~K~~ 127 (161)
T cd06129 64 ENPSIVKALHGIEGDLWKLLRDFGE--------KLQRLFD-TTIAANLKGLP-------ERWSLASLVEHFLGKTLDKSI 127 (161)
T ss_pred CCCCEEEEEeccHHHHHHHHHHcCC--------CcccHhH-HHHHHHHhCCC-------CCchHHHHHHHHhCCCCCccc
Confidence 9999999999999999999876666 1357799 89999999863 357999999999999999999
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009783 181 QCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (526)
Q Consensus 181 q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~ 213 (526)
++|||+.|||+++|+.|||.||++++.||+.|.
T Consensus 128 ~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 128 SCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred eeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999885
No 7
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=99.96 E-value=2.4e-28 Score=256.25 Aligned_cols=213 Identities=23% Similarity=0.341 Sum_probs=181.7
Q ss_pred EeCCChHHHHHHHHHhcCCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhH
Q 009783 14 VTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIW 93 (526)
Q Consensus 14 V~t~~~~el~~~~~~L~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~ 93 (526)
|+| .++++++++.+...++||||+||..... +.++++||||++. +.+|+||+..+. .+
T Consensus 2 I~t--~~~l~~~~~~l~~~~~ia~DtE~~~~~~---y~~~l~LiQia~~--------------~~~~liD~~~~~---~~ 59 (367)
T TIGR01388 2 ITT--DDELATVCEAVRTFPFVALDTEFVRERT---FWPQLGLIQVADG--------------EQLALIDPLVII---DW 59 (367)
T ss_pred cCC--HHHHHHHHHHHhcCCEEEEeccccCCCC---CCCcceEEEEeeC--------------CeEEEEeCCCcc---cH
Confidence 566 7899999999999999999999988763 7899999999984 689999998663 36
Q ss_pred HHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcC
Q 009783 94 ELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLD 173 (526)
Q Consensus 94 ~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg 173 (526)
..|+++|+|++|.||+|++++|+..|...++. ...++|| |++|+|+++++ .+.||+.|+++|||
T Consensus 60 ~~L~~lL~d~~i~KV~h~~k~Dl~~L~~~~~~--------~~~~~fD-tqlAa~lL~~~-------~~~~l~~Lv~~~Lg 123 (367)
T TIGR01388 60 SPLKELLRDESVVKVLHAASEDLEVFLNLFGE--------LPQPLFD-TQIAAAFCGFG-------MSMGYAKLVQEVLG 123 (367)
T ss_pred HHHHHHHCCCCceEEEeecHHHHHHHHHHhCC--------CCCCccc-HHHHHHHhCCC-------CCccHHHHHHHHcC
Confidence 78999999999999999999999999875433 2478999 99999999974 45799999999999
Q ss_pred CcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchhhhhhhhccCccc-CCC-CCCcccCCC
Q 009783 174 ISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGFAAGNSCSSISELDSSNLD-LGL-KGILEKPDI 251 (526)
Q Consensus 174 ~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~~~~~~~e~~~~~~~~~~-~~~-~~~~~~~~~ 251 (526)
+.++|+++.+||..|||+.+|+.|||.||++++.||+.|.++|++.|.. .|+.+||..+...... ... ..|++..+
T Consensus 124 ~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~~~g~~-~w~~ee~~~l~~~~~~~~~~~~~~~~i~~- 201 (367)
T TIGR01388 124 VELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLEESGRL-AWLEEECTLLTDRRTYVVNPEDAWRDIKN- 201 (367)
T ss_pred CCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcH-HHHHHHHHHHhccccCCCChHHHHHHhcc-
Confidence 9999999999999999999999999999999999999999999999998 8999999988653221 222 23776552
Q ss_pred CCcccccchhhHHHHHHHh
Q 009783 252 GNKTVRFKLCEALDIIRAT 270 (526)
Q Consensus 252 ~~~~~~~~~~~~~~~~~~~ 270 (526)
..++ .+++|+++|++
T Consensus 202 ---~~~l-~~~~l~~l~~L 216 (367)
T TIGR01388 202 ---AWQL-RPQQLAVLQAL 216 (367)
T ss_pred ---cccC-CHHHHHHHHHH
Confidence 2334 58999999999
No 8
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=99.95 E-value=1.7e-26 Score=216.86 Aligned_cols=163 Identities=33% Similarity=0.526 Sum_probs=142.6
Q ss_pred hHHHHHHHHHhc-CCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHH
Q 009783 19 SPEFTHLARALS-QSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLK 97 (526)
Q Consensus 19 ~~el~~~~~~L~-~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~ 97 (526)
.++++.+++.+. ...+||||+||.+.+.. ++.+++++||||+. +.+|+||+..+. .+...|+
T Consensus 4 ~~~~~~~~~~~~~~~~~ig~D~E~~~~~~~-~~~~~~~liQl~~~--------------~~~~l~~~~~~~--~~~~~l~ 66 (170)
T cd06141 4 AQDAEEAVKELLGKEKVVGFDTEWRPSFRK-GKRNKVALLQLATE--------------SRCLLFQLAHMD--KLPPSLK 66 (170)
T ss_pred HHHHHHHHHHHhcCCCEEEEeCccCCccCC-CCCCCceEEEEecC--------------CcEEEEEhhhhh--cccHHHH
Confidence 678899999998 99999999999987631 25689999999974 789999988753 3567899
Q ss_pred HhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCc
Q 009783 98 ELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS 177 (526)
Q Consensus 98 ~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~ 177 (526)
++|+++++.||||++++|+..|...||+ ...+++| +++++|++++. ....||+.|++++||..++
T Consensus 67 ~ll~~~~i~kv~~~~k~D~~~L~~~~g~--------~~~~~~D-l~~aa~ll~~~------~~~~~l~~l~~~~l~~~~~ 131 (170)
T cd06141 67 QLLEDPSILKVGVGIKGDARKLARDFGI--------EVRGVVD-LSHLAKRVGPR------RKLVSLARLVEEVLGLPLS 131 (170)
T ss_pred HHhcCCCeeEEEeeeHHHHHHHHhHcCC--------CCCCeee-HHHHHHHhCCC------cCCccHHHHHHHHcCcccC
Confidence 9999999999999999999999877776 1367799 89999999874 2346999999999999998
Q ss_pred --ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009783 178 --KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (526)
Q Consensus 178 --K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~ 213 (526)
|..++|||..|||+++|+.|||.||++++.||+.|.
T Consensus 132 k~k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 132 KPKKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCCCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 889999999999999999999999999999999885
No 9
>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins. The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.
Probab=99.94 E-value=4.6e-26 Score=219.78 Aligned_cols=170 Identities=25% Similarity=0.332 Sum_probs=141.9
Q ss_pred HHHHhcCCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCC
Q 009783 25 LARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPD 104 (526)
Q Consensus 25 ~~~~L~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~~~~ 104 (526)
+++.|....+||||+||.+.+. .++++|||||+. .+.+||||+..++...+...|+++|++++
T Consensus 3 ~~~~l~~~~~i~~D~E~~~~~~----~~~~~LiQia~~-------------~~~v~l~D~~~~~~~~~~~~L~~iLe~~~ 65 (197)
T cd06148 3 AIIHLKKQKVIGLDCEGVNLGR----KGKLCLVQIATR-------------TGQIYLFDILKLGSIVFINGLKDILESKK 65 (197)
T ss_pred hhhhhhhCCEEEEEcccccCCC----CCCEEEEEEeeC-------------CCcEEEEEhhhccchhHHHHHHHHhcCCC
Confidence 4566778999999999986652 468999999985 37899999988754346788999999999
Q ss_pred cEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccC-CCCCcCCccHHHHHHHHcCCcCcc-----
Q 009783 105 ILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLG-RKLPKETKSLANICKELLDISLSK----- 178 (526)
Q Consensus 105 i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~-~~~~~~~~gL~~Lv~~~Lg~~L~K----- 178 (526)
|.|||||+++|+..|...+|+ .+.++|| |++|+|++++... ...+....||+.+++++||.+++|
T Consensus 66 i~Kv~h~~k~D~~~L~~~~gi--------~~~~~fD-t~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~ 136 (197)
T cd06148 66 ILKVIHDCRRDSDALYHQYGI--------KLNNVFD-TQVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVK 136 (197)
T ss_pred ccEEEEechhHHHHHHHhcCc--------cccceee-HHHHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHH
Confidence 999999999999999766666 1367899 9999999987421 111123469999999999999865
Q ss_pred ---cccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 009783 179 ---ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKG 220 (526)
Q Consensus 179 ---~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g 220 (526)
..+++||..|||+++|+.|||.||++++.||+.|...|.+..
T Consensus 137 ~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~~~~ 181 (197)
T cd06148 137 KLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALISKF 181 (197)
T ss_pred HHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhhhhH
Confidence 467899999999999999999999999999999999998764
No 10
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=99.93 E-value=5.6e-25 Score=205.81 Aligned_cols=174 Identities=29% Similarity=0.451 Sum_probs=150.6
Q ss_pred EEEEeCCChHHHHHHHHHhcCCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCch
Q 009783 11 IHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLP 90 (526)
Q Consensus 11 i~~V~t~~~~el~~~~~~L~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~ 90 (526)
|++|++ .+++.+++..+...+++|||+||.+.... .....+++||+++. ..+|+++.......
T Consensus 1 y~~v~~--~~~l~~~~~~l~~~~~~a~D~E~~~~~~~-~~~~~~~~iq~~~~--------------~~~~i~~~~~~~~~ 63 (176)
T PF01612_consen 1 YQIVDT--EEELEEAIKKLKNAKVLAFDTETTGLDPY-SYNPKIALIQLATG--------------EGCYIIDPIDLGDN 63 (176)
T ss_dssp SEEEHS--HHHHHHHHHHHTTTSEEEEEEEEETSTST-TSSEEEEEEEEEES--------------CEEEEECGTTSTTT
T ss_pred CEecCC--HHHHHHHHHHHcCCCeEEEEEEECCCCcc-ccCCeEEEEEEecC--------------CCceeeeecccccc
Confidence 578888 89999999999999999999999988752 25789999999984 68899887765532
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
.++..|+++|++++++|||||+++|+..|.+.+|+ .+.+++| ++++++++++. ..+||++|+.+
T Consensus 64 ~~~~~l~~ll~~~~i~kv~~n~~~D~~~L~~~~~i--------~~~~~~D-~~l~~~~l~~~-------~~~~L~~L~~~ 127 (176)
T PF01612_consen 64 WILDALKELLEDPNIIKVGHNAKFDLKWLYRSFGI--------DLKNVFD-TMLAAYLLDPT-------RSYSLKDLAEE 127 (176)
T ss_dssp THHHHHHHHHTTTTSEEEESSHHHHHHHHHHHHTS----------SSEEE-HHHHHHHTTTS-------TTSSHHHHHHH
T ss_pred chHHHHHHHHhCCCccEEEEEEechHHHHHHHhcc--------ccCCccc-hhhhhhccccc-------ccccHHHHHHH
Confidence 26789999999999999999999999999987666 2478999 69999999874 34899999999
Q ss_pred HcC-CcCcccccccCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 171 LLD-ISLSKELQCSDWS-NRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (526)
Q Consensus 171 ~Lg-~~L~K~~q~sdW~-~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~ 217 (526)
++| ..++|..+.++|. .+||+++|+.|||.||+++++||+.|.++|+
T Consensus 128 ~l~~~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l~ 176 (176)
T PF01612_consen 128 YLGNIDLDKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQLE 176 (176)
T ss_dssp HHSEEE-GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHHC
T ss_pred HhhhccCcHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 999 7788999999999 8999999999999999999999999999873
No 11
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=99.83 E-value=3.3e-19 Score=167.75 Aligned_cols=174 Identities=29% Similarity=0.465 Sum_probs=140.6
Q ss_pred HHHHHHHhcCCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhC
Q 009783 22 FTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFV 101 (526)
Q Consensus 22 l~~~~~~L~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~ 101 (526)
+.++++.+...+.+++|+|+.+..+ ..+.++++|+++. +.+|+||+... .....|+++|+
T Consensus 2 ~~~~~~~l~~~~~l~~~~e~~~~~~---~~~~~~~i~l~~~--------------~~~~~i~~~~~---~~~~~l~~ll~ 61 (178)
T cd06142 2 LEDLCERLASAGVIAVDTEFMRLNT---YYPRLCLIQISTG--------------GEVYLIDPLAI---GDLSPLKELLA 61 (178)
T ss_pred HHHHHHHHhcCCeEEEECCccCCCc---CCCceEEEEEeeC--------------CCEEEEeCCCc---ccHHHHHHHHc
Confidence 3445555555669999999865542 3467899999873 44888886532 25667899999
Q ss_pred CCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCccccc
Q 009783 102 SPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQ 181 (526)
Q Consensus 102 ~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~K~~q 181 (526)
++++.|||||+|.|+..|.+.||+ . .++++| +++++|+++++ .+++|++++++++|..+.+...
T Consensus 62 ~~~i~kv~~d~K~~~~~L~~~~gi-------~-~~~~~D-~~laayLl~p~-------~~~~l~~l~~~~l~~~~~~~~~ 125 (178)
T cd06142 62 DPNIVKVFHAAREDLELLKRDFGI-------L-PQNLFD-TQIAARLLGLG-------DSVGLAALVEELLGVELDKGEQ 125 (178)
T ss_pred CCCceEEEeccHHHHHHHHHHcCC-------C-CCCccc-HHHHHHHhCCC-------ccccHHHHHHHHhCCCCCcccc
Confidence 999999999999999999886666 1 367899 89999999984 3469999999999998777668
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchhhhhhh
Q 009783 182 CSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGFAAGNSCSSISE 232 (526)
Q Consensus 182 ~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~~~~~~~e~~~ 232 (526)
.++|..+|++.+|+.|||.||+++++|++.|.++|++.|+. +-+..|++.
T Consensus 126 ~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~e~~l~-~L~~~~~~~ 175 (178)
T cd06142 126 RSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEEEGRL-EWAEEECEL 175 (178)
T ss_pred cccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCcH-HHHHHHHHH
Confidence 89999999999999999999999999999999999998876 444455543
No 12
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.76 E-value=5.7e-17 Score=150.48 Aligned_cols=169 Identities=32% Similarity=0.434 Sum_probs=132.8
Q ss_pred EEEeCCChHHHHHHHHHhc-CCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCch
Q 009783 12 HLVTSTESPEFTHLARALS-QSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLP 90 (526)
Q Consensus 12 ~~V~t~~~~el~~~~~~L~-~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~ 90 (526)
.+|++ .+++..+++.+. ....+++|+|+.+... ....++++|++.. ++.+|+++.... .
T Consensus 2 ~~i~~--~~~~~~~~~~~~~~~~~l~~~~e~~~~~~---~~~~~~~l~l~~~-------------~~~~~i~~~~~~--~ 61 (172)
T smart00474 2 RVVTD--SETLEELLEKLRAAGGEVALDTETTGLNS---YSGKLVLIQISVT-------------GEGAFIIDPLAL--G 61 (172)
T ss_pred EEecC--HHHHHHHHHHHHhcCCeEEEeccccCCcc---CCCCEEEEEEeEc-------------CCceEEEEeccc--h
Confidence 56777 677777666665 5669999999876653 3567899999963 235676554322 2
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
.....|+++|+++++.|||||+|.|+..|.+ +|+ . ..+++| +++++|+++++ ....+|+.++++
T Consensus 62 ~~~~~l~~~l~~~~~~kv~~d~k~~~~~L~~-~gi-~-------~~~~~D-~~laayll~p~------~~~~~l~~l~~~ 125 (172)
T smart00474 62 DDLEILKDLLEDETITKVGHNAKFDLHVLAR-FGI-E-------LENIFD-TMLAAYLLLGG------PSKHGLATLLKE 125 (172)
T ss_pred hhHHHHHHHhcCCCceEEEechHHHHHHHHH-CCC-c-------ccchhH-HHHHHHHHcCC------CCcCCHHHHHHH
Confidence 3356689999999999999999999999986 666 2 245699 99999999875 233699999999
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKV 216 (526)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L 216 (526)
++|..+++..+.++|..+|+..+|+.|||.||+++++|++.|.++|
T Consensus 126 ~l~~~~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 126 YLGVELDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred HhCCCCCcccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999876655567897788999999999999999999999998876
No 13
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.74 E-value=3.7e-18 Score=181.90 Aligned_cols=195 Identities=31% Similarity=0.495 Sum_probs=149.5
Q ss_pred CCCCccEEEEeCCChHHHHHHH-HHhcCC-CeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEE
Q 009783 5 YRKPLKIHLVTSTESPEFTHLA-RALSQS-SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLL 82 (526)
Q Consensus 5 ~~~~~~i~~V~t~~~~el~~~~-~~L~~~-~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~li 82 (526)
++....|++|++ +.++..+. +.+..+ -+||+|+||.|.-. +...+++++|+++ ++.+|||
T Consensus 386 ~~~~~~i~~V~~--e~El~~l~l~~l~~e~~yVGiDsEwkps~~--v~dsk~~IlQif~--------------~~~v~Li 447 (617)
T KOG2207|consen 386 PPWVESIGMVGN--EKELRDLLLESLSEELRYVGIDSEWKPSKK--VSDSKLAILQIFF--------------KDCVYLI 447 (617)
T ss_pred CCcccceeeeCC--HHHHHHHHHHHhhhcCEEEEEccccCcccC--CChhHHHHHHHHh--------------cCeEEEe
Confidence 455667889998 78888776 456655 78999999998832 3568999999998 4899999
Q ss_pred eCCCCC--chhhHH-HHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhcccc-CCCCC
Q 009783 83 DLSSIP--LPSIWE-LLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQL-GRKLP 158 (526)
Q Consensus 83 D~~~l~--~~~~~~-~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~-~~~~~ 158 (526)
|+..+. .++.|. .+..+|+++++.|||+++.+|+..|.++.|.+...-......++++...++..+.+-.. ....+
T Consensus 448 dc~~l~~~~se~w~~~~s~if~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~ 527 (617)
T KOG2207|consen 448 DCVKLENLASEIWHLLLSQIFESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLN 527 (617)
T ss_pred ehHHhhhchHHHHHHHHHHHccCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhc
Confidence 987754 245554 55779999999999999999999998644421110011223455665666666554321 12334
Q ss_pred cCCccHHHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 159 KETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (526)
Q Consensus 159 ~~~~gL~~Lv~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~ 217 (526)
....+|+.|....||..++|++|||||..|||+..|+.|||.||.++..++..+.+..+
T Consensus 528 ~~~~~L~~Lt~~llg~~lnKteqcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv~ 586 (617)
T KOG2207|consen 528 EATKGLADLTDCLLGKKLNKTEQCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVVE 586 (617)
T ss_pred chhhhhhhhhHHHhhhhcccccccchhhcCCchhhHHHHHHhcchhhHHHHHHHHhhcc
Confidence 45789999999999999999999999999999999999999999999999999987544
No 14
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=99.70 E-value=1.2e-15 Score=146.47 Aligned_cols=174 Identities=25% Similarity=0.396 Sum_probs=133.7
Q ss_pred CccEEEEeCCChHHHHHHHHHhcCCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCC
Q 009783 8 PLKIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSI 87 (526)
Q Consensus 8 ~~~i~~V~t~~~~el~~~~~~L~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l 87 (526)
.+.|.+|++ ++++..+++.+...+.+++|+|..+..+ ....+..+|++.. +++|+|++.
T Consensus 2 ~~~~~~i~~--~~~l~~~~~~l~~~~~l~~~~e~~~~~~---~~~~~~~l~l~~~--------------~~~~~i~~l-- 60 (192)
T cd06147 2 ETPLTFVDT--EEKLEELVEKLKNCKEIAVDLEHHSYRS---YLGFTCLMQISTR--------------EEDYIVDTL-- 60 (192)
T ss_pred CCCcEEECC--HHHHHHHHHHHhcCCeEEEEeEecCCcc---CCCceEEEEEecC--------------CCcEEEEec--
Confidence 356788865 5667776666655569999998654332 2457788888874 347777742
Q ss_pred CchhhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHH
Q 009783 88 PLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANI 167 (526)
Q Consensus 88 ~~~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L 167 (526)
........|+++|+++++.|+|||+|.|+..|...+|+ . ..+.|| ++|++||++++ +++|+.|
T Consensus 61 ~~~~~~~~L~~~L~~~~i~kv~~d~K~~~~~L~~~~gi-~-------~~~~fD-~~laaYLL~p~--------~~~l~~l 123 (192)
T cd06147 61 KLRDDMHILNEVFTDPNILKVFHGADSDIIWLQRDFGL-Y-------VVNLFD-TGQAARVLNLP--------RHSLAYL 123 (192)
T ss_pred ccccchHHHHHHhcCCCceEEEechHHHHHHHHHHhCC-C-------cCchHH-HHHHHHHhCCC--------cccHHHH
Confidence 22233556899999999999999999999999734555 1 133499 99999999983 3599999
Q ss_pred HHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 009783 168 CKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (526)
Q Consensus 168 v~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~ 219 (526)
+++||+..+.|..+.++|+.+||..+|..||+.+|.++++|++.|.++|+++
T Consensus 124 ~~~yl~~~~~k~~~~~~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~L~e~ 175 (192)
T cd06147 124 LQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELLER 175 (192)
T ss_pred HHHHhCCCcchhhhccccccCCCCHHHHHHHHhhHHHHHHHHHHHHHHHHHh
Confidence 9999998754555677898888899999999999999999999999999876
No 15
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=99.67 E-value=9.2e-17 Score=170.25 Aligned_cols=173 Identities=25% Similarity=0.344 Sum_probs=153.7
Q ss_pred EEEEeCCChHHHHHHHHHhcCCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCch
Q 009783 11 IHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLP 90 (526)
Q Consensus 11 i~~V~t~~~~el~~~~~~L~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~ 90 (526)
..+|.+ ..++.++.+.|.....+|+|.|..+.. ++.+-.||+||+|. .+-|+||...+.
T Consensus 193 ~~~I~t--~~el~~l~~~l~~~~Efavdlehhsyr---sf~gltclmqISTr--------------~ed~iIDt~~l~-- 251 (687)
T KOG2206|consen 193 KVWICT--LGELEALPEILDSVIEFAVDLEHHSYR---SFLGLTCLMQISTR--------------TEDFIIDTFKLR-- 251 (687)
T ss_pred ceeeec--hHHHHHHHHHHhhhhhhhhhccccchh---hhcCceeEEEeecc--------------chhheehhHHHH--
Confidence 567877 788999999998889999999987655 37789999999996 466999987664
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
+....|.+.|.+|.|+||.|+...|+.+|++.||+ .+.++|| |--|..+++- ..++|+.|.+.
T Consensus 252 ~~i~~l~e~fsdp~ivkvfhgaD~diiwlqrdfgi--------yvvnLfd-t~~a~r~L~~--------~r~sL~~ll~~ 314 (687)
T KOG2206|consen 252 DHIGILNEVFSDPGIVKVFHGADTDIIWLQRDFGI--------YVVNLFD-TIQASRLLGL--------PRPSLAYLLEC 314 (687)
T ss_pred HHHHHhhhhccCCCeEEEEecCccchhhhhccceE--------EEEechh-hHHHHHHhCC--------CcccHHHHHHH
Confidence 34568999999999999999999999999999988 2578999 8889999875 58999999999
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 009783 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGF 221 (526)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~ 221 (526)
+.|+..+|..|..||..|||+++++.||-.|.++++.||+.|+..|.+.+.
T Consensus 315 ~~~v~~nk~yqladwR~rpLp~~Mv~yar~dthyllyiyD~lr~el~~~a~ 365 (687)
T KOG2206|consen 315 VCGVLTNKKYQLADWRIRPLPEEMVRYAREDTHYLLYIYDVLRKELKRLAK 365 (687)
T ss_pred HHhhhhhhhhhhchhccccCcHHHHHHHhhcchhHHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999999999999999999999999987763
No 16
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=99.63 E-value=1.3e-14 Score=132.05 Aligned_cols=149 Identities=28% Similarity=0.310 Sum_probs=114.1
Q ss_pred eEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCcEEEEEecH
Q 009783 34 LVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFK 113 (526)
Q Consensus 34 ~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~~~~i~KVgh~~k 113 (526)
.+++|+|+.+... ..+.++++|+++. +++++++... ....+.+.|+++|+++.+.|||||++
T Consensus 2 ~l~~d~e~~~~~~---~~~~i~~~~l~~~--------------~~~~~i~~~~-~~~~~~~~l~~~l~~~~~~~v~~~~k 63 (155)
T cd00007 2 EVAFDTETTGLNY---HRGKLVGIQIATA--------------GEAAYIPDEL-ELEEDLEALKELLEDEDITKVGHDAK 63 (155)
T ss_pred ceEEEEecCCCCc---CCCeEEEEEEEEC--------------CcEEEEEcCC-CHHHHHHHHHHHHcCCCCcEEeccHH
Confidence 5899999876552 3578899999973 2244443221 12346677999999999999999999
Q ss_pred HhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcccccccCCC----CCC
Q 009783 114 QDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWS----NRP 189 (526)
Q Consensus 114 ~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~K~~q~sdW~----~RP 189 (526)
+|+..|... +. ....+++| +++++|++++. ..+++|+.|++++++..+.+..+..+|. .+|
T Consensus 64 ~d~~~L~~~-~~-------~~~~~~~D-~~~~ayll~~~------~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~ 128 (155)
T cd00007 64 FDLVVLARD-GI-------ELPGNIFD-TMLAAYLLNPG------EGSHSLDDLAKEYLGIELDKDEQIYGKGAKTFARP 128 (155)
T ss_pred HHHHHHHHC-CC-------CCCCCccc-HHHHHHHhCCC------CCcCCHHHHHHHHcCCCCccHHHHhcCCCCccccC
Confidence 999999874 22 12367899 99999999985 2157999999999998865534455553 478
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 190 LTEEQKNYAAIDAHCLIEIFNIFQVK 215 (526)
Q Consensus 190 L~~~qi~YAA~DA~~ll~L~~~L~~~ 215 (526)
++.+|+.||+.||.++++|++.|.++
T Consensus 129 ~~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 129 LSEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 89999999999999999999999864
No 17
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=99.61 E-value=1.8e-14 Score=131.44 Aligned_cols=147 Identities=26% Similarity=0.250 Sum_probs=112.5
Q ss_pred eEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCcEEEEEecH
Q 009783 34 LVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFK 113 (526)
Q Consensus 34 ~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~~~~i~KVgh~~k 113 (526)
++++|+|+.+..+ ...+++++|++.. ++.+|++++.... -....|+++|+++++.|+|||+|
T Consensus 1 ~~~~~~e~~~~~~---~~~~~~~l~l~~~-------------~~~~~~i~~~~~~--~~~~~l~~~l~~~~~~kv~~d~K 62 (150)
T cd09018 1 VFAFDTETDSLDN---ISANLVLIQLAIE-------------PGVAALIPVAHDY--LALELLKPLLEDEKALKVGQNLK 62 (150)
T ss_pred CEEEEeecCCCCC---CCceEEEEEEEcC-------------CCcEEEEEcCCcc--cCHHHHHHHhcCCCCceeeecHH
Confidence 4789998866553 3468899999974 2347888754311 02456899999999999999999
Q ss_pred HhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcccccc--cCCCCCCCC
Q 009783 114 QDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQC--SDWSNRPLT 191 (526)
Q Consensus 114 ~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~K~~q~--sdW~~RPL~ 191 (526)
.|+..|.+. |+ ...+++|| +++|+|++++. ..+.+|+.|++++|+..+.+..+. ++|..+++.
T Consensus 63 ~~~~~L~~~-~~-------~~~~~~~D-~~laayLl~p~------~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~ 127 (150)
T cd09018 63 YDRGILLNY-FI-------ELRGIAFD-TMLEAYILNSV------AGRWDMDSLVERWLGHKLIKFESIAGKLWFNQPLT 127 (150)
T ss_pred HHHHHHHHc-CC-------ccCCcchh-HHHHHHHhCCC------CCCCCHHHHHHHHhCCCcccHHHhcCCCCcccCCH
Confidence 999999763 43 12367899 99999999985 214699999999999886542222 248557889
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 009783 192 EEQKNYAAIDAHCLIEIFNIFQ 213 (526)
Q Consensus 192 ~~qi~YAA~DA~~ll~L~~~L~ 213 (526)
.+|+.||+.||+++++|++.|.
T Consensus 128 ~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 128 EEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999874
No 18
>PRK05755 DNA polymerase I; Provisional
Probab=99.60 E-value=3.2e-14 Score=165.29 Aligned_cols=187 Identities=18% Similarity=0.195 Sum_probs=147.7
Q ss_pred CccEEEEeCCChHHHHHHHHHhcCCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCC
Q 009783 8 PLKIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSI 87 (526)
Q Consensus 8 ~~~i~~V~t~~~~el~~~~~~L~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l 87 (526)
..+|.+|++ .+++..+++.+.....++||+|+.+..+ +.+++.++|++.. ++.+|++++..+
T Consensus 293 ~~~~~~I~~--~~~L~~~l~~l~~~~~~a~DtEt~~l~~---~~~~i~~i~ls~~-------------~g~~~~ip~~~i 354 (880)
T PRK05755 293 EEDYETILD--EEELEAWLAKLKAAGLFAFDTETTSLDP---MQAELVGLSFAVE-------------PGEAAYIPLDQL 354 (880)
T ss_pred CCceEEeCC--HHHHHHHHHHhhccCeEEEEeccCCCCc---ccccEEEEEEEeC-------------CCcEEEEecccc
Confidence 346778877 7889999998888899999999988764 6788999999875 345888887543
Q ss_pred CchhhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHH
Q 009783 88 PLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANI 167 (526)
Q Consensus 88 ~~~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L 167 (526)
.. ..+..|.++|+++.+.||+||+++|+..|.+ +|+ . ...+++| |++++|+++++ ..++|++|
T Consensus 355 ~~-~~l~~l~~~L~d~~v~kV~HNakfDl~~L~~-~gi---~----~~~~~~D-T~iAa~Ll~~~-------~~~~L~~L 417 (880)
T PRK05755 355 DR-EVLAALKPLLEDPAIKKVGQNLKYDLHVLAR-YGI---E----LRGIAFD-TMLASYLLDPG-------RRHGLDSL 417 (880)
T ss_pred cH-HHHHHHHHHHhCCCCcEEEeccHhHHHHHHh-CCC---C----cCCCccc-HHHHHHHcCCC-------CCCCHHHH
Confidence 21 4677899999999999999999999999986 454 1 1367999 99999999985 24899999
Q ss_pred HHHHcCCcCcccc----cccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchhhhhh
Q 009783 168 CKELLDISLSKEL----QCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGFAAGNSCSSIS 231 (526)
Q Consensus 168 v~~~Lg~~L~K~~----q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~~~~~~~e~~ 231 (526)
+++++|..+.... ...+|+..|+ +.+..||+.||.++++||..|.++|.+.+.. .|++.+++
T Consensus 418 ~~~ylg~~~~~~~~~~gk~~~~~~~pl-e~~~~YAa~Dv~~~~~L~~~L~~~L~~~~~l-~~l~~eiE 483 (880)
T PRK05755 418 AERYLGHKTISFEEVAGKQLTFAQVDL-EEAAEYAAEDADVTLRLHEVLKPKLLEEPGL-LELYEEIE 483 (880)
T ss_pred HHHHhCCCccchHHhcCCCCCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHHhcccH-HHHHHHhh
Confidence 9999998853211 1233444566 5789999999999999999999999887444 47776665
No 19
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.57 E-value=3.9e-17 Score=174.17 Aligned_cols=369 Identities=33% Similarity=0.417 Sum_probs=251.3
Q ss_pred CCceeeHHH--HHHHhhccccCCCCCcC-Cc---cHHHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHH-
Q 009783 135 VEPYLDITS--IYNHLHHKQLGRKLPKE-TK---SLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIE- 207 (526)
Q Consensus 135 ~~~~~Dlt~--La~yLl~~~~~~~~~~~-~~---gL~~Lv~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~- 207 (526)
...++|++. +..|+-+..++...+.. .+ +--++.+..+..-+.+..|+++|..+++++.|..|+..++.++..
T Consensus 154 ~~~~~Di~l~~i~e~lq~~~f~e~a~~~ik~~l~~~~~~e~~~ldlIls~k~q~a~~ll~~~~~~q~p~v~fld~~v~~~ 233 (617)
T KOG2207|consen 154 LKQTLDITLCKIDEYLQNQRFGEAAPKAIKSLLLSDNAFEQLMLDLILSKKLQIADELLRHLTELQKPYVEFLDQMVLDN 233 (617)
T ss_pred hhhhHhHhcchhHHHHHhHHHHHHHHHHHHhhhhhhhhHHHHhccHhhccchhHHHHHHhhhhhhhhhHHHHHHHHHHHH
Confidence 346788877 77777654332221111 11 111244555566667888999999999999999999999999999
Q ss_pred -HHHHHHHHHHhc-----CCCccchhhhhhhhccCcccCCCCCCcccCCCCCcccccchhhHHHHHHHhhhcccCCCCCc
Q 009783 208 -IFNIFQVKVAQK-----GFAAGNSCSSISELDSSNLDLGLKGILEKPDIGNKTVRFKLCEALDIIRATSYYSQCLPEGV 281 (526)
Q Consensus 208 -L~~~L~~~L~~~-----g~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 281 (526)
..+.+++.+.+. -.+ -...+||-. .+........ ....++++...|+++...+..++.++.+...-
T Consensus 234 ~~v~e~~~~~~e~~~~~~~tl-~~~v~~i~~--rn~~~~~f~~-----~~~~n~v~~~~~kal~~~~~~~e~~~~~~~~f 305 (617)
T KOG2207|consen 234 FIVDERCAHLLERTINLPKTL-TILVQEIIN--RNQKKYTFSD-----EYAKNYVQNKNCKALHYIRSEREKGQMADKGF 305 (617)
T ss_pred HHHHHHHHHHHhhccCCCchh-hhhHHHHHh--ccchhhhhhh-----hhhhhHhhcccHHHHHHHHHHhhhhhhHHHhh
Confidence 777777777655 011 112233311 1111111111 13346788899999999999999999877777
Q ss_pred ccccccCCCCCCchHHHHHHHHhh---hhhhhhcccCC-CCcc----ccccCCCCcccc-----ccccccccccCCCCCC
Q 009783 282 VSRVSYLNTMPMDESLVKIVRKYG---EKILLRECDKA-PKTS----KKKGRKRSSVIV-----DSREKRLDDIGDWQGP 348 (526)
Q Consensus 282 ~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~-~~~~----~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~ 348 (526)
++.+...+|.|+++.+++++...| |+|.+...+.- ||.= +++-.++..... ...+.++.+...|+.+
T Consensus 306 ~~~~~~~~t~~~d~~~lkyLw~~~~~iEai~~~~~~~i~~~d~~~el~~~~s~~~~~k~~~~~~~~~~~pl~~~~~~~~~ 385 (617)
T KOG2207|consen 306 VQHVVETKTKPDDENLLKYLWSFGEHIEAIYLATYDNIDPKDDAKELEKRTSRRGAGKTLFNQRMTTNVPLVCEDLFLFE 385 (617)
T ss_pred chhheeecccccchhHHHHHHHHHHhhhhhhhhhhhcCCCchhHHHHhchhhhcccChhhhhcccccccCccchhhhccC
Confidence 788888999999999999999998 88888887733 2221 111111111111 3445567778889999
Q ss_pred CCCCCCCCCCCCCEEEEecccHHHHHHHHhcCCceecCCCCCC-ChHHHHHhhhcCCcEEEecChhHHHhhc----ccCC
Q 009783 349 PPWDLSLGGDGYPKFLCDVMVEGLAKHLRCVGIDAATPRSKKP-EPRELIDQTSKEKRVLLTRDAKLLRHQY----LIKN 423 (526)
Q Consensus 349 ~p~~~~~~~~~~~kfl~D~mLg~Lar~LR~lG~D~~~~~~~~~-~d~~ll~~A~~E~RiiLTrd~~l~~~~~----~~~~ 423 (526)
|||+..++++++.+++-|.||++|.+.+|..|||+.+....+. +.+..|-++--+++|.|+...++.+.+. ....
T Consensus 386 ~~~~~~i~~V~~e~El~~l~l~~l~~e~~yVGiDsEwkps~~v~dsk~~IlQif~~~~v~Lidc~~l~~~~se~w~~~~s 465 (617)
T KOG2207|consen 386 PPWVESIGMVGNEKELRDLLLESLSEELRYVGIDSEWKPSKKVSDSKLAILQIFFKDCVYLIDCVKLENLASEIWHLLLS 465 (617)
T ss_pred CCcccceeeeCCHHHHHHHHHHHhhhcCEEEEEccccCcccCCChhHHHHHHHHhcCeEEEeehHHhhhchHHHHHHHHH
Confidence 9999999999999999999999999999999999998776333 3445555556789999999988754322 0101
Q ss_pred cEEEEcCCCH----HHHHHHHHH------HcCccccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCC
Q 009783 424 QIYRVKSLLK----NQQLLEVIE------AFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNL 493 (526)
Q Consensus 424 ~~~~v~~~~~----~~QL~~vl~------~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~ 493 (526)
+++-.++-.+ ..|..++++ +|++++...+..++|.+|+..+...+.+-++..++..+...++.+.+...-
T Consensus 466 ~if~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~Lt~~llg~~l 545 (617)
T KOG2207|consen 466 QIFESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADLTDCLLGKKL 545 (617)
T ss_pred HHccCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhhhhhhHHHhhhhc
Confidence 1222222111 134444444 677888777788999999998876666667777777777788888865332
Q ss_pred ---ce---eec--CCCCeEEecccch
Q 009783 494 ---QF---WQC--MDCNQLYWEVMSA 511 (526)
Q Consensus 494 ---~F---~~C--~~CgkvyW~GsH~ 511 (526)
++ |+| -+|+|+||.|.-.
T Consensus 546 nKteqcsnWqcrpLr~nQi~yaalDa 571 (617)
T KOG2207|consen 546 NKTEQCSNWQCRPLRRNQIYYAALDA 571 (617)
T ss_pred ccccccchhhcCCchhhHHHHHHhcc
Confidence 66 999 8999999999544
No 20
>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases. Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Probab=99.55 E-value=1.5e-13 Score=129.65 Aligned_cols=164 Identities=16% Similarity=0.120 Sum_probs=123.9
Q ss_pred CCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCcEEEEEe
Q 009783 32 SSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFK 111 (526)
Q Consensus 32 ~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~~~~i~KVgh~ 111 (526)
...+++|+|.....+ ....+..++++.. +++|++++... ......|+++|+++++.|++||
T Consensus 3 ~~~~~~~~~~~~~~~---~~~~l~~i~l~~~--------------~~~~~i~~~~~--~~~~~~l~~~l~~~~~~ki~~d 63 (178)
T cd06140 3 ADEVALYVELLGENY---HTADIIGLALANG--------------GGAYYIPLELA--LLDLAALKEWLEDEKIPKVGHD 63 (178)
T ss_pred CCceEEEEEEcCCCc---ceeeEEEEEEEeC--------------CcEEEEeccch--HHHHHHHHHHHhCCCCceeccc
Confidence 356788888776553 3467777777763 35777774321 0135568899999999999999
Q ss_pred cHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcccccccCCC---CC
Q 009783 112 FKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWS---NR 188 (526)
Q Consensus 112 ~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~K~~q~sdW~---~R 188 (526)
+|.|++.|.. +|+ ...+.+|| |+||+||++++ ...++|++++.+||+..+.+..+.+.|. .+
T Consensus 64 ~K~~~~~l~~-~gi-------~~~~~~fD-t~laaYLL~p~------~~~~~l~~l~~~yl~~~~~~~~~~~~~~~~~~~ 128 (178)
T cd06140 64 AKRAYVALKR-HGI-------ELAGVAFD-TMLAAYLLDPT------RSSYDLADLAKRYLGRELPSDEEVYGKGAKFAV 128 (178)
T ss_pred hhHHHHHHHH-CCC-------cCCCcchh-HHHHHHHcCCC------CCCCCHHHHHHHHcCCCCcchHHhcCCCCCccc
Confidence 9999999976 455 12356799 99999999985 2347999999999999876544444452 23
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchhhhhh
Q 009783 189 PLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGFAAGNSCSSIS 231 (526)
Q Consensus 189 PL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~~~~~~~e~~ 231 (526)
+....+..|++.||.+++.|++.|.++|+++++. .++++|+
T Consensus 129 ~~~~~~~~y~~~~a~~l~~l~~~l~~~L~~~~l~--~L~~~iE 169 (178)
T cd06140 129 PDEEVLAEHLARKAAAIARLAPKLEEELEENEQL--ELYYEVE 169 (178)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHH--HHHHHHH
Confidence 4457788999999999999999999999988776 6777775
No 21
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=99.46 E-value=3.1e-12 Score=121.69 Aligned_cols=168 Identities=20% Similarity=0.320 Sum_probs=121.9
Q ss_pred cCCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC------CCchhhHHHHHHhhCCC
Q 009783 30 SQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS------IPLPSIWELLKELFVSP 103 (526)
Q Consensus 30 ~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~------l~~~~~~~~L~~lL~~~ 103 (526)
.+.+.+++|+|..+..+ ...++..++++.. .+.+|++++.. .........|+++|++.
T Consensus 3 ~~~~~~a~d~e~~~~~~---~~~~i~~l~~~~~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~ 66 (193)
T cd06139 3 EKAKVFAFDTETTSLDP---MQAELVGISFAVE-------------PGEAYYIPLGHDYGGEQLPREEVLAALKPLLEDP 66 (193)
T ss_pred ccCCeEEEEeecCCCCc---CCCeEEEEEEEcC-------------CCCEEEEecCCCccccCCCHHHHHHHHHHHHhCC
Confidence 35678999998765543 3466777777763 23366665432 12234566689999998
Q ss_pred CcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCc------
Q 009783 104 DILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS------ 177 (526)
Q Consensus 104 ~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~------ 177 (526)
.+.+|+||++.|+..|.. +|+ . ....++| |++++|+++++ ...++|..++++++|....
T Consensus 67 ~~~~v~hn~k~d~~~l~~-~gi-~------~~~~~~D-t~l~a~ll~p~------~~~~~l~~l~~~~l~~~~~~~~~~~ 131 (193)
T cd06139 67 SIKKVGQNLKFDLHVLAN-HGI-E------LRGPAFD-TMLASYLLNPG------RRRHGLDDLAERYLGHKTISFEDLV 131 (193)
T ss_pred CCcEEeeccHHHHHHHHH-CCC-C------CCCCccc-HHHHHHHhCCC------CCCCCHHHHHHHHhCCCCccHHHHc
Confidence 889999999999999976 454 1 2356899 99999999985 2257999999999987631
Q ss_pred -ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCccchhhhhh
Q 009783 178 -KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ-KGFAAGNSCSSIS 231 (526)
Q Consensus 178 -K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~-~g~~~~~~~~e~~ 231 (526)
|..+..+|...|+ ..+..||+.||.++++|++.|.++|++ .++. +++++++
T Consensus 132 ~k~~~~~~~~~~~~-~~~~~ya~~d~~~~~~l~~~l~~~l~~~~~~~--~l~~~iE 184 (193)
T cd06139 132 GKGKKQITFDQVPL-EKAAEYAAEDADITLRLYELLKPKLKEEPGLL--ELYEEIE 184 (193)
T ss_pred CCCcCcCCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHH--HHHHHHh
Confidence 2223345654444 668899999999999999999999987 6544 6666664
No 22
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.34 E-value=5.5e-12 Score=139.64 Aligned_cols=146 Identities=22% Similarity=0.214 Sum_probs=119.2
Q ss_pred cEEEEeCCChHHHHHHHHHhcCCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCc
Q 009783 10 KIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPL 89 (526)
Q Consensus 10 ~i~~V~t~~~~el~~~~~~L~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~ 89 (526)
.+.+|++ .+++..++..+...+.+++|+|+.... ..++++|++.. +.+|++|+...
T Consensus 2 ~~~~I~~--~~~l~~~~~~l~~~~~~a~DtEf~r~~------t~l~liQ~~~~--------------~~~~liDpl~~-- 57 (553)
T PRK14975 2 DMKVILA--PEELGAALERLSPAGVVAGDTETTGDD------AAAAAAQEGEE--------------EPRWVWASTAA-- 57 (553)
T ss_pred CceEEec--cchhHHHHHHhccCCceeCCccccCCc------chhheeeecCC--------------CceEEECchHH--
Confidence 3567887 788999999999999999999987654 27899999863 67899996531
Q ss_pred hhhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHH
Q 009783 90 PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (526)
Q Consensus 90 ~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~ 169 (526)
+.+ + |.+ +|+ . +.++|| |+|++|+++++.+ ...++++.++.
T Consensus 58 ---l~~---~-------------------L~~-~Gv---~-----~~~~fD-T~LAa~lL~~~~~----~~~~~l~~la~ 98 (553)
T PRK14975 58 ---LYP---R-------------------LLA-AGV---R-----VERCHD-LMLASQLLLGSEG----RAGSSLSAAAA 98 (553)
T ss_pred ---hHH---H-------------------HHH-CCC---c-----cCCCch-HHHHHHHcCCCCC----cCCCCHHHHHH
Confidence 221 1 434 344 2 356999 9999999997511 01689999999
Q ss_pred HHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 009783 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (526)
Q Consensus 170 ~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~ 219 (526)
++|+..++|..+.+||. ||++++|+.|||.|+.+++.||..|.++|++.
T Consensus 99 ~~l~~~l~k~~~~sdw~-rpls~~q~~YAa~Dv~~l~~L~~~L~~qL~~~ 147 (553)
T PRK14975 99 RALGEGLDKPPQTSALS-DPPDEEQLLYAAADADVLLELYAVLADQLNRI 147 (553)
T ss_pred HHhCCCCCChhhhcccc-ccchHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Confidence 99999999988899997 99999999999999999999999999999876
No 23
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=99.17 E-value=2.1e-10 Score=125.10 Aligned_cols=179 Identities=17% Similarity=0.172 Sum_probs=127.3
Q ss_pred hHHHHHHHHHhcCCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCC-chhhHHHHH
Q 009783 19 SPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIP-LPSIWELLK 97 (526)
Q Consensus 19 ~~el~~~~~~L~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~-~~~~~~~L~ 97 (526)
...+..++..+...+.+++|+|..+..+ ....+++++... +..++++....-+ .-.....|+
T Consensus 9 ~~~~~~~~~~~~~~~~~a~~~et~~l~~-----~~~~lvg~s~~~------------~~~~~yi~~~~~~~~~~~~~~l~ 71 (593)
T COG0749 9 LAVLNAWLTKLNAAANIAFDTETDGLDP-----HGADLVGLSVAS------------EEEAAYIPLLHGPEQLNVLAALK 71 (593)
T ss_pred HHHHHHHHHHHhhcccceeeccccccCc-----ccCCeeEEEeec------------cccceeEeeccchhhhhhHHHHH
Confidence 4556666666665555999999988875 345677776652 2245555543311 112577899
Q ss_pred HhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCc
Q 009783 98 ELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS 177 (526)
Q Consensus 98 ~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~ 177 (526)
+||+++.+.|+|||.|.|.+.|++ +|+ . .+..+| |||++|+++++ ...+++++|++++++....
T Consensus 72 ~~l~~~~~~kv~~~~K~d~~~l~~-~Gi-------~-~~~~~D-tmlasYll~~~------~~~~~~~~l~~r~l~~~~~ 135 (593)
T COG0749 72 PLLEDEGIKKVGQNLKYDYKVLAN-LGI-------E-PGVAFD-TMLASYLLNPG------AGAHNLDDLAKRYLGLETI 135 (593)
T ss_pred HHhhCcccchhccccchhHHHHHH-cCC-------c-ccchHH-HHHHHhccCcC------cCcCCHHHHHHHhcCCccc
Confidence 999999999999999999999988 353 1 267899 99999999986 3579999999999998865
Q ss_pred ccccccCCC-----CCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchhhhhh
Q 009783 178 KELQCSDWS-----NRPLT-EEQKNYAAIDAHCLIEIFNIFQVKVAQKGFAAGNSCSSIS 231 (526)
Q Consensus 178 K~~q~sdW~-----~RPL~-~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~~~~~~~e~~ 231 (526)
......+-. ...++ +....|+|.||.++++|+..|.+++.+...+ ..++.+++
T Consensus 136 ~~~~i~~kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~l~~~~~L-~~l~~~iE 194 (593)
T COG0749 136 TFEDIAGKGKKQLTFADVKLEKATEYAAEDADATLRLESILEPELLKTPVL-LELYEEIE 194 (593)
T ss_pred hhHHhhccccccCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhH-HHHHHHHh
Confidence 433222111 11122 4458999999999999999999988877653 34555554
No 24
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.13 E-value=1.9e-09 Score=124.62 Aligned_cols=180 Identities=13% Similarity=0.052 Sum_probs=119.7
Q ss_pred EEEEeCCChHHHHHHHHHhcCCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCC-CEEEEEeCC---C
Q 009783 11 IHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNA-SVVFLLDLS---S 86 (526)
Q Consensus 11 i~~V~t~~~~el~~~~~~L~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~-~~v~liD~~---~ 86 (526)
+..|.+ .+++..+++. ...+.+++ .+..+ ....+..+.+++. . +.+|++++. .
T Consensus 304 ~~~~~~--~~~~~~~~~~-~~~~~~~~----~~~~~---~~~~~~~~~~~~~-------------~~~~~~~~~~~~~~~ 360 (887)
T TIGR00593 304 AKESEE--AAPLANPAEK-AEVGGFVL----ERLLD---QLKKALALAFATE-------------NQSYVAYASEADGIP 360 (887)
T ss_pred ceEeCC--HHHHHHHHHh-CcCCeEEE----cCccc---ccCceeEEEEEec-------------CCCceEEEecccchh
Confidence 345545 5667776655 44556777 12211 1233344445543 2 336666533 1
Q ss_pred CCchhhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHH
Q 009783 87 IPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLAN 166 (526)
Q Consensus 87 l~~~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~ 166 (526)
+......+.|+++|+++.+.|||||+|+|+..|.+ +|+ . ..+.++| |||++||++++ ..++|++
T Consensus 361 ~~~~~~~~~l~~~l~~~~~~~v~~n~K~d~~~l~~-~gi---~----~~~~~~D-t~la~yll~~~-------~~~~l~~ 424 (887)
T TIGR00593 361 LLTILTDDKFARWLLNEQIKKIGHDAKFLMHLLKR-EGI---E----LGGVIFD-TMLAAYLLDPA-------QVSTLDT 424 (887)
T ss_pred hhhHHHHHHHHHHHhCCCCcEEEeeHHHHHHHHHh-CCC---C----CCCcchh-HHHHHHHcCCC-------CCCCHHH
Confidence 12234566799999999999999999999999976 455 1 2256899 99999999985 3569999
Q ss_pred HHHHHcCCcCcccccccCCC--CCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchhhhhh
Q 009783 167 ICKELLDISLSKELQCSDWS--NRPLT-EEQKNYAAIDAHCLIEIFNIFQVKVAQKGFAAGNSCSSIS 231 (526)
Q Consensus 167 Lv~~~Lg~~L~K~~q~sdW~--~RPL~-~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~~~~~~~e~~ 231 (526)
++.+||+..+.+..+...+. ...++ +....||+.||.+++.||..|.++|+++++. .++.+++
T Consensus 425 la~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~~~~l~--~l~~~iE 490 (887)
T TIGR00593 425 LARRYLVEELILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKELDENKLL--SLYREIE 490 (887)
T ss_pred HHHHHcCcccccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHH--HHHHHHH
Confidence 99999998765433222221 12344 4457899999999999999999999877654 4455443
No 25
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=98.81 E-value=1.7e-08 Score=102.09 Aligned_cols=149 Identities=23% Similarity=0.254 Sum_probs=113.4
Q ss_pred CCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCcEEEEEe
Q 009783 32 SSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFK 111 (526)
Q Consensus 32 ~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~~~~i~KVgh~ 111 (526)
...+..+.||.+....++..+.+..+||++. ++.++|+.+.... .+...|+.+|+|++.++||.+
T Consensus 127 ~~~~~~~~e~~~~~d~~~~~P~~~~lqlcV~-------------en~C~I~ql~~~~--~IP~~LR~fl~D~~~~~vgv~ 191 (319)
T KOG4373|consen 127 PPFVCYRREAQPYLDMGRSDPPPDTLQLCVG-------------ENRCLIIQLIHCK--RIPHELRSFLEDPDHTFVGVW 191 (319)
T ss_pred CcceeecccccccccccccCCCcchhhhhhc-------------ccceeeEEeeccc--cchHHHHHhhcCCCceEEecc
Confidence 3456677788777554456678999999994 4788888665433 366788889999999999999
Q ss_pred cHHhHHHHHh-hcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcC-----CcCcccccccCC
Q 009783 112 FKQDLIYLSS-TFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLD-----ISLSKELQCSDW 185 (526)
Q Consensus 112 ~k~Dl~~L~~-~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg-----~~L~K~~q~sdW 185 (526)
.++|..+|.+ .|+. .+..+.||..+..-.++.+ ....+...|++..+| +.+++..+++||
T Consensus 192 ~d~D~~KL~r~~hql--------~I~~~~dlr~~~~d~~g~~------~~~~s~e~i~~~~~~~~~~~v~l~~~i~msdw 257 (319)
T KOG4373|consen 192 NDQDAGKLERKEHQL--------EIGELEDLRLLVNDSLGGS------MPNDSFEEIVSETLGYYGKDVRLDKEIRMSDW 257 (319)
T ss_pred ccccHHHHhhhhhcc--------cHHhhhhHHhhcchhhccC------ccCccHHHHHHHHhhccccccccChhcccccc
Confidence 9999999987 4443 2456778766665555442 234566666666655 446778899999
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHH
Q 009783 186 SNRPLTEEQKNYAAIDAHCLIEIF 209 (526)
Q Consensus 186 ~~RPL~~~qi~YAA~DA~~ll~L~ 209 (526)
+..||+.+|+.||+.|||+...++
T Consensus 258 ~~~~Ls~~Ql~~asidvy~c~~lg 281 (319)
T KOG4373|consen 258 SVYPLSDDQLLQASIDVYVCHKLG 281 (319)
T ss_pred eeeeccHHHHHHHHhHHHHHHHHH
Confidence 999999999999999999999999
No 26
>COG4634 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.58 E-value=2.1e-07 Score=79.68 Aligned_cols=73 Identities=21% Similarity=0.286 Sum_probs=60.2
Q ss_pred CEEEEecccH-HHHHHHHhcCCceecCCC---CCCChHHHHHhhhcCCcEEEecChhHHHhhccc--CCcEEEEcCCCH
Q 009783 361 PKFLCDVMVE-GLAKHLRCVGIDAATPRS---KKPEPRELIDQTSKEKRVLLTRDAKLLRHQYLI--KNQIYRVKSLLK 433 (526)
Q Consensus 361 ~kfl~D~mLg-~Lar~LR~lG~D~~~~~~---~~~~d~~ll~~A~~E~RiiLTrd~~l~~~~~~~--~~~~~~v~~~~~ 433 (526)
||+++|+.|. +||+||-..||++.+..+ .+..|-||.+.|+.++|||+|.|.+|....... ..+++.+++.+.
T Consensus 1 MkilvD~~Lp~rlad~l~~~g~e~~h~r~lg~~da~D~EI~a~A~~~~~iivTkDsDF~~la~~~G~Ppki~wLr~gNv 79 (113)
T COG4634 1 MKILVDAQLPPRLADWLPMAGIEAVHWRDLGLRDATDIEIWAYARRNNRIIVTKDSDFADLALTLGSPPKIVWLRCGNV 79 (113)
T ss_pred CcEeeecCCChHHHHHhhhcccceeeecccCcCCCccHHHHHHHHhcCcEEEEcCccHHHHHHHcCCCCeEEEEEecCC
Confidence 7999999999 899999999999988765 234578999999999999999999996543222 247888888664
No 27
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
Probab=98.55 E-value=1.5e-06 Score=79.89 Aligned_cols=118 Identities=19% Similarity=0.189 Sum_probs=78.9
Q ss_pred EEEEEeCCCCCchhhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCC
Q 009783 78 VVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKL 157 (526)
Q Consensus 78 ~v~liD~~~l~~~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~ 157 (526)
++|+|++.. .. ....|+++|+++.+.|++||.|.++..|.. +|+ . ..+.+|| ++||+||++|+
T Consensus 30 ~~~yi~~~~-~~--~~~~l~~~l~~~~~~ki~~d~K~~~~~l~~-~gi-~------l~~~~fD-~~LAaYLL~p~----- 92 (151)
T cd06128 30 VAAYIPVAH-DY--ALELLKPLLEDEKALKVGQNLKYDRVILAN-YGI-E------LRGIAFD-TMLEAYLLDPV----- 92 (151)
T ss_pred CeEEEeCCC-Cc--CHHHHHHHHcCCCCCEEeeehHHHHHHHHH-CCC-C------CCCcchh-HHHHHHHcCCC-----
Confidence 367775321 00 144588999999999999999999999976 455 1 2356799 99999999985
Q ss_pred CcCCccHHHHHHHHcCCcCcccccccCCCC--CCC-CHHHHHHHHHHHHHHHHHHHHHH
Q 009783 158 PKETKSLANICKELLDISLSKELQCSDWSN--RPL-TEEQKNYAAIDAHCLIEIFNIFQ 213 (526)
Q Consensus 158 ~~~~~gL~~Lv~~~Lg~~L~K~~q~sdW~~--RPL-~~~qi~YAA~DA~~ll~L~~~L~ 213 (526)
....+|++++++||+..+....+...+.. .++ ..+...|++..|.++.+|++.|.
T Consensus 93 -~~~~~l~~la~~yl~~~~~~~~~~~gkg~~~~~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 93 -AGRHDMDSLAERWLKEKTITFEEIAGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred -CCCCCHHHHHHHHcCCCCccHHHHcCCCCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 22159999999999887322011111110 012 12223488888889999988874
No 28
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=97.15 E-value=0.012 Score=60.95 Aligned_cols=102 Identities=14% Similarity=0.136 Sum_probs=68.4
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
+++..|..++.+. +.|+||+.+|+..|.+.+.-.+.. + ....++|...++..+ .+. ...++|++|++.
T Consensus 83 ev~~~l~~~l~~~--~lVaHNa~FD~~fL~~~~~r~g~~--~-~~~~~ldTl~lar~~-~~~------~~~~kL~~l~~~ 150 (313)
T PRK06063 83 DIAGEVAELLRGR--TLVAHNVAFDYSFLAAEAERAGAE--L-PVDQVMCTVELARRL-GLG------LPNLRLETLAAH 150 (313)
T ss_pred HHHHHHHHHcCCC--EEEEeCHHHHHHHHHHHHHHcCCC--C-CCCCEEehHHHHHHh-ccC------CCCCCHHHHHHH
Confidence 3556677777664 459999999999997654322221 1 124688943444443 332 247889999976
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 009783 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGF 221 (526)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~ 221 (526)
+|++....+ -|..||.++.+|+..+.+++.+.+.
T Consensus 151 -~gi~~~~~H----------------~Al~DA~ata~l~~~ll~~~~~~~~ 184 (313)
T PRK06063 151 -WGVPQQRPH----------------DALDDARVLAGILRPSLERARERDV 184 (313)
T ss_pred -cCCCCCCCC----------------CcHHHHHHHHHHHHHHHHHHHhcCC
Confidence 576643222 2789999999999999998887754
No 29
>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=97.11 E-value=0.0057 Score=57.08 Aligned_cols=86 Identities=20% Similarity=0.247 Sum_probs=55.9
Q ss_pred HHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcC
Q 009783 94 ELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLD 173 (526)
Q Consensus 94 ~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg 173 (526)
..|.+++.+.. +.||||+.+|+..|... ...++|+..++..+. +.. ....+++|..|++.++|
T Consensus 75 ~~~~~~i~~~~-vlVgHn~~fD~~fL~~~------------~~~~iDT~~l~~~~~-~~~---~~~~~~~L~~L~~~~~~ 137 (161)
T cd06137 75 AALWKFIDPDT-ILVGHSLQNDLDALRMI------------HTRVVDTAILTREAV-KGP---LAKRQWSLRTLCRDFLG 137 (161)
T ss_pred HHHHHhcCCCc-EEEeccHHHHHHHHhCc------------CCCeeEehhhhhhcc-CCC---cCCCCccHHHHHHHHCC
Confidence 45566666533 45999999999999652 135789555555443 320 00147999999999999
Q ss_pred CcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009783 174 ISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (526)
Q Consensus 174 ~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~ 209 (526)
+++.......+ |..||.++.+||
T Consensus 138 ~~~~~~~~~H~-------------A~~DA~at~~l~ 160 (161)
T cd06137 138 LKIQGGGEGHD-------------SLEDALAAREVV 160 (161)
T ss_pred chhcCCCCCCC-------------cHHHHHHHHHHh
Confidence 87743111122 678898888776
No 30
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=96.99 E-value=0.0052 Score=57.20 Aligned_cols=89 Identities=17% Similarity=0.173 Sum_probs=56.2
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHH--HHHh-hccccCCCCCcCCccHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSI--YNHL-HHKQLGRKLPKETKSLANI 167 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~L--a~yL-l~~~~~~~~~~~~~gL~~L 167 (526)
++...|.+++.+. +-||||+++|+..|...+. ...+.|+..+ +... ..+. ...++|..|
T Consensus 66 ~v~~~l~~~l~~~--vlV~Hn~~~D~~~l~~~~~----------~~~~~Dt~~l~~~~~~~~~p~------~~~~~L~~L 127 (157)
T cd06149 66 VAQKEILKILKGK--VVVGHAIHNDFKALKYFHP----------KHMTRDTSTIPLLNRKAGFPE------NCRVSLKVL 127 (157)
T ss_pred HHHHHHHHHcCCC--EEEEeCcHHHHHHhcccCC----------CcCEEECcccccchhhcCCcc------cCChhHHHH
Confidence 4566677777653 4599999999998865311 1356783222 2111 1221 246899999
Q ss_pred HHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009783 168 CKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (526)
Q Consensus 168 v~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~ 210 (526)
+++++|..+....+..+ |..||.++.+||+
T Consensus 128 ~~~~~~~~i~~~~~~H~-------------Al~DA~at~~l~~ 157 (157)
T cd06149 128 AKRLLHRDIQVGRQGHS-------------SVEDARATMELYK 157 (157)
T ss_pred HHHHcChhhcCCCCCcC-------------cHHHHHHHHHHhC
Confidence 99999876654222122 6789999988873
No 31
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=96.93 E-value=0.065 Score=53.17 Aligned_cols=90 Identities=16% Similarity=0.252 Sum_probs=57.8
Q ss_pred cEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcccccccC
Q 009783 105 ILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSD 184 (526)
Q Consensus 105 i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~K~~q~sd 184 (526)
...|+||..+|+..|.+.+.-.|..+ + ...+++| +......+.+. ....++|++|++. +|++....+.
T Consensus 94 ~~lVahNa~FD~~fL~~~~~r~~~~~-~-~~~~~iD-t~~l~~~~~~~-----~~~~~~L~~l~~~-~gi~~~~aH~--- 161 (232)
T PRK07942 94 VPVVVFNAPYDLTVLDRELRRHGLPS-L-VPGPVID-PYVIDKAVDRY-----RKGKRTLTALCEH-YGVRLDNAHE--- 161 (232)
T ss_pred CEEEEeCcHhhHHHHHHHHHHcCCCC-c-cCCcEee-HHHHHhhhhcc-----cCCCCCHHHHHHH-cCCCCCCCCC---
Confidence 34599999999998865533222111 0 1246889 55444333321 0135789999977 5876643332
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 009783 185 WSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (526)
Q Consensus 185 W~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~ 219 (526)
|..||.++.+|+..|.++..+-
T Consensus 162 -------------Al~Da~ata~l~~~l~~~~~~l 183 (232)
T PRK07942 162 -------------ATADALAAARVAWALARRFPEL 183 (232)
T ss_pred -------------hHHHHHHHHHHHHHHHHHHHHh
Confidence 8899999999999998766543
No 32
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=96.83 E-value=0.045 Score=54.97 Aligned_cols=150 Identities=19% Similarity=0.214 Sum_probs=86.0
Q ss_pred hcCCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-----------CCc--------
Q 009783 29 LSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-----------IPL-------- 89 (526)
Q Consensus 29 L~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~-----------l~~-------- 89 (526)
++....|.||+|+++..+ .+-.+||||.-. .+.+ .. .+.-..++.+.. +..
T Consensus 4 l~~~~~v~~D~ETTGl~~-----~~d~IIEIa~v~-v~~~--~~--~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~ 73 (250)
T PRK06310 4 LKDTEFVCLDCETTGLDV-----KKDRIIEFAAIR-FTFD--EV--IDSVEFLINPERVVSAESQRIHHISDAMLRDKPK 73 (250)
T ss_pred ccCCcEEEEEEeCCCCCC-----CCCeEEEEEEEE-EECC--eE--EEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCC
Confidence 345689999999988764 223477775421 0000 00 001223344321 110
Q ss_pred -hhhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCC-CCceeeHHHHHHHhhccccCCCCCcCCccHHHH
Q 009783 90 -PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDR-VEPYLDITSIYNHLHHKQLGRKLPKETKSLANI 167 (526)
Q Consensus 90 -~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~-~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L 167 (526)
.++...+.+++.+.. ..||||+.+|...|...+.-.|.. +.. -..++|+..++. .... ...++|+.|
T Consensus 74 ~~ev~~~~~~fl~~~~-~lvghn~~FD~~~L~~~~~r~g~~--~~~~~~~~iDtl~lar-~~~~-------~~~~~L~~l 142 (250)
T PRK06310 74 IAEVFPQIKGFFKEGD-YIVGHSVGFDLQVLSQESERIGET--FLSKHYYIIDTLRLAK-EYGD-------SPNNSLEAL 142 (250)
T ss_pred HHHHHHHHHHHhCCCC-EEEEECHHHHHHHHHHHHHHcCCC--ccccCCcEEehHHHHH-hccc-------CCCCCHHHH
Confidence 134456667776544 459999999999987643222221 111 146899444443 3322 236899999
Q ss_pred HHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 168 CKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKV 216 (526)
Q Consensus 168 v~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L 216 (526)
++.+ |+++...+ =|..||.++.+|+..+.+++
T Consensus 143 ~~~~-g~~~~~aH----------------~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 143 AVHF-NVPYDGNH----------------RAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred HHHC-CCCCCCCc----------------ChHHHHHHHHHHHHHHHHhc
Confidence 8775 76654322 28899999999999987644
No 33
>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=96.74 E-value=0.055 Score=50.27 Aligned_cols=95 Identities=18% Similarity=0.215 Sum_probs=58.3
Q ss_pred hHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHH-HHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITS-IYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 92 ~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~-La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
+...|.+++.+.. .||||..+|+..|.+.+.-.++.+.+.....++| |+ ++.. ..+. ..++|+++++.
T Consensus 71 v~~~l~~~l~~~~--lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~id-t~~~~~~-~~~~-------~~~~L~~l~~~ 139 (167)
T cd06131 71 IADEFLDFIRGAE--LVIHNASFDVGFLNAELSLLGLGKKIIDFCRVID-TLALARK-KFPG-------KPNSLDALCKR 139 (167)
T ss_pred HHHHHHHHHCCCe--EEEeChHHhHHHHHHHHHHhCCCcccccCCCceE-hHHHHHH-HcCC-------CCCCHHHHHHH
Confidence 4556667776643 4999999999988654322222111112246799 55 4443 3332 35799999988
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009783 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (526)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L 212 (526)
+ |++.... +..-|..||.++.+|+..|
T Consensus 140 ~-~i~~~~~--------------~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 140 F-GIDNSHR--------------TLHGALLDAELLAEVYLEL 166 (167)
T ss_pred C-CCCCCCC--------------CCCChHHHHHHHHHHHHHh
Confidence 5 6554211 0123889999999988765
No 34
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=96.73 E-value=0.085 Score=52.30 Aligned_cols=145 Identities=12% Similarity=0.109 Sum_probs=85.1
Q ss_pred CeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-----------CCc---------hhh
Q 009783 33 SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-----------IPL---------PSI 92 (526)
Q Consensus 33 ~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~-----------l~~---------~~~ 92 (526)
..+.||+|+++..+ .+-.+|+|+.-+ . ...+.-..++.+.. +.. .++
T Consensus 3 ~~vv~D~ETTGl~~-----~~d~IIeig~v~-~-------~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev 69 (232)
T PRK06309 3 ALIFYDTETTGTQI-----DKDRIIEIAAYN-G-------VTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEA 69 (232)
T ss_pred cEEEEEeeCCCCCC-----CCCEEEEEEEEc-C-------ccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHH
Confidence 46899999998764 223578886531 0 00012223444321 111 123
Q ss_pred HHHHHHhhCCCCcEEEEEec-HHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHH
Q 009783 93 WELLKELFVSPDILKLGFKF-KQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKEL 171 (526)
Q Consensus 93 ~~~L~~lL~~~~i~KVgh~~-k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~ 171 (526)
...+.+++.+. ...||||. ..|+..|.+.+.-.|+.. .....+|+..++..+ .++ ...++|..+++.+
T Consensus 70 ~~~~~~fi~~~-~~lVaHN~~~FD~~~L~~e~~r~g~~~---~~~~~iDt~~l~~~~-~~~------~~~~~L~~l~~~~ 138 (232)
T PRK06309 70 YQKFIEFCGTD-NILVAHNNDAFDFPLLRKECRRHGLEP---PTLRTIDSLKWAQKY-RPD------LPKHNLQYLRQVY 138 (232)
T ss_pred HHHHHHHHcCC-CEEEEeCCHHHHHHHHHHHHHHcCCCC---CCCcEEeHHHHHHHH-cCC------CCCCCHHHHHHHc
Confidence 44555666543 34599994 899999875532223221 124689955555544 232 2367899998776
Q ss_pred cCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 009783 172 LDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ 218 (526)
Q Consensus 172 Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~ 218 (526)
|++....+ -|..||.++.+|+..+..++..
T Consensus 139 -~~~~~~aH----------------~Al~Da~~t~~vl~~l~~~~~~ 168 (232)
T PRK06309 139 -GFEENQAH----------------RALDDVITLHRVFSALVGDLSP 168 (232)
T ss_pred -CCCCCCCC----------------CcHHHHHHHHHHHHHHHHHHHH
Confidence 66543322 2789999999999999877643
No 35
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=96.72 E-value=0.013 Score=58.40 Aligned_cols=95 Identities=22% Similarity=0.222 Sum_probs=64.1
Q ss_pred HHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHc
Q 009783 93 WELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELL 172 (526)
Q Consensus 93 ~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~L 172 (526)
-..+.++|.+. +.|||++++|+..|.-.++- .-+-| |.-+.-|... .....+.||..|++.+|
T Consensus 175 Q~ev~klL~gR--IlVGHaLhnDl~~L~l~hp~----------s~iRD-Ts~~~pl~k~----~~~~~tpSLK~Lt~~~L 237 (280)
T KOG2249|consen 175 QKEVLKLLKGR--ILVGHALHNDLQALKLEHPR----------SMIRD-TSKYPPLMKL----LSKKATPSLKKLTEALL 237 (280)
T ss_pred HHHHHHHHhCC--EEeccccccHHHHHhhhCch----------hhhcc-cccCchHHHH----hhccCCccHHHHHHHHh
Confidence 34566788774 34999999999999765433 22346 4322111110 00135789999999999
Q ss_pred CCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 009783 173 DISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (526)
Q Consensus 173 g~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~ 219 (526)
|+.+--++..| .+||.++.+||.....+-++.
T Consensus 238 g~~IQ~GeHsS---------------vEDA~AtM~LY~~vk~qwe~~ 269 (280)
T KOG2249|consen 238 GKDIQVGEHSS---------------VEDARATMELYKRVKVQWEKI 269 (280)
T ss_pred chhhhccccCc---------------HHHHHHHHHHHHHHHHHHHHH
Confidence 99886555433 589999999999998766554
No 36
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=96.72 E-value=0.08 Score=53.45 Aligned_cols=98 Identities=16% Similarity=0.181 Sum_probs=65.3
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
+++..+..++.+. +.|+||+..|...|.+.+.-.|..+ .....+|...++..+... ..++|+.|++
T Consensus 136 evl~~f~~fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~---~~~~~ldtl~la~~~~~~--------~~~~L~~L~~- 201 (257)
T PRK08517 136 EVLEEFRLFLGDS--VFVAHNVNFDYNFISRSLEEIGLGP---LLNRKLCTIDLAKRTIES--------PRYGLSFLKE- 201 (257)
T ss_pred HHHHHHHHHHCCC--eEEEECHHHHHHHHHHHHHHcCCCC---CCCCcEehHHHHHHHccC--------CCCCHHHHHH-
Confidence 3556677777764 4599999999999865432222211 124578855566554432 4689999987
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 009783 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ 218 (526)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~ 218 (526)
++|++....+ -|..||.++.+|+..+..++..
T Consensus 202 ~lgi~~~~~H----------------rAl~DA~ata~ll~~ll~~~~~ 233 (257)
T PRK08517 202 LLGIEIEVHH----------------RAYADALAAYEIFKICLLNLPS 233 (257)
T ss_pred HcCcCCCCCC----------------ChHHHHHHHHHHHHHHHHHhHH
Confidence 4687654322 2788999999999999877643
No 37
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=96.67 E-value=0.05 Score=56.48 Aligned_cols=96 Identities=14% Similarity=0.129 Sum_probs=64.4
Q ss_pred hHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHH
Q 009783 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKEL 171 (526)
Q Consensus 92 ~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~ 171 (526)
++..|.+++.+..+ ||||+.+|+..|.+.+...|+.. ....++|+..++..+.. . ...++|+.|++.
T Consensus 78 vl~~f~~fl~~~~l--VaHNa~FD~~fL~~~~~~~gl~~---~~~~~iDtl~la~~~~~-~------~~~~kL~~L~~~- 144 (313)
T PRK06807 78 VLPLFLAFLHTNVI--VAHNASFDMRFLKSNVNMLGLPE---PKNKVIDTVFLAKKYMK-H------APNHKLETLKRM- 144 (313)
T ss_pred HHHHHHHHHcCCeE--EEEcHHHHHHHHHHHHHHcCCCC---CCCCEeeHHHHHHHHhC-C------CCCCCHHHHHHH-
Confidence 45556666765433 99999999999976543333211 13568996666665543 2 246799999855
Q ss_pred cCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 172 LDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (526)
Q Consensus 172 Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~ 217 (526)
+|++. +.+ =|-.||.++.+|+..+.....
T Consensus 145 lgi~~-~~H----------------~Al~DA~~ta~l~~~l~~~~~ 173 (313)
T PRK06807 145 LGIRL-SSH----------------NAFDDCITCAAVYQKCASIEE 173 (313)
T ss_pred cCCCC-CCc----------------ChHHHHHHHHHHHHHHHHhhh
Confidence 67665 222 277899999999999987653
No 38
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=96.67 E-value=0.035 Score=67.02 Aligned_cols=103 Identities=22% Similarity=0.424 Sum_probs=72.0
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
+++..+..++.+. +.|+||+.+|+..|...+.-.|..+ ....++|+..++.. +.+. ...++|++|+.+
T Consensus 259 evl~~f~~fl~~~--iLVaHNa~FD~~fL~~~~~r~g~~~---~~~~~IDTl~lar~-l~p~------~k~~kL~~Lak~ 326 (1213)
T TIGR01405 259 EVLEKFKEFFKDS--ILVAHNASFDIGFLNTNFEKVGLEP---LENPVIDTLELARA-LNPE------YKSHRLGNICKK 326 (1213)
T ss_pred HHHHHHHHHhCCC--eEEEEChHHHHHHHHHHHHHcCCCc---cCCCEeEHHHHHHH-Hhcc------CCCCCHHHHHHH
Confidence 4566677777763 4599999999999875432223221 13578995445544 4443 357899999987
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009783 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGFA 222 (526)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~ 222 (526)
+|+++... +.|..||.++.+|+..+.+++++.|..
T Consensus 327 -lgi~~~~~----------------HrAl~DA~aTa~I~~~ll~~l~~~~i~ 361 (1213)
T TIGR01405 327 -LGVDLDDH----------------HRADYDAEATAKVFKVMVEQLKEKGIT 361 (1213)
T ss_pred -cCCCCCCC----------------cCHHHHHHHHHHHHHHHHHHHHHcCCc
Confidence 48765421 348899999999999999999887644
No 39
>PRK07883 hypothetical protein; Validated
Probab=96.60 E-value=0.057 Score=60.39 Aligned_cols=161 Identities=12% Similarity=0.136 Sum_probs=96.0
Q ss_pred HHHHhcCCCeEEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-----------CCc----
Q 009783 25 LARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-----------IPL---- 89 (526)
Q Consensus 25 ~~~~L~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~-----------l~~---- 89 (526)
+-..+.....|.||+|+++..+ ..-.+|+|+.-. -+.|- .. +.-..++++.. +..
T Consensus 8 ~~~~~~~~~~Vv~D~ETTGl~p-----~~~~IIEIgaV~-v~~g~--iv--~~f~~lV~P~~~i~~~~~~itGIt~e~l~ 77 (557)
T PRK07883 8 LGTPLRDVTFVVVDLETTGGSP-----AGDAITEIGAVK-VRGGE--VL--GEFATLVNPGRPIPPFITVLTGITTAMVA 77 (557)
T ss_pred hCCCCcCCCEEEEEEecCCCCC-----CCCeEEEEEEEE-EECCE--EE--EEEEEEECCCCCCChhHHhhcCCCHHHHh
Confidence 3344566789999999998764 223567765420 00000 00 00112333211 111
Q ss_pred -----hhhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccH
Q 009783 90 -----PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSL 164 (526)
Q Consensus 90 -----~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL 164 (526)
.+++..|..++.+ -+.|+||..+|+..|...+.-.|+.. .....+|+..++..+..+. ....++|
T Consensus 78 ~ap~~~evl~~f~~fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~~---~~~~~iDTl~lar~l~~~~-----~~~~~~L 147 (557)
T PRK07883 78 GAPPIEEVLPAFLEFARG--AVLVAHNAPFDIGFLRAAAARCGYPW---PGPPVLCTVRLARRVLPRD-----EAPNVRL 147 (557)
T ss_pred CCCCHHHHHHHHHHHhcC--CEEEEeCcHHHHHHHHHHHHHcCCCC---CCCCcEecHHHHHHhcccC-----CCCCCCH
Confidence 1345566667765 34589999999999876543333221 1245789555666655321 0247899
Q ss_pred HHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009783 165 ANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGFA 222 (526)
Q Consensus 165 ~~Lv~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~ 222 (526)
++|++ ++|++....+ -|..||.++.+|+..+..++.+.|..
T Consensus 148 ~~L~~-~~gi~~~~~H----------------~Al~DA~ata~l~~~l~~~~~~~~~~ 188 (557)
T PRK07883 148 STLAR-LFGATTTPTH----------------RALDDARATVDVLHGLIERLGNLGVH 188 (557)
T ss_pred HHHHH-HCCcccCCCC----------------CHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 99987 5687754322 28899999999999999999876654
No 40
>PRK07740 hypothetical protein; Provisional
Probab=96.60 E-value=0.11 Score=51.94 Aligned_cols=101 Identities=13% Similarity=0.184 Sum_probs=66.6
Q ss_pred hHHHHHHhhCCCCcEEEEEecHHhHHHHHhhc-ccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTF-CSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 92 ~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~-gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
++..|..++.+. ..||||+..|...|...+ ...+. .....++|+..++..+ .+. ...++|++++..
T Consensus 131 vl~~f~~fi~~~--~lVahna~fD~~fL~~~~~~~~~~----~~~~~~iDt~~l~r~l-~~~------~~~~sL~~l~~~ 197 (244)
T PRK07740 131 VLHRFYAFIGAG--VLVAHHAGHDKAFLRHALWRTYRQ----PFTHRLIDTMFLTKLL-AHE------RDFPTLDDALAY 197 (244)
T ss_pred HHHHHHHHhCCC--EEEEeCHHHHHHHHHHHHHHhcCC----CcCCCeechHHHHHHH-cCC------CCCCCHHHHHHH
Confidence 444555566553 458999999998886431 11111 1235789955555444 332 247899999965
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009783 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGFA 222 (526)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~ 222 (526)
+|++....+. |..||.++.+|+..+..++.+.|..
T Consensus 198 -~gi~~~~~H~----------------Al~Da~ata~l~~~ll~~~~~~~~~ 232 (244)
T PRK07740 198 -YGIPIPRRHH----------------ALGDALMTAKLWAILLVEAQQRGIT 232 (244)
T ss_pred -CCcCCCCCCC----------------cHHHHHHHHHHHHHHHHHHHHcCCc
Confidence 6877643221 7789999999999999998876643
No 41
>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=96.59 E-value=0.0085 Score=55.35 Aligned_cols=86 Identities=24% Similarity=0.360 Sum_probs=56.8
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
+++..|..++.+ .+ -||||+.+|+..|... . ....++| |........+. +..+++|+.|++.
T Consensus 66 ~~~~~l~~~l~~-~v-lVgHn~~fD~~~L~~~--~--------~~~~~~d-t~~l~~~~~~~-----~~~~~sL~~l~~~ 127 (152)
T cd06144 66 EVQKKVAELLKG-RI-LVGHALKNDLKVLKLD--H--------PKKLIRD-TSKYKPLRKTA-----KGKSPSLKKLAKQ 127 (152)
T ss_pred HHHHHHHHHhCC-CE-EEEcCcHHHHHHhcCc--C--------CCccEEE-eEEeecccccc-----CCCChhHHHHHHH
Confidence 456677788876 44 4999999999998642 1 0135778 44322222210 0257899999999
Q ss_pred HcCCcCcc-cccccCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009783 171 LLDISLSK-ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (526)
Q Consensus 171 ~Lg~~L~K-~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~ 210 (526)
++|+++.. .+ -|..||.++.+||+
T Consensus 128 ~lgi~~~~~~H----------------~Al~DA~at~~l~~ 152 (152)
T cd06144 128 LLGLDIQEGEH----------------SSVEDARAAMRLYR 152 (152)
T ss_pred HcCcccCCCCc----------------CcHHHHHHHHHHhC
Confidence 99987642 22 17789999988873
No 42
>PRK05168 ribonuclease T; Provisional
Probab=96.51 E-value=0.2 Score=48.97 Aligned_cols=93 Identities=16% Similarity=0.152 Sum_probs=60.0
Q ss_pred CcEEEEEecHHhHHHHHhhcccCCCcc-CcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcccccc
Q 009783 104 DILKLGFKFKQDLIYLSSTFCSQGCDI-GFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQC 182 (526)
Q Consensus 104 ~i~KVgh~~k~Dl~~L~~~~gi~~~~~-~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~K~~q~ 182 (526)
+.+.||||+.+|+..|.+.+.-.++.. .+ ....++|+..++..+. + ..+|..+++. +|+++.... .
T Consensus 114 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~-~~~~~iDt~~lar~~~-~---------~~~L~~l~~~-~gl~~~~~~-~ 180 (211)
T PRK05168 114 RAILVAHNAHFDLSFLMAAAERAGLKRNPF-HPFSTFDTATLSGLAL-G---------QTVLAKACQA-AGIEFDNKE-A 180 (211)
T ss_pred CceEEEeccHHhHHHHHHHHHHhCCCCCCC-CCCcEeeHHHHHHHHc-C---------CCCHHHHHHH-CCCCCCCCC-C
Confidence 456799999999998875432222110 00 0124899555655442 2 3579999887 476653111 1
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009783 183 SDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGFA 222 (526)
Q Consensus 183 sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~ 222 (526)
.-|..||.++.+|+..|..++.+.|.+
T Consensus 181 -------------H~Al~DA~ata~l~~~l~~~~~~~~~~ 207 (211)
T PRK05168 181 -------------HSALYDTEKTAELFCEIVNRWKRLGGW 207 (211)
T ss_pred -------------CChHHHHHHHHHHHHHHHHHHHHccCC
Confidence 128899999999999999999877644
No 43
>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=96.49 E-value=0.067 Score=51.52 Aligned_cols=113 Identities=19% Similarity=0.262 Sum_probs=70.4
Q ss_pred hhHHHHHHhhCC--CCcEEEEEecH-HhHHHHHhhcccCCCccCcCC-------------------CCceeeHHHHHHHh
Q 009783 91 SIWELLKELFVS--PDILKLGFKFK-QDLIYLSSTFCSQGCDIGFDR-------------------VEPYLDITSIYNHL 148 (526)
Q Consensus 91 ~~~~~L~~lL~~--~~i~KVgh~~k-~Dl~~L~~~~gi~~~~~~~~~-------------------~~~~~Dlt~La~yL 148 (526)
+++..+..++.. |++ .+|||.. +|+..|....-.+|+...+.. -...+|+-.++...
T Consensus 58 ~lL~~F~~~i~~~dpdi-ivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~ 136 (195)
T cd05780 58 EMIKRFIEIVKEKDPDV-IYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRT 136 (195)
T ss_pred HHHHHHHHHHHHcCCCE-EEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhh
Confidence 455555566655 775 4999976 599998654332333211100 12377865555433
Q ss_pred hccccCCCCCcCCccHHHHHHHHcCCcCcc--cccccC-CCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009783 149 HHKQLGRKLPKETKSLANICKELLDISLSK--ELQCSD-WSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (526)
Q Consensus 149 l~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~K--~~q~sd-W~~RPL~~~qi~YAA~DA~~ll~L~~~L 212 (526)
.. ..+++|+.+++++||.+... ..+... |...+-...-++|+..||..+++|.+.|
T Consensus 137 ~~--------l~sy~L~~v~~~~Lg~~k~d~~~~~i~~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 137 LN--------LTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred CC--------CCcCcHHHHHHHHhCCCCCcCCHHHHHHHHhCCCchHHHHHHhHHHHHHHHHHHhhC
Confidence 22 35899999999999986432 123332 4444344667899999999999998753
No 44
>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=96.48 E-value=0.0084 Score=56.77 Aligned_cols=80 Identities=20% Similarity=0.225 Sum_probs=54.2
Q ss_pred HHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCC
Q 009783 95 LLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDI 174 (526)
Q Consensus 95 ~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~ 174 (526)
.|..++ +++.+-|||++.+|+.+|.-.++. ..+.| |.+.-. .+. ....+|..|++++||.
T Consensus 94 ~l~~li-~~~tILVGHsL~nDL~aL~l~hp~----------~~viD-Ta~l~~--~~~------~r~~sLk~La~~~L~~ 153 (174)
T cd06143 94 KLRLLV-DLGCIFVGHGLAKDFRVINIQVPK----------EQVID-TVELFH--LPG------QRKLSLRFLAWYLLGE 153 (174)
T ss_pred HHHHHc-CCCCEEEeccchhHHHHhcCcCCC----------cceEE-cHHhcc--CCC------CCChhHHHHHHHHcCC
Confidence 455555 445566999999999998653221 46889 543211 121 1368999999999999
Q ss_pred cCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009783 175 SLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (526)
Q Consensus 175 ~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~ 209 (526)
.+..+. .| ..+||.+.++||
T Consensus 154 ~IQ~~~--Hd-------------SvEDArAam~Ly 173 (174)
T cd06143 154 KIQSET--HD-------------SIEDARTALKLY 173 (174)
T ss_pred cccCCC--cC-------------cHHHHHHHHHHh
Confidence 885421 11 468999999988
No 45
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.46 E-value=0.098 Score=52.27 Aligned_cols=98 Identities=16% Similarity=0.211 Sum_probs=60.3
Q ss_pred hHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCc-cCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCD-IGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 92 ~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~-~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
++..+.+++.+.. .|+||+.+|+..|.+.+.-+|.. +.+.....++|+..++.++ .++ ...+|+.|+++
T Consensus 76 v~~~f~~fi~~~~--lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~-~p~-------~~~~L~aL~~~ 145 (240)
T PRK05711 76 VADEFLDFIRGAE--LIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRM-FPG-------KRNSLDALCKR 145 (240)
T ss_pred HHHHHHHHhCCCE--EEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHH-cCC-------CCCCHHHHHHH
Confidence 4555666776644 48999999999887543222210 1111124589944444444 443 45799999987
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (526)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~ 214 (526)
| |++.... + ..-|..||.++.+||..|..
T Consensus 146 ~-gi~~~~r-~-------------~H~AL~DA~~~A~v~~~l~~ 174 (240)
T PRK05711 146 Y-GIDNSHR-T-------------LHGALLDAEILAEVYLAMTG 174 (240)
T ss_pred C-CCCCCCC-C-------------CCCHHHHHHHHHHHHHHHHC
Confidence 5 6543211 1 12288999999999988864
No 46
>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=96.46 E-value=0.15 Score=49.30 Aligned_cols=92 Identities=15% Similarity=0.119 Sum_probs=59.1
Q ss_pred cEEEEEecHHhHHHHHhhcccCCCccCcC-CCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCccccccc
Q 009783 105 ILKLGFKFKQDLIYLSSTFCSQGCDIGFD-RVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCS 183 (526)
Q Consensus 105 i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~-~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~K~~q~s 183 (526)
-..||||+..|+..|...+.-.+... .. ....++|+..++..+ .+ ..+|+.+++. +|++...
T Consensus 106 ~~lVaHNa~FD~~fL~~~~~r~~~~~-~~~~~~~~lDTl~lar~~-~~---------~~~L~~l~~~-~gi~~~~----- 168 (200)
T TIGR01298 106 AILVGHNANFDLGFLNAAVERTSLKR-NPFHPFSTFDTATLAGLA-YG---------QTVLAKACQA-AGXDFDS----- 168 (200)
T ss_pred CEEEEECchhhHHHHHHHHHHhCCCC-CCCCCCcEEEHHHHHHHH-cC---------cccHHHHHHH-cCCCccc-----
Confidence 45699999999999875431112110 00 013479955555433 32 3579999986 4665421
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009783 184 DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGFA 222 (526)
Q Consensus 184 dW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~ 222 (526)
.+..-|..||.++.+|+..+..++.+.|.+
T Consensus 169 ---------~~~H~Al~Da~ata~lf~~l~~~~~~~~~~ 198 (200)
T TIGR01298 169 ---------TQAHSALYDTEKTAELFCEIVNRWKRLGGW 198 (200)
T ss_pred ---------cchhhhHHhHHHHHHHHHHHHHHHHHccCC
Confidence 123348899999999999999999887654
No 47
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=96.44 E-value=0.14 Score=47.21 Aligned_cols=98 Identities=17% Similarity=0.185 Sum_probs=63.0
Q ss_pred hhHHHHHHhhCCCCcEEEEEec-HHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKF-KQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~-k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~ 169 (526)
++...|..++.+.. .|+|+. ++|+..|...+...++. +......+|+..++..+ .+. ...+|+++++
T Consensus 69 ~~~~~~~~~l~~~~--~v~~n~~~fD~~~L~~~~~~~~~~--~~~~~~~iD~~~~~~~~-~~~-------~~~~L~~l~~ 136 (169)
T smart00479 69 EVLEELLEFLKGKI--LVAGNALNFDLRFLKLEHPRLGIK--DPPKNPVIDTLKLARAL-NPG-------RKYSLKKLAE 136 (169)
T ss_pred HHHHHHHHHhcCCE--EEEeCCHHHhHHHHHHHHHHhCCC--CCcCCCeeEHHHHHHHH-CCC-------CCCCHHHHHH
Confidence 45667777887643 367777 99999987654332321 11124479954554433 332 3789999998
Q ss_pred HHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKV 216 (526)
Q Consensus 170 ~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L 216 (526)
.+ |++.... ...|..||..+.+|+..+.+++
T Consensus 137 ~~-~~~~~~~---------------~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 137 RL-GLEVIGR---------------AHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred HC-CCCCCCC---------------CcCcHHHHHHHHHHHHHHHHHh
Confidence 76 4433211 2448899999999999998754
No 48
>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=96.31 E-value=0.078 Score=51.95 Aligned_cols=104 Identities=17% Similarity=0.192 Sum_probs=63.8
Q ss_pred hHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHH
Q 009783 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKEL 171 (526)
Q Consensus 92 ~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~ 171 (526)
++..|..++.+. ..||||+.+|+..|.+.+.-.+.. ......++|+..++..+. +. .+..+.+|..+++.+
T Consensus 77 v~~~~~~~~~~~--~lVaHNa~FD~~fL~~~~~r~~~~--~~~~~~~~dtl~l~~~~~-~~----~~~~~~~L~~l~~~~ 147 (217)
T TIGR00573 77 IAEDFADYIRGA--ELVIHNASFDVGFLNYEFSKLYKV--EPKTNDVIDTTDTLQYAR-PE----FPGKRNTLDALCKRY 147 (217)
T ss_pred HHHHHHHHhCCC--EEEEeccHHHHHHHHHHHHHhcCC--CCCccceecHHHHHHHHH-Hh----CCCCCCCHHHHHHHc
Confidence 455666777653 348999999999998664311110 011246789444555443 21 112457899998775
Q ss_pred cCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 009783 172 LDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (526)
Q Consensus 172 Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~ 219 (526)
|++.... .. .=|..||.++.+|+..+..+..+.
T Consensus 148 -gl~~~~~-~~-------------H~Al~DA~~ta~l~~~l~~~~~~~ 180 (217)
T TIGR00573 148 -EITNSHR-AL-------------HGALADAFILAKLYLVMTGKQTKY 180 (217)
T ss_pred -CCCCCCc-cc-------------CCHHHHHHHHHHHHHHHHhcchhh
Confidence 6543200 11 128899999999999998765443
No 49
>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=96.23 E-value=0.029 Score=47.75 Aligned_cols=82 Identities=17% Similarity=0.228 Sum_probs=55.6
Q ss_pred EEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCC-cEEEEEecH
Q 009783 35 VGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPD-ILKLGFKFK 113 (526)
Q Consensus 35 Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~~~~-i~KVgh~~k 113 (526)
+++|+|+.+..+ +.+++.++|++... ++..|++| +.+++.+.. ..+|+||..
T Consensus 1 ~~~DiEt~~~~~---~~~~i~~i~~~~~~------------~~~~~~~~------------f~~~l~~~~~~v~V~hn~~ 53 (96)
T cd06125 1 IAIDTEATGLDG---AVHEIIEIALADVN------------PEDTAVID------------LKDILRDKPLAILVGHNGS 53 (96)
T ss_pred CEEEEECCCCCC---CCCcEEEEEEEEcc------------CCCEEEeh------------HHHHHhhCCCCEEEEeCcH
Confidence 479999988764 67889999998741 24567766 556777665 678999999
Q ss_pred HhHHHHHhhcccCCCccCcCCCCceeeHHHHH
Q 009783 114 QDLIYLSSTFCSQGCDIGFDRVEPYLDITSIY 145 (526)
Q Consensus 114 ~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La 145 (526)
.|+..|.+.+...+....+ ...+.+| |+.+
T Consensus 54 fD~~fL~~~~~~~~~~~p~-~~~~~lD-T~~l 83 (96)
T cd06125 54 FDLPFLNNRCAELGLKYPL-LAGSWID-TIKL 83 (96)
T ss_pred HhHHHHHHHHHHcCCCCCC-cCCcEEE-ehHH
Confidence 9998887654433322100 1356889 5544
No 50
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=96.21 E-value=0.23 Score=48.00 Aligned_cols=99 Identities=17% Similarity=0.199 Sum_probs=60.3
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhccc-CCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCS-QGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi-~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~ 169 (526)
+++..+..++.+. ..||||..+|+..|.+.+.- .+. ......+|+..++......... .....++|+++++
T Consensus 100 ~vl~~~~~~i~~~--~lv~hn~~fD~~fL~~~~~~~~~~----~~~~~~id~~~l~~~~~~~~~~--~~~~~~~L~~l~~ 171 (202)
T PRK09145 100 EALRQLLAFIGNR--PLVGYYLEFDVAMLNRYVRPLLGI----PLPNPLIEVSALYYDKKERHLP--DAYIDLRFDAILK 171 (202)
T ss_pred HHHHHHHHHHcCC--eEEEeCHHHHHHHHHHHHHHhcCC----CCCCCeeeHHHHHHHHhhccCC--CcccCCCHHHHHH
Confidence 3455666777764 35999999999998754210 111 1125678955554322211100 0123579999996
Q ss_pred HHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (526)
Q Consensus 170 ~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~ 214 (526)
. +|++....+. |..||.++.+||..|..
T Consensus 172 ~-~gi~~~~~H~----------------Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 172 H-LDLPVLGRHD----------------ALNDAIMAALIFLRLRK 199 (202)
T ss_pred H-cCCCCCCCCC----------------cHHHHHHHHHHHHHHHh
Confidence 6 4776533222 78899999999988853
No 51
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=96.16 E-value=0.23 Score=49.60 Aligned_cols=103 Identities=17% Similarity=0.117 Sum_probs=62.5
Q ss_pred hHHHHHHhhCCCCcEEEEEecHHhHHHHHhhccc-CCCccCcCCCCceeeHHHHHHHhhccccCC------CCCcCCccH
Q 009783 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTFCS-QGCDIGFDRVEPYLDITSIYNHLHHKQLGR------KLPKETKSL 164 (526)
Q Consensus 92 ~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi-~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~------~~~~~~~gL 164 (526)
++..|.+++.+. +-|+||...|...|.+.+.- .+. .....++|...++..+.....+. ......++|
T Consensus 119 vl~~l~~~~~~~--~lVaHna~FD~~fL~~~l~~~~~~----~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L 192 (239)
T PRK09146 119 ILDELLEALAGK--VVVVHYRRIERDFLDQALRNRIGE----GIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRL 192 (239)
T ss_pred HHHHHHHHhCCC--EEEEECHHHHHHHHHHHHHHhcCC----CCCCceechHHHHHHHcccccccccchhccCCCCCCCH
Confidence 445555566553 45899999999998654211 010 11256899666666654321000 001146789
Q ss_pred HHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 165 ANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (526)
Q Consensus 165 ~~Lv~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~ 217 (526)
+++++. +|++....+ -|..||.++.+|+..+..+.-
T Consensus 193 ~~l~~~-~gl~~~~~H----------------~Al~DA~ata~l~~~~~~~~~ 228 (239)
T PRK09146 193 ADSRLR-YGLPAYSPH----------------HALTDAIATAELLQAQIAHHF 228 (239)
T ss_pred HHHHHH-cCCCCCCCC----------------CcHHHHHHHHHHHHHHHHHHc
Confidence 999987 476543222 288999999999998887653
No 52
>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=96.14 E-value=0.19 Score=45.87 Aligned_cols=89 Identities=19% Similarity=0.242 Sum_probs=57.8
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
+++..|..++.+. ..||||+..|+..|...+.-.|+.+ .....+|+..+++.+. +. ....+|+.+++.
T Consensus 66 ~v~~~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~g~~~---~~~~~idt~~~~~~~~-~~------~~~~~L~~l~~~ 133 (156)
T cd06130 66 EVWPEIKPFLGGS--LVVAHNASFDRSVLRAALEAYGLPP---PPYQYLCTVRLARRVW-PL------LPNHKLNTVAEH 133 (156)
T ss_pred HHHHHHHHHhCCC--EEEEeChHHhHHHHHHHHHHcCCCC---CCCCEEEHHHHHHHHh-cc------CCCCCHHHHHHH
Confidence 3556777788763 4599999999999865433223221 1356889444555443 32 246899999986
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009783 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (526)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~ 209 (526)
+|++.. .+. |..||.++.+|+
T Consensus 134 -~g~~~~-~H~----------------Al~Da~~ta~l~ 154 (156)
T cd06130 134 -LGIELN-HHD----------------ALEDARACAEIL 154 (156)
T ss_pred -cCCCcc-CcC----------------chHHHHHHHHHH
Confidence 577654 322 678888888776
No 53
>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=96.14 E-value=0.021 Score=52.71 Aligned_cols=86 Identities=20% Similarity=0.255 Sum_probs=55.3
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
+++..+.+++.+ +-+.||||+.+|+..|... ...++|+..++..+..+ ..+++|..|+++
T Consensus 64 ~v~~~~~~fl~~-~~vlVgHn~~fD~~fL~~~------------~~~~iDT~~l~r~~~~~-------~~~~~L~~L~~~ 123 (150)
T cd06145 64 DVQKKLLSLISP-DTILVGHSLENDLKALKLI------------HPRVIDTAILFPHPRGP-------PYKPSLKNLAKK 123 (150)
T ss_pred HHHHHHHHHhCC-CCEEEEcChHHHHHHhhcc------------CCCEEEcHHhccccCCC-------CCChhHHHHHHH
Confidence 345566677753 2345999999999999652 13578944343332222 236899999999
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009783 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (526)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~ 209 (526)
++|..+....+.. -|..||.++.+||
T Consensus 124 ~~~~~i~~~~~~H-------------~Al~DA~~t~~l~ 149 (150)
T cd06145 124 YLGRDIQQGEGGH-------------DSVEDARAALELV 149 (150)
T ss_pred HCCcceeCCCCCC-------------CcHHHHHHHHHHh
Confidence 9986553211111 1678999988876
No 54
>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=96.12 E-value=0.12 Score=60.85 Aligned_cols=99 Identities=15% Similarity=0.259 Sum_probs=65.5
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
++...|.+++.+. +.||||+.+|+..|.+.+.-.|..+ .....+|+..++..+. +. ..+++|.+|++.
T Consensus 69 ev~~~l~~~l~~~--~~VahN~~fD~~fL~~~~~~~g~~~---~~~~~iDt~~l~~~~~-p~------~~~~~L~~l~~~ 136 (850)
T TIGR01407 69 QVAQEIYDLLEDG--IFVAHNVHFDLNFLAKALKDCGYEP---LPKPRIDTVELAQIFF-PT------EESYQLSELSEA 136 (850)
T ss_pred HHHHHHHHHhCCC--EEEEeCcHHHHHHHHHHHHHcCCCC---CCCCeEeHHHHHHHhc-CC------CCCCCHHHHHHH
Confidence 3456667777653 3599999999999976432223221 2357899544555443 32 257899999888
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 009783 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ 218 (526)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~ 218 (526)
+|++....++ |..||.++.+|+..+..++.+
T Consensus 137 -~gi~~~~~H~----------------Al~DA~ata~l~~~l~~~~~~ 167 (850)
T TIGR01407 137 -LGLTHENPHR----------------ADSDAQATAELLLLLFEKMEK 167 (850)
T ss_pred -CCCCCCCCCC----------------hHHHHHHHHHHHHHHHHHHHh
Confidence 5776543332 778888888888888777654
No 55
>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=96.09 E-value=0.11 Score=49.69 Aligned_cols=110 Identities=22% Similarity=0.282 Sum_probs=65.7
Q ss_pred hhHHHHHHhhCC--CCcEEEEEec-HHhHHHHHhhcccCCCcc--CcCC-----------------CCceeeHHHHHHHh
Q 009783 91 SIWELLKELFVS--PDILKLGFKF-KQDLIYLSSTFCSQGCDI--GFDR-----------------VEPYLDITSIYNHL 148 (526)
Q Consensus 91 ~~~~~L~~lL~~--~~i~KVgh~~-k~Dl~~L~~~~gi~~~~~--~~~~-----------------~~~~~Dlt~La~yL 148 (526)
+++..+.+++.+ |++ .+|||. .+|+..|......+|+.. ++.. ...++|+-.++...
T Consensus 65 ~lL~~f~~~i~~~dpdi-ivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~ 143 (199)
T cd05160 65 ELLKRFFDIIREYDPDI-LTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRD 143 (199)
T ss_pred HHHHHHHHHHHhcCCCE-EEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHh
Confidence 455555555554 555 499999 789999865433333321 0000 12478855454433
Q ss_pred hccccCCCCCcCCccHHHHHHHHcCCcCcc--cccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009783 149 HHKQLGRKLPKETKSLANICKELLDISLSK--ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (526)
Q Consensus 149 l~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~K--~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~ 209 (526)
.. ..+++|+.+++.+||..-.. .....+|....-...-++|.-.||..+++|+
T Consensus 144 ~~--------l~sy~L~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 144 FK--------LKSYTLDAVAEELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred cC--------cccCCHHHHHHHHhCCCCCcCCHHHHhhccCcchHHHHHHHHHHHHHHHHHhh
Confidence 22 35799999999999864322 2233332111223566899999999999886
No 56
>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=95.65 E-value=0.35 Score=43.33 Aligned_cols=91 Identities=18% Similarity=0.187 Sum_probs=58.1
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
++...+..++.+ ...||||...|...|.+.+...+..+ .....+|+..++..+... ...+++..+...
T Consensus 68 ~~~~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~---~~~~~iDt~~~~~~~~~~-------~~~~~l~~~~~~ 135 (159)
T cd06127 68 EVLPEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPP---LPNPWIDTLRLARRLLPG-------LRSHRLGLLLAE 135 (159)
T ss_pred HHHHHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCC---CCCCeeEHHHHHHHHcCC-------CCcCchHHHHHH
Confidence 356677778877 45699999999999876543222111 135789955566555432 245778887555
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009783 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (526)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~ 209 (526)
.+|....+.+ -|..||.++.+|+
T Consensus 136 ~~~~~~~~~H----------------~Al~Da~~t~~l~ 158 (159)
T cd06127 136 RYGIPLEGAH----------------RALADALATAELL 158 (159)
T ss_pred HcCCCCCCCC----------------CcHHHHHHHHHHh
Confidence 5665432222 2788999988876
No 57
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=95.57 E-value=0.43 Score=56.79 Aligned_cols=99 Identities=20% Similarity=0.237 Sum_probs=66.9
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
++...|..++.+. ..|+||+.+|+..|.+.+.-.|..+ .....+|+..++..+. +. ...++|++|++.
T Consensus 73 ev~~~l~~~l~~~--~~VaHN~~FD~~fL~~~~~~~g~~~---~~~~~iDt~~la~~~~-p~------~~~~~L~~l~~~ 140 (928)
T PRK08074 73 DVAPEIVELLEGA--YFVAHNVHFDLNFLNEELERAGYTE---IHCPKLDTVELARILL-PT------AESYKLRDLSEE 140 (928)
T ss_pred HHHHHHHHHhCCC--eEEEEChHHHHHHHHHHHHHcCCCC---CCCCeeeHHHHHHHhc-CC------CCCCCHHHHHHh
Confidence 3556677788754 4599999999999976533223221 1257899555655443 42 257899999987
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 009783 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ 218 (526)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~ 218 (526)
+|++....++ |-.||.++..|+..|.+++.+
T Consensus 141 -l~i~~~~~H~----------------Al~DA~ata~l~~~l~~~~~~ 171 (928)
T PRK08074 141 -LGLEHDQPHR----------------ADSDAEVTAELFLQLLNKLER 171 (928)
T ss_pred -CCCCCCCCCC----------------hHHHHHHHHHHHHHHHHHHHh
Confidence 5766543332 778999999998888887765
No 58
>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=94.80 E-value=0.78 Score=44.00 Aligned_cols=156 Identities=14% Similarity=0.200 Sum_probs=82.8
Q ss_pred CeEEEEEEEcCCC--CCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhC--CCCcEEE
Q 009783 33 SLVGLDAEWKPQR--SHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFV--SPDILKL 108 (526)
Q Consensus 33 ~~Vg~D~E~~~~~--~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~--~~~i~KV 108 (526)
.+++||.|..... +. ..... +++|+... . .+...++-.......+++..+..++. +|+++ +
T Consensus 4 ~~l~fDIEt~~~~gfp~-~~~d~--Ii~Is~~~---------~--~g~~~~~~~~~~~E~~lL~~F~~~i~~~dPd~i-~ 68 (188)
T cd05781 4 KTLAFDIEVYSKYGTPN-PRRDP--IIVISLAT---------S--NGDVEFILAEGLDDRKIIREFVKYVKEYDPDII-V 68 (188)
T ss_pred eEEEEEEEecCCCCCCC-CCCCC--EEEEEEEe---------C--CCCEEEEEecCCCHHHHHHHHHHHHHHcCCCEE-E
Confidence 4689999997322 21 12234 55554431 0 12222332111233345555555554 45643 7
Q ss_pred EEecH-HhHHHHHhhcccCCCccCcCCCC-----------------ceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 109 GFKFK-QDLIYLSSTFCSQGCDIGFDRVE-----------------PYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 109 gh~~k-~Dl~~L~~~~gi~~~~~~~~~~~-----------------~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
|||.. +|+..|......+|+...+.... ..+|+-.+...... ..+++|..+++
T Consensus 69 gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~--------l~~y~L~~Va~- 139 (188)
T cd05781 69 GYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPE--------VKVKTLENVAE- 139 (188)
T ss_pred ecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCC--------CCCCCHHHHHH-
Confidence 99965 79988754322233221110001 16785444443321 35799999997
Q ss_pred HcCCc--Ccc----ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009783 171 LLDIS--LSK----ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (526)
Q Consensus 171 ~Lg~~--L~K----~~q~s-dW~~RPL~~~qi~YAA~DA~~ll~L~~~L 212 (526)
+||.. ..| ..+.. -|...--...-+.|...|+..++.|++.+
T Consensus 140 ~Lg~~k~~~k~~~~~~~i~~~~~~~~~~~~l~~Y~~~D~~~t~~l~~~~ 188 (188)
T cd05781 140 YLGVMKKSERVLIEWYRIYEYWDDEKKRDILLKYNRDDARSTYGLAEKL 188 (188)
T ss_pred HHCCCccccccCCCHHHHHHHHcCcccHHHHHHHHHHHHHHHHHHHhhC
Confidence 58863 122 11222 24332134677899999999999998753
No 59
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=94.77 E-value=0.11 Score=61.01 Aligned_cols=103 Identities=19% Similarity=0.400 Sum_probs=75.0
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
+++..+++++.+. +-|.||+.+|+..|...|--.++.+ .-.+++|..++ ++.++|. ..+|+|..||.+
T Consensus 490 ~vL~kf~~~~~d~--IlVAHNasFD~gFl~~~~~k~~~~~---~~~pvIDTL~l-ar~L~P~------~ksh~Lg~l~kk 557 (1444)
T COG2176 490 EVLEKFREFIGDS--ILVAHNASFDMGFLNTNYEKYGLEP---LTNPVIDTLEL-ARALNPE------FKSHRLGTLCKK 557 (1444)
T ss_pred HHHHHHHHHhcCc--EEEeccCccchhHHHHHHHHhCCcc---ccCchhhHHHH-HHHhChh------hhhcchHHHHHH
Confidence 4677788888764 4499999999999865433223222 34789994445 5555664 368999999988
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009783 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGFA 222 (526)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~ 222 (526)
+ |+.+ ++..-|--||.++-.++-.+.+.+++.|..
T Consensus 558 ~-~v~l----------------e~hHRA~yDaeat~~vf~~f~~~~ke~Gi~ 592 (1444)
T COG2176 558 L-GVEL----------------ERHHRADYDAEATAKVFFVFLKDLKEKGIT 592 (1444)
T ss_pred h-CccH----------------HHhhhhhhhHHHHHHHHHHHHHHHHHhchh
Confidence 6 4443 445557889999999999999999998755
No 60
>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=94.67 E-value=0.29 Score=48.38 Aligned_cols=99 Identities=16% Similarity=0.212 Sum_probs=61.8
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCc-cCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCD-IGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~-~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~ 169 (526)
+++..|.+++.+..+ |+||+.+|+..|...+.-.|.. +.+.....++|+..++..+ .++ .+++|+.|++
T Consensus 71 ev~~~f~~fi~~~~l--VaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~-~p~-------~~~~L~~L~~ 140 (225)
T TIGR01406 71 EIADEFLDFIGGSEL--VIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARER-FPG-------QRNSLDALCK 140 (225)
T ss_pred HHHHHHHHHhCCCEE--EEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHH-cCC-------CCCCHHHHHH
Confidence 345566677776443 8999999999987553322310 0011125689944444443 343 4679999999
Q ss_pred HHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (526)
Q Consensus 170 ~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~ 214 (526)
+| |++.... + ..-|..||.++.+||..|..
T Consensus 141 ~~-gi~~~~r-~-------------~H~Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 141 RF-KVDNSHR-T-------------LHGALLDAHLLAEVYLALTG 170 (225)
T ss_pred hc-CCCCCCC-C-------------CcCHHHHHHHHHHHHHHHHc
Confidence 86 6553211 0 12288999999999998864
No 61
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=94.15 E-value=0.32 Score=56.99 Aligned_cols=100 Identities=20% Similarity=0.262 Sum_probs=67.4
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
+++..+.+++.+. +.||||+..|+..|.+.+...|. ....+.+|+..++..+ .+. ..+++|++|++.
T Consensus 75 ev~~~~~~~l~~~--~lVaHN~~FD~~fL~~~~~~~g~----~~~~~~iDT~~la~~~-~p~------~~~~~L~~L~~~ 141 (820)
T PRK07246 75 QVARHIYDLIEDC--IFVAHNVKFDANLLAEALFLEGY----ELRTPRVDTVELAQVF-FPT------LEKYSLSHLSRE 141 (820)
T ss_pred HHHHHHHHHhCCC--EEEEECcHHHHHHHHHHHHHcCC----CCCCCceeHHHHHHHH-hCC------CCCCCHHHHHHH
Confidence 3456667777763 35999999999999764321121 1235678944454444 343 247899999986
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 009783 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKG 220 (526)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g 220 (526)
+|++....++ |..||.++.+|+..|..++.+.+
T Consensus 142 -lgl~~~~~H~----------------Al~DA~ata~L~~~l~~~l~~l~ 174 (820)
T PRK07246 142 -LNIDLADAHT----------------AIADARATAELFLKLLQKIESLP 174 (820)
T ss_pred -cCCCCCCCCC----------------HHHHHHHHHHHHHHHHHHHhhcC
Confidence 6876543232 88999999999999998886543
No 62
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=93.53 E-value=1.5 Score=46.44 Aligned_cols=108 Identities=7% Similarity=0.021 Sum_probs=61.5
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCc------------------------cCcCCCCceeeHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCD------------------------IGFDRVEPYLDITSIYN 146 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~------------------------~~~~~~~~~~Dlt~La~ 146 (526)
+++..|.+++.+. +.|+||+.+|+..|.+.+.-.... .+......++|+..++.
T Consensus 114 eVl~el~~fL~g~--vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LAR 191 (377)
T PRK05601 114 QILKPLDRLIDGR--TLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATAR 191 (377)
T ss_pred HHHHHHHHHhCCC--EEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHH
Confidence 4677788888765 359999999999886542110000 00112246899445555
Q ss_pred HhhccccCCCCCcCCccHHHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009783 147 HLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (526)
Q Consensus 147 yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L 212 (526)
.+. +. ...+.|..|+++ +|++.+.. ..|. .++.-+..++ +-.||.++.+||..+
T Consensus 192 rl~-p~------l~~~rL~~La~~-lGi~~p~~-~A~~-~Ra~~p~~~l--~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 192 RQG-VA------LDDIRIRGVAHT-LGLDAPAA-EASV-ERAQVPHRQL--CREETLLVARLYFAL 245 (377)
T ss_pred HHc-CC------CCCCCHHHHHHH-hCCCCCch-hhhh-hhhcCChhhh--hhHHHHHHHHHHHHh
Confidence 554 32 357999999997 57765421 1110 0111112211 224888888888776
No 63
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=93.25 E-value=0.64 Score=48.12 Aligned_cols=99 Identities=18% Similarity=0.206 Sum_probs=64.4
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
+++..|.+++.+ -+-|+||+.+|+..|.+.+.-.+.. + ....++|+..++..+. ++ ...++|..|++.
T Consensus 69 ev~~~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~--~-~~~~~idT~~lar~l~-~~------~~~~~L~~L~~~ 136 (309)
T PRK06195 69 KIWEKIKHYFNN--NLVIAHNASFDISVLRKTLELYNIP--M-PSFEYICTMKLAKNFY-SN------IDNARLNTVNNF 136 (309)
T ss_pred HHHHHHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCC--C-CCCCEEEHHHHHHHHc-CC------CCcCCHHHHHHH
Confidence 355667777765 3459999999999886543222211 1 1246889445666554 32 246899999988
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 009783 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (526)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~ 219 (526)
+ |++. .. .-|..||.++.+|+..|.+++...
T Consensus 137 ~-gi~~-~~----------------H~Al~DA~ata~l~~~l~~~~~~~ 167 (309)
T PRK06195 137 L-GYEF-KH----------------HDALADAMACSNILLNISKELNSK 167 (309)
T ss_pred c-CCCC-cc----------------cCCHHHHHHHHHHHHHHHHHhccC
Confidence 5 6542 11 238899999999999888776543
No 64
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=93.23 E-value=1.2 Score=55.16 Aligned_cols=102 Identities=15% Similarity=0.259 Sum_probs=68.7
Q ss_pred hHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHH
Q 009783 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKEL 171 (526)
Q Consensus 92 ~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~ 171 (526)
++..+..++.+ ...|+|+...|+..|...+.-+|+.+ .....+|...++ +.+.+. ...++|..|+++
T Consensus 489 aL~~f~~figg--~vLVAHNa~FD~~fL~~~l~rlgl~~---l~~~~IDTLela-r~l~p~------~k~~kL~~LAk~- 555 (1437)
T PRK00448 489 VLPKFKEFCGD--SILVAHNASFDVGFINTNYEKLGLEK---IKNPVIDTLELS-RFLYPE------LKSHRLNTLAKK- 555 (1437)
T ss_pred HHHHHHHHhCC--CEEEEeCccccHHHHHHHHHHcCCcc---ccccceeHHHHH-HHHcCc------cccccHHHHHHH-
Confidence 44455555544 56699999999988754433233321 135688944444 444442 357899999987
Q ss_pred cCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009783 172 LDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGFA 222 (526)
Q Consensus 172 Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~ 222 (526)
+|+.+... +-|-.||.++.+|+..|.+++.+.|..
T Consensus 556 lGL~~~~~----------------HrAl~DA~aTa~lf~~ll~~l~~~gi~ 590 (1437)
T PRK00448 556 FGVELEHH----------------HRADYDAEATAYLLIKFLKDLKEKGIT 590 (1437)
T ss_pred cCCCCCCC----------------cChHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 57765432 238899999999999999999877654
No 65
>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=92.98 E-value=2.7 Score=40.50 Aligned_cols=110 Identities=23% Similarity=0.278 Sum_probs=62.8
Q ss_pred hhHHHHHHhhC--CCCcEEEEEecHH-hHHHHHhhcccCCCccCcCC--------------------CC-ceeeHHHHHH
Q 009783 91 SIWELLKELFV--SPDILKLGFKFKQ-DLIYLSSTFCSQGCDIGFDR--------------------VE-PYLDITSIYN 146 (526)
Q Consensus 91 ~~~~~L~~lL~--~~~i~KVgh~~k~-Dl~~L~~~~gi~~~~~~~~~--------------------~~-~~~Dlt~La~ 146 (526)
+++..+..++. +|+++ +|||..+ |+..|......+++.+.+.. .+ .++|+-.+..
T Consensus 53 ~lL~~f~~~i~~~dPDvi-~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k 131 (193)
T cd05784 53 SLLLALIAWFAQYDPDII-IGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALK 131 (193)
T ss_pred HHHHHHHHHHHhhCCCEE-EECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHH
Confidence 34555444444 45654 8999886 99887544333333321110 01 1677433333
Q ss_pred HhhccccCCCCCcCCccHHHHHHHHcCCcCcc-c-----cccc-CCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009783 147 HLHHKQLGRKLPKETKSLANICKELLDISLSK-E-----LQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (526)
Q Consensus 147 yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~K-~-----~q~s-dW~~RPL~~~qi~YAA~DA~~ll~L~~ 210 (526)
.-. ....+++|+++++++||..-.. . .++. -|...+ ..-++|+..||..+++|++
T Consensus 132 ~~~-------~kl~sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~~~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 132 TAT-------YHFESFSLENVAQELLGEGKLIHDVDDRGAEIERLFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred Hcc-------CCCCcCCHHHHHHHHhCCCccccCcccCHHHHHHHHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 210 1135899999999999964221 1 1222 244333 4668999999999999873
No 66
>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=92.89 E-value=0.99 Score=43.23 Aligned_cols=84 Identities=17% Similarity=0.184 Sum_probs=52.7
Q ss_pred cEEEEEecHHhHHHHHhhcccCCC-ccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCccccccc
Q 009783 105 ILKLGFKFKQDLIYLSSTFCSQGC-DIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCS 183 (526)
Q Consensus 105 i~KVgh~~k~Dl~~L~~~~gi~~~-~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~K~~q~s 183 (526)
.+.||||+..|+..|.+.+.-.|+ ...+ ....++|+..++..+. + ..+|+.++++ +|+++....
T Consensus 103 ~~lVaHna~FD~~fL~~~~~~~~~~~~~~-~~~~~lDt~~la~~~~-~---------~~~L~~l~~~-~gi~~~~~~--- 167 (189)
T cd06134 103 AILVGHNAHFDLGFLNAAVARCKIKRNPF-HPFSTFDTATLAGLAY-G---------QTVLAKACQA-AGIEFDNKE--- 167 (189)
T ss_pred CeEEEecchhhHHHHHHHHHHhCCCCCCC-CCCcEEEHHHHHHHHh-C---------CCcHHHHHHH-CCCCCCCCC---
Confidence 456999999999998754322222 1001 1134799555655443 2 3479999886 477642111
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 184 DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (526)
Q Consensus 184 dW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~ 214 (526)
..-|..||.++.+|+..|.+
T Consensus 168 -----------~H~Al~DA~ata~lf~~l~~ 187 (189)
T cd06134 168 -----------AHSALYDTQKTAELFCKIVN 187 (189)
T ss_pred -----------CcChHHHHHHHHHHHHHHHH
Confidence 12278999999999988865
No 67
>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=92.85 E-value=1.8 Score=42.21 Aligned_cols=158 Identities=16% Similarity=0.194 Sum_probs=80.7
Q ss_pred CeEEEEEEEcCCCCCC---CCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhC--CCCcEE
Q 009783 33 SLVGLDAEWKPQRSHQ---SNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFV--SPDILK 107 (526)
Q Consensus 33 ~~Vg~D~E~~~~~~~~---~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~--~~~i~K 107 (526)
.+++||.|..+..... .....-.++||+... . .+...++........+++..+..++. +|++ .
T Consensus 10 kilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~---------~--~~~~~~~~~~~~~E~~lL~~f~~~i~~~dPdi-i 77 (207)
T cd05785 10 RRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRD---------N--RGWEEVLHAEDAAEKELLEELVAIIRERDPDV-I 77 (207)
T ss_pred eEEEEEEEecCCCCccCCCCCCCCCeEEEEeccc---------C--CCceeeeccCCCCHHHHHHHHHHHHHHhCCCE-E
Confidence 5789999986533110 122334588888752 0 11111221111222345555555554 4675 3
Q ss_pred EEEec-HHhHHHHHhhcccCCCccCcCC--------------------------C-CceeeHHHHHHHhhccccCCCCCc
Q 009783 108 LGFKF-KQDLIYLSSTFCSQGCDIGFDR--------------------------V-EPYLDITSIYNHLHHKQLGRKLPK 159 (526)
Q Consensus 108 Vgh~~-k~Dl~~L~~~~gi~~~~~~~~~--------------------------~-~~~~Dlt~La~yLl~~~~~~~~~~ 159 (526)
+|||. .+|+..|......+|+...+.. . ..++|+-.++....... +. .
T Consensus 78 ~g~N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~--~~--l 153 (207)
T cd05785 78 EGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSS--RD--L 153 (207)
T ss_pred eccCCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccc--cC--C
Confidence 79999 6799988543222333221100 1 12368433333211100 11 2
Q ss_pred CCccHHHHHHHHcCCcCc-c----ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009783 160 ETKSLANICKELLDISLS-K----ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIF 209 (526)
Q Consensus 160 ~~~gL~~Lv~~~Lg~~L~-K----~~q~s-dW~~RPL~~~qi~YAA~DA~~ll~L~ 209 (526)
.+++|..+++.+ |..-. | ..+.. -|...+ +.-+.|+..||..++.|+
T Consensus 154 ~sysL~~Va~~~-g~~~~~k~d~~~~~I~~l~~~~~--~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 154 PSYGLKAVAKHF-GLASPDRTYIDGRQIAEVWRSDP--ARLLAYALDDVRETEGLA 206 (207)
T ss_pred CCCCHHHHHHHh-cccCCCcCCCCHHHHHHHHhcCH--HHHHHHHHHHHHHHHHhh
Confidence 478999999986 33111 1 11222 254432 667899999999998875
No 68
>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=92.26 E-value=2.6 Score=41.56 Aligned_cols=55 Identities=16% Similarity=0.174 Sum_probs=39.6
Q ss_pred CCccHHHHHHHHcCCcCcc--cccccC-CCCCCCC-HHHHHHHHHHHHHHHHHHHHHHH
Q 009783 160 ETKSLANICKELLDISLSK--ELQCSD-WSNRPLT-EEQKNYAAIDAHCLIEIFNIFQV 214 (526)
Q Consensus 160 ~~~gL~~Lv~~~Lg~~L~K--~~q~sd-W~~RPL~-~~qi~YAA~DA~~ll~L~~~L~~ 214 (526)
.+++|.++++++||..-.. ...... |...|-. ..-++|...||..+++|+..|.-
T Consensus 167 ~sy~L~~Va~~~Lg~~k~d~~~~~i~~~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl~~ 225 (230)
T cd05777 167 RSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLMC 225 (230)
T ss_pred ccCcHHHHHHHHhCCCCCCCCHHHHHHHHccCHhHhHHHHHhhHHHHHHHHHHHHHHhh
Confidence 5899999999999965321 223333 4333432 45689999999999999998853
No 69
>cd00814 MetRS_core catalytic core domain of methioninyl-tRNA synthetases. Methionine tRNA synthetase (MetRS) catalytic core domain. This class I enzyme aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. MetRS, which consists of the core domain and an anti-codon binding domain, functions as a monomer. However, in some species the anti-codon binding domain is followed by an EMAP domain. In this case, MetRS functions as a homodimer. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. As a result of a deletion event, MetRS has a significantly shorter core domain insertion than IleRS, ValRS, and LeuR. Consequently, the MetRS insertion lacks the editing function.
Probab=90.62 E-value=0.59 Score=48.53 Aligned_cols=102 Identities=12% Similarity=0.216 Sum_probs=59.0
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecChhHHHhhcccCCcEEEEcCCCHHHHHHHHHHHcCcccccc
Q 009783 372 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQLLEVIEAFQLKISED 451 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~RiiLTrd~~l~~~~~~~~~~~~~v~~~~~~~QL~~vl~~f~l~~~~~ 451 (526)
++|+||..|++|.++.+.+.-+..+...|+++|. | -+++.. ...+..++.++.+|+..+
T Consensus 29 ~~R~~r~~G~~V~~~~g~Dd~g~~i~~~a~~~g~---~-~~e~~~---------------~~~~~~~~~l~~LgI~~D-- 87 (319)
T cd00814 29 FARYQRLRGYDVLFVTGTDEHGTKIEQKAEEEGV---T-PQELCD---------------KYHEIFKDLFKWLNISFD-- 87 (319)
T ss_pred HHHHHHhCCCcccccCccCCCCcHHHHHHHHcCC---C-HHHHHH---------------HHHHHHHHHHHHcCCcCC--
Confidence 7999999999999987654334568888877663 1 111211 123566777888887643
Q ss_pred ccCccccC-CCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009783 452 QLMSRCTK-CNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 505 (526)
Q Consensus 452 ~~~sRC~~-CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 505 (526)
.+.|-.. -+... ..++.++... -..+|+...+-+.|+.|+..+
T Consensus 88 -~~~~tt~~~~~~~------v~~i~~~L~e----kG~iY~~~~~~~yc~~~~~~l 131 (319)
T cd00814 88 -YFIRTTSPRHKEI------VQEFFKKLYE----NGYIYEGEYEGLYCVSCERFL 131 (319)
T ss_pred -CCeeCCCHHHHHH------HHHHHHHHHH----CCCEEeeeeeeeECCCCCcEe
Confidence 2434211 00000 1122222211 124677778899999999754
No 70
>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=90.14 E-value=13 Score=36.11 Aligned_cols=161 Identities=16% Similarity=0.124 Sum_probs=84.8
Q ss_pred CeEEEEEEEcCC----CCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-----------------CCchh
Q 009783 33 SLVGLDAEWKPQ----RSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-----------------IPLPS 91 (526)
Q Consensus 33 ~~Vg~D~E~~~~----~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~-----------------l~~~~ 91 (526)
.+++||.|..+. ++. .....-.++||+.... ++...++++.... -+..+
T Consensus 6 rilsfDIE~~~~~~~~fP~-~~~~~d~IisI~~~~~---------~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~~~E~~ 75 (204)
T cd05783 6 KRIAIDIEVYTPIKGRIPD-PKTAEYPVISVALAGS---------DGLKRVLVLKREGVEGLEGLLPEGAEVEFFDSEKE 75 (204)
T ss_pred eEEEEEEEECCCCCCCCcC-CCCCCCeEEEEEEcCC---------CCCcEEEEEecCCcccccccCCCCCeEEecCCHHH
Confidence 578999999742 221 0112235788887520 0123455543100 11234
Q ss_pred hHHHHHHhhCCCCcEEEEEecH-HhHHHHHhhcccCCCc-----cCcC------CCCceeeHHHHHHH-hhc-cccCCCC
Q 009783 92 IWELLKELFVSPDILKLGFKFK-QDLIYLSSTFCSQGCD-----IGFD------RVEPYLDITSIYNH-LHH-KQLGRKL 157 (526)
Q Consensus 92 ~~~~L~~lL~~~~i~KVgh~~k-~Dl~~L~~~~gi~~~~-----~~~~------~~~~~~Dlt~La~y-Ll~-~~~~~~~ 157 (526)
++..+.+++.+.. ..+|||.. +|+..|......+|+. ..+. .....+|+-..... .+. -.++.
T Consensus 76 lL~~F~~~i~~~~-~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~-- 152 (204)
T cd05783 76 LIREAFKIISEYP-IVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGN-- 152 (204)
T ss_pred HHHHHHHHHhcCC-EEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhcc--
Confidence 5666666666654 45799977 6999885443333332 0000 01336775333322 100 00000
Q ss_pred CcCCccHHHHHHHHcCCcCc-ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009783 158 PKETKSLANICKELLDISLS-KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (526)
Q Consensus 158 ~~~~~gL~~Lv~~~Lg~~L~-K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~ 210 (526)
+..+++|..+++.+||..-. -..+. |.. =...-+.|+..||..++.|..
T Consensus 153 ~~~~~~L~~Va~~~lg~~K~~~~~~i--~~~--~~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 153 KYREYTLDAVAKALLGEGKVELEKNI--SEL--NLYELAEYNYRDAELTLELTT 202 (204)
T ss_pred ccccCcHHHHHHHhcCCCcccCCchh--hhh--cHHHHHHhhHHHHHHHHHHhc
Confidence 12578999999999996321 11111 211 125568999999999988864
No 71
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=89.40 E-value=0.27 Score=33.86 Aligned_cols=31 Identities=26% Similarity=0.732 Sum_probs=16.9
Q ss_pred ccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEe
Q 009783 457 CTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYW 506 (526)
Q Consensus 457 C~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW 506 (526)
|+.|+++|.. +||++ .+.+-+.|+.||.|..
T Consensus 3 C~~CG~~l~~----------------~ip~g---d~r~R~vC~~Cg~IhY 33 (34)
T PF14803_consen 3 CPQCGGPLER----------------RIPEG---DDRERLVCPACGFIHY 33 (34)
T ss_dssp -TTT--B-EE----------------E--TT----SS-EEEETTTTEEE-
T ss_pred cccccChhhh----------------hcCCC---CCccceECCCCCCEEe
Confidence 9999998742 34533 3577889999999854
No 72
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=89.27 E-value=1.6 Score=41.28 Aligned_cols=89 Identities=17% Similarity=0.072 Sum_probs=54.8
Q ss_pred hHHHHHHhhCC--CCcEEEEEec-HHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHH
Q 009783 92 IWELLKELFVS--PDILKLGFKF-KQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANIC 168 (526)
Q Consensus 92 ~~~~L~~lL~~--~~i~KVgh~~-k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv 168 (526)
+.+.|..++.. ...+.||||. .+|+..|.+.+.-.|+. +.....++| |+-....+. . +|++|+
T Consensus 84 ~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~--~~~~~~~iD-tl~l~r~~~----------~-~L~~l~ 149 (177)
T cd06136 84 TANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTK--LPDDILCVD-SLPAFRELD----------Q-SLGSLY 149 (177)
T ss_pred HHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCC--CCCCCEEEE-eHHHHhhhH----------h-hHHHHH
Confidence 34556666653 2356799998 89999986543222322 111234679 543322221 1 899999
Q ss_pred HHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009783 169 KELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (526)
Q Consensus 169 ~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~ 210 (526)
++++|++....+ -|..||.++.+++-
T Consensus 150 ~~~~~~~~~~~H----------------~A~~Da~at~~v~~ 175 (177)
T cd06136 150 KRLFGQEPKNSH----------------TAEGDVLALLKCAL 175 (177)
T ss_pred HHHhCCCccccc----------------chHHHHHHHHHHHh
Confidence 998887764433 28889999877763
No 73
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=89.23 E-value=0.04 Score=57.46 Aligned_cols=130 Identities=21% Similarity=0.270 Sum_probs=88.7
Q ss_pred CCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCcc
Q 009783 51 FPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDI 130 (526)
Q Consensus 51 ~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~ 130 (526)
++.+|.+|.++. ..+||+|+..++...+...++.++++.+|.|+-|++..-+.+++..||+
T Consensus 73 ~~~l~~~q~~~~--------------~~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~~~~~~i----- 133 (458)
T KOG2405|consen 73 HGKLCWLQVATN--------------CRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGI----- 133 (458)
T ss_pred cCcchhHHHHHH--------------HHHHHHHHHHhhhHHHHHHHHHHhhhhhHhhhHHHHHHHHHHhccccee-----
Confidence 358899999884 5789999877766667788999999999999999999999999998888
Q ss_pred CcCCCCceeeHHHHHHHhhcc-ccCCCCCcCCccH-HHHHHHHcCCcC------cc-----cccccCCCCCCCCHHHHHH
Q 009783 131 GFDRVEPYLDITSIYNHLHHK-QLGRKLPKETKSL-ANICKELLDISL------SK-----ELQCSDWSNRPLTEEQKNY 197 (526)
Q Consensus 131 ~~~~~~~~~Dlt~La~yLl~~-~~~~~~~~~~~gL-~~Lv~~~Lg~~L------~K-----~~q~sdW~~RPL~~~qi~Y 197 (526)
..+++|| |+++.-+-.. +.|..+|..-..+ ++|.. .|...+ .| .+...-|-.||.++.-+.-
T Consensus 134 ---~~n~v~~-~q~~d~~q~~~e~g~~~~n~~~~~q~sl~k-h~~~a~k~~~~l~~r~~~~~~n~e~~~i~~~~~s~~~~ 208 (458)
T KOG2405|consen 134 ---LLNNVFD-TQVADVLQFSMETGGYLPNCITTLQESLIK-HLQVAPKYLSFLEKRQKLIQENPEVWFIRPVSPSLLKI 208 (458)
T ss_pred ---eecchhh-hhhhhhhhhcccccccCCccccchHHHHHH-HHHhcccHHHHHHHHHHHHhhCcceeEeecCchhHHHh
Confidence 2589999 8887655432 2233333222223 33333 222221 12 1234458889988887666
Q ss_pred HHHHHHH
Q 009783 198 AAIDAHC 204 (526)
Q Consensus 198 AA~DA~~ 204 (526)
-|..|.+
T Consensus 209 ~~~e~~~ 215 (458)
T KOG2405|consen 209 LALEATY 215 (458)
T ss_pred hhhhhhh
Confidence 6655554
No 74
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=88.84 E-value=0.11 Score=54.28 Aligned_cols=126 Identities=22% Similarity=0.224 Sum_probs=76.9
Q ss_pred CEEEEEeCCCCCchhhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhcccc-CC
Q 009783 77 SVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQL-GR 155 (526)
Q Consensus 77 ~~v~liD~~~l~~~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~-~~ 155 (526)
...|++|...-+..-+..-.+..|++..+ +. |.+.+...|...|++ .+.+++| |++++.+..+.. |+
T Consensus 222 n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~--------~L~nVkD-tQia~sLve~~e~gr 289 (458)
T KOG2405|consen 222 NEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHS--------ALKNVKD-TQIASSLVEPSEYGR 289 (458)
T ss_pred chhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHH--------HHHhhHH-HHHHHHHhhhHHhcc
Confidence 67888886543321122335566776655 33 889999988888776 3578999 999999987653 43
Q ss_pred CCCcCC-ccHHHHHH--HHcCCcC------ccc-ccc-cCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 156 KLPKET-KSLANICK--ELLDISL------SKE-LQC-SDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (526)
Q Consensus 156 ~~~~~~-~gL~~Lv~--~~Lg~~L------~K~-~q~-sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~ 214 (526)
..|... .+.-.|-. .|.+... .+- .+. -+|..||.++....-++.|+.+|+.....|.+
T Consensus 290 r~p~~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll~~~~~l~a 359 (458)
T KOG2405|consen 290 RHPTSILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLLGIFDTLVA 359 (458)
T ss_pred cCCccceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHHHHHHHHHHHHhhHhh
Confidence 332110 00000000 0111110 111 122 26999999999999999999999997766554
No 75
>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=88.82 E-value=0.52 Score=43.48 Aligned_cols=148 Identities=17% Similarity=0.171 Sum_probs=68.1
Q ss_pred EEEEEEEcCCCCCCCCCCceEEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCc---hhhHHHHHHhhCCCCcEEEEEe
Q 009783 35 VGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPL---PSIWELLKELFVSPDILKLGFK 111 (526)
Q Consensus 35 Vg~D~E~~~~~~~~~~~~~vaLiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~---~~~~~~L~~lL~~~~i~KVgh~ 111 (526)
+.||+|+.+..+ ....+.+++++... .+...++.+...-.. ..+.+.+ ..+.+...+ |+||
T Consensus 1 l~~DIET~Gl~~---~~~~i~liG~~~~~-----------~~~~~~~~~~~~~~~~ee~~~~~~~-~~l~~~~~i-v~yn 64 (164)
T PF13482_consen 1 LFFDIETTGLSP---DNDTIYLIGVADFD-----------DDEIITFIQWFAEDPDEEEIILEFF-ELLDEADNI-VTYN 64 (164)
T ss_dssp --EEEEESS-GG----G---EEEEEEE-E-----------TTTTE-EEEE-GGGHHHHHHHHH---HHHHTT--E-EESS
T ss_pred CcEEecCCCCCC---CCCCEEEEEEEEeC-----------CCceEEeeHhhccCcHHHHHHHHHH-HHHhcCCeE-EEEe
Confidence 468999997764 34668888887631 012222222111111 1223333 344444333 7788
Q ss_pred c-HHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCc-c---ccccc---
Q 009783 112 F-KQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS-K---ELQCS--- 183 (526)
Q Consensus 112 ~-k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~-K---~~q~s--- 183 (526)
. .+|...|.+.+.-.++. .....+||-.++.... ..+.+|+.++.. ||..-. + +.+..
T Consensus 65 g~~FD~p~L~~~~~~~~~~----~~~~~iDl~~~~~~~~---------~~~~~Lk~ve~~-lg~~~~~~~~~G~~~~~~~ 130 (164)
T PF13482_consen 65 GKNFDIPFLKRRAKRYGLP----PPFNHIDLLKIIKKHF---------LESYSLKNVEKF-LGIERRDDDISGSESVKLY 130 (164)
T ss_dssp TTTTHHHHHHHHH-HHHH------GGGEEEHHHHHT-TT---------SCCTT--SHHH------------HHHHHHHHH
T ss_pred CcccCHHHHHHHHHHcCCC----cccchhhHHHHHHhcc---------CCCCCHHHHhhh-cccccccCCCCHHHHHHHH
Confidence 5 56999987654222222 2467899655442211 145688888776 676554 1 11111
Q ss_pred -CCCC---CCCCHHHHHHHHHHHHHHHHHHHHH
Q 009783 184 -DWSN---RPLTEEQKNYAAIDAHCLIEIFNIF 212 (526)
Q Consensus 184 -dW~~---RPL~~~qi~YAA~DA~~ll~L~~~L 212 (526)
.|.. ....+..+.|.-.|+..+..|++.|
T Consensus 131 ~~~~~~~~~~~~~~i~~yN~~Dv~~~~~L~~~l 163 (164)
T PF13482_consen 131 KEYLETGDPEALEEILEYNEDDVRATRRLYEWL 163 (164)
T ss_dssp H---TTGGTS--HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 1211 2344777999999999999999876
No 76
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=87.00 E-value=0.53 Score=32.98 Aligned_cols=33 Identities=21% Similarity=0.704 Sum_probs=22.1
Q ss_pred ccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009783 455 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 505 (526)
Q Consensus 455 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 505 (526)
.+|+.|+..+. ++.+. +|. ...--+|+.|+.+|
T Consensus 3 i~CP~C~~~f~---v~~~~----------l~~-----~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFR---VPDDK----------LPA-----GGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEE---cCHHH----------ccc-----CCcEEECCCCCcEe
Confidence 47999999873 43222 222 23466899999987
No 77
>PRK11779 sbcB exonuclease I; Provisional
Probab=87.00 E-value=10 Score=41.72 Aligned_cols=106 Identities=16% Similarity=0.155 Sum_probs=58.1
Q ss_pred hHHHHHHhhCCCCcEEEEEe-cHHhHHHHHhhcccCCCccC---cCCCCceeeHHHHHH--HhhccccCCCCC-----cC
Q 009783 92 IWELLKELFVSPDILKLGFK-FKQDLIYLSSTFCSQGCDIG---FDRVEPYLDITSIYN--HLHHKQLGRKLP-----KE 160 (526)
Q Consensus 92 ~~~~L~~lL~~~~i~KVgh~-~k~Dl~~L~~~~gi~~~~~~---~~~~~~~~Dlt~La~--yLl~~~~~~~~~-----~~ 160 (526)
+...+..++..+..+.|||| +.+|...|...+..-.+.+. +......+|+..++. +.+.++ +-..| ..
T Consensus 81 ~~~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~-~i~~P~~~~g~~ 159 (476)
T PRK11779 81 FAARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPE-GINWPENEDGLP 159 (476)
T ss_pred HHHHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccc-cccCcccccCCC
Confidence 45566667765555679997 78999887664311000000 000011234322222 222221 00011 24
Q ss_pred CccHHHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 161 TKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVK 215 (526)
Q Consensus 161 ~~gL~~Lv~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~ 215 (526)
++.|+.|++.+ |++....+ =|..||+++.+|+..|.++
T Consensus 160 s~rLe~L~~~~-gI~~~~AH----------------dALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 160 SFKLEHLTKAN-GIEHENAH----------------DAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CCcHHHHHHHc-CCCCCCCC----------------CcHHHHHHHHHHHHHHHHh
Confidence 68999999875 66543222 2789999999999999875
No 78
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=86.86 E-value=0.58 Score=32.02 Aligned_cols=29 Identities=28% Similarity=0.747 Sum_probs=21.6
Q ss_pred CccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009783 454 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 505 (526)
Q Consensus 454 ~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 505 (526)
..+|..||+.++. .+.+....|+.||.+|
T Consensus 3 ~~~C~~C~~~~i~-----------------------~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIV-----------------------NKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEE-----------------------EecCCeEEcccCCcEe
Confidence 3689999997641 1235577899999987
No 79
>PLN02224 methionine-tRNA ligase
Probab=85.75 E-value=2.4 Score=48.13 Aligned_cols=34 Identities=12% Similarity=0.192 Sum_probs=24.8
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009783 372 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 405 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 405 (526)
++||+|+.|++|.++.+.+.-...+...|.++|.
T Consensus 98 iaR~~r~~G~~V~fv~G~DehG~kI~~~A~~~g~ 131 (616)
T PLN02224 98 IARFQRLLGKKVIFITGTDEHGEKIATSAAANGR 131 (616)
T ss_pred HHHHHHhcCCceEEecCcCCcchHHHHHHHHcCC
Confidence 7999999999999987643222347777776663
No 80
>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=85.63 E-value=13 Score=36.25 Aligned_cols=111 Identities=15% Similarity=0.190 Sum_probs=62.4
Q ss_pred hhHHHHHHhhCC--CCcEEEEEecH-HhHHHHHhhcccCCCcc----CcCC---------CCceeeHHHHHHHhhccccC
Q 009783 91 SIWELLKELFVS--PDILKLGFKFK-QDLIYLSSTFCSQGCDI----GFDR---------VEPYLDITSIYNHLHHKQLG 154 (526)
Q Consensus 91 ~~~~~L~~lL~~--~~i~KVgh~~k-~Dl~~L~~~~gi~~~~~----~~~~---------~~~~~Dlt~La~yLl~~~~~ 154 (526)
+++..+.+++.+ |++ .+|||.. +|+..|......+|+.. ++.. ....+|+-.+.+.-..
T Consensus 75 ~lL~~f~~~i~~~~Pd~-i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~---- 149 (204)
T cd05779 75 ALLQRFFEHIREVKPHI-IVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSY---- 149 (204)
T ss_pred HHHHHHHHHHHHhCCCE-EEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhc----
Confidence 455555555543 555 4899876 69988754322233221 1110 0115675443332111
Q ss_pred CCCCcCCccHHHHHHHHcCCcCccc--cccc-CCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009783 155 RKLPKETKSLANICKELLDISLSKE--LQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (526)
Q Consensus 155 ~~~~~~~~gL~~Lv~~~Lg~~L~K~--~q~s-dW~~RPL~~~qi~YAA~DA~~ll~L~~ 210 (526)
++..+++|..+++.+||..-..- ..+. -|...+ +.-++|.-.||..++.||.
T Consensus 150 --l~~~sysLd~Va~~~Lg~~K~~~~~~~I~~~~~~~~--~~l~~Y~~~D~~~T~~l~~ 204 (204)
T cd05779 150 --LPQGSQGLKAVTKAKLGYDPVELDPEDMVPLAREDP--QTLASYSVSDAVATYYLYM 204 (204)
T ss_pred --CCCCCccHHHHHHHHhCCCcCcCCHHHHHHHHhCCc--HHHHhccHHHHHHHHHHhC
Confidence 11247899999999999742111 1111 355443 5678999999999999883
No 81
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=85.62 E-value=0.67 Score=32.28 Aligned_cols=32 Identities=22% Similarity=0.740 Sum_probs=21.9
Q ss_pred cccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009783 456 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 505 (526)
Q Consensus 456 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 505 (526)
+|+.|+.... ++.+ +||+. ..--+|+.||.+|
T Consensus 4 ~Cp~C~~~y~---i~d~----------~ip~~-----g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYE---IDDE----------KIPPK-----GRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEe---CCHH----------HCCCC-----CcEEECCCCCCEe
Confidence 6999999874 3322 34543 3456899999986
No 82
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=85.60 E-value=0.7 Score=49.16 Aligned_cols=91 Identities=20% Similarity=0.263 Sum_probs=58.5
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHH-HHHHhhccccCCCCCcCCccHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITS-IYNHLHHKQLGRKLPKETKSLANICK 169 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~-La~yLl~~~~~~~~~~~~~gL~~Lv~ 169 (526)
++-..|..++... -+-|||++..||.+|+-.| ..+.| |. +..+-.++ . ....+|..|++
T Consensus 282 dvq~~l~~~~~~~-TILVGHSLenDL~aLKl~H------------~~ViD-Ta~lf~~~~g~-----~-~~k~sLk~L~~ 341 (380)
T KOG2248|consen 282 DVQKELLELISKN-TILVGHSLENDLKALKLDH------------PSVID-TAVLFKHPTGP-----Y-PFKSSLKNLAK 341 (380)
T ss_pred HHHHHHHhhcCcC-cEEEeechhhHHHHHhhhC------------Cceee-eeEEEecCCCC-----c-cchHHHHHHHH
Confidence 3455677755554 4559999999999998643 35678 44 22222211 0 13567999999
Q ss_pred HHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (526)
Q Consensus 170 ~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~ 214 (526)
.+||..+.-+..-.+ .+.||.+.++|......
T Consensus 342 ~~L~~~Iq~~~~~Hd-------------S~eDA~acm~Lv~~k~~ 373 (380)
T KOG2248|consen 342 SYLGKLIQEGVGGHD-------------SVEDALACMKLVKLKIK 373 (380)
T ss_pred HHHHHHHhccCCCCc-------------cHHHHHHHHHHHHHHHh
Confidence 999987751111111 57899999988776543
No 83
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=85.16 E-value=25 Score=36.19 Aligned_cols=88 Identities=15% Similarity=0.123 Sum_probs=51.1
Q ss_pred HHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHc
Q 009783 93 WELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELL 172 (526)
Q Consensus 93 ~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~L 172 (526)
.+.+..++.... +.|+||+.+|...|.+.+.. |. .....+ ++.......+. ..+++|..|+..+
T Consensus 111 ~~~l~~fl~~~~-vlVAHNA~FD~~fL~~~~~~------~~-~~~~~c-t~~~i~~~~~~------~~~~kL~~La~~~- 174 (294)
T PRK09182 111 PAAVDALIAPAD-LIIAHNAGFDRPFLERFSPV------FA-TKPWAC-SVSEIDWSARG------FEGTKLGYLAGQA- 174 (294)
T ss_pred HHHHHHHhcCCC-EEEEeCHHHHHHHHHHHHHh------cc-CCcccc-cHHHHhhcccc------CCCCCHHHHHHHc-
Confidence 456777777644 45999999999999764221 11 122233 33211111111 2478999999875
Q ss_pred CCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009783 173 DISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (526)
Q Consensus 173 g~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~ 213 (526)
| ..... .=|..||.++.+|+....
T Consensus 175 g-~~~~a----------------HrAl~Da~Ata~ll~~~l 198 (294)
T PRK09182 175 G-FFHEG----------------HRAVDDCQALLELLARPL 198 (294)
T ss_pred C-CCCCC----------------cChHHHHHHHHHHHHHHH
Confidence 5 21111 228899999988877543
No 84
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=84.89 E-value=8.6 Score=37.21 Aligned_cols=99 Identities=16% Similarity=0.104 Sum_probs=60.1
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
+++..|.+++.+...+ +.|+...|+..|.+.+...|+. +.....++|+..++..+... ...++|+++++.
T Consensus 81 evl~~f~~~~~~~~~~-iv~~~~fD~~fL~~~~~~~~~~--~~~~~~~~dl~~~~~~~~~~-------~~~~~L~~~~~~ 150 (207)
T PRK07748 81 ELVEKLAEYDKRCKPT-IVTWGNMDMKVLKHNCEKAGVP--FPFKGQCRDLSLEYKKFFGE-------RNQTGLWKAIEE 150 (207)
T ss_pred HHHHHHHHHhCcCCeE-EEEECHHHHHHHHHHHHHcCCC--CcccccceeHHHHHHHHhCc-------CCCCCHHHHHHH
Confidence 4566777888773333 4455789999987553222322 11224677855444433322 245799998876
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVK 215 (526)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~ 215 (526)
+|++... + -.-|..||.++.+|+..|...
T Consensus 151 -~gi~~~~--~-------------~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 151 -YGKEGTG--K-------------HHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred -cCCCCCC--C-------------CcChHHHHHHHHHHHHHHHhC
Confidence 4655321 0 122889999999999988754
No 85
>PRK12268 methionyl-tRNA synthetase; Reviewed
Probab=84.50 E-value=1.3 Score=49.44 Aligned_cols=55 Identities=18% Similarity=0.111 Sum_probs=34.3
Q ss_pred CCCCC---CCCCCCCCCCEEEEecccHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009783 347 GPPPW---DLSLGGDGYPKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 405 (526)
Q Consensus 347 ~~~p~---~~~~~~~~~~kfl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 405 (526)
.|||. ++++|...++=++.| -++|++|+.|++|.++.+.+.-+..+...|+++|.
T Consensus 9 ~~~py~ng~~HiGH~~~~~~~~D----~~~R~~r~~G~~v~~~~g~d~~g~~i~~~a~~~g~ 66 (556)
T PRK12268 9 SAWPYANGPLHLGHLAGSGLPAD----VFARYQRLKGNEVLFVSGSDEHGTPIELAAKKEGV 66 (556)
T ss_pred cCCCCCCCCccccccccchhHHH----HHHHHHHhcCCceEecCcCCCcccHHHHHHHHcCC
Confidence 35555 456665443212233 36999999999999987643223457777776654
No 86
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=83.82 E-value=9.3 Score=37.60 Aligned_cols=87 Identities=9% Similarity=0.015 Sum_probs=53.8
Q ss_pred HHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcC
Q 009783 94 ELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLD 173 (526)
Q Consensus 94 ~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg 173 (526)
+.+..+..+ -.-||||+.+|...|... ....+|+..++..+ .++ ..++|..|++. +|
T Consensus 66 ev~~~~~~~--~~lVaHNa~FD~~~L~~~------------~~~~idTl~lar~l-~p~-------~~~~l~~L~~~-~~ 122 (219)
T PRK07983 66 DVIPHYYGS--EWYVAHNASFDRRVLPEM------------PGEWICTMKLARRL-WPG-------IKYSNMALYKS-RK 122 (219)
T ss_pred HHHHHHcCC--CEEEEeCcHhhHHHHhCc------------CCCcEeHHHHHHHH-ccC-------CCCCHHHHHHH-cC
Confidence 344444332 345999999999988641 14678944455444 443 34889888865 46
Q ss_pred CcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 174 ISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (526)
Q Consensus 174 ~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~ 214 (526)
+...... .. ...-|..||+++..|+..+.+
T Consensus 123 l~~~~~~-~~----------~aHrAl~Da~ata~ll~~l~~ 152 (219)
T PRK07983 123 LNVQTPP-GL----------HHHRALYDCYITAALLIDIMN 152 (219)
T ss_pred CCCCCCC-CC----------CCCcHHHHHHHHHHHHHHHHH
Confidence 5432100 00 123388999999999988864
No 87
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=83.24 E-value=2.3 Score=48.92 Aligned_cols=33 Identities=12% Similarity=0.100 Sum_probs=25.0
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCC
Q 009783 372 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 404 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~ 404 (526)
++||||..|++|.++.+.+.-...+...|+++|
T Consensus 31 ~aR~~r~~G~~V~~~~g~D~hG~~i~~~A~~~g 63 (673)
T PRK00133 31 WVRYQRMRGHEVLFVCADDAHGTPIMLKAEKEG 63 (673)
T ss_pred HHHHHHhcCCeeEEeCccCCCChHHHHHHHHcC
Confidence 799999999999998763322335777887765
No 88
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=83.17 E-value=1 Score=48.19 Aligned_cols=34 Identities=21% Similarity=0.181 Sum_probs=24.2
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009783 372 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 405 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 405 (526)
+|||+|+.|+||.++...+.-...+...|.++|.
T Consensus 28 ~aR~~r~~G~~v~~~tGtDehG~~i~~~A~~~g~ 61 (391)
T PF09334_consen 28 LARYLRLRGHDVLFVTGTDEHGSKIETAAEKQGI 61 (391)
T ss_dssp HHHHHHHTT-EEEEEEEEE-SSHHHHHHHHHTTS
T ss_pred HHHHHhhcccceeeEEecchhhHHHHHHHHHcCC
Confidence 7999999999998886533222357777877776
No 89
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=83.01 E-value=0.37 Score=36.71 Aligned_cols=18 Identities=17% Similarity=0.575 Sum_probs=14.7
Q ss_pred cCCceeecCCCCeEEecc
Q 009783 491 KNLQFWQCMDCNQLYWEV 508 (526)
Q Consensus 491 ~~~~F~~C~~CgkvyW~G 508 (526)
..++|.+||.||.+|=.-
T Consensus 13 DGE~~lrCPRC~~~FR~~ 30 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRR 30 (65)
T ss_pred CCceeeeCCchhHHHHHh
Confidence 357899999999998543
No 90
>TIGR00398 metG methionyl-tRNA synthetase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma
Probab=82.74 E-value=2.4 Score=47.11 Aligned_cols=34 Identities=12% Similarity=0.040 Sum_probs=26.9
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009783 372 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 405 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 405 (526)
++|+||..|+||.++.+.+.-+..++..|+++|.
T Consensus 28 l~R~~r~~G~~V~~v~g~D~~g~~i~~~a~~~g~ 61 (530)
T TIGR00398 28 YARYKRLRGYEVLFVCGTDEHGTKIELKAEQEGL 61 (530)
T ss_pred HHHHHHhcCCeEEEecccCCCCcHHHHHHHHcCC
Confidence 7999999999999987644334568888888773
No 91
>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=82.69 E-value=1.1 Score=31.29 Aligned_cols=34 Identities=18% Similarity=0.518 Sum_probs=21.5
Q ss_pred ccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEe
Q 009783 455 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYW 506 (526)
Q Consensus 455 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW 506 (526)
-.|+.|+..+. ++.+.. + ....--+|+.||..|+
T Consensus 3 ~~CP~C~~~~~---v~~~~~----------~-----~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFR---VVDSQL----------G-----ANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEE---eCHHHc----------C-----CCCCEEECCCCCCEEE
Confidence 36999999873 332221 1 1122567999999886
No 92
>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=82.53 E-value=2.7 Score=41.71 Aligned_cols=113 Identities=14% Similarity=0.191 Sum_probs=64.1
Q ss_pred hhHHHHHHhh--CCCCcEEEEEec-HHhHHHHHhhcccCCCccCcCCC-------------------------CceeeHH
Q 009783 91 SIWELLKELF--VSPDILKLGFKF-KQDLIYLSSTFCSQGCDIGFDRV-------------------------EPYLDIT 142 (526)
Q Consensus 91 ~~~~~L~~lL--~~~~i~KVgh~~-k~Dl~~L~~~~gi~~~~~~~~~~-------------------------~~~~Dlt 142 (526)
+++..+...+ .||+|+ +|||+ ..|+..|......+++. .|... .-++|+-
T Consensus 84 ~LL~~f~~~i~~~DPDii-vG~Ni~~fdl~~L~~R~~~l~i~-~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~ 161 (234)
T cd05776 84 ALLNFFLAKLQKIDPDVL-VGHDLEGFDLDVLLSRIQELKVP-HWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTY 161 (234)
T ss_pred HHHHHHHHHHhhcCCCEE-EeeccCCCCHHHHHHHHHHhCCC-ccccccccccccCccccccccccccccccCchhhccH
Confidence 3444444333 378875 89999 56998874332222321 11100 1255644
Q ss_pred HHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcc--ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009783 143 SIYNHLHHKQLGRKLPKETKSLANICKELLDISLSK--ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (526)
Q Consensus 143 ~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~K--~~q~s-dW~~RPL~~~qi~YAA~DA~~ll~L~~~L~ 213 (526)
.++..+.. ..+++|.++++.+||..-.. ..... -|....-...-+.|...||+..++|...|.
T Consensus 162 ~~~k~~~~--------~~sY~L~~va~~~Lg~~k~di~~~~i~~~~~~~~~l~~l~~y~~~Da~l~~~L~~kl~ 227 (234)
T cd05776 162 LSAKELIR--------CKSYDLTELSQQVLGIERQDIDPEEILNMYNDSESLLKLLEHTEKDAYLILQLMFKLN 227 (234)
T ss_pred HHHHHHhC--------CCCCChHHHHHHHhCcCcccCCHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence 44444432 35899999999999973211 11222 243301113348999999999999988773
No 93
>PRK11893 methionyl-tRNA synthetase; Reviewed
Probab=81.86 E-value=2.8 Score=46.21 Aligned_cols=34 Identities=15% Similarity=0.143 Sum_probs=25.8
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009783 372 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 405 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 405 (526)
++|+||..|++|.++.+.+.-+..++..|+++|.
T Consensus 30 ~~R~~r~~G~~v~~v~g~dd~g~~i~~~a~~~g~ 63 (511)
T PRK11893 30 LARFKRLRGYDVFFLTGTDEHGQKIQRKAEEAGI 63 (511)
T ss_pred HHHHHHhcCCcEEecCCCCCCChHHHHHHHHcCC
Confidence 7999999999999987644333467777777663
No 94
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=81.13 E-value=10 Score=36.67 Aligned_cols=92 Identities=14% Similarity=0.130 Sum_probs=55.6
Q ss_pred hhHHHHHHhhCCCCcEEEEEecH-HhHHHHHhhcccCCCccCcCCCCceeeHH--HHHHHhh-ccccCCCCCcCCccHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFK-QDLIYLSSTFCSQGCDIGFDRVEPYLDIT--SIYNHLH-HKQLGRKLPKETKSLAN 166 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k-~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt--~La~yLl-~~~~~~~~~~~~~gL~~ 166 (526)
+++..+..++.+.. .||||+. .|+..|.. +|. .+ . ....+|+. ....... .++ ...++|.+
T Consensus 73 evl~~f~~f~~~~~--lVaHNa~~fD~~fL~~-~g~-~~----~-~~~~idt~~~~~~~~~~~~~~------~~~~~L~~ 137 (195)
T PRK07247 73 EVLAAFKEFVGELP--LIGYNAQKSDLPILAE-NGL-DL----S-DQYQVDLYDEAFERRSSDLNG------IANLKLQT 137 (195)
T ss_pred HHHHHHHHHHCCCe--EEEEeCcHhHHHHHHH-cCC-Cc----C-CCceeehHHHHHHhhccccCC------CCCCCHHH
Confidence 35566777777654 4999996 79999976 343 11 0 11234521 1111111 111 24689999
Q ss_pred HHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 167 ICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVK 215 (526)
Q Consensus 167 Lv~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~ 215 (526)
|++. +|++. ..+ =|..||.++..|+..|...
T Consensus 138 La~~-~gi~~-~~H----------------rAl~DA~~ta~v~~~ll~~ 168 (195)
T PRK07247 138 VADF-LGIKG-RGH----------------NSLEDARMTARVYESFLES 168 (195)
T ss_pred HHHh-cCCCC-CCc----------------CCHHHHHHHHHHHHHHHhh
Confidence 9886 57653 112 1778999999999988664
No 95
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=80.27 E-value=0.54 Score=43.75 Aligned_cols=44 Identities=14% Similarity=0.301 Sum_probs=26.4
Q ss_pred cccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecccchhhHH
Q 009783 456 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVMSAYLFI 515 (526)
Q Consensus 456 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~GsH~~r~~ 515 (526)
+||.|+++.... ++.. ..+++ +...+|++|+.||+.| +|..++.
T Consensus 2 ~cp~c~~~~~~~-~~s~----------~~~~~--~~~~~~~~c~~c~~~f---~~~e~~~ 45 (154)
T PRK00464 2 RCPFCGHPDTRV-IDSR----------PAEDG--NAIRRRRECLACGKRF---TTFERVE 45 (154)
T ss_pred cCCCCCCCCCEe-Eecc----------ccCCC--CceeeeeeccccCCcc---eEeEecc
Confidence 799999976321 1111 22332 1245679999999988 4555443
No 96
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=79.90 E-value=3.1 Score=46.59 Aligned_cols=33 Identities=21% Similarity=0.156 Sum_probs=24.8
Q ss_pred HHHHHHhcCCceecCCCCCCChH-HHHHhhhcCCc
Q 009783 372 LAKHLRCVGIDAATPRSKKPEPR-ELIDQTSKEKR 405 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~~~~d~-~ll~~A~~E~R 405 (526)
+||++|+.|+||.++...+ ++. .|...|+++|.
T Consensus 34 ~aRy~Rl~G~~v~fvtGtD-eHGt~I~~~A~~~g~ 67 (558)
T COG0143 34 YARYLRLRGYEVFFLTGTD-EHGTKIELKAEKEGI 67 (558)
T ss_pred HHHHHHhcCCeEEEEeccC-CCCCHHHHHHHHcCC
Confidence 7999999999999987532 332 47777777774
No 97
>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=79.41 E-value=19 Score=34.99 Aligned_cols=110 Identities=21% Similarity=0.204 Sum_probs=62.4
Q ss_pred hhhHHHHHHhhCCCCcEEEEEecH-HhHHHHHhhcccCCCcc--CcCC-----------CCceeeHHHHHHHhhccccCC
Q 009783 90 PSIWELLKELFVSPDILKLGFKFK-QDLIYLSSTFCSQGCDI--GFDR-----------VEPYLDITSIYNHLHHKQLGR 155 (526)
Q Consensus 90 ~~~~~~L~~lL~~~~i~KVgh~~k-~Dl~~L~~~~gi~~~~~--~~~~-----------~~~~~Dlt~La~yLl~~~~~~ 155 (526)
.+++..+..++++.....||||.+ +|+..|....-.+|+.. .+.. ....+|+-.+.+....
T Consensus 79 ~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~~----- 153 (208)
T cd05782 79 KELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYGA----- 153 (208)
T ss_pred HHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccCc-----
Confidence 345666556666522345999995 69999865433333321 0100 0126785444322111
Q ss_pred CCCcCCccHHHHHHHHcCCcCcc----ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009783 156 KLPKETKSLANICKELLDISLSK----ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (526)
Q Consensus 156 ~~~~~~~gL~~Lv~~~Lg~~L~K----~~q~s-dW~~RPL~~~qi~YAA~DA~~ll~L~~ 210 (526)
..+.+|..+++ +||.+ .| +.+.. -|.... ...-..|...||..+..||.
T Consensus 154 ---~~~~~L~~va~-~lG~~-~K~d~~G~~v~~~y~~g~-~~~I~~Yc~~Dv~~t~~l~l 207 (208)
T cd05782 154 ---RARASLDLLAK-LLGIP-GKMDVDGSQVWELYAEGK-LDEIAEYCETDVLNTYLLYL 207 (208)
T ss_pred ---cCCCCHHHHHH-HhCCC-CCcCCCHHHHHHHHHcCC-hHHHHHHHHHHHHHHHHHHh
Confidence 25789999986 67773 22 11221 244433 45668999999999998874
No 98
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=79.38 E-value=6.2 Score=45.47 Aligned_cols=108 Identities=19% Similarity=0.213 Sum_probs=67.0
Q ss_pred CcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhcccc---CC-----------------CCC-----
Q 009783 104 DILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQL---GR-----------------KLP----- 158 (526)
Q Consensus 104 ~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~---~~-----------------~~~----- 158 (526)
.-+.||||..+|...++..|.+-|. -..++| ||-.+.-. .+. .+ ..|
T Consensus 241 e~liVGHNVsfDRaRirEeY~i~~S------k~rFlD-TMSlHia~-~Gm~S~Qrplw~ka~k~k~a~~d~~~~ps~~d~ 312 (1075)
T KOG3657|consen 241 EQLIVGHNVSFDRARIREEYNINGS------KIRFLD-TMSLHIAM-SGMCSRQRPLWFKARKAKSAMYDSETNPSISDY 312 (1075)
T ss_pred CceEEeccccchHHHHHHHHhcccc------ceeeee-chhhhhhh-hccccccchhHhhhhhhhhhhhhcccCCchhhh
Confidence 4566999999999999988877431 245789 76433211 110 00 000
Q ss_pred -------cCCccHHHHHHHHcCCc-Cccccccc--CCCCCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 009783 159 -------KETKSLANICKELLDIS-LSKELQCS--DWSNRPLT---EEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (526)
Q Consensus 159 -------~~~~gL~~Lv~~~Lg~~-L~K~~q~s--dW~~RPL~---~~qi~YAA~DA~~ll~L~~~L~~~L~~~ 219 (526)
..--||.++...+.|+. ++|+...+ .-...++. .+-++|.|.|++++.+++..+-+...+.
T Consensus 313 ~~pWL~~SS~NSL~dVhk~~c~~~~LdKt~Rd~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Fler 386 (1075)
T KOG3657|consen 313 DNPWLGRSSLNSLVDVHKFHCGIDALDKTPRDSFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLER 386 (1075)
T ss_pred hhhhhhhhhhHHHHHHHHhhCCCCccccchHHhhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHHh
Confidence 01135777777788887 77754322 11111222 1228999999999999999998877654
No 99
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=79.25 E-value=3.6 Score=46.98 Aligned_cols=33 Identities=18% Similarity=0.171 Sum_probs=25.4
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCC
Q 009783 372 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 404 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~ 404 (526)
++|++|+.|+||.++.+.+.-+..+...|+++|
T Consensus 33 ~~R~~r~~G~~v~~~~g~D~~g~~i~~~A~~~g 65 (648)
T PRK12267 33 LARYKRLQGYDVFFLTGTDEHGQKIQQAAEKAG 65 (648)
T ss_pred HHHHHHhcCCceEeecCCCCcchHHHHHHHHcC
Confidence 799999999999998764332346777777776
No 100
>PF09281 Taq-exonuc: Taq polymerase, exonuclease; InterPro: IPR015361 This domain is found in prokaryotic Taq DNA polymerase (thermostable), where it assumes a ribonuclease H-like motif. The domain confers 5'-3' exonuclease activity to the polymerase []. ; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 4DF4_A 3T3F_A 1QSY_A 3OJS_A 3PO5_A 3OJU_A 1QTM_A 1QSS_A 3PY8_A 4DFJ_A ....
Probab=78.79 E-value=10 Score=34.12 Aligned_cols=55 Identities=18% Similarity=0.289 Sum_probs=35.2
Q ss_pred CCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 135 VEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (526)
Q Consensus 135 ~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~ 214 (526)
+.+--| -+|.+||+++. +.+...++++|+|- +|... |+..|.+.-+|++.|..
T Consensus 84 v~PGDD-PlLlAYLlDPs--------Nt~p~~varRY~~~---------~W~~d---------A~~RA~~t~~L~~~L~p 136 (138)
T PF09281_consen 84 VEPGDD-PLLLAYLLDPS--------NTNPEGVARRYLGG---------EWPED---------AATRALATARLLRALPP 136 (138)
T ss_dssp --B----HHHHHHHH-TT----------SHHHHHHHH-TS------------SS---------HHHHHHHHHHHHHHHHH
T ss_pred cCCCCC-cchhhhhcCcc--------CCChHHHHHHhcCC---------CCCcc---------HHHHHHHHHHHHHHhhh
Confidence 355668 99999999984 67899999999873 45322 77888888888888877
Q ss_pred HH
Q 009783 215 KV 216 (526)
Q Consensus 215 ~L 216 (526)
+|
T Consensus 137 rL 138 (138)
T PF09281_consen 137 RL 138 (138)
T ss_dssp HT
T ss_pred cC
Confidence 54
No 101
>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=76.96 E-value=15 Score=34.77 Aligned_cols=99 Identities=18% Similarity=0.262 Sum_probs=53.0
Q ss_pred hHHHHHHhhCCCCcEEEEEe-cHHhHHHHHhhcccCCCccCcC----CCCceeeHHHHHHHhh--ccccCCCCC-----c
Q 009783 92 IWELLKELFVSPDILKLGFK-FKQDLIYLSSTFCSQGCDIGFD----RVEPYLDITSIYNHLH--HKQLGRKLP-----K 159 (526)
Q Consensus 92 ~~~~L~~lL~~~~i~KVgh~-~k~Dl~~L~~~~gi~~~~~~~~----~~~~~~Dlt~La~yLl--~~~~~~~~~-----~ 159 (526)
++..+..++..+....|||| +.+|+..|.+.+.-.+..+ +. .....+|+..++.... .+. ....| .
T Consensus 72 ~l~~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~-~~~~~~~~~~~~dtl~l~r~~~~~~~~-~~~~~~~~~~~ 149 (183)
T cd06138 72 FIAKIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDP-YTWEWKNGNSRWDLLDVVRAYYALRPD-GIVWPKNDDGK 149 (183)
T ss_pred HHHHHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcc-cceeccCCccccccHHHHHHHHhhChh-hccCccccCCC
Confidence 34556667765444458997 7899999876532212110 00 0122457444554332 121 00000 1
Q ss_pred CCccHHHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009783 160 ETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (526)
Q Consensus 160 ~~~gL~~Lv~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~ 209 (526)
.+++|++++++ +|++.... .-|..||.++.+|.
T Consensus 150 ~~~~L~~l~~~-~gi~~~~~----------------H~Al~Da~~ta~l~ 182 (183)
T cd06138 150 PSFKLEDLAQA-NGIEHSNA----------------HDALSDVEATIALA 182 (183)
T ss_pred cchhHHHHHHH-CCCCcccc----------------ccHHHHHHHHHHHh
Confidence 36789999986 57654222 33788998887663
No 102
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=76.09 E-value=3.3 Score=30.71 Aligned_cols=17 Identities=12% Similarity=0.098 Sum_probs=14.0
Q ss_pred ceeecCCCCeEEecccc
Q 009783 494 QFWQCMDCNQLYWEVMS 510 (526)
Q Consensus 494 ~F~~C~~CgkvyW~GsH 510 (526)
..+.|+.||-++..+..
T Consensus 19 ~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 19 RRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CEEECCcCCCeEECCCc
Confidence 48899999998887654
No 103
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=75.94 E-value=20 Score=35.30 Aligned_cols=98 Identities=19% Similarity=0.186 Sum_probs=62.1
Q ss_pred hHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHH
Q 009783 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKEL 171 (526)
Q Consensus 92 ~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~ 171 (526)
+.+.+..++.+. -.-|+||...|+..|...+...+..+ ....++|.-.++... .++ ....+|..|+. .
T Consensus 84 v~~~~~~~i~~~-~~~Vahna~fD~~fl~~~~~~~~~~~---~~~~~~~t~~~~r~~-~~~------~~~~~L~~l~~-~ 151 (243)
T COG0847 84 VLPEFLDFIGGL-RLLVAHNAAFDVGFLRVESERLGIEI---PGDPVLDTLALARRH-FPG------FDRSSLDALAE-R 151 (243)
T ss_pred HHHHHHHHHCCC-CeEEEEchhhcHHHHHHHHHHcCCCc---ccCceehHHHHHHHH-cCC------CccchHHHHHH-H
Confidence 445555666663 34499999999999875544333221 135677844444433 332 25789999999 6
Q ss_pred cCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 172 LDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVK 215 (526)
Q Consensus 172 Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~ 215 (526)
+|+...... . .-|..||.++..++..+...
T Consensus 152 ~gi~~~~~~-~-------------H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 152 LGIDRNPFH-P-------------HRALFDALALAELFLLLQTG 181 (243)
T ss_pred cCCCcCCcC-C-------------cchHHHHHHHHHHHHHHHhc
Confidence 677643111 1 22889999999999988763
No 104
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=75.77 E-value=1.9 Score=30.69 Aligned_cols=24 Identities=8% Similarity=0.324 Sum_probs=18.7
Q ss_pred CceeecCCCCeEEecccchhhHHh
Q 009783 493 LQFWQCMDCNQLYWEVMSAYLFIF 516 (526)
Q Consensus 493 ~~F~~C~~CgkvyW~GsH~~r~~~ 516 (526)
-...+|++||-++=.+.=+.++++
T Consensus 17 ~~id~C~~C~G~W~d~~el~~~~e 40 (41)
T PF13453_consen 17 VEIDVCPSCGGIWFDAGELEKLLE 40 (41)
T ss_pred EEEEECCCCCeEEccHHHHHHHHh
Confidence 467889999999887776666654
No 105
>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=75.66 E-value=25 Score=32.28 Aligned_cols=97 Identities=12% Similarity=0.065 Sum_probs=57.2
Q ss_pred hhHHHHHHhhCCC-CcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHH
Q 009783 91 SIWELLKELFVSP-DILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (526)
Q Consensus 91 ~~~~~L~~lL~~~-~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~ 169 (526)
++++.+.+++.+. ... +.++...|...+...+...+..+........+|+..++..+.+. ....+|++++.
T Consensus 77 ~vl~~~~~~l~~~~~~~-~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~-------~~~~~L~~l~~ 148 (176)
T cd06133 77 EVLKEFLEWLGKNGKYA-FVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGL-------KKRTGLSKALE 148 (176)
T ss_pred HHHHHHHHHHHhCCCeE-EEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCC-------CCCCCHHHHHH
Confidence 3556777788774 133 44455888766543211111110001235789977777766542 14789999986
Q ss_pred HHcCCcCc-ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009783 170 ELLDISLS-KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (526)
Q Consensus 170 ~~Lg~~L~-K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L 212 (526)
. +|++.. ..+ -|-.||.++.+|+..|
T Consensus 149 ~-~gi~~~~~~H----------------~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 149 Y-LGLEFEGRHH----------------RGLDDARNIARILKRL 175 (176)
T ss_pred H-CCCCCCCCCc----------------CcHHHHHHHHHHHHHh
Confidence 5 577664 122 2778999998888765
No 106
>PRK00420 hypothetical protein; Validated
Probab=75.59 E-value=2 Score=37.85 Aligned_cols=48 Identities=13% Similarity=0.095 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHHcCccccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEec
Q 009783 431 LLKNQQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWE 507 (526)
Q Consensus 431 ~~~~~QL~~vl~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~ 507 (526)
+++..++.+.+..-.-.. -..|+.|+.+|.. . .+.-.+||.||+++=.
T Consensus 5 ~~~~k~~a~~Ll~Ga~ml-----~~~CP~Cg~pLf~--l----------------------k~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 5 EDIVKKAAELLLKGAKML-----SKHCPVCGLPLFE--L----------------------KDGEVVCPVHGKVYIV 52 (112)
T ss_pred HHHHHHHHHHHHhHHHHc-----cCCCCCCCCccee--c----------------------CCCceECCCCCCeeee
Confidence 344556666654421111 1469999998741 0 1224569999998854
No 107
>PRK05762 DNA polymerase II; Reviewed
Probab=75.39 E-value=58 Score=38.29 Aligned_cols=112 Identities=18% Similarity=0.243 Sum_probs=64.0
Q ss_pred hhHHHHHHhhC--CCCcEEEEEecH-HhHHHHHhhcccCCCccCcCC---------------------C-CceeeHHHHH
Q 009783 91 SIWELLKELFV--SPDILKLGFKFK-QDLIYLSSTFCSQGCDIGFDR---------------------V-EPYLDITSIY 145 (526)
Q Consensus 91 ~~~~~L~~lL~--~~~i~KVgh~~k-~Dl~~L~~~~gi~~~~~~~~~---------------------~-~~~~Dlt~La 145 (526)
+++..+..++. ||+|+ +|||.. +|+..|.+....+|+...+.. . ..++|+-.++
T Consensus 205 ~LL~~F~~~i~~~DPDII-vGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~ 283 (786)
T PRK05762 205 ALLEKFNAWFAEHDPDVI-IGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDAL 283 (786)
T ss_pred HHHHHHHHHHHhcCCCEE-EEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHH
Confidence 45555555444 47765 899976 699888544333333211000 0 1266754443
Q ss_pred HHhhccccCCCCCcCCccHHHHHHHHcCCcCcc--c----cccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009783 146 NHLHHKQLGRKLPKETKSLANICKELLDISLSK--E----LQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (526)
Q Consensus 146 ~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~K--~----~q~s-dW~~RPL~~~qi~YAA~DA~~ll~L~~~L 212 (526)
...... ..+++|..+++++||..-.. . .++. -|... ....+.|...||..++.|+..+
T Consensus 284 k~~~~~-------l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~--~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 284 KSATWV-------FDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAED--KPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred HHhhcc-------CCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhh--HHHHHHHHHHHHHHHHHHHHHh
Confidence 332211 25789999999999854211 1 1111 23311 2556899999999999999843
No 108
>PRK12496 hypothetical protein; Provisional
Probab=75.12 E-value=4.1 Score=38.35 Aligned_cols=46 Identities=15% Similarity=0.103 Sum_probs=28.9
Q ss_pred cHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecChhHHHhh
Q 009783 369 VEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRDAKLLRHQ 418 (526)
Q Consensus 369 Lg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~RiiLTrd~~l~~~~ 418 (526)
+..+-+-.+.-| |...++ ..|.+++.+|.+.+-++||-|..+-+-+
T Consensus 60 i~~v~~~a~~tg-d~~~Ls---~~D~~~iaLA~el~~~lvtDD~~~~~vA 105 (164)
T PRK12496 60 IEKVEEAAIKTG-DLMRLS---NTDIEVLALALELNGTLYTDDYGIQNVA 105 (164)
T ss_pred HHHHHHHHHhcC-Cccccc---hhhHHHHHHHHHhCCcEECcHHHHHHHH
Confidence 444444444455 432232 3467899999988889999997764433
No 109
>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=74.94 E-value=2.7 Score=26.68 Aligned_cols=9 Identities=33% Similarity=0.899 Sum_probs=7.3
Q ss_pred ccCCCcccc
Q 009783 457 CTKCNGRFI 465 (526)
Q Consensus 457 C~~CN~~l~ 465 (526)
|..||..+.
T Consensus 1 C~sC~~~i~ 9 (24)
T PF07754_consen 1 CTSCGRPIA 9 (24)
T ss_pred CccCCCccc
Confidence 889999874
No 110
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=74.08 E-value=1.9 Score=30.10 Aligned_cols=11 Identities=27% Similarity=0.887 Sum_probs=9.9
Q ss_pred eecCCCCeEEe
Q 009783 496 WQCMDCNQLYW 506 (526)
Q Consensus 496 ~~C~~CgkvyW 506 (526)
|.|+.||++|=
T Consensus 2 r~C~~Cg~~Yh 12 (36)
T PF05191_consen 2 RICPKCGRIYH 12 (36)
T ss_dssp EEETTTTEEEE
T ss_pred cCcCCCCCccc
Confidence 68999999994
No 111
>PLN02610 probable methionyl-tRNA synthetase
Probab=73.78 E-value=6.4 Score=46.15 Aligned_cols=33 Identities=15% Similarity=0.055 Sum_probs=22.8
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCC
Q 009783 372 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 404 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~ 404 (526)
+|||+|+.|+||.++...+.-.-.+...|.++|
T Consensus 47 ~aRy~r~~G~~v~f~~GtDehG~~i~~~A~~~g 79 (801)
T PLN02610 47 FARYCRLRGYNAIYICGTDEYGTATETKALEEN 79 (801)
T ss_pred HHHHHHhCCCceEecccccCCcHHHHHHHHHcC
Confidence 699999999999998753322224555565555
No 112
>TIGR00435 cysS cysteinyl-tRNA synthetase. This model finds the cysteinyl-tRNA synthetase from most but not from all species. The enzyme from one archaeal species, Archaeoglobus fulgidus, is found but the equivalent enzymes from some other Archaea, including Methanococcus jannaschii, are not found, although biochemical evidence suggests that tRNA(Cys) in these species are charged directly with Cys rather than through a misacylation and correction pathway as for tRNA(Gln).
Probab=73.64 E-value=7.3 Score=42.78 Aligned_cols=35 Identities=14% Similarity=0.202 Sum_probs=27.6
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009783 371 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 405 (526)
Q Consensus 371 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 405 (526)
-++|+||..||+|.++.+.+.-|..++..|+++|.
T Consensus 48 vl~R~lr~~G~~V~~v~n~tD~ddkIi~~A~~~g~ 82 (465)
T TIGR00435 48 VLRRYLRYLGYKVQYVQNITDIDDKIIKRARENGE 82 (465)
T ss_pred HHHHHHHHcCCcEEEEEeeCCccHHHHHHHHHcCC
Confidence 48999999999999887643334578888988775
No 113
>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=73.48 E-value=1.7 Score=32.27 Aligned_cols=39 Identities=21% Similarity=0.484 Sum_probs=20.9
Q ss_pred cccCCCcccccCCCChHHHHHhhhcCcccCccc-cccCCceeecCCCCe
Q 009783 456 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCL-FDKNLQFWQCMDCNQ 503 (526)
Q Consensus 456 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v-~~~~~~F~~C~~Cgk 503 (526)
+|..|+-.--+.. .+. ...||+++ |+.-.+=|.||.|+-
T Consensus 3 ~C~~CgyvYd~~~---Gd~------~~~i~pGt~F~~Lp~~w~CP~C~a 42 (47)
T PF00301_consen 3 QCPVCGYVYDPEK---GDP------ENGIPPGTPFEDLPDDWVCPVCGA 42 (47)
T ss_dssp EETTTSBEEETTT---BBG------GGTB-TT--GGGS-TT-B-TTTSS
T ss_pred CCCCCCEEEcCCc---CCc------ccCcCCCCCHHHCCCCCcCcCCCC
Confidence 6999997543211 110 02466665 677777899999984
No 114
>PHA02119 hypothetical protein
Probab=72.45 E-value=1.4 Score=35.18 Aligned_cols=15 Identities=33% Similarity=0.578 Sum_probs=12.9
Q ss_pred HHHHHHHhcCCceec
Q 009783 371 GLAKHLRCVGIDAAT 385 (526)
Q Consensus 371 ~Lar~LR~lG~D~~~ 385 (526)
-+.-|||.+|||+..
T Consensus 58 divdylr~lgy~~~~ 72 (87)
T PHA02119 58 DIVDYLRSLGYDAKS 72 (87)
T ss_pred HHHHHHHHccchhcc
Confidence 478899999999874
No 115
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=72.32 E-value=0.92 Score=45.18 Aligned_cols=55 Identities=11% Similarity=0.282 Sum_probs=32.4
Q ss_pred HHHHHc-CccccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE-Eecccch
Q 009783 439 EVIEAF-QLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL-YWEVMSA 511 (526)
Q Consensus 439 ~vl~~f-~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv-yW~GsH~ 511 (526)
.+.+.+ |+.+-|-. --+|.-|+-.| |. ... ..|.+ .++.-+||.||+| ||.-+|.
T Consensus 182 ri~~~~kg~gvvpl~-g~~C~GC~m~l---~~--~~~-----------~~V~~-~d~iv~CP~CgRILy~~e~~~ 238 (239)
T COG1579 182 RIRKNKKGVGVVPLE-GRVCGGCHMKL---PS--QTL-----------SKVRK-KDEIVFCPYCGRILYYDESEE 238 (239)
T ss_pred HHHhcCCCceEEeec-CCcccCCeeee---cH--HHH-----------HHHhc-CCCCccCCccchHHHhhhccc
Confidence 344445 44443321 36899999876 21 111 12223 5677889999996 8876653
No 116
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=71.24 E-value=1.1 Score=51.78 Aligned_cols=89 Identities=18% Similarity=0.254 Sum_probs=61.1
Q ss_pred hhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcc
Q 009783 99 LFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSK 178 (526)
Q Consensus 99 lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~~Lg~~L~K 178 (526)
+|-+-.++.|||++++|...+- + -+ | .+.++| |...- +++. .+..+|.-||..+||..+--
T Consensus 1009 ~Li~~GviFVGHGL~nDFrvIN----i-~V-p----~~QiiD-Tv~lf-~~~s-------~R~LSLrfLa~~lLg~~IQ~ 1069 (1118)
T KOG1275|consen 1009 LLIQRGVIFVGHGLQNDFRVIN----I-HV-P----EEQIID-TVTLF-RLGS-------QRMLSLRFLAWELLGETIQM 1069 (1118)
T ss_pred HHHHcCcEEEcccccccceEEE----E-ec-C----hhhhee-eeEEE-eccc-------ccEEEHHHHHHHHhcchhhc
Confidence 6778899999999999988652 1 10 1 144778 54322 2222 25789999999999987632
Q ss_pred cccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009783 179 ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGFA 222 (526)
Q Consensus 179 ~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~ 222 (526)
+. .| ..+||..++.||++..+ |+++|+.
T Consensus 1070 ~~--HD-------------SIeDA~taLkLYk~Yl~-lkeq~~~ 1097 (1118)
T KOG1275|consen 1070 EA--HD-------------SIEDARTALKLYKKYLK-LKEQGKL 1097 (1118)
T ss_pred cc--cc-------------cHHHHHHHHHHHHHHHH-HHHhhHH
Confidence 21 11 45899999999999864 7888766
No 117
>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=71.17 E-value=2.6 Score=25.64 Aligned_cols=14 Identities=14% Similarity=0.503 Sum_probs=10.9
Q ss_pred eecCCCCeEEeccc
Q 009783 496 WQCMDCNQLYWEVM 509 (526)
Q Consensus 496 ~~C~~CgkvyW~Gs 509 (526)
|.|+.|++.|=.-+
T Consensus 1 y~C~~C~~~f~~~~ 14 (23)
T PF00096_consen 1 YKCPICGKSFSSKS 14 (23)
T ss_dssp EEETTTTEEESSHH
T ss_pred CCCCCCCCccCCHH
Confidence 68999999994433
No 118
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.15 E-value=3.7 Score=33.58 Aligned_cols=39 Identities=13% Similarity=0.329 Sum_probs=27.6
Q ss_pred cccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecccchhhHH
Q 009783 456 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVMSAYLFI 515 (526)
Q Consensus 456 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~GsH~~r~~ 515 (526)
-|+.||..|+. + -..+-||-+||+|+-|.-.+.--..+|
T Consensus 3 lCP~C~v~l~~--~-------------------~rs~vEiD~CPrCrGVWLDrGELdKli 41 (88)
T COG3809 3 LCPICGVELVM--S-------------------VRSGVEIDYCPRCRGVWLDRGELDKLI 41 (88)
T ss_pred ccCcCCceeee--e-------------------eecCceeeeCCccccEeecchhHHHHH
Confidence 59999998852 1 013457999999999987776555444
No 119
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=70.62 E-value=1.3 Score=43.54 Aligned_cols=54 Identities=17% Similarity=0.326 Sum_probs=28.8
Q ss_pred ccccCCCcccccCCCChHHHH--HhhhcCcccCccccccCCceeecCCCCeEEecc
Q 009783 455 SRCTKCNGRFIQKPLSTEEAV--EAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEV 508 (526)
Q Consensus 455 sRC~~CN~~l~~~~~~~e~~~--~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~G 508 (526)
..|++|+..+..+.|-....+ ....-+...-..|....-+.|.||.||=-++++
T Consensus 6 ~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 6 ITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred eECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 579999998854332111110 000000111111222345689999999988876
No 120
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=70.46 E-value=1 Score=32.92 Aligned_cols=43 Identities=16% Similarity=0.423 Sum_probs=27.2
Q ss_pred ccccCCCcccccCCCChHHHHHhhhcCcccCc--cccccCCceeecCCCC
Q 009783 455 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPD--CLFDKNLQFWQCMDCN 502 (526)
Q Consensus 455 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~--~v~~~~~~F~~C~~Cg 502 (526)
.-|+.|++.|. ++..+.+.+ ..+.+|. .|.+....-|.|+.||
T Consensus 3 ~~C~~Cg~~l~--~ig~~~~~q---~l~~~p~~~~V~e~~~~~y~C~~C~ 47 (47)
T PF13005_consen 3 RACPDCGGELK--EIGEEKVRQ---VLDLPPAKPEVTEHVRHKYACPCCG 47 (47)
T ss_pred CcCCCCCceee--ECCceeeEE---EEeecccceEEEEEEeceEECCCCC
Confidence 46999999985 343332322 1223333 3456778899999997
No 121
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=69.41 E-value=2.2 Score=37.71 Aligned_cols=27 Identities=11% Similarity=0.180 Sum_probs=21.8
Q ss_pred CCceeecCCCCeEEecccchhhHHhhh
Q 009783 492 NLQFWQCMDCNQLYWEVMSAYLFIFLT 518 (526)
Q Consensus 492 ~~~F~~C~~CgkvyW~GsH~~r~~~~~ 518 (526)
....|+|+.||-.|+...+..+...++
T Consensus 28 ~~~~~~C~~CGe~~~~~e~~~~~~~~i 54 (127)
T TIGR03830 28 GVPGWYCPACGEELLDPEESKRNSAAL 54 (127)
T ss_pred eeeeeECCCCCCEEEcHHHHHHHHHHH
Confidence 457889999999999988877755554
No 122
>PRK06722 exonuclease; Provisional
Probab=69.19 E-value=34 Score=35.11 Aligned_cols=100 Identities=19% Similarity=0.119 Sum_probs=57.5
Q ss_pred hhHHHHHHhhCCCCcEEEEEecHHhHHHHHhhcccCCCccCcCCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009783 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (526)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~~~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~Lv~~ 170 (526)
+++..+..++.+..+ |+|+...|+..|...+...|+...+......+|+..++..+... +.....+|+++++.
T Consensus 79 eVl~ef~~fig~~~l--vahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~-----l~~~~~sL~~l~~~ 151 (281)
T PRK06722 79 QIIEKFIQFIGEDSI--FVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEE-----LFEHTPSLQSAVEQ 151 (281)
T ss_pred HHHHHHHHHHCCCcE--EEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhh-----hccCCCCHHHHHHH
Confidence 456667777776444 67778999999876543323211000012246755444332211 00134689999987
Q ss_pred HcCCcCc-ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 009783 171 LLDISLS-KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (526)
Q Consensus 171 ~Lg~~L~-K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~ 214 (526)
+ |++.. ..+ -|-.||.++..|+..|..
T Consensus 152 l-gL~~~g~~H----------------rAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 152 L-GLIWEGKQH----------------RALADAENTANILLKAYS 179 (281)
T ss_pred C-CCCCCCCCc----------------CcHHHHHHHHHHHHHHhc
Confidence 5 66542 122 277899999999988863
No 123
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=67.97 E-value=3.5 Score=36.05 Aligned_cols=45 Identities=20% Similarity=0.428 Sum_probs=25.9
Q ss_pred ccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEeccc
Q 009783 452 QLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVM 509 (526)
Q Consensus 452 ~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~Gs 509 (526)
.+--||++||.+=. .-..-+-+-+. +....||.|++|+.-|=++|
T Consensus 72 ~I~~kCpkCghe~m--~Y~T~QlRSAD-----------EGQTVFYTC~kC~~k~~e~s 116 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEM--SYHTLQLRSAD-----------EGQTVFYTCPKCKYKFTENS 116 (116)
T ss_pred chhccCcccCCchh--hhhhhhccccc-----------CCceEEEEcCccceeeeccC
Confidence 34468999998521 01111111111 23567999999998775543
No 124
>cd00672 CysRS_core catalytic core domain of cysteinyl tRNA synthetase. Cysteinyl tRNA synthetase (CysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.
Probab=67.88 E-value=4 Score=40.03 Aligned_cols=34 Identities=15% Similarity=0.158 Sum_probs=26.1
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCC
Q 009783 371 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 404 (526)
Q Consensus 371 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~ 404 (526)
=|+|+||..|++|.++.+.+.-+..++..|+++|
T Consensus 47 vl~R~lr~~G~~V~~~~g~dd~g~ki~~~A~~~g 80 (213)
T cd00672 47 VLRRYLEDLGYKVRYVQNITDIDDKIIKRAREEG 80 (213)
T ss_pred HHHHHHHhcCCeeEEEeecCCCCCHHHHHHHHcC
Confidence 4899999999999988764333456888887764
No 125
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=67.66 E-value=4.7 Score=30.71 Aligned_cols=33 Identities=21% Similarity=0.574 Sum_probs=22.4
Q ss_pred ccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009783 455 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 504 (526)
Q Consensus 455 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 504 (526)
.+|.-|+-.+ +.....+ + ...++...||.||+|
T Consensus 23 ~~C~gC~~~l-----~~~~~~~-----------i-~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 23 GTCSGCHMEL-----PPQELNE-----------I-RKGDEIVFCPNCGRI 55 (56)
T ss_pred CccCCCCEEc-----CHHHHHH-----------H-HcCCCeEECcCCCcc
Confidence 5899999975 2333322 1 123678999999986
No 126
>PF14353 CpXC: CpXC protein
Probab=66.27 E-value=5.1 Score=35.74 Aligned_cols=19 Identities=21% Similarity=0.604 Sum_probs=14.3
Q ss_pred cccccCCceeecCCCCeEE
Q 009783 487 CLFDKNLQFWQCMDCNQLY 505 (526)
Q Consensus 487 ~v~~~~~~F~~C~~Cgkvy 505 (526)
.+++..--.+.||.||+.+
T Consensus 30 ~il~g~l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 30 KILDGSLFSFTCPSCGHKF 48 (128)
T ss_pred HHHcCCcCEEECCCCCCce
Confidence 3556666788999999854
No 127
>TIGR03447 mycothiol_MshC cysteine--1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase. Members of this protein family are MshC, l-cysteine:1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase, an enzyme that uses ATP to ligate a Cys residue to a mycothiol precursor molecule, in the second to last step in mycothiol biosynthesis. This enzyme shows considerable homology to Cys--tRNA ligases, and many instances are misannotated as such. Mycothiol is found in Mycobacterium tuberculosis, Corynebacterium glutamicum, Streptomyces coelicolor, and various other members of the Actinobacteria. Mycothiol is an analog to glutathione.
Probab=66.09 E-value=5.1 Score=43.23 Aligned_cols=34 Identities=9% Similarity=0.118 Sum_probs=27.7
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009783 372 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 405 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 405 (526)
|+|+||..||||.++.+.+.-|+.|+..|+++|.
T Consensus 64 l~R~lr~~G~~V~fV~nitD~dDKIi~~A~~~g~ 97 (411)
T TIGR03447 64 VNRVWRDAGHRVHYVQNVTDVDDPLFERAERDGV 97 (411)
T ss_pred HHHHHHhcCCceEEeeCCCchhHHHHHHHHHcCC
Confidence 8999999999999987643334579999988874
No 128
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=65.79 E-value=3 Score=43.29 Aligned_cols=11 Identities=27% Similarity=1.174 Sum_probs=9.5
Q ss_pred CceeecCCCCe
Q 009783 493 LQFWQCMDCNQ 503 (526)
Q Consensus 493 ~~F~~C~~Cgk 503 (526)
.-||.||+|++
T Consensus 366 ~l~W~CPsC~~ 376 (389)
T COG2956 366 TLYWHCPSCRA 376 (389)
T ss_pred eeeeeCCCccc
Confidence 45999999986
No 129
>PRK12418 cysteinyl-tRNA synthetase; Provisional
Probab=64.49 E-value=5.3 Score=42.75 Aligned_cols=36 Identities=11% Similarity=0.115 Sum_probs=28.8
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcE
Q 009783 371 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRV 406 (526)
Q Consensus 371 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~Ri 406 (526)
=|+|+||.+||+|.++.+.+.-|..|+..|+++|.-
T Consensus 36 vl~R~lr~~G~~V~~V~nitD~ddKIi~~A~~~G~~ 71 (384)
T PRK12418 36 LVNRVWRDAGHDVHYVQNVTDVDDPLLERAARDGVD 71 (384)
T ss_pred HHHHHHHHcCCceEEEEecCCcchHHHHHHHHcCCC
Confidence 389999999999999876443346799999988753
No 130
>PRK12366 replication factor A; Reviewed
Probab=64.36 E-value=2.4 Score=48.36 Aligned_cols=36 Identities=17% Similarity=0.371 Sum_probs=25.4
Q ss_pred cccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecccchhh
Q 009783 451 DQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVMSAYL 513 (526)
Q Consensus 451 ~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~GsH~~r 513 (526)
...+.+|+.||..+.. ...-|+|+.||++ ++.|.++
T Consensus 529 ~~~y~aCp~CnkKv~~-------------------------~~g~~~C~~c~~~--~p~~~~~ 564 (637)
T PRK12366 529 KIILYLCPNCRKRVEE-------------------------VDGEYICEFCGEV--EPNELLM 564 (637)
T ss_pred CEEEecccccCeEeEc-------------------------CCCcEECCCCCCC--CCcEEEE
Confidence 3456899999986420 1347999999998 6655543
No 131
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=64.07 E-value=1 Score=33.83 Aligned_cols=10 Identities=40% Similarity=0.929 Sum_probs=8.7
Q ss_pred ccccCCCccc
Q 009783 455 SRCTKCNGRF 464 (526)
Q Consensus 455 sRC~~CN~~l 464 (526)
-||..||..|
T Consensus 5 iRC~~CnklL 14 (51)
T PF10122_consen 5 IRCGHCNKLL 14 (51)
T ss_pred eeccchhHHH
Confidence 4999999977
No 132
>TIGR00396 leuS_bact leucyl-tRNA synthetase, eubacterial and mitochondrial family. The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both eubacterial and mitochondrial leucyl-tRNA synthetases. It generates higher scores for some valyl-tRNA synthetases than for any archaeal or eukaryotic cytosolic leucyl-tRNA synthetase. Note that the enzyme from Aquifex aeolicus is split into alpha and beta chains; neither chain is long enough to score above the trusted cutoff, but the alpha chain scores well above the noise cutoff. The beta chain must be found by a model and search designed for partial length matches.
Probab=63.26 E-value=15 Score=43.52 Aligned_cols=18 Identities=22% Similarity=0.320 Sum_probs=16.1
Q ss_pred HHHHHHhcCCceecCCCC
Q 009783 372 LAKHLRCVGIDAATPRSK 389 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~ 389 (526)
++|++|+.||+|.++.+.
T Consensus 58 i~Ry~rm~G~~V~~~~G~ 75 (842)
T TIGR00396 58 LSRYYRMKGYNVLHPMGW 75 (842)
T ss_pred HHHHHHhcCCceeccCCc
Confidence 799999999999998754
No 133
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=63.02 E-value=5.9 Score=34.34 Aligned_cols=43 Identities=19% Similarity=0.403 Sum_probs=26.9
Q ss_pred ccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecccch
Q 009783 455 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVMSA 511 (526)
Q Consensus 455 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~GsH~ 511 (526)
.+|+.|+++... ++-++ |-+..+....-+|+|+.|+- |.|-|-
T Consensus 3 ~~CpYCg~~~~l--~~~~~----------iYg~~~~~~~~~y~C~~C~A--yVG~H~ 45 (102)
T PF11672_consen 3 IICPYCGGPAEL--VDGSE----------IYGHRYDDGPYLYVCTPCDA--YVGCHP 45 (102)
T ss_pred cccCCCCCeeEE--cccch----------hcCccCCCCceeEECCCCCc--eeeeeC
Confidence 589999997653 22122 22233333445799999986 677775
No 134
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=61.37 E-value=4.3 Score=41.63 Aligned_cols=32 Identities=19% Similarity=0.572 Sum_probs=23.0
Q ss_pred ccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009783 450 EDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 503 (526)
Q Consensus 450 ~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 503 (526)
|+..+++|+.|+..+.. ++. ...++.||.||.
T Consensus 22 ~~~~~~~c~~c~~~~~~-----~~l-----------------~~~~~vc~~c~~ 53 (285)
T TIGR00515 22 PEGVWTKCPKCGQVLYT-----KEL-----------------ERNLEVCPKCDH 53 (285)
T ss_pred CCCCeeECCCCcchhhH-----HHH-----------------HhhCCCCCCCCC
Confidence 56678999999997642 222 134789999986
No 135
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=61.08 E-value=6.2 Score=28.33 Aligned_cols=14 Identities=14% Similarity=0.344 Sum_probs=9.5
Q ss_pred cCCceeecCCCCeE
Q 009783 491 KNLQFWQCMDCNQL 504 (526)
Q Consensus 491 ~~~~F~~C~~Cgkv 504 (526)
...-...|+.||-|
T Consensus 15 ~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 15 PERGELVCPNCGLV 28 (43)
T ss_dssp TTTTEEEETTT-BB
T ss_pred CCCCeEECCCCCCE
Confidence 34556799999976
No 136
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=60.74 E-value=8 Score=29.01 Aligned_cols=14 Identities=21% Similarity=0.776 Sum_probs=12.3
Q ss_pred ceeecCCCCeEEec
Q 009783 494 QFWQCMDCNQLYWE 507 (526)
Q Consensus 494 ~F~~C~~CgkvyW~ 507 (526)
..+.|+.||-.||.
T Consensus 36 ~r~~C~~Cgyt~~~ 49 (50)
T PRK00432 36 DRWHCGKCGYTEFK 49 (50)
T ss_pred CcEECCCcCCEEec
Confidence 57889999999985
No 137
>PHA02325 hypothetical protein
Probab=60.35 E-value=4.8 Score=31.63 Aligned_cols=16 Identities=31% Similarity=0.733 Sum_probs=11.7
Q ss_pred eecCCCC------eEEecccch
Q 009783 496 WQCMDCN------QLYWEVMSA 511 (526)
Q Consensus 496 ~~C~~Cg------kvyW~GsH~ 511 (526)
..||+|| |.||.|+--
T Consensus 4 k~CPkC~A~WldgqhYWsgTgk 25 (72)
T PHA02325 4 KICPKCGARWLDGQHYWSGTGK 25 (72)
T ss_pred cccCccCCEeEcceeeeccCCC
Confidence 4699995 678887643
No 138
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=59.84 E-value=6.5 Score=39.11 Aligned_cols=36 Identities=25% Similarity=0.683 Sum_probs=24.1
Q ss_pred ccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009783 452 QLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 505 (526)
Q Consensus 452 ~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 505 (526)
+.-|||-.|+.... ||..+. ....-++.|+.|++.|
T Consensus 130 KeVSRCr~C~~rYD--PVP~dk----------------mwG~aef~C~~C~h~F 165 (278)
T PF15135_consen 130 KEVSRCRKCRKRYD--PVPCDK----------------MWGIAEFHCPKCRHNF 165 (278)
T ss_pred cccccccccccccC--CCcccc----------------ccceeeeecccccccc
Confidence 44699999999764 332222 1234577899999876
No 139
>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=59.74 E-value=5.5 Score=29.93 Aligned_cols=39 Identities=21% Similarity=0.459 Sum_probs=23.8
Q ss_pred cccCCCcccccCCCChHHHHHhhhcCcccCccc-cccCCceeecCCCCe
Q 009783 456 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCL-FDKNLQFWQCMDCNQ 503 (526)
Q Consensus 456 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v-~~~~~~F~~C~~Cgk 503 (526)
+|..|+-.--+. +.+. ...||++. |+...+=|.||.||-
T Consensus 3 ~C~~CgyiYd~~---~Gd~------~~~i~pGt~f~~Lp~~w~CP~C~a 42 (50)
T cd00730 3 ECRICGYIYDPA---EGDP------DEGIPPGTPFEDLPDDWVCPVCGA 42 (50)
T ss_pred CCCCCCeEECCC---CCCc------ccCcCCCCCHhHCCCCCCCCCCCC
Confidence 699999754321 1111 12455554 556677899999984
No 140
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=59.05 E-value=6.5 Score=27.50 Aligned_cols=14 Identities=21% Similarity=0.831 Sum_probs=9.2
Q ss_pred CCceeecCCCCeEE
Q 009783 492 NLQFWQCMDCNQLY 505 (526)
Q Consensus 492 ~~~F~~C~~Cgkvy 505 (526)
..+||+|..||.|.
T Consensus 3 ~~~~YkC~~CGniV 16 (36)
T PF06397_consen 3 KGEFYKCEHCGNIV 16 (36)
T ss_dssp TTEEEE-TTT--EE
T ss_pred cccEEEccCCCCEE
Confidence 36899999999985
No 141
>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=58.72 E-value=3.6 Score=36.06 Aligned_cols=12 Identities=17% Similarity=0.415 Sum_probs=8.5
Q ss_pred ecCCCCeEEecc
Q 009783 497 QCMDCNQLYWEV 508 (526)
Q Consensus 497 ~C~~CgkvyW~G 508 (526)
.||.||..|=.-
T Consensus 28 vCP~CG~~~~~~ 39 (108)
T PF09538_consen 28 VCPKCGTEFPPE 39 (108)
T ss_pred cCCCCCCccCcc
Confidence 388888887544
No 142
>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=57.42 E-value=6.7 Score=23.39 Aligned_cols=12 Identities=25% Similarity=0.739 Sum_probs=8.0
Q ss_pred eecCCCCeEEec
Q 009783 496 WQCMDCNQLYWE 507 (526)
Q Consensus 496 ~~C~~CgkvyW~ 507 (526)
|.|+.|++.|=.
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 689999998843
No 143
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=57.26 E-value=8.5 Score=29.99 Aligned_cols=11 Identities=27% Similarity=0.594 Sum_probs=9.1
Q ss_pred eeecCCCCeEE
Q 009783 495 FWQCMDCNQLY 505 (526)
Q Consensus 495 F~~C~~Cgkvy 505 (526)
--+|+.|+..|
T Consensus 26 ~L~c~~~~~aY 36 (60)
T COG2835 26 ELICPRCKLAY 36 (60)
T ss_pred EEEecccCcee
Confidence 55699999988
No 144
>cd00812 LeuRS_core catalytic core domain of leucyl-tRNA synthetases. Leucyl tRNA synthetase (LeuRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. In Aquifex aeolicus, the gene encoding LeuRS is split in two, just before the KMSKS motif. Consequently, LeuRS is a heterodimer, which likely superimposes with the LeuRS monomer found in most other organisms. LeuRS has an insertion in the core domain, which is subject to both deletions and rearrangements and thus differs between prokaryotic LeuRS and archaeal/eukaryotic LeuRS. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
Probab=56.78 E-value=19 Score=37.27 Aligned_cols=35 Identities=17% Similarity=0.029 Sum_probs=25.8
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009783 371 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 405 (526)
Q Consensus 371 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 405 (526)
=++|+||..|++|.++.+.+.-+..+...|+++|.
T Consensus 28 v~~R~lr~~G~~V~~v~g~Dd~g~~i~~~a~~~g~ 62 (314)
T cd00812 28 IIARYKRMQGYNVLFPMGFDAFGLPAENAAIKIGR 62 (314)
T ss_pred HHHHHHHHcCCCcCCCCCcCCCCCHHHHHHHHcCC
Confidence 37999999999999887643223357777777765
No 145
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.76 E-value=3 Score=41.00 Aligned_cols=13 Identities=15% Similarity=0.166 Sum_probs=10.1
Q ss_pred ccCCceeecCCCC
Q 009783 490 DKNLQFWQCMDCN 502 (526)
Q Consensus 490 ~~~~~F~~C~~Cg 502 (526)
....+.|.||.|+
T Consensus 57 P~fY~VvvCP~C~ 69 (267)
T COG1655 57 PYFYDVVVCPICY 69 (267)
T ss_pred CceeEEEEcchhh
Confidence 3456789999996
No 146
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=56.68 E-value=6.1 Score=40.68 Aligned_cols=17 Identities=18% Similarity=0.575 Sum_probs=13.6
Q ss_pred cccccCccccCCCcccc
Q 009783 449 SEDQLMSRCTKCNGRFI 465 (526)
Q Consensus 449 ~~~~~~sRC~~CN~~l~ 465 (526)
.|+..+++|+.|+..+.
T Consensus 22 ~~~~~~~~c~~c~~~~~ 38 (292)
T PRK05654 22 VPEGLWTKCPSCGQVLY 38 (292)
T ss_pred CCCCCeeECCCccchhh
Confidence 35667899999999764
No 147
>PRK00390 leuS leucyl-tRNA synthetase; Validated
Probab=56.61 E-value=18 Score=42.55 Aligned_cols=18 Identities=22% Similarity=0.287 Sum_probs=16.1
Q ss_pred HHHHHHhcCCceecCCCC
Q 009783 372 LAKHLRCVGIDAATPRSK 389 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~ 389 (526)
++|+.|+.|++|.++.+.
T Consensus 61 i~Ry~rm~G~~V~~~~G~ 78 (805)
T PRK00390 61 IARYKRMQGYNVLHPMGW 78 (805)
T ss_pred HHHHHHhcCCcccccCcc
Confidence 799999999999998754
No 148
>PLN02946 cysteine-tRNA ligase
Probab=56.26 E-value=8.3 Score=43.27 Aligned_cols=35 Identities=14% Similarity=0.171 Sum_probs=28.0
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009783 371 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 405 (526)
Q Consensus 371 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 405 (526)
=|+|+||..||+|.++.+.+.-|+.|+..|+++|.
T Consensus 107 vl~R~Lr~~Gy~V~~V~niTDiDDKIi~~A~~~g~ 141 (557)
T PLN02946 107 VLYRYLKHLGYEVRYVRNFTDVDDKIIARANELGE 141 (557)
T ss_pred HHHHHHHhcCCcEEEEECCCCccCHHHHHHHHcCC
Confidence 48999999999999987643334579999988774
No 149
>COG1773 Rubredoxin [Energy production and conversion]
Probab=56.17 E-value=6.3 Score=30.22 Aligned_cols=40 Identities=20% Similarity=0.408 Sum_probs=25.1
Q ss_pred ccccCCCcccccCCCChHHHHHhhhcCcccCccc-cccCCceeecCCCCe
Q 009783 455 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCL-FDKNLQFWQCMDCNQ 503 (526)
Q Consensus 455 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v-~~~~~~F~~C~~Cgk 503 (526)
-+|..|+-...+..- +. ..-|+++. |+....-|.||.||-
T Consensus 4 ~~C~~CG~vYd~e~G---dp------~~gi~pgT~fedlPd~w~CP~Cg~ 44 (55)
T COG1773 4 WRCSVCGYVYDPEKG---DP------RCGIAPGTPFEDLPDDWVCPECGV 44 (55)
T ss_pred eEecCCceEeccccC---Cc------cCCCCCCCchhhCCCccCCCCCCC
Confidence 479999986532110 10 12455555 577788999999983
No 150
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=56.04 E-value=16 Score=41.63 Aligned_cols=58 Identities=16% Similarity=0.248 Sum_probs=37.6
Q ss_pred HHHHHHHHHH---cCcc-ccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEeccc
Q 009783 434 NQQLLEVIEA---FQLK-ISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVM 509 (526)
Q Consensus 434 ~~QL~~vl~~---f~l~-~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~Gs 509 (526)
.+.+.+|++. .++. ..-...+++|..|+.... .+.+.||.||.
T Consensus 544 ~~al~~lv~~~~~~~i~Y~~inp~~~~C~~CG~~~~---------------------------g~~~~CP~CGs------ 590 (625)
T PRK08579 544 PEALAKLTKRIMNTKLVYWSYTPAITVCNKCGRSTT---------------------------GLYTRCPRCGS------ 590 (625)
T ss_pred HHHHHHHHHHHHhcCCceEEeCCCCccCCCCCCccC---------------------------CCCCcCcCCCC------
Confidence 3677777765 2332 223345899999998421 11467999986
Q ss_pred chhhHHhhhhhhhhc
Q 009783 510 SAYLFIFLTPAYFSF 524 (526)
Q Consensus 510 H~~r~~~~~~~~~~~ 524 (526)
+---++++++-|+.-
T Consensus 591 ~~~~v~~Rv~GYl~~ 605 (625)
T PRK08579 591 EDVEVWSRIIGYYRP 605 (625)
T ss_pred chhHHHHHHHhhhcc
Confidence 334588888888753
No 151
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=55.98 E-value=3.8 Score=37.25 Aligned_cols=50 Identities=18% Similarity=0.474 Sum_probs=24.9
Q ss_pred cccccCccccCCCcccccCCCChHHHHHh-hhcCcccCccccccCCceeecCCCCe
Q 009783 449 SEDQLMSRCTKCNGRFIQKPLSTEEAVEA-AKGFQRIPDCLFDKNLQFWQCMDCNQ 503 (526)
Q Consensus 449 ~~~~~~sRC~~CN~~l~~~~~~~e~~~~~-~~~~~~vp~~v~~~~~~F~~C~~Cgk 503 (526)
......-+|..|+.... ++ ++.+. .+..+.-+.++-+....|+.||.||.
T Consensus 65 ~~~p~~~~C~~CG~~~~---~~--~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs 115 (135)
T PRK03824 65 EEEEAVLKCRNCGNEWS---LK--EVKESLDEEIREAIHFIPEVVHAFLKCPKCGS 115 (135)
T ss_pred EecceEEECCCCCCEEe---cc--cccccccccccccccccccccccCcCCcCCCC
Confidence 34445789999997652 21 10000 00011112222233456788999985
No 152
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=55.91 E-value=9.1 Score=27.08 Aligned_cols=31 Identities=26% Similarity=0.624 Sum_probs=22.3
Q ss_pred cccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCC---CCeEEec
Q 009783 456 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMD---CNQLYWE 507 (526)
Q Consensus 456 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~---CgkvyW~ 507 (526)
.|+.|++.|+.+. .+...||-|.. |.-++|-
T Consensus 3 ~CP~Cg~~lv~r~---------------------~k~g~F~~Cs~yP~C~~~~~~ 36 (39)
T PF01396_consen 3 KCPKCGGPLVLRR---------------------GKKGKFLGCSNYPECKYTEPL 36 (39)
T ss_pred CCCCCCceeEEEE---------------------CCCCCEEECCCCCCcCCeEeC
Confidence 5999999886421 01237999977 9988874
No 153
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=55.72 E-value=17 Score=41.50 Aligned_cols=97 Identities=15% Similarity=0.362 Sum_probs=53.1
Q ss_pred HHHHhhhcCCcEEEecChhHHHhhcccCCcEEEEcCCCHHHHHHHHH-HHc--CccccccccCccccCCCcccccCCCCh
Q 009783 395 ELIDQTSKEKRVLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQLLEVI-EAF--QLKISEDQLMSRCTKCNGRFIQKPLST 471 (526)
Q Consensus 395 ~ll~~A~~E~RiiLTrd~~l~~~~~~~~~~~~~v~~~~~~~QL~~vl-~~f--~l~~~~~~~~sRC~~CN~~l~~~~~~~ 471 (526)
.++.+|.-..|-+=|+++.|++-..... + ++..++|.+++. +-| +-..++...---|..|++++-+-.++.
T Consensus 1061 SllALaaca~raFGtCSKAfmkLe~~e~-----l-~~a~kq~ye~La~~iFsk~~p~d~~~~~vdc~~cg~~i~~~~~~c 1134 (1189)
T KOG2041|consen 1061 SLLALAACAVRAFGTCSKAFMKLEAFEE-----L-DDAEKQEYENLAFRIFSKNPPVDPNSAKVDCSVCGAKIDPYDLQC 1134 (1189)
T ss_pred HHHHHHHhhhhhhhhhHHHHHHHHhhhh-----C-CHHHHHHHHHHHHHHhccCCCCCCCccceeeeecCCcCCccCCCC
Confidence 5888888889999999999876433221 1 112244555542 223 112222222334788877653222222
Q ss_pred HHHHHhhhcCcccCccccc----cCCceeecCCCCe
Q 009783 472 EEAVEAAKGFQRIPDCLFD----KNLQFWQCMDCNQ 503 (526)
Q Consensus 472 e~~~~~~~~~~~vp~~v~~----~~~~F~~C~~Cgk 503 (526)
.|- ..+.|-++-. +...||.||.|+.
T Consensus 1135 ~ec------~~kfP~CiasG~pIt~~~fWlC~~CkH 1164 (1189)
T KOG2041|consen 1135 SEC------QTKFPVCIASGRPITDNIFWLCPRCKH 1164 (1189)
T ss_pred hhh------cCcCceeeccCCccccceEEEcccccc
Confidence 222 1355655521 3455999999974
No 154
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=55.50 E-value=6.3 Score=40.58 Aligned_cols=38 Identities=16% Similarity=0.379 Sum_probs=25.7
Q ss_pred HcCccccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009783 443 AFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 503 (526)
Q Consensus 443 ~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 503 (526)
.++.. .|+..+++|+.|+..+.. ++.. ..++.||.||.
T Consensus 28 ~~~~~-~p~~lw~kc~~C~~~~~~-----~~l~-----------------~~~~vcp~c~~ 65 (296)
T CHL00174 28 SWNTQ-KYKHLWVQCENCYGLNYK-----KFLK-----------------SKMNICEQCGY 65 (296)
T ss_pred ccCCC-CCCCCeeECCCccchhhH-----HHHH-----------------HcCCCCCCCCC
Confidence 34444 356679999999997642 2221 34789999986
No 155
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=55.11 E-value=17 Score=29.62 Aligned_cols=60 Identities=17% Similarity=0.432 Sum_probs=31.4
Q ss_pred HHHHHHHHHHcCccccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009783 434 NQQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 503 (526)
Q Consensus 434 ~~QL~~vl~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 503 (526)
..++.++.+...+++.++.--+-|..|+..|++- ++. . -+|-..-.....-.+.|-.||+
T Consensus 26 ~~~~~~i~~k~~~~l~~~~kr~~Ck~C~~~liPG-~~~-~--------vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 26 MKLMRKISKKTRIRLPPEIKRTICKKCGSLLIPG-VNC-S--------VRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp HHHHHHHHHHCT---STTCCCTB-TTT--B--CT-TTE-E--------EEEE---SSS-EEEEEETTTTE
T ss_pred HHHHHHHHHHhCCCCChHHhcccccCCCCEEeCC-Ccc-E--------EEEEecCCCCCEEEEEccccCC
Confidence 4688899999999888877678899999998741 110 0 0111000013345788999985
No 156
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=54.95 E-value=8.1 Score=26.51 Aligned_cols=15 Identities=27% Similarity=0.629 Sum_probs=12.2
Q ss_pred eeecCCCCeEEecccc
Q 009783 495 FWQCMDCNQLYWEVMS 510 (526)
Q Consensus 495 F~~C~~CgkvyW~GsH 510 (526)
+|+|+.||-+| +|.+
T Consensus 2 ~~~C~~CG~i~-~g~~ 16 (34)
T cd00729 2 VWVCPVCGYIH-EGEE 16 (34)
T ss_pred eEECCCCCCEe-ECCc
Confidence 79999999998 5554
No 157
>PRK07218 replication factor A; Provisional
Probab=54.84 E-value=5.7 Score=43.03 Aligned_cols=14 Identities=29% Similarity=0.800 Sum_probs=11.2
Q ss_pred cccCccccCCCccc
Q 009783 451 DQLMSRCTKCNGRF 464 (526)
Q Consensus 451 ~~~~sRC~~CN~~l 464 (526)
+-+..||+.||-.+
T Consensus 294 sgli~rCP~C~r~v 307 (423)
T PRK07218 294 SGLIERCPECGRVI 307 (423)
T ss_pred CcceecCcCccccc
Confidence 45679999999854
No 158
>PLN02563 aminoacyl-tRNA ligase
Probab=54.81 E-value=19 Score=43.13 Aligned_cols=18 Identities=28% Similarity=0.309 Sum_probs=16.1
Q ss_pred HHHHHHhcCCceecCCCC
Q 009783 372 LAKHLRCVGIDAATPRSK 389 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~ 389 (526)
+||+.|+.||+|.++.+.
T Consensus 140 iaRy~Rm~G~~Vl~~~G~ 157 (963)
T PLN02563 140 LARYKRMQGYNVLHPMGW 157 (963)
T ss_pred HHHHHHhcCCeecccccc
Confidence 799999999999998753
No 159
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=54.16 E-value=7 Score=37.42 Aligned_cols=13 Identities=23% Similarity=1.040 Sum_probs=11.3
Q ss_pred cCccccCCCcccc
Q 009783 453 LMSRCTKCNGRFI 465 (526)
Q Consensus 453 ~~sRC~~CN~~l~ 465 (526)
+++||+.|.++|.
T Consensus 148 I~A~CsrC~~~L~ 160 (188)
T COG1096 148 IYARCSRCRAPLV 160 (188)
T ss_pred EEEEccCCCcceE
Confidence 4799999999884
No 160
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=53.79 E-value=8.2 Score=35.49 Aligned_cols=17 Identities=24% Similarity=0.784 Sum_probs=13.7
Q ss_pred ccCCceeecCCCCeEEe
Q 009783 490 DKNLQFWQCMDCNQLYW 506 (526)
Q Consensus 490 ~~~~~F~~C~~CgkvyW 506 (526)
+....|+.||.||+.|=
T Consensus 94 e~~~~~Y~Cp~C~~~y~ 110 (147)
T smart00531 94 ETNNAYYKCPNCQSKYT 110 (147)
T ss_pred ccCCcEEECcCCCCEee
Confidence 34677999999998873
No 161
>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=53.55 E-value=5.4 Score=25.77 Aligned_cols=9 Identities=22% Similarity=0.674 Sum_probs=7.1
Q ss_pred ecCCCCeEE
Q 009783 497 QCMDCNQLY 505 (526)
Q Consensus 497 ~C~~Cgkvy 505 (526)
.||.||-.|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 399999765
No 162
>PRK11827 hypothetical protein; Provisional
Probab=53.21 E-value=12 Score=29.30 Aligned_cols=10 Identities=40% Similarity=1.135 Sum_probs=8.7
Q ss_pred cccCCCcccc
Q 009783 456 RCTKCNGRFI 465 (526)
Q Consensus 456 RC~~CN~~l~ 465 (526)
.|+.|.|+|.
T Consensus 10 aCP~ckg~L~ 19 (60)
T PRK11827 10 ACPVCNGKLW 19 (60)
T ss_pred ECCCCCCcCe
Confidence 6999999884
No 163
>PHA00616 hypothetical protein
Probab=52.32 E-value=3.4 Score=30.24 Aligned_cols=18 Identities=17% Similarity=0.610 Sum_probs=14.4
Q ss_pred eecCCCCeEEecccchhh
Q 009783 496 WQCMDCNQLYWEVMSAYL 513 (526)
Q Consensus 496 ~~C~~CgkvyW~GsH~~r 513 (526)
++|+.||++|=.-++..+
T Consensus 2 YqC~~CG~~F~~~s~l~~ 19 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIE 19 (44)
T ss_pred CccchhhHHHhhHHHHHH
Confidence 579999999977666555
No 164
>COG0215 CysS Cysteinyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=52.23 E-value=11 Score=41.06 Aligned_cols=35 Identities=20% Similarity=0.257 Sum_probs=28.5
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009783 371 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 405 (526)
Q Consensus 371 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 405 (526)
-|.||||.+||+|.|+.+...=|+.|++.|+++|-
T Consensus 49 vl~R~L~~~Gy~V~yV~NiTDIDDKIi~rA~~~g~ 83 (464)
T COG0215 49 VLRRYLRYLGYKVTYVRNITDIDDKIINRAREEGL 83 (464)
T ss_pred HHHHHHHHhCCeEEEEeccccccHHHHHHHHHhCC
Confidence 47999999999999987643224679999999886
No 165
>PRK00260 cysS cysteinyl-tRNA synthetase; Validated
Probab=52.00 E-value=13 Score=40.84 Aligned_cols=35 Identities=20% Similarity=0.276 Sum_probs=27.8
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009783 371 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 405 (526)
Q Consensus 371 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 405 (526)
=++|+||..||+|.++.+.+.-+..++..|+++|.
T Consensus 50 vl~R~lr~~G~~V~~v~~~tD~ddki~~~A~~~g~ 84 (463)
T PRK00260 50 VLRRYLRYLGYKVTYVRNITDIDDKIIKRANEEGE 84 (463)
T ss_pred HHHHHHHhcCCceEEeecCCCCcHHHHHHHHHcCC
Confidence 38999999999999987643334678899988873
No 166
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=50.36 E-value=6.2 Score=34.73 Aligned_cols=31 Identities=16% Similarity=0.227 Sum_probs=19.5
Q ss_pred HHHHHHHHHHc---------CccccccccCccccCCCccc
Q 009783 434 NQQLLEVIEAF---------QLKISEDQLMSRCTKCNGRF 464 (526)
Q Consensus 434 ~~QL~~vl~~f---------~l~~~~~~~~sRC~~CN~~l 464 (526)
.++|+.-++.+ .|.+......-||..|+...
T Consensus 41 pe~L~f~f~~~~~~T~~egA~L~I~~vp~~~~C~~Cg~~~ 80 (113)
T PRK12380 41 ESAVRFSFEIVCHGTVAQGCDLHIVYKPAQAWCWDCSQVV 80 (113)
T ss_pred HHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcccCCCEE
Confidence 46666655543 34444455568899999754
No 167
>TIGR00305 probable toxin-antitoxin system toxin component, PIN family. This uncharacterized protein family, part of the PIN domain superfamily, is restricted to bacteria and archaea. A comprehensive in silico study of toxin-antitoxin systems by Makarova, et al. (2009) finds evidence this family represents the toxin-like component of one class of type 2 toxin-antitoxin systems.
Probab=50.22 E-value=20 Score=30.94 Aligned_cols=28 Identities=21% Similarity=0.404 Sum_probs=22.6
Q ss_pred CCCChHHHHHhhhcCC-cEEEecChhHHH
Q 009783 389 KKPEPRELIDQTSKEK-RVLLTRDAKLLR 416 (526)
Q Consensus 389 ~~~~d~~ll~~A~~E~-RiiLTrd~~l~~ 416 (526)
.+++|..+++.|..-+ .+|+|+|++|+.
T Consensus 85 ~D~~D~~~l~~A~~~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 85 RDKKDNKFLNTAYASKANALITGDTDLLV 113 (114)
T ss_pred CCchhHHHHHHHHhcCCCEEEECCHHHhh
Confidence 4577888999988766 499999999864
No 168
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=50.19 E-value=44 Score=30.54 Aligned_cols=52 Identities=12% Similarity=0.110 Sum_probs=36.7
Q ss_pred HhcCCceecCCCCCCChHHHHHhhhcCC-cEEEecChhHHHhhcccCCcEEEEcC
Q 009783 377 RCVGIDAATPRSKKPEPRELIDQTSKEK-RVLLTRDAKLLRHQYLIKNQIYRVKS 430 (526)
Q Consensus 377 R~lG~D~~~~~~~~~~d~~ll~~A~~E~-RiiLTrd~~l~~~~~~~~~~~~~v~~ 430 (526)
...++.+.+.. ...|+-|++.|.+.| -|+.|.|++|-++....|..++.++.
T Consensus 73 ~~er~~~~~~~--~~aDe~i~~~a~~~~~~iVaTnD~eLk~rlr~~GIPvi~lr~ 125 (136)
T COG1412 73 YAERLECIHKG--RYADECLLEAALKHGRYIVATNDKELKRRLRENGIPVITLRQ 125 (136)
T ss_pred HhhccCccccC--CChHHHHHHHHHHcCCEEEEeCCHHHHHHHHHcCCCEEEEeC
Confidence 34566665542 234678999999999 77889999997765545556776664
No 169
>PRK08402 replication factor A; Reviewed
Probab=50.14 E-value=6.4 Score=41.69 Aligned_cols=29 Identities=17% Similarity=0.579 Sum_probs=20.6
Q ss_pred cCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009783 453 LMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 504 (526)
Q Consensus 453 ~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 504 (526)
.+.+|+.||..+.. +....-|+|+.||++
T Consensus 211 ~y~aCp~CnKkv~~-----------------------~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 211 VYDACPECRRKVDY-----------------------DPATDTWICPEHGEV 239 (355)
T ss_pred eEecCCCCCeEEEE-----------------------ecCCCCEeCCCCCCc
Confidence 46899999996521 112457999999974
No 170
>PRK14535 cysS cysteinyl-tRNA synthetase; Provisional
Probab=49.85 E-value=13 Score=42.59 Aligned_cols=55 Identities=20% Similarity=0.245 Sum_probs=36.4
Q ss_pred CCCCCCC-CCCCCCCCCEEEEecccHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009783 346 QGPPPWD-LSLGGDGYPKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 405 (526)
Q Consensus 346 ~~~~p~~-~~~~~~~~~kfl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 405 (526)
+||-++| +.+|.... -++.| =|+|+||..||+|.++.+...-|+.|+..|+++|.
T Consensus 254 CGPTVYd~~HIGHaRt-~V~~D----VL~R~Lr~~Gy~V~fV~NiTD~DDKII~~A~e~G~ 309 (699)
T PRK14535 254 CGMTVYDYCHLGHARV-MVVFD----MIARWLRECGYPLTYVRNITDIDDKIIARAAENGE 309 (699)
T ss_pred cCCcCCCCCcccchhH-HHHHH----HHHHHHHHcCCceEEEeCCcccchHHHHHHHHcCC
Confidence 4676664 34443322 12222 38999999999999987643334579999998874
No 171
>PRK05359 oligoribonuclease; Provisional
Probab=49.81 E-value=2.3e+02 Score=26.78 Aligned_cols=20 Identities=15% Similarity=0.107 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 009783 198 AAIDAHCLIEIFNIFQVKVA 217 (526)
Q Consensus 198 AA~DA~~ll~L~~~L~~~L~ 217 (526)
|-.|+...++.+..++..+.
T Consensus 157 al~D~~~s~~~~~~~~~~~~ 176 (181)
T PRK05359 157 ALADIRESIAELKYYREHFF 176 (181)
T ss_pred cHHHHHHHHHHHHHHHHHhc
Confidence 66788888888888877654
No 172
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=49.35 E-value=15 Score=28.10 Aligned_cols=27 Identities=22% Similarity=0.639 Sum_probs=20.0
Q ss_pred CccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009783 454 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 505 (526)
Q Consensus 454 ~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 505 (526)
-.+|..|+.+|.. .+.--+||.||..|
T Consensus 5 ~~~C~~Cg~~~~~-------------------------~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 5 GCKCPVCGKKFKD-------------------------GDDIVVCPECGAPY 31 (54)
T ss_pred CccChhhCCcccC-------------------------CCCEEECCCCCCcc
Confidence 4789999998731 13355799999988
No 173
>cd00668 Ile_Leu_Val_MetRS_core catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases. Catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases. These class I enzymes are all monomers. However, in some species, MetRS functions as a homodimer, as a result of an additional C-terminal domain. These enzymes aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. Enzymes in this subfamily share an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. MetRS has a significantly shorter insertion, which lacks the editing function.
Probab=49.16 E-value=33 Score=35.28 Aligned_cols=40 Identities=8% Similarity=-0.058 Sum_probs=28.0
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecC
Q 009783 372 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRD 411 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~RiiLTrd 411 (526)
++|+||..||+|.++.+.+.-+..+...|.+++.+-.+++
T Consensus 29 i~R~~r~~G~~v~~~~g~D~~g~~i~~~a~~~~~~~~~~~ 68 (312)
T cd00668 29 IARYKRMRGYEVPFLPGWDTHGLPIELKAERKGGRKKKTI 68 (312)
T ss_pred HHHHHHhCCCCCCCCCccCCCCHHHHHHHHHhcCcccccc
Confidence 7999999999999987653323457777777665444443
No 174
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=48.42 E-value=9.7 Score=29.17 Aligned_cols=11 Identities=18% Similarity=0.730 Sum_probs=8.6
Q ss_pred cCccccCCCcc
Q 009783 453 LMSRCTKCNGR 463 (526)
Q Consensus 453 ~~sRC~~CN~~ 463 (526)
.++.|+.|+..
T Consensus 25 ~l~~c~~cg~~ 35 (56)
T PF01783_consen 25 NLVKCPNCGEP 35 (56)
T ss_dssp SEEESSSSSSE
T ss_pred ceeeeccCCCE
Confidence 35789999974
No 175
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=48.37 E-value=12 Score=25.40 Aligned_cols=13 Identities=23% Similarity=0.639 Sum_probs=11.6
Q ss_pred CceeecCCCCeEE
Q 009783 493 LQFWQCMDCNQLY 505 (526)
Q Consensus 493 ~~F~~C~~Cgkvy 505 (526)
.+||+|..||.++
T Consensus 5 ~~~ykC~~Cgniv 17 (34)
T TIGR00319 5 GQVYKCEVCGNIV 17 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 5699999999987
No 176
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=48.23 E-value=8.7 Score=26.79 Aligned_cols=13 Identities=15% Similarity=0.278 Sum_probs=8.8
Q ss_pred ecCCCCeEEecccchhh
Q 009783 497 QCMDCNQLYWEVMSAYL 513 (526)
Q Consensus 497 ~C~~CgkvyW~GsH~~r 513 (526)
.|++||| |.||.+
T Consensus 4 ~CprC~k----g~Hwa~ 16 (36)
T PF14787_consen 4 LCPRCGK----GFHWAS 16 (36)
T ss_dssp C-TTTSS----SCS-TT
T ss_pred cCcccCC----Ccchhh
Confidence 4999997 778875
No 177
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=47.46 E-value=34 Score=26.82 Aligned_cols=48 Identities=19% Similarity=0.426 Sum_probs=29.8
Q ss_pred HHHHHHHHHHcCcccc---ccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009783 434 NQQLLEVIEAFQLKIS---EDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 504 (526)
Q Consensus 434 ~~QL~~vl~~f~l~~~---~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 504 (526)
.++|+...+..|+.+. +..--..|+.|+..... .....-+.|+.||..
T Consensus 5 ~~~L~yka~~~G~~v~~v~~~~TSq~C~~CG~~~~~-----------------------~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 5 RQRLEYKAEEYGIQVVEVDEAYTSQTCPRCGHRNKK-----------------------RRSGRVFTCPNCGFE 55 (69)
T ss_pred HHHHHHHHHHhCCEEEEECCCCCccCccCccccccc-----------------------ccccceEEcCCCCCE
Confidence 3556666666665542 22223469999996520 123568899999976
No 178
>PRK06386 replication factor A; Reviewed
Probab=47.45 E-value=7.6 Score=41.13 Aligned_cols=15 Identities=20% Similarity=0.753 Sum_probs=12.1
Q ss_pred ccccCccccCCCccc
Q 009783 450 EDQLMSRCTKCNGRF 464 (526)
Q Consensus 450 ~~~~~sRC~~CN~~l 464 (526)
..-++.|||.||-.+
T Consensus 232 gsgli~rCP~C~R~l 246 (358)
T PRK06386 232 GSRIFTKCSVCNKII 246 (358)
T ss_pred CcEeEecCcCCCeEc
Confidence 356789999999865
No 179
>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=47.43 E-value=17 Score=27.75 Aligned_cols=30 Identities=13% Similarity=0.404 Sum_probs=19.4
Q ss_pred ccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009783 455 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 505 (526)
Q Consensus 455 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 505 (526)
..|+.|+..+. ||..+. .+--.|+.||--|
T Consensus 3 ~~CP~CG~~ie------------------v~~~~~---GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIE------------------LENPEL---GELVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEe------------------cCCCcc---CCEEeCCCCCCEE
Confidence 37999999763 222221 2355899999765
No 180
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=47.31 E-value=16 Score=24.51 Aligned_cols=27 Identities=15% Similarity=0.294 Sum_probs=14.5
Q ss_pred cccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009783 456 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 505 (526)
Q Consensus 456 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 505 (526)
-|..|+++... . ....-.+|+.||..+
T Consensus 5 fC~~CG~~t~~--~---------------------~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 5 FCGRCGAPTKP--A---------------------PGGWARRCPSCGHEH 31 (32)
T ss_dssp B-TTT--BEEE------------------------SSSS-EEESSSS-EE
T ss_pred ccCcCCccccC--C---------------------CCcCEeECCCCcCEe
Confidence 49999998742 1 123456799999876
No 181
>PTZ00399 cysteinyl-tRNA-synthetase; Provisional
Probab=47.08 E-value=15 Score=42.10 Aligned_cols=34 Identities=18% Similarity=0.202 Sum_probs=28.2
Q ss_pred HHHHHH-hcCCceecCCCCCCChHHHHHhhhcCCc
Q 009783 372 LAKHLR-CVGIDAATPRSKKPEPRELIDQTSKEKR 405 (526)
Q Consensus 372 Lar~LR-~lG~D~~~~~~~~~~d~~ll~~A~~E~R 405 (526)
|+|+|| ..||||.++.+...-|+.|+..|+++|.
T Consensus 88 l~R~l~~~~Gy~V~~v~nitDidDKIi~~A~~~g~ 122 (651)
T PTZ00399 88 IRRILEDYFGYDVFYVMNITDIDDKIIKRAREEKL 122 (651)
T ss_pred HHHHHHHhcCCceEEEeCCCCcchHHHHHHHHhCC
Confidence 899999 8999999987643335679999999886
No 182
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=47.04 E-value=12 Score=35.70 Aligned_cols=16 Identities=25% Similarity=0.764 Sum_probs=13.1
Q ss_pred ccCCceeecCCCCeEE
Q 009783 490 DKNLQFWQCMDCNQLY 505 (526)
Q Consensus 490 ~~~~~F~~C~~Cgkvy 505 (526)
+....||.||.||+-|
T Consensus 112 e~~~~~Y~Cp~C~~ry 127 (178)
T PRK06266 112 EENNMFFFCPNCHIRF 127 (178)
T ss_pred ccCCCEEECCCCCcEE
Confidence 3567899999999776
No 183
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=46.32 E-value=14 Score=25.18 Aligned_cols=13 Identities=23% Similarity=0.805 Sum_probs=11.4
Q ss_pred CceeecCCCCeEE
Q 009783 493 LQFWQCMDCNQLY 505 (526)
Q Consensus 493 ~~F~~C~~Cgkvy 505 (526)
.+||+|..||.++
T Consensus 2 ~~~ykC~~CGniv 14 (34)
T cd00974 2 LEVYKCEICGNIV 14 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 3699999999987
No 184
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=46.22 E-value=15 Score=42.71 Aligned_cols=28 Identities=18% Similarity=0.388 Sum_probs=18.0
Q ss_pred HHHHHHHHH---cCccc-cccccCccccCCCc
Q 009783 435 QQLLEVIEA---FQLKI-SEDQLMSRCTKCNG 462 (526)
Q Consensus 435 ~QL~~vl~~---f~l~~-~~~~~~sRC~~CN~ 462 (526)
+.+.+|++. .++.. +.+..+++|..|+-
T Consensus 657 eal~~lvk~~~~~~i~Y~sin~~~~~C~~CG~ 688 (735)
T PRK07111 657 EAFEIIVKAMKNTNIGYGSINHPVDRCPVCGY 688 (735)
T ss_pred HHHHHHHHHHHhCCCceEEeCCCCeecCCCCC
Confidence 556666553 33432 44566899999995
No 185
>PF12813 XPG_I_2: XPG domain containing
Probab=46.01 E-value=21 Score=35.73 Aligned_cols=45 Identities=22% Similarity=0.206 Sum_probs=36.4
Q ss_pred HHHHHHHHhc---CCceecCCCCCCChHHHHHhhhcCCcEEEecChhHHH
Q 009783 370 EGLAKHLRCV---GIDAATPRSKKPEPRELIDQTSKEKRVLLTRDAKLLR 416 (526)
Q Consensus 370 g~Lar~LR~l---G~D~~~~~~~~~~d~~ll~~A~~E~RiiLTrd~~l~~ 416 (526)
.-+..-||.+ |..+..+.. ..|.++...|++-|..|||.|.+|+=
T Consensus 7 ~~~~e~L~~~~~~~~~~~~~~~--EAD~~~A~~A~~~~~~VLt~DSDf~I 54 (246)
T PF12813_consen 7 PAFIEALRESWRYGVPVVQCPG--EADRECAALARKWGCPVLTNDSDFLI 54 (246)
T ss_pred HHHHHHHHHHhhcCCcEEEcCc--cchHHHHHHHHHcCCeEEccCCCEEE
Confidence 3445567777 999988753 56889999999999999999999843
No 186
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=45.82 E-value=13 Score=25.26 Aligned_cols=12 Identities=25% Similarity=0.587 Sum_probs=9.9
Q ss_pred eeecCCCCeEEe
Q 009783 495 FWQCMDCNQLYW 506 (526)
Q Consensus 495 F~~C~~CgkvyW 506 (526)
.|+|+.||-+|=
T Consensus 1 ~~~C~~CGy~y~ 12 (33)
T cd00350 1 KYVCPVCGYIYD 12 (33)
T ss_pred CEECCCCCCEEC
Confidence 389999999883
No 187
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=45.64 E-value=8.8 Score=34.00 Aligned_cols=18 Identities=22% Similarity=0.678 Sum_probs=11.6
Q ss_pred cccccccCccccCCCccc
Q 009783 447 KISEDQLMSRCTKCNGRF 464 (526)
Q Consensus 447 ~~~~~~~~sRC~~CN~~l 464 (526)
.+......-||..|+...
T Consensus 64 ~Ie~vp~~~~C~~Cg~~~ 81 (117)
T PRK00564 64 DIVDEKVELECKDCSHVF 81 (117)
T ss_pred EEEecCCEEEhhhCCCcc
Confidence 334445567899999643
No 188
>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=45.43 E-value=16 Score=23.22 Aligned_cols=15 Identities=13% Similarity=0.452 Sum_probs=12.2
Q ss_pred CCceeecCCCCeEEe
Q 009783 492 NLQFWQCMDCNQLYW 506 (526)
Q Consensus 492 ~~~F~~C~~CgkvyW 506 (526)
.+.-+.|+.|+|.|.
T Consensus 11 ~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 11 GEKPYKCPYCGKSFS 25 (26)
T ss_dssp SSSSEEESSSSEEES
T ss_pred CCCCCCCCCCcCeeC
Confidence 355689999999985
No 189
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=45.22 E-value=14 Score=26.81 Aligned_cols=11 Identities=18% Similarity=0.736 Sum_probs=8.9
Q ss_pred ccccCCCcccc
Q 009783 455 SRCTKCNGRFI 465 (526)
Q Consensus 455 sRC~~CN~~l~ 465 (526)
-+|+.|+..+.
T Consensus 4 y~C~~CG~~~~ 14 (46)
T PRK00398 4 YKCARCGREVE 14 (46)
T ss_pred EECCCCCCEEE
Confidence 47999999763
No 190
>PHA00626 hypothetical protein
Probab=45.08 E-value=16 Score=28.01 Aligned_cols=16 Identities=19% Similarity=0.229 Sum_probs=12.1
Q ss_pred CCceeecCCCCeEEec
Q 009783 492 NLQFWQCMDCNQLYWE 507 (526)
Q Consensus 492 ~~~F~~C~~CgkvyW~ 507 (526)
...-|.|+.||--|=.
T Consensus 20 ~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 20 WSDDYVCCDCGYNDSK 35 (59)
T ss_pred cCcceEcCCCCCeech
Confidence 3567889999977644
No 191
>PRK14534 cysS cysteinyl-tRNA synthetase; Provisional
Probab=44.67 E-value=16 Score=40.36 Aligned_cols=36 Identities=11% Similarity=0.075 Sum_probs=26.3
Q ss_pred HHHHHHHhcCCceecCCCC-CC---------ChHHHHHhhhcCCcE
Q 009783 371 GLAKHLRCVGIDAATPRSK-KP---------EPRELIDQTSKEKRV 406 (526)
Q Consensus 371 ~Lar~LR~lG~D~~~~~~~-~~---------~d~~ll~~A~~E~Ri 406 (526)
=|+||||.+||+|.++.+. ++ .|+.|+..|+++|.-
T Consensus 48 vl~R~l~~~G~~V~~v~NiTDIghltg~~D~gddKIi~~A~~~g~~ 93 (481)
T PRK14534 48 LLIKSLRLLKYNVNYAMNITDIGHLTGDFDDGEDKVVKAARERGLT 93 (481)
T ss_pred HHHHHHHHcCCceEEEEeccccccccCCccCCCcHHHHHHHHcCCC
Confidence 3899999999999984331 11 245699999888753
No 192
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=44.64 E-value=14 Score=25.56 Aligned_cols=11 Identities=18% Similarity=0.631 Sum_probs=9.1
Q ss_pred cccCCCccccc
Q 009783 456 RCTKCNGRFIQ 466 (526)
Q Consensus 456 RC~~CN~~l~~ 466 (526)
-|+.||..|++
T Consensus 3 FCp~C~nlL~p 13 (35)
T PF02150_consen 3 FCPECGNLLYP 13 (35)
T ss_dssp BETTTTSBEEE
T ss_pred eCCCCCccceE
Confidence 49999998863
No 193
>PF01406 tRNA-synt_1e: tRNA synthetases class I (C) catalytic domain; InterPro: IPR015803 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Cysteinyl-tRNA synthetase (6.1.1.16 from EC) is an alpha monomer and belongs to class Ia.; GO: 0000166 nucleotide binding, 0004817 cysteine-tRNA ligase activity, 0005524 ATP binding, 0006423 cysteinyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3SP1_B 3TQO_A 3C8Z_B 1LI5_B 1LI7_B 1U0B_B.
Probab=43.78 E-value=12 Score=38.59 Aligned_cols=34 Identities=18% Similarity=0.220 Sum_probs=25.7
Q ss_pred HHHHHHhcCCceecCCCC-CCChHHHHHhhhcCCcE
Q 009783 372 LAKHLRCVGIDAATPRSK-KPEPRELIDQTSKEKRV 406 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~-~~~d~~ll~~A~~E~Ri 406 (526)
|.|+|+.+||+|.++.+. ++ |+.||+.|+++|--
T Consensus 36 l~R~L~~~g~~V~~V~NiTDi-DDKii~~A~~~g~~ 70 (300)
T PF01406_consen 36 LRRYLEYLGYDVTYVMNITDI-DDKIIKRAREEGVS 70 (300)
T ss_dssp HHHHHHHTT-EEEEEEEEB-S-SHHHHHHHHHTTS-
T ss_pred HHHHHHHcCCeEEEEEecccc-chHHHHHHHhccCC
Confidence 799999999999988653 34 45799999998743
No 194
>PHA02998 RNA polymerase subunit; Provisional
Probab=43.70 E-value=19 Score=34.21 Aligned_cols=48 Identities=21% Similarity=0.479 Sum_probs=26.4
Q ss_pred HcCccccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009783 443 AFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 505 (526)
Q Consensus 443 ~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 505 (526)
-|+|-.. +.-..|+.|++.-.. .. .-+.+-+ .-| ...|+.|..||+-|
T Consensus 134 yfnvlpk--kt~v~CPkCg~~~A~-f~-qlQTRSA-----DEP------mT~FYkC~~CG~~w 181 (195)
T PHA02998 134 YFNVLDE--KYNTPCPNCKSKNTT-PM-MIQTRAA-----DEP------PLVRHACRDCKKHF 181 (195)
T ss_pred heeccCc--ccCCCCCCCCCCceE-EE-EEeeccC-----CCC------ceEEEEcCCCCCcc
Confidence 5776543 245789999985210 00 0011100 112 35699999999864
No 195
>PRK12495 hypothetical protein; Provisional
Probab=43.27 E-value=27 Score=34.35 Aligned_cols=45 Identities=18% Similarity=0.263 Sum_probs=28.2
Q ss_pred HHHHHHHHHHcCccccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecc
Q 009783 434 NQQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEV 508 (526)
Q Consensus 434 ~~QL~~vl~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~G 508 (526)
.+++.++|....-.. ..-|..|+.+|- .+| --.+|+.|+++|=++
T Consensus 27 ~~~ma~lL~~gatms-----a~hC~~CG~PIp-----------------a~p--------G~~~Cp~CQ~~~~~~ 71 (226)
T PRK12495 27 TERMSELLLQGATMT-----NAHCDECGDPIF-----------------RHD--------GQEFCPTCQQPVTED 71 (226)
T ss_pred HHHHHHHHHhhcccc-----hhhcccccCccc-----------------CCC--------CeeECCCCCCccccc
Confidence 456666665443221 246999999862 122 245699999998664
No 196
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=43.02 E-value=13 Score=23.77 Aligned_cols=10 Identities=20% Similarity=0.720 Sum_probs=7.6
Q ss_pred ccccCCCccc
Q 009783 455 SRCTKCNGRF 464 (526)
Q Consensus 455 sRC~~CN~~l 464 (526)
..|+.|+..+
T Consensus 3 ~~Cp~Cg~~~ 12 (26)
T PF13248_consen 3 MFCPNCGAEI 12 (26)
T ss_pred CCCcccCCcC
Confidence 4699999853
No 197
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=42.57 E-value=20 Score=30.05 Aligned_cols=18 Identities=17% Similarity=0.540 Sum_probs=14.5
Q ss_pred CceeecCCCCeEEecccc
Q 009783 493 LQFWQCMDCNQLYWEVMS 510 (526)
Q Consensus 493 ~~F~~C~~CgkvyW~GsH 510 (526)
.-.|+|.+||..|=.|..
T Consensus 51 ~GIW~C~kCg~~fAGgay 68 (89)
T COG1997 51 TGIWKCRKCGAKFAGGAY 68 (89)
T ss_pred cCeEEcCCCCCeeccccc
Confidence 448999999999876654
No 198
>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=42.43 E-value=19 Score=33.60 Aligned_cols=34 Identities=21% Similarity=0.480 Sum_probs=23.7
Q ss_pred cccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009783 449 SEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 504 (526)
Q Consensus 449 ~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 504 (526)
..+..|-.|+.|+.. .|-++|.+ .-..||.||-.
T Consensus 104 e~~~~~Y~Cp~c~~r-----~tf~eA~~-----------------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 104 ETNNMFFICPNMCVR-----FTFNEAME-----------------LNFTCPRCGAM 137 (158)
T ss_pred ccCCCeEECCCCCcE-----eeHHHHHH-----------------cCCcCCCCCCE
Confidence 334567889999975 45677763 13569999975
No 199
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=42.14 E-value=11 Score=33.75 Aligned_cols=30 Identities=17% Similarity=0.278 Sum_probs=19.0
Q ss_pred HHHHHHHHHHc---------CccccccccCccccCCCccc
Q 009783 434 NQQLLEVIEAF---------QLKISEDQLMSRCTKCNGRF 464 (526)
Q Consensus 434 ~~QL~~vl~~f---------~l~~~~~~~~sRC~~CN~~l 464 (526)
.++|+.-++.+ .|.+.......|| .||...
T Consensus 41 pe~L~faf~~~~~gT~~egA~L~I~~vp~~~~C-~Cg~~~ 79 (124)
T PRK00762 41 PEQLRFMLDVLAEGTIAEDADLIVEMIPVEIEC-ECGYEG 79 (124)
T ss_pred HHHHHHHHHHHhCCCCcCCCEEEEEecCeeEEe-eCcCcc
Confidence 46666655433 3445555567899 999765
No 200
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=42.14 E-value=18 Score=25.21 Aligned_cols=13 Identities=23% Similarity=0.674 Sum_probs=10.4
Q ss_pred CCceeecCCCCeE
Q 009783 492 NLQFWQCMDCNQL 504 (526)
Q Consensus 492 ~~~F~~C~~Cgkv 504 (526)
.+-|++|..||-+
T Consensus 22 ~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 22 DDGFYYCDRCGHQ 34 (36)
T ss_pred cCCEEEhhhCceE
Confidence 3569999999965
No 201
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=41.97 E-value=6.5 Score=37.66 Aligned_cols=30 Identities=13% Similarity=0.530 Sum_probs=21.5
Q ss_pred ccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009783 452 QLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 505 (526)
Q Consensus 452 ~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 505 (526)
.++++|+.|..+++ |.+ -.--.|+.||+++
T Consensus 147 vv~a~~~~~g~~~~--~~~----------------------~~~~~c~~~~~~e 176 (189)
T PRK09521 147 VIYAMCSRCRTPLV--KKG----------------------ENELKCPNCGNIE 176 (189)
T ss_pred EEEEEccccCCceE--ECC----------------------CCEEECCCCCCEE
Confidence 45789999999885 221 1235699999876
No 202
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=41.74 E-value=17 Score=31.67 Aligned_cols=26 Identities=23% Similarity=0.567 Sum_probs=18.7
Q ss_pred ccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009783 455 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 504 (526)
Q Consensus 455 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 504 (526)
..|+.|++.. +|+. ...|.||.|+.-
T Consensus 3 p~CP~C~sey-----------------------tY~d-g~~~iCpeC~~E 28 (109)
T TIGR00686 3 PPCPKCNSEY-----------------------TYHD-GTQLICPSCLYE 28 (109)
T ss_pred CcCCcCCCcc-----------------------eEec-CCeeECcccccc
Confidence 5699999964 2332 457999999975
No 203
>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=41.67 E-value=36 Score=33.61 Aligned_cols=51 Identities=14% Similarity=0.198 Sum_probs=37.1
Q ss_pred cCCccHHHHHHHHcCCcCcc--cccccCC-CC-C-CCCHHHHHHHHHHHHHHHHHH
Q 009783 159 KETKSLANICKELLDISLSK--ELQCSDW-SN-R-PLTEEQKNYAAIDAHCLIEIF 209 (526)
Q Consensus 159 ~~~~gL~~Lv~~~Lg~~L~K--~~q~sdW-~~-R-PL~~~qi~YAA~DA~~ll~L~ 209 (526)
..+++|..++.++||...+. ..+.+.| .. . .-...-+.|...||...++|.
T Consensus 175 l~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l~l~Ll 230 (231)
T cd05778 175 LTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEIL 230 (231)
T ss_pred cccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHHHHHhh
Confidence 35899999999999987553 3455565 22 2 233556899999999998875
No 204
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=41.41 E-value=11 Score=33.28 Aligned_cols=31 Identities=16% Similarity=0.367 Sum_probs=18.9
Q ss_pred HHHHHHHHHHc---------CccccccccCccccCCCccc
Q 009783 434 NQQLLEVIEAF---------QLKISEDQLMSRCTKCNGRF 464 (526)
Q Consensus 434 ~~QL~~vl~~f---------~l~~~~~~~~sRC~~CN~~l 464 (526)
.++|+.-++.+ .|.+.......+|..|+...
T Consensus 41 p~~L~f~f~~~~~~t~~egA~L~i~~~p~~~~C~~Cg~~~ 80 (114)
T PRK03681 41 TSSLAFCFDLVCRGTVAEGCKLHLEEQEAECWCETCQQYV 80 (114)
T ss_pred HHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcccCCCee
Confidence 45666655443 34444445567899999743
No 205
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=41.29 E-value=16 Score=33.04 Aligned_cols=9 Identities=56% Similarity=1.280 Sum_probs=6.1
Q ss_pred cccCCCccc
Q 009783 456 RCTKCNGRF 464 (526)
Q Consensus 456 RC~~CN~~l 464 (526)
||+.|+..+
T Consensus 3 ~Ct~Cg~~f 11 (131)
T PF09845_consen 3 QCTKCGRVF 11 (131)
T ss_pred ccCcCCCCc
Confidence 577777665
No 206
>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=41.12 E-value=19 Score=30.51 Aligned_cols=17 Identities=18% Similarity=0.647 Sum_probs=13.1
Q ss_pred CceeecCCCCeEEeccc
Q 009783 493 LQFWQCMDCNQLYWEVM 509 (526)
Q Consensus 493 ~~F~~C~~CgkvyW~Gs 509 (526)
.-.|.|..||+.|=-|.
T Consensus 51 ~GIW~C~~C~~~~AGGA 67 (90)
T PF01780_consen 51 TGIWKCKKCGKKFAGGA 67 (90)
T ss_dssp TTEEEETTTTEEEE-BS
T ss_pred eEEeecCCCCCEEeCCC
Confidence 34799999999986664
No 207
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=40.94 E-value=22 Score=35.28 Aligned_cols=21 Identities=10% Similarity=0.028 Sum_probs=16.2
Q ss_pred CceeecCCCCeEEecccchhhH
Q 009783 493 LQFWQCMDCNQLYWEVMSAYLF 514 (526)
Q Consensus 493 ~~F~~C~~CgkvyW~GsH~~r~ 514 (526)
-++.+|+.||+++=. .+|...
T Consensus 33 i~v~~C~~Cg~~~~~-~~W~~~ 53 (236)
T PF04981_consen 33 IEVTICPKCGRYRIG-GRWVDP 53 (236)
T ss_pred cCceECCCCCCEECC-CEeeec
Confidence 479999999997765 666654
No 208
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=40.92 E-value=20 Score=32.38 Aligned_cols=26 Identities=15% Similarity=0.427 Sum_probs=15.8
Q ss_pred HHHHHHHHHcCccccccccCccccCCCcccc
Q 009783 435 QQLLEVIEAFQLKISEDQLMSRCTKCNGRFI 465 (526)
Q Consensus 435 ~QL~~vl~~f~l~~~~~~~~sRC~~CN~~l~ 465 (526)
+-+.++|..-.-.+. .-|++|+.+|.
T Consensus 14 k~iA~lLl~GAkML~-----~hCp~Cg~PLF 39 (131)
T COG1645 14 KKIAELLLQGAKMLA-----KHCPKCGTPLF 39 (131)
T ss_pred HHHHHHHHhhhHHHH-----hhCcccCCcce
Confidence 455565544332332 24999999985
No 209
>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=40.91 E-value=17 Score=33.93 Aligned_cols=16 Identities=19% Similarity=0.445 Sum_probs=13.0
Q ss_pred ccCCceeecCCCCeEE
Q 009783 490 DKNLQFWQCMDCNQLY 505 (526)
Q Consensus 490 ~~~~~F~~C~~Cgkvy 505 (526)
+....||.||.|++-|
T Consensus 104 e~~~~~Y~Cp~c~~r~ 119 (158)
T TIGR00373 104 ETNNMFFICPNMCVRF 119 (158)
T ss_pred ccCCCeEECCCCCcEe
Confidence 3567899999999765
No 210
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=39.98 E-value=7.1 Score=29.65 Aligned_cols=10 Identities=50% Similarity=1.072 Sum_probs=8.6
Q ss_pred ccccCCCccc
Q 009783 455 SRCTKCNGRF 464 (526)
Q Consensus 455 sRC~~CN~~l 464 (526)
-||..||..|
T Consensus 5 iRC~~CnKlL 14 (60)
T COG4416 5 IRCAKCNKLL 14 (60)
T ss_pred eehHHHhHHH
Confidence 4899999977
No 211
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=39.86 E-value=19 Score=24.79 Aligned_cols=16 Identities=25% Similarity=0.528 Sum_probs=9.6
Q ss_pred CceeecCCCCeEEecc
Q 009783 493 LQFWQCMDCNQLYWEV 508 (526)
Q Consensus 493 ~~F~~C~~CgkvyW~G 508 (526)
-..-+|+.||+++|.=
T Consensus 9 l~~~rC~~Cg~~~~pP 24 (37)
T PF12172_consen 9 LLGQRCRDCGRVQFPP 24 (37)
T ss_dssp EEEEE-TTT--EEES-
T ss_pred EEEEEcCCCCCEecCC
Confidence 3467899999999863
No 212
>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=39.61 E-value=16 Score=32.80 Aligned_cols=10 Identities=20% Similarity=0.644 Sum_probs=8.7
Q ss_pred cccCCCcccc
Q 009783 456 RCTKCNGRFI 465 (526)
Q Consensus 456 RC~~CN~~l~ 465 (526)
-|+.|+.+++
T Consensus 11 ~Cp~cg~kFY 20 (129)
T TIGR02300 11 ICPNTGSKFY 20 (129)
T ss_pred cCCCcCcccc
Confidence 4999999886
No 213
>PRK05978 hypothetical protein; Provisional
Probab=39.45 E-value=16 Score=33.77 Aligned_cols=9 Identities=22% Similarity=0.977 Sum_probs=7.4
Q ss_pred ecCCCCeEE
Q 009783 497 QCMDCNQLY 505 (526)
Q Consensus 497 ~C~~Cgkvy 505 (526)
.|+.||.-|
T Consensus 54 ~C~~CG~~~ 62 (148)
T PRK05978 54 HCAACGEDF 62 (148)
T ss_pred CccccCCcc
Confidence 399999877
No 214
>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=39.14 E-value=13 Score=32.86 Aligned_cols=31 Identities=23% Similarity=0.489 Sum_probs=18.5
Q ss_pred HHHHHHHHHHc---------CccccccccCccccCCCccc
Q 009783 434 NQQLLEVIEAF---------QLKISEDQLMSRCTKCNGRF 464 (526)
Q Consensus 434 ~~QL~~vl~~f---------~l~~~~~~~~sRC~~CN~~l 464 (526)
.++|+.-++.+ .|.+.......+|..|+...
T Consensus 41 p~~L~faf~~~~~~t~~ega~L~I~~~p~~~~C~~Cg~~~ 80 (115)
T TIGR00100 41 PSQLQFAFEVVREGTVAEGAKLNIEDEPVECECEDCSEEV 80 (115)
T ss_pred HHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcccCCCEE
Confidence 45666555433 34444445567899999654
No 215
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=39.09 E-value=25 Score=33.54 Aligned_cols=34 Identities=29% Similarity=0.737 Sum_probs=22.8
Q ss_pred cccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009783 449 SEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 504 (526)
Q Consensus 449 ~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 504 (526)
..+..|-.|+.|+..+ +-++|.+ .-..||.||-.
T Consensus 112 e~~~~~Y~Cp~C~~ry-----tf~eA~~-----------------~~F~Cp~Cg~~ 145 (178)
T PRK06266 112 EENNMFFFCPNCHIRF-----TFDEAME-----------------YGFRCPQCGEM 145 (178)
T ss_pred ccCCCEEECCCCCcEE-----eHHHHhh-----------------cCCcCCCCCCC
Confidence 3345578899999754 4567653 13569999864
No 216
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=38.76 E-value=21 Score=27.29 Aligned_cols=10 Identities=20% Similarity=0.670 Sum_probs=8.3
Q ss_pred CccccCCCcc
Q 009783 454 MSRCTKCNGR 463 (526)
Q Consensus 454 ~sRC~~CN~~ 463 (526)
++.|+.|+..
T Consensus 26 l~~C~~cG~~ 35 (55)
T TIGR01031 26 LVVCPNCGEF 35 (55)
T ss_pred ceECCCCCCc
Confidence 6789999984
No 217
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=38.12 E-value=28 Score=24.65 Aligned_cols=31 Identities=32% Similarity=0.804 Sum_probs=16.1
Q ss_pred ccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009783 455 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 504 (526)
Q Consensus 455 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 504 (526)
-||..|++-+- | =..+.....-|.|+-|+..
T Consensus 3 ~rC~~C~aylN--p-----------------~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 3 VRCRRCRAYLN--P-----------------FCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp -B-TTT--BS---T-----------------TSEEETTTTEEEETTT--E
T ss_pred cccCCCCCEEC--C-----------------cceEcCCCCEEECcCCCCc
Confidence 58999999652 1 1123445679999999874
No 218
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=37.87 E-value=18 Score=27.31 Aligned_cols=13 Identities=15% Similarity=0.674 Sum_probs=7.0
Q ss_pred CceeecCCCCeEE
Q 009783 493 LQFWQCMDCNQLY 505 (526)
Q Consensus 493 ~~F~~C~~Cgkvy 505 (526)
...++|++|+++|
T Consensus 19 ~~~y~C~~C~~~F 31 (51)
T PF07975_consen 19 SSRYRCPKCKNHF 31 (51)
T ss_dssp -EEE--TTTT--B
T ss_pred CCeEECCCCCCcc
Confidence 5688999999987
No 219
>PHA02768 hypothetical protein; Provisional
Probab=37.22 E-value=13 Score=28.55 Aligned_cols=18 Identities=22% Similarity=0.571 Sum_probs=15.5
Q ss_pred eecCCCCeEEecccchhh
Q 009783 496 WQCMDCNQLYWEVMSAYL 513 (526)
Q Consensus 496 ~~C~~CgkvyW~GsH~~r 513 (526)
+.|+.|||.|=.++|..+
T Consensus 6 y~C~~CGK~Fs~~~~L~~ 23 (55)
T PHA02768 6 YECPICGEIYIKRKSMIT 23 (55)
T ss_pred cCcchhCCeeccHHHHHH
Confidence 379999999999888766
No 220
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=37.18 E-value=41 Score=38.35 Aligned_cols=59 Identities=19% Similarity=0.264 Sum_probs=34.5
Q ss_pred HHHHHHHHHH---cCccc-cccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEeccc
Q 009783 434 NQQLLEVIEA---FQLKI-SEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVM 509 (526)
Q Consensus 434 ~~QL~~vl~~---f~l~~-~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~Gs 509 (526)
-+.+.+|++. .++.. +-+..+++|..|+-.- + .-+.||.||. .-.
T Consensus 535 ~~Al~~lvk~~~~~~i~Y~sin~~~~~C~~CGy~g--------~--------------------~~~~CP~CG~---~d~ 583 (618)
T PRK14704 535 KKALKQIVQAMAEHGVGYGSINHPVDRCKCCSYHG--------V--------------------IGNECPSCGN---EDE 583 (618)
T ss_pred HHHHHHHHHHHHhcCCceEEeCCCCeecCCCCCCC--------C--------------------cCccCcCCCC---CCc
Confidence 3455666553 22331 2344589999999621 0 0177999975 111
Q ss_pred chhhHHhhhhhhhh
Q 009783 510 SAYLFIFLTPAYFS 523 (526)
Q Consensus 510 H~~r~~~~~~~~~~ 523 (526)
+---++++++-|+.
T Consensus 584 ~~~~v~~Ri~GYl~ 597 (618)
T PRK14704 584 ANIERIRRITGYLV 597 (618)
T ss_pred chhHHHHHHHhHhc
Confidence 12458888888884
No 221
>PRK11032 hypothetical protein; Provisional
Probab=36.77 E-value=19 Score=33.85 Aligned_cols=11 Identities=27% Similarity=0.715 Sum_probs=8.8
Q ss_pred ccccCCCcccc
Q 009783 455 SRCTKCNGRFI 465 (526)
Q Consensus 455 sRC~~CN~~l~ 465 (526)
-+|..|+..+.
T Consensus 125 LvC~~Cg~~~~ 135 (160)
T PRK11032 125 LVCEKCHHHLA 135 (160)
T ss_pred EEecCCCCEEE
Confidence 47999998764
No 222
>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=36.62 E-value=19 Score=33.21 Aligned_cols=12 Identities=17% Similarity=0.440 Sum_probs=9.3
Q ss_pred CccccCCCcccc
Q 009783 454 MSRCTKCNGRFI 465 (526)
Q Consensus 454 ~sRC~~CN~~l~ 465 (526)
.-+|..|+..+.
T Consensus 112 ~l~C~~Cg~~~~ 123 (146)
T PF07295_consen 112 TLVCENCGHEVE 123 (146)
T ss_pred eEecccCCCEEE
Confidence 357999999764
No 223
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized 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.
Probab=36.50 E-value=24 Score=41.65 Aligned_cols=10 Identities=60% Similarity=1.428 Sum_probs=8.5
Q ss_pred ccccCCCccc
Q 009783 455 SRCTKCNGRF 464 (526)
Q Consensus 455 sRC~~CN~~l 464 (526)
-||++||...
T Consensus 1013 fRC~kC~~kY 1022 (1095)
T TIGR00354 1013 VRCTKCNTKY 1022 (1095)
T ss_pred eeecccCCcc
Confidence 5899999965
No 224
>PRK14536 cysS cysteinyl-tRNA synthetase; Provisional
Probab=36.47 E-value=31 Score=38.18 Aligned_cols=36 Identities=8% Similarity=0.218 Sum_probs=26.6
Q ss_pred HHHHHHHhcCCceecCCC----------CCCChHHHHHhhhcCCcE
Q 009783 371 GLAKHLRCVGIDAATPRS----------KKPEPRELIDQTSKEKRV 406 (526)
Q Consensus 371 ~Lar~LR~lG~D~~~~~~----------~~~~d~~ll~~A~~E~Ri 406 (526)
=|+|+||..||+|.++.+ .+..+..|+..|+++|.-
T Consensus 50 vl~R~l~~~G~~V~~v~NiTDv~hl~~~~De~ddKii~~A~~~g~~ 95 (490)
T PRK14536 50 TLRRTLHFLGYRVTHVMNITDVGHLTDDADSGEDKMVKSAQEHGKS 95 (490)
T ss_pred HHHHHHHhcCCceEEEEeeccccccccCCcCCChHHHHHHHHcCCC
Confidence 389999999999998752 122246788888887743
No 225
>PRK03954 ribonuclease P protein component 4; Validated
Probab=36.44 E-value=36 Score=30.48 Aligned_cols=33 Identities=15% Similarity=0.329 Sum_probs=25.8
Q ss_pred HHHHHHHHHHcCccccccccCccccCCCccccc
Q 009783 434 NQQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQ 466 (526)
Q Consensus 434 ~~QL~~vl~~f~l~~~~~~~~sRC~~CN~~l~~ 466 (526)
...+..|-....+.+.++---+-|-.||..|++
T Consensus 44 v~lar~Is~K~rirlp~~~KR~~CK~C~t~LiP 76 (121)
T PRK03954 44 VELALAVQQKAKVKLPRKWKRRYCKRCHSFLVP 76 (121)
T ss_pred HHHHHHHHHHhccCCCHHHHHHHhhcCCCeeec
Confidence 356777777888888777666789999999974
No 226
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=36.37 E-value=20 Score=24.87 Aligned_cols=12 Identities=25% Similarity=0.847 Sum_probs=9.8
Q ss_pred eecCCCCeEEec
Q 009783 496 WQCMDCNQLYWE 507 (526)
Q Consensus 496 ~~C~~CgkvyW~ 507 (526)
++|+.||+.|..
T Consensus 6 y~C~~Cg~~fe~ 17 (41)
T smart00834 6 YRCEDCGHTFEV 17 (41)
T ss_pred EEcCCCCCEEEE
Confidence 479999998863
No 227
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=36.34 E-value=42 Score=34.14 Aligned_cols=30 Identities=17% Similarity=0.119 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHcCccccccc-cC--ccccCCCc
Q 009783 433 KNQQLLEVIEAFQLKISEDQ-LM--SRCTKCNG 462 (526)
Q Consensus 433 ~~~QL~~vl~~f~l~~~~~~-~~--sRC~~CN~ 462 (526)
..+||+...+..++.+...+ .. ..|+.|+.
T Consensus 285 ~~~~l~yka~~~~~~v~~~~~~~tS~~C~~cg~ 317 (364)
T COG0675 285 LRRQLEYKAEWGGIVVKVVPPYYTSKTCPCCGH 317 (364)
T ss_pred HHHHHHHHHHhCCeEEEECCCCCCcccccccCC
Confidence 35666666666444433222 12 47999998
No 228
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=36.22 E-value=19 Score=23.60 Aligned_cols=10 Identities=20% Similarity=0.992 Sum_probs=5.7
Q ss_pred cccCCCcccc
Q 009783 456 RCTKCNGRFI 465 (526)
Q Consensus 456 RC~~CN~~l~ 465 (526)
.|++||+.|+
T Consensus 1 ~CP~C~s~l~ 10 (28)
T PF03119_consen 1 TCPVCGSKLV 10 (28)
T ss_dssp B-TTT--BEE
T ss_pred CcCCCCCEeE
Confidence 4999999885
No 229
>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=36.22 E-value=24 Score=29.94 Aligned_cols=17 Identities=18% Similarity=0.579 Sum_probs=13.8
Q ss_pred CceeecCCCCeEEeccc
Q 009783 493 LQFWQCMDCNQLYWEVM 509 (526)
Q Consensus 493 ~~F~~C~~CgkvyW~Gs 509 (526)
.-.|.|..||+.|=-|.
T Consensus 51 ~GIW~C~~C~~~~AGGA 67 (91)
T TIGR00280 51 TGIWTCRKCGAKFAGGA 67 (91)
T ss_pred eEEEEcCCCCCEEeCCc
Confidence 45899999999986664
No 230
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=36.13 E-value=25 Score=29.73 Aligned_cols=17 Identities=18% Similarity=0.602 Sum_probs=13.8
Q ss_pred CceeecCCCCeEEeccc
Q 009783 493 LQFWQCMDCNQLYWEVM 509 (526)
Q Consensus 493 ~~F~~C~~CgkvyW~Gs 509 (526)
.-.|.|..||+.|=-|.
T Consensus 52 ~GIW~C~~C~~~~AGGA 68 (90)
T PTZ00255 52 VGIWRCKGCKKTVAGGA 68 (90)
T ss_pred eEEEEcCCCCCEEeCCc
Confidence 35899999999986664
No 231
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=35.51 E-value=42 Score=29.20 Aligned_cols=56 Identities=14% Similarity=0.380 Sum_probs=34.4
Q ss_pred HHHHHHHHHcCccccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009783 435 QQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 505 (526)
Q Consensus 435 ~QL~~vl~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 505 (526)
+-+..+-....+.+.++---+-|-.|+..|++ -. .+. -+ +....-.+.|..||-++
T Consensus 37 ~la~~Is~K~rv~lp~~iKR~~CkkC~t~Lvp--g~--n~r------vR-----~~~~~v~vtC~~CG~~~ 92 (105)
T COG2023 37 KLARRISMKYRVRLPREIKRTICKKCYTPLVP--GK--NAR------VR-----LRKGRVVVTCLECGTIR 92 (105)
T ss_pred HHHHHHHHhhccccCHHHHHHhccccCccccc--Cc--ceE------EE-----EcCCeEEEEecCCCcEE
Confidence 34445555677777665445669999999964 11 110 01 12334689999999764
No 232
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=35.41 E-value=47 Score=30.43 Aligned_cols=39 Identities=15% Similarity=0.422 Sum_probs=23.8
Q ss_pred cccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009783 449 SEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 504 (526)
Q Consensus 449 ~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 504 (526)
..+..+-.|+.|+... +..+|.. ..+ | +.-..||.||..
T Consensus 94 e~~~~~Y~Cp~C~~~y-----~~~ea~~---~~d--~-------~~~f~Cp~Cg~~ 132 (147)
T smart00531 94 ETNNAYYKCPNCQSKY-----TFLEANQ---LLD--M-------DGTFTCPRCGEE 132 (147)
T ss_pred ccCCcEEECcCCCCEe-----eHHHHHH---hcC--C-------CCcEECCCCCCE
Confidence 3345577899999765 3455542 101 1 223789999975
No 233
>cd00758 MoCF_BD MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin.
Probab=35.38 E-value=78 Score=28.23 Aligned_cols=49 Identities=16% Similarity=0.156 Sum_probs=32.4
Q ss_pred EEEecccHHHHHHHHhcCCceecCCCCCCChH---HHHHhhhcCCcEEEecC
Q 009783 363 FLCDVMVEGLAKHLRCVGIDAATPRSKKPEPR---ELIDQTSKEKRVLLTRD 411 (526)
Q Consensus 363 fl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~---~ll~~A~~E~RiiLTrd 411 (526)
-+.|..-.-|+.+|+..|+++.+..-...+.. +.++.+.++-.+|||.+
T Consensus 15 ~i~d~n~~~l~~~l~~~G~~v~~~~~v~Dd~~~i~~~i~~~~~~~DlvittG 66 (133)
T cd00758 15 QIEDTNGPALEALLEDLGCEVIYAGVVPDDADSIRAALIEASREADLVLTTG 66 (133)
T ss_pred ceEEchHHHHHHHHHHCCCEEEEeeecCCCHHHHHHHHHHHHhcCCEEEECC
Confidence 45688888899999999999876532221222 34444555567777765
No 234
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=35.06 E-value=18 Score=38.93 Aligned_cols=30 Identities=27% Similarity=0.633 Sum_probs=21.1
Q ss_pred CccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEec
Q 009783 454 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWE 507 (526)
Q Consensus 454 ~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~ 507 (526)
..+|+.||+.+. . +| .. -|+|++||..|=.
T Consensus 350 ~p~Cp~Cg~~m~-------S-----~G-----------~~-g~rC~kCg~~~~~ 379 (421)
T COG1571 350 NPVCPRCGGRMK-------S-----AG-----------RN-GFRCKKCGTRARE 379 (421)
T ss_pred CCCCCccCCchh-------h-----cC-----------CC-CcccccccccCCc
Confidence 468999999862 1 12 12 7899999987643
No 235
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=35.02 E-value=53 Score=29.82 Aligned_cols=36 Identities=19% Similarity=0.263 Sum_probs=28.1
Q ss_pred ccHH--HHHHHHhcCCceecCCCCCCChHHHHHhhhcCC
Q 009783 368 MVEG--LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 404 (526)
Q Consensus 368 mLg~--Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~ 404 (526)
.+|. ++..||..||+|.++.. +...+++++.|.+++
T Consensus 17 ~lG~~iv~~~lr~~G~eVi~LG~-~vp~e~i~~~a~~~~ 54 (137)
T PRK02261 17 AVGNKILDRALTEAGFEVINLGV-MTSQEEFIDAAIETD 54 (137)
T ss_pred HHHHHHHHHHHHHCCCEEEECCC-CCCHHHHHHHHHHcC
Confidence 3553 69999999999999975 456678998887654
No 236
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=34.95 E-value=48 Score=33.54 Aligned_cols=49 Identities=24% Similarity=0.306 Sum_probs=32.8
Q ss_pred EEEecccHHHHHHHHhcCCceecCCCCCCCh---HHHHHhhhcCCcEEEecC
Q 009783 363 FLCDVMVEGLAKHLRCVGIDAATPRSKKPEP---RELIDQTSKEKRVLLTRD 411 (526)
Q Consensus 363 fl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d---~~ll~~A~~E~RiiLTrd 411 (526)
=++|.+...||+.|...||++....-...+. .+.+..|.+.-.++||.+
T Consensus 17 ~ivdtNa~~la~~L~~~G~~v~~~~~VgD~~~~I~~~l~~a~~r~D~vI~tG 68 (255)
T COG1058 17 RIVDTNAAFLADELTELGVDLARITTVGDNPDRIVEALREASERADVVITTG 68 (255)
T ss_pred ceecchHHHHHHHHHhcCceEEEEEecCCCHHHHHHHHHHHHhCCCEEEECC
Confidence 3689999999999999999996533222121 246666666655555543
No 237
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.88 E-value=1.5e+02 Score=36.52 Aligned_cols=102 Identities=14% Similarity=0.158 Sum_probs=59.6
Q ss_pred CCCcEEEEEecHH-hHHHHHhhcccCCCccCcCC-------------------CCceeeHHHHHHHhhccccCCCCCcCC
Q 009783 102 SPDILKLGFKFKQ-DLIYLSSTFCSQGCDIGFDR-------------------VEPYLDITSIYNHLHHKQLGRKLPKET 161 (526)
Q Consensus 102 ~~~i~KVgh~~k~-Dl~~L~~~~gi~~~~~~~~~-------------------~~~~~Dlt~La~yLl~~~~~~~~~~~~ 161 (526)
||+++ +|||..+ |+..|.+....+++. .|.. -.-++|+-.++..... ..+
T Consensus 599 DPDii-~g~n~~qfdlkvl~nR~~~l~i~-~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~~~~k~~~~--------~~s 668 (1172)
T TIGR00592 599 DPDEI-VGHDYQQRALKVLANRINDLKIP-TWSKIGRLRRSPKFGRRFGERTCGRMICDVEISAKELIR--------CKS 668 (1172)
T ss_pred CCCEE-EEEcccCccHHHHHHHHHHcCCC-cccccCccccCCCccccccceECCEEEEEHHHHHHHHhC--------cCC
Confidence 78764 7999875 777765432112211 1110 1236786666555543 258
Q ss_pred ccHHHHHHHHcCCcCcc--ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009783 162 KSLANICKELLDISLSK--ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (526)
Q Consensus 162 ~gL~~Lv~~~Lg~~L~K--~~q~s-dW~~RPL~~~qi~YAA~DA~~ll~L~~~L~ 213 (526)
++|..+++++||..-.. ..... -|....--..-+.|...||..+++|...|.
T Consensus 669 y~L~~v~~~~L~~~k~~~~~~~i~~~~~~~~~~~~~~~y~~~Da~l~~~L~~~l~ 723 (1172)
T TIGR00592 669 YDLSELVQQILKTERKVIPIDNINNMYSESSSLTYLLEHTWKDAMFILQIMCELN 723 (1172)
T ss_pred CCHHHHHHHHhCCCCcccCHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999853211 11111 133222224458899999999999887653
No 238
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=34.60 E-value=19 Score=39.77 Aligned_cols=41 Identities=15% Similarity=0.340 Sum_probs=25.6
Q ss_pred CccccCCCcccccCCCChHHHHHhhhcCcccCccc-cccCCceeecCCCCe
Q 009783 454 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCL-FDKNLQFWQCMDCNQ 503 (526)
Q Consensus 454 ~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v-~~~~~~F~~C~~Cgk 503 (526)
--+|..|+-.--+..- +. ...||++. |+...+=|.||.||-
T Consensus 425 ~~~c~~c~~~yd~~~g---~~------~~~~~~gt~~~~lp~~~~cp~c~~ 466 (479)
T PRK05452 425 RMQCSVCQWIYDPAKG---EP------MQDVAPGTPWSEVPDNFLCPECSL 466 (479)
T ss_pred eEEECCCCeEECCCCC---Cc------ccCCCCCCChhhCCCCCcCcCCCC
Confidence 3479999975432111 10 12477775 556667799999984
No 239
>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins.
Probab=34.56 E-value=71 Score=27.09 Aligned_cols=39 Identities=15% Similarity=0.235 Sum_probs=29.8
Q ss_pred ChHHHHHhhhcCC-cEEEecChhHHHhhc-ccCCcEEEEcC
Q 009783 392 EPRELIDQTSKEK-RVLLTRDAKLLRHQY-LIKNQIYRVKS 430 (526)
Q Consensus 392 ~d~~ll~~A~~E~-RiiLTrd~~l~~~~~-~~~~~~~~v~~ 430 (526)
.|+-|+++|.+.+ -++.|.|.+|.++.. .++..+++++.
T Consensus 53 addci~~~~~~~~~~~VaT~D~~Lr~~lr~~~GvPvi~l~~ 93 (101)
T PF04900_consen 53 ADDCILDLAGKNNKYIVATQDKELRRRLRKIPGVPVIYLRR 93 (101)
T ss_pred HHHHHHHHhccCCeEEEEecCHHHHHHHhcCCCCCEEEEEC
Confidence 4677999998777 688899999977654 56667777764
No 240
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.10 E-value=25 Score=32.69 Aligned_cols=33 Identities=30% Similarity=0.636 Sum_probs=22.6
Q ss_pred ccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009783 455 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 503 (526)
Q Consensus 455 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 503 (526)
-+|-+||.+-. +- +-+..|.....+-+|++|.-
T Consensus 80 yTCkvCntRs~-kt---------------isk~AY~~GvVivqC~gC~~ 112 (165)
T KOG3277|consen 80 YTCKVCNTRST-KT---------------ISKQAYEKGVVIVQCPGCKN 112 (165)
T ss_pred EEeeccCCccc-cc---------------cChhhhhCceEEEECCCCcc
Confidence 36999999753 12 22334556677999999973
No 241
>PRK04023 DNA polymerase II large subunit; Validated
Probab=33.91 E-value=29 Score=41.23 Aligned_cols=10 Identities=50% Similarity=1.308 Sum_probs=8.6
Q ss_pred ccccCCCccc
Q 009783 455 SRCTKCNGRF 464 (526)
Q Consensus 455 sRC~~CN~~l 464 (526)
.||++||...
T Consensus 1038 fRC~kC~~kY 1047 (1121)
T PRK04023 1038 FRCTKCGAKY 1047 (1121)
T ss_pred eeecccCccc
Confidence 5899999965
No 242
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=33.82 E-value=21 Score=22.26 Aligned_cols=9 Identities=22% Similarity=0.903 Sum_probs=7.2
Q ss_pred cccCCCccc
Q 009783 456 RCTKCNGRF 464 (526)
Q Consensus 456 RC~~CN~~l 464 (526)
+|+.|+..+
T Consensus 1 ~Cp~CG~~~ 9 (23)
T PF13240_consen 1 YCPNCGAEI 9 (23)
T ss_pred CCcccCCCC
Confidence 589999865
No 243
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=33.79 E-value=22 Score=30.64 Aligned_cols=10 Identities=40% Similarity=0.966 Sum_probs=4.7
Q ss_pred CccccCCCcc
Q 009783 454 MSRCTKCNGR 463 (526)
Q Consensus 454 ~sRC~~CN~~ 463 (526)
+|=|+.|++.
T Consensus 20 l~GCp~CG~n 29 (112)
T COG3364 20 LSGCPKCGCN 29 (112)
T ss_pred HccCccccch
Confidence 3445555543
No 244
>cd00671 ArgRS_core catalytic core domain of arginyl-tRNA synthetases. Arginyl tRNA synthetase (ArgRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. There are at least three subgroups of ArgRS. One type contains both characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The second subtype lacks the KMSKS motif; however, it has a lysine N-terminal to the HIGH motif, which serves as the functional counterpart to the second lysine of the KMSKS motif. A third group, which is found primarily in archaea and a few bacteria, lacks both the KMSKS motif and the HIGH loop lysine.
Probab=33.68 E-value=26 Score=34.00 Aligned_cols=38 Identities=16% Similarity=0.126 Sum_probs=25.5
Q ss_pred ccH-HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009783 368 MVE-GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 405 (526)
Q Consensus 368 mLg-~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 405 (526)
.+| -|+|+||.+||+|......+.-+.++...|.+.++
T Consensus 24 vigD~l~R~l~~~G~~V~~~~~~~D~G~qi~~~a~~~~~ 62 (212)
T cd00671 24 IIGDSLARILEFLGYDVTREYYINDWGRQIGLLILSLEK 62 (212)
T ss_pred HHHHHHHHHHHHCCCcEEEEeccCCcHHHHHHHHHHHHH
Confidence 355 48999999999998765432223457777655443
No 245
>TIGR03599 YloV DAK2 domain fusion protein YloV. This model describes a protein family that contains an N-terminal DAK2 domain (pfam02734), so named because of similarity to the dihydroxyacetone kinase family family. The GTP-binding protein CgtA (a member of the obg family) is a bacterial GTPase associated with ribosome biogenesis, and it has a characteristic extension (TIGR03595) in certain lineages. This protein family described here was found, by the method of partial phylognetic profiling, to have a phylogenetic distribution strongly correlated to that of TIGR03595. This correlation implies some form of functional coupling.
Probab=33.38 E-value=2.2e+02 Score=32.01 Aligned_cols=84 Identities=13% Similarity=0.271 Sum_probs=59.1
Q ss_pred CEEEEecccHHHHHHHHhcCCceecCCCC--CCChHHHHHhh---hcCCcEEEecChhHHHh----hcccCCcEEEEcCC
Q 009783 361 PKFLCDVMVEGLAKHLRCVGIDAATPRSK--KPEPRELIDQT---SKEKRVLLTRDAKLLRH----QYLIKNQIYRVKSL 431 (526)
Q Consensus 361 ~kfl~D~mLg~Lar~LR~lG~D~~~~~~~--~~~d~~ll~~A---~~E~RiiLTrd~~l~~~----~~~~~~~~~~v~~~ 431 (526)
..||+-+.=.++++.++.+|.|++..... .++-.++++.. ..++=|||..++..+-. ....+.++..|++.
T Consensus 315 ~~ivAv~~g~g~~~~f~~~Ga~~vi~ggqt~nPS~~dll~ai~~~~a~~V~iLPNn~nii~aA~qa~~~~~~~v~vvpT~ 394 (530)
T TIGR03599 315 YAIVAVAPGEGIAELFKSLGADVVIEGGQTMNPSTEDILKAIEKVNAKNVFVLPNNKNIILAAEQAAELADKNVVVIPTK 394 (530)
T ss_pred eEEEEEcCCchHHHHHHHCCCCEEEeCCCCCCCCHHHHHHHHHhCCCCeEEEecCCccHHHHHHHHHHHhCCcEEEEeCC
Confidence 35899888889999999999999887653 34445565444 44556888888775321 12234579999999
Q ss_pred CHHHHHHHHHHHcC
Q 009783 432 LKNQQLLEVIEAFQ 445 (526)
Q Consensus 432 ~~~~QL~~vl~~f~ 445 (526)
++.+.+..++ .|+
T Consensus 395 s~~qgiaAl~-~fd 407 (530)
T TIGR03599 395 TIVQGLAALL-VFD 407 (530)
T ss_pred CHHHHHHHHH-hhC
Confidence 8888887765 443
No 246
>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=33.29 E-value=27 Score=21.91 Aligned_cols=15 Identities=13% Similarity=0.713 Sum_probs=11.8
Q ss_pred eecCCCCeEEecccc
Q 009783 496 WQCMDCNQLYWEVMS 510 (526)
Q Consensus 496 ~~C~~CgkvyW~GsH 510 (526)
+.|..|++.|-..+-
T Consensus 2 ~~C~~C~~~F~~~~~ 16 (27)
T PF13912_consen 2 FECDECGKTFSSLSA 16 (27)
T ss_dssp EEETTTTEEESSHHH
T ss_pred CCCCccCCccCChhH
Confidence 579999999976443
No 247
>cd00802 class_I_aaRS_core catalytic core domain of class I amino acyl-tRNA synthetase. Class I amino acyl-tRNA synthetase (aaRS) catalytic core domain. These enzymes are mostly monomers which aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.
Probab=33.02 E-value=38 Score=30.42 Aligned_cols=33 Identities=18% Similarity=0.070 Sum_probs=22.1
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcC
Q 009783 371 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKE 403 (526)
Q Consensus 371 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E 403 (526)
-|+|+||..|++|..+...+.-+..+...|.+.
T Consensus 25 ~~~r~lr~~G~~v~~~~~~dd~~~~~~~~a~~~ 57 (143)
T cd00802 25 FLAQAYRKLGYKVRCIALIDDAGGLIGDPANKK 57 (143)
T ss_pred HHHHHHHHcCCCeEEEeeeCCCchHHHHHHHhc
Confidence 489999999999988765332233455555444
No 248
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=32.96 E-value=28 Score=29.47 Aligned_cols=17 Identities=18% Similarity=0.612 Sum_probs=13.6
Q ss_pred CceeecCCCCeEEeccc
Q 009783 493 LQFWQCMDCNQLYWEVM 509 (526)
Q Consensus 493 ~~F~~C~~CgkvyW~Gs 509 (526)
.-.|.|..||+.|=-|.
T Consensus 52 ~GIW~C~~C~~~~AGGA 68 (90)
T PRK03976 52 TGIWECRKCGAKFAGGA 68 (90)
T ss_pred EEEEEcCCCCCEEeCCc
Confidence 34899999999986554
No 249
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=32.77 E-value=23 Score=22.48 Aligned_cols=10 Identities=20% Similarity=0.630 Sum_probs=8.7
Q ss_pred eecCCCCeEE
Q 009783 496 WQCMDCNQLY 505 (526)
Q Consensus 496 ~~C~~Cgkvy 505 (526)
-.|+.|||-|
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 3699999998
No 250
>cd00817 ValRS_core catalytic core domain of valyl-tRNA synthetases. Valine amino-acyl tRNA synthetase (ValRS) catalytic core domain. This enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. ValRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
Probab=32.77 E-value=65 Score=34.35 Aligned_cols=18 Identities=22% Similarity=0.305 Sum_probs=15.9
Q ss_pred HHHHHHhcCCceecCCCC
Q 009783 372 LAKHLRCVGIDAATPRSK 389 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~ 389 (526)
++|++|+.|++|.++.+.
T Consensus 30 ~~Ry~r~~G~~V~~~~G~ 47 (382)
T cd00817 30 IARYKRMKGYNVLWPPGT 47 (382)
T ss_pred HHHHHHhcCCcccccCcc
Confidence 799999999999988753
No 251
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=32.71 E-value=24 Score=25.05 Aligned_cols=17 Identities=24% Similarity=0.620 Sum_probs=13.8
Q ss_pred CCceeecCCCCeEEecc
Q 009783 492 NLQFWQCMDCNQLYWEV 508 (526)
Q Consensus 492 ~~~F~~C~~CgkvyW~G 508 (526)
+-.-|+|+.||-.|+..
T Consensus 29 ~vp~~~C~~CGE~~~~~ 45 (46)
T TIGR03831 29 NVPALVCPQCGEEYLDA 45 (46)
T ss_pred CCCccccccCCCEeeCC
Confidence 44678899999999864
No 252
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=32.53 E-value=49 Score=28.90 Aligned_cols=59 Identities=24% Similarity=0.368 Sum_probs=28.1
Q ss_pred cCCcEEE--ecChhHHHhhcccCCcEEEEcCCCH-HHHHHHHHHHcCccccccc-cCccccCCCcc
Q 009783 402 KEKRVLL--TRDAKLLRHQYLIKNQIYRVKSLLK-NQQLLEVIEAFQLKISEDQ-LMSRCTKCNGR 463 (526)
Q Consensus 402 ~E~RiiL--Trd~~l~~~~~~~~~~~~~v~~~~~-~~QL~~vl~~f~l~~~~~~-~~sRC~~CN~~ 463 (526)
+|+|+|+ +|.-+.. ..+..+++.++.... .+.+..++.-..-+++.-. ..-.|++|+..
T Consensus 20 ked~~L~laCrnCd~v---e~A~s~~vY~~~~~~e~dE~t~ii~Dl~~DPTLPrts~~~C~~C~~~ 82 (113)
T KOG2691|consen 20 KEDRILLLACRNCDYV---EEADSSRVYVNELSHEHDELTQIIMDLASDPTLPRTSDKHCPKCGHR 82 (113)
T ss_pred ccccEEEEEecCCcce---EecCCcceEcCCcccchhhHHHHHHhhccCCCcCccccccCCccCCc
Confidence 3577776 3332221 123345566655432 4555555544322222111 23459999974
No 253
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=32.44 E-value=26 Score=23.51 Aligned_cols=27 Identities=15% Similarity=0.744 Sum_probs=13.1
Q ss_pred CccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009783 454 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 504 (526)
Q Consensus 454 ~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 504 (526)
++.|+.|++... | .....+.||.|+.-
T Consensus 2 ~p~Cp~C~se~~-----------------------y-~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 2 LPKCPLCGSEYT-----------------------Y-EDGELLVCPECGHE 28 (30)
T ss_dssp S---TTT----------------------------E-E-SSSEEETTTTEE
T ss_pred CCCCCCCCCcce-----------------------e-ccCCEEeCCccccc
Confidence 467999999641 1 13567889999853
No 254
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=32.32 E-value=24 Score=35.98 Aligned_cols=12 Identities=17% Similarity=0.501 Sum_probs=9.4
Q ss_pred CCceeecCCCCe
Q 009783 492 NLQFWQCMDCNQ 503 (526)
Q Consensus 492 ~~~F~~C~~Cgk 503 (526)
...+++||.|.+
T Consensus 262 gR~t~~CP~CQ~ 273 (273)
T COG0266 262 GRSTFYCPVCQK 273 (273)
T ss_pred CCcCEeCCCCCC
Confidence 356888999975
No 255
>PRK10220 hypothetical protein; Provisional
Probab=31.91 E-value=33 Score=29.99 Aligned_cols=12 Identities=17% Similarity=0.589 Sum_probs=9.4
Q ss_pred CceeecCCCCeE
Q 009783 493 LQFWQCMDCNQL 504 (526)
Q Consensus 493 ~~F~~C~~Cgkv 504 (526)
...|.||.|+.-
T Consensus 18 ~~~~vCpeC~hE 29 (111)
T PRK10220 18 NGMYICPECAHE 29 (111)
T ss_pred CCeEECCcccCc
Confidence 347999999864
No 256
>cd00885 cinA Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, where the domain is presumed to bind molybdopterin.
Probab=31.48 E-value=73 Score=29.99 Aligned_cols=49 Identities=20% Similarity=0.241 Sum_probs=31.5
Q ss_pred EEEecccHHHHHHHHhcCCceecCCCCCCChH---HHHHhhhcCCcEEEecC
Q 009783 363 FLCDVMVEGLAKHLRCVGIDAATPRSKKPEPR---ELIDQTSKEKRVLLTRD 411 (526)
Q Consensus 363 fl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~---~ll~~A~~E~RiiLTrd 411 (526)
-+.|.+..-|+++|+.+|+++....-...+.. +.++.+.++-.+|||.+
T Consensus 15 ~i~d~n~~~l~~~L~~~G~~v~~~~~v~Dd~~~I~~~l~~~~~~~dlVIttG 66 (170)
T cd00885 15 QIVDTNAAFLAKELAELGIEVYRVTVVGDDEDRIAEALRRASERADLVITTG 66 (170)
T ss_pred eEEEhHHHHHHHHHHHCCCEEEEEEEeCCCHHHHHHHHHHHHhCCCEEEECC
Confidence 57799899999999999999865322211222 34444444556666665
No 257
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=31.37 E-value=36 Score=34.30 Aligned_cols=32 Identities=19% Similarity=0.376 Sum_probs=22.2
Q ss_pred CccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecc
Q 009783 454 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEV 508 (526)
Q Consensus 454 ~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~G 508 (526)
+.-|+.|+.++... ....-..|+.||.++|.-
T Consensus 99 ~~fC~~CG~~~~~~-----------------------~~~~~~~C~~c~~~~yp~ 130 (256)
T PRK00241 99 HRFCGYCGHPMHPS-----------------------KTEWAMLCPHCRERYYPR 130 (256)
T ss_pred CccccccCCCCeec-----------------------CCceeEECCCCCCEECCC
Confidence 45699999987420 012245699999999974
No 258
>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=30.90 E-value=26 Score=36.96 Aligned_cols=58 Identities=22% Similarity=0.406 Sum_probs=20.1
Q ss_pred HHHHHHHHH-HcCccccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009783 434 NQQLLEVIE-AFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 503 (526)
Q Consensus 434 ~~QL~~vl~-~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 503 (526)
.||+.+-+. .+.+.+.- -.|..||-.-. ...... ++ ..-+-...+...+||.|++||+
T Consensus 235 kEkmeekm~~i~e~k~ka----v~C~~C~yt~~--~~~~~C-~~-----~~H~l~~~~a~KRFFkC~~C~~ 293 (344)
T PF09332_consen 235 KEKMEEKMESIREVKCKA----VTCKQCKYTAF--KPSDRC-KE-----EGHPLKWHDAVKRFFKCKDCGN 293 (344)
T ss_dssp ---------S-S--EEEE----EEETTT--EES--S--HHH-HH-----TT--EEEEEEE-EEEE-T-TS-
T ss_pred HHHHHHHHhhCcEEEEEE----EEcCCCCCccc--CcchhH-Hh-----cCCceEEeeeeeeeEECCCCCC
Confidence 455555443 34444432 46999997533 222222 22 1222234456688999999998
No 259
>PRK03673 hypothetical protein; Provisional
Probab=30.85 E-value=88 Score=33.71 Aligned_cols=49 Identities=14% Similarity=0.182 Sum_probs=31.7
Q ss_pred EEEecccHHHHHHHHhcCCceecCCCCCCChH---HHHHhhhcCCcEEEecC
Q 009783 363 FLCDVMVEGLAKHLRCVGIDAATPRSKKPEPR---ELIDQTSKEKRVLLTRD 411 (526)
Q Consensus 363 fl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~---~ll~~A~~E~RiiLTrd 411 (526)
-+.|.+-.-|+++|+.+|+++........+.+ +.++.|.++..++||.+
T Consensus 17 ~i~dtN~~~la~~L~~~G~~v~~~~~v~D~~~~i~~~l~~a~~~~DlVI~tG 68 (396)
T PRK03673 17 QIVDTNAAWLADFFFHQGLPLSRRNTVGDNLDALVAILRERSQHADVLIVNG 68 (396)
T ss_pred eEEEhHHHHHHHHHHHCCCEEEEEEEcCCCHHHHHHHHHHHhccCCEEEEcC
Confidence 67799999999999999999865432222333 23444555545555543
No 260
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 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 CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=30.69 E-value=26 Score=29.76 Aligned_cols=47 Identities=19% Similarity=0.516 Sum_probs=21.8
Q ss_pred HHHHHHHc-CccccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009783 437 LLEVIEAF-QLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 503 (526)
Q Consensus 437 L~~vl~~f-~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 503 (526)
|.+|++++ +++-.......+|+.|+..- |.-.++.....|.|=+||+
T Consensus 15 i~~v~~~~~~l~~~G~~~~~~CPfH~d~~--------------------pS~~i~~~k~~~~Cf~Cg~ 62 (97)
T PF01807_consen 15 IVDVIERYIKLKRRGREYRCLCPFHDDKT--------------------PSFSINPDKNRFKCFGCGK 62 (97)
T ss_dssp HHHHHCCCS--EEETTEEEE--SSS--SS----------------------EEEETTTTEEEETTT--
T ss_pred HHHHHHHhccccccCCeEEEECcCCCCCC--------------------CceEEECCCCeEEECCCCC
Confidence 34555554 33333334457788887531 3333444567999999996
No 261
>PRK03670 competence damage-inducible protein A; Provisional
Probab=30.68 E-value=76 Score=31.95 Aligned_cols=24 Identities=17% Similarity=-0.071 Sum_probs=21.0
Q ss_pred EEEecccHHHHHHHHhcCCceecC
Q 009783 363 FLCDVMVEGLAKHLRCVGIDAATP 386 (526)
Q Consensus 363 fl~D~mLg~Lar~LR~lG~D~~~~ 386 (526)
-+.|.+...|+++|+.+|+++...
T Consensus 16 ~i~dtN~~~la~~L~~~G~~v~~~ 39 (252)
T PRK03670 16 NTVDSNSAFIAQKLTEKGYWVRRI 39 (252)
T ss_pred eEEehhHHHHHHHHHHCCCEEEEE
Confidence 567999999999999999998654
No 262
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=30.67 E-value=9.5 Score=36.34 Aligned_cols=43 Identities=16% Similarity=0.507 Sum_probs=26.7
Q ss_pred cccCCCcccccCCCChHHHHHhhhcCcccCccc--cccCCceeecCCCCeE
Q 009783 456 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCL--FDKNLQFWQCMDCNQL 504 (526)
Q Consensus 456 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v--~~~~~~F~~C~~Cgkv 504 (526)
-|..||..+........++. ..+|+.+ |....++..|+.||-|
T Consensus 122 yc~~c~~~~~e~~f~~~d~~------~~~~~~~~~f~~~~e~rtC~~CG~v 166 (177)
T PRK13264 122 YCDECNHKVHEVEVQLTDIE------TDLPPVFAAFYASEELRTCDNCGTV 166 (177)
T ss_pred ECCCCCCeEEEEEEEecChh------hhhHHHHHHHhcCHhhccCCcCCcc
Confidence 39999998753322222221 1244443 4567899999999976
No 263
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=30.49 E-value=40 Score=27.34 Aligned_cols=43 Identities=19% Similarity=0.393 Sum_probs=25.7
Q ss_pred ccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecC--CCCeEEecccchh
Q 009783 455 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCM--DCNQLYWEVMSAY 512 (526)
Q Consensus 455 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~--~CgkvyW~GsH~~ 512 (526)
.+|+.|+..-.. .+... +-+. .-+.+++|. .||..|=--.-+.
T Consensus 2 m~CP~Cg~~a~i--rtSr~----------~s~~---~~~~Y~qC~N~eCg~tF~t~es~s 46 (72)
T PRK09678 2 FHCPLCQHAAHA--RTSRY----------ITDT---TKERYHQCQNVNCSATFITYESVQ 46 (72)
T ss_pred ccCCCCCCccEE--EEChh----------cChh---hheeeeecCCCCCCCEEEEEEEEE
Confidence 589999997632 11111 1122 235689999 9999884433333
No 264
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=29.77 E-value=38 Score=30.40 Aligned_cols=45 Identities=20% Similarity=0.567 Sum_probs=29.0
Q ss_pred HHHHHHHHHHcCccccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009783 434 NQQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 504 (526)
Q Consensus 434 ~~QL~~vl~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 504 (526)
.++|..+|+.| + ..|=.|+.|+.+-.. + +.+....|-.|..||..
T Consensus 79 ~~~i~~~L~~f-I-----~~yVlC~~C~spdT~--l------------------~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 79 SKQIQDLLDKF-I-----KEYVLCPECGSPDTE--L------------------IKEGRLIFLKCKACGAS 123 (125)
T ss_dssp CCHHHHHHHHH-H-----CHHSSCTSTSSSSEE--E------------------EEETTCCEEEETTTSCE
T ss_pred HHHHHHHHHHH-H-----HHEEEcCCCCCCccE--E------------------EEcCCEEEEEecccCCc
Confidence 45777777777 1 124579999997421 1 11234568899999964
No 265
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=29.63 E-value=37 Score=41.41 Aligned_cols=17 Identities=12% Similarity=0.241 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHHHh
Q 009783 202 AHCLIEIFNIFQVKVAQ 218 (526)
Q Consensus 202 A~~ll~L~~~L~~~L~~ 218 (526)
|.+++.+.+.+-..|++
T Consensus 844 a~yl~~va~fiDdLL~k 860 (1337)
T PRK14714 844 AEYLLKVAKFVDDLLEK 860 (1337)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 56677777777776665
No 266
>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.
Probab=29.58 E-value=73 Score=28.97 Aligned_cols=33 Identities=15% Similarity=0.206 Sum_probs=27.4
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009783 372 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 405 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 405 (526)
++..||..||+|.++.- +....++++.|++++-
T Consensus 21 v~~~l~~~GfeVi~LG~-~v~~e~~v~aa~~~~a 53 (134)
T TIGR01501 21 LDHAFTNAGFNVVNLGV-LSPQEEFIKAAIETKA 53 (134)
T ss_pred HHHHHHHCCCEEEECCC-CCCHHHHHHHHHHcCC
Confidence 69999999999999874 5567789999987654
No 267
>cd02072 Glm_B12_BD B12 binding domain of glutamate mutase (Glm). Glutamate mutase catalysis the conversion of (S)-glutamate with (2S,3S)-3-methylaspartate. The rearrangement reaction is initiated by the extraction of a hydrogen from the protein-bound substrate by a 5'-desoxyadenosyl radical, which is generated by the homolytic cleavage of the organometallic bond of the cofactor B12. Glm is a heterotetrameric molecule consisting of two alpha and two epsilon polypeptide chains.
Probab=29.32 E-value=75 Score=28.69 Aligned_cols=33 Identities=15% Similarity=0.209 Sum_probs=27.1
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009783 372 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 405 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 405 (526)
++..||..||++.++.- +....++++.|++++-
T Consensus 19 v~~~L~~~GfeVidLG~-~v~~e~~v~aa~~~~a 51 (128)
T cd02072 19 LDHAFTEAGFNVVNLGV-LSPQEEFIDAAIETDA 51 (128)
T ss_pred HHHHHHHCCCEEEECCC-CCCHHHHHHHHHHcCC
Confidence 68899999999999874 4567889999887654
No 268
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=29.29 E-value=35 Score=26.37 Aligned_cols=10 Identities=20% Similarity=0.826 Sum_probs=8.3
Q ss_pred CccccCCCcc
Q 009783 454 MSRCTKCNGR 463 (526)
Q Consensus 454 ~sRC~~CN~~ 463 (526)
++.|+.|+..
T Consensus 27 l~~C~~CG~~ 36 (57)
T PRK12286 27 LVECPNCGEP 36 (57)
T ss_pred ceECCCCCCc
Confidence 5789999985
No 269
>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=29.16 E-value=32 Score=33.82 Aligned_cols=30 Identities=13% Similarity=0.314 Sum_probs=20.7
Q ss_pred ccCccccccCCceeecCCCCeEEecccchhh
Q 009783 483 RIPDCLFDKNLQFWQCMDCNQLYWEVMSAYL 513 (526)
Q Consensus 483 ~vp~~v~~~~~~F~~C~~CgkvyW~GsH~~r 513 (526)
-|-..|.+..+.=|+|+-|+|.| .|.||=|
T Consensus 65 ~v~~~~~e~~~~K~~C~lc~KlF-kg~eFV~ 94 (214)
T PF04959_consen 65 FVQKNTKEEDEDKWRCPLCGKLF-KGPEFVR 94 (214)
T ss_dssp GEEEEE-SSSSEEEEE-SSS-EE-SSHHHHH
T ss_pred HHHHHHHHHcCCEECCCCCCccc-CChHHHH
Confidence 45566777788899999999998 6666655
No 270
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=29.08 E-value=37 Score=25.45 Aligned_cols=17 Identities=18% Similarity=0.561 Sum_probs=14.5
Q ss_pred CCceeecCCCCeEEecc
Q 009783 492 NLQFWQCMDCNQLYWEV 508 (526)
Q Consensus 492 ~~~F~~C~~CgkvyW~G 508 (526)
|.+-|.|.+||=..|..
T Consensus 34 H~dR~~CGkCgyTe~~~ 50 (51)
T COG1998 34 HKDRWACGKCGYTEFKK 50 (51)
T ss_pred cCceeEeccccceEeec
Confidence 55689999999999974
No 271
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=28.57 E-value=49 Score=33.34 Aligned_cols=54 Identities=17% Similarity=0.443 Sum_probs=32.8
Q ss_pred HHHHHHHHHcCccccccccCccccC--CCc-ccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEeccc
Q 009783 435 QQLLEVIEAFQLKISEDQLMSRCTK--CNG-RFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVM 509 (526)
Q Consensus 435 ~QL~~vl~~f~l~~~~~~~~sRC~~--CN~-~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~Gs 509 (526)
.-|..+.+.|. ...|.+|++ ||+ +++ |+.. ..+| .....-..||+|+.||=.-+
T Consensus 106 ~Gl~~M~eKY~-----~g~FG~CPRv~C~~q~~L--PvGl----------Sd~~----g~~~VKlyCP~C~DvY~p~s 162 (251)
T PTZ00396 106 KGLALMREKYL-----QGKFGHCPRVLCEGQNVL--PIGL----------SDVL----KTSRVKVYCPRCQEVYHPKK 162 (251)
T ss_pred HHHHHHHHHhh-----CCCCCCCCCccCCCCccc--cccc----------CCCc----CcCceeEeCCCchhhcCCCC
Confidence 45666677774 344889986 886 343 4421 1222 23445667999999995533
No 272
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=28.26 E-value=21 Score=27.27 Aligned_cols=10 Identities=20% Similarity=0.610 Sum_probs=7.9
Q ss_pred ccccCCCccc
Q 009783 455 SRCTKCNGRF 464 (526)
Q Consensus 455 sRC~~CN~~l 464 (526)
-.|+.||+.-
T Consensus 5 i~CP~CgnKT 14 (55)
T PF14205_consen 5 ILCPICGNKT 14 (55)
T ss_pred EECCCCCCcc
Confidence 4699999854
No 273
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=28.19 E-value=69 Score=36.28 Aligned_cols=41 Identities=10% Similarity=0.212 Sum_probs=23.6
Q ss_pred CCcEEEEcCCC---HHHHHHHHHHH-c--Ccc-ccccccCccccCCCc
Q 009783 422 KNQIYRVKSLL---KNQQLLEVIEA-F--QLK-ISEDQLMSRCTKCNG 462 (526)
Q Consensus 422 ~~~~~~v~~~~---~~~QL~~vl~~-f--~l~-~~~~~~~sRC~~CN~ 462 (526)
+|.+..+.-++ --+.+.+|++. + ++. .+-+..+++|..|+-
T Consensus 485 GG~i~~v~l~e~~~n~eal~~lv~~a~~~~i~Y~~~n~~~~~C~~CG~ 532 (579)
T TIGR02487 485 GGHITYIELDEAIPDPEALKDITKKAMKNGIGYFGINPPVDVCEDCGY 532 (579)
T ss_pred CceEEEEEcCCCCCCHHHHHHHHHHHHhcCCceEEeccCCccCCCCCC
Confidence 45555554321 14677777764 2 122 233455899999985
No 274
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=28.15 E-value=70 Score=29.27 Aligned_cols=46 Identities=15% Similarity=0.360 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHcCccccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009783 433 KNQQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 504 (526)
Q Consensus 433 ~~~QL~~vl~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 504 (526)
...++..+++.| + +.|=.|+.|+.+-.. +. .+...-|-.|..||..
T Consensus 87 ~~~~i~~~L~~y-I-----~~yVlC~~C~spdT~--l~------------------k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 87 SPRVINEKIDRY-V-----KEYVICPECGSPDTK--LI------------------KEGRIWVLKCEACGAE 132 (138)
T ss_pred CHHHHHHHHHHH-H-----HhcEECCCCCCCCcE--EE------------------EcCCeEEEEcccCCCC
Confidence 346888888877 1 125579999997531 11 1123458889999953
No 275
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=28.12 E-value=31 Score=27.29 Aligned_cols=15 Identities=20% Similarity=0.348 Sum_probs=11.9
Q ss_pred cCCceeecCCCCeEE
Q 009783 491 KNLQFWQCMDCNQLY 505 (526)
Q Consensus 491 ~~~~F~~C~~Cgkvy 505 (526)
-.+.--+|+.||+.|
T Consensus 49 i~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 49 IVEGELICPECGREY 63 (68)
T ss_dssp TTTTEEEETTTTEEE
T ss_pred ccCCEEEcCCCCCEE
Confidence 345567899999998
No 276
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=27.95 E-value=32 Score=34.97 Aligned_cols=12 Identities=17% Similarity=0.454 Sum_probs=9.5
Q ss_pred CCceeecCCCCe
Q 009783 492 NLQFWQCMDCNQ 503 (526)
Q Consensus 492 ~~~F~~C~~Cgk 503 (526)
....|.||.|.+
T Consensus 261 gR~t~~CP~CQ~ 272 (272)
T PRK14810 261 GRSSHYCPHCQK 272 (272)
T ss_pred CCccEECcCCcC
Confidence 366889999975
No 277
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=27.81 E-value=55 Score=34.72 Aligned_cols=20 Identities=15% Similarity=0.116 Sum_probs=18.5
Q ss_pred CceeecCCCCeEEecccchhh
Q 009783 493 LQFWQCMDCNQLYWEVMSAYL 513 (526)
Q Consensus 493 ~~F~~C~~CgkvyW~GsH~~r 513 (526)
-++.+|..|| -||.|.-|.+
T Consensus 41 ~~v~~C~~Cg-a~~~~~~W~~ 60 (355)
T COG1499 41 VNVEVCRHCG-AYRIRGRWVD 60 (355)
T ss_pred eEEEECCcCC-CccCCCccee
Confidence 5789999999 9999999998
No 278
>PRK12496 hypothetical protein; Provisional
Probab=27.80 E-value=26 Score=32.92 Aligned_cols=10 Identities=30% Similarity=0.823 Sum_probs=9.4
Q ss_pred eecCCCCeEE
Q 009783 496 WQCMDCNQLY 505 (526)
Q Consensus 496 ~~C~~Cgkvy 505 (526)
++|++||+.|
T Consensus 128 ~~C~gC~~~~ 137 (164)
T PRK12496 128 KVCKGCKKKY 137 (164)
T ss_pred EECCCCCccc
Confidence 7799999999
No 279
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=27.58 E-value=86 Score=27.05 Aligned_cols=32 Identities=22% Similarity=0.378 Sum_probs=25.0
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcC
Q 009783 371 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKE 403 (526)
Q Consensus 371 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E 403 (526)
-++..||..||+|.++.. ....+++++.+.++
T Consensus 18 ~~~~~l~~~G~~V~~lg~-~~~~~~l~~~~~~~ 49 (119)
T cd02067 18 IVARALRDAGFEVIDLGV-DVPPEEIVEAAKEE 49 (119)
T ss_pred HHHHHHHHCCCEEEECCC-CCCHHHHHHHHHHc
Confidence 369999999999998874 45667888877654
No 280
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=27.33 E-value=41 Score=23.71 Aligned_cols=13 Identities=23% Similarity=0.884 Sum_probs=11.2
Q ss_pred CceeecCCCCeEE
Q 009783 493 LQFWQCMDCNQLY 505 (526)
Q Consensus 493 ~~F~~C~~Cgkvy 505 (526)
..|+.|..||+.|
T Consensus 26 T~fy~C~~C~~~w 38 (39)
T PF01096_consen 26 TLFYVCCNCGHRW 38 (39)
T ss_dssp EEEEEESSSTEEE
T ss_pred eEEEEeCCCCCee
Confidence 5699999999875
No 281
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=27.24 E-value=73 Score=30.16 Aligned_cols=52 Identities=13% Similarity=0.429 Sum_probs=29.8
Q ss_pred CccccCCCcc------cccCCCChHHHHHhhh--cCc---ccCcc-ccccCCceeecCCCCeEE
Q 009783 454 MSRCTKCNGR------FIQKPLSTEEAVEAAK--GFQ---RIPDC-LFDKNLQFWQCMDCNQLY 505 (526)
Q Consensus 454 ~sRC~~CN~~------l~~~~~~~e~~~~~~~--~~~---~vp~~-v~~~~~~F~~C~~Cgkvy 505 (526)
...|+.||.+ |-++.-+++|-+-+.+ |.+ .|++. |.+...-.++|..|.+-|
T Consensus 71 ~~~C~~C~~~G~~c~pfr~r~T~kQEe~~ReeNgG~DPit~Vd~~lvnN~~nVLFRC~~C~Raw 134 (175)
T PF15446_consen 71 HGMCQQCKKPGPSCKPFRPRKTPKQEEKLREENGGVDPITPVDPELVNNPDNVLFRCTSCHRAW 134 (175)
T ss_pred CCcccccCCCCCCCcccCCCCCcHHHHHHHHHcCCCCCCccCCHHHccChhheEEecCCcccee
Confidence 6889999974 3223334433222211 111 34444 445667799999999875
No 282
>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=27.15 E-value=19 Score=33.27 Aligned_cols=12 Identities=17% Similarity=0.908 Sum_probs=9.6
Q ss_pred ceeecCCCCeEE
Q 009783 494 QFWQCMDCNQLY 505 (526)
Q Consensus 494 ~F~~C~~Cgkvy 505 (526)
.-..|+.||+-|
T Consensus 27 RRReC~~C~~RF 38 (147)
T TIGR00244 27 RRRECLECHERF 38 (147)
T ss_pred ecccCCccCCcc
Confidence 456799999977
No 283
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=26.86 E-value=49 Score=32.36 Aligned_cols=21 Identities=24% Similarity=0.491 Sum_probs=13.1
Q ss_pred CccccccccC-ccccCCCcccc
Q 009783 445 QLKISEDQLM-SRCTKCNGRFI 465 (526)
Q Consensus 445 ~l~~~~~~~~-sRC~~CN~~l~ 465 (526)
++.++...+| .||..||.=+.
T Consensus 32 glSiRL~TPF~~RCL~C~~YI~ 53 (272)
T COG5134 32 GLSIRLETPFPVRCLNCENYIQ 53 (272)
T ss_pred cceEEeccCcceeecchhhhhh
Confidence 3444444444 59999998653
No 284
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=26.85 E-value=37 Score=29.16 Aligned_cols=13 Identities=15% Similarity=0.593 Sum_probs=11.3
Q ss_pred CceeecCCCCeEE
Q 009783 493 LQFWQCMDCNQLY 505 (526)
Q Consensus 493 ~~F~~C~~Cgkvy 505 (526)
....+|+.||++|
T Consensus 77 g~~~rC~eCG~~f 89 (97)
T cd00924 77 GKPKRCPECGHVF 89 (97)
T ss_pred CCceeCCCCCcEE
Confidence 3688999999988
No 285
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=26.79 E-value=76 Score=36.26 Aligned_cols=69 Identities=7% Similarity=0.092 Sum_probs=39.9
Q ss_pred CCcEEEEcCCC--HHHHHHHHHHH---cCcc-ccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCce
Q 009783 422 KNQIYRVKSLL--KNQQLLEVIEA---FQLK-ISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQF 495 (526)
Q Consensus 422 ~~~~~~v~~~~--~~~QL~~vl~~---f~l~-~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F 495 (526)
+|.+..|.-++ -.+.++.+++. +++. ...+..+++|..|+-... .+.
T Consensus 528 GG~I~hi~l~e~~n~eal~~lv~~~~~~~i~Yf~in~~~~iC~~CG~~~~---------------------------g~~ 580 (623)
T PRK08271 528 GGSALHLNLDERLSEEGYRKLLNIAAKTGCNYFAFNVKITICNDCHHIDK---------------------------RTG 580 (623)
T ss_pred ceEEEEEEcCCCCCHHHHHHHHHHHHHcCCceEEeCCCCccCCCCCCcCC---------------------------CCC
Confidence 45566664321 23566666553 3333 233445899999997310 123
Q ss_pred eecCCCCeEEecccchhhHHhhhhhhhh
Q 009783 496 WQCMDCNQLYWEVMSAYLFIFLTPAYFS 523 (526)
Q Consensus 496 ~~C~~CgkvyW~GsH~~r~~~~~~~~~~ 523 (526)
+.||.||. +---+++|++-|+.
T Consensus 581 ~~CP~CGs------~~~ev~~RV~GYl~ 602 (623)
T PRK08271 581 KRCPICGS------ENIDYYTRVIGYLK 602 (623)
T ss_pred cCCcCCCC------cchhHHHHHhhhhc
Confidence 77999975 33456777777764
No 286
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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 DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=26.62 E-value=21 Score=28.52 Aligned_cols=34 Identities=26% Similarity=0.540 Sum_probs=20.9
Q ss_pred cccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009783 456 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 505 (526)
Q Consensus 456 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 505 (526)
-|..||.+-. + .+-...|++.-.+-+||+|+..-
T Consensus 6 TC~~C~~Rs~-~---------------~~sk~aY~~GvViv~C~gC~~~H 39 (66)
T PF05180_consen 6 TCNKCGTRSA-K---------------MFSKQAYHKGVVIVQCPGCKNRH 39 (66)
T ss_dssp EETTTTEEEE-E---------------EEEHHHHHTSEEEEE-TTS--EE
T ss_pred EcCCCCCccc-e---------------eeCHHHHhCCeEEEECCCCccee
Confidence 3999998753 1 23334456667799999998754
No 287
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=26.58 E-value=28 Score=35.53 Aligned_cols=11 Identities=18% Similarity=0.525 Sum_probs=9.0
Q ss_pred CceeecCCCCe
Q 009783 493 LQFWQCMDCNQ 503 (526)
Q Consensus 493 ~~F~~C~~Cgk 503 (526)
..-|+||.|.+
T Consensus 272 R~t~~CP~CQ~ 282 (282)
T PRK13945 272 RSTHWCPNCQK 282 (282)
T ss_pred CccEECCCCcC
Confidence 56888999975
No 288
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=26.08 E-value=68 Score=25.00 Aligned_cols=11 Identities=27% Similarity=0.764 Sum_probs=8.8
Q ss_pred ccccCCCcccc
Q 009783 455 SRCTKCNGRFI 465 (526)
Q Consensus 455 sRC~~CN~~l~ 465 (526)
..|+.||..+.
T Consensus 8 ~~CtSCg~~i~ 18 (59)
T PRK14890 8 PKCTSCGIEIA 18 (59)
T ss_pred ccccCCCCccc
Confidence 35999999874
No 289
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=26.03 E-value=32 Score=32.02 Aligned_cols=36 Identities=19% Similarity=0.439 Sum_probs=22.3
Q ss_pred ccccCCCcccccCCCChHHHHHhhhcCcccCcccc---ccCCceeecCCCCeEE
Q 009783 455 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLF---DKNLQFWQCMDCNQLY 505 (526)
Q Consensus 455 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~---~~~~~F~~C~~Cgkvy 505 (526)
+-|+.||.++. |. ...++|+ ..+..=.+|..||+-|
T Consensus 40 ~~Cp~C~~~Ir--------------G~-y~v~gv~~~g~~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 40 TSCPNCSTPIR--------------GD-YHVEGVFGLGGHYEAPSYCHNCGKPY 78 (158)
T ss_pred HHCcCCCCCCC--------------Cc-eecCCeeeeCCCCCCChhHHhCCCCC
Confidence 45888888752 11 2223333 2344567799999998
No 290
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=25.60 E-value=69 Score=28.12 Aligned_cols=44 Identities=18% Similarity=0.554 Sum_probs=28.3
Q ss_pred HHHHHHHHHHcCccccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009783 434 NQQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 503 (526)
Q Consensus 434 ~~QL~~vl~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 503 (526)
..++..+++.| + +.|-.|+.|+.+-.. + +.+...-|-.|..||.
T Consensus 66 ~~~i~~~l~~y-I-----~~yVlC~~C~spdT~--l------------------~k~~r~~~l~C~aCGa 109 (110)
T smart00653 66 PKKLQDLLRRY-I-----KEYVLCPECGSPDTE--L------------------IKENRLFFLKCEACGA 109 (110)
T ss_pred HHHHHHHHHHH-H-----HhcEECCCCCCCCcE--E------------------EEeCCeEEEEccccCC
Confidence 56788888777 1 125579999997431 1 1112345888999984
No 291
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=25.57 E-value=14 Score=34.58 Aligned_cols=40 Identities=23% Similarity=0.603 Sum_probs=0.0
Q ss_pred ccCCCcccccCCCChHHHHHhhhcCcccCccc--cccCCceeecCCCC
Q 009783 457 CTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCL--FDKNLQFWQCMDCN 502 (526)
Q Consensus 457 C~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v--~~~~~~F~~C~~Cg 502 (526)
|..||..+........++.- .+|+.+ |....+...|+.||
T Consensus 117 c~~c~~~~~e~~f~~~d~~~------~~~~~~~~f~~~~~~rtC~~Cg 158 (159)
T TIGR03037 117 CPQCGHKLHRAEVQLENIVT------DLPPVFEHFYSNEDARTCKNCG 158 (159)
T ss_pred CCCCCCeEEEEEEEecChhh------hhHHHHHHHhCChhhccCCccC
No 292
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.54 E-value=36 Score=34.61 Aligned_cols=13 Identities=23% Similarity=0.396 Sum_probs=10.4
Q ss_pred CceeecCCCCeEE
Q 009783 493 LQFWQCMDCNQLY 505 (526)
Q Consensus 493 ~~F~~C~~Cgkvy 505 (526)
..-|.||.|.+.+
T Consensus 253 R~ty~Cp~CQ~~~ 265 (269)
T PRK14811 253 RGTHFCPQCQPLR 265 (269)
T ss_pred CCcEECCCCcCCC
Confidence 5688899998753
No 293
>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=25.45 E-value=40 Score=24.09 Aligned_cols=10 Identities=20% Similarity=1.105 Sum_probs=7.6
Q ss_pred eecCCCCeEE
Q 009783 496 WQCMDCNQLY 505 (526)
Q Consensus 496 ~~C~~Cgkvy 505 (526)
++|+.||..|
T Consensus 6 y~C~~Cg~~f 15 (42)
T PF09723_consen 6 YRCEECGHEF 15 (42)
T ss_pred EEeCCCCCEE
Confidence 5688888766
No 294
>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=25.13 E-value=13 Score=32.68 Aligned_cols=31 Identities=29% Similarity=0.533 Sum_probs=18.9
Q ss_pred HHHHHHHHHHc---------CccccccccCccccCCCccc
Q 009783 434 NQQLLEVIEAF---------QLKISEDQLMSRCTKCNGRF 464 (526)
Q Consensus 434 ~~QL~~vl~~f---------~l~~~~~~~~sRC~~CN~~l 464 (526)
.++|..-++.+ .|.+......-||..||...
T Consensus 41 pe~L~f~f~~~~~~T~~e~a~L~Ie~~p~~~~C~~Cg~~~ 80 (113)
T PF01155_consen 41 PEALRFAFEVLAEGTILEGAELEIEEVPARARCRDCGHEF 80 (113)
T ss_dssp HHHHHHHHHHHHCCSTTTT-EEEEEEE--EEEETTTS-EE
T ss_pred HHHHHHHHHHHhCCCCccCCEEEEEecCCcEECCCCCCEE
Confidence 57777766544 34444455568999999976
No 295
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=24.97 E-value=48 Score=28.32 Aligned_cols=11 Identities=18% Similarity=0.534 Sum_probs=9.0
Q ss_pred eeecCCCCeEE
Q 009783 495 FWQCMDCNQLY 505 (526)
Q Consensus 495 F~~C~~Cgkvy 505 (526)
.+.|+.||..+
T Consensus 16 ~~~C~~C~~~~ 26 (104)
T TIGR01384 16 VYVCPSCGYEK 26 (104)
T ss_pred eEECcCCCCcc
Confidence 57799999874
No 296
>PRK10445 endonuclease VIII; Provisional
Probab=24.73 E-value=32 Score=34.84 Aligned_cols=28 Identities=21% Similarity=0.740 Sum_probs=18.9
Q ss_pred ccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009783 455 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 503 (526)
Q Consensus 455 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 503 (526)
.-|+.|++++... +| ....-|.||.|.+
T Consensus 236 ~~Cp~Cg~~I~~~---------------~~------~gR~t~~CP~CQ~ 263 (263)
T PRK10445 236 EACERCGGIIEKT---------------TL------SSRPFYWCPGCQK 263 (263)
T ss_pred CCCCCCCCEeEEE---------------EE------CCCCcEECCCCcC
Confidence 4599999986421 11 2356788999975
No 297
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=24.72 E-value=39 Score=34.45 Aligned_cols=31 Identities=19% Similarity=0.598 Sum_probs=22.5
Q ss_pred cccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009783 451 DQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 503 (526)
Q Consensus 451 ~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 503 (526)
+..++-|+.|..-+.. .|. ...+++||.|+.
T Consensus 25 e~lw~KCp~c~~~~y~-----~eL-----------------~~n~~vcp~c~~ 55 (294)
T COG0777 25 EGLWTKCPSCGEMLYR-----KEL-----------------ESNLKVCPKCGH 55 (294)
T ss_pred CCceeECCCccceeeH-----HHH-----------------HhhhhcccccCc
Confidence 6678999999997752 121 145899999974
No 298
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=24.44 E-value=29 Score=34.82 Aligned_cols=43 Identities=19% Similarity=0.516 Sum_probs=28.8
Q ss_pred CccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecccch
Q 009783 454 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVMSA 511 (526)
Q Consensus 454 ~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~GsH~ 511 (526)
|--|-.||..+- +| .|+-..+.=....+-|-.||+.||.-+..
T Consensus 3 ~FtCnvCgEsvK-Kp--------------~vekH~srCrn~~fSCIDC~k~F~~~sYk 45 (276)
T KOG2186|consen 3 FFTCNVCGESVK-KP--------------QVEKHMSRCRNAYFSCIDCGKTFERVSYK 45 (276)
T ss_pred EEehhhhhhhcc-cc--------------chHHHHHhccCCeeEEeecccccccchhh
Confidence 345999998752 22 23334444345788899999999986643
No 299
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=24.17 E-value=44 Score=31.55 Aligned_cols=11 Identities=18% Similarity=0.419 Sum_probs=8.5
Q ss_pred CccccCCCccc
Q 009783 454 MSRCTKCNGRF 464 (526)
Q Consensus 454 ~sRC~~CN~~l 464 (526)
.-+|.+|+-..
T Consensus 134 ~~vC~vCGy~~ 144 (166)
T COG1592 134 VWVCPVCGYTH 144 (166)
T ss_pred EEEcCCCCCcc
Confidence 35899999854
No 300
>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=24.13 E-value=42 Score=24.75 Aligned_cols=10 Identities=20% Similarity=1.072 Sum_probs=6.7
Q ss_pred eecCCCCeEE
Q 009783 496 WQCMDCNQLY 505 (526)
Q Consensus 496 ~~C~~Cgkvy 505 (526)
++|+.||+.|
T Consensus 6 y~C~~Cg~~f 15 (52)
T TIGR02605 6 YRCTACGHRF 15 (52)
T ss_pred EEeCCCCCEe
Confidence 4677777754
No 301
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=24.04 E-value=43 Score=31.06 Aligned_cols=30 Identities=20% Similarity=0.591 Sum_probs=21.3
Q ss_pred ccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009783 452 QLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 505 (526)
Q Consensus 452 ~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 505 (526)
-.+..|+.||..+.. ....-|+|+.|++.+
T Consensus 32 ~~Y~aC~~C~kkv~~------------------------~~~~~~~C~~C~~~~ 61 (166)
T cd04476 32 WWYPACPGCNKKVVE------------------------EGNGTYRCEKCNKSV 61 (166)
T ss_pred eEEccccccCcccEe------------------------CCCCcEECCCCCCcC
Confidence 345789999996531 012589999999975
No 302
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=23.82 E-value=48 Score=23.51 Aligned_cols=13 Identities=23% Similarity=0.851 Sum_probs=10.7
Q ss_pred CceeecCCCCeEE
Q 009783 493 LQFWQCMDCNQLY 505 (526)
Q Consensus 493 ~~F~~C~~Cgkvy 505 (526)
..|+.|..||+.+
T Consensus 26 T~fy~C~~C~~~w 38 (40)
T smart00440 26 TVFYVCTKCGHRW 38 (40)
T ss_pred eEEEEeCCCCCEe
Confidence 5699999999753
No 303
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=23.77 E-value=68 Score=34.69 Aligned_cols=47 Identities=21% Similarity=0.553 Sum_probs=29.1
Q ss_pred HHHHHHHc-CccccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009783 437 LLEVIEAF-QLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 503 (526)
Q Consensus 437 L~~vl~~f-~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 503 (526)
|.+|+..+ .++.........|+-|+..- |.........+|.|-+||.
T Consensus 16 i~~vi~~~~~l~~~G~~~~~~CPfh~ek~--------------------pSf~v~~~k~~~~Cf~Cg~ 63 (415)
T TIGR01391 16 IVDVISEYVKLKKKGRNYVGLCPFHHEKT--------------------PSFSVSPEKQFYHCFGCGA 63 (415)
T ss_pred HHHHHHhhCceeecCCceEeeCCCCCCCC--------------------CeEEEEcCCCcEEECCCCC
Confidence 45567665 44434444456788887631 3333344567999999997
No 304
>PHA02540 61 DNA primase; Provisional
Probab=23.51 E-value=72 Score=33.63 Aligned_cols=52 Identities=17% Similarity=0.399 Sum_probs=28.6
Q ss_pred HHHHHHHHc-CccccccccCccccCCCcccccCCCChHHHHHhhhcCcccCcc-ccc-cCCceeecCCCCe
Q 009783 436 QLLEVIEAF-QLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDC-LFD-KNLQFWQCMDCNQ 503 (526)
Q Consensus 436 QL~~vl~~f-~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~-v~~-~~~~F~~C~~Cgk 503 (526)
++.+++..| .++-... ...||+.||..-- .+ +-|.. |+. ...-||.|=+||.
T Consensus 9 ~~~~~~~~f~~~~~~~~-~~~~CPf~~ds~~------~~---------~kpsF~V~p~k~~~~yhCFgCGa 63 (337)
T PHA02540 9 RASPHLPKFKQVRRSSF-YNFRCPICGDSQK------DK---------NKARGWIYEKKDGGVFKCHNCGY 63 (337)
T ss_pred HHHHHHhhhheeccCce-EEecCCCCCCccc------cC---------cCCcEEEeccCCceEEEecCCCC
Confidence 445555555 3333322 5789999998421 11 11222 221 2234999999996
No 305
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=23.43 E-value=69 Score=33.18 Aligned_cols=10 Identities=30% Similarity=1.351 Sum_probs=8.4
Q ss_pred ceeecCCCCe
Q 009783 494 QFWQCMDCNQ 503 (526)
Q Consensus 494 ~F~~C~~Cgk 503 (526)
-+|.||+||=
T Consensus 367 ~~~~c~~c~~ 376 (389)
T PRK11788 367 LYWHCPSCKA 376 (389)
T ss_pred ceeECcCCCC
Confidence 4899999984
No 306
>PRK01215 competence damage-inducible protein A; Provisional
Probab=23.30 E-value=1.2e+02 Score=30.81 Aligned_cols=49 Identities=8% Similarity=0.070 Sum_probs=32.6
Q ss_pred EEEecccHHHHHHHHhcCCceecCCCCCCCh---HHHHHhhhcCCcEEEecC
Q 009783 363 FLCDVMVEGLAKHLRCVGIDAATPRSKKPEP---RELIDQTSKEKRVLLTRD 411 (526)
Q Consensus 363 fl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d---~~ll~~A~~E~RiiLTrd 411 (526)
-+.|.+-.-|+++|+.+|+++....-...+. .+.++.|.+...+|||.+
T Consensus 19 ~i~dtn~~~l~~~L~~~G~~v~~~~~v~Dd~~~I~~~l~~a~~~~DlVIttG 70 (264)
T PRK01215 19 RTVNTNASWIARRLTYLGYTVRRITVVMDDIEEIVSAFREAIDRADVVVSTG 70 (264)
T ss_pred eEEEhhHHHHHHHHHHCCCeEEEEEEeCCCHHHHHHHHHHHhcCCCEEEEeC
Confidence 6789999999999999999986543211122 244555555556666654
No 307
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=23.20 E-value=30 Score=30.58 Aligned_cols=9 Identities=33% Similarity=1.254 Sum_probs=6.9
Q ss_pred ccCCCcccc
Q 009783 457 CTKCNGRFI 465 (526)
Q Consensus 457 C~~CN~~l~ 465 (526)
|++|+++|.
T Consensus 1 CPvCg~~l~ 9 (113)
T PF09862_consen 1 CPVCGGELV 9 (113)
T ss_pred CCCCCCceE
Confidence 888888774
No 308
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=23.10 E-value=72 Score=30.84 Aligned_cols=15 Identities=13% Similarity=0.370 Sum_probs=12.0
Q ss_pred CceeecCCCCeEEec
Q 009783 493 LQFWQCMDCNQLYWE 507 (526)
Q Consensus 493 ~~F~~C~~CgkvyW~ 507 (526)
+...+|+.||.+|=.
T Consensus 28 ~~lvrC~eCG~V~~~ 42 (201)
T COG1326 28 EPLVRCEECGTVHPA 42 (201)
T ss_pred ceEEEccCCCcEeec
Confidence 457899999998744
No 309
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=23.08 E-value=46 Score=33.78 Aligned_cols=12 Identities=17% Similarity=0.548 Sum_probs=9.6
Q ss_pred CCceeecCCCCe
Q 009783 492 NLQFWQCMDCNQ 503 (526)
Q Consensus 492 ~~~F~~C~~Cgk 503 (526)
...-|.||.|.+
T Consensus 262 gR~t~~CP~CQ~ 273 (274)
T PRK01103 262 GRSTFFCPRCQK 273 (274)
T ss_pred CCCcEECcCCCC
Confidence 356888999986
No 310
>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=23.02 E-value=40 Score=21.38 Aligned_cols=10 Identities=20% Similarity=1.012 Sum_probs=8.6
Q ss_pred eecCCCCeEE
Q 009783 496 WQCMDCNQLY 505 (526)
Q Consensus 496 ~~C~~Cgkvy 505 (526)
+.|.-|++.|
T Consensus 2 ~~C~~C~k~f 11 (27)
T PF12171_consen 2 FYCDACDKYF 11 (27)
T ss_dssp CBBTTTTBBB
T ss_pred CCcccCCCCc
Confidence 5799999987
No 311
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=22.95 E-value=43 Score=24.56 Aligned_cols=35 Identities=17% Similarity=0.573 Sum_probs=21.9
Q ss_pred cccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCC--CCeEE
Q 009783 456 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMD--CNQLY 505 (526)
Q Consensus 456 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~--Cgkvy 505 (526)
+|+.|+++..++. .+.. -+.+ .+-+++|.. ||-.|
T Consensus 1 ~CP~Cg~~a~ir~--S~~~----------s~~~---~~~Y~qC~N~~Cg~tf 37 (47)
T PF04606_consen 1 RCPHCGSKARIRT--SRQL----------SPLT---RELYCQCTNPECGHTF 37 (47)
T ss_pred CcCCCCCeeEEEE--chhh----------Ccce---EEEEEEECCCcCCCEE
Confidence 6999999875422 1221 1111 246899999 99876
No 312
>PRK05667 dnaG DNA primase; Validated
Probab=22.94 E-value=76 Score=35.95 Aligned_cols=47 Identities=21% Similarity=0.554 Sum_probs=29.7
Q ss_pred HHHHHHHc-CccccccccCccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009783 437 LLEVIEAF-QLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 503 (526)
Q Consensus 437 L~~vl~~f-~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 503 (526)
+.+|+..+ .|+-........|+-||..- |.........+|.|-+||.
T Consensus 18 I~~vi~~~v~Lkk~G~~~~~~CPfH~ekt--------------------pSf~V~~~k~~~~CF~Cg~ 65 (580)
T PRK05667 18 IVDVIGEYVKLKKAGRNYKGLCPFHDEKT--------------------PSFTVSPDKQFYHCFGCGA 65 (580)
T ss_pred HHHHHHHhcceeecCCceeecCCCCCCCC--------------------CceEEECCCCeEEECCCCC
Confidence 44566655 44444445566799988631 3333344577999999997
No 313
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=22.91 E-value=1.4e+02 Score=27.84 Aligned_cols=65 Identities=14% Similarity=0.067 Sum_probs=40.9
Q ss_pred HHHhcCCceecCCCCCCChHHHHHhhhcCCc-----EEEecChhHHHhhcccCCcEEEEcCCCHHHHHHHHH
Q 009783 375 HLRCVGIDAATPRSKKPEPRELIDQTSKEKR-----VLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQLLEVI 441 (526)
Q Consensus 375 ~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R-----iiLTrd~~l~~~~~~~~~~~~~v~~~~~~~QL~~vl 441 (526)
.-+.-|+.+++.......|..|..++.+... +++|.|..+...... ..+..+.+....+++...-
T Consensus 62 ~~~~~gi~Vvft~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~~~~--~GA~~iss~ef~~~l~~~~ 131 (166)
T PF05991_consen 62 REEYGGIEVVFTKEGETADDYIERLVRELKNRPRQVTVVTSDREIQRAARG--RGAKRISSEEFLRELKAAK 131 (166)
T ss_pred eeeeCceEEEECCCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHHHHhh--CCCEEEcHHHHHHHHHHHH
Confidence 3344688888876544556667666665554 788999887655432 2467777765545544443
No 314
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=22.76 E-value=51 Score=24.79 Aligned_cols=21 Identities=19% Similarity=0.703 Sum_probs=13.7
Q ss_pred CCceeecCCCCeEEecccchhh
Q 009783 492 NLQFWQCMDCNQLYWEVMSAYL 513 (526)
Q Consensus 492 ~~~F~~C~~CgkvyW~GsH~~r 513 (526)
..-.|+|+.||. =|+-+=..|
T Consensus 25 ~~v~W~C~~Cgh-~w~~~v~~R 45 (55)
T PF14311_consen 25 KKVWWKCPKCGH-EWKASVNDR 45 (55)
T ss_pred CEEEEECCCCCC-eeEccHhhh
Confidence 345799999987 445444444
No 315
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=22.66 E-value=26 Score=32.43 Aligned_cols=38 Identities=13% Similarity=0.449 Sum_probs=21.1
Q ss_pred ccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009783 455 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 505 (526)
Q Consensus 455 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 505 (526)
.+|+.||..-.. -++.-.+ .++ +....-..|+.||+-|
T Consensus 1 M~CPfC~~~~tk-ViDSR~~----------edg--~aIRRRReC~~C~~RF 38 (156)
T COG1327 1 MKCPFCGHEDTK-VIDSRPA----------EEG--NAIRRRRECLECGERF 38 (156)
T ss_pred CCCCCCCCCCCe-eeecccc----------ccc--chhhhhhccccccccc
Confidence 379999986532 1221111 111 1223456799999877
No 316
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=22.57 E-value=44 Score=30.56 Aligned_cols=19 Identities=21% Similarity=0.532 Sum_probs=14.4
Q ss_pred CCceeecCCCCeEEecccc
Q 009783 492 NLQFWQCMDCNQLYWEVMS 510 (526)
Q Consensus 492 ~~~F~~C~~CgkvyW~GsH 510 (526)
.--..+|++||++|-.-..
T Consensus 26 kl~g~kC~~CG~v~~PPr~ 44 (140)
T COG1545 26 KLLGTKCKKCGRVYFPPRA 44 (140)
T ss_pred cEEEEEcCCCCeEEcCCcc
Confidence 3457789999999976543
No 317
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.54 E-value=38 Score=38.91 Aligned_cols=41 Identities=12% Similarity=0.151 Sum_probs=23.4
Q ss_pred CCcEEEEcCCC--H-HHHHHHHHHHc----Ccc-ccccccCccccCCCc
Q 009783 422 KNQIYRVKSLL--K-NQQLLEVIEAF----QLK-ISEDQLMSRCTKCNG 462 (526)
Q Consensus 422 ~~~~~~v~~~~--~-~~QL~~vl~~f----~l~-~~~~~~~sRC~~CN~ 462 (526)
||.+..|.-.+ + .+.+..+++.. ++. ..-+..+++|..|+-
T Consensus 586 GG~I~hv~l~e~~~n~~a~~~lv~~~~~~~~i~Y~~in~~~~~C~~CG~ 634 (656)
T PRK08270 586 GGTVFHLYLGEAISDAEACKKLVKKALENYRLPYITITPTFSICPKHGY 634 (656)
T ss_pred ceEEEEEECCCCCCCHHHHHHHHHHHHHhCCCceEEeCCCCcccCCCCC
Confidence 45565554321 2 46677776632 232 123445899999996
No 318
>PRK03094 hypothetical protein; Provisional
Probab=22.46 E-value=1.9e+02 Score=24.06 Aligned_cols=72 Identities=11% Similarity=0.122 Sum_probs=44.2
Q ss_pred EEEEecccHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEec-ChhHHHhhcccCCcEEEEcCCC-HHHHHHH
Q 009783 362 KFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTR-DAKLLRHQYLIKNQIYRVKSLL-KNQQLLE 439 (526)
Q Consensus 362 kfl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~RiiLTr-d~~l~~~~~~~~~~~~~v~~~~-~~~QL~~ 439 (526)
|+=+...|..+..+|+..||+|+-+.+. .+ ++.=+.+++|- |..++--+... .++..|.... ..+++.+
T Consensus 3 kIaVE~~Ls~i~~~L~~~GYeVv~l~~~--~~------~~~~Da~VitG~d~n~mgi~d~~-t~~pVI~A~G~TaeEI~~ 73 (80)
T PRK03094 3 KIGVEQSLTDVQQALKQKGYEVVQLRSE--QD------AQGCDCCVVTGQDSNVMGIADTS-TKGSVITASGLTADEICQ 73 (80)
T ss_pred eEEeecCcHHHHHHHHHCCCEEEecCcc--cc------cCCcCEEEEeCCCcceecccccc-cCCcEEEcCCCCHHHHHH
Confidence 5777888999999999999999877531 21 23347888886 34454333211 2345555443 2455555
Q ss_pred HHH
Q 009783 440 VIE 442 (526)
Q Consensus 440 vl~ 442 (526)
.++
T Consensus 74 ~ve 76 (80)
T PRK03094 74 QVE 76 (80)
T ss_pred HHH
Confidence 444
No 319
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.44 E-value=75 Score=28.66 Aligned_cols=14 Identities=21% Similarity=0.624 Sum_probs=11.2
Q ss_pred CceeecCCCCeEEe
Q 009783 493 LQFWQCMDCNQLYW 506 (526)
Q Consensus 493 ~~F~~C~~CgkvyW 506 (526)
..-|+|+.|++-|=
T Consensus 51 ~qRyrC~~C~~tf~ 64 (129)
T COG3677 51 HQRYKCKSCGSTFT 64 (129)
T ss_pred ccccccCCcCccee
Confidence 55789999998763
No 320
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=22.10 E-value=1.2e+02 Score=25.18 Aligned_cols=42 Identities=12% Similarity=0.215 Sum_probs=31.5
Q ss_pred EEEEecccHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecC
Q 009783 362 KFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRD 411 (526)
Q Consensus 362 kfl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~RiiLTrd 411 (526)
|+-+...|..+..+|+..||+|+.+.+. + -++.=+.|++|-.
T Consensus 3 kIAVE~~Ls~v~~~L~~~GyeVv~l~~~--~------~~~~~daiVvtG~ 44 (80)
T PF03698_consen 3 KIAVEEGLSNVKEALREKGYEVVDLENE--Q------DLQNVDAIVVTGQ 44 (80)
T ss_pred eEEecCCchHHHHHHHHCCCEEEecCCc--c------ccCCcCEEEEECC
Confidence 6778888999999999999999987642 1 1223377888864
No 321
>PLN02294 cytochrome c oxidase subunit Vb
Probab=22.05 E-value=45 Score=31.56 Aligned_cols=13 Identities=23% Similarity=0.656 Sum_probs=10.7
Q ss_pred CceeecCCCCeEE
Q 009783 493 LQFWQCMDCNQLY 505 (526)
Q Consensus 493 ~~F~~C~~Cgkvy 505 (526)
.+-.+|+.||++|
T Consensus 139 Gkp~RCpeCG~~f 151 (174)
T PLN02294 139 GKSFECPVCTQYF 151 (174)
T ss_pred CCceeCCCCCCEE
Confidence 4566799999998
No 322
>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=21.98 E-value=30 Score=40.40 Aligned_cols=12 Identities=33% Similarity=0.540 Sum_probs=0.0
Q ss_pred HHHHhcCCceec
Q 009783 374 KHLRCVGIDAAT 385 (526)
Q Consensus 374 r~LR~lG~D~~~ 385 (526)
-++++||+|...
T Consensus 557 ~~~~~Lg~~~~~ 568 (900)
T PF03833_consen 557 PLLRSLGLDLNL 568 (900)
T ss_dssp ------------
T ss_pred HHHHHhCCCccc
Confidence 367888888643
No 323
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=21.97 E-value=79 Score=36.78 Aligned_cols=41 Identities=12% Similarity=0.199 Sum_probs=22.8
Q ss_pred CCcEEEEcCCC---HHHHHHHHHHH-c-Ccc-ccccccCccccCCCc
Q 009783 422 KNQIYRVKSLL---KNQQLLEVIEA-F-QLK-ISEDQLMSRCTKCNG 462 (526)
Q Consensus 422 ~~~~~~v~~~~---~~~QL~~vl~~-f-~l~-~~~~~~~sRC~~CN~ 462 (526)
+|.+..+.-.+ --+.+++|++. + ++. ..-+..+++|..|+-
T Consensus 603 GG~I~yve~~~~~~n~~a~~~lv~~~~~~i~Y~~in~~~~~C~~CG~ 649 (711)
T PRK09263 603 GGFIHYCEYPNLQHNLKALEAVWDYSYDRVGYLGTNTPIDECYECGF 649 (711)
T ss_pred CeEEEEEecCCCcCCHHHHHHHHHHHHHCCCeEEeCCCCcccCCCCC
Confidence 45566664431 13566666553 2 322 123345899999996
No 324
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=21.88 E-value=2.4e+02 Score=25.02 Aligned_cols=71 Identities=15% Similarity=0.235 Sum_probs=40.9
Q ss_pred cHHHHHHHHhcCCceecCCC-------CCCChH---HHHHhhhc---CCcEEEecChhHH---HhhcccCCcEEEEcCC-
Q 009783 369 VEGLAKHLRCVGIDAATPRS-------KKPEPR---ELIDQTSK---EKRVLLTRDAKLL---RHQYLIKNQIYRVKSL- 431 (526)
Q Consensus 369 Lg~Lar~LR~lG~D~~~~~~-------~~~~d~---~ll~~A~~---E~RiiLTrd~~l~---~~~~~~~~~~~~v~~~- 431 (526)
..++..+|+..|+.+..... +..|-. ++++.|.. +.=||+|.|.+|. ++....+.+++.+...
T Consensus 54 ~~~~~~~L~~~g~~~~~~~~~~~~~~~~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~i~~lr~~G~~V~v~~~~~ 133 (149)
T cd06167 54 QRGFLDALRRLGFEPIQKPLRTRGSGKKGVDVALAIDALELAYKRRIDTIVLVSGDSDFVPLVERLRELGKRVIVVGFEA 133 (149)
T ss_pred HHHHHHHHHHCCcEEEEEcceecCCcccCccHHHHHHHHHHhhhcCCCEEEEEECCccHHHHHHHHHHcCCEEEEEccCc
Confidence 46789999999999976542 222221 45666655 3456679999873 2222223455555443
Q ss_pred CHHHHHHH
Q 009783 432 LKNQQLLE 439 (526)
Q Consensus 432 ~~~~QL~~ 439 (526)
.....|..
T Consensus 134 ~~s~~L~~ 141 (149)
T cd06167 134 KTSRELRK 141 (149)
T ss_pred cChHHHHH
Confidence 23334443
No 325
>PF09706 Cas_CXXC_CXXC: CRISPR-associated protein (Cas_CXXC_CXXC); InterPro: IPR019121 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved domain of about 65 amino acids found in otherwise highly divergent proteins encoded in CRISPR-associated regions. This domain features two CXXC motifs.
Probab=21.72 E-value=31 Score=27.59 Aligned_cols=24 Identities=25% Similarity=0.474 Sum_probs=19.8
Q ss_pred cccCccccccCCceeecCCCCeEE
Q 009783 482 QRIPDCLFDKNLQFWQCMDCNQLY 505 (526)
Q Consensus 482 ~~vp~~v~~~~~~F~~C~~Cgkvy 505 (526)
++.|..+.+.......||.|.-+|
T Consensus 38 ~~~~N~fwn~~~~~~iCp~C~~iy 61 (69)
T PF09706_consen 38 GRKPNFFWNFNNDADICPICELIY 61 (69)
T ss_pred CCcccccccCcCCCccCHHHHHHH
Confidence 477888888888999999997655
No 326
>cd00886 MogA_MoaB MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea, and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT). MogA, together with MoeA, is responsible for the metal incorporation into MPT, the third step in MoCF biosynthesis. The plant homolog Cnx1 is a MoeA-MogA fusion protein. The mammalian homolog gephyrin is a MogA-MoeA fusion protein, that plays a critical role in postsynaptic anchoring of inhibitory glycine receptors and major GABAa receptor subtypes. In contrast, MoaB shows high similarity to MogA, but little is known about its physiological role. All well studied members of this family form highly stable trimers.
Probab=21.69 E-value=1.2e+02 Score=27.75 Aligned_cols=48 Identities=15% Similarity=0.074 Sum_probs=29.6
Q ss_pred EEecccHHHHHHHHhcCCceecCCCCCCChH---HHHHhhhc--CCcEEEecC
Q 009783 364 LCDVMVEGLAKHLRCVGIDAATPRSKKPEPR---ELIDQTSK--EKRVLLTRD 411 (526)
Q Consensus 364 l~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~---~ll~~A~~--E~RiiLTrd 411 (526)
+.|.+-.-|+.+|+..|+++....-...|.+ +.++.+.+ +..+|||.+
T Consensus 17 i~d~n~~~l~~~l~~~G~~v~~~~~v~Dd~~~i~~~l~~~~~~~~~DlVittG 69 (152)
T cd00886 17 AEDRSGPALVELLEEAGHEVVAYEIVPDDKDEIREALIEWADEDGVDLILTTG 69 (152)
T ss_pred CccchHHHHHHHHHHcCCeeeeEEEcCCCHHHHHHHHHHHHhcCCCCEEEECC
Confidence 4477777899999999999865432222222 23333434 556777765
No 327
>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]
Probab=21.67 E-value=55 Score=31.82 Aligned_cols=18 Identities=17% Similarity=0.257 Sum_probs=15.3
Q ss_pred CCCCeEEecccchhhHHh
Q 009783 499 MDCNQLYWEVMSAYLFIF 516 (526)
Q Consensus 499 ~~CgkvyW~GsH~~r~~~ 516 (526)
|.+|.|||+|.|...+-.
T Consensus 54 p~~G~v~~~~~~i~~~~~ 71 (209)
T COG4133 54 PDAGEVYWQGEPIQNVRE 71 (209)
T ss_pred CCCCeEEecCCCCccchh
Confidence 679999999999887654
No 328
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=21.59 E-value=36 Score=36.65 Aligned_cols=44 Identities=25% Similarity=0.566 Sum_probs=27.5
Q ss_pred CccccCCCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009783 454 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 505 (526)
Q Consensus 454 ~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 505 (526)
--||.+|..++++.+- +||.+ +|=.--.+.|.+.|+|..||..-
T Consensus 394 APrCs~C~~PI~P~~G-~~etv-------Rvvamdr~fHv~CY~CEDCg~~L 437 (468)
T KOG1701|consen 394 APRCSVCGNPILPRDG-KDETV-------RVVAMDRDFHVNCYKCEDCGLLL 437 (468)
T ss_pred CcchhhccCCccCCCC-CcceE-------EEEEccccccccceehhhcCccc
Confidence 3689999999875332 23222 22111235678899999998653
No 329
>TIGR00177 molyb_syn molybdenum cofactor synthesis domain. The Drosophila protein cinnamon, the Arabidopsis protein cnx1, and rat protein gephyrin each have one domain like MoeA and one like MoaB and Mog. These domains are, however, distantly related to each other, as captured by this model. Gephyrin is unusual in that it seems to be a tubulin-binding neuroprotein involved in the clustering of both blycine receptors and GABA receptors, rather than a protein of molybdenum cofactor biosynthesis.
Probab=21.51 E-value=1.4e+02 Score=27.01 Aligned_cols=48 Identities=23% Similarity=0.254 Sum_probs=30.7
Q ss_pred EEEecccHHHHHHHHhcCCceecCCCCCCChH----HHHHhhhcCCcEEEecC
Q 009783 363 FLCDVMVEGLAKHLRCVGIDAATPRSKKPEPR----ELIDQTSKEKRVLLTRD 411 (526)
Q Consensus 363 fl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~----~ll~~A~~E~RiiLTrd 411 (526)
=+.|....-|+.+|+.+|+++....-. .|+. +.++.+.++-.+|||.+
T Consensus 23 ~i~d~n~~~l~~~l~~~G~~v~~~~~v-~Dd~~~i~~~l~~~~~~~DliIttG 74 (144)
T TIGR00177 23 QIYDSNGPLLAALLEEAGFNVSRLGIV-PDDPEEIREILRKAVDEADVVLTTG 74 (144)
T ss_pred eEEeCcHHHHHHHHHHCCCeEEEEeec-CCCHHHHHHHHHHHHhCCCEEEECC
Confidence 467999999999999999998754322 1222 23444444455666554
No 330
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=21.43 E-value=61 Score=25.83 Aligned_cols=20 Identities=20% Similarity=0.436 Sum_probs=14.5
Q ss_pred ccccCCceeecCCCCeEEec
Q 009783 488 LFDKNLQFWQCMDCNQLYWE 507 (526)
Q Consensus 488 v~~~~~~F~~C~~CgkvyW~ 507 (526)
||.+...--.|..||++-=+
T Consensus 31 vFshast~V~C~~CG~~l~~ 50 (67)
T COG2051 31 VFSHASTVVTCLICGTTLAE 50 (67)
T ss_pred EeccCceEEEecccccEEEe
Confidence 45556677889999987543
No 331
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=21.41 E-value=41 Score=30.70 Aligned_cols=13 Identities=23% Similarity=0.651 Sum_probs=10.7
Q ss_pred CceeecCCCCeEE
Q 009783 493 LQFWQCMDCNQLY 505 (526)
Q Consensus 493 ~~F~~C~~Cgkvy 505 (526)
.+-.+|+.||++|
T Consensus 110 g~~~RCpeCG~~f 122 (136)
T PF01215_consen 110 GKPQRCPECGQVF 122 (136)
T ss_dssp TSEEEETTTEEEE
T ss_pred CCccCCCCCCeEE
Confidence 3467999999988
No 332
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=21.28 E-value=57 Score=28.46 Aligned_cols=11 Identities=18% Similarity=0.616 Sum_probs=8.4
Q ss_pred eeecCCCCeEE
Q 009783 495 FWQCMDCNQLY 505 (526)
Q Consensus 495 F~~C~~Cgkvy 505 (526)
-..||.|+.-+
T Consensus 20 ~~~cpec~~ew 30 (112)
T COG2824 20 QLICPECAHEW 30 (112)
T ss_pred eEeCchhcccc
Confidence 67899998653
No 333
>COG5041 SKB2 Casein kinase II, beta subunit [Signal transduction mechanisms / Cell division and chromosome partitioning / Transcription]
Probab=21.24 E-value=91 Score=30.44 Aligned_cols=56 Identities=27% Similarity=0.618 Sum_probs=33.1
Q ss_pred HHHHHHHHHcCccccccccCccccC--CCcccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecccc
Q 009783 435 QQLLEVIEAFQLKISEDQLMSRCTK--CNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVMS 510 (526)
Q Consensus 435 ~QL~~vl~~f~l~~~~~~~~sRC~~--CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~GsH 510 (526)
.-|..+++.|. ...|.+|++ ||+--+. |+. ...+|. ....--.||+|--+|=+-|.
T Consensus 107 ~GL~~m~eKy~-----~~efG~CPRv~Cn~~~vL-PvG----------LsDi~g----~~~vkLyCpsC~dlY~p~Ss 164 (242)
T COG5041 107 SGLQAMLEKYK-----SREFGACPRVYCNGQQVL-PVG----------LSDIPG----KSSVKLYCPSCEDLYLPKSS 164 (242)
T ss_pred HHHHHHHHHHh-----hcccCCCCcccccCccee-ccc----------cccCCC----CceeEEecCchhhhcCcccc
Confidence 34666777774 334889986 6663221 332 223332 23445669999999966554
No 334
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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 C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=21.05 E-value=61 Score=21.43 Aligned_cols=14 Identities=21% Similarity=0.517 Sum_probs=11.4
Q ss_pred ecCCCCeEEecccc
Q 009783 497 QCMDCNQLYWEVMS 510 (526)
Q Consensus 497 ~C~~CgkvyW~GsH 510 (526)
-|-.|++.||..++
T Consensus 2 sCiDC~~~F~~~~y 15 (28)
T PF08790_consen 2 SCIDCSKDFDGDSY 15 (28)
T ss_dssp EETTTTEEEEGGGT
T ss_pred eeecCCCCcCcCCc
Confidence 59999999986654
No 335
>PHA02942 putative transposase; Provisional
Probab=20.84 E-value=1.2e+02 Score=32.44 Aligned_cols=11 Identities=18% Similarity=0.860 Sum_probs=9.2
Q ss_pred ceeecCCCCeE
Q 009783 494 QFWQCMDCNQL 504 (526)
Q Consensus 494 ~F~~C~~Cgkv 504 (526)
..|.|+.||-.
T Consensus 341 r~f~C~~CG~~ 351 (383)
T PHA02942 341 RYFHCPSCGYE 351 (383)
T ss_pred CEEECCCCCCE
Confidence 47999999964
No 336
>KOG3092 consensus Casein kinase II, beta subunit [Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Transcription]
Probab=20.75 E-value=1.1e+02 Score=29.65 Aligned_cols=54 Identities=26% Similarity=0.624 Sum_probs=33.2
Q ss_pred HHHHHHHHcCccccccccCccccC--CCc-ccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecccc
Q 009783 436 QLLEVIEAFQLKISEDQLMSRCTK--CNG-RFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVMS 510 (526)
Q Consensus 436 QL~~vl~~f~l~~~~~~~~sRC~~--CN~-~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~GsH 510 (526)
-|.++++.+. ...|.+|++ ||+ +++ |+ |...+|.. ...--.||+|.-||=.-|.
T Consensus 93 Gl~~M~eKy~-----~~dFG~CPRV~C~~q~~L--Pv----------GLsDipg~----~~VklYCP~C~dvY~P~ss 149 (216)
T KOG3092|consen 93 GLAAMLEKYK-----NGDFGRCPRVYCCGQPVL--PV----------GLSDIPGK----STVKLYCPSCEDVYIPKSS 149 (216)
T ss_pred HHHHHHHHHh-----cCCCCcCCcccccCCccc--cc----------cccCCCCc----ceEEEeCCCcccccccccc
Confidence 4556666664 234899997 554 332 33 22344432 3445679999999998773
No 337
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=20.51 E-value=27 Score=27.64 Aligned_cols=13 Identities=15% Similarity=0.519 Sum_probs=9.1
Q ss_pred CCceeecCCCCeE
Q 009783 492 NLQFWQCMDCNQL 504 (526)
Q Consensus 492 ~~~F~~C~~Cgkv 504 (526)
...+..|+.||-.
T Consensus 33 ~f~~v~C~~CGYT 45 (64)
T PF09855_consen 33 KFTTVSCTNCGYT 45 (64)
T ss_pred EEEEEECCCCCCE
Confidence 3446679999954
No 338
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=20.31 E-value=1.3e+02 Score=26.99 Aligned_cols=32 Identities=19% Similarity=0.249 Sum_probs=25.5
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCC
Q 009783 372 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 404 (526)
Q Consensus 372 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~ 404 (526)
++..||..||+|.+... ..+..++++.|.+++
T Consensus 22 v~~~l~~~GfeVi~lg~-~~s~e~~v~aa~e~~ 53 (132)
T TIGR00640 22 IATAYADLGFDVDVGPL-FQTPEEIARQAVEAD 53 (132)
T ss_pred HHHHHHhCCcEEEECCC-CCCHHHHHHHHHHcC
Confidence 68999999999998864 345678888887764
No 339
>PF02639 DUF188: Uncharacterized BCR, YaiI/YqxD family COG1671; InterPro: IPR003791 This entry describes proteins of unknown function.
Probab=20.24 E-value=2.4e+02 Score=25.48 Aligned_cols=29 Identities=14% Similarity=0.173 Sum_probs=22.4
Q ss_pred ChHHHHHhhhcCCcEEEecChhHHHhhccc
Q 009783 392 EPRELIDQTSKEKRVLLTRDAKLLRHQYLI 421 (526)
Q Consensus 392 ~d~~ll~~A~~E~RiiLTrd~~l~~~~~~~ 421 (526)
-|..|++.+ +.|-|+||.|-+|+.+....
T Consensus 41 aD~~I~~~~-~~gDiVITqDigLA~~~l~K 69 (130)
T PF02639_consen 41 ADFYIVNHA-KPGDIVITQDIGLASLLLAK 69 (130)
T ss_pred HHHHHHHcC-CCCCEEEECCHHHHHHHHHC
Confidence 366788877 46999999999998765533
No 340
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.20 E-value=37 Score=39.14 Aligned_cols=14 Identities=21% Similarity=0.615 Sum_probs=10.8
Q ss_pred ceeecCCCCeEEec
Q 009783 494 QFWQCMDCNQLYWE 507 (526)
Q Consensus 494 ~F~~C~~CgkvyW~ 507 (526)
..|.||.||--.+.
T Consensus 421 ~p~~Cp~Cgs~~l~ 434 (665)
T PRK14873 421 PDWRCPRCGSDRLR 434 (665)
T ss_pred cCccCCCCcCCcce
Confidence 47899999976554
No 341
>PF01214 CK_II_beta: Casein kinase II regulatory subunit; InterPro: IPR000704 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Casein kinase, a ubiquitous, well-conserved protein kinase involved in cell metabolism and differentiation, is characterised by its preference for Ser or Thr in acidic stretches of amino acids. The enzyme is a tetramer of 2 alpha- and 2 beta-subunits [, ]. However, some species (e.g., mammals) possess 2 related forms of the alpha-subunit (alpha and alpha'), while others (e.g., fungi) possess 2 related beta-subunits (beta and beta') []. The alpha-subunit is the catalytic unit and contains regions characteristic of serine/threonine protein kinases. The beta-subunit is believed to be regulatory, possessing an N-terminal auto-phosphorylation site, an internal acidic domain, and a potential metal-binding motif []. The beta subunit is a highly conserved protein of about 25kDa that contains, in its central section, a cysteine-rich motif, CX(n)C, that could be involved in binding a metal such as zinc []. The mammalian beta-subunit gene promoter shares common features with those of other mammalian protein kinases and is closely related to the promoter of the regulatory subunit of cAMP-dependent protein kinase [].; GO: 0019887 protein kinase regulator activity, 0005956 protein kinase CK2 complex; PDB: 2R6M_B 1RQF_K 1DS5_G 1QF8_B 3EED_A 4DGL_A 1JWH_D.
Probab=20.10 E-value=92 Score=29.90 Aligned_cols=52 Identities=23% Similarity=0.637 Sum_probs=26.9
Q ss_pred HHHHHHHHHcCccccccccCccccC--CCc-ccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEec
Q 009783 435 QQLLEVIEAFQLKISEDQLMSRCTK--CNG-RFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWE 507 (526)
Q Consensus 435 ~QL~~vl~~f~l~~~~~~~~sRC~~--CN~-~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~ 507 (526)
+-|.++.+.|. ...|.+|++ ||+ +++ |+. ....| .....-..||+|+.||=.
T Consensus 85 ~Gl~~m~eKy~-----~g~FG~CPRv~C~~~~lL--PiG----------lsd~~----g~~~vKlyCP~C~dvY~p 139 (184)
T PF01214_consen 85 RGLEQMKEKYE-----QGDFGRCPRVYCNGQPLL--PIG----------LSDTP----GESTVKLYCPRCKDVYHP 139 (184)
T ss_dssp HHHHHHHHHHH-----TTTT-B-SBGGGTT-B-E--EEB----------S-SST----TS-BBEEEETTTTEEE--
T ss_pred HHHHHHHHhhc-----CCcCCcCCcccCCCCcee--Ccc----------CCCCC----CccceeEECCCCccccCC
Confidence 55666777773 234889975 665 444 321 11112 234456679999999987
No 342
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=20.04 E-value=67 Score=19.59 Aligned_cols=15 Identities=27% Similarity=0.476 Sum_probs=11.7
Q ss_pred eecCCCCeEEecccc
Q 009783 496 WQCMDCNQLYWEVMS 510 (526)
Q Consensus 496 ~~C~~CgkvyW~GsH 510 (526)
|.|.-|++.|-.-..
T Consensus 1 ~~C~~C~~~f~s~~~ 15 (25)
T PF12874_consen 1 FYCDICNKSFSSENS 15 (25)
T ss_dssp EEETTTTEEESSHHH
T ss_pred CCCCCCCCCcCCHHH
Confidence 689999999865443
Done!