Query 009909
Match_columns 522
No_of_seqs 373 out of 1567
Neff 6.9
Searched_HMMs 46136
Date Thu Mar 28 18:46:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009909.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009909hhsearch_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 6.5E-46 1.4E-50 341.0 14.0 146 357-513 1-146 (147)
2 COG1656 Uncharacterized conser 100.0 1.7E-44 3.8E-49 327.4 11.5 148 354-512 4-151 (165)
3 cd06146 mut-7_like_exo DEDDy 3 100.0 1.3E-29 2.9E-34 243.3 19.8 184 11-213 1-192 (193)
4 cd06129 RNaseD_like DEDDy 3'-5 100.0 1.5E-28 3.3E-33 229.1 18.2 158 22-213 2-160 (161)
5 PRK10829 ribonuclease D; Provi 100.0 4.7E-28 1E-32 252.8 20.7 183 10-230 2-187 (373)
6 cd06141 WRN_exo DEDDy 3'-5' ex 99.9 1.1E-26 2.4E-31 218.0 18.9 163 19-213 4-169 (170)
7 cd06148 Egl_like_exo DEDDy 3'- 99.9 4.9E-26 1.1E-30 219.3 17.0 170 25-220 3-181 (197)
8 TIGR01388 rnd ribonuclease D. 99.9 3.2E-25 6.9E-30 232.4 20.1 180 14-231 2-184 (367)
9 COG0349 Rnd Ribonuclease D [Tr 99.9 1.3E-25 2.9E-30 229.1 16.6 179 19-232 4-185 (361)
10 PF01612 DNA_pol_A_exo1: 3'-5' 99.9 8.6E-25 1.9E-29 204.3 18.9 174 11-217 1-176 (176)
11 cd06142 RNaseD_exo DEDDy 3'-5' 99.8 9.4E-19 2E-23 164.4 19.4 164 23-222 3-166 (178)
12 smart00474 35EXOc 3'-5' exonuc 99.8 4.6E-17 1E-21 150.9 19.8 169 12-216 2-171 (172)
13 KOG2207 Predicted 3'-5' exonuc 99.7 2.6E-18 5.7E-23 182.8 9.1 195 5-217 386-586 (617)
14 cd06147 Rrp6p_like_exo DEDDy 3 99.7 7.3E-16 1.6E-20 147.7 20.2 175 8-220 2-176 (192)
15 KOG2206 Exosome 3'-5' exoribon 99.7 5.2E-17 1.1E-21 171.8 9.3 172 11-220 193-364 (687)
16 cd00007 35EXOc 3'-5' exonuclea 99.6 9E-15 1.9E-19 133.0 16.3 149 34-215 2-154 (155)
17 cd09018 DEDDy_polA_RNaseD_like 99.6 8.2E-15 1.8E-19 133.5 15.4 147 34-213 1-149 (150)
18 KOG2207 Predicted 3'-5' exonuc 99.6 2.3E-18 5E-23 183.2 -9.5 369 135-508 154-572 (617)
19 PRK05755 DNA polymerase I; Pro 99.6 8.4E-14 1.8E-18 161.5 20.5 179 8-222 293-475 (880)
20 cd06140 DNA_polA_I_Bacillus_li 99.5 5.4E-13 1.2E-17 125.7 16.4 156 32-221 3-161 (178)
21 cd06139 DNA_polA_I_Ecoli_like_ 99.4 1.6E-11 3.5E-16 116.6 18.2 157 30-218 3-172 (193)
22 PRK14975 bifunctional 3'-5' ex 99.3 2.7E-11 5.8E-16 134.0 13.0 146 10-219 2-147 (553)
23 COG0749 PolA DNA polymerase I 99.2 1.2E-10 2.6E-15 126.8 12.5 171 19-222 9-186 (593)
24 TIGR00593 pola DNA polymerase 99.1 4.3E-09 9.3E-14 121.6 19.7 172 11-221 304-482 (887)
25 KOG4373 Predicted 3'-5' exonuc 99.0 3.5E-09 7.6E-14 106.7 10.5 149 32-209 127-281 (319)
26 cd06128 DNA_polA_exo DEDDy 3'- 98.6 1.6E-06 3.4E-11 79.6 15.7 118 78-213 30-150 (151)
27 COG4634 Uncharacterized protei 98.6 2E-07 4.4E-12 79.6 8.1 73 357-429 1-79 (113)
28 cd06137 DEDDh_RNase DEDDh 3'-5 97.3 0.0033 7.1E-08 58.6 11.6 86 94-209 75-160 (161)
29 PRK06063 DNA polymerase III su 97.0 0.025 5.4E-07 58.6 15.9 102 91-221 83-184 (313)
30 cd06149 ISG20 DEDDh 3'-5' exon 96.9 0.008 1.7E-07 55.9 10.4 89 91-210 66-157 (157)
31 KOG2249 3'-5' exonuclease [Rep 96.8 0.0097 2.1E-07 59.1 10.8 96 92-219 174-269 (280)
32 cd06144 REX4_like DEDDh 3'-5' 96.7 0.01 2.2E-07 54.7 9.1 87 91-210 66-152 (152)
33 PRK07942 DNA polymerase III su 96.6 0.12 2.5E-06 51.3 16.6 89 105-218 94-182 (232)
34 PRK06310 DNA polymerase III su 96.5 0.061 1.3E-06 53.9 14.4 150 29-216 4-174 (250)
35 PRK06807 DNA polymerase III su 96.5 0.065 1.4E-06 55.5 14.9 97 91-217 77-173 (313)
36 PRK06309 DNA polymerase III su 96.5 0.12 2.7E-06 51.1 16.2 98 92-217 69-167 (232)
37 TIGR01405 polC_Gram_pos DNA po 96.4 0.073 1.6E-06 64.2 16.3 102 91-221 259-360 (1213)
38 PRK07740 hypothetical protein; 96.4 0.15 3.2E-06 51.0 16.0 100 91-220 130-230 (244)
39 cd06143 PAN2_exo DEDDh 3'-5' e 96.4 0.0093 2E-07 56.4 6.8 81 95-210 94-174 (174)
40 PRK08517 DNA polymerase III su 96.3 0.2 4.4E-06 50.4 16.7 97 91-217 136-232 (257)
41 PRK05168 ribonuclease T; Provi 96.3 0.25 5.3E-06 48.2 16.9 92 104-221 114-206 (211)
42 cd06145 REX1_like DEDDh 3'-5' 96.3 0.014 3.1E-07 53.7 7.6 86 91-209 64-149 (150)
43 PRK07883 hypothetical protein; 96.3 0.11 2.5E-06 58.0 16.1 156 24-221 7-187 (557)
44 cd06131 DNA_pol_III_epsilon_Ec 96.3 0.15 3.2E-06 47.3 14.5 97 91-212 70-166 (167)
45 smart00479 EXOIII exonuclease 96.1 0.24 5.1E-06 45.5 14.9 98 91-216 69-167 (169)
46 cd06125 DnaQ_like_exo DnaQ-lik 96.1 0.035 7.6E-07 47.2 8.4 82 35-145 1-83 (96)
47 PRK09145 DNA polymerase III su 96.0 0.3 6.6E-06 47.1 15.5 98 91-213 100-198 (202)
48 PRK05711 DNA polymerase III su 96.0 0.25 5.3E-06 49.3 15.0 99 91-214 75-174 (240)
49 cd05780 DNA_polB_Kod1_like_exo 96.0 0.19 4.1E-06 48.3 13.9 160 33-212 4-195 (195)
50 TIGR00573 dnaq exonuclease, DN 95.8 0.2 4.4E-06 48.9 13.6 105 91-219 76-180 (217)
51 PRK09146 DNA polymerase III su 95.8 0.41 9E-06 47.7 15.8 102 92-216 119-227 (239)
52 cd06130 DNA_pol_III_epsilon_li 95.6 0.45 9.6E-06 43.3 14.4 89 91-209 66-154 (156)
53 COG2176 PolC DNA polymerase II 95.6 0.056 1.2E-06 63.4 9.9 151 28-222 417-592 (1444)
54 PRK08074 bifunctional ATP-depe 95.5 0.25 5.5E-06 58.6 15.1 99 91-218 73-171 (928)
55 cd06127 DEDDh DEDDh 3'-5' exon 95.4 0.44 9.4E-06 42.7 13.5 91 91-209 68-158 (159)
56 cd05160 DEDDy_DNA_polB_exo DED 95.4 0.36 7.9E-06 46.1 13.4 110 91-209 65-198 (199)
57 TIGR01407 dinG_rel DnaQ family 95.2 0.56 1.2E-05 55.2 16.7 99 91-218 69-167 (850)
58 TIGR01298 RNaseT ribonuclease 93.9 0.67 1.5E-05 44.8 11.3 93 104-222 105-198 (200)
59 cd05781 DNA_polB_B3_exo DEDDy 93.7 1.7 3.7E-05 41.6 13.4 158 33-212 4-188 (188)
60 TIGR01406 dnaQ_proteo DNA poly 93.5 0.64 1.4E-05 45.8 10.4 99 91-214 71-170 (225)
61 cd06134 RNaseT DEDDh 3'-5' exo 93.3 0.88 1.9E-05 43.5 10.8 84 105-214 103-187 (189)
62 PRK07246 bifunctional ATP-depe 93.0 0.72 1.6E-05 54.0 11.6 100 91-220 75-174 (820)
63 PRK00448 polC DNA polymerase I 92.9 1.7 3.6E-05 53.7 14.7 103 91-222 488-590 (1437)
64 cd05784 DNA_polB_II_exo DEDDy 91.7 5.2 0.00011 38.5 13.8 110 91-210 53-193 (193)
65 PRK05601 DNA polymerase III su 91.6 4.1 8.9E-05 43.1 13.9 109 90-212 113-245 (377)
66 PRK06195 DNA polymerase III su 91.3 1.8 3.8E-05 44.8 10.9 98 91-218 69-166 (309)
67 cd05777 DNA_polB_delta_exo DED 90.9 2.9 6.3E-05 41.2 11.7 54 160-213 167-224 (230)
68 KOG2405 Predicted 3'-5' exonuc 90.6 0.026 5.6E-07 58.7 -3.4 130 51-204 73-215 (458)
69 cd05783 DNA_polB_B1_exo DEDDy 89.9 14 0.00031 35.8 15.1 161 33-210 6-202 (204)
70 cd00814 MetRS_core catalytic c 89.8 0.82 1.8E-05 47.4 6.9 101 368-501 29-131 (319)
71 cd05785 DNA_polB_like2_exo Unc 89.7 5.7 0.00012 38.6 12.3 159 32-209 9-206 (207)
72 PF14803 Nudix_N_2: Nudix N-te 88.6 0.33 7.2E-06 33.4 2.0 31 453-502 3-33 (34)
73 KOG2405 Predicted 3'-5' exonuc 88.6 0.12 2.7E-06 53.8 -0.2 126 77-214 222-359 (458)
74 cd06136 TREX1_2 DEDDh 3'-5' ex 88.4 2.1 4.5E-05 40.5 8.0 89 92-210 84-175 (177)
75 PRK11779 sbcB exonuclease I; P 88.1 9.2 0.0002 42.1 13.7 106 91-215 80-197 (476)
76 PF13719 zinc_ribbon_5: zinc-r 87.1 0.52 1.1E-05 32.9 2.2 33 451-501 3-35 (37)
77 PRK07247 DNA polymerase III su 87.0 3.2 6.9E-05 40.1 8.5 110 91-233 73-186 (195)
78 KOG2248 3'-5' exonuclease [Rep 86.7 0.66 1.4E-05 49.2 3.8 91 91-213 282-372 (380)
79 PF13717 zinc_ribbon_4: zinc-r 85.6 0.68 1.5E-05 32.2 2.2 32 452-501 4-35 (36)
80 PF08792 A2L_zn_ribbon: A2L zi 85.3 0.8 1.7E-05 31.3 2.4 29 450-501 3-31 (33)
81 PF09281 Taq-exonuc: Taq polym 85.1 4.2 9.1E-05 36.5 7.4 55 135-216 84-138 (138)
82 COG4049 Uncharacterized protei 84.7 0.3 6.6E-06 37.1 0.1 18 487-504 13-30 (65)
83 PRK12268 methionyl-tRNA synthe 84.6 1.3 2.9E-05 49.4 5.2 55 343-401 9-66 (556)
84 cd05779 DNA_polB_epsilon_exo D 84.3 17 0.00037 35.3 12.1 110 91-209 75-203 (204)
85 PLN02224 methionine-tRNA ligas 83.8 3.4 7.3E-05 46.9 7.9 34 368-401 98-131 (616)
86 PRK09182 DNA polymerase III su 83.8 29 0.00063 35.7 14.2 87 93-213 111-198 (294)
87 PF13482 RNase_H_2: RNase_H su 83.6 1.3 2.9E-05 40.6 4.0 148 35-212 1-163 (164)
88 PRK00133 metG methionyl-tRNA s 83.4 2.2 4.9E-05 48.9 6.4 33 368-400 31-63 (673)
89 TIGR02098 MJ0042_CXXC MJ0042 f 82.8 1 2.3E-05 31.3 2.2 34 451-502 3-36 (38)
90 KOG3657 Mitochondrial DNA poly 82.7 4.6 0.0001 46.4 8.3 109 103-219 240-386 (1075)
91 PF09334 tRNA-synt_1g: tRNA sy 82.7 1.1 2.3E-05 48.0 3.3 34 368-401 28-61 (391)
92 TIGR00398 metG methionyl-tRNA 82.1 2.8 6.1E-05 46.5 6.5 34 368-401 28-61 (530)
93 COG0143 MetG Methionyl-tRNA sy 81.8 2.4 5.3E-05 47.3 5.7 121 368-505 34-169 (558)
94 PRK11893 methionyl-tRNA synthe 81.6 2.9 6.4E-05 46.0 6.4 34 368-401 30-63 (511)
95 cd05776 DNA_polB_alpha_exo ina 80.1 3.9 8.5E-05 40.5 6.1 102 102-213 97-227 (234)
96 PRK07748 sporulation inhibitor 79.6 19 0.00042 34.7 10.6 99 91-215 81-179 (207)
97 KOG1275 PAB-dependent poly(A) 79.5 0.46 1E-05 54.5 -0.8 94 99-227 1009-1102(1118)
98 PRK12267 methionyl-tRNA synthe 79.3 4.1 8.8E-05 46.5 6.7 33 368-400 33-65 (648)
99 PRK00464 nrdR transcriptional 79.1 1.1 2.4E-05 41.6 1.7 44 452-511 2-45 (154)
100 smart00661 RPOL9 RNA polymeras 79.0 2.5 5.3E-05 31.3 3.3 17 490-506 19-35 (52)
101 PF07754 DUF1610: Domain of un 77.5 2.1 4.6E-05 27.1 2.1 9 453-461 1-9 (24)
102 PRK07983 exodeoxyribonuclease 77.2 20 0.00043 35.2 10.0 86 95-214 67-152 (219)
103 PF13453 zf-TFIIB: Transcripti 76.7 1.8 3.8E-05 30.8 1.8 24 489-512 17-40 (41)
104 PRK00420 hypothetical protein; 76.2 1.9 4.1E-05 37.9 2.2 47 428-503 6-52 (112)
105 cd05782 DNA_polB_like1_exo Unc 76.0 39 0.00084 32.8 11.6 110 90-210 79-207 (208)
106 COG1579 Zn-ribbon protein, pos 76.0 0.65 1.4E-05 46.2 -0.9 55 435-507 182-238 (239)
107 PF05191 ADK_lid: Adenylate ki 75.8 1.6 3.5E-05 30.4 1.3 11 492-502 2-12 (36)
108 PLN02610 probable methionyl-tR 75.0 5.8 0.00012 46.5 6.4 33 368-400 47-79 (801)
109 cd06138 ExoI_N N-terminal DEDD 73.0 21 0.00045 33.8 8.7 99 92-209 72-182 (183)
110 PRK05762 DNA polymerase II; Re 72.4 78 0.0017 37.2 14.8 112 91-212 205-348 (786)
111 COG0847 DnaQ DNA polymerase II 72.2 34 0.00074 33.5 10.4 99 91-215 83-181 (243)
112 PF02591 DUF164: Putative zinc 72.2 3.2 7E-05 31.5 2.4 33 451-500 23-55 (56)
113 PF00096 zf-C2H2: Zinc finger, 72.1 2.4 5.1E-05 25.7 1.3 15 492-506 1-15 (23)
114 PF13005 zf-IS66: zinc-finger 71.8 0.93 2E-05 33.0 -0.7 43 451-498 3-47 (47)
115 PF00301 Rubredoxin: Rubredoxi 71.5 1.9 4.2E-05 31.9 0.9 39 452-499 3-42 (47)
116 cd06133 ERI-1_3'hExo_like DEDD 71.4 39 0.00085 30.9 10.1 98 91-212 77-175 (176)
117 COG3809 Uncharacterized protei 70.8 3.8 8.3E-05 33.4 2.5 39 452-511 3-41 (88)
118 PRK00432 30S ribosomal protein 69.1 4.5 9.8E-05 30.3 2.5 14 490-503 36-49 (50)
119 cd00672 CysRS_core catalytic c 68.9 3.7 8E-05 40.2 2.6 34 367-400 47-80 (213)
120 PHA02119 hypothetical protein 68.8 1.8 3.9E-05 34.4 0.3 15 367-381 58-72 (87)
121 PF10122 Mu-like_Com: Mu-like 68.3 0.73 1.6E-05 34.5 -1.9 11 451-461 5-15 (51)
122 TIGR03830 CxxCG_CxxCG_HTH puta 68.1 2.4 5.2E-05 37.4 1.0 27 488-514 28-54 (127)
123 COG2956 Predicted N-acetylgluc 67.8 2.6 5.7E-05 43.6 1.3 12 488-499 365-376 (389)
124 PF14353 CpXC: CpXC protein 67.4 4.7 0.0001 35.9 2.8 19 483-501 30-48 (128)
125 PRK12366 replication factor A; 66.4 2 4.4E-05 48.9 0.2 36 447-509 529-564 (637)
126 TIGR03447 mycothiol_MshC cyste 66.3 5 0.00011 43.2 3.2 34 368-401 64-97 (411)
127 KOG2907 RNA polymerase I trans 65.9 4.2 9E-05 35.5 2.0 45 448-505 72-116 (116)
128 PRK12418 cysteinyl-tRNA synthe 64.7 5.3 0.00011 42.7 2.9 36 367-402 36-71 (384)
129 PF09986 DUF2225: Uncharacteri 64.3 2 4.3E-05 42.1 -0.3 54 451-504 6-61 (214)
130 TIGR00515 accD acetyl-CoA carb 63.0 4.3 9.4E-05 41.6 1.8 32 446-499 22-53 (285)
131 PHA02325 hypothetical protein 61.8 4.3 9.4E-05 31.8 1.2 16 492-507 4-25 (72)
132 PF15135 UPF0515: Uncharacteri 61.1 6.2 0.00014 39.2 2.4 36 448-501 130-165 (278)
133 COG2835 Uncharacterized conser 60.9 6.8 0.00015 30.4 2.1 27 452-501 10-36 (60)
134 PRK03824 hypA hydrogenase nick 60.6 2.7 5.8E-05 38.2 -0.1 47 444-499 64-115 (135)
135 PRK08579 anaerobic ribonucleos 60.2 12 0.00027 42.4 5.0 58 430-520 544-605 (625)
136 PF06397 Desulfoferrod_N: Desu 59.5 6.3 0.00014 27.5 1.6 14 488-501 3-16 (36)
137 TIGR00396 leuS_bact leucyl-tRN 59.3 18 0.00039 42.7 6.3 18 368-385 58-75 (842)
138 PF11672 DUF3268: Protein of u 59.3 7.5 0.00016 33.6 2.4 43 451-507 3-45 (102)
139 PRK07218 replication factor A; 59.2 4.4 9.4E-05 43.8 1.1 14 447-460 294-307 (423)
140 CHL00174 accD acetyl-CoA carbo 59.0 5.8 0.00012 40.8 1.9 38 439-499 28-65 (296)
141 PF08271 TF_Zn_Ribbon: TFIIB z 58.8 7.3 0.00016 27.9 1.9 13 488-500 16-28 (43)
142 PRK05654 acetyl-CoA carboxylas 58.8 6 0.00013 40.7 2.0 35 445-501 22-56 (292)
143 PF13894 zf-C2H2_4: C2H2-type 58.4 6.3 0.00014 23.5 1.3 12 492-503 1-12 (24)
144 cd00730 rubredoxin Rubredoxin; 57.7 6.2 0.00014 29.6 1.4 39 452-499 3-42 (50)
145 PRK06722 exonuclease; Provisio 57.5 70 0.0015 32.7 9.5 100 91-213 79-178 (281)
146 PRK11827 hypothetical protein; 57.2 9.3 0.0002 29.8 2.3 10 452-461 10-19 (60)
147 PF10571 UPF0547: Uncharacteri 56.4 4.6 0.0001 26.0 0.5 9 493-501 16-24 (26)
148 PRK12380 hydrogenase nickel in 56.3 4.1 8.8E-05 35.8 0.3 20 441-460 61-80 (113)
149 COG1655 Uncharacterized protei 55.5 3.3 7.1E-05 40.7 -0.5 12 487-498 58-69 (267)
150 PLN02946 cysteine-tRNA ligase 55.5 8.7 0.00019 43.0 2.7 35 367-401 107-141 (557)
151 PF04032 Rpr2: RNAse P Rpr2/Rp 55.2 17 0.00038 29.6 3.9 60 430-499 26-85 (85)
152 cd00729 rubredoxin_SM Rubredox 54.9 8.1 0.00018 26.4 1.5 15 491-506 2-16 (34)
153 cd00812 LeuRS_core catalytic c 54.8 22 0.00047 36.8 5.4 34 368-401 29-62 (314)
154 PF14787 zf-CCHC_5: GAG-polypr 54.6 6 0.00013 27.5 0.8 13 493-509 4-16 (36)
155 PF01396 zf-C4_Topoisom: Topoi 54.3 9.8 0.00021 26.8 1.9 31 452-503 3-36 (39)
156 COG1773 Rubredoxin [Energy pro 54.2 7.1 0.00015 29.9 1.2 40 451-499 4-44 (55)
157 TIGR00305 probable toxin-antit 53.8 17 0.00036 31.4 3.7 28 385-412 85-113 (114)
158 PRK00260 cysS cysteinyl-tRNA s 53.4 12 0.00026 41.0 3.3 35 367-401 50-84 (463)
159 PHA00616 hypothetical protein 53.2 3.2 6.9E-05 30.3 -0.7 18 492-509 2-19 (44)
160 PRK00390 leuS leucyl-tRNA synt 52.9 22 0.00048 41.8 5.6 18 368-385 61-78 (805)
161 COG1096 Predicted RNA-binding 52.8 7.3 0.00016 37.2 1.3 13 449-461 148-160 (188)
162 PRK00564 hypA hydrogenase nick 52.6 5.7 0.00012 35.1 0.6 19 442-460 63-81 (117)
163 PRK08402 replication factor A; 52.3 5.3 0.00012 42.2 0.4 29 449-500 211-239 (355)
164 PRK12495 hypothetical protein; 52.2 13 0.00028 36.4 3.0 45 430-504 27-71 (226)
165 PF02150 RNA_POL_M_15KD: RNA p 52.1 8.1 0.00017 26.7 1.1 10 452-461 3-12 (35)
166 TIGR00435 cysS cysteinyl-tRNA 52.0 11 0.00024 41.4 2.8 35 367-401 48-82 (465)
167 smart00531 TFIIE Transcription 52.0 9.1 0.0002 35.1 1.8 17 486-502 94-110 (147)
168 PRK06386 replication factor A; 52.0 5.7 0.00012 42.0 0.6 15 446-460 232-246 (358)
169 COG4416 Com Mu-like prophage p 51.9 3.5 7.5E-05 31.2 -0.7 11 451-461 5-15 (60)
170 PF09297 zf-NADH-PPase: NADH p 51.4 11 0.00024 25.2 1.7 28 451-501 4-31 (32)
171 PHA00626 hypothetical protein 51.0 12 0.00026 28.7 1.9 16 488-503 20-35 (59)
172 PLN02563 aminoacyl-tRNA ligase 50.3 24 0.00052 42.3 5.4 18 368-385 140-157 (963)
173 PRK07111 anaerobic ribonucleos 50.1 12 0.00026 43.4 2.8 29 430-458 656-688 (735)
174 TIGR00373 conserved hypothetic 49.5 15 0.00032 34.3 2.9 34 445-500 104-137 (158)
175 TIGR00319 desulf_FeS4 desulfof 49.5 11 0.00025 25.5 1.6 13 489-501 5-17 (34)
176 PRK14535 cysS cysteinyl-tRNA s 49.3 13 0.00029 42.4 3.0 55 342-401 254-309 (699)
177 COG0215 CysS Cysteinyl-tRNA sy 49.1 14 0.0003 40.4 2.9 35 367-401 49-83 (464)
178 PRK03681 hypA hydrogenase nick 49.0 6.5 0.00014 34.6 0.4 20 441-460 61-80 (114)
179 PF14446 Prok-RING_1: Prokaryo 48.8 16 0.00035 27.8 2.4 27 450-501 5-31 (54)
180 PF07282 OrfB_Zn_ribbon: Putat 48.7 28 0.0006 27.3 3.9 49 430-501 5-56 (69)
181 KOG2041 WD40 repeat protein [G 48.4 25 0.00054 40.2 4.7 97 391-499 1061-1164(1189)
182 PRK12496 hypothetical protein; 48.3 27 0.00058 32.8 4.4 46 365-414 60-105 (164)
183 cd00974 DSRD Desulforedoxin (D 47.4 13 0.00028 25.3 1.5 13 489-501 2-14 (34)
184 cd00350 rubredoxin_like Rubred 47.3 12 0.00025 25.4 1.3 12 491-502 1-12 (33)
185 PF13248 zf-ribbon_3: zinc-rib 47.1 10 0.00023 24.1 1.0 10 451-460 3-12 (26)
186 cd00668 Ile_Leu_Val_MetRS_core 46.7 36 0.00079 34.9 5.5 40 368-407 29-68 (312)
187 PRK00398 rpoP DNA-directed RNA 46.4 13 0.00029 26.9 1.6 11 451-461 4-14 (46)
188 PTZ00399 cysteinyl-tRNA-synthe 46.3 16 0.00035 41.8 3.0 34 368-401 88-122 (651)
189 PF12172 DUF35_N: Rubredoxin-l 46.1 14 0.00029 25.5 1.6 16 489-504 9-24 (37)
190 PRK00762 hypA hydrogenase nick 46.1 8.1 0.00018 34.5 0.5 19 441-460 61-79 (124)
191 PF09538 FYDLN_acid: Protein o 45.9 11 0.00024 33.0 1.3 30 451-504 10-39 (108)
192 PRK06266 transcription initiat 45.7 19 0.00041 34.3 3.0 35 444-500 111-145 (178)
193 TIGR01206 lysW lysine biosynth 45.6 19 0.00041 27.4 2.4 30 451-501 3-32 (54)
194 PF13465 zf-H2C2_2: Zinc-finge 45.5 16 0.00035 23.2 1.7 15 488-502 11-25 (26)
195 PF01783 Ribosomal_L32p: Ribos 45.4 11 0.00025 28.7 1.2 11 449-459 25-35 (56)
196 COG1997 RPL43A Ribosomal prote 45.3 18 0.00038 30.3 2.3 18 489-506 51-68 (89)
197 PRK12496 hypothetical protein; 45.2 14 0.00031 34.6 2.1 11 451-461 144-154 (164)
198 TIGR00100 hypA hydrogenase nic 45.0 8 0.00017 34.1 0.3 20 441-460 61-80 (115)
199 PRK06266 transcription initiat 44.8 14 0.00029 35.3 1.8 16 486-501 112-127 (178)
200 PRK14534 cysS cysteinyl-tRNA s 44.4 16 0.00035 40.2 2.6 36 367-402 48-93 (481)
201 PF12813 XPG_I_2: XPG domain c 43.8 25 0.00053 35.2 3.6 44 367-412 8-54 (246)
202 TIGR00686 phnA alkylphosphonat 43.4 16 0.00034 31.8 1.8 27 451-501 3-29 (109)
203 smart00531 TFIIE Transcription 43.3 32 0.0007 31.5 4.0 40 444-500 93-132 (147)
204 PF01780 Ribosomal_L37ae: Ribo 43.2 17 0.00037 30.7 1.9 17 489-505 51-67 (90)
205 PF06750 DiS_P_DiS: Bacterial 42.4 14 0.00031 31.2 1.4 12 449-460 32-43 (92)
206 PF04981 NMD3: NMD3 family ; 41.9 21 0.00046 35.4 2.8 21 489-510 33-53 (236)
207 PF01406 tRNA-synt_1e: tRNA sy 41.5 14 0.00031 38.1 1.5 34 368-402 36-70 (300)
208 PRK14704 anaerobic ribonucleos 41.3 32 0.00069 39.2 4.4 58 431-519 536-597 (618)
209 PF09845 DUF2072: Zn-ribbon co 41.0 16 0.00035 32.9 1.6 9 452-460 3-11 (131)
210 PHA02768 hypothetical protein; 41.0 10 0.00023 29.0 0.4 18 492-509 6-23 (55)
211 cd05778 DNA_polB_zeta_exo inac 41.0 38 0.00083 33.4 4.5 51 159-209 175-230 (231)
212 COG0675 Transposase and inacti 40.8 31 0.00066 35.1 3.9 44 429-500 285-331 (364)
213 PRK05978 hypothetical protein; 40.4 16 0.00034 33.8 1.4 9 493-501 54-62 (148)
214 PRK09521 exosome complex RNA-b 40.0 7.1 0.00015 37.3 -0.9 30 448-501 147-176 (189)
215 COG1645 Uncharacterized Zn-fin 39.6 22 0.00048 32.1 2.3 26 431-461 14-39 (131)
216 COG1412 Uncharacterized protei 39.6 73 0.0016 29.1 5.6 52 373-426 73-125 (136)
217 COG1571 Predicted DNA-binding 39.5 14 0.00031 39.7 1.2 30 450-503 350-379 (421)
218 PF11781 RRN7: RNA polymerase 39.4 21 0.00046 24.8 1.6 13 488-500 22-34 (36)
219 PRK14536 cysS cysteinyl-tRNA s 39.1 27 0.00059 38.6 3.3 35 368-402 51-95 (490)
220 PF07975 C1_4: TFIIH C1-like d 38.3 17 0.00038 27.3 1.2 13 489-501 19-31 (51)
221 TIGR00373 conserved hypothetic 38.2 20 0.00043 33.4 1.8 16 486-501 104-119 (158)
222 TIGR00280 L37a ribosomal prote 38.1 22 0.00047 30.1 1.8 17 489-505 51-67 (91)
223 smart00834 CxxC_CXXC_SSSS Puta 38.0 19 0.0004 25.0 1.3 12 492-503 6-17 (41)
224 PTZ00255 60S ribosomal protein 37.9 23 0.0005 29.9 2.0 17 489-505 52-68 (90)
225 PF04810 zf-Sec23_Sec24: Sec23 37.7 28 0.00062 24.6 2.1 31 451-500 3-33 (40)
226 PF03119 DNA_ligase_ZBD: NAD-d 37.6 17 0.00038 23.7 1.0 10 452-461 1-10 (28)
227 COG3364 Zn-ribbon containing p 37.4 18 0.00039 31.1 1.3 9 452-460 4-12 (112)
228 PF13240 zinc_ribbon_2: zinc-r 37.4 17 0.00038 22.6 0.9 9 452-460 1-9 (23)
229 PHA02998 RNA polymerase subuni 37.4 28 0.00061 33.0 2.6 48 439-501 134-181 (195)
230 PF07295 DUF1451: Protein of u 37.0 19 0.00041 33.2 1.5 12 450-461 112-123 (146)
231 PRK02261 methylaspartate mutas 36.7 43 0.00093 30.3 3.7 36 364-400 17-54 (137)
232 TIGR02300 FYDLN_acid conserved 36.7 19 0.00042 32.3 1.4 10 452-461 11-20 (129)
233 TIGR01031 rpmF_bact ribosomal 36.2 25 0.00054 26.9 1.8 11 449-459 25-35 (55)
234 cd00817 ValRS_core catalytic c 36.1 50 0.0011 35.1 4.7 17 368-384 30-46 (382)
235 PRK11032 hypothetical protein; 35.9 19 0.00042 33.6 1.4 11 451-461 125-135 (160)
236 PF13913 zf-C2HC_2: zinc-finge 35.7 19 0.00042 22.8 0.9 10 492-501 3-12 (25)
237 cd00671 ArgRS_core catalytic c 35.7 24 0.00051 34.3 2.0 38 364-401 24-62 (212)
238 PRK03954 ribonuclease P protei 35.6 32 0.00069 30.7 2.6 32 431-462 45-76 (121)
239 TIGR03831 YgiT_finger YgiT-typ 35.6 19 0.00042 25.5 1.0 17 488-504 29-45 (46)
240 PF01214 CK_II_beta: Casein ki 35.2 36 0.00077 32.6 3.1 52 431-503 85-139 (184)
241 COG0266 Nei Formamidopyrimidin 35.1 20 0.00044 36.4 1.4 12 488-499 262-273 (273)
242 COG5134 Uncharacterized conser 35.1 28 0.00061 33.9 2.3 21 441-461 32-53 (272)
243 PRK03976 rpl37ae 50S ribosomal 35.1 25 0.00054 29.7 1.7 17 489-505 52-68 (90)
244 cd00802 class_I_aaRS_core cata 34.7 35 0.00075 30.6 2.8 33 367-399 25-57 (143)
245 PRK00241 nudC NADH pyrophospha 34.0 31 0.00067 34.7 2.6 32 450-504 99-130 (256)
246 PTZ00396 Casein kinase II subu 33.9 48 0.001 33.4 3.8 54 431-505 106-162 (251)
247 PF04959 ARS2: Arsenite-resist 33.7 24 0.00053 34.6 1.7 30 479-509 65-94 (214)
248 PF13912 zf-C2H2_6: C2H2-type 33.2 27 0.00058 21.8 1.3 15 492-506 2-16 (27)
249 PRK10220 hypothetical protein; 33.2 31 0.00067 30.1 2.0 12 489-500 18-29 (111)
250 TIGR00354 polC DNA polymerase, 33.2 27 0.00059 41.2 2.2 10 451-460 1013-1022(1095)
251 COG1058 CinA Predicted nucleot 33.2 53 0.0011 33.1 4.0 49 359-407 17-68 (255)
252 PRK05452 anaerobic nitric oxid 32.8 21 0.00045 39.4 1.2 41 450-499 425-466 (479)
253 PRK14890 putative Zn-ribbon RN 32.3 47 0.001 25.8 2.7 11 451-461 8-18 (59)
254 PRK08271 anaerobic ribonucleos 32.3 53 0.0012 37.4 4.3 69 418-519 528-602 (623)
255 COG2023 RPR2 RNase P subunit R 32.2 48 0.001 28.8 3.1 53 433-501 39-92 (105)
256 PRK09678 DNA-binding transcrip 31.4 38 0.00083 27.4 2.2 44 451-509 2-47 (72)
257 cd00758 MoCF_BD MoCF_BD: molyb 31.4 99 0.0022 27.5 5.2 48 359-407 15-66 (133)
258 PF08274 PhnA_Zn_Ribbon: PhnA 31.2 28 0.0006 23.3 1.1 12 489-500 17-28 (30)
259 PF03966 Trm112p: Trm112p-like 31.1 25 0.00055 27.7 1.1 15 487-501 49-63 (68)
260 TIGR01384 TFS_arch transcripti 31.0 32 0.0007 29.3 1.9 11 491-501 16-26 (104)
261 TIGR03599 YloV DAK2 domain fus 31.0 2.5E+02 0.0055 31.4 9.3 81 357-437 315-404 (530)
262 PRK04023 DNA polymerase II lar 30.6 33 0.00072 40.7 2.4 10 451-460 1038-1047(1121)
263 PF01807 zf-CHC2: CHC2 zinc fi 30.4 25 0.00054 29.9 1.0 47 433-499 15-62 (97)
264 TIGR01501 MthylAspMutase methy 29.6 73 0.0016 28.9 4.0 33 368-401 21-53 (134)
265 KOG3277 Uncharacterized conser 29.5 28 0.0006 32.3 1.2 33 451-499 80-112 (165)
266 PRK08270 anaerobic ribonucleos 29.4 25 0.00054 40.3 1.1 41 418-458 586-634 (656)
267 PF09332 Mcm10: Mcm10 replicat 29.4 28 0.00061 36.6 1.4 58 430-499 235-293 (344)
268 cd04476 RPA1_DBD_C RPA1_DBD_C: 29.3 29 0.00063 32.2 1.4 30 448-501 32-61 (166)
269 cd02072 Glm_B12_BD B12 binding 29.2 76 0.0016 28.6 4.0 33 368-401 19-51 (128)
270 cd00924 Cyt_c_Oxidase_Vb Cytoc 29.1 32 0.0007 29.5 1.5 13 489-501 77-89 (97)
271 PF01873 eIF-5_eIF-2B: Domain 29.0 38 0.00082 30.4 2.0 53 422-500 71-123 (125)
272 cd02067 B12-binding B12 bindin 29.0 79 0.0017 27.2 4.1 32 367-399 18-49 (119)
273 PRK03988 translation initiatio 28.6 64 0.0014 29.5 3.4 46 429-500 87-132 (138)
274 PF04900 Fcf1: Fcf1; InterPro 28.5 1E+02 0.0023 26.0 4.6 39 388-426 53-93 (101)
275 PRK14810 formamidopyrimidine-D 28.0 32 0.00069 34.9 1.5 12 488-499 261-272 (272)
276 PRK09263 anaerobic ribonucleos 28.0 48 0.001 38.4 3.1 41 418-458 603-649 (711)
277 PRK03670 competence damage-ind 27.9 91 0.002 31.3 4.8 24 359-382 16-39 (252)
278 PF01155 HypA: Hydrogenase exp 27.7 9.3 0.0002 33.5 -2.1 31 430-460 41-80 (113)
279 PF10083 DUF2321: Uncharacteri 27.6 29 0.00064 32.2 1.0 36 451-501 40-78 (158)
280 PF15446 zf-PHD-like: PHD/FYVE 27.3 73 0.0016 30.1 3.6 54 448-501 69-134 (175)
281 PRK12286 rpmF 50S ribosomal pr 27.3 40 0.00087 26.0 1.6 10 450-459 27-36 (57)
282 PF09723 Zn-ribbon_8: Zinc rib 27.0 36 0.00078 24.3 1.2 10 492-501 6-15 (42)
283 COG4133 CcmA ABC-type transpor 26.9 38 0.00083 32.8 1.7 18 495-512 54-71 (209)
284 TIGR00244 transcriptional regu 26.7 19 0.00042 33.1 -0.3 12 490-501 27-38 (147)
285 COG3677 Transposase and inacti 26.7 57 0.0012 29.3 2.8 13 489-501 51-63 (129)
286 cd00885 cinA Competence-damage 26.7 99 0.0021 29.0 4.5 48 359-407 15-66 (170)
287 PRK13264 3-hydroxyanthranilate 26.6 13 0.00028 35.3 -1.4 43 452-500 122-166 (177)
288 TIGR00592 pol2 DNA polymerase 26.6 2.6E+02 0.0057 34.5 9.1 102 102-213 599-723 (1172)
289 PF04606 Ogr_Delta: Ogr/Delta- 26.2 42 0.0009 24.6 1.5 35 452-501 1-37 (47)
290 PRK14714 DNA polymerase II lar 26.1 43 0.00094 40.8 2.3 18 202-219 844-861 (1337)
291 COG0777 AccD Acetyl-CoA carbox 25.8 21 0.00046 36.2 -0.2 32 447-500 25-56 (294)
292 PF01096 TFIIS_C: Transcriptio 25.7 46 0.00099 23.4 1.5 14 488-501 25-38 (39)
293 PF14311 DUF4379: Domain of un 25.5 42 0.00091 25.2 1.4 21 488-509 25-45 (55)
294 COG1998 RPS31 Ribosomal protei 25.5 47 0.001 24.9 1.6 17 488-504 34-50 (51)
295 PRK13945 formamidopyrimidine-D 25.4 40 0.00087 34.4 1.7 11 489-499 272-282 (282)
296 TIGR01391 dnaG DNA primase, ca 25.1 62 0.0013 34.9 3.1 47 433-499 16-63 (415)
297 PRK14811 formamidopyrimidine-D 25.1 37 0.0008 34.4 1.3 13 489-501 253-265 (269)
298 smart00653 eIF2B_5 domain pres 25.0 72 0.0016 28.0 3.0 45 429-499 65-109 (110)
299 TIGR02605 CxxC_CxxC_SSSS putat 24.9 40 0.00086 24.8 1.2 10 492-501 6-15 (52)
300 PLN02294 cytochrome c oxidase 24.9 36 0.00079 32.1 1.1 13 489-501 139-151 (174)
301 COG1499 NMD3 NMD protein affec 24.9 69 0.0015 33.9 3.4 20 489-509 41-60 (355)
302 COG1326 Uncharacterized archae 24.5 65 0.0014 31.0 2.8 16 488-503 27-42 (201)
303 PRK05667 dnaG DNA primase; Val 24.4 68 0.0015 36.3 3.4 47 433-499 18-65 (580)
304 COG1545 Predicted nucleic-acid 24.2 39 0.00084 30.8 1.2 19 488-506 26-44 (140)
305 TIGR02487 NrdD anaerobic ribon 24.1 42 0.00092 37.9 1.7 41 418-458 485-532 (579)
306 PF05180 zf-DNL: DNL zinc fing 24.0 24 0.00052 28.1 -0.2 34 452-501 6-39 (66)
307 PF01215 COX5B: Cytochrome c o 24.0 34 0.00074 31.2 0.8 13 489-501 110-122 (136)
308 PF12171 zf-C2H2_jaz: Zinc-fin 23.6 37 0.00081 21.4 0.7 10 492-501 2-11 (27)
309 COG1933 Archaeal DNA polymeras 23.6 29 0.00063 34.5 0.3 8 367-374 130-137 (253)
310 COG1487 VapC Predicted nucleic 23.5 1.2E+02 0.0025 26.8 4.2 43 364-412 78-121 (133)
311 TIGR00375 conserved hypothetic 23.2 40 0.00087 35.9 1.2 34 450-506 240-273 (374)
312 PF03833 PolC_DP2: DNA polymer 23.2 27 0.00059 40.6 0.0 11 370-380 557-567 (900)
313 PHA02540 61 DNA primase; Provi 23.0 74 0.0016 33.5 3.1 52 432-499 9-63 (337)
314 COG0375 HybF Zn finger protein 23.0 42 0.00091 29.7 1.1 31 430-460 41-80 (115)
315 PRK10445 endonuclease VIII; Pr 22.7 47 0.001 33.5 1.6 28 451-499 236-263 (263)
316 TIGR03037 anthran_nbaC 3-hydro 22.7 17 0.00038 33.9 -1.4 40 453-498 117-158 (159)
317 PRK01103 formamidopyrimidine/5 22.7 48 0.001 33.6 1.6 12 488-499 262-273 (274)
318 PHA02942 putative transposase; 22.6 99 0.0021 33.1 4.1 11 490-500 341-351 (383)
319 smart00440 ZnF_C2C2 C2C2 Zinc 22.0 55 0.0012 23.2 1.4 13 489-501 26-38 (40)
320 COG2824 PhnA Uncharacterized Z 21.9 54 0.0012 28.5 1.5 11 491-501 20-30 (112)
321 COG1327 Predicted transcriptio 21.8 28 0.00062 32.1 -0.2 12 490-501 27-38 (156)
322 PF14205 Cys_rich_KTR: Cystein 21.5 34 0.00074 26.1 0.2 10 451-460 5-14 (55)
323 PF09862 DUF2089: Protein of u 21.5 55 0.0012 28.9 1.5 9 453-461 1-9 (113)
324 COG2331 Uncharacterized protei 21.4 44 0.00095 27.3 0.8 23 433-460 21-43 (82)
325 cd02071 MM_CoA_mut_B12_BD meth 21.3 1.3E+02 0.0029 26.3 4.0 31 368-399 19-49 (122)
326 KOG2186 Cell growth-regulating 21.3 36 0.00078 34.1 0.4 42 450-506 3-44 (276)
327 PF08790 zf-LYAR: LYAR-type C2 21.2 61 0.0013 21.4 1.3 14 493-506 2-15 (28)
328 PF05991 NYN_YacP: YacP-like N 21.1 1.7E+02 0.0037 27.3 4.9 65 372-438 63-132 (166)
329 PRK03094 hypothetical protein; 21.1 2.1E+02 0.0045 23.7 4.7 72 358-438 3-76 (80)
330 KOG1701 Focal adhesion adaptor 21.0 37 0.00081 36.4 0.5 44 450-501 394-437 (468)
331 cd02070 corrinoid_protein_B12- 20.9 1.2E+02 0.0027 29.0 4.1 34 365-399 97-132 (201)
332 PF06906 DUF1272: Protein of u 20.9 56 0.0012 25.1 1.3 15 451-465 42-56 (57)
333 PTZ00043 cytochrome c oxidase 20.8 50 0.0011 32.5 1.3 15 487-501 177-191 (268)
334 PRK11788 tetratricopeptide rep 20.7 87 0.0019 32.4 3.2 10 490-499 367-376 (389)
335 PF03698 UPF0180: Uncharacteri 20.7 1.3E+02 0.0028 24.8 3.5 43 357-407 2-44 (80)
336 TIGR00640 acid_CoA_mut_C methy 20.6 1.3E+02 0.0029 27.0 3.9 32 368-400 22-53 (132)
337 COG5047 SEC23 Vesicle coat com 20.4 50 0.0011 36.9 1.3 31 451-500 54-85 (755)
338 COG2888 Predicted Zn-ribbon RN 20.4 87 0.0019 24.4 2.2 11 450-460 9-19 (61)
339 PF13277 YmdB: YmdB-like prote 20.3 92 0.002 31.4 3.0 39 366-404 46-84 (253)
340 PRK03673 hypothetical protein; 20.3 1.4E+02 0.0029 32.2 4.5 49 359-407 17-68 (396)
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=6.5e-46 Score=340.96 Aligned_cols=146 Identities=35% Similarity=0.637 Sum_probs=134.0
Q ss_pred CEEEEecccHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecChhHHHhhcccCCcEEEEcCCCHHHHHHHH
Q 009909 357 PKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQLLEV 436 (522)
Q Consensus 357 ~rfl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~RiiLTrd~~l~~~~~~~~~~~~~v~~~~~~~QL~~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 MRFLVDAMLGRLARWLRLLGYDTLYSR--DIDDDEILELAREEGRILLTRDRDLLKRRRVSGG-VILIRSDDPEEQLREV 77 (147)
T ss_pred CEEEEeCCHHHHHHHHHHCCCcEEEeC--CCChHHHHHHhhhCCeEEEECCHHHHHHhhccCC-EEEEcCCCHHHHHHHH
Confidence 799999999999999999999999876 4689999999999999999999999998775544 7888999999999999
Q ss_pred HHhcCcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecccchhhHHhh
Q 009909 437 IEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVMSAYLFIFL 513 (522)
Q Consensus 437 ~~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvYW~GsH~~r~~~~ 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 68888875 479999999999999999999999999999998753
No 2
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.7e-44 Score=327.43 Aligned_cols=148 Identities=30% Similarity=0.494 Sum_probs=135.8
Q ss_pred CCCCEEEEecccHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecChhHHHhhcccCCcEEEEcCCCHHHHH
Q 009909 354 DGYPKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQL 433 (522)
Q Consensus 354 ~~~~rfl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~RiiLTrd~~l~~~~~~~~~~~~~v~~~~~~~QL 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 MGEMKFVVDAMLGKLARWLRLLGYDTVYSS--NESDDEIILIAKKEGRILLTRDRELYKRA-KLGIKAILIRSDSIEEQL 80 (165)
T ss_pred ccceeeeHHHhHHHHHHHHHHcCCceeeec--cCCcHHHHHHHhcCCeEEEeccHHHHHHh-hccCceEEEeCCCHHHHH
Confidence 467899999999999999999999999875 35788999999999999999999999987 567789999999999999
Q ss_pred HHHHHhcCcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecccchhhHHh
Q 009909 434 LEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVMSAYLFIF 512 (522)
Q Consensus 434 ~~v~~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvYW~GsH~~r~~~ 512 (522)
.+++.++++.......|+||+.||++|. ++++|+|++ .||+.|+..+++||+||.|||+||.||||+||-.
T Consensus 81 ~e~~~~~~l~~~~~~e~~RCp~CN~~L~--~vs~eev~~------~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw~~m~~ 151 (165)
T COG1656 81 AEFLARLGLKPRLFPEFSRCPECNGELE--KVSREEVKE------KVPEKVYRNYEEFYRCPKCGKIYWKGSHWRRMVE 151 (165)
T ss_pred HHHHHHhccchhcccccccCcccCCEec--cCcHHHHhh------ccchhhhhcccceeECCCCcccccCchHHHHHHH
Confidence 9999999998865556999999999996 799999885 7999999999999999999999999999999765
No 3
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=99.97 E-value=1.3e-29 Score=243.27 Aligned_cols=184 Identities=46% Similarity=0.765 Sum_probs=150.5
Q ss_pred EEEEcCCChHHHHHHHHH--hcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCC
Q 009909 11 IHLVTSTESPEFTHLARA--LSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIP 88 (522)
Q Consensus 11 i~~I~t~~~~el~~ll~~--l~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~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 688998 8999999999 8899999999999988742 23689999999985 689999998765
Q ss_pred ---chhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCC---CCCcCCc
Q 009909 89 ---LPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGR---KLPKETK 162 (522)
Q Consensus 89 ---~~~~~~~L~~lL~d~~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 013589999555555554321111 1113468
Q ss_pred cHHHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009909 163 SLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 163 sL~~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 4
>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=1.5e-28 Score=229.15 Aligned_cols=158 Identities=34% Similarity=0.581 Sum_probs=139.7
Q ss_pred HHHHHHHhc-CCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhh
Q 009909 22 FTHLARALS-QSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELF 100 (522)
Q Consensus 22 l~~ll~~l~-~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~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 567788888 9999999999999875 5689999999995 37899999987642 567899999
Q ss_pred CCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcccc
Q 009909 101 VSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKEL 180 (522)
Q Consensus 101 ~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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--------KLQRLFD-TTIAANLKGLP-------ERWSLASLVEHFLGKTLDKSI 127 (161)
T ss_pred CCCCEEEEEeccHHHHHHHHHHcCC--------CcccHhH-HHHHHHHhCCC-------CCchHHHHHHHHhCCCCCccc
Confidence 9999999999999999999876665 2467799 89999999863 357999999999999999999
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009909 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 5
>PRK10829 ribonuclease D; Provisional
Probab=99.96 E-value=4.7e-28 Score=252.83 Aligned_cols=183 Identities=24% Similarity=0.368 Sum_probs=162.1
Q ss_pred cEEEEcCCChHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCc
Q 009909 10 KIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPL 89 (522)
Q Consensus 10 ~i~~I~t~~~~el~~ll~~l~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~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 579999998764
Q ss_pred hhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHH
Q 009909 90 PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (522)
Q Consensus 90 ~~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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--------LPQPLID-TQILAAFCGRP-------LSCGFASMVE 123 (373)
T ss_pred --chHHHHHHHcCCCeEEEEeChHhHHHHHHHHcCC--------CcCCeee-HHHHHHHcCCC-------ccccHHHHHH
Confidence 3678999999999999999999999999777755 2579999 99999998753 3689999999
Q ss_pred HHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---ccchhccc
Q 009909 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS---CSSISELD 230 (522)
Q Consensus 170 ~~Lg~~l~K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~~~g~l---~~~~~~~~ 230 (522)
++||+.++|+++.|||.+|||+++|+.|||.|+++++.||+.|.++|.+.|.+ .+|+..+.
T Consensus 124 ~~lgv~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g~~~w~~ee~~~l~ 187 (373)
T PRK10829 124 EYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGWLPAALDECRLLC 187 (373)
T ss_pred HHhCCccCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999998886 45555443
No 6
>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=1.1e-26 Score=217.96 Aligned_cols=163 Identities=33% Similarity=0.526 Sum_probs=142.7
Q ss_pred hHHHHHHHHHhc-CCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHH
Q 009909 19 SPEFTHLARALS-QSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLK 97 (522)
Q Consensus 19 ~~el~~ll~~l~-~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~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 578889999998 99999999999987641 25689999999984 689999998753 4667899
Q ss_pred HhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCc
Q 009909 98 ELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS 177 (522)
Q Consensus 98 ~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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--------EVRGVVD-LSHLAKRVGPR------RKLVSLARLVEEVLGLPLS 131 (170)
T ss_pred HHhcCCCeeEEEeeeHHHHHHHHhHcCC--------CCCCeee-HHHHHHHhCCC------cCCccHHHHHHHHcCcccC
Confidence 9999999999999999999999877765 2467799 89999999874 2346999999999999998
Q ss_pred --ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009909 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 889999999999999999999999999999999885
No 7
>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins. The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.
Probab=99.94 E-value=4.9e-26 Score=219.27 Aligned_cols=170 Identities=25% Similarity=0.333 Sum_probs=141.7
Q ss_pred HHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCC
Q 009909 25 LARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPD 104 (522)
Q Consensus 25 ll~~l~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~l~~~~~~~~L~~lL~d~~ 104 (522)
.++.+..+++||||+||.+.+ ..++++|||||+. .+.+||||+..+....+...|+++|++++
T Consensus 3 ~~~~l~~~~~i~~D~E~~~~~----~~~~~~LiQia~~-------------~~~v~l~D~~~~~~~~~~~~L~~iLe~~~ 65 (197)
T cd06148 3 AIIHLKKQKVIGLDCEGVNLG----RKGKLCLVQIATR-------------TGQIYLFDILKLGSIVFINGLKDILESKK 65 (197)
T ss_pred hhhhhhhCCEEEEEcccccCC----CCCCEEEEEEeeC-------------CCcEEEEEhhhccchhHHHHHHHHhcCCC
Confidence 356677899999999998664 2578999999995 27999999998753346788999999999
Q ss_pred ceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccC-CCCCcCCccHHHHHHHHcCCcCcc-----
Q 009909 105 ILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLG-RKLPKETKSLANICKELLDISLSK----- 178 (522)
Q Consensus 105 I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~-~~~~~~~~sL~~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--------KLNNVFD-TQVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVK 136 (197)
T ss_pred ccEEEEechhHHHHHHHhcCc--------cccceee-HHHHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHH
Confidence 999999999999999766765 2467899 8999999987421 111223469999999999999865
Q ss_pred ---cccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 009909 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 467899999999999999999999999999999999998764
No 8
>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=99.93 E-value=3.2e-25 Score=232.43 Aligned_cols=180 Identities=26% Similarity=0.409 Sum_probs=157.6
Q ss_pred EcCCChHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhH
Q 009909 14 VTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIW 93 (522)
Q Consensus 14 I~t~~~~el~~ll~~l~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~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 7899999999999999999999987764 7889999999984 688999988653 36
Q ss_pred HHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcC
Q 009909 94 ELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLD 173 (522)
Q Consensus 94 ~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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---ccchhcccc
Q 009909 174 ISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS---CSSISELDS 231 (522)
Q Consensus 174 ~~l~K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~~~g~l---~~~~~~~~~ 231 (522)
+.++|..+.+||..|||+.+|+.|||.||++++.||+.|.++|++.|.+ .+|+..+.+
T Consensus 124 ~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~~~g~~~w~~ee~~~l~~ 184 (367)
T TIGR01388 124 VELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLEESGRLAWLEEECTLLTD 184 (367)
T ss_pred CCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999999999999999998886 555655443
No 9
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=1.3e-25 Score=229.15 Aligned_cols=179 Identities=27% Similarity=0.372 Sum_probs=159.4
Q ss_pred hHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHH
Q 009909 19 SPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKE 98 (522)
Q Consensus 19 ~~el~~ll~~l~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~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 4667888888888999999999998886 8899999999985 348999987632 13568899
Q ss_pred hhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcc
Q 009909 99 LFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSK 178 (522)
Q Consensus 99 lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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--------LPTPLFD-TQIAAKLAGFG-------TSHGLADLVEELLGVELDK 128 (361)
T ss_pred HhcCCceeeeeccccccHHHHHHhcCC--------CCCchhH-HHHHHHHhCCc-------ccccHHHHHHHHhCCcccc
Confidence 999999999999999999999988755 3589999 99999998764 3899999999999999999
Q ss_pred cccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---ccchhccccc
Q 009909 179 ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS---CSSISELDSS 232 (522)
Q Consensus 179 ~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~~~g~l---~~~~~~~~~~ 232 (522)
++|.|||.+||||++|+.|||.|+.+|+.||+.|.++|.++|.+ .++|..+...
T Consensus 129 ~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r~~~a~~ef~~l~~r 185 (361)
T COG0349 129 SEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAREGRLEWAEDEFRLLPTR 185 (361)
T ss_pred cccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHhhhc
Confidence 99999999999999999999999999999999999999999998 7778877766
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=8.6e-25 Score=204.34 Aligned_cols=174 Identities=29% Similarity=0.451 Sum_probs=149.9
Q ss_pred EEEEcCCChHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCch
Q 009909 11 IHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLP 90 (522)
Q Consensus 11 i~~I~t~~~~el~~ll~~l~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~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 578988 89999999999999999999999988752 24688999999984 67888887765432
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 26789999999999999999999999999987655 2578999 69999999875 23999999999
Q ss_pred HcC-CcCcccccccCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 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 8999999999999999999999999998873
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=9.4e-19 Score=164.44 Aligned_cols=164 Identities=31% Similarity=0.514 Sum_probs=134.8
Q ss_pred HHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCC
Q 009909 23 THLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVS 102 (522)
Q Consensus 23 ~~ll~~l~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~l~~~~~~~~L~~lL~d 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 344555555669999999866543 3467899999973 45888886532 256678999999
Q ss_pred CCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcccccc
Q 009909 103 PDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQC 182 (522)
Q Consensus 103 ~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 467899 89999999985 34699999999999987666688
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009909 183 SDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (522)
Q Consensus 183 sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~~~g~l 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 9999999999999999999999999999999999988653
No 12
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.76 E-value=4.6e-17 Score=150.91 Aligned_cols=169 Identities=32% Similarity=0.434 Sum_probs=132.5
Q ss_pred EEEcCCChHHHHHHHHHhc-CCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCch
Q 009909 12 HLVTSTESPEFTHLARALS-QSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLP 90 (522)
Q Consensus 12 ~~I~t~~~~el~~ll~~l~-~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~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 5669999999876653 3567889999963 235676544322 2
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 3456789999999999999999999999986 665 2 345699 99999999875 333699999999
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 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 9998876555567897788999999999999999999999998775
No 13
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.74 E-value=2.6e-18 Score=182.76 Aligned_cols=195 Identities=31% Similarity=0.500 Sum_probs=148.6
Q ss_pred CCCCccEEEEcCCChHHHHHHH-HHhcCC-CeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEE
Q 009909 5 YRKPLKIHLVTSTESPEFTHLA-RALSQS-SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLL 82 (522)
Q Consensus 5 ~~~~~~i~~I~t~~~~el~~ll-~~l~~~-~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~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--EKELRDLLLESLSEELRYVGIDSEWKPSK--KVSDSKLAILQIFFK--------------DCVYLI 447 (617)
T ss_pred CCcccceeeeCC--HHHHHHHHHHHhhhcCEEEEEccccCccc--CCChhHHHHHHHHhc--------------CeEEEe
Confidence 455667889988 78888776 456655 7899999999982 235689999999984 799999
Q ss_pred eCCCCC--chhhHH-HHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccc-CCCCC
Q 009909 83 DLSSIP--LPSIWE-LLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQL-GRKLP 158 (522)
Q Consensus 83 Dl~~l~--~~~~~~-~L~~lL~d~~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 45679999999999999999999998644421111011233555565666655544221 11233
Q ss_pred cCCccHHHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 159 KETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (522)
Q Consensus 159 ~~~~sL~~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 45789999999999999999999999999999999999999999999999999986654
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=99.71 E-value=7.3e-16 Score=147.66 Aligned_cols=175 Identities=25% Similarity=0.396 Sum_probs=133.9
Q ss_pred CccEEEEcCCChHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCC
Q 009909 8 PLKIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSI 87 (522)
Q Consensus 8 ~~~i~~I~t~~~~el~~ll~~l~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~l 87 (522)
+++|.+|++ ++++..+++.+...+.+++++|+.+..+ ..+.+..+|++.. +.+|+|++..
T Consensus 2 ~~~~~~i~~--~~~l~~~~~~l~~~~~l~~~~e~~~~~~---~~~~~~~l~l~~~--------------~~~~~i~~l~- 61 (192)
T cd06147 2 ETPLTFVDT--EEKLEELVEKLKNCKEIAVDLEHHSYRS---YLGFTCLMQISTR--------------EEDYIVDTLK- 61 (192)
T ss_pred CCCcEEECC--HHHHHHHHHHHhcCCeEEEEeEecCCcc---CCCceEEEEEecC--------------CCcEEEEecc-
Confidence 456788865 5667776666655569999998754432 3467778888874 2477777422
Q ss_pred CchhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHH
Q 009909 88 PLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANI 167 (522)
Q Consensus 88 ~~~~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L 167 (522)
.......|+++|+++++.|+|||+|.++..|...+|+ . ..+.|| ++|++||++++ +++|+.+
T Consensus 62 -~~~~~~~L~~~L~~~~i~kv~~d~K~~~~~L~~~~gi-~-------~~~~fD-~~laaYLL~p~--------~~~l~~l 123 (192)
T cd06147 62 -LRDDMHILNEVFTDPNILKVFHGADSDIIWLQRDFGL-Y-------VVNLFD-TGQAARVLNLP--------RHSLAYL 123 (192)
T ss_pred -cccchHHHHHHhcCCCceEEEechHHHHHHHHHHhCC-C-------cCchHH-HHHHHHHhCCC--------cccHHHH
Confidence 2234556899999999999999999999999733555 1 233499 99999999973 3599999
Q ss_pred HHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 009909 168 CKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKG 220 (522)
Q Consensus 168 ~~~~Lg~~l~K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~~~g 220 (522)
+++|||..++|..+.++|+.+||..+|..||+.+|.++++|++.|.++|+++.
T Consensus 124 ~~~yl~~~~~k~~~~~~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~L~e~~ 176 (192)
T cd06147 124 LQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELLERA 176 (192)
T ss_pred HHHHhCCCcchhhhccccccCCCCHHHHHHHHhhHHHHHHHHHHHHHHHHHhc
Confidence 99999987545556778987888999999999999999999999999998764
No 15
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=99.69 E-value=5.2e-17 Score=171.79 Aligned_cols=172 Identities=25% Similarity=0.352 Sum_probs=153.0
Q ss_pred EEEEcCCChHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCch
Q 009909 11 IHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLP 90 (522)
Q Consensus 11 i~~I~t~~~~el~~ll~~l~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~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 567877 7888899999888889999999877664 7899999999996 467999987664
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 45568999999999999999999999999999977 3578999 8888888874 47899999999
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 009909 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 99999999999999999999999999999999999999999999988876
No 16
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=99.63 E-value=9e-15 Score=133.02 Aligned_cols=149 Identities=28% Similarity=0.310 Sum_probs=114.4
Q ss_pred eEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCceEEEEech
Q 009909 34 LVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFK 113 (522)
Q Consensus 34 ~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~l~~~~~~~~L~~lL~d~~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 5799999876552 3578899999973 2244443322 12346677999999999999999999
Q ss_pred hhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcccccccCCC----CCC
Q 009909 114 QDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWS----NRP 189 (522)
Q Consensus 114 ~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L~~~~Lg~~l~K~~q~sdW~----~RP 189 (522)
+|+..|.+. +. ...++++| +++++|++++. ..+++|+++++++++..+.+..+..+|. .+|
T Consensus 64 ~d~~~L~~~-~~-------~~~~~~~D-~~~~ayll~~~------~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~ 128 (155)
T cd00007 64 FDLVVLARD-GI-------ELPGNIFD-TMLAAYLLNPG------EGSHSLDDLAKEYLGIELDKDEQIYGKGAKTFARP 128 (155)
T ss_pred HHHHHHHHC-CC-------CCCCCccc-HHHHHHHhCCC------CCcCCHHHHHHHHcCCCCccHHHHhcCCCCccccC
Confidence 999999774 22 13467899 99999999985 2157999999999998865534455653 478
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 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 89999999999999999999999865
No 17
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=99.63 E-value=8.2e-15 Score=133.54 Aligned_cols=147 Identities=26% Similarity=0.250 Sum_probs=113.1
Q ss_pred eEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCceEEEEech
Q 009909 34 LVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFK 113 (522)
Q Consensus 34 ~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~l~~~~~~~~L~~lL~d~~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 4789998876553 3578899999974 2447888754321 12456889999999999999999
Q ss_pred hhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcccccc--cCCCCCCCC
Q 009909 114 QDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQC--SDWSNRPLT 191 (522)
Q Consensus 114 ~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 43 13467899 99999999985 214599999999999886542222 248557889
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 009909 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 18
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.62 E-value=2.3e-18 Score=183.17 Aligned_cols=369 Identities=33% Similarity=0.411 Sum_probs=255.2
Q ss_pred CCceeeHHH--HHHHhhccccCCCCCcC-Cc---cHHHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHH-
Q 009909 135 VEPYLDITS--IYNHLHHKQLGRKLPKE-TK---SLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIE- 207 (522)
Q Consensus 135 ~~~~~Dlt~--La~yLl~~~~~~~~~~~-~~---sL~~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 346778877 77777664332222111 11 111234455555567888999999999999999999999999999
Q ss_pred -HHHHHHHHHHhc-----CCCccchhccccccccCCCCCCCCCCc-cCCccchhhhhhHHHHHHHhcccccCCCCCcccc
Q 009909 208 -IFNIFQVKVAQK-----GNSCSSISELDSSNLDLGLKGILEKPD-IGNKTVRFKLCEALDIIRATSYYSQCLPEGVVSR 280 (522)
Q Consensus 208 -L~~~L~~~L~~~-----g~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 280 (522)
+...+.+.+.+. ..+.--+..+-+. ........+ .+.++++...|+++.-.+.+++..+.+....++.
T Consensus 234 ~~v~e~~~~~~e~~~~~~~tl~~~v~~i~~r-----n~~~~~f~~~~~~n~v~~~~~kal~~~~~~~e~~~~~~~~f~~~ 308 (617)
T KOG2207|consen 234 FIVDERCAHLLERTINLPKTLTILVQEIINR-----NQKKYTFSDEYAKNYVQNKNCKALHYIRSEREKGQMADKGFVQH 308 (617)
T ss_pred HHHHHHHHHHHhhccCCCchhhhhHHHHHhc-----cchhhhhhhhhhhhHhhcccHHHHHHHHHHhhhhhhHHHhhchh
Confidence 777777777765 1221111111111 112222233 4566888999999999999999999988888888
Q ss_pred cccCCCCCCchHHHHHHHHhh---hhhhhhhccCC-CCcc----ccccCCCCcccc-----ccccccccccCCCCCCCCC
Q 009909 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 889999999999999999999 88888887733 2211 111111111111 3455667788889999999
Q ss_pred CCCCCCCCCCEEEEecccHHHHHHHHhcCCceecCCCCCC-ChHHHHHhhhcCCcEEEecChhHHHhhc----ccCCcEE
Q 009909 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 9999999999999999999999999999999988776333 3455555566789999999988754322 0111222
Q ss_pred EEcCCCH----HHHHHHHHH------hcCcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccC---C
Q 009909 423 RVKSLLK----NQQLLEVIE------AFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKN---L 489 (522)
Q Consensus 423 ~v~~~~~----~~QL~~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 2222111 244455555 67788887788899999999876656666777777777777888876433 2
Q ss_pred ce---eec--CCCCeEEecccchh
Q 009909 490 QF---WQC--MDCNQLYWEVMSAY 508 (522)
Q Consensus 490 ~F---~~C--~~CgkvYW~GsH~~ 508 (522)
++ |+| -+|+|+||.|.-..
T Consensus 549 eqcsnWqcrpLr~nQi~yaalDa~ 572 (617)
T KOG2207|consen 549 EQCSNWQCRPLRRNQIYYAALDAV 572 (617)
T ss_pred cccchhhcCCchhhHHHHHHhcch
Confidence 66 999 89999999995443
No 19
>PRK05755 DNA polymerase I; Provisional
Probab=99.57 E-value=8.4e-14 Score=161.53 Aligned_cols=179 Identities=18% Similarity=0.220 Sum_probs=142.6
Q ss_pred CccEEEEcCCChHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCC
Q 009909 8 PLKIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSI 87 (522)
Q Consensus 8 ~~~i~~I~t~~~~el~~ll~~l~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~l 87 (522)
++.|.+|++ .+++.++++.+.....+++|+|+.+..+ +.+++.++|+++. ++.+|++++..+
T Consensus 293 ~~~~~~I~~--~~~L~~~l~~l~~~~~~a~DtEt~~l~~---~~~~i~~i~ls~~-------------~g~~~~ip~~~i 354 (880)
T PRK05755 293 EEDYETILD--EEELEAWLAKLKAAGLFAFDTETTSLDP---MQAELVGLSFAVE-------------PGEAAYIPLDQL 354 (880)
T ss_pred CCceEEeCC--HHHHHHHHHHhhccCeEEEEeccCCCCc---ccccEEEEEEEeC-------------CCcEEEEecccc
Confidence 456778877 7889999988888899999999988765 6788999999875 355888887554
Q ss_pred CchhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHH
Q 009909 88 PLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANI 167 (522)
Q Consensus 88 ~~~~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L 167 (522)
+. ..++.|.++|+++.+.||+||+++|+..|.+ +|+ ...++++| |++++|+++++ . .++|+++
T Consensus 355 ~~-~~l~~l~~~L~d~~v~kV~HNakfDl~~L~~-~gi-------~~~~~~~D-T~iAa~Ll~~~------~-~~~L~~L 417 (880)
T PRK05755 355 DR-EVLAALKPLLEDPAIKKVGQNLKYDLHVLAR-YGI-------ELRGIAFD-TMLASYLLDPG------R-RHGLDSL 417 (880)
T ss_pred cH-HHHHHHHHHHhCCCCcEEEeccHhHHHHHHh-CCC-------CcCCCccc-HHHHHHHcCCC------C-CCCHHHH
Confidence 32 4677899999999999999999999999986 454 12367999 99999999985 2 4899999
Q ss_pred HHHHcCCcCcccc----cccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009909 168 CKELLDISLSKEL----QCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (522)
Q Consensus 168 ~~~~Lg~~l~K~~----q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~~~g~l 222 (522)
+++++|..+.... ...+|...|+ +.|..||+.|+.++++||..|.++|.+.+.+
T Consensus 418 ~~~ylg~~~~~~~~~~gk~~~~~~~pl-e~~~~YAa~Dv~~~~~L~~~L~~~L~~~~~l 475 (880)
T PRK05755 418 AERYLGHKTISFEEVAGKQLTFAQVDL-EEAAEYAAEDADVTLRLHEVLKPKLLEEPGL 475 (880)
T ss_pred HHHHhCCCccchHHhcCCCCCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHHhcccH
Confidence 9999998753211 1223444566 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=99.51 E-value=5.4e-13 Score=125.73 Aligned_cols=156 Identities=18% Similarity=0.142 Sum_probs=118.0
Q ss_pred CCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCceEEEEe
Q 009909 32 SSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFK 111 (522)
Q Consensus 32 ~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~l~~~~~~~~L~~lL~d~~I~KVgh~ 111 (522)
...+++|+|.....+ ..+++..++++.. +++|++++... . ...+.|+++|+++++.|++||
T Consensus 3 ~~~~~~~~~~~~~~~---~~~~l~~i~l~~~--------------~~~~~i~~~~~-~-~~~~~l~~~l~~~~~~ki~~d 63 (178)
T cd06140 3 ADEVALYVELLGENY---HTADIIGLALANG--------------GGAYYIPLELA-L-LDLAALKEWLEDEKIPKVGHD 63 (178)
T ss_pred CCceEEEEEEcCCCc---ceeeEEEEEEEeC--------------CcEEEEeccch-H-HHHHHHHHHHhCCCCceeccc
Confidence 356788888876554 4567777777763 35777774321 0 134568899999999999999
Q ss_pred chhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcccccccCCC---CC
Q 009909 112 FKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWS---NR 188 (522)
Q Consensus 112 ~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 1 2366799 99999999986 3347999999999999876544455552 23
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 009909 189 PLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGN 221 (522)
Q Consensus 189 PL~~~Qi~YAA~DA~~ll~L~~~L~~~L~~~g~ 221 (522)
+....+..|++.||.++++|++.|.++|+++++
T Consensus 129 ~~~~~~~~y~~~~a~~l~~l~~~l~~~L~~~~l 161 (178)
T cd06140 129 PDEEVLAEHLARKAAAIARLAPKLEEELEENEQ 161 (178)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 445678899999999999999999999988754
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=99.40 E-value=1.6e-11 Score=116.60 Aligned_cols=157 Identities=20% Similarity=0.321 Sum_probs=115.5
Q ss_pred cCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC------CCchhhHHHHHHhhCCC
Q 009909 30 SQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS------IPLPSIWELLKELFVSP 103 (522)
Q Consensus 30 ~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~------l~~~~~~~~L~~lL~d~ 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 34678999999766553 3456777777763 23366666432 12334566799999998
Q ss_pred CceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCc------
Q 009909 104 DILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS------ 177 (522)
Q Consensus 104 ~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 889999999999999976 454 1 2356899 99999999985 2257999999999987521
Q ss_pred -ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 009909 178 -KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ 218 (522)
Q Consensus 178 -K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~~ 218 (522)
|..+..+|...|+ ..+..||+.||.++++|++.|.+++++
T Consensus 132 ~k~~~~~~~~~~~~-~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 132 GKGKKQITFDQVPL-EKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred CCCcCcCCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 2223344654444 668899999999999999999999987
No 22
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.27 E-value=2.7e-11 Score=134.04 Aligned_cols=146 Identities=23% Similarity=0.229 Sum_probs=118.5
Q ss_pred cEEEEcCCChHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCc
Q 009909 10 KIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPL 89 (522)
Q Consensus 10 ~i~~I~t~~~~el~~ll~~l~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~l~~ 89 (522)
.+.+|++ .+++..++..+...+.+++|+|+.... ..++++|++.. +.+|++|....
T Consensus 2 ~~~~I~~--~~~l~~~~~~l~~~~~~a~DtEf~r~~------t~l~liQ~~~~--------------~~~~liDpl~~-- 57 (553)
T PRK14975 2 DMKVILA--PEELGAALERLSPAGVVAGDTETTGDD------AAAAAAQEGEE--------------EPRWVWASTAA-- 57 (553)
T ss_pred CceEEec--cchhHHHHHHhccCCceeCCccccCCc------chhheeeecCC--------------CceEEECchHH--
Confidence 4567887 688999999999999999999987654 27899999874 68899986531
Q ss_pred hhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHH
Q 009909 90 PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (522)
Q Consensus 90 ~~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L~~ 169 (522)
+. ++ |.+ +|+ .+.++|| |+|++|+++++.+ ..+++++.++.
T Consensus 58 ---l~---~~-------------------L~~-~Gv--------~~~~~fD-T~LAa~lL~~~~~----~~~~~l~~la~ 98 (553)
T PRK14975 58 ---LY---PR-------------------LLA-AGV--------RVERCHD-LMLASQLLLGSEG----RAGSSLSAAAA 98 (553)
T ss_pred ---hH---HH-------------------HHH-CCC--------ccCCCch-HHHHHHHcCCCCC----cCCCCHHHHHH
Confidence 11 11 334 344 1356899 9999999997510 11689999999
Q ss_pred HHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 009909 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 99999999988899996 99999999999999999999999999999876
No 23
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=99.19 E-value=1.2e-10 Score=126.76 Aligned_cols=171 Identities=17% Similarity=0.177 Sum_probs=125.4
Q ss_pred hHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCC-chhhHHHHH
Q 009909 19 SPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIP-LPSIWELLK 97 (522)
Q Consensus 19 ~~el~~ll~~l~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~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 4556666666665566999999988775 455677777652 2255565554311 112678899
Q ss_pred HhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCc
Q 009909 98 ELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS 177 (522)
Q Consensus 98 ~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 53 1 367899 99999999986 4579999999999998765
Q ss_pred ccccccCCCC-----CCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009909 178 KELQCSDWSN-----RPLT-EEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (522)
Q Consensus 178 K~~q~sdW~~-----RPL~-~~Qi~YAA~DA~~ll~L~~~L~~~L~~~g~l 222 (522)
..+...+-.. ..+. +.-..|+|.||.++++|+..|.+++.+...+
T Consensus 136 ~~~~i~~kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~l~~~~~L 186 (593)
T COG0749 136 TFEDIAGKGKKQLTFADVKLEKATEYAAEDADATLRLESILEPELLKTPVL 186 (593)
T ss_pred hhHHhhccccccCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhH
Confidence 4333222111 1122 4458999999999999999999988887764
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=99.08 E-value=4.3e-09 Score=121.64 Aligned_cols=172 Identities=13% Similarity=0.036 Sum_probs=115.3
Q ss_pred EEEEcCCChHHHHHHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCC-CEEEEEeCC---C
Q 009909 11 IHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNA-SVVFLLDLS---S 86 (522)
Q Consensus 11 i~~I~t~~~~el~~ll~~l~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~-~~v~liDl~---~ 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 12221 1233334445442 2 346666543 1
Q ss_pred CCchhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHH
Q 009909 87 IPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLAN 166 (522)
Q Consensus 87 l~~~~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~ 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 22234566799999999999999999999999986 455 2 2356899 99999999985 3469999
Q ss_pred HHHHHcCCcCcccccccCCC--CCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 009909 167 ICKELLDISLSKELQCSDWS--NRPLT-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 99999997754433322221 11343 445789999999999999999999987653
No 25
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=98.95 E-value=3.5e-09 Score=106.72 Aligned_cols=149 Identities=23% Similarity=0.254 Sum_probs=115.1
Q ss_pred CCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCceEEEEe
Q 009909 32 SSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFK 111 (522)
Q Consensus 32 ~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~l~~~~~~~~L~~lL~d~~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 4567777888877655556678999999995 4788888766543 367788889999999999999
Q ss_pred chhhHHHHHh-hcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcC-----CcCcccccccCC
Q 009909 112 FKQDLIYLSS-TFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLD-----ISLSKELQCSDW 185 (522)
Q Consensus 112 ~k~Dl~~L~~-~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 2566778766665555432 234566677776665 446778899999
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHH
Q 009909 186 SNRPLTEEQKNYAAIDAHCLIEIF 209 (522)
Q Consensus 186 ~~RPL~~~Qi~YAA~DA~~ll~L~ 209 (522)
+..||+.+|+.||+.|||+...++
T Consensus 258 ~~~~Ls~~Ql~~asidvy~c~~lg 281 (319)
T KOG4373|consen 258 SVYPLSDDQLLQASIDVYVCHKLG 281 (319)
T ss_pred eeeeccHHHHHHHHhHHHHHHHHH
Confidence 999999999999999999999999
No 26
>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=98.61 E-value=1.6e-06 Score=79.58 Aligned_cols=118 Identities=19% Similarity=0.189 Sum_probs=79.2
Q ss_pred EEEEEeCCCCCchhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCC
Q 009909 78 VVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKL 157 (522)
Q Consensus 78 ~v~liDl~~l~~~~~~~~L~~lL~d~~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 366775321 00 134588999999999999999999999976 455 2 2356799 99999999986
Q ss_pred CcCCccHHHHHHHHcCCcCcccccccCCCC--CCC-CHHHHHHHHHHHHHHHHHHHHHH
Q 009909 158 PKETKSLANICKELLDISLSKELQCSDWSN--RPL-TEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 158 ~~~~~sL~~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 -AGRHDMDSLAERWLKEKTITFEEIAGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred -CCCCCHHHHHHHHcCCCCccHHHHcCCCCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 33249999999999877321011111110 011 11223488888889999988874
No 27
>COG4634 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.59 E-value=2e-07 Score=79.59 Aligned_cols=73 Identities=21% Similarity=0.284 Sum_probs=60.5
Q ss_pred CEEEEecccH-HHHHHHHhcCCceecCCC---CCCChHHHHHhhhcCCcEEEecChhHHHhhcccC--CcEEEEcCCCH
Q 009909 357 PKFLCDVMVE-GLAKHLRCVGIDAATPRS---KKPEPRELIDQTSKEKRVLLTRDAKLLRHQYLIK--NQIYRVKSLLK 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 899999999999988765 3456889999999999999999999966543322 47899988653
No 28
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=97.27 E-value=0.0033 Score=58.63 Aligned_cols=86 Identities=20% Similarity=0.247 Sum_probs=56.9
Q ss_pred HHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcC
Q 009909 94 ELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLD 173 (522)
Q Consensus 94 ~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L~~~~Lg 173 (522)
+.|.+++.+.. +.||||+.+|+.+|... ...++|+..++..+. +.. ....+++|..|++.++|
T Consensus 75 ~~~~~~i~~~~-vlVgHn~~fD~~fL~~~------------~~~~iDT~~l~~~~~-~~~---~~~~~~~L~~L~~~~~~ 137 (161)
T cd06137 75 AALWKFIDPDT-ILVGHSLQNDLDALRMI------------HTRVVDTAILTREAV-KGP---LAKRQWSLRTLCRDFLG 137 (161)
T ss_pred HHHHHhcCCCc-EEEeccHHHHHHHHhCc------------CCCeeEehhhhhhcc-CCC---cCCCCccHHHHHHHHCC
Confidence 45666666533 46999999999999652 135789666655543 220 00147999999999999
Q ss_pred CcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009909 174 ISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (522)
Q Consensus 174 ~~l~K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~ 209 (522)
+++.......+ |..||.++.+||
T Consensus 138 ~~~~~~~~~H~-------------A~~DA~at~~l~ 160 (161)
T cd06137 138 LKIQGGGEGHD-------------SLEDALAAREVV 160 (161)
T ss_pred chhcCCCCCCC-------------cHHHHHHHHHHh
Confidence 87643112222 778999988876
No 29
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=96.99 E-value=0.025 Score=58.63 Aligned_cols=102 Identities=14% Similarity=0.130 Sum_probs=68.2
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 4566777777653 569999999999997654322321 1 124588944444443 332 247889999975
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 009909 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 -WGVPQQR---P-------------HDALDDARVLAGILRPSLERARERDV 184 (313)
T ss_pred -cCCCCCC---C-------------CCcHHHHHHHHHHHHHHHHHHHhcCC
Confidence 5765321 1 23889999999999999988877653
No 30
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=96.91 E-value=0.008 Score=55.86 Aligned_cols=89 Identities=17% Similarity=0.171 Sum_probs=57.3
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHH--HH-HhhccccCCCCCcCCccHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSI--YN-HLHHKQLGRKLPKETKSLANI 167 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~L--a~-yLl~~~~~~~~~~~~~sL~~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 35699999999999875321 2356783222 11 111221 246899999
Q ss_pred HHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009909 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 AKRLLHRDIQVGRQGHS-------------SVEDARATMELYK 157 (157)
T ss_pred HHHHcChhhcCCCCCcC-------------cHHHHHHHHHHhC
Confidence 99999876643222222 7789999988873
No 31
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=96.85 E-value=0.0097 Score=59.14 Aligned_cols=96 Identities=22% Similarity=0.211 Sum_probs=64.1
Q ss_pred hHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHH
Q 009909 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKEL 171 (522)
Q Consensus 92 ~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L~~~~ 171 (522)
+-..+.+||.+ -+-|||++.+|+..|.-.++- .-+-| |.-+.-|... .....+.||..|++.+
T Consensus 174 aQ~ev~klL~g--RIlVGHaLhnDl~~L~l~hp~----------s~iRD-Ts~~~pl~k~----~~~~~tpSLK~Lt~~~ 236 (280)
T KOG2249|consen 174 AQKEVLKLLKG--RILVGHALHNDLQALKLEHPR----------SMIRD-TSKYPPLMKL----LSKKATPSLKKLTEAL 236 (280)
T ss_pred HHHHHHHHHhC--CEEeccccccHHHHHhhhCch----------hhhcc-cccCchHHHH----hhccCCccHHHHHHHH
Confidence 34466778876 345999999999999755432 12336 3222111110 0013578999999999
Q ss_pred cCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 009909 172 LDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (522)
Q Consensus 172 Lg~~l~K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~~~ 219 (522)
||+.+--++..| .+||.++.+||.....+-++.
T Consensus 237 Lg~~IQ~GeHsS---------------vEDA~AtM~LY~~vk~qwe~~ 269 (280)
T KOG2249|consen 237 LGKDIQVGEHSS---------------VEDARATMELYKRVKVQWEKI 269 (280)
T ss_pred hchhhhccccCc---------------HHHHHHHHHHHHHHHHHHHHH
Confidence 999885555433 589999999999998776554
No 32
>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=96.67 E-value=0.01 Score=54.74 Aligned_cols=87 Identities=23% Similarity=0.339 Sum_probs=57.4
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 1235678 43322222211 0247999999999
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009909 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 LLGLDIQE--GE-------------HSSVEDARAAMRLYR 152 (152)
T ss_pred HcCcccCC--CC-------------cCcHHHHHHHHHHhC
Confidence 99987632 11 227899999998874
No 33
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=96.59 E-value=0.12 Score=51.29 Aligned_cols=89 Identities=16% Similarity=0.258 Sum_probs=56.6
Q ss_pred ceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcccccccC
Q 009909 105 ILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSD 184 (522)
Q Consensus 105 I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L~~~~Lg~~l~K~~q~sd 184 (522)
.+.|+||..+|+..|.+.+.-.|... + ...+++| +......+.+. ...+++|++|++. +|++....
T Consensus 94 ~~lVahNa~FD~~fL~~~~~r~~~~~-~-~~~~~iD-t~~l~~~~~~~-----~~~~~~L~~l~~~-~gi~~~~a----- 159 (232)
T PRK07942 94 VPVVVFNAPYDLTVLDRELRRHGLPS-L-VPGPVID-PYVIDKAVDRY-----RKGKRTLTALCEH-YGVRLDNA----- 159 (232)
T ss_pred CEEEEeCcHhhHHHHHHHHHHcCCCC-c-cCCcEee-HHHHHhhhhcc-----cCCCCCHHHHHHH-cCCCCCCC-----
Confidence 45599999999998866543222110 0 1246889 55444333221 0235789999977 57765321
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 009909 185 WSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ 218 (522)
Q Consensus 185 W~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~~ 218 (522)
+-|..||.++.+|+..|..+..+
T Consensus 160 -----------H~Al~Da~ata~l~~~l~~~~~~ 182 (232)
T PRK07942 160 -----------HEATADALAAARVAWALARRFPE 182 (232)
T ss_pred -----------CChHHHHHHHHHHHHHHHHHHHH
Confidence 22889999999999999876653
No 34
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=96.54 E-value=0.061 Score=53.94 Aligned_cols=150 Identities=19% Similarity=0.219 Sum_probs=85.4
Q ss_pred hcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCC-----------CCC---------
Q 009909 29 LSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLS-----------SIP--------- 88 (522)
Q Consensus 29 l~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~-----------~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 223477776531 00 0000 00112233321 111
Q ss_pred chhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCcc-CCCceeeHHHHHHHhhccccCCCCCcCCccHHHH
Q 009909 89 LPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFD-RVEPYLDITSIYNHLHHKQLGRKLPKETKSLANI 167 (522)
Q Consensus 89 ~~~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~-~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 569999999999987543222221 11 1146899444443 3221 236899999
Q ss_pred HHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 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~~~~~----------------aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 143 AVHF-NVPYDG----------------NHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred HHHC-CCCCCC----------------CcChHHHHHHHHHHHHHHHHhc
Confidence 8775 765422 1228899999999999987554
No 35
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=96.52 E-value=0.065 Score=55.54 Aligned_cols=97 Identities=12% Similarity=0.157 Sum_probs=64.9
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L~~~ 170 (522)
+++..|.+++.+. + -||||..+|+..|.+.+...|+. .....++|+..++..+.. . ...++|++|++.
T Consensus 77 evl~~f~~fl~~~-~-lVaHNa~FD~~fL~~~~~~~gl~---~~~~~~iDtl~la~~~~~-~------~~~~kL~~L~~~ 144 (313)
T PRK06807 77 EVLPLFLAFLHTN-V-IVAHNASFDMRFLKSNVNMLGLP---EPKNKVIDTVFLAKKYMK-H------APNHKLETLKRM 144 (313)
T ss_pred HHHHHHHHHHcCC-e-EEEEcHHHHHHHHHHHHHHcCCC---CCCCCEeeHHHHHHHHhC-C------CCCCCHHHHHHH
Confidence 3555666666654 3 49999999999998664333321 123568996666665543 2 236789999854
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 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-S----------------SHNAFDDCITCAAVYQKCASIEE 173 (313)
T ss_pred -cCCCC-C----------------CcChHHHHHHHHHHHHHHHHhhh
Confidence 67654 1 12388999999999999987653
No 36
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=96.51 E-value=0.12 Score=51.09 Aligned_cols=98 Identities=10% Similarity=0.070 Sum_probs=62.5
Q ss_pred hHHHHHHhhCCCCceEEEEe-chhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 92 IWELLKELFVSPDILKLGFK-FKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 92 ~~~~L~~lL~d~~I~KVgh~-~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L~~~ 170 (522)
+...+.+++.+. ..-|||| ...|+..|.+.+.-.|+.. ....++|+..++..+ .+. ...++|..+++.
T Consensus 69 v~~~~~~fi~~~-~~lVaHN~~~FD~~~L~~e~~r~g~~~---~~~~~iDt~~l~~~~-~~~------~~~~~L~~l~~~ 137 (232)
T PRK06309 69 AYQKFIEFCGTD-NILVAHNNDAFDFPLLRKECRRHGLEP---PTLRTIDSLKWAQKY-RPD------LPKHNLQYLRQV 137 (232)
T ss_pred HHHHHHHHHcCC-CEEEEeCCHHHHHHHHHHHHHHcCCCC---CCCcEEeHHHHHHHH-cCC------CCCCCHHHHHHH
Confidence 344556666543 4569999 4899999876543223221 124689955555443 232 236789999877
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (522)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~ 217 (522)
+ |++... .+-|..||.++.+|+..+..++.
T Consensus 138 ~-~~~~~~----------------aH~Al~Da~~t~~vl~~l~~~~~ 167 (232)
T PRK06309 138 Y-GFEENQ----------------AHRALDDVITLHRVFSALVGDLS 167 (232)
T ss_pred c-CCCCCC----------------CCCcHHHHHHHHHHHHHHHHHHH
Confidence 6 654321 12288999999999999987764
No 37
>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=96.41 E-value=0.073 Score=64.22 Aligned_cols=102 Identities=23% Similarity=0.408 Sum_probs=71.6
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 EVLEKFKEFFKD--SILVAHNASFDIGFLNTNFEKVGLEP---LENPVIDTLELARA-LNPE------YKSHRLGNICKK 326 (1213)
T ss_pred HHHHHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCc---cCCCEeEHHHHHHH-Hhcc------CCCCCHHHHHHH
Confidence 456677777765 35699999999999876432223221 23578995555544 4443 357899999987
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 009909 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 327 -lgi~~~~----------------~HrAl~DA~aTa~I~~~ll~~l~~~~i 360 (1213)
T TIGR01405 327 -LGVDLDD----------------HHRADYDAEATAKVFKVMVEQLKEKGI 360 (1213)
T ss_pred -cCCCCCC----------------CcCHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 4776532 244899999999999999999987754
No 38
>PRK07740 hypothetical protein; Provisional
Probab=96.38 E-value=0.15 Score=50.97 Aligned_cols=100 Identities=13% Similarity=0.180 Sum_probs=66.0
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhc-ccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTF-CSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~-gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 3445555566543 568999999999886532 11111 1236789955555444 332 24789999996
Q ss_pred HHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 009909 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKG 220 (522)
Q Consensus 170 ~~Lg~~l~K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~~~g 220 (522)
. +|++.... +-|..||.++.+|+..+..++.+.|
T Consensus 197 ~-~gi~~~~~----------------H~Al~Da~ata~l~~~ll~~~~~~~ 230 (244)
T PRK07740 197 Y-YGIPIPRR----------------HHALGDALMTAKLWAILLVEAQQRG 230 (244)
T ss_pred H-CCcCCCCC----------------CCcHHHHHHHHHHHHHHHHHHHHcC
Confidence 5 68765321 2278999999999999999987755
No 39
>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=96.36 E-value=0.0093 Score=56.35 Aligned_cols=81 Identities=19% Similarity=0.206 Sum_probs=54.6
Q ss_pred HHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCC
Q 009909 95 LLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDI 174 (522)
Q Consensus 95 ~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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-TVEL--FHLPG------QRKLSLRFLAWYLLGE 153 (174)
T ss_pred HHHHHc-CCCCEEEeccchhHHHHhcCcCC----------CcceEE-cHHh--ccCCC------CCChhHHHHHHHHcCC
Confidence 455555 44556799999999999965321 146789 5432 11221 2368999999999998
Q ss_pred cCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009909 175 SLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (522)
Q Consensus 175 ~l~K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~ 210 (522)
.+.... . -..+||.++++||+
T Consensus 154 ~IQ~~~--H-------------dSvEDArAam~Ly~ 174 (174)
T cd06143 154 KIQSET--H-------------DSIEDARTALKLYR 174 (174)
T ss_pred cccCCC--c-------------CcHHHHHHHHHHhC
Confidence 874321 1 14689999999983
No 40
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=96.34 E-value=0.2 Score=50.45 Aligned_cols=97 Identities=16% Similarity=0.194 Sum_probs=64.3
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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---LLNRKLCTIDLAKRTIE--------SPRYGLSFLKE- 201 (257)
T ss_pred HHHHHHHHHHCCC--eEEEECHHHHHHHHHHHHHHcCCCC---CCCCcEehHHHHHHHcc--------CCCCCHHHHHH-
Confidence 4566677777653 4699999999999865432222211 23557885556654432 24689999987
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (522)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~ 217 (522)
++|++... .+-|..||.++.+|+..+..++.
T Consensus 202 ~lgi~~~~----------------~HrAl~DA~ata~ll~~ll~~~~ 232 (257)
T PRK08517 202 LLGIEIEV----------------HHRAYADALAAYEIFKICLLNLP 232 (257)
T ss_pred HcCcCCCC----------------CCChHHHHHHHHHHHHHHHHHhH
Confidence 46766431 12288999999999999987764
No 41
>PRK05168 ribonuclease T; Provisional
Probab=96.33 E-value=0.25 Score=48.23 Aligned_cols=92 Identities=16% Similarity=0.200 Sum_probs=59.6
Q ss_pred CceEEEEechhhHHHHHhhcccCCCcc-CccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcccccc
Q 009909 104 DILKLGFKFKQDLIYLSSTFCSQGCDI-GFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQC 182 (522)
Q Consensus 104 ~I~KVgh~~k~Dl~~L~~~~gi~g~~~-~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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-AGIEFDNK-E- 179 (211)
T ss_pred CceEEEeccHHhHHHHHHHHHHhCCCCCCC-CCCcEeeHHHHHHHHc-C---------CCCHHHHHHH-CCCCCCCC-C-
Confidence 456799999999998875432222110 00 0124799656665442 2 3579999887 47664211 1
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 009909 183 SDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGN 221 (522)
Q Consensus 183 sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~~~g~ 221 (522)
.+-|..||.++.+|+..+..++.+.+.
T Consensus 180 ------------~H~Al~DA~ata~l~~~l~~~~~~~~~ 206 (211)
T PRK05168 180 ------------AHSALYDTEKTAELFCEIVNRWKRLGG 206 (211)
T ss_pred ------------CCChHHHHHHHHHHHHHHHHHHHHccC
Confidence 122889999999999999999887654
No 42
>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=96.30 E-value=0.014 Score=53.72 Aligned_cols=86 Identities=20% Similarity=0.260 Sum_probs=56.3
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 455667777753 3456999999999999652 13578944443332221 236899999999
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009909 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 12778999998886
No 43
>PRK07883 hypothetical protein; Validated
Probab=96.30 E-value=0.11 Score=57.95 Aligned_cols=156 Identities=12% Similarity=0.174 Sum_probs=95.3
Q ss_pred HHHHHhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCE-----EEEEeCC-----------CC
Q 009909 24 HLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASV-----VFLLDLS-----------SI 87 (522)
Q Consensus 24 ~ll~~l~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~-----v~liDl~-----------~l 87 (522)
++-..+.....|.||+|+++..+ ..-.+++|+.-. .. ++. ..++... .+
T Consensus 7 ~~~~~~~~~~~Vv~D~ETTGl~p-----~~~~IIEIgaV~--------v~--~g~iv~~f~~lV~P~~~i~~~~~~itGI 71 (557)
T PRK07883 7 DLGTPLRDVTFVVVDLETTGGSP-----AGDAITEIGAVK--------VR--GGEVLGEFATLVNPGRPIPPFITVLTGI 71 (557)
T ss_pred hhCCCCcCCCEEEEEEecCCCCC-----CCCeEEEEEEEE--------EE--CCEEEEEEEEEECCCCCCChhHHhhcCC
Confidence 33344566789999999998764 223566666521 00 111 1223221 11
Q ss_pred C---------chhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCC
Q 009909 88 P---------LPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLP 158 (522)
Q Consensus 88 ~---------~~~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~ 158 (522)
. ..+++..|..++.+ .+.||||..+|+..|...+.-.|+. + .....+|+..++..+..+. .
T Consensus 72 t~e~l~~ap~~~evl~~f~~fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~--~-~~~~~iDTl~lar~l~~~~-----~ 141 (557)
T PRK07883 72 TTAMVAGAPPIEEVLPAFLEFARG--AVLVAHNAPFDIGFLRAAAARCGYP--W-PGPPVLCTVRLARRVLPRD-----E 141 (557)
T ss_pred CHHHHhCCCCHHHHHHHHHHHhcC--CEEEEeCcHHHHHHHHHHHHHcCCC--C-CCCCcEecHHHHHHhcccC-----C
Confidence 1 12345566677765 4568999999999987654332321 1 1245789656666554321 1
Q ss_pred cCCccHHHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 009909 159 KETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGN 221 (522)
Q Consensus 159 ~~~~sL~~L~~~~Lg~~l~K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~~~g~ 221 (522)
..+++|++|++ ++|++... .+-|..||.++.+|+..+..++.+.+.
T Consensus 142 ~~~~~L~~L~~-~~gi~~~~----------------~H~Al~DA~ata~l~~~l~~~~~~~~~ 187 (557)
T PRK07883 142 APNVRLSTLAR-LFGATTTP----------------THRALDDARATVDVLHGLIERLGNLGV 187 (557)
T ss_pred CCCCCHHHHHH-HCCcccCC----------------CCCHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 24789999987 56876521 123899999999999999999876554
No 44
>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=96.28 E-value=0.15 Score=47.30 Aligned_cols=97 Identities=16% Similarity=0.180 Sum_probs=58.5
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L~~~ 170 (522)
++...|.+++.+. ..||||..+|+..|.+.+...+....+.....++|+..++..+ .+. ..++|+++++.
T Consensus 70 ~v~~~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~-~~~-------~~~~L~~l~~~ 139 (167)
T cd06131 70 EIADEFLDFIRGA--ELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKK-FPG-------KPNSLDALCKR 139 (167)
T ss_pred HHHHHHHHHHCCC--eEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHH-cCC-------CCCCHHHHHHH
Confidence 3456667777663 3489999999998865432212111011124678943344433 332 35799999988
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009909 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (522)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L 212 (522)
+ |++.... +.+-|..||.++.+|+..|
T Consensus 140 ~-~i~~~~~--------------~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 140 F-GIDNSHR--------------TLHGALLDAELLAEVYLEL 166 (167)
T ss_pred C-CCCCCCC--------------CCCChHHHHHHHHHHHHHh
Confidence 5 6543211 1233889999999998765
No 45
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=96.12 E-value=0.24 Score=45.52 Aligned_cols=98 Identities=17% Similarity=0.207 Sum_probs=62.9
Q ss_pred hhHHHHHHhhCCCCceEEEEec-hhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKF-KQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~-k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L~~ 169 (522)
++...|..++.+. ..|+||. ++|+..|...+...++. +......+|+..++..+ .+. .+.+|+++++
T Consensus 69 ~~~~~~~~~l~~~--~~v~~n~~~fD~~~L~~~~~~~~~~--~~~~~~~iD~~~~~~~~-~~~-------~~~~L~~l~~ 136 (169)
T smart00479 69 EVLEELLEFLKGK--ILVAGNALNFDLRFLKLEHPRLGIK--DPPKNPVIDTLKLARAL-NPG-------RKYSLKKLAE 136 (169)
T ss_pred HHHHHHHHHhcCC--EEEEeCCHHHhHHHHHHHHHHhCCC--CCcCCCeeEHHHHHHHH-CCC-------CCCCHHHHHH
Confidence 4566777788664 3467777 99999987654332321 11124479954444433 332 3789999998
Q ss_pred HHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 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 4433110 2458999999999999998664
No 46
>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=96.08 E-value=0.035 Score=47.19 Aligned_cols=82 Identities=17% Similarity=0.203 Sum_probs=54.9
Q ss_pred EEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCC-ceEEEEech
Q 009909 35 VGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPD-ILKLGFKFK 113 (522)
Q Consensus 35 Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~l~~~~~~~~L~~lL~d~~-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 479999988765 67889999988741 24567665 556777665 678999999
Q ss_pred hhHHHHHhhcccCCCccCccCCCceeeHHHHH
Q 009909 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 999888765433232110 02356889 5543
No 47
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=95.98 E-value=0.3 Score=47.08 Aligned_cols=98 Identities=17% Similarity=0.191 Sum_probs=59.7
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhccc-CCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCS-QGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi-~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 4556677777653 46999999999998754310 111 1235678965554322211100 0123689999996
Q ss_pred HHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009909 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 H-LDLPVLG---RH-------------DALNDAIMAALIFLRLR 198 (202)
T ss_pred H-cCCCCCC---CC-------------CcHHHHHHHHHHHHHHH
Confidence 6 4765421 12 28899999999998875
No 48
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=95.96 E-value=0.25 Score=49.34 Aligned_cols=99 Identities=16% Similarity=0.191 Sum_probs=60.5
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCc-cCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCD-IGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~-~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 EVADEFLDFIRGA--ELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRM-FPG-------KRNSLDALCK 144 (240)
T ss_pred HHHHHHHHHhCCC--EEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHH-cCC-------CCCCHHHHHH
Confidence 3455666676653 358999999999887543222210 0011124589944455444 343 3579999998
Q ss_pred HHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (522)
Q Consensus 170 ~~Lg~~l~K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~ 214 (522)
+| |++.... + .+-|..||.++.+||..|..
T Consensus 145 ~~-gi~~~~r-~-------------~H~AL~DA~~~A~v~~~l~~ 174 (240)
T PRK05711 145 RY-GIDNSHR-T-------------LHGALLDAEILAEVYLAMTG 174 (240)
T ss_pred HC-CCCCCCC-C-------------CCCHHHHHHHHHHHHHHHHC
Confidence 75 6542111 1 12388999999999988863
No 49
>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=95.95 E-value=0.19 Score=48.27 Aligned_cols=160 Identities=16% Similarity=0.210 Sum_probs=89.4
Q ss_pred CeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-------CCchhhHHHHHHhhCC--C
Q 009909 33 SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-------IPLPSIWELLKELFVS--P 103 (522)
Q Consensus 33 ~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~-------l~~~~~~~~L~~lL~d--~ 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----------EGGNKVITWKKFDLPFVEVVKTEKEMIKRFIEIVKEKDP 72 (195)
T ss_pred eEEEEEEEecCCCCC-CCCCCCcEEEEEEec----------CCCceEEEecCCCCCeEEEeCCHHHHHHHHHHHHHHcCC
Confidence 578999999743210 012334467777642 0123333221110 1113455555555554 7
Q ss_pred CceEEEEech-hhHHHHHhhcccCCCccCccC-------------------CCceeeHHHHHHHhhccccCCCCCcCCcc
Q 009909 104 DILKLGFKFK-QDLIYLSSTFCSQGCDIGFDR-------------------VEPYLDITSIYNHLHHKQLGRKLPKETKS 163 (522)
Q Consensus 104 ~I~KVgh~~k-~Dl~~L~~~~gi~g~~~~~~~-------------------~~~~~Dlt~La~yLl~~~~~~~~~~~~~s 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 5899976 699887544322333211100 0237785544443221 35899
Q ss_pred HHHHHHHHcCCcCcc--cccccC-CCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009909 164 LANICKELLDISLSK--ELQCSD-WSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (522)
Q Consensus 164 L~~L~~~~Lg~~l~K--~~q~sd-W~~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 999999999976421 123332 4444334666899999999999997653
No 50
>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=95.81 E-value=0.2 Score=48.94 Aligned_cols=105 Identities=17% Similarity=0.186 Sum_probs=64.8
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L~~~ 170 (522)
+++..|..++.+ -..||||+.+|+.+|.+.+.-.+.. ......++|+..++.++. +. .+..+++|..+++.
T Consensus 76 ev~~~~~~~~~~--~~lVaHNa~FD~~fL~~~~~r~~~~--~~~~~~~~dtl~l~~~~~-~~----~~~~~~~L~~l~~~ 146 (217)
T TIGR00573 76 EIAEDFADYIRG--AELVIHNASFDVGFLNYEFSKLYKV--EPKTNDVIDTTDTLQYAR-PE----FPGKRNTLDALCKR 146 (217)
T ss_pred HHHHHHHHHhCC--CEEEEeccHHHHHHHHHHHHHhcCC--CCCccceecHHHHHHHHH-Hh----CCCCCCCHHHHHHH
Confidence 355666677765 3458999999999998764311110 011245788544555443 21 11245789999877
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 009909 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 1228899999999999998765543
No 51
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=95.78 E-value=0.41 Score=47.67 Aligned_cols=102 Identities=18% Similarity=0.131 Sum_probs=62.2
Q ss_pred hHHHHHHhhCCCCceEEEEechhhHHHHHhhccc-CCCccCccCCCceeeHHHHHHHhhccccCC------CCCcCCccH
Q 009909 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTFCS-QGCDIGFDRVEPYLDITSIYNHLHHKQLGR------KLPKETKSL 164 (522)
Q Consensus 92 ~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi-~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~------~~~~~~~sL 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 44555555554 356899999999998664211 010 11356899666666654321000 001146789
Q ss_pred HHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 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 46553211 228899999999998887665
No 52
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=95.63 E-value=0.45 Score=43.30 Aligned_cols=89 Identities=19% Similarity=0.227 Sum_probs=57.9
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L~~~ 170 (522)
++++.|.+++.+ ...||||+..|+..|...+...|.. + .....+|+..+++.+. +. ..+.+|+.+++.
T Consensus 66 ~v~~~l~~~l~~--~~lv~hn~~fD~~~l~~~~~~~g~~--~-~~~~~idt~~~~~~~~-~~------~~~~~L~~l~~~ 133 (156)
T cd06130 66 EVWPEIKPFLGG--SLVVAHNASFDRSVLRAALEAYGLP--P-PPYQYLCTVRLARRVW-PL------LPNHKLNTVAEH 133 (156)
T ss_pred HHHHHHHHHhCC--CEEEEeChHHhHHHHHHHHHHcCCC--C-CCCCEEEHHHHHHHHh-cc------CCCCCHHHHHHH
Confidence 456677788876 3569999999999986543322322 1 2356889444554443 22 246899999986
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009909 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 576553 1 22778999888876
No 53
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=95.63 E-value=0.056 Score=63.38 Aligned_cols=151 Identities=18% Similarity=0.346 Sum_probs=99.8
Q ss_pred HhcCCCeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEE-----EEEeC-----------CCCC---
Q 009909 28 ALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVV-----FLLDL-----------SSIP--- 88 (522)
Q Consensus 28 ~l~~~~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v-----~liDl-----------~~l~--- 88 (522)
.|..+..|.||.|+++..+ ... .+||+|... -. .+++ +++++ ..+.
T Consensus 417 ~l~datyVVfDiETTGLs~---~~d--~iIE~aAvK--ik--------ng~iId~f~~Fi~P~~pl~~~~telTgITdem 481 (1444)
T COG2176 417 KLDDATYVVFDIETTGLSP---VYD--EIIEIAAVK--IK--------NGRIIDKFQFFIKPGRPLSATITELTGITDEM 481 (1444)
T ss_pred ccccccEEEEEeecCCcCc---ccc--hhhhheeee--ee--------CCcchHHHHHhcCCCCcCchhhhhccccCHHH
Confidence 3556789999999998876 233 377776531 00 1111 11111 1111
Q ss_pred ------chhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCc
Q 009909 89 ------LPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETK 162 (522)
Q Consensus 89 ------~~~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~ 162 (522)
..+++..+++++.+ -+-|.||+.+|+-.|...|--.++.+ .-++++|+.++ +..++|. -.+|
T Consensus 482 l~~a~~i~~vL~kf~~~~~d--~IlVAHNasFD~gFl~~~~~k~~~~~---~~~pvIDTL~l-ar~L~P~------~ksh 549 (1444)
T COG2176 482 LENAPEIEEVLEKFREFIGD--SILVAHNASFDMGFLNTNYEKYGLEP---LTNPVIDTLEL-ARALNPE------FKSH 549 (1444)
T ss_pred HcCCccHHHHHHHHHHHhcC--cEEEeccCccchhHHHHHHHHhCCcc---ccCchhhHHHH-HHHhChh------hhhc
Confidence 13567788888887 35699999999999865543223221 34789995555 4555564 3589
Q ss_pred cHHHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009909 163 SLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (522)
Q Consensus 163 sL~~L~~~~Lg~~l~K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~~~g~l 222 (522)
+|..||.++ |+.+ ++.+-|--||.++-.++-.+.+.+++.|..
T Consensus 550 ~Lg~l~kk~-~v~l----------------e~hHRA~yDaeat~~vf~~f~~~~ke~Gi~ 592 (1444)
T COG2176 550 RLGTLCKKL-GVEL----------------ERHHRADYDAEATAKVFFVFLKDLKEKGIT 592 (1444)
T ss_pred chHHHHHHh-CccH----------------HHhhhhhhhHHHHHHHHHHHHHHHHHhchh
Confidence 999999886 4332 556668899999999999999999998764
No 54
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=95.47 E-value=0.25 Score=58.59 Aligned_cols=99 Identities=20% Similarity=0.232 Sum_probs=65.4
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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---IHCPKLDTVELARIL-LPT------AESYKLRDLSEE 140 (928)
T ss_pred HHHHHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCC---CCCCeeeHHHHHHHh-cCC------CCCCCHHHHHHh
Confidence 455667777765 45699999999999976543223221 235789955555544 343 347899999987
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 009909 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 -LGLEHDQP----------------HRADSDAEVTAELFLQLLNKLER 171 (928)
T ss_pred -CCCCCCCC----------------CChHHHHHHHHHHHHHHHHHHHh
Confidence 57654311 22778888888888888777764
No 55
>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=95.44 E-value=0.44 Score=42.66 Aligned_cols=91 Identities=18% Similarity=0.204 Sum_probs=58.1
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 456677778876 5679999999999987654322210 1235689955565555432 245778877555
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009909 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 RYGIPLE---G-------------AHRALADALATAELL 158 (159)
T ss_pred HcCCCCC---C-------------CCCcHHHHHHHHHHh
Confidence 5664321 1 233889999998876
No 56
>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=95.36 E-value=0.36 Score=46.13 Aligned_cols=110 Identities=22% Similarity=0.282 Sum_probs=64.5
Q ss_pred hhHHHHHHhhCC--CCceEEEEec-hhhHHHHHhhcccCCCcc--CccC-----------------CCceeeHHHHHHHh
Q 009909 91 SIWELLKELFVS--PDILKLGFKF-KQDLIYLSSTFCSQGCDI--GFDR-----------------VEPYLDITSIYNHL 148 (522)
Q Consensus 91 ~~~~~L~~lL~d--~~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 355555555554 555 589999 789988854333233321 0000 12367854444433
Q ss_pred hccccCCCCCcCCccHHHHHHHHcCCcCcc--cccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009909 149 HHKQLGRKLPKETKSLANICKELLDISLSK--ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (522)
Q Consensus 149 l~~~~~~~~~~~~~sL~~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 21 35799999999999864321 2233332111123556899999999999886
No 57
>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=95.19 E-value=0.56 Score=55.20 Aligned_cols=99 Identities=15% Similarity=0.249 Sum_probs=65.4
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L~~~ 170 (522)
++...|.+++.+ -..||||+.+|+..|.+.+.-.|..+ .....+|+..++..+. +. ..+++|.+|++.
T Consensus 69 ev~~~l~~~l~~--~~~VahN~~fD~~fL~~~~~~~g~~~---~~~~~iDt~~l~~~~~-p~------~~~~~L~~l~~~ 136 (850)
T TIGR01407 69 QVAQEIYDLLED--GIFVAHNVHFDLNFLAKALKDCGYEP---LPKPRIDTVELAQIFF-PT------EESYQLSELSEA 136 (850)
T ss_pred HHHHHHHHHhCC--CEEEEeCcHHHHHHHHHHHHHcCCCC---CCCCeEeHHHHHHHhc-CC------CCCCCHHHHHHH
Confidence 355667777765 34699999999999876432223211 2357899555555443 32 347899999887
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 009909 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 57665321 22778888888888888777654
No 58
>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=93.94 E-value=0.67 Score=44.78 Aligned_cols=93 Identities=15% Similarity=0.138 Sum_probs=59.7
Q ss_pred CceEEEEechhhHHHHHhhcccCCCccCcc-CCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcccccc
Q 009909 104 DILKLGFKFKQDLIYLSSTFCSQGCDIGFD-RVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQC 182 (522)
Q Consensus 104 ~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~-~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 345799999999999875431112100 00 013479955555443 22 35799999864 65531
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009909 183 SDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (522)
Q Consensus 183 sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~~~g~l 222 (522)
..+.+-|..||.++.+|+..+..++.+.+.+
T Consensus 168 ---------~~~~H~Al~Da~ata~lf~~l~~~~~~~~~~ 198 (200)
T TIGR01298 168 ---------STQAHSALYDTEKTAELFCEIVNRWKRLGGW 198 (200)
T ss_pred ---------ccchhhhHHhHHHHHHHHHHHHHHHHHccCC
Confidence 1123458899999999999999998877653
No 59
>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=93.65 E-value=1.7 Score=41.62 Aligned_cols=158 Identities=15% Similarity=0.195 Sum_probs=82.1
Q ss_pred CeEEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhC--CCCceEEEE
Q 009909 33 SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFV--SPDILKLGF 110 (522)
Q Consensus 33 ~~Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~l~~~~~~~~L~~lL~--d~~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---------S--NGDVEFILAEGLDDRKIIREFVKYVKEYDPDI-IVGY 70 (188)
T ss_pred eEEEEEEEecCCCC-CCCCCCCCEEEEEEEe---------C--CCCEEEEEecCCCHHHHHHHHHHHHHHcCCCE-EEec
Confidence 57899999973221 0012233466666541 0 12223332111223345555555555 4564 4799
Q ss_pred ech-hhHHHHHhhcccCCCccCccCCC-----------------ceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHc
Q 009909 111 KFK-QDLIYLSSTFCSQGCDIGFDRVE-----------------PYLDITSIYNHLHHKQLGRKLPKETKSLANICKELL 172 (522)
Q Consensus 111 ~~k-~Dl~~L~~~~gi~g~~~~~~~~~-----------------~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 NSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIP--------EVKVKTLENVAE-YL 141 (188)
T ss_pred CCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhC--------CCCCCCHHHHHH-HH
Confidence 955 88877643322223221110001 1678544333222 135799999997 58
Q ss_pred CCc--Ccc----ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009909 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 11222 24332134677899999999999998753
No 60
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=93.47 E-value=0.64 Score=45.84 Aligned_cols=99 Identities=16% Similarity=0.177 Sum_probs=61.6
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCc-cCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCD-IGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~-~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 EIADEFLDFIGGS--ELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARER-FPG-------QRNSLDALCK 140 (225)
T ss_pred HHHHHHHHHhCCC--EEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHH-cCC-------CCCCHHHHHH
Confidence 4556666777653 348999999999987543222210 0011125689944444443 343 4679999998
Q ss_pred HHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (522)
Q Consensus 170 ~~Lg~~l~K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~ 214 (522)
+| |++.... + .+-|..||.++.+||..|..
T Consensus 141 ~~-gi~~~~r-~-------------~H~Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 141 RF-KVDNSHR-T-------------LHGALLDAHLLAEVYLALTG 170 (225)
T ss_pred hc-CCCCCCC-C-------------CcCHHHHHHHHHHHHHHHHc
Confidence 85 6543211 1 12388999999999988863
No 61
>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=93.26 E-value=0.88 Score=43.50 Aligned_cols=84 Identities=17% Similarity=0.202 Sum_probs=53.1
Q ss_pred ceEEEEechhhHHHHHhhcccCCC-ccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCccccccc
Q 009909 105 ILKLGFKFKQDLIYLSSTFCSQGC-DIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCS 183 (522)
Q Consensus 105 I~KVgh~~k~Dl~~L~~~~gi~g~-~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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-AGIEFDNK-E-- 167 (189)
T ss_pred CeEEEecchhhHHHHHHHHHHhCCCCCCC-CCCcEEEHHHHHHHHh-C---------CCcHHHHHHH-CCCCCCCC-C--
Confidence 467999999999998754322222 0000 1234799666665543 2 3579999886 47654211 1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 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 62
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=93.00 E-value=0.72 Score=54.02 Aligned_cols=100 Identities=20% Similarity=0.266 Sum_probs=67.4
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L~~~ 170 (522)
++...+.+++.+ -+.||||+..|+..|.+.+...|. ....+.+|+..++.. +.+. ..+++|.+|++.
T Consensus 75 ev~~~~~~~l~~--~~lVaHN~~FD~~fL~~~~~~~g~----~~~~~~iDT~~la~~-~~p~------~~~~~L~~L~~~ 141 (820)
T PRK07246 75 QVARHIYDLIED--CIFVAHNVKFDANLLAEALFLEGY----ELRTPRVDTVELAQV-FFPT------LEKYSLSHLSRE 141 (820)
T ss_pred HHHHHHHHHhCC--CEEEEECcHHHHHHHHHHHHHcCC----CCCCCceeHHHHHHH-HhCC------CCCCCHHHHHHH
Confidence 455667777775 356999999999999764321121 123567894444444 4443 247899999976
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 009909 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 142 -lgl~~~~~----------------H~Al~DA~ata~L~~~l~~~l~~l~ 174 (820)
T PRK07246 142 -LNIDLADA----------------HTAIADARATAELFLKLLQKIESLP 174 (820)
T ss_pred -cCCCCCCC----------------CCHHHHHHHHHHHHHHHHHHHhhcC
Confidence 68764311 2288999999999999988876543
No 63
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=92.88 E-value=1.7 Score=53.73 Aligned_cols=103 Identities=16% Similarity=0.246 Sum_probs=69.3
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 344555555544 56799999999988754433233221 2356789 44444444443 357899999986
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 009909 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (522)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~~~g~l 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 57665321 348899999999999999999876554
No 64
>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=91.67 E-value=5.2 Score=38.52 Aligned_cols=110 Identities=23% Similarity=0.267 Sum_probs=61.3
Q ss_pred hhHHHHHHhhC--CCCceEEEEechh-hHHHHHhhcccCCCccCccC--------------------C-CceeeHHHHHH
Q 009909 91 SIWELLKELFV--SPDILKLGFKFKQ-DLIYLSSTFCSQGCDIGFDR--------------------V-EPYLDITSIYN 146 (522)
Q Consensus 91 ~~~~~L~~lL~--d~~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 34444444444 4565 48999885 88877533322333221110 0 11677433332
Q ss_pred HhhccccCCCCCcCCccHHHHHHHHcCCcCcc-c-----cccc-CCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009909 147 HLHHKQLGRKLPKETKSLANICKELLDISLSK-E-----LQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (522)
Q Consensus 147 yLl~~~~~~~~~~~~~sL~~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 1 1222 244333 4568999999999999863
No 65
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=91.59 E-value=4.1 Score=43.12 Aligned_cols=109 Identities=7% Similarity=0.008 Sum_probs=61.4
Q ss_pred hhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCc------------------------cCccCCCceeeHHHHH
Q 009909 90 PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCD------------------------IGFDRVEPYLDITSIY 145 (522)
Q Consensus 90 ~~~~~~L~~lL~d~~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 35677788888753 469999999999886542110000 0011224689955555
Q ss_pred HHhhccccCCCCCcCCccHHHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009909 146 NHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (522)
Q Consensus 146 ~yLl~~~~~~~~~~~~~sL~~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 33 357999999987 577653210 000 0000111111 225888888888776
No 66
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=91.29 E-value=1.8 Score=44.79 Aligned_cols=98 Identities=16% Similarity=0.193 Sum_probs=64.3
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L~~~ 170 (522)
++++.|.+++.+ -+-|+||+.+|+..|.+.+.-.+.. + ....++|+..++..+. +. ..+++|..|++.
T Consensus 69 ev~~~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~--~-~~~~~idT~~lar~l~-~~------~~~~~L~~L~~~ 136 (309)
T PRK06195 69 KIWEKIKHYFNN--NLVIAHNASFDISVLRKTLELYNIP--M-PSFEYICTMKLAKNFY-SN------IDNARLNTVNNF 136 (309)
T ss_pred HHHHHHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCC--C-CCCCEEEHHHHHHHHc-CC------CCcCCHHHHHHH
Confidence 456677777764 3569999999999986543221211 1 1246889545666554 32 246899999987
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 009909 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~~~~~~ 166 (309)
T PRK06195 137 L-GYEF----K-------------HHDALADAMACSNILLNISKELNS 166 (309)
T ss_pred c-CCCC----c-------------ccCCHHHHHHHHHHHHHHHHHhcc
Confidence 5 6542 1 133889999999999888877643
No 67
>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=90.95 E-value=2.9 Score=41.17 Aligned_cols=54 Identities=17% Similarity=0.177 Sum_probs=39.0
Q ss_pred CCccHHHHHHHHcCCcCcc--cccccC-CCCCCCC-HHHHHHHHHHHHHHHHHHHHHH
Q 009909 160 ETKSLANICKELLDISLSK--ELQCSD-WSNRPLT-EEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 160 ~~~sL~~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 223333 4333322 4568999999999999999886
No 68
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=90.58 E-value=0.026 Score=58.70 Aligned_cols=130 Identities=21% Similarity=0.269 Sum_probs=88.1
Q ss_pred CCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCcc
Q 009909 51 FPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDI 130 (522)
Q Consensus 51 ~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~l~~~~~~~~L~~lL~d~~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 468899999884 6789999877765566778999999999999999999999999888877
Q ss_pred CccCCCceeeHHHHHHHhhcc-ccCCCCCcCCccHH-HHHHHHcCCcC------cc-----cccccCCCCCCCCHHHHHH
Q 009909 131 GFDRVEPYLDITSIYNHLHHK-QLGRKLPKETKSLA-NICKELLDISL------SK-----ELQCSDWSNRPLTEEQKNY 197 (522)
Q Consensus 131 ~~~~~~~~~Dlt~La~yLl~~-~~~~~~~~~~~sL~-~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 3589999 8887666542 12222332222232 2332 332222 12 1234458889988887666
Q ss_pred HHHHHHH
Q 009909 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 69
>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=89.87 E-value=14 Score=35.82 Aligned_cols=161 Identities=16% Similarity=0.120 Sum_probs=84.5
Q ss_pred CeEEEEEeEeCCC----CCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-----------------CCchh
Q 009909 33 SLVGLDAEWKPQR----SHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-----------------IPLPS 91 (522)
Q Consensus 33 ~~Vg~D~E~~~~~----~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~-----------------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 5799999987422 21 1122236889888520 0123455553100 11234
Q ss_pred hHHHHHHhhCCCCceEEEEech-hhHHHHHhhcccCCCc-----cCcc------CCCceeeHHHHHHH-hhc-cccCCCC
Q 009909 92 IWELLKELFVSPDILKLGFKFK-QDLIYLSSTFCSQGCD-----IGFD------RVEPYLDITSIYNH-LHH-KQLGRKL 157 (522)
Q Consensus 92 ~~~~L~~lL~d~~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 5666666666664 56799876 7888875433223332 0000 01336775333221 100 0000 0
Q ss_pred CcCCccHHHHHHHHcCCcC-cccccccCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009909 158 PKETKSLANICKELLDISL-SKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (522)
Q Consensus 158 ~~~~~sL~~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 KYREYTLDAVAKALLGEGKVELEKNI--SEL--NLYELAEYNYRDAELTLELTT 202 (204)
T ss_pred ccccCcHHHHHHHhcCCCcccCCchh--hhh--cHHHHHHhhHHHHHHHHHHhc
Confidence 1258899999999999632 111111 211 114558999999999998864
No 70
>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=89.77 E-value=0.82 Score=47.38 Aligned_cols=101 Identities=12% Similarity=0.208 Sum_probs=58.5
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecChhHHHhhcccCCcEEEEcCCCHHHHHHHHHHhcCcCcccC
Q 009909 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQLLEVIEAFQLKISED 447 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~RiiLTrd~~l~~~~~~~~~~~~~v~~~~~~~QL~~v~~~f~l~~~~~ 447 (522)
++|+||+.|++|.++.+.+.-+..+...|+++|. | -+++.. ...+...+.++.+|+..+
T Consensus 29 ~~R~~r~~G~~V~~~~g~Dd~g~~i~~~a~~~g~---~-~~e~~~---------------~~~~~~~~~l~~LgI~~D-- 87 (319)
T cd00814 29 FARYQRLRGYDVLFVTGTDEHGTKIEQKAEEEGV---T-PQELCD---------------KYHEIFKDLFKWLNISFD-- 87 (319)
T ss_pred HHHHHHhCCCcccccCccCCCCcHHHHHHHHcCC---C-HHHHHH---------------HHHHHHHHHHHHcCCcCC--
Confidence 7999999999999887644334568888877663 1 111211 123566777888887643
Q ss_pred cCCCcccC--CCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009909 448 QLMSRCTK--CNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 448 ~~~sRC~~--CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvY 501 (522)
.|.|-.. .+.. ..++.++... -..+++...+-+.|+.|+..+
T Consensus 88 -~~~~tt~~~~~~~-------v~~i~~~L~e----kG~iY~~~~~~~yc~~~~~~l 131 (319)
T cd00814 88 -YFIRTTSPRHKEI-------VQEFFKKLYE----NGYIYEGEYEGLYCVSCERFL 131 (319)
T ss_pred -CCeeCCCHHHHHH-------HHHHHHHHHH----CCCEEeeeeeeeECCCCCcEe
Confidence 2444211 0000 1122221111 124566778899999999765
No 71
>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=89.68 E-value=5.7 Score=38.60 Aligned_cols=159 Identities=16% Similarity=0.186 Sum_probs=80.5
Q ss_pred CCeEEEEEeEeCCCCCC---CCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhC--CCCce
Q 009909 32 SSLVGLDAEWKPQRSHQ---SNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFV--SPDIL 106 (522)
Q Consensus 32 ~~~Vg~D~E~~~~~~~~---~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~l~~~~~~~~L~~lL~--d~~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 36899999986533110 122345688888752 0 11111222111222345555555544 4664
Q ss_pred EEEEec-hhhHHHHHhhcccCCCccCccC--------------------------C-CceeeHHHHHHHhhccccCCCCC
Q 009909 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 6899887533222333211100 0 12368433222110000 0 1
Q ss_pred cCCccHHHHHHHHcCCcCc-c----ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009909 159 KETKSLANICKELLDISLS-K----ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIF 209 (522)
Q Consensus 159 ~~~~sL~~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 LPSYGLKAVAKHF-GLASPDRTYIDGRQIAEVWRSDP--ARLLAYALDDVRETEGLA 206 (207)
T ss_pred CCCCCHHHHHHHh-cccCCCcCCCCHHHHHHHHhcCH--HHHHHHHHHHHHHHHHhh
Confidence 2478999999986 33211 1 11222 254332 566899999999998875
No 72
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=88.64 E-value=0.33 Score=33.38 Aligned_cols=31 Identities=26% Similarity=0.732 Sum_probs=16.7
Q ss_pred ccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEe
Q 009909 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 2567889999999854
No 73
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=88.58 E-value=0.12 Score=53.80 Aligned_cols=126 Identities=22% Similarity=0.224 Sum_probs=76.6
Q ss_pred CEEEEEeCCCCCchhhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccc-CC
Q 009909 77 SVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQL-GR 155 (522)
Q Consensus 77 ~~v~liDl~~l~~~~~~~~L~~lL~d~~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 67888886543221122334556666544 33 999999999888765 3589999 999999987652 33
Q ss_pred CCCcCC-ccHHHHHH--HHcCCcC------cc-ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 156 KLPKET-KSLANICK--ELLDISL------SK-ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (522)
Q Consensus 156 ~~~~~~-~sL~~L~~--~~Lg~~l------~K-~~q~s-dW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~ 214 (522)
..|... .+...|-. .|.+... .+ -.++- +|..||.++...+-++.|+++|+.....|.+
T Consensus 290 r~p~~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll~~~~~l~a 359 (458)
T KOG2405|consen 290 RHPTSILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLLGIFDTLVA 359 (458)
T ss_pred cCCccceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHHHHHHHHHHHHhhHhh
Confidence 322110 01111100 0111111 11 11233 7999999999999999999999997766653
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=88.36 E-value=2.1 Score=40.47 Aligned_cols=89 Identities=18% Similarity=0.154 Sum_probs=54.4
Q ss_pred hHHHHHHhhCC--CCceEEEEec-hhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHH
Q 009909 92 IWELLKELFVS--PDILKLGFKF-KQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANIC 168 (522)
Q Consensus 92 ~~~~L~~lL~d--~~I~KVgh~~-k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L~ 168 (522)
+.+.|..++.. ...+-||||. ..|+..|.+.+.-.|.. +.....++|...++..+ . . +|++|+
T Consensus 84 ~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~--~~~~~~~iDtl~l~r~~-~----------~-~L~~l~ 149 (177)
T cd06136 84 TANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTK--LPDDILCVDSLPAFREL-D----------Q-SLGSLY 149 (177)
T ss_pred HHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCC--CCCCCEEEEeHHHHhhh-H----------h-hHHHHH
Confidence 34556666653 3456799998 89999986554222321 11123457833333322 1 1 899999
Q ss_pred HHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009909 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 98888765322 338899999987763
No 75
>PRK11779 sbcB exonuclease I; Provisional
Probab=88.08 E-value=9.2 Score=42.05 Aligned_cols=106 Identities=16% Similarity=0.134 Sum_probs=59.0
Q ss_pred hhHHHHHHhhCCCCceEEEEe-chhhHHHHHhhcccCCCccC---ccCCC---ceeeHHHHHHHhhccccCCCCC-----
Q 009909 91 SIWELLKELFVSPDILKLGFK-FKQDLIYLSSTFCSQGCDIG---FDRVE---PYLDITSIYNHLHHKQLGRKLP----- 158 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~-~k~Dl~~L~~~~gi~g~~~~---~~~~~---~~~Dlt~La~yLl~~~~~~~~~----- 158 (522)
++...+..++..++.+.|||| +.+|..++...+....+.+. +.... .++|+..+ .|.+.+.. -..|
T Consensus 80 e~~~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl-~~~lrp~~-i~~P~~~~g 157 (476)
T PRK11779 80 EFAARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRA-CYALRPEG-INWPENEDG 157 (476)
T ss_pred HHHHHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHH-HHHhcccc-ccCcccccC
Confidence 345566777765556679997 78999887664311000000 00001 23453222 23222210 0011
Q ss_pred cCCccHHHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 159 KETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVK 215 (522)
Q Consensus 159 ~~~~sL~~L~~~~Lg~~l~K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~ 215 (522)
..++.|+.|++.+ |++... .+-|..||+++.+|+..+..+
T Consensus 158 ~~s~rLe~L~~~~-gI~~~~----------------AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 158 LPSFKLEHLTKAN-GIEHEN----------------AHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CCCCcHHHHHHHc-CCCCCC----------------CCCcHHHHHHHHHHHHHHHHh
Confidence 2468999999875 655421 122889999999999998866
No 76
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=87.11 E-value=0.52 Score=32.94 Aligned_cols=33 Identities=21% Similarity=0.704 Sum_probs=22.1
Q ss_pred CcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009909 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 47999999873 44322 222 23456799999987
No 77
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=87.00 E-value=3.2 Score=40.07 Aligned_cols=110 Identities=13% Similarity=0.071 Sum_probs=65.7
Q ss_pred hhHHHHHHhhCCCCceEEEEech-hhHHHHHhhcccCCCccCccCCCceeeHHHHH--HHhh-ccccCCCCCcCCccHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFK-QDLIYLSSTFCSQGCDIGFDRVEPYLDITSIY--NHLH-HKQLGRKLPKETKSLAN 166 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k-~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La--~yLl-~~~~~~~~~~~~~sL~~ 166 (522)
+++..+..++.+. ..||||.. .|+..|... |. .. .....+|+...+ .... .++ ..+++|.+
T Consensus 73 evl~~f~~f~~~~--~lVaHNa~~fD~~fL~~~-g~-~~-----~~~~~idt~~~~~~~~~~~~~~------~~~~~L~~ 137 (195)
T PRK07247 73 EVLAAFKEFVGEL--PLIGYNAQKSDLPILAEN-GL-DL-----SDQYQVDLYDEAFERRSSDLNG------IANLKLQT 137 (195)
T ss_pred HHHHHHHHHHCCC--eEEEEeCcHhHHHHHHHc-CC-Cc-----CCCceeehHHHHHHhhccccCC------CCCCCHHH
Confidence 4566677777654 35899996 799999763 43 11 112234521111 1111 111 24689999
Q ss_pred HHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchhcccccc
Q 009909 167 ICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNSCSSISELDSSN 233 (522)
Q Consensus 167 L~~~~Lg~~l~K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~~~g~l~~~~~~~~~~~ 233 (522)
|++. +|++. +. +-|..||.++..|+..|...-+....++++-.+.+++|
T Consensus 138 La~~-~gi~~----~~-------------HrAl~DA~~ta~v~~~ll~~~~~~~~~~~~~~~~~~~~ 186 (195)
T PRK07247 138 VADF-LGIKG----RG-------------HNSLEDARMTARVYESFLESDQNKEYLEQQEEVTSDNP 186 (195)
T ss_pred HHHh-cCCCC----CC-------------cCCHHHHHHHHHHHHHHHhhccchhhhhcchhhccCCc
Confidence 9886 57652 11 22789999999999999876555554555545545444
No 78
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=86.66 E-value=0.66 Score=49.23 Aligned_cols=91 Identities=18% Similarity=0.236 Sum_probs=58.9
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L~~~ 170 (522)
++-..|+.++.. +-+-|||++..|+.+|+-.| ..++|+.++..+-..+ . ....+|..|++.
T Consensus 282 dvq~~l~~~~~~-~TILVGHSLenDL~aLKl~H------------~~ViDTa~lf~~~~g~-----~-~~k~sLk~L~~~ 342 (380)
T KOG2248|consen 282 DVQKELLELISK-NTILVGHSLENDLKALKLDH------------PSVIDTAVLFKHPTGP-----Y-PFKSSLKNLAKS 342 (380)
T ss_pred HHHHHHHhhcCc-CcEEEeechhhHHHHHhhhC------------CceeeeeEEEecCCCC-----c-cchHHHHHHHHH
Confidence 455677775555 45569999999999998643 3567833232222211 0 235689999999
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009909 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 171 ~Lg~~l~K~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~ 213 (522)
+||..+..+..-. -...||.++++|.....
T Consensus 343 ~L~~~Iq~~~~~H-------------dS~eDA~acm~Lv~~k~ 372 (380)
T KOG2248|consen 343 YLGKLIQEGVGGH-------------DSVEDALACMKLVKLKI 372 (380)
T ss_pred HHHHHHhccCCCC-------------ccHHHHHHHHHHHHHHH
Confidence 9997764111111 15789999999887765
No 79
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=85.59 E-value=0.68 Score=32.19 Aligned_cols=32 Identities=22% Similarity=0.740 Sum_probs=21.9
Q ss_pred cccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009909 452 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 452 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvY 501 (522)
+|+.|+.... ++.+ +||+. ..--+|+.||.+|
T Consensus 4 ~Cp~C~~~y~---i~d~----------~ip~~-----g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYE---IDDE----------KIPPK-----GRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEe---CCHH----------HCCCC-----CcEEECCCCCCEe
Confidence 6999999874 3322 34543 2356799999986
No 80
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=85.28 E-value=0.8 Score=31.26 Aligned_cols=29 Identities=28% Similarity=0.747 Sum_probs=21.4
Q ss_pred CCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009909 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 4689999997641 1234577899999987
No 81
>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=85.08 E-value=4.2 Score=36.52 Aligned_cols=55 Identities=18% Similarity=0.319 Sum_probs=36.1
Q ss_pred CCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 135 VEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (522)
Q Consensus 135 ~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 455668 99999999985 6788999999987 346432 78889999999999887
Q ss_pred HH
Q 009909 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 82
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=84.69 E-value=0.3 Score=37.07 Aligned_cols=18 Identities=17% Similarity=0.575 Sum_probs=14.7
Q ss_pred cCCceeecCCCCeEEecc
Q 009909 487 KNLQFWQCMDCNQLYWEV 504 (522)
Q Consensus 487 ~~~~F~~C~~CgkvYW~G 504 (522)
..++|.+||.||.+|-.-
T Consensus 13 DGE~~lrCPRC~~~FR~~ 30 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRR 30 (65)
T ss_pred CCceeeeCCchhHHHHHh
Confidence 357899999999998543
No 83
>PRK12268 methionyl-tRNA synthetase; Reviewed
Probab=84.64 E-value=1.3 Score=49.42 Aligned_cols=55 Identities=18% Similarity=0.111 Sum_probs=34.3
Q ss_pred CCCCC---CCCCCCCCCCEEEEecccHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009909 343 GPPPW---DLSLGGDGYPKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 343 ~~~p~---~~~~~~~~~~rfl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~R 401 (522)
.|||. ++++|....+=++.| -++||+|+.|++|.++.+.+.-+..+...|.++|.
T Consensus 9 ~~~py~ng~~HiGH~~~~~~~~D----~~~R~~r~~G~~v~~~~g~d~~g~~i~~~a~~~g~ 66 (556)
T PRK12268 9 SAWPYANGPLHLGHLAGSGLPAD----VFARYQRLKGNEVLFVSGSDEHGTPIELAAKKEGV 66 (556)
T ss_pred cCCCCCCCCccccccccchhHHH----HHHHHHHhcCCceEecCcCCCcccHHHHHHHHcCC
Confidence 34554 456665443212233 36999999999999987643223457777776654
No 84
>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=84.32 E-value=17 Score=35.33 Aligned_cols=110 Identities=15% Similarity=0.205 Sum_probs=60.5
Q ss_pred hhHHHHHHhhCC--CCceEEEEech-hhHHHHHhhcccCCCcc----CccC---------CCceeeHHHHHHHhhccccC
Q 009909 91 SIWELLKELFVS--PDILKLGFKFK-QDLIYLSSTFCSQGCDI----GFDR---------VEPYLDITSIYNHLHHKQLG 154 (522)
Q Consensus 91 ~~~~~L~~lL~d--~~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 345555555544 555 4788865 78877643322223221 1110 0115674333321000
Q ss_pred CCCCcCCccHHHHHHHHcCCcCcc--ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009909 155 RKLPKETKSLANICKELLDISLSK--ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIF 209 (522)
Q Consensus 155 ~~~~~~~~sL~~L~~~~Lg~~l~K--~~q~s-dW~~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 1124789999999999964211 11111 355443 466899999999999998
No 85
>PLN02224 methionine-tRNA ligase
Probab=83.77 E-value=3.4 Score=46.90 Aligned_cols=34 Identities=12% Similarity=0.192 Sum_probs=24.9
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009909 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~R 401 (522)
++||+|+.|++|.++.+.+.-...+...|.++|.
T Consensus 98 iaR~~r~~G~~V~fv~G~DehG~kI~~~A~~~g~ 131 (616)
T PLN02224 98 IARFQRLLGKKVIFITGTDEHGEKIATSAAANGR 131 (616)
T ss_pred HHHHHHhcCCceEEecCcCCcchHHHHHHHHcCC
Confidence 7999999999999887643222347777777663
No 86
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=83.76 E-value=29 Score=35.69 Aligned_cols=87 Identities=14% Similarity=0.117 Sum_probs=51.2
Q ss_pred HHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHH-HHHhhccccCCCCCcCCccHHHHHHHH
Q 009909 93 WELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSI-YNHLHHKQLGRKLPKETKSLANICKEL 171 (522)
Q Consensus 93 ~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~L-a~yLl~~~~~~~~~~~~~sL~~L~~~~ 171 (522)
.+.+..++... -+.|+||+.+|..+|.+.+.. +. .....+ ++. ..+. .+. ..+++|..|+..+
T Consensus 111 ~~~l~~fl~~~-~vlVAHNA~FD~~fL~~~~~~------~~-~~~~~c-t~~~i~~~-~~~------~~~~kL~~La~~~ 174 (294)
T PRK09182 111 PAAVDALIAPA-DLIIAHNAGFDRPFLERFSPV------FA-TKPWAC-SVSEIDWS-ARG------FEGTKLGYLAGQA 174 (294)
T ss_pred HHHHHHHhcCC-CEEEEeCHHHHHHHHHHHHHh------cc-CCcccc-cHHHHhhc-ccc------CCCCCHHHHHHHc
Confidence 45677777764 356999999999999764311 10 112233 332 1111 111 2478999999864
Q ss_pred cCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009909 172 LDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 172 Lg~~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-F--------HE--------GHRAVDDCQALLELLARPL 198 (294)
T ss_pred -CC-C--------CC--------CcChHHHHHHHHHHHHHHH
Confidence 52 1 11 1238899999988877544
No 87
>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=83.62 E-value=1.3 Score=40.62 Aligned_cols=148 Identities=17% Similarity=0.162 Sum_probs=67.0
Q ss_pred EEEEEeEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCc---hhhHHHHHHhhCCCCceEEEEe
Q 009909 35 VGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPL---PSIWELLKELFVSPDILKLGFK 111 (522)
Q Consensus 35 Vg~D~E~~~~~~~~~~~~~vaLiQla~~~~~~~~~~~~~~~~~~v~liDl~~l~~---~~~~~~L~~lL~d~~I~KVgh~ 111 (522)
+.||+|+++..+ ....+-+++++... .+...++.....-.. ..+.+.+ .++.+... .++||
T Consensus 1 l~~DIET~Gl~~---~~~~i~liG~~~~~-----------~~~~~~~~~~~~~~~~ee~~~~~~~-~~l~~~~~-iv~yn 64 (164)
T PF13482_consen 1 LFFDIETTGLSP---DNDTIYLIGVADFD-----------DDEIITFIQWFAEDPDEEEIILEFF-ELLDEADN-IVTYN 64 (164)
T ss_dssp --EEEEESS-GG----G---EEEEEEE-E-----------TTTTE-EEEE-GGGHHHHHHHHH---HHHHTT---EEESS
T ss_pred CcEEecCCCCCC---CCCCEEEEEEEEeC-----------CCceEEeeHhhccCcHHHHHHHHHH-HHHhcCCe-EEEEe
Confidence 468999997765 34567788877531 012221222111111 1123333 34555444 36777
Q ss_pred c-hhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCc-c---cccc----
Q 009909 112 F-KQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS-K---ELQC---- 182 (522)
Q Consensus 112 ~-k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 GKNFDIPFLKRRAKRYGL----PPPFNHIDLLKIIK---KHF------LESYSLKNVEKF-LGIERRDDDISGSESVKLY 130 (164)
T ss_dssp TTTTHHHHHHHHH-HHHH------GGGEEEHHHHHT----TT------SCCTT--SHHH------------HHHHHHHHH
T ss_pred CcccCHHHHHHHHHHcCC----CcccchhhHHHHHH---hcc------CCCCCHHHHhhh-cccccccCCCCHHHHHHHH
Confidence 5 5699888765422122 12467899654442 111 146788888776 676543 1 1111
Q ss_pred cCCCC---CCCCHHHHHHHHHHHHHHHHHHHHH
Q 009909 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 2344777999999999999999876
No 88
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=83.36 E-value=2.2 Score=48.87 Aligned_cols=33 Identities=12% Similarity=0.100 Sum_probs=25.1
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCC
Q 009909 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 400 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~ 400 (522)
++||||+.|++|.++.+.+.-...+...|.++|
T Consensus 31 ~aR~~r~~G~~V~~~~g~D~hG~~i~~~A~~~g 63 (673)
T PRK00133 31 WVRYQRMRGHEVLFVCADDAHGTPIMLKAEKEG 63 (673)
T ss_pred HHHHHHhcCCeeEEeCccCCCChHHHHHHHHcC
Confidence 799999999999998763322345788887766
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=82.78 E-value=1 Score=31.26 Aligned_cols=34 Identities=18% Similarity=0.519 Sum_probs=21.4
Q ss_pred CcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEe
Q 009909 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---VVDSQL----------GA-----NGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEE---eCHHHc----------CC-----CCCEEECCCCCCEEE
Confidence 36999999873 332221 11 122456999999886
No 90
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=82.74 E-value=4.6 Score=46.37 Aligned_cols=109 Identities=20% Similarity=0.206 Sum_probs=67.6
Q ss_pred CCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhcccc---CC-----------------CCC----
Q 009909 103 PDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQL---GR-----------------KLP---- 158 (522)
Q Consensus 103 ~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~---~~-----------------~~~---- 158 (522)
..-+.||||..+|...++..|.+-| .-..++| ||-.+.... +. .+ ..|
T Consensus 240 ke~liVGHNVsfDRaRirEeY~i~~------Sk~rFlD-TMSlHia~~-Gm~S~Qrplw~ka~k~k~a~~d~~~~ps~~d 311 (1075)
T KOG3657|consen 240 KEQLIVGHNVSFDRARIREEYNING------SKIRFLD-TMSLHIAMS-GMCSRQRPLWFKARKAKSAMYDSETNPSISD 311 (1075)
T ss_pred CCceEEeccccchHHHHHHHHhccc------cceeeee-chhhhhhhh-ccccccchhHhhhhhhhhhhhhcccCCchhh
Confidence 3457799999999999988887633 1245778 664433211 10 00 000
Q ss_pred -------c-CCccHHHHHHHHcCCc-CcccccccC--CCCCCCCH---HHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 009909 159 -------K-ETKSLANICKELLDIS-LSKELQCSD--WSNRPLTE---EQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (522)
Q Consensus 159 -------~-~~~sL~~L~~~~Lg~~-l~K~~q~sd--W~~RPL~~---~Qi~YAA~DA~~ll~L~~~L~~~L~~~ 219 (522)
. .-.||.++..-+.|.. ++|+...+- -...++.+ +-+.|.|.|++++.++|..+-+...+.
T Consensus 312 ~~~pWL~~SS~NSL~dVhk~~c~~~~LdKt~Rd~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Fler 386 (1075)
T KOG3657|consen 312 YDNPWLGRSSLNSLVDVHKFHCGIDALDKTPRDSFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLER 386 (1075)
T ss_pred hhhhhhhhhhhHHHHHHHHhhCCCCccccchHHhhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHHh
Confidence 0 1236777788888887 877654321 11112221 127899999999999999988876654
No 91
>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=82.67 E-value=1.1 Score=48.04 Aligned_cols=34 Identities=21% Similarity=0.181 Sum_probs=24.4
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009909 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~R 401 (522)
+|||+|+.|+||.++...+.-...+...|.++|.
T Consensus 28 ~aR~~r~~G~~v~~~tGtDehG~~i~~~A~~~g~ 61 (391)
T PF09334_consen 28 LARYLRLRGHDVLFVTGTDEHGSKIETAAEKQGI 61 (391)
T ss_dssp HHHHHHHTT-EEEEEEEEE-SSHHHHHHHHHTTS
T ss_pred HHHHHhhcccceeeEEecchhhHHHHHHHHHcCC
Confidence 7999999999998876533222457778887776
No 92
>TIGR00398 metG methionyl-tRNA synthetase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma
Probab=82.12 E-value=2.8 Score=46.51 Aligned_cols=34 Identities=12% Similarity=0.040 Sum_probs=26.7
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009909 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~R 401 (522)
++|+||+.|+||.++.+.+.-+..+...|+++|.
T Consensus 28 l~R~~r~~G~~V~~v~g~D~~g~~i~~~a~~~g~ 61 (530)
T TIGR00398 28 YARYKRLRGYEVLFVCGTDEHGTKIELKAEQEGL 61 (530)
T ss_pred HHHHHHhcCCeEEEecccCCCCcHHHHHHHHcCC
Confidence 7999999999999887644334568888888773
No 93
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=81.78 E-value=2.4 Score=47.31 Aligned_cols=121 Identities=13% Similarity=0.103 Sum_probs=61.5
Q ss_pred HHHHHHhcCCceecCCCCCCCh-HHHHHhhhcCCcEEEecChhHHHhhc--------ccCC-cEEEEcCCCH--HHHHHH
Q 009909 368 LAKHLRCVGIDAATPRSKKPEP-RELIDQTSKEKRVLLTRDAKLLRHQY--------LIKN-QIYRVKSLLK--NQQLLE 435 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~~~~d-~~ll~~A~~e~RiiLTrd~~l~~~~~--------~~~~-~~~~v~~~~~--~~QL~~ 435 (522)
+||++|+.|+||.++...+ ++ ..|...|.++|.- -..|..+.. ..+. -=.++++.++ .+..++
T Consensus 34 ~aRy~Rl~G~~v~fvtGtD-eHGt~I~~~A~~~g~t----P~el~d~~~~~~~~~~~~l~IsfD~F~rTt~~~h~~~vq~ 108 (558)
T COG0143 34 YARYLRLRGYEVFFLTGTD-EHGTKIELKAEKEGIT----PQELVDKNHEEFKELFKALNISFDNFIRTTSPEHKELVQE 108 (558)
T ss_pred HHHHHHhcCCeEEEEeccC-CCCCHHHHHHHHcCCC----HHHHHHHHHHHHHHHHHHhCCcccccccCCCHHHHHHHHH
Confidence 7999999999999987532 33 2577778777742 233322111 0010 1134444333 444455
Q ss_pred HHHhc---CcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEeccc
Q 009909 436 VIEAF---QLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVM 505 (522)
Q Consensus 436 v~~~f---~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvYW~Gs 505 (522)
+.+.. |.-......--.|+.|+.=| +-..+. +.-|.+=. ....=-+|..||+.|=...
T Consensus 109 ~f~~L~~~G~I~~~~~~~~Yc~~~e~fl-----~dr~v~------g~cp~cg~-~~arGD~Ce~Cg~~~~P~~ 169 (558)
T COG0143 109 FFLKLYENGDIYLREYEGLYCVSCERFL-----PDRYVE------GTCPKCGG-EDARGDQCENCGRTLDPTE 169 (558)
T ss_pred HHHHHHHCCCEeccceeeeEcccccccc-----cchhee------ccCCCcCc-cccCcchhhhccCcCCchh
Confidence 55443 11111122234688888754 222222 12232211 1223456889999887755
No 94
>PRK11893 methionyl-tRNA synthetase; Reviewed
Probab=81.59 E-value=2.9 Score=46.00 Aligned_cols=34 Identities=15% Similarity=0.143 Sum_probs=25.8
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009909 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~R 401 (522)
++|+||..|++|.++.+.+.-+..++..|.++|.
T Consensus 30 ~~R~~r~~G~~v~~v~g~dd~g~~i~~~a~~~g~ 63 (511)
T PRK11893 30 LARFKRLRGYDVFFLTGTDEHGQKIQRKAEEAGI 63 (511)
T ss_pred HHHHHHhcCCcEEecCCCCCCChHHHHHHHHcCC
Confidence 7999999999999987643333467777877764
No 95
>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=80.08 E-value=3.9 Score=40.46 Aligned_cols=102 Identities=16% Similarity=0.182 Sum_probs=59.5
Q ss_pred CCCceEEEEec-hhhHHHHHhhcccCCCccCccCC-------------------------CceeeHHHHHHHhhccccCC
Q 009909 102 SPDILKLGFKF-KQDLIYLSSTFCSQGCDIGFDRV-------------------------EPYLDITSIYNHLHHKQLGR 155 (522)
Q Consensus 102 d~~I~KVgh~~-k~Dl~~L~~~~gi~g~~~~~~~~-------------------------~~~~Dlt~La~yLl~~~~~~ 155 (522)
||+|+ +|||+ ..|+..|......+++. .|... .-++|+-..+..+..
T Consensus 97 DPDii-vG~Ni~~fdl~~L~~R~~~l~i~-~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~~~~k~~~~----- 169 (234)
T cd05776 97 DPDVL-VGHDLEGFDLDVLLSRIQELKVP-HWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYLSAKELIR----- 169 (234)
T ss_pred CCCEE-EeeccCCCCHHHHHHHHHHhCCC-ccccccccccccCccccccccccccccccCchhhccHHHHHHHhC-----
Confidence 78875 89999 57888764332222321 11111 114564444444432
Q ss_pred CCCcCCccHHHHHHHHcCCcCcc--ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009909 156 KLPKETKSLANICKELLDISLSK--ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 156 ~~~~~~~sL~~L~~~~Lg~~l~K--~~q~s-dW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~ 213 (522)
..+++|.++++.+||..-.. ..... -|....-...-++|...||+.+++|...|.
T Consensus 170 ---~~sY~L~~va~~~Lg~~k~di~~~~i~~~~~~~~~l~~l~~y~~~Da~l~~~L~~kl~ 227 (234)
T cd05776 170 ---CKSYDLTELSQQVLGIERQDIDPEEILNMYNDSESLLKLLEHTEKDAYLILQLMFKLN 227 (234)
T ss_pred ---CCCCChHHHHHHHhCcCcccCCHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence 35899999999999973211 11222 243201113348999999999999988774
No 96
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=79.60 E-value=19 Score=34.70 Aligned_cols=99 Identities=16% Similarity=0.093 Sum_probs=60.2
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L~~~ 170 (522)
+++..|.+++.+...+.+ |+...|+..|.+.+...|+. +.....++|+..++..+... ...++|+++++.
T Consensus 81 evl~~f~~~~~~~~~~iv-~~~~fD~~fL~~~~~~~~~~--~~~~~~~~dl~~~~~~~~~~-------~~~~~L~~~~~~ 150 (207)
T PRK07748 81 ELVEKLAEYDKRCKPTIV-TWGNMDMKVLKHNCEKAGVP--FPFKGQCRDLSLEYKKFFGE-------RNQTGLWKAIEE 150 (207)
T ss_pred HHHHHHHHHhCcCCeEEE-EECHHHHHHHHHHHHHcCCC--CcccccceeHHHHHHHHhCc-------CCCCCHHHHHHH
Confidence 466777888877444444 55789999987653222321 11235677855444433321 235799998876
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 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 -YGKEGT--GK-------------HHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred -cCCCCC--CC-------------CcChHHHHHHHHHHHHHHHhC
Confidence 465431 11 123889999999999988744
No 97
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=79.55 E-value=0.46 Score=54.55 Aligned_cols=94 Identities=19% Similarity=0.283 Sum_probs=64.9
Q ss_pred hhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCCcCcc
Q 009909 99 LFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSK 178 (522)
Q Consensus 99 lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~L~~~~Lg~~l~K 178 (522)
+|-+-.++.|||++++|.+.+--. + -.+.++| |...- ++.. .+..+|.-||-.+||..+--
T Consensus 1009 ~Li~~GviFVGHGL~nDFrvINi~--V--------p~~QiiD-Tv~lf-~~~s-------~R~LSLrfLa~~lLg~~IQ~ 1069 (1118)
T KOG1275|consen 1009 LLIQRGVIFVGHGLQNDFRVINIH--V--------PEEQIID-TVTLF-RLGS-------QRMLSLRFLAWELLGETIQM 1069 (1118)
T ss_pred HHHHcCcEEEcccccccceEEEEe--c--------Chhhhee-eeEEE-eccc-------ccEEEHHHHHHHHhcchhhc
Confidence 677888999999999998865211 1 1244778 43321 1211 25789999999999977622
Q ss_pred cccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchh
Q 009909 179 ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNSCSSIS 227 (522)
Q Consensus 179 ~~q~sdW~~RPL~~~Qi~YAA~DA~~ll~L~~~L~~~L~~~g~l~~~~~ 227 (522)
+. .| ..+||..+|.||+... +|+++|.+++++.
T Consensus 1070 ~~--HD-------------SIeDA~taLkLYk~Yl-~lkeq~~~~~~l~ 1102 (1118)
T KOG1275|consen 1070 EA--HD-------------SIEDARTALKLYKKYL-KLKEQGKLESELR 1102 (1118)
T ss_pred cc--cc-------------cHHHHHHHHHHHHHHH-HHHHhhHHHHHHH
Confidence 21 12 4689999999999985 6788888876655
No 98
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=79.33 E-value=4.1 Score=46.54 Aligned_cols=33 Identities=18% Similarity=0.171 Sum_probs=25.4
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCC
Q 009909 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 400 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~ 400 (522)
++|+||+.|+||.++.+.+.-+..+...|+++|
T Consensus 33 ~~R~~r~~G~~v~~~~g~D~~g~~i~~~A~~~g 65 (648)
T PRK12267 33 LARYKRLQGYDVFFLTGTDEHGQKIQQAAEKAG 65 (648)
T ss_pred HHHHHHhcCCceEeecCCCCcchHHHHHHHHcC
Confidence 799999999999998764332346777777776
No 99
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=79.09 E-value=1.1 Score=41.60 Aligned_cols=44 Identities=14% Similarity=0.309 Sum_probs=26.2
Q ss_pred cccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecccchhhHH
Q 009909 452 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVMSAYLFI 511 (522)
Q Consensus 452 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvYW~GsH~~r~~ 511 (522)
+||.|+++-.. -++. ...+++ +....|++|+.||+-| +|..++.
T Consensus 2 ~cp~c~~~~~~-~~~s----------~~~~~~--~~~~~~~~c~~c~~~f---~~~e~~~ 45 (154)
T PRK00464 2 RCPFCGHPDTR-VIDS----------RPAEDG--NAIRRRRECLACGKRF---TTFERVE 45 (154)
T ss_pred cCCCCCCCCCE-eEec----------cccCCC--CceeeeeeccccCCcc---eEeEecc
Confidence 79999997531 1111 123332 1234679999999988 4555443
No 100
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=78.97 E-value=2.5 Score=31.32 Aligned_cols=17 Identities=12% Similarity=0.098 Sum_probs=14.0
Q ss_pred ceeecCCCCeEEecccc
Q 009909 490 QFWQCMDCNQLYWEVMS 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 48899999998887654
No 101
>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=77.53 E-value=2.1 Score=27.08 Aligned_cols=9 Identities=33% Similarity=0.899 Sum_probs=7.3
Q ss_pred ccCCCCccc
Q 009909 453 CTKCNGRFI 461 (522)
Q Consensus 453 C~~CN~~l~ 461 (522)
|..||..+.
T Consensus 1 C~sC~~~i~ 9 (24)
T PF07754_consen 1 CTSCGRPIA 9 (24)
T ss_pred CccCCCccc
Confidence 889999774
No 102
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=77.16 E-value=20 Score=35.22 Aligned_cols=86 Identities=8% Similarity=0.004 Sum_probs=54.0
Q ss_pred HHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHHHcCC
Q 009909 95 LLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDI 174 (522)
Q Consensus 95 ~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 345699999999999864 1 14678955555544 343 34888888865 465
Q ss_pred cCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 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 0123488999999999988763
No 103
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=76.74 E-value=1.8 Score=30.83 Aligned_cols=24 Identities=8% Similarity=0.324 Sum_probs=18.5
Q ss_pred CceeecCCCCeEEecccchhhHHh
Q 009909 489 LQFWQCMDCNQLYWEVMSAYLFIF 512 (522)
Q Consensus 489 ~~F~~C~~CgkvYW~GsH~~r~~~ 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 467889999999877776666654
No 104
>PRK00420 hypothetical protein; Validated
Probab=76.23 E-value=1.9 Score=37.92 Aligned_cols=47 Identities=13% Similarity=0.117 Sum_probs=27.8
Q ss_pred CHHHHHHHHHHhcCcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEec
Q 009909 428 LKNQQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWE 503 (522)
Q Consensus 428 ~~~~QL~~v~~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvYW~ 503 (522)
++..++.+.+..-.-.. -..|+.|+.+|.. . .+.-.+||.||++|=.
T Consensus 6 ~~~k~~a~~Ll~Ga~ml-----~~~CP~Cg~pLf~--l----------------------k~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 6 DIVKKAAELLLKGAKML-----SKHCPVCGLPLFE--L----------------------KDGEVVCPVHGKVYIV 52 (112)
T ss_pred HHHHHHHHHHHhHHHHc-----cCCCCCCCCccee--c----------------------CCCceECCCCCCeeee
Confidence 34555666554421111 1569999998741 0 1234569999998854
No 105
>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=76.03 E-value=39 Score=32.82 Aligned_cols=110 Identities=21% Similarity=0.207 Sum_probs=61.6
Q ss_pred hhhHHHHHHhhCCCCceEEEEech-hhHHHHHhhcccCCCcc--CccC-----------CCceeeHHHHHHHhhccccCC
Q 009909 90 PSIWELLKELFVSPDILKLGFKFK-QDLIYLSSTFCSQGCDI--GFDR-----------VEPYLDITSIYNHLHHKQLGR 155 (522)
Q Consensus 90 ~~~~~~L~~lL~d~~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~~~~~~~~------ 152 (208)
T cd05782 79 KELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYG------ 152 (208)
T ss_pred HHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccC------
Confidence 345666556666533356999985 89988754322233310 0100 012678543332111
Q ss_pred CCCcCCccHHHHHHHHcCCcCcc----ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 009909 156 KLPKETKSLANICKELLDISLSK----ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (522)
Q Consensus 156 ~~~~~~~sL~~L~~~~Lg~~l~K----~~q~s-dW~~RPL~~~Qi~YAA~DA~~ll~L~~ 210 (522)
...+.+|..+++ +||.+ .| +.+.. -|.... ...-.+|...||..++.||.
T Consensus 153 --~~~~~~L~~va~-~lG~~-~K~d~~G~~v~~~y~~g~-~~~I~~Yc~~Dv~~t~~l~l 207 (208)
T cd05782 153 --ARARASLDLLAK-LLGIP-GKMDVDGSQVWELYAEGK-LDEIAEYCETDVLNTYLLYL 207 (208)
T ss_pred --ccCCCCHHHHHH-HhCCC-CCcCCCHHHHHHHHHcCC-hHHHHHHHHHHHHHHHHHHh
Confidence 124789999986 67773 22 11221 244433 45568999999999998874
No 106
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=75.99 E-value=0.65 Score=46.16 Aligned_cols=55 Identities=11% Similarity=0.254 Sum_probs=32.4
Q ss_pred HHHHhc-CcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE-Eecccch
Q 009909 435 EVIEAF-QLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL-YWEVMSA 507 (522)
Q Consensus 435 ~v~~~f-~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv-YW~GsH~ 507 (522)
.+.+.. |+.+-|- .--+|.-|+-.| |. ... ..|.+ .++.-+||.||+| ||.-+|.
T Consensus 182 ri~~~~kg~gvvpl-~g~~C~GC~m~l---~~--~~~-----------~~V~~-~d~iv~CP~CgRILy~~e~~~ 238 (239)
T COG1579 182 RIRKNKKGVGVVPL-EGRVCGGCHMKL---PS--QTL-----------SKVRK-KDEIVFCPYCGRILYYDESEE 238 (239)
T ss_pred HHHhcCCCceEEee-cCCcccCCeeee---cH--HHH-----------HHHhc-CCCCccCCccchHHHhhhccc
Confidence 344445 4444332 136899999876 21 111 12333 5677789999996 8877663
No 107
>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=75.83 E-value=1.6 Score=30.39 Aligned_cols=11 Identities=27% Similarity=0.887 Sum_probs=9.9
Q ss_pred eecCCCCeEEe
Q 009909 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 108
>PLN02610 probable methionyl-tRNA synthetase
Probab=75.03 E-value=5.8 Score=46.47 Aligned_cols=33 Identities=15% Similarity=0.055 Sum_probs=23.1
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCC
Q 009909 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 400 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~ 400 (522)
+|||+|+.|+||.++...+.-.-.+...|.++|
T Consensus 47 ~aRy~r~~G~~v~f~~GtDehG~~i~~~A~~~g 79 (801)
T PLN02610 47 FARYCRLRGYNAIYICGTDEYGTATETKALEEN 79 (801)
T ss_pred HHHHHHhCCCceEecccccCCcHHHHHHHHHcC
Confidence 699999999999988764322224555666655
No 109
>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=72.99 E-value=21 Score=33.75 Aligned_cols=99 Identities=18% Similarity=0.260 Sum_probs=53.4
Q ss_pred hHHHHHHhhCCCCceEEEEe-chhhHHHHHhhcccCCCccCcc----CCCceeeHHHHHHHhh--ccccCCCCC-----c
Q 009909 92 IWELLKELFVSPDILKLGFK-FKQDLIYLSSTFCSQGCDIGFD----RVEPYLDITSIYNHLH--HKQLGRKLP-----K 159 (522)
Q Consensus 92 ~~~~L~~lL~d~~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 44556667765444558997 7999999876532212110 00 0122457544554332 121 00001 2
Q ss_pred CCccHHHHHHHHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009909 160 ETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (522)
Q Consensus 160 ~~~sL~~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 36889999986 576541 1244888998887663
No 110
>PRK05762 DNA polymerase II; Reviewed
Probab=72.40 E-value=78 Score=37.18 Aligned_cols=112 Identities=18% Similarity=0.239 Sum_probs=62.5
Q ss_pred hhHHHHHHhhC--CCCceEEEEech-hhHHHHHhhcccCCCccCccC----------------------CCceeeHHHHH
Q 009909 91 SIWELLKELFV--SPDILKLGFKFK-QDLIYLSSTFCSQGCDIGFDR----------------------VEPYLDITSIY 145 (522)
Q Consensus 91 ~~~~~L~~lL~--d~~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 34444444444 57764 899966 699887533222333211000 01256743333
Q ss_pred HHhhccccCCCCCcCCccHHHHHHHHcCCcCcc--c----cccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009909 146 NHLHHKQLGRKLPKETKSLANICKELLDISLSK--E----LQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (522)
Q Consensus 146 ~yLl~~~~~~~~~~~~~sL~~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 KSATW-------VFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAED--KPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred HHhhc-------cCCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhh--HHHHHHHHHHHHHHHHHHHHHh
Confidence 32221 135789999999999854211 1 1121 23311 2455899999999999999843
No 111
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=72.22 E-value=34 Score=33.52 Aligned_cols=99 Identities=19% Similarity=0.216 Sum_probs=62.7
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 3455555666664 45599999999999875543333211 1356778444444333 32 25789999999
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 009909 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 6676642 1111 22889999999999988753
No 112
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=72.22 E-value=3.2 Score=31.55 Aligned_cols=33 Identities=21% Similarity=0.574 Sum_probs=22.4
Q ss_pred CcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009909 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 5899999875 2333332 1 123678899999986
No 113
>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=72.14 E-value=2.4 Score=25.74 Aligned_cols=15 Identities=13% Similarity=0.490 Sum_probs=11.3
Q ss_pred eecCCCCeEEecccc
Q 009909 492 WQCMDCNQLYWEVMS 506 (522)
Q Consensus 492 ~~C~~CgkvYW~GsH 506 (522)
|.|+.||+.|=.-+.
T Consensus 1 y~C~~C~~~f~~~~~ 15 (23)
T PF00096_consen 1 YKCPICGKSFSSKSN 15 (23)
T ss_dssp EEETTTTEEESSHHH
T ss_pred CCCCCCCCccCCHHH
Confidence 689999999944433
No 114
>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=71.80 E-value=0.93 Score=33.03 Aligned_cols=43 Identities=16% Similarity=0.425 Sum_probs=27.6
Q ss_pred CcccCCCCccccCCCChHHHHHhhhcCcccCcc--ccccCCceeecCCCC
Q 009909 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDC--LFDKNLQFWQCMDCN 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 46999999985 343332322 23334433 456778899999997
No 115
>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=71.46 E-value=1.9 Score=31.87 Aligned_cols=39 Identities=23% Similarity=0.497 Sum_probs=20.5
Q ss_pred cccCCCCccccCCCChHHHHHhhhcCcccCccc-cccCCceeecCCCCe
Q 009909 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 QCPVCGYVYDPEKGDPE---------NGIPPGTPFEDLPDDWVCPVCGA 42 (47)
T ss_dssp EETTTSBEEETTTBBGG---------GTB-TT--GGGS-TT-B-TTTSS
T ss_pred CCCCCCEEEcCCcCCcc---------cCcCCCCCHHHCCCCCcCcCCCC
Confidence 69999975432111110 2467765 566677899999984
No 116
>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=71.39 E-value=39 Score=30.94 Aligned_cols=98 Identities=12% Similarity=0.057 Sum_probs=57.1
Q ss_pred hhHHHHHHhhCCC-CceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHH
Q 009909 91 SIWELLKELFVSP-DILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (522)
Q Consensus 91 ~~~~~L~~lL~d~-~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 44455888766543211111100001246789977777665432 14789999986
Q ss_pred HHcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 009909 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--GR-------------HHRGLDDARNIARILKRL 175 (176)
T ss_pred H-CCCCCC--CC-------------CcCcHHHHHHHHHHHHHh
Confidence 5 576653 11 123788999999888765
No 117
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=70.84 E-value=3.8 Score=33.44 Aligned_cols=39 Identities=13% Similarity=0.329 Sum_probs=27.3
Q ss_pred cccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecccchhhHH
Q 009909 452 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVMSAYLFI 511 (522)
Q Consensus 452 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvYW~GsH~~r~~ 511 (522)
-|+.||..|+. + -...-+|-+||.|+-|.-.+.--..+|
T Consensus 3 lCP~C~v~l~~--~-------------------~rs~vEiD~CPrCrGVWLDrGELdKli 41 (88)
T COG3809 3 LCPICGVELVM--S-------------------VRSGVEIDYCPRCRGVWLDRGELDKLI 41 (88)
T ss_pred ccCcCCceeee--e-------------------eecCceeeeCCccccEeecchhHHHHH
Confidence 59999998852 1 012458999999999987766554444
No 118
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=69.06 E-value=4.5 Score=30.28 Aligned_cols=14 Identities=21% Similarity=0.776 Sum_probs=12.4
Q ss_pred ceeecCCCCeEEec
Q 009909 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 57889999999995
No 119
>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=68.88 E-value=3.7 Score=40.17 Aligned_cols=34 Identities=15% Similarity=0.158 Sum_probs=25.9
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCC
Q 009909 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 3899999999999988764333456888887764
No 120
>PHA02119 hypothetical protein
Probab=68.82 E-value=1.8 Score=34.39 Aligned_cols=15 Identities=33% Similarity=0.578 Sum_probs=12.7
Q ss_pred HHHHHHHhcCCceec
Q 009909 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 478899999999863
No 121
>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=68.30 E-value=0.73 Score=34.49 Aligned_cols=11 Identities=36% Similarity=0.821 Sum_probs=9.2
Q ss_pred CcccCCCCccc
Q 009909 451 SRCTKCNGRFI 461 (522)
Q Consensus 451 sRC~~CN~~l~ 461 (522)
-||..||..|.
T Consensus 5 iRC~~CnklLa 15 (51)
T PF10122_consen 5 IRCGHCNKLLA 15 (51)
T ss_pred eeccchhHHHh
Confidence 48999999873
No 122
>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=68.14 E-value=2.4 Score=37.36 Aligned_cols=27 Identities=11% Similarity=0.180 Sum_probs=21.7
Q ss_pred CCceeecCCCCeEEecccchhhHHhhh
Q 009909 488 NLQFWQCMDCNQLYWEVMSAYLFIFLT 514 (522)
Q Consensus 488 ~~~F~~C~~CgkvYW~GsH~~r~~~~~ 514 (522)
....|.|+.||-.|+...+..+...++
T Consensus 28 ~~~~~~C~~CGe~~~~~e~~~~~~~~i 54 (127)
T TIGR03830 28 GVPGWYCPACGEELLDPEESKRNSAAL 54 (127)
T ss_pred eeeeeECCCCCCEEEcHHHHHHHHHHH
Confidence 457889999999999988877755544
No 123
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=67.77 E-value=2.6 Score=43.63 Aligned_cols=12 Identities=25% Similarity=1.110 Sum_probs=9.9
Q ss_pred CCceeecCCCCe
Q 009909 488 NLQFWQCMDCNQ 499 (522)
Q Consensus 488 ~~~F~~C~~Cgk 499 (522)
+.-||.||+|++
T Consensus 365 ~~l~W~CPsC~~ 376 (389)
T COG2956 365 HTLYWHCPSCRA 376 (389)
T ss_pred eeeeeeCCCccc
Confidence 346999999986
No 124
>PF14353 CpXC: CpXC protein
Probab=67.36 E-value=4.7 Score=35.89 Aligned_cols=19 Identities=21% Similarity=0.604 Sum_probs=14.1
Q ss_pred cccccCCceeecCCCCeEE
Q 009909 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 3455566788999999854
No 125
>PRK12366 replication factor A; Reviewed
Probab=66.40 E-value=2 Score=48.88 Aligned_cols=36 Identities=17% Similarity=0.371 Sum_probs=25.5
Q ss_pred CcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecccchhh
Q 009909 447 DQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVMSAYL 509 (522)
Q Consensus 447 ~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvYW~GsH~~r 509 (522)
...+.+|+.||..+.. ...-|+|+.||++ ++.|.++
T Consensus 529 ~~~y~aCp~CnkKv~~-------------------------~~g~~~C~~c~~~--~p~~~~~ 564 (637)
T PRK12366 529 KIILYLCPNCRKRVEE-------------------------VDGEYICEFCGEV--EPNELLM 564 (637)
T ss_pred CEEEecccccCeEeEc-------------------------CCCcEECCCCCCC--CCcEEEE
Confidence 3457899999986420 1358999999998 6655543
No 126
>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=66.33 E-value=5 Score=43.19 Aligned_cols=34 Identities=9% Similarity=0.118 Sum_probs=27.6
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009909 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~R 401 (522)
|+||||..||||.++.+.+.-|..|+..|+++|.
T Consensus 64 l~R~lr~~G~~V~fV~nitD~dDKIi~~A~~~g~ 97 (411)
T TIGR03447 64 VNRVWRDAGHRVHYVQNVTDVDDPLFERAERDGV 97 (411)
T ss_pred HHHHHHhcCCceEEeeCCCchhHHHHHHHHHcCC
Confidence 8999999999999987643334579999998874
No 127
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=65.93 E-value=4.2 Score=35.55 Aligned_cols=45 Identities=20% Similarity=0.428 Sum_probs=26.2
Q ss_pred cCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEeccc
Q 009909 448 QLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVM 505 (522)
Q Consensus 448 ~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvYW~Gs 505 (522)
.+--||++||.+=. .-..-+-+-+. +....||-|++|+.-|=++|
T Consensus 72 ~I~~kCpkCghe~m--~Y~T~QlRSAD-----------EGQTVFYTC~kC~~k~~e~s 116 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEM--SYHTLQLRSAD-----------EGQTVFYTCPKCKYKFTENS 116 (116)
T ss_pred chhccCcccCCchh--hhhhhhccccc-----------CCceEEEEcCccceeeeccC
Confidence 34578999998521 11111111111 23567999999998775543
No 128
>PRK12418 cysteinyl-tRNA synthetase; Provisional
Probab=64.71 E-value=5.3 Score=42.70 Aligned_cols=36 Identities=11% Similarity=0.115 Sum_probs=28.7
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcE
Q 009909 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 389999999999999876433346799999988754
No 129
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=64.29 E-value=2 Score=42.09 Aligned_cols=54 Identities=17% Similarity=0.326 Sum_probs=27.7
Q ss_pred CcccCCCCccccCCCChHHHH--HhhhcCcccCccccccCCceeecCCCCeEEecc
Q 009909 451 SRCTKCNGRFIQKPLSTEEAV--EAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEV 504 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~--~~~~~~~~vp~~v~~~~~~F~~C~~CgkvYW~G 504 (522)
..||+|+..+..+.|-....+ ....-+...-..|....-+.|.||.||=-++++
T Consensus 6 ~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 6 ITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred eECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 579999998853322111110 000000001111222345789999999988876
No 130
>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=62.98 E-value=4.3 Score=41.55 Aligned_cols=32 Identities=22% Similarity=0.598 Sum_probs=23.1
Q ss_pred cCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009909 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 5667999999999764 2222 135789999986
No 131
>PHA02325 hypothetical protein
Probab=61.81 E-value=4.3 Score=31.77 Aligned_cols=16 Identities=31% Similarity=0.733 Sum_probs=11.9
Q ss_pred eecCCCC------eEEecccch
Q 009909 492 WQCMDCN------QLYWEVMSA 507 (522)
Q Consensus 492 ~~C~~Cg------kvYW~GsH~ 507 (522)
..||.|| |.||.|+--
T Consensus 4 k~CPkC~A~WldgqhYWsgTgk 25 (72)
T PHA02325 4 KICPKCGARWLDGQHYWSGTGK 25 (72)
T ss_pred cccCccCCEeEcceeeeccCCC
Confidence 4699995 678887753
No 132
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=61.14 E-value=6.2 Score=39.18 Aligned_cols=36 Identities=25% Similarity=0.683 Sum_probs=24.8
Q ss_pred cCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009909 448 QLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 448 ~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvY 501 (522)
+.-|||-.|+.... ||+.+. ....-++.|+.|++.|
T Consensus 130 KeVSRCr~C~~rYD--PVP~dk----------------mwG~aef~C~~C~h~F 165 (278)
T PF15135_consen 130 KEVSRCRKCRKRYD--PVPCDK----------------MWGIAEFHCPKCRHNF 165 (278)
T ss_pred cccccccccccccC--CCcccc----------------ccceeeeecccccccc
Confidence 44699999999764 343222 1234578899999876
No 133
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=60.89 E-value=6.8 Score=30.43 Aligned_cols=27 Identities=26% Similarity=0.666 Sum_probs=18.8
Q ss_pred cccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009909 452 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 452 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvY 501 (522)
-|+.|+|+|. +.. ...--.|+.||+.|
T Consensus 10 aCP~~kg~L~---~~~--------------------~~~~L~c~~~~~aY 36 (60)
T COG2835 10 ACPVCKGPLV---YDE--------------------EKQELICPRCKLAY 36 (60)
T ss_pred eccCcCCcce---Eec--------------------cCCEEEecccCcee
Confidence 4999999974 111 12255699999988
No 134
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=60.57 E-value=2.7 Score=38.16 Aligned_cols=47 Identities=23% Similarity=0.593 Sum_probs=25.2
Q ss_pred cccCcCCCcccCCCCccccCCCChHHHHH-----hhhcCcccCccccccCCceeecCCCCe
Q 009909 444 ISEDQLMSRCTKCNGRFIQKPLSTEEAVE-----AAKGFQRIPDCLFDKNLQFWQCMDCNQ 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---LK--EVKESLDEEIREAIHFIPE----VVHAFLKCPKCGS 115 (135)
T ss_pred EEecceEEECCCCCCEEe---cc--ccccccccccccccccccc----ccccCcCCcCCCC
Confidence 334456789999997652 21 1000 0011123333 3356788999984
No 135
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=60.16 E-value=12 Score=42.44 Aligned_cols=58 Identities=16% Similarity=0.248 Sum_probs=38.0
Q ss_pred HHHHHHHHHh---cCcC-cccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEeccc
Q 009909 430 NQQLLEVIEA---FQLK-ISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVM 505 (522)
Q Consensus 430 ~~QL~~v~~~---f~l~-~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvYW~Gs 505 (522)
.+.+.+|++. .++. .+-...+++|..|+.... .+.+.||.||.
T Consensus 544 ~~al~~lv~~~~~~~i~Y~~inp~~~~C~~CG~~~~---------------------------g~~~~CP~CGs------ 590 (625)
T PRK08579 544 PEALAKLTKRIMNTKLVYWSYTPAITVCNKCGRSTT---------------------------GLYTRCPRCGS------ 590 (625)
T ss_pred HHHHHHHHHHHHhcCCceEEeCCCCccCCCCCCccC---------------------------CCCCcCcCCCC------
Confidence 3577777775 3333 233456899999998321 12467999986
Q ss_pred chhhHHhhhhhhhhc
Q 009909 506 SAYLFIFLTPAYFSF 520 (522)
Q Consensus 506 H~~r~~~~~~~~~~~ 520 (522)
+---+++|++-|+.-
T Consensus 591 ~~~~v~~Rv~GYl~~ 605 (625)
T PRK08579 591 EDVEVWSRIIGYYRP 605 (625)
T ss_pred chhHHHHHHHhhhcc
Confidence 334588888888753
No 136
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=59.48 E-value=6.3 Score=27.49 Aligned_cols=14 Identities=21% Similarity=0.831 Sum_probs=9.2
Q ss_pred CCceeecCCCCeEE
Q 009909 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 35899999999985
No 137
>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=59.34 E-value=18 Score=42.72 Aligned_cols=18 Identities=22% Similarity=0.320 Sum_probs=16.1
Q ss_pred HHHHHHhcCCceecCCCC
Q 009909 368 LAKHLRCVGIDAATPRSK 385 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~ 385 (522)
++||+|+.||+|.++.+.
T Consensus 58 i~Ry~rm~G~~V~~~~G~ 75 (842)
T TIGR00396 58 LSRYYRMKGYNVLHPMGW 75 (842)
T ss_pred HHHHHHhcCCceeccCCc
Confidence 799999999999998754
No 138
>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=59.33 E-value=7.5 Score=33.61 Aligned_cols=43 Identities=19% Similarity=0.403 Sum_probs=26.9
Q ss_pred CcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecccch
Q 009909 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVMSA 507 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvYW~GsH~ 507 (522)
.+|+.|++.... ++-++ |-+..+....-+|+|+.|+- |-|-|-
T Consensus 3 ~~CpYCg~~~~l--~~~~~----------iYg~~~~~~~~~y~C~~C~A--yVG~H~ 45 (102)
T PF11672_consen 3 IICPYCGGPAEL--VDGSE----------IYGHRYDDGPYLYVCTPCDA--YVGCHP 45 (102)
T ss_pred cccCCCCCeeEE--cccch----------hcCccCCCCceeEECCCCCc--eeeeeC
Confidence 589999997643 22222 22233333445799999986 677775
No 139
>PRK07218 replication factor A; Provisional
Probab=59.21 E-value=4.4 Score=43.83 Aligned_cols=14 Identities=29% Similarity=0.800 Sum_probs=11.1
Q ss_pred CcCCCcccCCCCcc
Q 009909 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 45679999999854
No 140
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=59.04 E-value=5.8 Score=40.79 Aligned_cols=38 Identities=16% Similarity=0.389 Sum_probs=26.0
Q ss_pred hcCcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009909 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 44544 35667999999999764 2222 135789999986
No 141
>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=58.84 E-value=7.3 Score=27.90 Aligned_cols=13 Identities=15% Similarity=0.386 Sum_probs=9.2
Q ss_pred CCceeecCCCCeE
Q 009909 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 4456799999976
No 142
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=58.81 E-value=6 Score=40.68 Aligned_cols=35 Identities=17% Similarity=0.499 Sum_probs=23.8
Q ss_pred ccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009909 445 SEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 445 ~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvY 501 (522)
.|+..+++|+.|+..+.. .+. ...++.||.||.-|
T Consensus 22 ~~~~~~~~c~~c~~~~~~-----~~l-----------------~~~~~vc~~c~~h~ 56 (292)
T PRK05654 22 VPEGLWTKCPSCGQVLYR-----KEL-----------------EANLNVCPKCGHHM 56 (292)
T ss_pred CCCCCeeECCCccchhhH-----HHH-----------------HhcCCCCCCCCCCe
Confidence 356679999999997641 221 12468999998633
No 143
>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=58.41 E-value=6.3 Score=23.47 Aligned_cols=12 Identities=25% Similarity=0.739 Sum_probs=8.0
Q ss_pred eecCCCCeEEec
Q 009909 492 WQCMDCNQLYWE 503 (522)
Q Consensus 492 ~~C~~CgkvYW~ 503 (522)
|.|+.||+.|=.
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 689999998843
No 144
>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=57.70 E-value=6.2 Score=29.56 Aligned_cols=39 Identities=21% Similarity=0.405 Sum_probs=23.4
Q ss_pred cccCCCCccccCCCChHHHHHhhhcCcccCccc-cccCCceeecCCCCe
Q 009909 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 6999997543111010 12455554 455567899999984
No 145
>PRK06722 exonuclease; Provisional
Probab=57.50 E-value=70 Score=32.74 Aligned_cols=100 Identities=18% Similarity=0.123 Sum_probs=56.8
Q ss_pred hhHHHHHHhhCCCCceEEEEechhhHHHHHhhcccCCCccCccCCCceeeHHHHHHHhhccccCCCCCcCCccHHHHHHH
Q 009909 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (522)
Q Consensus 91 ~~~~~L~~lL~d~~I~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~~Dlt~La~yLl~~~~~~~~~~~~~sL~~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 456677777765433 66777999999876543323210000012246755444332211 00134689999887
Q ss_pred HcCCcCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009909 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 655311 1 1227889999999988876
No 146
>PRK11827 hypothetical protein; Provisional
Probab=57.19 E-value=9.3 Score=29.81 Aligned_cols=10 Identities=40% Similarity=1.135 Sum_probs=8.7
Q ss_pred cccCCCCccc
Q 009909 452 RCTKCNGRFI 461 (522)
Q Consensus 452 RC~~CN~~l~ 461 (522)
.|+.|.|+|.
T Consensus 10 aCP~ckg~L~ 19 (60)
T PRK11827 10 ACPVCNGKLW 19 (60)
T ss_pred ECCCCCCcCe
Confidence 6999999884
No 147
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=56.36 E-value=4.6 Score=26.01 Aligned_cols=9 Identities=22% Similarity=0.674 Sum_probs=7.1
Q ss_pred ecCCCCeEE
Q 009909 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 148
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=56.29 E-value=4.1 Score=35.84 Aligned_cols=20 Identities=20% Similarity=0.358 Sum_probs=13.7
Q ss_pred CcCcccCcCCCcccCCCCcc
Q 009909 441 QLKISEDQLMSRCTKCNGRF 460 (522)
Q Consensus 441 ~l~~~~~~~~sRC~~CN~~l 460 (522)
.|.+...+..-||..|+...
T Consensus 61 ~L~I~~vp~~~~C~~Cg~~~ 80 (113)
T PRK12380 61 DLHIVYKPAQAWCWDCSQVV 80 (113)
T ss_pred EEEEEeeCcEEEcccCCCEE
Confidence 44455556678999999754
No 149
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.54 E-value=3.3 Score=40.70 Aligned_cols=12 Identities=17% Similarity=0.199 Sum_probs=9.6
Q ss_pred cCCceeecCCCC
Q 009909 487 KNLQFWQCMDCN 498 (522)
Q Consensus 487 ~~~~F~~C~~Cg 498 (522)
...+.|.||.|+
T Consensus 58 ~fY~VvvCP~C~ 69 (267)
T COG1655 58 YFYDVVVCPICY 69 (267)
T ss_pred ceeEEEEcchhh
Confidence 345789999996
No 150
>PLN02946 cysteine-tRNA ligase
Probab=55.53 E-value=8.7 Score=43.02 Aligned_cols=35 Identities=14% Similarity=0.171 Sum_probs=27.8
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009909 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 38999999999999987643334579999988874
No 151
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=55.19 E-value=17 Score=29.57 Aligned_cols=60 Identities=17% Similarity=0.432 Sum_probs=31.2
Q ss_pred HHHHHHHHHhcCcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009909 430 NQQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 499 (522)
Q Consensus 430 ~~QL~~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 4678889999999888877778899999998641 111 0 0111000012345788999985
No 152
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=54.92 E-value=8.1 Score=26.44 Aligned_cols=15 Identities=27% Similarity=0.629 Sum_probs=12.2
Q ss_pred eeecCCCCeEEecccc
Q 009909 491 FWQCMDCNQLYWEVMS 506 (522)
Q Consensus 491 F~~C~~CgkvYW~GsH 506 (522)
+|+|+.||-+| +|.+
T Consensus 2 ~~~C~~CG~i~-~g~~ 16 (34)
T cd00729 2 VWVCPVCGYIH-EGEE 16 (34)
T ss_pred eEECCCCCCEe-ECCc
Confidence 79999999988 5554
No 153
>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=54.76 E-value=22 Score=36.79 Aligned_cols=34 Identities=18% Similarity=0.074 Sum_probs=25.3
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009909 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~R 401 (522)
++|+||..|++|.++.+.+.-+..+...|+++|.
T Consensus 29 ~~R~lr~~G~~V~~v~g~Dd~g~~i~~~a~~~g~ 62 (314)
T cd00812 29 IARYKRMQGYNVLFPMGFDAFGLPAENAAIKIGR 62 (314)
T ss_pred HHHHHHHcCCCcCCCCCcCCCCCHHHHHHHHcCC
Confidence 7999999999999887643223357777777775
No 154
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=54.65 E-value=6 Score=27.50 Aligned_cols=13 Identities=15% Similarity=0.278 Sum_probs=9.0
Q ss_pred ecCCCCeEEecccchhh
Q 009909 493 QCMDCNQLYWEVMSAYL 509 (522)
Q Consensus 493 ~C~~CgkvYW~GsH~~r 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 778876
No 155
>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=54.29 E-value=9.8 Score=26.84 Aligned_cols=31 Identities=26% Similarity=0.624 Sum_probs=22.2
Q ss_pred cccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCC---CCeEEec
Q 009909 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 11237999977 9988874
No 156
>COG1773 Rubredoxin [Energy production and conversion]
Probab=54.23 E-value=7.1 Score=29.87 Aligned_cols=40 Identities=20% Similarity=0.383 Sum_probs=25.2
Q ss_pred CcccCCCCccccCCCChHHHHHhhhcCcccCccc-cccCCceeecCCCCe
Q 009909 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 4799998765321111 0 12456665 477788999999983
No 157
>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=53.80 E-value=17 Score=31.45 Aligned_cols=28 Identities=21% Similarity=0.393 Sum_probs=22.9
Q ss_pred CCCChHHHHHhhhcCCc-EEEecChhHHH
Q 009909 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 46788889999888664 99999999864
No 158
>PRK00260 cysS cysteinyl-tRNA synthetase; Validated
Probab=53.38 E-value=12 Score=41.02 Aligned_cols=35 Identities=20% Similarity=0.276 Sum_probs=27.7
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009909 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 38999999999999887643335678899988873
No 159
>PHA00616 hypothetical protein
Probab=53.17 E-value=3.2 Score=30.28 Aligned_cols=18 Identities=17% Similarity=0.610 Sum_probs=14.5
Q ss_pred eecCCCCeEEecccchhh
Q 009909 492 WQCMDCNQLYWEVMSAYL 509 (522)
Q Consensus 492 ~~C~~CgkvYW~GsH~~r 509 (522)
++|+.||++|=.-++..+
T Consensus 2 YqC~~CG~~F~~~s~l~~ 19 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIE 19 (44)
T ss_pred CccchhhHHHhhHHHHHH
Confidence 589999999987766555
No 160
>PRK00390 leuS leucyl-tRNA synthetase; Validated
Probab=52.86 E-value=22 Score=41.76 Aligned_cols=18 Identities=22% Similarity=0.287 Sum_probs=16.0
Q ss_pred HHHHHHhcCCceecCCCC
Q 009909 368 LAKHLRCVGIDAATPRSK 385 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~ 385 (522)
++|+.|+.|++|.++.+.
T Consensus 61 i~Ry~rm~G~~V~~~~G~ 78 (805)
T PRK00390 61 IARYKRMQGYNVLHPMGW 78 (805)
T ss_pred HHHHHHhcCCcccccCcc
Confidence 799999999999998754
No 161
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=52.81 E-value=7.3 Score=37.22 Aligned_cols=13 Identities=23% Similarity=1.040 Sum_probs=11.2
Q ss_pred CCCcccCCCCccc
Q 009909 449 LMSRCTKCNGRFI 461 (522)
Q Consensus 449 ~~sRC~~CN~~l~ 461 (522)
++.||+.|.+.|.
T Consensus 148 I~A~CsrC~~~L~ 160 (188)
T COG1096 148 IYARCSRCRAPLV 160 (188)
T ss_pred EEEEccCCCcceE
Confidence 4799999999884
No 162
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=52.63 E-value=5.7 Score=35.13 Aligned_cols=19 Identities=26% Similarity=0.712 Sum_probs=12.3
Q ss_pred cCcccCcCCCcccCCCCcc
Q 009909 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 3344445677899999643
No 163
>PRK08402 replication factor A; Reviewed
Probab=52.34 E-value=5.3 Score=42.20 Aligned_cols=29 Identities=17% Similarity=0.579 Sum_probs=20.6
Q ss_pred CCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009909 449 LMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 449 ~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 500 (522)
.+.+|+.||..+.. +....-|+|+.||++
T Consensus 211 ~y~aCp~CnKkv~~-----------------------~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 211 VYDACPECRRKVDY-----------------------DPATDTWICPEHGEV 239 (355)
T ss_pred eEecCCCCCeEEEE-----------------------ecCCCCEeCCCCCCc
Confidence 56899999986520 113457999999975
No 164
>PRK12495 hypothetical protein; Provisional
Probab=52.18 E-value=13 Score=36.39 Aligned_cols=45 Identities=18% Similarity=0.266 Sum_probs=27.9
Q ss_pred HHHHHHHHHhcCcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecc
Q 009909 430 NQQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEV 504 (522)
Q Consensus 430 ~~QL~~v~~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvYW~G 504 (522)
.+++.++|....-. ...-|..|+.+|- .+|. -.+|+.|+++|=++
T Consensus 27 ~~~ma~lL~~gatm-----sa~hC~~CG~PIp-----------------a~pG--------~~~Cp~CQ~~~~~~ 71 (226)
T PRK12495 27 TERMSELLLQGATM-----TNAHCDECGDPIF-----------------RHDG--------QEFCPTCQQPVTED 71 (226)
T ss_pred HHHHHHHHHhhccc-----chhhcccccCccc-----------------CCCC--------eeECCCCCCccccc
Confidence 34566666544322 1346999999862 1232 44599999998664
No 165
>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=52.13 E-value=8.1 Score=26.65 Aligned_cols=10 Identities=20% Similarity=0.700 Sum_probs=8.7
Q ss_pred cccCCCCccc
Q 009909 452 RCTKCNGRFI 461 (522)
Q Consensus 452 RC~~CN~~l~ 461 (522)
-|+.||..|.
T Consensus 3 FCp~C~nlL~ 12 (35)
T PF02150_consen 3 FCPECGNLLY 12 (35)
T ss_dssp BETTTTSBEE
T ss_pred eCCCCCccce
Confidence 4999999986
No 166
>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=52.04 E-value=11 Score=41.36 Aligned_cols=35 Identities=14% Similarity=0.202 Sum_probs=27.8
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009909 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 38999999999999887643334578999988876
No 167
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=52.00 E-value=9.1 Score=35.13 Aligned_cols=17 Identities=24% Similarity=0.784 Sum_probs=13.6
Q ss_pred ccCCceeecCCCCeEEe
Q 009909 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 34577999999998873
No 168
>PRK06386 replication factor A; Reviewed
Probab=51.99 E-value=5.7 Score=41.97 Aligned_cols=15 Identities=20% Similarity=0.753 Sum_probs=12.0
Q ss_pred cCcCCCcccCCCCcc
Q 009909 446 EDQLMSRCTKCNGRF 460 (522)
Q Consensus 446 ~~~~~sRC~~CN~~l 460 (522)
..-++.|||.||-.+
T Consensus 232 gsgli~rCP~C~R~l 246 (358)
T PRK06386 232 GSRIFTKCSVCNKII 246 (358)
T ss_pred CcEeEecCcCCCeEc
Confidence 356789999999865
No 169
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=51.92 E-value=3.5 Score=31.20 Aligned_cols=11 Identities=45% Similarity=0.951 Sum_probs=9.1
Q ss_pred CcccCCCCccc
Q 009909 451 SRCTKCNGRFI 461 (522)
Q Consensus 451 sRC~~CN~~l~ 461 (522)
-||..||..|.
T Consensus 5 iRC~~CnKlLa 15 (60)
T COG4416 5 IRCAKCNKLLA 15 (60)
T ss_pred eehHHHhHHHH
Confidence 48999999773
No 170
>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=51.39 E-value=11 Score=25.16 Aligned_cols=28 Identities=14% Similarity=0.281 Sum_probs=14.9
Q ss_pred CcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009909 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvY 501 (522)
.-|+.|+++... . ....-.+||.||..+
T Consensus 4 rfC~~CG~~t~~--~---------------------~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 4 RFCGRCGAPTKP--A---------------------PGGWARRCPSCGHEH 31 (32)
T ss_dssp SB-TTT--BEEE------------------------SSSS-EEESSSS-EE
T ss_pred cccCcCCccccC--C---------------------CCcCEeECCCCcCEe
Confidence 359999998742 1 123466799999876
No 171
>PHA00626 hypothetical protein
Probab=50.99 E-value=12 Score=28.71 Aligned_cols=16 Identities=19% Similarity=0.229 Sum_probs=12.3
Q ss_pred CCceeecCCCCeEEec
Q 009909 488 NLQFWQCMDCNQLYWE 503 (522)
Q Consensus 488 ~~~F~~C~~CgkvYW~ 503 (522)
...-|.|+.||--|=.
T Consensus 20 ~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 20 WSDDYVCCDCGYNDSK 35 (59)
T ss_pred cCcceEcCCCCCeech
Confidence 4567899999977644
No 172
>PLN02563 aminoacyl-tRNA ligase
Probab=50.26 E-value=24 Score=42.30 Aligned_cols=18 Identities=28% Similarity=0.309 Sum_probs=16.1
Q ss_pred HHHHHHhcCCceecCCCC
Q 009909 368 LAKHLRCVGIDAATPRSK 385 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~ 385 (522)
+|||.|+.||+|.++.+.
T Consensus 140 iaRy~Rm~G~~Vl~~~G~ 157 (963)
T PLN02563 140 LARYKRMQGYNVLHPMGW 157 (963)
T ss_pred HHHHHHhcCCeecccccc
Confidence 799999999999998753
No 173
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=50.06 E-value=12 Score=43.45 Aligned_cols=29 Identities=17% Similarity=0.350 Sum_probs=18.8
Q ss_pred HHHHHHHHHh---cCcCc-ccCcCCCcccCCCC
Q 009909 430 NQQLLEVIEA---FQLKI-SEDQLMSRCTKCNG 458 (522)
Q Consensus 430 ~~QL~~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 3456666653 34443 45667999999995
No 174
>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=49.50 E-value=15 Score=34.26 Aligned_cols=34 Identities=21% Similarity=0.480 Sum_probs=24.0
Q ss_pred ccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009909 445 SEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 445 ~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 500 (522)
..+..|-.|+.|+.. .+-++|.+ .-+.||.||-.
T Consensus 104 e~~~~~Y~Cp~c~~r-----~tf~eA~~-----------------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 104 ETNNMFFICPNMCVR-----FTFNEAME-----------------LNFTCPRCGAM 137 (158)
T ss_pred ccCCCeEECCCCCcE-----eeHHHHHH-----------------cCCcCCCCCCE
Confidence 344567889999975 45677763 14679999965
No 175
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=49.45 E-value=11 Score=25.48 Aligned_cols=13 Identities=23% Similarity=0.639 Sum_probs=11.6
Q ss_pred CceeecCCCCeEE
Q 009909 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 176
>PRK14535 cysS cysteinyl-tRNA synthetase; Provisional
Probab=49.26 E-value=13 Score=42.37 Aligned_cols=55 Identities=20% Similarity=0.245 Sum_probs=36.1
Q ss_pred CCCCCCC-CCCCCCCCCEEEEecccHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009909 342 QGPPPWD-LSLGGDGYPKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 342 ~~~~p~~-~~~~~~~~~rfl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~R 401 (522)
+||-++| +.+|.... -++.| =|+|+||..||+|.++.+...-|+.|+..|+++|.
T Consensus 254 CGPTVYd~~HIGHaRt-~V~~D----VL~R~Lr~~Gy~V~fV~NiTD~DDKII~~A~e~G~ 309 (699)
T PRK14535 254 CGMTVYDYCHLGHARV-MVVFD----MIARWLRECGYPLTYVRNITDIDDKIIARAAENGE 309 (699)
T ss_pred cCCcCCCCCcccchhH-HHHHH----HHHHHHHHcCCceEEEeCCcccchHHHHHHHHcCC
Confidence 4666664 34443322 12222 38999999999999887643334679999998874
No 177
>COG0215 CysS Cysteinyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=49.10 E-value=14 Score=40.36 Aligned_cols=35 Identities=20% Similarity=0.257 Sum_probs=28.1
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009909 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 47999999999988887642224679999999886
No 178
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=49.01 E-value=6.5 Score=34.61 Aligned_cols=20 Identities=20% Similarity=0.528 Sum_probs=13.3
Q ss_pred CcCcccCcCCCcccCCCCcc
Q 009909 441 QLKISEDQLMSRCTKCNGRF 460 (522)
Q Consensus 441 ~l~~~~~~~~sRC~~CN~~l 460 (522)
.|.+...+...||..|+...
T Consensus 61 ~L~i~~~p~~~~C~~Cg~~~ 80 (114)
T PRK03681 61 KLHLEEQEAECWCETCQQYV 80 (114)
T ss_pred EEEEEeeCcEEEcccCCCee
Confidence 44445555678899999743
No 179
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=48.78 E-value=16 Score=27.85 Aligned_cols=27 Identities=22% Similarity=0.639 Sum_probs=19.8
Q ss_pred CCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009909 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 180
>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=48.66 E-value=28 Score=27.27 Aligned_cols=49 Identities=18% Similarity=0.416 Sum_probs=30.1
Q ss_pred HHHHHHHHHhcCcCcc---cCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009909 430 NQQLLEVIEAFQLKIS---EDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 430 ~~QL~~v~~~f~l~~~---~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvY 501 (522)
.++|......+|+.+. +..--..|+.|+..... .....-|.|+.||..+
T Consensus 5 ~~~L~yka~~~G~~v~~v~~~~TSq~C~~CG~~~~~-----------------------~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 5 RQRLEYKAEEYGIQVVEVDEAYTSQTCPRCGHRNKK-----------------------RRSGRVFTCPNCGFEM 56 (69)
T ss_pred HHHHHHHHHHhCCEEEEECCCCCccCccCccccccc-----------------------ccccceEEcCCCCCEE
Confidence 3456666666666542 22223569999996420 1235688999999763
No 181
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=48.37 E-value=25 Score=40.15 Aligned_cols=97 Identities=15% Similarity=0.367 Sum_probs=51.8
Q ss_pred HHHHhhhcCCcEEEecChhHHHhhcccCCcEEEEcCCCHHHHHHHHHH-hc--CcCcccCcCCCcccCCCCccccCCCCh
Q 009909 391 ELIDQTSKEKRVLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQLLEVIE-AF--QLKISEDQLMSRCTKCNGRFIQKPLST 467 (522)
Q Consensus 391 ~ll~~A~~e~RiiLTrd~~l~~~~~~~~~~~~~v~~~~~~~QL~~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 4788888889999999999876543221 111 12344444432 23 112223323344777777653211221
Q ss_pred HHHHHhhhcCcccCccccc----cCCceeecCCCCe
Q 009909 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 SECQ------TKFPVCIASGRPITDNIFWLCPRCKH 1164 (1189)
T ss_pred hhhc------CcCceeeccCCccccceEEEcccccc
Confidence 2211 255655532 3356999999974
No 182
>PRK12496 hypothetical protein; Provisional
Probab=48.33 E-value=27 Score=32.79 Aligned_cols=46 Identities=15% Similarity=0.103 Sum_probs=29.5
Q ss_pred cHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecChhHHHhh
Q 009909 365 VEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRDAKLLRHQ 414 (522)
Q Consensus 365 Lg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~RiiLTrd~~l~~~~ 414 (522)
+..+-+-.+.-| |...+. ..|.+++.+|...+-++||-|..+-+-+
T Consensus 60 i~~v~~~a~~tg-d~~~Ls---~~D~~~iaLA~el~~~lvtDD~~~~~vA 105 (164)
T PRK12496 60 IEKVEEAAIKTG-DLMRLS---NTDIEVLALALELNGTLYTDDYGIQNVA 105 (164)
T ss_pred HHHHHHHHHhcC-Cccccc---hhhHHHHHHHHHhCCcEECcHHHHHHHH
Confidence 455555555556 432222 3567899999988889999997764433
No 183
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=47.42 E-value=13 Score=25.26 Aligned_cols=13 Identities=23% Similarity=0.805 Sum_probs=11.4
Q ss_pred CceeecCCCCeEE
Q 009909 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 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=47.30 E-value=12 Score=25.38 Aligned_cols=12 Identities=25% Similarity=0.587 Sum_probs=9.9
Q ss_pred eeecCCCCeEEe
Q 009909 491 FWQCMDCNQLYW 502 (522)
Q Consensus 491 F~~C~~CgkvYW 502 (522)
.|+|+.||-+|=
T Consensus 1 ~~~C~~CGy~y~ 12 (33)
T cd00350 1 KYVCPVCGYIYD 12 (33)
T ss_pred CEECCCCCCEEC
Confidence 389999999883
No 185
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=47.12 E-value=10 Score=24.15 Aligned_cols=10 Identities=20% Similarity=0.720 Sum_probs=7.6
Q ss_pred CcccCCCCcc
Q 009909 451 SRCTKCNGRF 460 (522)
Q Consensus 451 sRC~~CN~~l 460 (522)
..|+.|+..+
T Consensus 3 ~~Cp~Cg~~~ 12 (26)
T PF13248_consen 3 MFCPNCGAEI 12 (26)
T ss_pred CCCcccCCcC
Confidence 4699999853
No 186
>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=46.67 E-value=36 Score=34.94 Aligned_cols=40 Identities=8% Similarity=-0.058 Sum_probs=28.0
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecC
Q 009909 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRD 407 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~RiiLTrd 407 (522)
++|+||+.||+|.++.+.+.-+..+...|.+++.+-.+.+
T Consensus 29 i~R~~r~~G~~v~~~~g~D~~g~~i~~~a~~~~~~~~~~~ 68 (312)
T cd00668 29 IARYKRMRGYEVPFLPGWDTHGLPIELKAERKGGRKKKTI 68 (312)
T ss_pred HHHHHHhCCCCCCCCCccCCCCHHHHHHHHHhcCcccccc
Confidence 7999999999999887643323457777777765444443
No 187
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=46.37 E-value=13 Score=26.91 Aligned_cols=11 Identities=18% Similarity=0.736 Sum_probs=8.9
Q ss_pred CcccCCCCccc
Q 009909 451 SRCTKCNGRFI 461 (522)
Q Consensus 451 sRC~~CN~~l~ 461 (522)
-+|+.|+..+.
T Consensus 4 y~C~~CG~~~~ 14 (46)
T PRK00398 4 YKCARCGREVE 14 (46)
T ss_pred EECCCCCCEEE
Confidence 47999999763
No 188
>PTZ00399 cysteinyl-tRNA-synthetase; Provisional
Probab=46.27 E-value=16 Score=41.85 Aligned_cols=34 Identities=18% Similarity=0.202 Sum_probs=28.0
Q ss_pred HHHHHH-hcCCceecCCCCCCChHHHHHhhhcCCc
Q 009909 368 LAKHLR-CVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 368 Lar~LR-~lG~D~~~~~~~~~~d~~ll~~A~~e~R 401 (522)
|+|+|| .+||||.++.+...-|+.|+..|+++|.
T Consensus 88 l~R~l~~~~Gy~V~~v~nitDidDKIi~~A~~~g~ 122 (651)
T PTZ00399 88 IRRILEDYFGYDVFYVMNITDIDDKIIKRAREEKL 122 (651)
T ss_pred HHHHHHHhcCCceEEEeCCCCcchHHHHHHHHhCC
Confidence 899999 8999999987643335679999999886
No 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=46.10 E-value=14 Score=25.53 Aligned_cols=16 Identities=25% Similarity=0.528 Sum_probs=9.7
Q ss_pred CceeecCCCCeEEecc
Q 009909 489 LQFWQCMDCNQLYWEV 504 (522)
Q Consensus 489 ~~F~~C~~CgkvYW~G 504 (522)
-...+|+.||+++|.=
T Consensus 9 l~~~rC~~Cg~~~~pP 24 (37)
T PF12172_consen 9 LLGQRCRDCGRVQFPP 24 (37)
T ss_dssp EEEEE-TTT--EEES-
T ss_pred EEEEEcCCCCCEecCC
Confidence 3577899999999963
No 190
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.05 E-value=8.1 Score=34.53 Aligned_cols=19 Identities=16% Similarity=0.253 Sum_probs=13.3
Q ss_pred CcCcccCcCCCcccCCCCcc
Q 009909 441 QLKISEDQLMSRCTKCNGRF 460 (522)
Q Consensus 441 ~l~~~~~~~~sRC~~CN~~l 460 (522)
.|.+...+...|| .|+...
T Consensus 61 ~L~I~~vp~~~~C-~Cg~~~ 79 (124)
T PRK00762 61 DLIVEMIPVEIEC-ECGYEG 79 (124)
T ss_pred EEEEEecCeeEEe-eCcCcc
Confidence 4455555667899 999764
No 191
>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=45.93 E-value=11 Score=32.96 Aligned_cols=30 Identities=20% Similarity=0.572 Sum_probs=20.2
Q ss_pred CcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecc
Q 009909 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEV 504 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvYW~G 504 (522)
..|+.|+.+++- +. + .=-.||.||..|=.-
T Consensus 10 R~Cp~CG~kFYD--Ln------------k----------~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYD--LN------------K----------DPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhcc--CC------------C----------CCccCCCCCCccCcc
Confidence 359999998861 21 1 223499999998554
No 192
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=45.66 E-value=19 Score=34.25 Aligned_cols=35 Identities=29% Similarity=0.691 Sum_probs=23.1
Q ss_pred cccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009909 444 ISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 444 ~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 500 (522)
...+..|-.|+.|+... +-++|.+ .-+.||.||-.
T Consensus 111 ~e~~~~~Y~Cp~C~~ry-----tf~eA~~-----------------~~F~Cp~Cg~~ 145 (178)
T PRK06266 111 EEENNMFFFCPNCHIRF-----TFDEAME-----------------YGFRCPQCGEM 145 (178)
T ss_pred hccCCCEEECCCCCcEE-----eHHHHhh-----------------cCCcCCCCCCC
Confidence 33345577899999754 5567653 24679999863
No 193
>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=45.59 E-value=19 Score=27.45 Aligned_cols=30 Identities=13% Similarity=0.404 Sum_probs=19.3
Q ss_pred CcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009909 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------------------LENPEL---GELVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEe------------------cCCCcc---CCEEeCCCCCCEE
Confidence 36999999763 222221 2345899999765
No 194
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=45.47 E-value=16 Score=23.18 Aligned_cols=15 Identities=13% Similarity=0.452 Sum_probs=12.2
Q ss_pred CCceeecCCCCeEEe
Q 009909 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 355689999999985
No 195
>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=45.40 E-value=11 Score=28.74 Aligned_cols=11 Identities=18% Similarity=0.730 Sum_probs=8.7
Q ss_pred CCCcccCCCCc
Q 009909 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 46889999974
No 196
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=45.29 E-value=18 Score=30.35 Aligned_cols=18 Identities=17% Similarity=0.540 Sum_probs=14.6
Q ss_pred CceeecCCCCeEEecccc
Q 009909 489 LQFWQCMDCNQLYWEVMS 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 458999999999876654
No 197
>PRK12496 hypothetical protein; Provisional
Probab=45.16 E-value=14 Score=34.60 Aligned_cols=11 Identities=18% Similarity=0.522 Sum_probs=8.5
Q ss_pred CcccCCCCccc
Q 009909 451 SRCTKCNGRFI 461 (522)
Q Consensus 451 sRC~~CN~~l~ 461 (522)
..|+.|+++|.
T Consensus 144 ~~C~~CG~~~~ 154 (164)
T PRK12496 144 DVCEICGSPVK 154 (164)
T ss_pred CcCCCCCChhh
Confidence 56889988874
No 198
>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=45.02 E-value=8 Score=34.09 Aligned_cols=20 Identities=20% Similarity=0.667 Sum_probs=13.1
Q ss_pred CcCcccCcCCCcccCCCCcc
Q 009909 441 QLKISEDQLMSRCTKCNGRF 460 (522)
Q Consensus 441 ~l~~~~~~~~sRC~~CN~~l 460 (522)
.|.+...+...||..|+...
T Consensus 61 ~L~I~~~p~~~~C~~Cg~~~ 80 (115)
T TIGR00100 61 KLNIEDEPVECECEDCSEEV 80 (115)
T ss_pred EEEEEeeCcEEEcccCCCEE
Confidence 34444455678899998653
No 199
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=44.76 E-value=14 Score=35.25 Aligned_cols=16 Identities=25% Similarity=0.764 Sum_probs=13.2
Q ss_pred ccCCceeecCCCCeEE
Q 009909 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 3467899999999876
No 200
>PRK14534 cysS cysteinyl-tRNA synthetase; Provisional
Probab=44.38 E-value=16 Score=40.21 Aligned_cols=36 Identities=11% Similarity=0.075 Sum_probs=26.3
Q ss_pred HHHHHHHhcCCceecCCCC-CC---------ChHHHHHhhhcCCcE
Q 009909 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 3899999999999984321 11 245699999888754
No 201
>PF12813 XPG_I_2: XPG domain containing
Probab=43.77 E-value=25 Score=35.24 Aligned_cols=44 Identities=23% Similarity=0.214 Sum_probs=35.8
Q ss_pred HHHHHHHhc---CCceecCCCCCCChHHHHHhhhcCCcEEEecChhHHH
Q 009909 367 GLAKHLRCV---GIDAATPRSKKPEPRELIDQTSKEKRVLLTRDAKLLR 412 (522)
Q Consensus 367 ~Lar~LR~l---G~D~~~~~~~~~~d~~ll~~A~~e~RiiLTrd~~l~~ 412 (522)
-+..-||.+ |..+..+.. ..|.+++..|++-|..|||.|.+|+-
T Consensus 8 ~~~e~L~~~~~~~~~~~~~~~--EAD~~~A~~A~~~~~~VLt~DSDf~I 54 (246)
T PF12813_consen 8 AFIEALRESWRYGVPVVQCPG--EADRECAALARKWGCPVLTNDSDFLI 54 (246)
T ss_pred HHHHHHHHHhhcCCcEEEcCc--cchHHHHHHHHHcCCeEEccCCCEEE
Confidence 345557777 999988753 56889999999999999999999854
No 202
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=43.40 E-value=16 Score=31.82 Aligned_cols=27 Identities=22% Similarity=0.597 Sum_probs=19.2
Q ss_pred CcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009909 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 4699999954 2332 3579999999753
No 203
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=43.27 E-value=32 Score=31.49 Aligned_cols=40 Identities=15% Similarity=0.407 Sum_probs=24.4
Q ss_pred cccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009909 444 ISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 444 ~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 500 (522)
...+..+-.|+.|+... +..+|... .+ | +.-..||.||..
T Consensus 93 ~e~~~~~Y~Cp~C~~~y-----~~~ea~~~---~d--~-------~~~f~Cp~Cg~~ 132 (147)
T smart00531 93 DETNNAYYKCPNCQSKY-----TFLEANQL---LD--M-------DGTFTCPRCGEE 132 (147)
T ss_pred cccCCcEEECcCCCCEe-----eHHHHHHh---cC--C-------CCcEECCCCCCE
Confidence 33445678899999764 34555431 01 1 233789999975
No 204
>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=43.24 E-value=17 Score=30.71 Aligned_cols=17 Identities=18% Similarity=0.647 Sum_probs=13.2
Q ss_pred CceeecCCCCeEEeccc
Q 009909 489 LQFWQCMDCNQLYWEVM 505 (522)
Q Consensus 489 ~~F~~C~~CgkvYW~Gs 505 (522)
.-.|.|..||+.|=.|.
T Consensus 51 ~GIW~C~~C~~~~AGGA 67 (90)
T PF01780_consen 51 TGIWKCKKCGKKFAGGA 67 (90)
T ss_dssp TTEEEETTTTEEEE-BS
T ss_pred eEEeecCCCCCEEeCCC
Confidence 35899999999986664
No 205
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=42.42 E-value=14 Score=31.21 Aligned_cols=12 Identities=25% Similarity=0.628 Sum_probs=10.4
Q ss_pred CCCcccCCCCcc
Q 009909 449 LMSRCTKCNGRF 460 (522)
Q Consensus 449 ~~sRC~~CN~~l 460 (522)
+-|+|..|+.+|
T Consensus 32 ~rS~C~~C~~~L 43 (92)
T PF06750_consen 32 PRSHCPHCGHPL 43 (92)
T ss_pred CCCcCcCCCCcC
Confidence 359999999987
No 206
>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=41.94 E-value=21 Score=35.38 Aligned_cols=21 Identities=10% Similarity=0.028 Sum_probs=16.1
Q ss_pred CceeecCCCCeEEecccchhhH
Q 009909 489 LQFWQCMDCNQLYWEVMSAYLF 510 (522)
Q Consensus 489 ~~F~~C~~CgkvYW~GsH~~r~ 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 378999999997765 666654
No 207
>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=41.54 E-value=14 Score=38.08 Aligned_cols=34 Identities=18% Similarity=0.220 Sum_probs=25.5
Q ss_pred HHHHHHhcCCceecCCCC-CCChHHHHHhhhcCCcE
Q 009909 368 LAKHLRCVGIDAATPRSK-KPEPRELIDQTSKEKRV 402 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~-~~~d~~ll~~A~~e~Ri 402 (522)
|.|+|+.+||++.++.+. ++ |+.|++.|+++|.-
T Consensus 36 l~R~L~~~g~~V~~V~NiTDi-DDKii~~A~~~g~~ 70 (300)
T PF01406_consen 36 LRRYLEYLGYDVTYVMNITDI-DDKIIKRAREEGVS 70 (300)
T ss_dssp HHHHHHHTT-EEEEEEEEB-S-SHHHHHHHHHTTS-
T ss_pred HHHHHHHcCCeEEEEEecccc-chHHHHHHHhccCC
Confidence 799999999999987653 34 45699999998843
No 208
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=41.34 E-value=32 Score=39.18 Aligned_cols=58 Identities=19% Similarity=0.271 Sum_probs=34.4
Q ss_pred HHHHHHHHh---cCcC-cccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecccc
Q 009909 431 QQLLEVIEA---FQLK-ISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVMS 506 (522)
Q Consensus 431 ~QL~~v~~~---f~l~-~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvYW~GsH 506 (522)
+.+..|++. .++. .+-+..+++|..|+-.-. .-+.||.||. .-.+
T Consensus 536 ~Al~~lvk~~~~~~i~Y~sin~~~~~C~~CGy~g~----------------------------~~~~CP~CG~---~d~~ 584 (618)
T PRK14704 536 KALKQIVQAMAEHGVGYGSINHPVDRCKCCSYHGV----------------------------IGNECPSCGN---EDEA 584 (618)
T ss_pred HHHHHHHHHHHhcCCceEEeCCCCeecCCCCCCCC----------------------------cCccCcCCCC---CCcc
Confidence 456666653 2333 233456899999986210 0177999975 1111
Q ss_pred hhhHHhhhhhhhh
Q 009909 507 AYLFIFLTPAYFS 519 (522)
Q Consensus 507 ~~r~~~~~~~~~~ 519 (522)
---+++|++-|+.
T Consensus 585 ~~~v~~Ri~GYl~ 597 (618)
T PRK14704 585 NIERIRRITGYLV 597 (618)
T ss_pred hhHHHHHHHhHhc
Confidence 1347888888874
No 209
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=41.04 E-value=16 Score=32.93 Aligned_cols=9 Identities=56% Similarity=1.280 Sum_probs=6.1
Q ss_pred cccCCCCcc
Q 009909 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 577777765
No 210
>PHA02768 hypothetical protein; Provisional
Probab=41.03 E-value=10 Score=28.99 Aligned_cols=18 Identities=22% Similarity=0.571 Sum_probs=15.7
Q ss_pred eecCCCCeEEecccchhh
Q 009909 492 WQCMDCNQLYWEVMSAYL 509 (522)
Q Consensus 492 ~~C~~CgkvYW~GsH~~r 509 (522)
+.|+.|||.|=.++|..+
T Consensus 6 y~C~~CGK~Fs~~~~L~~ 23 (55)
T PHA02768 6 YECPICGEIYIKRKSMIT 23 (55)
T ss_pred cCcchhCCeeccHHHHHH
Confidence 489999999999988766
No 211
>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=40.98 E-value=38 Score=33.41 Aligned_cols=51 Identities=14% Similarity=0.198 Sum_probs=37.2
Q ss_pred cCCccHHHHHHHHcCCcCcc--cccccCC-CC-C-CCCHHHHHHHHHHHHHHHHHH
Q 009909 159 KETKSLANICKELLDISLSK--ELQCSDW-SN-R-PLTEEQKNYAAIDAHCLIEIF 209 (522)
Q Consensus 159 ~~~~sL~~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 35899999999999986543 3455665 22 2 233556899999999999875
No 212
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=40.83 E-value=31 Score=35.09 Aligned_cols=44 Identities=16% Similarity=0.286 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhcCcCcccCc-CC--CcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009909 429 KNQQLLEVIEAFQLKISEDQ-LM--SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 429 ~~~QL~~v~~~f~l~~~~~~-~~--sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 500 (522)
..+||....+..++.+...+ .. ..|+.|+. + ....|.||.||..
T Consensus 285 ~~~~l~yka~~~~~~v~~~~~~~tS~~C~~cg~-~---------------------------~~r~~~C~~cg~~ 331 (364)
T COG0675 285 LRRQLEYKAEWGGIVVKVVPPYYTSKTCPCCGH-L---------------------------SGRLFKCPRCGFV 331 (364)
T ss_pred HHHHHHHHHHhCCeEEEECCCCCCcccccccCC-c---------------------------cceeEECCCCCCe
Confidence 35666666666444433222 12 47999998 2 1257889999965
No 213
>PRK05978 hypothetical protein; Provisional
Probab=40.35 E-value=16 Score=33.84 Aligned_cols=9 Identities=22% Similarity=0.977 Sum_probs=7.5
Q ss_pred ecCCCCeEE
Q 009909 493 QCMDCNQLY 501 (522)
Q Consensus 493 ~C~~CgkvY 501 (522)
.|+.||.-|
T Consensus 54 ~C~~CG~~~ 62 (148)
T PRK05978 54 HCAACGEDF 62 (148)
T ss_pred CccccCCcc
Confidence 399999877
No 214
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=39.97 E-value=7.1 Score=37.35 Aligned_cols=30 Identities=13% Similarity=0.559 Sum_probs=21.5
Q ss_pred cCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009909 448 QLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 448 ~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvY 501 (522)
.++++|+.|.++++ |.+. .--.|+.||+++
T Consensus 147 vv~a~~~~~g~~~~--~~~~----------------------~~~~c~~~~~~e 176 (189)
T PRK09521 147 VIYAMCSRCRTPLV--KKGE----------------------NELKCPNCGNIE 176 (189)
T ss_pred EEEEEccccCCceE--ECCC----------------------CEEECCCCCCEE
Confidence 45789999999875 3211 235699999876
No 215
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=39.61 E-value=22 Score=32.09 Aligned_cols=26 Identities=15% Similarity=0.427 Sum_probs=15.4
Q ss_pred HHHHHHHHhcCcCcccCcCCCcccCCCCccc
Q 009909 431 QQLLEVIEAFQLKISEDQLMSRCTKCNGRFI 461 (522)
Q Consensus 431 ~QL~~v~~~f~l~~~~~~~~sRC~~CN~~l~ 461 (522)
.-++++|..-.-.+. --|++|+.+|.
T Consensus 14 k~iA~lLl~GAkML~-----~hCp~Cg~PLF 39 (131)
T COG1645 14 KKIAELLLQGAKMLA-----KHCPKCGTPLF 39 (131)
T ss_pred HHHHHHHHhhhHHHH-----hhCcccCCcce
Confidence 445555544332222 34999999985
No 216
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=39.59 E-value=73 Score=29.06 Aligned_cols=52 Identities=12% Similarity=0.119 Sum_probs=35.9
Q ss_pred HhcCCceecCCCCCCChHHHHHhhhcCC-cEEEecChhHHHhhcccCCcEEEEcC
Q 009909 373 RCVGIDAATPRSKKPEPRELIDQTSKEK-RVLLTRDAKLLRHQYLIKNQIYRVKS 426 (522)
Q Consensus 373 R~lG~D~~~~~~~~~~d~~ll~~A~~e~-RiiLTrd~~l~~~~~~~~~~~~~v~~ 426 (522)
...++.+.+. . ...|+-|++.|.+.| -|+.|.|++|-++....|..++.++.
T Consensus 73 ~~er~~~~~~-~-~~aDe~i~~~a~~~~~~iVaTnD~eLk~rlr~~GIPvi~lr~ 125 (136)
T COG1412 73 YAERLECIHK-G-RYADECLLEAALKHGRYIVATNDKELKRRLRENGIPVITLRQ 125 (136)
T ss_pred HhhccCcccc-C-CChHHHHHHHHHHcCCEEEEeCCHHHHHHHHHcCCCEEEEeC
Confidence 3445555544 2 234778999999999 77789999997765545556666664
No 217
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=39.51 E-value=14 Score=39.67 Aligned_cols=30 Identities=27% Similarity=0.633 Sum_probs=21.0
Q ss_pred CCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEec
Q 009909 450 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWE 503 (522)
Q Consensus 450 ~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvYW~ 503 (522)
..+|+.|++.+. . +| .. -|+|++||..|=.
T Consensus 350 ~p~Cp~Cg~~m~-------S-----~G-----------~~-g~rC~kCg~~~~~ 379 (421)
T COG1571 350 NPVCPRCGGRMK-------S-----AG-----------RN-GFRCKKCGTRARE 379 (421)
T ss_pred CCCCCccCCchh-------h-----cC-----------CC-CcccccccccCCc
Confidence 468999999862 1 12 12 7899999987643
No 218
>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=39.40 E-value=21 Score=24.81 Aligned_cols=13 Identities=23% Similarity=0.674 Sum_probs=10.4
Q ss_pred CCceeecCCCCeE
Q 009909 488 NLQFWQCMDCNQL 500 (522)
Q Consensus 488 ~~~F~~C~~Cgkv 500 (522)
.+-|+.|..||-+
T Consensus 22 ~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 22 DDGFYYCDRCGHQ 34 (36)
T ss_pred cCCEEEhhhCceE
Confidence 4569999999964
No 219
>PRK14536 cysS cysteinyl-tRNA synthetase; Provisional
Probab=39.09 E-value=27 Score=38.60 Aligned_cols=35 Identities=9% Similarity=0.235 Sum_probs=26.4
Q ss_pred HHHHHHhcCCceecCCC----------CCCChHHHHHhhhcCCcE
Q 009909 368 LAKHLRCVGIDAATPRS----------KKPEPRELIDQTSKEKRV 402 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~----------~~~~d~~ll~~A~~e~Ri 402 (522)
|+||||..||+|.++.+ .+..|..|+..|+++|.-
T Consensus 51 l~R~l~~~G~~V~~v~NiTDv~hl~~~~De~ddKii~~A~~~g~~ 95 (490)
T PRK14536 51 LRRTLHFLGYRVTHVMNITDVGHLTDDADSGEDKMVKSAQEHGKS 95 (490)
T ss_pred HHHHHHhcCCceEEEEeeccccccccCCcCCChHHHHHHHHcCCC
Confidence 79999999999998742 122356788889888754
No 220
>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=38.27 E-value=17 Score=27.34 Aligned_cols=13 Identities=15% Similarity=0.674 Sum_probs=7.1
Q ss_pred CceeecCCCCeEE
Q 009909 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 221
>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=38.25 E-value=20 Score=33.43 Aligned_cols=16 Identities=19% Similarity=0.445 Sum_probs=12.9
Q ss_pred ccCCceeecCCCCeEE
Q 009909 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 3467899999999765
No 222
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=38.06 E-value=22 Score=30.13 Aligned_cols=17 Identities=18% Similarity=0.579 Sum_probs=13.9
Q ss_pred CceeecCCCCeEEeccc
Q 009909 489 LQFWQCMDCNQLYWEVM 505 (522)
Q Consensus 489 ~~F~~C~~CgkvYW~Gs 505 (522)
.--|.|..||+.|=.|.
T Consensus 51 ~GIW~C~~C~~~~AGGA 67 (91)
T TIGR00280 51 TGIWTCRKCGAKFAGGA 67 (91)
T ss_pred eEEEEcCCCCCEEeCCc
Confidence 45899999999986664
No 223
>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=38.03 E-value=19 Score=25.04 Aligned_cols=12 Identities=25% Similarity=0.847 Sum_probs=9.8
Q ss_pred eecCCCCeEEec
Q 009909 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 489999998853
No 224
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=37.89 E-value=23 Score=29.91 Aligned_cols=17 Identities=18% Similarity=0.602 Sum_probs=13.9
Q ss_pred CceeecCCCCeEEeccc
Q 009909 489 LQFWQCMDCNQLYWEVM 505 (522)
Q Consensus 489 ~~F~~C~~CgkvYW~Gs 505 (522)
.--|.|..||+.|=.|.
T Consensus 52 ~GIW~C~~C~~~~AGGA 68 (90)
T PTZ00255 52 VGIWRCKGCKKTVAGGA 68 (90)
T ss_pred eEEEEcCCCCCEEeCCc
Confidence 35899999999986664
No 225
>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=37.68 E-value=28 Score=24.55 Aligned_cols=31 Identities=32% Similarity=0.874 Sum_probs=15.9
Q ss_pred CcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009909 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--PF-----------------CQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp -B-TTT--BS---TT-----------------SEEETTTTEEEETTT--E
T ss_pred cccCCCCCEEC--Cc-----------------ceEcCCCCEEECcCCCCc
Confidence 58999999652 21 113345679999999874
No 226
>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=37.61 E-value=17 Score=23.73 Aligned_cols=10 Identities=20% Similarity=0.992 Sum_probs=5.6
Q ss_pred cccCCCCccc
Q 009909 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 4999999885
No 227
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=37.44 E-value=18 Score=31.10 Aligned_cols=9 Identities=44% Similarity=1.269 Sum_probs=4.2
Q ss_pred cccCCCCcc
Q 009909 452 RCTKCNGRF 460 (522)
Q Consensus 452 RC~~CN~~l 460 (522)
||++|+..+
T Consensus 4 ~CtrCG~vf 12 (112)
T COG3364 4 QCTRCGEVF 12 (112)
T ss_pred eeccccccc
Confidence 455554443
No 228
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=37.41 E-value=17 Score=22.58 Aligned_cols=9 Identities=22% Similarity=0.903 Sum_probs=7.2
Q ss_pred cccCCCCcc
Q 009909 452 RCTKCNGRF 460 (522)
Q Consensus 452 RC~~CN~~l 460 (522)
+|+.|+..+
T Consensus 1 ~Cp~CG~~~ 9 (23)
T PF13240_consen 1 YCPNCGAEI 9 (23)
T ss_pred CCcccCCCC
Confidence 589999865
No 229
>PHA02998 RNA polymerase subunit; Provisional
Probab=37.39 E-value=28 Score=33.01 Aligned_cols=48 Identities=21% Similarity=0.488 Sum_probs=26.3
Q ss_pred hcCcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009909 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-EP------mT~FYkC~~CG~~w 181 (195)
T PHA02998 134 YFNVLDE--KYNTPCPNCKSKNTT-PM-MIQTRAA----D-EP------PLVRHACRDCKKHF 181 (195)
T ss_pred heeccCc--ccCCCCCCCCCCceE-EE-EEeeccC----C-CC------ceEEEEcCCCCCcc
Confidence 4776543 235789999985210 00 0011100 1 12 35799999999864
No 230
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=36.95 E-value=19 Score=33.20 Aligned_cols=12 Identities=17% Similarity=0.440 Sum_probs=9.3
Q ss_pred CCcccCCCCccc
Q 009909 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 458999999763
No 231
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=36.74 E-value=43 Score=30.34 Aligned_cols=36 Identities=19% Similarity=0.263 Sum_probs=28.3
Q ss_pred ccHH--HHHHHHhcCCceecCCCCCCChHHHHHhhhcCC
Q 009909 364 MVEG--LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEK 400 (522)
Q Consensus 364 mLg~--Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~ 400 (522)
.+|. ++..||..||+++++.. +....++++.|.+++
T Consensus 17 ~lG~~iv~~~lr~~G~eVi~LG~-~vp~e~i~~~a~~~~ 54 (137)
T PRK02261 17 AVGNKILDRALTEAGFEVINLGV-MTSQEEFIDAAIETD 54 (137)
T ss_pred HHHHHHHHHHHHHCCCEEEECCC-CCCHHHHHHHHHHcC
Confidence 3553 69999999999999975 456678998887654
No 232
>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=36.74 E-value=19 Score=32.25 Aligned_cols=10 Identities=20% Similarity=0.644 Sum_probs=8.6
Q ss_pred cccCCCCccc
Q 009909 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 4999999885
No 233
>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=36.25 E-value=25 Score=26.85 Aligned_cols=11 Identities=18% Similarity=0.570 Sum_probs=8.8
Q ss_pred CCCcccCCCCc
Q 009909 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 234
>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=36.11 E-value=50 Score=35.14 Aligned_cols=17 Identities=24% Similarity=0.321 Sum_probs=15.4
Q ss_pred HHHHHHhcCCceecCCC
Q 009909 368 LAKHLRCVGIDAATPRS 384 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~ 384 (522)
+||++|+.|++|.++.+
T Consensus 30 ~~Ry~r~~G~~V~~~~G 46 (382)
T cd00817 30 IARYKRMKGYNVLWPPG 46 (382)
T ss_pred HHHHHHhcCCcccccCc
Confidence 79999999999998875
No 235
>PRK11032 hypothetical protein; Provisional
Probab=35.90 E-value=19 Score=33.64 Aligned_cols=11 Identities=27% Similarity=0.715 Sum_probs=8.8
Q ss_pred CcccCCCCccc
Q 009909 451 SRCTKCNGRFI 461 (522)
Q Consensus 451 sRC~~CN~~l~ 461 (522)
-+|..|+..+.
T Consensus 125 LvC~~Cg~~~~ 135 (160)
T PRK11032 125 LVCEKCHHHLA 135 (160)
T ss_pred EEecCCCCEEE
Confidence 57999998763
No 236
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=35.75 E-value=19 Score=22.77 Aligned_cols=10 Identities=20% Similarity=0.630 Sum_probs=8.7
Q ss_pred eecCCCCeEE
Q 009909 492 WQCMDCNQLY 501 (522)
Q Consensus 492 ~~C~~CgkvY 501 (522)
-.|+.|||-|
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 3599999998
No 237
>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=35.67 E-value=24 Score=34.27 Aligned_cols=38 Identities=16% Similarity=0.126 Sum_probs=25.3
Q ss_pred ccH-HHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009909 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 48999999999998765432223457776655443
No 238
>PRK03954 ribonuclease P protein component 4; Validated
Probab=35.62 E-value=32 Score=30.72 Aligned_cols=32 Identities=16% Similarity=0.362 Sum_probs=25.0
Q ss_pred HHHHHHHHhcCcCcccCcCCCcccCCCCcccc
Q 009909 431 QQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQ 462 (522)
Q Consensus 431 ~QL~~v~~~f~l~~~~~~~~sRC~~CN~~l~~ 462 (522)
..+..|.....+.+.++---+-|-.||..|++
T Consensus 45 ~lar~Is~K~rirlp~~~KR~~CK~C~t~LiP 76 (121)
T PRK03954 45 ELALAVQQKAKVKLPRKWKRRYCKRCHSFLVP 76 (121)
T ss_pred HHHHHHHHHhccCCCHHHHHHHhhcCCCeeec
Confidence 45677777888887776656779999999963
No 239
>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=35.56 E-value=19 Score=25.48 Aligned_cols=17 Identities=24% Similarity=0.620 Sum_probs=13.7
Q ss_pred CCceeecCCCCeEEecc
Q 009909 488 NLQFWQCMDCNQLYWEV 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 240
>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=35.16 E-value=36 Score=32.64 Aligned_cols=52 Identities=23% Similarity=0.606 Sum_probs=26.8
Q ss_pred HHHHHHHHhcCcCcccCcCCCccc--CCCC-ccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEec
Q 009909 431 QQLLEVIEAFQLKISEDQLMSRCT--KCNG-RFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWE 503 (522)
Q Consensus 431 ~QL~~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--PiG----------lsd~~----g~~~vKlyCP~C~dvY~p 139 (184)
T PF01214_consen 85 RGLEQMKEKYE-----QGDFGRCPRVYCNGQPLL--PIG----------LSDTP----GESTVKLYCPRCKDVYHP 139 (184)
T ss_dssp HHHHHHHHHHH-----TTTT-B-SBGGGTT-B-E--EEB----------S-SST----TS-BBEEEETTTTEEE--
T ss_pred HHHHHHHHhhc-----CCcCCcCCcccCCCCcee--Ccc----------CCCCC----CccceeEECCCCccccCC
Confidence 45677777774 23488997 4776 444 331 11111 223445569999999987
No 241
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=35.14 E-value=20 Score=36.44 Aligned_cols=12 Identities=17% Similarity=0.501 Sum_probs=9.5
Q ss_pred CCceeecCCCCe
Q 009909 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 456888999975
No 242
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=35.09 E-value=28 Score=33.87 Aligned_cols=21 Identities=24% Similarity=0.491 Sum_probs=13.1
Q ss_pred CcCcccCcCC-CcccCCCCccc
Q 009909 441 QLKISEDQLM-SRCTKCNGRFI 461 (522)
Q Consensus 441 ~l~~~~~~~~-sRC~~CN~~l~ 461 (522)
++.++...+| -||..||.=+.
T Consensus 32 glSiRL~TPF~~RCL~C~~YI~ 53 (272)
T COG5134 32 GLSIRLETPFPVRCLNCENYIQ 53 (272)
T ss_pred cceEEeccCcceeecchhhhhh
Confidence 3444444444 59999998653
No 243
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=35.06 E-value=25 Score=29.70 Aligned_cols=17 Identities=18% Similarity=0.612 Sum_probs=13.7
Q ss_pred CceeecCCCCeEEeccc
Q 009909 489 LQFWQCMDCNQLYWEVM 505 (522)
Q Consensus 489 ~~F~~C~~CgkvYW~Gs 505 (522)
.--|.|..||+.|=.|.
T Consensus 52 ~GIW~C~~C~~~~AGGA 68 (90)
T PRK03976 52 TGIWECRKCGAKFAGGA 68 (90)
T ss_pred EEEEEcCCCCCEEeCCc
Confidence 45899999999986554
No 244
>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=34.67 E-value=35 Score=30.64 Aligned_cols=33 Identities=18% Similarity=0.070 Sum_probs=21.9
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcC
Q 009909 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 489999999999988764322233455555444
No 245
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=34.00 E-value=31 Score=34.72 Aligned_cols=32 Identities=19% Similarity=0.353 Sum_probs=22.3
Q ss_pred CCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecc
Q 009909 450 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEV 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 HRFCGYCGHPMHP--S---------------------KTEWAMLCPHCRERYYPR 130 (256)
T ss_pred CccccccCCCCee--c---------------------CCceeEECCCCCCEECCC
Confidence 4679999998741 0 012245699999999974
No 246
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=33.95 E-value=48 Score=33.38 Aligned_cols=54 Identities=17% Similarity=0.443 Sum_probs=32.2
Q ss_pred HHHHHHHHhcCcCcccCcCCCcccC--CCC-ccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEeccc
Q 009909 431 QQLLEVIEAFQLKISEDQLMSRCTK--CNG-RFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVM 505 (522)
Q Consensus 431 ~QL~~v~~~f~l~~~~~~~~sRC~~--CN~-~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvYW~Gs 505 (522)
.-|..+.+.|. ...|.+|++ ||+ +++ |+-. ..+| .....-..||+|+.||=.-+
T Consensus 106 ~Gl~~M~eKY~-----~g~FG~CPRv~C~~q~~L--PvGl----------Sd~~----g~~~VKlyCP~C~DvY~p~s 162 (251)
T PTZ00396 106 KGLALMREKYL-----QGKFGHCPRVLCEGQNVL--PIGL----------SDVL----KTSRVKVYCPRCQEVYHPKK 162 (251)
T ss_pred HHHHHHHHHhh-----CCCCCCCCCccCCCCccc--cccc----------CCCc----CcCceeEeCCCchhhcCCCC
Confidence 35666677774 245899995 886 343 4421 1122 22344556999999995533
No 247
>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=33.71 E-value=24 Score=34.61 Aligned_cols=30 Identities=13% Similarity=0.314 Sum_probs=21.1
Q ss_pred ccCccccccCCceeecCCCCeEEecccchhh
Q 009909 479 RIPDCLFDKNLQFWQCMDCNQLYWEVMSAYL 509 (522)
Q Consensus 479 ~vp~~v~~~~~~F~~C~~CgkvYW~GsH~~r 509 (522)
-|-..|.+..+.=|+|+-|+|.| .|.||=|
T Consensus 65 ~v~~~~~e~~~~K~~C~lc~KlF-kg~eFV~ 94 (214)
T PF04959_consen 65 FVQKNTKEEDEDKWRCPLCGKLF-KGPEFVR 94 (214)
T ss_dssp GEEEEE-SSSSEEEEE-SSS-EE-SSHHHHH
T ss_pred HHHHHHHHHcCCEECCCCCCccc-CChHHHH
Confidence 45667777788899999999998 6676655
No 248
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=33.22 E-value=27 Score=21.85 Aligned_cols=15 Identities=13% Similarity=0.713 Sum_probs=11.8
Q ss_pred eecCCCCeEEecccc
Q 009909 492 WQCMDCNQLYWEVMS 506 (522)
Q Consensus 492 ~~C~~CgkvYW~GsH 506 (522)
+.|..|++.|-..+-
T Consensus 2 ~~C~~C~~~F~~~~~ 16 (27)
T PF13912_consen 2 FECDECGKTFSSLSA 16 (27)
T ss_dssp EEETTTTEEESSHHH
T ss_pred CCCCccCCccCChhH
Confidence 579999999976443
No 249
>PRK10220 hypothetical protein; Provisional
Probab=33.20 E-value=31 Score=30.10 Aligned_cols=12 Identities=17% Similarity=0.589 Sum_probs=9.6
Q ss_pred CceeecCCCCeE
Q 009909 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 357999999875
No 250
>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=33.19 E-value=27 Score=41.15 Aligned_cols=10 Identities=60% Similarity=1.428 Sum_probs=8.5
Q ss_pred CcccCCCCcc
Q 009909 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 251
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=33.18 E-value=53 Score=33.14 Aligned_cols=49 Identities=24% Similarity=0.306 Sum_probs=32.3
Q ss_pred EEEecccHHHHHHHHhcCCceecCCCCCCCh---HHHHHhhhcCCcEEEecC
Q 009909 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 4789999999999999999995533211111 245666666655555443
No 252
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=32.83 E-value=21 Score=39.37 Aligned_cols=41 Identities=12% Similarity=0.282 Sum_probs=25.2
Q ss_pred CCcccCCCCccccCCCChHHHHHhhhcCcccCccc-cccCCceeecCCCCe
Q 009909 450 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCL-FDKNLQFWQCMDCNQ 499 (522)
Q Consensus 450 ~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v-~~~~~~F~~C~~Cgk 499 (522)
--+|..|+-.--+..-+++ ..||+++ ++...+=|.||.||-
T Consensus 425 ~~~c~~c~~~yd~~~g~~~---------~~~~~gt~~~~lp~~~~cp~c~~ 466 (479)
T PRK05452 425 RMQCSVCQWIYDPAKGEPM---------QDVAPGTPWSEVPDNFLCPECSL 466 (479)
T ss_pred eEEECCCCeEECCCCCCcc---------cCCCCCCChhhCCCCCcCcCCCC
Confidence 3479999975432111111 2477775 455566799999984
No 253
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=32.35 E-value=47 Score=25.79 Aligned_cols=11 Identities=27% Similarity=0.764 Sum_probs=8.8
Q ss_pred CcccCCCCccc
Q 009909 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 35999999874
No 254
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=32.26 E-value=53 Score=37.42 Aligned_cols=69 Identities=9% Similarity=0.125 Sum_probs=40.1
Q ss_pred CCcEEEEcCC--CHHHHHHHHHHh---cCcC-cccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCce
Q 009909 418 KNQIYRVKSL--LKNQQLLEVIEA---FQLK-ISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQF 491 (522)
Q Consensus 418 ~~~~~~v~~~--~~~~QL~~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 4555555322 123556666653 3333 234456899999997310 124
Q ss_pred eecCCCCeEEecccchhhHHhhhhhhhh
Q 009909 492 WQCMDCNQLYWEVMSAYLFIFLTPAYFS 519 (522)
Q Consensus 492 ~~C~~CgkvYW~GsH~~r~~~~~~~~~~ 519 (522)
+.||.||. +---+++|++-|+.
T Consensus 581 ~~CP~CGs------~~~ev~~RV~GYl~ 602 (623)
T PRK08271 581 KRCPICGS------ENIDYYTRVIGYLK 602 (623)
T ss_pred cCCcCCCC------cchhHHHHHhhhhc
Confidence 77999975 33346777777764
No 255
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=32.17 E-value=48 Score=28.78 Aligned_cols=53 Identities=11% Similarity=0.367 Sum_probs=33.2
Q ss_pred HHHHHHhcCcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccc-cccCCceeecCCCCeEE
Q 009909 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~Lvp-g~---------------n~rvR~~~~~v~vtC~~CG~~~ 92 (105)
T COG2023 39 ARRISMKYRVRLPREIKRTICKKCYTPLVP-GK---------------NARVRLRKGRVVVTCLECGTIR 92 (105)
T ss_pred HHHHHHhhccccCHHHHHHhccccCccccc-Cc---------------ceEEEEcCCeEEEEecCCCcEE
Confidence 444555677777655445669999999863 11 0111 12233688999999775
No 256
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=31.45 E-value=38 Score=27.39 Aligned_cols=44 Identities=18% Similarity=0.357 Sum_probs=26.1
Q ss_pred CcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecC--CCCeEEecccchhh
Q 009909 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCM--DCNQLYWEVMSAYL 509 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~--~CgkvYW~GsH~~r 509 (522)
-+|+.|+..-.. .+... +-+.+ .+.+++|. .||..|=--.-+.|
T Consensus 2 m~CP~Cg~~a~i--rtSr~----------~s~~~---~~~Y~qC~N~eCg~tF~t~es~s~ 47 (72)
T PRK09678 2 FHCPLCQHAAHA--RTSRY----------ITDTT---KERYHQCQNVNCSATFITYESVQR 47 (72)
T ss_pred ccCCCCCCccEE--EEChh----------cChhh---heeeeecCCCCCCCEEEEEEEEEE
Confidence 589999997632 11111 22222 35689999 99998844333333
No 257
>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=31.37 E-value=99 Score=27.47 Aligned_cols=48 Identities=19% Similarity=0.212 Sum_probs=32.1
Q ss_pred EEEecccHHHHHHHHhcCCceecCCCCCCChH----HHHHhhhcCCcEEEecC
Q 009909 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 456888888999999999998764321 2332 34444555567777765
No 258
>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=31.20 E-value=28 Score=23.29 Aligned_cols=12 Identities=17% Similarity=0.534 Sum_probs=9.5
Q ss_pred CceeecCCCCeE
Q 009909 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 467899999853
No 259
>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=31.08 E-value=25 Score=27.71 Aligned_cols=15 Identities=20% Similarity=0.348 Sum_probs=11.9
Q ss_pred cCCceeecCCCCeEE
Q 009909 487 KNLQFWQCMDCNQLY 501 (522)
Q Consensus 487 ~~~~F~~C~~CgkvY 501 (522)
..+.--.||.||+.|
T Consensus 49 i~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 49 IVEGELICPECGREY 63 (68)
T ss_dssp TTTTEEEETTTTEEE
T ss_pred ccCCEEEcCCCCCEE
Confidence 345567899999999
No 260
>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=31.02 E-value=32 Score=29.33 Aligned_cols=11 Identities=18% Similarity=0.534 Sum_probs=9.0
Q ss_pred eeecCCCCeEE
Q 009909 491 FWQCMDCNQLY 501 (522)
Q Consensus 491 F~~C~~CgkvY 501 (522)
.+.|+.||..+
T Consensus 16 ~~~C~~C~~~~ 26 (104)
T TIGR01384 16 VYVCPSCGYEK 26 (104)
T ss_pred eEECcCCCCcc
Confidence 57799999874
No 261
>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=30.99 E-value=2.5e+02 Score=31.44 Aligned_cols=81 Identities=12% Similarity=0.251 Sum_probs=57.5
Q ss_pred CEEEEecccHHHHHHHHhcCCceecCCCC--CCChHHHHHh---hhcCCcEEEecChhHHHh----hcccCCcEEEEcCC
Q 009909 357 PKFLCDVMVEGLAKHLRCVGIDAATPRSK--KPEPRELIDQ---TSKEKRVLLTRDAKLLRH----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 35888888889999999999999877653 2344555543 344566888998875321 12234579999999
Q ss_pred CHHHHHHHHH
Q 009909 428 LKNQQLLEVI 437 (522)
Q Consensus 428 ~~~~QL~~v~ 437 (522)
++.+.+..++
T Consensus 395 s~~qgiaAl~ 404 (530)
T TIGR03599 395 TIVQGLAALL 404 (530)
T ss_pred CHHHHHHHHH
Confidence 8888877765
No 262
>PRK04023 DNA polymerase II large subunit; Validated
Probab=30.60 E-value=33 Score=40.71 Aligned_cols=10 Identities=50% Similarity=1.308 Sum_probs=8.5
Q ss_pred CcccCCCCcc
Q 009909 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 263
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=30.37 E-value=25 Score=29.87 Aligned_cols=47 Identities=19% Similarity=0.516 Sum_probs=21.8
Q ss_pred HHHHHHhc-CcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009909 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 33333333456788887531 2233344567999999996
No 264
>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.
Probab=29.65 E-value=73 Score=28.90 Aligned_cols=33 Identities=15% Similarity=0.206 Sum_probs=27.6
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009909 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~R 401 (522)
+++.||..||+++++.- +....++++.|++++-
T Consensus 21 v~~~l~~~GfeVi~LG~-~v~~e~~v~aa~~~~a 53 (134)
T TIGR01501 21 LDHAFTNAGFNVVNLGV-LSPQEEFIKAAIETKA 53 (134)
T ss_pred HHHHHHHCCCEEEECCC-CCCHHHHHHHHHHcCC
Confidence 69999999999999874 5667889999987754
No 265
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.53 E-value=28 Score=32.27 Aligned_cols=33 Identities=30% Similarity=0.636 Sum_probs=22.5
Q ss_pred CcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009909 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 46999999753 12 23334556677999999963
No 266
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=29.45 E-value=25 Score=40.35 Aligned_cols=41 Identities=12% Similarity=0.222 Sum_probs=23.6
Q ss_pred CCcEEEEcC--CCH-HHHHHHHHHhc----CcC-cccCcCCCcccCCCC
Q 009909 418 KNQIYRVKS--LLK-NQQLLEVIEAF----QLK-ISEDQLMSRCTKCNG 458 (522)
Q Consensus 418 ~~~~~~v~~--~~~-~~QL~~v~~~f----~l~-~~~~~~~sRC~~CN~ 458 (522)
||.+..|.- ..+ .+.+..+++.. ++. ..-+..+++|..|+-
T Consensus 586 GG~I~hv~l~e~~~n~~a~~~lv~~~~~~~~i~Y~~in~~~~~C~~CG~ 634 (656)
T PRK08270 586 GGTVFHLYLGEAISDAEACKKLVKKALENYRLPYITITPTFSICPKHGY 634 (656)
T ss_pred ceEEEEEECCCCCCCHHHHHHHHHHHHHhCCCceEEeCCCCcccCCCCC
Confidence 455555532 212 45677777642 233 233456899999986
No 267
>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=29.36 E-value=28 Score=36.63 Aligned_cols=58 Identities=26% Similarity=0.511 Sum_probs=19.7
Q ss_pred HHHHHHHHH-hcCcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009909 430 NQQLLEVIE-AFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 499 (522)
Q Consensus 430 ~~QL~~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-S-DRCKEE-----GHPLKWHDAVKRFFKCKDCGN 293 (344)
T ss_dssp ---------S-S--EEEE----EEETTT--EES-S----HHHHHT-----T--EEEEEEE-EEEE-T-TS-
T ss_pred HHHHHHHHhhCcEEEEEE----EEcCCCCCccc-Cc-c-hhHHhc-----CCceEEeeeeeeeEECCCCCC
Confidence 455555443 34444332 46999996532 12 2 222221 122233455678999999997
No 268
>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=29.26 E-value=29 Score=32.18 Aligned_cols=30 Identities=20% Similarity=0.591 Sum_probs=21.3
Q ss_pred cCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009909 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 346789999996521 012689999999975
No 269
>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=29.19 E-value=76 Score=28.58 Aligned_cols=33 Identities=15% Similarity=0.209 Sum_probs=27.2
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCCc
Q 009909 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKR 401 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~R 401 (522)
++..||..||+++++.- +....++++.|.+++-
T Consensus 19 v~~~L~~~GfeVidLG~-~v~~e~~v~aa~~~~a 51 (128)
T cd02072 19 LDHAFTEAGFNVVNLGV-LSPQEEFIDAAIETDA 51 (128)
T ss_pred HHHHHHHCCCEEEECCC-CCCHHHHHHHHHHcCC
Confidence 68999999999999874 5667889999887654
No 270
>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=29.06 E-value=32 Score=29.48 Aligned_cols=13 Identities=15% Similarity=0.593 Sum_probs=11.3
Q ss_pred CceeecCCCCeEE
Q 009909 489 LQFWQCMDCNQLY 501 (522)
Q Consensus 489 ~~F~~C~~CgkvY 501 (522)
....+|+.||++|
T Consensus 77 g~~~rC~eCG~~f 89 (97)
T cd00924 77 GKPKRCPECGHVF 89 (97)
T ss_pred CCceeCCCCCcEE
Confidence 4688999999988
No 271
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=29.05 E-value=38 Score=30.37 Aligned_cols=53 Identities=19% Similarity=0.492 Sum_probs=32.2
Q ss_pred EEEcCCCHHHHHHHHHHhcCcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009909 422 YRVKSLLKNQQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 422 ~~v~~~~~~~QL~~v~~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 500 (522)
+.|.-.-..+++..+|+.| +. .|-.|+.|+.+-.. + +.+...-|-.|..||-.
T Consensus 71 lii~G~~~~~~i~~~L~~f---I~---~yVlC~~C~spdT~--l------------------~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 71 LIINGRFSSKQIQDLLDKF---IK---EYVLCPECGSPDTE--L------------------IKEGRLIFLKCKACGAS 123 (125)
T ss_dssp EEEESSSSCCHHHHHHHHH---HC---HHSSCTSTSSSSEE--E------------------EEETTCCEEEETTTSCE
T ss_pred EEEEEecCHHHHHHHHHHH---HH---HEEEcCCCCCCccE--E------------------EEcCCEEEEEecccCCc
Confidence 3443333345788888877 11 25679999996421 1 11234568999999964
No 272
>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=28.99 E-value=79 Score=27.24 Aligned_cols=32 Identities=22% Similarity=0.378 Sum_probs=25.2
Q ss_pred HHHHHHHhcCCceecCCCCCCChHHHHHhhhcC
Q 009909 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 369999999999998874 46677888877543
No 273
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=28.62 E-value=64 Score=29.46 Aligned_cols=46 Identities=15% Similarity=0.403 Sum_probs=29.5
Q ss_pred HHHHHHHHHHhcCcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009909 429 KNQQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 429 ~~~QL~~v~~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 500 (522)
...++..+++.| + ..|-.|+.|+.+-.. + +.+...-|-.|..||-.
T Consensus 87 ~~~~i~~~L~~y---I---~~yVlC~~C~spdT~--l------------------~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 87 SPRVINEKIDRY---V---KEYVICPECGSPDTK--L------------------IKEGRIWVLKCEACGAE 132 (138)
T ss_pred CHHHHHHHHHHH---H---HhcEECCCCCCCCcE--E------------------EEcCCeEEEEcccCCCC
Confidence 346788888887 1 125679999996421 1 11122458899999953
No 274
>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins.
Probab=28.45 E-value=1e+02 Score=26.01 Aligned_cols=39 Identities=15% Similarity=0.235 Sum_probs=29.3
Q ss_pred ChHHHHHhhhcCC-cEEEecChhHHHhhc-ccCCcEEEEcC
Q 009909 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 4677999998777 688899999977654 45666777764
No 275
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=28.04 E-value=32 Score=34.92 Aligned_cols=12 Identities=17% Similarity=0.454 Sum_probs=9.5
Q ss_pred CCceeecCCCCe
Q 009909 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 357889999975
No 276
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=27.96 E-value=48 Score=38.44 Aligned_cols=41 Identities=12% Similarity=0.199 Sum_probs=22.9
Q ss_pred CCcEEEEcCCC---HHHHHHHHHHh-c-CcC-cccCcCCCcccCCCC
Q 009909 418 KNQIYRVKSLL---KNQQLLEVIEA-F-QLK-ISEDQLMSRCTKCNG 458 (522)
Q Consensus 418 ~~~~~~v~~~~---~~~QL~~v~~~-f-~l~-~~~~~~~sRC~~CN~ 458 (522)
||.+..+.-.+ .-+.+.+|++. + ++. ..-+..+++|..|+-
T Consensus 603 GG~I~yve~~~~~~n~~a~~~lv~~~~~~i~Y~~in~~~~~C~~CG~ 649 (711)
T PRK09263 603 GGFIHYCEYPNLQHNLKALEAVWDYSYDRVGYLGTNTPIDECYECGF 649 (711)
T ss_pred CeEEEEEecCCCcCCHHHHHHHHHHHHHCCCeEEeCCCCcccCCCCC
Confidence 45566654321 13556666653 2 322 133456899999996
No 277
>PRK03670 competence damage-inducible protein A; Provisional
Probab=27.93 E-value=91 Score=31.34 Aligned_cols=24 Identities=17% Similarity=-0.071 Sum_probs=21.0
Q ss_pred EEEecccHHHHHHHHhcCCceecC
Q 009909 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 577999999999999999998653
No 278
>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=27.72 E-value=9.3 Score=33.51 Aligned_cols=31 Identities=29% Similarity=0.533 Sum_probs=18.4
Q ss_pred HHHHHHHHHhc---------CcCcccCcCCCcccCCCCcc
Q 009909 430 NQQLLEVIEAF---------QLKISEDQLMSRCTKCNGRF 460 (522)
Q Consensus 430 ~~QL~~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 56776655543 34445455678999999976
No 279
>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=27.56 E-value=29 Score=32.19 Aligned_cols=36 Identities=19% Similarity=0.439 Sum_probs=22.7
Q ss_pred CcccCCCCccccCCCChHHHHHhhhcCcccCcccc---ccCCceeecCCCCeEE
Q 009909 451 SRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLF---DKNLQFWQCMDCNQLY 501 (522)
Q Consensus 451 sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~---~~~~~F~~C~~CgkvY 501 (522)
+-|+.||.++. |. ...++|+ ..+..=.+|..||+-|
T Consensus 40 ~~Cp~C~~~Ir--------------G~-y~v~gv~~~g~~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 40 TSCPNCSTPIR--------------GD-YHVEGVFGLGGHYEAPSYCHNCGKPY 78 (158)
T ss_pred HHCcCCCCCCC--------------Cc-eecCCeeeeCCCCCCChhHHhCCCCC
Confidence 45999998752 11 2233333 2345567799999998
No 280
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=27.28 E-value=73 Score=30.06 Aligned_cols=54 Identities=15% Similarity=0.400 Sum_probs=30.4
Q ss_pred cCCCcccCCCCc------cccCCCChHHHHHhh--hcCc---ccCccc-cccCCceeecCCCCeEE
Q 009909 448 QLMSRCTKCNGR------FIQKPLSTEEAVEAA--KGFQ---RIPDCL-FDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 448 ~~~sRC~~CN~~------l~~~~~~~e~~~~~~--~~~~---~vp~~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 346899999974 222333443322111 1111 344443 45557799999999875
No 281
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=27.27 E-value=40 Score=25.96 Aligned_cols=10 Identities=20% Similarity=0.826 Sum_probs=8.4
Q ss_pred CCcccCCCCc
Q 009909 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 6789999985
No 282
>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=27.03 E-value=36 Score=24.28 Aligned_cols=10 Identities=20% Similarity=1.105 Sum_probs=7.6
Q ss_pred eecCCCCeEE
Q 009909 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 5788888765
No 283
>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]
Probab=26.87 E-value=38 Score=32.82 Aligned_cols=18 Identities=17% Similarity=0.257 Sum_probs=15.5
Q ss_pred CCCCeEEecccchhhHHh
Q 009909 495 MDCNQLYWEVMSAYLFIF 512 (522)
Q Consensus 495 ~~CgkvYW~GsH~~r~~~ 512 (522)
|.+|.|||+|.|...+-.
T Consensus 54 p~~G~v~~~~~~i~~~~~ 71 (209)
T COG4133 54 PDAGEVYWQGEPIQNVRE 71 (209)
T ss_pred CCCCeEEecCCCCccchh
Confidence 679999999999888654
No 284
>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=26.75 E-value=19 Score=33.08 Aligned_cols=12 Identities=17% Similarity=0.908 Sum_probs=9.6
Q ss_pred ceeecCCCCeEE
Q 009909 490 QFWQCMDCNQLY 501 (522)
Q Consensus 490 ~F~~C~~CgkvY 501 (522)
.-..|+.||+-|
T Consensus 27 RRReC~~C~~RF 38 (147)
T TIGR00244 27 RRRECLECHERF 38 (147)
T ss_pred ecccCCccCCcc
Confidence 346799999977
No 285
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=26.74 E-value=57 Score=29.35 Aligned_cols=13 Identities=23% Similarity=0.761 Sum_probs=11.0
Q ss_pred CceeecCCCCeEE
Q 009909 489 LQFWQCMDCNQLY 501 (522)
Q Consensus 489 ~~F~~C~~CgkvY 501 (522)
..-|+|+.||+-|
T Consensus 51 ~qRyrC~~C~~tf 63 (129)
T COG3677 51 HQRYKCKSCGSTF 63 (129)
T ss_pred ccccccCCcCcce
Confidence 5678999999876
No 286
>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=26.70 E-value=99 Score=29.02 Aligned_cols=48 Identities=21% Similarity=0.250 Sum_probs=31.2
Q ss_pred EEEecccHHHHHHHHhcCCceecCCCCCCChH----HHHHhhhcCCcEEEecC
Q 009909 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~~~l~~~~~~~dlVIttG 66 (170)
T cd00885 15 QIVDTNAAFLAKELAELGIEVYRVTVV-GDDEDRIAEALRRASERADLVITTG 66 (170)
T ss_pred eEEEhHHHHHHHHHHHCCCEEEEEEEe-CCCHHHHHHHHHHHHhCCCEEEECC
Confidence 677999999999999999998543211 1222 33444444556666654
No 287
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=26.65 E-value=13 Score=35.32 Aligned_cols=43 Identities=16% Similarity=0.507 Sum_probs=26.3
Q ss_pred cccCCCCccccCCCChHHHHHhhhcCcccCccc--cccCCceeecCCCCeE
Q 009909 452 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCL--FDKNLQFWQCMDCNQL 500 (522)
Q Consensus 452 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v--~~~~~~F~~C~~Cgkv 500 (522)
-|..||..+....+...+.. ..+|+-+ |....++..|+.||-|
T Consensus 122 yc~~c~~~~~e~~f~~~d~~------~~~~~~~~~f~~~~e~rtC~~CG~v 166 (177)
T PRK13264 122 YCDECNHKVHEVEVQLTDIE------TDLPPVFAAFYASEELRTCDNCGTV 166 (177)
T ss_pred ECCCCCCeEEEEEEEecChh------hhhHHHHHHHhcCHhhccCCcCCcc
Confidence 49999998753322222221 1244443 4466889999999976
No 288
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.58 E-value=2.6e+02 Score=34.51 Aligned_cols=102 Identities=13% Similarity=0.138 Sum_probs=58.7
Q ss_pred CCCceEEEEech-hhHHHHHhhcccCCCccCccC-------------------CCceeeHHHHHHHhhccccCCCCCcCC
Q 009909 102 SPDILKLGFKFK-QDLIYLSSTFCSQGCDIGFDR-------------------VEPYLDITSIYNHLHHKQLGRKLPKET 161 (522)
Q Consensus 102 d~~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-TWSKIGRLRRSPKFGRRFGERTCGRMICDVEISAKELIR--------CKS 668 (1172)
T ss_pred CCCE-EEEEcccCccHHHHHHHHHHcCCC-cccccCccccCCCccccccceECCEEEEEHHHHHHHHhC--------cCC
Confidence 8875 5799976 4666654322111211 0100 1236786666655543 247
Q ss_pred ccHHHHHHHHcCCcCcc--ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 009909 162 KSLANICKELLDISLSK--ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (522)
Q Consensus 162 ~sL~~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 11122 133222124458899999999999887653
No 289
>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=26.18 E-value=42 Score=24.56 Aligned_cols=35 Identities=17% Similarity=0.611 Sum_probs=22.0
Q ss_pred cccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCC--CCeEE
Q 009909 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 6999999875421 112 11122 246899998 99776
No 290
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=26.07 E-value=43 Score=40.76 Aligned_cols=18 Identities=11% Similarity=0.167 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHHHhc
Q 009909 202 AHCLIEIFNIFQVKVAQK 219 (522)
Q Consensus 202 A~~ll~L~~~L~~~L~~~ 219 (522)
|.+++++.+.+...|++-
T Consensus 844 a~yl~~va~fiDdLL~k~ 861 (1337)
T PRK14714 844 AEYLLKVAKFVDDLLEKF 861 (1337)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 567777877777777653
No 291
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=25.83 E-value=21 Score=36.16 Aligned_cols=32 Identities=19% Similarity=0.560 Sum_probs=22.9
Q ss_pred CcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009909 447 DQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 447 ~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 500 (522)
+..++-|+.|...+.. .|. ...+|.||.||.-
T Consensus 25 e~lw~KCp~c~~~~y~-----~eL-----------------~~n~~vcp~c~~h 56 (294)
T COG0777 25 EGLWTKCPSCGEMLYR-----KEL-----------------ESNLKVCPKCGHH 56 (294)
T ss_pred CCceeECCCccceeeH-----HHH-----------------HhhhhcccccCcc
Confidence 6678999999997652 121 2368999999743
No 292
>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=25.66 E-value=46 Score=23.41 Aligned_cols=14 Identities=21% Similarity=0.769 Sum_probs=11.6
Q ss_pred CCceeecCCCCeEE
Q 009909 488 NLQFWQCMDCNQLY 501 (522)
Q Consensus 488 ~~~F~~C~~CgkvY 501 (522)
-..|+.|..||+.|
T Consensus 25 ~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 25 MTLFYVCCNCGHRW 38 (39)
T ss_dssp SEEEEEESSSTEEE
T ss_pred CeEEEEeCCCCCee
Confidence 35699999999875
No 293
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=25.55 E-value=42 Score=25.21 Aligned_cols=21 Identities=19% Similarity=0.703 Sum_probs=13.8
Q ss_pred CCceeecCCCCeEEecccchhh
Q 009909 488 NLQFWQCMDCNQLYWEVMSAYL 509 (522)
Q Consensus 488 ~~~F~~C~~CgkvYW~GsH~~r 509 (522)
..-.|+|+.||. =|+-+=..|
T Consensus 25 ~~v~W~C~~Cgh-~w~~~v~~R 45 (55)
T PF14311_consen 25 KKVWWKCPKCGH-EWKASVNDR 45 (55)
T ss_pred CEEEEECCCCCC-eeEccHhhh
Confidence 455799999987 445444443
No 294
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=25.54 E-value=47 Score=24.86 Aligned_cols=17 Identities=18% Similarity=0.561 Sum_probs=14.6
Q ss_pred CCceeecCCCCeEEecc
Q 009909 488 NLQFWQCMDCNQLYWEV 504 (522)
Q Consensus 488 ~~~F~~C~~CgkvYW~G 504 (522)
+.+-|.|.+||=.+|..
T Consensus 34 H~dR~~CGkCgyTe~~~ 50 (51)
T COG1998 34 HKDRWACGKCGYTEFKK 50 (51)
T ss_pred cCceeEeccccceEeec
Confidence 55689999999999974
No 295
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.38 E-value=40 Score=34.39 Aligned_cols=11 Identities=18% Similarity=0.525 Sum_probs=9.0
Q ss_pred CceeecCCCCe
Q 009909 489 LQFWQCMDCNQ 499 (522)
Q Consensus 489 ~~F~~C~~Cgk 499 (522)
..-|+||.|.+
T Consensus 272 R~t~~CP~CQ~ 282 (282)
T PRK13945 272 RSTHWCPNCQK 282 (282)
T ss_pred CccEECCCCcC
Confidence 56888999974
No 296
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=25.08 E-value=62 Score=34.94 Aligned_cols=47 Identities=21% Similarity=0.553 Sum_probs=29.1
Q ss_pred HHHHHHhc-CcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009909 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 16 i~~vi~~~~~l~~~G~~~~~~CPfh~ek~--------------------pSf~v~~~k~~~~Cf~Cg~ 63 (415)
T TIGR01391 16 IVDVISEYVKLKKKGRNYVGLCPFHHEKT--------------------PSFSVSPEKQFYHCFGCGA 63 (415)
T ss_pred HHHHHHhhCceeecCCceEeeCCCCCCCC--------------------CeEEEEcCCCcEEECCCCC
Confidence 55677765 44433344456788887631 2233334567999999997
No 297
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.07 E-value=37 Score=34.44 Aligned_cols=13 Identities=23% Similarity=0.396 Sum_probs=10.3
Q ss_pred CceeecCCCCeEE
Q 009909 489 LQFWQCMDCNQLY 501 (522)
Q Consensus 489 ~~F~~C~~CgkvY 501 (522)
..-|.||.|.+.+
T Consensus 253 R~ty~Cp~CQ~~~ 265 (269)
T PRK14811 253 RGTHFCPQCQPLR 265 (269)
T ss_pred CCcEECCCCcCCC
Confidence 5688899998753
No 298
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=24.97 E-value=72 Score=27.95 Aligned_cols=45 Identities=20% Similarity=0.551 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhcCcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009909 429 KNQQLLEVIEAFQLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQ 499 (522)
Q Consensus 429 ~~~QL~~v~~~f~l~~~~~~~~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgk 499 (522)
...++..+++.| + +.|-.|+.|+.+-.. + +.+...-|-.|..||.
T Consensus 65 ~~~~i~~~l~~y---I---~~yVlC~~C~spdT~--l------------------~k~~r~~~l~C~aCGa 109 (110)
T smart00653 65 TPKKLQDLLRRY---I---KEYVLCPECGSPDTE--L------------------IKENRLFFLKCEACGA 109 (110)
T ss_pred CHHHHHHHHHHH---H---HhcEECCCCCCCCcE--E------------------EEeCCeEEEEccccCC
Confidence 356788888877 1 125679999996421 1 1112345888999994
No 299
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=24.95 E-value=40 Score=24.84 Aligned_cols=10 Identities=20% Similarity=1.072 Sum_probs=6.8
Q ss_pred eecCCCCeEE
Q 009909 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 4677777754
No 300
>PLN02294 cytochrome c oxidase subunit Vb
Probab=24.93 E-value=36 Score=32.09 Aligned_cols=13 Identities=23% Similarity=0.656 Sum_probs=10.9
Q ss_pred CceeecCCCCeEE
Q 009909 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 301
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=24.91 E-value=69 Score=33.91 Aligned_cols=20 Identities=15% Similarity=0.116 Sum_probs=18.4
Q ss_pred CceeecCCCCeEEecccchhh
Q 009909 489 LQFWQCMDCNQLYWEVMSAYL 509 (522)
Q Consensus 489 ~~F~~C~~CgkvYW~GsH~~r 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 4789999999 9999999988
No 302
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=24.50 E-value=65 Score=31.05 Aligned_cols=16 Identities=13% Similarity=0.353 Sum_probs=12.4
Q ss_pred CCceeecCCCCeEEec
Q 009909 488 NLQFWQCMDCNQLYWE 503 (522)
Q Consensus 488 ~~~F~~C~~CgkvYW~ 503 (522)
++-..+|+.||.||=.
T Consensus 27 ~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 27 REPLVRCEECGTVHPA 42 (201)
T ss_pred CceEEEccCCCcEeec
Confidence 3457889999999744
No 303
>PRK05667 dnaG DNA primase; Validated
Probab=24.41 E-value=68 Score=36.29 Aligned_cols=47 Identities=21% Similarity=0.554 Sum_probs=29.8
Q ss_pred HHHHHHhc-CcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009909 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 45676665 44433444456799988631 2333344578999999997
No 304
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=24.19 E-value=39 Score=30.84 Aligned_cols=19 Identities=21% Similarity=0.532 Sum_probs=14.3
Q ss_pred CCceeecCCCCeEEecccc
Q 009909 488 NLQFWQCMDCNQLYWEVMS 506 (522)
Q Consensus 488 ~~~F~~C~~CgkvYW~GsH 506 (522)
.--..+|++||++|-.-..
T Consensus 26 kl~g~kC~~CG~v~~PPr~ 44 (140)
T COG1545 26 KLLGTKCKKCGRVYFPPRA 44 (140)
T ss_pred cEEEEEcCCCCeEEcCCcc
Confidence 3457789999999976543
No 305
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=24.06 E-value=42 Score=37.90 Aligned_cols=41 Identities=10% Similarity=0.216 Sum_probs=23.7
Q ss_pred CCcEEEEcCC---CHHHHHHHHHHh-c--CcC-cccCcCCCcccCCCC
Q 009909 418 KNQIYRVKSL---LKNQQLLEVIEA-F--QLK-ISEDQLMSRCTKCNG 458 (522)
Q Consensus 418 ~~~~~~v~~~---~~~~QL~~v~~~-f--~l~-~~~~~~~sRC~~CN~ 458 (522)
+|.+..+.-+ .--+.+.+|++. + ++. .+-+..+++|..|+-
T Consensus 485 GG~i~~v~l~e~~~n~eal~~lv~~a~~~~i~Y~~~n~~~~~C~~CG~ 532 (579)
T TIGR02487 485 GGHITYIELDEAIPDPEALKDITKKAMKNGIGYFGINPPVDVCEDCGY 532 (579)
T ss_pred CceEEEEEcCCCCCCHHHHHHHHHHHHhcCCceEEeccCCccCCCCCC
Confidence 4555555322 124677777774 2 222 234456899999975
No 306
>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=24.02 E-value=24 Score=28.06 Aligned_cols=34 Identities=26% Similarity=0.540 Sum_probs=20.7
Q ss_pred cccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009909 452 RCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 452 RC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvY 501 (522)
-|..||.+-. + .+-+..|.+..-+-+||+|+..-
T Consensus 6 TC~~C~~Rs~-~---------------~~sk~aY~~GvViv~C~gC~~~H 39 (66)
T PF05180_consen 6 TCNKCGTRSA-K---------------MFSKQAYHKGVVIVQCPGCKNRH 39 (66)
T ss_dssp EETTTTEEEE-E---------------EEEHHHHHTSEEEEE-TTS--EE
T ss_pred EcCCCCCccc-e---------------eeCHHHHhCCeEEEECCCCccee
Confidence 3999998653 1 23334466667799999998653
No 307
>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=24.00 E-value=34 Score=31.17 Aligned_cols=13 Identities=23% Similarity=0.651 Sum_probs=10.8
Q ss_pred CceeecCCCCeEE
Q 009909 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 3467999999988
No 308
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=23.65 E-value=37 Score=21.45 Aligned_cols=10 Identities=20% Similarity=1.012 Sum_probs=8.6
Q ss_pred eecCCCCeEE
Q 009909 492 WQCMDCNQLY 501 (522)
Q Consensus 492 ~~C~~CgkvY 501 (522)
+.|.-|++.|
T Consensus 2 ~~C~~C~k~f 11 (27)
T PF12171_consen 2 FYCDACDKYF 11 (27)
T ss_dssp CBBTTTTBBB
T ss_pred CCcccCCCCc
Confidence 5799999987
No 309
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=23.55 E-value=29 Score=34.46 Aligned_cols=8 Identities=38% Similarity=0.742 Sum_probs=5.0
Q ss_pred HHHHHHHh
Q 009909 367 GLAKHLRC 374 (522)
Q Consensus 367 ~Lar~LR~ 374 (522)
.||+.+|.
T Consensus 130 ~La~~iRa 137 (253)
T COG1933 130 DLARRIRA 137 (253)
T ss_pred hHHHHHHH
Confidence 46666665
No 310
>COG1487 VapC Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=23.55 E-value=1.2e+02 Score=26.84 Aligned_cols=43 Identities=21% Similarity=0.226 Sum_probs=33.8
Q ss_pred ccHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecC-hhHHH
Q 009909 364 MVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRD-AKLLR 412 (522)
Q Consensus 364 mLg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~RiiLTrd-~~l~~ 412 (522)
+-|.+.+-|+..|.- .+..|--|...|...|-.++|+| ++|.+
T Consensus 78 ~~~~i~~~l~~~G~~------~~~~D~lIAa~A~~~~~~LvT~d~~df~~ 121 (133)
T COG1487 78 IAAEIQARLRKEGIP------IGLNDLLIAATAIAHGLLLVTRDVKDFER 121 (133)
T ss_pred HHHHHHHHHHhcCCC------CChHHHHHHHHHHHcCCEEEEcCHHhccc
Confidence 357899999999991 23456778999999999999999 55543
No 311
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=23.25 E-value=40 Score=35.95 Aligned_cols=34 Identities=21% Similarity=0.396 Sum_probs=22.2
Q ss_pred CCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecccc
Q 009909 450 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVMS 506 (522)
Q Consensus 450 ~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvYW~GsH 506 (522)
++-|.+|+..+. .+++. ..-|+|| ||+-.=.|-.
T Consensus 240 ~~~c~~C~~~~~-----~~~~~-----------------~~~~~Cp-CG~~i~~GV~ 273 (374)
T TIGR00375 240 QTACEACGEPAV-----SEDAE-----------------TACANCP-CGGRIKKGVS 273 (374)
T ss_pred hhhhcccCCcCC-----chhhh-----------------hcCCCCC-CCCcceechH
Confidence 578999998652 23332 1258899 9987655543
No 312
>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=23.18 E-value=27 Score=40.63 Aligned_cols=11 Identities=36% Similarity=0.628 Sum_probs=0.0
Q ss_pred HHHHhcCCcee
Q 009909 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 36788888864
No 313
>PHA02540 61 DNA primase; Provisional
Probab=23.04 E-value=74 Score=33.46 Aligned_cols=52 Identities=15% Similarity=0.294 Sum_probs=28.2
Q ss_pred HHHHHHHhc-CcCcccCcCCCcccCCCCccccCCCChHHHHHhhhcCcccCccccccC--CceeecCCCCe
Q 009909 432 QLLEVIEAF-QLKISEDQLMSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKN--LQFWQCMDCNQ 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-YNFRCPICGDSQK------DK---------NKARGWIYEKKDGGVFKCHNCGY 63 (337)
T ss_pred HHHHHHhhhheeccCce-EEecCCCCCCccc------cC---------cCCcEEEeccCCceEEEecCCCC
Confidence 444555555 3333322 5689999997421 11 1122222222 34999999996
No 314
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=22.96 E-value=42 Score=29.70 Aligned_cols=31 Identities=23% Similarity=0.403 Sum_probs=18.5
Q ss_pred HHHHHHHHHhc---------CcCcccCcCCCcccCCCCcc
Q 009909 430 NQQLLEVIEAF---------QLKISEDQLMSRCTKCNGRF 460 (522)
Q Consensus 430 ~~QL~~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 45666655433 33344445567899998865
No 315
>PRK10445 endonuclease VIII; Provisional
Probab=22.72 E-value=47 Score=33.52 Aligned_cols=28 Identities=21% Similarity=0.724 Sum_probs=18.7
Q ss_pred CcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCe
Q 009909 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 EACERCGGIIEK--T-------------TL------SSRPFYWCPGCQK 263 (263)
T ss_pred CCCCCCCCEeEE--E-------------EE------CCCCcEECCCCcC
Confidence 459999997631 1 11 1356788999974
No 316
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=22.70 E-value=17 Score=33.93 Aligned_cols=40 Identities=23% Similarity=0.603 Sum_probs=0.0
Q ss_pred ccCCCCccccCCCChHHHHHhhhcCcccCccc--cccCCceeecCCCC
Q 009909 453 CTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCL--FDKNLQFWQCMDCN 498 (522)
Q Consensus 453 C~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v--~~~~~~F~~C~~Cg 498 (522)
|..||..+....+...+..- .+|+-+ |....+...|+.||
T Consensus 117 c~~c~~~~~e~~f~~~d~~~------~~~~~~~~f~~~~~~rtC~~Cg 158 (159)
T TIGR03037 117 CPQCGHKLHRAEVQLENIVT------DLPPVFEHFYSNEDARTCKNCG 158 (159)
T ss_pred CCCCCCeEEEEEEEecChhh------hhHHHHHHHhCChhhccCCccC
No 317
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=22.69 E-value=48 Score=33.64 Aligned_cols=12 Identities=17% Similarity=0.548 Sum_probs=9.5
Q ss_pred CCceeecCCCCe
Q 009909 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 356888999976
No 318
>PHA02942 putative transposase; Provisional
Probab=22.58 E-value=99 Score=33.08 Aligned_cols=11 Identities=18% Similarity=0.860 Sum_probs=9.2
Q ss_pred ceeecCCCCeE
Q 009909 490 QFWQCMDCNQL 500 (522)
Q Consensus 490 ~F~~C~~Cgkv 500 (522)
..|.|+.||-.
T Consensus 341 r~f~C~~CG~~ 351 (383)
T PHA02942 341 RYFHCPSCGYE 351 (383)
T ss_pred CEEECCCCCCE
Confidence 47999999965
No 319
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=21.98 E-value=55 Score=23.16 Aligned_cols=13 Identities=23% Similarity=0.851 Sum_probs=10.7
Q ss_pred CceeecCCCCeEE
Q 009909 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 320
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=21.88 E-value=54 Score=28.49 Aligned_cols=11 Identities=18% Similarity=0.616 Sum_probs=8.6
Q ss_pred eeecCCCCeEE
Q 009909 491 FWQCMDCNQLY 501 (522)
Q Consensus 491 F~~C~~CgkvY 501 (522)
.+.||.|+.-+
T Consensus 20 ~~~cpec~~ew 30 (112)
T COG2824 20 QLICPECAHEW 30 (112)
T ss_pred eEeCchhcccc
Confidence 67899998753
No 321
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=21.81 E-value=28 Score=32.14 Aligned_cols=12 Identities=17% Similarity=0.886 Sum_probs=9.6
Q ss_pred ceeecCCCCeEE
Q 009909 490 QFWQCMDCNQLY 501 (522)
Q Consensus 490 ~F~~C~~CgkvY 501 (522)
.-..|+.||+-|
T Consensus 27 RRReC~~C~~RF 38 (156)
T COG1327 27 RRRECLECGERF 38 (156)
T ss_pred hhhccccccccc
Confidence 456799999877
No 322
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=21.51 E-value=34 Score=26.10 Aligned_cols=10 Identities=20% Similarity=0.610 Sum_probs=7.9
Q ss_pred CcccCCCCcc
Q 009909 451 SRCTKCNGRF 460 (522)
Q Consensus 451 sRC~~CN~~l 460 (522)
-.|+.|++.-
T Consensus 5 i~CP~CgnKT 14 (55)
T PF14205_consen 5 ILCPICGNKT 14 (55)
T ss_pred EECCCCCCcc
Confidence 4799999854
No 323
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=21.50 E-value=55 Score=28.87 Aligned_cols=9 Identities=33% Similarity=1.254 Sum_probs=7.9
Q ss_pred ccCCCCccc
Q 009909 453 CTKCNGRFI 461 (522)
Q Consensus 453 C~~CN~~l~ 461 (522)
||.|++.|.
T Consensus 1 CPvCg~~l~ 9 (113)
T PF09862_consen 1 CPVCGGELV 9 (113)
T ss_pred CCCCCCceE
Confidence 999999884
No 324
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.39 E-value=44 Score=27.31 Aligned_cols=23 Identities=26% Similarity=0.780 Sum_probs=18.3
Q ss_pred HHHHHHhcCcCcccCcCCCcccCCCCcc
Q 009909 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 457788885 56689999999976
No 325
>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=21.31 E-value=1.3e+02 Score=26.27 Aligned_cols=31 Identities=23% Similarity=0.471 Sum_probs=24.4
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcC
Q 009909 368 LAKHLRCVGIDAATPRSKKPEPRELIDQTSKE 399 (522)
Q Consensus 368 Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e 399 (522)
++..||..||++.++.. ..+..++++.|.++
T Consensus 19 ~~~~l~~~G~~vi~lG~-~vp~e~~~~~a~~~ 49 (122)
T cd02071 19 IARALRDAGFEVIYTGL-RQTPEEIVEAAIQE 49 (122)
T ss_pred HHHHHHHCCCEEEECCC-CCCHHHHHHHHHHc
Confidence 58899999999999875 35666788877643
No 326
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=21.29 E-value=36 Score=34.09 Aligned_cols=42 Identities=19% Similarity=0.532 Sum_probs=28.0
Q ss_pred CCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEEecccc
Q 009909 450 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEVMS 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 345999998752 22 2333444434478889999999998664
No 327
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=21.20 E-value=61 Score=21.39 Aligned_cols=14 Identities=21% Similarity=0.517 Sum_probs=11.4
Q ss_pred ecCCCCeEEecccc
Q 009909 493 QCMDCNQLYWEVMS 506 (522)
Q Consensus 493 ~C~~CgkvYW~GsH 506 (522)
-|-.|++.||..++
T Consensus 2 sCiDC~~~F~~~~y 15 (28)
T PF08790_consen 2 SCIDCSKDFDGDSY 15 (28)
T ss_dssp EETTTTEEEEGGGT
T ss_pred eeecCCCCcCcCCc
Confidence 49999999987654
No 328
>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=21.09 E-value=1.7e+02 Score=27.27 Aligned_cols=65 Identities=14% Similarity=0.066 Sum_probs=40.6
Q ss_pred HHhcCCceecCCCCCCChHHHHHhhhcCCc-----EEEecChhHHHhhcccCCcEEEEcCCCHHHHHHHHHH
Q 009909 372 LRCVGIDAATPRSKKPEPRELIDQTSKEKR-----VLLTRDAKLLRHQYLIKNQIYRVKSLLKNQQLLEVIE 438 (522)
Q Consensus 372 LR~lG~D~~~~~~~~~~d~~ll~~A~~e~R-----iiLTrd~~l~~~~~~~~~~~~~v~~~~~~~QL~~v~~ 438 (522)
-+.-|+.++|.......|..|.+.+.+... +++|.|..+...... ..+..+.+....+++...-+
T Consensus 63 ~~~~gi~Vvft~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~~~~--~GA~~iss~ef~~~l~~~~~ 132 (166)
T PF05991_consen 63 EEYGGIEVVFTKEGETADDYIERLVRELKNRPRQVTVVTSDREIQRAARG--RGAKRISSEEFLRELKAAKR 132 (166)
T ss_pred eeeCceEEEECCCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHHHHhh--CCCEEEcHHHHHHHHHHHHH
Confidence 344688888876544456666666665554 788999988655432 24677777655445544433
No 329
>PRK03094 hypothetical protein; Provisional
Probab=21.07 E-value=2.1e+02 Score=23.74 Aligned_cols=72 Identities=11% Similarity=0.122 Sum_probs=43.4
Q ss_pred EEEEecccHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEec-ChhHHHhhcccCCcEEEEcCCC-HHHHHHH
Q 009909 358 KFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTR-DAKLLRHQYLIKNQIYRVKSLL-KNQQLLE 435 (522)
Q Consensus 358 rfl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~RiiLTr-d~~l~~~~~~~~~~~~~v~~~~-~~~QL~~ 435 (522)
|+-+...|..+..+|+..||+++-+.+. .+ ++.=+.+++|- |..++--+... ..+..|.... ..+++.+
T Consensus 3 kIaVE~~Ls~i~~~L~~~GYeVv~l~~~--~~------~~~~Da~VitG~d~n~mgi~d~~-t~~pVI~A~G~TaeEI~~ 73 (80)
T PRK03094 3 KIGVEQSLTDVQQALKQKGYEVVQLRSE--QD------AQGCDCCVVTGQDSNVMGIADTS-TKGSVITASGLTADEICQ 73 (80)
T ss_pred eEEeecCcHHHHHHHHHCCCEEEecCcc--cc------cCCcCEEEEeCCCcceecccccc-cCCcEEEcCCCCHHHHHH
Confidence 5777888999999999999999876531 22 23347788876 34454333211 2345555433 2444554
Q ss_pred HHH
Q 009909 436 VIE 438 (522)
Q Consensus 436 v~~ 438 (522)
.++
T Consensus 74 ~ve 76 (80)
T PRK03094 74 QVE 76 (80)
T ss_pred HHH
Confidence 443
No 330
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=21.03 E-value=37 Score=36.43 Aligned_cols=44 Identities=25% Similarity=0.566 Sum_probs=27.5
Q ss_pred CCcccCCCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeEE
Q 009909 450 MSRCTKCNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLY 501 (522)
Q Consensus 450 ~sRC~~CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~CgkvY 501 (522)
--||..|..++++.+- +||.+ +|-.--.+.|.+-|+|..||..-
T Consensus 394 APrCs~C~~PI~P~~G-~~etv-------Rvvamdr~fHv~CY~CEDCg~~L 437 (468)
T KOG1701|consen 394 APRCSVCGNPILPRDG-KDETV-------RVVAMDRDFHVNCYKCEDCGLLL 437 (468)
T ss_pred CcchhhccCCccCCCC-CcceE-------EEEEccccccccceehhhcCccc
Confidence 3689999998864322 22221 22222245678899999998643
No 331
>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=20.95 E-value=1.2e+02 Score=28.96 Aligned_cols=34 Identities=15% Similarity=0.316 Sum_probs=26.9
Q ss_pred cHH--HHHHHHhcCCceecCCCCCCChHHHHHhhhcC
Q 009909 365 VEG--LAKHLRCVGIDAATPRSKKPEPRELIDQTSKE 399 (522)
Q Consensus 365 Lg~--Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e 399 (522)
+|. ++..||..||+|.+++. +.+..++++.+.++
T Consensus 97 lG~~~v~~~l~~~G~~vi~lG~-~~p~~~l~~~~~~~ 132 (201)
T cd02070 97 IGKNLVATMLEANGFEVIDLGR-DVPPEEFVEAVKEH 132 (201)
T ss_pred HHHHHHHHHHHHCCCEEEECCC-CCCHHHHHHHHHHc
Confidence 563 69999999999998874 56777888887654
No 332
>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=20.94 E-value=56 Score=25.13 Aligned_cols=15 Identities=27% Similarity=0.986 Sum_probs=12.0
Q ss_pred CcccCCCCccccCCC
Q 009909 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 679999999976553
No 333
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=20.77 E-value=50 Score=32.53 Aligned_cols=15 Identities=20% Similarity=0.871 Sum_probs=12.2
Q ss_pred cCCceeecCCCCeEE
Q 009909 487 KNLQFWQCMDCNQLY 501 (522)
Q Consensus 487 ~~~~F~~C~~CgkvY 501 (522)
+..+-.+|+.||++|
T Consensus 177 rEGkpqRCpECGqVF 191 (268)
T PTZ00043 177 REGFLYRCGECDQIF 191 (268)
T ss_pred cCCCCccCCCCCcEE
Confidence 345678899999998
No 334
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=20.73 E-value=87 Score=32.38 Aligned_cols=10 Identities=30% Similarity=1.351 Sum_probs=8.5
Q ss_pred ceeecCCCCe
Q 009909 490 QFWQCMDCNQ 499 (522)
Q Consensus 490 ~F~~C~~Cgk 499 (522)
-+|.||+||=
T Consensus 367 ~~~~c~~c~~ 376 (389)
T PRK11788 367 LYWHCPSCKA 376 (389)
T ss_pred ceeECcCCCC
Confidence 4899999984
No 335
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=20.71 E-value=1.3e+02 Score=24.84 Aligned_cols=43 Identities=12% Similarity=0.206 Sum_probs=31.7
Q ss_pred CEEEEecccHHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEEecC
Q 009909 357 PKFLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRELIDQTSKEKRVLLTRD 407 (522)
Q Consensus 357 ~rfl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~~ll~~A~~e~RiiLTrd 407 (522)
.|+-+...|..+..+|+..||+++.+.+. + -++.=+.|++|-.
T Consensus 2 kkIAVE~~Ls~v~~~L~~~GyeVv~l~~~--~------~~~~~daiVvtG~ 44 (80)
T PF03698_consen 2 KKIAVEEGLSNVKEALREKGYEVVDLENE--Q------DLQNVDAIVVTGQ 44 (80)
T ss_pred CeEEecCCchHHHHHHHHCCCEEEecCCc--c------ccCCcCEEEEECC
Confidence 36778889999999999999999877642 1 1233467888764
No 336
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=20.55 E-value=1.3e+02 Score=26.96 Aligned_cols=32 Identities=19% Similarity=0.249 Sum_probs=25.4
Q ss_pred HHHHHHhcCCceecCCCCCCChHHHHHhhhcCC
Q 009909 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 68999999999998764 345678888887664
No 337
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=20.43 E-value=50 Score=36.89 Aligned_cols=31 Identities=39% Similarity=0.822 Sum_probs=23.1
Q ss_pred CcccC-CCCccccCCCChHHHHHhhhcCcccCccccccCCceeecCCCCeE
Q 009909 451 SRCTK-CNGRFIQKPLSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQL 500 (522)
Q Consensus 451 sRC~~-CN~~l~~~~~~~e~~~~~~~~~~~vp~~v~~~~~~F~~C~~Cgkv 500 (522)
--|.. ||..|- |-+..+....||.||-|.+-
T Consensus 54 v~C~~pC~avln-------------------pyC~id~r~~~W~CpfCnqr 85 (755)
T COG5047 54 VKCTAPCKAVLN-------------------PYCHIDERNQSWICPFCNQR 85 (755)
T ss_pred ceecccchhhcC-------------------cceeeccCCceEecceecCC
Confidence 35988 998662 44555666789999999974
No 338
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=20.42 E-value=87 Score=24.40 Aligned_cols=11 Identities=27% Similarity=0.679 Sum_probs=9.1
Q ss_pred CCcccCCCCcc
Q 009909 450 MSRCTKCNGRF 460 (522)
Q Consensus 450 ~sRC~~CN~~l 460 (522)
..+|+.||..|
T Consensus 9 ~~~CtSCg~~i 19 (61)
T COG2888 9 PPVCTSCGREI 19 (61)
T ss_pred CceeccCCCEe
Confidence 35899999987
No 339
>PF13277 YmdB: YmdB-like protein; PDB: 2CV9_B 2Z06_C.
Probab=20.33 E-value=92 Score=31.40 Aligned_cols=39 Identities=28% Similarity=0.347 Sum_probs=29.2
Q ss_pred HHHHHHHHhcCCceecCCCCCCChHHHHHhhhcCCcEEE
Q 009909 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 478999999999999988766677789988888888773
No 340
>PRK03673 hypothetical protein; Provisional
Probab=20.31 E-value=1.4e+02 Score=32.24 Aligned_cols=49 Identities=14% Similarity=0.182 Sum_probs=31.1
Q ss_pred EEEecccHHHHHHHHhcCCceecCCCCCCChHH---HHHhhhcCCcEEEecC
Q 009909 359 FLCDVMVEGLAKHLRCVGIDAATPRSKKPEPRE---LIDQTSKEKRVLLTRD 407 (522)
Q Consensus 359 fl~D~mLg~Lar~LR~lG~D~~~~~~~~~~d~~---ll~~A~~e~RiiLTrd 407 (522)
-+.|.+-.-|+++|+.+|+++....-...+..+ .++.|.++..++||.+
T Consensus 17 ~i~dtN~~~la~~L~~~G~~v~~~~~v~D~~~~i~~~l~~a~~~~DlVI~tG 68 (396)
T PRK03673 17 QIVDTNAAWLADFFFHQGLPLSRRNTVGDNLDALVAILRERSQHADVLIVNG 68 (396)
T ss_pred eEEEhHHHHHHHHHHHCCCEEEEEEEcCCCHHHHHHHHHHHhccCCEEEEcC
Confidence 678999999999999999998543322212222 3334555545555543
Done!