Query 009948
Match_columns 522
No_of_seqs 397 out of 1407
Neff 7.0
Searched_HMMs 46136
Date Thu Mar 28 19:14:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009948.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009948hhsearch_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 1.5E-46 3.3E-51 344.8 13.6 146 357-513 1-146 (147)
2 COG1656 Uncharacterized conser 100.0 6E-45 1.3E-49 329.8 13.1 156 354-520 4-159 (165)
3 PRK10829 ribonuclease D; Provi 100.0 4.1E-31 9E-36 275.5 21.4 215 10-267 2-221 (373)
4 cd06146 mut-7_like_exo DEDDy 3 100.0 1.1E-29 2.4E-34 243.6 19.9 184 11-213 1-192 (193)
5 COG0349 Rnd Ribonuclease D [Tr 100.0 1.4E-29 3E-34 257.9 17.0 215 19-273 4-223 (361)
6 cd06129 RNaseD_like DEDDy 3'-5 100.0 1.3E-28 2.9E-33 229.4 18.2 158 22-213 2-160 (161)
7 TIGR01388 rnd ribonuclease D. 100.0 2.7E-27 5.9E-32 247.8 21.3 211 14-267 2-217 (367)
8 cd06141 WRN_exo DEDDy 3'-5' ex 99.9 1.7E-26 3.6E-31 216.6 18.6 163 19-213 4-169 (170)
9 cd06148 Egl_like_exo DEDDy 3'- 99.9 2.5E-26 5.4E-31 221.1 17.1 170 25-220 3-181 (197)
10 PF01612 DNA_pol_A_exo1: 3'-5' 99.9 9.5E-25 2.1E-29 204.1 19.1 174 11-217 1-176 (176)
11 cd06142 RNaseD_exo DEDDy 3'-5' 99.8 5.2E-19 1.1E-23 166.2 18.7 164 23-222 3-166 (178)
12 smart00474 35EXOc 3'-5' exonuc 99.8 9E-17 1.9E-21 149.0 19.7 169 12-216 2-171 (172)
13 KOG2207 Predicted 3'-5' exonuc 99.7 4.6E-18 9.9E-23 180.7 9.0 195 5-217 386-586 (617)
14 cd06147 Rrp6p_like_exo DEDDy 3 99.7 1.3E-15 2.8E-20 145.9 20.2 173 9-219 3-175 (192)
15 KOG2207 Predicted 3'-5' exonuc 99.7 1.1E-18 2.4E-23 185.3 -7.3 382 135-521 154-585 (617)
16 KOG2206 Exosome 3'-5' exoribon 99.6 2.9E-16 6.3E-21 166.0 9.2 172 11-220 193-364 (687)
17 cd00007 35EXOc 3'-5' exonuclea 99.6 1.2E-14 2.5E-19 132.3 16.1 149 34-215 2-154 (155)
18 cd09018 DEDDy_polA_RNaseD_like 99.6 1.8E-14 3.9E-19 131.3 15.2 147 34-213 1-149 (150)
19 PRK05755 DNA polymerase I; Pro 99.6 1.1E-13 2.4E-18 160.5 20.8 180 7-222 292-475 (880)
20 cd06140 DNA_polA_I_Bacillus_li 99.5 6.4E-13 1.4E-17 125.2 15.7 157 32-222 3-162 (178)
21 cd06139 DNA_polA_I_Ecoli_like_ 99.4 1.7E-11 3.6E-16 116.5 17.6 160 30-221 3-176 (193)
22 PRK14975 bifunctional 3'-5' ex 99.3 5E-12 1.1E-16 139.7 11.9 146 10-219 2-147 (553)
23 COG0749 PolA DNA polymerase I 99.1 8.3E-10 1.8E-14 120.2 13.3 170 19-222 9-186 (593)
24 TIGR00593 pola DNA polymerase 99.0 9.1E-09 2E-13 118.9 19.6 172 11-221 304-482 (887)
25 KOG4373 Predicted 3'-5' exonuc 98.9 1.2E-08 2.6E-13 102.7 10.5 159 32-221 127-291 (319)
26 COG4634 Uncharacterized protei 98.7 1.1E-07 2.4E-12 81.0 8.6 73 357-429 1-79 (113)
27 cd06128 DNA_polA_exo DEDDy 3'- 98.5 1.6E-06 3.5E-11 79.5 13.4 117 78-213 30-150 (151)
28 PRK07942 DNA polymerase III su 97.0 0.036 7.8E-07 54.8 16.5 90 105-219 94-183 (232)
29 cd06149 ISG20 DEDDh 3'-5' exon 97.0 0.0052 1.1E-07 57.1 9.8 89 91-210 66-157 (157)
30 PRK06063 DNA polymerase III su 97.0 0.021 4.5E-07 59.1 15.2 102 91-221 83-184 (313)
31 cd06131 DNA_pol_III_epsilon_Ec 96.8 0.034 7.5E-07 51.5 13.7 96 91-212 70-166 (167)
32 KOG2249 3'-5' exonuclease [Rep 96.7 0.02 4.3E-07 56.9 11.6 95 93-219 175-269 (280)
33 PRK06310 DNA polymerase III su 96.7 0.043 9.4E-07 54.9 14.4 150 29-216 4-174 (250)
34 cd06144 REX4_like DEDDh 3'-5' 96.7 0.0077 1.7E-07 55.5 8.4 87 91-210 66-152 (152)
35 PRK06309 DNA polymerase III su 96.6 0.11 2.3E-06 51.5 16.5 144 33-217 3-167 (232)
36 PRK06807 DNA polymerase III su 96.6 0.061 1.3E-06 55.7 15.0 97 91-217 77-173 (313)
37 PRK08517 DNA polymerase III su 96.5 0.12 2.5E-06 52.1 16.3 98 91-218 136-233 (257)
38 TIGR01405 polC_Gram_pos DNA po 96.5 0.053 1.1E-06 65.3 15.8 103 91-222 259-361 (1213)
39 PRK05711 DNA polymerase III su 96.4 0.075 1.6E-06 52.9 14.2 98 91-213 75-173 (240)
40 PRK07740 hypothetical protein; 96.4 0.15 3.4E-06 50.8 16.3 101 91-221 130-231 (244)
41 PRK07883 hypothetical protein; 96.4 0.09 2E-06 58.7 15.9 162 24-222 7-188 (557)
42 cd05780 DNA_polB_Kod1_like_exo 96.3 0.087 1.9E-06 50.6 13.7 160 33-212 4-195 (195)
43 TIGR01406 dnaQ_proteo DNA poly 96.3 0.14 3E-06 50.5 15.0 98 91-213 71-169 (225)
44 PRK09145 DNA polymerase III su 96.2 0.18 4E-06 48.6 15.4 98 91-213 100-198 (202)
45 smart00479 EXOIII exonuclease 96.2 0.15 3.3E-06 46.8 14.1 98 91-216 69-167 (169)
46 cd06143 PAN2_exo DEDDh 3'-5' e 96.2 0.014 3.1E-07 55.0 7.2 81 95-210 94-174 (174)
47 PRK05168 ribonuclease T; Provi 96.2 0.34 7.3E-06 47.2 16.9 93 104-222 114-207 (211)
48 cd06145 REX1_like DEDDh 3'-5' 96.2 0.018 4E-07 52.9 7.7 86 91-209 64-149 (150)
49 TIGR00573 dnaq exonuclease, DN 96.2 0.093 2E-06 51.3 13.0 105 91-219 76-180 (217)
50 cd06125 DnaQ_like_exo DnaQ-lik 96.1 0.032 6.9E-07 47.4 8.4 82 35-145 1-83 (96)
51 cd06137 DEDDh_RNase DEDDh 3'-5 96.1 0.02 4.4E-07 53.3 7.8 87 93-209 74-160 (161)
52 cd05160 DEDDy_DNA_polB_exo DED 96.0 0.13 2.7E-06 49.3 13.0 110 91-209 65-198 (199)
53 TIGR01407 dinG_rel DnaQ family 95.9 0.12 2.5E-06 60.8 14.5 99 91-218 69-167 (850)
54 PRK07246 bifunctional ATP-depe 95.8 0.13 2.9E-06 60.0 14.3 101 91-221 75-175 (820)
55 PRK09146 DNA polymerase III su 95.8 0.39 8.4E-06 47.8 15.6 102 92-216 119-227 (239)
56 cd06130 DNA_pol_III_epsilon_li 95.7 0.38 8.3E-06 43.7 14.4 89 91-209 66-154 (156)
57 PRK08074 bifunctional ATP-depe 95.7 0.23 4.9E-06 59.0 16.0 99 91-218 73-171 (928)
58 cd06127 DEDDh DEDDh 3'-5' exon 95.5 0.39 8.5E-06 43.0 13.4 91 91-209 68-158 (159)
59 TIGR01298 RNaseT ribonuclease 94.6 0.4 8.8E-06 46.3 11.3 93 104-222 105-198 (200)
60 COG2176 PolC DNA polymerase II 94.5 0.16 3.5E-06 59.7 9.3 103 91-222 490-592 (1444)
61 PRK07247 DNA polymerase III su 94.3 0.7 1.5E-05 44.5 12.1 108 91-231 73-184 (195)
62 cd05781 DNA_polB_B3_exo DEDDy 94.3 1.2 2.6E-05 42.6 13.7 158 33-212 4-188 (188)
63 cd05784 DNA_polB_II_exo DEDDy 93.8 1.6 3.6E-05 41.9 13.7 110 91-210 53-193 (193)
64 cd05785 DNA_polB_like2_exo Unc 93.5 1.2 2.5E-05 43.4 12.2 160 32-209 9-206 (207)
65 cd06134 RNaseT DEDDh 3'-5' exo 93.0 0.86 1.9E-05 43.5 10.3 84 105-214 103-187 (189)
66 PRK00448 polC DNA polymerase I 92.9 1.7 3.7E-05 53.6 14.8 103 91-222 488-590 (1437)
67 PRK06195 DNA polymerase III su 92.6 0.83 1.8E-05 47.2 10.3 99 91-219 69-167 (309)
68 PRK05601 DNA polymerase III su 92.5 2.4 5.3E-05 44.7 13.4 109 90-212 113-245 (377)
69 cd05777 DNA_polB_delta_exo DED 92.2 3.8 8.3E-05 40.3 14.0 54 160-213 167-224 (230)
70 KOG2405 Predicted 3'-5' exonuc 92.1 0.02 4.3E-07 59.4 -2.4 130 51-204 73-215 (458)
71 cd05783 DNA_polB_B1_exo DEDDy 92.0 7.1 0.00015 37.9 15.3 161 33-210 6-202 (204)
72 cd05779 DNA_polB_epsilon_exo D 91.9 2.1 4.6E-05 41.5 11.4 110 91-209 75-203 (204)
73 KOG2405 Predicted 3'-5' exonuc 91.1 0.2 4.4E-06 52.2 3.6 125 77-213 222-358 (458)
74 cd06136 TREX1_2 DEDDh 3'-5' ex 89.6 1.6 3.4E-05 41.3 8.1 89 92-210 84-175 (177)
75 cd00814 MetRS_core catalytic c 87.5 1.5 3.3E-05 45.3 7.0 102 367-501 28-131 (319)
76 COG3809 Uncharacterized protei 86.9 0.6 1.3E-05 37.9 2.7 41 452-513 3-43 (88)
77 PF13482 RNase_H_2: RNase_H su 86.7 1 2.3E-05 41.3 4.8 148 35-212 1-163 (164)
78 PF14803 Nudix_N_2: Nudix N-te 86.5 0.52 1.1E-05 32.3 1.9 31 453-502 3-33 (34)
79 PF13719 zinc_ribbon_5: zinc-r 85.4 0.7 1.5E-05 32.2 2.2 33 451-501 3-35 (37)
80 PRK11779 sbcB exonuclease I; P 85.0 16 0.00035 40.1 13.6 107 91-215 80-197 (476)
81 COG4049 Uncharacterized protei 84.5 0.32 6.9E-06 36.9 0.2 23 487-509 13-35 (65)
82 PF08792 A2L_zn_ribbon: A2L zi 83.8 1 2.2E-05 30.7 2.3 29 450-501 3-31 (33)
83 PF13717 zinc_ribbon_4: zinc-r 83.7 0.92 2E-05 31.5 2.2 33 451-501 3-35 (36)
84 PRK00464 nrdR transcriptional 83.0 0.68 1.5E-05 42.9 1.7 51 452-518 2-52 (154)
85 KOG1275 PAB-dependent poly(A) 82.7 0.32 7E-06 55.7 -0.6 96 99-229 1009-1104(1118)
86 PRK09182 DNA polymerase III su 82.5 34 0.00075 35.1 14.1 88 93-213 111-198 (294)
87 cd05776 DNA_polB_alpha_exo ina 81.9 2.9 6.4E-05 41.3 5.9 112 92-213 85-227 (234)
88 KOG2248 3'-5' exonuclease [Rep 81.9 1.5 3.2E-05 46.6 4.0 90 91-213 282-372 (380)
89 TIGR02098 MJ0042_CXXC MJ0042 f 81.7 1.2 2.6E-05 30.9 2.2 34 451-502 3-36 (38)
90 PRK00133 metG methionyl-tRNA s 81.6 3 6.6E-05 47.8 6.7 34 367-400 30-63 (673)
91 PRK07748 sporulation inhibitor 81.4 14 0.00031 35.6 10.4 99 91-215 81-179 (207)
92 PF09281 Taq-exonuc: Taq polym 80.9 7.8 0.00017 34.8 7.4 55 135-216 84-138 (138)
93 PF13453 zf-TFIIB: Transcripti 80.1 1.6 3.4E-05 31.0 2.4 24 489-512 17-40 (41)
94 PRK07983 exodeoxyribonuclease 79.9 15 0.00032 36.1 10.0 86 95-214 67-152 (219)
95 PLN02224 methionine-tRNA ligas 79.8 4.5 9.7E-05 45.9 7.0 35 367-401 97-131 (616)
96 PRK11893 methionyl-tRNA synthe 79.1 4.1 8.8E-05 44.9 6.5 35 367-401 29-63 (511)
97 COG0143 MetG Methionyl-tRNA sy 79.0 3.7 7.9E-05 45.9 6.0 34 367-401 33-67 (558)
98 PRK05762 DNA polymerase II; Re 78.2 42 0.00091 39.4 14.6 112 91-212 205-348 (786)
99 PF09334 tRNA-synt_1g: tRNA sy 77.6 2.1 4.5E-05 45.8 3.5 35 367-401 27-61 (391)
100 smart00661 RPOL9 RNA polymeras 77.3 2.9 6.3E-05 30.9 3.2 17 490-506 19-35 (52)
101 cd05782 DNA_polB_like1_exo Unc 77.1 31 0.00066 33.5 11.2 110 90-210 79-207 (208)
102 TIGR03830 CxxCG_CxxCG_HTH puta 76.2 1.8 3.9E-05 38.1 2.1 30 488-517 28-57 (127)
103 cd06138 ExoI_N N-terminal DEDD 75.1 17 0.00036 34.3 8.6 99 92-209 72-182 (183)
104 PRK12268 methionyl-tRNA synthe 75.1 6.2 0.00013 44.1 6.5 35 367-401 32-66 (556)
105 KOG2907 RNA polymerase I trans 74.8 2 4.4E-05 37.4 1.9 46 447-505 71-116 (116)
106 cd06133 ERI-1_3'hExo_like DEDD 74.3 27 0.00059 32.0 9.7 98 91-212 77-175 (176)
107 PF00096 zf-C2H2: Zinc finger, 74.3 1.9 4.2E-05 26.1 1.3 16 492-507 1-16 (23)
108 PF05191 ADK_lid: Adenylate ki 74.0 1.9 4.1E-05 30.0 1.3 11 492-502 2-12 (36)
109 PF07754 DUF1610: Domain of un 73.1 3.3 7.1E-05 26.2 2.1 9 491-499 16-24 (24)
110 PHA02119 hypothetical protein 72.7 1.4 3E-05 34.9 0.4 15 367-381 58-72 (87)
111 PF00301 Rubredoxin: Rubredoxi 72.5 1.7 3.6E-05 32.1 0.8 39 452-499 3-42 (47)
112 PLN02610 probable methionyl-tR 72.5 7.6 0.00017 45.4 6.6 34 367-400 46-79 (801)
113 COG0847 DnaQ DNA polymerase II 72.2 35 0.00076 33.4 10.5 99 91-215 83-181 (243)
114 cd00672 CysRS_core catalytic c 69.6 3.7 8E-05 40.1 2.7 34 367-400 47-80 (213)
115 COG1579 Zn-ribbon protein, pos 69.5 1.5 3.3E-05 43.5 0.0 54 436-507 183-238 (239)
116 PRK00420 hypothetical protein; 69.5 3.4 7.3E-05 36.3 2.2 30 451-504 24-53 (112)
117 PF13005 zf-IS66: zinc-finger 69.3 1.2 2.6E-05 32.4 -0.6 43 451-498 3-47 (47)
118 PF14353 CpXC: CpXC protein 69.0 4.3 9.4E-05 36.1 2.9 19 483-501 30-48 (128)
119 CHL00174 accD acetyl-CoA carbo 68.2 3.7 8E-05 42.1 2.5 38 439-499 28-65 (296)
120 COG2956 Predicted N-acetylgluc 67.8 2.6 5.7E-05 43.6 1.3 11 489-499 366-376 (389)
121 PRK06722 exonuclease; Provisio 67.4 36 0.00078 34.8 9.4 100 91-213 79-178 (281)
122 PF02591 DUF164: Putative zinc 67.3 3.1 6.7E-05 31.6 1.3 33 451-500 23-55 (56)
123 TIGR03447 mycothiol_MshC cyste 66.7 5 0.00011 43.2 3.2 35 367-401 63-97 (411)
124 KOG3657 Mitochondrial DNA poly 65.8 12 0.00027 43.1 6.1 111 103-221 240-388 (1075)
125 PRK12418 cysteinyl-tRNA synthe 64.9 5.3 0.00012 42.6 3.0 36 367-402 36-71 (384)
126 TIGR00396 leuS_bact leucyl-tRN 62.1 15 0.00033 43.3 6.4 19 367-385 57-75 (842)
127 PF10122 Mu-like_Com: Mu-like 61.7 1.2 2.6E-05 33.3 -1.8 10 451-460 5-14 (51)
128 PF15135 UPF0515: Uncharacteri 61.3 6.2 0.00013 39.1 2.5 37 447-501 129-165 (278)
129 PF06397 Desulfoferrod_N: Desu 60.7 5.8 0.00013 27.6 1.5 14 488-501 3-16 (36)
130 PF13894 zf-C2H2_4: C2H2-type 60.0 5.7 0.00012 23.6 1.3 16 492-507 1-16 (24)
131 cd00730 rubredoxin Rubredoxin; 59.6 5.5 0.00012 29.8 1.4 39 452-499 3-42 (50)
132 PRK00432 30S ribosomal protein 58.8 9.2 0.0002 28.6 2.5 14 490-503 36-49 (50)
133 TIGR00515 accD acetyl-CoA carb 58.5 5.3 0.00011 40.9 1.6 32 446-499 22-53 (285)
134 PHA00616 hypothetical protein 58.4 2.3 5.1E-05 30.9 -0.7 17 492-508 2-18 (44)
135 PRK07218 replication factor A; 58.0 5.3 0.00011 43.2 1.5 14 447-460 294-307 (423)
136 PF08882 Acetone_carb_G: Aceto 57.2 6.5 0.00014 34.2 1.6 20 480-500 64-83 (112)
137 PLN02946 cysteine-tRNA ligase 57.2 8.2 0.00018 43.2 2.9 35 367-401 107-141 (557)
138 PRK03824 hypA hydrogenase nick 57.1 3.4 7.4E-05 37.4 -0.1 49 444-499 64-115 (135)
139 PF01396 zf-C4_Topoisom: Topoi 56.5 8.5 0.00018 27.1 1.9 31 452-503 3-36 (39)
140 PF04981 NMD3: NMD3 family ; 56.4 7.5 0.00016 38.5 2.2 21 489-510 33-53 (236)
141 cd00812 LeuRS_core catalytic c 56.1 22 0.00048 36.7 5.7 35 367-401 28-62 (314)
142 PF14787 zf-CCHC_5: GAG-polypr 56.0 4.8 0.0001 27.9 0.5 13 493-509 4-16 (36)
143 PF08271 TF_Zn_Ribbon: TFIIB z 55.8 8.7 0.00019 27.4 1.9 13 488-500 16-28 (43)
144 smart00531 TFIIE Transcription 55.5 7.3 0.00016 35.7 1.8 17 486-502 94-110 (147)
145 PRK00390 leuS leucyl-tRNA synt 55.2 20 0.00043 42.1 5.7 19 367-385 60-78 (805)
146 cd00729 rubredoxin_SM Rubredox 55.1 8 0.00017 26.4 1.5 16 490-506 1-16 (34)
147 COG1773 Rubredoxin [Energy pro 55.1 6.7 0.00014 29.9 1.2 40 451-499 4-44 (55)
148 COG2835 Uncharacterized conser 55.0 9.8 0.00021 29.5 2.1 11 491-501 26-36 (60)
149 PF09538 FYDLN_acid: Protein o 54.9 4.6 0.0001 35.2 0.4 10 452-461 11-20 (108)
150 PF11672 DUF3268: Protein of u 54.7 9.9 0.00021 32.8 2.3 42 451-506 3-44 (102)
151 PRK00260 cysS cysteinyl-tRNA s 54.4 11 0.00025 41.1 3.4 35 367-401 50-84 (463)
152 PF10571 UPF0547: Uncharacteri 54.4 5.4 0.00012 25.6 0.5 9 493-501 16-24 (26)
153 COG1655 Uncharacterized protei 54.2 3.6 7.8E-05 40.3 -0.4 43 452-498 21-69 (267)
154 PRK11827 hypothetical protein; 53.9 11 0.00025 29.2 2.3 11 451-461 9-19 (60)
155 PRK05654 acetyl-CoA carboxylas 53.2 7.7 0.00017 39.8 1.7 34 446-501 23-56 (292)
156 PLN02563 aminoacyl-tRNA ligase 52.9 21 0.00045 42.8 5.4 19 367-385 139-157 (963)
157 TIGR00435 cysS cysteinyl-tRNA 52.8 11 0.00023 41.4 2.9 35 367-401 48-82 (465)
158 TIGR00319 desulf_FeS4 desulfof 52.7 9.4 0.0002 25.8 1.5 13 489-501 5-17 (34)
159 PF04032 Rpr2: RNAse P Rpr2/Rp 51.8 21 0.00045 29.0 3.9 60 430-499 26-85 (85)
160 COG0215 CysS Cysteinyl-tRNA sy 51.6 12 0.00026 40.7 2.9 35 367-401 49-83 (464)
161 PF15446 zf-PHD-like: PHD/FYVE 51.4 18 0.00039 33.9 3.6 54 448-501 69-134 (175)
162 PRK12366 replication factor A; 51.3 7.2 0.00016 44.5 1.3 29 447-500 529-557 (637)
163 cd00974 DSRD Desulforedoxin (D 51.0 10 0.00022 25.6 1.5 13 489-501 2-14 (34)
164 PRK12380 hydrogenase nickel in 50.9 6.1 0.00013 34.7 0.5 31 430-460 41-80 (113)
165 PRK14535 cysS cysteinyl-tRNA s 50.6 13 0.00028 42.5 3.0 35 367-401 275-309 (699)
166 TIGR00305 probable toxin-antit 50.5 20 0.00043 30.9 3.7 28 385-412 85-113 (114)
167 TIGR00686 phnA alkylphosphonat 50.3 11 0.00023 32.8 1.8 27 451-501 3-29 (109)
168 PF10083 DUF2321: Uncharacteri 50.2 11 0.00025 34.7 2.1 55 451-520 40-98 (158)
169 PRK06386 replication factor A; 49.8 6.6 0.00014 41.5 0.6 19 442-460 227-246 (358)
170 PF13465 zf-H2C2_2: Zinc-finge 49.7 12 0.00027 23.6 1.7 15 488-502 11-25 (26)
171 PRK12496 hypothetical protein; 49.6 12 0.00027 35.0 2.3 93 365-461 60-154 (164)
172 cd00668 Ile_Leu_Val_MetRS_core 49.1 36 0.00078 34.9 6.0 41 367-407 28-68 (312)
173 KOG2041 WD40 repeat protein [G 49.0 27 0.00059 39.8 5.1 97 391-499 1061-1164(1189)
174 PRK00564 hypA hydrogenase nick 48.9 7.2 0.00016 34.4 0.6 19 442-460 63-81 (117)
175 PF12813 XPG_I_2: XPG domain c 48.9 19 0.00041 36.0 3.7 58 367-426 8-68 (246)
176 PHA02768 hypothetical protein; 48.7 8 0.00017 29.5 0.7 18 492-509 6-23 (55)
177 PRK06266 transcription initiat 48.5 11 0.00024 35.8 1.8 16 486-501 112-127 (178)
178 PHA00626 hypothetical protein 47.1 14 0.00031 28.2 1.9 17 488-504 20-36 (59)
179 COG5134 Uncharacterized conser 46.7 14 0.0003 35.9 2.2 20 441-460 32-52 (272)
180 PTZ00399 cysteinyl-tRNA-synthe 46.7 16 0.00034 41.8 3.1 35 367-401 87-122 (651)
181 PF04810 zf-Sec23_Sec24: Sec23 46.4 17 0.00036 25.7 2.1 31 451-500 3-33 (40)
182 PRK14534 cysS cysteinyl-tRNA s 46.3 15 0.00033 40.4 2.7 36 367-402 48-93 (481)
183 PF01783 Ribosomal_L32p: Ribos 46.2 16 0.00034 27.9 2.1 11 449-459 25-35 (56)
184 cd00350 rubredoxin_like Rubred 45.7 13 0.00027 25.1 1.3 11 491-501 1-11 (33)
185 PF09986 DUF2225: Uncharacteri 45.7 6.5 0.00014 38.4 -0.2 16 489-504 46-61 (214)
186 PRK03681 hypA hydrogenase nick 45.4 8.1 0.00017 34.0 0.4 31 430-460 41-80 (114)
187 PF01406 tRNA-synt_1e: tRNA sy 45.1 12 0.00026 38.5 1.6 36 367-402 35-70 (300)
188 COG1096 Predicted RNA-binding 45.0 11 0.00024 35.9 1.3 14 448-461 147-160 (188)
189 PF12172 DUF35_N: Rubredoxin-l 44.3 15 0.00033 25.2 1.6 15 489-503 9-23 (37)
190 TIGR00373 conserved hypothetic 43.4 19 0.00042 33.4 2.6 46 445-512 104-151 (158)
191 PHA02998 RNA polymerase subuni 43.0 21 0.00047 33.7 2.8 48 439-501 134-181 (195)
192 PRK00762 hypA hydrogenase nick 42.5 10 0.00022 33.9 0.6 30 430-460 41-79 (124)
193 TIGR00398 metG methionyl-tRNA 42.5 22 0.00047 39.5 3.4 35 367-401 27-61 (530)
194 TIGR00100 hypA hydrogenase nic 42.5 9.9 0.00022 33.4 0.5 19 442-460 62-80 (115)
195 PF14446 Prok-RING_1: Prokaryo 41.9 24 0.00052 26.8 2.4 27 450-501 5-31 (54)
196 TIGR00373 conserved hypothetic 41.8 16 0.00035 34.0 1.8 16 486-501 104-119 (158)
197 smart00834 CxxC_CXXC_SSSS Puta 41.6 15 0.00032 25.5 1.2 12 492-503 6-17 (41)
198 PF02150 RNA_POL_M_15KD: RNA p 40.9 14 0.00031 25.3 1.0 9 453-461 4-12 (35)
199 PF07282 OrfB_Zn_ribbon: Putat 40.8 44 0.00095 26.1 4.0 47 431-500 6-55 (69)
200 PRK10220 hypothetical protein; 40.4 20 0.00044 31.1 2.0 12 489-500 18-29 (111)
201 cd00674 LysRS_core_class_I cat 39.7 63 0.0014 34.2 6.0 18 367-384 46-63 (353)
202 PRK02261 methylaspartate mutas 39.4 39 0.00084 30.6 3.9 33 367-400 22-54 (137)
203 COG1412 Uncharacterized protei 39.3 77 0.0017 28.8 5.7 53 372-426 72-125 (136)
204 TIGR00354 polC DNA polymerase, 39.3 21 0.00045 42.0 2.5 10 451-460 1013-1022(1095)
205 PRK06266 transcription initiat 39.0 26 0.00057 33.3 2.8 34 445-500 112-145 (178)
206 PF07975 C1_4: TFIIH C1-like d 38.9 17 0.00036 27.4 1.2 13 489-501 19-31 (51)
207 PRK08402 replication factor A; 38.8 15 0.00032 38.8 1.2 30 448-500 210-239 (355)
208 smart00531 TFIIE Transcription 37.9 34 0.00074 31.3 3.3 39 445-500 94-132 (147)
209 cd05778 DNA_polB_zeta_exo inac 37.7 42 0.00091 33.1 4.2 51 159-209 175-230 (231)
210 TIGR01031 rpmF_bact ribosomal 37.4 23 0.0005 27.0 1.8 11 449-459 25-35 (55)
211 TIGR01206 lysW lysine biosynth 37.4 30 0.00065 26.3 2.3 30 451-501 3-32 (54)
212 PF09297 zf-NADH-PPase: NADH p 37.3 27 0.00058 23.2 1.9 12 490-501 20-31 (32)
213 cd00817 ValRS_core catalytic c 37.2 54 0.0012 34.9 5.2 18 367-384 29-46 (382)
214 cd00671 ArgRS_core catalytic c 36.9 22 0.00047 34.5 2.0 38 364-401 24-62 (212)
215 PRK05978 hypothetical protein; 36.9 19 0.00042 33.2 1.5 8 451-458 34-41 (148)
216 PRK14536 cysS cysteinyl-tRNA s 36.8 25 0.00053 38.9 2.5 36 367-402 50-95 (490)
217 PF08274 PhnA_Zn_Ribbon: PhnA 36.6 20 0.00043 23.9 1.1 12 489-500 17-28 (30)
218 PRK04023 DNA polymerase II lar 36.5 25 0.00055 41.6 2.6 10 451-460 1038-1047(1121)
219 PRK12495 hypothetical protein; 36.3 33 0.00071 33.6 3.0 14 491-504 58-71 (226)
220 PRK09521 exosome complex RNA-b 36.0 9.1 0.0002 36.5 -0.8 14 448-461 147-160 (189)
221 KOG2691 RNA polymerase II subu 35.7 39 0.00085 29.3 3.0 13 489-501 99-111 (113)
222 COG4416 Com Mu-like prophage p 35.7 14 0.0003 27.9 0.3 10 451-460 5-14 (60)
223 cd00802 class_I_aaRS_core cata 35.6 34 0.00073 30.7 2.9 33 367-399 25-57 (143)
224 PF13248 zf-ribbon_3: zinc-rib 35.6 21 0.00045 22.7 1.0 9 451-459 3-11 (26)
225 COG1571 Predicted DNA-binding 35.6 19 0.0004 38.8 1.3 31 450-504 350-380 (421)
226 PF13912 zf-C2H2_6: C2H2-type 35.4 24 0.00053 22.0 1.4 16 492-507 2-17 (27)
227 TIGR00592 pol2 DNA polymerase 35.4 1.5E+02 0.0032 36.6 9.0 102 102-213 599-723 (1172)
228 PRK12267 methionyl-tRNA synthe 35.3 35 0.00076 39.0 3.6 35 367-401 32-66 (648)
229 TIGR03831 YgiT_finger YgiT-typ 35.3 20 0.00043 25.4 1.0 17 488-504 29-45 (46)
230 PTZ00396 Casein kinase II subu 35.1 35 0.00076 34.3 3.1 52 431-503 106-160 (251)
231 PRK05452 anaerobic nitric oxid 34.8 18 0.00039 39.8 1.1 40 451-499 426-466 (479)
232 COG0266 Nei Formamidopyrimidin 34.5 21 0.00045 36.3 1.4 12 488-499 262-273 (273)
233 PRK03954 ribonuclease P protei 34.2 34 0.00074 30.5 2.6 59 431-501 45-103 (121)
234 PF07295 DUF1451: Protein of u 33.9 22 0.00048 32.7 1.4 12 450-461 112-123 (146)
235 PRK12496 hypothetical protein; 33.6 18 0.00039 33.9 0.8 11 491-501 127-137 (164)
236 PRK11032 hypothetical protein; 33.1 23 0.00049 33.2 1.3 10 451-460 125-134 (160)
237 PRK14873 primosome assembly pr 33.0 25 0.00053 40.4 1.9 27 490-516 421-449 (665)
238 PF01873 eIF-5_eIF-2B: Domain 32.9 36 0.00079 30.4 2.6 45 430-500 79-123 (125)
239 TIGR02300 FYDLN_acid conserved 32.7 25 0.00054 31.5 1.4 10 452-461 11-20 (129)
240 PF13913 zf-C2HC_2: zinc-finge 32.5 23 0.0005 22.3 0.9 11 492-502 3-13 (25)
241 PF03119 DNA_ligase_ZBD: NAD-d 32.4 23 0.0005 23.1 0.9 10 452-461 1-10 (28)
242 PF09845 DUF2072: Zn-ribbon co 32.2 28 0.0006 31.4 1.7 9 452-460 3-11 (131)
243 cd02067 B12-binding B12 bindin 32.1 66 0.0014 27.7 4.1 32 367-399 18-49 (119)
244 PRK14714 DNA polymerase II lar 32.1 32 0.00069 41.8 2.6 19 201-219 843-861 (1337)
245 COG4133 CcmA ABC-type transpor 32.0 26 0.00056 33.9 1.5 25 495-519 54-78 (209)
246 PRK03988 translation initiatio 32.0 54 0.0012 29.9 3.5 46 429-500 87-132 (138)
247 TIGR01501 MthylAspMutase methy 31.9 64 0.0014 29.2 4.0 37 367-404 20-56 (134)
248 PF01096 TFIIS_C: Transcriptio 31.8 31 0.00066 24.2 1.5 13 489-501 26-38 (39)
249 cd00758 MoCF_BD MoCF_BD: molyb 31.4 95 0.0021 27.5 5.1 48 359-407 15-66 (133)
250 PRK03673 hypothetical protein; 31.3 87 0.0019 33.6 5.6 50 358-407 16-68 (396)
251 PRK09678 DNA-binding transcrip 31.2 39 0.00085 27.3 2.2 36 451-501 2-39 (72)
252 KOG3092 Casein kinase II, beta 30.9 56 0.0012 31.5 3.5 57 433-509 94-153 (216)
253 PF09723 Zn-ribbon_8: Zinc rib 30.7 28 0.00061 24.8 1.2 10 492-501 6-15 (42)
254 COG3364 Zn-ribbon containing p 30.7 30 0.00066 29.7 1.5 10 450-459 20-29 (112)
255 COG1058 CinA Predicted nucleot 30.7 62 0.0013 32.6 4.0 49 359-407 17-68 (255)
256 COG0675 Transposase and inacti 30.4 57 0.0012 33.1 3.9 29 430-458 286-317 (364)
257 COG2023 RPR2 RNase P subunit R 30.1 45 0.00098 28.9 2.5 53 433-501 39-92 (105)
258 cd02072 Glm_B12_BD B12 binding 29.8 74 0.0016 28.6 4.0 34 367-401 18-51 (128)
259 PTZ00255 60S ribosomal protein 29.6 37 0.0008 28.6 1.9 16 490-505 53-68 (90)
260 PRK14810 formamidopyrimidine-D 29.3 29 0.00063 35.2 1.5 12 488-499 261-272 (272)
261 TIGR00280 L37a ribosomal prote 29.3 36 0.00078 28.8 1.7 16 490-505 52-67 (91)
262 PRK12286 rpmF 50S ribosomal pr 28.8 36 0.00078 26.1 1.6 10 450-459 27-36 (57)
263 PF03966 Trm112p: Trm112p-like 28.7 29 0.00064 27.3 1.1 14 488-501 50-63 (68)
264 cd00924 Cyt_c_Oxidase_Vb Cytoc 28.7 33 0.00071 29.4 1.5 14 488-501 76-89 (97)
265 PF11781 RRN7: RNA polymerase 28.6 40 0.00086 23.4 1.6 12 489-500 23-34 (36)
266 smart00653 eIF2B_5 domain pres 28.5 60 0.0013 28.4 3.1 44 430-499 66-109 (110)
267 PF12760 Zn_Tnp_IS1595: Transp 28.5 1.2E+02 0.0027 21.8 4.3 11 489-499 35-45 (46)
268 COG3357 Predicted transcriptio 28.5 35 0.00075 28.8 1.5 16 447-462 73-88 (97)
269 PRK07111 anaerobic ribonucleos 28.3 49 0.0011 38.5 3.2 29 430-458 656-688 (735)
270 PRK00241 nudC NADH pyrophospha 28.1 45 0.00098 33.5 2.6 32 450-504 99-130 (256)
271 TIGR02605 CxxC_CxxC_SSSS putat 27.8 33 0.00071 25.3 1.2 10 492-501 6-15 (52)
272 PF01214 CK_II_beta: Casein ki 27.7 60 0.0013 31.1 3.2 52 431-503 85-139 (184)
273 COG2824 PhnA Uncharacterized Z 27.7 36 0.00078 29.5 1.5 16 484-500 14-29 (112)
274 PRK14890 putative Zn-ribbon RN 27.5 63 0.0014 25.1 2.6 11 451-461 8-18 (59)
275 PRK14811 formamidopyrimidine-D 27.4 31 0.00068 34.9 1.3 14 488-501 252-265 (269)
276 PF01807 zf-CHC2: CHC2 zinc fi 27.3 30 0.00066 29.3 1.0 47 433-499 15-62 (97)
277 KOG3277 Uncharacterized conser 27.3 38 0.00083 31.3 1.7 33 451-499 80-112 (165)
278 PRK08271 anaerobic ribonucleos 27.2 68 0.0015 36.6 4.0 71 418-517 528-604 (623)
279 cd00885 cinA Competence-damage 27.1 92 0.002 29.2 4.4 49 358-407 14-66 (170)
280 PRK13945 formamidopyrimidine-D 27.0 36 0.00077 34.7 1.7 12 488-499 271-282 (282)
281 PF04959 ARS2: Arsenite-resist 26.9 42 0.00091 32.9 2.1 28 479-507 65-92 (214)
282 smart00440 ZnF_C2C2 C2C2 Zinc 26.8 39 0.00084 23.9 1.3 13 489-501 26-38 (40)
283 PRK03670 competence damage-ind 26.5 97 0.0021 31.1 4.6 24 359-382 16-39 (252)
284 PF04606 Ogr_Delta: Ogr/Delta- 26.4 40 0.00086 24.6 1.4 35 452-501 1-37 (47)
285 PF09332 Mcm10: Mcm10 replicat 26.0 37 0.0008 35.7 1.6 58 430-499 235-293 (344)
286 TIGR03599 YloV DAK2 domain fus 25.9 3.5E+02 0.0077 30.3 9.3 81 357-437 315-404 (530)
287 PRK08579 anaerobic ribonucleos 25.7 57 0.0012 37.2 3.1 30 430-459 544-577 (625)
288 PF12171 zf-C2H2_jaz: Zinc-fin 25.6 33 0.00072 21.6 0.7 11 492-502 2-12 (27)
289 COG1499 NMD3 NMD protein affec 25.5 77 0.0017 33.5 3.8 20 489-509 41-60 (355)
290 PF04900 Fcf1: Fcf1; InterPro 25.2 1.2E+02 0.0026 25.6 4.4 39 388-426 53-93 (101)
291 PLN02294 cytochrome c oxidase 25.1 36 0.00077 32.1 1.1 13 489-501 139-151 (174)
292 PRK08270 anaerobic ribonucleos 25.1 30 0.00065 39.6 0.8 29 430-458 601-634 (656)
293 COG1645 Uncharacterized Zn-fin 25.1 55 0.0012 29.6 2.3 10 452-461 30-39 (131)
294 COG1326 Uncharacterized archae 24.6 64 0.0014 31.0 2.7 15 488-502 27-41 (201)
295 PRK10445 endonuclease VIII; Pr 24.3 42 0.0009 33.9 1.6 28 451-499 236-263 (263)
296 PHA02325 hypothetical protein 24.3 37 0.0008 26.6 0.9 14 492-505 4-23 (72)
297 cd02071 MM_CoA_mut_B12_BD meth 24.2 1.1E+02 0.0023 26.8 4.0 32 367-399 18-49 (122)
298 PF01155 HypA: Hydrogenase exp 24.1 14 0.00029 32.4 -1.7 31 430-460 41-80 (113)
299 PHA02540 61 DNA primase; Provi 24.1 70 0.0015 33.6 3.2 52 432-499 9-63 (337)
300 PRK01103 formamidopyrimidine/5 24.1 43 0.00092 34.0 1.6 12 488-499 262-273 (274)
301 COG2185 Sbm Methylmalonyl-CoA 24.0 93 0.002 28.6 3.6 72 367-460 31-103 (143)
302 PF13277 YmdB: YmdB-like prote 23.9 76 0.0016 31.9 3.2 39 366-404 46-84 (253)
303 cd02070 corrinoid_protein_B12- 23.9 1E+02 0.0022 29.6 4.1 33 367-400 101-133 (201)
304 PF09706 Cas_CXXC_CXXC: CRISPR 23.7 28 0.00061 27.7 0.2 24 478-501 38-61 (69)
305 PF03698 UPF0180: Uncharacteri 23.7 1.1E+02 0.0023 25.3 3.5 42 358-407 3-44 (80)
306 TIGR00311 aIF-2beta translatio 23.4 98 0.0021 28.0 3.6 26 429-460 82-107 (133)
307 TIGR01391 dnaG DNA primase, ca 23.4 70 0.0015 34.5 3.2 52 433-507 16-68 (415)
308 COG0495 LeuS Leucyl-tRNA synth 23.4 1.3E+02 0.0027 35.5 5.3 35 367-401 62-96 (814)
309 TIGR00640 acid_CoA_mut_C methy 23.2 1.1E+02 0.0024 27.5 3.9 32 368-400 22-53 (132)
310 PF01215 COX5B: Cytochrome c o 23.1 38 0.00083 30.8 0.9 13 489-501 110-122 (136)
311 TIGR01384 TFS_arch transcripti 22.9 56 0.0012 27.8 1.9 12 491-502 16-27 (104)
312 PRK05667 dnaG DNA primase; Val 22.8 77 0.0017 35.8 3.5 47 433-499 18-65 (580)
313 cd06167 LabA_like LabA_like pr 22.7 2.6E+02 0.0057 24.7 6.4 63 365-427 54-132 (149)
314 PF08790 zf-LYAR: LYAR-type C2 22.6 65 0.0014 21.2 1.6 15 493-507 2-16 (28)
315 PF05180 zf-DNL: DNL zinc fing 22.4 26 0.00056 27.8 -0.3 33 453-501 7-39 (66)
316 PF14311 DUF4379: Domain of un 22.4 53 0.0011 24.6 1.4 18 487-505 24-41 (55)
317 cd04476 RPA1_DBD_C RPA1_DBD_C: 22.3 49 0.0011 30.6 1.5 30 448-501 32-61 (166)
318 COG1487 VapC Predicted nucleic 22.0 1.3E+02 0.0028 26.5 4.1 42 365-412 79-121 (133)
319 KOG2186 Cell growth-regulating 21.9 35 0.00076 34.1 0.4 42 450-506 3-44 (276)
320 PF10609 ParA: ParA/MinD ATPas 21.7 57 0.0012 27.0 1.6 14 488-501 62-75 (81)
321 PRK12336 translation initiatio 21.7 1E+02 0.0022 29.9 3.6 26 429-460 83-108 (201)
322 PRK00398 rpoP DNA-directed RNA 21.6 53 0.0012 23.7 1.3 11 491-501 3-13 (46)
323 PRK14715 DNA polymerase II lar 21.5 66 0.0014 39.4 2.6 9 451-460 1543-1551(1627)
324 PF05991 NYN_YacP: YacP-like N 21.3 1.8E+02 0.0039 27.1 5.1 62 373-436 64-130 (166)
325 COG1997 RPL43A Ribosomal prote 21.3 52 0.0011 27.6 1.3 18 489-506 51-68 (89)
326 COG0375 HybF Zn finger protein 21.3 47 0.001 29.3 1.1 31 430-460 41-80 (115)
327 COG0777 AccD Acetyl-CoA carbox 21.2 29 0.00064 35.1 -0.2 31 447-499 25-55 (294)
328 COG5041 SKB2 Casein kinase II, 21.1 93 0.002 30.2 3.1 52 432-503 108-161 (242)
329 PF09855 DUF2082: Nucleic-acid 21.0 27 0.00059 27.5 -0.4 14 489-502 34-47 (64)
330 COG1594 RPB9 DNA-directed RNA 21.0 51 0.0011 28.9 1.2 13 489-501 98-110 (113)
331 KOG1701 Focal adhesion adaptor 20.9 37 0.00081 36.4 0.5 43 451-501 395-437 (468)
332 PRK14704 anaerobic ribonucleos 20.8 81 0.0018 35.9 3.1 28 431-458 536-567 (618)
333 PF06906 DUF1272: Protein of u 20.7 57 0.0012 25.0 1.3 15 451-465 42-56 (57)
334 TIGR00244 transcriptional regu 20.6 61 0.0013 29.9 1.7 21 490-513 27-47 (147)
335 PF01780 Ribosomal_L37ae: Ribo 20.5 56 0.0012 27.6 1.3 16 490-505 52-67 (90)
336 PTZ00043 cytochrome c oxidase 20.4 52 0.0011 32.4 1.2 16 486-501 176-191 (268)
337 smart00355 ZnF_C2H2 zinc finge 20.3 38 0.00082 20.0 0.2 10 492-501 1-10 (26)
338 COG2331 Uncharacterized protei 20.2 47 0.001 27.1 0.8 23 433-460 21-43 (82)
339 PF03833 PolC_DP2: DNA polymer 20.2 34 0.00075 39.8 0.0 11 370-380 557-567 (900)
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=1.5e-46 Score=344.78 Aligned_cols=146 Identities=36% Similarity=0.719 Sum_probs=134.1
Q ss_pred CEEEEccccHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecChhHHHhhhhcCceEEEEccCChHHHHHHH
Q 009948 357 PKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQLLEV 436 (522)
Q Consensus 357 ~rfl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~RiiLTrd~~l~~~~~~~~~~~~~v~~~~~~eQl~~v 436 (522)
||||||.|||+||||||++||||++..+ .+|.+++++|++|+|||||+|++|+++....++ ++++.++++.+||.+|
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 MRFLVDAMLGRLARWLRLLGYDTLYSRD--IDDDEILELAREEGRILLTRDRDLLKRRRVSGG-VILIRSDDPEEQLREV 77 (147)
T ss_pred CEEEEeCCHHHHHHHHHHCCCcEEEeCC--CChHHHHHHhhhCCeEEEECCHHHHHHhhccCC-EEEEcCCCHHHHHHHH
Confidence 7999999999999999999999998864 588999999999999999999999988765544 7888999999999999
Q ss_pred HHHcccccccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeEeccchhhHHHHH
Q 009948 437 IEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEGTQYHNAVQK 513 (522)
Q Consensus 437 ~~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~GsH~~~~~~~ 513 (522)
+++|++.+.+++.||||+.||++|. +++++++. +.||++|++.+++||+|++||||||+||||+||.++
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 67777764 479999999999999999999999999999999985
No 2
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=6e-45 Score=329.80 Aligned_cols=156 Identities=29% Similarity=0.547 Sum_probs=140.9
Q ss_pred CCCCEEEEccccHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecChhHHHhhhhcCceEEEEccCChHHHH
Q 009948 354 DGYPKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQL 433 (522)
Q Consensus 354 ~~~~rfl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~RiiLTrd~~l~~~~~~~~~~~~~v~~~~~~eQl 433 (522)
.+.|||+||+|||+||||||++||||++.++ .+|.+++.+|..|||||||||+.|+++. +.+..+++|+++++++|+
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 MGEMKFVVDAMLGKLARWLRLLGYDTVYSSN--ESDDEIILIAKKEGRILLTRDRELYKRA-KLGIKAILIRSDSIEEQL 80 (165)
T ss_pred ccceeeeHHHhHHHHHHHHHHcCCceeeecc--CCcHHHHHHHhcCCeEEEeccHHHHHHh-hccCceEEEeCCCHHHHH
Confidence 4578999999999999999999999998753 4788999999999999999999999987 556789999999999999
Q ss_pred HHHHHHcccccccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeEeccchhhHHHHH
Q 009948 434 LEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEGTQYHNAVQK 513 (522)
Q Consensus 434 ~~v~~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~GsH~~~~~~~ 513 (522)
.+++.+|++.......|+||+.||++|. ++++|++++ .||+.|+..+++||+|+.|||+||.||||++|.+.
T Consensus 81 ~e~~~~~~l~~~~~~e~~RCp~CN~~L~--~vs~eev~~------~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw~~m~~~ 152 (165)
T COG1656 81 AEFLARLGLKPRLFPEFSRCPECNGELE--KVSREEVKE------KVPEKVYRNYEEFYRCPKCGKIYWKGSHWRRMVER 152 (165)
T ss_pred HHHHHHhccchhcccccccCcccCCEec--cCcHHHHhh------ccchhhhhcccceeECCCCcccccCchHHHHHHHH
Confidence 9999999988755555999999999996 688999874 79999999999999999999999999999999998
Q ss_pred HHHhccc
Q 009948 514 FIDVCKL 520 (522)
Q Consensus 514 ~~~~~~~ 520 (522)
+.+.++-
T Consensus 153 ~~~~~~~ 159 (165)
T COG1656 153 IVENLRP 159 (165)
T ss_pred HHHHhcc
Confidence 8776653
No 3
>PRK10829 ribonuclease D; Provisional
Probab=99.97 E-value=4.1e-31 Score=275.51 Aligned_cols=215 Identities=21% Similarity=0.307 Sum_probs=183.7
Q ss_pred cEEEEcCCChHHHHHHHHHhcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCc
Q 009948 10 KIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPL 89 (522)
Q Consensus 10 ~i~~I~t~~~~el~~l~~~L~~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~ 89 (522)
.|++|++ ++++.++++.+...++||||+|+.+... |.+++|||||++. +.+|+||+..+.
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 7899999999974 679999998774
Q ss_pred hhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHH
Q 009948 90 PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (522)
Q Consensus 90 ~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~ 169 (522)
.+..|+++|+|++|+||+|++++|+..|.+.+|+ . ..++|| |++|+.+++.+ .+.||+.|++
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 2678999999999999999999999999777655 2 379999 99999999853 3689999999
Q ss_pred HHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---ccchhhcccCcc--CCCCCCCccc
Q 009948 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS---CSSISELDSSNL--DLGLKGILEK 244 (522)
Q Consensus 170 ~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~---~~~~~~~~~~~~--~~~~~~~~~~ 244 (522)
++||+.++|+++.+||..|||+++|+.|||.||++++.||+.|.++|.+.|.+ .+||..+..... ......|++.
T Consensus 124 ~~lgv~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g~~~w~~ee~~~l~~~~~~~~~~~~~~~~i 203 (373)
T PRK10829 124 EYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGWLPAALDECRLLCQRRQEVLAPEEAYRDI 203 (373)
T ss_pred HHhCCccCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHhccccCCChHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999987 788888754211 1112347777
Q ss_pred CCCCCcchhhhhhhHHHHHHHhh
Q 009948 245 PDIGNKTVRFKLCEALDIIRATS 267 (522)
Q Consensus 245 ~~~~~~~~~~~~~~~~~~~~~~~ 267 (522)
.+.+ +.+ +++++++|+++
T Consensus 204 k~~~----~L~-~~~lavl~~L~ 221 (373)
T PRK10829 204 TNAW----QLR-TRQLACLQLLA 221 (373)
T ss_pred cccc----CCC-HHHHHHHHHHH
Confidence 6554 333 88999999994
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=1.1e-29 Score=243.56 Aligned_cols=184 Identities=46% Similarity=0.765 Sum_probs=150.1
Q ss_pred EEEEcCCChHHHHHHHHH--hcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCC
Q 009948 11 IHLVTSTESPEFTHLARA--LSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIP 88 (522)
Q Consensus 11 i~~I~t~~~~el~~l~~~--L~~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~ 88 (522)
||+|++ ++++.+++.. +....+||||+||.+.+.. +..++++|||||+. +.+|+||+..++
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 588998 8999999999 8899999999999988742 12578999999985 689999998765
Q ss_pred ---chhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCC---CCCcCcc
Q 009948 89 ---LPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGR---KLPKETK 162 (522)
Q Consensus 89 ---~~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~---~~~~~~~ 162 (522)
...+.+.|+++|+|++|+||||++++|+..|++.||+.+.. +....+++|+..++..+.....++ ..+....
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 23467789999999999999999999999999888762100 012489999545555554322111 1113478
Q ss_pred cHHHHHHHHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009948 163 SLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 163 gL~~L~~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~ 213 (522)
||++|++++||.+++|..|+|||+.|||+++|+.|||.||+++++||+.|.
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 999999999999999999999999999999999999999999999999986
No 5
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=1.4e-29 Score=257.90 Aligned_cols=215 Identities=24% Similarity=0.289 Sum_probs=185.9
Q ss_pred hHHHHHHHHHhcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHH
Q 009948 19 SPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKE 98 (522)
Q Consensus 19 ~~el~~l~~~L~~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~ 98 (522)
.+.++.++..+.+.+.|++|+|+...++ +.+++|||||+.. +++++||+.... .-+..|..
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 4678888889999999999999998885 8899999999985 348999988732 13678999
Q ss_pred hhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcCCcccc
Q 009948 99 LFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSK 178 (522)
Q Consensus 99 lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~K 178 (522)
+|.|++|+||+|.+.+|+..|.+.||. . ..++|| |++|+.+++.+ .++||++||++++|++++|
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 999999999999999999999998754 2 489999 99999999875 4899999999999999999
Q ss_pred ccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---ccchhhcccC--ccCCCCCCCcccCCCCCcchh
Q 009948 179 ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS---CSSISELDSS--NLDLGLKGILEKPDIGNKTVR 253 (522)
Q Consensus 179 ~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~---~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~ 253 (522)
++|.|||..||||++|+.|||.||.||+.||+.|.++|.++|.+ .+||..+.+. ......+.|++.... .
T Consensus 129 ~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r~~~a~~ef~~l~~r~~~~~~~~~~w~~i~~a-----~ 203 (361)
T COG0349 129 SEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAREGRLEWAEDEFRLLPTRRTYKVLPEDAWREIKIA-----H 203 (361)
T ss_pred cccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHhhhccccccChHhHHHHhhhh-----h
Confidence 99999999999999999999999999999999999999999998 8899999776 454677789987652 3
Q ss_pred hhhhhHHHHHHHhhcccccC
Q 009948 254 FKLCEALDIIRATSYYSQCL 273 (522)
Q Consensus 254 ~~~~~~~~~~~~~~~~~~~~ 273 (522)
...+++++++|.++.-..++
T Consensus 204 ~~~p~~la~l~~La~wRe~~ 223 (361)
T COG0349 204 SLDPRELAVLRELAAWRERE 223 (361)
T ss_pred cCChHHHHHHHHHHHHHHHH
Confidence 46688999999995443333
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=1.3e-28 Score=229.45 Aligned_cols=158 Identities=34% Similarity=0.573 Sum_probs=140.0
Q ss_pred HHHHHHHhc-CCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhh
Q 009948 22 FTHLARALS-QSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELF 100 (522)
Q Consensus 22 l~~l~~~L~-~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL 100 (522)
++++++.+. ..++||||+||.+.+. +.+++|+||||+. ++.+|+||+..++. .+..|+++|
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 26899999987652 467899999
Q ss_pred CCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcCCcccccc
Q 009948 101 VSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKEL 180 (522)
Q Consensus 101 ~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~K~~ 180 (522)
+|++|+||||++++|+..|.+.+|+ . ..++|| +++++|++++. .+.||+.+++++||.+++|..
T Consensus 64 ~d~~i~Kvg~~~k~D~~~L~~~~gi-~-------~~~~~D-~~~aa~ll~~~-------~~~~L~~l~~~~lg~~l~K~~ 127 (161)
T cd06129 64 ENPSIVKALHGIEGDLWKLLRDFGE-K-------LQRLFD-TTIAANLKGLP-------ERWSLASLVEHFLGKTLDKSI 127 (161)
T ss_pred CCCCEEEEEeccHHHHHHHHHHcCC-C-------cccHhH-HHHHHHHhCCC-------CCchHHHHHHHHhCCCCCccc
Confidence 9999999999999999999876665 1 367799 89999999863 357999999999999999999
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009948 181 QCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 181 q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~ 213 (522)
++|||+.|||+++|+.|||.||++++.||+.|.
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 999999999999999999999999999999985
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=99.95 E-value=2.7e-27 Score=247.83 Aligned_cols=211 Identities=23% Similarity=0.343 Sum_probs=176.7
Q ss_pred EcCCChHHHHHHHHHhcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhH
Q 009948 14 VTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIW 93 (522)
Q Consensus 14 I~t~~~~el~~l~~~L~~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~ 93 (522)
|++ .+++.++++.+...++||||+||.+... +.+++|||||++. +.+|+||+..+. .+
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 7899999999999999999999988764 7889999999984 689999998763 36
Q ss_pred HHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcC
Q 009948 94 ELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLD 173 (522)
Q Consensus 94 ~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg 173 (522)
..|+++|+|++|.||+|++++|+..|.+.++. ..+++|| |++|+|+++++ .+.||+.|++++||
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 99999999874 35799999999999
Q ss_pred CccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---ccchhhcccCcc-C-CCCCCCcccCCCC
Q 009948 174 ISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS---CSSISELDSSNL-D-LGLKGILEKPDIG 248 (522)
Q Consensus 174 ~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~---~~~~~~~~~~~~-~-~~~~~~~~~~~~~ 248 (522)
+.++|+++.+||..|||+.+|+.|||.||++++.||+.|.++|++.|.+ .+||..+.+... . ..-..|.+..+.+
T Consensus 124 ~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~~~g~~~w~~ee~~~l~~~~~~~~~~~~~~~~i~~~~ 203 (367)
T TIGR01388 124 VELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLEESGRLAWLEEECTLLTDRRTYVVNPEDAWRDIKNAW 203 (367)
T ss_pred CCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHhccccCCCChHHHHHHhcccc
Confidence 9999999999999999999999999999999999999999999999987 888887754321 1 1122466655433
Q ss_pred CcchhhhhhhHHHHHHHhh
Q 009948 249 NKTVRFKLCEALDIIRATS 267 (522)
Q Consensus 249 ~~~~~~~~~~~~~~~~~~~ 267 (522)
+. .+++++++|+++
T Consensus 204 ----~l-~~~~l~~l~~L~ 217 (367)
T TIGR01388 204 ----QL-RPQQLAVLQALA 217 (367)
T ss_pred ----cC-CHHHHHHHHHHH
Confidence 22 378899999883
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=216.61 Aligned_cols=163 Identities=33% Similarity=0.523 Sum_probs=142.3
Q ss_pred hHHHHHHHHHhc-CCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHH
Q 009948 19 SPEFTHLARALS-QSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLK 97 (522)
Q Consensus 19 ~~el~~l~~~L~-~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~ 97 (522)
.++++.+++.+. ...+||||+||.+.+.. +..+++++||||+. +.+|+||+..+. .+...|+
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 577889999998 99999999999987631 24678999999984 689999988763 3567899
Q ss_pred HhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcCCccc
Q 009948 98 ELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS 177 (522)
Q Consensus 98 ~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~ 177 (522)
++|++++|.||||++++|+..|.+.||+ . ..++|| +++++|++++. ....||++|++.+||.+++
T Consensus 67 ~ll~~~~i~kv~~~~k~D~~~L~~~~g~-~-------~~~~~D-l~~aa~ll~~~------~~~~~l~~l~~~~l~~~~~ 131 (170)
T cd06141 67 QLLEDPSILKVGVGIKGDARKLARDFGI-E-------VRGVVD-LSHLAKRVGPR------RKLVSLARLVEEVLGLPLS 131 (170)
T ss_pred HHhcCCCeeEEEeeeHHHHHHHHhHcCC-C-------CCCeee-HHHHHHHhCCC------cCCccHHHHHHHHcCcccC
Confidence 9999999999999999999999877765 1 367899 89999999874 2346999999999999998
Q ss_pred --cccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009948 178 --KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 178 --K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~ 213 (522)
|..++|||..|||+++|+.|||.||++++.||+.|.
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 788999999999999999999999999999999985
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=2.5e-26 Score=221.14 Aligned_cols=170 Identities=25% Similarity=0.327 Sum_probs=141.8
Q ss_pred HHHHhcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCC
Q 009948 25 LARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPD 104 (522)
Q Consensus 25 l~~~L~~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~~~~ 104 (522)
+++.+..+++||||+||.+.+. .+++||||||+. .+.+||||+..++...+...|+++|++++
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 4566778999999999986653 468999999995 27999999998754346788999999999
Q ss_pred ceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccC-CCCCcCcccHHHHHHHHcCCcccc-----
Q 009948 105 ILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLG-RKLPKETKSLANICKELLDISLSK----- 178 (522)
Q Consensus 105 i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~-~~~~~~~~gL~~L~~~~Lg~~L~K----- 178 (522)
|.|||||++.|+..|.+.||+ . ..++|| |++|+|++++... ...+....||+++++++||.+++|
T Consensus 66 i~Kv~h~~k~D~~~L~~~~gi---~-----~~~~fD-t~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~ 136 (197)
T cd06148 66 ILKVIHDCRRDSDALYHQYGI---K-----LNNVFD-TQVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVK 136 (197)
T ss_pred ccEEEEechhHHHHHHHhcCc---c-----ccceee-HHHHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHH
Confidence 999999999999999766665 1 367899 8999999987421 111223469999999999999865
Q ss_pred ---ccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 009948 179 ---ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKG 220 (522)
Q Consensus 179 ---~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g 220 (522)
..+++||..|||+++|+.|||.||++++.||+.|...|.+..
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 467899999999999999999999999999999999998763
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=9.5e-25 Score=204.07 Aligned_cols=174 Identities=29% Similarity=0.451 Sum_probs=150.1
Q ss_pred EEEEcCCChHHHHHHHHHhcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCch
Q 009948 11 IHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLP 90 (522)
Q Consensus 11 i~~I~t~~~~el~~l~~~L~~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~ 90 (522)
|++|++ .+++.+++..+...+++|||+||.+.... .....++++|+++. +.+|+++.......
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 89999999999999999999999987742 24678999999984 68889887765532
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
.++..|+++|++++|.|||||+++|+..|.+.+|+ ...+++| ++++++++++. ..+||++|+.+
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 36789999999999999999999999999987655 2478999 69999999875 33899999999
Q ss_pred HcC-CccccccccCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009948 171 LLD-ISLSKELQCSDWS-NRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (522)
Q Consensus 171 ~Lg-~~L~K~~q~sdW~-~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~ 217 (522)
++| ..++|..+.++|. .+||+++|+.|||.||+++++||+.|.++|+
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 7788899999999 8999999999999999999999999998874
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=99.82 E-value=5.2e-19 Score=166.16 Aligned_cols=164 Identities=31% Similarity=0.514 Sum_probs=135.0
Q ss_pred HHHHHHhcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCC
Q 009948 23 THLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVS 102 (522)
Q Consensus 23 ~~l~~~L~~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~~ 102 (522)
.++++.+...+.+|+|+|+.+..+ ..++++++|+++. +.+|+||+... .....|+++|++
T Consensus 3 ~~~~~~l~~~~~l~~~~e~~~~~~---~~~~~~~i~l~~~--------------~~~~~i~~~~~---~~~~~l~~ll~~ 62 (178)
T cd06142 3 EDLCERLASAGVIAVDTEFMRLNT---YYPRLCLIQISTG--------------GEVYLIDPLAI---GDLSPLKELLAD 62 (178)
T ss_pred HHHHHHHhcCCeEEEECCccCCCc---CCCceEEEEEeeC--------------CCEEEEeCCCc---ccHHHHHHHHcC
Confidence 444555555669999999865542 3467899999973 34888885532 256678999999
Q ss_pred CCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcCCcccccccc
Q 009948 103 PDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQC 182 (522)
Q Consensus 103 ~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~K~~q~ 182 (522)
+++.|||||+|.|++.|.++||+ . .++++| +++++|++++. .+++|+++++++||..+.+....
T Consensus 63 ~~i~kv~~d~K~~~~~L~~~~gi-------~-~~~~~D-~~laayLl~p~-------~~~~l~~l~~~~l~~~~~~~~~~ 126 (178)
T cd06142 63 PNIVKVFHAAREDLELLKRDFGI-------L-PQNLFD-TQIAARLLGLG-------DSVGLAALVEELLGVELDKGEQR 126 (178)
T ss_pred CCceEEEeccHHHHHHHHHHcCC-------C-CCCccc-HHHHHHHhCCC-------ccccHHHHHHHHhCCCCCccccc
Confidence 99999999999999999886665 2 367899 89999999985 34699999999999987666688
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009948 183 SDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (522)
Q Consensus 183 sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~ 222 (522)
++|..+|++.+|+.|||.||+++++|++.|.++|++.|+.
T Consensus 127 ~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~e~~l~ 166 (178)
T cd06142 127 SDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEEEGRL 166 (178)
T ss_pred ccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCcH
Confidence 9999999999999999999999999999999999988765
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=99.75 E-value=9e-17 Score=148.99 Aligned_cols=169 Identities=32% Similarity=0.434 Sum_probs=131.8
Q ss_pred EEEcCCChHHHHHHHHHhc-CCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCch
Q 009948 12 HLVTSTESPEFTHLARALS-QSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLP 90 (522)
Q Consensus 12 ~~I~t~~~~el~~l~~~L~-~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~ 90 (522)
.+|++ .+++..++..+. ....+++|+|+.+... ....++++|++.. ++.+|+++.... .
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 667777666665 5669999999876553 3467899999963 235676554322 2
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
.....|+++|+++++.|||||+|.|+..|.+ +|+ . ..+++| +++++|++++. ....+|+.++++
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 665 2 245699 99999999875 233699999999
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKV 216 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L 216 (522)
++|..+++..+.++|..+|+...|+.||+.||+++++|++.|.++|
T Consensus 126 ~l~~~~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 126 YLGVELDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred HhCCCCCcccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 9998876544556897788999999999999999999999998776
No 13
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.73 E-value=4.6e-18 Score=180.69 Aligned_cols=195 Identities=31% Similarity=0.498 Sum_probs=149.0
Q ss_pred CCCCccEEEEcCCChHHHHHHH-HHhcCC-CeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEE
Q 009948 5 YRKPLKIHLVTSTESPEFTHLA-RALSQS-SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLL 82 (522)
Q Consensus 5 ~~~~~~i~~I~t~~~~el~~l~-~~L~~~-~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~li 82 (522)
++....|++|++ +.++..++ +.+..+ -+||+|+||.+.-. ....+++++|+++. +.+|||
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--VSDSKLAILQIFFK--------------DCVYLI 447 (617)
T ss_pred CCcccceeeeCC--HHHHHHHHHHHhhhcCEEEEEccccCcccC--CChhHHHHHHHHhc--------------CeEEEe
Confidence 455567888988 78888776 456655 78999999998732 24679999999984 799999
Q ss_pred eCCCCC--chhhHH-HHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccc-CCCCC
Q 009948 83 DLSSIP--LPSIWE-LLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQL-GRKLP 158 (522)
Q Consensus 83 D~~~l~--~~~~~~-~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~-~~~~~ 158 (522)
|..++. .++.|. .+..+|++++|.|||+++.+|+..|.++.|.+...-.+...++++++..++..+.+-.. ....+
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 987653 245565 45679999999999999999999998644421110011234556666777766654321 11233
Q ss_pred cCcccHHHHHHHHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009948 159 KETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (522)
Q Consensus 159 ~~~~gL~~L~~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~ 217 (522)
....+|+.|....||.+++|++|||||..|||+..|+.|||.||.++..++..+....+
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 45789999999999999999999999999999999999999999999999999986544
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=1.3e-15 Score=145.92 Aligned_cols=173 Identities=25% Similarity=0.400 Sum_probs=132.2
Q ss_pred ccEEEEcCCChHHHHHHHHHhcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCC
Q 009948 9 LKIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIP 88 (522)
Q Consensus 9 ~~i~~I~t~~~~el~~l~~~L~~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~ 88 (522)
.+|.+|++ ++++..+++.+...+.+++++|..+..+ ....+..+|++.. +++|+|++..
T Consensus 3 ~~~~~i~~--~~~l~~~~~~l~~~~~l~~~~e~~~~~~---~~~~~~~l~l~~~--------------~~~~~i~~l~-- 61 (192)
T cd06147 3 TPLTFVDT--EEKLEELVEKLKNCKEIAVDLEHHSYRS---YLGFTCLMQISTR--------------EEDYIVDTLK-- 61 (192)
T ss_pred CCcEEECC--HHHHHHHHHHHhcCCeEEEEeEecCCcc---CCCceEEEEEecC--------------CCcEEEEecc--
Confidence 56788865 4667776666655569999998654332 2356778888874 2477777422
Q ss_pred chhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHH
Q 009948 89 LPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANIC 168 (522)
Q Consensus 89 ~~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~ 168 (522)
.......|+++|+++++.|+|||+|.|+..|.+.+|+ . ..+.|| ++|++||++++ +++|+.++
T Consensus 62 ~~~~~~~L~~~L~~~~i~kv~~d~K~~~~~L~~~~gi-~-------~~~~fD-~~laaYLL~p~--------~~~l~~l~ 124 (192)
T cd06147 62 LRDDMHILNEVFTDPNILKVFHGADSDIIWLQRDFGL-Y-------VVNLFD-TGQAARVLNLP--------RHSLAYLL 124 (192)
T ss_pred cccchHHHHHHhcCCCceEEEechHHHHHHHHHHhCC-C-------cCchHH-HHHHHHHhCCC--------cccHHHHH
Confidence 2223556889999999999999999999999733454 1 133499 99999999983 35999999
Q ss_pred HHHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 009948 169 KELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (522)
Q Consensus 169 ~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~ 219 (522)
++|||..++|..+.++|+.+||..+|..||+.+|.++++|++.|.++|+++
T Consensus 125 ~~yl~~~~~k~~~~~~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~L~e~ 175 (192)
T cd06147 125 QKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELLER 175 (192)
T ss_pred HHHhCCCcchhhhccccccCCCCHHHHHHHHhhHHHHHHHHHHHHHHHHHh
Confidence 999998754545667898888899999999999999999999999999876
No 15
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.66 E-value=1.1e-18 Score=185.32 Aligned_cols=382 Identities=32% Similarity=0.422 Sum_probs=263.2
Q ss_pred CCceeeHHH--HHHHhhccccCCCCCcC-cc---cHHHHHHHHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHH-
Q 009948 135 VEPYLDITS--IYNHLHHKQLGRKLPKE-TK---SLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIE- 207 (522)
Q Consensus 135 ~~~~~Dlt~--La~yLl~~~~~~~~~~~-~~---gL~~L~~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~- 207 (522)
...++|++. +..|+-+..++...+.. .+ +--++.+..+..-+.+..|+++|..+++++.|..|+...+.++..
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 346788777 77777664332222111 11 111344555666667888999999999999999999999999999
Q ss_pred -HHHHHHHHHHhc-----CCCccchhhc-ccCccCCCCCCCcccCCCCCcchhhhhhhHHHHHHHhhcccccCCcCcccc
Q 009948 208 -IFNIFQVKVAQK-----GNSCSSISEL-DSSNLDLGLKGILEKPDIGNKTVRFKLCEALDIIRATSYYSQCLPEGVVSR 280 (522)
Q Consensus 208 -L~~~L~~~L~~~-----g~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 280 (522)
....+.+.+.+. -.+..-+..+ ..+....+-+. ....++++...++++...+..++.+++....-+..
T Consensus 234 ~~v~e~~~~~~e~~~~~~~tl~~~v~~i~~rn~~~~~f~~-----~~~~n~v~~~~~kal~~~~~~~e~~~~~~~~f~~~ 308 (617)
T KOG2207|consen 234 FIVDERCAHLLERTINLPKTLTILVQEIINRNQKKYTFSD-----EYAKNYVQNKNCKALHYIRSEREKGQMADKGFVQH 308 (617)
T ss_pred HHHHHHHHHHHhhccCCCchhhhhHHHHHhccchhhhhhh-----hhhhhHhhcccHHHHHHHHHHhhhhhhHHHhhchh
Confidence 777888777765 1111111111 11111111111 13456778889999999999988888877777677
Q ss_pred cccCCCCCcchHHHHHHHHhh---hhhhhhcccCC-Cccc----ccccCCCCcccc-----ccccccccccCCCCCCCCC
Q 009948 281 VSYLNTMPMDESLVKIVRKYG---EKILLRECDKA-PKTS----KKKGRKRSSVIV-----DSREKRLDDIGDWQGPPPW 347 (522)
Q Consensus 281 ~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~-~~~~----~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~p~ 347 (522)
+-+..|.|+|+.+++++...| |.|.+...+.- ||-= +++-.++..... ...+.++.+...|+.+|||
T Consensus 309 ~~~~~t~~~d~~~lkyLw~~~~~iEai~~~~~~~i~~~d~~~el~~~~s~~~~~k~~~~~~~~~~~pl~~~~~~~~~~~~ 388 (617)
T KOG2207|consen 309 VVETKTKPDDENLLKYLWSFGEHIEAIYLATYDNIDPKDDAKELEKRTSRRGAGKTLFNQRMTTNVPLVCEDLFLFEPPW 388 (617)
T ss_pred heeecccccchhHHHHHHHHHHhhhhhhhhhhhcCCCchhHHHHhchhhhcccChhhhhcccccccCccchhhhccCCCc
Confidence 788899999999999999999 88888887733 2221 111111111111 3344557777889999999
Q ss_pred CCCCCCCCCCEEEEccccHHHHHHHHhcCCceecCCCCCC-ChHHHHHhhhcCCcEEEecChhHHHhhh----hcCceEE
Q 009948 348 DLSLGGDGYPKFLCDVMVEGLAKHLRCVGIDAATPRSKKP-EPRELIDQTSKEKRVLLTRDAKLLRHQY----LIKNQIY 422 (522)
Q Consensus 348 ~~~~~~~~~~rfl~D~mLg~Lar~LR~lG~D~~~~~~~~~-~d~~ll~~A~~E~RiiLTrd~~l~~~~~----~~~~~~~ 422 (522)
+..++..+..+++-|.||++|.+.+|..|||+.+..+.+. +.+..|-++-.+++|.|+....+.+.+. ....+++
T Consensus 389 ~~~i~~V~~e~El~~l~l~~l~~e~~yVGiDsEwkps~~v~dsk~~IlQif~~~~v~Lidc~~l~~~~se~w~~~~s~if 468 (617)
T KOG2207|consen 389 VESIGMVGNEKELRDLLLESLSEELRYVGIDSEWKPSKKVSDSKLAILQIFFKDCVYLIDCVKLENLASEIWHLLLSQIF 468 (617)
T ss_pred ccceeeeCCHHHHHHHHHHHhhhcCEEEEEccccCcccCCChhHHHHHHHHhcCeEEEeehHHhhhchHHHHHHHHHHHc
Confidence 9889999999999999999999999999999998776333 3344555556789999999987743321 0111222
Q ss_pred EEccCCh----HHHHHHHHH------HcccccccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCC---
Q 009948 423 RVKSLLK----NQQLLEVIE------AFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNL--- 489 (522)
Q Consensus 423 ~v~~~~~----~eQl~~v~~------~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~--- 489 (522)
-.++-.+ ..|..++++ +|++.+......++|.+|+..+...+.+-++..++..+...++.+.+...-
T Consensus 469 ~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~Lt~~llg~~lnKt 548 (617)
T KOG2207|consen 469 ESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADLTDCLLGKKLNKT 548 (617)
T ss_pred cCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhhhhhhHHHhhhhcccc
Confidence 2222211 234445555 577777777778999999998765556557777766777778888765332
Q ss_pred ce---eec--CCCCeeEeccchhhHHHHHHHHhcccc
Q 009948 490 QF---WQC--MDCNQLYWEGTQYHNAVQKFIDVCKLN 521 (522)
Q Consensus 490 ~F---~~C--~~CgkvyW~GsH~~~~~~~~~~~~~~~ 521 (522)
++ |+| -+|+|+||.|.-...+.+.|..+|+..
T Consensus 549 eqcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv 585 (617)
T KOG2207|consen 549 EQCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVV 585 (617)
T ss_pred cccchhhcCCchhhHHHHHHhcchhhHHHHHHHHhhc
Confidence 56 999 899999999999999999999999865
No 16
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=99.65 E-value=2.9e-16 Score=165.99 Aligned_cols=172 Identities=25% Similarity=0.352 Sum_probs=151.8
Q ss_pred EEEEcCCChHHHHHHHHHhcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCch
Q 009948 11 IHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLP 90 (522)
Q Consensus 11 i~~I~t~~~~el~~l~~~L~~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~ 90 (522)
.++|.+ ..++.++.+.+.....+|+|.|...... +.+-.|||||+|. ..-|+||...+.
T Consensus 193 ~~~I~t--~~el~~l~~~l~~~~Efavdlehhsyrs---f~gltclmqISTr--------------~ed~iIDt~~l~-- 251 (687)
T KOG2206|consen 193 KVWICT--LGELEALPEILDSVIEFAVDLEHHSYRS---FLGLTCLMQISTR--------------TEDFIIDTFKLR-- 251 (687)
T ss_pred ceeeec--hHHHHHHHHHHhhhhhhhhhccccchhh---hcCceeEEEeecc--------------chhheehhHHHH--
Confidence 567777 6888899999988889999999866553 6688999999996 467999987664
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
+....|++.|.+|.|+||+|++..|+.+|.+.||+ .+-++|| |.-|..+++- ..++|+.|.+.
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 34568999999999999999999999999999877 2478999 8889999875 47899999999
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKG 220 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g 220 (522)
+.|+..+|..|..||..|||+++++.||-.|.+|++.||+.|+..|.+.+
T Consensus 315 ~~~v~~nk~yqladwR~rpLp~~Mv~yar~dthyllyiyD~lr~el~~~a 364 (687)
T KOG2206|consen 315 VCGVLTNKKYQLADWRIRPLPEEMVRYAREDTHYLLYIYDVLRKELKRLA 364 (687)
T ss_pred HHhhhhhhhhhhchhccccCcHHHHHHHhhcchhHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999888876
No 17
>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=99.62 E-value=1.2e-14 Score=132.25 Aligned_cols=149 Identities=28% Similarity=0.303 Sum_probs=113.6
Q ss_pred eEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCceEEEEech
Q 009948 34 LVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFK 113 (522)
Q Consensus 34 ~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~~~~i~KVgh~~k 113 (522)
.+++|+|+.+... ..++++++|+++. +.+++++... ....+.+.|+++|+++.+.|||||++
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 3468899999973 2244443221 12346677999999999999999999
Q ss_pred hhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcCCccccccccCCCC----CCC
Q 009948 114 QDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWS----NRP 189 (522)
Q Consensus 114 ~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~K~~q~sdW~----~RP 189 (522)
+|+..|.+.+ . ...++++| +++++|++++. ..+++|+.+++++++..+.+..+..+|. .+|
T Consensus 64 ~d~~~L~~~~-~-------~~~~~~~D-~~~~ayll~~~------~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~ 128 (155)
T cd00007 64 FDLVVLARDG-I-------ELPGNIFD-TMLAAYLLNPG------EGSHSLDDLAKEYLGIELDKDEQIYGKGAKTFARP 128 (155)
T ss_pred HHHHHHHHCC-C-------CCCCCccc-HHHHHHHhCCC------CCcCCHHHHHHHHcCCCCccHHHHhcCCCCccccC
Confidence 9999998742 2 12467899 99999999985 2157999999999998865433355552 478
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHH
Q 009948 190 LTEEQKNYAAIDAHCLIEIFNIFQVK 215 (522)
Q Consensus 190 L~~~qi~YAA~DA~~ll~L~~~L~~~ 215 (522)
++..|+.||+.||.++++|++.|.++
T Consensus 129 ~~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 129 LSEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 89999999999999999999999864
No 18
>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=99.60 E-value=1.8e-14 Score=131.28 Aligned_cols=147 Identities=27% Similarity=0.265 Sum_probs=112.4
Q ss_pred eEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCceEEEEech
Q 009948 34 LVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFK 113 (522)
Q Consensus 34 ~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~~~~i~KVgh~~k 113 (522)
++++|+|+.+..+ ...+++++|+++. ++.+|++++.... -....|+++|+++++.|+|||+|
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 3467899999974 2347888754311 12456889999999999999999
Q ss_pred hhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcCCcccc-cc-ccCCCCCCCCC
Q 009948 114 QDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSK-EL-QCSDWSNRPLT 191 (522)
Q Consensus 114 ~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~K-~~-q~sdW~~RPL~ 191 (522)
.|+..|.+. |+ ...+++|| +++|+||+++. ..+.+|++|++++|+..+.+ .. ..++|..+++.
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 999999764 33 12467899 99999999985 21469999999999988554 22 12248557889
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 009948 192 EEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 192 ~~qi~YAA~DA~~ll~L~~~L~ 213 (522)
.+|+.||+.||+++++|++.|.
T Consensus 128 ~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 128 EEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999875
No 19
>PRK05755 DNA polymerase I; Provisional
Probab=99.57 E-value=1.1e-13 Score=160.54 Aligned_cols=180 Identities=18% Similarity=0.218 Sum_probs=142.7
Q ss_pred CCccEEEEcCCChHHHHHHHHHhcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC
Q 009948 7 KPLKIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS 86 (522)
Q Consensus 7 ~~~~i~~I~t~~~~el~~l~~~L~~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~ 86 (522)
+.++|.+|++ .+++..+++.+.....++||+|+.+..+ +.++++++|++.. ++.+|+|++..
T Consensus 292 ~~~~~~~I~~--~~~L~~~l~~l~~~~~~a~DtEt~~l~~---~~~~i~~i~ls~~-------------~g~~~~ip~~~ 353 (880)
T PRK05755 292 DEEDYETILD--EEELEAWLAKLKAAGLFAFDTETTSLDP---MQAELVGLSFAVE-------------PGEAAYIPLDQ 353 (880)
T ss_pred CCCceEEeCC--HHHHHHHHHHhhccCeEEEEeccCCCCc---ccccEEEEEEEeC-------------CCcEEEEeccc
Confidence 3456778877 7889999988888899999999988764 5678999999875 34588888754
Q ss_pred CCchhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHH
Q 009948 87 IPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLAN 166 (522)
Q Consensus 87 l~~~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~ 166 (522)
+. ...+..|.++|+++.+.||+||+++|+..|.+ +|+ . ...+++| |++++|+++++ ..++|++
T Consensus 354 i~-~~~l~~l~~~L~d~~v~kV~HNakfDl~~L~~-~gi---~----~~~~~~D-T~iAa~Ll~~~-------~~~~L~~ 416 (880)
T PRK05755 354 LD-REVLAALKPLLEDPAIKKVGQNLKYDLHVLAR-YGI---E----LRGIAFD-TMLASYLLDPG-------RRHGLDS 416 (880)
T ss_pred cc-HHHHHHHHHHHhCCCCcEEEeccHhHHHHHHh-CCC---C----cCCCccc-HHHHHHHcCCC-------CCCCHHH
Confidence 32 14678899999999999999999999999986 444 1 1367999 99999999985 2489999
Q ss_pred HHHHHcCCcccccc----ccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009948 167 ICKELLDISLSKEL----QCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (522)
Q Consensus 167 L~~~~Lg~~L~K~~----q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~ 222 (522)
++++++|.++.... ...+|+..|+ +.+..||+.||.++++||..|.++|.+.+.+
T Consensus 417 L~~~ylg~~~~~~~~~~gk~~~~~~~pl-e~~~~YAa~Dv~~~~~L~~~L~~~L~~~~~l 475 (880)
T PRK05755 417 LAERYLGHKTISFEEVAGKQLTFAQVDL-EEAAEYAAEDADVTLRLHEVLKPKLLEEPGL 475 (880)
T ss_pred HHHHHhCCCccchHHhcCCCCCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHHhcccH
Confidence 99999998852211 2234555577 5789999999999999999999999876443
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=99.49 E-value=6.4e-13 Score=125.16 Aligned_cols=157 Identities=17% Similarity=0.123 Sum_probs=117.3
Q ss_pred CCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCceEEEEe
Q 009948 32 SSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFK 111 (522)
Q Consensus 32 ~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~~~~i~KVgh~ 111 (522)
...+++|+|.....+ ...++..++++.. +++|+|++... ......|+++|+++++.|++||
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 3456777777763 35777774321 0134568899999999999999
Q ss_pred chhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcCCccccccccCCCC---CC
Q 009948 112 FKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWS---NR 188 (522)
Q Consensus 112 ~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~K~~q~sdW~---~R 188 (522)
+|.|++.|.+ +|+ . ..+++|| ++||+||++++ ..++++++++.+||+..+.+..+.+.|. .+
T Consensus 64 ~K~~~~~l~~-~gi-~------~~~~~fD-t~laaYLL~p~------~~~~~l~~l~~~yl~~~~~~~~~~~~~~~~~~~ 128 (178)
T cd06140 64 AKRAYVALKR-HGI-E------LAGVAFD-TMLAAYLLDPT------RSSYDLADLAKRYLGRELPSDEEVYGKGAKFAV 128 (178)
T ss_pred hhHHHHHHHH-CCC-c------CCCcchh-HHHHHHHcCCC------CCCCCHHHHHHHHcCCCCcchHHhcCCCCCccc
Confidence 9999999976 454 2 2356799 99999999985 2347999999999999875533344442 23
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009948 189 PLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (522)
Q Consensus 189 PL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~ 222 (522)
+....+..|++.||.++++|++.|.++|++++++
T Consensus 129 ~~~~~~~~y~~~~a~~l~~l~~~l~~~L~~~~l~ 162 (178)
T cd06140 129 PDEEVLAEHLARKAAAIARLAPKLEEELEENEQL 162 (178)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHH
Confidence 4456788999999999999999999999987653
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=99.39 E-value=1.7e-11 Score=116.50 Aligned_cols=160 Identities=21% Similarity=0.321 Sum_probs=116.4
Q ss_pred cCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC------CCchhhHHHHHHhhCCC
Q 009948 30 SQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS------IPLPSIWELLKELFVSP 103 (522)
Q Consensus 30 ~~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~------l~~~~~~~~L~~lL~~~ 103 (522)
.+...+++|+|..+..+ ...++..++++.. .+.+|++++.. .....+...|+++|++.
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 3456677777763 23366666432 12234566789999998
Q ss_pred CceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcCCccc------
Q 009948 104 DILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS------ 177 (522)
Q Consensus 104 ~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~------ 177 (522)
.+.+|+||++.|+..|.. +|+ . ..+.++| |++++|+++++ ..+++|.+++++++|..+.
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 889999999999999977 344 1 2356899 99999999985 2257999999999987621
Q ss_pred -cccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCC
Q 009948 178 -KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ-KGN 221 (522)
Q Consensus 178 -K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~-~g~ 221 (522)
|+.+..+|...|+ ..+..||+.||.++++|++.|.++|++ .++
T Consensus 132 ~k~~~~~~~~~~~~-~~~~~ya~~d~~~~~~l~~~l~~~l~~~~~~ 176 (193)
T cd06139 132 GKGKKQITFDQVPL-EKAAEYAAEDADITLRLYELLKPKLKEEPGL 176 (193)
T ss_pred CCCcCcCCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhH
Confidence 2223445654454 668899999999999999999999987 543
No 22
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.34 E-value=5e-12 Score=139.67 Aligned_cols=146 Identities=22% Similarity=0.215 Sum_probs=119.1
Q ss_pred cEEEEcCCChHHHHHHHHHhcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCc
Q 009948 10 KIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPL 89 (522)
Q Consensus 10 ~i~~I~t~~~~el~~l~~~L~~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~ 89 (522)
.+.+|++ .+++..++..+...+.+++|+|+..... .++++|++.. +.+|+||+...
T Consensus 2 ~~~~I~~--~~~l~~~~~~l~~~~~~a~DtEf~r~~t------~l~liQ~~~~--------------~~~~liDpl~~-- 57 (553)
T PRK14975 2 DMKVILA--PEELGAALERLSPAGVVAGDTETTGDDA------AAAAAQEGEE--------------EPRWVWASTAA-- 57 (553)
T ss_pred CceEEec--cchhHHHHHHhccCCceeCCccccCCcc------hhheeeecCC--------------CceEEECchHH--
Confidence 4567877 6889999999999999999999876552 7899999874 68899997531
Q ss_pred hhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHH
Q 009948 90 PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (522)
Q Consensus 90 ~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~ 169 (522)
+.+ + |.+ +|+ . +.++|| |+|++|+++++.+ ..++|++.++.
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 1 434 243 2 356999 9999999997510 01689999999
Q ss_pred HHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 009948 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (522)
Q Consensus 170 ~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~ 219 (522)
.+|+..++|..+.++|. ||++++|+.||+.|+.+++.||..|.++|++.
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 99999999988889997 99999999999999999999999999999876
No 23
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=99.09 E-value=8.3e-10 Score=120.20 Aligned_cols=170 Identities=18% Similarity=0.190 Sum_probs=124.1
Q ss_pred hHHHHHHHHHhcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCC-chhhHHHHH
Q 009948 19 SPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIP-LPSIWELLK 97 (522)
Q Consensus 19 ~~el~~l~~~L~~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~-~~~~~~~L~ 97 (522)
.+.+..+...+...+.+++|+|..+..+ ...++++++... +..++++.....+ .-.....|+
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 4556666666665555999999988774 456788887752 1245555544311 112577899
Q ss_pred HhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcCCccc
Q 009948 98 ELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS 177 (522)
Q Consensus 98 ~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~ 177 (522)
+||+++.+.|+|||.|.|.+.|.+. |+ . .+..+| |||++|+++++ ...+++++|++++++....
T Consensus 72 ~~l~~~~~~kv~~~~K~d~~~l~~~-Gi-------~-~~~~~D-tmlasYll~~~------~~~~~~~~l~~r~l~~~~~ 135 (593)
T COG0749 72 PLLEDEGIKKVGQNLKYDYKVLANL-GI-------E-PGVAFD-TMLASYLLNPG------AGAHNLDDLAKRYLGLETI 135 (593)
T ss_pred HHhhCcccchhccccchhHHHHHHc-CC-------c-ccchHH-HHHHHhccCcC------cCcCCHHHHHHHhcCCccc
Confidence 9999999999999999999999884 43 1 367899 99999999986 3579999999999998764
Q ss_pred ccc-------ccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009948 178 KEL-------QCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (522)
Q Consensus 178 K~~-------q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~ 222 (522)
..+ +.-+...-++ +....|+|.||.++++|+..|.+++.+...+
T Consensus 136 ~~~~i~~kg~~~~~~~~~~~-~~~~~y~a~~a~~~~~L~~~l~~~l~~~~~L 186 (593)
T COG0749 136 TFEDIAGKGKKQLTFADVKL-EKATEYAAEDADATLRLESILEPELLKTPVL 186 (593)
T ss_pred hhHHhhccccccCccccchH-HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhH
Confidence 322 1112222222 4468999999999999999999988887653
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=99.03 E-value=9.1e-09 Score=118.88 Aligned_cols=172 Identities=13% Similarity=0.040 Sum_probs=114.0
Q ss_pred EEEEcCCChHHHHHHHHHhcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCC-CEEEEEeCC---C
Q 009948 11 IHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNA-SVVFLLDLS---S 86 (522)
Q Consensus 11 i~~I~t~~~~el~~l~~~L~~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~-~~v~liD~~---~ 86 (522)
+..|.+ .+++..+++. ...+.+++ .+..+ ....+..+.+++. . +.+|+++.. .
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 445645 4667776654 44456777 12111 1123333344442 1 336666533 1
Q ss_pred CCchhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHH
Q 009948 87 IPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLAN 166 (522)
Q Consensus 87 l~~~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~ 166 (522)
+........|+++|+++.+.|+|||+|+|+..|.+ +|+ . ..+.+|| |||++||++++ ..++|++
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 12234556799999999999999999999999986 454 2 2356899 99999999985 3469999
Q ss_pred HHHHHcCCccccccccCCC--CCCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 009948 167 ICKELLDISLSKELQCSDW--SNRPLT-EEQKNYAAIDAHCLIEIFNIFQVKVAQKGN 221 (522)
Q Consensus 167 L~~~~Lg~~L~K~~q~sdW--~~RPL~-~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~ 221 (522)
++.+||+..+.+......| ....++ +.+..||+.||.++++||..|.++|+++++
T Consensus 425 la~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~~~~l 482 (887)
T TIGR00593 425 LARRYLVEELILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKELDENKL 482 (887)
T ss_pred HHHHHcCcccccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhccH
Confidence 9999999775432222111 112343 446789999999999999999999987654
No 25
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=98.86 E-value=1.2e-08 Score=102.74 Aligned_cols=159 Identities=22% Similarity=0.225 Sum_probs=117.6
Q ss_pred CCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCceEEEEe
Q 009948 32 SSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFK 111 (522)
Q Consensus 32 ~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~~~~i~KVgh~ 111 (522)
...+..+.||.+...++...+.+..+||++. ++.++|+.+.... .+...|+.+|+|++.++||.+
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 3456677788777554445677999999994 4788888665543 367788889999999999999
Q ss_pred chhhHHHHHh-hcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcC-----CccccccccCCC
Q 009948 112 FKQDLIYLSS-TFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLD-----ISLSKELQCSDW 185 (522)
Q Consensus 112 ~k~Dl~~L~~-~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg-----~~L~K~~q~sdW 185 (522)
..+|...|.+ .|+. .+..+.||..+..-.++.+ ....+...|++..+| +.+++..+++||
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 4432 2466778766665555542 234566666666654 446778899999
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 009948 186 SNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGN 221 (522)
Q Consensus 186 ~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~ 221 (522)
+..||+.+|+.||+.|||+...|+ ..+.+.+...
T Consensus 258 ~~~~Ls~~Ql~~asidvy~c~~lg--~~~~~w~~~~ 291 (319)
T KOG4373|consen 258 SVYPLSDDQLLQASIDVYVCHKLG--VLERLWEVKL 291 (319)
T ss_pred eeeeccHHHHHHHHhHHHHHHHHH--HHHHHHHHhc
Confidence 999999999999999999999999 3344444433
No 26
>COG4634 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.66 E-value=1.1e-07 Score=81.00 Aligned_cols=73 Identities=21% Similarity=0.265 Sum_probs=60.5
Q ss_pred CEEEEccccH-HHHHHHHhcCCceecCCC---CCCChHHHHHhhhcCCcEEEecChhHHHhhhh--cCceEEEEccCCh
Q 009948 357 PKFLCDVMVE-GLAKHLRCVGIDAATPRS---KKPEPRELIDQTSKEKRVLLTRDAKLLRHQYL--IKNQIYRVKSLLK 429 (522)
Q Consensus 357 ~rfl~D~mLg-~Lar~LR~lG~D~~~~~~---~~~~d~~ll~~A~~E~RiiLTrd~~l~~~~~~--~~~~~~~v~~~~~ 429 (522)
|||++|+.|. +||+||-..||++++..+ ++..|-||...|+.++|||+|.|.+|...... ...+++.+++.+.
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 999999999999988765 34568899999999999999999999654322 2257888887654
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=98.53 E-value=1.6e-06 Score=79.47 Aligned_cols=117 Identities=21% Similarity=0.207 Sum_probs=78.8
Q ss_pred EEEEEeCCCCCchhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCC
Q 009948 78 VVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKL 157 (522)
Q Consensus 78 ~v~liD~~~l~~~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~ 157 (522)
++|+|++.. .. ....|+++|+++++.|++||.|.++..|.+ +|+ . ..+.+|| ++||+||++|.
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 354 2 2356799 99999999985
Q ss_pred CcCcccHHHHHHHHcCCcccc-ccccCCCCC--CCC-CHHHHHHHHHHHHHHHHHHHHHH
Q 009948 158 PKETKSLANICKELLDISLSK-ELQCSDWSN--RPL-TEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 158 ~~~~~gL~~L~~~~Lg~~L~K-~~q~sdW~~--RPL-~~~qi~YAA~DA~~ll~L~~~L~ 213 (522)
....++++++++||+..+.. .. ...+.. .++ ......|++..|.++.+|++.|.
T Consensus 93 -~~~~~l~~la~~yl~~~~~~~~~-~~gkg~~~~~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 93 -AGRHDMDSLAERWLKEKTITFEE-IAGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred -CCCCCHHHHHHHHcCCCCccHHH-HcCCCCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 23149999999999877211 11 111100 012 12223488888999999998874
No 28
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=96.99 E-value=0.036 Score=54.84 Aligned_cols=90 Identities=16% Similarity=0.236 Sum_probs=57.4
Q ss_pred ceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcCCccccccccCC
Q 009948 105 ILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSD 184 (522)
Q Consensus 105 i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~K~~q~sd 184 (522)
.+.|+||+.+|+..|.+.+.-.|..+ + ...+++| +......+.+. ...+++|+++++. +|++....+
T Consensus 94 ~~lVahNa~FD~~fL~~~~~r~~~~~-~-~~~~~iD-t~~l~~~~~~~-----~~~~~~L~~l~~~-~gi~~~~aH---- 160 (232)
T PRK07942 94 VPVVVFNAPYDLTVLDRELRRHGLPS-L-VPGPVID-PYVIDKAVDRY-----RKGKRTLTALCEH-YGVRLDNAH---- 160 (232)
T ss_pred CEEEEeCcHhhHHHHHHHHHHcCCCC-c-cCCcEee-HHHHHhhhhcc-----cCCCCCHHHHHHH-cCCCCCCCC----
Confidence 34599999999988866543223211 0 1246889 55444333221 0135789999977 577654222
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 009948 185 WSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (522)
Q Consensus 185 W~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~ 219 (522)
-|..||.++.+|+..|.++..+-
T Consensus 161 ------------~Al~Da~ata~l~~~l~~~~~~l 183 (232)
T PRK07942 161 ------------EATADALAAARVAWALARRFPEL 183 (232)
T ss_pred ------------ChHHHHHHHHHHHHHHHHHHHHh
Confidence 28899999999999998766543
No 29
>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=96.98 E-value=0.0052 Score=57.06 Aligned_cols=89 Identities=17% Similarity=0.159 Sum_probs=57.0
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHH--HHHh-hccccCCCCCcCcccHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSI--YNHL-HHKQLGRKLPKETKSLANI 167 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~L--a~yL-l~~~~~~~~~~~~~gL~~L 167 (522)
++...|.+++.+ -+.||||+++|+..|...+. ..++.|+..+ +... ..+. ..+++|..|
T Consensus 66 ~v~~~l~~~l~~--~vlV~Hn~~~D~~~l~~~~~----------~~~~~Dt~~l~~~~~~~~~p~------~~~~~L~~L 127 (157)
T cd06149 66 VAQKEILKILKG--KVVVGHAIHNDFKALKYFHP----------KHMTRDTSTIPLLNRKAGFPE------NCRVSLKVL 127 (157)
T ss_pred HHHHHHHHHcCC--CEEEEeCcHHHHHHhcccCC----------CcCEEECcccccchhhcCCcc------cCChhHHHH
Confidence 456677777764 35699999999999865311 1356783222 1111 1221 246899999
Q ss_pred HHHHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009948 168 CKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (522)
Q Consensus 168 ~~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~ 210 (522)
+++++|..+..+.+.. -|..||.++.+||+
T Consensus 128 ~~~~~~~~i~~~~~~H-------------~Al~DA~at~~l~~ 157 (157)
T cd06149 128 AKRLLHRDIQVGRQGH-------------SSVEDARATMELYK 157 (157)
T ss_pred HHHHcChhhcCCCCCc-------------CcHHHHHHHHHHhC
Confidence 9999987665432212 27789999988873
No 30
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=96.98 E-value=0.021 Score=59.15 Aligned_cols=102 Identities=14% Similarity=0.138 Sum_probs=68.7
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
+++..|.+++.+. +.|+||+.+|+..|.+.+.-.|.. + ....++|...++..+ .+. ..+++|+++++.
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 4566777777663 459999999999997654322321 1 124688944444443 332 247889999976
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGN 221 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~ 221 (522)
+|++.... +-|..||.++.+|+..+.+++.+.+.
T Consensus 151 -~gi~~~~~----------------H~Al~DA~ata~l~~~ll~~~~~~~~ 184 (313)
T PRK06063 151 -WGVPQQRP----------------HDALDDARVLAGILRPSLERARERDV 184 (313)
T ss_pred -cCCCCCCC----------------CCcHHHHHHHHHHHHHHHHHHHhcCC
Confidence 57654222 23889999999999999988887754
No 31
>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=96.79 E-value=0.034 Score=51.54 Aligned_cols=96 Identities=18% Similarity=0.205 Sum_probs=58.8
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHH-HHHHhhccccCCCCCcCcccHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITS-IYNHLHHKQLGRKLPKETKSLANICK 169 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~-La~yLl~~~~~~~~~~~~~gL~~L~~ 169 (522)
++...|.+++.+.. .|+||+.+|+..|.+.+.-.|..+.+.....++| |+ ++..+ .+. ...+|+++++
T Consensus 70 ~v~~~l~~~l~~~~--lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~id-t~~~~~~~-~~~-------~~~~L~~l~~ 138 (167)
T cd06131 70 EIADEFLDFIRGAE--LVIHNASFDVGFLNAELSLLGLGKKIIDFCRVID-TLALARKK-FPG-------KPNSLDALCK 138 (167)
T ss_pred HHHHHHHHHHCCCe--EEEeChHHhHHHHHHHHHHhCCCcccccCCCceE-hHHHHHHH-cCC-------CCCCHHHHHH
Confidence 34566677776643 4899999999988654322122111111246799 55 44433 332 3579999998
Q ss_pred HHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009948 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (522)
Q Consensus 170 ~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L 212 (522)
++ |++.... +.+-|..||.++.+|+..|
T Consensus 139 ~~-~i~~~~~--------------~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 139 RF-GIDNSHR--------------TLHGALLDAELLAEVYLEL 166 (167)
T ss_pred HC-CCCCCCC--------------CCCChHHHHHHHHHHHHHh
Confidence 86 6543211 1234889999999998765
No 32
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=96.69 E-value=0.02 Score=56.88 Aligned_cols=95 Identities=22% Similarity=0.222 Sum_probs=63.9
Q ss_pred HHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHc
Q 009948 93 WELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELL 172 (522)
Q Consensus 93 ~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~L 172 (522)
-..+.++|.+. +.|||++.+|+..|.-.++- .-+-| |.-+.-|... .....+.||..|++.+|
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 34566788773 45999999999999754322 22346 4322222110 00135789999999999
Q ss_pred CCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 009948 173 DISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (522)
Q Consensus 173 g~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~ 219 (522)
|+.+--++..| .+||.++.+||.....+-++.
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 589999999999998766654
No 33
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=96.68 E-value=0.043 Score=54.95 Aligned_cols=150 Identities=19% Similarity=0.220 Sum_probs=85.8
Q ss_pred hcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-----------CC---------
Q 009948 29 LSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-----------IP--------- 88 (522)
Q Consensus 29 L~~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~-----------l~--------- 88 (522)
+.....|.||+|+++..+ .+-.+||||.-. -+ ++.. .+.-..++.+.. +.
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-FT--FDEV--IDSVEFLINPERVVSAESQRIHHISDAMLRDKPK 73 (250)
T ss_pred ccCCcEEEEEEeCCCCCC-----CCCeEEEEEEEE-EE--CCeE--EEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCC
Confidence 345689999999988764 233577775421 00 0000 001223344321 11
Q ss_pred chhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCcc-CCCceeeHHHHHHHhhccccCCCCCcCcccHHHH
Q 009948 89 LPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFD-RVEPYLDITSIYNHLHHKQLGRKLPKETKSLANI 167 (522)
Q Consensus 89 ~~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~-~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L 167 (522)
..++...+.+++.+.. +.||||+.+|...|...+.-.|.. +. ....++|+..++. .... ..+++|+.+
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 0234556667776544 469999999999987643222221 11 1146899444443 3321 236899999
Q ss_pred HHHHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009948 168 CKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKV 216 (522)
Q Consensus 168 ~~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L 216 (522)
++.+ |+++... +-|..||.++..|+..+.+++
T Consensus 143 ~~~~-g~~~~~a----------------H~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 143 AVHF-NVPYDGN----------------HRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred HHHC-CCCCCCC----------------cChHHHHHHHHHHHHHHHHhc
Confidence 8775 7654322 228899999999999987543
No 34
>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=96.68 E-value=0.0077 Score=55.51 Aligned_cols=87 Identities=23% Similarity=0.340 Sum_probs=57.3
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
+++..|..++.+ .+ .||||+..|+..|... . ....++| +.....+..+. +..+++|++|++.
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 466677788876 44 4999999999999642 1 1145678 43322222211 0247899999999
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~ 210 (522)
+||+++... . +-|..||.++.+||+
T Consensus 128 ~lgi~~~~~--~-------------H~Al~DA~at~~l~~ 152 (152)
T cd06144 128 LLGLDIQEG--E-------------HSSVEDARAAMRLYR 152 (152)
T ss_pred HcCcccCCC--C-------------cCcHHHHHHHHHHhC
Confidence 999876421 1 227889999988873
No 35
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=96.61 E-value=0.11 Score=51.49 Aligned_cols=144 Identities=13% Similarity=0.123 Sum_probs=84.8
Q ss_pred CeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-----------CCc---------hhh
Q 009948 33 SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-----------IPL---------PSI 92 (522)
Q Consensus 33 ~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~-----------l~~---------~~~ 92 (522)
..+.||+|+++..+ .+-.+|+|+.-. .. ..+.-..++.+.. +.. .++
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--GV------TSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEA 69 (232)
T ss_pred cEEEEEeeCCCCCC-----CCCEEEEEEEEc--Cc------cccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHH
Confidence 47899999988764 223688886531 00 0011222444321 111 134
Q ss_pred HHHHHHhhCCCCceEEEEec-hhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHH
Q 009948 93 WELLKELFVSPDILKLGFKF-KQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKEL 171 (522)
Q Consensus 93 ~~~L~~lL~~~~i~KVgh~~-k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~ 171 (522)
...+.+++.+. -..||||. ..|+..|.+.+.-.|+.. ....++|+..++..+ .+. ...++|..+++.+
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 44566666543 34599994 899999876542223221 124689955555443 332 2367899998776
Q ss_pred cCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009948 172 LDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (522)
Q Consensus 172 Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~ 217 (522)
|++.... +-|..||.++.+|+..+..++.
T Consensus 139 -~~~~~~a----------------H~Al~Da~~t~~vl~~l~~~~~ 167 (232)
T PRK06309 139 -GFEENQA----------------HRALDDVITLHRVFSALVGDLS 167 (232)
T ss_pred -CCCCCCC----------------CCcHHHHHHHHHHHHHHHHHHH
Confidence 6554222 2288999999999999887664
No 36
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=96.58 E-value=0.061 Score=55.71 Aligned_cols=97 Identities=12% Similarity=0.137 Sum_probs=65.1
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
+++..|.+++.+.. -||||+..|+..|.+.+...|+. .....++|+..++..+.. . ...++|.+|++.
T Consensus 77 evl~~f~~fl~~~~--lVaHNa~FD~~fL~~~~~~~gl~---~~~~~~iDtl~la~~~~~-~------~~~~kL~~L~~~ 144 (313)
T PRK06807 77 EVLPLFLAFLHTNV--IVAHNASFDMRFLKSNVNMLGLP---EPKNKVIDTVFLAKKYMK-H------APNHKLETLKRM 144 (313)
T ss_pred HHHHHHHHHHcCCe--EEEEcHHHHHHHHHHHHHHcCCC---CCCCCEeeHHHHHHHHhC-C------CCCCCHHHHHHH
Confidence 35556666776543 39999999999997654333431 123568996666665543 2 246799999855
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~ 217 (522)
+|++. +. +-|..||.++.+|+..+.....
T Consensus 145 -lgi~~-~~----------------H~Al~DA~~ta~l~~~l~~~~~ 173 (313)
T PRK06807 145 -LGIRL-SS----------------HNAFDDCITCAAVYQKCASIEE 173 (313)
T ss_pred -cCCCC-CC----------------cChHHHHHHHHHHHHHHHHhhh
Confidence 67654 21 2388999999999999987664
No 37
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=96.52 E-value=0.12 Score=52.12 Aligned_cols=98 Identities=16% Similarity=0.192 Sum_probs=65.4
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
+++..|..++.+. +.|+||+..|...|.+.+.-.|..+ .....+|...++..+... ..++|++|++
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 4566677777763 4699999999999865432223211 235578855566554432 4689999987
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ 218 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~ 218 (522)
++|++.... +-|..||.++.+|+..+..++..
T Consensus 202 ~lgi~~~~~----------------HrAl~DA~ata~ll~~ll~~~~~ 233 (257)
T PRK08517 202 LLGIEIEVH----------------HRAYADALAAYEIFKICLLNLPS 233 (257)
T ss_pred HcCcCCCCC----------------CChHHHHHHHHHHHHHHHHHhHH
Confidence 467665322 22889999999999999877643
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=96.50 E-value=0.053 Score=65.34 Aligned_cols=103 Identities=22% Similarity=0.416 Sum_probs=72.7
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
+++..|.+++.+. +.|+||+..|+..|...+.-.|..+ ....++|+..++.. +.+. ...++|++|+.+
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 4566777788763 4599999999999876432223221 13578995455544 4443 357899999987
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~ 222 (522)
+|+++.. .+.|..||.++.+|+..+..++++.|..
T Consensus 327 -lgi~~~~----------------~HrAl~DA~aTa~I~~~ll~~l~~~~i~ 361 (1213)
T TIGR01405 327 -LGVDLDD----------------HHRADYDAEATAKVFKVMVEQLKEKGIT 361 (1213)
T ss_pred -cCCCCCC----------------CcCHHHHHHHHHHHHHHHHHHHHHcCCc
Confidence 4776532 2458999999999999999999887654
No 39
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.44 E-value=0.075 Score=52.94 Aligned_cols=98 Identities=16% Similarity=0.223 Sum_probs=60.6
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCc-cCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCD-IGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~-~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~ 169 (522)
++...|.+++.+.. .|+||+.+|+..|.+.+.-+|.. +.+.....++|...++.++ .++ ...+|..|++
T Consensus 75 ev~~~f~~fi~~~~--lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~-~p~-------~~~~L~aL~~ 144 (240)
T PRK05711 75 EVADEFLDFIRGAE--LIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRM-FPG-------KRNSLDALCK 144 (240)
T ss_pred HHHHHHHHHhCCCE--EEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHH-cCC-------CCCCHHHHHH
Confidence 34556667776643 48999999999887544222210 1111124589944444444 343 3579999998
Q ss_pred HHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009948 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 170 ~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~ 213 (522)
+| |++.... +.+-|..||..+.+||..|.
T Consensus 145 ~~-gi~~~~r--------------~~H~AL~DA~~~A~v~~~l~ 173 (240)
T PRK05711 145 RY-GIDNSHR--------------TLHGALLDAEILAEVYLAMT 173 (240)
T ss_pred HC-CCCCCCC--------------CCCCHHHHHHHHHHHHHHHH
Confidence 75 6542211 11238899999999998886
No 40
>PRK07740 hypothetical protein; Provisional
Probab=96.41 E-value=0.15 Score=50.78 Aligned_cols=101 Identities=13% Similarity=0.169 Sum_probs=66.6
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhc-ccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTF-CSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~-gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~ 169 (522)
++...|..++.+. +.||||+..|...|.+.+ ...+. .....++|+..++..+ .+. ...++|++++.
T Consensus 130 evl~~f~~fi~~~--~lVahna~fD~~fL~~~~~~~~~~----~~~~~~iDt~~l~r~l-~~~------~~~~sL~~l~~ 196 (244)
T PRK07740 130 EVLHRFYAFIGAG--VLVAHHAGHDKAFLRHALWRTYRQ----PFTHRLIDTMFLTKLL-AHE------RDFPTLDDALA 196 (244)
T ss_pred HHHHHHHHHhCCC--EEEEeCHHHHHHHHHHHHHHhcCC----CcCCCeechHHHHHHH-cCC------CCCCCHHHHHH
Confidence 3455555666553 468999999998886532 11111 1236789955555444 332 24789999996
Q ss_pred HHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 009948 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGN 221 (522)
Q Consensus 170 ~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~ 221 (522)
. +|++.... +-|..||.++.+|+..+..++.+.|.
T Consensus 197 ~-~gi~~~~~----------------H~Al~Da~ata~l~~~ll~~~~~~~~ 231 (244)
T PRK07740 197 Y-YGIPIPRR----------------HHALGDALMTAKLWAILLVEAQQRGI 231 (244)
T ss_pred H-CCcCCCCC----------------CCcHHHHHHHHHHHHHHHHHHHHcCC
Confidence 5 68766422 22789999999999999999887654
No 41
>PRK07883 hypothetical protein; Validated
Probab=96.38 E-value=0.09 Score=58.71 Aligned_cols=162 Identities=13% Similarity=0.157 Sum_probs=96.3
Q ss_pred HHHHHhcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-----------CCc---
Q 009948 24 HLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-----------IPL--- 89 (522)
Q Consensus 24 ~l~~~L~~~~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~-----------l~~--- 89 (522)
++-..+.....|.||+|+++..+ . ...+++|+.-. -+.+ . . .+.-..++.+.. +..
T Consensus 7 ~~~~~~~~~~~Vv~D~ETTGl~p---~--~~~IIEIgaV~-v~~g-~-i--v~~f~~lV~P~~~i~~~~~~itGIt~e~l 76 (557)
T PRK07883 7 DLGTPLRDVTFVVVDLETTGGSP---A--GDAITEIGAVK-VRGG-E-V--LGEFATLVNPGRPIPPFITVLTGITTAMV 76 (557)
T ss_pred hhCCCCcCCCEEEEEEecCCCCC---C--CCeEEEEEEEE-EECC-E-E--EEEEEEEECCCCCCChhHHhhcCCCHHHH
Confidence 33344556789999999988764 1 24667765421 0000 0 0 000112333221 110
Q ss_pred ------hhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCccc
Q 009948 90 ------PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKS 163 (522)
Q Consensus 90 ------~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~g 163 (522)
.+++..|..++.+ -+.|+||+.+|+..|...+.-.|+. + .....+|+..++..+..+. ....++
T Consensus 77 ~~ap~~~evl~~f~~fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~--~-~~~~~iDTl~lar~l~~~~-----~~~~~~ 146 (557)
T PRK07883 77 AGAPPIEEVLPAFLEFARG--AVLVAHNAPFDIGFLRAAAARCGYP--W-PGPPVLCTVRLARRVLPRD-----EAPNVR 146 (557)
T ss_pred hCCCCHHHHHHHHHHHhcC--CEEEEeCcHHHHHHHHHHHHHcCCC--C-CCCCcEecHHHHHHhcccC-----CCCCCC
Confidence 2345566677765 3558999999999987654333332 1 1245789556666555321 024789
Q ss_pred HHHHHHHHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009948 164 LANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (522)
Q Consensus 164 L~~L~~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~ 222 (522)
|+++++ ++|++.... +-|..||.++.+|+..+..++.+.|..
T Consensus 147 L~~L~~-~~gi~~~~~----------------H~Al~DA~ata~l~~~l~~~~~~~~~~ 188 (557)
T PRK07883 147 LSTLAR-LFGATTTPT----------------HRALDDARATVDVLHGLIERLGNLGVH 188 (557)
T ss_pred HHHHHH-HCCcccCCC----------------CCHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 999987 568765322 338999999999999999999876653
No 42
>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=96.35 E-value=0.087 Score=50.60 Aligned_cols=160 Identities=16% Similarity=0.209 Sum_probs=90.3
Q ss_pred CeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-------CCchhhHHHHHHhhCC--C
Q 009948 33 SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-------IPLPSIWELLKELFVS--P 103 (522)
Q Consensus 33 ~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~-------l~~~~~~~~L~~lL~~--~ 103 (522)
.+++||.|..+.... .....-.++||+... . +.+.++.+.... -...+++..+..++.. |
T Consensus 4 ~i~~fDIEt~~~~g~-p~~~~d~Ii~Is~~~--------~--~~~~~~~~~~~~~~~v~~~~~E~~lL~~F~~~i~~~dp 72 (195)
T cd05780 4 KILSFDIEVLNHEGE-PNPEKDPIIMISFAD--------E--GGNKVITWKKFDLPFVEVVKTEKEMIKRFIEIVKEKDP 72 (195)
T ss_pred eEEEEEEEecCCCCC-CCCCCCcEEEEEEec--------C--CCceEEEecCCCCCeEEEeCCHHHHHHHHHHHHHHcCC
Confidence 578999999743210 012234567776642 0 123333221110 1113455555555655 7
Q ss_pred CceEEEEech-hhHHHHHhhcccCCCccCccC-------------------CCceeeHHHHHHHhhccccCCCCCcCccc
Q 009948 104 DILKLGFKFK-QDLIYLSSTFCSQGCDIGFDR-------------------VEPYLDITSIYNHLHHKQLGRKLPKETKS 163 (522)
Q Consensus 104 ~i~KVgh~~k-~Dl~~L~~~~gi~g~~~~~~~-------------------~~~~~Dlt~La~yLl~~~~~~~~~~~~~g 163 (522)
++ .+|||.. +|+..|....-.+|+...+.. -...+|+-.++..... ..+++
T Consensus 73 di-ivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~~--------l~sy~ 143 (195)
T cd05780 73 DV-IYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLN--------LTRYT 143 (195)
T ss_pred CE-EEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhCC--------CCcCc
Confidence 75 4899976 699988543322333211110 0236786555543322 35899
Q ss_pred HHHHHHHHcCCcccc--ccccC-CCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009948 164 LANICKELLDISLSK--ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (522)
Q Consensus 164 L~~L~~~~Lg~~L~K--~~q~s-dW~~RPL~~~qi~YAA~DA~~ll~L~~~L 212 (522)
|..+++++||.+... ..+.. -|...+-...-++|+..||..+++|...|
T Consensus 144 L~~v~~~~Lg~~k~d~~~~~i~~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 144 LERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred HHHHHHHHhCCCCCcCCHHHHHHHHhCCCchHHHHHHhHHHHHHHHHHHhhC
Confidence 999999999986422 12222 24444434667899999999999998753
No 43
>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=96.29 E-value=0.14 Score=50.52 Aligned_cols=98 Identities=16% Similarity=0.209 Sum_probs=61.6
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCc-cCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCD-IGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~-~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~ 169 (522)
+++..|.+++.+.. .|+||+.+|+..|...+.-.|.. +.+.....++|+..++..+ .++ .+++|++|++
T Consensus 71 ev~~~f~~fi~~~~--lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~-~p~-------~~~~L~~L~~ 140 (225)
T TIGR01406 71 EIADEFLDFIGGSE--LVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARER-FPG-------QRNSLDALCK 140 (225)
T ss_pred HHHHHHHHHhCCCE--EEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHH-cCC-------CCCCHHHHHH
Confidence 45566777777643 48999999999987543222310 0011125689944444443 343 4679999999
Q ss_pred HHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009948 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 170 ~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~ 213 (522)
+| |++.... +.+-|..||..+.+||..|.
T Consensus 141 ~~-gi~~~~r--------------~~H~Al~DA~~~a~v~~~l~ 169 (225)
T TIGR01406 141 RF-KVDNSHR--------------TLHGALLDAHLLAEVYLALT 169 (225)
T ss_pred hc-CCCCCCC--------------CCcCHHHHHHHHHHHHHHHH
Confidence 86 6543211 11238899999999998886
No 44
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=96.24 E-value=0.18 Score=48.56 Aligned_cols=98 Identities=17% Similarity=0.194 Sum_probs=59.9
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhccc-CCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCS-QGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi-~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~ 169 (522)
+++..|..++.+. ..||||+..|+..|.+.+.- .+. ......+|+..++......... ....+++|+++++
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 4556677777754 45999999999988654310 121 1125678965555332221100 0123579999996
Q ss_pred HHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009948 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 170 ~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~ 213 (522)
.+ |++....+ -|..||.++..|+..|.
T Consensus 172 ~~-gi~~~~~H----------------~Al~DA~ata~l~~~l~ 198 (202)
T PRK09145 172 HL-DLPVLGRH----------------DALNDAIMAALIFLRLR 198 (202)
T ss_pred Hc-CCCCCCCC----------------CcHHHHHHHHHHHHHHH
Confidence 64 76553222 27899999999998875
No 45
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=96.22 E-value=0.15 Score=46.83 Aligned_cols=98 Identities=17% Similarity=0.185 Sum_probs=63.1
Q ss_pred hhHHHHHHhhCCCCceEEEEec-hhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKF-KQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~-k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~ 169 (522)
++...|..++.+.. .|+|+. +.|+..|...+...|+. +......+|+..++..+ .+. ...+|.++++
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 467777 99999987754332321 11124479954544433 332 3789999998
Q ss_pred HHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009948 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKV 216 (522)
Q Consensus 170 ~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L 216 (522)
.+ |.+.... .+.|..||..+.+|+..+.+++
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 4333111 2558999999999999998654
No 46
>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=96.21 E-value=0.014 Score=55.01 Aligned_cols=81 Identities=20% Similarity=0.216 Sum_probs=54.7
Q ss_pred HHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcCC
Q 009948 95 LLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDI 174 (522)
Q Consensus 95 ~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~ 174 (522)
.|..++ +++.+.|||++.+|+.+|.-.++ -..+.| |.+.. ..+. ....+|..|+.++||.
T Consensus 94 ~l~~li-~~~tILVGHsL~nDL~aL~l~hp----------~~~viD-Ta~l~--~~~~------~r~~sLk~La~~~L~~ 153 (174)
T cd06143 94 KLRLLV-DLGCIFVGHGLAKDFRVINIQVP----------KEQVID-TVELF--HLPG------QRKLSLRFLAWYLLGE 153 (174)
T ss_pred HHHHHc-CCCCEEEeccchhHHHHhcCcCC----------CcceEE-cHHhc--cCCC------CCChhHHHHHHHHcCC
Confidence 455555 45566799999999999865321 146889 64321 1221 2368999999999998
Q ss_pred ccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009948 175 SLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (522)
Q Consensus 175 ~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~ 210 (522)
.+-.+. .| ..+||.++++||.
T Consensus 154 ~IQ~~~--Hd-------------SvEDArAam~Ly~ 174 (174)
T cd06143 154 KIQSET--HD-------------SIEDARTALKLYR 174 (174)
T ss_pred cccCCC--cC-------------cHHHHHHHHHHhC
Confidence 874321 11 4689999999983
No 47
>PRK05168 ribonuclease T; Provisional
Probab=96.17 E-value=0.34 Score=47.20 Aligned_cols=93 Identities=16% Similarity=0.170 Sum_probs=60.2
Q ss_pred CceEEEEechhhHHHHHhhcccCCCcc-CccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcCCcccccccc
Q 009948 104 DILKLGFKFKQDLIYLSSTFCSQGCDI-GFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQC 182 (522)
Q Consensus 104 ~i~KVgh~~k~Dl~~L~~~~gi~g~~~-~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~K~~q~ 182 (522)
+.+.||||+..|+..|.+.+.-.|+.. .+ ....++|+..++..+. + ..+|..+++. +|+++....
T Consensus 114 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~-~~~~~iDt~~lar~~~-~---------~~~L~~l~~~-~gl~~~~~~-- 179 (211)
T PRK05168 114 RAILVAHNAHFDLSFLMAAAERAGLKRNPF-HPFSTFDTATLSGLAL-G---------QTVLAKACQA-AGIEFDNKE-- 179 (211)
T ss_pred CceEEEeccHHhHHHHHHHHHHhCCCCCCC-CCCcEeeHHHHHHHHc-C---------CCCHHHHHHH-CCCCCCCCC--
Confidence 456799999999998876432222210 00 0124799556655443 2 3579999887 476643111
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009948 183 SDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (522)
Q Consensus 183 sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~ 222 (522)
.+-|..||.++.+|+..|..++.+.|.+
T Consensus 180 ------------~H~Al~DA~ata~l~~~l~~~~~~~~~~ 207 (211)
T PRK05168 180 ------------AHSALYDTEKTAELFCEIVNRWKRLGGW 207 (211)
T ss_pred ------------CCChHHHHHHHHHHHHHHHHHHHHccCC
Confidence 1228899999999999999999877653
No 48
>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=96.17 E-value=0.018 Score=52.93 Aligned_cols=86 Identities=20% Similarity=0.260 Sum_probs=56.0
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
+++..+.+++.+ +.+.||||+.+|+..|... ...++|+..++..+..+ ..+++|..|+++
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 355566777752 3456999999999999652 14578943343332221 236899999999
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~ 209 (522)
++|..+....+. +-|..||.++.+||
T Consensus 124 ~~~~~i~~~~~~-------------H~Al~DA~~t~~l~ 149 (150)
T cd06145 124 YLGRDIQQGEGG-------------HDSVEDARAALELV 149 (150)
T ss_pred HCCcceeCCCCC-------------CCcHHHHHHHHHHh
Confidence 998655321111 22778999998876
No 49
>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=96.16 E-value=0.093 Score=51.28 Aligned_cols=105 Identities=17% Similarity=0.189 Sum_probs=65.0
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
+++..|..++.+. ..||||+.+|+..|.+.+.-.+.. ......++|+..++.++. +. .+..+.+|..+++.
T Consensus 76 ev~~~~~~~~~~~--~lVaHNa~FD~~fL~~~~~r~~~~--~~~~~~~~dtl~l~~~~~-~~----~~~~~~~L~~l~~~ 146 (217)
T TIGR00573 76 EIAEDFADYIRGA--ELVIHNASFDVGFLNYEFSKLYKV--EPKTNDVIDTTDTLQYAR-PE----FPGKRNTLDALCKR 146 (217)
T ss_pred HHHHHHHHHhCCC--EEEEeccHHHHHHHHHHHHHhcCC--CCCccceecHHHHHHHHH-Hh----CCCCCCCHHHHHHH
Confidence 3556667777653 458999999999997764311110 011246788444555443 21 11246789999877
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~ 219 (522)
+ |++.... . .+=|..||.++.+|+..+..+..+.
T Consensus 147 ~-gl~~~~~-~-------------~H~Al~DA~~ta~l~~~l~~~~~~~ 180 (217)
T TIGR00573 147 Y-EITNSHR-A-------------LHGALADAFILAKLYLVMTGKQTKY 180 (217)
T ss_pred c-CCCCCCc-c-------------cCCHHHHHHHHHHHHHHHHhcchhh
Confidence 5 6543200 1 1228899999999999998765544
No 50
>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=96.14 E-value=0.032 Score=47.40 Aligned_cols=82 Identities=17% Similarity=0.203 Sum_probs=55.1
Q ss_pred EEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCC-ceEEEEech
Q 009948 35 VGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPD-ILKLGFKFK 113 (522)
Q Consensus 35 Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~~~~-i~KVgh~~k 113 (522)
+++|+|+.+..+ +.+++.++|++... .+..|++| +.+++.+.. ...|+||..
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 66889999998741 24567766 556777665 678999999
Q ss_pred hhHHHHHhhcccCCCccCccCCCceeeHHHHH
Q 009948 114 QDLIYLSSTFCSQGCDIGFDRVEPYLDITSIY 145 (522)
Q Consensus 114 ~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La 145 (522)
.|+..|.+.+...+.... ....+.+| |+.+
T Consensus 54 fD~~fL~~~~~~~~~~~p-~~~~~~lD-T~~l 83 (96)
T cd06125 54 FDLPFLNNRCAELGLKYP-LLAGSWID-TIKL 83 (96)
T ss_pred HhHHHHHHHHHHcCCCCC-CcCCcEEE-ehHH
Confidence 999888765433332110 01356889 5544
No 51
>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=96.14 E-value=0.02 Score=53.26 Aligned_cols=87 Identities=20% Similarity=0.236 Sum_probs=56.8
Q ss_pred HHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHc
Q 009948 93 WELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELL 172 (522)
Q Consensus 93 ~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~L 172 (522)
++.|.+++.+. .+.||||+..|+..|... ...++|+..++..+. +.. ....+++|..|+++++
T Consensus 74 ~~~~~~~i~~~-~vlVgHn~~fD~~fL~~~------------~~~~iDT~~l~~~~~-~~~---~~~~~~~L~~L~~~~~ 136 (161)
T cd06137 74 RAALWKFIDPD-TILVGHSLQNDLDALRMI------------HTRVVDTAILTREAV-KGP---LAKRQWSLRTLCRDFL 136 (161)
T ss_pred HHHHHHhcCCC-cEEEeccHHHHHHHHhCc------------CCCeeEehhhhhhcc-CCC---cCCCCccHHHHHHHHC
Confidence 34566666653 345999999999999652 135789555555443 320 0014789999999999
Q ss_pred CCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009948 173 DISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (522)
Q Consensus 173 g~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~ 209 (522)
|+++.......+ |..||.++.+||
T Consensus 137 ~~~~~~~~~~H~-------------A~~DA~at~~l~ 160 (161)
T cd06137 137 GLKIQGGGEGHD-------------SLEDALAAREVV 160 (161)
T ss_pred CchhcCCCCCCC-------------cHHHHHHHHHHh
Confidence 987743211122 778999888876
No 52
>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=96.02 E-value=0.13 Score=49.30 Aligned_cols=110 Identities=22% Similarity=0.282 Sum_probs=65.0
Q ss_pred hhHHHHHHhhCC--CCceEEEEec-hhhHHHHHhhcccCCCcc--CccC-----------------CCceeeHHHHHHHh
Q 009948 91 SIWELLKELFVS--PDILKLGFKF-KQDLIYLSSTFCSQGCDI--GFDR-----------------VEPYLDITSIYNHL 148 (522)
Q Consensus 91 ~~~~~L~~lL~~--~~i~KVgh~~-k~Dl~~L~~~~gi~g~~~--~~~~-----------------~~~~~Dlt~La~yL 148 (522)
+++..+.+++.+ |++ .+|||. ..|+..|......+|+.. .+.. -..++|+-.++...
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 599999 689999854332233321 0000 12367855454433
Q ss_pred hccccCCCCCcCcccHHHHHHHHcCCcccc--ccccCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009948 149 HHKQLGRKLPKETKSLANICKELLDISLSK--ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (522)
Q Consensus 149 l~~~~~~~~~~~~~gL~~L~~~~Lg~~L~K--~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~ 209 (522)
.. ..+++|.++++.+||..-.. .....+|....-...-+.|...||..+++|+
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 2223332111223557899999999999886
No 53
>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=95.91 E-value=0.12 Score=60.80 Aligned_cols=99 Identities=15% Similarity=0.259 Sum_probs=65.7
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
++...|.+++.+. +.||||+.+|+..|.+.+.-.|..+ .....+|...++..+. +. ..+++|.+|++.
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 3556677777653 4699999999999876432223221 2356899545555443 32 257899999888
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ 218 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~ 218 (522)
+|++.... +-|..||.++.+|+..+.+++.+
T Consensus 137 -~gi~~~~~----------------H~Al~DA~ata~l~~~l~~~~~~ 167 (850)
T TIGR01407 137 -LGLTHENP----------------HRADSDAQATAELLLLLFEKMEK 167 (850)
T ss_pred -CCCCCCCC----------------CChHHHHHHHHHHHHHHHHHHHh
Confidence 57765322 22778888888888888777764
No 54
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=95.80 E-value=0.13 Score=59.96 Aligned_cols=101 Identities=20% Similarity=0.273 Sum_probs=68.1
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
++...|.+++.+ -+.||||+..|+..|.+.+...|. ....+.+|...++..+ .+. ..+++|.+|++.
T Consensus 75 ev~~~~~~~l~~--~~lVaHN~~FD~~fL~~~~~~~g~----~~~~~~iDT~~la~~~-~p~------~~~~~L~~L~~~ 141 (820)
T PRK07246 75 QVARHIYDLIED--CIFVAHNVKFDANLLAEALFLEGY----ELRTPRVDTVELAQVF-FPT------LEKYSLSHLSRE 141 (820)
T ss_pred HHHHHHHHHhCC--CEEEEECcHHHHHHHHHHHHHcCC----CCCCCceeHHHHHHHH-hCC------CCCCCHHHHHHH
Confidence 456667777776 345999999999999764321122 1235678944455444 343 247899999976
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGN 221 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~ 221 (522)
+|++.... +-|..||.++.+|+..|..++...+.
T Consensus 142 -lgl~~~~~----------------H~Al~DA~ata~L~~~l~~~l~~l~~ 175 (820)
T PRK07246 142 -LNIDLADA----------------HTAIADARATAELFLKLLQKIESLPK 175 (820)
T ss_pred -cCCCCCCC----------------CCHHHHHHHHHHHHHHHHHHHhhcCc
Confidence 68765322 22889999999999999988865443
No 55
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=95.77 E-value=0.39 Score=47.82 Aligned_cols=102 Identities=18% Similarity=0.131 Sum_probs=62.0
Q ss_pred hHHHHHHhhCCCCceEEEEechhhHHHHHhhccc-CCCccCccCCCceeeHHHHHHHhhccccCC------CCCcCcccH
Q 009948 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTFCS-QGCDIGFDRVEPYLDITSIYNHLHHKQLGR------KLPKETKSL 164 (522)
Q Consensus 92 ~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi-~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~------~~~~~~~gL 164 (522)
++..|.+++.+ -+.|+||+..|...|.+.+.- .+. .....++|...++..+.....+. .....+++|
T Consensus 119 vl~~l~~~~~~--~~lVaHna~FD~~fL~~~l~~~~~~----~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L 192 (239)
T PRK09146 119 ILDELLEALAG--KVVVVHYRRIERDFLDQALRNRIGE----GIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRL 192 (239)
T ss_pred HHHHHHHHhCC--CEEEEECHHHHHHHHHHHHHHhcCC----CCCCceechHHHHHHHcccccccccchhccCCCCCCCH
Confidence 45555556655 345899999999998664211 011 11256899666666654321000 001146789
Q ss_pred HHHHHHHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009948 165 ANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKV 216 (522)
Q Consensus 165 ~~L~~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L 216 (522)
.+++.+ +|++.... +-|..||.++.+|+..+..+.
T Consensus 193 ~~l~~~-~gl~~~~~----------------H~Al~DA~ata~l~~~~~~~~ 227 (239)
T PRK09146 193 ADSRLR-YGLPAYSP----------------HHALTDAIATAELLQAQIAHH 227 (239)
T ss_pred HHHHHH-cCCCCCCC----------------CCcHHHHHHHHHHHHHHHHHH
Confidence 999887 46554221 228899999999998887665
No 56
>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=95.74 E-value=0.38 Score=43.70 Aligned_cols=89 Identities=19% Similarity=0.231 Sum_probs=57.9
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
+++..|.+++.+ ...||||+..|+..|...+.-.|+.+ .....+|+..++..+. +. ....+|..+++.
T Consensus 66 ~v~~~l~~~l~~--~~lv~hn~~fD~~~l~~~~~~~g~~~---~~~~~idt~~~~~~~~-~~------~~~~~L~~l~~~ 133 (156)
T cd06130 66 EVWPEIKPFLGG--SLVVAHNASFDRSVLRAALEAYGLPP---PPYQYLCTVRLARRVW-PL------LPNHKLNTVAEH 133 (156)
T ss_pred HHHHHHHHHhCC--CEEEEeChHHhHHHHHHHHHHcCCCC---CCCCEEEHHHHHHHHh-cc------CCCCCHHHHHHH
Confidence 456677788876 35699999999999865433223221 1356889444554443 32 246899999986
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~ 209 (522)
+|++.. . +-|..||..+.+|+
T Consensus 134 -~g~~~~-~----------------H~Al~Da~~ta~l~ 154 (156)
T cd06130 134 -LGIELN-H----------------HDALEDARACAEIL 154 (156)
T ss_pred -cCCCcc-C----------------cCchHHHHHHHHHH
Confidence 576653 2 22778898888876
No 57
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=95.74 E-value=0.23 Score=58.95 Aligned_cols=99 Identities=20% Similarity=0.222 Sum_probs=65.7
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
++...|..++.+ .+.|+||+.+|+..|.+.+.-.|..+ .....+|+..++..+. |. ..+++|++|++.
T Consensus 73 ev~~~l~~~l~~--~~~VaHN~~FD~~fL~~~~~~~g~~~---~~~~~iDt~~la~~~~-p~------~~~~~L~~l~~~ 140 (928)
T PRK08074 73 DVAPEIVELLEG--AYFVAHNVHFDLNFLNEELERAGYTE---IHCPKLDTVELARILL-PT------AESYKLRDLSEE 140 (928)
T ss_pred HHHHHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCC---CCCCeeeHHHHHHHhc-CC------CCCCCHHHHHHh
Confidence 455667778875 35599999999999976543223221 2357899555655443 42 247899999987
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ 218 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~ 218 (522)
||++....+ -|-.||.++..|+..|.+++.+
T Consensus 141 -l~i~~~~~H----------------~Al~DA~ata~l~~~l~~~~~~ 171 (928)
T PRK08074 141 -LGLEHDQPH----------------RADSDAEVTAELFLQLLNKLER 171 (928)
T ss_pred -CCCCCCCCC----------------ChHHHHHHHHHHHHHHHHHHHh
Confidence 576543222 2777888888888888777765
No 58
>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=95.51 E-value=0.39 Score=42.96 Aligned_cols=91 Identities=18% Similarity=0.203 Sum_probs=58.1
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
++...+..++.+ ...||||...|...|.+.+...+.. ......+|+..++..+... ...+++..+...
T Consensus 68 ~~~~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~---~~~~~~iDt~~~~~~~~~~-------~~~~~l~~~~~~ 135 (159)
T cd06127 68 EVLPEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGP---PLPNPWIDTLRLARRLLPG-------LRSHRLGLLLAE 135 (159)
T ss_pred HHHHHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCC---CCCCCeeEHHHHHHHHcCC-------CCcCchHHHHHH
Confidence 456677778877 4569999999999987754322211 0136689955565555432 245678877555
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~ 209 (522)
++|....+ .+-|..||.++.+|+
T Consensus 136 ~~~~~~~~----------------~H~Al~Da~~t~~l~ 158 (159)
T cd06127 136 RYGIPLEG----------------AHRALADALATAELL 158 (159)
T ss_pred HcCCCCCC----------------CCCcHHHHHHHHHHh
Confidence 55653321 233889999998876
No 59
>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=94.59 E-value=0.4 Score=46.26 Aligned_cols=93 Identities=15% Similarity=0.138 Sum_probs=60.0
Q ss_pred CceEEEEechhhHHHHHhhcccCCCccCcc-CCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcCCcccccccc
Q 009948 104 DILKLGFKFKQDLIYLSSTFCSQGCDIGFD-RVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQC 182 (522)
Q Consensus 104 ~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~-~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~K~~q~ 182 (522)
+-+.||||+..|+..|...+.-.+... .. ....++|...++..+ .+ ..+|..+++.+ |++..
T Consensus 105 ~~~lVaHNa~FD~~fL~~~~~r~~~~~-~~~~~~~~lDTl~lar~~-~~---------~~~L~~l~~~~-gi~~~----- 167 (200)
T TIGR01298 105 RAILVGHNANFDLGFLNAAVERTSLKR-NPFHPFSTFDTATLAGLA-YG---------QTVLAKACQAA-GXDFD----- 167 (200)
T ss_pred CCEEEEECchhhHHHHHHHHHHhCCCC-CCCCCCcEEEHHHHHHHH-cC---------cccHHHHHHHc-CCCcc-----
Confidence 345799999999999876432112110 00 012479955555443 22 35799999864 65532
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009948 183 SDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (522)
Q Consensus 183 sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~ 222 (522)
..+.+-|..||.++.+|+..+..++.+.|.+
T Consensus 168 ---------~~~~H~Al~Da~ata~lf~~l~~~~~~~~~~ 198 (200)
T TIGR01298 168 ---------STQAHSALYDTEKTAELFCEIVNRWKRLGGW 198 (200)
T ss_pred ---------ccchhhhHHhHHHHHHHHHHHHHHHHHccCC
Confidence 1133458899999999999999999877654
No 60
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=94.45 E-value=0.16 Score=59.67 Aligned_cols=103 Identities=19% Similarity=0.384 Sum_probs=76.3
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
+++..+++++.+. +-|.||+.+|+..|...|--.++.+ .-++++|..+++ ..++|. ..+++|..||..
T Consensus 490 ~vL~kf~~~~~d~--IlVAHNasFD~gFl~~~~~k~~~~~---~~~pvIDTL~la-r~L~P~------~ksh~Lg~l~kk 557 (1444)
T COG2176 490 EVLEKFREFIGDS--ILVAHNASFDMGFLNTNYEKYGLEP---LTNPVIDTLELA-RALNPE------FKSHRLGTLCKK 557 (1444)
T ss_pred HHHHHHHHHhcCc--EEEeccCccchhHHHHHHHHhCCcc---ccCchhhHHHHH-HHhChh------hhhcchHHHHHH
Confidence 5677888888874 4599999999999865433223322 347899944554 555565 368999999988
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~ 222 (522)
+ |+.+ ++.+-|-.||.++-.++-.+.+.+++.|..
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 4433 456668899999999999999999999875
No 61
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=94.28 E-value=0.7 Score=44.53 Aligned_cols=108 Identities=13% Similarity=0.086 Sum_probs=63.6
Q ss_pred hhHHHHHHhhCCCCceEEEEech-hhHHHHHhhcccCCCccCccCCCceeeHHHHH--HHhh-ccccCCCCCcCcccHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFK-QDLIYLSSTFCSQGCDIGFDRVEPYLDITSIY--NHLH-HKQLGRKLPKETKSLAN 166 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k-~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La--~yLl-~~~~~~~~~~~~~gL~~ 166 (522)
+++..|..++.+.. .||||+. .|+..|... |. .+ . ....+|+...+ .... .++ ..+++|.+
T Consensus 73 evl~~f~~f~~~~~--lVaHNa~~fD~~fL~~~-g~-~~----~-~~~~idt~~~~~~~~~~~~~~------~~~~~L~~ 137 (195)
T PRK07247 73 EVLAAFKEFVGELP--LIGYNAQKSDLPILAEN-GL-DL----S-DQYQVDLYDEAFERRSSDLNG------IANLKLQT 137 (195)
T ss_pred HHHHHHHHHHCCCe--EEEEeCcHhHHHHHHHc-CC-Cc----C-CCceeehHHHHHHhhccccCC------CCCCCHHH
Confidence 45667777787653 5999996 799999773 33 11 0 11234521111 1111 111 24689999
Q ss_pred HHHHHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchhhccc
Q 009948 167 ICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNSCSSISELDS 231 (522)
Q Consensus 167 L~~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~~~~~~~~~~ 231 (522)
|++. +|++. .. +-|..||.++..|+..|...-+.+..++++-++-++
T Consensus 138 La~~-~gi~~-~~----------------HrAl~DA~~ta~v~~~ll~~~~~~~~~~~~~~~~~~ 184 (195)
T PRK07247 138 VADF-LGIKG-RG----------------HNSLEDARMTARVYESFLESDQNKEYLEQQEEVTSD 184 (195)
T ss_pred HHHh-cCCCC-CC----------------cCCHHHHHHHHHHHHHHHhhccchhhhhcchhhccC
Confidence 9886 57653 11 227899999999999998665554444444444443
No 62
>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=94.27 E-value=1.2 Score=42.57 Aligned_cols=158 Identities=15% Similarity=0.208 Sum_probs=83.1
Q ss_pred CeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhC--CCCceEEEE
Q 009948 33 SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFV--SPDILKLGF 110 (522)
Q Consensus 33 ~~Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~--~~~i~KVgh 110 (522)
.+++||.|..+... ......-.+++|+... ..+...++-.......+++..+-.++. +|+++ +||
T Consensus 4 ~~l~fDIEt~~~~g-fp~~~~d~Ii~Is~~~-----------~~g~~~~~~~~~~~E~~lL~~F~~~i~~~dPd~i-~gy 70 (188)
T cd05781 4 KTLAFDIEVYSKYG-TPNPRRDPIIVISLAT-----------SNGDVEFILAEGLDDRKIIREFVKYVKEYDPDII-VGY 70 (188)
T ss_pred eEEEEEEEecCCCC-CCCCCCCCEEEEEEEe-----------CCCCEEEEEecCCCHHHHHHHHHHHHHHcCCCEE-Eec
Confidence 57899999974221 0011223566665541 012222332111223345555555555 45643 799
Q ss_pred ech-hhHHHHHhhcccCCCccCccCCC-----------------ceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHc
Q 009948 111 KFK-QDLIYLSSTFCSQGCDIGFDRVE-----------------PYLDITSIYNHLHHKQLGRKLPKETKSLANICKELL 172 (522)
Q Consensus 111 ~~k-~Dl~~L~~~~gi~g~~~~~~~~~-----------------~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~L 172 (522)
|.. +|+..|......+|+...+.... ..+|+-.+...... ..+++|.++++ +|
T Consensus 71 N~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~--------l~~y~L~~Va~-~L 141 (188)
T cd05781 71 NSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPE--------VKVKTLENVAE-YL 141 (188)
T ss_pred CCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCC--------CCCCCHHHHHH-HH
Confidence 966 79988743222233321111101 16775444433221 35799999997 58
Q ss_pred CCc--ccc----ccccC-CCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009948 173 DIS--LSK----ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (522)
Q Consensus 173 g~~--L~K----~~q~s-dW~~RPL~~~qi~YAA~DA~~ll~L~~~L 212 (522)
|.. ..| ..+.. -|....-...-+.|...|+..++.|+..+
T Consensus 142 g~~k~~~k~~~~~~~i~~~~~~~~~~~~l~~Y~~~D~~~t~~l~~~~ 188 (188)
T cd05781 142 GVMKKSERVLIEWYRIYEYWDDEKKRDILLKYNRDDARSTYGLAEKL 188 (188)
T ss_pred CCCccccccCCCHHHHHHHHcCcccHHHHHHHHHHHHHHHHHHHhhC
Confidence 863 122 11111 25432134667899999999999998753
No 63
>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=93.81 E-value=1.6 Score=41.90 Aligned_cols=110 Identities=23% Similarity=0.276 Sum_probs=62.5
Q ss_pred hhHHHHHHhhC--CCCceEEEEechh-hHHHHHhhcccCCCccCccC--------------------C-CceeeHHHHHH
Q 009948 91 SIWELLKELFV--SPDILKLGFKFKQ-DLIYLSSTFCSQGCDIGFDR--------------------V-EPYLDITSIYN 146 (522)
Q Consensus 91 ~~~~~L~~lL~--~~~i~KVgh~~k~-Dl~~L~~~~gi~g~~~~~~~--------------------~-~~~~Dlt~La~ 146 (522)
+++..+..++. +|+| .+|||..+ |+..|......+|+.+.+.+ . ...+|+-.+..
T Consensus 53 ~lL~~f~~~i~~~dPDv-i~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k 131 (193)
T cd05784 53 SLLLALIAWFAQYDPDI-IIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALK 131 (193)
T ss_pred HHHHHHHHHHHhhCCCE-EEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHH
Confidence 34555544444 4565 48999885 99887543322333321111 0 11677433333
Q ss_pred HhhccccCCCCCcCcccHHHHHHHHcCCcccc-cc-----ccC-CCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009948 147 HLHHKQLGRKLPKETKSLANICKELLDISLSK-EL-----QCS-DWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (522)
Q Consensus 147 yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~K-~~-----q~s-dW~~RPL~~~qi~YAA~DA~~ll~L~~ 210 (522)
.-. ....+++|.++++++||..-.. .. ... -|...+ ..-+.|+..||..+++|++
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 200 1135899999999999964221 11 122 244333 4578999999999999863
No 64
>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=93.53 E-value=1.2 Score=43.39 Aligned_cols=160 Identities=16% Similarity=0.163 Sum_probs=81.1
Q ss_pred CCeEEEEEEEeCCCCCC---CCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhC--CCCce
Q 009948 32 SSLVGLDAEWKPQRSHQ---SNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFV--SPDIL 106 (522)
Q Consensus 32 ~~~Vg~D~E~~~~~~~~---~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~--~~~i~ 106 (522)
-.+++||.|..+..... .....-.++||+... . .+...++........+++..+..++. +|++
T Consensus 9 lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~---------~--~~~~~~~~~~~~~E~~lL~~f~~~i~~~dPdi- 76 (207)
T cd05785 9 LRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRD---------N--RGWEEVLHAEDAAEKELLEELVAIIRERDPDV- 76 (207)
T ss_pred ceEEEEEEEecCCCCccCCCCCCCCCeEEEEeccc---------C--CCceeeeccCCCCHHHHHHHHHHHHHHhCCCE-
Confidence 36899999986543210 112334688888752 0 11111221111222345555555554 4675
Q ss_pred EEEEec-hhhHHHHHhhcccCCCccCccC--------------------------C-CceeeHHHHHHHhhccccCCCCC
Q 009948 107 KLGFKF-KQDLIYLSSTFCSQGCDIGFDR--------------------------V-EPYLDITSIYNHLHHKQLGRKLP 158 (522)
Q Consensus 107 KVgh~~-k~Dl~~L~~~~gi~g~~~~~~~--------------------------~-~~~~Dlt~La~yLl~~~~~~~~~ 158 (522)
.+|||. .+|+..|......+|+...+.+ . ..++|+-.++....... . .
T Consensus 77 i~g~N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~--~--~ 152 (207)
T cd05785 77 IEGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSS--R--D 152 (207)
T ss_pred EeccCCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccc--c--C
Confidence 479999 6799887543222333211100 0 12368433333211110 0 1
Q ss_pred cCcccHHHHHHHH--cCCc-cc-cccccC-CCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009948 159 KETKSLANICKEL--LDIS-LS-KELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIF 209 (522)
Q Consensus 159 ~~~~gL~~L~~~~--Lg~~-L~-K~~q~s-dW~~RPL~~~qi~YAA~DA~~ll~L~ 209 (522)
..+++|.++++.+ ++.. .+ ...+.. -|...+ +.-+.|...||..++.|+
T Consensus 153 l~sysL~~Va~~~g~~~~~k~d~~~~~I~~l~~~~~--~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 153 LPSYGLKAVAKHFGLASPDRTYIDGRQIAEVWRSDP--ARLLAYALDDVRETEGLA 206 (207)
T ss_pred CCCCCHHHHHHHhcccCCCcCCCCHHHHHHHHhcCH--HHHHHHHHHHHHHHHHhh
Confidence 2478999999986 2321 11 011111 254442 567899999999999875
No 65
>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=93.04 E-value=0.86 Score=43.53 Aligned_cols=84 Identities=17% Similarity=0.184 Sum_probs=52.8
Q ss_pred ceEEEEechhhHHHHHhhcccCCC-ccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcCCccccccccC
Q 009948 105 ILKLGFKFKQDLIYLSSTFCSQGC-DIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCS 183 (522)
Q Consensus 105 i~KVgh~~k~Dl~~L~~~~gi~g~-~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~K~~q~s 183 (522)
.+.||||+..|+..|.+.+.-.|+ ...+ ....++|+..++..+. + ..+|++++++ +|+++....
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 467999999999998754322232 0000 1134799556655543 2 3479999886 476542111
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 009948 184 DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (522)
Q Consensus 184 dW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~ 214 (522)
.+-|..||.++.+|+..|.+
T Consensus 168 -----------~H~Al~DA~ata~lf~~l~~ 187 (189)
T cd06134 168 -----------AHSALYDTQKTAELFCKIVN 187 (189)
T ss_pred -----------CcChHHHHHHHHHHHHHHHH
Confidence 12388999999999988864
No 66
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=92.91 E-value=1.7 Score=53.61 Aligned_cols=103 Identities=16% Similarity=0.246 Sum_probs=69.8
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
+++..+..++.+ ...|+|+...|+..|...+.-+|+.+ .....+| ++-.++.+.+. ...++|..|+++
T Consensus 488 EaL~~f~~figg--~vLVAHNa~FD~~fL~~~l~rlgl~~---l~~~~ID-TLelar~l~p~------~k~~kL~~LAk~ 555 (1437)
T PRK00448 488 EVLPKFKEFCGD--SILVAHNASFDVGFINTNYEKLGLEK---IKNPVID-TLELSRFLYPE------LKSHRLNTLAKK 555 (1437)
T ss_pred HHHHHHHHHhCC--CEEEEeCccccHHHHHHHHHHcCCcc---cccccee-HHHHHHHHcCc------cccccHHHHHHH
Confidence 344555555554 56799999999988754433233321 2356789 44444444443 357899999987
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~ 222 (522)
+|+.+... +-|..||.++.+|+..|..++.+.|..
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 57665322 348899999999999999999887665
No 67
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=92.61 E-value=0.83 Score=47.17 Aligned_cols=99 Identities=17% Similarity=0.200 Sum_probs=64.9
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
+++..|.+++.+ -+.|+||+.+|+..|.+.+.-.+... ....++|+..++..+. +. ...++|..|++.
T Consensus 69 ev~~~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~~---~~~~~idT~~lar~l~-~~------~~~~~L~~L~~~ 136 (309)
T PRK06195 69 KIWEKIKHYFNN--NLVIAHNASFDISVLRKTLELYNIPM---PSFEYICTMKLAKNFY-SN------IDNARLNTVNNF 136 (309)
T ss_pred HHHHHHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCCC---CCCCEEEHHHHHHHHc-CC------CCcCCHHHHHHH
Confidence 456677777765 35699999999998865432222211 1246889445666554 32 246899999888
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~ 219 (522)
+ |++.. -+-|..||.++.+|+..|.+++...
T Consensus 137 ~-gi~~~-----------------~H~Al~DA~ata~l~~~l~~~~~~~ 167 (309)
T PRK06195 137 L-GYEFK-----------------HHDALADAMACSNILLNISKELNSK 167 (309)
T ss_pred c-CCCCc-----------------ccCCHHHHHHHHHHHHHHHHHhccC
Confidence 5 65421 1338899999999998888766543
No 68
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=92.47 E-value=2.4 Score=44.74 Aligned_cols=109 Identities=7% Similarity=0.008 Sum_probs=61.7
Q ss_pred hhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCc------------------------cCccCCCceeeHHHHH
Q 009948 90 PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCD------------------------IGFDRVEPYLDITSIY 145 (522)
Q Consensus 90 ~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~------------------------~~~~~~~~~~Dlt~La 145 (522)
.+++..|.+++.+. +.|+||+.+|+..|.+.+.-.... .+......++|...++
T Consensus 113 ~eVl~el~~fL~g~--vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LA 190 (377)
T PRK05601 113 SQILKPLDRLIDGR--TLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATA 190 (377)
T ss_pred HHHHHHHHHHhCCC--EEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHH
Confidence 35677788888764 459999999999886543110000 0001224689944555
Q ss_pred HHhhccccCCCCCcCcccHHHHHHHHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009948 146 NHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (522)
Q Consensus 146 ~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L 212 (522)
..+. +. ..++.|..|+.+ +|++.+... .|. .++.-+..++ +-.||..+.+|+..+
T Consensus 191 Rrl~-p~------l~~~rL~~La~~-lGi~~p~~~-A~~-~Ra~~p~~~l--~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 191 RRQG-VA------LDDIRIRGVAHT-LGLDAPAAE-ASV-ERAQVPHRQL--CREETLLVARLYFAL 245 (377)
T ss_pred HHHc-CC------CCCCCHHHHHHH-hCCCCCchh-hhh-hhhcCChhhh--hhHHHHHHHHHHHHh
Confidence 5554 43 357999999987 577653211 000 0001111111 225899998888776
No 69
>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=92.19 E-value=3.8 Score=40.30 Aligned_cols=54 Identities=17% Similarity=0.177 Sum_probs=39.1
Q ss_pred CcccHHHHHHHHcCCcccc--ccccCC-CCCCCCC-HHHHHHHHHHHHHHHHHHHHHH
Q 009948 160 ETKSLANICKELLDISLSK--ELQCSD-WSNRPLT-EEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 160 ~~~gL~~L~~~~Lg~~L~K--~~q~sd-W~~RPL~-~~qi~YAA~DA~~ll~L~~~L~ 213 (522)
.+++|.++++++||..... ...... |+..|-. ..-+.|...||..+++|...|.
T Consensus 167 ~sy~L~~Va~~~Lg~~k~d~~~~~i~~~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl~ 224 (230)
T cd05777 167 RSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLM 224 (230)
T ss_pred ccCcHHHHHHHHhCCCCCCCCHHHHHHHHccCHhHhHHHHHhhHHHHHHHHHHHHHHh
Confidence 5899999999999965321 122233 4434432 4568999999999999999886
No 70
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=92.07 E-value=0.02 Score=59.38 Aligned_cols=130 Identities=21% Similarity=0.270 Sum_probs=88.2
Q ss_pred CCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCcc
Q 009948 51 FPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDI 130 (522)
Q Consensus 51 ~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~ 130 (522)
.+++|.+|.++. ..+|++|+..++...+-+.++.++++.+|.|+-|++..-+.+++..||+
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 458899999884 5789999877766566778999999999999999999999999998877
Q ss_pred CccCCCceeeHHHHHHHhhcc-ccCCCCCcCcccH-HHHHHHHcCCcc------cc-----ccccCCCCCCCCCHHHHHH
Q 009948 131 GFDRVEPYLDITSIYNHLHHK-QLGRKLPKETKSL-ANICKELLDISL------SK-----ELQCSDWSNRPLTEEQKNY 197 (522)
Q Consensus 131 ~~~~~~~~~Dlt~La~yLl~~-~~~~~~~~~~~gL-~~L~~~~Lg~~L------~K-----~~q~sdW~~RPL~~~qi~Y 197 (522)
..+++|| |+++.-+-.. +.|.-+|..-..+ +.|.. .|.+.+ .| .+...-|-.||.++.-+.-
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 8887666442 2233333222222 23333 222211 12 1234458899998877666
Q ss_pred HHHHHHH
Q 009948 198 AAIDAHC 204 (522)
Q Consensus 198 AA~DA~~ 204 (522)
-|..|.+
T Consensus 209 ~~~e~~~ 215 (458)
T KOG2405|consen 209 LALEATY 215 (458)
T ss_pred hhhhhhh
Confidence 6655555
No 71
>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=91.97 E-value=7.1 Score=37.85 Aligned_cols=161 Identities=16% Similarity=0.112 Sum_probs=85.2
Q ss_pred CeEEEEEEEeCCC----CCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-----------------CCchh
Q 009948 33 SLVGLDAEWKPQR----SHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-----------------IPLPS 91 (522)
Q Consensus 33 ~~Vg~D~E~~~~~----~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~-----------------l~~~~ 91 (522)
.+++||.|..+.. +. .....-.++||+..+. .+...++++.... -...+
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 5789999997422 21 0112236899988520 0113455553100 11234
Q ss_pred hHHHHHHhhCCCCceEEEEech-hhHHHHHhhcccCCCc-----cCcc------CCCceeeHHHHHHH-hhc-cccCCCC
Q 009948 92 IWELLKELFVSPDILKLGFKFK-QDLIYLSSTFCSQGCD-----IGFD------RVEPYLDITSIYNH-LHH-KQLGRKL 157 (522)
Q Consensus 92 ~~~~L~~lL~~~~i~KVgh~~k-~Dl~~L~~~~gi~g~~-----~~~~------~~~~~~Dlt~La~y-Ll~-~~~~~~~ 157 (522)
++..+.+++.+.. ..+|||.. +|+..|......+|+. ..+. .....+|+-...+. .+. ..++ .
T Consensus 76 lL~~F~~~i~~~~-~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~--~ 152 (204)
T cd05783 76 LIREAFKIISEYP-IVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFG--N 152 (204)
T ss_pred HHHHHHHHHhcCC-EEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhc--c
Confidence 5666666676654 45799987 6998875432223432 0000 01235775333322 110 0000 0
Q ss_pred CcCcccHHHHHHHHcCCccc-cccccCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009948 158 PKETKSLANICKELLDISLS-KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (522)
Q Consensus 158 ~~~~~gL~~L~~~~Lg~~L~-K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~ 210 (522)
+..+++|.++++.+||..-. -..+ -|.. =.+.-+.|+..||..++.|..
T Consensus 153 ~~~~~~L~~Va~~~lg~~K~~~~~~--i~~~--~~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 153 KYREYTLDAVAKALLGEGKVELEKN--ISEL--NLYELAEYNYRDAELTLELTT 202 (204)
T ss_pred ccccCcHHHHHHHhcCCCcccCCch--hhhh--cHHHHHHhhHHHHHHHHHHhc
Confidence 12578999999999996321 1111 1222 125568999999999998864
No 72
>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=91.86 E-value=2.1 Score=41.54 Aligned_cols=110 Identities=15% Similarity=0.180 Sum_probs=61.9
Q ss_pred hhHHHHHHhhCC--CCceEEEEech-hhHHHHHhhcccCCCccC----ccC---------CCceeeHHHHHHHhhccccC
Q 009948 91 SIWELLKELFVS--PDILKLGFKFK-QDLIYLSSTFCSQGCDIG----FDR---------VEPYLDITSIYNHLHHKQLG 154 (522)
Q Consensus 91 ~~~~~L~~lL~~--~~i~KVgh~~k-~Dl~~L~~~~gi~g~~~~----~~~---------~~~~~Dlt~La~yLl~~~~~ 154 (522)
+++..+.+++.+ |++ .+|||.. +|+..|......+|+... +.. ....+|+-.+.+.-..
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 455555555544 555 4899876 699887533222333211 100 0115674443331111
Q ss_pred CCCCcCcccHHHHHHHHcCCccccc--ccc-CCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009948 155 RKLPKETKSLANICKELLDISLSKE--LQC-SDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (522)
Q Consensus 155 ~~~~~~~~gL~~L~~~~Lg~~L~K~--~q~-sdW~~RPL~~~qi~YAA~DA~~ll~L~ 209 (522)
++..+.+|..+++.+||..-..- ... .-|...+ +.-+.|...||..++.||
T Consensus 150 --l~~~sysLd~Va~~~Lg~~K~~~~~~~I~~~~~~~~--~~l~~Y~~~D~~~T~~l~ 203 (204)
T cd05779 150 --LPQGSQGLKAVTKAKLGYDPVELDPEDMVPLAREDP--QTLASYSVSDAVATYYLY 203 (204)
T ss_pred --CCCCCccHHHHHHHHhCCCcCcCCHHHHHHHHhCCc--HHHHhccHHHHHHHHHHh
Confidence 11247899999999999742111 111 1465544 567899999999999987
No 73
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=91.06 E-value=0.2 Score=52.19 Aligned_cols=125 Identities=22% Similarity=0.241 Sum_probs=76.5
Q ss_pred CEEEEEeCCCCCchhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccc-CC
Q 009948 77 SVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQL-GR 155 (522)
Q Consensus 77 ~~v~liD~~~l~~~~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~-~~ 155 (522)
+..|++|...-+.--...-.+..|++..+ +. |.+.+...|..+|++ .+.+++| |++++.+..+.. |+
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 67888886543211122334556666554 34 999999999888766 3589999 999999987653 44
Q ss_pred CCCcC-cccHHHHHH--HHcCCc------cccc-cccC-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009948 156 KLPKE-TKSLANICK--ELLDIS------LSKE-LQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 156 ~~~~~-~~gL~~L~~--~~Lg~~------L~K~-~q~s-dW~~RPL~~~qi~YAA~DA~~ll~L~~~L~ 213 (522)
..|.. -.+...|-. .|.+.+ +.+- .++- +|..||.++...+-++.||.+|+.....|.
T Consensus 290 r~p~~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll~~~~~l~ 358 (458)
T KOG2405|consen 290 RHPTSILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLLGIFDTLV 358 (458)
T ss_pred cCCccceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHHHHHHHHHHHHhhHh
Confidence 33311 011111100 011111 0111 1233 699999999999999999999999776655
No 74
>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=89.57 E-value=1.6 Score=41.26 Aligned_cols=89 Identities=17% Similarity=0.083 Sum_probs=54.5
Q ss_pred hHHHHHHhhCC--CCceEEEEec-hhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHH
Q 009948 92 IWELLKELFVS--PDILKLGFKF-KQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANIC 168 (522)
Q Consensus 92 ~~~~L~~lL~~--~~i~KVgh~~-k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~ 168 (522)
+.+.|..++.. ...+.||||+ ..|+..|.+.+.-.|+. +.....++| |+-....+. . +|++|+
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 89999986544222321 111134578 443222221 1 899999
Q ss_pred HHHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009948 169 KELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (522)
Q Consensus 169 ~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~ 210 (522)
.+++|++.... +-|..||.++.+++.
T Consensus 150 ~~~~~~~~~~~----------------H~A~~Da~at~~v~~ 175 (177)
T cd06136 150 KRLFGQEPKNS----------------HTAEGDVLALLKCAL 175 (177)
T ss_pred HHHhCCCcccc----------------cchHHHHHHHHHHHh
Confidence 99888776432 338899999877753
No 75
>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=87.46 E-value=1.5 Score=45.33 Aligned_cols=102 Identities=12% Similarity=0.188 Sum_probs=57.5
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecChhHHHhhhhcCceEEEEccCChHHHHHHHHHHccccccc
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQLLEVIEAFQLKISE 446 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~RiiLTrd~~l~~~~~~~~~~~~~v~~~~~~eQl~~v~~~f~l~~~~ 446 (522)
=++|+||+.|++|.++.+.+.-+..+...|.++|. |. +++.. ...+...+.++.+|+.++
T Consensus 28 v~~R~~r~~G~~V~~~~g~Dd~g~~i~~~a~~~g~---~~-~e~~~---------------~~~~~~~~~l~~LgI~~D- 87 (319)
T cd00814 28 VFARYQRLRGYDVLFVTGTDEHGTKIEQKAEEEGV---TP-QELCD---------------KYHEIFKDLFKWLNISFD- 87 (319)
T ss_pred HHHHHHHhCCCcccccCccCCCCcHHHHHHHHcCC---CH-HHHHH---------------HHHHHHHHHHHHcCCcCC-
Confidence 46999999999999887644334568888877663 11 11211 123456777888887643
Q ss_pred CcCCCcccC--CCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeE
Q 009948 447 DQLMSRCTK--CNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 447 ~~~~sRC~~--CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 501 (522)
.|.|-.. .+.. ..++.+... --..+|+...+-+.|+.|+..+
T Consensus 88 --~~~~tt~~~~~~~-------v~~i~~~L~----ekG~iY~~~~~~~yc~~~~~~l 131 (319)
T cd00814 88 --YFIRTTSPRHKEI-------VQEFFKKLY----ENGYIYEGEYEGLYCVSCERFL 131 (319)
T ss_pred --CCeeCCCHHHHHH-------HHHHHHHHH----HCCCEEeeeeeeeECCCCCcEe
Confidence 3433211 0000 011211110 0124667778899999998544
No 76
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=86.86 E-value=0.6 Score=37.87 Aligned_cols=41 Identities=10% Similarity=0.405 Sum_probs=31.6
Q ss_pred cccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeEeccchhhHHHHH
Q 009948 452 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEGTQYHNAVQK 513 (522)
Q Consensus 452 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~GsH~~~~~~~ 513 (522)
-|+.||..|+. +. ...-+|-+||.|+-|.-.+.-..+++++
T Consensus 3 lCP~C~v~l~~--~~-------------------rs~vEiD~CPrCrGVWLDrGELdKli~r 43 (88)
T COG3809 3 LCPICGVELVM--SV-------------------RSGVEIDYCPRCRGVWLDRGELDKLIER 43 (88)
T ss_pred ccCcCCceeee--ee-------------------ecCceeeeCCccccEeecchhHHHHHHH
Confidence 59999998752 10 1245789999999999999888888774
No 77
>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=86.66 E-value=1 Score=41.34 Aligned_cols=148 Identities=17% Similarity=0.173 Sum_probs=67.4
Q ss_pred EEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCc---hhhHHHHHHhhCCCCceEEEEe
Q 009948 35 VGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPL---PSIWELLKELFVSPDILKLGFK 111 (522)
Q Consensus 35 Vg~D~E~~~~~~~~~~~~~v~LiQLa~~~~~~~~~~~~~~~~~~v~liD~~~l~~---~~~~~~L~~lL~~~~i~KVgh~ 111 (522)
+.||+|+.+..+ ....+.+++++... .+...++.....-.. ..+.+.+ ..+.+...+ ++||
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 33567888887631 012221222111111 1223333 344444433 6777
Q ss_pred c-hhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcCCcccc----cccc----
Q 009948 112 F-KQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSK----ELQC---- 182 (522)
Q Consensus 112 ~-k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~K----~~q~---- 182 (522)
. .+|...|.+.+.-.++. ...+.+||-.++.... ..+.+|+.++.. ||..-.+ +.+.
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 56999987654212221 2467899655442211 146688888776 6765431 1111
Q ss_pred CCCCC---CCCCHHHHHHHHHHHHHHHHHHHHH
Q 009948 183 SDWSN---RPLTEEQKNYAAIDAHCLIEIFNIF 212 (522)
Q Consensus 183 sdW~~---RPL~~~qi~YAA~DA~~ll~L~~~L 212 (522)
..|.. ....+..+.|.-.|+..+.+|++.|
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 11211 2344778999999999999999876
No 78
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=86.51 E-value=0.52 Score=32.34 Aligned_cols=31 Identities=26% Similarity=0.732 Sum_probs=16.6
Q ss_pred ccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeEe
Q 009948 453 CTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYW 502 (522)
Q Consensus 453 C~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW 502 (522)
|+.|+++|.. +||+. ...+-+.|+.||-|..
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 34432 3567889999999854
No 79
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=85.42 E-value=0.7 Score=32.18 Aligned_cols=33 Identities=21% Similarity=0.704 Sum_probs=21.8
Q ss_pred CcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeE
Q 009948 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 501 (522)
.+|+.|+..+. ++.+. +|+ ...--+|+.|+.+|
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 57999999873 33222 222 23456799999987
No 80
>PRK11779 sbcB exonuclease I; Provisional
Probab=85.04 E-value=16 Score=40.11 Aligned_cols=107 Identities=16% Similarity=0.164 Sum_probs=58.4
Q ss_pred hhHHHHHHhhCCCCceEEEEe-chhhHHHHHhhcccCCCccC---ccCCCceeeHHHHHH--HhhccccCCCCC-----c
Q 009948 91 SIWELLKELFVSPDILKLGFK-FKQDLIYLSSTFCSQGCDIG---FDRVEPYLDITSIYN--HLHHKQLGRKLP-----K 159 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~-~k~Dl~~L~~~~gi~g~~~~---~~~~~~~~Dlt~La~--yLl~~~~~~~~~-----~ 159 (522)
++...+..+|..+..+.|||| +.+|...|...+....+.+. +......+|+..++. +.+.+. +-..| .
T Consensus 80 e~~~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~-~i~~P~~~~g~ 158 (476)
T PRK11779 80 EFAARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPE-GINWPENEDGL 158 (476)
T ss_pred HHHHHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccc-cccCcccccCC
Confidence 345566677765556679997 68999887664311000000 000011234322222 222221 00011 2
Q ss_pred CcccHHHHHHHHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 009948 160 ETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVK 215 (522)
Q Consensus 160 ~~~gL~~L~~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~ 215 (522)
.++.|+.|++.+ |++.... +-|..||+++.+|+..+.++
T Consensus 159 ~s~rLe~L~~~~-gI~~~~A----------------HdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 159 PSFKLEHLTKAN-GIEHENA----------------HDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CCCcHHHHHHHc-CCCCCCC----------------CCcHHHHHHHHHHHHHHHHh
Confidence 468999999875 6554211 22889999999999998866
No 81
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=84.53 E-value=0.32 Score=36.86 Aligned_cols=23 Identities=17% Similarity=0.564 Sum_probs=17.3
Q ss_pred cCCceeecCCCCeeEeccchhhH
Q 009948 487 KNLQFWQCMDCNQLYWEGTQYHN 509 (522)
Q Consensus 487 ~~~~F~~C~~CgkvyW~GsH~~~ 509 (522)
..++|.+||.||.+|-.---|-|
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~R 35 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIR 35 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHH
Confidence 45789999999999976544433
No 82
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=83.79 E-value=1 Score=30.69 Aligned_cols=29 Identities=28% Similarity=0.747 Sum_probs=21.3
Q ss_pred CCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeE
Q 009948 450 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 450 ~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 501 (522)
..+|..||+.++. ...+....|+.||.+|
T Consensus 3 ~~~C~~C~~~~i~-----------------------~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIV-----------------------NKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEE-----------------------EecCCeEEcccCCcEe
Confidence 3589999997631 1235577899999987
No 83
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=83.68 E-value=0.92 Score=31.45 Aligned_cols=33 Identities=21% Similarity=0.699 Sum_probs=22.1
Q ss_pred CcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeE
Q 009948 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 501 (522)
-+|+.|+.... ++.+ .||+. ..--+|+.||.+|
T Consensus 3 i~Cp~C~~~y~---i~d~----------~ip~~-----g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYE---IDDE----------KIPPK-----GRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEe---CCHH----------HCCCC-----CcEEECCCCCCEe
Confidence 36999999873 3311 34543 2356799999987
No 84
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=83.02 E-value=0.68 Score=42.94 Aligned_cols=51 Identities=16% Similarity=0.328 Sum_probs=30.5
Q ss_pred cccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeEeccchhhHHHHHHHHhc
Q 009948 452 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEGTQYHNAVQKFIDVC 518 (522)
Q Consensus 452 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~GsH~~~~~~~~~~~~ 518 (522)
+||.|+++... -++. ...+++ +....|++|+.||+-| +|+.++..+...|.
T Consensus 2 ~cp~c~~~~~~-~~~s----------~~~~~~--~~~~~~~~c~~c~~~f---~~~e~~~~~~i~VI 52 (154)
T PRK00464 2 RCPFCGHPDTR-VIDS----------RPAEDG--NAIRRRRECLACGKRF---TTFERVELVPLLVI 52 (154)
T ss_pred cCCCCCCCCCE-eEec----------cccCCC--CceeeeeeccccCCcc---eEeEeccCcccEEE
Confidence 79999996531 1111 123342 2245679999999998 66666554444333
No 85
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=82.70 E-value=0.32 Score=55.67 Aligned_cols=96 Identities=19% Similarity=0.294 Sum_probs=67.6
Q ss_pred hhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcCCcccc
Q 009948 99 LFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSK 178 (522)
Q Consensus 99 lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~K 178 (522)
+|-+-.++.|||++.+|.+.+-- -+ | .+.++| |... +++.. ....+|.-||..+||..+--
T Consensus 1009 ~Li~~GviFVGHGL~nDFrvINi-----~V-p----~~QiiD-Tv~l-f~~~s-------~R~LSLrfLa~~lLg~~IQ~ 1069 (1118)
T KOG1275|consen 1009 LLIQRGVIFVGHGLQNDFRVINI-----HV-P----EEQIID-TVTL-FRLGS-------QRMLSLRFLAWELLGETIQM 1069 (1118)
T ss_pred HHHHcCcEEEcccccccceEEEE-----ec-C----hhhhee-eeEE-Eeccc-------ccEEEHHHHHHHHhcchhhc
Confidence 67788899999999999886522 11 1 244778 5332 22222 25789999999999987732
Q ss_pred ccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchhhc
Q 009948 179 ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNSCSSISEL 229 (522)
Q Consensus 179 ~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~~~~~~~~~ 229 (522)
+. .| ..+||..+|.||+... +|+++|++++++..+
T Consensus 1070 ~~--HD-------------SIeDA~taLkLYk~Yl-~lkeq~~~~~~l~ni 1104 (1118)
T KOG1275|consen 1070 EA--HD-------------SIEDARTALKLYKKYL-KLKEQGKLESELRNI 1104 (1118)
T ss_pred cc--cc-------------cHHHHHHHHHHHHHHH-HHHHhhHHHHHHHHH
Confidence 21 11 4689999999999986 688899988877655
No 86
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=82.53 E-value=34 Score=35.12 Aligned_cols=88 Identities=15% Similarity=0.138 Sum_probs=51.2
Q ss_pred HHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHc
Q 009948 93 WELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELL 172 (522)
Q Consensus 93 ~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~L 172 (522)
.+.+..++.... +.|+||+.+|...|.+.+.. |. .....+ ++.......+. ..+++|..|+..+
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 456777777643 56999999999999764211 10 122233 33211111111 2478999999875
Q ss_pred CCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009948 173 DISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 173 g~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~ 213 (522)
|. .. + .+-|..||.++.+|+....
T Consensus 175 g~-~~---~-------------aHrAl~Da~Ata~ll~~~l 198 (294)
T PRK09182 175 GF-FH---E-------------GHRAVDDCQALLELLARPL 198 (294)
T ss_pred CC-CC---C-------------CcChHHHHHHHHHHHHHHH
Confidence 42 11 1 1338899999988777543
No 87
>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=81.93 E-value=2.9 Score=41.31 Aligned_cols=112 Identities=14% Similarity=0.190 Sum_probs=63.8
Q ss_pred hHHHHHHhh--CCCCceEEEEec-hhhHHHHHhhcccCCCccCccCC-------------------------CceeeHHH
Q 009948 92 IWELLKELF--VSPDILKLGFKF-KQDLIYLSSTFCSQGCDIGFDRV-------------------------EPYLDITS 143 (522)
Q Consensus 92 ~~~~L~~lL--~~~~i~KVgh~~-k~Dl~~L~~~~gi~g~~~~~~~~-------------------------~~~~Dlt~ 143 (522)
++..+...+ .||+|+ +|||+ ..|+..|......+++. .|... .-++|+-.
T Consensus 85 LL~~f~~~i~~~DPDii-vG~Ni~~fdl~~L~~R~~~l~i~-~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~~ 162 (234)
T cd05776 85 LLNFFLAKLQKIDPDVL-VGHDLEGFDLDVLLSRIQELKVP-HWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYL 162 (234)
T ss_pred HHHHHHHHHhhcCCCEE-EeeccCCCCHHHHHHHHHHhCCC-ccccccccccccCccccccccccccccccCchhhccHH
Confidence 444443333 368875 89999 56998874322222321 11111 11456444
Q ss_pred HHHHhhccccCCCCCcCcccHHHHHHHHcCCcccc--ccccC-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009948 144 IYNHLHHKQLGRKLPKETKSLANICKELLDISLSK--ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 144 La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~K--~~q~s-dW~~RPL~~~qi~YAA~DA~~ll~L~~~L~ 213 (522)
++..+.. ..+++|.++++.+||..-.. ..... -|....-...-+.|...||+.+++|...|.
T Consensus 163 ~~k~~~~--------~~sY~L~~va~~~Lg~~k~di~~~~i~~~~~~~~~l~~l~~y~~~Da~l~~~L~~kl~ 227 (234)
T cd05776 163 SAKELIR--------CKSYDLTELSQQVLGIERQDIDPEEILNMYNDSESLLKLLEHTEKDAYLILQLMFKLN 227 (234)
T ss_pred HHHHHhC--------CCCCChHHHHHHHhCcCcccCCHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence 4444432 35899999999999973211 11111 244311113458999999999999998874
No 88
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=81.93 E-value=1.5 Score=46.57 Aligned_cols=90 Identities=20% Similarity=0.281 Sum_probs=58.6
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHH-HHHHhhccccCCCCCcCcccHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITS-IYNHLHHKQLGRKLPKETKSLANICK 169 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~-La~yLl~~~~~~~~~~~~~gL~~L~~ 169 (522)
++-..|..++. ++.+-|||+...||.+|+-.+ ..+.| |. +..+-.++ . ....+|..|++
T Consensus 282 dvq~~l~~~~~-~~TILVGHSLenDL~aLKl~H------------~~ViD-Ta~lf~~~~g~-----~-~~k~sLk~L~~ 341 (380)
T KOG2248|consen 282 DVQKELLELIS-KNTILVGHSLENDLKALKLDH------------PSVID-TAVLFKHPTGP-----Y-PFKSSLKNLAK 341 (380)
T ss_pred HHHHHHHhhcC-cCcEEEeechhhHHHHHhhhC------------Cceee-eeEEEecCCCC-----c-cchHHHHHHHH
Confidence 34556777554 555669999999999998642 35678 54 22222221 1 13568999999
Q ss_pred HHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009948 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 170 ~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~ 213 (522)
.+||..+..+..-.+ .+.||.+.++|.....
T Consensus 342 ~~L~~~Iq~~~~~Hd-------------S~eDA~acm~Lv~~k~ 372 (380)
T KOG2248|consen 342 SYLGKLIQEGVGGHD-------------SVEDALACMKLVKLKI 372 (380)
T ss_pred HHHHHHHhccCCCCc-------------cHHHHHHHHHHHHHHH
Confidence 999987741111111 5789999999887655
No 89
>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=81.72 E-value=1.2 Score=30.92 Aligned_cols=34 Identities=18% Similarity=0.558 Sum_probs=21.3
Q ss_pred CcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeEe
Q 009948 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYW 502 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW 502 (522)
-.|+.|+..+. ++.+. +++ ...--+|+.||..|+
T Consensus 3 ~~CP~C~~~~~---v~~~~----------~~~-----~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFR---VVDSQ----------LGA-----NGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEE---eCHHH----------cCC-----CCCEEECCCCCCEEE
Confidence 36999999763 33222 111 122566999999886
No 90
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=81.63 E-value=3 Score=47.78 Aligned_cols=34 Identities=12% Similarity=0.053 Sum_probs=25.4
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCC
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 400 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~ 400 (522)
=++||||+.|++|.++.+.+.-...+...|.++|
T Consensus 30 v~aR~~r~~G~~V~~~~g~D~hG~~i~~~A~~~g 63 (673)
T PRK00133 30 IWVRYQRMRGHEVLFVCADDAHGTPIMLKAEKEG 63 (673)
T ss_pred HHHHHHHhcCCeeEEeCccCCCChHHHHHHHHcC
Confidence 4699999999999998763222235888887766
No 91
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=81.40 E-value=14 Score=35.62 Aligned_cols=99 Identities=16% Similarity=0.104 Sum_probs=60.2
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
+++..|.+++.+...+ +.|+...|+..|.+.+...|+. +.....++|+..++..+... ...++|++++++
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 4667778888774444 4455789999987654222322 11235677855444433321 235799998877
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVK 215 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~ 215 (522)
+|++... + -+-|..||.++.+|+..|...
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 4654311 1 123889999999999988743
No 92
>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=80.90 E-value=7.8 Score=34.77 Aligned_cols=55 Identities=18% Similarity=0.319 Sum_probs=35.7
Q ss_pred CCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 009948 135 VEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (522)
Q Consensus 135 ~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~ 214 (522)
+.+--| -+|.+||+++. +.+...++++|+| .+|... |+..|....+|++.|..
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--------NTNPEGVARRYLG---------GEWPED---------AATRALATARLLRALPP 136 (138)
T ss_dssp --B----HHHHHHHH-TT----------SHHHHHHHH-T---------S---SS---------HHHHHHHHHHHHHHHHH
T ss_pred cCCCCC-cchhhhhcCcc--------CCChHHHHHHhcC---------CCCCcc---------HHHHHHHHHHHHHHhhh
Confidence 355668 99999999984 6789999999987 346432 78888888999998876
Q ss_pred HH
Q 009948 215 KV 216 (522)
Q Consensus 215 ~L 216 (522)
+|
T Consensus 137 rL 138 (138)
T PF09281_consen 137 RL 138 (138)
T ss_dssp HT
T ss_pred cC
Confidence 64
No 93
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=80.07 E-value=1.6 Score=31.02 Aligned_cols=24 Identities=8% Similarity=0.502 Sum_probs=19.7
Q ss_pred CceeecCCCCeeEeccchhhHHHH
Q 009948 489 LQFWQCMDCNQLYWEGTQYHNAVQ 512 (522)
Q Consensus 489 ~~F~~C~~CgkvyW~GsH~~~~~~ 512 (522)
-....|++||-++=.+.=++++.+
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 467889999999988887777664
No 94
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=79.94 E-value=15 Score=36.07 Aligned_cols=86 Identities=8% Similarity=0.004 Sum_probs=53.5
Q ss_pred HHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHHHcCC
Q 009948 95 LLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDI 174 (522)
Q Consensus 95 ~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~ 174 (522)
.+..+.. .-+.||||+.+|...|.. + ....+|...++..+ .++ ..+++..|+.. +|+
T Consensus 67 v~~~~~~--~~~lVaHNa~FD~~~L~~-~-----------~~~~idTl~lar~l-~p~-------~~~~l~~L~~~-~~l 123 (219)
T PRK07983 67 VIPHYYG--SEWYVAHNASFDRRVLPE-M-----------PGEWICTMKLARRL-WPG-------IKYSNMALYKS-RKL 123 (219)
T ss_pred HHHHHcC--CCEEEEeCcHhhHHHHhC-c-----------CCCcEeHHHHHHHH-ccC-------CCCCHHHHHHH-cCC
Confidence 3444433 335699999999998864 1 14678944555444 443 34788888865 465
Q ss_pred ccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 009948 175 SLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (522)
Q Consensus 175 ~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~ 214 (522)
...... . ...+-|..||+++..|+..+.+
T Consensus 124 ~~~~~~-~----------~~aHrAl~Da~ata~ll~~l~~ 152 (219)
T PRK07983 124 NVQTPP-G----------LHHHRALYDCYITAALLIDIMN 152 (219)
T ss_pred CCCCCC-C----------CCCCcHHHHHHHHHHHHHHHHH
Confidence 431100 0 0124489999999999988763
No 95
>PLN02224 methionine-tRNA ligase
Probab=79.76 E-value=4.5 Score=45.90 Aligned_cols=35 Identities=11% Similarity=0.190 Sum_probs=25.3
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 401 (522)
=++||+|+.|++|.++.+.+.-...+...|.++|.
T Consensus 97 viaR~~r~~G~~V~fv~G~DehG~kI~~~A~~~g~ 131 (616)
T PLN02224 97 SIARFQRLLGKKVIFITGTDEHGEKIATSAAANGR 131 (616)
T ss_pred HHHHHHHhcCCceEEecCcCCcchHHHHHHHHcCC
Confidence 56999999999999987543222347777777663
No 96
>PRK11893 methionyl-tRNA synthetase; Reviewed
Probab=79.11 E-value=4.1 Score=44.86 Aligned_cols=35 Identities=14% Similarity=0.108 Sum_probs=26.2
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 401 (522)
=++|+||+.|++|.++.+.+.-+..++..|.++|.
T Consensus 29 v~~R~~r~~G~~v~~v~g~dd~g~~i~~~a~~~g~ 63 (511)
T PRK11893 29 VLARFKRLRGYDVFFLTGTDEHGQKIQRKAEEAGI 63 (511)
T ss_pred HHHHHHHhcCCcEEecCCCCCCChHHHHHHHHcCC
Confidence 46999999999999987643223467777877763
No 97
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=79.01 E-value=3.7 Score=45.89 Aligned_cols=34 Identities=21% Similarity=0.127 Sum_probs=25.2
Q ss_pred HHHHHHHhcCCceecCCCCCCCh-HHHHHhhhcCCc
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEP-RELIDQTSKEKR 401 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d-~~ll~~A~~E~R 401 (522)
=+||++|+.|+||.++...+ ++ ..|...|.++|.
T Consensus 33 v~aRy~Rl~G~~v~fvtGtD-eHGt~I~~~A~~~g~ 67 (558)
T COG0143 33 VYARYLRLRGYEVFFLTGTD-EHGTKIELKAEKEGI 67 (558)
T ss_pred HHHHHHHhcCCeEEEEeccC-CCCCHHHHHHHHcCC
Confidence 46999999999999987532 23 257777877774
No 98
>PRK05762 DNA polymerase II; Reviewed
Probab=78.15 E-value=42 Score=39.35 Aligned_cols=112 Identities=18% Similarity=0.243 Sum_probs=63.5
Q ss_pred hhHHHHHHhhC--CCCceEEEEech-hhHHHHHhhcccCCCccCccC---------------------C-CceeeHHHHH
Q 009948 91 SIWELLKELFV--SPDILKLGFKFK-QDLIYLSSTFCSQGCDIGFDR---------------------V-EPYLDITSIY 145 (522)
Q Consensus 91 ~~~~~L~~lL~--~~~i~KVgh~~k-~Dl~~L~~~~gi~g~~~~~~~---------------------~-~~~~Dlt~La 145 (522)
+++..|..++. ||+|+ +|||.. +|+..|.+....+|+...+.+ . ..++|+-.++
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 34555444444 47764 899976 699887543222333211100 0 1256744443
Q ss_pred HHhhccccCCCCCcCcccHHHHHHHHcCCcccc--c----cccC-CCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009948 146 NHLHHKQLGRKLPKETKSLANICKELLDISLSK--E----LQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (522)
Q Consensus 146 ~yLl~~~~~~~~~~~~~gL~~L~~~~Lg~~L~K--~----~q~s-dW~~RPL~~~qi~YAA~DA~~ll~L~~~L 212 (522)
...... ..+++|..+++++||..-.. . .+.. .|... ....+.|...||..++.|+..+
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 35789999999999854211 1 1111 24321 2456899999999999999843
No 99
>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=77.57 E-value=2.1 Score=45.80 Aligned_cols=35 Identities=20% Similarity=0.145 Sum_probs=24.5
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 401 (522)
=+|||+|+.|+||.++...+.-...+...|.++|.
T Consensus 27 v~aR~~r~~G~~v~~~tGtDehG~~i~~~A~~~g~ 61 (391)
T PF09334_consen 27 VLARYLRLRGHDVLFVTGTDEHGSKIETAAEKQGI 61 (391)
T ss_dssp HHHHHHHHTT-EEEEEEEEE-SSHHHHHHHHHTTS
T ss_pred HHHHHHhhcccceeeEEecchhhHHHHHHHHHcCC
Confidence 46899999999998876532222357778887776
No 100
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=77.26 E-value=2.9 Score=30.86 Aligned_cols=17 Identities=12% Similarity=0.167 Sum_probs=14.2
Q ss_pred ceeecCCCCeeEeccch
Q 009948 490 QFWQCMDCNQLYWEGTQ 506 (522)
Q Consensus 490 ~F~~C~~CgkvyW~GsH 506 (522)
.+|.|+.||-.+..+..
T Consensus 19 ~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 19 RRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CEEECCcCCCeEECCCc
Confidence 48899999999887654
No 101
>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=77.13 E-value=31 Score=33.50 Aligned_cols=110 Identities=21% Similarity=0.207 Sum_probs=62.2
Q ss_pred hhhHHHHHHhhCCCCceEEEEech-hhHHHHHhhcccCCCcc--CccCC-----------CceeeHHHHHHHhhccccCC
Q 009948 90 PSIWELLKELFVSPDILKLGFKFK-QDLIYLSSTFCSQGCDI--GFDRV-----------EPYLDITSIYNHLHHKQLGR 155 (522)
Q Consensus 90 ~~~~~~L~~lL~~~~i~KVgh~~k-~Dl~~L~~~~gi~g~~~--~~~~~-----------~~~~Dlt~La~yLl~~~~~~ 155 (522)
.+++..+..++.+.....||||.+ +|+..|....-.+|+.. .+... ...+||-.+.+....
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 345666656666522345999996 69998854322234321 01000 126785443322111
Q ss_pred CCCcCcccHHHHHHHHcCCcccc----cccc-CCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009948 156 KLPKETKSLANICKELLDISLSK----ELQC-SDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (522)
Q Consensus 156 ~~~~~~~gL~~L~~~~Lg~~L~K----~~q~-sdW~~RPL~~~qi~YAA~DA~~ll~L~~ 210 (522)
..+.+|..+++ +||.+ .| +.+. .-|.... ...-..|...||..++.||.
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 24789999986 67763 22 1111 1355444 35568999999999998874
No 102
>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=76.17 E-value=1.8 Score=38.15 Aligned_cols=30 Identities=13% Similarity=0.379 Sum_probs=24.3
Q ss_pred CCceeecCCCCeeEeccchhhHHHHHHHHh
Q 009948 488 NLQFWQCMDCNQLYWEGTQYHNAVQKFIDV 517 (522)
Q Consensus 488 ~~~F~~C~~CgkvyW~GsH~~~~~~~~~~~ 517 (522)
....|.|+.||-.|+...+-+...+.+.+.
T Consensus 28 ~~~~~~C~~CGe~~~~~e~~~~~~~~i~~~ 57 (127)
T TIGR03830 28 GVPGWYCPACGEELLDPEESKRNSAALADF 57 (127)
T ss_pred eeeeeECCCCCCEEEcHHHHHHHHHHHHHH
Confidence 457889999999999999888777766544
No 103
>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=75.10 E-value=17 Score=34.32 Aligned_cols=99 Identities=18% Similarity=0.260 Sum_probs=53.6
Q ss_pred hHHHHHHhhCCCCceEEEEe-chhhHHHHHhhcccCCCccCcc----CCCceeeHHHHHHHhh--ccccCCCCC-----c
Q 009948 92 IWELLKELFVSPDILKLGFK-FKQDLIYLSSTFCSQGCDIGFD----RVEPYLDITSIYNHLH--HKQLGRKLP-----K 159 (522)
Q Consensus 92 ~~~~L~~lL~~~~i~KVgh~-~k~Dl~~L~~~~gi~g~~~~~~----~~~~~~Dlt~La~yLl--~~~~~~~~~-----~ 159 (522)
++..+..++..+....|||| +.+|+..|.+.+.-.+..+ +. .....+|...++..+. .+. ....| .
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 44556667765444458997 7899999876532212110 00 0122357444554332 121 00001 1
Q ss_pred CcccHHHHHHHHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009948 160 ETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (522)
Q Consensus 160 ~~~gL~~L~~~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~ 209 (522)
.+++|++++++ +|++.. +.+-|..||.++.+|.
T Consensus 150 ~~~~L~~l~~~-~gi~~~----------------~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 150 PSFKLEDLAQA-NGIEHS----------------NAHDALSDVEATIALA 182 (183)
T ss_pred cchhHHHHHHH-CCCCcc----------------ccccHHHHHHHHHHHh
Confidence 36789999986 576542 2244888998887663
No 104
>PRK12268 methionyl-tRNA synthetase; Reviewed
Probab=75.07 E-value=6.2 Score=44.05 Aligned_cols=35 Identities=14% Similarity=0.018 Sum_probs=25.5
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 401 (522)
-++||+|+.|++|.++.+.+.-+..+...|.++|.
T Consensus 32 ~~~R~~r~~G~~v~~~~g~d~~g~~i~~~a~~~g~ 66 (556)
T PRK12268 32 VFARYQRLKGNEVLFVSGSDEHGTPIELAAKKEGV 66 (556)
T ss_pred HHHHHHHhcCCceEecCcCCCcccHHHHHHHHcCC
Confidence 46999999999999987643223457777776654
No 105
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=74.82 E-value=2 Score=37.37 Aligned_cols=46 Identities=20% Similarity=0.429 Sum_probs=27.4
Q ss_pred CcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeEeccc
Q 009948 447 DQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEGT 505 (522)
Q Consensus 447 ~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~Gs 505 (522)
..+--||++||.+= +.-++-+-+-++ +....||-|++|+.-|=++|
T Consensus 71 a~I~~kCpkCghe~--m~Y~T~QlRSAD-----------EGQTVFYTC~kC~~k~~e~s 116 (116)
T KOG2907|consen 71 AVIKHKCPKCGHEE--MSYHTLQLRSAD-----------EGQTVFYTCPKCKYKFTENS 116 (116)
T ss_pred cchhccCcccCCch--hhhhhhhccccc-----------CCceEEEEcCccceeeeccC
Confidence 34457899999852 111111111111 34578999999998776553
No 106
>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=74.31 E-value=27 Score=32.03 Aligned_cols=98 Identities=12% Similarity=0.057 Sum_probs=57.5
Q ss_pred hhHHHHHHhhCCC-CceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHH
Q 009948 91 SIWELLKELFVSP-DILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (522)
Q Consensus 91 ~~~~~L~~lL~~~-~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~ 169 (522)
++++.|..++.+. ... +.|+...|...+...+...+..+........+|+..++..+... ....+|.+++.
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 4566777788774 133 44455888766543211111110001236789977777766532 14789999986
Q ss_pred HHcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009948 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (522)
Q Consensus 170 ~~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L 212 (522)
. +|++.. . +.+-|-.||.++.+++..|
T Consensus 149 ~-~gi~~~--~-------------~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 149 Y-LGLEFE--G-------------RHHRGLDDARNIARILKRL 175 (176)
T ss_pred H-CCCCCC--C-------------CCcCcHHHHHHHHHHHHHh
Confidence 6 476653 1 1123788999999888765
No 107
>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=74.28 E-value=1.9 Score=26.06 Aligned_cols=16 Identities=13% Similarity=0.528 Sum_probs=11.9
Q ss_pred eecCCCCeeEeccchh
Q 009948 492 WQCMDCNQLYWEGTQY 507 (522)
Q Consensus 492 ~~C~~CgkvyW~GsH~ 507 (522)
|.|+.||+.|=.-+.+
T Consensus 1 y~C~~C~~~f~~~~~l 16 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNL 16 (23)
T ss_dssp EEETTTTEEESSHHHH
T ss_pred CCCCCCCCccCCHHHH
Confidence 6899999999544433
No 108
>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=74.02 E-value=1.9 Score=29.95 Aligned_cols=11 Identities=27% Similarity=0.887 Sum_probs=9.8
Q ss_pred eecCCCCeeEe
Q 009948 492 WQCMDCNQLYW 502 (522)
Q Consensus 492 ~~C~~CgkvyW 502 (522)
|.|+.||++|=
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 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=73.12 E-value=3.3 Score=26.16 Aligned_cols=9 Identities=22% Similarity=0.748 Sum_probs=7.3
Q ss_pred eeecCCCCe
Q 009948 491 FWQCMDCNQ 499 (522)
Q Consensus 491 F~~C~~Cgk 499 (522)
-|.||.||+
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 567999995
No 110
>PHA02119 hypothetical protein
Probab=72.65 E-value=1.4 Score=34.93 Aligned_cols=15 Identities=33% Similarity=0.578 Sum_probs=12.8
Q ss_pred HHHHHHHhcCCceec
Q 009948 367 GLAKHLRCVGIDAAT 381 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~ 381 (522)
-+.-|||.+|||+..
T Consensus 58 divdylr~lgy~~~~ 72 (87)
T PHA02119 58 DIVDYLRSLGYDAKS 72 (87)
T ss_pred HHHHHHHHccchhcc
Confidence 578899999999864
No 111
>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=72.54 E-value=1.7 Score=32.13 Aligned_cols=39 Identities=21% Similarity=0.433 Sum_probs=20.8
Q ss_pred cccCCCCcCccCCCChHHHHHhhcccccCCccc-cccCCceeecCCCCe
Q 009948 452 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCL-FDKNLQFWQCMDCNQ 499 (522)
Q Consensus 452 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v-~~~~~~F~~C~~Cgk 499 (522)
+|..|+-.--+..-+. ...||+.+ |+...+=|.||.||-
T Consensus 3 ~C~~CgyvYd~~~Gd~---------~~~i~pGt~F~~Lp~~w~CP~C~a 42 (47)
T PF00301_consen 3 QCPVCGYVYDPEKGDP---------ENGIPPGTPFEDLPDDWVCPVCGA 42 (47)
T ss_dssp EETTTSBEEETTTBBG---------GGTB-TT--GGGS-TT-B-TTTSS
T ss_pred CCCCCCEEEcCCcCCc---------ccCcCCCCCHHHCCCCCcCcCCCC
Confidence 6999997542211110 12467765 677778899999984
No 112
>PLN02610 probable methionyl-tRNA synthetase
Probab=72.50 E-value=7.6 Score=45.43 Aligned_cols=34 Identities=15% Similarity=0.021 Sum_probs=23.1
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCC
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 400 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~ 400 (522)
=+|||+|+.|+||.++...+.-.-.+...|.++|
T Consensus 46 v~aRy~r~~G~~v~f~~GtDehG~~i~~~A~~~g 79 (801)
T PLN02610 46 VFARYCRLRGYNAIYICGTDEYGTATETKALEEN 79 (801)
T ss_pred HHHHHHHhCCCceEecccccCCcHHHHHHHHHcC
Confidence 3599999999999998753211224555666655
No 113
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=72.20 E-value=35 Score=33.43 Aligned_cols=99 Identities=19% Similarity=0.216 Sum_probs=62.7
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
++.+.+..++.+. -.-|+||...|+..|...+...+..+ ....++|...++.... ++ ....+|..|+.
T Consensus 83 ~v~~~~~~~i~~~-~~~Vahna~fD~~fl~~~~~~~~~~~---~~~~~~~t~~~~r~~~-~~------~~~~~L~~l~~- 150 (243)
T COG0847 83 EVLPEFLDFIGGL-RLLVAHNAAFDVGFLRVESERLGIEI---PGDPVLDTLALARRHF-PG------FDRSSLDALAE- 150 (243)
T ss_pred HHHHHHHHHHCCC-CeEEEEchhhcHHHHHHHHHHcCCCc---ccCceehHHHHHHHHc-CC------CccchHHHHHH-
Confidence 3455566666664 34599999999999875543333221 1356778444444333 32 25789999999
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVK 215 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~~~ 215 (522)
.+|+... .... +-|..||.++..++..+...
T Consensus 151 ~~gi~~~-~~~~-------------H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 151 RLGIDRN-PFHP-------------HRALFDALALAELFLLLQTG 181 (243)
T ss_pred HcCCCcC-CcCC-------------cchHHHHHHHHHHHHHHHhc
Confidence 6676643 1111 23889999999999998753
No 114
>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=69.60 E-value=3.7 Score=40.12 Aligned_cols=34 Identities=15% Similarity=0.158 Sum_probs=26.1
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCC
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 400 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~ 400 (522)
=++||||..|++|.++.+.+.-+..++..|+++|
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 5799999999999988764333456888887764
No 115
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=69.50 E-value=1.5 Score=43.52 Aligned_cols=54 Identities=11% Similarity=0.301 Sum_probs=31.8
Q ss_pred HHHHc-ccccccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCee-Eeccchh
Q 009948 436 VIEAF-QLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL-YWEGTQY 507 (522)
Q Consensus 436 v~~~f-~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv-yW~GsH~ 507 (522)
+.+.+ |+.+-|-. --+|.-|+-.| |. ... ..|.+ .++.-.||.||+| ||.-+|.
T Consensus 183 i~~~~kg~gvvpl~-g~~C~GC~m~l---~~--~~~-----------~~V~~-~d~iv~CP~CgRILy~~e~~~ 238 (239)
T COG1579 183 IRKNKKGVGVVPLE-GRVCGGCHMKL---PS--QTL-----------SKVRK-KDEIVFCPYCGRILYYDESEE 238 (239)
T ss_pred HHhcCCCceEEeec-CCcccCCeeee---cH--HHH-----------HHHhc-CCCCccCCccchHHHhhhccc
Confidence 34445 44443322 26899999865 21 111 12333 5677789999996 8876663
No 116
>PRK00420 hypothetical protein; Validated
Probab=69.49 E-value=3.4 Score=36.26 Aligned_cols=30 Identities=17% Similarity=0.283 Sum_probs=21.0
Q ss_pred CcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeEecc
Q 009948 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEG 504 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~G 504 (522)
..|+.|+.+|.. . .+--.+||.||++|=..
T Consensus 24 ~~CP~Cg~pLf~--l----------------------k~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 24 KHCPVCGLPLFE--L----------------------KDGEVVCPVHGKVYIVK 53 (112)
T ss_pred CCCCCCCCccee--c----------------------CCCceECCCCCCeeeec
Confidence 569999998741 0 12245699999998753
No 117
>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=69.31 E-value=1.2 Score=32.40 Aligned_cols=43 Identities=16% Similarity=0.423 Sum_probs=27.3
Q ss_pred CcccCCCCcCccCCCChHHHHHhhcccccCCc--cccccCCceeecCCCC
Q 009948 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPD--CLFDKNLQFWQCMDCN 498 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~--~v~~~~~~F~~C~~Cg 498 (522)
.-|+.|++.|. .+..+.+.+ ..+.+|. .|.+....-|.|+.||
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 46999999885 333332221 2233443 3457788899999997
No 118
>PF14353 CpXC: CpXC protein
Probab=69.02 E-value=4.3 Score=36.09 Aligned_cols=19 Identities=21% Similarity=0.604 Sum_probs=14.4
Q ss_pred cccccCCceeecCCCCeeE
Q 009948 483 CLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 483 ~v~~~~~~F~~C~~Cgkvy 501 (522)
.+++..--.+.||.||+.+
T Consensus 30 ~il~g~l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 30 KILDGSLFSFTCPSCGHKF 48 (128)
T ss_pred HHHcCCcCEEECCCCCCce
Confidence 3556666788999999864
No 119
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=68.19 E-value=3.7 Score=42.12 Aligned_cols=38 Identities=16% Similarity=0.389 Sum_probs=25.8
Q ss_pred HcccccccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCe
Q 009948 439 AFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 499 (522)
Q Consensus 439 ~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 499 (522)
.++.. .|+.++++|+.|+..+. +++. ...++.||.||.
T Consensus 28 ~~~~~-~p~~lw~kc~~C~~~~~-----~~~l-----------------~~~~~vcp~c~~ 65 (296)
T CHL00174 28 SWNTQ-KYKHLWVQCENCYGLNY-----KKFL-----------------KSKMNICEQCGY 65 (296)
T ss_pred ccCCC-CCCCCeeECCCccchhh-----HHHH-----------------HHcCCCCCCCCC
Confidence 34544 35667999999999753 2221 134789999986
No 120
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=67.79 E-value=2.6 Score=43.58 Aligned_cols=11 Identities=27% Similarity=1.174 Sum_probs=9.5
Q ss_pred CceeecCCCCe
Q 009948 489 LQFWQCMDCNQ 499 (522)
Q Consensus 489 ~~F~~C~~Cgk 499 (522)
.-||.||+|++
T Consensus 366 ~l~W~CPsC~~ 376 (389)
T COG2956 366 TLYWHCPSCRA 376 (389)
T ss_pred eeeeeCCCccc
Confidence 45999999986
No 121
>PRK06722 exonuclease; Provisional
Probab=67.40 E-value=36 Score=34.80 Aligned_cols=100 Identities=18% Similarity=0.123 Sum_probs=57.4
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCcccHHHHHHH
Q 009948 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~gL~~L~~~ 170 (522)
+++..|..++.+..+ |+|+...|+..|.+.+...|+...+-.....+|+..++..+... ......+|.++++.
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 456677777776433 67778999999877543333211000012246755444332211 00134689999887
Q ss_pred HcCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009948 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 171 ~Lg~~L~K~~q~sdW~~RPL~~~qi~YAA~DA~~ll~L~~~L~ 213 (522)
+ |++... + .+-|-.||..+..|+..|.
T Consensus 152 l-gL~~~g--~-------------~HrAL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 152 L-GLIWEG--K-------------QHRALADAENTANILLKAY 178 (281)
T ss_pred C-CCCCCC--C-------------CcCcHHHHHHHHHHHHHHh
Confidence 5 655321 1 1227889999999998886
No 122
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=67.32 E-value=3.1 Score=31.57 Aligned_cols=33 Identities=21% Similarity=0.574 Sum_probs=21.9
Q ss_pred CcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCee
Q 009948 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 500 (522)
.+|.-|+-.+ +.....+ + ...++...||.||++
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 5899999865 2223221 1 123678999999986
No 123
>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=66.66 E-value=5 Score=43.16 Aligned_cols=35 Identities=9% Similarity=0.073 Sum_probs=28.1
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 401 (522)
=|+||||..||+|.++.+.+.-|..|+..|+++|.
T Consensus 63 vl~R~lr~~G~~V~fV~nitD~dDKIi~~A~~~g~ 97 (411)
T TIGR03447 63 LVNRVWRDAGHRVHYVQNVTDVDDPLFERAERDGV 97 (411)
T ss_pred HHHHHHHhcCCceEEeeCCCchhHHHHHHHHHcCC
Confidence 47999999999999987643334679999998874
No 124
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=65.82 E-value=12 Score=43.08 Aligned_cols=111 Identities=19% Similarity=0.181 Sum_probs=68.8
Q ss_pred CCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccc---CC-----------------CCCc---
Q 009948 103 PDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQL---GR-----------------KLPK--- 159 (522)
Q Consensus 103 ~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~---~~-----------------~~~~--- 159 (522)
..-+.||||..+|-..++..|.+.|- -..++| ||-.+.-.. +. .+ ..|.
T Consensus 240 ke~liVGHNVsfDRaRirEeY~i~~S------k~rFlD-TMSlHia~~-Gm~S~Qrplw~ka~k~k~a~~d~~~~ps~~d 311 (1075)
T KOG3657|consen 240 KEQLIVGHNVSFDRARIREEYNINGS------KIRFLD-TMSLHIAMS-GMCSRQRPLWFKARKAKSAMYDSETNPSISD 311 (1075)
T ss_pred CCceEEeccccchHHHHHHHHhcccc------ceeeee-chhhhhhhh-ccccccchhHhhhhhhhhhhhhcccCCchhh
Confidence 34567999999999999888876431 245789 764432211 10 00 0000
Q ss_pred ---------CcccHHHHHHHHcCCc-cccccccCC--CCCCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 009948 160 ---------ETKSLANICKELLDIS-LSKELQCSD--WSNRPLT---EEQKNYAAIDAHCLIEIFNIFQVKVAQKGN 221 (522)
Q Consensus 160 ---------~~~gL~~L~~~~Lg~~-L~K~~q~sd--W~~RPL~---~~qi~YAA~DA~~ll~L~~~L~~~L~~~g~ 221 (522)
.--||.++...+.|.. |+|+...+- -...++. .+-+.|.|.|++++.+++..+-+...+.--
T Consensus 312 ~~~pWL~~SS~NSL~dVhk~~c~~~~LdKt~Rd~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~FlercP 388 (1075)
T KOG3657|consen 312 YDNPWLGRSSLNSLVDVHKFHCGIDALDKTPRDSFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLERCP 388 (1075)
T ss_pred hhhhhhhhhhhHHHHHHHHhhCCCCccccchHHhhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHHhCC
Confidence 1136777777778877 777543221 1111222 234789999999999999999988777643
No 125
>PRK12418 cysteinyl-tRNA synthetase; Provisional
Probab=64.92 E-value=5.3 Score=42.60 Aligned_cols=36 Identities=11% Similarity=0.115 Sum_probs=28.9
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcE
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRV 402 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~Ri 402 (522)
=|+||||.+||+|.++.+.+.-|..|+..|+++|.-
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 579999999999999876433356799999988753
No 126
>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=62.06 E-value=15 Score=43.26 Aligned_cols=19 Identities=21% Similarity=0.246 Sum_probs=16.4
Q ss_pred HHHHHHHhcCCceecCCCC
Q 009948 367 GLAKHLRCVGIDAATPRSK 385 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~ 385 (522)
=++||+|+.||+|.++.+.
T Consensus 57 vi~Ry~rm~G~~V~~~~G~ 75 (842)
T TIGR00396 57 VLSRYYRMKGYNVLHPMGW 75 (842)
T ss_pred HHHHHHHhcCCceeccCCc
Confidence 4699999999999998753
No 127
>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=61.67 E-value=1.2 Score=33.26 Aligned_cols=10 Identities=40% Similarity=0.929 Sum_probs=8.7
Q ss_pred CcccCCCCcC
Q 009948 451 SRCTKCNGRF 460 (522)
Q Consensus 451 sRC~~CN~~l 460 (522)
-||..||..|
T Consensus 5 iRC~~CnklL 14 (51)
T PF10122_consen 5 IRCGHCNKLL 14 (51)
T ss_pred eeccchhHHH
Confidence 4899999977
No 128
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=61.34 E-value=6.2 Score=39.11 Aligned_cols=37 Identities=24% Similarity=0.662 Sum_probs=24.9
Q ss_pred CcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeE
Q 009948 447 DQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 447 ~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 501 (522)
.+.-|||-.|+.... ||..+. ...--+|.|+.|++.|
T Consensus 129 rKeVSRCr~C~~rYD--PVP~dk----------------mwG~aef~C~~C~h~F 165 (278)
T PF15135_consen 129 RKEVSRCRKCRKRYD--PVPCDK----------------MWGIAEFHCPKCRHNF 165 (278)
T ss_pred ccccccccccccccC--CCcccc----------------ccceeeeecccccccc
Confidence 344699999999764 332111 1234588999999987
No 129
>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=60.74 E-value=5.8 Score=27.59 Aligned_cols=14 Identities=21% Similarity=0.831 Sum_probs=9.2
Q ss_pred CCceeecCCCCeeE
Q 009948 488 NLQFWQCMDCNQLY 501 (522)
Q Consensus 488 ~~~F~~C~~Cgkvy 501 (522)
..+||+|..||.|.
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 130
>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=60.05 E-value=5.7 Score=23.63 Aligned_cols=16 Identities=19% Similarity=0.598 Sum_probs=9.9
Q ss_pred eecCCCCeeEeccchh
Q 009948 492 WQCMDCNQLYWEGTQY 507 (522)
Q Consensus 492 ~~C~~CgkvyW~GsH~ 507 (522)
|.|+.|++.|=.-..+
T Consensus 1 ~~C~~C~~~~~~~~~l 16 (24)
T PF13894_consen 1 FQCPICGKSFRSKSEL 16 (24)
T ss_dssp EE-SSTS-EESSHHHH
T ss_pred CCCcCCCCcCCcHHHH
Confidence 6899999998544433
No 131
>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=59.64 E-value=5.5 Score=29.77 Aligned_cols=39 Identities=21% Similarity=0.405 Sum_probs=23.7
Q ss_pred cccCCCCcCccCCCChHHHHHhhcccccCCccc-cccCCceeecCCCCe
Q 009948 452 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCL-FDKNLQFWQCMDCNQ 499 (522)
Q Consensus 452 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v-~~~~~~F~~C~~Cgk 499 (522)
+|..|+-.--+..-+. ...||+.+ |+...+=|.||.||-
T Consensus 3 ~C~~CgyiYd~~~Gd~---------~~~i~pGt~f~~Lp~~w~CP~C~a 42 (50)
T cd00730 3 ECRICGYIYDPAEGDP---------DEGIPPGTPFEDLPDDWVCPVCGA 42 (50)
T ss_pred CCCCCCeEECCCCCCc---------ccCcCCCCCHhHCCCCCCCCCCCC
Confidence 6999997543211110 12456654 556677899999984
No 132
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=58.76 E-value=9.2 Score=28.55 Aligned_cols=14 Identities=21% Similarity=0.776 Sum_probs=12.3
Q ss_pred ceeecCCCCeeEec
Q 009948 490 QFWQCMDCNQLYWE 503 (522)
Q Consensus 490 ~F~~C~~CgkvyW~ 503 (522)
..+.|..||-.||.
T Consensus 36 ~r~~C~~Cgyt~~~ 49 (50)
T PRK00432 36 DRWHCGKCGYTEFK 49 (50)
T ss_pred CcEECCCcCCEEec
Confidence 57889999999996
No 133
>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=58.54 E-value=5.3 Score=40.87 Aligned_cols=32 Identities=22% Similarity=0.598 Sum_probs=22.9
Q ss_pred cCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCe
Q 009948 446 EDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 499 (522)
Q Consensus 446 ~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 499 (522)
|+..+++|+.|+..+. +++. ...++.||.||.
T Consensus 22 ~~~~~~~c~~c~~~~~-----~~~l-----------------~~~~~vc~~c~~ 53 (285)
T TIGR00515 22 PEGVWTKCPKCGQVLY-----TKEL-----------------ERNLEVCPKCDH 53 (285)
T ss_pred CCCCeeECCCCcchhh-----HHHH-----------------HhhCCCCCCCCC
Confidence 4667899999999653 2221 134789999986
No 134
>PHA00616 hypothetical protein
Probab=58.40 E-value=2.3 Score=30.88 Aligned_cols=17 Identities=18% Similarity=0.718 Sum_probs=13.0
Q ss_pred eecCCCCeeEeccchhh
Q 009948 492 WQCMDCNQLYWEGTQYH 508 (522)
Q Consensus 492 ~~C~~CgkvyW~GsH~~ 508 (522)
++|+.||++|=.-++..
T Consensus 2 YqC~~CG~~F~~~s~l~ 18 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVI 18 (44)
T ss_pred CccchhhHHHhhHHHHH
Confidence 68999999996655443
No 135
>PRK07218 replication factor A; Provisional
Probab=57.99 E-value=5.3 Score=43.17 Aligned_cols=14 Identities=29% Similarity=0.800 Sum_probs=11.3
Q ss_pred CcCCCcccCCCCcC
Q 009948 447 DQLMSRCTKCNGRF 460 (522)
Q Consensus 447 ~~~~sRC~~CN~~l 460 (522)
+.+..|||.||-.+
T Consensus 294 sgli~rCP~C~r~v 307 (423)
T PRK07218 294 SGLIERCPECGRVI 307 (423)
T ss_pred CcceecCcCccccc
Confidence 46789999999854
No 136
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=57.24 E-value=6.5 Score=34.24 Aligned_cols=20 Identities=20% Similarity=0.467 Sum_probs=12.3
Q ss_pred CCccccccCCceeecCCCCee
Q 009948 480 IPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 480 vp~~v~~~~~~F~~C~~Cgkv 500 (522)
.|+.-+....+| .||+||-.
T Consensus 64 aPdp~w~~irEy-yCP~Cgt~ 83 (112)
T PF08882_consen 64 APDPEWQVIREY-YCPGCGTQ 83 (112)
T ss_pred CCCCCcEEEEEE-ECCCCcce
Confidence 344445555555 49999953
No 137
>PLN02946 cysteine-tRNA ligase
Probab=57.19 E-value=8.2 Score=43.16 Aligned_cols=35 Identities=14% Similarity=0.171 Sum_probs=28.2
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 401 (522)
=|+||||..||+|.++.+...-|..|+..|+++|.
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 67999999999999987643335579999988874
No 138
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=57.10 E-value=3.4 Score=37.43 Aligned_cols=49 Identities=22% Similarity=0.560 Sum_probs=25.4
Q ss_pred cccCcCCCcccCCCCcCccCCCCh--HHH-HHhhcccccCCccccccCCceeecCCCCe
Q 009948 444 ISEDQLMSRCTKCNGRFIQKPLST--EEA-VEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 499 (522)
Q Consensus 444 ~~~~~~~sRC~~CN~~l~~~~~~~--e~~-~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 499 (522)
+......-||..|+.... ++. +.. .+.+...+.+|. ....|+.||.||.
T Consensus 64 i~~~p~~~~C~~CG~~~~---~~~~~~~~~~~~~~~~~~~~~----~~~~~~~CP~Cgs 115 (135)
T PRK03824 64 FEEEEAVLKCRNCGNEWS---LKEVKESLDEEIREAIHFIPE----VVHAFLKCPKCGS 115 (135)
T ss_pred EEecceEEECCCCCCEEe---ccccccccccccccccccccc----ccccCcCCcCCCC
Confidence 334456789999997652 210 000 000011123443 3356788999995
No 139
>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=56.47 E-value=8.5 Score=27.10 Aligned_cols=31 Identities=26% Similarity=0.624 Sum_probs=22.3
Q ss_pred cccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCC---CCeeEec
Q 009948 452 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMD---CNQLYWE 503 (522)
Q Consensus 452 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~---CgkvyW~ 503 (522)
.|+.|++.|+.+. .+...||-|.. |.-++|-
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 12237999987 9988874
No 140
>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=56.37 E-value=7.5 Score=38.54 Aligned_cols=21 Identities=10% Similarity=0.363 Sum_probs=16.6
Q ss_pred CceeecCCCCeeEeccchhhHH
Q 009948 489 LQFWQCMDCNQLYWEGTQYHNA 510 (522)
Q Consensus 489 ~~F~~C~~CgkvyW~GsH~~~~ 510 (522)
-++.+|+.||++|=. .+|.+.
T Consensus 33 i~v~~C~~Cg~~~~~-~~W~~~ 53 (236)
T PF04981_consen 33 IEVTICPKCGRYRIG-GRWVDP 53 (236)
T ss_pred cCceECCCCCCEECC-CEeeec
Confidence 378999999997665 777766
No 141
>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=56.14 E-value=22 Score=36.68 Aligned_cols=35 Identities=17% Similarity=0.029 Sum_probs=25.6
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 401 (522)
=++|+||..|++|.++.+.+.-+..+...|+++|.
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 56999999999999887643223357777777664
No 142
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=56.02 E-value=4.8 Score=27.88 Aligned_cols=13 Identities=23% Similarity=0.779 Sum_probs=8.7
Q ss_pred ecCCCCeeEeccchhhH
Q 009948 493 QCMDCNQLYWEGTQYHN 509 (522)
Q Consensus 493 ~C~~CgkvyW~GsH~~~ 509 (522)
.|++||| |.||.+
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 5999997 778864
No 143
>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=55.77 E-value=8.7 Score=27.45 Aligned_cols=13 Identities=15% Similarity=0.386 Sum_probs=9.1
Q ss_pred CCceeecCCCCee
Q 009948 488 NLQFWQCMDCNQL 500 (522)
Q Consensus 488 ~~~F~~C~~Cgkv 500 (522)
..-.+.|+.||-|
T Consensus 16 ~~g~~vC~~CG~V 28 (43)
T PF08271_consen 16 ERGELVCPNCGLV 28 (43)
T ss_dssp TTTEEEETTT-BB
T ss_pred CCCeEECCCCCCE
Confidence 3456799999976
No 144
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=55.53 E-value=7.3 Score=35.69 Aligned_cols=17 Identities=24% Similarity=0.784 Sum_probs=13.7
Q ss_pred ccCCceeecCCCCeeEe
Q 009948 486 DKNLQFWQCMDCNQLYW 502 (522)
Q Consensus 486 ~~~~~F~~C~~CgkvyW 502 (522)
+....||.||.||+.|=
T Consensus 94 e~~~~~Y~Cp~C~~~y~ 110 (147)
T smart00531 94 ETNNAYYKCPNCQSKYT 110 (147)
T ss_pred ccCCcEEECcCCCCEee
Confidence 34578999999999884
No 145
>PRK00390 leuS leucyl-tRNA synthetase; Validated
Probab=55.16 E-value=20 Score=42.10 Aligned_cols=19 Identities=21% Similarity=0.214 Sum_probs=16.3
Q ss_pred HHHHHHHhcCCceecCCCC
Q 009948 367 GLAKHLRCVGIDAATPRSK 385 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~ 385 (522)
=++|+.|+.|++|.++.+.
T Consensus 60 ii~Ry~rm~G~~V~~~~G~ 78 (805)
T PRK00390 60 VIARYKRMQGYNVLHPMGW 78 (805)
T ss_pred HHHHHHHhcCCcccccCcc
Confidence 4699999999999998753
No 146
>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=55.08 E-value=8 Score=26.40 Aligned_cols=16 Identities=31% Similarity=0.897 Sum_probs=12.5
Q ss_pred ceeecCCCCeeEeccch
Q 009948 490 QFWQCMDCNQLYWEGTQ 506 (522)
Q Consensus 490 ~F~~C~~CgkvyW~GsH 506 (522)
.+|+|..||-+| +|.+
T Consensus 1 ~~~~C~~CG~i~-~g~~ 16 (34)
T cd00729 1 KVWVCPVCGYIH-EGEE 16 (34)
T ss_pred CeEECCCCCCEe-ECCc
Confidence 379999999988 5543
No 147
>COG1773 Rubredoxin [Energy production and conversion]
Probab=55.08 E-value=6.7 Score=29.93 Aligned_cols=40 Identities=20% Similarity=0.382 Sum_probs=25.4
Q ss_pred CcccCCCCcCccCCCChHHHHHhhcccccCCccc-cccCCceeecCCCCe
Q 009948 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCL-FDKNLQFWQCMDCNQ 499 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v-~~~~~~F~~C~~Cgk 499 (522)
-||..|+-...+..-+ + ..-|++.+ |+....-|.||.||=
T Consensus 4 ~~C~~CG~vYd~e~Gd--------p-~~gi~pgT~fedlPd~w~CP~Cg~ 44 (55)
T COG1773 4 WRCSVCGYVYDPEKGD--------P-RCGIAPGTPFEDLPDDWVCPECGV 44 (55)
T ss_pred eEecCCceEeccccCC--------c-cCCCCCCCchhhCCCccCCCCCCC
Confidence 4799998865321100 0 12456655 578888999999983
No 148
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=55.05 E-value=9.8 Score=29.50 Aligned_cols=11 Identities=27% Similarity=0.594 Sum_probs=9.1
Q ss_pred eeecCCCCeeE
Q 009948 491 FWQCMDCNQLY 501 (522)
Q Consensus 491 F~~C~~Cgkvy 501 (522)
--.|+.||..|
T Consensus 26 ~L~c~~~~~aY 36 (60)
T COG2835 26 ELICPRCKLAY 36 (60)
T ss_pred EEEecccCcee
Confidence 55699999988
No 149
>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=54.85 E-value=4.6 Score=35.20 Aligned_cols=10 Identities=30% Similarity=1.095 Sum_probs=6.1
Q ss_pred cccCCCCcCc
Q 009948 452 RCTKCNGRFI 461 (522)
Q Consensus 452 RC~~CN~~l~ 461 (522)
.|+.|+.+|+
T Consensus 11 ~Cp~CG~kFY 20 (108)
T PF09538_consen 11 TCPSCGAKFY 20 (108)
T ss_pred cCCCCcchhc
Confidence 3666666654
No 150
>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=54.66 E-value=9.9 Score=32.82 Aligned_cols=42 Identities=21% Similarity=0.503 Sum_probs=25.4
Q ss_pred CcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeEeccch
Q 009948 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEGTQ 506 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~GsH 506 (522)
.+|+.|++..+. ++-++ |=+..+....-||.|+.|+- |-|-|
T Consensus 3 ~~CpYCg~~~~l--~~~~~----------iYg~~~~~~~~~y~C~~C~A--yVG~H 44 (102)
T PF11672_consen 3 IICPYCGGPAEL--VDGSE----------IYGHRYDDGPYLYVCTPCDA--YVGCH 44 (102)
T ss_pred cccCCCCCeeEE--cccch----------hcCccCCCCceeEECCCCCc--eeeee
Confidence 589999997643 22122 11133333445799999985 66666
No 151
>PRK00260 cysS cysteinyl-tRNA synthetase; Validated
Probab=54.39 E-value=11 Score=41.12 Aligned_cols=35 Identities=20% Similarity=0.276 Sum_probs=28.0
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 401 (522)
=++|+||..||+|.++.+.+.-|..++..|+++|.
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 57999999999999987643335678999988873
No 152
>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=54.38 E-value=5.4 Score=25.63 Aligned_cols=9 Identities=22% Similarity=0.674 Sum_probs=7.1
Q ss_pred ecCCCCeeE
Q 009948 493 QCMDCNQLY 501 (522)
Q Consensus 493 ~C~~Cgkvy 501 (522)
.||.||-.|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 399999765
No 153
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.23 E-value=3.6 Score=40.33 Aligned_cols=43 Identities=21% Similarity=0.362 Sum_probs=22.1
Q ss_pred cccCCCCcCccCCCChHHHHHhh------cccccCCccccccCCceeecCCCC
Q 009948 452 RCTKCNGRFIQKPLSTEEAVEAA------KGFQRIPDCLFDKNLQFWQCMDCN 498 (522)
Q Consensus 452 RC~~CN~~l~~~~~~~e~~~~~~------~~~~~vp~~v~~~~~~F~~C~~Cg 498 (522)
-||+||..+..+.+-...++-.+ -.++.|-|+ .-+.|.||.|+
T Consensus 21 eCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~----fY~VvvCP~C~ 69 (267)
T COG1655 21 ECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPY----FYDVVVCPICY 69 (267)
T ss_pred ccCcccchhhhhheeccceeEecccccceeeccccCCc----eeEEEEcchhh
Confidence 39999998853222111110000 012234444 34689999997
No 154
>PRK11827 hypothetical protein; Provisional
Probab=53.91 E-value=11 Score=29.23 Aligned_cols=11 Identities=36% Similarity=0.978 Sum_probs=9.0
Q ss_pred CcccCCCCcCc
Q 009948 451 SRCTKCNGRFI 461 (522)
Q Consensus 451 sRC~~CN~~l~ 461 (522)
-.|+.|.|+|.
T Consensus 9 LaCP~ckg~L~ 19 (60)
T PRK11827 9 IACPVCNGKLW 19 (60)
T ss_pred eECCCCCCcCe
Confidence 36999999874
No 155
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=53.22 E-value=7.7 Score=39.83 Aligned_cols=34 Identities=18% Similarity=0.507 Sum_probs=23.2
Q ss_pred cCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeE
Q 009948 446 EDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 446 ~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 501 (522)
++..+++|+.|+..+. .++. ...++.||.||.-|
T Consensus 23 ~~~~~~~c~~c~~~~~-----~~~l-----------------~~~~~vc~~c~~h~ 56 (292)
T PRK05654 23 PEGLWTKCPSCGQVLY-----RKEL-----------------EANLNVCPKCGHHM 56 (292)
T ss_pred CCCCeeECCCccchhh-----HHHH-----------------HhcCCCCCCCCCCe
Confidence 4667899999999653 1221 12368999998733
No 156
>PLN02563 aminoacyl-tRNA ligase
Probab=52.89 E-value=21 Score=42.79 Aligned_cols=19 Identities=26% Similarity=0.214 Sum_probs=16.4
Q ss_pred HHHHHHHhcCCceecCCCC
Q 009948 367 GLAKHLRCVGIDAATPRSK 385 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~ 385 (522)
=+|||.|+.||+|.++.+.
T Consensus 139 viaRy~Rm~G~~Vl~~~G~ 157 (963)
T PLN02563 139 ILARYKRMQGYNVLHPMGW 157 (963)
T ss_pred HHHHHHHhcCCeecccccc
Confidence 5699999999999998753
No 157
>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=52.84 E-value=11 Score=41.40 Aligned_cols=35 Identities=14% Similarity=0.202 Sum_probs=28.1
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 401 (522)
=++||||..||+|.++.+.+.-|..++..|+++|.
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 57999999999999887643335579999988876
No 158
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=52.69 E-value=9.4 Score=25.83 Aligned_cols=13 Identities=23% Similarity=0.639 Sum_probs=11.6
Q ss_pred CceeecCCCCeeE
Q 009948 489 LQFWQCMDCNQLY 501 (522)
Q Consensus 489 ~~F~~C~~Cgkvy 501 (522)
.+||+|..||.++
T Consensus 5 ~~~ykC~~Cgniv 17 (34)
T TIGR00319 5 GQVYKCEVCGNIV 17 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 5799999999987
No 159
>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=51.85 E-value=21 Score=29.04 Aligned_cols=60 Identities=17% Similarity=0.432 Sum_probs=31.2
Q ss_pred HHHHHHHHHHcccccccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCe
Q 009948 430 NQQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 499 (522)
Q Consensus 430 ~eQl~~v~~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 499 (522)
..++.++.+...+.+.++.--+-|..|+..|++. ++. . -+|-..-.....-.+.|..||+
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 4678889999998888777678899999998642 110 0 0111000013345888999985
No 160
>COG0215 CysS Cysteinyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=51.56 E-value=12 Score=40.71 Aligned_cols=35 Identities=20% Similarity=0.257 Sum_probs=28.6
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 401 (522)
=|.||||.+||+|.|+.+-..=|+.|++.|+++|-
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 57999999999998887643235679999999886
No 161
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=51.36 E-value=18 Score=33.95 Aligned_cols=54 Identities=19% Similarity=0.540 Sum_probs=30.9
Q ss_pred cCCCcccCCCCc------CccCCCCh-HHHH-Hhhcccc---cC-CccccccCCceeecCCCCeeE
Q 009948 448 QLMSRCTKCNGR------FIQKPLST-EEAV-EAAKGFQ---RI-PDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 448 ~~~sRC~~CN~~------l~~~~~~~-e~~~-~~~~~~~---~v-p~~v~~~~~~F~~C~~Cgkvy 501 (522)
.-...|+.||.. |-++.-++ |+.. +.-.|.+ .| |..|.+-.+..++|..|.+-|
T Consensus 69 P~~~~C~~C~~~G~~c~pfr~r~T~kQEe~~ReeNgG~DPit~Vd~~lvnN~~nVLFRC~~C~Raw 134 (175)
T PF15446_consen 69 PHHGMCQQCKKPGPSCKPFRPRKTPKQEEKLREENGGVDPITPVDPELVNNPDNVLFRCTSCHRAW 134 (175)
T ss_pred CCCCcccccCCCCCCCcccCCCCCcHHHHHHHHHcCCCCCCccCCHHHccChhheEEecCCcccee
Confidence 336899999974 22222333 2222 2212222 23 334456667899999999875
No 162
>PRK12366 replication factor A; Reviewed
Probab=51.33 E-value=7.2 Score=44.47 Aligned_cols=29 Identities=17% Similarity=0.443 Sum_probs=21.6
Q ss_pred CcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCee
Q 009948 447 DQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 447 ~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 500 (522)
...+.+|+.||..+.. ...-|+|+.||++
T Consensus 529 ~~~y~aCp~CnkKv~~-------------------------~~g~~~C~~c~~~ 557 (637)
T PRK12366 529 KIILYLCPNCRKRVEE-------------------------VDGEYICEFCGEV 557 (637)
T ss_pred CEEEecccccCeEeEc-------------------------CCCcEECCCCCCC
Confidence 4557999999985420 1347999999997
No 163
>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=50.95 E-value=10 Score=25.65 Aligned_cols=13 Identities=23% Similarity=0.805 Sum_probs=11.4
Q ss_pred CceeecCCCCeeE
Q 009948 489 LQFWQCMDCNQLY 501 (522)
Q Consensus 489 ~~F~~C~~Cgkvy 501 (522)
.+||+|..||.++
T Consensus 2 ~~~ykC~~CGniv 14 (34)
T cd00974 2 LEVYKCEICGNIV 14 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 3699999999987
No 164
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=50.86 E-value=6.1 Score=34.66 Aligned_cols=31 Identities=16% Similarity=0.227 Sum_probs=19.2
Q ss_pred HHHHHHHHHHc---------ccccccCcCCCcccCCCCcC
Q 009948 430 NQQLLEVIEAF---------QLKISEDQLMSRCTKCNGRF 460 (522)
Q Consensus 430 ~eQl~~v~~~f---------~l~~~~~~~~sRC~~CN~~l 460 (522)
.++|..-+..+ .|.+......-||..|+..+
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 45666555443 34455555668899999754
No 165
>PRK14535 cysS cysteinyl-tRNA synthetase; Provisional
Probab=50.63 E-value=13 Score=42.51 Aligned_cols=35 Identities=17% Similarity=0.209 Sum_probs=28.2
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 401 (522)
=|+|+||..||+|.++.+...-|..|+..|+++|.
T Consensus 275 VL~R~Lr~~Gy~V~fV~NiTD~DDKII~~A~e~G~ 309 (699)
T PRK14535 275 MIARWLRECGYPLTYVRNITDIDDKIIARAAENGE 309 (699)
T ss_pred HHHHHHHHcCCceEEEeCCcccchHHHHHHHHcCC
Confidence 48999999999999987643335679999998874
No 166
>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=50.47 E-value=20 Score=30.90 Aligned_cols=28 Identities=21% Similarity=0.393 Sum_probs=22.6
Q ss_pred CCCChHHHHHhhhcCCc-EEEecChhHHH
Q 009948 385 KKPEPRELIDQTSKEKR-VLLTRDAKLLR 412 (522)
Q Consensus 385 ~~~~d~~ll~~A~~E~R-iiLTrd~~l~~ 412 (522)
++++|..+++.|..-+- +|+|+|++|+.
T Consensus 85 ~D~~D~~~l~~A~~~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 85 RDKKDNKFLNTAYASKANALITGDTDLLV 113 (114)
T ss_pred CCchhHHHHHHHHhcCCCEEEECCHHHhh
Confidence 35678888999988764 99999999864
No 167
>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=50.31 E-value=11 Score=32.79 Aligned_cols=27 Identities=22% Similarity=0.597 Sum_probs=19.1
Q ss_pred CcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeE
Q 009948 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 501 (522)
..|+.|++.. +|+. ...|.||.|+.-+
T Consensus 3 p~CP~C~sey-----------------------tY~d-g~~~iCpeC~~EW 29 (109)
T TIGR00686 3 PPCPKCNSEY-----------------------TYHD-GTQLICPSCLYEW 29 (109)
T ss_pred CcCCcCCCcc-----------------------eEec-CCeeECccccccc
Confidence 5699999953 3333 3579999998753
No 168
>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=50.18 E-value=11 Score=34.74 Aligned_cols=55 Identities=18% Similarity=0.371 Sum_probs=34.0
Q ss_pred CcccCCCCcCccCCCChHHHHHhhcccccCCcccc---ccCCceeecCCCCeeE-eccchhhHHHHHHHHhccc
Q 009948 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLF---DKNLQFWQCMDCNQLY-WEGTQYHNAVQKFIDVCKL 520 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~---~~~~~F~~C~~Cgkvy-W~GsH~~~~~~~~~~~~~~ 520 (522)
+-|+.||.+.. |. ...+.|+ ..+..=..|..||+-| |--.-.+...+...++=+|
T Consensus 40 ~~Cp~C~~~Ir--------------G~-y~v~gv~~~g~~~~~PsYC~~CGkpyPWt~~~L~aa~el~ee~eeL 98 (158)
T PF10083_consen 40 TSCPNCSTPIR--------------GD-YHVEGVFGLGGHYEAPSYCHNCGKPYPWTENALEAANELIEEDEEL 98 (158)
T ss_pred HHCcCCCCCCC--------------Cc-eecCCeeeeCCCCCCChhHHhCCCCCchHHHHHHHHHHHHHHhhcC
Confidence 56999998652 11 2223332 2344556799999999 7777777766655444444
No 169
>PRK06386 replication factor A; Reviewed
Probab=49.78 E-value=6.6 Score=41.45 Aligned_cols=19 Identities=16% Similarity=0.690 Sum_probs=14.0
Q ss_pred cccc-cCcCCCcccCCCCcC
Q 009948 442 LKIS-EDQLMSRCTKCNGRF 460 (522)
Q Consensus 442 l~~~-~~~~~sRC~~CN~~l 460 (522)
+.+. ...++.|||.||-.+
T Consensus 227 v~i~~gsgli~rCP~C~R~l 246 (358)
T PRK06386 227 VSVGQGSRIFTKCSVCNKII 246 (358)
T ss_pred EEEcCCcEeEecCcCCCeEc
Confidence 3344 367789999999865
No 170
>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=49.70 E-value=12 Score=23.61 Aligned_cols=15 Identities=13% Similarity=0.452 Sum_probs=12.2
Q ss_pred CCceeecCCCCeeEe
Q 009948 488 NLQFWQCMDCNQLYW 502 (522)
Q Consensus 488 ~~~F~~C~~CgkvyW 502 (522)
.+.-+.|+.|+|.|.
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 345689999999985
No 171
>PRK12496 hypothetical protein; Provisional
Probab=49.64 E-value=12 Score=35.00 Aligned_cols=93 Identities=15% Similarity=0.133 Sum_probs=48.7
Q ss_pred cHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecChhHHHhhhhcCceEEEEccCChHHHHH--HHHHHccc
Q 009948 365 VEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQLL--EVIEAFQL 442 (522)
Q Consensus 365 Lg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~RiiLTrd~~l~~~~~~~~~~~~~v~~~~~~eQl~--~v~~~f~l 442 (522)
+..+-+..+.-| |...+. ..|-+++.+|.+.+-++||-|..+-+-+...+..+.-+....+.++.. .+....+=
T Consensus 60 i~~v~~~a~~tg-d~~~Ls---~~D~~~iaLA~el~~~lvtDD~~~~~vA~~lgi~v~~~~~~~i~~~~~w~~~C~gC~~ 135 (164)
T PRK12496 60 IEKVEEAAIKTG-DLMRLS---NTDIEVLALALELNGTLYTDDYGIQNVAKKLNIKFENIKTKGIKKVIKWRKVCKGCKK 135 (164)
T ss_pred HHHHHHHHHhcC-Cccccc---hhhHHHHHHHHHhCCcEECcHHHHHHHHHHcCCeEeccccccchhheeeeEECCCCCc
Confidence 445545445555 422222 356789999999999999999876544333333333333333333211 00111121
Q ss_pred ccccCcCCCcccCCCCcCc
Q 009948 443 KISEDQLMSRCTKCNGRFI 461 (522)
Q Consensus 443 ~~~~~~~~sRC~~CN~~l~ 461 (522)
.++.+.....|+.|++++.
T Consensus 136 ~~~~~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 136 KYPEDYPDDVCEICGSPVK 154 (164)
T ss_pred cccCCCCCCcCCCCCChhh
Confidence 1111123456999999874
No 172
>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=49.07 E-value=36 Score=34.92 Aligned_cols=41 Identities=7% Similarity=-0.099 Sum_probs=27.8
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecC
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRD 407 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~RiiLTrd 407 (522)
-++|+||+.||+|.++.+.+.-+..+...|.+++.+-.+.+
T Consensus 28 ~i~R~~r~~G~~v~~~~g~D~~g~~i~~~a~~~~~~~~~~~ 68 (312)
T cd00668 28 FIARYKRMRGYEVPFLPGWDTHGLPIELKAERKGGRKKKTI 68 (312)
T ss_pred HHHHHHHhCCCCCCCCCccCCCCHHHHHHHHHhcCcccccc
Confidence 46899999999999887643223357777777665444333
No 173
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=48.95 E-value=27 Score=39.75 Aligned_cols=97 Identities=15% Similarity=0.376 Sum_probs=52.7
Q ss_pred HHHHhhhcCCcEEEecChhHHHhhhhcCceEEEEccCChHHHHHHHH-HHcc--cccccCcCCCcccCCCCcCccCCCCh
Q 009948 391 ELIDQTSKEKRVLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQLLEVI-EAFQ--LKISEDQLMSRCTKCNGRFIQKPLST 467 (522)
Q Consensus 391 ~ll~~A~~E~RiiLTrd~~l~~~~~~~~~~~~~v~~~~~~eQl~~v~-~~f~--l~~~~~~~~sRC~~CN~~l~~~~~~~ 467 (522)
.++.+|.-..|-+=|+++.|++...... +++ ..++|..++. +-|. -..++...---|..|+++.-+-...-
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-----LDD-AEKQEYENLAFRIFSKNPPVDPNSAKVDCSVCGAKIDPYDLQC 1134 (1189)
T ss_pred HHHHHHHhhhhhhhhhHHHHHHHHhhhh-----CCH-HHHHHHHHHHHHHhccCCCCCCCccceeeeecCCcCCccCCCC
Confidence 4788888889999999999877543321 111 1234444442 2341 12222222345888887653211111
Q ss_pred HHHHHhhcccccCCccccc----cCCceeecCCCCe
Q 009948 468 EEAVEAAKGFQRIPDCLFD----KNLQFWQCMDCNQ 499 (522)
Q Consensus 468 e~~~~~~~~~~~vp~~v~~----~~~~F~~C~~Cgk 499 (522)
.|. ..+.|-++-. ....||.||.|..
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 121 1356666532 3355999999974
No 174
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=48.93 E-value=7.2 Score=34.43 Aligned_cols=19 Identities=26% Similarity=0.712 Sum_probs=12.0
Q ss_pred cccccCcCCCcccCCCCcC
Q 009948 442 LKISEDQLMSRCTKCNGRF 460 (522)
Q Consensus 442 l~~~~~~~~sRC~~CN~~l 460 (522)
|.+......-||..|+..+
T Consensus 63 L~Ie~vp~~~~C~~Cg~~~ 81 (117)
T PRK00564 63 LDIVDEKVELECKDCSHVF 81 (117)
T ss_pred EEEEecCCEEEhhhCCCcc
Confidence 3344445567899998643
No 175
>PF12813 XPG_I_2: XPG domain containing
Probab=48.86 E-value=19 Score=36.04 Aligned_cols=58 Identities=22% Similarity=0.194 Sum_probs=41.4
Q ss_pred HHHHHHHhc---CCceecCCCCCCChHHHHHhhhcCCcEEEecChhHHHhhhhcCceEEEEcc
Q 009948 367 GLAKHLRCV---GIDAATPRSKKPEPRELIDQTSKEKRVLLTRDAKLLRHQYLIKNQIYRVKS 426 (522)
Q Consensus 367 ~Lar~LR~l---G~D~~~~~~~~~~d~~ll~~A~~E~RiiLTrd~~l~~~~~~~~~~~~~v~~ 426 (522)
-+..-||.+ |..+..+.. ..|.+++..|++-|..+||.|.+|+-......++++.+.+
T Consensus 8 ~~~e~L~~~~~~~~~~~~~~~--EAD~~~A~~A~~~~~~VLt~DSDf~I~dlg~~~~yipl~~ 68 (246)
T PF12813_consen 8 AFIEALRESWRYGVPVVQCPG--EADRECAALARKWGCPVLTNDSDFLIHDLGQKGGYIPLDS 68 (246)
T ss_pred HHHHHHHHHhhcCCcEEEcCc--cchHHHHHHHHHcCCeEEccCCCEEEeccCCCceEEEeee
Confidence 345557777 999988764 4688999999999999999999985433322234555443
No 176
>PHA02768 hypothetical protein; Provisional
Probab=48.72 E-value=8 Score=29.54 Aligned_cols=18 Identities=17% Similarity=0.595 Sum_probs=15.5
Q ss_pred eecCCCCeeEeccchhhH
Q 009948 492 WQCMDCNQLYWEGTQYHN 509 (522)
Q Consensus 492 ~~C~~CgkvyW~GsH~~~ 509 (522)
|.|+.|||.|=.++|..+
T Consensus 6 y~C~~CGK~Fs~~~~L~~ 23 (55)
T PHA02768 6 YECPICGEIYIKRKSMIT 23 (55)
T ss_pred cCcchhCCeeccHHHHHH
Confidence 489999999999888754
No 177
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=48.49 E-value=11 Score=35.84 Aligned_cols=16 Identities=25% Similarity=0.764 Sum_probs=12.9
Q ss_pred ccCCceeecCCCCeeE
Q 009948 486 DKNLQFWQCMDCNQLY 501 (522)
Q Consensus 486 ~~~~~F~~C~~Cgkvy 501 (522)
+....||.||.||+-|
T Consensus 112 e~~~~~Y~Cp~C~~ry 127 (178)
T PRK06266 112 EENNMFFFCPNCHIRF 127 (178)
T ss_pred ccCCCEEECCCCCcEE
Confidence 3456899999999887
No 178
>PHA00626 hypothetical protein
Probab=47.06 E-value=14 Score=28.15 Aligned_cols=17 Identities=18% Similarity=0.217 Sum_probs=12.8
Q ss_pred CCceeecCCCCeeEecc
Q 009948 488 NLQFWQCMDCNQLYWEG 504 (522)
Q Consensus 488 ~~~F~~C~~CgkvyW~G 504 (522)
...-|.|+.||--|=..
T Consensus 20 ~snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 20 WSDDYVCCDCGYNDSKD 36 (59)
T ss_pred cCcceEcCCCCCeechh
Confidence 45678999999877543
No 179
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=46.68 E-value=14 Score=35.86 Aligned_cols=20 Identities=25% Similarity=0.547 Sum_probs=13.6
Q ss_pred ccccccCcCC-CcccCCCCcC
Q 009948 441 QLKISEDQLM-SRCTKCNGRF 460 (522)
Q Consensus 441 ~l~~~~~~~~-sRC~~CN~~l 460 (522)
++.++...+| -||..||.=+
T Consensus 32 glSiRL~TPF~~RCL~C~~YI 52 (272)
T COG5134 32 GLSIRLETPFPVRCLNCENYI 52 (272)
T ss_pred cceEEeccCcceeecchhhhh
Confidence 4455555555 5999999854
No 180
>PTZ00399 cysteinyl-tRNA-synthetase; Provisional
Probab=46.68 E-value=16 Score=41.82 Aligned_cols=35 Identities=17% Similarity=0.153 Sum_probs=28.6
Q ss_pred HHHHHHH-hcCCceecCCCCCCChHHHHHhhhcCCc
Q 009948 367 GLAKHLR-CVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 367 ~Lar~LR-~lG~D~~~~~~~~~~d~~ll~~A~~E~R 401 (522)
=|+|||| .+||||.++.+...-|..|+..|+++|.
T Consensus 87 il~R~l~~~~Gy~V~~v~nitDidDKIi~~A~~~g~ 122 (651)
T PTZ00399 87 IIRRILEDYFGYDVFYVMNITDIDDKIIKRAREEKL 122 (651)
T ss_pred HHHHHHHHhcCCceEEEeCCCCcchHHHHHHHHhCC
Confidence 4799999 8999999987643335679999999886
No 181
>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=46.44 E-value=17 Score=25.69 Aligned_cols=31 Identities=32% Similarity=0.804 Sum_probs=15.9
Q ss_pred CcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCee
Q 009948 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 500 (522)
-||..|++-+- | =..+......|.|+-|+..
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 58999998542 2 1123345679999999975
No 182
>PRK14534 cysS cysteinyl-tRNA synthetase; Provisional
Probab=46.28 E-value=15 Score=40.39 Aligned_cols=36 Identities=11% Similarity=0.075 Sum_probs=26.4
Q ss_pred HHHHHHHhcCCceecCCCC-CC---------ChHHHHHhhhcCCcE
Q 009948 367 GLAKHLRCVGIDAATPRSK-KP---------EPRELIDQTSKEKRV 402 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~-~~---------~d~~ll~~A~~E~Ri 402 (522)
=|+||||.+||+|.++.+- ++ .|..|+..|+++|.-
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 5799999999999984321 11 145699999888753
No 183
>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=46.21 E-value=16 Score=27.87 Aligned_cols=11 Identities=18% Similarity=0.730 Sum_probs=8.7
Q ss_pred CCCcccCCCCc
Q 009948 449 LMSRCTKCNGR 459 (522)
Q Consensus 449 ~~sRC~~CN~~ 459 (522)
.++.|+.|+..
T Consensus 25 ~l~~c~~cg~~ 35 (56)
T PF01783_consen 25 NLVKCPNCGEP 35 (56)
T ss_dssp SEEESSSSSSE
T ss_pred ceeeeccCCCE
Confidence 45889999974
No 184
>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=45.73 E-value=13 Score=25.13 Aligned_cols=11 Identities=27% Similarity=0.796 Sum_probs=9.5
Q ss_pred eeecCCCCeeE
Q 009948 491 FWQCMDCNQLY 501 (522)
Q Consensus 491 F~~C~~Cgkvy 501 (522)
.|+|+.||-+|
T Consensus 1 ~~~C~~CGy~y 11 (33)
T cd00350 1 KYVCPVCGYIY 11 (33)
T ss_pred CEECCCCCCEE
Confidence 38899999988
No 185
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=45.66 E-value=6.5 Score=38.44 Aligned_cols=16 Identities=25% Similarity=0.775 Sum_probs=14.1
Q ss_pred CceeecCCCCeeEecc
Q 009948 489 LQFWQCMDCNQLYWEG 504 (522)
Q Consensus 489 ~~F~~C~~CgkvyW~G 504 (522)
-+.|.||.||=-++++
T Consensus 46 Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 46 YEVWVCPHCGYAAFEE 61 (214)
T ss_pred eeEEECCCCCCccccc
Confidence 4689999999999986
No 186
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=45.35 E-value=8.1 Score=33.95 Aligned_cols=31 Identities=16% Similarity=0.367 Sum_probs=18.6
Q ss_pred HHHHHHHHHHc---------ccccccCcCCCcccCCCCcC
Q 009948 430 NQQLLEVIEAF---------QLKISEDQLMSRCTKCNGRF 460 (522)
Q Consensus 430 ~eQl~~v~~~f---------~l~~~~~~~~sRC~~CN~~l 460 (522)
.++|+.-+..+ .|.+...+...||..|+...
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 45666555433 34444455567899999743
No 187
>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=45.11 E-value=12 Score=38.55 Aligned_cols=36 Identities=17% Similarity=0.167 Sum_probs=26.3
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcE
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRV 402 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~Ri 402 (522)
=|.|+|+.+||+|.++.+-..=|+.|+..|+++|.-
T Consensus 35 ~l~R~L~~~g~~V~~V~NiTDiDDKii~~A~~~g~~ 70 (300)
T PF01406_consen 35 VLRRYLEYLGYDVTYVMNITDIDDKIIKRAREEGVS 70 (300)
T ss_dssp HHHHHHHHTT-EEEEEEEEB-SSHHHHHHHHHTTS-
T ss_pred HHHHHHHHcCCeEEEEEeccccchHHHHHHHhccCC
Confidence 468999999999998875322256799999998843
No 188
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=45.01 E-value=11 Score=35.91 Aligned_cols=14 Identities=21% Similarity=0.930 Sum_probs=11.5
Q ss_pred cCCCcccCCCCcCc
Q 009948 448 QLMSRCTKCNGRFI 461 (522)
Q Consensus 448 ~~~sRC~~CN~~l~ 461 (522)
-+|.||+.|.+.|.
T Consensus 147 VI~A~CsrC~~~L~ 160 (188)
T COG1096 147 VIYARCSRCRAPLV 160 (188)
T ss_pred EEEEEccCCCcceE
Confidence 34799999999874
No 189
>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=44.29 E-value=15 Score=25.21 Aligned_cols=15 Identities=27% Similarity=0.603 Sum_probs=9.7
Q ss_pred CceeecCCCCeeEec
Q 009948 489 LQFWQCMDCNQLYWE 503 (522)
Q Consensus 489 ~~F~~C~~CgkvyW~ 503 (522)
-...+|+.||+++|.
T Consensus 9 l~~~rC~~Cg~~~~p 23 (37)
T PF12172_consen 9 LLGQRCRDCGRVQFP 23 (37)
T ss_dssp EEEEE-TTT--EEES
T ss_pred EEEEEcCCCCCEecC
Confidence 357789999999996
No 190
>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=43.37 E-value=19 Score=33.41 Aligned_cols=46 Identities=17% Similarity=0.450 Sum_probs=29.3
Q ss_pred ccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCee--EeccchhhHHHH
Q 009948 445 SEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL--YWEGTQYHNAVQ 512 (522)
Q Consensus 445 ~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv--yW~GsH~~~~~~ 512 (522)
..+..|-.|+.|+.. .+-++|.+ .-+.||.||-. |=.-|+.-..++
T Consensus 104 e~~~~~Y~Cp~c~~r-----~tf~eA~~-----------------~~F~Cp~Cg~~L~~~dn~~~i~~l~ 151 (158)
T TIGR00373 104 ETNNMFFICPNMCVR-----FTFNEAME-----------------LNFTCPRCGAMLDYLDNSEAIEKLE 151 (158)
T ss_pred ccCCCeEECCCCCcE-----eeHHHHHH-----------------cCCcCCCCCCEeeeccCHHHHHHHH
Confidence 335568889999975 45577753 24679999985 344444433333
No 191
>PHA02998 RNA polymerase subunit; Provisional
Probab=42.96 E-value=21 Score=33.70 Aligned_cols=48 Identities=19% Similarity=0.468 Sum_probs=25.9
Q ss_pred HcccccccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeE
Q 009948 439 AFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 439 ~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 501 (522)
.|+|-.. ..-..|+.|++.-.. .. .-+...+ | +....|+.|..||+-|
T Consensus 134 yfnvlpk--kt~v~CPkCg~~~A~-f~-qlQTRSA----D-------EPmT~FYkC~~CG~~w 181 (195)
T PHA02998 134 YFNVLDE--KYNTPCPNCKSKNTT-PM-MIQTRAA----D-------EPPLVRHACRDCKKHF 181 (195)
T ss_pred heeccCc--ccCCCCCCCCCCceE-EE-EEeeccC----C-------CCceEEEEcCCCCCcc
Confidence 4776543 244789999985310 00 0001100 1 1135699999999863
No 192
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=42.55 E-value=10 Score=33.87 Aligned_cols=30 Identities=17% Similarity=0.278 Sum_probs=18.8
Q ss_pred HHHHHHHHHHc---------ccccccCcCCCcccCCCCcC
Q 009948 430 NQQLLEVIEAF---------QLKISEDQLMSRCTKCNGRF 460 (522)
Q Consensus 430 ~eQl~~v~~~f---------~l~~~~~~~~sRC~~CN~~l 460 (522)
.++|+.-+..+ .|.+......-|| .|+..+
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 45666555432 3455555667899 999764
No 193
>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=42.51 E-value=22 Score=39.45 Aligned_cols=35 Identities=11% Similarity=0.007 Sum_probs=27.2
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 401 (522)
=++|+||+.|+||.++.+.+.-+..++..|+++|.
T Consensus 27 vl~R~~r~~G~~V~~v~g~D~~g~~i~~~a~~~g~ 61 (530)
T TIGR00398 27 VYARYKRLRGYEVLFVCGTDEHGTKIELKAEQEGL 61 (530)
T ss_pred HHHHHHHhcCCeEEEecccCCCCcHHHHHHHHcCC
Confidence 46999999999999987644334568888888773
No 194
>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=42.51 E-value=9.9 Score=33.42 Aligned_cols=19 Identities=21% Similarity=0.676 Sum_probs=12.6
Q ss_pred cccccCcCCCcccCCCCcC
Q 009948 442 LKISEDQLMSRCTKCNGRF 460 (522)
Q Consensus 442 l~~~~~~~~sRC~~CN~~l 460 (522)
|.+.......||..|+...
T Consensus 62 L~I~~~p~~~~C~~Cg~~~ 80 (115)
T TIGR00100 62 LNIEDEPVECECEDCSEEV 80 (115)
T ss_pred EEEEeeCcEEEcccCCCEE
Confidence 4444455568899999643
No 195
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=41.87 E-value=24 Score=26.84 Aligned_cols=27 Identities=22% Similarity=0.639 Sum_probs=19.6
Q ss_pred CCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeE
Q 009948 450 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 450 ~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 501 (522)
-.+|+.|+..+.. .+.--+||.||-.|
T Consensus 5 ~~~C~~Cg~~~~~-------------------------~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 5 GCKCPVCGKKFKD-------------------------GDDIVVCPECGAPY 31 (54)
T ss_pred CccChhhCCcccC-------------------------CCCEEECCCCCCcc
Confidence 4789999997621 12345699999988
No 196
>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=41.83 E-value=16 Score=33.99 Aligned_cols=16 Identities=19% Similarity=0.445 Sum_probs=13.4
Q ss_pred ccCCceeecCCCCeeE
Q 009948 486 DKNLQFWQCMDCNQLY 501 (522)
Q Consensus 486 ~~~~~F~~C~~Cgkvy 501 (522)
+....||.||.|++-|
T Consensus 104 e~~~~~Y~Cp~c~~r~ 119 (158)
T TIGR00373 104 ETNNMFFICPNMCVRF 119 (158)
T ss_pred ccCCCeEECCCCCcEe
Confidence 3467899999999877
No 197
>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=41.65 E-value=15 Score=25.47 Aligned_cols=12 Identities=25% Similarity=0.847 Sum_probs=10.0
Q ss_pred eecCCCCeeEec
Q 009948 492 WQCMDCNQLYWE 503 (522)
Q Consensus 492 ~~C~~CgkvyW~ 503 (522)
++|+.||+.|..
T Consensus 6 y~C~~Cg~~fe~ 17 (41)
T smart00834 6 YRCEDCGHTFEV 17 (41)
T ss_pred EEcCCCCCEEEE
Confidence 489999998863
No 198
>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=40.90 E-value=14 Score=25.32 Aligned_cols=9 Identities=22% Similarity=0.896 Sum_probs=8.2
Q ss_pred ccCCCCcCc
Q 009948 453 CTKCNGRFI 461 (522)
Q Consensus 453 C~~CN~~l~ 461 (522)
|+.||..|.
T Consensus 4 Cp~C~nlL~ 12 (35)
T PF02150_consen 4 CPECGNLLY 12 (35)
T ss_dssp ETTTTSBEE
T ss_pred CCCCCccce
Confidence 999999885
No 199
>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=40.84 E-value=44 Score=26.08 Aligned_cols=47 Identities=19% Similarity=0.444 Sum_probs=28.6
Q ss_pred HHHHHHHHHccccc---ccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCee
Q 009948 431 QQLLEVIEAFQLKI---SEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 431 eQl~~v~~~f~l~~---~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 500 (522)
++|......+|+.+ ++..--..|+.|+..... .....-|.|+.||..
T Consensus 6 ~~L~yka~~~G~~v~~v~~~~TSq~C~~CG~~~~~-----------------------~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 6 QRLEYKAEEYGIQVVEVDEAYTSQTCPRCGHRNKK-----------------------RRSGRVFTCPNCGFE 55 (69)
T ss_pred HHHHHHHHHhCCEEEEECCCCCccCccCccccccc-----------------------ccccceEEcCCCCCE
Confidence 45555555566544 333323569999996420 123568899999976
No 200
>PRK10220 hypothetical protein; Provisional
Probab=40.40 E-value=20 Score=31.14 Aligned_cols=12 Identities=17% Similarity=0.589 Sum_probs=9.4
Q ss_pred CceeecCCCCee
Q 009948 489 LQFWQCMDCNQL 500 (522)
Q Consensus 489 ~~F~~C~~Cgkv 500 (522)
...|.||.|+.-
T Consensus 18 ~~~~vCpeC~hE 29 (111)
T PRK10220 18 NGMYICPECAHE 29 (111)
T ss_pred CCeEECCcccCc
Confidence 347999999864
No 201
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) 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. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=39.66 E-value=63 Score=34.18 Aligned_cols=18 Identities=28% Similarity=0.285 Sum_probs=15.9
Q ss_pred HHHHHHHhcCCceecCCC
Q 009948 367 GLAKHLRCVGIDAATPRS 384 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~ 384 (522)
-++|+||.+|++|.++..
T Consensus 46 ~i~R~lr~~G~~v~~v~~ 63 (353)
T cd00674 46 LVARALRDLGFEVRLIYS 63 (353)
T ss_pred HHHHHHHHcCCCEEEEEE
Confidence 679999999999988765
No 202
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=39.37 E-value=39 Score=30.58 Aligned_cols=33 Identities=18% Similarity=0.218 Sum_probs=26.9
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCC
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 400 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~ 400 (522)
-++..||..||+|+++.. +.+..++++.|.+++
T Consensus 22 iv~~~lr~~G~eVi~LG~-~vp~e~i~~~a~~~~ 54 (137)
T PRK02261 22 ILDRALTEAGFEVINLGV-MTSQEEFIDAAIETD 54 (137)
T ss_pred HHHHHHHHCCCEEEECCC-CCCHHHHHHHHHHcC
Confidence 459999999999999975 456678999887764
No 203
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=39.33 E-value=77 Score=28.83 Aligned_cols=53 Identities=11% Similarity=0.104 Sum_probs=36.5
Q ss_pred HHhcCCceecCCCCCCChHHHHHhhhcCC-cEEEecChhHHHhhhhcCceEEEEcc
Q 009948 372 LRCVGIDAATPRSKKPEPRELIDQTSKEK-RVLLTRDAKLLRHQYLIKNQIYRVKS 426 (522)
Q Consensus 372 LR~lG~D~~~~~~~~~~d~~ll~~A~~E~-RiiLTrd~~l~~~~~~~~~~~~~v~~ 426 (522)
....++.+.+. . .+.|+-|++.|.+.| -|+.|.|++|-++....+..++.++.
T Consensus 72 ~~~er~~~~~~-~-~~aDe~i~~~a~~~~~~iVaTnD~eLk~rlr~~GIPvi~lr~ 125 (136)
T COG1412 72 KYAERLECIHK-G-RYADECLLEAALKHGRYIVATNDKELKRRLRENGIPVITLRQ 125 (136)
T ss_pred HHhhccCcccc-C-CChHHHHHHHHHHcCCEEEEeCCHHHHHHHHHcCCCEEEEeC
Confidence 34556666554 2 245778999999999 77789999997664444555666653
No 204
>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=39.31 E-value=21 Score=42.04 Aligned_cols=10 Identities=60% Similarity=1.428 Sum_probs=8.5
Q ss_pred CcccCCCCcC
Q 009948 451 SRCTKCNGRF 460 (522)
Q Consensus 451 sRC~~CN~~l 460 (522)
.||++||...
T Consensus 1013 fRC~kC~~kY 1022 (1095)
T TIGR00354 1013 VRCTKCNTKY 1022 (1095)
T ss_pred eeecccCCcc
Confidence 5899999965
No 205
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=38.96 E-value=26 Score=33.25 Aligned_cols=34 Identities=29% Similarity=0.737 Sum_probs=23.8
Q ss_pred ccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCee
Q 009948 445 SEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 445 ~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 500 (522)
..+..|-.|+.|+..+ +-++|.+ .-+.||.||-.
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 3345678899999864 4566642 25679999974
No 206
>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=38.92 E-value=17 Score=27.37 Aligned_cols=13 Identities=15% Similarity=0.674 Sum_probs=7.0
Q ss_pred CceeecCCCCeeE
Q 009948 489 LQFWQCMDCNQLY 501 (522)
Q Consensus 489 ~~F~~C~~Cgkvy 501 (522)
...|+|+.|+++|
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 207
>PRK08402 replication factor A; Reviewed
Probab=38.78 E-value=15 Score=38.85 Aligned_cols=30 Identities=17% Similarity=0.542 Sum_probs=20.5
Q ss_pred cCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCee
Q 009948 448 QLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 448 ~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 500 (522)
..+.+|+.||-.+.. +....-|+|+.||++
T Consensus 210 ~~y~aCp~CnKkv~~-----------------------~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 210 LVYDACPECRRKVDY-----------------------DPATDTWICPEHGEV 239 (355)
T ss_pred eeEecCCCCCeEEEE-----------------------ecCCCCEeCCCCCCc
Confidence 357899999996420 112357899999963
No 208
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=37.88 E-value=34 Score=31.27 Aligned_cols=39 Identities=15% Similarity=0.450 Sum_probs=23.8
Q ss_pred ccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCee
Q 009948 445 SEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 445 ~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 500 (522)
..+..+-.|+.|+..+ +..+|... .+ | ..-+.||.||..
T Consensus 94 e~~~~~Y~Cp~C~~~y-----~~~ea~~~---~d--~-------~~~f~Cp~Cg~~ 132 (147)
T smart00531 94 ETNNAYYKCPNCQSKY-----TFLEANQL---LD--M-------DGTFTCPRCGEE 132 (147)
T ss_pred ccCCcEEECcCCCCEe-----eHHHHHHh---cC--C-------CCcEECCCCCCE
Confidence 3345578899999864 33455421 01 1 223789999975
No 209
>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=37.71 E-value=42 Score=33.06 Aligned_cols=51 Identities=14% Similarity=0.198 Sum_probs=36.9
Q ss_pred cCcccHHHHHHHHcCCcccc--ccccCCC-CC-C-CCCHHHHHHHHHHHHHHHHHH
Q 009948 159 KETKSLANICKELLDISLSK--ELQCSDW-SN-R-PLTEEQKNYAAIDAHCLIEIF 209 (522)
Q Consensus 159 ~~~~gL~~L~~~~Lg~~L~K--~~q~sdW-~~-R-PL~~~qi~YAA~DA~~ll~L~ 209 (522)
..+++|.+++.++||...+. ..+.+.| .. . .-...-+.|...||...++|.
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 35899999999999987543 2344555 22 2 233567899999999999875
No 210
>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=37.43 E-value=23 Score=26.96 Aligned_cols=11 Identities=18% Similarity=0.570 Sum_probs=8.7
Q ss_pred CCCcccCCCCc
Q 009948 449 LMSRCTKCNGR 459 (522)
Q Consensus 449 ~~sRC~~CN~~ 459 (522)
.++.|+.|+..
T Consensus 25 ~l~~C~~cG~~ 35 (55)
T TIGR01031 25 TLVVCPNCGEF 35 (55)
T ss_pred cceECCCCCCc
Confidence 36889999984
No 211
>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=37.41 E-value=30 Score=26.31 Aligned_cols=30 Identities=17% Similarity=0.418 Sum_probs=19.1
Q ss_pred CcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeE
Q 009948 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 501 (522)
..|+.|+..+. + |.... .+--.|+.||--|
T Consensus 3 ~~CP~CG~~ie---v---------------~~~~~---GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIE---L---------------ENPEL---GELVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEe---c---------------CCCcc---CCEEeCCCCCCEE
Confidence 36999999762 2 22211 2355899999765
No 212
>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=37.26 E-value=27 Score=23.24 Aligned_cols=12 Identities=17% Similarity=0.351 Sum_probs=8.1
Q ss_pred ceeecCCCCeeE
Q 009948 490 QFWQCMDCNQLY 501 (522)
Q Consensus 490 ~F~~C~~Cgkvy 501 (522)
.-.+|+.||..+
T Consensus 20 ~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 20 WARRCPSCGHEH 31 (32)
T ss_dssp S-EEESSSS-EE
T ss_pred CEeECCCCcCEe
Confidence 456799999876
No 213
>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=37.24 E-value=54 Score=34.87 Aligned_cols=18 Identities=22% Similarity=0.220 Sum_probs=15.7
Q ss_pred HHHHHHHhcCCceecCCC
Q 009948 367 GLAKHLRCVGIDAATPRS 384 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~ 384 (522)
=++|++|+.|++|.++.+
T Consensus 29 v~~Ry~r~~G~~V~~~~G 46 (382)
T cd00817 29 IIARYKRMKGYNVLWPPG 46 (382)
T ss_pred HHHHHHHhcCCcccccCc
Confidence 468999999999998875
No 214
>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=36.90 E-value=22 Score=34.47 Aligned_cols=38 Identities=16% Similarity=0.126 Sum_probs=26.0
Q ss_pred ccH-HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009948 364 MVE-GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 364 mLg-~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 401 (522)
.+| -|+|+||.+||+|...+..+.-+..+...|.+.++
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 455 78999999999998766432223457777755443
No 215
>PRK05978 hypothetical protein; Provisional
Probab=36.89 E-value=19 Score=33.19 Aligned_cols=8 Identities=38% Similarity=1.140 Sum_probs=5.6
Q ss_pred CcccCCCC
Q 009948 451 SRCTKCNG 458 (522)
Q Consensus 451 sRC~~CN~ 458 (522)
.||+.|+.
T Consensus 34 grCP~CG~ 41 (148)
T PRK05978 34 GRCPACGE 41 (148)
T ss_pred CcCCCCCC
Confidence 56777775
No 216
>PRK14536 cysS cysteinyl-tRNA synthetase; Provisional
Probab=36.79 E-value=25 Score=38.86 Aligned_cols=36 Identities=8% Similarity=0.218 Sum_probs=26.7
Q ss_pred HHHHHHHhcCCceecCCC----------CCCChHHHHHhhhcCCcE
Q 009948 367 GLAKHLRCVGIDAATPRS----------KKPEPRELIDQTSKEKRV 402 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~----------~~~~d~~ll~~A~~E~Ri 402 (522)
=|+||||..||+|.++.+ .+..|..++..|+++|.-
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 579999999999998852 112255788889888743
No 217
>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=36.63 E-value=20 Score=23.89 Aligned_cols=12 Identities=17% Similarity=0.534 Sum_probs=9.4
Q ss_pred CceeecCCCCee
Q 009948 489 LQFWQCMDCNQL 500 (522)
Q Consensus 489 ~~F~~C~~Cgkv 500 (522)
...+.||.|+.-
T Consensus 17 ~~~~vCp~C~~e 28 (30)
T PF08274_consen 17 GELLVCPECGHE 28 (30)
T ss_dssp SSSEEETTTTEE
T ss_pred CCEEeCCccccc
Confidence 467889999853
No 218
>PRK04023 DNA polymerase II large subunit; Validated
Probab=36.49 E-value=25 Score=41.61 Aligned_cols=10 Identities=50% Similarity=1.308 Sum_probs=8.6
Q ss_pred CcccCCCCcC
Q 009948 451 SRCTKCNGRF 460 (522)
Q Consensus 451 sRC~~CN~~l 460 (522)
.||++||...
T Consensus 1038 fRC~kC~~kY 1047 (1121)
T PRK04023 1038 FRCTKCGAKY 1047 (1121)
T ss_pred eeecccCccc
Confidence 5899999965
No 219
>PRK12495 hypothetical protein; Provisional
Probab=36.34 E-value=33 Score=33.64 Aligned_cols=14 Identities=29% Similarity=0.271 Sum_probs=10.9
Q ss_pred eeecCCCCeeEecc
Q 009948 491 FWQCMDCNQLYWEG 504 (522)
Q Consensus 491 F~~C~~CgkvyW~G 504 (522)
-.+|+.|+++|=++
T Consensus 58 ~~~Cp~CQ~~~~~~ 71 (226)
T PRK12495 58 QEFCPTCQQPVTED 71 (226)
T ss_pred eeECCCCCCccccc
Confidence 44699999998664
No 220
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=35.95 E-value=9.1 Score=36.54 Aligned_cols=14 Identities=14% Similarity=0.740 Sum_probs=11.6
Q ss_pred cCCCcccCCCCcCc
Q 009948 448 QLMSRCTKCNGRFI 461 (522)
Q Consensus 448 ~~~sRC~~CN~~l~ 461 (522)
.++++|+.|.++++
T Consensus 147 vv~a~~~~~g~~~~ 160 (189)
T PRK09521 147 VIYAMCSRCRTPLV 160 (189)
T ss_pred EEEEEccccCCceE
Confidence 45799999999874
No 221
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=35.74 E-value=39 Score=29.31 Aligned_cols=13 Identities=23% Similarity=0.817 Sum_probs=10.6
Q ss_pred CceeecCCCCeeE
Q 009948 489 LQFWQCMDCNQLY 501 (522)
Q Consensus 489 ~~F~~C~~Cgkvy 501 (522)
.-||.|..||..+
T Consensus 99 ~l~yvC~~C~h~w 111 (113)
T KOG2691|consen 99 RLFYVCCSCGHRW 111 (113)
T ss_pred EEEEEeccccccc
Confidence 4599999999764
No 222
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=35.68 E-value=14 Score=27.94 Aligned_cols=10 Identities=50% Similarity=1.072 Sum_probs=8.5
Q ss_pred CcccCCCCcC
Q 009948 451 SRCTKCNGRF 460 (522)
Q Consensus 451 sRC~~CN~~l 460 (522)
-||..||..|
T Consensus 5 iRC~~CnKlL 14 (60)
T COG4416 5 IRCAKCNKLL 14 (60)
T ss_pred eehHHHhHHH
Confidence 4899999976
No 223
>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=35.61 E-value=34 Score=30.69 Aligned_cols=33 Identities=18% Similarity=0.070 Sum_probs=22.4
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcC
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKE 399 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E 399 (522)
-++|+||..|+++.++...+.-+..+...|.+.
T Consensus 25 ~~~r~lr~~G~~v~~~~~~dd~~~~~~~~a~~~ 57 (143)
T cd00802 25 FLAQAYRKLGYKVRCIALIDDAGGLIGDPANKK 57 (143)
T ss_pred HHHHHHHHcCCCeEEEeeeCCCchHHHHHHHhc
Confidence 689999999999988765332233455555444
No 224
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=35.59 E-value=21 Score=22.71 Aligned_cols=9 Identities=22% Similarity=0.763 Sum_probs=7.2
Q ss_pred CcccCCCCc
Q 009948 451 SRCTKCNGR 459 (522)
Q Consensus 451 sRC~~CN~~ 459 (522)
..|+.|+..
T Consensus 3 ~~Cp~Cg~~ 11 (26)
T PF13248_consen 3 MFCPNCGAE 11 (26)
T ss_pred CCCcccCCc
Confidence 469999984
No 225
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=35.56 E-value=19 Score=38.77 Aligned_cols=31 Identities=26% Similarity=0.610 Sum_probs=21.6
Q ss_pred CCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeEecc
Q 009948 450 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEG 504 (522)
Q Consensus 450 ~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~G 504 (522)
-.+|+.|++... . +| .. -|+|++||..|=.-
T Consensus 350 ~p~Cp~Cg~~m~--------S----~G-----------~~-g~rC~kCg~~~~~~ 380 (421)
T COG1571 350 NPVCPRCGGRMK--------S----AG-----------RN-GFRCKKCGTRARET 380 (421)
T ss_pred CCCCCccCCchh--------h----cC-----------CC-CcccccccccCCcc
Confidence 468999999752 1 12 12 78999999887443
No 226
>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=35.44 E-value=24 Score=21.98 Aligned_cols=16 Identities=13% Similarity=0.573 Sum_probs=12.5
Q ss_pred eecCCCCeeEeccchh
Q 009948 492 WQCMDCNQLYWEGTQY 507 (522)
Q Consensus 492 ~~C~~CgkvyW~GsH~ 507 (522)
+.|..|++.|-..+-|
T Consensus 2 ~~C~~C~~~F~~~~~l 17 (27)
T PF13912_consen 2 FECDECGKTFSSLSAL 17 (27)
T ss_dssp EEETTTTEEESSHHHH
T ss_pred CCCCccCCccCChhHH
Confidence 5799999999765443
No 227
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.43 E-value=1.5e+02 Score=36.64 Aligned_cols=102 Identities=14% Similarity=0.142 Sum_probs=60.0
Q ss_pred CCCceEEEEechh-hHHHHHhhcccCCCccCccC-------------------CCceeeHHHHHHHhhccccCCCCCcCc
Q 009948 102 SPDILKLGFKFKQ-DLIYLSSTFCSQGCDIGFDR-------------------VEPYLDITSIYNHLHHKQLGRKLPKET 161 (522)
Q Consensus 102 ~~~i~KVgh~~k~-Dl~~L~~~~gi~g~~~~~~~-------------------~~~~~Dlt~La~yLl~~~~~~~~~~~~ 161 (522)
||++ .+|||..+ |+..|.+....+++. .|.. -.-++|+-.++...+.. .+
T Consensus 599 DPDi-i~g~n~~qfdlkvl~nR~~~l~i~-~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~~~~k~~~~~--------~s 668 (1172)
T TIGR00592 599 DPDE-IVGHDYQQRALKVLANRINDLKIP-TWSKIGRLRRSPKFGRRFGERTCGRMICDVEISAKELIRC--------KS 668 (1172)
T ss_pred CCCE-EEEEcccCccHHHHHHHHHHcCCC-cccccCccccCCCccccccceECCEEEEEHHHHHHHHhCc--------CC
Confidence 7875 47999875 777764422112211 1110 02367866666555432 57
Q ss_pred ccHHHHHHHHcCCcccc--ccccC-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009948 162 KSLANICKELLDISLSK--ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 162 ~gL~~L~~~~Lg~~L~K--~~q~s-dW~~RPL~~~qi~YAA~DA~~ll~L~~~L~ 213 (522)
++|..+++++||..-.. ..... -|....--..-+.|...||..+++|...|.
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 01111 243222224568999999999999887654
No 228
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=35.28 E-value=35 Score=38.97 Aligned_cols=35 Identities=17% Similarity=0.191 Sum_probs=26.3
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 401 (522)
=++|+||+.|+||.++.+.+.-+..+...|+++|.
T Consensus 32 v~~R~~r~~G~~v~~~~g~D~~g~~i~~~A~~~g~ 66 (648)
T PRK12267 32 ALARYKRLQGYDVFFLTGTDEHGQKIQQAAEKAGK 66 (648)
T ss_pred HHHHHHHhcCCceEeecCCCCcchHHHHHHHHcCC
Confidence 46999999999999987643223467778877773
No 229
>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=35.26 E-value=20 Score=25.39 Aligned_cols=17 Identities=24% Similarity=0.628 Sum_probs=13.7
Q ss_pred CCceeecCCCCeeEecc
Q 009948 488 NLQFWQCMDCNQLYWEG 504 (522)
Q Consensus 488 ~~~F~~C~~CgkvyW~G 504 (522)
+-.-|+|+.||-.|+..
T Consensus 29 ~vp~~~C~~CGE~~~~~ 45 (46)
T TIGR03831 29 NVPALVCPQCGEEYLDA 45 (46)
T ss_pred CCCccccccCCCEeeCC
Confidence 44678899999999864
No 230
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=35.07 E-value=35 Score=34.28 Aligned_cols=52 Identities=17% Similarity=0.507 Sum_probs=31.3
Q ss_pred HHHHHHHHHcccccccCcCCCcccC--CCCc-CccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeEec
Q 009948 431 QQLLEVIEAFQLKISEDQLMSRCTK--CNGR-FIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWE 503 (522)
Q Consensus 431 eQl~~v~~~f~l~~~~~~~~sRC~~--CN~~-l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~ 503 (522)
.-|..+.+.|. ...|.+|++ ||+- ++ |+...+ +| .....-..||.|+.||=.
T Consensus 106 ~Gl~~M~eKY~-----~g~FG~CPRv~C~~q~~L--PvGlSd----------~~----g~~~VKlyCP~C~DvY~p 160 (251)
T PTZ00396 106 KGLALMREKYL-----QGKFGHCPRVLCEGQNVL--PIGLSD----------VL----KTSRVKVYCPRCQEVYHP 160 (251)
T ss_pred HHHHHHHHHhh-----CCCCCCCCCccCCCCccc--ccccCC----------Cc----CcCceeEeCCCchhhcCC
Confidence 34666666674 345899997 8873 33 442111 11 223445569999999954
No 231
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=34.83 E-value=18 Score=39.78 Aligned_cols=40 Identities=13% Similarity=0.333 Sum_probs=25.3
Q ss_pred CcccCCCCcCccCCCChHHHHHhhcccccCCccc-cccCCceeecCCCCe
Q 009948 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCL-FDKNLQFWQCMDCNQ 499 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v-~~~~~~F~~C~~Cgk 499 (522)
-+|..|+-.--+..-+. ...|||.+ |+...+=|.||.||-
T Consensus 426 ~~c~~c~~~yd~~~g~~---------~~~~~~gt~~~~lp~~~~cp~c~~ 466 (479)
T PRK05452 426 MQCSVCQWIYDPAKGEP---------MQDVAPGTPWSEVPDNFLCPECSL 466 (479)
T ss_pred EEECCCCeEECCCCCCc---------ccCCCCCCChhhCCCCCcCcCCCC
Confidence 47999997543211111 12477775 556667799999984
No 232
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=34.47 E-value=21 Score=36.30 Aligned_cols=12 Identities=17% Similarity=0.501 Sum_probs=9.8
Q ss_pred CCceeecCCCCe
Q 009948 488 NLQFWQCMDCNQ 499 (522)
Q Consensus 488 ~~~F~~C~~Cgk 499 (522)
.+.+|+||.|.+
T Consensus 262 gR~t~~CP~CQ~ 273 (273)
T COG0266 262 GRSTFYCPVCQK 273 (273)
T ss_pred CCcCEeCCCCCC
Confidence 467889999975
No 233
>PRK03954 ribonuclease P protein component 4; Validated
Probab=34.22 E-value=34 Score=30.47 Aligned_cols=59 Identities=14% Similarity=0.366 Sum_probs=36.6
Q ss_pred HHHHHHHHHcccccccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeE
Q 009948 431 QQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 431 eQl~~v~~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 501 (522)
..+..|-....+.+.++---+-|-.||..|++. ++ ..+ ++-..- ...-...|..||.+.
T Consensus 45 ~lar~Is~K~rirlp~~~KR~~CK~C~t~LiPG-~n-~~v--------Ri~~~~--~~~vvitCl~CG~~k 103 (121)
T PRK03954 45 ELALAVQQKAKVKLPRKWKRRYCKRCHSFLVPG-VN-ARV--------RLRQKR--MPHVVITCLECGHIM 103 (121)
T ss_pred HHHHHHHHHhccCCCHHHHHHHhhcCCCeeecC-Cc-eEE--------EEecCC--cceEEEECccCCCEE
Confidence 456777778888877766567799999999742 11 000 111110 012477899999874
No 234
>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=33.93 E-value=22 Score=32.69 Aligned_cols=12 Identities=17% Similarity=0.440 Sum_probs=9.2
Q ss_pred CCcccCCCCcCc
Q 009948 450 MSRCTKCNGRFI 461 (522)
Q Consensus 450 ~sRC~~CN~~l~ 461 (522)
.-+|..|+....
T Consensus 112 ~l~C~~Cg~~~~ 123 (146)
T PF07295_consen 112 TLVCENCGHEVE 123 (146)
T ss_pred eEecccCCCEEE
Confidence 458999999653
No 235
>PRK12496 hypothetical protein; Provisional
Probab=33.63 E-value=18 Score=33.87 Aligned_cols=11 Identities=27% Similarity=0.652 Sum_probs=9.8
Q ss_pred eeecCCCCeeE
Q 009948 491 FWQCMDCNQLY 501 (522)
Q Consensus 491 F~~C~~Cgkvy 501 (522)
-++|++||+.|
T Consensus 127 ~~~C~gC~~~~ 137 (164)
T PRK12496 127 RKVCKGCKKKY 137 (164)
T ss_pred eEECCCCCccc
Confidence 37899999999
No 236
>PRK11032 hypothetical protein; Provisional
Probab=33.06 E-value=23 Score=33.16 Aligned_cols=10 Identities=30% Similarity=0.813 Sum_probs=8.2
Q ss_pred CcccCCCCcC
Q 009948 451 SRCTKCNGRF 460 (522)
Q Consensus 451 sRC~~CN~~l 460 (522)
-+|..|+..+
T Consensus 125 LvC~~Cg~~~ 134 (160)
T PRK11032 125 LVCEKCHHHL 134 (160)
T ss_pred EEecCCCCEE
Confidence 5799999865
No 237
>PRK14873 primosome assembly protein PriA; Provisional
Probab=33.04 E-value=25 Score=40.41 Aligned_cols=27 Identities=11% Similarity=0.261 Sum_probs=19.0
Q ss_pred ceeecCCCCeeEec--cchhhHHHHHHHH
Q 009948 490 QFWQCMDCNQLYWE--GTQYHNAVQKFID 516 (522)
Q Consensus 490 ~F~~C~~CgkvyW~--GsH~~~~~~~~~~ 516 (522)
..|.||.||.-.+. |.--+++.+.+.+
T Consensus 421 ~p~~Cp~Cgs~~l~~~g~Gter~eeeL~~ 449 (665)
T PRK14873 421 PDWRCPRCGSDRLRAVVVGARRTAEELGR 449 (665)
T ss_pred cCccCCCCcCCcceeeeccHHHHHHHHHH
Confidence 47899999987766 5555666665544
No 238
>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=32.95 E-value=36 Score=30.43 Aligned_cols=45 Identities=20% Similarity=0.533 Sum_probs=29.3
Q ss_pred HHHHHHHHHHcccccccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCee
Q 009948 430 NQQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 430 ~eQl~~v~~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 500 (522)
.+++..+++.|= .-|-.|+.|+.+-.. + +.+....|-.|..||-.
T Consensus 79 ~~~i~~~L~~fI------~~yVlC~~C~spdT~--l------------------~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 79 SKQIQDLLDKFI------KEYVLCPECGSPDTE--L------------------IKEGRLIFLKCKACGAS 123 (125)
T ss_dssp CCHHHHHHHHHH------CHHSSCTSTSSSSEE--E------------------EEETTCCEEEETTTSCE
T ss_pred HHHHHHHHHHHH------HHEEEcCCCCCCccE--E------------------EEcCCEEEEEecccCCc
Confidence 457888888871 125679999996321 1 11233568899999964
No 239
>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=32.66 E-value=25 Score=31.52 Aligned_cols=10 Identities=20% Similarity=0.644 Sum_probs=8.5
Q ss_pred cccCCCCcCc
Q 009948 452 RCTKCNGRFI 461 (522)
Q Consensus 452 RC~~CN~~l~ 461 (522)
-|+.|+.+++
T Consensus 11 ~Cp~cg~kFY 20 (129)
T TIGR02300 11 ICPNTGSKFY 20 (129)
T ss_pred cCCCcCcccc
Confidence 4999999875
No 240
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=32.48 E-value=23 Score=22.32 Aligned_cols=11 Identities=18% Similarity=0.465 Sum_probs=9.2
Q ss_pred eecCCCCeeEe
Q 009948 492 WQCMDCNQLYW 502 (522)
Q Consensus 492 ~~C~~CgkvyW 502 (522)
-.|+.|||-|=
T Consensus 3 ~~C~~CgR~F~ 13 (25)
T PF13913_consen 3 VPCPICGRKFN 13 (25)
T ss_pred CcCCCCCCEEC
Confidence 46999999993
No 241
>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=32.42 E-value=23 Score=23.09 Aligned_cols=10 Identities=20% Similarity=0.992 Sum_probs=5.5
Q ss_pred cccCCCCcCc
Q 009948 452 RCTKCNGRFI 461 (522)
Q Consensus 452 RC~~CN~~l~ 461 (522)
.|+.||+.++
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 4999999874
No 242
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=32.19 E-value=28 Score=31.38 Aligned_cols=9 Identities=56% Similarity=1.280 Sum_probs=5.3
Q ss_pred cccCCCCcC
Q 009948 452 RCTKCNGRF 460 (522)
Q Consensus 452 RC~~CN~~l 460 (522)
||+.|+..+
T Consensus 3 ~Ct~Cg~~f 11 (131)
T PF09845_consen 3 QCTKCGRVF 11 (131)
T ss_pred ccCcCCCCc
Confidence 566666654
No 243
>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=32.13 E-value=66 Score=27.74 Aligned_cols=32 Identities=22% Similarity=0.378 Sum_probs=25.5
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcC
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKE 399 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E 399 (522)
-++.+||..||+|.++.. ..+.+++++.+.++
T Consensus 18 ~~~~~l~~~G~~V~~lg~-~~~~~~l~~~~~~~ 49 (119)
T cd02067 18 IVARALRDAGFEVIDLGV-DVPPEEIVEAAKEE 49 (119)
T ss_pred HHHHHHHHCCCEEEECCC-CCCHHHHHHHHHHc
Confidence 559999999999998874 45677888887655
No 244
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=32.09 E-value=32 Score=41.80 Aligned_cols=19 Identities=11% Similarity=0.153 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHHHhc
Q 009948 201 DAHCLIEIFNIFQVKVAQK 219 (522)
Q Consensus 201 DA~~ll~L~~~L~~~L~~~ 219 (522)
-|.+++++...+...|++-
T Consensus 843 aa~yl~~va~fiDdLL~k~ 861 (1337)
T PRK14714 843 AAEYLLKVAKFVDDLLEKF 861 (1337)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 3567788888887777764
No 245
>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]
Probab=31.99 E-value=26 Score=33.87 Aligned_cols=25 Identities=20% Similarity=0.550 Sum_probs=20.5
Q ss_pred CCCCeeEeccchhhHHHHHHHHhcc
Q 009948 495 MDCNQLYWEGTQYHNAVQKFIDVCK 519 (522)
Q Consensus 495 ~~CgkvyW~GsH~~~~~~~~~~~~~ 519 (522)
|.+|.|||+|.|-.+..+.+.+-|.
T Consensus 54 p~~G~v~~~~~~i~~~~~~~~~~l~ 78 (209)
T COG4133 54 PDAGEVYWQGEPIQNVRESYHQALL 78 (209)
T ss_pred CCCCeEEecCCCCccchhhHHHHHH
Confidence 6799999999999998886655543
No 246
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=31.95 E-value=54 Score=29.90 Aligned_cols=46 Identities=15% Similarity=0.369 Sum_probs=29.4
Q ss_pred hHHHHHHHHHHcccccccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCee
Q 009948 429 KNQQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 429 ~~eQl~~v~~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 500 (522)
...++..+++.|= ..|-.|+.|+.+-.. + +.+...-|-.|..||-.
T Consensus 87 ~~~~i~~~L~~yI------~~yVlC~~C~spdT~--l------------------~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 87 SPRVINEKIDRYV------KEYVICPECGSPDTK--L------------------IKEGRIWVLKCEACGAE 132 (138)
T ss_pred CHHHHHHHHHHHH------HhcEECCCCCCCCcE--E------------------EEcCCeEEEEcccCCCC
Confidence 3467888888871 225679999996421 1 11122458889999953
No 247
>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=31.94 E-value=64 Score=29.23 Aligned_cols=37 Identities=14% Similarity=0.132 Sum_probs=29.0
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEE
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLL 404 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~RiiL 404 (522)
-++..||..||+++++.- +.+..++++.|++++--+|
T Consensus 20 iv~~~l~~~GfeVi~LG~-~v~~e~~v~aa~~~~adiV 56 (134)
T TIGR01501 20 ILDHAFTNAGFNVVNLGV-LSPQEEFIKAAIETKADAI 56 (134)
T ss_pred HHHHHHHHCCCEEEECCC-CCCHHHHHHHHHHcCCCEE
Confidence 458999999999999874 4566789999988764333
No 248
>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=31.77 E-value=31 Score=24.23 Aligned_cols=13 Identities=23% Similarity=0.884 Sum_probs=11.2
Q ss_pred CceeecCCCCeeE
Q 009948 489 LQFWQCMDCNQLY 501 (522)
Q Consensus 489 ~~F~~C~~Cgkvy 501 (522)
..|+.|..||+.|
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 249
>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=31.36 E-value=95 Score=27.55 Aligned_cols=48 Identities=19% Similarity=0.212 Sum_probs=32.4
Q ss_pred EEEccccHHHHHHHHhcCCceecCCCCCCChH----HHHHhhhcCCcEEEecC
Q 009948 359 FLCDVMVEGLAKHLRCVGIDAATPRSKKPEPR----ELIDQTSKEKRVLLTRD 407 (522)
Q Consensus 359 fl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~----~ll~~A~~E~RiiLTrd 407 (522)
-+.|.+-.-|+.+|+..|+++.+..-. .||. +.++.|.++-.+|||.+
T Consensus 15 ~i~d~n~~~l~~~l~~~G~~v~~~~~v-~Dd~~~i~~~i~~~~~~~DlvittG 66 (133)
T cd00758 15 QIEDTNGPALEALLEDLGCEVIYAGVV-PDDADSIRAALIEASREADLVLTTG 66 (133)
T ss_pred ceEEchHHHHHHHHHHCCCEEEEeeec-CCCHHHHHHHHHHHHhcCCEEEECC
Confidence 456888889999999999998765322 2332 34444555567777775
No 250
>PRK03673 hypothetical protein; Provisional
Probab=31.34 E-value=87 Score=33.64 Aligned_cols=50 Identities=14% Similarity=0.171 Sum_probs=31.9
Q ss_pred EEEEccccHHHHHHHHhcCCceecCCCCCCChHH---HHHhhhcCCcEEEecC
Q 009948 358 KFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRE---LIDQTSKEKRVLLTRD 407 (522)
Q Consensus 358 rfl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~~---ll~~A~~E~RiiLTrd 407 (522)
--+.|.+-.-|+++|+.+|+++........+..+ .++.|..+..++||.+
T Consensus 16 G~i~dtN~~~la~~L~~~G~~v~~~~~v~D~~~~i~~~l~~a~~~~DlVI~tG 68 (396)
T PRK03673 16 GQIVDTNAAWLADFFFHQGLPLSRRNTVGDNLDALVAILRERSQHADVLIVNG 68 (396)
T ss_pred CeEEEhHHHHHHHHHHHCCCEEEEEEEcCCCHHHHHHHHHHHhccCCEEEEcC
Confidence 3677999999999999999998654322222222 3334555545555544
No 251
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=31.20 E-value=39 Score=27.29 Aligned_cols=36 Identities=19% Similarity=0.496 Sum_probs=22.6
Q ss_pred CcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecC--CCCeeE
Q 009948 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCM--DCNQLY 501 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~--~Cgkvy 501 (522)
-+|+.|+..-.. .++.. +-+.+ .+.+++|+ .||..|
T Consensus 2 m~CP~Cg~~a~i--rtSr~----------~s~~~---~~~Y~qC~N~eCg~tF 39 (72)
T PRK09678 2 FHCPLCQHAAHA--RTSRY----------ITDTT---KERYHQCQNVNCSATF 39 (72)
T ss_pred ccCCCCCCccEE--EEChh----------cChhh---heeeeecCCCCCCCEE
Confidence 589999996532 11111 12222 35689999 999887
No 252
>KOG3092 consensus Casein kinase II, beta subunit [Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Transcription]
Probab=30.95 E-value=56 Score=31.45 Aligned_cols=57 Identities=23% Similarity=0.562 Sum_probs=33.0
Q ss_pred HHHHHHHcccccccCcCCCcccC--CCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeEeccc-hhhH
Q 009948 433 LLEVIEAFQLKISEDQLMSRCTK--CNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEGT-QYHN 509 (522)
Q Consensus 433 l~~v~~~f~l~~~~~~~~sRC~~--CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~Gs-H~~~ 509 (522)
|..+++.|. ...|.+|++ ||+.-+. |+. ...+|.. ...--.||+|.-||=.-| ++.+
T Consensus 94 l~~M~eKy~-----~~dFG~CPRV~C~~q~~L-PvG----------LsDipg~----~~VklYCP~C~dvY~P~ssr~~~ 153 (216)
T KOG3092|consen 94 LAAMLEKYK-----NGDFGRCPRVYCCGQPVL-PVG----------LSDIPGK----STVKLYCPSCEDVYIPKSSRHGN 153 (216)
T ss_pred HHHHHHHHh-----cCCCCcCCcccccCCccc-ccc----------ccCCCCc----ceEEEeCCCcccccccccccccc
Confidence 555566664 334899998 6663221 332 2233332 334456999999998866 4443
No 253
>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=30.74 E-value=28 Score=24.76 Aligned_cols=10 Identities=20% Similarity=1.105 Sum_probs=8.3
Q ss_pred eecCCCCeeE
Q 009948 492 WQCMDCNQLY 501 (522)
Q Consensus 492 ~~C~~Cgkvy 501 (522)
|+|+.||..|
T Consensus 6 y~C~~Cg~~f 15 (42)
T PF09723_consen 6 YRCEECGHEF 15 (42)
T ss_pred EEeCCCCCEE
Confidence 6799999776
No 254
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=30.68 E-value=30 Score=29.71 Aligned_cols=10 Identities=40% Similarity=0.966 Sum_probs=4.8
Q ss_pred CCcccCCCCc
Q 009948 450 MSRCTKCNGR 459 (522)
Q Consensus 450 ~sRC~~CN~~ 459 (522)
+|=|+.|++.
T Consensus 20 l~GCp~CG~n 29 (112)
T COG3364 20 LSGCPKCGCN 29 (112)
T ss_pred HccCccccch
Confidence 3445555543
No 255
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=30.65 E-value=62 Score=32.61 Aligned_cols=49 Identities=24% Similarity=0.306 Sum_probs=33.1
Q ss_pred EEEccccHHHHHHHHhcCCceecCCCCCCCh---HHHHHhhhcCCcEEEecC
Q 009948 359 FLCDVMVEGLAKHLRCVGIDAATPRSKKPEP---RELIDQTSKEKRVLLTRD 407 (522)
Q Consensus 359 fl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d---~~ll~~A~~E~RiiLTrd 407 (522)
=++|.+...||+.|...||++....-...+- .+.++.|.+.=.++||.+
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 3789999999999999999996543222121 245666666655555544
No 256
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=30.38 E-value=57 Score=33.07 Aligned_cols=29 Identities=17% Similarity=0.147 Sum_probs=16.1
Q ss_pred HHHHHHHHHHcccccccCc-CC--CcccCCCC
Q 009948 430 NQQLLEVIEAFQLKISEDQ-LM--SRCTKCNG 458 (522)
Q Consensus 430 ~eQl~~v~~~f~l~~~~~~-~~--sRC~~CN~ 458 (522)
.+||....+..++.+...+ -+ ..|+.|+.
T Consensus 286 ~~~l~yka~~~~~~v~~~~~~~tS~~C~~cg~ 317 (364)
T COG0675 286 RRQLEYKAEWGGIVVKVVPPYYTSKTCPCCGH 317 (364)
T ss_pred HHHHHHHHHhCCeEEEECCCCCCcccccccCC
Confidence 5566666666433332222 12 47999998
No 257
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=30.11 E-value=45 Score=28.90 Aligned_cols=53 Identities=11% Similarity=0.382 Sum_probs=32.8
Q ss_pred HHHHHHHcccccccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccc-cccCCceeecCCCCeeE
Q 009948 433 LLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCL-FDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 433 l~~v~~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v-~~~~~~F~~C~~Cgkvy 501 (522)
+..+-....+.+.++---+-|-.|+..|++. . . ..| +.....-+.|..||-++
T Consensus 39 a~~Is~K~rv~lp~~iKR~~CkkC~t~Lvpg-~---n------------~rvR~~~~~v~vtC~~CG~~~ 92 (105)
T COG2023 39 ARRISMKYRVRLPREIKRTICKKCYTPLVPG-K---N------------ARVRLRKGRVVVTCLECGTIR 92 (105)
T ss_pred HHHHHHhhccccCHHHHHHhccccCcccccC-c---c------------eEEEEcCCeEEEEecCCCcEE
Confidence 3444556777766554446699999998631 1 0 111 12233688999999775
No 258
>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=29.83 E-value=74 Score=28.62 Aligned_cols=34 Identities=15% Similarity=0.159 Sum_probs=27.5
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 401 (522)
=++..||..||+++++.- +.+..++++.|.+++-
T Consensus 18 iv~~~L~~~GfeVidLG~-~v~~e~~v~aa~~~~a 51 (128)
T cd02072 18 ILDHAFTEAGFNVVNLGV-LSPQEEFIDAAIETDA 51 (128)
T ss_pred HHHHHHHHCCCEEEECCC-CCCHHHHHHHHHHcCC
Confidence 358899999999999874 4567889999988754
No 259
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=29.63 E-value=37 Score=28.63 Aligned_cols=16 Identities=25% Similarity=0.835 Sum_probs=13.2
Q ss_pred ceeecCCCCeeEeccc
Q 009948 490 QFWQCMDCNQLYWEGT 505 (522)
Q Consensus 490 ~F~~C~~CgkvyW~Gs 505 (522)
--|.|..||+.|=.|.
T Consensus 53 GIW~C~~C~~~~AGGA 68 (90)
T PTZ00255 53 GIWRCKGCKKTVAGGA 68 (90)
T ss_pred EEEEcCCCCCEEeCCc
Confidence 4799999999986653
No 260
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.34 E-value=29 Score=35.19 Aligned_cols=12 Identities=17% Similarity=0.454 Sum_probs=9.8
Q ss_pred CCceeecCCCCe
Q 009948 488 NLQFWQCMDCNQ 499 (522)
Q Consensus 488 ~~~F~~C~~Cgk 499 (522)
....|+||.|.+
T Consensus 261 gR~t~~CP~CQ~ 272 (272)
T PRK14810 261 GRSSHYCPHCQK 272 (272)
T ss_pred CCccEECcCCcC
Confidence 467899999975
No 261
>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=29.28 E-value=36 Score=28.77 Aligned_cols=16 Identities=25% Similarity=0.875 Sum_probs=13.2
Q ss_pred ceeecCCCCeeEeccc
Q 009948 490 QFWQCMDCNQLYWEGT 505 (522)
Q Consensus 490 ~F~~C~~CgkvyW~Gs 505 (522)
-.|.|..||+.|=.|.
T Consensus 52 GIW~C~~C~~~~AGGA 67 (91)
T TIGR00280 52 GIWTCRKCGAKFAGGA 67 (91)
T ss_pred EEEEcCCCCCEEeCCc
Confidence 4799999999986653
No 262
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=28.82 E-value=36 Score=26.14 Aligned_cols=10 Identities=20% Similarity=0.826 Sum_probs=8.4
Q ss_pred CCcccCCCCc
Q 009948 450 MSRCTKCNGR 459 (522)
Q Consensus 450 ~sRC~~CN~~ 459 (522)
++.|+.|+..
T Consensus 27 l~~C~~CG~~ 36 (57)
T PRK12286 27 LVECPNCGEP 36 (57)
T ss_pred ceECCCCCCc
Confidence 5789999984
No 263
>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=28.73 E-value=29 Score=27.29 Aligned_cols=14 Identities=21% Similarity=0.422 Sum_probs=11.4
Q ss_pred CCceeecCCCCeeE
Q 009948 488 NLQFWQCMDCNQLY 501 (522)
Q Consensus 488 ~~~F~~C~~Cgkvy 501 (522)
.+.--.|+.||+.|
T Consensus 50 ~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 50 VEGELICPECGREY 63 (68)
T ss_dssp TTTEEEETTTTEEE
T ss_pred cCCEEEcCCCCCEE
Confidence 34567899999999
No 264
>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=28.72 E-value=33 Score=29.37 Aligned_cols=14 Identities=14% Similarity=0.570 Sum_probs=11.8
Q ss_pred CCceeecCCCCeeE
Q 009948 488 NLQFWQCMDCNQLY 501 (522)
Q Consensus 488 ~~~F~~C~~Cgkvy 501 (522)
.....+|+.||++|
T Consensus 76 ~g~~~rC~eCG~~f 89 (97)
T cd00924 76 KGKPKRCPECGHVF 89 (97)
T ss_pred CCCceeCCCCCcEE
Confidence 34688999999998
No 265
>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=28.59 E-value=40 Score=23.37 Aligned_cols=12 Identities=25% Similarity=0.670 Sum_probs=9.8
Q ss_pred CceeecCCCCee
Q 009948 489 LQFWQCMDCNQL 500 (522)
Q Consensus 489 ~~F~~C~~Cgkv 500 (522)
+-|+.|..||-+
T Consensus 23 dG~~yC~~cG~~ 34 (36)
T PF11781_consen 23 DGFYYCDRCGHQ 34 (36)
T ss_pred CCEEEhhhCceE
Confidence 459999999964
No 266
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=28.51 E-value=60 Score=28.38 Aligned_cols=44 Identities=18% Similarity=0.518 Sum_probs=28.2
Q ss_pred HHHHHHHHHHcccccccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCe
Q 009948 430 NQQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 499 (522)
Q Consensus 430 ~eQl~~v~~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 499 (522)
..++..+++.|= +.|-.|+.|+.+-.. + +.+...-|-.|..||.
T Consensus 66 ~~~i~~~l~~yI------~~yVlC~~C~spdT~--l------------------~k~~r~~~l~C~aCGa 109 (110)
T smart00653 66 PKKLQDLLRRYI------KEYVLCPECGSPDTE--L------------------IKENRLFFLKCEACGA 109 (110)
T ss_pred HHHHHHHHHHHH------HhcEECCCCCCCCcE--E------------------EEeCCeEEEEccccCC
Confidence 567888888771 225679999996421 1 1112345788999994
No 267
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=28.47 E-value=1.2e+02 Score=21.76 Aligned_cols=11 Identities=18% Similarity=0.676 Sum_probs=9.3
Q ss_pred CceeecCCCCe
Q 009948 489 LQFWQCMDCNQ 499 (522)
Q Consensus 489 ~~F~~C~~Cgk 499 (522)
...|+|..|++
T Consensus 35 ~~~~~C~~C~~ 45 (46)
T PF12760_consen 35 RGRYRCKACRK 45 (46)
T ss_pred CCeEECCCCCC
Confidence 56899999986
No 268
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=28.47 E-value=35 Score=28.77 Aligned_cols=16 Identities=38% Similarity=0.777 Sum_probs=11.8
Q ss_pred CcCCCcccCCCCcCcc
Q 009948 447 DQLMSRCTKCNGRFIQ 462 (522)
Q Consensus 447 ~~~~sRC~~CN~~l~~ 462 (522)
...-|||++|-+..++
T Consensus 73 ik~pSRCP~CKSE~Ie 88 (97)
T COG3357 73 IKKPSRCPKCKSEWIE 88 (97)
T ss_pred cCCcccCCcchhhccc
Confidence 3445999999997653
No 269
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=28.26 E-value=49 Score=38.50 Aligned_cols=29 Identities=17% Similarity=0.350 Sum_probs=18.7
Q ss_pred HHHHHHHHHH---ccccc-ccCcCCCcccCCCC
Q 009948 430 NQQLLEVIEA---FQLKI-SEDQLMSRCTKCNG 458 (522)
Q Consensus 430 ~eQl~~v~~~---f~l~~-~~~~~~sRC~~CN~ 458 (522)
.+.+.+|++. .++.. +.+..+++|..|+-
T Consensus 656 ~eal~~lvk~~~~~~i~Y~sin~~~~~C~~CG~ 688 (735)
T PRK07111 656 VEAFEIIVKAMKNTNIGYGSINHPVDRCPVCGY 688 (735)
T ss_pred HHHHHHHHHHHHhCCCceEEeCCCCeecCCCCC
Confidence 3556666664 23332 45667999999995
No 270
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=28.06 E-value=45 Score=33.50 Aligned_cols=32 Identities=19% Similarity=0.387 Sum_probs=21.7
Q ss_pred CCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeEecc
Q 009948 450 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEG 504 (522)
Q Consensus 450 ~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~G 504 (522)
+.-|+.|+.++... ....-..|+.||.++|.-
T Consensus 99 ~~fC~~CG~~~~~~-----------------------~~~~~~~C~~c~~~~yp~ 130 (256)
T PRK00241 99 HRFCGYCGHPMHPS-----------------------KTEWAMLCPHCRERYYPR 130 (256)
T ss_pred CccccccCCCCeec-----------------------CCceeEECCCCCCEECCC
Confidence 45699999986420 012235699999999864
No 271
>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=27.78 E-value=33 Score=25.25 Aligned_cols=10 Identities=20% Similarity=1.072 Sum_probs=8.0
Q ss_pred eecCCCCeeE
Q 009948 492 WQCMDCNQLY 501 (522)
Q Consensus 492 ~~C~~Cgkvy 501 (522)
|+|+.||+.|
T Consensus 6 y~C~~Cg~~f 15 (52)
T TIGR02605 6 YRCTACGHRF 15 (52)
T ss_pred EEeCCCCCEe
Confidence 5799999865
No 272
>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=27.73 E-value=60 Score=31.07 Aligned_cols=52 Identities=23% Similarity=0.616 Sum_probs=26.7
Q ss_pred HHHHHHHHHcccccccCcCCCcccC--CCC-cCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeEec
Q 009948 431 QQLLEVIEAFQLKISEDQLMSRCTK--CNG-RFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWE 503 (522)
Q Consensus 431 eQl~~v~~~f~l~~~~~~~~sRC~~--CN~-~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~ 503 (522)
+-|..+.+.|. ...|.+|++ ||+ .++ |+.. ...| .....-..||.|+.||=.
T Consensus 85 ~Gl~~m~eKy~-----~g~FG~CPRv~C~~~~lL--PiGl----------sd~~----g~~~vKlyCP~C~dvY~p 139 (184)
T PF01214_consen 85 RGLEQMKEKYE-----QGDFGRCPRVYCNGQPLL--PIGL----------SDTP----GESTVKLYCPRCKDVYHP 139 (184)
T ss_dssp HHHHHHHHHHH-----TTTT-B-SBGGGTT-B-E--EEBS-----------SST----TS-BBEEEETTTTEEE--
T ss_pred HHHHHHHHhhc-----CCcCCcCCcccCCCCcee--CccC----------CCCC----CccceeEECCCCccccCC
Confidence 45666777774 344889976 776 343 3321 1111 223445569999999976
No 273
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=27.67 E-value=36 Score=29.48 Aligned_cols=16 Identities=13% Similarity=0.401 Sum_probs=10.5
Q ss_pred ccccCCceeecCCCCee
Q 009948 484 LFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 484 v~~~~~~F~~C~~Cgkv 500 (522)
+|+... .+.||.|+.-
T Consensus 14 tYed~~-~~~cpec~~e 29 (112)
T COG2824 14 TYEDGG-QLICPECAHE 29 (112)
T ss_pred EEecCc-eEeCchhccc
Confidence 444333 7789999865
No 274
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=27.50 E-value=63 Score=25.07 Aligned_cols=11 Identities=27% Similarity=0.764 Sum_probs=8.6
Q ss_pred CcccCCCCcCc
Q 009948 451 SRCTKCNGRFI 461 (522)
Q Consensus 451 sRC~~CN~~l~ 461 (522)
..|+.||..+.
T Consensus 8 ~~CtSCg~~i~ 18 (59)
T PRK14890 8 PKCTSCGIEIA 18 (59)
T ss_pred ccccCCCCccc
Confidence 35999999763
No 275
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=27.41 E-value=31 Score=34.90 Aligned_cols=14 Identities=21% Similarity=0.377 Sum_probs=11.0
Q ss_pred CCceeecCCCCeeE
Q 009948 488 NLQFWQCMDCNQLY 501 (522)
Q Consensus 488 ~~~F~~C~~Cgkvy 501 (522)
...-|+||.|.+.+
T Consensus 252 gR~ty~Cp~CQ~~~ 265 (269)
T PRK14811 252 GRGTHFCPQCQPLR 265 (269)
T ss_pred CCCcEECCCCcCCC
Confidence 36788999998754
No 276
>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=27.32 E-value=30 Score=29.28 Aligned_cols=47 Identities=19% Similarity=0.516 Sum_probs=21.6
Q ss_pred HHHHHHHc-ccccccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCe
Q 009948 433 LLEVIEAF-QLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 499 (522)
Q Consensus 433 l~~v~~~f-~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 499 (522)
|.+|++++ ++.-.......+||.|+..- |.-.+......|.|=+||+
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 45566554 23323334457788888631 2222334456999999996
No 277
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.26 E-value=38 Score=31.33 Aligned_cols=33 Identities=30% Similarity=0.636 Sum_probs=22.8
Q ss_pred CcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCe
Q 009948 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 499 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 499 (522)
-+|-+||.+-. +. +.+..|.....|-+|++|.-
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 46999999642 12 33344566778999999973
No 278
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=27.15 E-value=68 Score=36.58 Aligned_cols=71 Identities=10% Similarity=0.118 Sum_probs=39.5
Q ss_pred CceEEEEcc--CChHHHHHHHHHH---cccc-cccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCce
Q 009948 418 KNQIYRVKS--LLKNQQLLEVIEA---FQLK-ISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQF 491 (522)
Q Consensus 418 ~~~~~~v~~--~~~~eQl~~v~~~---f~l~-~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F 491 (522)
++.+..|.- ....+.+..+++. +++. ...+..+|+|..|+.... .+.
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 344555532 2123556666654 3333 233556899999997310 124
Q ss_pred eecCCCCeeEeccchhhHHHHHHHHh
Q 009948 492 WQCMDCNQLYWEGTQYHNAVQKFIDV 517 (522)
Q Consensus 492 ~~C~~CgkvyW~GsH~~~~~~~~~~~ 517 (522)
+.||.||.-- =.+|.|+..-+..+
T Consensus 581 ~~CP~CGs~~--~ev~~RV~GYl~~v 604 (623)
T PRK08271 581 KRCPICGSEN--IDYYTRVIGYLKRV 604 (623)
T ss_pred cCCcCCCCcc--hhHHHHHhhhhcCc
Confidence 7799998521 24677776655443
No 279
>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=27.12 E-value=92 Score=29.18 Aligned_cols=49 Identities=20% Similarity=0.238 Sum_probs=31.9
Q ss_pred EEEEccccHHHHHHHHhcCCceecCCCCCCChH----HHHHhhhcCCcEEEecC
Q 009948 358 KFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPR----ELIDQTSKEKRVLLTRD 407 (522)
Q Consensus 358 rfl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~----~ll~~A~~E~RiiLTrd 407 (522)
--+.|.+..-|+++|+.+|+++....-. .|+. +.++.+.++-.+|||.+
T Consensus 14 G~i~d~n~~~l~~~L~~~G~~v~~~~~v-~Dd~~~I~~~l~~~~~~~dlVIttG 66 (170)
T cd00885 14 GQIVDTNAAFLAKELAELGIEVYRVTVV-GDDEDRIAEALRRASERADLVITTG 66 (170)
T ss_pred CeEEEhHHHHHHHHHHHCCCEEEEEEEe-CCCHHHHHHHHHHHHhCCCEEEECC
Confidence 3577999999999999999998653221 1222 33444444556777665
No 280
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=26.96 E-value=36 Score=34.72 Aligned_cols=12 Identities=17% Similarity=0.492 Sum_probs=9.6
Q ss_pred CCceeecCCCCe
Q 009948 488 NLQFWQCMDCNQ 499 (522)
Q Consensus 488 ~~~F~~C~~Cgk 499 (522)
...-|+||.|.+
T Consensus 271 gR~t~~CP~CQ~ 282 (282)
T PRK13945 271 GRSTHWCPNCQK 282 (282)
T ss_pred CCccEECCCCcC
Confidence 367889999975
No 281
>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=26.93 E-value=42 Score=32.91 Aligned_cols=28 Identities=18% Similarity=0.628 Sum_probs=19.3
Q ss_pred cCCccccccCCceeecCCCCeeEeccchh
Q 009948 479 RIPDCLFDKNLQFWQCMDCNQLYWEGTQY 507 (522)
Q Consensus 479 ~vp~~v~~~~~~F~~C~~CgkvyW~GsH~ 507 (522)
.|-..|.+....=|+|+-|+|.| +|.||
T Consensus 65 ~v~~~~~e~~~~K~~C~lc~KlF-kg~eF 92 (214)
T PF04959_consen 65 FVQKNTKEEDEDKWRCPLCGKLF-KGPEF 92 (214)
T ss_dssp GEEEEE-SSSSEEEEE-SSS-EE-SSHHH
T ss_pred HHHHHHHHHcCCEECCCCCCccc-CChHH
Confidence 45667777788899999999998 55655
No 282
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=26.83 E-value=39 Score=23.87 Aligned_cols=13 Identities=23% Similarity=0.851 Sum_probs=10.7
Q ss_pred CceeecCCCCeeE
Q 009948 489 LQFWQCMDCNQLY 501 (522)
Q Consensus 489 ~~F~~C~~Cgkvy 501 (522)
..||.|..||..+
T Consensus 26 T~fy~C~~C~~~w 38 (40)
T smart00440 26 TVFYVCTKCGHRW 38 (40)
T ss_pred eEEEEeCCCCCEe
Confidence 5699999999753
No 283
>PRK03670 competence damage-inducible protein A; Provisional
Probab=26.48 E-value=97 Score=31.11 Aligned_cols=24 Identities=17% Similarity=-0.071 Sum_probs=21.0
Q ss_pred EEEccccHHHHHHHHhcCCceecC
Q 009948 359 FLCDVMVEGLAKHLRCVGIDAATP 382 (522)
Q Consensus 359 fl~D~mLg~Lar~LR~lG~D~~~~ 382 (522)
-+.|.+..-|+++|+.+|+++...
T Consensus 16 ~i~dtN~~~la~~L~~~G~~v~~~ 39 (252)
T PRK03670 16 NTVDSNSAFIAQKLTEKGYWVRRI 39 (252)
T ss_pred eEEehhHHHHHHHHHHCCCEEEEE
Confidence 467999999999999999998653
No 284
>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=26.40 E-value=40 Score=24.62 Aligned_cols=35 Identities=17% Similarity=0.611 Sum_probs=21.6
Q ss_pred cccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCC--CCeeE
Q 009948 452 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMD--CNQLY 501 (522)
Q Consensus 452 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~--Cgkvy 501 (522)
+|+.|++....+. ++. +-+.+ -+-+++|.. ||-.|
T Consensus 1 ~CP~Cg~~a~ir~--S~~----------~s~~~---~~~Y~qC~N~~Cg~tf 37 (47)
T PF04606_consen 1 RCPHCGSKARIRT--SRQ----------LSPLT---RELYCQCTNPECGHTF 37 (47)
T ss_pred CcCCCCCeeEEEE--chh----------hCcce---EEEEEEECCCcCCCEE
Confidence 6999999764321 122 11222 246899998 99776
No 285
>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=26.01 E-value=37 Score=35.71 Aligned_cols=58 Identities=24% Similarity=0.507 Sum_probs=19.3
Q ss_pred HHHHHHHHH-HcccccccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCe
Q 009948 430 NQQLLEVIE-AFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 499 (522)
Q Consensus 430 ~eQl~~v~~-~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 499 (522)
.||+.+-+. .+.+.+.- -.|..||..-. .+ .+.-++. .-+-........||.|++||+
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-KP--SDRCKEE-----GHPLKWHDAVKRFFKCKDCGN 293 (344)
T ss_dssp ---------S-S--EEEE----EEETTT--EES-S----HHHHHT-----T--EEEEEEE-EEEE-T-TS-
T ss_pred HHHHHHHHhhCcEEEEEE----EEcCCCCCccc-Cc--chhHHhc-----CCceEEeeeeeeeEECCCCCC
Confidence 445554443 23444321 46999997432 12 2233321 112223455678999999997
No 286
>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=25.93 E-value=3.5e+02 Score=30.26 Aligned_cols=81 Identities=12% Similarity=0.245 Sum_probs=55.6
Q ss_pred CEEEEccccHHHHHHHHhcCCceecCCCC--CCChHHHHHhhh---cCCcEEEecChhHHHh----hhhcCceEEEEccC
Q 009948 357 PKFLCDVMVEGLAKHLRCVGIDAATPRSK--KPEPRELIDQTS---KEKRVLLTRDAKLLRH----QYLIKNQIYRVKSL 427 (522)
Q Consensus 357 ~rfl~D~mLg~Lar~LR~lG~D~~~~~~~--~~~d~~ll~~A~---~E~RiiLTrd~~l~~~----~~~~~~~~~~v~~~ 427 (522)
.-||+-+.=.++++.++.+|.|++..... .++-.++++... .++=|||..++..+.. .......++.|++.
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 36888888889999999999999876653 234456665443 4456888888875211 12224578999998
Q ss_pred ChHHHHHHHH
Q 009948 428 LKNQQLLEVI 437 (522)
Q Consensus 428 ~~~eQl~~v~ 437 (522)
++.+.+..++
T Consensus 395 s~~qgiaAl~ 404 (530)
T TIGR03599 395 TIVQGLAALL 404 (530)
T ss_pred CHHHHHHHHH
Confidence 8777766544
No 287
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.69 E-value=57 Score=37.16 Aligned_cols=30 Identities=20% Similarity=0.359 Sum_probs=19.3
Q ss_pred HHHHHHHHHH---cccc-cccCcCCCcccCCCCc
Q 009948 430 NQQLLEVIEA---FQLK-ISEDQLMSRCTKCNGR 459 (522)
Q Consensus 430 ~eQl~~v~~~---f~l~-~~~~~~~sRC~~CN~~ 459 (522)
.+.+.+|++. .++. ..-...+++|..|+..
T Consensus 544 ~~al~~lv~~~~~~~i~Y~~inp~~~~C~~CG~~ 577 (625)
T PRK08579 544 PEALAKLTKRIMNTKLVYWSYTPAITVCNKCGRS 577 (625)
T ss_pred HHHHHHHHHHHHhcCCceEEeCCCCccCCCCCCc
Confidence 3667777765 2333 2334568999999983
No 288
>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=25.58 E-value=33 Score=21.64 Aligned_cols=11 Identities=18% Similarity=0.821 Sum_probs=9.1
Q ss_pred eecCCCCeeEe
Q 009948 492 WQCMDCNQLYW 502 (522)
Q Consensus 492 ~~C~~CgkvyW 502 (522)
|.|.-|+|.|=
T Consensus 2 ~~C~~C~k~f~ 12 (27)
T PF12171_consen 2 FYCDACDKYFS 12 (27)
T ss_dssp CBBTTTTBBBS
T ss_pred CCcccCCCCcC
Confidence 57999999873
No 289
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=25.47 E-value=77 Score=33.51 Aligned_cols=20 Identities=15% Similarity=0.416 Sum_probs=18.4
Q ss_pred CceeecCCCCeeEeccchhhH
Q 009948 489 LQFWQCMDCNQLYWEGTQYHN 509 (522)
Q Consensus 489 ~~F~~C~~CgkvyW~GsH~~~ 509 (522)
-++-+|..|| .||.|.-|-+
T Consensus 41 ~~v~~C~~Cg-a~~~~~~W~~ 60 (355)
T COG1499 41 VNVEVCRHCG-AYRIRGRWVD 60 (355)
T ss_pred eEEEECCcCC-CccCCCccee
Confidence 4788999999 9999999988
No 290
>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins.
Probab=25.16 E-value=1.2e+02 Score=25.59 Aligned_cols=39 Identities=15% Similarity=0.235 Sum_probs=28.9
Q ss_pred ChHHHHHhhhcCC-cEEEecChhHHHhhh-hcCceEEEEcc
Q 009948 388 EPRELIDQTSKEK-RVLLTRDAKLLRHQY-LIKNQIYRVKS 426 (522)
Q Consensus 388 ~d~~ll~~A~~E~-RiiLTrd~~l~~~~~-~~~~~~~~v~~ 426 (522)
.|+-|+++|.+.+ -++.|.|.+|-++-. .++..+++++.
T Consensus 53 addci~~~~~~~~~~~VaT~D~~Lr~~lr~~~GvPvi~l~~ 93 (101)
T PF04900_consen 53 ADDCILDLAGKNNKYIVATQDKELRRRLRKIPGVPVIYLRR 93 (101)
T ss_pred HHHHHHHHhccCCeEEEEecCHHHHHHHhcCCCCCEEEEEC
Confidence 5678999998777 688899999976644 45656666664
No 291
>PLN02294 cytochrome c oxidase subunit Vb
Probab=25.13 E-value=36 Score=32.07 Aligned_cols=13 Identities=23% Similarity=0.656 Sum_probs=10.9
Q ss_pred CceeecCCCCeeE
Q 009948 489 LQFWQCMDCNQLY 501 (522)
Q Consensus 489 ~~F~~C~~Cgkvy 501 (522)
.+-.+|+.||++|
T Consensus 139 Gkp~RCpeCG~~f 151 (174)
T PLN02294 139 GKSFECPVCTQYF 151 (174)
T ss_pred CCceeCCCCCCEE
Confidence 4567799999998
No 292
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.11 E-value=30 Score=39.64 Aligned_cols=29 Identities=17% Similarity=0.228 Sum_probs=18.5
Q ss_pred HHHHHHHHHHc----ccc-cccCcCCCcccCCCC
Q 009948 430 NQQLLEVIEAF----QLK-ISEDQLMSRCTKCNG 458 (522)
Q Consensus 430 ~eQl~~v~~~f----~l~-~~~~~~~sRC~~CN~ 458 (522)
.+.+..+++.. ++. ..-+..+++|..|+-
T Consensus 601 ~~a~~~lv~~~~~~~~i~Y~~in~~~~~C~~CG~ 634 (656)
T PRK08270 601 AEACKKLVKKALENYRLPYITITPTFSICPKHGY 634 (656)
T ss_pred HHHHHHHHHHHHHhCCCceEEeCCCCcccCCCCC
Confidence 46677776642 233 233556899999997
No 293
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=25.10 E-value=55 Score=29.57 Aligned_cols=10 Identities=30% Similarity=0.943 Sum_probs=8.7
Q ss_pred cccCCCCcCc
Q 009948 452 RCTKCNGRFI 461 (522)
Q Consensus 452 RC~~CN~~l~ 461 (522)
-|++|+.+|.
T Consensus 30 hCp~Cg~PLF 39 (131)
T COG1645 30 HCPKCGTPLF 39 (131)
T ss_pred hCcccCCcce
Confidence 4999999885
No 294
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=24.63 E-value=64 Score=31.04 Aligned_cols=15 Identities=13% Similarity=0.377 Sum_probs=12.0
Q ss_pred CCceeecCCCCeeEe
Q 009948 488 NLQFWQCMDCNQLYW 502 (522)
Q Consensus 488 ~~~F~~C~~CgkvyW 502 (522)
++...+|+.||.||=
T Consensus 27 ~~~lvrC~eCG~V~~ 41 (201)
T COG1326 27 REPLVRCEECGTVHP 41 (201)
T ss_pred CceEEEccCCCcEee
Confidence 346889999999873
No 295
>PRK10445 endonuclease VIII; Provisional
Probab=24.35 E-value=42 Score=33.88 Aligned_cols=28 Identities=21% Similarity=0.742 Sum_probs=18.9
Q ss_pred CcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCe
Q 009948 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 499 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 499 (522)
.-|+.|++.+... . + ....-|.||.|.+
T Consensus 236 ~~Cp~Cg~~I~~~-----~----------~------~gR~t~~CP~CQ~ 263 (263)
T PRK10445 236 EACERCGGIIEKT-----T----------L------SSRPFYWCPGCQK 263 (263)
T ss_pred CCCCCCCCEeEEE-----E----------E------CCCCcEECCCCcC
Confidence 4599999976310 0 1 2367888999975
No 296
>PHA02325 hypothetical protein
Probab=24.27 E-value=37 Score=26.64 Aligned_cols=14 Identities=50% Similarity=1.146 Sum_probs=9.8
Q ss_pred eecCCCC------eeEeccc
Q 009948 492 WQCMDCN------QLYWEGT 505 (522)
Q Consensus 492 ~~C~~Cg------kvyW~Gs 505 (522)
..||.|| +-||.|+
T Consensus 4 k~CPkC~A~WldgqhYWsgT 23 (72)
T PHA02325 4 KICPKCGARWLDGQHYWSGT 23 (72)
T ss_pred cccCccCCEeEcceeeeccC
Confidence 4699996 5566655
No 297
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=24.22 E-value=1.1e+02 Score=26.81 Aligned_cols=32 Identities=22% Similarity=0.422 Sum_probs=25.0
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcC
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKE 399 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E 399 (522)
-++..||..||++.++... .+..++++.|.++
T Consensus 18 ~~~~~l~~~G~~vi~lG~~-vp~e~~~~~a~~~ 49 (122)
T cd02071 18 VIARALRDAGFEVIYTGLR-QTPEEIVEAAIQE 49 (122)
T ss_pred HHHHHHHHCCCEEEECCCC-CCHHHHHHHHHHc
Confidence 4488999999999998753 5567888887654
No 298
>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=24.14 E-value=14 Score=32.43 Aligned_cols=31 Identities=29% Similarity=0.533 Sum_probs=18.4
Q ss_pred HHHHHHHHHHc---------ccccccCcCCCcccCCCCcC
Q 009948 430 NQQLLEVIEAF---------QLKISEDQLMSRCTKCNGRF 460 (522)
Q Consensus 430 ~eQl~~v~~~f---------~l~~~~~~~~sRC~~CN~~l 460 (522)
.++|..-++.+ .|.+......-||..|+..+
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 56777666544 34444455568999999976
No 299
>PHA02540 61 DNA primase; Provisional
Probab=24.11 E-value=70 Score=33.60 Aligned_cols=52 Identities=17% Similarity=0.413 Sum_probs=27.6
Q ss_pred HHHHHHHHc-ccccccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCcc-ccc-cCCceeecCCCCe
Q 009948 432 QLLEVIEAF-QLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDC-LFD-KNLQFWQCMDCNQ 499 (522)
Q Consensus 432 Ql~~v~~~f-~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~-v~~-~~~~F~~C~~Cgk 499 (522)
.+.+++..| .+.-... ...|||.||..- +.+ +=|.. |+. ...-||.|=+||.
T Consensus 9 ~~~~~~~~f~~~~~~~~-~~~~CPf~~ds~------~~~---------~kpsF~V~p~k~~~~yhCFgCGa 63 (337)
T PHA02540 9 RASPHLPKFKQVRRSSF-YNFRCPICGDSQ------KDK---------NKARGWIYEKKDGGVFKCHNCGY 63 (337)
T ss_pred HHHHHHhhhheeccCce-EEecCCCCCCcc------ccC---------cCCcEEEeccCCceEEEecCCCC
Confidence 344555555 2332222 568999999842 011 01222 221 2235999999997
No 300
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=24.09 E-value=43 Score=33.96 Aligned_cols=12 Identities=17% Similarity=0.548 Sum_probs=9.8
Q ss_pred CCceeecCCCCe
Q 009948 488 NLQFWQCMDCNQ 499 (522)
Q Consensus 488 ~~~F~~C~~Cgk 499 (522)
...-|+||.|.+
T Consensus 262 gR~t~~CP~CQ~ 273 (274)
T PRK01103 262 GRSTFFCPRCQK 273 (274)
T ss_pred CCCcEECcCCCC
Confidence 367889999986
No 301
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=24.00 E-value=93 Score=28.55 Aligned_cols=72 Identities=15% Similarity=0.148 Sum_probs=44.0
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCC-cEEEecChhHHHhhhhcCceEEEEccCChHHHHHHHHHHcccccc
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK-RVLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQLLEVIEAFQLKIS 445 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~-RiiLTrd~~l~~~~~~~~~~~~~v~~~~~~eQl~~v~~~f~l~~~ 445 (522)
=+++-||-.||||.+..-.. ...++++.|.+|+ -+|.-+...- .....-.++.+.++..++.-
T Consensus 31 via~~l~d~GfeVi~~g~~~-tp~e~v~aA~~~dv~vIgvSsl~g--------------~h~~l~~~lve~lre~G~~~- 94 (143)
T COG2185 31 VIARALADAGFEVINLGLFQ-TPEEAVRAAVEEDVDVIGVSSLDG--------------GHLTLVPGLVEALREAGVED- 94 (143)
T ss_pred HHHHHHHhCCceEEecCCcC-CHHHHHHHHHhcCCCEEEEEeccc--------------hHHHHHHHHHHHHHHhCCcc-
Confidence 46999999999999987643 4578999886664 3333222110 01112456777777777552
Q ss_pred cCcCCCcccCCCCcC
Q 009948 446 EDQLMSRCTKCNGRF 460 (522)
Q Consensus 446 ~~~~~sRC~~CN~~l 460 (522)
+ ...+++.+
T Consensus 95 ---i---~v~~GGvi 103 (143)
T COG2185 95 ---I---LVVVGGVI 103 (143)
T ss_pred ---e---EEeecCcc
Confidence 1 26777754
No 302
>PF13277 YmdB: YmdB-like protein; PDB: 2CV9_B 2Z06_C.
Probab=23.95 E-value=76 Score=31.93 Aligned_cols=39 Identities=28% Similarity=0.347 Sum_probs=29.6
Q ss_pred HHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEE
Q 009948 366 EGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLL 404 (522)
Q Consensus 366 g~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~RiiL 404 (522)
.+.++.|..+|+|+++..+.-.+.+++++.-.++.|||=
T Consensus 46 ~~~~~~L~~~GvDviT~GNH~wdkkei~~~i~~~~~ilR 84 (253)
T PF13277_consen 46 PKIAEELFKAGVDVITMGNHIWDKKEIFDFIDKEPRILR 84 (253)
T ss_dssp HHHHHHHHHHT-SEEE--TTTTSSTTHHHHHHH-SSEE-
T ss_pred HHHHHHHHhcCCCEEecCcccccCcHHHHHHhcCCCcEE
Confidence 488999999999999988866777889998888889773
No 303
>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.
Probab=23.88 E-value=1e+02 Score=29.57 Aligned_cols=33 Identities=18% Similarity=0.301 Sum_probs=26.3
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCC
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 400 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~ 400 (522)
=++..||..||+|+++.. +.+..++++.+.+++
T Consensus 101 ~v~~~l~~~G~~vi~lG~-~~p~~~l~~~~~~~~ 133 (201)
T cd02070 101 LVATMLEANGFEVIDLGR-DVPPEEFVEAVKEHK 133 (201)
T ss_pred HHHHHHHHCCCEEEECCC-CCCHHHHHHHHHHcC
Confidence 448999999999998874 456788998887654
No 304
>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=23.75 E-value=28 Score=27.74 Aligned_cols=24 Identities=25% Similarity=0.474 Sum_probs=20.6
Q ss_pred ccCCccccccCCceeecCCCCeeE
Q 009948 478 QRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 478 ~~vp~~v~~~~~~F~~C~~Cgkvy 501 (522)
.+.|..+|+.......||.|.-+|
T Consensus 38 ~~~~N~fwn~~~~~~iCp~C~~iy 61 (69)
T PF09706_consen 38 GRKPNFFWNFNNDADICPICELIY 61 (69)
T ss_pred CCcccccccCcCCCccCHHHHHHH
Confidence 478888999999999999997665
No 305
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=23.66 E-value=1.1e+02 Score=25.33 Aligned_cols=42 Identities=12% Similarity=0.215 Sum_probs=31.3
Q ss_pred EEEEccccHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecC
Q 009948 358 KFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRD 407 (522)
Q Consensus 358 rfl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~RiiLTrd 407 (522)
|+=+...|..+..+|+..||+++.+.+. + -++.=+.|++|-.
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 6677888999999999999999987642 1 1223367888864
No 306
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=23.44 E-value=98 Score=28.01 Aligned_cols=26 Identities=27% Similarity=0.358 Sum_probs=17.8
Q ss_pred hHHHHHHHHHHcccccccCcCCCcccCCCCcC
Q 009948 429 KNQQLLEVIEAFQLKISEDQLMSRCTKCNGRF 460 (522)
Q Consensus 429 ~~eQl~~v~~~f~l~~~~~~~~sRC~~CN~~l 460 (522)
...++..+++.|= .-|--|+.|+.+-
T Consensus 82 ~~~~i~~~L~~yI------~~yVlC~~C~sPd 107 (133)
T TIGR00311 82 THFLLNERIEDYV------RKYVICRECNRPD 107 (133)
T ss_pred CHHHHHHHHHHHH------hheEECCCCCCCC
Confidence 3467778888771 1245699999964
No 307
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=23.39 E-value=70 Score=34.49 Aligned_cols=52 Identities=21% Similarity=0.531 Sum_probs=31.2
Q ss_pred HHHHHHHc-ccccccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeEeccchh
Q 009948 433 LLEVIEAF-QLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEGTQY 507 (522)
Q Consensus 433 l~~v~~~f-~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~GsH~ 507 (522)
+.+|+..+ .|+-........||-|+..- |.........+|.|-+||. .|+-+
T Consensus 16 i~~vi~~~~~l~~~G~~~~~~CPfh~ek~--------------------pSf~v~~~k~~~~Cf~Cg~---~Gd~i 68 (415)
T TIGR01391 16 IVDVISEYVKLKKKGRNYVGLCPFHHEKT--------------------PSFSVSPEKQFYHCFGCGA---GGDAI 68 (415)
T ss_pred HHHHHHhhCceeecCCceEeeCCCCCCCC--------------------CeEEEEcCCCcEEECCCCC---CCCHH
Confidence 56677765 33433344456788888631 2222233467999999997 45543
No 308
>COG0495 LeuS Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=23.37 E-value=1.3e+02 Score=35.52 Aligned_cols=35 Identities=14% Similarity=0.010 Sum_probs=22.4
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009948 367 GLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 367 ~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~R 401 (522)
=+|||.|+.||+|+++-.-+.----+.+.|.+-+.
T Consensus 62 v~aRykRm~GyNVL~PMGwdafGlPae~~A~~~~~ 96 (814)
T COG0495 62 VIARYKRMQGYNVLHPMGWDAFGLPAENAAIKIGT 96 (814)
T ss_pred HHHHHHHhcCCeecccCcccccCchHHHHHHHhCC
Confidence 57999999999999875432111134555554443
No 309
>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=23.25 E-value=1.1e+02 Score=27.47 Aligned_cols=32 Identities=19% Similarity=0.249 Sum_probs=25.4
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCC
Q 009948 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 400 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~ 400 (522)
++..||..||++++... ..+..++++.|.+++
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 48899999999998764 345678888888765
No 310
>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=23.10 E-value=38 Score=30.77 Aligned_cols=13 Identities=23% Similarity=0.651 Sum_probs=10.8
Q ss_pred CceeecCCCCeeE
Q 009948 489 LQFWQCMDCNQLY 501 (522)
Q Consensus 489 ~~F~~C~~Cgkvy 501 (522)
.+-.+|+.||++|
T Consensus 110 g~~~RCpeCG~~f 122 (136)
T PF01215_consen 110 GKPQRCPECGQVF 122 (136)
T ss_dssp TSEEEETTTEEEE
T ss_pred CCccCCCCCCeEE
Confidence 4467999999988
No 311
>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=22.91 E-value=56 Score=27.80 Aligned_cols=12 Identities=17% Similarity=0.371 Sum_probs=9.4
Q ss_pred eeecCCCCeeEe
Q 009948 491 FWQCMDCNQLYW 502 (522)
Q Consensus 491 F~~C~~CgkvyW 502 (522)
.+.|+.||..+=
T Consensus 16 ~~~C~~C~~~~~ 27 (104)
T TIGR01384 16 VYVCPSCGYEKE 27 (104)
T ss_pred eEECcCCCCccc
Confidence 577999998743
No 312
>PRK05667 dnaG DNA primase; Validated
Probab=22.83 E-value=77 Score=35.81 Aligned_cols=47 Identities=21% Similarity=0.554 Sum_probs=29.4
Q ss_pred HHHHHHHc-ccccccCcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCe
Q 009948 433 LLEVIEAF-QLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 499 (522)
Q Consensus 433 l~~v~~~f-~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 499 (522)
+.+|+..+ .|+-........||-||..- |.........+|.|-+||.
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 55676665 34433445556799998731 2222334567999999997
No 313
>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=22.73 E-value=2.6e+02 Score=24.72 Aligned_cols=63 Identities=17% Similarity=0.235 Sum_probs=38.0
Q ss_pred cHHHHHHHHhcCCceecCCC------CCCChH----HHHHhhhc---CCcEEEecChhHH---HhhhhcCceEEEEccC
Q 009948 365 VEGLAKHLRCVGIDAATPRS------KKPEPR----ELIDQTSK---EKRVLLTRDAKLL---RHQYLIKNQIYRVKSL 427 (522)
Q Consensus 365 Lg~Lar~LR~lG~D~~~~~~------~~~~d~----~ll~~A~~---E~RiiLTrd~~l~---~~~~~~~~~~~~v~~~ 427 (522)
..++..+|+..|+.+..... .+..|- ++++.|.. +.=||+|.|.+|. ++....+.+++.+...
T Consensus 54 ~~~~~~~L~~~g~~~~~~~~~~~~~~~~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~i~~lr~~G~~V~v~~~~ 132 (149)
T cd06167 54 QRGFLDALRRLGFEPIQKPLRTRGSGKKGVDVALAIDALELAYKRRIDTIVLVSGDSDFVPLVERLRELGKRVIVVGFE 132 (149)
T ss_pred HHHHHHHHHHCCcEEEEEcceecCCcccCccHHHHHHHHHHhhhcCCCEEEEEECCccHHHHHHHHHHcCCEEEEEccC
Confidence 56889999999999976652 112232 45666655 2356779999873 2222223455555443
No 314
>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=22.60 E-value=65 Score=21.18 Aligned_cols=15 Identities=20% Similarity=0.572 Sum_probs=11.9
Q ss_pred ecCCCCeeEeccchh
Q 009948 493 QCMDCNQLYWEGTQY 507 (522)
Q Consensus 493 ~C~~CgkvyW~GsH~ 507 (522)
-|-.|++.||..+.-
T Consensus 2 sCiDC~~~F~~~~y~ 16 (28)
T PF08790_consen 2 SCIDCSKDFDGDSYK 16 (28)
T ss_dssp EETTTTEEEEGGGTT
T ss_pred eeecCCCCcCcCCcC
Confidence 599999999876543
No 315
>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=22.41 E-value=26 Score=27.82 Aligned_cols=33 Identities=27% Similarity=0.558 Sum_probs=20.8
Q ss_pred ccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeE
Q 009948 453 CTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 453 C~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 501 (522)
|..||.+-. + .+.+..|.+.-.+-+||+|+..-
T Consensus 7 C~~C~~Rs~-~---------------~~sk~aY~~GvViv~C~gC~~~H 39 (66)
T PF05180_consen 7 CNKCGTRSA-K---------------MFSKQAYHKGVVIVQCPGCKNRH 39 (66)
T ss_dssp ETTTTEEEE-E---------------EEEHHHHHTSEEEEE-TTS--EE
T ss_pred cCCCCCccc-e---------------eeCHHHHhCCeEEEECCCCccee
Confidence 999998642 1 23344566677899999998754
No 316
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=22.37 E-value=53 Score=24.62 Aligned_cols=18 Identities=22% Similarity=1.010 Sum_probs=12.4
Q ss_pred cCCceeecCCCCeeEeccc
Q 009948 487 KNLQFWQCMDCNQLYWEGT 505 (522)
Q Consensus 487 ~~~~F~~C~~CgkvyW~Gs 505 (522)
...-.|+|+.||.- |+-+
T Consensus 24 ~~~v~W~C~~Cgh~-w~~~ 41 (55)
T PF14311_consen 24 NKKVWWKCPKCGHE-WKAS 41 (55)
T ss_pred CCEEEEECCCCCCe-eEcc
Confidence 34568999999874 4433
No 317
>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=22.34 E-value=49 Score=30.60 Aligned_cols=30 Identities=20% Similarity=0.591 Sum_probs=21.0
Q ss_pred cCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeE
Q 009948 448 QLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 448 ~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 501 (522)
..+..|+.||..+.. ....-|+|+.|++.+
T Consensus 32 ~~Y~aC~~C~kkv~~------------------------~~~~~~~C~~C~~~~ 61 (166)
T cd04476 32 WWYPACPGCNKKVVE------------------------EGNGTYRCEKCNKSV 61 (166)
T ss_pred eEEccccccCcccEe------------------------CCCCcEECCCCCCcC
Confidence 345789999996421 011579999999974
No 318
>COG1487 VapC Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=22.00 E-value=1.3e+02 Score=26.54 Aligned_cols=42 Identities=21% Similarity=0.211 Sum_probs=33.3
Q ss_pred cHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecC-hhHHH
Q 009948 365 VEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRD-AKLLR 412 (522)
Q Consensus 365 Lg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~E~RiiLTrd-~~l~~ 412 (522)
-+.+.+-|+..|.- .+..|--+...|...|-.++|+| ++|.+
T Consensus 79 ~~~i~~~l~~~G~~------~~~~D~lIAa~A~~~~~~LvT~d~~df~~ 121 (133)
T COG1487 79 AAEIQARLRKEGIP------IGLNDLLIAATAIAHGLLLVTRDVKDFER 121 (133)
T ss_pred HHHHHHHHHhcCCC------CChHHHHHHHHHHHcCCEEEEcCHHhccc
Confidence 56889999999991 13456778899999999999999 65543
No 319
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=21.85 E-value=35 Score=34.10 Aligned_cols=42 Identities=17% Similarity=0.503 Sum_probs=27.5
Q ss_pred CCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeEeccch
Q 009948 450 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEGTQ 506 (522)
Q Consensus 450 ~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~GsH 506 (522)
|--|-.||..+- +| .||-..+.=....+-|-.||+.||.-+-
T Consensus 3 ~FtCnvCgEsvK-Kp--------------~vekH~srCrn~~fSCIDC~k~F~~~sY 44 (276)
T KOG2186|consen 3 FFTCNVCGESVK-KP--------------QVEKHMSRCRNAYFSCIDCGKTFERVSY 44 (276)
T ss_pred EEehhhhhhhcc-cc--------------chHHHHHhccCCeeEEeecccccccchh
Confidence 445999998652 22 1233333334478889999999998653
No 320
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=21.74 E-value=57 Score=26.98 Aligned_cols=14 Identities=21% Similarity=0.814 Sum_probs=8.4
Q ss_pred CCceeecCCCCeeE
Q 009948 488 NLQFWQCMDCNQLY 501 (522)
Q Consensus 488 ~~~F~~C~~Cgkvy 501 (522)
+...+.||.||+.+
T Consensus 62 NMs~~~Cp~Cg~~~ 75 (81)
T PF10609_consen 62 NMSYFVCPHCGERI 75 (81)
T ss_dssp CT-EEE-TTT--EE
T ss_pred CCCccCCCCCCCee
Confidence 57899999999875
No 321
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=21.74 E-value=1e+02 Score=29.89 Aligned_cols=26 Identities=15% Similarity=0.424 Sum_probs=17.4
Q ss_pred hHHHHHHHHHHcccccccCcCCCcccCCCCcC
Q 009948 429 KNQQLLEVIEAFQLKISEDQLMSRCTKCNGRF 460 (522)
Q Consensus 429 ~~eQl~~v~~~f~l~~~~~~~~sRC~~CN~~l 460 (522)
...++..+++.| + .-|-.|+.|+.+-
T Consensus 83 ~~~~i~~~l~~y---i---~~yV~C~~C~~pd 108 (201)
T PRK12336 83 TEEDIQAAIDAY---V---DEYVICSECGLPD 108 (201)
T ss_pred CHHHHHHHHHHH---H---HheEECCCCCCCC
Confidence 356778888777 1 2255699998853
No 322
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=21.60 E-value=53 Score=23.65 Aligned_cols=11 Identities=18% Similarity=0.658 Sum_probs=8.1
Q ss_pred eeecCCCCeeE
Q 009948 491 FWQCMDCNQLY 501 (522)
Q Consensus 491 F~~C~~Cgkvy 501 (522)
-|+|+.||..+
T Consensus 3 ~y~C~~CG~~~ 13 (46)
T PRK00398 3 EYKCARCGREV 13 (46)
T ss_pred EEECCCCCCEE
Confidence 46788888765
No 323
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=21.48 E-value=66 Score=39.44 Aligned_cols=9 Identities=44% Similarity=1.361 Sum_probs=7.4
Q ss_pred CcccCCCCcC
Q 009948 451 SRCTKCNGRF 460 (522)
Q Consensus 451 sRC~~CN~~l 460 (522)
-|| +||...
T Consensus 1543 ~RC-kC~~ky 1551 (1627)
T PRK14715 1543 FRC-KCGAKY 1551 (1627)
T ss_pred eee-cCCCcc
Confidence 589 999965
No 324
>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=21.35 E-value=1.8e+02 Score=27.13 Aligned_cols=62 Identities=15% Similarity=0.094 Sum_probs=37.9
Q ss_pred HhcCCceecCCCCCCChHHHHHhhhcCCc-----EEEecChhHHHhhhhcCceEEEEccCChHHHHHHH
Q 009948 373 RCVGIDAATPRSKKPEPRELIDQTSKEKR-----VLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQLLEV 436 (522)
Q Consensus 373 R~lG~D~~~~~~~~~~d~~ll~~A~~E~R-----iiLTrd~~l~~~~~~~~~~~~~v~~~~~~eQl~~v 436 (522)
+.-|+.++|.......|..|.+++.+... +++|.|..+...... .++..+.+....+++...
T Consensus 64 ~~~gi~Vvft~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~~~~--~GA~~iss~ef~~~l~~~ 130 (166)
T PF05991_consen 64 EYGGIEVVFTKEGETADDYIERLVRELKNRPRQVTVVTSDREIQRAARG--RGAKRISSEEFLRELKAA 130 (166)
T ss_pred eeCceEEEECCCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHHHHhh--CCCEEEcHHHHHHHHHHH
Confidence 34688888876534456666666655554 778999887554332 246777766544444443
No 325
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=21.31 E-value=52 Score=27.55 Aligned_cols=18 Identities=22% Similarity=0.750 Sum_probs=14.4
Q ss_pred CceeecCCCCeeEeccch
Q 009948 489 LQFWQCMDCNQLYWEGTQ 506 (522)
Q Consensus 489 ~~F~~C~~CgkvyW~GsH 506 (522)
.-.|+|.+||..|=.|.-
T Consensus 51 ~GIW~C~kCg~~fAGgay 68 (89)
T COG1997 51 TGIWKCRKCGAKFAGGAY 68 (89)
T ss_pred cCeEEcCCCCCeeccccc
Confidence 348999999999876654
No 326
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=21.28 E-value=47 Score=29.33 Aligned_cols=31 Identities=23% Similarity=0.403 Sum_probs=18.5
Q ss_pred HHHHHHHHHHc---------ccccccCcCCCcccCCCCcC
Q 009948 430 NQQLLEVIEAF---------QLKISEDQLMSRCTKCNGRF 460 (522)
Q Consensus 430 ~eQl~~v~~~f---------~l~~~~~~~~sRC~~CN~~l 460 (522)
.+||+.-++.+ .+.+.....--+|..|+..+
T Consensus 41 ~~~l~FaFev~~egT~aega~l~Ie~~p~~~~C~~C~~~~ 80 (115)
T COG0375 41 PEALRFAFEVVAEGTIAEGAELHIEEEPAECWCLDCGQEV 80 (115)
T ss_pred HHHHHHHHHHHhccCcccCCEEEEEEeccEEEeccCCCee
Confidence 46776655543 23344444557899998854
No 327
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=21.19 E-value=29 Score=35.14 Aligned_cols=31 Identities=19% Similarity=0.598 Sum_probs=22.2
Q ss_pred CcCCCcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCe
Q 009948 447 DQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 499 (522)
Q Consensus 447 ~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 499 (522)
+.+++-|+.|..-+.. .|. ...+|+||.|+.
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 6778999999997641 121 245899999974
No 328
>COG5041 SKB2 Casein kinase II, beta subunit [Signal transduction mechanisms / Cell division and chromosome partitioning / Transcription]
Probab=21.08 E-value=93 Score=30.23 Aligned_cols=52 Identities=25% Similarity=0.611 Sum_probs=30.1
Q ss_pred HHHHHHHHcccccccCcCCCcccC--CCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeEec
Q 009948 432 QLLEVIEAFQLKISEDQLMSRCTK--CNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWE 503 (522)
Q Consensus 432 Ql~~v~~~f~l~~~~~~~~sRC~~--CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvyW~ 503 (522)
-|..+++.|. ...|.+|++ ||+.-+. |+.- ..+|.. ...--.||.|--+|=+
T Consensus 108 GL~~m~eKy~-----~~efG~CPRv~Cn~~~vL-PvGL----------sDi~g~----~~vkLyCpsC~dlY~p 161 (242)
T COG5041 108 GLQAMLEKYK-----SREFGACPRVYCNGQQVL-PVGL----------SDIPGK----SSVKLYCPSCEDLYLP 161 (242)
T ss_pred HHHHHHHHHh-----hcccCCCCcccccCccee-cccc----------ccCCCC----ceeEEecCchhhhcCc
Confidence 3566666664 345899997 7774331 4321 222221 2334559999999944
No 329
>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=21.03 E-value=27 Score=27.51 Aligned_cols=14 Identities=14% Similarity=0.484 Sum_probs=9.7
Q ss_pred CceeecCCCCeeEe
Q 009948 489 LQFWQCMDCNQLYW 502 (522)
Q Consensus 489 ~~F~~C~~CgkvyW 502 (522)
-.+..|+.||-.=|
T Consensus 34 f~~v~C~~CGYTE~ 47 (64)
T PF09855_consen 34 FTTVSCTNCGYTEF 47 (64)
T ss_pred EEEEECCCCCCEEE
Confidence 34567999996533
No 330
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=21.00 E-value=51 Score=28.94 Aligned_cols=13 Identities=23% Similarity=0.909 Sum_probs=11.3
Q ss_pred CceeecCCCCeeE
Q 009948 489 LQFWQCMDCNQLY 501 (522)
Q Consensus 489 ~~F~~C~~Cgkvy 501 (522)
..||.|+.||..|
T Consensus 98 T~Fy~C~~Cg~~w 110 (113)
T COG1594 98 TRFYKCTRCGYRW 110 (113)
T ss_pred eEEEEecccCCEe
Confidence 5799999999875
No 331
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=20.93 E-value=37 Score=36.36 Aligned_cols=43 Identities=26% Similarity=0.585 Sum_probs=26.8
Q ss_pred CcccCCCCcCccCCCChHHHHHhhcccccCCccccccCCceeecCCCCeeE
Q 009948 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkvy 501 (522)
-||..|..++++.+- +||.+ +|-.--.+.+.+.|+|..||..-
T Consensus 395 PrCs~C~~PI~P~~G-~~etv-------Rvvamdr~fHv~CY~CEDCg~~L 437 (468)
T KOG1701|consen 395 PRCSVCGNPILPRDG-KDETV-------RVVAMDRDFHVNCYKCEDCGLLL 437 (468)
T ss_pred cchhhccCCccCCCC-CcceE-------EEEEccccccccceehhhcCccc
Confidence 689999998764332 22221 22222245678899999998653
No 332
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.81 E-value=81 Score=35.94 Aligned_cols=28 Identities=21% Similarity=0.390 Sum_probs=17.2
Q ss_pred HHHHHHHHH-c--ccc-cccCcCCCcccCCCC
Q 009948 431 QQLLEVIEA-F--QLK-ISEDQLMSRCTKCNG 458 (522)
Q Consensus 431 eQl~~v~~~-f--~l~-~~~~~~~sRC~~CN~ 458 (522)
+.+..|++. + ++. ++-+..+++|..|+-
T Consensus 536 ~Al~~lvk~~~~~~i~Y~sin~~~~~C~~CGy 567 (618)
T PRK14704 536 KALKQIVQAMAEHGVGYGSINHPVDRCKCCSY 567 (618)
T ss_pred HHHHHHHHHHHhcCCceEEeCCCCeecCCCCC
Confidence 455666554 2 233 233556899999996
No 333
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=20.70 E-value=57 Score=25.00 Aligned_cols=15 Identities=27% Similarity=0.986 Sum_probs=12.3
Q ss_pred CcccCCCCcCccCCC
Q 009948 451 SRCTKCNGRFIQKPL 465 (522)
Q Consensus 451 sRC~~CN~~l~~~~~ 465 (522)
.+|+-|+|.|+.+|+
T Consensus 42 ~~CPNCgGelv~RP~ 56 (57)
T PF06906_consen 42 GVCPNCGGELVRRPR 56 (57)
T ss_pred CcCcCCCCccccCCC
Confidence 679999999986654
No 334
>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=20.62 E-value=61 Score=29.86 Aligned_cols=21 Identities=19% Similarity=0.601 Sum_probs=14.3
Q ss_pred ceeecCCCCeeEeccchhhHHHHH
Q 009948 490 QFWQCMDCNQLYWEGTQYHNAVQK 513 (522)
Q Consensus 490 ~F~~C~~CgkvyW~GsH~~~~~~~ 513 (522)
.=..|+.||+-| |-|+++...
T Consensus 27 RRReC~~C~~RF---TTyErve~~ 47 (147)
T TIGR00244 27 RRRECLECHERF---TTFERAELL 47 (147)
T ss_pred ecccCCccCCcc---ceeeecccc
Confidence 346699999988 555555443
No 335
>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=20.52 E-value=56 Score=27.59 Aligned_cols=16 Identities=25% Similarity=0.947 Sum_probs=12.5
Q ss_pred ceeecCCCCeeEeccc
Q 009948 490 QFWQCMDCNQLYWEGT 505 (522)
Q Consensus 490 ~F~~C~~CgkvyW~Gs 505 (522)
-.|.|..||+.|=.|.
T Consensus 52 GIW~C~~C~~~~AGGA 67 (90)
T PF01780_consen 52 GIWKCKKCGKKFAGGA 67 (90)
T ss_dssp TEEEETTTTEEEE-BS
T ss_pred EEeecCCCCCEEeCCC
Confidence 4799999999986654
No 336
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=20.36 E-value=52 Score=32.37 Aligned_cols=16 Identities=19% Similarity=0.750 Sum_probs=12.8
Q ss_pred ccCCceeecCCCCeeE
Q 009948 486 DKNLQFWQCMDCNQLY 501 (522)
Q Consensus 486 ~~~~~F~~C~~Cgkvy 501 (522)
-+..+-.+|+.||++|
T Consensus 176 LrEGkpqRCpECGqVF 191 (268)
T PTZ00043 176 CREGFLYRCGECDQIF 191 (268)
T ss_pred ecCCCCccCCCCCcEE
Confidence 3445678999999998
No 337
>smart00355 ZnF_C2H2 zinc finger.
Probab=20.29 E-value=38 Score=20.00 Aligned_cols=10 Identities=20% Similarity=1.255 Sum_probs=8.5
Q ss_pred eecCCCCeeE
Q 009948 492 WQCMDCNQLY 501 (522)
Q Consensus 492 ~~C~~Cgkvy 501 (522)
+.|+.|++.|
T Consensus 1 ~~C~~C~~~f 10 (26)
T smart00355 1 YRCPECGKVF 10 (26)
T ss_pred CCCCCCcchh
Confidence 4699999887
No 338
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.19 E-value=47 Score=27.06 Aligned_cols=23 Identities=26% Similarity=0.780 Sum_probs=18.2
Q ss_pred HHHHHHHcccccccCcCCCcccCCCCcC
Q 009948 433 LLEVIEAFQLKISEDQLMSRCTKCNGRF 460 (522)
Q Consensus 433 l~~v~~~f~l~~~~~~~~sRC~~CN~~l 460 (522)
.-+|+++|. +++++-|..||+++
T Consensus 21 ~~dvvq~~~-----ddplt~ce~c~a~~ 43 (82)
T COG2331 21 RFDVVQAMT-----DDPLTTCEECGARL 43 (82)
T ss_pred HHHHHHhcc-----cCccccChhhChHH
Confidence 456788885 56689999999976
No 339
>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=20.18 E-value=34 Score=39.81 Aligned_cols=11 Identities=36% Similarity=0.628 Sum_probs=0.0
Q ss_pred HHHHhcCCcee
Q 009948 370 KHLRCVGIDAA 380 (522)
Q Consensus 370 r~LR~lG~D~~ 380 (522)
-++++||+|..
T Consensus 557 ~~~~~Lg~~~~ 567 (900)
T PF03833_consen 557 PLLRSLGLDLN 567 (900)
T ss_dssp -----------
T ss_pred HHHHHhCCCcc
Confidence 46788888864
Done!